Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018351.1 Corchorus olitorius cultivar O-4 contig18384, 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: 40924
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:800 original size:11 final size:11
Alignment explanation
Indices: 784--823 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
774 CAAGGCTAGG
784 CCCGGCCCGAA
1 CCCGGCCCGAA
795 CCCGGCCCGAA
1 CCCGGCCCGAA
*
806 CCCGGCCCG-G
1 CCCGGCCCGAA
816 CCCGGCCC
1 CCCGGCCC
824 ATGAACAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.10, C:0.60, G:0.30, T:0.00
Consensus pattern (11 bp):
CCCGGCCCGAA
Found at i:3027 original size:2 final size:2
Alignment explanation
Indices: 3020--3049 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3010 TTCCTTGATA
3020 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3050 AATACCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4363 original size:205 final size:205
Alignment explanation
Indices: 4004--4421 Score: 782
Period size: 205 Copynumber: 2.0 Consensus size: 205
3994 AACTGAAAAA
4004 AAAAAACGAAACATGAACCATTAATGAACAAAATAATAATAATAATATAAGCTTACATTATCCAA
1 AAAAAA-GAAACATGAACCATTAATGAACAAAATAATAATAATAATATAAGCTTACATTATCCAA
*
4069 GTCACTTGAACTTGGTTTATGGCTGTTTTGTGCTAACTAGGAATGAAAAATTAGGATCAAAATCT
65 GTCACTTGAACTTGGTTTATGGATGTTTTGTGCTAACTAGGAATGAAAAATTAGGATCAAAATCT
4134 CAAAGCCTGTATACATAAATACAAAATTCAGTTGTATTGAACTAAAAAAATTTGCTAGGTTAGAT
130 CAAAGCCTGTATACATAAATACAAAATTCAGTTGTATTGAACTAAAAAAATTTGCTAGGTTAGAT
4199 ACAACAAATGG
195 ACAACAAATGG
4210 AAAAAAGAAACATGAACCATTAATGAACAAAATAATAATAATAATATAAGCTTACATTATCCAAG
1 AAAAAAGAAACATGAACCATTAATGAACAAAATAATAATAATAATATAAGCTTACATTATCCAAG
*
4275 TCACTTGAACTTGGTTTATGGATGTTTTGTGCTAACTAGGAATGAAAAGTTAGGATCAAAATCTC
66 TCACTTGAACTTGGTTTATGGATGTTTTGTGCTAACTAGGAATGAAAAATTAGGATCAAAATCTC
* *
4340 AAAGCCTGTATACATAAATACAAAATTCAGTTGTATTGAACTAAAAATATTTGCTGGGTTAGATA
131 AAAGCCTGTATACATAAATACAAAATTCAGTTGTATTGAACTAAAAAAATTTGCTAGGTTAGATA
4405 CAACAAATGG
196 CAACAAATGG
*
4415 ACAAAAG
1 AAAAAAG
4422 TTGGATGCAA
Statistics
Matches: 207, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
205 201 0.97
206 6 0.03
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (205 bp):
AAAAAAGAAACATGAACCATTAATGAACAAAATAATAATAATAATATAAGCTTACATTATCCAAG
TCACTTGAACTTGGTTTATGGATGTTTTGTGCTAACTAGGAATGAAAAATTAGGATCAAAATCTC
AAAGCCTGTATACATAAATACAAAATTCAGTTGTATTGAACTAAAAAAATTTGCTAGGTTAGATA
CAACAAATGG
Found at i:9785 original size:46 final size:46
Alignment explanation
Indices: 9728--9846 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
9718 CATGAAATGG
* *
9728 TAAGTGTTTTATGAAGTTTTTGAATTAGGAATTTACAATTCATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
9774 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
*
9820 TAAGTGCTTTATGAATGGTTTTGAATT
1 TAAGTGCTTTATGAA-GTTTTTGAATT
9847 TATGCAGAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 59 0.86
47 10 0.14
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.43
Consensus pattern (46 bp):
TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
Found at i:10171 original size:14 final size:14
Alignment explanation
Indices: 10152--10178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10142 CTGCAGAAAA
10152 TTATAGGCTCACTG
1 TTATAGGCTCACTG
10166 TTATAGGCTCACT
1 TTATAGGCTCACT
10179 TTTGCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:10571 original size:14 final size:14
Alignment explanation
Indices: 10552--10578 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10542 CTGCAGAAAA
10552 TTATAGGCTCACTG
1 TTATAGGCTCACTG
10566 TTATAGGCTCACT
1 TTATAGGCTCACT
10579 TTTGCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:10765 original size:400 final size:398
Alignment explanation
Indices: 10026--10807 Score: 1451
Period size: 400 Copynumber: 2.0 Consensus size: 398
10016 GACTACTGAT
*
10026 CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGATTTAAAGTTTCATATTGAT
1 CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGATTGAAAGTTTCATATTGAT
10091 GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
66 GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
10156 AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
131 AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
*
10221 TAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
196 TAAGAATCTATCACGAAAGAGAGCTGCGGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
10286 AGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATT
261 AGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATT
*
10351 GCCTAAATGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
326 GCCTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
10416 AGGGTTCA
391 AGGGTTCA
*
10424 CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTGAAAGTTTCATATTGAT
1 CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGATTGAAAGTTTCATATTGAT
10489 GCCAAGAATTAAAAGAATAAAAAAAAAAT-AGAAGTGAATATTGGTTACTAACACTGCAGAAAAT
66 GCCAAGAATTAAAAGAAT--AAAAAAAATGAG-AGTGAATATTGGTTACTAACACTGCAGAAAAT
10553 TATAGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAA
128 TATAGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAA
10618 ATATAAGAATCTATCACGAAAGAGAGCTGCGGATGTTTATTCTTACTTACTATGCCTTAAGTACG
193 ATATAAGAATCTATCACGAAAGAGAGCTGCGGATGTTTATTCTTACTTACTATGCCTTAAGTACG
10683 TATAGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTC
258 TATAGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTC
* * *
10748 ATTGCAGT-AGGGTTCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTA
323 ATTGC-CTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTA
10808 CCAATCTTTA
Statistics
Matches: 373, Mismatches: 7, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
398 81 0.22
399 2 0.01
400 289 0.77
401 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (398 bp):
CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGATTGAAAGTTTCATATTGAT
GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
TAAGAATCTATCACGAAAGAGAGCTGCGGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
AGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCATT
GCCTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
AGGGTTCA
Found at i:12771 original size:6 final size:6
Alignment explanation
Indices: 12757--12798 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
12747 CATCTGGTGC
*
12757 TTCTGT TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT
1 TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT TTCTAT
12799 ATATATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.14, C:0.17, G:0.02, T:0.67
Consensus pattern (6 bp):
TTCTAT
Found at i:21939 original size:12 final size:13
Alignment explanation
Indices: 21922--21950 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21912 CGGTGATCCT
21922 AAAAAATAAAA-A
1 AAAAAATAAAATA
21934 AAAAAATAAAATA
1 AAAAAATAAAATA
21947 AAAA
1 AAAA
21951 CAGGGTAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:23211 original size:18 final size:17
Alignment explanation
Indices: 23188--23222 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
23178 ACCTCATCTA
*
23188 TCAAAATCAAAACAAAAG
1 TCAAAAACAAAA-AAAAG
23206 TCAAAAACAAAAAAAAG
1 TCAAAAACAAAAAAAAG
23223 CTAGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.14, G:0.06, T:0.09
Consensus pattern (17 bp):
TCAAAAACAAAAAAAAG
Found at i:26095 original size:2 final size:2
Alignment explanation
Indices: 26088--26125 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26078 GAGTTACTCA
26088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26126 AATACTTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31368 original size:14 final size:14
Alignment explanation
Indices: 31349--31376 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31339 TACCTGGATC
31349 ATGATTATGAGACT
1 ATGATTATGAGACT
31363 ATGATTATGAGACT
1 ATGATTATGAGACT
31377 CATAATTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
ATGATTATGAGACT
Found at i:38976 original size:18 final size:19
Alignment explanation
Indices: 38945--38982 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
38935 TACTTCAAAA
*
38945 AAAAAAAACTTAGTTTGGTT
1 AAAAAAAAC-TAGTTGGGTT
38965 AAAAAAAA-TAGTTGGGTT
1 AAAAAAAACTAGTTGGGTT
38983 TTTTAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (19 bp):
AAAAAAAACTAGTTGGGTT
Found at i:39389 original size:14 final size:13
Alignment explanation
Indices: 39371--39404 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
39361 TACATTTTAG
39371 AAGAAAAAAG-AA
1 AAGAAAAAAGAAA
39383 AAGAGAAAAAGAAA
1 AAGA-AAAAAGAAA
39397 AAGAAAAA
1 AAGAAAAA
39405 TATAGAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 10 0.50
14 6 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:39395 original size:6 final size:6
Alignment explanation
Indices: 39375--39404 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
39365 TTTTAGAAGA
39375 AAAAAG AAAAGAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAA
39405 TATAGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:39639 original size:31 final size:31
Alignment explanation
Indices: 39558--39628 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
39548 TTCACTTTTG
* * *
39558 AAACGTAAGGGATTAATTTGTCACAAAAAAA
1 AAACATAAGAGATTATTTTGTCACAAAAAAA
* *
39589 AAACATAAGAGATTATTTTGTCCCAAAAGAA
1 AAACATAAGAGATTATTTTGTCACAAAAAAA
39620 AAACATAAG
1 AAACATAAG
39629 GGTTTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (31 bp):
AAACATAAGAGATTATTTTGTCACAAAAAAA
Found at i:39959 original size:42 final size:43
Alignment explanation
Indices: 39908--40000 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 43
39898 AGTGCATTAC
*
39908 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
39949 CTAATATTCTACCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA-CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
39993 TTAATATT
1 CTAATATT
40001 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 37 0.79
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Done.