Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019530.1 Corchorus olitorius cultivar O-4 contig19563, 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: 73372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1115 original size:15 final size:15
Alignment explanation
Indices: 1066--1117 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1056 AAAAAAAAGT
1066 CTAATTATTGTACTA
1 CTAATTATTGTACTA
* * *
1081 CT-TTTTTTGAAC-A
1 CTAATTATTGTACTA
1094 TCTAATTATTGTACTA
1 -CTAATTATTGTACTA
1110 CTAATTAT
1 CTAATTAT
1118 ACCGATTAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.32
15 17 0.61
16 1 0.04
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (15 bp):
CTAATTATTGTACTA
Found at i:1285 original size:11 final size:11
Alignment explanation
Indices: 1269--1293 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1259 CCATGTTGGC
1269 TATATTATATA
1 TATATTATATA
1280 TATATTATATA
1 TATATTATATA
1291 TAT
1 TAT
1294 GTCTCTTCAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATTATATA
Found at i:1789 original size:2 final size:2
Alignment explanation
Indices: 1782--1818 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1772 ACCAAGGCTT
1782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1819 CATAATAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2953 original size:60 final size:60
Alignment explanation
Indices: 2882--3005 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
2872 TTATAGTCTA
* * * * *
2882 ATTTAATCAAATTCAAAGCATGGACC-ATAAATTGAACATTTTCATATGCGTAAGGGTCCT
1 ATTTAACCAAATTAAAAGCATGG-CCTATAAATTGAACATTTTCACATACGTAAGGGACCT
* * *
2942 ATTTAACCAAATTAAAAGCATGGCCTCTAAATTGAGCATTTTCACATACGTTAGGGACCT
1 ATTTAACCAAATTAAAAGCATGGCCTATAAATTGAACATTTTCACATACGTAAGGGACCT
3002 ATTT
1 ATTT
3006 GAACAATTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (60 bp):
ATTTAACCAAATTAAAAGCATGGCCTATAAATTGAACATTTTCACATACGTAAGGGACCT
Found at i:14325 original size:5 final size:5
Alignment explanation
Indices: 14315--14354 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
14305 AGGTAACTTC
14315 TCTTT TCTTT TCTTT TCTTT T-TTT ATCTTT T-TTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT -TCTTT TCTTT TCTTT T
14355 ATGGCAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 7 0.22
5 22 0.69
6 3 0.09
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TCTTT
Found at i:14838 original size:10 final size:10
Alignment explanation
Indices: 14823--14855 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
14813 AGAGAGGGAT
14823 TTTTTTTTTC
1 TTTTTTTTTC
14833 TTTTTTTTTC
1 TTTTTTTTTC
14843 TTTTTTTTTC
1 TTTTTTTTTC
14853 TTT
1 TTT
14856 CTAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:29060 original size:21 final size:19
Alignment explanation
Indices: 29035--29088 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
29025 GCTGCTCTAA
29035 TAATCTCATCTGTACAATACC
1 TAATCTCATCTGTACAAT--C
* * * *
29056 TAATCTAATATGTACAGTG
1 TAATCTCATCTGTACAATC
29075 TAATCTCATCTGTA
1 TAATCTCATCTGTA
29089 GAGTTGCTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 12 0.44
21 15 0.56
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (19 bp):
TAATCTCATCTGTACAATC
Found at i:31590 original size:24 final size:24
Alignment explanation
Indices: 31562--31609 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
31552 CGGTAGACTA
* *
31562 TTTGGTTCGTATCGGCTTAAATTT
1 TTTGGTTCGTACCAGCTTAAATTT
31586 TTTGGTTCGTACCAGCTTAAATTT
1 TTTGGTTCGTACCAGCTTAAATTT
31610 CAGTGATTTC
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:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (24 bp):
TTTGGTTCGTACCAGCTTAAATTT
Found at i:32381 original size:34 final size:34
Alignment explanation
Indices: 32338--32407 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
32328 TATTGTCAAT
32338 TGTGGCTCAACATTGAGATAGGAAGAGTTCTGAG
1 TGTGGCTCAACATTGAGATAGGAAGAGTTCTGAG
32372 TGTGGCTCAACATTGAGATAGGAAGAGTTCTGAG
1 TGTGGCTCAACATTGAGATAGGAAGAGTTCTGAG
32406 TG
1 TG
32408 AAGGAGTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (34 bp):
TGTGGCTCAACATTGAGATAGGAAGAGTTCTGAG
Found at i:32430 original size:1 final size:1
Alignment explanation
Indices: 32424--32453 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
32414 TTGCCAGTAA
32424 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32454 ATATGGGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35642 original size:24 final size:23
Alignment explanation
Indices: 35601--35650 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
35591 CCATCATGGT
35601 TTATTAGTAATTTATTCCTTAAG
1 TTATTAGTAATTTATTCCTTAAG
* *
35624 TTATTGGTATATTTGTTCCTTAAG
1 TTATTAGTA-ATTTATTCCTTAAG
35648 TTA
1 TTA
35651 ATGACATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.54
Consensus pattern (23 bp):
TTATTAGTAATTTATTCCTTAAG
Found at i:48503 original size:30 final size:30
Alignment explanation
Indices: 48469--48525 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
48459 TTATCTTGAT
48469 TTTCCTCTTATACCCTCAAATTTTAATGAC
1 TTTCCTCTTATACCCTCAAATTTTAATGAC
48499 TTTCCTCTTATACCCTCAAATTTTAAT
1 TTTCCTCTTATACCCTCAAATTTTAAT
48526 ATCTTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (30 bp):
TTTCCTCTTATACCCTCAAATTTTAATGAC
Found at i:51460 original size:12 final size:12
Alignment explanation
Indices: 51443--51489 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
51433 GGAAGGAGAA
51443 GGAGTTGGGGTT
1 GGAGTTGGGGTT
*
51455 GGAGTTGGGGTG
1 GGAGTTGGGGTT
* *
51467 GGTGATGGGGTT
1 GGAGTTGGGGTT
*
51479 GGAGTGGGGGT
1 GGAGTTGGGGT
51490 GGCAGCCGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.09, C:0.00, G:0.64, T:0.28
Consensus pattern (12 bp):
GGAGTTGGGGTT
Found at i:54277 original size:10 final size:9
Alignment explanation
Indices: 54258--54282 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54248 GTCGAAGTAG
54258 TTTTTATTT
1 TTTTTATTT
54267 TTTTTATTT
1 TTTTTATTT
54276 TTTTTAT
1 TTTTTAT
54283 ATGCCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:59511 original size:18 final size:18
Alignment explanation
Indices: 59488--59535 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
59478 TCTTCTTCTT
*
59488 CTTCTTCCCTCATTCGAG
1 CTTCTTCCCTCATCCGAG
** *
59506 CTTCTTTTCTTATCCGAG
1 CTTCTTCCCTCATCCGAG
*
59524 CTTCGTCCCTCA
1 CTTCTTCCCTCA
59536 AATCTGTGAT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.38, G:0.10, T:0.42
Consensus pattern (18 bp):
CTTCTTCCCTCATCCGAG
Done.