Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018489.1 Corchorus olitorius cultivar O-4 contig18522, 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: 61800
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1022 original size:33 final size:34
Alignment explanation
Indices: 965--1032 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
955 TCTTTTTTTT
965 ATTTCTTTTTTCCTTTCTCTTTTCCCCACAAGGTC
1 ATTTCTTTTTTCC-TTCTCTTTTCCCCACAAGGTC
1000 ATTTCTTTTTTCC-TCTCTTTTCCCCACAAGGTC
1 ATTTCTTTTTTCCTTCTCTTTTCCCCACAAGGTC
1033 TTTTAGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 20 0.61
35 13 0.39
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (34 bp):
ATTTCTTTTTTCCTTCTCTTTTCCCCACAAGGTC
Found at i:1052 original size:35 final size:33
Alignment explanation
Indices: 965--1052 Score: 113
Period size: 33 Copynumber: 2.5 Consensus size: 33
955 TCTTTTTTTT
965 ATTTCTTTTTTCCTTTCTCTTTTCCCCACAAGGTC
1 ATTTCTTTTTT-C-TTCTCTTTTCCCCACAAGGTC
*
1000 ATTTCTTTTTTCCTCTCTTTTCCCCACAAGGTC
1 ATTTCTTTTTTCTTCTCTTTTCCCCACAAGGTC
* *
1033 TTTTAGTATTTTTCTTCTCT
1 ATTT-CT-TTTTTCTTCTCT
1053 ACACGTGTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 23 0.49
34 2 0.04
35 22 0.47
ACGTcount: A:0.11, C:0.28, G:0.06, T:0.55
Consensus pattern (33 bp):
ATTTCTTTTTTCTTCTCTTTTCCCCACAAGGTC
Found at i:5732 original size:233 final size:234
Alignment explanation
Indices: 5313--5770 Score: 846
Period size: 233 Copynumber: 2.0 Consensus size: 234
5303 GGGAGGAAGG
*
5313 TACGGGACAGGGAGAGAGAAAAAGTGAGGAAAAGTCATAGATATTTATTAGGTAAGCCAATAACT
1 TACGGGACAGGGAGAGAGAAAAAGTGAGGAAAAGTCATAGATATTTATTAGGTAAGACAATAACT
5378 GATGGATACATAGTTATTGAGGGAATAAAAAAATGGGAACTTTCTAGAATTTGGTTAGGTGTGGG
66 GATGGATACATAGTTATTGAGGGAATAAAAAAATGGGAACTTTCTAGAATTTGGTTAGGTGTGGG
*
5443 AGAAGAATCCGTTCAATTATAATGAAATTGGTCTGGTTAACCAAACGGGTAATGGTGTGAACAGT
131 AGAAGAATCCGTTCAATTATAATGAAATTGGTCTGGTTAACCAAACGGGTAATGGTGTGAACAAT
5508 GCAATGGGACACCTGCGTATTTATTGACTTAGAGTGAAT
196 GCAATGGGACACCTGCGTATTTATTGACTTAGAGTGAAT
* *
5547 TACGGGAGAGGGAGAGAGAAAAAGTGAGGAAAAGTTATAGATATTTATTAGGTAAGACAATAACT
1 TACGGGACAGGGAGAGAGAAAAAGTGAGGAAAAGTCATAGATATTTATTAGGTAAGACAATAACT
*
5612 GATGGATACATAGTTATTGAGGGAAT-AAAAAATGGGAACTTTTTAGAATTTGGTTAGGTGTGGG
66 GATGGATACATAGTTATTGAGGGAATAAAAAAATGGGAACTTTCTAGAATTTGGTTAGGTGTGGG
5676 AGAAGAATCCGTTCAATTATAATGAAATTGGTCTGGTTAACCAAACGGGTAATGGTGTGAACAAT
131 AGAAGAATCCGTTCAATTATAATGAAATTGGTCTGGTTAACCAAACGGGTAATGGTGTGAACAAT
**
5741 GCAATGGGACATGTGCGTATTTATTGACTT
196 GCAATGGGACACCTGCGTATTTATTGACTT
5771 CTTGTAGAGT
Statistics
Matches: 217, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
233 129 0.59
234 88 0.41
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (234 bp):
TACGGGACAGGGAGAGAGAAAAAGTGAGGAAAAGTCATAGATATTTATTAGGTAAGACAATAACT
GATGGATACATAGTTATTGAGGGAATAAAAAAATGGGAACTTTCTAGAATTTGGTTAGGTGTGGG
AGAAGAATCCGTTCAATTATAATGAAATTGGTCTGGTTAACCAAACGGGTAATGGTGTGAACAAT
GCAATGGGACACCTGCGTATTTATTGACTTAGAGTGAAT
Found at i:7937 original size:3 final size:3
Alignment explanation
Indices: 7931--7957 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7921 AAATTTAGAT
7931 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
7958 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9722 original size:13 final size:13
Alignment explanation
Indices: 9704--9728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9694 ACATGAATCA
9704 CACAATGTAAAGC
1 CACAATGTAAAGC
9717 CACAATGTAAAG
1 CACAATGTAAAG
9729 GGTTTTACAT
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
CACAATGTAAAGC
Found at i:13318 original size:187 final size:188
Alignment explanation
Indices: 12993--13365 Score: 640
Period size: 187 Copynumber: 2.0 Consensus size: 188
12983 TATATATATA
*
12993 TTTGCAATAGAAACGATAGGAAGATAAATTAAAACATAGAAACAGAGTTTCATACATATTACAAC
1 TTTGCAATAGAAACGATAGGAAGATAAATTAAAACATAGAAACAAAGTTTCATACATATTACAAC
*
13058 ATCATTTTAAGATAAGTAGATAAAAGCTAATACACTTAGTAGTCACCCTTCCTTCCAATCTTCCA
66 ATCATTTTAACATAAGTAGATAAAAGCTAATACACTTAGTAGTCACCCTTCCTTCCAATCTTCCA
* *
13123 CCCGAGACA-TCAAAGGGTAAAAGAGGATCATCAGAAGCTAAAATTGGAGGATATTTT
131 CCCGAGACACTCAAAGGATAAAAAAGGATCATCAGAAGCTAAAATTGGAGGATATTTT
* * *
13180 TTTGCAATAGAAATGATAGGAAGATAAATTAAAACATAGAAACAAAGTTTCATACATATTGCAGC
1 TTTGCAATAGAAACGATAGGAAGATAAATTAAAACATAGAAACAAAGTTTCATACATATTACAAC
* *
13245 ATCATTTTAACATAAGTAGATAAAAGCTAATACACTTAGTAGTCACCCTTCTTTCCAATCTTCTA
66 ATCATTTTAACATAAGTAGATAAAAGCTAATACACTTAGTAGTCACCCTTCCTTCCAATCTTCCA
*
13310 CTCGAGACATCTCAAAGGATAAAAAAGGATCATCAGAAGCTAAAATTGGAGGATAT
131 CCCGAGACA-CTCAAAGGATAAAAAAGGATCATCAGAAGCTAAAATTGGAGGATAT
13366 GAACAAAACG
Statistics
Matches: 174, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
187 131 0.75
189 43 0.25
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (188 bp):
TTTGCAATAGAAACGATAGGAAGATAAATTAAAACATAGAAACAAAGTTTCATACATATTACAAC
ATCATTTTAACATAAGTAGATAAAAGCTAATACACTTAGTAGTCACCCTTCCTTCCAATCTTCCA
CCCGAGACACTCAAAGGATAAAAAAGGATCATCAGAAGCTAAAATTGGAGGATATTTT
Found at i:24625 original size:13 final size:14
Alignment explanation
Indices: 24601--24633 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
24591 ATTAATTACT
24601 TATAAGTAAAATTC
1 TATAAGTAAAATTC
24615 TATAA-TAAAATTC
1 TATAAGTAAAATTC
24628 TATAAG
1 TATAAG
24634 GGGGGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (14 bp):
TATAAGTAAAATTC
Found at i:26176 original size:6 final size:6
Alignment explanation
Indices: 26168--26232 Score: 89
Period size: 6 Copynumber: 11.0 Consensus size: 6
26158 TGTCTTGTAA
*
26168 TTATAA TTATA- TT-TAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
26214 TTATAT CTATAT TATATAT
1 TTATAT TTATAT T-TATAT
26233 AAAAATACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
4 2 0.04
5 4 0.07
6 43 0.80
7 5 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (6 bp):
TTATAT
Found at i:31917 original size:27 final size:27
Alignment explanation
Indices: 31875--31935 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
31865 TCTTCATTAT
* *
31875 AGGGGTAAAATCGTAATTTTATCAATC
1 AGGGGTAAAATAGTAAATTTATCAATC
* * *
31902 AGGGGTAACATAGTAAATTTGTCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
31929 ACGGGTA
1 AGGGGTA
31936 TTTTTGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Found at i:40906 original size:18 final size:18
Alignment explanation
Indices: 40883--40917 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40873 CCTGTTAGTC
* *
40883 GCTGACTTGGCTTTTTCT
1 GCTGACATGGATTTTTCT
40901 GCTGACATGGATTTTTC
1 GCTGACATGGATTTTTC
40918 CACGTCAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (18 bp):
GCTGACATGGATTTTTCT
Found at i:41935 original size:13 final size:13
Alignment explanation
Indices: 41917--41954 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
41907 AAGAAGGAGG
*
41917 GAGAAAGAAAAGA
1 GAGAAAAAAAAGA
41930 GAGAAAAAAAAGA
1 GAGAAAAAAAAGA
41943 -AGGAAAAAAAAG
1 GA-GAAAAAAAAG
41955 GTTTGCCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
GAGAAAAAAAAGA
Found at i:43846 original size:11 final size:11
Alignment explanation
Indices: 43832--43862 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43822 AATCTACTTA
43832 AATCTTCAGAT
1 AATCTTCAGAT
*
43843 AATCTCCAGAT
1 AATCTTCAGAT
43854 AATCTTCAG
1 AATCTTCAG
43863 TTGAAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (11 bp):
AATCTTCAGAT
Found at i:43893 original size:13 final size:13
Alignment explanation
Indices: 43855--43894 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
43845 TCTCCAGATA
* *
43855 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
43868 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
43881 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
43894 A
1 A
43895 ATATTCTCCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Found at i:52333 original size:10 final size:11
Alignment explanation
Indices: 52309--52338 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52299 CCCTTGGCCT
52309 AAAACTAGAGA
1 AAAACTAGAGA
52320 AAAACTAGAGA
1 AAAACTAGAGA
52331 AAAA-TAGA
1 AAAACTAGA
52339 AGATGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.67, C:0.07, G:0.17, T:0.10
Consensus pattern (11 bp):
AAAACTAGAGA
Found at i:53435 original size:2 final size:2
Alignment explanation
Indices: 53430--53466 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53420 TCTCTCTCTG
53430 TA TA TA TA TA TA TA TA 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 TA T
53467 TGTGGCTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54532 original size:19 final size:21
Alignment explanation
Indices: 54508--54552 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54498 CGTGGAGATT
* *
54508 CTTGAGA-AA-AAGCGCGGAG
1 CTTGAGAGAATAAGCACGAAG
54527 CTTGAGAGAATAAGCACGAAG
1 CTTGAGAGAATAAGCACGAAG
54548 CTTGA
1 CTTGA
54553 TTTTTTGCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 13 0.59
ACGTcount: A:0.38, C:0.16, G:0.31, T:0.16
Consensus pattern (21 bp):
CTTGAGAGAATAAGCACGAAG
Found at i:56210 original size:22 final size:22
Alignment explanation
Indices: 56160--56288 Score: 77
Period size: 22 Copynumber: 5.9 Consensus size: 22
56150 TCTTACAGAG
56160 AGGTTATTGAAAA-TT-ATAGGA
1 AGGTTATT-AAAATTTCATAGGA
**
56181 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATTAAAATTTCATAGGA
* *
56204 AGGTTATTAAAGTTTCATATGA
1 AGGTTATTAAAATTTCATAGGA
* * * *
56226 AGTTTATCACAATTTCATAAGTA
1 AGGTTATTAAAATTTCAT-AGGA
* * * *
56249 A-ATTATCAAAATTTCATAACGT
1 AGGTTATTAAAATTTCAT-AGGA
*
56271 A-GTTATCAAAATTTCATA
1 AGGTTATTAAAATTTCATA
56289 AAAATATTCA
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
21 8 0.09
22 68 0.79
23 10 0.12
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
AGGTTATTAAAATTTCATAGGA
Found at i:56289 original size:22 final size:22
Alignment explanation
Indices: 56229--56289 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
56219 CATATGAAGT
*
56229 TTATCACAATTTCATAAGTAAA
1 TTATCAAAATTTCATAAGTAAA
*
56251 TTATCAAAATTTCATAACGT-AG
1 TTATCAAAATTTCATAA-GTAAA
56273 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
56290 AAATATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGTAAA
Found at i:56350 original size:12 final size:12
Alignment explanation
Indices: 56318--56356 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
56308 ATGAAATTAA
56318 ATATCCGTCG--
1 ATATCCGTCGAT
56328 ATA-CC-TCGAT
1 ATATCCGTCGAT
56338 ATATCCGTCGAT
1 ATATCCGTCGAT
56350 ATATCCG
1 ATATCCG
56357 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:57441 original size:2 final size:2
Alignment explanation
Indices: 57434--57462 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57424 TAAAACTAAA
57434 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 A
57463 ATGGTACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60612 original size:19 final size:19
Alignment explanation
Indices: 60562--60618 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
60552 GCTCTATTAG
*
60562 TCTCATCTGTACAGTACTTAA
1 TCTCATCTGTACAGT--GTAA
* * *
60583 TTTAATTTGTACAGTGTAA
1 TCTCATCTGTACAGTGTAA
60602 TCTCATCTGTACAGTGT
1 TCTCATCTGTACAGTGT
60619 CTAAACAGAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 17 0.59
21 12 0.41
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (19 bp):
TCTCATCTGTACAGTGTAA
Found at i:60751 original size:3 final size:3
Alignment explanation
Indices: 60743--60794 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
60733 TTGTCCTTAC
60743 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
60791 TTA T
1 TTA T
60795 ACTAAACTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61793 original size:15 final size:16
Alignment explanation
Indices: 61752--61799 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
61742 AGGAAATAGG
61752 AAAGAAAGG--AAGAA
1 AAAGAAAGGAAAAGAA
61766 AAAGAAAGGAAAA-AA
1 AAAGAAAGGAAAAGAA
**
61781 AAAGAAATTAAAAGAA
1 AAAGAAAGGAAAAGAA
61797 AAA
1 AAA
61800 A
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 9 0.31
15 13 0.45
16 7 0.24
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (16 bp):
AAAGAAAGGAAAAGAA
Done.