Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 129 of 284
Found at i:43159097 original size:21 final size:21
Alignment explanation
Indices: 43159073--43159112 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
43159063 TATATTTTAT
43159073 AGCATA-AGTAATAAAATAAAG
1 AGCATAGA-TAATAAAATAAAG
43159094 AGCATAGATAATAAAATAA
1 AGCATAGATAATAAAATAA
43159113 TAGTGGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (21 bp):
AGCATAGATAATAAAATAAAG
Found at i:43161055 original size:40 final size:40
Alignment explanation
Indices: 43161000--43161141 Score: 189
Period size: 40 Copynumber: 3.6 Consensus size: 40
43160990 TGTTCAAATG
* *
43161000 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
43161040 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
43161080 ATATCCGGGCTAAGACCCGACGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
43161120 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
43161142 TACTTGGGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
39 13 0.15
40 74 0.83
41 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:43165749 original size:46 final size:46
Alignment explanation
Indices: 43165697--43166607 Score: 1655
Period size: 46 Copynumber: 19.8 Consensus size: 46
43165687 ATTTGGGCAT
* * * *
43165697 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGTATGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *** * * * *
43165743 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC
43165788 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43165836 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43165882 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43165928 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43165974 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166020 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166066 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166112 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166158 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166204 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166250 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166296 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166342 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166388 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166434 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166480 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
43166526 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
43166572 CCAAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43166608 GCGGGTTACA
Statistics
Matches: 843, Mismatches: 17, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
45 2 0.00
46 804 0.95
47 34 0.04
48 3 0.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:43169401 original size:15 final size:15
Alignment explanation
Indices: 43169353--43169436 Score: 82
Period size: 15 Copynumber: 5.7 Consensus size: 15
43169343 TATCGTACCT
*
43169353 TGGGTTTCTTTATCC
1 TGGGTTTCTTTATTC
* *
43169368 TGGATCTCTTTATTC
1 TGGGTTTCTTTATTC
43169383 TGGGTTTCTTTATTC
1 TGGGTTTCTTTATTC
*
43169398 TGGGTTTCTCTA-TC
1 TGGGTTTCTTTATTC
* *
43169412 TTGGATTTTTTTATTC
1 -TGGGTTTCTTTATTC
*
43169428 -GGTTTTCTT
1 TGGGTTTCTT
43169437 ATTATCTTTG
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.80
16 2 0.04
ACGTcount: A:0.08, C:0.15, G:0.18, T:0.58
Consensus pattern (15 bp):
TGGGTTTCTTTATTC
Found at i:43171123 original size:38 final size:38
Alignment explanation
Indices: 43171072--43171146 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
43171062 GCTAGCAATA
*
43171072 ATTCAACCTAGGGTTCATATTTGGAAAAATACCCATAG
1 ATTCAACCTAGGGTTCATATTTAGAAAAATACCCATAG
43171110 ATTCAACCTAGGGTTCATATTTAGAAAAATACCCATA
1 ATTCAACCTAGGGTTCATATTTAGAAAAATACCCATA
43171147 CGTGAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (38 bp):
ATTCAACCTAGGGTTCATATTTAGAAAAATACCCATAG
Found at i:43171920 original size:46 final size:46
Alignment explanation
Indices: 43171867--43172078 Score: 379
Period size: 46 Copynumber: 4.6 Consensus size: 46
43171857 ATCCGAACTT
* * *
43171867 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
43171913 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
43171959 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
*
43172005 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCAAGCTC
1 GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
*
43172051 GTTGAGTTGAGTCTGAGTTCACTTATGG
1 GTTGAGTTGAGTCCGAGTTCACTTATGG
43172079 GCGGGTTACA
Statistics
Matches: 161, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 161 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
GTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTC
Found at i:43181480 original size:47 final size:47
Alignment explanation
Indices: 43181429--43181670 Score: 340
Period size: 47 Copynumber: 5.1 Consensus size: 47
43181419 TTAGGATTTT
*
43181429 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
** * *
43181476 ATGTGATGAATGTGAACCTCTATATATATGCGTGATAAAGCCGAATGGCCA
1 ATGTGATGAATGTGAA---C-ATGCATATGTGTGATAAGGCCGAATGGCCA
*
43181527 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
43181574 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
43181621 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
43181668 ATG
1 ATG
43181671 CGAAATGTGT
Statistics
Matches: 174, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
47 131 0.75
48 1 0.01
50 1 0.01
51 41 0.24
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:43181539 original size:98 final size:94
Alignment explanation
Indices: 43181429--43181670 Score: 360
Period size: 98 Copynumber: 2.5 Consensus size: 94
43181419 TTAGGATTTT
*
43181429 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
43181494 T-CTATATATATGCGTGATAAAGCCGAATGGCCA
66 TGC---ATATAT--GAGATAAAGCCGAATGGCCA
43181527 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
*
43181592 TGCATATATGAGATAAGGCCGAATGGCCA
66 TGCATATATGAGATAAAGCCGAATGGCCA
** * * *
43181621 ATGTGATGAATGTGAACATGTATATATGTGGTAAGGCCGAATGGCTAATG
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATG
43181671 CGAAATGTGT
Statistics
Matches: 135, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
94 63 0.47
96 6 0.04
98 65 0.48
99 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (94 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
TGCATATATGAGATAAAGCCGAATGGCCA
Found at i:43181780 original size:46 final size:46
Alignment explanation
Indices: 43181644--43181780 Score: 193
Period size: 46 Copynumber: 3.0 Consensus size: 46
43181634 GAACATGTAT
* *
43181644 ATATGTGGTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * *
43181690 ATATGAGGTAAAGCTGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * *
43181736 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
43181781 TGTATATATA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.34, C:0.08, G:0.31, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:43191895 original size:44 final size:44
Alignment explanation
Indices: 43191834--43191919 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
43191824 CATGTGCGAG
* *
43191834 GCATCCGAGCTCATTGAGTTGGTCCGAGTTTATTATGGATGCAA
1 GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATGGATGCAA
* * *
43191878 GCATCTGAGCTCGTTGAGTTGGTCTAAGTTCATTATGGATGC
1 GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATGGATGC
43191920 GATACATGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (44 bp):
GCATCCGAGCTCATTGAGTTGGTCCAAGTTCATTATGGATGCAA
Found at i:43208479 original size:47 final size:47
Alignment explanation
Indices: 43208408--43208575 Score: 246
Period size: 47 Copynumber: 3.6 Consensus size: 47
43208398 CCCTTCGGGA
* * * * * * *
43208408 CTTATCACATTTATACACTTTCACATCCACCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43208455 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
43208502 CTTATCACATATATACACTTTCACATTCATCACATCGGTGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43208549 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
43208576 TATTCAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 110 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43210908 original size:39 final size:40
Alignment explanation
Indices: 43210865--43211029 Score: 133
Period size: 40 Copynumber: 4.2 Consensus size: 40
43210855 CTCGTTCAAG
* * * *
43210865 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
43210904 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
43210944 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * * *
43210984 GGCCTTCGGGACTTGACCCGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
43211024 TGCCTT
1 TGCCTT
43211030 TTGATCTTAG
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 26 0.24
40 77 0.72
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:43210954 original size:40 final size:39
Alignment explanation
Indices: 43210902--43211029 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 39
43210892 TAACTCATAC
* *
43210902 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
43210942 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
* *
43210982 AAGGCCTTCGGGACTTGACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
43211022 AATGCCTT
1 AATGCCTT
43211030 TTGATCTTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:43211045 original size:80 final size:79
Alignment explanation
Indices: 43210865--43211085 Score: 202
Period size: 80 Copynumber: 2.8 Consensus size: 79
43210855 CTCGTTCAAG
* * * * * * * *
43210865 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCA-TACAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTT-ACCCGGATAT
*
43210929 TAAAACTCGCACGAA
65 TAAAACTCGCACAAA
*
43210944 TGCCTTCGGGACTTAACCCGGA-ATTAGT-A-TCTCGCACAAAGGCCTTCGGGACTTGACCCGGA
1 TGCCTTCGGGACTTAACCCGGATA-TAGTCACT-TAGCACAAA-GCCTTCGGGACTT-ACCCGGA
43211006 -ATTAATAACTCGCACAAA
62 TATTAA-AACTCGCACAAA
** **
43211024 TGCCTT-TTGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTA-CCCGGA
43211086 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 34 0.29
80 69 0.59
81 10 0.09
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (79 bp):
TGCCTTCGGGACTTAACCCGGATATAGTCACTTAGCACAAAGCCTTCGGGACTTACCCGGATATT
AAAACTCGCACAAA
Found at i:43218276 original size:39 final size:40
Alignment explanation
Indices: 43218231--43218415 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
43218221 GCTCCTCGTT
* * *
43218231 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
43218271 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
43218310 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
43218350 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
43218391 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
43218416 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:43218331 original size:40 final size:39
Alignment explanation
Indices: 43218198--43218415 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
43218188 AAATCACGTA
* * **
43218198 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
43218237 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
43218276 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
43218316 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
43218356 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
43218396 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
43218416 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:43221765 original size:40 final size:40
Alignment explanation
Indices: 43221666--43221987 Score: 371
Period size: 40 Copynumber: 8.1 Consensus size: 40
43221656 ACTATTTGAT
* * * *
43221666 TCAGGGTTACCAAAGTATAAATAGGGGCTCGTATGTGCAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
* ** * *
43221706 TCA-AGGTACTGAAGTACAAACAGGGGCACATTTGTGCAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
* ** *
43221745 TTAGGGGTACCAAAGTACAAACAGGGGCATATATGTACAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
* *
43221785 TCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTACAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
* *
43221825 TC-GGGGTTATCAAAGTACAAATAGGGGCACGTATGTGCAA
1 TCAGGGG-TACCAAAGTACAAACAGGGGCACGTATGTGCAA
* * * *
43221865 TTATGGGTATCGAAA-TACAAACAGGGGCACATATGTGCAA
1 TCAGGGGTA-CCAAAGTACAAACAGGGGCACGTATGTGCAA
*
43221905 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
* * * *
43221945 TCAGGGGCACCGAAGTACAAATAGGGGAACGTATGTGCAA
1 TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
43221985 TCA
1 TCA
43221988 TACAATAATT
Statistics
Matches: 239, Mismatches: 38, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
39 37 0.15
40 196 0.82
41 6 0.03
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (40 bp):
TCAGGGGTACCAAAGTACAAACAGGGGCACGTATGTGCAA
Found at i:43221770 original size:20 final size:20
Alignment explanation
Indices: 43221747--43221931 Score: 72
Period size: 20 Copynumber: 9.2 Consensus size: 20
43221737 TTGTGCAATT
43221747 AGGGGTACCAAAGTACAAAC
1 AGGGGTACCAAAGTACAAAC
* * * *
43221767 AGGGGCA-TATATGTACAATC
1 AGGGGTACCA-AAGTACAAAC
*
43221787 AGGGGTACCGAAGTACAAAC
1 AGGGGTACCAAAGTACAAAC
* ** * *
43221807 AGGGGCACGTATGTACAATC
1 AGGGGTACCAAAGTACAAAC
* *
43221827 -GGGGTTATCAAAGTACAAAT
1 AGGGG-TACCAAAGTACAAAC
* ** * * **
43221847 AGGGGCACGTATGTGCAATT
1 AGGGGTACCAAAGTACAAAC
* *
43221867 ATGGGTATCGAAA-TACAAAC
1 AGGGGTA-CCAAAGTACAAAC
* * * *
43221887 AGGGGCA-CATATGTGCAATC
1 AGGGGTACCA-AAGTACAAAC
*
43221907 AGGGGTACCAAAGTACAAAT
1 AGGGGTACCAAAGTACAAAC
43221927 AGGGG
1 AGGGG
43221932 CACGTATGTG
Statistics
Matches: 111, Mismatches: 46, Indels: 16
0.64 0.27 0.09
Matches are distributed among these distances:
18 1 0.01
19 6 0.05
20 95 0.86
21 9 0.08
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (20 bp):
AGGGGTACCAAAGTACAAAC
Found at i:43221950 original size:20 final size:20
Alignment explanation
Indices: 43221886--43221987 Score: 75
Period size: 20 Copynumber: 5.1 Consensus size: 20
43221876 GAAATACAAA
*
43221886 CAGGGGCACATATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* ** * *
43221906 CAGGGGTACCAAAGTACAAAT
1 CAGGGGCACGTATGTGC-AAT
43221927 -AGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* *
43221946 CAGGGGCACCG-AAGTACAAAT
1 CAGGGGCA-CGTATGTGC-AAT
*
43221967 -AGGGGAACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
43221986 CA
1 CA
43221988 TACAATAATT
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
19 8 0.13
20 45 0.74
21 8 0.13
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:43221987 original size:80 final size:80
Alignment explanation
Indices: 43221666--43221987 Score: 423
Period size: 80 Copynumber: 4.0 Consensus size: 80
43221656 ACTATTTGAT
* * * * *
43221666 TCAGGGTTACCAAAGTATAAATAGGGGCTCGTATGTGCAATCA-AGGTACTGAAGTACAAACAGG
1 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGG
*
43221730 GGCACATTTGTGCAA
66 GGCACATATGTGCAA
* * ** *
43221745 TTAGGGGTACCAAAGTACAAACAGGGGCATATATGTACAATCAGGGGTACCGAAGTACAAACAGG
1 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGG
* *
43221810 GGCACGTATGTACAA
66 GGCACATATGTGCAA
* * * * *
43221825 TC-GGGGTTATCAAAGTACAAATAGGGGCACGTATGTGCAATTATGGGTATCGAAATACAAACAG
1 TCAGGGG-TACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAG
43221889 GGGCACATATGTGCAA
65 GGGCACATATGTGCAA
* *
43221905 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGCACCGAAGTACAAATAGG
1 TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGG
* *
43221970 GGAACGTATGTGCAA
66 GGCACATATGTGCAA
43221985 TCA
1 TCA
43221988 TACAATAATT
Statistics
Matches: 206, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
79 39 0.19
80 163 0.79
81 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (80 bp):
TCAGGGGTACCAAAGTACAAATAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTACAAACAGG
GGCACATATGTGCAA
Found at i:43223477 original size:54 final size:54
Alignment explanation
Indices: 43223395--43223502 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
43223385 TGAATTTTCT
*
43223395 CAAGTTTAGGAGGTAAAGCTAATCTGTAAGCTACAAGACTGATTCTTTTAGTAA
1 CAAGTTTAGGAGGTAAAGCTAATCTGTAAGCTACAAAACTGATTCTTTTAGTAA
*
43223449 CAAGTTTAGGAGGTAAAGTTAATCTGTAAGCTACAAAACTGATTCTTTTAGTAA
1 CAAGTTTAGGAGGTAAAGCTAATCTGTAAGCTACAAAACTGATTCTTTTAGTAA
43223503 TCTCGTACGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (54 bp):
CAAGTTTAGGAGGTAAAGCTAATCTGTAAGCTACAAAACTGATTCTTTTAGTAA
Found at i:43225438 original size:23 final size:23
Alignment explanation
Indices: 43225403--43225457 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
43225393 CGCAAAGTTT
* *
43225403 GCATGACCACTCTTAAATGCTCA
1 GCATGATCTCTCTTAAATGCTCA
43225426 GCATGATCTCTCTTAAATGCTCA
1 GCATGATCTCTCTTAAATGCTCA
43225449 GCATGATCT
1 GCATGATCT
43225458 GACTGATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (23 bp):
GCATGATCTCTCTTAAATGCTCA
Found at i:43228385 original size:40 final size:40
Alignment explanation
Indices: 43228327--43228478 Score: 243
Period size: 40 Copynumber: 3.8 Consensus size: 40
43228317 CGGATGATAA
*
43228327 CCGGGCTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
43228367 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
43228407 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AAT
* *
43228447 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
43228479 AGCTATATCC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 102 0.98
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:43236392 original size:40 final size:40
Alignment explanation
Indices: 43236333--43236448 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
43236323 TATTCGGATG
43236333 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
* *
43236373 A-AATCCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT
1 ATAA-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
* *
43236413 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
43236449 AGATATATCC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
39 2 0.03
40 65 0.94
41 2 0.03
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
Found at i:43240835 original size:27 final size:27
Alignment explanation
Indices: 43240804--43240981 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
43240794 TAAATTGTAC
43240804 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43240831 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43240857 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43240885 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
43240913 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43240940 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43240967 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43240982 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43240918 original size:82 final size:81
Alignment explanation
Indices: 43240805--43240960 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
43240795 AAATTGTACA
*
43240805 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
43240869 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43240886 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
43240951 TGCGAGTTGA
65 TGCGAATTGA
43240961 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43240972 original size:82 final size:81
Alignment explanation
Indices: 43240801--43240981 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
43240791 GATTAAATTG
*
43240801 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
43240866 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43240882 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
43240946 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43240964 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43240982 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43241524 original size:169 final size:169
Alignment explanation
Indices: 43241234--43241576 Score: 627
Period size: 169 Copynumber: 2.0 Consensus size: 169
43241224 ATTTATGAAA
*
43241234 ATGCTTCAATGTCCTATTGATGAGTATATGGAATGTGAATGCATGAATTGATATGAAATTGAATT
1 ATGCTTCAATGTCCTATTGATGAGTATATGGAATGTGAATGCATGAATTGATATGAAATTGAATC
43241299 GATAGGTTGGAGGAACTATGGTATGGTTCGGAATGGATGGAGTAATTAGCCTCGTTCCATTTTGT
66 GATAGGTTGGAGGAACTATGGTATGGTTCGGAATGGATGGAGTAATTAGCCTCGTTCCATTTTGT
*
43241364 TTTCTCTTGTGATAATGTTATTGATGGATGGTAGTGCAT
131 TTCCTCTTGTGATAATGTTATTGATGGATGGTAGTGCAT
43241403 ATGCTTCAATGTCCTATTGATGAGTATATGGAATGTGAATGCATGAATTGATATGAAATTGAATC
1 ATGCTTCAATGTCCTATTGATGAGTATATGGAATGTGAATGCATGAATTGATATGAAATTGAATC
* *
43241468 GATAGGTTGGAGGAACTATGGTATGGTTCGGTATGGATGGAGTAAATT-GTCTCGTTCCATTTTG
66 GATAGGTTGGAGGAACTATGGTATGGTTCGGAATGGATGGAGT-AATTAGCCTCGTTCCATTTTG
43241532 TTTCCTCTTGTGATAATGTTATTGATGGATGGTAGTGCAT
130 TTTCCTCTTGTGATAATGTTATTGATGGATGGTAGTGCAT
43241572 -TGCTT
1 ATGCTT
43241577 ATGACTTACT
Statistics
Matches: 169, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
168 5 0.03
169 160 0.95
170 4 0.02
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.38
Consensus pattern (169 bp):
ATGCTTCAATGTCCTATTGATGAGTATATGGAATGTGAATGCATGAATTGATATGAAATTGAATC
GATAGGTTGGAGGAACTATGGTATGGTTCGGAATGGATGGAGTAATTAGCCTCGTTCCATTTTGT
TTCCTCTTGTGATAATGTTATTGATGGATGGTAGTGCAT
Found at i:43249059 original size:27 final size:27
Alignment explanation
Indices: 43249028--43249205 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
43249018 TAAATTGTAC
43249028 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
43249055 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43249081 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
43249109 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
43249137 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
43249164 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
43249191 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
43249206 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:43249142 original size:82 final size:81
Alignment explanation
Indices: 43249029--43249184 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
43249019 AAATTGTACA
*
43249029 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
43249093 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
43249110 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
43249175 TGCGAGTTGA
65 TGCGAATTGA
43249185 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:43249196 original size:82 final size:81
Alignment explanation
Indices: 43249025--43249205 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
43249015 GATTAAATTG
*
43249025 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
43249090 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
43249106 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
43249170 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
43249188 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
43249206 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:43250601 original size:37 final size:37
Alignment explanation
Indices: 43250559--43250629 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
43250549 TGTTACACAA
43250559 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
43250596 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
43250630 ATATATTTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:43250827 original size:48 final size:48
Alignment explanation
Indices: 43250769--43251721 Score: 1807
Period size: 48 Copynumber: 19.9 Consensus size: 48
43250759 ATATACACAC
* * *
43250769 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43250817 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43250865 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43250913 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43250961 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43251009 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
*
43251057 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251105 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251153 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251201 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251249 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251297 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251345 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251393 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251441 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251489 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251537 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251585 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
43251633 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
* *
43251681 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACA
1 ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACA
43251722 CACATATATA
Statistics
Matches: 900, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 900 1.00
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCGTTCGGCTTTACCACATATACAT
Found at i:43254130 original size:49 final size:48
Alignment explanation
Indices: 43254058--43254271 Score: 208
Period size: 46 Copynumber: 4.5 Consensus size: 48
43254048 AGTTGTCGAA
* * * *
43254058 GCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTTCGATGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTATCATATTCG-TGCTGAT
* *
43254107 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACGTGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTATC--ATATTCGTGCTGAT
*
43254157 G-CATGTCCCAGACAT-GTCTTACACTAGC-ACTCATAAT-GTGGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATATTCGT-GCTGAT
* * * ***
43254203 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGT-CTCAACACTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTATCATATTC-GTGCTGAT
43254249 GCCATGTCCCAGACATGGTCTTA
1 GCCATGTCCCAGACATGGTCTTA
43254272 GACTGGCGTA
Statistics
Matches: 141, Mismatches: 15, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
45 3 0.02
46 46 0.33
47 14 0.10
48 21 0.15
49 45 0.32
50 7 0.05
51 5 0.04
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTATCATATTCGTGCTGAT
Found at i:43254248 original size:46 final size:47
Alignment explanation
Indices: 43254058--43254271 Score: 202
Period size: 49 Copynumber: 4.5 Consensus size: 47
43254048 AGTTGTCGAA
* * * * * * * *
43254058 GCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTTCGATGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-AT-AACGCTGAT
43254107 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATATACGTGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATA-AC--GCTGAT
* * ***
43254157 G-CATGTCCCAGACAT-GTCTTACACTAGCACTCATAATGTGGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGT-ATAACGCTGAT
* *
43254203 G-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAACACTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTAT-AACGCTGAT
43254249 GCCATGTCCCAGACATGGTCTTA
1 GCCATGTCCCAGACATGGTCTTA
43254272 GACTGGCGTA
Statistics
Matches: 138, Mismatches: 20, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
45 1 0.01
46 44 0.32
47 14 0.10
48 25 0.18
49 48 0.35
50 6 0.04
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTATAACGCTGAT
Found at i:43257847 original size:90 final size:89
Alignment explanation
Indices: 43257699--43257929 Score: 214
Period size: 90 Copynumber: 2.6 Consensus size: 89
43257689 TCTGGGACAT
* ** * * * *
43257699 GGCATTGGCATCGATATGAGATCTAGTGTAAGACCATAT-TAGGGATATGGCTTTGACATCAATA
1 GGCA-TGGCATCGATATGAGGTCCCGTGTAAGACCATGTCT-GGGACATGGCGTCGACATCAATA
* * *
43257763 AGTGA-TTTCGTATAAGACCATGTCTTG
64 AGAGACTTT-GTATAAGACCATAT-TAG
* * **
43257790 GGCATGGCATCGATATGAGGTCCCGTATAAGACCATGTCTGGGACATGGCGTCGACATCGATTCG
1 GGCATGGCATCGATATGAGGTCCCGTGTAAGACCATGTCTGGGACATGGCGTCGACATCAATAAG
43257855 AGACTTTGTATAAGACCATATTAG
66 AGACTTTGTATAAGACCATATTAG
* * * * * * *
43257879 GGATATGGAATCGATGTGTGGTTCCATGTAAGACCATGTCTTGGACATGGC
1 GG-CATGGCATCGATATGAGGTCCCGTGTAAGACCATGTCTGGGACATGGC
43257930 TTTGGCACCC
Statistics
Matches: 115, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
89 4 0.03
90 103 0.90
91 8 0.07
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (89 bp):
GGCATGGCATCGATATGAGGTCCCGTGTAAGACCATGTCTGGGACATGGCGTCGACATCAATAAG
AGACTTTGTATAAGACCATATTAG
Found at i:43281414 original size:24 final size:25
Alignment explanation
Indices: 43281367--43281422 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
43281357 AACACTTCGA
* *
43281367 TGCAATTTTGTGAAAGGCATTTTGG
1 TGCAACTTTGTGAAAGGCACTTTGG
*
43281392 TGCAACTTTGTG-ATGGCACTTTGG
1 TGCAACTTTGTGAAAGGCACTTTGG
43281416 TGCAACT
1 TGCAACT
43281423 CTATTAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.38
Consensus pattern (25 bp):
TGCAACTTTGTGAAAGGCACTTTGG
Found at i:43282809 original size:17 final size:17
Alignment explanation
Indices: 43282789--43282839 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
43282779 TGGTTTAATG
* *
43282789 ATTTTTATTGTTTGTTT
1 ATTTTTATTATTTATTT
*
43282806 ATTTTTCTTATTTATTT
1 ATTTTTATTATTTATTT
**
43282823 ATTTTCGTTATTTATTT
1 ATTTTTATTATTTATTT
43282840 TTATCTCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.75
Consensus pattern (17 bp):
ATTTTTATTATTTATTT
Found at i:43288166 original size:46 final size:46
Alignment explanation
Indices: 43288099--43288273 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
43288089 TGTAACCCGC
* * * *
43288099 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43288145 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43288191 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
43288237 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43288274 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43293360 original size:35 final size:35
Alignment explanation
Indices: 43293314--43293383 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
43293304 AATCTCGAGT
43293314 TCCCTACACTGGCTGCAGAAGTATTCTGAGATTTA
1 TCCCTACACTGGCTGCAGAAGTATTCTGAGATTTA
43293349 TCCCTACACTGGCTGCAGAAGTATTCTGAGATTTA
1 TCCCTACACTGGCTGCAGAAGTATTCTGAGATTTA
43293384 GGACCCACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (35 bp):
TCCCTACACTGGCTGCAGAAGTATTCTGAGATTTA
Found at i:43302608 original size:40 final size:40
Alignment explanation
Indices: 43302547--43302729 Score: 271
Period size: 40 Copynumber: 4.6 Consensus size: 40
43302537 AACCCAAGTA
* * *
43302547 CCTTCGGGATTTA-ACCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
43302586 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
43302626 CCTTCGGGACTTAGTCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
43302666 CCTTTGGGACTTAGCCCGGATATAGTCACTAGCACAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-AAATG
*
43302707 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
43302730 CATCGAATAA
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 11 0.08
40 93 0.71
41 27 0.21
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:43304703 original size:18 final size:18
Alignment explanation
Indices: 43304650--43304704 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
43304640 TAAGTAAACC
*
43304650 AATAATACAAATGATACA
1 AATAATACAAATGATATA
* *
43304668 ATTAATACAAA-CATTATA
1 AATAATACAAATGA-TATA
*
43304686 AATAATATAAATGATATA
1 AATAATACAAATGATATA
43304704 A
1 A
43304705 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (18 bp):
AATAATACAAATGATATA
Found at i:43306129 original size:24 final size:23
Alignment explanation
Indices: 43306085--43306128 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43306075 GGTTTTCATC
*
43306085 TTAATTTATTTTTTTGTTTTTGT
1 TTAATTTATTTTTGTGTTTTTGT
43306108 TTAATTTTATTTTTG-GTTTTT
1 TTAA-TTTATTTTTGTGTTTTT
43306129 TTTTTAGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (23 bp):
TTAATTTATTTTTGTGTTTTTGT
Found at i:43310866 original size:47 final size:47
Alignment explanation
Indices: 43310812--43310907 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
43310802 GTTGAATTTA
*
43310812 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
*
43310859 AAGCTTGTTAAATTTTCCCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
43310906 AA
1 AA
43310908 AGAAAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
Found at i:43311778 original size:45 final size:44
Alignment explanation
Indices: 43311714--43311880 Score: 246
Period size: 45 Copynumber: 3.7 Consensus size: 44
43311704 CGCACAGTAT
43311714 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAC
1 TATTC-GGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAC
* *
43311759 TATTCGAGCCTTTGAGCCTAGCAGGCTGTAATGCCGGTG-GAATAC
1 TATTCG-GCCTTTGAGCCTAGCAGGCTATAATACCGGTGAG-ATAC
*
43311804 TATTCGGCCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGATAC
1 TATTCGG-CCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAC
*
43311849 TATTCGGGCTTTCGAGCCTAGCAGGCTATAAT
1 TATTCGGCCTTT-GAGCCTAGCAGGCTATAAT
43311881 GTCGATGAAA
Statistics
Matches: 111, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
44 7 0.06
45 103 0.93
46 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.28
Consensus pattern (44 bp):
TATTCGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAC
Found at i:43311867 original size:90 final size:90
Alignment explanation
Indices: 43311714--43311881 Score: 284
Period size: 90 Copynumber: 1.9 Consensus size: 90
43311704 CGCACAGTAT
* *
43311714 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATACTATTCGAGCCTTTGAGCCTA
1 TATTCGGCCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGATACTATTCGAGCCTTTGAGCCTA
*
43311779 GCAGGCTGTAATGCCGGTGGAATAC
66 GCAGGCTATAATGCCGGTGGAATAC
*
43311804 TATTCGGCCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGATACTATTCG-GGCTTTCGAGCCT
1 TATTCGGCCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGATACTATTCGAGCCTTT-GAGCCT
43311868 AGCAGGCTATAATG
65 AGCAGGCTATAATG
43311882 TCGATGAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
89 5 0.07
90 68 0.93
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (90 bp):
TATTCGGCCCTTTGAGCCTAGCAGGCTATAATACCAGTGAGATACTATTCGAGCCTTTGAGCCTA
GCAGGCTATAATGCCGGTGGAATAC
Found at i:43318260 original size:47 final size:47
Alignment explanation
Indices: 43318206--43318301 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
43318196 GTTGAATTTA
*
43318206 AAGCTTGTTAAATTTGCTCTTAATATTTCCGGATAAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
* *
43318253 AAGCTTGTTAAATTTGCCCTTAATATTTCTGGATGAGTTACTTAGTT
1 AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
43318300 AA
1 AA
43318302 AGAAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (47 bp):
AAGCTTGTTAAATTTGCCCTTAATATTTCCGGATAAGTTACTTAGTT
Found at i:43319206 original size:45 final size:45
Alignment explanation
Indices: 43319110--43319325 Score: 291
Period size: 45 Copynumber: 4.9 Consensus size: 45
43319100 CGCACAGTAT
* *
43319110 TATTCGGGCTTTTGAGCCTAGCAGGCTA-AATGTCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* *
43319154 TATTCGGGCCTTTGAGCCTAGCATGCTATAATGCCGGTAAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
43319199 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
* * *
43319244 TATTCGGGCTTTTGAGCCTAGCAGGCTATAATGCGGGTGAAATGA-
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGAT-AC
* *
43319289 TA-TCGGG-CTTCGAGCCTAACAGG-TGA-AATGCCGGTGA
1 TATTCGGGCCTTTGAGCCTAGCAGGCT-ATAATGCCGGTGA
43319326 ATGAATTCAG
Statistics
Matches: 156, Mismatches: 13, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
42 11 0.07
43 14 0.09
44 31 0.20
45 99 0.63
46 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAC
Found at i:43320261 original size:14 final size:15
Alignment explanation
Indices: 43320239--43320287 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
43320229 ATTTTGGGAA
43320239 GAATGTTTTTTTAAG
1 GAATGTTTTTTTAAG
*
43320254 GAA---TTTTTCAAG
1 GAATGTTTTTTTAAG
43320266 G-ATGTTTTTTTAAG
1 GAATGTTTTTTTAAG
43320280 GAAT-TTTT
1 GAATGTTTT
43320288 CAAGGGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.04
12 9 0.32
14 13 0.46
15 5 0.18
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.53
Consensus pattern (15 bp):
GAATGTTTTTTTAAG
Found at i:43320266 original size:12 final size:12
Alignment explanation
Indices: 43320245--43320292 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
43320235 GGAAGAATGT
*
43320245 TTTTTTAAGGAA
1 TTTTTCAAGGAA
*
43320257 TTTTTCAAGGATGT
1 TTTTTCAAGGA--A
*
43320271 TTTTTTAAGGAA
1 TTTTTCAAGGAA
43320283 TTTTTCAAGG
1 TTTTTCAAGG
43320293 GTGTTTCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.27, C:0.04, G:0.19, T:0.50
Consensus pattern (12 bp):
TTTTTCAAGGAA
Found at i:43320272 original size:26 final size:26
Alignment explanation
Indices: 43320241--43320298 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
43320231 TTTGGGAAGA
43320241 ATGTTTTTTTAAGGAATTTTTCAAGG
1 ATGTTTTTTTAAGGAATTTTTCAAGG
43320267 ATGTTTTTTTAAGGAATTTTTCAAGG
1 ATGTTTTTTTAAGGAATTTTTCAAGG
*
43320293 GTGTTT
1 ATGTTT
43320299 CCAATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.21, T:0.52
Consensus pattern (26 bp):
ATGTTTTTTTAAGGAATTTTTCAAGG
Found at i:43333923 original size:40 final size:40
Alignment explanation
Indices: 43333863--43334046 Score: 178
Period size: 40 Copynumber: 4.6 Consensus size: 40
43333853 TATTCGAATG
* *
43333863 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATACTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
43333903 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * * *
43333943 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
* *
43333983 ATATCCAGGCTAAG-TCCCGAAGGCATTTATGCAAGTGACCT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGA-CT
* *
43334024 -TATCTGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
43334047 CTTGTGCGAG
Statistics
Matches: 117, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 1 0.01
40 112 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:43333996 original size:80 final size:79
Alignment explanation
Indices: 43333863--43334082 Score: 243
Period size: 80 Copynumber: 2.8 Consensus size: 79
43333853 TATTCGAATG
* * * *
43333863 ATATCCGGGCTAAGTCCCGAAGGCTTTTATACTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGG-CTAAGATCCCGAAGGC
* *
43333927 ATTTGTGCGAGTTG-CT
64 ATTTATGCAAG-TGACT
* *
43333943 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTAGCGATTATATCCAGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCC-GGCTAAGATCCCGAAGGC
43334007 ATTTATGCAAGTGACCT
64 ATTTATGCAAGTGA-CT
* * * *
43334024 -TATCTGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCCGGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGCTAAGATCCCGAAG
43334083 ATACTTGGGT
Statistics
Matches: 120, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
78 14 0.12
79 20 0.17
80 82 0.68
81 4 0.03
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (79 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGCTAAGATCCCGAAGGCAT
TTATGCAAGTGACT
Found at i:43342086 original size:40 final size:40
Alignment explanation
Indices: 43342026--43342209 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 40
43342016 TATTCGAATG
* *
43342026 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * *
43342066 ATATCCGGACTAATATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* * * *
43342106 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* *
43342146 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
43342186 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
43342210 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 118 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:43342166 original size:80 final size:78
Alignment explanation
Indices: 43342026--43342245 Score: 255
Period size: 80 Copynumber: 2.8 Consensus size: 78
43342016 TATTCGAATG
* * * * *
43342026 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAATATCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAT-CCCGAAGGCA
* *
43342091 TTTGTGCGAGTTG-CT
64 TTTATGCGAG-TGACC
* *
43342106 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAA-TCCCGAAGGCA
*
43342171 TTTATGCTAGTGACC
64 TTTATGCGAGTGACC
* * *
43342186 ATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCT-AATCCCGAAG
43342246 ATACTTGGGT
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
78 12 0.10
79 21 0.17
80 87 0.72
81 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (78 bp):
ATATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAATCCCGAAGGCATT
TATGCGAGTGACC
Found at i:43351478 original size:89 final size:89
Alignment explanation
Indices: 43351355--43351536 Score: 337
Period size: 89 Copynumber: 2.0 Consensus size: 89
43351345 GTTCAGGGGC
43351355 AAAATTGTAATTTTTCCAAAGGTTGAGTTAAGGACTATTTTGAATAGTAAATTAATTAAATAAGT
1 AAAATTGTAATTTTTCCAAAGGTTGAGTTAAGGACTATTTTGAATAGTAAATTAATTAAATAAGT
*
43351420 GAAATATGATGTTTTAGATCCCGA
66 AAAATATGATGTTTTAGATCCCGA
* *
43351444 AAAATTGTAATTTTTCCAAAGGTTGAGTTAAGGACTGTTTTGAATAGTAATTTAATTAAATAAGT
1 AAAATTGTAATTTTTCCAAAGGTTGAGTTAAGGACTATTTTGAATAGTAAATTAATTAAATAAGT
43351509 AAAATATGATGTTTTAGATCCCGA
66 AAAATATGATGTTTTAGATCCCGA
43351533 AAAA
1 AAAA
43351537 CGAGATTTGA
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (89 bp):
AAAATTGTAATTTTTCCAAAGGTTGAGTTAAGGACTATTTTGAATAGTAAATTAATTAAATAAGT
AAAATATGATGTTTTAGATCCCGA
Found at i:43352249 original size:68 final size:66
Alignment explanation
Indices: 43352177--43352348 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
43352167 CATCATGTGT
* * * *
43352177 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
43352240 TGTAG
62 TGTAG
** * *
43352245 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
43352310 AG
65 AG
* * * *
43352312 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
43352349 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:43352282 original size:64 final size:64
Alignment explanation
Indices: 43352201--43352384 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
43352191 AGACATTATG
* * *
43352201 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
43352265 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
43352330 AA
63 AA
* * *
43352332 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
43352385 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:43353283 original size:22 final size:21
Alignment explanation
Indices: 43353253--43353300 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
43353243 AATGAAATAA
*
43353253 ATGATATGTGTATATATATAT
1 ATGACATGTGTATATATATAT
43353274 CATGACATGTGTATATATATAT
1 -ATGACATGTGTATATATATAT
43353296 ATGAC
1 ATGAC
43353301 TAGTCTCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (21 bp):
ATGACATGTGTATATATATAT
Found at i:43354603 original size:180 final size:180
Alignment explanation
Indices: 43354295--43354654 Score: 657
Period size: 180 Copynumber: 2.0 Consensus size: 180
43354285 CTACATATGC
*
43354295 TGTTGCATGCTTGACTAAATTAATCAGTAAATGTGATTACTAAAGTTATTCAAAATTCATAAAAT
1 TGTTGCATGCTTGACTAAATTAATCAGTAAATGTGATGACTAAAGTTATTCAAAATTCATAAAAT
43354360 GTATGAGTGAGTGCACTTGTTTGAAATGAGATAATTGGAAATTTTATGTAAGACAGATATGAATA
66 GTATGAGTGAGTGCACTTGTTTGAAATGAGATAATTGGAAATTTTATGTAAGACAGATATGAATA
43354425 ATAAATTGTTTGAAGTGGATAGTATGATTATAATGACATATGTGGATAAT
131 ATAAATTGTTTGAAGTGGATAGTATGATTATAATGACATATGTGGATAAT
* * *
43354475 TGTTGCATGCTTGACTAAATTAATTAGTAAATGTGATGATTAAAGTTATTCAAAATTCATAGAAT
1 TGTTGCATGCTTGACTAAATTAATCAGTAAATGTGATGACTAAAGTTATTCAAAATTCATAAAAT
*
43354540 GTATGAGTGAGTGCACTTGTTTGAAATGAGATAATTGGAAATTTTATGTAAGACAGGTATGAATA
66 GTATGAGTGAGTGCACTTGTTTGAAATGAGATAATTGGAAATTTTATGTAAGACAGATATGAATA
* *
43354605 ATAAATTGTTTGACGTGGATAGTATGATTATACTGACATATGTGGATAAT
131 ATAAATTGTTTGAAGTGGATAGTATGATTATAATGACATATGTGGATAAT
43354655 GAAAAAAATG
Statistics
Matches: 173, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 173 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.36
Consensus pattern (180 bp):
TGTTGCATGCTTGACTAAATTAATCAGTAAATGTGATGACTAAAGTTATTCAAAATTCATAAAAT
GTATGAGTGAGTGCACTTGTTTGAAATGAGATAATTGGAAATTTTATGTAAGACAGATATGAATA
ATAAATTGTTTGAAGTGGATAGTATGATTATAATGACATATGTGGATAAT
Found at i:43356682 original size:68 final size:67
Alignment explanation
Indices: 43356610--43356759 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
43356600 CATCATGTGT
* * * *
43356610 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
43356672 ATGTAG
62 ATGTAG
** * *
43356678 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
43356743 AG
66 AG
43356745 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
43356760 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:43356715 original size:64 final size:64
Alignment explanation
Indices: 43356634--43356817 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
43356624 AGACATTATG
* *
43356634 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
43356698 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
43356763 AA
63 AA
* * * *
43356765 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
43356818 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:43357878 original size:22 final size:22
Alignment explanation
Indices: 43357848--43357890 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43357838 AATGAAATAA
*
43357848 ATGATATGTGTATATATATATC
1 ATGACATGTGTATATATATATC
43357870 ATGACATGTGTATATATATAT
1 ATGACATGTGTATATATATAT
43357891 GACTAGTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (22 bp):
ATGACATGTGTATATATATATC
Found at i:43359463 original size:40 final size:40
Alignment explanation
Indices: 43359389--43359607 Score: 327
Period size: 40 Copynumber: 5.5 Consensus size: 40
43359379 AACCCAAGTA
* * *
43359389 CCTTTGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
43359428 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
43359468 CCTTCTGGACTTAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
43359508 CCTTCGGGACTTAGCTCGGATATAGTCACTAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
43359548 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
43359587 CCTTTGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
43359608 GTCATCCGAA
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 34 0.21
40 130 0.79
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:43375449 original size:23 final size:21
Alignment explanation
Indices: 43375410--43375451 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
43375400 TTACAAAATA
43375410 TTTCTCTTTTCTTTGTTTTCC
1 TTTCTCTTTTCTTTGTTTTCC
43375431 TTTCTCTTTTGTCTTTGTTTT
1 TTTCTC-TTT-TCTTTGTTTT
43375452 GTAGGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTCTCTTTTCTTTGTTTTCC
Found at i:43376280 original size:50 final size:50
Alignment explanation
Indices: 43376123--43376332 Score: 163
Period size: 50 Copynumber: 4.2 Consensus size: 50
43376113 GATTTGATTT
** * * * * *
43376123 TGTAGCTTCATCTCGCTCCACTACATCTTTAGGGAGATAAAATTTGCTAT
1 TGTAGCTTCATCTTACTCCACTACATCTTCAAGGAGATGAGATTTGCTAC
* * * * * * **
43376173 TGTAGCTTCA-CTTCATTCCACTACAACTTCAAGGATAT-AGGAGTCGTTGT
1 TGTAGCTTCATCTT-ACTCCACTACATCTTCAAGGAGATGA-GATTTGCTAC
**
43376223 TGTAGCTTCATCTTGTTCCACTACATCTTCAAGGAGATGAGATTTGCTAC
1 TGTAGCTTCATCTTACTCCACTACATCTTCAAGGAGATGAGATTTGCTAC
* * * * * * *
43376273 TGCAGCTTTATCTTACTGCATTGCATCTTCAGGGAGATGAGGTTTGCTAC
1 TGTAGCTTCATCTTACTCCACTACATCTTCAAGGAGATGAGATTTGCTAC
*
43376323 TGTAACTTCA
1 TGTAGCTTCA
43376333 CTCCATCTCA
Statistics
Matches: 124, Mismatches: 32, Indels: 8
0.76 0.20 0.05
Matches are distributed among these distances:
49 3 0.02
50 117 0.94
51 4 0.03
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (50 bp):
TGTAGCTTCATCTTACTCCACTACATCTTCAAGGAGATGAGATTTGCTAC
Found at i:43377387 original size:15 final size:15
Alignment explanation
Indices: 43377349--43377390 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
43377339 TAATTATGTT
43377349 ATTAGTAGAAAAAAC
1 ATTAGTAGAAAAAAC
* *
43377364 ATTTA-TAGAAATACC
1 A-TTAGTAGAAAAAAC
43377379 ATTAGTAGAAAA
1 ATTAGTAGAAAA
43377391 TCATAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 3 0.14
15 16 0.73
16 3 0.14
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.26
Consensus pattern (15 bp):
ATTAGTAGAAAAAAC
Found at i:43379364 original size:6 final size:6
Alignment explanation
Indices: 43379353--43379377 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43379343 ACGGATGAGT
43379353 ATGGCA ATGGCA ATGGCA ATGGCA A
1 ATGGCA ATGGCA ATGGCA ATGGCA A
43379378 CAATGGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (6 bp):
ATGGCA
Found at i:43382210 original size:68 final size:67
Alignment explanation
Indices: 43382102--43382233 Score: 246
Period size: 68 Copynumber: 2.0 Consensus size: 67
43382092 TAGCACATGT
*
43382102 AAAATTTATCATAAAACTGATAATCAGATAGTTAAACATTTCCTTACTAATAAAAGTTTGGAAAT
1 AAAATTTATCATAAAACTGATAATCAGACAGTTAAACATTTCCTTACTAATAAAAGTTTGGAAAT
43382167 GG
66 GG
43382169 AAAATTTATCATAAAAACTGATAATCAGACAGTTAAACATTTCCTTACTAATAAAAGTTTGGAAA
1 AAAATTTATCAT-AAAACTGATAATCAGACAGTTAAACATTTCCTTACTAATAAAAGTTTGGAAA
43382234 CTGTACCTAG
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
67 12 0.19
68 51 0.81
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (67 bp):
AAAATTTATCATAAAACTGATAATCAGACAGTTAAACATTTCCTTACTAATAAAAGTTTGGAAAT
GG
Found at i:43386424 original size:16 final size:17
Alignment explanation
Indices: 43386403--43386435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43386393 GACATTACGG
*
43386403 TAATTAT-TTTGTCAAA
1 TAATTATCTTTGACAAA
43386419 TAATTATCTTTGACAAA
1 TAATTATCTTTGACAAA
43386436 AACTACCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
TAATTATCTTTGACAAA
Found at i:43386493 original size:13 final size:13
Alignment explanation
Indices: 43386475--43386502 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43386465 CATCGTCTCT
43386475 TTATTTATTATTA
1 TTATTTATTATTA
43386488 TTATTTATTATTA
1 TTATTTATTATTA
43386501 TT
1 TT
43386503 GACACATCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:43389339 original size:34 final size:34
Alignment explanation
Indices: 43389294--43389362 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
43389284 ATTCTCCGCC
*
43389294 TAAGACTCATCAACTGCCTTTCCATTGGCTTGGG
1 TAAGACCCATCAACTGCCTTTCCATTGGCTTGGG
43389328 TAAGACCCATCAACTGCCTTTCCATTGGCTTGGG
1 TAAGACCCATCAACTGCCTTTCCATTGGCTTGGG
43389362 T
1 T
43389363 GTCTTATTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (34 bp):
TAAGACCCATCAACTGCCTTTCCATTGGCTTGGG
Found at i:43395768 original size:48 final size:48
Alignment explanation
Indices: 43395665--43395768 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
43395655 AAGAAAATAC
* ** * *
43395665 AAAACTATGTCATTTTGATAAATATTTACATTTTAAGTTAAAAAAGAT
1 AAAATTATGTCATTTTGATAAATATTTACACATTAAATTAAAAAACAT
* *
43395713 AAAATTATGTCA-TTTGAATAAATATTTACCCATTAAATTAAAAGACA-
1 AAAATTATGTCATTTTG-ATAAATATTTACACATTAAATTAAAAAACAT
43395760 AAATATTAT
1 AAA-ATTAT
43395769 ATTGTTTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 7 0.15
48 40 0.85
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (48 bp):
AAAATTATGTCATTTTGATAAATATTTACACATTAAATTAAAAAACAT
Found at i:43396068 original size:33 final size:33
Alignment explanation
Indices: 43396031--43396102 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
43396021 AAAATTATAA
* * *
43396031 TTTATATATTATTCTATTAAATTATTTAAATAT
1 TTTATATATCATTATATTAAATTACTTAAATAT
* *
43396064 TTTATGTATCGTTATATTAAATTACTTAAATAT
1 TTTATATATCATTATATTAAATTACTTAAATAT
*
43396097 GTTATA
1 TTTATA
43396103 AAATATATAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (33 bp):
TTTATATATCATTATATTAAATTACTTAAATAT
Found at i:43396980 original size:9 final size:9
Alignment explanation
Indices: 43396966--43396997 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
43396956 TTTCGAATTT
43396966 GAATAACTC
1 GAATAACTC
*
43396975 GAATAATTC
1 GAATAACTC
43396984 GAATAACTC
1 GAATAACTC
43396993 GAATA
1 GAATA
43396998 TCAAACTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (9 bp):
GAATAACTC
Found at i:43396982 original size:18 final size:18
Alignment explanation
Indices: 43396961--43396997 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
43396951 TGAGTTTTCG
*
43396961 AATTTGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
43396979 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCGAAT
43396997 A
1 A
43396998 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:43405938 original size:29 final size:29
Alignment explanation
Indices: 43405863--43406099 Score: 223
Period size: 29 Copynumber: 8.2 Consensus size: 29
43405853 TCAGATTTTC
* *
43405863 GCCACAAAGGCATCC-TTTAACAGA-ATTT
1 GCCACAAAGGCATCCTTTTAATAGAGA-TA
*
43405891 G-CA-AGAAGGCATTCC-TTTAATAGAGATG
1 GCCACA-AAGGCA-TCCTTTTAATAGAGATA
*
43405919 GCCATAAAGGCATCCTTTTAATAGAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* *
43405948 GTCACAAAGGTATCCTTTTAATAGAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* * * * *
43405977 GCCATAAAGGTATCCTTCTAACAGGGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
** * *
43406006 GCCACAAAAACATCCTTTTAACAGAGATC
1 GCCACAAAGGCATCCTTTTAATAGAGATA
* *
43406035 GCCACAAAGGCATCCTTTTAACAAAGATA
1 GCCACAAAGGCATCCTTTTAATAGAGATA
** * *
43406064 GCCACAAAAACATCCTGTTAATAGAGATC
1 GCCACAAAGGCATCCTTTTAATAGAGATA
43406093 GCCACAA
1 GCCACAA
43406100 TGCTTCCTTT
Statistics
Matches: 175, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.01
27 8 0.05
28 17 0.10
29 148 0.85
30 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (29 bp):
GCCACAAAGGCATCCTTTTAATAGAGATA
Found at i:43405981 original size:58 final size:58
Alignment explanation
Indices: 43405906--43406096 Score: 256
Period size: 58 Copynumber: 3.3 Consensus size: 58
43405896 AAGGCATTCC
* * * ***
43405906 TTTAATAGAGATGGCCATAAAGGCATCCTTTTAATAGAGATAGTCACAAAGGTATCCT
1 TTTAATAGAGATCGCCATAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCT
* * * *
43405964 TTTAATAGAGATAGCCATAAAGGTATCCTTCTAACAGGGATAGCCACAAAAACATCCT
1 TTTAATAGAGATCGCCATAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCT
* * *
43406022 TTTAACAGAGATCGCCACAAAGGCATCCTTTTAACAAAGATAGCCACAAAAACATCCT
1 TTTAATAGAGATCGCCATAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCT
*
43406080 GTTAATAGAGATCGCCA
1 TTTAATAGAGATCGCCA
43406097 CAATGCTTCC
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 115 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (58 bp):
TTTAATAGAGATCGCCATAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCT
Found at i:43406097 original size:58 final size:58
Alignment explanation
Indices: 43405861--43406099 Score: 254
Period size: 58 Copynumber: 4.2 Consensus size: 58
43405851 CTTCAGATTT
* **
43405861 TCGCCACAAAGGCATCC-TTTAACAGA-ATTTG-CA-AGAAGGCATTCC-TTTAATAGAGA
1 TCGCCACAAAGGCATCCTTTTAACAGAGA-TAGCCACA-AAAACA-TCCTTTTAATAGAGA
* * * * ***
43405917 TGGCCATAAAGGCATCCTTTTAATAGAGATAGTCACAAAGGTATCCTTTTAATAGAGA
1 TCGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCTTTTAATAGAGA
* * * * * *
43405975 TAGCCATAAAGGTATCCTTCTAACAGGGATAGCCACAAAAACATCCTTTTAACAGAGA
1 TCGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCTTTTAATAGAGA
* *
43406033 TCGCCACAAAGGCATCCTTTTAACAAAGATAGCCACAAAAACATCCTGTTAATAGAGA
1 TCGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCTTTTAATAGAGA
43406091 TCGCCACAA
1 TCGCCACAA
43406100 TGCTTCCTTT
Statistics
Matches: 155, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
56 15 0.10
57 13 0.08
58 126 0.81
59 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (58 bp):
TCGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAACATCCTTTTAATAGAGA
Found at i:43406704 original size:31 final size:31
Alignment explanation
Indices: 43406669--43406732 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
43406659 AACCTAAAAT
43406669 ACATGGAAACCCTAGGAGAGAGAGAGAATAA
1 ACATGGAAACCCTAGGAGAGAGAGAGAATAA
43406700 ACATGGAAACCCTAGGAGAGAGAGAGAATAA
1 ACATGGAAACCCTAGGAGAGAGAGAGAATAA
43406731 AC
1 AC
43406733 TTTCATGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.09
Consensus pattern (31 bp):
ACATGGAAACCCTAGGAGAGAGAGAGAATAA
Found at i:43410108 original size:15 final size:15
Alignment explanation
Indices: 43410082--43410120 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
43410072 TGGCGTGGCC
43410082 TCATTCTTCATAACCA
1 TCATT-TTCATAACCA
43410098 TCATTTTCATAACCA
1 TCATTTTCATAACCA
43410113 TCACTTTT
1 TCA-TTTT
43410121 GTTTCTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TCATTTTCATAACCA
Found at i:43417776 original size:38 final size:40
Alignment explanation
Indices: 43417725--43418010 Score: 161
Period size: 38 Copynumber: 6.8 Consensus size: 40
43417715 ATGAAAACAT
43417725 GTGGTGCTAAGTGGATATACCACGGTTATA-TG-TGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATATTGATGTAAC
*
43417763 GTGGTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTT----ATATTG----ATGTAAC
* *
43417811 GTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAAC
1 GTGGTGCTAAGTGGATATACCACGG-T---TATATTGA-T--GTAAC
* * * * **
43417858 ATAGTGCTAAGTGGATATACCATGATTA-A-ACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATATTGATGTAAC
* * *
43417896 GTGGTGCTAAGTGGATATTCCACGGCTACATATACTGATTCATTAAC
1 GTGGTGCTAAGTGGATATACCACGG-T---TATATTGA-T--GTAAC
* *** *
43417943 GTGGTGCTAAGTGGATATGCCACGG--ATAAACATGGAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATATTGATGTAAC
* *
43417981 ATGGTGCTAAGTGGATATGCCACGGTTATA
1 GTGGTGCTAAGTGGATATACCACGGTTATA
43418011 CATGTTAATT
Statistics
Matches: 193, Mismatches: 27, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
38 77 0.40
39 1 0.01
40 5 0.03
41 5 0.03
42 6 0.03
43 5 0.03
44 2 0.01
45 2 0.01
46 1 0.01
47 52 0.27
48 35 0.18
49 1 0.01
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (40 bp):
GTGGTGCTAAGTGGATATACCACGGTTATATTGATGTAAC
Found at i:43417913 original size:85 final size:85
Alignment explanation
Indices: 43417802--43418008 Score: 317
Period size: 85 Copynumber: 2.4 Consensus size: 85
43417792 ACATATTGAT
*
43417802 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATAGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATACTGATTCATTAACATAGTGCTA
*
43417867 AGTGGATATACCA-TGATTAA
66 AGTGGATATACCACGGA-TAA
* * * *
43417887 ACATGTAACGTGGTGCTAAGTGGATATTCCACGGCTACATATACTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATACTGATTCATTAACATAGTGCTA
*
43417952 AGTGGATATGCCACGGATAA
66 AGTGGATATACCACGGATAA
* *
43417972 ACATGGAACATGGTGCTAAGTGGATATGCCACGGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
43418009 TACATGTTAA
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
85 108 0.98
86 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATACTGATTCATTAACATAGTGCTA
AGTGGATATACCACGGATAA
Found at i:43423295 original size:128 final size:128
Alignment explanation
Indices: 43423067--43423451 Score: 761
Period size: 128 Copynumber: 3.0 Consensus size: 128
43423057 CAGTTGTAAG
*
43423067 GTAACTAATGAATTAATTATTTAAATGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
1 GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
43423132 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
66 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
43423195 GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
1 GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
43423260 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
66 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
43423323 GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
1 GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
43423388 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
66 TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
43423451 G
1 G
43423452 CGTTGCATAA
Statistics
Matches: 256, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 256 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (128 bp):
GTAACTAATGAATTAATTATTTAAACGGTTTGAAATTATAATTAATTGACATGATACTTAATCAT
TGCATGTTTAATCATCTAAGGTAGCTGAAGGTTAAATTAGCAACGGTATCTAACGATACACTA
Found at i:43428689 original size:42 final size:42
Alignment explanation
Indices: 43428574--43428735 Score: 153
Period size: 42 Copynumber: 3.8 Consensus size: 42
43428564 TACCGTACCA
* * * **
43428574 ATGCCATATCCCAGATATAGTCTTATATGTAATCTTGTATCG
1 ATGCCATATCCCAGATATAGTCTTACACGAAATCTCATATCG
** * * **
43428616 ATGTGAATAGCCCAGCTATAGTCTTACACGAAATCTCACGTCG
1 ATG-CCATATCCCAGATATAGTCTTACACGAAATCTCATATCG
* * * *
43428659 ATGCCATATCCCAGATATGGTCTTATACGAAGTCTCATACCG
1 ATGCCATATCCCAGATATAGTCTTACACGAAATCTCATATCG
* * *
43428701 ATACCATATCCCAGATATGGTCTTACACGTAATCT
1 ATGCCATATCCCAGATATAGTCTTACACGAAATCT
43428736 TAGTAACCCT
Statistics
Matches: 94, Mismatches: 25, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
42 63 0.67
43 31 0.33
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATAGTCTTACACGAAATCTCATATCG
Found at i:43434477 original size:22 final size:22
Alignment explanation
Indices: 43434448--43434494 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
43434438 TATCCCCACA
* *
43434448 TGGAGGAGTGTATTGTAG-GGC
1 TGGAGGAGTGGAGTGTAGAGGC
43434469 TGGACGGAGTGGAGTGTAGAGGC
1 TGGA-GGAGTGGAGTGTAGAGGC
43434492 TGG
1 TGG
43434495 TGGGGTAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 12 0.55
23 6 0.27
ACGTcount: A:0.19, C:0.06, G:0.51, T:0.23
Consensus pattern (22 bp):
TGGAGGAGTGGAGTGTAGAGGC
Found at i:43437615 original size:39 final size:40
Alignment explanation
Indices: 43437572--43437739 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 40
43437562 CTCGTTCAAG
* * * *
43437572 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
43437611 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
43437651 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * * *
43437691 GGCCTTCGGGACTTAACCCGGAATTA-ATAACGCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
43437731 TGCCTTCGG
1 TGCCTTCGG
43437740 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 26 0.24
40 80 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:43437727 original size:80 final size:80
Alignment explanation
Indices: 43437607--43437792 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
43437597 AGTAACTCAT
* * * *
43437607 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACGCGCACAAATGCCTTC-GGATCTTAACCCG
*
43437671 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
43437686 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACGCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACGCGCACAAATGCCTTCGGATCTTAACCC
43437750 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
43437767 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
43437793 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 11 0.12
80 71 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACGCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:43437752 original size:40 final size:40
Alignment explanation
Indices: 43437609--43437792 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
43437599 TAACTCATAC
* *
43437609 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
43437649 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* *
43437689 AAGGCCTTCGGGACTTAACCCGGAATTAATAACGCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
43437729 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
43437770 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43437793 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 104 0.85
41 10 0.08
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:43438226 original size:121 final size:121
Alignment explanation
Indices: 43438012--43438252 Score: 455
Period size: 121 Copynumber: 2.0 Consensus size: 121
43438002 TCGAACGATC
*
43438012 CCGCTAACTATTCGACCACTTTTTCCTTCCCTTTATCGAATTTATTTCCCCTTTGCTCTTGAGCT
1 CCGCTAACTATTCAACCACTTTTTCCTTCCCTTTATCGAATTTATTTCCCCTTTGCTCTTGAGCT
43438077 TAATTAAACAAATAAATTGATTTCATCATTTAGGCATCAAAAAGATGAACACGAAT
66 TAATTAAACAAATAAATTGATTTCATCATTTAGGCATCAAAAAGATGAACACGAAT
* *
43438133 CCGCTAGCTATTCAACCACTTTTTCCTTCCCTTTATCGGATTTATTTCCCCTTTGCTCTTGAGCT
1 CCGCTAACTATTCAACCACTTTTTCCTTCCCTTTATCGAATTTATTTCCCCTTTGCTCTTGAGCT
43438198 TAATTAAACAAATAAATTGATTTCATCATTTAGGCATCAAAAAGATGAACACGAA
66 TAATTAAACAAATAAATTGATTTCATCATTTAGGCATCAAAAAGATGAACACGAA
43438253 GCACTTAGCC
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (121 bp):
CCGCTAACTATTCAACCACTTTTTCCTTCCCTTTATCGAATTTATTTCCCCTTTGCTCTTGAGCT
TAATTAAACAAATAAATTGATTTCATCATTTAGGCATCAAAAAGATGAACACGAAT
Found at i:43447238 original size:103 final size:103
Alignment explanation
Indices: 43447113--43447450 Score: 493
Period size: 103 Copynumber: 3.3 Consensus size: 103
43447103 GGGGTTCTGT
* * *
43447113 GTGCTGATTCCCCTATTCATTGGTGGTTGTTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAG
1 GTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAG
43447178 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAA
66 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAA
*
43447216 GTGCTGATTCCCCTAC-CTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAA
1 GTGCTGATTCCCCGACTC-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAA
*
43447280 GGGGGTTGCTAAGTGCTGATTCCCCCGAGTGGTTGCTAA
65 GGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAA
* * * * *
43447319 GCGCTGATTCCCCGAC-CTATTTTGTGGTTGCTAAGTGCTGATTCCACCGCATCTGAAATGTG-A
1 GTGCTGATTCCCCGACTC-A-TTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAA
* * **
43447382 AGGGGGTTGCTAAGTGCTGATTACCCCAAGGGGTTGCTGT
64 AGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAA
*
43447422 GTGCTGATTCCCCGATTCATTGGTGGTTG
1 GTGCTGATTCCCCGACTCATTGGTGGTTG
43447451 TTAACTGCGG
Statistics
Matches: 215, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
102 10 0.05
103 166 0.77
104 39 0.18
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.33
Consensus pattern (103 bp):
GTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAG
GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAA
Found at i:43447414 original size:27 final size:26
Alignment explanation
Indices: 43447384--43447434 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
43447374 AAATGTGAAG
43447384 GGGGTTGCTAAGTGCTGATTACCCCAA
1 GGGGTTGCTAAGTGCTGATT-CCCCAA
**
43447411 GGGGTTGCTGTGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
43447435 GATTCATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCAA
Found at i:43453926 original size:103 final size:103
Alignment explanation
Indices: 43453798--43454148 Score: 483
Period size: 103 Copynumber: 3.4 Consensus size: 103
43453788 ATTGCATATA
** * * **
43453798 AAGGGGTTGCTGTGTGCTGATTCCCCTA-TTCATTGGTGGTTGCTAAGTGCTGATTCCAATGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACCT-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
*
43453862 TTTAAATGTGAAAGGGGGTTGCTAAGTGTTGATTCCCCC
65 TTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
*
43453901 AAGGGGTTGCTAAGTGCTGATTCCCCTACCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
43453966 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* * * * *
43454004 GAGTGGTTGCTAAGCGCTGATTCCCCGACCTATTTTGTGGTTGCTAAGTGCTGATTCCACCGCAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACCTA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTAT
* * *
43454069 CTGAAATGTG-AAGGGGGTTGCTAAGTACTGATTCCCCC
65 TTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
** *
43454107 AAGGGGTTGCTGTGTGCTGATTCCCCGA-TTCATTGGTGGTTG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACCT-ATTGGTGGTTG
43454149 TTAATTGCGG
Statistics
Matches: 223, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
102 10 0.04
103 174 0.78
104 39 0.17
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:43453947 original size:33 final size:33
Alignment explanation
Indices: 43453905--43454061 Score: 110
Period size: 34 Copynumber: 4.6 Consensus size: 33
43453895 TCCCCCAAGG
43453905 GGTTGCTAAGTGCTGATTCCCCTACCTATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTACCTATTGGT
** *
43453938 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA-CCT--AT-T----GGT
*
43453981 GGTTGCTAAGTGCTGATT-CCC--CCGA---GT
1 GGTTGCTAAGTGCTGATTCCCCTACCTATTGGT
* * *
43454008 GGTTGCTAAGCGCTGATTCCCCGACCTATTTTGT
1 GGTTGCTAAGTGCTGATTCCCCTACCTA-TTGGT
43454042 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
43454062 ACCGCATCTG
Statistics
Matches: 97, Mismatches: 10, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
27 18 0.19
28 3 0.03
30 3 0.03
33 20 0.21
34 23 0.24
35 3 0.03
36 1 0.01
38 2 0.02
39 1 0.01
41 2 0.02
42 1 0.01
43 20 0.21
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTACCTATTGGT
Found at i:43456620 original size:31 final size:31
Alignment explanation
Indices: 43456584--43456651 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
43456574 GAAAAATAAT
*
43456584 AATTTAACTCTT-TTTGAAAGGTTAATGG-TCA
1 AATTTAAC-CTTATTTGAAAAGTTAATGGCT-A
*
43456615 AATTTAACCTTATTTTAAAAGTTAATGGCTA
1 AATTTAACCTTATTTGAAAAGTTAATGGCTA
43456646 AATTTA
1 AATTTA
43456652 GTTAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 29 0.88
32 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (31 bp):
AATTTAACCTTATTTGAAAAGTTAATGGCTA
Found at i:43457219 original size:54 final size:55
Alignment explanation
Indices: 43457136--43457275 Score: 237
Period size: 55 Copynumber: 2.5 Consensus size: 55
43457126 TTGCCCATGT
* *
43457136 TTTTTAGGATTAGAGTTTTTTAGGGTTTAATTAATTTAAGGTTAAA-TTTTTTTAG
1 TTTTTAGGGTTAG-GGTTTTTAGGGTTTAATTAATTTAAGGTTAAATTTTTTTTAG
43457191 TTTTTAGGGTTAGGGTTTTTAGGGTTTAATTAATTTAAGGTTAAATTTTTTTTAG
1 TTTTTAGGGTTAGGGTTTTTAGGGTTTAATTAATTTAAGGTTAAATTTTTTTTAG
43457246 TTTTTAGGGTTAGGGTTTTTTAGGGTTTAA
1 TTTTTAGGGTTAGGG-TTTTTAGGGTTTAA
43457276 AATTAAGGTT
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
54 31 0.38
55 36 0.44
56 14 0.17
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (55 bp):
TTTTTAGGGTTAGGGTTTTTAGGGTTTAATTAATTTAAGGTTAAATTTTTTTTAG
Found at i:43457388 original size:34 final size:34
Alignment explanation
Indices: 43457345--43457421 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 34
43457335 AATACTAAAT
*
43457345 ATTAAATTAGAGTTTAAGGT-ATTAGGGTTAATTG
1 ATTAAATTAGAGATTAA-GTAATTAGGGTTAATTG
* *
43457379 ATTAAATTAGAGATTGATTAAATTAGGGTTAATTG
1 ATTAAATTAGAGATTAAGT-AATTAGGGTTAATTG
43457414 ATTAAATT
1 ATTAAATT
43457422 TAGGGTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 1 0.03
34 15 0.39
35 22 0.58
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (34 bp):
ATTAAATTAGAGATTAAGTAATTAGGGTTAATTG
Found at i:43457415 original size:19 final size:19
Alignment explanation
Indices: 43457365--43457454 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
43457355 AGTTTAAGGT
43457365 ATTAGGGTTAATTGATTAA
1 ATTAGGGTTAATTGATTAA
*
43457384 ATTAGAG---ATTGATTAA
1 ATTAGGGTTAATTGATTAA
43457400 ATTAGGGTTAATTGATTAA
1 ATTAGGGTTAATTGATTAA
*
43457419 ATTTAGGGTTAATTAATTAA
1 A-TTAGGGTTAATTGATTAA
* *
43457439 TTTAGGATTAATTGAT
1 ATTAGGGTTAATTGAT
43457455 ACATAATCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
16 15 0.25
19 29 0.48
20 17 0.28
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (19 bp):
ATTAGGGTTAATTGATTAA
Found at i:43457450 original size:39 final size:35
Alignment explanation
Indices: 43457365--43457454 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 35
43457355 AGTTTAAGGT
*
43457365 ATTAGGGTTAATTGATTAAATTAGAGATTGATTAA
1 ATTAGGGTTAATTGATTAAATTAGAGATTAATTAA
*
43457400 ATTAGGGTTAATTGATTAAATTTAGGGTTAATTAATTAA
1 ATTAGGGTTAATTGATTAAA-TTAGAG---ATTAATTAA
* *
43457439 TTTAGGATTAATTGAT
1 ATTAGGGTTAATTGAT
43457455 ACATAATCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 20 0.43
36 5 0.11
39 22 0.47
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (35 bp):
ATTAGGGTTAATTGATTAAATTAGAGATTAATTAA
Found at i:43458275 original size:125 final size:126
Alignment explanation
Indices: 43457998--43458377 Score: 532
Period size: 125 Copynumber: 3.0 Consensus size: 126
43457988 TTTCTGTAAG
* * * * *
43457998 AATAATTTTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAAAGCTTCAAGCAAGATGCATTGTT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAAAGCTTCAAGTAGGATGCACTGTC
* * * * * * *
43458063 AGCAAAATTTTTGAAAAAATCTCCCAAATGGACGCTCTTTTGCTACAATAGTTCGTTGAAA
66 AGTAAAATTTCTGAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
43458124 AATAATTCTGAGTAGACATTTATGAACAAATAGTGTTGAAAACGCTTCAAGTAGGATGCACTGTC
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAAAGCTTCAAGTAGGATGCACTGTC
43458189 AGTAAAATTTCTGAAAAAA-CTCCTACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGTAAAATTTCTGAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
*
43458249 AATAATTCTGAGTAGACGTTTCTGAACAAATAGAGTCGAAAATA-CTTCAAGTAGGATGCACTGT
1 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAA-AGCTTCAAGTAGGATGCACTGT
* * * *
43458313 CAGTCAAATTTCTAAAAAAAGC-CCTCACGTGGACGCTCTTTTGATACAGTAGTTCGTAGAAA
65 CAGTAAAATTTCTGAAAAAAGCTCCT-ACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
43458375 AAT
1 AAT
43458378 GAGGTTATAA
Statistics
Matches: 227, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
125 116 0.51
126 111 0.49
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (126 bp):
AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTCGAAAAAGCTTCAAGTAGGATGCACTGTC
AGTAAAATTTCTGAAAAAAGCTCCTACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:43461856 original size:18 final size:18
Alignment explanation
Indices: 43461830--43461872 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
43461820 GATTAGGAAA
* *
43461830 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
43461848 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
43461866 AGGATAC
1 AGGATAC
43461873 GCACCTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:43463515 original size:48 final size:46
Alignment explanation
Indices: 43463461--43463595 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 46
43463451 ATGCAAACAT
* *
43463461 CATAAATGAAAAAAAAATCAAGCAGTATTGAAATTTTAATTATAA-TTG
1 CATAAATGAAAAAAATATCAA-TAGTATTGAAA-TTTAATTA-AATTTG
* *
43463509 CATAAATGAATAATATATCAAATAGTATTGCAAATTTAATTAAATTTG
1 CATAAATGAAAAAAATATC-AATAGTATTG-AAATTTAATTAAATTTG
*
43463557 CATAAATTAAAAAAATATCGAATAGTATTGAAAATTTAA
1 CATAAATGAAAAAAATATC-AATAGTATTG-AAATTTAA
43463596 AATTATCACT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 2 0.03
48 68 0.91
49 5 0.07
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (46 bp):
CATAAATGAAAAAAATATCAATAGTATTGAAATTTAATTAAATTTG
Found at i:43463744 original size:11 final size:11
Alignment explanation
Indices: 43463728--43463789 Score: 65
Period size: 11 Copynumber: 5.7 Consensus size: 11
43463718 ATTTAAACAA
43463728 AGAAATTTGAT
1 AGAAATTTGAT
43463739 AGAAATTTGAT
1 AGAAATTTGAT
* *
43463750 AGAAGTTTGAG
1 AGAAATTTGAT
*
43463761 A-AAATTTCA-
1 AGAAATTTGAT
43463770 ATGAAATTTGAT
1 A-GAAATTTGAT
*
43463782 AGATATTT
1 AGAAATTT
43463790 TAAGGGAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 6 0.14
11 34 0.81
12 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.37
Consensus pattern (11 bp):
AGAAATTTGAT
Found at i:43465769 original size:15 final size:15
Alignment explanation
Indices: 43465749--43465777 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43465739 TTTCTGAAAT
43465749 TTTTTATATTTTTTA
1 TTTTTATATTTTTTA
43465764 TTTTTATATTTTTT
1 TTTTTATATTTTTT
43465778 TAAAAAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATATTTTTTA
Found at i:43466527 original size:13 final size:13
Alignment explanation
Indices: 43466511--43466535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43466501 ACACAAGCCC
43466511 AAAAATAAAAAAT
1 AAAAATAAAAAAT
43466524 AAAAATAAAAAA
1 AAAAATAAAAAA
43466536 ATGCACGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:43467261 original size:20 final size:19
Alignment explanation
Indices: 43467232--43467315 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 19
43467222 GATATTAATG
*
43467232 AAATCATTAGAAATTTTGGT
1 AAATC-TTAGAAATATTGGT
* *
43467252 AAATCGTTAGAAATAATAGT
1 AAATC-TTAGAAATATTGGT
43467272 AAATCTTTA-AATATATTGGT
1 AAATC-TTAGAA-ATATTGGT
* * *
43467292 CAAAACTTAGAAATTTTGGA
1 -AAATCTTAGAAATATTGGT
43467312 AAAT
1 AAAT
43467316 TCTAAAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 5 0.10
20 39 0.78
21 6 0.12
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (19 bp):
AAATCTTAGAAATATTGGT
Found at i:43467517 original size:20 final size:20
Alignment explanation
Indices: 43467479--43467517 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43467469 AAATTATTGG
*
43467479 AAATAATGGTAAATCATTAC
1 AAATAATGGTAAAGCATTAC
* *
43467499 AAATATTGGTAAAGGATTA
1 AAATAATGGTAAAGCATTA
43467518 GATGTGTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATAATGGTAAAGCATTAC
Found at i:43467748 original size:20 final size:20
Alignment explanation
Indices: 43467725--43467768 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
43467715 AGATATTTTT
*
43467725 GTAAACCATTAGAAATAATG
1 GTAAACCATTAAAAATAATG
* * *
43467745 GTAAATCTTTAAAAATATTG
1 GTAAACCATTAAAAATAATG
43467765 GTAA
1 GTAA
43467769 CGTCATAGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (20 bp):
GTAAACCATTAAAAATAATG
Found at i:43469311 original size:20 final size:20
Alignment explanation
Indices: 43469282--43469322 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43469272 AAACTTTTAT
* *
43469282 AAATATTAGTAAATCGTTAG
1 AAATAATAGTAAATCCTTAG
43469302 AAATAATAGTAAATCCTTAG
1 AAATAATAGTAAATCCTTAG
43469322 A
1 A
43469323 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (20 bp):
AAATAATAGTAAATCCTTAG
Found at i:43469572 original size:23 final size:23
Alignment explanation
Indices: 43469527--43469572 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
43469517 GAAATATTGG
*
43469527 TAAATCCTTTAAAAAATTGGTAA
1 TAAATCCTTTAAAAAATTAGTAA
*
43469550 TAAAT-CTTTAGAAATATTAGTAA
1 TAAATCCTTTA-AAAAATTAGTAA
43469573 AGGATTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.37
Consensus pattern (23 bp):
TAAATCCTTTAAAAAATTAGTAA
Found at i:43469694 original size:40 final size:39
Alignment explanation
Indices: 43469635--43469728 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
43469625 TATTAAAGGG
* *
43469635 TTTAGAAATTTTGTGAAATCCTTAAAAATACAT-GTAAATC
1 TTTAGATATTTTG-GAAATCATTAAAAATA-ATGGTAAATC
* *
43469675 TTTAGATATTTTGGCAAATCATTAGAAATAATGGTAATTC
1 TTTAGATATTTTGG-AAATCATTAAAAATAATGGTAAATC
*
43469715 CTTAGATATTTTGG
1 TTTAGATATTTTGG
43469729 TAAAGGCTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.06
40 44 0.94
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (39 bp):
TTTAGATATTTTGGAAATCATTAAAAATAATGGTAAATC
Found at i:43469729 original size:20 final size:20
Alignment explanation
Indices: 43469668--43469732 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
43469658 AAAAATACAT
*
43469668 GTAAATCTTTAGATATTTTG
1 GTAAATCATTAGATATTTTG
* * **
43469688 GCAAATCATTAGAAATAATG
1 GTAAATCATTAGATATTTTG
* *
43469708 GTAATTCCTTAGATATTTTG
1 GTAAATCATTAGATATTTTG
43469728 GTAAA
1 GTAAA
43469733 GGCTTAGATA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (20 bp):
GTAAATCATTAGATATTTTG
Found at i:43469845 original size:40 final size:40
Alignment explanation
Indices: 43469787--43469893 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 40
43469777 AGAAATATTG
* * * * *
43469787 GTAAATTTTTAGAAATTTTGGTAAGT-CATTAT-AACTACT
1 GTAAATTATTAGATATTTTGGTAAATAAAATATAAAC-ACT
* *
43469826 AGTAAATTGTTAGATATTTTAGTAAATAAAATATAAACACT
1 -GTAAATTATTAGATATTTTGGTAAATAAAATATAAACACT
43469867 GATAAATTATTAGATATTTTGGTAAAT
1 G-TAAATTATTAGATATTTTGGTAAAT
43469894 TGTTAGAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
40 23 0.41
41 30 0.54
42 3 0.05
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (40 bp):
GTAAATTATTAGATATTTTGGTAAATAAAATATAAACACT
Found at i:43469956 original size:20 final size:20
Alignment explanation
Indices: 43469928--43469978 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
43469918 AGATATTTTA
* *
43469928 GTAAGGTCTTAAAATTATTG
1 GTAAAGTCTTAAAACTATTG
43469948 GTAAAGTCTTAAAACTATTG
1 GTAAAGTCTTAAAACTATTG
*
43469968 GTAAAGGCTTA
1 GTAAAGTCTTA
43469979 GATGTGTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (20 bp):
GTAAAGTCTTAAAACTATTG
Found at i:43475371 original size:9 final size:9
Alignment explanation
Indices: 43475357--43475387 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43475347 TAGGCTTGGG
*
43475357 AATTGAAGA
1 AATTGAATA
43475366 AATTGAATA
1 AATTGAATA
43475375 AATTGAATA
1 AATTGAATA
43475384 AATT
1 AATT
43475388 TCATTTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (9 bp):
AATTGAATA
Found at i:43478222 original size:49 final size:49
Alignment explanation
Indices: 43478097--43478412 Score: 450
Period size: 49 Copynumber: 6.6 Consensus size: 49
43478087 CCCTTCGGGA
* * * * *
43478097 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43478144 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
43478191 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43478240 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
43478287 CTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43478336 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43478385 CTTATCAC--ATATATACACTTTCACATTC
1 CTTATCACATATATATACACTTTCACATTC
43478413 CAATGAATAA
Statistics
Matches: 243, Mismatches: 20, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
46 1 0.00
47 107 0.44
49 135 0.56
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43478259 original size:96 final size:96
Alignment explanation
Indices: 43478097--43478412 Score: 478
Period size: 96 Copynumber: 3.3 Consensus size: 96
43478087 CCCTTCGGGA
* * * * *
43478097 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
43478160 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
43478191 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
*
43478256 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43478287 CTTATCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATAT
* * *
43478352 ACACTTTCACATTCATCACATTGGCCATTCGAC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
43478385 CTTATCAC--ATATATACACTTTCACATTC
1 CTTATCACATATATATACACTTTCACATTC
43478413 CAATGAATAA
Statistics
Matches: 204, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
94 10 0.05
95 1 0.00
96 150 0.74
98 43 0.21
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43478358 original size:145 final size:143
Alignment explanation
Indices: 43478097--43478412 Score: 515
Period size: 145 Copynumber: 2.2 Consensus size: 143
43478087 CCCTTCGGGA
* * * * * *
43478097 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
43478162 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
43478227 TTGGCCATTCGGC
131 TTGGCCATTCGAC
* * *
43478240 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCAC--ATATATAC
43478305 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
43478370 CATTGGCCATTCGAC
129 CATTGGCCATTCGAC
43478385 CTTATCACATATATACACTTTCACATTC
1 CTTATCACATATATACACTTTCACATTC
43478413 CAATGAATAA
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
143 46 0.29
145 114 0.71
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TTGGCCATTCGAC
Found at i:43480041 original size:13 final size:13
Alignment explanation
Indices: 43480023--43480047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43480013 TACTAAATTT
43480023 TCATGGATTCAAA
1 TCATGGATTCAAA
43480036 TCATGGATTCAA
1 TCATGGATTCAA
43480048 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:43484668 original size:46 final size:45
Alignment explanation
Indices: 43484578--43484703 Score: 146
Period size: 46 Copynumber: 2.7 Consensus size: 45
43484568 ACATTATGAG
*
43484578 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTGAGACG-A
1 AGCCAGTGTAAGA-CATGTCT-GGACAT-GCATCAGCATTGAGACGTA
* * * *
43484625 GTGCTAGTGTAAGACATGTCTAGGACATGCTTCAGCCTTGAGACGTA
1 -AGCCAGTGTAAGACATGTCT-GGACATGCATCAGCATTGAGACGTA
43484672 AGCCAGTGTAAGACATGTCTGAGACATGCATC
1 AGCCAGTGTAAGACATGTCTG-GACATGCATC
43484704 GTCTACGAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 1 0.01
46 42 0.63
47 13 0.19
48 11 0.16
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (45 bp):
AGCCAGTGTAAGACATGTCTGGACATGCATCAGCATTGAGACGTA
Done.