Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014941.1 Corchorus olitorius cultivar O-4 contig14974, 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: 116464
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8044 original size:14 final size:14
Alignment explanation
Indices: 8025--8055 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
8015 AATCATGCAG
8025 ATATCCAATTCAAT
1 ATATCCAATTCAAT
*
8039 ATATCCAATTCCAT
1 ATATCCAATTCAAT
8053 ATA
1 ATA
8056 CATGAGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATCCAATTCAAT
Found at i:9366 original size:21 final size:19
Alignment explanation
Indices: 9340--9388 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
9330 GCTGCTCTAA
*
9340 TAATCTCATTTGTACAATGTC
1 TAATCTCATATGTAC-A-GTC
* *
9361 TAATCTAATATGTACAGTG
1 TAATCTCATATGTACAGTC
9380 TAATCTCAT
1 TAATCTCAT
9389 CTATACAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.42
20 1 0.04
21 13 0.54
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (19 bp):
TAATCTCATATGTACAGTC
Found at i:10424 original size:21 final size:19
Alignment explanation
Indices: 10386--10443 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 19
10376 AATTAAATAT
*
10386 ATATTATTTTATTTATTTTGA
1 ATATTA-TTTA-TTATTTAGA
10407 ACTCATTATTTATTATTTAGA
1 A-T-ATTATTTATTATTTAGA
10428 ATA-TATTTATTATTTA
1 ATATTATTTATTATTTA
10444 TTTAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 13 0.38
19 1 0.03
20 1 0.03
21 10 0.29
22 5 0.15
23 4 0.12
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
ATATTATTTATTATTTAGA
Found at i:16627 original size:19 final size:19
Alignment explanation
Indices: 16603--16642 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
16593 GACAGATCCA
*
16603 AATCGAAACGTTGATGATG
1 AATCGAAACGTCGATGATG
16622 AATCGAAACGTCGATGATG
1 AATCGAAACGTCGATGATG
16641 AA
1 AA
16643 ATTCAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (19 bp):
AATCGAAACGTCGATGATG
Found at i:21625 original size:18 final size:18
Alignment explanation
Indices: 21602--21638 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21592 AGCTATGCTC
*
21602 TGGAATTCCAAATTAATG
1 TGGAATTCAAAATTAATG
21620 TGGAATTCAAAATTAATG
1 TGGAATTCAAAATTAATG
21638 T
1 T
21639 TCCAGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (18 bp):
TGGAATTCAAAATTAATG
Found at i:23854 original size:28 final size:30
Alignment explanation
Indices: 23813--23872 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
23803 AGGGTGAGTG
23813 AGGAAGAACAAAG-AGAAAAAAGA-AAAAA
1 AGGAAGAACAAAGAAGAAAAAAGAGAAAAA
** *
23841 AGGAAGAATGAAGAAGAAAAAATAGAAAAA
1 AGGAAGAACAAAGAAGAAAAAAGAGAAAAA
23871 AG
1 AG
23873 AATAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 9 0.33
30 7 0.26
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.03
Consensus pattern (30 bp):
AGGAAGAACAAAGAAGAAAAAAGAGAAAAA
Found at i:23873 original size:19 final size:18
Alignment explanation
Indices: 23815--23879 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
23805 GGTGAGTGAG
*
23815 GAAGAACAAAGAGAAAAAA
1 GAAGAA-AAAAAGAAAAAA
**
23834 GAA-AAAAAGGAAGAATGAA
1 GAAGAAAAA--AAGAAAAAA
23853 GAAGAAAAAATAGAAAAAA
1 GAAGAAAAAA-AGAAAAAA
*
23872 GAATAAAA
1 GAAGAAAA
23880 GAAAAACACA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 3 0.08
18 3 0.08
19 25 0.69
20 5 0.14
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.05
Consensus pattern (18 bp):
GAAGAAAAAAAGAAAAAA
Found at i:25516 original size:3 final size:3
Alignment explanation
Indices: 25502--25548 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
25492 TTCGGTACAA
* * * *
25502 CAG CAA CAG CAG CAG CAG CAA CAG CAA CAA CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
25549 AATAGCGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:28132 original size:24 final size:25
Alignment explanation
Indices: 28100--28265 Score: 160
Period size: 24 Copynumber: 6.5 Consensus size: 25
28090 CCACCACTTG
28100 AGCAGCAGCAGCAACAACAACCA-C
1 AGCAGCAGCAGCAACAACAACCAGC
*
28124 AGCAGCAGCAACAACAACAACCACAGCAGC
1 AGCAGCAGCAGCAACAAC-A--AC--CAGC
**
28154 AGCAGCAGCAGCAACAACAACAACCAC
1 AGCAGCAGCAGCAACAACAAC--CAGC
28181 AGCAGCAGCAGCAACAACAACCA-C
1 AGCAGCAGCAGCAACAACAACCAGC
* * *
28205 AGCAGCAGCAGCAGCAGC-AGCAGC
1 AGCAGCAGCAGCAACAACAACCAGC
* * *
28229 AGCAGCAGCAGCAGCAGC-AGCAGC
1 AGCAGCAGCAGCAACAACAACCAGC
28253 AGCAGCAGCAGCA
1 AGCAGCAGCAGCA
28266 GCAGCAATTT
Statistics
Matches: 126, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.02
24 72 0.57
25 2 0.02
27 28 0.22
29 3 0.02
30 18 0.14
ACGTcount: A:0.42, C:0.36, G:0.22, T:0.00
Consensus pattern (25 bp):
AGCAGCAGCAGCAACAACAACCAGC
Found at i:28210 original size:3 final size:3
Alignment explanation
Indices: 28147--28271 Score: 155
Period size: 3 Copynumber: 41.7 Consensus size: 3
28137 ACAACAACCA
* * * *
28147 CAG CAG CAG CAG CAG CAG CAA CAA CAA CAAC CA- CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG C-AG CAG CAG CAG CAG CAG
* * *
28192 CAA CAA CAAC CA- CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG C-AG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
28237 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
28272 ATTTCCTCCT
Statistics
Matches: 114, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
2 4 0.04
3 106 0.93
4 4 0.04
ACGTcount: A:0.39, C:0.35, G:0.26, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:45736 original size:40 final size:39
Alignment explanation
Indices: 45677--45753 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
45667 TATTTATAAC
45677 TAGGGGCTAAACCTGGATTTAATTTATTACCTTAATTAT
1 TAGGGGCTAAACCTGGATTTAATTTATTACCTTAATTAT
* *
45716 TAGGAGGCTAAACTTGGATTTAATTTATTTCCTTAATT
1 TAGG-GGCTAAACCTGGATTTAATTTATTACCTTAATT
45754 TAATTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (39 bp):
TAGGGGCTAAACCTGGATTTAATTTATTACCTTAATTAT
Found at i:45756 original size:18 final size:18
Alignment explanation
Indices: 45733--45771 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
45723 CTAAACTTGG
45733 ATTTAATTTATTTCCTTA
1 ATTTAATTTATTTCCTTA
45751 ATTTAATTTATTTCCTTA
1 ATTTAATTTATTTCCTTA
45769 ATT
1 ATT
45772 ATTAGGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTAATTTATTTCCTTA
Found at i:85680 original size:17 final size:16
Alignment explanation
Indices: 85654--85685 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
85644 TATCCCTCCC
85654 TCCCTTTTAGGGTTTT
1 TCCCTTTTAGGGTTTT
85670 TCCCATTTTAGGGTTT
1 TCCC-TTTTAGGGTTT
85686 CAAGAAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (16 bp):
TCCCTTTTAGGGTTTT
Found at i:97775 original size:2 final size:2
Alignment explanation
Indices: 97768--97792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97758 TATCTTATGC
97768 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 A
97793 GATTAGATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98841 original size:28 final size:29
Alignment explanation
Indices: 98775--98842 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
98765 TGAGAGGGCG
* *
98775 CAAAACGTCCCAAAATTGAAATTCAGGGAA
1 CAAAACAT-CCAAAATTAAAATTCAGGGAA
98805 CAAAACATCCAAAATTAAAATTCA-GGAA
1 CAAAACATCCAAAATTAAAATTCAGGGAA
98833 CAAAACATCC
1 CAAAACATCC
98843 GAACACTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 14 0.39
29 15 0.42
30 7 0.19
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.16
Consensus pattern (29 bp):
CAAAACATCCAAAATTAAAATTCAGGGAA
Found at i:100470 original size:24 final size:24
Alignment explanation
Indices: 100438--100496 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
100428 GTTATCCAAA
**
100438 AGCTTTGTCCATTTCTTGTATTAT
1 AGCTTTGTCCATTTCTTGTAACAT
* * *
100462 AGCTTTGTCCTTTTTTTTTAACAT
1 AGCTTTGTCCATTTCTTGTAACAT
100486 AGCTTTGTCCA
1 AGCTTTGTCCA
100497 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.53
Consensus pattern (24 bp):
AGCTTTGTCCATTTCTTGTAACAT
Found at i:116081 original size:40 final size:40
Alignment explanation
Indices: 115947--116316 Score: 426
Period size: 41 Copynumber: 9.2 Consensus size: 40
115937 TTGAGGGCCA
* *
115947 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGA
1 ATGTGAA-TAAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
* *
115988 ATGTGAATGAAGGCAAGTTCAATGTCATTTGGG--A-TTGA
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
*
116026 ATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
** * *
116066 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
* * *
116106 ATGTGAATCAAGGCTAGTTCAATGTCAATT-GGAAAATTCAG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTT-GG
* * *
116147 ATGTGAATAAGGCAAGTTCAATGTTAATT-GGAAAATTCAG
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTT-GG
* * * *
116187 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGA
1 ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
*
116227 ATGTGAATCAAGGCAAGTTCAATGTCAATTGGTAAAGTTGG
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
** **
116268 ATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTAA
1 ATGTGAAT-AAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
116309 ATGTGAAT
1 ATGTGAAT
116317 GTGCCGTGTA
Statistics
Matches: 293, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
37 24 0.08
38 12 0.04
39 2 0.01
40 120 0.41
41 135 0.46
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (40 bp):
ATGTGAATAAGGCAAGTTCAATGTCAATTGGGAAAGTTGG
Found at i:116082 original size:20 final size:20
Alignment explanation
Indices: 115945--116292 Score: 156
Period size: 20 Copynumber: 17.3 Consensus size: 20
115935 CATTGAGGGC
115945 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAA-TAAGGCAAGTT
* ** * *
115966 CAATGTCAATTGGGAAATTT
1 CAATGTGAATAAGGCAAGTT
*
115986 GAATGTGAATGAAGGCAAGTT
1 CAATGTGAAT-AAGGCAAGTT
* ** *
116007 CAATGT-CATTTGG-GA-TT
1 CAATGTGAATAAGGCAAGTT
*
116024 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATAAGGCAAGTT
* * ** *
116044 CAATGTCATTTGGGAAAGTT
1 CAATGTGAATAAGGCAAGTT
**
116064 GGATGTGAATAAGGCAAGTT
1 CAATGTGAATAAGGCAAGTT
* * *
116084 CAATGTTG-AT-TGGAAAATTT
1 CAATG-TGAATAAGG-CAAGTT
** *
116104 GGATGTGAATCAAGGCTAGTT
1 CAATGTGAAT-AAGGCAAGTT
* * * *
116125 CAATGTCAAT-TGGAAAATT
1 CAATGTGAATAAGGCAAGTT
116144 CAGATGTGAATAAGGCAAGTT
1 CA-ATGTGAATAAGGCAAGTT
* * * *
116165 CAATGTTAAT-TGGAAAATT
1 CAATGTGAATAAGGCAAGTT
116184 CAGATGTGAATAAGGCAAGTT
1 CA-ATGTGAATAAGGCAAGTT
* * * *
116205 CAATGTTAAT-TGGAAAATTT
1 CAATGTGAATAAGG-CAAGTT
*
116225 GAATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-AAGGCAAGTT
* * *
116246 CAATGTCAAT-TGGTAAAGTT
1 CAATGTGAATAAGG-CAAGTT
**
116266 GGATGTGAATCAAGGCAAGTT
1 CAATGTGAAT-AAGGCAAGTT
116287 CAATGT
1 CAATGT
116293 TTATTGGGAA
Statistics
Matches: 224, Mismatches: 84, Indels: 38
0.65 0.24 0.11
Matches are distributed among these distances:
17 7 0.03
18 5 0.02
19 26 0.12
20 112 0.50
21 68 0.30
22 6 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (20 bp):
CAATGTGAATAAGGCAAGTT
Found at i:116207 original size:121 final size:120
Alignment explanation
Indices: 115947--116316 Score: 514
Period size: 121 Copynumber: 3.1 Consensus size: 120
115937 TTGAGGGCCA
* * *
115947 ATGTGAATTAAGGCAAGTTCAATGTCAATTGGGAAATTTGAATGTGAATGAAGGCAAGTTCAATG
1 ATGTGAA-TAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATG
* * * * *
116012 TCATTTGG--GATT-GAATGTGAATAAGGCAAGTTCAATGTCATTTGGGAAAGTTGG
65 TCAATTGGAAAATTAG-ATGTGAATAAGGCAAGTTCAATGTTAATTGGGAAAGTTAG
* * *
116066 ATGTGAATAAGGCAAGTTCAATGTTGATTGGAAAATTTGGATGTGAATCAAGGCTAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
*
116131 CAATTGGAAAATTCAGATGTGAATAAGGCAAGTTCAATGTTAATT-GGAAAATTCAG
66 CAATTGGAAAATT-AGATGTGAATAAGGCAAGTTCAATGTTAATTGGGAAAGTT-AG
116187 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
1 ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
* * * *
116252 CAATTGGTAAAGTTGGATGTGAATCAAGGCAAGTTCAATGTTTATTGGGAAAGTTAA
66 CAATTGG-AAAATTAGATGTGAAT-AAGGCAAGTTCAATGTTAATTGGGAAAGTTAG
116309 ATGTGAAT
1 ATGTGAAT
116317 GTGCCGTGTA
Statistics
Matches: 223, Mismatches: 20, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
118 58 0.26
119 7 0.03
120 10 0.04
121 106 0.48
122 35 0.16
123 7 0.03
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (120 bp):
ATGTGAATAAGGCAAGTTCAATGTTAATTGGAAAATTTGAATGTGAATCAAGGCAAGTTCAATGT
CAATTGGAAAATTAGATGTGAATAAGGCAAGTTCAATGTTAATTGGGAAAGTTAG
Done.