Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015041.1 Corchorus capsularis cultivar CVL-1 contig15062, 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: 78816
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3260 original size:13 final size:13
Alignment explanation
Indices: 3242--3266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3232 GTCCTTCTAG
3242 AGATATAAATGTT
1 AGATATAAATGTT
3255 AGATATAAATGT
1 AGATATAAATGT
3267 ATCTATCAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (13 bp):
AGATATAAATGTT
Found at i:7496 original size:32 final size:31
Alignment explanation
Indices: 7418--7503 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
7408 CGTCAGCGTC
* * *
7418 TTGGTCTGACGTGGCCTTACCACGTGGTATT
1 TTGGTCCGACGTGGCATTACCACGTGGCATT
* * *
7449 TTGGTCCAATGTGGCATTACCATGTGGCATTT
1 TTGGTCCGACGTGGCATTACCACGTGGCA-TT
* *
7481 TTGGTCCGACATGGCATTGCCAC
1 TTGGTCCGACGTGGCATTACCAC
7504 ATCAGCAATA
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.53
32 20 0.47
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (31 bp):
TTGGTCCGACGTGGCATTACCACGTGGCATT
Found at i:8338 original size:30 final size:30
Alignment explanation
Indices: 8302--8363 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
8292 GATGGCAAAC
8302 GTTGAGGAATCCTAATTCGTTTACTGTAAT
1 GTTGAGGAATCCTAATTCGTTTACTGTAAT
8332 GTTGAGGAATCCTAATTCGTTTACTGTAAT
1 GTTGAGGAATCCTAATTCGTTTACTGTAAT
8362 GT
1 GT
8364 GTGGTCCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (30 bp):
GTTGAGGAATCCTAATTCGTTTACTGTAAT
Found at i:21182 original size:2 final size:2
Alignment explanation
Indices: 21175--21213 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
21165 TAGTCCTCAT
* * *
21175 TA TA TA TA TA AA TC TA TA AA 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 TA TA TA TA TA T
21214 CTTGAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:23097 original size:2 final size:2
Alignment explanation
Indices: 23090--23117 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23080 AAATAATGGA
23090 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
23118 GTACTTACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24980 original size:108 final size:107
Alignment explanation
Indices: 24795--25092 Score: 430
Period size: 108 Copynumber: 2.8 Consensus size: 107
24785 TTAGTCATAG
* * *
24795 TAATTT-TTATTAT-AGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTATCCCCAA
1 TAATTTATTGTTATAAG-GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACTCCAA
24858 ATTAAAATTATATTTTTATTTTAAGGGTAAATTTCAAAATTAA
65 ATTAAAATTATATTTTTATTTTAAGGGTAAATTTCAAAATTAA
*
24901 TAATTTATTGTTATAAGGTTTTAGAAATAAAATACAAAACTAAATTTCACTAAGTTTAACTCCAA
1 TAATTTATTGTTATAAGGTTTTAGAAATAAAATATAAAACT-AATTTCACTAAGTTTAACTCCAA
*
24966 ATTAAAAATT-TATTTTTATTTTAAGGGTAAATTTCATAATTAA
65 ATT-AAAATTATATTTTTATTTTAAGGGTAAATTTCAAAATTAA
* * *
25009 TAA--TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTT-AGTCCAAA
1 TAATTTATTGTTATAAGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACTCCAAA
* *
25070 TTAAAATTAAAATTTTATTTTAA
66 TTAAAATTATATTTTTATTTTAA
25093 AGGTTAGAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
102 6 0.03
103 21 0.12
104 12 0.07
105 2 0.01
106 39 0.22
107 29 0.16
108 61 0.35
109 6 0.03
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (107 bp):
TAATTTATTGTTATAAGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAACTCCAAA
TTAAAATTATATTTTTATTTTAAGGGTAAATTTCAAAATTAA
Found at i:25130 original size:106 final size:102
Alignment explanation
Indices: 24804--25118 Score: 311
Period size: 106 Copynumber: 3.0 Consensus size: 102
24794 GTAATTTTTA
*
24804 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTATCCCCAAATTAAAATTAT
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAT--CCAAATTAAAATTAT
*
24869 ATTTTTATTTTAAGGGTAAATTTCAAAATTAATAA-TTT--ATTG
64 ATTTTTATTTTAA-GGTAGA----AAAATTAA-AATTTTAAATTG
* *
24911 TTATAAGGTTTTAGAAATAAAATACAAAACTAAATTTCACTAAGTTTAACTCCAAATTAAAAATT
1 TTATAGGGTTTTAGAAATAAAATATAAAACT-AATTTCACTAAGTTT-A-TCCAAATT-AAAATT
* * * *
24976 -TATTTTTATTTTAAGG--GTAAATTTCATAATTAATAATATTG
62 ATATTTTTATTTTAAGGTAGAAAAATT-AAAATT-TTAA-ATTG
* *
25017 TTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAGTCCAAATTAAAATTAAA
1 TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTA-TCCAAATTAAAATTATA
*
25081 ATTTTATTTTAAAGGTTAGAAAAATTAAAATTTGTAAA
65 TTTTTATTTT-AAGG-TAGAAAAATTAAAATTT-TAAA
25119 GGGTGTATAG
Statistics
Matches: 174, Mismatches: 18, Indels: 34
0.77 0.08 0.15
Matches are distributed among these distances:
101 7 0.04
102 8 0.05
103 20 0.11
104 16 0.09
105 3 0.02
106 40 0.23
107 36 0.21
108 36 0.21
109 7 0.04
110 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (102 bp):
TTATAGGGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTATCCAAATTAAAATTATAT
TTTTATTTTAAGGTAGAAAAATTAAAATTTTAAATTG
Found at i:25774 original size:16 final size:16
Alignment explanation
Indices: 25753--25785 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25743 ATAGTAATCA
25753 AAGAATACTCCATTGT
1 AAGAATACTCCATTGT
25769 AAGAATACTCCATTGT
1 AAGAATACTCCATTGT
25785 A
1 A
25786 GAGATTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (16 bp):
AAGAATACTCCATTGT
Found at i:34680 original size:22 final size:22
Alignment explanation
Indices: 34655--34697 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
34645 CCATTAAGGC
* * *
34655 TTGGGTTAGTCCAAGTAAGAAA
1 TTGGGTGAGCCCAAGCAAGAAA
34677 TTGGGTGAGCCCAAGCAAGAA
1 TTGGGTGAGCCCAAGCAAGAA
34698 GTATAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21
Consensus pattern (22 bp):
TTGGGTGAGCCCAAGCAAGAAA
Found at i:37947 original size:21 final size:22
Alignment explanation
Indices: 37914--37959 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
37904 AAAAATTATA
* **
37914 AAAATGGGGGGCGGTATTTAGC
1 AAAATGGGAGGCGGTAAATAGC
37936 AAAA-GGGAGGCGGTAAATAGC
1 AAAATGGGAGGCGGTAAATAGC
37957 AAA
1 AAA
37960 CCCCTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.39, C:0.09, G:0.37, T:0.15
Consensus pattern (22 bp):
AAAATGGGAGGCGGTAAATAGC
Found at i:38697 original size:34 final size:34
Alignment explanation
Indices: 38654--38722 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
38644 TAATCTATGT
38654 AAAATTATTTGATACACCATTAGTGGTATTTAGC
1 AAAATTATTTGATACACCATTAGTGGTATTTAGC
*
38688 AAAATTATTTGGTACACCATTAGTGGTATTTAGC
1 AAAATTATTTGATACACCATTAGTGGTATTTAGC
38722 A
1 A
38723 GACCATCCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.38
Consensus pattern (34 bp):
AAAATTATTTGATACACCATTAGTGGTATTTAGC
Found at i:43896 original size:14 final size:16
Alignment explanation
Indices: 43879--43914 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
43869 ATATAGTGAG
*
43879 TATAAAATTTCATCTA
1 TATAGAATTTCATCTA
43895 TATTAGAATTTCATCTA
1 TA-TAGAATTTCATCTA
43912 TAT
1 TAT
43915 TAATGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (16 bp):
TATAGAATTTCATCTA
Found at i:43906 original size:17 final size:17
Alignment explanation
Indices: 43884--43916 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
43874 GTGAGTATAA
43884 AATTTCATCTATATTAG
1 AATTTCATCTATATTAG
43901 AATTTCATCTATATTA
1 AATTTCATCTATATTA
43917 ATGTATAATA
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:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (17 bp):
AATTTCATCTATATTAG
Found at i:44734 original size:2 final size:2
Alignment explanation
Indices: 44727--44756 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44717 GTTAAAGATA
44727 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
44757 TAAACCGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50643 original size:13 final size:13
Alignment explanation
Indices: 50625--50652 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
50615 CTTTCTATCA
50625 AAATTGCAATTTT
1 AAATTGCAATTTT
50638 AAATTGCAATTTT
1 AAATTGCAATTTT
50651 AA
1 AA
50653 TAACTGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
AAATTGCAATTTT
Found at i:61362 original size:1 final size:1
Alignment explanation
Indices: 61356--61400 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
61346 TCAGGTTTAG
61356 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
61401 ATCTTCCTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:76275 original size:180 final size:181
Alignment explanation
Indices: 75954--76279 Score: 453
Period size: 180 Copynumber: 1.8 Consensus size: 181
75944 AAATCTCCTA
* * *
75954 ATTATTTATTTCTTTCCTTTTTAACTAATATATCCATTTTAGACATTTTATCATTCTACCACATT
1 ATTATTTATTTCATTCCTTTTTAACTAACATATCCATTTTAGACATTTTATCATTCAACCACATT
* * * *
76019 TTCTAACAGCAATACCAAACATTATATATATTTTTAAACTGTAATTTCAAAAAGCACTTCTTTAA
66 TTCTAACAGCAATACCAAACATTATATAAATTTTTAAACCGTAATTTAAAAAAGCACTTCTTCAA
* *
76084 ATAAGTTTTTTCAAACTTCAACTTCAATGTCAAACTAAGCCTTTGCGTTTC
131 AAAACTTTTTTCAAACTTCAACTTCAATGTCAAACTAAGCCTTTGCGTTTC
* * *
76135 ATTATTT-TTCTCATTCCTTTTTAACTAGCATATCCTTTTTAGACATTTTATCCTTCAACC-CAA
1 ATTATTTATT-TCATTCCTTTTTAACTAACATATCCATTTTAGACATTTTATCATTCAACCAC-A
* * **
76198 TTTT-TCACAGCAATACCAAACATTATTTAAATTTTTCTACCGTAATTTAAAAAAGCACTTC-TC
64 TTTTCTAACAGCAATACCAAACATTATATAAATTTTTAAACCGTAATTTAAAAAAGCACTTCTTC
76261 AAAAACACTTTTTTCAAAC
129 AAAAA-ACTTTTTTCAAAC
76280 CAAATTTTTT
Statistics
Matches: 126, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
179 5 0.04
180 65 0.52
181 56 0.44
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.42
Consensus pattern (181 bp):
ATTATTTATTTCATTCCTTTTTAACTAACATATCCATTTTAGACATTTTATCATTCAACCACATT
TTCTAACAGCAATACCAAACATTATATAAATTTTTAAACCGTAATTTAAAAAAGCACTTCTTCAA
AAAACTTTTTTCAAACTTCAACTTCAATGTCAAACTAAGCCTTTGCGTTTC
Found at i:76677 original size:2 final size:2
Alignment explanation
Indices: 76672--76702 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76662 ACACAGATAG
76672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76703 CTGAACATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78559 original size:2 final size:2
Alignment explanation
Indices: 78552--78583 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
78542 TACTATGCTA
78552 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
78584 GTATTTTGGA
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
Done.