Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012024.1 Corchorus olitorius cultivar O-4 contig12057, 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: 25403
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1268 original size:2 final size:2
Alignment explanation
Indices: 1225--1252 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1215 TTATTTTAGT
1225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1253 AACTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5087 original size:13 final size:13
Alignment explanation
Indices: 5069--5100 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
5059 TAAGTACAAA
5069 AATTATTTGTATT
1 AATTATTTGTATT
5082 AATTATTTGTATT
1 AATTATTTGTATT
5095 AATTAT
1 AATTAT
5101 CAGCATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
AATTATTTGTATT
Found at i:7294 original size:25 final size:24
Alignment explanation
Indices: 7244--7299 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
7234 CTATTGTTTT
*
7244 TTTTATCAAATTTAAAAAATATTA
1 TTTTATCAAATTTAAAAAATAATA
7268 TTTTAT-ATAATTTAAAAAATTAATA
1 TTTTATCA-AATTTAAAAAA-TAATA
7293 TTATTAT
1 TT-TTAT
7300 TATTATGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 1 0.04
24 17 0.61
25 6 0.21
26 4 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATCAAATTTAAAAAATAATA
Found at i:8163 original size:98 final size:99
Alignment explanation
Indices: 7994--8187 Score: 273
Period size: 98 Copynumber: 2.0 Consensus size: 99
7984 CATTTAGGGC
* * * * ** *
7994 ATAGTTTTGAATTTCACAAACAAAATTAATCAAGAAAGTGTATATGTGTCAACTTTTTAATGTGC
1 ATAGTTTTGAATTTCAAAAACAAAACTAATCAAGAAAATGTATATGTGTCAACTTCTTAACCTAC
8059 TTGTAGAGTCCAAAATTTAC-TTGATAATGTGGA
66 TTGTAGAGTCCAAAATTTACATTGATAATGTGGA
* * *
8092 ATAGTTTTGAATTTCAAAAACAAAACTAATTAAGAAAATGTGTATGTGTCATCTTCTTAACCTAC
1 ATAGTTTTGAATTTCAAAAACAAAACTAATCAAGAAAATGTATATGTGTCAACTTCTTAACCTAC
**
8157 TTGTAGAGTTTAAAATTTACATTGATAATGT
66 TTGTAGAGTCCAAAATTTACATTGATAATGT
8188 ATTGTATAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
98 73 0.88
99 10 0.12
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (99 bp):
ATAGTTTTGAATTTCAAAAACAAAACTAATCAAGAAAATGTATATGTGTCAACTTCTTAACCTAC
TTGTAGAGTCCAAAATTTACATTGATAATGTGGA
Found at i:9370 original size:59 final size:59
Alignment explanation
Indices: 9293--9418 Score: 159
Period size: 58 Copynumber: 2.1 Consensus size: 59
9283 TTTTACAAAA
* * * * *
9293 GGACATTTTCCCACTTGAATTTTTATTTTGGAA-CTTGT-AGTCCTTAAACTATCAAAATCG
1 GGACAATTTCCCACTTGAACTTTTAATTT-GAATCTT-TCA-CCCCTAAACTATCAAAATCG
9353 GGACAATTTCCC-CTTGAACTTTTAATTTGAATCTTTCACCCCTAAACTATCAAAATCG
1 GGACAATTTCCCACTTGAACTTTTAATTTGAATCTTTCACCCCTAAACTATCAAAATCG
9411 GGACAATT
1 GGACAATT
9419 GTACCCCGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
58 30 0.51
59 18 0.31
60 11 0.19
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (59 bp):
GGACAATTTCCCACTTGAACTTTTAATTTGAATCTTTCACCCCTAAACTATCAAAATCG
Found at i:9985 original size:35 final size:35
Alignment explanation
Indices: 9946--10055 Score: 93
Period size: 35 Copynumber: 3.1 Consensus size: 35
9936 TATTAAAGTA
9946 AATTTCTTTTATCTAATTTATCTCATATTAAACCT
1 AATTTCTTTTATCTAATTTATCTCATATTAAACCT
* * * *** *
9981 AATTTAATATTT-GCTCAA--AAAAACATATTAAA-GT
1 AATTT-CT-TTTATCT-AATTTATCTCATATTAAACCT
10015 AAATTTCTTTTATCTAATTTATCTCATATTAAACCT
1 -AATTTCTTTTATCTAATTTATCTCATATTAAACCT
10051 AATTT
1 AATTT
10056 AATATTTGCT
Statistics
Matches: 53, Mismatches: 14, Indels: 16
0.64 0.17 0.19
Matches are distributed among these distances:
33 5 0.09
34 4 0.08
35 35 0.66
36 4 0.08
37 5 0.09
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (35 bp):
AATTTCTTTTATCTAATTTATCTCATATTAAACCT
Found at i:10012 original size:70 final size:70
Alignment explanation
Indices: 9935--10074 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
9925 TTACTTGTAT
9935 ATATTAAAGTAAATTTCTTTTATCTAATTTATCTCATATTAAACCTAATTTAATATTTGCTCAAA
1 ATATTAAAGTAAATTTCTTTTATCTAATTTATCTCATATTAAACCTAATTTAATATTTGCTCAAA
10000 AAAAC
66 AAAAC
10005 ATATTAAAGTAAATTTCTTTTATCTAATTTATCTCATATTAAACCTAATTTAATATTTGCTCAAA
1 ATATTAAAGTAAATTTCTTTTATCTAATTTATCTCATATTAAACCTAATTTAATATTTGCTCAAA
10070 AAAAC
66 AAAAC
10075 CTAATTTATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (70 bp):
ATATTAAAGTAAATTTCTTTTATCTAATTTATCTCATATTAAACCTAATTTAATATTTGCTCAAA
AAAAC
Found at i:16253 original size:2 final size:2
Alignment explanation
Indices: 16246--16280 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
16236 ATTGTTATGT
*
16246 TA TA TA TA TA TA TA TC TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
16281 AAAGTACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16611 original size:47 final size:48
Alignment explanation
Indices: 16549--16649 Score: 195
Period size: 47 Copynumber: 2.1 Consensus size: 48
16539 AATCATCCAC
16549 TGGAATGACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCT
1 TGGAATGACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCT
16597 TGGAA-GACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCT
1 TGGAATGACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCT
16644 TGGAAT
1 TGGAAT
16650 CCTCTTTCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 47 0.90
48 5 0.10
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.27
Consensus pattern (48 bp):
TGGAATGACAGAATTAGGTCTCGAGGTAAACATAAAAGTTGTAGATCT
Found at i:17152 original size:21 final size:22
Alignment explanation
Indices: 17126--17232 Score: 110
Period size: 23 Copynumber: 4.9 Consensus size: 22
17116 TCTCACAGAG
*
17126 AGGTTATCAAAA-ATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
17147 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
17168 AGGTTTATTAAAATTTCATAGGA
1 AGG-TTATCAAAATTTCATAGGA
** * **
17191 ATATTTATTAAAATTTCATAGTT
1 A-GGTTATCAAAATTTCATAGGA
*
17214 AGGTTATCAAAGTTTCATA
1 AGGTTATCAAAATTTCATA
17233 TTTCATAGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
20 5 0.07
21 17 0.24
22 17 0.24
23 33 0.46
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:17236 original size:29 final size:29
Alignment explanation
Indices: 17203--17259 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
17193 ATTTATTAAA
* ** *
17203 ATTTCATAGTTAGGTTATCAAAGTTTCAT
1 ATTTCATAGGTAAATTATCAAAATTTCAT
17232 ATTTCATAGGTAAATTATCAAAATTTCA
1 ATTTCATAGGTAAATTATCAAAATTTCA
17260 CAAAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (29 bp):
ATTTCATAGGTAAATTATCAAAATTTCAT
Found at i:19806 original size:20 final size:20
Alignment explanation
Indices: 19778--19822 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
19768 TAAGGAAATG
*
19778 ACCCATTGAAAACCGG-TGTA
1 ACCCGTTGAAAACCGGAT-TA
*
19798 ACCCGTTGAAACCCGGATTA
1 ACCCGTTGAAAACCGGATTA
19818 ACCCG
1 ACCCG
19823 GTGACCCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (20 bp):
ACCCGTTGAAAACCGGATTA
Found at i:20492 original size:19 final size:19
Alignment explanation
Indices: 20467--20523 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 19
20457 GTAACTAAAT
20467 TATGAAATTTTGATAA-AC
1 TATGAAATTTTGATAACAC
20485 TCATGAAATTTTGATGACCACAC
1 T-ATGAAATTTTGAT-A--ACAC
20508 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
20524 TTGATAACCT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.03
19 14 0.41
20 1 0.03
21 1 0.03
22 14 0.41
23 3 0.09
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (19 bp):
TATGAAATTTTGATAACAC
Found at i:20607 original size:22 final size:21
Alignment explanation
Indices: 20557--20767 Score: 146
Period size: 22 Copynumber: 9.8 Consensus size: 21
20547 TTTGATAAAG
*
20557 CTCATTATGAAATTTTG-ATAC
1 CTCACTATGAAATTTTGTA-AC
* *
20578 CTCCCTATGTAATTTTAGTAAC
1 CTCACTATGAAATTTT-GTAAC
20600 CTCACTATGAAATTTTGATAAC
1 CTCACTATGAAATTTTG-TAAC
* * * *
20622 CACCCTACGAAATTTTAATAAC
1 CTCACTATGAAATTTT-GTAAC
* *
20644 CACATTATGAAATTTTGGT--C
1 CTCACTATGAAATTTT-GTAAC
20664 CTCACTATGAAATTTTGATAAC
1 CTCACTATGAAATTTTG-TAAC
*
20686 CTCA-TATGAAACTTTGATAAC
1 CTCACTATGAAATTTTG-TAAC
* * *
20707 CTCCCTATGTAATTTTATTAAC
1 CTCACTATGAAATTTT-GTAAC
*
20729 CTCGCTAT-ATAATTTTGATAAC
1 CTCACTATGA-AATTTTG-TAAC
*
20751 CACA-TAATGAAATTTTG
1 CTCACT-ATGAAATTTTG
20768 ATAAGCTTCC
Statistics
Matches: 151, Mismatches: 26, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.01
20 16 0.11
21 34 0.23
22 98 0.65
23 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (21 bp):
CTCACTATGAAATTTTGTAAC
Found at i:20750 original size:107 final size:107
Alignment explanation
Indices: 20557--20767 Score: 259
Period size: 107 Copynumber: 2.0 Consensus size: 107
20547 TTTGATAAAG
* * * *
20557 CTCATTATGAAATTTTGATACCTCCCTATGTAATTTTAGTAACCTCACTATGAAATTTTGATAAC
1 CTCACTATGAAATTTTGATACCTCCATATGAAATTTGAGTAACCTCACTATGAAATTTTGATAAC
*
20622 CACCCTACGAAATTTTAATAACCACATTATGAAATTTTGGTC
66 CACCCTACGAAATTTTAATAACCACATAATGAAATTTTGGTC
* *
20664 CTCACTATGAAATTTTGATAACCT-CATATGAAACTTTGA-TAACCTCCCTATGTAATTTT-ATT
1 CTCACTATGAAATTTTGAT-ACCTCCATATGAAA-TTTGAGTAACCTCACTATGAAATTTTGA-T
* * * *
20726 AACCTCGCTA-TATAATTTTGATAACCACATAATGAAATTTTG
63 AACCACCCTACGA-AATTTTAATAACCACATAATGAAATTTTG
20768 ATAAGCTTCC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
106 2 0.02
107 79 0.89
108 8 0.09
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (107 bp):
CTCACTATGAAATTTTGATACCTCCATATGAAATTTGAGTAACCTCACTATGAAATTTTGATAAC
CACCCTACGAAATTTTAATAACCACATAATGAAATTTTGGTC
Found at i:21508 original size:22 final size:22
Alignment explanation
Indices: 21483--21606 Score: 96
Period size: 22 Copynumber: 5.7 Consensus size: 22
21473 TAATCTCACA
*
21483 ATGAAATTTTGATAAGCACAAT
1 ATGAAATTTTGATAAGCACATT
* *
21505 ATGAAATTTT-A-ATG-ACCTT
1 ATGAAATTTTGATAAGCACATT
* * *
21524 CCATCAAATTTTTG-TAACCATATT
1 --ATGAAA-TTTTGATAAGCACATT
21548 ATGAAATTTTGATAAGCACATT
1 ATGAAATTTTGATAAGCACATT
* * *
21570 ATGAAATTTTGGT-GGCCACACT
1 ATGAAATTTTGATAAG-CACATT
21592 ATGAAATTTTGATAA
1 ATGAAATTTTGATAA
21607 TCTGTAAAGT
Statistics
Matches: 77, Mismatches: 16, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.04
20 2 0.03
21 12 0.16
22 56 0.73
23 1 0.01
24 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAAGCACATT
Found at i:21959 original size:22 final size:22
Alignment explanation
Indices: 21928--21976 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
21918 ATTTATTTTT
* * *
21928 AAAATGAAATTATATTTTGTAG
1 AAAATAAAATTATATTTTATAA
21950 AAAATAAAATTATATTTTATAA
1 AAAATAAAATTATATTTTATAA
21972 AAAAT
1 AAAAT
21977 TAAGTTGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (22 bp):
AAAATAAAATTATATTTTATAA
Done.