Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 54 of 91
Found at i:12200921 original size:2 final size:2
Alignment explanation
Indices: 12200914--12200948 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12200904 AAATATTAAA
12200914 AT AT AT AT 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 AT AT AT AT A
12200949 ATGAGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12201014 original size:18 final size:18
Alignment explanation
Indices: 12200944--12201018 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 18
12200934 ATATATATAT
* *
12200944 ATATAATGAGTAAAATAGA
1 ATATAAT-AGTAATATAAA
*
12200963 A-A-AATAATAATCATAACA
1 ATATAATAGTAAT-ATAA-A
12200981 ATAATAATAGTAATATGAAA
1 AT-ATAATAGTAATAT-AAA
12201001 ATATAATA-TAATATAAA
1 ATATAATAGTAATATAAA
12201018 A
1 A
12201019 AAAACCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.09
17 10 0.22
18 9 0.20
19 7 0.15
20 6 0.13
21 10 0.22
ACGTcount: A:0.63, C:0.03, G:0.07, T:0.28
Consensus pattern (18 bp):
ATATAATAGTAATATAAA
Found at i:12201019 original size:18 final size:19
Alignment explanation
Indices: 12200905--12201019 Score: 61
Period size: 22 Copynumber: 5.5 Consensus size: 19
12200895 AAATAAATGA
*
12200905 AATATTAAAATATATATATAT
1 AATATAAAAATA-ATA-ATAT
* *
12200926 ATATATATATATATATATATAT
1 A-ATATAAAAATA-ATA-ATAT
* *
12200948 AATGAGTAAAATAGAAAAATAAT
1 AAT-A-TAAAA-ATAATAAT-AT
*
12200971 AATCATAACAATAATAATAGT
1 AAT-ATAAAAATAATAATA-T
*
12200992 AATATGAAAAT-ATAATAT
1 AATATAAAAATAATAATAT
12201010 AATATAAAAA
1 AATATAAAAA
12201020 AAACCAAAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
18 10 0.14
19 6 0.08
20 7 0.09
21 13 0.18
22 25 0.34
23 11 0.15
24 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (19 bp):
AATATAAAAATAATAATAT
Found at i:12201020 original size:19 final size:19
Alignment explanation
Indices: 12200965--12201019 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
12200955 AAAATAGAAA
* *
12200965 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAAAAAT-AT
*
12200986 AATAGTAATATGAAAATAT
1 AATAGTAATATAAAAATAT
12201005 AATA-TAATATAAAAA
1 AATAGTAATATAAAAA
12201020 AAACCAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 6 0.20
21 8 0.27
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAGTAATATAAAAATAT
Found at i:12201160 original size:2 final size:2
Alignment explanation
Indices: 12201153--12201181 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12201143 GATAATTACA
12201153 AT 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 AT A
12201182 GTAATAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12201239 original size:21 final size:22
Alignment explanation
Indices: 12201226--12201330 Score: 83
Period size: 22 Copynumber: 4.8 Consensus size: 22
12201216 AAAAGTATAT
12201226 ATATA-TATAAAAAAATAATAA
1 ATATAGTATAAAAAAATAATAA
* *
12201247 ATATAGTATTAAAAAATAACCAA
1 ATATAGTATAAAAAAATAA-TAA
* *
12201270 ATGA-A-TATAAATAAATAAAAA
1 AT-ATAGTATAAAAAAATAATAA
* *
12201291 ATATATGTAT-AGATAATAATAA
1 ATATA-GTATAAAAAAATAATAA
*
12201313 TATATAGTGTAAAAAAAT
1 -ATATAGTATAAAAAAAT
12201331 CAATTGAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.02
21 10 0.16
22 34 0.53
23 18 0.28
24 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (22 bp):
ATATAGTATAAAAAAATAATAA
Found at i:12202081 original size:21 final size:21
Alignment explanation
Indices: 12202055--12202142 Score: 106
Period size: 21 Copynumber: 4.2 Consensus size: 21
12202045 GAAGAAGCAG
*
12202055 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
12202076 AAGTAG-TAGAAGTACCTTGGT
1 AAGTAGAT-GAAGTACCTTGGT
* *
12202097 AAGTAGATGAAGTACCTTCGA
1 AAGTAGATGAAGTACCTTGGT
* * *
12202118 AAATAGATGAAGTACTTTGGC
1 AAGTAGATGAAGTACCTTGGT
12202139 AAGT
1 AAGT
12202143 GTCTCTGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
20 1 0.02
21 55 0.96
22 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:12204693 original size:30 final size:30
Alignment explanation
Indices: 12204653--12204717 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
12204643 AATGGATTTA
* * * *
12204653 TTTAATGACCAAATTATAAATTTTGTAAAG
1 TTTAGTGACCAAAGTATAAACTTTGAAAAG
12204683 TTTAGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGTGACCAAAGTATAAACTTTGAAAAG
12204713 TTTAG
1 TTTAG
12204718 GGACTAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.37
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAACTTTGAAAAG
Found at i:12208408 original size:25 final size:25
Alignment explanation
Indices: 12208374--12208431 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
12208364 TTTTACTGCT
*
12208374 AAGAAATTGTTGTCACGTGGATGTC
1 AAGAAATTGTTGTCACATGGATGTC
12208399 AAGAAATTGTTGTCACATGGATGTC
1 AAGAAATTGTTGTCACATGGATGTC
*
12208424 AAGCAATT
1 AAGAAATT
12208432 TTAGCAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (25 bp):
AAGAAATTGTTGTCACATGGATGTC
Found at i:12208591 original size:15 final size:15
Alignment explanation
Indices: 12208571--12208626 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
12208561 ATAAGAGCTA
*
12208571 AAAAATAGAAAGAAG
1 AAAAATAAAAAGAAG
12208586 AAAAATAAAAAGAAG
1 AAAAATAAAAAGAAG
* *
12208601 AAGAAGAAAATAGAA-
1 AAAAATAAAA-AGAAG
*
12208616 AAAAAGAAAAA
1 AAAAATAAAAA
12208627 AATGAGAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 1 0.03
15 31 0.86
16 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAAATAAAAAGAAG
Found at i:12208604 original size:21 final size:19
Alignment explanation
Indices: 12208579--12208629 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
12208569 TAAAAAATAG
12208579 AAAGAAGAAAAATAAAAAGA
1 AAAGAAGAAAAATAAAAA-A
*
12208599 AGAAGAAG-AAAATAGAAAA
1 A-AAGAAGAAAAATAAAAAA
12208618 AAAGAA-AAAAAT
1 AAAGAAGAAAAAT
12208630 GAGAGATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 10 0.36
21 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (19 bp):
AAAGAAGAAAAATAAAAAA
Found at i:12210230 original size:28 final size:28
Alignment explanation
Indices: 12210190--12210251 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
12210180 ATTTTATTCC
*
12210190 ATAAACGGATTTATTTAGTGACCAAATT
1 ATAAATGGATTTATTTAGTGACCAAATT
12210218 ATAAATGGATTTATTTAGTGACCAAATT
1 ATAAATGGATTTATTTAGTGACCAAATT
*
12210246 AGAAAT
1 ATAAAT
12210252 TTGGTAAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (28 bp):
ATAAATGGATTTATTTAGTGACCAAATT
Found at i:12210267 original size:30 final size:30
Alignment explanation
Indices: 12210231--12210303 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
12210221 AATGGATTTA
* *
12210231 TTTAGTGACCAAATTAGAAA-TTTGGTAAAG
1 TTTAGTGACCAAAGTAGAAACTTT-GAAAAG
* *
12210261 TTTAGTGACTAAAGTATAAACTTTGAAAAG
1 TTTAGTGACCAAAGTAGAAACTTTGAAAAG
*
12210291 TTTAGGGACCAAA
1 TTTAGTGACCAAA
12210304 ATGTAATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (30 bp):
TTTAGTGACCAAAGTAGAAACTTTGAAAAG
Found at i:12212624 original size:46 final size:46
Alignment explanation
Indices: 12212447--12212617 Score: 267
Period size: 46 Copynumber: 3.8 Consensus size: 46
12212437 ATAAACTGGC
* * *
12212447 AAATAAGCTTACGAGCTTAT-GGAAT-AATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
* *
12212491 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAATTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
12212537 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
*
12212583 AAATAAGCTTACGATCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAG
12212618 AGATTTTATC
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
44 20 0.17
45 15 0.13
46 83 0.70
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
Found at i:12214360 original size:45 final size:46
Alignment explanation
Indices: 12214268--12214371 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 46
12214258 TGCACATACC
* *
12214268 ATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTG
* *
12214314 ATGCATCGATGCACTCCGGCTATTT-TG-AAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTG
12214359 ATGCATCGATGCA
1 ATGCATCGATGCA
12214372 ATCTTAGTGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
45 30 0.57
46 20 0.38
47 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTG
Found at i:12217137 original size:111 final size:110
Alignment explanation
Indices: 12216916--12217129 Score: 272
Period size: 111 Copynumber: 2.0 Consensus size: 110
12216906 ACTGAAGATC
* * * * *
12216916 GGTATTTTCTATTACAATGCTGCTAGTATCGTATTCATCGATGTCATTGTCTAATTCAGTATCAT
1 GGTATCTTCTATTACAATGCTACTAGCATCATATTCATCGATGTCATTGTCTAATTCAATATCAT
* * *
12216981 CGGTAGAAGGTGGAGTGGAAGAAGAAGTGGAAGTAGGTGAACCTTG
66 CGGTAGAAAGT-GAGTAGAAGAAGAAGTGGAAGTAGATGAACCTTG
* * *
12217027 GGTATCTTCTATTACAATGCTACTAGCGTCATATTCATCGATGTCATTGTCTGATTGAATATC-T
1 GGTATCTTCTATTACAATGCTACTAGCATCATATTCATCGATGTCATTGTCTAATTCAATATCAT
* *
12217091 GTGGTAGAAAGT-A-TAGTAGAAGAAGTGGAAGTAGATGAA
66 -CGGTAGAAAGTGAGTAGAAGAAGAAGTGGAAGTAGATGAA
12217130 TTACCTTGCG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
108 23 0.26
109 1 0.01
110 1 0.01
111 64 0.72
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (110 bp):
GGTATCTTCTATTACAATGCTACTAGCATCATATTCATCGATGTCATTGTCTAATTCAATATCAT
CGGTAGAAAGTGAGTAGAAGAAGAAGTGGAAGTAGATGAACCTTG
Found at i:12221517 original size:13 final size:13
Alignment explanation
Indices: 12221501--12221533 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12221491 TATGACACGT
*
12221501 ATTTATGGCGCTC
1 ATTTATGGCGCAC
12221514 ATTTATGGCGCAC
1 ATTTATGGCGCAC
12221527 ATTTATG
1 ATTTATG
12221534 ACATGCATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (13 bp):
ATTTATGGCGCAC
Found at i:12221705 original size:2 final size:2
Alignment explanation
Indices: 12221698--12221781 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
12221688 TTTCGTAAAT
12221698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12221740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12221782 CATTATAGAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12242137 original size:51 final size:51
Alignment explanation
Indices: 12242082--12242187 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 51
12242072 TACAATAGAT
* * *
12242082 AAATTTAACACATAATTCCAACATTGAATTCATAACAGATTTACACCATTC
1 AAATTTAACACATAATTCCAACATTAAACTCATAACAGACTTACACCATTC
* *
12242133 AAATTTAACATATAATTCCAATATTAAACTCATAACAGACTTACACCATTC
1 AAATTTAACACATAATTCCAACATTAAACTCATAACAGACTTACACCATTC
12242184 AAAT
1 AAAT
12242188 AATTTCTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (51 bp):
AAATTTAACACATAATTCCAACATTAAACTCATAACAGACTTACACCATTC
Found at i:12245211 original size:16 final size:16
Alignment explanation
Indices: 12245186--12245217 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12245176 TATGTATTCA
*
12245186 TAATATTAATTATATT
1 TAATACTAATTATATT
12245202 TAATACTAATTATATT
1 TAATACTAATTATATT
12245218 AAGAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATACTAATTATATT
Found at i:12247150 original size:34 final size:34
Alignment explanation
Indices: 12247107--12247176 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
12247097 TAATTAACCA
12247107 TTCAAATTCCTTTTATCCCAACTTCATATAACAT
1 TTCAAATTCCTTTTATCCCAACTTCATATAACAT
12247141 TTCAAATTCCTTTTATCCCAACTTCATATAACAT
1 TTCAAATTCCTTTTATCCCAACTTCATATAACAT
12247175 TT
1 TT
12247177 TCACTTAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (34 bp):
TTCAAATTCCTTTTATCCCAACTTCATATAACAT
Found at i:12247572 original size:23 final size:23
Alignment explanation
Indices: 12247535--12247588 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
12247525 TTTTGATTCT
*
12247535 ATTCAAGCATGAAATCAACTTCG
1 ATTCAACCATGAAATCAACTTCG
*
12247558 ATTGAACCATGAAATCAACTTCG
1 ATTCAACCATGAAATCAACTTCG
12247581 ATTCAACC
1 ATTCAACC
12247589 TTATAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (23 bp):
ATTCAACCATGAAATCAACTTCG
Found at i:12255195 original size:51 final size:52
Alignment explanation
Indices: 12255140--12255841 Score: 550
Period size: 51 Copynumber: 13.8 Consensus size: 52
12255130 AATTTAACAC
* * * *
12255140 ATAATTCTAATATTAAACTCATAACGA-ACTTAAACCAGTCAAGTATAGTAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * * *
12255191 ATAATT-TCAATATTTAACTCATAA--AAAATTAACACCAGTCCAATATAGCAT
1 ATAATTCT-AATATTGAACTCATAACGAGACTT-ACACCAGTCAAATATAGCAT
* *
12255242 ATAATTCAAATATTGAACTCATAAC-AGACTTACACTAGTCAAATATAGCAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * * * ** *
12255293 ATAAGTCAAACATTTAACTCATAACG-GACTTACATGAGTCAAATATAACAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* *
12255344 ATAATT-TCAATATTGAACTCATAAC-AAACTTACACCAGTCAAATATAACAT
1 ATAATTCT-AATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
** * * *
12255395 ATTTTTCTAGTATTGAACTCACAA-GAGACTTACACCAGTCAAATATGGCAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
** * * ** * * *
12255446 ATTCTTCTAGTATTGAACTCACAAC-AGAAATACACTAGTTAAATATAGCTT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * * *
12255497 ATAATT-TCAATATT-AACTAATAAC-AAACTTACACCAGTCAAATTTAACAT
1 ATAATTCT-AATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * ** * *
12255547 ATAATTCAAATATTGATCTCCA-AAATAGACTTACACTAGTTAAATATAGCAT
1 ATAATTCTAATATTGAACT-CATAACGAGACTTACACCAGTCAAATATAGCAT
* * * * *
12255599 ATAATT-TCAATA-TCATACTCATAAC-ATACTTATACTAGTCAAATTTAGCAT
1 ATAATTCT-AATATTGA-ACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * * * *
12255650 ATAATTCAAATATTGAACTCAGAAC-ATACTTACACCAGTTAAATATAGAAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
** ** * * * *
12255701 ATAATTGC-AATATCAAACT--TATTGTAGACTTAAACTAGTCAAATTTGGCAT
1 ATAATT-CTAATATTGAACTCATAACG-AGACTTACACCAGTCAAATATAGCAT
* * *
12255752 ATAATTCAAATATTGAACTCACAAC-AGACTTACATCAGTCAAATATAGCAT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
* * * *
12255803 ATAATTCCAATATTAAACTCATAAC-AAAGTTACACCAGT
1 ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGT
12255842 GAATGAACGC
Statistics
Matches: 519, Mismatches: 105, Indels: 54
0.77 0.15 0.08
Matches are distributed among these distances:
49 2 0.00
50 44 0.08
51 428 0.82
52 44 0.08
53 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (52 bp):
ATAATTCTAATATTGAACTCATAACGAGACTTACACCAGTCAAATATAGCAT
Found at i:12255219 original size:102 final size:102
Alignment explanation
Indices: 12255105--12255837 Score: 681
Period size: 102 Copynumber: 7.2 Consensus size: 102
12255095 CCAACATTGT
* * * * * * * *
12255105 ACTCATAAAAAATTTACACTATTGAAATTTAACACATAATTCTAATATTAAACTCATAAC-GAAC
1 ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAG-AC
* * *
12255169 TTAAACCAGTCAAGTATAGTATATAATTTCAATATTTA
65 TTACACCAGTCAAATATAGCATATAATTTCAATATTTA
* * * *
12255207 ACTCATAA-AAAATTAACACCAGTCCAATATAGCATATAATTCAAATATTGAACTCATAACAGAC
1 ACTCATAACAAACTT-ACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAGAC
* * *
12255271 TTACACTAGTCAAATATAGCATATAA-GTCAAACATTTA
65 TTACACCAGTCAAATATAGCATATAATTTC-AATATTTA
** * * *
12255309 ACTCATAACGGACTTACA-TGAGTCAAATATAACATATAATTTC-AATATTGAACTCATAACAAA
1 ACTCATAACAAACTTACACT-AGTCAAATTTAGCATATAA-TTCAAATATTGAACTCATAACAGA
* * * *
12255372 CTTACACCAGTCAAATATAACATAT-TTTTCTAGTATTGA
64 CTTACACCAGTCAAATATAGCATATAATTTC-AATATTTA
* * * * * * ** * * * **
12255411 ACTCACAAGAGACTTACACCAGTCAAATATGGCATATTCTTCTAGTATTGAACTCACAACAGAAA
1 ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAGACT
* * *
12255476 TACACTAGTTAAATATAGCTTATAATTTCAATA-TTA
66 TACACCAGTCAAATATAGCATATAATTTCAATATTTA
* * * * * *
12255512 ACTAATAACAAACTTACACCAGTCAAATTTAACATATAATTCAAATATTGATCTCCAAAATAGAC
1 ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACT-CATAACAGAC
* * *
12255577 TTACACTAGTTAAATATAGCATATAATTTCAATA-TCA
65 TTACACCAGTCAAATATAGCATATAATTTCAATATTTA
* * * *
12255614 TACTCATAACATACTTATACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCAGAACATAC
1 -ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAGAC
* * * **
12255679 TTACACCAGTTAAATATAGAATATAATTGCAATATCAA
65 TTACACCAGTCAAATATAGCATATAATTTCAATATTTA
* *** * * * *
12255717 ACTTATTGTAGACTTAAACTAGTCAAATTTGGCATATAATTCAAATATTGAACTCACAACAGACT
1 ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAGACT
* * *
12255782 TACATCAGTCAAATATAGCATATAATTCCAATATTAA
66 TACACCAGTCAAATATAGCATATAATTTCAATATTTA
*
12255819 ACTCATAACAAAGTTACAC
1 ACTCATAACAAACTTACAC
12255838 CAGTGAATGA
Statistics
Matches: 514, Mismatches: 104, Indels: 26
0.80 0.16 0.04
Matches are distributed among these distances:
101 54 0.11
102 400 0.78
103 60 0.12
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.31
Consensus pattern (102 bp):
ACTCATAACAAACTTACACTAGTCAAATTTAGCATATAATTCAAATATTGAACTCATAACAGACT
TACACCAGTCAAATATAGCATATAATTTCAATATTTA
Found at i:12255367 original size:153 final size:152
Alignment explanation
Indices: 12255089--12255841 Score: 696
Period size: 153 Copynumber: 4.9 Consensus size: 152
12255079 AATTCAGCAC
* * * * * * * * * * * * *
12255089 ATAATTCCAACATTGTACTCATAAAAAATTTACACTATTGAAATTTAACACATAATTCTAATATT
1 ATAATTCAAATATTGAACTCATAATAGACTTACACTAGTCAAATATAGCATATAATTCAAACATT
* * * * * *
12255154 AAACTCATAAC-GAACTTAAACCAGTCAAGTATAGTATATAATTTCAATATTTAACTCATAA-AA
66 GAACTCATAACAG-ACTTACA-TAGTCAAATATAGCATATAATTTCAATATTGAACTCATAACAA
* * *
12255217 AATTAACACCAGTCCAATATAGCAT
129 ACTT-ACACCAGTCAAATATAACAT
* *
12255242 ATAATTCAAATATTGAACTCATAACAGACTTACACTAGTCAAATATAGCATATAAGTCAAACATT
1 ATAATTCAAATATTGAACTCATAATAGACTTACACTAGTCAAATATAGCATATAATTCAAACATT
* * *
12255307 TAACTCATAACGGACTTACATGAGTCAAATATAACATATAATTTCAATATTGAACTCATAACAAA
66 GAACTCATAACAGACTTACAT-AGTCAAATATAGCATATAATTTCAATATTGAACTCATAACAAA
12255372 CTTACACCAGTCAAATATAACAT
130 CTTACACCAGTCAAATATAACAT
** * * * * * * ** * **
12255395 ATTTTTCTAGTATTGAACTCACAAGAGACTTACACCAGTCAAATATGGCATATTCTTCTAGTATT
1 ATAATTCAAATATTGAACTCATAATAGACTTACACTAGTCAAATATAGCATATAATTCAAACATT
* ** * * *
12255460 GAACTCACAACAGAAATACACTAGTTAAATATAGCTTATAATTTCAATATT-AACTAATAACAAA
66 GAACTCATAACAGACTTACA-TAGTCAAATATAGCATATAATTTCAATATTGAACTCATAACAAA
*
12255524 CTTACACCAGTCAAATTTAACAT
130 CTTACACCAGTCAAATATAACAT
* * *
12255547 ATAATTCAAATATTGATCTCCAAAATAGACTTACACTAGTTAAATATAGCATATAATTTCAATAT
1 ATAATTCAAATATTGAACT-CATAATAGACTTACACTAGTCAAATATAGCATATAA-TTCAA-A-
* * * *
12255612 CA-T--ACTCATAACATACTTATACTAGTCAAATTTAGCATATAA-TTCAAATATTGAACTCAGA
62 CATTGAACTCATAACAGACTTACA-TAGTCAAATATAGCATATAATTTC-AATATTGAACTCATA
* *
12255673 ACATACTTACACCAGTTAAATATAGA-AT
125 ACAAACTTACACCAGTCAAATATA-ACAT
** * ** * * * *
12255701 ATAATTGC-AATATCAAACTTATTGTAGACTTAAACTAGTCAAATTTGGCATATAATTCAAATAT
1 ATAATT-CAAATATTGAACTCATAATAGACTTACACTAGTCAAATATAGCATATAATTCAAACAT
* * *
12255765 TGAACTCACAACAGACTTACATCAGTCAAATATAGCATATAATTCCAATATTAAACTCATAACAA
65 TGAACTCATAACAGACTTACAT-AGTCAAATATAGCATATAATTTCAATATTGAACTCATAACAA
*
12255830 AGTTACACCAGT
129 ACTTACACCAGT
12255842 GAATGAACGC
Statistics
Matches: 486, Mismatches: 97, Indels: 34
0.79 0.16 0.06
Matches are distributed among these distances:
150 1 0.00
151 2 0.00
152 57 0.12
153 366 0.75
154 56 0.12
155 3 0.01
156 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (152 bp):
ATAATTCAAATATTGAACTCATAATAGACTTACACTAGTCAAATATAGCATATAATTCAAACATT
GAACTCATAACAGACTTACATAGTCAAATATAGCATATAATTTCAATATTGAACTCATAACAAAC
TTACACCAGTCAAATATAACAT
Found at i:12255922 original size:51 final size:51
Alignment explanation
Indices: 12255832--12256003 Score: 181
Period size: 51 Copynumber: 3.4 Consensus size: 51
12255822 CATAACAAAG
* * * * * *
12255832 TTACACCAGTG-AATGAACGCTTAATACCAGCGATGGAAGTTAACATAGAC
1 TTACACCAGTGAAATTAACACTTAATTCCTGAGGTGGAAGTTAACATAGAC
*
12255882 TTACACCAGTGAAATTAACACTTAATTCCTGAGGTGGAAGTTAACATAGGC
1 TTACACCAGTGAAATTAACACTTAATTCCTGAGGTGGAAGTTAACATAGAC
* * *
12255933 ATT-CACC-GATGAAATTAACACTTAATTCTTGTA-GTGAAAGTTAATATAGAC
1 -TTACACCAG-TGAAATTAACACTTAATTCCTG-AGGTGGAAGTTAACATAGAC
* *
12255984 TTGCACCGGTGAAATTAACA
1 TTACACCAGTGAAATTAACA
12256004 TAGACTTATA
Statistics
Matches: 105, Mismatches: 11, Indels: 11
0.83 0.09 0.09
Matches are distributed among these distances:
50 14 0.13
51 87 0.83
52 4 0.04
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (51 bp):
TTACACCAGTGAAATTAACACTTAATTCCTGAGGTGGAAGTTAACATAGAC
Found at i:12273570 original size:14 final size:14
Alignment explanation
Indices: 12273551--12273592 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
12273541 AATGTTCTCT
12273551 CTTTGATTATCCTC
1 CTTTGATTATCCTC
12273565 CTTTGATTATCCTC
1 CTTTGATTATCCTC
12273579 CTTTGATTATCCTC
1 CTTTGATTATCCTC
12273593 ATAGACTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTTGATTATCCTC
Found at i:12275290 original size:16 final size:13
Alignment explanation
Indices: 12275255--12275280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12275245 CTTTCATTGA
12275255 GTTAGTTCTGAGG
1 GTTAGTTCTGAGG
12275268 GTTAGTTCTGAGG
1 GTTAGTTCTGAGG
12275281 TGAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.38, T:0.38
Consensus pattern (13 bp):
GTTAGTTCTGAGG
Found at i:12281445 original size:46 final size:46
Alignment explanation
Indices: 12281370--12281586 Score: 283
Period size: 46 Copynumber: 4.7 Consensus size: 46
12281360 TAACATACCG
* ** * * * *
12281370 TTATGTATTTTCATTGGTGGCATCATTTCATGTCGATAATACATCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCATCA
* * *
12281416 TGATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTTACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCATCA
* *
12281462 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAATTCA-CTT
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCATC-A
* *
12281508 TTATGCATTTTCATTTATGGAATCCTTTCATGCCTATAATTCATCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCATCA
*
12281554 TTATGCATTTTCATTTACGGCATCCTTTCATGC
1 TTATGCATTTTCATTTATGGCATCCTTTCATGC
12281587 TAAAGGCATT
Statistics
Matches: 150, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 148 0.99
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATTCATCA
Found at i:12282174 original size:18 final size:18
Alignment explanation
Indices: 12282151--12282196 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
12282141 ATAATCCATG
12282151 GTATCGATACCCACATCA
1 GTATCGATACCCACATCA
12282169 GTATCGATACCCACATCA
1 GTATCGATACCCACATCA
12282187 GTATCGATAC
1 GTATCGATAC
12282197 TAATTACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.30, G:0.13, T:0.24
Consensus pattern (18 bp):
GTATCGATACCCACATCA
Found at i:12284996 original size:2 final size:2
Alignment explanation
Indices: 12284989--12285057 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
12284979 CCACAAAAGC
* *
12284989 TA TA TA TA TA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12285031 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12285058 CTTTCTGACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12286952 original size:46 final size:46
Alignment explanation
Indices: 12286895--12287342 Score: 617
Period size: 46 Copynumber: 9.7 Consensus size: 46
12286885 TAATATACTA
** *
12286895 TTATGCATTTTCATTGGTGGCATCCTTTCATGCCGATAATGCAACG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
**
12286941 TTATGTGTTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
12286987 TTATGCATTTTCATTTACGGCATCCGTTCATGCCGAAAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
12287033 TTATGCATTTTCATTTATGGCATCCTTCCATGCCCATAATGCAACG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * *
12287079 TTATGCATTTTCATTTATGGCATTCTTTCATACCTATAATGTACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
12287125 TTATGCATTTTCATTTATGGCATCTTTTCATGCTGATAATGCACTG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * *
12287171 TTATGTATTTTCATTTATGGCATCCTTTCATGACGATAATACACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
12287217 TTATGCATTTTCATTTATGGTATCCTTTCATGCCTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * *
12287263 TTCTGCATTTTCATTTATGACATCATTTCATGCCTATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
12287309 TTATACGTTTTCATTTATGGCATCCTTTTATGCC
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCC
12287343 AAAGGCATTT
Statistics
Matches: 350, Mismatches: 52, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 350 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
Found at i:12287978 original size:21 final size:21
Alignment explanation
Indices: 12287948--12288013 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
12287938 TCGATACCCA
12287948 CATCAGTATCGATACTCATTG
1 CATCAGTATCGATACTCATTG
*
12287969 CATCAATATCGATACTCATTG
1 CATCAGTATCGATACTCATTG
12287990 CATCAGTATCGATACT-ATT-
1 CATCAGTATCGATACTCATTG
12288009 CATCA
1 CATCA
12288014 TAATTCTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.12
20 3 0.07
21 35 0.81
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (21 bp):
CATCAGTATCGATACTCATTG
Found at i:12291874 original size:22 final size:22
Alignment explanation
Indices: 12291825--12291874 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
12291815 TTGTTTACCG
* * *
12291825 ATCCAACCTGCTGACCCGTTTG
1 ATCCAACCTACTGACCCGTCTA
* *
12291847 ACCCAACCTATTGACCCGTCTA
1 ATCCAACCTACTGACCCGTCTA
12291869 ATCCAA
1 ATCCAA
12291875 AACTTAAGCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.38, G:0.12, T:0.24
Consensus pattern (22 bp):
ATCCAACCTACTGACCCGTCTA
Found at i:12293669 original size:20 final size:21
Alignment explanation
Indices: 12293639--12293688 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
12293629 TGCTGCCATG
*
12293639 ATATGTAAATGATAT-GAAAAC
1 ATATATAAATGA-ATCGAAAAC
*
12293660 ATA-ATAAATGAATCTAAAAC
1 ATATATAAATGAATCGAAAAC
12293680 ATATATAAA
1 ATATATAAA
12293689 CATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 15 0.60
21 8 0.32
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (21 bp):
ATATATAAATGAATCGAAAAC
Found at i:12296174 original size:20 final size:20
Alignment explanation
Indices: 12296149--12296189 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12296139 AGTTCTTTTC
* *
12296149 TTTTTCTTTTTTTTTTTTGT
1 TTTTTCTTCTTTCTTTTTGT
12296169 TTTTTCTTCTTTCTTTTTGT
1 TTTTTCTTCTTTCTTTTTGT
12296189 T
1 T
12296190 GCTGCACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (20 bp):
TTTTTCTTCTTTCTTTTTGT
Found at i:12299424 original size:3 final size:3
Alignment explanation
Indices: 12299402--12299478 Score: 52
Period size: 3 Copynumber: 24.7 Consensus size: 3
12299392 AAAAGAGAAG
* * *
12299402 ATT ATT A-T ATAT ATT GTT ATT ATTT ATT ATT ATT AAAT AGT ATTT ATT
1 ATT ATT ATT AT-T ATT ATT ATT A-TT ATT ATT ATT -ATT ATT A-TT ATT
12299450 ATT CA-T ATTT ATT -TT ATT ATT ATT ATT AT
1 ATT -ATT A-TT ATT ATT ATT ATT ATT ATT AT
12299479 ATGTTGTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
2 5 0.08
3 42 0.70
4 13 0.22
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12299467 original size:9 final size:10
Alignment explanation
Indices: 12299403--12299476 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 10
12299393 AAAGAGAAGA
12299403 TTATTATATAT
1 TTATTAT-TAT
*
12299414 ATTGTTATTAT
1 -TTATTATTAT
12299425 TTATTATTAT
1 TTATTATTAT
* * *
12299435 TAAATAGTAT
1 TTATTATTAT
12299445 TTATTATTCATAT
1 TTATTA-T--TAT
12299458 TTATT-TTA-
1 TTATTATTAT
12299466 TTATTATTAT
1 TTATTATTAT
12299476 T
1 T
12299477 ATATGTTGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
8 5 0.10
9 5 0.10
10 21 0.43
11 4 0.08
12 6 0.12
13 8 0.16
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (10 bp):
TTATTATTAT
Found at i:12299472 original size:24 final size:24
Alignment explanation
Indices: 12299445--12299504 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
12299435 TAAATAGTAT
12299445 TTATTATTCATAT-TTATTTTATTA
1 TTATTATT-ATATGTTATTTTATTA
*
12299469 TTATTATTATATGTTGTTTTATATAA
1 TTATTATTATATGTTATTTTAT-T-A
*
12299495 ATATTATTAT
1 TTATTATTAT
12299505 TACTTGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.52
25 1 0.03
26 10 0.32
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (24 bp):
TTATTATTATATGTTATTTTATTA
Found at i:12301406 original size:17 final size:17
Alignment explanation
Indices: 12301386--12301421 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12301376 TAACGAACGG
12301386 CTACTTTCGACGACCGA
1 CTACTTTCGACGACCGA
12301403 CTACTTTCGACGACCGA
1 CTACTTTCGACGACCGA
12301420 CT
1 CT
12301422 GAAGAAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (17 bp):
CTACTTTCGACGACCGA
Found at i:12303993 original size:2 final size:2
Alignment explanation
Indices: 12303981--12304011 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12303971 TAATACCTCC
*
12303981 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12304012 GCAATCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12315727 original size:14 final size:14
Alignment explanation
Indices: 12315687--12315727 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
12315677 TAATTACTTA
12315687 GTTGGAATCTTCTT
1 GTTGGAATCTTCTT
* *
12315701 -TTCGAATCGTCTT
1 GTTGGAATCTTCTT
12315714 GTTGGAATCTTCTT
1 GTTGGAATCTTCTT
12315728 CTTTGAAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (14 bp):
GTTGGAATCTTCTT
Found at i:12317143 original size:22 final size:22
Alignment explanation
Indices: 12317115--12317162 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
12317105 TCAAGAGTTA
12317115 AGTACAAATCAGATTAGGACTG
1 AGTACAAATCAGATTAGGACTG
12317137 AGTACAAATCAGATTAGGACTG
1 AGTACAAATCAGATTAGGACTG
12317159 AGTA
1 AGTA
12317163 TTAATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (22 bp):
AGTACAAATCAGATTAGGACTG
Found at i:12317609 original size:15 final size:15
Alignment explanation
Indices: 12317589--12317619 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12317579 CAACAAATAG
12317589 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
12317604 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
12317619 A
1 A
12317620 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:12318635 original size:15 final size:16
Alignment explanation
Indices: 12318617--12318648 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12318607 CTACTAATAG
12318617 TGACAAAATT-AATTT
1 TGACAAAATTAAATTT
12318632 TGACAAAATTAAATTT
1 TGACAAAATTAAATTT
12318648 T
1 T
12318649 TCATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TGACAAAATTAAATTT
Found at i:12319936 original size:19 final size:20
Alignment explanation
Indices: 12319894--12319938 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
12319884 ACCAAGCTGT
*
12319894 AAATTTATGTTAGAGTGTTG
1 AAATTGATGTTAGAGTGTTG
*
12319914 AAATTGATGTTAGATTG-TG
1 AAATTGATGTTAGAGTGTTG
12319933 AAATTG
1 AAATTG
12319939 GGTGTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
AAATTGATGTTAGAGTGTTG
Found at i:12329705 original size:17 final size:17
Alignment explanation
Indices: 12329680--12329716 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12329670 AAATTAAAAC
*
12329680 TAAATTATTTGAAAATT
1 TAAAATATTTGAAAATT
12329697 TAAAATATTTGAAAATT
1 TAAAATATTTGAAAATT
12329714 TAA
1 TAA
12329717 TGCTAGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
TAAAATATTTGAAAATT
Found at i:12333032 original size:6 final size:6
Alignment explanation
Indices: 12333023--12333078 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
12333013 AGACGATGAC
* * * *
12333023 GAAGAT GAAGAT GAATAT GAATAT GAATAT GAAGAT GATGAT GGAA-AT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT -GAAGAT
*
12333071 GGAGAT GA
1 GAAGAT GA
12333079 GGATAGAGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
5 2 0.05
6 38 0.90
7 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.23
Consensus pattern (6 bp):
GAAGAT
Found at i:12333042 original size:12 final size:12
Alignment explanation
Indices: 12333027--12333060 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
12333017 GATGACGAAG
12333027 ATGAAGATGAAT
1 ATGAAGATGAAT
*
12333039 ATGAATATGAAT
1 ATGAAGATGAAT
12333051 ATGAAGATGA
1 ATGAAGATGA
12333061 TGATGGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (12 bp):
ATGAAGATGAAT
Found at i:12336771 original size:85 final size:83
Alignment explanation
Indices: 12336606--12336759 Score: 204
Period size: 85 Copynumber: 1.8 Consensus size: 83
12336596 ATATACTCTC
* *
12336606 TGACACACAATATGTGTCATCTCCATTTATGACGAGGGCTTCAATGACAGGCAATGTAAGTCATA
1 TGACACACAATATGTGTCATCTCCATTTATGACGAGGGCTTCAATGACACGCAATGCAAGTCATA
*
12336671 CATGCATGTCATAAATTTA
66 AATGCA-GTCATAAATTTA
* **
12336690 TGACACACAA-ATGTGTGCCATCTTCATTTATGAC-AGGGGCTTCAATGACACGCAATGCGCGTC
1 TGACACACAATATGTGT--CATCTCCATTTATGACGA-GGGCTTCAATGACACGCAATGCAAGTC
12336753 ATAAATG
63 ATAAATG
12336760 AGCATCATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
83 6 0.10
84 11 0.18
85 44 0.72
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (83 bp):
TGACACACAATATGTGTCATCTCCATTTATGACGAGGGCTTCAATGACACGCAATGCAAGTCATA
AATGCAGTCATAAATTTA
Found at i:12336805 original size:13 final size:13
Alignment explanation
Indices: 12336743--12336810 Score: 73
Period size: 13 Copynumber: 5.2 Consensus size: 13
12336733 AATGACACGC
12336743 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
12336756 AATGAGCATCATA
1 AATGCGCGTCATA
* *
12336769 AATGTGTGTCATA
1 AATGCGCGTCATA
* *
12336782 AATGTGTGTCATA
1 AATGCGCGTCATA
*
12336795 AATGCACGTCATA
1 AATGCGCGTCATA
12336808 AAT
1 AAT
12336811 TTATGACACA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:12336805 original size:26 final size:26
Alignment explanation
Indices: 12336743--12336810 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
12336733 AATGACACGC
12336743 AATGCGCGTCATAAATGAGCATCATA
1 AATGCGCGTCATAAATGAGCATCATA
* * * **
12336769 AATGTGTGTCATAAATGTGTGTCATA
1 AATGCGCGTCATAAATGAGCATCATA
*
12336795 AATGCACGTCATAAAT
1 AATGCGCGTCATAAAT
12336811 TTATGACACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (26 bp):
AATGCGCGTCATAAATGAGCATCATA
Found at i:12339301 original size:19 final size:18
Alignment explanation
Indices: 12339268--12339304 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12339258 TTATATTATC
12339268 CTTATTTTATTGTCTTAA
1 CTTATTTTATTGTCTTAA
*
12339286 CTTATTATTCTTGTCTTAA
1 CTTATT-TTATTGTCTTAA
12339305 TCTCAAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.14, G:0.05, T:0.59
Consensus pattern (18 bp):
CTTATTTTATTGTCTTAA
Found at i:12339347 original size:52 final size:52
Alignment explanation
Indices: 12339288--12339392 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
12339278 TGTCTTAACT
12339288 TATTATTCTTGTCTTAATCTCAAGAACTAAAAACCTTAATCCAATTACCTTG
1 TATTATTCTTGTCTTAATCTCAAGAACTAAAAACCTTAATCCAATTACCTTG
*
12339340 TATTATTCTTGTCTTAATCTCAAGAACTAAAAGCCTTAATCCAATTACCTTG
1 TATTATTCTTGTCTTAATCTCAAGAACTAAAAACCTTAATCCAATTACCTTG
12339392 T
1 T
12339393 TGCCATCCAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (52 bp):
TATTATTCTTGTCTTAATCTCAAGAACTAAAAACCTTAATCCAATTACCTTG
Found at i:12339708 original size:4 final size:4
Alignment explanation
Indices: 12339699--12339726 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12339689 AAAAAGGCAA
12339699 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12339727 CCATAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:12341178 original size:21 final size:21
Alignment explanation
Indices: 12341145--12341220 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
12341135 TTTCAGAGAC
* *
12341145 ACTTACTAGGGTACTTCATCT
1 ACTTACCAAGGTACTTCATCT
* *
12341166 A-TTTCGCAAGGTACTTTATCT
1 ACTTAC-CAAGGTACTTCATCT
** *
12341187 ACTTACCAAGGTACTTTTTCC
1 ACTTACCAAGGTACTTCATCT
*
12341208 ATTTACCAAGGTA
1 ACTTACCAAGGTA
12341221 ATTTTTCTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (21 bp):
ACTTACCAAGGTACTTCATCT
Found at i:12345493 original size:15 final size:16
Alignment explanation
Indices: 12345470--12345503 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12345460 TCATTTTTTG
12345470 CATTATTTATTC-TTT
1 CATTATTTATTCATTT
*
12345485 CATTTTTTATTCATTT
1 CATTATTTATTCATTT
12345501 CAT
1 CAT
12345504 AAGTATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (16 bp):
CATTATTTATTCATTT
Found at i:12352690 original size:19 final size:19
Alignment explanation
Indices: 12352658--12352695 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12352648 CATTTCCTCA
*
12352658 ATGATTCAAGAATACCAAAG
1 ATGATTCAACAATA-CAAAG
12352678 ATGA-TCAACAATACAAAG
1 ATGATTCAACAATACAAAG
12352696 CATTCATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.53, C:0.16, G:0.13, T:0.18
Consensus pattern (19 bp):
ATGATTCAACAATACAAAG
Found at i:12361703 original size:23 final size:23
Alignment explanation
Indices: 12361659--12361703 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
12361649 GTTTGAGATA
**
12361659 CAACATCACCACCATCTTCCATT
1 CAACATCACCACCATCAACCATT
* *
12361682 CAACATCATCATCATCAACCAT
1 CAACATCACCACCATCAACCAT
12361704 CTTCCATTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (23 bp):
CAACATCACCACCATCAACCATT
Found at i:12382741 original size:45 final size:45
Alignment explanation
Indices: 12382692--12382789 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
12382682 TCATCTTGTT
* *
12382692 ATTTTCTCTCCAATCAAGATTGTTTCCATCGTATTTCTTGTTACC
1 ATTTTCTCTCCAATCAAGATTGTTTCAATCATATTTCTTGTTACC
* * **
12382737 ATTTTCTCTCCAATCAAGATTGTTTCAATTATCTTTCTTGTTGTC
1 ATTTTCTCTCCAATCAAGATTGTTTCAATCATATTTCTTGTTACC
12382782 ATTTTCTC
1 ATTTTCTC
12382790 CTTTGTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.50
Consensus pattern (45 bp):
ATTTTCTCTCCAATCAAGATTGTTTCAATCATATTTCTTGTTACC
Found at i:12384205 original size:8 final size:8
Alignment explanation
Indices: 12384192--12384217 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
12384182 AAAAGGTAAT
12384192 TGTGCATG
1 TGTGCATG
12384200 TGTGCATG
1 TGTGCATG
12384208 TGTGCATG
1 TGTGCATG
12384216 TG
1 TG
12384218 ATTTGCTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.38, T:0.38
Consensus pattern (8 bp):
TGTGCATG
Found at i:12394687 original size:26 final size:26
Alignment explanation
Indices: 12394651--12394764 Score: 183
Period size: 26 Copynumber: 4.4 Consensus size: 26
12394641 AGTTTGACTT
12394651 GACTTGAAAAGTATAAAATGGAATTC
1 GACTTGAAAAGTATAAAATGGAATTC
*
12394677 GACTTGAAAAGTGTAAAATGGAATTC
1 GACTTGAAAAGTATAAAATGGAATTC
*
12394703 GACTTGAAAAGTGTAAAATGGAATTC
1 GACTTGAAAAGTATAAAATGGAATTC
* *
12394729 GACTTGAAAAATATAAAATTGAATTC
1 GACTTGAAAAGTATAAAATGGAATTC
*
12394755 CACTTGAAAA
1 GACTTGAAAA
12394765 TTCACGAGTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 83 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (26 bp):
GACTTGAAAAGTATAAAATGGAATTC
Found at i:12396002 original size:37 final size:37
Alignment explanation
Indices: 12395921--12396200 Score: 325
Period size: 37 Copynumber: 7.4 Consensus size: 37
12395911 TTTATTTAAT
** * *
12395921 ATATATATTGTATATAGTTTTTTTAAAACATTTTGAAA
1 ATATATATAATATATAG-TTTTTGAAAATATTTTGAAA
* * *
12395959 ATATATATAATATAT-GATTTTAGAAAACATTTTTAAAAA
1 ATATATATAATATATAG-TTTTTGAAAATA-TTTT-GAAA
12395998 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
** *
12396035 ATATATATAATATATAGTTTTCAAAAATATTATGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* *
12396072 ATATGTATAATATATAGTTTTTGAAAACA-TTT-AAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* *
12396107 GCATATATATAATATAGACTTTTTGAAAATATTTTGAAA
1 --ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
12396146 ATATATAT-ATAATATAGTATTTTGAAAATATTTTGAAA
1 ATATATATAAT-ATATAGT-TTTTGAAAATATTTTGAAA
12396184 ATATATATATATATATA
1 ATATATATA-ATATATA
12396201 TATATATATA
Statistics
Matches: 208, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
35 3 0.01
36 4 0.02
37 111 0.53
38 51 0.25
39 36 0.17
40 3 0.01
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:12396143 original size:11 final size:11
Alignment explanation
Indices: 12396127--12396187 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 11
12396117 AATATAGACT
12396127 TTTTGAAAATA
1 TTTTGAAAATA
12396138 TTTTGAAAATA
1 TTTTGAAAATA
12396149 TATATAT-AATATAGTA
1 T-T-T-TGAA-A-A-TA
12396165 TTTTGAAAATA
1 TTTTGAAAATA
12396176 TTTTGAAAATA
1 TTTTGAAAATA
12396187 T
1 T
12396188 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
11 26 0.60
12 2 0.05
13 5 0.12
14 5 0.12
15 2 0.05
16 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:12396191 original size:2 final size:2
Alignment explanation
Indices: 12396184--12396219 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
12396174 TATTTTGAAA
12396184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
12396220 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12396217 original size:56 final size:55
Alignment explanation
Indices: 12396146--12396258 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 55
12396136 TATTTTGAAA
*
12396146 ATATATATATAATATAGTA-TTTTGAAAATATTTTGAAAATATATATATATATATAT
1 ATATATATATAATATA-TAGTTTTGAAAATATTTTGAAAATATATATA-AGATATAT
*
12396202 ATATATATATCATATATAGTTTTTGAAAATATTTTGAAAATATATATAAGATATAT
1 ATATATATATAATATATAG-TTTTGAAAATATTTTGAAAATATATATAAGATATAT
12396258 A
1 A
12396259 ACTTTTGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 2 0.04
56 23 0.43
57 28 0.53
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (55 bp):
ATATATATATAATATATAGTTTTGAAAATATTTTGAAAATATATATAAGATATAT
Found at i:12396245 original size:39 final size:36
Alignment explanation
Indices: 12396202--12396315 Score: 106
Period size: 39 Copynumber: 3.0 Consensus size: 36
12396192 ATATATATAT
12396202 ATATATATATCATATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATAT-ATATATA-TTTTTGAAAATATTTT-AAA
* * * * *
12396241 ATATATATAAGATATATAACTTTTGAAAACATATATATA
1 ATATATAT-ATATATAT-ATTTTTGAAAATAT-TTTAAA
12396280 ATATATA-ATATATA-ATTTTTGAAAATATTTTTAAA
1 ATATATATATATATATATTTTTGAAAATA-TTTTAAA
12396315 A
1 A
12396316 CATTTTGAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
35 16 0.26
36 1 0.02
37 6 0.10
39 34 0.56
40 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (36 bp):
ATATATATATATATATATTTTTGAAAATATTTTAAA
Found at i:12396246 original size:132 final size:130
Alignment explanation
Indices: 12396072--12396315 Score: 300
Period size: 132 Copynumber: 1.9 Consensus size: 130
12396062 TATTATGAAA
* *
12396072 ATATGTATAATATATAGTTTTTGAAAACATTTAAAGCATATATAT-A-ATATA-GACTTTTTGAA
1 ATATATATAATATATAGTTTTTGAAAACATTTAAA-CATATATATAAGATATATAAC-TTTTGAA
* * *
12396134 AATAT-TTTGAAAATATATATATAATATAGTATTTTGAAAATATTTTGAAAATATATATATATAT
64 AACATATAT-AAAATATATA-AT-ATATAAT-TTTTGAAAATATTTTGAAAATATATATATATAT
12396198 ATATAT
125 ATATAT
* *
12396204 ATATATATCATATATAGTTTTTGAAAATATTTTGAAA-ATATATATAAGATATATAACTTTTGAA
1 ATATATATAATATATAGTTTTTGAAAACA-TTT-AAACATATATATAAGATATATAACTTTTGAA
* *
12396268 AACATATATATAATATATAATATATAATTTTTGAAAATATTTTTAAAA
64 AACATATATAAAATATATAATATATAATTTTTGAAAATATTTTGAAAA
12396316 CATTTTGAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 13
0.82 0.08 0.11
Matches are distributed among these distances:
131 19 0.20
132 40 0.41
133 6 0.06
134 28 0.29
135 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (130 bp):
ATATATATAATATATAGTTTTTGAAAACATTTAAACATATATATAAGATATATAACTTTTGAAAA
CATATATAAAATATATAATATATAATTTTTGAAAATATTTTGAAAATATATATATATATATATAT
Found at i:12396264 original size:28 final size:28
Alignment explanation
Indices: 12396233--12396287 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
12396223 TTTGAAAATA
*
12396233 TTTTGAAAATATATATA-AGATATATAAC
1 TTTTGAAAACATATATATA-ATATATAAC
12396261 TTTTGAAAACATATATATAATATATAA
1 TTTTGAAAACATATATATAATATATAA
12396288 TATATAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTTGAAAACATATATATAATATATAAC
Found at i:12396275 original size:85 final size:85
Alignment explanation
Indices: 12396176--12396333 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 85
12396166 TTTGAAAATA
* * *
12396176 TTTTGAAAATATATATAT-ATATAT-ATATAT-ATATATCATATATAGTTTTTGAAAATATTTTG
1 TTTTGAAAACATATATATAATATATAATATATAATATATCA-AAATA-TTTTT-AAAACATTTTG
12396238 AAAATATATATAAGATATATAAC
63 AAAATATATATAAGATATATAAC
* * *
12396261 TTTTGAAAACATATATATAATATATAATATATAATTTTTGAAAATATTTTTAAAACATTTTGAAA
1 TTTTGAAAACATATATATAATATATAATATATAATATATCAAAATATTTTTAAAACATTTTGAAA
12396326 ATATATAT
66 ATATATAT
12396334 TATATAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
85 38 0.59
86 11 0.17
87 10 0.16
88 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (85 bp):
TTTTGAAAACATATATATAATATATAATATATAATATATCAAAATATTTTTAAAACATTTTGAAA
ATATATATAAGATATATAAC
Found at i:12396291 original size:95 final size:95
Alignment explanation
Indices: 12396109--12396293 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 95
12396099 CATTTAAAGC
12396109 ATATATATAATATAGACTTTTTGAAAATATTTTGAAAATATATATATAATATAGTATTTTGAAAA
1 ATATATATAATATAGACTTTTTGAAAATATTTTGAAAATATATATATAATATAGTATTTTGAAAA
* *
12396174 TATTTTGAAAATATATATATATATATATAT
66 CATTATGAAAATATATATATATATATATAT
* * *
12396204 ATATATATCATATATAGTTTTTGAAAATATTTTGAAAATATATATA-AGATATA-TAACTTTTGA
1 ATATATATAATATAGACTTTTTGAAAATATTTTGAAAATATATATATA-ATATAGT-A-TTTTGA
*
12396267 AAACATATAT-ATAATATATA-ATATATA
63 AAACAT-TATGAAAATATATATATATATA
12396294 ATTTTTGAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
94 2 0.03
95 56 0.70
96 20 0.25
97 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (95 bp):
ATATATATAATATAGACTTTTTGAAAATATTTTGAAAATATATATATAATATAGTATTTTGAAAA
CATTATGAAAATATATATATATATATATAT
Found at i:12396345 original size:169 final size:169
Alignment explanation
Indices: 12396035--12396347 Score: 402
Period size: 169 Copynumber: 1.9 Consensus size: 169
12396025 TATTTTGAAA
* **
12396035 ATATATATAATATATAGTTTTCAAAAATATTATGAAAATATGTATAATATATAGTTTTTGAAAAC
1 ATATATATAATATATAGTTTTCAAAAATATTATGAAAATATATATAATATATAACTTTTGAAAAC
* * * *
12396100 ATTTAAAGCATATATATAATATAGACTTTTTGAAAATATTTTGAAAATATATATATAATATAGTA
66 ATATAAAGCATATATATAATATAGAATTTTTGAAAATATTTTGAAAACATATATAAAATATAGTA
12396165 TTTTGAAAATATTTTGAAAATATATATATATATATATAT
131 TTTTGAAAATATTTTGAAAATATATATATATATATATAT
* ** *
12396204 ATATATATCATATATAGTTTTTGAAAATATTTTGAAAATATATATAAGATATATAACTTTTGAAA
1 ATATATATAATATATAGTTTTCAAAAATATTATGAAAATATATAT-A-ATATATAACTTTTGAAA
* * * * *
12396269 ACATATATA-TA-ATATATAATATATAATTTTTGAAAATATTTTTAAAACAT-TTTGAAAATATA
64 ACATATAAAGCATATATATAATATAGAATTTTTGAAAATATTTTGAAAACATATAT-AAAATATA
12396331 -TATTATAT-AAAATATTT
128 GTATT-T-TGAAAATATTT
12396348 ATGTATTATA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
168 6 0.05
169 92 0.75
170 3 0.02
171 22 0.18
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (169 bp):
ATATATATAATATATAGTTTTCAAAAATATTATGAAAATATATATAATATATAACTTTTGAAAAC
ATATAAAGCATATATATAATATAGAATTTTTGAAAATATTTTGAAAACATATATAAAATATAGTA
TTTTGAAAATATTTTGAAAATATATATATATATATATAT
Found at i:12396361 original size:5 final size:5
Alignment explanation
Indices: 12396351--12396400 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
12396341 AATATTTATG
*
12396351 TATTA TATTA TATTA TATTA TATTA TATTA T-TTT TATT- TATT- TATT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
12396397 TATT
1 TATT
12396401 TTCTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
4 15 0.35
5 28 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TATTA
Found at i:12396394 original size:8 final size:9
Alignment explanation
Indices: 12396342--12396401 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 9
12396332 ATTATATAAA
12396342 ATATTTATGT
1 ATATTTAT-T
*
12396352 AT-TATATT
1 ATATTTATT
12396360 ATATTATATT
1 ATATT-TATT
12396370 ATATTATATT
1 ATATT-TATT
*
12396380 ATTTTTATT
1 ATATTTATT
12396389 -TATTTATT
1 ATATTTATT
12396397 -TATTT
1 ATATTT
12396402 TCTTTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
8 15 0.34
9 9 0.20
10 20 0.45
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
ATATTTATT
Found at i:12396414 original size:18 final size:19
Alignment explanation
Indices: 12396345--12396415 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 19
12396335 ATATAAAATA
*
12396345 TTTATGTATTATA-TTATAT
1 TTTATTTATTATATTTAT-T
*
12396364 TATATTATATTATA-TTATT
1 TTTATT-TATTATATTTATT
12396383 TTTATTTATT-TATTTATT
1 TTTATTTATTATATTTATT
12396401 TTCT-TTT-TTATATTT
1 TT-TATTTATTATATTT
12396416 TGGTTCAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 4 0.09
18 19 0.42
19 11 0.24
20 11 0.24
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (19 bp):
TTTATTTATTATATTTATT
Found at i:12397588 original size:6 final size:6
Alignment explanation
Indices: 12397572--12397612 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
12397562 ATTTATTTCA
*
12397572 TTTATTT TTTATT TTTA-A TTT-TT TTTATT TTTATT TTTATT
1 TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
12397613 CATTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
5 6 0.20
6 20 0.67
7 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:12397595 original size:16 final size:15
Alignment explanation
Indices: 12397576--12397628 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
12397566 ATTTCATTTA
12397576 TTTTTTATTTTTAATT
1 TTTTTTATTTTT-ATT
12397592 TTTTTTATTTTTATT
1 TTTTTTATTTTTATT
*
12397607 TTTATTCA-TTTTATT
1 TTT-TTTATTTTTATT
12397622 TTATTTT
1 TT-TTTT
12397629 CTTTAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 17 0.52
16 16 0.48
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTTTATTTTTATT
Found at i:12397637 original size:20 final size:21
Alignment explanation
Indices: 12397572--12397637 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
12397562 ATTTATTTCA
**
12397572 TTTATTTTTTATTTTTAATTTTT
1 TTTA-TTTTTATTTTT-ATTAAT
*
12397595 TTTATTTTTATTTTTATTCAT
1 TTTATTTTTATTTTTATTAAT
12397616 TTTA-TTTTATTTTCT-TTAAT
1 TTTATTTTTATTTT-TATTAAT
12397636 TT
1 TT
12397638 AATTAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 15 0.38
21 9 0.23
22 11 0.28
23 4 0.10
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTATTTTTATTTTTATTAAT
Found at i:12405844 original size:32 final size:32
Alignment explanation
Indices: 12405803--12405879 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
12405793 AGTCGAGGGT
*
12405803 TTACCTATGTTCTACGAAACATATTGACAGAA
1 TTACCTATGTTCTACGAAACATATGGACAGAA
* * *
12405835 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 TTACCTATGTTC-TACGAAACATATGGACAGAA
*
12405867 -TACCTTTGTTCTA
1 TTACCTATGTTCTA
12405880 AGGAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
31 10 0.27
32 27 0.73
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (32 bp):
TTACCTATGTTCTACGAAACATATGGACAGAA
Found at i:12407609 original size:12 final size:12
Alignment explanation
Indices: 12407586--12407619 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
12407576 TGGGGATTGA
12407586 TAAGAA-GAGTT
1 TAAGAATGAGTT
*
12407597 TAATAATGAGTT
1 TAAGAATGAGTT
12407609 TAAGAATGAGT
1 TAAGAATGAGT
12407620 ATATTGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
TAAGAATGAGTT
Found at i:12409576 original size:24 final size:20
Alignment explanation
Indices: 12409549--12409606 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
12409539 GCATGGGTAG
12409549 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
12409573 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
12409593 TGTATCGATGCACT
1 TGCATCGATGCACT
12409607 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:12412208 original size:17 final size:16
Alignment explanation
Indices: 12412188--12412246 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
12412178 TCTTATTTTA
12412188 TTTCTTTTGAACTCAAT
1 TTTCTTTTGAA-TCAAT
* * *
12412205 TTTCTTTAATTAATTACT
1 TTTCTTT--TGAATCAAT
12412223 TTTCTTTTGAATTCAAT
1 TTTCTTTTGAA-TCAAT
12412240 TTTCTTT
1 TTTCTTT
12412247 CATCCAGTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 3 0.09
17 17 0.52
18 10 0.30
19 3 0.09
ACGTcount: A:0.22, C:0.14, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTCTTTTGAATCAAT
Found at i:12412258 original size:35 final size:35
Alignment explanation
Indices: 12412188--12412259 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
12412178 TCTTATTTTA
* *
12412188 TTTCTTTTGAACTCAATTTTCTTTAATTAATTACT
1 TTTCTTTTGAACTCAATTTTCTTTAATCAAGTACT
* * *
12412223 TTTCTTTTGAATTCAATTTTCTTTCATCCAGTACT
1 TTTCTTTTGAACTCAATTTTCTTTAATCAAGTACT
12412258 TT
1 TT
12412260 GTTTTATCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (35 bp):
TTTCTTTTGAACTCAATTTTCTTTAATCAAGTACT
Found at i:12414943 original size:45 final size:45
Alignment explanation
Indices: 12414850--12414944 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
12414840 GTATTTTGCT
* * * **
12414850 AAAAAATGCTTAGGGTGAAAACCTGAAAGGGCATCCTAAGTTGGA
1 AAAAAATGCTTAGGGTGAAAACCCGAAAGGGCAGCCTAAATTAAA
*
12414895 AAAAAATGTTTAGGGTGAAAACCCGAAAGGGC-GCCTTAAATTAAA
1 AAAAAATGCTTAGGGTGAAAACCCGAAAGGGCAGCC-TAAATTAAA
12414940 AAAAA
1 AAAAA
12414945 TGGGTCCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (45 bp):
AAAAAATGCTTAGGGTGAAAACCCGAAAGGGCAGCCTAAATTAAA
Found at i:12416368 original size:2 final size:2
Alignment explanation
Indices: 12416361--12416412 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
12416351 GTTTTATTTG
*
12416361 AT AT AT AT A- AT AT AC AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12416401 AT AT AT AT AT AT
1 AT AT AT AT AT AT
12416413 TTAAAACACT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12416436 original size:37 final size:38
Alignment explanation
Indices: 12416393--12416757 Score: 336
Period size: 37 Copynumber: 9.9 Consensus size: 38
12416383 ATATATATAT
* *
12416393 ATATATATATATATATA-TATTT-AAAACACTTTGAAAA
1 ATATATATATATATATAGTTTTTGAAAATA-TTTGAAAA
* * * *
12416430 AAATATATATAATATATTA-TTTTGGAAAACATTTTCAAAA
1 ATATATATAT-ATATA-TAGTTTTTGAAAATA-TTTGAAAA
*
12416470 ATATATATATAATATATAGTTTTTGAAAATATTTTAAAA
1 ATATATATAT-ATATATAGTTTTTGAAAATATTTGAAAA
* *
12416509 ATATATATA-ATATATAATTTTTGAAAATATTTTAAAA
1 ATATATATATATATATAGTTTTTGAAAATATTTGAAAA
* *
12416546 ATATATATA-ATATATAGTTTTCGAAAATATTTTAAAA
1 ATATATATATATATATAGTTTTTGAAAATATTTGAAAA
12416583 ATATATATA-ATATATAGTTTTTGAAAATATTTTG-AAA
1 ATATATATATATATATAGTTTTTGAAAATA-TTTGAAAA
* * *
12416620 ATATATATA-GTATATAGTTTTTGAAAACATTTTGAAAGC
1 ATATATATATATATATAGTTTTTGAAAATA-TTTGAAA-A
12416659 ATATATATATAATATATAGTTTTTGAAAATA--T-----
1 ATATATATAT-ATATATAGTTTTTGAAAATATTTGAAAA
* * **
12416691 ATATA-ATATATATA-A-CTTTTGAAAACATTTTTAAA
1 ATATATATATATATATAGTTTTTGAAAATATTTGAAAA
* *
12416726 ATATATATA-ATATATAATTTTTGAATATATTT
1 ATATATATATATATATAGTTTTTGAAAATATTT
12416758 TTAAAACATT
Statistics
Matches: 285, Mismatches: 24, Indels: 38
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.04
29 1 0.00
30 6 0.02
31 4 0.01
32 5 0.02
35 10 0.04
36 4 0.01
37 146 0.51
38 11 0.04
39 32 0.11
40 38 0.13
41 18 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (38 bp):
ATATATATATATATATAGTTTTTGAAAATATTTGAAAA
Found at i:12416580 original size:74 final size:74
Alignment explanation
Indices: 12416393--12416763 Score: 413
Period size: 74 Copynumber: 5.0 Consensus size: 74
12416383 ATATATATAT
* * * *
12416393 ATATATATATATATATA-TATTT-AAAACACTTTGAAAAAAATATATATAATATATTATTTTGGA
1 ATATATATA-ATATATAGTTTTTGAAAACA-TTT--TAAAAATATATATAATATATAATTTTTGA
*
12416456 AAACATTTTCAAAAA
62 AAATATTTT--AAAA
*
12416471 TATATATATAATATATAGTTTTTGAAAATATTTTAAAAATATATATAATATATAATTTTTGAAAA
1 -ATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAATTTTTGAAAA
12416536 TATTTTAAAA
65 TATTTTAAAA
* * *
12416546 ATATATATAATATATAGTTTTCGAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAAT
1 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAATTTTTGAAAAT
*
12416611 ATTTTGAAA
66 ATTTTAAAA
* *
12416620 ATATATATAGTATATAGTTTTTGAAAACATTTTGAAAGCATATATATATAATATATAGTTTTTGA
1 ATATATATAATATATAGTTTTTGAAAACATTTT-AAA--A-ATATATATAATATATAATTTTTGA
12416685 AAATA---T----
62 AAATATTTTAAAA
** * *
12416691 ATATA-AT-ATATATAACTTTTGAAAACATTTTTAAAATATATATAATATATAATTTTTGAATAT
1 ATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAATTTTTGAAAAT
*
12416754 ATTTTTAAA
66 ATTTTAAAA
12416763 A
1 A
12416764 CATTTTGAAA
Statistics
Matches: 261, Mismatches: 18, Indels: 33
0.84 0.06 0.11
Matches are distributed among these distances:
65 27 0.10
66 1 0.00
68 3 0.01
69 21 0.08
70 2 0.01
71 5 0.02
72 1 0.00
74 101 0.39
75 8 0.03
77 35 0.13
78 36 0.14
79 16 0.06
80 5 0.02
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (74 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATATAATTTTTGAAAAT
ATTTTAAAA
Found at i:12416683 original size:30 final size:28
Alignment explanation
Indices: 12416661--12416715 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 28
12416651 TTGAAAGCAT
12416661 ATATATATAATATATAGT---TTTTGAAA
1 ATATATATAATATATA-TAACTTTTGAAA
12416687 ATATATATAATATATATAACTTTTGAAA
1 ATATATATAATATATATAACTTTTGAAA
12416715 A
1 A
12416716 CATTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 1 0.04
26 16 0.62
28 9 0.35
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (28 bp):
ATATATATAATATATATAACTTTTGAAA
Found at i:12416729 original size:28 final size:28
Alignment explanation
Indices: 12416649--12416732 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
12416639 TTTGAAAACA
* **
12416649 TTTTGAAAGCATATATATATAATATATAGT
1 TTTTGAAAACATATATA-A-AATATATAAC
* *
12416679 TTTTGAAAATATATATAATATATATAAC
1 TTTTGAAAACATATATAAAATATATAAC
* *
12416707 TTTTGAAAACATTTTTAAAATATATA
1 TTTTGAAAACATATATAAAATATATA
12416733 TAATATATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 29 0.64
29 1 0.02
30 15 0.33
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTTGAAAACATATATAAAATATATAAC
Found at i:12416778 original size:37 final size:37
Alignment explanation
Indices: 12416678--12416766 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
12416668 TAATATATAG
*
12416678 TTTTTGAAAATATATATAATATATATAACTTTTGAAAACA
1 TTTTT-AAAACATATATAA-A-ATATAACTTTTGAAAACA
* * * * *
12416718 TTTTTAAAATATATATAATATATAATTTTTGAATATA
1 TTTTTAAAACATATATAAAATATAACTTTTGAAAACA
12416755 TTTTTAAAACAT
1 TTTTTAAAACAT
12416767 TTTGAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 26 0.59
39 13 0.30
40 5 0.11
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTTTAAAACATATATAAAATATAACTTTTGAAAACA
Found at i:12416817 original size:13 final size:12
Alignment explanation
Indices: 12416801--12416868 Score: 59
Period size: 13 Copynumber: 5.5 Consensus size: 12
12416791 AATATTTACG
*
12416801 TATTATATTTTA
1 TATTTTATTTTA
*
12416813 T-TATTTATTATTT
1 TAT-TTTATT-TTA
12416826 TATTTTATTATT-
1 TATTTTATT-TTA
12416838 TATTTTATTTTA
1 TATTTTATTTTA
*
12416850 TTTATTTATTTTA
1 TAT-TTTATTTTA
12416863 TATTTT
1 TATTTT
12416869 TGTTATTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
11 3 0.06
12 20 0.43
13 23 0.49
14 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:12416850 original size:30 final size:29
Alignment explanation
Indices: 12416801--12416877 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 29
12416791 AATATTTACG
12416801 TATTATATTTTATTATT-TATTATTTTATTTTA
1 TATT-TATTTTATT-TTAT-TTA-TTTATTTTA
12416833 TTATTTATTTTATTTTATTTATTTATTTTA
1 -TATTTATTTTATTTTATTTATTTATTTTA
12416863 TATTT-TTGTTATTTT
1 TATTTATT-TTATTTT
12416878 GGTCCAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
28 2 0.05
29 12 0.29
30 9 0.21
31 5 0.12
32 10 0.24
33 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (29 bp):
TATTTATTTTATTTTATTTATTTATTTTA
Found at i:12416876 original size:20 final size:19
Alignment explanation
Indices: 12416803--12416868 Score: 91
Period size: 20 Copynumber: 3.5 Consensus size: 19
12416793 TATTTACGTA
12416803 TTATATTTTATTATTTATT
1 TTATATTTTATTATTTATT
*
12416822 ATTTTATTTTATTATTTA-T
1 -TTATATTTTATTATTTATT
12416841 TT-TATTTTATTTATTTATT
1 TTATATTTTA-TTATTTATT
12416860 TTATATTTT
1 TTATATTTT
12416869 TGTTATTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 7 0.17
18 9 0.21
19 4 0.10
20 22 0.52
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTATATTTTATTATTTATT
Found at i:12416877 original size:9 final size:8
Alignment explanation
Indices: 12416816--12416869 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
12416806 TATTTTATTA
*
12416816 TTTATTAT
1 TTTATTTT
12416824 TTTATTTT
1 TTTATTTT
*
12416832 ATTATTTAT
1 TTTATTT-T
12416841 TTTATTTT
1 TTTATTTT
12416849 ATTTATTTAT
1 -TTTATTT-T
12416859 TTTATATTT
1 TTTAT-TTT
12416868 TT
1 TT
12416870 GTTATTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
8 14 0.36
9 22 0.56
10 3 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATTTT
Found at i:12424354 original size:20 final size:20
Alignment explanation
Indices: 12424326--12424375 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
12424316 TTATGTGGGC
12424326 ATCGATACTAAGAGGAAGGT
1 ATCGATACTAAGAGGAAGGT
* *
12424346 GTTGATACTAAGAGGAAGGT
1 ATCGATACTAAGAGGAAGGT
12424366 ATCGATACTA
1 ATCGATACTA
12424376 TGGATTATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.24
Consensus pattern (20 bp):
ATCGATACTAAGAGGAAGGT
Found at i:12435658 original size:19 final size:19
Alignment explanation
Indices: 12435631--12435695 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
12435621 ATCTAACCAG
* * *
12435631 TTGAATTTGACCCGCCCCA
1 TTGACTTTGACCTGACCCA
*
12435650 TTTACTTTGACCTGACCCA
1 TTGACTTTGACCTGACCCA
12435669 TTGACTTTGACCTGACCCA
1 TTGACTTTGACCTGACCCA
12435688 TTGACTTT
1 TTGACTTT
12435696 TACCAAAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.35
Consensus pattern (19 bp):
TTGACTTTGACCTGACCCA
Found at i:12441282 original size:13 final size:14
Alignment explanation
Indices: 12441264--12441293 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12441254 CATTCATTCC
12441264 AAAACAAAAC-ATA
1 AAAACAAAACAATA
12441277 AAAACAAAACAATA
1 AAAACAAAACAATA
12441291 AAA
1 AAA
12441294 TATAAATTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAACAAAACAATA
Found at i:12447902 original size:18 final size:18
Alignment explanation
Indices: 12447871--12447906 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12447861 GTGGCATCAT
*
12447871 ATGTGACTAGGTATAATG
1 ATGTGACTAAGTATAATG
*
12447889 ATGTGGCTAAGTATAATG
1 ATGTGACTAAGTATAATG
12447907 CTACTAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
ATGTGACTAAGTATAATG
Found at i:12460879 original size:2 final size:2
Alignment explanation
Indices: 12460872--12460933 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
12460862 TACTCTGAAT
12460872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12460914 TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
12460934 TTAAAAGAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12466855 original size:2 final size:2
Alignment explanation
Indices: 12466848--12466890 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
12466838 AACAAACATA
12466848 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12466890 A
1 A
12466891 CGTTGTTACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12469196 original size:2 final size:2
Alignment explanation
Indices: 12469189--12469213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12469179 TATTCTTAAT
12469189 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12469214 CAATTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12485723 original size:56 final size:56
Alignment explanation
Indices: 12485569--12486067 Score: 709
Period size: 56 Copynumber: 8.9 Consensus size: 56
12485559 TACGATACGA
* * * ***
12485569 AAATTCATAAACTTATTTTGAATTTCTTAG-TTTTGCACGCACAA-TGCCCATACAT
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACA-AAGTGCCCATATGG
* * * *
12485624 AAATTCATTAACTTATTATGAATTTATTAGTTTTTTTGCACACAAAGTGCCCACATGG
1 AAATTCATAAACTCATTATGAATTTCTTAG--TTTTTGCACACAAAGTGCCCATATGG
* *
12485682 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTACCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
*
12485738 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
* *
12485794 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTTCTCACAAAGTGCCCATACT-G
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATA-TGG
*
12485850 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCTCACAAAGTGCCCATATGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
*
12485906 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACCCAAAGTGCCCATATGG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
* * **
12485962 AAATTCATAAACTCATTATAAATTTCTTAGTTTTTGCACACAAAGTTCCCATACAG
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
* *
12486018 AATTTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACATATAGTGCC
1 AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACA-A-AGTGCC
12486068 ATTCGGTAAT
Statistics
Matches: 406, Mismatches: 30, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
55 39 0.10
56 316 0.78
57 7 0.02
58 44 0.11
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (56 bp):
AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATATGG
Found at i:12497138 original size:18 final size:19
Alignment explanation
Indices: 12497115--12497150 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12497105 AATATGAATG
12497115 TAAAAA-CATGGAAAATAT
1 TAAAAACCATGGAAAATAT
12497133 TAAAAACCATGGAAAATA
1 TAAAAACCATGGAAAATA
12497151 AAGATGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.19
Consensus pattern (19 bp):
TAAAAACCATGGAAAATAT
Found at i:12508032 original size:12 final size:12
Alignment explanation
Indices: 12508017--12508067 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
12508007 TGAAAAAAAG
*
12508017 ACAAGGAAAATA
1 ACAAGTAAAATA
12508029 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
*
12508042 TACAA-AAAAATAA
1 -ACAAGTAAAAT-A
12508055 ACAAGTAAAATA
1 ACAAGTAAAATA
12508067 A
1 A
12508068 AAATGTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:12510381 original size:14 final size:14
Alignment explanation
Indices: 12510362--12510426 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
12510352 TGTTAAATAG
12510362 GAAATAAAAGAAAT
1 GAAATAAAAGAAAT
*
12510376 GAAATAAATGAAAT
1 GAAATAAAAGAAAT
* *
12510390 AAAATAAATGAAAT
1 GAAATAAAAGAAAT
*
12510404 GAAATGAAAGAAAT
1 GAAATAAAAGAAAT
12510418 -AAGATAAAA
1 GAA-ATAAAA
12510427 ATATAGATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
13 2 0.05
14 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (14 bp):
GAAATAAAAGAAAT
Found at i:12510389 original size:5 final size:5
Alignment explanation
Indices: 12510362--12510417 Score: 66
Period size: 5 Copynumber: 12.0 Consensus size: 5
12510352 TGTTAAATAG
* *
12510362 GAAAT -AAAA GAAAT GAAAT -AAAT GAAAT AAAAT -AAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT
12510409 GAAA- GAAAT
1 GAAAT GAAAT
12510418 AAGATAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
4 15 0.34
5 29 0.66
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (5 bp):
GAAAT
Found at i:12510398 original size:4 final size:4
Alignment explanation
Indices: 12510372--12510551 Score: 63
Period size: 4 Copynumber: 43.8 Consensus size: 4
12510362 GAAATAAAAG
*
12510372 AAAT GAAAT AAAT GAAAT AAAAT AAAT GAAAT GAAAT GAAAG AAAT AAGAT
1 AAAT -AAAT AAAT -AAAT -AAAT AAAT -AAAT -AAAT -AAAT AAAT AA-AT
* * *
12510423 AAA- AATAT AGAT -AA- AAAT AAAAT AAAAT AATT AAAAT AAAG AATAT
1 AAAT AA-AT AAAT AAAT AAAT -AAAT -AAAT AAAT -AAAT AAAT AA-AT
* * * ** * *
12510469 ATAT ATAT ATAT AAA- AAGG AAAT AAA- AAAT AAAGAT AAAG ACA- AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AA-AT AAAT AAAT AAAT
*
12510515 AAAT AAAT AAAT AAAT AAAT AAAT --AT AAAG AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
12510552 GAAAAGAGAT
Statistics
Matches: 139, Mismatches: 19, Indels: 35
0.72 0.10 0.18
Matches are distributed among these distances:
2 2 0.01
3 15 0.11
4 72 0.52
5 48 0.35
6 2 0.01
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:12510402 original size:28 final size:28
Alignment explanation
Indices: 12510363--12510426 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
12510353 GTTAAATAGG
12510363 AAATAAAAGAAATGAAAT-AAATGAAATA
1 AAATAAAAGAAATGAAATGAAA-GAAATA
*
12510391 AAATAAATGAAATGAAATGAAAGAAATA
1 AAATAAAAGAAATGAAATGAAAGAAATA
*
12510419 AGATAAAA
1 AAATAAAA
12510427 ATATAGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.17
Consensus pattern (28 bp):
AAATAAAAGAAATGAAATGAAAGAAATA
Found at i:12510436 original size:12 final size:11
Alignment explanation
Indices: 12510414--12510449 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
12510404 GAAATGAAAG
12510414 AAATAAGATAA
1 AAATAAGATAA
12510425 AAATATAGATAA
1 AAATA-AGATAA
*
12510437 AAATAAAATAA
1 AAATAAGATAA
12510448 AA
1 AA
12510450 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAATAAGATAA
Found at i:12510528 original size:22 final size:22
Alignment explanation
Indices: 12510487--12510555 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
12510477 ATATAAAAAG
12510487 GAAATAAAAAATAAAG--ATAAA
1 GAAAT-AAAAATAAAGAAATAAA
*
12510508 GACAA-AAAAATAAATAAATAAA
1 GA-AATAAAAATAAAGAAATAAA
* *
12510530 TAAATAAATATAAAGAAATAAA
1 GAAATAAAAATAAAGAAATAAA
12510552 GAAA
1 GAAA
12510556 AGAGATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 9 0.23
21 4 0.10
22 26 0.67
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.16
Consensus pattern (22 bp):
GAAATAAAAATAAAGAAATAAA
Found at i:12510564 original size:70 final size:69
Alignment explanation
Indices: 12510367--12510586 Score: 161
Period size: 70 Copynumber: 3.2 Consensus size: 69
12510357 AATAGGAAAT
* * * *
12510367 AAAAGAAATGAAATAAATGAAATAAAATAAATGA-AATGAAATGAAAGAAATA-AGAT-AAAAAT
1 AAAAAAAATAAAATAAATAAAAT-AAATAAAT-ATAAAGAAAT-AAAGAAA-AGAGATAAAAAAT
*
12510429 ATAGATAA
62 AAAGATAA
* * * * * * * *
12510437 AAATAAAATAAAATAATTAAAATAAAGAATATATATATATATATAA-AAAGGAAATAAAAAATAA
1 AAAAAAAATAAAATAAATAAAATAAATAA-ATATAAAGAAATA-AAGAAAAGAGATAAAAAATAA
12510501 AGATAA
64 AGATAA
12510507 AGACAAAAAA-ATAAATAAAT-AAATAAATAAATATAAAGAAATAAAGAAAAGAGAT--AAAATA
1 A-A-AAAAAATA-AAATAAATAAAATAAATAAATATAAAGAAATAAAGAAAAGAGATAAAAAATA
12510568 GAA-ATAA
63 -AAGATAA
*
12510575 AAATAAAATAAA
1 AAAAAAAATAAA
12510587 GAAAAAATAA
Statistics
Matches: 117, Mismatches: 22, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
66 7 0.06
67 2 0.02
68 11 0.09
69 17 0.15
70 57 0.49
71 11 0.09
72 12 0.10
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (69 bp):
AAAAAAAATAAAATAAATAAAATAAATAAATATAAAGAAATAAAGAAAAGAGATAAAAAATAAAG
ATAA
Found at i:12510608 original size:15 final size:16
Alignment explanation
Indices: 12510573--12510613 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
12510563 AAATAGAAAT
*
12510573 AAAAATAAAATAAAGA
1 AAAAATAAAAGAAAGA
12510589 AAAAATAAAAGAAAGGA
1 AAAAATAAAAGAAA-GA
12510606 AAATAATA
1 AAA-AATA
12510614 GTAAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.59
17 5 0.23
18 4 0.18
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (16 bp):
AAAAATAAAAGAAAGA
Found at i:12510620 original size:43 final size:44
Alignment explanation
Indices: 12510490--12510610 Score: 113
Period size: 43 Copynumber: 2.7 Consensus size: 44
12510480 TAAAAAGGAA
* *
12510490 ATAAA-AAATAAAGATAAAGACAAAAAAATAAATAAATAAATAAATAAAT
1 ATAAAGAAATAAAGA-AAAGA-AAGAAAAT--AGAAAT-AA-AAATAAAT
* *
12510539 ATAAAGAAATAAAGAAAAGAGATAAAATAGAAATAAAAATAAA-
1 ATAAAGAAATAAAGAAAAGAAAGAAAATAGAAATAAAAATAAAT
*
12510582 ATAAAGAAA-AAATAAAAGAAAGGAAAATA
1 ATAAAGAAATAAAGAAAAGAAA-GAAAATA
12510611 ATAGTAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 10 0.16
43 15 0.23
44 7 0.11
45 2 0.03
46 5 0.08
48 6 0.09
49 10 0.16
50 9 0.14
ACGTcount: A:0.75, C:0.01, G:0.09, T:0.15
Consensus pattern (44 bp):
ATAAAGAAATAAAGAAAAGAAAGAAAATAGAAATAAAAATAAAT
Found at i:12510628 original size:2 final size:2
Alignment explanation
Indices: 12510623--12510649 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12510613 AGTAAAAAAG
12510623 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
12510650 AAATATTAAA
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:12510795 original size:21 final size:20
Alignment explanation
Indices: 12510757--12510818 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
12510747 ATAAAACACT
**
12510757 AAAAAATCAAAATCAAAATCA
1 AAAAAATCAAAAAAAAAAT-A
12510778 AAAAAATCAAAAAAAAAATA
1 AAAAAATCAAAAAAAAAATA
* *
12510798 TAAAAAT-AATAAAAATAATA
1 AAAAAATCAA-AAAAAAAATA
12510818 A
1 A
12510819 TAATAAATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 17 0.49
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAAATCAAAAAAAAAATA
Found at i:12510820 original size:15 final size:16
Alignment explanation
Indices: 12510792--12510825 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
12510782 AATCAAAAAA
12510792 AAAATATAAAAATAAT
1 AAAATATAAAAATAAT
*
12510808 AAAA-ATAATAATAAT
1 AAAATATAAAAATAAT
12510823 AAA
1 AAA
12510826 TCCCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATATAAAAATAAT
Found at i:12510823 original size:9 final size:9
Alignment explanation
Indices: 12510791--12510824 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
12510781 AAATCAAAAA
12510791 AAAAAT-AT
1 AAAAATAAT
12510799 AAAAATAAT
1 AAAAATAAT
12510808 AAAAATAAT
1 AAAAATAAT
*
12510817 AATAATAA
1 AAAAATAA
12510825 ATCCCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATAAT
Found at i:12510851 original size:2 final size:2
Alignment explanation
Indices: 12510846--12510871 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12510836 ATAGTAAATA
12510846 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12510872 GAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12524307 original size:90 final size:90
Alignment explanation
Indices: 12524197--12524363 Score: 289
Period size: 90 Copynumber: 1.9 Consensus size: 90
12524187 ATTTAATTTT
* * *
12524197 AATTAATTAAATTTAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACTT
12524262 AGATATAAAAGGATTATTAAATTCC
66 AGATATAAAAGGATTATTAAATTCC
*
12524287 AATTAATTAAATATAGATTTAATAAATTTGATATAATAAAAACCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACTT
*
12524352 AGTTATAAAAGG
66 AGATATAAAAGG
12524364 GAGTGTTAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (90 bp):
AATTAATTAAATATAGATTTAATAAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACTT
AGATATAAAAGGATTATTAAATTCC
Found at i:12531127 original size:90 final size:90
Alignment explanation
Indices: 12531006--12531183 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 90
12530996 TAATCCCGAA
* * *
12531006 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
12531071 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
12531096 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
12531161 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
12531184 GTGTGTTAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Done.