Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023312.1 Corchorus olitorius cultivar O-4 contig23345, 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: 41166
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:2655 original size:24 final size:24
Alignment explanation
Indices: 2627--2672 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2617 GAAAAGCCAA
*
2627 ATACTGAGCATACAGCAGTTTGAG
1 ATACTGAGCATACAACAGTTTGAG
2651 ATACTGAGCATACAACAGTTTG
1 ATACTGAGCATACAACAGTTTG
2673 GGGATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (24 bp):
ATACTGAGCATACAACAGTTTGAG
Found at i:5280 original size:3 final size:3
Alignment explanation
Indices: 5272--5319 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5262 ATATATATAG
5272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5320 GGATTAAGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5945 original size:32 final size:32
Alignment explanation
Indices: 5904--5984 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
5894 AGTTGGTTTT
5904 TGAGATGAGTGATATCTCTGAGAGATGGTCTG
1 TGAGATGAGTGATATCTCTGAGAGATGGTCTG
* *
5936 TGAGATGAGTGATATCACTGAGAGATGGTTTG
1 TGAGATGAGTGATATCTCTGAGAGATGGTCTG
*
5968 TAAGATGAGTGATATCT
1 TGAGATGAGTGATATCT
5985 GTTTAAAGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.28, C:0.07, G:0.32, T:0.32
Consensus pattern (32 bp):
TGAGATGAGTGATATCTCTGAGAGATGGTCTG
Found at i:7203 original size:18 final size:20
Alignment explanation
Indices: 7161--7205 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
7151 AGATGGAATT
7161 TTTAATAATAATTATTCTGA
1 TTTAATAATAATTATTCTGA
*
7181 --AAATAATAATTATT-T-A
1 TTTAATAATAATTATTCTGA
7197 TTTAATAAT
1 TTTAATAAT
7206 TAATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
16 1 0.05
17 1 0.05
18 19 0.90
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAATAATAATTATTCTGA
Found at i:12508 original size:105 final size:105
Alignment explanation
Indices: 12327--12578 Score: 373
Period size: 107 Copynumber: 2.4 Consensus size: 105
12317 TTTTCTAACA
* ** * *
12327 CTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTGAATTTATTTATATATTTTATTTC
1 CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTATTTATATATTTTATTTA
*
12392 TAAAACCCTATAACAAT-ATTATTAATTATGGAATTTACC
66 TAAAACCCTATAACAATAATTATTAATTATGAAATTTACC
* *
12431 CTTAAAATAAATATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTT-TGTATTTTATT
1 CTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTA-TTTATATATTTTATT
*
12495 TATAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACC
64 TATAAAACCCTATAACAAT-AATTATTAATTATGAAATTTACC
12538 CTTAAAATAAAAATAAAATTTTAATTTCGGGCTAAACTTAG
1 CTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAG
12579 GTTCTGTTTG
Statistics
Matches: 133, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
104 23 0.17
105 48 0.36
106 3 0.02
107 59 0.44
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (105 bp):
CTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTATTTATATATTTTATTTA
TAAAACCCTATAACAATAATTATTAATTATGAAATTTACC
Found at i:26007 original size:17 final size:17
Alignment explanation
Indices: 25963--26009 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
25953 AAACGGTCTA
25963 AACCGCCTAAACCGCAT
1 AACCGCCTAAACCGCAT
25980 AACCG-----ACCGCAT
1 AACCGCCTAAACCGCAT
25992 AACCGCCTAAACCGCAT
1 AACCGCCTAAACCGCAT
26009 A
1 A
26010 TTCAGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 12 0.48
17 13 0.52
ACGTcount: A:0.36, C:0.40, G:0.13, T:0.11
Consensus pattern (17 bp):
AACCGCCTAAACCGCAT
Found at i:26813 original size:11 final size:11
Alignment explanation
Indices: 26797--26821 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26787 AACTACAAAG
26797 AGAAAATAAAA
1 AGAAAATAAAA
26808 AGAAAATAAAA
1 AGAAAATAAAA
26819 AGA
1 AGA
26822 TTTCCATGAC
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:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (11 bp):
AGAAAATAAAA
Found at i:29092 original size:35 final size:35
Alignment explanation
Indices: 29052--29127 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
29042 AGTTTGTTTA
*
29052 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCATTTATTGTTCATTTAAG
*
29087 TGTTCACGAACAGGCTCATTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCATTTATTGTTCATTTAAG
29122 TGTTCA
1 TGTTCA
29128 TTTATATAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCATTTATTGTTCATTTAAG
Found at i:29237 original size:17 final size:17
Alignment explanation
Indices: 29153--29284 Score: 66
Period size: 17 Copynumber: 7.8 Consensus size: 17
29143 AACGTTCATT
*
29153 TATTATATAATTATTTATA
1 TATTATATAA-TA-TAATA
*
29172 TATTA-ATAATA-ATATG
1 TATTATATAATATA-ATA
29188 TATTAT-TAATA-AA-A
1 TATTATATAATATAATA
*
29202 -ATTATA-AAAATAATAA
1 TATTATATAATATAAT-A
*
29218 TATTATATAATCTAATA
1 TATTATATAATATAATA
* *
29235 TATTTAAATTAAAATTTAAT-
1 TA-TT--A-TATAATATAATA
29255 TATTATATAATAT-ATA
1 TATTATATAATATAATA
29271 TAATTATATAATAT
1 T-ATTATATAATAT
29285 TTTATTCGTT
Statistics
Matches: 89, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
13 8 0.09
14 2 0.02
15 3 0.03
16 21 0.24
17 24 0.27
18 12 0.13
19 7 0.08
20 3 0.03
21 9 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
TATTATATAATATAATA
Found at i:29350 original size:18 final size:18
Alignment explanation
Indices: 29323--29357 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29313 AATTATTACA
29323 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
29341 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
29358 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:29491 original size:35 final size:35
Alignment explanation
Indices: 29451--29549 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 35
29441 GAACGAGCTT
*
29451 CGAACACTCTAAAT-TTTAAACGAGCCGAGCTCGAA
1 CGAACAC-CAAAATATTTAAACGAGCCGAGCTCGAA
29486 CGAACACCAAAATATTTAAACGAACACGAGCCGAGCTCGAA
1 CGAACACCAAAATATTT-----AA-ACGAGCCGAGCTCGAA
29527 CGAACACCAAAATATTTAAACGA
1 CGAACACCAAAATATTTAAACGA
29550 ACACGAGCCG
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
34 5 0.09
35 14 0.25
36 2 0.04
40 2 0.04
41 33 0.59
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.16
Consensus pattern (35 bp):
CGAACACCAAAATATTTAAACGAGCCGAGCTCGAA
Found at i:29509 original size:20 final size:20
Alignment explanation
Indices: 29484--29553 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
29474 GCCGAGCTCG
29484 AACGAACACCAAAATATTTA
1 AACGAACACCAAAATATTTA
* **** * **
29504 AACGAACACGAGCCGAGCTCG
1 AACGAACACCAAAATA-TTTA
29525 AACGAACACCAAAATATTTA
1 AACGAACACCAAAATATTTA
29545 AACGAACAC
1 AACGAACAC
29554 GAGCCGAGCT
Statistics
Matches: 33, Mismatches: 16, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (20 bp):
AACGAACACCAAAATATTTA
Found at i:29522 original size:41 final size:41
Alignment explanation
Indices: 29470--29568 Score: 189
Period size: 41 Copynumber: 2.4 Consensus size: 41
29460 TAAATTTTAA
29470 ACGAGCCGAGCTCGAACGAACACCAAAATATTTAAACGAAC
1 ACGAGCCGAGCTCGAACGAACACCAAAATATTTAAACGAAC
29511 ACGAGCCGAGCTCGAACGAACACCAAAATATTTAAACGAAC
1 ACGAGCCGAGCTCGAACGAACACCAAAATATTTAAACGAAC
*
29552 ACGAGCCGAGCTTGAAC
1 ACGAGCCGAGCTCGAAC
29569 AAAGCAAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.41, C:0.27, G:0.19, T:0.12
Consensus pattern (41 bp):
ACGAGCCGAGCTCGAACGAACACCAAAATATTTAAACGAAC
Found at i:30579 original size:8 final size:8
Alignment explanation
Indices: 30566--30599 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
30556 GGATTAGTTT
30566 TAATATTA
1 TAATATTA
30574 TAATATTA
1 TAATATTA
30582 TAATATTA
1 TAATATTA
*
30590 TAATAATA
1 TAATATTA
30598 TA
1 TA
30600 TTTATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAATATTA
Found at i:30587 original size:16 final size:16
Alignment explanation
Indices: 30566--30612 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
30556 GGATTAGTTT
*
30566 TAATATTATAATATTA
1 TAATATTATAATAATA
30582 TAATATTATAATAATA
1 TAATATTATAATAATA
30598 T-AT-TTATATATAATA
1 TAATATTATA-ATAATA
30613 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 16 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATATTATAATAATA
Found at i:31407 original size:22 final size:22
Alignment explanation
Indices: 31379--31422 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31369 AGTTTACTAC
*
31379 TACATTATATATATATATATAT
1 TACATTATATAAATATATATAT
*
31401 TACATTATTTAAATATATATAT
1 TACATTATATAAATATATATAT
31423 ATATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TACATTATATAAATATATATAT
Found at i:31438 original size:2 final size:2
Alignment explanation
Indices: 31384--31430 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
31374 ACTACTACAT
* * *
31384 TA TA TA TA TA TA TA TA T- TA CA T- TA TT TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31424 TA TA TA T
1 TA TA TA T
31431 TTTATATACG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38686 original size:3 final size:3
Alignment explanation
Indices: 38674--38720 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
38664 TCGAACTCCG
38674 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38721 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41083 original size:2 final size:2
Alignment explanation
Indices: 41076--41113 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41066 CTCTTATAGA
41076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41114 GATTGAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.