Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001791.1 Hibiscus syriacus cultivar Beakdansim tig00003615_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: 100928
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1562 original size:16 final size:17
Alignment explanation
Indices: 1538--1573 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1528 AATGTTAAAC
*
1538 TATGTTCAATTT-ATGT
1 TATGATCAATTTGATGT
1554 TATGATCAATTTGATGT
1 TATGATCAATTTGATGT
1571 TAT
1 TAT
1574 ACTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (17 bp):
TATGATCAATTTGATGT
Found at i:4115 original size:32 final size:34
Alignment explanation
Indices: 4053--4117 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 34
4043 CAAAATTATT
*
4053 AAATATTGACATACATTATATAAAAATTAAATAAA
1 AAATATTGACATA-ATTATAAAAAAATTAAATAAA
4088 AAATATTGACAT-ATTA-AAAAAAATTAAATA
1 AAATATTGACATAATTATAAAAAAATTAAATA
4118 TAGGATCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
35 12 0.41
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (34 bp):
AAATATTGACATAATTATAAAAAAATTAAATAAA
Found at i:6562 original size:33 final size:33
Alignment explanation
Indices: 6520--6586 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
6510 ACTCGGCTTT
6520 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
1 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
*
6553 TAAATGTTCTTCCTTCCTTATAAATAACAACCC
1 TAAATGTTCTTCCTTCCCTATAAATAACAACCC
6586 T
1 T
6587 CTTAATGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (33 bp):
TAAATGTTCTTCCTTCCCTATAAATAACAACCC
Found at i:12184 original size:23 final size:24
Alignment explanation
Indices: 12158--12202 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12148 TGTATTATAG
12158 ACTTGTA-TATCTGCTGTTCTGTC
1 ACTTGTATTATCTGCTGTTCTGTC
*
12181 ACTTGTATTTTCTGCTGTTCTG
1 ACTTGTATTATCTGCTGTTCTG
12203 CCTGCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (24 bp):
ACTTGTATTATCTGCTGTTCTGTC
Found at i:17323 original size:51 final size:51
Alignment explanation
Indices: 17263--17364 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
17253 TTTAAGGCAT
17263 TGAATAGAGAAAATGTATGTTAGGTAATGACAGTCATCATTTACATGGATA
1 TGAATAGAGAAAATGTATGTTAGGTAATGACAGTCATCATTTACATGGATA
17314 TGAATAGAGAAAATGTATGTTAGGTAATGACAGTCATCATTTACATGGATA
1 TGAATAGAGAAAATGTATGTTAGGTAATGACAGTCATCATTTACATGGATA
17365 AAGATTGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (51 bp):
TGAATAGAGAAAATGTATGTTAGGTAATGACAGTCATCATTTACATGGATA
Found at i:20542 original size:27 final size:27
Alignment explanation
Indices: 20512--20609 Score: 115
Period size: 27 Copynumber: 3.5 Consensus size: 27
20502 CTCCGAGTCT
20512 CGTGCTGCACCACCTTCTCCCGATCCC
1 CGTGCTGCACCACCTTCTCCCGATCCC
* * *
20539 CGTGCTGCACCACCGCTCCTTCCTGATCCT
1 CGTGCTGCACCA-C-CTTC-TCCCGATCCC
*
20569 CATGCTGCACCACCTTCTCCCGATCCC
1 CGTGCTGCACCACCTTCTCCCGATCCC
* *
20596 TGTGCTGCGCCACC
1 CGTGCTGCACCACC
20610 GCTCCCACCT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
27 31 0.53
28 4 0.07
29 4 0.07
30 19 0.33
ACGTcount: A:0.11, C:0.49, G:0.16, T:0.23
Consensus pattern (27 bp):
CGTGCTGCACCACCTTCTCCCGATCCC
Found at i:20575 original size:30 final size:29
Alignment explanation
Indices: 20514--20863 Score: 279
Period size: 30 Copynumber: 12.0 Consensus size: 29
20504 CCGAGTCTCG
* * * *
20514 TGCTGCACCA-C-CTTCTCCCGATCCCCG
1 TGCTGCACCACCGCTCCTCCTGATCCTCA
20541 TGCTGCACCACCGCTCCTTCCTGATCCTCA
1 TGCTGCACCACCGCTCC-TCCTGATCCTCA
* * *
20571 TGCTGCACCA-C-CTTCTCCCGATCC-CTG
1 TGCTGCACCACCGCTCCTCCTGATCCTC-A
* * *
20598 TGCTGCGCCACCGCTCCCACCTGATCCCCA
1 TGCTGCACCACCGCT-CCTCCTGATCCTCA
* *
20628 TGCTGCGCCACCGCTCCCACCTGATCCTCA
1 TGCTGCACCACCGCT-CCTCCTGATCCTCA
*
20658 TGCCGCACCACCGCCTCCTCCTGATCCTCA
1 TGCTGCACCACCG-CTCCTCCTGATCCTCA
*
20688 TGCTGCACCACCGCCTCCTCCTGATTCTCA
1 TGCTGCACCACCG-CTCCTCCTGATCCTCA
*
20718 TGCTGCACCACTG--CCTCCTGATCCTCA
1 TGCTGCACCACCGCTCCTCCTGATCCTCA
* *
20745 TGCTGCACCTCCTCCTCCTCCTCCTGATCCTCA
1 TGCTGCA---CCACC-GCTCCTCCTGATCCTCA
* * * *
20778 TGCTGCACCATCGACTCCTGCTGTTCCTCG
1 TGCTGCACCACCG-CTCCTCCTGATCCTCA
* * *
20808 TGCTGCACAACTAC-CTCCTCCTGTTCCTCG
1 TGCTGCACCAC--CGCTCCTCCTGATCCTCA
* *
20838 TGTTGCACCA-C-CTTCTCCTGATCCTC
1 TGCTGCACCACCGCTCCTCCTGATCCTC
20864 GTCAGAAGCT
Statistics
Matches: 269, Mismatches: 36, Indels: 36
0.79 0.11 0.11
Matches are distributed among these distances:
26 1 0.00
27 61 0.23
28 5 0.02
29 6 0.02
30 171 0.64
31 3 0.01
32 1 0.00
33 21 0.08
ACGTcount: A:0.12, C:0.48, G:0.14, T:0.26
Consensus pattern (29 bp):
TGCTGCACCACCGCTCCTCCTGATCCTCA
Found at i:20575 original size:57 final size:56
Alignment explanation
Indices: 20514--20815 Score: 248
Period size: 57 Copynumber: 5.1 Consensus size: 56
20504 CCGAGTCTCG
*
20514 TGCTGCACCACCTTCTCCCGATCCCCGTGCTGCACCACCGCTCCTTCCTGATCCTCA
1 TGCTGCACCACCTTCTCCCGATCCCCATGCTGCACCACCGCTCC-TCCTGATCCTCA
** * * *
20571 TGCTGCACCACCTTCTCCCGATCCCTGTGCTGCGCCACCGCTCCCACCTGATCCCCA
1 TGCTGCACCACCTTCTCCCGATCCCCATGCTGCACCACCGCT-CCTCCTGATCCTCA
* * * * *
20628 TGCTGCGCCACCGCTCCCACCTGATCCTCATGCCGCACCACCGCCTCCTCCTGATCCTCA
1 TGCTGCACCACC-TTCTC-CC-GATCCCCATGCTGCACCACCG-CTCCTCCTGATCCTCA
* * * * *
20688 TGCTGCACCACCGCCTCCTCCTGATTCTCATGCTGCACCACTG--CCTCCTGATCCTCA
1 TGCTGCACCA---CCTTCTCCCGATCCCCATGCTGCACCACCGCTCCTCCTGATCCTCA
* * * * * *
20745 TGCTGCACCTCCTCCTCCTCCTCCTGATCCTCATGCTGCACCATCGACTCCTGCTGTTCCTCG
1 TGCTGCACCACCT--T-CT-C-CC-GATCCCCATGCTGCACCACCG-CTCCTCCTGATCCTCA
20808 TGCTGCAC
1 TGCTGCAC
20816 AACTACCTCC
Statistics
Matches: 197, Mismatches: 31, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
54 3 0.02
57 86 0.44
58 6 0.03
59 3 0.02
60 73 0.37
61 3 0.02
62 2 0.01
63 21 0.11
ACGTcount: A:0.12, C:0.48, G:0.15, T:0.25
Consensus pattern (56 bp):
TGCTGCACCACCTTCTCCCGATCCCCATGCTGCACCACCGCTCCTCCTGATCCTCA
Found at i:23969 original size:28 final size:28
Alignment explanation
Indices: 23929--23984 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
23919 AATGAAATCG
23929 GCAAACATTTACAAAGCTCTCATTTTAT
1 GCAAACATTTACAAAGCTCTCATTTTAT
*
23957 GCAAACATTTACAGAGCTCTCATTTTAT
1 GCAAACATTTACAAAGCTCTCATTTTAT
23985 ATGAAGTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (28 bp):
GCAAACATTTACAAAGCTCTCATTTTAT
Found at i:35271 original size:20 final size:21
Alignment explanation
Indices: 35232--35271 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35222 CCCCCTTTGA
*
35232 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
35253 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
35272 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:40642 original size:63 final size:63
Alignment explanation
Indices: 40569--40690 Score: 160
Period size: 63 Copynumber: 1.9 Consensus size: 63
40559 CTAATGTGAC
* *
40569 TCTTAGGTAGG-CTCTACGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATATG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATATG
40631 T
63 T
* *
40632 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGAT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGAT
40691 GTTCCCTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
62 1 0.02
63 47 0.90
64 4 0.08
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATATGT
Found at i:40643 original size:32 final size:31
Alignment explanation
Indices: 40569--40653 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
40559 CTAATGTGAC
* *
40569 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** *
40600 TCTCGGGTAGGCCCTGCGGCCCTAAGAT-ATGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCA--T
40632 TCTTAGGTAGG-CCTCACGGCCC
1 TCTTAGGTAGGCCCT-ACGGCCC
40654 CGAAATCTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.02
31 26 0.60
32 16 0.37
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:43872 original size:20 final size:20
Alignment explanation
Indices: 43829--43875 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43819 GAAATTTGCG
* *
43829 TTGCAAAAAATAAAACCGCG
1 TTGCGAAAAATAAAACCGCA
*
43849 TTGCGAAAAATAAAATCGCA
1 TTGCGAAAAATAAAACCGCA
43869 TTGCGAA
1 TTGCGAA
43876 TTCGGAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (20 bp):
TTGCGAAAAATAAAACCGCA
Found at i:44110 original size:28 final size:28
Alignment explanation
Indices: 44070--44129 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
44060 TAATCCACAA
* *
44070 TCCCCATTTGATTGGCCGAGAATGTCAT
1 TCCCCATTTGATTAGCCGAAAATGTCAT
*
44098 TCCCCGTTTGATTAGCCGAAAATGTCAT
1 TCCCCATTTGATTAGCCGAAAATGTCAT
44126 TCCC
1 TCCC
44130 GGGAATCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (28 bp):
TCCCCATTTGATTAGCCGAAAATGTCAT
Found at i:44463 original size:36 final size:36
Alignment explanation
Indices: 44298--44466 Score: 259
Period size: 36 Copynumber: 4.7 Consensus size: 36
44288 CAAAAGTTTA
**
44298 TTCCGATTCAAGTCGAACGG-AGAGAAGCATTTGCAC
1 TTCCGATTCAAGTCGAACGGAAG-GAAGCATCGGCAC
* *
44334 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGACAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
44370 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAT
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
44406 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
44442 TTCCGATTCAAGTCAAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
44467 TGTGTCTTAC
Statistics
Matches: 123, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
36 122 0.99
37 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:46859 original size:21 final size:21
Alignment explanation
Indices: 46835--46884 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
46825 ATAATATATG
* * *
46835 ATTTTTAAAATCATAACGTGA
1 ATTTGTAAAATCACAACGCGA
46856 ATTTGT-AAATCACAACGCGA
1 ATTTGTAAAATCACAACGCGA
46876 ATTTGTAAA
1 ATTTGTAAA
46885 TCGCAACACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
ATTTGTAAAATCACAACGCGA
Found at i:46867 original size:20 final size:20
Alignment explanation
Indices: 46842--46891 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
46832 ATGATTTTTA
* *
46842 AAATCATAACGTGAATTTGT
1 AAATCACAACGCGAATTTGT
46862 AAATCACAACGCGAATTTGT
1 AAATCACAACGCGAATTTGT
*
46882 AAATCGCAAC
1 AAATCACAAC
46892 ACAGTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (20 bp):
AAATCACAACGCGAATTTGT
Found at i:47033 original size:20 final size:20
Alignment explanation
Indices: 47010--47137 Score: 161
Period size: 20 Copynumber: 6.4 Consensus size: 20
47000 GAAAATCGCG
47010 TTGCGATATCACTGTTCACA
1 TTGCGATATCACTGTTCACA
* *
47030 TTGCAATATTACTGTTCACA
1 TTGCGATATCACTGTTCACA
*
47050 TTGTGATATCACTGTTCACA
1 TTGCGATATCACTGTTCACA
*
47070 TTGCGATATCACTATTCACA
1 TTGCGATATCACTGTTCACA
* *
47090 TTGTGATAGT-ATTGTTCACA
1 TTGCGATA-TCACTGTTCACA
*
47110 TTACGATAGT-ACTGTTCACA
1 TTGCGATA-TCACTGTTCACA
47130 TTGCGATA
1 TTGCGATA
47138 GTACTTATAT
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 92 0.99
21 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (20 bp):
TTGCGATATCACTGTTCACA
Found at i:47316 original size:19 final size:20
Alignment explanation
Indices: 47292--47333 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
47282 CGGTGTTAGT
47292 GAACCG-CTTTGAACCATTC
1 GAACCGACTTTGAACCATTC
*
47311 GAACCGACTTTGAACCGTTC
1 GAACCGACTTTGAACCATTC
47331 GAA
1 GAA
47334 TCGGATCGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (20 bp):
GAACCGACTTTGAACCATTC
Found at i:47899 original size:24 final size:24
Alignment explanation
Indices: 47872--47944 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
47862 CGTTCATTTA
47872 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
47896 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
47920 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
47944 C
1 C
47945 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:47901 original size:14 final size:14
Alignment explanation
Indices: 47882--47937 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
47872 CGTTCGTGAA
47882 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
47896 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
47910 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
47920 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
47934 CGTT
1 CGTT
47938 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:47954 original size:24 final size:23
Alignment explanation
Indices: 47883--47957 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
47873 GTTCGTGAAC
* *
47883 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
47907 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
47931 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
47955 GTT
1 GTT
47958 TAACACAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:48698 original size:16 final size:16
Alignment explanation
Indices: 48677--48743 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
48667 GTCTCCAACG
48677 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
48693 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
48709 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
48725 TTTATGCTCGT-TT-A
1 TTTATGTTCGTGTTCA
48739 TTTAT
1 TTTAT
48744 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:48716 original size:32 final size:32
Alignment explanation
Indices: 48675--48735 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
48665 GGGTCTCCAA
*
48675 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGCTCGTGTT
*
48707 CGTTTATGTTCGTGTTCGTTTATGCTCGT
1 CGTTTATGTTCGTGTTCATTTATGCTCGT
48736 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.08, C:0.15, G:0.23, T:0.54
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGCTCGTGTT
Found at i:48826 original size:16 final size:16
Alignment explanation
Indices: 48805--48837 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
48795 AAAAAAAATT
48805 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
48821 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
48837 T
1 T
48838 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:49054 original size:13 final size:13
Alignment explanation
Indices: 49036--49061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49026 ATAAGATATA
49036 AATTTTATATTTT
1 AATTTTATATTTT
49049 AATTTTATATTTT
1 AATTTTATATTTT
49062 GATAGATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTTATATTTT
Found at i:49304 original size:21 final size:22
Alignment explanation
Indices: 49270--49315 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
49260 CCATAAATGT
*
49270 TAAAAAATATTAATATTTTAGG
1 TAAAAAATAATAATATTTTAGG
*
49292 TAAAAAA-AATAATGTTTTAGG
1 TAAAAAATAATAATATTTTAGG
49313 TAA
1 TAA
49316 TTTTTTAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (22 bp):
TAAAAAATAATAATATTTTAGG
Found at i:51062 original size:228 final size:228
Alignment explanation
Indices: 50660--51957 Score: 1674
Period size: 228 Copynumber: 5.7 Consensus size: 228
50650 TTCAAAATAG
* * * * * * * *
50660 ATGCAAATTTTCGTCAAGACGCTCACTGGCAAGACCATCACCCTT-GAGGTGGAAAGTTCTGATA
1 ATGCAAATTTTCGTGAAGACACTCACCGGAAAGACCATCA-CCTTGGAGGTTGAAAGCTCCGACA
* * * * * * * * *
50724 CCATTGATAATGTAAAGGCCAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAACAGCGGCTT
65 CAATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGG-TT
* * * * * * *
50789 -ATTTTTGCTGGTAAACAGCTGGAGGATGGCCGGACCCTT-GCTGACTACAACATCCAGAAGGAA
129 GATTTTTGCTGGTAAGCAACTAGAGGATGGCCGCA-CCTTGGCTGACTATAACATCCAAAAGGAG
* * * ** *
50852 TCCACACTCCACTTGGTTCTTCGAT-TGAGGGGTGGT
193 TCCACCCTCCACTTGGTGCTCCG-TCTTCGTGGTGGT
* * * * * * * * *
50888 ATGCAAATCTTT-GTTAAGACCCTCACCGGAAAGACCATTACATTGGAGGTGGAGAGTTCAGATA
1 ATGCAAAT-TTTCGTGAAGACACTCACCGGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACA
* *
50952 CAATTGACAATGTCAAGGCAAAGATTCAGGACAAGGAAGGTATCCCCCCAGACCAGCAGAGGTTG
65 CAATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTG
51017 ATTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTC
130 ATTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTC
51082 CACCCTCCA-TCTGGTGCTCCGTCTTCGTGGTGGT
195 CACCCTCCACT-TGGTGCTCCGTCTTCGTGGTGGT
* * * * *
51116 ATGCAGATTTTTGTGAAGACACTTACCGGGAAGACCATCACCTTGGAAGTTGAAAGCTCCGACAC
1 ATGCAAATTTTCGTGAAGACACTCACCGGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* *
51181 AATTGACAATGTGAAGGCCAAGATTCAGGACAAGGAGGGTATCCCTCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* * *
51246 TTTTTGCTGGTAAGCAATTGGAGGATGGCCGCACTTTGGCTGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
*
51311 ACCCTACACTTGGTGCTCCGTCTTCGTGGTGGT
196 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* * * * *
51344 ATGCAGATTTTTGTGAAGACACTAACCGGGAAGACCATCACCTTGGAAGTTGAAAGCTCCGACAC
1 ATGCAAATTTTCGTGAAGACACTCACCGGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
*
51409 GATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* * * *
51474 TCTTTGCTGGGAAGCAACTAGAGGATGGGCGCACCTTGGCCGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
51539 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
196 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* * * * *
51572 ATGCAGATTTTCGTGAAGACACTTACCGGAAAGACCATCACCCTGGAGGTAGAAAGTTCCGACAC
1 ATGCAAATTTTCGTGAAGACACTCACCGGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
* * * *
51637 AATCGATAATGTCAAGGCCAAAATTCAGGACAAGGAGGGTATCCCGCCAGACCAGCAGAGGTTGA
66 AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
* * *
51702 TTTTTGCTGGTAAGCAACTTGAGGATGGGCGCACCTTGGCCGACTATAACATCCAAAAGGAGTCC
131 TTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
*
51767 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGG
196 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
* * * * *
51800 ATGCAAATTTTCGTGAAGACCCTCACCGGGAAA-ACCATCACCCTAGAGGTTGAGAGCTCGGACA
1 ATGCAAATTTTCGTGAAGACACTCACC-GGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACA
* * * * * * *
51864 CGATTGATAATGTCAAGGCCAAGATTCAGGATAAGGAAGGAATCCCCCCGGATCAGCAGAGGTTG
65 CAATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTG
* * *
51929 ATCTTTGCTGGGAAGCAACTTGAGGATGG
130 ATTTTTGCTGGTAAGCAACTAGAGGATGG
51958 GAGGACCCTT
Statistics
Matches: 961, Mismatches: 100, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
227 14 0.01
228 938 0.98
229 9 0.01
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (228 bp):
ATGCAAATTTTCGTGAAGACACTCACCGGAAAGACCATCACCTTGGAGGTTGAAAGCTCCGACAC
AATTGACAATGTCAAGGCCAAGATTCAGGACAAGGAGGGTATCCCCCCAGACCAGCAGAGGTTGA
TTTTTGCTGGTAAGCAACTAGAGGATGGCCGCACCTTGGCTGACTATAACATCCAAAAGGAGTCC
ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
Found at i:52585 original size:29 final size:28
Alignment explanation
Indices: 52519--52588 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
52509 TTCTAAAATA
* *
52519 ATTTAAATTCGTTTAAATTTGTAGTATT
1 ATTTATATTTGTTTAAATTTGTAGTATT
*
52547 ATTTGTATTTGTTTAAATTT-TAGTACTAT
1 ATTTATATTTGTTTAAATTTGTAGTA-T-T
52576 ATTTATATTTGTT
1 ATTTATATTTGTT
52589 CATATGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 5 0.14
28 18 0.50
29 13 0.36
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.59
Consensus pattern (28 bp):
ATTTATATTTGTTTAAATTTGTAGTATT
Found at i:52669 original size:23 final size:23
Alignment explanation
Indices: 52643--52693 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
52633 AGTATATTCG
* *
52643 TTTAATGTTTATGAATATCTTTA
1 TTTAATGTTTATAAATATATTTA
*
52666 TTTAATGTTTGTAAATATATTTA
1 TTTAATGTTTATAAATATATTTA
52689 TTTAA
1 TTTAA
52694 CGTCTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (23 bp):
TTTAATGTTTATAAATATATTTA
Found at i:53672 original size:23 final size:23
Alignment explanation
Indices: 53646--53692 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
53636 TAGAAGAGAA
53646 TAAAATATTTTAGTGATGAATGG
1 TAAAATATTTTAGTGATGAATGG
*
53669 TAAAATGTTTTAGTGATGAATGG
1 TAAAATATTTTAGTGATGAATGG
53692 T
1 T
53693 GTAATTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.40
Consensus pattern (23 bp):
TAAAATATTTTAGTGATGAATGG
Found at i:63671 original size:22 final size:24
Alignment explanation
Indices: 63625--63679 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
63615 CATCAAATTT
63625 ATAA-ATAATGTTTTTATAATCAA
1 ATAATATAATGTTTTTATAATCAA
*
63648 ATATTATAAT-TTTATTA-AAT-AA
1 ATAATATAATGTTT-TTATAATCAA
63670 ATAATATAAT
1 ATAATATAAT
63680 ATAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.39
23 9 0.32
24 8 0.29
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
ATAATATAATGTTTTTATAATCAA
Found at i:63680 original size:5 final size:5
Alignment explanation
Indices: 63666--63694 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
63656 ATTTTATTAA
63666 ATAA- ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
63695 GTTTTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:63690 original size:22 final size:22
Alignment explanation
Indices: 63639--63690 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
63629 ATAATGTTTT
* * *
63639 TATAATCAAATATTATAATTTTA
1 TATAAT-AAATAATATAATATAA
63662 T-TAAATAAATAATATAATATAA
1 TAT-AATAAATAATATAATATAA
63684 TATAATA
1 TATAATA
63691 TAATGTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAATAAATAATATAATATAA
Found at i:80012 original size:68 final size:68
Alignment explanation
Indices: 79931--80064 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 68
79921 ATTTAATATT
* * * * *
79931 ATATATATTTATTATATAATTATATTAATGGAATAATATAATTTAATA-TATCAAATAATTCTTA
1 ATATATATATATTAAATAATAATATTAATGAAATAATATAATTTAATAGAAT-AAATAATTCTTA
79995 ATAA
65 ATAA
* *
79999 ATATATATATATTAAATTATAATTTTAATGAAATAATATAATTTAATAGAATAAATAATTCTTAA
1 ATATATATATATTAAATAATAATATTAATGAAATAATATAATTTAATAGAATAAATAATTCTTAA
80064 T
66 T
80065 TTTTAATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 56 0.97
69 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (68 bp):
ATATATATATATTAAATAATAATATTAATGAAATAATATAATTTAATAGAATAAATAATTCTTAA
TAA
Found at i:80040 original size:19 final size:19
Alignment explanation
Indices: 80016--80064 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
80006 TATATTAAAT
80016 TATAATTTTAAT-GAAATAA
1 TATAATTTTAATAG-AATAA
80035 TATAA-TTTAATAGAATAA
1 TATAATTTTAATAGAATAA
80053 -ATAATTCTTAAT
1 TATAATT-TTAAT
80065 TTTTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.15
18 12 0.44
19 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (19 bp):
TATAATTTTAATAGAATAA
Found at i:80164 original size:28 final size:29
Alignment explanation
Indices: 80116--80175 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
80106 ATTCTTAAGA
**
80116 AATATTAAATTATAATTAAT-AAATATAT
1 AATATTAAATTATAAAAAATAAAATATAT
80144 AATATTAAATTA-ACAAAAATACAAATATAT
1 AATATTAAATTATA-AAAAATA-AAATATAT
80174 AA
1 AA
80176 AATATACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 16 0.59
30 10 0.37
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AATATTAAATTATAAAAAATAAAATATAT
Found at i:80979 original size:21 final size:21
Alignment explanation
Indices: 80955--80996 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
80945 AAAATAGCCA
80955 CAAATGTTAAGACGTAGCTTG
1 CAAATGTTAAGACGTAGCTTG
80976 CAAATGTTAAGACGTAGCTTG
1 CAAATGTTAAGACGTAGCTTG
80997 ATAGAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
CAAATGTTAAGACGTAGCTTG
Found at i:86278 original size:33 final size:31
Alignment explanation
Indices: 86235--86305 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
86225 GATCAGATTA
*
86235 TTTTTAAAAAAAATTAGGGATCGGGTCGCATTT
1 TTTTTAAAAAAAA-TAGGGATCGGGTCG-AGTT
* * *
86268 TTTTTTAAAAAAATCGGGTTCGGGTCGAGTT
1 TTTTTAAAAAAAATAGGGATCGGGTCGAGTT
86299 TTTTTAA
1 TTTTTAA
86306 GTTTGATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 9 0.27
32 12 0.36
33 12 0.36
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (31 bp):
TTTTTAAAAAAAATAGGGATCGGGTCGAGTT
Found at i:86317 original size:28 final size:28
Alignment explanation
Indices: 86286--86351 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
86276 AAAAATCGGG
*
86286 TTCGGGTC-GAGTTTTTTTAAGTTTGATA
1 TTCGGGTCGGA-TTTTTTTAAGTGTGATA
86314 TTCGGGTCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
*
86342 TTCTGGTCGG
1 TTCGGGTCGG
86352 GTGAAACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.15, C:0.09, G:0.29, T:0.47
Consensus pattern (28 bp):
TTCGGGTCGGATTTTTTTAAGTGTGATA
Found at i:87043 original size:22 final size:22
Alignment explanation
Indices: 87001--87077 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 22
86991 ATTCTGACTA
*
87001 TCGCATTGCGA-TTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAAT
* *
87022 TCGCGTTGCGGTTTTCCTAAA-
1 TCGCATTGCGATTTTCCTAAAT
* *
87043 TCACAATGCGATTTTCCT-AAT
1 TCGCATTGCGATTTTCCTAAAT
87064 TCGCATTGCGATTT
1 TCGCATTGCGATTT
87078 ACATAGCGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 2 0.04
21 35 0.78
22 8 0.18
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (22 bp):
TCGCATTGCGATTTTCCTAAAT
Found at i:87635 original size:20 final size:19
Alignment explanation
Indices: 87606--87677 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
87596 TTCTAAACTT
*
87606 AAAATTGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
87626 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
87646 ACTATCACAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
87667 AAAATCGCAAC
1 AAAATCGCAAC
87678 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:87666 original size:21 final size:21
Alignment explanation
Indices: 87621--87684 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
87611 TGCAACATGA
*
87621 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCACAACGA-GAG
**
87641 AAATGACTATCACAACGAGAG
1 AAATGAAAATCACAACGAGAG
*
87662 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCACAACGAGAG
87683 AA
1 AA
87685 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.53, C:0.17, G:0.19, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCACAACGAGAG
Found at i:87698 original size:33 final size:33
Alignment explanation
Indices: 87661--87741 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
87651 CACAACGAGA
87661 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
87694 GAAATGAAAATCGCAACGATATAATTGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
87727 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
87742 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:87807 original size:20 final size:20
Alignment explanation
Indices: 87742--87830 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
87732 CAAAATCGCA
87742 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
*
87761 TTGCGA--TT-A--T-CTCG
1 TTGCGATTTTCATTTCCGCG
**
87775 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
87795 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
87815 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
87831 AACCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:89736 original size:92 final size:93
Alignment explanation
Indices: 89626--89970 Score: 565
Period size: 93 Copynumber: 3.7 Consensus size: 93
89616 CGGCTGCTGC
89626 CTAAACTGTGTATTCTTTAACA-TGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
89690 GTAAATTTGTTCGTTGCTGCCAATTCTG
66 GTAAATTTGTTCGTTGCTGCCAATTCTG
*
89718 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTTTTTGTCTTTGTTTTGTC-TTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
* *
89782 GTAAATTTGTTCGGTTGCTGCTAATTCAG
66 GTAAATTTGTTC-GTTGCTGCCAATTCTG
*
89811 CTAAACTGTGTATTC-TTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAAA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
* *
89875 GTAAATTTGTTCGTTTACTGTCAATTCTG
66 GTAAATTTGTTCG-TTGCTGCCAATTCTG
* *
89904 CTAAACTGTGTATTCTTTAATA-TCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-AA
1 CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
89967 GTAA
66 GTAA
89971 TGCAATCCAT
Statistics
Matches: 237, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
92 88 0.37
93 144 0.61
94 5 0.02
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
CTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAA
GTAAATTTGTTCGTTGCTGCCAATTCTG
Found at i:89861 original size:185 final size:177
Alignment explanation
Indices: 89516--89970 Score: 638
Period size: 185 Copynumber: 2.5 Consensus size: 177
89506 TAGATTGCTT
* * *
89516 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
89577 ATTTGTCTTT-TGTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTC
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTC
*
89641 TTTAACATGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TTTAACATGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
*
89689 AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTT
1 AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA
* *
89754 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCTAATTCAGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTC-G--GCTGC---TGC--CTAAACT
89818 GTGTATTC-TTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
122 GTGTATTCTTTAACA-TGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
* * * *
89874 AGTAAATTTGTTCGTTTACTGTCAATTCTGCTAAACTGTGTATTCTTTAATA-TCTGAAGTTAGT
1 AGTAAATTTGTTCG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
89938 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
89971 TGCAATCCAT
Statistics
Matches: 252, Mismatches: 13, Indels: 22
0.88 0.05 0.08
Matches are distributed among these distances:
172 21 0.08
173 12 0.05
174 3 0.01
175 2 0.01
176 36 0.14
177 19 0.08
178 1 0.00
180 5 0.02
183 2 0.01
184 6 0.02
185 103 0.41
186 42 0.17
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (177 bp):
AGTAAATTTGTTCGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGCTGCTGCCTAAACTGTGTATTCT
TTAACATGTGAAGTTAGTATTTGTCTTTGTTTTGTCCTTTGGTTGAA
Found at i:90097 original size:19 final size:19
Alignment explanation
Indices: 90048--90168 Score: 161
Period size: 19 Copynumber: 6.3 Consensus size: 19
90038 TCTTTTGGTT
* *
90048 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
*
90067 GAGAATGAAAATCGCAACGC
1 GA-AACGAAAATCGCAACGC
90087 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
90106 GAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
* *
90125 GAAACCAAAAACGCAACGC
1 GAAACGAAAATCGCAACGC
*
90144 GAAATCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
90164 GAAAC
1 GAAAC
90169 TATAATCGCG
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 57 0.62
20 35 0.38
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:90120 original size:38 final size:38
Alignment explanation
Indices: 90048--90177 Score: 179
Period size: 39 Copynumber: 3.4 Consensus size: 38
90038 TCTTTTGGTT
* *
90048 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
90087 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
* * *
90125 GAAACCAAAAACGCAACGCGAAATCAAAAATCGCAACGC
1 GAAACGAAAATCGCAACGCGAAAT-GAAAATCGCAACGC
* *
90164 GAAACTATAATCGC
1 GAAACGAAAATCGC
90178 GTTGCGATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 39 0.48
39 43 0.52
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.09
Consensus pattern (38 bp):
GAAACGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:90177 original size:58 final size:58
Alignment explanation
Indices: 90048--90167 Score: 179
Period size: 58 Copynumber: 2.1 Consensus size: 58
90038 TCTTTTGGTT
** * *
90048 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAACCAAAAACGCAACGCGAAACAAAAATCGCAACGC
*
90106 GAAATGAAAATCGCAACGCGA-AACCAAAAACGCAACGCGAAATCAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAACCAAAAACGCAACGCGAAA-CAAAAATCGCAACGC
90164 GAAA
1 GAAA
90168 CTATAATCGC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 18 0.32
58 38 0.68
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (58 bp):
GAAATGAAAATCGCAACGAGAGAACCAAAAACGCAACGCGAAACAAAAATCGCAACGC
Found at i:90201 original size:19 final size:19
Alignment explanation
Indices: 90174--90280 Score: 89
Period size: 19 Copynumber: 5.8 Consensus size: 19
90164 GAAACTATAA
90174 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
90193 ACGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
90207 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
90226 TCGCGTTACGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
**
90245 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
90266 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
90281 AAGTTCCAGA
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 8 0.12
16 3 0.05
17 3 0.05
19 38 0.58
21 14 0.21
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:90758 original size:42 final size:42
Alignment explanation
Indices: 90679--90767 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
90669 GACTCGCCTG
* * * *
90679 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
* * * * *
90721 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAAAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
90763 TCATC
1 TCATC
90768 GTTGAAGAGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAAAGGCCCCTA
Found at i:92168 original size:13 final size:14
Alignment explanation
Indices: 92143--92177 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
92133 ATTGTTTAAT
92143 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
92157 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
92170 TGATTTGT
1 TGATTTGT
92178 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:92186 original size:13 final size:14
Alignment explanation
Indices: 92130--92178 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
92120 TGCTTATTTT
*
92130 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
92142 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
92156 ATGATTTG-TAAAG
1 TTGATTTGTTAAAG
92169 TTGATTTGTT
1 TTGATTTGTT
92179 TAATTGATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.14
13 17 0.59
14 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:92338 original size:19 final size:19
Alignment explanation
Indices: 92314--92352 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
92304 GCAACGAGAG
*
92314 AATCGCAACGCGAAACTAA
1 AATCGCAACACGAAACTAA
92333 AATCGCAACACGAAACTAA
1 AATCGCAACACGAAACTAA
92352 A
1 A
92353 TTCGTGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.26, G:0.13, T:0.10
Consensus pattern (19 bp):
AATCGCAACACGAAACTAA
Found at i:92401 original size:33 final size:33
Alignment explanation
Indices: 92358--92483 Score: 207
Period size: 33 Copynumber: 3.8 Consensus size: 33
92348 CTAAATTCGT
* * *
92358 GTTGCGATTTTCATTTCGCTTTGTGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
92391 GTTGCAATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
*
92424 GTTGCGATTTTTATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
92457 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
92484 AGTCATTTCC
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
Found at i:92449 original size:19 final size:19
Alignment explanation
Indices: 92425--92483 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
92415 GATTCTCTCG
92425 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTTATTTCGCA
* *
92444 TTGCGA---TTCTCTCG--
1 TTGCGATTTTTATTTCGCA
*
92458 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTTATTTCGCA
92477 TTGCGAT
1 TTGCGAT
92484 AGTCATTTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 6 0.20
16 6 0.20
17 5 0.17
19 13 0.43
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTTATTTCGCA
Found at i:92502 original size:20 final size:19
Alignment explanation
Indices: 92456--92510 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
92446 GCGATTCTCT
**
92456 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
92475 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
92495 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
92511 AAGATGATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:95885 original size:20 final size:20
Alignment explanation
Indices: 95870--95957 Score: 124
Period size: 20 Copynumber: 4.3 Consensus size: 20
95860 AGAATCTCGT
95870 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
95890 TGCGATTTACTAAATCGCAA
1 TGCGATTTACTAAATCGCAA
95910 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTAC-TAAATCGCAA
* **
95930 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTA-CTAAATCGCAA
95951 TGCGATT
1 TGCGATT
95958 ATTGCAATGC
Statistics
Matches: 62, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.06
20 40 0.65
21 18 0.29
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (20 bp):
TGCGATTTACTAAATCGCAA
Found at i:95945 original size:21 final size:21
Alignment explanation
Indices: 95881--96007 Score: 110
Period size: 21 Copynumber: 6.5 Consensus size: 21
95871 GCGATTTACT
* **
95881 AAATCGCAATGCGATTTA-CT
1 AAATCGCAATGCGAATTAGGA
* *
95901 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
95921 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
95942 AAATCGCAATGCG-ATT----
1 AAATCGCAATGCGAATTAGGA
*
95958 --ATTGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
95977 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
95998 AAATCGCAAT
1 AAATCGCAAT
96008 ACGATAGTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 3 0.03
20 30 0.34
21 42 0.48
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:95993 original size:56 final size:55
Alignment explanation
Indices: 95906--96012 Score: 151
Period size: 56 Copynumber: 1.9 Consensus size: 55
95896 TTACTAAATC
* * *
95906 GCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTATT
1 GCAATGCGATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGATTATT
* * *
95961 GCAATGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAATACGAT
1 GCAATGCG-ATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGAT
96013 AGTTAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
55 8 0.18
56 37 0.82
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (55 bp):
GCAATGCGATTACGAAAATCGCAACGCGAATTAGGAAAATCGCAATACGATTATT
Done.