Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015953.1 Corchorus olitorius cultivar O-4 contig15986, 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: 10461
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1299 original size:27 final size:27
Alignment explanation
Indices: 1261--1314 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1251 TCCCTAGGTC
1261 AGTAATCATCTTGAATTTAATATTGAA
1 AGTAATCATCTTGAATTTAATATTGAA
1288 AGTAATCATCTTGAATTTAATATTGAA
1 AGTAATCATCTTGAATTTAATATTGAA
1315 TTTATCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (27 bp):
AGTAATCATCTTGAATTTAATATTGAA
Found at i:1308 original size:15 final size:15
Alignment explanation
Indices: 1263--1308 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1253 CCTAGGTCAG
1263 TAATCATCTTGAATT
1 TAATCATCTTGAATT
**
1278 TAAT-A--TTGAAAG
1 TAATCATCTTGAATT
1290 TAATCATCTTGAATT
1 TAATCATCTTGAATT
1305 TAAT
1 TAAT
1309 ATTGAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 1 0.04
15 13 0.54
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATCATCTTGAATT
Found at i:1315 original size:12 final size:12
Alignment explanation
Indices: 1271--1318 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1261 AGTAATCATC
1271 TTGAATTTAATA
1 TTGAATTTAATA
**
1283 TTGAAAGTAATCA
1 TTGAATTTAAT-A
1296 TCTTGAATTTAATA
1 --TTGAATTTAATA
1310 TTGAATTTA
1 TTGAATTTA
1319 TCTTTTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 18 0.62
13 1 0.03
14 1 0.03
15 9 0.31
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (12 bp):
TTGAATTTAATA
Found at i:1468 original size:15 final size:15
Alignment explanation
Indices: 1438--1479 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1428 TTACTTTGTT
*
1438 TTGTTCTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
1454 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
1469 TTGTTTACTGT
1 TTGTTTTCTGT
1480 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:7785 original size:21 final size:21
Alignment explanation
Indices: 7759--7799 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7749 TTTAAACCTT
7759 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
7780 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
7800 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:9670 original size:5 final size:5
Alignment explanation
Indices: 9660--9695 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
9650 AGCAATAAAC
9660 AACAA AAC-A AACAA AAC-A AACAA AAC-A AACAA AACA
1 AACAA AACAA AACAA AACAA AACAA AACAA AACAA AACA
9696 GAGCAACCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 12 0.43
5 16 0.57
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:9672 original size:9 final size:9
Alignment explanation
Indices: 9656--9695 Score: 73
Period size: 9 Copynumber: 4.6 Consensus size: 9
9646 TAAAAGCAAT
9656 AAAC-AACA
1 AAACAAACA
9664 AAACAAACA
1 AAACAAACA
9673 AAACAAACA
1 AAACAAACA
9682 AAACAAACA
1 AAACAAACA
9691 AAACA
1 AAACA
9696 GAGCAACCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 4 0.13
9 27 0.87
ACGTcount: A:0.78, C:0.23, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAACA
Done.