Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015156.1 Corchorus capsularis cultivar CVL-1 contig15177, 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, 772
Length: 1288
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:714 original size:321 final size:321
Alignment explanation
Indices: 1--1288 Score: 1709
Period size: 320 Copynumber: 4.0 Consensus size: 321
*
1 GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATCCGGAACGCGTTTTTAGCCAAAA
1 GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATCCGGAACGCGTTTTTAGCCCAAA
66 ACTGTGATGGTTAGTACACGATTTCGGCTAAAAAC---CCCGAAAAGTTTTTTTTCTCAATTTTT
66 ACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG--TTTTTTCTCAATTTTT
*
128 AGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAAATTGACGAGCTTTTCATGCTT
129 AGCCACAATACACA-AAAAAATATATAATTCAAAGCC-AAAAAAATTGACGAGCTTTTCATGCTT
*
193 TTAATATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATGC
192 CTAATATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATGC
* * *
258 TCG-AAAAA-AAATCATTATATCTAACATGGCTAAGATTTGATTCGATGAATATTGATATTTAAA
257 TCGTAAAAACAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCAA
* * * * *
321 GGAGTTTTTGTGCCAAAAATCATGCAAAATTTAGTCGGGGCTCCAGAATGCGTTTTTAG-CCAAA
1 GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATCCGGAACGCGTTTTTAGCCCAAA
385 ACCTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG-TTTTTCTCAATTTTTA
66 A-CTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTA
* *
449 GCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAAATTGACGAGCTTTTCATGCTTTT
130 GCCACAATACACA-AAAAAATATATAATTCAAAGCCAAAAAAATTGACGAGCTTTTCATGCTTCT
*
514 AATATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATACTC
194 AATATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATGCTC
579 G-AACAAACAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCAA
259 GTAA-AAACAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCAA
* * *
642 GAAGTCTTTGTGCCAAAAATCTTGCAAAATTGAGTTGGGGATCCGGAACGCGTTTTTAGCCCAAA
1 GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATCCGGAACGCGTTTTTAGCCCAAA
* * * * * *
707 ACTGTGATGGTTAGTACACGATTTGGGCTAAAAACTTAGCAGAAAAGTTTTTTCCCAATTTTTTG
66 ACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTAG
* * * * *
772 CCACAATACACAAAAATATATATAATTCAATGTCAAAAAGATTGACGAGCTTTTCAAGCTTCTAA
131 CCACAATACACAAAAAAATATATAATTCAAAGCCAAAAAAATTGACGAGCTTTTCATGCTTCTAA
* * * * * *
837 TATTGCTTTTTCA-TTTTTTCCGAATTCATTTCTAATAAAATTGAAACAACATTAAGACGCTTGT
196 TATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATGCTCGT
* * ** *
901 AAAAACCAATTC-TTATAACTAATTTGGCTCAAATTTGATTCGATGAATATAGATATTTCAA
261 AAAAA-CAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCAA
* * * * * * * * *
962 GGAGTTTTTGTACAAAAAATCATGCTAAACTGAGTCGGGGCTCTCGAAACACGTTTTTAACCCAA
1 GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATC-CGGAACGCGTTTTTAGCCC-A
* * * *
1027 AAACCGTGATGGTTAGTACATGATTTTGACTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTT
64 AAACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTT
* * * * * * * * *
1092 -TCCACAATACACAAAAAATATATATAGTTCTACGCCAGAAAGATTGATGGGCTTTTCACGCTTC
129 AGCCACAATACACAAAAAA-ATATATAATTCAAAGCCAAAAAAATTGACGAGCTTTTCATGCTTC
* * *
1156 TAATATCGGTTTTTTCATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAA-ATG
193 TAATAT-TGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATT-AAGATG
* * * ** * * * * *
1220 CTCGTAAAAAGAAATCCTTATATCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTCA
256 CTCGTAAAAACAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCA
1285 A
321 A
1286 GGA
1 GGA
Statistics
Matches: 859, Mismatches: 92, Indels: 30
0.88 0.09 0.03
Matches are distributed among these distances:
319 101 0.12
320 269 0.31
321 243 0.28
322 133 0.15
323 21 0.02
324 90 0.10
325 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (321 bp):
GGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGATCCGGAACGCGTTTTTAGCCCAAA
ACTGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTAG
CCACAATACACAAAAAAATATATAATTCAAAGCCAAAAAAATTGACGAGCTTTTCATGCTTCTAA
TATTGTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAACATTAAGATGCTCGT
AAAAACAAATCATTATATCTAACATGGCTCAGATTTGATTCGATGAATATAGATATTTCAA
Done.