Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 124 of 310
Found at i:39838963 original size:49 final size:49
Alignment explanation
Indices: 39838838--39839285 Score: 718
Period size: 49 Copynumber: 9.3 Consensus size: 49
39838828 CCCTTCGGGA
* * * * * *
39838838 CTTATCACAT-T-TATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39838885 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39838932 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39838981 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39839030 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39839079 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCC--ATTAGGC
*
39839130 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39839177 CTTATCAC--ACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39839224 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39839271 CTTATCACATATATA
1 CTTATCACATATATA
39839286 CACTGTCTTG
Statistics
Matches: 379, Mismatches: 14, Indels: 14
0.93 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 148 0.39
49 215 0.57
51 15 0.04
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39868807 original size:46 final size:46
Alignment explanation
Indices: 39868739--39868913 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
39868729 TGTAACCTGC
39868739 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * * *
39868785 CCATAAGTGAACTTGGATTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * * * * * *
39868835 -C-TCA-CGAACTCAGACTCAACTAAACGAGTTCAGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
39868878 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
39868914 CTGCCCAAAT
Statistics
Matches: 100, Mismatches: 20, Indels: 18
0.72 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 58 0.58
47 22 0.22
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:39868855 original size:93 final size:93
Alignment explanation
Indices: 39868747--39868918 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
39868737 GCCCATAAGT
* * * * * * *
39868747 GAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAGTGAACTTGGATTCAACTCAA
1 GAACTCAGACTCAACTAAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39868812 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
39868840 GAACTCAGACTCAACTAAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTAAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
39868905 CGAGTTCGGCTGCC
66 CGAGCTCGGATGCC
39868919 CAAATATCCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTAAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:39878375 original size:33 final size:33
Alignment explanation
Indices: 39878338--39878407 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
39878328 GAAAGGTAAG
39878338 TATAACAAATCAAAAAGTGTTGGTAAGAATATA
1 TATAACAAATCAAAAAGTGTTGGTAAGAATATA
*
39878371 TATAACAAATCAAAGAGTGTTGGTAAGAATATA
1 TATAACAAATCAAAAAGTGTTGGTAAGAATATA
39878404 TATA
1 TATA
39878408 TGTGTAAGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.29
Consensus pattern (33 bp):
TATAACAAATCAAAAAGTGTTGGTAAGAATATA
Found at i:39892249 original size:11 final size:11
Alignment explanation
Indices: 39892233--39892262 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
39892223 CTTGTTCTCA
39892233 TTGCATATTAT
1 TTGCATATTAT
39892244 TTGCATATTAT
1 TTGCATATTAT
39892255 TTGCATAT
1 TTGCATAT
39892263 GGACTTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (11 bp):
TTGCATATTAT
Found at i:39894829 original size:23 final size:25
Alignment explanation
Indices: 39894761--39894830 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
39894751 TCTTCTCTCA
* *
39894761 AGCCATATAACAGGAAGCTCACAAAG
1 AGCCATA-ATCAGGAAGCTTACAAAG
*
39894787 AGCCATTAATCGGGAAGCTTACAAAG
1 AGCCA-TAATCAGGAAGCTTACAAAG
39894813 AGCC-T-ATCAGGAAGCTTA
1 AGCCATAATCAGGAAGCTTA
39894831 TCCGGGCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
23 12 0.31
24 1 0.03
26 24 0.62
27 2 0.05
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (25 bp):
AGCCATAATCAGGAAGCTTACAAAG
Found at i:39896131 original size:25 final size:24
Alignment explanation
Indices: 39896093--39896182 Score: 119
Period size: 24 Copynumber: 3.8 Consensus size: 24
39896083 GGACTCACCA
* *
39896093 CAGCTCGTATGAGCTTATTGATTAT
1 CAGCTCGTAAGAGCTTACTGATT-T
*
39896118 CAGCTCGTAAGAGCTTACTGTTTT
1 CAGCTCGTAAGAGCTTACTGATTT
*
39896142 CAGCTCGTAGGAGCTTACTGA-TT
1 CAGCTCGTAAGAGCTTACTGATTT
*
39896165 CAGCTCGTCAGAGCTTAC
1 CAGCTCGTAAGAGCTTAC
39896183 CATTTTAGCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 18 0.31
24 20 0.34
25 20 0.34
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
CAGCTCGTAAGAGCTTACTGATTT
Found at i:39896224 original size:24 final size:23
Alignment explanation
Indices: 39896094--39896225 Score: 90
Period size: 23 Copynumber: 5.6 Consensus size: 23
39896084 GACTCACCAC
* * *
39896094 AGCTCGTATGAGCTTATTGATTATC
1 AGCTCGTAAGAGCTTACT-ATT-TT
*
39896119 AGCTCGTAAGAGCTTACTGTTTT
1 AGCTCGTAAGAGCTTACTATTTT
* *
39896142 CAGCTCGTAGGAGCTTACTGA-TTC
1 -AGCTCGTAAGAGCTTACT-ATTTT
* *
39896166 AGCTCGTCAGAGCTTACCATTTT
1 AGCTCGTAAGAGCTTACTATTTT
*
39896189 AGCT--TAATAGAGCTTACTATTCAT
1 AGCTCGT-A-AGAGCTTACTATT-TT
*
39896213 AGCTCGAAAGAGC
1 AGCTCGTAAGAGC
39896226 GGAAATGATA
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 34 0.40
24 31 0.37
25 17 0.20
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
AGCTCGTAAGAGCTTACTATTTT
Found at i:39898021 original size:65 final size:65
Alignment explanation
Indices: 39897896--39898045 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 65
39897886 CGAGCCATAT
* * *
39897896 CAAGATGCTCACAAAGAGCTGCGTTTGTGCTTGCAACATATGCAAGATCAAAATGTATCATAAAA
1 CAAGATGCTCACAAAGAGCTACGTTTGTGCTGGCAACATATGCAAGATCAAAACGTATCATAAAA
* * * * * * *
39897961 CAGGATGCTCACTAAGAGCTACGTTTGTG-TCGGTAATATATGCAAGATCACTACCG-ATCATAT
1 CAAGATGCTCACAAAGAGCTACGTTTGTGCT-GGCAACATATGCAAGATCA-AAACGTATCATAA
39898024 AA
64 AA
*
39898026 CAAGACGCTCACAAAGAGCT
1 CAAGATGCTCACAAAGAGCT
39898046 GTGGTAATCC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
64 1 0.01
65 67 0.96
66 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (65 bp):
CAAGATGCTCACAAAGAGCTACGTTTGTGCTGGCAACATATGCAAGATCAAAACGTATCATAAAA
Found at i:39903276 original size:47 final size:46
Alignment explanation
Indices: 39903214--39903312 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 46
39903204 TCTTAAATAG
*
39903214 GTCTTAAGTCTATTAATACATG-T-TAATTAGTACAGCATTTTAATGT
1 GTCTTAAGTCTATTAAT--ATGTTATAATAAGTACAGCATTTTAATGT
* *
39903260 GTCTTAAGTTTAATTAATATGTTATAATAAGTACAGCTTTTTAATGT
1 GTCTTAAGTCT-ATTAATATGTTATAATAAGTACAGCATTTTAATGT
39903307 GTCTTA
1 GTCTTA
39903313 GATTAAGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
45 3 0.06
46 11 0.23
47 33 0.70
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (46 bp):
GTCTTAAGTCTATTAATATGTTATAATAAGTACAGCATTTTAATGT
Found at i:39904342 original size:170 final size:170
Alignment explanation
Indices: 39904035--39904348 Score: 504
Period size: 170 Copynumber: 1.8 Consensus size: 170
39904025 AAAACTATTC
* *
39904035 AACTATTTAGCTATTCAAGGCAGCCCCTTAAAGGTAGTTCACATCTCTTGGCTGATCATATTCAG
1 AACTATTCAACTATTCAAGGCAGCCCCTTAAAGGTAGTTCACATCTCTTGGCTGATCATATTCAG
* * * * *
39904100 GTCCATTCATCTCATCTTTCACTTCAATTAATCAAGCTGGCCTAGAAAGCATTAACGGATGTTTT
66 CTCCATTCATCTCATCTTTCACTTCAATTAATCAAGCTAGCCTAGAAAGCATCAACGGACGTTTC
*
39904165 GGAAGGTTCAAGGATGCCCAAGCTTCCATTTGAAGTCCAA
131 AGAAGGTTCAAGGATGCCCAAGCTTCCATTTGAAGTCCAA
* *
39904205 AACTATTCAACTATTCAAGGCAGCCCCTTAAAGGCT-GTTCACATCTCTTGGTTGATTATATTCA
1 AACTATTCAACTATTCAAGGCAGCCCCTTAAAGG-TAGTTCACATCTCTTGGCTGATCATATTCA
* *
39904269 GCTCCATTCATCTCATCTTTCACTTCAATTAATCAAGCTAGCCTAGGAAGCATCAAGGGACGTTT
65 GCTCCATTCATCTCATCTTTCACTTCAATTAATCAAGCTAGCCTAGAAAGCATCAACGGACGTTT
39904334 CAGAAGGTTCAAGGA
130 CAGAAGGTTCAAGGA
39904349 AGTTTCCAGC
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
170 130 0.99
171 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (170 bp):
AACTATTCAACTATTCAAGGCAGCCCCTTAAAGGTAGTTCACATCTCTTGGCTGATCATATTCAG
CTCCATTCATCTCATCTTTCACTTCAATTAATCAAGCTAGCCTAGAAAGCATCAACGGACGTTTC
AGAAGGTTCAAGGATGCCCAAGCTTCCATTTGAAGTCCAA
Found at i:39905071 original size:22 final size:22
Alignment explanation
Indices: 39905044--39905098 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
39905034 ATTTTTGTAC
39905044 AAAGTTGTGAAA-TATAAAAAA
1 AAAGTTGTGAAATTATAAAAAA
*
39905065 AAGAGTTCG-AAAATTATAAAAAA
1 AA-AGTT-GTGAAATTATAAAAAA
*
39905088 AAAGTTTTGAA
1 AAAGTTGTGAA
39905099 GTGCTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
21 2 0.07
22 13 0.48
23 12 0.44
ACGTcount: A:0.58, C:0.02, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAGTTGTGAAATTATAAAAAA
Found at i:39906715 original size:65 final size:65
Alignment explanation
Indices: 39906571--39906717 Score: 177
Period size: 65 Copynumber: 2.3 Consensus size: 65
39906561 AAGCCATATC
* * * * **
39906571 AGGATGCTCACAAAGAACTGCGTTTGTGTCTGCAACACATGCAAGATCACAACCGATTATAAAAA
1 AGGACGCTCACAAAGAGCTACGTTTGTGTCTGCAACACATGCAAGACCACAACCGACCATAAAAA
* * * * *
39906636 AGGATGCTCACAAAGAGCTACGTTTGTGTCTGCAATATATGCAAGACCACAACCGACCATATAAT
1 AGGACGCTCACAAAGAGCTACGTTTGTGTCTGCAACACATGCAAGACCACAACCGACCATAAAAA
* *
39906701 AGTACGCTCTCAAAGAG
1 AGGACGCTCACAAAGAG
39906718 TTGCGGTAGT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (65 bp):
AGGACGCTCACAAAGAGCTACGTTTGTGTCTGCAACACATGCAAGACCACAACCGACCATAAAAA
Found at i:39908076 original size:22 final size:22
Alignment explanation
Indices: 39908051--39908094 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39908041 CCAAGTTCCC
* *
39908051 ATGGAGACTTGGGTTGAGTTAA
1 ATGGAAACTTGGGTTAAGTTAA
*
39908073 ATGGAAACTTTGGTTAAGTTAA
1 ATGGAAACTTGGGTTAAGTTAA
39908095 GAAGAAGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.34
Consensus pattern (22 bp):
ATGGAAACTTGGGTTAAGTTAA
Found at i:39909093 original size:32 final size:32
Alignment explanation
Indices: 39909050--39909128 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
39909040 AACTCTGGAT
*
39909050 AGGAAAGCCTTTGTGACAAGCACTAGATATAA
1 AGGATAGCCTTTGTGACAAGCACTAGATATAA
* * * *
39909082 AGGATAGCCTTTGTGGCGAGTACTGGATATAA
1 AGGATAGCCTTTGTGACAAGCACTAGATATAA
* *
39909114 AGAATAGGCTTTGTG
1 AGGATAGCCTTTGTG
39909129 GCACAATTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.27
Consensus pattern (32 bp):
AGGATAGCCTTTGTGACAAGCACTAGATATAA
Found at i:39909249 original size:29 final size:29
Alignment explanation
Indices: 39909206--39909274 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
39909196 GTTTAAGAAC
* *
39909206 GCCTTTGTCGTAAATCTTTGAAAGGAAAT
1 GCCTTTGTGGCAAATCTTTGAAAGGAAAT
39909235 GCCTTTGTGGCAAATCTTTGAAAGGAAAT
1 GCCTTTGTGGCAAATCTTTGAAAGGAAAT
*
39909264 GCCTTTATGGC
1 GCCTTTGTGGC
39909275 GATCTCTGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (29 bp):
GCCTTTGTGGCAAATCTTTGAAAGGAAAT
Found at i:39915989 original size:60 final size:60
Alignment explanation
Indices: 39915892--39916011 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
39915882 GGCATTATAG
* *
39915892 AGGGATTATATGCTTATGTATTCTGGAGGAGATCTCACTCCTATTGGTTATATCAATTCT
1 AGGGATTATATGCTTATGTATTCTGGAAGAGACCTCACTCCTATTGGTTATATCAATTCT
* * *
39915952 AGGGATTATATGTTTATGTATTTTGGAAGAGACCTCACTCCTATTGGTTATATCGATTCT
1 AGGGATTATATGCTTATGTATTCTGGAAGAGACCTCACTCCTATTGGTTATATCAATTCT
39916012 TACTTCCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (60 bp):
AGGGATTATATGCTTATGTATTCTGGAAGAGACCTCACTCCTATTGGTTATATCAATTCT
Found at i:39918354 original size:34 final size:34
Alignment explanation
Indices: 39918311--39918383 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
39918301 TATGTATGTG
39918311 ATTATATGACTGGTTACTTCAGAATATTTATGAA
1 ATTATATGACTGGTTACTTCAGAATATTTATGAA
*
39918345 ATTATATGACTGGTTACTTCAGAATATTTATGAC
1 ATTATATGACTGGTTACTTCAGAATATTTATGAA
39918379 ATTAT
1 ATTAT
39918384 GAATGTCTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (34 bp):
ATTATATGACTGGTTACTTCAGAATATTTATGAA
Found at i:39918829 original size:41 final size:41
Alignment explanation
Indices: 39918772--39918857 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
39918762 GAGTTTAGGA
39918772 AAATCCATTGTAACACCCTATACCAACCTGGACACTAAGCC
1 AAATCCATTGTAACACCCTATACCAACCTGGACACTAAGCC
*
39918813 AAATCCATTGTAACACCCTATACCGACCTGGACACTAAGCC
1 AAATCCATTGTAACACCCTATACCAACCTGGACACTAAGCC
39918854 AAAT
1 AAAT
39918858 ATCGAGATGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (41 bp):
AAATCCATTGTAACACCCTATACCAACCTGGACACTAAGCC
Found at i:39922649 original size:8 final size:8
Alignment explanation
Indices: 39922636--39922665 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
39922626 TATGTCTATG
39922636 ATTTCACA
1 ATTTCACA
39922644 ATTTCACA
1 ATTTCACA
39922652 ATTTCACA
1 ATTTCACA
*
39922660 AATTCA
1 ATTTCA
39922666 AAAATTGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (8 bp):
ATTTCACA
Found at i:39922671 original size:17 final size:16
Alignment explanation
Indices: 39922636--39922678 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
39922626 TATGTCTATG
* *
39922636 ATTTCACAATTTCACA
1 ATTTCACAAATTCAAA
39922652 ATTTCACAAATTCAAA
1 ATTTCACAAATTCAAA
* *
39922668 AATTGACAAAT
1 ATTTCACAAAT
39922679 AAACATATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTTCACAAATTCAAA
Found at i:39932076 original size:46 final size:46
Alignment explanation
Indices: 39931561--39932055 Score: 936
Period size: 46 Copynumber: 10.8 Consensus size: 46
39931551 TGTAACCCGC
* * * *
39931561 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931607 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931653 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931699 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931745 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931791 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931837 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931883 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931929 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39931975 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
39932021 CCATAAGTGAAATCAGACTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
39932056 AATGCTCAAC
Statistics
Matches: 443, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 443 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:39936335 original size:49 final size:49
Alignment explanation
Indices: 39936263--39936361 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
39936253 GCTGTGAAAA
*
39936263 TGAACTGCTCATCGGTCTTTTCTTCCAATTTCTAGTCTCAGCCTCTACC
1 TGAACCGCTCATCGGTCTTTTCTTCCAATTTCTAGTCTCAGCCTCTACC
39936312 TGAACCGCTCATCGGTCTTTTCTTCCAATTTCTAGTCTCAGCCTCTACC
1 TGAACCGCTCATCGGTCTTTTCTTCCAATTTCTAGTCTCAGCCTCTACC
39936361 T
1 T
39936362 TTTTCTTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.16, C:0.33, G:0.12, T:0.38
Consensus pattern (49 bp):
TGAACCGCTCATCGGTCTTTTCTTCCAATTTCTAGTCTCAGCCTCTACC
Found at i:39938665 original size:46 final size:46
Alignment explanation
Indices: 39938598--39939094 Score: 908
Period size: 46 Copynumber: 10.8 Consensus size: 46
39938588 TGTAACCCGC
* * *
39938598 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938644 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938690 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938736 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938782 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938828 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938874 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938920 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39938966 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
39939011 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
39939058 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39939095 TGCTCAACCA
Statistics
Matches: 438, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
45 5 0.01
46 428 0.98
47 5 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:39939003 original size:20 final size:20
Alignment explanation
Indices: 39938978--39939049 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 20
39938968 ATAAGTGAAC
39938978 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
**
39938998 TCGGACATTCGCTACATCTC-ACGAAC
1 TCGGAC--T--C-A-A-CTCAACGAGT
39939024 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
39939044 TCGGAC
1 TCGGAC
39939050 ATTCGCATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
19 3 0.08
20 17 0.43
21 1 0.03
22 2 0.05
24 2 0.05
25 1 0.03
26 11 0.28
27 3 0.08
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGGACTCAACTCAACGAGT
Found at i:39940029 original size:22 final size:22
Alignment explanation
Indices: 39939997--39940040 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39939987 ATGGAATAAG
*
39939997 AACACTCAATTTTGGGATTACT
1 AACACTCAATTTCGGGATTACT
* *
39940019 AACACTTAATTTCGGGGTTACT
1 AACACTCAATTTCGGGATTACT
39940041 TCCACCTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (22 bp):
AACACTCAATTTCGGGATTACT
Found at i:39940137 original size:32 final size:31
Alignment explanation
Indices: 39940096--39940158 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
39940086 TCAAGAGAAC
39940096 TACATCTATAGCACGCACCGCTCTTCATCTG
1 TACATCTATAGCACGCACCGCTCTTCATCTG
* *
39940127 NTACATCTATAGCCCGCCCCGCTCTTCATCTG
1 -TACATCTATAGCACGCACCGCTCTTCATCTG
39940159 CCACTCTCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.38, G:0.13, T:0.29
Consensus pattern (31 bp):
TACATCTATAGCACGCACCGCTCTTCATCTG
Found at i:39944671 original size:27 final size:27
Alignment explanation
Indices: 39944628--39944760 Score: 144
Period size: 27 Copynumber: 4.9 Consensus size: 27
39944618 GCGAGGCTGC
39944628 CAGATAT-TGTGGCAGAGCCACCAGAA
1 CAGATATATGTGGCAGAGCCACCAGAA
* * *
39944654 CAGATATATGTGGTAGAGCCACTAGAT
1 CAGATATATGTGGCAGAGCCACCAGAA
* * *
39944681 CAGATA-ATTATGGCATAGCCACCAGGA
1 CAGATATA-TGTGGCAGAGCCACCAGAA
*
39944708 CAGATATATGTGGCAGAGCCACCAGAT
1 CAGATATATGTGGCAGAGCCACCAGAA
* * *
39944735 TAGATAAATTGTGGCATAGCCACCAG
1 CAGATATA-TGTGGCAGAGCCACCAG
39944761 GACGCTTCCT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
26 8 0.09
27 62 0.71
28 17 0.20
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATATGTGGCAGAGCCACCAGAA
Found at i:39944711 original size:54 final size:54
Alignment explanation
Indices: 39944628--39944763 Score: 202
Period size: 54 Copynumber: 2.5 Consensus size: 54
39944618 GCGAGGCTGC
* * * *
39944628 CAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGTAGAGCCACTAGAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGAT
*
39944681 CAGATAATTATGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGAT
1 CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGAT
*
39944735 TAGATAAATTGTGGCATAGCCACCAGGAC
1 CAGAT-AATTGTGGCATAGCCACCAGGAC
39944764 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
53 5 0.07
54 47 0.64
55 22 0.30
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (54 bp):
CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGAT
Found at i:39946345 original size:26 final size:26
Alignment explanation
Indices: 39946314--39946421 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
39946304 TGAAATGGCC
*
39946314 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39946340 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
39946366 ACCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39946392 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39946418 ATCA
1 ATCA
39946422 ATTTGTACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39952555 original size:27 final size:27
Alignment explanation
Indices: 39952521--39952649 Score: 147
Period size: 27 Copynumber: 4.8 Consensus size: 27
39952511 AGACTGCCAA
39952521 ATAT-TGTGGCAGAGCCACCAGAACAG
1 ATATATGTGGCAGAGCCACCAGAACAG
*
39952547 ATATATGTGGCAGAGCCACCAGATCAG
1 ATATATGTGGCAGAGCCACCAGAACAG
* *
39952574 ATA-ATTGTGGCATAGCCACTA-AGACAG
1 ATATA-TGTGGCAGAGCCACCAGA-ACAG
**
39952601 ATATATGTGGCAGAGCCACCAGATTAG
1 ATATATGTGGCAGAGCCACCAGAACAG
* *
39952628 ATAAATTGTGGCATAGCCACCA
1 ATATA-TGTGGCAGAGCCACCA
39952650 AGACGCTTCC
Statistics
Matches: 87, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.07
27 64 0.74
28 17 0.20
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (27 bp):
ATATATGTGGCAGAGCCACCAGAACAG
Found at i:39952591 original size:54 final size:55
Alignment explanation
Indices: 39952523--39952653 Score: 212
Period size: 54 Copynumber: 2.4 Consensus size: 55
39952513 ACTGCCAAAT
*
39952523 ATTGTGGCAGAGCCACC-AGAACAGATATATGTGGCAGAGCCACCAGATCAGAT-A
1 ATTGTGGCATAGCCACCAAG-ACAGATATATGTGGCAGAGCCACCAGATCAGATAA
* *
39952577 ATTGTGGCATAGCCACTAAGACAGATATATGTGGCAGAGCCACCAGATTAGATAA
1 ATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGCCACCAGATCAGATAA
39952632 ATTGTGGCATAGCCACCAAGAC
1 ATTGTGGCATAGCCACCAAGAC
39952654 GCTTCCTCCA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
54 47 0.66
55 24 0.34
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (55 bp):
ATTGTGGCATAGCCACCAAGACAGATATATGTGGCAGAGCCACCAGATCAGATAA
Found at i:39954240 original size:26 final size:26
Alignment explanation
Indices: 39954205--39954312 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
39954195 TGAAATGGCC
* *
39954205 ATCATAGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39954231 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
39954257 ACCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39954283 ACCATGGAACATTTACCTAACCCGTT
1 ATCATGGAACATTTACCTAACCCATT
39954309 ATCA
1 ATCA
39954313 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39958927 original size:47 final size:47
Alignment explanation
Indices: 39958869--39959310 Score: 695
Period size: 47 Copynumber: 9.4 Consensus size: 47
39958859 CAGCCAAGAC
*
39958869 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
39958916 AGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
39958963 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
39959010 AATGTATATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
39959057 AGTGTATATGTGTGCTAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
39959104 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
39959151 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
39959198 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGAGGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
39959245 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
39959292 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
39959311 TCCCGAAGGG
Statistics
Matches: 365, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 365 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:39959485 original size:37 final size:37
Alignment explanation
Indices: 39959429--39959507 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
39959419 CCGAGCTCTA
* *
39959429 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTGTGTCCGGGT
*
39959466 AAGACCCGATAACTTCGTGTGGAGATTGTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTGTGTCCGGGT
39959503 AAGAC
1 AAGAC
39959508 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTGTGTCCGGGT
Found at i:39961291 original size:41 final size:41
Alignment explanation
Indices: 39961245--39961334 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
39961235 CACAAAAATA
* * * *
39961245 AATTCATGGTTACCGAAGTACAAACGAGGGCA-TGTATGTGC
1 AATTCAAGGGTACCGAAGTACAAACAAGGG-AGCGTATGTGC
*
39961286 AATTCAAGGGTACCGAAGTACAAATAAGGGAGCGTATGTGC
1 AATTCAAGGGTACCGAAGTACAAACAAGGGAGCGTATGTGC
39961327 AATTCAAG
1 AATTCAAG
39961335 AATAATTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.02
41 42 0.98
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (41 bp):
AATTCAAGGGTACCGAAGTACAAACAAGGGAGCGTATGTGC
Found at i:39965019 original size:14 final size:16
Alignment explanation
Indices: 39964997--39965030 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
39964987 AGTGATCGAA
39964997 AAAAGTAC-AAAAAAT
1 AAAAGTACAAAAAAAT
39965012 AAAA-TACAAAAAAAT
1 AAAAGTACAAAAAAAT
39965027 AAAA
1 AAAA
39965031 AATATTACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAGTACAAAAAAAT
Found at i:39970789 original size:45 final size:45
Alignment explanation
Indices: 39970710--39970872 Score: 256
Period size: 45 Copynumber: 3.6 Consensus size: 45
39970700 TAGCATTTTC
*
39970710 CCTGCTAGGCTCGAA-GCCCGAATAGTATCTCACCGGCATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATAG
* * *
39970754 CCTGCTAGGCTCAAAGGCCCGAGTGGTATTTCACCGGCATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATAG
*
39970799 CCTGCTAGGCTCAAAGACCCGAATAGTATCTCACCGGCATTATAG
1 CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATAG
* *
39970844 CCTGCTAGGTTCAAAGGCCTGAATAGTAT
1 CCTGCTAGGCTCAAAGGCCCGAATAGTAT
39970873 TGTGCGGTGT
Statistics
Matches: 107, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 14 0.13
45 93 0.87
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (45 bp):
CCTGCTAGGCTCAAAGGCCCGAATAGTATCTCACCGGCATTATAG
Found at i:39978510 original size:45 final size:45
Alignment explanation
Indices: 39978425--39978555 Score: 203
Period size: 45 Copynumber: 3.0 Consensus size: 45
39978415 TTTTATCAAT
** *
39978425 TCACCGGCATT-TTTCCTACTAGGCTCAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
39978468 TCACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
39978513 TCACCGGCATTATAGCCTGCTACGCTCAAAGGCCCGAATAGTA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
39978556 CTGTGCGATA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 10 0.12
44 15 0.19
45 55 0.69
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:39985468 original size:28 final size:27
Alignment explanation
Indices: 39985423--39985505 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 27
39985413 ATGCCATTGA
39985423 ATACTCAATATTCTGCACACTAAGTGCC
1 ATACTCAATA-TCTGCACACTAAGTGCC
*
39985451 ATACTCGATATCTAGCACACTAAGTGCC
1 ATACTCAATATCT-GCACACTAAGTGCC
** *
39985479 ATTTTCAATGTCTCGCACACTAAGTGC
1 ATACTCAATATCT-GCACACTAAGTGC
39985506 AATGCTCGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 3 0.06
28 45 0.94
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (27 bp):
ATACTCAATATCTGCACACTAAGTGCC
Found at i:39985505 original size:56 final size:56
Alignment explanation
Indices: 39985437--39985562 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 56
39985427 TCAATATTCT
*
39985437 GCACACTAAGTGCCATACTCGATATCTAGCACACTAAGTGCCATTTTCAATGTCTC
1 GCACACTAAGTGCCATACTCGATATCTAGCACACTAAATGCCATTTTCAATGTCTC
* * * * *
39985493 GCACACTAAGTGCAATGCTCGATGTCTTGCACATTAAATGCCATTTTCAATGTCTC
1 GCACACTAAGTGCCATACTCGATATCTAGCACACTAAATGCCATTTTCAATGTCTC
* *
39985549 ACACACTAACTGCC
1 GCACACTAAGTGCC
39985563 GTACATAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (56 bp):
GCACACTAAGTGCCATACTCGATATCTAGCACACTAAATGCCATTTTCAATGTCTC
Found at i:39985517 original size:28 final size:28
Alignment explanation
Indices: 39985437--39985562 Score: 126
Period size: 28 Copynumber: 4.5 Consensus size: 28
39985427 TCAATATTCT
* * * *
39985437 GCACACTAAGTGCCATACTCGATATCTA
1 GCACACTAAGTGCCATTCTCAATGTCTC
*
39985465 GCACACTAAGTGCCATTTTCAATGTCTC
1 GCACACTAAGTGCCATTCTCAATGTCTC
* * * *
39985493 GCACACTAAGTGCAATGCTCGATGTCTT
1 GCACACTAAGTGCCATTCTCAATGTCTC
* * *
39985521 GCACATTAAATGCCATTTTCAATGTCTC
1 GCACACTAAGTGCCATTCTCAATGTCTC
* *
39985549 ACACACTAACTGCC
1 GCACACTAAGTGCC
39985563 GTACATAGCC
Statistics
Matches: 78, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 78 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATGTCTC
Found at i:39985647 original size:40 final size:40
Alignment explanation
Indices: 39985569--39985647 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
39985559 TGCCGTACAT
* * *
39985569 AGCCGAAGATATCTCAAATCGCACACTAAGTTCCATATTC
1 AGCCGAAGATATCTCAAATCGCACACAAAATGCCATATTC
* * * *
39985609 AGCCGAAGCTATGTCGAATCGCACACAAAATGCTATATT
1 AGCCGAAGATATCTCAAATCGCACACAAAATGCCATATT
39985648 TAGTCGATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
AGCCGAAGATATCTCAAATCGCACACAAAATGCCATATTC
Found at i:39990027 original size:40 final size:40
Alignment explanation
Indices: 39989983--39990244 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39989973 GCTCCTCGTT
* *
39989983 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39990023 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39990063 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39990102 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39990141 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39990180 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39990221 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39990245 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39998235 original size:29 final size:29
Alignment explanation
Indices: 39998172--39998239 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
39998162 TAATCAACCG
39998172 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
39998201 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
39998230 CGCACACTTA
1 CGCACACTTA
39998240 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:39998351 original size:174 final size:174
Alignment explanation
Indices: 39998061--39998388 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
39998051 AACTCAAGGT
* *
39998061 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
39998126 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
39998191 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
39998235 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
39998300 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
*
39998365 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
39998389 TGTACAATTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:39998380 original size:29 final size:30
Alignment explanation
Indices: 39998341--39998419 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
39998331 CTTAATAATC
39998341 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
39998371 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
39998400 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
39998420 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:40003847 original size:20 final size:22
Alignment explanation
Indices: 40003819--40003868 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
40003809 TGTTATGTAT
*
40003819 GTATCGATATTGCCTTT-A-TG
1 GTATTGATATTGCCTTTAAGTG
* *
40003839 GTATTGATATTTCTTTTAAGTG
1 GTATTGATATTGCCTTTAAGTG
40003861 GTATTGAT
1 GTATTGAT
40003869 GCCACATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.56
21 1 0.04
22 10 0.40
ACGTcount: A:0.22, C:0.08, G:0.20, T:0.50
Consensus pattern (22 bp):
GTATTGATATTGCCTTTAAGTG
Found at i:40009509 original size:38 final size:38
Alignment explanation
Indices: 40009458--40009534 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
40009448 GTGTTCGATT
*
40009458 TTTTTTGGGGGGGGGGGGGGGGGTTCTATTCTTTAGGC
1 TTTTTTGGGGGGGGGGGGAGGGGTTCTATTCTTTAGGC
*
40009496 TTTTTTGGGGGGGGGGGGAGGTGTTCTATTCTTTAGGC
1 TTTTTTGGGGGGGGGGGGAGGGGTTCTATTCTTTAGGC
40009534 T
1 T
40009535 CATTCACTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.06, C:0.08, G:0.47, T:0.39
Consensus pattern (38 bp):
TTTTTTGGGGGGGGGGGGAGGGGTTCTATTCTTTAGGC
Found at i:40014863 original size:13 final size:13
Alignment explanation
Indices: 40014845--40014884 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40014835 AGTTTGGCAA
*
40014845 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
40014858 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
40014871 TGTTTTTGAAAAG
1 TGCTTTTGAAAAG
40014884 T
1 T
40014885 TTGGTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40029114 original size:184 final size:184
Alignment explanation
Indices: 40028805--40029172 Score: 736
Period size: 184 Copynumber: 2.0 Consensus size: 184
40028795 GAAAATGTCC
40028805 TTTAGTTTAAAGAAGATATATTATTTGAGGGAATTTTACTATTTTTAGTTTTTCTTTAAAAAACC
1 TTTAGTTTAAAGAAGATATATTATTTGAGGGAATTTTACTATTTTTAGTTTTTCTTTAAAAAACC
40028870 AATTAAAACTTTGCATATGGTGAAATTTGAACCCATGAAATTTGCAATAATAAAACATTAATTTT
66 AATTAAAACTTTGCATATGGTGAAATTTGAACCCATGAAATTTGCAATAATAAAACATTAATTTT
40028935 CACACTCAACTAAAACTTTACTTTAATTTCTTTAATACATTTTAATATTATTTT
131 CACACTCAACTAAAACTTTACTTTAATTTCTTTAATACATTTTAATATTATTTT
40028989 TTTAGTTTAAAGAAGATATATTATTTGAGGGAATTTTACTATTTTTAGTTTTTCTTTAAAAAACC
1 TTTAGTTTAAAGAAGATATATTATTTGAGGGAATTTTACTATTTTTAGTTTTTCTTTAAAAAACC
40029054 AATTAAAACTTTGCATATGGTGAAATTTGAACCCATGAAATTTGCAATAATAAAACATTAATTTT
66 AATTAAAACTTTGCATATGGTGAAATTTGAACCCATGAAATTTGCAATAATAAAACATTAATTTT
40029119 CACACTCAACTAAAACTTTACTTTAATTTCTTTAATACATTTTAATATTATTTT
131 CACACTCAACTAAAACTTTACTTTAATTTCTTTAATACATTTTAATATTATTTT
40029173 ACTTACTTTA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 184 1.00
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (184 bp):
TTTAGTTTAAAGAAGATATATTATTTGAGGGAATTTTACTATTTTTAGTTTTTCTTTAAAAAACC
AATTAAAACTTTGCATATGGTGAAATTTGAACCCATGAAATTTGCAATAATAAAACATTAATTTT
CACACTCAACTAAAACTTTACTTTAATTTCTTTAATACATTTTAATATTATTTT
Found at i:40035760 original size:26 final size:27
Alignment explanation
Indices: 40035710--40035761 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
40035700 TTTGATTGGT
*
40035710 TAAGATTATTTTATTATTATTTTAATA
1 TAAGATTATTTTATTATTATGTTAATA
40035737 TAAGA-TATTTTATTATT-TAGTTAAT
1 TAAGATTATTTTATTATTAT-GTTAAT
40035762 GGTTAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.74
27 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (27 bp):
TAAGATTATTTTATTATTATGTTAATA
Found at i:40037727 original size:223 final size:223
Alignment explanation
Indices: 40037318--40037768 Score: 667
Period size: 223 Copynumber: 2.0 Consensus size: 223
40037308 CCTATAGAGG
*
40037318 TCATACGACACTTTCAGAATAATCGCAGCATTGCTGCCAATATATTGGCGAAATATTACCTTACA
1 TCATACGACACTTTCAGAATAATCGCAGCATTGCTGCCAATATATTGGCGAAATATCACCTTACA
40037383 TAGAATACTTACTCCTCATAAAACATAACCCGTCCCATAGCCAGATACAGACAGAACATCAGATA
66 TAGAATACTTACTCCTCATAAAACATAACCCGTCCCATAGCCAGATACAGACAGAACATCAGATA
* * * *
40037448 AAATAGAATAACATATACCAGAATGTATATCACATGCATGCTTGTATAACAAATACTAAACATGC
131 AAACAAAATAACAGATACCAGAACGTATATCACATGCATGCTTGTATAACAAATACTAAACATGC
40037513 TCATACATAACAGAATAGATCATACATA
196 TCATACATAACAGAATAGATCATACATA
* * * * * *
40037541 -CATACGACACTTTTCAGAATAATTGCAGCATTGGTGCGAGTATATTGGTGAAATATCGCCTTAC
1 TCATACGACAC-TTTCAGAATAATCGCAGCATTGCTGCCAATATATTGGCGAAATATCACCTTAC
* * * *
40037605 ATAGAATACTTCCTTCTCATAAAACATAACCCG-CCTTATAGCCAGATACAGACAGAGCATCAGA
65 ATAGAATACTTACTCCTCATAAAACATAACCCGTCC-CATAGCCAGATACAGACAGAACATCAGA
* *
40037669 TAAAACAAAATAACAGATACCAGAACGTATATTACATGTATGCTCATGTA-AA-AAATACTAAAC
129 TAAAACAAAATAACAGATACCAGAACGTATATCACATGCATGCT--TGTATAACAAATACTAAAC
* *
40037732 ATGCTCATACATAACATAATATATCATACATA
192 ATGCTCATACATAACAGAATAGATCATACATA
40037764 TCATA
1 TCATA
40037769 TTACACTATA
Statistics
Matches: 204, Mismatches: 19, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
222 12 0.06
223 182 0.89
224 6 0.03
225 4 0.02
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (223 bp):
TCATACGACACTTTCAGAATAATCGCAGCATTGCTGCCAATATATTGGCGAAATATCACCTTACA
TAGAATACTTACTCCTCATAAAACATAACCCGTCCCATAGCCAGATACAGACAGAACATCAGATA
AAACAAAATAACAGATACCAGAACGTATATCACATGCATGCTTGTATAACAAATACTAAACATGC
TCATACATAACAGAATAGATCATACATA
Found at i:40038584 original size:13 final size:13
Alignment explanation
Indices: 40038566--40038617 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
40038556 TGGCAGCTAG
40038566 GAAAAATAAAGAA
1 GAAAAATAAAGAA
40038579 GAAAAATAAAG-A
1 GAAAAATAAAGAA
* *
40038591 GTAAAGAGAAAGAA
1 G-AAAAATAAAGAA
* *
40038605 CAAAAAAAAAGAA
1 GAAAAATAAAGAA
40038618 ACATGAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 2 0.06
13 29 0.91
14 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06
Consensus pattern (13 bp):
GAAAAATAAAGAA
Found at i:40039613 original size:22 final size:22
Alignment explanation
Indices: 40039581--40039625 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40039571 GATGATTGTG
40039581 GCACTTCGGTGCAAATGAAAGT
1 GCACTTCGGTGCAAATGAAAGT
* * *
40039603 GCACTTTGGTGCAAGTGATAGT
1 GCACTTCGGTGCAAATGAAAGT
40039625 G
1 G
40039626 GCTCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (22 bp):
GCACTTCGGTGCAAATGAAAGT
Found at i:40042085 original size:47 final size:48
Alignment explanation
Indices: 40042020--40042148 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 48
40042010 ATCTCTACGC
* *
40042020 CGATTCCATGTCCCAGACATGGTCTTACACTAGCTA-TCG-T-AATGT
1 CGATGCCATGTCCTAGACATGGTCTTACACTAGCTACTCGCTCAATGT
40042065 GGCTGATG-CATGTCCTAGACAT-GTCTTACACTAGC-ACTCGTCTCAATGT
1 --C-GATGCCATGTCCTAGACATGGTCTTACACTAGCTACTCG-CTCAATGT
* *
40042114 CGATGCCATATCCTAGATATGGTCTTACACTAGCT
1 CGATGCCATGTCCTAGACATGGTCTTACACTAGCT
40042149 CTCACAAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
45 1 0.01
46 20 0.29
47 27 0.39
48 17 0.24
49 5 0.07
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (48 bp):
CGATGCCATGTCCTAGACATGGTCTTACACTAGCTACTCGCTCAATGT
Found at i:40042102 original size:94 final size:92
Alignment explanation
Indices: 40041784--40042148 Score: 288
Period size: 94 Copynumber: 3.8 Consensus size: 92
40041774 CAAAATTGCC
* * *
40041784 GATGCCATGTCCTAGACATGGTCTTACACTGGCTATCTTCAT-TGAGGCCGATGCCATATCCCAG
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-A-C-TCATCTTA-GCCGATGCCATATCCCAG
* * *
40041848 ACATGGTCTTACACTAGCTCTTGTGTATAAGT-GCT
60 ACATGGTCTTACACTAGCT-AT-CGTA-ATGTGGCT
** * * ** *
40041883 GATGCATGTCCCAGACATGTCTTACACTAGCACGAAGCTTAGCCGATG-CATGTCCCAGTTA-CG
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTTAGCCGATGCCATATCCCAGACATGG
* * * * * *
40041946 TCTTACACTGGCTACCATCATTGAGGCC
66 TCTTACACTAGCTATCGT-AATGTGGCT
* * * * * *
40041974 AATGCATGTCCCCAGCCACGTCTTACACTGGCACTCATCTCTACGCCGATTCCATGTCCCAGACA
1 GATGCATGT-CCCAGACATGTCTTACACTAGCACTCATCT-TA-GCCGATGCCATATCCCAGACA
40042039 TGGTCTTACACTAGCTATCGTAATGTGGCT
63 TGGTCTTACACTAGCTATCGTAATGTGGCT
* * * * * *
40042069 GATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCAATGTCGATGCCATATCCTAGATAT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCT-TA-GCCGATGCCATATCCCAGACAT
40042134 GGTCTTACACTAGCT
64 GGTCTTACACTAGCT
40042149 CTCACAAAAC
Statistics
Matches: 209, Mismatches: 49, Indels: 21
0.75 0.18 0.08
Matches are distributed among these distances:
90 2 0.01
91 11 0.05
92 37 0.18
93 12 0.06
94 73 0.35
95 28 0.13
96 17 0.08
97 12 0.06
98 13 0.06
99 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTTAGCCGATGCCATATCCCAGACATGG
TCTTACACTAGCTATCGTAATGTGGCT
Found at i:40042145 original size:48 final size:48
Alignment explanation
Indices: 40041993--40042147 Score: 151
Period size: 48 Copynumber: 3.3 Consensus size: 48
40041983 CCCCAGCCAC
* * * * * * *
40041993 GTCTTACACTGGCACTCATCTCTACGCCGATTCCATGTCCCAGACATG
1 GTCTTACACTAGCACTCGTCTCAATGTCGATGCCATGTCCTAGACATG
40042041 GTCTTACACTAGCTA-TCG--T-AATGTGGCTGATG-CATGTCCTAGACAT-
1 GTCTTACACTAGC-ACTCGTCTCAATGT--C-GATGCCATGTCCTAGACATG
* *
40042087 GTCTTACACTAGCACTCGTCTCAATGTCGATGCCATATCCTAGATATG
1 GTCTTACACTAGCACTCGTCTCAATGTCGATGCCATGTCCTAGACATG
40042135 GTCTTACACTAGC
1 GTCTTACACTAGC
40042148 TCTCACAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
45 3 0.03
46 21 0.24
47 27 0.31
48 31 0.35
49 6 0.07
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (48 bp):
GTCTTACACTAGCACTCGTCTCAATGTCGATGCCATGTCCTAGACATG
Found at i:40046383 original size:47 final size:47
Alignment explanation
Indices: 40046277--40046446 Score: 152
Period size: 47 Copynumber: 3.6 Consensus size: 47
40046267 ACGAAGTTTA
* * * *
40046277 GCCGATGCATGTCCTAGTCACGTCTTACACTGGCTACCTTCATTGAG
1 GCCGATGCATGTCCCAGACACGTCTTACATTGGCTACCTTCATTGAC
*
40046324 GCCGATGCATGTCCCAGACACGTCTTACATTGGC-A-C-TCATCTCTAC
1 GCCGATGCATGTCCCAGACACGTCTTACATTGGCTACCTTCAT-T-GAC
* ** * *
40046370 GCCGATGCGATGTCCCAGACATGGTCTTACATTGGCTGTCGTAATATG--
1 GCCGATGC-ATGTCCCAGACA-CGTCTTACATTGGCTACCTTCAT-TGAC
* *
40046418 GCTGATGCATGTCCTAGACACGTCTTACA
1 GCCGATGCATGTCCCAGACACGTCTTACA
40046447 CTAGCCCTCG
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 18 0.17
47 54 0.52
48 20 0.19
50 1 0.01
51 4 0.04
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACACGTCTTACATTGGCTACCTTCATTGAC
Found at i:40046427 original size:94 final size:94
Alignment explanation
Indices: 40046327--40046500 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
40046317 CATTGAGGCC
* * * *
40046327 GATGCATGTCCCAGACACGTCTTACATTGGCACTCATCTCTACGCCGATGCGATGTCCCAGACAT
1 GATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAACGCCGATGCCATGTCCCAGACAT
*
40046392 GGTCTTACATTGGCTGTCGTAATATGGCT
66 GGTCTTACACTGGCTGTCGTAATATGGCT
* * * * *
40046421 GATGCATGTCCTAGACACGTCTTACACTAGCCCTCGTTTCAATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAACGCCGATGCCATGTCCCAGACAT
40046486 GGTCTTACACTGGCT
66 GGTCTTACACTGGCT
40046501 CTCATAAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 70 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.28
Consensus pattern (94 bp):
GATGCATGTCCCAGACACGTCTTACACTAGCACTCATCTCAACGCCGATGCCATGTCCCAGACAT
GGTCTTACACTGGCTGTCGTAATATGGCT
Found at i:40049547 original size:51 final size:50
Alignment explanation
Indices: 40049486--40049591 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 50
40049476 TGAATAGCCA
40049486 TTGAAGTCGTTCGACAACATCTGAGGTAAGTCTTCGAGTAATGACCCTAC
1 TTGAAGTCGTTCGACAACATCTGAGGTAAGTCTTCGAGTAATGACCCTAC
* *
40049536 GTTGAAGTCGTTCGACGACATTTGAGGTAAGTCTTCGAGTAATGACCCTAC
1 -TTGAAGTCGTTCGACAACATCTGAGGTAAGTCTTCGAGTAATGACCCTAC
40049587 TTGAA
1 TTGAA
40049592 TTATATTGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 5 0.09
51 48 0.91
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (50 bp):
TTGAAGTCGTTCGACAACATCTGAGGTAAGTCTTCGAGTAATGACCCTAC
Found at i:40051067 original size:40 final size:40
Alignment explanation
Indices: 40049801--40051066 Score: 2084
Period size: 40 Copynumber: 31.6 Consensus size: 40
40049791 AGCATTGGAT
* *
40049801 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40049841 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40049881 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40049921 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40049961 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050001 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050041 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050081 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050121 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050161 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050201 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050241 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050281 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050321 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050361 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050401 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050441 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050481 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050521 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
40050561 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * *
40050601 TATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* ** * *
40050641 TATATCCGGGCTGTGACCCGAAGGCAATTATGCGAGA-TGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGA-ATTGA
* * * *
40050681 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050721 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050761 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050801 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050841 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050881 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050921 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40050961 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* * * *
40051001 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
* *
40051041 TATGTCCGGGTTAAGACCCGAAGGCA
1 TATATCCGGGATAAGACCCGAAGGCA
40051067 AATGTGTTTG
Statistics
Matches: 1210, Mismatches: 14, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
40 1210 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (40 bp):
TATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGA
Found at i:40055415 original size:40 final size:40
Alignment explanation
Indices: 40055360--40055489 Score: 233
Period size: 40 Copynumber: 3.2 Consensus size: 40
40055350 ATGTGCATGA
*
40055360 GCATTTGTGCGAGTTGATATATCTGGGCTAAGACCCGAAG
1 GCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAG
40055400 GCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAG
1 GCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAG
* *
40055440 GCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAGG
1 GCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAG
40055480 GCATTTGTGC
1 GCATTTGTGC
40055490 TTGTGGTTAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (40 bp):
GCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAG
Found at i:40055501 original size:80 final size:79
Alignment explanation
Indices: 40055360--40055509 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 79
40055350 ATGTGCATGA
* * *
40055360 GCATTTGTGCGAGTTGATATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCG
1 GCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGATATATCC-
40055425 GGCTAAGACCCGAAG
65 GGCTAAGACCCGAAG
* ** *
40055440 GCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAGGGCATTTGTGCTTGTGGTTATATCCG
1 GCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGATATATCCG
40055505 GCTAA
66 GCTAA
40055510 ATTCCGAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 6 0.10
80 57 0.90
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (79 bp):
GCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGGATATATCCG
GCTAAGACCCGAAG
Found at i:40057530 original size:67 final size:67
Alignment explanation
Indices: 40057452--40057761 Score: 593
Period size: 67 Copynumber: 4.6 Consensus size: 67
40057442 ATATATATAT
*
40057452 ATATATGTGGCGAAGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
40057517 AG
66 AG
40057519 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
40057584 AG
66 AG
40057586 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
40057651 AG
66 AG
40057653 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
1 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
40057718 AG
66 AG
* *
40057720 ATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCTGCCAGA
1 ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGA
40057762 ATGCTTCCTC
Statistics
Matches: 240, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 240 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (67 bp):
ATATATGTGGCGAGGCCACCAGATTGCAGTGAGGGTGCCAGATATTGTGACGAAATCACCAGAAC
AG
Found at i:40062749 original size:27 final size:26
Alignment explanation
Indices: 40062701--40062760 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
40062691 GCGAGGTTGC
* *
40062701 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCA-AAA
* * *
40062728 CAGATATTGTGGCTAGGCCACCAAAA
1 CAGATATTGTGACGAAGCCACCAAAA
40062754 CAGATAT
1 CAGATAT
40062761 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAAAA
Found at i:40062803 original size:71 final size:67
Alignment explanation
Indices: 40062728--40062869 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
40062718 TCACCAGATA
* * * *
40062728 CAGATATTGTGGCTAGGCCACCAAAACAGATATATATATGTGGCGAAGCCACCAGATTGTAGCGA
1 CAGATATTGTGACGAAGCCACCAAAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
40062793 GGCTGC
62 GGCTGC
* * *
40062799 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAAAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
40062864 GC
66 GC
40062866 CAGA
1 CAGA
40062870 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 40 0.62
71 24 0.38
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAAAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:40062847 original size:27 final size:26
Alignment explanation
Indices: 40062799--40062850 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40062789 GCGAGGCTGC
*
40062799 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40062825 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
40062851 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40068824 original size:30 final size:30
Alignment explanation
Indices: 40068790--40068858 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
40068780 TCCTCCAGTA
*
40068790 GCCAAAGCTAGTTTAAATCGCACACTTAGT
1 GCCAAAGCTAATTTAAATCGCACACTTAGT
**
40068820 GCCAAAATTAATTTAAATCGCACACTTAGT
1 GCCAAAGCTAATTTAAATCGCACACTTAGT
40068850 GCCAAAGCT
1 GCCAAAGCT
40068859 TCCGATTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (30 bp):
GCCAAAGCTAATTTAAATCGCACACTTAGT
Found at i:40075625 original size:27 final size:27
Alignment explanation
Indices: 40075595--40075744 Score: 124
Period size: 27 Copynumber: 5.6 Consensus size: 27
40075585 CCTTAATCGA
40075595 TAAAATAACTGTTTTGCCCTTTTGTGG
1 TAAAATAACTGTTTTGCCCTTTTGTGG
* * * *
40075622 TAAAATGATTGTTTTGCCCTTATGAGG
1 TAAAATAACTGTTTTGCCCTTTTGTGG
40075649 TAAAATGAA-TGTTTTG-CCTTTATGTGG
1 TAAAAT-AACTGTTTTGCCCTTT-TGTGG
* * * **
40075676 TAAAATTATTGTTTTGCCCTTATAAGG
1 TAAAATAACTGTTTTGCCCTTTTGTGG
* * ** *
40075703 TAAAATTACTATTTTGTTCTTTTATGG
1 TAAAATAACTGTTTTGCCCTTTTGTGG
* *
40075730 TAAGATGACTGTTTT
1 TAAAATAACTGTTTT
40075745 ACCCCTATGT
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
26 5 0.05
27 89 0.90
28 5 0.05
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (27 bp):
TAAAATAACTGTTTTGCCCTTTTGTGG
Found at i:40075698 original size:54 final size:54
Alignment explanation
Indices: 40075595--40075744 Score: 187
Period size: 54 Copynumber: 2.8 Consensus size: 54
40075585 CCTTAATCGA
*
40075595 TAAAATAACTGTTTTGCCCTTTTGTGGTAAAATGATTGTTTTGCCCTTATGAGG
1 TAAAATAACTGTTTTGCCCTTTTGTGGTAAAATGATTGTTTTGCCCTTATAAGG
*
40075649 TAAAATGAA-TGTTTTG-CCTTTATGTGGTAAAATTATTGTTTTGCCCTTATAAGG
1 TAAAAT-AACTGTTTTGCCCTTT-TGTGGTAAAATGATTGTTTTGCCCTTATAAGG
* * ** * * *
40075703 TAAAATTACTATTTTGTTCTTTTATGGTAAGATGACTGTTTT
1 TAAAATAACTGTTTTGCCCTTTTGTGGTAAAATGATTGTTTT
40075745 ACCCCTATGT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
53 6 0.07
54 71 0.86
55 6 0.07
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (54 bp):
TAAAATAACTGTTTTGCCCTTTTGTGGTAAAATGATTGTTTTGCCCTTATAAGG
Found at i:40076925 original size:31 final size:30
Alignment explanation
Indices: 40076848--40076960 Score: 122
Period size: 31 Copynumber: 3.7 Consensus size: 30
40076838 TTAGTCTTGA
*
40076848 CATATACTGGGCCGAAGCC-TTTCATTTAAT
1 CATATACTGGGCCGAAGCCTTTTCA-TAAAT
** **
40076878 GGT-TACTGGGTTGAAGCCTTTTCATAAAT
1 CATATACTGGGCCGAAGCCTTTTCATAAAT
*
40076907 TATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
*
40076938 CATATCATTGGGCCGAAGCCTTT
1 CATAT-ACTGGGCCGAAGCCTTT
40076961 ACTGTAAACG
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.26
30 7 0.10
31 44 0.64
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (30 bp):
CATATACTGGGCCGAAGCCTTTTCATAAAT
Found at i:40077249 original size:26 final size:26
Alignment explanation
Indices: 40077179--40077274 Score: 144
Period size: 26 Copynumber: 3.8 Consensus size: 26
40077169 CTCTTTTAAT
*
40077179 AACTGGAGCA-AAGCCC-TTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
40077203 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
* *
40077228 AACTGAGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
40077254 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
40077275 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 15 0.23
25 17 0.26
26 34 0.52
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:40078101 original size:27 final size:27
Alignment explanation
Indices: 40078071--40078162 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
40078061 GGGCACATTC
*
40078071 GTCATTTTACCATACAGGGG-TATTACG
1 GTCATTTTACCCTACAGGGGCT-TTACG
* *
40078098 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCCTACAGGGGCTTTACG
40078125 GTC-TCTTTACCCTACAGGGGCTTTACG
1 GTCAT-TTTACCCTACAGGGGCTTTACG
*
40078152 GTCTTTTTACC
1 GTCATTTTACC
40078163 TAATAGGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
27 55 0.96
28 2 0.04
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCTTTACG
Found at i:40078255 original size:28 final size:28
Alignment explanation
Indices: 40078215--40078299 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 28
40078205 GGTAAATCTA
40078215 TAAACCAAGGGTATTT-CAGTAATTTTGT
1 TAAACCAAGGGTATTTCCA-TAATTTTGT
*
40078243 TAAACCAATGGTATTTCCATAATTTT-T
1 TAAACCAAGGGTATTTCCATAATTTTGT
* * *
40078270 AGAAAGTCAAGGGTATTTCCATAACTTTGT
1 -TAAA-CCAAGGGTATTTCCATAATTTTGT
40078300 AAATTAGGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 25 0.52
29 21 0.44
30 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (28 bp):
TAAACCAAGGGTATTTCCATAATTTTGT
Found at i:40078393 original size:81 final size:81
Alignment explanation
Indices: 40078304--40078539 Score: 323
Period size: 81 Copynumber: 2.9 Consensus size: 81
40078294 CTTTGTAAAT
* *
40078304 TAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCATAAACCAGTGGTATTT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTATAAACCAGTGGTATTT
*
40078369 TGGTAATTTTACAAAC
66 TAGTAATTTTACAAAC
* * * *
40078385 TAGGGGTATTTTGATAATTTTACAAATTGAGGGTATTTCAGTAATTTTACAAACCAATGGTATTT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTATAAACCAGTGGTATTT
* *
40078450 TAGCAATTTTACAGAC
66 TAGTAATTTTACAAAC
** * * *
40078466 TA-GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTATAAACTGAG-GGTATT
1 TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTATAAAC-CAGTGGTATT
40078529 TTAGTAATTTT
65 TTAGTAATTTT
40078540 GTAAATCGAG
Statistics
Matches: 135, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 60 0.44
81 75 0.56
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (81 bp):
TAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTATAAACCAGTGGTATTT
TAGTAATTTTACAAAC
Found at i:40078544 original size:27 final size:27
Alignment explanation
Indices: 40078307--40078539 Score: 231
Period size: 27 Copynumber: 8.7 Consensus size: 27
40078297 TGTAAATTAG
* *
40078307 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTTACAAACTGA
* * * *
40078334 GGGTATTTCGGTAATTTCATAAAC-CA
1 GGGTATTTTGGTAATTTTACAAACTGA
40078360 GTGGTATTTTGGTAATTTTACAAACT-A
1 G-GGTATTTTGGTAATTTTACAAACTGA
* *
40078387 GGGGTATTTTGATAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAACTGA
** **
40078415 GGGTATTTCAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTGA
* * * *
40078442 TGGTATTTTAGCAATTTTACAGACT-A
1 GGGTATTTTGGTAATTTTACAAACTGA
**
40078468 GGGTATTTTGGTAATTTTACTGA-TCGA
1 GGGTATTTTGGTAATTTTACAAACT-GA
*
40078495 GGGTATTTTGGTAATTTTATAAACTGA
1 GGGTATTTTGGTAATTTTACAAACTGA
*
40078522 GGGTATTTTAGTAATTTT
1 GGGTATTTTGGTAATTTT
40078540 GTAAATCGAG
Statistics
Matches: 170, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
25 1 0.01
26 22 0.13
27 144 0.85
28 3 0.02
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTGA
Found at i:40078550 original size:27 final size:27
Alignment explanation
Indices: 40078307--40078673 Score: 204
Period size: 27 Copynumber: 13.6 Consensus size: 27
40078297 TGTAAATTAG
* **
40078307 GGGTATTTTGGTAATTTTACAAATTAA
1 GGGTATTTTGGTAATTTTATAAATCGA
* * *
40078334 GGGTATTTCGGTAATTTCATAAA-CCA
1 GGGTATTTTGGTAATTTTATAAATCGA
* *
40078360 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTTTATAAATCGA
* * *
40078387 GGGGTATTTTGATAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTATAAATCGA
** * * *
40078415 GGGTATTTCAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAATCGA
* * * * * *
40078442 TGGTATTTTAGCAATTTTACAGA-CTA
1 GGGTATTTTGGTAATTTTATAAATCGA
*
40078468 GGGTATTTTGGTAATTTTACT-GATCGA
1 GGGTATTTTGGTAATTTTA-TAAATCGA
40078495 GGGTATTTTGGTAATTTTATAAA-CTGA
1 GGGTATTTTGGTAATTTTATAAATC-GA
* *
40078522 GGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
*** ** * **
40078549 GGGTAAAATAATAATTTTGTAAATTAA
1 GGGTATTTTGGTAATTTTATAAATCGA
***** * *
40078576 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
**** *
40078603 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
* * * *
40078630 GGGTACTTTGGTAATTTTACAATTTGA
1 GGGTATTTTGGTAATTTTATAAATCGA
**
40078657 GGGTATTTCAGTAATTT
1 GGGTATTTTGGTAATTT
40078674 GGTAAACTAA
Statistics
Matches: 277, Mismatches: 55, Indels: 16
0.80 0.16 0.05
Matches are distributed among these distances:
26 24 0.09
27 250 0.90
28 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAATCGA
Found at i:40078565 original size:107 final size:107
Alignment explanation
Indices: 40078362--40078566 Score: 241
Period size: 107 Copynumber: 1.9 Consensus size: 107
40078352 ATAAACCAGT
* *
40078362 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAATTGAGGGTATTTCAGT
1 GGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCAGT
* *** *
40078427 AATTTTACAAACCAATGGTATTTTAGCAATTTTACAGACTAG
66 AATTTTACAAACCAAGGGTAAAATAACAATTTTACAGACTAG
* * * * *
40078469 GGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGTAATTTTATAAACTGAGGGTATTTTAG
1 GGTATTTTGGTAATTTTAC-AAACGAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCAG
** * * *
40078533 TAATTTTGTAAATCGAGGGTAAAATAATAATTTT
65 TAATTTTACAAACCAAGGGTAAAATAACAATTTT
40078567 GTAAATTAAG
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
107 77 0.96
108 3 0.04
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (107 bp):
GGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGATAATTTTACAAACTGAGGGTATTTCAGT
AATTTTACAAACCAAGGGTAAAATAACAATTTTACAGACTAG
Found at i:40084702 original size:19 final size:20
Alignment explanation
Indices: 40084667--40084704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40084657 CATTTCATGT
*
40084667 TTATTTTATTATTTTACTAA
1 TTATTTTACTATTTTACTAA
40084687 TTATTTTACT-TTTTACTA
1 TTATTTTACTATTTTACTA
40084705 TTTTAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTACTATTTTACTAA
Found at i:40095024 original size:68 final size:66
Alignment explanation
Indices: 40094952--40095123 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
40094942 CATCATGTGT
* * * *
40094952 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCACTGAAGGACACCA
40095015 TGTAG
62 TGTAG
** * *
40095020 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGCTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-CTGAAGGACACCATGT
40095085 AG
65 AG
* * * *
40095087 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
40095124 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:0.28, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCACTGAAGGACACCATGTA
G
Found at i:40095057 original size:64 final size:64
Alignment explanation
Indices: 40094976--40095158 Score: 201
Period size: 67 Copynumber: 2.8 Consensus size: 64
40094966 AGACATTATG
* * *
40094976 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
40095040 ATGTAGCTAGGTCGCATGCGTGGTTCCAGCTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40095105 AA
63 AA
* * *
40095107 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAG
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAG
40095159 TCAAACTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 25 0.26
66 21 0.21
67 33 0.34
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40096715 original size:50 final size:50
Alignment explanation
Indices: 40096640--40096734 Score: 181
Period size: 50 Copynumber: 1.9 Consensus size: 50
40096630 CCACATAGGT
*
40096640 AGAGACACGACCATGTGTCTCAGCCGTGTATGGAACGCGACTTTGCAGGC
1 AGAGACACGACCATGTGTCTCAGCCGTGTATGGAACACGACTTTGCAGGC
40096690 AGAGACACGACCATGTGTCTCAGCCGTGTATGGAACACGACTTTG
1 AGAGACACGACCATGTGTCTCAGCCGTGTATGGAACACGACTTTG
40096735 GGACACGGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.21
Consensus pattern (50 bp):
AGAGACACGACCATGTGTCTCAGCCGTGTATGGAACACGACTTTGCAGGC
Found at i:40106347 original size:22 final size:22
Alignment explanation
Indices: 40106316--40106361 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
40106306 GTGTCTCAAC
*
40106316 TGTGTGTGACACACAGCTATGT
1 TGTGTATGACACACAGCTATGT
*
40106338 TGTGTATGACACATAGCTATGT
1 TGTGTATGACACACAGCTATGT
40106360 TG
1 TG
40106362 CACAGTCGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (22 bp):
TGTGTATGACACACAGCTATGT
Found at i:40110557 original size:44 final size:43
Alignment explanation
Indices: 40110485--40110646 Score: 134
Period size: 43 Copynumber: 3.8 Consensus size: 43
40110475 CTTTGACGTT
* * * *
40110485 GATTTGAGATATCATGTAACACCGTGTCTGGGACATAGGCCTC
1 GATTTGAGATTTCATGTAAGACCATGTCTGGGACATAGGCATC
* **
40110528 GATTTGAGATTTACGTGTAAGACCATGTCTAAGACATAGGCATC
1 GATTTGAGATTT-CATGTAAGACCATGTCTGGGACATAGGCATC
* * *
40110572 GTATCTT---ATTTCATGTAAGACCCTGTCTGGGACAGAAGCATC
1 G-AT-TTGAGATTTCATGTAAGACCATGTCTGGGACATAGGCATC
* * * *
40110614 GATACTGA-ATTACATGTAAGACCACGTCCGGGA
1 GAT-TTGAGATTTCATGTAAGACCATGTCTGGGA
40110647 TGTCGGCATT
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 3 0.03
42 26 0.27
43 36 0.38
44 26 0.27
45 2 0.02
46 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
GATTTGAGATTTCATGTAAGACCATGTCTGGGACATAGGCATC
Found at i:40110613 original size:42 final size:43
Alignment explanation
Indices: 40110538--40110637 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
40110528 GATTTGAGAT
* * * *
40110538 TTACGTGTAAGACCATGTCTAAGACATAGGCATCG-TATCT-TA
1 TTACATGTAAGACCATGTCTAAGACAGAAGCATCGATA-CTGAA
* * **
40110580 TTTCATGTAAGACCCTGTCTGGGACAGAAGCATCGATACTGAA
1 TTACATGTAAGACCATGTCTAAGACAGAAGCATCGATACTGAA
40110623 TTACATGTAAGACCA
1 TTACATGTAAGACCA
40110638 CGTCCGGGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
42 30 0.65
43 16 0.35
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTAAGACAGAAGCATCGATACTGAA
Found at i:40111585 original size:6 final size:6
Alignment explanation
Indices: 40111574--40111607 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
40111564 CTAAGTATCA
40111574 CACGGC CACGGC ACACGGC CACGGC ACACGGC CA
1 CACGGC CACGGC -CACGGC CACGGC -CACGGC CA
40111608 TGTCTATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.24, C:0.47, G:0.29, T:0.00
Consensus pattern (6 bp):
CACGGC
Found at i:40111590 original size:13 final size:13
Alignment explanation
Indices: 40111572--40111607 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
40111562 AGCTAAGTAT
40111572 CACACGGCCACGG
1 CACACGGCCACGG
40111585 CACACGGCCACGG
1 CACACGGCCACGG
40111598 CACACGGCCA
1 CACACGGCCA
40111608 TGTCTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.25, C:0.47, G:0.28, T:0.00
Consensus pattern (13 bp):
CACACGGCCACGG
Found at i:40111592 original size:7 final size:7
Alignment explanation
Indices: 40111572--40111605 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
40111562 AGCTAAGTAT
40111572 CACACGG
1 CACACGG
40111579 C-CACGG
1 CACACGG
40111585 CACACGG
1 CACACGG
40111592 C-CACGG
1 CACACGG
40111598 CACACGG
1 CACACGG
40111605 C
1 C
40111606 CATGTCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.24, C:0.47, G:0.29, T:0.00
Consensus pattern (7 bp):
CACACGG
Found at i:40112117 original size:10 final size:10
Alignment explanation
Indices: 40112075--40112121 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
40112065 AAGCGGTCCC
40112075 TGAGGCCCAT
1 TGAGGCCCAT
40112085 T-AGGCCCAT
1 TGAGGCCCAT
*
40112094 T-TGGCCC-T
1 TGAGGCCCAT
40112102 TCGAGGCCCAT
1 T-GAGGCCCAT
40112113 TGAGGCCCA
1 TGAGGCCCA
40112122 GAACAGCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 2 0.06
9 14 0.44
10 14 0.44
11 2 0.06
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (10 bp):
TGAGGCCCAT
Found at i:40113861 original size:27 final size:27
Alignment explanation
Indices: 40113830--40114032 Score: 230
Period size: 27 Copynumber: 7.6 Consensus size: 27
40113820 CCTTAATCAA
* *
40113830 TAAAATGACTATTTTTCCATTATGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
*
40113857 TAAAATGACTGTTTTGCCCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* *
40113884 TAAAATGACTGTTTTGCTCTTATGAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
*
40113911 TAAAATGATTATTTTGCCCTTATG-GG
1 TAAAATGACTATTTTGCCCTTATGAGG
** * *
40113937 GGAAATGACTGTTTTGCCCTTATAAGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* * * *
40113964 TAAAATGATTGTTTTACCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGAGG
* *
40113991 TAAAATGATTATTTTGCCCTT-TTATGG
1 TAAAATGACTATTTTGCCCTTATGA-GG
*
40114018 TAATATGACTATTTT
1 TAAAATGACTATTTT
40114033 ACGCCTATGT
Statistics
Matches: 150, Mismatches: 24, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
26 22 0.15
27 128 0.85
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGAGG
Found at i:40113965 original size:80 final size:81
Alignment explanation
Indices: 40113830--40114011 Score: 267
Period size: 80 Copynumber: 2.3 Consensus size: 81
40113820 CCTTAATCAA
* * * * *
40113830 TAAAATGACTATTTTTCCATTATGAGGTAAAATGACTGTTTTGCCCTTATGAGGTAAAATGACTG
1 TAAAATGATTATTTTGCCCTTATGAGGGAAAATGACTGTTTTGCCCTTATAAGGTAAAATGACTG
* *
40113895 TTTTGCTCTTATGAGG
66 TTTTACCCTTATGAGG
* *
40113911 TAAAATGATTATTTTGCCCTTATG-GGGGAAATGACTGTTTTGCCCTTATAAGGTAAAATGATTG
1 TAAAATGATTATTTTGCCCTTATGAGGGAAAATGACTGTTTTGCCCTTATAAGGTAAAATGACTG
*
40113975 TTTTACCCTTATGTGG
66 TTTTACCCTTATGAGG
40113991 TAAAATGATTATTTTGCCCTT
1 TAAAATGATTATTTTGCCCTT
40114012 TTATGGTAAT
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 70 0.77
81 21 0.23
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (81 bp):
TAAAATGATTATTTTGCCCTTATGAGGGAAAATGACTGTTTTGCCCTTATAAGGTAAAATGACTG
TTTTACCCTTATGAGG
Found at i:40118019 original size:33 final size:33
Alignment explanation
Indices: 40117977--40118045 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
40117967 TTATGACATG
40117977 TTAATTGCTTAAATTGTGTATATACGGTAAGTT
1 TTAATTGCTTAAATTGTGTATATACGGTAAGTT
*
40118010 TTAATTGCTTAAATTGTGTATATATGGTAAGTT
1 TTAATTGCTTAAATTGTGTATATACGGTAAGTT
40118043 TTA
1 TTA
40118046 CTTTAATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.48
Consensus pattern (33 bp):
TTAATTGCTTAAATTGTGTATATACGGTAAGTT
Found at i:40119998 original size:32 final size:32
Alignment explanation
Indices: 40119962--40120040 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
40119952 ACAGTCTTAA
* *
40119962 TTGGGCCTAGCCTATCTCAGAA-TCAATATCAG
1 TTGGGCCTAGCCCATATCAGAACT-AATATCAG
*
40119994 TTGGGCCTAGCCCATATCAGAACTAGTATCAG
1 TTGGGCCTAGCCCATATCAGAACTAATATCAG
40120026 TTGGGCCTAGCCCAT
1 TTGGGCCTAGCCCAT
40120041 TTCAATATCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (32 bp):
TTGGGCCTAGCCCATATCAGAACTAATATCAG
Found at i:40123827 original size:28 final size:28
Alignment explanation
Indices: 40123785--40123839 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
40123775 CCGATTTGCT
*
40123785 CCCTCCGTTTCTTTTCTTTTCTTTTCTG
1 CCCTCCGTTTATTTTCTTTTCTTTTCTG
*
40123813 CCCTCTGTTTATTTTCTTTTCTTTTCT
1 CCCTCCGTTTATTTTCTTTTCTTTTCT
40123840 ACCGATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (28 bp):
CCCTCCGTTTATTTTCTTTTCTTTTCTG
Found at i:40123860 original size:38 final size:39
Alignment explanation
Indices: 40123813--40123886 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
40123803 TTCTTTTCTG
*
40123813 CCCTCTGTTTATTTTC-TTTTCTTTTCTACCGATTTGCT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
* * * *
40123851 CCCTTTGTTTCTTCTCATTTTCTTTTTTGCCGATTT
1 CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTT
40123887 CTGAGTTAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 13 0.43
39 17 0.57
ACGTcount: A:0.07, C:0.26, G:0.08, T:0.59
Consensus pattern (39 bp):
CCCTCTGTTTATTCTCATTTTCTTTTCTACCGATTTGCT
Found at i:40131059 original size:40 final size:40
Alignment explanation
Indices: 40130975--40131158 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
40130965 TTGAATGCTG
* * * *
40130975 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
40131014 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * * *
40131055 TCCGGGTCAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
40131095 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
40131135 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40131159 GTATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:40137005 original size:31 final size:31
Alignment explanation
Indices: 40136965--40137047 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
40136955 AATATTAAAC
*
40136965 TATACATGAATTTTAATTTGATGTGCAATGT
1 TATATATGAATTTTAATTTGATGTGCAATGT
* * *
40136996 TATATATGAATTTTGATTT--TGTGCGATTT
1 TATATATGAATTTTAATTTGATGTGCAATGT
*
40137025 TATATATTAAATTTTAATTTGAT
1 TATATA-TGAATTTTAATTTGAT
40137048 TAAATTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 14 0.33
30 11 0.26
31 17 0.40
32 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (31 bp):
TATATATGAATTTTAATTTGATGTGCAATGT
Found at i:40137045 original size:29 final size:29
Alignment explanation
Indices: 40136986--40137045 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
40136976 TTTAATTTGA
* *
40136986 TGTGCAATGTTATATATGAATTTTGATTT
1 TGTGCAATGTTATATATAAATTTTGAATT
* *
40137015 TGTGCGATTTTATATATTAAATTTT-AATT
1 TGTGCAATGTTATATA-TAAATTTTGAATT
40137044 TG
1 TG
40137046 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.53
Consensus pattern (29 bp):
TGTGCAATGTTATATATAAATTTTGAATT
Found at i:40138082 original size:29 final size:30
Alignment explanation
Indices: 40138049--40138117 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
40138039 TACAAGTTTT
* * *
40138049 ATGTATATAATTACA-CT-AAATCAAAGTTC
1 ATGTATA-AATTACATATGAAAACAAAGTTA
40138078 ATGTATCAAATTACATATGAAAACAAAGTTA
1 ATGTAT-AAATTACATATGAAAACAAAGTTA
40138109 ATGTATAAA
1 ATGTATAAA
40138118 ATCGATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 13 0.38
30 5 0.15
31 16 0.47
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (30 bp):
ATGTATAAATTACATATGAAAACAAAGTTA
Found at i:40159841 original size:24 final size:24
Alignment explanation
Indices: 40159797--40159848 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
40159787 TTTATTAGAG
*
40159797 TTTTATATTTTTATGAGTTTTT-T
1 TTTTATATTTTTATGAATTTTTAT
40159820 TTTTATAATTTTTA-GAAATTTTTAT
1 TTTTAT-ATTTTTATG-AATTTTTAT
40159845 TTTT
1 TTTT
40159849 TATGATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 7 0.28
24 13 0.52
25 5 0.20
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTTATATTTTTATGAATTTTTAT
Found at i:40166178 original size:25 final size:25
Alignment explanation
Indices: 40166150--40166201 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40166140 CTTTTCATCC
40166150 CTCCACTTTTCTATTCAACCAAACA
1 CTCCACTTTTCTATTCAACCAAACA
40166175 CTCCACTTTTCTATTCAACCAAACA
1 CTCCACTTTTCTATTCAACCAAACA
40166200 CT
1 CT
40166202 TCCTAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.37, G:0.00, T:0.33
Consensus pattern (25 bp):
CTCCACTTTTCTATTCAACCAAACA
Found at i:40174796 original size:87 final size:87
Alignment explanation
Indices: 40174650--40174824 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
40174640 AAGTAGTTAA
*
40174650 GAAATGATTAAGGGCCTAAACTATAAATACATAAACATGGTGTAAAAAAAATTTTCAAGCTTCAA
1 GAAATGATTAAGGGCCTAAACTATAAATACATAAACATGGTGTAAAAAAAATTTTCAAGCTACAA
40174715 TATTCAGAATACAGAACTCTCT
66 TATTCAGAATACAGAACTCTCT
* * *
40174737 GAAATGATTAAGGGCCTAAACTATAAATGCATAAACATGGTGTAAAAAAGATTTTCAAGCTACAG
1 GAAATGATTAAGGGCCTAAACTATAAATACATAAACATGGTGTAAAAAAAATTTTCAAGCTACAA
40174802 TATTCAGAATACAGAACTCTCT
66 TATTCAGAATACAGAACTCTCT
40174824 G
1 G
40174825 TTTCTAAAAC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (87 bp):
GAAATGATTAAGGGCCTAAACTATAAATACATAAACATGGTGTAAAAAAAATTTTCAAGCTACAA
TATTCAGAATACAGAACTCTCT
Found at i:40177264 original size:38 final size:39
Alignment explanation
Indices: 40177205--40177286 Score: 139
Period size: 38 Copynumber: 2.1 Consensus size: 39
40177195 AATAGTATTA
*
40177205 AAATAAAATAAAATAGAAAATACAATGGACTTAAAATAT
1 AAATAAAATAAAATAGAAAATACAATAGACTTAAAATAT
40177244 AAATAAAAT-AAATAGAAAATACAATAGACTTAAAATAT
1 AAATAAAATAAAATAGAAAATACAATAGACTTAAAATAT
*
40177282 TAATA
1 AAATA
40177287 TATAATGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 32 0.78
39 9 0.22
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.24
Consensus pattern (39 bp):
AAATAAAATAAAATAGAAAATACAATAGACTTAAAATAT
Found at i:40177715 original size:17 final size:17
Alignment explanation
Indices: 40177693--40177735 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
40177683 ATCCTTCTCG
40177693 GGTCGGGTCACCGTTCA
1 GGTCGGGTCACCGTTCA
40177710 GGTCGGGTCACCGTTCA
1 GGTCGGGTCACCGTTCA
*
40177727 GATCGGGTC
1 GGTCGGGTC
40177736 TTCAAAACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.28, G:0.37, T:0.23
Consensus pattern (17 bp):
GGTCGGGTCACCGTTCA
Found at i:40178354 original size:17 final size:16
Alignment explanation
Indices: 40178325--40178356 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40178315 AGGTGGACGA
40178325 AGGCGCACACGCGCGT
1 AGGCGCACACGCGCGT
40178341 AGGCGCAGCACGCGCG
1 AGGCGCA-CACGCGCG
40178357 AGGAGGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.19, C:0.38, G:0.41, T:0.03
Consensus pattern (16 bp):
AGGCGCACACGCGCGT
Found at i:40190751 original size:18 final size:19
Alignment explanation
Indices: 40190704--40190757 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 19
40190694 GATAATTCAT
40190704 AACAAATTTTAAAAAAAATAC
1 AACAAATTTT--AAAAAATAC
40190725 AA-AATATTTTAAAAAAT-C
1 AACAA-ATTTTAAAAAATAC
40190743 AACAAA-TTTAAAAAA
1 AACAAATTTTAAAAAA
40190758 AGTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.29
18 4 0.13
19 9 0.29
20 2 0.06
21 7 0.23
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (19 bp):
AACAAATTTTAAAAAATAC
Found at i:40190758 original size:18 final size:19
Alignment explanation
Indices: 40190704--40190758 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
40190694 GATAATTCAT
40190704 AACAAATTTTAAAAAAAATAC
1 AACAAA-TTT-AAAAAAATAC
*
40190725 AA-AATATTTTAAAAAAT-C
1 AACAA-ATTTAAAAAAATAC
40190743 AACAAATTTAAAAAAA
1 AACAAATTTAAAAAAA
40190759 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 13 0.43
19 9 0.30
20 5 0.17
21 3 0.10
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (19 bp):
AACAAATTTAAAAAAATAC
Found at i:40192355 original size:29 final size:28
Alignment explanation
Indices: 40192283--40192437 Score: 148
Period size: 29 Copynumber: 5.3 Consensus size: 28
40192273 GGTGTATTAG
*
40192283 CGACCATCGAATATGAAAAGGGATGGTTT
1 CGACCATC-AATATGAAAAGGGATGGTTA
* ** * *
40192312 TGAATATCTATTATGAAAAGGGATGGTGA
1 CGACCATC-AATATGAAAAGGGATGGTTA
*
40192341 CGACCATCAACTATGAAAAGGGATGGTGA
1 CGACCATCAA-TATGAAAAGGGATGGTTA
* * *
40192370 CGACCATCGATTAATGAAAATGGATGGTTT
1 CGACCATC-AAT-ATGAAAAGGGATGGTTA
**
40192400 CGACCATCGAATATGAAAAGGGACAGTTA
1 CGACCATC-AATATGAAAAGGGATGGTTA
40192429 CGACCATCA
1 CGACCATCA
40192438 TTTAGCACAC
Statistics
Matches: 103, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.02
29 75 0.73
30 26 0.25
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (28 bp):
CGACCATCAATATGAAAAGGGATGGTTA
Found at i:40192406 original size:59 final size:58
Alignment explanation
Indices: 40192283--40192436 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 58
40192273 GGTGTATTAG
** ** *
40192283 CGACCATCGAATATGAAAAGGGATGGTTTTGAATATCTATTATGAAAAGGGATGGTGA
1 CGACCATCGAATATGAAAAGGGATGGTTACGACCATCGATTATGAAAAGGGATGGTGA
* * **
40192341 CGACCATC-AACTATGAAAAGGGATGGTGACGACCATCGATTAATGAAAATGGATGGTTT
1 CGACCATCGAA-TATGAAAAGGGATGGTTACGACCATCGATT-ATGAAAAGGGATGGTGA
**
40192400 CGACCATCGAATATGAAAAGGGACAGTTACGACCATC
1 CGACCATCGAATATGAAAAGGGATGGTTACGACCATC
40192437 ATTTAGCACA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
57 2 0.02
58 32 0.40
59 45 0.56
60 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (58 bp):
CGACCATCGAATATGAAAAGGGATGGTTACGACCATCGATTATGAAAAGGGATGGTGA
Found at i:40194687 original size:25 final size:26
Alignment explanation
Indices: 40194649--40194756 Score: 91
Period size: 25 Copynumber: 4.3 Consensus size: 26
40194639 CATGTAAACT
**
40194649 GGAAGCTCTTTCGAGCCATATAA-CG
1 GGAAGCTCAATCGAGCCATATAATCG
***
40194674 GGAAGCTCAATCGAGTTGTAT-ATCG
1 GGAAGCTCAATCGAGCCATATAATCG
*
40194699 AGAAGCTC-ATGCGAGCCATA-AATCG
1 GGAAGCTCAAT-CGAGCCATATAATCG
** *
40194724 GGAAGCTCAAGAGAGTCAT-TAATCG
1 GGAAGCTCAATCGAGCCATATAATCG
40194749 GGAAGCTC
1 GGAAGCTC
40194757 GTGAGAGCCA
Statistics
Matches: 65, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
24 3 0.05
25 61 0.94
26 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (26 bp):
GGAAGCTCAATCGAGCCATATAATCG
Found at i:40194754 original size:50 final size:50
Alignment explanation
Indices: 40194649--40194766 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 50
40194639 CATGTAAACT
* * **
40194649 GGAAGCTCTTTCGAGCCATATAACGGGAAGCTCAATCGAGTTGTATATCG
1 GGAAGCTCATGCGAGCCATATAACGGGAAGCTCAAGAGAGTTGTATATCG
*
40194699 AGAAGCTCATGCGAGCCATA-AATCGGGAAGCTCAAGAGAGTCAT-TA-ATCG
1 GGAAGCTCATGCGAGCCATATAA-CGGGAAGCTCAAGAGAGT--TGTATATCG
* *
40194749 GGAAGCTCGTGAGAGCCA
1 GGAAGCTCATGCGAGCCA
40194767 AATATTGGGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
49 2 0.04
50 52 0.91
51 2 0.04
52 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (50 bp):
GGAAGCTCATGCGAGCCATATAACGGGAAGCTCAAGAGAGTTGTATATCG
Found at i:40194762 original size:25 final size:25
Alignment explanation
Indices: 40194695--40194783 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
40194685 CGAGTTGTAT
* *
40194695 ATCGAGAAGCTCATGCGAGCCATAA
1 ATCGGGAAGCTCATGAGAGCCATAA
* * *
40194720 ATCGGGAAGCTCAAGAGAGTCATTA
1 ATCGGGAAGCTCATGAGAGCCATAA
*
40194745 ATCGGGAAGCTCGTGAGAGCCA-AA
1 ATCGGGAAGCTCATGAGAGCCATAA
* *
40194769 TATTGGGATGCTCAT
1 -ATCGGGAAGCTCAT
40194784 AAATGATGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 1 0.02
25 50 0.98
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (25 bp):
ATCGGGAAGCTCATGAGAGCCATAA
Found at i:40196308 original size:27 final size:27
Alignment explanation
Indices: 40196251--40196310 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
40196241 TTTGCCTTTT
* *
40196251 TTATATTATTTATTATTGTATTTGTCG
1 TTATATTATTTATTATTGTATGTGTCA
* *
40196278 TTATATTA-TTATTATTATTATGTGTTA
1 TTATATTATTTATTATT-GTATGTGTCA
40196305 TTATAT
1 TTATAT
40196311 ATATCTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (27 bp):
TTATATTATTTATTATTGTATGTGTCA
Found at i:40196528 original size:9 final size:9
Alignment explanation
Indices: 40196514--40196539 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40196504 TATAATATAG
40196514 GTATATATT
1 GTATATATT
40196523 GTATATATT
1 GTATATATT
40196532 GTATATAT
1 GTATATAT
40196540 ATTATGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (9 bp):
GTATATATT
Found at i:40196863 original size:23 final size:21
Alignment explanation
Indices: 40196826--40196867 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
40196816 TATTACTATA
40196826 ACTATTATTTATTAGTATTTT
1 ACTATTATTTATTAGTATTTT
40196847 ACTATTACTATTATTAGTATT
1 ACTATTA-T-TTATTAGTATT
40196868 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 1 0.05
23 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
ACTATTATTTATTAGTATTTT
Found at i:40196873 original size:27 final size:25
Alignment explanation
Indices: 40196812--40196873 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 25
40196802 TTATACGTTC
*
40196812 TTATTATTACTATAACTATTATTTA
1 TTATTTTTACTATAACTATTATTTA
*
40196837 TTAGTATTTTACTATTACTATTATTAGTA
1 TTA-T-TTTTACTATAACTATTATT--TA
40196866 TTATTTTT
1 TTATTTTT
40196874 TTTAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 3 0.10
26 1 0.03
27 21 0.68
28 1 0.03
29 5 0.16
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (25 bp):
TTATTTTTACTATAACTATTATTTA
Found at i:40196997 original size:26 final size:26
Alignment explanation
Indices: 40196943--40197002 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
40196933 ATATGTATGG
*
40196943 TGTATATTCTTAATATTATATATTGTA
1 TGTATATTCTTAATA-TATATATTATA
*
40196970 TGTATTTTCTTAATA-ACTATATTATA
1 TGTATATTCTTAATATA-TATATTATA
40196996 TGTATAT
1 TGTATAT
40197003 ATAGTATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 14 0.48
27 14 0.48
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (26 bp):
TGTATATTCTTAATATATATATTATA
Found at i:40197042 original size:20 final size:20
Alignment explanation
Indices: 40197017--40197056 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40197007 TATGTACATA
40197017 TTTTTAATAT-TATTATGTAT
1 TTTTTAATATATA-TATGTAT
40197037 TTTTTAATATATATATGTAT
1 TTTTTAATATATATATGTAT
40197057 ATGTGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTAATATATATATGTAT
Found at i:40197357 original size:27 final size:27
Alignment explanation
Indices: 40197327--40197379 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
40197317 ATATTATATA
*
40197327 TATTTTTAATACTA-TGTATATATTTTT
1 TATTCTTAATACTACT-TATATATTTTT
* *
40197354 TATTCTTATTATTACTTATATATTTT
1 TATTCTTAATACTACTTATATATTTT
40197380 AATACATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTCTTAATACTACTTATATATTTTT
Done.