Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 267 of 284
Found at i:89710664 original size:79 final size:79
Alignment explanation
Indices: 89710511--89710675 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
89710501 AGACTAAGAT
* * * **
89710511 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGCCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
*
89710576 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
89710590 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGCCTATGTCCCAAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGCCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
* *
89710653 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
89710669 CCGAAGG
1 CCGAAGG
89710676 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.66
80 23 0.32
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGCCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:89720114 original size:10 final size:11
Alignment explanation
Indices: 89720088--89720120 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
89720078 CAATTCAATT
*
89720088 TAATCATCACC
1 TAATCATCACA
89720099 TAATCA-CACA
1 TAATCATCACA
89720109 TAATCATCACA
1 TAATCATCACA
89720120 T
1 T
89720121 GTTAGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.27
Consensus pattern (11 bp):
TAATCATCACA
Found at i:89720389 original size:24 final size:23
Alignment explanation
Indices: 89720362--89720457 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 23
89720352 AAATAGCAAA
89720362 CTCTATTGAGCTGAAAACGATAAG
1 CTCTATTGAGCTGAAAACG-TAAG
* *
89720386 CTCTATTGAGCTGAACA-GTTAG
1 CTCTATTGAGCTGAAAACGTAAG
*
89720408 CTCT-TTCGAGCTG-AATCGGTAAG
1 CTCTATT-GAGCTGAAAAC-GTAAG
* *
89720431 CTCCAATGAGCTGAAATA-GTAAG
1 CTCTATTGAGCTGAAA-ACGTAAG
89720454 CTCT
1 CTCT
89720458 TACAAGCTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
21 3 0.05
22 13 0.23
23 22 0.39
24 19 0.33
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
CTCTATTGAGCTGAAAACGTAAG
Found at i:89726399 original size:15 final size:17
Alignment explanation
Indices: 89726370--89726408 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
89726360 CACGGTCAAG
89726370 ACACACGCTCGTGTGTC
1 ACACACGCTCGTGTGTC
89726387 ACACACGC-CTGTGTGTC
1 ACACACGCTC-GTGTGTC
89726404 ACACA
1 ACACA
89726409 TAGTCATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (17 bp):
ACACACGCTCGTGTGTC
Found at i:89748500 original size:66 final size:66
Alignment explanation
Indices: 89748391--89748521 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
89748381 GGGAGAGATT
* *
89748391 TTAGGAGAAGAATATGAAAGTTGAGGTGTGGGGTGCTTCTTGCCGAAAGAGGGACTCTTCTAGTG
1 TTAGGAGAAGAATATAAAAGTTGAGGTGTGGGGTGCTTATTGCCGAAAGAGGGACTCTTCTAGTG
89748456 G
66 G
89748457 TTAGGAGAAGAATATAAAAGTTGAGGTGTGGGGTGCTTATTGCCGAAAGAGGGACTCTTCTAGTG
1 TTAGGAGAAGAATATAAAAGTTGAGGTGTGGGGTGCTTATTGCCGAAAGAGGGACTCTTCTAGTG
89748522 ACAAATTTAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.27, C:0.10, G:0.35, T:0.27
Consensus pattern (66 bp):
TTAGGAGAAGAATATAAAAGTTGAGGTGTGGGGTGCTTATTGCCGAAAGAGGGACTCTTCTAGTG
G
Found at i:89750108 original size:26 final size:26
Alignment explanation
Indices: 89750077--89750151 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
89750067 TCTGCCACAT
*
89750077 ATACTGATACTGGCAGCTTTGCTGCA
1 ATACTGATATTGGCAGCTTTGCTGCA
* * * *
89750103 TTACTGTTATTAGCAGCTTTGTTGCA
1 ATACTGATATTGGCAGCTTTGCTGCA
*
89750129 ATAAT-ATTATTGGCAGCTTTGCT
1 ATACTGA-TATTGGCAGCTTTGCT
89750152 ACGTTATTGG
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (26 bp):
ATACTGATATTGGCAGCTTTGCTGCA
Found at i:89752859 original size:26 final size:26
Alignment explanation
Indices: 89752790--89752885 Score: 111
Period size: 26 Copynumber: 3.7 Consensus size: 26
89752780 CTTTACATAT
* **
89752790 ATGCTCACACGAGTTACGAAAAGAGC
1 ATGCTCACACGAGCTGTGAAAAGAGC
* * *
89752816 ATGCTCACATGAGTTGTGAAAAGAGT
1 ATGCTCACACGAGCTGTGAAAAGAGC
* *
89752842 ATGCTCACACGAGCTGTGAAATGGGC
1 ATGCTCACACGAGCTGTGAAAAGAGC
*
89752868 CTGCTCACACGAGCTGTG
1 ATGCTCACACGAGCTGTG
89752886 GGTCAAAACG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (26 bp):
ATGCTCACACGAGCTGTGAAAAGAGC
Found at i:89769959 original size:48 final size:48
Alignment explanation
Indices: 89769872--89770007 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 48
89769862 TCTCATATCG
* * * * * *
89769872 ATGCCATGTCCCAGACATGGTTTTATATGAAATCACATATCGATGCCA
1 ATGCCATATCCCAAACATGGTATTACATGGAATCTCATATCGATGCCA
* *
89769920 ATGCCATATCCCAAATATTGTATTACATGGAATCTCATATCGATGCCA
1 ATGCCATATCCCAAACATGGTATTACATGGAATCTCATATCGATGCCA
* * * * *
89769968 ATGCCATGTCTCAGACATGGTCTTACATGGGATCTCATAT
1 ATGCCATATCCCAAACATGGTATTACATGGAATCTCATAT
89770008 AACCCTAATG
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (48 bp):
ATGCCATATCCCAAACATGGTATTACATGGAATCTCATATCGATGCCA
Found at i:89771006 original size:331 final size:332
Alignment explanation
Indices: 89770362--89771027 Score: 1239
Period size: 331 Copynumber: 2.0 Consensus size: 332
89770352 TCAAAAAATA
** *
89770362 TTTTAAATTTATTTTCTATGTTTATTTTGTGTGAATTTATATCTGTGAAATTTTCGTGATTTAAT
1 TTTTAAAAGTATTTTCTATGTTTATTTTGTGTGAATTTATACCTGTGAAATTTTCGTGATTTAAT
* *
89770427 TTTATCGTTTGAGTGTTCGATTTAATAAAAAGACTTAATTGCTTAAAATGAAAATTTGGTGGTTA
66 TTTATCGTTTGAGTGTTCGATTTAATAAAAAGACTTAATCGCGTAAAATGAAAATTTGGTGGTTA
89770492 TTTCTAAAAGGTACCTAGTTGTTATTGGCTTTATTAATGGGAGTCTTTATGTTGCAATTAGTCCA
131 TTTCTAAAAGGTACCTAGTTGTTATTGGCTTTATTAATGGGAGTCTTTATGTTGCAATTAGTCCA
89770557 TTTAATAGGGTGGACAGTAATGGGCTTATAATATATGATTTTGCTATAATTTTATTAAGGTTAAA
196 TTTAATAGGGTGGACAGTAATGGGCTTATAATATATGATTTTGCTATAATTTTATTAAGGTTAAA
89770622 AATGTAATTAGATAAAAAAATGTTAATATAAGTTATTATATCATAAAATAAGCCATGTTTTTATT
261 AATGTAATTAGATAAAAAAATGTTAATATAAGTTATTATATCATAAAATAAGCCATGTTTTTATT
89770687 CATTCTC
326 CATTCTC
*
89770694 TTTTAAAAGTATTTTCTGTGTTTATTTTGTGTGAA-TTATACCTGTGAAATTTTCGTGATTTAAT
1 TTTTAAAAGTATTTTCTATGTTTATTTTGTGTGAATTTATACCTGTGAAATTTTCGTGATTTAAT
89770758 TTTATCGTTTGAGTG-TCTGATTTAAT-AAAAGAACTTAATCGCGTAAAATGAAAATTTGGTGGT
66 TTTATCGTTTGAGTGTTC-GATTTAATAAAAAG-ACTTAATCGCGTAAAATGAAAATTTGGTGGT
89770821 TATTTCTAAAAGGTACCTAGTTGTTATTGGCTTTATTAATGGGAGTCTTTATGTTGCAATTAGTC
129 TATTTCTAAAAGGTACCTAGTTGTTATTGGCTTTATTAATGGGAGTCTTTATGTTGCAATTAGTC
89770886 CATTTAATAGGGTGGACAGTAATGGGCTTATAATATATGATTTTGCTATAATTTTATTAAGGTTA
194 CATTTAATAGGGTGGACAGTAATGGGCTTATAATATATGATTTTGCTATAATTTTATTAAGGTTA
89770951 AAAATGTAATTAGATAAAAAAATGTTAATATAAGTTATTATATCATAAAATAAGCCATGTTTTTA
259 AAAATGTAATTAGATAAAAAAATGTTAATATAAGTTATTATATCATAAAATAAGCCATGTTTTTA
89771016 TTCATTCTC
324 TTCATTCTC
89771025 TTT
1 TTT
89771028 GACAGAAATT
Statistics
Matches: 326, Mismatches: 6, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
330 7 0.02
331 287 0.88
332 32 0.10
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (332 bp):
TTTTAAAAGTATTTTCTATGTTTATTTTGTGTGAATTTATACCTGTGAAATTTTCGTGATTTAAT
TTTATCGTTTGAGTGTTCGATTTAATAAAAAGACTTAATCGCGTAAAATGAAAATTTGGTGGTTA
TTTCTAAAAGGTACCTAGTTGTTATTGGCTTTATTAATGGGAGTCTTTATGTTGCAATTAGTCCA
TTTAATAGGGTGGACAGTAATGGGCTTATAATATATGATTTTGCTATAATTTTATTAAGGTTAAA
AATGTAATTAGATAAAAAAATGTTAATATAAGTTATTATATCATAAAATAAGCCATGTTTTTATT
CATTCTC
Found at i:89775233 original size:24 final size:24
Alignment explanation
Indices: 89775201--89775270 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
89775191 CTGTCAGGAG
89775201 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
89775225 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
89775249 AGGATTTAGGAGCTGATCAAGG
1 AGGATTTAGGAGTTGAT-AAGG
89775271 AATAAGAGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 40 0.91
25 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.37, T:0.27
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:89777742 original size:40 final size:40
Alignment explanation
Indices: 89777561--89777738 Score: 243
Period size: 40 Copynumber: 4.5 Consensus size: 40
89777551 AAGCCAAGTA
* * *
89777561 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
89777600 CCTTCGTGACATAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
89777640 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
89777680 CCTTCGGGACTTAGCCCAGTTATGGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
89777720 CATTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
89777739 TTATCATCCA
Statistics
Matches: 123, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 11 0.09
40 112 0.91
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:89779456 original size:16 final size:15
Alignment explanation
Indices: 89779430--89779459 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
89779420 ACTAGATCGG
89779430 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
89779445 CAAAATGCCGAAAAG
1 CAAAA-GCCGAAAAG
89779460 TTGGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.23, G:0.20, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:89779925 original size:27 final size:27
Alignment explanation
Indices: 89779876--89779953 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
89779866 AGGAAGTGTC
* *
89779876 CTGGTGGCTATGCCATA-ATTATCTAAT
1 CTGGTGGCTCTGCCACATA-TATCTAAT
**
89779903 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTAAT
* *
89779930 CTGGTGGTTCTACCACGAT-TATCT
1 CTGGTGGCTCTGCCAC-ATATATCT
89779954 GTATTTGGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
27 40 0.93
28 3 0.07
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTAAT
Found at i:89779954 original size:27 final size:26
Alignment explanation
Indices: 89779893--89779987 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 26
89779883 CTATGCCATA
** *
89779893 ATTATCTAATCTGGTGGCTCTGCCAC
1 ATTATCTGTTCTGGTGGCTCTACCAC
*
89779919 ATATATCTGTTCTGGTGGTTCTACCAC
1 AT-TATCTGTTCTGGTGGCTCTACCAC
* * * **
89779946 GATTATCTGTATTTGGTGACTTTGTCAC
1 -ATTATCTGT-TCTGGTGGCTCTACCAC
89779974 ATTATCTGTTCTGG
1 ATTATCTGTTCTGG
89779988 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
26 6 0.11
27 36 0.65
28 13 0.24
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (26 bp):
ATTATCTGTTCTGGTGGCTCTACCAC
Found at i:89786303 original size:24 final size:24
Alignment explanation
Indices: 89786238--89786308 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
89786228 CTGTCAGGAG
*
89786238 AGGATTTAGGAGTTGATAAAGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
89786262 AAGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
89786286 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
89786309 GGAAATCTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.38, C:0.01, G:0.35, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:89787756 original size:27 final size:26
Alignment explanation
Indices: 89787716--89787826 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
89787706 AGGAAGCGTC
*
89787716 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
89787743 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
89787770 CTGGTGGTTCTG-CACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
89787797 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
89787823 CTGG
1 CTGG
89787827 AAGCCATGCT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
26 16 0.22
27 54 0.74
28 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:89795357 original size:46 final size:46
Alignment explanation
Indices: 89795264--89795392 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
89795254 TGTAACCCGC
** * * * *
89795264 CCATAAGCAAACTCGGACTCAACTCAATGAGCTCGGTCGTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* * **
89795310 CCATGAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
89795356 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
89795393 TGCTCAACCA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:89795411 original size:46 final size:46
Alignment explanation
Indices: 89795273--89795411 Score: 128
Period size: 46 Copynumber: 3.0 Consensus size: 46
89795263 CCCATAAGCA
* *
89795273 AACTCGGACTCAACTCAATGAGCTCGG-TCGTTC-A-CATCCATGAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGAT-GTTCAACCATCC-T-AGTG
* * *
89795319 AACTCAGACTCAACTCAACGAGTTCGGACAT-TTGCATCCAT--AAGTG
1 AACTCGGACTCAACTCAACGAGTTCGG--ATGTT-CAACCATCCTAGTG
*
89795365 AACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGTTCAACCATCCTAGTG
89795411 A
1 A
89795412 CATGTCACTT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
44 8 0.11
45 1 0.01
46 59 0.79
47 2 0.03
48 1 0.01
49 1 0.01
50 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGTTCAACCATCCTAGTG
Found at i:89795539 original size:35 final size:35
Alignment explanation
Indices: 89795493--89795562 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
89795483 TTCTACGGAA
*
89795493 TGCCGTTACCGATACTCGGTAGTATTTCACATTTT
1 TGCCGATACCGATACTCGGTAGTATTTCACATTTT
89795528 TGCCGATACCGATACTCGGTAGTATTTCACATTTT
1 TGCCGATACCGATACTCGGTAGTATTTCACATTTT
89795563 CCAAGTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (35 bp):
TGCCGATACCGATACTCGGTAGTATTTCACATTTT
Found at i:89802383 original size:43 final size:43
Alignment explanation
Indices: 89802309--89802394 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 43
89802299 TATGTGATTC
*
89802309 CGATATGTGTTTACGAGTAAGACCCTATCTGGGACAG-TGGCAT
1 CGATATGTGGTTACGAGTAAGACCCTATCTGGGAC-GTTGGCAT
*
89802352 CGATATGTGGTTAC-ATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 CGATATGTGGTTACGA-GTAAGACC-CTATCTGGGACGTTGGCAT
89802395 TGTGCGATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
42 2 0.05
43 35 0.92
44 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
CGATATGTGGTTACGAGTAAGACCCTATCTGGGACGTTGGCAT
Found at i:89806311 original size:25 final size:25
Alignment explanation
Indices: 89806256--89806364 Score: 141
Period size: 25 Copynumber: 4.4 Consensus size: 25
89806246 CTGGAGGCCT
* *
89806256 AGCCTCTTTTAAT-AACTGGGG-TAA
1 AGCC-CTTTTGATAAACTGGGGCAAA
89806280 AGCCCTTTTGATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
89806305 AGCCCTTTTCGGTAAACTGGGGCAAA
1 AGCCCTTTT-GATAAACTGGGGCAAA
* *
89806331 AGCCTTTTTGGTAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
89806356 AGCCCTTTT
1 AGCCCTTTT
89806365 TGCACTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.09
24 12 0.16
25 35 0.45
26 23 0.30
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:89806327 original size:26 final size:25
Alignment explanation
Indices: 89806269--89806364 Score: 149
Period size: 25 Copynumber: 3.8 Consensus size: 25
89806259 CTCTTTTAAT
* *
89806269 AACTGGGG-TAAAGCCCTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTGGTA
89806293 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAAGCCCTTTT-GGTA
*
89806319 AACTGGGGCAAAAGCCTTTTTGGTA
1 AACTGGGGCAAAAGCCCTTTTGGTA
89806344 AACTGGGGCAAAAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
89806365 TGCACTTCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
24 8 0.12
25 35 0.53
26 23 0.35
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAAGCCCTTTTGGTA
Found at i:89806346 original size:51 final size:50
Alignment explanation
Indices: 89806269--89806364 Score: 156
Period size: 51 Copynumber: 1.9 Consensus size: 50
89806259 CTCTTTTAAT
*
89806269 AACTGGGGTAAAGCCCTTTTGATAAACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGAAAAGCCCTTTTGATAAACTGGGGCAAAAGCCCTTTTCGGTA
* *
89806319 AACTGGGGCAAAAGCCTTTTTGGTAAACTGGGGCAAAAGCCCTTTT
1 AACTGGGG-AAAAGCCCTTTTGATAAACTGGGGCAAAAGCCCTTTT
89806365 TGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 8 0.19
51 34 0.81
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (50 bp):
AACTGGGGAAAAGCCCTTTTGATAAACTGGGGCAAAAGCCCTTTTCGGTA
Found at i:89806435 original size:20 final size:20
Alignment explanation
Indices: 89806412--89806458 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
89806402 TTATGAATAC
89806412 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
89806432 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
89806452 ATCATGT
1 ATCATGT
89806459 ATATTAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:89812062 original size:46 final size:46
Alignment explanation
Indices: 89812005--89812180 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
89811995 TATTTGGGCA
*
89812005 TCCGAGTTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
89812051 TCCGAGCTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
89812096 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
89812144 -CTCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGG
1 TC-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89812181 GTGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 61 0.56
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:89812172 original size:93 final size:93
Alignment explanation
Indices: 89812001--89812172 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
89811991 AGGATATTTG
* *
89812001 GGCATCCGAGTTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAG
**
89812066 TTGAGTCTGAGTTCGTGAGATGTAACTA
66 TTGAGTCCAAGTTCGTGAGATGTAACTA
89812094 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAGCTCGTTGA
89812158 GTTGAGTCCAAGTTC
65 GTTGAGTCCAAGTTC
89812173 ACTTATGGGT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.30
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAG
TTGAGTCCAAGTTCGTGAGATGTAACTA
Found at i:89817685 original size:24 final size:24
Alignment explanation
Indices: 89817653--89817836 Score: 145
Period size: 24 Copynumber: 7.5 Consensus size: 24
89817643 TCGATTTCAT
*
89817653 ACACATAGTGCTATTCAAATCCGC
1 ACACATAGTGCCATTCAAATCCGC
* * *
89817677 ACACTTAGTGCCATGCTAATCCGC
1 ACACATAGTGCCATTCAAATCCGC
* * * *
89817701 ACACTTAGTGCCATGCTAACCCGC
1 ACACATAGTGCCATTCAAATCCGC
* * *
89817725 ACAGATAGTGCC-TTAGAAATCCAC
1 ACACATAGTGCCATT-CAAATCCGC
* * * *
89817749 ACACTCGTACTGACATTCAAATCAGC
1 ACA--CATAGTGCCATTCAAATCCGC
* *
89817775 ACACATAGTGCTATTCAATTCCGC
1 ACACATAGTGCCATTCAAATCCGC
*
89817799 ACACATAGTGCCATTCAAAATCCTC
1 ACACATAGTGCCATTC-AAATCCGC
**
89817824 ACATTTAGTGCCA
1 ACACATAGTGCCA
89817837 ATGTCATTTC
Statistics
Matches: 125, Mismatches: 30, Indels: 9
0.76 0.18 0.05
Matches are distributed among these distances:
23 1 0.01
24 91 0.73
25 17 0.14
26 14 0.11
27 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (24 bp):
ACACATAGTGCCATTCAAATCCGC
Found at i:89827889 original size:15 final size:15
Alignment explanation
Indices: 89827866--89827898 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
89827856 GTTAAACTTA
89827866 AATTATGGTTTGTAT
1 AATTATGGTTTGTAT
*
89827881 AATTTTGGTTTGTAT
1 AATTATGGTTTGTAT
89827896 AAT
1 AAT
89827899 CTAAGCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (15 bp):
AATTATGGTTTGTAT
Found at i:89837053 original size:70 final size:71
Alignment explanation
Indices: 89836934--89837078 Score: 256
Period size: 70 Copynumber: 2.1 Consensus size: 71
89836924 AGCCACCATG
89836934 TGTAAGAGGTTTGAGGACGGCCTCAATAAAGATATCCGAGTGTTTGTTGGCATCATAGAGCTGTG
1 TGTAAGAGGTTTGAGGACGGCCTCAATAAAGATATCCGAGTGTTTGTTGGCATCATAGAGCTGTG
89836999 GGAATT
66 GGAATT
* * *
89837005 TGTAA-AGGTTTGAGGACGGCCTCAGTAAAGATATCCGAGTGTTTGTTGGCATCTTAGAGCTTTG
1 TGTAAGAGGTTTGAGGACGGCCTCAATAAAGATATCCGAGTGTTTGTTGGCATCATAGAGCTGTG
89837069 GGAATT
66 GGAATT
89837075 TGTA
1 TGTA
89837079 GCACTTGTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 66 0.93
71 5 0.07
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (71 bp):
TGTAAGAGGTTTGAGGACGGCCTCAATAAAGATATCCGAGTGTTTGTTGGCATCATAGAGCTGTG
GGAATT
Found at i:89844882 original size:16 final size:16
Alignment explanation
Indices: 89844863--89844893 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89844853 CTTCTTCACT
89844863 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
89844879 TACTTACTTACTTAA
1 TACTCACTTACTTAA
89844894 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:89844899 original size:20 final size:20
Alignment explanation
Indices: 89844860--89844899 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
89844850 AAACTTCTTC
* *
89844860 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
89844880 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
89844900 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:89845283 original size:108 final size:110
Alignment explanation
Indices: 89845132--89845330 Score: 305
Period size: 108 Copynumber: 1.8 Consensus size: 110
89845122 TATCCTTTTC
* *
89845132 AAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCA
1 AAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCA
89845195 A-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAG
65 ACTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAG
* * * * *
89845240 AAACTTATCAATGCCATGTCTTGACATGGTCTTATATGATATCCTTGCTTTAGAAACCTTACCAA
1 AAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAA
89845305 CTGCCATGCCTTGGCATGGTCTTACA
66 CTGCCATGCCTTGGCATGGTCTTACA
89845331 AGGTATCCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.59
109 7 0.09
110 25 0.31
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (110 bp):
AAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAA
CTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAG
Found at i:89845310 original size:55 final size:53
Alignment explanation
Indices: 89845086--89845340 Score: 252
Period size: 55 Copynumber: 4.8 Consensus size: 53
89845076 ACACGGGTAC
* * * * *
89845086 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T--TTT-CAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
* * * *
89845135 CTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTA-GAAA
* * *
89845188 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTG-CTT-TAGAAA
* * * *
89845243 CTTATCAATGCCATGTCTTGACATGGTCTTATATGATATCCTTGCTTTAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
* *
89845296 CCTTACCAACTGCCATGCCTTGGCATGGTCTTACAAGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
89845341 AAACCCTAAT
Statistics
Matches: 168, Mismatches: 26, Indels: 18
0.79 0.12 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 4 0.02
53 43 0.26
54 13 0.08
55 68 0.40
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCTTTAGAAA
Found at i:89848666 original size:8 final size:9
Alignment explanation
Indices: 89848640--89848675 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
89848630 GGGGTTGTTT
89848640 ATTAAACTA
1 ATTAAACTA
89848649 ATTAAACTA
1 ATTAAACTA
89848658 ATT-AACTA
1 ATTAAACTA
*
89848666 AGTAAACTA
1 ATTAAACTA
89848675 A
1 A
89848676 AGTAAAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.31
Consensus pattern (9 bp):
ATTAAACTA
Found at i:89851645 original size:18 final size:18
Alignment explanation
Indices: 89851593--89851646 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
89851583 AAGAAAATAA
* *
89851593 TAAAATTGAAATGAAAAT
1 TAAAATTAAAATAAAAAT
* * *
89851611 GAAAATAAAAAGAAAAAT
1 TAAAATTAAAATAAAAAT
*
89851629 TAAAATTAAAATTAAAAT
1 TAAAATTAAAATAAAAAT
89851647 AACAATATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (18 bp):
TAAAATTAAAATAAAAAT
Found at i:89855583 original size:9 final size:9
Alignment explanation
Indices: 89855569--89855604 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
89855559 GAGGTTGTTT
89855569 ATTAAACTA
1 ATTAAACTA
89855578 ATTAAACTA
1 ATTAAACTA
89855587 ATT-AACTA
1 ATTAAACTA
89855595 ATTAAACTA
1 ATTAAACTA
89855604 A
1 A
89855605 AGTAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTAAACTA
Found at i:89860952 original size:16 final size:16
Alignment explanation
Indices: 89860928--89860958 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
89860918 TTTCTTCACG
89860928 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
89860944 TACTTACTTACTTAA
1 TACTCACTTACTTAA
89860959 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:89861280 original size:53 final size:50
Alignment explanation
Indices: 89861154--89861295 Score: 153
Period size: 53 Copynumber: 2.8 Consensus size: 50
89861144 CGGGTACCTT
* * *
89861154 ACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-TTTTGAAACTT
1 ACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTTTTTGAAACTC
* *
89861203 ACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AACTC
1 ACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTT---TT-TGAAACTC
* * * *
89861256 ACCAATGCCATGCCTTGGCATGGTCTTACAAGGTATCCTT
1 ACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTT
89861296 AAACCTTAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
49 34 0.44
50 1 0.01
53 41 0.53
54 2 0.03
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (50 bp):
ACCATTGCCATGACTTGACATGGTCTTACATGGTATCCTTTTTGAAACTC
Found at i:89862587 original size:46 final size:47
Alignment explanation
Indices: 89862520--89862689 Score: 217
Period size: 47 Copynumber: 3.7 Consensus size: 47
89862510 CACGAGAGCT
89862520 AGTGTAAGA-CATGTCTAGGACAT-GCATCGACCTCGAAATGTAAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGA-CTCGAAATGTAAGCC
*
89862566 AGTGTAAGA-CATGTCTAGGACAT-GCATCAACTAC-AAGATG-ATAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGACT-CGAA-ATGTA-AGCC
* * * *
89862612 AGTGTAAGACCATGTCTAGGACATGGCATCGACTTGAGATATGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGACTCGAAATGTAAGCC
89862659 AGTGTAAGACCATGTCTAGGACATGGCATCG
1 AGTGTAAGACCATGTCTAGGACATGGCATCG
89862690 GCACCTTACC
Statistics
Matches: 111, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
45 5 0.05
46 46 0.41
47 51 0.46
48 9 0.08
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGACTCGAAATGTAAGCC
Found at i:89865052 original size:14 final size:14
Alignment explanation
Indices: 89865033--89865059 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89865023 CAAAATCGAT
89865033 AAAATTTTCTTATC
1 AAAATTTTCTTATC
89865047 AAAATTTTCTTAT
1 AAAATTTTCTTAT
89865060 AACGTTCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
AAAATTTTCTTATC
Found at i:89871017 original size:17 final size:17
Alignment explanation
Indices: 89870995--89871030 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
89870985 ATTTCAAATC
89870995 TTACTTTTCATTATTTA
1 TTACTTTTCATTATTTA
89871012 TTACTTTTCATTATTTA
1 TTACTTTTCATTATTTA
89871029 TT
1 TT
89871031 TGTATGTTAT
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:0.11, G:0.00, T:0.67
Consensus pattern (17 bp):
TTACTTTTCATTATTTA
Found at i:89874606 original size:26 final size:29
Alignment explanation
Indices: 89874577--89874632 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 29
89874567 AAAGTTCGAG
*
89874577 ATGTTTTTCT-GTTTTTT-TTTATA-AAA
1 ATGTTTTTCTACTTTTTTGTTTATATAAA
89874603 ATGTTTTTCTACTTTTTTGTTTATATAAA
1 ATGTTTTTCTACTTTTTTGTTTATATAAA
89874632 A
1 A
89874633 ATTATATCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.38
27 6 0.23
28 6 0.23
29 4 0.15
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (29 bp):
ATGTTTTTCTACTTTTTTGTTTATATAAA
Found at i:89893250 original size:19 final size:20
Alignment explanation
Indices: 89893223--89893274 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
89893213 AAGTCATAAG
89893223 AAAATTATAAAAAATGTAAA
1 AAAATTATAAAAAATGTAAA
* **
89893243 GAAA-TATAAAATTTGTAAA
1 AAAATTATAAAAAATGTAAA
89893262 AAAATTATAAAAA
1 AAAATTATAAAAA
89893275 TTATTGTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAATTATAAAAAATGTAAA
Found at i:89893487 original size:19 final size:19
Alignment explanation
Indices: 89893465--89893536 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 19
89893455 TATTTTTATT
89893465 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* * * *
89893484 ATTTTTTTATATTTTTACG
1 ATTTTTATAAAATTTTACA
* * *
89893503 ATTTATATATATTTTCTA-A
1 ATTTTTATAAAATTT-TACA
*
89893522 ATTTTAATAAAATTT
1 ATTTTTATAAAATTT
89893537 AAATGATTTT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 39 0.95
20 2 0.05
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:89893567 original size:39 final size:39
Alignment explanation
Indices: 89893502--89893576 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
89893492 ATATTTTTAC
*
89893502 GATTTATATATATTTTCTAAATTTTAATAAAATTTAAAT
1 GATTTATATATATTTTCTAAAATTTAATAAAATTTAAAT
* * *
89893541 GATTT-TATATTTTTTATTAAAATTTAATAAATTTTA
1 GATTTATATATATTTT-CTAAAATTTAATAAAATTTA
89893577 TAACTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 9 0.29
39 22 0.71
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (39 bp):
GATTTATATATATTTTCTAAAATTTAATAAAATTTAAAT
Found at i:89893574 original size:29 final size:29
Alignment explanation
Indices: 89893503--89893587 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
89893493 TATTTTTACG
* * * *
89893503 ATTTATATATATTTTCTAAATTTTAATAAA
1 ATTTAAATA-ATTTTATAACTTTTATTAAA
* **
89893533 ATTTAAATGATTTTATATTTTTTATTAAA
1 ATTTAAATAATTTTATAACTTTTATTAAA
89893562 ATTT-AATAAATTTTATAACTTTTATT
1 ATTTAAAT-AATTTTATAACTTTTATT
89893588 GATTTTTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.07
29 35 0.78
30 7 0.16
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTAAATAATTTTATAACTTTTATTAAA
Found at i:89893869 original size:85 final size:86
Alignment explanation
Indices: 89893711--89893869 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 86
89893701 GAGTGCCAAA
* * ** * ** * *
89893711 AAAAAAGTAGGGACTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTTTTTTTGATGCATTTTGACA
1 AAAAAAGTAGGGACTTAAATGCTTTTTTCGAAAAAAATTAAGGGCCTTTTTGATACATTTTGAAA
** *
89893776 GTTTAAGTACTCAATTGAGTG
66 ACTCAAGTACTCAATTGAGTG
89893797 AAAAAAGT--GGAGCTTAAATGCTTTTTTCGAAAAAAATTAAGGGCCTTTTTGATACATTTTGAA
1 AAAAAAGTAGGGA-CTTAAATGCTTTTTTCGAAAAAAATTAAGGGCCTTTTTGATACATTTTGAA
89893860 AACTCAAGTA
65 AACTCAAGTA
89893870 ACTGATTAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
84 3 0.05
85 49 0.82
86 8 0.13
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (86 bp):
AAAAAAGTAGGGACTTAAATGCTTTTTTCGAAAAAAATTAAGGGCCTTTTTGATACATTTTGAAA
ACTCAAGTACTCAATTGAGTG
Found at i:89905180 original size:27 final size:27
Alignment explanation
Indices: 89905150--89905327 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
89905140 ATATTGAGTC
* * * *
89905150 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
89905177 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89905204 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
89905232 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
89905259 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
89905286 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
89905313 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89905328 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:89905289 original size:82 final size:81
Alignment explanation
Indices: 89905171--89905326 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
89905161 TGCTATATAA
* *
89905171 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
89905236 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
89905253 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
89905317 CACTTAGTGC
65 CACTTAGTGC
89905327 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:89907806 original size:27 final size:26
Alignment explanation
Indices: 89907780--89908085 Score: 147
Period size: 27 Copynumber: 11.4 Consensus size: 26
89907770 ATCTATAAAC
*
89907780 CAAGGGTATTTCGATAATTTTGCAAAC
1 CAAGGGTATTTCG-TAATTTTGCAAAT
* *
89907807 CAATGGTATTTTTGTAATTTTTG-AAAGT
1 CAAGGGTA-TTTCGTAA-TTTTGCAAA-T
* **
89907835 CTA-GGTATTTCTGTAATTTTATAAAT
1 CAAGGGTATTTC-GTAATTTTGCAAAT
* * *
89907861 TAGGGGTATTTCTGTAATTTT-CTAAGT
1 CAAGGGTATTTC-GTAATTTTGC-AAAT
* * *
89907888 CAACGGTATTTCGACAATTTTCCAAAT
1 CAAGGGTATTTCG-TAATTTTGCAAAT
* * *
89907915 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTA-TTTCGTAATTTTGCAAAT
* **
89907942 CAAAGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTC-GTAATTTTGCAAAT
* * *
89907969 AAAGGGTATTTTGGTAA-TTTACAAA-
1 CAAGGGTA-TTTCGTAATTTTGCAAAT
* * *
89907994 CTAGGGGTATTTTGGTAATTTTGCTAAT
1 C-AAGGGTA-TTTCGTAATTTTGCAAAT
* * * * *
89908022 CGATGGTATTTTTGTAATTTTGTAAAC
1 CAAGGGTA-TTTCGTAATTTTGCAAAT
* * *
89908049 CATGGGTA-TTCAGTAATTTTGTAAAC
1 CAAGGGTATTTC-GTAATTTTGCAAAT
89908075 CAAGGGTATTT
1 CAAGGGTATTT
89908086 TAGTAATTCT
Statistics
Matches: 217, Mismatches: 45, Indels: 34
0.73 0.15 0.11
Matches are distributed among these distances:
25 2 0.01
26 55 0.25
27 140 0.65
28 20 0.09
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (26 bp):
CAAGGGTATTTCGTAATTTTGCAAAT
Found at i:89907842 original size:54 final size:53
Alignment explanation
Indices: 89907784--89908093 Score: 186
Period size: 54 Copynumber: 5.8 Consensus size: 53
89907774 ATAAACCAAG
* * *
89907784 GGTATTTCGATAATTTTGCAAACCAATGGTATTTTTGTAATTTTTGAAAGTCTA
1 GGTATTTCGATAATTTTGCAAATCAAGGGTATTTTTGTAATTTTTCAAA-TCTA
** * * * * *
89907838 GGTATTTCTG-TAATTTTATAAATTAGGGGTATTTCTGTAA-TTTTCTAAGTCAA
1 GGTATTTC-GATAATTTTGCAAATCAAGGGTATTTTTGTAATTTTTC-AAATCTA
* * * * * *
89907891 CGGTATTTCGACAATTTTCCAAATCAGGGGTATTTTGGTAATTTTACAAATCAAA
1 -GGTATTTCGATAATTTTGCAAATCAAGGGTATTTTTGTAATTTTTCAAATC-TA
** * * *
89907946 GGTATTTC-AGTAATTTCACAAATAAAGGGTATTTTGGTAA-TTTACAAA-CTA
1 GGTATTTCGA-TAATTTTGCAAATCAAGGGTATTTTTGTAATTTTTCAAATCTA
* * * * * * *
89907997 GGGGTATTTTGGTAATTTTGCTAATCGATGGTATTTTTGTAATTTTGT-AAACCATG
1 --GGTATTTCGATAATTTTGCAAATCAAGGGTATTTTTGTAATTTT-TCAAATC-TA
* * *
89908053 GGTA-TTC-AGTAATTTTGTAAACCAAGGGTATTTTAGTAATT
1 GGTATTTCGA-TAATTTTGCAAATCAAGGGTATTTTTGTAATT
89908094 CTATCCTACA
Statistics
Matches: 198, Mismatches: 43, Indels: 31
0.73 0.16 0.11
Matches are distributed among these distances:
51 1 0.01
52 1 0.01
53 75 0.38
54 112 0.57
55 8 0.04
56 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (53 bp):
GGTATTTCGATAATTTTGCAAATCAAGGGTATTTTTGTAATTTTTCAAATCTA
Found at i:89908112 original size:27 final size:27
Alignment explanation
Indices: 89908082--89908158 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
89908072 AACCAAGGGT
* *
89908082 ATTTTAGTAATTCTATCCTACAGGTGC
1 ATTTTAGTAATTCTACCCTACAGGGGC
* *
89908109 ATTTTAGTAATTCTACCCTAAAGGGGT
1 ATTTTAGTAATTCTACCCTACAGGGGC
* *
89908136 ATTTTAGTAATACTAGCCTACAG
1 ATTTTAGTAATTCTACCCTACAG
89908159 ATATGAGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (27 bp):
ATTTTAGTAATTCTACCCTACAGGGGC
Found at i:89911080 original size:22 final size:20
Alignment explanation
Indices: 89911055--89911110 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
89911045 TTTGGCACAC
89911055 AGCCATAATTAGGTTGGCATA
1 AGCCATAATTAGGTTGGCA-A
89911076 GAGCCAT-ATGTAGGTTGGTGCAA
1 -AGCCATAAT-TAGGTT-G-GCAA
89911099 AGCCATAATTAG
1 AGCCATAATTAG
89911111 ACTAATTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.07
22 21 0.70
23 4 0.13
24 3 0.10
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (20 bp):
AGCCATAATTAGGTTGGCAA
Found at i:89911299 original size:41 final size:41
Alignment explanation
Indices: 89911242--89911321 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
89911232 AAAGCCACCG
89911242 GTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATCA
1 GTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATCA
*
89911283 GTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
1 GTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAAT
89911322 TTCTTCCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.20
Consensus pattern (41 bp):
GTGGATCCACGATCGTCAAGCAACCATGCGATCCTCAATCA
Found at i:89912934 original size:40 final size:39
Alignment explanation
Indices: 89912836--89913098 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
89912826 TCCTCGTTCA
* * * *
89912836 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
89912875 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
89912914 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
89912954 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
89912994 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
89913034 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
89913075 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
89913099 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:89913058 original size:120 final size:119
Alignment explanation
Indices: 89912836--89913098 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
89912826 TCCTCGTTCA
* * *
89912836 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
89912901 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
89912954 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
89913019 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
89913075 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
89913099 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:89913107 original size:41 final size:41
Alignment explanation
Indices: 89913030--89913107 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
89913020 TTTGTATCTC
* * *
89913030 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
89913071 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
89913108 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:89919224 original size:29 final size:29
Alignment explanation
Indices: 89919191--89919258 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
89919181 TGTAAAAAGG
89919191 TAAGTGTGCGAACTTGAAA-TGCATGGCAC
1 TAAGTGTGCG-ACTTGAAAGTGCATGGCAC
* * *
89919220 TAAGTGTGTGAGTTTAAAGTGCATGGCAC
1 TAAGTGTGCGACTTGAAAGTGCATGGCAC
89919249 TAAGTGTGCG
1 TAAGTGTGCG
89919259 CGGTTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (29 bp):
TAAGTGTGCGACTTGAAAGTGCATGGCAC
Found at i:89924927 original size:27 final size:27
Alignment explanation
Indices: 89924856--89925162 Score: 205
Period size: 27 Copynumber: 11.4 Consensus size: 27
89924846 TTTCACCTTA
* * * *
89924856 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTGCAAAC
*
89924883 CAAGGGTATTTCGGTAATTTTGCAAAC
1 CAAGGGTATTTTGGTAATTTTGCAAAC
* * *
89924910 CAATGGTATTTTTGTAATTTTTG-AAAGT
1 CAAGGGTATTTTGGTAA-TTTTGCAAA-C
* ** *
89924938 CTAGGGTAATTTT-GTAATTTTATAAAT
1 CAAGGGT-ATTTTGGTAATTTTGCAAAC
* * * *
89924965 CAGGGGTATTTCT-ATAAATTTT-CGAAT
1 CAAGGGTATTT-TGGT-AATTTTGCAAAC
* * * * **
89924992 GAAAGGTATTTCGGTAATTTTCCAAGT
1 CAAGGGTATTTTGGTAATTTTGCAAAC
* *
89925019 CAGGGGTATTTTGGTAA-TTTACAAAC
1 CAAGGGTATTTTGGTAATTTTGCAAAC
*
89925045 CAAGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTGCAAAC
* * *
89925071 CTAGAGGTATTTTGGTAATTTTGCTAAT
1 CAAG-GGTATTTTGGTAATTTTGCAAAC
* *
89925099 CGAGGGTATTTTGGTAATTTTGAAAAC
1 CAAGGGTATTTTGGTAATTTTGCAAAC
* ** *
89925126 TAAGGGTA-TTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTGCAAAC
89925152 CAAGGGTATTT
1 CAAGGGTATTT
89925163 CAGTAATTCT
Statistics
Matches: 223, Mismatches: 45, Indels: 24
0.76 0.15 0.08
Matches are distributed among these distances:
26 57 0.26
27 135 0.61
28 26 0.12
29 5 0.02
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTGCAAAC
Found at i:89925079 original size:80 final size:79
Alignment explanation
Indices: 89924859--89925135 Score: 228
Period size: 80 Copynumber: 3.4 Consensus size: 79
89924849 CACCTTACAA
* * * * * *
89924859 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAATGGTATTTTTG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTT-CAAACTAA-GGTATTTTGG
*
89924924 TAATTTTTGAAAGTCTA-
64 TAA-TTTTCAAAGTC-AG
* * * * *
89924941 GGGTAATTTT-GTAATTTTATAAATCAGGGGTATTTCT-ATAAATTTTCGAA-TGAAAGGTATTT
1 GGGT-ATTTTGGTAATTTTACAAACCAAGGGTATTT-TGGT-AATTTTCAAACT--AAGGTATTT
* *
89925003 CGGTAATTTTCCAAGTCAG
61 TGGTAATTTTCAAAGTCAG
89925022 GGGTATTTTGGTAA-TTTACAAACCAAGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTT-CAAACTA-AGGTATTTTGG
*
89925086 TAATTTTGCTAA-TC-G
64 TAATTTT-CAAAGTCAG
*
89925101 AGGGTATTTTGGTAATTTTGA-AAACTAAGGGTATT
1 -GGGTATTTTGGTAATTTT-ACAAACCAAGGGTATT
89925136 CAGTAATTTT
Statistics
Matches: 158, Mismatches: 22, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
79 9 0.06
80 60 0.38
81 37 0.23
82 40 0.25
83 12 0.08
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (79 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTCAAACTAAGGTATTTTGGTA
ATTTTCAAAGTCAG
Found at i:89925118 original size:54 final size:54
Alignment explanation
Indices: 89924885--89925162 Score: 166
Period size: 53 Copynumber: 5.2 Consensus size: 54
89924875 CTACAAACCA
* * * * *
89924885 AGGGTATTTCGGTAATTTTGCAAACCA-ATGGTATTTTTGTAATTTTTG-AAAGTCT
1 AGGGTATTTTGGTAATTTTACAAACTAGA-GGTATTTTGGTAA-TTTTGCAAA-TCG
* * * *
89924940 AGGGTAATTTT-GTAATTTTATAAA-TCAGGGGTATTTCT-ATAAATTTT-CGAAT-G
1 AGGGT-ATTTTGGTAATTTTACAAACT-AGAGGTATTT-TGGT-AATTTTGCAAATCG
* * * * * * * *
89924993 AAAGGTATTTCGGTAATTTT-CCAAGTCAGGGGTATTTTGGTAA-TTTACAAACCA
1 -AGGGTATTTTGGTAATTTTACAAACT-AGAGGTATTTTGGTAATTTTGCAAATCG
*
89925047 AGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTTGGTAATTTTGCTAATCG
1 AGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTTGGTAATTTTGCAAATCG
** * * *
89925101 AGGGTATTTTGGTAATTTTGA-AAACTA-AGGGTA-TTCAGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTT-ACAAACTAGA-GGTATTTTGGTAATTTTGCAAATCG
89925154 AGGGTATTT
1 AGGGTATTT
89925163 CAGTAATTCT
Statistics
Matches: 176, Mismatches: 31, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
52 3 0.02
53 68 0.39
54 66 0.38
55 32 0.18
56 7 0.04
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTTGGTAATTTTGCAAATCG
Found at i:89925169 original size:80 final size:80
Alignment explanation
Indices: 89924859--89925170 Score: 214
Period size: 80 Copynumber: 3.9 Consensus size: 80
89924849 CACCTTACAA
* * * * * **
89924859 GGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCGGTAATTTTGCAAACCAA-TGGTATTTTT
1 GGGTATTTTGGT-AATTTACAAACCAAGGGTATTTCAGTAATTTTACAAA-CAAGAGGTATTTCG
**
89924923 GTAATTTTTGAAAGTCTA-
64 GTAA-TTTTCCAAGTC-AG
* * * **
89924941 GGGTAATTTT-GTAATTTTATAAATCAGGGGTATTTCTA-TAAATTTT-CGAATGAA-AGGTATT
1 GGGT-ATTTTGGTAA-TTTACAAACCAAGGGTATTTC-AGT-AATTTTAC-AAACAAGAGGTATT
89925002 TCGGTAATTTTCCAAGTCAG
61 TCGGTAATTTTCCAAGTCAG
** * *
89925022 GGGTATTTTGGTAATTTACAAACCAAGGGTATTTTGGTAATTTTACAAACTAGAGGTATTTTGGT
1 GGGTATTTTGGTAATTTACAAACCAAGGGTATTTCAGTAATTTTACAAACAAGAGGTATTTCGGT
*
89925087 AATTTTGCTAA-TC-G
66 AATTTT-CCAAGTCAG
* **
89925101 AGGGTATTTTGGTAATTTTGA-AAACTAAGGGTA-TTCAGTAATTTTGTAAACCAAG-GGTATTT
1 -GGGTATTTTGGTAA-TTT-ACAAACCAAGGGTATTTCAGTAATTTTACAAA-CAAGAGGTATTT
*
89925163 CAGTAATT
62 CGGTAATT
89925171 CTACCCTATG
Statistics
Matches: 184, Mismatches: 31, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
79 10 0.05
80 84 0.46
81 39 0.21
82 39 0.21
83 12 0.07
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTACAAACCAAGGGTATTTCAGTAATTTTACAAACAAGAGGTATTTCGGT
AATTTTCCAAGTCAG
Found at i:89925230 original size:27 final size:27
Alignment explanation
Indices: 89925153--89925230 Score: 115
Period size: 25 Copynumber: 3.0 Consensus size: 27
89925143 TTTGTAAACC
89925153 AAGGGTATTTCAGTAATTCTACCCTAT
1 AAGGGTATTTCAGTAATTCTACCCTAT
*
89925180 --GGGCATTTCAGTAATTCTACCCTAT
1 AAGGGTATTTCAGTAATTCTACCCTAT
* *
89925205 AAGGGTATTTCAGTAATACTAGCCTA
1 AAGGGTATTTCAGTAATTCTACCCTA
89925231 CAGATATGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
25 24 0.53
27 21 0.47
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (27 bp):
AAGGGTATTTCAGTAATTCTACCCTAT
Found at i:89925581 original size:70 final size:70
Alignment explanation
Indices: 89925468--89925604 Score: 238
Period size: 70 Copynumber: 2.0 Consensus size: 70
89925458 TGGCATTTGC
* * *
89925468 CGTTCTACAGATAGAGTAGTACGAAAGACACACCTGTTTATGAGAACGGGCCGAAGTCCACGATC
1 CGTTCTACAGATACAGTAGTACGAAACACACACCTGTTTATGAGAACGAGCCGAAGTCCACGATC
89925533 ACTAT
66 ACTAT
*
89925538 CGTTCTACAGATACAGTAGTACGAAACACACACCTGTTTATGAGAACGAGCCGAAGTCCATGATC
1 CGTTCTACAGATACAGTAGTACGAAACACACACCTGTTTATGAGAACGAGCCGAAGTCCACGATC
89925603 AC
66 AC
89925605 CAACCTTGGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (70 bp):
CGTTCTACAGATACAGTAGTACGAAACACACACCTGTTTATGAGAACGAGCCGAAGTCCACGATC
ACTAT
Found at i:89927001 original size:23 final size:23
Alignment explanation
Indices: 89926971--89927019 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
89926961 ACTAAATGTG
89926971 TTAAAAGTTAATGTGATTTATGC
1 TTAAAAGTTAATGTGATTTATGC
*
89926994 TTAAAAGTTAATGTGCTTTATGC
1 TTAAAAGTTAATGTGATTTATGC
89927017 TTA
1 TTA
89927020 GTTACTAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (23 bp):
TTAAAAGTTAATGTGATTTATGC
Found at i:89928353 original size:42 final size:44
Alignment explanation
Indices: 89928276--89928388 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 44
89928266 CCTCGATTGA
* **
89928276 GATTTACGTATAAGACCATGTCTGGGGCATCGGCATC-ATATCT
1 GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATATCT
* *
89928319 GATTT-CGTATAAGACCCTTTCTGGGACAGAGGCATCGATAT-T
1 GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATATCT
* * * *
89928361 GAATTACATGTAAGACCACGTCTGGGAC
1 GATTTACGTATAAGACCATGTCTGGGAC
89928389 GTCGGCGTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 31 0.54
43 26 0.46
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
GATTTACGTATAAGACCATGTCTGGGACAGAGGCATCGATATCT
Found at i:89936548 original size:79 final size:81
Alignment explanation
Indices: 89936406--89936588 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
89936396 TACTCGTTCA
* *
89936406 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
89936470 TTTAGT-AGC-TCGCACC
66 TATAGTCA-CTTAGCA-C
**
89936486 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
*
89936548 ATATGGTCACTTAGCAC
65 ATATAGTCACTTAGCAC
*
89936565 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
89936589 CATCATTCGA
Statistics
Matches: 90, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
78 3 0.03
79 58 0.64
80 29 0.32
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTCACTTAGCAC
Found at i:89936588 original size:40 final size:40
Alignment explanation
Indices: 89936385--89936588 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
89936375 CAGAATTTAA
** *
89936385 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
89936425 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
89936465 CCGGATTTAGTAGCTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
89936504 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
89936544 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
89936584 CCGGA
1 CCGGA
89936589 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:89941202 original size:30 final size:30
Alignment explanation
Indices: 89941135--89941294 Score: 132
Period size: 30 Copynumber: 5.4 Consensus size: 30
89941125 AGCAAAAGCT
* *
89941135 ATCCCTATTCA-TATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTCGATGGTCGTCACC
89941164 AT-CCTTTTCATTATTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTCGATGGTCGTCACC
** * * * *
89941193 ATCCCTTTTCAAAATTTGATAGTCG-AAGCT
1 ATCCCTTTTCATTATTCGATGGTCGTCA-CC
** * *
89941223 ATCCCTTTTCATGGTTCGATAGTCG-AAGCC
1 ATCCCTTTTCATTATTCGATGGTCGTCA-CC
* *
89941253 ATCCCTTTCCA-TAGTTCGATGGTTGTCACC
1 ATCCCTTTTCATTA-TTCGATGGTCGTCACC
89941283 ATCCCTTTTCAT
1 ATCCCTTTTCAT
89941295 AATCGATAGC
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
28 7 0.07
29 22 0.21
30 75 0.71
31 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATTATTCGATGGTCGTCACC
Found at i:89941315 original size:29 final size:29
Alignment explanation
Indices: 89941283--89941352 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
89941273 GGTTGTCACC
* *
89941283 ATCCCTTTTCATAATCGATAGCCAAAGTT
1 ATCCCTTTTCATAATCGATAACCAAAGCT
** * *
89941312 ATCCCTTTTTGTATTCGATAACCGAAGCT
1 ATCCCTTTTCATAATCGATAACCAAAGCT
89941341 ATCCCTTTTCAT
1 ATCCCTTTTCAT
89941353 TTGTCTATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAACCAAAGCT
Found at i:89942852 original size:27 final size:27
Alignment explanation
Indices: 89942822--89943216 Score: 475
Period size: 27 Copynumber: 14.6 Consensus size: 27
89942812 TTAGTTTACC
89942822 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** * *
89942849 AAATTACTAAAATACCATTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
89942876 AAATTACCAAAATGCCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
89942903 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** *
89942930 AAATTACTAAAATACCTTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
89942957 AAATCACCAAAATACCCGTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** **
89942984 AAATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
89943011 AAATTACCAAAATACCCATGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** * *
89943038 AAATTACTAAAATACCATTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
89943065 AAATTACCAAAATGCCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
89943092 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
89943119 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** *
89943146 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
** *
89943173 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
89943200 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
89943217 TCGACCTGTA
Statistics
Matches: 317, Mismatches: 51, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 317 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:89943269 original size:27 final size:27
Alignment explanation
Indices: 89942822--89943277 Score: 413
Period size: 27 Copynumber: 16.9 Consensus size: 27
89942812 TTAGTTTACC
*
89942822 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* ** *
89942849 AAATTACTAAAATACCATTTG-TTTATA
1 AAATTACCAAAATACC-CCTGATTTGTA
*
89942876 AAATTACCAAAATGCCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
89942903 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* ** * *
89942930 AAATTACTAAAATACCTTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
89942957 AAATCACCAAAATACCCGTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
** * **
89942984 AAATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
89943011 AAATTACCAAAATACCCATGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* ** *
89943038 AAATTACTAAAATACCATTTG-TTTATA
1 AAATTACCAAAATACC-CCTGATTTGTA
*
89943065 AAATTACCAAAATGCCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
89943092 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
89943119 AAATTATCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
89943146 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
* *
89943173 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
** **
89943200 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*** *
89943227 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
* *
89943254 AAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCCCTGATTT
89943278 ACAGAATTAC
Statistics
Matches: 359, Mismatches: 58, Indels: 24
0.81 0.13 0.05
Matches are distributed among these distances:
26 6 0.02
27 345 0.96
28 8 0.02
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:89943296 original size:27 final size:26
Alignment explanation
Indices: 89943266--89943336 Score: 115
Period size: 27 Copynumber: 2.7 Consensus size: 26
89943256 ATTACCAAAG
*
89943266 TACCCTTGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACA-AATTACCGTTT
89943293 TACCCTCGATTTACAAATTTACCGTTT
1 TACCCTCGATTTACAAA-TTACCGTTT
89943320 TACCCTCGATTTACAAA
1 TACCCTCGATTTACAAA
89943337 ATTATCGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.38
Consensus pattern (26 bp):
TACCCTCGATTTACAAATTACCGTTT
Found at i:89943350 original size:27 final size:26
Alignment explanation
Indices: 89943200--89943352 Score: 90
Period size: 27 Copynumber: 5.7 Consensus size: 26
89943190 CTAATTTGTG
** **
89943200 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTAC-GAAATACCCTCGATTTACA
* * **
89943227 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTA-CGAAATACCCTCGATTTACA
* *
89943254 AAATTACCAAAGTACCCTTGATTTACA
1 AAATTACGAAA-TACCCTCGATTTACA
* ***
89943281 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTA-CGAAATACCCTCGATTTACA
* ***
89943308 AATTTACCGTTTTACCCTCGATTTACA
1 AAATTA-CGAAATACCCTCGATTTACA
89943335 AAATTATCGAAATACCCT
1 AAATTA-CGAAATACCCT
89943353 TGTAGGGTAG
Statistics
Matches: 102, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
26 3 0.03
27 98 0.96
28 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (26 bp):
AAATTACGAAATACCCTCGATTTACA
Found at i:89943351 original size:54 final size:54
Alignment explanation
Indices: 89942979--89943352 Score: 129
Period size: 54 Copynumber: 6.9 Consensus size: 54
89942969 TACCCGTGGT
* * * * * * **
89942979 TTGTAAAATTACCAAAATACCTTTGGTTTACAAAATTACCAAAATACCCAT-GGT
1 TTGTAAAATTACCAAAGTACCCTCGATTTACAAAATTATCGAAATACCC-TCGAC
* * * * * * * * * *
89943033 TTGTAAAATTACTAAAATACCATTTG-TTTATAAAATTACCAAAATGCCC-CTAGT
1 TTGTAAAATTACCAAAGTACC-CTCGATTTACAAAATTATCGAAATACCCTCGA-C
* * ** * * *
89943087 TTGTAAAATTACCAAAATACCC-CTGGTTTGTAAAATTATCAAAATACCC-CTAGT
1 TTGTAAAATTACCAAAGTACCCTC-GATTTACAAAATTATCGAAATACCCTCGA-C
* * *** * * * *
89943141 TTGTAAAATTACCAAAATACCC-CTAATTTGTGAAATTACCAAAATACCC-CTAAT
1 TTGTAAAATTACCAAAGTACCCTC-GATTTACAAAATTATCGAAATACCCTC-GAC
* * ** ** *
89943195 TTGTGAAATTACTGAAA-TACCCTCGACCTGTAAAATTATTGAAATACCCTCGAC
1 TTGTAAAATTAC-CAAAGTACCCTCGATTTACAAAATTATCGAAATACCCTCGAC
* * * ***
89943249 TTGTAAAATTACCAAAGTACCCTTGATTTACAGAATTACCGTTTTACCCTCGA-
1 TTGTAAAATTACCAAAGTACCCTCGATTTACAAAATTATCGAAATACCCTCGAC
****
89943302 TT-TACAAATTTACCGTTTTACCCTCGATTTACAAAATTATCGAAATACCCT
1 TTGTA-AAA-TTACCAAAGTACCCTCGATTTACAAAATTATCGAAATACCCT
89943353 TGTAGGGTAG
Statistics
Matches: 258, Mismatches: 50, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
52 2 0.01
53 9 0.03
54 237 0.92
55 10 0.04
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (54 bp):
TTGTAAAATTACCAAAGTACCCTCGATTTACAAAATTATCGAAATACCCTCGAC
Found at i:89943372 original size:27 final size:27
Alignment explanation
Indices: 89943336--89943638 Score: 410
Period size: 27 Copynumber: 11.3 Consensus size: 27
89943326 CGATTTACAA
* *
89943336 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
89943363 AAATACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
89943390 AATTACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
89943417 AATTAGCGAAATACCCCTGTAGGGCAG
1 AATTACCGAAATACCCCTGTAGGGTAG
89943444 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
89943471 AATTATCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
89943498 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
89943525 AATTACTGAAATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
89943552 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
89943579 AATTACTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
89943606 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
89943632 AATTACC
1 AATTACC
89943639 ATTTTGCCCC
Statistics
Matches: 240, Mismatches: 36, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
26 16 0.07
27 224 0.93
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:89944098 original size:22 final size:22
Alignment explanation
Indices: 89944065--89944129 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
89944055 TTAAAGCTTT
* *
89944065 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
89944087 CT-ATATATGGCTCTGTGCCAAC
1 CTGAT-TATGGCTCTGTGCCAAC
*
89944109 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
89944130 ACGTATTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 34 0.89
23 2 0.05
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:89944352 original size:27 final size:27
Alignment explanation
Indices: 89944294--89944387 Score: 127
Period size: 27 Copynumber: 3.5 Consensus size: 27
89944284 TAAGTGGCTT
* *
89944294 TGCCACATTATCTGT-TCTGGTGGCTC
1 TGCCACAATATCTGTATCTGGTGACTC
* * *
89944320 TACCACAATATCTATATCTAGTGACTC
1 TGCCACAATATCTGTATCTGGTGACTC
89944347 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGACTC
*
89944374 TGTCACAATATCTG
1 TGCCACAATATCTG
89944388 ATAATTGAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
26 12 0.21
27 46 0.79
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGACTC
Found at i:89944541 original size:6 final size:6
Alignment explanation
Indices: 89944527--89944659 Score: 85
Period size: 6 Copynumber: 21.7 Consensus size: 6
89944517 TTCTGTTACT
* * * * *
89944527 TGATAC TGATTC TGATTT TGATTC TG-TTACC TGATAC TGATTT TGATTT
1 TGATTC TGATTC TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC
* * * *
89944576 TGATTC TG-TTACC TGATAC TGATTC TGATTT TGATTC TG-TTACC TAATAC
1 TGATTC TGATT--C TGATTC TGATTC TGATTC TGATTC TGATT--C TGATTC
*
89944626 TGATTC TGATTC TGATTT TGATTC T-AGTTC TGAT
1 TGATTC TGATTC TGATTC TGATTC TGA-TTC TGAT
89944660 AATGTTTCTT
Statistics
Matches: 99, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
5 7 0.07
6 80 0.81
7 9 0.09
8 3 0.03
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (6 bp):
TGATTC
Found at i:89944554 original size:31 final size:31
Alignment explanation
Indices: 89944503--89944642 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
89944493 TTGCATTCAC
* *
89944503 ATTCTGATTTTATATTCTGTTACTTGATACTG
1 ATTCTGATTTT-GATTCTGTTACCTGATACTG
89944535 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
89944566 ATTTTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
89944597 ATTCTGATTTTGATTCTGTTACCTAATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
*
89944628 ATTCTGATTCTGATT
1 ATTCTGATTTTGATT
89944643 TTGATTCTAG
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
31 91 0.89
32 11 0.11
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:89945930 original size:29 final size:29
Alignment explanation
Indices: 89945896--89946260 Score: 242
Period size: 29 Copynumber: 12.7 Consensus size: 29
89945886 AACATGCTAG
* *
89945896 AAAAGAAAAGCCTTTATGGTGAACCTCTA
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
*
89945925 AAAAGAAAAAGCCTTTGTGATAAACCTCTA
1 AAAAG-AAAAGCCTTTGTGGTAAACCTCTA
** * ** * *
89945955 AAAAGAAAATACTTTTTGGCGAACCTATG
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* **
89945984 AAAAGAAAAGACTTTGTGGGGAACCTCTA
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
*
89946013 AAAAGAAAAGCCTTTGTGGCAAACCTCTA
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* * * * *
89946042 TAAATGGAAAGCCTTTGTGGAAAATCTTTA
1 -AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* *
89946072 CAAAAG-AAAGCCTATAT-GTCAAACCTCT-
1 -AAAAGAAAAGCCTTTGTGGT-AAACCTCTA
* * * *
89946100 TAAAGGAAAGCCTATGTGGCAAACCTCT-
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* * * **
89946128 AAAAGGAAAGCTTTTTTGGCGAA-C-CTA
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* * * *
89946155 CAAAAGGAAAGCCTTTTTGGTGAACCTCTG
1 -AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* *
89946185 AAAAG-AAAGCCTTTGTGGCAAATCTCTA
1 AAAAGAAAAGCCTTTGTGGTAAACCTCTA
* * * *
89946213 CAAAGGAAAGCCTATATGGCT-AACCTCTA
1 AAAAGAAAAGCCTTTGTGG-TAAACCTCTA
* *
89946242 AAAATAAAAGCCTTGGTGG
1 AAAAGAAAAGCCTTTGTGG
89946261 CAATTTTAAA
Statistics
Matches: 267, Mismatches: 58, Indels: 22
0.77 0.17 0.06
Matches are distributed among these distances:
26 2 0.01
27 5 0.02
28 80 0.30
29 124 0.46
30 56 0.21
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAAGAAAAGCCTTTGTGGTAAACCTCTA
Found at i:89946038 original size:58 final size:57
Alignment explanation
Indices: 89945896--89946263 Score: 283
Period size: 59 Copynumber: 6.4 Consensus size: 57
89945886 AACATGCTAG
* ** * * **
89945896 AAAAGAAAAGCCTTTATGGTGAACCTCTAAAAAGAAAAAGCCTTTGTGATAAACCTCTA
1 AAAAGAAAAGCCTTTGTGGCAAACCTAT-AAAAG-GAAAGCCTTTGTGGCAAACCTCTA
** * * * * **
89945955 AAAAGAAAATACTTTTTGGCGAACCTATGAAAAGAAAAGACTTTGTGGGGAACCTCTA
1 AAAAGAAAAGCCTTTGTGGCAAACCTAT-AAAAGGAAAGCCTTTGTGGCAAACCTCTA
* * * *
89946013 AAAAGAAAAGCCTTTGTGGCAAACCTCTATAAATGGAAAGCCTTTGTGGAAAATCTTTA
1 AAAAGAAAAGCCTTTGTGGCAAA-C-CTATAAAAGGAAAGCCTTTGTGGCAAACCTCTA
* * * * * *
89946072 CAAAAG-AAAGCCTATATGTCAAACCTCTTAAAGGAAAGCCTATGTGGCAAACCTCT-
1 -AAAAGAAAAGCCTTTGTGGCAAACCTATAAAAGGAAAGCCTTTGTGGCAAACCTCTA
* * * * * * ** *
89946128 AAAAGGAAAGCTTTTTTGGCGAACCTACAAAAGGAAAGCCTTTTTGGTGAACCTCTG
1 AAAAGAAAAGCCTTTGTGGCAAACCTATAAAAGGAAAGCCTTTGTGGCAAACCTCTA
* * * * *
89946185 AAAAG-AAAGCCTTTGTGGCAAATCTCTACAAAGGAAAGCCTATATGGCTAACCTCTA
1 AAAAGAAAAGCCTTTGTGGCAAACCTATA-AAAGGAAAGCCTTTGTGGCAAACCTCTA
* *
89946242 AAAATAAAAGCCTTGGTGGCAA
1 AAAAGAAAAGCCTTTGTGGCAA
89946264 TTTTAAAAAG
Statistics
Matches: 246, Mismatches: 56, Indels: 15
0.78 0.18 0.05
Matches are distributed among these distances:
55 5 0.02
56 55 0.22
57 57 0.23
58 55 0.22
59 65 0.26
60 9 0.04
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (57 bp):
AAAAGAAAAGCCTTTGTGGCAAACCTATAAAAGGAAAGCCTTTGTGGCAAACCTCTA
Found at i:89946112 original size:28 final size:28
Alignment explanation
Indices: 89946005--89946244 Score: 187
Period size: 28 Copynumber: 8.4 Consensus size: 28
89945995 CTTTGTGGGG
* * *
89946005 AACCTCTAAAAAGAAAAGCCTTTGTGGCA
1 AACCTCT-AAAAGGAAAGCCTATATGGCA
* * *
89946034 AACCTCTATAAATGGAAAGCCTTTGTGGAA
1 AACCTCTA-AAA-GGAAAGCCTATATGGCA
* * * *
89946064 AATCTTTACAAAAGAAAGCCTATATGTCA
1 AACCTCTA-AAAGGAAAGCCTATATGGCA
* *
89946093 AACCTCTTAAAGGAAAGCCTATGTGGCA
1 AACCTCTAAAAGGAAAGCCTATATGGCA
* * * *
89946121 AACCTCTAAAAGGAAAGCTTTTTTGGCG
1 AACCTCTAAAAGGAAAGCCTATATGGCA
* * **
89946149 AACCTAC-AAAAGGAAAGCCTTTTTGGTG
1 AACCT-CTAAAAGGAAAGCCTATATGGCA
* *
89946177 AACCTCTGAAAA-GAAAGCCTTTGTGGCA
1 AACCTCT-AAAAGGAAAGCCTATATGGCA
* *
89946205 AATCTCTACAAAGGAAAGCCTATATGGCT
1 AACCTCTA-AAAGGAAAGCCTATATGGCA
89946234 AACCTCTAAAA
1 AACCTCTAAAA
89946245 ATAAAAGCCT
Statistics
Matches: 173, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.01
28 95 0.55
29 52 0.30
30 24 0.14
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (28 bp):
AACCTCTAAAAGGAAAGCCTATATGGCA
Found at i:89946224 original size:57 final size:57
Alignment explanation
Indices: 89945896--89946263 Score: 278
Period size: 58 Copynumber: 6.4 Consensus size: 57
89945886 AACATGCTAG
* ** * * *
89945896 AAAAGAAAAGCCTTTATGGTGAACCTCTAAAAAGAAAAAGCCTTTGTGATAAACCTCTA
1 AAAAG-AAAGCCTTTGTGGCAAACCTCTACAAAG-GAAAGCCTTTGTGGTAAACCTCTA
** * * * * * **
89945955 AAAAGAAAATACTTTTTGGCGAACCTATGA-AAAGAAAAGACTTTGTGGGGAACCTCTA
1 AAAAG-AAAGCCTTTGTGGCAAACCTCT-ACAAAGGAAAGCCTTTGTGGTAAACCTCTA
* * * *
89946013 AAAAGAAAAGCCTTTGTGGCAAACCTCTATAAATGGAAAGCCTTTGTGGAAAATCTTTA
1 AAAAG-AAAGCCTTTGTGGCAAACCTCTACAAA-GGAAAGCCTTTGTGGTAAACCTCTA
* * * * * *
89946072 CAAAAGAAAGCCTATATGTCAAACCTCT-TAAAGGAAAGCCTATGTGGCAAACCTCTA
1 -AAAAGAAAGCCTTTGTGGCAAACCTCTACAAAGGAAAGCCTTTGTGGTAAACCTCTA
* * * * * * *
89946129 AAAGGAAAGCTTTTTTGGCGAA-C-CTACAAAAGGAAAGCCTTTTTGGTGAACCTCTG
1 AAAAGAAAGCCTTTGTGGCAAACCTCTAC-AAAGGAAAGCCTTTGTGGTAAACCTCTA
* * *
89946185 AAAAGAAAGCCTTTGTGGCAAATCTCTACAAAGGAAAGCCTATATGGCT-AACCTCTA
1 AAAAGAAAGCCTTTGTGGCAAACCTCTACAAAGGAAAGCCTTTGTGG-TAAACCTCTA
* *
89946242 AAAATAAAAGCCTTGGTGGCAA
1 AAAA-GAAAGCCTTTGTGGCAA
89946264 TTTTAAAAAG
Statistics
Matches: 251, Mismatches: 48, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
54 2 0.01
55 1 0.00
56 57 0.23
57 50 0.20
58 70 0.28
59 65 0.26
60 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.24
Consensus pattern (57 bp):
AAAAGAAAGCCTTTGTGGCAAACCTCTACAAAGGAAAGCCTTTGTGGTAAACCTCTA
Found at i:89946862 original size:13 final size:13
Alignment explanation
Indices: 89946844--89946869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89946834 CATGAGAGTA
89946844 CTTTTAGGAAACC
1 CTTTTAGGAAACC
89946857 CTTTTAGGAAACC
1 CTTTTAGGAAACC
89946870 TTATCAAGTG
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CTTTTAGGAAACC
Found at i:89948475 original size:48 final size:46
Alignment explanation
Indices: 89948406--89948525 Score: 159
Period size: 46 Copynumber: 2.6 Consensus size: 46
89948396 TGTCTTCGAC
* * *
89948406 ATGGACTTACATGGATTATTCCTGTCTCCAATGCCATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCC--ATATATCTAAT
* * *
89948454 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCCATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
*
89948500 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
89948526 CTGCCCTGTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 33 0.52
48 30 0.48
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
Found at i:89948510 original size:46 final size:47
Alignment explanation
Indices: 89948406--89948519 Score: 158
Period size: 48 Copynumber: 2.4 Consensus size: 47
89948396 TGTCTTCGAC
* * * *
89948406 ATGGACTTACATGGATTATTCCTGTCTCCAATGCCATATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCA-ATATATCTAAT
* *
89948454 ATGGGCTTACATGGCTCATTCCTATCTCCAAAGCC-ATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCAATATATCTAAT
89948500 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
89948520 TCTGTCCTGC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 29 0.49
48 30 0.51
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (47 bp):
ATGGACTTACATGGCTCATTCCTATCTCCAAAGCCAATATATCTAAT
Found at i:89952041 original size:56 final size:57
Alignment explanation
Indices: 89951981--89952359 Score: 235
Period size: 56 Copynumber: 6.7 Consensus size: 57
89951971 GAAAATGCAA
* *
89951981 GAAAAGAAAAGCATTTGTGATGAACCTCT-AAAGAAAACCCTTTATGGCGAACATCT
1 GAAAAGAAAAGCCTTTGTGATGAACCTCTGAAAGAAAACCCTTTATGGCGAACCTCT
* * * * *
89952037 GAAAAGAAAAGCCTTTGT-A-GCAAACCTTTGATAGGAAAGCCTTTGTGGC-AAGCCTCT
1 GAAAAGAAAAGCCTTTGTGATG--AACCTCTGAAAGAAAACCCTTTATGGCGAA-CCTCT
** * * *
89952094 -AAAA-AAAATTCTTTGT-A-GCAAACCTCTGAAA-AAATAGCCTTTTGTGGCAAACCTCT
1 GAAAAGAAAAGCCTTTGTGATG--AACCTCTGAAAGAAA-A-CCCTTTATGGCGAACCTCT
* * *** * * * * *
89952150 AAAAAGAAAAGCCTTTATGGCAAACCTCT-ACAAAACAAACCCTTTGTGCCTAATCTCT
1 GAAAAGAAAAGCCTTTGTGATGAACCTCTGA-AAGA-AAACCCTTTATGGCGAACCTCT
* * * * * * *
89952208 -ACAAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTATATGGCGAACCTCT
1 GA-AAAGAAAAGCCTTTGTGATGAACCTCTGAAAGAAAACCCTTTATGGCGAACCTCT
* * * * *
89952265 GAAAAG-AAAGCCTATGTTG-TGAACCTCTGAAAGGAAAGCCTTTATGGTGAACCTAT
1 GAAAAGAAAAGCCTTTG-TGATGAACCTCTGAAAGAAAACCCTTTATGGCGAACCTCT
* *
89952321 GAAAAGAAAAGCCTTTGTGGTGAACCTCTAAACAGAAAA
1 GAAAAGAAAAGCCTTTGTGATGAACCTCTGAA-AGAAAA
89952360 GCATTTGTTG
Statistics
Matches: 259, Mismatches: 43, Indels: 40
0.76 0.13 0.12
Matches are distributed among these distances:
54 3 0.01
55 25 0.10
56 94 0.36
57 69 0.27
58 63 0.24
59 3 0.01
60 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (57 bp):
GAAAAGAAAAGCCTTTGTGATGAACCTCTGAAAGAAAACCCTTTATGGCGAACCTCT
Found at i:89952081 original size:15 final size:14
Alignment explanation
Indices: 89952044--89952091 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
89952034 TCTGAAAAGA
89952044 AAAGCCTTTGTAGC
1 AAAGCCTTTGTAGC
*
89952058 AAA-CCTTTGATAGG
1 AAAGCCTTTG-TAGC
*
89952072 AAAGCCTTTGTGGC
1 AAAGCCTTTGTAGC
89952086 -AAGCCT
1 AAAGCCT
89952092 CTAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 12 0.41
14 11 0.38
15 6 0.21
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (14 bp):
AAAGCCTTTGTAGC
Found at i:89952110 original size:55 final size:56
Alignment explanation
Indices: 89952049--89952154 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 56
89952039 AAAGAAAAGC
* ** *
89952049 CTTTGTAGCAAACCTTTGATAGGAA-AGCC-TTTGTGGCAAGCCTCTAAAAAAAATT
1 CTTTGTAGCAAACCTCTGA-AAAAATAGCCTTTTGTGGCAAACCTCTAAAAAAAATT
89952104 CTTTGTAGCAAACCTCTGAAAAAATAGCCTTTTGTGGCAAACCTCTAAAAA
1 CTTTGTAGCAAACCTCTGAAAAAATAGCCTTTTGTGGCAAACCTCTAAAAA
89952155 GAAAAGCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
54 3 0.07
55 22 0.49
56 20 0.44
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (56 bp):
CTTTGTAGCAAACCTCTGAAAAAATAGCCTTTTGTGGCAAACCTCTAAAAAAAATT
Found at i:89952392 original size:200 final size:200
Alignment explanation
Indices: 89952114--89952496 Score: 466
Period size: 200 Copynumber: 1.9 Consensus size: 200
89952104 CTTTGTAGCA
* * *
89952114 AACCTCTGAAAAAATAGCCTTTTGTGGCAAACCTCTAAAAAGAAAAGCCTTTATGGCAAACCTCT
1 AACCTATGAAAAAAAAGCCTTTTGTGGCAAACCTCTAAAAAGAAAAGCATTTATGGCAAACCTCT
** * **
89952179 ACAAAACAAACCCTTTGTGCCTAATC-TCTACAAAGGAAAGCCTATGTGGTGAA-CCTCTAAAAG
66 ACAAAACAAACCCTTTGTGCAAAATCAT-TACAAAGGAAAGCCTATATGGCAAACCCT-TAAAAG
** * *
89952242 GAAAGCCTATATGGCGAACCTCTGAAAAGAAAGCCTATGTTGTGAACCTCTGAAAGGAAAGCCTT
129 GAAAGCCTATATGGAAAACCTCTGAAAAGAAAGCCTATGTGGTAAACCTCTGAAAGGAAAGCCTT
89952307 TATGGTG
194 TATGGTG
** * * *
89952314 AACCTATGAAAAGAAAAGCC-TTTGTGGTGAACCTCTAAACAGAAAAGCATTTGTTGCAAACCTC
1 AACCTATGAAAA-AAAAGCCTTTTGTGGCAAACCTCTAAAAAGAAAAGCATTTATGGCAAACCTC
* ** * * *
89952378 TAGAAAGGAAACCCTTTGTGGAAAATCATTATAAAGGAAAGCCTATATGGCAAACCCTTGAAAGG
65 TACAAAACAAACCCTTTGTGCAAAATCATTACAAAGGAAAGCCTATATGGCAAACCCTTAAAAGG
* * * * *
89952443 AATGCCTATGTGGAAAACCTCTGAAAGGATAGCCTTTGTGGTAAACCTCTGAAA
130 AAAGCCTATATGGAAAACCTCTGAAAAGAAAGCCTATGTGGTAAACCTCTGAAA
89952497 AAAAAAGGCC
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
200 142 0.93
201 10 0.07
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (200 bp):
AACCTATGAAAAAAAAGCCTTTTGTGGCAAACCTCTAAAAAGAAAAGCATTTATGGCAAACCTCT
ACAAAACAAACCCTTTGTGCAAAATCATTACAAAGGAAAGCCTATATGGCAAACCCTTAAAAGGA
AAGCCTATATGGAAAACCTCTGAAAAGAAAGCCTATGTGGTAAACCTCTGAAAGGAAAGCCTTTA
TGGTG
Found at i:89952395 original size:29 final size:29
Alignment explanation
Indices: 89952039--89952496 Score: 287
Period size: 29 Copynumber: 16.1 Consensus size: 29
89952029 GAACATCTGA
* * *
89952039 AAAGAAAAGCCTTTGTAGCAAACCT-TTG
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* *
89952067 ATAGGAAAGCCTTTGTGGCAAGCCTCTA-
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* ** *
89952095 AAA-AAAATTCTTTGTAGCAAACCTCT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* *
89952122 AAA-AAATAGCCTTTTGTGGCAAACCTCTAA
1 AAAGGAA-AGCC-TTTGTGGCAAACCTCTAG
* * *
89952152 AAAGAAAAGCCTTTATGGCAAACCTCTAC
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
** * * * * *
89952181 AAAACAAACCCTTTGTGCCTAATCTCTAC
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* **
89952210 AAAGGAAAGCCTATGTGGTGAACCTCTA-
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* * *
89952238 AAAGGAAAGCCTATATGGCGAACCTCT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* * * **
89952266 AAAAGAAAGCCTATGTTGTGAACCTCT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* ** *
89952294 AAAGGAAAGCCTTTATGGTGAACCTAT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* **
89952322 AAAAGAAAAGCCTTTGTGGTGAACCTCTA-
1 -AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* * *
89952351 AACAGAAAAGCATTTGTTGCAAACCTCTAG
1 AA-AGGAAAGCCTTTGTGGCAAACCTCTAG
* * * *
89952381 AAAGGAAACCCTTTGTGGAAAATCAT-TAT
1 AAAGGAAAGCCTTTGTGGCAAA-CCTCTAG
* * *
89952410 AAAGGAAAGCCTATATGGCAAACC-CTTG
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* * *
89952438 AAAGGAATGCCTATGTGGAAAACCTCT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
* *
89952466 AAAGGATAGCCTTTGTGGTAAACCTCT-G
1 AAAGGAAAGCCTTTGTGGCAAACCTCTAG
89952494 AAA
1 AAA
89952497 AAAAAAGGCC
Statistics
Matches: 345, Mismatches: 71, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
27 24 0.07
28 150 0.43
29 157 0.46
30 11 0.03
31 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (29 bp):
AAAGGAAAGCCTTTGTGGCAAACCTCTAG
Found at i:89952496 original size:56 final size:56
Alignment explanation
Indices: 89952210--89952496 Score: 263
Period size: 56 Copynumber: 5.1 Consensus size: 56
89952200 TAATCTCTAC
* *
89952210 AAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTATATGGCGAACCTCTG
1 AAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTTTATGGCAAACCTCTG
* * * ** *
89952266 AAAAGAAAGCCTATGTTGTGAACCTCTGAAAGGAAAGCCTTTATGGTGAACCTATG
1 AAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTTTATGGCAAACCTCTG
* * * * * *
89952322 AAAAGAAAAGCCTTTGTGGTGAACCTCTAAACAGAAAAGCATTTGTTGCAAACCTCTAG
1 -AAAGGAAAGCCTATGTGGTGAACCTCTAAA-AGGAAAGCCTTTATGGCAAACCTCT-G
* * ** * *
89952381 AAAGGAAACCCTTTGTGGAAAATCAT-TATAAAGGAAAGCCTATATGGCAAACC-CTTG
1 AAAGGAAAGCCTATGTGGTGAA-CCTCTA-AAAGGAAAGCCTTTATGGCAAACCTC-TG
* ** * * * *
89952438 AAAGGAATGCCTATGTGGAAAACCTCTGAAAGGATAGCCTTTGTGGTAAACCTCTG
1 AAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTTTATGGCAAACCTCTG
89952494 AAA
1 AAA
89952497 AAAAAAGGCC
Statistics
Matches: 186, Mismatches: 37, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
56 77 0.41
57 48 0.26
58 56 0.30
59 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (56 bp):
AAAGGAAAGCCTATGTGGTGAACCTCTAAAAGGAAAGCCTTTATGGCAAACCTCTG
Found at i:89954600 original size:43 final size:43
Alignment explanation
Indices: 89954556--89954717 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 43
89954546 CTGAGATGTG
* * *
89954556 ATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTG
1 ATTACATGTAAGACCATATCTGGGACATTGGCATCGTATTGTA
* * ** * * *
89954599 ATCACGTGTAAGACCATGCCTGGGACATTGGCCTCGTTAAT-CA
1 ATTACATGTAAGACCATATCTGGGACATTGGCATCG-TATTGTA
* * *
89954642 ATTTCATGTAAGACCCTATCTGGGACAGTGGCATCG-ATATGTA
1 ATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT-TGTA
* *
89954685 ATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 ATTACATGTAAGACCATATCTGGGACATTGGCAT
89954718 TGTACGAGCT
Statistics
Matches: 94, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 83 0.88
44 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
ATTACATGTAAGACCATATCTGGGACATTGGCATCGTATTGTA
Found at i:89959002 original size:29 final size:29
Alignment explanation
Indices: 89958977--89959310 Score: 217
Period size: 29 Copynumber: 11.6 Consensus size: 29
89958967 GGAAGCCTCA
*
89958977 GTGGCAAACCTCTAAAAAGAAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* * *
89959006 GTGGTGAACCTATAAAAAGAAAAGTCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* ** *
89959035 GTGGCGAACCTCTGAAGGGAAAATCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* ** * *
89959064 GTTGAAAACCTCTACAAAGGAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* ** * * *
89959093 GTTGTAAATCTCTACAAAGGAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* * * ** *
89959122 CTGGTGAATCT-TTGAAAGGAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
** * * * *
89959150 GCAG-TAAGCCTTTAAAATGAAAGGCCTTT
1 GTGGCGAA-CCTCTAAAAAGAAAAGCCTTT
* *
89959179 GTGGTGAACCTCTGAAAAGAAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
** * * *
89959208 GTGGAAAACCTCT-GAAAGGAAAGCCTAT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
** * * * *
89959236 GTTCCAAACCTAT-GAAAGGAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
* *
89959264 ATGGTGAACCTCTAAAAAGAAAAGCCTTT
1 GTGGCGAACCTCTAAAAAGAAAAGCCTTT
89959293 GTGGCGAACCTCTAAAAA
1 GTGGCGAACCTCTAAAAA
89959311 AATCCTTTAT
Statistics
Matches: 237, Mismatches: 64, Indels: 8
0.77 0.21 0.03
Matches are distributed among these distances:
27 2 0.01
28 60 0.25
29 173 0.73
30 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (29 bp):
GTGGCGAACCTCTAAAAAGAAAAGCCTTT
Found at i:89959022 original size:57 final size:57
Alignment explanation
Indices: 89958953--89959403 Score: 300
Period size: 57 Copynumber: 7.9 Consensus size: 57
89958943 GCCTTTACAA
* * ** *
89958953 TGAAACTCTAAAAGGGAAGCCTCAGTGGCAAACCTCTAAAAAGAAAAGCCTTTGTGG
1 TGAACCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
* * * ** * ** * *
89959010 TGAACCTATAAAAAGAAAAGTCTTTGTGGCGAACCTCTGAAGGGAAAATCCTTTGTTG
1 TGAACCTCT-AAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
** * * * * *
89959068 AAAACCTCTACAAAGGAAAGCCTTTGTTGTAAATCTCTACAAAGGAAAGCCTTTCTGG
1 TGAACCTCTA-AAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
* * * ** * * * *
89959126 TGAATCTTTGAAAGGAAAGCCTTTGCAGTAAGCCTTTAAAATGAAAGGCCTTTGTGG
1 TGAACCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
* * * * * **
89959183 TGAACCTCTGAAAAGAAAAGCCTTTGTGGAAAACCTCT-GAAAGGAAAGCCTATGTTC
1 TGAACCTCT-AAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
** * * * *
89959240 CAAACCTATGAAAGGAAAGCCTTTATGGTGAACCTCTAAAAAGAAAAGCCTTTGTGG
1 TGAACCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
* * * * * * * **
89959297 CGAACCTCTAAAA--AAATCCTTTATAGTAAATCTTTACAAACG-AAAGCCAGTGTGG
1 TGAACCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTA-AAAAGAAAAGCCTTTGTGG
* * * * *
89959352 -AAAGCCTCTAAAAGGAAAGCCTATGTGGTGAACCACTAAAAAGAAAAACCTT
1 TGAA-CCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTT
89959404 GGAGGCAATT
Statistics
Matches: 287, Mismatches: 98, Indels: 18
0.71 0.24 0.04
Matches are distributed among these distances:
54 2 0.01
55 38 0.13
56 31 0.11
57 114 0.40
58 102 0.36
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (57 bp):
TGAACCTCTAAAAGGAAAGCCTTTGTGGTAAACCTCTAAAAAGAAAAGCCTTTGTGG
Found at i:89959244 original size:28 final size:28
Alignment explanation
Indices: 89959185--89959261 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
89959175 CTTTGTGGTG
* * *
89959185 AACCTCTGAAAAGAAAAGCCTTTGTGGAA
1 AACCTCTG-AAAGGAAAGCCTATGTGCAA
* *
89959214 AACCTCTGAAAGGAAAGCCTATGTTCCA
1 AACCTCTGAAAGGAAAGCCTATGTGCAA
*
89959242 AACCTATGAAAGGAAAGCCT
1 AACCTCTGAAAGGAAAGCCT
89959262 TTATGGTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 34 0.81
29 8 0.19
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (28 bp):
AACCTCTGAAAGGAAAGCCTATGTGCAA
Found at i:89959378 original size:28 final size:27
Alignment explanation
Indices: 89958954--89959397 Score: 210
Period size: 29 Copynumber: 15.7 Consensus size: 27
89958944 CCTTTACAAT
* **
89958954 GAAA-CTCTAAAAGGGAAGCCTCAGTG
1 GAAACCTCTAAAAGGAAAGCCTTTGTG
*
89958980 GCAAACCTCTAAAAAGAAAAGCCTTTGTG
1 G-AAACCTCT-AAAAGGAAAGCCTTTGTG
* * * *
89959009 GTGAACCTATAAAAAGAAAAGTCTTTGTG
1 G-AAACCTCT-AAAAGGAAAGCCTTTGTG
* * * *
89959038 GCGAACCTCTGAAGGGAAAATCCTTTGTTG
1 G-AAACCTCTAAAAGG-AAAGCCTTTG-TG
*
89959068 AAAACCTCTACAAAGGAAAGCCTTTGTTG
1 GAAACCTCTA-AAAGGAAAGCCTTTG-TG
* * *
89959097 TAAATCTCTACAAAGGAAAGCCTTTCTG
1 GAAACCTCTA-AAAGGAAAGCCTTTGTG
* * * * *
89959125 GTGAATCTTTGAAAGGAAAGCCTTTGCAG
1 G-AAACCTCTAAAAGGAAAGCCTTTG-TG
* * * *
89959154 TAAGCCTTTAAAATGAAAGGCCTTTGTG
1 GAAACCTCTAAAAGGAAA-GCCTTTGTG
* *
89959182 GTGAACCTCTGAAAAGAAAAGCCTTTGTG
1 G-AAACCTCT-AAAAGGAAAGCCTTTGTG
* * *
89959211 GAAAACCTCTGAAAGGAAAGCCTATGTTC
1 G-AAACCTCTAAAAGGAAAGCCTTTG-TG
* * * *
89959240 CAAACCTATGAAAGGAAAGCCTTTATG
1 GAAACCTCTAAAAGGAAAGCCTTTGTG
* *
89959267 GTGAACCTCTAAAAAGAAAAGCCTTTGTG
1 G-AAACCTCT-AAAAGGAAAGCCTTTGTG
* * *
89959296 GCGAACCTCTAAAA--AAATCCTTTATAG
1 G-AAACCTCTAAAAGGAAAGCCTTTGT-G
* * * * **
89959323 TAAATCTTTACAAACGAAAGCCAGTGTG
1 GAAACCTCTA-AAAGGAAAGCCTTTGTG
*
89959351 GAAAGCCTCTAAAAGGAAAGCCTATGTG
1 GAAA-CCTCTAAAAGGAAAGCCTTTGTG
* * *
89959379 GTGAACCACTAAAAAGAAA
1 G-AAACCTCTAAAAGGAAA
89959398 AACCTTGGAG
Statistics
Matches: 319, Mismatches: 79, Indels: 38
0.73 0.18 0.09
Matches are distributed among these distances:
26 16 0.05
27 8 0.03
28 111 0.35
29 171 0.54
30 13 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (27 bp):
GAAACCTCTAAAAGGAAAGCCTTTGTG
Found at i:89965574 original size:43 final size:43
Alignment explanation
Indices: 89965526--89965688 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 43
89965516 ATTGAGATGT
*
89965526 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * *
89965569 GATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TATTGA
* * * * * *
89965612 GATTACGTGTAAGACCCTGTCTAGGAAAGTGGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TGA
* * *
89965655 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCAT
89965689 TGTACTAGCT
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 88 0.89
44 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:89965680 original size:86 final size:85
Alignment explanation
Indices: 89965526--89965688 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 85
89965516 ATTGAGATGT
* * * * * * * *
89965526 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTACGTGTAAGACCATGTTT
1 GATTACATGTAAGACCATGTCTAGGAAAGTGGCATCGTATTGAGATAACATGTAAGACCATATCT
89965591 GGGACATTGGCATCGTTAATC
66 GGGACA-TGGCATCGTTAATC
* * *
89965612 GATTACGTGTAAGACCCTGTCTAGGAAAGTGGCATCG-ATATGTGATAACATGTAAGACCATATC
1 GATTACATGTAAGACCATGTCTAGGAAAGTGGCATCGTAT-TGAGATAACATGTAAGACCATATC
*
89965676 TGGGATATGGCAT
65 TGGGACATGGCAT
89965689 TGTACTAGCT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
85 8 0.12
86 56 0.88
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (85 bp):
GATTACATGTAAGACCATGTCTAGGAAAGTGGCATCGTATTGAGATAACATGTAAGACCATATCT
GGGACATGGCATCGTTAATC
Found at i:89966838 original size:87 final size:87
Alignment explanation
Indices: 89966710--89966871 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
89966700 GCTGCACGAC
* * *
89966710 CGTGTGTCCCTTGGGGAACCCTTTTGAATTAAGTCAATATACCCTACATTTTTGACATGGCTTAG
1 CGTGTGTCCCTTGGGGAACCCTTTCGAATTAAGTCAATATACCCTACAGTTCTGACATGGCTTAG
89966775 ACACACGGGCGTGTGTCTCAGT
66 ACACACGGGCGTGTGTCTCAGT
* * *
89966797 CGTGTGTCCTTTGGGGTACCCTTTCGAATTAAGTCAGTATACCCTACAGTTCTGACATGGCTTAG
1 CGTGTGTCCCTTGGGGAACCCTTTCGAATTAAGTCAATATACCCTACAGTTCTGACATGGCTTAG
89966862 ACACACGGGC
66 ACACACGGGC
89966872 ACGTCTACTG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (87 bp):
CGTGTGTCCCTTGGGGAACCCTTTCGAATTAAGTCAATATACCCTACAGTTCTGACATGGCTTAG
ACACACGGGCGTGTGTCTCAGT
Found at i:89972089 original size:29 final size:28
Alignment explanation
Indices: 89972003--89972109 Score: 99
Period size: 29 Copynumber: 3.8 Consensus size: 28
89971993 TATATACATG
89972003 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTC-TATT
* * * * ** *
89972031 GAAATGGCCCATTTGGATCAGTTCATATT
1 CATATGGCCCACTAGGCCCAATTC-TATT
*
89972060 CTTATGGCCCACTAGGCCCAATTCTCATT
1 CATATGGCCCACTAGGCCCAATTCT-ATT
*
89972089 CATATGGCCCATTAGGCCCAA
1 CATATGGCCCACTAGGCCCAA
89972110 ATCATATTAT
Statistics
Matches: 59, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
28 15 0.25
29 44 0.75
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (28 bp):
CATATGGCCCACTAGGCCCAATTCTATT
Found at i:89976793 original size:16 final size:15
Alignment explanation
Indices: 89976768--89976819 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
89976758 GTAGCCTAAC
*
89976768 TTTTGACTTTTCGAT
1 TTTTGGCTTTTCGAT
*
89976783 ATTTTGGCTTTTTGAT
1 -TTTTGGCTTTTCGAT
* *
89976799 TTTTCGGCGTTTCGAC
1 TTTT-GGCTTTTCGAT
89976815 TTTTG
1 TTTTG
89976820 CCGATTCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.58
Consensus pattern (15 bp):
TTTTGGCTTTTCGAT
Found at i:89979909 original size:26 final size:26
Alignment explanation
Indices: 89979848--89979933 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
89979838 TGGAGGAAGC
*
89979848 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
89979875 GTTCTGGTGGCTCTACCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* *
89979901 GTATC-GGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
89979927 GTTCTGG
1 GTTCTGG
89979934 CAGACATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.04
26 31 0.60
27 19 0.37
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:89984550 original size:83 final size:84
Alignment explanation
Indices: 89984400--89984556 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 84
89984390 TAGGGTTTTC
* *
89984400 AAGCTTCCCAAGCTCAATTGTAAGTCCGTTCTAACCCCGTTTTTCAAGTTCTTTACGTTTTTTGA
1 AAGCTTCCCAAGCTCAATTGTAAGTCCGTTCTAACCCCATTTTTCAAGTTCTTTACGTTTTTGGA
89984465 GTCCCGGTAACTTGATTTG
66 GTCCCGGTAACTTGATTTG
* * * *
89984484 AAGCTT-CCAAGCTCGATTGTAAGTCCGTTTTAGCCTCATTTTT-AATGATT-TTTACGTTTTTG
1 AAGCTTCCCAAGCTCAATTGTAAGTCCGTTCTAACCCCATTTTTCAA-G-TTCTTTACGTTTTTG
89984546 GAGTCCCGGTA
64 GAGTCCCGGTA
89984557 GCTCGATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
82 2 0.03
83 55 0.85
84 8 0.12
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (84 bp):
AAGCTTCCCAAGCTCAATTGTAAGTCCGTTCTAACCCCATTTTTCAAGTTCTTTACGTTTTTGGA
GTCCCGGTAACTTGATTTG
Found at i:89987730 original size:15 final size:15
Alignment explanation
Indices: 89987707--89987762 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
89987697 GTATCTTGGG
89987707 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
89987722 TTACTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
89987737 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
89987752 TTTCTTTATTC
1 TTTCTTTATTC
89987763 GGTTTCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 2 0.06
15 31 0.89
16 2 0.06
ACGTcount: A:0.14, C:0.16, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:89990210 original size:46 final size:46
Alignment explanation
Indices: 89990160--89990285 Score: 171
Period size: 46 Copynumber: 2.7 Consensus size: 46
89990150 TTGAGCATCT
* * * *
89990160 GAACTCATTGAGTTGAGTCCGAATTCACTTATGGATGCAAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCC
* * *
89990206 GAACTCGTTGAGTTGAGCCCGAGTTCACTCATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCC
* *
89990252 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
89990286 GTGGGTTACA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCC
Found at i:89995250 original size:26 final size:26
Alignment explanation
Indices: 89995195--89995274 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
89995185 AAGTGTTCCA
89995195 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCAC-AATATCTGTTCTG
* *
89995222 GTGGCTCTACCACAATATCTGTATC-G
1 GTGGCTATGCCACAATATCTGT-TCTG
* * *
89995248 GTGACTTTGTCACAATATCTGTTCTG
1 GTGGCTATGCCACAATATCTGTTCTG
89995274 G
1 G
89995275 CAGCCATGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.04
26 30 0.67
27 13 0.29
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTGTTCTG
Found at i:89995964 original size:49 final size:49
Alignment explanation
Indices: 89995899--89995995 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
89995889 AATCACCCTG
* * *
89995899 ATTACCAAAAATAAAGAACACAACCAATCGTAAGTCAATTTGACGCGTT
1 ATTACCAAAAACAAAGAACACAACCAACCGTAAGTCAATATGACGCGTT
* *
89995948 ATTACCATAAACAAAGAACACAACCGACCGTAAGTCAATATGACGCGT
1 ATTACCAAAAACAAAGAACACAACCAACCGTAAGTCAATATGACGCGT
89995996 CAGACTTGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.20
Consensus pattern (49 bp):
ATTACCAAAAACAAAGAACACAACCAACCGTAAGTCAATATGACGCGTT
Found at i:90021387 original size:47 final size:47
Alignment explanation
Indices: 90021267--90021388 Score: 163
Period size: 47 Copynumber: 2.6 Consensus size: 47
90021257 GTGCGAATAA
* * ** *
90021267 TACCTTGATTTGGCTACGGGCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGAGAAGT
* *
90021314 TACCTTGATTTGACTACGGGCCATGGTATAGGTACTCCGAGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGAGAAGT
* *
90021361 TACCTTGATTTGGCTACAGGCTATGGTA
1 TACCTTGATTTGGCTACGGGCCATGGTA
90021389 CAAGTACTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGAGAGAAGT
Found at i:90036573 original size:39 final size:40
Alignment explanation
Indices: 90036465--90036649 Score: 182
Period size: 40 Copynumber: 4.7 Consensus size: 40
90036455 TCGAATGATG
* * *
90036465 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
90036504 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGGTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
90036545 TCCGGGCTAAG-CCTGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
90036584 TCCGAGTTAAGTCCCGAAGGCATTTGTACGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
90036623 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
90036650 AACGAGTAGC
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 33 0.28
40 76 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:90045360 original size:43 final size:43
Alignment explanation
Indices: 90045285--90045367 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
90045275 ACATGTAACA
*
90045285 CATCCATAATGAACTCAGACCACCCAACGAGCTTGGATGCTCG
1 CATCCATAATGAACACAGACCACCCAACGAGCTTGGATGCTCG
* * * *
90045328 CATCCATAATGAACACGGACTACTCAATGAGCTTGGATGC
1 CATCCATAATGAACACAGACCACCCAACGAGCTTGGATGC
90045368 CACATATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
CATCCATAATGAACACAGACCACCCAACGAGCTTGGATGCTCG
Found at i:90045451 original size:43 final size:42
Alignment explanation
Indices: 90045344--90045451 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
90045334 TAATGAACAC
* * * * * *
90045344 GGACTACTCAATGAGCTTGGATGCCACATATATCATGAACTT
1 GGACCACTCAACGAGCTTAGATTCCACATATATCACGAACCT
* * *
90045386 GGACCACTTAACAAG-TTCAGATTCTCATATATATCACGAACCT
1 GGACCACTCAACGAGCTT-AGATTC-CACATATATCACGAACCT
90045429 GGACCACTCAACGAGCTTAGATT
1 GGACCACTCAACGAGCTTAGATT
90045452 TCTAAATTCC
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
41 2 0.04
42 15 0.29
43 33 0.63
44 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
GGACCACTCAACGAGCTTAGATTCCACATATATCACGAACCT
Found at i:90050325 original size:46 final size:46
Alignment explanation
Indices: 90050255--90050343 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
90050245 TTAAAATTCC
*
90050255 GATGTGGAAGTGGGAAAGAATAACTATGGACTTTGTGAGTGGGTCT
1 GATGTGGAAGTGGAAAAGAATAACTATGGACTTTGTGAGTGGGTCT
*
90050301 GATGTGGAAGTGGAAAAGAGTAACTATGGACTTTGTGAGTGGG
1 GATGTGGAAGTGGAAAAGAATAACTATGGACTTTGTGAGTGGG
90050344 CTACCCCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.29, C:0.06, G:0.38, T:0.27
Consensus pattern (46 bp):
GATGTGGAAGTGGAAAAGAATAACTATGGACTTTGTGAGTGGGTCT
Found at i:90052814 original size:16 final size:16
Alignment explanation
Indices: 90052790--90052820 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
90052780 TGCAAAGGTT
90052790 GAAAAGCTGAAAAGCC
1 GAAAAGCTGAAAAGCC
*
90052806 GAAAGGCTGAAAAGC
1 GAAAAGCTGAAAAGC
90052821 TAAAAAATCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.29, T:0.06
Consensus pattern (16 bp):
GAAAAGCTGAAAAGCC
Found at i:90052832 original size:24 final size:24
Alignment explanation
Indices: 90052783--90052832 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
90052773 GTGAAACTGC
* * *
90052783 AAAGGTTGAAAAGCTGAAAAGCCG
1 AAAGGCTGAAAAGCTAAAAAACCG
*
90052807 AAAGGCTGAAAAGCTAAAAAATCG
1 AAAGGCTGAAAAGCTAAAAAACCG
90052831 AA
1 AA
90052833 GAGTGCATCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.12, G:0.24, T:0.12
Consensus pattern (24 bp):
AAAGGCTGAAAAGCTAAAAAACCG
Found at i:90053630 original size:33 final size:33
Alignment explanation
Indices: 90053557--90053631 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 33
90053547 TTGCATACTA
*
90053557 TACTGAAATGGGCTAAGGCTCAGACTACCTCTGT
1 TACTGAAATGGGCTAAGGCCCAGACTA-CTCTGT
*
90053591 TACTGAAATGGGCTCAGGCCCAGACTA-TACTGT
1 TACTGAAATGGGCTAAGGCCCAGACTACT-CTGT
*
90053624 TTCTGAAA
1 TACTGAAA
90053632 AAAAAAGAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 11 0.30
34 25 0.68
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (33 bp):
TACTGAAATGGGCTAAGGCCCAGACTACTCTGT
Found at i:90055725 original size:26 final size:26
Alignment explanation
Indices: 90055693--90055744 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
90055683 AATTTTAAAC
90055693 CATAAAAACATAATAAAAATAAGTTT
1 CATAAAAACATAATAAAAATAAGTTT
*
90055719 CATAAAAATATAATAAAAATAAGTTT
1 CATAAAAACATAATAAAAATAAGTTT
90055745 TCTTACGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (26 bp):
CATAAAAACATAATAAAAATAAGTTT
Found at i:90059553 original size:16 final size:16
Alignment explanation
Indices: 90059532--90059562 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
90059522 ATAAATTTGA
90059532 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
90059548 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
90059563 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:90062354 original size:32 final size:32
Alignment explanation
Indices: 90062313--90062380 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
90062303 AGGGACACGC
*
90062313 CCGTGTTGATTTCCTATGTTGACCCATTTTCT
1 CCGTGTTGATTTCCCATGTTGACCCATTTTCT
90062345 CCGTGTTGATTTCCCATGTTGACCCATTTTCT
1 CCGTGTTGATTTCCCATGTTGACCCATTTTCT
90062377 CCGT
1 CCGT
90062381 TTTTGGCCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.12, C:0.28, G:0.16, T:0.44
Consensus pattern (32 bp):
CCGTGTTGATTTCCCATGTTGACCCATTTTCT
Done.