Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016379.1 Corchorus capsularis cultivar CVL-1 contig16400, 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: 24073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1182 original size:31 final size:30
Alignment explanation
Indices: 1147--1242 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 30
1137 TAAACGGAGA
1147 GACTAAATTGATCGTTTTCCAATAGTAGAGG
1 GACTAAATTGATCGTTTTCC-ATAGTAGAGG
* * *
1178 GACTAAATTGA-CAGATTT-CATAATGGAGG
1 GACTAAATTGATC-GTTTTCCATAGTAGAGG
* * * *
1207 GACTAAAATGATCTTTTTCTGATAGTACAGG
1 GACTAAATTGATCGTTTTC-CATAGTAGAGG
1238 GACTA
1 GACTA
1243 TTTAGGTTCT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 21 0.41
30 3 0.06
31 27 0.53
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (30 bp):
GACTAAATTGATCGTTTTCCATAGTAGAGG
Found at i:1760 original size:14 final size:14
Alignment explanation
Indices: 1725--1760 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1715 AAAAGCTTGG
1725 TTTGCAAAAAGTGCT
1 TTTG-AAAAAGTGCT
1740 TTT-AAAAAGTGCT
1 TTTGAAAAAGTGCT
1753 TTTGAAAA
1 TTTGAAAA
1761 TAGCCGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.65
14 4 0.20
15 3 0.15
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (14 bp):
TTTGAAAAAGTGCT
Found at i:4413 original size:2 final size:2
Alignment explanation
Indices: 4406--4430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4396 AAACTATTTC
4406 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 A
4431 CAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10655 original size:20 final size:20
Alignment explanation
Indices: 10630--10669 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10620 AGTCTCTGTT
*
10630 TCGAGACCTTACGTATGCAA
1 TCGAGACCTTACGTACGCAA
10650 TCGAGACCTTACGTACGCAA
1 TCGAGACCTTACGTACGCAA
10670 CCGCCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGAGACCTTACGTACGCAA
Found at i:10764 original size:24 final size:24
Alignment explanation
Indices: 10732--10779 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
10722 GTTGAATCCG
10732 GATTAGTTGGATATCAAATGGAAA
1 GATTAGTTGGATATCAAATGGAAA
*
10756 GATTAGTTGGATATCGAATGGAAA
1 GATTAGTTGGATATCAAATGGAAA
10780 AAGAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (24 bp):
GATTAGTTGGATATCAAATGGAAA
Found at i:13237 original size:13 final size:13
Alignment explanation
Indices: 13219--13244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13209 AGGTTTGAAA
13219 TCTGATGATGATG
1 TCTGATGATGATG
13232 TCTGATGATGATG
1 TCTGATGATGATG
13245 AGAAAATTGA
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:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
TCTGATGATGATG
Found at i:18530 original size:78 final size:77
Alignment explanation
Indices: 18448--18686 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
18438 TTGTTTAGGT
*
18448 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
18508 AAT-TATTTT--A
65 ATTATATTTTACA
*
18518 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
18583 TTATATTTTACCA
66 TTATATTTTA-CA
*
18596 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
18661 TTATATTTTACAA
66 TTATATTTTAC-A
18674 TTTTACTATTTTA
1 TTTTACTATTTTA
18687 GTTAAAAAAC
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 88 0.57
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACA
Found at i:18531 original size:70 final size:70
Alignment explanation
Indices: 18448--18680 Score: 306
Period size: 70 Copynumber: 3.2 Consensus size: 70
18438 TTGTTTAGGT
*
18448 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATT
18512 ATTTTA
65 ATTTTA
*
18518 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAT-CTT-T-A-TA
*
18583 TTATATTTTACCA
62 AT-TATTTT---A
* * *
18596 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
*
18661 TTATA
66 TTTTA
*
18666 TTTTACAATTTTACT
1 TTTTACTATTTTACT
18681 ATTTTAGTTA
Statistics
Matches: 144, Mismatches: 10, Indels: 18
0.84 0.06 0.10
Matches are distributed among these distances:
70 64 0.44
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 53 0.37
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:20456 original size:50 final size:50
Alignment explanation
Indices: 20402--20558 Score: 129
Period size: 50 Copynumber: 3.0 Consensus size: 50
20392 TAAAATTTTT
20402 TCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA
1 TCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA
* * * * * * ** ***
20452 TCTAATATCTTTATAATTACTTATTTTACAAAAAAATTTGGA-TAT-ATAAAATTTTT
1 TCTAATA----TACAATT--TTATTCTACTAAAAACTCT--ATTTTCATTTAATTAAA
20508 TCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA
1 TCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA
20558 T
1 T
20559 TCAATGTTTT
Statistics
Matches: 75, Mismatches: 22, Indels: 20
0.64 0.19 0.17
Matches are distributed among these distances:
48 1 0.01
49 2 0.03
50 29 0.39
52 6 0.08
54 6 0.08
56 28 0.37
57 2 0.03
58 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.47
Consensus pattern (50 bp):
TCTAATATACAATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAA
Found at i:20515 original size:17 final size:18
Alignment explanation
Indices: 20495--20529 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20485 AAATTTGGAT
20495 ATATAAAATTTT-TTCTA
1 ATATAAAATTTTATTCTA
*
20512 ATATACAATTTTATTCTA
1 ATATAAAATTTTATTCTA
20530 CTAAAAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAAAATTTTATTCTA
Found at i:20524 original size:106 final size:109
Alignment explanation
Indices: 20300--20558 Score: 425
Period size: 106 Copynumber: 2.4 Consensus size: 109
20290 ACTATTATAG
* *
20300 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
20365 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
20414 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTAC-TTA-TT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
20477 TTACAAAAAAATTTGGATATA-TAAAATTTTTTCTAATATACAA
66 TTACAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
20520 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT
20559 TCAATGTTTT
Statistics
Matches: 142, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
106 61 0.43
107 22 0.15
108 3 0.02
109 30 0.21
110 3 0.02
111 2 0.01
114 21 0.15
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACAAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.