Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002280.1 Hibiscus syriacus cultivar Beakdansim tig00004640_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: 63955
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:823 original size:21 final size:20
Alignment explanation
Indices: 799--843 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
789 TTTAGTAAAC
799 TATGATCTA-TTTATTGAATTT
1 TATGAT-TATTTTATTG-ATTT
820 TATGATTATTTTTATTGATTT
1 TATGATTA-TTTTATTGATTT
841 TAT
1 TAT
844 ATACTAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 13 0.59
22 7 0.32
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (20 bp):
TATGATTATTTTATTGATTT
Found at i:1382 original size:13 final size:13
Alignment explanation
Indices: 1364--1388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1354 TCTCTAACCT
1364 TTTATTTATTTTA
1 TTTATTTATTTTA
1377 TTTATTTATTTT
1 TTTATTTATTTT
1389 TGAGTGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:12506 original size:44 final size:44
Alignment explanation
Indices: 12458--12601 Score: 157
Period size: 44 Copynumber: 3.2 Consensus size: 44
12448 CCAGATCTCT
12458 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
* * * * * ** * *
12502 TCATCACGTAGGAACCATGTTATCACCTTTA-GATGGCCAGATC-TCT
1 TCATCACGTAAGAGCC--G-TGTCAACATTAGGATAACCAG-CCGTCC
12548 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
12592 TCATCACGTA
1 TCATCACGTA
12602 GGAACCGAGT
Statistics
Matches: 76, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
43 9 0.12
44 34 0.45
46 24 0.32
47 9 0.12
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (44 bp):
TCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
Found at i:12558 original size:90 final size:93
Alignment explanation
Indices: 12446--12664 Score: 347
Period size: 90 Copynumber: 2.4 Consensus size: 93
12436 TCATCCCCTG
12446 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
12511 AGGAACC-ATGTTATCA-CCTT-T-AGAT
66 AGGAACCGA-GTTATCACCCTTCTAAGAT
*
12536 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
12601 AGGAACCGAGTTATCACCCTTCCTAAAGAT
66 AGGAACCGAGTTATCACCCTT-CT-AAGAT
* * *
12631 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
12665 CCCTTAGACG
Statistics
Matches: 118, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
90 78 0.66
91 5 0.04
93 1 0.01
95 34 0.29
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (93 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGT
AGGAACCGAGTTATCACCCTTCTAAGAT
Found at i:21106 original size:45 final size:46
Alignment explanation
Indices: 21015--21119 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 46
21005 TGTACATACC
* *
21015 ATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATGCTTTTT
1 ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTT
*
21061 ATGCATCGATGCACTTAGGCTATTT-T-AAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGG-TATTTATGAAAACATCGAATGCATTTT
* *
21106 ATGAATTGATGCAC
1 ATGCATCGATGCAC
21120 CCTTAGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 30 0.57
46 19 0.36
47 4 0.08
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGTATTTATGAAAACATCGAATGCATTTT
Found at i:27834 original size:64 final size:65
Alignment explanation
Indices: 27679--27839 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 65
27669 TGAATAAATT
* *
27679 AAACATCGAATGCATTTTATGCTTCGATGCACATACCATGCATCAATACACTCAGGTTTTTATGA
1 AAACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCAATACACTCAGGTATTTATGA
* *
27744 AAACATCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTATTT-T
1 AAACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCAATACACTCAGG-TATTTAT
27807 -A
64 GA
*
27808 AAACATCGAATGTATTTTATGCATCGATGCAC
1 AAACATCGAATGCATTTTATGCATCGATGCAC
27840 CCCTTAGTGC
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 33 0.37
65 52 0.58
66 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (65 bp):
AAACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCAATACACTCAGGTATTTATGA
Found at i:31063 original size:21 final size:21
Alignment explanation
Indices: 31039--31079 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31029 CCGAAGCTGA
31039 AGCGAGAGAAGCAGAAAGAGC
1 AGCGAGAGAAGCAGAAAGAGC
*
31060 AGCGAGAGAAGCAGAGAGAG
1 AGCGAGAGAAGCAGAAAGAG
31080 AAGCATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.41, T:0.00
Consensus pattern (21 bp):
AGCGAGAGAAGCAGAAAGAGC
Found at i:34945 original size:22 final size:22
Alignment explanation
Indices: 34920--34975 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
34910 ATTTTTAGTG
34920 TTTTTTATTTTTAGTAATTTAA
1 TTTTTTATTTTTAGTAATTTAA
* *
34942 TTTTTTATTTTTAGTAGTTTTA
1 TTTTTTATTTTTAGTAATTTAA
* *
34964 TATTTGATTTTT
1 TTTTTTATTTTT
34976 TTAATATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTTTATTTTTAGTAATTTAA
Found at i:34995 original size:15 final size:16
Alignment explanation
Indices: 34959--34992 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
34949 TTTTTAGTAG
34959 TTTT-ATATTTGATTT
1 TTTTAATATTTGATTT
34974 TTTTAATATTTGATTT
1 TTTTAATATTTGATTT
34990 TTT
1 TTT
34993 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTAATATTTGATTT
Found at i:39376 original size:20 final size:20
Alignment explanation
Indices: 39343--39393 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
39333 TAGTTATTTG
**
39343 TATATAAATTTTATTAAATA
1 TATATAAAAATTATTAAATA
39363 TATATAAAAATTA-TAAATA
1 TATATAAAAATTATTAAATA
*
39382 -ATA-GAAAATTAT
1 TATATAAAAATTAT
39394 ATTAAGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 6 0.22
20 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TATATAAAAATTATTAAATA
Found at i:39395 original size:64 final size:62
Alignment explanation
Indices: 39321--39441 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 62
39311 AAAAAAATTT
* * *
39321 AAAATATATATTTAGTTATTTGTATATAAATTTTATTAAATATATATAAAAATTATAAATAATAG
1 AAAATATATATTAAGTTATTTGTATA-AAAATTTA-GAAATATA-ATAAAAATTATAAATAATAG
* * *
39386 AAAAT-TATATTAAGTTATTTGTGTAAAAATTTAGAAATATAATTATAATTATAAAT
1 AAAATATATATTAAGTTATTTGTATAAAAATTTAGAAATATAATAAAAATTATAAAT
39442 TTAATTTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 13 0.26
62 7 0.14
63 7 0.14
64 18 0.36
65 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (62 bp):
AAAATATATATTAAGTTATTTGTATAAAAATTTAGAAATATAATAAAAATTATAAATAATAG
Found at i:45342 original size:22 final size:22
Alignment explanation
Indices: 45294--45336 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
45284 AACTTTTTTG
*
45294 GTCAAAGTAAACGGTCATACCC
1 GTCAAAGTAAACGGTCAGACCC
* *
45316 GTCAAAGTCAATGGTCAGACC
1 GTCAAAGTAAACGGTCAGACC
45337 GATCAACGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (22 bp):
GTCAAAGTAAACGGTCAGACCC
Found at i:53823 original size:102 final size:102
Alignment explanation
Indices: 53647--53911 Score: 336
Period size: 102 Copynumber: 2.6 Consensus size: 102
53637 TATTAGAATA
* * * * * *
53647 TGACATTGAGTATGCGAGA-TAAAAGAAGATTGAAAAGAAGTGTCGTAACATATTTTCTAGCTAG
1 TGACATTGTGTATGCGA-ACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAG
*
53711 TCATGCATCAGATGATTATGAGTCCCTCAGTTTTAATT
65 TCATGCATCAGATGATTATGAGTCACTCAGTTTTAATT
* * * * *
53749 TGACATTTTGTATGCGAACTAAAAGATGATCGAAAGGAAATGTCATAGCAGATTTTCTGGCCAGT
1 TGACATTGTGTATGCGAACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAGT
** *
53814 CATTTATCAGATGATTATGTGTCACTCAGTTTTAATT
66 CATGCATCAGATGATTATGAGTCACTCAGTTTTAATT
* * *
53851 TGACATTGTGTATGC-AAGCTAAAAGACGCTCGAAAAGAAGTGTCGTAGCAGATTTTGTGGC
1 TGACATTGTGTATGCGAA-CTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGC
53912 ACCAGATGAT
Statistics
Matches: 139, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
101 3 0.02
102 136 0.98
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (102 bp):
TGACATTGTGTATGCGAACTAAAAGAAGATCGAAAAGAAGTGTCGTAGCAGATTTTCTGGCCAGT
CATGCATCAGATGATTATGAGTCACTCAGTTTTAATT
Found at i:54659 original size:8 final size:8
Alignment explanation
Indices: 54648--54678 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
54638 AAGAAAAAGA
54648 AAAAAATG
1 AAAAAATG
54656 AAAAAATG
1 AAAAAATG
54664 AAAAAAATG
1 -AAAAAATG
54673 AAAAAA
1 AAAAAA
54679 AAGAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:54667 original size:6 final size:6
Alignment explanation
Indices: 54580--54651 Score: 144
Period size: 6 Copynumber: 12.0 Consensus size: 6
54570 AAAGACAGAG
54580 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
54628 GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA
54652 AATGAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:54694 original size:9 final size:8
Alignment explanation
Indices: 54587--54714 Score: 85
Period size: 9 Copynumber: 14.4 Consensus size: 8
54577 GAGGAAAAAG
54587 AAAAAGAA
1 AAAAAGAA
*
54595 AAAGAAAAA
1 AAA-AAGAA
54604 GAAAAAGAA
1 -AAAAAGAA
*
54613 AAAGAAAAA
1 AAA-AAGAA
54622 GAAAAAGAA
1 -AAAAAGAA
*
54631 AAAGAAAAA
1 AAA-AAGAA
54640 GAAAAAGAA
1 -AAAAAGAA
54649 AAAAATGAA
1 AAAAA-GAA
*
54658 AAAATGAA
1 AAAAAGAA
54666 AAAAATGAAA
1 AAAAA-G-AA
54676 AAAAAGAA
1 AAAAAGAA
*
54684 AGAAAACAA
1 A-AAAAGAA
*
54693 AGGATAAGAA
1 A--AAAAGAA
54703 TAAAAAGAA
1 -AAAAAGAA
54712 AAA
1 AAA
54715 CAAAAAACTG
Statistics
Matches: 96, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
8 27 0.28
9 46 0.48
10 22 0.23
11 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:56914 original size:36 final size:36
Alignment explanation
Indices: 56872--57049 Score: 123
Period size: 36 Copynumber: 5.3 Consensus size: 36
56862 TGAGGTTGTT
* *
56872 TCTTGAAACAAATTTTGTCTCGCATGAGACAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
* * * *
56908 TCTTGAAACATAA-----AC-C-TTTGAGATTGTTTA
1 TCTTGAAACA-AATTTTGTCTCGCTTGAGATAGTTTC
*
56938 TCTTGAAACAAATTTTGTCTCGCTTAAGATAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
* * * * *
56974 TCTTGAAACATAA-----AC-C-TTTAAGATTGTTTA
1 TCTTGAAACA-AATTTTGTCTCGCTTGAGATAGTTTC
*
57004 TCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTC
1 TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
57040 TCTTGAAACA
1 TCTTGAAACA
57050 TAAACATTTG
Statistics
Matches: 105, Mismatches: 21, Indels: 32
0.66 0.13 0.20
Matches are distributed among these distances:
29 4 0.04
30 40 0.38
31 2 0.02
32 2 0.02
34 2 0.02
35 2 0.02
36 49 0.47
37 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (36 bp):
TCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTC
Found at i:56942 original size:30 final size:30
Alignment explanation
Indices: 56903--57013 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
56893 GCATGAGACA
* *
56903 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTATCTTGAAACATAAACCTTTAAGATT
* * *
56933 GTTTATCTTGAAACA-AATTTTGTCTCGCTTAAGATA
1 GTTTATCTTGAAACATAA-----AC-C-TTTAAGATT
*
56969 GTTTCTCTTGAAACATAAACCTTTAAGATT
1 GTTTATCTTGAAACATAAACCTTTAAGATT
56999 GTTTATCTTGAAACA
1 GTTTATCTTGAAACA
57014 AATTTTGTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
29 2 0.03
30 35 0.56
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 20 0.32
37 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.41
Consensus pattern (30 bp):
GTTTATCTTGAAACATAAACCTTTAAGATT
Found at i:56978 original size:66 final size:66
Alignment explanation
Indices: 56822--57106 Score: 421
Period size: 66 Copynumber: 4.3 Consensus size: 66
56812 AGAAGATTGC
* * *
56822 TTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAATTTGAGGTTG-TT-TCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
56885 T
66 T
* *
56886 TTGTCTCGCATGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTATCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
56951 T
66 T
* * * *
56952 TTGTCTCGCTTAAGATAGTTTCTCTTGAAACATAAACCTTTAAGATTGTTTATCTTGAAACAAAT
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
57017 T
66 T
*
57018 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAAG
1 TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAA-
57083 TT
65 TT
** * *
57085 ACGTCTCACTTGAGACAATTTC
1 TTGTCTCGCTTGAGACAGTTTC
57107 CCATAAAAAC
Statistics
Matches: 200, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
64 43 0.22
65 2 0.01
66 135 0.68
67 20 0.10
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (66 bp):
TTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTATCTTGAAACAAAT
T
Found at i:57133 original size:67 final size:66
Alignment explanation
Indices: 56824--57141 Score: 205
Period size: 66 Copynumber: 4.8 Consensus size: 66
56814 AAGATTGCTT
* * * ** * ** *
56824 GTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAAATTTGAGGTTG-TT-TCTTGAAACAAATTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
*
56887 T
66 C
* * * * ** * * * *
56888 GTCTCGCATGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTATCTTGAAACAAATTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
*
56953 T
66 C
* * * * * ** * *
56954 GTCTCGCTTAAGATAGTTTCTCTTGAAACATAAACCTTT-AAGATTGTTTATCTTGAAACAAATT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAA-ATTGTTTCTCTTGAAACAAATT
**
57018 TT
65 AC
* * * ** *
57020 GTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACATTTGAGATTGTTTCTCTTGAAACAAAGTT
1 GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAA-TT
57085 AC
65 AC
* *
57087 GTCTCACTTGAGACAATTTCCCATAAAAAC-TCAAA-TTTTGAAATTGTTTCACTTG
1 GTCTCACTTGAGACAATTTCCC-TAAAAACAT-AAACATTTGAAATTGTTTCTCTTG
57142 GAAAAAAAAG
Statistics
Matches: 223, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
64 41 0.18
65 3 0.01
66 131 0.59
67 40 0.18
68 8 0.04
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (66 bp):
GTCTCACTTGAGACAATTTCCCTAAAAACATAAACATTTGAAATTGTTTCTCTTGAAACAAATTA
C
Found at i:57286 original size:103 final size:102
Alignment explanation
Indices: 57057--57290 Score: 233
Period size: 103 Copynumber: 2.3 Consensus size: 102
57047 ACATAAACAT
* *
57057 TTGAGATTGTTTCTCTTGAAACAAAGTTACGTCTCACTTGAGACAATTTCCCATAAAAACTCAAA
1 TTGAGATAG-TTCTCTTGAAACAAA-TTACGTCTCACTTGAGACAATTTCCCATAAAAACACAAA
*
57122 TTTTGAAATTGTTTCACTTGGAAAAAAAAGTAATCTCAT
64 TTTTGAAATTGTTTCACTTGGAAAAAAAAGTAATCTCAC
* * * * * * **
57161 TTGAGATTGTTTTC-CGAAAAACAAA-TATCGTCTCGCTTGAGGCAGTTTTCCC-TTGAAACACA
1 TTGAGATAGTTCTCTTG--AAACAAATTA-CGTCTCACTTGAGACA-ATTTCCCATAAAAACACA
** *
57223 AATTTTGAAATTGTTTCACTT-GAAACAAAATTTTATCTCAC
62 AATTTTGAAATTGTTTCACTTGGAAA-AAAAAGTAATCTCAC
*
57264 TTGATATAGCTTCTCTTGAAACAAATT
1 TTGAGATAG-TTCTCTTGAAACAAATT
57291 TCTTTCCACT
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
102 7 0.07
103 71 0.67
104 27 0.25
105 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (102 bp):
TTGAGATAGTTCTCTTGAAACAAATTACGTCTCACTTGAGACAATTTCCCATAAAAACACAAATT
TTGAAATTGTTTCACTTGGAAAAAAAAGTAATCTCAC
Found at i:59252 original size:14 final size:14
Alignment explanation
Indices: 59233--59264 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
59223 TTTTTATTTA
59233 TTTAATGTCATTCC
1 TTTAATGTCATTCC
*
59247 TTTAATTTCATTCC
1 TTTAATGTCATTCC
59261 TTTA
1 TTTA
59265 GTTTTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (14 bp):
TTTAATGTCATTCC
Found at i:60585 original size:24 final size:25
Alignment explanation
Indices: 60558--60608 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
60548 TGATTTTATT
*
60558 TTTTTATAATTA-GTTTACCTTTTA
1 TTTTTATAATTATGTTTACATTTTA
* *
60582 -TTTTATATTTATGTTTATATTTTA
1 TTTTTATAATTATGTTTACATTTTA
60606 TTT
1 TTT
60609 AATTGTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
23 10 0.45
24 10 0.45
25 2 0.09
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTATAATTATGTTTACATTTTA
Found at i:62037 original size:16 final size:16
Alignment explanation
Indices: 61995--62037 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
61985 TTTCTCCTAA
* *
61995 AAAATAATTCATAAAT
1 AAAATAATCCTTAAAT
*
62011 -AAATAACCCTTAAAT
1 AAAATAATCCTTAAAT
62026 AAAATAATCCTT
1 AAAATAATCCTT
62038 CTCAACTGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAATCCTTAAAT
Found at i:63340 original size:29 final size:29
Alignment explanation
Indices: 63235--63441 Score: 223
Period size: 29 Copynumber: 7.3 Consensus size: 29
63225 TCATATATAT
*
63235 AAATAGTTTTGTA-CTTATTATAATTTAG
1 AAATAGTTTTGTACCTTATTGTAATTTAG
*
63263 AAATAG-TTT-TA-CTTATTGT-TTTTAG
1 AAATAGTTTTGTACCTTATTGTAATTTAG
* *
63288 AAATAG-TTTGTACTTTATTTTAATTTAG
1 AAATAGTTTTGTACCTTATTGTAATTTAG
* *
63316 AAATAGTTTTGCACTTTATTGTAATTTAG
1 AAATAGTTTTGTACCTTATTGTAATTTAG
* *
63345 AAATAGTTATGTACCTTATTGTAATTTAT
1 AAATAGTTTTGTACCTTATTGTAATTTAG
* *
63374 AAATACTTTTTTACCTTATTGTAATTTA-
1 AAATAGTTTTGTACCTTATTGTAATTTAG
* *
63402 ATAA-AATTTATGTACCTTATTGTAATTTAT
1 A-AATAGTTT-TGTACCTTATTGTAATTTAG
*
63432 AAATACTTTT
1 AAATAGTTTT
63442 ATATTTTATT
Statistics
Matches: 154, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
25 14 0.09
26 11 0.07
27 9 0.06
28 22 0.14
29 93 0.60
30 5 0.03
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.51
Consensus pattern (29 bp):
AAATAGTTTTGTACCTTATTGTAATTTAG
Found at i:63450 original size:29 final size:29
Alignment explanation
Indices: 63232--63489 Score: 196
Period size: 29 Copynumber: 9.2 Consensus size: 29
63222 TTATCATATA
* *
63232 TATAAATAGTTTTGTA-CTTATTATAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
* * *
63260 TAGAAATA-GTTT-TA-CTTATTGT-TTT
1 TATAAATACTTTTGTACCTTATTGTAATT
* * * *
63285 TAGAAATA-GTTTGTACTTTATTTTAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
* * * *
63313 TAGAAATAGTTTTGCACTTTATTGTAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
* * *
63342 TAGAAATAGTTATGTACCTTATTGTAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
*
63371 TATAAATACTTTTTTACCTTATTGTAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
63400 TAATAAA-A-TTTATGTACCTTATTGTAATT
1 T-ATAAATACTTT-TGTACCTTATTGTAATT
* ** *
63429 TATAAATACTTTTATATTTTATTATAATT
1 TATAAATACTTTTGTACCTTATTGTAATT
* * *
63458 TCTAAA-ACGTTTGT-CTTTATTGT-ATT
1 TATAAATACTTTTGTACCTTATTGTAATT
*
63484 TCTAAA
1 TATAAA
63490 AAGATATGTC
Statistics
Matches: 195, Mismatches: 27, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
25 14 0.07
26 20 0.10
27 16 0.08
28 31 0.16
29 106 0.54
30 8 0.04
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (29 bp):
TATAAATACTTTTGTACCTTATTGTAATT
Found at i:63536 original size:28 final size:27
Alignment explanation
Indices: 63446--63537 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
63436 ACTTTTATAT
**
63446 TTTATTATAATTTCTAAAACGTTTGT-C
1 TTTATTAT-ATTTCTAAAAAATTTGTCC
* *
63473 TTTATTGTATTTCTAAAAAGATATGTCC
1 TTTATTATATTTCTAAAAA-ATTTGTCC
* *
63501 TTCATTATATTTCTAAAATATTTTGTCC
1 TTTATTATATTTCTAAAA-AATTTGTCC
*
63529 TTTTTTATA
1 TTTATTATA
63538 AATTTTAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
26 10 0.19
27 11 0.21
28 30 0.58
29 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.07, T:0.53
Consensus pattern (27 bp):
TTTATTATATTTCTAAAAAATTTGTCC
Done.