Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023078.1 Corchorus olitorius cultivar O-4 contig23111, 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: 84218
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:7705 original size:58 final size:58
Alignment explanation
Indices: 7615--7731 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
7605 ACAATGTGAA
* *
7615 TTTTATTGAATATAATATAATTTTAGTTTATAATATTCTTGCATCATTTGGATTAACT
1 TTTTATTGAATATAATATAACTTTAATTTATAATATTCTTGCATCATTTGGATTAACT
*
7673 TTTTATTGAATATAATATAACTTTAATTTATAATATTCTTGCATCATTTGGGTTAACT
1 TTTTATTGAATATAATATAACTTTAATTTATAATATTCTTGCATCATTTGGATTAACT
7731 T
1 T
7732 CTCGAGTCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (58 bp):
TTTTATTGAATATAATATAACTTTAATTTATAATATTCTTGCATCATTTGGATTAACT
Found at i:7848 original size:32 final size:32
Alignment explanation
Indices: 7807--7904 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 32
7797 TACTTTTGTC
7807 TAATCAAATCAGGTTTGGCCGAGTTAAACGAG
1 TAATCAAATCAGGTTTGGCCGAGTTAAACGAG
* *** **
7839 TAATCAAATCAGGTTTGGCCG-TTTACTTTTGTC
1 TAATCAAATCAGGTTTGGCCGAGTTA--AACGAG
*
7872 TAATCAAATCAGGTTTGGCCGAGTTAGACGAG
1 TAATCAAATCAGGTTTGGCCGAGTTAAACGAG
7904 T
1 T
7905 TATCTGATTC
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.06
32 23 0.45
33 22 0.43
34 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (32 bp):
TAATCAAATCAGGTTTGGCCGAGTTAAACGAG
Found at i:7881 original size:33 final size:33
Alignment explanation
Indices: 7793--7892 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 33
7783 GGATTCGGGT
7793 CGTTTACTTTTGTCTAATCAAATCAGGTTTGGC
1 CGTTTACTTTTGTCTAATCAAATCAGGTTTGGC
* *** **
7826 CGAGTTA--AACGAGTAATCAAATCAGGTTTGGC
1 CG-TTTACTTTTGTCTAATCAAATCAGGTTTGGC
7858 CGTTTACTTTTGTCTAATCAAATCAGGTTTGGC
1 CGTTTACTTTTGTCTAATCAAATCAGGTTTGGC
7891 CG
1 CG
7893 AGTTAGACGA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.06
32 22 0.42
33 24 0.46
34 3 0.06
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (33 bp):
CGTTTACTTTTGTCTAATCAAATCAGGTTTGGC
Found at i:11305 original size:19 final size:19
Alignment explanation
Indices: 11281--11323 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
11271 AAACTATAAT
11281 TTATTCAATAATAATTATA
1 TTATTCAATAATAATTATA
11300 TTATTCAATAATAATTATA
1 TTATTCAATAATAATTATA
11319 TTATT
1 TTATT
11324 GTTATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTCAATAATAATTATA
Found at i:11320 original size:16 final size:16
Alignment explanation
Indices: 11276--11320 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
11266 ATTCTAAACT
11276 ATAATT-TATTCAATA
1 ATAATTATATTCAATA
11291 ATAATTATATTATTCAATA
1 ATAA-T-TA-TATTCAATA
11310 ATAATTATATT
1 ATAATTATATT
11321 ATTGTTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 3 0.12
18 1 0.04
19 13 0.50
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATTATATTCAATA
Found at i:11682 original size:25 final size:24
Alignment explanation
Indices: 11654--11710 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
11644 GTGGATTGTA
*
11654 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
11679 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
11703 AAA-AAATT
1 AAATAAATT
11711 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:16313 original size:23 final size:23
Alignment explanation
Indices: 16285--16331 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16275 CCATATGAAC
16285 TAACATAACATGCAGATTCCAAT
1 TAACATAACATGCAGATTCCAAT
16308 TAACATAACATGCAGATTCCAAT
1 TAACATAACATGCAGATTCCAAT
16331 T
1 T
16332 GAACTTGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (23 bp):
TAACATAACATGCAGATTCCAAT
Found at i:20231 original size:1 final size:1
Alignment explanation
Indices: 20227--20254 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
20217 TTTTTCTTGA
20227 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
20255 AGCAACTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39526 original size:37 final size:37
Alignment explanation
Indices: 39473--39551 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
39463 GGCATTTGGA
* *
39473 ATGTGGTAATCGTCTTAAATCTAAGGTGGTATATGGT
1 ATGTGGTAATCGTCTTAAATCTAAGGTAGTATATGAT
* * *
39510 ATGTGGTAATCTTCTTAAATTTAAGGTAGTATTTGAT
1 ATGTGGTAATCGTCTTAAATCTAAGGTAGTATATGAT
39547 ATGTG
1 ATGTG
39552 TGGTAGTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (37 bp):
ATGTGGTAATCGTCTTAAATCTAAGGTAGTATATGAT
Found at i:53346 original size:4 final size:4
Alignment explanation
Indices: 53337--53363 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53327 TGTAACATGT
53337 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
53364 TATTCCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:55541 original size:5 final size:5
Alignment explanation
Indices: 55531--55566 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
55521 GTAATTATAA
* *
55531 CTTTT CTTTT CTTTT CCTTT CTTTT CTTTT ATTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C
55567 CTCTCTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (5 bp):
CTTTT
Found at i:55556 original size:20 final size:22
Alignment explanation
Indices: 55531--55578 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 22
55521 GTAATTATAA
*
55531 CTTTTCTTTTCTTTTCCT-T-T
1 CTTTTCTTTTATTTTCCTCTCT
55551 CTTTTCTTTTATTTTCCTCTCT
1 CTTTTCTTTTATTTTCCTCTCT
55573 CTTTTC
1 CTTTTC
55579 CTCTCATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.68
21 1 0.04
22 7 0.28
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTTCTTTTATTTTCCTCTCT
Found at i:70205 original size:30 final size:31
Alignment explanation
Indices: 70171--70242 Score: 74
Period size: 36 Copynumber: 2.2 Consensus size: 31
70161 GAACCACCCG
70171 CTTTAGGA-GGAGGAGGTGGCGGAGCAGGAC
1 CTTTAGGACGGAGGAGGTGGCGGAGCAGGAC
* *
70201 CTTTAGCTGGAGCCGGTGGAGGTGGCGGGGCAGGAC
1 CTTTA---GGA--CGGAGGAGGTGGCGGAGCAGGAC
70237 CTTTAG
1 CTTTAG
70243 CTGGAACTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
30 5 0.15
33 4 0.12
36 25 0.74
ACGTcount: A:0.18, C:0.17, G:0.47, T:0.18
Consensus pattern (31 bp):
CTTTAGGACGGAGGAGGTGGCGGAGCAGGAC
Found at i:70234 original size:36 final size:36
Alignment explanation
Indices: 70182--70264 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
70172 TTTAGGAGGA
*
70182 GGAGGTGGCGGAGCAGGACCTTTAGCTGGAGCCGGT
1 GGAGGTGGCGGAGCAGGACCTTTAGCTGGAACCGGT
* *
70218 GGAGGTGGCGGGGCAGGACCTTTAGCTGGAACTGGT
1 GGAGGTGGCGGAGCAGGACCTTTAGCTGGAACCGGT
70254 GGAGGTGGCGG
1 GGAGGTGGCGG
70265 TGGTGGAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.16, C:0.17, G:0.51, T:0.17
Consensus pattern (36 bp):
GGAGGTGGCGGAGCAGGACCTTTAGCTGGAACCGGT
Found at i:74940 original size:3 final size:3
Alignment explanation
Indices: 74924--74983 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
74914 ATTGTGATTG
* * *
74924 TGA TGA TGGA -GA TGA TGA TGA TGA TGC TGG GGA TGA TGA TGA TGA
1 TGA TGA T-GA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
74969 TGG TGG TGA TGA TGA
1 TGA TGA TGA TGA TGA
74984 GGATAAAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.42, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:74942 original size:21 final size:21
Alignment explanation
Indices: 74903--74983 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
74893 AAAAAGACGG
74903 TGATGATGGAGATTG-TGATTG-
1 TGATGATGGAGA-TGATGA-TGA
74924 TGATGATGGAGATGATGATGA
1 TGATGATGGAGATGATGATGA
* *
74945 TGATGCTGGGGATGATGATGA
1 TGATGATGGAGATGATGATGA
* *
74966 TGATGGTGGTGATGATGA
1 TGATGATGGAGATGATGA
74984 GGATAAAATG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.07
21 50 0.93
ACGTcount: A:0.26, C:0.01, G:0.41, T:0.32
Consensus pattern (21 bp):
TGATGATGGAGATGATGATGA
Found at i:74958 original size:18 final size:19
Alignment explanation
Indices: 74937--74983 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
74927 TGATGGAGAT
*
74937 GATGATGATGATGCTGG-G
1 GATGATGATGATGATGGTG
74955 GATGATGATGATGATGGTG
1 GATGATGATGATGATGGTG
74974 G-TGATGATGA
1 GATGATGATGA
74984 GGATAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.43, T:0.30
Consensus pattern (19 bp):
GATGATGATGATGATGGTG
Found at i:77854 original size:25 final size:25
Alignment explanation
Indices: 77822--77871 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
77812 TTCTTTCTCT
77822 CTCTCTCTCGTCTTCTTCAACCTTC
1 CTCTCTCTCGTCTTCTTCAACCTTC
77847 CTCTCTCTCGTCTTCTTCAACCTTC
1 CTCTCTCTCGTCTTCTTCAACCTTC
77872 AGTCTCCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.44, G:0.04, T:0.44
Consensus pattern (25 bp):
CTCTCTCTCGTCTTCTTCAACCTTC
Found at i:78481 original size:19 final size:19
Alignment explanation
Indices: 78441--78481 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
78431 GAGAATTTTG
* *
78441 AAGGTTTATTCATTATTGT
1 AAGGTTTATTCATTAATAT
78460 AAGGTTTATTCATTAATAT
1 AAGGTTTATTCATTAATAT
78479 AAG
1 AAG
78482 TTTTGGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (19 bp):
AAGGTTTATTCATTAATAT
Found at i:78495 original size:21 final size:21
Alignment explanation
Indices: 78471--78511 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
78461 AGGTTTATTC
78471 ATTAATATAAGTTTTGGTGAT
1 ATTAATATAAGTTTTGGTGAT
*
78492 ATTAATGTAAGTTTTGGTGA
1 ATTAATATAAGTTTTGGTGA
78512 GAATTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (21 bp):
ATTAATATAAGTTTTGGTGAT
Found at i:80100 original size:16 final size:16
Alignment explanation
Indices: 80079--80112 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
80069 TTTACCTCTA
80079 AGCCAACGTTAAGTGT
1 AGCCAACGTTAAGTGT
80095 AGCCAACGTTAAGTGT
1 AGCCAACGTTAAGTGT
80111 AG
1 AG
80113 ACGTGGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (16 bp):
AGCCAACGTTAAGTGT
Done.