Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 62 of 345
Found at i:17214347 original size:25 final size:27
Alignment explanation
Indices: 17214301--17214357 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
17214291 TAAGCCCTTT
17214301 TAAAATTTATAAATTACTAAAAAATCA
1 TAAAATTTATAAATTACTAAAAAATCA
*
17214328 TAAAA-TTAT-AATTA-TAAAAAAGTTA
1 TAAAATTTATAAATTACTAAAAAA-TCA
17214353 TAAAA
1 TAAAA
17214358 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.25
25 12 0.43
26 4 0.14
27 5 0.18
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATTTATAAATTACTAAAAAATCA
Found at i:17214358 original size:26 final size:27
Alignment explanation
Indices: 17214301--17214358 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
17214291 TAAGCCCTTT
*
17214301 TAAAATTTATAAATTACTAAAAAATCA
1 TAAAAATTATAAATTACTAAAAAATCA
*
17214328 T-AAAATTAT-AATTA-TAAAAAAGTTA
1 TAAAAATTATAAATTACTAAAAAA-TCA
17214353 TAAAAA
1 TAAAAA
17214359 ATTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 7 0.26
25 8 0.30
26 11 0.41
27 1 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAAATTATAAATTACTAAAAAATCA
Found at i:17214370 original size:17 final size:17
Alignment explanation
Indices: 17214311--17214371 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
17214301 TAAAATTTAT
17214311 AAATTACTAAAAAATCATA
1 AAATTA-TAAAAAAT-ATA
** *
17214330 AAATTAT-AATTATAAA
1 AAATTATAAAAAATATA
*
17214346 AAAGTTATAAAAAATTTA
1 AAA-TTATAAAAAATATA
17214364 AAATTATA
1 AAATTATA
17214372 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
16 5 0.15
17 13 0.39
18 9 0.27
19 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATTATAAAAAATATA
Found at i:17214516 original size:10 final size:10
Alignment explanation
Indices: 17214486--17214518 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
17214476 TAAAAAAATT
17214486 ATAATTTTT-
1 ATAATTTTTA
17214495 ATAAATTTTTA
1 AT-AATTTTTA
17214506 ATAATTTTTA
1 ATAATTTTTA
17214516 ATA
1 ATA
17214519 TTTAAAAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:17220765 original size:13 final size:13
Alignment explanation
Indices: 17220747--17220772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17220737 GCTCGGCAGG
17220747 GACACGCCCGTGT
1 GACACGCCCGTGT
17220760 GACACGCCCGTGT
1 GACACGCCCGTGT
17220773 ACGATTACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:17227246 original size:13 final size:13
Alignment explanation
Indices: 17227228--17227253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17227218 CTGCCAAAGG
17227228 GACACGCCCGTGT
1 GACACGCCCGTGT
17227241 GACACGCCCGTGT
1 GACACGCCCGTGT
17227254 AAGAAAGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:17240739 original size:13 final size:13
Alignment explanation
Indices: 17240721--17240764 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17240711 AGAAAGGCTA
17240721 GTGGGTAAGCCGT
1 GTGGGTAAGCCGT
*
17240734 GTGGGTACATGCCCAT
1 GTGGGTA-A-G-CCGT
17240750 GTGGGTAAGCCGT
1 GTGGGTAAGCCGT
17240763 GT
1 GT
17240765 CTCTCACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 12 0.46
14 2 0.08
15 2 0.08
16 10 0.38
ACGTcount: A:0.16, C:0.18, G:0.41, T:0.25
Consensus pattern (13 bp):
GTGGGTAAGCCGT
Found at i:17243864 original size:11 final size:11
Alignment explanation
Indices: 17243850--17243880 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
17243840 TATGATTTGA
17243850 TTAAATGTATG
1 TTAAATGTATG
17243861 TTAAATGTATG
1 TTAAATGTATG
17243872 TATAAATGT
1 T-TAAATGT
17243881 GTTGTAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (11 bp):
TTAAATGTATG
Found at i:17244724 original size:19 final size:18
Alignment explanation
Indices: 17244696--17244732 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17244686 TGTCGATAAT
*
17244696 TTTATTTTTTTCATTTTA
1 TTTATTTTTTTAATTTTA
17244714 TTTATTATTTTTAATTTTA
1 TTTATT-TTTTTAATTTTA
17244733 ATTTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTTTAATTTTA
Found at i:17244743 original size:19 final size:18
Alignment explanation
Indices: 17244692--17244745 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
17244682 TCAGTGTCGA
*
17244692 TAATTTTATTTTTTTCATTT
1 TAATTTTA--TTTTTAATTT
*
17244712 TATTTATTATTTTTAATTT
1 TAATT-TTATTTTTAATTT
17244731 TAATTTTAGTTTTTA
1 TAATTTTA-TTTTTA
17244746 TCTTAGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.10
19 19 0.66
20 4 0.14
21 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TAATTTTATTTTTAATTT
Found at i:17247450 original size:27 final size:26
Alignment explanation
Indices: 17247413--17247527 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
17247403 AACATGGCTG
** *
17247413 CCAGAACAGATAATGTGAAAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
17247439 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
17247467 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
17247494 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
17247521 CCAGAAC
1 CCAGAAC
17247528 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 16 0.20
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:17247477 original size:54 final size:54
Alignment explanation
Indices: 17247413--17247527 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
17247403 AACATGGCTG
*
17247413 CCAGAACAGATA-ATGTGAAAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGAAAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
** * * *
17247467 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGAAAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
17247521 CCAGAAC
1 CCAGAAC
17247528 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGAAAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:17249179 original size:26 final size:26
Alignment explanation
Indices: 17249143--17249252 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
17249133 CATGAAATTC
17249143 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
17249169 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
17249195 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
17249221 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
17249247 TTATCA
1 TTATCA
17249253 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:17252761 original size:10 final size:9
Alignment explanation
Indices: 17252735--17252765 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17252725 TTATGTGTTC
17252735 TTTATTTTA
1 TTTATTTTA
17252744 TTTATTTTA
1 TTTATTTTA
17252753 TTCTATTTTA
1 TT-TATTTTA
17252763 TTT
1 TTT
17252766 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:17257216 original size:10 final size:9
Alignment explanation
Indices: 17257190--17257220 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17257180 TTATGTGTTC
17257190 TTTATTTTA
1 TTTATTTTA
17257199 TTTATTTTA
1 TTTATTTTA
17257208 TTCTATTTTA
1 TT-TATTTTA
17257218 TTT
1 TTT
17257221 TTCACAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:17257826 original size:20 final size:21
Alignment explanation
Indices: 17257801--17257861 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
17257791 GGTAAATTAT
17257801 AAAAAAATATT-CTTTAACAA
1 AAAAAAATATTACTTTAACAA
* * *
17257821 AAAAAATTATTATTTTAATAA
1 AAAAAAATATTACTTTAACAA
*
17257842 AATAATAAATATTATTTTAA
1 AA-AA-AAATATTACTTTAA
17257862 AAATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 2 0.06
23 13 0.38
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAAATATTACTTTAACAA
Found at i:17258678 original size:11 final size:11
Alignment explanation
Indices: 17258662--17258686 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17258652 AAAGTAAGAG
17258662 TAATTTTTATC
1 TAATTTTTATC
17258673 TAATTTTTATC
1 TAATTTTTATC
17258684 TAA
1 TAA
17258687 AGTCAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTTTATC
Found at i:17258737 original size:2 final size:2
Alignment explanation
Indices: 17258727--17258755 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17258717 AAAAAATAGA
17258727 AT AT A- 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
17258756 TAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17259207 original size:21 final size:21
Alignment explanation
Indices: 17259183--17259222 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17259173 AATACCATGT
17259183 GTCAAGTTAAAATTATTATAG
1 GTCAAGTTAAAATTATTATAG
*
17259204 GTCAAGTTAAAATTTTTAT
1 GTCAAGTTAAAATTATTAT
17259223 GGATGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
GTCAAGTTAAAATTATTATAG
Found at i:17261037 original size:47 final size:47
Alignment explanation
Indices: 17260966--17261065 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 47
17260956 ACCAACACAC
* * * **
17260966 CAGTACGGCACTCAGTGCCTCATCGGCTT-TGCCAAAGTAAACAGTAA
1 CAGTACGGCACTCAGTACCCCATCGGATTAAACCAAAGT-AACAGTAA
* * *
17261013 CAGTACGGTACTTAGTACCCCATCGGATTAAACCGAAGTAACAGTAA
1 CAGTACGGCACTCAGTACCCCATCGGATTAAACCAAAGTAACAGTAA
17261060 CAGTAC
1 CAGTAC
17261066 TACACACAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (47 bp):
CAGTACGGCACTCAGTACCCCATCGGATTAAACCAAAGTAACAGTAA
Found at i:17261767 original size:25 final size:25
Alignment explanation
Indices: 17261733--17261780 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
17261723 CATTTGTTAC
*
17261733 AATTCAATTTATTTTATAATATAAT
1 AATTCAATTTAATTTATAATATAAT
*
17261758 AATTTAATTTAATTTATAATATA
1 AATTCAATTTAATTTATAATATA
17261781 CTTTTTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTCAATTTAATTTATAATATAAT
Found at i:17261925 original size:3 final size:3
Alignment explanation
Indices: 17261917--17261949 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
17261907 TTAATTTATT
*
17261917 TAA TAA TAA TAG TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17261950 TAATCTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17267614 original size:22 final size:22
Alignment explanation
Indices: 17267589--17267641 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
17267579 ACCCCTACTT
17267589 AATTAATATGCAAACCCTGATA
1 AATTAATATGCAAACCCTGATA
*
17267611 AATTAATATGCGAACCCTGATA
1 AATTAATATGCAAACCCTGATA
17267633 AATTAATAT
1 AATTAATAT
17267642 AAGAACCCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (22 bp):
AATTAATATGCAAACCCTGATA
Found at i:17267647 original size:22 final size:22
Alignment explanation
Indices: 17267601--17267649 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
17267591 TTAATATGCA
**
17267601 AACCCTGATAAATTAATATGCG
1 AACCCTGATAAATTAATATAAG
17267623 AACCCTGATAAATTAATATAAG
1 AACCCTGATAAATTAATATAAG
17267645 AACCC
1 AACCC
17267650 CTACATTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.24
Consensus pattern (22 bp):
AACCCTGATAAATTAATATAAG
Found at i:17267722 original size:24 final size:24
Alignment explanation
Indices: 17267689--17267776 Score: 133
Period size: 24 Copynumber: 3.6 Consensus size: 24
17267679 GTTAGTATAT
17267689 AACCACCTATCACCAGACATGTGCA
1 AACC-CCTATCACCAGACATGTGCA
17267714 AACCCCTATCACCAGACATGTGCA
1 AACCCCTATCACCAGACATGTGCA
* *
17267738 AACCCTTATCACCA-ATCATGTGCG
1 AACCCCTATCACCAGA-CATGTGCA
17267762 AACCCCTATCACCAG
1 AACCCCTATCACCAG
17267777 TGACATGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.91
25 4 0.07
ACGTcount: A:0.33, C:0.38, G:0.11, T:0.18
Consensus pattern (24 bp):
AACCCCTATCACCAGACATGTGCA
Found at i:17267790 original size:48 final size:46
Alignment explanation
Indices: 17267694--17267797 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 46
17267684 TATATAACCA
*
17267694 CCTATCACCAGACATGTGCAAACCCCTATCACCAGACATGTGCAAAC
1 CCTATCACCAGACATGTGCAAACCCCTATCACCAGACATGAG-AAAC
*
17267741 CCTTATCACCA-ATCATGTGCGAACCCCTATCACCAGTGACATGAG-AAC
1 CC-TATCACCAGA-CATGTGCAAACCCCTATCACCA--GACATGAGAAAC
17267789 CCTATCACC
1 CCTATCACC
17267798 TTATATGTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 10 0.20
48 34 0.67
50 7 0.14
ACGTcount: A:0.32, C:0.37, G:0.12, T:0.19
Consensus pattern (46 bp):
CCTATCACCAGACATGTGCAAACCCCTATCACCAGACATGAGAAAC
Found at i:17267894 original size:33 final size:31
Alignment explanation
Indices: 17267857--17267941 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 31
17267847 GTCAAATCCT
*
17267857 TGTGTGAATC-TACCTATGTGCAAACCTTACCAC
1 TGTGTGAACCATACC-ATGTG--AACCTTACCAC
* *
17267890 TGTGTGAACCATACCATGTGAGCCTTACCAT
1 TGTGTGAACCATACCATGTGAACCTTACCAC
17267921 TGTGTGAAACC-TACCCATGTG
1 TGTGTG-AACCATA-CCATGTG
17267942 TGAGCTTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 17 0.37
32 11 0.24
33 14 0.30
34 4 0.09
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
TGTGTGAACCATACCATGTGAACCTTACCAC
Found at i:17267899 original size:17 final size:16
Alignment explanation
Indices: 17267857--17267944 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 16
17267847 GTCAAATCCT
*
17267857 TGTGTGAATC-TACCTA
1 TGTGTGAACCTTACC-A
**
17267873 TGTGCAAACCTTACCA
1 TGTGTGAACCTTACCA
*
17267889 CTGTGTGAACCATACCA
1 -TGTGTGAACCTTACCA
*
17267906 --TGTGAGCCTTACCA
1 TGTGTGAACCTTACCA
17267920 TTGTGTGAAACC-TACCCA
1 -TGTGTG-AACCTTA-CCA
17267938 TGTGTGA
1 TGTGTGA
17267945 GCTTACTTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.21
16 9 0.16
17 29 0.52
18 6 0.11
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (16 bp):
TGTGTGAACCTTACCA
Found at i:17267919 original size:31 final size:32
Alignment explanation
Indices: 17267881--17267941 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
17267871 TATGTGCAAA
17267881 CCTTACCACTGTGTG-AACCATA-CCATGTGAG
1 CCTTACCACTGTGTGAAACC-TACCCATGTGAG
*
17267912 CCTTACCATTGTGTGAAACCTACCCATGTG
1 CCTTACCACTGTGTGAAACCTACCCATGTG
17267942 TGAGCTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (32 bp):
CCTTACCACTGTGTGAAACCTACCCATGTGAG
Found at i:17268088 original size:22 final size:22
Alignment explanation
Indices: 17268063--17268143 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
17268053 ATTGTGTGAT
*
17268063 TGCCATGTGATATGTGAACCTA
1 TGCCATGTGATATGTGAACATA
*
17268085 TGCCATGTGATATGTGAACTTA
1 TGCCATGTGATATGTGAACATA
* * *
17268107 TGCTAAAGTGATATGCGAACATA
1 TGC-CATGTGATATGTGAACATA
*
17268130 TACCATGTGATATG
1 TGCCATGTGATATG
17268144 CAAACTATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
22 33 0.66
23 17 0.34
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (22 bp):
TGCCATGTGATATGTGAACATA
Found at i:17268144 original size:22 final size:21
Alignment explanation
Indices: 17268065--17268162 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 21
17268055 TGTGTGATTG
* *
17268065 CCATGTGATATGTGAACCTATG
1 CCATGTGATATGCGAA-CTATA
* *
17268087 CCATGTGATATGTGAACTTATG
1 CCATGTGATATGCGAAC-TATA
* *
17268109 CTAAAGTGATATGCGAACATATA
1 C-CATGTGATATGCGAAC-TATA
*
17268132 CCATGTGATATGCAAACTATGA
1 CCATGTGATATGCGAACTAT-A
17268154 CCTATGTGA
1 CC-ATGTGA
17268163 GCTACATGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
21 4 0.06
22 37 0.58
23 23 0.36
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (21 bp):
CCATGTGATATGCGAACTATA
Found at i:17268703 original size:76 final size:76
Alignment explanation
Indices: 17268563--17268706 Score: 171
Period size: 76 Copynumber: 1.9 Consensus size: 76
17268553 CCAAGATGGG
* * * * * * * ***
17268563 AAGTCATCATCATCGGACAACCCGGGATGACATATTTGAATCGATAAACCCTCATTGTTTGGCAA
1 AAGTCATCATCACCGGACAACCCAGGAGGACAAATCTAAATCGATAAACCATCATTGCCAGGCAA
17268628 TCCGGGATGAC
66 TCCGGGATGAC
* * *
17268639 AAGTCATCATCACCGGGCAACCCAGGAGGACAAATCTAAATTGATAAACCATTATTGCCAGGCAA
1 AAGTCATCATCACCGGACAACCCAGGAGGACAAATCTAAATCGATAAACCATCATTGCCAGGCAA
17268704 TCC
66 TCC
17268707 TGGGTGGTAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
76 55 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (76 bp):
AAGTCATCATCACCGGACAACCCAGGAGGACAAATCTAAATCGATAAACCATCATTGCCAGGCAA
TCCGGGATGAC
Found at i:17271804 original size:2 final size:2
Alignment explanation
Indices: 17271797--17271821 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17271787 ATTTCCGGAA
17271797 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 A
17271822 AATAAAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17277293 original size:30 final size:30
Alignment explanation
Indices: 17277259--17277318 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
17277249 AAGTTTAAAT
17277259 ATGAATGATCACACTTGAACATACCTAATA
1 ATGAATGATCACACTTGAACATACCTAATA
**
17277289 ATGAATGATCACACTTGAATGTACCTAATA
1 ATGAATGATCACACTTGAACATACCTAATA
17277319 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (30 bp):
ATGAATGATCACACTTGAACATACCTAATA
Found at i:17289717 original size:29 final size:29
Alignment explanation
Indices: 17289685--17289755 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
17289675 TATTTACTTC
* * * *
17289685 ATATTACATTTTAGTCATTTATATTTGAA
1 ATATTACGTTTTAGTCACTTACATTCGAA
* *
17289714 ATATTACGTTTTAGTTACTTACGTTCGAA
1 ATATTACGTTTTAGTCACTTACATTCGAA
17289743 ATATTACGTTTTA
1 ATATTACGTTTTA
17289756 CTTACTTGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
ATATTACGTTTTAGTCACTTACATTCGAA
Found at i:17289760 original size:29 final size:29
Alignment explanation
Indices: 17289711--17289767 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
17289701 ATTTATATTT
*
17289711 GAAATATTACGTTTTAGTTACTTACGTTC
1 GAAATATTACGTTTTACTTACTTACGTTC
*
17289740 GAAATATTACGTTTTACTTACTTGCGTT
1 GAAATATTACGTTTTACTTACTTACGTT
17289768 ATCGTTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
GAAATATTACGTTTTACTTACTTACGTTC
Found at i:17296709 original size:20 final size:19
Alignment explanation
Indices: 17296658--17296711 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
17296648 AATTAGATAA
17296658 TTATTATTTATTTAATATT
1 TTATTATTTATTTAATATT
* ** *
17296677 TTAATAAGATATTTATTATT
1 TT-ATTATTTATTTAATATT
17296697 TTATTATTTTATTTA
1 TTATTA-TTTATTTA
17296712 GTATATATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTATTTATTTAATATT
Found at i:17300415 original size:78 final size:78
Alignment explanation
Indices: 17300286--17300443 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
17300276 AGAATAGAGA
17300286 AAATTCAAGGGATTAAATTAGAAATTATACCATAAGGTGACAAGTGTGTGGTAAGTATAAATACA
1 AAATTCAAGGGATTAAATTAGAAATTATACCATAAGGTGACAAGTGTGTGGTAAGTATAAATACA
17300351 TGTGTATTAATTT
66 TGTGTATTAATTT
17300364 AAATTCAAGGGATTAAATTAGAAATTATACCATAAGGTGACAAGTGTGTGGTAAGTATAAATACA
1 AAATTCAAGGGATTAAATTAGAAATTATACCATAAGGTGACAAGTGTGTGGTAAGTATAAATACA
17300429 TGTGTATTAATTT
66 TGTGTATTAATTT
17300442 AA
1 AA
17300444 CTAGTACAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (78 bp):
AAATTCAAGGGATTAAATTAGAAATTATACCATAAGGTGACAAGTGTGTGGTAAGTATAAATACA
TGTGTATTAATTT
Found at i:17303054 original size:13 final size:13
Alignment explanation
Indices: 17303036--17303060 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17303026 ATTGTAACAC
17303036 CCCTCGCCGGAAT
1 CCCTCGCCGGAAT
17303049 CCCTCGCCGGAA
1 CCCTCGCCGGAA
17303061 CAGGGTTCGA
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:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
CCCTCGCCGGAAT
Found at i:17303945 original size:45 final size:45
Alignment explanation
Indices: 17303844--17304339 Score: 721
Period size: 45 Copynumber: 11.1 Consensus size: 45
17303834 TTTTCTCAAA
* * * *
17303844 TCACTGGCATT-TCGCCTGCTAGGCTC-GAGGCCCG-ATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * * ** *
17303886 TCACCAGCATTATAGCCTGTTAGGCTCGAAA-GTCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAACATT
* *
17303931 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* *
17303976 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* *
17304021 TCACCGGCATTATAGCCTGCTAGCCTCAAAGGCCAGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
*
17304066 TCACCGGCATTATAGCCTGCTAGCCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* *
17304111 TCACCAGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
*
17304156 TCACCCGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* *
17304201 TCACCCGCATTATAGCCTGCTAGGCTCAAAGGCCTGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * * *
17304246 TCACTGGCATTATAGCCTGCTAGGGTCAAAAGCCTGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
17304291 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
17304336 TCAC
1 TCAC
17304340 TAGTTCTTTC
Statistics
Matches: 417, Mismatches: 32, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
42 9 0.02
43 13 0.03
44 7 0.02
45 388 0.93
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
Found at i:17311317 original size:49 final size:48
Alignment explanation
Indices: 17311259--17311503 Score: 283
Period size: 49 Copynumber: 4.9 Consensus size: 48
17311249 TAGCCAAAGC
* * *
17311259 TATCTGGTACGCATAGTAGTCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAG-CTGCACTTAGTACTACACATGTGACCAAT
* * *
17311308 TATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAG-CTGCACTTAGTACTACACATGTGACC-AAT
* * * *
17311358 CATCTGATACACGTAGTAGCTTGCACTTAGTACTACACATATGATCGAAGT
1 TATCTGGTACACGTAGTAGC-TGCACTTAGTACTACACATGTGA-CCAA-T
* * * *
17311409 TATCGGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGC-TGCACTTAGTACTACACATGTGACCAAT
*
17311458 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACC
1 TATCTGGTACACGTAGTAG-CTGCACTTAGTACTACACATGTGACC
17311504 TCACAATAGA
Statistics
Matches: 165, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
49 82 0.50
50 45 0.27
51 38 0.23
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (48 bp):
TATCTGGTACACGTAGTAGCTGCACTTAGTACTACACATGTGACCAAT
Found at i:17311447 original size:101 final size:98
Alignment explanation
Indices: 17311272--17311497 Score: 274
Period size: 100 Copynumber: 2.3 Consensus size: 98
17311262 CTGGTACGCA
* ** *
17311272 TAGTAG-TCTGCACTTAGTACTACACATGCGACCAATTATTTGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCT-TGCACTTAGTACTACACATACGACCAATTATCGGGTACACATAGTAGCCTGCACTT
* *
17311336 AGTACTACACACGTGACCTAACCATCTGATACACG
65 AGTACTACACACGCGACC-AACCATCCGATACACG
* * * *
17311371 TAGTAGCTTGCACTTAGTACTACACATATGATCGAAGTTATCGGGTACGCATAGTAGCTTGCACT
1 TAGTAGCTTGCACTTAGTACTACACATACGA-CCAA-TTATCGGGTACACATAGTAGCCTGCACT
* ** *
17311436 TAGTACTACACATGCGACCAATTATCCGGTACACG
64 TAGTACTACACACGCGACCAACCATCCGATACACG
*
17311471 TAGTAGCCTGCACTTAGTACTACACAT
1 TAGTAGCTTGCACTTAGTACTACACAT
17311498 GTGACCTCAC
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
99 27 0.25
100 42 0.39
101 40 0.37
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (98 bp):
TAGTAGCTTGCACTTAGTACTACACATACGACCAATTATCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATCCGATACACG
Found at i:17316542 original size:67 final size:68
Alignment explanation
Indices: 17316468--17316618 Score: 179
Period size: 67 Copynumber: 2.2 Consensus size: 68
17316458 CATCATGTGT
* * *
17316468 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCA-CG-GGTATACTA-TG-TGTACACC
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCAGCGTGGT-TACAAGTGAAGGACACC
17316529 ATGTAG
63 ATGTAG
* *
17316535 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCA-GCGTGGTTACAAGTGAAGGACACCAT
17316598 GTAG
65 GTAG
17316602 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
17316619 TAAACTGGCT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
63 16 0.22
64 3 0.04
65 6 0.08
66 6 0.08
67 40 0.56
68 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCAGCGTGGTTACAAGTGAAGGACACCATG
TAG
Found at i:17317761 original size:2 final size:2
Alignment explanation
Indices: 17317754--17317792 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17317744 TCATGACATG
17317754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17317793 GACTAGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17323714 original size:141 final size:141
Alignment explanation
Indices: 17323460--17323717 Score: 385
Period size: 141 Copynumber: 1.8 Consensus size: 141
17323450 CGACTGTCTC
* * *
17323460 CTTGCCTTTCTCTATGGCATGCCCGAGAAGAGTTTGGAGCTAGTGGTCGGAAGCGAAGCAAGCAA
1 CTTGCCTTTCTCTATGGCATGCCCAAGAAGAGTTTGGAGCTAGTGGCCAGAAGCGAAGCAAGCAA
**
17323525 TAGAGGCTAGGTGAGAAGGGCTATCGGGTTGAGTAACAAAGGTTTCAGAATGAAGAAAAACAAAG
66 TAGAGGCTAGGTGAGAAGGGCTATCAAGTTGAGTAACAAAGGTTTCAGAATGAAGAAAAACAAAG
17323590 GCAGCTCTCTT
131 GCAGCTCTCTT
* * * *
17323601 CTTGCCTTTCTTTATGGCATGCCCAAGAAGAGTTTGGGGCTAGTGGCCAGAGGCGAAGCAAGTAA
1 CTTGCCTTTCTCTATGGCATGCCCAAGAAGAGTTTGGAGCTAGTGGCCAGAAGCGAAGCAAGCAA
* *
17323666 TAGAGGCT-GAGTGAG-AGAGGCTATCAAGTTGAGTGAGAAAGGTTTCAGAATG
66 TAGAGGCTAG-GTGAGAAG-GGCTATCAAGTTGAGTAACAAAGGTTTCAGAATG
17323718 GTGAGGGTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
140 3 0.03
141 101 0.97
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.23
Consensus pattern (141 bp):
CTTGCCTTTCTCTATGGCATGCCCAAGAAGAGTTTGGAGCTAGTGGCCAGAAGCGAAGCAAGCAA
TAGAGGCTAGGTGAGAAGGGCTATCAAGTTGAGTAACAAAGGTTTCAGAATGAAGAAAAACAAAG
GCAGCTCTCTT
Found at i:17330351 original size:43 final size:43
Alignment explanation
Indices: 17330296--17330482 Score: 214
Period size: 43 Copynumber: 4.3 Consensus size: 43
17330286 TTTTTTAAAT
* *
17330296 AAACGCCGCTAAAGATCATGACCTTTAGCGACGCTTTTTTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACACTTTTTTCAC
* * * *
17330339 AAACGCCTCTAAAGACCATGGCCTTTAGCGACACTTTTTCCAGA
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACACTTTTTTCA-C
* * *
17330383 AAACGCCGCTAAAAACCATGACCTTTAGCGGCACTTTTTTTAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACACTTTTTTCAC
* * * * * * *
17330426 AAACGCCACTACAGAACA-AACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCATGACCTTTAGCGACACTTTTTTCAC
17330468 AAACGCCGCTAAAGA
1 AAACGCCGCTAAAGA
17330483 ATATAACCTT
Statistics
Matches: 120, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
42 33 0.28
43 51 0.43
44 36 0.30
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCTTTAGCGACACTTTTTTCAC
Found at i:17330515 original size:20 final size:20
Alignment explanation
Indices: 17330492--17330529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17330482 AATATAACCT
17330492 TTAAAAAATATATATTTTTA
1 TTAAAAAATATATATTTTTA
* *
17330512 TTAAATAATATTTATTTT
1 TTAAAAAATATATATTTT
17330530 CTATATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAAAAATATATATTTTTA
Found at i:17335033 original size:20 final size:19
Alignment explanation
Indices: 17334983--17335033 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
17334973 TTTCCAACAG
17334983 TAAACCCTAAACCTAAACC
1 TAAACCCTAAACCTAAACC
** *
17335002 TCAAACTATAAACCTATATCC
1 T-AAACCCTAAACCTA-AACC
17335023 TAAACCCTAAA
1 TAAACCCTAAA
17335034 TATATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACCCTAAACCTAAACC
Found at i:17335220 original size:14 final size:14
Alignment explanation
Indices: 17335203--17335241 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17335193 ATAAAACAAA
*
17335203 AAACTACAAACTCT
1 AAACCACAAACTCT
*
17335217 AAACCATAAACTCT
1 AAACCACAAACTCT
*
17335231 AAACCAAAAAC
1 AAACCACAAAC
17335242 AATAAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCACAAACTCT
Found at i:17335937 original size:41 final size:41
Alignment explanation
Indices: 17335872--17336015 Score: 236
Period size: 41 Copynumber: 3.5 Consensus size: 41
17335862 TTACTTTTTT
*
17335872 GCGGCGTTTTT-CTAAAGCGCCGCTAAAACCTCGATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
17335912 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
* * * *
17335953 GCGGCGTTTTACCAAAAGTGCCGCTAAAACCTCAACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
17335994 GCGGCGTTTTTCCAAAAGCGCC
1 GCGGCGTTTTTCCAAAAGCGCC
17336016 CTATTGTTCA
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 11 0.11
41 85 0.89
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATA
Found at i:17336072 original size:41 final size:39
Alignment explanation
Indices: 17335992--17336082 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 39
17335982 CCTCAACCTA
** * *
17335992 TAGCGGCGTTTTTCCAAAAGCGCCCTATTGTTCAATTTT
1 TAGCGGCGTTTGACCAAAAACGCCCTATTGCTCAATTTT
17336031 TAGCGGCGTTTGGACCAAAAACGCCGCTATTGCT-AAGTTTT
1 TAGCGGCGTTT-GACCAAAAACGCC-CTATTGCTCAA-TTTT
17336072 TAGCGGCGTTT
1 TAGCGGCGTTT
17336083 TATTGCAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 11 0.24
40 12 0.27
41 22 0.49
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (39 bp):
TAGCGGCGTTTGACCAAAAACGCCCTATTGCTCAATTTT
Found at i:17344404 original size:21 final size:21
Alignment explanation
Indices: 17344371--17344411 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17344361 CAACGTGGCA
*
17344371 AGTTACTTGGCCATATCAGCT
1 AGTTACTTGGCCACATCAGCT
17344392 AGTTAACTT-GCCACATCAGC
1 AGTT-ACTTGGCCACATCAGC
17344412 GGTCCAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
AGTTACTTGGCCACATCAGCT
Found at i:17345875 original size:20 final size:20
Alignment explanation
Indices: 17345850--17345920 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
17345840 TATTCTTTAG
17345850 AATTTTTTTAAAATTATTAT
1 AATTTTTTTAAAATTATTAT
* *
17345870 AATTTTTTTAAAA-AAATAT
1 AATTTTTTTAAAATTATTAT
*
17345889 AATTTTTTTGGAAATT-TTAT
1 AATTTTTTT-AAAATTATTAT
* *
17345909 AAATATTTTAAA
1 AATTTTTTTAAA
17345921 TATTTTAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTTTTAAAATTATTAT
Found at i:17345877 original size:19 final size:19
Alignment explanation
Indices: 17345850--17345897 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
17345840 TATTCTTTAG
* *
17345850 AATTTTTTTAAAATTATTAT
1 AATTTTTTTAAAA-AAATAT
17345870 AATTTTTTTAAAAAAATAT
1 AATTTTTTTAAAAAAATAT
17345889 AATTTTTTT
1 AATTTTTTT
17345898 GGAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTTTAAAAAAATAT
Found at i:17346199 original size:24 final size:24
Alignment explanation
Indices: 17346172--17346222 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
17346162 AGTTTTACTC
17346172 ACCTTAAATTTCTCAATAAAGTAT
1 ACCTTAAATTTCTCAATAAAGTAT
* *
17346196 ACCTTAAATTTCTTAATCAAGTAT
1 ACCTTAAATTTCTCAATAAAGTAT
17346220 ACC
1 ACC
17346223 AAAATAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (24 bp):
ACCTTAAATTTCTCAATAAAGTAT
Found at i:17360799 original size:46 final size:42
Alignment explanation
Indices: 17360727--17360815 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 42
17360717 AGTAAAAATG
17360727 AAATTATTAATTAAAATAAAAAATTATTAATTAAAATAAAAA
1 AAATTATTAATTAAAATAAAAAATTATTAATTAAAATAAAAA
17360769 AAATTATTAATTAAATATTAAAAACCATTATTAATTAAAATAAAAA
1 AAATTATTAATTAAA-A-TAAAAA--ATTATTAATTAAAATAAAAA
17360815 A
1 A
17360816 TTATGAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
42 15 0.35
43 1 0.02
44 6 0.14
46 21 0.49
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (42 bp):
AAATTATTAATTAAAATAAAAAATTATTAATTAAAATAAAAA
Found at i:17360830 original size:20 final size:20
Alignment explanation
Indices: 17360727--17360819 Score: 132
Period size: 22 Copynumber: 4.3 Consensus size: 20
17360717 AGTAAAAATG
17360727 AAATTATTAATTAAAATAAA
1 AAATTATTAATTAAAATAAA
17360747 AAATTATTAATTAAAATAAAAA
1 AAATTATTAATTAAAAT--AAA
17360769 AAATTATTAATTAAATATTAAA
1 AAATTATTAATTAAA-A-TAAA
17360791 AACCATTATTAATTAAAATAAA
1 AA--ATTATTAATTAAAATAAA
17360813 AAATTAT
1 AAATTAT
17360820 GAATAACAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
20 22 0.33
22 29 0.43
23 2 0.03
24 14 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTATTAATTAAAATAAA
Found at i:17361424 original size:29 final size:28
Alignment explanation
Indices: 17361392--17361483 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 28
17361382 TAAATTTTAG
17361392 AAAAATTATTAAATTTTAATAAAAAT-AT-
1 AAAAATTA-TAAATTTT-ATAAAAATCATA
* ** *
17361420 AAAAATTAGATTTTTTATAAAAATCGTA
1 AAAAATTATAAATTTTATAAAAATCATA
*
17361448 TAAAAATTGTAAAATTTTATAAAAAATCATA
1 -AAAAATTAT-AAATTTTAT-AAAAATCATA
17361479 AAAAA
1 AAAAA
17361484 ATAACAAACC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 8 0.16
27 6 0.12
28 8 0.16
29 7 0.14
30 12 0.24
31 9 0.18
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAAATTATAAATTTTATAAAAATCATA
Found at i:17366126 original size:18 final size:20
Alignment explanation
Indices: 17366085--17366134 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
17366075 TTTAAGAGCC
*
17366085 ACACACCCGTGTGGCTTAGG
1 ACACACCCGTGTGGCTCAGG
*
17366105 ACACACCCGTGTGG-TCA-T
1 ACACACCCGTGTGGCTCAGG
17366123 ACACACCCGTGT
1 ACACACCCGTGT
17366135 CCCTAACCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.43
19 2 0.07
20 14 0.50
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (20 bp):
ACACACCCGTGTGGCTCAGG
Found at i:17367067 original size:15 final size:16
Alignment explanation
Indices: 17367049--17367078 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17367039 AAACTCTTAT
17367049 AATCATAA-CTTACTC
1 AATCATAATCTTACTC
17367064 AATCATAATCTTACT
1 AATCATAATCTTACT
17367079 AAGGGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (16 bp):
AATCATAATCTTACTC
Found at i:17367361 original size:42 final size:42
Alignment explanation
Indices: 17367250--17367404 Score: 231
Period size: 43 Copynumber: 3.7 Consensus size: 42
17367240 TACCATACCA
* * *
17367250 ATGCCATATCCCATATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
17367292 ATGCCAATAGCCCAGTTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
17367335 ATGCCATATCCCAGATATAGTCTTACACGAAATCCCATA-CG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
17367376 ATGCCATATCCCAGATATGGTCTTACACG
1 ATGCCATATCCCAGATATGGTCTTACACG
17367405 TAGTCTTAGT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
41 30 0.29
42 35 0.34
43 37 0.36
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:17370823 original size:93 final size:93
Alignment explanation
Indices: 17370711--17370881 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
17370701 GCCCATAAGT
* *
17370711 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17370776 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
17370804 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
17370869 CGAGTTCGGATGC
66 CGAGTTCGGATGC
17370882 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:17370878 original size:46 final size:46
Alignment explanation
Indices: 17370703--17370878 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
17370693 TGTAACCCGC
* * *
17370703 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
17370749 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
17370799 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
17370842 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
17370879 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17372883 original size:12 final size:12
Alignment explanation
Indices: 17372866--17372896 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17372856 GAAGCAGGGG
17372866 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
17372878 AGAAAAAGGGAA
1 AGAAAAAGAGAA
17372890 AGAAAAA
1 AGAAAAA
17372897 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:17380466 original size:12 final size:12
Alignment explanation
Indices: 17380449--17380479 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17380439 GAAGCAGGGG
17380449 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
17380461 AGAAAAAGGGAA
1 AGAAAAAGAGAA
17380473 AGAAAAA
1 AGAAAAA
17380480 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:17387142 original size:22 final size:24
Alignment explanation
Indices: 17387112--17387166 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
17387102 TTATTTCATT
17387112 TTATT-TTATTT-TTTTAC-TTTA
1 TTATTATTATTTATTTTACGTTTA
*
17387133 TTATTATTATTTATTTTCCTGTTTA
1 TTATTATTATTTATTTTAC-GTTTA
17387158 TTATTATTA
1 TTATTATTA
17387167 CCTCGCCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 5 0.17
25 13 0.45
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (24 bp):
TTATTATTATTTATTTTACGTTTA
Found at i:17387149 original size:25 final size:24
Alignment explanation
Indices: 17387097--17387166 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
17387087 CCTTTTAATG
17387097 ATTTTTTATTTCATT-TTA-T-TTT
1 ATTTTTTATTT-ATTATTATTATTT
17387119 ATTTTTTTACTTTATTATTATTATTT
1 A-TTTTTTA-TTTATTATTATTATTT
* *
17387145 ATTTTCCTGTTTATTATTATTA
1 ATTTT-TTATTTATTATTATTA
17387167 CCTCGCCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.03
23 10 0.25
24 6 0.15
25 18 0.45
26 5 0.12
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.71
Consensus pattern (24 bp):
ATTTTTTATTTATTATTATTATTT
Found at i:17389036 original size:2 final size:2
Alignment explanation
Indices: 17389025--17389061 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
17389015 ATTAAGTAAG
17389025 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17389062 TACAACTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17391302 original size:4 final size:4
Alignment explanation
Indices: 17391293--17391326 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
17391283 TATTTTGCAA
17391293 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
17391327 GTTTGTACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:17395756 original size:2 final size:2
Alignment explanation
Indices: 17395751--17395780 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17395741 AAAATCAAGC
17395751 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17395781 ACAATGATAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17397814 original size:5 final size:5
Alignment explanation
Indices: 17397804--17397845 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
17397794 TTATGTTTTA
* *
17397804 ATTAT ATTAT ATTAT ATTAT GTTAT ATTAT GTTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
17397846 ATAAACTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:17404413 original size:5 final size:5
Alignment explanation
Indices: 17404403--17404438 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
17404393 TTATGTTTTA
17404403 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
17404439 AAACTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:17404507 original size:13 final size:13
Alignment explanation
Indices: 17404489--17404514 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17404479 GGGACGAAAC
17404489 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
17404502 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
17404515 GAAATTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:17405708 original size:20 final size:20
Alignment explanation
Indices: 17405671--17405708 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17405661 TGATGGGGAG
*
17405671 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
17405691 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
17405709 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:17407621 original size:46 final size:46
Alignment explanation
Indices: 17407554--17407781 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
17407544 AGTCTGCTCT
*
17407554 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
17407600 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
17407646 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *** * *
17407692 GTGAGATGAAATGAACAAGACCATGGTCGAAAGATTCCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
17407738 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
17407782 TCATGTCAAA
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 163 0.99
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:17417795 original size:29 final size:29
Alignment explanation
Indices: 17417762--17417824 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
17417752 GTAATCGAGC
17417762 TTGTAAATATGTTAAATTGAATGTTGTGT
1 TTGTAAATATGTTAAATTGAATGTTGTGT
17417791 TTGTAAATATGTTAAATTGAATGTTGTGT
1 TTGTAAATATGTTAAATTGAATGTTGTGT
17417820 TTGTA
1 TTGTA
17417825 TGGAATGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (29 bp):
TTGTAAATATGTTAAATTGAATGTTGTGT
Found at i:17419165 original size:21 final size:21
Alignment explanation
Indices: 17419139--17419196 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
17419129 ACATGGCTTC
*
17419139 TCACACGAGCGTGTCCTAGGG
1 TCACACGGGCGTGTCCTAGGG
17419160 TCACACGGGCGTGTCCTAGGG
1 TCACACGGGCGTGTCCTAGGG
17419181 TCACACGGGCGTGTCC
1 TCACACGGGCGTGTCC
17419197 CTTAGACCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (21 bp):
TCACACGGGCGTGTCCTAGGG
Found at i:17419210 original size:22 final size:21
Alignment explanation
Indices: 17419140--17419216 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
17419130 CATGGCTTCT
* **
17419140 CACACGAGCGTGTCCTAGGGT
1 CACACGGGCGTGTCCTAGGAC
**
17419161 CACACGGGCGTGTCCTAGGGT
1 CACACGGGCGTGTCCTAGGAC
17419182 CACACGGGCGTGTCCCTTA-GAC
1 CACACGGGCGTGT-CC-TAGGAC
17419204 CACACGGGCGTGT
1 CACACGGGCGTGT
17419217 GAGCCCTGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
21 33 0.65
22 16 0.31
23 2 0.04
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.18
Consensus pattern (21 bp):
CACACGGGCGTGTCCTAGGAC
Found at i:17423687 original size:17 final size:17
Alignment explanation
Indices: 17423647--17423680 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17423637 TATATTAAAA
* *
17423647 TTATTATTATTATGGTT
1 TTATAATTATTATGATT
17423664 TTATAATTATTATGATT
1 TTATAATTATTATGATT
17423681 ATTTAATGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
TTATAATTATTATGATT
Found at i:17424097 original size:12 final size:12
Alignment explanation
Indices: 17424080--17424110 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17424070 GAAGCAGGGG
17424080 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
17424092 AGAAAAAGGGAA
1 AGAAAAAGAGAA
17424104 AGAAAAA
1 AGAAAAA
17424111 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:17425266 original size:18 final size:18
Alignment explanation
Indices: 17425243--17425283 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17425233 AAATAAAAAA
17425243 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
17425261 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
17425279 AGAAA
1 AGAAA
17425284 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:17425794 original size:20 final size:20
Alignment explanation
Indices: 17425771--17425808 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17425761 GTTATTAAGT
17425771 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
17425791 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
17425809 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:17426936 original size:2 final size:2
Alignment explanation
Indices: 17426929--17426957 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17426919 TGGAAGTCGA
17426929 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17426958 TTTGAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17428048 original size:38 final size:38
Alignment explanation
Indices: 17427997--17428119 Score: 219
Period size: 38 Copynumber: 3.2 Consensus size: 38
17427987 TCGAAATATG
17427997 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
17428035 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
* *
17428073 ATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATT
1 ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
*
17428111 ATATTCGGG
1 ATATCCGGG
17428120 CCTTTGAGCC
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 82 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (38 bp):
ATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATT
Found at i:17428195 original size:46 final size:44
Alignment explanation
Indices: 17428112--17428225 Score: 126
Period size: 46 Copynumber: 2.6 Consensus size: 44
17428102 GCTGGTATTA
* * * *
17428112 TATTCGGGCCTTT-GAGCCTAGTAGACTATTATGCCGGTGAGACAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATACCGGTGA-A-AT
17428157 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATACCGGTGAAAT
1 TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATACCGGTGAAAT
* *
17428201 GATATCAGGCC--TCGAGCCTAGCAGG
1 TAT-TCGGGCCTTTCGAGCCTAGCAGG
17428226 TGAAATGCCG
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 14 0.23
44 4 0.07
45 20 0.33
46 23 0.38
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (44 bp):
TATTCGGGCCTTTCGAGCCTAGCAGGCTATAATACCGGTGAAAT
Found at i:17435824 original size:16 final size:19
Alignment explanation
Indices: 17435805--17435853 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
17435795 TCTTCCAAAA
17435805 TTCTTCTC-TC-TAATTCT
1 TTCTTCTCTTCGTAATTCT
17435822 TCTCTTCTCTTTCGTAATTC-
1 T-TCTTCTC-TTCGTAATTCT
17435842 TTCTTCTTCTTC
1 TTCTTC-TCTTC
17435854 TATTCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.04
18 7 0.26
19 8 0.30
20 5 0.19
21 6 0.22
ACGTcount: A:0.08, C:0.31, G:0.02, T:0.59
Consensus pattern (19 bp):
TTCTTCTCTTCGTAATTCT
Found at i:17436714 original size:96 final size:96
Alignment explanation
Indices: 17436553--17436746 Score: 370
Period size: 96 Copynumber: 2.0 Consensus size: 96
17436543 TAGTTATTAC
* *
17436553 ATAAAGTATGAATCAACTACTCTAGTAACTAATTTTTAATTGATGATGGGTTGATTAAAAATTAA
1 ATAAAGTATGAATCAACAACTCTAGTAACTAATTTCTAATTGATGATGGGTTGATTAAAAATTAA
17436618 GGCTAATGTGTAAAAATTATATATTAAGAGT
66 GGCTAATGTGTAAAAATTATATATTAAGAGT
17436649 ATAAAGTATGAATCAACAACTCTAGTAACTAATTTCTAATTGATGATGGGTTGATTAAAAATTAA
1 ATAAAGTATGAATCAACAACTCTAGTAACTAATTTCTAATTGATGATGGGTTGATTAAAAATTAA
17436714 GGCTAATGTGTAAAAATTATATATTAAGAGT
66 GGCTAATGTGTAAAAATTATATATTAAGAGT
17436745 AT
1 AT
17436747 GGTCCCCAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (96 bp):
ATAAAGTATGAATCAACAACTCTAGTAACTAATTTCTAATTGATGATGGGTTGATTAAAAATTAA
GGCTAATGTGTAAAAATTATATATTAAGAGT
Found at i:17449903 original size:17 final size:17
Alignment explanation
Indices: 17449881--17449914 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17449871 CAGTTTGACC
17449881 TTAGTCTACATCCAAAG
1 TTAGTCTACATCCAAAG
17449898 TTAGTCTACATCCAAAG
1 TTAGTCTACATCCAAAG
17449915 CAATGATCCA
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:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAGTCTACATCCAAAG
Found at i:17450313 original size:21 final size:21
Alignment explanation
Indices: 17450289--17450348 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
17450279 AAGTGACTTT
*
17450289 ACTTGATTCATAAGTAACCAA
1 ACTTGATCCATAAGTAACCAA
17450310 ACTTGATCCATAAGTAACCAA
1 ACTTGATCCATAAGTAACCAA
* * *
17450331 AGTTGACCCACAAGTAAC
1 ACTTGATCCATAAGTAAC
17450349 TAATCTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
ACTTGATCCATAAGTAACCAA
Found at i:17450526 original size:21 final size:21
Alignment explanation
Indices: 17450502--17450561 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
17450492 AAGTGACTTT
*
17450502 ACTTGATTCATAAGTAACCAA
1 ACTTGATCCATAAGTAACCAA
17450523 ACTTGATCCATAAGTAACCAA
1 ACTTGATCCATAAGTAACCAA
* * *
17450544 AGTTGACCCACAAGTAAC
1 ACTTGATCCATAAGTAAC
17450562 TAATCTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
ACTTGATCCATAAGTAACCAA
Found at i:17450580 original size:213 final size:213
Alignment explanation
Indices: 17450213--17450638 Score: 843
Period size: 213 Copynumber: 2.0 Consensus size: 213
17450203 GCTAAAAATT
17450213 AACATAGGATAATCTTGACATAATTCGGTAAGAGTTTTGGTGTAAAGCAATGTCTTCAAATATAG
1 AACATAGGATAATCTTGACATAATTCGGTAAGAGTTTTGGTGTAAAGCAATGTCTTCAAATATAG
17450278 AAAGTGACTTTACTTGATTCATAAGTAACCAAACTTGATCCATAAGTAACCAAAGTTGACCCACA
66 AAAGTGACTTTACTTGATTCATAAGTAACCAAACTTGATCCATAAGTAACCAAAGTTGACCCACA
17450343 AGTAACTAATCTTCAAATCTTCAATTTTAACTCAATTGGTCTTCATGGTTTAAGCTCTAACTTGT
131 AGTAACTAATCTTCAAATCTTCAATTTTAACTCAATTGGTCTTCATGGTTTAAGCTCTAACTTGT
17450408 CCAAATATCTTCAAAGCA
196 CCAAATATCTTCAAAGCA
17450426 AACATAGGATAATCTTGACATAATTCGGTAAGAGTTTTGGTGTAAAGCAATGTCTTCAAATATAG
1 AACATAGGATAATCTTGACATAATTCGGTAAGAGTTTTGGTGTAAAGCAATGTCTTCAAATATAG
17450491 AAAGTGACTTTACTTGATTCATAAGTAACCAAACTTGATCCATAAGTAACCAAAGTTGACCCACA
66 AAAGTGACTTTACTTGATTCATAAGTAACCAAACTTGATCCATAAGTAACCAAAGTTGACCCACA
*
17450556 AGTAACTAATCTTCAAATCTTCAATTTTAACTCAATTGGTCTTCATGGTTTAGGCTCTAACTTGT
131 AGTAACTAATCTTCAAATCTTCAATTTTAACTCAATTGGTCTTCATGGTTTAAGCTCTAACTTGT
17450621 CCAAATATCTTCAAAGCA
196 CCAAATATCTTCAAAGCA
17450639 TGTAGTCTAA
Statistics
Matches: 212, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 212 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (213 bp):
AACATAGGATAATCTTGACATAATTCGGTAAGAGTTTTGGTGTAAAGCAATGTCTTCAAATATAG
AAAGTGACTTTACTTGATTCATAAGTAACCAAACTTGATCCATAAGTAACCAAAGTTGACCCACA
AGTAACTAATCTTCAAATCTTCAATTTTAACTCAATTGGTCTTCATGGTTTAAGCTCTAACTTGT
CCAAATATCTTCAAAGCA
Found at i:17459772 original size:21 final size:21
Alignment explanation
Indices: 17459746--17459831 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
17459736 GGCTTTATCG
* *
17459746 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
17459767 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
*
17459788 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
* * * *
17459809 TTTAGGCACTTTATGTGTCGT
1 ATCAGGCACCTCATGTGTCGT
17459830 AT
1 AT
17459832 ACTGATCAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCAGGCACCTCATGTGTCGT
Found at i:17461812 original size:3 final size:3
Alignment explanation
Indices: 17461804--17461890 Score: 97
Period size: 3 Copynumber: 28.7 Consensus size: 3
17461794 AATTTATTTC
17461804 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* ** *
17461850 TCTA AT- ATA A-A ACC ATA ATA ATAA ATA ATG ATA ATA ATA AT
1 -ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT
17461891 TTAATATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
2 4 0.06
3 60 0.83
4 8 0.11
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17463543 original size:19 final size:20
Alignment explanation
Indices: 17463508--17463546 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17463498 AATACATGTG
17463508 TAATAATAAACATATGTATT
1 TAATAATAAACATATGTATT
17463528 TAATAATAAA-ATATGTATT
1 TAATAATAAACATATGTATT
17463547 GCTTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATAATAAACATATGTATT
Found at i:17464429 original size:26 final size:26
Alignment explanation
Indices: 17464400--17464559 Score: 248
Period size: 26 Copynumber: 6.2 Consensus size: 26
17464390 TGGTACAAAT
17464400 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
17464426 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17464452 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * * *
17464478 TGATAATGGATTAAGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17464504 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17464530 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17464556 TGAT
1 TGAT
17464560 GGGCATTTCA
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 119 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17464464 original size:52 final size:52
Alignment explanation
Indices: 17464400--17464559 Score: 275
Period size: 52 Copynumber: 3.1 Consensus size: 52
17464390 TGGTACAAAT
17464400 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* * *
17464452 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAAGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
17464504 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
17464556 TGAT
1 TGAT
17464560 GGGCATTTCA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:17474568 original size:46 final size:44
Alignment explanation
Indices: 17474468--17474575 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
17474458 TGTCTTTGAC
** * * *
17474468 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
* *
17474512 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATA--TATAAT
17474558 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
17474576 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 32 0.58
46 23 0.42
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTATCTCCAAAGCCATATATAAT
Found at i:17476123 original size:2 final size:2
Alignment explanation
Indices: 17476116--17476150 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17476106 AACCGGAATT
17476116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17476151 TAAAACAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17478106 original size:21 final size:22
Alignment explanation
Indices: 17478076--17478118 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17478066 GCTTAAATGA
*
17478076 AATCAGT-AAAATAACATATAT
1 AATCAGTAAAAATAAAATATAT
*
17478097 AATCATTAAAAATAAAATATAT
1 AATCAGTAAAAATAAAATATAT
17478119 GTTGAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
AATCAGTAAAAATAAAATATAT
Found at i:17479012 original size:22 final size:25
Alignment explanation
Indices: 17478971--17479016 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
17478961 GTATCATAAT
17478971 TATTTAGCAAACTATGTAATTTATA
1 TATTTAGCAAACTATGTAATTTATA
17478996 TATTTA-CAAA-T-TGTAATTTAT
1 TATTTAGCAAACTATGTAATTTAT
17479017 GTTTGCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 4 0.19
25 6 0.29
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (25 bp):
TATTTAGCAAACTATGTAATTTATA
Found at i:17481411 original size:3 final size:3
Alignment explanation
Indices: 17481403--17481444 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17481393 GAATTGAAGG
17481403 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17481445 TGACGAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17482773 original size:21 final size:21
Alignment explanation
Indices: 17482749--17482789 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17482739 ACAATAAATA
*
17482749 TTATTATAAAAAGGAAAATTT
1 TTATAATAAAAAGGAAAATTT
* *
17482770 TTATAATAAAAGGGTAAATT
1 TTATAATAAAAAGGAAAATT
17482790 ATAAAAATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (21 bp):
TTATAATAAAAAGGAAAATTT
Found at i:17483535 original size:5 final size:5
Alignment explanation
Indices: 17483525--17483556 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17483515 TGAAGTGTGA
17483525 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
17483557 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17483550 original size:9 final size:9
Alignment explanation
Indices: 17483526--17483556 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17483516 GAAGTGTGAA
17483526 AAATAAAAT
1 AAATAAAAT
17483535 AAAATAAAAT
1 -AAATAAAAT
17483545 AAATAAAAT
1 AAATAAAAT
17483554 AAA
1 AAA
17483557 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:17485704 original size:22 final size:22
Alignment explanation
Indices: 17485677--17485721 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17485667 CTATTCTCAA
17485677 TTTTTGTTCTGGCTTGAGGAGT
1 TTTTTGTTCTGGCTTGAGGAGT
17485699 TTTTTGTTCTGGCTTGAGGAGT
1 TTTTTGTTCTGGCTTGAGGAGT
17485721 T
1 T
17485722 GACTCTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.31, T:0.51
Consensus pattern (22 bp):
TTTTTGTTCTGGCTTGAGGAGT
Found at i:17488004 original size:5 final size:5
Alignment explanation
Indices: 17487994--17488025 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
17487984 CAATTTGTGA
17487994 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
17488026 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:17488019 original size:9 final size:9
Alignment explanation
Indices: 17487995--17488025 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
17487985 AATTTGTGAA
17487995 AAATAAAAT
1 AAATAAAAT
17488004 AAAATAAAAT
1 -AAATAAAAT
17488014 AAATAAAAT
1 AAATAAAAT
17488023 AAA
1 AAA
17488026 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:17488504 original size:17 final size:17
Alignment explanation
Indices: 17488484--17488517 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17488474 AGGTTTAGGT
17488484 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
17488501 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
17488518 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:17498077 original size:16 final size:17
Alignment explanation
Indices: 17498056--17498090 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17498046 ACATACATAC
*
17498056 ATTATAT-TTTAAATAA
1 ATTATATATTTAAAAAA
17498072 ATTATATATTTAAAAAA
1 ATTATATATTTAAAAAA
17498089 AT
1 AT
17498091 ATTCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATATATTTAAAAAA
Found at i:17505793 original size:22 final size:22
Alignment explanation
Indices: 17505753--17505795 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
17505743 AAAGAGATTT
17505753 AAAATAAATAATGATAAAACAGA
1 AAAATAAATAA-GATAAAACAGA
17505776 AAAATAAATAA-ATCAAAACA
1 AAAATAAATAAGAT-AAAACA
17505796 AGTTAAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 2 0.11
22 6 0.32
23 11 0.58
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (22 bp):
AAAATAAATAAGATAAAACAGA
Found at i:17508304 original size:45 final size:45
Alignment explanation
Indices: 17508204--17508330 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
17508194 TTTTCTCAAA
* *
17508204 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
17508246 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
17508290 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
17508331 ATCAAGTCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 40 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:17508733 original size:38 final size:38
Alignment explanation
Indices: 17508678--17508957 Score: 371
Period size: 38 Copynumber: 7.3 Consensus size: 38
17508668 GGCACGAAGG
* * * *
17508678 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* *
17508716 CTCGGATATAATACCAGCACAAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** * *
17508754 CCCGGATATTTTACTAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
17508793 GCCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
17508832 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
*
17508871 GCCTGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* * *
17508910 CTCGAATATAATACCAGCATGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
17508948 CCCGGATATA
1 CCCGGATATA
17508958 TATCGAATAT
Statistics
Matches: 210, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
38 132 0.63
39 20 0.10
40 58 0.28
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:17508809 original size:78 final size:78
Alignment explanation
Indices: 17508718--17508957 Score: 385
Period size: 78 Copynumber: 3.1 Consensus size: 78
17508708 GGATTTATCT
* *
17508718 CGGATATAATACCAGCACAAAGCCTGCGGGATTTAACCCGGATATTTTACTAGCACGAAGCCTGC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGC
17508783 GGGTCTTTAAGCC
66 GGGTCTTTAAGCC
17508796 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGC
17508861 GGGTCTTTAAGCC
66 GGGTCTTTAAGCC
* * * ** *
17508874 TGGATATAATACCAGCACGAAGCCTGCGGGATTTAACTCGAATATAATACCAGCATGAAGCCTGC
1 CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGC
*
17508939 GGG-ATTTAA-CC
66 GGGTCTTTAAGCC
17508950 CGGATATA
1 CGGATATA
17508958 TATCGAATAT
Statistics
Matches: 152, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
76 9 0.06
77 5 0.03
78 138 0.91
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (78 bp):
CGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCCTGC
GGGTCTTTAAGCC
Found at i:17508919 original size:116 final size:116
Alignment explanation
Indices: 17508677--17508957 Score: 386
Period size: 116 Copynumber: 2.4 Consensus size: 116
17508667 AGGCACGAAG
* * * *
17508677 GCCCGAATATAATACCAGCACTAGGCCTGCGGGATTTATCTCGGATATAATACCAGCACAAAGCC
1 GCCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACAAAGCC
** * *
17508742 TGCGGGATTTAACCCGGATATTTTACTAGCACGAAGCCTGCGGGTCTTTAA
66 TGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGGTATTTAA
* ** *
17508793 GCCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGCC
1 GCCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACAAAGCC
* *
17508858 TGCGGGTCTTTAAGCCTGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
66 TGCGGG-ATTTAA-CCCGGATATAATACCAGCACGAAGCCTGCGGGTATTTAA
* *
17508910 -CTCGAATATAATACCAGCATGAAGCCTGCGGGATTTAACCCGGATATA
1 GCCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA
17508958 TATCGAATAT
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
116 107 0.74
117 10 0.07
118 28 0.19
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (116 bp):
GCCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACAAAGCC
TGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGGTATTTAA
Found at i:17508959 original size:78 final size:78
Alignment explanation
Indices: 17508678--17508957 Score: 379
Period size: 78 Copynumber: 3.6 Consensus size: 78
17508668 GGCACGAAGG
* * * * *
17508678 CCCGAATATAATACCAGCACTAGGCCTGCGGG-ATTT-ATCTCGGATATAATACCAGCACAAAGC
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGTATTTAAGCCCGGATATAATACCAGCACGAAGC
17508741 CTGCGGGATTTAA
66 CTGCGGGATTTAA
* ** * *
17508754 CCCGGATATTTTACTAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATATAATACCAGCACGAAGC
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGTATTTAAGCCCGGATATAATACCAGCACGAAGC
17508819 CTGCGGGATTTAA
66 CTGCGGGATTTAA
* ** * *
17508832 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAAGCCTGGATATAATACCAGCACGAAGC
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGTATTTAAGCCCGGATATAATACCAGCACGAAGC
17508897 CTGCGGGATTTAA
66 CTGCGGGATTTAA
* *
17508910 CTCGAATATAATACCAGCATGAAGCCTGCGGG-ATTTAA-CCCGGATATA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGTATTTAAGCCCGGATATA
17508958 TATCGAATAT
Statistics
Matches: 183, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
76 35 0.19
77 8 0.04
78 140 0.77
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (78 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGTATTTAAGCCCGGATATAATACCAGCACGAAGC
CTGCGGGATTTAA
Found at i:17516884 original size:19 final size:18
Alignment explanation
Indices: 17516837--17516903 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 18
17516827 ATTCTAAATG
* *
17516837 AATTCAAAAA-TATAAAG
1 AATTTAAAAATTATAAAA
17516854 AATTTAAAAATTATAAAA
1 AATTTAAAAATTATAAAA
*
17516872 AATATTAATAATTATTAAAA
1 AAT-TTAAAAATTA-TAAAA
17516892 GAATTATAAAAA
1 -AATT-TAAAAA
17516904 ATTGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.22
18 9 0.22
19 9 0.22
20 6 0.15
21 8 0.20
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (18 bp):
AATTTAAAAATTATAAAA
Found at i:17516896 original size:12 final size:10
Alignment explanation
Indices: 17516842--17516906 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 10
17516832 AAATGAATTC
17516842 AAAAA-TATA
1 AAAAATTATA
*
17516851 AAGAATT-T-
1 AAAAATTATA
17516859 AAAAATTATA
1 AAAAATTATA
*
17516869 AAAAA-TATT
1 AAAAATTATA
*
17516878 AATAATTATTA
1 AAAAATTA-TA
17516889 AAAGAATTATA
1 AAA-AATTATA
17516900 AAAAATT
1 AAAAATT
17516907 GAAAAAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.14
9 13 0.30
10 12 0.27
11 8 0.18
12 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:17519152 original size:15 final size:16
Alignment explanation
Indices: 17519132--17519164 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17519122 AATAATTTAA
*
17519132 TTAAATTAGTT-ATAT
1 TTAAATTAATTAATAT
17519147 TTAAATTAATTAATAT
1 TTAAATTAATTAATAT
17519163 TT
1 TT
17519165 TTAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAAATTAATTAATAT
Found at i:17522319 original size:2 final size:2
Alignment explanation
Indices: 17522312--17522336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17522302 CACTAAAATT
17522312 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17522337 GTGAGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17522521 original size:17 final size:18
Alignment explanation
Indices: 17522487--17522522 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17522477 CTTCTCTAAT
*
17522487 TTTAATTAAATTAAAAAA
1 TTTAATTAAATAAAAAAA
17522505 TTTAATT-AATAAAAAAA
1 TTTAATTAAATAAAAAAA
17522522 T
1 T
17522523 ATGTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTAATTAAATAAAAAAA
Done.