Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011248.1 Corchorus capsularis cultivar CVL-1 contig11269, 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: 32868
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:355 original size:22 final size:21
Alignment explanation
Indices: 311--355 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
301 GCTAAAAGGG
*
311 AGGGGAAAGGAAAAAGATAAA
1 AGGGGAAAGGAAAAAGACAAA
332 AGGGGAGAAGGAAAAA-ACAGAA
1 AGGGGA-AAGGAAAAAGACA-AA
354 AG
1 AG
356 AAAGGAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.02
Consensus pattern (21 bp):
AGGGGAAAGGAAAAAGACAAA
Found at i:3816 original size:14 final size:14
Alignment explanation
Indices: 3798--3903 Score: 72
Period size: 14 Copynumber: 7.6 Consensus size: 14
3788 TATAAATACT
3798 TTTAAGAAAATTCA
1 TTTAAGAAAATTCA
* * *
3812 ATTAAGAAATTTTA
1 TTTAAGAAAATTCA
* * *
3826 TTTTA-TAAATTCT
1 TTTAAGAAAATTCA
3839 TTTAAGAAAATTCA
1 TTTAAGAAAATTCA
* * *
3853 GTTAAGAAATTTTA
1 TTTAAGAAAATTCA
* * *
3867 TTTTA-TAAATTCT
1 TTTAAGAAAATTCA
3880 TTTAAGAAAAATTCA
1 TTTAAG-AAAATTCA
*
3895 GTTAAGAAA
1 TTTAAGAAA
3904 TGAAATTTTG
Statistics
Matches: 64, Mismatches: 25, Indels: 6
0.67 0.26 0.06
Matches are distributed among these distances:
13 16 0.25
14 37 0.58
15 11 0.17
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (14 bp):
TTTAAGAAAATTCA
Found at i:3841 original size:41 final size:41
Alignment explanation
Indices: 3780--3904 Score: 223
Period size: 41 Copynumber: 3.0 Consensus size: 41
3770 CGTGCGGTTG
* *
3780 TTTTATTTTATAAATACTTTTAAGAAAATTCAATTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
3821 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
3862 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
3904 T
1 T
3905 GAAATTTTGT
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
41 63 0.78
42 18 0.22
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (41 bp):
TTTTATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAA
Found at i:3986 original size:16 final size:16
Alignment explanation
Indices: 3965--3995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3955 GAAGCATGGA
3965 AAAGACAAGAGAATAG
1 AAAGACAAGAGAATAG
*
3981 AAAGACAATAGAATA
1 AAAGACAAGAGAATA
3996 TGGAGAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.19, T:0.10
Consensus pattern (16 bp):
AAAGACAAGAGAATAG
Found at i:10267 original size:6 final size:6
Alignment explanation
Indices: 10256--10286 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
10246 CATCTTTGGT
10256 TGATTA TGATTA TGATTA TGATTA TGATTA T
1 TGATTA TGATTA TGATTA TGATTA TGATTA T
10287 TATCATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTA
Found at i:17784 original size:21 final size:21
Alignment explanation
Indices: 17758--17816 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
17748 TGTTGCAGAA
* *
17758 GTAGAACCGGCCCTTGTCATT
1 GTAGAACCAGCCATTGTCATT
*
17779 GTAGAAGCAGCCATTGTCATT
1 GTAGAACCAGCCATTGTCATT
* *
17800 GTAGAAGCAGCCTTTGT
1 GTAGAACCAGCCATTGT
17817 TGCAGCTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (21 bp):
GTAGAACCAGCCATTGTCATT
Found at i:20912 original size:27 final size:24
Alignment explanation
Indices: 20864--20948 Score: 125
Period size: 24 Copynumber: 3.4 Consensus size: 24
20854 TGTGGGGCTT
*
20864 CATTTAAACCCTCACTACCTACTG
1 CATTTAAACCCTCACCACCTACTG
*
20888 CATTTATACCCGGTTCACCACCTACTG
1 CATTTAAACCC---TCACCACCTACTG
20915 CATTTAAACCCTCACCACCTACTG
1 CATTTAAACCCTCACCACCTACTG
20939 CATTTAAACC
1 CATTTAAACC
20949 ATCATCTACT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 33 0.60
27 22 0.40
ACGTcount: A:0.28, C:0.38, G:0.06, T:0.28
Consensus pattern (24 bp):
CATTTAAACCCTCACCACCTACTG
Found at i:25182 original size:26 final size:26
Alignment explanation
Indices: 25153--25270 Score: 111
Period size: 26 Copynumber: 4.7 Consensus size: 26
25143 TTCCTTCATT
25153 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
25179 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
25205 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * * * *
25228 GTAAT-TTTAATTAACTAATTA-AAA
1 TTAATCATAAACTAATTAAATACTAA
25252 TTAATCATAAACTAATTAA
1 TTAATCATAAACTAATTAA
25271 TATTTAAAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
22 6 0.08
23 9 0.13
24 8 0.11
25 11 0.15
26 37 0.52
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:25301 original size:12 final size:13
Alignment explanation
Indices: 25279--25306 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
25269 AATATTTAAA
25279 AATTAAAAAAAAT
1 AATTAAAAAAAAT
25292 AATTAAAAAAAAT
1 AATTAAAAAAAAT
25305 AA
1 AA
25307 AGAAAATGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATTAAAAAAAAT
Found at i:26884 original size:29 final size:28
Alignment explanation
Indices: 26850--26926 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
26840 ACTTGTAGCG
* **
26850 TTTGGACGTTTTGCCCCCTGAATTTTGAT
1 TTTGGAC-TTTTGCCCCCTGAACTTCAAT
*
26879 TTTGGACATTTTGTCCCCTGAACTTCAAT
1 TTTGGAC-TTTTGCCCCCTGAACTTCAAT
*
26908 TTTGGGACTTTTTCCCCCT
1 TTT-GGACTTTTGCCCCCT
26927 TAACCTAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (28 bp):
TTTGGACTTTTGCCCCCTGAACTTCAAT
Found at i:27739 original size:19 final size:20
Alignment explanation
Indices: 27715--27754 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
27705 AATTAAATAT
27715 CCATA-TCAAATTTTGATAA
1 CCATATTCAAATTTTGATAA
*
27734 CCATATTTGAAATTTTGATAA
1 CCATA-TTCAAATTTTGATAA
27755 TCACCCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
CCATATTCAAATTTTGATAA
Found at i:27748 original size:21 final size:20
Alignment explanation
Indices: 27722--27798 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
27712 TATCCATATC
*
27722 AAATTTTGATAACCATATTT
1 AAATTTTGATAACCACATTT
* **
27742 GAAATTTTGATAATCACCCTT
1 -AAATTTTGATAACCACATTT
*
27763 ACAATTTTGATAATCACATTAT
1 A-AATTTTGATAACCACATT-T
27785 AAATTTTGATAACC
1 AAATTTTGATAACC
27799 GTACACTACA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.40
Consensus pattern (20 bp):
AAATTTTGATAACCACATTT
Found at i:28040 original size:131 final size:131
Alignment explanation
Indices: 27831--28086 Score: 295
Period size: 131 Copynumber: 2.0 Consensus size: 131
27821 CCTCATTATG
* *** *
27831 GAAATTTTGATAATCTCTCTATTAAAATTTAATAACCTCCTTCTGAAATTTTGATAACTTCCCTA
1 GAAATTTTGATAATCTCCCTATTAAAATTTAATAACCTCCCAATGAAATTTTGATAACCTCCCTA
** * * **
27896 TGGTTTTTGATAACTTA-GTTATGAAATTTTGATAACCACATAATAAAATTTCGACAACCTTCCT
66 TGAATTTTAATAAC-CACACTATGAAATTTTGATAACCACATAATAAAATTTCGACAACCTTCCT
27960 AT
130 AT
* *
27962 GAAATTTTGATAATCTCCCTA-TAAAATTTTGATAACCTCCCAATGAAATTTTGGT-ACCTCCC-
1 GAAATTTTGATAATCTCCCTATTAAAA-TTTAATAACCTCCCAATGAAATTTTGATAACCTCCCT
* * * *
28024 ATTGAAATTTTAATAACCACACTATGAAATTTTGATAACCTCATTATAAAATTTTGATAACCT
65 A-TG-AATTTTAATAACCACACTATGAAATTTTGATAACCACATAATAAAATTTCGACAACCT
28087 CTTTGATAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
129 1 0.01
130 14 0.13
131 89 0.86
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.39
Consensus pattern (131 bp):
GAAATTTTGATAATCTCCCTATTAAAATTTAATAACCTCCCAATGAAATTTTGATAACCTCCCTA
TGAATTTTAATAACCACACTATGAAATTTTGATAACCACATAATAAAATTTCGACAACCTTCCTA
T
Found at i:28076 original size:65 final size:66
Alignment explanation
Indices: 27915--28087 Score: 188
Period size: 65 Copynumber: 2.6 Consensus size: 66
27905 ATAACTTAGT
* * * * * * *
27915 TATGAAATTTTGATAACCACATAATAAAATTTCGACAACCTTCCTATGAAATTTTGATAATCTCC
1 TATGAAATTTTGATAACCTCATAATAAAATTTTGACAACCTCCCTATGAAATTTTAATAACCACA
27980 C
66 C
* ** * **
27981 TATAAAATTTTGATAACCTCCCAATGAAATTTTG-GTACCTCCC-ATTGAAATTTTAATAACCAC
1 TATGAAATTTTGATAACCTCATAATAAAATTTTGACAACCTCCCTA-TGAAATTTTAATAACCAC
28044 AC
65 AC
* *
28046 TATGAAATTTTGATAACCTCATTATAAAATTTTGATAACCTC
1 TATGAAATTTTGATAACCTCATAATAAAATTTTGACAACCTC
28088 TTTGATAACA
Statistics
Matches: 85, Mismatches: 20, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
64 1 0.01
65 51 0.60
66 33 0.39
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (66 bp):
TATGAAATTTTGATAACCTCATAATAAAATTTTGACAACCTCCCTATGAAATTTTAATAACCACA
C
Found at i:28085 original size:22 final size:22
Alignment explanation
Indices: 27722--28087 Score: 184
Period size: 22 Copynumber: 16.7 Consensus size: 22
27712 TATCCATATC
27722 AAATTTTGATAACCAT-ATT-TG
1 AAATTTTGATAACC-TCATTATG
*
27743 AAATTTTGATAATCAC-CCTTA--
1 AAATTTTGATAA-C-CTCATTATG
* * *
27764 CAATTTTGATAATCACATTAT-
1 AAATTTTGATAACCTCATTATG
* *
27785 AAATTTTGATAACCGTACACTA-C
1 AAATTTTGATAACC-T-CATTATG
**
27808 AAAGTTTCAATAACCTCATTATGG
1 AAA-TTTTGATAACCTCATTAT-G
* *
27832 AAATTTTGATAATCTC-TCTATT
1 AAATTTTGATAACCTCAT-TATG
* * * *
27854 AAAATTTAATAACCTCCTTCTG
1 AAATTTTGATAACCTCATTATG
* **
27876 AAATTTTGATAACTTCCCTATG
1 AAATTTTGATAACCTCATTATG
** *
27898 -GTTTTTGATAA-CTTAGTTATG
1 AAATTTTGATAACCTCA-TTATG
* * *
27919 AAATTTTGATAACCACATAATA
1 AAATTTTGATAACCTCATTATG
* * *
27941 AAATTTCGACAACCTTC-CTATG
1 AAATTTTGATAACC-TCATTATG
* ** *
27963 AAATTTTGATAATCTCCCTATA
1 AAATTTTGATAACCTCATTATG
***
27985 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCTCATTATG
*
28007 AAATTTTGGT-ACCTCCCA-T-TG
1 AAATTTTGATAACCT--CATTATG
* * *
28028 AAATTTTAATAACCACACTATG
1 AAATTTTGATAACCTCATTATG
*
28050 AAATTTTGATAACCTCATTATA
1 AAATTTTGATAACCTCATTATG
28072 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
28088 TTTGATAACA
Statistics
Matches: 260, Mismatches: 61, Indels: 47
0.71 0.17 0.13
Matches are distributed among these distances:
19 1 0.00
20 7 0.03
21 65 0.25
22 148 0.57
23 27 0.10
24 12 0.05
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:30191 original size:22 final size:22
Alignment explanation
Indices: 30166--30314 Score: 95
Period size: 22 Copynumber: 6.8 Consensus size: 22
30156 ACTCCCCATA
* *
30166 AAATTTTGGTAAACACGTTATG
1 AAATTTTGATAAACACATTATG
* * * *
30188 AAATTCTGATAACCGCACTATG
1 AAATTTTGATAAACACATTATG
* *
30210 AAATTTTGATAATCTCATTATG
1 AAATTTTGATAAACACATTATG
* *
30232 AAATTTTGATAACCACACTAT-
1 AAATTTTGATAAACACATTATG
* * *
30253 AACATATTGATAACCTCCA-TATG
1 AA-ATTTTGATAAAC-ACATTATG
* * * * *
30276 AAATTTTTACAACCTCATTATA
1 AAATTTTGATAAACACATTATG
*
30298 AAATTTTGATAACCACA
1 AAATTTTGATAAACACA
30315 CAAAGACAAC
Statistics
Matches: 100, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
21 4 0.04
22 92 0.92
23 4 0.04
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAAACACATTATG
Found at i:30192 original size:44 final size:44
Alignment explanation
Indices: 30144--30314 Score: 110
Period size: 44 Copynumber: 3.9 Consensus size: 44
30134 TTACACAATA
* * * *
30144 AAATTTTGATAAACTCCCCATAAAATTTTGGTAAACACGTTATG
1 AAATTTTGATAAACGCACCATAAAATTTTGATAAACACATTATG
* * * * * *
30188 AAATTCTGATAACCGCACTATGAAATTTTGATAATCTCATTATG
1 AAATTTTGATAAACGCACCATAAAATTTTGATAAACACATTATG
* * * * * * *
30232 AAATTTTGATAACCACACTATAACATATTGATAACCTCCA-TATG
1 AAATTTTGATAAACGCACCATAAAATTTTGATAAAC-ACATTATG
* * * * ** *
30276 AAATTTTTACAACCTCATTATAAAATTTTGATAACCACA
1 AAATTTTGATAAACGCACCATAAAATTTTGATAAACACA
30315 CAAAGACAAC
Statistics
Matches: 102, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
43 2 0.02
44 98 0.96
45 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAAACGCACCATAAAATTTTGATAAACACATTATG
Found at i:30236 original size:66 final size:66
Alignment explanation
Indices: 30163--30315 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 66
30153 TAAACTCCCC
* ** * *
30163 ATAAAATTTTGGTAAACACGTTATGAA-AT-TCTGATAACCG-CACTATGAAATTTTGATAATCT
1 ATAAAATTTTGATAAACACACTAT-AACATAT-TGATAACCGCCA-TATGAAATTTTGACAACCT
30225 CATT
63 CATT
* * * *
30229 ATGAAATTTTGATAACCACACTATAACATATTGATAACCTCCATATGAAATTTTTACAACCTCAT
1 ATAAAATTTTGATAAACACACTATAACATATTGATAACCGCCATATGAAATTTTGACAACCTCAT
30294 T
66 T
*
30295 ATAAAATTTTGATAACCACAC
1 ATAAAATTTTGATAAACACAC
30316 AAAGACAACA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 2 0.03
66 69 0.93
67 3 0.04
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (66 bp):
ATAAAATTTTGATAAACACACTATAACATATTGATAACCGCCATATGAAATTTTGACAACCTCAT
T
Found at i:31087 original size:109 final size:109
Alignment explanation
Indices: 30891--31186 Score: 450
Period size: 109 Copynumber: 2.7 Consensus size: 109
30881 ACTATTATAG
* *
30891 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
30956 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
31005 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
31070 TTACCAAAAAATTTGGATATATTAAGATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
31114 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
31178 TTTTTACCA
63 TTTTTACCA
31187 TTTTAATTTA
Statistics
Matches: 172, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 125 0.73
110 8 0.05
111 17 0.10
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.