Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019945.1 Corchorus olitorius cultivar O-4 contig19978, 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: 37259
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:100 original size:2 final size:2
Alignment explanation
Indices: 93--126 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
83 TGTTCGATTA
93 AT AT 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 AT AT
127 TACATCTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:798 original size:27 final size:27
Alignment explanation
Indices: 768--821 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
758 GCTGTAGTAG
768 AAGATACTAAACTCAAACCTTTTTTTT
1 AAGATACTAAACTCAAACCTTTTTTTT
795 AAGATACTAAACTCAAACCTTTTTTTT
1 AAGATACTAAACTCAAACCTTTTTTTT
822 TATTAAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (27 bp):
AAGATACTAAACTCAAACCTTTTTTTT
Found at i:2128 original size:13 final size:13
Alignment explanation
Indices: 2110--2137 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2100 TTCTTTATAA
2110 TTTGTTTGTTTAT
1 TTTGTTTGTTTAT
2123 TTTGTTTGTTTAT
1 TTTGTTTGTTTAT
2136 TT
1 TT
2138 GGTAGGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (13 bp):
TTTGTTTGTTTAT
Found at i:2410 original size:2 final size:2
Alignment explanation
Indices: 2403--2436 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
2393 ACTTTTTGAG
*
2403 AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
2437 AAAGTACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4783 original size:15 final size:15
Alignment explanation
Indices: 4765--4802 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
4755 ATATGCTATG
4765 TGGAGGAATGCTGAA
1 TGGAGGAATGCTGAA
4780 TGGAGGAATGCTGAA
1 TGGAGGAATGCTGAA
4795 TGGAGGAA
1 TGGAGGAA
4803 CTCAGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.05, G:0.42, T:0.18
Consensus pattern (15 bp):
TGGAGGAATGCTGAA
Found at i:5214 original size:43 final size:44
Alignment explanation
Indices: 5153--5251 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 44
5143 CATAGTTAGG
* * * * *
5153 TTATCAAAGTTTTTTATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA
* *
5196 TTATCAAAATTTTATATGGTGGTTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA
*
5240 TTATCGAAATTT
1 TTATCAAAATTT
5252 CATAAAACTA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 32 0.68
44 15 0.32
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.44
Consensus pattern (44 bp):
TTATCAAAATTTTATATGGAGGTTATCAAAATTTAATAGGGTAA
Found at i:5224 original size:22 final size:22
Alignment explanation
Indices: 5153--5251 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
5143 CATAGTTAGG
* * * *
5153 TTATCAAAGTTTTTTATGGAGT
1 TTATCAAAATTTTATATGGTGA
* *
5175 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTTATATGGTGA
*
5196 TTATCAAAATTTTATATGGTGG
1 TTATCAAAATTTTATATGGTGA
* *
5218 TTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTTATATGGTGA
*
5240 TTATCGAAATTT
1 TTATCAAAATTT
5252 CATAAAACTA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
21 17 0.27
22 46 0.73
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.44
Consensus pattern (22 bp):
TTATCAAAATTTTATATGGTGA
Found at i:6776 original size:19 final size:19
Alignment explanation
Indices: 6729--6776 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
6719 TTTAATGTGG
6729 GTATACTTG-TTTGTACAT
1 GTATACTTGTTTTGTACAT
*
6747 GT-TATTTGTTTTGTA-AGT
1 GTATACTTGTTTTGTACA-T
6765 GTATACTTGTTT
1 GTATACTTGTTT
6777 CCACACATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 11 0.44
19 8 0.32
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (19 bp):
GTATACTTGTTTTGTACAT
Found at i:8677 original size:21 final size:21
Alignment explanation
Indices: 8653--8710 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
8643 AATCACATCT
8653 TAAAATTATCAATGAATAAAA
1 TAAAATTATCAATGAATAAAA
*
8674 TAAAGTATATCAA--AATAAAA
1 TAAAAT-TATCAATGAATAAAA
*
8694 AAAAATTAT-AATTGAAT
1 TAAAATTATCAA-TGAAT
8711 CACTAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 11 0.37
21 8 0.27
22 6 0.20
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAAATTATCAATGAATAAAA
Found at i:12393 original size:2 final size:2
Alignment explanation
Indices: 12386--12422 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12376 TGTTAAGAGG
12386 AT 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 AT A
12423 CTAGGTAAGA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13050 original size:178 final size:177
Alignment explanation
Indices: 12730--13068 Score: 495
Period size: 178 Copynumber: 1.9 Consensus size: 177
12720 AAGCACAAAC
** * *
12730 TATATAATATTAAGTAGATTGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCATTTT
1 TATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACGAATTCTTTGGAAGCATTTT
*
12795 TATACCTTGAATATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGGAAAAACCT
66 TATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGGAAAAACCT
* *
12860 TTCAAGAGACACTTGAATCATCTCAATCAGACCTCTGGAACAAAAGT
131 TTCAAGAGACACTTAAATCACCTCAATCAGACCTCTGGAACAAAAGT
* *
12907 TATATAATATTAAGTGGACCGTCTATTCCCGTTAACTGAAACAACGAATT-TTTCGGAAGCATTT
1 TATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACGAATTCTTT-GGAAGCATTT
* *
12971 TTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAA
65 TT-ATACCTTG-AACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGGAAAAA
* * *
13035 TC-TTCTAATAGACACTTAAATCACCTTAATCAGA
128 CCTTTC-AAGAGACACTTAAATCACCTCAATCAGA
13069 TAACCGGAGA
Statistics
Matches: 144, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
176 3 0.02
177 63 0.44
178 78 0.54
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (177 bp):
TATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACGAATTCTTTGGAAGCATTTT
TATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATCATGGAAAAACCT
TTCAAGAGACACTTAAATCACCTCAATCAGACCTCTGGAACAAAAGT
Found at i:13223 original size:23 final size:25
Alignment explanation
Indices: 13174--13223 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
13164 TGCCCTTAAA
* *
13174 AATATGTGAGAATAACGACAAAGTC
1 AATATGTGAGAATAACGAAAAAATC
*
13199 AATAT-TGA-AATGACGAAAAAATC
1 AATATGTGAGAATAACGAAAAAATC
13222 AA
1 AA
13224 GCTAAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 3 0.14
25 5 0.23
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (25 bp):
AATATGTGAGAATAACGAAAAAATC
Found at i:13318 original size:7 final size:7
Alignment explanation
Indices: 13293--13333 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
13283 CTTCCTATAA
13293 TTATTGTT
1 TTATT-TT
*
13301 TT-TTAT
1 TTATTTT
13307 TTATTTT
1 TTATTTT
13314 TTATTTT
1 TTATTTT
13321 TTA-TTT
1 TTATTTT
13327 TTATTTT
1 TTATTTT
13334 ATATAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
6 9 0.31
7 18 0.62
8 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:13322 original size:18 final size:18
Alignment explanation
Indices: 13299--13335 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13289 ATAATTATTG
13299 TTTTTTATTTATT-TTTTA
1 TTTTTTATTT-TTATTTTA
13317 TTTTTTATTTTTATTTTA
1 TTTTTTATTTTTATTTTA
13335 T
1 T
13336 ATAATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTATTTTTATTTTA
Found at i:13323 original size:14 final size:14
Alignment explanation
Indices: 13293--13333 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
13283 CTTCCTATAA
*
13293 TTATTGTTTT-TTAT
1 TTATT-TTTTATTTT
13307 TTATTTTTTATTTT
1 TTATTTTTTATTTT
13321 TTA-TTTTTATTTT
1 TTATTTTTTATTTT
13334 ATATAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (14 bp):
TTATTTTTTATTTT
Found at i:14467 original size:40 final size:40
Alignment explanation
Indices: 14409--14489 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
14399 TTTATAACTA
* *
14409 GGGGCTAAACATGGATTTAATTTCTTAT-CTTAATTATTAG
1 GGGGCTAAACATGAATTTAATTTATT-TCCTTAATTATTAG
*
14449 GGGGCTAAACCTGAATTTAATTTATTTCCTTAATTATTAG
1 GGGGCTAAACATGAATTTAATTTATTTCCTTAATTATTAG
14489 G
1 G
14490 AGGGTCAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACATGAATTTAATTTATTTCCTTAATTATTAG
Found at i:14545 original size:13 final size:13
Alignment explanation
Indices: 14527--14559 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
14517 ATTTCTTGAT
14527 TCTCCAATTTGTC
1 TCTCCAATTTGTC
14540 TCTCCAATTTGTC
1 TCTCCAATTTGTC
*
14553 CCTCCAA
1 TCTCCAA
14560 CTTGACCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.06, T:0.39
Consensus pattern (13 bp):
TCTCCAATTTGTC
Found at i:14631 original size:40 final size:40
Alignment explanation
Indices: 14569--14649 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
14559 ACTTGACCCT
* *
14569 CCTAATAATTAAGAAAATAAATTAAATTCA-GATTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATCCATG-TTTAGCCC
*
14609 CCTAATAATTAAGATAAGAAATTAAATCCATGTTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATCCATGTTTAGCCC
14649 C
1 C
14650 TAGTTATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (40 bp):
CCTAATAATTAAGAAAAGAAATTAAATCCATGTTTAGCCC
Found at i:14767 original size:13 final size:13
Alignment explanation
Indices: 14749--14780 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
14739 TGACACGTCA
14749 GGAGGGACAAATT
1 GGAGGGACAAATT
*
14762 GGAGGGACAAGTT
1 GGAGGGACAAATT
14775 GGAGGG
1 GGAGGG
14781 TCATGTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.50, T:0.12
Consensus pattern (13 bp):
GGAGGGACAAATT
Found at i:21320 original size:25 final size:26
Alignment explanation
Indices: 21291--21342 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
21281 GTATAATATG
*
21291 TTTTGTTTG-CCTGTTACTCTGTTTT
1 TTTTGTTTGTCCTGTTAATCTGTTTT
*
21316 TTTTGTTTGTTGCTGTTAATCTGTTTT
1 TTTTGTTTG-TCCTGTTAATCTGTTTT
21343 ACTGATATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.06, C:0.12, G:0.17, T:0.65
Consensus pattern (26 bp):
TTTTGTTTGTCCTGTTAATCTGTTTT
Found at i:28997 original size:24 final size:24
Alignment explanation
Indices: 28968--29015 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28958 GTGAATATAA
28968 AAATATTGCTTGTTGTATTTGTAT
1 AAATATTGCTTGTTGTATTTGTAT
28992 AAATATTGCTTGTTGTATTTGTAT
1 AAATATTGCTTGTTGTATTTGTAT
29016 GTTATGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (24 bp):
AAATATTGCTTGTTGTATTTGTAT
Found at i:29962 original size:11 final size:11
Alignment explanation
Indices: 29939--29973 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29929 TTGACAGCGC
29939 AACAAAAACAA
1 AACAAAAACAA
* *
29950 AACGAAAATAA
1 AACAAAAACAA
29961 AACAAAAACAA
1 AACAAAAACAA
29972 AA
1 AA
29974 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:33786 original size:30 final size:30
Alignment explanation
Indices: 33752--33813 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
33742 ATTTTTATCT
*
33752 TGACTTTCCTCTTATACCTTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
*
33782 TGACTTTTCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATACCCTCAAATTTTAA
33812 TG
1 TG
33814 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATACCCTCAAATTTTAA
Found at i:34452 original size:18 final size:20
Alignment explanation
Indices: 34417--34454 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
34407 AAAAAAGAAA
*
34417 TTTGATTTTTCTTCTTTTCT
1 TTTGATTTTCCTTCTTTTCT
34437 TTTG-TTTTCCTT-TTTTCT
1 TTTGATTTTCCTTCTTTTCT
34455 GTTTTTTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 7 0.41
20 4 0.24
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTGATTTTCCTTCTTTTCT
Done.