Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 48 of 93
Found at i:18490920 original size:93 final size:90
Alignment explanation
Indices: 18490760--18491092 Score: 292
Period size: 93 Copynumber: 3.6 Consensus size: 90
18490750 AAAAAAATCT
* * * * **
18490760 AATATCTTAAGAATTCTTCCATTAAGGTTCCAATATCTTAAGAATTCCTCCTCCAAGAATCTTAT
1 AATATCTTAAGAATTCCTCCACTAAGGTTCCAATATCTTAAGAATTCTTCCACCAAG-ATCCAAT
*
18490825 ATCTTAAAAATTCCTCGATCGAGGTTAC
65 ATCTTAAGAATTCCTC-ATCGAGGTT-C
* * *
18490853 AATATCTTAAGAATTCCTCGACTGAGGTTCCAATATTTTAAGAATTCTTCCACCAAGATTCCAAT
1 AATATCTTAAGAATTCCTCCACTAAGGTTCCAATATCTTAAGAATTCTTCCACCAAGA-TCCAAT
* * * *
18490918 ATCATAAGATTTCCTTCATCGAGAATTT
65 ATCTTAAGAATTCC-TCATCGAG-GTTC
* * * * * * * * *
18490946 AATATCATAAAAATCCCTCGACCAAAGTTCCAATATCTTAAGTATCCTTCCACAAAGGATCCAAT
1 AATATCTTAAGAATTCCTCCACTAAGGTTCCAATATCTTAAGAATTCTTCCACCAA-GATCCAAT
* * * *
18491011 GTCTTAAGAATTCCTCCCTTC-AAGATC
65 ATCTTAAGAATTCCT--CATCGAGGTTC
* *
18491038 TAATATCTTAAGAATTCCTCCA-TCAAGCTTTCAATATCTTAAGAATTCTTCCACC
1 -AATATCTTAAGAATTCCTCCACT-AAGGTTCCAATATCTTAAGAATTCTTCCACC
18491093 GATGTTCTAA
Statistics
Matches: 189, Mismatches: 43, Indels: 16
0.76 0.17 0.06
Matches are distributed among these distances:
92 3 0.02
93 177 0.94
94 9 0.05
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (90 bp):
AATATCTTAAGAATTCCTCCACTAAGGTTCCAATATCTTAAGAATTCTTCCACCAAGATCCAATA
TCTTAAGAATTCCTCATCGAGGTTC
Found at i:18494995 original size:36 final size:36
Alignment explanation
Indices: 18494948--18495040 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
18494938 TAACCGTGCA
*
18494948 TGTGCGGTGTGGGAGTGCACATGACGGTGCCAGTAG
1 TGTGCGGTGTGGGAGTGCACATGACGATGCCAGTAG
18494984 TGTGCGGTGTGGGAGTGCACATGACGATGCCAGTAG
1 TGTGCGGTGTGGGAGTGCACATGACGATGCCAGTAG
*
18495020 TGTGCAGTGTGGGAGTGCACA
1 TGTGCGGTGTGGGAGTGCACA
18495041 CGCCAATGAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.18, C:0.16, G:0.43, T:0.23
Consensus pattern (36 bp):
TGTGCGGTGTGGGAGTGCACATGACGATGCCAGTAG
Found at i:18516297 original size:20 final size:20
Alignment explanation
Indices: 18516272--18516322 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
18516262 TGAATTTTTT
18516272 TTACATCAACATCAACTTTC
1 TTACATCAACATCAACTTTC
*
18516292 TTACATCAACATCACCTTTC
1 TTACATCAACATCAACTTTC
18516312 TTACATCAACA
1 TTACATCAACA
18516323 ATATACATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (20 bp):
TTACATCAACATCAACTTTC
Found at i:18517223 original size:7 final size:7
Alignment explanation
Indices: 18517202--18517232 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
18517192 GTAAATGGAC
18517202 TAGTGGG
1 TAGTGGG
18517209 TAAGTGGG
1 T-AGTGGG
18517217 TAGTGGG
1 TAGTGGG
18517224 TAGTGGG
1 TAGTGGG
18517231 TA
1 TA
18517233 AATGGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (7 bp):
TAGTGGG
Found at i:18517230 original size:22 final size:22
Alignment explanation
Indices: 18517176--18517249 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
18517166 GTTTTTGTTA
* *
18517176 GGTAATGGGTAAATGGGTAAATG
1 GGTAGTGGGTAAATGGAT-AATG
* * * *
18517199 GACTAGTGGGTAAGTGGGTAGTG
1 G-GTAGTGGGTAAATGGATAATG
18517222 GGTAGTGGGTAAATGGATAATG
1 GGTAGTGGGTAAATGGATAATG
18517244 GGTAGT
1 GGTAGT
18517250 CCAAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 23 0.55
23 5 0.12
24 14 0.33
ACGTcount: A:0.28, C:0.01, G:0.43, T:0.27
Consensus pattern (22 bp):
GGTAGTGGGTAAATGGATAATG
Found at i:18517538 original size:13 final size:13
Alignment explanation
Indices: 18517520--18517659 Score: 96
Period size: 12 Copynumber: 10.5 Consensus size: 13
18517510 ACTTACCATA
*
18517520 TTTTTTTTGAAGTTT
1 TTTTTTTTGAA--AT
*
18517535 TTTTTTTTG-AGT
1 TTTTTTTTGAAAT
*
18517547 TTTTTTTT-TAA-
1 TTTTTTTTGAAAT
18517558 TTTTTTTT-AAAT
1 TTTTTTTTGAAAT
18517570 TTTTTTCTTGAAAT
1 TTTTTT-TTGAAAT
18517584 TTTTTTTTGAAAT
1 TTTTTTTTGAAAT
18517597 ATTTTTTTGACATGAAAT
1 -TTTTTTT----TGAAAT
18517615 TTTTTTTTG-AA-
1 TTTTTTTTGAAAT
*
18517626 TTTTTTATGAAAT
1 TTTTTTTTGAAAT
18517639 ATATTTTTATTG-AAT
1 -T-TTTTT-TTGAAAT
18517654 TTTTTT
1 TTTTTT
18517660 AAATTTAAAA
Statistics
Matches: 106, Mismatches: 5, Indels: 30
0.75 0.04 0.21
Matches are distributed among these distances:
11 18 0.17
12 20 0.19
13 16 0.15
14 20 0.19
15 17 0.16
16 2 0.02
17 7 0.07
18 6 0.06
ACGTcount: A:0.22, C:0.01, G:0.08, T:0.69
Consensus pattern (13 bp):
TTTTTTTTGAAAT
Found at i:18517539 original size:14 final size:13
Alignment explanation
Indices: 18517520--18517631 Score: 86
Period size: 13 Copynumber: 8.3 Consensus size: 13
18517510 ACTTACCATA
18517520 TTTTTTTTGAAGTTT
1 TTTTTTTTGAA--TT
*
18517535 TTTTTTTTGAGTT
1 TTTTTTTTGAATT
18517548 TTTTTTTT-AA--
1 TTTTTTTTGAATT
*
18517558 TTTTTTTTAAATT
1 TTTTTTTTGAATT
* *
18517571 TTTTTCTTGAAAT
1 TTTTTTTTGAATT
18517584 TTTTTTTTGAAATAT
1 TTTTTTTTG-AAT-T
* *
18517599 TTTTTTGACATGAAAT
1 TTTTTT---TTGAATT
18517615 TTTTTTTTGAATT
1 TTTTTTTTGAATT
18517628 TTTT
1 TTTT
18517632 ATGAAATATA
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.10
11 2 0.03
12 1 0.01
13 37 0.47
14 2 0.03
15 17 0.22
16 7 0.09
17 2 0.03
18 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:18517540 original size:15 final size:14
Alignment explanation
Indices: 18517520--18517555 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
18517510 ACTTACCATA
18517520 TTTTTTTTGAAGTTT
1 TTTTTTTTG-AGTTT
18517535 TTTTTTTTGAGTTT
1 TTTTTTTTGAGTTT
18517549 TTTTTTT
1 TTTTTTT
18517556 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (14 bp):
TTTTTTTTGAGTTT
Found at i:18517561 original size:11 final size:11
Alignment explanation
Indices: 18517547--18517591 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
18517537 TTTTTTGAGT
18517547 TTTTTTTTTAA
1 TTTTTTTTTAA
*
18517558 TTTTTTTTAAA
1 TTTTTTTTTAA
18517569 TTTTTTTCTTGAAA
1 TTTTTTT-TT--AA
18517583 TTTTTTTTT
1 TTTTTTTTT
18517592 GAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.59
12 1 0.03
13 2 0.07
14 9 0.31
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:18517660 original size:28 final size:24
Alignment explanation
Indices: 18517534--18517665 Score: 81
Period size: 27 Copynumber: 5.1 Consensus size: 24
18517524 TTTTGAAGTT
* * **
18517534 TTTTTTTTTGAGTTTTTTTTTTAA
1 TTTTTTTTTGAATTTTTTATGAAA
* *
18517558 -TTTTTTTTAAATTTTTTTCTTGAAA
1 TTTTTTTTTGAA-TTTTTT-ATGAAA
18517583 TTTTTTTTTGAAATATTTTTTTGACATGAAA
1 TTTTTTTTTG--A-A-TTTTTT---ATGAAA
18517614 TTTTTTTTTGAATTTTTTATGAAA
1 TTTTTTTTTGAATTTTTTATGAAA
18517638 TATATTTTTATTGAATTTTTT-T-AAA
1 T-T-TTTTT-TTGAATTTTTTATGAAA
18517663 TTT
1 TTT
18517666 AAAAAAATTC
Statistics
Matches: 91, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
23 10 0.11
24 14 0.15
25 9 0.10
26 14 0.15
27 17 0.19
28 2 0.02
29 9 0.10
31 16 0.18
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (24 bp):
TTTTTTTTTGAATTTTTTATGAAA
Found at i:18520002 original size:20 final size:20
Alignment explanation
Indices: 18519974--18520050 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
18519964 GAGATCAGTT
18519974 GGAAGAAAGGAGAAAGGAAA
1 GGAAGAAAGGAGAAAGGAAA
* *
18519994 GGAATAAAGGAGAAATGAAA
1 GGAAGAAAGGAGAAAGGAAA
*
18520014 -GATAGAAAGGAGAAAGAAAAA
1 GGA-AGAAAGGAGAAAG-GAAA
*
18520035 GAAAGAAAGGAAGAAA
1 GGAAGAAAGG-AGAAA
18520051 AAGCTTGGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.62
21 10 0.21
22 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (20 bp):
GGAAGAAAGGAGAAAGGAAA
Found at i:18530141 original size:14 final size:14
Alignment explanation
Indices: 18530124--18530171 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
18530114 CTCTCTCTTT
*
18530124 CTTTCTTTCCTCTC
1 CTTTCTTTCTTCTC
*
18530138 CTTTCTCTT-TTCTT
1 CTTTCT-TTCTTCTC
*
18530152 TTTTCTTTCTTCTC
1 CTTTCTTTCTTCTC
18530166 CTTTCT
1 CTTTCT
18530172 CTTTTTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTCTTTCTTCTC
Found at i:18530156 original size:28 final size:29
Alignment explanation
Indices: 18530108--18530182 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
18530098 AAACCTTCAT
*
18530108 TCCTTTCTC-TCTCTTTCTTTCTTTCCTC
1 TCCTTTCTCTTTTCTTTCTTTCTTTCCTC
*
18530136 TCCTTTCTCTTTTCTTT-TTTCTTTCTTC
1 TCCTTTCTCTTTTCTTTCTTTCTTTCCTC
18530164 TCCTTTCTCTTTT-TTTCTT
1 TCCTTTCTCTTTTCTTTCTT
18530183 GGTAATGAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 3 0.07
28 34 0.79
29 6 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (29 bp):
TCCTTTCTCTTTTCTTTCTTTCTTTCCTC
Found at i:18530164 original size:21 final size:20
Alignment explanation
Indices: 18530140--18530182 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
18530130 TTCCTCTCCT
* *
18530140 TTCTCTTTTCTTTTTTCTTTC
1 TTCTCCTTTCTCTTTT-TTTC
18530161 TTCTCCTTTCTCTTTTTTTC
1 TTCTCCTTTCTCTTTTTTTC
18530181 TT
1 TT
18530183 GGTAATGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTCTCCTTTCTCTTTTTTTC
Found at i:18532993 original size:20 final size:20
Alignment explanation
Indices: 18532968--18533014 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
18532958 CCAAGCAAGG
18532968 GAACAAAGAGAAAAAGAGAA
1 GAACAAAGAGAAAAAGAGAA
18532988 GAACAAAGAGAAAAAGAGAA
1 GAACAAAGAGAAAAAGAGAA
18533008 GAACAAA
1 GAACAAA
18533015 CTCTAGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.70, C:0.06, G:0.23, T:0.00
Consensus pattern (20 bp):
GAACAAAGAGAAAAAGAGAA
Found at i:18546104 original size:64 final size:64
Alignment explanation
Indices: 18546027--18546152 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 64
18546017 TGGCACCATA
* * *
18546027 TGTGGAACATTACCTCACGCCATGTGGAACGCCATCATCCATCATACTAGATGCATTCACCACG
1 TGTGGAACATTACCTCACACCATGTGAAACGCCATCATCCATCATACTACATGCATTCACCACG
** ** * *
18546091 TGTGGAATGTTACCTCACACTGTGTGAAACGCCATCATTCATCATGCTACATGCATTCACCA
1 TGTGGAACATTACCTCACACCATGTGAAACGCCATCATCCATCATACTACATGCATTCACCA
18546153 TATATGGGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (64 bp):
TGTGGAACATTACCTCACACCATGTGAAACGCCATCATCCATCATACTACATGCATTCACCACG
Found at i:18546165 original size:64 final size:64
Alignment explanation
Indices: 18546049--18546172 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 64
18546039 CCTCACGCCA
* * * *
18546049 TGTGGAACGCCATCATCCATCATACTAGATGCATTCACCACGTGTGGAATGTTACCTCACACTG
1 TGTGAAACGCCATCATCCATCATACTACATGCATTCACCACATATGGAATGTTACCTCACACTG
* * * * *
18546113 TGTGAAACGCCATCATTCATCATGCTACATGCATTCACCATATATGGGATGTTGCCTCAC
1 TGTGAAACGCCATCATCCATCATACTACATGCATTCACCACATATGGAATGTTACCTCAC
18546173 TGTAATGACT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (64 bp):
TGTGAAACGCCATCATCCATCATACTACATGCATTCACCACATATGGAATGTTACCTCACACTG
Found at i:18554131 original size:14 final size:14
Alignment explanation
Indices: 18554114--18554162 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
18554104 GTTTCTTTCC
18554114 TCTTCTTTCTCTTT
1 TCTTCTTTCTCTTT
*
18554128 TCTTCTTTCT-TACT
1 TCTTCTTTCTCT-TT
*
18554142 TCTCCTTTCTCTTT
1 TCTTCTTTCTCTTT
*
18554156 TCCTCTT
1 TCTTCTT
18554163 GGTTATAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (14 bp):
TCTTCTTTCTCTTT
Found at i:18554138 original size:28 final size:28
Alignment explanation
Indices: 18554105--18554162 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
18554095 TGTTTCTTTG
* * *
18554105 TTTCTTTCCTCTTCTTTCTCTTTTCTTC
1 TTTCTTACCTCTCCTTTCTCTTTTCCTC
*
18554133 TTTCTTACTTCTCCTTTCTCTTTTCCTC
1 TTTCTTACCTCTCCTTTCTCTTTTCCTC
18554161 TT
1 TT
18554163 GGTTATAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTCTTACCTCTCCTTTCTCTTTTCCTC
Found at i:18557239 original size:2 final size:2
Alignment explanation
Indices: 18557232--18557267 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
18557222 TGTTATGTTG
* *
18557232 AT AT AT AT AT AT AT AT AT AT AT AT CT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18557268 GGTATGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18561064 original size:13 final size:13
Alignment explanation
Indices: 18561020--18561076 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
18561010 CACGCATTGA
*
18561020 AAATACATAATAAT
1 AAATA-ATAAAAAT
**
18561034 AAATAATAATTAT
1 AAATAATAAAAAT
*
18561047 GAATAA-AATAAAT
1 AAATAATAA-AAAT
18561060 AAATAATAAAAAT
1 AAATAATAAAAAT
18561073 AAAT
1 AAAT
18561077 TAGAGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.06
13 27 0.75
14 7 0.19
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AAATAATAAAAAT
Found at i:18569637 original size:36 final size:37
Alignment explanation
Indices: 18569590--18569715 Score: 159
Period size: 36 Copynumber: 3.5 Consensus size: 37
18569580 GCTCACCAGC
*
18569590 TCATGTGCACTCCCACACCGCACATAGCTGAA-ATCA
1 TCATGTGCACTCCCACACCGCACATAGCTAAATATCA
** * *
18569626 TCATGTGCACTCCCACACTACACATAG-TTAATACCA
1 TCATGTGCACTCCCACACCGCACATAGCTAAATATCA
*
18569662 TCATGTGCACTCCCACACCGCACATGGC-AAATATCA
1 TCATGTGCACTCCCACACCGCACATAGCTAAATATCA
* *
18569698 TCATGTACACCCCCACAC
1 TCATGTGCACTCCCACAC
18569716 TACATAATCA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 3 0.04
36 74 0.96
ACGTcount: A:0.31, C:0.37, G:0.11, T:0.21
Consensus pattern (37 bp):
TCATGTGCACTCCCACACCGCACATAGCTAAATATCA
Found at i:18575384 original size:42 final size:42
Alignment explanation
Indices: 18575288--18575440 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 42
18575278 AGCTCATATG
* ** * * *
18575288 CACTCCCACTAGCACATGGCTGGGTCAGCATCGACTTATGCG
1 CACTCCCACTCGCACATAACCGGGTCAGCATCGGCTTATGCA
**
18575330 CACTCTTACTCGCACATAACCGGGTCAGCATCGGCTTATGCA
1 CACTCCCACTCGCACATAACCGGGTCAGCATCGGCTTATGCA
* * *** *
18575372 CACTCCCCCTCGCACATAGCCAAATTAGCATCGGCTTATGCA
1 CACTCCCACTCGCACATAACCGGGTCAGCATCGGCTTATGCA
* * **
18575414 CACTCCTACTAGCACATAGTCGGGTCA
1 CACTCCCACTCGCACATAACCGGGTCA
18575441 ATATCATTAC
Statistics
Matches: 87, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (42 bp):
CACTCCCACTCGCACATAACCGGGTCAGCATCGGCTTATGCA
Found at i:18591794 original size:19 final size:19
Alignment explanation
Indices: 18591770--18591824 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
18591760 TGCCCGTGTG
18591770 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
****
18591789 CACGATG-GCACTGATTGTA
1 CACGATGTGGGGGGA-TGTA
18591808 CACGATGTGGGGGGATG
1 CACGATGTGGGGGGATG
18591825 CACATGATGA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
18 3 0.12
19 20 0.77
20 3 0.12
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.22
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:18591863 original size:40 final size:38
Alignment explanation
Indices: 18591766--18591871 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 38
18591756 ATAGTGCCCG
* * * **
18591766 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGCACATGATGACACCAAT
* *
18591804 TGTACACGATGTGGGGGGATGCACATGATGACTCCAACT
1 TGTGCACGATGTGGGGGGATGCACATGATGACACCAA-T
*
18591843 ATGTGCACGATGTGGGGGGATGCAAATGA
1 -TGTGCACGATGTGGGGGGATGCACATGA
18591872 GTTGGATGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 30 0.53
39 1 0.02
40 26 0.46
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.23
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACATGATGACACCAAT
Found at i:18592397 original size:19 final size:19
Alignment explanation
Indices: 18592373--18592411 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18592363 GGAGGTTTGG
18592373 TAAGAAACCCTTGGCCAGT
1 TAAGAAACCCTTGGCCAGT
*
18592392 TAAGAAACCCTTGGCTAGT
1 TAAGAAACCCTTGGCCAGT
18592411 T
1 T
18592412 GATAATTTAA
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:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (19 bp):
TAAGAAACCCTTGGCCAGT
Found at i:18592893 original size:2 final size:2
Alignment explanation
Indices: 18592886--18592913 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18592876 ATAGAAAATG
18592886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18592914 CTTGATCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18592955 original size:2 final size:2
Alignment explanation
Indices: 18592948--18592977 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18592938 TAGCAANTAG
18592948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18592978 CTTGATCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18592978 original size:64 final size:63
Alignment explanation
Indices: 18592886--18593008 Score: 237
Period size: 64 Copynumber: 1.9 Consensus size: 63
18592876 ATAGAAAATG
18592886 TATATATATATATATATATATATATATACTTGATCGATATGCCACTATGAGTTAGCAANTAGTA
1 TATATATATATATATATATATATATATACTTGATCGATATGCCACTATGAGTTAGCAA-TAGTA
18592950 TATATATATATATATATATATATATATACTTGATCGATATGCCACTATGAGTTAGCAAT
1 TATATATATATATATATATATATATATACTTGATCGATATGCCACTATGAGTTAGCAAT
18593009 GTTTAGTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 1 0.02
64 58 0.98
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (63 bp):
TATATATATATATATATATATATATATACTTGATCGATATGCCACTATGAGTTAGCAATAGTA
Found at i:18595875 original size:32 final size:32
Alignment explanation
Indices: 18595834--18595898 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
18595824 GAGAATCAAT
18595834 ACCTCAGTCATGCGCCAATGAAGACATTTTCA
1 ACCTCAGTCATGCGCCAATGAAGACATTTTCA
* *
18595866 ACCTCAGTCATGTGCGAATGAAGACATTTTCA
1 ACCTCAGTCATGCGCCAATGAAGACATTTTCA
18595898 A
1 A
18595899 ACCCATCGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (32 bp):
ACCTCAGTCATGCGCCAATGAAGACATTTTCA
Found at i:18601221 original size:37 final size:36
Alignment explanation
Indices: 18601180--18601298 Score: 166
Period size: 37 Copynumber: 3.2 Consensus size: 36
18601170 AATGCAATAT
18601180 CATCATCATGTGTGCACTCCCTACTCGCACAGTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACA-TTCAA
* * *
18601217 CATCATCATGTGTGAACTCCTTACTCGCACACTCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACATTC-AA
* *
18601254 CATCATCATGTGTGCATTCCCTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACA-TTCAA
18601291 CATCATCA
1 CATCATCA
18601299 CACAACATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
36 2 0.03
37 68 0.94
38 2 0.03
ACGTcount: A:0.27, C:0.34, G:0.10, T:0.29
Consensus pattern (36 bp):
CATCATCATGTGTGCACTCCCTACTCGCACATTCAA
Found at i:18616374 original size:15 final size:16
Alignment explanation
Indices: 18616354--18616386 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18616344 ATTATATATA
18616354 TTTTCTTT-TCTTTTT
1 TTTTCTTTCTCTTTTT
18616369 TTTTCTTTCTCTTTTT
1 TTTTCTTTCTCTTTTT
18616385 TT
1 TT
18616387 CTCTCTCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTCTCTTTTT
Found at i:18616377 original size:14 final size:14
Alignment explanation
Indices: 18616354--18616393 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
18616344 ATTATATATA
*
18616354 TTTTCTTTTCTTTTT
1 TTTTC-TTTCTCTTT
18616369 TTTTCTTTCTCTTT
1 TTTTCTTTCTCTTT
*
18616383 TTTTCTCTCTC
1 TTTTCTTTCTC
18616394 CTCTCTCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTCTCTTT
Found at i:18616666 original size:36 final size:36
Alignment explanation
Indices: 18616591--18616701 Score: 145
Period size: 36 Copynumber: 3.1 Consensus size: 36
18616581 ATTTTTTCTC
* * *
18616591 AAAAATCAGTAGCTAAGCTGCTCTATT--CTCCCTCA
1 AAAAATTAATAGCTAAGCTTCTCT-TTGCCTCCCTCA
18616626 AAAAATTTAATAGCTAAGCTTCTCTTTGCCTCCCTCA
1 AAAAA-TTAATAGCTAAGCTTCTCTTTGCCTCCCTCA
**
18616663 AAAAATTAGCAGCTAAGCTTCTCTTTGCCTCCCTCA
1 AAAAATTAATAGCTAAGCTTCTCTTTGCCTCCCTCA
18616699 AAA
1 AAA
18616702 CTCGACAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
35 7 0.10
36 48 0.71
37 13 0.19
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.31
Consensus pattern (36 bp):
AAAAATTAATAGCTAAGCTTCTCTTTGCCTCCCTCA
Found at i:18616771 original size:34 final size:35
Alignment explanation
Indices: 18616716--18616801 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 35
18616706 ACAGCCAAAG
* * *
18616716 CTTCAAAGATCAGTAGACAAAATCGCACC-TTCAGC
1 CTTCAAA-ATCAGCAGCCAAAATCGCACCTTTCAAC
18616751 CTTCAAAATCAGCAGCCAAAATCGCACCTTTCAAC
1 CTTCAAAATCAGCAGCCAAAATCGCACCTTTCAAC
*
18616786 CTTCAAAATCAACAGC
1 CTTCAAAATCAGCAGC
18616802 TAAAGCTGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 19 0.41
35 27 0.59
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.20
Consensus pattern (35 bp):
CTTCAAAATCAGCAGCCAAAATCGCACCTTTCAAC
Found at i:18627642 original size:37 final size:37
Alignment explanation
Indices: 18627585--18627679 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 37
18627575 CCTCAGCTCT
*
18627585 TGTGCACTCCTTACAT-GCACAAGGCAAT-ACGACCATA
1 TGTGCACTCCCTAC-TCGCACAAGGCAATGAC-ACCATA
*** * * *
18627622 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACAAGGCAATGACACCATA
18627659 TGTGCACTCCCTACTCGCACA
1 TGTGCACTCCCTACTCGCACA
18627680 CCTCATTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
36 1 0.02
37 47 0.96
38 1 0.02
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACAAGGCAATGACACCATA
Found at i:18627692 original size:37 final size:37
Alignment explanation
Indices: 18627622--18627694 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
18627612 TACGACCATA
** *
18627622 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
*
18627659 TGTGCACTCCCTACTCGCACACCTCATTATCATCAT
1 TGTGCACTCCCTACTCGCACACCTCAATATCATCAT
18627695 ACAACATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.22, C:0.36, G:0.11, T:0.32
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACACCTCAATATCATCATG
Found at i:18633233 original size:21 final size:21
Alignment explanation
Indices: 18633197--18633247 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18633187 TACAGTTGAG
18633197 TAGTT-AA-TTTAAGTTATTT
1 TAGTTAAATTTTAAGTTATTT
*
18633216 TAGTTAAATTTTATGTTATTT
1 TAGTTAAATTTTAAGTTATTT
*
18633237 TATTTTAAATT
1 TA-GTTAAATT
18633248 ACTTTAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 13 0.48
22 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (21 bp):
TAGTTAAATTTTAAGTTATTT
Found at i:18645803 original size:43 final size:43
Alignment explanation
Indices: 18645749--18645864 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
18645739 GGCTATGTAT
****
18645749 GAGTAGGGAGTGCGCATAAGCTGAG-GATGACCCGGTTATGTGC
1 GAGTAGGGAGTGCGCATAAGCTG-GTGATGACCCAACCATGTGC
** * *
18645792 GAGTAGGGAGTGCATATAACCCGGTGATGACCCAACCATGTGC
1 GAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAACCATGTGC
*
18645835 GAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 GAGTAGGGAGTGCGCATAAGCTGGTGATGA
18645865 TGATGATGTG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (43 bp):
GAGTAGGGAGTGCGCATAAGCTGGTGATGACCCAACCATGTGC
Found at i:18645891 original size:23 final size:23
Alignment explanation
Indices: 18645861--18645920 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
18645851 TGAGCTGGTG
* * *
18645861 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGC
18645884 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGC
*
18645907 ATGATAATGATGGG
1 ATGATGATGATGGG
18645921 TATACATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGC
Found at i:18648089 original size:12 final size:13
Alignment explanation
Indices: 18648074--18648102 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18648064 GAGAAAGGAA
18648074 GAAAG-AAAAAAG
1 GAAAGAAAAAAAG
18648086 GAAAGAAAAAAAG
1 GAAAGAAAAAAAG
18648099 GAAA
1 GAAA
18648103 AAAGAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAAGAAAAAAAG
Found at i:18650200 original size:42 final size:42
Alignment explanation
Indices: 18650144--18650247 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
18650134 CTTCCTAAGT
*
18650144 GCACATAGCAGGGTCATCATCAACTCATGTGCACTCCCACAC
1 GCACATAGCTGGGTCATCATCAACTCATGTGCACTCCCACAC
* *
18650186 GCACATAGCTGGGTCATCATCAGCTCATGTGCACTCCCACAT
1 GCACATAGCTGGGTCATCATCAACTCATGTGCACTCCCACAC
*
18650228 ACACATAGCTGGGTCATCAT
1 GCACATAGCTGGGTCATCAT
18650248 TATCACATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (42 bp):
GCACATAGCTGGGTCATCATCAACTCATGTGCACTCCCACAC
Found at i:18653289 original size:2 final size:2
Alignment explanation
Indices: 18653282--18653307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18653272 TACCTCTAAC
18653282 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
18653308 CCTTGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18657503 original size:42 final size:44
Alignment explanation
Indices: 18657369--18657545 Score: 181
Period size: 43 Copynumber: 4.2 Consensus size: 44
18657359 AGCTAGGTCA
* * *
18657369 TCATCATCGGCTTATGCGCACTCT-ATACTCGCACATAGCTGGG
1 TCATCATCAGCTCATGCGCACTCTCACACTCGCACATAGCTGGG
* * * *
18657412 TCATCAT-AGGCTTATGCGCACTC-CATACTCGTACATA-ATCGGG
1 TCATCATCA-GCTCATGCGCACTCTCACACTCGCACATAGCT-GGG
* *
18657455 TCATCATCAGCTCATGTGCACTCTCACAC-C-CACATAGTTGGG
1 TCATCATCAGCTCATGCGCACTCTCACACTCGCACATAGCTGGG
* *
18657497 TCATCATCAGCTCATGTGCACTC-C-CACACGCACATAGCTGGG
1 TCATCATCAGCTCATGCGCACTCTCACACTCGCACATAGCTGGG
18657539 TCATCAT
1 TCATCAT
18657546 TATCACATAA
Statistics
Matches: 117, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
40 3 0.03
41 2 0.02
42 50 0.43
43 57 0.49
44 5 0.04
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.27
Consensus pattern (44 bp):
TCATCATCAGCTCATGCGCACTCTCACACTCGCACATAGCTGGG
Found at i:18658412 original size:13 final size:14
Alignment explanation
Indices: 18658385--18658416 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
18658375 CAAGGTTTTC
18658385 TTCCTTTCTTTCTT
1 TTCCTTTCTTTCTT
18658399 TTCCTTTC-TTCTT
1 TTCCTTTCTTTCTT
18658412 TTCCT
1 TTCCT
18658417 AGGGTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCCTTTCTTTCTT
Found at i:18660421 original size:39 final size:39
Alignment explanation
Indices: 18660371--18660547 Score: 216
Period size: 39 Copynumber: 4.6 Consensus size: 39
18660361 GTGCCGGTAG
* ** *
18660371 TGTGCGGTGTGGGAGAGCACAAGCCGATGATATATGTCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
*
18660410 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCC
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
18660449 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
* * * * *
18660488 TGTGCGGTGTGAGAGTGTACATGAGGAT-AT-TA-GCTA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
** *
18660524 TGTGTTGTGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGAGCACATGA
18660548 GCTAAGTTGC
Statistics
Matches: 123, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 23 0.19
37 2 0.02
38 2 0.02
39 96 0.78
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (39 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATATATGCCA
Found at i:18694622 original size:267 final size:266
Alignment explanation
Indices: 18694144--18694679 Score: 975
Period size: 267 Copynumber: 2.0 Consensus size: 266
18694134 GGTGATGGGT
*
18694144 GAAAGGAATGTTTTGGAGTAATATATTCTGCACACGAAAAAATAATAATTAAATAATAATATTTT
1 GAAAGGAATGTTTAGGAGTAATATATTCTGCACACGAAAAAATAATAATTAAATAATAATATTTT
18694209 TATTGAGAATGAATTAGCAAGTTAAAAGATGATTTAGAAGTGAATGGGGTATAATAAGACATTTT
66 TATTGAGAATGAATTAGCAAGTTAAAAGATGATTTAGAAGTGAATGGGGTATAATAAGACATTTT
18694274 GGGACCCAAGGAGACAAGTGGAGAATTTTGGAATAAAATATTATTTTATTAATAAAATAATATTA
131 GGGACCCAAGGAGACAAGTGGAGAATTTTGGAATAAAATATTATTTTATTAATAAAATAATATTA
18694339 AATGATTAATATTTTATCTGATGTCGAGATTAGTCATGAAGGAGGATTATATGGCTAATCTAAGT
196 AATGATTAATATTTTATCTGATGTCGAGATTAGTCATGAAGGAGGATTATATGGCTAATCTAAGT
*
18694404 GGGGGA
261 GCGGGA
* *
18694410 GAAAGGAATGTTTAGGAGTAATATATTCTGCACACGAGAAAATAATAATTAAATAATAATTTTTT
1 GAAAGGAATGTTTAGGAGTAATATATTCTGCACACGAAAAAATAATAATTAAATAATAATATTTT
* *
18694475 TATTGAGAATGAATTAGCAAGTTAAAAGGTGATTTGGAAGTGAATCGGGGTATAATAAGACATTT
66 TATTGAGAATGAATTAGCAAGTTAAAAGATGATTTAGAAGTGAAT-GGGGTATAATAAGACATTT
*
18694540 TGGGACCCGAGGAGACAAGTGGAGAATTTTGGAATAAAATATTATTTTATTAATAAAATAATATT
130 TGGGACCCAAGGAGACAAGTGGAGAATTTTGGAATAAAATATTATTTTATTAATAAAATAATATT
*
18694605 AAAAT-ATTAATATTTTATCTGATGTCGAGATTAGTTATGAAGGAGGATTATATGGCTAATCTAA
195 -AAATGATTAATATTTTATCTGATGTCGAGATTAGTCATGAAGGAGGATTATATGGCTAATCTAA
18694669 GTGCGGGA
259 GTGCGGGA
18694677 GAA
1 GAA
18694680 GAAGAACAAG
Statistics
Matches: 260, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
266 105 0.40
267 151 0.58
268 4 0.02
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (266 bp):
GAAAGGAATGTTTAGGAGTAATATATTCTGCACACGAAAAAATAATAATTAAATAATAATATTTT
TATTGAGAATGAATTAGCAAGTTAAAAGATGATTTAGAAGTGAATGGGGTATAATAAGACATTTT
GGGACCCAAGGAGACAAGTGGAGAATTTTGGAATAAAATATTATTTTATTAATAAAATAATATTA
AATGATTAATATTTTATCTGATGTCGAGATTAGTCATGAAGGAGGATTATATGGCTAATCTAAGT
GCGGGA
Found at i:18705851 original size:23 final size:22
Alignment explanation
Indices: 18705795--18705853 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
18705785 TGAAAATTCA
*
18705795 AGGTTTTTGCTGTTGAATTTTG
1 AGGTTTTTGCTGTTAAATTTTG
18705817 AGGTTATGTTGCTG-TAAATTTTTAG
1 AGGTT-T-TTGCTGTTAAA-TTTT-G
18705842 AGGTTTTTGCTG
1 AGGTTTTTGCTG
18705854 CCATTGAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.16
23 10 0.31
24 11 0.34
25 6 0.19
ACGTcount: A:0.17, C:0.05, G:0.27, T:0.51
Consensus pattern (22 bp):
AGGTTTTTGCTGTTAAATTTTG
Found at i:18705925 original size:34 final size:34
Alignment explanation
Indices: 18705887--18705951 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
18705877 CTGAAAATTT
18705887 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATG
1 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATG
* *
18705921 GAGCTGTTTGCTGTCAATTTGTGCAACAAAA
1 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAA
18705952 TTAGAGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (34 bp):
GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATG
Found at i:18705965 original size:34 final size:34
Alignment explanation
Indices: 18705887--18705967 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
18705877 CTGAAAATTT
*
18705887 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATG
1 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATA
* * *
18705921 GAGCTGTTTGCTGTCAATTTGTGCAACAAAATTA
1 GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATA
* *
18705955 GAGTTTTTTGCTG
1 GAGCTGTTTGCTG
18705968 GTAGTTTGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (34 bp):
GAGCTGTTTGCTGCCAATTTGTGCAAAAAAAATA
Found at i:18706002 original size:23 final size:23
Alignment explanation
Indices: 18705972--18706024 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
18705962 TTGCTGGTAG
*
18705972 TTTGTGCAGGAAAATTGGATAGC
1 TTTGTGCAGGAAAATTGGACAGC
18705995 TTTGTGCAGGAAAATTGGACAGC
1 TTTGTGCAGGAAAATTGGACAGC
18706018 TTTGTGC
1 TTTGTGC
18706025 TGCTAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.32
Consensus pattern (23 bp):
TTTGTGCAGGAAAATTGGACAGC
Found at i:18706045 original size:24 final size:25
Alignment explanation
Indices: 18705982--18706051 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 25
18705972 TTTGTGCAGG
* * *
18705982 AAAATTGGATAGCTTTG-TGCAG-G
1 AAAATTGGACAGCTTTGTTGCTGCT
18706005 AAAATTGGACAGCTTTG-TGCTGCT
1 AAAATTGGACAGCTTTGTTGCTGCT
*
18706029 AAAATTGAGA-AGTTTTGTTGCTG
1 AAAATTG-GACAGCTTTGTTGCTG
18706052 AAAATTTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 20 0.50
24 13 0.32
25 7 0.17
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (25 bp):
AAAATTGGACAGCTTTGTTGCTGCT
Found at i:18706286 original size:25 final size:25
Alignment explanation
Indices: 18706256--18706318 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
18706246 AAAGAAAATA
18706256 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGACCC
* *
18706281 AATAGAAAATAAGTGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGACCC
* *
18706306 AATGGGAAATAAA
1 AATAGAAAATAAA
18706319 AATAAATGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.24, T:0.16
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGACCC
Found at i:18706700 original size:2 final size:2
Alignment explanation
Indices: 18706693--18706720 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18706683 AAAAATTCCG
18706693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18706721 CGTATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18713399 original size:12 final size:12
Alignment explanation
Indices: 18713384--18713465 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
18713374 TGGTGGCTTG
*
18713384 GGCGGTGGTGTT
1 GGCGGTGGAGTT
* *
18713396 GGCGGTGGTGCT
1 GGCGGTGGAGTT
*
18713408 GGTGGTGGAGTT
1 GGCGGTGGAGTT
* **
18713420 GGAGGTGCCGTT
1 GGCGGTGGAGTT
*
18713432 GGTGGTGGAGTT
1 GGCGGTGGAGTT
* * *
18713444 GGAGTTGGAGGT
1 GGCGGTGGAGTT
*
18713456 GGAGGTGGAG
1 GGCGGTGGAG
18713466 CTGGTGCTGG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 56 1.00
ACGTcount: A:0.09, C:0.06, G:0.59, T:0.27
Consensus pattern (12 bp):
GGCGGTGGAGTT
Found at i:18713414 original size:24 final size:24
Alignment explanation
Indices: 18713387--18713447 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
18713377 TGGCTTGGGC
* * **
18713387 GGTGGTGTTGGCGGTGGTGCTGGT
1 GGTGGAGTTGGAGGTGCCGCTGGT
*
18713411 GGTGGAGTTGGAGGTGCCGTTGGT
1 GGTGGAGTTGGAGGTGCCGCTGGT
18713435 GGTGGAGTTGGAG
1 GGTGGAGTTGGAG
18713448 TTGGAGGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.07, C:0.07, G:0.57, T:0.30
Consensus pattern (24 bp):
GGTGGAGTTGGAGGTGCCGCTGGT
Found at i:18713450 original size:18 final size:18
Alignment explanation
Indices: 18713419--18713471 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
18713409 GTGGTGGAGT
**
18713419 TGGAGGTGCCGTTGGTGG
1 TGGAGGTGGAGTTGGTGG
* *
18713437 TGGAGTTGGAGTTGGAGG
1 TGGAGGTGGAGTTGGTGG
*
18713455 TGGAGGTGGAGCTGGTG
1 TGGAGGTGGAGTTGGTG
18713472 CTGGTATCGG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.11, C:0.06, G:0.57, T:0.26
Consensus pattern (18 bp):
TGGAGGTGGAGTTGGTGG
Found at i:18713462 original size:24 final size:24
Alignment explanation
Indices: 18713411--18713465 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
18713401 TGGTGCTGGT
* * *
18713411 GGTGGAGTTGGAGGTGCCGTTGGT
1 GGTGGAGTTGGAGGTGCAGGTGGA
* *
18713435 GGTGGAGTTGGAGTTGGAGGTGGA
1 GGTGGAGTTGGAGGTGCAGGTGGA
18713459 GGTGGAG
1 GGTGGAG
18713466 CTGGTGCTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.04, G:0.58, T:0.25
Consensus pattern (24 bp):
GGTGGAGTTGGAGGTGCAGGTGGA
Found at i:18716851 original size:28 final size:28
Alignment explanation
Indices: 18716820--18716874 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
18716810 TATGAAAGCA
*
18716820 GATATTCCTCCACCAATTGAACTAATGT
1 GATATTCCTACACCAATTGAACTAATGT
*
18716848 GATATTTCTACACCAATTGAACTAATG
1 GATATTCCTACACCAATTGAACTAATG
18716875 GAGGAGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (28 bp):
GATATTCCTACACCAATTGAACTAATGT
Found at i:18718735 original size:13 final size:13
Alignment explanation
Indices: 18718717--18718741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18718707 TTCTAGAAAA
18718717 TTTATAAAATCAT
1 TTTATAAAATCAT
18718730 TTTATAAAATCA
1 TTTATAAAATCA
18718742 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18723882 original size:39 final size:39
Alignment explanation
Indices: 18723779--18724047 Score: 270
Period size: 39 Copynumber: 6.9 Consensus size: 39
18723769 ATCCAATCCT
* * * * * * *
18723779 ATCCAAGTATTCCAAATAAATACGAGTGTTTAGAATCGA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
* * * *
18723818 ATTCGAGTACTTT-AATTGAAAATGAATGATTATAATCAA
1 ATCCGAGTA-TTTCAAATAAAAATGAATGTTTATAATCAA
** * *
18723857 ATTTGAGTATTTCAAATAAAGATGAAGGTTTATAATCAA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
* *
18723896 ATCCGAGTATTTCAAACAAAAATGAATGTTTACAATCAA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
* *
18723935 ATCCAAGTATTTCAAATAAAAATGATTGTTTATAATCAA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
* * * *
18723974 ATCCAAGTATTTTAAATAAAAACGAATGTGTATAATCAA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
** * * *
18724013 ATATGAGTATTTTAATTAAAAACGAATGTTTATAA
1 ATCCGAGTATTTCAAATAAAAATGAATGTTTATAA
18724048 AGCTTAGTAG
Statistics
Matches: 192, Mismatches: 36, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
38 3 0.02
39 187 0.97
40 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (39 bp):
ATCCGAGTATTTCAAATAAAAATGAATGTTTATAATCAA
Found at i:18726930 original size:64 final size:64
Alignment explanation
Indices: 18726786--18727096 Score: 259
Period size: 64 Copynumber: 4.9 Consensus size: 64
18726776 TCATTAATGT
** * *
18726786 TAGTGGCAATACCACATAATCATTATCACTATCGATGGCC-TAGCCACATAATCATAACCAACAC
1 TAGTGGCAGCACCACATAATCATTATCAATATCGATGGCCTTA-CCACATAATCATAATCAACAC
* ** * * * * *
18726850 TAGTAGCCTCGA-TACATAATCATCATCATTGTCGATGGCCTTTCCACATAATCATAATCAACAC
1 TAGTGGCAGC-ACCACATAATCATTATCAATATCGATGGCCTTACCACATAATCATAATCAACAC
** * * * * * * * *
18726914 TAGTGGTTGCGCTACATAATCA-TAGTCAATATTGGTGGCCTCACTACATACTCATAATCAAAAC
1 TAGTGGCAGCACCACATAATCATTA-TCAATATCGATGGCCTTACCACATAATCATAATCAACAC
* * * * * *
18726978 TAGTGGCAGTACCACATAATCATAATCAATATTGGTGGCCTTACCACGTAATCATAATCTACAC
1 TAGTGGCAGCACCACATAATCATTATCAATATCGATGGCCTTACCACATAATCATAATCAACAC
* * * * * **
18727042 TAGCGGTAGCACCACATAATCATTATCAATATTGGTGACCTCGCCACATAATCAT
1 TAGTGGCAGCACCACATAATCATTATCAATATCGATGGCCTTACCACATAATCAT
18727097 CGACCTTATA
Statistics
Matches: 197, Mismatches: 45, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
63 1 0.01
64 193 0.98
65 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (64 bp):
TAGTGGCAGCACCACATAATCATTATCAATATCGATGGCCTTACCACATAATCATAATCAACAC
Found at i:18726931 original size:32 final size:32
Alignment explanation
Indices: 18726895--18727006 Score: 109
Period size: 32 Copynumber: 3.5 Consensus size: 32
18726885 TGGCCTTTCC
* * *
18726895 ACATAATCATAATCAACACTAGTGGTTGCGCT
1 ACATAATCATAATCAAAACTAGTGGCTGCACT
* * * *
18726927 ACATAATCATAGTCAATATTGGTGGCCT-CACT
1 ACATAATCATAATCAAAACTAGTGG-CTGCACT
* * * *
18726959 ACATACTCATAATCAAAACTAGTGGCAGTACC
1 ACATAATCATAATCAAAACTAGTGGCTGCACT
18726991 ACATAATCATAATCAA
1 ACATAATCATAATCAA
18727007 TATTGGTGGC
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
31 1 0.02
32 61 0.97
33 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (32 bp):
ACATAATCATAATCAAAACTAGTGGCTGCACT
Found at i:18726953 original size:128 final size:128
Alignment explanation
Indices: 18726796--18727096 Score: 322
Period size: 128 Copynumber: 2.4 Consensus size: 128
18726786 TAGTGGCAAT
* * * * *
18726796 ACCACATAATCATTATCACTATCGATGGCCTAGCCACATAATCATAACCAACACTAGTAGCCTCG
1 ACCACATAATCATTATCAATATTGGTGGCCTAGCCACATAATCATAACCAAAACTAGT-GCC-AG
* * * * * * *
18726861 -A-TACATAATCATCATCATTGTCGATGGCCTTTCCACATAATCATAATCAACACTAGTGGTTGC
64 TACCACATAATCATAATCAATATCGATGGCCTTACCACATAATCATAATCAACACTAGCGGTAGC
* * * * * *
18726924 GCTACATAATCA-TAGTCAATATTGGTGGCCTCA-CTACATACTCATAATCAAAACTAGTGGCAG
1 ACCACATAATCATTA-TCAATATTGGTGGCCT-AGCCACATAATCATAACCAAAACTAGTGCCAG
* * * *
18726987 TACCACATAATCATAATCAATATTGGTGGCCTTACCACGTAATCATAATCTACACTAGCGGTAGC
64 TACCACATAATCATAATCAATATCGATGGCCTTACCACATAATCATAATCAACACTAGCGGTAGC
* *
18727052 ACCACATAATCATTATCAATATTGGTGACCTCGCCACATAATCAT
1 ACCACATAATCATTATCAATATTGGTGGCCTAGCCACATAATCAT
18727097 CGACCTTATA
Statistics
Matches: 139, Mismatches: 28, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
126 1 0.01
127 5 0.04
128 130 0.94
129 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (128 bp):
ACCACATAATCATTATCAATATTGGTGGCCTAGCCACATAATCATAACCAAAACTAGTGCCAGTA
CCACATAATCATAATCAATATCGATGGCCTTACCACATAATCATAATCAACACTAGCGGTAGC
Found at i:18727016 original size:32 final size:32
Alignment explanation
Indices: 18726927--18727078 Score: 126
Period size: 32 Copynumber: 4.8 Consensus size: 32
18726917 TGGTTGCGCT
* * *
18726927 ACATAATCATAGTCAATATTGGTGGC-CTCACT
1 ACATAATCATAATCAATATTGGTGGCAGT-ACC
* * * *
18726959 ACATACTCATAATCAAAACTAGTGGCAGTACC
1 ACATAATCATAATCAATATTGGTGGCAGTACC
**
18726991 ACATAATCATAATCAATATTGGTGGCCTTACC
1 ACATAATCATAATCAATATTGGTGGCAGTACC
* * * * * * * *
18727023 ACGTAATCATAATCTACACTAGCGGTAGCACC
1 ACATAATCATAATCAATATTGGTGGCAGTACC
*
18727055 ACATAATCATTATCAATATTGGTG
1 ACATAATCATAATCAATATTGGTG
18727079 ACCTCGCCAC
Statistics
Matches: 89, Mismatches: 30, Indels: 2
0.74 0.25 0.02
Matches are distributed among these distances:
32 88 0.99
33 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (32 bp):
ACATAATCATAATCAATATTGGTGGCAGTACC
Found at i:18728218 original size:10 final size:11
Alignment explanation
Indices: 18728191--18728245 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
18728181 ACACTTTAAT
18728191 TTGCATTTCAC
1 TTGCATTTCAC
*
18728202 ATGCATTT-AC
1 TTGCATTTCAC
18728212 TTGCATTTCAC
1 TTGCATTTCAC
*
18728223 TTACATTTCA-
1 TTGCATTTCAC
*
18728233 TGTGCATTCCAC
1 T-TGCATTTCAC
18728245 T
1 T
18728246 CATTATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 10 0.28
11 25 0.69
12 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.44
Consensus pattern (11 bp):
TTGCATTTCAC
Found at i:18728229 original size:21 final size:21
Alignment explanation
Indices: 18728191--18728230 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18728181 ACACTTTAAT
*
18728191 TTGCATTTCACATGCATTTAC
1 TTGCATTTCACATACATTTAC
*
18728212 TTGCATTTCACTTACATTT
1 TTGCATTTCACATACATTT
18728231 CATGTGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (21 bp):
TTGCATTTCACATACATTTAC
Found at i:18729750 original size:37 final size:37
Alignment explanation
Indices: 18729674--18729750 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
18729664 ACATACATCG
*
18729674 TCATCATGTGTGCACTCCCTACTCGCACACTCTATCA
1 TCATCATGTGTGCACTCCCTACTCGCACACTCTAACA
* * *
18729711 TCATCATGTTTGCACTCCCTATTTGCACACT-TCAACA
1 TCATCATGTGTGCACTCCCTACTCGCACACTCT-AACA
18729748 TCA
1 TCA
18729751 CCACCCAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.23, C:0.35, G:0.09, T:0.32
Consensus pattern (37 bp):
TCATCATGTGTGCACTCCCTACTCGCACACTCTAACA
Found at i:18731523 original size:43 final size:43
Alignment explanation
Indices: 18731461--18731566 Score: 133
Period size: 43 Copynumber: 2.5 Consensus size: 43
18731451 CTAGGCTATA
** * * **
18731461 TGCGAGTAGGGAGTGCGCATAAGTCGAG-GATGACCCGGTTATG
1 TGCGAGTAGGGAGTGCGCATAACCCG-GTAATGACCCAGCCATG
*
18731504 TGCGAGTAGGGAGTACGCATAACCCGGTAATGACCCAGCCATG
1 TGCGAGTAGGGAGTGCGCATAACCCGGTAATGACCCAGCCATG
18731547 TGCGAGTAGGGAGTGCGCAT
1 TGCGAGTAGGGAGTGCGCAT
18731567 GAGCTGGTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 53 0.98
ACGTcount: A:0.25, C:0.20, G:0.37, T:0.19
Consensus pattern (43 bp):
TGCGAGTAGGGAGTGCGCATAACCCGGTAATGACCCAGCCATG
Found at i:18732013 original size:60 final size:60
Alignment explanation
Indices: 18731935--18732078 Score: 216
Period size: 60 Copynumber: 2.4 Consensus size: 60
18731925 TGAAATACAT
* * *
18731935 TCTCGCTGCAGTGAGAAACTTTCTGTTTCTGGGTTGCAATTTCACTGCAGCGAGATTGAA
1 TCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATTTCACTGCAACGAGATTGAA
* * * *
18731995 TTTTGCTGCAGCGAGAAACATTCTGTTTCTGGGTTACAATTTCGCTGCAACGAGATTGAA
1 TCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATTTCACTGCAACGAGATTGAA
*
18732055 TCTCGCTGCAGCGAAAAACTTTCT
1 TCTCGCTGCAGCGAGAAACTTTCT
18732079 ATTTTGGTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (60 bp):
TCTCGCTGCAGCGAGAAACTTTCTGTTTCTGGGTTACAATTTCACTGCAACGAGATTGAA
Found at i:18735543 original size:50 final size:50
Alignment explanation
Indices: 18735486--18735585 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
18735476 TAGCATCATC
* *
18735486 ATGGGTTACATGTCCCTAACATGTTTTGTTATGTGCTTCATCACGTTTTG
1 ATGGGTTACATGTCCCTAACATGTTTTGTTATGTGCCTCACCACGTTTTG
* *
18735536 ATGGGTTACATGTCTCTAACATGTTTTGTTATGTGCCTCACCATGTTTTG
1 ATGGGTTACATGTCCCTAACATGTTTTGTTATGTGCCTCACCACGTTTTG
18735586 TACATGCCCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (50 bp):
ATGGGTTACATGTCCCTAACATGTTTTGTTATGTGCCTCACCACGTTTTG
Found at i:18736695 original size:2 final size:2
Alignment explanation
Indices: 18736688--18736740 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
18736678 TGTGACAATA
18736688 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18736730 TG TG TG TG TG T
1 TG TG TG TG TG T
18736741 AAATGGTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:18743813 original size:35 final size:35
Alignment explanation
Indices: 18743774--18743846 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
18743764 CTTACTCAAC
* *
18743774 TCATGTGCACTCTCTACACGCACAAGGCAATATCA
1 TCATGTGCACTCCCTACAAGCACAAGGCAATATCA
***
18743809 TCATGTGCACTCCCTACAAGCACATTTCAATATCA
1 TCATGTGCACTCCCTACAAGCACAAGGCAATATCA
18743844 TCA
1 TCA
18743847 CAAGCACTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.26
Consensus pattern (35 bp):
TCATGTGCACTCCCTACAAGCACAAGGCAATATCA
Found at i:18744794 original size:20 final size:20
Alignment explanation
Indices: 18744741--18744794 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
18744731 AGGATGGGAA
18744741 GAAGAAGAAGAAGAAGCTGCTG
1 GAAGAA-AAG-AGAAGCTGCTG
** * *
18744763 GAAGCGAGGAGAAGGTGCTG
1 GAAGAAAAGAGAAGCTGCTG
18744783 GAAGAAAAGAGA
1 GAAGAAAAGAGA
18744795 TATTTATCCT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 19 0.76
21 2 0.08
22 4 0.16
ACGTcount: A:0.44, C:0.07, G:0.41, T:0.07
Consensus pattern (20 bp):
GAAGAAAAGAGAAGCTGCTG
Found at i:18745937 original size:36 final size:36
Alignment explanation
Indices: 18745897--18746018 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
18745887 CATGTAGTTG
*
18745897 ATTAAAATTGTTTAATTAAGTTGTTAGGCTTAATTA
1 ATTAAAATTGTTTAATTAAGTTGTTGGGCTTAATTA
* ** * *
18745933 ATT-AAATTGTTTAAGTAAGTCATTGGGCCTAATTG
1 ATTAAAATTGTTTAATTAAGTTGTTGGGCTTAATTA
*
18745968 ATTAAAATTATTTAATTAAGTTGTTGGGCTTAATTA
1 ATTAAAATTGTTTAATTAAGTTGTTGGGCTTAATTA
18746004 A-TAAAATTGTTTAAT
1 ATTAAAATTGTTTAAT
18746019 CAAATTACTG
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
35 42 0.58
36 30 0.42
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (36 bp):
ATTAAAATTGTTTAATTAAGTTGTTGGGCTTAATTA
Found at i:18747611 original size:29 final size:29
Alignment explanation
Indices: 18747578--18747719 Score: 133
Period size: 30 Copynumber: 4.8 Consensus size: 29
18747568 TCAACTTTGT
* *
18747578 AAAAGTGGAAAGGCTT-TACCTTAGCCTTA
1 AAAAGTAGAAAGG-TTCTAACTTAGCCTTA
18747607 AAAAGGTAGAAAGGTTCTAACTTAGCCTTA
1 AAAA-GTAGAAAGGTTCTAACTTAGCCTTA
* *
18747637 AAAGGTAGAGAGGTTCTAACTTAGCCTTGA
1 AAAAGTAGAAAGGTTCTAACTTAGCCTT-A
* ** * * * *
18747667 AAAGGTAGGGAGATTATAACTTAGTCTTC
1 AAAAGTAGAAAGGTTCTAACTTAGCCTTA
*
18747696 AAAAGCTAGAAAGGTTTTAACTTA
1 AAAAG-TAGAAAGGTTCTAACTTA
18747720 AACTTGAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
29 33 0.35
30 62 0.65
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (29 bp):
AAAAGTAGAAAGGTTCTAACTTAGCCTTA
Found at i:18747661 original size:59 final size:60
Alignment explanation
Indices: 18747597--18747719 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 60
18747587 AAGGCTTTAC
* * * *
18747597 CTTAGCCTTAAAAAGGTAGAAAGGTTCTAACTTAGCCTT-AAAAGGTAGAGAGGTTCTAA
1 CTTAGCCTTAAAAAGGTAGAAAGATTATAACTTAGCCTTCAAAAGCTAGAAAGGTTCTAA
* ** * *
18747656 CTTAGCCTTGAAAAGGTAGGGAGATTATAACTTAGTCTTCAAAAGCTAGAAAGGTTTTAA
1 CTTAGCCTTAAAAAGGTAGAAAGATTATAACTTAGCCTTCAAAAGCTAGAAAGGTTCTAA
18747716 CTTA
1 CTTA
18747720 AACTTGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 33 0.61
60 21 0.39
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (60 bp):
CTTAGCCTTAAAAAGGTAGAAAGATTATAACTTAGCCTTCAAAAGCTAGAAAGGTTCTAA
Found at i:18747730 original size:30 final size:30
Alignment explanation
Indices: 18747597--18747730 Score: 153
Period size: 30 Copynumber: 4.5 Consensus size: 30
18747587 AAGGCTTTAC
*
18747597 CTTAGCCTTAAAAAGGTAGAAAGGTTCTAA
1 CTTAGCCTTGAAAAGGTAGAAAGGTTCTAA
*
18747627 CTTAGCCTT-AAAAGGTAGAGAGGTTCTAA
1 CTTAGCCTTGAAAAGGTAGAAAGGTTCTAA
** * *
18747656 CTTAGCCTTGAAAAGGTAGGGAGATTATAA
1 CTTAGCCTTGAAAAGGTAGAAAGGTTCTAA
* * * *
18747686 CTTAGTCTTCAAAAGCTAGAAAGGTTTTAA
1 CTTAGCCTTGAAAAGGTAGAAAGGTTCTAA
**
18747716 CTTAAACTTGAAAAG
1 CTTAGCCTTGAAAAG
18747731 ATATGGACGT
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
29 28 0.31
30 61 0.69
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (30 bp):
CTTAGCCTTGAAAAGGTAGAAAGGTTCTAA
Found at i:18749339 original size:27 final size:27
Alignment explanation
Indices: 18749308--18749512 Score: 99
Period size: 27 Copynumber: 7.4 Consensus size: 27
18749298 AACACACATT
* * *
18749308 TTGAAAAAAATGTTTTTACATGCCATG
1 TTGAAAAAAAAGTTGTTACACGCCATG
18749335 TTGAAAAAAAAGTTGTTACACGCCATG
1 TTGAAAAAAAAGTTGTTACACGCCATG
* **** *
18749362 TTTAAAAATTTTTTTTGTTACACACCATG
1 TTGAAAAA--AAAGTTGTTACACGCCATG
* **
18749391 TTCACAAAAAAAGTTGTTACACATCATG
1 TTGA-AAAAAAAGTTGTTACACGCCATG
* * * * *
18749419 TT-TAAAAAATGTTATTATTATACGCTATG
1 TTGAAAAAAAAG---TTGTTACACGCCATG
* * * *
18749448 TTGAAAAAAAAATTATTACATGCCATA
1 TTGAAAAAAAAGTTGTTACACGCCATG
* * * *
18749475 TTTAAAAAATGTAGTTGTTACATGCCATC
1 TTGAAAAAA--AAGTTGTTACACGCCATG
18749504 TT-AAAAAAA
1 TTGAAAAAAA
18749513 TTTGTTAAAC
Statistics
Matches: 134, Mismatches: 35, Indels: 19
0.71 0.19 0.10
Matches are distributed among these distances:
26 7 0.05
27 50 0.37
28 22 0.16
29 45 0.34
30 10 0.07
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (27 bp):
TTGAAAAAAAAGTTGTTACACGCCATG
Found at i:18749449 original size:57 final size:55
Alignment explanation
Indices: 18749312--18749545 Score: 199
Period size: 56 Copynumber: 4.3 Consensus size: 55
18749302 CACATTTTGA
*
18749312 AAAAAATG-T-TT-TTACATGCCATGTTGAAAAAAAAGTTGTTACACGCCATGTTT
1 AAAAAATGTTATTATTACACGCCATGTT-AAAAAAAAGTTGTTACACGCCATGTTT
* * * * * **
18749365 AAAAATTTTTTTTGTTACACACCATGTTCACAAAAAAAGTTGTTACACATCATGTTT
1 AAAAAATGTTATTATTACACGCCATGTT-A-AAAAAAAGTTGTTACACGCCATGTTT
* * * * * *
18749422 AAAAAATGTTATTATTATACGCTATGTTGAAAAAAAAATTATTACATGCCATATTT
1 AAAAAATGTTATTATTACACGCCATGTT-AAAAAAAAGTTGTTACACGCCATGTTT
* * * * * **
18749478 AAAAAATG-TAGTTGTTACATGCCATCTT-AAAAAAATTTGTTAAACGTAATGTTT
1 AAAAAATGTTA-TTATTACACGCCATGTTAAAAAAAAGTTGTTACACGCCATGTTT
18749532 AAAAAATGTTATTA
1 AAAAAATGTTATTA
18749546 ATAACTTTAT
Statistics
Matches: 141, Mismatches: 34, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
53 6 0.04
54 30 0.21
55 6 0.04
56 53 0.38
57 46 0.33
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (55 bp):
AAAAAATGTTATTATTACACGCCATGTTAAAAAAAAGTTGTTACACGCCATGTTT
Found at i:18749473 original size:113 final size:110
Alignment explanation
Indices: 18749332--18749545 Score: 266
Period size: 113 Copynumber: 1.9 Consensus size: 110
18749322 TTTACATGCC
* * * * * ** *
18749332 ATGTTGAAAAAAAAGTTGTTACACGCCATGTTTAAAAATTTTTTTTGTTACACACCATGTTCACA
1 ATGTTGAAAAAAAAATTATTACACGCCATATTTAAAAAATGTAGTTGTTACACACCATCTT---A
* *
18749397 AAAAAAGTTGTTACACATCATGTTTAAAAAATGTTATTATTATACGCT
63 AAAAAAGTTGTTAAACATAATGTTTAAAAAATGTTATTATTATACGCT
* **
18749445 ATGTTGAAAAAAAAATTATTACATGCCATATTTAAAAAATGTAGTTGTTACATGCCATCTTAAAA
1 ATGTTGAAAAAAAAATTATTACACGCCATATTTAAAAAATGTAGTTGTTACACACCATCTTAAAA
* *
18749510 AAATTTGTTAAACGTAATGTTTAAAAAATGTTATTA
66 AAAGTTGTTAAACATAATGTTTAAAAAATGTTATTA
18749546 ATAACTTTAT
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
110 36 0.42
113 50 0.58
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (110 bp):
ATGTTGAAAAAAAAATTATTACACGCCATATTTAAAAAATGTAGTTGTTACACACCATCTTAAAA
AAAGTTGTTAAACATAATGTTTAAAAAATGTTATTATTATACGCT
Found at i:18751810 original size:38 final size:38
Alignment explanation
Indices: 18751748--18751850 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 38
18751738 AAAGTGCCCG
* *
18751748 TGTGCACGATGTGGGGGGAAGCACACGATGGCACT-AA
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTGAA
* * *
18751785 TGTTGCATGATGTGGGGGGATGCACACGATGACTCTGGCTA
1 TG-TGCACGATGTGGGGGGATGCACACGATGACACT-G-AA
18751826 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
18751851 TGAGTTGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 2 0.04
38 29 0.52
40 22 0.39
41 3 0.05
ACGTcount: A:0.22, C:0.17, G:0.39, T:0.21
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACTGAA
Found at i:18774891 original size:35 final size:36
Alignment explanation
Indices: 18774817--18774904 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
18774807 GTCTTGGTAG
* * *
18774817 AGGTTATGTTTGATCTTGCAAATAGGCAAGTTGTGA
1 AGGTTACGCTTGATCTTGCAAATAGGCAAGTTGTAA
*
18774853 AGGTTACGCTTGATCTTGCAAA-AGGCATGTTGTAA
1 AGGTTACGCTTGATCTTGCAAATAGGCAAGTTGTAA
*
18774888 AGGTTACGCTTCATCTT
1 AGGTTACGCTTGATCTT
18774905 ATTGAAAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 27 0.57
36 20 0.43
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (36 bp):
AGGTTACGCTTGATCTTGCAAATAGGCAAGTTGTAA
Found at i:18786879 original size:47 final size:47
Alignment explanation
Indices: 18786823--18787237 Score: 453
Period size: 47 Copynumber: 8.8 Consensus size: 47
18786813 TGTGACATGG
* * *
18786823 CTGTGACACGCCAGCGTTCAAAGTTGGTGAAACACCATGGAGGGAAT
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
* * * *
18786870 -TCGTGACACGCCAGTG-TAAAGAGTTGGTGACACGACATGGTGGGAAT
1 CT-GTGACACGCCAGAGTTCAA-AGTTGGTGACACGCCATGGAGGGAAT
* * * * * * *
18786917 CTATGAGATGTCAGCA-TTCAGAGTTGGTGAGACACCATGGAGGGAAT
1 CTGTGACACGCCAG-AGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
*
18786964 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGGCATGGAGGGAAT
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
* * * * * * *
18787011 CTGTAACACACTAGCGTTCAGAGTTAGTGAGACGCCATGGAGGGAAT
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
* *
18787058 CTGTGACACGCTAGAGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
* * * *
18787105 TTGTGACACGCCAGTGTT-AAGAGTTGGTGAGACGGCATGGAGGGAAT
1 CTGTGACACGCCAGAGTTCAA-AGTTGGTGACACGCCATGGAGGGAAT
* *
18787152 CTGTGACACGCCAGAGTTCAGAGTTGGTGACACGGCATGGAGGGAAGT
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAA-T
* * *
18787200 -TGTGACAAGCCAAAGTTCACAGTTGGTGACACGCCATG
1 CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATG
18787238 TTTAGAGTGT
Statistics
Matches: 307, Mismatches: 52, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
46 6 0.02
47 296 0.96
48 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (47 bp):
CTGTGACACGCCAGAGTTCAAAGTTGGTGACACGCCATGGAGGGAAT
Found at i:18787068 original size:23 final size:22
Alignment explanation
Indices: 18787037--18787164 Score: 64
Period size: 23 Copynumber: 5.5 Consensus size: 22
18787027 TTCAGAGTTA
*
18787037 GTGAGACGCCATGGAGGGAATCT
1 GTGACACGCCATGGAGGGAAT-T
* * *
18787060 GTGACACG-C-TAGAGTTCAGAGTT
1 GTGACACGCCATGGAG---GGAATT
18787083 GGTGACACGCCATGGAGGGAATTT
1 G-TGACACGCCATGGAGGGAA-TT
* * *
18787107 GTGACACGCCAGTGTTA-AGAGTT
1 GTGACACGCCA-TG-GAGGGAATT
* *
18787130 GGTGAGACGGCATGGAGGGAATCT
1 -GTGACACGCCATGGAGGGAAT-T
18787154 GTGACACGCCA
1 GTGACACGCCA
18787165 GAGTTCAGAG
Statistics
Matches: 76, Mismatches: 17, Indels: 24
0.65 0.15 0.21
Matches are distributed among these distances:
21 4 0.05
22 2 0.03
23 37 0.49
24 27 0.36
25 2 0.03
26 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.36, T:0.20
Consensus pattern (22 bp):
GTGACACGCCATGGAGGGAATT
Found at i:18787324 original size:29 final size:29
Alignment explanation
Indices: 18787282--18787341 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
18787272 TGACACTCCA
18787282 TGGTTTAGAGTGTGTGACACGGCATTGCT
1 TGGTTTAGAGTGTGTGACACGGCATTGCT
* *
18787311 TGGTTTAGAGTGTGTGACAGGGCATTTCT
1 TGGTTTAGAGTGTGTGACACGGCATTGCT
18787340 TG
1 TG
18787342 AACGACTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.12, G:0.35, T:0.37
Consensus pattern (29 bp):
TGGTTTAGAGTGTGTGACACGGCATTGCT
Found at i:18787853 original size:31 final size:31
Alignment explanation
Indices: 18787811--18788229 Score: 500
Period size: 31 Copynumber: 13.5 Consensus size: 31
18787801 GGCATTGTTA
* *
18787811 GCGTGTGACAACATTTGACTCT-ATATGCATG
1 GCGTGTCACAACATTTTACT-TGATATGCATG
* *
18787842 GCGTGTCACAACATTTGACTTGATATTCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* *
18787873 GCGGGTCACAACATTTGACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
** *
18787904 GCAAGTAACAACATTTTACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
18787935 GCATGTCACAATATTTTACTTGGTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
*
18787966 GCGTGTCACAACATTTTAC-TCAGTATGCATG
1 GCGTGTCACAACATTTTACTTGA-TATGCATG
* * *
18787997 GCGTGTTACAAGATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
18788028 GGGTGTCACAACATTTTACTTGTTATGCATT
1 GCGTGTCACAACATTTTACTTGATATGCATG
*
18788059 GTGTGTCACAACATTTTACTTGATATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
18788090 GTGTGTCACAACATTTTACTTGTTATGGATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* * *
18788121 GCTTGTCACAATATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
** * *
18788152 GTTTGTCACAACATTTTGCTTGCTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* *
18788183 GCGTGTCACAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGATATGCATG
* *
18788214 TCGTTTCACAACATTT
1 GCGTGTCACAACATTT
18788230 ATTCCTTATT
Statistics
Matches: 343, Mismatches: 42, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
30 2 0.01
31 340 0.99
32 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGATATGCATG
Found at i:18790158 original size:22 final size:22
Alignment explanation
Indices: 18790133--18790185 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
18790123 ATTTTTTTTC
18790133 TTATAAAACAAT-ATTTTTATAG
1 TTATAAAA-AATAATTTTTATAG
**
18790155 TTATACGTAAATAATTTTTATAG
1 TTATA-AAAAATAATTTTTATAG
18790178 -TATAAAAA
1 TTATAAAAA
18790186 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
TTATAAAAAATAATTTTTATAG
Found at i:18792058 original size:20 final size:20
Alignment explanation
Indices: 18792032--18792077 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
18792022 AATCTTACCT
* *
18792032 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
18792053 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
18792074 TTTT
1 TTTT
18792078 TTCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:18792078 original size:22 final size:22
Alignment explanation
Indices: 18792037--18792077 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18792027 TACCTTTTTT
*
18792037 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
18792059 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
18792078 TTCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:18793496 original size:94 final size:93
Alignment explanation
Indices: 18793336--18793885 Score: 444
Period size: 94 Copynumber: 5.9 Consensus size: 93
18793326 CTTGTTATGG
* * * * * ** *
18793336 ATGGCGTGTCAGAACATTTTTGGTGGT-TATACATGGCATGTCAAAACATTTT-G-TAGGGCATC
1 ATGGCGTGTCAGAACA-TTTTGCTTGTGT-TGCATGGCGTGTCAGAACATTTTGGCT-GGTTATG
*
18793398 CATGGCGTGTTAGAACATTTTGCTTGTG-TTGC
63 CATGGCGTGTCAGAACATTTTG-TTG-GCTTGC
* * *
18793430 ATGGCGTGTCAGAATATTTTGCTTGTGTTGCATGGCGTGTTAGAACATTTTGGGTGGTTATGCAT
1 ATGGCGTGTCAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAACATTTTGGCTGGTTATGCAT
* * *
18793495 GGCGCGTCAGAACATTTTGTATGGCATCC
66 GGCGTGTCAGAACATTTTGT-TGGCTTGC
* * * *
18793524 ATGGCATGTCAGAACATTTTACTTGTGTTGCATGGCGTGTCAAAACATTTTGGGTGGTTATGCAT
1 ATGGCGTGTCAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAACATTTTGGCTGGTTATGCAT
* * *
18793589 GGCGTGTCTA-AACATTTTGTAAGGCATCC
66 GGCGTGTC-AGAACATTTTGT-TGGCTTGC
* ** *
18793618 ATGGCGTGTCAGAA-ATTTTGCTTGTGTTGCATGGCGTGTCA-CA-ATGTTTAACTTGTTATGCA
1 ATGGCGTGTCAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAACAT-TTTGGCTGGTTATGCA
* * *
18793680 TGGCATGTCAGAACATTTTGGGTGGTTATGC
65 TGGCGTGTCAGAACATTTT-GTTGGCT-TGC
* ** *
18793711 ATGGCGTGTCATAACATTTTGCTTGTGTTGCATCACATGTCAGAACATTTT-GCTTGTGTTA--C
1 ATGGCGTGTCAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAACATTTTGGC-TG-GTTATGC
* * ** *
18793773 ATGGCGTGTCACAACGTTTAACTT-GTTATGC
64 ATGGCGTGTCAGAACATTT-TGTTGGCT-TGC
* * * * * *
18793804 ATGACGTGTCAAAACATTTTGCTTGT-TATCCATGGCGTATCACAACATTTT-GCTTGTTATGCA
1 ATGGCGTGTCAGAACATTTTGCTTGTGT-TGCATGGCGTGTCAGAACATTTTGGCTGGTTATGCA
* *
18793867 TGGTGTGTCACAACATTTT
65 TGGCGTGTCAGAACATTTT
18793886 ACTTATTATG
Statistics
Matches: 378, Mismatches: 59, Indels: 40
0.79 0.12 0.08
Matches are distributed among these distances:
91 7 0.02
92 33 0.09
93 139 0.37
94 186 0.49
95 7 0.02
96 6 0.02
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (93 bp):
ATGGCGTGTCAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAACATTTTGGCTGGTTATGCAT
GGCGTGTCAGAACATTTTGTTGGCTTGC
Found at i:18793549 original size:125 final size:126
Alignment explanation
Indices: 18793329--18793731 Score: 388
Period size: 125 Copynumber: 3.2 Consensus size: 126
18793319 CGTTTAACTT
* * * *
18793329 GTTATGGATGGCGTGTCAGAACATTTTTGGTGGTTATACATGGCATGTCAAAACATTTTGTAGGG
1 GTTATGCATGGCGTGTTAGAACATTTTGGGTGGTTATACATGGCACGTCAAAACATTTTGTAGGG
* * * * * *
18793394 CATCCATGGCGTGTTAGAACATTTTGCTTGTGTTGCATGGCGTGTCAGAATATTTTGC-TT
66 CATCCATGGCATGTCAGAACATTTTACTTGTGTTGCATGGCGTGTCAAAACATTTTGCGTG
* * * *
18793454 GTGT-TGCATGGCGTGTTAGAACATTTTGGGTGGTTATGCATGGCGCGTCAGAACATTTTGTATG
1 GT-TATGCATGGCGTGTTAGAACATTTTGGGTGGTTATACATGGCACGTCAAAACATTTTGTAGG
*
18793518 GCATCCATGGCATGTCAGAACATTTTACTTGTGTTGCATGGCGTGTCAAAACATTTTGGGTG
65 GCATCCATGGCATGTCAGAACATTTTACTTGTGTTGCATGGCGTGTCAAAACATTTTGCGTG
*** * * ** * *
18793580 GTTATGCATGGCGTGTCTA-AACATTTTGTAAGG-CATCCATGGCGTGTCAGAA-ATTTTGCTTG
1 GTTATGCATGGCGTGT-TAGAACATTTTGGGTGGTTATACATGGCACGTCAAAACATTTTG-TAG
* * * * * ** * * * *
18793642 TG-TTGCATGGCGTGTCACAATGTTTAACTTGT-TATGCATGGCATGTCAGAACATTTTGGGTG
64 GGCATCCATGGCATGTCAGAACATTTTACTTGTGT-TGCATGGCGTGTCAAAACATTTTGCGTG
* *
18793704 GTTATGCATGGCGTGTCATAACATTTTG
1 GTTATGCATGGCGTGTTAGAACATTTTG
18793732 CTTGTGTTGC
Statistics
Matches: 237, Mismatches: 34, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
123 2 0.01
124 80 0.34
125 126 0.53
126 27 0.11
127 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (126 bp):
GTTATGCATGGCGTGTTAGAACATTTTGGGTGGTTATACATGGCACGTCAAAACATTTTGTAGGG
CATCCATGGCATGTCAGAACATTTTACTTGTGTTGCATGGCGTGTCAAAACATTTTGCGTG
Found at i:18793695 original size:124 final size:125
Alignment explanation
Indices: 18793523--18793857 Score: 412
Period size: 124 Copynumber: 2.7 Consensus size: 125
18793513 GTATGGCATC
* * * *
18793523 CATGGCATGTCAGAACATTTTACTTGTGT-TGCATGGCGTGTCAAAACATTTTGGGTGGTTATGC
1 CATGGCGTGTCACAACGTTTAACTTGT-TATGCATGGCGTGTCAAAACATTTTGGGTGGTTATGC
** * *
18793587 ATGGCGTGTCTA-AACATTTTG-TAAG-GCATCCATGGCGTGTCAGAA-ATTTTGCTTGTGTTG
65 ATGGCGTGTC-ACAACATTTTGCT-AGTG-ATCCATCACATGTCAGAACATTTTGCTTGTGTTA
* * *
18793647 CATGGCGTGTCACAATGTTTAACTTGTTATGCATGGCATGTCAGAACATTTTGGGTGGTTATGCA
1 CATGGCGTGTCACAACGTTTAACTTGTTATGCATGGCGTGTCAAAACATTTTGGGTGGTTATGCA
* * * *
18793712 TGGCGTGTCATAACATTTTGCTTGTGTTGCATCACATGTCAGAACATTTTGCTTGTGTTA
66 TGGCGTGTCACAACATTTTGCTAGTGATCCATCACATGTCAGAACATTTTGCTTGTGTTA
* * * *
18793772 CATGGCGTGTCACAACGTTTAACTTGTTATGCATGACGTGTCAAAACATTTT-GCTTGTTATCCA
1 CATGGCGTGTCACAACGTTTAACTTGTTATGCATGGCGTGTCAAAACATTTTGGGTGGTTATGCA
*
18793836 TGGCGTATCACAACATTTTGCT
66 TGGCGTGTCACAACATTTTGCT
18793858 TGTTATGCAT
Statistics
Matches: 183, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
123 2 0.01
124 117 0.64
125 64 0.35
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (125 bp):
CATGGCGTGTCACAACGTTTAACTTGTTATGCATGGCGTGTCAAAACATTTTGGGTGGTTATGCA
TGGCGTGTCACAACATTTTGCTAGTGATCCATCACATGTCAGAACATTTTGCTTGTGTTA
Found at i:18793895 original size:31 final size:31
Alignment explanation
Indices: 18793325--18793895 Score: 318
Period size: 31 Copynumber: 18.3 Consensus size: 31
18793315 TTTACGTTTA
* *
18793325 ACTTGTTATGGATGGCGTGTCAGAACATTTTT
1 ACTTGTTATGCATGGCGTGTCACAACA-TTTT
** * * * *
18793357 GGTGGTTATACATGGCATGTCAAAACATTTT
1 ACTTGTTATGCATGGCGTGTCACAACATTTT
* * ** * * *
18793388 -GTAGGGCATCCATGGCGTGTTAGAACATTTT
1 ACT-TGTTATGCATGGCGTGTCACAACATTTT
* * *
18793419 GCTTGTGT-TGCATGGCGTGTCAGAATATTTT
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
* * *
18793450 GCTTGTGT-TGCATGGCGTGTTAGAACATTTT
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
** * * *
18793481 GGGTGGTTATGCATGGCGCGTCAGAACATTTT
1 -ACTTGTTATGCATGGCGTGTCACAACATTTT
* ** * * *
18793513 -GTATGGCATCCATGGCATGTCAGAACATTTT
1 ACT-TGTTATGCATGGCGTGTCACAACATTTT
*
18793544 ACTTGTGT-TGCATGGCGTGTCAAAACATTTT
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
** *
18793575 GGGTGGTTATGCATGGCGTGTCTA-AACATTTT
1 -ACTTGTTATGCATGGCGTGTC-ACAACATTTT
* * ** * *
18793607 -GTAAGGCATCCATGGCGTGTCAGAA-ATTTT
1 ACT-TGTTATGCATGGCGTGTCACAACATTTT
* ** *
18793637 GCTTGTGT-TGCATGGCGTGTCACAATGTTTA
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
* *
18793668 ACTTGTTATGCATGGCATGTCAGAACATTTT
1 ACTTGTTATGCATGGCGTGTCACAACATTTT
** * *
18793699 GGGTGGTTATGCATGGCGTGTCATAACATTTT
1 -ACTTGTTATGCATGGCGTGTCACAACATTTT
* ** * *
18793731 GCTTGTGT-TGCATCACATGTCAGAACATTTT
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
* * * *
18793762 GCTTGTGT-TACATGGCGTGTCACAACGTTTA
1 ACTTGT-TATGCATGGCGTGTCACAACATTTT
* *
18793793 ACTTGTTATGCATGACGTGTCAAAACATTTT
1 ACTTGTTATGCATGGCGTGTCACAACATTTT
* * *
18793824 GCTTGTTATCCATGGCGTATCACAACATTTT
1 ACTTGTTATGCATGGCGTGTCACAACATTTT
* *
18793855 GCTTGTTATGCATGGTGTGTCACAACATTTT
1 ACTTGTTATGCATGGCGTGTCACAACATTTT
*
18793886 ACTTATTATG
1 ACTTGTTATG
18793896 GTTTGTGGTA
Statistics
Matches: 426, Mismatches: 93, Indels: 41
0.76 0.17 0.07
Matches are distributed among these distances:
30 30 0.07
31 297 0.70
32 98 0.23
33 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (31 bp):
ACTTGTTATGCATGGCGTGTCACAACATTTT
Found at i:18798233 original size:219 final size:219
Alignment explanation
Indices: 18797854--18798274 Score: 727
Period size: 219 Copynumber: 1.9 Consensus size: 219
18797844 GGCGATTATA
* * *
18797854 ACGGGCTCGAGGGGAGTACCGAGTCGTGACACCAGATGAGTTACGGGGGTACGTGGAGGGTGAAA
1 ACGGGCTCGAGAGGAGTACCGAGTCATGACACCAGATGAGTTACGGGGGTACATGGAGGGTGAAA
* * *
18797919 GGCCTATATATGGCAAAAAATGAGAATATGTAGATTTCATCCTCGCTCCTTGCAACGTTGTAGGG
66 GGCCGATATACGGCAAAAAATGAGAAGATGTAGATTTCATCCTCGCTCCTTGCAACGTTGTAGGG
18797984 CATTGGGTAGTTGCGAAGATCGACTTGGTGAGATGGACGATCAAGGTGATGGACTCCACAAGAAC
131 CATTGGGTAGTTGCGAAGATCGACTTGGTGAGATGGACGATCAAGGTGATGGACTCCACAAGAAC
18798049 TTCGGATACGTCGCGACGATTGTC
196 TTCGGATACGTCGCGACGATTGTC
*
18798073 ACGGGCTCGAGAGGAGTACC-AGGTCATGACACCAGATGAGTTGCGGGGGTACATGGAGGGTGAA
1 ACGGGCTCGAGAGGAGTACCGA-GTCATGACACCAGATGAGTTACGGGGGTACATGGAGGGTGAA
* *
18798137 AGGCCGATATACGGTAAAAAATGAGAAGATGTGGATTTCATCCTCGCTCCTTGCAACGTTGTAGG
65 AGGCCGATATACGGCAAAAAATGAGAAGATGTAGATTTCATCCTCGCTCCTTGCAACGTTGTAGG
*
18798202 GCATTGGGTAGTTGCGAAGATCGACTTGGTGAGATGGACGATCAAGGTGATGGACTCCATAAGAA
130 GCATTGGGTAGTTGCGAAGATCGACTTGGTGAGATGGACGATCAAGGTGATGGACTCCACAAGAA
*
18798267 CTTTGGAT
195 CTTCGGAT
18798275 GCTAAGGATA
Statistics
Matches: 190, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
218 1 0.01
219 189 0.99
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (219 bp):
ACGGGCTCGAGAGGAGTACCGAGTCATGACACCAGATGAGTTACGGGGGTACATGGAGGGTGAAA
GGCCGATATACGGCAAAAAATGAGAAGATGTAGATTTCATCCTCGCTCCTTGCAACGTTGTAGGG
CATTGGGTAGTTGCGAAGATCGACTTGGTGAGATGGACGATCAAGGTGATGGACTCCACAAGAAC
TTCGGATACGTCGCGACGATTGTC
Found at i:18798689 original size:19 final size:17
Alignment explanation
Indices: 18798618--18798694 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
18798608 TTCTGTACAT
*
18798618 TTTTTTTGTATACAGAA
1 TTTTTTTGTATACACAA
*
18798635 TTATTTT-TAT--ACAA
1 TTTTTTTGTATACACAA
**
18798649 -TTAATTGTATACACAA
1 TTTTTTTGTATACACAA
18798665 TTTTTTTGTATACACAA
1 TTTTTTTGTATACACAA
18798682 TTTTTTT-TATACA
1 TTTTTTTGTATACA
18798695 ATTCATTGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.06
14 6 0.12
16 13 0.27
17 27 0.55
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTTTTTGTATACACAA
Found at i:18798708 original size:16 final size:15
Alignment explanation
Indices: 18798623--18798714 Score: 53
Period size: 14 Copynumber: 6.0 Consensus size: 15
18798613 TACATTTTTT
* *
18798623 TTGTATACAGAATTA
1 TTGTATATACAATTA
*
18798638 TT-TTTATACAATTAA
1 TTGTATATACAATT-A
* *
18798653 TTGTATACACAATTTTT
1 TTGTATATACAA--TTA
*
18798670 TTGTATACACAATT-
1 TTGTATATACAATTA
* *
18798684 TTTTTTATACAATTCA
1 TTGTATATACAATT-A
*
18798700 TTGTATATAGAATTA
1 TTGTATATACAATTA
18798715 ATTCTTTTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 19 0.32
15 8 0.14
16 18 0.31
17 12 0.20
18 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (15 bp):
TTGTATATACAATTA
Found at i:18798894 original size:31 final size:31
Alignment explanation
Indices: 18798853--18799001 Score: 104
Period size: 31 Copynumber: 4.8 Consensus size: 31
18798843 AGTCGCAAGA
*
18798853 AGTCAGCGTGTCACACCATAAATCTACTACC
1 AGTCAGCGTGTCACACCATAAATCTACTAGC
* * * * *
18798884 AGTCAACGTGTC-CCCACATACATCTGCTTGC
1 AGTCAGCGTGTCACAC-CATAAATCTACTAGC
* * * * * *
18798915 ACTTAGCGTGTCACCCCATAAATCTGCAAGA
1 AGTCAGCGTGTCACACCATAAATCTACTAGC
* * *
18798946 AGTCAGCGTGTCACACCGTAAATCCACTAAC
1 AGTCAGCGTGTCACACCATAAATCTACTAGC
* * *
18798977 ACTCAACATGTCAGC-CCATAAATCT
1 AGTCAGCGTGTCA-CACCATAAATCT
18799002 GCTTCCACTC
Statistics
Matches: 88, Mismatches: 27, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
30 2 0.02
31 82 0.93
32 4 0.05
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.23
Consensus pattern (31 bp):
AGTCAGCGTGTCACACCATAAATCTACTAGC
Found at i:18799016 original size:93 final size:93
Alignment explanation
Indices: 18798847--18799018 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
18798837 ATACACAGTC
* * * * *
18798847 GCAAGAAGTCAGCGTGTCACACCATAAATCTACTACCAGTCAACGTGTCCCCACATACATCTGCT
1 GCAAGAAGTCAGCGTGTCACACCATAAATCCACTAACACTCAACATGTCCCCACATAAATCTGCT
* *
18798912 TGCACTTAGCGTGTCACCCCATAAATCT
66 TCCACTCAGCGTGTCACCCCATAAATCT
* *
18798940 GCAAGAAGTCAGCGTGTCACACCGTAAATCCACTAACACTCAACATGTCAGCC-CATAAATCTGC
1 GCAAGAAGTCAGCGTGTCACACCATAAATCCACTAACACTCAACATGTC-CCCACATAAATCTGC
18799004 TTCCACTCAGCGTGT
65 TTCCACTCAGCGTGT
18799019 GAGAACAATT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
93 67 0.97
94 2 0.03
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (93 bp):
GCAAGAAGTCAGCGTGTCACACCATAAATCCACTAACACTCAACATGTCCCCACATAAATCTGCT
TCCACTCAGCGTGTCACCCCATAAATCT
Found at i:18799159 original size:86 final size:86
Alignment explanation
Indices: 18798979--18799169 Score: 203
Period size: 86 Copynumber: 2.2 Consensus size: 86
18798969 CCACTAACAC
* * * *
18798979 TCAACATGTCA-GCCCATAAATCTGCTTCCACTCAGCGTGTGAGAACAATTGGGCCTTGTCGTGT
1 TCAACGTGTCACG-CCATAAATCTGCTTCCACTCAGCGTGTCAGAACAATTGGCCCCTGTCGTGT
* *
18799043 CACGCTAGAAATCTGCAGATAT
65 CACGCCAGAAATCTGCAGATAG
* *
18799065 TCAACGTGTGACGCCATAAATCTGCTTCCACTC-GACGTGTCATAACAATTGGCCCCTGTCGTGT
1 TCAACGTGTCACGCCATAAATCTGCTTCCACTCAG-CGTGTCAGAACAATTGGCCCCTGTCGTGT
*
18799129 CACCCGCCA-AGA-CTGCAAGA-AG
65 CA--CGCCAGAAATCTGC-AGATAG
* *
18799151 TCAGCGTGTCATGCCATAA
1 TCAACGTGTCACGCCATAA
18799170 GTTTGAATTA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
85 1 0.01
86 77 0.88
87 6 0.07
88 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (86 bp):
TCAACGTGTCACGCCATAAATCTGCTTCCACTCAGCGTGTCAGAACAATTGGCCCCTGTCGTGTC
ACGCCAGAAATCTGCAGATAG
Found at i:18799159 original size:117 final size:117
Alignment explanation
Indices: 18799038--18799310 Score: 273
Period size: 117 Copynumber: 2.3 Consensus size: 117
18799028 TGGGCCTTGT
* * *
18799038 CGTGTCACGCTAGAAATCTGCAGA-T-ATTCAACGTGTGACGCCATAAATCTGCTTCCACTC-GA
1 CGTGTCACGCCAGAAATCTG-A-ATTAACTCAACGTGTCACGCCATAAATCTGCTTCCACTCAG-
* ** *
18799100 CGTGTCATAACAATTGGCCCCTGTCGTGTCACCCGCCAAGACTGCAAGAAGTCAG
63 CGTGTCACAACAATTGGCCCCTACCGTGTCACCCGCCAAGACTGCAACAAGTCAG
* * * * * * * *
18799155 CGTGTCATGCCATAAGTTTGAATTAACTCAGCGTGTCACGCTATAAGTCTGCTTGCACTCAGCGT
1 CGTGTCACGCCAGAAATCTGAATTAACTCAACGTGTCACGCCATAAATCTGCTTCCACTCAGCGT
* *
18799220 GTCACCACAATTGGCCCCTACCGTGTCACCCGCCAAGACTGCAACAGGTCAG
66 GTCACAACAATTGGCCCCTACCGTGTCACCCGCCAAGACTGCAACAAGTCAG
* * * * * * * *
18799272 AGTGTCAAGTCATAAGTCTGCATTCACTCAGCGTGTCAC
1 CGTGTCACGCCAGAAATCTGAATTAACTCAACGTGTCAC
18799311 CAGAAGACTT
Statistics
Matches: 130, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
115 1 0.01
116 2 0.02
117 126 0.97
118 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.24
Consensus pattern (117 bp):
CGTGTCACGCCAGAAATCTGAATTAACTCAACGTGTCACGCCATAAATCTGCTTCCACTCAGCGT
GTCACAACAATTGGCCCCTACCGTGTCACCCGCCAAGACTGCAACAAGTCAG
Found at i:18802888 original size:31 final size:31
Alignment explanation
Indices: 18802852--18802926 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
18802842 TAGTCATGTT
*
18802852 ACACGCCATGCATAT-AACGTAAAATGTTATA
1 ACACGCCATGCATATCAA-GTAAAATGTCATA
* *
18802883 ACACGCCATGCATATCAAGTCAAATGTCGTA
1 ACACGCCATGCATATCAAGTAAAATGTCATA
18802914 ACACGCCATGCAT
1 ACACGCCATGCAT
18802927 CACTGTCGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (31 bp):
ACACGCCATGCATATCAAGTAAAATGTCATA
Found at i:18803063 original size:56 final size:55
Alignment explanation
Indices: 18802959--18803080 Score: 172
Period size: 56 Copynumber: 2.2 Consensus size: 55
18802949 CTGTAATTGC
* * * *
18802959 TGACATGCTAAGAACCCAAAAAACCAGTTTACCCACAACACGCCAGGAACAGCCG
1 TGACACGCTAACAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAGCCA
* * *
18803014 TGACACGCTAACAACCCAAAAAAACTAGTTAACCCACTACACGCTAGGAACAGCCA
1 TGACACGCTAACAACCC-AAAAAACCAGTTAACCCACAACACGCCAGGAACAGCCA
18803070 TGACACGCTAA
1 TGACACGCTAA
18803081 AATAACGCTA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
55 15 0.25
56 44 0.75
ACGTcount: A:0.41, C:0.32, G:0.15, T:0.12
Consensus pattern (55 bp):
TGACACGCTAACAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAGCCA
Found at i:18804089 original size:15 final size:14
Alignment explanation
Indices: 18804065--18804094 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18804055 GTAACATATC
18804065 ATAATATTTAAATA
1 ATAATATTTAAATA
18804079 ATAATTATTTAAATA
1 ATAA-TATTTAAATA
18804094 A
1 A
18804095 ATAGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATATTTAAATA
Found at i:18804608 original size:10 final size:11
Alignment explanation
Indices: 18804593--18804621 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
18804583 TTTCATATCC
18804593 ACATGGCAC-A
1 ACATGGCACTA
18804603 ACATGGCACTA
1 ACATGGCACTA
18804614 ACATGGCA
1 ACATGGCA
18804622 TTGATGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (11 bp):
ACATGGCACTA
Found at i:18804817 original size:30 final size:30
Alignment explanation
Indices: 18804783--18804841 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
18804773 ATAAGAGTTT
*
18804783 ATTTGAATCGAAATAAAAATATAAAGGCTC
1 ATTTGAATCAAAATAAAAATATAAAGGCTC
* *
18804813 ATTTGACTCAAAATAAAAGTATAAAGGCT
1 ATTTGAATCAAAATAAAAATATAAAGGCT
18804842 TGATTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (30 bp):
ATTTGAATCAAAATAAAAATATAAAGGCTC
Found at i:18808015 original size:29 final size:29
Alignment explanation
Indices: 18807941--18808104 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 29
18807931 TAAAATGTTG
*
18807941 TCTTAATTTAGACAAGAAAATATGTTTGG
1 TCTTAATTTAGACAAGAAAATATGTTTGC
* *
18807970 TCGTAATTTAGATAAGAAAATATGTTT-C
1 TCTTAATTTAGACAAGAAAATATGTTTGC
* * * **
18807998 TCTTAATTAAAGAGAAGAAAAATATTTTTTT
1 TCTTAATT-TAGACAAG-AAAATATGTTTGC
* * * *
18808029 TCTTAATCTAGACAATAAAACATATTTG-
1 TCTTAATTTAGACAAGAAAATATGTTTGC
* * *
18808057 TCTCAATTTAGATAAGATAAAATATTTTTG-
1 TCTTAATTTAGACAAG--AAAATATGTTTGC
*
18808087 TCTTAATTAAAGACAAGA
1 TCTTAATT-TAGACAAGA
18808105 GTTGTCTTAA
Statistics
Matches: 105, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
28 19 0.18
29 41 0.39
30 32 0.30
31 13 0.12
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (29 bp):
TCTTAATTTAGACAAGAAAATATGTTTGC
Found at i:18808262 original size:17 final size:17
Alignment explanation
Indices: 18808240--18808272 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18808230 ATAATAATAA
18808240 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
18808257 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
18808273 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:18817254 original size:2 final size:2
Alignment explanation
Indices: 18817247--18817273 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18817237 AACACTTTAT
18817247 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
18817274 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18817322 original size:11 final size:12
Alignment explanation
Indices: 18817299--18817327 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
18817289 TATATTCATA
18817299 TTTTTCTTCTTC
1 TTTTTCTTCTTC
18817311 TTTTTCTT-TTC
1 TTTTTCTTCTTC
18817322 TTTTTC
1 TTTTTC
18817328 ATTCACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:18822325 original size:28 final size:28
Alignment explanation
Indices: 18822281--18822337 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
18822271 TTTAGGTTAT
*
18822281 TTCCTTGATAAACTACTTATATTTTGGG
1 TTCCTTGAGAAACTACTTATATTTTGGG
*
18822309 TTCCTTGAGAAATTACTTATATTTTGGG
1 TTCCTTGAGAAACTACTTATATTTTGGG
18822337 T
1 T
18822338 ATGGCCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (28 bp):
TTCCTTGAGAAACTACTTATATTTTGGG
Found at i:18823835 original size:44 final size:44
Alignment explanation
Indices: 18823772--18823858 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
18823762 ATATGGCAGC
18823772 GATGCTCAAGTAATTGAGTTTTGAGAGTCCCACATGGGATCTTT
1 GATGCTCAAGTAATTGAGTTTTGAGAGTCCCACATGGGATCTTT
18823816 GATGCTCAAGTAATTGAGTTTTGAGAGTCCCACATGGGATCTT
1 GATGCTCAAGTAATTGAGTTTTGAGAGTCCCACATGGGATCTT
18823859 CTCAAAAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (44 bp):
GATGCTCAAGTAATTGAGTTTTGAGAGTCCCACATGGGATCTTT
Found at i:18827989 original size:74 final size:74
Alignment explanation
Indices: 18827902--18828043 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 74
18827892 AAATCTATAC
* *
18827902 TTATAAATATGTATTCATTAAATGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAACGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
18827967 TTAAATTTA
66 TTAAATTTA
* ** *
18827976 TTATAAATGTGTATTCATCAAACGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAACGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
18828041 TTA
66 TTA
18828044 TTTCATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAACGACAATCATTAAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAATTTA
Found at i:18828173 original size:35 final size:34
Alignment explanation
Indices: 18828119--18828214 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 34
18828109 TTTAATAGTG
* *
18828119 TTTTATAATTTAAATATTAATATTTTAAATTAATT
1 TTTTTTAAGTTAAATATTAATATTTT-AATTAATT
* **
18828154 TTTTTTAAGTTAAATATTAATATTTTTATTTTTT
1 TTTTTTAAGTTAAATATTAATATTTTAATTAATT
18828188 TAATATTTTAAGTTAAATATTAATATT
1 T--T-TTTTAAGTTAAATATTAATATT
18828215 CATCAAACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
34 6 0.11
35 24 0.45
36 1 0.02
37 22 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TTTTTTAAGTTAAATATTAATATTTTAATTAATT
Found at i:18835208 original size:7 final size:7
Alignment explanation
Indices: 18835198--18835223 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18835188 CTTGACACTG
18835198 CCTCCCT
1 CCTCCCT
18835205 CCTCCCT
1 CCTCCCT
18835212 CCTCCCT
1 CCTCCCT
18835219 CCTCC
1 CCTCC
18835224 AATCATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (7 bp):
CCTCCCT
Found at i:18838466 original size:21 final size:20
Alignment explanation
Indices: 18838440--18838496 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
18838430 AATACCACTA
**
18838440 ATCTATTAATAGATCTTCTTC
1 ATCTATTAATAGAT-GACTTC
** *
18838461 ATCTATCGATAGATGACTTT
1 ATCTATTAATAGATGACTTC
18838481 ATCTATTAATAGATGA
1 ATCTATTAATAGATGA
18838497 AGAACATCAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
ATCTATTAATAGATGACTTC
Found at i:18838877 original size:21 final size:21
Alignment explanation
Indices: 18838853--18838892 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18838843 TATTTTCACA
* *
18838853 TTTAATGCATCATCAACTACC
1 TTTAAAGCATCAGCAACTACC
*
18838874 TTTAAAGCTTCAGCAACTA
1 TTTAAAGCATCAGCAACTA
18838893 TAATTCAAGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTAAAGCATCAGCAACTACC
Found at i:18840968 original size:2 final size:2
Alignment explanation
Indices: 18840894--18840952 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
18840884 ATTGCACTAA
* * *
18840894 AT AT A- AT AT AT AT AT AT -T AT AT AT AT AT TT TT AA 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
*
18840934 GT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
18840953 TACTTTATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18841067 original size:15 final size:15
Alignment explanation
Indices: 18841047--18841124 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
18841037 TAGTAATGTT
18841047 TATATATAAATTAAA
1 TATATATAAATTAAA
*
18841062 TATATATAAA-TAACG
1 TATATATAAATTAA-A
* *
18841077 TTTATAT-AATTATA
1 TATATATAAATTAAA
*
18841091 TATATATATA-T-AA
1 TATATATAAATTAAA
18841104 TATATA-ATAATATAAA
1 TATATATA-AAT-TAAA
18841120 TATAT
1 TATAT
18841125 TCCACTATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
12 1 0.02
13 8 0.17
14 12 0.25
15 20 0.42
16 7 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
TATATATAAATTAAA
Found at i:18841091 original size:8 final size:8
Alignment explanation
Indices: 18841078--18841124 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
18841068 TAAATAACGT
18841078 TTATATAA
1 TTATATAA
18841086 TTATATATA
1 TTATATA-A
18841095 TATATATAA
1 T-TATATAA
18841104 -TATATAA
1 TTATATAA
*
18841111 TAATATAA
1 TTATATAA
*
18841119 ATATAT
1 TTATAT
18841125 TCCACTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 17 0.52
9 3 0.09
10 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTATATAA
Done.