Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013663.1 Corchorus capsularis cultivar CVL-1 contig13684, 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: 47598
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4779 original size:25 final size:27
Alignment explanation
Indices: 4750--4803 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
4740 GAAAATAGGA
4750 TTTTTGCT-G-CAAAACTGTAAACTTT
1 TTTTTGCTAGACAAAACTGTAAACTTT
*
4775 TTTTTGGTAGAAACAAAACTGTAAACTTT
1 TTTTTGCTAG--ACAAAACTGTAAACTTT
4804 GTTATTATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 1 0.04
29 16 0.67
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (27 bp):
TTTTTGCTAGACAAAACTGTAAACTTT
Found at i:17223 original size:45 final size:45
Alignment explanation
Indices: 17172--17260 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
17162 AAATTTTTTT
17172 CTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAATTTCTTTTCTA
1 CTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAATTTCTTTTCTA
*
17217 CTTCCTTTTCTTCTTCGTTTTCTGCTTTTATCAATTTCTTTTCT
1 CTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAATTTCTTTTCT
17261 TAAATTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.08, C:0.26, G:0.04, T:0.62
Consensus pattern (45 bp):
CTTCCTTTTCTTCTCCGTTTTCTGCTTTTATCAATTTCTTTTCTA
Found at i:17312 original size:12 final size:11
Alignment explanation
Indices: 17289--17377 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
17279 TCTTCCCCAA
17289 TTTCTTAATTT
1 TTTCTTAATTT
17300 TTTCTTAAGTTT
1 TTTCTTAA-TTT
17312 TTATACGTTGTATATTT
1 TT-T-C--T-TA-ATTT
17329 TTTCTTAAATTT
1 TTTCTT-AATTT
17341 TTTCTTAATTT
1 TTTCTTAATTT
***
17352 CACCTT--TTT
1 TTTCTTAATTT
17361 TTTCTTAATTT
1 TTTCTTAATTT
17372 TTTCTT
1 TTTCTT
17378 TTCTTTTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
9 6 0.10
11 25 0.40
12 16 0.26
13 3 0.05
14 1 0.02
15 1 0.02
16 2 0.03
17 7 0.11
18 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTCTTAATTT
Found at i:18895 original size:40 final size:40
Alignment explanation
Indices: 18844--18922 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
18834 TTTATAACTA
*
18844 GGGCTAAACCTGGATATAATTTCTTACCTTAATTATTAGG
1 GGGCTAAACCTGGATATAATTTATTACCTTAATTATTAGG
* **
18884 GGGCTAAACCTGGATTTAATTTATTTTCTTAATTATTAG
1 GGGCTAAACCTGGATATAATTTATTACCTTAATTATTAG
18923 TAGGGTCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (40 bp):
GGGCTAAACCTGGATATAATTTATTACCTTAATTATTAGG
Found at i:26817 original size:41 final size:41
Alignment explanation
Indices: 26770--26847 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
26760 ATAACTAGGA
*
26770 CTAAACCTGAATTTAATTTCTTAT-CTTAATTATTAGGGGAG
1 CTAAACCTGAATTTAATTTATT-TCCTTAATTATTAGGGGAG
*
26811 CTAAACCTGGATTTAATTTATTTCCTTAATTATTAGG
1 CTAAACCTGAATTTAATTTATTTCCTTAATTATTAGG
26848 AGGGTCAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (41 bp):
CTAAACCTGAATTTAATTTATTTCCTTAATTATTAGGGGAG
Found at i:27957 original size:41 final size:41
Alignment explanation
Indices: 27905--27984 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 41
27895 AAATAATTAT
27905 AAAAATATTGAATTTAATAA-AAA-AAATAATAGAGTTTACA
1 AAAAATATTGAATTTAATAATAAATAAA-AATAGAGTTTACA
27945 AAAATATATTGAATTTAATAATTAAATAAAAATAGAGTTT
1 AAAA-ATATTGAATTTAATAA-TAAATAAAAATAGAGTTT
27985 TTAGTAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
40 4 0.11
41 16 0.44
43 13 0.36
44 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (41 bp):
AAAAATATTGAATTTAATAATAAATAAAAATAGAGTTTACA
Found at i:29916 original size:2 final size:2
Alignment explanation
Indices: 29911--29943 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29901 TGTGTGTGTG
29911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29944 TATTATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31574 original size:210 final size:212
Alignment explanation
Indices: 31210--31605 Score: 663
Period size: 210 Copynumber: 1.9 Consensus size: 212
31200 ATTTAATTAC
* *
31210 AAAGCAAATCATTTATTTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTTGCTTATTGA
1 AAAGCAAATCATCTATTTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTTACTTATTGA
31275 ATTATTTAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGATTTAATAGTTGCTTAATTT
66 ATTATTTAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGATTTAATAGTTGCTTAATTT
* *
31340 TCCTTTTTTGTTTGATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAACTAATTACG
131 TCCTTTTTTGTTTAATGAAAATGAATCATCTGTTTAAACTTAAAGATTTTAAATAACTAATTACG
31405 CTTTATTTCCTTTAAGG
196 CTTTATTTCCTTTAAGG
31422 AAAGCAAATCATCTATTTTTTTT-ATCAAATAGATTGATTACGTTTGATA-TTTTTACTTATTGA
1 AAAGCAAATCATCTATTTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTTACTTATTGA
* * *
31485 ATTATTTAATTTCAAGCATTATCATAGTCAATAATTACTTATTTGCTTTAATAGTTGCTTAA-TT
66 ATTATTTAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGATTTAATAGTTGCTTAATTT
* ** *
31549 TCCTTTTTTTTTTTAATGAAAATGAATCATCTGTTTTTACTTAAAGATTTTTAATAA
131 TCC-TTTTTTGTTTAATGAAAATGAATCATCTGTTTAAACTTAAAGATTTTAAATAA
31606 GTTGTAAGGT
Statistics
Matches: 172, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
209 5 0.03
210 119 0.69
211 26 0.15
212 22 0.13
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (212 bp):
AAAGCAAATCATCTATTTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTTACTTATTGA
ATTATTTAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGATTTAATAGTTGCTTAATTT
TCCTTTTTTGTTTAATGAAAATGAATCATCTGTTTAAACTTAAAGATTTTAAATAACTAATTACG
CTTTATTTCCTTTAAGG
Found at i:32017 original size:139 final size:138
Alignment explanation
Indices: 31784--32149 Score: 484
Period size: 139 Copynumber: 2.6 Consensus size: 138
31774 CCAAAAGCTA
* *
31784 ATGATTATTTAATTTTACCACAAATAAATGAATCAATTAGT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTT-ATTTTACCATAAATAAATGAATCAATTAGTAATTATATTAC-AAAAAA-AAATT
* * * * * *
31848 GATCGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTT-AGTTAACTTTGCCAATCAAAGT
63 GATTGAACATACTAAATAAATAAATGAATCAAGTTAGTCCTTGA-TCAACTTTGCCAACCAAAGT
31912 TATAATTGATGG
127 TATAATTGATGG
* * *
31924 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTAGTAATTATATTACCAAAAAAAATTGA
1 ATGATTATTTA-TTTTACCATAAATAAATGAATCAATTAGTAATTATATTACAAAAAAAAATTGA
* * *
31989 TTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTGATCAACTTTGTCAACCAAAGTTAT
65 TTGAACATACTAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGCCAACCAAAGTTAT
* *
32054 AATTTATTG
130 AATTGATGG
*
32063 ATGATTATTTGATTTTGCCATAAATAAATGAATCAATTAGTAATTATATTAGCAAAAAAATAGAT
1 ATGATTATTT-ATTTTACCATAAATAAATGAATCAATTAGTAATTATATTA-CAAAAAAA-A-AT
32128 TGATTGAACATACTAAATAAAT
62 TGATTGAACATACTAAATAAAT
32150 TAGGGAATCA
Statistics
Matches: 200, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
139 117 0.58
140 50 0.25
141 10 0.05
142 23 0.12
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (138 bp):
ATGATTATTTATTTTACCATAAATAAATGAATCAATTAGTAATTATATTACAAAAAAAAATTGAT
TGAACATACTAAATAAATAAATGAATCAAGTTAGTCCTTGATCAACTTTGCCAACCAAAGTTATA
ATTGATGG
Found at i:32588 original size:140 final size:139
Alignment explanation
Indices: 32458--32789 Score: 524
Period size: 140 Copynumber: 2.4 Consensus size: 139
32448 AAGTTAGTGA
* *
32458 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
*
32522 CGCTACAAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
66 -GCCACAAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
32587 TATTGAACATG
130 TATT-AACATG
32598 TCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
1 TCGTTAGTTAATTTT-TCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
* * **
32662 TGCCACCAAAAAGATTGCCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
65 TGCCACAAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAAT
32727 TATTGAACATG
130 TATT-AACATG
* * *
32738 TTGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATGATTATCTAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAAT
32790 CAAAGTTGTA
Statistics
Matches: 179, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
140 174 0.97
141 5 0.03
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (139 bp):
TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAAT
GCCACAAAAAAAATTAACATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATT
ATTAACATG
Found at i:35265 original size:310 final size:311
Alignment explanation
Indices: 34701--35295 Score: 706
Period size: 310 Copynumber: 1.9 Consensus size: 311
34691 TGGCGTCAAG
* * * * *
34701 ACTCCTTGAGATATCTATATTCATCTAATCAAATCTCAGTCATATTGGATTTAAAAATTTGTTTT
1 ACTCCTTGAAATAACTATATCCATCTAATCAAATCTCAGTCACATTGCATTTAAAAATTTGTTTT
* * *
34766 TATAAGCATCTAAATCTTGTTTCAATTTAATTGAAAATTAATACAGAAAAATATGAAAAACGATA
66 TACAAGCATCTAAATCATGTTTCAATTTAATTGAAAATTAATACAAAAAAATATGAAAAACGATA
* * * *
34831 TTAAAATCGTGAAAAGACCTCCAATATTTTTTCACTTAAATTATAGATATTTTATGAGTATTTTA
131 TTAAAAGCGTCAAAAGACCTCCAATATTTTTGCACTTAAATTATA-ATATTTTATGAGTATTATA
* * * *
34896 TCTAAAAATTGAAGAAAAATTTTTCAAGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTA
195 GCTAAAAATTGAAGAAAAATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATA
* **
34961 ACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGGGCATTTTTGCCGCCGAC
260 ACCATCACAGTTTTTAACTAAAAACGCGTTTCGGGGCATTTTTGCCGCCGAC
*
35013 ACTCCTTGAAATAACTATATCCATCTAAT-AGAATCAT-AG-CTACATTGCATTT-AATATTT-T
1 ACTCCTTGAAATAACTATATCCATCTAATCA-AATC-TCAGTC-ACATTGCATTTAAAAATTTGT
* * * * *
35073 TTTTACAATCATCTGAATCATGTTTCGATTTAATT-AGAAATTAATTCAAAAAGAATATGAATAA
63 TTTTACAAGCATCTAAATCATGTTTCAATTTAATTGA-AAATTAATACAAAAA-AATATGAAAAA
* * * * *
35137 CGATATTAAAAGCGTCAAAA-ACCCTTCAATCTTTTTGGC-GTTGAATTAT-ATATCTTTCTGAG
126 CGATATTAAAAGCGTCAAAAGA-CCTCCAATATTTTT-GCACTTAAATTATAATAT-TTTATGAG
* * ** *
35199 TATTATGGCTAAAATTTG-AGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTTAGGCAAAATC
188 TATTATAGCTAAAAATTGAAGAAAA-ATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATC
*
35263 GTGTAATAATCATCACAGTTTTTAACTAAAAAC
252 GTGTAATAACCATCACAGTTTTTAACTAAAAAC
35296 AAGTGGATTT
Statistics
Matches: 238, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
309 11 0.05
310 128 0.54
311 56 0.24
312 42 0.18
313 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (311 bp):
ACTCCTTGAAATAACTATATCCATCTAATCAAATCTCAGTCACATTGCATTTAAAAATTTGTTTT
TACAAGCATCTAAATCATGTTTCAATTTAATTGAAAATTAATACAAAAAAATATGAAAAACGATA
TTAAAAGCGTCAAAAGACCTCCAATATTTTTGCACTTAAATTATAATATTTTATGAGTATTATAG
CTAAAAATTGAAGAAAAATCTTTCAAGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTAATAA
CCATCACAGTTTTTAACTAAAAACGCGTTTCGGGGCATTTTTGCCGCCGAC
Found at i:35584 original size:17 final size:17
Alignment explanation
Indices: 35558--35596 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35548 GTTCTTTCAT
35558 TAAATCAATTAA-AATTA
1 TAAATCAATTAATAA-TA
*
35575 TAAATTAATTAATAATA
1 TAAATCAATTAATAATA
35592 TAAAT
1 TAAAT
35597 ATCCAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATCAATTAATAATA
Found at i:42512 original size:329 final size:328
Alignment explanation
Indices: 41834--44738 Score: 1892
Period size: 329 Copynumber: 8.8 Consensus size: 328
41824 GCAAAAAAGT
* * * * * *
41834 ACGATTTAAGCTAAAATTTTGCGAAAACTGACCC-AAAAGTTATTTCCTCAACTTCTCA-CCAAA
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAATT-TTT-CTCAA-TTTTTAGCCACA
* * * * * * *
41897 ATGCTCA-TAGATAATATATAATTCAACGACAAAATA-ATTTGAGGGCTTTTCACTCTTCTAATA
63 ATACT-ATTAAAAAATATATAATTCAACGCCAAAA-AGA-TTGAAGGCTTTTCACGCTTATAATA
** * * * *
41960 TCGCTTTTCTTATTTTTTCTAAATTAATTT-TTAATTAATCGAAAAAAGATTCATATGCTCGTAA
125 TCGCTTTTCCCA--TTTTCTAAATTAATTTCTCAATAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
42024 AAACAAATCCTTAAATCCAATGTCG-CTAAAATTTGGTTACATAAATATAGATATTTCAAGGAGT
188 AAACAAATCCTTAAATCCAAT-TTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGT
* * ** * * * * *
42088 ATGGGCACCAAAAATCATGTAAAACTGAGCCGG-GACCCC-GAAA-CGCGTTTTAGCCATAAACC
252 CTTGGTGCCAAAAATCATGCAAAAATGAGCCGGAG-CCCCGGAAAGCG-GTTTTAGCAAAAAACT
42150 GTGATGGTTAGTATAC
315 GTGATGGTTAG--TAC
* ** * *
42166 ATGATTTCTGCTAAAATTTTGCAAAAATTGCCCCGAAAAATTTTTCTTCAATTTTTAGTCACAAT
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTC-TCAATTTTTAGCCACAAT
* * * *
42231 ACTATTAAAAAACATATAATTCAAAGACAAAAAGATTAGAAGGTTTTTCACGCTTATAATATCG-
65 ACTATTAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGCTTTTCACGCTTATAATATCGC
* * *
42295 TTTTCCCATTTTCTGAATTAATTTCTCAATAAATCGAAATAAGATTCAGATGCTCGT-AAAAGAA
129 TTTTCCCATTTTCTAAATTAATTTCTCAATAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * *
42359 ATCCTTAAATCGAATTTGACTGAGATTTGACTAGATCAATATACATATTTCAAGGAGTCTTGGTT
194 ATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGTG
* * * * * **
42424 CCAAAAAAACATGCAAAAATGAGTCGGTGTCCCAGAAAGCGGTTTTAG-ACAAAAACCATGATGG
259 CC-AAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAGCA-AAAAACTGTGATGG
*
42488 TTAGCAC
322 TTAGTAC
* * * *
42495 ACGATTTAAGTTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTT-GTCTACAA
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TTTTCTCAATTTTTAG-CCACAA
* * * * * *
42559 TAC--TCAAAAAATATATTATTCAACACCAAAACA-ATTGAAAGACTTTTCACGCTTCTAAAATC
64 TACTATTAAAAAATATATAATTCAACGCCAAAA-AGATTG-AAGGCTTTTCACGCTTATAATATC
** * * * * * *
42621 ATTTTTCCTATTGTTTTCCAAATTAATTTCTCATTAAAACGAAACATGAAGT-AGATGCTCGTAA
127 GCTTTTCCCA---TTTTCTAAATTAATTTCTCAATAAATCGAAACAAG-ATTCAGATGCTCGTAA
* * * ** * * * ** *
42685 AAACAAATCCTTAATTTCAATGTGGTTGATATTTGATTAGATGAAGATAGATATTTCAAATAGAC
188 AAACAAATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTC
* * * * * *
42750 TCGGTGCC-AAAATCATGCAAAAATGAGTCGGAGCCCCAGAACGTGTTTTTAGTC-AAAAA-T-T
253 TTGGTGCCAAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAG-CAAAAAACTGT
**
42811 G-TAATT-GTAC
317 GATGGTTAGTAC
** * * * * * * * *** *
42821 ACGATTTCGGCTAAGATTTTGCGGAAAA-TGACTCGTAAGATATTTCATCAACTTACCGCCAAAA
1 ACGATTTAAGCTAAAATTTTGC-AAAAATTGACCCGAAAAATTTTTC-TCAATTTTTAGCCACAA
* * * * * * * * *
42885 TGCTCA-TAGATAATATATAATTCAAAGGCAAATAGATTGGAGGGATTTTCACTCTTCA-AATAT
64 TACT-ATTAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGCTTTTCACGCTT-ATAATAT
* ** * * * **
42948 CGTTTTTCTTATTTTTTCTAAATTAATTTTTC-ATTAATCGACAA-AAGAAT-ATGATAATTC-T
126 CGCTTTTCCCA--TTTTCTAAATTAATTTCTCAATAAATCGA-AACAAGATTCA-GAT-GCTCGT
* * * * *
43009 AAAAACAAATCCTTAAATCTAATAT-AGCTGAGATTTGGTTAGATAAATATAAATATATCAAGGA
186 AAAAACAAATCCTTAAATCCAATTTGA-CTGAGATTTGATTAGATAAATATAGATATTTCAAGGA
* * * * * * *
43073 GT-ATGGACGCCAAAAATCATGTAAAACTGAGCCGGGGCCCCGGAACGCGATTTTAGCAAAAAAC
250 GTCTTGG-TGCCAAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAGCAAAAAAC
43137 TGTGATGGTTAGTAC
314 TGTGATGGTTAGTAC
*** * * *
43152 ACGATTTCTGCAAAAAAAAAAAAATATATACAAAAATTGGCCCGAAAAATTTTTCATCAATTTTT
1 ACGA-TT-T------AAGCTAAAAT-TTTGCAAAAATTGACCCGAAAAATTTTTC-TCAATTTTT
* * * * * * *
43217 AGCCACAATATTAATAAAAAATATATAATTCAATGCTAAAAATATTAAAAGTCTTTTCACGCTTA
56 AGCCACAATACTATTAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGCTTTTCACGCTTA
* * * * * * *
43282 TAACATCG-TTTTCCCTTTTTTTCCCAAATTATTTTCTCATTAAATCGAAACAATATTCAAATGC
120 TAATATCGCTTTTCCC--ATTTT-CTAAATTAATTTCTCAATAAATCGAAACAAGATTCAGATGC
* * * * *
43346 AT-GTAAAAAGAAATTCTTAAATCCAATTTGCCTGAGATTTGACTT-GATCAATATAGATACTTC
182 -TCGTAAAAACAAATCCTTAAATCCAATTTGACTGAGATTTGA-TTAGATAAATATAGATATTTC
* * *
43409 AAGGAGTCTTGGTGCCAAAAATCATG-AAAAACTGAGCCAGAGTCCCGGAAAACGGTTTTAGACC
245 AAGGAGTCTTGGTGCCAAAAATCATGCAAAAA-TGAGCCGGAGCCCCGGAAAGCGGTTTTAG--C
* *
43473 AAAAAAAAACTCTGATGGTTAGCAC
307 ---AAAAAACTGTGATGGTTAGTAC
* * * * *
43498 ATGATTTAAGCTAAAATTTTGCAAAAATTGATCCGAAATATATATTCTCAATTTTTATCCACAAT
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TTTTCTCAATTTTTAGCCACAAT
* * * *
43563 ACTCATT-AAAAATATATAATTCAACGCCAAAACA-ATTGAAAGACTTTTCGCGCTTCTAAAATC
65 ACT-ATTAAAAAATATATAATTCAACGCCAAAA-AGATTG-AAGGCTTTTCACGCTTATAATATC
** * * * * * * *
43626 ATTTTTCCTATTATTTTCTAAATTAATTTCTCATTAAAACGAAACATGAAGT-AAATGTTCGTAA
127 GCTTTTCC---CATTTTCTAAATTAATTTCTCAATAAATCGAAACAAG-ATTCAGATGCTCGTAA
* * * * ** * * * * *
43690 AAACAAATCTTTAATTTCAATATGGTTGATATTTGATAAGATGAATATAGATATTTCAAGTAGAC
188 AAACAAATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTC
* * * * *
43755 TCGGTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAATGCGTTTTTAGCAAAAAA-T-T-
253 TTGGTGCCAAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAGCAAAAAACTGTG
* *
43817 AT-GATGGTAC
318 ATGGTTAGTAC
** ** * * * * * *** *
43827 ACGATTTTGGCTATGATTTTGCGAAAACTGACCAGAAAGATATTTTCTCAACTTACCGCCAAAAT
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAAT-TTTTCTCAATTTTTAGCCACAAT
* * * * * * * * *
43892 GCTCA-TAGATAATATATAATTCAACGGCAAACAGATTGAAGGGTTTTTCACTCTTCTAATATTG
65 ACT-ATTAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCACGCTTATAATATCG
* * * *
43956 CTTTT--C-TTAT-T---TT--TTT-T-AATTAATCGAAAAAAGATTCAGATGCTCGTAAAAATA
128 CTTTTCCCATTTTCTAAATTAATTTCTCAATAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * *
44010 AATCCTTAAATCCAATGTGACTGAGATTTGTTTAGATAAATGA-AGATATTTCAAGGAGTATTGG
193 AATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAAT-ATAGATATTTCAAGGAGTCTTGG
* * * *
44074 CGCCAAAAATAATG-AAAAACCGAGCC-GAGGCCCCGGAAGAACGCGTTTATAGCAAAAAACTGT
257 TGCCAAAAATCATGCAAAAA-TGAGCCGGA-GCCCCGGAA-AGCG-GTTT-TAGCAAAAAACTGT
44137 GATGGTTAGTAC
317 GATGGTTAGTAC
** * ** *
44149 ACGATTTTTGCTAAAATTTTGCAGAAATTGACATGAAAAAATTTTCTTCAATTTTGT-GCCACAA
1 ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTC-TCAATTTT-TAGCCACAA
* *
44213 TACTAGTAAAAAATATATAATTCAACGCCAAAAAGATTAAAAGGCTTTTCACGCTTATAATATCG
64 TACTATTAAAAAATATATAATTCAACGCCAAAAAGATT-GAAGGCTTTTCACGCTTATAATATCG
* * * * *
44278 TTTTTCCCCTTTTTTTTCCAAATTATTTTGTC-ATCAAATCGAAACAAGATTCAGATGCTCGTAA
128 CTTTT-CCC---ATTTTCTAAATTAATTTCTCAAT-AAATCGAAACAAGATTCAGATGCTCGTAA
* * * * * * *
44342 AAACAAATTCTTATATCGAATTTGGCTGAGATTTGACTAGATCAATATAGATACTTCAAGGAGTC
188 AAACAAATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTC
* * *
44407 TTGGTGCCAAAAATCATGCAAAACTGAGCCGGAGTCTCGGAAAGCGGTTTTAG-ACAAAAACTGT
253 TTGGTGCCAAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAGCA-AAAAACTGT
*
44471 GATGGTTAGCAC
317 GATGGTTAGTAC
* * ** *
44483 ACGATTTAAGCTAAAATTTTGCAAAAAAATGACCC-AAAAGATATTTCCTCAATTTTTTTCCACG
1 ACGATTTAAGCTAAAATTTTGC-AAAAATTGACCCGAAAA-AT-TTTTCTCAATTTTTAGCCACA
* * * * *
44547 ATACTCA-T-AAAAATATATAATTCAACGTCAAAACA-ATTGAAAGGCTTTTCATGGTTCTAAAA
63 ATACT-ATTAAAAAATATATAATTCAACGCCAAAA-AGATTG-AAGGCTTTTCACGCTTATAATA
* *** * * *** * *
44609 TCGTTTTTCTTTTTGTTTTCCAAATTAATTTCTCATTAAATCGAAAGGTGAAGT-AGATACTCGT
125 TCGCTTTTC---CCATTTTCTAAATTAATTTCTCAATAAATCGAAACAAG-ATTCAGATGCTCGT
* * * * * * *
44673 AAAAACAAATCATTAATTTCAATATGACTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAG
186 AAAAACAAATCCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAG
44738 T
251 T
44739 ATGTAAAACT
Statistics
Matches: 1987, Mismatches: 450, Indels: 271
0.73 0.17 0.10
Matches are distributed among these distances:
314 7 0.00
315 99 0.05
316 4 0.00
317 6 0.00
318 10 0.01
319 3 0.00
320 1 0.00
321 8 0.00
322 104 0.05
323 5 0.00
325 9 0.00
326 111 0.06
327 118 0.06
328 65 0.03
329 233 0.12
330 103 0.05
331 91 0.05
332 152 0.08
333 106 0.05
334 104 0.05
335 35 0.02
336 13 0.01
337 193 0.10
338 150 0.08
339 29 0.01
340 92 0.05
341 103 0.05
342 6 0.00
343 1 0.00
344 1 0.00
345 2 0.00
346 23 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (328 bp):
ACGATTTAAGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTTCTCAATTTTTAGCCACAATA
CTATTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCACGCTTATAATATCGCTT
TTCCCATTTTCTAAATTAATTTCTCAATAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
CCTTAAATCCAATTTGACTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTGGTGCC
AAAAATCATGCAAAAATGAGCCGGAGCCCCGGAAAGCGGTTTTAGCAAAAAACTGTGATGGTTAG
TAC
Found at i:45204 original size:29 final size:29
Alignment explanation
Indices: 45164--45221 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
45154 CGCAGGTTAG
45164 CAACAGGCGGTATTAATGCCGGCACTGAA
1 CAACAGGCGGTATTAATGCCGGCACTGAA
45193 CAACAGGCGGTATTAATGCCGGCACTGAA
1 CAACAGGCGGTATTAATGCCGGCACTGAA
45222 TCACTATCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (29 bp):
CAACAGGCGGTATTAATGCCGGCACTGAA
Found at i:45578 original size:108 final size:106
Alignment explanation
Indices: 45372--45643 Score: 424
Period size: 108 Copynumber: 2.6 Consensus size: 106
45362 TACAAATTTT
*
45372 AATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTA-TAAC
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATTAAC
**
45434 AATATTATTAATTATGGAATTTACCCTTAAAATAAAAATAA
66 AATATTATTAATTATAAAATTTACCCTTAAAATAAAAATAA
*
45475 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATTAAC
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATTAAC
* *
45540 AATAAATTATTAATTTTAAAATTTACCCTTAAAATAAAAATAC
66 AAT--ATTATTAATTATAAAATTTACCCTTAAAATAAAAATAA
* * *
45583 AATTTTAATTTGGGACTAAATTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACTCTAT
1 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTAT
45644 GACAAAAAGT
Statistics
Matches: 154, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 11 0.07
104 15 0.10
105 30 0.19
106 7 0.05
108 91 0.59
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (106 bp):
AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATTAAC
AATATTATTAATTATAAAATTTACCCTTAAAATAAAAATAA
Done.