Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 131 of 310
Found at i:42364593 original size:40 final size:40
Alignment explanation
Indices: 42364495--42364797 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
42364485 TCCTCGTTCA
* * * ** *
42364495 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
42364534 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42364574 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42364614 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
42364654 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
42364694 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
42364734 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
42364774 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42364798 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:42370594 original size:36 final size:36
Alignment explanation
Indices: 42370547--42370618 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
42370537 TTAGTAGCCC
42370547 CATGTTTTCGGATTCTATCAACTGGGGGCTTATTTG
1 CATGTTTTCGGATTCTATCAACTGGGGGCTTATTTG
*
42370583 CATGTTTTCGGATTCTGTCAACTGGGGGCTTATTTG
1 CATGTTTTCGGATTCTATCAACTGGGGGCTTATTTG
42370619 ACCTTATTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.17, G:0.26, T:0.42
Consensus pattern (36 bp):
CATGTTTTCGGATTCTATCAACTGGGGGCTTATTTG
Found at i:42372434 original size:39 final size:40
Alignment explanation
Indices: 42372389--42372573 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
42372379 GCTCCTCGTT
* * *
42372389 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
42372429 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
42372468 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
42372508 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
42372549 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
42372574 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:42372489 original size:40 final size:39
Alignment explanation
Indices: 42372356--42372573 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
42372346 AAATCACGTA
* * **
42372356 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
42372395 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
42372434 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
42372474 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
42372514 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
42372554 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
42372574 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:42376165 original size:43 final size:43
Alignment explanation
Indices: 42376047--42376203 Score: 153
Period size: 43 Copynumber: 3.7 Consensus size: 43
42376037 CTCGTACAAA
**
42376047 GCCAACGTCCCAGACGTAGTCTTACATGT-AATCAAATATAGAT
1 GCCAACGTCCCAGACGTAGTCTTACACATAAATCAAATAT-GAT
* * *
42376090 GCC-ACTATCCCAGAC-AAGGTCTTACAC-GAAATCAAATATGAT
1 GCCAAC-GTCCCAGACGTA-GTCTTACACATAAATCAAATATGAT
* *
42376132 GCCAACGTCCCAGACGTGGTCTTACACATAAATCATAAGT-CGAT
1 GCCAACGTCCCAGACGTAGTCTTACACATAAATCA-AA-TATGAT
* *
42376176 ACCAGCGTCCCAGACGTAGTCTTACACA
1 GCCAACGTCCCAGACGTAGTCTTACACA
42376204 ATAACACATA
Statistics
Matches: 94, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
42 26 0.28
43 37 0.39
44 30 0.32
45 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTAGTCTTACACATAAATCAAATATGAT
Found at i:42376447 original size:11 final size:11
Alignment explanation
Indices: 42376431--42376465 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
42376421 AACAGAAGTA
42376431 GACGGCTATTC
1 GACGGCTATTC
42376442 GACGGCTATTC
1 GACGGCTATTC
*
42376453 GACGACT-TTC
1 GACGGCTATTC
42376463 GAC
1 GAC
42376466 TTTCCCCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.26
Consensus pattern (11 bp):
GACGGCTATTC
Found at i:42378230 original size:44 final size:44
Alignment explanation
Indices: 42378182--42378271 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 44
42378172 ACATAGGACT
* ** * *
42378182 TCGATATGTGATTTTTGTGTTAGACCATGTCTGGGAAATTGGCA
1 TCGATATGAGATTTACGTGTAAGACCATGTCTGGGAAAGTGGCA
* * * *
42378226 TCGATTTGAGATTTACGTGTAAGACCTTGTTTGGGACAGTGGCA
1 TCGATATGAGATTTACGTGTAAGACCATGTCTGGGAAAGTGGCA
42378270 TC
1 TC
42378272 AATAGTTGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (44 bp):
TCGATATGAGATTTACGTGTAAGACCATGTCTGGGAAAGTGGCA
Found at i:42385110 original size:26 final size:26
Alignment explanation
Indices: 42385073--42385149 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
42385063 GCCAACACAC
*
42385073 CAATATCGCAGCAAAGCTACCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* * *
42385099 TAATATCACAGCAGAGCTGCCAGTAA
1 CAATATCGCAGCAAAGCTGCCAGTAA
* *
42385125 CAGTAACGCAGCAAAGCTGCCAGTA
1 CAATATCGCAGCAAAGCTGCCAGTA
42385150 TTTGTATATG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (26 bp):
CAATATCGCAGCAAAGCTGCCAGTAA
Found at i:42388803 original size:68 final size:68
Alignment explanation
Indices: 42388655--42388810 Score: 156
Period size: 68 Copynumber: 2.2 Consensus size: 68
42388645 AGCCGATTTG
* * * * **
42388655 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGTGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGTGACCTAGCTACACA
*
42388720 TATC
65 TATA
*
42388724 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGTGACCTAGCTAC-
42388786 ACATAGTA
62 ACATA-TA
*
42388794 TCTCGTAGCTTTCTTGT
1 TCTCGTAGCTCTCTTGT
42388811 ACACATGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
68 35 0.48
69 6 0.08
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGTGACCTAGCTACACAT
ATA
Found at i:42400368 original size:50 final size:48
Alignment explanation
Indices: 42400310--42400679 Score: 262
Period size: 50 Copynumber: 7.7 Consensus size: 48
42400300 TTATGTGCGC
*
42400310 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGA-AGATGAGAT
* * * * *
42400359 CTAGTGTAAGACCATGTCTGGGGCATGGCATC--AACTTG-ATATGTG-T
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGAAGATGAGAT
* * * * * *
42400405 CAGTGTAAGATCATGTTTGGGACATGGCATTGACATCGACAAATGAGAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGA-AGATGAGAT
* * *
42400454 CCAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTG-ATATGTG-T
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGAAGATGAGAT
* * * *
42400500 CAGTGTAAGACCATGCCTGGGACATGGCATTGGCACCAACAGATGAGAG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGA-AGATGAGAT
* * * ** *
42400549 CTAGTGTAAGGCCATGTCTAGGACATGGCATCAGC-TTG--GTATGTG-T
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAAG-ATGAGAT
*
42400595 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATATATGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGA-AGATGAGA-T
* * * * *
42400645 CAATATAAAACCATATCTGGGATATGGCATCGGCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
42400680 TCGATATGTG
Statistics
Matches: 246, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
45 85 0.35
46 7 0.03
47 17 0.07
48 17 0.07
49 5 0.02
50 115 0.47
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAAGATGAGAT
Found at i:42400412 original size:45 final size:45
Alignment explanation
Indices: 42400361--42400625 Score: 251
Period size: 45 Copynumber: 5.7 Consensus size: 45
42400351 GATGAGAGCT
*
42400361 AGTGTAAGACCATGTCTGGGGCATGGCATCAACTTGATATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATATGTGTC
* * ** * * *
42400406 AGTGTAAGATCATGTTTGGGACATGGCATTGACATCGACAAATGAGATCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAAC-TTG--ATATGTG-T-C
*
42400456 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATATGTGTC
* * *** * * *
42400501 AGTGTAAGACCATGCCTGGGACATGGCATTGGCACCAACAGATGAGAGC
1 AGTGTAAGACCATGTCTGGGACATGGCA-T--CAACTTGATATGTG-TC
* * * *
42400550 TAGTGTAAGGCCATGTCTAGGACATGGCATCAGCTTGGTATGTGTC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATATGTGTC
42400596 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
42400626 GGCCTCGATA
Statistics
Matches: 174, Mismatches: 36, Indels: 20
0.76 0.16 0.09
Matches are distributed among these distances:
45 84 0.48
46 5 0.03
47 12 0.07
48 12 0.07
49 5 0.03
50 56 0.32
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATATGTGTC
Found at i:42400473 original size:95 final size:95
Alignment explanation
Indices: 42400310--42400624 Score: 486
Period size: 95 Copynumber: 3.3 Consensus size: 95
42400300 TTATGTGCGC
*
42400310 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
*
42400375 TCTGGGGCATGGCATCAACTTGATATGTGT
66 TCTGGGACATGGCATCAACTTGATATGTGT
* * * * * * *
42400405 CAGTGTAAGATCATGTTTGGGACATGGCATTGACATCGACAAATGAGATCCAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
*
42400470 TCTGGGACATGGCATCGACTTGATATGTGT
66 TCTGGGACATGGCATCAACTTGATATGTGT
* * *
42400500 CAGTGTAAGACCATGCCTGGGACATGGCATTGGCACCAACAGATGAGAGCTAGTGTAAGGCCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
* * *
42400565 TCTAGGACATGGCATCAGCTTGGTATGTGT
66 TCTGGGACATGGCATCAACTTGATATGTGT
42400595 CAGTGTAAGACCATGTCTGGGACATGGCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCAT
42400625 CGGCCTCGAT
Statistics
Matches: 195, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 195 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATTGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
TCTGGGACATGGCATCAACTTGATATGTGT
Found at i:42400641 original size:95 final size:95
Alignment explanation
Indices: 42400310--42400690 Score: 480
Period size: 95 Copynumber: 4.0 Consensus size: 95
42400300 TTATGTGCGC
42400310 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
* *
42400375 TCTGGGGCATGGCATCAACTTGATATGTGT
66 TCTGGGACATGGCATCAGCTTGATATGTGT
* * * * * * * *
42400405 CAGTGTAAGATCATGTTTGGGACATGGCATTGACATCGACAAATGAGATCCAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
42400470 TCTGGGACATGGCATC-GACTTGATATGTGT
66 TCTGGGACATGGCATCAG-CTTGATATGTGT
* * * *
42400500 CAGTGTAAGACCATGCCTGGGACATGGCATTGGCACCAACAGATGAGAGCTAGTGTAAGGCCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
* *
42400565 TCTAGGACATGGCATCAGCTTGGTATGTGT
66 TCTGGGACATGGCATCAGCTTGATATGTGT
* * * * *
42400595 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATATATGAGAG-TCAATATAAAACCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGACAGATGAGAGCT-AGTGTAAGACCA
* * * *
42400658 TATCTGGGATATGGCATCGGCATCGATATGTGT
64 TGTCTGGGACATGGCATCAGC-TTGATATGTGT
42400691 AAGATTTCTC
Statistics
Matches: 244, Mismatches: 37, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
94 2 0.01
95 232 0.95
96 10 0.04
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (95 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
TCTGGGACATGGCATCAGCTTGATATGTGT
Found at i:42400666 original size:190 final size:191
Alignment explanation
Indices: 42400310--42400690 Score: 541
Period size: 190 Copynumber: 2.0 Consensus size: 191
42400300 TTATGTGCGC
* *
42400310 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGCCTGGGACATGGCATCGGCACCAACAGATGAGAGCTAGTGTAAGACCATG
* * * * *
42400375 TCTGGGGCATGGCATCAACTTGATATGTGTCAGTGTAAGATCATGTTTGGGACATGGCATTGACA
66 TCTAGGACATGGCATCAACTTGATATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACA
* * * * *
42400440 TCGACAAATGAGATCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTGATATGTGT
131 TCGACAAATGAGATCCAATATAAAACCATATCTGGGACATGGCATCGACATCGATATGTGT
* *
42400500 CAGTGTAAGACCATGCCTGGGACATGGCATTGGCACCAACAGATGAGAGCTAGTGTAAGGCCATG
1 CAGTGTAAGACCATGCCTGGGACATGGCATCGGCACCAACAGATGAGAGCTAGTGTAAGACCATG
* * * *
42400565 TCTAGGACATGGCATCAGCTTGGTATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCC
66 TCTAGGACATGGCATCAACTTGATATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACA
* * * *
42400630 TCGATATATGAGAGT-CAATATAAAACCATATCTGGGATATGGCATCGGCATCGATATGTGT
131 TCGACAAATGAGA-TCCAATATAAAACCATATCTGGGACATGGCATCGACATCGATATGTGT
42400691 AAGATTTCTC
Statistics
Matches: 167, Mismatches: 22, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
190 156 0.93
191 11 0.07
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (191 bp):
CAGTGTAAGACCATGCCTGGGACATGGCATCGGCACCAACAGATGAGAGCTAGTGTAAGACCATG
TCTAGGACATGGCATCAACTTGATATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACA
TCGACAAATGAGATCCAATATAAAACCATATCTGGGACATGGCATCGACATCGATATGTGT
Found at i:42406205 original size:70 final size:70
Alignment explanation
Indices: 42406094--42406373 Score: 537
Period size: 70 Copynumber: 4.0 Consensus size: 70
42406084 TTATTTGCAT
*
42406094 GAAAAATGAAGTT--AAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
1 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
42406157 ATAAG
66 ATAAG
42406162 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
1 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
42406227 ATAAG
66 ATAAG
42406232 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
1 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
42406297 ATAAG
66 ATAAG
42406302 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
1 GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
42406367 ATAAG
66 ATAAG
42406372 GA
1 GA
42406374 TGCTTGAGGT
Statistics
Matches: 209, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
68 12 0.06
70 197 0.94
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (70 bp):
GAAAAATGAAATTAAAAAAAATGACCCATGCTAGATAATTATGCATTTTGATGTTTAATGGTAGA
ATAAG
Found at i:42407220 original size:45 final size:45
Alignment explanation
Indices: 42407155--42407327 Score: 175
Period size: 45 Copynumber: 3.7 Consensus size: 45
42407145 TATGTGAGCC
* *
42407155 AGTGTAAGACCATGTTTGGGACATGGCATCGGCTTGATATCTATT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATATATT
* ** * * *
42407200 AGTGTAAGACCATGTCTGGGACATGGCCTCGGCACCGACAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTG--ATAT-ATA-TT
* * * * * *
42407250 AGTGTAAGACCATATTTGGGACATAGCATCGGCTTGATATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATATATT
42407295 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
42407328 ACCGACAGAT
Statistics
Matches: 100, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
45 61 0.61
46 1 0.01
47 3 0.03
48 3 0.03
49 2 0.02
50 30 0.30
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGATATATATT
Found at i:42407270 original size:50 final size:50
Alignment explanation
Indices: 42407199--42407352 Score: 183
Period size: 50 Copynumber: 3.2 Consensus size: 50
42407189 TGATATCTAT
*
42407199 TAGTGTAAGACCATGTCTGGGACATGGCCTCGGCACCGACAGATGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGC
* * * ** * * *
42407249 TAGTGTAAGACCATATTTGGGACATAGCATCGGC-TTG--ATATGTG-TC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGC
42407295 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGC
*
42407344 CAGTGTAAG
1 TAGTGTAAG
42407353 TTATGCCTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
45 30 0.37
46 2 0.02
47 5 0.06
48 5 0.06
49 2 0.02
50 38 0.46
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (50 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACAGATGAGAGC
Found at i:42407318 original size:95 final size:95
Alignment explanation
Indices: 42407150--42407352 Score: 343
Period size: 95 Copynumber: 2.1 Consensus size: 95
42407140 GCTGTTATGT
* * *
42407150 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCTTGATATCTATTAGTGTAAGACCATGT
1 GAGCCAGTGTAAGACCATATTTGGGACATAGCATCGGCTTGATATCTATCAGTGTAAGACCATGT
*
42407215 CTGGGACATGGCCTCGGCACCGACAGATGA
66 CTGGGACATGGCATCGGCACCGACAGATGA
* * *
42407245 GAGCTAGTGTAAGACCATATTTGGGACATAGCATCGGCTTGATATGTGTCAGTGTAAGACCATGT
1 GAGCCAGTGTAAGACCATATTTGGGACATAGCATCGGCTTGATATCTATCAGTGTAAGACCATGT
42407310 CTGGGACATGGCATCGGCACCGACAGATGA
66 CTGGGACATGGCATCGGCACCGACAGATGA
42407340 GAGCCAGTGTAAG
1 GAGCCAGTGTAAG
42407353 TTATGCCTAT
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 100 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (95 bp):
GAGCCAGTGTAAGACCATATTTGGGACATAGCATCGGCTTGATATCTATCAGTGTAAGACCATGT
CTGGGACATGGCATCGGCACCGACAGATGA
Found at i:42409580 original size:11 final size:11
Alignment explanation
Indices: 42409558--42409587 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42409548 TTTTAAATGA
42409558 TATTTT-TTAT
1 TATTTTATTAT
42409568 TATTTTATTAT
1 TATTTTATTAT
42409579 TATTTTATT
1 TATTTTATT
42409588 TAGTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:42416954 original size:40 final size:40
Alignment explanation
Indices: 42416856--42417118 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
42416846 TCCTCGTTCA
* * * ** *
42416856 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
42416895 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42416935 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
42416975 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
42417015 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
42417055 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
42417095 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
42417119 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:42418588 original size:10 final size:11
Alignment explanation
Indices: 42418569--42418601 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42418559 TTGATATGTT
42418569 AATGAAGAGAA
1 AATGAAGAGAA
42418580 AAT-AAGAGAA
1 AATGAAGAGAA
*
42418590 AGTGAAGAGAA
1 AATGAAGAGAA
42418601 A
1 A
42418602 TAGTGTAGAG
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:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (11 bp):
AATGAAGAGAA
Found at i:42420358 original size:46 final size:46
Alignment explanation
Indices: 42420310--42420538 Score: 305
Period size: 46 Copynumber: 5.0 Consensus size: 46
42420300 ACTCTCTGAT
** * *
42420310 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
42420356 ATGAAACGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
42420402 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
42420448 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * * *
42420494 AAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 -ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
42420539 TCAAAGATAA
Statistics
Matches: 161, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 124 0.77
47 37 0.23
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:42424668 original size:43 final size:43
Alignment explanation
Indices: 42424573--42424674 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
42424563 ACCAAGATGT
* * * * *
42424573 GATTACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGT
1 GATTACGTGTAAGACCATGTCTGGGACATTAGCATCGTAATGC
42424616 GATTACGTGTAAGACCATGTCTGGGACATTAGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTAGCATCG-TAATGC
*
42424659 GATTTCGTGTAAGACC
1 GATTACGTGTAAGACC
42424675 CAGTTCGGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 49 0.94
44 3 0.06
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTAGCATCGTAATGC
Found at i:42427104 original size:40 final size:40
Alignment explanation
Indices: 42427049--42427270 Score: 324
Period size: 40 Copynumber: 5.6 Consensus size: 40
42427039 TATTCGAATG
* *
42427049 ATATCCGGGCTAAGTCCCAAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
42427089 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
42427129 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
42427169 ATATCCGGGCTAAGTCTCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
42427209 ATATCCGGGCTAAGACCCGAAGGCATTTGTG-TGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TGACT
*
42427249 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
42427271 TACTTGGGTT
Statistics
Matches: 165, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 15 0.09
40 148 0.90
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:42433752 original size:53 final size:53
Alignment explanation
Indices: 42433574--42433776 Score: 160
Period size: 53 Copynumber: 3.8 Consensus size: 53
42433564 GGGTTTAAGG
* * * *
42433574 ATACCAAGTAATACCATGCCAATG-CATGGCATTGGTAAGTTCTACAAGGCAAGAA
1 ATACCACGTAAGACCATGCCAA-GACATGGCAATGGTAAGTTC-ATAAGGCAA-AA
* * * * * *
42433629 A-ATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTAAT-ATAAGGCAAAA
1 ATACCACGTAAGACCATGCCAAGACATGGCAATGGT-AAGT--TCATAAGGCAAAA
* * * * * **
42433683 ATCCCATGTAAGACCATGCCAAGGCGTGGCAATGGTGAGTTCATAAGGCAAGG
1 ATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAAA
* *
42433736 ATACCACGTAAGACCATGTCAAGACATGGCAGTGGTAAGTT
1 ATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
42433777 TAAAAAGGAA
Statistics
Matches: 117, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
52 1 0.01
53 44 0.38
54 32 0.27
55 39 0.33
57 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (53 bp):
ATACCACGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGCAAAA
Found at i:42439882 original size:16 final size:16
Alignment explanation
Indices: 42439857--42439895 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42439847 GTAGATCAAC
* *
42439857 AAAAGCCGAAATGCCG
1 AAAAGTCGAAATACCG
42439873 AAAAGTCGAAATACCG
1 AAAAGTCGAAATACCG
42439889 AAAAGTC
1 AAAAGTC
42439896 AAAGGTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (16 bp):
AAAAGTCGAAATACCG
Found at i:42440154 original size:29 final size:30
Alignment explanation
Indices: 42440112--42440195 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 30
42440102 AAGCATGTAT
*
42440112 ATGAATGTGATTTGTGCCTAATGGGCTG-C
1 ATGAATGTGATTTGGGCCTAATGGGCTGAC
* *
42440141 ATGAATGTGATTTGGGTCTAATGGG-TGAT
1 ATGAATGTGATTTGGGCCTAATGGGCTGAC
* *
42440170 ATGAATATGATTTGGGCTTAATGGGC
1 ATGAATGTGATTTGGGCCTAATGGGC
42440196 ATATGAATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.04
29 45 0.96
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (30 bp):
ATGAATGTGATTTGGGCCTAATGGGCTGAC
Found at i:42440221 original size:27 final size:29
Alignment explanation
Indices: 42440149--42440228 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
42440139 GCATGAATGT
** *
42440149 GATTTGGG-TCTAATGGGTGATATGAATAT
1 GATTTGGGCT-TAATGGGCCATATGAATAA
42440178 GATTTGGGCTTAATGGG-CATATGAATAA
1 GATTTGGGCTTAATGGGCCATATGAATAA
*
42440206 GA-TTGGGCTTAGTGGGCCATATG
1 GATTTGGGCTTAATGGGCCATATG
42440229 CATGTATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 13 0.28
28 17 0.37
29 15 0.33
30 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.34
Consensus pattern (29 bp):
GATTTGGGCTTAATGGGCCATATGAATAA
Found at i:42440524 original size:99 final size:99
Alignment explanation
Indices: 42440349--42440549 Score: 366
Period size: 99 Copynumber: 2.0 Consensus size: 99
42440339 AGGCTAAGGT
*
42440349 GTGGTGATAGGTATATGCATGTCTAGGATTGGATGTAGGGAGAGCTTGGTACTTAAGCGGTCTTA
1 GTGGTGATAGGTATATGCATGTCTAGGATTGGATGTAGGGAGAGCTTGGTACTTAAACGGTCTTA
*
42440414 ATGACTCACCTCCTCTTCTCTAGAATCCTATCTG
66 ATGACTCACCTCCTCTTCTCTAGAATCCTACCTG
*
42440448 GTGGTGATAGGTATATGCATGTCTAGGATTGTATGTAGGGAGAGCTTGGTACTTAAACGGTCTTA
1 GTGGTGATAGGTATATGCATGTCTAGGATTGGATGTAGGGAGAGCTTGGTACTTAAACGGTCTTA
*
42440513 ATGACTTACCTCCTCTTCTCTAGAATCCTACCTG
66 ATGACTCACCTCCTCTTCTCTAGAATCCTACCTG
42440547 GTG
1 GTG
42440550 CATAGTATCT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (99 bp):
GTGGTGATAGGTATATGCATGTCTAGGATTGGATGTAGGGAGAGCTTGGTACTTAAACGGTCTTA
ATGACTCACCTCCTCTTCTCTAGAATCCTACCTG
Found at i:42461882 original size:12 final size:13
Alignment explanation
Indices: 42461867--42461896 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42461857 TATAGCATAT
42461867 TATTT-CATTTAC
1 TATTTCCATTTAC
42461879 TATTTCCATTTAC
1 TATTTCCATTTAC
42461892 TATTT
1 TATTT
42461897 TAACCTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTCCATTTAC
Found at i:42468445 original size:43 final size:42
Alignment explanation
Indices: 42468397--42468566 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 42
42468387 AGGTCACACA
* *
42468397 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT-G
* *
42468440 ATGCCACTGTCCCAGACAG-GGTCTTACACAAAATCAAATATG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATATG
* * * *
42468482 ATGCCGATGTCTCAGACATGATCTTACACGTAAATCTCAAAT-TG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAA--TCAAATATG
* * * * *
42468526 ATGCCAACGACCCAGATGTGCTCTTACACGAAATCACATAT
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT
42468567 CGAAATCCTA
Statistics
Matches: 103, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
41 5 0.05
42 25 0.24
43 41 0.40
44 26 0.25
45 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATG
Found at i:42474238 original size:46 final size:46
Alignment explanation
Indices: 42474182--42474318 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
42474172 TATATATACA
* * * * *
42474182 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCGCATGTC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
* * **
42474228 CATCTTATACACGTTTCGCATTAGCCATTCGGCTTTACTTCATATC
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
* *
42474274 CATCTCATACACATTTCGTATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATAT
42474319 ATACACTTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.36
Consensus pattern (46 bp):
CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCGCATATC
Found at i:42474363 original size:47 final size:46
Alignment explanation
Indices: 42474297--42474456 Score: 205
Period size: 47 Copynumber: 3.4 Consensus size: 46
42474287 TTTCGTATTA
* * * * *
42474297 GCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCACATTG
1 GCCATTC-GCCTTATCACATATATGCA-TGTTCACATTCATCACATTG
*
42474344 GCCATTCTGCCTTGTCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTC-GCCTTATCACATATATGCATGTTCACATTCATCACATTG
42474391 GCCATTCGACCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCG-CCTTATCACATATATGCATGTTCACATTCATCACATTG
*
42474438 GCCATTCGGCCTTACCACA
1 GCCATTC-GCCTTATCACA
42474457 CTACGGCTTT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
46 2 0.02
47 98 0.97
48 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.33
Consensus pattern (46 bp):
GCCATTCGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:42474540 original size:47 final size:47
Alignment explanation
Indices: 42474489--42474639 Score: 230
Period size: 47 Copynumber: 3.2 Consensus size: 47
42474479 CACTTCCACG
* *
42474489 TTCATCACATTGGCCATTCTGCCTTGTCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
42474536 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
** * * **
42474583 TTCATCACATTTTCCATTCGGCCTTATCTCATATATCCACATTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
42474630 TTCATCACAT
1 TTCATCACAT
42474640 AAAATCCTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 96 1.00
ACGTcount: A:0.25, C:0.29, G:0.09, T:0.36
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:42474589 original size:157 final size:157
Alignment explanation
Indices: 42474303--42474608 Score: 585
Period size: 157 Copynumber: 1.9 Consensus size: 157
42474293 ATTAGCCATT
42474303 CGGCTTTACCACATATATACACTTCCACGTTCATCACATTGGCCATTCTGCCTTGTCACATATAT
1 CGGCTTTACCACATATATACACTTCCACGTTCATCACATTGGCCATTCTGCCTTGTCACATATAT
42474368 GCATGTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCATCA
66 GCATGTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCATCA
42474433 CATTGGCCATTCGGCCTTACCACACTA
131 CATTGGCCATTCGGCCTTACCACACTA
42474460 CGGCTTTACCACATATATACACTTCCACGTTCATCACATTGGCCATTCTGCCTTGTCACATATAT
1 CGGCTTTACCACATATATACACTTCCACGTTCATCACATTGGCCATTCTGCCTTGTCACATATAT
*
42474525 GCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
66 GCATGTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCATCA
**
42474590 CATTTTCCATTCGGCCTTA
131 CATTGGCCATTCGGCCTTA
42474609 TCTCATATAT
Statistics
Matches: 146, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
157 146 1.00
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (157 bp):
CGGCTTTACCACATATATACACTTCCACGTTCATCACATTGGCCATTCTGCCTTGTCACATATAT
GCATGTTCACATTCATCACATTGGCCATTCGACCTTATCACATATATGCATGTTCACATTCATCA
CATTGGCCATTCGGCCTTACCACACTA
Found at i:42474640 original size:25 final size:25
Alignment explanation
Indices: 42474561--42474640 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
42474551 ATTCGGCCTT
* **
42474561 ATCACATATATGCATGTTCACATTC
1 ATCACATATATCCACATTCACATTC
* * *
42474586 ATCACAT-T-TTC-CATTCGGCCTT-
1 ATCACATATATCCACATTC-ACATTC
*
42474608 ATCTCATATATCCACATTCACATTC
1 ATCACATATATCCACATTCACATTC
42474633 ATCACATA
1 ATCACATA
42474641 AAATCCTAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 6 0.15
25 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (25 bp):
ATCACATATATCCACATTCACATTC
Found at i:42488640 original size:85 final size:85
Alignment explanation
Indices: 42488543--42488712 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
42488533 ACTAGTTAAT
*
42488543 ACTTAAGTGTTAGTATTTGTACATGAAATAGATGAATGTGGAATTGTTGAGTTATTTGAACAAAT
1 ACTTAAGTGTTAGTATTTGTACATGAAATAGATGAATGTGGAATTGTGGAGTTATTTGAACAAAT
42488608 TCGGCTTTGTAATGGATTTC
66 TCGGCTTTGTAATGGATTTC
42488628 ACTTAAGTGTTAGTATTTGTACATGAAATAGATGAATGTGGAATTGTGGAGTTATTTGAACAAAT
1 ACTTAAGTGTTAGTATTTGTACATGAAATAGATGAATGTGGAATTGTGGAGTTATTTGAACAAAT
42488693 TCGGCTTTGTAATGGATTTC
66 TCGGCTTTGTAATGGATTTC
42488713 TTTTTAGTAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.39
Consensus pattern (85 bp):
ACTTAAGTGTTAGTATTTGTACATGAAATAGATGAATGTGGAATTGTGGAGTTATTTGAACAAAT
TCGGCTTTGTAATGGATTTC
Found at i:42497333 original size:40 final size:40
Alignment explanation
Indices: 42497228--42497444 Score: 325
Period size: 40 Copynumber: 5.5 Consensus size: 40
42497218 CGGATGATAA
* *
42497228 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
42497268 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42497307 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42497347 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42497387 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
42497427 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42497445 TACTTGGTTT
Statistics
Matches: 167, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 51 0.31
40 116 0.69
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42497442 original size:119 final size:119
Alignment explanation
Indices: 42497224--42497444 Score: 340
Period size: 119 Copynumber: 1.9 Consensus size: 119
42497214 TATTCGGATG
* *
42497224 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
* *
42497289 TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGAGCGAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
*
42497343 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGC
*
42497407 ATTTGAGCGAG-TAGCTATATCC-GGCTAAATTCCGAAGG
64 ATTTGAGCGAGTTA-CTATATCCGGGCTAAATCCCGAAGG
42497445 TACTTGGTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
118 2 0.02
119 64 0.69
120 27 0.29
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCAT
TTGAGCGAGTTACTATATCCGGGCTAAATCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42504857 original size:27 final size:27
Alignment explanation
Indices: 42504847--42505040 Score: 280
Period size: 27 Copynumber: 7.2 Consensus size: 27
42504837 TCTTAGCCTG
*
42504847 ATGTGGTAAAATGACTGTTTTTCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
*
42504874 ATGTGGTAAAATGACTGTTTTGCTCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
42504901 ATGTGGTAAAATGACTGTTTTGCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
*
42504928 ATATGGTAAAATGACTGTTTTGCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
*
42504955 ATGTGGTAAAATGACTATTTTGCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
* *
42504982 ATATGGTAAAATGACTATTTTGCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
* * * * *
42505009 ATATGGTAAGATGAGTATTTTTCCCTT
1 ATGTGGTAAAATGACTGTTTTGCCCTT
*
42505036 GTGTG
1 ATGTG
42505041 TTGTATATAT
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 155 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.42
Consensus pattern (27 bp):
ATGTGGTAAAATGACTGTTTTGCCCTT
Found at i:42507556 original size:27 final size:27
Alignment explanation
Indices: 42507526--42507729 Score: 270
Period size: 27 Copynumber: 7.6 Consensus size: 27
42507516 TCAAAATTAT
* *
42507526 TATTTTGTCATTATGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
42507553 TATTTTGCCCTTATGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
*
42507580 TGTTTTGCCCTTATGTGGTAAAATGGA-
1 TATTTTGCCCTTATGTGGTAAAAT-GAC
* * *
42507607 TGTTTTTCCCTTTTGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
* * *
42507634 TCTTTTTCCCCTATGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
42507661 TATTTTGCCCTTATGTGGTAAAAT-AC
1 TATTTTGCCCTTATGTGGTAAAATGAC
* * *
42507687 TGTTTTGCCCTTA-ATGGTAAGATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
42507713 TATTTTGCCCTTATGTG
1 TATTTTGCCCTTATGTG
42507730 ATGTGTGTAT
Statistics
Matches: 157, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
25 8 0.05
26 30 0.19
27 117 0.75
28 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (27 bp):
TATTTTGCCCTTATGTGGTAAAATGAC
Found at i:42508008 original size:23 final size:24
Alignment explanation
Indices: 42507982--42508026 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
42507972 ATATCCCCAC
*
42507982 ATGGAGTGTAG-GGTTAGATGGAG
1 ATGGAGTGTAGAGGCTAGATGGAG
42508005 ATGGAGTGTAGAGGCTAGATGG
1 ATGGAGTGTAGAGGCTAGATGG
42508027 GTAGGACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.47, T:0.24
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTAGATGGAG
Found at i:42508083 original size:18 final size:18
Alignment explanation
Indices: 42508039--42508087 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42508029 AGGACTTGTA
*
42508039 TATTGTTACTGCACTGAT
1 TATTGTTACTGCACTGAC
* * *
42508057 TACTATTACTGCACTGCC
1 TATTGTTACTGCACTGAC
42508075 TATTGTTACTGCA
1 TATTGTTACTGCA
42508088 ATGGGCCAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (18 bp):
TATTGTTACTGCACTGAC
Found at i:42512399 original size:43 final size:43
Alignment explanation
Indices: 42512303--42512416 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
42512293 ACCGAGATGT
* * * *
42512303 GATTACTTGTAAGACCATGTCTGGGACATTGGCATTATATTAT
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAAC
* *
42512346 GATTACGTGTAAGACCATGTCTGGGACATTGATATTGT-TAACC
1 GATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAA-C
** * *
42512389 GATTTTGTGTAAGACCCTGTTTGGGACA
1 GATTACGTGTAAGACCATGTCTGGGACA
42512417 GTGGCATTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 2 0.03
43 58 0.97
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAAC
Found at i:42524074 original size:11 final size:11
Alignment explanation
Indices: 42524058--42524083 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42524048 CGAAGCCCAC
42524058 ATCACAATAAT
1 ATCACAATAAT
42524069 ATCACAATAAT
1 ATCACAATAAT
42524080 ATCA
1 ATCA
42524084 TACATGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (11 bp):
ATCACAATAAT
Found at i:42524570 original size:26 final size:27
Alignment explanation
Indices: 42524539--42524616 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
42524529 AAGGGCAAAA
* * *
42524539 CAGTCATTTTACCCTATAGGGGTATGT
1 CAGTCATTTTACACTACAAGGGTATGT
*
42524566 C-GTCATTTTACACTACAAGGGTATTT
1 CAGTCATTTTACACTACAAGGGTATGT
* *
42524592 CAGTAATTTTACACTACAAAGGTAT
1 CAGTCATTTTACACTACAAGGGTAT
42524617 TTCGATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 22 0.50
27 22 0.50
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (27 bp):
CAGTCATTTTACACTACAAGGGTATGT
Found at i:42524600 original size:27 final size:27
Alignment explanation
Indices: 42524581--42525064 Score: 457
Period size: 27 Copynumber: 18.0 Consensus size: 27
42524571 TTTTACACTA
*
42524581 CAAGGGTATTTCAGTAATTTTAC-ACT
1 CAAGGGTATTTCAGTAATTTTACAAAT
*
42524607 ACAAAGGTATTTC-GATAATTTTACAAAT
1 -CAAGGGTATTTCAG-TAATTTTACAAAT
* *
42524635 C-AGGGATGTTTCGGTAATTTTACAAAT
1 CAAGGG-TATTTCAGTAATTTTACAAAT
*
42524662 CGAGGGTATTTC-GATAATTTTACAAAT
1 CAAGGGTATTTCAG-TAATTTTACAAAT
*
42524689 CAAGGGTATTTTAGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
42524716 CGAGGGTGTTTC-GATAATTTTACAAAT
1 CAAGGGTATTTCAG-TAATTTTACAAAT
* * **
42524743 CGAGGGTGTTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
42524770 -AGAGGGTGTTTTAGTAATTTTACAAAT
1 CA-AGGGTATTTCAGTAATTTTACAAAT
*
42524797 CAAGGGTATTTTTA-TAATTTTAC-AAT
1 CAAGGGTA-TTTCAGTAATTTTACAAAT
** *
42524823 TGAGGGTATTTCGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* *
42524850 TAAGGGTATTTCAATAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* * *
42524877 CGAGGGTATTTTAGTAATTTTATAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
***
42524904 TGGGGGTATTTCAGTAATTTTACAAAGT
1 CAAGGGTATTTCAGTAATTTTACAAA-T
* * *
42524932 -AAAGGTATTTTAGTAACTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
** * *
42524958 TGAGGGTGTTTCGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
** *
42524985 TGAGGGTATTTCAGTAATTTTA-GAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
* * * *
42525011 CAATGATATTTCTGTAATATTACAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
*
42525038 CAAGGGTATTTCAGTAATTTTGCAAAT
1 CAAGGGTATTTCAGTAATTTTACAAAT
42525065 TGATAGTATT
Statistics
Matches: 384, Mismatches: 56, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.01
26 44 0.11
27 321 0.84
28 16 0.04
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTACAAAT
Found at i:42524668 original size:81 final size:81
Alignment explanation
Indices: 42524583--42525076 Score: 520
Period size: 81 Copynumber: 6.1 Consensus size: 81
42524573 TTACACTACA
* * *
42524583 AGGGTATTTCAGTAATTTTAC-ACTACAAAGGTA-TTTCGATAATTTTACAAATC-AGGGATGTT
1 AGGGTATTTCAGTAATTTTACAAAT-CAAGGGTATTTTAG-TAATTTTACAAATCAAGGG-TGTT
*
42524645 TCGGTAATTTTACAAATCG
63 TCGGTAATTTTACAAATTG
*
42524664 AGGGTATTTC-GATAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCGAGGGTGTTTC
1 AGGGTATTTCAG-TAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTGTTTC
* *
42524728 GATAATTTTACAAATCG
65 GGTAATTTTACAAATTG
* ** * * *
42524745 AGGGTGTTTTGGTAATTTTACAAAT-AGAGGGTGTTTTAGTAATTTTACAAATCAAGGGTATTTT
1 AGGGTATTTCAGTAATTTTACAAATCA-AGGGTATTTTAGTAATTTTACAAATCAAGGGTGTTTC
**
42524809 TATAATTTTAC-AATTG
65 GGTAATTTTACAAATTG
* * * * * * **
42524825 AGGGTATTTCGGTAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTTA
1 AGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTGTTTCG
*
42524890 GTAATTTTATAAATTG
66 GTAATTTTACAAATTG
* * * **
42524906 GGGGTATTTCAGTAATTTTACAAAGT-AAAGGTATTTTAGTAACTTTACAAATTGAGGGTGTTTC
1 AGGGTATTTCAGTAATTTTACAAA-TCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTGTTTC
42524970 GGTAATTTTACAAATTG
65 GGTAATTTTACAAATTG
* * * * *
42524987 AGGGTATTTCAGTAATTTTA-GAATCAATGATATTTCT-GTAATATTACAAATCAAGGGTATTTC
1 AGGGTATTTCAGTAATTTTACAAATCAAGGGTATTT-TAGTAATTTTACAAATCAAGGGTGTTTC
* *
42525050 AGTAATTTTGCAAATTG
65 GGTAATTTTACAAATTG
**
42525067 ATAGTATTTC
1 AGGGTATTTC
42525077 GATTGTAACA
Statistics
Matches: 357, Mismatches: 45, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
79 1 0.00
80 124 0.35
81 220 0.62
82 12 0.03
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTACAAATCAAGGGTGTTTCG
GTAATTTTACAAATTG
Found at i:42525749 original size:25 final size:25
Alignment explanation
Indices: 42525716--42525785 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
42525706 AATCAAAATG
42525716 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
*
42525741 AGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGGTGAC
* *
42525766 AGAATTAGAATCATAATCAG
1 AGAATCAGAATCAGAATCAG
42525786 TATCAGGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTGAC
Found at i:42525753 original size:31 final size:30
Alignment explanation
Indices: 42525716--42525813 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 30
42525706 AATCAAAATG
42525716 AGAATCAGAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATCAG-ATCAGGTGACAGAATC
*
42525747 AGAATCAGAAT----T-AGGTGACAGAATT
1 AGAATCAGAATCAGATCAGGTGACAGAATC
* *
42525772 AGAATCATAATCAGTATCAGGTAACAGAATC
1 AGAATCAGAATCAG-ATCAGGTGACAGAATC
* *
42525803 AAAATAAGAAT
1 AGAATCAGAAT
42525814 GTGAATGCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
25 22 0.41
26 1 0.02
30 1 0.02
31 30 0.56
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.20
Consensus pattern (30 bp):
AGAATCAGAATCAGATCAGGTGACAGAATC
Found at i:42525776 original size:6 final size:6
Alignment explanation
Indices: 42525695--42525757 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
42525685 AAGAAACATT
* * *
42525695 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
42525744 ATCAGA ATCAGA AT
1 ATCAGA ATCAGA AT
42525758 TAGGTGACAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 2 0.04
6 39 0.85
7 4 0.09
8 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:42525980 original size:27 final size:26
Alignment explanation
Indices: 42525932--42525991 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42525922 GCGAGGCTGC
*
42525932 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
42525959 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
42525985 CAGATAT
1 CAGATAT
42525992 ATAGATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42526615 original size:91 final size:91
Alignment explanation
Indices: 42526460--42526641 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
42526450 TCCATAGCTA
*
42526460 GGGTTTGTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAACCCTGTTTTTAATGATTTTTA
1 GGGTTTGTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAACCCCGTTTTTAATGATTTTTA
42526525 CGTTTTTGAGATCCCGGTAACTCGAT
66 CGTTTTTGAGATCCCGGTAACTCGAT
*
42526551 GGGTTTGTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTTTAATGATTTTTA
1 GGGTTTGTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAACCCCGTTTTTAATGATTTTTA
42526616 CGTTTTTGAGATCCCGGTAACTCGAT
66 CGTTTTTGAGATCCCGGTAACTCGAT
42526642 AAAGCTTATG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (91 bp):
GGGTTTGTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAACCCCGTTTTTAATGATTTTTA
CGTTTTTGAGATCCCGGTAACTCGAT
Found at i:42527465 original size:46 final size:46
Alignment explanation
Indices: 42527415--42527629 Score: 412
Period size: 46 Copynumber: 4.7 Consensus size: 46
42527405 AGCATCCGAA
* *
42527415 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
42527461 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
1 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
42527507 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
1 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
42527553 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
1 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
42527599 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
42527630 GCGGGTTACA
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 167 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCGCTTATGGATGCGAACGCACGAG
Found at i:42528826 original size:79 final size:79
Alignment explanation
Indices: 42528695--42528851 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 79
42528685 GAGAAAGCAG
42528695 AGTTCTGGCTCGAAAATTCTATCTGGGTATTTGATGAATTATCTTGTACACCTGAAGAATGTTTG
1 AGTTCTGGCTCGAAAATTCTATCTGGGTATTTGATGAATTATCTTGTACACCTGAAGAATGTTTG
42528760 AAATGTGCTACATA
66 AAATGTGCTACATA
*
42528774 AGTTCTGGCTTGAAAATTCTATCTGGGTATTTGATGAATTATCTTGTACACCTGAAGAATGTTTG
1 AGTTCTGGCTCGAAAATTCTATCTGGGTATTTGATGAATTATCTTGTACACCTGAAGAATGTTTG
42528839 AAATGTGCTACAT
66 AAATGTGCTACAT
42528852 CTTTGTTGAG
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (79 bp):
AGTTCTGGCTCGAAAATTCTATCTGGGTATTTGATGAATTATCTTGTACACCTGAAGAATGTTTG
AAATGTGCTACATA
Found at i:42530365 original size:77 final size:77
Alignment explanation
Indices: 42530238--42530391 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 77
42530228 TTTGCGGACG
*
42530238 TATTTCCAGAAGAATTGCCGGGTTTGCCTCCAGTCAGGGAAGTAGAATTTGGTATTGAGTTGATA
1 TATTTCCAGAAGAATTGCCGGGTTTGCCTCCACTCAGGGAAGTAGAATTTGGTATTGAGTTGATA
*
42530303 CTGGGAACAGCT
66 CCGGGAACAGCT
* * *
42530315 TATTTCCAGAAGAGTTGCTGGGTTTGCCTCCACTTAGGGAAGTAGAATTTGGTATTGAGTTGATA
1 TATTTCCAGAAGAATTGCCGGGTTTGCCTCCACTCAGGGAAGTAGAATTTGGTATTGAGTTGATA
42530380 CCGGGAACAGCT
66 CCGGGAACAGCT
42530392 CCGATCTCGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (77 bp):
TATTTCCAGAAGAATTGCCGGGTTTGCCTCCACTCAGGGAAGTAGAATTTGGTATTGAGTTGATA
CCGGGAACAGCT
Found at i:42533918 original size:46 final size:46
Alignment explanation
Indices: 42533817--42534032 Score: 407
Period size: 46 Copynumber: 4.7 Consensus size: 46
42533807 GGTTGAGCAT
* *
42533817 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
42533862 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
42533908 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
42533954 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
42534000 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTA
1 CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTA
42534033 CAAATTATCC
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
45 32 0.19
46 136 0.81
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGC
Found at i:42535620 original size:27 final size:27
Alignment explanation
Indices: 42535590--42535784 Score: 255
Period size: 27 Copynumber: 7.2 Consensus size: 27
42535580 TAACACCCTA
* * *
42535590 AGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTAAAACGGTAATTTTGTAAATCG
*
42535617 AGGGTAAAACGGTAATTTTCTAAATCG
1 AGGGTAAAACGGTAATTTTGTAAATCG
42535644 AGGGTAAAACGGTAATTTTGTAAATCG
1 AGGGTAAAACGGTAATTTTGTAAATCG
* * *
42535671 AGGGTAAAACGGTAATTCTGTCAATTG
1 AGGGTAAAACGGTAATTTTGTAAATCG
*
42535698 AGGGTAAAACGGTAATTTTGTAAATCA
1 AGGGTAAAACGGTAATTTTGTAAATCG
* ** * *
42535725 ATGGTAAAATAGTAATTCTGTAAATTG
1 AGGGTAAAACGGTAATTTTGTAAATCG
* *
42535752 AGGGTAAAACAGTAATTTTGTAATTCG
1 AGGGTAAAACGGTAATTTTGTAAATCG
42535779 AGGGTA
1 AGGGTA
42535785 CTTTGATAAT
Statistics
Matches: 146, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
AGGGTAAAACGGTAATTTTGTAAATCG
Found at i:42535794 original size:27 final size:26
Alignment explanation
Indices: 42535764--42535851 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
42535754 GGTAAAACAG
42535764 TAATTTTGTAATTCGAGGGTACTTTGA
1 TAATTTTGTAATTCGAGGGTA-TTTGA
*
42535791 TAA-TTT-TACATGTCGAGGGTATTTCA
1 TAATTTTGTA-AT-TCGAGGGTATTTGA
* *
42535817 GTAATTTTGCAA-ACTGAGGGTATTTCGA
1 -TAATTTTGTAATTC-GAGGGTATTT-GA
42535845 TAATTTT
1 TAATTTT
42535852 ACAAATCGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
25 2 0.04
26 10 0.20
27 32 0.64
28 5 0.10
29 1 0.02
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.43
Consensus pattern (26 bp):
TAATTTTGTAATTCGAGGGTATTTGA
Found at i:42535868 original size:54 final size:53
Alignment explanation
Indices: 42535761--42535909 Score: 165
Period size: 54 Copynumber: 2.8 Consensus size: 53
42535751 GAGGGTAAAA
* * ** * *
42535761 CAGTAATTTTGTAATTCGAGGGTACTTTGATAATTTTACATGTCGAGGGTATTT
1 CAGTAATTTTGAAACT-GAGGGTACTTTGATAATTTTACAAATCGAAGATATTT
42535815 CAGTAATTTTGCAAACTGAGGGTA-TTTCGATAATTTTACAAATCGAAGATATTT
1 CAGTAATTTTG-AAACTGAGGGTACTTT-GATAATTTTACAAATCGAAGATATTT
** * *
42535869 GGGTAATTTTATAAACTGAGGGTACTTTGGTAATTTTACAA
1 CAGTAATTTT-GAAACTGAGGGTACTTTGATAATTTTACAA
42535910 CTGGGGGTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.04
54 72 0.89
55 6 0.07
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (53 bp):
CAGTAATTTTGAAACTGAGGGTACTTTGATAATTTTACAAATCGAAGATATTT
Found at i:42535927 original size:26 final size:26
Alignment explanation
Indices: 42535778--42535930 Score: 114
Period size: 27 Copynumber: 5.7 Consensus size: 26
42535768 TTTGTAATTC
* **
42535778 GAGGGTACTTTGA-TAATTTTACATGT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
42535804 CGAGGGTATTTCAGTAATTTTGCAAACT
1 -GAGGGTATTTCAGTAATTTTAC-AACT
*
42535832 GAGGGTATTTC-GATAATTTTACAAAT
1 GAGGGTATTTCAG-TAATTTTACAACT
* * ** *
42535858 CGAAGATATTTGGGTAATTTTATAAACT
1 -GAGGGTATTTCAGTAATTTTA-CAACT
*
42535886 GAGGGTACTTT-GGTAATTTTACAACT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
42535912 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCAGTAATTT
42535931 GGTAAACTAA
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
25 3 0.03
26 25 0.25
27 65 0.64
28 9 0.09
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.39
Consensus pattern (26 bp):
GAGGGTATTTCAGTAATTTTACAACT
Found at i:42538032 original size:14 final size:15
Alignment explanation
Indices: 42538013--42538042 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42538003 TTACAGACCC
42538013 ATACTCA-AGGCCCA
1 ATACTCATAGGCCCA
42538027 ATACTCATAGGCCCA
1 ATACTCATAGGCCCA
42538042 A
1 A
42538043 ATTCAGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (15 bp):
ATACTCATAGGCCCA
Found at i:42541443 original size:40 final size:40
Alignment explanation
Indices: 42541388--42541612 Score: 265
Period size: 40 Copynumber: 5.6 Consensus size: 40
42541378 TATTCGGATG
*
42541388 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
42541428 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
42541471 ATA-CTTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
42541511 ATTTCCGGGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
42541551 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
42541591 ATATCC-GGCTAAATCCCTAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
42541613 TACTTGGTTT
Statistics
Matches: 159, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 13 0.08
40 108 0.68
41 2 0.01
42 1 0.01
43 35 0.22
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:42541533 original size:83 final size:80
Alignment explanation
Indices: 42541388--42541582 Score: 266
Period size: 83 Copynumber: 2.4 Consensus size: 80
42541378 TATTCGGATG
* * *
42541388 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
42541453 TTTGTGCGAGTAGTTGCT
66 TGTGTGC--G-AGTTACT
* * *
42541471 ATA-CTTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTCCGGGCTAAGACCCGAAGGC
1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGC
42541535 ATGTGTGCGAGTTACT
65 ATGTGTGCGAGTTACT
*
42541551 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
42541583 GAGTTGCGAT
Statistics
Matches: 100, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
80 34 0.34
81 2 0.02
82 1 0.01
83 63 0.63
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TGTGTGCGAGTTACT
Found at i:42543693 original size:242 final size:242
Alignment explanation
Indices: 42543268--42543760 Score: 950
Period size: 242 Copynumber: 2.0 Consensus size: 242
42543258 AACAAGCTGC
*
42543268 TAATCAAATATTAGGCTTAACAGCCGTCGATGGATCCACGGTCGTCAAGAAACTATGCGATTCAC
1 TAATCAAATATTAGGCTTAACAGCCGTCGATGGATCCACGGTCGTCAAGAAACTATGCGATCCAC
42543333 ATATACTTCCTCCATTCCATAATTCCCAGCCCATGCAATATGTCGTGTATGTCATGCTCAATCAT
66 ATATACTTCCTCCATTCCATAATTCCCAGCCCATGCAATATGTCGTGTATGTCATGCTCAATCAT
42543398 CACACGTGTATGCAGAATGGCCGTACTCAATAACAGTATTTTAAAAAAGATATTAAGAGCATATC
131 CACACGTGTATGCAGAATGGCCGTACTCAATAACAGTATTTTAAAAAAGATATTAAGAGCATATC
42543463 AGTCATACAACCACAGTCAAGTCAATTAAAACGCAGTCATACTTTCA
196 AGTCATACAACCACAGTCAAGTCAATTAAAACGCAGTCATACTTTCA
42543510 TAATCAAATATTAGGCTTAACAGCCGTCGATGGATCCACGGTCGTCAAGAAACTATGCGATCCAC
1 TAATCAAATATTAGGCTTAACAGCCGTCGATGGATCCACGGTCGTCAAGAAACTATGCGATCCAC
*
42543575 ATATACTTCCTCCATTCCATAATTCCCAGGCCATGCAATATGTCGTGTATGTCATGCTCAATCAT
66 ATATACTTCCTCCATTCCATAATTCCCAGCCCATGCAATATGTCGTGTATGTCATGCTCAATCAT
* *
42543640 CACACGTGTATGCAGAATGGCCGTACTCAATAACAGTCTTTTAAAAAAGATATTAAGAGCATGTC
131 CACACGTGTATGCAGAATGGCCGTACTCAATAACAGTATTTTAAAAAAGATATTAAGAGCATATC
42543705 AGTCATACAACCACAGTCAAGTCAATTAAAACGCAGTCATACTTTCA
196 AGTCATACAACCACAGTCAAGTCAATTAAAACGCAGTCATACTTTCA
42543752 TAATCAAAT
1 TAATCAAAT
42543761 TAGTCAAATT
Statistics
Matches: 247, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
242 247 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (242 bp):
TAATCAAATATTAGGCTTAACAGCCGTCGATGGATCCACGGTCGTCAAGAAACTATGCGATCCAC
ATATACTTCCTCCATTCCATAATTCCCAGCCCATGCAATATGTCGTGTATGTCATGCTCAATCAT
CACACGTGTATGCAGAATGGCCGTACTCAATAACAGTATTTTAAAAAAGATATTAAGAGCATATC
AGTCATACAACCACAGTCAAGTCAATTAAAACGCAGTCATACTTTCA
Found at i:42543933 original size:27 final size:27
Alignment explanation
Indices: 42543817--42544321 Score: 357
Period size: 27 Copynumber: 18.9 Consensus size: 27
42543807 ACAGTTATTG
* * * *
42543817 GGGTATGTCGGTCATTTTAC-ACTACGA
1 GGGTATTTCGGTAATTTTACAAAT-CAA
*
42543844 GGGTA-TTCTGGTAATTTTAC-ACTACAA
1 GGGTATTTC-GGTAATTTTACAAAT-CAA
* * * *
42543871 AGGTATTTCGATGATTTTACAAATC-G
1 GGGTATTTCGGTAATTTTACAAATCAA
*
42543897 GGGATGTTTCGGTAATTTTACAAATCAA
1 GGG-TATTTCGGTAATTTTACAAATCAA
* *
42543925 AGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTCGGTAATTTTACAAATCAA
** *
42543952 GGGTATTTTAGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCAA
* * * *
42543979 TGGTGTTTCGATAATTCTACAAATCGAA
1 GGGTATTTCGGTAATTTTACAAATC-AA
*
42544007 GGTGT-TTT-GGTAATTTTACAAATCGA
1 GG-GTATTTCGGTAATTTTACAAATCAA
* *
42544033 GGGTATTTCAGTAATTTTAC-AATCGA
1 GGGTATTTCGGTAATTTTACAAATCAA
* * *
42544059 TGGTATTTCGGTAATTTTAAAAATTAA
1 GGGTATTTCGGTAATTTTACAAATCAA
** *
42544086 GGGTATTTCAATAATTTTACAAA-CTGA
1 GGGTATTTCGGTAATTTTACAAATC-AA
** * *
42544113 GGGTATTTTAGTAATTTTACAAATTAG
1 GGGTATTTCGGTAATTTTACAAATCAA
* *
42544140 GGGTATTTCAGTAATTTTACAAATTAA
1 GGGTATTTCGGTAATTTTACAAATCAA
* * **
42544167 GGGTATTTTGGTAATTTTAAAAATTGA
1 GGGTATTTCGGTAATTTTACAAATCAA
* **
42544194 GGGT-GTTCGAAAATTTTACAAATCAA
1 GGGTATTTCGGTAATTTTACAAATCAA
** * *
42544220 GGGTATTTTAGTAATTTTA-GAATCGA
1 GGGTATTTCGGTAATTTTACAAATCAA
** * * **
42544246 GAATATTTCGGTAATATTACAATTTGA
1 GGGTATTTCGGTAATTTTACAAATCAA
** * *
42544273 -GGTATTTCAATAATTTTGCAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCAA
* *
42544299 TGGTATTTCGATAATTTTACAAA
1 GGGTATTTCGGTAATTTTACAAA
42544322 CCGGGGGTGT
Statistics
Matches: 378, Mismatches: 85, Indels: 30
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.01
26 89 0.24
27 273 0.72
28 12 0.03
29 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAATCAA
Found at i:42544695 original size:28 final size:28
Alignment explanation
Indices: 42544659--42544722 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
42544649 TGGCCCTTTT
* *
42544659 AGGCCCAATCTCGTTCATATAGCCCATC
1 AGGCCCAATCACATTCATATAGCCCATC
* *
42544687 AGGCCCAATCACATTCATATGGCCCATT
1 AGGCCCAATCACATTCATATAGCCCATC
42544715 AGGCCCAA
1 AGGCCCAA
42544723 CTACTTCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATAGCCCATC
Found at i:42546053 original size:56 final size:56
Alignment explanation
Indices: 42545962--42546095 Score: 180
Period size: 56 Copynumber: 2.4 Consensus size: 56
42545952 CATGGCATCA
*
42545962 ATATATGTGTGCGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATT-TCG
1 ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCT-G
* * * * * *
42546018 ATATATGTGCACGAGTAAGGCCACGTTTTATACGTTGGCATCGATATGTGATTCTG
1 ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCTG
*
42546074 ATATATATGTACGAGTAAGACC
1 ATATATGTGTACGAGTAAGACC
42546096 CTATCTGGGA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
56 66 0.99
57 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (56 bp):
ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCTG
Found at i:42558093 original size:94 final size:94
Alignment explanation
Indices: 42557721--42558101 Score: 622
Period size: 94 Copynumber: 4.1 Consensus size: 94
42557711 ATTTAGGATT
42557721 TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
42557786 CATGCATATATGTGATAAGGCCGAATGGC
66 CATGCATATATGTGATAAGGCCGAATGGC
*
42557815 CAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
42557880 CATGCATATATGTGATAAGGCCGAATGGC
66 CATGCATATATGTGATAAGGCCGAATGGC
*
42557909 CAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
42557974 CATGCATATATGTGATAAGGACGAATGGA
66 CATGCATATATGTGATAAGGCCGAATGGC
* ** *
42558003 TAATGTGATGAATGTGAGCATGCATATATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGA
1 TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GA
* * **
42558068 A-GTGTATATATGTGGCGAA-GCCGAATGGC
65 ACATGCATATATGT-GATAAGGCCGAATGGC
42558097 TAATG
1 TAATG
42558102 CGAAATTATG
Statistics
Matches: 271, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
94 265 0.98
95 6 0.02
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (94 bp):
TAATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
CATGCATATATGTGATAAGGCCGAATGGC
Found at i:42558096 original size:47 final size:47
Alignment explanation
Indices: 42557722--42558061 Score: 626
Period size: 47 Copynumber: 7.2 Consensus size: 47
42557712 TTTAGGATTT
42557722 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
42557769 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
42557816 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
42557863 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
42557910 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* **
42557957 AATGTGATGAATGTGAACATGCATATATGTGATAAGGACGAATGGAT
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
* **
42558004 AATGTGATGAATGTGAGCATGCATATATGTGATAAGGTAGAATGGCC
1 AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
42558051 AATGTGATGAA
1 AATGTGATGAA
42558062 CGTGGAAGTG
Statistics
Matches: 285, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 285 1.00
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (47 bp):
AATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCC
Found at i:42558128 original size:79 final size:79
Alignment explanation
Indices: 42558029--42558185 Score: 314
Period size: 79 Copynumber: 2.0 Consensus size: 79
42558019 AGCATGCATA
42558029 TATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTGGCGAAGCCGAAT
1 TATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTGGCGAAGCCGAAT
42558094 GGCTAATGCGAAAT
66 GGCTAATGCGAAAT
42558108 TATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTGGCGAAGCCGAAT
1 TATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTGGCGAAGCCGAAT
42558173 GGCTAATGCGAAA
66 GGCTAATGCGAAA
42558186 CGTGTATGAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (79 bp):
TATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTGGCGAAGCCGAAT
GGCTAATGCGAAAT
Found at i:42560202 original size:27 final size:27
Alignment explanation
Indices: 42560172--42560377 Score: 288
Period size: 27 Copynumber: 7.6 Consensus size: 27
42560162 TCAAAATTAT
* * *
42560172 TATTTTGTCATTATATGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
* *
42560199 TATTTTTCCCTTATGTGATAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
*
42560226 TGTTTTGCCCTTATGTGGTAAAATGGA-
1 TATTTTGCCCTTATGTGGTAAAAT-GAC
* *
42560253 TGTTTTGCCCTTTTGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
42560280 TATTTTGCCCTTATGTGGTAAAATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
*
42560307 TATTTTGCCCTTATGTGGTAAAATGAT
1 TATTTTGCCCTTATGTGGTAAAATGAC
* * *
42560334 TGTTTTGCCCTTATATGGTAAGATGAC
1 TATTTTGCCCTTATGTGGTAAAATGAC
42560361 TATTTTGCCCTTATGTG
1 TATTTTGCCCTTATGTG
42560378 ATGTGTGTAT
Statistics
Matches: 159, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 2 0.01
27 155 0.97
28 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (27 bp):
TATTTTGCCCTTATGTGGTAAAATGAC
Found at i:42560302 original size:81 final size:81
Alignment explanation
Indices: 42560164--42560379 Score: 326
Period size: 81 Copynumber: 2.7 Consensus size: 81
42560154 CTGATTGATC
* * * * * *
42560164 AAAATTATTATTTTGTCATTATATGGTAAAATGACTATTTTTCCCTTATGTGATAAAATGACTGT
1 AAAATGATTGTTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGACTAT
42560229 TTTGCCCTTATGTGGT
66 TTTGCCCTTATGTGGT
* * *
42560245 AAAATGGA-TGTTTTGCCCTTTTGTGGTAAAATGACTATTTTGCCCTTATGTGGTAAAATGACTA
1 AAAAT-GATTGTTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGACTA
42560309 TTTTGCCCTTATGTGGT
65 TTTTGCCCTTATGTGGT
*
42560326 AAAATGATTGTTTTGCCCTTATATGGTAAGATGACTATTTTGCCCTTATGTGAT
1 AAAATGATTGTTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGTGAT
42560380 GTGTGTATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 2 0.02
81 117 0.98
82 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (81 bp):
AAAATGATTGTTTTGCCCTTATATGGTAAAATGACTATTTTGCCCTTATGTGATAAAATGACTAT
TTTGCCCTTATGTGGT
Found at i:42560655 original size:23 final size:24
Alignment explanation
Indices: 42560629--42560673 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
42560619 ATATCCCCAC
*
42560629 ATGGAGTGTAG-GGTTAGATGGAG
1 ATGGAGTGTAGAGGCTAGATGGAG
42560652 ATGGAGTGTAGAGGCTAGATGG
1 ATGGAGTGTAGAGGCTAGATGG
42560674 GTAGGACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.47, T:0.24
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTAGATGGAG
Found at i:42560730 original size:18 final size:18
Alignment explanation
Indices: 42560686--42560734 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
42560676 AGGACTTGTA
42560686 TATTGTTACTGCACTGAT
1 TATTGTTACTGCACTGAT
* *
42560704 TACTATTACTGCACTG-T
1 TATTGTTACTGCACTGAT
42560721 CTATTGTTACTGCA
1 -TATTGTTACTGCA
42560735 ATGGGCCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.43
Consensus pattern (18 bp):
TATTGTTACTGCACTGAT
Found at i:42564112 original size:30 final size:30
Alignment explanation
Indices: 42564076--42564136 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
42564066 ATTTGTGTTC
42564076 ATCTTTCTTGCTATCAACTAAAATTGAGAA
1 ATCTTTCTTGCTATCAACTAAAATTGAGAA
42564106 ATCTTTCTTGCTATCAACTAAAATTGAGAA
1 ATCTTTCTTGCTATCAACTAAAATTGAGAA
42564136 A
1 A
42564137 GAAAAAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (30 bp):
ATCTTTCTTGCTATCAACTAAAATTGAGAA
Found at i:42565031 original size:43 final size:43
Alignment explanation
Indices: 42564936--42565036 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
42564926 TCGAGATGTG
* * * * *
42564936 ATTACTTGTAAGACCATGTCTGGGACATTGGCGTTATATTATG
1 ATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAATA
*
42564979 ATTACGTGTAAGACCATGTCTGGGACATTGACATTGT-TAATCA
1 ATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAAT-A
**
42565022 ATTTTGTGTAAGACC
1 ATTACGTGTAAGACC
42565037 CTGTTTCGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.06
43 46 0.94
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (43 bp):
ATTACGTGTAAGACCATGTCTGGGACATTGACATTATATAATA
Found at i:42567487 original size:46 final size:48
Alignment explanation
Indices: 42567369--42567497 Score: 142
Period size: 46 Copynumber: 2.8 Consensus size: 48
42567359 AACTTGAGTT
* * *
42567369 CCGAGCTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCA
1 CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAAC-AGGCA
* * *
42567415 TCCGAACTCGTTGAGTTGAGTTTGAGTTCACTTATGGATGCAA-ATGC-
1 -CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAACAGGCA
*
42567462 CCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
42567498 GCGGGTTACA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
46 33 0.47
47 26 0.37
48 5 0.07
50 6 0.09
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (48 bp):
CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCAACAGGCA
Found at i:42571711 original size:43 final size:41
Alignment explanation
Indices: 42571621--42571712 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
42571611 TGTGGTTACC
* * * ** *
42571621 TGTAAGACCATGTTTGGGACATTGGCATCGTATTTGATTCA
1 TGTAAGACCATGTCTGGAACAGTGGCATCGTATGAGATGCA
*
42571662 TGTAAGACCCTGTCTGGAACAGTGGCATCGATATGAGATAGCA
1 TGTAAGACCATGTCTGGAACAGTGGCATCG-TATGAGAT-GCA
42571705 TGTAAGAC
1 TGTAAGAC
42571713 GACATTTGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 26 0.62
42 6 0.14
43 10 0.24
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGAACAGTGGCATCGTATGAGATGCA
Found at i:42574295 original size:11 final size:11
Alignment explanation
Indices: 42574279--42574311 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
42574269 GCCCACATCG
42574279 CAATAATATCA
1 CAATAATATCA
42574290 CAATAATATCA
1 CAATAATATCA
42574301 CAATAATATCA
1 CAATAATATCA
42574312 TACATGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (11 bp):
CAATAATATCA
Found at i:42574817 original size:27 final size:27
Alignment explanation
Indices: 42574768--42574845 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
42574758 AGGGCAAAAC
* * **
42574768 AGTCATTTTACCCTATAGGGGTATGTT
1 AGTCATTTTACACTACAAAGGTATGTT
*
42574795 AGTCATTTTACACTACAAAGGTATTTT
1 AGTCATTTTACACTACAAAGGTATGTT
*
42574822 AGTAATTTTACACTACAAAGGTAT
1 AGTCATTTTACACTACAAAGGTAT
42574846 TTCGATAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (27 bp):
AGTCATTTTACACTACAAAGGTATGTT
Found at i:42574846 original size:27 final size:27
Alignment explanation
Indices: 42574787--42574860 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
42574777 ACCCTATAGG
* *
42574787 GGTATGTTAGTCATTTTACACTACAAA
1 GGTATTTTAGTAATTTTACACTACAAA
42574814 GGTATTTTAGTAATTTTACACTACAAA
1 GGTATTTTAGTAATTTTACACTACAAA
*
42574841 GGTA-TTTCGATAATTTTACA
1 GGTATTTTAG-TAATTTTACA
42574861 AATCAGGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41
Consensus pattern (27 bp):
GGTATTTTAGTAATTTTACACTACAAA
Found at i:42574875 original size:27 final size:26
Alignment explanation
Indices: 42574845--42575266 Score: 219
Period size: 27 Copynumber: 15.7 Consensus size: 26
42574835 TACAAAGGTA
42574845 TTTCGATAATTTTACAAATCAGGGAT
1 TTTCGATAATTTTACAAATCAGGGAT
*
42574871 GTTTCGGTAATTTTACAAATCAAGGGTAT
1 -TTTCGATAATTTTACAAATC-AGGG-AT
42574900 TTT--ACTAATTTTACAAATCGAGGG-T
1 TTTCGA-TAATTTTACAAATC-AGGGAT
42574925 GTTTCGATAATTTTACAAATCAAGGG-T
1 -TTTCGATAATTTTACAAATC-AGGGAT
* * * *
42574952 GTTTTGGTAATTTTACAAATAGAGGGTGT
1 -TTTCGATAATTTTACAAAT-CAGGG-AT
*
42574981 TTTAGA-AATTTTACAAATCAAGGG-T
1 TTTCGATAATTTTACAAATC-AGGGAT
* *
42575006 ATTTCAATAATTTTAC-AAT-AGAGGGT
1 -TTTCGATAATTTTACAAATCAG-GGAT
*
42575032 ATTTCGATAATTTTACAAATTAAGGG-T
1 -TTTCGATAATTTTACAAA-TCAGGGAT
*
42575059 ATTTCAATAATTTTACAAATCGAGGGTAT
1 -TTTCGATAATTTTACAAATC-AGGG-AT
* ** * ** *
42575088 TTTAG-TAATTTTGTAGATTGGGGGT
1 TTTCGATAATTTTACAAATCAGGGAT
* *
42575113 ATTTCGGTAATTTTACAAAGTAAGGGTAT
1 -TTTCGATAATTTTACAAA-TCAGGG-AT
* * *
42575142 TTTAG-TAACTTTACAAATTGAGGG-T
1 TTTCGATAATTTTACAAA-TCAGGGAT
42575167 GTTTCGATAATTTTACAAATCGAGGGTAT
1 -TTTCGATAATTTTACAAATC-AGGG-AT
* *
42575196 TTT-GGTAATTTTA-GAATC-GAGGAT
1 TTTCGATAATTTTACAAATCAG-GGAT
* *
42575220 ATTTCGGTAATATTACAAATCAAGGGTAT
1 -TTTCGATAATTTTACAAATC-AGGG-AT
* *
42575249 TTTAG-TAATTTTGCAAAT
1 TTTCGATAATTTTACAAAT
42575267 TGATAGTATT
Statistics
Matches: 315, Mismatches: 44, Indels: 72
0.73 0.10 0.17
Matches are distributed among these distances:
24 5 0.02
25 11 0.03
26 52 0.17
27 201 0.64
28 35 0.11
29 11 0.03
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (26 bp):
TTTCGATAATTTTACAAATCAGGGAT
Found at i:42574881 original size:54 final size:54
Alignment explanation
Indices: 42574823--42575266 Score: 312
Period size: 54 Copynumber: 8.3 Consensus size: 54
42574813 AGGTATTTTA
* * * *
42574823 GTAATTTTAC-ACTACAAAGGTATTTCGATAATTTTACAAATCAGGGATGTTTCG
1 GTAATTTTACAAAT-CAAGGGTATTTCAATAATTTTACAAATCAGGGGTGTTTCG
* *
42574877 GTAATTTTACAAATCAAGGGTATTTTACTAATTTTACAAATC-GAGGGTGTTTCG
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAG-GGGTGTTTCG
* * *** **
42574931 ATAATTTTACAAATCAAGGGTGTTTTGGTAATTTTACAAAT-AGAGGGTGTTTTA
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAG-GGGTGTTTCG
* *
42574985 GAAATTTTACAAATCAAGGGTATTTCAATAATTTTAC-AAT-AGAGGGTATTTCG
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAG-GGGTGTTTCG
* * * **
42575038 ATAATTTTACAAATTAAGGGTATTTCAATAATTTTACAAATC-GAGGGTATTTTA
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAG-GGGTGTTTCG
** * *** ** * * **
42575092 GTAATTTTGTAGATTGGGGGTATTTCGGTAATTTTACAAAGT-AAGGGTATTTTA
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAA-TCAGGGGTGTTTCG
* ** * * * *
42575146 GTAACTTTACAAATTGAGGGTGTTTCGATAATTTTACAAATC-GAGGGTATTTTG
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAG-GGGTGTTTCG
* * * ** * * * **
42575200 GTAATTTTA-GAATCGAGGATATTTCGGTAATATTACAAATCAAGGGTATTTTA
1 GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAGGGGTGTTTCG
*
42575253 GTAATTTTGCAAAT
1 GTAATTTTACAAAT
42575267 TGATAGTATT
Statistics
Matches: 324, Mismatches: 55, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
53 92 0.28
54 229 0.71
55 3 0.01
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (54 bp):
GTAATTTTACAAATCAAGGGTATTTCAATAATTTTACAAATCAGGGGTGTTTCG
Found at i:42574909 original size:81 final size:80
Alignment explanation
Indices: 42574814--42575250 Score: 429
Period size: 81 Copynumber: 5.4 Consensus size: 80
42574804 ACACTACAAA
* * * *
42574814 GGTATTTTAGTAATTTTAC-ACTACAAAGGTATTTCGATAATTTTACAAATCAGGGATGTTTCGG
1 GGTATTTTAGTAATTTTACAAAT-CGAGGGTATTTCGATAATTTTACAAATCAGGGATATTTCGG
42574878 TAATTTTACAAATCAAG
65 TAATTTTACAAAT-AAG
* * * *
42574895 GGTATTTTACTAATTTTACAAATCGAGGGTGTTTCGATAATTTTACAAATCAAGGG-TGTTTTGG
1 GGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATC-AGGGATATTTCGG
42574959 TAATTTTACAAATAGAG
65 TAATTTTACAAATA-AG
* * * * * *
42574976 GGTGTTTTAGAAATTTTACAAATCAAGGGTATTTCAATAATTTTAC-AAT-AGAGGGTATTTCGA
1 GGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCAG-GGATATTTCGG
42575039 TAATTTTACAAATTAAG
65 TAATTTTACAAA-TAAG
* * * ** * ** *
42575056 GGTATTTCAATAATTTTACAAATCGAGGGTATTT-TAGTAATTTTGTAGATTGGGGGTATTTCGG
1 GGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGA-TAATTTTACAAATCAGGGATATTTCGG
42575120 TAATTTTACAAAGTAAG
65 TAATTTTACAAA-TAAG
* * * *
42575137 GGTATTTTAGTAACTTTACAAATTGAGGGTGTTTCGATAATTTTACAAATCGAGGG-TATTTTGG
1 GGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATC-AGGGATATTTCGG
* *
42575201 TAATTTTA-GAATCGAG
65 TAATTTTACAAAT-AAG
* ** * *
42575217 GATATTTCGGTAATATTACAAATCAAGGGTATTT
1 GGTATTTTAGTAATTTTACAAATCGAGGGTATTT
42575251 TAGTAATTTT
Statistics
Matches: 295, Mismatches: 49, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
78 2 0.01
79 4 0.01
80 89 0.30
81 189 0.64
82 11 0.04
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (80 bp):
GGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCAGGGATATTTCGGT
AATTTTACAAATAAG
Found at i:42575958 original size:6 final size:6
Alignment explanation
Indices: 42575937--42576039 Score: 77
Period size: 6 Copynumber: 16.8 Consensus size: 6
42575927 TATTAGAACT
* * *
42575937 AGAATC AAAATG AGAATC AGAATC AGAATC AGAATC AGAATT AGGTGAA--
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC A---GAATC
* * * *
42575986 AGAATT AGAATC AGAATC AGTATC AGTATC AGGTAA-C AGAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC
42576035 AGAAT
1 AGAAT
42576040 GTGAATGCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.04
5 2 0.03
6 66 0.84
7 4 0.05
8 1 0.01
9 3 0.04
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:42575990 original size:37 final size:37
Alignment explanation
Indices: 42575949--42576039 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
42575939 AATCAAAATG
*
42575949 AGAATCAGAATCAGAATCAGAATCAGAATTAGGTGAA-
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGT-AAC
* * *
42575986 AGAATTAGAATCAGAATCAGTATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGAATCAGAATCAGGTAAC
*
42576023 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
42576040 GTGAATGCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.04
37 45 0.96
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (37 bp):
AGAATCAGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:42576206 original size:27 final size:26
Alignment explanation
Indices: 42576158--42576217 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42576148 GCGAGGCTGC
*
42576158 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
42576185 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
42576211 CAGATAT
1 CAGATAT
42576218 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42576304 original size:27 final size:26
Alignment explanation
Indices: 42576256--42576307 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42576246 GCGAGGCTGC
*
42576256 CAGATATTGTGACGAAGTCACCAGAG
1 CAGATATTGTGACGAAGCCACCAGAG
* *
42576282 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
42576308 ATGCAATGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.33, C:0.21, G:0.29, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAG
Found at i:42576737 original size:27 final size:27
Alignment explanation
Indices: 42576542--42576723 Score: 247
Period size: 27 Copynumber: 6.7 Consensus size: 27
42576532 TTAACACCTT
*
42576542 AAGGGTAAAATGGTAATTCTGTAAATC
1 AAGGGTAAAATGGTAATTTTGTAAATC
42576569 AAGGGTAAAATGGTAATTTTGTAAATC
1 AAGGGTAAAATGGTAATTTTGTAAATC
* *
42576596 AAGGGTAAAACGGTAATTTTGTAAATT
1 AAGGGTAAAATGGTAATTTTGTAAATC
* * *
42576623 AAGGGTAAAATGGTAATTCTATCAATC
1 AAGGGTAAAATGGTAATTTTGTAAATC
* *
42576650 AAGGGTAAAACGGTAATTTTGTAAAAC
1 AAGGGTAAAATGGTAATTTTGTAAATC
* *
42576677 AAGGGTAAAATAGTAATTCTGTAAATC
1 AAGGGTAAAATGGTAATTTTGTAAATC
* * *
42576704 GATGGTAAAATAGTAATTTT
1 AAGGGTAAAATGGTAATTTT
42576724 ATAATTTGAG
Statistics
Matches: 135, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 135 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (27 bp):
AAGGGTAAAATGGTAATTTTGTAAATC
Found at i:42576788 original size:54 final size:54
Alignment explanation
Indices: 42576730--42576862 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 54
42576720 TTTTATAATT
* ** * * *
42576730 TGAGGGTACTTTGATAATTTTACATGTTAAGGGTATTTCAATAATTTTGCAAAC
1 TGAGGGTACTTTGGTAATTTTACAAATCAAGGATATTTCAATAATTTTACAAAC
* *** *
42576784 TGAGGGTA-TTTCGGTAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAAC
1 TGAGGGTACTTT-GGTAATTTTACAAATCAAGGATATTTCAATAATTTTACAAAC
*
42576838 CGAGGGTACTTTGGTAATTTTACAA
1 TGAGGGTACTTTGGTAATTTTACAA
42576863 CTGGGGGTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
53 3 0.05
54 59 0.91
55 3 0.05
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
TGAGGGTACTTTGGTAATTTTACAAATCAAGGATATTTCAATAATTTTACAAAC
Found at i:42576789 original size:27 final size:27
Alignment explanation
Indices: 42576759--42576883 Score: 130
Period size: 27 Copynumber: 4.7 Consensus size: 27
42576749 TTACATGTTA
** *
42576759 AGGGTATTTCAATAATTTTGCAAACTG
1 AGGGTATTTCGGTAATTTTACAAACTG
42576786 AGGGTATTTCGGTAATTTTACAAA-TCG
1 AGGGTATTTCGGTAATTTTACAAACT-G
* * * *
42576813 AGGATATTTGGGTAATTTTATAAACCG
1 AGGGTATTTCGGTAATTTTACAAACTG
42576840 AGGGTACTTT-GGTAATTTTAC-AACTG
1 AGGGTA-TTTCGGTAATTTTACAAACTG
* *
42576866 GGGGTATTTCAGTAATTT
1 AGGGTATTTCGGTAATTT
42576884 GGTAAACTGA
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
25 3 0.04
26 17 0.21
27 59 0.72
28 3 0.04
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAACTG
Found at i:42579012 original size:14 final size:15
Alignment explanation
Indices: 42578993--42579022 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42578983 TTACAAACCC
42578993 ATACTCA-AGGCCCA
1 ATACTCATAGGCCCA
42579007 ATACTCATAGGCCCA
1 ATACTCATAGGCCCA
42579022 A
1 A
42579023 ATTCTGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (15 bp):
ATACTCATAGGCCCA
Found at i:42581045 original size:134 final size:133
Alignment explanation
Indices: 42580788--42581236 Score: 485
Period size: 134 Copynumber: 3.4 Consensus size: 133
42580778 TTACACTACA
* *
42580788 AAGGTATTTCGATGATTTTACAAATT--GGGTATGTTTCGGTAATTTTACAAATCAAAGGTATTT
1 AAGGTATTTCGATAATTTTACAAATTGAGGGTA--TTTCGGTAATTTTAC-AATCGAAGGTATTT
* * * * *
42580851 CGGTAATTTTACAAATAAATGGTATTTTAGTAATTTTACAAATCGATGGTGTTTCGGTAATTCTA
63 CGGTAATTTTACAAATAAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGGTAATT-TA
42580916 CAAATCG
127 CAAATCG
* * * *
42580923 AAGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAATCGATGGTATTTCGG
1 AAGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAATCGAAGGTATTTCGG
* * * **
42580988 TAATTTTAAAAATTAAGGGTATTTCAATAATTTTACAAACCGAGGGTATTTTAGTAATTTTACAA
66 TAATTTTACAAATAAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGGTAA-TTTACAA
42581053 ATC-
130 ATCG
* * * * * * * *
42581056 AGGGGTATTTCGGTAATTTTACAAATTAAGGGTATTTTGGTAATTTTAAAAATTGAGGGT-GTTC
1 A-AGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTT-ACAATCGAAGGTATTTC
* * * *
42581120 GGTAATTTTACGAATCAAGGGTATTTCAATAATTTTA-GAATCGAGGATATTTCGGTAATATTAC
64 GGTAATTTTACAAATAAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGGTAAT-TTAC
*
42581184 AAATTG
128 AAATCG
* * * * *
42581190 ATGGTATTTCAATAATTTTGCAAATTGACGGTATTTCGATAATTTTA
1 AAGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTA
42581237 GAAACCGGGG
Statistics
Matches: 265, Mismatches: 42, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
132 2 0.01
133 62 0.23
134 148 0.56
135 48 0.18
137 5 0.02
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (133 bp):
AAGGTATTTCGATAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAATCGAAGGTATTTCGG
TAATTTTACAAATAAAGGGTATTTCAATAATTTTACAAATCGAGGGTATTTCGGTAATTTACAAA
TCG
Found at i:42581155 original size:27 final size:27
Alignment explanation
Indices: 42580764--42581261 Score: 407
Period size: 27 Copynumber: 18.6 Consensus size: 27
42580754 CACTATGAGA
* * * *
42580764 GTATTTTGGTAATTTTAC-ACTACAAAG
1 GTATTTCGGTAATTTTACAAAT-CGAGG
* * *
42580791 GTATTTCGATGATTTTACAAAT--TGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
42580816 GTATGTTTCGGTAATTTTACAAATCAAAG
1 GTA--TTTCGGTAATTTTACAAATCGAGG
** *
42580845 GTATTTCGGTAATTTTACAAATAAATG
1 GTATTTCGGTAATTTTACAAATCGAGG
** *
42580872 GTATTTTAGTAATTTTACAAATCGATG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * *
42580899 GTGTTTCGGTAATTCTACAAATCGAAG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
42580926 GTATTTTGGTAATTTTACAAATTGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
42580953 GTATTTCAGTAATTTTAC-AATCGATG
1 GTATTTCGGTAATTTTACAAATCGAGG
* **
42580979 GTATTTCGGTAATTTTAAAAATTAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
** *
42581006 GTATTTCAATAATTTTACAAACCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
**
42581033 GTATTTTAGTAATTTTACAAATC-AGGG
1 GTATTTCGGTAATTTTACAAATCGA-GG
**
42581060 GTATTTCGGTAATTTTACAAATTAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * *
42581087 GTATTTTGGTAATTTTAAAAATTGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * *
42581114 GT-GTTCGGTAATTTTACGAATCAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
** *
42581140 GTATTTCAATAATTTTA-GAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * * *
42581166 ATATTTCGGTAATATTACAAATTGATG
1 GTATTTCGGTAATTTTACAAATCGAGG
** * * *
42581193 GTATTTCAATAATTTTGCAAATTGACG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * * *
42581220 GTATTTCGATAATTTTAGAAACCGGGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
42581247 GTGTTTCGATAATTT
1 GTATTTCGGTAATTT
42581262 CTCTTTATTA
Statistics
Matches: 380, Mismatches: 81, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
25 4 0.01
26 64 0.17
27 305 0.80
28 3 0.01
29 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACAAATCGAGG
Found at i:42581611 original size:28 final size:28
Alignment explanation
Indices: 42581578--42581634 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
42581568 TGGCCCTTTT
* * *
42581578 AGGCCCAATCTCGTTCGTATAGCCCATC
1 AGGCCCAATCACATTCATATAGCCCATC
42581606 AGGCCCAATCACATTCATATAGCCCATC
1 AGGCCCAATCACATTCATATAGCCCATC
42581634 A
1 A
42581635 AACCCAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATAGCCCATC
Found at i:42581640 original size:28 final size:28
Alignment explanation
Indices: 42581581--42581641 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
42581571 CCCTTTTAGG
* * * **
42581581 CCCAATCTCGTTCGTATAGCCCATCAGG
1 CCCAATCACATTCATATAGCCCATCAAA
42581609 CCCAATCACATTCATATAGCCCATCAAA
1 CCCAATCACATTCATATAGCCCATCAAA
42581637 CCCAA
1 CCCAA
42581642 CTACTTCCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.31, C:0.38, G:0.10, T:0.21
Consensus pattern (28 bp):
CCCAATCACATTCATATAGCCCATCAAA
Found at i:42584573 original size:47 final size:47
Alignment explanation
Indices: 42584504--42584666 Score: 208
Period size: 47 Copynumber: 3.5 Consensus size: 47
42584494 GCCCATAAGT
42584504 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
* * * * ***
42584551 GAACTCGGACTCAACTCAACGAGTTCTGACATTCGC-A--TCCATAAGT-
1 GAACTCGGACTCAACTCAACGAGCTC-G-GATGC-CTAGTTACATCTCTC
42584597 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
1 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
42584644 GAACTCGGACTCAACTCAACGAG
1 GAACTCGGACTCAACTCAACGAG
42584667 TTCTGACATT
Statistics
Matches: 95, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 30 0.32
47 53 0.56
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42584618 original size:46 final size:46
Alignment explanation
Indices: 42584551--42584714 Score: 190
Period size: 46 Copynumber: 3.5 Consensus size: 46
42584541 TACATCTCTC
42584551 GAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGT
* * * * ***
42584597 GAACTCGGACTCAACTCAACGAGCTC-G-GATGC-CTAGTTACATCTCT
1 GAACTCGGACTCAACTCAACGAGTTCTGACATTCGC-A--TCCATAAGT
42584643 CGAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGT
1 -GAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGT
* *
42584690 GAACTCGGACTCATCTCAACAAGTT
1 GAACTCGGACTCAACTCAACGAGTT
42584715 TGGATGCCCA
Statistics
Matches: 95, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 1 0.01
46 53 0.56
47 30 0.32
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCTGACATTCGCATCCATAAGT
Found at i:42584722 original size:93 final size:93
Alignment explanation
Indices: 42584496--42584709 Score: 419
Period size: 93 Copynumber: 2.3 Consensus size: 93
42584486 TGTAACCCGC
42584496 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGGAC
42584561 TCAACTCAACGAGTTCTGACATTCGCAT
66 TCAACTCAACGAGTTCTGACATTCGCAT
42584589 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGGAC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGGAC
42584654 TCAACTCAACGAGTTCTGACATTCGCAT
66 TCAACTCAACGAGTTCTGACATTCGCAT
*
42584682 CCATAAGTGAACTCGGACTCATCTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
42584710 AAGTTTGGAT
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 120 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (93 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCTCGAACTCGGAC
TCAACTCAACGAGTTCTGACATTCGCAT
Found at i:42590962 original size:134 final size:131
Alignment explanation
Indices: 42590739--42591176 Score: 407
Period size: 134 Copynumber: 3.3 Consensus size: 131
42590729 TATTTCGATG
* * * * *
42590739 ATTTTACAAATCG-GGGATGTTTCGGTAATTTTACAAATCAAAGGTATTTTGGTAATTTTACAAA
1 ATTTTACAAATTGAGGG-TATTTCGATAATTTTAC-AATCGAAGGTATTTCGGTAATTTTACAAA
* * * *
42590803 TCAAGGGTATTTTAGTAATTTTACAAATCGATGGTGTTTCGGTAATTCTACAAATCGAAGGTGTT
64 TCAAGGGTATTTCAATAATTTTACAAATCGA-GGTATTTTGGTAATT-TACAAAT-GAAGGTGTT
42590868 TTGGTA
126 TTGGTA
* * * *
42590874 ATTTTACAAATTGAGGGTATTTCAATAATTTTACAATCGATGGTATTTCGGTAATTTTAAAAATT
1 ATTTTACAAATTGAGGGTATTTCGATAATTTTACAATCGAAGGTATTTCGGTAATTTTACAAATC
* * * * *
42590939 AAGGGTATTTCAATAATTTTACAAACCGAGGGAATTTTAGTAATTTTACAAAT-TAGGGGTATTT
66 AAGGGTATTTCAATAATTTTACAAATCGA-GGTATTTTGGTAA-TTTACAAATGAAGGTGT-TTT
42591003 CGGTA
128 -GGTA
* * * * * * * *
42591008 ATTTTATAAATTAAGGGTATTTTGGTAATTTTAAAAATTGAGGGT-GTTCGGTAATTTTACAAAT
1 ATTTTACAAATTGAGGGTATTTCGATAATTTT-ACAATCGAAGGTATTTCGGTAATTTTACAAAT
* * * * *
42591072 CGAGGGTATTTCAATAATTTTA-GAATCGAGGATATTTTGGTAATATTACAATTTGAGGGTATTT
65 CAAGGGTATTTCAATAATTTTACAAATCGAGG-TATTTTGGTAAT-TTACAA-ATGAAGGTGTTT
**
42591136 CAGTA
127 TGGTA
* * *
42591141 ATTTTGCAAATCGATGGTATTTCGATAATTTTACAA
1 ATTTTACAAATTGAGGGTATTTCGATAATTTTACAA
42591177 ACCGGGGGTG
Statistics
Matches: 244, Mismatches: 50, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
132 11 0.05
133 51 0.21
134 139 0.57
135 40 0.16
136 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (131 bp):
ATTTTACAAATTGAGGGTATTTCGATAATTTTACAATCGAAGGTATTTCGGTAATTTTACAAATC
AAGGGTATTTCAATAATTTTACAAATCGAGGTATTTTGGTAATTTACAAATGAAGGTGTTTTGGT
A
Found at i:42591190 original size:27 final size:27
Alignment explanation
Indices: 42590672--42591198 Score: 438
Period size: 27 Copynumber: 19.6 Consensus size: 27
42590662 ACAGTTATTG
* * *
42590672 GGGTATGTCGGTCATTTTAC-ACTACGA
1 GGGTATTTCGGTAATTTTACAAAT-CGA
* * *
42590699 GGGTATTTTGGTAATTTTAC-ACTACAA
1 GGGTATTTCGGTAATTTTACAAAT-CGA
* * *
42590726 AGGTATTTCGATGATTTTACAAATCG-
1 GGGTATTTCGGTAATTTTACAAATCGA
* *
42590752 GGGATGTTTCGGTAATTTTACAAATCAA
1 GGG-TATTTCGGTAATTTTACAAATCGA
* * *
42590780 AGGTATTTTGGTAATTTTACAAATCAA
1 GGGTATTTCGGTAATTTTACAAATCGA
**
42590807 GGGTATTTTAGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * *
42590834 TGGTGTTTCGGTAATTCTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * * *
42590861 AGGTGTTTTGGTAATTTTACAAATTGA
1 GGGTATTTCGGTAATTTTACAAATCGA
**
42590888 GGGTATTTCAATAATTTTAC-AATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * **
42590914 TGGTATTTCGGTAATTTTAAAAATTAA
1 GGGTATTTCGGTAATTTTACAAATCGA
** *
42590941 GGGTATTTCAATAATTTTACAAACCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* ** *
42590968 GGGAATTTTAGTAATTTTACAAAT-TA
1 GGGTATTTCGGTAATTTTACAAATCGA
* **
42590994 GGGGTATTTCGGTAATTTTATAAATTAA
1 -GGGTATTTCGGTAATTTTACAAATCGA
* * *
42591022 GGGTATTTTGGTAATTTTAAAAATTGA
1 GGGTATTTCGGTAATTTTACAAATCGA
*
42591049 GGGT-GTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
** *
42591075 GGGTATTTCAATAATTTTA-GAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * * * *
42591101 GGATATTTTGGTAATATTACAATTTGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* *
42591128 GGGTATTTCAGTAATTTTGCAAATCGA
1 GGGTATTTCGGTAATTTTACAAATCGA
* * * *
42591155 TGGTATTTCGATAATTTTACAAACCGG
1 GGGTATTTCGGTAATTTTACAAATCGA
* *
42591182 GGGTGTTTCGATAATTT
1 GGGTATTTCGGTAATTT
42591199 CTCTCTATTA
Statistics
Matches: 399, Mismatches: 93, Indels: 16
0.79 0.18 0.03
Matches are distributed among these distances:
26 66 0.17
27 328 0.82
28 5 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAATCGA
Found at i:42591551 original size:28 final size:28
Alignment explanation
Indices: 42591515--42591578 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
42591505 TGGCCCTTTT
* *
42591515 AGGCCCAATCTCGTTCATAT-AGCCCATC
1 AGGCCCAATCACATTCATATGA-CCCATC
*
42591543 AGGCCCAATCACATTCATATGACCCATT
1 AGGCCCAATCACATTCATATGACCCATC
42591571 AGGCCCAA
1 AGGCCCAA
42591579 CTACTTCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGACCCATC
Found at i:42593724 original size:56 final size:56
Alignment explanation
Indices: 42593633--42593766 Score: 178
Period size: 56 Copynumber: 2.4 Consensus size: 56
42593623 CATGGCATCA
* * *
42593633 ATATATGTGTGCGAGTAAGATCACATTTTAAACGTTGGCATCAATACGTGATTTCG
1 ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCCG
* * * * * *
42593689 ATATATGTGTACGAGTAAGGCCACGTTTTATACGTTTGCATCGATATGTGATTCCG
1 ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCCG
*
42593745 ATATATATGTACGAGTAAGACC
1 ATATATGTGTACGAGTAAGACC
42593767 CTATCTGGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 67 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (56 bp):
ATATATGTGTACGAGTAAGACCACATTTTAAACGTTGGCATCAATACGTGATTCCG
Found at i:42597414 original size:14 final size:14
Alignment explanation
Indices: 42597395--42597423 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42597385 TCGGCTAAAT
42597395 GCTTTGAAAATTTG
1 GCTTTGAAAATTTG
42597409 GCTTTGAAAATTTG
1 GCTTTGAAAATTTG
42597423 G
1 G
42597424 AGGCATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (14 bp):
GCTTTGAAAATTTG
Found at i:42602354 original size:12 final size:12
Alignment explanation
Indices: 42602318--42602354 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
42602308 ACAGATCATT
42602318 TTGTACAAAATA
1 TTGTACAAAATA
**
42602330 CCGTACAAAATA
1 TTGTACAAAATA
42602342 TTGTACAAAATA
1 TTGTACAAAATA
42602354 T
1 T
42602355 GAGATCGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (12 bp):
TTGTACAAAATA
Found at i:42609658 original size:34 final size:34
Alignment explanation
Indices: 42609615--42609684 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
42609605 GAGAGCAAGT
42609615 AACTTGGGAGTTTTTCCAAACTGAGTTTCGGAAA
1 AACTTGGGAGTTTTTCCAAACTGAGTTTCGGAAA
42609649 AACTTGGGAGTTTTTCCAAACTGAGTTTCGGAAA
1 AACTTGGGAGTTTTTCCAAACTGAGTTTCGGAAA
42609683 AA
1 AA
42609685 GTATATCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (34 bp):
AACTTGGGAGTTTTTCCAAACTGAGTTTCGGAAA
Found at i:42620218 original size:505 final size:505
Alignment explanation
Indices: 42619268--42620277 Score: 2020
Period size: 505 Copynumber: 2.0 Consensus size: 505
42619258 TAAGGTAATG
42619268 ATTATTGGAAGTGGTTTCTAAGGGTATGTACTATTAAAAAATTATTATGGGACAAGATATTTATG
1 ATTATTGGAAGTGGTTTCTAAGGGTATGTACTATTAAAAAATTATTATGGGACAAGATATTTATG
42619333 AAATGTTTAGAAGGATTCCTTAGTTAGATAAGGAAGATGGAGTATGACAAGAGTAGGATAACTAG
66 AAATGTTTAGAAGGATTCCTTAGTTAGATAAGGAAGATGGAGTATGACAAGAGTAGGATAACTAG
42619398 TGTTTAAGAGTATGGTAAACTATGGTGGTATCCACCAAAATAAATGAGGCAGAACTAATTGGCAC
131 TGTTTAAGAGTATGGTAAACTATGGTGGTATCCACCAAAATAAATGAGGCAGAACTAATTGGCAC
42619463 CCAGTGGTTCACACTAGATTCCAAAGTATCTAATAAGGTATTATTATAATGAGACCATTAAGTAC
196 CCAGTGGTTCACACTAGATTCCAAAGTATCTAATAAGGTATTATTATAATGAGACCATTAAGTAC
42619528 TCCTGTACTTATAAGTTTTGTTATTTCTTTTAGGTAACTGTGAGGAGACTGTGTCTAGAGGGACG
261 TCCTGTACTTATAAGTTTTGTTATTTCTTTTAGGTAACTGTGAGGAGACTGTGTCTAGAGGGACG
42619593 ATGCCAAAAGCATGCCAAGTTGGTGACAGGGTGGTCTATTATGCATATAGTAGAGTTGTAGAGTA
326 ATGCCAAAAGCATGCCAAGTTGGTGACAGGGTGGTCTATTATGCATATAGTAGAGTTGTAGAGTA
42619658 GTCTGGGAATACACCCTTAGAATATGTCTTAAATGAACTTCCACCTTTTAGGGATATGTATCAAA
391 GTCTGGGAATACACCCTTAGAATATGTCTTAAATGAACTTCCACCTTTTAGGGATATGTATCAAA
42619723 AATGATGTAATCAAGTATATTTTAAATACTTCACTTGTTTTCTGTAAAGA
456 AATGATGTAATCAAGTATATTTTAAATACTTCACTTGTTTTCTGTAAAGA
42619773 ATTATTGGAAGTGGTTTCTAAGGGTATGTACTATTAAAAAATTATTATGGGACAAGATATTTATG
1 ATTATTGGAAGTGGTTTCTAAGGGTATGTACTATTAAAAAATTATTATGGGACAAGATATTTATG
42619838 AAATGTTTAGAAGGATTCCTTAGTTAGATAAGGAAGATGGAGTATGACAAGAGTAGGATAACTAG
66 AAATGTTTAGAAGGATTCCTTAGTTAGATAAGGAAGATGGAGTATGACAAGAGTAGGATAACTAG
42619903 TGTTTAAGAGTATGGTAAACTATGGTGGTATCCACCAAAATAAATGAGGCAGAACTAATTGGCAC
131 TGTTTAAGAGTATGGTAAACTATGGTGGTATCCACCAAAATAAATGAGGCAGAACTAATTGGCAC
42619968 CCAGTGGTTCACACTAGATTCCAAAGTATCTAATAAGGTATTATTATAATGAGACCATTAAGTAC
196 CCAGTGGTTCACACTAGATTCCAAAGTATCTAATAAGGTATTATTATAATGAGACCATTAAGTAC
42620033 TCCTGTACTTATAAGTTTTGTTATTTCTTTTAGGTAACTGTGAGGAGACTGTGTCTAGAGGGACG
261 TCCTGTACTTATAAGTTTTGTTATTTCTTTTAGGTAACTGTGAGGAGACTGTGTCTAGAGGGACG
42620098 ATGCCAAAAGCATGCCAAGTTGGTGACAGGGTGGTCTATTATGCATATAGTAGAGTTGTAGAGTA
326 ATGCCAAAAGCATGCCAAGTTGGTGACAGGGTGGTCTATTATGCATATAGTAGAGTTGTAGAGTA
42620163 GTCTGGGAATACACCCTTAGAATATGTCTTAAATGAACTTCCACCTTTTAGGGATATGTATCAAA
391 GTCTGGGAATACACCCTTAGAATATGTCTTAAATGAACTTCCACCTTTTAGGGATATGTATCAAA
42620228 AATGATGTAATCAAGTATATTTTAAATACTTCACTTGTTTTCTGTAAAGA
456 AATGATGTAATCAAGTATATTTTAAATACTTCACTTGTTTTCTGTAAAGA
42620278 GTATTTAAAT
Statistics
Matches: 505, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
505 505 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.33
Consensus pattern (505 bp):
ATTATTGGAAGTGGTTTCTAAGGGTATGTACTATTAAAAAATTATTATGGGACAAGATATTTATG
AAATGTTTAGAAGGATTCCTTAGTTAGATAAGGAAGATGGAGTATGACAAGAGTAGGATAACTAG
TGTTTAAGAGTATGGTAAACTATGGTGGTATCCACCAAAATAAATGAGGCAGAACTAATTGGCAC
CCAGTGGTTCACACTAGATTCCAAAGTATCTAATAAGGTATTATTATAATGAGACCATTAAGTAC
TCCTGTACTTATAAGTTTTGTTATTTCTTTTAGGTAACTGTGAGGAGACTGTGTCTAGAGGGACG
ATGCCAAAAGCATGCCAAGTTGGTGACAGGGTGGTCTATTATGCATATAGTAGAGTTGTAGAGTA
GTCTGGGAATACACCCTTAGAATATGTCTTAAATGAACTTCCACCTTTTAGGGATATGTATCAAA
AATGATGTAATCAAGTATATTTTAAATACTTCACTTGTTTTCTGTAAAGA
Found at i:42621773 original size:226 final size:226
Alignment explanation
Indices: 42621379--42621836 Score: 916
Period size: 226 Copynumber: 2.0 Consensus size: 226
42621369 AACAAAGAAA
42621379 ATTATGTTGGAAAATATGGACATCACATATATAATAAGGGTAATTACATGTTATGATTTACTATC
1 ATTATGTTGGAAAATATGGACATCACATATATAATAAGGGTAATTACATGTTATGATTTACTATC
42621444 ATGATACTTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAAATGTTATTGGGCTTTAATTATT
66 ATGATACTTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAAATGTTATTGGGCTTTAATTATT
42621509 AAATAAAGTATGGGTCAAATATGTGTAGATACTCTAGTAATTGAGTTCTAATCAAATTCTAATTA
131 AAATAAAGTATGGGTCAAATATGTGTAGATACTCTAGTAATTGAGTTCTAATCAAATTCTAATTA
42621574 ATGATAGGCTAATTAGAATTTGAGTAGAACT
196 ATGATAGGCTAATTAGAATTTGAGTAGAACT
42621605 ATTATGTTGGAAAATATGGACATCACATATATAATAAGGGTAATTACATGTTATGATTTACTATC
1 ATTATGTTGGAAAATATGGACATCACATATATAATAAGGGTAATTACATGTTATGATTTACTATC
42621670 ATGATACTTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAAATGTTATTGGGCTTTAATTATT
66 ATGATACTTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAAATGTTATTGGGCTTTAATTATT
42621735 AAATAAAGTATGGGTCAAATATGTGTAGATACTCTAGTAATTGAGTTCTAATCAAATTCTAATTA
131 AAATAAAGTATGGGTCAAATATGTGTAGATACTCTAGTAATTGAGTTCTAATCAAATTCTAATTA
42621800 ATGATAGGCTAATTAGAATTTGAGTAGAACT
196 ATGATAGGCTAATTAGAATTTGAGTAGAACT
42621831 ATTATG
1 ATTATG
42621837 CCAATGTTAT
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 232 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (226 bp):
ATTATGTTGGAAAATATGGACATCACATATATAATAAGGGTAATTACATGTTATGATTTACTATC
ATGATACTTTAGCCCAAATTAAAAGTGATCTAATTTGGTTAAAATGTTATTGGGCTTTAATTATT
AAATAAAGTATGGGTCAAATATGTGTAGATACTCTAGTAATTGAGTTCTAATCAAATTCTAATTA
ATGATAGGCTAATTAGAATTTGAGTAGAACT
Found at i:42633651 original size:93 final size:93
Alignment explanation
Indices: 42633539--42633710 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42633529 CGCCCATAAG
* *
42633539 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42633604 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
42633632 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42633697 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42633711 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42633707 original size:46 final size:46
Alignment explanation
Indices: 42633532--42633707 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42633522 TGTAACCCGC
* * *
42633532 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42633578 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
42633628 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42633671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42633708 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42641227 original size:93 final size:93
Alignment explanation
Indices: 42641115--42641286 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42641105 CGCCCATAAG
* *
42641115 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42641180 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
42641208 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42641273 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42641287 TCAATCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42641283 original size:46 final size:46
Alignment explanation
Indices: 42641108--42641283 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42641098 TGTAACCCGC
* * *
42641108 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42641154 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
42641204 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42641247 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42641284 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42648361 original size:24 final size:24
Alignment explanation
Indices: 42648329--42648377 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42648319 GAAGCGGCAT
42648329 CGGAAGAGGGTCATCTCCATTGGC
1 CGGAAGAGGGTCATCTCCATTGGC
42648353 CGGAAGAGGGTCATCTCCATTGGC
1 CGGAAGAGGGTCATCTCCATTGGC
42648377 C
1 C
42648378 CCTATGTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.33, T:0.20
Consensus pattern (24 bp):
CGGAAGAGGGTCATCTCCATTGGC
Found at i:42663098 original size:34 final size:34
Alignment explanation
Indices: 42663052--42663120 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
42663042 GCACAGTTAA
* *
42663052 AACAGTCTTGGGCCCAAGCCCTTTTCAGTATCAGT
1 AACAGTCTTGGGCCCAAGCCCATCTCAGTA-CAGT
*
42663087 AACAGT-TTGGGCCCTAGCCCATCTCAGTACAGT
1 AACAGTCTTGGGCCCAAGCCCATCTCAGTACAGT
42663120 A
1 A
42663121 TCGAATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 5 0.16
34 20 0.65
35 6 0.19
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (34 bp):
AACAGTCTTGGGCCCAAGCCCATCTCAGTACAGT
Found at i:42667219 original size:41 final size:41
Alignment explanation
Indices: 42667158--42667280 Score: 201
Period size: 41 Copynumber: 3.0 Consensus size: 41
42667148 TAAAAGCTAC
* * *
42667158 CGGTGGATCCACGGTCGTCAAGCAGCCATGCGATCCTTAAT
1 CGGTGGATCCACGGTTGTCAAGCAACCATGCGATCCTCAAT
*
42667199 CGGTGGATCCACGGTTGTCAAGCAACCATACGATCCTCAAT
1 CGGTGGATCCACGGTTGTCAAGCAACCATGCGATCCTCAAT
*
42667240 CGGTAGATCCACGGTTGTCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTTGTCAAGCAACCATGCGATCCTCAAT
42667281 TTCTTCCTCT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (41 bp):
CGGTGGATCCACGGTTGTCAAGCAACCATGCGATCCTCAAT
Found at i:42667569 original size:27 final size:27
Alignment explanation
Indices: 42667537--42667833 Score: 227
Period size: 27 Copynumber: 11.0 Consensus size: 27
42667527 TTGATAAATC
* *
42667537 TACAAACCAATGGTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* * * **
42667564 TGCAAACCAATGGTATTTATGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
** **
42667591 TTGAAAGTCAAGGGTATTTTTGTAATTT
1 TACAAA-TCAAGGGTATTTCGGTAATTT
* *
42667619 TCCAAATCAAGGGTATTTCGATAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* **
42667646 TCCAAATCAAGGGTATTTCTATAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* * *
42667673 TACAAGTCTAGGTTATTTCGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* * *
42667700 TACAAGTCTAGGGTATTTCGATAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
** * * *
42667727 TACAGGTCGAGGGTATTTGGGAAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* * *
42667754 CACAAATCATGGGTATTTTGGTAATTT
1 TACAAATCAAGGGTATTTCGGTAATTT
* * *
42667781 TACAAA-CTAGAGGTATTTTGTTAATTT
1 TACAAATCAAG-GGTATTTCGGTAATTT
** * * *
42667808 TGTAAACCAATGGTATTTCAGTAATT
1 TACAAATCAAGGGTATTTCGGTAATT
42667834 CTACCCTACA
Statistics
Matches: 222, Mismatches: 45, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
26 2 0.01
27 196 0.88
28 24 0.11
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (27 bp):
TACAAATCAAGGGTATTTCGGTAATTT
Found at i:42667899 original size:21 final size:21
Alignment explanation
Indices: 42667866--42667906 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42667856 CATGGGTCGG
* *
42667866 GCCGCGCTGGGTTCGGGCCGA
1 GCCGCGCTAGGTTCAGGCCGA
*
42667887 GCCGGGCTAGGTTCAGGCCG
1 GCCGCGCTAGGTTCAGGCCG
42667907 GGCCCAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.32, G:0.46, T:0.15
Consensus pattern (21 bp):
GCCGCGCTAGGTTCAGGCCGA
Found at i:42670383 original size:48 final size:48
Alignment explanation
Indices: 42670319--42670424 Score: 158
Period size: 48 Copynumber: 2.2 Consensus size: 48
42670309 CAAGATAAAT
* * * *
42670319 ATATATATGTGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
42670367 ATATGTATATGTGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
42670415 ATGTGTATAT
1 ATATGTATAT
42670425 ATTGTGGCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:42670608 original size:37 final size:37
Alignment explanation
Indices: 42670558--42670629 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
42670548 GAAATATATT
*
42670558 CCGGGTAAGACCCGATGGCTACGTGTGGAGATTATGC
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
*
42670595 CCGGGTAAGACCCGATGACTACGTGTGGGGATTAT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTAT
42670630 TCAGGCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGC
Done.