Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014734.1 Corchorus olitorius cultivar O-4 contig14767, 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: 84735
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:8977 original size:39 final size:40
Alignment explanation
Indices: 8921--9001 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
8911 TTTAATTCCT
*
8921 ATGTAATATATATAATAAGTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
8961 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
9000 AT
1 AT
9002 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:9450 original size:202 final size:200
Alignment explanation
Indices: 9088--9494 Score: 751
Period size: 202 Copynumber: 2.0 Consensus size: 200
9078 TTCCTTAATA
9088 ATAAATAAATCGGATCTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
1 ATAAATAAATCGGATCTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
* *
9153 TTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAGTAAT
66 TTTAATAAATCAACCACTAATGTTCAAATAATTTTTTTTGGTATAGTTCTATATATAATAATAAT
9218 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
131 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
9283 CATTG
196 CATTG
9288 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC--TAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* * *
9353 AATTTAATAAATCAACCACTAATGTTCAAATACTTTTTTTTGGTATAGTTTTTTATATAATAATA
64 AATTTAATAAATCAACCACTAATGTTCAAATAATTTTTTTTGGTATAGTTCTATATATAATAATA
9418 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
129 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
9483 ACCATTG
194 ACCATTG
9490 ATAAA
1 ATAAA
9495 GTTATTAAGC
Statistics
Matches: 200, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
200 16 0.08
202 184 0.92
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (200 bp):
ATAAATAAATCGGATCTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTAA
TTTAATAAATCAACCACTAATGTTCAAATAATTTTTTTTGGTATAGTTCTATATATAATAATAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCAC
CATTG
Found at i:10054 original size:36 final size:36
Alignment explanation
Indices: 10007--10076 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
9997 GAGATTTTGG
* *
10007 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
* *
10043 AGAAATATGATAACCAAAATCACAGAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
10077 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:12375 original size:19 final size:21
Alignment explanation
Indices: 12351--12389 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
12341 TACTCCTCAA
12351 TAAATTGA-TAAA-ATGTTAC
1 TAAATTGATTAAAGATGTTAC
*
12370 TAAATTTATTAAAGATGTTA
1 TAAATTGATTAAAGATGTTA
12390 GGTTACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (21 bp):
TAAATTGATTAAAGATGTTAC
Found at i:14384 original size:32 final size:32
Alignment explanation
Indices: 14347--14416 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
14337 AGGTTATTAC
14347 TTATTTTCTTTCCTTAATATATTATTATTAAG
1 TTATTTTCTTTCCTTAATATATTATTATTAAG
14379 TTATTTTCTTTCCTTAATATATTATTATTAAG
1 TTATTTTCTTTCCTTAATATATTATTATTAAG
14411 TTATTT
1 TTATTT
14417 ATTTACTACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (32 bp):
TTATTTTCTTTCCTTAATATATTATTATTAAG
Found at i:42762 original size:26 final size:26
Alignment explanation
Indices: 42701--42806 Score: 149
Period size: 26 Copynumber: 3.8 Consensus size: 26
42691 ACCTCAATTT
*
42701 TTCAAGTAAAATAATATCAAAAATCTCAA
1 TTCAAGTAAAATAACATCAAAAA--TC-A
42730 TTTTTCAAGTAAAATAACATCAAAAATCA
1 ---TTCAAGTAAAATAACATCAAAAATCA
42759 TTCAAGTAAAATAACATCAAAAATCA
1 TTCAAGTAAAATAACATCAAAAATCA
42785 TTCAAGTAAAATAACATCAAAA
1 TTCAAGTAAAATAACATCAAAA
42807 GTAAAATAAC
Statistics
Matches: 73, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
26 48 0.66
29 1 0.01
30 2 0.03
32 22 0.30
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (26 bp):
TTCAAGTAAAATAACATCAAAAATCA
Found at i:42810 original size:17 final size:17
Alignment explanation
Indices: 42788--42823 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42778 AAAATCATTC
42788 AAGTAAAATAACATCAA
1 AAGTAAAATAACATCAA
42805 AAGTAAAATAACATCAA
1 AAGTAAAATAACATCAA
42822 AA
1 AA
42824 CTCATGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (17 bp):
AAGTAAAATAACATCAA
Found at i:60946 original size:3 final size:3
Alignment explanation
Indices: 60938--60999 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
60928 TATCTTATAT
* * *
60938 ATA ATA ATA ATA ATA CTA ATA ATA AT- ATA CA-A ATG ATG ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA AT-A ATA
60983 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
61000 TGAATAGAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 3 0.06
3 45 0.88
4 3 0.06
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:63780 original size:29 final size:29
Alignment explanation
Indices: 63710--63782 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
63700 GGTTGAGGGG
*
63710 GCAAAACATCTCAAAATTGAAGTTCATGGG
1 GCAAAACATC-CAAAATTGAAGTTCATGGA
* **
63740 GTAAAATGTCCAAAATTGAAGTTCATGGA
1 GCAAAACATCCAAAATTGAAGTTCATGGA
63769 GCAAAACATCCAAA
1 GCAAAACATCCAAA
63783 CGCTATAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (29 bp):
GCAAAACATCCAAAATTGAAGTTCATGGA
Found at i:67790 original size:2 final size:2
Alignment explanation
Indices: 67783--67824 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
67773 GAAGTAGATT
67783 TA TA TA TA TA TA -A TA -A TGA TGA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A T-A TA TA TA TA TA TA TA TA TA TA
67825 CAAGAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 30 0.81
3 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:67796 original size:26 final size:28
Alignment explanation
Indices: 67767--67822 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
67757 TATAAGTTAT
*
67767 TAATAA-GAAG-TAGATTTATATATATA
1 TAATAATGAAGATAGATATATATATATA
* *
67793 TAATAATGATGATATATATATATATATA
1 TAATAATGAAGATAGATATATATATATA
67821 TA
1 TA
67823 TACAAGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 3 0.12
28 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (28 bp):
TAATAATGAAGATAGATATATATATATA
Found at i:71800 original size:29 final size:29
Alignment explanation
Indices: 71765--71834 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
71755 ACACAAAACG
71765 GCCAAATAAGCCACTGAACTTTAATTGTA
1 GCCAAATAAGCCACTGAACTTTAATTGTA
71794 GCCAAATAAGCCACTGAACTTTAATTGTA
1 GCCAAATAAGCCACTGAACTTTAATTGTA
71823 GCCAAATAAGCC
1 GCCAAATAAGCC
71835 CTTTTCAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (29 bp):
GCCAAATAAGCCACTGAACTTTAATTGTA
Done.