Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018535.1 Corchorus olitorius cultivar O-4 contig18568, 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: 22249
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35 GTATGTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:556 original size:15 final size:15
Alignment explanation
Indices: 536--565 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
526 ACAGTCTACT
536 AAAGTAATTGATTTA
1 AAAGTAATTGATTTA
*
551 AAAGTAATTGGTTTA
1 AAAGTAATTGATTTA
566 GAAGAGGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (15 bp):
AAAGTAATTGATTTA
Found at i:880 original size:18 final size:17
Alignment explanation
Indices: 857--890 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
847 AGGAAGAGAG
857 AGAAAAAAAAAAGAAAAA
1 AGAAAAAAAAAA-AAAAA
875 AGAAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAAA
891 GAACGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAAAAAA
Found at i:882 original size:15 final size:15
Alignment explanation
Indices: 861--893 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
851 AGAGAGAGAA
861 AAAAAAAAGAAAAAAG
1 AAAAAAAA-AAAAAAG
877 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
892 AA
1 AA
894 CGTGTGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:3035 original size:25 final size:24
Alignment explanation
Indices: 3007--3068 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
2997 GTGGATTGTA
*
3007 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
3032 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
3056 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
3069 CTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:6169 original size:49 final size:49
Alignment explanation
Indices: 6112--6210 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
6102 TTCGTGTTAT
6112 ATATCCTTTGTGGGTTCATGTGTGAAATTAAATTTCATGTCCAATTCCA
1 ATATCCTTTGTGGGTTCATGTGTGAAATTAAATTTCATGTCCAATTCCA
6161 ATATCCTTTGTGGGTTCATGTGTGAAATTAAATTTCATGTCCAATTCCA
1 ATATCCTTTGTGGGTTCATGTGTGAAATTAAATTTCATGTCCAATTCCA
6210 A
1 A
6211 ACCTCCTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (49 bp):
ATATCCTTTGTGGGTTCATGTGTGAAATTAAATTTCATGTCCAATTCCA
Found at i:11506 original size:76 final size:76
Alignment explanation
Indices: 11376--11640 Score: 345
Period size: 76 Copynumber: 3.5 Consensus size: 76
11366 CGCTAGGGAA
* *
11376 GACGAACGGGGGCGCCAGTTTAGGCACTCCA-CCATTGAGTGAGCGGCGTCAGCGTGGACGCTCT
1 GACGAACGGGGGCGCCAGTCTAGGCACT-CAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCT
*
11440 GTCCCACTGGTG
65 GTCTCACTGGTG
* * * * *
11452 GACGAACGAGGGCGCCAGTCTAGGCACTCAGTCGTTGAGTGAGCTGCGTAAGCGTGGATGCTCTG
1 GACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCTG
* *
11517 TTTCACTGGTA
66 TCTCACTGGTG
** * * *
11528 GACGAACGGGGATGCCAGTCTAGGCACTCAGCCGTTGAGTGAGAGGCGTCTGCGTGAACGCTCTG
1 GACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCTG
11593 TCTCACTGGTG
66 TCTCACTGGTG
* *
11604 GGCGAACGGGGGTGCCAGTCTAGGCACTCCA-CCGTTG
1 GACGAACGGGGGCGCCAGTCTAGGCACT-CAGCCGTTG
11641 TTTGAAATAT
Statistics
Matches: 163, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
75 2 0.01
76 159 0.98
77 2 0.01
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.20
Consensus pattern (76 bp):
GACGAACGGGGGCGCCAGTCTAGGCACTCAGCCGTTGAGTGAGCGGCGTCAGCGTGGACGCTCTG
TCTCACTGGTG
Found at i:18666 original size:18 final size:19
Alignment explanation
Indices: 18627--18666 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
18617 GTGCTCCCGT
18627 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
18648 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
18666 T
1 T
18667 TCTGACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Done.