Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005406.1 Corchorus capsularis cultivar CVL-1 contig05424, 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: 3400
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:775 original size:328 final size:328
Alignment explanation
Indices: 1--817 Score: 826
Period size: 328 Copynumber: 2.5 Consensus size: 328
* *
1 AAAATTTGGCAAAAATTGATCC-GAGAAATTTCTCATCAATTTCTGGCCACTATATTCATAAAAA
1 AAAATTTTGCAAAAATTGATCCTGAGAAATTTCTCCTCAATTT-TGGCCA-TATATTCATAAAAA
* * *
65 ATATATAATTCAACGCCAAAAAGGTTGAAGGGCTTCTCACGCTTCTAAT-TTGTTTTTTTTTTTC
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCG-----TTTTTCC
* *
129 TATTTTTCCGAATTAATTTCTAATTAAATCGAAATCGGATTGAGATGCTCATAAAGCAAATCCTT
124 TATTTTTCCGAATTAATTTCTAATTAAACCGAAATCGGATTGAGATGCTCATAAAACAAATCCTT
** * *
194 AAATCCAAAGTGGCTGAGATTTTGTTAGATAAATATAGAAATTTTAATGAGTCTTGACACCAAAA
189 AAATCCAAAGTGAATAAGATTTTGTTAGATAAATATAGAAATTTCAATGAGTCTTGACACCAAAA
* * *
259 ATCATGCAAAACTGAGTTGGAGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACA
254 ATCATGCAAAACTGAGTGGGAGCCCAGAAACGCGTTTTTAGCAAAAAACCGTGATAG-T-GTACA
324 CAGATTTCAGCT
317 CAGATTTCAGCT
* * *
336 AAAATTTTGAAAAAAATT-ATCCAT-AGGAATTT-TCCTCAATTTTTGGCCACGATATTCATAAA
1 AAAATTTTG-CAAAAATTGATCC-TGAGAAATTTCTCCTCAA-TTTTGGCCA-TATATTCATAAA
* * * *
398 AAATATATAATTCAACACCAAAATGATTGAAAGACTAT-TCACGCTTCTAATATCGTTTTTCCTA
62 AAATATATAATTCAACGCCAAAAAGATTGAAGGGCT-TCTCACGCTTCTAATATCGTTTTTCCTA
* * * * * * *
462 TTTTTTCCGAATTAATTTTTAATTGAACCGAAA-CATGTTTTATATGCTCGTAAAAACAAAT-CT
126 -TTTTTCCGAATTAATTTCTAATTAAACCGAAATC-GGATTGAGATGCTCAT-AAAACAAATCCT
* ** * * * *
525 ATAAATCTAATA-TGAATAAGA-TTTGTTAGATGGATATA-AATATTTCAATTAGATTTTGGCGC
188 -TAAATCCAA-AGTGAATAAGATTTTGTTAGATAAATATAGAA-ATTTCAATGAG-TCTTGACAC
** *
587 CAAAAATTGTGCAAAACTGAGTCGGGA-CTCCAG-AACGCGTTTTTAGTAAAAAACCGTGAT-G-
249 CAAAAATCATGCAAAACTGAGT-GGGAGC-CCAGAAACGCGTTTTTAGCAAAAAACCGTGATAGT
648 GTACAC-GATTTCAGCT
312 GTACACAGATTTCAGCT
* * *
664 AAAATTTTGCAAAAATTGA-CCTGAGAAATTTCTCCTCAATTTTGGGTCATAATACTAATAAAAA
1 AAAATTTTGCAAAAATTGATCCTGAGAAATTTCTCCTCAATTTT-GGCCAT-ATATTCATAAAAA
* * * * *
728 ATATATAACTCTACGCCAAAAAAAATGAAGGGCTTCTCACACTTCTAATATC-TCTTTTCAAAC-
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGT-TTTTC---CT
791 ATTTTTCCGAATTAATTTCTAATTAAA
125 ATTTTTCCGAATTAATTTCTAATTAAA
818 AAAATTATAT
Statistics
Matches: 402, Mismatches: 55, Indels: 56
0.78 0.11 0.11
Matches are distributed among these distances:
326 1 0.00
327 22 0.05
328 88 0.22
329 30 0.07
330 1 0.00
331 12 0.03
332 67 0.17
333 74 0.18
334 7 0.02
335 80 0.20
336 20 0.05
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (328 bp):
AAAATTTTGCAAAAATTGATCCTGAGAAATTTCTCCTCAATTTTGGCCATATATTCATAAAAAAT
ATATAATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTTT
CCGAATTAATTTCTAATTAAACCGAAATCGGATTGAGATGCTCATAAAACAAATCCTTAAATCCA
AAGTGAATAAGATTTTGTTAGATAAATATAGAAATTTCAATGAGTCTTGACACCAAAAATCATGC
AAAACTGAGTGGGAGCCCAGAAACGCGTTTTTAGCAAAAAACCGTGATAGTGTACACAGATTTCA
GCT
Found at i:1202 original size:65 final size:64
Alignment explanation
Indices: 1102--1222 Score: 208
Period size: 65 Copynumber: 1.9 Consensus size: 64
1092 ACTCTTGAAC
1102 TTTTTTTTTTCACCAAAAAGAAAAAACTCTTGAACTTTTTTTGGAGTATATTCTTTCTAACTTT
1 TTTTTTTTTTCACCAAAAAGAAAAAACTCTTGAACTTTTTTTGGAGTATATTCTTTCTAACTTT
*
1166 TTTTTTTCATTTCACCAAAAA-AAAAAACTCTTGAACTTTTTTTGTAGTATATTCTTT
1 TTTTTTT--TTTCACCAAAAAGAAAAAACTCTTGAACTTTTTTTGGAGTATATTCTTT
1223 TTTATGAACC
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
64 7 0.13
65 35 0.65
66 12 0.22
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.49
Consensus pattern (64 bp):
TTTTTTTTTTCACCAAAAAGAAAAAACTCTTGAACTTTTTTTGGAGTATATTCTTTCTAACTTT
Found at i:3056 original size:18 final size:18
Alignment explanation
Indices: 3033--3069 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3023 GTTTGGAAGT
*
3033 AGGAAAAATAGTAGGGAA
1 AGGAAAAATAGTAAGGAA
*
3051 AGGAAAAATTGTAAGGAA
1 AGGAAAAATAGTAAGGAA
3069 A
1 A
3070 ATTAAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.30, T:0.14
Consensus pattern (18 bp):
AGGAAAAATAGTAAGGAA
Done.