Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010878.1 Corchorus capsularis cultivar CVL-1 contig10899, 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: 23261
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:5150 original size:24 final size:23
Alignment explanation
Indices: 5118--5168 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
5108 AAATCCTATC
*
5118 TTCCACATCAGGCAATGAAGCAT
1 TTCCACATCAGGCAATGAAACAT
5141 TTCCAACATCAGGCAATGAAACAT
1 TTCC-ACATCAGGCAATGAAACAT
5165 TTCC
1 TTCC
5169 TCTTGTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (23 bp):
TTCCACATCAGGCAATGAAACAT
Found at i:20232 original size:40 final size:40
Alignment explanation
Indices: 20181--20326 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
20171 TTCCGTTGTT
*
20181 TGTGTGGGGAGCATCACTGCCGAGAGTTGCGTCTGTGTTG
1 TGTGTGGGGAGCATCACTGCCGAGAGTTGCGTCTGCGTTG
* * * **
20221 TGTGCGGGGAGCATCACTTCTGAGAGTTGCGTCTGCAATG
1 TGTGTGGGGAGCATCACTGCCGAGAGTTGCGTCTGCGTTG
* * *
20261 TATTTGGGGAGCATCACTGCCGAGAGTCGCGTCTGCGTTG
1 TGTGTGGGGAGCATCACTGCCGAGAGTTGCGTCTGCGTTG
*
20301 TGTGTGGGGAGCATCACTGTCGAGAG
1 TGTGTGGGGAGCATCACTGCCGAGAG
20327 CCGTTTAATA
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.27
Consensus pattern (40 bp):
TGTGTGGGGAGCATCACTGCCGAGAGTTGCGTCTGCGTTG
Found at i:20491 original size:39 final size:40
Alignment explanation
Indices: 20395--20620 Score: 291
Period size: 39 Copynumber: 5.8 Consensus size: 40
20385 AATAATCTTC
* *** *
20395 CGTTGTGTGTGGGGAGCATCACTTCCGAGAGTCACGTTTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
*
20435 CG--ATGTGT-GGGAGCATCACTGCCGAGAGTTGTGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
20472 CGTTGTGTGT-GGGAGCATCACTGCCGAGAGTTGTGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
* *** *
20511 CGTTGTGTGTGGGGAGCATCACTTCCGAGAGTCACGTTTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
* *
20551 TGATGTGTGT-GGGAGCATCACTGCCGAGAGTTGTGTCTG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
*
20590 CGCTGTGTGTGGGGAGCATCACTGCCGAGAG
1 CGTTGTGTGTGGGGAGCATCACTGCCGAGAG
20621 CCGTTTAATA
Statistics
Matches: 161, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
37 26 0.16
38 5 0.03
39 76 0.47
40 54 0.34
ACGTcount: A:0.15, C:0.19, G:0.38, T:0.28
Consensus pattern (40 bp):
CGTTGTGTGTGGGGAGCATCACTGCCGAGAGTTGTGTCTG
Found at i:20542 original size:79 final size:78
Alignment explanation
Indices: 20395--20620 Score: 294
Period size: 79 Copynumber: 2.9 Consensus size: 78
20385 AATAATCTTC
* *** * *
20395 CGTTGTGTGTGGGGAGCATCACTTCCGAGAGTCACGTTTGCG-ATGTGT-GGGAGCATCACTGCC
1 CGTTGTGTGT-GGGAGCATCACTGCCGAGAGTTGTGTCTGCGTGTGTGTGGGGAGCATCACTGCC
***
20458 GAGAGTTGTGTCTG
65 GAGAGTCACGTCTG
*
20472 CGTTGTGTGTGGGAGCATCACTGCCGAGAGTTGTGTCTGCGTTGTGTGTGGGGAGCATCACTTCC
1 CGTTGTGTGTGGGAGCATCACTGCCGAGAGTTGTGTCTGCG-TGTGTGTGGGGAGCATCACTGCC
*
20537 GAGAGTCACGTTTG
65 GAGAGTCACGTCTG
* *
20551 TGATGTGTGTGGGAGCATCACTGCCGAGAGTTGTGTCTGCGCTGTGTGTGGGGAGCATCACTGCC
1 CGTTGTGTGTGGGAGCATCACTGCCGAGAGTTGTGTCTGCG-TGTGTGTGGGGAGCATCACTGCC
20616 GAGAG
65 GAGAG
20621 CCGTTTAATA
Statistics
Matches: 131, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
76 26 0.20
77 10 0.08
78 5 0.04
79 90 0.69
ACGTcount: A:0.15, C:0.19, G:0.38, T:0.28
Consensus pattern (78 bp):
CGTTGTGTGTGGGAGCATCACTGCCGAGAGTTGTGTCTGCGTGTGTGTGGGGAGCATCACTGCCG
AGAGTCACGTCTG
Found at i:20821 original size:22 final size:25
Alignment explanation
Indices: 20774--20825 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
20764 CCGTTTAATA
*
20774 AATTATTATAACTTTATAATAGCTT
1 AATTATAATAACTTTATAATAGCTT
20799 AATTATAATAACTTTA-AA-A-CTT
1 AATTATAATAACTTTATAATAGCTT
20821 AATTA
1 AATTA
20826 CAACTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.31
23 1 0.04
24 2 0.08
25 15 0.58
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTATAATAACTTTATAATAGCTT
Found at i:23209 original size:323 final size:323
Alignment explanation
Indices: 21907--23260 Score: 1890
Period size: 323 Copynumber: 4.2 Consensus size: 323
21897 AGATCCCTTT
* * *
21907 GTTTTTCAATTTTTTTCCGAAATAATTTCCAATTAAATCGAAACAAGATTTAGATGGTCTTAAAA
1 GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAA
* * * *
21972 CTAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAATATATATATTCCAAGGAGTTTT
66 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
* * * *
22037 TCTGCCAAAAATCTTGCATAACTGAGTCGGGGCCTCGAAACGCGTTTTTATGCCAAAAACCGTGA
131 TCTGCCAAAAATCTTGAATAACTGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGA
** * * *
22102 TGGTTAGTACACGATTTCGAATAAAAATTGACCCAAAAAGTTTGTTCTCTATTTTTTGCCACAAT
196 TGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
* * * * * *
22167 ACTTAGAAAAAATATTTAATTCAACACCAAAAAGAATGATGGGCTTTTCACGCTTCTAATATC
261 ACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACACTCCTAATATC
* *
22230 GTTTTTCAATTTTTTTCCGAAATAATTTTTAATTAAATCGAAACAAGATTCAGATACTCTTAAAA
1 GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAA
* *
22295 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTTAGAAGAATATAGATATTCCAAGGAATCTT
66 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
* * *
22360 TCTGCCAAAAAATCTTGCAA-AACTGAGTCGGGGTCCCGAAACTCGTTTTTATGCCAAAAAGTCA
131 TCTGCC-AAAAATCTTG-AATAACTGAGCCGGGGCCCCGAAACGCGTTTTTATG-C------T-A
* * * ***
22424 AAAACCGTGATAGTTAGTACACGATTTCGGCTAAAAACTGACACGAGTCGTTTTTTTTTCTCAAT
186 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAG---TTTTTTCTCAAT
* * * ** *
22489 TTTTTGCTAGAATACTCAGTAAATGTATATAATTCAACACCAAAAAGATTGACGGGCTTTTTC-T
248 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGC-TTTTCAC
* **
22553 GCTTTTAATATC
312 ACTCCTAATATC
* *
22565 ATTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGAAGCTCTT-AAA
1 GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAA
* ** ** *
22629 ACAAATCCTTAAATCCATTGTACCTAAGATTTGGTAAGGTGAATAGAGATATTCCAAGGAGTCTT
66 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
* * * *
22694 TCTGCCAAAAATCTTGCATAATTGAGCTGGGGCTCCGAAACGCGTTTTTATGC-AAAAACCGTGA
131 TCTGCCAAAAATCTTGAATAACTGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGA
* *
22758 TTGTTAGTACACGAATTCGGCTAAAAATTGACCCGAAAA-TTTTTTCTCAATTTTTTGCCACAAT
196 TGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
*
22822 ACTCAGAAAAAATTATATAATTCAACACCAAAAAGATTGATGGGCTTTTCACACTCCTAATATC
261 ACTCAGAAAAAA-TATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACACTCCTAATATC
* *
22886 GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAATAAGATTCGGATGCTCTTAAAA
1 GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAA
22951 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
66 ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
* *
23016 TCTTCCAAAAATCTTGAATAACTGGGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGA
131 TCTGCCAAAAATCTTGAATAACTGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGA
* * * * *
23081 TGGTTAGTACAAGATTTTGGCTAAAAATTGACCCGAAAAGTTTTTTCTTAAATTTTTACCACAAT
196 TGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
* *
23146 ACTCAGAAAAAATATAGAATTCAACACCATAAAGATTGACGGGCTTTTCACACTCCTAATATC
261 ACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACACTCCTAATATC
*
23209 GTTTTTCAATTTTTTTTCCGAAATAATTTCTAATTAAATCGAAATAAGATTC
1 GTTTTTCAA-TTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTC
23261 G
Statistics
Matches: 912, Mismatches: 98, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
320 37 0.04
321 97 0.11
322 109 0.12
323 230 0.25
324 159 0.17
325 2 0.00
332 44 0.05
333 37 0.04
334 66 0.07
335 126 0.14
336 5 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (323 bp):
GTTTTTCAATTTTTTTCCGAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCTTAAAA
ATAAATCCTTAAATCCATTGTGTCTAAGATTTGGTAAGAAGAATATAGATATTCCAAGGAGTCTT
TCTGCCAAAAATCTTGAATAACTGAGCCGGGGCCCCGAAACGCGTTTTTATGCTAAAAACCGTGA
TGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
ACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACACTCCTAATATC
Done.