Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004988.1 Hibiscus syriacus cultivar Beakdansim tig00011189_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: 61449
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:12437 original size:2 final size:2
Alignment explanation
Indices: 12430--12464 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12420 TAATATTTTG
12430 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 A
12465 AAGTGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20535 original size:43 final size:46
Alignment explanation
Indices: 20447--20551 Score: 128
Period size: 49 Copynumber: 2.3 Consensus size: 46
20437 AGAATTAGAT
20447 TTATTATTTTATTAGGAATTAAGTTTAAGTTAAAATATTTTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGTTTAAG-TAAAATA--TTTTAGTTTA
* *
20496 TTATTATTTTATTAGGAATTAGAG-TTAAG-AACA-A-TTTAGTTTG
1 TTATTATTTTATTAGGAATTA-AGTTTAAGTAAAATATTTTAGTTTA
20539 TTATTATTTTATT
1 TTATTATTTTATT
20552 CATTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
43 21 0.40
46 1 0.02
47 3 0.06
49 26 0.49
50 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.11, T:0.54
Consensus pattern (46 bp):
TTATTATTTTATTAGGAATTAAGTTTAAGTAAAATATTTTAGTTTA
Found at i:20895 original size:58 final size:59
Alignment explanation
Indices: 20781--20900 Score: 163
Period size: 58 Copynumber: 2.1 Consensus size: 59
20771 GGAGGGTTGG
* * *
20781 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTGGAACTAGAAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTACCTATTCATTCGAACTAGAAGGGTTCGATAGGACAC
* * *
20840 TTAGATCCATATTATCGAGTTTACC-ATTCATTACG-ATTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTACCTATTCATT-CGAACTAGAAGGGTTCGATAGGACAC
20898 TTA
1 TTA
20901 TCCACCTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
58 30 0.56
59 24 0.44
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTACCTATTCATTCGAACTAGAAGGGTTCGATAGGACAC
Found at i:23064 original size:17 final size:17
Alignment explanation
Indices: 23038--23079 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
23028 GGAGGTAGAG
23038 AAAG-AAAAAAAA-GAA
1 AAAGCAAAAAAAACGAA
*
23053 AAAGCTAAAAAAAACGCA
1 AAAGC-AAAAAAAACGAA
23071 AAAGCAAAA
1 AAAGCAAAA
23080 GAGGTCACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.76, C:0.10, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAGCAAAAAAAACGAA
Found at i:24857 original size:20 final size:22
Alignment explanation
Indices: 24832--24877 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
24822 TAATTTAATA
24832 TTAGGA-TA-ATGCATTATCTT
1 TTAGGATTAGATGCATTATCTT
**
24852 TTAGGATTAGATTTATTATCTT
1 TTAGGATTAGATGCATTATCTT
24874 TTAG
1 TTAG
24878 TTTATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 2 0.09
22 14 0.64
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (22 bp):
TTAGGATTAGATGCATTATCTT
Found at i:25593 original size:16 final size:16
Alignment explanation
Indices: 25574--25604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25564 TTTAAAAGGC
25574 CAAAAAATAAAAAATA
1 CAAAAAATAAAAAATA
*
25590 CAAAAAATACAAAAT
1 CAAAAAATAAAAAAT
25605 TTCAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (16 bp):
CAAAAAATAAAAAATA
Found at i:29441 original size:59 final size:59
Alignment explanation
Indices: 29378--29491 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
29368 TGGTTAGAGT
**
29378 CATATTATCGAGTTTTTCTTTGCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAAC
1 CATATTATCGAGTTTACCTTTGCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAAC
* *
29437 CATATTATCGAGTTTACCTTTTCATTGCGACTAGGAGGGTTTGATAGGACACTTA
1 CATATTATCGAGTTTACCTTTGCATTGCGACTAGGAGGGTTCGATAGGACACTTA
29492 TCCATCTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (59 bp):
CATATTATCGAGTTTACCTTTGCATTGCGACTAGGAGGGTTCGATAGGACACTTAGAAC
Found at i:33393 original size:24 final size:24
Alignment explanation
Indices: 33366--33423 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
33356 ACCTTTGGGT
* *
33366 ACTCATGTTTCAGTGCAATTATGC
1 ACTCATGTATCAGTCCAATTATGC
* *
33390 ACTCTTGTATCAGTCCAATTGTGC
1 ACTCATGTATCAGTCCAATTATGC
*
33414 ACTCTTGTAT
1 ACTCATGTAT
33424 TAGTGCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (24 bp):
ACTCATGTATCAGTCCAATTATGC
Found at i:33435 original size:24 final size:25
Alignment explanation
Indices: 33377--33453 Score: 97
Period size: 24 Copynumber: 3.2 Consensus size: 25
33367 CTCATGTTTC
* *
33377 AGTG-CAATTATGCACTCTTGTATC
1 AGTGCCAATTGTGCACTCTTGTATT
33401 AGT-CCAATTGTGCACTCTTGTATT
1 AGTGCCAATTGTGCACTCTTGTATT
* *
33425 AGTGCC-TTTGTGCACTCCTGTATT
1 AGTGCCAATTGTGCACTCTTGTATT
33449 AGTGC
1 AGTGC
33454 ATTCTTACAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (25 bp):
AGTGCCAATTGTGCACTCTTGTATT
Found at i:33464 original size:24 final size:24
Alignment explanation
Indices: 33411--33596 Score: 157
Period size: 24 Copynumber: 7.7 Consensus size: 24
33401 AGTCCAATTG
* *
33411 TGCACTCTTGTATTAGTGCCTT-T
1 TGCACTCCTGTATTAGTGCATTCT
33434 GTGCACTCCTGTATTAGTGCATTCT
1 -TGCACTCCTGTATTAGTGCATTCT
* * *
33459 TACACTCCTATATTAGTGCATTCA
1 TGCACTCCTGTATTAGTGCATTCT
*
33483 TACACTCCTGTATTAGTGCAATT-T
1 TGCACTCCTGTATTAGTGC-ATTCT
* * * *
33507 TTCACTCCTGAATTAGTTCATTCA
1 TGCACTCCTGTATTAGTGCATTCT
* *
33531 TGCACTCCTG-ATTCTATTACA-TCT
1 TGCACTCCTGTA-T-TAGTGCATTCT
* *
33555 GTGTACTCCAGTATTAGTGCATT-T
1 -TGCACTCCTGTATTAGTGCATTCT
33579 GTGCACTCCTGTATTAGT
1 -TGCACTCCTGTATTAGT
33597 ACCATTGCGT
Statistics
Matches: 133, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
23 4 0.03
24 109 0.82
25 19 0.14
26 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (24 bp):
TGCACTCCTGTATTAGTGCATTCT
Found at i:33465 original size:72 final size:71
Alignment explanation
Indices: 33389--33596 Score: 195
Period size: 72 Copynumber: 2.9 Consensus size: 71
33379 TGCAATTATG
* * * *
33389 CACTCTTGTATCAGTCCAATTGTGCACTCTTGTATTAGTGCCTTTGTGCACTCCTGTATTAGTGC
1 CACTCCTGTATCAGTAC-ATTGTGCACTCCTGTATTAGTGCATTTGTGCACTCCTGTATTAGTGC
*
33454 ATTCTTA
65 ATTCATA
* * * * * * * *
33461 CACTCCTATATTAGTGCATTCATACACTCCTGTATTAGTGCAATTT-TTCACTCCTGAATTAGTT
1 CACTCCTGTATCAGTACATT-GTGCACTCCTGTATTAGTGC-ATTTGTGCACTCCTGTATTAGTG
*
33525 CATTCATG
64 CATTCATA
* * *
33533 CACTCCTG-ATTCTATTACATCTGTGTACTCCAGTATTAGTGCATTTGTGCACTCCTGTATTAGT
1 CACTCCTGTA-TC-AGTACAT-TGTGCACTCCTGTATTAGTGCATTTGTGCACTCCTGTATTAGT
33597 ACCATTGCGT
Statistics
Matches: 107, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
71 4 0.04
72 63 0.59
73 39 0.36
74 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (71 bp):
CACTCCTGTATCAGTACATTGTGCACTCCTGTATTAGTGCATTTGTGCACTCCTGTATTAGTGCA
TTCATA
Found at i:33610 original size:24 final size:24
Alignment explanation
Indices: 33554--33659 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
33544 CTATTACATC
* *
33554 TGTGTACTCCAGTATTAGT-GCATT
1 TGTGTACTCCTGTATTAGTACCA-T
*
33578 TGTGCACTCCTGTATTAGTACCAT
1 TGTGTACTCCTGTATTAGTACCAT
* * *
33602 TGCGTACTCCTGTGTTAGTACCTT
1 TGTGTACTCCTGTATTAGTACCAT
* *
33626 TGTGTAATCATGTATTTAGTA-CAT
1 TGTGTACTCCTGTA-TTAGTACCAT
33650 TAGTGTACTC
1 T-GTGTACTC
33660 TTGGCATTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
24 51 0.77
25 15 0.23
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (24 bp):
TGTGTACTCCTGTATTAGTACCAT
Found at i:48390 original size:23 final size:23
Alignment explanation
Indices: 48364--48422 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
48354 TAGATTTTTG
*
48364 ATACAAAAATGGGTAGAGTTTCA
1 ATACAAAAATGGGTAGAGATTCA
* * * *
48387 ATACAATAATAGGTCGAGATTCT
1 ATACAAAAATGGGTAGAGATTCA
*
48410 GTACAAAAATGGG
1 ATACAAAAATGGG
48423 AAAAGTGTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.25
Consensus pattern (23 bp):
ATACAAAAATGGGTAGAGATTCA
Found at i:50260 original size:18 final size:18
Alignment explanation
Indices: 50237--50271 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50227 CTCGATTAAT
*
50237 ATTTATTTTAATTTTTTA
1 ATTTATATTAATTTTTTA
50255 ATTTATATTAATTTTTT
1 ATTTATATTAATTTTTT
50272 GGAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATATTAATTTTTTA
Found at i:51349 original size:68 final size:68
Alignment explanation
Indices: 51268--51399 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 68
51258 CGAGCAAGAG
* **
51268 TTTAATGACCTTAACGAGCAACGAGTCGACCAAAAAACTTTCTTATTGAGCACAAGTCAAGCAAA
1 TTTAACGACCTTAACGAGCAACGAGTCGACCAAAAAACTTTCTTAACGAGCACAAGTCAAGCAAA
51333 AAT
66 AAT
* * ** * * * *
51336 TTTAACGAGCTTAACGAGCAATGAGTCGTGCAATAAATTTTCTTAACGAGCACGAGTCGAGCAA
1 TTTAACGACCTTAACGAGCAACGAGTCGACCAAAAAACTTTCTTAACGAGCACAAGTCAAGCAA
51400 CAAAAGTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 53 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (68 bp):
TTTAACGACCTTAACGAGCAACGAGTCGACCAAAAAACTTTCTTAACGAGCACAAGTCAAGCAAA
AAT
Found at i:51381 original size:32 final size:32
Alignment explanation
Indices: 51345--51429 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
51335 TTTTAACGAG
* * *
51345 CTTAACGAGCAATGAGTCGTGCAA-TAAATTTT
1 CTTAACGAGC-ATGAGTCGAGCAACAAAAGTTT
*
51377 CTTAACGAGCACGAGTCGAGCAACAAAAGTTT
1 CTTAACGAGCATGAGTCGAGCAACAAAAGTTT
*
51409 -TTAATGAGCATGAGTCGAGCA
1 CTTAACGAGCATGAGTCGAGCA
51430 CAGTCCAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.65
32 16 0.35
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (32 bp):
CTTAACGAGCATGAGTCGAGCAACAAAAGTTT
Found at i:51946 original size:19 final size:19
Alignment explanation
Indices: 51922--51969 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
51912 ACATGTTTTT
51922 AATCACTTATAAGGCTCCC
1 AATCACTTATAAGGCTCCC
51941 AATCACTTATAAGGCTCCC
1 AATCACTTATAAGGCTCCC
51960 AATCACTTAT
1 AATCACTTAT
51970 TTACTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
AATCACTTATAAGGCTCCC
Done.