Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014327.1 Corchorus olitorius cultivar O-4 contig14360, 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: 46012
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1053 original size:122 final size:126
Alignment explanation
Indices: 824--1069 Score: 392
Period size: 122 Copynumber: 2.0 Consensus size: 126
814 AATATATTCA
*
824 AAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
1 AAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT---ACA-GTATA
*
889 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATTT
62 AGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
*
954 AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-CA-TA-AA-GA
1 AAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATACAGTATAAGGA
*
1015 TATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
66 TATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
1070 TTAAACAATG
Statistics
Matches: 112, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
122 55 0.49
123 2 0.02
124 2 0.02
126 1 0.01
130 52 0.46
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (126 bp):
AAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATACAGTATAAGGA
TATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTT
Found at i:1175 original size:11 final size:11
Alignment explanation
Indices: 1155--1201 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
1145 GTACTTTTTA
1155 ATATAGTATAG
1 ATATAGTATAG
* *
1166 ATATAATATAT
1 ATATAGTATAG
1177 ATATAGTATAG
1 ATATAGTATAG
1188 ATATAGTATAG
1 ATATAGTATAG
1199 ATA
1 ATA
1202 ATATAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
ATATAGTATAG
Found at i:1645 original size:18 final size:17
Alignment explanation
Indices: 1619--1652 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1609 AAAAAAAGAG
1619 AGAAAAATAAAAGAAAA
1 AGAAAAATAAAAGAAAA
*
1636 AGAAAGAATAGAAGAAA
1 AGAAA-AATAAAAGAAA
1653 TGAGGACTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AGAAAAATAAAAGAAAA
Found at i:2588 original size:2 final size:2
Alignment explanation
Indices: 2581--2608 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2571 TTTAGTGAAT
2581 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2609 CCAGGGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9311 original size:16 final size:16
Alignment explanation
Indices: 9290--9323 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
9280 CCGAATTATT
9290 TTCCTTTATCTAAAAC
1 TTCCTTTATCTAAAAC
9306 TTCCTTTATCTAAAAC
1 TTCCTTTATCTAAAAC
9322 TT
1 TT
9324 GAACTTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCCTTTATCTAAAAC
Found at i:9450 original size:43 final size:43
Alignment explanation
Indices: 9402--9490 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
9392 AACCTAACCT
* *
9402 AACTTGAACTAGGAATTGATCCGAATTATTTTCCTTTATCTAA
1 AACTTGAACTAGGAATTGATCCAAATAATTTTCCTTTATCTAA
*
9445 AACTTGAACTCGGAATTGATCCAAATAATTTTCCTTTATCTAA
1 AACTTGAACTAGGAATTGATCCAAATAATTTTCCTTTATCTAA
9488 AAC
1 AAC
9491 GATCCAACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (43 bp):
AACTTGAACTAGGAATTGATCCAAATAATTTTCCTTTATCTAA
Found at i:10373 original size:7 final size:7
Alignment explanation
Indices: 10358--10394 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
10348 GACGCTGACG
10358 AAAAA-A
1 AAAAAGA
10364 AAAAAGA
1 AAAAAGA
10371 AAAAAGA
1 AAAAAGA
10378 AAAAAGA
1 AAAAAGA
10385 AAAAAGA
1 AAAAAGA
10392 AAA
1 AAA
10395 GTTAATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:11893 original size:25 final size:24
Alignment explanation
Indices: 11857--11903 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
11847 TCCTTCTATT
11857 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
11880 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
11904 AATTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:12384 original size:21 final size:21
Alignment explanation
Indices: 12358--12398 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12348 TTGAAGCCCT
12358 ATTGGAAAC-AAGTGGTACTAA
1 ATTGG-AACTAAGTGGTACTAA
*
12379 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
12399 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:30974 original size:11 final size:13
Alignment explanation
Indices: 30958--30989 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
30948 TTTGGTTGGG
30958 GGTGATCTTG-C-
1 GGTGATCTTGACA
30969 GGTGATCTTGACA
1 GGTGATCTTGACA
30982 GGTGATCT
1 GGTGATCT
30990 CAGATCACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.53
12 1 0.05
13 8 0.42
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (13 bp):
GGTGATCTTGACA
Found at i:31139 original size:17 final size:16
Alignment explanation
Indices: 31099--31149 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
31089 CATGTAATCT
*
31099 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
31115 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
31132 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
31149 T
1 T
31150 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:36512 original size:29 final size:29
Alignment explanation
Indices: 36478--36760 Score: 314
Period size: 29 Copynumber: 9.8 Consensus size: 29
36468 ATTCGCATGC
*
36478 CCAGGGGCATTTTGGTCATTTTTGCACGT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* *
36507 ACAGGGGCATTTTGGTCATTTTTACACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* *
36536 CCAGGGGCATTATGGTTATTTTTGCACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* * * *
36565 TCAGGGGCATTTTTGTCATTTTTGTATAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
** * * *
36594 TTAGGGGCATTTAGATCATCTTTGCACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
** * *
36623 CCAGGTTCATTATGGTCATCTTTGCACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* * *
36652 CCAGGGGCATTATGGTCATTTTCGCATAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* *
36681 CTAGGGGCATTTTGGTCATCTTTGCACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* * *
36710 CCAGGGGCATTATGGTCAATTCTGCACAT
1 CCAGGGGCATTTTGGTCATTTTTGCACAT
* *
36739 CCAGGGGCATTGTGATCATTTT
1 CCAGGGGCATTTTGGTCATTTT
36761 GGATGCTTTA
Statistics
Matches: 208, Mismatches: 46, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 208 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (29 bp):
CCAGGGGCATTTTGGTCATTTTTGCACAT
Found at i:36625 original size:87 final size:87
Alignment explanation
Indices: 36478--36760 Score: 368
Period size: 87 Copynumber: 3.3 Consensus size: 87
36468 ATTCGCATGC
** * * *
36478 CCAGGGGCATTTTGGTCATTTTTGCACGTACAGGGGCATTTTGGTCATTTTTACACATCCAGGGG
1 CCAGGGGCATTTTGGTCATTTTTGCATATATAGGGGCATTTTGGTCATCTTTGCACATCCAGGGG
*
36543 CATTATGGTTATTTTTGCACAT
66 CATTATGGTCATTTTTGCACAT
* * * * * * **
36565 TCAGGGGCATTTTTGTCATTTTTGTATATTTAGGGGCATTTAGATCATCTTTGCACATCCAGGTT
1 CCAGGGGCATTTTGGTCATTTTTGCATATATAGGGGCATTTTGGTCATCTTTGCACATCCAGGGG
*
36630 CATTATGGTCATCTTTGCACAT
66 CATTATGGTCATTTTTGCACAT
* * *
36652 CCAGGGGCATTATGGTCATTTTCGCATATCTAGGGGCATTTTGGTCATCTTTGCACATCCAGGGG
1 CCAGGGGCATTTTGGTCATTTTTGCATATATAGGGGCATTTTGGTCATCTTTGCACATCCAGGGG
* *
36717 CATTATGGTCAATTCTGCACAT
66 CATTATGGTCATTTTTGCACAT
* *
36739 CCAGGGGCATTGTGATCATTTT
1 CCAGGGGCATTTTGGTCATTTT
36761 GGATGCTTTA
Statistics
Matches: 166, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 166 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (87 bp):
CCAGGGGCATTTTGGTCATTTTTGCATATATAGGGGCATTTTGGTCATCTTTGCACATCCAGGGG
CATTATGGTCATTTTTGCACAT
Found at i:40716 original size:13 final size:13
Alignment explanation
Indices: 40698--40722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40688 TAAAAAAAAT
40698 CAAAAGTGTTTTC
1 CAAAAGTGTTTTC
40711 CAAAAGTGTTTT
1 CAAAAGTGTTTT
40723 TAAGTATGTT
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:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
CAAAAGTGTTTTC
Found at i:45802 original size:29 final size:29
Alignment explanation
Indices: 45770--46012 Score: 362
Period size: 29 Copynumber: 8.4 Consensus size: 29
45760 CGCACTCCCT
*
45770 GGGGTATTTTGGTCATTTTTGCACATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
*
45799 GGGGCATTTTGGTCATTTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
* **
45828 GGGGCATTATCATCATTTTTGCACATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
45857 GGGGCATTTTGGTCATTTTTGCACATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
*
45886 GGGGCATTTTGGTCATTTTTGCACATTCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
* *
45915 GGGGCATTTTGATCATCTTTGCACAT-CA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
* *
45943 GGGGCATTATGGTCATCTTTGCACATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
* * *
45972 GGGGCATTATGGTAATTTTTGCATATCCA
1 GGGGCATTTTGGTCATTTTTGCACATCCA
46001 GGGGCATTTTGG
1 GGGGCATTTTGG
Statistics
Matches: 195, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
28 26 0.13
29 169 0.87
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTTGCACATCCA
Done.