Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005100.1 Hibiscus syriacus cultivar Beakdansim tig00011466_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: 60584
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1486 original size:20 final size:20
Alignment explanation
Indices: 1458--1501 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1448 CGCCATTAAC
1458 TTTAGACATATAGCAACATT
1 TTTAGACATATAGCAACATT
* * *
1478 TTTATACATATAGGAGCATT
1 TTTAGACATATAGCAACATT
1498 TTTA
1 TTTA
1502 ATAAAGGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (20 bp):
TTTAGACATATAGCAACATT
Found at i:3762 original size:15 final size:18
Alignment explanation
Indices: 3724--3764 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
3714 AGGTTGACTC
3724 ATTATGCATTAATTATTT
1 ATTATGCATTAATTATTT
3742 AATTATGCATTATATT-TTT
1 -ATTATGCATTA-ATTATTT
3761 ATTA
1 ATTA
3765 ATAATTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 14 0.67
20 3 0.14
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
ATTATGCATTAATTATTT
Found at i:10206 original size:21 final size:21
Alignment explanation
Indices: 10182--10234 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
10172 GGAAGAAGAG
* *
10182 AGAGCAGCAGCAGAAGCAGCC
1 AGAGAAGCAGCAGAAACAGCC
* * *
10203 AGAGAAGCAACGGAAACAGCT
1 AGAGAAGCAGCAGAAACAGCC
10224 AGAGAAGCAGC
1 AGAGAAGCAGC
10235 GGCAGCACAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.23, G:0.32, T:0.02
Consensus pattern (21 bp):
AGAGAAGCAGCAGAAACAGCC
Found at i:10701 original size:43 final size:42
Alignment explanation
Indices: 10673--10917 Score: 239
Period size: 43 Copynumber: 5.8 Consensus size: 42
10663 CTAAAAATGT
*
10673 CGCAAAACATCAACACCTACTACGGCGTTTGTGGGAAAAACGC
1 CGCAAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAA-GC
* * *
10716 CACAAAACATCAACACATACTGCGACGTTTGTGGGAAAACA-C
1 CGCAAAACATCAACACCTACTGCGGCGTTTGTGGGAAAA-AGC
* *
10758 CGCAAAACATTAACACCTACTGCGACGTTTGTGGGAAAACA-C
1 CGCAAAACATCAACACCTACTGCGGCGTTTGTGGGAAAA-AGC
* * * *
10800 CGCAAAACATCAACATCTACTGCTGTGTTTGTGAGAAAAATGC
1 CGCAAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAA-GC
* * *
10843 CACAAAACATCAACACCTACTAG-GGCGTTT-TAGAGAAAATCGC
1 CGCAAAACATCAACACCTACT-GCGGCGTTTGT-GGGAAAA-AGC
* * *
10886 CGCTAAACATCATA-ACTTATTGCGGCGTTTGT
1 CGCAAAACATCA-ACACCTACTGCGGCGTTTGT
10918 CTAAAAAATA
Statistics
Matches: 171, Mismatches: 22, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 75 0.44
43 91 0.53
44 4 0.02
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
CGCAAAACATCAACACCTACTGCGGCGTTTGTGGGAAAAAGC
Found at i:10773 original size:42 final size:42
Alignment explanation
Indices: 10673--10863 Score: 242
Period size: 42 Copynumber: 4.5 Consensus size: 42
10663 CTAAAAATGT
* * *
10673 CGCAAAACATCAACACCTACTACGGCGTTTGTGGGAAAAACGC
1 CGCAAAACATCAACACCTACTGCGACGTTTGTGGG-AAAACAC
* *
10716 CACAAAACATCAACACATACTGCGACGTTTGTGGGAAAACAC
1 CGCAAAACATCAACACCTACTGCGACGTTTGTGGGAAAACAC
*
10758 CGCAAAACATTAACACCTACTGCGACGTTTGTGGGAAAACAC
1 CGCAAAACATCAACACCTACTGCGACGTTTGTGGGAAAACAC
* * *
10800 CGCAAAACATCAACATCTACTGCTG-TGTTTGTGAGAAAA-ATGC
1 CGCAAAACATCAACACCTACTGC-GACGTTTGTGGGAAAACA--C
*
10843 CACAAAACATCAACACCTACT
1 CGCAAAACATCAACACCTACT
10864 AGGGCGTTTT
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 78 0.60
43 52 0.40
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.19
Consensus pattern (42 bp):
CGCAAAACATCAACACCTACTGCGACGTTTGTGGGAAAACAC
Found at i:10778 original size:85 final size:84
Alignment explanation
Indices: 10673--10872 Score: 253
Period size: 85 Copynumber: 2.4 Consensus size: 84
10663 CTAAAAATGT
*
10673 CGCAAAACATCAACACCTACTACGGCGTTTGTGGGAAAAACGCCACAAAACATCAACA-CATACT
1 CGCAAAACATCAACACCTACTACGGCGTTTGTGGG-AAAACACCACAAAACATCAACATC-TACT
*
10737 GC-GACGTTTGTGGGAAAACA-C
64 GCTG-CGTTTGTGAGAAAA-AGC
* * * *
10758 CGCAAAACATTAACACCTACTGCGACGTTTGTGGGAAAACACCGCAAAACATCAACATCTACTGC
1 CGCAAAACATCAACACCTACTACGGCGTTTGTGGGAAAACACCACAAAACATCAACATCTACTGC
*
10823 TGTGTTTGTGAGAAAAATGC
66 TGCGTTTGTGAGAAAAA-GC
* *
10843 CACAAAACATCAACACCTACTAGGGCGTTT
1 CGCAAAACATCAACACCTACTACGGCGTTT
10873 TAGAGAAAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
83 1 0.01
84 38 0.38
85 60 0.61
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (84 bp):
CGCAAAACATCAACACCTACTACGGCGTTTGTGGGAAAACACCACAAAACATCAACATCTACTGC
TGCGTTTGTGAGAAAAAGC
Found at i:10950 original size:43 final size:43
Alignment explanation
Indices: 10903--10992 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
10893 CATCATAACT
10903 TATTGCGGCGTTTGTCTAAAAAATACCGTTAAATATCAACACC
1 TATTGCGGCGTTTGTCTAAAAAATACCGTTAAATATCAACACC
* * * * **
10946 TATTGCGGTGTTTTTCTGACAAATGTCGTTAAATATCAACACC
1 TATTGCGGCGTTTGTCTAAAAAATACCGTTAAATATCAACACC
10989 TATT
1 TATT
10993 ACAACGTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (43 bp):
TATTGCGGCGTTTGTCTAAAAAATACCGTTAAATATCAACACC
Found at i:11011 original size:43 final size:43
Alignment explanation
Indices: 10928--11035 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
10918 CTAAAAAATA
* *** * ** *
10928 CCGTTAAATATCAACACCTATTGCGGTGTTTTTCTGACAAATG
1 CCGTTAAATATCAACACCTATTACAACGTTTGTCACACAAACG
*
10971 TCGTTAAATATCAACACCTATTACAACGTTTGTCACACAAACG
1 CCGTTAAATATCAACACCTATTACAACGTTTGTCACACAAACG
** *
11014 CCGCAAAATATCAATACCTATT
1 CCGTTAAATATCAACACCTATT
11036 GCGGCATTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (43 bp):
CCGTTAAATATCAACACCTATTACAACGTTTGTCACACAAACG
Found at i:11379 original size:8 final size:8
Alignment explanation
Indices: 11366--11396 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
11356 ATTTGTAAAT
11366 TATATATC
1 TATATATC
11374 TATATATC
1 TATATATC
*
11382 TATATATA
1 TATATATC
11390 TATATAT
1 TATATAT
11397 ATTTATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (8 bp):
TATATATC
Found at i:15021 original size:19 final size:19
Alignment explanation
Indices: 15001--15035 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
14991 TAATAATATT
15001 TTTTTA-TTAAA-ATATAC
1 TTTTTATTTAAACATATAC
15018 TTTTTATTTAAACATATA
1 TTTTTATTTAAACATATA
15036 TTAAAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTATTTAAACATATAC
Found at i:16650 original size:31 final size:31
Alignment explanation
Indices: 16615--16675 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
16605 TCGCGAGCCT
* *
16615 AAAATTTTCAAGCTCGACTCGAACTCGAAAG
1 AAAATATTCAAACTCGACTCGAACTCGAAAG
*
16646 AAAATATTGAAACTCGACTCGAACTCGAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAA
16676 AGGCTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAG
Found at i:16803 original size:17 final size:17
Alignment explanation
Indices: 16781--16814 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16771 TTGAGTTCGG
16781 TTCAAGCTCAAACTCGA
1 TTCAAGCTCAAACTCGA
16798 TTCAAGCTCAAACTCGA
1 TTCAAGCTCAAACTCGA
16815 ACTCGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (17 bp):
TTCAAGCTCAAACTCGA
Found at i:19420 original size:21 final size:21
Alignment explanation
Indices: 19394--19442 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
19384 AACCATTAAC
*
19394 CATAAATTATAAAC-CTTAAAT
1 CATAAACTATAAACTC-TAAAT
*
19415 CCTAAACTATAAACTCTAAAT
1 CATAAACTATAAACTCTAAAT
19436 CATAAAC
1 CATAAAC
19443 CCTAAAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (21 bp):
CATAAACTATAAACTCTAAAT
Found at i:19426 original size:28 final size:28
Alignment explanation
Indices: 19424--19491 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
19414 TCCTAAACTA
* *
19424 TAAACTCTAAATCATAAACCCTAAAACC
1 TAAACTATAAATTATAAACCCTAAAACC
**
19452 TAAACTATAAATCCTAAACCCTAAAACC
1 TAAACTATAAATTATAAACCCTAAAACC
*
19480 TAAACCATAAAT
1 TAAACTATAAAT
19492 CCTATCACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAACTATAAATTATAAACCCTAAAACC
Found at i:19427 original size:14 final size:14
Alignment explanation
Indices: 19424--19495 Score: 81
Period size: 14 Copynumber: 5.1 Consensus size: 14
19414 TCCTAAACTA
* *
19424 TAAACTCTAAATCA
1 TAAACCCTAAATCC
*
19438 TAAACCCTAAAACC
1 TAAACCCTAAATCC
**
19452 TAAACTATAAATCC
1 TAAACCCTAAATCC
*
19466 TAAACCCTAAAACC
1 TAAACCCTAAATCC
*
19480 TAAACCATAAATCC
1 TAAACCCTAAATCC
19494 TA
1 TA
19496 TCACATAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:19492 original size:28 final size:28
Alignment explanation
Indices: 19431--19495 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
19421 CTATAAACTC
* *
19431 TAAATCATAAACCCTAAAACCTAAACTA
1 TAAATCCTAAACCCTAAAACCTAAACCA
19459 TAAATCCTAAACCCTAAAACCTAAACCA
1 TAAATCCTAAACCCTAAAACCTAAACCA
19487 TAAATCCTA
1 TAAATCCTA
19496 TCACATAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (28 bp):
TAAATCCTAAACCCTAAAACCTAAACCA
Found at i:20098 original size:20 final size:19
Alignment explanation
Indices: 20054--20111 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
20044 AAGGGTTCAC
*
20054 GGAATATAAGATTATCGGT
1 GGAATATAAGATTATCAGT
*
20073 GAGAATGTAAGATTATCAGT
1 G-GAATATAAGATTATCAGT
*
20093 AGGAATAAAAGATTATCAG
1 -GGAATATAAGATTATCAG
20112 AGAATAGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.28
Consensus pattern (19 bp):
GGAATATAAGATTATCAGT
Found at i:21130 original size:2 final size:2
Alignment explanation
Indices: 21123--21196 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
21113 GTTCACATCA
21123 AT 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 AT
* *
21165 AT AT AT AT AT AT AT AT AT AT AT GT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21197 TGCATCAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26249 original size:30 final size:30
Alignment explanation
Indices: 26210--26283 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
26200 TATGATTGTC
*
26210 TTTTGAATTAAATCTATCTAATGAAAAATG
1 TTTTTAATTAAATCTATCTAATGAAAAATG
*
26240 TTTTTAATTAAATCTATCTAATGACAAATG
1 TTTTTAATTAAATCTATCTAATGAAAAATG
26270 TTTTTAATTAAATC
1 TTTTTAATTAAATC
26284 CTTCGTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (30 bp):
TTTTTAATTAAATCTATCTAATGAAAAATG
Found at i:27672 original size:21 final size:21
Alignment explanation
Indices: 27629--27672 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27619 AAAATGACCC
*
27629 AAAATAATAATATTTTAGATA
1 AAAATAATAATATTTCAGATA
27650 AAAATAATAATATTATCAG-TA
1 AAAATAATAATATT-TCAGATA
27671 AA
1 AA
27673 TTTTTACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAATAATAATATTTCAGATA
Found at i:28711 original size:25 final size:25
Alignment explanation
Indices: 28677--28727 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28667 AATTTCTGTA
28677 TCTGATCGGCTTCCCATGTCGTTTT
1 TCTGATCGGCTTCCCATGTCGTTTT
28702 TCTGATCGGCTTCCCATGTCGTTTT
1 TCTGATCGGCTTCCCATGTCGTTTT
28727 T
1 T
28728 GTCTTCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.08, C:0.27, G:0.20, T:0.45
Consensus pattern (25 bp):
TCTGATCGGCTTCCCATGTCGTTTT
Found at i:29248 original size:169 final size:169
Alignment explanation
Indices: 28969--29307 Score: 678
Period size: 169 Copynumber: 2.0 Consensus size: 169
28959 TCTGTTCTCT
28969 TCCACTTGACTTAAGAGTCATTAAACACGTTGTTTTGTGGGGTTACTTTAGGATATTATGTCTTA
1 TCCACTTGACTTAAGAGTCATTAAACACGTTGTTTTGTGGGGTTACTTTAGGATATTATGTCTTA
29034 TTGCCAAGGTGATTCAATTTGGATATGTTTGCTTTGAGTTGTAAGTGGTAAATGGTTATACGTGG
66 TTGCCAAGGTGATTCAATTTGGATATGTTTGCTTTGAGTTGTAAGTGGTAAATGGTTATACGTGG
29099 TGTTTCTATATTTAATTTTTTGGTGTTCCTTTTTTGGTA
131 TGTTTCTATATTTAATTTTTTGGTGTTCCTTTTTTGGTA
29138 TCCACTTGACTTAAGAGTCATTAAACACGTTGTTTTGTGGGGTTACTTTAGGATATTATGTCTTA
1 TCCACTTGACTTAAGAGTCATTAAACACGTTGTTTTGTGGGGTTACTTTAGGATATTATGTCTTA
29203 TTGCCAAGGTGATTCAATTTGGATATGTTTGCTTTGAGTTGTAAGTGGTAAATGGTTATACGTGG
66 TTGCCAAGGTGATTCAATTTGGATATGTTTGCTTTGAGTTGTAAGTGGTAAATGGTTATACGTGG
29268 TGTTTCTATATTTAATTTTTTGGTGTTCCTTTTTTGGTA
131 TGTTTCTATATTTAATTTTTTGGTGTTCCTTTTTTGGTA
29307 T
1 T
29308 TTTGTAGATG
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 170 1.00
ACGTcount: A:0.21, C:0.10, G:0.22, T:0.46
Consensus pattern (169 bp):
TCCACTTGACTTAAGAGTCATTAAACACGTTGTTTTGTGGGGTTACTTTAGGATATTATGTCTTA
TTGCCAAGGTGATTCAATTTGGATATGTTTGCTTTGAGTTGTAAGTGGTAAATGGTTATACGTGG
TGTTTCTATATTTAATTTTTTGGTGTTCCTTTTTTGGTA
Found at i:30729 original size:21 final size:20
Alignment explanation
Indices: 30643--30800 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
30633 AAATGACCAA
**
30643 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
30662 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
30682 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
30702 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
30723 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
30744 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
30764 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
30785 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
30801 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:30829 original size:20 final size:20
Alignment explanation
Indices: 30767--30960 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
30757 CGATTTTCCA
* ** *
30767 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
30787 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
30807 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30827 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
30847 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
30867 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
30887 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
30907 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
30927 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
30948 AAATCGCAACGCG
1 AAATCGCAACGCG
30961 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:30851 original size:60 final size:60
Alignment explanation
Indices: 30767--30960 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
30757 CGATTTTCCA
* ** * *
30767 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
30827 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
30887 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
30948 AAATCGCAACGCG
1 AAATCGCAACGCG
30961 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:31380 original size:33 final size:33
Alignment explanation
Indices: 31341--31411 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
31331 TTCACTTAGA
* *
31341 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
31374 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
31407 TTTCA
1 TTTCA
31412 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:31517 original size:21 final size:20
Alignment explanation
Indices: 31491--31596 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
31481 TGCAGAAGAG
31491 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
31512 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
31532 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
31553 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
31567 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
31586 TCGCAACGAGA
1 TCGCAACGAGA
31597 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:31535 original size:20 final size:21
Alignment explanation
Indices: 31489--31567 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
31479 TTTGCAGAAG
*
31489 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
31511 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
31530 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
31552 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
31568 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:31548 original size:41 final size:38
Alignment explanation
Indices: 31484--31600 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
31474 TTCAATTTGC
* *
31484 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
31522 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
31563 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
31596 AGAAT
1 AGAAT
31601 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:31573 original size:14 final size:14
Alignment explanation
Indices: 31554--31607 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
31544 AAATGAAAAG
31554 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
31568 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
31587 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
31601 CGCAACG
1 CGCAACG
31608 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:31583 original size:33 final size:33
Alignment explanation
Indices: 31543--31612 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
31533 CGCAACGAGA
31543 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
31576 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
31609 GAAA
1 GAAA
31613 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:31619 original size:33 final size:33
Alignment explanation
Indices: 31549--31623 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
31539 GAGAGAAATG
* **
31549 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
31582 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
31615 AAAATCGCA
1 AAAATCGCA
31624 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:31641 original size:19 final size:19
Alignment explanation
Indices: 31619--31716 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
31609 GAAACCAAAA
*
31619 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31638 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
31652 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
31671 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
31685 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
31704 TCGCGTTGCGATT
1 TCGCGTTGCGATT
31717 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31660 original size:14 final size:14
Alignment explanation
Indices: 31641--31730 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
31631 TTTCATTTCG
31641 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31655 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
31674 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
31688 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
31705 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
31721 CGTTGCGATT
1 CGTTGCGATT
31731 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31666 original size:33 final size:33
Alignment explanation
Indices: 31624--31738 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
31614 CAAAATCGCA
31624 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31657 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
31690 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
31723 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
31739 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:33446 original size:18 final size:18
Alignment explanation
Indices: 33400--33449 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
33390 TTTACTCGTA
*
33400 ATTTCACTTAAATTAGCC
1 ATTTCACTTAGATTAGCC
33418 ATTTCACTTAGATTAGCC
1 ATTTCACTTAGATTAGCC
33436 ATTTCACTTAGATT
1 ATTTCACTTAGATT
33450 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAGCC
Found at i:33613 original size:93 final size:93
Alignment explanation
Indices: 33454--33927 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
33444 TAGATTGCTT
*
33454 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33519 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33547 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33612 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33640 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33705 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
33733 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33798 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33826 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
33891 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
33919 AGTAAATTT
1 AGTAAATTT
33928 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:34011 original size:19 final size:19
Alignment explanation
Indices: 33971--34099 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
33961 TAGTTTACTT
* *
33971 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
33991 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* **
34010 TCGCAACGCGCAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
34029 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
34043 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
34062 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
34076 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
34095 TCGCA
1 TCGCA
34100 TTGCGATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:34050 original size:33 final size:32
Alignment explanation
Indices: 34007--34099 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
33997 CGCGAAACCA
* **
34007 AAATCGCAACGCGCAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
34039 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
34072 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
34100 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.45, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:34097 original size:52 final size:54
Alignment explanation
Indices: 33971--34099 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 54
33961 TAGTTTACTT
* *
33971 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGCAATGAAAA
1 TCGCAAC-CGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAACGCACAATG--AA
*
34029 TCGCAA-CG--A-CAGAATCGCAACGCGAAACCAAAATCGCAACG-ACAA-G-A
1 TCGCAACCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCACAATGAA
34076 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAAC-CGAAACCAAAATCGCA
34100 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
47 7 0.11
49 2 0.03
50 1 0.02
51 4 0.06
52 39 0.63
54 1 0.02
56 2 0.03
58 6 0.10
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (54 bp):
TCGCAACCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCACAATGAA
Found at i:34117 original size:19 final size:18
Alignment explanation
Indices: 34095--34145 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
34085 GAAACCAAAA
34095 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
34114 TCGCGTTGCGA--TTC-TT
1 TCGC-TTGCGATTTTCATT
34130 TCG-TTGCGATTTTCAT
1 TCGCTTGCGATTTTCAT
34146 AGAATTCGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 6 0.21
16 8 0.29
17 4 0.14
19 10 0.36
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:34532 original size:14 final size:14
Alignment explanation
Indices: 34513--34548 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34503 ATTGTTTAAT
34513 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34527 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34541 TGATTTGT
1 TGATTTGT
34549 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34679 original size:19 final size:19
Alignment explanation
Indices: 34655--34754 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
34645 AAAATTGACT
34655 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34674 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34693 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34707 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34726 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
34746 ATCGCAATG
1 ATCGCAATG
34755 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34784 original size:53 final size:53
Alignment explanation
Indices: 34655--34771 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
34645 AAAATTGACT
34655 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
34707 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
34760 ATCGCAATGCGA
1 ATCGCAATGCGA
34772 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:34789 original size:19 final size:19
Alignment explanation
Indices: 34761--34909 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
34751 AATGGGAGAA
* *
34761 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
34780 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
34796 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
34813 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
34832 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
34848 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
34865 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
34881 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
34898 TCCGCATTGCGA
1 T-CGCATTGCGA
34910 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:34824 original size:52 final size:52
Alignment explanation
Indices: 34761--34877 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
34751 AATGGGAGAA
*
34761 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
34813 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
34865 TCGCATTGCGATT
1 TCGCATTGCGATT
34878 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:34855 original size:33 final size:33
Alignment explanation
Indices: 34818--34909 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
34808 TCATTTCGCA
34818 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
34851 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
34884 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
34910 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:34856 original size:14 final size:14
Alignment explanation
Indices: 34837--34891 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
34827 TCATTTCGCA
34837 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
34851 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
34868 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
34884 TTGCGATT
1 TTGCGATT
34892 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:34992 original size:19 final size:19
Alignment explanation
Indices: 34968--35065 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
34958 AAAATTGACT
*
34968 ATCGCAATGCGAAGTGAAA
1 ATCGCAATGCGAAATGAAA
34987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
35006 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
35020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
35039 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
35059 ATCGCAA
1 ATCGCAA
35066 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 16 0.23
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:35097 original size:53 final size:53
Alignment explanation
Indices: 34968--35084 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
34958 AAAATTGACT
*
34968 ATCGCAATGCGAAGTGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35020 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35073 ATCGCAATGCGA
1 ATCGCAATGCGA
35085 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.44
53 35 0.56
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:37415 original size:12 final size:12
Alignment explanation
Indices: 37398--37422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37388 TCTTCGGGGA
37398 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37410 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37422 C
1 C
37423 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37631 original size:24 final size:24
Alignment explanation
Indices: 37597--37643 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37587 CTGAAACATC
37597 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
37621 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37644 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:38352 original size:20 final size:20
Alignment explanation
Indices: 38324--38573 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
38314 AAATTTCAGT
* * *
38324 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38344 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38364 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38384 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38404 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
38424 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
38444 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
38464 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
38484 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
38504 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
38524 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
38544 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
38564 GTTGCGATTT
1 GTTGCGATTT
38574 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:38590 original size:21 final size:21
Alignment explanation
Indices: 38560--38642 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
38550 ATTTTCATAT
*
38560 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
38581 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
38602 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
38623 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
38643 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:38633 original size:42 final size:43
Alignment explanation
Indices: 38540--38638 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
38530 ATTTATGTGT
* *
38540 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
38581 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
38623 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
38639 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:41402 original size:9 final size:9
Alignment explanation
Indices: 41388--41420 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
41378 TATCTTATGC
41388 TAATTAATT
1 TAATTAATT
41397 TAATTAATT
1 TAATTAATT
*
41406 TTA-TAATT
1 TAATTAATT
41414 TAATTAA
1 TAATTAA
41421 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:47082 original size:18 final size:17
Alignment explanation
Indices: 47059--47131 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 17
47049 ATCCATCAGG
47059 AAAAAAAGAGAAAAGAA
1 AAAAAAAGAGAAAAGAA
* *
47076 CAAAAAAAAAGGAAAAAGGA
1 -AAAAAAAGA-G-AAAAGAA
*
47096 AAAAAAAGAGAAAAAAA
1 AAAAAAAGAGAAAAGAA
*
47113 AGAAAAAAGAAAAAAGAA
1 A-AAAAAAGAGAAAAGAA
47131 A
1 A
47132 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 6 0.13
18 24 0.53
19 9 0.20
20 6 0.13
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAGAAAAGAA
Found at i:47091 original size:11 final size:11
Alignment explanation
Indices: 47088--47131 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
47078 AAAAAAAAGG
47088 AAAAAG-GAAA
1 AAAAAGAGAAA
47098 AAAAAGAGAAA
1 AAAAAGAGAAA
*
47109 AAAAAGAAAAA
1 AAAAAGAGAAA
*
47120 AGAAAAAAGAAA
1 A-AAAAGAGAAA
47132 TTGAATCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 6 0.21
11 15 0.52
12 8 0.28
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:47100 original size:28 final size:28
Alignment explanation
Indices: 47060--47130 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
47050 TCCATCAGGA
*
47060 AAAAAAGAGAAAAGAACA-AAAAAAAAGG
1 AAAAAAGAAAAAAGAACAGAAAAAAAA-G
* *
47088 AAAAAGGAAAAAA-AAGAGAAAAAAAAG
1 AAAAAAGAAAAAAGAACAGAAAAAAAAG
47115 AAAAAAGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
47131 ATTGAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.43
28 21 0.57
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAAAAAGAACAGAAAAAAAAG
Found at i:47130 original size:7 final size:7
Alignment explanation
Indices: 47060--47131 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
47050 TCCATCAGGA
47060 AAAAAAG
1 AAAAAAG
*
47067 AGAAAAG
1 AAAAAAG
47074 AACAAAA-
1 AA-AAAAG
*
47081 AAAAAGG
1 AAAAAAG
*
47088 AAAAAGG
1 AAAAAAG
47095 AAAAAA-
1 AAAAAAG
*
47101 AAGAGAA-
1 AA-AAAAG
47108 AAAAAAG
1 AAAAAAG
47115 AAAAAAG
1 AAAAAAG
47122 AAAAAAG
1 AAAAAAG
47129 AAA
1 AAA
47132 TTGAATCAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
6 8 0.15
7 43 0.78
8 4 0.07
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:48090 original size:28 final size:28
Alignment explanation
Indices: 48050--48116 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
48040 TTACCCTATT
48050 CAAAAAGGGCATATATCCCAGTGCATAG
1 CAAAAAGGGCATATATCCCAGTGCATAG
*
48078 CAAAAAGGGCATATATTCCAGTGCATAG
1 CAAAAAGGGCATATATCCCAGTGCATAG
48106 CAAAAAGGGCA
1 CAAAAAGGGCA
48117 AGAATGCGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (28 bp):
CAAAAAGGGCATATATCCCAGTGCATAG
Found at i:48523 original size:51 final size:52
Alignment explanation
Indices: 48458--48591 Score: 189
Period size: 51 Copynumber: 2.6 Consensus size: 52
48448 ATCTATCTGG
* * *
48458 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACATAAGTTATCCATGTG-
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATATGA
* * * *
48509 GGTATCTTAAAGGCTCACATCAACATGAAAAAGACAGAAGTAATCCATATGA
1 GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATATGA
*
48561 GGCATCTTGAAGGCTCACACCAGCATAAAAA
1 GGCATCTTGAAGGCTCACATCAGCATAAAAA
48592 GGTTGGGATA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
51 44 0.63
52 26 0.37
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (52 bp):
GGCATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATATGA
Found at i:50161 original size:119 final size:119
Alignment explanation
Indices: 50008--50761 Score: 1134
Period size: 119 Copynumber: 6.4 Consensus size: 119
49998 ATTTCTCACA
*
50008 AATTT-TAAATCCTTCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
*
50072 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCAGGT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
*
50126 AATTTTTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
*
50191 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
* *
50245 AATTTGGAAATTCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
** * * *
50310 AAGCAACTACCAAAGTTTCTTATTTAATGTTCTAGAAAATTAAAACCTCCGGGT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
*
50364 AATTTGTAAATCCTCCGGGTCTTCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
*
50429 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAATATTAAAA-CTTCCGGGT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTT-CGGGT
* *
50483 AATTTGTAAATCCTCTGGGTCATCTGT-AAA----A---TAGGATGTTTTCGCATGAAAATGCGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* * * * *
50540 AAATGATTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGAGT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
* * *
50594 AATTTGTAAATCC-CTGGGTCATCTATAAAACCTCAGGGTAGGATGTTTTCACATGAAAATGAGA
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
* * * * * **
50658 AAGCGGTTACCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTCCGAAT
66 AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
* *
50712 AATTTGTAAATCCTCCAGGTCATCTATAAAACCTCAGGGTAGGATGTTTT
1 AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
50762 TACTTTAATT
Statistics
Matches: 587, Mismatches: 37, Indels: 23
0.91 0.06 0.04
Matches are distributed among these distances:
110 12 0.02
111 86 0.15
112 2 0.00
114 1 0.00
115 1 0.00
118 97 0.17
119 388 0.66
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (119 bp):
AATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGA
AAGTGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTTCGGGT
Found at i:50391 original size:20 final size:20
Alignment explanation
Indices: 50350--50404 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
50340 TCTAGAAAAT
50350 TAAAACCTCCGGGTAATTTG
1 TAAAACCTCCGGGTAATTTG
* *
50370 TAAATCCTCCGGGT-CTTCTG
1 TAAAACCTCCGGGTAATT-TG
*
50390 TAAAACCTCAGGGTA
1 TAAAACCTCCGGGTA
50405 GGATGTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATTTG
Found at i:50903 original size:3 final size:3
Alignment explanation
Indices: 50895--50944 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
50885 TGAGACTATA
* *
50895 TAT TAT TAT TAT TAT TA- TAT TAC AAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50942 TAT
1 TAT
50945 ATATATTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:57520 original size:2 final size:2
Alignment explanation
Indices: 57513--57539 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57503 AACAAGGTAA
57513 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 A
57540 CTTTTAGCCC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57717 original size:17 final size:19
Alignment explanation
Indices: 57687--57725 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
57677 AAACTATAAA
57687 AAATAATAAAAATATTT-T
1 AAATAATAAAAATATTTAT
57705 AAATAAT-AAAATATTTAT
1 AAATAATAAAAATATTTAT
57723 AAA
1 AAA
57726 AATGTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAAAAATATTTAT
Done.