Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004947.1 Corchorus capsularis cultivar CVL-1 contig04965, 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: 5502
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 19--43 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9 AATACTCATA
19 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44 ATCAACGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:768 original size:346 final size:347
Alignment explanation
Indices: 118--775 Score: 801
Period size: 347 Copynumber: 1.9 Consensus size: 347
108 TAGTTTCTAT
* * * *
118 TTAAATCAAAACAAGATTCAGATGCGCGTAAAAGCAAATCCTTAAATTCAAATGCCTAAGATTTG
1 TTAAATCAAAACAAAATTCAGATACGCGTAAAAGAAAATCCTTAAATTCAAATGCCTAAGATTCG
* * *
183 ATTAGATGAATATAGATATTTCAAGTAGTCTTGGTGCCAAAAATCATACAAAACTATGCCGAGGC
66 ATTAGATGAATATAGATATCTCAAGTAGTCTTGGCGCAAAAAATCATACAAAACTATGCCGAGGC
* * * *
248 CTCGAAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCTGCTAAAATTTTGCAA
131 CTCGAAACACGTTTTTAGCCAAAAACCGTGAAGATTAGTACACGATTTCTGCTAAAATTTTACAA
* * * * * *
313 AAAATGACCCGAAAAATTTTTCTGTCAATTTTTAGCTAAAATACTCATAAAATTTATATAATTTA
196 AAAATAAACCGAAAAATTTTTCTGTCAATTTTTAGCCAAAATACTCATAAAAATCATATAATTCA
*
378 ATGCCAAAAAAATTGAAGGACTTTTCACGATTTTAATATCGTTTTTCATATTTGTCTGAATTATC
261 ATGCCAAAAAAATTGAAGGACTTTTCACGATTCTAATATCGTTTTTCATATTTGTCTGAATTATC
443 TAAATTATTTGAATTATTTTAA
326 TAAATTATTTGAATTATTTTAA
** * * * * *
465 TTAAATCAAAACAAAATTCAGATATTCGTAAAATAAAATTCTTAAA-TCCAATGTAGCTGAGATT
1 TTAAATCAAAACAAAATTCAGATACGCGTAAAAGAAAATCCTTAAATTCAAATG--CCTAAGATT
* * **
529 CGATTAGATGAATATGGATATCTCAAAG-AGTCTTGGCGCAAAAAATCATGCAAAACT-TAGTTG
64 CGATTAGATGAATATAGATATCTC-AAGTAGTCTTGGCGCAAAAAATCATACAAAACTAT-GCCG
* * * * * *
592 GGGCC-CGGAACACGTTTTTAGTCAAAAACCGTTAAGATTATTACACGATTTC-GACTAGAATTT
127 AGGCCTCGAAACACGTTTTTAGCCAAAAACCGTGAAGATTAGTACACGATTTCTG-CTAAAATTT
* * ** *
655 TACAAAAATTAAATCGAAAGTTTATTTCT-TC-ATTTTTAGCCACAATACTCATAAAAATCATAT
191 TACAAAAAATAAACCGAAAAATT-TTTCTGTCAATTTTTAGCCAAAATACTCATAAAAATCATAT
* * * *
718 AATTCAATG-GAAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATT
255 AATTCAATGCCAAAAAA-ATTGAAGGACTTTTCACGATTCTAATATCGTTTTTCATATT
776 ATTTTCCGAA
Statistics
Matches: 260, Mismatches: 44, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
345 6 0.02
346 80 0.31
347 106 0.41
348 65 0.25
349 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (347 bp):
TTAAATCAAAACAAAATTCAGATACGCGTAAAAGAAAATCCTTAAATTCAAATGCCTAAGATTCG
ATTAGATGAATATAGATATCTCAAGTAGTCTTGGCGCAAAAAATCATACAAAACTATGCCGAGGC
CTCGAAACACGTTTTTAGCCAAAAACCGTGAAGATTAGTACACGATTTCTGCTAAAATTTTACAA
AAAATAAACCGAAAAATTTTTCTGTCAATTTTTAGCCAAAATACTCATAAAAATCATATAATTCA
ATGCCAAAAAAATTGAAGGACTTTTCACGATTCTAATATCGTTTTTCATATTTGTCTGAATTATC
TAAATTATTTGAATTATTTTAA
Found at i:1856 original size:28 final size:29
Alignment explanation
Indices: 1810--1864 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1800 ATGTGACTGA
1810 GATTTGATTAGATGAATATAT-TATATTT
1 GATTTGATTAGATGAATATATATATATTT
* *
1838 GATTTGATTATATGTATATATATATAT
1 GATTTGATTAGATGAATATATATATAT
1865 ATTATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (29 bp):
GATTTGATTAGATGAATATATATATATTT
Found at i:3357 original size:2 final size:2
Alignment explanation
Indices: 3350--3381 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3340 TTTTATTTAG
3350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3382 TGCAATCCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4537 original size:305 final size:305
Alignment explanation
Indices: 3968--4546 Score: 763
Period size: 305 Copynumber: 1.9 Consensus size: 305
3958 ACGTCAGGCA
* * *
3968 GAGAAATTATTAGATGGACCCGGTCCACCACGTCATCTATGGTTCCAACCAATAAGATCGTGACA
1 GAGAAATTATTAGATGGACCCGGTCCACCACGTCATCCATGATCCCAACCAATAAGATCGTGACA
* * * *
4033 CGTCAAATTTATTCTTAAAATTCAGGCACAAAATTAGCACCAGGTTTAACCCCAAGTTTAACCAT
66 AGTCAAATTTATTCCTAAAATTCAGACACAAAATTAGCACCAGGTTTAACCCCAAGTTTAACCAG
* * * *
4098 ATGAGATTCACAGGGTAAGTCCCTAAATTTAGTACATTAATTTGGTAGGGTTTTAGAAATTGTAG
131 ATGAAATTAACAGGGTAAGTCCCTAAATTTAGGACATTAATTTGCTAGGGTTTTAGAAATTGTAG
* * *
4163 GAAAAAATCTGACGTGTCACAATCTTATTGATCGGGACCATGGATGACGTGGTAGACCTGATCCA
196 GAAAAAATCTGACGTGTCACAATCTTATTGATCGGGACCATGGATGACATGGTAGACCCGATACA
4228 TGTAATAATTTCTCCGTCAGGCGGGACATTTTGCGGGTCAAATAG
261 TGTAATAATTTCTCCGTCAGGCGGGACATTTTGCGGGTCAAATAG
** ** * * *
4273 GAGAAATTATTTTATGGACTGGGTCCACCACGTCATCCATTATCCCGACCAATACA-ATTGTGAC
1 GAGAAATTATTAGATGGACCCGGTCCACCACGTCATCCATGATCCCAACCAATA-AGATCGTGAC
* * * * * * * *
4337 AAGTCAGATTTCTTCCTAAAATTTAGACACAAATTTAGGACCAGGTTTAGCCCCGAGTTTCACCA
65 AAGTCAAATTTATTCCTAAAATTCAGACACAAAATTAGCACCAGGTTTAACCCCAAGTTTAACCA
*
4402 GATGAAATTAACAGGGTATA-TCCCTAAATTTAGGATATTAATTTGCT-GGGATTTTAGAAATTG
130 GATGAAATTAACAGGGTA-AGTCCCTAAATTTAGGACATTAATTTGCTAGGG-TTTTAGAAATTG
** * *
4465 TAGGAAAAAATCTGATTTGTCA-AGATCTTATTGGTTGGGACCATGGATGACATGGT-GAACCCG
193 TAGGAAAAAATCTGACGTGTCACA-ATCTTATTGATCGGGACCATGGATGACATGGTAG-ACCCG
*
4528 GTACATGTAATAATTTCTC
256 ATACATGTAATAATTTCTC
4547 ATCAAATAGG
Statistics
Matches: 234, Mismatches: 35, Indels: 10
0.84 0.13 0.04
Matches are distributed among these distances:
304 5 0.02
305 227 0.97
306 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (305 bp):
GAGAAATTATTAGATGGACCCGGTCCACCACGTCATCCATGATCCCAACCAATAAGATCGTGACA
AGTCAAATTTATTCCTAAAATTCAGACACAAAATTAGCACCAGGTTTAACCCCAAGTTTAACCAG
ATGAAATTAACAGGGTAAGTCCCTAAATTTAGGACATTAATTTGCTAGGGTTTTAGAAATTGTAG
GAAAAAATCTGACGTGTCACAATCTTATTGATCGGGACCATGGATGACATGGTAGACCCGATACA
TGTAATAATTTCTCCGTCAGGCGGGACATTTTGCGGGTCAAATAG
Done.