Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010473.1 Corchorus olitorius cultivar O-4 contig10505, 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, 628
Length: 1047
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Found at i:459 original size:126 final size:126
Alignment explanation
Indices: 234--486 Score: 418
Period size: 126 Copynumber: 2.0 Consensus size: 126
224 GGGTCAGTTT
* *
234 TTTTGCAAAATTTTAGTCGATATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCT
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCT
*
299 AGGCCCTGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCA
66 AGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCA
* * * *
360 TTTTGCAAAATTTTAGCCGAAATCGTTTACT-ACTATCACGGTTTTTTGGCTAAAAATGTGTTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAATGCGTTTC
*
424 TAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCA
65 TAGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCA
486 T
1 T
487 CTAAAAATCT
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 7 0.06
126 111 0.94
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (126 bp):
TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCT
AGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCA
Found at i:1012 original size:332 final size:333
Alignment explanation
Indices: 360--1047 Score: 1116
Period size: 334 Copynumber: 2.1 Consensus size: 333
350 TCTATATTCA
* * * * *
360 TTTTGCAAAATTTTAGCCGAAATCGTTTACTACTATCACGGTTTTTTGGCTAAAAATGTGTTTCT
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTACCATCACGGATTTTTGGCTAAAAATGCGTTTCG
*
425 AGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATCTA
66 AGGCCCTGACTCAGTTTTGCATGATTTTTGGAAGAATGACTTCTCGAAATATCTATATTCATCTA
* * * *
490 AAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACATGTATTTGGATCTTGTTTCGATT
131 AAAATCTCTCAGCCACAATGCATTTACAGATTTATTTTTACAAGTATCTGGATCTTGTTTCAATT
*
555 TATTTAGAAATAAATTCAGAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAATAGT
196 TATTTAAAAATAAATTCAGAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAATAGT
* *
620 TTTGGCGTTAAATTATATGATTTTTCTGAGTATTGTGGCGAAGAAATTGGGGGAAAACTTTACGG
261 TTTGGCATTAAATTATATGATTTTTCTGAGTATTGTGGCGAAAAAATTGGGGGAAAACTTTACGG
*
685 GTAAG-TT
326 ATAAGTTT
692 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAATGCGTTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACT-ACCATCACGGATTTTTGGCTAAAAATGCGTTTC
* * *
756 GAGTCCCTGGCTCAGTTTTGCATGATTTTTGGAAGAATGACTTCTCGAAATATTTATATTCATCT
65 GAGGCCCTGACTCAGTTTTGCATGATTTTTGGAAGAATGACTTCTCGAAATATCTATATTCATCT
* *
821 AATCAAATCTCTCAGCCACAATGCATTTACAGATTTATTTTTACAAGTGTCTGTATCTTGTTTCA
130 AA--AAATCTCTCAGCCACAATGCATTTACAGATTTATTTTTACAAGTATCTGGATCTTGTTTCA
886 ATTTA-TTAAAAATAAATTCAGAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAA
193 ATTTATTTAAAAATAAATTCAG-AAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAA
*
950 TAGTTTTGGCATTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAAAATT-GGGGAAAACTTT
257 TAGTTTTGGCATTAAATTATATGATTTTTCTGAGTATTGTGGCGAAAAAATTGGGGGAAAACTTT
*
1013 TCGGATAAGTTT
322 ACGGATAAGTTT
1025 TTTTGCAAAATTTTAGCCGAAAT
1 TTTTGCAAAATTTTAGCCGAAAT
Statistics
Matches: 330, Mismatches: 21, Indels: 9
0.92 0.06 0.03
Matches are distributed among these distances:
332 133 0.40
333 54 0.16
334 143 0.43
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (333 bp):
TTTTGCAAAATTTTAGCCGAAATCGTGTACTACCATCACGGATTTTTGGCTAAAAATGCGTTTCG
AGGCCCTGACTCAGTTTTGCATGATTTTTGGAAGAATGACTTCTCGAAATATCTATATTCATCTA
AAAATCTCTCAGCCACAATGCATTTACAGATTTATTTTTACAAGTATCTGGATCTTGTTTCAATT
TATTTAAAAATAAATTCAGAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAATAGT
TTTGGCATTAAATTATATGATTTTTCTGAGTATTGTGGCGAAAAAATTGGGGGAAAACTTTACGG
ATAAGTTT
Done.