Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008754.1 Corchorus capsularis cultivar CVL-1 contig08775, 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: 17320
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:404 original size:56 final size:57
Alignment explanation
Indices: 317--431 Score: 178
Period size: 56 Copynumber: 2.0 Consensus size: 57
307 ATCAAACCTC
317 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGC-TGCAAGAGACCCAAG
1 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGCATGCAAGAGACCCAAG
**
373 CAAAAGGTGCACAATAAGAAGCAGGGTAAAAAATGAGATGCATAATGCAAGAGACCCAA
1 CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGC---ATGCAAGAGACCCAA
432 CCTGAAATCT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 39 0.74
60 14 0.26
ACGTcount: A:0.49, C:0.17, G:0.24, T:0.10
Consensus pattern (57 bp):
CAAAAGGTGCACAATAAGAAGCAGGCAAAAAAATGAGATGCATGCAAGAGACCCAAG
Found at i:702 original size:64 final size:64
Alignment explanation
Indices: 613--745 Score: 266
Period size: 64 Copynumber: 2.1 Consensus size: 64
603 GCGAGAAAGT
613 GAAGAATAATCGAAGTGATAAAGCGAGAAGGGAAAAACAGATGAGCAGAGGAAGAAAGGGAAGA
1 GAAGAATAATCGAAGTGATAAAGCGAGAAGGGAAAAACAGATGAGCAGAGGAAGAAAGGGAAGA
677 GAAGAATAATCGAAGTGATAAAGCGAGAAGGGAAAAACAGATGAGCAGAGGAAGAAAGGGAAGA
1 GAAGAATAATCGAAGTGATAAAGCGAGAAGGGAAAAACAGATGAGCAGAGGAAGAAAGGGAAGA
741 GAAGA
1 GAAGA
746 GAGCGACCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.52, C:0.06, G:0.35, T:0.08
Consensus pattern (64 bp):
GAAGAATAATCGAAGTGATAAAGCGAGAAGGGAAAAACAGATGAGCAGAGGAAGAAAGGGAAGA
Found at i:1367 original size:31 final size:31
Alignment explanation
Indices: 1332--1429 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
1322 AACGTCCAAA
* *
1332 GTCCAAACGCTACAAATTCAATGGACAAAAT
1 GTCCAAACGCTACAAGTTCAATGGGCAAAAT
* ** *
1363 GTCCAAA--ATTGAAGTTC-ATGAGGCAAAAC
1 GTCCAAACGCTACAAGTTCAATG-GGCAAAAT
*
1392 GTCCAAACGCTACAAGTTCAAGGGGCAAAAT
1 GTCCAAACGCTACAAGTTCAATGGGCAAAAT
1423 GTCCAAA
1 GTCCAAA
1430 ATTGAATTTC
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
28 3 0.06
29 19 0.37
31 28 0.54
32 2 0.04
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (31 bp):
GTCCAAACGCTACAAGTTCAATGGGCAAAAT
Found at i:1380 original size:29 final size:29
Alignment explanation
Indices: 1348--1440 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
1338 ACGCTACAAA
*
1348 TTCAATGGACAAAATGTCCAAAATTGAAG
1 TTCAATGGGCAAAATGTCCAAAATTGAAG
* * **
1377 TTC-ATGAGGCAAAACGTCCAAACGCTACAAG
1 TTCAATG-GGCAAAATGTCCAAA--ATTGAAG
* *
1408 TTCAAGGGGCAAAATGTCCAAAATTGAAT
1 TTCAATGGGCAAAATGTCCAAAATTGAAG
1437 TTCA
1 TTCA
1441 GATGCAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 3 0.06
29 23 0.47
31 21 0.43
32 2 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (29 bp):
TTCAATGGGCAAAATGTCCAAAATTGAAG
Found at i:1451 original size:60 final size:60
Alignment explanation
Indices: 1332--1449 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
1322 AACGTCCAAA
*
1332 GTCCAAACGCTACAAATTCAATGGACAAAATGTCCAAAATTGAAGTTCATGAGGCAAAAC
1 GTCCAAACGCTACAAATTCAAGGGACAAAATGTCCAAAATTGAAGTTCATGAGGCAAAAC
* * * *
1392 GTCCAAACGCTACAAGTTCAAGGGGCAAAATGTCCAAAATTGAATTTCA-GATGCAAAA
1 GTCCAAACGCTACAAATTCAAGGGACAAAATGTCCAAAATTGAAGTTCATGAGGCAAAA
1450 ACATCCAATG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 8 0.15
60 45 0.85
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (60 bp):
GTCCAAACGCTACAAATTCAAGGGACAAAATGTCCAAAATTGAAGTTCATGAGGCAAAAC
Found at i:6333 original size:11 final size:11
Alignment explanation
Indices: 6317--6346 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6307 GTCCCTGAAT
6317 AATCTATAGAA
1 AATCTATAGAA
*
6328 AATCTATAGAT
1 AATCTATAGAA
6339 AATCTATA
1 AATCTATA
6347 AAGAAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (11 bp):
AATCTATAGAA
Found at i:6500 original size:29 final size:29
Alignment explanation
Indices: 6458--6515 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6448 AAGAGGGACT
6458 AATCTATCATCACTGTTACTAGCTGATAC
1 AATCTATCATCACTGTTACTAGCTGATAC
6487 AATCTATCATCACTGTTACTAGCTGATAC
1 AATCTATCATCACTGTTACTAGCTGATAC
6516 CATGAATCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (29 bp):
AATCTATCATCACTGTTACTAGCTGATAC
Found at i:6596 original size:16 final size:16
Alignment explanation
Indices: 6575--6606 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6565 CCCACATATG
*
6575 TAAAAAAAATATTAAA
1 TAAAAAAAATAATAAA
6591 TAAAAAAAATAATAAA
1 TAAAAAAAATAATAAA
6607 AAGTTTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAAAAATAATAAA
Found at i:13577 original size:2 final size:2
Alignment explanation
Indices: 13570--13596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13560 TTCTACGTAC
13570 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13597 GAGTAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13647 original size:42 final size:42
Alignment explanation
Indices: 13600--13689 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
13590 ATATATAGAG
*
13600 TAATTTGGGTAAATAATTAAATCAAGATAAGACTTGTCTCTT
1 TAATTTGGGTAAATAATTAAATCAAGATAAGACTTGCCTCTT
*
13642 TAATTTGGGTAAATAATTAAATCAAGATAAGATTTGCCTCTT
1 TAATTTGGGTAAATAATTAAATCAAGATAAGACTTGCCTCTT
13684 TAATTT
1 TAATTT
13690 TGAGATTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (42 bp):
TAATTTGGGTAAATAATTAAATCAAGATAAGACTTGCCTCTT
Found at i:14800 original size:175 final size:175
Alignment explanation
Indices: 14022--15196 Score: 1444
Period size: 175 Copynumber: 6.7 Consensus size: 175
14012 TGCATTTTTT
* * * * * * * * *
14022 TTTTATGAAAAATAGTGGGCAACTGAGGTTTGTAAGTTTAGTGGGCGAGAAAATTCAAAATTGGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTGGA
* *
14087 AAGAG-T--AAGGTGAATGACAACAAGGGAGGAACACGTGAAATCTGTGAAGTTTATAAAATTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAGTTTA
* * *** *
14149 GTAGGCGATCGAGATAACCTGCCTCGCAATCGGTGCAAAGGTATC
131 GCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * * * ** *
14194 TTTATTTTGAAATACAGTGGGCGACCGAGGTTTGTAAGTTTAGTGGGCAAGATAATCGAAAATTG
1 -TT-TTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTG
** * * * * * * *
14259 GAAAGAGCGCAACGTTGAATGACAACGAGGGAGGAACACATGAAACCTGTGAAGTTTATAACGTT
64 GAAAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAGTT
* * *
14324 TAGCAGGCGGTTGAGATAACCCATCTCGCAATCAGTGCAAACGTGTC
129 TAGCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * *
14371 TTTTGT-AAAAACAGTGGGCGACAGAGGTTTGTAATTAAGTTTAGTGGGTGAGATAATCCAAAAT
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTG----TAAGTTCAGTGGGTGAGATAATCCAAAAT
* * * *
14435 TGGAAAGAGTTTAAAGATGAATGACAACAAGGGAGGAACACGTGAAATCTGTGAAGTTTAAAAAG
62 TGGAAAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAG
* *
14500 TTTAGCAGGCGGTCGAGAGATAACCCACCTCGCAATCGGTGCAAAGGTTTC
127 TTTAGCAGGCGGTC--GAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * *
14551 TTTTGTGAAAAACAATGGGCGACCGAGGTTTATAAGTTCAGTGGGTGAGATAATCTAAAATTAGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTGGA
* * * ** *
14616 AAGAGTTCAAAGGTGAACGAAAACAAGGGAAGAACACGCGGGATCTATGAAGTTTATAAAGTTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAGTTTA
* * * * *
14681 GCTGGCGGTCGAGATAATCCATCTCGGAGTCGGTGCAAATGTGTC
131 GCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * * *
14726 GTTTGTGAAAAACAATGGGCGATCGAGGTATGTAAGTTCAATGGGTGAGATAATCCAAAATTGGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTGGA
* * * * ** *
14791 AATAGTTCAAATGTGAATGAAAACAAGGGAAGAACACGCGGGATCTATGAAGTTTATAAAGTTTA
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAGTTTA
* * *
14856 GCAGGCGGTCGAGATAACCCATCTCGGAGTCGGTGCAAATGTGTC
131 GCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
*
14901 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAATGGGTGAGATAATCCAAAATTGGA
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTGGA
* *
14966 AATAGTTCAAAGGTGAATGACAACAA-GGAAGGAACACGTGGAATCTGTGAAGTTTATAAAGTTT
66 AAGAGTTCAAAGGTGAATGACAACAAGGGAA-GAACACGTGAAATCTGTGAAGTTTATAAAGTTT
** *
15030 AGCAGGCGGTTAAGATAACCCATCTTGCAATCGGTGCAAAGGTGTC
130 AGCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
* * ** * *
15076 TTTTGTG-AAAACTATGGACGATTGAGGTTTGTAAGTTCAGAGGGACGAGATAATCCAAAATTGG
1 TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGG-TGAGATAATCCAAAATTGG
*
15140 TAAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTA
65 AAAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTA
15197 AAGAGTTCAA
Statistics
Matches: 882, Mismatches: 106, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
173 2 0.00
174 117 0.13
175 425 0.48
176 6 0.01
177 179 0.20
178 94 0.11
180 37 0.04
181 22 0.02
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (175 bp):
TTTTGTGAAAAACAATGGGCGACCGAGGTTTGTAAGTTCAGTGGGTGAGATAATCCAAAATTGGA
AAGAGTTCAAAGGTGAATGACAACAAGGGAAGAACACGTGAAATCTGTGAAGTTTATAAAGTTTA
GCAGGCGGTCGAGATAACCCATCTCGCAATCGGTGCAAAGGTGTC
Done.