Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001617.1 Hibiscus syriacus cultivar Beakdansim tig00003214_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: 73843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2773 original size:21 final size:23
Alignment explanation
Indices: 2730--2778 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
2720 TTTTACCGAA
2730 AAATATTAAAAAATAATTATTTT
1 AAATATTAAAAAATAATTATTTT
*
2753 AAATA-TAAATAATAA-TATTTT
1 AAATATTAAAAAATAATTATTTT
2774 AAATA
1 AAATA
2779 ATTCTTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.44
22 9 0.36
23 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATTAAAAAATAATTATTTT
Found at i:15244 original size:2 final size:2
Alignment explanation
Indices: 15237--15263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15227 AGTGTTTATT
15237 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
15264 TAAATGATTA
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:21849 original size:22 final size:21
Alignment explanation
Indices: 21824--21888 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 21
21814 ATAATTAATT
21824 TGTTCATATTATAAAAAGTTAA
1 TGTTCATATTATAAAAAGTT-A
*
21846 TGTT-AT-TGT-TAATAA-TT-
1 TGTTCATAT-TATAAAAAGTTA
*
21863 TGTACATATTATAAAAAGTTTA
1 TGTTCATATTATAAAAAG-TTA
21885 TGTT
1 TGTT
21889 AATAATATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 8 0.25
20 6 0.19
21 5 0.16
22 7 0.22
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (21 bp):
TGTTCATATTATAAAAAGTTA
Found at i:21889 original size:33 final size:36
Alignment explanation
Indices: 21819--21894 Score: 95
Period size: 39 Copynumber: 2.1 Consensus size: 36
21809 TAACAATAAT
*
21819 TAATTTGTTCATATTATAAAAAGTTAATGTTATTGTTAA
1 TAATTTGTACATATTATAAAAAG---ATGTTATTGTTAA
21858 TAATTTGTACATATTATAAAAAG-T-TTA-TGTTAA
1 TAATTTGTACATATTATAAAAAGATGTTATTGTTAA
21891 TAAT
1 TAAT
21895 ATTGATGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 10 0.28
34 3 0.08
35 1 0.03
39 22 0.61
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (36 bp):
TAATTTGTACATATTATAAAAAGATGTTATTGTTAA
Found at i:23068 original size:40 final size:40
Alignment explanation
Indices: 23024--23112 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 40
23014 AAAATTAGTG
* *
23024 TCGTCACAAATTACCAACTAAGACTAGTGACAAAAATAAT
1 TCGTCACAAATCACCAACTAAGACTAGAGACAAAAATAAT
* *
23064 TCGTCACAAATCACCAACTAAGACTAGAGACAAAATTATT
1 TCGTCACAAATCACCAACTAAGACTAGAGACAAAAATAAT
*
23104 TCATCACAA
1 TCGTCACAA
23113 TTATGAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.22
Consensus pattern (40 bp):
TCGTCACAAATCACCAACTAAGACTAGAGACAAAAATAAT
Found at i:25176 original size:18 final size:18
Alignment explanation
Indices: 25155--25196 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25145 ATTAATATTA
*
25155 TTTATATGAATTATAATG
1 TTTAAATGAATTATAATG
* *
25173 TTTAAATTAATTATAATT
1 TTTAAATGAATTATAATG
25191 TTTAAA
1 TTTAAA
25197 CTAAATATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTAAATGAATTATAATG
Found at i:25205 original size:18 final size:18
Alignment explanation
Indices: 25166--25208 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
25156 TTATATGAAT
* * *
25166 TATAATGTTTAAATTAAT
1 TATAATTTTTAAACTAAA
25184 TATAATTTTTAAACTAAA
1 TATAATTTTTAAACTAAA
25202 TATAATT
1 TATAATT
25209 ATACTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TATAATTTTTAAACTAAA
Found at i:26312 original size:28 final size:25
Alignment explanation
Indices: 26279--26332 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
26269 TAGTATATAA
26279 ATAATTATAAGTACTACATATATATTAT
1 ATAATTATAA-T--TACATATATATTAT
* *
26307 ATAATTCTAATTACTTATATATTAT
1 ATAATTATAATTACATATATATTAT
26332 A
1 A
26333 ATGAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.58
27 1 0.04
28 9 0.38
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (25 bp):
ATAATTATAATTACATATATATTAT
Found at i:31559 original size:16 final size:17
Alignment explanation
Indices: 31532--31567 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
31522 ATATGAGAAA
31532 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
31549 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
31565 AAA
1 AAA
31568 ATAACATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:33005 original size:33 final size:34
Alignment explanation
Indices: 32948--33013 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
32938 TGCCTAACTC
* *
32948 TCACCTAACTAATTTGATGTAAGCAATGACATCT
1 TCACCTAACAAAATTGATGTAAGCAATGACATCT
32982 TCACCTAACAAAATT-ATGTAAGCAATGACATC
1 TCACCTAACAAAATTGATGTAAGCAATGACATC
33014 AAATTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.57
34 13 0.43
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (34 bp):
TCACCTAACAAAATTGATGTAAGCAATGACATCT
Found at i:46834 original size:19 final size:21
Alignment explanation
Indices: 46802--46841 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
46792 AATTGGTTTA
*
46802 AAAAATATATTTAT-AATTTT
1 AAAAATATAATTATAAATTTT
46822 AAAAATA-AATTATAAATTTT
1 AAAAATATAATTATAAATTTT
46842 TATATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATATAATTATAAATTTT
Found at i:47386 original size:20 final size:19
Alignment explanation
Indices: 47363--47404 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
47353 ATTGGTTCAC
*
47363 GAAATTTAAGATTACCAGTG
1 GAAATGTAAGATTACCAG-G
47383 GAAATGTAAGATTACCAGG
1 GAAATGTAAGATTACCAGG
47402 GAA
1 GAA
47405 TATGATTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (19 bp):
GAAATGTAAGATTACCAGG
Found at i:49511 original size:60 final size:60
Alignment explanation
Indices: 49408--49583 Score: 203
Period size: 60 Copynumber: 2.9 Consensus size: 60
49398 ATAATGTGGT
* * * * *
49408 ATGAAATTGAAATGTTCAAAAAGTTTGTTGACCAATTTAGAATGAAGATCATAGTTTGGGG
1 ATGAAATTGAAATATTC-AAAAGTTTGATGACTAATTTAGAATGAAGATCATAATTTAGGG
49469 ATGAAATTGAAATATTCAAAAGTTTGATGACTAATTTAGAATGATAG-TCATAATTTAGGG
1 ATGAAATTGAAATATTCAAAAGTTTGATGACTAATTTAGAATGA-AGATCATAATTTAGGG
* * * * * * *
49529 ATGGAATTAAAATATTTAAAACTTT-AAGAATTAATTTAGAAGGAAGATCATAATT
1 ATGAAATTGAAATATTCAAAAGTTTGATG-ACTAATTTAGAATGAAGATCATAATT
49584 GAAGGACTTG
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
59 4 0.04
60 78 0.78
61 18 0.18
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (60 bp):
ATGAAATTGAAATATTCAAAAGTTTGATGACTAATTTAGAATGAAGATCATAATTTAGGG
Found at i:51606 original size:12 final size:12
Alignment explanation
Indices: 51589--51613 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51579 TATAATCAAT
51589 AAAAAATCTAAA
1 AAAAAATCTAAA
51601 AAAAAATCTAAA
1 AAAAAATCTAAA
51613 A
1 A
51614 TATAAGTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATCTAAA
Found at i:51705 original size:2 final size:2
Alignment explanation
Indices: 51698--51737 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
51688 TAAAATTAAA
51698 AT AT 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
51738 GAACACAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60068 original size:20 final size:20
Alignment explanation
Indices: 60032--60069 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60022 ATCCTATTTC
**
60032 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
60052 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
60070 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:64515 original size:9 final size:9
Alignment explanation
Indices: 64485--64536 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
64475 TTAGCAAAAA
*
64485 AAATTAATT
1 AAATTAAAT
64494 AAA-TAAA-
1 AAATTAAAT
*
64501 ATATTAAAT
1 AAATTAAAT
64510 AAATTAAAT
1 AAATTAAAT
*
64519 -ACTTAAAT
1 AAATTAAAT
64527 AAATTAAAT
1 AAATTAAAT
64536 A
1 A
64537 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:64517 original size:17 final size:17
Alignment explanation
Indices: 64482--64534 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
64472 ATATTAGCAA
* *
64482 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
64498 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
64515 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
64532 AAA
1 AAA
64535 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:64535 original size:17 final size:17
Alignment explanation
Indices: 64488--64537 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
64478 GCAAAAAAAA
* *
64488 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
64504 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
64521 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
64538 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:72664 original size:2 final size:2
Alignment explanation
Indices: 72657--72706 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
72647 CCAATCTGAA
72657 AT AT AT AT AT AT AT AT AT AT AT AT A- 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 AT
72697 AT AT AT AT AT
1 AT AT AT AT AT
72707 TATTATTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73676 original size:4 final size:4
Alignment explanation
Indices: 73658--73759 Score: 133
Period size: 4 Copynumber: 26.5 Consensus size: 4
73648 CTGGAATATA
*
73658 TATG TATA TAT- TATG TATG TATG TATG TATG TA-- TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
73703 TATG TATG TA-G TATG TATG TATA TATG TA-G TATG TAATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T-ATG TATG TATG
*
73750 TATA TATG TA
1 TATG TATG TA
73760 ATATATTTAA
Statistics
Matches: 87, Mismatches: 5, Indels: 12
0.84 0.05 0.12
Matches are distributed among these distances:
2 2 0.02
3 9 0.10
4 72 0.83
5 4 0.05
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:73682 original size:19 final size:20
Alignment explanation
Indices: 73658--73759 Score: 120
Period size: 19 Copynumber: 5.1 Consensus size: 20
73648 CTGGAATATA
73658 TATGTATATAT-TATGTATG
1 TATGTATATATGTATGTATG
*
73677 TATGTATGTATGTATATGTATG
1 TATGTATATATG--TATGTATG
*
73699 TATGTATGTATGTA-GTATG
1 TATGTATATATGTATGTATG
73718 TATGTATATATGTA-GTATG
1 TATGTATATATGTATGTATG
* *
73737 TAATGTATGTATGTATATATG
1 T-ATGTATATATGTATGTATG
73758 TA
1 TA
73760 ATATATTTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
19 34 0.46
20 15 0.20
21 5 0.07
22 20 0.27
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (20 bp):
TATGTATATATGTATGTATG
Done.