Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014009.1 Corchorus olitorius cultivar O-4 contig14042, 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: 6729
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Found at i:162 original size:72 final size:72
Alignment explanation
Indices: 45--189 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
35 ATTTCGAAAG
45 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
1 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
110 TCCTAGT
66 TCCTAGT
* * * *
117 AAGAAGAAAAGAAAATATAAATGAATAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCA
1 AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
182 TCCTAGT
66 TCCTAGT
189 A
1 A
190 CTACTCTCGC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
TCCTAGT
Found at i:663 original size:288 final size:289
Alignment explanation
Indices: 117--703 Score: 1032
Period size: 288 Copynumber: 2.0 Consensus size: 289
107 CCATCCTAGT
* * *
117 AAGAAGAAAAGAAAATATAAATGAATAAAGGGGTGCAACACGAGGACTTCCCAGGAGGTCACCCA
1 AAGAAGAAAAGAAAATAAAAATGAATAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
* * * *
182 TCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGAACCGGTGCATTAGT
66 TCCAAGTACTACTCTCGCCCAAGCACGCTTAACTACGGAGTTCTAATGGGAACCAGTGCATTAGT
* *
247 GTTGGTATGATCGCACCCATCAATCTTCGCATAATAAATATGTATAAGCACATCTCATTGGATCC
131 GCTGGTATGATCGCACCCATCAATCTTCGCATAATAAATATATATAAGCACATCTCATTGGATCC
312 GGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACGAACTTGAAC
196 GGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACGAACTTGAAC
377 CGATACCTACCCAAAAAAATTTTCGAAAG
261 CGATACCTACCCAAAAAAATTTTCGAAAG
*
406 AAGAAGAAAAGAAAATAAAAATGAA-AAAAGGGTGCAACACGAGGACTTCCTAAGAGGTCACCCA
1 AAGAAGAAAAGAAAATAAAAATGAATAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
*
470 TCCAAGTACTACTCTCGCCCAAGCACGCTTAACTACGGAGTTCTAATGGGATCCAGTGCATTAGT
66 TCCAAGTACTACTCTCGCCCAAGCACGCTTAACTACGGAGTTCTAATGGGAACCAGTGCATTAGT
* * * *
535 GCTGGTATGATCGCACCCATTAGTCTTTGCATAATAAATATATATAAGCACTTCTCATTGGATCC
131 GCTGGTATGATCGCACCCATCAATCTTCGCATAATAAATATATATAAGCACATCTCATTGGATCC
600 GGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACGAACTTGAAC
196 GGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACGAACTTGAAC
665 CGATACCTACCCAAAAAAATTTTCGAAAG
261 CGATACCTACCCAAAAAAATTTTCGAAAG
694 AAGAAGAAAA
1 AAGAAGAAAA
704 CAACATTTCT
Statistics
Matches: 283, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
288 259 0.92
289 24 0.08
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (289 bp):
AAGAAGAAAAGAAAATAAAAATGAATAAAAGGGTGCAACACGAGGACTTCCCAAGAGGTCACCCA
TCCAAGTACTACTCTCGCCCAAGCACGCTTAACTACGGAGTTCTAATGGGAACCAGTGCATTAGT
GCTGGTATGATCGCACCCATCAATCTTCGCATAATAAATATATATAAGCACATCTCATTGGATCC
GGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACGAACTTGAAC
CGATACCTACCCAAAAAAATTTTCGAAAG
Found at i:1604 original size:453 final size:453
Alignment explanation
Indices: 397--2012 Score: 2748
Period size: 453 Copynumber: 3.5 Consensus size: 453
387 CCAAAAAAAT
* *
397 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATG-AAAAAAGGGTGCAACACGAGGACTTCCTAAGA
1 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAGGA
* * * *
461 GGTCACCCATCCAAGTACTACTCTCGCCCAAGCACGCTTAACTACGGAGTTCTAATGGGATCCAG
66 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
* * *
526 TGCATTAGTGCTGGTATGATCGCACCCATTAGTCTTTGCATAATAAATATATATAAGCACTTCTC
131 TGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTGCATAATAAATATATATAAGCACATCTC
591 ATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACG
196 ATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACG
*
656 AACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTACT
261 TACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTACT
721 AACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACATG
326 AACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACATG
*
786 CTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
391 TTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
*
849 TTTCGAAAGAAGAAGAAAATAAAATAAAAATGAAAAAAAGGGCTGCAACACGAGGACTTCCCAGG
1 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGG-TGCAACACGAGGACTTCCCAGG
* * *
914 AGGTCACCCATCCTAGTACTATTCACGCCCAAGCACCCTTAACTGCGGAGTTCTGATGGGATCCG
65 AGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCG
* * *
979 GTGCATTAGTGCTGGTATGATCGTACCAATCAGTCTTTGCATAATAAATATATATAAGCACATCT
130 GTGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTGCATAATAAATATATATAAGCACATCT
* *
1044 CATTGGATCCGGTGCATTGTCGCCGACATATGATCGTACACGCCATACCTTCTAAGACTTAATAC
195 CATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATAC
1109 GTACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTAC
260 GTACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTAC
* *
1174 TAACCCAACCAAGCGAACATATACGAGCTTTAATAGAGTTTGCTCACGAGCCGTTCATCGAACAT
325 TAACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACAT
*
1239 GTTGTTCATTCGCAGACATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
390 GTTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
* *
1303 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACAAGAGGATTTCCCAGGA
1 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAGGA
*
1368 GGTCACCCAACCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
66 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
* *
1433 TGCATTAATACTGGTATGATCGCACCCATCAATCTTTGCATAATAAATATATATAAGCACATCTC
131 TGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTGCATAATAAATATATATAAGCACATCTC
1498 ATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACG
196 ATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACG
* * *
1563 TACTTGAATCGATACCTACTCAAAAAATTTTTCGAAAGAAGAAGAAAACAACATTTCTCATTACT
261 TACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTACT
1628 AACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACATG
326 AACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACATG
1693 TTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
391 TTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
* *
1756 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAGGGGTGCAACACGAGGACTTCCTAGGA
1 TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAGGA
*
1821 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTATCTGCGGAGTTCTGATGGGATCCGG
66 GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
*
1886 TGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTGTATAATATATATATATATATATATATA
131 TGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTG-----------CATA-ATA-A-ATATA
* * *
1951 TATAAACACATCTCATTGGATTCGGTGCATTGTTGCCGACATATGATCGTACACGCTATACG
182 TATAAGCACATCTCATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACG
2013 CCATATGATC
Statistics
Matches: 1095, Mismatches: 53, Indels: 17
0.94 0.05 0.01
Matches are distributed among these distances:
452 31 0.03
453 561 0.51
454 432 0.39
464 3 0.00
465 3 0.00
466 1 0.00
467 64 0.06
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (453 bp):
TTTCGAAAGAAGAAGAAAAGAAAATAAAAATGAAAAAAAGGGTGCAACACGAGGACTTCCCAGGA
GGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTCTGATGGGATCCGG
TGCATTAGTGCTGGTATGATCGCACCCATCAATCTTTGCATAATAAATATATATAAGCACATCTC
ATTGGATCCGGTGCATTGTTGCCGACATATGATCGTACACGCCATACGTTCTAAGACTTAATACG
TACTTGAACCGATACCTACCCAAAAAAATTTTCGAAAGAAGAAGAAAACAACATTTCTCATTACT
AACCCAACCAAGCGAACATAAACGAGCTTTAATCGAGTTTGCTCACGAGCCGTTCATCGAACATG
TTGTTCATTCGCAGCCATACTAAGACTTAATGCTTACTTGAAACGATTGTCTACCATAAGAAA
Found at i:1935 original size:2 final size:2
Alignment explanation
Indices: 1924--1954 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1914 TCAATCTTTG
1924 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1955 AACACATCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2022 original size:24 final size:24
Alignment explanation
Indices: 1990--2036 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1980 TTGTTGCCGA
*
1990 CATATGATCGTACACGCTATACGC
1 CATATGATCGTACACGCCATACGC
2014 CATATGATCGTACACGCCATACG
1 CATATGATCGTACACGCCATACG
2037 TTCTCAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (24 bp):
CATATGATCGTACACGCCATACGC
Found at i:6066 original size:16 final size:17
Alignment explanation
Indices: 6037--6078 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
6027 CAAACAGGAA
*
6037 TTTTCTCAATAATTTTT
1 TTTTTTCAATAATTTTT
6054 TTTTTTCAA-AA-TTTT
1 TTTTTTCAATAATTTTT
6069 TTTTTTCAAT
1 TTTTTTCAAT
6079 TTTTTTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 13 0.57
16 2 0.09
17 8 0.35
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTCAATAATTTTT
Found at i:6083 original size:15 final size:15
Alignment explanation
Indices: 6047--6084 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
6037 TTTTCTCAAT
6047 AATTTTTTTTTTTCA
1 AATTTTTTTTTTTCA
*
6062 AAATTTTTTTTTTC-
1 AATTTTTTTTTTTCA
6076 AATTTTTTT
1 AATTTTTTT
6085 GACACTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (15 bp):
AATTTTTTTTTTTCA
Done.