Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023505.1 Corchorus olitorius cultivar O-4 contig23538, 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: 54394
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1045 original size:43 final size:42
Alignment explanation
Indices: 993--1236 Score: 343
Period size: 43 Copynumber: 5.8 Consensus size: 42
983 TAAGGAGAAA
*
993 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
1035 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGA-
1 -TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
* *
1077 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAGAG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
*
1119 TTGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGA-
1 -TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
* *
1161 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-G
*
1204 TGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
1237 TTGGCTTTTG
Statistics
Matches: 180, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
41 72 0.40
42 4 0.02
43 104 0.58
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (42 bp):
TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:1104 original size:84 final size:84
Alignment explanation
Indices: 992--1236 Score: 463
Period size: 84 Copynumber: 2.9 Consensus size: 84
982 ATAAGGAGAA
992 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1057 TTTGGGGACTTTGATATAG
66 TTTGGGGACTTTGATATAG
*
1076 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAGTAGAGTTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1141 TTTGGGGACTTTGATATAG
66 TTTGGGGACTTTGATATAG
* *
1160 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATGTG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
1225 TTTGGGGACTTT
66 TTTGGGGACTTT
1237 TTGGCTTTTG
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 157 1.00
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.43
Consensus pattern (84 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATATAG
Found at i:8042 original size:15 final size:15
Alignment explanation
Indices: 8022--8052 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8012 AGATGATGAG
8022 AAAGTTGAAGAAGAA
1 AAAGTTGAAGAAGAA
*
8037 AAAGTTGAGGAAGAA
1 AAAGTTGAAGAAGAA
8052 A
1 A
8053 GGCTAACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.13
Consensus pattern (15 bp):
AAAGTTGAAGAAGAA
Found at i:10037 original size:29 final size:30
Alignment explanation
Indices: 9982--10057 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
9972 GATTTTGGTT
* * * *
9982 AAGTGCGGGTTGTGTACTTGTGTTTG-TTC
1 AAGTGTGGGTTGTGCACTTGGGATTGTTTC
*
10011 AAGTGTGGGTTGTGCACTTGGGATTGTTTT
1 AAGTGTGGGTTGTGCACTTGGGATTGTTTC
*
10041 GAGTGTGGGTT-TGCACT
1 AAGTGTGGGTTGTGCACT
10058 CGTGTCAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.42
Consensus pattern (30 bp):
AAGTGTGGGTTGTGCACTTGGGATTGTTTC
Found at i:16596 original size:9 final size:9
Alignment explanation
Indices: 16582--16616 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
16572 TCAACTCACG
16582 AAGAGATGA
1 AAGAGATGA
16591 AAGAGATGA
1 AAGAGATGA
*
16600 AAGAAATGA
1 AAGAGATGA
16609 AAGAGATG
1 AAGAGATG
16617 GTTCAGTCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.31, T:0.11
Consensus pattern (9 bp):
AAGAGATGA
Found at i:20361 original size:25 final size:26
Alignment explanation
Indices: 20331--20379 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
20321 TGTCCCTCTG
*
20331 AAAAG-AAAAGAGTGTTAGTAACCTC
1 AAAAGAAAAAGAGAGTTAGTAACCTC
*
20356 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAGAAAAAGAGAGTTAGTAACC
20380 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.16
Consensus pattern (26 bp):
AAAAGAAAAAGAGAGTTAGTAACCTC
Found at i:21441 original size:21 final size:21
Alignment explanation
Indices: 21391--21435 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21381 GTGACACTGC
*
21391 CCACCTGGGTCCTCAAGCAAA
1 CCACATGGGTCCTCAAGCAAA
* *
21412 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTCCTCAAGCAAA
21433 CCA
1 CCA
21436 TGTGGGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.22, T:0.13
Consensus pattern (21 bp):
CCACATGGGTCCTCAAGCAAA
Found at i:23412 original size:11 final size:11
Alignment explanation
Indices: 23388--23422 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
23378 GTAAAACTGG
*
23388 AAAAGTAAATA
1 AAAAGTAAAGA
*
23399 AAAAGAAAAGA
1 AAAAGTAAAGA
23410 AAAAGTAAAGA
1 AAAAGTAAAGA
23421 AA
1 AA
23423 GCAAACACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAGTAAAGA
Found at i:41667 original size:16 final size:17
Alignment explanation
Indices: 41646--41677 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41636 GTCTAACGTG
41646 TCGTGTAA-CGTGTTAT
1 TCGTGTAACCGTGTTAT
41662 TCGTGTAACCGTGTTA
1 TCGTGTAACCGTGTTA
41678 ACCCGGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.16, G:0.25, T:0.41
Consensus pattern (17 bp):
TCGTGTAACCGTGTTAT
Found at i:50607 original size:21 final size:21
Alignment explanation
Indices: 50582--50664 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
50572 TATCTTAGAT
50582 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
50603 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
50624 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
50646 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
50665 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:50615 original size:25 final size:25
Alignment explanation
Indices: 50584--50632 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
50574 TCTTAGATAT
*
50584 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
50609 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
50633 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:51390 original size:85 final size:86
Alignment explanation
Indices: 51284--51470 Score: 290
Period size: 85 Copynumber: 2.2 Consensus size: 86
51274 AAAAATATAT
* * **
51284 TTAAAAAA-TTATAATATATCTAAGTTTTGCAATTACAATAGT-TTAATGGTAAAAATAAAATAG
1 TTAAAAAATTTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAAATGGTAAAAATAAAATAG
51347 TTATAAAGAGATTAGATTTAA
66 TTATAAAGAGATTAGATTTAA
* *
51368 TTAAAAAATTTCTAATATATCTAAGTTTTGTAATTAAAATAGTAAAAATGGTAAAAATTAAATAG
1 TTAAAAAATTTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAAATGGTAAAAATAAAATAG
*
51433 TTATAAAGAGATTAGGTTTAA
66 TTATAAAGAGATTAGATTTAA
51454 TT-AAAAATTTCTAATAT
1 TTAAAAAATTTCTAATAT
51471 GGGTTATTAT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
84 8 0.09
85 46 0.49
86 40 0.43
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (86 bp):
TTAAAAAATTTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAAATGGTAAAAATAAAATAG
TTATAAAGAGATTAGATTTAA
Found at i:52561 original size:16 final size:16
Alignment explanation
Indices: 52540--52571 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52530 AAGAATGTGG
52540 ATGTCAACATTGTAGA
1 ATGTCAACATTGTAGA
52556 ATGTCAACATTGTAGA
1 ATGTCAACATTGTAGA
52572 TTTAACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTCAACATTGTAGA
Found at i:54062 original size:56 final size:56
Alignment explanation
Indices: 53995--54107 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
53985 TGTTTTATCA
*
53995 ATTAGTATGTAATGTCATCCCATCAAAATGAAAAATTGATGGTATTGCATCTTTGG
1 ATTAGTATGTAATCTCATCCCATCAAAATGAAAAATTGATGGTATTGCATCTTTGG
54051 ATTAGTATGTAATCTCATCCCATCAAAATGAAAAATTGATGGTATTGCATCTTTGG
1 ATTAGTATGTAATCTCATCCCATCAAAATGAAAAATTGATGGTATTGCATCTTTGG
54107 A
1 A
54108 AGTCAGGGAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (56 bp):
ATTAGTATGTAATCTCATCCCATCAAAATGAAAAATTGATGGTATTGCATCTTTGG
Done.