Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000892.1 Hibiscus syriacus cultivar Beakdansim tig00001746_pilon, 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: 61379
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12768 original size:40 final size:42
Alignment explanation
Indices: 12724--12802 Score: 117
Period size: 40 Copynumber: 1.9 Consensus size: 42
12714 AACAAGCCCT
* *
12724 TTGTTCGTGTTCGTTTATTT-A-AATAAACAAACATAAAATA
1 TTGTTCATGTTCGTTCATTTAATAATAAACAAACATAAAATA
*
12764 TTGTTCATGTTCGTTCATTTAATAATAAACGAACATAAA
1 TTGTTCATGTTCGTTCATTTAATAATAAACAAACATAAA
12803 CGAACTTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 18 0.53
41 1 0.03
42 15 0.44
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (42 bp):
TTGTTCATGTTCGTTCATTTAATAATAAACAAACATAAAATA
Found at i:13253 original size:14 final size:14
Alignment explanation
Indices: 13224--13270 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
13214 TATACTTTAT
*
13224 CTCTAACTTA-AAA
1 CTCTAAATTATAAA
13237 CTCTAAATTATAAA
1 CTCTAAATTATAAA
13251 CTCTAAATTATAAA
1 CTCTAAATTATAAA
*
13265 CACTAA
1 CTCTAA
13271 GGTTATTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
CTCTAAATTATAAA
Found at i:14285 original size:28 final size:29
Alignment explanation
Indices: 14254--14319 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
14244 TCTGAATTCC
**
14254 TAAAATTTTGTGGGTCAAATTA-AATTTT
1 TAAAATTTTAAGGGTCAAATTATAATTTT
**
14282 TAAAACATTAAGGGTCAAATTATAATTTT
1 TAAAATTTTAAGGGTCAAATTATAATTTT
14311 TCAAAATTT
1 T-AAAATTT
14320 GGGGAACCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 18 0.60
29 7 0.23
30 5 0.17
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (29 bp):
TAAAATTTTAAGGGTCAAATTATAATTTT
Found at i:27088 original size:22 final size:21
Alignment explanation
Indices: 27053--27093 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
27043 AATATTAAAT
27053 TAAAAATAAAATATTTAAAAG
1 TAAAAATAAAATATTTAAAAG
*
27074 TAAAGAATAATATATTTAAA
1 TAAA-AATAAAATATTTAAA
27094 TTTGTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAAATAAAATATTTAAAAG
Found at i:28505 original size:20 final size:19
Alignment explanation
Indices: 28480--28545 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
28470 TAATAGTATC
28480 TAATTAATATACTTTTAATA
1 TAATTAATATACTTTT-ATA
* * *
28500 TAATT-ATTTAATCTTTTGTT
1 TAATTAATAT-A-CTTTTATA
*
28520 TAATTAATATATTTTTCATA
1 TAATTAATATACTTTT-ATA
28540 TAATTA
1 TAATTA
28546 TAATATTATT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 7 0.20
20 20 0.57
21 8 0.23
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
TAATTAATATACTTTTATA
Found at i:37622 original size:23 final size:23
Alignment explanation
Indices: 37592--37637 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
37582 AGAGACCTAT
37592 CTTAAAATTTT-ATTGGTGTCCAC
1 CTTAAAATTTTGATT-GTGTCCAC
37615 CTTAAAATTTTGATTGTGTCCAC
1 CTTAAAATTTTGATTGTGTCCAC
37638 TCATTGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (23 bp):
CTTAAAATTTTGATTGTGTCCAC
Found at i:39228 original size:27 final size:28
Alignment explanation
Indices: 39163--39351 Score: 124
Period size: 27 Copynumber: 6.8 Consensus size: 28
39153 CCAGAATTTA
* *
39163 GATTGAAGCACAGAGGTGCTCAGTCATA
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
**
39191 G-TTGGCTGCACAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* *
39218 GATTGAAGCACAGAGGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
39246 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
** * *
39272 GGCTGAAGCACAGAGGTGCTCAGTCATTT
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
** * *
39301 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
39330 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
39352 ATCACTTTTG
Statistics
Matches: 121, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
26 7 0.06
27 59 0.49
28 31 0.26
29 8 0.07
30 5 0.04
31 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:39233 original size:55 final size:55
Alignment explanation
Indices: 39163--39408 Score: 282
Period size: 55 Copynumber: 4.4 Consensus size: 55
39153 CCAGAATTTA
* ** * *
39163 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
*
39218 GATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
** * * * *
39272 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
39330 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTC
* *
39385 GATTGAAGCACATATGTGCTCAAT
1 GATTGAAGCACAGAGGTGCTCAAT
39409 TGTTAATTCT
Statistics
Matches: 162, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
54 43 0.27
55 73 0.45
57 2 0.01
58 44 0.27
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:39430 original size:55 final size:55
Alignment explanation
Indices: 39109--39408 Score: 267
Period size: 54 Copynumber: 5.4 Consensus size: 55
39099 CTTGATTTTA
* * * * * * *
39109 GATTGTAGCACAGAGGTGCTCAATCA---TTCCAATGCACAGAGGTGCCAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTGCTA-GCACAGAGGTGTCAG-CTCTC
* *
39163 GATTGAAGCACAGAGGTGCTCAGTCA-TAGTTGGCT-GCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCACT--TTTGCTAGCACAGAGGTGTCAGCT-CTC
* *
39218 GATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTA-CACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCACT-TTTGCTAGCACAGAGGTGTCAGCTCTC
** * * ** *
39272 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCACTTTTGCT-A--GCACAGAGGTGTCAGCTCTC
39330 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTA-CACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCACTTTT-GCTAGCACAGAGGTGTCAGCTCTC
* *
39385 GATTGAAGCACATATGTGCTCAAT
1 GATTGAAGCACAGAGGTGCTCAAT
39409 TGTTAATTCT
Statistics
Matches: 204, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
54 72 0.35
55 70 0.34
56 14 0.07
58 47 0.23
59 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCACTTTTGCTAGCACAGAGGTGTCAGCTCTC
Found at i:39663 original size:81 final size:81
Alignment explanation
Indices: 39528--39682 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 81
39518 AGTTACAAAG
* ** * * *
39528 AATGGTTCGCATACGAAATGGTGGAGCAACAAGCTCTCATAGAGGTGTAGAGCAGGAAGTTACTG
1 AATGGTTCGCACACGAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTACCG
*
39593 AGCCGGTTGCACCGAT
66 AGCCAGTTGCACCGAT
* *
39609 AATGGTTCGCACACGAAATGGCAGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTACCG
1 AATGGTTCGCACACGAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTACCG
39674 AGCCAGTTG
66 AGCCAGTTG
39683 TACAAGAGAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (81 bp):
AATGGTTCGCACACGAAATGGCAGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTACCG
AGCCAGTTGCACCGAT
Found at i:45647 original size:26 final size:26
Alignment explanation
Indices: 45604--45664 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
45594 TATACATGTA
* *
45604 TTTTTATATTTGTAGTATGATTTTAAG
1 TTTTT-TATTAGTAGTATGATTTGAAG
*
45631 TTTTTTATTAGTCGTATGATTTGAAG
1 TTTTTTATTAGTAGTATGATTTGAAG
*
45657 TTTATTAT
1 TTTTTTAT
45665 CATGTATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.59
Consensus pattern (26 bp):
TTTTTTATTAGTAGTATGATTTGAAG
Found at i:53756 original size:6 final size:6
Alignment explanation
Indices: 53745--53769 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53735 TGCTCAATCG
53745 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
53770 TGTAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Done.