Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011956.1 Corchorus olitorius cultivar O-4 contig11989, 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: 47993
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7455 original size:34 final size:34
Alignment explanation
Indices: 7412--7479 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
7402 TGCAATGCTT
7412 TTCCTGGCGAATTCGATCTTTTATAAACAAGTTC
1 TTCCTGGCGAATTCGATCTTTTATAAACAAGTTC
7446 TTCCTGGCGAATTCGATCTTTTATAAACAAGTTC
1 TTCCTGGCGAATTCGATCTTTTATAAACAAGTTC
7480 ACGCTGAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (34 bp):
TTCCTGGCGAATTCGATCTTTTATAAACAAGTTC
Found at i:7887 original size:56 final size:56
Alignment explanation
Indices: 7801--7915 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
7791 TAACAAAGTA
*
7801 AGTGGCATATTTATAGGCACATAGATACATCACCATAAATATAAAGGGATGAACTT
1 AGTGGCATATTTATAGGCACATAGATACATCACCATAAATATAAAGAGATGAACTT
7857 AGTGGCATATTTATAGGCACATAGATACATCACCATAAATATAAAGAGATGAACTT
1 AGTGGCATATTTATAGGCACATAGATACATCACCATAAATATAAAGAGATGAACTT
7913 AGT
1 AGT
7916 ACATAGGTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (56 bp):
AGTGGCATATTTATAGGCACATAGATACATCACCATAAATATAAAGAGATGAACTT
Found at i:8041 original size:38 final size:38
Alignment explanation
Indices: 7991--8067 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
7981 GACATCCACA
*
7991 ACATACATGTATATTCATAACAAGTTTATAATTAATTT
1 ACATACATGTATATTCATAACAAATTTATAATTAATTT
8029 ACATACATGTATATTCATAACAAATTTATAATTAATTT
1 ACATACATGTATATTCATAACAAATTTATAATTAATTT
8067 A
1 A
8068 TAATTATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (38 bp):
ACATACATGTATATTCATAACAAATTTATAATTAATTT
Found at i:8065 original size:11 final size:11
Alignment explanation
Indices: 8051--8088 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8041 ATTCATAACA
8051 AATTTATAATT
1 AATTTATAATT
8062 AATTTATAATT
1 AATTTATAATT
8073 -ATTTGATAATT
1 AATTT-ATAATT
*
8084 TATTT
1 AATTT
8089 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:19349 original size:6 final size:6
Alignment explanation
Indices: 19338--19383 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
19328 AATTAGTATC
*
19338 TATCTA TATCTA TATCTA TATTTA TATCTA TTTATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA --TATCTA TATCTA TAT
19384 TAAAAAGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
8 6 0.17
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (6 bp):
TATCTA
Found at i:19751 original size:16 final size:16
Alignment explanation
Indices: 19730--19760 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19720 GAAAGTGCTT
19730 GAGAAAGTATTTGGGA
1 GAGAAAGTATTTGGGA
19746 GAGAAAGTATTTGGG
1 GAGAAAGTATTTGGG
19761 TCAGTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (16 bp):
GAGAAAGTATTTGGGA
Found at i:20015 original size:77 final size:77
Alignment explanation
Indices: 19886--20044 Score: 230
Period size: 77 Copynumber: 2.1 Consensus size: 77
19876 GCTCTTATAG
* * * ** * *
19886 TTTTACTCAACTAAAAATTTTATTTTTATTTAATTAAATCTAATATTTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTA-TGTAGTT
*
19951 TACCATTTTATTA
65 TACCATTTTACTA
19964 TTTTACTCAACT-AAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATGTAGTTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATGTAGTTT
20028 ACCATTTTACTA
66 ACCATTTTACTA
20040 TTTTA
1 TTTTA
20045 ATTAAAAAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 22 0.30
77 39 0.53
78 12 0.16
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.53
Consensus pattern (77 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATAACTATGTAGTTT
ACCATTTTACTA
Found at i:20157 original size:26 final size:25
Alignment explanation
Indices: 20102--20158 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
20092 TGTAATTGTT
* *
20102 TAAACTTTTACATTTTTTTTAGAAA
1 TAAACTTTTACATTTTTTCTACAAA
*
20127 TAAACTTTTACAGTTTTATTCTACTAA
1 TAAACTTTTACA-TTTT-TTCTACAAA
20154 -AAACT
1 TAAACT
20159 CTATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.44
26 9 0.33
27 6 0.22
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (25 bp):
TAAACTTTTACATTTTTTCTACAAA
Found at i:21125 original size:17 final size:18
Alignment explanation
Indices: 21092--21128 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
21082 CTTTCATTAC
21092 ATTAATTTAAAATTATAA
1 ATTAATTTAAAATTATAA
21110 ATTAA-TTAATAA-TATAA
1 ATTAATTTAA-AATTATAA
21127 AT
1 AT
21129 ATCCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATTTAAAATTATAA
Found at i:29001 original size:43 final size:44
Alignment explanation
Indices: 28954--29056 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
28944 CATAGTTAGG
* * * * **
28954 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTCAATAGGGTAA
* *
28997 TTATCAAAATTTCATATGGTGGTTATCAAAATTCAATAGGGTGA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTCAATAGGGTAA
29041 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
29057 AAAATATTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 31 0.61
44 20 0.39
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTCAATAGGGTAA
Found at i:29023 original size:22 final size:21
Alignment explanation
Indices: 28917--29056 Score: 106
Period size: 22 Copynumber: 6.6 Consensus size: 21
28907 AGGAAGGTTA
*
28917 CAAAA-TTCATAGG-AATTAT
1 CAAAATTTCATAGGTGATTAT
* * *
28936 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGT-GATTAT
* * * *
28958 CAAAGTTTCTTATGGAGTTTAT
1 CAAAATTTCATA-GGTGATTAT
* * *
28980 CACAATTTTATAGGTAATTAT
1 CAAAATTTCATAGGTGATTAT
*
29001 CAAAATTTCATATGGTGGTTAT
1 CAAAATTTCATA-GGTGATTAT
29023 CAAAA-TTCAATAGGGTGATTAT
1 CAAAATTTC-ATA-GGTGATTAT
29045 CAAAATTTCATA
1 CAAAATTTCATA
29057 AAAATATTCA
Statistics
Matches: 91, Mismatches: 23, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.04
20 7 0.08
21 19 0.21
22 57 0.63
23 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
CAAAATTTCATAGGTGATTAT
Found at i:29045 original size:65 final size:64
Alignment explanation
Indices: 28917--29052 Score: 143
Period size: 65 Copynumber: 2.1 Consensus size: 64
28907 AGGAAGGTTA
* * * * * * *
28917 CAAAA-TTCATAGGAATTATTAAAATTTCATAGTTAGGTTATCAAAGTTTCTTATGGAGTTTAT
1 CAAAATTTTATAGGAATTATCAAAATTTCATAGGTAGGTTATCAAAGATTCATAGGGAGATTAT
* *
28980 CACAATTTTATAGGTAATTATCAAAATTTCATATGGT-GGTTATCAAA-ATTCAATAGGGTGATT
1 CAAAATTTTATAGG-AATTATCAAAATTTCATA-GGTAGGTTATCAAAGATTC-ATAGGGAGATT
29043 AT
63 AT
29045 CAAAATTT
1 CAAAATTT
29053 CATAAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
63 4 0.07
64 10 0.17
65 43 0.73
66 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (64 bp):
CAAAATTTTATAGGAATTATCAAAATTTCATAGGTAGGTTATCAAAGATTCATAGGGAGATTAT
Found at i:38597 original size:18 final size:18
Alignment explanation
Indices: 38570--38629 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
38560 ACCATAGGTG
*
38570 GCAACGGCATACGCAGAT
1 GCAACAGCATACGCAGAT
38588 GCAACAGCATACGCAGAT
1 GCAACAGCATACGCAGAT
38606 GCAACAGCATACGCAGAT
1 GCAACAGCATACGCAGAT
38624 GCAACA
1 GCAACA
38630 TATGATGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.38, C:0.28, G:0.23, T:0.10
Consensus pattern (18 bp):
GCAACAGCATACGCAGAT
Found at i:47971 original size:2 final size:2
Alignment explanation
Indices: 47964--47991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47954 AAGTGAAGAT
47964 TA 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
47992 CT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.