Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005361.1 Corchorus capsularis cultivar CVL-1 contig05379, 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: 5696
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--58 Score: 107
Period size: 2 Copynumber: 28.5 Consensus size: 2
1 CT CT CT CAT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
44 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
59 CTTTTTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 53 0.96
3 2 0.04
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1561 original size:29 final size:30
Alignment explanation
Indices: 1510--1569 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1500 ATACTACTAT
* * *
1510 AAACTTAAATAGATTTATGCAAAAAAAAAA
1 AAACTAAAATAGAATTATACAAAAAAAAAA
*
1540 AAACTAAAATA-AATTATACAAAAAGAAAA
1 AAACTAAAATAGAATTATACAAAAAAAAAA
1569 A
1 A
1570 TCAAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (30 bp):
AAACTAAAATAGAATTATACAAAAAAAAAA
Found at i:3598 original size:27 final size:28
Alignment explanation
Indices: 3560--3631 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
3550 TACTACTACT
*
3560 ATAAACTAAAATAGATTTATG-AAACAA
1 ATAAACTAAAATAGATTTATGAAAAAAA
* *
3587 ATAAACTAAAATA-AATTGTGAAAAAAA
1 ATAAACTAAAATAGATTTATGAAAAAAA
*
3614 AAAAACTAAAAT-GATTTA
1 ATAAACTAAAATAGATTTA
3632 CATAAGAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 5 0.14
27 32 0.86
ACGTcount: A:0.62, C:0.06, G:0.07, T:0.25
Consensus pattern (28 bp):
ATAAACTAAAATAGATTTATGAAAAAAA
Found at i:5210 original size:387 final size:383
Alignment explanation
Indices: 4496--5255 Score: 1398
Period size: 387 Copynumber: 2.0 Consensus size: 383
4486 CACTTTGCCC
4496 TTGTTCTCAAAGTTGGGCCCAGGCTTGGGCCTATGGCTTCTTAACATTTTACAAAATGCTTAAGC
1 TTGTTCTCAAAGTTGGGCCCAGGCTTGGGCCTATGGCTTCTTAACATTTTACAAAATGCTTAAGC
4561 TATGCTTTAATATAGGTTTTTTTGGTTTTTTTAATGAGGGCGTTATGATAAAGTTTAATGAACTT
66 TATGCTTTAATATAGGTTTTTTTGGTTTTTTTAATGAGGGCGTTATGATAAAGTTTAATGAACTT
4626 TTTTTTAGGAGTACAACTCAAATTTCGTTACAATTACAATAATTCATCTAAAATTATATTGTTTT
131 TTTTTTAGGAGTACAACTCAAATTTCGTTACAATTACAATAATTCATCTAAAATTATATTGTTTT
4691 GGCCTAAAAAAAACTAAAATTATATTGAATAAACTACCAACGTATAAAAGAAGCAAGCAAACAAA
196 GGCCTAAAAAAAACTAAAATTATATTGAATAAACTACCAACGTATAAAAGAAGCAAGCAAACAAA
**
4756 TAAACTAAATTTATATACACATTCCGTAATACTTGAACTCATAACCTTACAATTTAGGTAGGGTG
261 TAAACTAAATTTATATACACATTCCGTAATACTTGAACTCATAACCTTACAATTTAGACAGGGTG
4821 TACTCACCAATTGAGTTAATAATACTAATACAAAGTTTAATAATGTTGGGCTACAGAA
326 TACTCACCAATTGAGTTAATAATACTAATACAAAGTTTAATAATGTTGGGCTACAGAA
4879 TTGTTCTCAAAGTTGGGCCCAGGCTTGGGCCTATGGCTTCTTAACATTTTACAAAATGCTTAAGC
1 TTGTTCTCAAAGTTGGGCCCAGGCTTGGGCCTATGGCTTCTTAACATTTTACAAAATGCTTAAGC
*
4944 TATGCTTTAATATAGG-TTTTTTGGTTTTTTTAATGAGGGTCGTTNTGATAAAGTTTTAA-GAAA
66 TATGCTTTAATATAGGTTTTTTTGGTTTTTTTAATGAGGG-CGTTATGATAAAG-TTTAATG-AA
5007 CTTTTTTTTTAGGAGTTACAACTCAAATTTCGTTTACAATTACAATAATTCATCTAAAATTATAT
128 C-TTTTTTTTAGGAG-TACAACTCAAATTTCG-TTACAATTACAATAATTCATCTAAAATTATAT
*
5072 TGTTTTGGCCTTAAAAAAACTAAAATTATATTGAATAAACTACCAACGTATAAAAGAAGCAAGCA
190 TGTTTTGGCCTAAAAAAAACTAAAATTATATTGAATAAACTACCAACGTATAAAAGAAGCAAGCA
*
5137 AACAAATAAACTGAATTTATATACACATTCCGTAATACTTGAACTCATAACCTTACAATTTAGAC
255 AACAAATAAACTAAATTTATATACACATTCCGTAATACTTGAACTCATAACCTTACAATTTAGAC
*
5202 ATGGTGTACTCACCAATTGAGTTAATAATACTAATACAAAGTTTAATAATGTTG
320 AGGGTGTACTCACCAATTGAGTTAATAATACTAATACAAAGTTTAATAATGTTG
5256 TAGAATTGAA
Statistics
Matches: 365, Mismatches: 6, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
382 23 0.06
383 94 0.26
384 8 0.02
385 13 0.04
386 16 0.04
387 211 0.58
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (383 bp):
TTGTTCTCAAAGTTGGGCCCAGGCTTGGGCCTATGGCTTCTTAACATTTTACAAAATGCTTAAGC
TATGCTTTAATATAGGTTTTTTTGGTTTTTTTAATGAGGGCGTTATGATAAAGTTTAATGAACTT
TTTTTTAGGAGTACAACTCAAATTTCGTTACAATTACAATAATTCATCTAAAATTATATTGTTTT
GGCCTAAAAAAAACTAAAATTATATTGAATAAACTACCAACGTATAAAAGAAGCAAGCAAACAAA
TAAACTAAATTTATATACACATTCCGTAATACTTGAACTCATAACCTTACAATTTAGACAGGGTG
TACTCACCAATTGAGTTAATAATACTAATACAAAGTTTAATAATGTTGGGCTACAGAA
Done.