Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold493
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: 575764
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:356042 original size:32 final size:32
Alignment explanation
Indices: 356001--356076 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
355991 AAACAGTAAC
356001 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
356033 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
356065 TGTATCGCTACA
1 TGTATCGATACA
356077 AAGCTACTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:356113 original size:13 final size:13
Alignment explanation
Indices: 356095--356122 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
356085 GCCAAGGAAA
356095 TGTATCGATACAT
1 TGTATCGATACAT
356108 TGTATCGATACAT
1 TGTATCGATACAT
356121 TG
1 TG
356123 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:359298 original size:58 final size:58
Alignment explanation
Indices: 359187--359300 Score: 131
Period size: 58 Copynumber: 2.0 Consensus size: 58
359177 TGAGGGATAT
* ** * *
359187 TAAGTCGAGCATGCCTCATTTGCCCTATCGCTGGGGTCGAGTGCACATTACGACAATA
1 TAAGTCGAGCACGCCTCATTTGCCCTATCGCCAGGGTCGAGCGCACATCACGACAATA
* * * *
359245 TAAGTCGAGCACGCCTCATCTT-CTCTATTGCCAGGGTTGAGCGCACGTCACGACAA
1 TAAGTCGAGCACGCCTCAT-TTGCCCTATCGCCAGGGTCGAGCGCACATCACGACAA
359301 GGCCCATTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
58 44 0.96
59 2 0.04
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (58 bp):
TAAGTCGAGCACGCCTCATTTGCCCTATCGCCAGGGTCGAGCGCACATCACGACAATA
Found at i:366063 original size:74 final size:74
Alignment explanation
Indices: 365977--366802 Score: 520
Period size: 74 Copynumber: 11.3 Consensus size: 74
365967 TATATTTCTC
* * * * *
365977 CAGTCCTCAAAGAGTAGGACGTCTTCTCTTTTTCTTTAAAGCCCATATAAGCTAGTGGCATCTTT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCTT
366042 TATCTTTTT
66 TATCTTTTT
* * * *
366051 CAATCCTCAAAGAGTAGGACGCCTTTTGTTTTT-TTTCAAAGCCCACACAAGCTAGTGGAACCCT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTT-AAAGCCCACACAAGCTAGTGGCACCCT
366115 TTATCTTTTT
65 TTATCTTTTT
* * * * * * ** * *
366125 CAGTCATCAAAGAGTAAGATG-CGTTTTCTTTTTCTTCAAGGTCTGCACAAGTTGGTGGCACCCT
1 CAGTCCTCAAAGAGTAGGACGTC-TTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCT
366189 TTATCTTTTT
65 TTATCTTTTT
* * * * * *** *
366199 CAATCTTTAAATAGTATGATACCTTTT-TTTTTC---AAAGCCCACACAAGCTAGTGGCACCTTT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCTT
*
366260 TATCATTTT
66 TATCTTTTT
* * * * * * * *
366269 CATTCCTCAAAGAGTAGGAC-ACTTTTCATTTTT-TTCAAAGCCCGCATAAGCTTGTGGCATCAT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTC-TTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCT
*
366332 TTATC-TTCT
65 TTATCTTTTT
* * * * * *
366341 CTAGTCCTCAAAAAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGGTGGCACCCT
1 C-AGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCT
* *
366406 TTATC-CTCT
65 TTATCTTTTT
* * * * * * * * *
366415 CTAGTCTTCAAAGAGTAGGATGCCTTATCTTTTTTTTTCAAAGACCATACAGGCTGGTGGCACCC
1 C-AGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTT-AAAGCCCACACAAGCTAGTGGCACCC
*
366480 CTTATCTTTTT
64 TTTATCTTTTT
* * * * *
366491 CAGTCCTTAAAGAGCATGATG-CATTTTCTTTTTCTTCT-AAGCCCACACAAGCTGGTGGCACCC
1 CAGTCCTCAAAGAGTAGGACGTC-TTTTCTTTTTCTT-TAAAGCCCACACAAGCTAGTGGCACCC
*
366554 TTCATCTTTTT
64 TTTATCTTTTT
* *** * * * * *
366565 TAGTCCTCAAAGTCCAAGACGTCTTTTCTTTTTC---AAAGCCCACATAAACTAATCGCACCCTT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCTT
366627 TATCTTTTT
66 TATCTTTTT
* * * * * * * * * **
366636 CAGTCTTCAAA-ATGCA-AAGCG-CCTTTCATTTTT-ATTAAAACCTACATAAGCTGGTGGCATA
1 CAGTCCTCAAAGA-GTAGGA-CGTCTTTTC-TTTTTCTTTAAAGCCCACACAAGCTAGTGGCACC
* *
366697 ATTTATCTTTTC
63 CTTTATCTTTTT
** * * * * * * * * * *
366709 CAGTCCTTGAAGAGTAAGATGCCTTTTCTTCTTCTTCAAAGCCTATACAAGTTGGTGGCACTCTT
1 CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCTT
**
366774 TAAATTTTT
66 TATCTTTTT
* *
366783 CAGTCCTCGAATAGTAGGAC
1 CAGTCCTCAAAGAGTAGGAC
366803 ATTTACCTAT
Statistics
Matches: 589, Mismatches: 135, Indels: 56
0.76 0.17 0.07
Matches are distributed among these distances:
69 5 0.01
70 49 0.08
71 53 0.09
72 4 0.01
73 99 0.17
74 316 0.54
75 59 0.10
76 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (74 bp):
CAGTCCTCAAAGAGTAGGACGTCTTTTCTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCCTT
TATCTTTTT
Found at i:366407 original size:217 final size:217
Alignment explanation
Indices: 366004--366410 Score: 548
Period size: 217 Copynumber: 1.9 Consensus size: 217
365994 GACGTCTTCT
* * * *
366004 CTTTTTCTTTAAAGCCCATATAAGCTAGTGGCATCTTTTATCTTTTTCAATCCTCAAAGAGTAGG
1 CTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCTTTTATCATTTTCAATCCTCAAAGAGTAGG
* ** * *
366069 ACGCCTTTTGTTTTTTTTCAAAGCCCACACAAGCTAGTGGAACCCTTTATCTTTTTCAGTCATCA
66 ACGACTTTTCATTTTTTTCAAAGCCCACACAAGCTAGTGGAACCATTTATCTTTCTCAGTCATCA
* * * * * ** *
366134 AAGAGTAAGATGCGTTTTCTTTTTCTTCAAGGTCTGCACAAGTTGGTGGCACCCTTTATCTTTTT
131 AAAAGTAAGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTT
366199 CAATCTTTAAATAGTATGATAC
196 CAATCTTTAAATAGTATGATAC
* *
366221 CTTTTTTTTTCAAAGCCCACACAAGCTAGTGGCACCTTTTATCATTTTCATTCCTCAAAGAGTAG
1 CTTTTTCTTT-AAAGCCCACACAAGCTAGTGGCACCTTTTATCATTTTCAATCCTCAAAGAGTAG
* * * * * *
366286 GAC-ACTTTTCATTTTTTTCAAAGCCCGCATAAGCTTGTGGCATCATTTATC-TTCTCTAGTCCT
65 GACGACTTTTCATTTTTTTCAAAGCCCACACAAGCTAGTGGAACCATTTATCTTTCTC-AGTCAT
*
366349 CAAAAAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATC
129 CAAAAAGTAAGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATC
366411 CTCTCTAGTC
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
216 4 0.02
217 106 0.65
218 52 0.32
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (217 bp):
CTTTTTCTTTAAAGCCCACACAAGCTAGTGGCACCTTTTATCATTTTCAATCCTCAAAGAGTAGG
ACGACTTTTCATTTTTTTCAAAGCCCACACAAGCTAGTGGAACCATTTATCTTTCTCAGTCATCA
AAAAGTAAGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTTATCTTTTT
CAATCTTTAAATAGTATGATAC
Found at i:366801 original size:367 final size:364
Alignment explanation
Indices: 365966--366802 Score: 873
Period size: 367 Copynumber: 2.3 Consensus size: 364
365956 GTATCTAAAC
* * * * * * * *
365966 TTATATTTCTCCAGTCCTCAAAGAGTAGGACGTCTTCTCTTTTTCTTTAAAGCCCATATAAGCTA
1 TTATCTTT-TCCAGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCATACAAGCTG
* * *
366031 GTGGCA-TCTTTTATCTTTTTCAATCCTCAAAGAGTAGGACGCCTTTTGTTTTTTTTCAAAGCCC
65 GTGGCACTC-TTTA-ATTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTGTTTTTTTTCAAAGACC
* * *
366095 ACACAAGCTAGTGGAACCCTTTATCTTTTTCAGTCATCAAAGAGTAAGATGCGTTTTCTTTTTCT
128 ACACAAGCTAGTGGAACCCCTTATCTTTTTCAGTCATCAAAGAGCAAGATGCATTTTCTTTTTCT
* ** * * * * *
366160 TCAAGGTCTGCACAAGTTGGTGGCACCCTTTATCTTTTTCAATCTTTAAATAGTATGATACCTTT
193 TCAAGGCCCACACAAGCTGGTGGCACCCTTCATCTTTTTCAATCTCTAAATAGTAAGACACCTTT
* * * * * * *
366225 TTTTTTCAAAGCCCACACAAGCTAGTGGCACCTTTTATCATTTTCATTCCTCAAAGAGTAGGACA
258 TTTTTTCAAAGCCCACACAAACTAATCGCACCCTTTATCATTTTCAGTCCTCAAAGAGAAAGACA
* * * * *
366290 CTTTTCATTTTTTTCAAAGCCCGCATAAGCTTGTGGCATCAT
323 CCTTTCATTTTTTTCAAAACCCACATAAGCTGGTGGCATAAT
* * * *
366332 TTATCTTCTCTAGTCCTCAAAAAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCACACAAGCTGG
1 TTATCTTTTCCAGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCATACAAGCTGG
* * * * *
366397 TGGCACCCTTT-ATCCTCTCTAGTCTTCAAAGAGTAGGATGCCTTATCT-TTTTTTTTCAAAGAC
66 TGGCACTCTTTAAT-TTTTC-AGTCCTCAAAGAGTAGGACGCCTT-T-TGTTTTTTTTCAAAGAC
* * * * * * *
366460 CATACAGGCTGGTGGCACCCCTTATCTTTTTCAGTCCTTAAAGAGCATGATGCATTTTCTTTTTC
127 CACACAAGCTAGTGGAACCCCTTATCTTTTTCAGTCATCAAAGAGCAAGATGCATTTTCTTTTTC
* * * **
366525 TTCTAA-GCCCACACAAGCTGGTGGCACCCTTCATCTTTTTTAGTC-CTCAA-AGTCCAAGACGT
192 TTC-AAGGCCCACACAAGCTGGTGGCACCCTTCATCTTTTTCAATCTCTAAATAGT--AAGACAC
* * *
366587 CTTTTCTTTTTCAAAGCCCACATAAACTAATCGCACCCTTTATCTTTTTCAGTCTTCAAA-ATGC
254 CTTTT-TTTTTCAAAGCCCACACAAACTAATCGCACCCTTTATCATTTTCAGTCCTCAAAGA-G-
* *
366651 AAAG-CGCCTTTCATTTTTATT-AAAACCTACATAAGCTGGTGGCATAAT
316 AAAGACACCTTTCATTTTT-TTCAAAACCCACATAAGCTGGTGGCATAAT
** * * *
366699 TTATCTTTTCCAGTCCTTGAAGAGTAAGATGCCTTTTCTTCTTCTTCAAAGCCTATACAAGTTGG
1 TTATCTTTTCCAGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCATACAAGCTGG
* *
366764 TGGCACTCTTTAAATTTTTCAGTCCTCGAATAGTAGGAC
66 TGGCACTCTTT-AATTTTTCAGTCCTCAAAGAGTAGGAC
366803 ATTTACCTAT
Statistics
Matches: 381, Mismatches: 76, Indels: 27
0.79 0.16 0.06
Matches are distributed among these distances:
363 1 0.00
364 6 0.02
365 79 0.21
366 121 0.32
367 165 0.43
368 7 0.02
369 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (364 bp):
TTATCTTTTCCAGTCCTCAAAGAGTAGGATGCCTTTTCTTCTTCTTCAAAGCCCATACAAGCTGG
TGGCACTCTTTAATTTTTCAGTCCTCAAAGAGTAGGACGCCTTTTGTTTTTTTTCAAAGACCACA
CAAGCTAGTGGAACCCCTTATCTTTTTCAGTCATCAAAGAGCAAGATGCATTTTCTTTTTCTTCA
AGGCCCACACAAGCTGGTGGCACCCTTCATCTTTTTCAATCTCTAAATAGTAAGACACCTTTTTT
TTTCAAAGCCCACACAAACTAATCGCACCCTTTATCATTTTCAGTCCTCAAAGAGAAAGACACCT
TTCATTTTTTTCAAAACCCACATAAGCTGGTGGCATAAT
Found at i:375528 original size:20 final size:20
Alignment explanation
Indices: 375503--375555 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
375493 GTTAGGCCCA
** *
375503 ATGTATCGATACGTTTTACC
1 ATGTATCGATACAATGTACC
*
375523 ATGTATCGATACAATGTCCC
1 ATGTATCGATACAATGTACC
375543 ATGTATCGATACA
1 ATGTATCGATACA
375556 TTTCACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:375630 original size:19 final size:20
Alignment explanation
Indices: 375584--375637 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
375574 CTGCTAGTTT
*
375584 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
**
375604 TGTGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
375623 CATGTATCGATACAA
1 CATGTATCGATACAA
375638 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:385950 original size:103 final size:104
Alignment explanation
Indices: 385795--386046 Score: 278
Period size: 104 Copynumber: 2.4 Consensus size: 104
385785 GATGAAACTA
* * * * *
385795 ACAAGTCAACAAAAAGGTGACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAA-TC
1 ACAAGTCAAC-AAAGGGTGACTAAGATAAAACCTAACTCAGAAAAAGGTAACCAAGGCAAAACT-
* * *
385859 AATAGGTCAACAAGTTAAAAA-GTTGATCGA-GACAAAATTG
64 AATAAGTCAACAAGCTAAAAAGGTTGATC-ATGACAAAATCG
* * *
385899 ACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACTCA-AAAAAGGTTAACCAGGGCGAAACTG
1 ACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACTCAGAAAAAGG-TAACCAAGGCAAAACTA
* **
385963 ATAAGTCAACAAGCTAAAAAGGTTGGTCATGATGAAATCG
65 ATAAGTCAACAAGCTAAAAAGGTTGATCATGACAAAATCG
* * * *
386003 ACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAA
1 ACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACTCAGAAAA
386047 GGTTGTTTAG
Statistics
Matches: 125, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
102 6 0.05
103 56 0.45
104 59 0.47
105 4 0.03
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (104 bp):
ACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACTCAGAAAAAGGTAACCAAGGCAAAACTAA
TAAGTCAACAAGCTAAAAAGGTTGATCATGACAAAATCG
Found at i:387624 original size:939 final size:939
Alignment explanation
Indices: 385806--387692 Score: 3711
Period size: 939 Copynumber: 2.0 Consensus size: 939
385796 CAAGTCAACA
*
385806 AAAAGGTGACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAATCAATAGGTCAACA
1 AAAAGGTTACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAATCAATAGGTCAACA
385871 AGTTAAAAAGTTGATCGAGACAAAATTGACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACT
66 AGTTAAAAAGTTGATCGAGACAAAATTGACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACT
*
385936 CAAAAAAGGTTAACCAGGGCGAAACTGATAAGTCAACAAGCTAAAAAGGTTGGTCATGATGAAAT
131 CAAAAAAGGTTAACCAGGGCGAAACTGATAAGTCAACAAGCTAAAAAGGTTGGTCAGGATGAAAT
386001 CGACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAAGGTTGTTTAGGGCAAAACT
196 CGACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAAGGTTGTTTAGGGCAAAACT
386066 GATAAATAATATTTGACACTTGATTAGTTGAACAAGATAAAGGATTTGATTTTAAAGGAATAAGC
261 GATAAATAATATTTGACACTTGATTAGTTGAACAAGATAAAGGATTTGATTTTAAAGGAATAAGC
386131 ATGGCCATCACTTTCTAGTGTTACACTTAACTTTCCTTACAAATTATTGAATACAAATGCATGCA
326 ATGGCCATCACTTTCTAGTGTTACACTTAACTTTCCTTACAAATTATTGAATACAAATGCATGCA
386196 GAATGATATGATTAATTTATATGACTTTATTAAATTTGAAAGTGAAAATATTCTGAAGCTTTTCT
391 GAATGATATGATTAATTTATATGACTTTATTAAATTTGAAAGTGAAAATATTCTGAAGCTTTTCT
*
386261 TTTCTTATGGAAAAGTGAGCCTATGCCTCTGCTTGGAGTTGAAGCATTTTTAGAAAATGTTAAAG
456 TTTCTTATGGAAAAGTGAGCCTACGCCTCTGCTTGGAGTTGAAGCATTTTTAGAAAATGTTAAAG
386326 AAATCTCTTTTTTTCTAGCCAAGGGAGCTAGTGCCTGAACTTGTAATCAACGGCATCTTCAAAGA
521 AAATCTCTTTTTTTCTAGCCAAGGGAGCTAGTGCCTGAACTTGTAATCAACGGCATCTTCAAAGA
386391 TCATGGTAAACAAGATATAATTACTTTTGGGAGATCAAACTAGATGACGCACCGATATCATATAG
586 TCATGGTAAACAAGATATAATTACTTTTGGGAGATCAAACTAGATGACGCACCGATATCATATAG
386456 GAGCTGAAAAAAGTAAATATGATTAGGAAACATGTGGTTATAATTTTCAACAATAGCCGAAACAA
651 GAGCTGAAAAAAGTAAATATGATTAGGAAACATGTGGTTATAATTTTCAACAATAGCCGAAACAA
*
386521 ACTGATAACAAGTTGAAAAAGAAAAACATGATGGGGAATATGCGATTTTAATTTCCCATCAACAT
716 ACTGATAACAAGTTGAAAAAGAAAAACATGATGGGGAATATGCGATTTTAATTTCCCATCAACAA
386586 TTGAACAAACTGATAACAAAATGTTGTTCGTCCCCTTAATCCTTCCTAAAACGTCCTAATGACTT
781 TTGAACAAACTGATAACAAAATGTTGTTCGTCCCCTTAATCCTTCCTAAAACGTCCTAATGACTT
386651 TGGAACATTAACTAAGATCCCTATAATGTTTTGATTCCATCCCAAAGTAATGCAAGAAATTCATT
846 TGGAACATTAACTAAGATCCCTATAATGTTTTGATTCCATCCCAAAGTAATGCAAGAAATTCATT
386716 CATCATTTTTCATCCATCTCCATTTCCTT
911 CATCATTTTTCATCCATCTCCATTTCCTT
386745 AAAAGGTTACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAATCAATAGGTCAACA
1 AAAAGGTTACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAATCAATAGGTCAACA
*
386810 AGTTAAAAAGTTGATCGAGACAAAATTGACAAGTCAACAAAGGGTGACTAAGATAAAACCTAATT
66 AGTTAAAAAGTTGATCGAGACAAAATTGACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACT
386875 CAAAAAAGGTTAACCAGGGCGAAACTGATAAGTCAACAAGCTAAAAAGGTTGGTCAGGATGAAAT
131 CAAAAAAGGTTAACCAGGGCGAAACTGATAAGTCAACAAGCTAAAAAGGTTGGTCAGGATGAAAT
386940 CGACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAAGGTTGTTTAGGGCAAAACT
196 CGACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAAGGTTGTTTAGGGCAAAACT
387005 GATAAATAATATTTGACACTTGATTAGTTGAACAAGATAAAGGATTTGATTTTAAAGGAATAAGC
261 GATAAATAATATTTGACACTTGATTAGTTGAACAAGATAAAGGATTTGATTTTAAAGGAATAAGC
387070 ATGGCCATCACTTTCTAGTGTTACACTTAACTTTCCTTACAAATTATTGAATACAAATGCATGCA
326 ATGGCCATCACTTTCTAGTGTTACACTTAACTTTCCTTACAAATTATTGAATACAAATGCATGCA
*
387135 GAATGATATGATTAATTTATATGACTTTATTAAATTTGAAAGTGAAAATATTCTGAGGCTTTTCT
391 GAATGATATGATTAATTTATATGACTTTATTAAATTTGAAAGTGAAAATATTCTGAAGCTTTTCT
387200 TTTCTTATGGAAAAGTGAGCCTACGCCTCTGCTTGGAGTTGAAGCATTTTTAGAAAATGTTAAAG
456 TTTCTTATGGAAAAGTGAGCCTACGCCTCTGCTTGGAGTTGAAGCATTTTTAGAAAATGTTAAAG
387265 AAATCTCTTTTTTTCTAGCCAAGGGAGCTAGTGCCTGAACTTGTAATCAACGGCATCTTCAAAGA
521 AAATCTCTTTTTTTCTAGCCAAGGGAGCTAGTGCCTGAACTTGTAATCAACGGCATCTTCAAAGA
387330 TCATGGTAAACAAGATATAATTACTTTTGGGAGATCAAACTAGATGACGCACCGATATCATATAG
586 TCATGGTAAACAAGATATAATTACTTTTGGGAGATCAAACTAGATGACGCACCGATATCATATAG
387395 GAGCTGAAAAAAGTAAATATGATTAGGAAACATGTGGTTATAATTTTCAACAATAGCCGAAACAA
651 GAGCTGAAAAAAGTAAATATGATTAGGAAACATGTGGTTATAATTTTCAACAATAGCCGAAACAA
387460 ACTGATAACAAGTTGAAAAAGAAAAACATGATGGGGAATATGCGATTTTAATTTCCCATCAACAA
716 ACTGATAACAAGTTGAAAAAGAAAAACATGATGGGGAATATGCGATTTTAATTTCCCATCAACAA
387525 TTGAACAAACTGATAACAAAATGTTGTTCGTCCCCTTAATCCTTCCTAAAACGTCCTAATGACTT
781 TTGAACAAACTGATAACAAAATGTTGTTCGTCCCCTTAATCCTTCCTAAAACGTCCTAATGACTT
*
387590 TGGAACATTAACTAAGATCCCTATAATGTTTTGATTTCATCCCAAAGTAATGCAAGAAATTCATT
846 TGGAACATTAACTAAGATCCCTATAATGTTTTGATTCCATCCCAAAGTAATGCAAGAAATTCATT
387655 CATCATTTTTCATCCATCTCCATTTCCTT
911 CATCATTTTTCATCCATCTCCATTTCCTT
387684 AAAAGGTTA
1 AAAAGGTTA
387693 ATTTTTATTT
Statistics
Matches: 941, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
939 941 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (939 bp):
AAAAGGTTACTAAGGTAAAACATAAGTCAGAAAGAGGTAACCAAGGCAAAATCAATAGGTCAACA
AGTTAAAAAGTTGATCGAGACAAAATTGACAAGTCAACAAAGGGTGACTAAGATAAAACCTAACT
CAAAAAAGGTTAACCAGGGCGAAACTGATAAGTCAACAAGCTAAAAAGGTTGGTCAGGATGAAAT
CGACAAGTCAATAAAGGGTGACTAGGATAAAACCTAAGTTAGAAAAGGTTGTTTAGGGCAAAACT
GATAAATAATATTTGACACTTGATTAGTTGAACAAGATAAAGGATTTGATTTTAAAGGAATAAGC
ATGGCCATCACTTTCTAGTGTTACACTTAACTTTCCTTACAAATTATTGAATACAAATGCATGCA
GAATGATATGATTAATTTATATGACTTTATTAAATTTGAAAGTGAAAATATTCTGAAGCTTTTCT
TTTCTTATGGAAAAGTGAGCCTACGCCTCTGCTTGGAGTTGAAGCATTTTTAGAAAATGTTAAAG
AAATCTCTTTTTTTCTAGCCAAGGGAGCTAGTGCCTGAACTTGTAATCAACGGCATCTTCAAAGA
TCATGGTAAACAAGATATAATTACTTTTGGGAGATCAAACTAGATGACGCACCGATATCATATAG
GAGCTGAAAAAAGTAAATATGATTAGGAAACATGTGGTTATAATTTTCAACAATAGCCGAAACAA
ACTGATAACAAGTTGAAAAAGAAAAACATGATGGGGAATATGCGATTTTAATTTCCCATCAACAA
TTGAACAAACTGATAACAAAATGTTGTTCGTCCCCTTAATCCTTCCTAAAACGTCCTAATGACTT
TGGAACATTAACTAAGATCCCTATAATGTTTTGATTCCATCCCAAAGTAATGCAAGAAATTCATT
CATCATTTTTCATCCATCTCCATTTCCTT
Found at i:399658 original size:21 final size:21
Alignment explanation
Indices: 399625--399665 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
399615 CTAAGTAAAA
399625 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
399646 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
399666 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:399730 original size:20 final size:19
Alignment explanation
Indices: 399705--399775 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
399695 ACCCTGAAAA
399705 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
399725 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
399744 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
399765 GTATCGATACA
1 GTATCGATACA
399776 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:399828 original size:53 final size:53
Alignment explanation
Indices: 399745--399881 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
399735 AAATTGCATA
399745 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
399799 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
399852 GTATCGATACACAAAATATGTATTGATACA
1 GTATCGATACACACAATATGTATCGATACA
399882 TTGGAAGTAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:399947 original size:21 final size:22
Alignment explanation
Indices: 399913--399968 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
399903 TTTCACTGTT
399913 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
399935 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
399956 CATCACTGTTCAT
1 CATCACTGTTCAT
399969 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:400077 original size:13 final size:13
Alignment explanation
Indices: 400059--400083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
400049 CATATTTGTA
400059 TGTATCGATACAG
1 TGTATCGATACAG
400072 TGTATCGATACA
1 TGTATCGATACA
400084 TCATAAATAG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:405887 original size:22 final size:22
Alignment explanation
Indices: 405859--405913 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
405849 TGGACATGTT
405859 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
405881 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
405903 AAAAATGCATG
1 AAAAATGCATG
405914 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:406854 original size:20 final size:19
Alignment explanation
Indices: 406825--406896 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
406815 AAAAGGACAT
406825 AATGTATCGATATATTGTA
1 AATGTATCGATATATTGTA
* * *
406844 GAATATATCGATACATTCATA
1 -AATGTATCGATATATT-GTA
* *
406865 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-TA
406885 AATGTATCGATA
1 AATGTATCGATA
406897 CATCAAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
AATGTATCGATATATTGTA
Found at i:406881 original size:40 final size:39
Alignment explanation
Indices: 406822--406899 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
406812 GGTAAAAGGA
* *
406822 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
406861 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
406900 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:408194 original size:114 final size:114
Alignment explanation
Indices: 407461--408470 Score: 1329
Period size: 114 Copynumber: 8.8 Consensus size: 114
407451 AAAAAAAAAT
** * *
407461 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAGGAG-TGCCACTG--ACTTGTGGGCTTTG-AAAGGG
** * *
407525 TGTTACTGACTTGCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTG-AAAGG
59 TGCCACTGACTT--GTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAAGA
* * * *
407585 GTGCCACTAACTCGTGGGCTTTAAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * *
407649 GACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT-AAAAGGA
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAA-GA
* *
407700 GTGCCACTGACTTGTGTGGGCTTTAAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
* * * * ** * * * *
407764 CTGAATTGCGGGCTTCGCAATAGTGCCACTAACATGTGGGCTTCG-AAAGG
64 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
407814 GTGCCACTGACTTGTGGGCTCTGAAAGG-GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * *
407878 GACTTATGGGCTTTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAAGA
66 GACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
407928 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * *
407993 GACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTCTAGGCTTTGAAAAGA
66 GACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
408043 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
408108 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
408157 GTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCAC
408222 TGACTTGT-GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
65 TGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
*
408271 GTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCAC
* * *
408335 TAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGG
65 TGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
408384 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCAC
*
408449 TTACTTGTGGGCTTTGAAAGGG
65 TGACTTGTGGGCTTTGAAAGGG
408471 ATGAACATTC
Statistics
Matches: 806, Mismatches: 63, Indels: 44
0.88 0.07 0.05
Matches are distributed among these distances:
112 60 0.07
113 97 0.12
114 305 0.38
115 210 0.26
116 1 0.00
117 88 0.11
118 13 0.02
120 8 0.01
122 10 0.01
124 13 0.02
125 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (114 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:408468 original size:29 final size:29
Alignment explanation
Indices: 407461--408469 Score: 1354
Period size: 28 Copynumber: 35.0 Consensus size: 29
407451 AAAAAAAAAT
**
407461 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAGGA
* *
407492 GTTGCCACTGACACATGTGGGCTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAGGA
** *
407524 GTGTTACTGACTTGCGTGGGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
407555 GTGCCACTGACTTGTGTGGGCTTTGAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
* * *
407585 GTGCCACTAACTCGTGGGCTTTAAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
407614 -TGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
407641 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
407669 GTACCACTGACTTGCGTGAGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
407700 GTGCCACTGACTTGTGTGGGCTTTAAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
407730 GTGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
407758 GTGCCACTGAATTGCGGGCTTCGCAA-TA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
407786 GTGCCACTAACATGTGGGCTTCGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
407814 GTGCCACTGACTTGTGGGCTCTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
407842 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
407870 GTGCCACTGACTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
407899 GTGCCACTAATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
407928 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
407957 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
407985 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
408014 GTGCCACTGATTTCTAGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408043 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408072 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408100 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408128 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408157 GTGCCACTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408186 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408215 GTGCCACTGACTTGT-GGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408242 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408271 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408299 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408328 GTGCCACTAACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
408357 -TGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408384 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408413 GTGCCACTGATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
408442 GTGCCACTTACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
408470 GATGAACATT
Statistics
Matches: 876, Mismatches: 76, Indels: 54
0.87 0.08 0.05
Matches are distributed among these distances:
27 18 0.02
28 386 0.44
29 341 0.39
30 33 0.04
31 68 0.08
32 22 0.03
33 2 0.00
34 5 0.01
35 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:409702 original size:1 final size:1
Alignment explanation
Indices: 409698--409761 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
409688 TTTTTTGCTA
* * * * * * * *
409698 TTTTTTTCTTTTTTTTGTTTTTTTGTTTTGTTTTTTGTTGTTTTTTTTTTGTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
409762 GGGTGTAAAG
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (1 bp):
T
Found at i:409721 original size:20 final size:20
Alignment explanation
Indices: 409683--409761 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 20
409673 ATCTAGACCC
* * *
409683 TTCTATTTTTTGCTATTTTT
1 TTCTTTTTTTTGTTTTTTTT
409703 TTCTTTTTTTTGTTTTTTTGTT
1 TTCTTTTTTTTG-TTTTTT-TT
*
409725 TTGTTTTTTGTTGTTTTTTTT
1 TTCTTTTTT-TTGTTTTTTTT
*
409746 TTGTTGTTTTTT-TTTT
1 TTCTT-TTTTTTGTTTT
409762 GGGTGTAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
20 15 0.29
21 13 0.25
22 20 0.39
23 3 0.06
ACGTcount: A:0.03, C:0.04, G:0.10, T:0.84
Consensus pattern (20 bp):
TTCTTTTTTTTGTTTTTTTT
Found at i:409726 original size:14 final size:13
Alignment explanation
Indices: 409688--409761 Score: 78
Period size: 14 Copynumber: 5.3 Consensus size: 13
409678 GACCCTTCTA
409688 TTTTTTGCTATTTTT
1 TTTTTTG-T-TTTTT
*
409703 TTCTTTT-TTTTGT
1 TT-TTTTGTTTTTT
409716 TTTTTTGTTTTGTT
1 TTTTTTGTTTT-TT
409730 TTTTGTTGTTTTTT
1 TTTT-TTGTTTTTT
409744 TTTTGTTGTTTTTT
1 TTTT-TTGTTTTTT
409758 TTTT
1 TTTT
409762 GGGTGTAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.08
13 10 0.19
14 26 0.49
15 9 0.17
16 4 0.08
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:409731 original size:29 final size:28
Alignment explanation
Indices: 409698--409761 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
409688 TTTTTTGCTA
*
409698 TTTTTTTCTT-TTTTTTGTTTTTTTGTTT
1 TTTTTTTCTTGTTTTTT-TTTTGTTGTTT
*
409726 TGTTTTTTGTTGTTTTTTTTTTGTTGTTT
1 T-TTTTTTCTTGTTTTTTTTTTGTTGTTT
409755 TTTTTTT
1 TTTTTTT
409762 GGGTGTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.22
29 19 0.59
30 6 0.19
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (28 bp):
TTTTTTTCTTGTTTTTTTTTTGTTGTTT
Found at i:409762 original size:14 final size:14
Alignment explanation
Indices: 409698--409762 Score: 87
Period size: 14 Copynumber: 4.6 Consensus size: 14
409688 TTTTTTGCTA
*
409698 TTTTTTTCTT-TTT
1 TTTTTTTGTTGTTT
*
409711 TTTGTTTTTTTGTTT
1 TTT-TTTTGTTGTTT
409726 TGTTTTTTGTTGTTT
1 T-TTTTTTGTTGTTT
409741 TTTTTTTGTTGTTT
1 TTTTTTTGTTGTTT
409755 TTTTTTTG
1 TTTTTTTG
409763 GGTGTAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
13 3 0.06
14 27 0.57
15 15 0.32
16 2 0.04
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (14 bp):
TTTTTTTGTTGTTT
Found at i:419500 original size:21 final size:22
Alignment explanation
Indices: 419476--419517 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
419466 ATAATGGGAA
*
419476 TGAATAGCAA-AAAAAAAAAAT
1 TGAACAGCAATAAAAAAAAAAT
*
419497 TGAACATCAATAAAAAAAAAA
1 TGAACAGCAATAAAAAAAAAA
419518 GTGGCCCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (22 bp):
TGAACAGCAATAAAAAAAAAAT
Found at i:421564 original size:75 final size:75
Alignment explanation
Indices: 421421--421564 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 75
421411 TAATTTTCTT
* * *
421421 GATTGAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAGTATCCCCAATGATGACA
1 GATTGAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCAATAATGAAA
421486 ATTTAAGAGA
66 ATTTAAGAGA
* * * *
421496 GATTTAAAAGCGGGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGGAGTATCCCCGATAAAT-AA
1 GATTGAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCAAT-AATGAA
421560 AATTT
65 AATTT
421565 TTGATTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 59 0.97
76 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (75 bp):
GATTGAAAAACGGGGTTGGAGTATCCCCTCGGAAGAATAGGGTTGGAGTATCCCCAATAATGAAA
ATTTAAGAGA
Found at i:422849 original size:22 final size:23
Alignment explanation
Indices: 422803--422858 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
422793 TGGACATGTT
422803 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
422826 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
422848 AAAAATGCATG
1 AAAAATGCATG
422859 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:423818 original size:20 final size:20
Alignment explanation
Indices: 423771--423845 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
423761 AAAAAGACAT
*
423771 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
423790 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
423811 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
423831 AATGTATCGATACAT
1 AATGTATCGATACAT
423846 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:423839 original size:40 final size:39
Alignment explanation
Indices: 423768--423845 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
423758 GGTAAAAAGA
* *
423768 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
423807 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
423846 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:425337 original size:21 final size:20
Alignment explanation
Indices: 425297--425335 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
425287 TTAAGTATAA
425297 ATATTTTTCAAGCATTAAATC
1 ATATTTTTCAA-CATTAAATC
425318 ATATGTTTTCAA-ATTAAA
1 ATAT-TTTTCAACATTAAA
425336 ATAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATTTTTCAACATTAAATC
Found at i:442611 original size:10 final size:10
Alignment explanation
Indices: 442596--442655 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 10
442586 TGTCCTTCTC
442596 AAAAAAACAA
1 AAAAAAACAA
442606 AAAAAAACAAA
1 AAAAAAAC-AA
*
442617 AAACAAGAAAAA
1 AAA-AA-AACAA
442629 AATAAAAACCAA
1 AA-AAAAA-CAA
442641 AAAAAACACAA
1 AAAAAA-ACAA
442652 AAAA
1 AAAA
442656 GGGAGGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.19
11 18 0.43
12 13 0.31
13 3 0.07
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:442617 original size:17 final size:17
Alignment explanation
Indices: 442597--442655 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 17
442587 GTCCTTCTCA
442597 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
*
442614 AAAAAACAAGAAAAAAAT
1 AAAAAACAA-AAAAAAAC
*
442632 AAAAACCAAAAAAAACAC
1 AAAAAACAAAAAAAA-AC
442650 AAAAAA
1 AAAAAA
442656 GGGAGGGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 15 0.42
18 21 0.58
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:443990 original size:28 final size:28
Alignment explanation
Indices: 443950--444424 Score: 449
Period size: 28 Copynumber: 16.7 Consensus size: 28
443940 AATACGACCT
* *
443950 CTTTTCAAAGCCCACAAGTTAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
443978 CTTTTTAAAGCCCACAAGTTAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
*
444008 CTTTTCAACGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
444037 C-TTTCAAAG-CCATAAGTGAGTGACATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* **
444064 C-TTTCAGAGCCCACAAGTCAGTGGCTT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
444091 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
** *
444119 CTTTTCAAAGCCCGTAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
444147 CTTCTCAAAACCCACAAGTGAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
444175 CTTTTCAAAGCCCACAATTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
444204 CTTCTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
444232 CTTCTCAAAGCCCATAAGTCAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
444260 CTTTTCAAAGCCCACAACTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
444287 CTTTCTCAAAGCCCACAAGTCAGTCGTATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCA-C
* * *
444317 C-TTCCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
444344 CTTTTCAAAACCCACAAGCCAGTGGTATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
444373 C-TTTCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
444402 CTTTCTCTAAAGCCTACACAAGT
1 CTTT-TC-AAAGCC--CACAAGT
444425 TGGTGGCAAC
Statistics
Matches: 372, Mismatches: 59, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
27 29 0.08
28 253 0.68
29 35 0.09
30 39 0.10
31 4 0.01
32 12 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:444216 original size:141 final size:139
Alignment explanation
Indices: 443949--444432 Score: 506
Period size: 141 Copynumber: 3.4 Consensus size: 139
443939 CAATACGACC
* * * *
443949 TCTTTTCAAAGCCCACAAGTTAGTGGTACCTTTTTAAAGCCCACAAGTTAGTGGCAACCCTTTTC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGC-A-CCTTCTC
* * * *
444014 AACGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCATAAGTGAGTGACATCCTTTCAGAGCCCAC
64 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTG-CATCCTTTCAAAGCCCAC
444078 AAGTCAGTGGCT
128 AAGTCAGTGGCT
**
444090 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCGTAAGTTAGTGGCACCTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * *
444155 AACCCACAAGTGAGTGGCA-CCTTTTCAAAGCCCACAATTTAGTAGCATCCTTCTCAAAGCCCAC
66 AGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGT-GCATCCTT-TCAAAGCCCAC
* *
444219 AAGTTAGTGGCA
128 AAGTCAGTGGCT
* * * * * * * *
444231 CCTTCTCAAAGCCCATAAGTCAGTAGCACCTTTTCAAAGCCCACAACTCAATGGCACTTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * * * *
444296 AGCCCACAAGTCAGTCGTATCCTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAACCCACAA
66 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGT-GCATCCTTTCAAAGCCCACAA
*
444361 GCCAGTGG-T
130 GTCAGTGGCT
* * * *
444370 ATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTCTCTAAAGCCTACACAAGTTGGTGGCA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGCACCTTT-TC-AAAGCC--CACAAGTTAGTGGCA
444433 ACCCTTCTAA
Statistics
Matches: 281, Mismatches: 50, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
138 2 0.01
139 32 0.11
140 43 0.15
141 167 0.59
142 18 0.06
143 2 0.01
144 6 0.02
146 11 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (139 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGCATCCTTTCAAAGCCCACAAG
TCAGTGGCT
Found at i:445472 original size:20 final size:20
Alignment explanation
Indices: 445447--445571 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
445437 TTTTACCTAG
* *
445447 ATGTATCGATGCATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
445467 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
445487 ATATATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
445507 ATGTATCGATACATTCTGATTTTTTACGTA
1 ATGTATCGAT--A--C--A-TTTTT-C--A
445537 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
445558 ATGTATCGATACAT
1 ATGTATCGATACAT
445572 CTAGTTAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 52 0.64
21 1 0.01
22 1 0.01
23 1 0.01
24 5 0.06
25 1 0.01
26 1 0.01
27 6 0.07
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:455350 original size:11 final size:11
Alignment explanation
Indices: 455334--455394 Score: 70
Period size: 11 Copynumber: 5.3 Consensus size: 11
455324 TGTCCTTCTC
455334 AAAAAAACAAA
1 AAAAAAACAAA
455345 AAAAAAACAAA
1 AAAAAAACAAA
455356 AAACAAGAA-AAA
1 AAA-AA-AACAAA
455368 AATAAAAACCAAA
1 AA-AAAAA-CAAA
*
455381 AAAAACACAAA
1 AAAAAAACAAA
455392 AAA
1 AAA
455395 GGGAGGGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
11 23 0.52
12 13 0.30
13 8 0.18
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:455356 original size:18 final size:18
Alignment explanation
Indices: 455335--455394 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
455325 GTCCTTCTCA
455335 AAAAAACAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
* *
455353 AAAAAACAAGAAAAAAAT
1 AAAAAACAAAAAAAAAAC
* *
455371 AAAAACCAAAAAAAACAC
1 AAAAAACAAAAAAAAAAC
455389 AAAAAA
1 AAAAAA
455395 GGGAGGGGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAC
Found at i:456729 original size:28 final size:28
Alignment explanation
Indices: 456689--457163 Score: 449
Period size: 28 Copynumber: 16.7 Consensus size: 28
456679 AATACGACCT
* *
456689 CTTTTCAAAGCCCACAAGTTAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
456717 CTTTTTAAAGCCCACAAGTTAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
*
456747 CTTTTCAACGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
456776 C-TTTCAAAG-CCATAAGTGAGTGACATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* **
456803 C-TTTCAGAGCCCACAAGTCAGTGGCTT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
456830 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
** *
456858 CTTTTCAAAGCCCGTAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
456886 CTTCTCAAAACCCACAAGTGAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
456914 CTTTTCAAAGCCCACAATTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
456943 CTTCTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
456971 CTTCTCAAAGCCCATAAGTCAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
456999 CTTTTCAAAGCCCACAACTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
457026 CTTTCTCAAAGCCCACAAGTCAGTCGTATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCA-C
* * *
457056 C-TTCCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
457083 CTTTTCAAAACCCACAAGCCAGTGGTATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
457112 C-TTTCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
457141 CTTTCTCTAAAGCCTACACAAGT
1 CTTT-TC-AAAGCC--CACAAGT
457164 TGGTGGCAAC
Statistics
Matches: 372, Mismatches: 59, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
27 29 0.08
28 253 0.68
29 35 0.09
30 39 0.10
31 4 0.01
32 12 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:456955 original size:141 final size:139
Alignment explanation
Indices: 456688--457171 Score: 506
Period size: 141 Copynumber: 3.4 Consensus size: 139
456678 CAATACGACC
* * * *
456688 TCTTTTCAAAGCCCACAAGTTAGTGGTACCTTTTTAAAGCCCACAAGTTAGTGGCAACCCTTTTC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGC-A-CCTTCTC
* * * *
456753 AACGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCATAAGTGAGTGACATCCTTTCAGAGCCCAC
64 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTG-CATCCTTTCAAAGCCCAC
456817 AAGTCAGTGGCT
128 AAGTCAGTGGCT
**
456829 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCGTAAGTTAGTGGCACCTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * *
456894 AACCCACAAGTGAGTGGCA-CCTTTTCAAAGCCCACAATTTAGTAGCATCCTTCTCAAAGCCCAC
66 AGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGT-GCATCCTT-TCAAAGCCCAC
* *
456958 AAGTTAGTGGCA
128 AAGTCAGTGGCT
* * * * * * * *
456970 CCTTCTCAAAGCCCATAAGTCAGTAGCACCTTTTCAAAGCCCACAACTCAATGGCACTTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * * * *
457035 AGCCCACAAGTCAGTCGTATCCTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAACCCACAA
66 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGT-GCATCCTTTCAAAGCCCACAA
*
457100 GCCAGTGG-T
130 GTCAGTGGCT
* * * *
457109 ATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTCTCTAAAGCCTACACAAGTTGGTGGCA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGCACCTTT-TC-AAAGCC--CACAAGTTAGTGGCA
457172 ACCCTTCTAA
Statistics
Matches: 281, Mismatches: 50, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
138 2 0.01
139 32 0.11
140 43 0.15
141 167 0.59
142 18 0.06
143 2 0.01
144 6 0.02
146 11 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (139 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGCATCCTTTCAAAGCCCACAAG
TCAGTGGCT
Found at i:458212 original size:20 final size:20
Alignment explanation
Indices: 458187--458311 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
458177 TTTTACCTAG
* *
458187 ATGTATCGATGCATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
458207 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
458227 ATATATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
458247 ATGTATCGATACATTCTGATTTTTTACGTA
1 ATGTATCGAT--A--C--A-TTTTT-C--A
458277 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
458298 ATGTATCGATACAT
1 ATGTATCGATACAT
458312 CTAGTTAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 52 0.64
21 1 0.01
22 1 0.01
23 1 0.01
24 5 0.06
25 1 0.01
26 1 0.01
27 6 0.07
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:468093 original size:11 final size:11
Alignment explanation
Indices: 468077--468137 Score: 70
Period size: 11 Copynumber: 5.3 Consensus size: 11
468067 TGTCCTTCTC
468077 AAAAAAACAAA
1 AAAAAAACAAA
468088 AAAAAAACAAA
1 AAAAAAACAAA
468099 AAACAAGAA-AAA
1 AAA-AA-AACAAA
468111 AATAAAAACCAAA
1 AA-AAAAA-CAAA
*
468124 AAAAACACAAA
1 AAAAAAACAAA
468135 AAA
1 AAA
468138 GGGAGGGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
11 23 0.52
12 13 0.30
13 8 0.18
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:468099 original size:18 final size:18
Alignment explanation
Indices: 468078--468137 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
468068 GTCCTTCTCA
468078 AAAAAACAAAAAAAAAAC
1 AAAAAACAAAAAAAAAAC
* *
468096 AAAAAACAAGAAAAAAAT
1 AAAAAACAAAAAAAAAAC
* *
468114 AAAAACCAAAAAAAACAC
1 AAAAAACAAAAAAAAAAC
468132 AAAAAA
1 AAAAAA
468138 GGGAGGGGTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAACAAAAAAAAAAC
Found at i:469472 original size:28 final size:28
Alignment explanation
Indices: 469432--469906 Score: 449
Period size: 28 Copynumber: 16.7 Consensus size: 28
469422 AATACGACCT
* *
469432 CTTTTCAAAGCCCACAAGTTAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
469460 CTTTTTAAAGCCCACAAGTTAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
*
469490 CTTTTCAACGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
469519 C-TTTCAAAG-CCATAAGTGAGTGACATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* **
469546 C-TTTCAGAGCCCACAAGTCAGTGGCTT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
469573 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
** *
469601 CTTTTCAAAGCCCGTAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
469629 CTTCTCAAAACCCACAAGTGAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
469657 CTTTTCAAAGCCCACAATTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
469686 CTTCTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
469714 CTTCTCAAAGCCCATAAGTCAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
469742 CTTTTCAAAGCCCACAACTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
469769 CTTTCTCAAAGCCCACAAGTCAGTCGTATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCA-C
* * *
469799 C-TTCCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
469826 CTTTTCAAAACCCACAAGCCAGTGGTATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
469855 C-TTTCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
469884 CTTTCTCTAAAGCCTACACAAGT
1 CTTT-TC-AAAGCC--CACAAGT
469907 TGGTGGCAAC
Statistics
Matches: 372, Mismatches: 59, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
27 29 0.08
28 253 0.68
29 35 0.09
30 39 0.10
31 4 0.01
32 12 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:469698 original size:141 final size:139
Alignment explanation
Indices: 469431--469914 Score: 506
Period size: 141 Copynumber: 3.4 Consensus size: 139
469421 CAATACGACC
* * * *
469431 TCTTTTCAAAGCCCACAAGTTAGTGGTACCTTTTTAAAGCCCACAAGTTAGTGGCAACCCTTTTC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGC-A-CCTTCTC
* * * *
469496 AACGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCATAAGTGAGTGACATCCTTTCAGAGCCCAC
64 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTG-CATCCTTTCAAAGCCCAC
469560 AAGTCAGTGGCT
128 AAGTCAGTGGCT
**
469572 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCGTAAGTTAGTGGCACCTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * *
469637 AACCCACAAGTGAGTGGCA-CCTTTTCAAAGCCCACAATTTAGTAGCATCCTTCTCAAAGCCCAC
66 AGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGT-GCATCCTT-TCAAAGCCCAC
* *
469701 AAGTTAGTGGCA
128 AAGTCAGTGGCT
* * * * * * * *
469713 CCTTCTCAAAGCCCATAAGTCAGTAGCACCTTTTCAAAGCCCACAACTCAATGGCACTTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * * * *
469778 AGCCCACAAGTCAGTCGTATCCTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAACCCACAA
66 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGT-GCATCCTTTCAAAGCCCACAA
*
469843 GCCAGTGG-T
130 GTCAGTGGCT
* * * *
469852 ATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTCTCTAAAGCCTACACAAGTTGGTGGCA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGCACCTTT-TC-AAAGCC--CACAAGTTAGTGGCA
469915 ACCCTTCTAA
Statistics
Matches: 281, Mismatches: 50, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
138 2 0.01
139 32 0.11
140 43 0.15
141 167 0.59
142 18 0.06
143 2 0.01
144 6 0.02
146 11 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (139 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGCATCCTTTCAAAGCCCACAAG
TCAGTGGCT
Found at i:470952 original size:20 final size:20
Alignment explanation
Indices: 470927--471051 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
470917 TTTTACCTAG
* *
470927 ATGTATCGATGCATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
470947 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
470967 ATATATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
470987 ATGTATCGATACATTCTGATTTTTTACGTA
1 ATGTATCGAT--A--C--A-TTTTT-C--A
471017 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
471038 ATGTATCGATACAT
1 ATGTATCGATACAT
471052 CTAGTTAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 52 0.64
21 1 0.01
22 1 0.01
23 1 0.01
24 5 0.06
25 1 0.01
26 1 0.01
27 6 0.07
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:480827 original size:10 final size:10
Alignment explanation
Indices: 480812--480871 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 10
480802 TGTCCTTCTC
480812 AAAAAAACAA
1 AAAAAAACAA
480822 AAAAAAACAAA
1 AAAAAAAC-AA
*
480833 AAACAAGAAAAA
1 AAA-AA-AACAA
480845 AATAAAAACCAA
1 AA-AAAAA-CAA
480857 AAAAAACACAA
1 AAAAAA-ACAA
480868 AAAA
1 AAAA
480872 GGGAGGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 8 0.19
11 18 0.43
12 13 0.31
13 3 0.07
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:480833 original size:17 final size:17
Alignment explanation
Indices: 480813--480871 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 17
480803 GTCCTTCTCA
480813 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
*
480830 AAAAAACAAGAAAAAAAT
1 AAAAAACAA-AAAAAAAC
*
480848 AAAAACCAAAAAAAACAC
1 AAAAAACAAAAAAAA-AC
480866 AAAAAA
1 AAAAAA
480872 GGGAGGGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 15 0.42
18 21 0.58
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.02
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:482206 original size:28 final size:28
Alignment explanation
Indices: 482166--482640 Score: 449
Period size: 28 Copynumber: 16.7 Consensus size: 28
482156 AATACGACCT
* *
482166 CTTTTCAAAGCCCACAAGTTAGTGGTAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
482194 CTTTTTAAAGCCCACAAGTTAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-A-C
*
482224 CTTTTCAACGCCCACAAGTCAGTGGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* * *
482253 C-TTTCAAAG-CCATAAGTGAGTGACATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* **
482280 C-TTTCAGAGCCCACAAGTCAGTGGCTT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
482307 CTTTTCAAAGCCCACAAGTCAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
** *
482335 CTTTTCAAAGCCCGTAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
482363 CTTCTCAAAACCCACAAGTGAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
482391 CTTTTCAAAGCCCACAATTTAGTAGCATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
482420 CTTCTCAAAGCCCACAAGTTAGTGGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
482448 CTTCTCAAAGCCCATAAGTCAGTAGCAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
482476 CTTTTCAAAGCCCACAACTCAATGGCA-
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* *
482503 CTTTCTCAAAGCCCACAAGTCAGTCGTATC
1 CTTT-TCAAAGCCCACAAGTCAGTGGCA-C
* * *
482533 C-TTCCAAAGCCCACAAGTCAGTGGTAT
1 CTTTTCAAAGCCCACAAGTCAGTGGCAC
* * *
482560 CTTTTCAAAACCCACAAGCCAGTGGTATC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-C
* *
482589 C-TTTCAAAGCCCACACAAGTCGGTGGCAA
1 CTTTTCAAAG-CC-CACAAGTCAGTGGCAC
482618 CTTTCTCTAAAGCCTACACAAGT
1 CTTT-TC-AAAGCC--CACAAGT
482641 TGGTGGCAAC
Statistics
Matches: 372, Mismatches: 59, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
27 29 0.08
28 253 0.68
29 35 0.09
30 39 0.10
31 4 0.01
32 12 0.03
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (28 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:482432 original size:141 final size:139
Alignment explanation
Indices: 482165--482648 Score: 506
Period size: 141 Copynumber: 3.4 Consensus size: 139
482155 CAATACGACC
* * * *
482165 TCTTTTCAAAGCCCACAAGTTAGTGGTACCTTTTTAAAGCCCACAAGTTAGTGGCAACCCTTTTC
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGC-A-CCTTCTC
* * * *
482230 AACGCCCACAAGTCAGTGGCATCCTTTCAAAG-CCATAAGTGAGTGACATCCTTTCAGAGCCCAC
64 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTG-CATCCTTTCAAAGCCCAC
482294 AAGTCAGTGGCT
128 AAGTCAGTGGCT
**
482306 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCGTAAGTTAGTGGCACCTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * *
482371 AACCCACAAGTGAGTGGCA-CCTTTTCAAAGCCCACAATTTAGTAGCATCCTTCTCAAAGCCCAC
66 AGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGT-GCATCCTT-TCAAAGCCCAC
* *
482435 AAGTTAGTGGCA
128 AAGTCAGTGGCT
* * * * * * * *
482447 CCTTCTCAAAGCCCATAAGTCAGTAGCACCTTTTCAAAGCCCACAACTCAATGGCACTTTCTCAA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
* * * * * *
482512 AGCCCACAAGTCAGTCGTATCCTTCCAAAGCCCACAAGTCAGTGGTATCTTTTCAAAACCCACAA
66 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGT-GCATCCTTTCAAAGCCCACAA
*
482577 GCCAGTGG-T
130 GTCAGTGGCT
* * * *
482586 ATCCTTTCAAAGCCCACACAAGTCGGTGGCAACTTTCTCTAAAGCCTACACAAGTTGGTGGCA
1 -TCTTTTCAAAG-CC-CACAAGTCAGTGGCACCTTT-TC-AAAGCC--CACAAGTTAGTGGCA
482649 ACCCTTCTAA
Statistics
Matches: 281, Mismatches: 50, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
138 2 0.01
139 32 0.11
140 43 0.15
141 167 0.59
142 18 0.06
143 2 0.01
144 6 0.02
146 11 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (139 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAA
AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGCATCCTTTCAAAGCCCACAAG
TCAGTGGCT
Found at i:483687 original size:20 final size:20
Alignment explanation
Indices: 483662--483786 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
483652 TTTTACCTAG
* *
483662 ATGTATCGATGCATTTTTTA
1 ATGTATCGATACATTTTTCA
* * * *
483682 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
483702 ATATATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
483722 ATGTATCGATACATTCTGATTTTTTACGTA
1 ATGTATCGAT--A--C--A-TTTTT-C--A
483752 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
483773 ATGTATCGATACAT
1 ATGTATCGATACAT
483787 CTAGTTAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 52 0.64
21 1 0.01
22 1 0.01
23 1 0.01
24 5 0.06
25 1 0.01
26 1 0.01
27 6 0.07
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:487006 original size:20 final size:19
Alignment explanation
Indices: 486963--487014 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
486953 ACATTATGCT
***
486963 TTGTATCGATACATGTTCA
1 TTGTATCGATACACACTCA
486982 TTGTATCGATACACACTCAA
1 TTGTATCGATACACACTC-A
*
487002 TTGTATCAATACA
1 TTGTATCGATACA
487015 TGAGACTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACACACTCA
Found at i:488685 original size:3 final size:3
Alignment explanation
Indices: 488677--488716 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
488667 ACCATCAAAA
* *
488677 ATG ATG ATG ATG AAG ATG ATG ATG ATG ATG ATA ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
488717 AGTTGACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:488927 original size:24 final size:24
Alignment explanation
Indices: 488900--488953 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 24
488890 ATTCGACATT
488900 GAAGAAAAAGAGTTTAAATAAGCC
1 GAAGAAAAAGAGTTTAAATAAGCC
488924 GAAG---AAGAGTTTAAATAAGCC
1 GAAGAAAAAGAGTTTAAATAAGCC
*
488945 AAAGAAAAA
1 GAAGAAAAA
488954 AGCAATGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 20 0.77
24 6 0.23
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.15
Consensus pattern (24 bp):
GAAGAAAAAGAGTTTAAATAAGCC
Found at i:488933 original size:21 final size:21
Alignment explanation
Indices: 488907--488950 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
488897 ATTGAAGAAA
*
488907 AAGAGTTTAAATAAGCCGAAG
1 AAGAGTTTAAATAAGCCAAAG
488928 AAGAGTTTAAATAAGCCAAAG
1 AAGAGTTTAAATAAGCCAAAG
488949 AA
1 AA
488951 AAAAGCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.18
Consensus pattern (21 bp):
AAGAGTTTAAATAAGCCAAAG
Found at i:493227 original size:13 final size:13
Alignment explanation
Indices: 493209--493233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
493199 CAAAGATCTT
493209 TGTATCGATACAC
1 TGTATCGATACAC
493222 TGTATCGATACA
1 TGTATCGATACA
493234 AGGGTTACTA
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:495098 original size:21 final size:19
Alignment explanation
Indices: 495074--495127 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
495064 TTTCAACAAT
495074 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
495095 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
495114 TTGTATCGATACAA
1 TTGTATCGATACAA
495128 TGTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:495119 original size:19 final size:19
Alignment explanation
Indices: 495074--495156 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
495064 TTTCAACAAT
* *
495074 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
495095 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
495114 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
495128 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
495146 TTGTATCGATA
1 TTGTATCGATA
495157 TAATGTATCG
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 22 0.41
20 3 0.06
21 14 0.26
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:495133 original size:13 final size:13
Alignment explanation
Indices: 495115--495139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
495105 ACATAAGTGT
495115 TGTATCGATACAA
1 TGTATCGATACAA
495128 TGTATCGATACA
1 TGTATCGATACA
495140 TAAGTGTTGT
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:495137 original size:32 final size:32
Alignment explanation
Indices: 495096--495171 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
495086 AAACAGTAAT
495096 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
495128 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
495160 TGTATCGCTACA
1 TGTATCGATACA
495172 AAGCTATTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:504105 original size:13 final size:13
Alignment explanation
Indices: 504087--504111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
504077 CAATTCTTCA
504087 TGTATCGATACAT
1 TGTATCGATACAT
504100 TGTATCGATACA
1 TGTATCGATACA
504112 ATGTGCCATG
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:504122 original size:33 final size:32
Alignment explanation
Indices: 504067--504131 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
504057 TTTGGGATAA
504067 TGTATCGATACAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTC-TCATGTATCGATACAT
*
504100 TGTATCGATACAATGTGC-CATGTATTGATACA
1 TGTATCGATACAAT-T-CTCATGTATCGATACA
504132 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATGTATCGATACAT
Found at i:504184 original size:20 final size:19
Alignment explanation
Indices: 504155--504217 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
504145 TAGCTACTGC
504155 CAAT-TTCATGTATCGATA
1 CAATGTTCATGTATCGATA
*
504173 CATTTGTTCATGTATCGATA
1 CA-ATGTTCATGTATCGATA
**
504193 CAATGAACATGTATCGATA
1 CAATGTTCATGTATCGATA
504212 CAATGT
1 CAATGT
504218 ATGATACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 16 0.42
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
CAATGTTCATGTATCGATA
Found at i:514436 original size:20 final size:19
Alignment explanation
Indices: 514411--514464 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
514401 ACCCTAGAAA
514411 GTATCGATACATATCCAGAT
1 GTATCGATACATATCC-GAT
* **
514431 GTATCGATACATTATGCTTT
1 GTATCGATACA-TATCCGAT
514451 GTATCGATACATAT
1 GTATCGATACATAT
514465 TCATTATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 4 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATCCGAT
Found at i:514496 original size:20 final size:19
Alignment explanation
Indices: 514449--514500 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
514439 ACATTATGCT
* *
514449 TTGTATCGATACATATTCA
1 TTGTATCGATACACACTCA
* *
514468 TTATATCGATACACCCTCAA
1 TTGTATCGATACACACTC-A
514488 TTGTATCGATACA
1 TTGTATCGATACA
514501 TGAAACTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACACACTCA
Found at i:514565 original size:13 final size:13
Alignment explanation
Indices: 514547--514580 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
514537 CGATATATGG
*
514547 TACATTGTATCGA
1 TACATTGTATCCA
514560 TACATTGTATCCA
1 TACATTGTATCCA
*
514573 TAAATTGT
1 TACATTGT
514581 GAAAAGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (13 bp):
TACATTGTATCCA
Found at i:516836 original size:51 final size:52
Alignment explanation
Indices: 516732--516860 Score: 172
Period size: 52 Copynumber: 2.5 Consensus size: 52
516722 AATGTATAGG
* * *
516732 TACATTGAAGAATGTATCTATACATTTGGGTAAAAAACCCAAAATATATCAA
1 TACAATGAAAAATGTATCGATACATTTGGGTAAAAAACCCAAAATATATCAA
* * * * *
516784 TACAATGAAAAATGTATCGATATATTTGGGT-TAAAACCCAGATTGTATCAA
1 TACAATGAAAAATGTATCGATACATTTGGGTAAAAAACCCAAAATATATCAA
516835 TACAAT-AAAAATGTATCGATACATTT
1 TACAATGAAAAATGTATCGATACATTT
516861 TCTTCAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 19 0.28
51 22 0.32
52 27 0.40
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (52 bp):
TACAATGAAAAATGTATCGATACATTTGGGTAAAAAACCCAAAATATATCAA
Found at i:522071 original size:52 final size:52
Alignment explanation
Indices: 521986--522114 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
521976 AGAAATATGA
*
521986 AAATTTGCCTGCATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
522038 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
522090 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
522115 AAGATCTGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:522761 original size:49 final size:49
Alignment explanation
Indices: 522676--522955 Score: 322
Period size: 49 Copynumber: 5.8 Consensus size: 49
522666 CGAAGAATGA
* * * * * *
522676 CAATGTGCTGCTTCATGGCTAGCGACATT-GATCTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGA-CTTAAAGATGAAGGTGC
* ** *
522725 CAATATGCTGATTCAAAGCCAGCGATACCGGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * *
522774 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
522823 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
* * * * *
522866 CAATGTGTTGGTTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
*
522915 CAATATGCTGATTCAAGGCCAGCGATATTGGATTTAGAAGA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
522956 AGATGCCACC
Statistics
Matches: 193, Mismatches: 30, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
43 38 0.20
45 1 0.01
47 1 0.01
49 147 0.76
50 6 0.03
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
Found at i:522862 original size:22 final size:22
Alignment explanation
Indices: 522837--522904 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
522827 ATGCTGATTC
522837 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
** * *
522859 AAGGTGCCAATG-TGTTGG--TTC
1 AA-G-GCCAGCGATATTGGACTTA
*
522880 AAGGCCAGCGACATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
522902 AAG
1 AAG
522905 ATGACGGTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 5 0.16
20 5 0.16
21 4 0.12
22 7 0.22
23 6 0.19
24 5 0.16
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (22 bp):
AAGGCCAGCGATATTGGACTTA
Found at i:522914 original size:92 final size:97
Alignment explanation
Indices: 522676--522963 Score: 394
Period size: 92 Copynumber: 3.0 Consensus size: 97
522666 CGAAGAATGA
* * *
522676 CAATGTGCTGCTTCATGGCTAGCGACATT-GATCTTAAAGATGACGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGA-CTTAAAGATGACGGTGCCAATATGCTGATTCA
* **
522740 AAGCCAGCGATACCGGACTTAAAGATGAAGATGC
65 AGGCCAGCGATATTGGACTTAAAGATG-AGATGC
* *
522774 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
522839 GGCCAGCGATATTGGACTT-AA-A-G-G-TGC
66 GGCCAGCGATATTGGACTTAAAGATGAGATGC
* *
522866 CAATGTGTTGGTTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
*
522931 GGCCAGCGATATTGGATTTAGAAGA--AGATGC
66 GGCCAGCGATATTGGACTTA-AAGATGAGATGC
522962 CA
1 CA
522964 CCAACTTGTG
Statistics
Matches: 171, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
92 82 0.48
93 1 0.01
94 2 0.01
95 3 0.02
96 6 0.04
97 2 0.01
98 74 0.43
99 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (97 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGACTTAAAGATGAGATGC
Found at i:523133 original size:58 final size:56
Alignment explanation
Indices: 522972--523621 Score: 650
Period size: 58 Copynumber: 11.3 Consensus size: 56
522962 CACCAACTTG
** * *
522972 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTT-TGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGA-A-GGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
* * * * * *
523029 TGTGGGCTTTTGAAAAGATACCACTAACTTGTGGGCTTT-TGAAGGTTGGCACTGACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
* * * *
523086 TATGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTT-TGAAGGTTGCCACTAACT
1 TGTGGGCTTT-G--AAGGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
* * * ** *
523144 TGTGAGCTTTAGGAGAAGAG-TGCCACTAATTTGTGGGCTTTGAAAAAGAGTGCCACTGACT
1 TGTGGGCTTT----GAAG-GTTGCCACTGACTTGTGGGCTTTG-TGAAGGGTGCCACTGACT
* *
523205 TGTGGGCTTTTGAAGGTTGCCATTGACTTGTGGGCTTTAG-GAAAAGGGTGCCACTGATT
1 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTT-GTG--AAGGGTGCCACTGACT
* * *
523264 TGTGGGCTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT--GTGAAGGGTGCCACTGACT
* *
523322 TGTGGGCTTTGAAGGTTGCCACTGATTTGTGGGC-TT-TGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
* * * *
523376 TGTGGGCTTTGAAGGTTGCCACTAACTTATGGGCTTTGGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGTG--AAGGGTGCCACTGACT
* *
523434 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT--GTGAAGGGTGCCACTGACT
* *
523492 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTT--GTGAAGGGTGCCACTGACT
** * *
523550 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
523606 TGTGGGCTTTTGAAGG
1 TGTGGGC-TTTGAAGG
523622 GTGAGGAATA
Statistics
Matches: 518, Mismatches: 51, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
54 46 0.09
55 2 0.00
56 28 0.05
57 64 0.12
58 306 0.59
59 45 0.09
60 4 0.01
61 20 0.04
62 3 0.01
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (56 bp):
TGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGTGAAGGGTGCCACTGACT
Found at i:523286 original size:27 final size:27
Alignment explanation
Indices: 522972--523621 Score: 604
Period size: 27 Copynumber: 22.6 Consensus size: 27
522962 CACCAACTTG
**
522972 TGTGGGCTTTTGATAGGGTTG-CACCAACT
1 TGTGGGC-TTTGA-A-GGTTGCCACTGACT
*
523001 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACT
* * * *
523029 TGTGGGCTTTTGAAAAGATACCACTAACT
1 TGTGGGC-TTTG-AAGGTTGCCACTGACT
*
523058 TGTGGGCTTTTGAAGGTTGGCACTGACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACT
* *
523086 TATGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTT-G--AAGGTTGCCACTGACT
*
523116 TGTGGGCTTTTGAAGGTTGCCACTAACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACT
* * *
523144 TGTGAGCTTTAGGAGAAGAG-TGCCACTAATT
1 TGTGGGCTTT----GAAG-GTTGCCACTGACT
523175 TGTGGGCTTTGAAAAAGAG-TGCCACTGACT
1 TGTGGGCTTTG---AAG-GTTGCCACTGACT
*
523205 TGTGGGCTTTTGAAGGTTGCCATTGACT
1 TGTGGGC-TTTGAAGGTTGCCACTGACT
* *
523233 TGTGGGCTTTAGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT--G--AAGGTTGCCACTGACT
*
523264 TGTGGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* *
523291 TGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTT----GAAGGTTGCCACTGACT
*
523322 TGTGGGCTTTGAAGGTTGCCACTGATT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
523349 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
*
523376 TGTGGGCTTTGAAGGTTGCCACTAACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* * *
523403 TATGGGCTTTGGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT--G--AAGGTTGCCACTGACT
523434 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* *
523461 TGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTT----GAAGGTTGCCACTGACT
523492 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* *
523519 TGTGGGCTTTGGGAGAAGGGTGCCACTGATT
1 TGTGGGCTTT----GAAGGTTGCCACTGACT
523550 TGTGGGCTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAGGTTGCCACTGACT
* *
523577 TGTGGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTTG--AAGGTTGCCACTGACT
523606 TGTGGGCTTTTGAAGG
1 TGTGGGC-TTTGAAGG
523622 GTGAGGAATA
Statistics
Matches: 527, Mismatches: 55, Indels: 79
0.80 0.08 0.12
Matches are distributed among these distances:
27 191 0.36
28 79 0.15
29 61 0.12
30 46 0.09
31 149 0.28
32 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (27 bp):
TGTGGGCTTTGAAGGTTGCCACTGACT
Found at i:523462 original size:228 final size:227
Alignment explanation
Indices: 522972--523621 Score: 821
Period size: 228 Copynumber: 2.8 Consensus size: 227
522962 CACCAACTTG
** * * * *
522972 TGTGGGCTTTTGATAGGGTTG-CACCAACTTGTGTGCTTT-TG--AAGGTTGCCACTGACTTGTG
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTGGGCTTTAGGAAAAGGGTGCCACTGATTTGTG
* * * * * * * *
523033 GGCTTTTGAAAAGATACCACTAACTTGTGGGCTTT---TGAAGGTTGGCACTGACTTATGGGCTT
64 GGC-TTTG-AAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTT
* * *
523095 TGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGAGCTTTAGGAGA
127 T-G--AAGGTTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTT----GA
* *
523160 AGAGTGCCACTAATTTGTGGGCTTTGAAAAAGAGTGCCACTGACT
184 AG-GTGCCACTAACTTATGGGCTTTGAAAAAGAGTGCCACTGACT
*
523205 TGTGGGCTTTTGAAGGTTGCCATTGACTTGTGGGCTTTAGGAAAAGGGTGCCACTGATTTGTGGG
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGGAAAAGGGTGCCACTGATTTGTGGG
523270 CTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTTGAA
66 CTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTTGAA
*
523335 GGTTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTA
131 GGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAGG-TGCCACTA
* * *
523400 ACTTATGGGCTTTGGGAAAAGGGTGCCACTGATT
195 ACTTATGGGCTTT-GAAAAAGAGTGCCACTGACT
* *
523434 TGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGG
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGGAAAAGGGTGCCACTGATTTGTGGG
*
523498 CTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTTGAA
66 CTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTTGAA
* *
523563 GGTTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGG
131 GGTTGCCACTGACTTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGGGC-TTTGAAGG
523622 GTGAGGAATA
Statistics
Matches: 374, Mismatches: 31, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
227 1 0.00
228 165 0.44
229 24 0.06
230 21 0.06
231 13 0.03
232 43 0.11
233 58 0.16
234 4 0.01
235 22 0.06
236 23 0.06
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (227 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTAGGAAAAGGGTGCCACTGATTTGTGGG
CTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGGAGAAGGGTGCCACTGATTTGTGGGCTTTGAA
GGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAGGTGCCACTAA
CTTATGGGCTTTGAAAAAGAGTGCCACTGACT
Found at i:525073 original size:1 final size:1
Alignment explanation
Indices: 525069--525166 Score: 70
Period size: 1 Copynumber: 98.0 Consensus size: 1
525059 GTTGTTGTTG
* * * * * * * *
525069 TTTTTGTTTTTTTTTCTTTGTTTTTTTGTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * **
525134 CTTCTTTTTTTTTGTTTATTTGGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
525167 GTGGAGGACG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:525088 original size:14 final size:13
Alignment explanation
Indices: 525054--525166 Score: 104
Period size: 14 Copynumber: 8.2 Consensus size: 13
525044 ATCCGGACCC
*
525054 TTTTTGTTGTTGTTG
1 TTTTTGTT-TT-TTT
525069 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
525082 TTCTTTGTTTTTTT
1 TT-TTTGTTTTTTT
525096 GTTTTTGTTTTTTGT
1 -TTTTTGTTTTTT-T
525111 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
525124 TTGTTT-TTTTCTTCT
1 TT-TTTGTTTT-TT-T
*
525139 TTTTT-TTTGTTT
1 TTTTTGTTTTTTT
* *
525151 ATTTGGTTTTTTT
1 TTTTTGTTTTTTT
525164 TTT
1 TTT
525167 GTGGAGGACG
Statistics
Matches: 85, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.05
13 21 0.25
14 46 0.54
15 14 0.16
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (13 bp):
TTTTTGTTTTTTT
Found at i:525093 original size:21 final size:20
Alignment explanation
Indices: 525069--525166 Score: 110
Period size: 22 Copynumber: 4.8 Consensus size: 20
525059 GTTGTTGTTG
525069 TTTTTGTTTTTTTTTCTTTGTT
1 TTTTTGTTTTTTTTT-TTTG-T
*
525091 TTTTTGTTTTTGTTTTTTGT
1 TTTTTGTTTTTTTTTTTTGT
*
525111 TTTTTG-TTTTTTTTTGT-T
1 TTTTTGTTTTTTTTTTTTGT
* *
525129 TTTTTCTTCTTTTTTTTTGT
1 TTTTTGTTTTTTTTTTTTGT
525149 TTATTTGGTTTTTTTTTT
1 TT-TTT-GTTTTTTTTTT
525167 GTGGAGGACG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.09
19 18 0.28
20 10 0.16
21 7 0.11
22 23 0.36
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTTTTGT
Found at i:525165 original size:51 final size:53
Alignment explanation
Indices: 525054--525168 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 53
525044 ATCCGGACCC
* *
525054 TTTTTGTTGTTGTTGTTTTTGTTTTTTTTTCTTTGTTTTTTTGTTTTTGTTTT
1 TTTTTTTTGTTGTTGTTTTTGTTTTTTTTTCTTTGTTTTTTTGTTTTTGTGTT
525107 TTGTTTTTTGTT-TT-TTTTTGTTTTTTTCTTC-TT-TTTTTTTGTTTATT-TGGTT
1 TT-TTTTTTGTTGTTGTTTTTGTTTTTTT-TTCTTTGTTTTTTTGTTT-TTGT-GTT
525159 TTTTTTTTGT
1 TTTTTTTTGT
525169 GGAGGACGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
51 20 0.36
52 21 0.38
53 7 0.12
54 8 0.14
ACGTcount: A:0.01, C:0.03, G:0.13, T:0.83
Consensus pattern (53 bp):
TTTTTTTTGTTGTTGTTTTTGTTTTTTTTTCTTTGTTTTTTTGTTTTTGTGTT
Found at i:525166 original size:20 final size:20
Alignment explanation
Indices: 525063--525168 Score: 101
Period size: 21 Copynumber: 5.2 Consensus size: 20
525053 CTTTTTGTTG
*
525063 TTGTTGTTTTTGTTTTTTTTTCT
1 TTGTT-TTTTTG-GTTTTTTT-T
*
525086 TTGTTTTTTTGTTTTTGTTTT
1 TTGTTTTTTTGGTTTT-TTTT
525107 TTG-TTTTTT-G-TTTTTTT
1 TTGTTTTTTTGGTTTTTTTT
**
525124 TTGTTTTTTTCTTCTTTTTTT
1 TTGTTTTTTTGGT-TTTTTTT
*
525145 TTGTTTATTTGGTTTTTTTT
1 TTGTTTTTTTGGTTTTTTTT
525165 TTGT
1 TTGT
525169 GGAGGACGCC
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
17 7 0.10
18 9 0.12
20 17 0.23
21 26 0.36
22 9 0.12
23 5 0.07
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (20 bp):
TTGTTTTTTTGGTTTTTTTT
Found at i:539083 original size:52 final size:52
Alignment explanation
Indices: 538935--539063 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
538925 CGAAATATGA
538935 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTTGGC
*
538987 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTTGGC
539039 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
539064 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTTGGC
Found at i:539090 original size:13 final size:13
Alignment explanation
Indices: 539072--539096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
539062 CAAAGATCAG
539072 TGTATCGATACAA
1 TGTATCGATACAA
539085 TGTATCGATACA
1 TGTATCGATACA
539097 TTTGAGTAAT
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:539138 original size:86 final size:84
Alignment explanation
Indices: 538999--539182 Score: 212
Period size: 86 Copynumber: 2.2 Consensus size: 84
538989 ATTTGCCTGC
* * * *
538999 ATGTATCGATACATTTTATAGTGTATCGATACATCTTGGCAAATTTGCCTGCA-TGTATCGATAC
1 ATGTATCGATACATTTGATAATGTATCGATACATCTTGGC-AAGTAGCCTGCATTGTATCGATAC
539063 AAAGA-TCAGTGTATCGATACA
65 AAA-ACTCA-TGTATCGATACA
* *
539084 ATGTATCGATACATTTGAGTAATGTATCGATACATTTTTTGGC-AGTAGCTTGCATTGTATCGAT
1 ATGTATCGATACATTTGA-TAATGTATCGATACA--TCTTGGCAAGTAGCCTGCATTGTATCGAT
*
539148 ACAAAACTTATGTATCGATACA
63 ACAAAACTCATGTATCGATACA
* *
539170 TTGTATTGATACA
1 ATGTATCGATACA
539183 ACACTTATGT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
85 17 0.20
86 46 0.54
87 16 0.19
88 6 0.07
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (84 bp):
ATGTATCGATACATTTGATAATGTATCGATACATCTTGGCAAGTAGCCTGCATTGTATCGATACA
AAACTCATGTATCGATACA
Found at i:539163 original size:19 final size:18
Alignment explanation
Indices: 539139--539236 Score: 72
Period size: 19 Copynumber: 5.8 Consensus size: 18
539129 TAGCTTGCAT
539139 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
539158 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
539171 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
539190 TGTATCGATAC--A-TTA
1 TGTATCGATACAAACTTA
539205 --TATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
*
539223 TGTATCAATACAAA
1 TGTATCGATACAAA
539237 TTGTTGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 26
0.68 0.03 0.28
Matches are distributed among these distances:
13 19 0.30
14 1 0.02
15 3 0.05
16 4 0.06
18 4 0.06
19 22 0.35
20 10 0.16
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:539181 original size:32 final size:32
Alignment explanation
Indices: 539136--539234 Score: 153
Period size: 32 Copynumber: 3.1 Consensus size: 32
539126 CAGTAGCTTG
*
539136 CATTGTATCGATACAAAACTTATGTATCGATA
1 CATTGTATCGATACAACACTTATGTATCGATA
*
539168 CATTGTATTGATACAACACTTATGTATCGATA
1 CATTGTATCGATACAACACTTATGTATCGATA
* *
539200 CATTATATCGATACAACACTTTATGTATCAATA
1 CATTGTATCGATACAACAC-TTATGTATCGATA
539233 CA
1 CA
539235 AATTGTTGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 47 0.77
33 14 0.23
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.35
Consensus pattern (32 bp):
CATTGTATCGATACAACACTTATGTATCGATA
Found at i:540357 original size:20 final size:20
Alignment explanation
Indices: 540312--540383 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
540302 CGTTGAACTC
* * *
540312 AGTGTATGGATACATTTATGA
1 AGTGTATTGATACATTCA-CA
540333 A-TGTATTGATACATTCTA-A
1 AGTGTATTGATACATTC-ACA
* * *
540352 ATTGTATCGAAACATTCACA
1 AGTGTATTGATACATTCACA
540372 AGTGTATTGATA
1 AGTGTATTGATA
540384 TGAATGAGGG
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
AGTGTATTGATACATTCACA
Found at i:540471 original size:20 final size:21
Alignment explanation
Indices: 540426--540472 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
540416 GCCAACAAAT
* *
540426 TGTATCAATACATTCATATGA
1 TGTATCAATACATTCACATAA
540447 TGTATCAATACA-TCACATAA
1 TGTATCAATACATTCACATAA
540467 TGTATC
1 TGTATC
540473 GATAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (21 bp):
TGTATCAATACATTCACATAA
Found at i:542966 original size:20 final size:20
Alignment explanation
Indices: 542941--543007 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
542931 ATATAGAGAA
*
542941 TGTATCGATAGATTATTCAT
1 TGTATCGATACATTATTCAT
542961 TGTATCGATACA--A-T--T
1 TGTATCGATACATTATTCAT
542976 TGTATCGATACATTATTCAT
1 TGTATCGATACATTATTCAT
*
542996 TGTATCAATACA
1 TGTATCGATACA
543008 ATCTGGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 13 0.32
17 2 0.05
18 2 0.05
20 23 0.57
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATTCAT
Found at i:542991 original size:35 final size:35
Alignment explanation
Indices: 542941--543009 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
542931 ATATAGAGAA
* *
542941 TGTATCGATAGATTATTCATTGTATCGATACAATT
1 TGTATCGATACATTATTCATTGTATCAATACAATT
542976 TGTATCGATACATTATTCATTGTATCAATACAAT
1 TGTATCGATACATTATTCATTGTATCAATACAAT
543010 CTGGAAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (35 bp):
TGTATCGATACATTATTCATTGTATCAATACAATT
Found at i:545765 original size:20 final size:19
Alignment explanation
Indices: 545722--545773 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
545712 ACATTATGCT
***
545722 TTGTATCGATACATGTTCA
1 TTGTATCGATACACACTCA
545741 TTGTATCGATACACACTCAA
1 TTGTATCGATACACACTC-A
*
545761 TTGTATCAATACA
1 TTGTATCGATACA
545774 TGAGACTAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACACACTCA
Found at i:547445 original size:3 final size:3
Alignment explanation
Indices: 547437--547476 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
547427 ACCATCAAAA
* *
547437 ATG ATG ATG ATG AAG ATG ATG ATG ATG ATG ATA ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
547477 AGTTGACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:547687 original size:24 final size:24
Alignment explanation
Indices: 547660--547713 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 24
547650 ATTCGACATT
547660 GAAGAAAAAGAGTTTAAATAAGCC
1 GAAGAAAAAGAGTTTAAATAAGCC
547684 GAAG---AAGAGTTTAAATAAGCC
1 GAAGAAAAAGAGTTTAAATAAGCC
*
547705 AAAGAAAAA
1 GAAGAAAAA
547714 AGCAATGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 20 0.77
24 6 0.23
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.15
Consensus pattern (24 bp):
GAAGAAAAAGAGTTTAAATAAGCC
Found at i:547693 original size:21 final size:21
Alignment explanation
Indices: 547667--547710 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
547657 ATTGAAGAAA
*
547667 AAGAGTTTAAATAAGCCGAAG
1 AAGAGTTTAAATAAGCCAAAG
547688 AAGAGTTTAAATAAGCCAAAG
1 AAGAGTTTAAATAAGCCAAAG
547709 AA
1 AA
547711 AAAAGCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.18
Consensus pattern (21 bp):
AAGAGTTTAAATAAGCCAAAG
Found at i:551987 original size:13 final size:13
Alignment explanation
Indices: 551969--551993 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551959 CAAAGATCTT
551969 TGTATCGATACAC
1 TGTATCGATACAC
551982 TGTATCGATACA
1 TGTATCGATACA
551994 AGGGTTACTA
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:553858 original size:21 final size:19
Alignment explanation
Indices: 553834--553887 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
553824 TTTCAACAAT
553834 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
553855 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
553874 TTGTATCGATACAA
1 TTGTATCGATACAA
553888 TGTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:553879 original size:19 final size:19
Alignment explanation
Indices: 553834--553916 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
553824 TTTCAACAAT
* *
553834 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
553855 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
553874 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
553888 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
553906 TTGTATCGATA
1 TTGTATCGATA
553917 TAATGTATCG
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 22 0.41
20 3 0.06
21 14 0.26
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:553893 original size:13 final size:13
Alignment explanation
Indices: 553875--553899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553865 ACATAAGTGT
553875 TGTATCGATACAA
1 TGTATCGATACAA
553888 TGTATCGATACA
1 TGTATCGATACA
553900 TAAGTGTTGT
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:553897 original size:32 final size:32
Alignment explanation
Indices: 553856--553931 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
553846 AAACAGTAAT
553856 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
553888 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
553920 TGTATCGCTACA
1 TGTATCGATACA
553932 AAGCTATTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:559048 original size:21 final size:21
Alignment explanation
Indices: 559022--559097 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
559012 CTGCCAAGAA
559022 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
559043 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
559063 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
559084 ATGTATCGATACAT
1 ATGTATCGATACAT
559098 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:559067 original size:20 final size:20
Alignment explanation
Indices: 559042--559115 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
559032 ACATCTTTTT
559042 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
559062 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
559083 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
559103 CATGTATCGATAC
1 CATGTATCGATAC
559116 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:559079 original size:41 final size:41
Alignment explanation
Indices: 559022--559115 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
559012 CTGCCAAGAA
559022 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
559063 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
559104 ATGTATCGATAC
1 ATGTATCGATAC
559116 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:560042 original size:64 final size:63
Alignment explanation
Indices: 559936--560067 Score: 246
Period size: 64 Copynumber: 2.1 Consensus size: 63
559926 CAACTAATAT
*
559936 CAAAAGTTTATGCAAGCTCTCCCCCTTAATACAAGTGTTCTTCCCTTTAATACAAAATTTATAA
1 CAAACGTTTATGCAAGCTCTCCCCCTTAATACAAGTGTTCTTCCCTTTAATACAAAATTTAT-A
560000 CAAACGTTTATGCAAGCTCTCCCCCTTAATACAAGTGTTCTTCCCTTTAATACAAAATTTATA
1 CAAACGTTTATGCAAGCTCTCCCCCTTAATACAAGTGTTCTTCCCTTTAATACAAAATTTATA
560063 CAAAC
1 CAAAC
560068 TCTCCCCCTT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
63 6 0.09
64 61 0.91
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (63 bp):
CAAACGTTTATGCAAGCTCTCCCCCTTAATACAAGTGTTCTTCCCTTTAATACAAAATTTATA
Found at i:560939 original size:13 final size:13
Alignment explanation
Indices: 560921--560945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560911 ACTGAAGCAA
560921 TGTATCGATATAT
1 TGTATCGATATAT
560934 TGTATCGATATA
1 TGTATCGATATA
560946 ATCTGGAAAA
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATCGATATAT
Found at i:564734 original size:21 final size:21
Alignment explanation
Indices: 564708--564783 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
564698 CTGCCAAGAA
564708 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
564729 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
564749 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
564770 ATGTATCGATACAT
1 ATGTATCGATACAT
564784 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:564753 original size:20 final size:20
Alignment explanation
Indices: 564728--564801 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
564718 ACATCTTTTT
564728 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
564748 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
564769 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
564789 CATGTATCGATAC
1 CATGTATCGATAC
564802 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:564765 original size:41 final size:41
Alignment explanation
Indices: 564708--564801 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
564698 CTGCCAAGAA
564708 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
564749 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
564790 ATGTATCGATAC
1 ATGTATCGATAC
564802 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:569779 original size:13 final size:13
Alignment explanation
Indices: 569761--569785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
569751 CAATTCTTCA
569761 TGTATCGATACAT
1 TGTATCGATACAT
569774 TGTATCGATACA
1 TGTATCGATACA
569786 ATGTGCCATG
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:569796 original size:33 final size:32
Alignment explanation
Indices: 569741--569805 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
569731 TTTGGGATAA
569741 TGTATCGATACAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTC-TCATGTATCGATACAT
*
569774 TGTATCGATACAATGTGC-CATGTATTGATACA
1 TGTATCGATACAAT-T-CTCATGTATCGATACA
569806 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATGTATCGATACAT
Found at i:569858 original size:20 final size:19
Alignment explanation
Indices: 569829--569891 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
569819 TAGCTACTGC
569829 CAAT-TTCATGTATCGATA
1 CAATGTTCATGTATCGATA
*
569847 CATTTGTTCATGTATCGATA
1 CA-ATGTTCATGTATCGATA
**
569867 CAATGAACATGTATCGATA
1 CAATGTTCATGTATCGATA
569886 CAATGT
1 CAATGT
569892 ATGATACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 2 0.05
19 20 0.53
20 16 0.42
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
CAATGTTCATGTATCGATA
Done.