Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008451.1 Corchorus capsularis cultivar CVL-1 contig08472, 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: 11849
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:425 original size:25 final size:24
Alignment explanation
Indices: 386--457 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 24
376 ACCGCTTACC
* *
386 TTTATATATAAATTAATATTATTAGT
1 TTTA-ATATATATTAATATAATTA-T
412 TTTAATATATATTACTATATAATTAT
1 TTTAATATATATTA--ATATAATTAT
*
438 ATT-ATATATATATAATATAA
1 TTTAATATATAT-TAATATAA
458 ATATATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 6 0.15
25 17 0.43
26 9 0.22
27 8 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (24 bp):
TTTAATATATATTAATATAATTAT
Found at i:1137 original size:8 final size:8
Alignment explanation
Indices: 1115--1171 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
1105 TTATTAGTTT
1115 TAATATATA
1 TAAT-TATA
*
1124 TTATTATA
1 TAATTATA
1132 TAATTATA
1 TAATTATA
1140 TATTATATATA
1 TA--AT-TATA
*
1151 TAATAATA
1 TAATTATA
*
1159 TAAATATA
1 TAATTATA
1167 TAATT
1 TAATT
1172 TATCTTAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 26 0.67
9 5 0.13
10 2 0.05
11 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TAATTATA
Found at i:1174 original size:29 final size:27
Alignment explanation
Indices: 1117--1168 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1107 ATTAGTTTTA
* * *
1117 ATATATATTATTATATAATTATATATT
1 ATATATATAATAATATAAATATATATT
1144 ATATATATAATAATATAAATATATA
1 ATATATATAATAATATAAATATATA
1169 ATTTATCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATATAATAATATAAATATATATT
Found at i:4811 original size:22 final size:22
Alignment explanation
Indices: 4786--4870 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
4776 AATCATATGG
4786 AGGTTATCAAAATTTCATTGAA
1 AGGTTATCAAAATTTCATTGAA
* * **
4808 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAATTTCATTGAA
* ** *
4831 AGGTTAACAGTATTTCATTGAG
1 AGGTTATCAAAATTTCATTGAA
*
4853 AGTTTATCAAAATTTCAT
1 AGGTTATCAAAATTTCAT
4871 AGGGTAATTA
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
22 29 0.62
23 18 0.38
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.41
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATTGAA
Found at i:4834 original size:23 final size:23
Alignment explanation
Indices: 4789--4894 Score: 78
Period size: 22 Copynumber: 4.7 Consensus size: 23
4779 CATATGGAGG
*
4789 TTATCAAAATTTCATTGAAAGGT
1 TTATCAAAATTTCATAGAAAGGT
* **
4812 TTATTAAAATTTCATAGTTAGG-
1 TTATCAAAATTTCATAGAAAGGT
* ** * *
4834 TTAACAGTATTTCATTGAGA-GT
1 TTATCAAAATTTCATAGAAAGGT
4856 TTATCAAAATTTCATAG---GGT
1 TTATCAAAATTTCATAGAAAGGT
4876 AATTATCAAAATTTCATAG
1 --TTATCAAAATTTCATAG
4895 GGTGGTTCTC
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.03
21 1 0.02
22 43 0.67
23 18 0.28
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTCATAGAAAGGT
Found at i:4881 original size:22 final size:22
Alignment explanation
Indices: 4856--4915 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
4846 CATTGAGAGT
4856 TTATCAAAATTTCATAGGGTAA
1 TTATCAAAATTTCATAGGGTAA
**
4878 TTATCAAAATTTCATAGGGTGG
1 TTATCAAAATTTCATAGGGTAA
*
4900 TTCTCAAAATTTCATA
1 TTATCAAAATTTCATA
4916 AAAATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAA
Found at i:4890 original size:44 final size:44
Alignment explanation
Indices: 4789--4915 Score: 121
Period size: 44 Copynumber: 2.9 Consensus size: 44
4779 CATATGGAGG
* * * *
4789 TTATCAAAATTTCATTGAAAGGTTTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATTGAGA-GTTTATCAAAATTTCATAGGTAGA
* **
4834 TTAACAGTATTTCATTGAGAGTTTATCAAAATTTCATAGGGTA-A
1 TTATCAAAATTTCATTGAGAGTTTATCAAAATTTCATA-GGTAGA
* * * * *
4878 TTATCAAAATTTCATAGGGTGGTTCTCAAAATTTCATA
1 TTATCAAAATTTCATTGAGAGTTTATCAAAATTTCATA
4916 AAAATATTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
44 47 0.71
45 19 0.29
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATTGAGAGTTTATCAAAATTTCATAGGTAGA
Found at i:5111 original size:11 final size:11
Alignment explanation
Indices: 5087--5121 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
5077 CAATGCCTCC
5087 TTCTTCTT-CT
1 TTCTTCTTCCT
5097 TTCTTCTTCCT
1 TTCTTCTTCCT
*
5108 TTCTTCTTCAT
1 TTCTTCTTCCT
5119 TTC
1 TTC
5122 AATTTCAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (11 bp):
TTCTTCTTCCT
Found at i:7273 original size:24 final size:24
Alignment explanation
Indices: 7246--7293 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
7236 TATCAAGCAT
*
7246 CTAAGAGGGGTCAATGAAGAAATA
1 CTAAGAGAGGTCAATGAAGAAATA
*
7270 CTAAGAGAGGTCTATGAAGAAATA
1 CTAAGAGAGGTCAATGAAGAAATA
7294 TTACTGGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.19
Consensus pattern (24 bp):
CTAAGAGAGGTCAATGAAGAAATA
Done.