Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009860.1 Corchorus capsularis cultivar CVL-1 contig09881, 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: 13674
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:624 original size:118 final size:118
Alignment explanation
Indices: 416--641 Score: 364
Period size: 118 Copynumber: 1.9 Consensus size: 118
406 ATTCAGGTGC
* * *
416 TTGTAAAAAGAAATCCTTAAGCCCATTGTTACTGAGATTTGGTTCGTTGAATATAGATATTTCAA
1 TTGTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTAGTTCGATGAATATAGATATTTCAA
* * *
481 GGAGTCCTTCTGCCAAATATCATACAAAATTGAGTCGGGGCCCTAAAACGCAT
66 GGAGTCCATCAGCCAAAAATCATACAAAATTGAGTCGGGGCCCTAAAACGCAT
* *
534 TTGTAAAAAGAAATCCTTAAGCCCATTGTGA-TCGAGATTTAGTTCGATGATTATAGATATTTTA
1 TTGTAAAAAGAAATCCTTAAGCCCATTGTGACT-GAGATTTAGTTCGATGAATATAGATATTTCA
598 AGGAGTCCATCAGCCAAAAATCATACAAAATTGAGTCGGGGCCC
65 AGGAGTCCATCAGCCAAAAATCATACAAAATTGAGTCGGGGCCC
642 CGAAATGCGT
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 1 0.01
118 98 0.99
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (118 bp):
TTGTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTAGTTCGATGAATATAGATATTTCAA
GGAGTCCATCAGCCAAAAATCATACAAAATTGAGTCGGGGCCCTAAAACGCAT
Found at i:1632 original size:323 final size:321
Alignment explanation
Indices: 536--2304 Score: 2605
Period size: 323 Copynumber: 5.5 Consensus size: 321
526 AAACGCATTT
* *
536 GTAAAAAGAAATCCTTAAGCCCATTGTGA-TCGAGATTT-AGTTCGATGATTATAGATATTTTAA
1 GTAAAAAGAAATCCTTAAGCCCATTGTGACT-GAGATTTGA-TTCGATGAATATAGATATTTCAA
* * * *
599 GGAGTCCATCAGCCAAAAATCATACAAAATTGAGTCGGGGCCCCGAAATGCGTTTTTAACT-AAA
64 GGAGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAA
* * * *
663 ACTGTGAGTGTTAGTACACAATTTCAGCTAAGAATTAACCCGAAATATTTTTTTCTCAATTTTTT
129 ACTGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAT-TTTTTTTCTCAATTTTTT
* * * *
728 GCAACAATACTTATAAAAAATATATAATTGAATGCCAGAAAGATTGAAGGGTTTTTCACGCTTCT
193 GCCACAATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTTCT
*
793 AATATCGTTATTCAATTTTTTTCCGAATTAA-TTCTAATTAAATCGAAACAAGATTCAGATGCTC
258 AATATCGTTTTTCAATTTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
857 GAAAAAAGAAATCCTTAAACCCATTATGACTGAGATTTGCTTCGATAAATATAGATATTTCAAGT
1 GTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAAGG
* * * *
922 AGTTCTTCTG-CAAAATATCATGCAAAATT-ATTCGGGGCCCCGAACCGCGTTTTTAGCTAAAAA
66 AGTCCATCTGCCAAAA-ATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAA
* * * *
985 CTATGAGTGTTAGTACACGATTTAAGCTAAAAACTGACCCGAAAATTTGTTTTCTCAATTTGTTG
130 CTGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCG-AAATTTTTTTTCTCAATTTTTTG
*
1050 CCACAATACTCATAAAAAATATATAATTCAACGCCAGAAAGATTGAAGGATTTTTCACGCTTCTA
194 CCACAATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTTCTA
*
1115 ATAACGTTTTTCAATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
259 ATATCGTTTTTCAATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
** *
1178 GT-AAAAGAAAATCCTTAAGTCTAATT-TGGCTGAGATTTGATTCGATGAATATAGATATTTCAA
1 GTAAAAAG-AAATCCTTAAG-CCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAA
1241 GGAGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAA
64 GGAGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAA
*
1306 ACTGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATTCTATTTTCTCAATTTTTT
129 ACTGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATT-TTTTTTCTCAATTTTTT
1371 GCCACAATACTCATAAAAAATATATAATTCAACT-CCAGAAAGATTGAAGGATTTTTCACGCTTC
193 GCCACAATACTCATAAAAAATATATAATTCAA-TGCCAGAAAGATTGAAGGATTTTTCACGCTTC
* * *
1435 TAATAACGTTTTTCAAATTTTTTTCGAATTAATTTCTAATTAAATCGTAACAAGATTCAGGTGCT
257 TAATATCGTTTTTC-AATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
1500 C
321 C
* *
1501 GTAAAAAGAAATCCTTAAGCCCATTTTGACTGAGATTTGATTCAATGAATATAGATATTTCAAGG
1 GTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAAGG
* * * *
1566 AGTCCATCTGTCAAAAATCATGCAAAATTGAGTCGAGGCCCTGAAACGCGTTTTTAGCTTAAAAC
66 AGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAAC
* * * *
1631 TGTGACTGTAAGTACACGCTTTCAGCTAAAAACTGACCCGAAAATTTTTTTTCTCAATTTGTTGC
131 TGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCG-AAATTTTTTTTCTCAATTTTTTGC
1696 CA-ATATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTTCTA
195 CACA-ATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTTCTA
*
1760 ATATCGTTTTTCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTC
259 ATATCGTTTTTCAATTTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * *
1824 GTAAAAAGAAATCCTTAAGCCCATTGTGACCGAGATTTGGTTCGATGAATATAGATATTTCAAAG
1 GTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAAGG
* * *
1889 AGTCCTTCTGCCAAAAATCATACAAAATTGAG-CAGGGGCCCCGAAACGCGTTTTTAACTAAAAA
66 AGTCCATCTGCCAAAAATCATGCAAAATTGAGTC-GGGGCCCCGAAACGCGTTTTTAGCTAAAAA
1953 CTGTGAGTGTTGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATTTTTTTTTCTCAATTTT
130 CTGTGA--G-TGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAA-TTTTTTTTCTCAATTTT
*
2018 TTGCCACAATACTC--AAAAAATATATAATTCAATGCCAAAAAGATTGAAGGATTTTTCACGCTT
191 TTGCCACAATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTT
* *
2081 CTAATATCGTTTTTCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGTTTCAGATGCT
256 CTAATATCGTTTTTCAATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
2146 C
321 C
* * * * * *
2147 GT-AAAAGAAAATCCTTAAGTCTAATGTGGCTGAGATTTGGTTCGATGAATATAGTTATTTCAAG
1 GTAAAAAG-AAATCCTTAAGCCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAAG
* * * * *
2211 GAGTCCTTCAGCCAAAAATCATGCAAAATTGAGTC-GCGCCCCGAAACACGTTTCTAGCTAAAAA
65 GAGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAA
* * *
2275 CCGTGAGTGTTTGTATACGATTTCAGCTAA
130 CTGTGAGTGTTAGTACACGATTTCAGCTAA
2305 TTGCTGAAGT
Statistics
Matches: 1318, Mismatches: 103, Indels: 56
0.89 0.07 0.04
Matches are distributed among these distances:
319 21 0.02
320 44 0.03
321 313 0.24
322 227 0.17
323 567 0.43
324 82 0.06
325 3 0.00
326 60 0.05
327 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (321 bp):
GTAAAAAGAAATCCTTAAGCCCATTGTGACTGAGATTTGATTCGATGAATATAGATATTTCAAGG
AGTCCATCTGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGAAACGCGTTTTTAGCTAAAAAC
TGTGAGTGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAATTTTTTTTCTCAATTTTTTGCC
ACAATACTCATAAAAAATATATAATTCAATGCCAGAAAGATTGAAGGATTTTTCACGCTTCTAAT
ATCGTTTTTCAATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
Found at i:7596 original size:15 final size:15
Alignment explanation
Indices: 7571--7618 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
7561 GGAAGTTGAG
7571 GAGGAAGAAGAAGAT
1 GAGGAAGAAGAAGAT
* *
7586 GATGACA-AAGAAGAG
1 GAGGA-AGAAGAAGAT
7601 GAGGAAGAAGAAGAT
1 GAGGAAGAAGAAGAT
7616 GAG
1 GAG
7619 AGTGAGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.40, T:0.06
Consensus pattern (15 bp):
GAGGAAGAAGAAGAT
Found at i:7700 original size:15 final size:16
Alignment explanation
Indices: 7682--7723 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
7672 AGTTGATCAT
7682 GAAGATGATGATGA-A
1 GAAGATGATGATGATA
* *
7697 GAAGTTGACGATGATA
1 GAAGATGATGATGATA
7713 -AAGATGATGAT
1 GAAGATGATGAT
7724 CATGGTGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.31, T:0.24
Consensus pattern (16 bp):
GAAGATGATGATGATA
Found at i:10403 original size:48 final size:48
Alignment explanation
Indices: 10306--10433 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 48
10296 AGCGTGCTGC
* * *
10306 TGATGCATCTTATAAGGCCCCTGTTCCTACTTCTAATCTTCGAAAGGA
1 TGATGGATCTTATAAGACCCCTGTTCCTACTACTAATCTTCGAAAGGA
* * ** *
10354 TGGTGGATCTTATAAGACCCCTGTTCCTCCTACTGCTGTTC-AAAGGGA
1 TGATGGATCTTATAAGACCCCTGTTCCTACTACTAATCTTCGAAA-GGA
* * * *
10402 TGATGTAACTTACAAGACCCCTGCTCCTACTA
1 TGATGGATCTTATAAGACCCCTGTTCCTACTA
10434 AGTCACTTTC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
47 3 0.05
48 62 0.95
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (48 bp):
TGATGGATCTTATAAGACCCCTGTTCCTACTACTAATCTTCGAAAGGA
Found at i:12804 original size:7 final size:7
Alignment explanation
Indices: 12792--12816 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12782 GGTTTGATTG
12792 AAATTAC
1 AAATTAC
12799 AAATTAC
1 AAATTAC
12806 AAATTAC
1 AAATTAC
12813 AAAT
1 AAAT
12817 CCGTGTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTAC
Found at i:13185 original size:45 final size:44
Alignment explanation
Indices: 13115--13207 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 44
13105 TTTATAGTAA
* * * * *
13115 AAATGCTAGTGTCTCGTTTTTATTTTAATGGAGAAAATTGATGGT
1 AAATGCCAGTGCCTCGCTTTCATTTTAATGGAGAAAATT-AAGGT
13160 AAATGCCAGTGCCTCGCTTTCATTTTAATGGAGAAAATTAAGGT
1 AAATGCCAGTGCCTCGCTTTCATTTTAATGGAGAAAATTAAGGT
13204 AAAT
1 AAAT
13208 TCTCTCTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 8 0.19
45 35 0.81
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (44 bp):
AAATGCCAGTGCCTCGCTTTCATTTTAATGGAGAAAATTAAGGT
Done.