Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013459.1 Corchorus capsularis cultivar CVL-1 contig13480, 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: 37132
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:790 original size:26 final size:27
Alignment explanation
Indices: 753--818 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 27
743 TAAAAAAAAT
*
753 AAATGACTAAAATGCCCCTGAGTG-AA
1 AAATGACCAAAATGCCCCTGAGTGCAA
*
779 AAATGACCAAAATGCCCCTGGGTGCAA
1 AAATGACCAAAATGCCCCTGAGTGCAA
806 AAATGACCAAAAT
1 AAATGACCAAAAT
819 ACCCTTGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
26 22 0.59
27 15 0.41
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGAGTGCAA
Found at i:815 original size:27 final size:26
Alignment explanation
Indices: 753--827 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
743 TAAAAAAAAT
* *
753 AAATGACTAAAATGCCCCTGAGTGAA
1 AAATGACCAAAATGCCCCTGGGTGAA
779 AAATGACCAAAATGCCCCTGGGTGCAA
1 AAATGACCAAAATGCCCCTGGGTG-AA
* *
806 AAATGACCAAAATACCCTTGGG
1 AAATGACCAAAATGCCCCTGGG
828 CGACTCTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 22 0.50
27 22 0.50
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (26 bp):
AAATGACCAAAATGCCCCTGGGTGAA
Found at i:5832 original size:13 final size:13
Alignment explanation
Indices: 5814--5842 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5804 AAAACAGTGA
5814 AATGGTAAAATAT
1 AATGGTAAAATAT
5827 AATGGTAAAATAT
1 AATGGTAAAATAT
5840 AAT
1 AAT
5843 AGCTATAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (13 bp):
AATGGTAAAATAT
Found at i:5840 original size:91 final size:93
Alignment explanation
Indices: 5736--5916 Score: 242
Period size: 100 Copynumber: 1.9 Consensus size: 93
5726 AAAATAGTAA
*
5736 AATGGTAAAATATAATAG-TA-ATAAGG-ATATTAGATTTTATTATATAAAAATAGAGTTTTTAG
1 AATGGTAAAATATAATAGATACATAAGGAATATTAGATTTAATTATAT-AAAATAGAGTTTTTAG
*
5798 TTGAGTAAAACAGTGAAATGGTAAAATAT
65 TTGAGTAAAACAGTAAAATGGTAAAATAT
5827 AATGGTAAAATATAATAGCTATAGCCTATAAGGATAATATTAGATTTAATTATATAAAATAGAGT
1 AATGGTAAAATATAATAG--ATA--C-ATAAGG--AATATTAGATTTAATTATATAAAATAGAGT
*
5892 TTTTAGTTGAGTAAAATAGTAAAAT
59 TTTTAGTTGAGTAAAACAGTAAAAT
5917 AAAATAGTTA
Statistics
Matches: 77, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
91 18 0.23
94 2 0.03
98 6 0.08
100 33 0.43
101 18 0.23
ACGTcount: A:0.47, C:0.02, G:0.15, T:0.35
Consensus pattern (93 bp):
AATGGTAAAATATAATAGATACATAAGGAATATTAGATTTAATTATATAAAATAGAGTTTTTAGT
TGAGTAAAACAGTAAAATGGTAAAATAT
Found at i:12733 original size:17 final size:17
Alignment explanation
Indices: 12695--12727 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12685 CTCATGATAC
12695 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
12712 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
12728 GATAGGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:16723 original size:8 final size:8
Alignment explanation
Indices: 16710--16734 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16700 TATATGTGTA
16710 TCTTAGAT
1 TCTTAGAT
16718 TCTTAGAT
1 TCTTAGAT
16726 TCTTAGAT
1 TCTTAGAT
16734 T
1 T
16735 TTTTTCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TCTTAGAT
Found at i:21978 original size:20 final size:21
Alignment explanation
Indices: 21950--22004 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
21940 CTTGGTCTCG
*
21950 AGTCATTTG-CTCTTTAAGTA
1 AGTCATTTGACTCCTTAAGTA
* *
21970 AGTCGTTTGACTCCTTAAGTTG
1 AGTCATTTGACTCCTTAAG-TA
21992 AG-CATTTGACTCC
1 AGTCATTTGACTCC
22005 ATTATTAGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
AGTCATTTGACTCCTTAAGTA
Found at i:25131 original size:135 final size:135
Alignment explanation
Indices: 24967--25249 Score: 406
Period size: 135 Copynumber: 2.1 Consensus size: 135
24957 TCAAGTGGCC
* *
24967 GTTGGTTTTGCCCCCCGAGTCCTTCCCCCCCAAGTCTTTCATCGATAAGGCCAACCTGAGCCATG
1 GTTGGTTTTGCCCCCCGAGTCCTTCCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCATG
* ** * *
25032 ACCTGTTGATTGTTCACCTGATGGTTAACTTGTTGAAGGGGAAGAGGATCGAGCTGGGCACCAAG
66 ACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAGCACCGAGCTGGGCACCAAG
25097 CAGTT
131 CAGTT
* * *
25102 GTTGGTTTTGCCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATCGATGAGACCAATCTCAGCCATG
1 GTTGGTTTTGCCCCCCGAGTCCTTCCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCATG
* * * ** * *
25167 ACTTGTGGGTTGTTCACCTGATGGTTGACTTGTTGAAAAGGTTGAGCACCGGGTTGGGCACCAAG
66 ACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAGCACCGAGCTGGGCACCAAG
25232 CAGTT
131 CAGTT
25237 GTTGGTTTT-CCCC
1 GTTGGTTTTGCCCC
25250 TCCAAGTCTT
Statistics
Matches: 131, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
134 4 0.03
135 127 0.97
ACGTcount: A:0.19, C:0.27, G:0.26, T:0.29
Consensus pattern (135 bp):
GTTGGTTTTGCCCCCCGAGTCCTTCCCCCCCAAGTCTTTCATCGATAAGACCAACCTCAGCCATG
ACCTGTGGATTGTTCACCTGATGGTTAACTTGTTGAAAAGGAAGAGCACCGAGCTGGGCACCAAG
CAGTT
Found at i:26374 original size:21 final size:21
Alignment explanation
Indices: 26350--26390 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
26340 ACTGGCGGGC
*
26350 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTACTGAGGAAGGCGT
26371 TTTACTTACTGAGGAAGGCG
1 TTTACTTACTGAGGAAGGCG
26391 AACTCTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (21 bp):
TTTACTTACTGAGGAAGGCGT
Found at i:28853 original size:38 final size:35
Alignment explanation
Indices: 28795--28874 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
28785 CCTTATTCTC
28795 CCATTTTCTCCTTGCCCGAAACCCCAAAATCAAAACTA
1 CCATTTTCTCCTTGCCCGAAA--CC-AAATCAAAACTA
* * * *
28833 CCATTTTCTTCTTTCTCGAAACCAAATCAAAACTG
1 CCATTTTCTCCTTGCCCGAAACCAAATCAAAACTA
28868 CCATTTT
1 CCATTTT
28875 ATTTTATTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.47
36 2 0.05
38 18 0.47
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (35 bp):
CCATTTTCTCCTTGCCCGAAACCAAATCAAAACTA
Found at i:30635 original size:19 final size:19
Alignment explanation
Indices: 30606--30650 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
30596 GCGGCAAACG
30606 TTTGACCCCAAATTGAGCAT
1 TTTG-CCCCAAATTGAGCAT
30626 TTTGCCCCAAATTGAGCAT
1 TTTGCCCCAAATTGAGCAT
30645 TTTGCC
1 TTTGCC
30651 AAAGTTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (19 bp):
TTTGCCCCAAATTGAGCAT
Found at i:32013 original size:41 final size:41
Alignment explanation
Indices: 31968--32052 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
31958 GGATGAATTC
31968 GTTACTGTTTTTGAACAAAATTCAAAGCTCCTTTGATTCGA
1 GTTACTGTTTTTGAACAAAATTCAAAGCTCCTTTGATTCGA
*
32009 GTTACTGTTTTTGAACAAAATTCAAAGCTCCTTTGATTTGA
1 GTTACTGTTTTTGAACAAAATTCAAAGCTCCTTTGATTCGA
32050 GTT
1 GTT
32053 GTATGGTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (41 bp):
GTTACTGTTTTTGAACAAAATTCAAAGCTCCTTTGATTCGA
Found at i:33837 original size:26 final size:27
Alignment explanation
Indices: 33790--33841 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
33780 CAAAATCTGA
33790 TCCGAACCCGATAACCCACCCAACCCG
1 TCCGAACCCGATAACCCACCCAACCCG
*
33817 TCCGAACCCG-TAACCCGCCCAACCC
1 TCCGAACCCGATAACCCACCCAACCC
33842 AATTTGACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.27, C:0.54, G:0.12, T:0.08
Consensus pattern (27 bp):
TCCGAACCCGATAACCCACCCAACCCG
Found at i:33915 original size:32 final size:32
Alignment explanation
Indices: 33878--33977 Score: 80
Period size: 32 Copynumber: 3.1 Consensus size: 32
33868 AAACTCACCC
*
33878 GACCTG-AGACCC-GACGAACCCGTGACCCGAAT
1 GACCTGCA-ACCCAGACG-ACCCGAGACCCGAAT
*
33910 GACCTGCAACCCAGATGACCCGAGACCCGAAT
1 GACCTGCAACCCAGACGACCCGAGACCCGAAT
* * * * * *
33942 -AACTCGTAACCCAGATGACCTGAAACCTGAAT
1 GACCT-GCAACCCAGACGACCCGAGACCCGAAT
33974 GACC
1 GACC
33978 CGAGACCCGT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
31 3 0.05
32 47 0.84
33 6 0.11
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (32 bp):
GACCTGCAACCCAGACGACCCGAGACCCGAAT
Found at i:33939 original size:48 final size:48
Alignment explanation
Indices: 33878--33986 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
33868 AAACTCACCC
* * * *
33878 GACCTGAGACCCGACGAACCCGTGACCC-GAATGACCTGCAACCCAG-AT
1 GACCCGAGACCCGAAGAACCCGTAACCCAG-ATGACCTG-AAACCAGAAT
* * *
33926 GACCCGAGACCCGAATAACTCGTAACCCAGATGACCTGAAACCTGAAT
1 GACCCGAGACCCGAAGAACCCGTAACCCAGATGACCTGAAACCAGAAT
33974 GACCCGAGACCCG
1 GACCCGAGACCCG
33987 TATGACCCGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 5 0.10
48 46 0.88
49 1 0.02
ACGTcount: A:0.31, C:0.36, G:0.22, T:0.11
Consensus pattern (48 bp):
GACCCGAGACCCGAAGAACCCGTAACCCAGATGACCTGAAACCAGAAT
Found at i:33994 original size:16 final size:16
Alignment explanation
Indices: 33895--33996 Score: 68
Period size: 16 Copynumber: 6.4 Consensus size: 16
33885 GACCCGACGA
*
33895 ACCCGTGACCCGAATG
1 ACCCGAGACCCGAATG
*
33911 ACCTGCA-ACCC-AGATG
1 ACCCG-AGACCCGA-ATG
*
33927 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
*
33943 ACTCGTA-ACCC-AGATG
1 ACCCG-AGACCCGA-ATG
* * *
33959 ACCTGAAACCTGAATG
1 ACCCGAGACCCGAATG
*
33975 ACCCGAGACCCGTATG
1 ACCCGAGACCCGAATG
33991 ACCCGA
1 ACCCGA
33997 ATAACCCGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
15 4 0.06
16 58 0.89
17 3 0.05
ACGTcount: A:0.31, C:0.35, G:0.21, T:0.13
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:34139 original size:21 final size:21
Alignment explanation
Indices: 34114--34160 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
34104 TACAATTTAT
34114 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
34135 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
34156 ATTAT
1 ATTAT
34161 AAATTGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:34640 original size:16 final size:17
Alignment explanation
Indices: 34606--34650 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
34596 AACCCGCCCA
*
34606 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAATAG
34622 ACCCGAGACCCGAAT-G
1 ACCCGAGACCCGAATAG
*
34638 ACCCGAAACCCGA
1 ACCCGAGACCCGA
34651 TACCAGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.31, C:0.40, G:0.24, T:0.04
Consensus pattern (17 bp):
ACCCGAGACCCGAATAG
Found at i:34648 original size:23 final size:22
Alignment explanation
Indices: 34622--34682 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
34612 GACCCGGTAG
*
34622 ACCCGAGACCCGAATGACCCGAA
1 ACCCGAGACCCGAATAACCCG-A
* *
34645 ACCCGATACCAGAATAACCCGA
1 ACCCGAGACCCGAATAACCCGA
34667 ACCCAGATGACCCGAA
1 ACCC-GA-GACCCGAA
34683 ACTCGATGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 5 0.16
23 20 0.65
24 6 0.19
ACGTcount: A:0.38, C:0.38, G:0.18, T:0.07
Consensus pattern (22 bp):
ACCCGAGACCCGAATAACCCGA
Found at i:35236 original size:16 final size:16
Alignment explanation
Indices: 35215--35255 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
35205 AGTTGAAAGT
35215 AAAAGATCAAGTTTGA
1 AAAAGATCAAGTTTGA
35231 AAAAGATCAAGTTTGA
1 AAAAGATCAAGTTTGA
35247 AAAAGATCA
1 AAAAGATCA
35256 GACGAATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.22
Consensus pattern (16 bp):
AAAAGATCAAGTTTGA
Found at i:37091 original size:2 final size:2
Alignment explanation
Indices: 37086--37132 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
37076 ACACACATAC
37086 AT AT AT AT AT AT AT A- 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 AT AT AT AT AT
37127 ACT AT A
1 A-T AT A
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.