Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014147.1 Corchorus capsularis cultivar CVL-1 contig14168, 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: 10437
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Found at i:823 original size:36 final size:34
Alignment explanation
Indices: 775--939 Score: 161
Period size: 36 Copynumber: 4.6 Consensus size: 34
765 CTAAAATAAG
775 TAACTGAAGAAAGACCACCCTAGATCATTCCGAAC
1 TAACTGAAGAAAGACCACCCT-GATCATTCCGAAC
*
810 TGAACTGAAGAAAGACCACCCTGGATCATTCCGATGC
1 T-AACTGAAGAAAGACCACCCT-GATCATTCCGA-AC
* * ** *
847 TAACTGAAGGAAGACCACCCTGAGTCA-ACTAAAA
1 TAACTGAAGAAAGACCACCCTGA-TCATTCCGAAC
* * *
881 TAAACTGAAGAACGACCACTCTTGATCATTCCGACTC
1 T-AACTGAAGAAAGACCAC-CCTGATCATTCCGA-AC
*
918 TAACTGAAGAAGGACCACCCTG
1 TAACTGAAGAAAGACCACCCTG
940 GGTCATTGAA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
34 1 0.01
35 26 0.25
36 75 0.71
37 3 0.03
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (34 bp):
TAACTGAAGAAAGACCACCCTGATCATTCCGAAC
Found at i:908 original size:71 final size:71
Alignment explanation
Indices: 812--944 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 71
802 TTCCGAACTG
812 AACTGAAGAAAGACCACCCTGGATCATTCCGA-TGCTAACTGAAGGAA-GACCACCCTGAGTCAA
1 AACTGAAGAAAGACCACCCTGGATCATTCCGACT-CTAACTGAA-GAAGGACCACCCTGAGTCAA
875 CTAAAATA
64 CTAAAATA
* * * *
883 AACTGAAGAACGACCACTCTTGATCATTCCGACTCTAACTGAAGAAGGACCACCCTGGGTCA
1 AACTGAAGAAAGACCACCCTGGATCATTCCGACTCTAACTGAAGAAGGACCACCCTGAGTCA
945 TTGAAGTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
70 3 0.05
71 52 0.93
72 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (71 bp):
AACTGAAGAAAGACCACCCTGGATCATTCCGACTCTAACTGAAGAAGGACCACCCTGAGTCAACT
AAAATA
Found at i:998 original size:29 final size:29
Alignment explanation
Indices: 965--1020 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
955 TTGAAGCATT
*
965 GATCACCTTGGACCAATTAACTAAAGAAA
1 GATCACCCTGGACCAATTAACTAAAGAAA
* * *
994 GATCACCCTGGATCAATTGACTTAAGA
1 GATCACCCTGGACCAATTAACTAAAGA
1021 TGGACCTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (29 bp):
GATCACCCTGGACCAATTAACTAAAGAAA
Found at i:1103 original size:100 final size:99
Alignment explanation
Indices: 987--1171 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 99
977 CCAATTAACT
* * * * *
987 AAAGAAAGATCACCCTGGATCAATTGACTTAAGATGGACCTCCCTGGGTCAGTTGAAATTCACTT
1 AAAGAAAGATCACCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCAC-T
*
1052 TTAGAGAGATCACCCTGGATCAACCGAAATTCACA
65 TTAGAAAGATCACCCTGGATCAACCGAAATTCACA
* *
1087 AAAGGAAGATCGCCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTT
1 AAAGAAAGATCACCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTT
1152 TAGAAAGATCACCCTGGATC
66 TAGAAAGATCACCCTGGATC
1172 GACTTGAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 21 0.27
100 56 0.73
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (99 bp):
AAAGAAAGATCACCCTGGATCAATTAACTAAAGATGGACCGCCCTGGGTCAATTGAAAGTCACTT
TAGAAAGATCACCCTGGATCAACCGAAATTCACA
Found at i:2309 original size:17 final size:19
Alignment explanation
Indices: 2289--2324 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2279 ACCCTAGGGC
2289 TTCTTTTT-TCT-TTTTTT
1 TTCTTTTTCTCTCTTTTTT
2306 TTCTTTTTCTCTCTTTTTT
1 TTCTTTTTCTCTCTTTTTT
2325 ATGCACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
TTCTTTTTCTCTCTTTTTT
Found at i:3103 original size:15 final size:16
Alignment explanation
Indices: 3083--3112 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3073 CCCCGAGTGC
3083 TTTTTCT-TTTTTTTT
1 TTTTTCTCTTTTTTTT
3098 TTTTTCTCTTTTTTT
1 TTTTTCTCTTTTTTT
3113 GGTCTCTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTCTCTTTTTTTT
Found at i:7962 original size:35 final size:36
Alignment explanation
Indices: 7916--8430 Score: 447
Period size: 35 Copynumber: 14.9 Consensus size: 36
7906 TTCTTACTAA
*
7916 ACTTAATTACCCTGAATTGAGTT-ACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTGA-TTATTGAACTC
*
7951 ACTTAATTACCCTGAATTAAGTT-ACTCATT-AACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTATTGAACTC
*
7986 ACTTAATTACCCCGAATTAAAGTTGATTATTG-ACTC
1 ACTTAATTACCCTGAATT-AAGTTGATTATTGAACTC
* *
8022 ACTTAATTACCCTGAATTAAGTTGATTATCGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* * * * *
8057 ACTTAATTACCCCGAATTAAATTGATTACTG-AGTT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* * * * *
8092 ACTT--TT----T---TTGAGGTAGATTACTG-AGTT
1 ACTTAATTACCCTGAATT-AAGTTGATTATTGAACTC
* * *
8119 ACTTAATTACCCTGAATTAAGTT-ACTAGCTGACCTGC
1 ACTTAATTACCCTGAATTAAGTTGATTA-TTGAACT-C
* * * * *
8156 -C-TAATTTCCCTAAATTGAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
*
8189 ACTTAATTACCCTGAATTAAGTAT-ATTACTG-ACTC
1 ACTTAATTACCCTGAATTAAGT-TGATTATTGAACTC
* * * *
8224 ACTTAATTAGCCAGAATTAAGTTGATTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* *
8259 ACTTAATTGCCCTGAATTAAGTTGATTACTG-ACTC
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* *
8294 ACTTAATTACCCTGACTTAAGTTGATTATTGAA-TT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* *
8329 ACTTAATTACCCTGAATTAAGTTGATTACTG-ACTT
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
* *
8364 ACTTAATTACCCTGAATTAAGTTGATTACTG-ACCC
1 ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
8399 ACTTAATTACCCTGAATTAAGTTGATTATTGA
1 ACTTAATTACCCTGAATTAAGTTGATTATTGA
8431 TTCACCTTTT
Statistics
Matches: 403, Mismatches: 47, Indels: 59
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.00
27 18 0.04
29 2 0.00
33 3 0.01
34 14 0.03
35 322 0.80
36 41 0.10
37 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTGATTATTGAACTC
Done.