Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019207.1 Corchorus olitorius cultivar O-4 contig19240, 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: 105281
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:738 original size:30 final size:30
Alignment explanation
Indices: 704--762 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
694 TTAATCATAG
704 TTCAAAAGCAAATCTCAATTAAGCTCGAGC
1 TTCAAAAGCAAATCTCAATTAAGCTCGAGC
734 TTCAAAAGCAAATCTCAATTAAGCTCGAG
1 TTCAAAAGCAAATCTCAATTAAGCTCGAG
763 TCGAGTTTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (30 bp):
TTCAAAAGCAAATCTCAATTAAGCTCGAGC
Found at i:8617 original size:11 final size:11
Alignment explanation
Indices: 8601--8626 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8591 GAAAGTTATT
8601 AAGATTTCGAA
1 AAGATTTCGAA
8612 AAGATTTCGAA
1 AAGATTTCGAA
8623 AAGA
1 AAGA
8627 AAAGGCCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (11 bp):
AAGATTTCGAA
Found at i:9360 original size:18 final size:17
Alignment explanation
Indices: 9337--9374 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
9327 GAAGGGGGAG
9337 AAGGAG-ATAAGGAAGGTA
1 AAGGAGAATAA-GAAGG-A
9355 AAGGAGAATAAGAAGGA
1 AAGGAGAATAAGAAGGA
9372 AAG
1 AAG
9375 AAAAGGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.37, T:0.08
Consensus pattern (17 bp):
AAGGAGAATAAGAAGGA
Found at i:14665 original size:15 final size:17
Alignment explanation
Indices: 14639--14671 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
14629 ATCTACTTAC
14639 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
14655 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
14671 C
1 C
14672 TCACATTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:45424 original size:16 final size:16
Alignment explanation
Indices: 45395--45432 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
45385 GTCTCAAGTT
45395 TTTTGTTTTCTTTATA
1 TTTTGTTTTCTTTATA
45411 TTTT-TTTTCTTT-TA
1 TTTTGTTTTCTTTATA
45425 -TTTGTTTT
1 TTTTGTTTT
45433 GAATAAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 3 0.14
14 6 0.29
15 8 0.38
16 4 0.19
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (16 bp):
TTTTGTTTTCTTTATA
Found at i:47305 original size:18 final size:18
Alignment explanation
Indices: 47278--47315 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
47268 ACAATATGAT
* *
47278 TATATTTATATGAATATA
1 TATATGTATATAAATATA
47296 TATATGTATATAAATATA
1 TATATGTATATAAATATA
47314 TA
1 TA
47316 CACTTCTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TATATGTATATAAATATA
Found at i:47892 original size:29 final size:28
Alignment explanation
Indices: 47838--47893 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
47828 AATTACCCAT
*
47838 ATATATATATAGTTTTCAACTTTATGAA
1 ATATATATATAGTTTTCAACTATATGAA
*
47866 ATATATCATATAGTTTTCAAGTATATGA
1 ATATAT-ATATAGTTTTCAACTATATGA
47894 TTGGTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (28 bp):
ATATATATATAGTTTTCAACTATATGAA
Found at i:51601 original size:60 final size:60
Alignment explanation
Indices: 51513--51628 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
51503 TAAAAGTCTA
** * *
51513 ATCTTTTAATTTGCCAAATTAAAAGCCTAACGTTATTGGA-AATGCTCAAATAAGGGCCCG
1 ATCTTTTAATTTGCCAAATTAAAAGCCTAAAATTA-TCGACAATGCTAAAATAAGGGCCCG
* **
51573 ATCTTTTAATTTGGTCAAA-TAAGGGCCTAAAATTATCGACAATGCTAAAATAAGGG
1 ATCTTTTAATTT-GCCAAATTAAAAGCCTAAAATTATCGACAATGCTAAAATAAGGG
51629 TCTGACGTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 3 0.06
60 39 0.83
61 5 0.11
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (60 bp):
ATCTTTTAATTTGCCAAATTAAAAGCCTAAAATTATCGACAATGCTAAAATAAGGGCCCG
Found at i:66850 original size:29 final size:31
Alignment explanation
Indices: 66815--66887 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
66805 CATTACACTG
66815 TATGTTTCATTATTTTTTGGGTT-TAACTAA
1 TATGTTTCATTATTTTTTGGGTTGTAACTAA
** *
66845 -ATGTTTCATT-TTTTTTGTTTTGTGACTAA
1 TATGTTTCATTATTTTTTGGGTTGTAACTAA
66874 TATGTTTCATTATT
1 TATGTTTCATTATT
66888 GCTAACTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.24
29 16 0.43
30 10 0.27
31 2 0.05
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (31 bp):
TATGTTTCATTATTTTTTGGGTTGTAACTAA
Found at i:72356 original size:236 final size:235
Alignment explanation
Indices: 71927--72638 Score: 1025
Period size: 236 Copynumber: 3.0 Consensus size: 235
71917 ATTTCTTTCA
* * * * * * *
71927 GATGCAGTCAGCGCATCAGGTAATGACAGCAATGCATCTATCCCGCCAGGTGAACATCTGCTTCG
1 GATGCAGTCTGCACTTCAGGTAATGACAGCAATGTATCTGTCCAGCCAGGTGAACAGCTGCTTCG
*
71992 TGAGAACAATGAGGTTATTGTCTGTTCCATGT-TTTGATTTAGAAATGAATTCTCTGATGTCAAA
66 TGAGAACAATGAGGTTATTGTCTGTTCCATGTCTTTGATTTATAAATGAATTCTCTGATGTCAAA
* * *
72056 TTTTGCTTTCTTTTTCTTCAATAATATTTCCTGTGCTTTGTAGGACTCACTGGACCGGATAGTAT
131 ATTTGCTTTTTTTTTCTTCAATAATATTTCCTGT-CTTTGTAGGACTCACTGGACCAGATAGTAT
* * **
72121 CACCTAAGGAAGCTGCATGTACTCAGCAGCCACACCCGGTT
195 CACCTAAGGAAGTTGAACATACTCAGCAGCCACACCCGGTT
* * *
72162 GATGCAGTTTGCACTTCAGGTGATGACAGCACTGTATCTGTCCAGCCAGGTGAACAGCTGCTTCG
1 GATGCAGTCTGCACTTCAGGTAATGACAGCAATGTATCTGTCCAGCCAGGTGAACAGCTGCTTCG
* *
72227 TGAGAACAATGAGGTTATTGTTTGTTCCATGTCTTTGATTTATAAATGGATTCT-TAGATGTCAA
66 TGAGAACAATGAGGTTATTGTCTGTTCCATGTCTTTGATTTATAAATGAATTCTCT-GATGTCAA
** *
72291 AATTTGCTTTTTTTTTCTTCAATAATATTTCCTTGTCTTTGTAGGACTTGCTGGATCAGATAGTA
130 AATTTGCTTTTTTTTTCTTCAATAATATTTCC-TGTCTTTGTAGGACTCACTGGACCAGATAGTA
72356 TCACCTAAGGAAGTTGAACATACTCAGCAGCCACACCCGGTT
194 TCACCTAAGGAAGTTGAACATACTCAGCAGCCACACCCGGTT
* *
72398 GATGCAGTCTGCACTTCAGGTAATGACAGCAGTGTATCTGTCCAGCCAGGTGAACAGCTGCTTCT
1 GATGCAGTCTGCACTTCAGGTAATGACAGCAATGTATCTGTCCAGCCAGGTGAACAGCTGCTTCG
* * * * *
72463 TGAGAACAATGAGGTAATGGTCTGTTCCTTGTCTTTGATTTATAAGTGAATTGTCTGATGTCAAA
66 TGAGAACAATGAGGTTATTGTCTGTTCCATGTCTTTGATTTATAAATGAATTCTCTGATGTCAAA
* * * *
72528 ATTTCCTTTTTTTTT-TCTCTAATAATATTTCCTGCACTTTGTAGGACTCACTAGACCAGAAAGT
131 ATTTGCTTTTTTTTTCT-TC-AATAATATTTCCTG-TCTTTGTAGGACTCACTGGACCAGATAGT
* *
72592 ATCACCTAAGGAAGTTGAACATACTCAGCAGCCACAACTGGTT
193 ATCACCTAAGGAAGTTGAACATACTCAGCAGCCACACCCGGTT
72635 GATG
1 GATG
72639 TGCCTAATAT
Statistics
Matches: 427, Mismatches: 43, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
235 88 0.21
236 255 0.60
237 84 0.20
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (235 bp):
GATGCAGTCTGCACTTCAGGTAATGACAGCAATGTATCTGTCCAGCCAGGTGAACAGCTGCTTCG
TGAGAACAATGAGGTTATTGTCTGTTCCATGTCTTTGATTTATAAATGAATTCTCTGATGTCAAA
ATTTGCTTTTTTTTTCTTCAATAATATTTCCTGTCTTTGTAGGACTCACTGGACCAGATAGTATC
ACCTAAGGAAGTTGAACATACTCAGCAGCCACACCCGGTT
Found at i:77174 original size:115 final size:115
Alignment explanation
Indices: 76972--77198 Score: 350
Period size: 115 Copynumber: 2.0 Consensus size: 115
76962 TATCTATTTG
* *
76972 AACCCTGTCTTACACGTAGCTATGCTACTCGGGTTTATGTTGCACCACGTAGTTATCTTCTATAA
1 AACCCTGTCTTACACGTAGCTATGCTACTCGCGTTTATGTTGCACCACGTAGTCATCTTCTATAA
* *
77037 CACTAAATTATTGAAAAGATGTATCATTTGGGGACATTTTTGGCATCATA
66 CACTAAATGATTGAAAAGATGTATCATTTGGGCACATTTTTGGCATCATA
77087 AACCCTGTCTTACACGTAGCTATGCTACTC-CGTATTATGTTGCACCACGTAGTCA-CTTTCTAT
1 AACCCTGTCTTACACGTAGCTATGCTACTCGCGT-TTATGTTGCACCACGTAGTCATC-TTCTAT
* * **
77150 TACACTGAATGATTGACGAGATGTATCATTTGGGCACATTTTTGGCATC
64 AACACTAAATGATTGAAAAGATGTATCATTTGGGCACATTTTTGGCATC
77199 TTAACCGATA
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
114 3 0.03
115 99 0.97
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (115 bp):
AACCCTGTCTTACACGTAGCTATGCTACTCGCGTTTATGTTGCACCACGTAGTCATCTTCTATAA
CACTAAATGATTGAAAAGATGTATCATTTGGGCACATTTTTGGCATCATA
Found at i:83857 original size:1 final size:1
Alignment explanation
Indices: 83851--83879 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
83841 ATAGCTACAT
83851 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
83880 GCAATTAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:89065 original size:17 final size:17
Alignment explanation
Indices: 89045--89083 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
89035 TTGATCAACG
89045 GTGATCTT-GCATTACCA
1 GTGATCTTAG-ATTACCA
*
89062 GTGATCTTAGATTACTA
1 GTGATCTTAGATTACCA
89079 GTGAT
1 GTGAT
89084 TTGGAGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (17 bp):
GTGATCTTAGATTACCA
Found at i:103282 original size:4 final size:4
Alignment explanation
Indices: 103275--103301 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
103265 TATATATACC
103275 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
103302 ATGTACTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:103725 original size:117 final size:114
Alignment explanation
Indices: 103519--103750 Score: 338
Period size: 117 Copynumber: 2.0 Consensus size: 114
103509 ACTAAAAAGC
* * *
103519 TAAATTGAGGATTAATGTGATGTCACCTTTTGGCTTTTTTTGGTATTTTCTCACTTTTCGGATGA
1 TAAATTGAGGATTAATATGATGCCACCTTTTGACTTTTTTTGGTATTTTCTCACTTTTCGGATGA
* *
103584 CTAAAAAGCCCCTCTATGAGTTTCCCCCTTTCCTTTTCCTGCTACCCTT
66 CTAAAAAGCCCCTCTATGAATTTCCCCCATTCCTTTTCCTGCTACCCTT
* * * *
103633 TAAATTGAGGATTAATATGGTGCCACCTTTTGACTTTTTTTTTTTGTCTTTTCTCACTTTTTGGA
1 TAAATTGAGGATTAATATGATGCCACCTTTTGAC---TTTTTTTGGTATTTTCTCACTTTTCGGA
* *
103698 TGACTAAAAAGCCCCTCTATGAATTTCCTCCATTCCTTTTCCTGCTATCCTT
63 TGACTAAAAAGCCCCTCTATGAATTTCCCCCATTCCTTTTCCTGCTACCCTT
103750 T
1 T
103751 TTTGTAATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
114 30 0.29
117 74 0.71
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (114 bp):
TAAATTGAGGATTAATATGATGCCACCTTTTGACTTTTTTTGGTATTTTCTCACTTTTCGGATGA
CTAAAAAGCCCCTCTATGAATTTCCCCCATTCCTTTTCCTGCTACCCTT
Done.