Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004970.1 Corchorus capsularis cultivar CVL-1 contig04988, 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: 8816
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30
Found at i:785 original size:25 final size:25
Alignment explanation
Indices: 736--785 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
726 TTAGTAGAAT
*
736 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
761 AATTGTAAAAGAATATATTT-TAAAA
1 AATTGTAAAAG--TATATTTCTAAAA
786 TTTCTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 5 0.23
27 6 0.27
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:1084 original size:133 final size:133
Alignment explanation
Indices: 938--1207 Score: 540
Period size: 133 Copynumber: 2.0 Consensus size: 133
928 AAAAGTATAT
938 TTAAAATTTTCTAATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGATATAGT
1 TTAAAATTTTCTAATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGATATAGT
1003 TATAAGAATGGGAGATTTTTTTTAATTATACAGCAAGTAATATATCAAGCAATATATCAAGTAAA
66 TATAAGAATGGGAGATTTTTTTTAATTATACAGCAAGTAATATATCAAGCAATATATCAAGTAAA
1068 AAA
131 AAA
1071 TTAAAATTTTCTAATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGATATAGT
1 TTAAAATTTTCTAATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGATATAGT
1136 TATAAGAATGGGAGATTTTTTTTAATTATACAGCAAGTAATATATCAAGCAATATATCAAGTAAA
66 TATAAGAATGGGAGATTTTTTTTAATTATACAGCAAGTAATATATCAAGCAATATATCAAGTAAA
1201 AAA
131 AAA
1204 TTAA
1 TTAA
1208 GTAATGGTAT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 137 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (133 bp):
TTAAAATTTTCTAATACATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATGATATAGT
TATAAGAATGGGAGATTTTTTTTAATTATACAGCAAGTAATATATCAAGCAATATATCAAGTAAA
AAA
Found at i:1570 original size:13 final size:13
Alignment explanation
Indices: 1552--1579 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1542 GCCAAGATTA
1552 TTGATTTGGCCTT
1 TTGATTTGGCCTT
1565 TTGATTTGGCCTT
1 TTGATTTGGCCTT
1578 TT
1 TT
1580 CTTTTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (13 bp):
TTGATTTGGCCTT
Found at i:3973 original size:16 final size:16
Alignment explanation
Indices: 3954--3986 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3944 AATCCGCCTG
3954 AACCCGAATCCGAAAA
1 AACCCGAATCCGAAAA
*
3970 AACCCGAATTCGAAAA
1 AACCCGAATCCGAAAA
3986 A
1 A
3987 GCTCAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (16 bp):
AACCCGAATCCGAAAA
Found at i:4221 original size:16 final size:15
Alignment explanation
Indices: 4202--4251 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
4192 GATCGAACCC
4202 AACCCGAACCCGAATT
1 AACCCG-ACCCGAATT
* *
4218 AACCTGACCCAAATT
1 AACCCGACCCGAATT
4233 CAACCCGACCCGAATT
1 -AACCCGACCCGAATT
4249 AAC
1 AAC
4252 TTGACTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.14
Consensus pattern (15 bp):
AACCCGACCCGAATT
Found at i:4232 original size:15 final size:16
Alignment explanation
Indices: 4209--4268 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 16
4199 CCCAACCCGA
*
4209 ACCCGAATT-AACCTG
1 ACCCAAATTCAACCTG
*
4224 ACCCAAATTCAACCCG
1 ACCCAAATTCAACCTG
* *
4240 ACCCGAATT-AACTTG
1 ACCCAAATTCAACCTG
*
4255 ACTCAAATTCAACC
1 ACCCAAATTCAACC
4269 CGATCTAACT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 19 0.54
16 16 0.46
ACGTcount: A:0.37, C:0.35, G:0.08, T:0.20
Consensus pattern (16 bp):
ACCCAAATTCAACCTG
Found at i:4247 original size:31 final size:31
Alignment explanation
Indices: 4201--4271 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
4191 AGATCGAACC
4201 CAACCCGAACCCGAATTAACCTGACCCAAATT
1 CAACCCG-ACCCGAATTAACCTGACCCAAATT
* *
4233 CAACCCGACCCGAATTAACTTGACTCAAATT
1 CAACCCGACCCGAATTAACCTGACCCAAATT
4264 CAACCCGA
1 CAACCCGA
4272 TCTAACTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
31 30 0.81
32 7 0.19
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (31 bp):
CAACCCGACCCGAATTAACCTGACCCAAATT
Found at i:8046 original size:54 final size:54
Alignment explanation
Indices: 7964--8143 Score: 258
Period size: 54 Copynumber: 3.4 Consensus size: 54
7954 CCCAATAATT
7964 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTATATC
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTATATC
* ** * *
8018 AAAGTCTTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCACCTCTCTCA-A
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTAT-ATC
* *
8072 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAATACAGAGGC-ATT-TACATC
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTATATC
*
8124 AAAGTCCTCAAGCACAAGGG
1 AAAGTCCTCAAACACAAGGG
8144 CATCCACATT
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
51 1 0.01
52 20 0.18
53 1 0.01
54 88 0.79
55 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (54 bp):
AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCAATTCTATATC
Found at i:8176 original size:30 final size:30
Alignment explanation
Indices: 8098--8199 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
8088 AGGGTATTCA
* * *
8098 TCCCTAAATACAGAGGCATTTACATCAAAG
1 TCCCTAAACACAGAGGCATCTACATTAAAG
* *
8128 T-CCTCAAGCACA-AGGGCATCCACATTAAAG
1 TCCCT-AAACACAGA-GGCATCTACATTAAAG
* *
8158 TCCCTAAACACAGAGGCATCTATACTAAAG
1 TCCCTAAACACAGAGGCATCTACATTAAAG
*
8188 TCCCCAAACACA
1 TCCCTAAACACA
8200 TATAGCACAG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.07
30 50 0.86
31 4 0.07
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCTACATTAAAG
Done.