Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015182.1 Corchorus capsularis cultivar CVL-1 contig15203, 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, 947
Length: 1579
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:707 original size:325 final size:326
Alignment explanation
Indices: 1--738 Score: 1017
Period size: 325 Copynumber: 2.3 Consensus size: 326
*
1 CAAATCCTTATAT-CAAATATGGCTGAGA-TTTAGTTTGATGTATATAGATATTTCAAGGAGTCT
1 CAAATCCTTATATCCAAA-ATGGCTGAGACTTT-GTTTGATGAATATAGATATTTCAAGGAGTCT
* * * * * * * ** * *
64 TTCTGCCAAAAATAATGCGAAATTGATCATGGGGCTCCCGGAATGCGTTTTTAACCAAAAACCGT
64 TTCTGCCAAAAATCATGCAAAATTAAGCACGGAGCTCCCGAAACACATTTTTAACCAAAAACAGT
* * * *
129 GATGATTAGTACACGATTTCGGCTGCAAACTACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAA
129 GATGATTAATACAAGATTTCGGCTGCAAACTACCCGAAAAGTTCTTTCTCAATTTGTTGCCACAA
* * * *
194 TATTCAGAAAAAATATATAAGTTAATGCCAAAAAGATTGACGGGCTTTTCAGGCTTCTAATATCG
194 TACTCAGAAAAAATATATAAGTTAATGCCAAAAAGATTGACGGGCTTTCCAAGCTTCGAATATCG
* *
259 TTTTTTCTTTTTTTTTTCCCAATTAATTTCAAATTGAATAGAAACAAGATTGAGATGCTCGAAAA
259 TTTTTTCTATTTTTTTTCCCAATTAATTTCAAATTAAATAGAAACAAGATTGAGATGCTCGAAAA
*
324 CAA
324 AAA
* *
327 CAAATCCTTATATCCAAAATGGCTGAGACTTTGTTCGATGAATATAGATATTTCAAGGAGTCTTC
1 CAAATCCTTATATCCAAAATGGCTGAGACTTTGTTTGATGAATATAGATATTTCAAGGAGTCTTT
* *
392 CTGCCAAAAATCATGCAAAATTAAGC-CGGAGCTCCCGAAACACA-TTTTATCATAAAAACAGTG
66 CTGCCAAAAATCATGCAAAATTAAGCACGGAGCTCCCGAAACACATTTTTAAC-CAAAAACAGTG
* *
455 ATGGA-TAATATAAGATTTCGGCTGCAAACTGACCTGAAAAGTTCTTTCTCAATTTGTTGCCACA
130 AT-GATTAATACAAGATTTCGGCTGCAAACT-ACCCGAAAAGTTCTTTCTCAATTTGTTGCCACA
* *
519 ATACTCTGAAAAAATATATAA-TTCAATGCCAAAAAGATTGACGGGCTTTCCAAGCTTGGAATAT
193 ATACTCAGAAAAAATATATAAGTT-AATGCCAAAAAGATTGACGGGCTTTCCAAGCTTCGAATAT
* *
583 CGTTTTTTC-ATTTTTTTTCCGAATTAATTTCTAATTAAATCA-AAACAAGATTGAGATGCTCGA
257 CGTTTTTTCTATTTTTTTTCCCAATTAATTTCAAATTAAAT-AGAAACAAGATTGAGATGCTCGA
646 AAAAAA
321 AAAAAA
* * *
652 CAAATCC-TATTATCCAAAATGGCTGAGACTTTGTTTGGTGAACATAGAAATTTCAAGGAGTCTT
1 CAAATCCTTA-TATCCAAAATGGCTGAGACTTTGTTTGATGAATATAGATATTTCAAGGAGTCTT
716 TCTGCCAAAAATCATGCAAAATT
65 TCTGCCAAAAATCATGCAAAATT
739 GAGCTGGGGC
Statistics
Matches: 366, Mismatches: 38, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
324 8 0.02
325 179 0.49
326 172 0.47
327 7 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (326 bp):
CAAATCCTTATATCCAAAATGGCTGAGACTTTGTTTGATGAATATAGATATTTCAAGGAGTCTTT
CTGCCAAAAATCATGCAAAATTAAGCACGGAGCTCCCGAAACACATTTTTAACCAAAAACAGTGA
TGATTAATACAAGATTTCGGCTGCAAACTACCCGAAAAGTTCTTTCTCAATTTGTTGCCACAATA
CTCAGAAAAAATATATAAGTTAATGCCAAAAAGATTGACGGGCTTTCCAAGCTTCGAATATCGTT
TTTTCTATTTTTTTTCCCAATTAATTTCAAATTAAATAGAAACAAGATTGAGATGCTCGAAAAAA
A
Found at i:1058 original size:273 final size:272
Alignment explanation
Indices: 556--1072 Score: 777
Period size: 273 Copynumber: 1.9 Consensus size: 272
546 GCCAAAAAGA
*
556 TTGACGGGCTTTCCAAGCTTGGAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAA
1 TTGACGGGCTTTCCAAGCTTCGAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAA
621 ATCAAAACAAGATTGAGATGCTCGAAAAAAACAAATCCTATTATCCAAAATGGCTGAGACTTTGT
66 ATCAAAACAAGATTGAGATGCTCGAAAAAAACAAATCCTATTATCCAAAATGGCTGAGACTTTGT
* * * * *
686 TTGGTGAACATAGAAATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCTGGGGCTC
131 TCGATGAACATAGAAATTTCAAGGAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGGGGCTC
* * * * ** *
751 CTGGAACGCGTTTTTACCCCAAAAACTGTGATGGTTTGTACACGATTTCGTCTGAAAACTGTCCC
196 CCGAAACACGTTTTTACCCAAAAAACCATGATGGTTAGTACACGATTTCGTCTGAAAACTGTCCC
816 GAAATATGGTTT
261 GAAATATGGTTT
* * *
828 TTGATGGGCTTTCCAAGCTTCTAATATGGTTTTTTCATTTTTTTTTCCGAATTAATTTCTAATTA
1 TTGACGGGCTTTCCAAGCTTCGAATATCGTTTTTTCA-TTTTTTTTCCGAATTAATTTCTAATTA
* * *
893 AAT-AGAAACAAGATTGAGATGCTCGAAAAAAATAAATCCT-TATATCCAAAATGGTTGAGATTT
65 AATCA-AAACAAGATTGAGATGCTCGAAAAAAACAAATCCTAT-TATCCAAAATGGCTGAGACTT
* * *
956 TGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATAATGCGAAATTGAGCCGGGG
128 TGTTCGATGAACATAGAAATTTCAAGGAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGGGG
* *
1021 CTCCCGAAACACGTTTTTATCCAAAAAACCATGATGGTTAGTGCACGATTTC
193 CTCCCGAAACACGTTTTTACCCAAAAAACCATGATGGTTAGTACACGATTTC
1073 TGCTAAAAAC
Statistics
Matches: 218, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
272 35 0.16
273 183 0.84
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (272 bp):
TTGACGGGCTTTCCAAGCTTCGAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAA
ATCAAAACAAGATTGAGATGCTCGAAAAAAACAAATCCTATTATCCAAAATGGCTGAGACTTTGT
TCGATGAACATAGAAATTTCAAGGAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGGGGCTC
CCGAAACACGTTTTTACCCAAAAAACCATGATGGTTAGTACACGATTTCGTCTGAAAACTGTCCC
GAAATATGGTTT
Found at i:1468 original size:317 final size:323
Alignment explanation
Indices: 845--1579 Score: 901
Period size: 317 Copynumber: 2.3 Consensus size: 323
835 GCTTTCCAAG
*
845 CTTCTAATATGGTTTTTTCATTTTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTGA
1 CTTCTAATATCGTTTTTTCA--TTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTGA
* * * * *
910 GATGCTCGAAAAAAATAAATCCTTATATCCAAAATGGTTGAGATTTTGTTCGATGAATATAGATA
64 GATGCTC--AAAAAACAAATCCTTATATCCAAAATGGCTGAGAATTGGTTCGATAAATATAGATA
* * * *
975 TTTCAAGGAGTCTTTCTACCAAAAATAATGCGAAATTGAGCCGGGGCTCCCGAAACACGTTTTTA
127 TTTCAAGAAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGAGACTCCCGAAACACGTTTTTA
* * * *
1040 TCCAAAAAACCATGATGGTTAGTGCACGATTTCTGCTAAAAACTTGCCCGAAAAGATTTTTCACA
192 GCCAAAAAACCATGATGGATAGTACACGATTTCGGCTAAAAACTTGCCCGAAAAGATTTTTCACA
* * * * * *
1105 ATTTTTCGCCATAATACTCAGAAAAAATATATAATTCAACGTCAAAAAGATTGACGGGCTTTTCA
257 ATTTTTCACAACAATACTCAAAAAAAATATATAAGTCAACGTCAAAAAGATTAACGGGCTTTTCA
**
1170 TT
322 GA
* * * * * *
1172 CTTCTAATATCGTTTTTTCAATTTTTTCTGAATTAATTTCTAAATAAATCGAAATAAGATTCAGA
1 CTTCTAATATCGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTGAGA
* ** *
1237 TGCTCATAAAAACAAAACCTTATATCCAATGTGGCTGATAATTGGTTCGATAAATATAGATATTT
66 TGCTCA-AAAAACAAATCCTTATATCCAAAATGGCTGAGAATTGGTTCGATAAATATAGATATTT
* * * * * * *
1302 CATGAAGTCTTTGTACCAAAAATCATGCAAAATTGAGTCGAGACT-CCGAAACGCTTTTTTAGGC
130 CAAGAAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGAGACTCCCGAAACACGTTTTTAGCC
* * *
1366 -AAAAA-C-TG-T-GAT-GTACACGATTTCGGTTAAAAAC-TGACCCGAAAAGTTTTTTCTCAAT
195 AAAAAACCATGATGGATAGTACACGATTTCGGCTAAAAACTTG-CCCGAAAAGATTTTTCACAAT
* * *
1424 TTTTTACAACAATACTCAAAAAAAATATATAAGTCAATGTCAAAAAGATTAACGGGCTTTTTAGA
259 TTTTCACAACAATACTCAAAAAAAATATATAAGTCAACGTCAAAAAGATTAACGGGCTTTTCAGA
* * *
1489 CTTCTAATATCATTTTTTTCTTTTTTTTTCCGAATTAATTTCTAATTGAATAGAAACAAGATTGA
1 CTTCTAATATC-GTTTTTTC-ATTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTGA
*
1554 GATGCTCAAATAACAAATCCTTATAT
64 GATGCTCAAAAAACAAATCCTTATAT
Statistics
Matches: 348, Mismatches: 56, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
316 2 0.01
317 103 0.30
318 25 0.07
319 45 0.13
320 2 0.01
321 1 0.00
322 5 0.01
323 16 0.05
324 86 0.25
325 44 0.13
327 19 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (323 bp):
CTTCTAATATCGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTGAGA
TGCTCAAAAAACAAATCCTTATATCCAAAATGGCTGAGAATTGGTTCGATAAATATAGATATTTC
AAGAAGTCTTTCTACCAAAAATAATGCAAAATTGAGCCGAGACTCCCGAAACACGTTTTTAGCCA
AAAAACCATGATGGATAGTACACGATTTCGGCTAAAAACTTGCCCGAAAAGATTTTTCACAATTT
TTCACAACAATACTCAAAAAAAATATATAAGTCAACGTCAAAAAGATTAACGGGCTTTTCAGA
Done.