Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014499.1 Corchorus capsularis cultivar CVL-1 contig14520, 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: 2462
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34
Found at i:491 original size:275 final size:274
Alignment explanation
Indices: 1--518 Score: 903
Period size: 275 Copynumber: 1.9 Consensus size: 274
*
1 TCTTAGCAATATTGGATATAAGGATTTGTTTTTTCGAGAATCTCAATCTTGTTTCGATTTAATTA
1 TCTTAGCAATATTGGATATAAGGATTTGTTTTTTCGAGAATCTCAATCTTCTTTCGATTTAATTA
* **
66 GAAATCAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGTTTGTCAATATTTCTGG
66 GAAATCAATTCGGAAAAAATGGAAAAAAGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGG
* *
131 CGATGAATTATATACTTTTTCTGTGTATTGTGTCAAAAAATTGAGAAAAAAAATGTTCGGGTAAG
131 CGATGAATTATATACTTTTTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAATGTTCGGGTAAG
196 TTTTTAGCAGAAATTGTGTACTAACCATCACGG-TTTTGGCGTAAAAACTCCTTCAAATATATAT
196 TTTTTAGCAGAAATTGTGTACTAACCATCACGGTTTTTGGC-TAAAAACTCCTTCAAATATATAT
260 ATTCATCGAAGCAAA
260 ATTCATCGAAGCAAA
*
275 TCTTAGCAATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTCTTTCGATTTAATTA
1 TCTTAGCAATATTGGATATAAGGATTTGTTTTTTCGAGAATCTCAATCTTCTTTCGATTTAATTA
*
340 GAAATTAATTCGGAAAAAAATGGAAAAAAGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTG
66 GAAATCAATTCGG-AAAAAATGGAAAAAAGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTG
* *
405 GCGATGAATTATATACTTTTTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCA
130 GCGATGAATTATATACTTTTTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAATGTTCGGGTAA
* *
470 GTTTTTAGCCGAAATTGTGTACTAACCATCATGGTTTTTGGCTAAAAAC
195 GTTTTTAGCAGAAATTGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
519 GCGTTCCGGA
Statistics
Matches: 230, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
274 75 0.33
275 148 0.64
276 7 0.03
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (274 bp):
TCTTAGCAATATTGGATATAAGGATTTGTTTTTTCGAGAATCTCAATCTTCTTTCGATTTAATTA
GAAATCAATTCGGAAAAAATGGAAAAAAGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGG
CGATGAATTATATACTTTTTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAATGTTCGGGTAAG
TTTTTAGCAGAAATTGTGTACTAACCATCACGGTTTTTGGCTAAAAACTCCTTCAAATATATATA
TTCATCGAAGCAAA
Found at i:1317 original size:321 final size:320
Alignment explanation
Indices: 229--2462 Score: 3170
Period size: 323 Copynumber: 7.0 Consensus size: 320
219 ACCATCACGG
* *
229 TTTTGGCGTAAAAACTCCTTCAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
*
294 AAGGATTTGTTTTTTCGAGCATCTCAATCTTCTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
66 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
*
359 ATGGAAAAAAGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCGATGAATTATATACTTT
131 ATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGC-ATGAATTATATACTTT
*
424 TTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATTGTG
195 TTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATTGTG
* * * **
489 TACTAACCATCATGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCAGAATTTTGCATGAT
259 TACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
** * * * * *
552 TTTTGGCACAAAGACTCCTAGAAATATCTATATTTATCGAGGCAAATCTCAGCAATATTGGATAT
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
* * * *
617 ACGGATTTGTTTTTTCGAGTATCTCAATCTTTTTTCGATTTAATTAGAAATTACA-TCGGAATAA
66 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTA-ATTCGGAAAAA
* * * * * *
681 AATGGAAAAGCGATATTAGAAGCATGAAAAGTTCATCAATATTTTTGGCATTGAAGTATATATCT
130 AATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCA-TGAATTATATA-CT
* * *
746 TTTT-TGT-TTTTTTGAG-AAAAAATTGAG-AAAGAAATTTCGGGTCAGTTTTTAGCCGAAATTG
193 TTTTCTGTGTATTGTG-GCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTG
*
807 TGTACTAACCATCACGGTTTTTGGCTAAGAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
257 TGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
*
872 TTTTGGCGTAAAGACTCCTTGAATATATATATATATTCATCGAACCAAATCTTAGCAATATTGGA
1 TTTTGGCGTAAAGACTCCTTG-A-A-ATATATATATTCATCGAAGCAAATCTTAGCAATATTGGA
937 TATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
63 TATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA
*
1002 AAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATATTTCTGGCGATGAATTATATAC
128 AAAATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGC-ATGAATTATATAC
1067 TTTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATT
192 TTTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAA-TTTCGGGTCAGTTTTTAGCCGAAATT
1132 GTGTACTAA-ATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
256 GTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
*
1196 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAACCAAATCTTAGCAATATTGGATAT
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
* * ** *
1261 AAGGATATGTTATTTCGAGCATCTCAATCTTAATTCGATTTAATTAGAAATTAATTCGGAGAAAA
66 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* * *
1326 ATGGGAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTTGCATTGAATTATAAACTTT
131 ATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCA-TGAATTATATACTTT
* * * *
1391 TTCTGTGTATTGCGACAAAAAATTCAGAAAAAAAATTTCGGGTCAGTTTTTACCCGAAATTGTGT
195 TTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTGTGT
* * * *
1456 ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTGAATTTTACATGAT
260 ACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
** * * ** * * *
1518 TTTTGGCACAAAGACTCCTAGAATTATCCATATTTATCGAGGCAAATC-TACGAAATATTGGATA
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTA-GCAATATTGGATA
*
1582 TAAGGATTTGCTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
65 TAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
* * *
1647 AATGGAAAAACGATATTAGAAGCGTGAAAAGTTCGTCAAGATTTTCTGGCATTGAATGATATA-T
130 AATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATA-TTTCTGGCA-TGAATTATATACT
* * *
1711 TTTTCCTGTTTGTTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAA---
193 TTTT-CTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTG
* *
1773 --TACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGTGCCCTGACTCAATTTTGCATGAT
257 TGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
* *
1836 TTTTGGCGTAAAGACTCCTTGAAGTATATATATTCATCGAACCAAATCTTAGCAATATTGGATAT
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
* *
1901 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAAATCGGAGAAAA
66 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* * * *
1966 ATGGGAAAACGATATTAGAAGCGTAAAAAGTCCGTCAATATTTCTTGCATCGAATTATAAACTTT
131 ATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCAT-GAATTATATACTTT
* * * *
2031 TTCTGTCTATTTGTGGCAAAAAATGGAGAAAAAAAATTTCGGGTCAATTTTTCGCCGAAATTGTG
195 TTCTGTGTA-TTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTGTG
* * * * *
2096 TACTAACCATCACGGTTTTTGGCTAAAAACGCATTTCGGAGGCCCGGCTGAATTTTGCATAAT
259 TACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
** * * * * * * *
2159 TTTTGGCACAAAGACTGCTAGAAATATCTATATTTATCGAGGCAAATCTCAGCAATATTAGATAT
1 TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
* * *
2224 AAGGATTTGTTTTTTC--GTATCTCAATCTTGTTTCGATTTAATAAGAAGTTAATTCGG--AAAA
66 AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
*
2285 ATAGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCAATGAATTATATACTTT
131 ATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGC-ATGAATTATATACTTT
*
2350 TTCTGTGTAATGTGGCAAAAAATTGAGAAAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTGT
195 TTCTGTGTATTGTGGCAAAAAATTGAG--AAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTGT
* * * * *
2415 GTAGTAACCATCTCTGTTTTTGACTAAGAACGCGTTTCGGAGCCCCGA
258 GTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGA
Statistics
Matches: 1708, Mismatches: 171, Indels: 67
0.88 0.09 0.03
Matches are distributed among these distances:
316 1 0.00
317 21 0.01
318 274 0.16
319 71 0.04
320 215 0.13
321 239 0.14
322 229 0.13
323 518 0.30
324 99 0.06
325 6 0.00
326 35 0.02
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
TTTTGGCGTAAAGACTCCTTGAAATATATATATTCATCGAAGCAAATCTTAGCAATATTGGATAT
AAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
ATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTCTGGCATGAATTATATACTTTT
TCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCGGGTCAGTTTTTAGCCGAAATTGTGTA
CTAACATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGCCCCGACTCAATTTTGCATGAT
Done.