Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016468.1 Corchorus capsularis cultivar CVL-1 contig16489, 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: 59195
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6882 original size:66 final size:66
Alignment explanation
Indices: 6776--6907 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
6766 GATATTTTTT
6776 AGTCAATCAGATTTAGGTTAGTTTGGATTAGAACTTTTTTGAGTGAATTTTTCGAGTTCATATTT
1 AGTCAATCAGATTTAGGTTAGTTTGGATTAGAACTTTTTTGAGTGAATTTTTCGAGTTCATATTT
6841 A
66 A
*
6842 AGTCAATCAGATTTAGGTTAGTTTGGATTAGAGCTTTTTTGAGTGAATTTTTCGAGTTCATATTT
1 AGTCAATCAGATTTAGGTTAGTTTGGATTAGAACTTTTTTGAGTGAATTTTTCGAGTTCATATTT
6907 A
66 A
6908 TTTTGCCATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (66 bp):
AGTCAATCAGATTTAGGTTAGTTTGGATTAGAACTTTTTTGAGTGAATTTTTCGAGTTCATATTT
A
Found at i:6970 original size:2 final size:2
Alignment explanation
Indices: 6927--6959 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6917 CTTTAGTTAT
6927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6960 AAACATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15377 original size:13 final size:13
Alignment explanation
Indices: 15359--15383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15349 ATCATTATTG
15359 TTTTTTATTTTTA
1 TTTTTTATTTTTA
15372 TTTTTTATTTTT
1 TTTTTTATTTTT
15384 TATAATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:15883 original size:26 final size:26
Alignment explanation
Indices: 15832--15883 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
15822 TATTCTATAC
* **
15832 CTCCAAACTATTTGAACTGATTTATT
1 CTCCAAACAATTTGAACTGACCTATT
*
15858 CTCCAAACAATTTGCACTGACCTATT
1 CTCCAAACAATTTGAACTGACCTATT
15884 GAAAAGGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.37
Consensus pattern (26 bp):
CTCCAAACAATTTGAACTGACCTATT
Found at i:22258 original size:85 final size:85
Alignment explanation
Indices: 22156--22324 Score: 338
Period size: 85 Copynumber: 2.0 Consensus size: 85
22146 TGTTGGCTAC
22156 ACTTATATCAAATTAAGTACCATTATTATTATAGTTATTTATTCGCAATTAATTAAGCTGAATAA
1 ACTTATATCAAATTAAGTACCATTATTATTATAGTTATTTATTCGCAATTAATTAAGCTGAATAA
22221 TTTAATGAATTCAATTATAA
66 TTTAATGAATTCAATTATAA
22241 ACTTATATCAAATTAAGTACCATTATTATTATAGTTATTTATTCGCAATTAATTAAGCTGAATAA
1 ACTTATATCAAATTAAGTACCATTATTATTATAGTTATTTATTCGCAATTAATTAAGCTGAATAA
22306 TTTAATGAATTCAATTATA
66 TTTAATGAATTCAATTATA
22325 CTTGAGCTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (85 bp):
ACTTATATCAAATTAAGTACCATTATTATTATAGTTATTTATTCGCAATTAATTAAGCTGAATAA
TTTAATGAATTCAATTATAA
Found at i:27013 original size:32 final size:31
Alignment explanation
Indices: 26925--27017 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
26915 GCTGCCCTAC
* *
26925 TGGGGCGGCTTCGCCACGACAAGCCGCCCCA
1 TGGGGCGGCTTCGCCACGGCAAGCCGCCCAA
** *
26956 TGAGGGCGGCTT-GCCGTGGCGAAGCCTCCCAA
1 TG-GGGCGGCTTCGCCACGGC-AAGCCGCCCAA
*
26988 GTGGGGCGGCTTCGCCACGGTAAGCCGCCC
1 -TGGGGCGGCTTCGCCACGGCAAGCCGCCC
27018 TCTTGGGACG
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
31 7 0.14
32 35 0.71
33 7 0.14
ACGTcount: A:0.14, C:0.37, G:0.37, T:0.13
Consensus pattern (31 bp):
TGGGGCGGCTTCGCCACGGCAAGCCGCCCAA
Found at i:33284 original size:16 final size:17
Alignment explanation
Indices: 33245--33313 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 17
33235 GCGGGTTAGG
* *
33245 TTGGGTTCGGGTTTAAG
1 TTGGGTTCGGGTTGAAT
*
33262 TTAGG-TCGGGTTGAAT
1 TTGGGTTCGGGTTGAAT
**
33278 TTGGG-TCAAGTT-AAT
1 TTGGGTTCGGGTTGAAT
* *
33293 TCGGGTTTGGGTTGAAT
1 TTGGGTTCGGGTTGAAT
33310 TTGG
1 TTGG
33314 ATTTTGACCA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
15 7 0.18
16 22 0.56
17 10 0.26
ACGTcount: A:0.16, C:0.06, G:0.38, T:0.41
Consensus pattern (17 bp):
TTGGGTTCGGGTTGAAT
Found at i:33511 original size:32 final size:32
Alignment explanation
Indices: 33473--33562 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
33463 GGGTCGGGTT
* * *
33473 TTTTCGGAATCTGATTTTTTCGGGTTTGAGCA
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCA
33505 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCA
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCA
33537 TTTTCGGATTCGGGTTTTTTCGGGTT
1 TTTTCGGATTCGGGTTTTTTCGGGTT
33563 CGGGTTTAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.49
Consensus pattern (32 bp):
TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCA
Found at i:33556 original size:16 final size:16
Alignment explanation
Indices: 33466--33569 Score: 82
Period size: 16 Copynumber: 6.5 Consensus size: 16
33456 CGAATTCGGG
*
33466 TCGGGTTTTTTCGGAA
1 TCGGGTTTTTTCGGAT
* * *
33482 TCTGATTTTTTCGGGT
1 TCGGGTTTTTTCGGAT
* * **
33498 TTGAGCATTTTCGGAT
1 TCGGGTTTTTTCGGAT
*
33514 TCGGGTTTTTTCGGGT
1 TCGGGTTTTTTCGGAT
* * **
33530 TTGAGCATTTTCGGAT
1 TCGGGTTTTTTCGGAT
*
33546 TCGGGTTTTTTCGGGT
1 TCGGGTTTTTTCGGAT
33562 TCGGGTTT
1 TCGGGTTT
33570 AGATGGGTTC
Statistics
Matches: 62, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.09, C:0.12, G:0.31, T:0.48
Consensus pattern (16 bp):
TCGGGTTTTTTCGGAT
Found at i:33960 original size:117 final size:112
Alignment explanation
Indices: 33731--33963 Score: 245
Period size: 117 Copynumber: 2.0 Consensus size: 112
33721 AGGATTTTAG
* * * *
33731 AAAAATAAGTTTAAACACTTTTGAATAAGGTTTAACCCCAACTAAAATATGTTTATTTTTTTAAG
1 AAAAAAAAGTTTAAACACTTGTAAATAAGGTTTAACCCCAACTAAAATATGTTTATTTTTTAAAG
* **
33796 GGTAAATCTTAAATGGTAAGATCCACTATCTTAGGGTTTTATTAAAA
66 GGTAAATCTTAAATGGTAAGATCCACTATCATAGGGTTTTAGGAAAA
* * * * *
33843 AAAAAAAAGTTTGAACACTTGTAAATAAGGTTTAGCCCCAATTATAAAGTTTTTTTTTATTTTTT
1 AAAAAAAAGTTTAAACACTTGTAAATAAGGTTTAACCCCAACTA-AAA---TATGTTTATTTTTT
** * *
33908 AAAAGGGTAAAT-TTCAAATTTTAAGATCCATTATCA-ATGTGTTTTAGGAAAA
62 -AAAGGGTAAATCTT-AAATGGTAAGATCCACTATCATA-GGGTTTTAGGAAAA
33960 AAAA
1 AAAA
33964 TTATATACCT
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
112 38 0.39
113 3 0.03
116 15 0.15
117 42 0.43
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (112 bp):
AAAAAAAAGTTTAAACACTTGTAAATAAGGTTTAACCCCAACTAAAATATGTTTATTTTTTAAAG
GGTAAATCTTAAATGGTAAGATCCACTATCATAGGGTTTTAGGAAAA
Found at i:35746 original size:45 final size:45
Alignment explanation
Indices: 35696--35784 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
35686 GATTACTTCT
35696 CCAGCTCATCATTAA-TCTGGGGTA-GGAATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATTC-GGGGTATGG-ATCTTTTAGTAATTCCAC
35741 CCAGCTCATCATTAATTCGGGGTATGGATCTTTTAGTAATTCCA
1 CCAGCTCATCATTAATTCGGGGTATGGATCTTTTAGTAATTCCA
35785 TTACTCTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
45 38 0.90
46 4 0.10
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (45 bp):
CCAGCTCATCATTAATTCGGGGTATGGATCTTTTAGTAATTCCAC
Found at i:35950 original size:21 final size:21
Alignment explanation
Indices: 35908--35951 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
35898 TTCAAATAAC
** * *
35908 ATAATACTTTTTTTTTTGAAA
1 ATAATACTTCATTATTTCAAA
35929 ATAATACTTCATTATTTCAAA
1 ATAATACTTCATTATTTCAAA
35950 AT
1 AT
35952 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (21 bp):
ATAATACTTCATTATTTCAAA
Found at i:36415 original size:31 final size:31
Alignment explanation
Indices: 36378--36460 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
36368 CAAAGAACAT
** *
36378 ATTCAACCAAGAAAA-AACATTACAGTATCAA
1 ATTCAACCAAGAAAACAA-ATTACAACACCAA
*
36409 ATTCAACCAAGAAAACAAATTACAACACCAG
1 ATTCAACCAAGAAAACAAATTACAACACCAA
*
36440 ATTCAACCAAGAAAATAAATT
1 ATTCAACCAAGAAAACAAATT
36461 GCAGCACAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 44 0.96
32 2 0.04
ACGTcount: A:0.55, C:0.20, G:0.06, T:0.18
Consensus pattern (31 bp):
ATTCAACCAAGAAAACAAATTACAACACCAA
Found at i:42170 original size:21 final size:21
Alignment explanation
Indices: 42146--42223 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 21
42136 ATATGGCTTC
42146 ACATGATTAATTTACTTGCAA
1 ACATGATTAATTTACTTGCAA
42167 ACATGATT-ATGCTGATAAAACTTGCAA
1 ACATGATTAAT--T--T---ACTTGCAA
42194 ACATGATTAATTTACTTGCAA
1 ACATGATTAATTTACTTGCAA
42215 ACATGATTA
1 ACATGATTA
42224 TGCTGATAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
20 2 0.04
21 25 0.51
22 1 0.02
24 2 0.04
26 1 0.02
27 16 0.33
28 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (21 bp):
ACATGATTAATTTACTTGCAA
Found at i:42197 original size:27 final size:27
Alignment explanation
Indices: 42159--42233 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 27
42149 TGATTAATTT
42159 ACTTGCAAACATGATTATGCTGATAAA
1 ACTTGCAAACATGATTATGCTGATAAA
42186 ACTTGCAAACATGATTAAT--T--T---
1 ACTTGCAAACATGATT-ATGCTGATAAA
42207 ACTTGCAAACATGATTATGCTGATAAA
1 ACTTGCAAACATGATTATGCTGATAAA
42234 TGTGAAGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
20 2 0.05
21 16 0.40
22 1 0.03
24 2 0.05
26 1 0.03
27 16 0.40
28 2 0.05
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (27 bp):
ACTTGCAAACATGATTATGCTGATAAA
Found at i:56092 original size:21 final size:22
Alignment explanation
Indices: 56045--56092 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
56035 TTCATTGAGT
*
56045 ATTAATGAGTTAAATAATCGAA
1 ATTAATGAGTTAAAAAATCGAA
*
56067 GTTAA-GAGTTAAAGAAAT-GAA
1 ATTAATGAGTTAAA-AAATCGAA
56088 ATTAA
1 ATTAA
56093 AGCACTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.17, T:0.29
Consensus pattern (22 bp):
ATTAATGAGTTAAAAAATCGAA
Done.