Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009597.1 Corchorus olitorius cultivar O-4 contig09629, 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: 11572
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:686 original size:17 final size:15
Alignment explanation
Indices: 648--727 Score: 68
Period size: 15 Copynumber: 5.7 Consensus size: 15
638 TATTAGTTAT
648 TTGATATATTGTAAA
1 TTGATATATTGTAAA
663 TTGATATATTGTAAA
1 TTGATATATTGTAAA
**
678 TT-AT-TATATG-ATT
1 TTGATATAT-TGTAAA
691 TTG-T-TAGTTGT---
1 TTGATATA-TTGTAAA
702 TTGATATATTGTAAA
1 TTGATATATTGTAAA
717 TTGATATATTG
1 TTGATATATTG
728 ATGTATTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
11 3 0.06
12 5 0.09
13 13 0.24
14 5 0.09
15 28 0.52
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (15 bp):
TTGATATATTGTAAA
Found at i:705 original size:54 final size:56
Alignment explanation
Indices: 609--727 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 56
599 CAAAATTGAT
609 ATATATTGTAAATTATTATCTAAGGATTTTATTAGTTATTTGATATATTGTAAATTG
1 ATATATTGTAAATTATTA-CTAAGGATTTTATTAGTTATTTGATATATTGTAAATTG
* * *
666 ATATATTGTAAATTATTA-T-ATGATTTTGTTAGTTGTTTGATATATTGTAAATTG
1 ATATATTGTAAATTATTACTAAGGATTTTATTAGTTATTTGATATATTGTAAATTG
720 ATATATTG
1 ATATATTG
728 ATGTATTTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
54 40 0.68
55 1 0.02
57 18 0.31
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (56 bp):
ATATATTGTAAATTATTACTAAGGATTTTATTAGTTATTTGATATATTGTAAATTG
Found at i:5065 original size:19 final size:19
Alignment explanation
Indices: 5045--5081 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5035 AATTAATTAT
5045 TTTA-ATATTATATTTTTA
1 TTTATATATTATATTTTTA
5063 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
5082 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:5092 original size:19 final size:19
Alignment explanation
Indices: 5051--5092 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5041 TTATTTTAAT
* * *
5051 ATTATATTTTTATTTATAT
1 ATTATATTTTTACTTAAAA
5070 ATTATATTTTTACTTAAAA
1 ATTATATTTTTACTTAAAA
5089 ATTA
1 ATTA
5093 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTTTACTTAAAA
Found at i:5492 original size:19 final size:19
Alignment explanation
Indices: 5481--5521 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5471 AATTTTTAAG
5481 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
5500 TAAAAATTTAATACTA-AAA
1 TAAAAATATAATA-TATAAA
5519 TAA
1 TAA
5522 CTAATTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:7873 original size:9 final size:9
Alignment explanation
Indices: 7859--7886 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
7849 ATTTCTTGAA
7859 AAAAAACCG
1 AAAAAACCG
7868 AAAAAACCG
1 AAAAAACCG
7877 AAAAAACCG
1 AAAAAACCG
7886 A
1 A
7887 CTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.68, C:0.21, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAACCG
Found at i:11075 original size:14 final size:13
Alignment explanation
Indices: 11056--11089 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
11046 ATTTCTATGT
11056 TATCATATATATCA
1 TATCATATATAT-A
11070 TATCATATATATA
1 TATCATATATATA
11083 TAT-ATAT
1 TATCATAT
11090 TAAAACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 4 0.20
14 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
TATCATATATATA
Found at i:11273 original size:4 final size:4
Alignment explanation
Indices: 11264--11294 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
11254 ATCATATTAA
11264 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
11295 TGAATATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:11290 original size:77 final size:76
Alignment explanation
Indices: 11199--11355 Score: 237
Period size: 77 Copynumber: 2.0 Consensus size: 76
11189 TATATATTAA
*
11199 ATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAATCATATT
1 ATTGATTGATTGA-TTGATATAATATCTTGATCCAATTAGAATCAATTAGTACT--AATCATATT
11262 AAATTGATTGATTG
63 AAATTGATTGATTG
* *
11276 ATTGATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
1 ATTGATTGATTGATTGATAT-AATATCTTGATCCAATTAGAATCAATTAGTACTAATCATATTAA
11341 ATTGATTGATTG
65 ATTGATTGATTG
11353 ATT
1 ATT
11356 TGAATATTGA
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
76 4 0.05
77 39 0.53
79 31 0.42
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (76 bp):
ATTGATTGATTGATTGATATAATATCTTGATCCAATTAGAATCAATTAGTACTAATCATATTAAA
TTGATTGATTG
Found at i:11345 original size:61 final size:59
Alignment explanation
Indices: 11280--11392 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 59
11270 TGATTGATTG
* *
11280 ATTGATTGATTGATTTGAATATCTTGATCCAATTAGAATCAATTAGTACTAATGATATTAA
1 ATTGATTGATTGATTTGAATA--TTGATCAAATTAAAATCAATTAGTACTAATGATATTAA
*
11341 ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTATTAATG
1 ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTACTAATG
11393 TCATTTAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
59 28 0.57
61 21 0.43
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (59 bp):
ATTGATTGATTGATTTGAATATTGATCAAATTAAAATCAATTAGTACTAATGATATTAA
Found at i:11365 original size:77 final size:80
Alignment explanation
Indices: 11201--11366 Score: 259
Period size: 79 Copynumber: 2.1 Consensus size: 80
11191 TATATTAAAT
*
11201 TGATTGATTGATTTGAATATATTTTGATCCAATTAGAATCAATTAGTACTAAAATCATATTAAAT
1 TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACT-AAATCATATTAAAT
*
11266 TGATTGATTGATTGAT
65 TGATTGATTGATTGAA
*
11282 TGATTGATTGATTTG-A-ATATCTTGATCCAATTAGAATCAATTAGTACT-AATGATATTAAATT
1 TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATCATATTAAATT
11344 GATTGATTGATTTGAA
66 GATTGATTGA-TTGAA
11360 T-ATTGAT
1 TGATTGAT
11367 CAAATTAAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
77 29 0.36
78 5 0.06
79 31 0.38
80 1 0.01
81 15 0.19
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (80 bp):
TGATTGATTGATTTGAATATATCTTGATCCAATTAGAATCAATTAGTACTAAATCATATTAAATT
GATTGATTGATTGAA
Done.