Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009206.1 Corchorus capsularis cultivar CVL-1 contig09227, 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: 78568
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:7551 original size:6 final size:6
Alignment explanation
Indices: 7513--7541 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
7503 TAACTGTATT
7513 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
7542 TTTAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:7616 original size:3 final size:3
Alignment explanation
Indices: 7608--7645 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
7598 TAATAACTAA
7608 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
7646 ATAAAGTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11617 original size:2 final size:2
Alignment explanation
Indices: 11610--11638 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11600 AATTACAATG
11610 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 T
11639 CTCTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13168 original size:6 final size:6
Alignment explanation
Indices: 13157--13185 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
13147 CAAAGCACTC
13157 TTTGTT TTTGTT TTTGTT TTTGTT TTTGT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGT
13186 CAACTAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTGTT
Found at i:18138 original size:93 final size:93
Alignment explanation
Indices: 17997--18167 Score: 342
Period size: 93 Copynumber: 1.8 Consensus size: 93
17987 ATCTGGTATA
17997 TAGAAGAACCTTGGTATATTTCATTGGGCATTCCAAGCTTACATTGAATCTCAACAAAGATTACA
1 TAGAAGAACCTTGGTATATTTCATTGGGCATTCCAAGCTTACATTGAATCTCAACAAAGATTACA
18062 TCATCTTGAGTTCAAAGCCAAATACAGG
66 TCATCTTGAGTTCAAAGCCAAATACAGG
18090 TAGAAGAACCTTGGTATATTTCATTGGGCATTCCAAGCTTACATTGAATCTCAACAAAGATTACA
1 TAGAAGAACCTTGGTATATTTCATTGGGCATTCCAAGCTTACATTGAATCTCAACAAAGATTACA
18155 TCATCTTGAGTTC
66 TCATCTTGAGTTC
18168 TTGACAAGTA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (93 bp):
TAGAAGAACCTTGGTATATTTCATTGGGCATTCCAAGCTTACATTGAATCTCAACAAAGATTACA
TCATCTTGAGTTCAAAGCCAAATACAGG
Found at i:34939 original size:4 final size:3
Alignment explanation
Indices: 34886--34930 Score: 54
Period size: 3 Copynumber: 13.7 Consensus size: 3
34876 AGAAAAAGTG
34886 TTC TTCC TTC TTTC TTTC TTTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TT-C TTC -TTC -TTC -TTC TTC TTC TTC TTC TTC TTC TTC TT
34931 TCTTTCTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 26 0.65
4 14 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:56143 original size:24 final size:24
Alignment explanation
Indices: 56100--56147 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
56090 CCTTTTAGGG
*
56100 CTTAGGCTCAATTCAGTGTCCTAA
1 CTTAGGCCCAATTCAGTGTCCTAA
56124 CTTAGGGCCCAATTCA-TGTCCTAA
1 CTTA-GGCCCAATTCAGTGTCCTAA
56148 TCAAATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (24 bp):
CTTAGGCCCAATTCAGTGTCCTAA
Found at i:59997 original size:14 final size:14
Alignment explanation
Indices: 59978--60008 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59968 CACATTCCTC
59978 TGTCTTCAATTAGA
1 TGTCTTCAATTAGA
59992 TGTCTTCAATTAGA
1 TGTCTTCAATTAGA
60006 TGT
1 TGT
60009 GACTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (14 bp):
TGTCTTCAATTAGA
Found at i:65012 original size:13 final size:14
Alignment explanation
Indices: 64989--65018 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
64979 GGTTGAAATT
64989 GAAAGAGAAAAAAA
1 GAAAGAGAAAAAAA
65003 GAAA-AGAAAAAAA
1 GAAAGAGAAAAAAA
65016 GAA
1 GAA
65019 GGGGGAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
GAAAGAGAAAAAAA
Found at i:68479 original size:29 final size:31
Alignment explanation
Indices: 68416--68480 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
68406 GCATCCGACG
* * *
68416 TGGCATGCCACGTGTACCAAAAAATGCCACG
1 TGGCATGCCACGTGTACCAAAAAAGGACACA
68447 TGGCATGCCACGTGTA-C-AAAAAGGACACA
1 TGGCATGCCACGTGTACCAAAAAAGGACACA
68476 TGGCA
1 TGGCA
68481 CGTCACATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 14 0.45
30 1 0.03
31 16 0.52
ACGTcount: A:0.34, C:0.26, G:0.25, T:0.15
Consensus pattern (31 bp):
TGGCATGCCACGTGTACCAAAAAAGGACACA
Found at i:69335 original size:28 final size:28
Alignment explanation
Indices: 69295--69364 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
69285 GGCTAGGCTA
*
69295 TTTTTTTTAAAAAATA-ATAATTAGTTAT
1 TTTTTTTTTAAAAATAGATAATTA-TTAT
*
69323 TTTTTTTTTAAAAATAGCTAATTATTAT
1 TTTTTTTTTAAAAATAGATAATTATTAT
*
69351 TATTTTTTTAAAAA
1 TTTTTTTTTAAAAA
69365 ATAGCCTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 32 0.84
29 6 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTTTTTTTAAAAATAGATAATTATTAT
Found at i:69369 original size:29 final size:29
Alignment explanation
Indices: 69295--69369 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 29
69285 GGCTAGGCTA
*
69295 TTTTTTTTAAAAAATA-ATAATTAGTTAT
1 TTTTTTTTAAAAAATAGCTAATTAGTTAT
*
69323 TTTTTTTTTAAAAATAGCTAATTA-TTAT
1 TTTTTTTTAAAAAATAGCTAATTAGTTAT
69351 TATTTTTTTAAAAAATAGC
1 T-TTTTTTTAAAAAATAGC
69370 CTAACCGTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (29 bp):
TTTTTTTTAAAAAATAGCTAATTAGTTAT
Found at i:69461 original size:37 final size:33
Alignment explanation
Indices: 69372--69469 Score: 133
Period size: 33 Copynumber: 2.8 Consensus size: 33
69362 AAAATAGCCT
* *
69372 AACCGTCTTATTGGGGAGGCTCCGCCGTGGCTG
1 AACCGTCCTAGTGGGGAGGCTCCGCCGTGGCTG
*
69405 AACCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG
1 AACCGTCCTAGTGGGGAGGCTCCGCCGTGGCTG
69438 ACTGAGCCGTCCTAGTGGGGAGGCTCCGCCGT
1 A---A-CCGTCCTAGTGGGGAGGCTCCGCCGT
69470 AGTTAAGGAC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 31 0.54
36 1 0.02
37 25 0.44
ACGTcount: A:0.12, C:0.31, G:0.38, T:0.19
Consensus pattern (33 bp):
AACCGTCCTAGTGGGGAGGCTCCGCCGTGGCTG
Found at i:72470 original size:331 final size:331
Alignment explanation
Indices: 71884--74270 Score: 2765
Period size: 331 Copynumber: 7.2 Consensus size: 331
71874 ACACGTTTTA
* * * * *
71884 GGTCCCGA-CTCAGTTTTGCATGATTTTTAGCGTCAAAACTCATTGAAAAATCTATATTCATTTA
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATCTATATTCATCTA
* * *
71948 ACCAAATCTCAACCACATTGGATTTAAGGAATTTGTTTTACGAGCATCTGAATAATGTTTCGATT
66 ACCAAATATCAGCCACATTGGATTTAAGG-ATTTGTTTTACGAGCATCTGAATCATGTTTCGATT
* * * * *
72013 TAATTATAAATTAATTCGAAAAAAATAGCAAATATGATATTAGAAGCGTGATAAGCCCTTCAATC
130 TAATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTC
* * **
72078 TTTTTGACATTGAATTATATTTTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAATTTTTTTTG
195 TTTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTTG
* *
72143 GGTCAGTTTGTGAAAAATTTTAGGCGAAATCGTGTACTAACCATCACAGTTTTTGACTAAAAACG
260 GGTCAGTTTTTGAAAAATTTTAGGCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACG
* *
72208 TGTTCCA
325 CGTTCCG
* * * * **
72215 GGTTCCCTGCTCAGTTTTACATGATTTTTGGCGCCAAGACTCACTG-AATTTCCTATATTCATCT
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAAT-CTATATTCATCT
* *
72279 AACCAAATATCAGCCACATTGGATTTACGGATTTGTTTTACGAGCATCTGAATTATGTTTCGATT
65 AACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCATGTTTCGATT
* * **
72344 TAATCAGCAATTAATTCGGGAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTC
130 TAATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTC
* **
72409 TTTTGGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAATTTTTTTTG
195 TTTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTTG
* *
72474 GGTCAGTTTTTGAAAAATTTCAGGAGAAA-----T-C-AACCATCACAGTTTTTGGCTAAAAACG
260 GGTCAGTTTTTGAAAAATTTTAGGCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACG
*
72532 CGTCCCG
325 CGTTCCG
* * * * * * * *
72539 AGTCCCCAGCTCAATTTTGCATGAATTTTATCGCCAGGACTCACTGAAATATCTATAATCATCCA
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATCTATATTCATCTA
* * * * *
72604 ACTAAATATCAGCCACATTGAATATACGGATTTTTTTGTACGAGCATCTGAATCATGTTTCGATT
66 ACCAAATATCAGCCACATTGGATTTAAGGATTTGTTT-TACGAGCATCTGAATCATGTTTCGATT
* * * * *
72669 TAATTAGAAATTAATACGGAAAAAATAGGAAATACGATATTAGAAACGTGAAAGGCCCTTCAATC
130 TAATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTC
* *
72734 TTTTTTGCATTGAATTATATATTTTTTACGAGTAATTTGGCCAAAAATTAAGGAAAAATTTTTTG
195 TTTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTTG
* *
72799 GGTAAGTTTTTGAAAAATTTTA-GCTGAAATCGTGTACTAACCATCACAGTTGTTGGCTAAAAAC
260 GGTCAGTTTTTGAAAAATTTTAGGC-GAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAC
*
72863 GTGTTCCG
324 GCGTTCCG
* * * * * * * * *
72871 GCTCTCCGGCTCAGTTTTGAATGATTTTTGGCGCCAAGACTCATTGAAATA-CAAATATTCATTT
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATC-TATATTCATCT
* * * *
72935 AACCAAATCTCAGCCACATTTGATTTAAGAATTTGTTTTTACGAGTATCTGAATCATGTTTCGAT
65 AACCAAATATCAGCCACATTGGATTTAAGGATTTG-TTTTACGAGCATCTGAATCATGTTTCGAT
* * * * *
73000 TTAATCAGAAATTAATTC-AAAAAAATAGGAAATACGATATTAGAAGTGTAAAAAGTCTTTCATT
129 TTAATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATT
* * * * *
73064 CTTTTTGGCATTAAATTATATATTTTTTATGAGTATTGTGGCAAAAAAAAATTAAGGAAAAATAT
194 CTTTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGC---CAAAAATTAAGGAAAAATTT
* * * ** **
73129 TTCGGGTTAGTTTTTGCAAAATTTTAGTTGAAATCGTGTACTAACAACCATCACA-TTTTTCACT
256 TTTGGGTCAGTTTTTGAAAAATTTTAGGCGAAATCGTGTACT---AACCATCACAGTTTTTGGCT
73193 AAAAACGCG-TCCTG
318 AAAAACGCGTTCC-G
* * * * *
73207 GGTCCCCAGCTCAGTTTTGCATGATTTTTATCGCCAAGACTCACTGATATATCTATAATCCTCTA
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATCTATATTCATCTA
* *
73272 ACCAAATATCAGTCACATTGGATTTACGGATTT-TTTTACGAGCATCTGAATCATGTTTCGATTT
66 ACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCATGTTTCGATTT
* * * *
73336 ATTTAGAAATTAATT--AAAAAAATCGCAAATATGATATTAGAAGCGTGAAAAGCCCTTCATTCT
131 AATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCT
* * * **
73399 TTTTGACATTGAATTATATATTTATTACGAGTAATATGGCCAAAAATTAAGGAAAAATTTTTCAG
196 TTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTTGG
* ** *
73464 GTCAGTTTTT-ACAAAATTTTAGGCGAAATCGTGTACTAACCACCACAGTTCATGGCTAAAACCG
261 GTCAGTTTTTGA-AAAATTTTAGGCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACG
73528 CGTTCCG
325 CGTTCCG
* * * * *
73535 GGTCCCCGGCTAAGTTTTGCATGATTTTTGGCACCAAGACTCACTGAAAATACCTATATTCATCT
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAA-ATCTATATTCATCT
* * * *
73600 AACCAAATCTCAGCCACATTTGATTTAAGGATTTGTTTTTACGAGTATCTGAATTATGTTTCGAT
65 AACCAAATATCAGCCACATTGGATTTAAGGATTTG-TTTTACGAGCATCTGAATCATGTTTCGAT
* * * *
73665 TTAATCAGAAATTAGTTC-AGAAAAAATATGAAATACGATATT-GAAATCGTGAAAAGCCCTTCA
129 TTAATTAGAAATTAATTCGA-AAAAAATAGGAAATACGATATTAG-AAGCGTGAAAAGCCCTTCA
* * *
73728 TTCTATTTT-GCATTGAATTATATATTTTTTATGAGTACTGTGGCCAAAAATTAAGGAAAAAATT
192 TTCT-TTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTT
* * * * * *
73792 TTAGGGTCAGTTTTTGCAAAATTTTA-GCAGAAATCGTGCATTAACCATCATAGTTTTAT-ACTA
256 TTTGGGTCAGTTTTTGAAAAATTTTAGGC-GAAATCGTGTACTAACCATCACAGTTTT-TGGCTA
* * *
73855 GAAAGGCGTCCCG
319 AAAACGCGTTCCG
* * * ** * * *
73868 AGTCCCCAGCTCAGCTTTACATGATTTTTATTGCCAAGACTCACTGAAATATCTATAATCCTCTA
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATCTATATTCATCTA
* * * * *
73933 ACCAAATATTAGCCATATTGGATTTATGGATTTTCTTTTACGAGCATATGAATCATGTTTCGATT
66 ACCAAATATCAGCCACATTGGATTTAAGGA-TTTGTTTTACGAGCATCTGAATCATGTTTCGATT
* * * * *
73998 TATTTAGAAATTAATTAGAAAAAAATCA-CAAATACGAAATTAGAAGGGTG-AAAGCCCTTCATT
130 TAATTAGAAATTAATTCGAAAAAAAT-AGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATT
* * * * * * * *
74061 ATTTTTGGTATTTAATTATATATTTTTTATGAGTAGTGTGGCCAACAATTAAAGAAAAATTGTTT
194 CTTTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTT
* * *
74126 GGGTCAGTTTTTGAAAATTTTTAGGGGAAATCGTGTACTAAACATCACAGTTTAAGTTTTTGGCT
259 GGGTCAGTTTTTGAAAAATTTTAGGCGAAATCGTGTACTAACCATCAC------AGTTTTTGGCT
**
74191 AAAAACATGTTCCG
318 AAAAACGCGTTCCG
* * * * *
74205 GGTCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCGAGACTAACTGAAATA-CGTATATTCATCT
1 GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATC-TATATTCATCT
74269 AA
65 AA
74271 ATCCATTGTG
Statistics
Matches: 1734, Mismatches: 272, Indels: 94
0.83 0.13 0.04
Matches are distributed among these distances:
324 112 0.06
325 173 0.10
326 1 0.00
327 9 0.01
328 57 0.03
329 44 0.03
330 59 0.03
331 407 0.23
332 321 0.19
333 269 0.16
334 102 0.06
335 3 0.00
336 96 0.06
337 81 0.05
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (331 bp):
GGTCCCCAGCTCAGTTTTGCATGATTTTTAGCGCCAAGACTCACTGAAAAATCTATATTCATCTA
ACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCATGTTTCGATTT
AATTAGAAATTAATTCGAAAAAAATAGGAAATACGATATTAGAAGCGTGAAAAGCCCTTCATTCT
TTTTGGCATTGAATTATATATTTTTTACGAGTAATGTGGCCAAAAATTAAGGAAAAATTTTTTGG
GTCAGTTTTTGAAAAATTTTAGGCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGC
GTTCCG
Found at i:76864 original size:344 final size:342
Alignment explanation
Indices: 76186--76821 Score: 832
Period size: 344 Copynumber: 1.9 Consensus size: 342
76176 TTTCTGCCAA
* *
76186 AAATCATGTAAAACTGAGCCGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
1 AAATCATGGAAAACAGAGCCGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
* * * ** *
76251 CACGATTTCAGCTAAAGACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAA
66 CACGATTTCAGCTAAAAACTAACCCGAAGAGTTTTTCTCAATTTTCCCAGAAAATATTAAGAAAA
* * * * * * *
76316 AAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTTTCAT
131 AAATATAAAATTCAACACCAAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTTCCAT
** * *
76381 TTTTTTCGAATTTATTTAAAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
196 TCATTTCGAATTAATTTAAAATTAAATAGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTA
* *** * * * * * *
76446 AATCCATTATTACTGAGATTTGGTTAGATGAAATATAGATATTTCAAAGAGTCTTTCTTCCAAAA
261 AATCCATTATGACT-AGATTTAAATACATGAAACATAGATATTTCAAAAAATCTATCGT-CAAAA
76511 AGCCGGAGCCGGAACCCCG
324 AGCCGGAGCCGGAACCCCG
* *
76530 AAATCATGGACAACAGAGCCGGAGACCC-GAAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
1 AAATCATGGAAAACAGAGCCGGAG-CCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
76594 ACACGATTTCAGCTAAAAACTAACCCGAAGAGTTTTTCTCAATTTTCCCAGAAAAT-TTAAG-AA
65 ACACGATTTCAGCTAAAAACTAACCCGAAGAGTTTTTCTCAATTTTCCCAGAAAATATTAAGAAA
* * *
76657 AAAATATAAAATTCGACATCAAAATAAATT-AAGGGATTTTCACGCTTCTAATATTGTTTTTTCC
130 AAAATATAAAATTCAACACCAAAA-AAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTTCC
** *
76721 ATTCATTTCAGAATTAATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATCC
194 ATTCATTTC-GAATTAATTTAAAATTAAATAGAAACAAGATCCAGATGCTCGTAAAAACAAATCC
* * *
76786 TTAAATCCATTGTGACT-GATTTAAATCCATTAAACA
258 TTAAATCCATTATGACTAGATTTAAATACATGAAACA
76822 AGGAGCCTTT
Statistics
Matches: 253, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
341 12 0.05
342 58 0.23
343 73 0.29
344 107 0.42
345 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (342 bp):
AAATCATGGAAAACAGAGCCGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
CACGATTTCAGCTAAAAACTAACCCGAAGAGTTTTTCTCAATTTTCCCAGAAAATATTAAGAAAA
AAATATAAAATTCAACACCAAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTTCCAT
TCATTTCGAATTAATTTAAAATTAAATAGAAACAAGATCCAGATGCTCGTAAAAACAAATCCTTA
AATCCATTATGACTAGATTTAAATACATGAAACATAGATATTTCAAAAAATCTATCGTCAAAAAG
CCGGAGCCGGAACCCCG
Found at i:77127 original size:653 final size:628
Alignment explanation
Indices: 75795--77726 Score: 2609
Period size: 633 Copynumber: 3.0 Consensus size: 628
75785 AAAAATCATG
* * ** * *
75795 CAAATCCGTAAATCCATTGTGACTGGGATTT-GATTTGATGAATATCGATATTTCAAG-GAGTCT
1 CAAATCCTTAAATCCATTATGACTCAGATTTAG-TTAGATGAATATAGATATTTCAAGAG-GT-T
* ** *
75858 -TTCTGCCAAAAATCATGTA-AAATTGAGCCGGAGCCCCAAAACGCGTTTTTAGCCAAAAACCGT
63 ATTTTGCCAAAAATCATG-ACAAACAGAGCCGGAG-CCCGAAACGCGTTTTTAGCCAAAAACCGT
* * * **
75921 TATCGTTAGTACACAATTTCAGCT-AAAACTGACCCAAAGAG-TTTTCT-AATTTTTTCTGGAAA
126 GATGGTTAGTACACGATTTCAGCTAAAAACTGACCCAAAGAGTTTTTCTCAA--TTTTCCAGAAA
* * * *
75983 ATATTCAGAAAAAAATTTATAATTCAACGCCAAAA-ATATTGATGGGTTTTTCACGCTTCTAATA
189 ATATTCAG-AAAAAATATATAATTCAACGCCAAAATAAATTGAAGGGATTTTCACGCTTCTAATA
* ** * * * *
76047 TCGTTTTTTCATTTTTTTCGAATTTATTTAAAATTAAATCAAAACAAAATTCAGATTCTCGTAAA
253 TTGTTTTTTCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAA
* ** *
76112 AACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTTGATGAATATCGA-TATTTCAAGGAGTC
318 AACAAATCCTTAAATCCATTGTGACT--GA------TT--T-AA-ATCCATTA-AACAAGGAGCC
* * * * *
76176 TTTCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTG
370 TTTCTGCAAAAAATCATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTT
* * *
76241 ATGGTTAGTACACGATTTCAGCTAAAGACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAAT
435 ATGGTTAGTACACAATTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAAT
76306 ATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCG
500 ATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCG
* *
76371 TTTTTTTCATTTTTTTCGAATTTATTTAAAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAA
565 -TTTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
76436 CAAATCCTTAAATCCATTATTACTGAGATTTGGTTAGATGAAATATAGATATTTCAA-AGAGTCT
1 CAAATCCTTAAATCCATTATGACTCAGATTTAGTTAGATG-AATATAGATATTTCAAGAG-GT-T
*
76500 -TTCTTCCAAAAAGCCGGAGCCGGAACCCCGAAATCATGGAC-AACAGAGCCGGAGACCCGAAAT
63 ATT-TT-------------GCC--AA-----AAATCAT-GACAAACAGAGCCGGAG-CCCGAAAC
* *
76563 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTAACCCGAAGAGTT
105 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCAAAGAGTT
* * * **
76628 TTTCTCAATTTTCCCAGAAAAT-TTAAGAAAAAATATAAAATTCGACATCAAAATAAATT-AAGG
170 TTTCTCAATTTT-CCAGAAAATATTCAGAAAAAATATATAATTCAACGCCAAAATAAATTGAAGG
** *
76691 GATTTTCACGCTTCTAATATTGTTTTTTCCATTCATTTCAGAATTAATTTCTAATTAAATCGAAA
234 GATTTTCACGCTTCTAATATTGTTTTTT-CATTTTTTTC-GAATTTATTTCTAATTAAATCGAAA
76756 CAAGATCCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGACTGATTTAAATCCATTAAAC
297 CAAGATCCAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGACTGATTTAAATCCATTAAAC
76821 AAGGAGCCTTTCTGCAAAAAATCATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAA
362 AAGGAGCCTTTCTGCAAAAAATCATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAA
76886 AAACCGTTATGGTTAGTACACAATTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTC
427 AAACCGTTATGGTTAGTACACAATTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTC
76951 TGGAAAATATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTC
492 TGGAAAATATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTC
77016 TAATATCGTTTTTTCATTTGTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCT
557 TAATATCGTTTTTTCATTT-TTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCT
77081 CGTAAAAA
621 CGTAAAAA
*
77089 CAAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATATAGATATTTCAAGAGGTTATT
1 CAAATCCTTAAATCCATTATGACTCAGATTTAGTTAGATGAATATAGATATTTCAAGAGGTTATT
* * * *
77154 TTGCCAAAAATCATGCCAAACAGAGCCAGAGCCTCGAAACGCGTTTTTATCCAAAAAACTGTGAT
66 TTGCCAAAAATCATGACAAACAGAGCCGGAGCC-CGAAACGCGTTTTTAGCC-AAAAACCGTGAT
* * *
77219 GGTTAGTATATGATTTCAGCTAAAAACTGACCCAAAGAGTTTTTCTCAATTTTTCAGGAAAATAT
129 GGTTAGTACACGATTTCAGCTAAAAACTGACCCAAAGAGTTTTTCTCAATTTTCCA-GAAAATAT
* * *
77284 TCAGAAAAAATATATAATTCAACGCCAAAAT-GATTGAAGGGCTTTTCACGTTTCTAATATTG-T
193 TCAGAAAAAATATATAATTCAACGCCAAAATAAATTGAAGGGATTTTCACGCTTCTAATATTGTT
77347 TTTTCAGTTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAA
258 TTTTCA---TTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAA
77412 CAAATCCTTAAATCCATTGTGACTGATTTAAATCCATTAAACAAGGAGCCTTTCTGCAAAAAATC
320 CAAATCCTTAAATCCATTGTGACTGATTTAAATCCATTAAACAAGGAGCCTTTCTGCAAAAAATC
*
77477 ATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTTATGGTTAGTACAGAA
385 ATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTTATGGTTAGTACACAA
77542 TTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAAATT
450 TTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAAATT
77607 TATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTT
515 TATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTTCA-TTTTTT
* *
77672 TCGAGTTTATTTCAAATTAAATCGAAACAAGATTCAGAAGCTCGTAAAAA
579 TCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
77722 CAAAT
1 CAAAT
77727 TGTGATGGTT
Statistics
Matches: 1164, Mismatches: 80, Indels: 102
0.86 0.06 0.08
Matches are distributed among these distances:
630 4 0.00
631 39 0.03
632 74 0.06
633 406 0.35
634 9 0.01
636 2 0.00
638 3 0.00
641 33 0.03
642 24 0.02
643 1 0.00
651 3 0.00
652 31 0.03
653 288 0.25
654 4 0.00
655 1 0.00
656 3 0.00
657 2 0.00
658 2 0.00
663 119 0.10
664 36 0.03
665 78 0.07
666 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (628 bp):
CAAATCCTTAAATCCATTATGACTCAGATTTAGTTAGATGAATATAGATATTTCAAGAGGTTATT
TTGCCAAAAATCATGACAAACAGAGCCGGAGCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
TTAGTACACGATTTCAGCTAAAAACTGACCCAAAGAGTTTTTCTCAATTTTCCAGAAAATATTCA
GAAAAAATATATAATTCAACGCCAAAATAAATTGAAGGGATTTTCACGCTTCTAATATTGTTTTT
TCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAACAAATC
CTTAAATCCATTGTGACTGATTTAAATCCATTAAACAAGGAGCCTTTCTGCAAAAAATCATGTAA
AACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTTATGGTTAGTACACAATTTCAG
CTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATATTCAGAAAAAAATTTATAAT
TCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCGAATT
TATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
Found at i:77343 original size:322 final size:322
Alignment explanation
Indices: 75795--77726 Score: 1864
Period size: 310 Copynumber: 6.0 Consensus size: 322
75785 AAAAATCATG
* * * *
75795 CAAATCCGTAAATCCATTGTGACTGGGATTT-GATTTGATGAATATCGATATTTCAAG-GAGTCT
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAG-TTAGATGAATATAGATATTTCAAGAGAGTCT
* * *
75858 TTCTGCCAAAAATCATGTAAAATTGAGCCGGAGCCCCAAAACGCGTTTTTAGCCAAAAACCGTTA
65 TTCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
* * *
75923 TCGTTAGTACACAATTTCAGCT-AAAACTGACCCAAAGAG-TTTTCT-AATTTTTTCTGGAAAAT
130 TGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAA-TTTTTCTGGAAAAT
*
75985 ATTCAGAAAAAAATTTATAATTCAACGCCAAAAATATTGATGGGTTTTTCACGCTTCTAATATCG
194 ATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCG
* * * *
76050 TTTTTTCATTTTTTTCGAATTTATTTAAAATTAAATCAAAACAAAATTCAGATTCTCGTAAAAA
259 TTTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
76114 CAAATCCTTAAATCCATTGTGACTGAGATTTGGTTTGATGAATATCGATATTTCAAG-GAGTCTT
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATGAATATAGATATTTCAAGAGAGTCTT
*
76178 TCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGAT
66 TCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
*
76243 GGTTAGTACACGATTTCAGCTAAAGACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATAT
131 GGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATAT
76308 TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTT
196 TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCG-T
* *
76373 TTTTTCATTTTTTTCGAATTTATTTAAAATTAAATAGAAACAAGATTCAGATGCTCGTAAAAA
260 TTTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
76436 CAAATCCTTAAATCCATTATTACTGAGATTTGGTTAGATGAAATATAGATATTTCAA-AGAGTCT
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATG-AATATAGATATTTCAAGAGAGTCT
* * * * ** * * *
76500 TTCTTCC-AAAA--A-G----CCGGAGCCGGAACCCCGAAA-----TCATGGACAACAGAGCCG-
65 TTCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAA-A-AACCGT
**** * * * * ** * * * * * ** *
76551 GA-GACCCG-AAATGCGTTTTTAGCCAAAAAC---CGTGATG-GTTAGTACACGATTTCAGCT-A
128 GATGGTTAGTACA--CGATTTCAGCTAAAAACTGACCCGAAGAGTT-TTTCTCAATTT-TTCTGG
** * * *** * ** * **** *
76609 AAAACTAACCCGAAGAGTTTTTCTCAATT-TTC-CCAGAAAA-TTTAAGAAAAAATATAAAATTC
189 AAAA-TATTCAGAAAAAAATTTAT-AATTCAACGCCA-AAAAGATT--G-ATGGGT-T---TTTC
* *** ** *
76671 GACATCAAAATAAATTAAGGGATTTTCACGCTTCTAATATTGTTTTTTCCATTCATTTCAGAATT
244 -AC-GC-TTCT-AA-T-ATCG-TTTT-----TTC----A-T-TTTTTTCGA---ATTT----ATT
* *
76736 AATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAAAA
284 ----TCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
** *
76779 CAAATCCTTAAATCCATTGTGACT--GATTTA---A-ATCCAT-TA-A-A---CAAG-GAGCCTT
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATGAATATAGATATTTCAAGAGAGTCTT
* * * *
76831 TCTGCAAAAAATCATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTTAT
66 TCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
* *
76896 GGTTAGTACACAATTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATAT
131 GGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATAT
76961 TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTT
196 TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTT
77026 TTTTCATTTGTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
261 TTTTCATTT-TTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
*
77089 CAAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATATAGATATTTCAAGAG-GT-TA
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATGAATATAGATATTTCAAGAGAGTCT-
* ** * * * * *
77152 TTTTGCCAAAAATCATGCCAAACAGAGCCAGAGCCTCGAAACGCGTTTTTATCCAAAAAACTGTG
65 TTCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCC-AAAAACCGTG
* * * *
77217 ATGGTTAGTATATGATTTCAGCTAAAAACTGACCCAAAGAGTTTTTCTCAATTTTTCAGGAAAAT
129 ATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAAT
* * * * * *
77282 ATTCAG-AAAAAATATATAATTCAACGCCAAAATGATTGAAGGGCTTTTCACGTTTCTAATATTG
194 ATTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCG
* *
77346 -TTTTTCAGTTTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATCCAGATGCTCGTAAA
259 TTTTTTCA---TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
77410 AA
321 AA
** *
77412 CAAATCCTTAAATCCATTGTGACT--GATTTA---A-ATCCAT-TA-A-A---CAAG-GAGCCTT
1 CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATGAATATAGATATTTCAAGAGAGTCTT
* * * *
77464 TCTGCAAAAAATCATGTAAAACTGTGTCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTTAT
66 TCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
*
77529 GGTTAGTACA-GAATTTCAGCTAAAAACTGGCCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATA
131 GGTTAGTACACG-ATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATA
77593 TTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGT
195 TTCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGT
* *
77658 TTTTTCATTTTTTTTCGAGTTTATTTCAAATTAAATCGAAACAAGATTCAGAAGCTCGTAAAAA
260 TTTTTCA-TTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
77722 CAAAT
1 CAAAT
77727 TGTGATGGTT
Statistics
Matches: 1316, Mismatches: 197, Indels: 209
0.76 0.11 0.12
Matches are distributed among these distances:
307 3 0.00
308 20 0.02
309 21 0.02
310 206 0.16
311 119 0.09
312 19 0.01
314 4 0.00
315 21 0.02
316 8 0.01
317 7 0.01
318 7 0.01
319 144 0.11
320 20 0.02
321 111 0.08
322 205 0.16
323 176 0.13
324 3 0.00
326 6 0.00
330 14 0.01
331 9 0.01
332 10 0.01
333 3 0.00
334 4 0.00
335 7 0.01
336 3 0.00
337 4 0.00
338 19 0.01
339 3 0.00
341 10 0.01
342 17 0.01
343 70 0.05
344 20 0.02
345 20 0.02
346 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
CAAATCCTTAAATCCATTGTGACTGAGATTTAGTTAGATGAATATAGATATTTCAAGAGAGTCTT
TCTGCCAAAAATCATGTAAAACTGAGCCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT
GGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCTGGAAAATAT
TCAGAAAAAAATTTATAATTCAACGCCAAAAAGATTGATGGGTTTTTCACGCTTCTAATATCGTT
TTTTCATTTTTTTCGAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
Found at i:77878 original size:11 final size:11
Alignment explanation
Indices: 77862--77896 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
77852 CTAATATCGT
*
77862 TTTTTTTTAAA
1 TTTTTTTCAAA
77873 TTTTTTTCAAA
1 TTTTTTTCAAA
*
77884 TTTATTTCAAA
1 TTTTTTTCAAA
77895 TT
1 TT
77897 AAATCGAAAC
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:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:78340 original size:323 final size:321
Alignment explanation
Indices: 77798--78509 Score: 993
Period size: 323 Copynumber: 2.2 Consensus size: 321
77788 TATGCAGAAC
* **
77798 ATTCAG-AAAAATATATAAATCAACATCAAAAAGATTGACGGGCTTTTCAC-TCTTCTAATATCG
1 ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-GGGCTTTTCACGT-TTCTAATATCG
* *
77861 TTTTTTTTTAAATTTTTTTCAAATTTATTTCAAATTAAATCGAAACAAGATTTAGATGCTCGTAA
64 TTTTTATTT--ATTTTTTTCAAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * ** *
77926 AAACAAATCCTTAAATCCATTGTGACTGAGATTTGGTTTGATGAATACCGATATTTCAAGGAGTT
127 AAACAAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATACAAATATTTCAAGGAGTC
* * *
77991 ATTTTGCCAAAAATCATGCAAAACAGAGCCGGAGCCCCGAAACGCGTTTCTAGCCAAAAATTGTG
192 ATTTTGCCAAAAATCAAGCAAAACAGAGCCAGAGCCCCGAAACGCGTTTCTAGCCAAAAACTGTG
* * *
78056 ATGGTTAGTACACGATTTCATCTAAAAACTGACCCGAAGAGTTTTTCTCAATTTTTCAGGAAAAA
257 ATGATTAGTACACGATTTCAACTAAAAACTGACCCGAAGAGTTTTTCCCAATTTTTCAGG-AAAA
78121 A
321 A
*
78122 ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCACGTTTCTAATATTGT
1 ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATT-GAGGGCTTTTCACGTTTCTAATATCGT
* *
78187 TTTTCATTT-TTTTTTTCGAATTTATTTCAAATTTAATCGAAACAAGATTCAGATGCTCGTAAAA
65 TTTT-ATTTATTTTTTTCAAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
*
78251 ACAAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATATAAATATTTCAA-GAGGTCA
129 ACAAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATACAAATATTTCAAGGA-GTCA
* * * * *
78315 TTTTGTCAGAAATCAAGCCAAACAGAGCCAGAGCCCCGAAACGCGTTTTTATCCAAAAACTGTGA
193 TTTTGCCAAAAATCAAGCAAAACAGAGCCAGAGCCCCGAAACGCGTTTCTAGCCAAAAACTGTGA
* * * * *
78380 TGATTAGTATATGATTTCAACTAAAAACTTACCCGAAGAGTTTTTCCCAATTTTTCCGGAAAAT
258 TGATTAGTACACGATTTCAACTAAAAACTGACCCGAAGAGTTTTTCCCAATTTTTCAGGAAAAA
* * * *
78444 ATTCAGAAAAAATATATAATTTAATGCCATAAAA-ATTGAGGGATTTTCACGCTTCTAATATCGT
1 ATTCAGAAAAAATATATAATTCAACGCCA-AAAAGATTGAGGGCTTTTCACGTTTCTAATATCGT
78508 TT
65 TT
78510 GATAAATATA
Statistics
Matches: 346, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
321 26 0.08
322 36 0.10
323 219 0.63
324 6 0.02
325 53 0.15
326 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (321 bp):
ATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAGGGCTTTTCACGTTTCTAATATCGTT
TTTATTTATTTTTTTCAAATTTATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
AAATCCTTAAATCCATTGTGACTCAGATTTAGTTAGATGAATACAAATATTTCAAGGAGTCATTT
TGCCAAAAATCAAGCAAAACAGAGCCAGAGCCCCGAAACGCGTTTCTAGCCAAAAACTGTGATGA
TTAGTACACGATTTCAACTAAAAACTGACCCGAAGAGTTTTTCCCAATTTTTCAGGAAAAA
Done.