Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011569.1 Corchorus capsularis cultivar CVL-1 contig11590, 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: 43741
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1864 original size:22 final size:22
Alignment explanation
Indices: 1839--1891 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1829 AGGTCGCGCG
*
1839 CGGGTCGCGACCCGCCATGGTC
1 CGGGTCGCGACCCGCCACGGTC
*
1861 CGGGTCGCGACCCGCCACGGTG
1 CGGGTCGCGACCCGCCACGGTC
*
1883 TGGGTCGCG
1 CGGGTCGCG
1892 TGCGATCGCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.38, G:0.42, T:0.13
Consensus pattern (22 bp):
CGGGTCGCGACCCGCCACGGTC
Found at i:11477 original size:40 final size:40
Alignment explanation
Indices: 11418--11497 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
11408 TGAAGTATTT
* *
11418 CAGATGTTTTTATTCTGATCTTCACCAAAGTTTAAGAAGA
1 CAGATGTTCTTATTATGATCTTCACCAAAGTTTAAGAAGA
11458 CAGATGTTCTTATTATGATCTTCACCAAAGTTTAAGAAGA
1 CAGATGTTCTTATTATGATCTTCACCAAAGTTTAAGAAGA
11498 TTAATGAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (40 bp):
CAGATGTTCTTATTATGATCTTCACCAAAGTTTAAGAAGA
Found at i:11571 original size:26 final size:26
Alignment explanation
Indices: 11542--11625 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
11532 TTCTTTCAAA
11542 GAAGATTCAATTATTGGAGAATTACT
1 GAAGATTCAATTATTGGAGAATTACT
** * *
11568 GAAGACCCAGTTATTGG-GAAATTATT
1 GAAGATTCAATTATTGGAG-AATTACT
*
11594 GAAAAATTCAATTATTGGAGAATTACT
1 G-AAGATTCAATTATTGGAGAATTACT
*
11621 AAAGA
1 GAAGA
11626 CCCAGTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
25 1 0.02
26 24 0.55
27 18 0.41
28 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (26 bp):
GAAGATTCAATTATTGGAGAATTACT
Found at i:11626 original size:53 final size:53
Alignment explanation
Indices: 11546--11650 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
11536 TTCAAAGAAG
*
11546 ATTCAATTATTGGAGAATTACTGAAGACCCAGTTATTGGGAAATTATTGAAAA
1 ATTCAATTATTGGAGAATTACTAAAGACCCAGTTATTGGGAAATTATTGAAAA
11599 ATTCAATTATTGGAGAATTACTAAAGACCCAGTTATTGGGAAATTATTGAAA
1 ATTCAATTATTGGAGAATTACTAAAGACCCAGTTATTGGGAAATTATTGAAA
11651 GAAGATCCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (53 bp):
ATTCAATTATTGGAGAATTACTAAAGACCCAGTTATTGGGAAATTATTGAAAA
Found at i:11644 original size:26 final size:26
Alignment explanation
Indices: 11552--11637 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
11542 GAAGATTCAA
*
11552 TTATTGGAGAATTACTGAAGACCCAG
1 TTATTGGAGAATTACTAAAGACCCAG
* * ** *
11578 TTATTGG-GAAATTATTGAAAAATTCAA
1 TTATTGGAG-AATTACT-AAAGACCCAG
11605 TTATTGGAGAATTACTAAAGACCCAG
1 TTATTGGAGAATTACTAAAGACCCAG
11631 TTATTGG
1 TTATTGG
11638 GAAATTATTG
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
25 1 0.02
26 26 0.57
27 18 0.39
28 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (26 bp):
TTATTGGAGAATTACTAAAGACCCAG
Found at i:12651 original size:16 final size:17
Alignment explanation
Indices: 12622--12654 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12612 CCCATTTAAT
*
12622 CCATCTTTCTCCAAAGC
1 CCATCTTTCACCAAAGC
12639 CCAT-TTTCACCAAAGC
1 CCATCTTTCACCAAAGC
12655 AAACTGGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.39, G:0.06, T:0.27
Consensus pattern (17 bp):
CCATCTTTCACCAAAGC
Found at i:13316 original size:107 final size:107
Alignment explanation
Indices: 13103--13358 Score: 381
Period size: 107 Copynumber: 2.4 Consensus size: 107
13093 TTCTTTTTAT
* * * *
13103 TAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTA
1 TAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAACTCCAAAATTAATAATATA
13168 TTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCAC
66 TTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCAC
* *
13210 TAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAACTCCATAATTAATAGTAAT
1 TAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAACTCCAAAATTAATAAT-AT
* * *
13275 ATTGTTATAGGGTTTTAGAAATAAAATATATAATTAA-TTCAC
65 ATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCAC
** *
13317 TAAGTTTAG-CCCAAATTAAAATTAAAATTTAATTTTAAGGGT
1 TAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGT
13359 TAGAAAAATT
Statistics
Matches: 136, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
106 30 0.22
107 71 0.52
108 35 0.26
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (107 bp):
TAAGTTTAGCCCCAAATTAAAATTTTAATTTTATTTTAAGGGTAAACTCCAAAATTAATAATATA
TTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCAC
Found at i:13915 original size:15 final size:15
Alignment explanation
Indices: 13895--13923 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13885 GGCTAAATTT
13895 AATAAAAAAAAAGAA
1 AATAAAAAAAAAGAA
13910 AATAAAAAAAAAGA
1 AATAAAAAAAAAGA
13924 GAAGACACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AATAAAAAAAAAGAA
Found at i:14810 original size:1 final size:1
Alignment explanation
Indices: 14804--14832 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
14794 ACCAAAGATC
14804 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14833 CCAATTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20232 original size:25 final size:25
Alignment explanation
Indices: 20201--20250 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20191 CATTATTATT
20201 GGTAGTTTTCTGTTTTCATAACTTG
1 GGTAGTTTTCTGTTTTCATAACTTG
*
20226 GGTAGTTTTCTGTTTTCCTAACTTG
1 GGTAGTTTTCTGTTTTCATAACTTG
20251 TTGGAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (25 bp):
GGTAGTTTTCTGTTTTCATAACTTG
Found at i:24273 original size:58 final size:56
Alignment explanation
Indices: 24202--24319 Score: 182
Period size: 58 Copynumber: 2.1 Consensus size: 56
24192 TCTCTCTTCC
**
24202 TAAACTAGAACTAGAAGCTTTGATTGAGGGATGTCCCCGTACTTCTACACATTTTATT
1 TAAACTAGAACTAGAAGCTTTGATTGAGGGATGTCCCCGTA--TAAACACATTTTATT
* *
24260 TAAACTGGAACTAGAAGCTTTGATTGAGGGATTTCCCCGTATAAACACATTTTATT
1 TAAACTAGAACTAGAAGCTTTGATTGAGGGATGTCCCCGTATAAACACATTTTATT
24316 TAAA
1 TAAA
24320 ACAATTTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
56 17 0.30
58 39 0.70
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (56 bp):
TAAACTAGAACTAGAAGCTTTGATTGAGGGATGTCCCCGTATAAACACATTTTATT
Found at i:30330 original size:187 final size:183
Alignment explanation
Indices: 30013--30376 Score: 529
Period size: 187 Copynumber: 2.0 Consensus size: 183
30003 TATGATTCAG
*
30013 TTATTGCAAAACAAACATCAGGAAATTTCCTCGTTTGGAATCCGAATTCAAATCCAAATTAGTGA
1 TTATTGCAAAACAAACATCAGGAAATTTCCTCATTTGGAATCCGAATTCAAATCCAAATTAGTGA
* * *
30078 AGTCTCTCTGTTACGTACATATAAACCAGAAGGACCAGAACAGAAGGAGATAAAAATCTGAGCCT
66 AGTCCCCCTGTTACGTACATATAAACCAGAAGGACCAGAACAGAAGGAGAGAAAAATCTGAGCCT
* *
30143 TTTTTTAAACA-TTTTCCTTCATGGTG-ATACAACAATAAGAAAACTATATTGT
131 TTTTTT-AACATTTTTCATTCACGGTGAATACAACAATAAGAAAACTATATTGT
*
30195 TTATTGC-AAACAAACATCAGGAAGAATTTTCCTCATTTGGAATCCGACGTTATTCTAATCCAAA
1 TTATTGCAAAACAAACATCAGG-A-AA-TTTCCTCATTTGGAATCCGA----ATTCAAATCCAAA
* *
30259 TTAGTGAAGTCCCCCTG-TACGTACATATAATCCAGAAGGACCAGAACAGAAGGAGAGAAAAATG
59 TTAGTGAAGTCCCCCTGTTACGTACATATAAACCAGAAGGACCAGAACAGAAGGAGAGAAAAATC
* *
30323 TGAGCCTTTTTTTAACATTTTTCATTCACGGTGAATATAACAATAAGGAAACTA
124 TGAGCCTTTTTTTAACATTTTTCATTCACGGTGAATACAACAATAAGAAAACTA
30377 AAATGAAAAT
Statistics
Matches: 162, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
181 14 0.09
182 8 0.05
183 2 0.01
184 19 0.12
186 4 0.02
187 70 0.43
188 45 0.28
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (183 bp):
TTATTGCAAAACAAACATCAGGAAATTTCCTCATTTGGAATCCGAATTCAAATCCAAATTAGTGA
AGTCCCCCTGTTACGTACATATAAACCAGAAGGACCAGAACAGAAGGAGAGAAAAATCTGAGCCT
TTTTTTAACATTTTTCATTCACGGTGAATACAACAATAAGAAAACTATATTGT
Found at i:30818 original size:22 final size:22
Alignment explanation
Indices: 30792--30857 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
30782 CATTGATTTC
30792 TCTTTTCCTTTCTATGTTTGTT
1 TCTTTTCCTTTCTATGTTTGTT
** *
30814 TCTTTCTATTTTC-AT-TATGTT
1 TCTTT-TCCTTTCTATGTTTGTT
*
30835 TGTTTTCCTTTCTATGTTTGTT
1 TCTTTTCCTTTCTATGTTTGTT
30857 T
1 T
30858 AGTTTAGGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.15
21 11 0.32
22 13 0.38
23 5 0.15
ACGTcount: A:0.08, C:0.15, G:0.09, T:0.68
Consensus pattern (22 bp):
TCTTTTCCTTTCTATGTTTGTT
Found at i:33447 original size:167 final size:168
Alignment explanation
Indices: 33113--33453 Score: 587
Period size: 167 Copynumber: 2.0 Consensus size: 168
33103 TTTTCTCTTT
*
33113 TTTGGGGGGTTTCTGTGTTTGTTTGGTGGACAAGAAAATTTTGGAATTTATGGGTCAAATCGTGT
1 TTTGGGGGGTTTCTGTGTTTGTTTGGTGGACAAGAAAATTGTGGAATTTATGGGTCAAATCGTGT
* *
33178 TTAATTACCTGTTTGGTTGATGTGAAATTTGTGGAAGAGGGAAATGGAACCTGAAATATCAGGCG
66 TTAATTACC-GTTTGGTTGATGGGAAATTGGTGGAAGAGGGAAATGGAACCTGAAATATCAGGCG
33243 TGTTTCTACTTAGAAAGTGGAAAAGGATGGTTAATGAAC
130 TGTTTCTACTTAGAAAGTGGAAAAGGATGGTTAATGAAC
*
33282 TTTGGGGGGTTTCTGTGTTTGTTTGGTGGACAAGAAAATTGTGGAATTTATGGGTCAAATTGTGT
1 TTTGGGGGGTTTCTGTGTTTGTTTGGTGGACAAGAAAATTGTGGAATTTATGGGTCAAATCGTGT
*
33347 TTAATTACC-TTTGGTTGATGGGAAATTGGTGGAAGAGGGAAATGGAACCTGAAATATCAGGTGT
66 TTAATTACCGTTTGGTTGATGGGAAATTGGTGGAAGAGGGAAATGGAACCTGAAATATCAGGCGT
* *
33411 GTTTCTACTTTGAAACTTGG-AAAGGATGGTTAATGAAC
131 GTTTCTACTTAGAAA-GTGGAAAAGGATGGTTAATGAAC
33449 TTTGG
1 TTTGG
33454 ACTTATTTAG
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
167 89 0.54
168 3 0.02
169 72 0.44
ACGTcount: A:0.27, C:0.07, G:0.30, T:0.35
Consensus pattern (168 bp):
TTTGGGGGGTTTCTGTGTTTGTTTGGTGGACAAGAAAATTGTGGAATTTATGGGTCAAATCGTGT
TTAATTACCGTTTGGTTGATGGGAAATTGGTGGAAGAGGGAAATGGAACCTGAAATATCAGGCGT
GTTTCTACTTAGAAAGTGGAAAAGGATGGTTAATGAAC
Found at i:36142 original size:31 final size:31
Alignment explanation
Indices: 36104--36174 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
36094 GCCCTAATTT
*
36104 GACATTTTCTAAAGTTGAGGCTCTTAATTGA
1 GACATTTTCTAAAGTGGAGGCTCTTAATTGA
36135 GACATTTTCTAAAGTGGAGGCTCTTAATTGA
1 GACATTTTCTAAAGTGGAGGCTCTTAATTGA
*
36166 GAAATTTTC
1 GACATTTTC
36175 AAAATTCAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (31 bp):
GACATTTTCTAAAGTGGAGGCTCTTAATTGA
Found at i:39087 original size:19 final size:19
Alignment explanation
Indices: 39063--39099 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39053 TAATAATCTA
39063 CATAAACCGAAAAACCGAC
1 CATAAACCGAAAAACCGAC
* *
39082 CATAAATCGACAAACCGA
1 CATAAACCGAAAAACCGA
39100 ACTTATCGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.30, G:0.11, T:0.08
Consensus pattern (19 bp):
CATAAACCGAAAAACCGAC
Found at i:39456 original size:25 final size:26
Alignment explanation
Indices: 39383--39457 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 26
39373 GGCTTAATAC
* *
39383 ACAAATTAGCCCCTTAACTATCCATTGGG
1 ACAAATTGGCCCCTTAACT-T--TTTGGG
39412 ACAAATTGGCCCCTTAACTTTTTGGG
1 ACAAATTGGCCCCTTAACTTTTTGGG
39438 ACAAATTGG-CCCTTAACTTT
1 ACAAATTGGCCCCTTAACTTT
39458 AAAAACGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.25
26 14 0.32
28 1 0.02
29 18 0.41
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (26 bp):
ACAAATTGGCCCCTTAACTTTTTGGG
Found at i:40224 original size:31 final size:29
Alignment explanation
Indices: 40146--40226 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
40136 TCTCGTTTTT
* *
40146 AAAACTTAAGGGGCCAATTTGTCACCAAA
1 AAAAGTTAAGGGGCTAATTTGTCACCAAA
* *
40175 AAAAGTTAAGAGGTTAATTTGTC-CCAAA
1 AAAAGTTAAGGGGCTAATTTGTCACCAAA
*
40203 ATGGATAGTTAAGGGGCTAATTTG
1 A---AAAGTTAAGGGGCTAATTTG
40227 GGTATTAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.14
29 19 0.45
31 17 0.40
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.27
Consensus pattern (29 bp):
AAAAGTTAAGGGGCTAATTTGTCACCAAA
Found at i:42276 original size:12 final size:12
Alignment explanation
Indices: 42237--42305 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
42227 TTTTTTGGGT
42237 TCAGGAACGAC-
1 TCAGGAACGACA
* * *
42248 TCCAAGATCGACT
1 T-CAGGAACGACA
*
42261 TCAGGAACAACA
1 TCAGGAACGACA
*
42273 TCAGGAACGACG
1 TCAGGAACGACA
*
42285 TCAGGAACGACT
1 TCAGGAACGACA
42297 TCAGGAACG
1 TCAGGAACG
42306 GGAATATCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
11 1 0.02
12 45 0.96
13 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.25, T:0.13
Consensus pattern (12 bp):
TCAGGAACGACA
Done.