Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021078.1 Corchorus olitorius cultivar O-4 contig21111, 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: 13174
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1213 original size:498 final size:495
Alignment explanation
Indices: 2--1590 Score: 2738
Period size: 498 Copynumber: 3.2 Consensus size: 495
1 C
* *
2 TTTTTTTTTTTTGCTAAAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACT
1 TTTTTTTTTTTGGCT-AAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACC
* * *
67 GAGACTCCTTGAAATATCTTTATTCATCTATTCAAATCAAGGAAAAATCTTTCGGATTAATTTTT
65 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAATCTTTCGGATCAATTTTT
*
132 GCAAAGTTTTAGCCGAAATCATGTACCAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGT
130 GCAAAGTTTTAGCCGAAATCATGTACTAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGT
*
197 CCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAATAAA
195 CCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAA
262 ATCTCAGCGACATTAAATTTAAGCG-TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
260 ATCTCAGCGACATTAAATTTAAG-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
326 TAGAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATCTTTTTG
324 TAGAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATCTTTTTG
* *
391 ATGTCGAATTATATTTTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCAGGTCCA
389 ATGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCCA
*
456 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAATCATCACA
454 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACA
* *
498 GTTTTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGTCTCTGTTTTGTATGATTTTTCGCACC
1 -TTTTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACC
** *
563 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAAAATTTCAGATCAATTTTT
65 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAATCTTTCGGATCAATTTTT
* *
628 GCAAAGTTTTAGCCGAAATCATGTACTAACTATCACAGTTTTCAGCTAAAACCGAGTTCCGGGGT
130 GCAAAGTTTTAGCCGAAATCATGTACTAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGT
*
693 CCAGCTCAGTTTTGCATGATTTTTGATGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAA
195 CCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAA
* *
758 ATCTCAACGACATTAAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
260 ATCTCAGCGACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
*
823 AGAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATATTTTTGA
325 AGAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATCTTTTTGA
*
888 TGTC-ATATTATATACTTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCC
390 TGTCGA-ATTATATA-TTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCC
* *
952 ATTTTTGTAAAATTTTAGCCGAAATCGTATACTAACCATCACAA
453 ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-A
* * * *
996 TTTTTTTTTTTTTGCTAAAAACGTGTTTCAGGGCCACGGCTCTGTTTTCTATGATTTTTGGCACT
1 -TTTTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACC
1061 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAATCTTTCGGATCAATTTTT
65 GAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAATCTTTCGGATCAATTTTT
1126 GCAAAGTTTTAGCCGAAATCATGTACTAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGT
130 GCAAAGTTTTAGCCGAAATCATGTACTAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGT
1191 CCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAA
195 CCAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAA
* *
1256 ATCTCAGCGATATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATT
260 ATCTCAGCGACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
*
1321 AGAAATTAATTTGGAAAAATAGGAAAAACAATATTTGAAGTGTGAAAGCCCTTCAATCTTTTTGA
325 AGAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATCTTTTTGA
* *
1386 TGTCGAATTACATATTTTTTATGAGTATTTCAGCCAAAAATTGAGGAAATATCTTTCGGGTCCAT
390 TGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCCAT
* *
1451 TTTTGCAAAATTTTAGCCGAAATTGTGCACTAACCATCACA
455 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACA
* * *
1492 ---GTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGTTCTGTTTTGTATGATTTTTGGTACCG
1 TTTTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACCG
1554 AGACTCCTTGAAATATCTTTATTCATCTAATCAAATC
66 AGACTCCTTGAAATATCTTTATTCATCTAATCAAATC
1591 TCAGGCATAT
Statistics
Matches: 1030, Mismatches: 57, Indels: 15
0.93 0.05 0.01
Matches are distributed among these distances:
492 92 0.09
495 2 0.00
496 367 0.36
497 185 0.18
498 383 0.37
499 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (495 bp):
TTTTTTTTTTTGGCTAAAAACGCGTTTCAGGGCCACGGCTCTGTTTTGTATGATTTTTGGCACCG
AGACTCCTTGAAATATCTTTATTCATCTAATCAAATCGAGGAAAAATCTTTCGGATCAATTTTTG
CAAAGTTTTAGCCGAAATCATGTACTAACTATCACGGTTTTCAGCTAAAACCGCGTTCCGGGGTC
CAGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTATATTCATCTAACAAAA
TCTCAGCGACATTAAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
GAAATTAATTTGGAAAAATAGGAAAAACAATATTAGAAGTGTGAAAGCCCTTCAATCTTTTTGAT
GTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCCATT
TTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACA
Found at i:3555 original size:102 final size:102
Alignment explanation
Indices: 3290--3583 Score: 401
Period size: 103 Copynumber: 2.9 Consensus size: 102
3280 TTTGCCACAA
* * ** * *
3290 AATTAATTTTCGTGGCAAATTAAAATTTGAATTCCCACTCCCTCAAAAATTTTGTGCCAAAATAA
1 AATTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGTTCAAATATTTTGCGCCAAAATAA
*
3355 ATTTTTGCAACGGAAATTATTACAAAATTTTGCAACG
66 ATTTTTGCAACGGAAATTACTACAAAATTTTGCAACG
* * * *
3392 AATTTAGTTATCGTAACAAATCAAAATTTGAATTCCCGCTCGATT-AAATATTTTGCGCCAAAAT
1 AA-TTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCG-TTCAAATATTTTGCGCCAAAAT
* *
3456 ACATTTTTGCAACGGAAATTACTACAAATTTTTGCAACG
64 AAATTTTTGCAACGGAAATTACTACAAAATTTTGCAACG
* * *
3495 AATTAATTTTCGTGTCAAATTAAAATTTGAATTCCCGCTAGTTCAAATATTTTGCACCAAAATAA
1 AATTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGTTCAAATATTTTGCGCCAAAATAA
* *
3560 ATTGTTCCAACGGAAATTACTACA
66 ATTTTTGCAACGGAAATTACTACA
3584 GAAAAATCCG
Statistics
Matches: 166, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
101 2 0.01
102 76 0.46
103 87 0.52
104 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (102 bp):
AATTAATTTTCGTGACAAATTAAAATTTGAATTCCCGCTCGTTCAAATATTTTGCGCCAAAATAA
ATTTTTGCAACGGAAATTACTACAAAATTTTGCAACG
Done.