Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014007.1 Corchorus capsularis cultivar CVL-1 contig14028, 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: 52045
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:581 original size:34 final size:34
Alignment explanation
Indices: 538--615 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
528 TTTGAAATAC
538 TTTTTTTTTTTTCGAAAAATGGAACACAAGACTT
1 TTTTTTTTTTTTCGAAAAATGGAACACAAGACTT
572 TTTTTTTTTTTTCGAAAAATGGAACACAAGACTT
1 TTTTTTTTTTTTCGAAAAATGGAACACAAGACTT
606 TTTTTTTTTT
1 TTTTTTTTTT
616 AACGGCAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (34 bp):
TTTTTTTTTTTTCGAAAAATGGAACACAAGACTT
Found at i:1727 original size:42 final size:42
Alignment explanation
Indices: 1658--1755 Score: 126
Period size: 42 Copynumber: 2.3 Consensus size: 42
1648 AAAATAAATA
* *
1658 CTCCTACCACAAAATAATTCTAAAATGATCAA-GTTGATTTCAAT
1 CTCCTACCAC--AATAATCCTAAAATGAT-AATGTTGATTCCAAT
* *
1702 CTCCTACCACAATAATCCTGAAATGATAATGTTGATTCCAGT
1 CTCCTACCACAATAATCCTAAAATGATAATGTTGATTCCAAT
1744 CTCCTACCACAA
1 CTCCTACCACAA
1756 AATACTCCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 2 0.04
42 37 0.76
44 10 0.20
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.30
Consensus pattern (42 bp):
CTCCTACCACAATAATCCTAAAATGATAATGTTGATTCCAAT
Found at i:2020 original size:13 final size:13
Alignment explanation
Indices: 2002--2037 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1992 CCAACATACC
2002 AGGGAGAATTTTG
1 AGGGAGAATTTTG
*
2015 AGGGAGAA-CTTG
1 AGGGAGAATTTTG
2027 AGGGAGAATTT
1 AGGGAGAATTT
2038 CAGTCAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.33, C:0.03, G:0.39, T:0.25
Consensus pattern (13 bp):
AGGGAGAATTTTG
Found at i:3072 original size:21 final size:21
Alignment explanation
Indices: 3019--3076 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 21
3009 AGGGGCAATA
3019 TGACT-CTAAATAAAAGTTTT
1 TGACTCCTAAATAAAAGTTTT
* * * *
3039 TTAGTCACAAAATAAAGGTTTT
1 TGACTC-CTAAATAAAAGTTTT
3061 TGACTCCTAAATAAAA
1 TGACTCCTAAATAAAA
3077 ATTTAGAAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
20 3 0.11
21 8 0.29
22 17 0.61
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
TGACTCCTAAATAAAAGTTTT
Found at i:6870 original size:27 final size:27
Alignment explanation
Indices: 6820--6872 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
6810 TTAATAGCAC
* *
6820 TGCTTTGTTCAACCTTCTATTTGGAAG
1 TGCTTTGTTCAACCTTCGACTTGGAAG
*
6847 TGCTTTGTTCAACCTTGGACTTGGAA
1 TGCTTTGTTCAACCTTCGACTTGGAA
6873 TTTTGGGTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (27 bp):
TGCTTTGTTCAACCTTCGACTTGGAAG
Found at i:11217 original size:22 final size:21
Alignment explanation
Indices: 11167--11217 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
11157 TATTATTACC
11167 TACAAAAAATACAAACCAAAA
1 TACAAAAAATACAAACCAAAA
*
11188 TA-AGAAAAA-ACAATACTTAAAA
1 TACA-AAAAATACAA-AC-CAAAA
11210 TACAAAAA
1 TACAAAAA
11218 TAAAATTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 10 0.40
23 1 0.04
ACGTcount: A:0.71, C:0.14, G:0.02, T:0.14
Consensus pattern (21 bp):
TACAAAAAATACAAACCAAAA
Found at i:18273 original size:27 final size:27
Alignment explanation
Indices: 18247--18297 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
18237 TTTATTTTAT
18247 TTAAATAAAT-AAAATAA-TAAAAATTA
1 TTAAA-AAATAAAAATAATTAAAAATTA
*
18273 TTAAAAATTAAAAATAATTAAAAAT
1 TTAAAAAATAAAAATAATTAAAAAT
18298 GAATTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 12 0.55
27 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TTAAAAAATAAAAATAATTAAAAATTA
Found at i:18286 original size:17 final size:17
Alignment explanation
Indices: 18249--18297 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
18239 TATTTTATTT
* *
18249 AAATAAATAAAATAATAA
1 AAATAATTAAAA-ATTAA
*
18267 AAATTATTAAAAATTAA
1 AAATAATTAAAAATTAA
18284 AAATAATTAAAAAT
1 AAATAATTAAAAAT
18298 GAATTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATAATTAAAAATTAA
Found at i:19460 original size:17 final size:17
Alignment explanation
Indices: 19438--19471 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19428 ACAAGAATTG
*
19438 ATTTTTAATTATTTTTA
1 ATTTTTAATAATTTTTA
19455 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTTTA
19472 TTATTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Found at i:25584 original size:3 final size:3
Alignment explanation
Indices: 25576--25624 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
25566 CGAATCCACT
25576 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
25624 T
1 T
25625 GCCTGAGTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:30318 original size:3 final size:3
Alignment explanation
Indices: 30310--30341 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30300 TTTTTCCAAT
30310 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30342 TTACTTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:32310 original size:21 final size:21
Alignment explanation
Indices: 32284--32324 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
32274 ACGCCGCATC
*
32284 TGCTTCTGTCTTGGATGCCTT
1 TGCTTCGGTCTTGGATGCCTT
32305 TGCTTCGGTCTTGGATGCCT
1 TGCTTCGGTCTTGGATGCCT
32325 CTAGTCCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.24, G:0.27, T:0.44
Consensus pattern (21 bp):
TGCTTCGGTCTTGGATGCCTT
Found at i:35508 original size:23 final size:24
Alignment explanation
Indices: 35410--35538 Score: 74
Period size: 22 Copynumber: 5.5 Consensus size: 24
35400 ATAAGCAGAC
* * *
35410 ATTTTGATAATCTCCTTCCTTATGAG
1 ATTTTGATAA-CT-CTTTCTTAAGAA
* *
35436 ATTTTGTTAAC-C-TTCTTATGAA
1 ATTTTGATAACTCTTTCTTAAGAA
* * *
35458 ATTTTGATAGACACATT-AT-A-AA
1 ATTTTGATA-ACTCTTTCTTAAGAA
35480 ATTTTGATAAC-CTTTCTTAAGAA
1 ATTTTGATAACTCTTTCTTAAGAA
* * *
35503 ATTTTGAT-ACTTTTTTTTTATGAA
1 ATTTTGATAAC-TCTTTCTTAAGAA
35527 ATTTTGATAACT
1 ATTTTGATAACT
35539 GCTGTATGAA
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
20 3 0.04
21 3 0.04
22 30 0.36
23 13 0.16
24 20 0.24
25 5 0.06
26 9 0.11
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (24 bp):
ATTTTGATAACTCTTTCTTAAGAA
Found at i:38753 original size:30 final size:29
Alignment explanation
Indices: 38647--38753 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 29
38637 TAATCTACCA
** * *
38647 TTTTGCCCCCTGAACTTGTAGCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
*
38678 TTTTGTCCCCC-GAACTTCAATCTTGGACA
1 TTTTG-CCCCCTGAACTTCAATCTTGGACG
* * *
38707 TTTTGTCCCTTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
*
38737 TTTTGCCCCCTCAACTT
1 TTTTGCCCCCTGAACTT
38754 AACGGCTCCA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 3 0.05
29 22 0.36
30 18 0.30
31 13 0.21
32 5 0.08
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Found at i:38811 original size:32 final size:32
Alignment explanation
Indices: 38770--38917 Score: 278
Period size: 32 Copynumber: 4.6 Consensus size: 32
38760 TCCATTAAGT
38770 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
1 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
*
38802 CGCTGACGTGGCATTGCCAGGTTGGACCAAAC
1 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
38834 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
1 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
38866 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
1 CGCTGACGTGGCATTGCCACGTTGGACCAAAC
*
38898 CGCTGACGTGGCAATGCCAC
1 CGCTGACGTGGCATTGCCAC
38918 ACGACATTTT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 113 1.00
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (32 bp):
CGCTGACGTGGCATTGCCACGTTGGACCAAAC
Found at i:39035 original size:29 final size:30
Alignment explanation
Indices: 38978--39049 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
38968 CGTTAGGTTG
38978 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
* * * *
39008 ATGGGGCAAAATGT-TCAAGATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
*
39037 GGGGGGCAAAACG
1 AGGGGGCAAAACG
39050 CATAAACGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 23 0.66
30 12 0.34
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:50826 original size:53 final size:52
Alignment explanation
Indices: 50749--50861 Score: 190
Period size: 53 Copynumber: 2.2 Consensus size: 52
50739 ATAAAAGCTG
* *
50749 AAAAAGAAATCTAGTACTACTAGAAAAGCTTTAAAGTTACTATAGTACCCAAA
1 AAAAAAAAATCTAGTACTACTAGAAAAGCTTAAAAGTTACTATAGTA-CCAAA
*
50802 AAAAAAAAATCTAGTACTACTAGAAAAGCTTAAAAGTTAGTATAGTACCAAA
1 AAAAAAAAATCTAGTACTACTAGAAAAGCTTAAAAGTTACTATAGTACCAAA
50854 AAAAAAAA
1 AAAAAAAA
50862 CTGAAAAATC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 13 0.23
53 44 0.77
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.22
Consensus pattern (52 bp):
AAAAAAAAATCTAGTACTACTAGAAAAGCTTAAAAGTTACTATAGTACCAAA
Found at i:50887 original size:52 final size:54
Alignment explanation
Indices: 50770--50888 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 54
50760 TAGTACTACT
** * *
50770 AGAAAAGCTTT-AAAGTTACTATAGTACCCAAAAAAAAAAAATCTAGTACTACT
1 AGAAAAGCTTTAAAAGTTACTATAGTACCCAAAAAAAAAAAATCTAAAAATACA
*
50823 AGAAAAGC-TTAAAAGTTAGTATAGTA-CC-AAAAAAAAAAA-CTGAAAAAT-CGA
1 AGAAAAGCTTTAAAAGTTACTATAGTACCCAAAAAAAAAAAATCT-AAAAATAC-A
50874 AGAAAAGCTTTAAAA
1 AGAAAAGCTTTAAAA
50889 AAAAAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
50 3 0.05
51 22 0.39
52 10 0.18
53 22 0.39
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (54 bp):
AGAAAAGCTTTAAAAGTTACTATAGTACCCAAAAAAAAAAAATCTAAAAATACA
Done.