Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012779.1 Corchorus olitorius cultivar O-4 contig12812, 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: 71264
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2030 original size:21 final size:21
Alignment explanation
Indices: 2004--2043 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1994 CAGCACTATG
2004 TGAAAAATTCCTTAATTCCAA
1 TGAAAAATTCCTTAATTCCAA
2025 TGAAAAATTCCTTAATTCC
1 TGAAAAATTCCTTAATTCC
2044 TTAATTCGGC
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:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (21 bp):
TGAAAAATTCCTTAATTCCAA
Found at i:9031 original size:41 final size:41
Alignment explanation
Indices: 8983--9089 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
8973 GGCTCGATCA
8983 CCCTTCCTCATCGGAAGGTGTTGTTTA-AGTTCACCAGTTTG
1 CCCTTCCTCATCGGAAGGTGTTGTTTACAGTTC-CCAGTTTG
* * * * *
9024 GCCTTCCTCATTGGAAGGTGTTGTCTACATTTCTCAGTTTG
1 CCCTTCCTCATCGGAAGGTGTTGTTTACAGTTCCCAGTTTG
*
9065 CCCTCCCTCATCAGG-AGGTGTTGTT
1 CCCTTCCTCATC-GGAAGGTGTTGTT
9090 CCTATTCCTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 49 0.89
42 6 0.11
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.37
Consensus pattern (41 bp):
CCCTTCCTCATCGGAAGGTGTTGTTTACAGTTCCCAGTTTG
Found at i:16458 original size:22 final size:22
Alignment explanation
Indices: 16432--16473 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
16422 CTTGTCTTGA
16432 CAATGTATTTATGGTTGTGAGC
1 CAATGTATTTATGGTTGTGAGC
*
16454 CAATGTTTTTATGGTTGTGA
1 CAATGTATTTATGGTTGTGA
16474 TGATTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.45
Consensus pattern (22 bp):
CAATGTATTTATGGTTGTGAGC
Found at i:18164 original size:21 final size:22
Alignment explanation
Indices: 18140--18187 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
18130 TCGCTGATTA
*
18140 TAATCTT-ATCTGTACAATGTT
1 TAATCTTGATCTATACAATGTT
18161 TAAT-TTGATCTATACAATGTT
1 TAATCTTGATCTATACAATGTT
18182 TAATCT
1 TAATCT
18188 CATAACTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (22 bp):
TAATCTTGATCTATACAATGTT
Found at i:20109 original size:2 final size:2
Alignment explanation
Indices: 20102--20130 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20092 TAGTAATCTC
20102 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 A
20131 ATGATATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31096 original size:48 final size:48
Alignment explanation
Indices: 31018--31114 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
31008 ACCTGGAGAT
*
31018 ATAGCAACTTTAATAAAATTCTTTCCTTTATGATACTTCTGATGCCTG
1 ATAGCAACTTTAATAAAATTATTTCCTTTATGATACTTCTGATGCCTG
*
31066 ATAGCAACTTT-ATGAAAATTATTTCTTTTATGATACTTCTGATGCCTG
1 ATAGCAACTTTAAT-AAAATTATTTCCTTTATGATACTTCTGATGCCTG
31114 A
1 A
31115 GGCAGTGTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 2 0.04
48 44 0.96
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.42
Consensus pattern (48 bp):
ATAGCAACTTTAATAAAATTATTTCCTTTATGATACTTCTGATGCCTG
Found at i:33080 original size:56 final size:56
Alignment explanation
Indices: 33014--33142 Score: 240
Period size: 56 Copynumber: 2.3 Consensus size: 56
33004 ACAGTACTAT
33014 AGTATTAACCATCGAGATTACATGCATCCCTTAGACATCAAACCCTAAACCAAATAA
1 AGTA-TAACCATCGAGATTACATGCATCCCTTAGACATCAAACCCTAAACCAAATAA
*
33071 AGTATAACCATCGAGATTACGTGCATCCCTTAGACATCAAACCCTAAACCAAATAA
1 AGTATAACCATCGAGATTACATGCATCCCTTAGACATCAAACCCTAAACCAAATAA
33127 AGTATAACCATCGAGA
1 AGTATAACCATCGAGA
33143 GTCACAGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
56 67 0.94
57 4 0.06
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (56 bp):
AGTATAACCATCGAGATTACATGCATCCCTTAGACATCAAACCCTAAACCAAATAA
Found at i:34964 original size:2 final size:2
Alignment explanation
Indices: 34957--35011 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
34947 AAAATTAAAA
*
34957 AG AG AG AG AG AG AG AG AG AA 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 AG AG AG AG AG
34999 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
35012 AGAAGAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:51294 original size:2 final size:2
Alignment explanation
Indices: 51287--51316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51277 TTTAAGCTCC
51287 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
51317 CTAAATATTA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56321 original size:2 final size:2
Alignment explanation
Indices: 56308--56338 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
56298 TTACACTAGG
*
56308 AT AT AT AC 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
56339 CTAAATAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58855 original size:26 final size:28
Alignment explanation
Indices: 58812--58864 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
58802 TTTTCCTAGA
*
58812 AGGCTTATTCAAATCCTTT-TTCTTTGT
1 AGGCTTATCCAAATCCTTTCTTCTTTGT
*
58839 AGGCTTCTCCAAA-CCTTTCTTCTTTG
1 AGGCTTATCCAAATCCTTTCTTCTTTG
58865 AAGTCTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.17, C:0.25, G:0.11, T:0.47
Consensus pattern (28 bp):
AGGCTTATCCAAATCCTTTCTTCTTTGT
Found at i:62324 original size:12 final size:12
Alignment explanation
Indices: 62307--62333 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62297 GCACACCCAA
62307 AGGAAATTAAAC
1 AGGAAATTAAAC
62319 AGGAAATTAAAC
1 AGGAAATTAAAC
62331 AGG
1 AGG
62334 GTCTCGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (12 bp):
AGGAAATTAAAC
Found at i:67197 original size:16 final size:17
Alignment explanation
Indices: 67176--67239 Score: 64
Period size: 16 Copynumber: 4.0 Consensus size: 17
67166 ACCTGAATCC
67176 GAACCCGAACCC-AAAA
1 GAACCCGAACCCGAAAA
67192 GAACCCGAACCCG-AAA
1 GAACCCGAACCCGAAAA
* *
67208 -AACTCAAACCCGAAAA
1 GAACCCGAACCCGAAAA
* *
67224 -AATCAGAACCCGAAAA
1 GAACCCGAACCCGAAAA
67240 ATCTAAAACC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 10 0.25
16 30 0.75
ACGTcount: A:0.52, C:0.33, G:0.12, T:0.03
Consensus pattern (17 bp):
GAACCCGAACCCGAAAA
Found at i:67219 original size:15 final size:15
Alignment explanation
Indices: 67199--67253 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 15
67189 AAAGAACCCG
67199 AACCCGAAAAACTCA
1 AACCCGAAAAACTCA
*
67214 AACCCGAAAAAATCA
1 AACCCGAAAAACTCA
*
67229 GAACCCGAAAAATCTAA
1 -AACCCGAAAAA-CTCA
67246 AACCCGAA
1 AACCCGAA
67254 CCCGAACCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 14 0.40
16 19 0.54
17 2 0.06
ACGTcount: A:0.55, C:0.29, G:0.09, T:0.07
Consensus pattern (15 bp):
AACCCGAAAAACTCA
Found at i:67240 original size:16 final size:16
Alignment explanation
Indices: 67198--67253 Score: 71
Period size: 15 Copynumber: 3.6 Consensus size: 16
67188 AAAAGAACCC
*
67198 GAACCCGAAAAACTCA
1 GAACCCGAAAAAATCA
67214 -AACCCGAAAAAATCA
1 GAACCCGAAAAAATCA
67229 GAACCCG-AAAAATCTA
1 GAACCCGAAAAAATC-A
*
67245 AAACCCGAA
1 GAACCCGAA
67254 CCCGAACCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 21 0.60
16 13 0.37
17 1 0.03
ACGTcount: A:0.54, C:0.29, G:0.11, T:0.07
Consensus pattern (16 bp):
GAACCCGAAAAAATCA
Found at i:68607 original size:11 final size:11
Alignment explanation
Indices: 68591--68615 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
68581 AAAAAATAAT
68591 AATTAATTATA
1 AATTAATTATA
68602 AATTAATTATA
1 AATTAATTATA
68613 AAT
1 AAT
68616 CAAACGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAATTATA
Found at i:71194 original size:2 final size:2
Alignment explanation
Indices: 71183--71217 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
71173 GAATTTCTTT
71183 TA TA -A 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 TA TA
71218 GGTTCTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.