Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010050.1 Corchorus capsularis cultivar CVL-1 contig10071, 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: 98392
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:355 original size:2 final size:2
Alignment explanation
Indices: 348--379 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
338 ATTAGTTACG
348 TA TA 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 TA TA
380 ATAAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21986 original size:14 final size:15
Alignment explanation
Indices: 21962--21990 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
21952 TACTATTACA
21962 AAAAAGTGAAAAACC
1 AAAAAGTGAAAAACC
21977 AAAAAG-GAAAAACC
1 AAAAAGTGAAAAACC
21991 CCTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.14, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAGTGAAAAACC
Found at i:24361 original size:21 final size:21
Alignment explanation
Indices: 24336--24375 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24326 ATTGAGTTTG
24336 TTTTTATTCAATTTTCCTTTT
1 TTTTTATTCAATTTTCCTTTT
* **
24357 TTTTTTTTGGATTTTCCTT
1 TTTTTATTCAATTTTCCTT
24376 CTTAATTAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTATTCAATTTTCCTTTT
Found at i:27912 original size:5 final size:5
Alignment explanation
Indices: 27871--27896 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
27861 AAAAAATCTG
27871 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
27897 CAATAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:30939 original size:21 final size:21
Alignment explanation
Indices: 30915--30954 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
30905 TCTTTTATGA
30915 AGAATAGTTATTCTTGGTTGG
1 AGAATAGTTATTCTTGGTTGG
30936 AGAATAGTTATTCTTGGTT
1 AGAATAGTTATTCTTGGTT
30955 TTTTACTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (21 bp):
AGAATAGTTATTCTTGGTTGG
Found at i:41321 original size:6 final size:6
Alignment explanation
Indices: 41310--41334 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41300 AGTAGAAAAT
41310 GAACCA GAACCA GAACCA GAACCA G
1 GAACCA GAACCA GAACCA GAACCA G
41335 TTAACAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.20, T:0.00
Consensus pattern (6 bp):
GAACCA
Found at i:41407 original size:18 final size:18
Alignment explanation
Indices: 41384--41419 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41374 AGGAAGCAGA
*
41384 TGTTGAACAATCTGAACC
1 TGTTGAACAATCAGAACC
*
41402 TGTTGAAGAATCAGAACC
1 TGTTGAACAATCAGAACC
41420 AGGACCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (18 bp):
TGTTGAACAATCAGAACC
Found at i:44719 original size:2 final size:2
Alignment explanation
Indices: 44712--44741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44702 CATGGAATTT
44712 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
44742 AATGGGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:44945 original size:14 final size:14
Alignment explanation
Indices: 44928--44957 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44918 AATTAAAATT
44928 AAAAGCAAAAAAAA
1 AAAAGCAAAAAAAA
*
44942 AAAAGGAAAAAAAA
1 AAAAGCAAAAAAAA
44956 AA
1 AA
44958 GAAAGAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAGCAAAAAAAA
Found at i:44952 original size:15 final size:17
Alignment explanation
Indices: 44934--44967 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
44924 AATTAAAAGC
44934 AAAAAAAAA-AAAG-GA
1 AAAAAAAAAGAAAGAGA
44949 AAAAAAAAAGAAAGAGA
1 AAAAAAAAAGAAAGAGA
44966 AA
1 AA
44968 CTACTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 4 0.24
17 4 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAGAGA
Found at i:44953 original size:16 final size:17
Alignment explanation
Indices: 44934--44967 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44924 AATTAAAAGC
44934 AAAAAAAAAAAAG-GAA
1 AAAAAAAAAAAAGAGAA
*
44950 AAAAAAAAGAAAGAGAA
1 AAAAAAAAAAAAGAGAA
44967 A
1 A
44968 CTACTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAGAA
Found at i:45314 original size:15 final size:15
Alignment explanation
Indices: 45294--45322 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45284 AGATTAGTGA
45294 TTTTAATTAATCTTT
1 TTTTAATTAATCTTT
45309 TTTTAATTAATCTT
1 TTTTAATTAATCTT
45323 AACATTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATTAATCTTT
Found at i:50418 original size:13 final size:14
Alignment explanation
Indices: 50395--50424 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
50385 AGAAAGTTAG
50395 TTATGATTCAAACT
1 TTATGATTCAAACT
50409 TTAT-ATTCAAACT
1 TTATGATTCAAACT
50422 TTA
1 TTA
50425 ATGTACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (14 bp):
TTATGATTCAAACT
Found at i:60044 original size:14 final size:14
Alignment explanation
Indices: 60027--60055 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60017 ATATTTTAAA
60027 AAAATTCTATATTG
1 AAAATTCTATATTG
60041 AAAATTCTATATTG
1 AAAATTCTATATTG
60055 A
1 A
60056 TTTTTGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAATTCTATATTG
Found at i:81486 original size:31 final size:30
Alignment explanation
Indices: 81438--81515 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
81428 GCTTATTGCT
* *
81438 CAAAAAGGCTCCTGAACTTACATAA-AACAGC
1 CAAATAGGCCCCTGAACTT-C-TAATAACAGC
**
81469 CAAATAGGCCCCTGAAC-TCTAATTGCAGC
1 CAAATAGGCCCCTGAACTTCTAATAACAGC
*
81498 CAAATAAGCCCCTGAACT
1 CAAATAGGCCCCTGAACT
81516 CTTTAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 3 0.08
29 21 0.52
30 1 0.03
31 15 0.38
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.18
Consensus pattern (30 bp):
CAAATAGGCCCCTGAACTTCTAATAACAGC
Found at i:83014 original size:21 final size:21
Alignment explanation
Indices: 82969--83015 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
82959 TTCAAAATAA
* *
82969 AATAAAAACTACCCATTTTAG
1 AATAAAAACTACCCACTATAG
82990 -ATAAAAACTACCCACTATAG
1 AATAAAAACTACCCACTATAG
83010 AATAAA
1 AATAAA
83016 TACAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.23
Consensus pattern (21 bp):
AATAAAAACTACCCACTATAG
Found at i:83722 original size:221 final size:214
Alignment explanation
Indices: 83335--83755 Score: 542
Period size: 221 Copynumber: 1.9 Consensus size: 214
83325 ATGTCAAACG
* *
83335 TCCAACCTAAAATCAATTGGCCATAGGTGGAGAGGCCCTTCATGTATATAAAGCACTCAGTCATG
1 TCCAACCTAAAATCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAAGCACACAGTCATG
* * * * *
83400 TTGAATATAATCAATGTGAGATATTACCATTTTAACACACCCCCTCACATGTAGTCCGGAATAAC
66 TCGAACATAACCAATGTGAGATATTACCACTTTAACACACCCCCTCACATGTAGCCCGGAATAAC
* * * * * * *
83465 ACTCGAAATAGAACGGACCTACACGTGGACAACCGAGTCTGGGGCGCAACAGGACAGACCT-AAG
131 ACTCGAAACAAAACGGACCTACACATGAACAACCGAGTCTGAGACACAACAGGACAGACCTGAA-
83529 CTCTGACACTATGTCACGCA
195 CTCTGACACTATGTCACGCA
*
83549 TCCAACCTAAAATCAATTGGTAATAGGTGGAGAGGCCCTTCATGTATATATAATATAAGGCACAC
1 TCCAACCTAAAATCAATTGGCAATAGGTGGAGAGGCCCTTCATG----TAT-ATA-AA-GCACAC
* * *
83614 AGTCATGTCGAACATAACCAATGT-AGAATATTACCACTTTAAGACGCCCCCTCACGTGTAGCCC
59 AGTCATGTCGAACATAACCAATGTGAG-ATATTACCACTTTAACACACCCCCTCACATGTAGCCC
* * *
83678 GGGATAACACTCGAAGCAAAAC-GAGTCTACACATGAACAACCGAGTCTGAGACACAACAGGACA
123 GGAATAACACTCGAAACAAAACGGA-CCTACACATGAACAACCGAGTCTGAGACACAACAGGACA
83742 GACCTGAACTCTGA
187 GACCTGAACTCTGA
83756 AACTGAAACC
Statistics
Matches: 176, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
214 42 0.24
218 3 0.02
219 3 0.02
220 6 0.03
221 120 0.68
222 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (214 bp):
TCCAACCTAAAATCAATTGGCAATAGGTGGAGAGGCCCTTCATGTATATAAAGCACACAGTCATG
TCGAACATAACCAATGTGAGATATTACCACTTTAACACACCCCCTCACATGTAGCCCGGAATAAC
ACTCGAAACAAAACGGACCTACACATGAACAACCGAGTCTGAGACACAACAGGACAGACCTGAAC
TCTGACACTATGTCACGCA
Found at i:85793 original size:15 final size:15
Alignment explanation
Indices: 85773--85802 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
85763 TTTAACATGG
85773 GGCTAATTGTTCAAC
1 GGCTAATTGTTCAAC
85788 GGCTAATTGTTCAAC
1 GGCTAATTGTTCAAC
85803 TTAGGGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
GGCTAATTGTTCAAC
Found at i:87188 original size:12 final size:12
Alignment explanation
Indices: 87158--87197 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
87148 AGATCCTTTT
*
87158 AGCCACCCTAACT
1 AGCCACCC-AACC
*
87171 AGCCACCCAGCC
1 AGCCACCCAACC
87183 AGCCACCCAACC
1 AGCCACCCAACC
87195 AGC
1 AGC
87198 GCACTTCTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.30, C:0.53, G:0.12, T:0.05
Consensus pattern (12 bp):
AGCCACCCAACC
Found at i:92901 original size:66 final size:65
Alignment explanation
Indices: 92825--92953 Score: 222
Period size: 66 Copynumber: 2.0 Consensus size: 65
92815 ACTCGAACAT
92825 TAGCCGGGTAATCACACCCAACCATTTGACTCCGTGATTAGTGCATGATCCTTTTGTTTAAAGAG
1 TAGCCGGGTAATCACACCCAACCATTTGACTCCGTGATTAGTGCATGAT-CTTTTGTTTAAAGAG
92890 C
65 C
* * *
92891 TAGCCGGGTAATTACACCCGACCATTTGACTCTGTGATTAGTGCATGATCTTTTGTTTAAAGA
1 TAGCCGGGTAATCACACCCAACCATTTGACTCCGTGATTAGTGCATGATCTTTTGTTTAAAGA
92954 ACGGGTTCGG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
65 14 0.23
66 46 0.77
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (65 bp):
TAGCCGGGTAATCACACCCAACCATTTGACTCCGTGATTAGTGCATGATCTTTTGTTTAAAGAGC
Found at i:95288 original size:107 final size:104
Alignment explanation
Indices: 95014--95274 Score: 336
Period size: 107 Copynumber: 2.5 Consensus size: 104
95004 ATAAAATTTT
* *
95014 AATTTTAATTTGGACTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAACCCTATAAAGA
1 AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAA-A
* *
95078 T--ATTATTAATTATGGAATTTACCCTTAAAATAAAAAAA
65 TAAATTATAAATTATGAAATTTACCCTTAAAATAAAAAAA
* * * *
95116 AA---TGATTTGGGGCTAAATTTAATGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA-A
* * *
95178 ATAAATTGTAAATTTTGAAATTTACTCTTAAAATAAAAATAA
64 ATAAATTATAAATTATGAAATTTACCCTTAAAATAAAAA-AA
95220 AATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
1 AATTTTAATTTG-GGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAA
95275 TTATATAATA
Statistics
Matches: 134, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
99 5 0.04
100 12 0.09
101 35 0.26
102 3 0.02
103 30 0.22
104 4 0.03
106 1 0.01
107 44 0.33
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAAT
AAATTATAAATTATGAAATTTACCCTTAAAATAAAAAAA
Found at i:97377 original size:32 final size:32
Alignment explanation
Indices: 97336--97408 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
97326 GATGACCCGT
97336 GCCGTCCCAAGAGGGCGGCTTACCGTGGCGAA
1 GCCGTCCCAAGAGGGCGGCTTACCGTGGCGAA
97368 GCCGTCCCAAGAGGGCGGCTTACCGTGGCGAA
1 GCCGTCCCAAGAGGGCGGCTTACCGTGGCGAA
*
97400 GCCGCCCCA
1 GCCGTCCCA
97409 CTGAGGAGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.18, C:0.36, G:0.36, T:0.11
Consensus pattern (32 bp):
GCCGTCCCAAGAGGGCGGCTTACCGTGGCGAA
Found at i:97592 original size:32 final size:33
Alignment explanation
Indices: 97551--97625 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
97541 AATTTGGTCT
*
97551 AGCCGCCCCACCG-GGGCGGCCTG-CCGTGGCGA
1 AGCCGCCCCA-CGAGGGCGGCCTGCCCATGGCGA
* * *
97583 AGCCGCCCCATGAGGGCGGCTTGCCCATGGTGA
1 AGCCGCCCCACGAGGGCGGCCTGCCCATGGCGA
97616 AGCCGCCCCA
1 AGCCGCCCCA
97626 GTGGGGAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 19 0.51
33 17 0.46
ACGTcount: A:0.13, C:0.41, G:0.36, T:0.09
Consensus pattern (33 bp):
AGCCGCCCCACGAGGGCGGCCTGCCCATGGCGA
Done.