Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012026.1 Corchorus olitorius cultivar O-4 contig12059, 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: 21705
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:900 original size:55 final size:55
Alignment explanation
Indices: 821--929 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
811 TATAGTATAG
821 ATATATATATATATATTTATGATAATCATTTGATTTCTCAAAGGCATTGTGATAT
1 ATATATATATATATATTTATGATAATCATTTGATTTCTCAAAGGCATTGTGATAT
*
876 ATATATATATATTTATTTATGATAATCATTTGATTTCTCAAAGGCATTGTGATA
1 ATATATATATATATATTTATGATAATCATTTGATTTCTCAAAGGCATTGTGATA
930 ATTGCCCAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (55 bp):
ATATATATATATATATTTATGATAATCATTTGATTTCTCAAAGGCATTGTGATAT
Found at i:1347 original size:15 final size:16
Alignment explanation
Indices: 1327--1359 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1317 ATTTGAAAAA
1327 AAAATTAATTT-ATTT
1 AAAATTAATTTAATTT
1342 AAAATTAATTTAATTT
1 AAAATTAATTTAATTT
1358 AA
1 AA
1360 CCAGAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATTAATTTAATTT
Found at i:2583 original size:21 final size:21
Alignment explanation
Indices: 2558--2690 Score: 113
Period size: 21 Copynumber: 6.2 Consensus size: 21
2548 ATATGAGAAA
*
2558 GAAAATCCAGTTGAAGGAGTT
1 GAAAATCCAGTTGATGGAGTT
** **
2579 GAAAATCCAGGAGATGGTTTT
1 GAAAATCCAGTTGATGGAGTT
** **
2600 GAAAATCCAGGAGATGGTTTT
1 GAAAATCCAGTTGATGGAGTT
2621 GAAAATCCAGTTGATGGAGTT
1 GAAAATCCAGTTGATGGAGTT
* *
2642 GAAAAGCCAGTAGATGATGGTGTT
1 GAAAATCCAGT---TGATGGAGTT
* * *
2666 GGAAATCCAGTTGAAGAAGTT
1 GAAAATCCAGTTGATGGAGTT
2687 GAAA
1 GAAA
2691 TGCCTGAAAA
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
21 74 0.80
24 18 0.20
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.26
Consensus pattern (21 bp):
GAAAATCCAGTTGATGGAGTT
Found at i:6295 original size:19 final size:19
Alignment explanation
Indices: 6271--6307 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6261 AATATTTTCC
6271 TAAACTTCATTGCATTATT
1 TAAACTTCATTGCATTATT
*
6290 TAAACTTTATTGCATTAT
1 TAAACTTCATTGCATTAT
6308 GTCCTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (19 bp):
TAAACTTCATTGCATTATT
Found at i:7510 original size:18 final size:18
Alignment explanation
Indices: 7489--7533 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
7479 CAATTTTAAA
7489 TTTTACTTTT-TTTTCTTT
1 TTTTA-TTTTCTTTTCTTT
7507 TTTTATTTTCGTTTTC-TT
1 TTTTATTTTC-TTTTCTTT
7525 TTTTATTTT
1 TTTTATTTT
7534 AAGTAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.16
18 16 0.64
19 5 0.20
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTATTTTCTTTTCTTT
Found at i:7587 original size:22 final size:22
Alignment explanation
Indices: 7530--7578 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
7520 TTCTTTTTTA
7530 TTTTAAGTAATTAAAAAATACTT
1 TTTTAA-TAATTAAAAAATACTT
7553 TTTTAATAATTAAAAAATA-TT
1 TTTTAATAATTAAAAAATACTT
7574 TTTTA
1 TTTTA
7579 TTGACTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 6 0.23
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAATAATTAAAAAATACTT
Found at i:12031 original size:47 final size:47
Alignment explanation
Indices: 11962--12051 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
11952 AACGTTGGGT
*
11962 TCTTACACTCAAGTTGTTAGCTCAACTGGGAGGAGTGCCATACATGC
1 TCTTACACTCAAGTTGTTAGCTCAACTAGGAGGAGTGCCATACATGC
*
12009 TCTTACACTCGAGTTGTTAGCTCAACTAGGAGGAGTGCCATAC
1 TCTTACACTCAAGTTGTTAGCTCAACTAGGAGGAGTGCCATAC
12052 TTGACCATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
TCTTACACTCAAGTTGTTAGCTCAACTAGGAGGAGTGCCATACATGC
Found at i:12752 original size:19 final size:19
Alignment explanation
Indices: 12712--12748 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12702 AATTTTTAAG
12712 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
12731 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
12749 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:17053 original size:23 final size:22
Alignment explanation
Indices: 17020--17095 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 22
17010 ATTACACCTT
17020 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
* * * *
17042 GTAAATGACAAGGTTGATCACAACTT
1 GTAAA-AACAAGGGTGATGA-AA--A
17068 GTAAAAACAAGGGTGATGAAAA
1 GTAAAAACAAGGGTGATGAAAA
17090 GTAAAA
1 GTAAAA
17096 GATAGGGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
22 11 0.26
23 11 0.26
24 4 0.10
25 11 0.26
26 5 0.12
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (22 bp):
GTAAAAACAAGGGTGATGAAAA
Found at i:17088 original size:48 final size:48
Alignment explanation
Indices: 17017--17109 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
17007 AAGATTACAC
*
17017 CTTGTAAAAACAAGGGTGATGAAAAGTAAATGACAAGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCACAA
* *
17065 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCA
17110 AACAAGAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.22
Consensus pattern (48 bp):
CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGACAAGGTTGATCACAA
Done.