Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022421.1 Corchorus olitorius cultivar O-4 contig22454, 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: 2558
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Found at i:1121 original size:336 final size:335
Alignment explanation
Indices: 1--2536 Score: 4024
Period size: 335 Copynumber: 7.6 Consensus size: 335
* * * **
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTTGAGGCCCTGACTCACTTTTGCGT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
*
66 GATTTTTGGCAGAAAGACTTCTCGTAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
* *
131 CATTTTCGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATAAGAAATAAATTCAG-
131 CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
* ** * *
195 AAAAAATAGAAAAACGATATTAGAAATGTGAAAAACCATAAAATATTTTTTGCGTTGAATTATAT
196 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATAT
* * *
260 GATTTTTCTGAATATTGTGGCAACAAATTGGGGAAAAACTTTTCGAGTCAGTTTTTTGCATAATT
261 GATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATT
325 TGAGCCGAAA
326 TGAGCCGAAA
335 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
* *
400 GATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATG
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
*
465 CATTTACGGAGTTATTATTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
131 CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
* ** *
530 AAAAAATGGGAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGATGTTGAATTATAC
196 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATAT
* * **
595 GATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAATTTTTCGGGTCAGTTTTTTAAAAAATT
261 GATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATT
660 TGAG-CGAAA
326 TGAGCCGAAA
*
669 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGCAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
734 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
* * *
799 CATTTACGGAGTTATTTTTACGAGTCTCTGAAACTTGTTTCGATTTAATTAGATATAAATTCAGA
131 CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
* *
864 AAAAAATGTAAAAACGATATTTGAAGCGTGAAAAAACCTTAAAATATTTTTGGCGTTGAATTATA
196 AAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAACCTTAAAATATTTTTGGCGTTGAATTATA
* * * *
929 TGATTTTTCTGAATATTGTGGCAATAAATTGGGCAAAAAATTTTCGGGTCAGTTTTTTACAAAAT
260 TGATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAAT
994 TTGAGCCGAAA
325 TTGAGCCGAAA
* * * * *
1005 TCATGTAGTAACCATCATGGTTTATGGCTAAAAATGCGTTTTGGGGCCCTGACTCAGTTTTGAAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
* * * *
1070 GATTTTCGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTATCAGCCACAATG
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
* *
1135 CATTTACGGAGTTATTATTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAATTTCAGA
131 CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
* *
1200 AAAAATATGGAAAAACGATATTAGAAGTGTGAAAAACCTTAAAATATTTTTTGCGTTGAATTATA
196 AAAAA-ATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATA
* * *
1265 TGATTTTTCTGAATATTGTGGCAAATAATTGGGGTAAAACTTTTCGGGTCAGTTTTTTGTAAAAT
260 TGATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAAT
*
1330 TTTAGCCGAAA
325 TTGAGCCGAAA
* * *
1341 TCGTGTACTAACCATCACGGTTTTTAAGCTAAAAATGTGTTTTGGGACCCTGACTCAGTTTTGAA
1 TCTTGTACTAACCATCACGGTTTTT-GGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAA
1406 TGATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAAT
65 TGATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAAT
*
1471 GCATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATAAGAAATAAATTCAG
130 GCATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG
* * *
1536 AAAAAAAATGGAAAAATGATATTAGAAGTGTGAAAAACCTTAAAATATTTTTTGCGTTGAATTAT
195 -AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTAT
*
1601 ATGATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAATTTTTCGGGTCAGTTTTTTGCAAAA
259 ATGATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAA
*
1666 TTTTAGCCGAAA
324 TTTGAGCCGAAA
* *
1678 TCATGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGCAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
* * *
1743 GATTTTTAGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATG
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
* * *
1808 CATTTATGGAGTTATTTTTACGAGTATCTGAAACTTGTTTCGATTTAATTAGATATAAATTCAGA
131 CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
* * *
1873 AAAAAATGTAAAAACGATATTAGAAGCGTGAAAAAACTTAAAATATTTTTGTCGTTGAATTATAT
196 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATAT
* * *
1938 GATTTTTCTGAATATTGTGGCAAATAATTGGGGTAAAACTTTTTGGGTCAGTTTTTTGCAAAAAT
261 GATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGC-AAAAT
2003 TT-AGCCGAAA
325 TTGAGCCGAAA
* * * *
2013 TCGTGTACAAACCATCACAGTTTTTGGCTAAAAATGCGTTTTGGGGCCCTGACTCAGTTTTGAAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
2078 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAAT-TTCTCAGCCACAAT
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTT-TCAGCCACAAT
*
2142 GCATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAA
130 GCATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG
* * * *
2207 AAAAAAATGGGAAAACGATATTAGAAGCGTGAAAAACCTTAAAATAATTTCGGTGTTGAATTATA
195 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATA
* * * *
2272 TGATTTTTCTGAGTATTGTGGCAAAAAATTAGGGAAAAATTTTTCGGGTCGGTTTTTTGCAAAAT
260 TGATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAAT
* *
2337 TTGAGTCGATA
325 TTGAGCCGAAA
* * *
2348 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGAGGCCCTGACTCACTTTTGCAT
1 TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
* * * * *
2413 GATTTTTGACAGAAAGACTTCTTGAAATATCAATATTCATCTAAAT-AAAT-TTCTCTGCCACAA
66 GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCT-AATCAAATCTT-TCAGCCACAA
* * *
2476 TGCATTTACAGATTTATTTTTACGAGTATCTGAATCTTATTTCGATTTAATTAGAAA-AAAT
129 TGCATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
2537 GTAAAAACGA
Statistics
Matches: 2037, Mismatches: 155, Indels: 20
0.92 0.07 0.01
Matches are distributed among these distances:
334 415 0.20
335 800 0.39
336 481 0.24
337 335 0.16
338 6 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (335 bp):
TCTTGTACTAACCATCACGGTTTTTGGCTAAAAATGTGTTTTGGGGCCCTGACTCAGTTTTGAAT
GATTTTTGGCAGAAAGACTTCTCGAAATAGCTATATTCATCTAATCAAATCTTTCAGCCACAATG
CATTTACGGAGTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCTTAAAATATTTTTGGCGTTGAATTATAT
GATTTTTCTGAATATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATT
TGAGCCGAAA
Done.