Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009728.1 Corchorus capsularis cultivar CVL-1 contig09749, 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: 80673
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:3174 original size:16 final size:16
Alignment explanation
Indices: 3114--3174 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
3104 ATTCTTCTCT
*
3114 CATTTTTA-TTAACTAC
1 CATTTTTACTT-ATTAC
*
3130 CATTTTTACTAATTATC
1 CATTTTTACTTATTA-C
3147 C-TCTTCTTACTTATTAC
1 CAT-TT-TTACTTATTAC
3164 CATTTTTACTT
1 CATTTTTACTT
3175 TTGCTACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 18 0.49
17 9 0.24
18 10 0.27
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (16 bp):
CATTTTTACTTATTAC
Found at i:3192 original size:24 final size:25
Alignment explanation
Indices: 3154--3200 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3144 ATCCTCTTCT
3154 TACTTATTACCATTTTTACTTTTGC
1 TACTTATTACCATTTTTACTTTTGC
*
3179 TACTT-TTATCATTTTTACTTTT
1 TACTTATTACCATTTTTACTTTT
3201 ACCATTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.62
Consensus pattern (25 bp):
TACTTATTACCATTTTTACTTTTGC
Found at i:3197 original size:15 final size:15
Alignment explanation
Indices: 3179--3209 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3169 TTACTTTTGC
*
3179 TACTTTTATCATTTT
1 TACTTTTACCATTTT
3194 TACTTTTACCATTTT
1 TACTTTTACCATTTT
3209 T
1 T
3210 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:3209 original size:24 final size:24
Alignment explanation
Indices: 3155--3209 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
3145 TCCTCTTCTT
* * *
3155 ACTTATTACCATTTTTACTTTTGCT
1 ACTT-TTATCATTTTTACTTTTACC
3180 ACTTTTATCATTTTTACTTTTACC
1 ACTTTTATCATTTTTACTTTTACC
*
3204 ATTTTT
1 ACTTTT
3210 CTTACTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.20, C:0.18, G:0.02, T:0.60
Consensus pattern (24 bp):
ACTTTTATCATTTTTACTTTTACC
Found at i:3267 original size:42 final size:42
Alignment explanation
Indices: 3219--3333 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
3209 TCTTACTCTT
*
3219 TTACTTAATACCATATTTCACTTAATACCATTCTTGACCTTC
1 TTACTTAATACCATATTTTACTTAATACCATTCTTGACCTTC
* * * *
3261 TTACTTAGTACCATATTTTACTTGATACCATTGTTGACCTTT
1 TTACTTAATACCATATTTTACTTAATACCATTCTTGACCTTC
*
3303 TTACTCAATACCAT-TTTTACTTAATACCATT
1 TTACTTAATACCATATTTTACTTAATACCATT
3334 TTTACTCTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 16 0.25
42 49 0.75
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (42 bp):
TTACTTAATACCATATTTTACTTAATACCATTCTTGACCTTC
Found at i:3336 original size:17 final size:16
Alignment explanation
Indices: 3300--3340 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
3290 ATTGTTGACC
3300 TTTTTACTCAATACCA
1 TTTTTACTCAATACCA
*
3316 TTTTTACTTAATACCA
1 TTTTTACTCAATACCA
3332 TTTTTACTC
1 TTTTTACTC
3341 TTTTGTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTTACTCAATACCA
Found at i:3902 original size:37 final size:35
Alignment explanation
Indices: 3809--3902 Score: 86
Period size: 37 Copynumber: 2.7 Consensus size: 35
3799 TACTCCCTTT
* *
3809 TTAATTATCAATTTACTGATTA-ATCACTCAACTC
1 TTAATTATCGATTTACAGATTACATCACTCAACTC
* **
3843 TTAATTA-CTGATTTGCTA-ATTACCATCACTTTGACTC
1 TTAATTATC-GATTTAC-AGATTA-CATCAC-TCAACTC
3880 TTAATTATCGATTTACAGATTAC
1 TTAATTATCGATTTACAGATTAC
3903 TATTTTTACC
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
33 1 0.02
34 16 0.34
36 7 0.15
37 22 0.47
38 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (35 bp):
TTAATTATCGATTTACAGATTACATCACTCAACTC
Found at i:4130 original size:55 final size:52
Alignment explanation
Indices: 4059--4166 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 52
4049 GATTAATCTT
* *
4059 TGATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATCA-CTTGACTC
4112 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATCACTTGACTC
1 TGATTAA--TCTTTTTACTTAATTACTGATTTACTGATTACTATCACTTGACTC
4166 T
1 T
4167 TAATTATCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 7 0.14
54 9 0.18
55 35 0.69
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (52 bp):
TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATCACTTGACTC
Found at i:4189 original size:55 final size:55
Alignment explanation
Indices: 4061--4179 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 55
4051 TTAATCTTTG
* * * *
4061 ATTAATC--TTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTCTG
1 ATTAATCAATTTTGACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTA
** *
4114 ATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATCA-CTTGACTCTTA
1 ATTAATCAATTTTGACTTAATTACTGATTTACTGATTACTATCACCTTGACTC-TA
4169 ATT-ATCAATTT
1 ATTAATCAATTT
4180 ACTGATTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
53 7 0.12
54 14 0.24
55 37 0.64
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (55 bp):
ATTAATCAATTTTGACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTA
Found at i:4211 original size:71 final size:71
Alignment explanation
Indices: 4111--4256 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
4101 TACCTTGACT
*
4111 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATCA-CTTGACTCTTAATTATC
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTTAACTATC
4175 AATTTA
66 AATTTA
*
4181 CTGATTAATCTCTTTTTTGCTTAATTACTGATTTACTGATTACTATCACCTTGACTCTTAACTAT
1 CTGATTAATCTC-TTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTTAACTAT
4246 CAATTTA
65 CAATTTA
4253 CTGA
1 CTGA
4257 CTAGTCTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
70 12 0.17
71 34 0.47
72 26 0.36
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.47
Consensus pattern (71 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATCACCTTGACTCTTAACTATC
AATTTA
Found at i:12869 original size:2 final size:2
Alignment explanation
Indices: 12862--12921 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
12852 TTCATGACAA
*
12862 CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12904 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
12922 ATATATATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12926 original size:2 final size:2
Alignment explanation
Indices: 12921--12962 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
12911 TCTCTCTCTC
* * *
12921 TA TA TA TA TA TA TA TA TA CA TA CA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12963 AGGAAATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:15605 original size:2 final size:2
Alignment explanation
Indices: 15598--15628 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15588 TGTCAAAGAA
15598 AT AT AT 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 AT AT AT A
15629 GCATGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23355 original size:18 final size:18
Alignment explanation
Indices: 23334--23371 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23324 ATATGTGAGG
*
23334 GTGATATTTTGGAATTTC
1 GTGATACTTTGGAATTTC
*
23352 GTGATACTTTGGAGTTTC
1 GTGATACTTTGGAATTTC
23370 GT
1 GT
23372 AATAATAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.47
Consensus pattern (18 bp):
GTGATACTTTGGAATTTC
Found at i:33357 original size:18 final size:18
Alignment explanation
Indices: 33317--33358 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33307 TCCTTGGGGA
* *
33317 GCTTCTTCTCGGCTCTGG
1 GCTTCTTCTCAGCTCGGG
33335 GCTTCTTCTCAGCT-GGG
1 GCTTCTTCTCAGCTCGGG
33352 GCCTTCT
1 G-CTTCT
33359 CGGCTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.02, C:0.33, G:0.26, T:0.38
Consensus pattern (18 bp):
GCTTCTTCTCAGCTCGGG
Found at i:41459 original size:21 final size:21
Alignment explanation
Indices: 41433--41482 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
41423 GAAGAGGAAA
* * *
41433 AAGAAGAAAGTGAGAACGAGG
1 AAGAAGAAAGTGAAAAAGACG
*
41454 AAGAAGGAAGTGAAAAAGACG
1 AAGAAGAAAGTGAAAAAGACG
41475 AAGAAGAA
1 AAGAAGAA
41483 GAACCTGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.34, T:0.04
Consensus pattern (21 bp):
AAGAAGAAAGTGAAAAAGACG
Found at i:44335 original size:17 final size:17
Alignment explanation
Indices: 44285--44335 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
44275 TAAAATAGTT
*
44285 TTCTTCTCCATTCAATC
1 TTCTTCTCCATTCAGTC
* *
44302 TTCTTCTCAAAAT-AGTC
1 TTCTTCTC-CATTCAGTC
44319 TTCTTCTCCATTCAGTC
1 TTCTTCTCCATTCAGTC
44336 ATCGATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.07
17 23 0.85
18 2 0.07
ACGTcount: A:0.20, C:0.31, G:0.04, T:0.45
Consensus pattern (17 bp):
TTCTTCTCCATTCAGTC
Found at i:47882 original size:18 final size:18
Alignment explanation
Indices: 47861--47896 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47851 GAAACCAAAT
47861 GGATTAAATAGAAAAAGA
1 GGATTAAATAGAAAAAGA
*
47879 GGATTAAATAGGAAAAGA
1 GGATTAAATAGAAAAAGA
47897 ATAGAGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (18 bp):
GGATTAAATAGAAAAAGA
Found at i:48981 original size:70 final size:73
Alignment explanation
Indices: 48842--48994 Score: 222
Period size: 70 Copynumber: 2.1 Consensus size: 73
48832 AACTCAGACT
* * * *
48842 TGTAAAGACTATCTTTTGAGAGGAACTCTTATGTAAAGATTGTTTTATATGTTTTTGTTATGTTA
1 TGTAAAGACCATCTTTTGAGAGGAACTCTGATGTAAAGA-TCTTTTATATGTTTCTGTTATGTTA
48907 TTTTGAATA
65 TTTTGAATA
48916 TGTAAAGACCATCTTTTGAGAGGAACTC-GA-GTAAAGA-CTTTTATATGTTTCTGTTATGTTAT
1 TGTAAAGACCATCTTTTGAGAGGAACTCTGATGTAAAGATCTTTTATATGTTTCTGTTATGTTAT
* *
48978 TTTGGATG
66 TTTGAATA
48986 TGTAAAGAC
1 TGTAAAGAC
48995 TCGTCTATTT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
70 38 0.52
72 7 0.10
73 1 0.01
74 27 0.37
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.44
Consensus pattern (73 bp):
TGTAAAGACCATCTTTTGAGAGGAACTCTGATGTAAAGATCTTTTATATGTTTCTGTTATGTTAT
TTTGAATA
Found at i:49059 original size:2 final size:2
Alignment explanation
Indices: 49054--49085 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49044 TTTAAAAAAA
49054 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
49086 GAAAGAACAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60705 original size:13 final size:15
Alignment explanation
Indices: 60689--60717 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60679 TTTTATAGTG
60689 TTTTT-TCTTTTTTT
1 TTTTTATCTTTTTTT
60703 TTTTTATCTTTTTTT
1 TTTTTATCTTTTTTT
60718 GTTTGATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTATCTTTTTTT
Found at i:65521 original size:77 final size:74
Alignment explanation
Indices: 65382--65531 Score: 221
Period size: 77 Copynumber: 2.0 Consensus size: 74
65372 AGCAAATAAC
*
65382 AGTTACTTAGGAAACTGTTCCACTTAAGAATATACAAACTTTAGCATTAAACATTTAAATTTAGT
1 AGTTACTTAGGAAACTGTTCCACTAAAGAATATACAAACTTTAGCATTAAACATTTAAATTTAGT
65447 AACGCCTAT
66 AACGCCTAT
* * *
65456 AGTTACTTAGGAAACTGTTCCACTAAGAGTCAATATATAGAA-TTTAGTATTAAACATTTAGATT
1 AGTTACTTAGGAAACTGTTCCACTAA-AG--AATATACA-AACTTTAGCATTAAACATTTAAATT
65520 TAGTAACGCCTA
62 TAGTAACGCCTA
65532 AAGGTCACAT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
74 25 0.37
75 2 0.03
77 39 0.57
78 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (74 bp):
AGTTACTTAGGAAACTGTTCCACTAAAGAATATACAAACTTTAGCATTAAACATTTAAATTTAGT
AACGCCTAT
Found at i:69097 original size:4 final size:4
Alignment explanation
Indices: 69090--69115 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
69080 CTTTCATACA
69090 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
69116 ATATTCTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:75612 original size:70 final size:69
Alignment explanation
Indices: 75477--75614 Score: 161
Period size: 70 Copynumber: 2.0 Consensus size: 69
75467 TGAGTAAATC
* * * ** *
75477 AAGTCATCCGTTTCTTACATTTCCCCGTTTTTAAGATTGAGTCTGATTTAATTATTGGAACTAAG
1 AAGTCATCCATTTCTTACATTTCCCCATTCTTAAGATTGAGTCTGATTTAACCATTGCAACTAAG
75542 AGTT
66 AGTT
* * * *
75546 AAGTTATCCATTTCTTTACATTTCCTCATTCTTAAGATTGGGTC-GAATTTAACCATTGCAATTA
1 AAGTCATCCATTTC-TTACATTTCCCCATTCTTAAGATTGAGTCTG-ATTTAACCATTGCAACTA
75610 AGAGT
64 AGAGT
75615 CTAACACTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
69 13 0.23
70 44 0.77
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (69 bp):
AAGTCATCCATTTCTTACATTTCCCCATTCTTAAGATTGAGTCTGATTTAACCATTGCAACTAAG
AGTT
Found at i:80337 original size:33 final size:33
Alignment explanation
Indices: 80271--80338 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
80261 CCTCCAATCA
* * **
80271 TTTCAACCAAAGGGCGATTTTTTTTTTTTTTTT
1 TTTCAACCAAAGGGCGAATTTTTATTTAATTTT
80304 TTTCAACCAAAGGGCGAATTTTTATTTAATTTT
1 TTTCAACCAAAGGGCGAATTTTTATTTAATTTT
80337 TT
1 TT
80339 CGTATAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (33 bp):
TTTCAACCAAAGGGCGAATTTTTATTTAATTTT
Done.