Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013314.1 Corchorus capsularis cultivar CVL-1 contig13335, 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: 29982
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:749 original size:70 final size:71
Alignment explanation
Indices: 666--898 Score: 310
Period size: 70 Copynumber: 3.2 Consensus size: 71
656 TAACTAAAAT
* *
666 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
730 TAGTTG
66 TAGTTG
*
736 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
801 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
814 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
878 TAGTTG
66 TAGTTG
884 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
899 ATCTGACAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
70 71 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 63 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:749 original size:78 final size:77
Alignment explanation
Indices: 660--898 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
650 TTTTTTTAAC
*
660 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
725 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
738 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
803 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
816 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
874 TTTTTAGTTGAG
66 TTTTTAGTTGAG
886 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
899 ATCTGACAAT
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:2235 original size:25 final size:25
Alignment explanation
Indices: 2201--2251 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2191 CAATATGGGC
2201 ACTTTAGGCCAAACAAAAGGGGAAA
1 ACTTTAGGCCAAACAAAAGGGGAAA
*
2226 ACTTTAGGCCAAACAATAGGGGAAA
1 ACTTTAGGCCAAACAAAAGGGGAAA
2251 A
1 A
2252 GAGCTGAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.14
Consensus pattern (25 bp):
ACTTTAGGCCAAACAAAAGGGGAAA
Found at i:3752 original size:142 final size:142
Alignment explanation
Indices: 3496--3752 Score: 379
Period size: 142 Copynumber: 1.8 Consensus size: 142
3486 TTTAGAGAGC
* *
3496 TAACTAGTGTACCTTAAGCATCTAATTATTTCTGCCGAACGAGCTTCCTTGTTTTCATAAGGGTA
1 TAACTAGTGTACCTCAAGCATCTAATTATTTCTGCAGAACGAGCTTCCTTGTTTTCATAAGGGTA
**
3561 ATCAACAACAAAAGTATTTATTGAGTCCTTTTTTACTCTCGTTTTGGTTCTGATCCTTTTTGTGG
66 ATCAACAACAAAAGTATTTATTGAGTAATTTTTTACTCTCGTTTTGGTTCTGATCCTTTTTGTGG
3626 AGAATGACAACT
131 AGAATGACAACT
* * * * * *
3638 TAACTAGTGTTCCTCAAGCATCTACTTATTTCTGCAGAATGAGCTTCCTTGTTTTGATTAGGGTG
1 TAACTAGTGTACCTCAAGCATCTAATTATTTCTGCAGAACGAGCTTCCTTGTTTTCATAAGGGTA
*** * *
3703 ATCAACAATTTAAGTATTTATTGAGTAATTTTTTACTGTGGTTTTGGTTC
66 ATCAACAACAAAAGTATTTATTGAGTAATTTTTTACTCTCGTTTTGGTTC
3753 ATAATGATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
142 100 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (142 bp):
TAACTAGTGTACCTCAAGCATCTAATTATTTCTGCAGAACGAGCTTCCTTGTTTTCATAAGGGTA
ATCAACAACAAAAGTATTTATTGAGTAATTTTTTACTCTCGTTTTGGTTCTGATCCTTTTTGTGG
AGAATGACAACT
Found at i:12054 original size:9 final size:9
Alignment explanation
Indices: 12040--12069 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
12030 TTATGGTTCG
12040 TTAAAATCA
1 TTAAAATCA
12049 TTAAAATCA
1 TTAAAATCA
12058 TTTAAAATCA
1 -TTAAAATCA
12068 TT
1 TT
12070 TATTTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAAATCA
Found at i:12064 original size:10 final size:10
Alignment explanation
Indices: 12040--12071 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
12030 TTATGGTTCG
12040 TTAAAATCA-
1 TTAAAATCAT
12049 TTAAAATCAT
1 TTAAAATCAT
12059 TTAAAATCAT
1 TTAAAATCAT
12069 TTA
1 TTA
12072 TTTGTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAAATCAT
Found at i:16340 original size:53 final size:53
Alignment explanation
Indices: 16233--16351 Score: 161
Period size: 53 Copynumber: 2.2 Consensus size: 53
16223 ATTTCAACCC
* **
16233 AAATCAGACAAATACCCATGAACCCAAATCCTTTCAGCTTTAAAGCAAACAAGGA
1 AAATCA-AC-AATACCCATGAACCCAAATCCTCTCAGCTAAAAAGCAAACAAGGA
16288 AAATCAACAATCACCCATGAACCCAAATCC-CTCAGC-AAACAAGCAAACAAGGA
1 AAATCAACAAT-ACCCATGAACCCAAATCCTCTCAGCTAAA-AAGCAAACAAGGA
16341 AAATCAACAAT
1 AAATCAACAAT
16352 TTCTTCCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
52 1 0.02
53 32 0.54
54 20 0.34
55 6 0.10
ACGTcount: A:0.49, C:0.28, G:0.09, T:0.14
Consensus pattern (53 bp):
AAATCAACAATACCCATGAACCCAAATCCTCTCAGCTAAAAAGCAAACAAGGA
Found at i:16687 original size:3 final size:3
Alignment explanation
Indices: 16679--16711 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
16669 AGGGGAAGGG
*
16679 AGA AGA AGA AGA AGA AGA AGA AGA ATA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
16712 TAGTGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:16806 original size:15 final size:15
Alignment explanation
Indices: 16777--16815 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16767 TATTAATGTA
16777 TTTTTC-TTT-TTTT
1 TTTTTCGTTTGTTTT
16790 TTTTTCGTTTGTTTT
1 TTTTTCGTTTGTTTT
*
16805 TTTTTTGTTTG
1 TTTTTCGTTTG
16816 AATTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 3 0.13
15 14 0.61
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (15 bp):
TTTTTCGTTTGTTTT
Found at i:16821 original size:16 final size:16
Alignment explanation
Indices: 16786--16824 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
16776 ATTTTTCTTT
16786 TTTTTTTTTCGTTTG-
1 TTTTTTTTTCGTTTGA
*
16801 TTTTTTTTTTGTTTGAA
1 TTTTTTTTTCGTTTG-A
16818 TTTTTTT
1 TTTTTTT
16825 GAATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
17 7 0.33
ACGTcount: A:0.05, C:0.03, G:0.10, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTCGTTTGA
Found at i:17922 original size:65 final size:65
Alignment explanation
Indices: 17818--18012 Score: 284
Period size: 65 Copynumber: 3.0 Consensus size: 65
17808 AATAATTTTG
* * * **
17818 AGTGCCTACCCCAATTGGATTAAACCATGTTAAGTGTCCATTGGGTGCATATAAAACATTAGTAA
1 AGTGCCCACCTCAATTGGATTAAACCATGTTAAATGTCCATTGGGCCCATATAAAACATTAGTAA
*
17883 AGTGCCCACCTCAATTGGATTAAACCATGTTAAATGTCCATTGGGCCCATATTAAACATTAGTAA
1 AGTGCCCACCTCAATTGGATTAAACCATGTTAAATGTCCATTGGGCCCATATAAAACATTAGTAA
* ** * *
17948 AGTGCTCATTTCAATTGGATTAAACCATGTTAAATGTCCATT-GACCCATATGAAACATTAGTAA
1 AGTGCCCACCTCAATTGGATTAAACCATGTTAAATGTCCATTGGGCCCATATAAAACATTAGTAA
18012 A
1 A
18013 AATATGTGTA
Statistics
Matches: 119, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 21 0.18
65 98 0.82
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (65 bp):
AGTGCCCACCTCAATTGGATTAAACCATGTTAAATGTCCATTGGGCCCATATAAAACATTAGTAA
Found at i:19180 original size:30 final size:28
Alignment explanation
Indices: 19146--19212 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 28
19136 AATAAATTAC
*
19146 TAATTATAAATTTATTATAAATTATTCATA
1 TAATTATAAATTT-TAATAAA-TATTCATA
* *
19176 TAATTAATTTAATTTTAATAAATATTCCTA
1 TAATT-A-TAAATTTTAATAAATATTCATA
19206 TAATTAT
1 TAATTAT
19213 TGTTTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 17 0.53
31 7 0.22
32 6 0.19
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TAATTATAAATTTTAATAAATATTCATA
Found at i:22036 original size:20 final size:20
Alignment explanation
Indices: 22011--22051 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
22001 ATGAGATGTC
**
22011 TTAAAAACCTTCTTAACATA
1 TTAAAAACCCACTTAACATA
22031 TTAAAAACCCACTTAACATA
1 TTAAAAACCCACTTAACATA
22051 T
1 T
22052 CAATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAAACCCACTTAACATA
Found at i:22091 original size:73 final size:72
Alignment explanation
Indices: 22000--22137 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 72
21990 GGGTTACCAA
*
22000 AATGAGATGTCTTAAAAAC-CTTCTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAG
1 AATGAGATGTCTTAAAAACAC-ACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAG
22064 GAAACCTT
65 GAAACCTT
* * *
22072 AATGAAGATGTCTTAAAAACACACTTAATATATTTAAAACCCACTTAATATATCAATAATTAAAG
1 AATG-AGATGTCTTAAAAACACACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAG
22137 G
65 G
22138 GAATCTCAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
72 4 0.07
73 55 0.92
74 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (72 bp):
AATGAGATGTCTTAAAAACACACTTAACATATTAAAAACCCACTTAACATATCAATAATTAAAGG
AAACCTT
Found at i:22116 original size:20 final size:20
Alignment explanation
Indices: 22087--22124 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
22077 AGATGTCTTA
22087 AAAACACACTTAATATATTT
1 AAAACACACTTAATATATTT
*
22107 AAAACCCACTTAATATAT
1 AAAACACACTTAATATAT
22125 CAATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAACACACTTAATATATTT
Found at i:22401 original size:16 final size:16
Alignment explanation
Indices: 22347--22402 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
22337 CGGGTTAAAT
22347 TCTCGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
* * ** *
22363 TTTTGGGTCAACCGTG
1 TCTCGGGTCATTCGGG
*
22379 TCACGGGTCATTCGGG
1 TCTCGGGTCATTCGGG
22395 TCTCGGGT
1 TCTCGGGT
22403 TCGGACGGGT
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.23, G:0.36, T:0.32
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:26836 original size:24 final size:24
Alignment explanation
Indices: 26795--26845 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
26785 AAACTTTAAT
** * *
26795 AATTTTATATTATTAAAACAAATA
1 AATTTTATATTACCAAAAAAAAAA
*
26819 AATTTTCTATTACCAAAAAAAAAA
1 AATTTTATATTACCAAAAAAAAAA
26843 AAT
1 AAT
26846 ACAAATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTTTATATTACCAAAAAAAAAA
Done.