Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010493.1 Corchorus capsularis cultivar CVL-1 contig10514, 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: 19258
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Found at i:1043 original size:21 final size:22
Alignment explanation
Indices: 998--1046 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
988 TAAAATTGGT
*
998 AATCA-AGAGTTTTCAAGATTT
1 AATCAGAGAGTTTTCAAGATTA
1019 AATCAGAG-GTTTTCAA-ATTCA
1 AATCAGAGAGTTTTCAAGATT-A
1040 AATCAGA
1 AATCAGA
1047 CTTAGTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCAGAGAGTTTTCAAGATTA
Found at i:3306 original size:265 final size:266
Alignment explanation
Indices: 2819--3319 Score: 914
Period size: 265 Copynumber: 1.9 Consensus size: 266
2809 CATAATTAAA
* *
2819 CAATCTGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTAATTTCTT
1 CAATCCGGCCATATAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTAATTTCTT
* * ***
2884 GCCCAAATGATCACCAAAGCTCTTCAATTGAAATTTTGTTGGTCTTCAAGTCTTCAAGATGAGTT
66 GCCCAAATCATCACCAAAGCTCTTCAATTGAAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTT
2949 CGAACAAGGCCCATGAGTGCAACCTTGAACCTTTTAGCTCTTGCTCTTGTCATCGGACCAATAAG
131 CGAACAAGGCCCATGAGTGCAACCTTGAACCTTTTAGCTCTTGCTCTTGTCATCGGACCAATAAG
3014 CATCTTCAATGGATCGAATGACATCTTTTTAGTGCTTGGAAACTAAAGCTAATGGGCTCATGCCA
196 CATCTTCAATGGATCGAATGACATCTTTTTAGTGCTTGGAAACTAAAGCTAATGGGCTCATGCCA
3079 TGATGT
261 TGATGT
*
3085 CAATCCGGCCATATAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTTTAATTTCTT
1 CAATCCGGCCATATAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTAATTTCTT
3150 GCCCAAATCATCACCAAAGCTCTTCAATTG-AACTTCAATGGTCTTCAAGTCTTCAAGATGAGTT
66 GCCCAAATCATCACCAAAGCTCTTCAATTGAAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTT
3214 CGAACAAGGCCCATGAGTGCAACCTTGAACCTTTTAGCTCTTGCTCTTGTCATCGGACCAATAAG
131 CGAACAAGGCCCATGAGTGCAACCTTGAACCTTTTAGCTCTTGCTCTTGTCATCGGACCAATAAG
*
3279 CATCTTCAATGGATCGAATGGCATCTTTTTAGTGCTTGGAA
196 CATCTTCAATGGATCGAATGACATCTTTTTAGTGCTTGGAA
3320 CATGATTATC
Statistics
Matches: 226, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
265 135 0.60
266 91 0.40
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (266 bp):
CAATCCGGCCATATAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTAATTTCTT
GCCCAAATCATCACCAAAGCTCTTCAATTGAAACTTCAATGGTCTTCAAGTCTTCAAGATGAGTT
CGAACAAGGCCCATGAGTGCAACCTTGAACCTTTTAGCTCTTGCTCTTGTCATCGGACCAATAAG
CATCTTCAATGGATCGAATGACATCTTTTTAGTGCTTGGAAACTAAAGCTAATGGGCTCATGCCA
TGATGT
Found at i:3750 original size:33 final size:33
Alignment explanation
Indices: 3713--3809 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
3703 AGCACTAGTG
* *
3713 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
3746 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
3779 ACCGGCCACGCGACATGGACATGTCCGGCCA
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCA
3810 CAACTGGCCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.23, C:0.37, G:0.30, T:0.10
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:4800 original size:8 final size:8
Alignment explanation
Indices: 4787--4820 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4777 CACCTTCTTG
4787 AAAAATTC
1 AAAAATTC
4795 AAAAATTC
1 AAAAATTC
*
4803 AGAAACTTC
1 A-AAAATTC
4812 AAAAATTC
1 AAAAATTC
4820 A
1 A
4821 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:10287 original size:33 final size:33
Alignment explanation
Indices: 10250--10356 Score: 135
Period size: 33 Copynumber: 3.2 Consensus size: 33
10240 AGCACTAGTG
* *
10250 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* * *
10283 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
* *
10316 ACCGGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
10348 AACCGGCCA
1 -ACCGGCCA
10357 TCGCTAGGCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 2 0.03
33 61 0.97
ACGTcount: A:0.23, C:0.38, G:0.29, T:0.09
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC
Found at i:15883 original size:9 final size:9
Alignment explanation
Indices: 15853--15906 Score: 65
Period size: 9 Copynumber: 5.9 Consensus size: 9
15843 ATTTCCCAGA
*
15853 AAAAAAAAG
1 AAAAAAGAG
*
15862 AAAGAAGAG
1 AAAAAAGAG
15871 -AAAAAGAG
1 AAAAAAGAG
15879 AAAAAAGAAG
1 AAAAAAG-AG
15889 AATAAAAGAG
1 AA-AAAAGAG
15899 AAAAAAGA
1 AAAAAAGA
15907 AAAGAGAAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
8 7 0.18
9 19 0.49
10 8 0.21
11 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:15885 original size:20 final size:20
Alignment explanation
Indices: 15850--15907 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
15840 ACAATTTCCC
15850 AGAAAAA-A-AAAGAAAGAAG
1 AGAAAAAGAGAAA-AAAGAAG
15869 AGAAAAAGAGAAAAAAGAAG
1 AGAAAAAGAGAAAAAAGAAG
15889 A-ATAAAAGAGAAAAAAGAA
1 AGA-AAAAGAGAAAAAAGAA
15908 AAGAGAAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.22
20 25 0.69
21 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AGAAAAAGAGAAAAAAGAAG
Found at i:15889 original size:27 final size:27
Alignment explanation
Indices: 15850--15917 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
15840 ACAATTTCCC
* *
15850 AGAAAAAAAAAGAA-AGAAGAGAAAAA
1 AGAAAAAAGAAGAATAAAAGAGAAAAA
15876 GAGAAAAAAGAAGAATAAAAGAGAAAAA
1 -AGAAAAAAGAAGAATAAAAGAGAAAAA
*
15904 AGAAAAGAGAAGAA
1 AGAAAAAAGAAGAA
15918 GCAATGATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 26 0.70
28 11 0.30
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (27 bp):
AGAAAAAAGAAGAATAAAAGAGAAAAA
Found at i:16404 original size:21 final size:22
Alignment explanation
Indices: 16361--16418 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 22
16351 ATGAAGAAGG
16361 GAAGAA-AAGAAAAAAAAAGAA
1 GAAGAAGAAGAAAAAAAAAGAA
*
16382 GAAGAAGAAGAAAAAATAA-AA
1 GAAGAAGAAGAAAAAAAAAGAA
* *
16403 G-AGAGGAGGAAAAAAA
1 GAAGAAGAAGAAAAAAA
16419 TGAAAGTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 12 0.38
21 9 0.28
22 11 0.34
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (22 bp):
GAAGAAGAAGAAAAAAAAAGAA
Found at i:16788 original size:17 final size:17
Alignment explanation
Indices: 16748--16791 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
16738 GTGAAAGAAA
16748 AAGAAGAAAATAAAAAG
1 AAGAAGAAAATAAAAAG
* *
16765 AAAAAGAAAA-AAAGAG
1 AAGAAGAAAATAAAAAG
16781 AATGAAGAAAA
1 AA-GAAGAAAA
16792 GAGGCTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAATAAAAAG
Found at i:16794 original size:14 final size:14
Alignment explanation
Indices: 16735--16794 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
16725 GTGCATATGT
*
16735 AAAGTGAAAGAAAA
1 AAAGAGAAAGAAAA
* *
16749 AGA-AGAAA-ATAA
1 AAAGAGAAAGAAAA
*
16761 AAAGAAAAAGAAAA
1 AAAGAGAAAGAAAA
* *
16775 AAAGAGAATGAAGA
1 AAAGAGAAAGAAAA
16789 AAAGAG
1 AAAGAG
16795 GCTCTATGGT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
12 5 0.14
13 8 0.23
14 22 0.63
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (14 bp):
AAAGAGAAAGAAAA
Found at i:17138 original size:50 final size:50
Alignment explanation
Indices: 17052--17151 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
17042 ATTTCAAAAC
* ** *
17052 AAATAAGATGGCATTCCATTTGTGAGTCTATTATCAAGATTCGA-TTTTCA
1 AAATAAGATGGCATTCCATTTGTGAGTCCAAGATCAAAATTC-ACTTTTCA
* *
17102 AAATAAGATTGCATTCTATTTGTGAGTCCAAGATCAAAATTCACTTTTCA
1 AAATAAGATGGCATTCCATTTGTGAGTCCAAGATCAAAATTCACTTTTCA
17152 GAGGGCGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (50 bp):
AAATAAGATGGCATTCCATTTGTGAGTCCAAGATCAAAATTCACTTTTCA
Found at i:17388 original size:29 final size:29
Alignment explanation
Indices: 17346--17404 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
17336 GATCAATAAA
*
17346 AGAATTTTTCAAAGCATACTATTCAAGTC
1 AGAATCTTTCAAAGCATACTATTCAAGTC
*
17375 AGAATCTTTCAAAGCATATTATTCAAGTC
1 AGAATCTTTCAAAGCATACTATTCAAGTC
17404 A
1 A
17405 AATTTGGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (29 bp):
AGAATCTTTCAAAGCATACTATTCAAGTC
Found at i:17873 original size:139 final size:139
Alignment explanation
Indices: 17649--17944 Score: 416
Period size: 139 Copynumber: 2.1 Consensus size: 139
17639 CGAATGCTCC
* * * *
17649 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGTGTAGCCTTGGTTCCATCCAAGCATT
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACACAAGTCAGTGTAGACTTGGTTCCATCCAAGCATT
* *
17714 CAGGGGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCAGATCCAGCTTCGATTCCATCCAG
66 CAAGGGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCAGATCCAGCTTCGATTCCATCCAA
*
17779 GCA-AGAGA
131 GCATACAGA
* * *
17787 GGCTTTTCCATAAGCCAAACTCGCTTCCACGCAAGAT-AGTTTAAGATTTGGTTCCATCCAAGCA
1 GGCTTTTCCATAAGCCAAACTCGCTTCCACACAAG-TCAGTGT-AGACTTGGTTCCATCCAAGCA
* * * *
17851 TTCAAGGGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTTCATCC
64 TTCAAGGGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCAGATCCAGCTTCGATTCCATCC
* *
17916 AAGCATTCAGG
129 AAGCATACAGA
17927 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCATAAGCCAA
17945 GTTCAGTGCG
Statistics
Matches: 139, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
138 35 0.25
139 84 0.60
140 20 0.14
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (139 bp):
GGCTTTTCCATAAGCCAAACTCGCTTCCACACAAGTCAGTGTAGACTTGGTTCCATCCAAGCATT
CAAGGGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCAGATCCAGCTTCGATTCCATCCAA
GCATACAGA
Found at i:17877 original size:70 final size:70
Alignment explanation
Indices: 17649--17944 Score: 359
Period size: 70 Copynumber: 4.3 Consensus size: 70
17639 CGAATGCTCC
** *
17649 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAG-TGTAGCCTTGGTTCCATCCAAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
*
17713 TCAGG
66 TCAAG
* * * *
17718 GGCTTTTCCACAAGCCAAACTCATTTCCACACGAGTCAGATCCAGCTTCGATTCCATCCAGGCA-
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
17782 --AGAG
66 TCA-AG
* * * * * ** *
17786 AGGCTTTTCCATAAGCCAAACTCGCTTCCACGCAAGAT-AGTTTAAGATTTGGTTCCATCCAAGC
1 -GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGC
17850 ATTCAAG
64 ATTCAAG
*
17857 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTTCATCCAAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
*
17922 TCAGG
66 TCAAG
*
17927 GGCTTTTCCATAAGCCAA
1 GGCTTTTCCACAAGCCAA
17945 GTTCAGTGCG
Statistics
Matches: 188, Mismatches: 31, Indels: 15
0.80 0.13 0.06
Matches are distributed among these distances:
67 1 0.01
68 1 0.01
69 89 0.47
70 94 0.50
71 2 0.01
72 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (70 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCAT
TCAAG
Found at i:18128 original size:47 final size:47
Alignment explanation
Indices: 18054--18290 Score: 357
Period size: 47 Copynumber: 5.0 Consensus size: 47
18044 ATCCAGGCAA
*
18054 TCTTGTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
** *
18101 TCTTTTCTCGCTTTTACGTGAGTTTTCAATCTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* *
18148 TCTTTTCTCGCTTCCATGCGAGTTTTCAATCTAGTGACCCAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
** * *
18195 TCTTTTCTCGCTTCCACGCGAGTTAGCAGTTTAGTGACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
* * *
18242 TCTTCTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
18289 TC
1 TC
18291 AACGGGTTTT
Statistics
Matches: 170, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 170 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATCTAGTGACCAAAGATGG
Done.