Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002342.1 Hibiscus syriacus cultivar Beakdansim tig00004780_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: 46001
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5288 original size:4 final size:4
Alignment explanation
Indices: 5279--5309 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5269 TAGCCTGATC
*
5279 CATA CATA CATA CATA CATA TATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
5310 GAGGGTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:5524 original size:18 final size:19
Alignment explanation
Indices: 5492--5529 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5482 GATGACGTAA
5492 AACAATAATTTTTTTATTT
1 AACAATAATTTTTTTATTT
5511 AACAATAA-TTTTTTATTT
1 AACAATAATTTTTTTATTT
5529 A
1 A
5530 GTTTGATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
AACAATAATTTTTTTATTT
Found at i:5642 original size:2 final size:2
Alignment explanation
Indices: 5630--5677 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5620 TAAATTCACA
5630 AT AT A- AT 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 AT AT AT AT
5671 AT AT AT A
1 AT AT AT A
5678 CTAGATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6419 original size:30 final size:28
Alignment explanation
Indices: 6384--6443 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
6374 TTAAACAATT
6384 AAAATAAAAATTTGAAAATTTTCAAAAAAA
1 AAAATAAAAATTTG--AATTTTCAAAAAAA
* * *
6414 AAAATAGAAGTTTGAGTTTTCAAAAAAA
1 AAAATAAAAATTTGAATTTTCAAAAAAA
6442 AA
1 AA
6444 TCTTGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 15 0.56
30 12 0.44
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (28 bp):
AAAATAAAAATTTGAATTTTCAAAAAAA
Found at i:13995 original size:2 final size:2
Alignment explanation
Indices: 13990--14016 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13980 ATTTTTAAAG
13990 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14017 TAATAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16579 original size:23 final size:24
Alignment explanation
Indices: 16538--16590 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
16528 ATAATGATTC
16538 ATAATGCATTGTAAGTTGGCAAC-A
1 ATAATGCATTGTAAGTTGGC-ACTA
16562 ATAATG-ATT-TATAGTTGGCACTA
1 ATAATGCATTGTA-AGTTGGCACTA
16585 ATAATG
1 ATAATG
16591 GTTGAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.15
23 17 0.63
24 6 0.22
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (24 bp):
ATAATGCATTGTAAGTTGGCACTA
Found at i:24333 original size:57 final size:59
Alignment explanation
Indices: 24244--24369 Score: 175
Period size: 58 Copynumber: 2.2 Consensus size: 59
24234 TACTGTTTCA
* * * * *
24244 TTTTAGTTACCGAACTATCTTTTTTTCGAAATCATATCTAAAGTTACA-TTTGATTCCG
1 TTTTAGTCACCCAACTATCTTTTTTTCAAAATCATACCTAAAGTTACATTTTGATTCCC
*
24302 TTTTAGTCACCCAACT-TTTTTTTTTCAAAATCATACCTAAAGTTACATTTTGATTCCC
1 TTTTAGTCACCCAACTATCTTTTTTTCAAAATCATACCTAAAGTTACATTTTGATTCCC
*
24360 TTTTGGTCAC
1 TTTTAGTCAC
24370 TCGTCGTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 28 0.47
58 32 0.53
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (59 bp):
TTTTAGTCACCCAACTATCTTTTTTTCAAAATCATACCTAAAGTTACATTTTGATTCCC
Found at i:27437 original size:2 final size:2
Alignment explanation
Indices: 27430--27456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27420 CACCTACTTT
27430 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
27457 AAGACGCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30068 original size:2 final size:2
Alignment explanation
Indices: 30061--30101 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30051 TCTACTTTCA
30061 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
30102 GATTGATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30170 original size:53 final size:53
Alignment explanation
Indices: 30079--30205 Score: 155
Period size: 53 Copynumber: 2.4 Consensus size: 53
30069 ATATATATAT
* * * * * *
30079 ATATATATATATATATATATATAGATTGATATACGAATAACGACAAAAGTATGA
1 ATAT-TATAAATATATTTTTATAGATTAAAATAAGAATAACGACAAAAGTATGA
* *
30133 ATATTATAAATATATTTTTATAGATTAAAATAAGAATAACGATAAAAGTATTA
1 ATATTATAAATATATTTTTATAGATTAAAATAAGAATAACGACAAAAGTATGA
* *
30186 ATGTTATAAATATAGTTTTA
1 ATATTATAAATATATTTTTA
30206 ATTAATTATA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 59 0.94
54 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38
Consensus pattern (53 bp):
ATATTATAAATATATTTTTATAGATTAAAATAAGAATAACGACAAAAGTATGA
Found at i:30216 original size:22 final size:22
Alignment explanation
Indices: 30189--30235 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
30179 AGTATTAATG
*
30189 TTATAAATATAGTTTTA-ATTAA
1 TTATAAA-ATAGTTATATATTAA
*
30211 TTATAAAATTGTTATATATTAA
1 TTATAAAATAGTTATATATTAA
30233 TTA
1 TTA
30236 GATTTTATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
TTATAAAATAGTTATATATTAA
Found at i:39158 original size:20 final size:20
Alignment explanation
Indices: 39125--39182 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
39115 TGAAATTTAA
39125 AATAATATAAATAAAA-TTT
1 AATAATATAAATAAAATTTT
*
39144 AATAGATATAGATAAAATTTT
1 AATA-ATATAAATAAAATTTT
39165 AATAATATAAATTAAAAT
1 AATAATATAAA-TAAAAT
39183 AAATCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.12
20 17 0.50
21 13 0.38
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AATAATATAAATAAAATTTT
Found at i:39534 original size:17 final size:18
Alignment explanation
Indices: 39491--39541 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
39481 GGAATGTTTA
39491 TGAAGGAATTGAAATCTG
1 TGAAGGAATTGAAATCTG
39509 TGAAGGAATTGAAATCTG
1 TGAAGGAATTGAAATCTG
* *
39527 T-CAGGAATTGGAATC
1 TGAAGGAATTGAAATC
39542 CAATTCCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.27
Consensus pattern (18 bp):
TGAAGGAATTGAAATCTG
Found at i:40410 original size:185 final size:184
Alignment explanation
Indices: 40086--40475 Score: 622
Period size: 185 Copynumber: 2.1 Consensus size: 184
40076 TTTTCTAATT
* * * * *
40086 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAAATAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
40150 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
* * *
40215 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGCTTAGCTCATATGTTA
131 GGATCTTAAATTAATAATTAGGTTTTAAATGATTTGGGCTGAGCCCATATGTTA
40269 TATATAATATATTTAATATTTTTTAAATAAAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAAATAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* *
40334 TTATAAAATAAAAATTTTATAT-AATTTTTTAAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 TTATAAAATAAAAATTTCAGATAAATTTTTT-AATTAATTAATATTGATTTAGGTTTAAAAGTTA
* *
40398 TTGGATCTTAAATTAATAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
129 TTGGATCTTAAATTAATAATTAGGTTTTAAATGATTTGGGCTGAGCCCATATGTTA
*
40454 TATATATATATATTTAAAATTT
1 TATATA-ATATATTTAATATTT
40476 AATTTCAGTT
Statistics
Matches: 190, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
183 7 0.04
184 31 0.16
185 138 0.73
186 14 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAAATAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT
GGATCTTAAATTAATAATTAGGTTTTAAATGATTTGGGCTGAGCCCATATGTTA
Done.