Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008313.1 Corchorus capsularis cultivar CVL-1 contig08334, 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: 38228
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:271 original size:15 final size:16
Alignment explanation
Indices: 239--272 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
229 AAAGAAGAAT
*
239 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
255 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
270 TAA
1 TAA
273 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:8814 original size:13 final size:13
Alignment explanation
Indices: 8796--8823 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8786 GGATTTTTTT
8796 AACACACATGCTG
1 AACACACATGCTG
8809 AACACACATGCTG
1 AACACACATGCTG
8822 AA
1 AA
8824 ATTCCCACAT
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:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (13 bp):
AACACACATGCTG
Found at i:14142 original size:11 final size:11
Alignment explanation
Indices: 14128--14169 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
14118 ATTCATAACA
14128 AATTTATAATT
1 AATTTATAATT
14139 AATTTATAATT
1 AATTTATAATT
14150 -ATTTGATAATTT
1 AATTT-ATAA-TT
14162 AATTTATA
1 AATTTATA
14170 TAGGAAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.14
11 15 0.54
12 5 0.18
13 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:14147 original size:22 final size:23
Alignment explanation
Indices: 14122--14169 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
14112 ATGTATATTC
14122 ATAACAAATTT-ATAA-TTAATTT
1 ATAA-AAATTTGATAATTTAATTT
**
14144 ATAATTATTTGATAATTTAATTT
1 ATAAAAATTTGATAATTTAATTT
14167 ATA
1 ATA
14170 TAGGAAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAAAAATTTGATAATTTAATTT
Found at i:14594 original size:33 final size:33
Alignment explanation
Indices: 14557--14620 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
14547 GTACATTACC
* *
14557 TTCCTAGATAAAATTCTATATTTACTTAACTCT
1 TTCCTAGATAAAAGTCTATATTTACTAAACTCT
14590 TTCCTAGATAAAAGTCTATATTTACTAAACT
1 TTCCTAGATAAAAGTCTATATTTACTAAACT
14621 AAGTTCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (33 bp):
TTCCTAGATAAAAGTCTATATTTACTAAACTCT
Found at i:15166 original size:16 final size:16
Alignment explanation
Indices: 15145--15177 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15135 ACCGGTGAAC
15145 AACTGTAACTATAACA
1 AACTGTAACTATAACA
15161 AACTGTAACTATAACA
1 AACTGTAACTATAACA
15177 A
1 A
15178 TTCGGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.06, T:0.24
Consensus pattern (16 bp):
AACTGTAACTATAACA
Found at i:22233 original size:2 final size:2
Alignment explanation
Indices: 22226--22251 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22216 GAAGCACAAC
22226 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
22252 ATTGGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27617 original size:19 final size:19
Alignment explanation
Indices: 27593--27630 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
27583 AGTAGAGTCT
27593 TAATTCAGAA-CAATTAAGA
1 TAATTCA-AAGCAATTAAGA
27612 TAATTCAAAGCAATTAAGA
1 TAATTCAAAGCAATTAAGA
27631 AAAGTATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
TAATTCAAAGCAATTAAGA
Found at i:27735 original size:37 final size:37
Alignment explanation
Indices: 27649--27789 Score: 151
Period size: 37 Copynumber: 3.7 Consensus size: 37
27639 CATAGTTGAG
*
27649 GACTTAATTCATAGAAATTAAGTAAAAACAGTTGTCAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAGCAG-T-T-AAAA
*
27689 GACTTAATTCATAAAAATTAAGTAAAAGCAGTTAAAA
1 GACTTAATTCATAGAAATTAAGTAAAAGCAGTTAAAA
** ** *
27726 GACTTAATTCAGGGAAATTAAGTAACTGCAG-TCAAA
1 GACTTAATTCATAGAAATTAAGTAAAAGCAGTTAAAA
*
27762 GTACTTAATTCA-AGGAAATCAAGTAAAA
1 G-ACTTAATTCATA-GAAATTAAGTAAAA
27790 ATAGACTGAC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
36 5 0.06
37 51 0.59
38 1 0.01
39 1 0.01
40 29 0.33
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (37 bp):
GACTTAATTCATAGAAATTAAGTAAAAGCAGTTAAAA
Found at i:27915 original size:36 final size:36
Alignment explanation
Indices: 27827--27974 Score: 149
Period size: 36 Copynumber: 4.2 Consensus size: 36
27817 AGAACATTAG
* * * *
27827 AAGACTGACTTAAATTCAAGGAAATTAAGAAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
* * *
27862 TAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
* *
27898 AAGATTGGCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
* * * * *
27932 AAGACTGACTTAGTTTCAAGTAAACTAGGTAGAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
27968 AAGACTG
1 AAGACTG
27975 CCTCAGTTTT
Statistics
Matches: 91, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
34 26 0.29
35 30 0.33
36 35 0.38
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
Found at i:27957 original size:70 final size:71
Alignment explanation
Indices: 27835--27971 Score: 215
Period size: 70 Copynumber: 1.9 Consensus size: 71
27825 AGAAGACTGA
*
27835 CTTAAATTCAAGGAAATTAAGAAAAGATAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAA
1 CTTAAATTCAAGGAAATTAAGAAAAGATAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAAAA
27900 GATTGG
66 GATTGG
* * *
27906 CTTAATTTCAAGGAAATTAAGTAAAA-A-AGACTGACTTAGTTTCAAGTAAACTAGGTAGAGAAA
1 CTTAAATTCAAGGAAATTAAG-AAAAGATAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAAA
27969 AGA
65 AGA
27972 CTGCCTCAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 36 0.59
71 21 0.34
72 4 0.07
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (71 bp):
CTTAAATTCAAGGAAATTAAGAAAAGATAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAAAA
GATTGG
Found at i:28039 original size:41 final size:42
Alignment explanation
Indices: 27987--28067 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 42
27977 TCAGTTTTAA
* *
27987 GAAAGGAAATTAGGTAAAGATAAGCACAGACTTGATTTCAAG
1 GAAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAG
*
28029 GAAA-GAAATTAGGTAAAGACCAGCACAGACTTAATTTCA
1 GAAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCA
28068 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (42 bp):
GAAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTTCAAG
Found at i:28131 original size:36 final size:36
Alignment explanation
Indices: 28050--28153 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
28040 GGTAAAGACC
*
28050 AGCACAGACTTAATTTCACAAGAATTAAGT-AAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
*
28085 AGCAAGGACTTAATTTCACAAGAATTAAGTAAAATT
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
28121 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
1 AGCAAAGACTTAATTTCACAAGAATTAAGTAAA
28154 GTCATCAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 28 0.43
36 37 0.57
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (36 bp):
AGCAAAGACTTAATTTCACAAGAATTAAGTAAAATT
Found at i:28242 original size:11 final size:11
Alignment explanation
Indices: 28226--28337 Score: 161
Period size: 11 Copynumber: 10.1 Consensus size: 11
28216 AAATTAGGCA
*
28226 AAAGAATACTG
1 AAAGAAGACTG
28237 AAAGAAGACTG
1 AAAGAAGACTG
28248 AAAAGAAGACTG
1 -AAAGAAGACTG
28260 AAAGAAGACTG
1 AAAGAAGACTG
28271 AAAGAAGACTG
1 AAAGAAGACTG
*
28282 AAAGGAGACTG
1 AAAGAAGACTG
*
28293 AAAGGAGACTG
1 AAAGAAGACTG
* *
28304 AAAGAAAACTA
1 AAAGAAGACTG
*
28315 AAAGAATACTG
1 AAAGAAGACTG
28326 AAAGAAGACTG
1 AAAGAAGACTG
28337 A
1 A
28338 CTTAATTTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
11 81 0.88
12 11 0.12
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.11
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:28415 original size:36 final size:36
Alignment explanation
Indices: 28330--28560 Score: 257
Period size: 36 Copynumber: 6.7 Consensus size: 36
28320 ATACTGAAAG
* * *
28330 AAGACTGACTTAATTTCAAGCAAATTAGGTAAA-AGA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGA-A
*
28366 AA-ACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* *
28401 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAGAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
*
28437 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* * * *
28472 TAGACTGG-ATAGTTTCAAGGAAACTAGGTAAAG-G
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
* *
28506 AAGACTGGCTTAA-TTCAAGGAAATTAAGT--A-AA
1 AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
*
28538 AAGACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
28561 GGAAATTAAG
Statistics
Matches: 170, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
32 19 0.11
33 3 0.02
34 43 0.25
35 39 0.23
36 66 0.39
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAACTAGGTAAAGAA
Found at i:28587 original size:37 final size:35
Alignment explanation
Indices: 28522--28593 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 35
28512 GGCTTAATTC
28522 AAGGAAATTAAGTAAAAAGACAGGCTTAATTTCAGGA
1 AAGGAAATTAAGTAAAAAGACA-GCTTAA-TTCAGGA
28559 AAGGAAATTAAGTAGAATAAAGA-A-CTTAATTCAGG
1 AAGGAAATTAAGT--AA-AAAGACAGCTTAATTCAGG
28594 GTAATTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
36 6 0.19
37 18 0.56
39 3 0.09
40 5 0.16
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.22
Consensus pattern (35 bp):
AAGGAAATTAAGTAAAAAGACAGCTTAATTCAGGA
Found at i:28601 original size:32 final size:32
Alignment explanation
Indices: 28564--28670 Score: 126
Period size: 32 Copynumber: 3.2 Consensus size: 32
28554 CAGGAAAGGA
28564 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
*
28596 AATTAAGTGAGGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-A-G--AATAAAGA-ACTTAATTCAGGGT
* * *
28632 AATTAAATAGAATAAAGAATTTAATTCAAGGT
1 AATTAAGTAGAATAAAGAACTTAATTCAGGGT
28664 AATTAAG
1 AATTAAG
28671 CGAAGTCAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
32 31 0.49
33 2 0.03
34 2 0.03
35 2 0.03
36 26 0.41
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.29
Consensus pattern (32 bp):
AATTAAGTAGAATAAAGAACTTAATTCAGGGT
Found at i:28614 original size:36 final size:35
Alignment explanation
Indices: 28574--28692 Score: 138
Period size: 36 Copynumber: 3.4 Consensus size: 35
28564 AATTAAGTAG
28574 AATAAAGAACTTAATTCAGGGTAATTAAGTGAGGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTGA-GTC
* *
28610 AATAAA-AGGCTTAATTCAGGGTAATTAAAT-AG--
1 AATAAAGA-ACTTAATTCAGGGTAATTAAGTGAGTC
* * *
28642 AATAAAGAATTTAATTCAAGGTAATTAAGCGAAGTC
1 AATAAAGAACTTAATTCAGGGTAATTAAGTG-AGTC
28678 AATAAAGAACTTAAT
1 AATAAAGAACTTAAT
28693 CTAAAAAGAG
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
32 23 0.33
33 1 0.01
34 3 0.04
35 2 0.03
36 40 0.58
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.28
Consensus pattern (35 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTGAGTC
Found at i:28691 original size:68 final size:68
Alignment explanation
Indices: 28564--28692 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 68
28554 CAGGAAAGGA
* * * * *
28564 AATTAAGTAGAATAAAGAACTTAATTCAGGGTAATTAAGTGAGGTCAATAAAAGGCTTAATTCAG
1 AATTAAATAGAATAAAGAACTTAATTCAAGGTAATTAAGCGAAGTCAATAAAAGACTTAATTCAG
28629 GGT
66 GGT
*
28632 AATTAAATAGAATAAAGAATTTAATTCAAGGTAATTAAGCGAAGTCAAT-AAAGAACTTAAT
1 AATTAAATAGAATAAAGAACTTAATTCAAGGTAATTAAGCGAAGTCAATAAAAG-ACTTAAT
28693 CTAAAAAGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 4 0.07
68 50 0.93
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (68 bp):
AATTAAATAGAATAAAGAACTTAATTCAAGGTAATTAAGCGAAGTCAATAAAAGACTTAATTCAG
GGT
Found at i:33287 original size:17 final size:17
Alignment explanation
Indices: 33265--33297 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33255 TTTTACCCTT
*
33265 ATTTGTTCATCTCATAA
1 ATTTGTTCAACTCATAA
33282 ATTTGTTCAACTCATA
1 ATTTGTTCAACTCATA
33298 TATGATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
ATTTGTTCAACTCATAA
Found at i:34078 original size:24 final size:25
Alignment explanation
Indices: 34033--34087 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
34023 CCAAACAGCA
* **
34033 TTAATTAGTTTTAACATTAGA-TAT
1 TTAATTAGTTTAAACAGGAGATTAT
34057 TTAATTAGTTTAAACAGGAGATTAT
1 TTAATTAGTTTAAACAGGAGATTAT
34082 TATAAT
1 T-TAAT
34088 CACCTTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 18 0.69
25 4 0.15
26 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (25 bp):
TTAATTAGTTTAAACAGGAGATTAT
Found at i:37882 original size:21 final size:22
Alignment explanation
Indices: 37858--37900 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
37848 ATATAGGGGA
37858 TTACTAAATACCGCCC-CCTTT
1 TTACTAAATACCGCCCTCCTTT
**
37879 TTACTAGGTACCGCCCTCCTTT
1 TTACTAAATACCGCCCTCCTTT
37901 GGATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (22 bp):
TTACTAAATACCGCCCTCCTTT
Done.