Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008776.1 Corchorus capsularis cultivar CVL-1 contig08797, 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: 12521
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--45 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
*
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43 AT A
1 AT A
46 CTAATTATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60 original size:19 final size:19
Alignment explanation
Indices: 36--72 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
26 TATATATATA
36 TATATCTATACTAATTATC
1 TATATCTATACTAATTATC
55 TATATCTATACTAATTAT
1 TATATCTATACTAATTAT
73 AATGTGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATCTATACTAATTATC
Found at i:506 original size:22 final size:22
Alignment explanation
Indices: 403--1069 Score: 258
Period size: 22 Copynumber: 30.7 Consensus size: 22
393 TATGATCCCA
*
403 TTATGAAATTTTGATAACATTC
1 TTATGAAATTTTGATAACCTTC
* * ** *
425 CTATGAAATTTTAATAATGATAC
1 TTATGAAATTTTGATAA-CCTTC
* * *
448 -TATGAAATTTCGAGAACCTTT
1 TTATGAAATTTTGATAACCTTC
* **
469 TTAT-AATTTTTTTTAACCTTC
1 TTATGAAATTTTGATAACCTTC
* *
490 TTATGAAATTTTGTTAACCTCC
1 TTATGAAATTTTGATAACCTTC
*
512 TTGA-GTAATTTTGA-AGACC-TC
1 TT-ATGAAATTTTGATA-ACCTTC
* *
533 AATATGGAATTTTGATAA-CTTCC
1 -TTATGAAATTTTGATAACCTT-C
** **
556 CAATGAAATTTTGATAACCAAC
1 TTATGAAATTTTGATAACCTTC
* * *
578 ATTATGAGATGTTGATAACCTCC
1 -TTATGAAATTTTGATAACCTTC
* * * * *
601 ATATGATATATTCATAACC-AC
1 TTATGAAATTTTGATAACCTTC
* * * *
622 GTTATGAAAATTTAAAAACCTCC
1 -TTATGAAATTTTGATAACCTTC
* *
645 GTATG-AATTGTTCG-TAATCAC-AC
1 TTATGAAATT-TT-GATAA-C-CTTC
* *
668 -TCTGAAATTTTGATAATCAC-AC
1 TTATGAAATTTTGATAA-C-CTTC
* *
690 -TATGAAATTGTGATAA-CATC
1 TTATGAAATTTTGATAACCTTC
* **
710 GCTATGAAATTTTGATAAATTTTC
1 -TTATGAAATTTTGAT-AACCTTC
* *
734 TTATAAAATTTTGATAAACCTCC
1 TTATGAAATTTTGAT-AACCTTC
* * * *
757 CTATAAAATTATGATAACTTTC
1 TTATGAAATTTTGATAACCTTC
*
779 TTATGAAATCTTGATAA----C
1 TTATGAAATTTTGATAACCTTC
* * *
797 -TA-CAAATTTTTATAACCTCC
1 TTATGAAATTTTGATAACCTTC
* **
817 CTATGATTTTTTGATAACC-TC
1 TTATGAAATTTTGATAACCTTC
* *
838 ATTATGAAATTTTGTTAATC-TC
1 -TTATGAAATTTTGATAACCTTC
* * * *
860 CTAGTGAAATTTTGATCTACATAC
1 TTA-TGAAATTTTGAT-AACCTTC
*
884 -TATGAAATTTTGATAACCCTC
1 TTATGAAATTTTGATAACCTTC
905 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
* * *
927 ATATGAAATTTTGTTAATC-TC
1 TTATGAAATTTTGATAACCTTC
* * * *
948 CTAGTGAAATTTTGATCTACATAC
1 TTA-TGAAATTTTGAT-AACCTTC
*
972 -TATGAAATTTTGATAACCCTC
1 TTATGAAATTTTGATAACCTTC
993 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTGATAACCTTC
* *
1015 ATATGAAATTTTGATATCC-TC
1 TTATGAAATTTTGATAACCTTC
** *
1036 -CCTGAAATTTTGATATCC-TC
1 TTATGAAATTTTGATAACCTTC
*
1056 -TCTGAAATTTTGAT
1 TTATGAAATTTTGAT
1070 TACTCCATAA
Statistics
Matches: 489, Mismatches: 116, Indels: 82
0.71 0.17 0.12
Matches are distributed among these distances:
16 10 0.02
17 2 0.00
18 1 0.00
19 1 0.00
20 33 0.07
21 42 0.09
22 326 0.67
23 69 0.14
24 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCTTC
Found at i:744 original size:23 final size:23
Alignment explanation
Indices: 716--795 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
706 CATCGCTATG
*
716 AAATTTTGATAAATTTTCTTATA
1 AAATTTTGATAAACTTTCTTATA
* * *
739 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACTTTCTTATA
* *
762 AAATTATGAT-AACTTTCTTATG
1 AAATTTTGATAAACTTTCTTATA
*
784 AAATCTTGATAA
1 AAATTTTGATAA
796 CTACAAATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 16 0.36
23 29 0.64
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAACTTTCTTATA
Found at i:779 original size:45 final size:46
Alignment explanation
Indices: 694--795 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 46
684 TCACACTATG
* * * * *
694 AAATTGTGAT-AACATCGCTATGAAATTTTGATAAATTTTCTTATA
1 AAATTTTGATAAACATCCCTATAAAATTATGATAAACTTTCTTATA
* *
739 AAATTTTGATAAACCTCCCTATAAAATTATGAT-AACTTTCTTATG
1 AAATTTTGATAAACATCCCTATAAAATTATGATAAACTTTCTTATA
*
784 AAATCTTGATAA
1 AAATTTTGATAA
796 CTACAAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 30 0.62
46 18 0.38
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (46 bp):
AAATTTTGATAAACATCCCTATAAAATTATGATAAACTTTCTTATA
Found at i:873 original size:44 final size:42
Alignment explanation
Indices: 482--1069 Score: 288
Period size: 44 Copynumber: 13.5 Consensus size: 42
472 TAATTTTTTT
* * *
482 TAACCTTCTTATGAAATTTTGTTAACCTCCT-TGAGTAATTTTGA
1 TAACC-TCATATGAAATTTTGATAATCTCCTATGA--AATTTTGA
* *
526 -AGACCTCAATATGGAATTTTGATAA-CTTCCCAATGAAATTTTGA
1 TA-ACCTC-ATATGAAATTTTGATAATC-T-CCTATGAAATTTTGA
* * * * * * *
570 TAACCAACATTATGAGATGTTGATAACCTCCATATGATATATTCA
1 TAACC-TCA-TATGAAATTTTGATAATCTCC-TATGAAATTTTGA
* * * * * *
615 TAACCACGTTATGAAAATTTAAAAACCTCCGTATG-AATTGTTCG-
1 TAACCTC-ATATGAAATTTTGATAATCTCC-TATGAAATT-TT-GA
* * * * *
659 TAATCACACTCTGAAATTTTGATAATCACACTATGAAATTGTGA
1 TAACCTCA-TATGAAATTTTGATAATCTC-CTATGAAATTTTGA
* * * * *
703 TAACATCGCTATGAAATTTTGATAAATTTTCTTATAAAATTTTGA
1 TAACCTC-ATATGAAATTTTGAT-AA-TCTCCTATGAAATTTTGA
* * * * * *
748 TAAACCTCCCTATAAAATTATGATAACTTTCTTATGAAATCTTGA
1 T-AACCT-CATATGAAATTTTGATAA-TCTCCTATGAAATTTTGA
* * * **
793 TAA---C-TA-CAAATTTTTATAACCTCCCTATGATTTTTTGA
1 TAACCTCATATGAAATTTTGATAATCT-CCTATGAAATTTTGA
*
831 TAACCTCATTATGAAATTTTGTTAATCTCCTAGTGAAATTTTGA
1 TAACCTCA-TATGAAATTTTGATAATCTCCTA-TGAAATTTTGA
* * * *
875 TCTACAT-ACTATGAAATTTTGATAACCCTCTTATGAAATTTTGA
1 T-AACCTCA-TATGAAATTTTGATAA-TCTCCTATGAAATTTTGA
*
919 TAACCTTCATATGAAATTTTGTTAATCTCCTAGTGAAATTTTGA
1 TAACC-TCATATGAAATTTTGATAATCTCCTA-TGAAATTTTGA
* * * *
963 TCTACAT-ACTATGAAATTTTGATAACCCTCTTATGAAATTTTGA
1 T-AACCTCA-TATGAAATTTTGATAA-TCTCCTATGAAATTTTGA
*
1007 TAACCTTCATATGAAATTTTGAT-ATCCTCC-CTGAAATTTTGA
1 TAACC-TCATATGAAATTTTGATAAT-CTCCTATGAAATTTTGA
* *
1049 TATCCTC-TCTGAAATTTTGAT
1 TAACCTCATATGAAATTTTGAT
1070 TACTCCATAA
Statistics
Matches: 418, Mismatches: 85, Indels: 86
0.71 0.14 0.15
Matches are distributed among these distances:
37 1 0.00
38 24 0.06
39 2 0.00
40 14 0.03
41 3 0.01
42 15 0.04
43 27 0.06
44 221 0.53
45 87 0.21
46 23 0.06
47 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (42 bp):
TAACCTCATATGAAATTTTGATAATCTCCTATGAAATTTTGA
Found at i:917 original size:88 final size:88
Alignment explanation
Indices: 825--1027 Score: 390
Period size: 88 Copynumber: 2.3 Consensus size: 88
815 CCCTATGATT
825 TTTTGATAACC-TCATTATGAAATTTTGTTAATCTCCTAGTGAAATTTTGATCTACATACTATGA
1 TTTTGATAACCTTCA-TATGAAATTTTGTTAATCTCCTAGTGAAATTTTGATCTACATACTATGA
889 AATTTTGATAACCCTCTTATGAAA
65 AATTTTGATAACCCTCTTATGAAA
913 TTTTGATAACCTTCATATGAAATTTTGTTAATCTCCTAGTGAAATTTTGATCTACATACTATGAA
1 TTTTGATAACCTTCATATGAAATTTTGTTAATCTCCTAGTGAAATTTTGATCTACATACTATGAA
978 ATTTTGATAACCCTCTTATGAAA
66 ATTTTGATAACCCTCTTATGAAA
1001 TTTTGATAACCTTCATATGAAATTTTG
1 TTTTGATAACCTTCATATGAAATTTTG
1028 ATATCCTCCC
Statistics
Matches: 114, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
88 111 0.97
89 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (88 bp):
TTTTGATAACCTTCATATGAAATTTTGTTAATCTCCTAGTGAAATTTTGATCTACATACTATGAA
ATTTTGATAACCCTCTTATGAAA
Found at i:1043 original size:20 final size:20
Alignment explanation
Indices: 1018--1069 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1008 AACCTTCATA
1018 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
1038 TGAAATTTTGATATCCTCTC
1 TGAAATTTTGATATCCTCCC
1058 TGAAATTTTGAT
1 TGAAATTTTGAT
1070 TACTCCATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:1377 original size:22 final size:22
Alignment explanation
Indices: 1150--1378 Score: 117
Period size: 22 Copynumber: 10.3 Consensus size: 22
1140 AGAAATACCA
1150 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * *
1173 -TTTGAAAATTTGATAATCTCT
1 CTATGAAATTTTGATAATCACT
* ***
1194 TTATGAAATTTTGATAACTTTTT
1 CTATGAAATTTTGATAA-TCACT
* * * * * *
1217 TTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
* **
1239 CTATAAAATTCCGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
* * * *
1262 -TATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACT
* * *
1283 CTTTGAAATTTTGATAATAACA
1 CTATGAAATTTTGATAATCACT
*
1305 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCACT
*
1326 CCTAT-AAATTTTGATAATTTGATCT
1 -CTATGAAATTTTGATAA--TCA-CT
*
1351 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
1373 CTATGA
1 CTATGA
1379 GATATGATAA
Statistics
Matches: 153, Mismatches: 42, Indels: 23
0.70 0.19 0.11
Matches are distributed among these distances:
21 17 0.11
22 99 0.65
23 21 0.14
24 4 0.03
25 12 0.08
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:1493 original size:22 final size:22
Alignment explanation
Indices: 1428--1785 Score: 112
Period size: 22 Copynumber: 16.5 Consensus size: 22
1418 AAATTGAGAC
1428 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACC-TCACTATGAAA
** *
1449 TTTTGATAACCAGACTATAAAA
1 TTTTGATAACCTCACTATGAAA
*
1471 TTTTGATAATCTC-CTCATGAAA
1 TTTTGATAACCTCACT-ATGAAA
*
1493 TATT-AGTAACCTC-CTAATGAAA
1 TTTTGA-TAACCTCACT-ATGAAA
* * *
1515 TTTTGTTAACCACACTGTGAAA
1 TTTTGATAACCTCACTATGAAA
* *
1537 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTCACTATGAAA
* *
1559 TTTTGATAA--TCTCTTTGATAA
1 TTTTGATAACCTCACTATGA-AA
* * *
1580 CCTTTCT-ATAA---AATTGTGATAA
1 --TTT-TGATAACCTCACTATGA-AA
* *
1602 ---T--TAACCACCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
** * *
1619 TTTCAATAACC-AACCTAAGAAA
1 TTTTGATAACCTCA-CTATGAAA
* *
1641 TTTTAATAACCTGATCCTATGAAA
1 TTTTGATAACCTCA--CTATGAAA
* *
1665 TTTTGATAA-TTAAACTATGAAA
1 TTTTGATAACCT-CACTATGAAA
*
1687 TTTTGATAACTTTCA-TATGAAA
1 TTTTGATAAC-CTCACTATGAAA
* * * *
1709 TTTTGGTAACCACACAATGGAA
1 TTTTGATAACCTCACTATGAAA
1731 TTTTGATAACCTC-CTCATGAAA
1 TTTTGATAACCTCACT-ATGAAA
* * *
1753 TTATAATAACCATC-TTATGAAA
1 TTTTGATAACC-TCACTATGAAA
1775 TTTTGATAACC
1 TTTTGATAACC
1786 ACATAGAGAC
Statistics
Matches: 253, Mismatches: 55, Indels: 57
0.69 0.15 0.16
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 2 0.01
18 4 0.02
20 7 0.03
21 14 0.06
22 185 0.73
23 17 0.07
24 20 0.08
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:1786 original size:22 final size:22
Alignment explanation
Indices: 1603--1786 Score: 147
Period size: 22 Copynumber: 8.3 Consensus size: 22
1593 TTGTGATAAT
* **
1603 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
1625 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
1647 TAACCTGATCCTATGAAATTTTGA
1 TAACC--ATCCTATGAAATTTTGA
** **
1671 TAATTAAACTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
** * *
1693 TAACTTTCATATGAAATTTTGG
1 TAACCATCCTATGAAATTTTGA
* *
1715 TAACCA-CACAATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
1737 TAACC-TCCTCATGAAATTATAA
1 TAACCATCCT-ATGAAATTTTGA
*
1759 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
1781 TAACCA
1 TAACCA
1787 CATAGAGACA
Statistics
Matches: 127, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.02
22 105 0.83
23 3 0.02
24 17 0.13
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:2100 original size:32 final size:32
Alignment explanation
Indices: 2064--2132 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
2054 TTTAGTAATG
2064 ACAATTTAGAAATATGTTTTTTAAAAA-AA-GGT
1 ACAATTTAGAAATATG--TTTTAAAAATAAGGGT
*
2096 ACAA-TTGGAAATATGTTTTAAAAATAAGGGT
1 ACAATTTAGAAATATGTTTTAAAAATAAGGGT
2127 ACAATT
1 ACAATT
2133 GGAAAACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.27
30 2 0.06
31 17 0.52
32 5 0.15
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (32 bp):
ACAATTTAGAAATATGTTTTAAAAATAAGGGT
Found at i:2108 original size:31 final size:31
Alignment explanation
Indices: 2072--2137 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
2062 TGACAATTTA
2072 GAAATATGTTTTTTAAAAA-AA-GGTACAATTG
1 GAAATATG--TTTTAAAAATAAGGGTACAATTG
2103 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
2134 GAAA
1 GAAA
2138 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 9 0.27
30 2 0.06
31 22 0.67
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:2346 original size:75 final size:73
Alignment explanation
Indices: 2221--2422 Score: 233
Period size: 75 Copynumber: 2.7 Consensus size: 73
2211 TAAAGGCTGT
* * *
2221 CATCAACTTTTAACATGGGAGAACATTTTCGCCTCGTTTTGGTCTTTTCTCACCCCGGAATTTAC
1 CATCAACTTTTAACGTGGGA-AAC-TTTTCGCCCCGTTTTGGTCTTTTCTCACCCCGAAATTTAC
2286 CAATAGCTCC
64 CAATAGCTCC
* * *
2296 CTTCAACTTTTAACGTGGGAAAGCTGTTTCGCCCCGTTTTGGTCTTTTCTCACTCTGAAATTTAC
1 CATCAACTTTTAACGTGGGAAA-CT-TTTCGCCCCGTTTTGGTCTTTTCTCACCCCGAAATTTAC
*
2361 TAATAGCTCC
64 CAATAGCTCC
* * *** *
2371 CATCAACTTTTAATGTTGTAGATTTTTTTTGCCCCGTTTTGGTCTTTTCTCA
1 CATCAACTTTTAACG-TG-GGAAACTTTTCGCCCCGTTTTGGTCTTTTCTCA
2423 ATTTATTAGT
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
74 3 0.03
75 101 0.93
76 3 0.03
77 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.41
Consensus pattern (73 bp):
CATCAACTTTTAACGTGGGAAACTTTTCGCCCCGTTTTGGTCTTTTCTCACCCCGAAATTTACCA
ATAGCTCC
Found at i:2927 original size:71 final size:71
Alignment explanation
Indices: 2794--2925 Score: 196
Period size: 70 Copynumber: 1.9 Consensus size: 71
2784 GCTTGAAATT
* *
2794 CATTGTTTTTATATGTAATTTTAGCATTTGGATGTAATTAAAGACGTTCCTACCATTTTTTTCCC
1 CATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAAAGACGTTCCCACCATTTTTTTCCC
2859 TTAATG
66 TTAATG
* **
2865 CATTGTCTTTATATGTAA-TTTAGCA-TTGGAATGTAATTAATGGTGTTCCCACCATTTTTTT
1 CATTGTCTTTATATGTAATTTTAGCATTTGG-ATGTAATTAAAGACGTTCCCACCATTTTTTT
2926 TCTTAGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
69 4 0.07
70 34 0.62
71 17 0.31
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48
Consensus pattern (71 bp):
CATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAAAGACGTTCCCACCATTTTTTTCCC
TTAATG
Found at i:3889 original size:12 final size:13
Alignment explanation
Indices: 3871--3903 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3861 GTAGGTTTAG
3871 TAGTTTGTTTATT
1 TAGTTTGTTTATT
*
3884 TA-TTTGTTTGTT
1 TAGTTTGTTTATT
3896 TAGTTTGT
1 TAGTTTGT
3904 AATTAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70
Consensus pattern (13 bp):
TAGTTTGTTTATT
Found at i:4869 original size:29 final size:29
Alignment explanation
Indices: 4837--4897 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
4827 CTTTAACAAT
*
4837 CAAGTGCAAAACCTGCACTTCA-TCAACCA
1 CAAGTGCAAAACCCGCACTT-AGTCAACCA
*
4866 CAAGTGCACAACCCGCACTTAGTCAACCA
1 CAAGTGCAAAACCCGCACTTAGTCAACCA
4895 CAA
1 CAA
4898 TAAACAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.15
Consensus pattern (29 bp):
CAAGTGCAAAACCCGCACTTAGTCAACCA
Found at i:9374 original size:45 final size:42
Alignment explanation
Indices: 9282--9401 Score: 165
Period size: 45 Copynumber: 2.9 Consensus size: 42
9272 TCCTATTTTA
*
9282 TTAA-TTTCCAAAATCTTCTTTTGG-ATTTCTT-AAAAAACT
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAAAAAACT
9321 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAGAGAAAACCT
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAA-A-AAAA-CT
**
9366 TTGTTTTTCCAAAATCTTCTTTTGGAATTACTTAAA
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAA
9402 TTGAAAATAT
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
39 4 0.06
40 20 0.28
41 6 0.08
42 1 0.01
43 1 0.01
44 5 0.07
45 35 0.49
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (42 bp):
TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAAAAAACT
Found at i:11749 original size:33 final size:33
Alignment explanation
Indices: 11674--11749 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
11664 AGCCGCGCAA
* * *
11674 CACCGGCCACGCGACTTGGAGATGCCCGACCAT
1 CACCAGCCACGCGACATGGACATGCCCGACCAT
* *
11707 CACCGGCCACGCGACATGGACATGCCCGGCCA-
1 CACCAGCCACGCGACATGGACATGCCCGACCAT
11739 CAACCAGCCAC
1 C-ACCAGCCAC
11750 ATGATTCGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 1 0.03
33 37 0.97
ACGTcount: A:0.24, C:0.43, G:0.25, T:0.08
Consensus pattern (33 bp):
CACCAGCCACGCGACATGGACATGCCCGACCAT
Done.