Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012592.1 Corchorus olitorius cultivar O-4 contig12625, 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: 22013
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1159 original size:18 final size:20
Alignment explanation
Indices: 1136--1177 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1126 GCAAGGACAA
1136 AAATTT-TTTTT-ATGACGC
1 AAATTTGTTTTTCATGACGC
1154 AAATTTGTTTTTCGATGACGC
1 AAATTTGTTTTTC-ATGACGC
1175 AAA
1 AAA
1178 ACACAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 5 0.24
21 10 0.48
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (20 bp):
AAATTTGTTTTTCATGACGC
Found at i:2370 original size:11 final size:11
Alignment explanation
Indices: 2354--2379 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2344 CTTGCCTAAA
2354 AAAACTAGAAG
1 AAAACTAGAAG
2365 AAAACTAGAAG
1 AAAACTAGAAG
2376 AAAA
1 AAAA
2380 TAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:5428 original size:29 final size:29
Alignment explanation
Indices: 5354--5422 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
5344 TTTGCTTGCC
5354 CAGGGGCATTTTGGTCATTTTTGCACATT
1 CAGGGGCATTTTGGTCATTTTTGCACATT
* *
5383 CAGGGGTATTTTGGTCATTTTTGCATATT
1 CAGGGGCATTTTGGTCATTTTTGCACATT
5412 CAGGGGCATTT
1 CAGGGGCATTT
5423 GAGTCAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.42
Consensus pattern (29 bp):
CAGGGGCATTTTGGTCATTTTTGCACATT
Found at i:7381 original size:16 final size:17
Alignment explanation
Indices: 7360--7401 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
7350 TGCCTTATGA
7360 TTTATGTTGATGAAAG-
1 TTTATGTTGATGAAAGC
7376 TTTATGTT--TGAAAGC
1 TTTATGTTGATGAAAGC
7391 TTTAT-TTGATG
1 TTTATGTTGATG
7402 TTTCCATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.35
15 5 0.22
16 10 0.43
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.50
Consensus pattern (17 bp):
TTTATGTTGATGAAAGC
Found at i:10920 original size:28 final size:27
Alignment explanation
Indices: 10889--10947 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
10879 CTAAATCGAC
10889 ATTTTCAACAACTAAGGGTAAAATAGTA
1 ATTTTC-ACAACTAAGGGTAAAATAGTA
* * *
10917 ATTTTCCCCACTAAGGGTAAAATGGTA
1 ATTTTCACAACTAAGGGTAAAATAGTA
10944 ATTT
1 ATTT
10948 CACTTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (27 bp):
ATTTTCACAACTAAGGGTAAAATAGTA
Found at i:14264 original size:21 final size:21
Alignment explanation
Indices: 14238--14277 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14228 GAGAGATTGA
* *
14238 GTGATAGTTATTGGTAATTAT
1 GTGATAATTATTGATAATTAT
14259 GTGATAATTATTGATAATT
1 GTGATAATTATTGATAATT
14278 TGATAGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (21 bp):
GTGATAATTATTGATAATTAT
Found at i:14273 original size:10 final size:10
Alignment explanation
Indices: 14239--14277 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
14229 AGAGATTGAG
*
14239 TGATAGTTAT
1 TGATAATTAT
*
14249 TGGTAATTAT
1 TGATAATTAT
14259 GTGATAATTAT
1 -TGATAATTAT
14270 TGATAATT
1 TGATAATT
14278 TGATAGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (10 bp):
TGATAATTAT
Done.