Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021526.1 Corchorus olitorius cultivar O-4 contig21559, 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: 56412
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2516 original size:48 final size:47
Alignment explanation
Indices: 2440--2582 Score: 171
Period size: 49 Copynumber: 3.0 Consensus size: 47
2430 CGAGCGTGCC
* * *
2440 AATCAATTTTGTCAAAAAATTGATAAAAAGTGCGGTGAAAATTAAAA
1 AATCAATTTTGTCTAAAAATTGATAAAAAGTGCAGTGAAAAATAAAA
*
2487 AATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAA
1 AATCAATTTTGTC-TAAAAATTGATAAAAAG-TGC-AGTGAAAAATAAAA
** * *
2536 GTTCAATTTTGTAGTAAAAATTGATAAAAAGTGCAGTGAAAAGTAAA
1 AATCAATTTTGT-CTAAAAATTGATAAAAAGTGCAGTGAAAAATAAA
2583 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 16 0.20
48 26 0.32
49 38 0.46
50 2 0.02
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (47 bp):
AATCAATTTTGTCTAAAAATTGATAAAAAGTGCAGTGAAAAATAAAA
Found at i:3868 original size:9 final size:9
Alignment explanation
Indices: 3850--3889 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
3840 TTAATTCATT
3850 TAATTT-CA
1 TAATTTCCA
3858 TAATTTCCA
1 TAATTTCCA
*
3867 TAATTTCCT
1 TAATTTCCA
3876 TAATTTCC-
1 TAATTTCCA
3884 TAATTT
1 TAATTT
3890 GGGAGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 12 0.40
9 18 0.60
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTTCCA
Found at i:3870 original size:17 final size:17
Alignment explanation
Indices: 3850--3889 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3840 TTAATTCATT
3850 TAATTT-CATAATTTCC
1 TAATTTCCATAATTTCC
*
3866 ATAATTTCCTTAATTTCC
1 -TAATTTCCATAATTTCC
3884 TAATTT
1 TAATTT
3890 GGGAGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTTCCATAATTTCC
Found at i:10716 original size:5 final size:5
Alignment explanation
Indices: 10690--10728 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
10680 TAGTATATAG
10690 TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TAA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAA
10729 ATTTATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 2 0.07
4 8 0.27
5 20 0.67
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:10728 original size:10 final size:8
Alignment explanation
Indices: 10686--10722 Score: 56
Period size: 8 Copynumber: 4.4 Consensus size: 8
10676 TATATAGTAT
10686 ATAGTAAG
1 ATAGTAAG
10694 ATAGTAAG
1 ATAGTAAG
10702 ATAGTAAG
1 ATAGTAAG
10710 ATAAGATAAG
1 AT-AG-TAAG
10720 ATA
1 ATA
10723 AGATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 18 0.67
9 3 0.11
10 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (8 bp):
ATAGTAAG
Found at i:11140 original size:121 final size:126
Alignment explanation
Indices: 10998--11245 Score: 382
Period size: 121 Copynumber: 2.0 Consensus size: 126
10988 CATTGTTTAA
*
10998 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTA-TTTTATTTAATTAAATCTAATATCCTTATACT
*
11060 A-ATTTTTACCATTTTACTATTTTAATTAAAAAAC-T-TATATATTATAATTTTTTAAATAT
65 ATATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
11119 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTATTTAATTAAATCTAATATCCTTATACCT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTATTTAATTAAATCTAATATCCTTATA-CT
*
11184 ATTTTATTTTTACCATTTTACTATTTTAATTTAAAAACTTATATATATTAGAATTTTTTAAA
65 A---TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAA
11246 CATATTTCTT
Statistics
Matches: 114, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
120 23 0.20
121 34 0.30
122 2 0.02
124 2 0.02
128 32 0.28
129 1 0.01
130 20 0.18
ACGTcount: A:0.37, C:0.11, G:0.01, T:0.50
Consensus pattern (126 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTATTTAATTAAATCTAATATCCTTATACTA
TATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:12653 original size:1 final size:1
Alignment explanation
Indices: 12647--12671 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12637 CAATGACTTC
12647 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12672 CTCATCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27861 original size:125 final size:121
Alignment explanation
Indices: 27639--27873 Score: 337
Period size: 125 Copynumber: 1.9 Consensus size: 121
27629 TACTTCATGC
* *
27639 AAATCCACCTTATCTTCACTAACTGCCCTAAAAATCATCAACCAACAACAGAAAATCTCAAAATA
1 AAATCCACCTTATCTTCACTAACCGCCCTAAAAATCATCAACCAACAACAAAAAATCTCAAAATA
*
27704 AAACTGAGACAACAATGAAAGTTAAAATCATTTTGCTGTAACAACTAGAATGAAGT
66 AAACTGAGAAAACAATGAAAGTTAAAATCATTTTGCTGTAACAACTAGAATGAAGT
* ** *
27760 AAATCCA-CTGTATCTTCACTAACCGCCCTACAAATCATCAATTAACAAACACAAAATAATCTCT
1 AAATCCACCT-TATCTTCACTAACCGCCCTAAAAATCATCAACCAAC--A-ACAAAA-AATCTCA
* *
27824 AAATAAAACTGAGAAAACAATGAAAGTTGAAATCATTTTTCTGTAACAAC
61 AAATAAAACTGAGAAAACAATGAAAGTTAAAATCATTTTGCTGTAACAAC
27874 AATTAGAACT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
120 2 0.02
121 39 0.39
123 1 0.01
124 5 0.05
125 53 0.53
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (121 bp):
AAATCCACCTTATCTTCACTAACCGCCCTAAAAATCATCAACCAACAACAAAAAATCTCAAAATA
AAACTGAGAAAACAATGAAAGTTAAAATCATTTTGCTGTAACAACTAGAATGAAGT
Found at i:29432 original size:24 final size:24
Alignment explanation
Indices: 29393--29438 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29383 GATTAGTAAG
* *
29393 AAATTTAATAATAAAAAGAAAAAT
1 AAATTTAAAAAAAAAAAGAAAAAT
*
29417 AAATTTAAAAAAAAAAGGAAAA
1 AAATTTAAAAAAAAAAAGAAAA
29439 GTGTTATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (24 bp):
AAATTTAAAAAAAAAAAGAAAAAT
Found at i:55653 original size:254 final size:252
Alignment explanation
Indices: 55206--55711 Score: 913
Period size: 254 Copynumber: 2.0 Consensus size: 252
55196 AGCAAAAAAG
**
55206 GGTAAAAGTACCCGGGAGGTCTTTGTACTATACGAAATGTTGATTTTGGTCCCTATACTTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTATACTTTTTTT
**
55271 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGTGTGCCGT
66 TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
*
55336 GACAGACCCGTTAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
131 GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
*
55401 ACGTGGAATAAAAATTAAATATTTTTTGATATATTTTATTTTATTGAAATTTATTTT
196 ACGTGGAATAAAAATTAAATATTTTTTAATATATTTTATTTTATTGAAATTTATTTT
*
55458 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCCTGTACTTTTTT
1 GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGT-CCCTATAC-TTTTT
* *
55523 TTTTCTACAAATTCGTCCCTCTACTATCATAACCTATCACCCGAGGTCCCTCATGTTAGCATGCC
64 TTTTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCC
55588 GTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTG
129 GTGACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTG
55653 ACACGTGGAATAAAAATTAAATATTTTTTAATATATTTTATTTTATTGAAATTTATTTT
194 ACACGTGGAATAAAAATTAAATATTTTTTAATATATTTTATTTTATTGAAATTTATTTT
55712 TAAAAAAAAT
Statistics
Matches: 243, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
252 48 0.20
253 7 0.03
254 188 0.77
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (252 bp):
GGTAAAAGTACCCGGGAGGTCCCTGTACTATACGAAATGTTGATTTTGGTCCCTATACTTTTTTT
TTCTACAAATTCGTCCCTCTACTATCAGAACCTATCACCCGAGGTCCCTCACGTTAGCATGCCGT
GACAGACCCGTCAAATATGCTGACGTGGCACTAACACCGTCTTTTTTGCTGACGTGGCAGGTGAC
ACGTGGAATAAAAATTAAATATTTTTTAATATATTTTATTTTATTGAAATTTATTTT
Done.