Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011817.1 Corchorus capsularis cultivar CVL-1 contig11838, 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: 88583
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:317 original size:81 final size:81
Alignment explanation
Indices: 182--335 Score: 281
Period size: 81 Copynumber: 1.9 Consensus size: 81
172 ATAAAAAGTA
*
182 ATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTTCCTTTTGTCCAACTTCCTCAGTT
1 ATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTTCCTTTTGTCCAACTTCCTCAATT
247 ATAATATATATATATG
66 ATAATATATATATATG
*
263 ATTAATATATTTCTCAATCAACCTAAAGTAATTAATTTATTTCCTTTTGTCCAACTTCCTCAATT
1 ATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTTCCTTTTGTCCAACTTCCTCAATT
*
328 TTAATATA
66 ATAATATA
336 CTAGTATTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.04, T:0.44
Consensus pattern (81 bp):
ATTAATATATTTCCCAATCAACCTAAAGTAATTAATTTATTTCCTTTTGTCCAACTTCCTCAATT
ATAATATATATATATG
Found at i:1189 original size:25 final size:25
Alignment explanation
Indices: 1140--1190 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1130 TTAGTAGAAT
*
1140 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
1165 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
1191 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:1912 original size:2 final size:2
Alignment explanation
Indices: 1907--1939 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1897 AAAAAAAAAA
1907 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
1940 GATTGCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2614 original size:140 final size:141
Alignment explanation
Indices: 2430--2696 Score: 375
Period size: 142 Copynumber: 1.9 Consensus size: 141
2420 TTACACCCAA
* * *
2430 TTTTTTTTTTTAATTAAAACGCACCATAAAGTTTTATTTCTGTGCCA-TGTTGTATCCTCCGTC-
1 TTTTTTTTTTTAATCAAAACGCACCATAAAGTTTTATTTCTGTGCCAGT-TTGCACCCTCCGTCA
**
2493 CGG-TGGACAAA-AGGATCCATCATGGCGTCCGACGTGGCATGTTACGTGGACAAAAAATGACAC
65 CGGTTGGACAAACA-GATCCATCATGGCGTCCGACGTGGCATGCCACGTGGACAAAAAATGACAC
2556 GTCACCCATTTTT
129 GTCACCCATTTTT
* *
2569 TTTTTTTATTTTGATCAAAACGCATCCTATAAA-TTTTATTT-TGTGCCAGTTTGCACCCTTCGT
1 TTTTTTT-TTTTAATCAAAACGCA-CC-ATAAAGTTTTATTTCTGTGCCAGTTTGCACCCTCCGT
*
2632 CACGGTTGGACAAACAGCTCCATCATGGCGTCCGACGTGGCATGCCACGTGGACAAAAAATGACA
63 CACGGTTGGACAAACAGATCCATCATGGCGTCCGACGTGGCATGCCACGTGGACAAAAAATGACA
2697 TGTGGCACGT
Statistics
Matches: 113, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
139 7 0.06
140 32 0.28
141 14 0.12
142 59 0.52
143 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (141 bp):
TTTTTTTTTTTAATCAAAACGCACCATAAAGTTTTATTTCTGTGCCAGTTTGCACCCTCCGTCAC
GGTTGGACAAACAGATCCATCATGGCGTCCGACGTGGCATGCCACGTGGACAAAAAATGACACGT
CACCCATTTTT
Found at i:6171 original size:83 final size:83
Alignment explanation
Indices: 6032--6198 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
6022 GTCAATTTCT
6032 TAAAGGGTGGAACTTGGTAGTGGTTGTAACTTGGAAGTCATAATCCATCACAGCACTAAGAAATT
1 TAAAGGGTGGAACTTGGTAGTGGTTGTAACTTGGAAGTCATAATCCATCACAGCACTAAGAAATT
6097 TCCAACCAAATTTAATGA
66 TCCAACCAAATTTAATGA
6115 TAAAGGGTGGAACTTGGTAGTGGTTGTAACTTGGAAGTCATAATCCATCACAGCACTAAGAAATT
1 TAAAGGGTGGAACTTGGTAGTGGTTGTAACTTGGAAGTCATAATCCATCACAGCACTAAGAAATT
6180 TCCAACCAAATTTAATGA
66 TCCAACCAAATTTAATGA
6198 T
1 T
6199 TTTGGTATTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (83 bp):
TAAAGGGTGGAACTTGGTAGTGGTTGTAACTTGGAAGTCATAATCCATCACAGCACTAAGAAATT
TCCAACCAAATTTAATGA
Found at i:25142 original size:45 final size:45
Alignment explanation
Indices: 25078--25169 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
25068 CTCAACTCTG
25078 TCTGCTGAGTTATGAATGCACATAAGCCAAGGGATTTGTATTTAA
1 TCTGCTGAGTTATGAATGCACATAAGCCAAGGGATTTGTATTTAA
25123 TCTGCTGAGTTATGAATGCACATAAGCCAAGGGATTTGTATTTAA
1 TCTGCTGAGTTATGAATGCACATAAGCCAAGGGATTTGTATTTAA
25168 TC
1 TC
25170 GGTGTTTGGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (45 bp):
TCTGCTGAGTTATGAATGCACATAAGCCAAGGGATTTGTATTTAA
Found at i:25411 original size:56 final size:56
Alignment explanation
Indices: 25344--25450 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
25334 TGAGGAAATA
25344 AACGTACTGTATCATAGTAACATAAAGATGCTTCACTTCATTGTCTATCTACCATT
1 AACGTACTGTATCATAGTAACATAAAGATGCTTCACTTCATTGTCTATCTACCATT
* *
25400 AACGTACTGTATTATAGTAACATAAAGATGCTTTACTTCATTGTCTATCTA
1 AACGTACTGTATCATAGTAACATAAAGATGCTTCACTTCATTGTCTATCTA
25451 AGATAATCAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (56 bp):
AACGTACTGTATCATAGTAACATAAAGATGCTTCACTTCATTGTCTATCTACCATT
Found at i:33898 original size:2 final size:2
Alignment explanation
Indices: 33891--33923 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33881 AAGGGTATCA
33891 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33924 GTGTGACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35506 original size:9 final size:9
Alignment explanation
Indices: 35492--35516 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
35482 TCATACATAC
35492 ATATATATT
1 ATATATATT
35501 ATATATATT
1 ATATATATT
35510 ATATATA
1 ATATATA
35517 GTACTACTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATATATATT
Found at i:37771 original size:2 final size:2
Alignment explanation
Indices: 37755--37787 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
37745 TATTGATCTT
37755 TA TA -A TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37788 TCTTAAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55481 original size:16 final size:16
Alignment explanation
Indices: 55450--55480 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55440 AAGCCATTGC
55450 CTCTCTTTTCTTTTTT
1 CTCTCTTTTCTTTTTT
55466 CTCTCTTTT-TTTTTT
1 CTCTCTTTTCTTTTTT
55481 TTTTGAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
CTCTCTTTTCTTTTTT
Found at i:60276 original size:27 final size:27
Alignment explanation
Indices: 60245--60304 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 27
60235 TGCCCTACCC
*
60245 AATTT-CATAAAAATGAATTAATAATCA
1 AATTTGCAAAAAAAT-AATTAATAATCA
60272 AATTTTGGCCAAAAAAATAATTAATAATCA
1 AA-TTT-G-CAAAAAAATAATTAATAATCA
60302 AAT
1 AAT
60305 ATGACAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
27 2 0.07
28 3 0.11
29 1 0.04
30 14 0.50
31 8 0.29
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (27 bp):
AATTTGCAAAAAAATAATTAATAATCA
Found at i:60751 original size:21 final size:20
Alignment explanation
Indices: 60727--60770 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
60717 ATAATCCCAC
*
60727 AAAATAAAGAATAGAAGGAAA
1 AAAAAAAAGAATAGAA-GAAA
60748 AAAAAAAAGAATAGAAGAAA
1 AAAAAAAAGAATAGAAGAAA
60768 AAA
1 AAA
60771 TGTAGGGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
AAAAAAAAGAATAGAAGAAA
Found at i:63106 original size:10 final size:11
Alignment explanation
Indices: 63085--63109 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
63075 TGCAATTAGC
63085 AAAAAGGAAAA
1 AAAAAGGAAAA
63096 AAAAAGGAAAA
1 AAAAAGGAAAA
63107 AAA
1 AAA
63110 GGTTAGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGGAAAA
Found at i:63333 original size:3 final size:3
Alignment explanation
Indices: 63325--63377 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
63315 GGTCAAAAGG
* * * * * *
63325 GGT GGT GGT GGC GGT GGA GGA GGA GGA GGT GGT GGT GGT GGT GGT GAT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
63373 GGT GG
1 GGT GG
63378 AGGAGGAGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.09, C:0.02, G:0.66, T:0.23
Consensus pattern (3 bp):
GGT
Found at i:70611 original size:2 final size:2
Alignment explanation
Indices: 70604--70630 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
70594 AATATGTAAA
70604 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
70631 CCTTACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70783 original size:13 final size:13
Alignment explanation
Indices: 70765--70789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70755 TTGGAATTCC
70765 AAATAATATTTAT
1 AAATAATATTTAT
70778 AAATAATATTTA
1 AAATAATATTTA
70790 GAACATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:71015 original size:2 final size:2
Alignment explanation
Indices: 71008--71042 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
70998 TTATCTAGTG
71008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71043 AATTTAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:78211 original size:45 final size:45
Alignment explanation
Indices: 78160--78249 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
78150 ATATTATCCT
*
78160 TAATTGAACCACTAAAAAACTTTGAGAACTAAACTAACCTAAATA
1 TAATTGAACCACTAAAAAACTTTGAGAACTAAACTAAACTAAATA
* *
78205 TAATTGAGCCACTAAAAAACTTTGGGAACTAAACTAAACTAAATA
1 TAATTGAACCACTAAAAAACTTTGAGAACTAAACTAAACTAAATA
78250 AACCGCACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (45 bp):
TAATTGAACCACTAAAAAACTTTGAGAACTAAACTAAACTAAATA
Found at i:80061 original size:30 final size:30
Alignment explanation
Indices: 80016--80085 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
80006 TAGTACTAAT
*
80016 CTCATTTTATCCTCCTTTCTTGCATTTCTTG
1 CTCA-TTTGTCCTCCTTTCTTGCATTTCTTG
80047 CTCATTTGTCCTCCTTTCTTGCATTTCTTG
1 CTCATTTGTCCTCCTTTCTTGCATTTCTTG
80077 CATC-TTTGT
1 C-TCATTTGT
80086 AATGGAACTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 31 0.84
31 6 0.16
ACGTcount: A:0.09, C:0.29, G:0.09, T:0.54
Consensus pattern (30 bp):
CTCATTTGTCCTCCTTTCTTGCATTTCTTG
Found at i:81801 original size:17 final size:17
Alignment explanation
Indices: 81779--81812 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
81769 AAGAACTCTT
81779 TAGGTTTTAAGTTTGAG
1 TAGGTTTTAAGTTTGAG
81796 TAGGTTTTAAGTTTGAG
1 TAGGTTTTAAGTTTGAG
81813 ATCAGGAAAC
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:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (17 bp):
TAGGTTTTAAGTTTGAG
Found at i:81848 original size:29 final size:29
Alignment explanation
Indices: 81806--81864 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
81796 TAGGTTTTAA
81806 GTTTGAGATCAGGAAACAGTGTAGTTGTG
1 GTTTGAGATCAGGAAACAGTGTAGTTGTG
81835 GTTTGAGATCAGGAAACAGTGTAGTTGTG
1 GTTTGAGATCAGGAAACAGTGTAGTTGTG
81864 G
1 G
81865 AAAACAGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.31
Consensus pattern (29 bp):
GTTTGAGATCAGGAAACAGTGTAGTTGTG
Found at i:82157 original size:31 final size:31
Alignment explanation
Indices: 82084--82147 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
82074 GTAAAGTTGC
*
82084 CTTAAAAATCAACATTCTTCCATATTCTGCT
1 CTTAAAAATCAACAGTCTTCCATATTCTGCT
82115 CTTAAAAATCAACAGTCTTCCATATTCTGCT
1 CTTAAAAATCAACAGTCTTCCATATTCTGCT
82146 CT
1 CT
82148 GTTCTATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.38
Consensus pattern (31 bp):
CTTAAAAATCAACAGTCTTCCATATTCTGCT
Found at i:83170 original size:105 final size:105
Alignment explanation
Indices: 83045--83255 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
83035 CAACAGCAGC
83045 AGCAGAAACTTCAATAGAAGAAGAACCACTAACAAACTTCGCAACAGATATACCAACAGGAATAA
1 AGCAGAAACTTCAATAGAAGAAGAACCACTAACAAACTTCGCAACAGATATACCAACAGGAATAA
83110 AGAAAAGTCCGCCCATTGTCGGGGTTCTCCTCTTTCTGGA
66 AGAAAAGTCCGCCCATTGTCGGGGTTCTCCTCTTTCTGGA
83150 AGCAGAAACTTCAATAGAAGAAGAACCACTAACAAACTTCGCAACAGATATACCAACAGGAATAA
1 AGCAGAAACTTCAATAGAAGAAGAACCACTAACAAACTTCGCAACAGATATACCAACAGGAATAA
83215 AGAAAAGTCCGCCCATTGTCGGGGTTCTCCTCTTTCTGGA
66 AGAAAAGTCCGCCCATTGTCGGGGTTCTCCTCTTTCTGGA
83255 A
1 A
83256 TGTCTTGCAG
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (105 bp):
AGCAGAAACTTCAATAGAAGAAGAACCACTAACAAACTTCGCAACAGATATACCAACAGGAATAA
AGAAAAGTCCGCCCATTGTCGGGGTTCTCCTCTTTCTGGA
Found at i:85137 original size:2 final size:2
Alignment explanation
Indices: 85130--85159 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
85120 AATATCTGAG
85130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85160 GTAGTAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.