Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold296
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 679504
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.24
Warning! 166439 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:160247 original size:10 final size:11
Alignment explanation
Indices: 160232--160260 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
160222 CCACTAGATG
160232 ATTTTTCAAA-
1 ATTTTTCAAAC
160242 ATTTTTCAAAC
1 ATTTTTCAAAC
160253 ATTTTTCA
1 ATTTTTCA
160261 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:329862 original size:156 final size:156
Alignment explanation
Indices: 329625--330378 Score: 592
Period size: 156 Copynumber: 4.8 Consensus size: 156
329615 CTAGGACTAA
* * * *
329625 GTTCTTAAGAAATTACCAAAATGCCCTTAGGGGTATACCTTT-GACGTAAAAGAATCCTGGCA-A
1 GTTC-TAAAAAATTACAAAAATGCCCTTA-GGGTATA-CTTTCGACGTAAAAGTAT-CTCG-ATA
* * * *
329688 -CCCTAAAGGACTTAAAAA-GACTCATA-AGGGGATAAACCTATCCTAAATGCCAACCTTTGACA
61 CCCCTAAAGGACTTAAAAAGGACT-AGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGACA
* * *
329750 TAAAAAGCGGACCCGGTGATGACCTAGGAATTT
125 T-AAAAGCGAACCCGGTGATGACTTAGGAATTG
* *
329783 ATTCTAAAAAATTACAAAAATGCCCTTAGAGG-ATACTTTCGATGTAAAAGTATCTCGATACCCC
1 GTTCTAAAAAATTACAAAAATGCCCTTAG-GGTATACTTTCGACGTAAAAGTATCTCGATACCCC
*
329847 TAAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATG-CCACC-TTCAGCATAAA
65 TAAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGA-CATAAA
* * *
329910 AGCAAACTCGGTGATGACTTAGGAGTTG
129 AGCGAACCCGGTGATGACTTAGGAATTG
* * * * ** *
329938 GTTCTAGAAAATTACAAAAATACCCCTATGGGTATACCTTCGACGTAAAAGTATC-CGGCAACCC
1 GTTCTAAAAAATTACAAAAATGCCCTTA-GGGTATACTTTCGACGTAAAAGTATCTCGATACCCC
**
330002 TAAAGGACTTAAACAA-GACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGTA-AAA
65 TAAAGGACTTAAA-AAGGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGACATAAA
* * **
330065 AACGAACCCGGGTGACGACTTAGGTGTTG
129 AGCGAACCC-GGTGATGACTTAGGAATTG
* ** * * * ** * * *
330094 GTTTTAGAAAAATTATGAGAATGCCCCTAAGGG-ATACCTTCGACGTGGAAGT-GCCCAATACCC
1 GTTCTA-AAAAATTACAAAAATG-CCCTTAGGGTATACTTTCGACGTAAAAGTATCTCGATACCC
* * * * * *
330157 TTAAAGGACTTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATGCCCACCTTTGGCATAAA
64 CTAAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGACATAAA
* * *
330222 AGCGGAA-CCAGTGA-CATCGTA-GAACTTG
129 AGC-GAACCCGGTGATGA-CTTAGGAA-TTG
* * * * * * *
330250 GTTCTAAAAAATTACGAGAATGCCCTTAGGGTATACCTTT-GATGTAGAAGT-GCCCGATACGCT
1 GTTCTAAAAAATTACAAAAATGCCCTTAGGGTATA-CTTTCGACGTAAAAGTATCTCGATAC-CC
* * * * * * * * * * *
330313 TTAAAGAACTTAAAAAGG-TTATAAAAGGAATGAACATATCCTAAATACCCACCTTCGATATAAA
64 CTAAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGACATAAA
330377 AG
129 AG
330379 TAGACCCGGT
Statistics
Matches: 494, Mismatches: 78, Indels: 51
0.79 0.13 0.08
Matches are distributed among these distances:
154 9 0.02
155 201 0.41
156 202 0.41
157 72 0.15
158 10 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (156 bp):
GTTCTAAAAAATTACAAAAATGCCCTTAGGGTATACTTTCGACGTAAAAGTATCTCGATACCCCT
AAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGACATAAAAG
CGAACCCGGTGATGACTTAGGAATTG
Found at i:329957 original size:155 final size:156
Alignment explanation
Indices: 329634--330288 Score: 607
Period size: 156 Copynumber: 4.2 Consensus size: 156
329624 AGTTCTTAAG
* * * * * *
329634 AAATTACCAAAATGCCCTTAGGGGTATACCTTTGACGTAAAAGAATCCTGGCA-A-CCCTAAAGG
1 AAATTACAAAAATGCCCCTAGAGGTATACCTTCGACGTAAAAGTAT-CTCG-ATACCCCTAAAGG
* * * * * *
329697 ACTTAAAAAGACTCATA-AGGGGATAAACCTATCCTAAATGCCAACCTTTGACATAAAAAGCGGA
64 ACTTAAAAAGACT-AGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGCAT-AAAAGCGAA
* * ** *
329761 CCCGGTGATGACCTAGGAATTTATTCTAAA
127 CCCGGTGATGACTTAGGAGTTGGTTCTAGA
* * *
329791 AAATTACAAAAATGCCCTTAGAGG-ATACTTTCGATGTAAAAGTATCTCGATACCCCTAAAGGAC
1 AAATTACAAAAATGCCCCTAGAGGTATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGAC
** * *
329855 TTAAAAAGGACTAGAGATGGGATGAACCTATCCTAAATG-CCACCTTCAGCATAAAAGCAAACTC
66 TTAAAAA-GACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGAACCC
329919 GGTGATGACTTAGGAGTTGGTTCTAGA
130 GGTGATGACTTAGGAGTTGGTTCTAGA
* ** *
329946 AAATTACAAAAATACCCCTATG-GGTATACCTTCGACGTAAAAGTATC-CGGCAACCCTAAAGGA
1 AAATTACAAAAATGCCCCTA-GAGGTATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGA
* *
330009 CTTAAACAAGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGTA-AAAAACGAACC
65 CTTAAA-AAGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGAACC
* * *
330073 CGGGTGACGACTTAGGTGTTGGTTTTAGAA
129 C-GGTGATGACTTAGGAGTTGGTTCTAG-A
** * * ** * * * *
330103 AAATTATGAGAATGCCCCTA-AGGGATACCTTCGACGTGGAAGT-GCCCAATACCCTTAAAGGAC
1 AAATTACAAAAATGCCCCTAGAGGTATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGAC
* * * *
330166 TTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGGAA-C
66 TTAAAAA-GACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGC-GAACC
* * * * * *
330230 CAGTGA-CATCGTAGAACTTGGTTCTAAA
129 CGGTGATGA-CTTAGGAGTTGGTTCTAGA
* * *
330258 AAATTACGAGAATGCCCTTAG-GGTATACCTT
1 AAATTACAAAAATGCCCCTAGAGGTATACCTT
330289 TGATGTAGAA
Statistics
Matches: 413, Mismatches: 68, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
154 1 0.00
155 146 0.35
156 192 0.46
157 71 0.17
158 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (156 bp):
AAATTACAAAAATGCCCCTAGAGGTATACCTTCGACGTAAAAGTATCTCGATACCCCTAAAGGAC
TTAAAAAGACTAGAGATGGGATGAACCTATCCTAAATGCCCACCTTTGGCATAAAAGCGAACCCG
GTGATGACTTAGGAGTTGGTTCTAGA
Found at i:330253 original size:312 final size:310
Alignment explanation
Indices: 329625--330288 Score: 748
Period size: 312 Copynumber: 2.1 Consensus size: 310
329615 CTAGGACTAA
* * *
329625 GTTCTTAAGAAATTACCAAAATGCCCTTAGGGGTATACCTTTGACGTAAAAGAATCCTGGCAACC
1 GTTC-TAAAAAATTACAAAAATGCCCTTA-GGGTATACCTTCGACGTAAAAGAATCCTGGCAACC
*
329690 CTAAAGGACTTAAAAAGACTCATAAGGGGATAAACCTATCCTAAATGCCAACCTTTGACATAAAA
64 CTAAAGGACTTAAAAAGACTCAGAAGGGGATAAACCTATCCTAAATGCCAACCTTTGA-ATAAAA
* * * * * *
329755 AGCGGACCCGGTGATGACCTAGGAATTTATTCTAAAAAATTACAAAAATGCCCTTAGAGGATACT
128 AACGAACCCGGTGACGACCTAGGAATTGATTCTAAAAAATTACAAAAATGCCCTAAGAGGATACC
* * * * * *
329820 TTCGATGTAAAAGTATCTCGATACCCCTAAAGGACTTAAAAAGGACTAGAGATGGGATGAACCTA
193 TTCGACGTAAAAGTAGCCCAATACCCCTAAAGGACTTAAAAAGGACTAGAAAAGGGATGAACCTA
* * * * *
329885 TCCTAAATGCCACCTTCAGCATAAAAGCAAACTCGGTGATGACTTAGGAGTTG
258 TCCTAAATGCCACCTTCAGCATAAAAGCAAACTCAGTGATCACGTAGAACTTG
* * * *
329938 GTTCTAGAAAATTACAAAAATACCCCTATGGGTATACCTTCGACGTAAAAGTATCC-GGCAACCC
1 GTTCTAAAAAATTACAAAAATGCCCTTA-GGGTATACCTTCGACGTAAAAGAATCCTGGCAACCC
* * * *
330002 TAAAGGACTTAAACAAGACT-AGAGATGGGATGAACCTATCCTAAATGCCCACCTTTG-GTAAAA
65 TAAAGGACTTAAA-AAGACTCAGA-AGGGGATAAACCTATCCTAAATGCCAACCTTTGAATAAAA
* ** * * ** *
330065 AACGAACCCGGGTGACGACTTAGGTGTTGGTTTTAGAAAAATTATGAGAATGCCCCTAAG-GGAT
128 AACGAACCC-GGTGACGACCTAGGAATTGATTCTA-AAAAATTACAAAAATG-CCCTAAGAGGAT
** * * *
330129 ACCTTCGACGTGGAAGT-GCCCAATACCCTTAAAGGACTTAAAAAGGACTATAAAAGTGATGAAC
190 ACCTTCGACGTAAAAGTAGCCCAATACCCCTAAAGGACTTAAAAAGGACTAGAAAAGGGATGAAC
** *
330193 CTATCCTAAATGCCCACCTTTGGCATAAAAGCGGAAC-CAGTGA-CATCGTAGAACTTG
255 CTATCCTAAATG-CCACCTTCAGCATAAAAGC-AAACTCAGTGATCA-CGTAGAACTTG
* *
330250 GTTCTAAAAAATTACGAGAATGCCCTTAGGGTATACCTT
1 GTTCTAAAAAATTACAAAAATGCCCTTAGGGTATACCTT
330289 TGATGTAGAA
Statistics
Matches: 292, Mismatches: 51, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
310 12 0.04
311 104 0.36
312 163 0.56
313 13 0.04
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (310 bp):
GTTCTAAAAAATTACAAAAATGCCCTTAGGGTATACCTTCGACGTAAAAGAATCCTGGCAACCCT
AAAGGACTTAAAAAGACTCAGAAGGGGATAAACCTATCCTAAATGCCAACCTTTGAATAAAAAAC
GAACCCGGTGACGACCTAGGAATTGATTCTAAAAAATTACAAAAATGCCCTAAGAGGATACCTTC
GACGTAAAAGTAGCCCAATACCCCTAAAGGACTTAAAAAGGACTAGAAAAGGGATGAACCTATCC
TAAATGCCACCTTCAGCATAAAAGCAAACTCAGTGATCACGTAGAACTTG
Found at i:330376 original size:155 final size:156
Alignment explanation
Indices: 330091--330378 Score: 386
Period size: 155 Copynumber: 1.9 Consensus size: 156
330081 GACTTAGGTG
* * *
330091 TTGGTTTTAGAAAAATTATGAGAATGCCCCTAAGGGATACCTTCGACGTGGAAGTGCCCAATACC
1 TTGGTTCTAGAAAAATTACGAGAATGCCCCTAAGGGATACCTTCGACGTAGAAGTGCCCAATACC
* * * * *
330156 CTTAAAGGACTTAAAAAGGACTATAAAAGTGATGAACCTATCCTAAATGCCCACCTTTGGCATAA
66 CTTAAAGAACTTAAAAAGGACTATAAAAGTGATGAACATATCCTAAATACCCACCTTCGACATAA
330221 AAGCGGAACCAGTGACATCGTAGAAC
131 AAGCGGAACCAGTGACATCGTAGAAC
* * * *
330247 TTGGTTCTA-AAAAATTACGAGAATG-CCCTTAGGGTATACCTTTGATGTAGAAGTGCCCGATAC
1 TTGGTTCTAGAAAAATTACGAGAATGCCCCTAAGGG-ATACCTTCGACGTAGAAGTGCCCAATAC
* * *
330310 GCTTTAAAGAACTTAAAAAGG-TTATAAAAG-GAATGAACATATCCTAAATACCCACCTTCGATA
65 -CCTTAAAGAACTTAAAAAGGACTATAAAAGTG-ATGAACATATCCTAAATACCCACCTTCGACA
330373 TAAAAG
128 TAAAAG
330379 TAGACCCGGT
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
154 9 0.08
155 79 0.69
156 26 0.23
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (156 bp):
TTGGTTCTAGAAAAATTACGAGAATGCCCCTAAGGGATACCTTCGACGTAGAAGTGCCCAATACC
CTTAAAGAACTTAAAAAGGACTATAAAAGTGATGAACATATCCTAAATACCCACCTTCGACATAA
AAGCGGAACCAGTGACATCGTAGAAC
Found at i:331132 original size:129 final size:130
Alignment explanation
Indices: 330963--331293 Score: 431
Period size: 130 Copynumber: 2.5 Consensus size: 130
330953 ATACAAAAAA
* *
330963 TTTGAAATCTTTTAATACCCCTATGGATATCC-ATAGGAATATAAAAGATTAAAAACT-ATTAAT
1 TTTGAAATCTTTT-ATATCCCTATGGATA-CCTATAGGAATATAAAAAATTAAAAA-TAATTAAT
* * *
331026 ATTTATTTAT-TTTTGAAAAAAAA-ATCATTTCATACGTTAATGGATACCTAAAAAGATACGAAA
63 ATTTATTTATGTTTTGAAAAAAAATAT-ATTTCATACCTTAATAGATACCCAAAAAGATACGAAA
331089 AGTT
127 AGTT
* * * * *
331093 TTTTAAATCTTTTATATCCCTACGGATACCTATAAGAATATAAAAAACTT-AAAATGATAAATAT
1 TTTGAAATCTTTTATATCCCTATGGATACCTATAGGAATATAAAAAA-TTAAAAATAATTAATAT
* * *
331157 TTATTTATGTTTTTAAAAAAAATATATTTCGTACCTTAATAGATACCCGAAAAGATACGAAAAGT
65 TTATTTATGTTTTGAAAAAAAATATATTTCATACCTTAATAGATACCCAAAAAGATACGAAAAGT
331222 T
130 T
*
331223 TTTGAAATCTTTTATATCCCTATGGATA-CTCATAGGAATATAAAAAATTAAAAATAATTAACAT
1 TTTGAAATCTTTTATATCCCTATGGATACCT-ATAGGAATATAAAAAATTAAAAATAATTAATAT
*
331287 TTGTTTA
65 TTATTTA
331294 AATTAACGGG
Statistics
Matches: 175, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
128 3 0.02
129 50 0.29
130 120 0.69
131 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (130 bp):
TTTGAAATCTTTTATATCCCTATGGATACCTATAGGAATATAAAAAATTAAAAATAATTAATATT
TATTTATGTTTTGAAAAAAAATATATTTCATACCTTAATAGATACCCAAAAAGATACGAAAAGTT
Found at i:331544 original size:127 final size:130
Alignment explanation
Indices: 331321--331585 Score: 403
Period size: 127 Copynumber: 2.1 Consensus size: 130
331311 TTTAATATTA
* *
331321 TTTATTTATTTTTGGAAAAAAAATCATTTCCTATCTTAATGGATACCCGAAAAGATACGAAAAGT
1 TTTATTTATGTTTGG-AAAAAAATCATTTCCTACCTTAATGGATACCCGAAAAGATACGAAAAGT
*
331386 TTTTCAGAATCTTATATACCCCTACGAATACCCATAGGAATATAAAAGATTAAAAAA-TATTAGA
65 TTTTCAGAATCTTATATACCCCTACGAATACCCATAAGAATATAAAAGATTAAAAAATTATTA-A
331450 TG
129 TG
* **
331452 TTTATTTATGTTTGG-AAAAAATCATTTCGTACCTTAATGGATACTTG-AAAGATACGAAAAGTT
1 TTTATTTATGTTTGGAAAAAAATCATTTCCTACCTTAATGGATACCCGAAAAGATACGAAAAGTT
* * *
331515 TTTGA-AATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATG
66 TTTCAGAATCTTATATACCCCTACGAATACCCATAAGAATATAAAAGATTAAAAAATTATTAATG
331579 TTTATTT
1 TTTATTT
331586 TAATTATCGA
Statistics
Matches: 124, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
127 57 0.46
128 25 0.20
129 28 0.23
131 14 0.11
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (130 bp):
TTTATTTATGTTTGGAAAAAAATCATTTCCTACCTTAATGGATACCCGAAAAGATACGAAAAGTT
TTTCAGAATCTTATATACCCCTACGAATACCCATAAGAATATAAAAGATTAAAAAATTATTAATG
Found at i:331631 original size:293 final size:292
Alignment explanation
Indices: 331025--331749 Score: 996
Period size: 292 Copynumber: 2.5 Consensus size: 292
331015 AAACTATTAA
* **
331025 TATTTATTTATTTTTGAAAAAAAAATCATTTCATACGTTAATGGATACCTAAAAAGATACGAAAA
1 TATTTATTTATTTTTGGAAAAAAAATCATTTCATAC-TTAATGGATACCCGAAAAGATACGAAAA
* * * * *
331090 GTTTTTTAAATCTTTTATATCCCTACGGATACCTATAAGAATATAAAAAACTT--AAAATGATAA
65 GTTTTTCAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGA-TTAAAAAAT-ATTA
* *
331153 ATATTTATTTATGTTTTTAAAAAAAATATATTTCGTACCTTAATAGATACCCGAAAAGATACGAA
128 ATGTTTATTTATG-TTTTAAAAAAAATACATTTCGTACCTTAATAGATACCCGAAAAGATACGAA
* * * *
331218 AAGTTTTTGAAATCTTTTATATCCCTATGGATACTCATAGGAATATAAAAAATTAAAAATAATTA
192 AAGTTTTTGAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAAATTAAAAATAATTA
*
331283 ACATTTGTTTAAATTAACGGGGAGTGAATTTAATAT
257 ACATTTATTTAAATTAACGGGGAGTGAATTTAATAT
*
331319 TATTTATTTATTTTTGGAAAAAAAATCATTTCCTATCTTAATGGATACCCGAAAAGATACGAAAA
1 TATTTATTTATTTTTGGAAAAAAAATCATTTCATA-CTTAATGGATACCCGAAAAGATACGAAAA
* * *
331384 GTTTTTCAGAATCTTATATACCCCTACGAATACCCATAGGAATATAAAAGATTAAAAAATATTAG
65 GTTTTTCA-AATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATATTA-
** * **
331449 ATGTTTATTTATG-TTTGGAAAAAAT-CATTTCGTACCTTAATGGATACTTG-AAAGATACGAAA
128 ATGTTTATTTATGTTTTAAAAAAAATACATTTCGTACCTTAATAGATACCCGAAAAGATACGAAA
* *
331511 AGTTTTTGAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTA
193 AGTTTTTGAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAAATT-AAAAATAATTA
** * *
331576 ATGTTTATTTTAATTATCGAGGG-GTGAATTTAATAT
257 ACATTTATTTAAATTAACG-GGGAGTGAATTTAATAT
* * *
331612 TATTTGTTTATTTTTGG-AAAAAAATCATTTCGTACCTTAATGGATACTCGAAAAGATACGAAAA
1 TATTTATTTATTTTTGGAAAAAAAATCATTTCATA-CTTAATGGATACCCGAAAAGATACGAAAA
*
331676 GTTTTTGAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAA
65 GTTTTTCAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAA-TATTAA
331741 TGTTTATTT
129 TGTTTATTT
331750 TAATTATCGA
Statistics
Matches: 385, Mismatches: 38, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
291 57 0.15
292 116 0.30
293 74 0.19
294 81 0.21
295 40 0.10
296 17 0.04
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (292 bp):
TATTTATTTATTTTTGGAAAAAAAATCATTTCATACTTAATGGATACCCGAAAAGATACGAAAAG
TTTTTCAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATATTAATG
TTTATTTATGTTTTAAAAAAAATACATTTCGTACCTTAATAGATACCCGAAAAGATACGAAAAGT
TTTTGAAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAAATTAAAAATAATTAACAT
TTATTTAAATTAACGGGGAGTGAATTTAATAT
Found at i:331692 original size:164 final size:164
Alignment explanation
Indices: 331456--331905 Score: 823
Period size: 164 Copynumber: 2.8 Consensus size: 164
331446 TAGATGTTTA
*
331456 TTTATGTTTGG-AAAAAATCATTTCGTACCTTAATGGATACTTG-AAAGATACGAAAAGTTTTTG
1 TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTTGAAAAGATACGAAAAGTTTTTG
331519 AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATGTTTAT
66 AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATGTTTAT
331584 TTTAATTATCGAGGGGTGAATTTAATATTATTTG
131 TTTAATTATCGAGGGGTGAATTTAATATTATTTG
*
331618 TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTCGAAAAGATACGAAAAGTTTTTG
1 TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTTGAAAAGATACGAAAAGTTTTTG
331683 AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATGTTTAT
66 AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATGTTTAT
331748 TTTAATTATCGAGGGGTGAATTTAATATTATTTG
131 TTTAATTATCGAGGGGTGAATTTAATATTATTTG
331782 TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTTGAAAAGATACGAAAAGTTTTTG
1 TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTTGAAAAGATACGAAAAGTTTTTG
* * * * *
331847 AAATCTTTTATACTCCTACGGATACTCATAGGAATATAAAAGATTTAAAAATGATTAAT
66 AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAAT
331906 ATTAAAATAT
Statistics
Matches: 278, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
162 10 0.04
163 31 0.11
164 237 0.85
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (164 bp):
TTTATTTTTGGAAAAAAATCATTTCGTACCTTAATGGATACTTGAAAAGATACGAAAAGTTTTTG
AAATCTTTTATACCCCTACGGATACCCATAAGAATATAAAAGATTAAAAAATTATTAATGTTTAT
TTTAATTATCGAGGGGTGAATTTAATATTATTTG
Found at i:332903 original size:15 final size:15
Alignment explanation
Indices: 332865--332903 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
332855 TTTGTCTTTC
*
332865 TTCATTTATTTGATT
1 TTCATTAATTTGATT
*
332880 TTCTTTTAATTTGATT
1 TTC-ATTAATTTGATT
332896 TTCATTAA
1 TTCATTAA
332904 ATTTTGTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (15 bp):
TTCATTAATTTGATT
Found at i:332906 original size:16 final size:16
Alignment explanation
Indices: 332872--332907 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
332862 TTCTTCATTT
* *
332872 ATTTGATTTTCTTTTA
1 ATTTGATTTTCATTAA
332888 ATTTGATTTTCATTAA
1 ATTTGATTTTCATTAA
332904 ATTT
1 ATTT
332908 TGTTAGACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (16 bp):
ATTTGATTTTCATTAA
Found at i:335122 original size:155 final size:154
Alignment explanation
Indices: 334829--335677 Score: 775
Period size: 155 Copynumber: 5.5 Consensus size: 154
334819 GTAACTACTA
* * * * * * *
334829 GGTCCGTTTTTATGCCAAAGGTGGGTATTTAGGATATGTTCATTCCTTTTATA-ACCTTTTTATG
1 GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAG
* *
334893 T-TCTTTAGGGGTATC-GGTACTTCTACGTCAAAGGTATCCCCTAGGGGCATTCTCATAATTTTT
66 TCT-TTTAGGGGTATCAGGTACTTCAACGTCGAAGGTATCCCCTAGGGGCATT-TCATAATTTTT
* *
334956 TAGAACCAAGTCTTAGGTTGTCACCG
129 TAGAACCAACTCTTAGGTCGTCACCG
* * * *
334982 GGTTTGCTTTTATGCTGAAGGTGGGCATTTAGGAGAGGTTCATCCCTTTTATAGTCCTTTTTAAG
1 GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAG
* *
335047 TCTTTTAGGGGTATCAGGTACTTCAACGTCGAAGGTATCCCCCAGGGGCATTCTCGTAATTTTTT
66 TCTTTTAGGGGTATCAGGTACTTCAACGTCGAAGGTATCCCCTAGGGGCATT-TCATAATTTTTT
* * * * **
335112 TGAACTAAGTCTTAGGTTGTCACTA
130 AGAACCAACTCTTAGGTCGTCACCG
* * * *
335137 GGTCTGCTTTTATGACGAAGGTGCGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAT
1 GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAG
* * ** *
335202 TCCTTTAGGGGTATCAGGTACTTCAATGTCGAAGGTATACCTATAAGGGCATTTTCATAATTTTT
66 TCTTTTAGGGGTATCAGGTACTTCAACGTCGAAGGTAT-CCCCTAGGGGCA-TTTCATAATTTTT
* * * *
335267 CTAAAACCAACTCCTAGGTCATTACCG
129 -TAGAACCAACTCTTAGGTCGTCACCG
* * * * * * * *
335294 AGTCCGTTTTTATGACGAAGGT-GCCATTTAGGATAGGTTCATCCCATATCTAGT-CTTTTCAAG
1 GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAG
* * * * *** * *** *
335357 TCTTTTAGGGTTTTCGGGAAACTTGTTCGTCAAAGGTATACTTATAGGGGTAGTTTCATAATTTT
66 TCTTTTAGGGGTATCAGG-TACTTCAACGTCGAAGGTAT-CCCCTAGGGGCA-TTTCATAATTTT
* * *
335422 CTAAAACCAACTCCTAGGTCGTCACCG
128 TTAGAACCAACTCTTAGGTCGTCACCG
* * * * *
335449 AGT-TAGTTTTTATGCCGAAGGTGGGCATTTAGGATAGATTCATCCCATCTCTAGTCCTTTTTAA
1 GGTCT-GTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAA
* * * * * *
335513 GTCCTTTAGGGGTACCAAGATACTTTC-ACCTCGAAAGTATCCCCTAGGGGCAATTTTATAA-TT
65 GTCTTTTAGGGGTATC-AGGTAC-TTCAACGTCGAAGGTATCCCCTAGGGGC-ATTTCATAATTT
* * *
335576 TTTGGAACTAACTCTTAGGTCGTCACCA
127 TTTAGAACCAACTCTTAGGTCGTCACCG
* * *** *
335604 GGTCTATTTTTATGCCGAAAGAAAGCATTTAGGATAGGTTCATCCC-TTTATGAGT-TTTTTTAA
1 GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTAT-AGTCCTTTTTAA
335667 GT-TCTTTAGGG
65 GTCT-TTTAGGG
335678 TTGCCGTGAT
Statistics
Matches: 571, Mismatches: 109, Indels: 31
0.80 0.15 0.04
Matches are distributed among these distances:
153 44 0.08
154 41 0.07
155 290 0.51
156 125 0.22
157 68 0.12
158 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.37
Consensus pattern (154 bp):
GGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAAG
TCTTTTAGGGGTATCAGGTACTTCAACGTCGAAGGTATCCCCTAGGGGCATTTCATAATTTTTTA
GAACCAACTCTTAGGTCGTCACCG
Found at i:335481 original size:312 final size:309
Alignment explanation
Indices: 334828--335526 Score: 712
Period size: 312 Copynumber: 2.3 Consensus size: 309
334818 GGTAACTACT
* * * * * *
334828 AGGTCCGTTTTTATGCCAAAGGTGGGTATTTAGGATATGTTCATTCCTTTTATA-ACCTTTTT-A
1 AGGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAA
* * * *
334891 TGTTCTTTAGGGGTATCGGTACTTCTACGTCAAAGGTATCCCCTAGGGGCATTCTCATAATTTTT
66 T-TCCTTTAGGGGTATCGGTACTTCAACGTCAAAGGTATCCCATAAGGGCATTCTCATAATTTTT
* * * ** * ** *
334956 TAGAACCAAGTCTTAGGTTGTCACCGGGTTTGCTTTTATGCTGAAGGTGGGCATTTAGGAGAGGT
130 TAAAACCAACTCCTAGGTCATCACCGAGTCCGCTTTTATGCTGAAGGTGGCCATTTAGGAGAGGT
* * * * *
335021 TCATCCCTTTTATAGTCCTTTTTAAGTCTTTTAGGGGTATCAGGTACTTCAACGTCGAAGGTATC
195 TCATCCCATATATAGTCCTTTTCAAGTCTTTTAGGGGTATCAGGAACTTCAACGTCAAAGGTATC
* * * ** * * * * *
335086 CCCCAGGGGCATTCTCGTAATTTTTTTGAACTAAGTCTTAGGTTGTCACT
260 CCACAGGGGCATTCTCATAATTTTCTAAAACCAACTCCTAGGTCGTCACG
* * *
335136 AGGTCTGCTTTTATGACGAAGGTGCGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAA
1 AGGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAA
* * * *
335201 TTCCTTTAGGGGTATCAGGTACTTCAATGTCGAAGGTATACCTATAAGGGCATTTTCATAATTTT
66 TTCCTTTAGGGGTATC-GGTACTTCAACGTCAAAGGTAT-CCCATAAGGGCATTCTCATAATTTT
* * *
335266 TCTAAAACCAACTCCTAGGTCATTACCGAGTCCGTTTTTATGAC-GAAGGT-GCCATTTAGGATA
129 T-TAAAACCAACTCCTAGGTCATCACCGAGTCCGCTTTTATG-CTGAAGGTGGCCATTTAGGAGA
* * * * ***
335329 GGTTCATCCCATATCTAGT-CTTTTCAAGTCTTTTAGGGTTTTCGGGAAACTTGTTCGTCAAAGG
192 GGTTCATCCCATATATAGTCCTTTTCAAGTCTTTTAGGGGTATCAGG-AACTTCAACGTCAAAGG
** * *
335393 TATACTTATAGGGGTAGTT-TCATAATTTTCTAAAACCAACTCCTAGGTCGTCACCG
256 TAT-CCCACAGGGGCA-TTCTCATAATTTTCTAAAACCAACTCCTAGGTCGTCA-CG
* * * *
335449 A-GT-TAGTTTTTATGCCGAAGGTGGGCATTTAGGATAGATTCATCCCATCTCTAGTCCTTTTTA
1 AGGTCT-GTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTA
*
335512 AGTCCTTTAGGGGTA
65 ATTCCTTTAGGGGTA
335527 CCAAGATACT
Statistics
Matches: 317, Mismatches: 63, Indels: 18
0.80 0.16 0.05
Matches are distributed among these distances:
308 46 0.15
309 21 0.07
310 44 0.14
311 65 0.21
312 136 0.43
313 5 0.02
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (309 bp):
AGGTCTGTTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCTTTTATAGTCCTTTTTAA
TTCCTTTAGGGGTATCGGTACTTCAACGTCAAAGGTATCCCATAAGGGCATTCTCATAATTTTTT
AAAACCAACTCCTAGGTCATCACCGAGTCCGCTTTTATGCTGAAGGTGGCCATTTAGGAGAGGTT
CATCCCATATATAGTCCTTTTCAAGTCTTTTAGGGGTATCAGGAACTTCAACGTCAAAGGTATCC
CACAGGGGCATTCTCATAATTTTCTAAAACCAACTCCTAGGTCGTCACG
Found at i:337757 original size:155 final size:154
Alignment explanation
Indices: 337489--337773 Score: 367
Period size: 155 Copynumber: 1.8 Consensus size: 154
337479 CCGGGTCTGT
*
337489 TTTTATGTCGAAGGTGAGTACTTAGGATAGTTTCATACTTTTATAACCTTTTAAAGTTCTTTAAG
1 TTTTATGTCGAAGGTGAGCACTTAGGATAGTTTCATACTTTTATAACCTTTTAAAGTTCTTTAAG
* * ** *
337554 GGTGTCGGGTACTTCTACGTCAAAGGTATCTCCTAGGGGCATCCTTGTAATTTTT-TAGAGCCAA
66 GGTATCAGGTACTTCTACGTCAAAGGTATCTCCTAAAGGCATCCTTGTAATTTTTCTAGAACCAA
337618 GTCTTAGATTGTCACCGAGTCCAC
131 GTCTTAGATTGTCACCGAGTCCAC
* * * * * * *
337642 TTTTATGTCGAAGGTGGGCATTTATGATAAG-TTCATCCCTTTTATAGTCTTTTTTAAGTTCTTT
1 TTTTATGTCGAAGGTGAGCACTTAGGAT-AGTTTCAT-ACTTTTATA-ACCTTTTAAAGTTCTTT
* * * **
337706 AGGGGTATCAGGTACTTCTACGTCGAAGGTATCTCCTAAAGGTATTTTTGTAATTTTTCTAGAAC
63 AAGGGTATCAGGTACTTCTACGTCAAAGGTATCTCCTAAAGGCATCCTTGTAATTTTTCTAGAAC
337771 CAA
128 CAA
337774 CTCCTATGTC
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
153 29 0.26
154 10 0.09
155 63 0.57
156 8 0.07
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (154 bp):
TTTTATGTCGAAGGTGAGCACTTAGGATAGTTTCATACTTTTATAACCTTTTAAAGTTCTTTAAG
GGTATCAGGTACTTCTACGTCAAAGGTATCTCCTAAAGGCATCCTTGTAATTTTTCTAGAACCAA
GTCTTAGATTGTCACCGAGTCCAC
Found at i:337850 original size:156 final size:154
Alignment explanation
Indices: 337536--338226 Score: 544
Period size: 156 Copynumber: 4.5 Consensus size: 154
337526 CTTTTATAAC
* * * * * **
337536 CTTTTAAAGTTCTTTAAGGGTGTCGGGTACTTCTACGTCAAAGGTATCTCCTAGGGGCATCCTTG
1 CTTTTTAAGTTCTTTAAGGGTATCAGGTACTTCTACGTCGAAGGTATCTCCTAAGGGCATTTTTG
* * * * ** * * *
337601 TAATTTTTTAGAGCCAAGTCTTAGATTGTCACCGAGTC-CACTTTTATGTCGAAGGTGGGCATTT
66 TAATTTTTTAGAACCAACTCCTAGGTCATCACC-AGGCTCGCTTTTATGCCGAAGGTGGGCATTT
* * * * *
337665 ATGATAAGTTCATCCCTTTTATAGT
130 AGGATAGGTTCATCCCATCTCTAGT
* * *
337690 CTTTTTTAAGTTCTTTAGGGGTATCAGGTACTTCTACGTCGAAGGTATCTCCTAAAGGTATTTTT
1 C-TTTTTAAGTTCTTTAAGGGTATCAGGTACTTCTACGTCGAAGGTATCTCCTAAGGGCATTTTT
* *
337755 GTAATTTTTCTAGAACCAACTCCTATGTCATCACCAGGCTCGGC-TTTATGCCGGAGGTGGGCAT
65 GTAATTTTT-TAGAACCAACTCCTAGGTCATCACCAGGCTC-GCTTTTATGCCGAAGGTGGGCAT
337819 TTAGGATAGGTTCATCCCATCTCTAGT
128 TTAGGATAGGTTCATCCCATCTCTAGT
* ** * * * *
337846 CTTTTTAAG-TCATTT-AGGGTTGTTGGGAAACTTTTACGTCGAAGGTAT-ACCTATAGGGGTAT
1 CTTTTTAAGTTC-TTTAAGGG-TATCAGG-TACTTCTACGTCGAAGGTATCTCCTA-A-GGGCAT
** * * * *
337908 TTTCATAATTTTTTAGAACCAACTCCTAGGTCATCACTAGGTTCGCTTTTATGCCAAATGTGGGC
61 TTTTGTAATTTTTTAGAACCAACTCCTAGGTCATCACCAGGCTCGCTTTTATGCCGAAGGTGGGC
337973 ATTTAGGATAGG-T--T--CATC-CTA--
126 ATTTAGGATAGGTTCATCCCATCTCTAGT
* * * * * *
337994 -TTTCT-AGTCCTTCAAGGGTACCGAGATACTT-TCACGTCGAAGGTATCCCCTAAGGGCATTTT
1 CTTTTTAAGTTCTTTAAGGGTATC-AGGTACTTCT-ACGTCGAAGGTATCTCCTAAGGGCATTTT
* * *
338056 TGTAATTTTTTAGAATCAACTCCTAGGTCATCACCGAGTC-CAG-TTTTATGCCGAAGGTTGGCA
64 TGTAATTTTTTAGAACCAACTCCTAGGTCATCACC-AGGCTC-GCTTTTATGCCGAAGGTGGGCA
* *
338119 TTTAGGATAGGTTCATCCCCT-TATGAGT
127 TTTAGGATAGGTTCATCCCATCTCT-AGT
* * * * * *
338147 CTTTTTAAG-TCTTTTAGGGT-TGCCGGGATACTT-TACATCAAAGGTATACCCCTACGGGCATT
1 CTTTTTAAGTTCTTTAAGGGTAT--CAGG-TACTTCTACGTCGAAGGTAT-CTCCTAAGGGCATT
*
338209 TTAGTAATTTTCTTAGAA
62 TTTGTAATTTT-TTAGAA
338227 ATTAGTCTTA
Statistics
Matches: 429, Mismatches: 75, Indels: 64
0.76 0.13 0.11
Matches are distributed among these distances:
145 69 0.16
146 27 0.06
147 14 0.03
148 1 0.00
150 6 0.01
151 5 0.01
153 1 0.00
154 30 0.07
155 119 0.28
156 140 0.33
157 17 0.04
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (154 bp):
CTTTTTAAGTTCTTTAAGGGTATCAGGTACTTCTACGTCGAAGGTATCTCCTAAGGGCATTTTTG
TAATTTTTTAGAACCAACTCCTAGGTCATCACCAGGCTCGCTTTTATGCCGAAGGTGGGCATTTA
GGATAGGTTCATCCCATCTCTAGT
Found at i:338274 original size:301 final size:302
Alignment explanation
Indices: 337725--338287 Score: 688
Period size: 301 Copynumber: 1.9 Consensus size: 302
337715 AGGTACTTCT
* * *
337725 ACGTCGAAGGTATCTCCTAAAGGTATTTTTGTAATTTTTCTAGAACCAACTCCTATGTCATCACC
1 ACGTCGAAGGTATCCCCTAAAGGCATTTTTGTAATTTTTCTAGAACCAACTCCTAGGTCATCACC
* * *
337790 AGGCTCGGCTTTATGCCGGAGGTGGGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAG
66 AGGCTCAGCTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCATCTATAGTCTTTTTAAG
** * * * * *
337855 TCATTTAGGGTTGTTGGGAAACTTTTACGTCGAAGGTATACCTATAGGGGTATTTTCATAATTTT
131 TCATTTAGGGTTGCCGGGAAACTTTTACATCAAAGGTATACCCATACGGGCATTTTCATAATTTT
* * * * * * * * * *
337920 TTAGAACCAACTCCTAGGTCATCACTAGGTTCGCTTTTATGCCAAATGTGGGCATTTAGGATAGG
196 TTAGAAACAACTCCTAGATAACCACGAGGTCCACTTTTACGCCAAAGGTGGGCATTGAGGATAGG
337985 TTCATCCTATTTCTAGTCCTTCAAGGGTACCGAGATACTTTC
261 TTCATCCTATTTCTAGTCCTTCAAGGGTACCGAGATACTTTC
* *
338027 ACGTCGAAGGTATCCCCTAAGGGCATTTTTGTAATTTTT-TAGAATCAACTCCTAGGTCATCACC
1 ACGTCGAAGGTATCCCCTAAAGGCATTTTTGTAATTTTTCTAGAACCAACTCCTAGGTCATCACC
* * * *
338091 GAGTC-CAGTTTTATGCCGAAGGTTGGCATTTAGGATAGGTTCATCCCCT-TATGAGTCTTTTTA
66 -AGGCTCAGCTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCATCTAT-AGTCTTTTTA
* * *
338154 AGTCTTTTAGGGTTGCCGGGATAC-TTTACATCAAAGGTATACCCCTACGGGCATTTT-AGTAAT
129 AGTCATTTAGGGTTGCCGGGAAACTTTTACATCAAAGGTATACCCATACGGGCATTTTCA-TAAT
** * * * *
338217 TTTCTTAGAAATTAGTCTTAGATAACCACCGA-GTCCACTTTTACGTCAAGGGTGGGCATTGAGG
193 TTT-TTAGAAACAACTCCTAGATAACCA-CGAGGTCCACTTTTACGCCAAAGGTGGGCATTGAGG
*
338281 GTAGGTT
256 ATAGGTT
338288 TGCCTTTTCA
Statistics
Matches: 217, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
299 1 0.00
300 36 0.17
301 139 0.64
302 41 0.19
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (302 bp):
ACGTCGAAGGTATCCCCTAAAGGCATTTTTGTAATTTTTCTAGAACCAACTCCTAGGTCATCACC
AGGCTCAGCTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCCCATCTATAGTCTTTTTAAG
TCATTTAGGGTTGCCGGGAAACTTTTACATCAAAGGTATACCCATACGGGCATTTTCATAATTTT
TTAGAAACAACTCCTAGATAACCACGAGGTCCACTTTTACGCCAAAGGTGGGCATTGAGGATAGG
TTCATCCTATTTCTAGTCCTTCAAGGGTACCGAGATACTTTC
Found at i:345452 original size:33 final size:33
Alignment explanation
Indices: 345387--345452 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
345377 AAATTCCCAG
* *
345387 ATGTATCGATACAAAGATCAATTTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCAATACA
**
345420 ATGTATCGATACATTGAAT-AATGTATCAATACA
1 ATGTATCGATACAAAG-ATCAATGTATCAATACA
345453 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCAATACA
Found at i:347016 original size:45 final size:45
Alignment explanation
Indices: 346952--347044 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
346942 CTCCAACCCC
346952 ATTTTTTAATCAAAAATTAAATCATTTTCTCTCTCCCAAAGTTTG
1 ATTTTTTAATCAAAAATTAAATCATTTTCTCTCTCCCAAAGTTTG
*
346997 ATTTTTTAATCAAAAATTAAATCATTTTCTCTCTCCCGAAGTTTG
1 ATTTTTTAATCAAAAATTAAATCATTTTCTCTCTCCCAAAGTTTG
347042 ATT
1 ATT
347045 CATTCTATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.45
Consensus pattern (45 bp):
ATTTTTTAATCAAAAATTAAATCATTTTCTCTCTCCCAAAGTTTG
Found at i:358451 original size:13 final size:13
Alignment explanation
Indices: 358426--358464 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
358416 ACAACATTCC
*
358426 TTGTATTGATACA
1 TTGTATCGATACA
*
358439 TTTTATCGATACA
1 TTGTATCGATACA
358452 TTGTATCGATACA
1 TTGTATCGATACA
358465 ATGGGTACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:360924 original size:13 final size:13
Alignment explanation
Indices: 360906--360930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
360896 CATTTTGCTT
360906 TGTATCGATACAC
1 TGTATCGATACAC
360919 TGTATCGATACA
1 TGTATCGATACA
360931 TGTTCAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:360930 original size:33 final size:32
Alignment explanation
Indices: 360888--360949 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
360878 CACCCAGATA
* **
360888 TATCGATACATTTTGCTTTGTATCGATACACTG
1 TATCGATACATGTT-CAATGTATCGATACACTG
360921 TATCGATACATGTTCAATGTATCGATACA
1 TATCGATACATGTTCAATGTATCGATACA
360950 TGAACAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (32 bp):
TATCGATACATGTTCAATGTATCGATACACTG
Found at i:360943 original size:19 final size:21
Alignment explanation
Indices: 360919--360974 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
360909 ATCGATACAC
**
360919 TGTATCGATACATGTTC-AA-
1 TGTATCGATACATGAACAAAT
360938 TGTATCGATACATGAACAAAT
1 TGTATCGATACATGAACAAAT
360959 TGTATCGATACATGAA
1 TGTATCGATACATGAA
360975 ATTGGCAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 2 0.06
21 16 0.48
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATGAACAAAT
Found at i:361043 original size:33 final size:32
Alignment explanation
Indices: 361001--361067 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
360991 CTATCACTAT
361001 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
*
361034 TTGTATCGATATATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
361067 T
1 T
361068 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:365452 original size:1 final size:1
Alignment explanation
Indices: 365446--365488 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
365436 TCCTTCGTAC
** * *
365446 AAAAAAAAACCAAAAAAAAAACAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
365489 CCCAAGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:365463 original size:12 final size:11
Alignment explanation
Indices: 365444--365571 Score: 96
Period size: 12 Copynumber: 10.7 Consensus size: 11
365434 CATCCTTCGT
365444 ACAAAAAAAAA
1 ACAAAAAAAAA
*
365455 CCAAAAAAAAA
1 ACAAAAAAAAA
365466 ACAAAAAAAAAA
1 AC-AAAAAAAAA
365478 ACAAAAAAAAA
1 ACAAAAAAAAA
*
365489 CCCAAGAAAAGAAA
1 -ACAA-AAAA-AAA
365503 ACAAAAAAATAGA
1 ACAAAAAAA-A-A
*
365516 A-AAAACCAAAA
1 ACAAAA-AAAAA
*
365527 GCAAAAAAAGTAA
1 ACAAAAAAA--AA
*
365540 AAAAAACAAAAA
1 ACAAAA-AAAAA
*
365552 ACAAACAAATAA
1 ACAAA-AAAAAA
365564 ACAAAAAA
1 ACAAAAAA
365572 GGGGCCTAGA
Statistics
Matches: 94, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
11 27 0.29
12 43 0.46
13 18 0.19
14 6 0.06
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.02
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:365476 original size:10 final size:10
Alignment explanation
Indices: 365444--365560 Score: 65
Period size: 10 Copynumber: 10.5 Consensus size: 10
365434 CATCCTTCGT
365444 ACAAAAAAAA
1 ACAAAAAAAA
365454 ACCAAAAAAAAA
1 A-C-AAAAAAAA
365466 ACAAAAAAAAAA
1 AC--AAAAAAAA
365478 ACAAAAAAAA
1 ACAAAAAAAA
365488 ACCCAAGAAAAGAAA
1 A--C-A-AAAA-AAA
*
365503 ACAAAAAAAT
1 ACAAAAAAAA
*
365513 AGAAAAAACCAA
1 ACAAAAAA--AA
*
365525 A-AGCAAAAAA
1 ACA-AAAAAAA
**
365535 AGTAAAAAAA
1 ACAAAAAAAA
365545 ACAAAAAACAA
1 ACAAAAAA-AA
365556 ACAAA
1 ACAAA
365561 TAAACAAAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 25
0.72 0.07 0.21
Matches are distributed among these distances:
10 34 0.40
11 14 0.16
12 28 0.33
13 2 0.02
14 4 0.05
15 4 0.05
ACGTcount: A:0.81, C:0.13, G:0.04, T:0.02
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:365478 original size:24 final size:23
Alignment explanation
Indices: 365446--365571 Score: 103
Period size: 25 Copynumber: 5.2 Consensus size: 23
365436 TCCTTCGTAC
*
365446 AAAAAAAAACCAAAAAAAAAACA
1 AAAAAAAAAACAAAAAAAAAACA
*
365469 AAAAAAAAAACAAAAAAAAACCCA
1 AAAAAAAAAACAAAAAAAAA-ACA
*
365493 AGAAAAGAAAACAAAAAAATAGAA-A
1 A-AAAAAAAAACAAAAAAA-A-AACA
** *
365518 AAACCAAAAGCAAAAAAAGTAAA-A
1 AAAAAAAAAACAAAAAAA--AAACA
*
365542 AAAACAAAAAACAAACAAATAAACA
1 AAAA-AAAAAACAAA-AAAAAAACA
365567 AAAAA
1 AAAAA
365572 GGGGCCTAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
23 19 0.23
24 26 0.31
25 33 0.40
26 4 0.05
27 1 0.01
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAACAAAAAAAAAACA
Found at i:366849 original size:28 final size:28
Alignment explanation
Indices: 366809--367612 Score: 904
Period size: 28 Copynumber: 28.3 Consensus size: 28
366799 CTAGAACGTT
366809 CATCTCTTT-AAAGCCTC-CAAGTTAGTGG
1 CATC-CTTTCAAAGCC-CACAAGTTAGTGG
** *
366837 CATCCTTTCAAAGCCCGTAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* * * *
366865 CATCTTTTCGAAGCCCACAAGTCAGTTG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* * *
366893 CACCCTTTCAAAGCCCATAAATTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
366921 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* * *
366949 CATCTTTTCAAAGCCCGCAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* *
366977 CAT-CTCTTCAAAAGACCACAAGTCAGTGG
1 CATCCT-TTC-AAAGCCCACAAGTTAGTGG
* * *
367006 CATCCTTTCAAAGCCCATAAGTCAATGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* *
367034 CACCCTTTCAAAGCCCACAAGTTAGTAG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
*
367062 TA-CCTTTTCAAAGCCCACAAGTTAGTGG
1 CATCC-TTTCAAAGCCCACAAGTTAGTGG
* *
367090 CATCCTTTCAAAGCCCATAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
367118 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
*
367146 CATCCTTTCAAAGCCCATAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
*
367174 CAT-CTCTTCAAAAGACCACAAGTTAGTGG
1 CATCCT-TTC-AAAGCCCACAAGTTAGTGG
*
367203 CACCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* *
367231 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* *
367259 CATCCTTTCAAAGCCCAGAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
*
367287 CAT-CTCTTCAAAAGACCACAAGTTAGTGG
1 CATCCT-TTC-AAAGCCCACAAGTTAGTGG
* *
367316 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
367344 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* **
367372 CATACCCTTTCAAAGCCCACACAAATCGGTGG
1 CAT--CCTTTCAAAG-CC-CACAAGTTAGTGG
367404 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
*
367432 CACCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* **
367460 CA-CCTTTTCAGAGCCCACAAGTCGGTGG
1 CATCC-TTTCAAAGCCCACAAGTTAGTGG
* * **
367488 CACCCTTTCAAAGCCCATAAGTCGGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* * * **
367516 CACCCTTTCAAGGCCCACCAGTCGGTGG
1 CATCCTTTCAAAGCCCACAAGTTAGTGG
* *
367544 CACCCTTTCAAAGCCCACACAAGTTGGTGG
1 CATCCTTTCAAAG-CC-CACAAGTTAGTGG
*
367574 CAACTCTTTTCAAAGCCCACACAAGTTAGTGG
1 C-A-TCCTTTCAAAG-CC-CACAAGTTAGTGG
367606 CA-CCTTT
1 CATCCTTT
367613 TTTTTTAAAA
Statistics
Matches: 677, Mismatches: 76, Indels: 45
0.85 0.10 0.06
Matches are distributed among these distances:
27 14 0.02
28 504 0.74
29 78 0.12
30 38 0.06
31 4 0.01
32 39 0.06
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
CATCCTTTCAAAGCCCACAAGTTAGTGG
Found at i:367047 original size:113 final size:112
Alignment explanation
Indices: 366814--367609 Score: 907
Period size: 113 Copynumber: 7.0 Consensus size: 112
366804 ACGTTCATCT
* ** * * * *
366814 CTTT-AAAGCCTC-CAAGTTAGTGGCATCCTTTCAAAGCCCGTAAGTCAGTGGCATCTTTTCGAA
1 CTTTCAAAGCC-CACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAA
* * * * * *
366877 GCCCACAAGTCAGTTGCACCCTTTCAAAGCCCATAAATTAGTGGCATC
65 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
366925 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCGCAAGTCAGTGGCA-TCTCTTCAAA
1 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCT-TTC-AA
* * *
366989 AGACCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAATGGCACC
64 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
367038 CTTTCAAAGCCCACAAGTTAGTAGTACCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAG
1 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG
* * *
367103 CCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATC
66 CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
367150 CTTTCAAAGCCCATAAGTTAGTGGCATCTCTTCAAAAGACCACAAGTTAGTGGCACCCTTTCAAA
1 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTC-AAAGCCCACAAGTTAGTGGCACCCTTTCAAA
* * *
367215 GCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATC
65 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
367263 CTTTCAAAGCCCAGAAGTCAGTGGCATCTCTTCAAAAGACCACAAGTTAGTGGCACCCTTTCAAA
1 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTC-AAAGCCCACAAGTTAGTGGCACCCTTTCAAA
*
367328 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATACC
65 GCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC--ACC
* ** *
367378 CTTTCAAAGCCCACACAAATCGGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAA
1 CTTTCAAAG-CC-CACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAA
* * *
367443 AGCCCACAAGTTAGTGGCA-CCTTTTCAGAGCCCACAAGTCGGTGGCACC
64 AGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACC
* ** * * * * **
367492 CTTTCAAAGCCCATAAGTCGGTGGCACCCTTTCAAGGCCCACCAGTCGGTGGCACCCTTTCAAAG
1 CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG
** * *
367557 CCCACACAAGTTGGTGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
66 -CC-CACAAGTCAGTGGC-A-TCCTTTCAAAG-CC-CACAAGTCAGTGGCACC
367610 TTTTTTTTTA
Statistics
Matches: 604, Mismatches: 63, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
111 6 0.01
112 168 0.28
113 277 0.46
114 27 0.04
115 14 0.02
116 77 0.13
117 20 0.03
118 15 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (112 bp):
CTTTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:368550 original size:20 final size:20
Alignment explanation
Indices: 368522--368780 Score: 185
Period size: 20 Copynumber: 11.8 Consensus size: 20
368512 TTTTTACCCA
*
368522 AATGCATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
368542 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
368562 AATGTATCGATACATTCTGTCTTTTTTACC
1 AATGTATCGATACA--------TTTTT--C
368592 TAGATGTATCGATACATTTTTC
1 -A-ATGTATCGATACATTTTTC
* * *
368614 AATGTATCGATACATGTATA
1 AATGTATCGATACATTTTTC
368634 AATGTATCGATACATTCTATCTTTTTATGC
1 AATGTATCGAT--A--C-A---TTTT-T-C
368664 AGATGTATCGATACATTTTTC
1 A-ATGTATCGATACATTTTTC
* * *
368685 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
368705 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
368725 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
368745 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
368765 AATGTATTGATACATT
1 AATGTATCGATACATT
368781 CTGTCTTTTT
Statistics
Matches: 190, Mismatches: 26, Indels: 46
0.73 0.10 0.18
Matches are distributed among these distances:
20 139 0.73
21 3 0.02
22 3 0.02
23 4 0.02
24 6 0.03
25 1 0.01
26 1 0.01
27 1 0.01
28 5 0.03
29 2 0.01
30 1 0.01
31 11 0.06
32 13 0.07
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:368629 original size:72 final size:70
Alignment explanation
Indices: 368512--368807 Score: 360
Period size: 71 Copynumber: 4.3 Consensus size: 70
368502 AAAAGTCACA
* *
368512 TTTTTACCCAAATGCATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTA-CCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
368577 TCTGTC
65 TCTGTC
*
368583 TTTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATAAATGTATCGATACA
1 -TTTTTACC-AGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA
*
368648 TTCTATC
64 TTCTGTC
*
368655 TTTTTATGCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA-
1 TTTTTA-CCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
368719 ------
65 TCTGTC
* * * * * * *
368719 TTTTT--CA-ATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATTGATACATT
1 TTTTTACCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
368781 CTGTC
66 CTGTC
*
368786 TTTTTACCCAGATATATCGATA
1 TTTTTA-CCAGATGTATCGATA
368808 TATTGAATGA
Statistics
Matches: 197, Mismatches: 14, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
60 46 0.23
61 2 0.01
64 5 0.03
67 5 0.03
70 2 0.01
71 72 0.37
72 65 0.33
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (70 bp):
TTTTTACCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATT
CTGTC
Found at i:368639 original size:40 final size:40
Alignment explanation
Indices: 368595--368779 Score: 228
Period size: 40 Copynumber: 4.8 Consensus size: 40
368585 TTTTACCTAG
368595 ATGTATCGATACATTTTTCAATGTATCGATACATGTATAA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATAA
* * * *
368635 ATGTATCGATACATTCTATC--T-T-T---T-TATG--CAG
1 ATGTATCGATACATT-TTTCAATGTATCGATACATGTATAA
*
368666 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATAA
*
368706 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATAA
*
368746 ATGTATCGATACATTTTTCAATGTATTGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
368780 TCTGTCTTTT
Statistics
Matches: 124, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
30 3 0.02
31 16 0.13
32 1 0.01
33 4 0.03
34 2 0.02
37 2 0.02
38 4 0.03
39 1 0.01
40 88 0.71
41 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (40 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATGTATAA
Found at i:368700 original size:71 final size:72
Alignment explanation
Indices: 368512--368720 Score: 341
Period size: 72 Copynumber: 2.9 Consensus size: 72
368502 AAAAGTCACA
* * *
368512 TTTTTACCCAAATGCATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
*
368577 TCTGTCT
66 TCTATCT
*
368584 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATAAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
368649 TCTATC-
66 TCTATCT
*
368655 TTTTTATGC-AGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA
1 TTTTTA-CCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA
368719 TT
65 TT
368721 TTTCAATGTA
Statistics
Matches: 129, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
71 62 0.48
72 67 0.52
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (72 bp):
TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTATCT
Found at i:368821 original size:131 final size:131
Alignment explanation
Indices: 368512--368830 Score: 334
Period size: 131 Copynumber: 2.3 Consensus size: 131
368502 AAAAGTCACA
* ** **
368512 TTTTTACCCAAATGCATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTAATCAATGTATCGATACATGTATGAATGTATCGATACA-
* *
368577 TCTGTCTTTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATGTATAAATGTATC
65 -------TTTTT--C-A-ATGTATCGATACATGTATCAATGTATCGATACATGTATAAATGTATC
368642 GATACATTCTATC
119 GATACATTCTATC
** * **
368655 TTTTTATGCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTAATCAATGTATCGATACATGTATGAATGTATCGATACAT
* * * * * *
368720 TTTTCAATGTATCGATACATGTATGAATGTATCGATACATTTTTCAATGTATTGATACATTCTGT
66 TTTTCAATGTATCGATACATGTATCAATGTATCGATACATGTATAAATGTATCGATACATTCTAT
368785 C
131 C
* *
368786 TTTTTACCCAGATATATCGATATATTGAAT-GATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATT-AATCAATGTATCGATACAT
368831 CTAGTTAAAA
Statistics
Matches: 156, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
131 88 0.56
132 2 0.01
133 1 0.01
135 5 0.03
143 60 0.38
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (131 bp):
TTTTTACCCAGATATATCGATACATTAATCAATGTATCGATACATGTATGAATGTATCGATACAT
TTTTCAATGTATCGATACATGTATCAATGTATCGATACATGTATAAATGTATCGATACATTCTAT
C
Found at i:375922 original size:20 final size:21
Alignment explanation
Indices: 375872--375928 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
375862 GTAAAAAGAC
*
375872 AGAATGTATCGATACATTCAT
1 AGAATGTATCGATACATTGAT
* *
375893 A-CATGCATCGATACATTGA-
1 AGAATGTATCGATACATTGAT
375912 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
375929 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AGAATGTATCGATACATTGAT
Found at i:375944 original size:71 final size:70
Alignment explanation
Indices: 375828--375999 Score: 229
Period size: 71 Copynumber: 2.4 Consensus size: 70
375818 AACTAGATGT
* *
375828 ATCGATACATTGAAAACTATATAGATACATCCGGGTAAAAAGACAGAATGTATCGATACATTCAT
1 ATCGATACATTGAAAA-TGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACATTCA-
*
375893 A-CATGC
64 AGAATGC
* *
375899 ATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAA
1 ATCGATACATTGAA-AATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACATTCAA
*
375964 GAATGT
65 GAATGC
* *
375970 ATCGATACATTCATACATGTATCGATACAT
1 ATCGATACATTGA-AAATGTATCGATACAT
376000 TGAAGAATGT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
70 1 0.01
71 86 0.96
72 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (70 bp):
ATCGATACATTGAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACATTCAAG
AATGC
Found at i:375968 original size:20 final size:20
Alignment explanation
Indices: 375943--376019 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
375933 GTAAAAAGAC
375943 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
375963 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
375983 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
376003 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
376020 CTGGGTACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 49 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:376798 original size:49 final size:45
Alignment explanation
Indices: 376720--376843 Score: 122
Period size: 49 Copynumber: 2.7 Consensus size: 45
376710 AGATGAGAGG
* ** *
376720 AGTGCCAATGTGCCAATTTAAGGCCAGCGACATTAGGCTAAGGGAAA
1 AGTGTCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAA--GAAA
* * *
376767 AGTGGATCAATGTGCTGATTCAAGGGCAGCGACATTGGGCTAATAAA
1 AGT-G-TCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAAGAAA
* * *
376814 AGTGTCAATATGCTGATTCAATGCTAGCGA
1 AGTGTCAATGTGCTGATTCAAGGCCAGCGA
376844 TGTCAGATAG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 22 0.34
46 1 0.02
47 9 0.14
48 1 0.02
49 31 0.48
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (45 bp):
AGTGTCAATGTGCTGATTCAAGGCCAGCGACATTAGGCTAAGAAA
Found at i:376834 original size:45 final size:48
Alignment explanation
Indices: 376739--376843 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 48
376729 GTGCCAATTT
*
376739 AAGGCCAGCGACATTAGGCTAAGGGAAAAGTGGATCAATGTGCTGATTC
1 AAGGCCAGCGACATTAGGCTAA-GGAAAAGTGGATCAATATGCTGATTC
* * *
376788 AAGGGCAGCGACATTGGGCTAA-TAAAAGT-G-TCAATATGCTGATTC
1 AAGGCCAGCGACATTAGGCTAAGGAAAAGTGGATCAATATGCTGATTC
* *
376833 AATGCTAGCGA
1 AAGGCCAGCGA
376844 TGTCAGATAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
45 22 0.45
46 1 0.02
47 6 0.12
49 20 0.41
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (48 bp):
AAGGCCAGCGACATTAGGCTAAGGAAAAGTGGATCAATATGCTGATTC
Found at i:377033 original size:28 final size:29
Alignment explanation
Indices: 376922--377107 Score: 297
Period size: 29 Copynumber: 6.4 Consensus size: 29
376912 CATTAACTTG
*
376922 TGTGGGCTTTGAAAAGAGTTACCACT-AGCT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGA-CT
376952 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
376981 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
* *
377010 TGTGGGCTTTGAAAGGA-TGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
377038 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
*
377067 TGTAGGCTTTG-AAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACT
377095 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
377108 GAGATGAGCG
Statistics
Matches: 146, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
28 53 0.36
29 74 0.51
30 19 0.13
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACT
Found at i:377048 original size:57 final size:57
Alignment explanation
Indices: 376922--377107 Score: 295
Period size: 57 Copynumber: 3.2 Consensus size: 57
376912 CATTAACTTG
*
376922 TGTGGGCTTTGAAAAGAGTTACCACT-AGCTTGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAG-TGCCACTGA-CTTGTGGGCTTTG-AAAGAGTGCCACTGACT
*
376981 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTAACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACT
*
377038 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTAGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
377095 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
377108 GAGATGAGCG
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
56 1 0.01
57 80 0.67
58 20 0.17
59 19 0.16
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (57 bp):
TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:383799 original size:32 final size:30
Alignment explanation
Indices: 383763--383821 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
383753 GAAAACAAAT
383763 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
383795 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
383822 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:384110 original size:13 final size:13
Alignment explanation
Indices: 384092--384117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384082 CAATTTTTTG
384092 TGTATCGATACAT
1 TGTATCGATACAT
384105 TGTATCGATACAT
1 TGTATCGATACAT
384118 ATTTGATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:384133 original size:32 final size:33
Alignment explanation
Indices: 384072--384135 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
384062 TACAAGCCAA
*
384072 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTGTGTATCGATACAT
384105 TGTATCGATAC-A-TATTTGATGTATCGATACA
1 TGTATCGATACAATTATTTG-TGTATCGATACA
384136 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 13 0.45
33 11 0.38
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATTATTTGTGTATCGATACAT
Found at i:388774 original size:15 final size:15
Alignment explanation
Indices: 388754--388784 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
388744 ATTTCGTTTG
*
388754 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
388769 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
388784 G
1 G
388785 GACATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:390616 original size:21 final size:21
Alignment explanation
Indices: 390587--390631 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
390577 AAGTTTTTAT
*
390587 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
390607 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
390629 TTT
1 TTT
390632 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:396553 original size:55 final size:57
Alignment explanation
Indices: 396469--396575 Score: 164
Period size: 55 Copynumber: 1.9 Consensus size: 57
396459 TTTTTTTTTT
* *
396469 CTTTCATGTTTCATGCATGCGTATGTTCATTTCATGCATA-A-GCATTTCATGCTCA
1 CTTTCATGTTTCATGCATGCATATGTTCATTTCATGCAAACATGCATTTCATGCTCA
* *
396524 CTTTCTTGTTTCATGCATGCATATGTTCATTTTATGCAAACATGCATTTCAT
1 CTTTCATGTTTCATGCATGCATATGTTCATTTCATGCAAACATGCATTTCAT
396576 ATGTTTATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 36 0.78
56 1 0.02
57 9 0.20
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (57 bp):
CTTTCATGTTTCATGCATGCATATGTTCATTTCATGCAAACATGCATTTCATGCTCA
Found at i:396866 original size:45 final size:45
Alignment explanation
Indices: 396811--396935 Score: 198
Period size: 45 Copynumber: 2.8 Consensus size: 45
396801 CAGCAATGAT
* * *
396811 GAAGACAAAGCAACA-TGGAACAGCAAAGCAACAATGAAGAAAGTG
1 GAAGACAAAGCAA-AGTGGAACAACAAAGCAACAAGGAAAAAAGTG
*
396856 GAAGAAAAAGCAAAGTGGAACAACAAAGCAACAAGGAAAAAAGTG
1 GAAGACAAAGCAAAGTGGAACAACAAAGCAACAAGGAAAAAAGTG
396901 GAAGACAAAGCAAAGTGGAACAACAAAGCAACAAG
1 GAAGACAAAGCAAAGTGGAACAACAAAGCAACAAG
396936 TTAAAGGGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
44 1 0.01
45 73 0.99
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (45 bp):
GAAGACAAAGCAAAGTGGAACAACAAAGCAACAAGGAAAAAAGTG
Found at i:396872 original size:17 final size:18
Alignment explanation
Indices: 396850--396886 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
396840 AACAATGAAG
*
396850 AAAGTGGAAGAA-AAAGC
1 AAAGTGGAACAACAAAGC
396867 AAAGTGGAACAACAAAGC
1 AAAGTGGAACAACAAAGC
396885 AA
1 AA
396887 CAAGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.11, G:0.24, T:0.05
Consensus pattern (18 bp):
AAAGTGGAACAACAAAGC
Found at i:396917 original size:17 final size:18
Alignment explanation
Indices: 396895--396931 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
396885 AACAAGGAAA
*
396895 AAAGTGGAA-GACAAAGC
1 AAAGTGGAACAACAAAGC
396912 AAAGTGGAACAACAAAGC
1 AAAGTGGAACAACAAAGC
396930 AA
1 AA
396932 CAAGTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (18 bp):
AAAGTGGAACAACAAAGC
Found at i:397152 original size:40 final size:40
Alignment explanation
Indices: 397105--397226 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
397095 TAACTTCCAA
* * *
397105 CAGCTCCCACGATAGCCTCTAGCAGCTCAGCAACCACCAG
1 CAGCTCCCACGACAGCCTCCAGCAGCTCAGCAACCACAAG
* * * * **
397145 TAGCTCCCATGGCAGTCTCCAATAGCTCAGCAACCACAAG
1 CAGCTCCCACGACAGCCTCCAGCAGCTCAGCAACCACAAG
* * *
397185 CAGCTCCCAC-AGCAGCTTCCAGCAGGTCAGCAACCACGAG
1 CAGCTCCCACGA-CAGCCTCCAGCAGCTCAGCAACCACAAG
397225 CA
1 CA
397227 ACTCTGCAGC
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.29, C:0.39, G:0.19, T:0.13
Consensus pattern (40 bp):
CAGCTCCCACGACAGCCTCCAGCAGCTCAGCAACCACAAG
Found at i:397289 original size:22 final size:22
Alignment explanation
Indices: 397262--397303 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
397252 CAGCTTTAGC
*
397262 AGCTCCCACAGCAACCTCCAGT
1 AGCTCCAACAGCAACCTCCAGT
*
397284 AGCTCCAACAGCAGCCTCCA
1 AGCTCCAACAGCAACCTCCA
397304 ACAGCTCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.45, G:0.14, T:0.12
Consensus pattern (22 bp):
AGCTCCAACAGCAACCTCCAGT
Found at i:397309 original size:22 final size:22
Alignment explanation
Indices: 397261--397310 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
397251 ACAGCTTTAG
* *
397261 CAGCTCCCACAGCAACCTCCAG
1 CAGCTCCAACAGCAACCTCCAA
* *
397283 TAGCTCCAACAGCAGCCTCCAA
1 CAGCTCCAACAGCAACCTCCAA
397305 CAGCTC
1 CAGCTC
397311 AGTAACCATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.46, G:0.14, T:0.12
Consensus pattern (22 bp):
CAGCTCCAACAGCAACCTCCAA
Found at i:400032 original size:21 final size:21
Alignment explanation
Indices: 399991--400032 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
399981 TTTTGGGCAT
* **
399991 CACGAGATGGTCGATTTTTAC
1 CACGAGAGGGTCGATCATTAC
400012 CACGAGAGGGTCGATCATTAC
1 CACGAGAGGGTCGATCATTAC
400033 TTGTGGCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
CACGAGAGGGTCGATCATTAC
Found at i:402363 original size:79 final size:77
Alignment explanation
Indices: 402258--402959 Score: 639
Period size: 79 Copynumber: 8.9 Consensus size: 77
402248 GAAATAATGG
** * * *
402258 GAGTATCCCCAATGGTGGAAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTTGA
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTT-AAAATAAAA-CGGGGTTGGAGTATCCCCTTGA
*
402323 AAATAACGGGGTTA
64 AAATAATGGGGTTA
* * * * *
402337 GAGTATCTCTAATTGTGAAAAATTGATATTTTGGAAATAAAATCGGGGTTGGAGTAT-CCCTTCG
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTT-AAAATAAAA-CGGGGTTGGAGTATCCCCTT-G
*
402401 AAAATAATGGGGTTG
63 AAAATAATGGGGTTA
* ** * * * **
402416 GAGTATCCCTGATTGTGAAAAATTTGTGTTTTAGAAATAAGATTGGGTTTAGAGTATCCTCTCAA
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTTA-AAATAA-AACGGGGTTGGAGTATCCCCTTGA
*
402481 AAATAATGGGGTCA
64 AAATAATGGGGTTA
**
402495 GAGTAT-CCTCGATTGTGAAAAATTGGTGTTTTCAAAATAAAACGGGGTTGGAGTATCCCCTAAA
1 GAGTATCCCT-GATTGTGAAAAATTGGTGTTTT-AAAATAAAACGGGGTTGGAGTATCCCCTTGA
402559 AAATAATGGGGTTA
64 AAATAATGGGGTTA
* * * *
402573 GAATATCCCTGATTATGGAAAATTGGTGTTGTAGAAATAAAACTGGGGTTGGAGTATCCCCTTCG
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTTA-AAATAAAAC-GGGGTTGGAGTATCCCCTT-G
* *
402638 -AAATAA-CGGGATA
63 AAAATAATGGGGTTA
*
402651 GGAGTAT-CCTCAATTGTGAAAAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTAT-CCCTT
1 -GAGTATCCCT-GATTGTGAAAAATTGGTGTTTTA-AAATAAAA-CGGGGTTGGAGTATCCCCTT
* * ** **
402714 AAAAAACAACAGGGTCG
62 -GAAAATAATGGGGTTA
* * * *
402731 GAGTAT-CCTCGATTGTGGAAAATTGGTGTTTTGGAAATAAAACCAGGGTTCGAGTATCCCCTTG
1 GAGTATCCCT-GATTGTGAAAAATTGGTGTTTT-AAAATAAAA-CGGGGTTGGAGTATCCCCTTG
* *
402795 GAAATAATGGGGTTG
63 AAAATAATGGGGTTA
* * *
402810 GAGTACCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCTCCCTAG
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTT-AAAATAAAAC-GGGGTTGGAGTATC-CCCTTG
*
402875 -GAATAATGGGGTTA
63 AAAATAATGGGGTTA
* * * * *
402889 AAGTATCCCCGATTGTAAAAAATTGGTG-TTTAAGGAATAAAACTAGGGTTGGAGTATCCCCTCG
1 GAGTATCCCTGATTGTGAAAAATTGGTGTTTTAA--AATAAAAC-GGGGTTGGAGTATCCCCTTG
*
402953 GAAATAA
63 AAAATAA
402960 AAACATGAAT
Statistics
Matches: 522, Mismatches: 78, Indels: 46
0.81 0.12 0.07
Matches are distributed among these distances:
77 3 0.01
78 94 0.18
79 404 0.77
80 21 0.04
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (77 bp):
GAGTATCCCTGATTGTGAAAAATTGGTGTTTTAAAATAAAACGGGGTTGGAGTATCCCCTTGAAA
ATAATGGGGTTA
Found at i:402849 original size:315 final size:315
Alignment explanation
Indices: 402259--402959 Score: 873
Period size: 315 Copynumber: 2.2 Consensus size: 315
402249 AAATAATGGG
* ** * *
402259 AGTATCCCCAATGGTGGAAAATTGATGTTTTGAAAATAAAA-TCGGGGTTGGAGTATCCCCTT-G
1 AGTATCCCCGATTATGGAAAATTGGTGTTTAG-AAATAAAACT-GGGGTTGGAGTATCCCCTTCG
* *
402322 AAAATAACGGGGTTAGAGTATCTCTAATTGTGAAAAATTGATATTTTGGAAATAAAATCGGGGTT
64 -AAATAACGGGGATAGAGTATCTCTAATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTT
** * ** * *
402387 GGAGTATCCCTTCGAAAATAATGGGGTTGGAGTATCCCTGATTGTGAAAAATTTGTGTTTTAGAA
128 GGAGTATCCCTTAAAAAACAACAGGGTCGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAA
* ** * * *
402452 ATAAGATTGGGTTTAGAGTATCCTCTCAAAAATAATGGGGTCAGAGTATCCTCGATTGTGAAAAA
193 ATAAAACAGGGTTTAGAGTATCCCCTCAAAAATAATGGGGTCAGAGTACCCCCGATTGTGAAAAA
402517 TTGGTGTTTTCAAAATAAAAC-GGGGTTGGAGTATC-CCCTAAAAAATAATGGGGTTAGA
258 TTGGTGTTTTCAAAATAAAACTGGGGTTGGAGTATCTCCCT-AAAAATAATGGGGTTA-A
*
402575 A-TATCCCTGATTATGGAAAATTGGTGTTGTAGAAATAAAACTGGGGTTGGAGTATCCCCTTCGA
1 AGTATCCCCGATTATGGAAAATTGGTGTT-TAGAAATAAAACTGGGGTTGGAGTATCCCCTTCGA
* *
402639 AATAAC-GGGATAGGAGTATC-CTCAATTGTGAAAAATTGGTGTTTTAGAAATAAAATCGGGGTT
65 AATAACGGGGATA-GAGTATCTCT-AATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTT
* *
402702 GGAGTATCCCTTAAAAAACAACAGGGTCGGAGTAT-CCTCGATTGTGGAAAATTGGTGTTTTGGA
128 GGAGTATCCCTTAAAAAACAACAGGGTCGGAGTATCCCT-GATTGTGAAAAATTGGTGTTTTAGA
* *** **
402766 AATAAAACCAGGG-TTCGAGTATCCCCTTGGAAATAATGGGGTTGGAGTACCCCCGATTGTGAAA
192 AATAAAA-CAGGGTTTAGAGTATCCCCTCAAAAATAATGGGGTCAGAGTACCCCCGATTGTGAAA
* **
402830 AATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCTCCCTAGGAATAATGGGGTTAA
256 AATTGGTGTTTTCAAAATAAAACTGGGGTTGGAGTATCTCCCTAAAAATAATGGGGTTAA
* ** * *
402890 AGTATCCCCGATTGTAAAAAATTGGTGTTTAAGGAATAAAACTAGGGTTGGAGTATCCCC-TCGG
1 AGTATCCCCGATTATGGAAAATTGGTGTTT-AGAAATAAAACTGGGGTTGGAGTATCCCCTTC-G
402954 AAATAA
64 AAATAA
402960 AAACATGAAT
Statistics
Matches: 333, Mismatches: 40, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
314 10 0.03
315 226 0.68
316 93 0.28
317 4 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (315 bp):
AGTATCCCCGATTATGGAAAATTGGTGTTTAGAAATAAAACTGGGGTTGGAGTATCCCCTTCGAA
ATAACGGGGATAGAGTATCTCTAATTGTGAAAAATTGATATTTTAGAAATAAAATCGGGGTTGGA
GTATCCCTTAAAAAACAACAGGGTCGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTAGAAATA
AAACAGGGTTTAGAGTATCCCCTCAAAAATAATGGGGTCAGAGTACCCCCGATTGTGAAAAATTG
GTGTTTTCAAAATAAAACTGGGGTTGGAGTATCTCCCTAAAAATAATGGGGTTAA
Found at i:406205 original size:117 final size:120
Alignment explanation
Indices: 405999--406436 Score: 573
Period size: 117 Copynumber: 3.6 Consensus size: 120
405989 TAAAGCGCGC
* * * * *
405999 CCTGCTCTTTGGGGACTAGAAGGTGCCACCAACTTTTGTGGGCTTTGAAAGTAAAGCATCCTACT
1 CCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACATCCTGCT
* * *
406064 TTTTGAGGACTAGAAGGTGCCACCAA-TTGTGTGGGCTTTGAAAGG-AAA-GCAT
66 CTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGCAT
* * * *
406116 CCTGCTCTTTGAGGATTGGAAGCTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACGTCCTGCT
1 CCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACATCCTGCT
* *
406181 CTTTGAGGACTGGAAGGTGCCACCAACTTATGTAGGCTTTGAAAGGAAAAGGCGT
66 CTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGCAT
*
406236 CCTGCTCTTTGAGGA-TAGACA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAACAAGCATCCT
1 CCTGCTCTTTGAGGACTAGA-AGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAA-AA-CATCCT
* *
406299 GCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCAT
63 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGCAT
* * * * *
406357 CCTACTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAAAGAAAGGGCGTCC
1 CCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAA--ACATCC
406421 TGCTCTTTGAGGACTG
62 TGCTCTTTGAGGACTG
406437 AAAGATAAAA
Statistics
Matches: 281, Mismatches: 28, Indels: 18
0.86 0.09 0.06
Matches are distributed among these distances:
117 80 0.28
118 17 0.06
119 36 0.13
120 21 0.07
121 75 0.27
122 26 0.09
123 26 0.09
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (120 bp):
CCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAACATCCTGCT
CTTTGAGGACTGGAAGGTGCCACCAACTTATGTGGGCTTTGAAAGGAAAAGGCAT
Found at i:406341 original size:61 final size:60
Alignment explanation
Indices: 405999--406440 Score: 558
Period size: 59 Copynumber: 7.4 Consensus size: 60
405989 TAAAGCGCGC
* * *
405999 CCTGCTCTTTGGGGACT-AGAAGGTGCCACCAACTTTTGTGGGCTTTGAAA-GTAAAGCAT
1 CCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCAT
* *
406058 CCTACTTTTTGAGGACT-AGAAGGTGCCACCAA-TTGTGTGGGCTTTGAAAGG-AAAGCAT
1 CCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCAT
* * * *
406116 CCTGCTCTTTGAGGATTGGAAGCTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-CGT
1 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCAT
* * * *
406175 CCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTATGTAGGCTTTGAAAGGAAAAGGCGT
1 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-GCAT
* *
406236 CCTGCTCTTTGAGGA-TAGACA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAACAAGCAT
1 CCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAA-AAGCAT
* *
406296 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAGGCAT
1 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAA-GCAT
* * * * *
406357 CCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAAAGAAAGGGCGT
1 CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAA-AGCAT
406419 CCTGCTCTTTGAGGACTGAAAG
1 CCTGCTCTTTGAGGACTGAAAG
406441 ATAAAAGGTT
Statistics
Matches: 340, Mismatches: 30, Indels: 23
0.87 0.08 0.06
Matches are distributed among these distances:
58 49 0.14
59 103 0.30
60 56 0.16
61 101 0.30
62 31 0.09
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (60 bp):
CCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGCAT
Found at i:407465 original size:15 final size:15
Alignment explanation
Indices: 407439--407499 Score: 86
Period size: 15 Copynumber: 3.9 Consensus size: 15
407429 TTTTTCTCTT
407439 TTTTTGTTGTTTTTTG
1 TTTTT-TTGTTTTTTG
*
407455 GTTTTTTGTTTTTTG
1 TTTTTTTGTTTTTTG
*
407470 TTTTTTTGGTTTTTG
1 TTTTTTTGTTTTTTG
407485 TTGTTTTTGTTTTTT
1 TT-TTTTTGTTTTTT
407500 TTTGTTTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 25 0.62
16 15 0.38
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (15 bp):
TTTTTTTGTTTTTTG
Found at i:407466 original size:25 final size:24
Alignment explanation
Indices: 407438--407499 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
407428 TTTTTTCTCT
407438 TTTTTTGTTGTTTTTTGGTTTTTTG
1 TTTTTTGTTGTTTTTTGG-TTTTTG
407463 TTTTTTG-T-TTTTTTGGTTTTTG
1 TTTTTTGTTGTTTTTTGGTTTTTG
*
407485 TTGTTT-TTGTTTTTT
1 TTTTTTGTTGTTTTTT
407500 TTTGTTTAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 12 0.35
23 14 0.41
24 1 0.03
25 7 0.21
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (24 bp):
TTTTTTGTTGTTTTTTGGTTTTTG
Found at i:407499 original size:7 final size:7
Alignment explanation
Indices: 407421--407499 Score: 70
Period size: 7 Copynumber: 10.9 Consensus size: 7
407411 TTCTTTTCTC
*
407421 TTTTTTC
1 TTTTTTG
*
407428 TTTTTTC
1 TTTTTTG
*
407435 TCTTTT-
1 TTTTTTG
*
407441 TTTGTTG
1 TTTTTTG
407448 TTTTTTGG
1 TTTTTT-G
407456 TTTTTTG
1 TTTTTTG
407463 TTTTTTG
1 TTTTTTG
407470 TTTTTTTG
1 -TTTTTTG
*
407478 GTTTTTG
1 TTTTTTG
407485 TTGTTTTTG
1 -T-TTTTTG
407494 TTTTTT
1 TTTTTT
407500 TTTGTTTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
6 4 0.07
7 36 0.59
8 15 0.25
9 6 0.10
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (7 bp):
TTTTTTG
Found at i:407500 original size:25 final size:24
Alignment explanation
Indices: 407439--407506 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
407429 TTTTTCTCTT
407439 TTTTTGTTGTTTTTTGG-TTTTTTG
1 TTTTTGTT-TTTTTTGGTTTTTTTG
407463 TTTTT-TGTTTTTTTGGTTTTTGTTG
1 TTTTTGT-TTTTTTTGGTTTTT-TTG
*
407488 TTTTTGTTTTTTTTTGTTT
1 TTTTTGTTTTTTTTGGTTT
407507 AGAAAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 9 0.23
24 10 0.26
25 19 0.49
26 1 0.03
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (24 bp):
TTTTTGTTTTTTTTGGTTTTTTTG
Found at i:410009 original size:33 final size:33
Alignment explanation
Indices: 409972--410039 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
409962 TTTGGATGGC
409972 CTTAGCCTTGTCAAGATCAAATTCTATTCCTTT
1 CTTAGCCTTGTCAAGATCAAATTCTATTCCTTT
410005 CTTAGCCTTGTCAAGATCAAATTCTATTCCTTT
1 CTTAGCCTTGTCAAGATCAAATTCTATTCCTTT
410038 CT
1 CT
410040 CACTTACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.43
Consensus pattern (33 bp):
CTTAGCCTTGTCAAGATCAAATTCTATTCCTTT
Found at i:410597 original size:19 final size:19
Alignment explanation
Indices: 410573--410610 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
410563 CCACCTCGAG
410573 AAAACCTGCTTCAAATTGT
1 AAAACCTGCTTCAAATTGT
410592 AAAACCTGCTTCAAATTGT
1 AAAACCTGCTTCAAATTGT
410611 TTCCTGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAACCTGCTTCAAATTGT
Found at i:414907 original size:20 final size:19
Alignment explanation
Indices: 414845--414916 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 19
414835 CACATCTAGA
* **
414845 TGTATCGATACATTATGCT
1 TGTATCGATACATTTTAAT
* *
414864 GTGTATCGATACATGTTCAT
1 -TGTATCGATACATTTTAAT
414884 TGTATCGATACATATTTAAT
1 TGTATCGATACAT-TTTAAT
414904 TGTATCGATACAT
1 TGTATCGATACAT
414917 GAAACTGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.29
20 32 0.71
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTAAT
Found at i:415423 original size:23 final size:23
Alignment explanation
Indices: 415380--415423 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
415370 GCATTCAACC
* *
415380 TTGGGTTATAATCTCTTAAGAAT
1 TTGGGGTATAATCTCTGAAGAAT
415403 TTGGGGTATAATACT-TGAAGA
1 TTGGGGTATAAT-CTCTGAAGA
415424 GATTGAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39
Consensus pattern (23 bp):
TTGGGGTATAATCTCTGAAGAAT
Found at i:416582 original size:12 final size:12
Alignment explanation
Indices: 416567--416599 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
416557 ACCATCAAAG
416567 ATGATGAAGATA
1 ATGATGAAGATA
*
416579 ATGATGATGATA
1 ATGATGAAGATA
416591 ATGATGAAG
1 ATGATGAAG
416600 TTGACTCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.27, T:0.27
Consensus pattern (12 bp):
ATGATGAAGATA
Found at i:417045 original size:16 final size:15
Alignment explanation
Indices: 417019--417066 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
417009 GGAAGAAAAT
417019 AAATAAAAATTTGTTGA
1 AAAT-AAAA-TTGTTGA
*
417036 AAATAAAATTCTTGA
1 AAATAAAATTGTTGA
*
417051 AAAGAAAATTGTTGA
1 AAATAAAATTGTTGA
417066 A
1 A
417067 CTAGAAAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 20 0.71
16 4 0.14
17 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.31
Consensus pattern (15 bp):
AAATAAAATTGTTGA
Found at i:427812 original size:51 final size:51
Alignment explanation
Indices: 427750--427895 Score: 231
Period size: 50 Copynumber: 2.9 Consensus size: 51
427740 TTTTAACTAG
* *
427750 ATGTATTGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
427801 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGT-AAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
427851 ATGTATCGATACATTGAAAAATGTATTGATACATCTGGGCAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
427896 TGTGACTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 45 0.52
51 41 0.48
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:429852 original size:31 final size:31
Alignment explanation
Indices: 429817--429891 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
429807 TGGAGGCTAG
* * *
429817 TGTGGGAGCTGTTGGAGCTG-TTGAAAGTTGC
1 TGTGGGAGCTGCTAGAGCTGCTAG-AAGTTGC
*
429848 TGTGGGAGCAGCTAGAGCTGCTAGAAGTTGC
1 TGTGGGAGCTGCTAGAGCTGCTAGAAGTTGC
*
429879 TGTGGGGGCTGCT
1 TGTGGGAGCTGCT
429892 CGTATTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 35 0.95
32 2 0.05
ACGTcount: A:0.16, C:0.13, G:0.43, T:0.28
Consensus pattern (31 bp):
TGTGGGAGCTGCTAGAGCTGCTAGAAGTTGC
Found at i:430168 original size:45 final size:44
Alignment explanation
Indices: 430052--430175 Score: 158
Period size: 45 Copynumber: 2.8 Consensus size: 44
430042 ATTTTTCAAC
* * * *
430052 TTGTTGCTTTGCTGTTCCACTTTGATTTATCTTCCACTTTCTTCC
1 TTGTTGCTTTGCTATTCCA-TTTGCTTTGTCTTCCACTTTCTTCA
* **
430097 TTGTTGCTTTGTTATTCCACACTGCTTTGTCTTCCACTTTCTTCA
1 TTGTTGCTTTGCTATTCCA-TTTGCTTTGTCTTCCACTTTCTTCA
430142 TTGTTGCTTTGCTATTCCATGTTGCTTTGTCTTC
1 TTGTTGCTTTGCTATTCCAT-TTGCTTTGTCTTC
430176 ATCATTGCTG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.09, C:0.25, G:0.13, T:0.53
Consensus pattern (44 bp):
TTGTTGCTTTGCTATTCCATTTGCTTTGTCTTCCACTTTCTTCA
Found at i:430439 original size:30 final size:30
Alignment explanation
Indices: 430393--430451 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
430383 AATGAAAGCA
*
430393 ATGCAATGAGATGAACATATGAAATGCATGT
1 ATGCAATGAAATGAACATATG-AATGCATGT
*
430424 ATGC-ATGAAATGAACATATGCATGCATG
1 ATGCAATGAAATGAACATATGAATGCATG
430452 AAACAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (30 bp):
ATGCAATGAAATGAACATATGAATGCATGT
Found at i:430489 original size:55 final size:55
Alignment explanation
Indices: 430423--430572 Score: 264
Period size: 55 Copynumber: 2.7 Consensus size: 55
430413 GAAATGCATG
*
430423 TATGCATGAAATGAACATATGCATGCATGAAACAAGAAAGTAAGCATGAAATGTT
1 TATGCACGAAATGAACATATGCATGCATGAAACAAGAAAGTAAGCATGAAATGTT
430478 TATGCACGAAATGAACATATGCATGCATGAAACAAGAAAGTAAGCATGAAATGTT
1 TATGCACGAAATGAACATATGCATGCATGAAACAAGAAAGTAAGCATGAAATGTT
* * *
430533 TATGCACGAAATGAACATACGCATGCATAAAACATGAAAG
1 TATGCACGAAATGAACATATGCATGCATGAAACAAGAAAG
430573 AAAAAAAAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.21
Consensus pattern (55 bp):
TATGCACGAAATGAACATATGCATGCATGAAACAAGAAAGTAAGCATGAAATGTT
Found at i:430675 original size:24 final size:24
Alignment explanation
Indices: 430643--430698 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
430633 ATCCTTTCAC
430643 ATTTTTTTTGGAATTTT-TTATTTT
1 ATTTTTTTTGG-ATTTTATTATTTT
* *
430667 CTTTTTTTTGGATTTTATTTTTTT
1 ATTTTTTTTGGATTTTATTATTTT
430691 ATTTTTTT
1 ATTTTTTT
430699 AAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (24 bp):
ATTTTTTTTGGATTTTATTATTTT
Found at i:431307 original size:87 final size:87
Alignment explanation
Indices: 431205--431646 Score: 348
Period size: 85 Copynumber: 5.1 Consensus size: 87
431195 GATTCCCCTG
* * * *
431205 GGTCAAAGCCAACAAGAAGACAAAAAAGAATGGAAAAGTCTCTAGAGTCAAAG-CTGATAGGTAG
1 GGTCAAAGCCGACAAGCAGACAAAAAAGAATGGAAAAGTCTCTAGAGTCAAAGTC-GACAGGCAG
**
431269 ACTTTAGATGAGACAGTCTCCAA
65 ACTTTAGATGAGGTAGTCTCCAA
* ** * ** * * * *
431292 GGTCAAAGCCGACAAGCAGAC-TAAGGGTA-GG-GCAGTCTCCTAGGGTCAAAGCCAACAGGCAC
1 GGTCAAAGCCGACAAGCAGACAAAAAAGAATGGAAAAGTCT-CTAGAGTCAAAGTCGACAGGCAG
* * * **
431354 AC-TAAGGGTAAGAAAGTCTCCAA
65 ACTTTA-GATGAGGTAGTCTCCAA
** * * * * *
431377 GGTCAAAGTTGACAGGCAGAC-AAAAAG-ATAGAAAAGTATCCA-AGGTCAAAGTCGACAGGTAG
1 GGTCAAAGCCGACAAGCAGACAAAAAAGAATGGAAAAGTCTCTAGA-GTCAAAGTCGACAGGCAG
431439 ACTTTAGATGAGGTAGTCTCCAA
65 ACTTTAGATGAGGTAGTCTCCAA
* * * * *
431462 GGTCAAAGCTGACAAGCAGATAAAAAA-AAGTGAAAAAGTCTCTAGGGTCAAAGTCGACAAGCAG
1 GGTCAAAGCCGACAAGCAGACAAAAAAGAA-TGGAAAAGTCTCTAGAGTCAAAGTCGACAGGCAG
* *
431526 ACTTTAGATGAGGTAGTCTCTAG
65 ACTTTAGATGAGGTAGTCTCCAA
* * * * * *
431549 GGTCAAAGCTGACAGGCAGATTAAAAAA-AATTGAAAAAGTCTCCA-AGGTCAAAGTCGACATGC
1 GGTCAAAGCCGACAAGCAGA-CAAAAAAGAA-TGGAAAAGTCTCTAGA-GTCAAAGTCGACAGGC
* *
431612 AGACTTTAGATGAGGTAGTCTCGAG
63 AGACTTTAGATGAGGTAGTCTCCAA
431637 GGTCAAAGCC
1 GGTCAAAGCC
431647 AAAAGGCAGA
Statistics
Matches: 285, Mismatches: 57, Indels: 25
0.78 0.16 0.07
Matches are distributed among these distances:
84 8 0.03
85 105 0.37
86 17 0.06
87 85 0.30
88 70 0.25
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (87 bp):
GGTCAAAGCCGACAAGCAGACAAAAAAGAATGGAAAAGTCTCTAGAGTCAAAGTCGACAGGCAGA
CTTTAGATGAGGTAGTCTCCAA
Found at i:431313 original size:42 final size:42
Alignment explanation
Indices: 431251--432753 Score: 535
Period size: 42 Copynumber: 35.5 Consensus size: 42
431241 AGTCTCTAGA
* * * *
431251 GTCAAAGCTGATAGGTAGACTTTAGATGAGACAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * ** *
431293 GTCAAAGCCGACAAGCAGAC-TAAG-GGTAGGGCAGTCTCCTAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCC-AAG
* * * * *
431336 GTCAAAGCCAACAGGCACAC-TAAGGGTAAGAAAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTA-GATGAGAAAGTCTCCAAG
** *** *
431378 GTCAAAGTTGACAGGCAGACAAAAAGAT-AGAAAAGTATCCAAG
1 GTCAAAGCCGACAGGCAGAC-TTTAGATGAG-AAAGTCTCCAAG
* * **
431421 GTCAAAGTCGACAGGTAGACTTTAGATGAGGTAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * ** * * * *
431463 GTCAAAGCTGACAAGCAGA-TAAAAAAAAGTGAAAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACT---TTAGA-TGAGAAAGTCTCCAAG
* * ** * *
431508 GTCAAAGTCGACAAGCAGACTTTAGATGAGGTAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * *
431550 GTCAAAGCTGACAGGCAGA-TTAAAAAAAATTGAAAAAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTT----TAGA-TGAGAAAGTCTCCAAG
* * ** * *
431596 GTCAAAGTCGACATGCAGACTTTAGATGAGGTAGTCTCGAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * * * *
431638 GTCAAAGCCAAAAGGCAGAC-TGAGGGTAAGAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTTTA-GATGAGAAAGTCTCCAAG
* * * *** * * *
431680 GTCAAAGCCAAGAGGCAGCCAAAAAGATGAAAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGAC-TTTAGATGAGAAAGTCTCCAAG
* * ** ** *
431723 GTCAAAGCCGATAGGTAGACTTTAGATGAGGCAGTCTTTAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * * *
431765 GTCAAAGTCGACAGGCAGAC-TAAAAGGTAGGAAACTCTCCACG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
* ** * *
431808 GTCAAAGCTGATTGGCAGAC-TAAGATG-GAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAG-AAAGTCTCCAAG
* * ** *
431849 GTCAAAGCCGATAGGTAGACTTTAGATGAGGCAGTCTCCAAC
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * *
431891 GTCAAAGCCGATAGGCAGAC-TAAG-GGTAGAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-AGAAAGTCTCCAAG
* * * * ** **
431932 GTCAAAGCTGACATGTAGACTTTAGATGGGGCAGTCTTTAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * * * **
431974 GTCAAAGCCAATAGGCAAAC-TGAG-GGTAGGAAAGTAT-TTAG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
** * ** * ***
432015 GATCAAAGCTAACAGACAGACTTTAGATGAGGCAGCCTCTTGG
1 G-TCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * ** * ***
432058 GTCAAAGTCGACATGTAGACTGAAG-GGTAGGAAAGTCTCTGGG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
* *
432101 GTCAAAGCTGACAGGCAGACTTTAGATGAGACAGTCTCCAGAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCA-AG
* * * * * * * * *
432144 TTCTAAGCCGATAGGCAAAC-TGAGGGTGAAGAAACTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTTTA-GATG-AGAAAGTCTCCAAG
* * * **
432187 GTCAAAGCCGACAAGCAAACTTTGGATGAGTCAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * *
432229 GCCAAAGCC-ATCAAGCAGAC-TGAG-GGTAGGAAAGTTTCCAAG
1 GTCAAAGCCGA-CAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
* * * ** * *
432271 GTCAAAGTCGACAGGTAGACTTTAGATAAGGTAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * *
432313 GTCAAAGCCGACATGAAGAC-TGA-ATGTAGGAAAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
* * * ** ** *
432355 GTTAAAGCTGATAGGCAGACTTTAGATGAGGCAGTCTTTAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* *
432397 GTCAAAGCCGACAGGCAGAC-TGAGGATGAAGAAAGCCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTA-GATG-AGAAAGTCTCCAAG
* * * * ** *
432440 GTCAAAGTCGATAAGTAGACTTTAGATGAGGCA-TCTCCAGG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * *
432481 GTCAAAGTCGTCAGGCAGAC-TAAG-GGTAGGAAAGTCTTCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATG-A-GAAAGTCTCCAAG
* **
432523 GTCAAAGCCAACAGGC-GAACTTTAGATGAGGTAGTCTCCAAG
1 GTCAAAGCCGACAGGCAG-ACTTTAGATGAGAAAGTCTCCAAG
** * *
432565 GTCAAAGCCGACAGGCAGACTGAAGGT-AGGAAAGTCTCCATG
1 GTCAAAGCCGACAGGCAGACTTTAGATGA-GAAAGTCTCCAAG
** * * * * ** * *
432607 GTCAAAGATGGCAGGTAGTCTTTAGATAAGGCAGTCTCTATG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* * * * * *
432649 GTCAAAGCCGACAGGCAAAC-TGAGGGTAAGAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTTTA-GATGAGAAAGTCTCCAAG
* ** * * **
432691 GTCAAACCCGAGGGGTAAACTTTAGATGAGGCAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
* *
432733 GTTAAAGCCAACAGGCAGACT
1 GTCAAAGCCGACAGGCAGACT
432754 GAAGGCAGAC
Statistics
Matches: 1052, Mismatches: 341, Indels: 136
0.69 0.22 0.09
Matches are distributed among these distances:
39 1 0.00
40 11 0.01
41 114 0.11
42 593 0.56
43 248 0.24
44 25 0.02
45 30 0.03
46 28 0.03
47 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (42 bp):
GTCAAAGCCGACAGGCAGACTTTAGATGAGAAAGTCTCCAAG
Found at i:431358 original size:43 final size:42
Alignment explanation
Indices: 431282--431384 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 42
431272 TTAGATGAGA
* *
431282 CAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAAGGGTAGGG
1 CAGTCTCCAAGGTCAAAGCCAACAAGCACACTAAGGGTAGGG
* * * *
431324 CAGTCTCCTAGGGTCAAAGCCAACAGGCACACTAAGGGTAAGA
1 CAGTCTCC-AAGGTCAAAGCCAACAAGCACACTAAGGGTAGGG
*
431367 AAGTCTCCAAGGTCAAAG
1 CAGTCTCCAAGGTCAAAG
431385 TTGACAGGCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 17 0.33
43 35 0.67
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (42 bp):
CAGTCTCCAAGGTCAAAGCCAACAAGCACACTAAGGGTAGGG
Found at i:431435 original size:85 final size:85
Alignment explanation
Indices: 431368--431645 Score: 353
Period size: 87 Copynumber: 3.2 Consensus size: 85
431358 AGGGTAAGAA
* * *
431368 AGTCTCCAAGGTCAAAGTTGACAGGCAGACAAAAAGATAG-AAAAGTATCCAAGGTCAAAGTCGA
1 AGTCTCCAAGGTCAAAGCTGACAGGCAGA-AAAAAAATAGAAAAAGTCTCCAAGGTCAAAGTCGA
*
431432 CAGGTAGACTTTAGATGAGGT
65 CAGGCAGACTTTAGATGAGGT
* * *
431453 AGTCTCCAAGGTCAAAGCTGACAAGCAGATAAAAAAA-AGTGAAAAAGTCTCTAGGGTCAAAGTC
1 AGTCTCCAAGGTCAAAGCTGACAGGCAGA-AAAAAAATA--GAAAAAGTCTCCAAGGTCAAAGTC
*
431517 GACAAGCAGACTTTAGATGAGGT
63 GACAGGCAGACTTTAGATGAGGT
* * *
431540 AGTCTCTAGGGTCAAAGCTGACAGGCAGATTAAAAAAAATTGAAAAAGTCTCCAAGGTCAAAGTC
1 AGTCTCCAAGGTCAAAGCTGACAGGCAG---AAAAAAAATAGAAAAAGTCTCCAAGGTCAAAGTC
*
431605 GACATGCAGACTTTAGATGAGGT
63 GACAGGCAGACTTTAGATGAGGT
* *
431628 AGTCTCGAGGGTCAAAGC
1 AGTCTCCAAGGTCAAAGC
431646 CAAAAGGCAG
Statistics
Matches: 169, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
84 1 0.01
85 33 0.20
86 1 0.01
87 65 0.38
88 61 0.36
89 7 0.04
90 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.19
Consensus pattern (85 bp):
AGTCTCCAAGGTCAAAGCTGACAGGCAGAAAAAAAATAGAAAAAGTCTCCAAGGTCAAAGTCGAC
AGGCAGACTTTAGATGAGGT
Found at i:431578 original size:88 final size:87
Alignment explanation
Indices: 431368--431645 Score: 373
Period size: 88 Copynumber: 3.2 Consensus size: 87
431358 AGGGTAAGAA
* * * * * *
431368 AGTCTCCAAGGTCAAAGTTGACAGGCAGA-CAAAAAGA-T-AGAAAAGTATCCAAGGTCAAAGTC
1 AGTCTCCAGGGTCAAAGCTGACAAGCAGATAAAAAAAAGTGA-AAAAGTCTCCAAGGTCAAAGTC
* *
431430 GACAGGTAGACTTTAGATGAGGT
65 GACAAGCAGACTTTAGATGAGGT
* * *
431453 AGTCTCCAAGGTCAAAGCTGACAAGCAGATAAAAAAAAGTGAAAAAGTCTCTAGGGTCAAAGTCG
1 AGTCTCCAGGGTCAAAGCTGACAAGCAGATAAAAAAAAGTGAAAAAGTCTCCAAGGTCAAAGTCG
431518 ACAAGCAGACTTTAGATGAGGT
66 ACAAGCAGACTTTAGATGAGGT
* * *
431540 AGTCTCTAGGGTCAAAGCTGACAGGCAGATTAAAAAAAATTGAAAAAGTCTCCAAGGTCAAAGTC
1 AGTCTCCAGGGTCAAAGCTGACAAGCAGA-TAAAAAAAAGTGAAAAAGTCTCCAAGGTCAAAGTC
*
431605 GACATGCAGACTTTAGATGAGGT
65 GACAAGCAGACTTTAGATGAGGT
*
431628 AGTCTCGAGGGTCAAAGC
1 AGTCTCCAGGGTCAAAGC
431646 CAAAAGGCAG
Statistics
Matches: 172, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
85 27 0.16
86 6 0.03
87 67 0.39
88 72 0.42
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.19
Consensus pattern (87 bp):
AGTCTCCAGGGTCAAAGCTGACAAGCAGATAAAAAAAAGTGAAAAAGTCTCCAAGGTCAAAGTCG
ACAAGCAGACTTTAGATGAGGT
Found at i:432049 original size:84 final size:83
Alignment explanation
Indices: 431239--432755 Score: 890
Period size: 84 Copynumber: 17.9 Consensus size: 83
431229 AAAGAATGGA
* * * *
431239 AAAGTCTCTAGAGTCAAAGCTGATAGGTAGACTTTAGATGAGACAGTCTCCAAGGTCAAAGCCGA
1 AAAGTCTCAAG-GTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
* *
431304 CAAGCAGACTAAGGGTAGG
65 CAGGCAGACTGAGGGTAGG
** * ** * * * * ** **
431323 GCAGTCTCCTAGGGTCAAAGCCAACAGGCACAC-TAAGGGTAAGAAAGTCTCCAAGGTCAAAGTT
1 AAAGTCT-C-AAGGTCAAAGCTGACAGGCAGACTTTA-GATGAGGCAGTCTCCAAGGTCAAAGCC
** * * *
431387 GACAGGCAGACAAAAAGATAGA
63 GACAGGCAGAC-TGAGGGTAGG
* * * *
431409 AAAGTATCCAAGGTCAAAG-TCGACAGGTAGACTTTAGATGAGGTAGTCTCCAAGGTCAAAGCTG
1 AAAGTCT-CAAGGTCAAAGCT-GACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* * ****
431473 ACAAGCAGA-TAAAAAAAAGTG
64 ACAGGCAGACT-GAGGGTAG-G
* * * * *
431494 AAAAAGTCTCTAGGGTCAAAG-TCGACAAGCAGACTTTAGATGAGGTAGTCTCTAGGGTCAAAGC
1 --AAAGTCTC-AAGGTCAAAGCT-GACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGC
* * * *** * *
431558 TGACAGGCAGATTAAAAAAAATTGAA
62 CGACAGGCAGACT---GAGGGTAG-G
* * * * *
431584 AAAGTCTCCAAGGTCAAAG-TCGACATGCAGACTTTAGATGAGGTAGTCTCGAGGGTCAAAGCCA
1 AAAGTCT-CAAGGTCAAAGCT-GACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* *
431648 AAAGGCAGACTGAGGGTAAG
64 ACAGGCAGACTGAGGGTAGG
* ** * * *** *** * *
431668 AAAGTCTCTAGGGTCAAAGCCAAGAGGCAGCCAAAAAGATGAAAAAGTCTCTAGGGTCAAAGCCG
1 AAAGTCTC-AAGGTCAAAGCTGACAGGCAGAC-TTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* * * *
431733 ATAGGTAGACTTTA-GATGAGG
64 ACAGGCAGAC-TGAGGGT-AGG
* * * * * * * * *
431754 -CAGTCTTTAGGGTCAAAG-TCGACAGGCAGAC-TAAAAGGTAGGAAACTCTCCACGGTCAAAGC
1 AAAGTC-TCAAGGTCAAAGCT-GACAGGCAGACTTTAGATG-AGG-CAGTCTCCAAGGTCAAAGC
* ** * *
431816 TGATTGGCAGACT-AAGAT-GG
62 CGACAGGCAGACTGAGGGTAGG
* * * * *
431836 AAAAGTCTCCAGGGTCAAAGCCGATAGGTAGACTTTAGATGAGGCAGTCTCCAACGTCAAAGCCG
1 -AAAGTCT-CAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* *
431901 ATAGGCAGACTAAGGGTA-G
64 ACAGGCAGACTGAGGGTAGG
* * * * ** *
431920 AAAGTCTCCAGGGTCAAAGCTGACATGTAGACTTTAGATGGGGCAGTCTTTAAGGTCAAAGCCAA
1 AAAGTCT-CAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
* *
431985 TAGGCAAACTGAGGGTAGG
65 CAGGCAGACTGAGGGTAGG
* ** * * * *** *
432004 AAAGTATTTAGGATCAAAGCTAACAGACAGACTTTAGATGAGGCAGCCTCTTGGGTCAAAGTCGA
1 AAAGTCTCAAGG-TCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
* *
432069 CATGTAGACTGAAGGGTAGG
65 CAGGCAGACTG-AGGGTAGG
** * * *
432089 AAAGTCTCTGGGGTCAAAGCTGACAGGCAGACTTTAGATGAGACAGTCTCCAGAGTTCTAAGCCG
1 AAAGTCTC-AAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCA-AGGTCAAAGCCG
* * *
432154 ATAGGCAAACTGAGGGTGAAG
64 ACAGGCAGACTGAGGGT-AGG
* * * * * * * *
432175 AAACTCTCTAGGGTCAAAGCCGACAAGCAAACTTTGGATGAGTCAGTCTCCAAGGCCAAAGCC-A
1 AAAGTCTC-AAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
*
432239 TCAAGCAGACTGAGGGTAGG
65 -CAGGCAGACTGAGGGTAGG
* * * * * *
432259 AAAGTTTCCAAGGTCAAAG-TCGACAGGTAGACTTTAGATAAGGTAGTCTCTAGGGTCAAAGCCG
1 AAAGTCT-CAAGGTCAAAGCT-GACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* * **
432323 ACATGAAGACTGAATGTAGG
64 ACAGGCAGACTGAGGGTAGG
* * ** *
432343 AAAGTCTCCAAGGTTAAAGCTGATAGGCAGACTTTAGATGAGGCAGTCTTTAGGGTCAAAGCCGA
1 AAAGTCT-CAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
* *
432408 CAGGCAGACTGAGGATGAAG
65 CAGGCAGACTGAGGGT-AGG
* * * * * *
432428 AAAGCCTCCAAGGTCAAAG-TCGATAAGTAGACTTTAGATGAGGCA-TCTCCAGGGTCAAAGTCG
1 AAAGTCT-CAAGGTCAAAGCT-GACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
* *
432491 TCAGGCAGACTAAGGGTAGG
64 ACAGGCAGACTGAGGGTAGG
** *
432511 AAAGTCTTCAAGGTCAAAGCCAACAGGC-GAACTTTAGATGAGGTAGTCTCCAAGGTCAAAGCCG
1 AAAGTC-TCAAGGTCAAAGCTGACAGGCAG-ACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCG
*
432575 ACAGGCAGACTGAAGGTAGG
64 ACAGGCAGACTGAGGGTAGG
* * * * * * * *
432595 AAAGTCTCCATGGTCAAAGATGGCAGGTAGTCTTTAGATAAGGCAGTCTCTATGGTCAAAGCCGA
1 AAAGTCT-CAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
* *
432660 CAGGCAAACTGAGGGTAAG
65 CAGGCAGACTGAGGGTAGG
* * * ** * * * *
432679 AAAGTCTCTAGGGTCAAACCCGAGGGGTAAACTTTAGATGAGGCAGTCTCCAAGGTTAAAGCCAA
1 AAAGTCTC-AAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGA
432744 CAGGCAGACTGA
65 CAGGCAGACTGA
432756 AGGCAGACAA
Statistics
Matches: 1120, Mismatches: 261, Indels: 104
0.75 0.18 0.07
Matches are distributed among these distances:
82 3 0.00
83 144 0.13
84 447 0.40
85 301 0.27
86 86 0.08
87 64 0.06
88 67 0.06
89 1 0.00
90 7 0.01
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (83 bp):
AAAGTCTCAAGGTCAAAGCTGACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGAC
AGGCAGACTGAGGGTAGG
Found at i:432758 original size:168 final size:167
Alignment explanation
Indices: 431251--432758 Score: 1053
Period size: 168 Copynumber: 8.9 Consensus size: 167
431241 AGTCTCTAGA
* * * * * * *
431251 GTCAAAGCTGATAGGTAGACTTTAGATGAGACAGTCTCCAAGGTCAAAGCCGACAAGCAGACTAA
1 GTCAAAG-TGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGA
** * * * * * **
431316 GGGTAGGGCAGTCTCCTAGGGTCAAAGCCAACAGGCACAC-TAAGGGTAAGAAAGTCTCCAAGGT
65 GGGTAGGAAAGTCT-CTAGGGTCAAAGCCGACAGGCAAACTTTA-GATGAGGCAGTCTCCAAGGT
** ** * * *
431380 CAAAGTTGACAGGCAGACAAAAAGATAGAAAAGTATCCAAG
128 CAAAGCCGACAGGCAGAC-TGAAGGTAGGAAAGTCTCCAAG
* * * * * *
431421 GTCAAAGTCGACAGGTAGACTTTAGATGAGGTAGTCTCCAAGGTCAAAGCTGACAAGCAGATAAA
1 GTCAAAGT-GACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGC--A-AAC
** ** * * * * * * *
431486 AAAAAGT-GAAAAAGTCTCTAGGGTCAAAGTCGACAAGCAGACTTTAGATGAGGTAGTCTCTAGG
62 TGAGGGTAG-GAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAG
* * * ** * *
431550 GTCAAAGCTGACAGGCAGATTAAAAAAAATTGAAAAAGTCTCCAAG
126 GTCAAAGCCGACAGGCAGACT---GAAGGTAG-GAAAGTCTCCAAG
* * * * * * *
431596 GTCAAAGTCGACATGCAGACTTTAGATGAGGTAGTCTCGAGGGTCAAAGCCAAAAGGCAGACTGA
1 GTCAAAGT-GACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGA
* * * ** *** *** * *
431661 GGGTAAGAAAGTCTCTAGGGTCAAAGCCAAGAGGCAGCCAAAAAGATGAAAAAGTCTCTAGGGTC
65 GGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAAC-TTTAGATGAGGCAGTCTCCAAGGTC
* * ** * * ** *
431726 AAAGCCGATAGGTAGACTTTAGATGAGG-CAGTCTTTAGG
129 AAAGCCGACAGGCAGACTGAAGGT-AGGAAAGTCTCCAAG
* * * * * * * * * ** *
431765 GTCAAAGTCGACAGGCAGAC-TAAAAGGTAGGAAACTCTCCACGGTCAAAGCTGATTGGCAGACT
1 GTCAAAGT-GACAGGTAGACTTTAGATG-AGG-CAGTCTCTAGGGTCAAAGCCGACAGGCAAACT
* * * * * * *
431829 -AAGAT-GGAAAAGTCTCCAGGGTCAAAGCCGATAGGTAGACTTTAGATGAGGCAGTCTCCAACG
63 GAGGGTAGG-AAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGG
* *
431892 TCAAAGCCGATAGGCAGACT-AAGGGTA-GAAAGTCTCCAGG
127 TCAAAGCCGACAGGCAGACTGAA-GGTAGGAAAGTCTCCAAG
* * * * * *
431932 GTCAAAGCTGACATGTAGACTTTAGATGGGGCAGTCTTTAAGGTCAAAGCCAATAGGCAAACTGA
1 GTCAAAG-TGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGA
* * * ** * * * ***
431997 GGGTAGGAAAGTATTTAGGATCAAAGCTAACAGACAGACTTTAGATGAGGCAGCCTCTTGGGTCA
65 GGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGTCA
* * * ***
432062 AAGTCGACATGTAGACTGAAGGGTAGGAAAGTCTCTGGG
130 AAGCCGACAGGCAGACTGAA-GGTAGGAAAGTCTCCAAG
* * * * * *
432101 GTCAAAGCTGACAGGCAGACTTTAGATGAGACAGTCTCCAGAGTTCTAAGCCGATAGGCAAACTG
1 GTCAAAG-TGACAGGTAGACTTTAGATGAGGCAGTCTCTAG-GGTCAAAGCCGACAGGCAAACTG
* * * * * *
432166 AGGGTGAAGAAACTCTCTAGGGTCAAAGCCGACAAGCAAACTTTGGATGAGTCAGTCTCCAAGGC
64 AGGGT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGT
* * *
432231 CAAAGCC-ATCAAGCAGACTGAGGGTAGGAAAGTTTCCAAG
128 CAAAGCCGA-CAGGCAGACTGAAGGTAGGAAAGTCTCCAAG
* * *
432271 GTCAAAGTCGACAGGTAGACTTTAGATAAGGTAGTCTCTAGGGTCAAAGCCGACATG-AAGACTG
1 GTCAAAGT-GACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAA-ACTG
** * * * * * * ** *
432335 AATGTAGGAAAGTCTCCAAGGTTAAAGCTGATAGGCAGACTTTAGATGAGGCAGTCTTTAGGGTC
64 AGGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGTC
* *
432400 AAAGCCGACAGGCAGACTG-AGGATGAAGAAAGCCTCCAAG
129 AAAGCCGACAGGCAGACTGAAGG-T-AGGAAAGTCTCCAAG
* * * * * * *
432440 GTCAAAGTCGATAAGTAGACTTTAGATGAGGCA-TCTCCAGGGTCAAAGTCGTCAGGCAGACTAA
1 GTCAAAGT-GACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGA
* * * *
432504 GGGTAGGAAAGTCT-TCAAGGTCAAAGCCAACAGGCGAACTTTAGATGAGGTAGTCTCCAAGGTC
65 GGGTAGGAAAGTCTCT-AGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGTC
*
432568 AAAGCCGACAGGCAGACTGAAGGTAGGAAAGTCTCCATG
129 AAAGCCGACAGGCAGACTGAAGGTAGGAAAGTCTCCAAG
* * * *
432607 GTCAAAGATGGCAGGTAGTCTTTAGATAAGGCAGTCTCTATGGTCAAAGCCGACAGGCAAACTGA
1 GTCAAAG-TGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGA
* * ** * *
432672 GGGTAAGAAAGTCTCTAGGGTCAAACCCGAGGGGTAAACTTTAGATGAGGCAGTCTCCAAGGTTA
65 GGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGTCA
*
432737 AAGCCAACAGGCAGACTGAAGG
130 AAGCCGACAGGCAGACTGAAGG
432759 CAGACAAAAA
Statistics
Matches: 1045, Mismatches: 255, Indels: 78
0.76 0.19 0.06
Matches are distributed among these distances:
166 24 0.02
167 128 0.12
168 311 0.30
169 172 0.16
170 153 0.15
171 59 0.06
172 84 0.08
173 46 0.04
174 6 0.01
175 62 0.06
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (167 bp):
GTCAAAGTGACAGGTAGACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGACAGGCAAACTGAG
GGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAAGGTCAA
AGCCGACAGGCAGACTGAAGGTAGGAAAGTCTCCAAG
Found at i:436030 original size:59 final size:59
Alignment explanation
Indices: 435938--436051 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
435928 TTCCAACTTA
* * * * *
435938 TCCTATTATAACGCTTACCTATTTCTTAATTTTAAATGTTCTCCCCCTATGTGTTCTCC
1 TCCTATTATAACACTTACCTATTACTCAATTTTAAACGTTCTCCCCATATGTGTTCTCC
435997 TCCTATTATAACACTT-CTCTATTACTCAATTTTAAACGTTCTCCCCATATGTGTT
1 TCCTATTATAACACTTAC-CTATTACTCAATTTTAAACGTTCTCCCCATATGTGTT
436052 ATAAGCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
58 1 0.02
59 48 0.98
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (59 bp):
TCCTATTATAACACTTACCTATTACTCAATTTTAAACGTTCTCCCCATATGTGTTCTCC
Found at i:438005 original size:40 final size:40
Alignment explanation
Indices: 437947--438038 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
437937 TATCGATGCA
*
437947 ATGTATCGATACTGAGTGAGTTTTAGCTACTGCTAATTTT
1 ATGTATCGATACTAAGTGAGTTTTAGCTACTGCTAATTTT
*
437987 CTGTATCGATACTAAGTGAGTTTTAGCTACTGCTAATTTT
1 ATGTATCGATACTAAGTGAGTTTTAGCTACTGCTAATTTT
*
438027 ATATATCGATAC
1 ATGTATCGATAC
438039 AATTTAATGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACTAAGTGAGTTTTAGCTACTGCTAATTTT
Found at i:440787 original size:20 final size:21
Alignment explanation
Indices: 440756--440795 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
440746 ATCTGGGTTT
*
440756 TTTAGATGTATTGATACATTA
1 TTTAGATGTATTAATACATTA
440777 TTTAG-TGTATTAATACATT
1 TTTAGATGTATTAATACATT
440796 CTGAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (21 bp):
TTTAGATGTATTAATACATTA
Found at i:446837 original size:13 final size:13
Alignment explanation
Indices: 446819--446856 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
446809 ACATTTCACC
446819 ATGTATCGATACA
1 ATGTATCGATACA
446832 ATGTATCGATACA
1 ATGTATCGATACA
*
446845 CTGTATCGATAC
1 ATGTATCGATAC
446857 TAAGTGAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:446941 original size:13 final size:13
Alignment explanation
Indices: 446923--446948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
446913 TACCAAGAAC
446923 ATGTATCGATACA
1 ATGTATCGATACA
446936 ATGTATCGATACA
1 ATGTATCGATACA
446949 TCTAGGTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:447931 original size:13 final size:13
Alignment explanation
Indices: 447913--447938 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
447903 CATTATGCTG
447913 TGTATCGATACAT
1 TGTATCGATACAT
447926 TGTATCGATACAT
1 TGTATCGATACAT
447939 GTTCATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:447968 original size:20 final size:19
Alignment explanation
Indices: 447922--447978 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
447912 GTGTATCGAT
*
447922 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
447941 TCATTGTATCGGTACATGG
1 ACATTGTATCGATACATGG
447960 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
447979 AAACTGGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:448050 original size:33 final size:33
Alignment explanation
Indices: 448008--448072 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
447998 TACCACTGTT
* *
448008 TGTATCGATACATG-TTACATTGTATGGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
448041 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
448073 TTGCTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:451024 original size:10 final size:10
Alignment explanation
Indices: 451009--451034 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
450999 TTTGGAAGAA
451009 GAATTTGATG
1 GAATTTGATG
451019 GAATTTGATG
1 GAATTTGATG
451029 GAATTT
1 GAATTT
451035 TGTTGATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (10 bp):
GAATTTGATG
Found at i:454890 original size:20 final size:19
Alignment explanation
Indices: 454865--454942 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 19
454855 ACTACCAAGG
454865 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATT-AT
*
454885 AAATGTATCGATACATGCTTT
1 AAATGTATCGATACAT--TAT
454906 AAATTGTATCGATACATTTAT
1 AAA-TGTATCGATACA-TTAT
* *
454927 CATTGTATCGATACAT
1 AAATGTATCGATACAT
454943 GCAGACAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
19 1 0.02
20 28 0.56
21 7 0.14
22 13 0.26
23 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (19 bp):
AAATGTATCGATACATTAT
Found at i:459660 original size:13 final size:13
Alignment explanation
Indices: 459642--459666 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459632 CATAAAGTGT
459642 TGTATCGATACAA
1 TGTATCGATACAA
459655 TGTATCGATACA
1 TGTATCGATACA
459667 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:459664 original size:33 final size:33
Alignment explanation
Indices: 459622--459688 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
459612 TTCAACGATT
459622 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
459655 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
459688 T
1 T
459689 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:459749 original size:13 final size:13
Alignment explanation
Indices: 459731--459755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459721 ATTACTCAAA
459731 TGTATCGATACAT
1 TGTATCGATACAT
459744 TGTATCGATACA
1 TGTATCGATACA
459756 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:459805 original size:32 final size:32
Alignment explanation
Indices: 459764--459838 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
459754 CACTGATCTT
459764 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGA
*
459796 TGTATCGATACATGCAGGCAAATTTGCCTAGA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGA
459828 TGTATCGATAC
1 TGTATCGATAC
459839 TTTATAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (32 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:459851 original size:52 final size:52
Alignment explanation
Indices: 459795--459920 Score: 198
Period size: 52 Copynumber: 2.4 Consensus size: 52
459785 ATTTGCCCAG
* * **
459795 ATGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGATACTTTATAAA
1 ATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAA
*
459847 ATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATTAA
1 ATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAA
*
459899 ATGTATCGATACATGCAAGCAA
1 ATGTATCGATACATGCAGGCAA
459921 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAA
Found at i:465575 original size:24 final size:24
Alignment explanation
Indices: 465548--465595 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
465538 GCGGAAGCAT
465548 AAAAAAATGA-AAAAAAAAAAGAAG
1 AAAAAAAT-ACAAAAAAAAAAGAAG
* *
465572 AAAAACATACACAAAAAAAAGAAG
1 AAAAAAATACAAAAAAAAAAGAAG
465596 TGCAAAGGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.79, C:0.06, G:0.10, T:0.04
Consensus pattern (24 bp):
AAAAAAATACAAAAAAAAAAGAAG
Found at i:466788 original size:33 final size:33
Alignment explanation
Indices: 466751--466815 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
466741 TACCACTGTT
*
466751 TGTATCGATACATGCT-ACATTGTATAGATACAA
1 TGTATCGATACATGATGA-ATTGTATAGATACAA
*
466784 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATAGATACA
466816 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATAGATACAA
Found at i:473700 original size:79 final size:77
Alignment explanation
Indices: 473603--473785 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 77
473593 GGTGTTTTGT
** * *
473603 AAATAAAATTGGGGTTGGAGTATCCTCT-CGAAAATAACAGGG-TTGGAGTATCCACGATTGTGA
1 AAATAAAA-TGGGGTTGGAGTATCC-CTACGAAAATAAC-GGGATTACAGTATCCACGATTATCA
473666 AAAATCGATGCTTTAG
63 AAAAT-GATGCTTTAG
** *
473682 AAATAAGGCTGGGGTTGGAGTATCCCTACGAAAATAACGGGATTACAGTATCCTCGATTATCAAA
1 AAATAA-AATGGGGTTGGAGTATCCCTACGAAAATAACGGGATTACAGTATCCACGATTATCAAA
* *
473747 AATTATGTTTTAG
65 AATGATGCTTTAG
473760 AAATAAAATAGGGGTTGGAGTATCCC
1 AAATAAAAT-GGGGTTGGAGTATCCC
473786 CGATTGTAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 35 0.39
79 53 0.60
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (77 bp):
AAATAAAATGGGGTTGGAGTATCCCTACGAAAATAACGGGATTACAGTATCCACGATTATCAAAA
ATGATGCTTTAG
Found at i:473790 original size:50 final size:51
Alignment explanation
Indices: 473728--473837 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
473718 ACGGGATTAC
* * *
473728 AGTATCCTCGATTATCAA-AAAT-TATGTTTTAGAAATAAAATAGGGGTTGG
1 AGTATCCCCGATTAT-AAGAAATCAATATTTTAGAAATAAAATAGGGGTTGG
* * *
473778 AGTATCCCCGATTGTAAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGG
1 AGTATCCCCGATTATAAGAAATCAATATTTTAGAAATAAAATAGGGGTTGG
473829 AGTATCCCC
1 AGTATCCCC
473838 TCGGAAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.04
50 17 0.33
51 33 0.63
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (51 bp):
AGTATCCCCGATTATAAGAAATCAATATTTTAGAAATAAAATAGGGGTTGG
Found at i:473921 original size:52 final size:51
Alignment explanation
Indices: 473853--473966 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
473843 AATAACAGGA
* * *** * **
473853 TTGGAGTATCCTCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAATTGGGG
1 TTGGAGTATCCCCGATTATGAAAA-ATCAATATTTTAGAAATAAAACCGGGG
*
473905 TTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAACCGGGG
1 TTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGG
473956 TTGGAGTATCC
1 TTGGAGTATCC
473967 TTCCGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 32 0.60
52 21 0.40
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCGGGG
Found at i:473938 original size:131 final size:128
Alignment explanation
Indices: 473642--474047 Score: 485
Period size: 129 Copynumber: 3.1 Consensus size: 128
473632 GAAAATAACA
* * * ** * *
473642 GGGTTGGAGTATCCACGATTGTGAAAAATCGATGCTTTAGAAATAAGGCTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCC
*
473707 CTACGAAAATAACGGGATTACAGTATCCTCGATTATCAAAAATT-ATGTTTTAGAAATAAAATAG
66 CTACGAAAATAACGGGATT--AGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAATAG
* *
473771 GGGTTGGAGTATCCCCGATTGTAAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT-C
* * * *
473836 CCT-CGGAAATAACAGGATTGGAGTATCCTCGATTGTGAAAAGATTGGTGTTTTAGAAATAAAAT
65 CCTACGAAAATAACGGGATT--AGTATCCTCGATTATGAAAA-ATTGATGTTTTAGAAATAAAAT
*
473900 TG
127 AG
* *
473902 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAACCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCC
* * * * * * * **
473967 TTCCGAAAATGAGGGGATTAGTATCCCCGATTATGAAAAATTGTTGTCTTTA-AAACAAAACCG
66 CTACGAAAATAACGGGATTAGTATCCTCGATTATGAAAAATTGATGT-TTTAGAAATAAAATAG
*
474030 GGGTTGGAGTATGCCCGA
1 GGGTTGGAGTATCCCCGA
474048 GATAAAAAAT
Statistics
Matches: 239, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
128 32 0.13
129 108 0.45
130 10 0.04
131 89 0.37
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (128 bp):
GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCC
CTACGAAAATAACGGGATTAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAATAG
Found at i:476390 original size:20 final size:20
Alignment explanation
Indices: 476365--476418 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
476355 GTAAACCCAG
476365 AATGTATCGATACAATAAAC
1 AATGTATCGATACAATAAAC
*
476385 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATAAAC
476405 AATGTATCGATACA
1 AATGTATCGATACA
476419 TCTGGGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATAAAC
Found at i:476428 original size:69 final size:70
Alignment explanation
Indices: 476316--476469 Score: 220
Period size: 70 Copynumber: 2.2 Consensus size: 70
476306 AAAATGCCTG
* *
476316 AATGTATCAATACATTGAAAAATGTATCGATACATCTGAGT-AAACCCAGAATGTATCGATACAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGAGTAAAACCCAGAATGTATCGATACAA
476380 TAAAC
66 TAAAC
* * * * *
476385 AATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCTAGAATTTATCGATATAA
1 AATGTATCGATACAATGAAAAATGTATCGATACATCTGAGTAAAACCCAGAATGTATCGATACAA
*
476450 TGAAC
66 TAAAC
*
476455 AATGTATCGACACAA
1 AATGTATCGATACAA
476470 ATTGTGAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 37 0.49
70 38 0.51
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (70 bp):
AATGTATCGATACAATGAAAAATGTATCGATACATCTGAGTAAAACCCAGAATGTATCGATACAA
TAAAC
Found at i:477159 original size:61 final size:61
Alignment explanation
Indices: 477067--477426 Score: 429
Period size: 61 Copynumber: 5.9 Consensus size: 61
477057 AATAAAATGG
* * * ** *
477067 GTCCTGCTCCTTG-GGAACT-AGAAGCTACCACCAACTTGTATGGGCTTTGCAAGGAGAAA-AC
1 GTCCTGCTCCTTGAGG-ACTAAAAAG-TGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGC
* * ** *
477128 ATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
** * * *
477189 GTCCTATTCTTTGAGGACTAAAAAAGTGTCACCAACTTGTGTGGTCTTTAAAAGGAAAAGGC
1 GTCCTGCTCCTTGAGGACT-AAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
477251 ATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
1 GTCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * * *
477312 GTCCTACTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
477373 GTCCTGCTCCTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGG
1 GTCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
477427 CATTCTGCTC
Statistics
Matches: 257, Mismatches: 38, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
60 3 0.01
61 197 0.77
62 57 0.22
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
GTCCTGCTCCTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
Found at i:477314 original size:123 final size:122
Alignment explanation
Indices: 477094--477426 Score: 479
Period size: 123 Copynumber: 2.7 Consensus size: 122
477084 CTAGAAGCTA
* ** * *
477094 CCACCAACTTGTATGGGCTTTGCAAGGAGAAA-ACATCCTGCTCTTTGAGGACTGGAAGGTGCCA
1 CCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCA
* *
477158 CCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTATTCTTTGAGGACTAAAAAAGTG
65 CCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTGAGGA-TAAAAAAGTG
* *
477217 TCACCAACTTGTGTGGTCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCAC
1 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCAC
**
477282 CAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTGAGGATTGAAAAGTG
66 CAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTGAGGATAAAAAAGTG
** * * **
477339 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCTCCTTGAGGACTAAAAAATGCCAC
1 CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCAC
*
477404 CAACTTGTGTGGGCTTTGAAAGG
66 CAACTTGTGTGGGCTTTAAAAGG
477427 CATTCTGCTC
Statistics
Matches: 189, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
122 90 0.48
123 99 0.52
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (122 bp):
CCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCAC
CAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTCCTTGAGGATAAAAAAGTG
Found at i:477389 original size:184 final size:177
Alignment explanation
Indices: 477068--477454 Score: 490
Period size: 184 Copynumber: 2.1 Consensus size: 177
477058 ATAAAATGGG
* * * **
477068 TCCTGCTCCTTG-GGAACTAGAAGCTACCACCAACTTGTATGGGCTTTGCAAGGAGAAAACATCC
1 TCCTGCTCTTTGAGG-ACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAGAAAACATCC
* * * * *
477132 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTATT
65 TACTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
* * *
477197 CTTTGAGGACTAAAAAAGTGTCACCAACTTGTGTGGTCTTTAAAAGGAAAAGGCA
130 CCTTGAGGACTAAAAAA-TGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCA
* * *
477252 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGCGTCC
1 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAGAAA-ACATCC
* * *
477316 TACTCCTTGAGGATTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGTGTCCTGCT
65 TACTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACT
477381 CCTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
130 CCTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
* *
477429 TTCTGCTCTTTGAGGACTAAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAGGTG
477455 AAAGGAGAGA
Statistics
Matches: 180, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
177 31 0.17
178 1 0.01
183 24 0.13
184 122 0.68
185 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (177 bp):
TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAGAAAACATCCT
ACTCCTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTACTC
CTTGAGGACTAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
Found at i:478565 original size:11 final size:11
Alignment explanation
Indices: 478534--478573 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
478524 TTTTCTCTCC
*
478534 TTTTTCTTTGTT
1 TTTTTTTTTG-T
478546 TTGTTTTTTTGT
1 TT-TTTTTTTGT
478558 TTTTTTTTTGT
1 TTTTTTTTTGT
478569 TTTTT
1 TTTTT
478574 CATTTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 14 0.54
12 5 0.19
13 7 0.27
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:478568 original size:19 final size:19
Alignment explanation
Indices: 478544--478583 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
478534 TTTTTCTTTG
**
478544 TTTTGTTTTTTTGTTTTTT
1 TTTTGTTTTTTCATTTTTT
478563 TTTTGTTTTTTCATTTTTT
1 TTTTGTTTTTTCATTTTTT
478582 TT
1 TT
478584 AAAGGTGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (19 bp):
TTTTGTTTTTTCATTTTTT
Found at i:491103 original size:79 final size:80
Alignment explanation
Indices: 490945--491129 Score: 209
Period size: 79 Copynumber: 2.4 Consensus size: 80
490935 GGTATTTTGA
* *
490945 AAATAAAATCGGGGTTGGAGTAT-CCC-TCGAAAATAACGAGGTTGCAATATCCACGATTGTGGA
1 AAATAAAATAGGGGTTGGAGTATCCCCGTCGAAAATAACGAGGTTGCAATATCCACGATTGTGAA
491008 AAATCGATGCTATAG
66 AAATCGATGCTATAG
** * * * *
491023 AAATAAGGCT-GGGGTTGGAGTATCCCCGT-GAAAATAATG-GGATTGGAGTATCCCCGATTGTG
1 AAATAA-AATAGGGGTTGGAGTATCCCCGTCGAAAATAACGAGG-TTGCAATATCCACGATTGTG
* * * *
491085 AAAAATTGGTGTTTTAG
64 AAAAATCGATGCTATAG
491102 AAATAAAATAGGGGTTGGAGTATCCCCG
1 AAATAAAATAGGGGTTGGAGTATCCCCG
491130 ATTGTGAGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
78 22 0.25
79 66 0.74
80 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.26
Consensus pattern (80 bp):
AAATAAAATAGGGGTTGGAGTATCCCCGTCGAAAATAACGAGGTTGCAATATCCACGATTGTGAA
AAATCGATGCTATAG
Found at i:491127 original size:51 final size:51
Alignment explanation
Indices: 491059--491179 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
491049 CGTGAAAATA
* *** *
491059 ATGGGATTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAA-
1 ATGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAG
*
491109 ATAGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAG
1 AT-GGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAG
*
491161 CTGGGGTTGGAGTATCCCC
1 ATGGGGTTGGAGTATCCCC
491180 TCGGAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.03
51 59 0.95
52 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
ATGGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAATAAAG
Found at i:491133 original size:130 final size:129
Alignment explanation
Indices: 491020--491387 Score: 513
Period size: 131 Copynumber: 2.8 Consensus size: 129
491010 ATCGATGCTA
* * *
491020 TAGAAATAAGGCTGGGGTTGGAGTATCCCCGTGAAAATAATGGGATTGGAGTATCCCCGATTGTG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCC-TGAAAATAACGGGATTGGAGTATCCCCGATTATG
491085 AAAAATTGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
65 AAAAATTGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
* ** * *
491150 TAGAAATAAAGCTGGGGTTGGAGTATCCCCTCGGAAATAACAAGATTGGAGCATCCTCGATTATG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCCT-GAAAATAACGGGATTGGAGTATCCCCGATTATG
* * *
491215 AAAAGATTGGTGTTTTAGAAATAAAATTGCGGTTGGAGTATCCCCAATTGTGAGAAATCAATATT
65 AAAA-ATTGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATT
491280 T
129 T
* * * *
491281 TAGAAATAAAGCCGGGGTTAGAGTATCCCCTTAGAAATAAGGGGATTGGAGTATCCCCGATTATG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCCTGA-AAATAACGGGATTGGAGTATCCCCGATTATG
* ** *
491346 AAAAATTGATGTTTT-GAAAATAAAACCGGGGTTAGAGTATCC
65 AAAAATTGGTGTTTTAG-AAATAAAATAGGGGTTGGAGTATCC
491388 TCGAGATGAA
Statistics
Matches: 209, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
129 2 0.01
130 90 0.43
131 117 0.56
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (129 bp):
TAGAAATAAAGCTGGGGTTGGAGTATCCCCTGAAAATAACGGGATTGGAGTATCCCCGATTATGA
AAAATTGGTGTTTTAGAAATAAAATAGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
Found at i:493704 original size:49 final size:50
Alignment explanation
Indices: 493651--493780 Score: 192
Period size: 49 Copynumber: 2.6 Consensus size: 50
493641 AAAAATGCCT
* * *
493651 GAATGTATCGATACATTGAAAAATGTATCGATACATCTAGGT-AAACCTA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
*
493700 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
* *
493750 AAATGTATTGATACAAT-AACAATGTATCGAT
1 GAATGTATCGATACAATGAACAATGTATCGAT
493781 GCAAATTATG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
49 53 0.72
50 21 0.28
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTAGGTAAAACCCA
Found at i:494567 original size:22 final size:22
Alignment explanation
Indices: 494529--494578 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
494519 ATCAAATCTT
494529 CTTC-AAATATCTTATTTTTCA
1 CTTCAAAATATCTTATTTTTCA
494550 CTTCAAAATA-CTTCATTTTTCA
1 CTTCAAAATATCTT-ATTTTTCA
494572 --TCAAAAT
1 CTTCAAAAT
494579 CATCAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.26
21 7 0.26
22 13 0.48
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (22 bp):
CTTCAAAATATCTTATTTTTCA
Found at i:496947 original size:20 final size:19
Alignment explanation
Indices: 496904--496957 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
496894 ACATTATGCT
*
496904 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGTCCA
496923 TTGTATCGATACATAG-CCAA
1 TTGTATCGATACAT-GTCC-A
496943 TTGTATCGATACATG
1 TTGTATCGATACATG
496958 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGTCCA
Found at i:497039 original size:20 final size:21
Alignment explanation
Indices: 496986--497039 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
496976 CTACCACTGT
496986 TTGTATCGATAC-ATGGTACA
1 TTGTATCGATACAATGGTACA
497006 TTGTATCGATACAAT-GTACCA
1 TTGTATCGATACAATGGTA-CA
497027 -TGTATCGATACAA
1 TTGTATCGATACAA
497040 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAATGGTACA
Found at i:498472 original size:97 final size:97
Alignment explanation
Indices: 498298--498799 Score: 413
Period size: 97 Copynumber: 5.2 Consensus size: 97
498288 CTTTCAAATC
*
498298 TTTT-TCTAAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
*
498362 TTTCTTCCAAGTCCACGATTTAGTGGCATTAT
66 TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
* * *
498394 TTTTCTCTCAAAGCCCATGACTTAATGGCATCTCTTTTCCAAGTCCATGACTTAGTGGCATATTT
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
*
498459 TTTCTTCCAAGTCCACGGTTTAGTGGCATCAT
66 TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
** *
498491 TTTTCTCTCAAAGCCCATGACTCAGTGGTGTCTCTTTTCCAAGTCCACGACTCT-GTGGC--A-C
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACT-TAGTGGCATATT
** ** * *
498552 CCTTC--CCAAAGTCCATAACTTAGTAGCATC-T
65 TTTTCTTCC-AAGTCCACGATTTAGTGGCATCAT
* * * ** * *
498583 TTTT-TC-C-AAGTCCACGACTCAGTGGCATTCTTTTTCTTCCAAGTCCATAATTTAGTGGCATC
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCA-TC-TCTT-TTCCAAGTCCACGACTTAGTGGCATA
* * * *
498645 CTTTTTCTTCCAAGTCCATGACTCAGTGGCATC--
63 TTTTTTCTTCCAAGTCCACGATTTAGTGGCATCAT
* * * * * * * * * * *
498678 --TCCTCTCTAAGTCCATGACTTAGTGGCATCTTTTTTCTTCCAAGCCCATGACTCAATGGTATC
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATC--TCTT-TTCCAAGTCCACGACTTAGTGGCATA
* * ** * *
498741 CTTTTTCTTCCAAGTCCATGACATAGTGGCAACCT
63 TTTTTTCTTCCAAGTCCACGATTTAGTGGCATCAT
* *
498776 TTTTCTTTTCAAAGCCCATAACTC
1 TTTTC-TCTCAAAGCCCATGACTC
498800 TTTGGTACCC
Statistics
Matches: 333, Mismatches: 52, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
89 16 0.05
90 3 0.01
91 6 0.02
92 25 0.08
93 18 0.05
94 5 0.02
95 7 0.02
96 97 0.29
97 140 0.42
98 1 0.00
100 2 0.01
101 13 0.04
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (97 bp):
TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
Found at i:498690 original size:63 final size:63
Alignment explanation
Indices: 498381--498782 Score: 244
Period size: 63 Copynumber: 6.3 Consensus size: 63
498371 AGTCCACGAT
** * * * * * * * * *
498381 TTAGTGGCATTATTTTTCTCTCAAAGCCCATGACTTAATGGCATCTCTTTTCCAAGTCCATGAC
1 TTAGTGGCATCCTTTTTCT-TCCAAGTCCACGACTCAGTGGCATCTCCTCTCAAAGTCCATAAC
** ** * * * *
498445 TTAGTGGCATATTTTTTCTTCCAAGTCCACGGTTTAGTGGCATCATTTTTCTCTCAAAGCCCATG
1 TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATC----TCCTCTCAAAGTCCATA
498510 AC
62 AC
* ** * * *
498512 TCAGTGGTGT-C-TCTT-TTCCAAGTCCACGACTCTGTGGCA-C-CCTTCCCAAAGTCCATAAC
1 TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTCC-TCTCAAAGTCCATAAC
* ** *
498571 TTAGTAGCAT-C-TTTT-TTCCAAGTCCACGACTCAGTGGCATTCTTTTTCTTCCAAGTCCATAA
1 TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCA-TC-TCCTC-TCAAAGTCCATAA
*
498633 T
63 C
* * *
498634 TTAGTGGCATCCTTTTTCTTCCAAGTCCATGACTCAGTGGCATCTCCTCTCTAAGTCCATGAC
1 TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTCCTCTCAAAGTCCATAAC
* * * * * ** * *
498697 TTAGTGGCATCTTTTTTCTTCCAAGCCCATGACTCAATGGTATCCTTTTTCTTCCAAGTCCATGA
1 TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCAT-C-TCCTC-TCAAAGTCCATAA
498762 C
63 C
* *
498763 ATAGTGGCAACCTTTTTCTT
1 TTAGTGGCATCCTTTTTCTT
498783 TTCAAAGCCC
Statistics
Matches: 268, Mismatches: 54, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
58 1 0.00
59 46 0.17
61 1 0.00
62 2 0.01
63 90 0.34
64 42 0.16
65 12 0.04
66 53 0.20
67 21 0.08
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (63 bp):
TTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTCCTCTCAAAGTCCATAAC
Found at i:498690 original size:96 final size:96
Alignment explanation
Indices: 498590--498771 Score: 260
Period size: 96 Copynumber: 1.9 Consensus size: 96
498580 TCTTTTTTCC
* * * *
498590 AAGTCCACGACTCAGTGGCAT-TCTTTTTCTTCCAAGTCCATAATTTAGTGGCATCCTTTTTCTT
1 AAGTCCACGACTCAGTGGCATCT-TTTTTCTTCCAAGCCCATAACTCAATGGCATCCTTTTTCTT
498654 CCAAGTCCATGAC-TCAGTGGCATCTCCTCTCT
65 CCAAGTCCATGACAT-AGTGGCATCTCCTCTCT
* * * *
498686 AAGTCCATGACTTAGTGGCATCTTTTTTCTTCCAAGCCCATGACTCAATGGTATCCTTTTTCTTC
1 AAGTCCACGACTCAGTGGCATCTTTTTTCTTCCAAGCCCATAACTCAATGGCATCCTTTTTCTTC
498751 CAAGTCCATGACATAGTGGCA
66 CAAGTCCATGACATAGTGGCA
498772 ACCTTTTTCT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
96 74 0.97
97 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (96 bp):
AAGTCCACGACTCAGTGGCATCTTTTTTCTTCCAAGCCCATAACTCAATGGCATCCTTTTTCTTC
CAAGTCCATGACATAGTGGCATCTCCTCTCT
Found at i:498777 original size:33 final size:33
Alignment explanation
Indices: 498311--498782 Score: 329
Period size: 33 Copynumber: 14.8 Consensus size: 33
498301 TTCTAAAAGC
*
498311 CCATGACTCAGTGGCAT-C-TCTT-TTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* * **
498341 CCACGACTTAGTGGCATATTTTTTCTTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* * * ** * *
498374 CCACGATTTAGTGGCATTATTTTTCTCTCAAAGC
1 CCATGACTCAGTGGCATCCTTTTTCT-TCCAAGT
* * *
498408 CCATGACTTAATGGCAT-C-TCTT-TTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* **
498438 CCATGACTTAGTGGCATATTTTTTCTTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* ** * * * *
498471 CCACGGTTTAGTGGCATCATTTTTCTCTCAAAGC
1 CCATGACTCAGTGGCATCCTTTTTCT-TCCAAGT
** *
498505 CCATGACTCAGTGGTGT-C-TCTT-TTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* * *
498535 CCACGACTCTGTGGCA-CC--CTTC--CCAAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCC-AAGT
* * *
498564 CCATAACTTAGTAGCAT-C-TTTT-TTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* *
498594 CCACGACTCAGTGGCATTCTTTTTCTTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* * *
498627 CCATAATTTAGTGGCATCCTTTTTCTTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
** *
498660 CCATGACTCAGTGGCAT-C-TCCTC-TCTAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* * *
498690 CCATGACTTAGTGGCATCTTTTTTCTTCCAAGC
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
* *
498723 CCATGACTCAATGGTATCCTTTTTCTTCCAAGT
1 CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
*
498756 CCATGACAT-AGTGGCAACCTTTTTCTT
1 CCATGAC-TCAGTGGCATCCTTTTTCTT
498783 TTCAAAGCCC
Statistics
Matches: 345, Mismatches: 75, Indels: 41
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.06
30 95 0.28
31 8 0.02
32 20 0.06
33 165 0.48
34 36 0.10
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (33 bp):
CCATGACTCAGTGGCATCCTTTTTCTTCCAAGT
Done.