Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008181.1 Corchorus capsularis cultivar CVL-1 contig08202, 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: 46298
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:87 original size:30 final size:31
Alignment explanation
Indices: 51--117 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
41 GTGCAAATGG
51 GTCCCTGAAG-TGAACTT-AGTGAGCAATTGA
1 GTCCCTGAAGTTG-ACTTAAGTGAGCAATTGA
* * *
81 GTCCCTGAAGTTGAGTTAATTGAGCAATTGG
1 GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
112 GTCCCT
1 GTCCCT
118 CACCAAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (31 bp):
GTCCCTGAAGTTGACTTAAGTGAGCAATTGA
Found at i:1757 original size:100 final size:100
Alignment explanation
Indices: 1630--1830 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
1620 ATGGTTACTA
1630 AAAAAGTTTTAGAAGTTATCAAAACAATTATGATCCTATATATCAATAAATTCAATAATATTGTA
1 AAAAAGTTTTAGAAGTTATCAAAACAATTATGATCCTATATATCAATAAATTCAATAATATTGTA
1695 TTCTTAGCATCTTTAGTAAATGTTACCAATTTTTT
66 TTCTTAGCATCTTTAGTAAATGTTACCAATTTTTT
*
1730 AAAAAGTTTTAGAAGTTATCAAAACAATTATGATCCTATATATCAATAAATTCAATAATCTTGTA
1 AAAAAGTTTTAGAAGTTATCAAAACAATTATGATCCTATATATCAATAAATTCAATAATATTGTA
1795 TTCTTAGCATCTTTAGTAAATGTTACCAATTTTTT
66 TTCTTAGCATCTTTAGTAAATGTTACCAATTTTTT
1830 A
1 A
1831 TTTATCTAAG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.41
Consensus pattern (100 bp):
AAAAAGTTTTAGAAGTTATCAAAACAATTATGATCCTATATATCAATAAATTCAATAATATTGTA
TTCTTAGCATCTTTAGTAAATGTTACCAATTTTTT
Found at i:2698 original size:28 final size:31
Alignment explanation
Indices: 2634--2696 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
2624 TTCATTAATG
2634 GTGAAGATCACCAATTTTCTATCTAATTTTTT
1 GTGAAGATCACCAATTTTCTATCT-ATTTTTT
* *
2666 GTGAAGATTACCAATTTTCTAT-TTTTTTTT
1 GTGAAGATCACCAATTTTCTATCTATTTTTT
2696 G
1 G
2697 AAAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.24
31 1 0.03
32 21 0.72
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (31 bp):
GTGAAGATCACCAATTTTCTATCTATTTTTT
Found at i:7256 original size:79 final size:80
Alignment explanation
Indices: 7159--7352 Score: 354
Period size: 79 Copynumber: 2.4 Consensus size: 80
7149 AAGAATGTTA
* *
7159 TTGGATTTGCTTGGTGGTAGTTAATAGGAATATTGTAAACTTGTTTTTGCTTGCTGGTATTTCAT
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGTAAACTTGTTTTTGCTTGCTGGTATTTCAT
7224 ATGCAGATTGCATAC
66 ATGCAGATTGCATAC
7239 TT-GTTTTGCTTGCTGGTAGTTAATAGGAATATTGTAAACTTGTTTTTGCTTGCTGGTATTTCAT
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGTAAACTTGTTTTTGCTTGCTGGTATTTCAT
7303 ATGCAGATTGCATAC
66 ATGCAGATTGCATAC
*
7318 TTGGTTTTGCTTGCTGGTAGTTGATAGGAATATTG
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTG
7353 CATACCTATT
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
79 77 0.70
80 33 0.30
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (80 bp):
TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGTAAACTTGTTTTTGCTTGCTGGTATTTCAT
ATGCAGATTGCATAC
Found at i:7353 original size:40 final size:40
Alignment explanation
Indices: 7159--7357 Score: 220
Period size: 40 Copynumber: 5.0 Consensus size: 40
7149 AAGAATGTTA
* * * *
7159 TTGGATTTGCTTGGTGGTAGTTAATAGGAATATTGTAAAC
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
* * * * * *
7199 TTGTTTTTGCTTGCTGGTATTTCATATGCAGATTGCATAC
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
* *
7239 TT-GTTTTGCTTGCTGGTAGTTAATAGGAATATTGTAAAC
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
* * * * * *
7278 TTGTTTTTGCTTGCTGGTATTTCATATGCAGATTGCATAC
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
*
7318 TTGGTTTTGCTTGCTGGTAGTTGATAGGAATATTGCATAC
1 TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
7358 CTATTCTGAT
Statistics
Matches: 126, Mismatches: 32, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
39 31 0.25
40 95 0.75
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.44
Consensus pattern (40 bp):
TTGGTTTTGCTTGCTGGTAGTTAATAGGAATATTGCATAC
Found at i:10765 original size:2 final size:2
Alignment explanation
Indices: 10751--10789 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
10741 ACGAAAAGAA
*
10751 AT AT AT -T AA 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 AT AT AT AT AT
10790 TATTACTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13006 original size:16 final size:16
Alignment explanation
Indices: 12987--13033 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
12977 AATTTTTGGG
12987 TACCCGAACCCGAAAT
1 TACCCGAACCCGAAAT
* *
13003 TACCCGAATCC-AAAC
1 TACCCGAACCCGAAAT
*
13018 GACCCGAACCCGAAAT
1 TACCCGAACCCGAAAT
13034 GACTAAAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.38, C:0.38, G:0.13, T:0.11
Consensus pattern (16 bp):
TACCCGAACCCGAAAT
Found at i:13047 original size:31 final size:32
Alignment explanation
Indices: 12988--13061 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 32
12978 ATTTTTGGGT
* ** *
12988 ACCCGAACCCGAAATTACCCGAATCC-AAACG
1 ACCCGAACCCGAAATGACCAAAACCCAAAACG
* *
13019 ACCCGAACCCGAAATGACTAAAACCCAAAATG
1 ACCCGAACCCGAAATGACCAAAACCCAAAACG
13051 A-CCGAACCCGA
1 ACCCGAACCCGA
13062 TCAACCCGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.42, C:0.36, G:0.14, T:0.08
Consensus pattern (32 bp):
ACCCGAACCCGAAATGACCAAAACCCAAAACG
Found at i:14413 original size:15 final size:17
Alignment explanation
Indices: 14378--14415 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
14368 AACCGAAAAC
14378 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
14394 GACCCGAACCCAG-A-T
1 GACCCGAACCCAGAATT
14409 GACCCGA
1 GACCCGA
14416 CGTTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.34, C:0.39, G:0.18, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:17417 original size:19 final size:19
Alignment explanation
Indices: 17374--17417 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17364 TTGTCAATCC
*
17374 TCTTCTCTTCTTCTGTAAT
1 TCTTTTCTTCTTCTGTAAT
* * *
17393 TTTTTTCTTTTTCTGTTAT
1 TCTTTTCTTCTTCTGTAAT
17412 TCTTTT
1 TCTTTT
17418 GATTTCATGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.18, G:0.05, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTCTTCTGTAAT
Found at i:28271 original size:21 final size:21
Alignment explanation
Indices: 28233--28273 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28223 GCTAAAGCAG
*
28233 AAATAAAAGCATTAGAGCTAA
1 AAATAAAAGCATCAGAGCTAA
* *
28254 AAATAAAGGCATCCGAGCTA
1 AAATAAAAGCATCAGAGCTA
28274 TTAGCAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATAAAAGCATCAGAGCTAA
Found at i:29585 original size:21 final size:21
Alignment explanation
Indices: 29561--29607 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29551 CAGTAGCTTA
* *
29561 TTCTTCCTCTTTTTCACTTCC
1 TTCTTCCTCGTTCTCACTTCC
*
29582 TTCTTCCTCGTTCTCACTTTC
1 TTCTTCCTCGTTCTCACTTCC
29603 TTCTT
1 TTCTT
29608 TTTCTTCTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.36, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTTCCTCGTTCTCACTTCC
Found at i:30244 original size:18 final size:18
Alignment explanation
Indices: 30217--30257 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
30207 AGTCCACCAG
30217 TGTTGATCCACCTAAACC
1 TGTTGATCCACCTAAACC
* *
30235 TGTTGCTCCACCTGAACC
1 TGTTGATCCACCTAAACC
30253 TGTTG
1 TGTTG
30258 TGAGAAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.32
Consensus pattern (18 bp):
TGTTGATCCACCTAAACC
Found at i:32418 original size:15 final size:15
Alignment explanation
Indices: 32400--32432 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32390 CCAACTCCTC
*
32400 CCCCTCCCTACCCCA
1 CCCCTCCCCACCCCA
32415 CCCCTCCCCACCCCA
1 CCCCTCCCCACCCCA
32430 CCC
1 CCC
32433 TTCTCCCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.79, G:0.00, T:0.09
Consensus pattern (15 bp):
CCCCTCCCCACCCCA
Found at i:33326 original size:31 final size:31
Alignment explanation
Indices: 33249--33310 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
33239 TAAGACTGTC
33249 ATTACAACCTCTTTTTTAATAATTTTTAAGT
1 ATTACAACCTCTTTTTTAATAATTTTTAAGT
33280 ATTACAACCTCTTTTTTAATAATTTTTAAGT
1 ATTACAACCTCTTTTTTAATAATTTTTAAGT
33311 GTTTCATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTACAACCTCTTTTTTAATAATTTTTAAGT
Found at i:33990 original size:107 final size:105
Alignment explanation
Indices: 33705--33982 Score: 380
Period size: 106 Copynumber: 2.6 Consensus size: 105
33695 AAGGTTTTTT
* * *
33705 TTATTATAGAGTTGTAGAAATAAAATATAAAACGAATTTCACTAAGTTTAGCCCCAAATCAAAAT
1 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAAT
* *
33770 TTTATTTTTATTTAAGGGTAAATTTCAAAATTAATAACTTA
65 TTTATTTTTATTTAAGAGTAAATTCCAAAATTAATAACTTA
* * *
33811 TTGTTATAGAGTTTTAGAAATAAAATACAAAACTAATTTCACTAAGTTTAACTCCAAATTAAAAT
1 TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGC-CCAAATTAAAAT
** *
33876 TTTATTTTTATTTCAAGAGTAAATTCCATGATTAATAATTTA
65 TTTATTTTTATTT-AAGAGTAAATTCCAAAATTAATAACTTA
* *
33918 TTATTATAGGGTTTTAGAAATAAAATATATATAACTAA-TTCA-TAAGTTTAGCCAAAATTAAAA
1 TTATTATAGAGTTTTAGAAATAAAATATA-A-AACTAATTTCACTAAGTTTAGCCCAAATTAAAA
33981 TT
64 TT
33983 AAAATTTTAT
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
105 1 0.01
106 82 0.54
107 58 0.38
108 5 0.03
109 6 0.04
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (105 bp):
TTATTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT
TTATTTTTATTTAAGAGTAAATTCCAAAATTAATAACTTA
Found at i:35869 original size:33 final size:33
Alignment explanation
Indices: 35832--35894 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
35822 TCCTAGGACT
35832 TGTAACATTCGGGAAACTCTCCCAAACTCTGAC
1 TGTAACATTCGGGAAACTCTCCCAAACTCTGAC
* **
35865 TGTAATATTCGGGAGTCTCTCCCAAACTCT
1 TGTAACATTCGGGAAACTCTCCCAAACTCT
35895 ATTGTCATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTAACATTCGGGAAACTCTCCCAAACTCTGAC
Found at i:37627 original size:33 final size:33
Alignment explanation
Indices: 37585--37650 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
37575 AAGTCATCAA
37585 ATTTGGTATTACAAATGATTTCATATGACCCCT
1 ATTTGGTATTACAAATGATTTCATATGACCCCT
*
37618 ATTTGGTATTACAAATTATTTCATATGACCCCT
1 ATTTGGTATTACAAATGATTTCATATGACCCCT
37651 CTTTTAACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (33 bp):
ATTTGGTATTACAAATGATTTCATATGACCCCT
Done.