Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009192.1 Corchorus capsularis cultivar CVL-1 contig09213, 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: 65615
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11258 original size:15 final size:16
Alignment explanation
Indices: 11233--11262 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11223 GAACAATATA
11233 AGAAGAAGAAATTGAG
1 AGAAGAAGAAATTGAG
11249 AGAA-AAGAAATTGA
1 AGAAGAAGAAATTGA
11263 TGAAGAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (16 bp):
AGAAGAAGAAATTGAG
Found at i:35234 original size:13 final size:13
Alignment explanation
Indices: 35210--35248 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
35200 AAGTTAATAT
35210 CAGCACGAAACAAG
1 CAGCA-GAAACAAG
35224 CAGCAGAAACAAG
1 CAGCAGAAACAAG
35237 CAGCAGAAACAA
1 CAGCAGAAACAA
35249 CCATGTGGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.54, C:0.26, G:0.21, T:0.00
Consensus pattern (13 bp):
CAGCAGAAACAAG
Found at i:35761 original size:23 final size:23
Alignment explanation
Indices: 35731--35774 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35721 CACCAATAAA
* *
35731 AGATTTTTACCCCCTAGTCCTTT
1 AGATTTTTAACCCCTAATCCTTT
35754 AGATTTTTAACCCCTAATCCT
1 AGATTTTTAACCCCTAATCCT
35775 ATGAAGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.41
Consensus pattern (23 bp):
AGATTTTTAACCCCTAATCCTTT
Found at i:44475 original size:1 final size:1
Alignment explanation
Indices: 44469--44508 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
44459 AACGATTAGG
44469 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44509 GTTGTGTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:45009 original size:49 final size:49
Alignment explanation
Indices: 44956--45109 Score: 124
Period size: 49 Copynumber: 3.1 Consensus size: 49
44946 AAGATCTGGA
44956 GACTCAAACATTTGTAAATTCAAAAGACATCAAACAAACTGAATAAACT
1 GACTCAAACATTTGTAAATTCAAAAGACATCAAACAAACTGAATAAACT
** * * * * * *
45005 GACTC-AACAAACTGAACAAACTC--AA-ACATCCAA-GATCT-AA-AGATCT
1 GACTCAAAC-ATTTG--TAAATTCAAAAGACATCAAACAAACTGAATA-AACT
45051 GGAGACTCAAACATTTGTAAATTCAAAAGACATCAAACAAACTGAATAAACT
1 ---GACTCAAACATTTGTAAATTCAAAAGACATCAAACAAACTGAATAAACT
45103 GACTCAA
1 GACTCAA
45110 CAAACTGAAC
Statistics
Matches: 75, Mismatches: 16, Indels: 28
0.63 0.13 0.24
Matches are distributed among these distances:
45 1 0.01
46 5 0.07
47 8 0.11
48 10 0.13
49 27 0.36
50 10 0.13
51 8 0.11
52 5 0.07
53 1 0.01
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (49 bp):
GACTCAAACATTTGTAAATTCAAAAGACATCAAACAAACTGAATAAACT
Found at i:45038 original size:98 final size:98
Alignment explanation
Indices: 44869--45162 Score: 570
Period size: 98 Copynumber: 3.0 Consensus size: 98
44859 CCCCAATCTA
* *
44869 TTGTAAACTCAAAATACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
1 TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
44934 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
66 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
44967 TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
1 TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
45032 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
66 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
45065 TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
1 TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
45130 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
66 ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
45163 CTAAGATCTA
Statistics
Matches: 194, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 194 1.00
ACGTcount: A:0.49, C:0.22, G:0.10, T:0.19
Consensus pattern (98 bp):
TTGTAAATTCAAAAGACATCAAACAAACTGAATAAACTGACTCAACAAACTGAACAAACTCAAAC
ATCCAAGATCTAAAGATCTGGAGACTCAAACAT
Found at i:45157 original size:31 final size:31
Alignment explanation
Indices: 45122--45186 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
45112 AACTGAACAA
45122 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
*
45153 ACTCAAACATCTAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
45184 ACT
1 ACT
45187 GATAATCCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:45404 original size:111 final size:109
Alignment explanation
Indices: 45212--45432 Score: 415
Period size: 111 Copynumber: 2.0 Consensus size: 109
45202 TCAACAGATC
45212 TGTGGGACTTTATTCTAAAACTAAAGAAAAAAACAAGATACGAAATAAAAAAACCAAACCCCTCC
1 TGTGGGACTTTATTCTAAAACTAAAGAAAAAAACAAGATACGAAATAAAAAAACCAAACCCCTCC
45277 TCCCCCTTGACAGTAATAGCCAAGGAGGAGGAGCGAAAAGAGAA
66 TCCCCCTTGACAGTAATAGCCAAGGAGGAGGAGCGAAAAGAGAA
*
45321 TGTGGGACTTTATTCTAAAACTAAAGAAAAAAAACAAGATACGAAATAAAAAAAATCAAACCCCT
1 TGTGGGACTTTATTCTAAAACTAAAG-AAAAAAACAAGATACGAAAT-AAAAAAACCAAACCCCT
45386 CCTCCCCCTTGACAGTAATAGCCAAGGAGGAGGAGCGAAAAGAGAA
64 CCTCCCCCTTGACAGTAATAGCCAAGGAGGAGGAGCGAAAAGAGAA
45432 T
1 T
45433 AAAGCAAGAA
Statistics
Matches: 109, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
109 26 0.24
110 20 0.18
111 63 0.58
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.16
Consensus pattern (109 bp):
TGTGGGACTTTATTCTAAAACTAAAGAAAAAAACAAGATACGAAATAAAAAAACCAAACCCCTCC
TCCCCCTTGACAGTAATAGCCAAGGAGGAGGAGCGAAAAGAGAA
Found at i:57614 original size:70 final size:70
Alignment explanation
Indices: 57501--57634 Score: 268
Period size: 70 Copynumber: 1.9 Consensus size: 70
57491 GATCATTGAG
57501 CTTACTTATTCTACACTACACTGTTACCATCTCGCTCGTGAACCCAAAATACTTAATAATTATTA
1 CTTACTTATTCTACACTACACTGTTACCATCTCGCTCGTGAACCCAAAATACTTAATAATTATTA
57566 ATGAT
66 ATGAT
57571 CTTACTTATTCTACACTACACTGTTACCATCTCGCTCGTGAACCCAAAATACTTAATAATTATT
1 CTTACTTATTCTACACTACACTGTTACCATCTCGCTCGTGAACCCAAAATACTTAATAATTATT
57635 GAAACCCTGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (70 bp):
CTTACTTATTCTACACTACACTGTTACCATCTCGCTCGTGAACCCAAAATACTTAATAATTATTA
ATGAT
Found at i:59407 original size:2 final size:2
Alignment explanation
Indices: 59400--59424 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59390 ATAATACAGA
59400 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
59425 AGGAGAAAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.