Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020030.1 Corchorus olitorius cultivar O-4 contig20063, 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: 47885
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4027 original size:27 final size:27
Alignment explanation
Indices: 3996--4059 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
3986 TGGAACACTG
*
3996 GATTGGCACAAGTGTAAGTTGTACTTA
1 GATTGTCACAAGTGTAAGTTGTACTTA
4023 GATTGTCACAAGTGTAAGTTGTACTTA
1 GATTGTCACAAGTGTAAGTTGTACTTA
4050 GATTGTCACA
1 GATTGTCACA
4060 GTAGATAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (27 bp):
GATTGTCACAAGTGTAAGTTGTACTTA
Found at i:5297 original size:11 final size:10
Alignment explanation
Indices: 5281--5333 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
5271 AAGTTCGTTT
5281 TTGAAGACTTA
1 TTGAAGA-TTA
*
5292 TTGAAGATAA
1 TTGAAGATTA
5302 TTTGAAGA-T-
1 -TTGAAGATTA
5311 TTGAAGATTA
1 TTGAAGATTA
5321 TTGAAGAATTA
1 TTGAAG-ATTA
5332 TT
1 TT
5334 TGCAAGAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:5305 original size:22 final size:21
Alignment explanation
Indices: 5280--5333 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
5270 GAAGTTCGTT
5280 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
5302 TTTGAAGA-T-TTGAAGATTA
1 TTTGAAGATTATTGAAGATAA
5321 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
5334 TGCAAGAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.41
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:12811 original size:22 final size:22
Alignment explanation
Indices: 12728--12825 Score: 103
Period size: 22 Copynumber: 4.5 Consensus size: 22
12718 GTCGACTAAG
12728 AATTGTCGACTTC-AAGGAGAGA
1 AATTGTCGAC-TCAAAGGAGAGA
*
12750 AATTGTCGACTCTAAGGAGAGA
1 AATTGTCGACTCAAAGGAGAGA
* *
12772 AATAGTCGACTGAAAGGAG-GA
1 AATTGTCGACTCAAAGGAGAGA
*
12793 AATTTTCGACTCAAGAGGA-AGCA
1 AATTGTCGACTCAA-AGGAGAG-A
*
12816 AATCGTCGAC
1 AATTGTCGAC
12826 AAGAAGGCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
21 15 0.23
22 40 0.62
23 9 0.14
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGTCGACTCAAAGGAGAGA
Found at i:14037 original size:9 final size:9
Alignment explanation
Indices: 14020--14053 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
14010 AAGTGTGTGT
*
14020 GTGGTGGGG
1 GTGGGGGGG
14029 GTGGGGGGG
1 GTGGGGGGG
14038 G-GGGGGGG
1 GTGGGGGGG
14046 GTGGGGGG
1 GTGGGGGG
14054 TGAATACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.00, C:0.00, G:0.88, T:0.12
Consensus pattern (9 bp):
GTGGGGGGG
Found at i:21117 original size:14 final size:15
Alignment explanation
Indices: 21098--21127 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
21088 GCTAATTAAA
21098 ATTTTATT-ATATAT
1 ATTTTATTCATATAT
21112 ATTTTATTCATATAT
1 ATTTTATTCATATAT
21127 A
1 A
21128 CTATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTCATATAT
Found at i:25521 original size:205 final size:200
Alignment explanation
Indices: 25128--25537 Score: 723
Period size: 201 Copynumber: 2.0 Consensus size: 200
25118 GCTTAATAAC
*
25128 TTTATCAATGGGGAATGTTATTATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGGGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
25193 GATACAAAACATTATTATTATATATAAAACTATACCAAAAAAAATAGTTGAACATTAGTGGTTGA
66 GATACAAAACATTACTATTATATATAAAACTATACCAAAAAAAATAGTTGAACATTAGTGGTTGA
25258 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
25323 GATTTA
195 GATTTA
*
25329 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGGGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
25394 GATACAACACATTACTATTATATATATAGAACTAT-CCAAAAAAAAAAATAGTTGAACATTAGTG
66 GATACAAAACATTACTATTATATATA-A-AACTATACC---AAAAAAAATAGTTGAACATTAGTG
25458 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
126 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAG
25523 ATCCGATTTA
191 ATCCGATTTA
25533 TTTAT
1 TTTAT
25538 TATTAAGGAA
Statistics
Matches: 200, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
201 87 0.44
202 3 0.01
203 6 0.03
204 18 0.09
205 86 0.43
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGGGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAAAACATTACTATTATATATAAAACTATACCAAAAAAAATAGTTGAACATTAGTGGTTGA
TTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCG
ATTTA
Found at i:25704 original size:39 final size:40
Alignment explanation
Indices: 25650--25730 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
25640 ATACCTAAGA
*
25650 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
25689 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
25729 AT
1 AT
25731 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:27498 original size:29 final size:29
Alignment explanation
Indices: 27448--27503 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
27438 ACATTTAGGG
** *
27448 AAAAGGTCATTTAAGTATCTAAACTTTAA
1 AAAAGGTCAAATAAGTAACTAAACTTTAA
* *
27477 AAAAGGTCAAATAGGTAACTAACCTTT
1 AAAAGGTCAAATAAGTAACTAAACTTT
27504 TTGATTTGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (29 bp):
AAAAGGTCAAATAAGTAACTAAACTTTAA
Found at i:36769 original size:21 final size:19
Alignment explanation
Indices: 36743--36801 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
36733 CGCTACTCTA
36743 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
36762 ACATAATCTAATCTGTACAGT
1 --ATAATCTCATCTGTACAGT
* *
36783 GTAATTTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
36802 TGTCAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:43496 original size:21 final size:21
Alignment explanation
Indices: 43471--43513 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
43461 TTTGGGTATA
43471 GAGATTTCACTGGGTTTGTTT
1 GAGATTTCACTGGGTTTGTTT
43492 GAGATTTCACTGGGTTTGTTT
1 GAGATTTCACTGGGTTTGTTT
43513 G
1 G
43514 TTAGGGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.30, T:0.47
Consensus pattern (21 bp):
GAGATTTCACTGGGTTTGTTT
Found at i:47404 original size:14 final size:14
Alignment explanation
Indices: 47385--47413 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47375 GGGAAGGTGT
47385 AAATTAAGAAACTA
1 AAATTAAGAAACTA
47399 AAATTAAGAAACTA
1 AAATTAAGAAACTA
47413 A
1 A
47414 CATTCATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATTAAGAAACTA
Done.