Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008101.1 Corchorus capsularis cultivar CVL-1 contig08122, 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: 90815
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2618 original size:33 final size:33
Alignment explanation
Indices: 2581--2743 Score: 162
Period size: 33 Copynumber: 4.9 Consensus size: 33
2571 GGCGGCTGAG
2581 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
* *
2614 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
2647 CCATGG--ATAGACCGCCC-CCTTGGGGCGGCACTA
1 CCATGGCCA-AG-CCGCCCTCC-TGGGGCGGCACTA
* *
2680 CCATGGCCAGGCCG-CCTCCCTGGGGCGGCCCTA
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTA
2713 CCATGG--ATAGACCGCCC-CCTTGGGGCGGCAC
1 CCATGGCCA-AG-CCGCCCTCC-TGGGGCGGCAC
2744 CGGTACTAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
31 2 0.02
32 11 0.10
33 88 0.81
34 7 0.06
35 1 0.01
ACGTcount: A:0.13, C:0.42, G:0.32, T:0.13
Consensus pattern (33 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTA
Found at i:2671 original size:66 final size:66
Alignment explanation
Indices: 2592--2743 Score: 288
Period size: 66 Copynumber: 2.3 Consensus size: 66
2582 CATGGCCAAG
2592 CCGCCCTCC-TGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATA
1 CCGCCC-CCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATA
2656 GA
65 GA
2658 CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG
1 CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG
2723 A
66 A
2724 CCGCCCCCTTGGGGCGGCAC
1 CCGCCCCCTTGGGGCGGCAC
2744 CGGTACTAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
65 2 0.02
66 83 0.98
ACGTcount: A:0.12, C:0.42, G:0.32, T:0.13
Consensus pattern (66 bp):
CCGCCCCCTTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCTACCATGGATAG
A
Found at i:2896 original size:32 final size:32
Alignment explanation
Indices: 2804--2887 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
2794 AAAAAGCCTT
* *
2804 GCCGCCCTAGTGGGGTGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
2836 GCCGTCCTAGT-GGGACGGCTAGCCGTGGCGGA
1 GCCGTCCTAGTGGGGA-GGCTAGCCGTGGCAGA
2868 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
2888 CCGCGTGGCT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
31 3 0.06
32 40 0.85
33 4 0.09
ACGTcount: A:0.12, C:0.27, G:0.44, T:0.17
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:4529 original size:2 final size:2
Alignment explanation
Indices: 4522--4557 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4512 CACAACACAA
* *
4522 CT CT CT CT CT CT CT GT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4558 AATTTTCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (2 bp):
CT
Found at i:7125 original size:19 final size:19
Alignment explanation
Indices: 7101--7137 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7091 TGTTTAGTAC
7101 ACCGTTTCACCACCGTTTG
1 ACCGTTTCACCACCGTTTG
7120 ACCGTTTCACCACCGTTT
1 ACCGTTTCACCACCGTTT
7138 TGGGTCTAAA
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:0.16, C:0.38, G:0.14, T:0.32
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTG
Found at i:18390 original size:28 final size:31
Alignment explanation
Indices: 18358--18438 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 31
18348 TTCCCCCAAT
18358 ATCCTG-T-AACCGC-TTTGGGTCTCGACTA
1 ATCCTGTTGAACCGCGTTTGGGTCTCGACTA
*
18386 ATCCTGAGTTGAGCCGCGTTTGGGTCTCGACTA
1 ATCCT--GTTGAACCGCGTTTGGGTCTCGACTA
*
18419 ATCCTGAGTTGAGCCGCGTT
1 ATCCT--GTTGAACCGCGTT
18439 GAACCCCCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 5 0.11
30 1 0.02
31 1 0.02
32 5 0.11
33 35 0.74
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31
Consensus pattern (31 bp):
ATCCTGTTGAACCGCGTTTGGGTCTCGACTA
Found at i:18413 original size:33 final size:33
Alignment explanation
Indices: 18367--18438 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
18357 TATCCTGTAA
18367 CCGC-TTTGGGTCTCGACTAATCCTGAGTTGAG
1 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG
18399 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG
1 CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG
18432 CCGCGTT
1 CCGCGTT
18439 GAACCCCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 4 0.10
33 35 0.90
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.31
Consensus pattern (33 bp):
CCGCGTTTGGGTCTCGACTAATCCTGAGTTGAG
Found at i:22840 original size:18 final size:18
Alignment explanation
Indices: 22817--22852 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
22807 TTTGAGTACT
22817 CTACAGGCCCAGGTGATG
1 CTACAGGCCCAGGTGATG
*
22835 CTACAGGTCCAGGTGATG
1 CTACAGGCCCAGGTGATG
22853 GTAAGCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.19
Consensus pattern (18 bp):
CTACAGGCCCAGGTGATG
Found at i:27591 original size:18 final size:18
Alignment explanation
Indices: 27558--27634 Score: 109
Period size: 19 Copynumber: 4.1 Consensus size: 18
27548 CATTCTCTAT
27558 TTTCCATCTCCAAAAATA
1 TTTCCATCTCCAAAAATA
*
27576 TCTCCATTCTCCAAAAATA
1 TTTCCA-TCTCCAAAAATA
27595 TTTTCCATCTCCAAAAATA
1 -TTTCCATCTCCAAAAATA
*
27614 TTTCCATTCTCTAAAAATA
1 TTTCCA-TCTCCAAAAATA
27633 TT
1 TT
27635 ATGCTTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
18 11 0.21
19 37 0.70
20 5 0.09
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTCCATCTCCAAAAATA
Found at i:27606 original size:38 final size:38
Alignment explanation
Indices: 27555--27634 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
27545 GAACATTCTC
27555 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA
1 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA
* *
27593 TATTTTCCATCTCCAAAAATATTTCCATTCTCTAAAAA
1 TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA
27631 TATT
1 TATT
27635 ATGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (38 bp):
TATTTTCCATCTCCAAAAATATCTCCATTCTCCAAAAA
Found at i:39944 original size:70 final size:70
Alignment explanation
Indices: 39862--40094 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
39852 TTGTTTAGGT
* * *
39862 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
39926 ATTTTA
65 ATTTTA
*
39932 TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-TA--TA
*
39997 TTATATTTTACCA
62 AT-TATTTT---A
* * *
40010 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
40075 TTATA
66 TTTTA
*
40080 TTTTACAATTTTACT
1 TTTTACTATTTTACT
40095 ATTTTAGTTA
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
70 62 0.44
71 5 0.04
72 2 0.01
73 5 0.04
74 5 0.04
75 6 0.04
76 2 0.01
77 2 0.01
78 53 0.37
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:39944 original size:78 final size:77
Alignment explanation
Indices: 39862--40100 Score: 332
Period size: 78 Copynumber: 3.2 Consensus size: 77
39852 TTGTTTAGGT
* * *
39862 TTTTA-TAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
39922 AAT-TATTTT--A
65 ATTATATTTTACA
* *
39932 TTTTACTATTTTACTCAACTAAAAACTATATTTTTATATAATTAAATCTAATATCCTTATAGCTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
39997 TTATATTTTACCA
66 TTATATTTTA-CA
*
40010 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
40075 TTATATTTTACAA
66 TTATATTTTAC-A
40088 TTTTACTATTTTA
1 TTTTACTATTTTA
40101 GTTAAAAAAA
Statistics
Matches: 150, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
70 47 0.31
71 5 0.03
72 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.58
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:41976 original size:5 final size:5
Alignment explanation
Indices: 41966--42005 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
41956 ACTCTGCAGC
41966 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA
1 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA
42006 GCTTCCATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (5 bp):
ACAGA
Found at i:50111 original size:2 final size:2
Alignment explanation
Indices: 50058--50099 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
50048 CCAAACCAAT
* *
50058 TA TA CA TA TA TA T- TG TA 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 TA TA TA TA
50099 T
1 T
50100 GTACACATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56770 original size:27 final size:28
Alignment explanation
Indices: 56740--56792 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
56730 CGGTATTCAG
* *
56740 GACTTTGTCTTGACTAATCC-GATCCAA
1 GACTTTGCCCTGACTAATCCGGATCCAA
56767 GACTTTGCCCTGACTAATCCGGATCC
1 GACTTTGCCCTGACTAATCCGGATCC
56793 GACCCGCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (28 bp):
GACTTTGCCCTGACTAATCCGGATCCAA
Found at i:58815 original size:138 final size:138
Alignment explanation
Indices: 58586--58845 Score: 448
Period size: 138 Copynumber: 1.9 Consensus size: 138
58576 CTAGGGGCAG
** *
58586 ATCAATCAGAAGTGAACCGCTCATGAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA
1 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA
* * * *
58651 TATATGTCTAATGCCTTATAATCTCAAATTCTCATTTCATATTATCTCAAGACAACATCCGATCT
66 TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACATCCGATCT
58716 AAAGGCGC
131 AAAGGCGC
58724 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA
1 ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA
*
58789 TACATGCCTAATGCCTCATAATCTCAAATTCTCGTTTCATATTAACTCAAGACAACA
66 TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACA
58846 AAGTTCATAC
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 114 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.26
Consensus pattern (138 bp):
ATCAATCAGAAGTGAAAAGCTCATAAACATTGTAGATAAAGGACAAGCACACCATCAACCATTCA
TACATGCCTAATGCCTCATAATCTCAAATTCTCATTTCATATTAACTCAAGACAACATCCGATCT
AAAGGCGC
Found at i:63836 original size:51 final size:51
Alignment explanation
Indices: 63776--63878 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
63766 TCTTTCTGCC
63776 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA
1 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA
63827 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA
1 TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA
63878 T
1 T
63879 AATTGAATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (51 bp):
TTTCCCCTGCAAGTAAACTGAAGATGATTAAAGTTCAATCTATCTTTGGCA
Found at i:66579 original size:5 final size:5
Alignment explanation
Indices: 66569--66602 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
66559 GTGAAATTCT
66569 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
66603 GAATGAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:67387 original size:94 final size:92
Alignment explanation
Indices: 67129--67396 Score: 321
Period size: 91 Copynumber: 2.9 Consensus size: 92
67119 CCACGTGTGT
* * * *
67129 CTAGAAACATGGTCAACTATCGACTATCAAGAAATAAACCCTAAGTCGACATGGCATTTCCTAGT
1 CTAGAAACATGGCCAACTATC-ACTATCAAGAAATAAACACTAAGTTGACATGGCATTTTCTAGT
* *
67194 CGCATAGCATGCTGATGTTGCCACGTGC
65 CACATAGCATGCTGATGTTGCCACGTAC
* *
67222 CAAGAAACGTGGCCAA--AT---TATCAAGAAATAAACCTCACTCAAGTTGACATGGCATTTTCT
1 CTAGAAACATGGCCAACTATCACTATCAAGAAATAAA---CACT-AAGTTGACATGGCATTTTCT
*
67282 AGTCACATAGCATGTTGATGTTGCCACGTAC
62 AGTCACATAGCATGCTGATGTTGCCACGTAC
* * *
67313 CTAGAAACATAGCCAAACTATCACTATCAGGAAATAAACACTAAAGTTGACGTGGCATTTTCTAG
1 CTAGAAACATGGCC-AACTATCACTATCAAGAAATAAACACT-AAGTTGACATGGCATTTTCTAG
*
67378 TCACATAGCAAGCTGATGT
64 TCACATAGCATGCTGATGT
67397 GGACCTTTTA
Statistics
Matches: 148, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
87 14 0.09
90 3 0.02
91 59 0.40
92 2 0.01
93 13 0.09
94 44 0.30
97 13 0.09
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.25
Consensus pattern (92 bp):
CTAGAAACATGGCCAACTATCACTATCAAGAAATAAACACTAAGTTGACATGGCATTTTCTAGTC
ACATAGCATGCTGATGTTGCCACGTAC
Done.