Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011294.1 Corchorus capsularis cultivar CVL-1 contig11315, 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: 62315
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3625 original size:16 final size:16
Alignment explanation
Indices: 3604--3638 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3594 CTCCAAAAGG
*
3604 AAATATATATACATAA
1 AAATATATATAAATAA
3620 AAATATATATAAATAA
1 AAATATATATAAATAA
3636 AAA
1 AAA
3639 AAAACTCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATATATATAAATAA
Found at i:8741 original size:22 final size:22
Alignment explanation
Indices: 8702--8746 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8692 AAAACTCAGG
**
8702 AGAAAGGAGAGATTGAAAGGAAA
1 AGAAAGGAGAGAAAGAAA-GAAA
8725 AGAAA-GAGAGAAAGAAAGAAA
1 AGAAAGGAGAGAAAGAAAGAAA
8746 A
1 A
8747 TGTGTCGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.04
Consensus pattern (22 bp):
AGAAAGGAGAGAAAGAAAGAAA
Found at i:21382 original size:22 final size:22
Alignment explanation
Indices: 21354--21396 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21344 CGCCTTTAGA
21354 GGTCATGGGCATGACGTGCTCT
1 GGTCATGGGCATGACGTGCTCT
*
21376 GGTCATGGGCATGACTTGCTC
1 GGTCATGGGCATGACGTGCTC
21397 AGGCTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.35, T:0.28
Consensus pattern (22 bp):
GGTCATGGGCATGACGTGCTCT
Found at i:22063 original size:5 final size:5
Alignment explanation
Indices: 22053--22078 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
22043 TTTTGATCAT
22053 TTTCA TTTCA TTTCA TTTCA TTTCA T
1 TTTCA TTTCA TTTCA TTTCA TTTCA T
22079 GGGGCTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:22359 original size:108 final size:109
Alignment explanation
Indices: 22170--22391 Score: 347
Period size: 108 Copynumber: 2.0 Consensus size: 109
22160 ACTTATGCAT
* *
22170 TTAAGATGCCTTGCATACTCGTAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTATGATAC
1 TTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTATGATAC
*
22235 CGAACCCCGTGTGCTCCACT-TCCAAAAACAGCGGAGTAATTTA
66 CGAACCCCGTGTGCTCCACTACCCAAAAACAGCGGAGTAATTTA
* * *
22278 TTAAGGTGCATTGCATACTCATAATTTTGGTTTGTGACTGACGCGAAGGTTGATATTTGTGATAC
1 TTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTATGATAC
** **
22343 CGAACCCCGTGTGCTCCACTACCCAAAAACATTGGAGTTGTTTA
66 CGAACCCCGTGTGCTCCACTACCCAAAAACAGCGGAGTAATTTA
22387 TTAAG
1 TTAAG
22392 TTCCTCTTTT
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
108 80 0.78
109 23 0.22
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (109 bp):
TTAAGATGCATTGCATACTCATAATTTTGGTTCGTGACTGACGCGAAGGTTGATATTTATGATAC
CGAACCCCGTGTGCTCCACTACCCAAAAACAGCGGAGTAATTTA
Found at i:35038 original size:62 final size:62
Alignment explanation
Indices: 34940--35137 Score: 342
Period size: 63 Copynumber: 3.2 Consensus size: 62
34930 AGTTCATTCA
*
34940 TTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
1 TTTTTTTTT-TGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
35003 TTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
1 TTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
* **
35065 TTTTTTTTTTGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTATCAACTTAGCGAGGG
1 TTTTTTTTTT-GCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
35128 TTTTTTTTTT
1 TTTTTTTTTT
35138 TGGGTTGACT
Statistics
Matches: 130, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
62 62 0.48
63 68 0.52
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (62 bp):
TTTTTTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCC
Found at i:35102 original size:63 final size:63
Alignment explanation
Indices: 34940--35137 Score: 344
Period size: 62 Copynumber: 3.1 Consensus size: 63
34930 AGTTCATTCA
*
34940 TTTTTTTTTGTGCTCTAAGTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
1 TTTTTTTTTG-GCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
35004 TTTTTTTTT-GCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
1 TTTTTTTTTGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
* **
35066 TTTTTTTTTGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTATCAACTTAGCGAGGGT
1 TTTTTTTTTGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
35129 TTTTTTTTT
1 TTTTTTTTT
35138 TGGGTTGACT
Statistics
Matches: 129, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
62 61 0.47
63 59 0.46
64 9 0.07
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (63 bp):
TTTTTTTTTGGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGCCT
Found at i:54656 original size:20 final size:20
Alignment explanation
Indices: 54631--54672 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
54621 AAAAAAAAAG
54631 AGAAAAATAATAGTCTGCAA
1 AGAAAAATAATAGTCTGCAA
*
54651 AGAAAAATAATGGTCTGCAA
1 AGAAAAATAATAGTCTGCAA
54671 AG
1 AG
54673 TTATCATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (20 bp):
AGAAAAATAATAGTCTGCAA
Found at i:54819 original size:92 final size:92
Alignment explanation
Indices: 54662--54900 Score: 469
Period size: 92 Copynumber: 2.6 Consensus size: 92
54652 GAAAAATAAT
*
54662 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
54727 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
54754 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
54819 TGGATGAAGAGAAAGCCAAATTATGAA
66 TGGATGAAGAGAAAGCCAAATTATGAA
54846 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAA
54901 TAGTACAAAG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 146 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (92 bp):
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGGATGAAGAGAAAGCCAAATTATGAA
Found at i:55194 original size:2 final size:2
Alignment explanation
Indices: 55187--55247 Score: 50
Period size: 2 Copynumber: 35.0 Consensus size: 2
55177 TAATTATAAT
*
55187 TA TA TA TA TA -A T- TA TA TA -A TA -A TA T- TA GA 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
55224 -A T- TA TA TA TA TA -A TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55248 ATTATTAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
1 9 0.19
2 39 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:55198 original size:12 final size:12
Alignment explanation
Indices: 55181--55252 Score: 92
Period size: 12 Copynumber: 5.8 Consensus size: 12
55171 ATCCTCTAAT
55181 TATAATTATATA
1 TATAATTATATA
55193 TATAATTATATA
1 TATAATTATATA
55205 -ATAATATTAGATATA
1 TAT-A-ATT--ATATA
55220 TATAATTATATA
1 TATAATTATATA
*
55232 TATAATAATATA
1 TATAATTATATA
55244 TATAATTAT
1 TATAATTAT
55253 TAAACGGTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.04
12 37 0.70
13 3 0.06
14 3 0.06
15 6 0.11
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
TATAATTATATA
Found at i:55232 original size:14 final size:14
Alignment explanation
Indices: 55187--55247 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
55177 TAATTATAAT
55187 TATATATATAATTA
1 TATATATATAATTA
55201 TATA-ATA-ATATTA
1 TATATATATA-ATTA
*
55214 GATATATATAATTA
1 TATATATATAATTA
55228 TATATATAATAA-TA
1 TATATAT-ATAATTA
55242 TATATA
1 TATATA
55248 ATTATTAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 1 0.02
13 10 0.24
14 25 0.61
15 5 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TATATATATAATTA
Found at i:55784 original size:121 final size:121
Alignment explanation
Indices: 55568--55810 Score: 389
Period size: 121 Copynumber: 2.0 Consensus size: 121
55558 TCAAAAAAAA
*
55568 TCATTAAATTGTCAATCTAGAGGGGTCCAACATGGCAACACCAATGAAAACTAAGGCTATGTTTA
1 TCATTAAATTGTCAATCTAGAGGGGCCCAACATGGCAACACCAATGAAAACTAAGGCTATGTTTA
* *
55633 ATGCACTGGTTCACCAGCTGTTGGATCGGTGCACCGGTCAAATGGAGTCTTAAGTG
66 ATGCACTGGTTCACCAGCTGTTGGACCGGTGCACCGGTCAAATGAAGTCTTAAGTG
* * * *
55689 TCATTAAGTTGTCAAT-TGGAGGGGGCCCAACGTGGCAACACCAATGAAAACTAAGGTTATGTTT
1 TCATTAAATTGTCAATCTAGA-GGGGCCCAACATGGCAACACCAATGAAAACTAAGGCTATGTTT
* *
55753 AGTGCACTGGTTCACCGGCTGTTGGACCGGTGCACCGGTCAAATGAAGTCTTAAGTG
65 AATGCACTGGTTCACCAGCTGTTGGACCGGTGCACCGGTCAAATGAAGTCTTAAGTG
55810 T
1 T
55811 AATCTCCGTT
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
120 3 0.03
121 109 0.97
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (121 bp):
TCATTAAATTGTCAATCTAGAGGGGCCCAACATGGCAACACCAATGAAAACTAAGGCTATGTTTA
ATGCACTGGTTCACCAGCTGTTGGACCGGTGCACCGGTCAAATGAAGTCTTAAGTG
Found at i:58384 original size:83 final size:83
Alignment explanation
Indices: 58288--58455 Score: 257
Period size: 83 Copynumber: 2.0 Consensus size: 83
58278 CACAGCCTCA
* * *
58288 CACCACACTGAACACACCTGA-ATTTATTCCAATGTTTTGGAGTTTAATGGAAGTTTTTATTCAC
1 CACCACACTGAACACACCT-ATATTTATTCCAAAGTTTTGGAGTTTAATGGAAGCTTTTACTCAC
58352 AAAATCCAAACTGGATTTG
65 AAAATCCAAACTGGATTTG
* **
58371 CACCACACTGAACACACCTATATTTATTGCAAAGTTTTGGAGTTTAATGGTTGCTTTTACTCACA
1 CACCACACTGAACACACCTATATTTATTCCAAAGTTTTGGAGTTTAATGGAAGCTTTTACTCACA
*
58436 AAATCCAAATTGGATTTG
66 AAATCCAAACTGGATTTG
58454 CA
1 CA
58456 ATTATACCTT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 1 0.01
83 76 0.99
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (83 bp):
CACCACACTGAACACACCTATATTTATTCCAAAGTTTTGGAGTTTAATGGAAGCTTTTACTCACA
AAATCCAAACTGGATTTG
Found at i:62121 original size:73 final size:73
Alignment explanation
Indices: 62033--62180 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
62023 CTGAAATTGC
62033 ATGTTTCCAAACAACTAAAAAATATATCTTGTATCCAAACACCTAAATATCCTTTATATTTGTAC
1 ATGTTTCCAAACAACTAAAAAATATATCTTGTATCCAAACACCTAAATATCCTTTATATTTGTAC
62098 AAAATGTT
66 AAAATGTT
62106 ATGTTTCCAAACAACTAAAAAATATATCTTGTATCCAAACACCTAAATATCCTTTATATTTGTAC
1 ATGTTTCCAAACAACTAAAAAATATATCTTGTATCCAAACACCTAAATATCCTTTATATTTGTAC
62171 AAAATGTT
66 AAAATGTT
62179 AT
1 AT
62181 TGTGTAGTAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (73 bp):
ATGTTTCCAAACAACTAAAAAATATATCTTGTATCCAAACACCTAAATATCCTTTATATTTGTAC
AAAATGTT
Found at i:62288 original size:2 final size:2
Alignment explanation
Indices: 62281--62309 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62271 AATTAATTAC
62281 TA TA TA TA TA 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 T
62310 TACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.