Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022188.1 Corchorus olitorius cultivar O-4 contig22221, 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: 8582
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Found at i:332 original size:96 final size:96
Alignment explanation
Indices: 196--470 Score: 347
Period size: 96 Copynumber: 2.8 Consensus size: 96
186 AATGGGTCGG
* * * *
196 AAGGTCCCAATTTTCCATCAATATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCCCAGTTTTCA
1 AAGGT-CCAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTTC-
** * *
261 TTCAATATTCGGAAAATGCCCCTTCC-CTATCAA
64 TTCAATATTCCAAAAATACCCCTTCCACGA-CAA
* *
294 AAGGTCCAATTTTCCTTCAAAATT-CAAAAATGCCCCTTCCCGGTCGGGAGGTCTTAGTTTTCCT
1 AAGGTCCAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTT-CT
* * *
358 TCAAAATTCCAAAAATACCCCTTCCAGGACGA
65 TCAATATTCCAAAAATACCCCTTCCACGACAA
* * *
390 AAGGTCTCAGTTTTTCTACAAAATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTTCT
1 AAGGTC-CAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTTCT
455 TCAATATTCCAAAAAT
65 TCAATATTCCAAAAAT
471 TTGCCCTTCC
Statistics
Matches: 154, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
96 63 0.41
97 51 0.33
98 40 0.26
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (96 bp):
AAGGTCCAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTTCTT
CAATATTCCAAAAATACCCCTTCCACGACAA
Found at i:359 original size:48 final size:49
Alignment explanation
Indices: 190--492 Score: 326
Period size: 49 Copynumber: 6.2 Consensus size: 49
180 GACTAAAATG
* * * *
190 GGTCGGAAGGTCCCAATTTTCCATCAATATTCCAAAAATGCCCCTTCCC
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
* * * * **
239 GGTCAGAAGGTCCCAGTTTTCATTCAATATTCGGAAAATGCCCCTTCCC
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
** ** *
288 TATCAAAAGGTC-CAATTTTCCTTCAAAATT-CAAAAATGCCCCTTCCC
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
* * * *
335 GGTCGGGAGGTCTTAGTTTTCCTTCAAAATTCCAAAAATACCCCTTCCA
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
* * * *
384 GGACGAAAGGTCTCAGTTTTTCTACAAAATTCCAAAAATGCCCCTTCCC
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
* *
433 GGTCGGAAGGTCTCAGTTTT-CTTCAATATTCCAAAAATTTG-CCCTTCCT
1 GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAA--TGCCCCTTCCC
*
482 AGTCGGAAGGT
1 GGTCGGAAGGT
493 GTTGTTTACG
Statistics
Matches: 213, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
47 22 0.10
48 46 0.22
49 143 0.67
50 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (49 bp):
GGTCGGAAGGTCTCAGTTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
Found at i:457 original size:145 final size:146
Alignment explanation
Indices: 206--470 Score: 331
Period size: 145 Copynumber: 1.8 Consensus size: 146
196 AAGGTCCCAA
* * * * * *
206 TTTTCCATCAATATTCCAAAAATGCCCCTTCCCGGTCAGAAGGTCCCAGTTTTCATTCAATATTC
1 TTTTCCATCAAAATTCCAAAAATACCCCTTCCAGGACAGAAGGTCCCAGTTTTCATACAAAATTC
** *
271 GGAAAATGCCCCTTCCCTATCAAAAGGTCCAATTTTCCTTCAAAATT-CAAAAATGCCCCTTCCC
66 CAAAAATGCCCCTTCCCGATCAAAAGGTCCAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
335 GGTCGGGAGGTCTTAG
131 GGTCGGGAGGTCTTAG
* *
351 TTTTCCTTCAAAATTCCAAAAATACCCCTTCCAGGAC-GAAAGGTCTCAGTTTTTC-TACAAAAT
1 TTTTCCATCAAAATTCCAAAAATACCCCTTCCAGGACAG-AAGGTCCCAG-TTTTCATACAAAAT
* ** * *
414 TCCAAAAATGCCCCTTCCCGGTCGGAAGGTCTCAGTTTT-CTTCAATATTCCAAAAAT
64 TCCAAAAATGCCCCTTCCCGATCAAAAGGTC-CAATTTTCCTTCAAAATTCCAAAAAT
471 TTGCCCTTCC
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
144 1 0.01
145 81 0.81
146 18 0.18
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (146 bp):
TTTTCCATCAAAATTCCAAAAATACCCCTTCCAGGACAGAAGGTCCCAGTTTTCATACAAAATTC
CAAAAATGCCCCTTCCCGATCAAAAGGTCCAATTTTCCTTCAAAATTCCAAAAATGCCCCTTCCC
GGTCGGGAGGTCTTAG
Found at i:527 original size:41 final size:41
Alignment explanation
Indices: 470--717 Score: 254
Period size: 41 Copynumber: 6.1 Consensus size: 41
460 ATTCCAAAAA
* *
470 TTTGCCCTTCCTAGTCGGAAGGTGTTGTTTACGTTTCTCAG
1 TTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCAG
* * * *
511 TTTGCCCTTTCCAGTCGGGAGGTGTTGTCTT-CTTTTCCCAA
1 TTTGCCCTTCCCAGTCGGAAGGTGTTGT-TTACGTTTCCCAG
* *
552 TTTGCCCTTCCCAGTCGGAAGGTATTATTTACGTTTCCGC-G
1 TTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCC-CAG
* * * * * *
593 TTTGCCCTCCCCGGTCGGGAGGTGTTGTTTTCTTTTCCCAA
1 TTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCAG
* * *
634 TTTGCCCTTCCCAGTCAGAAAGTGTTGTTTACTTTTCCCCA-
1 TTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTT-CCCAG
* *
675 TTTGCCCTTCCCAGT-GTGAAGGTGTTGTTCA-GTTTCTCAG
1 TTTGCCCTTCCCAGTCG-GAAGGTGTTGTTTACGTTTCCCAG
715 TTT
1 TTT
718 CTCGGTCTGC
Statistics
Matches: 169, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
39 3 0.02
40 9 0.05
41 150 0.89
42 7 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (41 bp):
TTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCAG
Found at i:703 original size:82 final size:82
Alignment explanation
Indices: 468--703 Score: 314
Period size: 82 Copynumber: 2.9 Consensus size: 82
458 ATATTCCAAA
* * *
468 AATTTGCCCTTCCTAGTCGGAAGGTGTTGTTTACGTTT-CTCAGTTTGCCCTTTCCAGTCGGGAG
1 AATTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCCA-TTTGCCCTTCCCAGTCGGGAG
*
532 GTGTTGTCTTCTTTTCCC
65 GTGTTGTTTTCTTTTCCC
* * * * * *
550 AATTTGCCCTTCCCAGTCGGAAGGTATTATTTACGTTTCCGCGTTTGCCCTCCCCGGTCGGGAGG
1 AATTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCCATTTGCCCTTCCCAGTCGGGAGG
615 TGTTGTTTTCTTTTCCC
66 TGTTGTTTTCTTTTCCC
* * * *
632 AATTTGCCCTTCCCAGTCAGAAAGTGTTGTTTACTTTTCCCCATTTGCCCTTCCCAGT-GTGAAG
1 AATTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCCATTTGCCCTTCCCAGTCG-GGAG
696 GTGTTGTT
65 GTGTTGTT
704 CAGTTTCTCA
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 1 0.01
82 130 0.98
83 2 0.02
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (82 bp):
AATTTGCCCTTCCCAGTCGGAAGGTGTTGTTTACGTTTCCCCATTTGCCCTTCCCAGTCGGGAGG
TGTTGTTTTCTTTTCCC
Found at i:4316 original size:17 final size:15
Alignment explanation
Indices: 4280--4328 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4270 TTTGAGAAGG
* *
4280 GAAAGGAGAAAATAA
1 GAAAGGAAAAAAAAA
*
4295 GAGGAGG-AAAAAAAA
1 GA-AAGGAAAAAAAAA
4310 GAAAGGAAAAAAAAA
1 GAAAGGAAAAAAAAA
4325 GAAA
1 GAAA
4329 AGCATAAGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
GAAAGGAAAAAAAAA
Found at i:6249 original size:24 final size:24
Alignment explanation
Indices: 6217--6279 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
6207 TAATATATAG
6217 CGGCGTCTAGACGCCACTATTTAA
1 CGGCGTCTAGACGCCACTATTTAA
6241 CGGCGTCTAGACGCCACTATTTAA
1 CGGCGTCTAGACGCCACTATTTAA
6265 CGGCGTCTAGACGCC
1 CGGCGTCTAGACGCC
6280 GTTATCTGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (24 bp):
CGGCGTCTAGACGCCACTATTTAA
Found at i:6446 original size:32 final size:32
Alignment explanation
Indices: 6352--6519 Score: 194
Period size: 32 Copynumber: 5.3 Consensus size: 32
6342 ACTATTTAGC
** *
6352 GGCGTTTTGTTCTGAAGACGCCACTAAATAAG
1 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
* *
6384 GGCGATTT-TTCTTTAGACGCTGCTAAATAAG
1 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
* *
6415 GGCGTTTTGTTTTTTAAACGCCGCTAAATAAG
1 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
* * * * * *
6447 GGCATTTTCTTCTATAGACGACGCTAAATTAT
1 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
**
6479 GGCGTTTTGTTCCATAGACGCCGCTAAATAAG
1 GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
6511 GGCGTTTTG
1 GGCGTTTTG
6520 AAACTTGACA
Statistics
Matches: 112, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
31 26 0.23
32 86 0.77
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (32 bp):
GGCGTTTTGTTCTTTAGACGCCGCTAAATAAG
Done.