Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 106 of 427
Found at i:28039290 original size:8 final size:8
Alignment explanation
Indices: 28039277--28039303 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28039267 GTCTCTCTAT
28039277 TTTTAAAA
1 TTTTAAAA
28039285 TTTTAAAA
1 TTTTAAAA
28039293 TTTTAAAA
1 TTTTAAAA
28039301 TTT
1 TTT
28039304 AAGTCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTAAAA
Found at i:28044110 original size:21 final size:23
Alignment explanation
Indices: 28044086--28044136 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
28044076 TCATAATATT
28044086 TTTTATAAAT-AT-TTTAATTAA
1 TTTTATAAATCATGTTTAATTAA
*
28044107 TTTTAT-AATCATGTTTAATTAT
1 TTTTATAAATCATGTTTAATTAA
28044129 TTATTATA
1 TT-TTATA
28044137 TTAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 8 0.32
22 10 0.40
23 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATAAATCATGTTTAATTAA
Found at i:28044123 original size:22 final size:20
Alignment explanation
Indices: 28044086--28044127 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 20
28044076 TCATAATATT
28044086 TTTTATAAATATTTTAATTAA
1 TTTTAT-AATATTTTAATTAA
28044107 TTTTATAATCATGTTTAATTA
1 TTTTATAAT-AT-TTTAATTA
28044128 TTTATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTATAATATTTTAATTAA
Found at i:28057030 original size:19 final size:18
Alignment explanation
Indices: 28056994--28057032 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
28056984 ACTTTTTTGT
28056994 ATTCATCGCATTCATTGC
1 ATTCATCGCATTCATTGC
28057012 ATTCAT-GCATCTGCATTGC
1 ATTCATCGCAT-T-CATTGC
28057031 AT
1 AT
28057033 CATACGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (18 bp):
ATTCATCGCATTCATTGC
Found at i:28065118 original size:43 final size:43
Alignment explanation
Indices: 28065070--28065153 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 43
28065060 GTGAAATCGG
* * *
28065070 TGAATTCACA-AGCCTTATCTCCCTAAGCAGTAGGGTAACAGGC
1 TGAATTCACAGA-CCTTAACCCCCTAAGCAGTAGGGAAACAGGC
* * *
28065113 TGAATTTACAGATCTTAACCCCCTATGCAGTAGGGAAACAG
1 TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGAAACAG
28065154 ATCGAAGATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (43 bp):
TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGAAACAGGC
Found at i:28065187 original size:44 final size:43
Alignment explanation
Indices: 28065090--28065370 Score: 211
Period size: 44 Copynumber: 6.5 Consensus size: 43
28065080 AGCCTTATCT
* * * * *
28065090 CCCTAAGCAGTAGGGTAACAG-GCTGAATTTACA-GATCTTAACC
1 CCCTAAGCAGTAGGGTAACAGATC-GAAATGA-AGGGTCTTAAAC
* *
28065133 CCCTATGCAGTAGGGAAACAGATCGAAGATGAAGGGTCTTAAAC
1 CCCTAAGCAGTAGGGTAACAGATCGAA-ATGAAGGGTCTTAAAC
* * * * * *
28065177 CCCTAAGCAGTAGGGTAACAGACCGAATTGCA-GATATT-ATC
1 CCCTAAGCAGTAGGGTAACAGATCGAAATGAAGGGTCTTAAAC
* *
28065218 TCCCTAAGTAGTAGTGG-AGCAGATCGAAAATGAAGGGTCTTAAAC
1 -CCCTAAGCAGTAG-GGTAACAGATCG-AAATGAAGGGTCTTAAAC
* * * *
28065263 CCCTAAGCAGTAGGGTAACAGA-CCAAATTGCA-GATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGATCGAAA-TGAAGGGTCTTAAAC
* *
28065304 TCCCTAAGCAGTAGTGG-AGCAGATCGAAGACGAAGGGTCTTAAAC
1 -CCCTAAGCAGTAG-GGTAACAGATCGAA-ATGAAGGGTCTTAAAC
*
28065349 CCCTAAACAGTAGGGTAACAGA
1 CCCTAAGCAGTAGGGTAACAGA
28065371 CCAAATTGCA
Statistics
Matches: 184, Mismatches: 37, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
41 4 0.02
42 49 0.27
43 48 0.26
44 79 0.43
45 4 0.02
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGATCGAAATGAAGGGTCTTAAAC
Found at i:28065251 original size:86 final size:86
Alignment explanation
Indices: 28065090--28065402 Score: 466
Period size: 86 Copynumber: 3.6 Consensus size: 86
28065080 AGCCTTATCT
* * * * * * * * *
28065090 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTATGCAGTAG-GGAAACAG
1 CCCTAAGCAGTAGGGTAACAGAC-CAAATTGCAGATATTATCTCCCTAAGCAGTAGTGG-AGCAG
28065154 ATCGAAGATGAAGGGTCTTAAAC
64 ATCGAAGATGAAGGGTCTTAAAC
* *
28065177 CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGATATTATCTCCCTAAGTAGTAGTGGAGCAGAT
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGAT
*
28065242 CGAAAATGAAGGGTCTTAAAC
66 CGAAGATGAAGGGTCTTAAAC
*
28065263 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGAT
*
28065328 CGAAGACGAAGGGTCTTAAAC
66 CGAAGATGAAGGGTCTTAAAC
*
28065349 CCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTA
1 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTA
28065403 AGGTAACAGA
Statistics
Matches: 206, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
86 182 0.88
87 24 0.12
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (86 bp):
CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATATTATCTCCCTAAGCAGTAGTGGAGCAGAT
CGAAGATGAAGGGTCTTAAAC
Found at i:28065311 original size:42 final size:42
Alignment explanation
Indices: 28065083--28065459 Score: 264
Period size: 42 Copynumber: 8.8 Consensus size: 42
28065073 ATTCACAAGC
* * * *
28065083 CTTATCTCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGAT
1 CTTATCTCCCTAAGCAGTAGGGTAACAGAC-CAAATTGCAGAT
* * * * * * *
28065126 CTTAACCCCCTATGCAGTAGGGAAACAGATCGAAGA-TGAAGGGT
1 CTTATCTCCCTAAGCAGTAGGGTAACAGA-CCAA-ATTGCA-GAT
* *
28065170 CTTAAAC-CCCTAAGCAGTAGGGTAACAGACCGAATTGCAGAT
1 CTT-ATCTCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
* * * * * * *
28065212 ATTATCTCCCTAAGTAGTAGTGG-AGCAGATCGAAAATGAAGGGT
1 CTTATCTCCCTAAGCAGTAG-GGTAACAGA-CCAAATTGCA-GAT
*
28065256 CTTAAAC-CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
1 CTT-ATCTCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
* * * * *
28065298 CTTATCTCCCTAAGCAGTAGTGG-AGCAGATCGAAGA-CGAAGGGT
1 CTTATCTCCCTAAGCAGTAG-GGTAACAGA-CCAA-ATTGCA-GAT
* *
28065342 CTTAAAC-CCCTAAACAGTAGGGTAACAGACCAAATTGCAGAT
1 CTT-ATCTCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
* * * *
28065384 ATTATCTCCCTAAGCAGTAAGGTAACAGACCAAATTACAAAT
1 CTTATCTCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
* * *
28065426 CTTATCTACCTAAGCAGTAGGGAAACAGATCAAA
1 CTTATCTCCCTAAGCAGTAGGGTAACAGACCAAA
28065460 GGTGACAAGC
Statistics
Matches: 258, Mismatches: 56, Indels: 41
0.73 0.16 0.12
Matches are distributed among these distances:
41 6 0.02
42 110 0.43
43 65 0.25
44 70 0.27
45 7 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (42 bp):
CTTATCTCCCTAAGCAGTAGGGTAACAGACCAAATTGCAGAT
Found at i:28065398 original size:128 final size:128
Alignment explanation
Indices: 28065263--28065497 Score: 348
Period size: 128 Copynumber: 1.8 Consensus size: 128
28065253 GGTCTTAAAC
* * * * *
28065263 CCCTAAGCAGTAGGGTAACAGACCAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGA
1 CCCTAAGCAGTAAGGTAACAGACCAAATTACAAATCTTATCTACCTAAGCAGTAG-GGAAACAGA
* * *
28065327 TCGAAGACGA-AGGGTCTTAAACCCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATCT
65 TCAAAGACGACA-AGCCTTAAACCCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATCT
28065391 CCCTAAGCAGTAAGGTAACAGACCAAATTACAAATCTTATCTACCTAAGCAGTAGGGAAACAGAT
1 CCCTAAGCAGTAAGGTAACAGACCAAATTACAAATCTTATCTACCTAAGCAGTAGGGAAACAGAT
**
28065456 CAAAGGTGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAG
66 CAAAGACGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAG
28065498 GCTGAAGATT
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
127 2 0.02
128 92 0.97
129 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (128 bp):
CCCTAAGCAGTAAGGTAACAGACCAAATTACAAATCTTATCTACCTAAGCAGTAGGGAAACAGAT
CAAAGACGACAAGCCTTAAACCCCTAAACAGTAGGGTAACAGACCAAATTGCAGATATTATCT
Found at i:28065561 original size:89 final size:87
Alignment explanation
Indices: 28065391--28065604 Score: 225
Period size: 89 Copynumber: 2.4 Consensus size: 87
28065381 GATATTATCT
* * * * *
28065391 CCCTAAGCAGTAAGGTAACAGAC-CAAATTACAAATCTTATCTACCTAAGCAGTAGGGAAACAGA
1 CCCTAAGCAGTAGGGTAACAGGCTGAAATTACAAATCTTAACCACCTAAGCAGTAGGGAAACAGA
*
28065455 TCAAAGGTGACAAGCCTTAAAC
66 GCAAAGGTGACAAGCCTTAAAC
* * *
28065477 CCCTAAACAGTAGGGTAACAGGCTGAAGATTGACAAATCTTAACCCCCTAAGCAGTAGGGAAGCA
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-ATT-ACAAATCTTAACCACCTAAGCAGTAGGGAAACA
* ***
28065542 TAGCAGAA-GTGATGGGCCTTAAAC
64 GAGCA-AAGGTGACAAGCCTTAAAC
* * * *
28065566 CCCTGAGCAATAGGGTCACAAGCTGGAAATTACAAATCT
1 CCCTAAGCAGTAGGGTAACAGGCT-GAAATTACAAATCT
28065605 CTTCTCCTTA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
86 20 0.19
87 2 0.02
88 11 0.10
89 67 0.64
90 5 0.05
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAAATTACAAATCTTAACCACCTAAGCAGTAGGGAAACAGA
GCAAAGGTGACAAGCCTTAAAC
Found at i:28065724 original size:44 final size:45
Alignment explanation
Indices: 28065648--28065769 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 45
28065638 GCCACAGTAG
* * * * **
28065648 ATCTCCTTGAAGTTTCAGCGGAGTAGATTGAAG-TCA-CATGTCTT
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGAT-AGCAAATCTT
*
28065692 ATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGATAGCAAATCTT
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGCAAATCTT
* ** *
28065737 ATTTCCCTGAAGTTGTAGTGGAACAGATTGAAG
1 ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAG
28065770 CTAAATAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 29 0.45
45 35 0.55
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
ATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGATAGCAAATCTT
Found at i:28067388 original size:2 final size:2
Alignment explanation
Indices: 28067381--28067416 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28067371 CTAACTCTAC
*
28067381 AT AT AT AT AT AT AT AT AC 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
28067417 TAGCGTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28074860 original size:13 final size:14
Alignment explanation
Indices: 28074844--28074879 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28074834 CAATCTCATA
28074844 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
28074857 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
28074870 TCTC-ATTTCA
1 TCTCAATTTCA
28074880 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:28074869 original size:18 final size:19
Alignment explanation
Indices: 28074831--28074871 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28074821 TGGTTCATGT
28074831 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
28074850 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
28074868 TTTC
1 TTTC
28074872 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:28075061 original size:39 final size:38
Alignment explanation
Indices: 28074994--28075128 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
28074984 ACCAATATGG
* * *
28074994 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
28075033 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
28075071 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
28075112 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
28075129 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:28075393 original size:18 final size:19
Alignment explanation
Indices: 28075367--28075405 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28075357 TTTCAATTCA
28075367 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
28075386 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
28075404 AT
1 AT
28075406 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:28076739 original size:12 final size:12
Alignment explanation
Indices: 28076722--28076768 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
28076712 TTTACTTATT
28076722 TATATAATATAA
1 TATATAATATAA
28076734 TATATAATATAA
1 TATATAATATAA
28076746 TATACT-ATAATAA
1 TATA-TAAT-ATAA
28076759 TA-ATAATATA
1 TATATAATATA
28076769 TATTTTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.12
12 21 0.66
13 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATAATATAA
Found at i:28081305 original size:13 final size:14
Alignment explanation
Indices: 28081289--28081324 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28081279 CAATCTCATA
28081289 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
28081302 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
28081315 TCTC-ATTTCA
1 TCTCAATTTCA
28081325 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:28081314 original size:18 final size:19
Alignment explanation
Indices: 28081276--28081316 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28081266 TGGTTCATGT
28081276 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
28081295 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
28081313 TTTC
1 TTTC
28081317 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:28081506 original size:39 final size:38
Alignment explanation
Indices: 28081439--28081573 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
28081429 ACCAATATGG
* * *
28081439 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
28081478 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
28081516 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
28081557 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
28081574 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:28081838 original size:18 final size:19
Alignment explanation
Indices: 28081812--28081850 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
28081802 TTTCAATTCA
28081812 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
28081831 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
28081849 AT
1 AT
28081851 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:28082728 original size:5 final size:5
Alignment explanation
Indices: 28082718--28082765 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
28082708 TTACTTATTT
* *
28082718 ATATA ATATA ATATAA TATATA ATATA CTATA ATAATA ATTTA ATATA
1 ATATA ATATA ATAT-A -ATATA ATATA ATATA AT-ATA ATATA ATATA
28082766 TATTTTAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 25 0.69
6 7 0.19
7 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:28082739 original size:17 final size:17
Alignment explanation
Indices: 28082717--28082765 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
28082707 TTTACTTATT
28082717 TATATAATATAATATAA
1 TATATAATATAATATAA
*
28082734 TATATAATATACTATAA
1 TATATAATATAATATAA
*
28082751 TA-ATAATTTAATATA
1 TATATAATATAATATA
28082766 TATTTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATATAATATAATATAA
Found at i:28083710 original size:19 final size:19
Alignment explanation
Indices: 28083682--28083728 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
28083672 ACCTGTCAGA
28083682 AGTAAATAAAAGAAAAATT
1 AGTAAATAAAAGAAAAATT
* *
28083701 AGTAATTAAAATAAAAA-T
1 AGTAAATAAAAGAAAAATT
28083719 AG-AAATAAAA
1 AGTAAATAAAA
28083729 ATAAATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 15 0.60
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (19 bp):
AGTAAATAAAAGAAAAATT
Found at i:28083729 original size:18 final size:18
Alignment explanation
Indices: 28083685--28083733 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
28083675 TGTCAGAAGT
*
28083685 AAATAAAAGA-AAAATTAG
1 AAATAAAA-ATAAAAATAG
* *
28083703 TAATTAAAATAAAAATAG
1 AAATAAAAATAAAAATAG
28083721 AAATAAAAATAAA
1 AAATAAAAATAAA
28083734 TTTCAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAAATAAAAATAG
Found at i:28098610 original size:22 final size:22
Alignment explanation
Indices: 28098582--28098657 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
28098572 ACATGCATAT
28098582 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
28098604 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
28098628 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
28098651 ATGTGAT
1 ATGTGAT
28098658 GAATGTGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 15 0.37
23 9 0.22
24 9 0.22
25 8 0.20
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:28098798 original size:22 final size:22
Alignment explanation
Indices: 28098723--28098798 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
28098713 ACATGCATAT
*
28098723 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
28098745 ATGTGATAAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
28098769 CATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
28098792 ATGTGAT
1 ATGTGAT
28098799 GAACGTGGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:28098835 original size:47 final size:47
Alignment explanation
Indices: 28098400--28098801 Score: 642
Period size: 47 Copynumber: 8.6 Consensus size: 47
28098390 ATACATAAGC
* * * *
28098400 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGC
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
** * *
28098447 TAAGGCCGAATGGAAAATGTGATGAATGTGAACATGCATTTGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * *
28098494 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
28098541 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
28098588 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
28098635 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
28098682 TAAGGCCGAATGGCCAATGTGAAGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
28098729 TAAGGCCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
28098776 TAAGGCAGAATGGCCAATGTGATGAA
1 TAAGGCCGAATGGCCAATGTGATGAA
28098802 CGTGGATGTG
Statistics
Matches: 333, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 333 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
Found at i:28098868 original size:46 final size:46
Alignment explanation
Indices: 28098815--28098905 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
28098805 GGATGTGTAT
* * *
28098815 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
28098861 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
28098906 TGTGTATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:28109151 original size:19 final size:19
Alignment explanation
Indices: 28109127--28109165 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
28109117 TCAGTGAATA
28109127 TTTTAAAAAA-AATAATTTT
1 TTTTAAAAAACAA-AATTTT
28109146 TTTTAAAAAACAAAATTTT
1 TTTTAAAAAACAAAATTTT
28109165 T
1 T
28109166 ATAATGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAAAAACAAAATTTT
Found at i:28109153 original size:18 final size:19
Alignment explanation
Indices: 28109127--28109165 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28109117 TCAGTGAATA
*
28109127 TTTTAAAAAAA-ATAATTT
1 TTTTAAAAAAACAAAATTT
*
28109145 TTTTTAAAAAACAAAATTT
1 TTTTAAAAAAACAAAATTT
28109164 TT
1 TT
28109166 ATAATGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTAAAAAAACAAAATTT
Found at i:28109368 original size:21 final size:22
Alignment explanation
Indices: 28109333--28109374 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28109323 AAAAAACTCT
*
28109333 AAAATATTAATAAAAATTAATA
1 AAAATATTAATAAAAACTAATA
*
28109355 AAAATATTTA-AAAAACTAAT
1 AAAATATTAATAAAAACTAAT
28109375 CTTCATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATATTAATAAAAACTAATA
Found at i:28109795 original size:31 final size:31
Alignment explanation
Indices: 28109751--28109823 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
28109741 TTTATTGTAA
* **
28109751 ATTTAAATA-TTTCTTATTGTTTCTAATAAT
1 ATTTTAATATTTTCTTATAATTTCTAATAAT
*
28109781 ATTTTAATATTTTCTTATAATTTTTAATAAT
1 ATTTTAATATTTTCTTATAATTTCTAATAAT
28109812 -TTTCT-ATATTTT
1 ATTT-TAATATTTT
28109824 AAATTGATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 18 0.49
31 19 0.51
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (31 bp):
ATTTTAATATTTTCTTATAATTTCTAATAAT
Found at i:28109800 original size:21 final size:21
Alignment explanation
Indices: 28109770--28109817 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28109760 TTTCTTATTG
28109770 TTTCTAATAATATTTTAAT-AT
1 TTTCTAATAAT-TTTTAATAAT
*
28109791 TTTCTTATAATTTTTAATAAT
1 TTTCTAATAATTTTTAATAAT
28109812 TTTCTA
1 TTTCTA
28109818 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTCTAATAATTTTTAATAAT
Found at i:28109803 original size:11 final size:11
Alignment explanation
Indices: 28109770--28109817 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
28109760 TTTCTTATTG
28109770 TTTCTAATAAT
1 TTTCTAATAAT
28109781 ATTT-TAAT-AT
1 -TTTCTAATAAT
*
28109791 TTTCTTATAAT
1 TTTCTAATAAT
28109802 TTT-TAATAAT
1 TTTCTAATAAT
28109812 TTTCTA
1 TTTCTA
28109818 TATTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 3 0.10
10 14 0.45
11 11 0.35
12 3 0.10
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTCTAATAAT
Found at i:28109819 original size:20 final size:19
Alignment explanation
Indices: 28109770--28109823 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
28109760 TTTCTTATTG
28109770 TTTCTAATAATATTTTAATAT
1 TTTCT-ATAAT-TTTTAATAT
28109791 TTTCTTATAATTTTTAATAAT
1 TTTC-TATAATTTTTAAT-AT
28109812 TTTCTAT-ATTTT
1 TTTCTATAATTTT
28109824 AAATTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 15 0.48
22 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTCTATAATTTTTAATAT
Found at i:28111801 original size:25 final size:26
Alignment explanation
Indices: 28111760--28111832 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
28111750 ATACACCTTA
28111760 GCTC-TTATGAGCATTCCGATT-ATAG
1 GCTCTTTATGAGC-TTCCGATTAATAG
*
28111785 GCTCTTTATGAGCTTCCCG-TTAAATTG
1 GCTCTTTATGAGCTT-CCGATT-AATAG
*
28111812 GCTCTTTGTGAGCTTCTCGAT
1 GCTCTTTATGAGCTTC-CGAT
28111833 AGTGTCTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 8 0.20
26 12 0.30
27 19 0.47
28 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (26 bp):
GCTCTTTATGAGCTTCCGATTAATAG
Found at i:28114357 original size:12 final size:12
Alignment explanation
Indices: 28114342--28114367 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28114332 GTAAATAATG
28114342 AAAATAATAGTA
1 AAAATAATAGTA
28114354 AAAATAATAGTA
1 AAAATAATAGTA
28114366 AA
1 AA
28114368 GGAGAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAATAATAGTA
Found at i:28115315 original size:10 final size:10
Alignment explanation
Indices: 28115288--28115347 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
28115278 TGAAATTCTA
*
28115288 AAAGATAATT
1 AAAGATAAAT
28115298 ACAA-ATAAAT
1 A-AAGATAAAT
28115308 AAAGATAAAT
1 AAAGATAAAT
28115318 AAAGATAAAT
1 AAAGATAAAT
28115328 AAAGATAAAT
1 AAAGATAAAT
28115338 GAAA-ATAAAT
1 -AAAGATAAAT
28115348 CCTAAAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
9 2 0.04
10 39 0.85
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28117600 original size:11 final size:11
Alignment explanation
Indices: 28117586--28117610 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28117576 ATTTATCATC
28117586 TATTATTATTT
1 TATTATTATTT
28117597 TATTATTATTT
1 TATTATTATTT
28117608 TAT
1 TAT
28117611 CCTACATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:28125588 original size:21 final size:21
Alignment explanation
Indices: 28125555--28125594 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28125545 GACTAAATCA
28125555 AAAACATTTAAAAATTTAAGG
1 AAAACATTTAAAAATTTAAGG
28125576 AAAA-ATTTAAAAAATTTAA
1 AAAACATTT-AAAAATTTAA
28125595 TTACAGGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAACATTTAAAAATTTAAGG
Found at i:28132193 original size:19 final size:19
Alignment explanation
Indices: 28132164--28132210 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28132154 TTAAATATGA
28132164 TGGCC-TTAAATG-GTAAG
1 TGGCCATTAAATGTGTAAG
28132181 TAGGCCATTAAATGTGTAAG
1 T-GGCCATTAAATGTGTAAG
*
28132201 TGGACATTAA
1 TGGCCATTAA
28132211 TGGACATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
19 15 0.58
20 6 0.23
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (19 bp):
TGGCCATTAAATGTGTAAG
Found at i:28140915 original size:30 final size:30
Alignment explanation
Indices: 28140879--28140946 Score: 122
Period size: 28 Copynumber: 2.3 Consensus size: 30
28140869 CGTGTGTCTT
28140879 AGCCGTGTGCGACACACGGTCATGTTACAC
1 AGCCGTGTGCGACACACGGTCATGTTACAC
28140909 AGCC--GTGCGACACACGGTCATGTTACAC
1 AGCCGTGTGCGACACACGGTCATGTTACAC
28140937 AGCCGTGTGC
1 AGCCGTGTGC
28140947 CCCTGGTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 28 0.78
30 8 0.22
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (30 bp):
AGCCGTGTGCGACACACGGTCATGTTACAC
Found at i:28142090 original size:29 final size:30
Alignment explanation
Indices: 28142034--28142099 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
28142024 CGTATTTCGG
* *
28142034 TGATGGACGATTTAATTGATGGTTGTATTT
1 TGATGGACAATTTAATTGATGCTTGTATTT
28142064 TGATGGACAATTT-ATTGATGCTTGTATTT
1 TGATGGACAATTTAATTGATGCTTGTATTT
28142093 TGATGGA
1 TGATGGA
28142100 TGGTTCAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (30 bp):
TGATGGACAATTTAATTGATGCTTGTATTT
Found at i:28146286 original size:17 final size:16
Alignment explanation
Indices: 28146249--28146287 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
28146239 AACAAAAAAT
28146249 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
28146264 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
28146282 TAAATT
1 TAAATT
28146288 CGGGTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:28151672 original size:42 final size:42
Alignment explanation
Indices: 28151564--28151724 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 42
28151554 AGCACATATA
* * * *
28151564 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCGAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAATA-CG
* *
28151607 ATGCC-ACTGTGCCAGACAGGGTCTTACACGAAATCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAATACG
* * * *
28151649 ATGCCAATGTCCCAAACATGGTCTTACATGTAAATCATAAGT-CA
1 ATGCCAACGTCCCAGACATGGTCTTACACG-AAATCA-AA-TACG
*
28151693 ATGCCAACGTCCCAGACGT-GTCTTACACGAAA
1 ATGCCAACGTCCCAGACATGGTCTTACACGAAA
28151725 ACACATATCG
Statistics
Matches: 97, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 30 0.31
43 47 0.48
44 19 0.20
45 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAATACG
Found at i:28151716 original size:85 final size:85
Alignment explanation
Indices: 28151564--28151724 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 85
28151554 AGCACATATA
* * * *
28151564 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCGAATATCGATGCCACTGTGCCAGACAGGGT
1 ATGCCAACGTCCCAAACATGGTCTTACATGTAATCGAATATCAATGCCACTGTCCCAGACAGGGT
28151629 CTTACACGAAATCAAATACG
66 CTTACACGAAATCAAATACG
*
28151649 ATGCCAATGTCCCAAACATGGTCTTACATGTAAATC--ATAAGTCAATGCCAAC-GTCCCAGAC-
1 ATGCCAACGTCCCAAACATGGTCTTACATGT-AATCGAAT-A-TCAATGCC-ACTGTCCCAGACA
*
28151710 GTGTCTTACACGAAA
62 GGGTCTTACACGAAA
28151725 ACACATATCG
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
84 2 0.03
85 43 0.65
86 19 0.29
87 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (85 bp):
ATGCCAACGTCCCAAACATGGTCTTACATGTAATCGAATATCAATGCCACTGTCCCAGACAGGGT
CTTACACGAAATCAAATACG
Found at i:28158772 original size:42 final size:43
Alignment explanation
Indices: 28158713--28158831 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 43
28158703 TTGAATATCA
* *
28158713 ATGCCACTGTCCTAGACAGGGTCTTACACGAAATCA-AA-TACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCATAAGT-CG
* *
28158755 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAAGTTG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-AAATCATAAGTCG
*
28158799 ATGCCAACGTCCCAGAC-GTGGTCTTACACGAAA
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGAAA
28158832 ACACATATCA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
42 27 0.40
43 9 0.13
44 30 0.45
45 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGAAATCATAAGTCG
Found at i:28158814 original size:44 final size:42
Alignment explanation
Indices: 28158665--28158831 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 42
28158655 CGGAAAGCAC
* * * * * * **
28158665 ATACAATGCCAACATCCTAGACGTGGTCTTACATGTAATTGA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACACGAAATCAA
* * *
28158707 ATATCAATGCC-ACTGTCCTAGACAGGGTCTTACACGAAATCAA
1 ATA-CGATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAA
*
28158750 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATA
1 ATACGATGCCAACGTCCCAGACATGGTCTTACACG-AAATCA-A
* *
28158794 AGT-TGATGCCAACGTCCCAGACGTGGTCTTACACGAAA
1 A-TACGATGCCAACGTCCCAGACATGGTCTTACACGAAA
28158832 ACACATATCA
Statistics
Matches: 105, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
42 31 0.30
43 42 0.40
44 31 0.30
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAGACATGGTCTTACACGAAATCAA
Found at i:28158990 original size:3 final size:3
Alignment explanation
Indices: 28158982--28159023 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28158972 ATATCATATG
28158982 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28159024 TCAATTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28161269 original size:17 final size:16
Alignment explanation
Indices: 28161232--28161270 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
28161222 AATAGACAAT
28161232 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
28161247 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
28161265 TAAATT
1 TAAATT
28161271 CAGGATTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:28174255 original size:26 final size:29
Alignment explanation
Indices: 28174226--28174283 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 29
28174216 AAGTTTTCAA
*
28174226 TTATTTTTAAT-TTTATATA-T-TTTAAT
1 TTATTTTAAATATTTATATATTATTTAAT
28174252 TTATTTTAAATACTTTATATATTATTTAAT
1 TTATTTTAAATA-TTTATATATTATTTAAT
28174282 TT
1 TT
28174284 TTATACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 10 0.37
28 8 0.30
29 1 0.04
30 8 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATTTTAAATATTTATATATTATTTAAT
Found at i:28174259 original size:19 final size:21
Alignment explanation
Indices: 28174235--28174278 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
28174225 ATTATTTTTA
* *
28174235 ATTTTATATATTTTA-AT-TT
1 ATTTTAAATACTTTATATATT
28174254 ATTTTAAATACTTTATATATT
1 ATTTTAAATACTTTATATATT
28174275 ATTT
1 ATTT
28174279 AATTTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.62
20 2 0.10
21 6 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTAAATACTTTATATATT
Found at i:28174355 original size:3 final size:3
Alignment explanation
Indices: 28174337--28174439 Score: 51
Period size: 3 Copynumber: 35.0 Consensus size: 3
28174327 TATATTATCC
* * *
28174337 ATT A-T ATT ATT TTT ATT ATT ATTT ATTT ATAA ATT ATAT GTT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT A-TT A-TT AT-T ATT AT-T ATT ATT ATT
* *
28174384 ATT -TT ATT A-T ATAT ATT A-T ATT A-T ATT A-T ATT ATT TTT A-A
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28174424 ATT ATGT ATT ATT ATT
1 ATT AT-T ATT ATT ATT
28174440 CATTGATTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
2 15 0.19
3 45 0.58
4 17 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28174363 original size:10 final size:10
Alignment explanation
Indices: 28174341--28174439 Score: 52
Period size: 10 Copynumber: 10.0 Consensus size: 10
28174331 TTATCCATTA
28174341 TATTATT-TT
1 TATTATTATT
28174350 TATTATTATT
1 TATTATTATT
*
28174360 TA-T-TTATA
1 TATTATTATT
*
28174368 AATTA-TATGT
1 TATTATTAT-T
28174378 TATTA-TATTT
1 TATTATTA-TT
28174388 TATTATATATAT
1 TATTAT-TAT-T
28174400 TA-TATTATAT
1 TATTATTAT-T
28174410 TA-TATTATT
1 TATTATTATT
*
28174419 T-TTAAATTATG
1 TATT--ATTATT
28174430 TATTATTATT
1 TATTATTATT
28174440 CATTGATTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
8 5 0.07
9 15 0.21
10 34 0.47
11 11 0.15
12 7 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TATTATTATT
Found at i:28174365 original size:39 final size:37
Alignment explanation
Indices: 28174314--28174422 Score: 120
Period size: 39 Copynumber: 3.0 Consensus size: 37
28174304 AAATGATATA
*
28174314 TATTTTTTATTTATATATTATCCATTATATTATTTTTAT
1 TATTATTTATTTATATATTAT--ATTATATTATTTTTAT
*
28174353 TATTATTTATTTATAAATTATATGT-TATTATATTTTAT
1 TATTATTTATTTATATATTATAT-TATATTAT-TTTTAT
*
28174391 TA-TA--TATAT-TATATTATATTATATTATTTTTA
1 TATTATTTATTTATATATTATATTATATTATTTTTA
28174423 AATTATGTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
33 6 0.10
34 15 0.24
35 4 0.06
37 10 0.16
38 9 0.14
39 19 0.30
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (37 bp):
TATTATTTATTTATATATTATATTATATTATTTTTAT
Found at i:28174391 original size:5 final size:5
Alignment explanation
Indices: 28174327--28174417 Score: 77
Period size: 5 Copynumber: 18.6 Consensus size: 5
28174317 TTTTTATTTA
* *
28174327 TATAT TATCCAT TATAT TAT-T TTTAT TATTAT T-TAT T-TA- TAAAT
1 TATAT TAT--AT TATAT TATAT TATAT TA-TAT TATAT TATAT TATAT
*
28174371 TATAT GT-TAT TATAT TTTAT TATA- TATAT TATAT TATAT TATAT TAT
1 TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
28174418 TTTTAAATTA
Statistics
Matches: 71, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
3 1 0.01
4 15 0.21
5 45 0.63
6 5 0.07
7 5 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:28174398 original size:24 final size:24
Alignment explanation
Indices: 28174321--28174417 Score: 84
Period size: 24 Copynumber: 4.2 Consensus size: 24
28174311 ATATATTTTT
28174321 TATT-TATATATTATCCATTATATTA
1 TATTATATATATTAT--ATTATATTA
*
28174346 T-TTTTAT-TATTAT-TTAT-TTA
1 TATTATATATATTATATTATATTA
* *
28174366 TA-AAT-TATATGT-TATTATATTT
1 TATTATATATAT-TATATTATATTA
28174388 TATTATATATATTATATTATATTA
1 TATTATATATATTATATTATATTA
28174412 TATTAT
1 TATTAT
28174418 TTTTAAATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
19 1 0.02
20 9 0.16
21 9 0.16
22 4 0.07
23 3 0.05
24 28 0.48
25 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (24 bp):
TATTATATATATTATATTATATTA
Found at i:28174410 original size:29 final size:29
Alignment explanation
Indices: 28174309--28174415 Score: 93
Period size: 28 Copynumber: 3.8 Consensus size: 29
28174299 GTATAAAATG
* * *
28174309 ATATATATT-TTTTAT-TTATATATTATCC
1 ATATATATTATATTATATTATATTTTAT-T
*
28174337 AT-TATATTAT-TTTTATTAT-TATTTATT
1 ATATATATTATATTATATTATAT-TTTATT
*
28174364 -TATAAATTATATGT-TATTATATTTTATT
1 ATATATATTATAT-TATATTATATTTTATT
28174392 ATATATATTATATTATATTATATT
1 ATATATATTATATTATATTATATT
28174416 ATTTTTAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
26 1 0.02
27 17 0.26
28 25 0.38
29 22 0.34
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.63
Consensus pattern (29 bp):
ATATATATTATATTATATTATATTTTATT
Found at i:28174436 original size:55 final size:52
Alignment explanation
Indices: 28174337--28174438 Score: 134
Period size: 55 Copynumber: 1.9 Consensus size: 52
28174327 TATATTATCC
*
28174337 ATTATATTATTTTTATTATTATTTATTTATAAATTATATGTTATTATATTTT
1 ATTATATTATTTTTATTATTATTTATTTATAAATTATATATTATTATATTTT
* *
28174389 ATTATATATATTATATTA-TATTATATTATTTTTAAATTATGTATTATTAT
1 ATTATAT-TATT-T-TTATTATTAT-TTATTTATAAATTATATATTATTAT
28174439 TCATTGATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
52 7 0.16
53 4 0.09
54 7 0.16
55 25 0.58
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (52 bp):
ATTATATTATTTTTATTATTATTTATTTATAAATTATATATTATTATATTTT
Found at i:28174641 original size:26 final size:26
Alignment explanation
Indices: 28174592--28174641 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
28174582 ATCATATGGT
**
28174592 TTATATTATTATATTTTGGTTATAAG
1 TTATATTATTATATTTTGACTATAAG
28174618 TTATATTATATATATTTT-ACTATA
1 TTATATTAT-TATATTTTGACTATA
28174642 TTATCTCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (26 bp):
TTATATTATTATATTTTGACTATAAG
Found at i:28178039 original size:18 final size:18
Alignment explanation
Indices: 28178018--28178300 Score: 119
Period size: 18 Copynumber: 15.3 Consensus size: 18
28178008 GAACAATTAT
28178018 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
28178036 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
28178054 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
28178072 TTATTCAGTATCGATCAATTGATC-G
1 TTATTCAGTA---A-C-A--G-TCAG
* *
28178097 ATTATCCAGTAACAGTCAA
1 -TTATTCAGTAACAGTCAG
* *
28178116 TTATTCAATAA-AATCAAG
1 TTATTCAGTAACAGTC-AG
* *
28178134 -TATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
28178152 TTATTCATTAACAGTCA-
1 TTATTCAGTAACAGTCAG
* *
28178169 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
28178188 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* * *
28178206 TTATTCAGTAATATTTAG
1 TTATTCAGTAACAGTCAG
28178224 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
28178242 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * * *
28178260 TTATCCGGTAACAGTTAA
1 TTATTCAGTAACAGTCAG
* * *
28178278 TTATTTAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
28178296 TTATT
1 TTATT
28178301 TTATACCTTT
Statistics
Matches: 195, Mismatches: 50, Indels: 40
0.68 0.18 0.14
Matches are distributed among these distances:
17 15 0.08
18 148 0.76
19 16 0.08
21 2 0.01
22 1 0.01
23 2 0.01
25 1 0.01
26 10 0.05
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:28178058 original size:36 final size:36
Alignment explanation
Indices: 28178005--28178300 Score: 177
Period size: 36 Copynumber: 8.0 Consensus size: 36
28177995 TCATTAACAA
* * *
28178005 TCAG-AACAATTATTTATTCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
28178040 TCGGTAACAATCAATTATTCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
28178076 TCAGTATCGATCAATTGATCGATTATCCAGTAACAGTCAATTAT
1 TCAGTA---A-C-A---ATCAATTATTCAGTAACAATCAGTTAT
* * *
28178120 TCAATAA-AATCAAGTATTCAGTAACAATTAAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAA-TCAGTTAT
* * *
28178156 TCATTAACAGTC-ATTCATTCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATT-ATTCAGTAACAATCAGTTAT
** * * *
28178192 TCAGTAATGATCAATTATTCAGTAATATTTAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
* * * *
28178228 TCAGTAACAGTCTAA-TATCCAGTAACAGTCAATTAT
1 TCAGTAACAATC-AATTATTCAGTAACAATCAGTTAT
* * * * * *
28178264 CCGGTAACAGTTAATTATTTAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
28178300 T
1 T
28178301 TTATACCTTT
Statistics
Matches: 194, Mismatches: 52, Indels: 29
0.71 0.19 0.11
Matches are distributed among these distances:
35 20 0.10
36 125 0.64
37 19 0.10
38 1 0.01
39 1 0.01
40 1 0.01
41 2 0.01
44 25 0.13
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAGTAACAATCAGTTAT
Found at i:28178137 original size:17 final size:18
Alignment explanation
Indices: 28178106--28178164 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
28178096 GATTATCCAG
* *
28178106 TAACAGTCAATTATTCAA
1 TAACAATCAAGTATTCAA
*
28178124 TAA-AATCAAGTATTCAG
1 TAACAATCAAGTATTCAA
* *
28178141 TAACAATTAAGTTATTCAT
1 TAACAATCAAG-TATTCAA
28178160 TAACA
1 TAACA
28178165 GTCATTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 14 0.41
18 9 0.26
19 11 0.32
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (18 bp):
TAACAATCAAGTATTCAA
Found at i:28178280 original size:72 final size:70
Alignment explanation
Indices: 28178099--28178300 Score: 197
Period size: 72 Copynumber: 2.8 Consensus size: 70
28178089 ATTGATCGAT
* * * * *
28178099 TATCCAGTAACAGTCAATTATTCAATAAAATCAAGTATTCAGTAACAATTAAGTTATTCATTAAC
1 TATCCAGTAACAGTCAATTATTCAGTAAAGTCAATTATTCAGTAA-TATTAAGTTATTCAGTAAC
*
28178164 AGTCAT
65 AGTCAA
* * * * * *
28178170 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTTAGTTATTCAGTAA
1 T-ATCCAGTAACAGTCAATTATTCAGTAAAG-TCAATTATTCAGTAATATTAAGTTATTCAGTAA
28178235 CAGTCTAA
64 CAGTC-AA
* * * * * *
28178243 TATCCAGTAACAGTCAATTATCCGGTAACAGTTAATTATTTAGTAATAATCAGTTATT
1 TATCCAGTAACAGTCAATTATTCAGTAA-AGTCAATTATTCAGTAATATTAAGTTATT
28178301 TTATACCTTT
Statistics
Matches: 104, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
71 1 0.01
72 86 0.83
73 17 0.16
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (70 bp):
TATCCAGTAACAGTCAATTATTCAGTAAAGTCAATTATTCAGTAATATTAAGTTATTCAGTAACA
GTCAA
Found at i:28178468 original size:59 final size:56
Alignment explanation
Indices: 28178370--28178488 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 56
28178360 CCAATACACT
* * * * *
28178370 AGTACGGCACATAGTGCCTCATCGGCCAAAGCCGGAATAGTAACAGTAAGAGTAGC
1 AGTACGGCACAAAGTACCTCATCGGACAAAGCCGGAATAGTAACAGTAACAGTAAC
*
28178426 AGTACGGTACACAAAGTACCTCATCGGAACAAATCCGGAATAGTAACAGTAACAGTAAC
1 AGTACGG--CACAAAGTACCTCATCGG-ACAAAGCCGGAATAGTAACAGTAACAGTAAC
28178485 AGTA
1 AGTA
28178489 TTCAACACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
56 7 0.13
58 16 0.30
59 31 0.57
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (56 bp):
AGTACGGCACAAAGTACCTCATCGGACAAAGCCGGAATAGTAACAGTAACAGTAAC
Found at i:28178517 original size:45 final size:45
Alignment explanation
Indices: 28178468--28178578 Score: 195
Period size: 45 Copynumber: 2.5 Consensus size: 45
28178458 ATCCGGAATA
*
28178468 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
* *
28178513 GTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
28178558 GTAACAGTAACAGTAACAGTA
1 GTAACAGTAACAGTAACAGTA
28178579 ACAGTAGTCG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCG
Found at i:28178569 original size:6 final size:6
Alignment explanation
Indices: 28178558--28178584 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28178548 TGCCGAATCG
28178558 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
28178585 GTCGGCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:28180221 original size:2 final size:2
Alignment explanation
Indices: 28180214--28180248 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28180204 GTTTTACTTG
28180214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28180249 GTTAACTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28180381 original size:31 final size:32
Alignment explanation
Indices: 28180325--28180387 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
28180315 CACACTTGTC
*
28180325 ATAATTTAATATATTTATTACATAAAAATCTT
1 ATAATATAATATATTTATTACATAAAAATCTT
*
28180357 ATAATATAAT-TATTTAATTA-ATAAATATCTT
1 ATAATATAATATATTT-ATTACATAAAAATCTT
28180388 TTATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAATATAATATATTTATTACATAAAAATCTT
Found at i:28180788 original size:31 final size:31
Alignment explanation
Indices: 28180750--28180812 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
28180740 ATTACAAATG
28180750 TATGTACATTATTTATCACACATGTATTTTA
1 TATGTACATTATTTATCACACATGTATTTTA
28180781 TATGTACATTATTTATCACACATGTATTTTA
1 TATGTACATTATTTATCACACATGTATTTTA
28180812 T
1 T
28180813 TTTTATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (31 bp):
TATGTACATTATTTATCACACATGTATTTTA
Found at i:28180811 original size:16 final size:16
Alignment explanation
Indices: 28180761--28180812 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
28180751 ATGTACATTA
28180761 TTTATCACACATGTAT
1 TTTATCACACATGTAT
*
28180777 TTTAT-ATGTACAT-TA-
1 TTTATCA--CACATGTAT
28180792 TTTATCACACATGTAT
1 TTTATCACACATGTAT
28180808 TTTAT
1 TTTAT
28180813 TTTTATCACA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.14
15 8 0.28
16 13 0.45
17 4 0.14
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTATCACACATGTAT
Found at i:28184976 original size:40 final size:39
Alignment explanation
Indices: 28184932--28185235 Score: 403
Period size: 40 Copynumber: 7.7 Consensus size: 39
28184922 GCCACTAGCT
*
28184932 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
28184972 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
*
28185011 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* *
28185051 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
28185090 CAAACGCCTTCGGGACTTAGCCCAGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGTATAGTAACTCGCA
* *
28185130 CGAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
28185170 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
28185210 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
28185236 TATCATCCGA
Statistics
Matches: 238, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
39 76 0.32
40 162 0.68
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:28185030 original size:79 final size:79
Alignment explanation
Indices: 28184932--28185235 Score: 441
Period size: 79 Copynumber: 3.8 Consensus size: 79
28184922 GCCACTAGCT
*
28184932 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
28184997 TATAATAACTCGCA
66 TATAATAACTCGCA
28185011 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
*
28185076 TATAATAACTTGCA
66 TATAATAACTCGCA
* * * * *
28185090 CAAACGCCTTCGGGACTTAGCCCAGATATAGTAGCTCGCACGAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
* *
28185155 ATATAGTAGCTCGCA
66 -TATAATAACTCGCA
* ** * *
28185170 CGAATGCCTTCGGGACTTAGCCCGGA-ATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTTGCACAAATGCCT-TCGGGACTTAGCCC
28185233 GGT
64 GGT
28185236 TATCATCCGA
Statistics
Matches: 203, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
79 141 0.69
80 62 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
TATAATAACTCGCA
Found at i:28185136 original size:119 final size:119
Alignment explanation
Indices: 28184909--28185194 Score: 432
Period size: 119 Copynumber: 2.4 Consensus size: 119
28184899 CCTTCGGAGT
** * *
28184909 TTAG-CCGGATATAGCCACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTTGCAC
* *
28184973 AAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCACAAATGCCTTCGGGAC
66 AAACGCCTTCGGGACTTAGCCCGATATAATAACTCGCACAAATGCCTTCGGGAC
*
28185027 TTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG-TATAATAACTTGCAC
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTTGCAC
* * *
28185091 AAACGCCTTCGGGACTTAGCCCAGATATAGTAGCTCGCACGAATGCCTTCGGGAC
66 AAACGCCTTCGGGACTTAGCCC-GATATAATAACTCGCACAAATGCCTTCGGGAC
* * *
28185146 TTAGCCCGGATATAGTAGCTCGCACGAATGCCTTCGGGACTTAGCCCGG
1 TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
28185195 AATTAGCCAC
Statistics
Matches: 153, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
118 39 0.25
119 114 0.75
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (119 bp):
TTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTTGCAC
AAACGCCTTCGGGACTTAGCCCGATATAATAACTCGCACAAATGCCTTCGGGAC
Found at i:28193937 original size:44 final size:44
Alignment explanation
Indices: 28193795--28194196 Score: 222
Period size: 44 Copynumber: 9.1 Consensus size: 44
28193785 GATCCAAGAT
* * * *
28193795 GATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGA-AACA
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAGCA
* * *
28193838 GATTTGCCATCTCTGTA-T-TCGAAGGGGAGCAGATCGAAGACATAGCT
1 GATTTGGCATCTCTGTATTGTC-AA--AGAGCAGATCGAAG--ATAGCA
* *
28193885 GATTTGGCGTCTTTGTATTGTCAAAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAGCA
* * * *
28193929 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGTA
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAGCA
* *
28193973 GATTTGGCATCTCTGTA-T-TCAACAGGGAGCAGATCGAAGACATAACT
1 GATTTGGCATCTCTGTATTGTCAA-A--GAGCAGATCGAAG--ATAGCA
* * ** * *
28194020 GATTTGGCTTTCACGTGT-TTACGT-TGA-AGCAAATCTAAGAT----
1 GATTTGGC-ATCTC-TGTATT--GTCAAAGAGCAGATCGAAGATAGCA
* * *
28194061 GATTTGGCATCTCTGTATGGTCAGAGAGCAGATCAAAGAT-GACA
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAG-CA
* * * * *
28194105 GATTTGGCGTCACTGTATTGTCAGAGAGCCGATTGAAGAT-GACA
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAG-CA
* * * * * * *
28194149 GATCTGGCGTCTCTATATTGGT-AGAGAGCAGATCAAAAATAACA
1 GATTTGGCATCTCTGTATT-GTCAAAGAGCAGATCGAAGATAGCA
28194193 GATT
1 GATT
28194197 GGTGTTCTTG
Statistics
Matches: 282, Mismatches: 49, Indels: 55
0.73 0.13 0.14
Matches are distributed among these distances:
38 2 0.01
39 5 0.02
40 16 0.06
41 10 0.04
42 5 0.02
43 18 0.06
44 145 0.51
45 16 0.06
46 14 0.05
47 37 0.13
48 6 0.02
49 6 0.02
50 1 0.00
52 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGATAGCA
Found at i:28193962 original size:90 final size:87
Alignment explanation
Indices: 28193794--28194012 Score: 230
Period size: 90 Copynumber: 2.5 Consensus size: 87
28193784 AGATCCAAGA
* * *
28193794 TGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATTTGCCATCTCTGTATTCG
1 TGATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGAAACAGATTTGCCATCTCTGTATTCG
*
28193859 AAGGGGAGCAGATCGAAGACATAG
66 AAGGAGAGCAGATCGAAG--ATAG
* * * * *
28193883 CTGATTTGGCGTCTTTGTATTGTCAAAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATT
1 -TGATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGA-AACAGATTTGCCATCTCTGTATT
* *
28193948 -GTCA-GAGAGTAGATCGAAGATAG
64 CG-AAGGAGAGCAGATCGAAGATAG
28193971 TAGATTTGGCATCTCTGTA-T-TCAACAGGGAGCAGATCGAAGA
1 T-GATTTGGCATCTCTGTATTGTCAA-A--GAGCAGATCGAAGA
28194013 CATAACTGAT
Statistics
Matches: 110, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
86 4 0.04
87 3 0.03
88 19 0.17
89 14 0.13
90 49 0.45
91 21 0.19
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (87 bp):
TGATTTGGCATCTCTGTATTGTCAAAGAGCAGATCGAAGAAACAGATTTGCCATCTCTGTATTCG
AAGGAGAGCAGATCGAAGATAG
Found at i:28194121 original size:132 final size:129
Alignment explanation
Indices: 28193777--28194123 Score: 376
Period size: 132 Copynumber: 2.6 Consensus size: 129
28193767 AGTATTTACA
* * *
28193777 CTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAAACAGATT
1 CTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATACAGATT
* * * **
28193842 TGCCATCTCTGTATTCGAAGGGGAGCAGATCGAAGACATAGCTGATTTGGCGTCTTTGTATTGT
66 TGGCATCTCTGTATTCGAAAGGGAGCAGATCGAAGACATAACTGATTTGGCGTCCGTGTATTGT
** * * *
28193906 CAAAGAGCAGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAG
1 CTGA-AGCAGATCCAAGAT----GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATA-
* *
28193971 TAGATTTGGCATCTCTGTATTC-AACAGGGAGCAGATCGAAGACATAACTGATTTGGCTTTCACG
60 CAGATTTGGCATCTCTGTATTCGAA-AGGGAGCAGATCGAAGACATAACTGATTTGGC-GTC-CG
28194035 TGT-TTACGT
122 TGTATT--GT
* * * *
28194044 -TGAAGCAAATCTAAGATGATTTGGCATCTCTGTATGGTCAGAGAGCAGATCAAAGATGACAGAT
1 CTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGAT-ACAGAT
* *
28194108 TTGGCGTCACTGTATT
65 TTGGCATCTCTGTATT
28194124 GTCAGAGAGC
Statistics
Matches: 180, Mismatches: 26, Indels: 21
0.79 0.11 0.09
Matches are distributed among these distances:
129 2 0.01
130 13 0.07
132 54 0.30
133 1 0.01
134 38 0.21
135 50 0.28
136 16 0.09
137 4 0.02
138 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (129 bp):
CTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATACAGATT
TGGCATCTCTGTATTCGAAAGGGAGCAGATCGAAGACATAACTGATTTGGCGTCCGTGTATTGT
Found at i:28195818 original size:21 final size:19
Alignment explanation
Indices: 28195776--28195818 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28195766 ATTTTAATCC
* *
28195776 TTTTATATATTTTAATTTA
1 TTTTAAATACTTTAATTTA
28195795 TTTTAAATACTTTATATATTA
1 TTTTAAATACTTTA-AT-TTA
28195816 TTT
1 TTT
28195819 AATTTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAAATACTTTAATTTA
Found at i:28195944 original size:5 final size:5
Alignment explanation
Indices: 28195927--28195956 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
28195917 TATTATACGT
28195927 TATTA TA-TA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA T
28195957 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:28196146 original size:21 final size:20
Alignment explanation
Indices: 28196088--28196147 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
28196078 ATACTACATT
28196088 TTATTATATATTT--TTATA
1 TTATTATATATTTGGTTATA
*
28196106 TTATT-TATCATATGGTTTATA
1 TTATTATAT-ATTTGG-TTATA
28196127 TTATTATATATTTTGGTTATA
1 TTATTATATA-TTTGGTTATA
28196148 AGTTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 8 0.24
21 16 0.47
22 7 0.21
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (20 bp):
TTATTATATATTTGGTTATA
Found at i:28197607 original size:21 final size:21
Alignment explanation
Indices: 28197582--28197646 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
28197572 TAGCCTTCAG
28197582 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
28197603 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
28197621 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
28197642 GCTTC
1 GCTTC
28197647 AGTTAGACTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.20
19 8 0.23
20 8 0.23
21 12 0.34
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:28197613 original size:39 final size:39
Alignment explanation
Indices: 28197566--28197663 Score: 178
Period size: 39 Copynumber: 2.5 Consensus size: 39
28197556 TCATACGAGT
*
28197566 TTCAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGTGC
1 TTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGC
28197605 TTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGC
1 TTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGC
*
28197644 TTCAGTTAGACTTCGGGCTT
1 TTCAGTTAGCCTTCGGGCTT
28197664 TAGATCACGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.39
Consensus pattern (39 bp):
TTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGTGC
Found at i:28200898 original size:40 final size:40
Alignment explanation
Indices: 28200799--28201036 Score: 344
Period size: 40 Copynumber: 6.0 Consensus size: 40
28200789 ATGATAACCT
* *
28200799 GGCTAAGTCCCGAAGG-ATTTGTGCTAGTGACTA-ATTCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
28200837 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
28200876 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
28200916 GGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATATCCG
**
28200956 GGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* **
28200996 GGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
28201036 G
1 G
28201037 TTAAAGCCCG
Statistics
Matches: 186, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
37 7 0.04
38 28 0.15
39 9 0.05
40 139 0.75
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:28209167 original size:40 final size:39
Alignment explanation
Indices: 28209112--28209354 Score: 330
Period size: 40 Copynumber: 6.1 Consensus size: 39
28209102 CGGATGATAA
*
28209112 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ACTATA-T
*
28209152 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATA-T
*
28209192 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TACTATAT
28209231 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTACTATAT
*
28209271 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTACTATAT
* * *
28209311 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGT-ACTATAT
28209351 CCGG
1 CCGG
28209355 TTAAAGCCCG
Statistics
Matches: 191, Mismatches: 7, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
39 39 0.20
40 149 0.78
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTACTATAT
Found at i:28209244 original size:79 final size:80
Alignment explanation
Indices: 28209112--28209354 Score: 368
Period size: 80 Copynumber: 3.0 Consensus size: 80
28209102 CGGATGATAA
* *
28209112 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
28209176 GTGCGAGTTACTA-ATT
65 GTGCGAGTTACTATA-T
28209192 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
28209256 TGCGAAG-TACTATAT
66 TGCG-AGTTACTATAT
**
28209271 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* **
28209336 AGCGAGTGGCTATAT
66 TGCGAGTTACTATAT
28209351 CCGG
1 CCGG
28209355 TTAAAGCCCG
Statistics
Matches: 151, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
79 72 0.48
80 79 0.52
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:28209323 original size:119 final size:120
Alignment explanation
Indices: 28209112--28209354 Score: 377
Period size: 119 Copynumber: 2.0 Consensus size: 120
28209102 CGGATGATAA
*
28209112 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
** * *
28209177 TGCGAGTTACTAATTCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
66 TGCGAACTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
28209231 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATT
*
28209294 TGTGCGAACTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
64 TGTGCGAACTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
28209351 CCGG
1 CCGG
28209355 TTAAAGCCCG
Statistics
Matches: 114, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
118 4 0.04
119 78 0.68
120 32 0.28
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (120 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAACTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
Found at i:28211527 original size:23 final size:25
Alignment explanation
Indices: 28211467--28211525 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
28211457 TTTTTTTAAA
*
28211467 AAAATTTTAAAATATATTTATATAT
1 AAAATTTTAAAATATATTCATATAT
*
28211492 AAAATTGTAAAATATA-TCAT-TAT
1 AAAATTTTAAAATATATTCATATAT
28211515 -AAATTTTAAAA
1 AAAATTTTAAAA
28211526 ATTCAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.32
23 3 0.10
24 3 0.10
25 15 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAATTTTAAAATATATTCATATAT
Found at i:28211669 original size:22 final size:22
Alignment explanation
Indices: 28211636--28211678 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28211626 AAAAAATTAT
*
28211636 TTTTAAACTTTTTTTAATTTTC
1 TTTTAAACTTTTTATAATTTTC
28211658 TTTTACAA-TTTTTATAATTTT
1 TTTTA-AACTTTTTATAATTTT
28211679 TTTACGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTAAACTTTTTATAATTTTC
Found at i:28211734 original size:16 final size:15
Alignment explanation
Indices: 28211693--28211731 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28211683 CGTTTTTAAT
*
28211693 AATATTATTAATTTC
1 AATATTTTTAATTTC
28211708 AATATTTTTAATTATC
1 AATATTTTTAATT-TC
28211724 -ATATTTTT
1 AATATTTTT
28211732 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTTAATTTC
Found at i:28211742 original size:20 final size:19
Alignment explanation
Indices: 28211717--28211769 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
28211707 CAATATTTTT
28211717 AATTATCATATTTTTTAAAA
1 AATTAT-ATATTTTTTAAAA
* *
28211737 AATTATA-ATTTTTTTATA
1 AATTATATATTTTTTAAAA
*
28211755 AATTATATGTTTTTT
1 AATTATATATTTTTT
28211770 TTCTAGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 16 0.55
19 7 0.24
20 6 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTATATATTTTTTAAAA
Found at i:28211770 original size:20 final size:20
Alignment explanation
Indices: 28211745--28211782 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28211735 AAAATTATAA
28211745 TTTTTTTATAAATTATATGT
1 TTTTTTTATAAATTATATGT
* *
28211765 TTTTTTTCTAGATTATAT
1 TTTTTTTATAAATTATAT
28211783 ATATTCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTTTTTATAAATTATATGT
Found at i:28219847 original size:40 final size:39
Alignment explanation
Indices: 28219792--28220031 Score: 378
Period size: 40 Copynumber: 6.1 Consensus size: 39
28219782 CGGATGATAA
*
28219792 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATA-T
28219832 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
28219871 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
28219910 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAT
*
28219950 CCGGGCTAAGTCCCGAAGGCATTTGTGCGACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
* *
28219989 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
28220028 CCGG
1 CCGG
28220032 TTAAAGCCCG
Statistics
Matches: 191, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
38 25 0.13
39 74 0.39
40 89 0.47
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:28220000 original size:118 final size:118
Alignment explanation
Indices: 28219792--28220031 Score: 380
Period size: 118 Copynumber: 2.0 Consensus size: 118
28219782 CGGATGATAA
*
28219792 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
* *
28219857 TGCGAGTTACTAATCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAT
66 TGCGAGCTACTAATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TACTATAT
28219910 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATT
*
28219973 TGTGCGA-CTACTATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGCTATAT
64 TGTGCGAGCTACTA-ATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTACTATAT
28220028 CCGG
1 CCGG
28220032 TTAAAGCCCG
Statistics
Matches: 114, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
117 7 0.06
118 86 0.75
119 21 0.18
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (118 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGCTACTAATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTACTATAT
Found at i:28222400 original size:16 final size:15
Alignment explanation
Indices: 28222359--28222397 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28222349 CGTTTTTAAT
*
28222359 AATATTATTAATTTC
1 AATATTTTTAATTTC
28222374 AATATTTTTAATTATC
1 AATATTTTTAATT-TC
28222390 -ATATTTTT
1 AATATTTTT
28222398 TAAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTTAATTTC
Found at i:28222433 original size:20 final size:20
Alignment explanation
Indices: 28222393--28222450 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
28222383 AATTATCATA
*
28222393 TTTTTTAAAAATTATA-ATT
1 TTTTTTATAAATTATATATT
*
28222412 TTTTTTATAAATTATATGTT
1 TTTTTTATAAATTATATATT
* *
28222432 TTTTTTCTAGATTATATAT
1 TTTTTTATAAATTATATAT
28222451 ATTCTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTTATAAATTATATATT
Found at i:28222436 original size:19 final size:19
Alignment explanation
Indices: 28222383--28222436 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
28222373 CAATATTTTT
* *
28222383 AATTATCATATTTTTTAAA
1 AATTATAATTTTTTTTAAA
*
28222402 AATTATAATTTTTTTTATA
1 AATTATAATTTTTTTTAAA
28222421 AATTAT-ATGTTTTTTT
1 AATTATAAT-TTTTTTT
28222437 TCTAGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 2 0.06
19 29 0.94
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
AATTATAATTTTTTTTAAA
Found at i:28222462 original size:27 final size:27
Alignment explanation
Indices: 28222431--28222486 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
28222421 AATTATATGT
* *
28222431 TTTTTTTCTAGATTATATATATTCTAAA
1 TTTTTTTATAAATT-TATATATTCTAAA
*
28222459 TTTTTTTATAAATTTATATATTTTAAA
1 TTTTTTTATAAATTTATATATTCTAAA
28222486 T
1 T
28222487 GTGTAGGACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTTTTATAAATTTATATATTCTAAA
Found at i:28230577 original size:40 final size:40
Alignment explanation
Indices: 28230471--28230712 Score: 368
Period size: 40 Copynumber: 6.1 Consensus size: 40
28230461 CGGATGATAA
* *
28230471 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
28230511 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
28230550 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28230590 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
28230630 CCGGGCTAAGTCCCGAAGGCATTTGTGCGA-CTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
28230669 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
28230709 CCGG
1 CCGG
28230713 TTAAAGCCCG
Statistics
Matches: 191, Mismatches: 6, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
39 75 0.39
40 113 0.59
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28230602 original size:79 final size:80
Alignment explanation
Indices: 28230471--28230712 Score: 368
Period size: 79 Copynumber: 3.0 Consensus size: 80
28230461 CGGATGATAA
* *
28230471 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGT-CCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTT
28230534 GTGCGAGTTACTA-ATT
65 GTGCGAGTTACTATA-T
28230550 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
28230615 TGCGAAG-TACTATAT
66 TGCG-AGTTACTATAT
*
28230630 CCGGGCTAAGTCCCGAAGGCATTTGTGCGA-CTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* **
28230694 AGCGAGTGGCTATAT
66 TGCGAGTTACTATAT
28230709 CCGG
1 CCGG
28230713 TTAAAGCCCG
Statistics
Matches: 152, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
78 2 0.01
79 93 0.61
80 54 0.36
81 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATAT
Found at i:28230682 original size:119 final size:119
Alignment explanation
Indices: 28230471--28230712 Score: 375
Period size: 119 Copynumber: 2.0 Consensus size: 119
28230461 CGGATGATAA
*
28230471 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGT
* * *
28230536 GCGAGTTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
66 GCGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
28230590 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACT-ATATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTGACTAAT-TCCGGGCTAAGT-CCGAAGGCATT
*
28230653 TGTGCGA-CTACT-ATATCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
63 TGTGCGAGCTACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
28230709 CCGG
1 CCGG
28230713 TTAAAGCCCG
Statistics
Matches: 114, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
118 4 0.04
119 89 0.78
120 21 0.18
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTAATTCCGGGCTAAGTCCGAAGGCATTTGT
GCGAGCTACTAATTCCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGACTATAT
Found at i:28232882 original size:23 final size:25
Alignment explanation
Indices: 28232822--28232880 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
28232812 ATTTTTTAAA
*
28232822 AAAATTTTAAAATATATTTATATAT
1 AAAATTTTAAAATATATTCATATAT
*
28232847 AAAATTGTAAAATATA-TCAT-TAT
1 AAAATTTTAAAATATATTCATATAT
28232870 -AAATTTTAAAA
1 AAAATTTTAAAA
28232881 ATTCAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.32
23 3 0.10
24 3 0.10
25 15 0.48
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAATTTTAAAATATATTCATATAT
Found at i:28233024 original size:22 final size:22
Alignment explanation
Indices: 28232991--28233033 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28232981 AAAAAATTAT
*
28232991 TTTTAAACTTTTTTTAATTTTC
1 TTTTAAACTTTTTATAATTTTC
28233013 TTTTACAA-TTTTTATAATTTT
1 TTTTA-AACTTTTTATAATTTT
28233034 TTTACGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTAAACTTTTTATAATTTTC
Found at i:28233089 original size:16 final size:15
Alignment explanation
Indices: 28233048--28233086 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28233038 CGTTTTTAAT
*
28233048 AATATTATTAATTTC
1 AATATTTTTAATTTC
28233063 AATATTTTTAATTATC
1 AATATTTTTAATT-TC
28233079 -ATATTTTT
1 AATATTTTT
28233087 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTTTAATTTC
Found at i:28233123 original size:19 final size:19
Alignment explanation
Indices: 28233072--28233126 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
28233062 CAATATTTTT
* *
28233072 AATTATCATATTTTTTAAAA
1 AATTATAAT-TTTTTTTAAA
*
28233092 AATTATAATTTTTTTTATA
1 AATTATAATTTTTTTTAAA
28233111 AATTAT-ATGTTTTTTT
1 AATTATAAT-TTTTTTT
28233127 TCTAGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.06
19 21 0.68
20 8 0.26
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTATAATTTTTTTTAAA
Found at i:28233126 original size:20 final size:20
Alignment explanation
Indices: 28233072--28233140 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
28233062 CAATATTTTT
* *
28233072 AATTATCATA-TTTTTTAAAA
1 AATTAT-ATATTTTTTTTATA
28233092 AATTATA-ATTTTTTTTATA
1 AATTATATATTTTTTTTATA
* *
28233111 AATTATATGTTTTTTTTCTA
1 AATTATATATTTTTTTTATA
*
28233131 GATTATATAT
1 AATTATATAT
28233141 ATTCTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.02
19 16 0.39
20 24 0.59
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTATATATTTTTTTTATA
Found at i:28239529 original size:18 final size:17
Alignment explanation
Indices: 28239498--28239543 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
28239488 AAAAGACTAT
28239498 TTTAACTTTA-TTACAAA
1 TTTAA-TTTATTTACAAA
28239515 TATTAATTTATTTACAAA
1 T-TTAATTTATTTACAAA
*
28239533 TTAAATTTATT
1 TTTAATTTATT
28239544 AAATAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATTTATTTACAAA
Found at i:28239630 original size:22 final size:22
Alignment explanation
Indices: 28239605--28239651 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
28239595 TAAAATAACA
28239605 TTTTA-TTAATATTAATTTATTT
1 TTTTACTTAATA-TAATTTATTT
* *
28239627 TTTTACTTATTATGATTTATTT
1 TTTTACTTAATATAATTTATTT
28239649 TTT
1 TTT
28239652 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTACTTAATATAATTTATTT
Found at i:28244511 original size:46 final size:46
Alignment explanation
Indices: 28244444--28244618 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
28244434 TGTAACCCGC
*
28244444 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * *
28244490 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* ** *
28244540 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGCACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
28244583 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
28244619 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:28244563 original size:93 final size:93
Alignment explanation
Indices: 28244451--28244622 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
28244441 CGCCCATAAG
** *
28244451 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGCACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28244516 ACAAGTTCGGATGCCTAGTTACATCTCA
66 ACAAGTTCGGATGCCTAGTTACATCTCA
*
28244544 CGAACTCGGACTCAACTCAACGAGTTCGCACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGCACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
28244609 ACGAGTTCGGATGC
66 ACAAGTTCGGATGC
28244623 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGCACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACAAGTTCGGATGCCTAGTTACATCTCA
Found at i:28249255 original size:20 final size:21
Alignment explanation
Indices: 28249217--28249255 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28249207 TCATAATGAC
28249217 CACACGGGCGTGTTGCCCTTT
1 CACACGGGCGTGTTGCCCTTT
28249238 CACACGGGCGTG-TGCCCT
1 CACACGGGCGTGTTGCCCT
28249256 GTTTGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.23
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTT
Found at i:28261826 original size:13 final size:13
Alignment explanation
Indices: 28261808--28261834 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28261798 ACCTTATTAT
28261808 GGGCTGAGGACAC
1 GGGCTGAGGACAC
28261821 GGGCTGAGGACAC
1 GGGCTGAGGACAC
28261834 G
1 G
28261835 AGCGTATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.48, T:0.07
Consensus pattern (13 bp):
GGGCTGAGGACAC
Found at i:28262497 original size:58 final size:58
Alignment explanation
Indices: 28262401--28262608 Score: 242
Period size: 58 Copynumber: 3.6 Consensus size: 58
28262391 GAGTAGCTTT
* * * *
28262401 ATACTTGAGAAAA-TTTG-AAGATAACAAACTGGGGATGTGGATCTGCGAGCTATTTC
1 ATACTTAAGAAAATTTTGAAAGATAACCAGCTGGGGATGTGGATCTGCGAGCTATTTA
* * * * *
28262457 ATACCTAAGAGAATTTTGAAAGATAACTAGCTGGGGATGTGGATCCGCGAGCTATTTT
1 ATACTTAAGAAAATTTTGAAAGATAACCAGCTGGGGATGTGGATCTGCGAGCTATTTA
* * * * *
28262515 ATACTTTAA-AAAATTTTGAAGGATAACCAGCTGGGGATGTGAATTTGCAAGCTACTTA
1 ATAC-TTAAGAAAATTTTGAAAGATAACCAGCTGGGGATGTGGATCTGCGAGCTATTTA
*
28262573 ATACTTGAGAAAATTTTGAAAGATAACACAGCTGGG
1 ATACTTAAGAAAATTTTGAAAGATAAC-CAGCTGGG
28262609 AGTTTCCAAC
Statistics
Matches: 128, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
56 10 0.08
57 7 0.05
58 100 0.78
59 11 0.09
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (58 bp):
ATACTTAAGAAAATTTTGAAAGATAACCAGCTGGGGATGTGGATCTGCGAGCTATTTA
Found at i:28262730 original size:69 final size:69
Alignment explanation
Indices: 28262618--28262944 Score: 318
Period size: 69 Copynumber: 4.8 Consensus size: 69
28262608 GAGTTTCCAA
* * ** * * *
28262618 CTCTCGCTAACTATGTTTGAGGTTGTGGTTTTTATCCTACGAGCCTTAATATGACACTTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACGATTTTTATCTTGCGAGCCTTAATATGACACTTGGGAGC
28262683 TTTG
66 TTTG
* * * ** * *
28262687 ATCTCGCTGACTGTGTTGGAGGCTATTATTTTTAAAC-TGCGAGCCTTAATATGACAGTTGGGAG
1 CTCTCGCTAACTATGTTGGAGGCTACGATTTTT-ATCTTGCGAGCCTTAATATGACACTTGGGAG
*
28262751 CTTAG
65 CTTTG
* ** * * *
28262756 CTCTCGCTAACTGTGTTAAAGGCTGCGGTTTTTATCTTGCGAGCCTTAATATGACAAC-TAGG-G
1 CTCTCGCTAACTATGTTGGAGGCTACGATTTTTATCTTGCGAGCCTTAATATGAC-ACTTGGGAG
28262819 CTTTG
65 CTTTG
* * * ** * * * *
28262824 CTTTCACTAGCTATGTTGGAGGCTGTGGTTTTTATCTTGCGAGCCTTTATATGATAGTTGGGAGC
1 CTCTCGCTAACTATGTTGGAGGCTACGATTTTTATCTTGCGAGCCTTAATATGACACTTGGGAGC
28262889 TTTG
66 TTTG
* * *
28262893 CTCTAGCTAACTATGTTGGAGGTTACGATTTTTATCCTGCGAGCCTTAATAT
1 CTCTCGCTAACTATGTTGGAGGCTACGATTTTTATCTTGCGAGCCTTAATAT
28262945 TACATAAATG
Statistics
Matches: 208, Mismatches: 45, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
67 1 0.00
68 56 0.27
69 148 0.71
70 3 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (69 bp):
CTCTCGCTAACTATGTTGGAGGCTACGATTTTTATCTTGCGAGCCTTAATATGACACTTGGGAGC
TTTG
Found at i:28262877 original size:137 final size:138
Alignment explanation
Indices: 28262618--28262944 Score: 392
Period size: 137 Copynumber: 2.4 Consensus size: 138
28262608 GAGTTTCCAA
* * * *
28262618 CTCTCGCTAACTATGTTTGAGGTTGTGGTTTTTATCCTACGAGCCTTAATATGACACTTGGGAGC
1 CTCTCGCTAACTATGTTAGAGGTTGCGGTTTTTATCCTGCGAGCCTTAATATGACACTTAGGAGC
* * *
28262683 TTTGATCTCGCTGACTGTGTTGGAGGCTATTATTTTTAAACTGCGAGCCTTAATATGACAGTTGG
66 TTTGATCTCACTGACTATGTTGGAGGCTATGATTTTTAAACTGCGAGCCTTAATATGACAGTTGG
28262748 GAGCTTAG
131 GAGCTTAG
* * * *
28262756 CTCTCGCTAACTGTGTTAAAGGCTGCGGTTTTTATCTTGCGAGCCTTAATATGACAAC-TAGG-G
1 CTCTCGCTAACTATGTTAGAGGTTGCGGTTTTTATCCTGCGAGCCTTAATATGAC-ACTTAGGAG
* * * * * * *
28262819 CTTTGCTTTCACT-AGCTATGTTGGAGGCTGTGGTTTTT-ATCTTGCGAGCCTTTATATGATAGT
65 CTTTGATCTCACTGA-CTATGTTGGAGGCTATGATTTTTAAAC-TGCGAGCCTTAATATGACAGT
*
28262882 TGGGAGCTTTG
128 TGGGAGCTTAG
* * * *
28262893 CTCTAGCTAACTATGTTGGAGGTTACGATTTTTATCCTGCGAGCCTTAATAT
1 CTCTCGCTAACTATGTTAGAGGTTGCGGTTTTTATCCTGCGAGCCTTAATAT
28262945 TACATAAATG
Statistics
Matches: 159, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
136 3 0.02
137 103 0.65
138 51 0.32
139 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (138 bp):
CTCTCGCTAACTATGTTAGAGGTTGCGGTTTTTATCCTGCGAGCCTTAATATGACACTTAGGAGC
TTTGATCTCACTGACTATGTTGGAGGCTATGATTTTTAAACTGCGAGCCTTAATATGACAGTTGG
GAGCTTAG
Found at i:28274055 original size:24 final size:24
Alignment explanation
Indices: 28274027--28274078 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
28274017 GGCCGATGTG
28274027 GTGAATGTGAAAGTGTATGTATAT
1 GTGAATGTGAAAGTGTATGTATAT
28274051 GTGAATGTGAAAGTGTATGTATAT
1 GTGAATGTGAAAGTGTATGTATAT
28274075 GTGA
1 GTGA
28274079 TGAGGCCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.37
Consensus pattern (24 bp):
GTGAATGTGAAAGTGTATGTATAT
Found at i:28274058 original size:73 final size:73
Alignment explanation
Indices: 28273979--28274127 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
28273969 GCCGATGTGA
28273979 TGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
1 TGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
28274044 TGTATATG
66 TGTATATG
28274052 TGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
1 TGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
28274117 TGTATATG
66 TGTATATG
28274125 TGA
1 TGA
28274128 TAAGGCCTAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (73 bp):
TGAATGTGAAAGTGTATGTATATGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTA
TGTATATG
Found at i:28274060 original size:55 final size:49
Alignment explanation
Indices: 28273952--28274054 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 49
28273942 TACATATATG
28273952 TGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
* * *
28274001 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
28274050 TGTGA
1 TGTGA
28274055 ATGTGAAAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (49 bp):
TGTGATAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
Found at i:28274293 original size:37 final size:37
Alignment explanation
Indices: 28274243--28274364 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
28274233 GGAATATGTT
*
28274243 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
28274280 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
28274317 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
28274354 CCGGGTAAGAC
1 CCGGGTAAGAC
28274365 TTCTTTTATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:28276460 original size:29 final size:29
Alignment explanation
Indices: 28276418--28276552 Score: 252
Period size: 29 Copynumber: 4.7 Consensus size: 29
28276408 GCGAATGATT
28276418 GAGGCACTATGTGTGCGAGATCAGTAATC
1 GAGGCACTATGTGTGCGAGATCAGTAATC
28276447 GAGGCACTATGTGTGCGAGATCAGTAATC
1 GAGGCACTATGTGTGCGAGATCAGTAATC
28276476 GAGGCACTATGTGTGCGAGATCAGTAATC
1 GAGGCACTATGTGTGCGAGATCAGTAATC
*
28276505 GAGGCACTATGTGTGCGAGATCAGTAATT
1 GAGGCACTATGTGTGCGAGATCAGTAATC
*
28276534 GAGGCACTGTGTGTGCGAG
1 GAGGCACTATGTGTGCGAG
28276553 TTTTTCAACA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 104 1.00
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GAGGCACTATGTGTGCGAGATCAGTAATC
Done.