Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023882.1 Corchorus olitorius cultivar O-4 contig23915, 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: 71719
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:24158 original size:17 final size:17
Alignment explanation
Indices: 24136--24169 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
24126 TTTTTATATA
24136 AAATAATAATACAAAGT
1 AAATAATAATACAAAGT
24153 AAATAATAATACAAAGT
1 AAATAATAATACAAAGT
24170 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAATAATAATACAAAGT
Found at i:29536 original size:14 final size:14
Alignment explanation
Indices: 29517--29544 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29507 ATATTTGCTT
29517 AAACATGAATATGA
1 AAACATGAATATGA
29531 AAACATGAATATGA
1 AAACATGAATATGA
29545 TACATGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAACATGAATATGA
Found at i:33891 original size:45 final size:45
Alignment explanation
Indices: 33813--34040 Score: 368
Period size: 45 Copynumber: 5.1 Consensus size: 45
33803 GAGTATACCT
* * * * *
33813 CAATCTGATAACTTCTTTTATCATTTAAGTCGTCATGATCATCTG
1 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
33858 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
1 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
*
33903 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCACCTG
1 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
33948 CAATCTGATAACTTG-TTTCATCACTCAACTCGTCATGATCATCTG
1 CAATCTGATAAC-TGCTTTCATCACTCAACTCGTCATGATCATCTG
* *
33993 CAATCTGATAACTTCTTTCATCATTCAACTCGTCATGATCATCTG
1 CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
34038 CAA
1 CAA
34041 AATCTGCTTG
Statistics
Matches: 172, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
44 1 0.01
45 169 0.98
46 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.36
Consensus pattern (45 bp):
CAATCTGATAACTGCTTTCATCACTCAACTCGTCATGATCATCTG
Found at i:45134 original size:17 final size:17
Alignment explanation
Indices: 45108--45142 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45098 AAAATATATT
* *
45108 AATTACTTGAGCTCAAA
1 AATTAATTGAGATCAAA
45125 AATTAATTGAGATCAAA
1 AATTAATTGAGATCAAA
45142 A
1 A
45143 TATATATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (17 bp):
AATTAATTGAGATCAAA
Found at i:48827 original size:14 final size:15
Alignment explanation
Indices: 48803--48831 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48793 AAAATCTAAA
48803 ATATGAATATACTAC
1 ATATGAATATACTAC
48818 ATAT-AATATACTAC
1 ATATGAATATACTAC
48832 TCTTATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.34
Consensus pattern (15 bp):
ATATGAATATACTAC
Found at i:48922 original size:18 final size:17
Alignment explanation
Indices: 48894--48929 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
48884 TAAAATATGG
48894 TGTACATATATATTATA
1 TGTACATATATATTATA
48911 TGTACTATATATATTATA
1 TGTAC-ATATATATTATA
48929 T
1 T
48930 ATCAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (17 bp):
TGTACATATATATTATA
Found at i:49312 original size:22 final size:22
Alignment explanation
Indices: 49137--49317 Score: 66
Period size: 22 Copynumber: 8.2 Consensus size: 22
49127 TTATATTATA
49137 AAATTTTGATAACCTCTCCTTATG
1 AAATTTTGATAACCTC-CC-TATG
* * * *
49161 AAATCTTGATAATCACAC-ATG
1 AAATTTTGATAACCTCCCTATG
** *
49182 AAATTTTGATAACGGCACTATG
1 AAATTTTGATAACCTCCCTATG
* * * * *
49204 GAA-TTTCAGGAACCTTCATATG
1 AAATTTTGA-TAACCTCCCTATG
* * * *
49226 AAATTTTGTTAACTTTCCTACG
1 AAATTTTGATAACCTCCCTATG
* * *
49248 AAACTTT-ATTA-GTCTCCTGATG
1 AAATTTTGATAACCTC-CCT-ATG
* **
49270 GAATTTT-ATAGACCTTACTATG
1 AAATTTTGATA-ACCTCCCTATG
*
49292 AAATTTTGATAACCTCCCTATA
1 AAATTTTGATAACCTCCCTATG
49314 AAAT
1 AAAT
49318 ATATCACACT
Statistics
Matches: 110, Mismatches: 39, Indels: 18
0.66 0.23 0.11
Matches are distributed among these distances:
20 1 0.01
21 26 0.24
22 59 0.54
23 10 0.09
24 14 0.13
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:49472 original size:22 final size:22
Alignment explanation
Indices: 49447--49677 Score: 172
Period size: 22 Copynumber: 10.5 Consensus size: 22
49437 GGTTATTTTC
49447 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAATCACA
49469 CTATGAAATTTTGATAATCACA
1 CTATGAAATTTTGATAATCACA
* * * * *
49491 TTA-AAAAGTTTGATAACCGCA
1 CTATGAAATTTTGATAATCACA
*
49512 CTATGAAGTTTTGATAA-C-CTA
1 CTATGAAATTTTGATAATCAC-A
* *
49533 GCTATGAAAATTTGATAATCTC-
1 -CTATGAAATTTTGATAATCACA
* * *
49555 CTTATGGAATCTTGATAAT-ATCC
1 C-TATGAAATTTTGATAATCA-CA
* *
49578 CTAAT-AAATTTTGATAACCATA
1 CT-ATGAAATTTTGATAATCACA
* * *
49600 TTATGAAATTTCGATAATCATA
1 CTATGAAATTTTGATAATCACA
* * *
49622 CTATGAAATTGTGATAACCTC-
1 CTATGAAATTTTGATAATCACA
49643 CTTATGAAATTTTGATAAT-ATCA
1 C-TATGAAATTTTGATAATCA-CA
49666 CTATGAAATTTT
1 CTATGAAATTTT
49678 AATAGAAAAA
Statistics
Matches: 163, Mismatches: 32, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
20 1 0.01
21 22 0.13
22 133 0.82
23 6 0.04
24 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACA
Found at i:59328 original size:62 final size:62
Alignment explanation
Indices: 59252--59376 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
59242 TATTCCATAC
59252 AATTACTAAAACTCTAAAAAATTATTACAT-GACACTGACCCACCTTATCAGCCATGAGACCA
1 AATTACTAAAACTCTAAAAAATTATTACATAG-CACTGACCCACCTTATCAGCCATGAGACCA
*
59314 AATTACTAAAACTCTGAAAAATTATTACATAGCACTGACCCACCTTATCAGCCATGAGACCA
1 AATTACTAAAACTCTAAAAAATTATTACATAGCACTGACCCACCTTATCAGCCATGAGACCA
59376 A
1 A
59377 CCACCTTGCT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 60 0.98
63 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.24
Consensus pattern (62 bp):
AATTACTAAAACTCTAAAAAATTATTACATAGCACTGACCCACCTTATCAGCCATGAGACCA
Found at i:67457 original size:21 final size:21
Alignment explanation
Indices: 67431--67470 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
67421 TAAAGGGACA
67431 GTAAAAGCACTGCCAGAGACG
1 GTAAAAGCACTGCCAGAGACG
*
67452 GTAAAAGCATTGCCAGAGA
1 GTAAAAGCACTGCCAGAGA
67471 GTCTCCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.28, T:0.12
Consensus pattern (21 bp):
GTAAAAGCACTGCCAGAGACG
Found at i:68710 original size:18 final size:19
Alignment explanation
Indices: 68669--68716 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
68659 GATCGTTTAG
68669 TAATATT-TATA-ATTAAA
1 TAATATTATATATATTAAA
68686 T-ATATTATATATA-TAAA
1 TAATATTATATATATTAAA
68703 TAATATTATATATA
1 TAATATTATATATA
68717 CTAGTTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.18
17 10 0.36
18 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATATTATATATATTAAA
Found at i:68804 original size:22 final size:22
Alignment explanation
Indices: 68775--68879 Score: 104
Period size: 22 Copynumber: 4.8 Consensus size: 22
68765 TGAATATTTT
* *
68775 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACCACCA
* *
68797 TATTAAATTTTGATGACCACCA
1 TATGAAATTTTGATAACCACCA
** *
68819 TATGAAATTTTGATAATTATC-
1 TATGAAATTTTGATAACCACCA
* * *
68840 TATGAAATTATGATAAACGCCA
1 TATGAAATTTTGATAACCACCA
*
68862 TATGAAACTTTGATAACC
1 TATGAAATTTTGATAACC
68880 TGACTATAAA
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
21 16 0.25
22 49 0.75
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCA
Found at i:68845 original size:21 final size:21
Alignment explanation
Indices: 68775--68899 Score: 101
Period size: 22 Copynumber: 5.8 Consensus size: 21
68765 TGAATATTTT
68775 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTA-CC
* * *
68797 TATTAAATTTTGATGACCACC
1 TATGAAATTTTGATAACTACC
* *
68818 ATATGAAATTTTGATAATTATC
1 -TATGAAATTTTGATAACTACC
* *
68840 TATGAAATTATGATAAAC-GCC
1 TATGAAATTTTGAT-AACTACC
*
68861 ATATGAAACTTTGATAACCTGA-C
1 -TATGAAATTTTGATAA-CT-ACC
*
68884 TATAAAATTTTGATAA
1 TATGAAATTTTGATAA
68900 GCTTTTCTAT
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
21 18 0.22
22 61 0.76
23 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:68864 original size:43 final size:44
Alignment explanation
Indices: 68775--68878 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
68765 TGAATATTTT
* * * *
68775 TATGAAATTTTGATAACTACCCTATTAAATTTTGATGACCACCA
1 TATGAAATTTTGATAACTACCCTATGAAATTATGATAAACACCA
* * *
68819 TATGAAATTTTGATAATTA-TCTATGAAATTATGATAAACGCCA
1 TATGAAATTTTGATAACTACCCTATGAAATTATGATAAACACCA
*
68862 TATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
68879 CTGACTATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 33 0.65
44 18 0.35
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACTACCCTATGAAATTATGATAAACACCA
Found at i:68947 original size:37 final size:37
Alignment explanation
Indices: 68882--68956 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
68872 TGATAACCTG
* * *
68882 ACTATAAAATTTTGATAAGCTTTTCTATAAATTTTGT
1 ACTATAAAATTTTAATAAACTTTCCTATAAATTTTGT
68919 ACTATAAAATTTTAATAAACTTTCCTATAAATTTTGT
1 ACTATAAAATTTTAATAAACTTTCCTATAAATTTTGT
68956 A
1 A
68957 ATCTTCCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (37 bp):
ACTATAAAATTTTAATAAACTTTCCTATAAATTTTGT
Found at i:70394 original size:3 final size:3
Alignment explanation
Indices: 70386--70452 Score: 116
Period size: 3 Copynumber: 22.3 Consensus size: 3
70376 TAGGTTGGCC
*
70386 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
70434 AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
70453 TAGATATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:71355 original size:22 final size:22
Alignment explanation
Indices: 71313--71368 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
71303 TATTTTTATT
71313 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCACACTATA
* ** *
71335 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAACCACACTATA
*
71357 AAATTCTGATAA
1 AAATTTTGATAA
71369 ACTCCCAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:71702 original size:22 final size:22
Alignment explanation
Indices: 71660--71719 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
71650 TAATAACTAC
*
71660 ACTATGAAATTCTGATAACCAT
1 ACTATGAAATTTTGATAACCAT
* * *
71682 CCTATGAAATTTTGGTCACCAT
1 ACTATGAAATTTTGATAACCAT
*
71704 ACTCTGAAATTTTGAT
1 ACTATGAAATTTTGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAT
Done.