Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013681.1 Corchorus capsularis cultivar CVL-1 contig13702, 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: 71903
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:183 original size:22 final size:22
Alignment explanation
Indices: 150--191 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
140 GAGAAACTTT
*
150 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTATTAACCTTC
172 TTATGAAA-TTTTATTAACCT
1 TTAT-AAATTTTTATTAACCT
192 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTATTAACCTTC
Found at i:421 original size:23 final size:23
Alignment explanation
Indices: 390--474 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
380 GATAACCTCG
*
390 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
413 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
436 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
458 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
475 CTATAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:473 original size:45 final size:45
Alignment explanation
Indices: 351--474 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
341 TCACATTCTG
* * *
351 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTATA
*
395 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTATA
* *
441 AAATTTTGATAACT-TTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
475 CTATAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 11 0.16
45 31 0.46
46 26 0.38
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.39
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTATA
Found at i:529 original size:22 final size:22
Alignment explanation
Indices: 173--604 Score: 161
Period size: 22 Copynumber: 19.9 Consensus size: 22
163 TTAACCTTCT
*
173 TATGAAATTTT-ATTAACCTCCC
1 TATGAAATTTTGA-TAACCTCAC
* * *
195 TAAGGAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCAC
* * *
217 TATGAAATTTTAATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
239 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* * * *
262 CATGAGATGTTGTTAA-C-CA-
1 TATGAAATTTTGATAACCTCAC
* *
281 TATGATATATTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
* * *
301 GTTATGAAAATTTAAAAACCTC-C
1 --TATGAAATTTTGATAACCTCAC
* * *
324 ATATG-AATTGTT-AGTAATCACAT
1 -TATGAAATT-TTGA-TAACCTCAC
* * *
347 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
369 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
*
391 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCTCAC
* *
414 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
437 TATAAAATTTTGATAACTTTC-T
1 TATGAAATTTTGATAAC-CTCAC
*
459 TATGAAATCTTGAT-A----AC
1 TATGAAATTTTGATAACCTCAC
*
476 TAT-AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
497 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* ** *
519 TATGAAATTTTGTTAATATCCC
1 TATGAAATTTTGATAACCTCAC
*
541 TATGAAATTTGGAT---CTGCATGC
1 TATGAAATTTTGATAACCT-CA--C
* *
563 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
*
585 TATGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
605 CCTTAAATTT
Statistics
Matches: 304, Mismatches: 73, Indels: 66
0.69 0.16 0.15
Matches are distributed among these distances:
16 9 0.03
17 4 0.01
19 15 0.05
20 3 0.01
21 10 0.03
22 194 0.64
23 63 0.21
24 6 0.02
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:817 original size:22 final size:21
Alignment explanation
Indices: 764--1309 Score: 156
Period size: 22 Copynumber: 24.9 Consensus size: 21
754 TGTTGACCCT
*
764 CTATGAAATTCTGATAATCA-C
1 CTATGAAATTTTGATAA-CATC
* * *
785 ATTATGTAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACATC
* * *
807 GCTTTGAAATTTTGGTAACAAC
1 -CTATGAAATTTTGATAACATC
*
829 ACTATGAAATTTTGATAATCTTC
1 -CTATGAAATTTTGATAA-CATC
852 CTAT-AAATTTTGATAATCTGATC
1 CTATGAAATTTTGATAA-C--ATC
*
875 TCTATGAAATTTCGATAATCA-C
1 -CTATGAAATTTTGATAA-CATC
* * * *
897 TCTATGAGA-TTTAATAACCTT
1 -CTATGAAATTTTGATAACATC
* *
918 CTATCAAATTTTGGT-AC-TC
1 CTATGAAATTTTGATAACATC
* *
937 CTTATGAAATTGAGACTTTTATAACCTTC
1 C-TATGAAA-T-----TTTGATAA-CATC
* *
966 ATATGAAATTTTGATAACCATA
1 CTATGAAATTTTGATAA-CATC
* *
988 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACAT-C
* * *
1010 CCATGAAATATT-AGTAACCTC
1 CTATGAAATTTTGA-TAACATC
* *
1031 CTAATGAAATTTTGTTAACAAC
1 CT-ATGAAATTTTGATAACATC
*
1053 ACTATGAAATTCTT-ATAACCTC
1 -CTATGAAATT-TTGATAACATC
*
1075 GCTATGACATTTTGAT-AC-TC
1 -CTATGAAATTTTGATAACATC
* *
1095 TCTTTGATAACCTTTCT-ATAAAAT-
1 -CTATGA-AA--TTT-TGATAACATC
* * * *
1119 -TGTGAAA-ATT-A-ACCACC
1 CTATGAAATTTTGATAACATC
** *
1136 CTATGAAATTTCAATAACCAAC
1 CTATGAAATTTTGATAA-CATC
* *
1158 CTAAGAAATTTTAATAACCTGATC
1 CTATGAAATTTTGATAA-C--ATC
*
1182 CTATGAAATTTTGGTAACCA-C
1 CTATGAAATTTTGATAA-CATC
* *
1203 ACTATGAAGTTTTGATAACTTC
1 -CTATGAAATTTTGATAACATC
*
1225 CATATGAAATTTTGGTAACCA-C
1 C-TATGAAATTTTGATAA-CATC
* *
1247 ACTATGGAATTTTGATAACCTC
1 -CTATGAAATTTTGATAACATC
* *
1269 CTCATGAAATTATAATAACCATC
1 CT-ATGAAATTTTGATAA-CATC
*
1292 TTATGAAATTTTGATAAC
1 CTATGAAATTTTGATAAC
1310 CACATAGAGA
Statistics
Matches: 389, Mismatches: 88, Indels: 95
0.68 0.15 0.17
Matches are distributed among these distances:
16 2 0.01
17 2 0.01
18 7 0.02
19 3 0.01
20 23 0.06
21 46 0.12
22 232 0.60
23 20 0.05
24 24 0.06
25 14 0.04
26 4 0.01
27 2 0.01
28 8 0.02
29 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
CTATGAAATTTTGATAACATC
Found at i:817 original size:65 final size:66
Alignment explanation
Indices: 713--848 Score: 159
Period size: 65 Copynumber: 2.1 Consensus size: 66
703 AAAATTTTTG
* * * * * *
713 TAATCACATTCTGAAAATTTGATAACCTCTTTATAAAATTTTGTTGAC-CCTCTATGAAATTCTG
1 TAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGGTAACAACACTATGAAATTCTG
777 A
66 A
* * * *
778 TAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGGTAACAACACTATGAAATTTT
1 TAATCACATTATGAAAATTTGATAACCTC-CTTATAAAATTTTGGTAACAACACTATGAAATTCT
842 GA
65 GA
844 TAATC
1 TAATC
849 TTCCTATAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
65 38 0.64
66 21 0.36
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (66 bp):
TAATCACATTATGAAAATTTGATAACCTCCTTATAAAATTTTGGTAACAACACTATGAAATTCTG
A
Found at i:1016 original size:44 final size:44
Alignment explanation
Indices: 724--1310 Score: 180
Period size: 44 Copynumber: 13.4 Consensus size: 44
714 AATCACATTC
* ** * * * *
724 TGAAAATTTGATAACCTCTTTATAAAATTTTGTTGACCCT-CTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
* * * ** * * *
767 TGAAATTCTGATAATCACATTATGTAATTTTGATAACC-TCGCTT
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCAT-ACTA
* ** * * * *
811 TGAAATTTTGGTAACAACACTATGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
* * * *
855 T-AAATTTTGATAATCTGATCTCTATGAAATTTCGATAATCACT-CTA
1 TGAAATTTTGATAA-C--CTCCCTATGAAATTTTGATAACCA-TACTA
* * * * * * *
901 TGAGA-TTTAATAACCT-TCTATCAAATTTTGGTACTCCTTATGA-AA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATA-ACC--AT-ACTA
* * *
946 TTGAGACTTTT-ATAACCTTCATATGAAATTTTGATAACCATACTA
1 -TGA-AATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
* * * *
991 TAAAATTTTGATAACCTCCCCATGAAATATT-AGTAACC-TCCTAA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGA-TAACCATACT-A
* ** * *
1035 TGAAATTTTGTTAACAACACTATGAAATTCTT-ATAACC-TCGCTA
1 TGAAATTTTGATAACCTCCCTATGAAATT-TTGATAACCAT-ACTA
* * * *
1079 TGACATTTTGAT-A-CT--C--T----CTTTGATAACCTTTCTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
* * * **
1113 TAAAATTGTGAAAATTAACCACCCTATGAAATTTCAATAACCA-ACCTA
1 TGAAATTTTG---A-TAACCTCCCTATGAAATTTTGATAACCATA-CTA
* * * * *
1161 AGAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCT--CCCTATGAAATTTTGATAACCATACTA
* * * * *
1207 TGAAGTTTTGATAACTTCCATATGAAATTTTGGTAACCACACTA
1 TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
* * *
1251 TGGAATTTTGATAACCT-CCTCATGAAATTATAATAACCAT-CTTA
1 TGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCATAC-TA
1295 TGAAATTTTGATAACC
1 TGAAATTTTGATAACC
1311 ACATAGAGAC
Statistics
Matches: 404, Mismatches: 95, Indels: 89
0.69 0.16 0.15
Matches are distributed among these distances:
33 2 0.00
34 17 0.04
35 1 0.00
37 1 0.00
38 2 0.00
39 1 0.00
40 2 0.00
42 16 0.04
43 55 0.14
44 180 0.45
45 13 0.03
46 68 0.17
47 13 0.03
48 33 0.08
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCATACTA
Found at i:1310 original size:22 final size:22
Alignment explanation
Indices: 1128--1311 Score: 160
Period size: 22 Copynumber: 8.3 Consensus size: 22
1118 TTGTGAAAAT
* **
1128 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
1150 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
*
1172 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
*
1196 TAACCA-CACTATGAAGTTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
1218 TAA-CTTCCATATGAAATTTTGG
1 TAACCATCC-TATGAAATTTTGA
*
1240 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
1262 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
1284 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
1306 TAACCA
1 TAACCA
1312 CATAGAGACA
Statistics
Matches: 131, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.04
22 103 0.79
23 5 0.04
24 18 0.14
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:1507 original size:19 final size:20
Alignment explanation
Indices: 1476--1513 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1466 TATTGATATT
1476 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
1495 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
1514 ACTAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:1823 original size:2 final size:2
Alignment explanation
Indices: 1816--1850 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
1806 TTCGTACTTT
*
1816 TA TA TA TA GTG TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
1851 GTACTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2650 original size:31 final size:31
Alignment explanation
Indices: 2613--2685 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
2603 TATATTTGAG
2613 GACAATTTGCC-TATCAAACTTCCAAATTC-AA
1 GACAATTTGCCGT-T-AAACTTCCAAATTCAAA
* *
2644 GACAATTAGTCCGTTGAACTTCCAAATTCAAA
1 GACAATTTG-CCGTTAAACTTCCAAATTCAAA
*
2676 GACAGTTTGC
1 GACAATTTGC
2686 TTCATCATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 22 0.63
32 12 0.34
33 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (31 bp):
GACAATTTGCCGTTAAACTTCCAAATTCAAA
Found at i:6614 original size:1 final size:1
Alignment explanation
Indices: 6608--6642 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
6598 TTCTCACACC
6608 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6643 CTAATGGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14436 original size:33 final size:33
Alignment explanation
Indices: 14393--14520 Score: 188
Period size: 33 Copynumber: 3.9 Consensus size: 33
14383 TTTGCCCTTA
*
14393 GCCAC-GCGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGGCGGCTCT
*
14425 GCCACGGCGGAGCCTCCCCACTAGGGCGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGGCGGCTCT
* *
14458 GCCACGGTGGAGCCGCCCCACTAGGACGGCTCT
1 GCCACGGCGGAGCCGCCCCACTAGGGCGGCTCT
*
14491 GCCACGGC-TAGCCGCCCCACTTAGGGCGGC
1 GCCACGGCGGAGCCGCCCCAC-TAGGGCGGC
14521 AAGGCTTTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.18
33 72 0.82
ACGTcount: A:0.13, C:0.42, G:0.33, T:0.12
Consensus pattern (33 bp):
GCCACGGCGGAGCCGCCCCACTAGGGCGGCTCT
Found at i:14633 original size:33 final size:35
Alignment explanation
Indices: 14561--14636 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 35
14551 TTAGTACCGG
* * *
14561 TGCCGCCCCAGGGGGGGCGGTCTATCCATGGCAGA
1 TGCCGCCCCAGGGGAGGCGGCCTAGCCATGGCAGA
*
14596 -GCCGCCCCA-GGGAGGCGGCCTAGCCATGGTA-A
1 TGCCGCCCCAGGGGAGGCGGCCTAGCCATGGCAGA
14628 TGCCGCCCC
1 TGCCGCCCC
14637 TGGTGCGTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 1 0.03
33 26 0.72
34 9 0.25
ACGTcount: A:0.14, C:0.37, G:0.37, T:0.12
Consensus pattern (35 bp):
TGCCGCCCCAGGGGAGGCGGCCTAGCCATGGCAGA
Found at i:14685 original size:33 final size:33
Alignment explanation
Indices: 14648--14711 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
14638 GGTGCGTCAT
*
14648 TACCATGGC-CAGGCCG-CTCCCCTGGGGCGGCCC
1 TACCATGGCTCA-GCCGTC-CCCCTAGGGCGGCCC
14681 TACCATGGCTCAGCCGTCCCCCTAGGGCGGC
1 TACCATGGCTCAGCCGTCCCCCTAGGGCGGC
14712 ATGAGCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.11, C:0.44, G:0.31, T:0.14
Consensus pattern (33 bp):
TACCATGGCTCAGCCGTCCCCCTAGGGCGGCCC
Found at i:17769 original size:2 final size:2
Alignment explanation
Indices: 17762--17786 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17752 TCAGCAAACT
17762 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 T
17787 TCTCTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24544 original size:57 final size:57
Alignment explanation
Indices: 24456--24569 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
24446 AAAAATTCCT
24456 AATATACCTTCCAATCCAAATTCAAGTGTCAGAAGAAGTTCAAGAATCAAAACAAAG
1 AATATACCTTCCAATCCAAATTCAAGTGTCAGAAGAAGTTCAAGAATCAAAACAAAG
*
24513 AATATACCTTCTAATCCAAATTCAAGTGTCAGAAGAAGTTCAAGAATCAAAACAAAG
1 AATATACCTTCCAATCCAAATTCAAGTGTCAGAAGAAGTTCAAGAATCAAAACAAAG
24570 CCTCCATACT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (57 bp):
AATATACCTTCCAATCCAAATTCAAGTGTCAGAAGAAGTTCAAGAATCAAAACAAAG
Found at i:29559 original size:15 final size:15
Alignment explanation
Indices: 29541--29570 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29531 CTCCCGAAAT
29541 AGACATGTCAACTTG
1 AGACATGTCAACTTG
29556 AGACATGTCAACTTG
1 AGACATGTCAACTTG
29571 TGGAGGCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
AGACATGTCAACTTG
Found at i:30371 original size:6 final size:6
Alignment explanation
Indices: 30361--30395 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
30351 AGTAACTGAG
*
30361 TTTTTG TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
30396 TTAATTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:45205 original size:2 final size:2
Alignment explanation
Indices: 45200--45231 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45190 TCTTTGCTTC
45200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45232 GTCATAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62481 original size:12 final size:12
Alignment explanation
Indices: 62464--62488 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62454 TTCTCACATC
62464 TCACTCATAATT
1 TCACTCATAATT
62476 TCACTCATAATT
1 TCACTCATAATT
62488 T
1 T
62489 TATGTGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCACTCATAATT
Found at i:62965 original size:17 final size:17
Alignment explanation
Indices: 62943--62978 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
62933 AAAGGACTTG
62943 ATAGAAAAGACATTGAA
1 ATAGAAAAGACATTGAA
62960 ATAGAAAAGACATTGAA
1 ATAGAAAAGACATTGAA
62977 AT
1 AT
62979 TCAGTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.19
Consensus pattern (17 bp):
ATAGAAAAGACATTGAA
Done.