Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010733.1 Corchorus capsularis cultivar CVL-1 contig10754, 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: 25041
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:48 original size:22 final size:21
Alignment explanation
Indices: 23--589 Score: 143
Period size: 22 Copynumber: 26.0 Consensus size: 21
13 ATGATTCCAT
23 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* ** *
45 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAA-CCTCC
* ** * **
67 TATGGAATTTCAAGAACCTTTT
1 TATGAAATTTTGATAACC-TCC
* ** *
89 TAT-AATTTTTTTTAACCTTCT
1 TATGAAATTTTGATAACC-TCC
* * *
110 TATTAAATTTTGTTCACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
132 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTC-C
* *
154 TATGGAATTTTGATAACTTTCC
1 TATGAAATTTTGATAAC-CTCC
* *
176 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
199 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
220 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
243 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
264 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTC-C
* *
287 T-TCGAAATTTTGATAATCACAC
1 TAT-GAAATTTTGATAACCTC-C
*
309 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
331 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
* *
354 TATAAAAATTTGATAAACCTCC
1 TATGAAATTTTGAT-AACCTCC
* * * * *
376 GTGTG-ATTTTCTTATAACATCAT
1 -TATGAAATTT-TGATAACCTC-C
* *
399 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
* * * *
421 TATGAAATTTTGTTCTACATAC
1 TATGAAATTTTGAT-AACCTCC
* *
443 TATGAAATTTTAATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* * *
465 TATCAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
* *
487 TATGAAATTTTTATATCCTCC
1 TATGAAATTTTGATAACCTCC
* *
508 -CTGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
* * *
528 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACC-TCC
* *
552 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACC-TCC
569 TATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
590 CCAGAAATAC
Statistics
Matches: 394, Mismatches: 110, Indels: 83
0.67 0.19 0.14
Matches are distributed among these distances:
17 10 0.03
18 2 0.01
19 1 0.00
20 21 0.05
21 30 0.08
22 253 0.64
23 71 0.18
24 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:514 original size:20 final size:20
Alignment explanation
Indices: 489--527 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
479 AACTAAACTA
*
489 TGAAATTTTTATATCCTCCC
1 TGAAATTTTGATATCCTCCC
509 TGAAATTTTGATATCCTCC
1 TGAAATTTTGATATCCTCC
528 ATAATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:700 original size:44 final size:44
Alignment explanation
Indices: 651--771 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 44
641 CCTCTGCATA
* * * *
651 AAATTTTGTTGACCCCTCTATGAAATTTTGATAATC-ACATTATG
1 AAATTTTGATAACCCCACTATGAAATTTTGATAA-CAACACTATG
* * *
695 TAATTTTGATAACCTCACTTTGAAATTTTGATAACAACACTATG
1 AAATTTTGATAACCCCACTATGAAATTTTGATAACAACACTATG
**
739 AAATTTTGATAATCTTC-CTAT-AAATTTTGATAA
1 AAATTTTGATAA-CCCCACTATGAAATTTTGATAA
772 TCTGATCTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
43 13 0.20
44 49 0.75
45 3 0.05
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (44 bp):
AAATTTTGATAACCCCACTATGAAATTTTGATAACAACACTATG
Found at i:721 original size:66 final size:66
Alignment explanation
Indices: 600--752 Score: 175
Period size: 66 Copynumber: 2.3 Consensus size: 66
590 CCAGAAATAC
* * * *
600 CACTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTGCATAAAATTTTGTTGAC
1 CACTATGAAA-TTTTGATAATCACATTATGAAAATTTGATAACCTCTACATAAAATTTTGATAAC
**
664 CC
65 AA
* * * * *
666 CTCTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTC-ACTTTGAAATTTTGATAAC
1 CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTAC-ATAAAATTTTGATAAC
730 AA
65 AA
732 CACTATGAAATTTTGATAATC
1 CACTATGAAATTTTGATAATC
753 TTCCTATAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
65 6 0.08
66 67 0.92
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (66 bp):
CACTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTACATAAAATTTTGATAACA
A
Found at i:765 original size:21 final size:23
Alignment explanation
Indices: 668--774 Score: 125
Period size: 22 Copynumber: 4.9 Consensus size: 23
658 GTTGACCCCT
668 CTATGAAATTTTGATAATC-ACA
1 CTATGAAATTTTGATAATCTACA
* * *
690 TTATGTAATTTTGATAACCT-CA
1 CTATGAAATTTTGATAATCTACA
* *
712 CTTTGAAATTTTGATAA-CAACA
1 CTATGAAATTTTGATAATCTACA
*
734 CTATGAAATTTTGATAATCTTC-
1 CTATGAAATTTTGATAATCTACA
756 CTAT-AAATTTTGATAATCT
1 CTATGAAATTTTGATAATCT
775 GATCTCTACG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
21 16 0.22
22 54 0.75
23 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
CTATGAAATTTTGATAATCTACA
Found at i:952 original size:22 final size:20
Alignment explanation
Indices: 856--990 Score: 72
Period size: 22 Copynumber: 6.2 Consensus size: 20
846 AAATTGAGAC
* *
856 TTTTTTAACCTTCATATGAAA
1 TTTTGTAACC-TCCTATGAAA
* * *
877 TTTTGATAATCACACTATAAAA
1 TTTTG-TAACCTC-CTATGAAA
* *
899 TTTTGACAACCTCCCCATGAAA
1 TTTTG-TAACCT-CCTATGAAA
*
921 TATTAGTAACCTCCTAATGAAA
1 T-TTTGTAACCTCCT-ATGAAA
*
943 TTTTGTTAACCACACTATGAAA
1 TTTTG-TAACCTC-CTATGAAA
* *
965 TTCTTATAACCTCGCTATGACA
1 TT-TTGTAACCTC-CTATGAAA
987 TTTT
1 TTTT
991 CATAATCTCT
Statistics
Matches: 87, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
21 12 0.14
22 67 0.77
23 8 0.09
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTTGTAACCTCCTATGAAA
Found at i:1057 original size:22 final size:22
Alignment explanation
Indices: 1031--1210 Score: 139
Period size: 22 Copynumber: 8.1 Consensus size: 22
1021 TGTGATAATA
**
1031 AACCACCCTATGAAATTTCAAT
1 AACCACCCTATGAAATTTTGAT
* * *
1053 AACCAACCTAAGAAATTTTAAT
1 AACCACCCTATGAAATTTTGAT
* *
1075 AACCTGATCCTATGAAATTTTGGT
1 AACC--ACCCTATGAAATTTTGAT
1099 AACCACACC-ATGAAATTTTGAT
1 AACCAC-CCTATGAAATTTTGAT
** * *
1121 AACTTCCATATGAAATTTTGGT
1 AACCACCCTATGAAATTTTGAT
* *
1143 AACCACACTATGGAATTTTGAT
1 AACCACCCTATGAAATTTTGAT
* * * *
1165 AACC-TCTTCATGAAATTATAAT
1 AACCACCCT-ATGAAATTTTGAT
* *
1187 AACCATCTTATGAAATTTTGAT
1 AACCACCCTATGAAATTTTGAT
1209 AA
1 AA
1211 ATACATAGAG
Statistics
Matches: 125, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
21 2 0.02
22 99 0.79
23 6 0.05
24 18 0.14
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (22 bp):
AACCACCCTATGAAATTTTGAT
Found at i:1102 original size:46 final size:44
Alignment explanation
Indices: 1037--1210 Score: 158
Period size: 44 Copynumber: 3.9 Consensus size: 44
1027 AATAAACCAC
*** * *
1037 CCTATGAAATTTCAATAACCAACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCAACCTATGAAATTTTGATAACCT--T
1083 CCTATGAAATTTTGGTAACCACACC-ATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACCA-ACCTATGAAATTTTGATAACCTT
*
1126 CCATATGAAATTTTGGTAACC-ACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCAAC-CTATGAAATTTTGATAACCTT
* * ** * *
1170 CTTCATGAAATTATAATAACCATCTTATGAAATTTTGATAA
1 CCT-ATGAAATTTTGGTAACCAACCTATGAAATTTTGATAA
1211 ATACATAGAG
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 63 0.58
45 4 0.04
46 31 0.29
47 3 0.03
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACCTATGAAATTTTGATAACCTT
Found at i:2482 original size:7 final size:7
Alignment explanation
Indices: 2470--2525 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
2460 AATTTTATTT
2470 TAATATA
1 TAATATA
2477 TAATATA
1 TAATATA
*
2484 TATTAT-
1 TAATATA
*
2490 TAATATG
1 TAATATA
2497 TAATATA
1 TAATATA
2504 T-ATATA
1 TAATATA
* *
2510 TGTATGTA
1 T-AATATA
2518 TAATATA
1 TAATATA
2525 T
1 T
2526 TCAAACTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
6 11 0.28
7 24 0.60
8 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:2490 original size:22 final size:20
Alignment explanation
Indices: 2465--2525 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
2455 GTAAGAATTT
2465 TATT-TTAATATATAATATA
1 TATTATTAATATATAATATA
*
2484 TATTATTAATATGTAATATA
1 TATTATTAATATATAATATA
*
2504 TATATATGT-ATGTATAATATA
1 TAT-TAT-TAATATATAATATA
2525 T
1 T
2526 TCAAACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.11
20 17 0.47
21 14 0.39
22 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
TATTATTAATATATAATATA
Found at i:4784 original size:19 final size:19
Alignment explanation
Indices: 4760--4797 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4750 TTTATCAATT
4760 TATGGTCAAAATTGATTGG
1 TATGGTCAAAATTGATTGG
4779 TATGGTCAAAATTGATTGG
1 TATGGTCAAAATTGATTGG
4798 CATGCTCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
TATGGTCAAAATTGATTGG
Found at i:4954 original size:37 final size:37
Alignment explanation
Indices: 4864--4960 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 37
4854 TATCTAAGCC
* * *
4864 CAAATAGGACATTGGAGACAAAGGCAAAAAGCAAAAT
1 CAAATAGGACGTTGGAAACAAAGACAAAAAGCAAAAT
* * *
4901 CAAATA-CATCGATTGGAAACAAAGACAAAAGGTAAAAT
1 CAAATAGGA-CG-TTGGAAACAAAGACAAAAAGCAAAAT
*
4939 TAAATAGGACGTTGGAAACAAA
1 CAAATAGGACGTTGGAAACAAA
4961 AAGTCAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
36 1 0.02
37 18 0.37
38 29 0.59
39 1 0.02
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.14
Consensus pattern (37 bp):
CAAATAGGACGTTGGAAACAAAGACAAAAAGCAAAAT
Found at i:5116 original size:30 final size:30
Alignment explanation
Indices: 5057--5152 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 30
5047 TGGCAATTTA
* *
5057 GAAATATGTTTTAAAAAAATGGATACAATTG
1 GAAATATATTTTAAAAAAA-GGGTACAATTG
**
5088 GAAATATATTTTTTAAAAAGGGTACAATTG
1 GAAATATATTTTAAAAAAAGGGTACAATTG
*
5118 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAA-AAGGGTACAATTG
5149 GAAA
1 GAAA
5153 ACATAAAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.44
31 32 0.56
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (30 bp):
GAAATATATTTTAAAAAAAGGGTACAATTG
Found at i:6134 original size:437 final size:438
Alignment explanation
Indices: 5489--6498 Score: 1274
Period size: 438 Copynumber: 2.3 Consensus size: 438
5479 TCACAAAAGT
* * * * * * *
5489 ATTTTTTAGAACTGAAACATGAAAATTAGCTTTTGAGTCTTTAATGAAAAGTTGTATATCATAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATG-AAAGTTGTAGATCATGAA
* * ** * * *
5554 ATTACCTTTTAATAAACACCTGAAT-TGCTTTAATTGGACAAATAGAACAAAGAAAATAAAAAAG
65 ATTACCTTTTAATAGACACATGAATCAAC-TTAATCGGACAAATAGAACAAAGAATA-AAAAAAT
* * * *
5618 AAATGAAGCGTTAAATCGAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGT
128 AAATGAAACGTT-AA-CGAATAAGATAGAATTTCTAAAGGACTAAGTAGCATAAAATAGAAAAAT
* * *
5683 ATGAGAGTCATTTGATAACTAATTCAAATAAGAAAATATTTCTTAATGAATATCTTGAAACATAA
191 ATGAGAGTCATTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGAAGATCTCGAAACATAA
* * * *
5748 AAATTCTCTTTTAAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCAGGTTCTTCATGAAA
256 AAATTCCCTTTTAAACCCTTCATGAAACTCGCAGATCAAATTTAACTTTCAGATCCTTCATGAAA
* * * * * *
5812 GTCGTAGATCATACAGTAACCTTTTAACCGACACTTGAATAACTTTAATCGGAAATGTGGATC-G
321 GTCGTAAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGA-CAA
* * * * *
5876 AAAATTATATGATATTAAATAGACCACCAATCGAAACGACCAAATTTAGGAAGC
385 AAAATTATACGAAATTAAATAGACCACCAATCAAAACCACAAAATTTAGGAAGC
* *
5930 ATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
5995 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAA
66 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAA
* * * *
6060 TCTTAAACGTT-A-GATTAAGATAGAATTTCTAAAGGACTAAGTAGTATAAAGTAGAAAAATATG
131 --TGAAACGTTAACGAATAAGATAGAATTTCTAAAGGACTAAGTAGCATAAAATAGAAAAATATG
* * * * *
6123 AGGGTCATTTGATAAATAATTCAAATAAGAAAATGTTTGTTAATGGAGATCTCGAAGCATAAAAA
194 AGAGTCATTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGAAGATCTCGAAACATAAAAA
* * * *
6188 TTCCCTTTTGAACCCTTCATGAAATTCGCAGATCAAATTTAGCTTTCTGATCCTTCATGAAAGTC
259 TTCCCTTTTAAACCCTTCATGAAACTCGCAGATCAAATTTAACTTTCAGATCCTTCATGAAAGTC
* * *
6253 GTAAATCATGCAATAACCTTTTAACTAACACTTCAATAACTTCAATCGGACATGTGGACAAAAAA
324 GTAAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGACAAAAAA
* ** *
6318 TTATACGAAATTAAATTGACCGGCAATCAAAACCACAAAATTTCGGAAGC
389 TTATACGAAATTAAATAGACCACCAATCAAAACCACAAAATTTAGGAAGC
* * * * * *
6368 ATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATTCTTCATGAAAATTGTAGATCATGAAA
1 ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
* * * * * *
6433 TTACCTTTTAATAGACACTTGAATCACCTTAATCAGACAAATAGAGAAAAAAAATACAAAAATAA
66 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGA-ACAAAGAATAAAAAAATAA
6498 A
130 A
6499 AGTCAACGCG
Statistics
Matches: 492, Mismatches: 71, Indels: 14
0.85 0.12 0.02
Matches are distributed among these distances:
437 136 0.28
438 218 0.44
439 27 0.05
440 64 0.13
441 47 0.10
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (438 bp):
ATTTTTTAGAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAA
TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAAAAAAATAAA
TGAAACGTTAACGAATAAGATAGAATTTCTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAG
AGTCATTTGATAAATAATTCAAATAAGAAAATATTTCTTAATGAAGATCTCGAAACATAAAAATT
CCCTTTTAAACCCTTCATGAAACTCGCAGATCAAATTTAACTTTCAGATCCTTCATGAAAGTCGT
AAATCATACAATAACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGACAAAAAATT
ATACGAAATTAAATAGACCACCAATCAAAACCACAAAATTTAGGAAGC
Found at i:7035 original size:31 final size:32
Alignment explanation
Indices: 6987--7055 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
6977 TAAAAGTTGT
* * *
6987 TTAAAGGTCTCACCTTTT-AGA-TTTGGGTCAA
1 TTAAGGGTCCCACCTTTTCA-ACTTTAGGTCAA
7018 TTAAGGGTCCCACCTTTTCAACTTTAGGTCAA
1 TTAAGGGTCCCACCTTTTCAACTTTAGGTCAA
7050 TTAAGG
1 TTAAGG
7056 TTAGCAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (32 bp):
TTAAGGGTCCCACCTTTTCAACTTTAGGTCAA
Found at i:19607 original size:31 final size:30
Alignment explanation
Indices: 19531--19631 Score: 132
Period size: 31 Copynumber: 3.3 Consensus size: 30
19521 AACATGCCAT
19531 GCCACGTGTACCAAAAAAGGACACGTGACAC
1 GCCACGTGTACCAAAAAAGGACACGTG-CAC
* *
19562 GCCATGTATA-CAAAAAAGGACACGTAGCAC
1 GCCACGTGTACCAAAAAAGGACACGT-GCAC
*
19592 GCCACGTGTACCAAAAAAGGGCACGTGGCAC
1 GCCACGTGTACCAAAAAAGGACACGT-GCAC
*
19623 GTCACGTGT
1 GCCACGTGT
19632 TAATACGACG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
30 26 0.43
31 35 0.57
ACGTcount: A:0.36, C:0.27, G:0.25, T:0.13
Consensus pattern (30 bp):
GCCACGTGTACCAAAAAAGGACACGTGCAC
Found at i:23811 original size:2 final size:2
Alignment explanation
Indices: 23804--23841 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
23794 GTAGCTAAGA
*
23804 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23842 GTGAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Done.