Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021728.1 Corchorus olitorius cultivar O-4 contig21761, 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: 17044
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7213 original size:2 final size:2
Alignment explanation
Indices: 7206--7230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7196 AAAAGGAATC
7206 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7231 AACTGTAGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7234 original size:52 final size:49
Alignment explanation
Indices: 7153--7250 Score: 160
Period size: 50 Copynumber: 1.9 Consensus size: 49
7143 GCAAAATGAC
7153 ATCATATATATATATATATATATTAAAACTGTAGACATTGGAGAAAAGGA
1 ATCATATATATATATATATATATTAAAACTGTAGACATTGG-GAAAAGGA
*
7203 ATCATATATATATATATATATATATATAAACTGTAGACGTTGGGAAAA
1 ATCATATATATATATATATATAT-TA-AAACTGTAGACATTGGGAAAA
7251 AAGAAAGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
50 23 0.51
51 7 0.16
52 15 0.33
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (49 bp):
ATCATATATATATATATATATATTAAAACTGTAGACATTGGGAAAAGGA
Found at i:7399 original size:51 final size:51
Alignment explanation
Indices: 7334--7433 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
7324 AATTTATATA
7334 TATTAGATTGATTGATTAATTGATTTGAATATTTTGATCAAATTAAAATAC
1 TATTAGATTGATTGATTAATTGATTTGAATATTTTGATCAAATTAAAATAC
* *
7385 TATTTGATTGATTGATTGATTGATTTGAATATTTTGATCAAATTAAAAT
1 TATTAGATTGATTGATTAATTGATTTGAATATTTTGATCAAATTAAAAT
7434 CAATTAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (51 bp):
TATTAGATTGATTGATTAATTGATTTGAATATTTTGATCAAATTAAAATAC
Found at i:9587 original size:16 final size:15
Alignment explanation
Indices: 9549--9590 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
9539 ACAGAGGTTG
*
9549 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
9564 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
9579 ACTAGAAAACAA
1 AC-AGAAAACAA
9591 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:11007 original size:29 final size:31
Alignment explanation
Indices: 10970--11029 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
10960 CAATCCTTGC
* *
10970 TCTTGAAATAAATGTTC-A-AAGTCTTCAAA
1 TCTTCAAATAAATCTTCAATAAGTCTTCAAA
*
10999 TCTTCAAATAAGTCTTCAATAAGTCTTCAAA
1 TCTTCAAATAAATCTTCAATAAGTCTTCAAA
11030 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
30 1 0.04
31 11 0.42
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAATAAGTCTTCAAA
Found at i:11016 original size:12 final size:12
Alignment explanation
Indices: 10999--11029 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
10989 AGTCTTCAAA
10999 TCTTCAAATAAG
1 TCTTCAAATAAG
11011 TCTTC-AATAAG
1 TCTTCAAATAAG
11022 TCTTCAAA
1 TCTTCAAA
11030 CACGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (12 bp):
TCTTCAAATAAG
Found at i:11021 original size:11 final size:11
Alignment explanation
Indices: 10988--11028 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
10978 TAAATGTTCA
10988 AAGTCTTC-A-
1 AAGTCTTCAAT
10997 AA-TCTTCAAAT
1 AAGTCTTC-AAT
11008 AAGTCTTCAAT
1 AAGTCTTCAAT
11019 AAGTCTTCAA
1 AAGTCTTCAA
11029 ACACGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.18
9 2 0.07
10 1 0.04
11 15 0.54
12 5 0.18
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (11 bp):
AAGTCTTCAAT
Found at i:12913 original size:21 final size:21
Alignment explanation
Indices: 12889--12943 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
12879 GGCACTGAAT
* *
12889 GGTGATGGCACGGGCATAGCC
1 GGTGGTGGCACGGGCATAACC
**
12910 GGTGGTGGCACGGGTTTAACC
1 GGTGGTGGCACGGGCATAACC
12931 GGTGGTGGCACGG
1 GGTGGTGGCACGG
12944 TGAATGGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.15, C:0.20, G:0.47, T:0.18
Consensus pattern (21 bp):
GGTGGTGGCACGGGCATAACC
Found at i:16306 original size:30 final size:29
Alignment explanation
Indices: 16205--16296 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
16195 ATGACGCAGA
**
16205 AAAACT-TTTTTTTTATGACGCAAAACAC
1 AAAACTCTTTTTTTTATGACGCAAAACTG
* **
16233 AAAACTTTTTTTTTTCCGACGCAAAACTG
1 AAAACTCTTTTTTTTATGACGCAAAACTG
16262 AAAACTCTTTTTTTTATGACGCAGAAACTG
1 AAAACTCTTTTTTTTATGACGCA-AAACTG
16292 AAAAC
1 AAAAC
16297 AGATTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 6 0.11
29 38 0.69
30 11 0.20
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (29 bp):
AAAACTCTTTTTTTTATGACGCAAAACTG
Found at i:16725 original size:16 final size:15
Alignment explanation
Indices: 16687--16728 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
16677 ACATAGGTTG
*
16687 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
16702 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
16717 ACTAGAAAACAA
1 AC-AGAAAACAA
16729 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.