Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019360.1 Corchorus olitorius cultivar O-4 contig19393, 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: 40122
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2585 original size:37 final size:37
Alignment explanation
Indices: 2481--2592 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 37
2471 ATAATCTTCA
2481 TATTATAATAATTGGTTAATCTAATAATCTTCAACTT
1 TATTATAATAATTGGTTAATCTAATAATCTTCAACTT
* * * ** * *
2518 TA-CAAACAAAATT-GAAAATTTTATAATCTTCATA-TT
1 TATTATA-ATAATTGGTTAATCTAATAATCTTCA-ACTT
*
2554 TATTATAATAATTGGTTAATCTCATAATCTTCAACTT
1 TATTATAATAATTGGTTAATCTAATAATCTTCAACTT
2591 TA
1 TA
2593 CAAATGTAAA
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
36 27 0.48
37 29 0.52
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (37 bp):
TATTATAATAATTGGTTAATCTAATAATCTTCAACTT
Found at i:5292 original size:1 final size:1
Alignment explanation
Indices: 5286--5315 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
5276 CACGTGCATG
5286 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5316 GAAGAACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10763 original size:31 final size:30
Alignment explanation
Indices: 10728--10787 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
10718 ACATGTAAAC
***
10728 TAAATAGTGGTGTTTTGGTGCCAAAAAAAAA
1 TAAATAGTGGTAAATTGGTG-CAAAAAAAAA
10759 TAAATAGTGGTAAATTGGTGCAAAAAAAA
1 TAAATAGTGGTAAATTGGTGCAAAAAAAA
10788 TAGGGGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.27
Consensus pattern (30 bp):
TAAATAGTGGTAAATTGGTGCAAAAAAAAA
Found at i:11920 original size:15 final size:15
Alignment explanation
Indices: 11878--11920 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
11868 AATTTTCTCG
*
11878 GGTCATTCGGGTTCC
1 GGTCATTCGGGTTCA
11893 GGCTCA-TCTGGGTTCA
1 GG-TCATTC-GGGTTCA
11909 GGTCATTCGGGT
1 GGTCATTCGGGT
11921 CTCGGGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.09, C:0.23, G:0.35, T:0.33
Consensus pattern (15 bp):
GGTCATTCGGGTTCA
Found at i:12098 original size:25 final size:24
Alignment explanation
Indices: 12043--12099 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
12033 GTCAGCCTTG
*
12043 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
* *
12066 AATTTATTTAATGTCTTTATTATTC
1 AATTTATTTAATGT-TTAATTATTA
12091 AATTTATTT
1 AATTTATTT
12100 TACAATCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.28
25 16 0.55
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:12380 original size:17 final size:17
Alignment explanation
Indices: 12354--12387 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12344 TAATCTTATT
*
12354 TAATATTTATTCATATA
1 TAATAATTATTCATATA
12371 TAATAATTATTCATATA
1 TAATAATTATTCATATA
12388 ATGAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAATTATTCATATA
Found at i:13023 original size:12 final size:12
Alignment explanation
Indices: 13006--13032 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12996 GCTTCGCTAC
13006 TGAAGGAGCAGA
1 TGAAGGAGCAGA
13018 TGAAGGAGCAGA
1 TGAAGGAGCAGA
13030 TGA
1 TGA
13033 GAGAATTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.41, T:0.11
Consensus pattern (12 bp):
TGAAGGAGCAGA
Found at i:13338 original size:48 final size:48
Alignment explanation
Indices: 13267--13371 Score: 201
Period size: 48 Copynumber: 2.2 Consensus size: 48
13257 ATTCATCGCT
13267 GAAGTGTTGGGAGGATATGAAGAAGCTGTCAAAAAGCTGTCAAAGCAA
1 GAAGTGTTGGGAGGATATGAAGAAGCTGTCAAAAAGCTGTCAAAGCAA
13315 GAAGTGTTGGGAGGATATGAAGAAGCTGTCAAAAAGCTGTCAAAGCAA
1 GAAGTGTTGGGAGGATATGAAGAAGCTGTCAAAAAGCTGTCAAAGCAA
*
13363 AAAGTGTTG
1 GAAGTGTTG
13372 TTGTTTGCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (48 bp):
GAAGTGTTGGGAGGATATGAAGAAGCTGTCAAAAAGCTGTCAAAGCAA
Found at i:14581 original size:25 final size:25
Alignment explanation
Indices: 14538--14589 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
14528 ATGCAATCTC
*
14538 TCATAGAAAGACACATTTTCATGTT
1 TCATAGAAAGACACATTTTCATATT
* * *
14563 TCATAGAAATATACCTTTTCATATT
1 TCATAGAAAGACACATTTTCATATT
14588 TC
1 TC
14590 TGCAGATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (25 bp):
TCATAGAAAGACACATTTTCATATT
Found at i:18165 original size:17 final size:17
Alignment explanation
Indices: 18143--18188 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
18133 TCTGACAATC
18143 ATTTATCAAAAACTTCA
1 ATTTATCAAAAACTTCA
18160 ATTTATCAAAAACTTCA
1 ATTTATCAAAAACTTCA
18177 ATTTATCAAAAA
1 ATTTATCAAAAA
18189 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTATCAAAAACTTCA
Found at i:18991 original size:49 final size:50
Alignment explanation
Indices: 18914--19015 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 50
18904 GTACTCTTTC
*
18914 AAAGGATGCGAGGAAAAGTAAATATTCAATTTTGATGCAAAAATTGAGAA
1 AAAGGATGCGAGAAAAAGTAAATATTCAATTTTGATGCAAAAATTGAGAA
* * *
18964 AAAGG-TGCGAGAAAAATTAAA-AGTTCAATTTTGTTGTAAAAATTGAGAA
1 AAAGGATGCGAGAAAAAGTAAATA-TTCAATTTTGATGCAAAAATTGAGAA
19013 AAA
1 AAA
19016 AAAAGAGTGC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
48 1 0.02
49 41 0.87
50 5 0.11
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.25
Consensus pattern (50 bp):
AAAGGATGCGAGAAAAAGTAAATATTCAATTTTGATGCAAAAATTGAGAA
Found at i:22686 original size:21 final size:20
Alignment explanation
Indices: 22660--22709 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
22650 GCAAGATTTG
22660 TCATTACACCTTAAAAT-GATA
1 TCATTACACCTT-AAATGGA-A
*
22681 TCATTACA-CTTAACTGGAA
1 TCATTACACCTTAAATGGAA
22700 TCATTACACC
1 TCATTACACC
22710 AAATAATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 12 0.46
20 6 0.23
21 8 0.31
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (20 bp):
TCATTACACCTTAAATGGAA
Found at i:23025 original size:20 final size:20
Alignment explanation
Indices: 23000--23043 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
22990 CGACGGTGTA
* *
23000 AATTTTGGACTCTATAAGCG
1 AATTTTGGACTCCACAAGCG
23020 AATTTTGGACTCCACAAGCG
1 AATTTTGGACTCCACAAGCG
23040 AATT
1 AATT
23044 GTGAAGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
AATTTTGGACTCCACAAGCG
Found at i:26441 original size:13 final size:13
Alignment explanation
Indices: 26423--26448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26413 ACAGATATCC
26423 ACGGATATATCGA
1 ACGGATATATCGA
26436 ACGGATATATCGA
1 ACGGATATATCGA
26449 GGTATCGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
ACGGATATATCGA
Found at i:27575 original size:10 final size:10
Alignment explanation
Indices: 27560--27597 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
27550 AATTTAATAT
27560 GGATATTTAC
1 GGATATTTAC
*
27570 GGATATTTAT
1 GGATATTTAC
27580 GGATATTTAC
1 GGATATTTAC
27590 GGAATATT
1 GG-ATATT
27598 GAGGTATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:27580 original size:20 final size:21
Alignment explanation
Indices: 27557--27597 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
27547 TTTAATTTAA
27557 TATGGATATTTACGG-ATATT
1 TATGGATATTTACGGAATATT
27577 TATGGATATTTACGGAATATT
1 TATGGATATTTACGGAATATT
27598 GAGGTATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (21 bp):
TATGGATATTTACGGAATATT
Found at i:28330 original size:20 final size:21
Alignment explanation
Indices: 28294--28334 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28284 TTTAAATTGG
28294 AGGTGTTATTAAAATTTTTTA
1 AGGTGTTATTAAAATTTTTTA
*
28315 AGGTGTTATTAAATTTTTTT
1 AGGTGTTATTAAAATTTTTT
28335 TATTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (21 bp):
AGGTGTTATTAAAATTTTTTA
Found at i:29047 original size:20 final size:19
Alignment explanation
Indices: 29013--29058 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
29003 CTTCACTTCT
29013 TCTTCTTCATCAATCATCA
1 TCTTCTTCATCAATCATCA
* *
29032 TCTTCATTCTTCAATCTTCA
1 TCTTC-TTCATCAATCATCA
29052 TC-TCTTC
1 TCTTCTTC
29059 CTTGTTCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 7 0.29
20 14 0.58
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.48
Consensus pattern (19 bp):
TCTTCTTCATCAATCATCA
Found at i:29139 original size:15 final size:15
Alignment explanation
Indices: 29119--29151 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29109 CAAATCTTCT
29119 TCTTCTTCTCTG-TCC
1 TCTTCTTCT-TGTTCC
29134 TCTTCTTCTTGTTCC
1 TCTTCTTCTTGTTCC
29149 TCT
1 TCT
29152 CACCTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.00, C:0.36, G:0.06, T:0.58
Consensus pattern (15 bp):
TCTTCTTCTTGTTCC
Found at i:39937 original size:24 final size:22
Alignment explanation
Indices: 39908--39962 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 22
39898 GTGGATTATA
*
39908 AAATAATTGAATAATTAAGACATT
1 AAATAATT-AAGAATTAA-ACATT
39932 AAATAAATTAAGAATTAAACATT
1 AAAT-AATTAAGAATTAAACATT
*
39955 AAAAAATT
1 AAATAATT
39963 CAAGGCTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 4 0.14
23 8 0.29
24 12 0.43
25 4 0.14
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (22 bp):
AAATAATTAAGAATTAAACATT
Done.