Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021143.1 Corchorus olitorius cultivar O-4 contig21176, whole genome shotgun sequence
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: 114085
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:833 original size:12 final size:12
Alignment explanation
Indices: 816--857 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
806 TGAACTCTAA
*
816 GCAACAGCCGCC
1 GCAACAGCAGCC
*
828 GCAACAGCAGCA
1 GCAACAGCAGCC
*
840 GCAGCAGCAGCC
1 GCAACAGCAGCC
852 GCAACA
1 GCAACA
858 AAACGGTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.40, G:0.26, T:0.00
Consensus pattern (12 bp):
GCAACAGCAGCC
Found at i:838 original size:3 final size:3
Alignment explanation
Indices: 832--896 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
822 GCCGCCGCAA
* * * * * **
832 CAG CAG CAG CAG CAG CAG CCG CAA CA- AAA CGG TCAG CAG CAG TTG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG -CAG CAG CAG CAG
877 CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CA
897 TCCTCAGCCA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 1 0.02
3 45 0.94
4 2 0.04
ACGTcount: A:0.34, C:0.32, G:0.29, T:0.05
Consensus pattern (3 bp):
CAG
Found at i:2096 original size:18 final size:18
Alignment explanation
Indices: 2073--2109 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2063 TCTTTAATCC
*
2073 TTTTGAAAGTTTAGACCT
1 TTTTGAAAATTTAGACCT
2091 TTTTGAAAATTTAGACCT
1 TTTTGAAAATTTAGACCT
2109 T
1 T
2110 CTCTACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTTGAAAATTTAGACCT
Found at i:11072 original size:130 final size:130
Alignment explanation
Indices: 10902--11141 Score: 453
Period size: 130 Copynumber: 1.8 Consensus size: 130
10892 GAGATAAGAA
*
10902 TCATTTTCATTTCTTAAAGAGATTGAGATTACAAAGGCACAGGAATACCCGTACAACGCTGCATG
1 TCATTTTCATTTCTTAAAGAGATTGAGATTACAAACGCACAGGAATACCCGTACAACGCTGCATG
10967 ATTAGCTACATTATCGAAACGCTAATCTATGAGATAACAAACTACAACAAACAAATTACAAACAT
66 ATTAGCTACATTATCGAAACGCTAATCTATGAGATAACAAACTACAACAAACAAATTACAAACAT
* *
11032 TCATTTTCATTTCTTGAAGAGATTGAGATTACAAACGCACATGAATACCCGTACAACGCTGCATG
1 TCATTTTCATTTCTTAAAGAGATTGAGATTACAAACGCACAGGAATACCCGTACAACGCTGCATG
11097 ATTAGCTACATTATCGAAACGCTAATCTATGAGATAACAAACTAC
66 ATTAGCTACATTATCGAAACGCTAATCTATGAGATAACAAACTAC
11142 CTACCTATTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (130 bp):
TCATTTTCATTTCTTAAAGAGATTGAGATTACAAACGCACAGGAATACCCGTACAACGCTGCATG
ATTAGCTACATTATCGAAACGCTAATCTATGAGATAACAAACTACAACAAACAAATTACAAACAT
Found at i:21296 original size:152 final size:150
Alignment explanation
Indices: 21021--21296 Score: 322
Period size: 152 Copynumber: 1.8 Consensus size: 150
21011 CCAAAAATAT
* *
21021 GACAATTGACCTGATAAAATGAAGGCCATGTGTCAATCAGGCTTTGCTTCTTGAACATCAAAAAC
1 GACAATTGACCTGAGAAAATGAAGGCCATATGTCAATCAGGCTTT-CTTCTTGAACATCAAAAAC
* * * * * * * *
21086 CAAGTTAATACAAAAACATAAGTTAAGCTGGTTTTTCCTGGCAGCTTGCAATCGTGATAGAATGC
65 CAAGTTAAGACAAAAACAAAAGTTAAGCAGGGTTTGCCTGGCAGCTTACAAACATGATAGAATGC
21151 CTATCTGTAAACCCAAAGTAA
130 CTATCTGTAAACCCAAAGTAA
* ** ** ***
21172 GACAATTGGACCTGAGAAAATTAAGGCCATATGTCTGTCAGGCTTT-TATCTTGGGCATCACCTA
1 GACAATT-GACCTGAGAAAATGAAGGCCATATGTCAATCAGGCTTTCT-TCTTGAACATCAAAAA
*
21236 CCAAGTT-AGACAAAAACAAAATTTAAGCAGGGTTTGCCTGGCAGCTCTCACAAACATGATA
64 CCAAGTTAAGACAAAAACAAAAGTTAAGCAGGGTTTGCCTGGCAGCT-T-ACAAACATGATA
21297 TATCATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
150 34 0.33
151 26 0.25
152 42 0.41
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (150 bp):
GACAATTGACCTGAGAAAATGAAGGCCATATGTCAATCAGGCTTTCTTCTTGAACATCAAAAACC
AAGTTAAGACAAAAACAAAAGTTAAGCAGGGTTTGCCTGGCAGCTTACAAACATGATAGAATGCC
TATCTGTAAACCCAAAGTAA
Found at i:39792 original size:30 final size:30
Alignment explanation
Indices: 39758--39816 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
39748 TTTTATCTTC
39758 ACTTTCCTCTTATACCCTCAAATTTTAATG
1 ACTTTCCTCTTATACCCTCAAATTTTAATG
* *
39788 ACTTTCCTCTTATATCTTCAAATTTTAAT
1 ACTTTCCTCTTATACCCTCAAATTTTAAT
39817 ATCTTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAATG
Found at i:49767 original size:11 final size:11
Alignment explanation
Indices: 49751--49785 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
49741 TTTTTCTGTT
49751 TTTTGTTTTTG
1 TTTTGTTTTTG
*
49762 TTTTGTTTTCG
1 TTTTGTTTTTG
49773 TTTTGTTTTTG
1 TTTTGTTTTTG
49784 TT
1 TT
49786 GTGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:52800 original size:41 final size:41
Alignment explanation
Indices: 52737--52818 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
52727 ACTTGACCCT
*
52737 CCTAATAATTAAGGAAATAAATTAAATCCAGATTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
* *
52778 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
52819 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTAGCCCC
Found at i:52936 original size:13 final size:13
Alignment explanation
Indices: 52918--52949 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
52908 TGACACGTCA
52918 GGAGGGACAAATT
1 GGAGGGACAAATT
52931 GGAGGGACAAATT
1 GGAGGGACAAATT
52944 GGAGGG
1 GGAGGG
52950 TCATGTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.06, G:0.47, T:0.12
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:57232 original size:40 final size:40
Alignment explanation
Indices: 57183--57268 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
57173 CTCCAACTTG
* * *
57183 ACCCTCCTAATAATTAAGGAAATAAATTTAATCCAGGTTTA
1 ACCC-CCTAATAATTAAGGAAAGAAATTAAATCCAGATTTA
*
57224 ACCCCCTAATAATTAAGGTAAGAAATTAAATCCAGATTTA
1 ACCCCCTAATAATTAAGGAAAGAAATTAAATCCAGATTTA
*
57264 GCCCC
1 ACCCC
57269 TAGTTATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (40 bp):
ACCCCCTAATAATTAAGGAAAGAAATTAAATCCAGATTTA
Found at i:61523 original size:6 final size:6
Alignment explanation
Indices: 61512--61540 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
61502 CTAATTTATA
61512 ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
61541 GTATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
ATCTAT
Found at i:61851 original size:116 final size:116
Alignment explanation
Indices: 61628--61842 Score: 306
Period size: 116 Copynumber: 1.8 Consensus size: 116
61618 CATTGTTTAA
* * *
61628 ACTTCTATAGTTTTAGTCAACTAAAAACTCTATTTTTATCTAATTAAATCTAATATCCTTTAACT
1 ACTTCTATAGTTTTACTCAACTAAAAACTCTATTTTAATCTAATTAAATCTAATATCATTTAACT
* **
61693 ATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTAAATATATTAT
66 ATTTTATGTTTACCATTTTACTATAATAATTAAAAAACTTAAATATATTAT
* * *
61744 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTAATTTAATTAAATCTAATATCATTATACC
1 ACTTCTATAGTTTTACTCAACTAAAAACTCTATTTTAATCTAATTAAATCTAATATCATT-TAAC
* *
61809 TTTTTTTATGTTTACCATTTTACTA-AATATTTAA
65 -TATTTTATGTTTACCATTTTACTATAATAATTAA
61843 TTAATTAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
116 55 0.64
117 9 0.10
118 22 0.26
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (116 bp):
ACTTCTATAGTTTTACTCAACTAAAAACTCTATTTTAATCTAATTAAATCTAATATCATTTAACT
ATTTTATGTTTACCATTTTACTATAATAATTAAAAAACTTAAATATATTAT
Found at i:63437 original size:30 final size:30
Alignment explanation
Indices: 63401--63461 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
63391 CATTCTCATT
63401 TCTCTAGAATGGAAGAAGAAAAAGAACAAG
1 TCTCTAGAATGGAAGAAGAAAAAGAACAAG
63431 TCTCTAGAATGGAAGAAGAAAAAGAACAAG
1 TCTCTAGAATGGAAGAAGAAAAAGAACAAG
63461 T
1 T
63462 ACAACTGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (30 bp):
TCTCTAGAATGGAAGAAGAAAAAGAACAAG
Found at i:66539 original size:26 final size:25
Alignment explanation
Indices: 66495--66543 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
66485 GCCTATATTT
66495 ATTTTTTAAAATAAAATAATAATTAA
1 ATTTTTTAAAATAAAATAA-AATTAA
*
66521 ATTTTTTAATAA-AAGATAAAATT
1 ATTTTTTAA-AATAAAATAAAATT
66544 TAAACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 15 0.71
27 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
ATTTTTTAAAATAAAATAAAATTAA
Found at i:66694 original size:29 final size:30
Alignment explanation
Indices: 66644--66703 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
66634 CTAATTAATG
* *
66644 TATACATATAAATTATTCAATTTTATTATA
1 TATAAATATAAATTATTCAATTATATTATA
*
66674 TATAAATAT-AATTATTTAATTATATTATA
1 TATAAATATAAATTATTCAATTATATTATA
66703 T
1 T
66704 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TATAAATATAAATTATTCAATTATATTATA
Found at i:67933 original size:332 final size:331
Alignment explanation
Indices: 67167--69715 Score: 2087
Period size: 332 Copynumber: 7.8 Consensus size: 331
67157 AGCTGAGATT
* * * * * *
67167 TTTCGGCTAAAATTTTACAAAAATTGACCCG-AAAGTTATTTTCTTAATTTTTAGCCACAATACT
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTTCCTCAATTTTTAGCTAAAATACT
* * * ** * *
67231 CATAAAAATTATATAATTCAAAGCAAAAAAGATTGAAAAACTTTTCATGCTTCCAATATCGTTTT
65 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTT
* * * **
67296 TCCTATTATTTTTC-GAATTAAATTCTAATTAAATCGAAACATGATTCAGATGCTTGCT--TTAC
130 T-C-A-TATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAAAAAC
* *
67358 AAATCCTTAAATCCAATGTAGCTGAGATTTGGTTAGATAAAT-ATATATAGATATTTCAAGGAGT
191 AAATCCTTAAATCCAATGTGGCTGAGATTTGATT--AT--ATGA-ATATAGATATTTCAAGGAGT
* ** * * * * * * * * *
67422 CTCGGTGCCAGAAATCATGCAACATTAAACCGGGGCCTCGCAATGCGTTTTTAGCCAAAAACCGT
251 CTTGACGCCAAAAATCATGCAAAACTGAACCAGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGT
* *
67487 GATTTCGACTAACATACACGA
316 GA--T-GA-TTA-GTACACGA
* * * * * * *
67508 TTTCAGTTAATATTTTACAAAAATTGACCTG-AAATTTTTTCCCTCAAATTTT-GTCTAAAATAC
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTT-CCTCAATTTTTAG-CTAAAATAC
* * * * * *
67571 TCATAAAATATATATAATTCAACTCCAAAAAGATTGGAGAACTTTTCACGCTTTTAATTTCGTTT
64 TCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTT
* * * * *
67636 TTCATATTTTTC-GAATTAATTTTTGATTGAATCGAAACAAGATTCAAATGATCGTAAAAACAAA
129 TTCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * *
67700 TCCTTAAATGCAATGTGGCTGAGATTTGATTATATGGATATATATATTTCAAGGAGTCTTGACGT
194 TCCTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTGACGC
* * * *
67765 AAAAAATTATGCAAAACTGAACCAGGGCCCCGAAACACGTTTTTAGCAAAAAAAACCGTGATGGT
259 CAAAAATCATGCAAAACTGAACCAGGGCCCCGAAACGCGTTTTTAGC--AAAAAACCGTGATGAT
67830 TAGTACACGA
322 TAGTACACGA
* * *
67840 TTTCGGCTAAAATTTTGCAAAAAGTGACTCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTC
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTC
** * * ** * * *
67905 AGGAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTTTCGCTTTTCATATCGATTTT
66 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTT
* * *
67970 CATATTTTTCAGAATTACTTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAAAC
131 CATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* ** * * * *
68035 TTTAAATGTAATGTGGCTGAGA-TTGATTAGATGACTATAGATATCTT--AGGGGTCTTGGCGCC
196 CTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATAT-TTCAAGGAGTCTTGACGCC
* * * * * *
68097 AAAAATCATGCAAAACTGACCCAAGGCCCTGTAACGCGTTTTTTAGCCAAAAATCGTGATGATTA
260 AAAAATCATGCAAAACTGAACCAGGGCCCCGAAACGCG-TTTTTAGCAAAAAACCGTGATGATTA
* *
68162 TTACACTA
324 GTACACGA
* * *
68170 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTC
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTC
* * * * * *
68235 AT-AAAAAGATATAATTCAACGCCAAAAATATTTTAAGG-TTTTTTACGCTTCTAATATTGTTTT
66 ATAAAAAATATATAATTCAACGCCAAAAAGA-TTGAAGGACTTTTCACGCTTCTAATATCGTTTT
* * * * ** *
68298 TCCTACTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTTATTTGCTCGTAAAAATAAA
130 TCATA-TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * *
68363 TCCTCAAATCCAATGTGACTGAGATTTGATTAGATGAATATAGATATTTCAATGAGTCTTGGA-G
194 TCCTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTT-GACG
* * *
68427 CCGAAAATCATGCAAAACTG-ACCTGGGGCCCC-ATAACGCGTTTTTAGCCAAAAAAAAAAC-TG
258 CCAAAAATCATGCAAAACTGAACC-AGGGCCCCGA-AACGCGTTTTTAG-C---AAAAAACCGTG
* *
68489 -TGA-TGGTACACAA
317 ATGATTAGTACACGA
* * * * * * * *
68502 ATTCGGTTAATATTTTACAAAAATTGACCCGAAATATTTTAT-CTCAATTTTTAGCCATAATCCT
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTT-TCCTCAATTTTTAGCTAAAATACT
* ** * * * *
68566 CATAAAAAATATATAATTCAATGTTAAAAAGAATGAAGGTCTTTCCACGCTTCTAATATCGTTTA
65 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTT
* * * * *
68631 TCCTATTTTTCCGAATTAATTTCTAATTAAATTGAAACATGATTCAGATGCTTGT-------AA-
130 TCATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * *
68688 ----AAA--C-A-GTGGTTGCGATTTGGTTAGATGAATATAGGTATTTCAAGGAGTCTCGACACC
195 CCTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTGACGCC
* * * * *
68745 GAAAATCATGCGAAACTGAATC-GGGCCCCGGAAA-ACGTTTTTAGC-CAAAACCGTGATGATTA
260 AAAAATCATGCAAAACTGAACCAGGGCCCC-GAAACGCGTTTTTAGCAAAAAACCGTGATGATTA
*
68807 TTACACGA
324 GTACACGA
* * ** * * * * *
68815 TTTC-G-----A-----CAAAAATTGACGCGAAAGATAATTCGTTAATTTTTATCCACAATACTC
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTC
* * * * * *
68869 ATAAAAAATATATAATTTAATGCCAAAAAGATTAAAGGGCTTTTCATG-ATCTTAATATCGTTTT
66 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTC-TAATATCGTTTT
* * * * * *
68933 TCATATTTTTTCAGAACTAAATTCTAATTTAATCGAAACGAGATTGAGATGTTCGTAAAAACAAA
130 TCATA-TTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * **
68998 TCCTTAAATGCAATGTGGCT-ATGATTTTATTAAATGAATATAGATATTTC---GAGTCTCGGTG
194 TCCTTAAATCCAATGTGGCTGA-GATTTGATTATATGAATATAGATATTTCAAGGAGTCTTGACG
* * * * * * * * * *
69059 CCCAAAATCATGCAAAACTGAGCCAGAGCTCCAAAATGCGTTTTTAGCCAAATACCGTGATGGTC
258 CCAAAAATCATGCAAAACTGAACCAGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATT
*
69124 AGAACACGA
323 AGTACACGA
* * * * *
69133 TTTTGGCTAAAATTTTGC-AAAA-T---CCGAAAAAAATCTTCCTCAATTTTTGGATAAAATACT
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCG-AAAAATTTTTCCTCAATTTTTAGCTAAAATACT
* * * * * * *
69193 CATAAAAAATATATAATTTAATGCCAAAAATATCGGAGGACTTTTCACGCTTTTAATATC-ATTT
65 CATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTT
* * *
69257 TCATATTTTTTCTA-AATTAATTTCTAATTAAATCGAAACAAGATTCAAATGTTTGTAAAAAAAA
130 TCATA-TTTTTC-AGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-----AAA
* * * * *
69321 AAAAAAT-CTTAAATCCAATGTGGCCGAGATTTGATTATATGAATGTGGATATCTCAAGGAGTCT
188 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCT
* * * * * *
69385 TGACGTCAAAAATCATGCAAAACTGAACTAGGGCCCTTG-AATGCATTTTTAGCAAAAAACTGTG
253 TGACGCCAAAAATCATGCAAAACTGAACCAGGGCCC-CGAAACGCGTTTTTAGCAAAAAACCGTG
* *
69449 ATGATTATTATACGA
317 ATGATTAGTACACGA
* * * ** *
69464 TTTCGGGTAAAATTTTGTATAAATTGACCCGAATGATATTTCCTCAATTTTTAGCTAAAATACTC
1 TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTC
* * * * * * *
69529 ATAAAAAATATATAATTCAACGTCAAAAAGATTTAAGGGCTTTTGACGCTTCCAAAACCGTTTTT
66 ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTT
* * * * * * *
69594 CCTATTTTTCTGAATTAATTCCTAATTAAA-CGGAAACAAGATTCAGATTCCCGAAAAAATAAAT
131 CATATTTTTCAGAATTAATTTCTAATTAAATC-GAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * *
69658 TCTTAAATCCAATGTGGCTGAGATTTGATTGTATGAATATAAATGTTTCAAGTAGTCT
195 CCTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCT
69716 CGGAGCCAAT
Statistics
Matches: 1771, Mismatches: 347, Indels: 190
0.77 0.15 0.08
Matches are distributed among these distances:
301 3 0.00
302 92 0.05
303 40 0.02
307 1 0.00
310 7 0.00
311 2 0.00
312 4 0.00
313 10 0.01
314 1 0.00
315 21 0.01
316 91 0.05
317 20 0.01
318 24 0.01
319 30 0.02
320 3 0.00
324 53 0.03
325 75 0.04
326 1 0.00
327 1 0.00
328 43 0.02
329 59 0.03
330 168 0.09
331 201 0.11
332 296 0.17
333 133 0.08
334 4 0.00
335 180 0.10
336 10 0.01
337 14 0.01
338 42 0.02
339 34 0.02
340 5 0.00
341 103 0.06
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (331 bp):
TTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTC
ATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTT
CATATTTTTCAGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
CTTAAATCCAATGTGGCTGAGATTTGATTATATGAATATAGATATTTCAAGGAGTCTTGACGCCA
AAAATCATGCAAAACTGAACCAGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGATTAGT
ACACGA
Found at i:69873 original size:21 final size:21
Alignment explanation
Indices: 69849--69901 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
69839 AATATCTTTA
69849 CATAATTAAAATAAAAAGT-TT
1 CATAATTAAAATAAAAA-TATT
* *
69870 CATAAGTATAAATAATAATATT
1 CATAATTA-AAATAAAAATATT
69892 -ATAATTAAAA
1 CATAATTAAAA
69902 ATATATTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 14 0.52
22 10 0.37
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
CATAATTAAAATAAAAATATT
Found at i:69909 original size:17 final size:18
Alignment explanation
Indices: 69887--69926 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
69877 ATAAATAATA
69887 ATATTATAAT-TAAAAAT
1 ATATTATAATCTAAAAAT
69904 ATATTATAATCTAAAAAT
1 ATATTATAATCTAAAAAT
69922 A-ATTA
1 ATATTA
69927 ATTTTTTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTATAATCTAAAAAT
Found at i:76197 original size:25 final size:25
Alignment explanation
Indices: 76148--76197 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
76138 CTTACCTTAC
**
76148 TTATTAGCCGATATAACAGGTAGTA
1 TTATTAGCCGATATAACAGACAGTA
* *
76173 TTATTAGGCGGTATAACAGACAGTA
1 TTATTAGCCGATATAACAGACAGTA
76198 AAATTAGAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (25 bp):
TTATTAGCCGATATAACAGACAGTA
Found at i:79100 original size:334 final size:327
Alignment explanation
Indices: 78441--80793 Score: 1839
Period size: 334 Copynumber: 7.1 Consensus size: 327
78431 GGTTCGGTTG
* * *
78441 TTTTTTTACAAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTCAGAAGAAATAGGAAA
1 TTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA-AAATAGGAAA
* * * *
78506 AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATCATATATTTTTTATGAG
65 AACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAG
* ** * * * * *
78571 TATTGTGGTTAAAACTTGAGGAAAAATATTTCGGGTCACTTTCTGCAAAATATTAGCCGAAATCG
130 TATTGTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTTCAAAAT-TTAGCCGAAATCG
* * ** *
78636 TG---TACCATCACGGTTTTTTTGGGCTAAAAACGCGTTCCGATGCCCCGGGTCAGTTTTGCATG
194 TGTAATATCATCACGG--TTTTT-GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATG
* * * * * * *
78698 ATTTTTGACGCCAAGAATCCTTGAAATATCTAAATTCATCAAATCAAAT-TTCAACCATATTGCA
256 ATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTT-AGCCACATTACA
78762 TTTAAGGA
320 TTTAAGGA
* * *
78770 TTTGCTTTTACGAGCATCTAAATCTTGGTTCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGA
1 TTT--TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA-TAGGA
* * * *
78835 AAAACGATATTAGAATCGTAAAAAATCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTGAA
63 AAAACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTT-AT
* *
78900 GAGTATTGTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAAATTTTATCTAAAATTTAGCCGAA
127 GAGTATTGTAGCCAAAAATTGAGGAAAAATCTTTCGGGTC-AATTTTTTC-AAAATTTAGCCGAA
* * * *
78965 ATCGTGTAATAGTCATCACGGTTTTTTGCTAAAAACGCGTTTCAGGGCCCCGGGTCAGCTTTGCA
190 ATCGTGTAATA-TCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCA
* * *
79030 TGATTTTTGGCGCCAAGACTCCTTGAGATATCCATATTCATCTTATCAAATCTTAGCCACATTAC
254 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTAC
79095 ATTTAAGGA
319 ATTTAAGGA
79104 TTTATTTTTACGAGCATCT-AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATATA
1 -TT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG---AAAA-ATA
* * * * *
79168 GGAAAAACG--A-T------GTGAAAAGTCCTTTAATATTTTTGGTGTTAAATTATATATATTTC
60 GGAAAAACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTT
* * * * *
79224 ATTAGTATTTTTGCCAAAATTTGAGGAAAAATTTTTCGGGTC-ATTTTTTGCAAAATTT----GA
125 ATGAGTATTGTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTT-CAAAATTTAGCCGA
* * *
79284 GA-C--G--A-A--AT--C--------G-T-AAATCGCGTTTCGGGGCCCCGACTCAGTTTTGCA
189 AATCGTGTAATATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCA
* * * * * *
79329 AGATTTTTGGGGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTTC
254 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTAC
79394 ATTTAAGGA
319 ATTTAAGGA
* * * *
79403 TTTTTTTTACGA-CTATCCGTATCTTGTTTCGATTTAATTAGAAATTAATTCAGTAAAATATGAA
1 -TTTTTTTACGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAA
* * * * ** *
79467 AAAC-ATTACTAAAAGCGTGAAAAGTACTCCAATCCTTTTGGAGTTGAAATATATATATATATAT
64 AAACGA-TATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTG--A-AT-TATATAT-T-T
* * * * * *
79531 ATATTATGAGTATTTTAGGCAAAAATTGAGGAAAAATATTTCTGATCAA-TTTTTCAAAATATTT
122 -T-TTATGAGTATTGTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTTCAAAAT-TTA
** * * *
79595 GTTGAAATCGTGTACGTTAGTCGAAATCACGGTTTTTGGCTAAAAATGCG-TTCTGGGGCCCCTG
184 GCCGAAATCGTGTA--ATA-TC---ATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGGCCCCGG
* * * * *
79659 TTCAGTGTTGCATGATTTTTTGCGCCAAGACTCCTTGTAATATCTATATTCATCTAACCAAAT-T
242 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
*
79723 TCAGCCACATTAGATTTAAGGA
307 T-AGCCACATTACATTTAAGGA
** * * *
79745 TTTTTGAAACAAGCATCTGAAT-TATGTTTCGATTTAATTAGAAAATAATTCGGAAAATTATAGG
1 TTTTT-TTACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTCAGAAAA--ATAGG
* * * * * * *
79809 AAAAAAGATATTAGAAGCATGAAAAGCCCATCAA-ATTTTTTAGCATTGAATTATATAATTTTTA
62 AAAAACGATATTAGAAGCGTGAAAAGTCCTTCAATA-TTTTTGGCGTTGAATTATATATTTTTTA
** * *
79873 TGAGTATTGT-GGTAGAAAATTGA-GATAATAA-CTTTCGGGTCAATTTTTACAAAATTTTAGCT
126 TGAGTATTGTAGCCA-AAAATTGAGGA-AA-AATCTTTCGGGTCAATTTTTTCAAAA-TTTAGCC
* * * * * ** *
79935 GAAATCGTGTAATAATCTTTACGATTTTTGGCTAAAAACGCGTTGCGAGGCCTTGGCTAAGTTTT
187 GAAATCGTGTAAT-ATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTT
*** * * * * * * *
80000 GCATGATTTTTGATACCTAGACTAGTCTCTGAGATATCCATATTCATTTAATCAAATCTCAGCTA
251 GCATGATTTTTGGCGCCAAGACT--CCT-TGAAATATCTATATTCATCTAATCAAATCTTAGCCA
** * * *
80065 CATTGGATATATGAA
313 CATTACATTTAAGGA
* * * * *
80080 TTTGTTTTCACGAGCTTCTGAATCTTGTTTCGA-TTAATAAAAAATTAATTTAGAAAAATATGAA
1 TTT-TTTT-ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAA
* * * * * * * * * *
80144 AAATGATATCAAAAGCGTGAAAAGTCCTCCAATCTTTTTTGTGTTAAATATTGTATATATTTTAT
64 AAACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTT-GA-ATTATATATTTTTTAT
* * ** * *
80209 GAGTATTTTTGCC-AAAATCAAGGAAAAAAT-TTTCGGGT-ATTTTTTTGCAAAATTTTAGCTGA
127 GAGTATTGTAGCCAAAAATTGAGG-AAAAATCTTTCGGGTCAATTTTTT-CAAAA-TTTAGCCGA
* * * * *
80271 AATCGTGTAGTGACCATCA-GAGTTTTTGGCTAAAAACGCGTTTCGGAGCCTCGGCTTAGTTTTG
189 AATCGTGTAAT-ATCATCACG-GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTG
* *
80335 CATGATTTTTTTGGCGCCGAGACTCCTTAAAATATCTATATTCATCTAATCAAAT-TTCAGCCAC
252 CATGA--TTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTT-AGCCAC
*
80399 ATTGA-ATTTAAGTA
314 ATT-ACATTTAAGGA
* * * *
80413 TTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAGTAGAAATTAATTTAGAAAAATATGAA
1 -TT-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAA
* * * * * * *
80478 AAACGATATTAAAAGCATGAAAAGTCCTCCAAT-CTTTTAGTGTTGAATTATATATATTTTATGA
64 AAACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGA
* * * *
80542 GTATTATGGCTAAAAATTGAGGAAAAATACTTT-GGGTC-ATTTTTTGCAAAATTTTAGCCAAAA
129 GTATTGTAGCCAAAAATTGAGGAAAAAT-CTTTCGGGTCAATTTTTT-CAAAA-TTTAGCCGAAA
* * * *
80605 TCGTGTACTATCA--ATGGTTTTTTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCAGG-TTAGTT
191 TCGTGTAATATCATCACGG------TTTTTGGCTAAAAACGCGTTTCGGGGCCCC-GGCTCAGTT
* * ** * * *
80667 TTGCATGATTTTTTGTGGAAAAACTCCTTGAAATATCTATATTTATCTAA-CGAAAATCTTAGTC
249 TTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC--AAATCTTAGCC
*
80731 ACATT-GATTTAAGGA
312 ACATTACATTTAAGGA
* * *
80746 -TTTTTTACGAGCATTTGAATCATGTTTTGATTTAATTAGAAATTAATT
1 TTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
80794 TGAAAAAATA
Statistics
Matches: 1631, Mismatches: 268, Indels: 249
0.76 0.12 0.12
Matches are distributed among these distances:
295 10 0.01
296 3 0.00
297 2 0.00
298 13 0.01
299 130 0.08
300 1 0.00
301 1 0.00
304 23 0.01
306 1 0.00
307 2 0.00
308 7 0.00
309 1 0.00
310 1 0.00
311 9 0.01
312 43 0.03
313 1 0.00
314 1 0.00
315 1 0.00
316 3 0.00
317 2 0.00
319 2 0.00
320 3 0.00
324 14 0.01
325 1 0.00
326 35 0.02
327 38 0.02
329 5 0.00
330 50 0.03
331 140 0.09
332 132 0.08
333 215 0.13
334 282 0.17
335 145 0.09
336 90 0.06
337 37 0.02
338 2 0.00
339 1 0.00
340 7 0.00
341 13 0.01
342 126 0.08
343 1 0.00
344 36 0.02
345 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (327 bp):
TTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAA
ACGATATTAGAAGCGTGAAAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGT
ATTGTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTTCAAAATTTAGCCGAAATCGTG
TAATATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTT
TGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTACATTTAAG
GA
Found at i:85021 original size:31 final size:31
Alignment explanation
Indices: 84986--85045 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
84976 TCAATTTAAT
** *
84986 CCCTCTACTTGTAAAATTGTGTCAATTGAGC
1 CCCTCTACTTACAAAATTGGGTCAATTGAGC
*
85017 CCCTCTACTTACCAAATTGGGTCAATTGA
1 CCCTCTACTTACAAAATTGGGTCAATTGA
85046 ATCCAATCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (31 bp):
CCCTCTACTTACAAAATTGGGTCAATTGAGC
Found at i:87484 original size:15 final size:16
Alignment explanation
Indices: 87451--87482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
87441 GTTGGGACCA
87451 TAAAAAATTATTAATT
1 TAAAAAATTATTAATT
*
87467 TAAAAAGTTATTAATT
1 TAAAAAATTATTAATT
87483 AATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAAAAATTATTAATT
Found at i:97714 original size:321 final size:316
Alignment explanation
Indices: 97032--99025 Score: 1652
Period size: 321 Copynumber: 6.3 Consensus size: 316
97022 GGCGTGACAG
* * * ** * ** *
97032 AATCAAATCCCAGCCACATTCGATTTAATAATTTATTTTTACGAGCAT-TCGAATCTTACTTCTA
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCT-GAATCTTGTTTCGA
* * * * **
97096 TCTAATTTGAAATTAATTCGGAAAAATATGGAAAAAAGATATTAGAAGTGTGAAAAA-TAC-TAC
65 TTTAATTAGAAATTAATTCAGAAAAA-AT-GAAAAACGATATTAGAAGTGT-AAAAAGCCCGT-C
* * * * *
97159 AAATTTTTTGA-CGTTGAATTATATTCTTTTTATGAGTATTGTGCCAAAAAATTGAGAAAAATAT
126 -AATTTTTTGAGCGTTGAATTAT-TTATTTTTCTGAGTATTCTGGCAAAAAATTGAGAAAAAAAT
* *
97223 TTCGGGTCAGTTTTTAGCCGAAATCGTGTACT-ACCATCACGGTTGTTGGCTAAAAACGCGTTCC
189 TTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT-AAAACGCGTTTC
* * * * **
97287 CGAGCCTGGACTCAATTTCGCATGATTTTTGGC-GCAAAAACTCATTGAAATATCCATATTCATC
253 CGAGCC-CGACTCAGTTTTGCATGATTTTTGGCAG-AAAAACTCCTTGAAATATTTATATTCATC
*
97351 G
316 T
* ** * *
97352 AATCAATTCTCAGCCACATTGGATAGGAGGATTTATTTTTACGAGCATCTTAATCTTGTTTCGAT
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * *
97417 TTGACTATAAATTAATTCTGAAAAAATGAAAAAACGATATTAGAAGTGTAAAAAGCCCGTCAATC
66 TTAATTAGAAATTAATTCAGAAAAAATG-AAAAACGATATTAGAAGTGTAAAAAGCCCGTCAATT
* * ** * *
97482 CTTTGAGCATTGAATTATTTATTTTTCTGAGTATTCTGAAAAAAAAATTCATAAAAAAATCTTCG
130 TTTTGAGCGTTGAATTATTTATTTTTCTGAGTATTCTG-GCAAAAAATTGAGAAAAAAAT-TTCG
* * * *
97547 GGTCAGTTTTTAGCCGAAATCATGTACTAATCATCACGGTTTTTGGGCTAAAACGCGTTTCGGGG
193 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GGCTAAAACGCGTTTCCGAG
* *
97612 TCCCGATTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCT
257 -CCCGACTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATTTATATTCATCT
* * * * * * * * *
97673 AACCAAATCTCAGACACATTGAATTTAATGATTTGTTTTTACGAGAATCCGAATCATGTTTTGAT
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * *
97738 TTAATTATAAATAAATTCACAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAAA-CCCTTCAA
66 TTAATTAGAAATTAATTCA-GAAAAAAT-GAAAAACGATATTAGAAGTGT-AAAAAGCCCGTCAA
* * * * **
97802 TTTGTTT--GCGTTGAATTATATATTCTTTATGAGTATTGTGGCTAAAAA-TGAAGGAAAAACTT
128 TTT-TTTGAGCGTTGAATTATTTATT-TTTCTGAGTATTCTGGCAAAAAATTG-A-GAAAAAAAT
* * * *
97864 TTCGTGTCAGTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCGTCATGGTTTTTGGTTAAA
189 TTCGGGTCA------GT----TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT-AA
* * ** *
97929 AACGCG-TTCCGGAGCCCCGACTCAGTTTTGCATGATTTTTTGCACAATTACTCCTTGAAACATT
243 AACGCGTTTCC-GAG-CCCGACTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATT
*
97993 TATATTCATCG
306 TATATTCATCT
* *
98004 AATCAAATCTCAGCCACATTGGATATAAGGATTT-CTTTTACGAGCA-CTTGAATATTGTTTCGA
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATC-TGAATCTTGTTTCGA
* * * ** *
98067 TTTAATTAGAAATTAATTCGGAAAAGGAAATGGAAAAACGATATTAGATGCGTGGAAAGCCCATC
65 TTTAATTAGAAATTAATTCAG-AAA--AAAT-GAAAAACGATATTAGAAGTGTAAAAAGCCCGTC
* *
98132 AATATTTTTGA-CATTGAATTATATATTTTTTCTGAGTA-TCTTGGCAAAAAATTGAGAAAAAAC
126 AAT-TTTTTGAGCGTTGAATTATTTA-TTTTTCTGAGTATTC-TGGCAAAAAATTGAGAAAAAA-
* * *
98195 TTTTCGGGTCAGTTTTTATAGCCGAAATCGTGTACTAA-C-TCACGGTTTTTGGCTAGAAACACA
187 ATTTCGGGTCAG-TTTT-TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA-AAACGCG
* * *
98258 TTT-C---CCC-ATCTCAATTTTGCATGATTTTTGGTAGAAAAACTCCTTGAAATATCTATATTC
249 TTTCCGAGCCCGA-CTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATTTATATTC
98318 ATCT
313 ATCT
* * *
98322 TACCAAATCTCAGCCAGATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * * *
98387 ATAATTAGAAATTAATTCAGAAAAAATGGAAAACGATATTTGAAGCGTGAAAAGCTCGTCAATTT
66 TTAATTAGAAATTAATTCAGAAAAAATGAAAAACGATATTAGAAGTGTAAAAAGCCCGTCAATTT
* * *
98452 TTTG-GCGTTGAATTATATTTTTTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAACATTTC
131 TTTGAGCGTTGAA-T-TA-TTTATTTTTCTGAGTATTCTGGCAAAAAATTGA-GAAAAAAATTTC
* * * * *
98516 GGGTCAGTTTTTAGCCGAAATCGTGTTCTAACCATCACAGTTTTTGACAAAAAAACGCG-GTCCG
192 GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGC--TAAAACGCGTTTCCG
* * * ** *
98580 GGACCACGACTCTGTTTGGCAT-ATTTTTGGC-GCTGAGACTCCTTGAAATATCTT-TATTCATC
255 AG-CC-CGACTCAGTTTTGCATGATTTTTGGCAG-AAAAACTCCTTGAAATAT-TTATATTCATC
98642 T
316 T
* * *
98643 AATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATTTTGTTTCGAT
1 AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * **
98708 TTAATTAGAAATTAATTCAAAAAAATATGAAAAACGA-ATTAAAATTGTGAAAA-CCCCCCAATC
66 TTAATTAGAAATTAATTCAGAAAAA-ATGAAAAACGATATTAGAAGTGTAAAAAGCCCGTCAAT-
* * ** * * *
98771 TTTTTG-GCGTTGAATTATATGTA-TTTTATGAGTATTTTTACCAAAAATTGAGGGAAAATATTT
129 TTTTTGAGCGTTGAATTAT-T-TATTTTTCTGAGTATTCTGGCAAAAAATTGA-GAAAAAAATTT
* * *
98834 TGGGTCA-ATTTTA-CC---ATC----A-T-----T----GTTTTTGGCTAAAAACACG-TTCCG
191 CGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCT-AAAACGCGTTTCCG
* ** * * *
98879 AGCCCGGCTCAGTTTTGCATGATTTTTGGC-GCCAGACTCCTTGAAAGATCTATATT-ATCT
255 AGCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATTTATATTCATCT
* * * * * * *
98939 AATCAAATCTCAAG-CATATCGGATTTAAGGATTT-TTTTTATGAGTATTTGAATCTTATTTCGA
1 AATCAAATCTC-AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
99002 TTTAATTAGAAATTAATTCA-AAAA
65 TTTAATTAGAAATTAATTCAGAAAA
99026 TCATGAAACA
Statistics
Matches: 1382, Mismatches: 216, Indels: 178
0.78 0.12 0.10
Matches are distributed among these distances:
294 4 0.00
295 43 0.03
296 34 0.02
297 34 0.02
298 12 0.01
299 12 0.01
300 8 0.01
304 1 0.00
309 1 0.00
314 34 0.02
315 36 0.03
316 56 0.04
317 18 0.01
318 121 0.09
319 135 0.10
320 113 0.08
321 311 0.23
322 84 0.06
323 29 0.02
324 6 0.00
325 20 0.01
327 3 0.00
328 1 0.00
329 1 0.00
330 47 0.03
331 128 0.09
332 42 0.03
333 44 0.03
334 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (316 bp):
AATCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGAT
TTAATTAGAAATTAATTCAGAAAAAATGAAAAACGATATTAGAAGTGTAAAAAGCCCGTCAATTT
TTTGAGCGTTGAATTATTTATTTTTCTGAGTATTCTGGCAAAAAATTGAGAAAAAAATTTCGGGT
CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAACGCGTTTCCGAGCCCG
ACTCAGTTTTGCATGATTTTTGGCAGAAAAACTCCTTGAAATATTTATATTCATCT
Found at i:100071 original size:61 final size:61
Alignment explanation
Indices: 99976--100097 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
99966 TTACTATTTT
*
99976 TTTCGAGAAATATTAATTTGTATTAAACTCAAAGATCTGGGTTACAAATATCAGGTGGTAA
1 TTTCGAGAAATATTAATTTGTATTAAACTCAAAGATCTGGGTTACAAACATCAGGTGGTAA
100037 TTTCGAGAAATATTAATTTGTATTAAACTCAAAGATCTGGGTTACAAACATCAGGTGGTAA
1 TTTCGAGAAATATTAATTTGTATTAAACTCAAAGATCTGGGTTACAAACATCAGGTGGTAA
100098 ACACCTGTAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (61 bp):
TTTCGAGAAATATTAATTTGTATTAAACTCAAAGATCTGGGTTACAAACATCAGGTGGTAA
Found at i:102936 original size:30 final size:32
Alignment explanation
Indices: 102882--102946 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
102872 TAGTTGCATG
102882 AGGGAGAGAGAGGCTGAGGCTGCTCGGATG-TAT
1 AGGGAGAGAGAGGCT--GGCTGCTCGGATGCTAT
*
102915 AGGGAGAGGGAGGCT-GCTGCTCGGATGCTAT
1 AGGGAGAGAGAGGCTGGCTGCTCGGATGCTAT
102946 A
1 A
102947 TTCAGCAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 12 0.40
31 4 0.13
33 14 0.47
ACGTcount: A:0.23, C:0.14, G:0.45, T:0.18
Consensus pattern (32 bp):
AGGGAGAGAGAGGCTGGCTGCTCGGATGCTAT
Found at i:111014 original size:30 final size:30
Alignment explanation
Indices: 110989--111399 Score: 615
Period size: 30 Copynumber: 13.6 Consensus size: 30
110979 TTACAAATGG
* *
110989 CACCAGAAGTTGTCATGGTCTTACAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
* * *
111019 CACCAGAAGTTGTCATGGTCTTACAAATGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111049 CACCAGAAGTTGTCATGGTCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111079 CACCAGAAGTTGTCATGCTCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111109 CACCAGAAGTTGTCATAATCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111139 CACCAGAAGTTGTCATAATCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111169 CACCAGAAGTTGTCATGATTTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111199 CACCAGAAGTTGTCATGATTTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111229 CACCAGAAGTTGTCATGATGTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111259 CACCAGAAGTTGTCATGATGTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
111289 CACCAGAAGTTGTCATGATCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
*
111319 CACCATAAGTTGTCATGATCTTGCAATTGA
1 CACCAGAAGTTGTCATGATCTTGCAATTGA
* ** * * * *
111349 TACTTGAAGATGTCATAATTTTATTCAATTGA
1 CACCAGAAGTTGTCATGA-TCT-TGCAATTGA
111381 CACCAGAAGTTGTCATGAT
1 CACCAGAAGTTGTCATGAT
111400 AAATTTCCAA
Statistics
Matches: 355, Mismatches: 24, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
30 331 0.93
31 3 0.01
32 21 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (30 bp):
CACCAGAAGTTGTCATGATCTTGCAATTGA
Found at i:111379 original size:32 final size:32
Alignment explanation
Indices: 111342--111448 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
111332 CATGATCTTG
*
111342 CAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
** * ** *
111374 CAATTGACACCAGAAGTTGTCATGATAAATT-TC
1 CAATTGACACTTGAAGATGTCAT-A-ATTTTATT
* *
111407 CAATAGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACTTGAAGATGTCATAATTTTATT
111439 CAATTGACAC
1 CAATTGACAC
111449 CAGAAGTTCT
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
31 3 0.05
32 29 0.53
33 20 0.36
34 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (32 bp):
CAATTGACACTTGAAGATGTCATAATTTTATT
Found at i:111441 original size:65 final size:62
Alignment explanation
Indices: 111012--111464 Score: 343
Period size: 60 Copynumber: 7.4 Consensus size: 62
111002 CATGGTCTTA
* * ** * ** * *
111012 CAATTGACACCAGAAGTTGTCATGGTCTTACAA-ATGACACCAGAAGTTGTCAT-GGTCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATA-GACACTTGAAGATGTCATAATTTTATT
* * * ** * * *
111072 CAATTGACACCAGAAGTTGTCATGCTCTTGCAATTGACACCAGAAGTTGTCATAA-TCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * *
111132 CAATTGACACCAGAAGTTGTCATAATCTTGCAATTGACACCAGAAGTTGTCATGA-TTT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * * *
111192 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGA-TGT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * ** * * * *
111252 CAATTGACACCAGAAGTTGTCATGATGTTGCAATTGACACCAGAAGTTGTCATGA-TCT-TG
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* * * *
111312 CAATTGACACCATAAGTTGTCATGATCTTGCAATTGATACTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
* *
111374 CAATTGACACCAGAAGTTGTCATGATAAATTTCCAATAGACATTTGAAGATGTCATAATTTTATT
1 CAATTGACACCAGAAGTTGTCATGAT---CTTCCAATAGACACTTGAAGATGTCATAATTTTATT
*
111439 CAATTGACACCAGAAGTTCTCATGAT
1 CAATTGACACCAGAAGTTGTCATGAT
111465 TTTACCTTTC
Statistics
Matches: 357, Mismatches: 29, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
60 273 0.76
61 2 0.01
62 26 0.07
65 56 0.16
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (62 bp):
CAATTGACACCAGAAGTTGTCATGATCTTCCAATAGACACTTGAAGATGTCATAATTTTATT
Done.