Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 58 of 130
Found at i:12413592 original size:29 final size:28
Alignment explanation
Indices: 12413560--12413628 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
12413550 TTTTTTTTAT
12413560 TTAAAAAAATGAAATAAATAAAATAAAAA
1 TTAAAAAAAT-AAATAAATAAAATAAAAA
* *
12413589 TTAAAAAAAATAAATAAGTAAAATGAAAA
1 TT-AAAAAAATAAATAAATAAAATAAAAA
* *
12413618 TGAATAAAATA
1 TTAAAAAAATA
12413629 TAGAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.23
29 19 0.54
30 8 0.23
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (28 bp):
TTAAAAAAATAAATAAATAAAATAAAAA
Found at i:12414577 original size:12 final size:12
Alignment explanation
Indices: 12414562--12414601 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
12414552 ATAAATCAAA
12414562 AAATTAACAGAT
1 AAATTAACAGAT
12414574 AAATTAA-A-ATT
1 AAATTAACAGA-T
12414585 AAA-TAACAGAT
1 AAATTAACAGAT
12414596 AAATTA
1 AAATTA
12414602 TAACATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.17
11 10 0.42
12 10 0.42
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (12 bp):
AAATTAACAGAT
Found at i:12414725 original size:6 final size:6
Alignment explanation
Indices: 12414692--12414804 Score: 81
Period size: 6 Copynumber: 18.5 Consensus size: 6
12414682 AGTAATAAAT
* * * *
12414692 AAATAA ATAATAA ATACAT-A AGATAA AAAT-A AAAGAA AAATAT ATATAA
1 AAATAA A-AATAA A-A-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * *
12414741 AAACAA TAATAA AAATAA AAATAA AAAT-A AAATAA AAATGTAA AATACAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA--TAA AA-ATAA
12414791 AAATAA AAA-AA AAA
1 AAATAA AAATAA AAA
12414805 AGGAAATAGA
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
5 16 0.19
6 47 0.55
7 14 0.16
8 7 0.08
9 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:12414733 original size:41 final size:39
Alignment explanation
Indices: 12414688--12414776 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 39
12414678 TAATAGTAAT
*
12414688 AAATAAATAAATAATAAATACAT-AAGATAAAAATAAAAGA-A
1 AAATAAATAAA-AA-AAATA-ATAAAAATAAAAATAAAA-ATA
*
12414729 AAATATATATAAAAACAATAATAAAAATAAAAATAAAAATA
1 AAATA-A-ATAAAAAAAATAATAAAAATAAAAATAAAAATA
12414770 AAATAAA
1 AAATAAA
12414777 AATGTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
39 1 0.02
40 4 0.10
41 29 0.69
42 3 0.07
43 5 0.12
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (39 bp):
AAATAAATAAAAAAAATAATAAAAATAAAAATAAAAATA
Found at i:12417786 original size:16 final size:16
Alignment explanation
Indices: 12417761--12417791 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12417751 ATGAAATAAA
12417761 ATTTTCTTTTATATTT
1 ATTTTCTTTTATATTT
*
12417777 ATTTTTTTTTATATT
1 ATTTTCTTTTATATT
12417792 GAAACTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTCTTTTATATTT
Found at i:12421990 original size:72 final size:75
Alignment explanation
Indices: 12421851--12421994 Score: 186
Period size: 72 Copynumber: 2.0 Consensus size: 75
12421841 AAAATAAAAT
* * * *
12421851 AATAAAAATTTTTAAAAAATATATTTTTAGGAAAAAGTTAAAAATATTAATATTCTTTGAAAATA
1 AATAAAAATTTTTAAAAAATATATTTTGAGGAAAAAGTTAAAAAGATCAATATTCCTTGAAAATA
12421916 AAATTTCTAA
66 AAATTTCTAA
* * * * *
12421926 AATAAAAA-TTTTCAAAAA-GTATTTTGAGG-AAAAGTTGAAAAGATCAATTTTCCTTGAAATTA
1 AATAAAAATTTTTAAAAAATATATTTTGAGGAAAAAGTTAAAAAGATCAATATTCCTTGAAAATA
12421988 AAATTTC
66 AAATTTC
12421995 AGGAAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
72 34 0.57
73 9 0.15
74 9 0.15
75 8 0.13
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (75 bp):
AATAAAAATTTTTAAAAAATATATTTTGAGGAAAAAGTTAAAAAGATCAATATTCCTTGAAAATA
AAATTTCTAA
Found at i:12422016 original size:61 final size:60
Alignment explanation
Indices: 12421925--12422103 Score: 206
Period size: 61 Copynumber: 3.0 Consensus size: 60
12421915 AAAATTTCTA
* * *
12421925 AAATAAAAATTTTC--AAAAAGTA-TTTTGAGGAAAAGTTGAAAAG-ATCAATTTTCCTTG
1 AAATAAAAATTATCAAAAAAAATATTTTTGAGGAAAAGTTG-AAAGTATCAATTTTTCTTG
* * *
12421982 AAATTAAAATT-TCAGGAAAAAAATATTTTTGAGGAAAAGTTGAAAGTACCAATTTTTCTTAA
1 AAATAAAAATTATCA--AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-G
* * *
12422044 AAATAAAAATTATCAAGAAAAATATTTTTAAGGAAAAGTTGCAAGTATCAATTTTTCTTG
1 AAATAAAAATTATCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTG
12422104 TATAAAAGCA
Statistics
Matches: 103, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
56 2 0.02
57 10 0.10
60 11 0.11
61 67 0.65
62 10 0.10
63 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (60 bp):
AAATAAAAATTATCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:12426279 original size:31 final size:30
Alignment explanation
Indices: 12426175--12426287 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 30
12426165 CCATTCTTTT
* *
12426175 AAACCCCTAAATCAACTGAACTCAAT-ATTTA
1 AAACCCCTAAATTAACTGAAC-CAATCA-CTA
** * * *
12426206 AAAATCCTAAATCAACTGAAACAATCTCTA
1 AAACCCCTAAATTAACTGAACCAATCACTA
* * *
12426236 GAACCTCTAAATTAACTGAACCTAGTCACTA
1 AAACCCCTAAATTAACTGAACC-AATCACTA
*
12426267 AAACCCCTAAATTAATTGAAC
1 AAACCCCTAAATTAACTGAAC
12426288 GTCCAATTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
30 22 0.34
31 42 0.66
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (30 bp):
AAACCCCTAAATTAACTGAACCAATCACTA
Found at i:12432097 original size:3 final size:3
Alignment explanation
Indices: 12432091--12432126 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
12432081 GATGATGATG
12432091 ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12432127 TTAATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:12432113 original size:11 final size:11
Alignment explanation
Indices: 12432094--12432131 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12432084 GATGATGATA
12432094 ATAATAATAAT
1 ATAATAATAAT
12432105 A-ATATAATAAT
1 ATA-ATAATAAT
12432116 ATAATAATAAT
1 ATAATAATAAT
*
12432127 TTAAT
1 ATAAT
12432132 GAAAAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:12432131 original size:8 final size:8
Alignment explanation
Indices: 12432091--12432124 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
12432081 GATGATGATG
12432091 ATAATAAT
1 ATAATAAT
12432099 AATAATAAT
1 -ATAATAAT
12432108 ATAATAAT
1 ATAATAAT
12432116 ATAATAAT
1 ATAATAAT
12432124 A
1 A
12432125 ATTTAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:12432391 original size:13 final size:13
Alignment explanation
Indices: 12432346--12432395 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
12432336 TGAAACTTTC
*
12432346 AAATTGAAACCCT
1 AAATGGAAACCCT
12432359 AAAT-GAAACCCT
1 AAATGGAAACCCT
*
12432371 AAAAGGAAACTCC-
1 AAATGGAAAC-CCT
12432384 AAATGG-AACCCT
1 AAATGGAAACCCT
12432396 TAGAAAAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 14 0.44
13 14 0.44
14 2 0.06
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATGGAAACCCT
Found at i:12432862 original size:12 final size:12
Alignment explanation
Indices: 12432842--12432874 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12432832 TTACACTCAT
*
12432842 TATACATGTATA
1 TATATATGTATA
12432854 TATATATGTATA
1 TATATATGTATA
12432866 TATATATGT
1 TATATATGT
12432875 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (12 bp):
TATATATGTATA
Found at i:12438260 original size:35 final size:35
Alignment explanation
Indices: 12438214--12438285 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
12438204 CCTTCCGTGA
12438214 ATCGCACTACTAGAAAAGTAGATTATGTATGAGTG
1 ATCGCACTACTAGAAAAGTAGATTATGTATGAGTG
12438249 ATCGCACTACTAGAAAAGTAGATTATGTATGAGTG
1 ATCGCACTACTAGAAAAGTAGATTATGTATGAGTG
12438284 AT
1 AT
12438286 AAGGGGCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (35 bp):
ATCGCACTACTAGAAAAGTAGATTATGTATGAGTG
Found at i:12438312 original size:6 final size:6
Alignment explanation
Indices: 12438301--12438329 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12438291 GCACATCAAA
12438301 AAAAAG AAAAAG AAAAA- AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
12438330 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12438320 original size:17 final size:18
Alignment explanation
Indices: 12438298--12438339 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
12438288 GGGGCACATC
12438298 AAAAAAAAGAAAAAG-AA
1 AAAAAAAAGAAAAAGTAA
*
12438315 AAAAAAAAGAAAAAGTAC
1 AAAAAAAAGAAAAAGTAA
12438333 AAAAAAA
1 AAAAAAA
12438340 TGGTTATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAAAAGTAA
Found at i:12438321 original size:11 final size:12
Alignment explanation
Indices: 12438301--12438329 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
12438291 GCACATCAAA
12438301 AAAAAGAAAAAG
1 AAAAAGAAAAAG
12438313 AAAAA-AAAAAG
1 AAAAAGAAAAAG
12438324 AAAAAG
1 AAAAAG
12438330 TACAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:12438862 original size:4 final size:4
Alignment explanation
Indices: 12438833--12438892 Score: 68
Period size: 4 Copynumber: 14.5 Consensus size: 4
12438823 AGGAAAAGTG
* *
12438833 AAGA AAAA AGAGA AAAA AATGA AAGA AAGA AAGAA AAGA AAGA AA-A AAGA
1 AAGA AAGA A-AGA AAGA AA-GA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA
12438883 AAGA AAGA AA
1 AAGA AAGA AA
12438893 TGGGTGGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.06
4 35 0.73
5 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:12438869 original size:28 final size:28
Alignment explanation
Indices: 12438833--12438892 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
12438823 AGGAAAAGTG
12438833 AAGAAAA-AAGAGAAAAAAATGAAAGAAAGA
1 AAGAAAAGAA-AG-AAAAAA-GAAAGAAAGA
12438863 AAGAAAAGAAAGAAAAAAGAAAGAAAGA
1 AAGAAAAGAAAGAAAAAAGAAAGAAAGA
12438891 AA
1 AA
12438893 TGGGTGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 12 0.41
29 6 0.21
30 9 0.31
31 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (28 bp):
AAGAAAAGAAAGAAAAAAGAAAGAAAGA
Found at i:12439896 original size:65 final size:68
Alignment explanation
Indices: 12439749--12439896 Score: 175
Period size: 67 Copynumber: 2.2 Consensus size: 68
12439739 AGCTGGAACC
** *
12439749 CAAT-GAAAATTTAAGCATAGTTTAGTTGGCACTAATGACAAGATTTAAGCCTAACTTAGTTAAC
1 CAATAGAAAATTTAAGCATAGTTTAACTGGCACTAATGACAAGATTTAAGCCTAACTTAGCTAAC
12439813 CCT
66 CCT
* * *
12439816 CAATA-AAAATTTAAGCTTAGTTTAACTGGTACTAATGA-AA-ATTTAAGCCT-ACTGTAGCTAG
1 CAATAGAAAATTTAAGCATAGTTTAACTGGCACTAATGACAAGATTTAAGCCTAACT-TAGCTAA
12439877 CACCT
65 C-CCT
12439882 -AA-AGAAAATTTAAGC
1 CAATAGAAAATTTAAGC
12439897 CCAATCTGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
64 4 0.06
65 29 0.41
66 5 0.07
67 33 0.46
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (68 bp):
CAATAGAAAATTTAAGCATAGTTTAACTGGCACTAATGACAAGATTTAAGCCTAACTTAGCTAAC
CCT
Found at i:12440033 original size:22 final size:21
Alignment explanation
Indices: 12439918--12440040 Score: 90
Period size: 22 Copynumber: 5.8 Consensus size: 21
12439908 GGCATGCAAC
*
12439918 CCCATATTAGCTAGCACATAAG
1 CCCAT-TTAGCTGGCACATAAG
* *
12439940 CCCAATTTAGCTAGCACATAAA
1 CCC-ATTTAGCTGGCACATAAG
*
12439962 CCCAGTTTAGTTGGCACATAAG
1 CCCA-TTTAGCTGGCACATAAG
* * *
12439984 CTCATATTAGCTGACACATGAG
1 CCCAT-TTAGCTGGCACATAAG
*
12440006 ---TTTTAGCTGGCACATAAG
1 CCCATTTAGCTGGCACATAAG
* *
12440024 TCCAGTTTAGTTGGCAC
1 CCCA-TTTAGCTGGCAC
12440041 GTAAAGCCAT
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
18 14 0.17
19 1 0.01
21 2 0.02
22 62 0.77
23 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (21 bp):
CCCATTTAGCTGGCACATAAG
Found at i:12440250 original size:32 final size:32
Alignment explanation
Indices: 12440203--12440280 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 32
12440193 ATTCCTAAGA
*
12440203 AAAATTTAAGTCTAGATTATCTAGCACCAAT-
1 AAAATTTAAGCCTAGATTATCTAGCACCAATG
*
12440234 AAAGTTTTAAGCCTAGATTATCTAGCACCAATG
1 AAA-ATTTAAGCCTAGATTATCTAGCACCAATG
12440267 AAAATTTAAGCCTA
1 AAAATTTAAGCCTA
12440281 ATTTAGTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
31 3 0.07
32 36 0.86
33 3 0.07
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (32 bp):
AAAATTTAAGCCTAGATTATCTAGCACCAATG
Found at i:12440631 original size:22 final size:23
Alignment explanation
Indices: 12440583--12440637 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
12440573 TAAGCTCAGT
* *
12440583 TTAGCTGGCACATAAGCCCAAAA
1 TTAGTTGGCACAAAAGCCCAAAA
12440606 TTAGTTGGCACAAAAGCCC-AAA
1 TTAGTTGGCACAAAAGCCCAAAA
12440628 TTAGTTGGCA
1 TTAGTTGGCA
12440638 TGCAGGCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
TTAGTTGGCACAAAAGCCCAAAA
Found at i:12441135 original size:19 final size:19
Alignment explanation
Indices: 12441111--12441148 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12441101 ACTAAATAAT
12441111 AATAATAAT-TAAATTAAAA
1 AATAATAATATAAA-TAAAA
12441130 AATAATAATATAAATAAAA
1 AATAATAATATAAATAAAA
12441149 TAAAACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAATATAAATAAAA
Found at i:12441138 original size:25 final size:24
Alignment explanation
Indices: 12441104--12441153 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
12441094 AAACAAAACT
* *
12441104 AAATAATAATAATAATTAAATTAAA
1 AAATAATAAT-ATAAATAAAATAAA
12441129 AAATAATAATATAAATAAAATAAA
1 AAATAATAATATAAATAAAATAAA
12441153 A
1 A
12441154 CAACAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAATAATATAAATAAAATAAA
Found at i:12443182 original size:3 final size:3
Alignment explanation
Indices: 12443174--12443220 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
12443164 TAAATAGATG
* *
12443174 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATC ATA ATC ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12443221 TTAATGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12443476 original size:24 final size:24
Alignment explanation
Indices: 12443449--12443500 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
12443439 CGTTCAAATT
12443449 GAAACCCCAAATAAAACCCTAAAA
1 GAAACCCCAAATAAAACCCTAAAA
*
12443473 GAAACCCCAAATGAAACCCTAAAA
1 GAAACCCCAAATAAAACCCTAAAA
12443497 GAAA
1 GAAA
12443501 ATTATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.27, G:0.08, T:0.08
Consensus pattern (24 bp):
GAAACCCCAAATAAAACCCTAAAA
Found at i:12443500 original size:12 final size:12
Alignment explanation
Indices: 12443449--12443500 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
12443439 CGTTCAAATT
12443449 GAAACCCCAAATA
1 GAAACCCCAAA-A
*
12443462 -AAACCCTAAAA
1 GAAACCCCAAAA
*
12443473 GAAACCCCAAAT
1 GAAACCCCAAAA
*
12443485 GAAACCCTAAAA
1 GAAACCCCAAAA
12443497 GAAA
1 GAAA
12443501 ATTATAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 1 0.03
12 32 0.97
ACGTcount: A:0.58, C:0.27, G:0.08, T:0.08
Consensus pattern (12 bp):
GAAACCCCAAAA
Found at i:12443578 original size:19 final size:19
Alignment explanation
Indices: 12443556--12443604 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12443546 TCCTGAATTG
12443556 AACCC-AAAACCTTAAATAA
1 AACCCTAAAA-CTTAAATAA
*
12443575 AACCCTAAAACTTAAGTAA
1 AACCCTAAAACTTAAATAA
*
12443594 AACCCTGAAAC
1 AACCCTAAAAC
12443605 CCTAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.53, C:0.27, G:0.04, T:0.16
Consensus pattern (19 bp):
AACCCTAAAACTTAAATAA
Found at i:12443627 original size:32 final size:31
Alignment explanation
Indices: 12443580--12443640 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
12443570 AATAAAACCC
*
12443580 TAAAACTTAAGTAAAACCCTGAAACCCTAGT
1 TAAAACTTAAATAAAACCCTGAAACCCTAGT
*
12443611 TAAAATCTTAAATAAAACCTTGAAACCCTA
1 TAAAA-CTTAAATAAAACCCTGAAACCCTA
12443641 AGTCTACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (31 bp):
TAAAACTTAAATAAAACCCTGAAACCCTAGT
Found at i:12445534 original size:4 final size:4
Alignment explanation
Indices: 12445525--12445660 Score: 51
Period size: 4 Copynumber: 35.8 Consensus size: 4
12445515 CATTTTTATT
*
12445525 TTTA TTTA -TTA -TTA -TTA -TTA -TTA TTTA TTAATA TTTT TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA
* * * * *
12445569 TTTA TCTA TTAATA TTT- TTTA -TTA ATTA TCTA TTAA TATA TTTA TTTA
1 TTTA TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * *
12445617 TTTA -TTA GTTA TCTA TTAA TATA TATA -TT- TTTA TCTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
12445661 TACTTTTTCT
Statistics
Matches: 101, Mismatches: 20, Indels: 22
0.71 0.14 0.15
Matches are distributed among these distances:
3 30 0.30
4 63 0.62
6 8 0.08
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (4 bp):
TTTA
Found at i:12445534 original size:10 final size:10
Alignment explanation
Indices: 12445519--12445659 Score: 78
Period size: 10 Copynumber: 13.6 Consensus size: 10
12445509 CATTTGCATT
*
12445519 TTTATTTTTA
1 TTTATTATTA
12445529 TTTATTATTA
1 TTTATTATTA
12445539 -TTATTATTA
1 TTTATTATTA
*
12445548 TTTATTAATA
1 TTTATTATTA
*
12445558 TTTTTTTATTA
1 -TTTATTATTA
12445569 TTTATCTATTAA
1 TTTAT-TATT-A
12445581 TATT-TT-TTA
1 T-TTATTATTA
*
12445590 TTAATTATCTA
1 TTTATTAT-TA
*
12445601 TTAATATATTTA
1 TTTAT-TA-TTA
12445613 TTTATTTATTA
1 TTTA-TTATTA
*
12445624 GTTATCTATTA
1 TTTAT-TATTA
*
12445635 -ATA-TATATA
1 TTTATTAT-TA
12445644 TTT-TTATCTA
1 TTTATTAT-TA
12445654 TTTATT
1 TTTATT
12445660 TTACTTTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
8 4 0.04
9 15 0.14
10 36 0.35
11 33 0.32
12 12 0.12
13 4 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTATTATTA
Found at i:12445538 original size:3 final size:3
Alignment explanation
Indices: 12445520--12445634 Score: 58
Period size: 3 Copynumber: 36.0 Consensus size: 3
12445510 ATTTGCATTT
* * *
12445520 TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTTA TTA ATA TT- TTT TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* *
12445566 TTA TTTA TCTA TTA ATA TT- TT- TTA TTAA TTA TCTA TTA ATA -TA TTTA
1 TTA -TTA T-TA TTA TTA TTA TTA TTA TT-A TTA T-TA TTA TTA TTA -TTA
12445613 TTTA TTTA TTA GTTA TCTA TTA
1 -TTA -TTA TTA -TTA T-TA TTA
12445635 ATATATATAT
Statistics
Matches: 92, Mismatches: 8, Indels: 24
0.74 0.06 0.19
Matches are distributed among these distances:
2 8 0.09
3 50 0.54
4 34 0.37
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12445586 original size:24 final size:24
Alignment explanation
Indices: 12445539--12445621 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
12445529 TTTATTATTA
*
12445539 TTATTA-TTATTTATTAATATTTTT
1 TTATTATTTATCTATTAATA-TTTT
12445563 TTATTATTTATCTATTAATATTTT
1 TTATTATTTATCTATTAATATTTT
* *
12445587 TTATTAATTATCTATTAATA-TAT
1 TTATTATTTATCTATTAATATTTT
12445610 TTATTTATTTAT
1 TTA-TTATTTAT
12445622 TAGTTATCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.09
24 36 0.68
25 12 0.23
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTATTTATCTATTAATATTTT
Found at i:12445590 original size:38 final size:37
Alignment explanation
Indices: 12445523--12445594 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
12445513 TGCATTTTTA
*
12445523 TTTTTATTTATTATTATTATTATTATTTATTAATATT
1 TTTTTATTTATTATTATTAATATTATTTATTAATATT
*
12445560 TTTTTA-TTATTTATCTATTAATATTTTTTATTAAT
1 TTTTTATTTA-TTAT-TATTAATATTATTTATTAAT
12445595 TATCTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.10
37 10 0.32
38 18 0.58
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (37 bp):
TTTTTATTTATTATTATTAATATTATTTATTAATATT
Found at i:12445622 original size:31 final size:29
Alignment explanation
Indices: 12445525--12445646 Score: 110
Period size: 31 Copynumber: 4.1 Consensus size: 29
12445515 CATTTTTATT
12445525 TTTATTTATTATTATTATT-AT-TATTTA
1 TTTATTTATTATTATTATTAATATATTTA
* *
12445552 TTAATATTT-TT-TTATTATTTATCTATTAATA
1 TT--TATTTATTATTATTATTAATATATT--TA
12445583 TTT-TTTATTAATTATCTATTAATATATTTA
1 TTTATTTATT-ATTAT-TATTAATATATTTA
*
12445613 TTTATTTATTAGTTATCTATTAATATATATA
1 TTTATTTATTA-TTAT-TATTAATATATTTA
12445644 TTT
1 TTT
12445647 TTATCTATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
27 10 0.12
28 7 0.09
29 12 0.15
30 6 0.08
31 35 0.44
32 10 0.12
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTATTTATTATTATTATTAATATATTTA
Found at i:12445623 original size:55 final size:53
Alignment explanation
Indices: 12445527--12445655 Score: 145
Period size: 55 Copynumber: 2.4 Consensus size: 53
12445517 TTTTTATTTT
* * *
12445527 TATTTATTATTATTATTATTATTTATTAATATTTTTTTATTATTTATCTATTAA
1 TATTTATTATTATTATTATTATATATT-ATATTTATTTATTAGTTATCTATTAA
*
12445581 TATTTTTTATTAATTATCTATTAATATATT-TATTTATTTATTAGTTATCTATTAA
1 TATTTATTATT-ATTAT-TATT-ATATATTATATTTATTTATTAGTTATCTATTAA
* *
12445636 TATATA-TATTTTTATCTATT
1 TATTTATTATTATTAT-TATT
12445656 TATTTTACTT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
53 9 0.14
54 14 0.22
55 32 0.49
56 4 0.06
57 6 0.09
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (53 bp):
TATTTATTATTATTATTATTATATATTATATTTATTTATTAGTTATCTATTAA
Found at i:12445949 original size:9 final size:10
Alignment explanation
Indices: 12445924--12445950 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12445914 ATTTGTGGGA
12445924 AATTTTTTAG
1 AATTTTTTAG
12445934 AATTTTTTAG
1 AATTTTTTAG
12445944 AATTTTT
1 AATTTTT
12445951 GGCATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:12446498 original size:26 final size:25
Alignment explanation
Indices: 12446467--12446528 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
12446457 TGGGCATTCC
* *
12446467 TTAATTTTTTTATTTTTTTTTAATTT
1 TTAATTTTTTTACTTTATTTT-ATTT
*
12446493 TTAA-TTTTTAACTTTATTTTATTT
1 TTAATTTTTTTACTTTATTTTATTT
*
12446517 TTATTTTTTTTA
1 TTAATTTTTTTA
12446529 GTGATTTCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.23
25 19 0.63
26 4 0.13
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (25 bp):
TTAATTTTTTTACTTTATTTTATTT
Found at i:12446516 original size:17 final size:16
Alignment explanation
Indices: 12446475--12446528 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 16
12446465 CCTTAATTTT
12446475 TTTATTTT-TTTTTAA
1 TTTATTTTATTTTTAA
*
12446490 -TT-TTTAATTTTTAA
1 TTTATTTTATTTTTAA
12446504 CTTTATTTTATTTTT-A
1 -TTTATTTTATTTTTAA
*
12446520 TTTTTTTTA
1 TTTATTTTA
12446529 GTGATTTCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.09
14 9 0.28
15 8 0.25
16 3 0.09
17 9 0.28
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTATTTTTAA
Found at i:12446524 original size:6 final size:6
Alignment explanation
Indices: 12446473--12446524 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
12446463 TTCCTTAATT
* **
12446473 TTTTTA TTTTT- TTTTAA TTTTTAA TTTTTA ACTTTA -TTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA
12446520 TTTTT
1 TTTTT
12446525 TTTAGTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 8 0.21
6 24 0.63
7 6 0.16
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:12446717 original size:62 final size:61
Alignment explanation
Indices: 12446540--12446723 Score: 262
Period size: 61 Copynumber: 3.0 Consensus size: 61
12446530 TGATTTCCTA
** **
12446540 AAATTAAAATTTCAAAAAAAAAACCATTTCGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAATTAAAATTTCAAAAAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * *
12446601 AAATTAAAATTTTAGAAAACAAAATATTTTAAGAAAAAGTT-AAGAGTATCAATTTTTCTTG
1 AAATTAAAATTTCAAAAAAAAAAATATTTTAAGAAAAAGTTGAA-AGTATCAATTTTTCTTG
* *
12446662 AAATTAAAATTTCAAAAAAATAAAATATTTTAAGGAAAAGTTGAAAATATCAATTTTTCTTG
1 AAATTAAAATTTCAAAAAAA-AAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
12446724 TATAAAAGCA
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
60 2 0.02
61 68 0.63
62 36 0.33
63 2 0.02
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (61 bp):
AAATTAAAATTTCAAAAAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:12461590 original size:2 final size:2
Alignment explanation
Indices: 12461583--12461609 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12461573 TAAAATAAAC
12461583 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12461610 CATGTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12462019 original size:20 final size:20
Alignment explanation
Indices: 12461968--12462013 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
12461958 TTTATTTAAT
12461968 GTTTCAGCTAGGGCTTCAGG
1 GTTTCAGCTAGGGCTTCAGG
12461988 GTTTCAGCTAGGGCTTCAGG
1 GTTTCAGCTAGGGCTTCAGG
12462008 GTTTCA
1 GTTTCA
12462014 CTTAGGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.20, G:0.33, T:0.33
Consensus pattern (20 bp):
GTTTCAGCTAGGGCTTCAGG
Found at i:12462056 original size:19 final size:19
Alignment explanation
Indices: 12462005--12462060 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
12461995 CTAGGGCTTC
12462005 AGGGTTTCACTTAGG-TTT
1 AGGGTTTCACTTAGGATTT
* *
12462023 AGGGTTTTATTTAGGATTT
1 AGGGTTTCACTTAGGATTT
* *
12462042 TGGGTTTCACCTAGGATTT
1 AGGGTTTCACTTAGGATTT
12462061 CATGTTTCAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.18, C:0.09, G:0.27, T:0.46
Consensus pattern (19 bp):
AGGGTTTCACTTAGGATTT
Found at i:12462096 original size:24 final size:24
Alignment explanation
Indices: 12462064--12462123 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
12462054 AGGATTTCAT
*
12462064 GTTTCATTTAGAGCTT-TTTTAAGG
1 GTTTCATTTAGAG-TTCCTTTAAGG
* *
12462088 GTTTCATTTGGAGTTGCCTTTCAGG
1 GTTTCATTTAGAGTT-CCTTTAAGG
12462113 GTTTCATTTAG
1 GTTTCATTTAG
12462124 GGTTTCAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 2 0.07
24 12 0.40
25 16 0.53
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (24 bp):
GTTTCATTTAGAGTTCCTTTAAGG
Found at i:12462127 original size:12 final size:12
Alignment explanation
Indices: 12462064--12462130 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
12462054 AGGATTTCAT
12462064 GTTTCATTTAGAG
1 GTTTCATTTAG-G
*
12462077 CTTT--TTTAAGG
1 GTTTCATTT-AGG
12462088 GTTTCATTT-GG
1 GTTTCATTTAGG
* *
12462099 AGTTGCCTTTCAGG
1 -GTTTCATTT-AGG
12462113 GTTTCATTTAGG
1 GTTTCATTTAGG
12462125 GTTTCA
1 GTTTCA
12462131 ATTTGAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
11 9 0.21
12 18 0.43
13 13 0.31
14 2 0.05
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.48
Consensus pattern (12 bp):
GTTTCATTTAGG
Found at i:12462362 original size:3 final size:3
Alignment explanation
Indices: 12462354--12462385 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12462344 TTTTCATTAA
12462354 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
12462386 CATCATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12463255 original size:18 final size:18
Alignment explanation
Indices: 12463208--12463257 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 18
12463198 ATTGAAATAA
*
12463208 CATA-GAAAATTAAAATG
1 CATATGAAAATTAAATTG
12463225 C-T-TGAAACA-TAAATTG
1 CATATGAAA-ATTAAATTG
12463241 CATATGAAAATTAAATT
1 CATATGAAAATTAAATT
12463258 ACCAGAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 12 0.44
17 4 0.15
18 11 0.41
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (18 bp):
CATATGAAAATTAAATTG
Found at i:12468245 original size:31 final size:30
Alignment explanation
Indices: 12468204--12468311 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
12468194 TTGGACGTTT
* *
12468204 AGTTGATTTAGGGGTTTTAGTGACTAGGTTC
1 AGTTGATTTAGGGGTTCTAGAGA-TAGGTTC
* * * *
12468235 AGTTAATTTAGAGGTTCTAGAGATTGTTTC
1 AGTTGATTTAGGGGTTCTAGAGATAGGTTC
** * * * *
12468265 AGTTGATTTAGGATTTTTAAATATTGAGTTC
1 AGTTGATTTAGGGGTTCTAGAGATAG-GTTC
12468296 AGTTGATTTAGGGGTT
1 AGTTGATTTAGGGGTT
12468312 TAAAAGAATG
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
30 24 0.40
31 36 0.60
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (30 bp):
AGTTGATTTAGGGGTTCTAGAGATAGGTTC
Found at i:12472498 original size:61 final size:61
Alignment explanation
Indices: 12472381--12472545 Score: 176
Period size: 61 Copynumber: 2.7 Consensus size: 61
12472371 TGCTTTTATA
* * * * * *
12472381 CAAGGAAAATTGATACTTTCAACTTTTCTTTAAAA-ATGTTTTTCTTGATAATTTTTATTTT
1 CAAGAAAAATTG-TACTTTCAACTTTTCCTCAAAATATTTTTTTCCTGATAATTTTTAATTT
*
12472442 TAAGAAAAATTTGTACTTTCAACTTTTCCTCAAAAATATTTTTTTCCTGA-AA-TTTTAATTT
1 CAAGAAAAA-TTGTACTTTCAACTTTTCCTC-AAAATATTTTTTTCCTGATAATTTTTAATTT
* *
12472503 CAAGGAAAATTG-ATCTTTTCAACTTTTCCTCAAAATACTTTTT
1 CAAGAAAAATTGTA-C-TTTCAACTTTTCCTCAAAATATTTTTT
12472546 GAAAATTTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
59 1 0.01
60 15 0.17
61 53 0.60
62 9 0.10
63 11 0.12
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (61 bp):
CAAGAAAAATTGTACTTTCAACTTTTCCTCAAAATATTTTTTTCCTGATAATTTTTAATTT
Found at i:12472570 original size:72 final size:73
Alignment explanation
Indices: 12472490--12472628 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 73
12472480 TTTTTTTCCT
* * * *
12472490 GAAATTTTAATTTCAAGGAAAATTGATCTTTTCAACTTTT-CCTCAAAATACT-TTTTGAAAATT
1 GAAATTTTAATTTCAAAGAAAATTAATATTTTCAACTTTTCCCTAAAAATA-TATTTTGAAAATT
12472553 TTTATTTTA
65 TTTATTTTA
* * *
12472562 GAAATTTTATTTTCAAAGAATATTAATATTTTCAACTTTTCCCTAAAAATATATTTTTAAAATTT
1 GAAATTTTAATTTCAAAGAAAATTAATATTTTCAACTTTTCCCTAAAAATATATTTTGAAAATTT
12472627 TT
66 TT
12472629 TATTATTTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
72 36 0.62
73 22 0.38
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (73 bp):
GAAATTTTAATTTCAAAGAAAATTAATATTTTCAACTTTTCCCTAAAAATATATTTTGAAAATTT
TTATTTTA
Found at i:12479232 original size:3 final size:3
Alignment explanation
Indices: 12479219--12479260 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
12479209 TTAAATATAT
* *
12479219 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12479261 ATTTTCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:12480370 original size:14 final size:14
Alignment explanation
Indices: 12480351--12480381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12480341 TGATCAAATT
12480351 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
12480365 AAAAAAAAACAAAG
1 AAAAAAAAAAAAAG
12480379 AAA
1 AAA
12480382 GCTTGAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:12482247 original size:15 final size:16
Alignment explanation
Indices: 12482220--12482254 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
12482210 ATCTTGTAAA
12482220 TTCTCTCAAATTCTAC
1 TTCTCTCAAATTCTAC
*
12482236 TTCTCT-AAATTCTTC
1 TTCTCTCAAATTCTAC
12482251 TTCT
1 TTCT
12482255 TTACTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (16 bp):
TTCTCTCAAATTCTAC
Found at i:12486493 original size:16 final size:16
Alignment explanation
Indices: 12486469--12486503 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12486459 CTTAAGATTT
*
12486469 TTTTTAGGACTTTGGA
1 TTTTAAGGACTTTGGA
*
12486485 TTTTAAGGATTTTGGA
1 TTTTAAGGACTTTGGA
12486501 TTT
1 TTT
12486504 CGGGGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTTAAGGACTTTGGA
Found at i:12486532 original size:16 final size:15
Alignment explanation
Indices: 12486474--12486536 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
12486464 GATTTTTTTT
*
12486474 AGGACTTTGGATTTTA
1 AGGATTTTGGA-TTTA
*
12486490 AGGATTTTGGATTTCGG
1 AGGATTTTGGATTT--A
* *
12486507 GGGGTTTTGGATTTA
1 AGGATTTTGGATTTA
12486522 ATGGATTTTGGATTT
1 A-GGATTTTGGATTT
12486537 TTAGGGGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
15 3 0.08
16 22 0.59
17 12 0.32
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (15 bp):
AGGATTTTGGATTTA
Found at i:12486544 original size:33 final size:33
Alignment explanation
Indices: 12486479--12486547 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
12486469 TTTTTAGGAC
*
12486479 TTTGGATTTTAAGGATTTTGGATTTCGGGGGGT
1 TTTGGATTTTAAGGATTTTGGATTTCGAGGGGT
**
12486512 TTTGGA-TTTAATGGATTTTGGATTTTTAGGGGT
1 TTTGGATTTTAA-GGATTTTGGATTTCGAGGGGT
12486545 TTT
1 TTT
12486548 AGAATCCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.16, C:0.01, G:0.32, T:0.51
Consensus pattern (33 bp):
TTTGGATTTTAAGGATTTTGGATTTCGAGGGGT
Found at i:12487933 original size:21 final size:21
Alignment explanation
Indices: 12487899--12487940 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12487889 CTGAGAGAGC
12487899 TGGTCAGGGGGTTGGTTGGGT
1 TGGTCAGGGGGTTGGTTGGGT
12487920 TGGTC-GGGGAGTTGGTTGGGT
1 TGGTCAGGGG-GTTGGTTGGGT
12487941 GGCTGACAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.05, C:0.05, G:0.57, T:0.33
Consensus pattern (21 bp):
TGGTCAGGGGGTTGGTTGGGT
Found at i:12489325 original size:15 final size:16
Alignment explanation
Indices: 12489299--12489333 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
12489289 ATCTTTTAAA
12489299 TTCTCTTAAATTTTTC
1 TTCTCTTAAATTTTTC
12489315 TTCTC-TAAATTTTTC
1 TTCTCTTAAATTTTTC
12489330 TTCT
1 TTCT
12489334 TTATCAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (16 bp):
TTCTCTTAAATTTTTC
Found at i:12493028 original size:125 final size:125
Alignment explanation
Indices: 12492888--12493150 Score: 409
Period size: 125 Copynumber: 2.1 Consensus size: 125
12492878 TATTGATGGC
* * * *
12492888 GTTTATTCTAGAAAAATACCTTGACTAATTCGTTTTATTTTTTGAAAAAATTTATTGAAGGCATC
1 GTTTATTTTAGAAAAATACCTTGACTAATTCATTTTATTTTCTGAAAAAATTTACTGAAGGCATC
* * * * *
12492953 TTCTAGTGCAAAACGCCTTCAATGTTCCACTATTCAAATTTTAAGACGGTTAGTAAAGGT
66 TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
*
12493013 GTTTATTTTAGAAAAATACCTTGACTAATTCATTTTATTTTCTGAAGAAATTTACTGAAGGCATC
1 GTTTATTTTAGAAAAATACCTTGACTAATTCATTTTATTTTCTGAAAAAATTTACTGAAGGCATC
* * *
12493078 TTATAATATAAAACGCTTTTAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
66 TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
12493138 GTTTATTTTAGAA
1 GTTTATTTTAGAA
12493151 GAAAAAATTT
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (125 bp):
GTTTATTTTAGAAAAATACCTTGACTAATTCATTTTATTTTCTGAAAAAATTTACTGAAGGCATC
TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
Found at i:12493197 original size:125 final size:125
Alignment explanation
Indices: 12492888--12493201 Score: 362
Period size: 125 Copynumber: 2.5 Consensus size: 125
12492878 TATTGATGGC
* ** * ** * *
12492888 GTTTATTCTAGAAAAATACCTTGACTAATTCGTTTTATTTTTTGAAAAAATTTATTGAAGGCATC
1 GTTTATTTTAGAAAAATAAATTGACTAATTCATTTTAAGTTATGAACAAATTTATTGAAGGCATC
* * * * *
12492953 TTCTAGTGCAAAACGCCTTCAATGTTCCACTATTCAAATTTTAAGACGGTTAGTAAAGGT
66 TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
** ** * * *
12493013 GTTTATTTTAGAAAAATACCTTGACTAATTCATTTTATTTTCTGAAGAAATTTACTGAAGGCATC
1 GTTTATTTTAGAAAAATAAATTGACTAATTCATTTTAAGTTATGAACAAATTTATTGAAGGCATC
* * *
12493078 TTATAATATAAAACGCTTTTAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
66 TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
* * *
12493138 GTTTATTTTAGAAGAAA-AAATTTACTAATTCCTTTTAAGTTATGTACATAA-TTATTGAAGGCA
1 GTTTATTTTAGAA-AAATAAATTGACTAATTCATTTTAAGTTATGAACA-AATTTATTGAAGGCA
12493201 T
64 T
12493202 TTTTTGAAAA
Statistics
Matches: 164, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
125 159 0.97
126 5 0.03
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (125 bp):
GTTTATTTTAGAAAAATAAATTGACTAATTCATTTTAAGTTATGAACAAATTTATTGAAGGCATC
TTATAATACAAAACGCCTTCAATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGT
Found at i:12493664 original size:186 final size:186
Alignment explanation
Indices: 12493098--12493898 Score: 837
Period size: 185 Copynumber: 4.3 Consensus size: 186
12493088 AAACGCTTTT
* * * * * * *
12493098 AATATTCCACTATTCAAATTTTAAGACAGTTAGTAAAGGTGTTTATTTTAGAAGAAAA-A-ATTT
1 AATATTCCACTACTCAAATTTTAAGACGGTTAGTGAAGGCGTTTATTCTA-AA-AAAACACCTTC
* * * * * *
12493161 ACTAATTCCTTTTAAGTTATGTACATAATTATTGAAGGCATTTTTTGAAAACAAA-TGCCTTCAA
64 AATAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACT-CCTTCAA
* ** * * * *
12493225 TAATTTCATTTTAAAAATTTTTGGGATTATTAAATGCGTCTTCTACTTAAAAACACCTTC
128 TAATTTC-TTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * * * * * *
12493285 AGTATACCAGTACTCAAAATTTAAGACAGG-TAGTGAAGGCATTTATTCCAAAAAAAATACCTTC
1 AATATTCCACTACTCAAATTTTAAGAC-GGTTAGTGAAGGCGTTTATT-CTAAAAAAACACCTTC
* * * *
12493349 AATAATTCTTTTTAAATTTTGTACATAATTATTAAAGGCATATTTTTGGAACAAACGCCTTCAAT
64 AATAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAAT
* * * *
12493414 AATTT-TTTTAAAAAATTTTTAAGATTATTAAAGACATCTTTCAGTGAAAAACACCTTT
129 AATTTCTTTTAAAAAA-TTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * * * * *
12493472 AATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTGTTTATTTTAGAAAAACACTTTCAT
1 AATATTCCACTACTCAAATTTTAAGACGGTTAGTGAAGGCGTTTATTCTAAAAAAACACCTTCAA
* * * * ** *
12493537 TGATTCCATTT-AATTTATGTACATAATTATTGAA-GTATTTTTTTAGAACAAACTTTTTTAATA
66 TAATTCCTTTTAAATTT-TGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATA
* * **
12493600 ATTTCATTTTAAAAAATTTTAGGATTATTAAAGGCGTCTTCCAATGAAAAATGCCTTC
130 ATTTC-TTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * *
12493658 AATATTCTACTACTCAAA-CTTAAGACGATTAGTGAA-GCGTTTATTCTAAAAAAACACCTTCAA
1 AATATTCCACTACTCAAATTTTAAGACGGTTAGTGAAGGCGTTTATTCTAAAAAAACACCTTCAA
* * **
12493721 TAATTCTTTTTAAATTTTGTACATAATTATTAAATGCATTTTTTTAGAACAAACAACTTCAATAA
66 TAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATAA
* * * *
12493786 TTTTCTTTTAAAAAGTTTTAAGATTATTAAAGGTGTCTTCTAGTGAAAAACACATTC
131 -TTTCTTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * * * *
12493843 AATATTTCAGTACTCAAATTTTAACACGGTTAGTGAAGGCATTTATTCCAAAAAAA
1 AATATTCCACTACTCAAATTTTAAGACGGTTAGTGAAGGCGTTTATTCTAAAAAAA
12493899 TGACTTCACT
Statistics
Matches: 499, Mismatches: 100, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
184 46 0.09
185 135 0.27
186 121 0.24
187 134 0.27
188 63 0.13
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (186 bp):
AATATTCCACTACTCAAATTTTAAGACGGTTAGTGAAGGCGTTTATTCTAAAAAAACACCTTCAA
TAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATAA
TTTCTTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
Found at i:12493767 original size:185 final size:186
Alignment explanation
Indices: 12493098--12493898 Score: 803
Period size: 187 Copynumber: 4.3 Consensus size: 186
12493088 AAACGCTTTT
* * ** * *
12493098 AATATTCCACTATTCAAATTTTAAGAC-AGTTAGTAAAGGTGTTTATTTTAGAAGAAAA-A-ATT
1 AATATTCCACTACTCAAATTTTAAGACGA-TTAGTGAAGGCATTTATTCTA-AA-AAAACACCTT
* * * * * * *
12493160 TACTAATTCCTTTTAAGTTATGTACATAATTATTGAAGGCATTTTTTGAAAACAAA-TGCCTTCA
63 CAATAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACT-CCTTCA
* ** * * * *
12493224 ATAATTTCATTTTAAAAATTTTTGGGATTATTAAATGCGTCTTCTACTTAAAAACACCTTC
127 ATAATTTC-TTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * * * * * *
12493285 AGTATACCAGTACTCAAAATTTAAGAC-AGGTAGTGAAGGCATTTATTCCAAAAAAAATACCTTC
1 AATATTCCACTACTCAAATTTTAAGACGA-TTAGTGAAGGCATTTATT-CTAAAAAAACACCTTC
* * * *
12493349 AATAATTCTTTTTAAATTTTGTACATAATTATTAAAGGCATATTTTTGGAACAAACGCCTTCAAT
64 AATAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAAT
* * * *
12493414 AATTT-TTTTAAAAAATTTTTAAGATTATTAAAGACATCTTTCAGTGAAAAACACCTTT
129 AATTTCTTTTAAAAAA-TTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * ** * * * *
12493472 AATATTCCACTACTCAAATTTTAAGATGGTTAGTGAAGGTGTTTATTTTAGAAAAACACTTTCAT
1 AATATTCCACTACTCAAATTTTAAGACGATTAGTGAAGGCATTTATTCTAAAAAAACACCTTCAA
* * * * ** *
12493537 TGATTCCATTT-AATTTATGTACATAATTATTGAA-GTATTTTTTTAGAACAAACTTTTTTAATA
66 TAATTCCTTTTAAATTT-TGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATA
* * **
12493600 ATTTCATTTTAAAAAATTTTAGGATTATTAAAGGCGTCTTCCAATGAAAAATGCCTTC
130 ATTTC-TTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * *
12493658 AATATTCTACTACTCAAA-CTTAAGACGATTAGTGAA-GCGTTTATTCTAAAAAAACACCTTCAA
1 AATATTCCACTACTCAAATTTTAAGACGATTAGTGAAGGCATTTATTCTAAAAAAACACCTTCAA
* * **
12493721 TAATTCTTTTTAAATTTTGTACATAATTATTAAATGCATTTTTTTAGAACAAACAACTTCAATAA
66 TAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATAA
* * * *
12493786 TTTTCTTTTAAAAAGTTTTAAGATTATTAAAGGTGTCTTCTAGTGAAAAACACATTC
131 -TTTCTTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
* * * * *
12493843 AATATTTCAGTACTCAAATTTTAACACGGTTAGTGAAGGCATTTATTCCAAAAAAA
1 AATATTCCACTACTCAAATTTTAAGACGATTAGTGAAGGCATTTATTCTAAAAAAA
12493899 TGACTTCACT
Statistics
Matches: 498, Mismatches: 102, Indels: 28
0.79 0.16 0.04
Matches are distributed among these distances:
184 46 0.09
185 135 0.27
186 119 0.24
187 136 0.27
188 62 0.12
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (186 bp):
AATATTCCACTACTCAAATTTTAAGACGATTAGTGAAGGCATTTATTCTAAAAAAACACCTTCAA
TAATTCCTTTTAAATTTTGTACATAATTATTAAAGGCATTTTTTTAGAACAAACTCCTTCAATAA
TTTCTTTTAAAAAATTTTAAGATTATTAAAGGCGTCTTCCAGTGAAAAACACCTTC
Found at i:12494603 original size:12 final size:12
Alignment explanation
Indices: 12494586--12494613 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12494576 GATATTGGTA
12494586 TGCTGAATCATT
1 TGCTGAATCATT
12494598 TGCTGAATCATT
1 TGCTGAATCATT
12494610 TGCT
1 TGCT
12494614 AAATGATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (12 bp):
TGCTGAATCATT
Found at i:12496494 original size:14 final size:13
Alignment explanation
Indices: 12496472--12496524 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 13
12496462 CCAATTTTGC
*
12496472 TTTTATTTTGTAT
1 TTTTATTTTATAT
12496485 TTTATATTTT-T-T
1 TTT-TATTTTATAT
*
12496497 TATTATTTT-TA-
1 TTTTATTTTATAT
12496508 TTTTATTTTATAT
1 TTTTATTTTATAT
12496521 TTTT
1 TTTT
12496525 TTCTTTGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 15 0.44
12 5 0.15
13 8 0.24
14 6 0.18
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTATTTTATAT
Found at i:12496499 original size:10 final size:9
Alignment explanation
Indices: 12496484--12496526 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
12496474 TTATTTTGTA
12496484 TTTTATATTT
1 TTTTAT-TTT
*
12496494 TTTTATTAT
1 TTTTATTTT
12496503 TTTTATTTT
1 TTTTATTTT
12496512 ATTTTATATTT
1 -TTTTAT-TTT
12496523 TTTT
1 TTTT
12496527 CTTTGTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 10 0.34
10 16 0.55
11 3 0.10
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTTT
Found at i:12496521 original size:18 final size:18
Alignment explanation
Indices: 12496472--12496524 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
12496462 CCAATTTTGC
*
12496472 TTTTATTTTGTA-TTTTA
1 TTTTATTTTATATTTTTA
12496489 TATTT-TTTTATTATTTTTA
1 T-TTTATTTTA-TATTTTTA
12496508 TTTTATTTTATATTTTT
1 TTTTATTTTATATTTTT
12496525 TTCTTTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.16
18 15 0.48
19 11 0.35
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTATTTTATATTTTTA
Found at i:12496525 original size:19 final size:19
Alignment explanation
Indices: 12496472--12496525 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
12496462 CCAATTTTGC
* *
12496472 TTTTATTTTGTATTTTATA
1 TTTTATTTTATATTTTTTA
12496491 -TTT-TTTTAT-TATTTTTA
1 TTTTATTTTATAT-TTTTTA
12496508 TTTTATTTTATATTTTTT
1 TTTTATTTTATATTTTTT
12496526 TCTTTGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 6 0.21
19 11 0.38
20 1 0.03
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTATTTTATATTTTTTA
Found at i:12496690 original size:26 final size:25
Alignment explanation
Indices: 12496633--12496806 Score: 90
Period size: 25 Copynumber: 7.2 Consensus size: 25
12496623 TTTCTGTTAA
*
12496633 TATTTATATATGTATTTTATTTATC
1 TATTTATATATTTATTTTATTTATC
*
12496658 TAGTTATATATTTATTATTATTTAT-
1 TATTTATATATTTATT-TTATTTATC
*
12496683 TCATTTATATA-TTA--TGATTTATC
1 T-ATTTATATATTTATTTTATTTATC
*
12496706 T-GTTATTATTATTT-TTTTATTTATC
1 TATTTA-TA-TATTTATTTTATTTATC
*
12496731 T-TGTA-ATA-TT-TTTTATTT-TC
1 TATTTATATATTTATTTTATTTATC
*
12496751 T-TATTAT-T-TTT-TTTCTAATTATC
1 TAT-TTATATATTTATTT-TATTTATC
* *
12496774 TATTAATATTTTTTTATTTTATTTATC
1 TATT--TATATATTTATTTTATTTATC
12496801 TGATTT
1 T-ATTT
12496807 TCTTTTTCTT
Statistics
Matches: 118, Mismatches: 11, Indels: 39
0.70 0.07 0.23
Matches are distributed among these distances:
20 4 0.03
21 21 0.18
22 15 0.13
23 8 0.07
24 3 0.03
25 32 0.27
26 18 0.15
27 11 0.09
28 6 0.05
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (25 bp):
TATTTATATATTTATTTTATTTATC
Found at i:12496743 original size:22 final size:21
Alignment explanation
Indices: 12496647--12496792 Score: 82
Period size: 21 Copynumber: 6.4 Consensus size: 21
12496637 TATATATGTA
12496647 TTTTATTTATCTAGTTATATATTT
1 TTTTATTTATCT--TTA-ATATTT
*
12496671 ATTATTATTTATTCATTT-ATATAT
1 -TT-TTATTTA-TC-TTTAATATTT
* *
12496695 TATGATTTATCTGTTATTATTATTT
1 TTTTATTTATCT-TTA--A-TATTT
12496720 TTTTATTTATCTTGTAATA-TT
1 TTTTATTTATCTT-TAATATTT
* *
12496741 TTTTATTT-TCTTATTATTTTT
1 TTTTATTTATCTT-TAATATTT
*
12496762 TTTCTAATTATCTATTAATATTT
1 TTT-TATTTATCT-TTAATATTT
12496785 TTTTATTT
1 TTTTATTT
12496793 TATTTATCTG
Statistics
Matches: 95, Mismatches: 13, Indels: 29
0.69 0.09 0.21
Matches are distributed among these distances:
20 8 0.08
21 19 0.20
22 16 0.17
23 14 0.15
24 8 0.08
25 18 0.19
26 9 0.09
27 2 0.02
28 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTATTTATCTTTAATATTT
Found at i:12496755 original size:43 final size:44
Alignment explanation
Indices: 12496708--12496793 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
12496698 GATTTATCTG
*
12496708 TTATTATTATTTTTT-TATTTATCT-TGTAATA-TTTTTTATTTTC
1 TTATTATT-TTTTTTCTAATTATCTAT-TAATATTTTTTTATTTTC
12496751 TTATTATTTTTTTTCTAATTATCTATTAATATTTTTTTATTTT
1 TTATTATTTTTTTTCTAATTATCTATTAATATTTTTTTATTTT
12496794 ATTTATCTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
42 6 0.15
43 21 0.54
44 12 0.31
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (44 bp):
TTATTATTTTTTTTCTAATTATCTATTAATATTTTTTTATTTTC
Found at i:12497676 original size:3 final size:3
Alignment explanation
Indices: 12497670--12497724 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
12497660 CGTTTTCATT
*
12497670 TTA TTA TTT TTA TTA TT- TTA TT- TTA TT- TTA TTTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA
12497714 TTA TTA -TA TTA
1 TTA TTA TTA TTA
12497725 GGGTTGTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 8 0.18
3 30 0.67
4 7 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:12497679 original size:14 final size:14
Alignment explanation
Indices: 12497670--12497724 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 14
12497660 CGTTTTCATT
12497670 TTATTATTTTTATTA
1 TTATTA-TTTTATTA
12497685 TT-TTATTTTATT-
1 TTATTATTTTATTA
12497697 TTATT-TATTTATTA
1 TTATTAT-TTTATTA
*
12497711 TTATTATTATATTA
1 TTATTATTTTATTA
12497725 GGGTTGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.09
13 15 0.43
14 14 0.40
15 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATTTTATTA
Found at i:12497717 original size:27 final size:27
Alignment explanation
Indices: 12497662--12497805 Score: 81
Period size: 27 Copynumber: 5.5 Consensus size: 27
12497652 TTTTTTTTCG
*
12497662 TTTTCATTTTATTATTTTTATTATT-TTA
1 TTTT-ATTTTATT-TATTTATTATTATTA
12497690 TTTTATTTTATTTATTTATTATTATTA
1 TTTTATTTTATTTATTTATTATTATTA
* **** *
12497717 TTATATTAGGGTTGTTTA--A-TATT-
1 TTTTATTTTATTTATTTATTATTATTA
* *
12497740 TTTTCTATTATTTATTTATT-TT-TTA
1 TTTTATTTTATTTATTTATTATTATTA
*
12497765 -TTTA-TTTATTTATTTTATTCTTATTTA
1 TTTTATTTTATTTA-TTTATTATTA-TTA
* *
12497792 TTTCATTTTCTTTA
1 TTTTATTTTATTTA
12497806 AATAAAATTA
Statistics
Matches: 86, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
23 17 0.20
24 15 0.17
25 4 0.05
26 10 0.12
27 26 0.30
28 7 0.08
29 7 0.08
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (27 bp):
TTTTATTTTATTTATTTATTATTATTA
Found at i:12497756 original size:4 final size:4
Alignment explanation
Indices: 12497747--12497799 Score: 63
Period size: 4 Copynumber: 12.5 Consensus size: 4
12497737 ATTTTTTCTA
12497747 TTAT TTAT TTAT TT-T TTAT TTAT TTAT TTATT TTATT CTTAT TTAT TTCAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA-T -TTAT TTAT TT-AT
12497798 TT
1 TT
12497800 TCTTTAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.07
4 28 0.62
5 11 0.24
6 3 0.07
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:12497767 original size:15 final size:15
Alignment explanation
Indices: 12497747--12497794 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 15
12497737 ATTTTTTCTA
12497747 TTATTTATTTATTTT
1 TTATTTATTTATTTT
12497762 TTATTTATTTATTTATT
1 TTATTTATTTA-TT-TT
12497779 TTATTCTTATTTATTT
1 TTA-T-TTATTTATTT
12497795 CATTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.38
16 2 0.07
17 6 0.21
18 3 0.10
19 7 0.24
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTATTTATTTT
Found at i:12497791 original size:19 final size:19
Alignment explanation
Indices: 12497667--12497800 Score: 104
Period size: 19 Copynumber: 7.3 Consensus size: 19
12497657 TTTCGTTTTC
12497667 ATTTTATTATT-TTTA-TT
1 ATTTTATTATTATTTATTT
12497684 ATTTTATT-TTATTTTATTT
1 ATTTTATTATTA-TTTATTT
12497703 A-TTTATTATTA-TTA-TT
1 ATTTTATTATTATTTATTT
* *** * *
12497719 ATATTAGGGTTGTTTA-AT
1 ATTTTATTATTATTTATTT
*
12497737 ATTTTTTCTATTATTTATTT
1 ATTTTAT-TATTATTTATTT
12497757 ATTTT-TTATTTATTTATTT
1 ATTTTATTA-TTATTTATTT
*
12497776 ATTTTATTCTTATTTATTT
1 ATTTTATTATTATTTATTT
12497795 CATTTT
1 -ATTTT
12497801 CTTTAAATAA
Statistics
Matches: 92, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.05
17 16 0.17
18 20 0.22
19 38 0.41
20 13 0.14
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (19 bp):
ATTTTATTATTATTTATTT
Found at i:12497927 original size:29 final size:29
Alignment explanation
Indices: 12497835--12497927 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
12497825 CAAAAAAACA
12497835 TTTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATT
* * * * ** ****
12497864 TTTCTTAAGAATAAATTTTCAAAAAAAGGTTT
1 TTT-TTGAGGA-AAA-GTTGAAAGTATCAATT
12497896 TTTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTTTGAGGAAAAGTTGAAAGTATCAATT
12497925 TTT
1 TTT
12497928 CTCAAAATTA
Statistics
Matches: 41, Mismatches: 20, Indels: 6
0.61 0.30 0.09
Matches are distributed among these distances:
29 14 0.34
30 8 0.20
31 8 0.20
32 11 0.27
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTTTGAGGAAAAGTTGAAAGTATCAATT
Found at i:12497959 original size:120 final size:117
Alignment explanation
Indices: 12497826--12498459 Score: 694
Period size: 120 Copynumber: 5.4 Consensus size: 117
12497816 AAAAAAAAAC
*
12497826 AAAAAAACATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAA
1 AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTTAA-AATAAATTTTC-AAAAA
* * * *
12497890 AGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAATTCC
64 A-G-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAATTTCA
* * * *
12497946 AAAGAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATCTTCAAAAAG
1 AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTTAA-AATAAATTTTCAAAAAA
* * *
12498010 GTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAACGATTTCA
65 GTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAA-AATTTCA
* * * *
12498064 AAAAAAATATTTTT-AGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAGAATTTCAAAAA
1 AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCT-TAAAATAA-ATTTTC-AAAA
* * * *
12498128 GAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCA
63 -AAGTATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAATTTCA
* * * *
12498184 AAAAAAAAATTTTTGAG-GAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAA
1 AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCT-TAAAATAAA-TTTTCAAAAA
* * **
12498248 A-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TAAGCTTTCCA
64 AGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TCAAAATTAAAATTT-CA
* * *
12498302 CAAAAAAATATTTTTTG-GAGAAAAGTTGAAAGTAACAATTTTCCTTAAAAATAAGTTTTCAAAA
1 -AAAAAAATA-TTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAATTTTCAAAA
* * * * *
12498366 ATGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTC-
63 AAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAATTTCA
* *
12498420 AAAAGAATATTTTTG-GAGAAAAATTGAAAGTATCAATTTT
1 AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTT
12498460 CTCTACACAA
Statistics
Matches: 445, Mismatches: 51, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
116 29 0.07
117 88 0.20
118 60 0.13
119 42 0.09
120 186 0.42
121 40 0.09
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (117 bp):
AAAAAAATATTTTTGAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAATTTTCAAAAAAG
TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAATTTCA
Found at i:12498088 original size:238 final size:234
Alignment explanation
Indices: 12497824--12498459 Score: 773
Period size: 238 Copynumber: 2.7 Consensus size: 234
12497814 TAAAAAAAAA
* *
12497824 ACAAAAAAACATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAA
1 ACAAAAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTTCAAAAA
* * *
12497889 AAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAAATTCCAAAGAAAT
64 AA-G-TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTTCAAAAGAAAT
* * *
12497954 ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTTCT-TAAGAATAAA-TCTTCAAAAAGGTTTTTT
127 ATTTTT-GGGAAAAGTTGAAAGTATCAATTTTTCTCGAA-AATAAAGTCTTCAAAAA-ATATTTT
* *
12498017 TGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAACGATTT-C
189 TGAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAA-GATTTCC
* * *
12498063 A-AAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAGAATTTCAAAA
1 ACAAAAAAATATTTTT-GAGAAAAGTTGAAAGTATCAATTTTCCT-TAAAATAA-ATTTTCAAAA
* * * * * *
12498127 AGAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAA
63 A-AAGTATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTTCAAAAGAAA
* * * *
12498191 AATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAAATATTTTT
126 TATTTTTG-GGAAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAGTCTTCAAAAAATATTTTT
* *
12498256 GAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCC
190 GAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAAATAAGATTTCC
* *
12498301 ACAAAAAAATATTTTTTGGAGAAAAGTTGAAAGTAACAATTTTCCTTAAAAATAAGTTTTC-AAA
1 ACAAAAAAATA-TTTTT-GAGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTTTCAAAA
* * * *
12498365 AATGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTCAAAAG-AATA
63 AAAGTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTTCAAAAGAAATA
*
12498429 TTTTTGGAGAAAAATTGAAAGTATCAATTTT
128 TTTTTGG-GAAAAGTTGAAAGTATCAATTTT
12498460 CTCTACACAA
Statistics
Matches: 339, Mismatches: 44, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
235 1 0.00
236 30 0.09
237 53 0.16
238 176 0.52
239 39 0.12
240 40 0.12
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (234 bp):
ACAAAAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTCAAAAAAA
GTATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTTCAAAAGAAATATTT
TTGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAAATAAAGTCTTCAAAAAATATTTTTGAGAAA
AAGTTGAAAGTATCAATTTTCCTCGAAAATAAGATTTCC
Found at i:12498375 original size:178 final size:177
Alignment explanation
Indices: 12497825--12498460 Score: 797
Period size: 178 Copynumber: 3.6 Consensus size: 177
12497815 AAAAAAAAAA
* * * *
12497825 CAAAAAA-ACATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCT-TAAGAATAAATTTTCAAAA
1 CAAAAAAGA-ATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAA-ATTAAAATTTCAAAA
* * * * * * *
12497888 AAAGGTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TCAAAATTAAAAATTC-CAAAGA
64 AAA---TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TAAGATTTCACAAAAA
* * *
12497951 AATATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATCTT
125 AATATTTTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* ** * * *
12498003 CAAAAAGGTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAACGATTTCAAAAA
1 CAAAAAAGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAA-AATTTC-AAAA
* *
12498068 AAATATTTTT-AGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAGAATTTCA-AAAAGAA
64 AAATATTTTTGAGA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-ATTTCACAAAA-AA
12498131 ATATTTTTAGGA-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
126 ATATTTTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* *
12498182 CAAAAAAAAAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTTC-AAA
1 C-AAAAAAGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAA-ATTTCAAAA
*
12498246 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCCACAAAAAAAT
64 AAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTT-CACAAAAAAAT
* * *
12498311 ATTTTTTGGAGAAAAGTTGAAAGTAACAATTTTCCTTAAAAATAAGTTTT
128 ATTTTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* *
12498361 CAAAAATGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTCAAAAGA
1 CAAAAAAGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTCAAAAAA
12498426 ATATTTTTGGAGAAAAA-TTGAAAGTATCAATTTTC
66 ATATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTC
12498461 TCTACACAAA
Statistics
Matches: 402, Mismatches: 38, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
176 2 0.00
177 39 0.10
178 195 0.49
179 109 0.27
180 57 0.14
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (177 bp):
CAAAAAAGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTCAAAAAA
ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGATTTCACAAAAAAATATT
TTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
Found at i:12508733 original size:9 final size:9
Alignment explanation
Indices: 12508719--12508870 Score: 72
Period size: 9 Copynumber: 15.8 Consensus size: 9
12508709 CGCTCCAGAT
*
12508719 TTTTTTTTC
1 TTTTTTTTA
12508728 TTTTTTTTA
1 TTTTTTTTA
*
12508737 TTATTTTTA
1 TTTTTTTTA
*
12508746 TTATTTTTA
1 TTTTTTTTA
*
12508755 TTTTATTTA
1 TTTTTTTTA
12508764 TTTATTTATTA
1 TTT-TTT-TTA
* *
12508775 -TTATATTA
1 TTTTTTTTA
* * *
12508783 GGGTTGTTTAA
1 --TTTTTTTTA
*
12508794 TATTTTTTA
1 TTTTTTTTA
12508803 TTTTTTATTTA
1 -TTTTT-TTTA
12508814 TTTTCATTTTA
1 TTTT--TTTTA
*
12508825 TTTATTCTTA
1 TTT-TTTTTA
12508835 TTTTATTCTTA
1 TTTT-TT-TTA
*
12508846 TTTATTTTA
1 TTTTTTTTA
* *
12508855 TTTATTTCA
1 TTTTTTTTA
12508864 TTTTTTT
1 TTTTTTT
12508871 AAATAAAATT
Statistics
Matches: 111, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
8 3 0.03
9 59 0.53
10 22 0.20
11 25 0.23
12 2 0.02
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:12508752 original size:18 final size:20
Alignment explanation
Indices: 12508731--12508857 Score: 77
Period size: 19 Copynumber: 6.2 Consensus size: 20
12508721 TTTTTTCTTT
12508731 TTTTTATTATT-TTTA-TTA
1 TTTTTATTATTATTTATTTA
12508749 TTTTTATT-TTATTTATTTA
1 TTTTTATTATTATTTATTTA
* *
12508768 TTTATTATTATATTAGGGTTGTTTAA
1 TTT-TTA-T-TATTA--TTTATTT-A
*
12508794 TATTTT-TTATTTTTTATTTA
1 T-TTTTATTATTATTTATTTA
*
12508814 TTTTCATT-TTATTTATTCT-
1 TTTTTATTATTATTTATT-TA
*
12508833 TATTTTATTCTTATTTATTTTA
1 T-TTTTATTATTATTTA-TTTA
12508855 TTT
1 TTT
12508858 ATTTCATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 29
0.70 0.07 0.24
Matches are distributed among these distances:
17 2 0.02
18 12 0.14
19 18 0.21
20 14 0.16
21 16 0.19
22 4 0.05
23 7 0.08
24 1 0.01
25 5 0.06
26 4 0.05
27 2 0.02
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.73
Consensus pattern (20 bp):
TTTTTATTATTATTTATTTA
Found at i:12508757 original size:15 final size:15
Alignment explanation
Indices: 12508737--12508853 Score: 55
Period size: 15 Copynumber: 7.5 Consensus size: 15
12508727 CTTTTTTTTA
12508737 TTATTTTTATTATTT
1 TTATTTTTATTATTT
*
12508752 TTA-TTTTATT-TAT
1 TTATTTTTATTATTT
*
12508765 TTATTTATTATTA-TA
1 TTATTT-TTATTATTT
*
12508780 TTAGGGTTGTTTAATATTTT
1 TTA---TT-TTTATTA-TTT
12508800 TTATTTTTTATTTATTT
1 TTA-TTTTTA-TTATTT
* *
12508817 TCA-TTTTATTTATTC
1 TTATTTTTA-TTATTT
*
12508832 TTA-TTTTATTCTTAT
1 TTATTTTTATTATT-T
12508847 TTATTTT
1 TTATTTT
12508854 ATTTATTTCA
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
13 5 0.06
14 13 0.17
15 32 0.41
16 3 0.04
17 9 0.12
18 11 0.14
19 1 0.01
20 4 0.05
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (15 bp):
TTATTTTTATTATTT
Found at i:12508822 original size:6 final size:5
Alignment explanation
Indices: 12508798--12508867 Score: 65
Period size: 5 Copynumber: 13.8 Consensus size: 5
12508788 GTTTAATATT
*
12508798 TTTTA TTTTT TATTTA TTTTCA TTTTA -TTTA TTCTTA TTTTA TTCTTA
1 TTTTA TTTTA T-TTTA TTTT-A TTTTA TTTTA TT-TTA TTTTA TT-TTA
*
12508846 -TTTA TTTTA -TTTA TTTCA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
12508868 TTTAAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
4 11 0.20
5 26 0.48
6 17 0.31
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:12508837 original size:21 final size:20
Alignment explanation
Indices: 12508806--12508857 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
12508796 TTTTTTATTT
12508806 TTTA-TTTATTTTCATT-TTA
1 TTTATTTTATTTT-ATTCTTA
12508825 TTTATTCTTATTTTATTCTTA
1 TTTATT-TTATTTTATTCTTA
12508846 TTTATTTTATTT
1 TTTATTTTATTT
12508858 ATTTCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.13
20 10 0.33
21 16 0.53
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTTTATTTTATTCTTA
Found at i:12508978 original size:58 final size:57
Alignment explanation
Indices: 12508889--12509331 Score: 443
Period size: 58 Copynumber: 7.6 Consensus size: 57
12508879 TTAAAAAAAA
*
12508889 CAAAAAAACATTTTT-GAGG-AAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTT
1 CAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTT
*
12508946 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATCTT
1 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTT
* * *
12509004 CAAAAAGAT-TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATCTT
1 CAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTT
** * * * * * *
12509062 CAAAAAGGT-TTTTTTGAGAAAAAGTCGAAAGTATCAATTTTTCTTGAAATTAAAAATTT
1 CAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-AAATTTT
*
12509121 CAAAAAGAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTT
1 C-AAAA-AAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAA-TTTT
* * * * * * *
12509182 AAAAAAAAGATTTTGA-GGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTT
1 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-TAAAATAAA-TTTT
* *
12509240 C-AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAGATAAATTTT
1 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAA-ATAAATTTT
*** * *
12509297 CAAAGGGAT-TTTTGA-GAAAAAGTTGAAAGTATCAA
1 CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAA
12509332 AAATAAGCTT
Statistics
Matches: 333, Mismatches: 40, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
56 20 0.06
57 47 0.14
58 199 0.60
59 16 0.05
60 11 0.03
61 34 0.10
62 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (57 bp):
CAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTT
Found at i:12509049 original size:116 final size:113
Alignment explanation
Indices: 12508889--12509504 Score: 532
Period size: 116 Copynumber: 5.4 Consensus size: 113
12508879 TTAAAAAAAA
* * *
12508889 CAAAAAAACATTTTTGAGG-AAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAA
1 CAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTTCAAAAAG
12508953 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATCTT
65 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAAT-TT
* *
12509004 CAAAAAGATTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATCTTCAAAAAG
1 CAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAATTTTCAAAAAG
* * * * * *
12509069 GT-TTTTTTGAGAAAAAGTCGAAAGTATCAATTTTTCTTGAAATTAAAAATTT
65 ATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-AAA--ATAAATTT
* *
12509121 CAAAAAGAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTTAAAA
1 CAAAAAG--ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAA-TTTTCAAA
* * * * * * *
12509186 AAAAGATTTTGA-GGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTT
62 AAGATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT-TAAAATAAA--TTT
* **
12509240 CAAAAA-ATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAGATAAATTTTCAAAGG
1 CAAAAAGATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAA-ATAAATTTTCAAAAA
* * *
12509303 GAT-TTTTGA-GAAAAAGTTGAAAGTATC-A--------AAAATAAGCTTT
64 GATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAA-ATTT
* * * *
12509343 CCACAAAAAAATATTTTTGGGAGAAAAGTTAAAAGTATCAATTTTCCTTCAAAATAAGTTTTCAA
1 ---CAAAAAGATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAATTTTCAA
* * *
12509408 AAATGA-ATTTTT-GAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAATTAAAATTT
61 AAA-GATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCT-TAAAAT-AAATTT
* *
12509463 C-AAAAGAATATTTTTGGGGAAAAATTGAAAGTATCAATTTTC
1 CAAAAAG-ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
12509505 TCTACACAAA
Statistics
Matches: 411, Mismatches: 51, Indels: 77
0.76 0.09 0.14
Matches are distributed among these distances:
103 3 0.01
104 6 0.01
106 6 0.01
107 8 0.02
108 37 0.09
109 10 0.02
110 16 0.04
111 1 0.00
113 1 0.00
114 22 0.05
115 35 0.09
116 134 0.33
117 26 0.06
118 5 0.01
119 78 0.19
120 17 0.04
121 6 0.01
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (113 bp):
CAAAAAGATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTTTCAAAAAGA
TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAATTT
Found at i:12509385 original size:108 final size:108
Alignment explanation
Indices: 12509241--12509441 Score: 289
Period size: 108 Copynumber: 1.9 Consensus size: 108
12509231 TAAAGTTTTC
* * *
12509241 AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAGATAAATTTTC-AAAGGG
1 AAAAAATATTTTTAGGAAAAAGTTAAAAGTATCAATTTTCCTTCAAA-ATAAATTTTCAAAAGGA
*
12509304 ATTTTTGAGAAAAAGTTGAAAGTATCAAAAATAAGCTTTCCACA
65 ATTTTTGAGAAAAAGTTAAAAGTATCAAAAATAAGCTTTCCACA
* * *
12509348 AAAAAATATTTTTGGGAGAAAAGTTAAAAGTATCAATTTTCCTTCAAAATAAGTTTTCAAAAATG
1 AAAAAATATTTTTAGGA-AAAAGTTAAAAGTATCAATTTTCCTTCAAAATAAATTTTC-AAAAGG
*
12509413 AATTTTTGAGGAAAAGTTAAAAGTATCAA
64 AATTTTTGAGAAAAAGTTAAAAGTATCAA
12509442 TTTTCCTCGA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
107 16 0.20
108 33 0.40
109 3 0.04
110 30 0.37
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (108 bp):
AAAAAATATTTTTAGGAAAAAGTTAAAAGTATCAATTTTCCTTCAAAATAAATTTTCAAAAGGAA
TTTTTGAGAAAAAGTTAAAAGTATCAAAAATAAGCTTTCCACA
Found at i:12509436 original size:58 final size:58
Alignment explanation
Indices: 12509346--12509504 Score: 198
Period size: 58 Copynumber: 2.7 Consensus size: 58
12509336 AAGCTTTCCA
* **
12509346 CAAAAAAATATTTTTGGGAGAAAAGTTAAAAGTATCAATTTTCCTTC-AAAATAAGTTTT
1 CAAAAGAATATTTTTGGG-GAAAAGTTAAAAGTATCAATTTTCC-TCGAAAATAAAATTT
* *
12509405 C-AAA-AATGAATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAATTAAAATTT
1 CAAAAGAAT--ATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAATTT
* *
12509463 CAAAAGAATATTTTTGGGGAAAAATTGAAAGTATCAATTTTC
1 CAAAAGAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTC
12509505 TCTACACAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
57 5 0.06
58 68 0.77
59 12 0.14
60 3 0.03
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (58 bp):
CAAAAGAATATTTTTGGGGAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAATTT
Found at i:12509466 original size:166 final size:166
Alignment explanation
Indices: 12509183--12509499 Score: 398
Period size: 166 Copynumber: 1.9 Consensus size: 166
12509173 TAAATTTTTA
* *
12509183 AAAAAAAGATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAGTTTTCAAAAAAT
1 AAAAAAAGATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAT
* * * * *
12509248 ATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAAGATAAATTTTC-AAAG-GGATTTTT-
66 ATTTTTAGGAAAAAGTTAAAAGTATCAATTTTCCTGAAAGATAAAATTTCAAAAGAAGATTTTTG
12509310 GAGAAAAAGTTGAAAGTATCAAAAATAAGCTTTCCAC
131 GAGAAAAA-TTGAAAGTATCAAAAATAAGCTTTCCAC
* *
12509347 AAAAAAATATTTTTGGGAGAAAAGTTAAAAGTATCAATTTTCCTTC-AAAAT-AAGTTTTC-AAA
1 AAAAAAAGA-TTTTGAG-GAAAAGTTAAAAGTATCAATTTTCC-TCGAAAATAAAGTTTTCAAAA
* *
12509409 AATGAATTTTTGAGG-AAAAGTTAAAAGTATCAATTTTCCTCGAAA-TTAAAATTTCAAAAGAAT
63 AAT--ATTTTT-AGGAAAAAGTTAAAAGTATCAATTTTCCT-GAAAGATAAAATTTCAAAAGAAG
*
12509472 ATTTTTGGGGAAAAATTGAAAGTATCAA
124 ATTTTTGGAGAAAAATTGAAAGTATCAA
12509500 TTTTCTCTAC
Statistics
Matches: 131, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
164 14 0.11
165 14 0.11
166 65 0.50
167 12 0.09
168 19 0.15
169 7 0.05
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.33
Consensus pattern (166 bp):
AAAAAAAGATTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAGTTTTCAAAAAAT
ATTTTTAGGAAAAAGTTAAAAGTATCAATTTTCCTGAAAGATAAAATTTCAAAAGAAGATTTTTG
GAGAAAAATTGAAAGTATCAAAAATAAGCTTTCCAC
Found at i:12511527 original size:160 final size:160
Alignment explanation
Indices: 12511260--12511574 Score: 533
Period size: 160 Copynumber: 2.0 Consensus size: 160
12511250 AACTTCTTCA
12511260 AAAATGTGATCAATGGCTGTAATCCTTCAACGGTAATATTAACAGAGACTATCAGATCTTTGAGT
1 AAAATGTGATCAATGGCTGTAATCCTTCAACGGTAATATTAACAGAGACTATCAGATCTTTGAGT
* * * * * *
12511325 TATTGTCGTCAGAATAGAAGGTGCTTCATAGGTTGTATACAGTTATTGTACTTATGGATGAAAGC
66 TATTATCATCAGAATAGAAGGCGCTTCATAGGTTGCATACAGTTATTGTACTTATAGATGAAAAC
12511390 CATTTTGAATAGGAAAATGGTGCTTCTTTG
131 CATTTTGAATAGGAAAATGGTGCTTCTTTG
* *
12511420 AAAATGTGATCAATGGCTGTAATCCTTCAATGGTAATATTAGCAGAGACTATCAGATCTTTGAGT
1 AAAATGTGATCAATGGCTGTAATCCTTCAACGGTAATATTAACAGAGACTATCAGATCTTTGAGT
*
12511485 TATTATCATC-GAAATAGAGGGCGCTTCATAGGTTGCATACAGTTATTGTACTTATAGATGAAAA
66 TATTATCATCAG-AATAGAAGGCGCTTCATAGGTTGCATACAGTTATTGTACTTATAGATGAAAA
12511549 CCATTTTGAATAGGAAAATGGTGCTT
130 CCATTTTGAATAGGAAAATGGTGCTT
12511575 TCTTGAAGCT
Statistics
Matches: 145, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
159 1 0.01
160 144 0.99
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (160 bp):
AAAATGTGATCAATGGCTGTAATCCTTCAACGGTAATATTAACAGAGACTATCAGATCTTTGAGT
TATTATCATCAGAATAGAAGGCGCTTCATAGGTTGCATACAGTTATTGTACTTATAGATGAAAAC
CATTTTGAATAGGAAAATGGTGCTTCTTTG
Found at i:12515421 original size:8 final size:8
Alignment explanation
Indices: 12515408--12515446 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
12515398 CTATGCTTGA
12515408 AAAAAAAT
1 AAAAAAAT
12515416 AAAAAAAT
1 AAAAAAAT
12515424 -AAAAAAT
1 AAAAAAAT
12515431 AAAAAAAT
1 AAAAAAAT
12515439 GAAAAAAA
1 -AAAAAAA
12515447 AATGAATGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12515429 original size:15 final size:16
Alignment explanation
Indices: 12515409--12515445 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
12515399 TATGCTTGAA
12515409 AAAAAATAAAAAAAT-
1 AAAAAATAAAAAAATG
12515424 AAAAAATAAAAAAATG
1 AAAAAATAAAAAAATG
12515440 AAAAAA
1 AAAAAA
12515446 AAATGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAATAAAAAAATG
Found at i:12516490 original size:41 final size:41
Alignment explanation
Indices: 12516445--12516657 Score: 185
Period size: 41 Copynumber: 5.1 Consensus size: 41
12516435 ATGATTGTCA
* * *
12516445 AGGAGCAATTTACTTTTCAAAATCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAG
* * * *
12516486 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCCCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAG
* * * * *
12516527 ATGAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAA
1 AGGAGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAG
* * *
12516568 ATGAGCCATTTA-TTTTCCAAAGTCATTGAGCCTCTGATTAG
1 AGGAGCAATTTACTTTT-CAAAGTCATGGAGCCTCTGATTAG
* * * ** ** *
12516609 AAGAGCCATTTATGTTTCTCAAAGTTGTTAAGCCTCTGCTTAG
1 AGGAGCAATTTA-CTTT-TCAAAGTCATGGAGCCTCTGATTAG
12516652 AGGAGC
1 AGGAGC
12516658 TTTGATCAAA
Statistics
Matches: 149, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 4 0.03
41 116 0.78
43 28 0.19
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCATGGAGCCTCTGATTAG
Found at i:12516560 original size:82 final size:82
Alignment explanation
Indices: 12516447--12516657 Score: 217
Period size: 82 Copynumber: 2.5 Consensus size: 82
12516437 GATTGTCAAG
* * * * * * *
12516447 GAGCAATTTACTTTTCAAAATCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCG
1 GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCAATTTA-TTTTCCAAAGTCA
* * *
12516511 TGGTGCCCCTGTTTAGAT
65 TGGAGCCCCTGATTAGAA
* * *
12516529 GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAAATGAGCCATTTATTTTCCAAAGTCAT
1 GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCAATTTATTTTCCAAAGTCAT
* *
12516594 TGAGCCTCTGATTAGAA
66 GGAGCCCCTGATTAGAA
* * * *
12516611 GAGCCATTTATGTTTCTCAAAGTTGTTAAGCCTCTGCTTAGAGGAGC
1 GAGCAATTTAT-TTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
12516658 TTTGATCAAA
Statistics
Matches: 105, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
81 4 0.04
82 72 0.69
83 3 0.03
84 26 0.25
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (82 bp):
GAGCAATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCAATTTATTTTCCAAAGTCAT
GGAGCCCCTGATTAGAA
Found at i:12516646 original size:43 final size:42
Alignment explanation
Indices: 12516474--12516657 Score: 187
Period size: 41 Copynumber: 4.4 Consensus size: 42
12516464 AAATCATGGT
* * * * * *
12516474 GCCTCTGTTTAGAGGAGCAATTTACTTT-TCAAAGTCGTGGT
1 GCCTCTGATTAGAAGAGCCATTTATTTTCTCAAAGTCGTTGA
* * * *
12516515 GCCCCTGTTTAGATGAGCAATTTATTTT-TCAAAGTCGTTGA
1 GCCTCTGATTAGAAGAGCCATTTATTTTCTCAAAGTCGTTGA
*
12516556 GCCTCTGATTA-AATGAGCCATTTATTTTC-CAAAGTCATTGA
1 GCCTCTGATTAGAA-GAGCCATTTATTTTCTCAAAGTCGTTGA
* *
12516597 GCCTCTGATTAGAAGAGCCATTTATGTTTCTCAAAGTTGTTAA
1 GCCTCTGATTAGAAGAGCCATTTAT-TTTCTCAAAGTCGTTGA
* *
12516640 GCCTCTGCTTAGAGGAGC
1 GCCTCTGATTAGAAGAGC
12516658 TTTGATCAAA
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
40 1 0.01
41 91 0.74
42 6 0.05
43 25 0.20
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (42 bp):
GCCTCTGATTAGAAGAGCCATTTATTTTCTCAAAGTCGTTGA
Found at i:12516686 original size:8 final size:8
Alignment explanation
Indices: 12516673--12516725 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
12516663 TCAAATTAAA
12516673 AAAAAAAT
1 AAAAAAAT
12516681 AAAAAAAT
1 AAAAAAAT
12516689 AAAAAAAAT
1 -AAAAAAAT
* *
12516698 AAACAAAC
1 AAAAAAAT
12516706 AAAAAAAGT
1 AAAAAAA-T
12516715 AAAAAAA-
1 AAAAAAAT
12516722 AAAA
1 AAAA
12516726 TTACCTCTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
7 4 0.10
8 20 0.51
9 15 0.38
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12516686 original size:9 final size:9
Alignment explanation
Indices: 12516672--12516722 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 9
12516662 ATCAAATTAA
12516672 AAAAAAAAT
1 AAAAAAAAT
12516681 -AAAAAAAT
1 AAAAAAAAT
12516689 AAAAAAAAT
1 AAAAAAAAT
* *
12516698 -AAACAAAC
1 AAAAAAAAT
*
12516706 AAAAAAAGT
1 AAAAAAAAT
12516715 AAAAAAAA
1 AAAAAAAA
12516723 AAATTACCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 14 0.41
9 20 0.59
ACGTcount: A:0.86, C:0.04, G:0.02, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:12516694 original size:17 final size:16
Alignment explanation
Indices: 12516670--12516725 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
12516660 TGATCAAATT
12516670 AAAAAAAAAATAAAAA
1 AAAAAAAAAATAAAAA
12516686 AATAAAAAAAATAAACAA
1 AA-AAAAAAAATAAA-AA
* *
12516704 ACAAAAAAAGTAAAAA
1 AAAAAAAAAATAAAAA
12516720 AAAAAA
1 AAAAAA
12516726 TTACCTCTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.26
17 23 0.66
18 3 0.09
ACGTcount: A:0.88, C:0.04, G:0.02, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAATAAAAA
Found at i:12517028 original size:7 final size:7
Alignment explanation
Indices: 12517016--12517064 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
12517006 ATTTTGCTTT
*
12517016 TATTTTG
1 TATTTTA
12517023 TATTTTA
1 TATTTTA
12517030 TATTTTA
1 TATTTTA
*
12517037 TATTATTTT
1 TA-T-TTTA
12517046 TATTTT-
1 TATTTTA
12517052 TATTTTA
1 TATTTTA
12517059 TATTTT
1 TATTTT
12517065 TTCCTTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 6 0.16
7 24 0.65
8 2 0.05
9 5 0.14
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (7 bp):
TATTTTA
Found at i:12517030 original size:12 final size:11
Alignment explanation
Indices: 12517013--12517064 Score: 59
Period size: 12 Copynumber: 4.4 Consensus size: 11
12517003 CCAATTTTGC
12517013 TTTTATTTTGTA
1 TTTTATTTT-TA
12517025 TTTTATATTTTA
1 TTTTAT-TTTTA
*
12517037 TATTATTTTTA
1 TTTTATTTTTA
12517048 TTTTTATTTTATA
1 -TTTTATTTT-TA
12517061 TTTT
1 TTTT
12517065 TTCCTTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 5 0.14
12 25 0.71
13 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:12517228 original size:4 final size:4
Alignment explanation
Indices: 12517188--12517353 Score: 53
Period size: 4 Copynumber: 41.8 Consensus size: 4
12517178 TTTTTGTTAA
* * * * *
12517188 TATT TATA TATG TATTT TATT TATC TAGT TATA TATT TA-T TA-T TATT
1 TATT TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT
* * * * *
12517235 TATT CATT TATA TATT ATGATT TATC T-GT TA-T TATT TTTT TATT TATCT
1 TATT TATT TATT TATT -T-ATT TATT TATT TATT TATT TATT TATT TAT-T
* * * * * *
12517284 TGTAA TATT T-TT TATT TATCT TATT T-TT T-TC TAAT TATC TATT AATAT
1 TAT-T TATT TATT TATT TAT-T TATT TATT TATT TATT TATT TATT TAT-T
12517332 T-TT T-TT TATT TATTT TATT TAT
1 TATT TATT TATT TA-TT TATT TAT
12517354 CTGATTTTCT
Statistics
Matches: 118, Mismatches: 31, Indels: 26
0.67 0.18 0.15
Matches are distributed among these distances:
3 23 0.19
4 73 0.62
5 19 0.16
6 3 0.03
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:12517245 original size:26 final size:25
Alignment explanation
Indices: 12517188--12517250 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 25
12517178 TTTTTGTTAA
*
12517188 TATTTATATATGTATTTTATTTATC
1 TATTTATATATTTATTTTATTTATC
*
12517213 TAGTTATATATTTATTATTATTTAT-
1 TATTTATATATTTATT-TTATTTATC
12517238 TCATTTATATATT
1 T-ATTTATATATT
12517251 ATGATTTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.45
26 18 0.55
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (25 bp):
TATTTATATATTTATTTTATTTATC
Found at i:12517259 original size:26 final size:25
Alignment explanation
Indices: 12517188--12517259 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
12517178 TTTTTGTTAA
12517188 TATTTATATATGTAT-TTTATTTATC
1 TATTTATATAT-TATATTTATTTATC
*
12517213 TAGTTATATATT-TATTATTATTTAT-
1 TATTTATATATTATA-T-TTATTTATC
12517238 TCATTTATATATTATGATTTAT
1 T-ATTTATATATTAT-ATTTAT
12517260 CTGTTATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 12 0.31
26 22 0.56
27 2 0.05
28 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.62
Consensus pattern (25 bp):
TATTTATATATTATATTTATTTATC
Found at i:12517279 original size:22 final size:21
Alignment explanation
Indices: 12517202--12517350 Score: 101
Period size: 21 Copynumber: 6.8 Consensus size: 21
12517192 TATATATGTA
12517202 TTTTATTTATCTAGTTATATATTT
1 TTTTATTTATCT--TTAT-TATTT
*
12517226 ATTATTATTTATTCATTTA-TATAT
1 -TT-TTATTTA-TC-TTTATTATTT
* *
12517250 TATGATTTATCTGTTATTATTT
1 TTTTATTTATCT-TTATTATTT
*
12517272 TTTTATTTATCTTGTAATA-TT
1 TTTTATTTATCTT-TATTATTT
12517293 TTTTATTTATC-TTATT-TTT
1 TTTTATTTATCTTTATTATTT
* * *
12517312 TTCTAATTATCTATTAATATTTT
1 TTTTATTTATCT-TTATTA-TTT
12517335 TTTTATTTAT-TTTATT
1 TTTTATTTATCTTTATT
12517351 TATCTGATTT
Statistics
Matches: 99, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
19 14 0.14
20 2 0.02
21 27 0.27
22 25 0.25
23 12 0.12
24 4 0.04
25 2 0.02
26 10 0.10
27 2 0.02
28 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (21 bp):
TTTTATTTATCTTTATTATTT
Found at i:12517313 original size:40 final size:41
Alignment explanation
Indices: 12517254--12517351 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 41
12517244 ATATATTATG
* *
12517254 ATTTATCTGTTATTATTTTTTTATTTATCT-TGTAATA-TTTTTT
1 ATTTATC--TTATT-TTTTTCTAATTATCTAT-TAATATTTTTTT
12517297 ATTTATCTTATTTTTTTCTAATTATCTATTAATATTTTTTTT
1 ATTTATCTTATTTTTTTCTAATTATCTATTAATA-TTTTTTT
*
12517339 ATTTATTTTATTT
1 ATTTATCTTATTT
12517352 ATCTGATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
40 18 0.37
41 6 0.12
42 18 0.37
43 7 0.14
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.70
Consensus pattern (41 bp):
ATTTATCTTATTTTTTTCTAATTATCTATTAATATTTTTTT
Found at i:12517347 original size:13 final size:13
Alignment explanation
Indices: 12517190--12517353 Score: 51
Period size: 14 Copynumber: 12.7 Consensus size: 13
12517180 TTTGTTAATA
* *
12517190 TTTATATATGTAT
1 TTTATTTATTTAT
*
12517203 TTTATTTATCTA-
1 TTTATTTATTTAT
* *
12517215 GTTATATATTTAT
1 TTTATTTATTTAT
*
12517228 TATTATTTATTCAT
1 T-TTATTTATTTAT
*
12517242 TTATATATTA-TGAT
1 TT-TAT-TTATTTAT
*
12517256 TTATCTGTTA-TTAT
1 TT-TAT-TTATTTAT
12517270 TTT-TTTATTTAT
1 TTTATTTATTTAT
*
12517282 CTTGTA-ATA-TT-T
1 -TT-TATTTATTTAT
12517294 TTTATTTATCTTAT
1 TTTATTTAT-TTAT
* *
12517308 TTTTTTCTAATTA-
1 TTTATT-TATTTAT
* *
12517321 TCTA-TTA-ATAT
1 TTTATTTATTTAT
*
12517332 TTTTTTTATTTAT
1 TTTATTTATTTAT
12517345 TTTATTTAT
1 TTTATTTAT
12517354 CTGATTTTCT
Statistics
Matches: 112, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
10 4 0.04
11 11 0.10
12 19 0.17
13 31 0.28
14 42 0.38
15 5 0.04
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:12518301 original size:4 final size:4
Alignment explanation
Indices: 12518287--12518374 Score: 72
Period size: 4 Copynumber: 20.2 Consensus size: 4
12518277 TATTTTTTTC
12518287 TATT T-TT TATT TATTT TCATTT TATT TATT TATT TATT TATT TATT T-TT
1 TATT TATT TATT TA-TT T-A-TT TATT TATT TATT TATT TATT TATT TATT
*
12518336 ATTTT TATTT TATTCT TATT TATTT TATT TATT TCATT T
1 -TATT TA-TT TA-T-T TATT TA-TT TATT TATT T-ATT T
12518375 TCTTTAAATA
Statistics
Matches: 74, Mismatches: 1, Indels: 17
0.80 0.01 0.18
Matches are distributed among these distances:
3 5 0.07
4 40 0.54
5 21 0.28
6 8 0.11
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:12518356 original size:75 final size:74
Alignment explanation
Indices: 12518215--12518374 Score: 173
Period size: 75 Copynumber: 2.1 Consensus size: 74
12518205 TTTTTTTTTC
* *
12518215 TTTTTA-TTATTTTTATTTTATTTTATTTATTTATTTATTATTATTATATTATGGTTGCTTAATA
1 TTTTTATTTATTTTCATTTTATTTTATTTATTTATTTATTATTATTATATTAT-GTTGATTAATA
*
12518279 TTTTTTTCTAT
65 TTTATTT-TAT
* * * **
12518290 TTTTTATTTATTTTCATTTTA-TTTATTTATTTATTTATTTATTTTTATTTTTAT-TTTATTCTT
1 TTTTTATTTATTTTCATTTTATTTTATTTATTTATTTA-TTATTATTA-TATTATGTTGATTAAT
12518353 ATTTATTTTAT
64 ATTTATTTTAT
12518364 TTATTTCATTT
1 TT-TTT-ATTT
12518375 TCTTTAAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
74 5 0.07
75 37 0.51
76 25 0.35
77 5 0.07
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (74 bp):
TTTTTATTTATTTTCATTTTATTTTATTTATTTATTTATTATTATTATATTATGTTGATTAATAT
TTATTTTAT
Found at i:12518463 original size:67 final size:64
Alignment explanation
Indices: 12518394--12518696 Score: 200
Period size: 64 Copynumber: 4.8 Consensus size: 64
12518384 AAAATTCAAA
12518394 AAAAAAATAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTT
1 AAAAAAA-AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTT
* *** * * *
12518459 AAAAAAAAAAGATTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTT
1 AAAAAAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTT
** ****** * * * *
12518523 -TCAAAAAAGGTTTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTC-CT-CG---AAA-TT
1 AAAAAAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTT
*** * *
12518580 AAAAATTTCAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCTTTGAA-AACAAGC
1 AAAAA-AAAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCTTT-AAGAATAA-A
12518643 TTT
62 TTT
** * * *
12518646 ----CCATAAAAAAATATTTTTGAGGGAAAAGTTGAAAGTATTAATTTTCCTTAA
1 AAAAAAAAAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCTTTAA
12518697 AACTAAGTTT
Statistics
Matches: 192, Mismatches: 34, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
57 2 0.01
58 6 0.03
59 32 0.17
60 1 0.01
61 17 0.09
62 29 0.15
63 44 0.23
64 52 0.27
65 7 0.04
66 2 0.01
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (64 bp):
AAAAAAAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTT
Found at i:12518465 original size:58 final size:58
Alignment explanation
Indices: 12518402--12518807 Score: 317
Period size: 58 Copynumber: 6.7 Consensus size: 58
12518392 AAAAAAAAAT
*
12518402 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTTAAA
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAA-AATAAATTT-CA
* * *
12518462 AAAAAAAGATTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCA
1 AAAAAAA-A---TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAA-AATAAA-TTTCA
*** * * ** *
12518526 AAAAAGGTTTTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAATTTC-
1 AAAAA---AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTTTAAA--ATAAATTTCA
* *
12518589 -AAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAACAAGCTTTCCA
1 AAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCTTT-AAAATAA-ATTT-CA
* * * *
12518649 TAAAAAAATATTTTTGAGGGAAAAGTTGAAAGTATTAATTTTCCTTAAAACTAAGTTTTC-
1 AAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCTTTAAAA-TAA-ATTTCA
** * *
12518709 AAAAATGA-ATTTTTGAGAAAAAGTTGAAAGTATCAATTTT-TCTCAAAATTAAAGTTTC-
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCT-TTAAAA-TAAA-TTTCA
*
12518767 -AAAAGAATATTTTTG-GAGAAAAGTTGAAAGTATCAATTTTC
1 AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTC
12518808 CCTGCACAAA
Statistics
Matches: 287, Mismatches: 35, Indels: 49
0.77 0.09 0.13
Matches are distributed among these distances:
57 9 0.03
58 69 0.24
59 42 0.15
60 12 0.04
61 20 0.07
62 38 0.13
63 34 0.12
64 56 0.20
65 7 0.02
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (58 bp):
AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAAATAAATTTCA
Found at i:12518561 original size:63 final size:64
Alignment explanation
Indices: 12518412--12518572 Score: 261
Period size: 63 Copynumber: 2.5 Consensus size: 64
12518402 AAAAAAAATA
* *
12518412 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGAATAAATTTAAAAAAAAAAGATTTTT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTAAAAAAAAAAGATTTTT
** * *
12518476 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTT-TCAAAAAAGGTTTTTT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTAAAAAAAAAAGATTTTT
12518539 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCT
12518573 CGAAATTAAA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 46 0.51
64 45 0.49
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (64 bp):
TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTAAAAAAAAAAGATTTTT
Found at i:12518589 original size:64 final size:61
Alignment explanation
Indices: 12518412--12518629 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 61
12518402 AAAAAAAATA
* * * *
12518412 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTAAGA-ATAAATTTAAAAAAAAAAGATTTTT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGATAAAAATTT---CAAAAAAG-TTTTT
*
12518476 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGA-ATAAATTTTCAAAAAAGGTTTTTT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGATA-AAAATTTCAAAAAA-G-TTTTT
* *
12518539 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTCGAA-ATTAAAAATTTCAAAAAA----AT
1 TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCT-TAAGA-TAAAAATTTCAAAAAAGTTTTT
*
12518597 ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTC
1 TTTTTTA-GGAAAAGTTGAAAGTATCAATTTTC
12518630 TTTGAAAACA
Statistics
Matches: 138, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
58 7 0.05
59 25 0.18
62 6 0.04
63 41 0.30
64 53 0.38
65 6 0.04
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (61 bp):
TTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGATAAAAATTTCAAAAAAGTTTTT
Found at i:12520012 original size:35 final size:35
Alignment explanation
Indices: 12519957--12520024 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
12519947 ATATATAAAC
** *
12519957 CAAATGTTTTTTGGGTATAAA-TATACAACTGACTT
1 CAAATGTTTTTCAGGCATAAACT-TACAACTGACTT
12519992 CAAATGTTTTTCAGGCATAAACTTACAACTGAC
1 CAAATGTTTTTCAGGCATAAACTTACAACTGAC
12520025 CTGACATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (35 bp):
CAAATGTTTTTCAGGCATAAACTTACAACTGACTT
Found at i:12525647 original size:15 final size:14
Alignment explanation
Indices: 12525601--12525652 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
12525591 TTCTCTCATA
12525601 TTTATCTTTC-AAGT
1 TTTATCTTTCTAA-T
*
12525615 TTTATCATTTTCTTAT
1 TTTATC--TTTCTAAT
12525631 TTCTATCTTTCTAAT
1 TT-TATCTTTCTAAT
12525646 TTTATCT
1 TTTATCT
12525653 CTATTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 11 0.34
15 9 0.28
16 7 0.22
17 5 0.16
ACGTcount: A:0.19, C:0.15, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATCTTTCTAAT
Found at i:12531242 original size:3 final size:3
Alignment explanation
Indices: 12531234--12531275 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
12531224 TAAACACCAT
12531234 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12531276 TTTTTCTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:12531320 original size:32 final size:33
Alignment explanation
Indices: 12531268--12531330 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
12531258 TTATTATTTT
*
12531268 ATTTTATTTTTTTCTTTCTTT-CTCGTTTTCTAC
1 ATTTTATTTTCTTCTTTCTTTCCTC-TTTTCTAC
12531301 ATTTT-TTTTCTTCTTTCTTTCCTCTTTTCT
1 ATTTTATTTTCTTCTTTCTTTCCTCTTTTCT
12531331 TTTCCCTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (33 bp):
ATTTTATTTTCTTCTTTCTTTCCTCTTTTCTAC
Found at i:12531823 original size:21 final size:20
Alignment explanation
Indices: 12531806--12531843 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12531796 CCTTTTAGTG
12531806 AAAAGGAGGTTAGATTTATC
1 AAAAGGAGGTTAGATTTATC
*
12531826 CAAAGGAGGTTAGATTTA
1 AAAAGGAGGTTAGATTTA
12531844 CGCTTAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.29
Consensus pattern (20 bp):
AAAAGGAGGTTAGATTTATC
Done.