Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009712.1 Corchorus capsularis cultivar CVL-1 contig09733, 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: 68463
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--183 Score: 132
Period size: 31 Copynumber: 6.0 Consensus size: 31
*
1 ATTTTCGATAACGTTATGCCCTTATTTGAGC
1 ATTTTCGATAACGTTAGGCCCTTATTTGAGC
32 ATTTTCGATAACGTTAGGCCCTTATTTG-GCC
1 ATTTTCGATAACGTTAGGCCCTTATTTGAG-C
** * * *
63 AAATT--A-AAAGACTGGGCCCTTATTTGAGC
1 ATTTTCGATAACG-TTAGGCCCTTATTTGAGC
*
92 ATTTTCGATAACATTAGGCCCTTATTTG-GCC
1 ATTTTCGATAACGTTAGGCCCTTATTTGAG-C
** * **
123 AAATT--A-AAAGATCGGGCCCTTATTTGAGC
1 ATTTTCGATAACG-TTAGGCCCTTATTTGAGC
* *
152 ATTTTGGCA-AATGTTAGGCCCTTATTTGAGC
1 ATTTTCG-ATAACGTTAGGCCCTTATTTGAGC
183 A
1 A
184 ATTAGCCTTG
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.04
29 36 0.31
30 4 0.03
31 66 0.56
32 6 0.05
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (31 bp):
ATTTTCGATAACGTTAGGCCCTTATTTGAGC
Found at i:87 original size:29 final size:28
Alignment explanation
Indices: 48--148 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 28
38 GATAACGTTA
48 GGCCCTTATTTGGCCAAATTAAAAGACTG
1 GGCCCTTATTTGGCCAAATTAAAAGA-TG
** * * *
77 GGCCCTTATTTGAG-CATTTTCGATAACATTA
1 GGCCCTTATTTG-GCCAAATT--AAAAGA-TG
108 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGAT-G
137 GGCCCTTATTTG
1 GGCCCTTATTTG
149 AGCATTTTGG
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
28 1 0.02
29 32 0.57
30 2 0.04
31 21 0.38
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (28 bp):
GGCCCTTATTTGGCCAAATTAAAAGATG
Found at i:111 original size:60 final size:60
Alignment explanation
Indices: 18--179 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
8 ATAACGTTAT
18 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGA-CTGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC-GG
*
78 GCCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
* *
138 GCCCTTATTTGAGCATTTTGGCA-AATGTTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
180 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
60 94 0.98
61 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:2696 original size:54 final size:54
Alignment explanation
Indices: 2610--2750 Score: 255
Period size: 54 Copynumber: 2.6 Consensus size: 54
2600 TAAAAACAAA
2610 TAGCTTTTCTTTCAAATATTGAAATAGAGGAATCTCTTTTCTCTTAATTCTTGT
1 TAGCTTTTCTTTCAAATATTGAAATAGAGGAATCTCTTTTCTCTTAATTCTTGT
* *
2664 TGGGTTTTCTTTCAAATATTGAAATAGAGGAATCTCTTTTCTCTTAATTCTTGT
1 TAGCTTTTCTTTCAAATATTGAAATAGAGGAATCTCTTTTCTCTTAATTCTTGT
*
2718 TAGCTTTTATTTCAAATATTGAAATAGAGGAAT
1 TAGCTTTTCTTTCAAATATTGAAATAGAGGAAT
2751 TATTAGAGAC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (54 bp):
TAGCTTTTCTTTCAAATATTGAAATAGAGGAATCTCTTTTCTCTTAATTCTTGT
Found at i:4919 original size:1 final size:1
Alignment explanation
Indices: 4876--4900 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4866 AAGAATCACG
4876 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4901 GACAATCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16362 original size:31 final size:31
Alignment explanation
Indices: 16284--16402 Score: 134
Period size: 31 Copynumber: 3.9 Consensus size: 31
16274 ACGGTGCCCG
* *
16284 ACGTGGCTTGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* * *
16315 ACATGTCACGCCACATGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
* ** *
16346 ACGTGGCATGCGACATGTTTCAAAATGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGAC
16377 ACGTGGCATGCCAC--GTACACAAAAAG
1 ACGTGGCATGCCACATGTAC-CAAAAAG
16403 ATACGTGCCA
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
29 2 0.03
30 6 0.08
31 63 0.89
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (31 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGAC
Found at i:21849 original size:31 final size:31
Alignment explanation
Indices: 21786--21884 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
21776 TTTTGTGCAC
* * **
21786 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
21817 GTGGCATGCCACGTGTCACTTTTTGGTGCAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * *
21848 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
21879 GTGGCA
1 GTGGCA
21885 CGACTTTTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:30921 original size:72 final size:71
Alignment explanation
Indices: 30804--30950 Score: 204
Period size: 72 Copynumber: 2.1 Consensus size: 71
30794 TTAATTATAC
* * *
30804 AAATTAAGAAAATCAGAATAATAGTTGATCCACGAAACCGCAATTTTACATCCAACAGACCCCAA
1 AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAACGCAATTTTACATCCAACAGA-CCCAA
30869 AACTAAT
65 AACTAAT
* * * * * *
30876 AAATTAAGAAAATTAAAATAGTACTTGATCCACGAAAATGTAATTTTACATCCAATAGACCCTAA
1 AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAACGCAATTTTACATCCAACAGACCCAAA
30941 ACTAAT
66 ACTAAT
30947 AAAT
1 AAAT
30951 AGAATTATAA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 15 0.23
72 51 0.77
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (71 bp):
AAATTAAGAAAATCAAAATAATACTTGATCCACGAAAACGCAATTTTACATCCAACAGACCCAAA
ACTAAT
Found at i:48002 original size:12 final size:12
Alignment explanation
Indices: 47985--48028 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
47975 TTTAATACAG
*
47985 GTATCGATGGAT
1 GTATCGACGGAT
47997 GTATCGACGGAT
1 GTATCGACGGAT
48009 GTATCGAACGGAT
1 GTATCG-ACGGAT
*
48022 ATATCGA
1 GTATCGA
48029 AGTATTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (12 bp):
GTATCGACGGAT
Found at i:48021 original size:13 final size:13
Alignment explanation
Indices: 47993--48029 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
47983 AGGTATCGAT
47993 GGATGTATCG-AC
1 GGATGTATCGAAC
48005 GGATGTATCGAAC
1 GGATGTATCGAAC
*
48018 GGATATATCGAA
1 GGATGTATCGAA
48030 GTATTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (13 bp):
GGATGTATCGAAC
Found at i:50097 original size:20 final size:19
Alignment explanation
Indices: 50062--50119 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
50052 TGGATATTTA
50062 CGGATATATCGA--GATAT
1 CGGATATATCGACGGATAT
*
50079 C-GATAAATATCGACGGATACA
1 CGGAT--ATATCGACGGATA-T
50100 CGGATATATCGACGGATAT
1 CGGATATATCGACGGATAT
50119 C
1 C
50120 CCGTGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 7 0.21
19 1 0.03
20 17 0.52
21 1 0.03
22 3 0.09
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CGGATATATCGACGGATAT
Found at i:50186 original size:12 final size:12
Alignment explanation
Indices: 50169--50207 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
50159 GTACAGATAT
50169 CGGATATATCGA
1 CGGATATATCGA
50181 CGGATATATCGA
1 CGGATATATCGA
50193 -GG---TATCGA
1 CGGATATATCGA
50201 CGGATAT
1 CGGATAT
50208 TTAATAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:54463 original size:184 final size:183
Alignment explanation
Indices: 53918--54465 Score: 621
Period size: 184 Copynumber: 3.0 Consensus size: 183
53908 GTTATTTTGA
* * * * *
53918 GGTGTATAAATATGAAAATCTTATTTTTCAATGTTTTTTACAGTGTTATTATGAATATCACCATT
1 GGTGTAAAAATACGAAAATCTTTTTTTTCAATGTTTTTGACAGTGTTATTATGAATATCACCTTT
* ** * * *
53983 ATCAGATTCACAATTAAGAACAAAGTCTACGTTTGCACAAGCACAATTTATATCACTGGTGACGA
66 ATCAGATTCAAAATTAAGAACAAAGGATACGTTTGCACAAACACAATCTATATCACAGGTGACGA
* * * * * * ** * *
54048 TCACGGTAGCCTGCAATTTCATAAATCAAGGTTCAAACACCCTATCATGTTTG
131 TCACGGTCGCCTGCAATTTCAAAAATCAAGGTTCAGACGCCTTGTTGTGTGTC
* * * *
54101 GGTGTAATAATATGAAAATCTCTTTTTTTCAATGTTTTTGACAATTTTATTATGAATATCACCTT
1 GGTGTAAAAATACGAAAATCT-TTTTTTTCAATGTTTTTGACAGTGTTATTATGAATATCACCTT
* * *
54166 TA-CGAGATTCAAAATTAAGAACAAATGATACATTTGCACAAACACAATCTATATCACGGGTGAC
65 TATC-AGATTCAAAATTAAGAACAAAGGATACGTTTGCACAAACACAATCTATATCACAGGTGAC
* * *
54230 GCTCACGGTCACCTGCAATTTCAAAAATCAAGGTTTAGACGCCTTGTTGTGTGTC
129 GATCACGGTCGCCTGCAATTTCAAAAATCAAGGTTCAGACGCCTTGTTGTGTGTC
* ** *
54285 GGTGTAAAAATCCGAAAATCTTGTTTTTTGGATGTTTCTGACAGTGTTATTATGAATATCACCTT
1 GGTGTAAAAATACGAAAATCTT-TTTTTTCAATGTTTTTGACAGTGTTATTATGAATATCACCTT
* ** * * * *
54350 TATCAGATCCGTATTTAAAAACAAAGGATACGTTTGCACAAACACAATCTATATCACAGGCGATG
65 TATCAGATTCAAAATTAAGAACAAAGGATACGTTTGCACAAACACAATCTATATCACAGGTGACG
* * * ** * *
54415 ATCGCGGTCGCCTGTAATTTCAGAGGTCAGGGTTCAGACGCTTTGTTGTGT
130 ATCACGGTCGCCTGCAATTTCAAAAATCAAGGTTCAGACGCCTTGTTGTGT
54466 CTGTATATAT
Statistics
Matches: 305, Mismatches: 56, Indels: 7
0.83 0.15 0.02
Matches are distributed among these distances:
183 21 0.07
184 283 0.93
185 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (183 bp):
GGTGTAAAAATACGAAAATCTTTTTTTTCAATGTTTTTGACAGTGTTATTATGAATATCACCTTT
ATCAGATTCAAAATTAAGAACAAAGGATACGTTTGCACAAACACAATCTATATCACAGGTGACGA
TCACGGTCGCCTGCAATTTCAAAAATCAAGGTTCAGACGCCTTGTTGTGTGTC
Found at i:59654 original size:22 final size:21
Alignment explanation
Indices: 59606--59654 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
59596 TTTATGGAAG
**
59606 TTAA-ATATATTTTTATTGTA
1 TTAATATATATTTTTATTCCA
59626 TTAATATATATTTATTATTCCA
1 TTAATATATATTT-TTATTCCA
*
59648 TTTATAT
1 TTAATAT
59655 TACTACGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 8 0.33
22 12 0.50
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAATATATATTTTTATTCCA
Found at i:63293 original size:2 final size:2
Alignment explanation
Indices: 63286--63315 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63276 GGTAAATTAC
63286 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
63316 CATGTGGTTT
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
Done.