Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013395.1 Corchorus olitorius cultivar O-4 contig13428, 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: 46691
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Found at i:1076 original size:14 final size:14
Alignment explanation
Indices: 1053--1086 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1043 AAATGGAAAG
*
1053 AAATTCTTGTTTAT
1 AAATTTTTGTTTAT
*
1067 GAATTTTTGTTTAT
1 AAATTTTTGTTTAT
1081 AAATTT
1 AAATTT
1087 GGACTCAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (14 bp):
AAATTTTTGTTTAT
Found at i:1156 original size:29 final size:28
Alignment explanation
Indices: 1111--1168 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 28
1101 TCAAATTTCA
1111 AGTAGATGGACTCAATTGACAG-TTTTTGT
1 AGTAGATGGACTCAATT-A-AGATTTTTGT
1140 AGTAGATGGAC-CAAATTAAGATTTTTGT
1 AGTAGATGGACTC-AATTAAGATTTTTGT
1168 A
1 A
1169 TAAGTAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 2 0.07
28 10 0.37
29 15 0.56
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (28 bp):
AGTAGATGGACTCAATTAAGATTTTTGT
Found at i:1643 original size:27 final size:27
Alignment explanation
Indices: 1613--1673 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
1603 GCTTATCTCA
* *
1613 TCTTCAAGGTCAAGACAAGTCACTAAT
1 TCTTAAAGGTCAAGACAAGCCACTAAT
*
1640 TCTTAAAGGTCAAGACAAGCCGCTAAT
1 TCTTAAAGGTCAAGACAAGCCACTAAT
1667 TCTTAAA
1 TCTTAAA
1674 ATTTACGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (27 bp):
TCTTAAAGGTCAAGACAAGCCACTAAT
Found at i:21388 original size:11 final size:11
Alignment explanation
Indices: 21364--21398 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
21354 TTGACAACGC
21364 AACAAAAACAA
1 AACAAAAACAA
* *
21375 AACGAAAACGA
1 AACAAAAACAA
21386 AACAAAAACAA
1 AACAAAAACAA
21397 AA
1 AA
21399 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:26680 original size:12 final size:12
Alignment explanation
Indices: 26661--26690 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26651 ACAGATTAGT
26661 CAAAACCGAAAC
1 CAAAACCGAAAC
*
26673 CGAAACCGAAAC
1 CAAAACCGAAAC
26685 CAAAAC
1 CAAAAC
26691 TGCAGCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.33, G:0.10, T:0.00
Consensus pattern (12 bp):
CAAAACCGAAAC
Found at i:37943 original size:28 final size:28
Alignment explanation
Indices: 37887--37942 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
37877 CAGCTCATTT
37887 AATTAAGGTTTCGATTTCCCTAAAAAAA
1 AATTAAGGTTTCGATTTCCCTAAAAAAA
*
37915 AATTAAGGTTTCGA-TT-CTTAAAAAAA
1 AATTAAGGTTTCGATTTCCCTAAAAAAA
37941 AA
1 AA
37943 AGTTTTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 11 0.41
27 2 0.07
28 14 0.52
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
AATTAAGGTTTCGATTTCCCTAAAAAAA
Found at i:44469 original size:18 final size:20
Alignment explanation
Indices: 44433--44469 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
44423 TGTACAGACT
44433 AATTAGTAGGGATTTGACAG
1 AATTAGTAGGGATTTGACAG
44453 AATTAG-AGGGA-TTGACA
1 AATTAGTAGGGATTTGACA
44470 ACCTAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (20 bp):
AATTAGTAGGGATTTGACAG
Done.