Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011755.1 Corchorus capsularis cultivar CVL-1 contig11776, 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: 17623
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Found at i:525 original size:2 final size:2
Alignment explanation
Indices: 520--548 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
510 TTTTGGATCT
520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
549 CCTTATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5787 original size:330 final size:327
Alignment explanation
Indices: 4679--6003 Score: 1218
Period size: 330 Copynumber: 4.0 Consensus size: 327
4669 TCGTGATGAT
* * * *
4679 AAAAATGACCCGAAAGATTTTTCCACATTTTTTGGC-AAAACTACTCATAAAATTTATATATAAT
1 AAAAATTACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAA-TACTCAT-AAA--TATATATAAT
* * * *
4743 TCAACGTCAAAAGGATTGGAGGACTTTTCATGCTTTTAATATCGTTTTTCATATTTTTTGCGAAT
62 TCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTT-TGAAT
* * * * * * *
4808 CAATTTCTAATTAAATCGAAAAAATATTCAGATTCACATTAAAAAAATCCTTAAATTCAATGTGA
126 TAATTTCTAATTAAATCG-AAAAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATTCAATGTGG
* * * * * * *
4873 CTGAGATTTGATTAGATAAATAAAGATATTTCAAGGAATCTCGGCGCCGAAAA-TCATGCAAAAC
190 TTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT--ACGTCAAAAATTCATGCAAAAC
* * * * * *
4937 -AGAGTTGTGGCAGTGGAAC-AAGTTTTTAGCCAAAAACTGTGATGGTTAGTACACAATTTCGGC
253 TA-AGTTGGGGCACTGGAACGCA-TTTTTAGCCAAAAACTGCGATGGTTAGTACACGATTTCGAC
5000 TAAAATTTTGC-
316 TAAAATTTTGCA
* * * * **
5011 AAAAATTGACTCG-AAAGTTATTTCCTCAATTTTTGGTTAAAATACTCATAAAAAGTATGCAATT
1 AAAAATT-ACCCGAAAAATT-TTTCCTCAATTTTTGGCTAAAATACTCATAAATA-TATATAATT
* * ** * * * * * *
5075 CGATGTAAAAAAGATTGAAGGGCTTTTAAGGCTTCTAATAATATTGTTTTTCCTA-TTTTTTGAA
63 CAACGCCAAAAAGATTGGAGGACTTTTCACGCTT-T--TAATATCGTTTTTCATATTTTTTTG-A
* *
5139 ATTAATTTCTAATTAAATCTAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAGTCTAAT
124 ATTAATTTCTAATTAAATCGAAA-AAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATTC-AAT
* * * * * *
5203 ATGG-CGGGATTTGGTTAGACGAATATAGATATTTCAAGGATTGC-AC--CAAAAATTCATGCAA
186 GTGGTTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT-CTACGTCAAAAATTCATGCAA
* * * * * * * *
5264 AACTGAG-TCGAGCCCTGGAATGCATTTTTAGTCGAAAAC--C-ATGGTTAGTACACGATTTCGG
250 AACTAAGTTGGGGCACTGGAACGCATTTTTAGCCAAAAACTGCGATGGTTAGTACACGATTTCGA
*
5325 CTAAAATTTTACA
315 CTAAAATTTTGCA
* * * * * ** *
5338 AAAAATTTATCCGAAAGATTTTTCCTCGATTTCTAGAGAAAATACTCATTATAA-ACATATAATT
1 AAAAA-TTACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCA-TA-AATATATATAATT
* * * * *
5402 CATCACCAAAAA-ATTTGGAAGCCTTTTTTCACGCTTTTAATATCATTTTTCATATTTTTTTGAA
63 CAACGCCAAAAAGA-TTGGAGGAC--TTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTGAA
5466 TTAATTTCTAATTAAATCGAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
125 TTAATTTCTAATTAAATCGAAAAAGATTCAGATGCTCGTAAAAA-AAATCCTTAAATTCAATGTG
* *
5531 GTTGAGATTTGATTAGATGAATATAGATATTTTAAGGAGTCTACGTGCCAAAATTCATGCAAAAC
189 GTTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTACGT-CAAAAATTCATGCAAAAC
* * * * * *
5596 TAAGTTGGGGCCCCGAAACGCGTTTTTAGCCAAAAACTGCGCTGTTTAGTACACGATTTC-ACTA
253 TAAGTTGGGGCACTGGAACGCATTTTTAGCCAAAAACTGCGATGGTTAGTACACGATTTCGACTA
* *
5660 GAATTTTGTA
318 AAATTTTGCA
*
5670 AAAAATTACCCGAAAAATTTTTCCGTCAATTTTTGGCTAAAATACTCATGAAATATATATAAATC
1 AAAAATTACCCGAAAAATTTTTCC-TCAATTTTTGGCTAAAATACTCAT-AAATATATATAATTC
* *
5735 AACGCCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
64 AACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTGAATTAA
* * * * * *
5800 TTTCTAATTAAATAGAAGCAAGATTCATATGCTCGTAAAAAAAATTCTTAAATTCAATTTAGTTG
129 TTTCTAATTAAATCGAA-AAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATTCAATGTGGTTG
* * * * * * *
5865 AGATTTGATTAAATGAATATGGATATCTCAAAGAGTTTAGCGT-AAAAAATCATGCAAAACTTAG
193 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTA-CGTCAAAAATTCATGCAAAACTAAG
* * * * * * *
5929 TCGGGGCACTGGAACGCATTTTTAGCAAAAAAACCGTGATGATTAATACACGA-TTC-AGCTAGA
257 TTGGGGCACTGGAACGCATTTTTAGC-CAAAAACTGCGATGGTTAGTACACGATTTCGA-CTAAA
5992 ATTTTGCA
320 ATTTTGCA
6000 AAAA
1 AAAA
6004 TTGATTCGAA
Statistics
Matches: 805, Mismatches: 146, Indels: 86
0.78 0.14 0.08
Matches are distributed among these distances:
325 38 0.05
326 107 0.13
327 56 0.07
328 10 0.01
329 100 0.12
330 186 0.23
331 78 0.10
332 78 0.10
333 119 0.15
334 33 0.04
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (327 bp):
AAAAATTACCCGAAAAATTTTTCCTCAATTTTTGGCTAAAATACTCATAAATATATATAATTCAA
CGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTGAATTAATT
TCTAATTAAATCGAAAAAGATTCAGATGCTCGTAAAAAAAATCCTTAAATTCAATGTGGTTGAGA
TTTGATTAGATGAATATAGATATTTCAAGGAGTCTACGTCAAAAATTCATGCAAAACTAAGTTGG
GGCACTGGAACGCATTTTTAGCCAAAAACTGCGATGGTTAGTACACGATTTCGACTAAAATTTTG
CA
Found at i:8141 original size:15 final size:16
Alignment explanation
Indices: 8104--8155 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 16
8094 AAATTTCATG
*
8104 ATTATAAAT-AATAAT
1 ATTATAATTAAATAAT
8119 ATTATAATTAAAT-AT
1 ATTATAATTAAATAAT
8134 ATTATAATCTAAA-AAT
1 ATTATAAT-TAAATAAT
8150 AATTAT
1 -ATTAT
8156 TAGAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 18 0.56
16 9 0.28
17 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATAATTAAATAAT
Found at i:11364 original size:21 final size:21
Alignment explanation
Indices: 11325--11363 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11315 CCTTTTCTTC
11325 TTTTCTCTCCCAAGTTTTTAG
1 TTTTCTCTCCCAAGTTTTTAG
*
11346 TTTT-TCTTCCAAGTTTTT
1 TTTTCTCTCCCAAGTTTTT
11364 TTATACTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.13, C:0.21, G:0.08, T:0.59
Consensus pattern (21 bp):
TTTTCTCTCCCAAGTTTTTAG
Found at i:12186 original size:2 final size:2
Alignment explanation
Indices: 12179--12206 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12169 GTCAATTCAG
12179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12207 ACGTTATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12495 original size:21 final size:20
Alignment explanation
Indices: 12458--12500 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
12448 GATGCACCCC
12458 TTGTGGTGCACCACCTTACAA
1 TTGTGGTGCACCACCTTA-AA
*
12479 TTGTGGATGCA-CTCCTTAAA
1 TTGTGG-TGCACCACCTTAAA
12499 TT
1 TT
12501 TTGATTCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (20 bp):
TTGTGGTGCACCACCTTAAA
Found at i:16700 original size:60 final size:60
Alignment explanation
Indices: 16598--16713 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 60
16588 TGGTCGGGGA
* *
16598 GAAATTGTTCCAATTTTGATAGTTTGGGGAGTGAAAGTTCCAAATTAAAAGTTCAGAAGG
1 GAAATTGTTCCAATTTTGATAGTTTAGGGAGTGAAAGTTCCAAATTAAAAATTCAGAAGG
16658 GAAATTTGTTCCAATTTTGATAGTTTAGGG-GTGAAAGTTCCAAATTAAAAATTCAG
1 GAAA-TTGTTCCAATTTTGATAGTTTAGGGAGTGAAAGTTCCAAATTAAAAATTCAG
16714 TGGAGAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 29 0.55
61 24 0.45
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (60 bp):
GAAATTGTTCCAATTTTGATAGTTTAGGGAGTGAAAGTTCCAAATTAAAAATTCAGAAGG
Found at i:17603 original size:2 final size:2
Alignment explanation
Indices: 17596--17623 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17586 ATACTTCGGC
17596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.