Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 90 of 135
Found at i:28112016 original size:165 final size:165
Alignment explanation
Indices: 28111761--28112068 Score: 397
Period size: 165 Copynumber: 1.9 Consensus size: 165
28111751 AATTAGTATA
* * *
28111761 AAATCCAAAAATAGAATATAATCTATTACTCGGCAGGAATAAATCTCGAAACAGATTTAGTCAAC
1 AAATCCAAAAATAGAATATAATCTATTACACGACAGGAATAAATCCCGAAACAGATTTAGTCAAC
* * *
28111826 TTATTTTATTTTGGAAACAAAATCAATTGGAATAAAATCTATTGAATGGCGGAAATAAATCCCGA
66 TTATTTTATTTTGGAAACAAAATCAAATAGAATAAAATCTATTAAATGGCGGAAATAAATCCCGA
* *
28111891 AACAGATTTATTTACTTAATTATTATTTGGAACTG
131 AACAAATTAATTTACTTAATTATTATTTGGAACTG
* * * * **
28111926 AAATCCAAATATAGACT-TAATCTATT-CAACGACGGGAATAAATCCCGAAACATATTTA-TTTA
1 AAATCCAAAAATAGAATATAATCTATTAC-ACGACAGGAATAAATCCCGAAACAGATTTAGTCAA
* * * *
28111988 CTTATTTTCTTTTTTGGAAATAAAATCAAATAGAATAAAATCTGTTAAATGGTGGAAATAAATCC
65 CTTA-TTT-TATTTTGGAAACAAAATCAAATAGAATAAAATCTATTAAATGGCGGAAATAAATCC
*
28112053 GGAAACAAATTAATTT
128 CGAAACAAATTAATTT
28112069 CCAATTTTAG
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
163 7 0.06
164 37 0.31
165 77 0.64
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (165 bp):
AAATCCAAAAATAGAATATAATCTATTACACGACAGGAATAAATCCCGAAACAGATTTAGTCAAC
TTATTTTATTTTGGAAACAAAATCAAATAGAATAAAATCTATTAAATGGCGGAAATAAATCCCGA
AACAAATTAATTTACTTAATTATTATTTGGAACTG
Found at i:28115216 original size:87 final size:86
Alignment explanation
Indices: 28115104--28115270 Score: 257
Period size: 87 Copynumber: 1.9 Consensus size: 86
28115094 AAATTTAAGT
* *
28115104 TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAA-CTCTGGGATTTGAATTCATTAAG
1 TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAATCT-TGGGATATGAACTCATTAAG
28115168 AGTAATAAACTCAACCTCTCATG
65 AGTAA-AAACTCAACCTCTCATG
28115191 TCGGTGAATTCATCAAGTCTC-TCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAG
1 TCGGTGAATTCATCAAGTC-CGTCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAG
* *
28115255 AGTGAGAACTCAACCT
65 AGTAAAAACTCAACCT
28115271 TATGCATGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
86 10 0.14
87 61 0.82
88 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (86 bp):
TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAATCTTGGGATATGAACTCATTAAGA
GTAAAAACTCAACCTCTCATG
Found at i:28115290 original size:87 final size:86
Alignment explanation
Indices: 28115111--28115293 Score: 221
Period size: 87 Copynumber: 2.1 Consensus size: 86
28115101 AGTTCGGTGA
* *
28115111 ATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATTTGAATTCATTAAGAGTAATAA
1 ATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTAATAA
* *
28115176 ACTCAACCTCTCATGTCGGTG
66 ACTCAACCTATCATGTCAGTG
*
28115197 AATTCATCAAGTCTC-TCTCAATAGGACCACCCAAA-TCTTGGGATATGAACTCATTAAGAGTGA
1 -ATTCATCAAGTC-CGTCTCAATAGGACCACCCAAACTC-TGGGATATGAACTCATTAAGAGTAA
* *
28115260 -GAACTCAACCTTATGCATGTACATTG
63 TAAACTCAACC-TAT-CATGT-CAGTG
28115286 -TTCATCAA
1 ATTCATCAA
28115294 AGGGATAGGT
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
86 11 0.13
87 64 0.76
88 6 0.07
89 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (86 bp):
ATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTAATAA
ACTCAACCTATCATGTCAGTG
Found at i:28127716 original size:29 final size:29
Alignment explanation
Indices: 28127674--28127779 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
28127664 CATTTATGGT
28127674 TGATTCTGTTATATGAGAGCCTTTGTGGC
1 TGATTCTGTTATATGAGAGCCTTTGTGGC
* * * *
28127703 TGATTCTATTATATGTGAGCTTTTGTGGT
1 TGATTCTGTTATATGAGAGCCTTTGTGGC
* * * *
28127732 TGATTTTGTTATATGCGAGCCTTTATGAC
1 TGATTCTGTTATATGAGAGCCTTTGTGGC
*
28127761 TAAATT-TGTTATATGAGAG
1 T-GATTCTGTTATATGAGAG
28127780 TCTTCATTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
29 60 0.95
30 3 0.05
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (29 bp):
TGATTCTGTTATATGAGAGCCTTTGTGGC
Found at i:28127887 original size:26 final size:26
Alignment explanation
Indices: 28127851--28127951 Score: 121
Period size: 26 Copynumber: 3.9 Consensus size: 26
28127841 TGGCGTAGAT
*
28127851 ATTGGACGCCTATATGGCTATCTCTG
1 ATTGGACGCCTATATGGCTATCTCTA
* * *
28127877 ATTGGAAGCCTATATGGCTATTTCTT
1 ATTGGACGCCTATATGGCTATCTCTA
* *
28127903 ATTGGACGCCTATATGACTATCTCAA
1 ATTGGACGCCTATATGGCTATCTCTA
* * *
28127929 ATTGGATGCCTCTATAGCTATCT
1 ATTGGACGCCTATATGGCTATCT
28127952 ATGCTTATGG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 63 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (26 bp):
ATTGGACGCCTATATGGCTATCTCTA
Found at i:28127907 original size:52 final size:52
Alignment explanation
Indices: 28127850--28127949 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
28127840 ATGGCGTAGA
* ** *
28127850 TATTGGACGCCTATATGGCTATCTCTGATTGGAAGCCTATATGGCTATTTCT
1 TATTGGACGCCTATATGACTATCTCAAATTGGAAGCCTATATAGCTATTTCT
* *
28127902 TATTGGACGCCTATATGACTATCTCAAATTGGATGCCTCTATAGCTAT
1 TATTGGACGCCTATATGACTATCTCAAATTGGAAGCCTATATAGCTAT
28127950 CTATGCTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (52 bp):
TATTGGACGCCTATATGACTATCTCAAATTGGAAGCCTATATAGCTATTTCT
Found at i:28136015 original size:61 final size:62
Alignment explanation
Indices: 28135935--28136050 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 62
28135925 ATGCTCAATT
* ** * *
28135935 TACATTAGATATTATAATTACTTTATTTTATTTTTACCTAATTAATATTTAGATATCATTTA
1 TACATTAGATATTAAAATTACTAAACTTTATTTTTACCAAATTAATATTTAGATATCATTTA
* *
28135997 TACA-TAGATATTAAAATTAGTAAACTTTATTTTTATCAAATTAATATTTAGATA
1 TACATTAGATATTAAAATTACTAAACTTTATTTTTACCAAATTAATATTTAGATA
28136051 GTACTTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
61 43 0.91
62 4 0.09
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (62 bp):
TACATTAGATATTAAAATTACTAAACTTTATTTTTACCAAATTAATATTTAGATATCATTTA
Found at i:28136116 original size:21 final size:21
Alignment explanation
Indices: 28136066--28136129 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
28136056 TTATATTGAT
*
28136066 TTACTAAATTAAATTAAAAATA
1 TTACTAAATT-TATTAAAAATA
28136088 TTACTAAATTTATTATAAAATA
1 TTACTAAATTTATTA-AAAATA
*
28136110 TTA-TAAATTCTATAAAAAAT
1 TTACTAAATT-TATTAAAAAT
28136130 TAAACTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TTACTAAATTTATTAAAAATA
Found at i:28144119 original size:29 final size:29
Alignment explanation
Indices: 28144087--28144150 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
28144077 AAAACGGGAC
28144087 TTTTTGGA-TACCCGGGGGCAAAATAGTAA
1 TTTTTGGACT-CCCGGGGGCAAAATAGTAA
***
28144116 -TTTTGGACTTTTGGGGGCAAAATAGTAA
1 TTTTTGGACTCCCGGGGGCAAAATAGTAA
28144144 TTTTTGG
1 TTTTTGG
28144151 TAAAATCGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTTGGACTCCCGGGGGCAAAATAGTAA
Found at i:28144161 original size:29 final size:29
Alignment explanation
Indices: 28144129--28144217 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
28144119 TGGACTTTTG
28144129 GGGGCAAAATAGTAATTTTTGGTAAAATC
1 GGGGCAAAATAGTAATTTTTGGTAAAATC
* *
28144158 GGGGTCAAAA-A-TGAAATTTTAG-AAAGTATC
1 GGGG-CAAAATAGT-AATTTTTGGTAAA--ATC
* * *
28144188 GGGGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGCAAAATAGTAATTTTTGGTAAAATC
28144217 G
1 G
28144218 AGATCAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
30 19 0.41
31 3 0.07
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (29 bp):
GGGGCAAAATAGTAATTTTTGGTAAAATC
Found at i:28144176 original size:30 final size:31
Alignment explanation
Indices: 28144142--28144227 Score: 74
Period size: 30 Copynumber: 2.9 Consensus size: 31
28144132 GCAAAATAGT
28144142 AATTTTTGGTAAAATCGGGGTCAAAAAT-GA
1 AATTTTTGGTAAAATCGGGGTCAAAAATGGA
* *
28144172 AA-TTTTAG-AAAGTATCGGGGT--AAAATGGT
1 AATTTTTGGTAAA--ATCGGGGTCAAAAATGGA
* * *
28144201 AATTTTTGGTGAAATCGAGATCAAAAA
1 AATTTTTGGTAAAATCGGGGTCAAAAA
28144228 CGGGATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
28 8 0.19
29 14 0.33
30 15 0.35
31 6 0.14
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (31 bp):
AATTTTTGGTAAAATCGGGGTCAAAAATGGA
Found at i:28144236 original size:59 final size:59
Alignment explanation
Indices: 28144129--28144265 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
28144119 TGGACTTTTG
* * * * *
28144129 GGGGCAAAATAGTAATTTTTGGTAAAATCGGGGTCAAAAATGAAATTTTAGAAAGTATC-
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGATCAAAAACGAAATTTTAGAAAGT-TCA
* ** * * *
28144188 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGATCAAAAACGGGATTTTTGGACGTTCA
1 GGGGTAAAATGGTAATTTTTGGTAAAATCGAGATCAAAAACGAAATTTTAGAAAGTTCA
*
28144247 AGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
28144266 AGGGGTTTCG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 2 0.03
59 63 0.97
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTAAAATCGAGATCAAAAACGAAATTTTAGAAAGTTCA
Found at i:28144320 original size:58 final size:59
Alignment explanation
Indices: 28144252--28144382 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 59
28144242 GTTCAAGGGT
**
28144252 AAAATGGTAATTTTAGGGGTTTCGA-GGTCAAAAATGGAATTTTTGGAAG-TTTGGGGGCA
1 AAAAT-GTAATTTTAGGAATTT-GAGGGTCAAAAATGGAATTTTTGGAAGTTTTGGGGGCA
* * * **
28144311 AAAATGTAATTTTTGGAATTTTAGGGTTAAAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGTAATTTTAGGAATTTGAGGGTCAAAAATGGAATTTTTGGAAGTTTTGGGGGCA
28144370 AAAATGTAATTTT
1 AAAATGTAATTTT
28144383 GGAGAAGTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 1 0.02
58 36 0.57
59 26 0.41
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (59 bp):
AAAATGTAATTTTAGGAATTTGAGGGTCAAAAATGGAATTTTTGGAAGTTTTGGGGGCA
Found at i:28144370 original size:30 final size:30
Alignment explanation
Indices: 28144281--28144391 Score: 145
Period size: 29 Copynumber: 3.7 Consensus size: 30
28144271 TTTCGAGGTC
**
28144281 AAAAATGGAATTTTTGGAAG-TTTGGGGGC
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
* *
28144310 AAAAATGTAATTTTTGGAA-TTTTAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
28144339 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTGGGGTT
* *
28144369 AAAAATGTAATTTTGGAGAAGTT
1 AAAAATGGAATTTTTG-GAAGTT
28144392 CGAGGCTTGG
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
29 42 0.59
30 23 0.32
31 6 0.08
ACGTcount: A:0.34, C:0.01, G:0.27, T:0.38
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTTGGGGTT
Found at i:28144754 original size:205 final size:205
Alignment explanation
Indices: 28144402--28144828 Score: 746
Period size: 205 Copynumber: 2.1 Consensus size: 205
28144392 CGAGGCTTGG
28144402 GTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGC
1 GTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGC
* * * * *
28144467 TTCTCTAGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACC
66 TTCTCTAAATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTGCCTCATCAGGAAGCTAACA
* *
28144532 ATTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCG
131 ATTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCA
28144597 TTGAGCCTGA
196 TTGAGCCTGA
28144607 GTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGC
1 GTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGC
*
28144672 TTTTCTAAATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTGCCTCATCAGGAAGCTAACA
66 TTCTCTAAATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTGCCTCATCAGGAAGCTAACA
* * *
28144737 ATTTATTACTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTTGAAGATTTGCTCGCA
131 ATTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCA
*
28144802 TTGAGCCTGG
196 TTGAGCCTGA
28144812 GTTTGATTTGGTCTTCT
1 GTTTGATTTGGTCTTCT
28144829 CCTCTTTTTT
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
205 210 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (205 bp):
GTTTGATTTGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGC
TTCTCTAAATCTCCTCAGGAAGACAAATTTAGTCCACTTCTCTGTGCCTCATCAGGAAGCTAACA
ATTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCGCA
TTGAGCCTGA
Found at i:28144842 original size:8 final size:8
Alignment explanation
Indices: 28144831--28144923 Score: 70
Period size: 8 Copynumber: 12.1 Consensus size: 8
28144821 GGTCTTCTCC
28144831 TCTTTTTT
1 TCTTTTTT
28144839 TC--TTTT
1 TCTTTTTT
28144845 TC-TTTTT
1 TCTTTTTT
*
28144852 TCTTTTAT
1 TCTTTTTT
*
28144860 TCTTTTAT
1 TCTTTTTT
*
28144868 TCTTTTAT
1 TCTTTTTT
28144876 TCTTTTTT
1 TCTTTTTT
* *
28144884 TGTTTTTG
1 TCTTTTTT
*
28144892 T-TTTTGT
1 TCTTTTTT
28144899 T-TTTTTT
1 TCTTTTTT
* *
28144906 ACTTCTTCT
1 TCTT-TTTT
28144915 TCTTTTTT
1 TCTTTTTT
28144923 T
1 T
28144924 TTGATATCAC
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
6 6 0.09
7 16 0.23
8 42 0.60
9 6 0.09
ACGTcount: A:0.04, C:0.12, G:0.03, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:28149200 original size:58 final size:58
Alignment explanation
Indices: 28149109--28149331 Score: 211
Period size: 58 Copynumber: 3.8 Consensus size: 58
28149099 AATGGGGAAT
* * ** *
28149109 AAAAATGGGATTTTTGGACA-TTCGAGGGT-AAAATGGTAATTTCAGG-GGTTTCGAGGTC
1 AAAAATGGAATTTTTGGA-AGTT-TAGGGTCAAAATGG-AATTTTTGGAAGTTTCGAGGTC
*
28149167 AAAAATGGAATTTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAAGTTTTGAGG-C
1 AAAAATGGAATTTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * *
28149224 AAAAATGTAATGTTTGGAAGTTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTCAAGGTC
1 AAAAATGGAATTTTTGGAAG-TTTAGGGTC-AAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * * *
28149284 AAAAAAGTAATTTTGGAGAAGTTTGAGGGTTAAAATGTAATATTTGGA
1 AAAAATGGAATTTTTG-GAAGTTT-AGGGTCAAAATGGAATTTTTGGA
28149332 TAATTTAGGG
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
57 32 0.23
58 42 0.30
59 25 0.18
60 32 0.23
61 8 0.06
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:28149257 original size:30 final size:30
Alignment explanation
Indices: 28149163--28149331 Score: 177
Period size: 30 Copynumber: 5.7 Consensus size: 30
28149153 GGGGTTTCGA
28149163 GGTCAAAAATGGAATTTTTGGAAG-TTTAG
1 GGTCAAAAATGGAATTTTTGGAAGTTTTAG
28149192 GGTC-AAAATGGAATTTTTGGAAGTTTT-G
1 GGTCAAAAATGGAATTTTTGGAAGTTTTAG
* * *
28149220 AGG-CAAAAATGTAATGTTTGGAAGTTTTTG
1 -GGTCAAAAATGGAATTTTTGGAAGTTTTAG
* *
28149250 GGTCAAAAATGGAATTTTTGGAAGTTTCAA
1 GGTCAAAAATGGAATTTTTGGAAGTTTTAG
* * * *
28149280 GGTCAAAAAAGTAATTTTGGAGAAGTTTGAG
1 GGTCAAAAATGGAATTTTTG-GAAGTTTTAG
* * *
28149311 GGT-TAAAATGTAATATTTGGA
1 GGTCAAAAATGGAATTTTTGGA
28149332 TAATTTAGGG
Statistics
Matches: 118, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
28 21 0.18
29 34 0.29
30 52 0.44
31 11 0.09
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
GGTCAAAAATGGAATTTTTGGAAGTTTTAG
Found at i:28149273 original size:59 final size:57
Alignment explanation
Indices: 28149156--28149331 Score: 210
Period size: 60 Copynumber: 3.0 Consensus size: 57
28149146 AATTTCAGGG
*
28149156 GTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAA
1 GTTTCGAGGTCAAAAATGTAA-TTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAA
* *
28149214 GTTTTGAGG-CAAAAATGTAATGTTTGGAAGTTTTTGGGTCAAAAATGGAATTTTTGGAA
1 GTTTCGAGGTCAAAAATGTAAT-TTTGGAAG-TTTAGGGTC-AAAATGGAATTTTTGGAA
* * * * *
28149273 GTTTCAAGGTCAAAAAAGTAATTTTGGAGAAGTTTGAGGGTTAAAATGTAATATTTGGA
1 GTTTCGAGGTCAAAAATGTAATTTT-G-GAAGTTT-AGGGTCAAAATGGAATTTTTGGA
28149332 TAATTTAGGG
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
56 1 0.01
57 18 0.18
58 16 0.16
59 28 0.28
60 30 0.30
61 8 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (57 bp):
GTTTCGAGGTCAAAAATGTAATTTTGGAAGTTTAGGGTCAAAATGGAATTTTTGGAA
Found at i:28158406 original size:13 final size:13
Alignment explanation
Indices: 28158381--28158414 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
28158371 TAATCACACC
28158381 AATATAT-TTAAA
1 AATATATATTAAA
28158393 AATATATATTAAA
1 AATATATATTAAA
28158406 AATATATAT
1 AATATATAT
28158415 ATTTTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATATATTAAA
Found at i:28158414 original size:15 final size:14
Alignment explanation
Indices: 28158382--28158417 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
28158372 AATCACACCA
*
28158382 ATATATTTAAAAAT
1 ATATATTAAAAAAT
28158396 ATATATTAAAAATAT
1 ATATATTAAAAA-AT
28158411 ATATATT
1 ATATATT
28158418 TTTTCGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTAAAAAAT
Found at i:28168470 original size:18 final size:18
Alignment explanation
Indices: 28168447--28168482 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28168437 ATGTACCTAT
*
28168447 GTATTTTTTTTAAATACG
1 GTATTTTATTTAAATACG
*
28168465 GTATTTTATTTATATACG
1 GTATTTTATTTAAATACG
28168483 AAAATACGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (18 bp):
GTATTTTATTTAAATACG
Found at i:28168597 original size:15 final size:15
Alignment explanation
Indices: 28168575--28168605 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28168565 CCTTTTTCTC
28168575 GAAAAAAAAATTTTCA
1 GAAAAAAAAA-TTTCA
28168591 GAAAAAAAAATTTCA
1 GAAAAAAAAATTTCA
28168606 AAATTTCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (15 bp):
GAAAAAAAAATTTCA
Found at i:28168723 original size:61 final size:57
Alignment explanation
Indices: 28168612--28168909 Score: 349
Period size: 61 Copynumber: 5.2 Consensus size: 57
28168602 TTCAAAATTT
**
28168612 CGACACCCCCTTTTCTCGAAAAAAAA-TTGCATTTTTGGGTGTTGGCCATCAAATGGC
1 CGACA-CCCCTTTTCTCGAAAAAAAATTTAAATTTTTGGGTGTTGGCCATCAAATGGC
* *
28168669 CGACACTTCCCTTTTCTCGAGAAAAAAATTTAAATTTTTTTGGTG-TGGATCATCAAATGGC
1 CGACAC--CCCTTTTCTCGA-AAAAAAATTTAAA-TTTTTGGGTGTTGG-CCATCAAATGGC
** * *
28168730 CGACACCCCTTTTCTCGAAAAAAAA-TTGCATTTTTGGGTGTTGGCCATCATATGAC
1 CGACACCCCTTTTCTCGAAAAAAAATTTAAATTTTTGGGTGTTGGCCATCAAATGGC
* *
28168786 CGACACCCCCTATTCTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
1 CGACA-CCCCTTTTCTCGA-AAAAAAATTT-AAA-TTTTTGGGTGTTGGCCATCAAATGGC
*
28168847 CGACACCCCTTTT-TC-AAAAAAAATTGT--ATTTTTGGGTGTTGGCCATTAAATGGC
1 CGACACCCCTTTTCTCGAAAAAAAATT-TAAATTTTTGGGTGTTGGCCATCAAATGGC
28168901 CGACACCCC
1 CGACACCCC
28168910 CAACTTCTTA
Statistics
Matches: 209, Mismatches: 19, Indels: 29
0.81 0.07 0.11
Matches are distributed among these distances:
54 33 0.16
55 1 0.00
56 24 0.11
57 32 0.15
58 28 0.13
59 23 0.11
60 14 0.07
61 54 0.26
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (57 bp):
CGACACCCCTTTTCTCGAAAAAAAATTTAAATTTTTGGGTGTTGGCCATCAAATGGC
Found at i:28168762 original size:117 final size:117
Alignment explanation
Indices: 28168612--28168910 Score: 480
Period size: 117 Copynumber: 2.6 Consensus size: 117
28168602 TTCAAAATTT
*
28168612 CGACACCCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACTT
1 CGACA-CCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACAC-C
* *
28168677 CCCTTTTCTCGAGAAAAAAATTT-AAATTTTTTTGGTG-TGGATCATCAAATGGC
64 CCCTATTCTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGG-CCATCAAATGGC
* *
28168730 CGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCATATGACCGACACCCC
1 CGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCC
28168795 CTATTCTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
66 CTATTCTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
* *
28168847 CGACACCCCTTTT-TC-AAAAAAAATTGTATTTTTGGGTGTTGGCCATTAAATGGCCGACACCCC
1 CGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCC
28168910 C
66 C
28168911 AACTTCTTAT
Statistics
Matches: 170, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
115 45 0.26
116 24 0.14
117 93 0.55
118 8 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (117 bp):
CGACACCCCTTTTCTCGAAAAAAAATTGCATTTTTGGGTGTTGGCCATCAAATGGCCGACACCCC
CTATTCTCGAGAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATCAAATGGC
Found at i:28172668 original size:12 final size:12
Alignment explanation
Indices: 28172626--28172673 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
28172616 ATTTCTGTAA
*
28172626 AAATTAATTTGA
1 AAATTAATTTGG
28172638 AAATTAATTTAAGTTG
1 AAATTAATTT--G--G
28172654 AAATTAATTTGG
1 AAATTAATTTGG
28172666 AAATTAAT
1 AAATTAAT
28172674 GAACATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (12 bp):
AAATTAATTTGG
Found at i:28172733 original size:22 final size:22
Alignment explanation
Indices: 28172681--28172733 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
28172671 AATGAACATG
*
28172681 TTTAAATTTAAATAATTTAAAC
1 TTTAAAATTAAATAATTTAAAC
* * *
28172703 TTCATAATTATATAAGTTTAAA-
1 TTTAAAATTAAATAA-TTTAAAC
28172725 TTTAAAATT
1 TTTAAAATT
28172734 CTACTTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTAAAATTAAATAATTTAAAC
Found at i:28172895 original size:84 final size:81
Alignment explanation
Indices: 28172804--28173124 Score: 340
Period size: 89 Copynumber: 3.8 Consensus size: 81
28172794 AAAAAGATAG
* * * *
28172804 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-AAATTTTC
28172869 ATAATTAAAGTTCAAATTA
65 ATAATTAAA-TT-AAATTA
* * *
28172888 TTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATATATTATTTATTAATTTTAT
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTA-TAA-ATT-T
* * *
28172953 ATCTTTAAATAAAAATTATTATTA
63 -TC-AT-AAT-TAAATTA-AATTA
*
28172977 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATTTT-A
1 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATAAATTTTCA
* *
28173041 TATCTTTAAATAAAAATTA
66 TA--ATTAAAT-TAAATTA
* *
28173060 TTATTATATTACAATTTTTATCATATTTTAA-ATGTTGATTTGACAATACATTATTTATTAATTT
1 TTATTATATTACAATTTTTATCATA---TAATGTGTTGATTTGACAATACATTATTTATAAATTT
28173124 T
63 T
28173125 ATATCTTTAA
Statistics
Matches: 203, Mismatches: 20, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
82 1 0.00
83 34 0.17
84 53 0.26
85 37 0.18
86 5 0.02
87 4 0.02
88 4 0.02
89 62 0.31
90 3 0.01
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (81 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATAAATTTTCA
TAATTAAATTAAATTA
Found at i:28172948 original size:45 final size:46
Alignment explanation
Indices: 28172889--28173044 Score: 139
Period size: 45 Copynumber: 3.5 Consensus size: 46
28172879 TTCAAATTAT
28172889 TATTATATTA-TAATTTT-TATCATATAATGTGTTGATTTGACAATA
1 TATTAT-TTATTAATTTTATATCATATAATGTGTTGATTTGACAATA
* * *** * **
28172934 TATTATTTATTAATTTTATATC-TTTAA-AT-AAAAATT-ATTAT-
1 TATTATTTATTAATTTTATATCATATAATGTGTTGATTTGACAATA
28172975 TATTATTATATTACAATTTT-TATCATATAATGTGTTGATTTGACAATA
1 TATTATT-TATT--AATTTTATATCATATAATGTGTTGATTTGACAATA
*
28173023 CATTATTTATTAATTTTATATC
1 TATTATTTATTAATTTTATATC
28173045 TTTAAATAAA
Statistics
Matches: 83, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
41 7 0.08
42 7 0.08
43 7 0.08
44 14 0.17
45 24 0.29
46 11 0.13
47 7 0.08
48 6 0.07
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (46 bp):
TATTATTTATTAATTTTATATCATATAATGTGTTGATTTGACAATA
Found at i:28173005 original size:89 final size:88
Alignment explanation
Indices: 28172884--28173176 Score: 472
Period size: 89 Copynumber: 3.3 Consensus size: 88
28172874 TAAAGTTCAA
* *
28172884 ATTATTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATATATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
28172949 TTATATCTTTAAATAAAAATTATT
66 TTATATCTTTAAATAAAAA-TATT
28172973 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
28173038 TTATATCTTTAAAT--AAA-A--
66 TTATATCTTTAAATAAAAATATT
*
28173056 ATTATTATTATATTACAATTTTTATCATATTTTAA-ATGTTGATTTGACAATACATTATTTATTA
1 ATTATTATTATATTACAATTTTTATCATA---TAATGTGTTGATTTGACAATACATTATTTATTA
28173120 ATTTTATATCTTTAAATAAAAAATATT
63 ATTTTATATCTTTAAAT-AAAAATATT
28173147 ATTATTATTATATTACAATTTTTATCATAT
1 ATTATTATTATATTACAATTTTTATCATAT
28173177 TTTAAATTTA
Statistics
Matches: 192, Mismatches: 3, Indels: 19
0.90 0.01 0.09
Matches are distributed among these distances:
83 29 0.15
85 46 0.24
86 3 0.02
87 3 0.02
88 4 0.02
89 78 0.41
91 29 0.15
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (88 bp):
ATTATTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTATTAATT
TTATATCTTTAAATAAAAATATT
Found at i:28173130 original size:174 final size:173
Alignment explanation
Indices: 28172804--28173176 Score: 565
Period size: 174 Copynumber: 2.2 Consensus size: 173
28172794 AAAAAGATAG
* * *
28172804 TTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTTC
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
** * *
28172869 ATAATTAAAGTTCAAATTATTATTATATTATAATTTTTATCATATAATGTGTTGATTTGACAATA
66 ATAATTAAAGTAAAAATTATTATTATATTACAATTTTTATCATATAATATGTTGATTTGACAATA
* *
28172934 TATTATTTATTAATTTTATATCTTTAAATAAAAATTATTATTA
131 CATTATTTATTAATTTTATATCTTTAAATAAAAAATATTATTA
* *
28172977 TTATTATATTACAATTTTTATCATATAATGTGTTGATTTGACAATACATTATTTAT-TAATTTT-
1 TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
*
28173040 ATATCTTTAAA-TAAAAATTATTATTATATTACAATTTTTATCATATTTTAA-ATGTTGATTTGA
66 ATA--ATTAAAGTAAAAATTATTATTATATTACAATTTTTATCATA---TAATATGTTGATTTGA
28173103 CAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATATTATTA
126 CAATACATTATTTATTAATTTTATATCTTTAAATAAAAAATATTATTA
28173151 TTATTATATTACAATTTTTATCATAT
1 TTATTATATTACAATTTTTATCATAT
28173177 TTTAAATTTA
Statistics
Matches: 183, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
171 3 0.02
172 37 0.20
173 57 0.31
174 83 0.45
175 3 0.02
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (173 bp):
TTATTATATTACAATTTTTATCATATAATGTGTTAATTTGACAATACATTATTTATCAAATTTTC
ATAATTAAAGTAAAAATTATTATTATATTACAATTTTTATCATATAATATGTTGATTTGACAATA
CATTATTTATTAATTTTATATCTTTAAATAAAAAATATTATTA
Found at i:28173366 original size:10 final size:10
Alignment explanation
Indices: 28173340--28173381 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
28173330 TGTCTTGAGA
28173340 CGCCGTTGAC
1 CGCCGTTGAC
**
28173350 CATCGTTGAC
1 CGCCGTTGAC
*
28173360 CGCCGTTGAT
1 CGCCGTTGAC
28173370 CGCCGTTGAC
1 CGCCGTTGAC
28173380 CG
1 CG
28173382 ACTTTGTTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.12, C:0.36, G:0.29, T:0.24
Consensus pattern (10 bp):
CGCCGTTGAC
Found at i:28174278 original size:18 final size:18
Alignment explanation
Indices: 28174244--28174278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28174234 TAAATTTTAT
*
28174244 TAATTATTATTCTATTTC
1 TAATTATTATTCAATTTC
*
28174262 TAATTATTTTTCAATTT
1 TAATTATTATTCAATTT
28174279 TTCAGATGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATTATTATTCAATTTC
Found at i:28175637 original size:30 final size:30
Alignment explanation
Indices: 28175603--28175694 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
28175593 TCCCTTTACT
*
28175603 TTTTAAATTTAA-TTTGTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTTG-AATTTC-TTGTATA
28175633 TTTTAAATTTAATTTTGAATTTCTTGTATA
1 TTTTAAATTTAATTTTGAATTTCTTGTATA
* ** *
28175663 TTTTAATTTTTCTTTCT-AATTTCCTGTATA
1 TTTTAAATTTAATTT-TGAATTTCTTGTATA
28175693 TT
1 TT
28175695 CTAATTATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.04
30 47 0.87
31 5 0.09
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTTGAATTTCTTGTATA
Found at i:28181699 original size:18 final size:18
Alignment explanation
Indices: 28181678--28181713 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28181668 GTAACTTAGT
28181678 TTGTAAGTGTTTTCCACA
1 TTGTAAGTGTTTTCCACA
28181696 TTGTAAGTGTTTTCCACA
1 TTGTAAGTGTTTTCCACA
28181714 AAAAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
TTGTAAGTGTTTTCCACA
Found at i:28182367 original size:18 final size:18
Alignment explanation
Indices: 28182344--28182382 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28182334 TTTAAACTAG
28182344 TTAGAATTCTAGTTTA-AT
1 TTAGAATTCTA-TTTAGAT
*
28182362 TTAGAATTTTATTTAGAT
1 TTAGAATTCTATTTAGAT
28182380 TTA
1 TTA
28182383 TTTAGCTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (18 bp):
TTAGAATTCTATTTAGAT
Found at i:28183878 original size:24 final size:24
Alignment explanation
Indices: 28183833--28183878 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28183823 AAAGAAACAA
* *
28183833 TAAAAGTAAAAACAAATGAAAACT
1 TAAAACTAAAAACAAATAAAAACT
28183857 TAAAACTAAAAATC-AATAAAAA
1 TAAAACTAAAAA-CAAATAAAAA
28183879 TTACTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (24 bp):
TAAAACTAAAAACAAATAAAAACT
Found at i:28184942 original size:17 final size:18
Alignment explanation
Indices: 28184909--28184951 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
28184899 TAAATAAATC
*
28184909 TAAA-TAAAACTATTAAT
1 TAAACTAAAACTACTAAT
28184926 TAAACTAAAACT-CTAAT
1 TAAACTAAAACTACTAAT
*
28184943 TAATCTAAA
1 TAAACTAAA
28184952 CAAGAAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAACTAAAACTACTAAT
Found at i:28185129 original size:15 final size:14
Alignment explanation
Indices: 28185103--28185138 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
28185093 TTGTTTCACT
28185103 AAAAATGATTTTCG
1 AAAAATGATTTTCG
*
28185117 AAAAATGATTTTTG
1 AAAAATGATTTTCG
*
28185131 GAAAATGA
1 AAAAATGA
28185139 CTTACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (14 bp):
AAAAATGATTTTCG
Found at i:28185549 original size:15 final size:15
Alignment explanation
Indices: 28185529--28185580 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 15
28185519 ACTACAAAAG
28185529 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
28185544 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
28185563 ATTTATTATTAATAT
1 ATTTATTATTAATAT
28185578 ATT
1 ATT
28185581 AATATTGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.39
16 1 0.03
17 8 0.26
18 1 0.03
19 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:28189725 original size:26 final size:26
Alignment explanation
Indices: 28189453--28189726 Score: 279
Period size: 26 Copynumber: 10.5 Consensus size: 26
28189443 CTCTAGTAGT
* * *
28189453 GTAAACGCATAACCATGCTGGCGAGC
1 GTAAACGTATAATCATGCTGACGAGC
* *
28189479 GTAAATGTATAATCATGCTAACGAGC
1 GTAAACGTATAATCATGCTGACGAGC
*
28189505 GTAAATGTATAATCATGCTGACGAGC
1 GTAAACGTATAATCATGCTGACGAGC
* *
28189531 ATAAACATAT-ATCCATGCTGACGAGC
1 GTAAACGTATAAT-CATGCTGACGAGC
28189557 GTAAACGTAT-ATCCATGCTGACGAGC
1 GTAAACGTATAAT-CATGCTGACGAGC
* * *
28189583 ATAAATGTAT-ATCCATGCTAACGAGC
1 GTAAACGTATAAT-CATGCTGACGAGC
* * *
28189609 GTAAACGTATAATCATGTTGACAAGT
1 GTAAACGTATAATCATGCTGACGAGC
*
28189635 GTAAACGTAT-ATCCATGCTGATGAGC
1 GTAAACGTATAAT-CATGCTGACGAGC
* *
28189661 GTAAACGTATATTCATGGT-ATCGAGC
1 GTAAACGTATAATCATGCTGA-CGAGC
* * *
28189687 ATAAACGCATAATCATGCTTACGAGC
1 GTAAACGTATAATCATGCTGACGAGC
*
28189713 GTAAACGTGTAATC
1 GTAAACGTATAATC
28189727 GGGAAAATGG
Statistics
Matches: 208, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
25 5 0.02
26 199 0.96
27 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (26 bp):
GTAAACGTATAATCATGCTGACGAGC
Found at i:28197057 original size:26 final size:26
Alignment explanation
Indices: 28196731--28197058 Score: 335
Period size: 26 Copynumber: 12.7 Consensus size: 26
28196721 GAACTCTAGT
* * *
28196731 AGCGTAAACGCATAACCATGCTGGCG
1 AGCGTAAACGTATAATCATGCTGACG
*
28196757 AGCGTAAACGTATAATCATGTTGACG
1 AGCGTAAACGTATAATCATGCTGACG
*
28196783 AGCGTAAACATAT-ATCCATGCTGACG
1 AGCGTAAACGTATAAT-CATGCTGACG
* *
28196809 AGCATAAATGTAT-ATCCATGCTGACG
1 AGCGTAAACGTATAAT-CATGCTGACG
* * *
28196835 AGCATAAACGTAT-ATCCATGTTGATG
1 AGCGTAAACGTATAAT-CATGCTGACG
* *
28196861 AGCGTAAACATATAATCATGTTGACG
1 AGCGTAAACGTATAATCATGCTGACG
* * *
28196887 AGCATAAACGTATAATCATGTTGACA
1 AGCGTAAACGTATAATCATGCTGACG
28196913 AGCGTAAACGTAT-ATCCATGCTGACG
1 AGCGTAAACGTATAAT-CATGCTGACG
*
28196939 AGCATAAACGTAT-ATCCATGC-GACG
1 AGCGTAAACGTATAAT-CATGCTGACG
*
28196964 AGCGTAAAAGTATAATCATGCTGACG
1 AGCGTAAACGTATAATCATGCTGACG
* * **
28196990 AGCGTCAACGTATATTCATGCTGGTG
1 AGCGTAAACGTATAATCATGCTGACG
* * * *
28197016 AGCGTAAATGCATAATCAAGCTTACG
1 AGCGTAAACGTATAATCATGCTGACG
*
28197042 AGCGTAAACGTGTAATC
1 AGCGTAAACGTATAATC
28197059 GGGAATACGA
Statistics
Matches: 257, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
25 24 0.09
26 231 0.90
27 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (26 bp):
AGCGTAAACGTATAATCATGCTGACG
Found at i:28198474 original size:52 final size:51
Alignment explanation
Indices: 28198314--28198479 Score: 197
Period size: 52 Copynumber: 3.2 Consensus size: 51
28198304 TAAATGTAAA
* *
28198314 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAGTCCTTTACGGATTATG
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATGA-ACCTTTACGGATTATG
* * * * *
28198366 AGATCCGATGACCACGTTTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATGAA-CCTTTACGGATTATG
* * * * *
28198418 AGGTTTGATGACTACGTGTCATCATGAGTATCTGAACCTTTTACGGATTGTA
1 AGGTTCGATGACTACGTGTCATCGTGAGTATATGAACC-TTTACGGATTATG
28198470 AGGTTCGATG
1 AGGTTCGATG
28198480 CATTGTGAGT
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
51 2 0.02
52 94 0.98
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (51 bp):
AGGTTCGATGACTACGTGTCATCGTGAGTATATGAACCTTTACGGATTATG
Found at i:28205243 original size:52 final size:52
Alignment explanation
Indices: 28205162--28205348 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 52
28205152 TAAATGTAAA
* *
28205162 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAGTCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* ** * *
28205214 AGGTCCAATGACTATGTGTCATCAAGAGTATATGAATCCTTTACGGATTAGG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * * * *
28205266 AGGTCTGATAACTATGTGTCATTGTGAGTATCTGAACCCTTTATGGATTGTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
28205318 AGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
28205349 TAAATTAAAT
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 114 1.00
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
Found at i:28211880 original size:40 final size:38
Alignment explanation
Indices: 28211825--28212052 Score: 197
Period size: 40 Copynumber: 5.7 Consensus size: 38
28211815 TCAATTCACT
*
28211825 GGCTCATAGCCTGCTAAGCCATAGCTTGAACTTTAACATC
1 GGCTCATAGCCTGCTAAGCCA-AGCTTGAA-TTTATCATC
* * * * *
28211865 GGCTCGTAGCATGCTAAGCTATAGCTTGAATTTTAACACC
1 GGCTCATAGCCTGCTAAGCCA-AGCTTGAA-TTTATCATC
** * ** *
28211905 GGCTTGTAACCTGCTAAGTCGTAGCTTGAATTTATTCATT
1 GGCTCATAGCCTGCTAAG-CCAAGCTTGAATTTA-TCATC
*
28211945 GGCTCATAGCCTGCTAAGTCGAAGCTTGAATTCTATCA-C
1 GGCTCATAGCCTGCTAAG-CCAAGCTTGAATT-TATCATC
28211984 TGGCTCATAGCCTGCTAAGCCGAAGCTTGAATTCTATCATC
1 -GGCTCATAGCCTGCTAAGCC-AAGCTTGAATT-TATCATC
* * * *
28212025 GGCTCGTAACGTGCTAAGCGAAGCTTGA
1 GGCTCATAGCCTGCTAAGCCAAGCTTGA
28212053 CTTCTTTTCA
Statistics
Matches: 159, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
39 13 0.08
40 142 0.89
41 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (38 bp):
GGCTCATAGCCTGCTAAGCCAAGCTTGAATTTATCATC
Found at i:28211971 original size:80 final size:78
Alignment explanation
Indices: 28211825--28212057 Score: 259
Period size: 80 Copynumber: 2.9 Consensus size: 78
28211815 TCAATTCACT
* * * *
28211825 GGCTCATAGCCTGCTAAGCCATAGCTTGAACTTTAACATCGGCTCGTAGCATGCTAAGCTATAGC
1 GGCTCATAACCTGCTAAGCCGTAGCTTGAA-TTTATCATCGGCTCGTAGCATGCTAAGCGA-AGC
*
28211890 TTGAATTTTAACACC
64 TTGAATTCTAACACC
** * * * *
28211905 GGCTTGTAACCTGCTAAGTCGTAGCTTGAATTTATTCATTGGCTCATAGCCTGCTAAGTCGAAGC
1 GGCTCATAACCTGCTAAGCCGTAGCTTGAATTTA-TCATCGGCTCGTAGCATGCTAAG-CGAAGC
* *
28211970 TTGAATTCTATCACT
64 TTGAATTCTAACACC
* * * *
28211985 GGCTCATAGCCTGCTAAGCCGAAGCTTGAATTCTATCATCGGCTCGTAACGTGCTAAGCGAAGCT
1 GGCTCATAACCTGCTAAGCCGTAGCTTGAATT-TATCATCGGCTCGTAGCATGCTAAGCGAAGCT
*
28212050 TGACTTCT
65 TGAATTCT
28212058 TTTCAACGTA
Statistics
Matches: 127, Mismatches: 23, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
79 18 0.14
80 105 0.83
81 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (78 bp):
GGCTCATAACCTGCTAAGCCGTAGCTTGAATTTATCATCGGCTCGTAGCATGCTAAGCGAAGCTT
GAATTCTAACACC
Found at i:28212034 original size:120 final size:119
Alignment explanation
Indices: 28211818--28212052 Score: 289
Period size: 120 Copynumber: 2.0 Consensus size: 119
28211808 TTACTAATCA
*
28211818 ATTCACTGGCTCATAGCCTGCTAAGCCATAGCTTGAACTTTAACATCGGCTCGTAGCATGCTAAG
1 ATTCACTGGCTCATAGCCTGCTAAGCCATAGCTTGAACTTTAACATCGGCTCATAGCATGCTAAG
* * * *
28211883 CTATAGCTTGAATTTTAACACCGGCTTGTAACCTGCTAAGTCGTAGCTTGAATTT
66 CGATAGCTTGAATTCTAACACCGGCTCGTAACCTGCTAAG-CGAAGCTTGAATTT
* * * *
28211938 ATTCATTGGCTCATAGCCTGCTAAGTCGA-AGCTTGAA-TTCTATCA-CTGGCTCATAGCCTGCT
1 ATTCACTGGCTCATAGCCTGCTAAG-CCATAGCTTGAACTT-TAACATC-GGCTCATAGCATGCT
* * *
28212000 AAGCCGA-AGCTTGAATTCTATCATCGGCTCGTAACGTGCTAAGCGAAGCTTGA
63 AAG-CGATAGCTTGAATTCTAACACCGGCTCGTAACCTGCTAAGCGAAGCTTGA
28212053 CTTCTTTTCA
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
119 12 0.12
120 83 0.84
121 4 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (119 bp):
ATTCACTGGCTCATAGCCTGCTAAGCCATAGCTTGAACTTTAACATCGGCTCATAGCATGCTAAG
CGATAGCTTGAATTCTAACACCGGCTCGTAACCTGCTAAGCGAAGCTTGAATTT
Found at i:28214017 original size:40 final size:40
Alignment explanation
Indices: 28213955--28214233 Score: 210
Period size: 40 Copynumber: 6.9 Consensus size: 40
28213945 TTGTTACTAA
*
28213955 TTAATTCACCGGCTCATAGCCTGCTAAGCCATAGCTTGAATT
1 TTAA-TCACCGGCTCGTAGCCTGCTAAGCCA-AGCTTGAATT
* **
28213997 TTAAT-ACCGGCTCGTGGCCTGCTAAGCTGTAGCTTGAATT
1 TTAATCACCGGCTCGTAGCCTGCTAAGC-CAAGCTTGAATT
** * * * *
28214037 TTAAT-ATTGGCTTGTAGCTTGCGAAGCCGTAGCTTGAA-T
1 TTAATCACCGGCTCGTAGCCTGCTAAGCC-AAGCTTGAATT
* * * * *
28214076 TTATTCATCAGCTCGTAGCTTGCTAAGTCGAAGCTTGAATT
1 TTAATCACCGGCTCGTAGCCTGCTAAG-CCAAGCTTGAATT
* * *
28214117 CT-ACCACTGGCTCGTAGCCTGCTAAGCCGAAGCTTGAATT
1 TTAATCACCGGCTCGTAGCCTGCTAAGCC-AAGCTTGAATT
* * * * *
28214157 TT-ATCACCAGCTCGTAACTTTCTAAGCCGAAGCTTGAAAT
1 TTAATCACCGGCTCGTAGCCTGCTAAGCC-AAGCTTGAATT
* * *
28214197 CT-ATCATCGGCTCGTAACCTGCTAAGCCAAAGCTTGA
1 TTAATCACCGGCTCGTAGCCTGCTAAGCC-AAGCTTGA
28214234 CTTCTTTTCA
Statistics
Matches: 191, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
39 6 0.03
40 177 0.93
41 4 0.02
42 4 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (40 bp):
TTAATCACCGGCTCGTAGCCTGCTAAGCCAAGCTTGAATT
Found at i:28214113 original size:80 final size:80
Alignment explanation
Indices: 28213965--28214233 Score: 249
Period size: 80 Copynumber: 3.4 Consensus size: 80
28213955 TTAATTCACC
* * * ** * * *
28213965 GGCTCATAGCCTGCTAAGCC-ATAGCTTGAATTTTAAT-ACCGGCTCGTGGCCTGCTAAGCTGTA
1 GGCTCGTAGCCTGCGAAGCCGA-AGCTTGAATTTT-ATCACCAGCTCGTAACTTGCTAAGCCGAA
* * *
28214028 GCTTGAATTTTAATATT
64 GCTTGAATTCTAACACT
* * * * * *
28214045 GGCTTGTAGCTTGCGAAGCCGTAGCTTGAA-TTTATTCATCAGCTCGTAGCTTGCTAAGTCGAAG
1 GGCTCGTAGCCTGCGAAGCCGAAGCTTGAATTTTA-TCACCAGCTCGTAACTTGCTAAGCCGAAG
*
28214109 CTTGAATTCTACCACT
65 CTTGAATTCTAACACT
* *
28214125 GGCTCGTAGCCTGCTAAGCCGAAGCTTGAATTTTATCACCAGCTCGTAACTTTCTAAGCCGAAGC
1 GGCTCGTAGCCTGCGAAGCCGAAGCTTGAATTTTATCACCAGCTCGTAACTTGCTAAGCCGAAGC
* *
28214190 TTGAAATCTATCA-T
66 TTGAATTCTAACACT
* * *
28214204 CGGCTCGTAACCTGCTAAGCCAAAGCTTGA
1 -GGCTCGTAGCCTGCGAAGCCGAAGCTTGA
28214234 CTTCTTTTCA
Statistics
Matches: 156, Mismatches: 28, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
79 5 0.03
80 146 0.94
81 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (80 bp):
GGCTCGTAGCCTGCGAAGCCGAAGCTTGAATTTTATCACCAGCTCGTAACTTGCTAAGCCGAAGC
TTGAATTCTAACACT
Found at i:28214184 original size:120 final size:120
Alignment explanation
Indices: 28213974--28214238 Score: 291
Period size: 120 Copynumber: 2.2 Consensus size: 120
28213964 CGGCTCATAG
* * * * * *
28213974 CCTGCTAAGCCATAGCTTGAATTTTAATACCGGCTCGTGGCCTGCTAAGCTGTAGCTTGAATTTT
1 CCTGCTAAGCCAAAGCTTGAATTCTAACACCGGCTCGTAGCCTGCTAAGCCGAAGCTTGAATTTT
*** * * * * *
28214039 AATATTGGCTTGTAGCTTGCGAAGCCGTAGCTTG-AATTTATTCATCAGCTCGTAG
66 AATACCAGCTCGTAACTTGCGAAGCCGAAGCTTGAAATCTA-TCATCAGCTCGTAA
* * * * *
28214094 CTTGCTAAGTCGAAGCTTGAATTCTACCACTGGCTCGTAGCCTGCTAAGCCGAAGCTTGAATTTT
1 CCTGCTAAGCCAAAGCTTGAATTCTAACACCGGCTCGTAGCCTGCTAAGCCGAAGCTTGAATTTT
* * *
28214159 -ATCACCAGCTCGTAACTTTCTAAGCCGAAGCTTGAAATCTATCATCGGCTCGTAA
66 AAT-ACCAGCTCGTAACTTGCGAAGCCGAAGCTTGAAATCTATCATCAGCTCGTAA
*
28214214 CCTGCTAAGCCAAAGCTTGACTTCT
1 CCTGCTAAGCCAAAGCTTGAATTCT
28214239 TTTCAACGTA
Statistics
Matches: 117, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
119 2 0.02
120 110 0.94
121 5 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (120 bp):
CCTGCTAAGCCAAAGCTTGAATTCTAACACCGGCTCGTAGCCTGCTAAGCCGAAGCTTGAATTTT
AATACCAGCTCGTAACTTGCGAAGCCGAAGCTTGAAATCTATCATCAGCTCGTAA
Found at i:28225001 original size:47 final size:47
Alignment explanation
Indices: 28224932--28225041 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 47
28224922 ACAGTAACGT
* * *
28224932 AGATAAATTGCCACTTTGTAATATTGTGGACAAGCCACCACATTTGC
1 AGATAAACTGCCACTTTGTAATATTGTGAACAAGCCACCACATTTAC
* *
28224979 AGATAAACTGTCACTTTGTAATATTGTGAACAAGCCACCACTTTTAC
1 AGATAAACTGCCACTTTGTAATATTGTGAACAAGCCACCACATTTAC
*
28225026 AGATAAACTACCACTT
1 AGATAAACTGCCACTT
28225042 CTTCCTCCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (47 bp):
AGATAAACTGCCACTTTGTAATATTGTGAACAAGCCACCACATTTAC
Found at i:28233666 original size:30 final size:29
Alignment explanation
Indices: 28233630--28233740 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 29
28233620 ATTAGAAATT
* *
28233630 AAAATAACTTAATAATTTTATTATTTCAAA
1 AAAATAATTTAATAATTTTA-TATTTAAAA
* *
28233660 AAAATAATTTTTATATTTTTATATTTAAAA
1 AAAATAA-TTTAATAATTTTATATTTAAAA
* * **
28233690 AATAATAATTTAAAAAAATTTATATTT-TGA
1 AA-AATAATTT-AATAATTTTATATTTAAAA
28233720 AAAATAATTTTAATAATTTTA
1 AAAATAA-TTTAATAATTTTA
28233741 AAATCATTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
29 13 0.20
30 26 0.40
31 26 0.40
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATAATTTAATAATTTTATATTTAAAA
Found at i:28233740 original size:29 final size:29
Alignment explanation
Indices: 28233630--28233740 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 29
28233620 ATTAGAAATT
* *
28233630 AAAATAA-CTTAATAATTTTATTATTTCAAA
1 AAAATAATTTTAATAATTTTA-TATTT-TAA
* *
28233660 AAAATAATTTTTATATTTTTATA-TTTAA
1 AAAATAATTTTAATAATTTTATATTTTAA
* * *
28233688 AAAATAATAATTTAAAAAAATTTATATTTTGA
1 AAAATAAT--TTT-AATAATTTTATATTTTAA
28233720 AAAATAATTTTAATAATTTTA
1 AAAATAATTTTAATAATTTTA
28233741 AAATCATTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
28 10 0.15
29 10 0.15
30 15 0.23
31 18 0.28
32 12 0.18
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
AAAATAATTTTAATAATTTTATATTTTAA
Found at i:28233743 original size:20 final size:20
Alignment explanation
Indices: 28233692--28233749 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
28233682 ATTTAAAAAA
*
28233692 TAATAA-TTTAAAA-AAATT
1 TAATAATTTTAAAATAATTT
28233710 T-AT-ATTTTGAAAAATAATTT
1 TAATAATTTT--AAAATAATTT
*
28233730 TAATAATTTTAAAATCATTT
1 TAATAATTTTAAAATAATTT
28233750 GCTGACGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 1 0.03
17 5 0.16
18 1 0.03
19 4 0.12
20 14 0.44
21 2 0.06
22 5 0.16
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATAATTTTAAAATAATTT
Found at i:28236487 original size:655 final size:657
Alignment explanation
Indices: 28235302--28236542 Score: 1897
Period size: 655 Copynumber: 1.9 Consensus size: 657
28235292 GACCGATGAA
* *** * * *
28235302 GGAGGAAGAAAAGAAGATGTGGGTTTTGTTCACTCACTTAAAGAAGAAGAAAGGAGGAGAGAAAA
1 GGAGGAAGAAAAGAAGATATCAATTTCGATCACTCACTTAAAGAAGAAGAAAGGAGAAGAGAAAA
** * *
28235367 TAAAAAAATGGGTGGTGTTGTGTGGTGGTTGTCACGGTGGAGGAAGGCGGTGCTAAAGGAAATAG
66 TAAAAAAATGGGTGGTGTTACGCGGTGGTTGTCACGGTGGAGGAAGGCGGTGCTAAAGGAAACAG
*
28235432 TGGAGAAAAATGGAAAAGAGTGGTGACAAGGTGGAGGTCCGGTGGTGATGATGGGTGTTTGAGGA
131 TGGAGAAAAATGGAAAAGAGTGGCGACAAGGTGGAGGTCCGGTGGTGATGATGGGTGTTTGAGGA
* *
28235497 AAAGGAGTGGTAGAAGAGAGGAGAAAAATAATAGAAATGGTGGTTGCTAGGTAAAACAAAATGAA
196 AAACGAGTGGTAGAAGAGAGGAGAAAAATAATAGAAATGGTGGTTGATAGGTAAAACAAAATGAA
* * * *
28235562 AAGAGACAAAATACGGAAGAGCAAAAGAGGAGGGTTTCAAAAATGAATAGGAAAATAAAATATGA
261 AAGAGACAAAATACGGAACAACAAAAGAAGAGGGTTGCAAAAATGAATAGGAAAATAAAATATGA
* * * **
28235627 ACAATTAAAGGTGGTCATTCATCTTGTCCAAGTTCAATATATGTCACACAAGGTACAGGTGGTGA
326 ACAATAAAAGGTGGTCATTCACCTTGTCCAACTTCAATATATGTCACACAAGGTACAGGTGCAGA
*
28235692 AATATGCATGTTGAGGGGACGAAGAGTAAAAGAAGATAATGAGAGTGAAAAGGGGGTCTGGGGGG
391 AATATGCATGTTGAGGGGACGAAGAGTAAAAGAAGATAATGAGAGTGAAAAGGGGGGCTGGGGGG
*
28235757 GAAAGTTGACTAACTAAAGGAGGAAACAATTTGCATTTACTTACTTGACATAGTCCATAACGTTG
456 GAAAGTTGACTAACTAAAGGAGGAAACAATTTGCATTTACTTACTTGACATAGTCCATAACGATG
* *
28235822 AATGTTATCTCTCTTTATGGATACTTAAAATATCCTTATTTAATCATAATTTAAAATAATAATGA
521 AATGTTATCTCTCTTTATGGAAACTTAAAATATCATTATTTAATCATAATTTAAAATAATAATGA
28235887 TATTTTGAAATGAAGAAGAAAAAGAGAAAGGATCTTCATCGTCGGCGACGATGATAGCGATGGTC
586 TATTTTGAAATGAAGAAGAAAAAGAGAAAGGATCTTCATCGTCGGCGACGATGATAGCGATGGTC
28235952 CGACGAC
651 CGACGAC
*
28235959 GGAGGAAGAAAAGAAGATATCAATTTCGATCACTCACTTAAAGAAGAA-AAGATGAGAAGAGAAA
1 GGAGGAAGAAAAGAAGATATCAATTTCGATCACTCACTTAAAGAAGAAGAA-AGGAGAAGAGAAA
* * **
28236023 ATAAGAAAATGGGTGGTGTTACGCGGTGGTTGTCACGGTGGAGGAAGGCGGTGCTAAGGGCTACA
65 ATAAAAAAATGGGTGGTGTTACGCGGTGGTTGTCACGGTGGAGGAAGGCGGTGCTAAAGGAAACA
* *
28236088 GTGGAG-AAAATGGAGGAGAGATGTGGCGATAAGGTGGAGGTCCGGTGGTGATGAT-GGTGGTTT
130 GTGGAGAAAAATGGA--AAAGA-GTGGCGACAAGGTGGAGGTCCGGTGGTGATGATGGGT-GTTT
* * * * *
28236151 TAGGAAAACGAGTGTTGGAGGAGAGGAGGAAAATAATAGAAATGGTGGTTGAT-GGCTAAAACAA
191 GAGGAAAACGAGTGGTAGAAGAGAGGAGAAAAATAATAGAAATGGTGGTTGATAGG-TAAAACAA
* * **
28236215 AA-G-AGAG-GAGAAAATGGGGAACAACAAAAGAAG-GGGTTGCAAAAATGAATAGGAAAATAAA
255 AATGAAAAGAGACAAAATACGGAACAACAAAAGAAGAGGGTTGCAAAAATGAATAGGAAAATAAA
* * * * *
28236276 ATATGAACAATAAAAGTTGTTCATTCACCTTGTCCAGACTT-AGTATATGTCAGACAAGGTACGG
320 ATATGAACAATAAAAGGTGGTCATTCACCTTGTCCA-ACTTCAATATATGTCACACAAGGTACAG
*
28236340 GTGCAGAAATATGCATGTTGAGGGGACGAAGAGTAAAAGAAGATAATGAGAGTGAAAAGGGGGGG
384 GTGCAGAAATATGCATGTTGAGGGGACGAAGAGTAAAAGAAGATAATGAGAGTGAAAAGGGGGGC
*
28236405 TGTGGGGGAAAGTTGACTAACTAAAGGAGGAAACAATTTGCATTTACTTACTTGACATAGTCCAT
449 TGGGGGGGAAAGTTGACTAACTAAAGGAGGAAACAATTTGCATTTACTTACTTGACATAGTCCAT
*
28236470 AATGATGAATGTTATCTCTCTTTATGGAAACTTAAAATATCATTATTTAATCATAATTTAAAATA
514 AACGATGAATGTTATCTCTCTTTATGGAAACTTAAAATATCATTATTTAATCATAATTTAAAATA
28236535 ATAATGAT
579 ATAATGAT
28236543 TTTAACAATG
Statistics
Matches: 526, Mismatches: 51, Indels: 16
0.89 0.09 0.03
Matches are distributed among these distances:
655 273 0.52
656 33 0.06
657 119 0.23
658 10 0.02
659 91 0.17
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (657 bp):
GGAGGAAGAAAAGAAGATATCAATTTCGATCACTCACTTAAAGAAGAAGAAAGGAGAAGAGAAAA
TAAAAAAATGGGTGGTGTTACGCGGTGGTTGTCACGGTGGAGGAAGGCGGTGCTAAAGGAAACAG
TGGAGAAAAATGGAAAAGAGTGGCGACAAGGTGGAGGTCCGGTGGTGATGATGGGTGTTTGAGGA
AAACGAGTGGTAGAAGAGAGGAGAAAAATAATAGAAATGGTGGTTGATAGGTAAAACAAAATGAA
AAGAGACAAAATACGGAACAACAAAAGAAGAGGGTTGCAAAAATGAATAGGAAAATAAAATATGA
ACAATAAAAGGTGGTCATTCACCTTGTCCAACTTCAATATATGTCACACAAGGTACAGGTGCAGA
AATATGCATGTTGAGGGGACGAAGAGTAAAAGAAGATAATGAGAGTGAAAAGGGGGGCTGGGGGG
GAAAGTTGACTAACTAAAGGAGGAAACAATTTGCATTTACTTACTTGACATAGTCCATAACGATG
AATGTTATCTCTCTTTATGGAAACTTAAAATATCATTATTTAATCATAATTTAAAATAATAATGA
TATTTTGAAATGAAGAAGAAAAAGAGAAAGGATCTTCATCGTCGGCGACGATGATAGCGATGGTC
CGACGAC
Found at i:28246990 original size:24 final size:24
Alignment explanation
Indices: 28246952--28247017 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
28246942 TTCATTAAGC
*
28246952 TTACGCTCGTTAGCTAATGTACGT
1 TTACGCTCGTCAGCTAATGTACGT
* *
28246976 TTATGCTCGTCAGCTAATGTATGT
1 TTACGCTCGTCAGCTAATGTACGT
* *
28247000 TTACACTCGTCATCTAAT
1 TTACGCTCGTCAGCTAAT
28247018 CAAATAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (24 bp):
TTACGCTCGTCAGCTAATGTACGT
Found at i:28258981 original size:22 final size:21
Alignment explanation
Indices: 28258956--28258996 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28258946 AGAAATGGAA
*
28258956 TGATTATAATGGGGCGACACTG
1 TGATT-TAACGGGGCGACACTG
*
28258978 TGATTTTACGGGGCGACAC
1 TGATTTAACGGGGCGACAC
28258997 CTCAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (21 bp):
TGATTTAACGGGGCGACACTG
Found at i:28259258 original size:95 final size:94
Alignment explanation
Indices: 28259107--28259304 Score: 211
Period size: 95 Copynumber: 2.1 Consensus size: 94
28259097 TAGGGTTATG
* * * * *
28259107 TTGTGTAAGACCATAGCTCGACTATGGAAGCATATGGAGTTCGCTAGGATAGTAAACACAAGGTA
1 TTGTGTAAGACCATAACTCAACTATGGAAGCATATGAAGTTCGCTAGGACAATAAACACAAGGTA
* * *
28259172 GTCTGTCAGGATGTTAAACATGGGGCTACA
66 ATCTATCAAGATGTTAAA-ATGGGGCTACA
* * * **
28259202 TTGTGTAAGACCATAACTCAATTAT-GATAGCATATGAAGTTTG-TCGGGACAATAAACACGGGG
1 TTGTGTAAGACCATAACTCAACTATGGA-AGCATATGAAGTTCGCT-AGGACAATAAACACAAGG
* * *
28259265 TAATTTATCAAGATGTTAAAATGGGGTTATA
64 TAATCTATCAAGATGTTAAAATGGGGCTACA
28259296 TTGTGTAAG
1 TTGTGTAAG
28259305 GCTATAGTTC
Statistics
Matches: 85, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
94 21 0.25
95 64 0.75
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (94 bp):
TTGTGTAAGACCATAACTCAACTATGGAAGCATATGAAGTTCGCTAGGACAATAAACACAAGGTA
ATCTATCAAGATGTTAAAATGGGGCTACA
Found at i:28259370 original size:94 final size:94
Alignment explanation
Indices: 28259157--28259372 Score: 222
Period size: 94 Copynumber: 2.3 Consensus size: 94
28259147 TCGCTAGGAT
* * *
28259157 AGTAAACACAAGGTAGTCTGTCAGGATGTTAAACATGGGGCTACATTGTGTAAGACCATAACTCA
1 AGTAAACACAGGGTA-TCTTTCAAGATGTTAAACATGGGGCTACATTGTGTAAGACCATAACTCA
* **
28259222 ATTATGATAGCATATGAAGTTTGTCGGGAC
65 ATTATGATAGCATATGAAGTCTACCGGGAC
* * * * * * **
28259252 AATAAACACGGGGTAAT-TTATCAAGATGTTAAA-ATGGGGTTATATTGTGTAAGGCTATAGTTC
1 AGTAAACACAGGGT-ATCTT-TCAAGATGTTAAACATGGGGCTACATTGTGTAAGACCATAACTC
* *
28259315 GAA-TATGATAGTATATGTAGTCTACCGGGAC
64 -AATTATGATAGCATATGAAGTCTACCGGGAC
28259346 AGTAAACACAGGGTATCTCTTCAAGAT
1 AGTAAACACAGGGTATCT-TTCAAGAT
28259373 AATAACAATG
Statistics
Matches: 98, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
93 2 0.02
94 68 0.69
95 27 0.28
96 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (94 bp):
AGTAAACACAGGGTATCTTTCAAGATGTTAAACATGGGGCTACATTGTGTAAGACCATAACTCAA
TTATGATAGCATATGAAGTCTACCGGGAC
Found at i:28265788 original size:27 final size:29
Alignment explanation
Indices: 28265758--28265815 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 29
28265748 AGTTTAATTT
28265758 ATTTAAAAAT-AAAAATAAAA-AATATGA
1 ATTTAAAAATGAAAAATAAAACAATATGA
* *
28265785 ATTTAAACATGAAATATAAAATCAATATGA
1 ATTTAAAAATGAAAAATAAAA-CAATATGA
28265815 A
1 A
28265816 AAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 9 0.35
30 8 0.31
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (29 bp):
ATTTAAAAATGAAAAATAAAACAATATGA
Found at i:28266113 original size:30 final size:29
Alignment explanation
Indices: 28266079--28266150 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
28266069 TTAAATTAGT
*
28266079 AATAATAAAATTATATTTTAATCTTTTAAA
1 AATAATAAAATT-TAATTTAATCTTTTAAA
*
28266109 AATAATAATAATTTAATTTAATTTTTTAAA
1 AATAATAA-AATTTAATTTAATCTTTTAAA
*
28266139 AATTATGAAAAT
1 AATAAT-AAAAT
28266151 ATAAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 31 0.84
31 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
AATAATAAAATTTAATTTAATCTTTTAAA
Found at i:28266156 original size:16 final size:17
Alignment explanation
Indices: 28266137--28266175 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
28266127 TAATTTTTTA
28266137 AAAATTATGAAAATA-T
1 AAAATTATGAAAATATT
*
28266153 AAAA-TATTAAAATATT
1 AAAATTATGAAAATATT
28266169 AAAATTA
1 AAAATTA
28266176 CATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 9 0.45
17 2 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTATGAAAATATT
Found at i:28273610 original size:21 final size:21
Alignment explanation
Indices: 28273568--28273616 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
28273558 CCACGTTAAT
*
28273568 AAATTA-TTTTAAAATTATTA
1 AAATTATTTTTAAAAATATTA
28273588 AAATTATTTTTGAAAAATA-TA
1 AAATTATTTTT-AAAAATATTA
28273609 AAATTATT
1 AAATTATT
28273617 AAAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 14 0.54
22 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATTATTTTTAAAAATATTA
Found at i:28273613 original size:30 final size:31
Alignment explanation
Indices: 28273576--28273651 Score: 120
Period size: 32 Copynumber: 2.5 Consensus size: 31
28273566 ATAAATTATT
28273576 TTAAAATTATTAAAATTA-TTTTTGAAA-AA
1 TTAAAATTATTAAAATTATTTTTTGAAATAA
28273605 TATAAAATTATTAAAATTATTTTTTTGAAATAA
1 T-TAAAATTATTAAAATTA-TTTTTTGAAATAA
28273638 TTAAAATTATTAAA
1 TTAAAATTATTAAA
28273652 TAATTTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
29 1 0.02
30 17 0.40
32 22 0.51
33 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TTAAAATTATTAAAATTATTTTTTGAAATAA
Found at i:28274549 original size:31 final size:31
Alignment explanation
Indices: 28274511--28274585 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
28274501 ATTAAAATTA
28274511 TTTAATAATTTTAT-TATTTCAAAAAAATAAT
1 TTTAATAATTTTATAT-TTTCAAAAAAATAAT
*
28274542 TTTAATAATTTTATATTTTTAAAAAAATAAT
1 TTTAATAATTTTATATTTTCAAAAAAATAAT
*
28274573 TTTAATAAATTTA
1 TTTAATAATTTTA
28274586 AAATAATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTAATAATTTTATATTTTCAAAAAAATAAT
Found at i:28274588 original size:22 final size:22
Alignment explanation
Indices: 28274545--28274588 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
28274535 AAATAATTTT
**
28274545 AATAATTTTATATTTTTAAAAA
1 AATAATTTTATAAATTTAAAAA
28274567 AATAATTTTAATAAATTTAAAA
1 AATAATTTT-ATAAATTTAAAA
28274589 TAATTTGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATAAATTTAAAAA
Found at i:28282416 original size:68 final size:64
Alignment explanation
Indices: 28282307--28282458 Score: 187
Period size: 68 Copynumber: 2.3 Consensus size: 64
28282297 GTGGGGAGTA
* ** * *
28282307 GTTGTAGAGACGTGAAGAGGCAGCAATTGAATGGCAAAGCAGTTGATAGAAAAAAATAGCAGCAG
1 GTTGTAGAGACGTGAAGAGGCAACAATTGAACAGCAAAGCAGTTG---CAAAAAAATAGCAACAG
28282372 GCG
63 G-G
** *
28282375 GTTGTAGAGACGTGAAGAGGCAACAATTGTCCAGCAAAGCAGTTGCCAAAAAATAGCAACAGGG
1 GTTGTAGAGACGTGAAGAGGCAACAATTGAACAGCAAAGCAGTTGCAAAAAAATAGCAACAGGG
*
28282439 ATTGTAGAGACGTGAAGAGG
1 GTTGTAGAGACGTGAAGAGG
28282459 AAATTTTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 20 0.27
65 15 0.20
68 40 0.53
ACGTcount: A:0.39, C:0.13, G:0.32, T:0.16
Consensus pattern (64 bp):
GTTGTAGAGACGTGAAGAGGCAACAATTGAACAGCAAAGCAGTTGCAAAAAAATAGCAACAGGG
Found at i:28285670 original size:18 final size:18
Alignment explanation
Indices: 28285647--28285695 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
28285637 CTCTTTTCTT
*
28285647 TAGGCTGTATTCTATCAC
1 TAGGCTATATTCTATCAC
28285665 TAGGCTATATTCTATCAC
1 TAGGCTATATTCTATCAC
28285683 TAGGCTATATTCT
1 TAGGCTATATTCT
28285696 GCAGGGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (18 bp):
TAGGCTATATTCTATCAC
Found at i:28288604 original size:26 final size:26
Alignment explanation
Indices: 28288566--28288619 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
28288556 ATTTTAGGCG
*
28288566 CAATTCTGGACATGTTCATGCAGTGA
1 CAATTCTGGACATGTTCATGCAGCGA
* *
28288592 CAATTTTGTACATGTTCATGCAGCGA
1 CAATTCTGGACATGTTCATGCAGCGA
28288618 CA
1 CA
28288620 TTCCTGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (26 bp):
CAATTCTGGACATGTTCATGCAGCGA
Found at i:28288650 original size:37 final size:38
Alignment explanation
Indices: 28288609--28288706 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
28288599 GTACATGTTC
28288609 ATGCAGCGACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
* * *
28288646 ATGCAGCGATAGTT-CTGGATGCAATTTGAAGAATATTT
1 ATGCAGCGACA-TTCCTGGGTGCAATTTGAAGAATACTT
* *
28288684 ATGCAGCGACAGTCTTGGGTGCA
1 ATGCAGCGACATTCCTGGGTGCA
28288707 TTTCGGAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 20 0.39
38 31 0.61
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (38 bp):
ATGCAGCGACATTCCTGGGTGCAATTTGAAGAATACTT
Found at i:28290337 original size:7 final size:7
Alignment explanation
Indices: 28290327--28290359 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
28290317 ATATTTTATG
28290327 GAATTTT
1 GAATTTT
28290334 GAATTTT
1 GAATTTT
28290341 GAATTTT
1 GAATTTT
28290348 -AATTATT
1 GAATT-TT
28290355 GAATT
1 GAATT
28290360 AAAATTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 4 0.17
7 16 0.67
8 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (7 bp):
GAATTTT
Found at i:28290346 original size:14 final size:14
Alignment explanation
Indices: 28290322--28290359 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28290312 AATAAATATT
*
28290322 TTATGGAATTTTGAA
1 TTATTGAATTTT-AA
28290337 TT-TTGAATTTTAA
1 TTATTGAATTTTAA
28290350 TTATTGAATT
1 TTATTGAATT
28290360 AAAATTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 15 0.71
15 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
TTATTGAATTTTAA
Found at i:28292293 original size:44 final size:44
Alignment explanation
Indices: 28292243--28292375 Score: 187
Period size: 44 Copynumber: 3.0 Consensus size: 44
28292233 ATATGCTGGT
*
28292243 AACAGGCATGACCTGTGGGTCAACA-AGGAGTAAATCAGATATCG
1 AACAGGCATGACCTTTGGGTCAACAGA-GAGTAAATCAGATATCG
* * * *
28292287 AACAGGCATGACCTTTGGGTTAATAGAGAGTAAATCAAATATCA
1 AACAGGCATGACCTTTGGGTCAACAGAGAGTAAATCAGATATCG
* *
28292331 AATAGACATGACCTTTGGGTCAACAGAGAGTAAATCAGATATCG
1 AACAGGCATGACCTTTGGGTCAACAGAGAGTAAATCAGATATCG
28292375 A
1 A
28292376 TCATTGAAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 76 0.99
45 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (44 bp):
AACAGGCATGACCTTTGGGTCAACAGAGAGTAAATCAGATATCG
Found at i:28298705 original size:123 final size:123
Alignment explanation
Indices: 28298481--28298726 Score: 447
Period size: 123 Copynumber: 2.0 Consensus size: 123
28298471 ACAAATATGC
* *
28298481 GGTGGCATCAGAAGAACAAATCCTACCTGAATGTGATCACATAACTGAGGCTAATAGTTGTGATC
1 GGTGACATCAGAAGAACAAATCCTACCTGAATGCGATCACATAACTGAGGCTAATAGTTGTGATC
*
28298546 TGAGACAGGGCTGGCAATTGGAATCTTTTGATTTGTCTAATAGGACGATCCTTGTTTT
66 TGAGACAGGGCTGGCAATTGGAATCTTTGGATTTGTCTAATAGGACGATCCTTGTTTT
28298604 GGTGACATCAGAAGAACAAATCCTACCTGAATGCGATCACATAACTGAGGCTAATAGTTGTGATC
1 GGTGACATCAGAAGAACAAATCCTACCTGAATGCGATCACATAACTGAGGCTAATAGTTGTGATC
* *
28298669 TGAGATAGGGCTGGCAATTGGAATCTTTGGATTTGTCTAATAGGACGGTCCTTGTTTT
66 TGAGACAGGGCTGGCAATTGGAATCTTTGGATTTGTCTAATAGGACGATCCTTGTTTT
28298727 TAAACCATCA
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 118 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (123 bp):
GGTGACATCAGAAGAACAAATCCTACCTGAATGCGATCACATAACTGAGGCTAATAGTTGTGATC
TGAGACAGGGCTGGCAATTGGAATCTTTGGATTTGTCTAATAGGACGATCCTTGTTTT
Found at i:28304020 original size:17 final size:17
Alignment explanation
Indices: 28303998--28304035 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28303988 GTCATTGCAT
28303998 TTTTATTTGTCACTACA
1 TTTTATTTGTCACTACA
* *
28304015 TTTTATTTGTTAGTACA
1 TTTTATTTGTCACTACA
28304032 TTTT
1 TTTT
28304036 CATTGTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTATTTGTCACTACA
Found at i:28304635 original size:19 final size:19
Alignment explanation
Indices: 28304613--28304649 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28304603 ATAAAAATAG
28304613 AGAAGAAGAAAAAAAGCAA
1 AGAAGAAGAAAAAAAGCAA
*
28304632 AGAAGAAGAGAAAAAGCA
1 AGAAGAAGAAAAAAAGCA
28304650 GAAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.70, C:0.05, G:0.24, T:0.00
Consensus pattern (19 bp):
AGAAGAAGAAAAAAAGCAA
Found at i:28307661 original size:34 final size:34
Alignment explanation
Indices: 28307618--28307684 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
28307608 GCTATTATGC
*
28307618 ATACAAAGAAAGCTATGTGGAGAAGTTAAAGTCA
1 ATACAAAGAAAGCTAAGTGGAGAAGTTAAAGTCA
*
28307652 ATACAAAGAAAGCTAAGTGGTGAAGTTAAAGTC
1 ATACAAAGAAAGCTAAGTGGAGAAGTTAAAGTC
28307685 TGTGCATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.21
Consensus pattern (34 bp):
ATACAAAGAAAGCTAAGTGGAGAAGTTAAAGTCA
Found at i:28316315 original size:29 final size:29
Alignment explanation
Indices: 28316282--28316379 Score: 126
Period size: 29 Copynumber: 3.4 Consensus size: 29
28316272 TCTCTTATAC
** *
28316282 ATAGATAGCCATAGAGGTGTCCTTAAACA
1 ATAGATAGCCATAGAGGCATCCTCAAACA
* *
28316311 ATAGATAACCA-CGAAGGCATCCTCAAACA
1 ATAGATAGCCATAG-AGGCATCCTCAAACA
*
28316340 ATAGATAGCCATAAAGGCATCCTCAAACA
1 ATAGATAGCCATAGAGGCATCCTCAAACA
28316369 ATAGATAGCCA
1 ATAGATAGCCA
28316380 CGAAGGCATC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.02
29 58 0.98
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (29 bp):
ATAGATAGCCATAGAGGCATCCTCAAACA
Found at i:28316350 original size:58 final size:58
Alignment explanation
Indices: 28316282--28316391 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
28316272 TCTCTTATAC
* ** *
28316282 ATAGATAGCCATAGAGGTGTCCTTAAACAATAGATAACCACGAAGGCATCCTCAAACA
1 ATAGATAGCCATAAAGGCATCCTCAAACAATAGATAACCACGAAGGCATCCTCAAACA
*
28316340 ATAGATAGCCATAAAGGCATCCTCAAACAATAGATAGCCACGAAGGCATCCT
1 ATAGATAGCCATAAAGGCATCCTCAAACAATAGATAACCACGAAGGCATCCT
28316392 TTAAAGAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (58 bp):
ATAGATAGCCATAAAGGCATCCTCAAACAATAGATAACCACGAAGGCATCCTCAAACA
Found at i:28316385 original size:29 final size:29
Alignment explanation
Indices: 28316301--28316391 Score: 146
Period size: 29 Copynumber: 3.1 Consensus size: 29
28316291 CATAGAGGTG
* *
28316301 TCCTTAAACAATAGATAACCACGAAGGCA
1 TCCTCAAACAATAGATAGCCACGAAGGCA
**
28316330 TCCTCAAACAATAGATAGCCATAAAGGCA
1 TCCTCAAACAATAGATAGCCACGAAGGCA
28316359 TCCTCAAACAATAGATAGCCACGAAGGCA
1 TCCTCAAACAATAGATAGCCACGAAGGCA
28316388 TCCT
1 TCCT
28316392 TTAAAGAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (29 bp):
TCCTCAAACAATAGATAGCCACGAAGGCA
Found at i:28316439 original size:28 final size:28
Alignment explanation
Indices: 28316375--28316533 Score: 171
Period size: 28 Copynumber: 5.7 Consensus size: 28
28316365 AACAATAGAT
*
28316375 AGCCACGAAGGCATC-CTTTAA-AGAATC
1 AGCCACAAAGGC-TCACTTTAACAGAATC
* *
28316402 AGCCAAAAAGGCTCACTTTAATAGAATC
1 AGCCACAAAGGCTCACTTTAACAGAATC
* *
28316430 AGTCACAAAGGCTTTA-TTTAACAGAATC
1 AGCCACAAAGGC-TCACTTTAACAGAATC
* *
28316458 AGGCACAAAGGCTCTCTTTAACAGAATC
1 AGCCACAAAGGCTCACTTTAACAGAATC
* * *
28316486 ATCCAAAAAGGCTCACATTTAACAGATTC
1 AGCCACAAAGGCTCAC-TTTAACAGAATC
*
28316515 AGCCACAAAAGCTCACTTT
1 AGCCACAAAGGCTCACTTT
28316534 TCGGTAATGC
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
26 2 0.02
27 17 0.15
28 65 0.59
29 26 0.24
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.23
Consensus pattern (28 bp):
AGCCACAAAGGCTCACTTTAACAGAATC
Found at i:28320285 original size:20 final size:20
Alignment explanation
Indices: 28320238--28320275 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28320228 TACCCTTTGT
28320238 AATTTTTATAATATATTTTC
1 AATTTTTATAATATATTTTC
28320258 AATTTTTATAATAT-TTTT
1 AATTTTTATAATATATTTT
28320276 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTATAATATATTTTC
Found at i:28320616 original size:19 final size:19
Alignment explanation
Indices: 28320594--28320630 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28320584 CTATTGTCAC
28320594 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
28320613 CCACCGTAATCAAATTTG
1 CCACCGTAATCAAATTTG
28320631 CTATTAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:28322403 original size:23 final size:23
Alignment explanation
Indices: 28322373--28322447 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
28322363 ACAAATTACA
*
28322373 AGAGAATATTCACTGTTTATGCT
1 AGAGAATATTCACTGTTTATGCC
*
28322396 AGAGAATATTTACTGTTTATGCC
1 AGAGAATATTCACTGTTTATGCC
* * *
28322419 AGAGAAT-CTCACTATTCATGCC
1 AGAGAATATTCACTGTTTATGCC
*
28322441 AAAGAAT
1 AGAGAAT
28322448 CTCACTATTC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 17 0.38
23 28 0.62
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
AGAGAATATTCACTGTTTATGCC
Found at i:28322446 original size:22 final size:22
Alignment explanation
Indices: 28322414--28322460 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28322404 TTTACTGTTT
*
28322414 ATGCCAGAGAATCTCACTATTC
1 ATGCCAAAGAATCTCACTATTC
28322436 ATGCCAAAGAATCTCACTATTC
1 ATGCCAAAGAATCTCACTATTC
28322458 ATG
1 ATG
28322461 TCACTGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (22 bp):
ATGCCAAAGAATCTCACTATTC
Found at i:28333953 original size:31 final size:30
Alignment explanation
Indices: 28333903--28333963 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
28333893 AAAAATTAAA
28333903 CCCTAATATGAGAACAATTATTAAGTTTAG
1 CCCTAATATGAGAACAATTATTAAGTTTAG
* *
28333933 CCCTCAATGTGAGAATAATTATTAAGTTTAG
1 CCCT-AATATGAGAACAATTATTAAGTTTAG
28333964 GGTTTAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (30 bp):
CCCTAATATGAGAACAATTATTAAGTTTAG
Found at i:28337206 original size:22 final size:22
Alignment explanation
Indices: 28337181--28337251 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
28337171 CAGCAATTCA
*
28337181 GTGCTATCTGCTTAGCACTTTG
1 GTGCTATCTGTTTAGCACTTTG
* *
28337203 GTGCTCTCTATTTAGCA-TTTCG
1 GTGCTATCTGTTTAGCACTTT-G
* * *
28337225 GTGATATCTGTTTAACACTTCG
1 GTGCTATCTGTTTAGCACTTTG
28337247 GTGCT
1 GTGCT
28337252 CTCTAGTGTA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
21 3 0.08
22 33 0.87
23 2 0.05
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.42
Consensus pattern (22 bp):
GTGCTATCTGTTTAGCACTTTG
Found at i:28337244 original size:44 final size:44
Alignment explanation
Indices: 28337147--28337256 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 44
28337137 GTGCTCACTA
* * * * *
28337147 CTTATCACTCTGGTACTCCCTATTCAGCAATTCAGTGCTATCTG
1 CTTAACACTTTGGTGCTCTCTATTCAGCAATTCAGTGATATCTG
* * * *
28337191 CTTAGCACTTTGGTGCTCTCTATTTAGCATTTCGGTGATATCTG
1 CTTAACACTTTGGTGCTCTCTATTCAGCAATTCAGTGATATCTG
* *
28337235 TTTAACACTTCGGTGCTCTCTA
1 CTTAACACTTTGGTGCTCTCTA
28337257 GTGTAGTGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.40
Consensus pattern (44 bp):
CTTAACACTTTGGTGCTCTCTATTCAGCAATTCAGTGATATCTG
Found at i:28354501 original size:21 final size:21
Alignment explanation
Indices: 28354460--28354533 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
28354450 AAAGTTTTTA
28354460 GTATCGGTAGAGGTAAG--ACTT
1 GTATCGGTAGAGG--AGTCACTT
28354481 GTATCGGTAGAGGAGTCACTT
1 GTATCGGTAGAGGAGTCACTT
* ***
28354502 ATATCGGTAGAACTGTCACTT
1 GTATCGGTAGAGGAGTCACTT
*
28354523 GTATCGATAGA
1 GTATCGGTAGA
28354534 AATATGTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.04
21 43 0.96
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAGGAGTCACTT
Found at i:28355200 original size:15 final size:15
Alignment explanation
Indices: 28355180--28355218 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
28355170 AGTCACCGCC
28355180 CTCCTGACCAC-TCAG
1 CTCCTG-CCACGTCAG
28355195 CTCCTGCCACGTCAG
1 CTCCTGCCACGTCAG
*
28355210 CACCTGCCA
1 CTCCTGCCA
28355219 TGTAAGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.18, C:0.49, G:0.15, T:0.18
Consensus pattern (15 bp):
CTCCTGCCACGTCAG
Found at i:28356599 original size:30 final size:31
Alignment explanation
Indices: 28356564--28356622 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
28356554 TATTTTGTTG
* * *
28356564 AAAAATTATATTTTGACC-CTAAACTTTCTA
1 AAAAATCACATTTTGACCTCCAAACTTTCTA
28356594 AAAAATCACATTTTGACCTCCAAACTTTC
1 AAAAATCACATTTTGACCTCCAAACTTTC
28356623 CCAAAGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATCACATTTTGACCTCCAAACTTTCTA
Found at i:28356668 original size:45 final size:46
Alignment explanation
Indices: 28356583--28356672 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 46
28356573 ATTTTGACCC
* * *
28356583 TAAACTTTCTAAAAAATCACATTTTGACCTCCAAACTTTCCCAAAG
1 TAAACTTTCTAAAAAATCACAATTTAACCTCCAAAATTTCCCAAAG
* *
28356629 TAAACTTTCT-CAAAATCATAATTTAACC-CACAAAATTTCCCAAA
1 TAAACTTTCTAAAAAATCACAATTTAACCTC-CAAAATTTCCCAAA
28356673 ATCACATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 1 0.03
45 27 0.71
46 10 0.26
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (46 bp):
TAAACTTTCTAAAAAATCACAATTTAACCTCCAAAATTTCCCAAAG
Found at i:28356688 original size:30 final size:30
Alignment explanation
Indices: 28356630--28356764 Score: 117
Period size: 30 Copynumber: 4.5 Consensus size: 30
28356620 TTCCCAAAGT
* * * *
28356630 AAACTTTCTCAAAATCATAATTTAACCCAC
1 AAACTTTCCCAAAATCACATTTTGACCCAC
* *
28356660 AAAATTTCCCAAAATCACATTTTGACCCAT
1 AAACTTTCCCAAAATCACATTTTGACCCAC
* * * **
28356690 ATACCTTCCCAAAATCGCATTTTGACCCTT
1 AAACTTTCCCAAAATCACATTTTGACCCAC
* * * *
28356720 AAACTTACCTAAAATTACATTTTGACCCTC
1 AAACTTTCCCAAAATCACATTTTGACCCAC
* *
28356750 AAATTTTTCCAAAAT
1 AAACTTTCCCAAAAT
28356765 TGTATTTTAA
Statistics
Matches: 83, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (30 bp):
AAACTTTCCCAAAATCACATTTTGACCCAC
Found at i:28356772 original size:30 final size:29
Alignment explanation
Indices: 28356698--28356772 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
28356688 ATATACCTTC
* *
28356698 CCAAAATCGCATTTTGACCCTTAAACTTA
1 CCAAAATTGCATTTTGACCCTCAAACTTA
* * *
28356727 CCTAAAATTACATTTTGACCCTCAAATTTTT
1 CC-AAAATTGCATTTTGACCCTCAAA-CTTA
*
28356758 CCAAAATTGTATTTT
1 CCAAAATTGCATTTT
28356773 AACCTTAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 2 0.05
30 31 0.84
31 4 0.11
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
CCAAAATTGCATTTTGACCCTCAAACTTA
Found at i:28372028 original size:134 final size:133
Alignment explanation
Indices: 28371839--28372102 Score: 456
Period size: 134 Copynumber: 2.0 Consensus size: 133
28371829 GTCAATATTT
* *
28371839 ACCCAAAAGAGGTGTATGAGGACGTGTATGCTCCGGTGATCCGATCCAAGTAGTAACAAAAGTTC
1 ACCCAAAAGAGGTGTATGAAGACGTGTATGCTCCGGTGATCCGATCCAAGAAGTAACAAAAGTTC
* * *
28371904 ACAAAATCTACAAAACAATTAAACAAGGTAAGTTTCTTTGAAGATTTATCATTCTTAAGAAGAGT
66 ACAAAATCTACAAAACAATTAAACAAGGTAAGCTT-ATTGAAGATTTATCATTCTGAAGAAGAGT
28371969 TCAA
130 TCAA
28371973 ACCCAAAAGAGGTGTATGAAGACGTGTATGCTCCGGTGATCCGATCCAAGAAGTAACAAAAGTTC
1 ACCCAAAAGAGGTGTATGAAGACGTGTATGCTCCGGTGATCCGATCCAAGAAGTAACAAAAGTTC
* *
28372038 ACAAAATCTACAAAACAATTAAACAAGGTAAGCTTATTGAATATTTATCATTCTGAGGAAGAGTT
66 ACAAAATCTACAAAACAATTAAACAAGGTAAGCTTATTGAAGATTTATCATTCTGAAGAAGAGTT
28372103 AAAATATAAT
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
133 26 0.21
134 97 0.79
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (133 bp):
ACCCAAAAGAGGTGTATGAAGACGTGTATGCTCCGGTGATCCGATCCAAGAAGTAACAAAAGTTC
ACAAAATCTACAAAACAATTAAACAAGGTAAGCTTATTGAAGATTTATCATTCTGAAGAAGAGTT
CAA
Found at i:28372181 original size:24 final size:24
Alignment explanation
Indices: 28372154--28372240 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
28372144 CAGCTAATAC
*
28372154 ACGTTTATGCTCATC-GATCACTAT
1 ACGTTTATGCTCATCAG-CCACTAT
* * *
28372178 ACGTATATGCTCGTTAGCCACTAT
1 ACGTTTATGCTCATCAGCCACTAT
*
28372202 ACGTTTATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCATCAGCCACTAT
28372226 ACGTTTATGACTCAT
1 ACGTTTATG-CTCAT
28372241 ATACTTAGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 49 0.91
25 5 0.09
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (24 bp):
ACGTTTATGCTCATCAGCCACTAT
Found at i:28378509 original size:8 final size:9
Alignment explanation
Indices: 28378493--28378521 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
28378483 TATATATATA
28378493 TTTCTTTTT
1 TTTCTTTTT
28378502 TTTCTTTTT
1 TTTCTTTTT
28378511 TTTCTTTTT
1 TTTCTTTTT
28378520 TT
1 TT
28378522 ATGTGACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:28379057 original size:17 final size:17
Alignment explanation
Indices: 28379018--28379065 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
28379008 ATATATATGG
28379018 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
* *
28379035 AGATGCAGTGACAA-GAA
1 AAATGCAATGACAATG-A
28379052 AAATGCAATGACAA
1 AAATGCAATGACAA
28379066 ACGAAATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:28379072 original size:17 final size:16
Alignment explanation
Indices: 28379017--28379073 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
28379007 AATATATATG
*
28379017 GAAATGCAATGACAAT
1 GAAATGCAATGACAAA
*
28379033 GAAGATGCAGTGACAAGA
1 GAA-ATGCAATGACAA-A
*
28379051 AAAATGCAATGACAAA
1 GAAATGCAATGACAAA
28379067 CGAAATG
1 -GAAATG
28379074 TGATAACAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (16 bp):
GAAATGCAATGACAAA
Found at i:28394622 original size:15 final size:15
Alignment explanation
Indices: 28394580--28394623 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28394570 AATTTGTCTT
*
28394580 AGCATCTTTTTTCTC
1 AGCATCTTTTTCCTC
*
28394595 AGCATATTTTTCCTC
1 AGCATCTTTTTCCTC
* *
28394610 GGCATCTTCTTCCT
1 AGCATCTTTTTCCT
28394624 TATCGTTTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.14, C:0.30, G:0.09, T:0.48
Consensus pattern (15 bp):
AGCATCTTTTTCCTC
Found at i:28396569 original size:55 final size:55
Alignment explanation
Indices: 28396452--28396570 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 55
28396442 CAGATGCTAT
* * * ** *
28396452 GACAATTTTGGGCACAATTTAGGATATGCTCATGCAACGAGCTGTCAAATGCGGT
1 GACAATTCTGAGCACAATTTAGGATATGCTCATGCAACGAGCTATCAAATAAGGC
* * *
28396507 GATAATTCTGAGCACAATTCTA-GATATGCTCATTCAACGAGCTATCAGATAAGGC
1 GACAATTCTGAGCACAATT-TAGGATATGCTCATGCAACGAGCTATCAAATAAGGC
28396562 GACAATTCT
1 GACAATTCT
28396571 AGGCATGCTC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 51 0.96
56 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (55 bp):
GACAATTCTGAGCACAATTTAGGATATGCTCATGCAACGAGCTATCAAATAAGGC
Found at i:28396647 original size:38 final size:38
Alignment explanation
Indices: 28396593--28396675 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
28396583 GCAGTGACAT
28396593 TTCTGAACATCATCATGCAGTGACAATTTTGGGCGCAA
1 TTCTGAACATCATCATGCAGTGACAATTTTGGGCGCAA
* *
28396631 TTCTGGACATCGTCATGCAGTGACAATTTTGGGCGCAA
1 TTCTGAACATCATCATGCAGTGACAATTTTGGGCGCAA
28396669 TTCTGAA
1 TTCTGAA
28396676 TAGACTCATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (38 bp):
TTCTGAACATCATCATGCAGTGACAATTTTGGGCGCAA
Found at i:28397869 original size:21 final size:22
Alignment explanation
Indices: 28397836--28397882 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
28397826 AAAGAACAAG
*
28397836 AAATAAAGTAAAA-TAAAACCT
1 AAATAAAGAAAAACTAAAACCT
*
28397857 AAATAGAGAAAAACTAAAACCT
1 AAATAAAGAAAAACTAAAACCT
28397879 AAAT
1 AAAT
28397883 GAAAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (22 bp):
AAATAAAGAAAAACTAAAACCT
Found at i:28403773 original size:17 final size:16
Alignment explanation
Indices: 28403751--28403795 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
28403741 TGGCAATGTA
28403751 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
28403768 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
28403784 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
28403796 TGCGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:28403794 original size:10 final size:11
Alignment explanation
Indices: 28403751--28403796 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
28403741 TGGCAATGTA
28403751 TTTCTTTTCTT
1 TTTCTTTTCTT
28403762 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
28403774 CTTC-TTTCTT
1 TTTCTTTTCTT
28403784 TTTC-TTTCTT
1 TTTCTTTTCTT
28403794 TTT
1 TTT
28403797 GCGATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:28404356 original size:18 final size:18
Alignment explanation
Indices: 28404316--28404361 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
28404306 GCAGATAAAC
*
28404316 TAACAAAT-AAAATGCAG
1 TAACAAATAAAAATGCAA
*
28404333 TGACAAATAAAAATGCAA
1 TAACAAATAAAAATGCAA
*
28404351 TAACAACTAAA
1 TAACAAATAAA
28404362 TAAAATGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.61, C:0.13, G:0.09, T:0.17
Consensus pattern (18 bp):
TAACAAATAAAAATGCAA
Found at i:28404376 original size:22 final size:23
Alignment explanation
Indices: 28404337--28404382 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
28404327 ATGCAGTGAC
28404337 AAATAAAAATGCAATAAC-AACT
1 AAATAAAAATGCAATAACTAACT
*
28404359 AAAT-AAAATGCATGTAACTAACT
1 AAATAAAAATGCA-ATAACTAACT
28404382 A
1 A
28404383 CTGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.22
Consensus pattern (23 bp):
AAATAAAAATGCAATAACTAACT
Found at i:28407811 original size:22 final size:22
Alignment explanation
Indices: 28407768--28407809 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28407758 ATTCACATGT
28407768 TTTCTTAATCATGATTCTTTTG
1 TTTCTTAATCATGATTCTTTTG
**
28407790 TTTC-TAATCATTTTTCTTTT
1 TTTCTTAATCATGATTCTTTT
28407810 TGATCTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.14, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTAATCATGATTCTTTTG
Found at i:28408430 original size:9 final size:9
Alignment explanation
Indices: 28408402--28408435 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28408392 CACACATAAT
28408402 AAAAACTAA
1 AAAAACTAA
**
28408411 AAAAAGAAA
1 AAAAACTAA
28408420 AAAAACTAA
1 AAAAACTAA
28408429 AAAAACT
1 AAAAACT
28408436 TGATGCCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.79, C:0.09, G:0.03, T:0.09
Consensus pattern (9 bp):
AAAAACTAA
Found at i:28412515 original size:17 final size:16
Alignment explanation
Indices: 28412480--28412520 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
28412470 TTATTCTATA
28412480 TTTTTTTTCTTTTACC
1 TTTTTTTTCTTTTACC
28412496 TTTTTCTTTCTTTT-CTC
1 TTTTT-TTTCTTTTAC-C
28412513 TTTTTTTT
1 TTTTTTTT
28412521 ATGCTATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTTTACC
Found at i:28413535 original size:21 final size:21
Alignment explanation
Indices: 28413511--28413550 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28413501 TCTTTCCCTC
28413511 CTTCCT-TTTCTACTTCCTTCT
1 CTTCCTCTTTCT-CTTCCTTCT
*
28413532 CTTCTTCTTTCTCTTCCTT
1 CTTCCTCTTTCTCTTCCTT
28413551 AATACCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.60
Consensus pattern (21 bp):
CTTCCTCTTTCTCTTCCTTCT
Found at i:28431402 original size:147 final size:148
Alignment explanation
Indices: 28431053--28431692 Score: 859
Period size: 147 Copynumber: 4.3 Consensus size: 148
28431043 CTTTTGATTA
* * * *
28431053 AAAGAAAATTACTACTTTACTTTAAAA-TCAAAAATTTTATTTCGAAATAGTTTAAAAAAATCAA
1 AAAGAAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTCGAAATAG-TTAAAAAAATCAA
* * *
28431117 AACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATCACTAAAAAAACATATTTTTATTTTTTTT
64 AACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACATATTTTTA--TTTTTA
*
28431182 AAAATCTAAACTTTCTTTCTTTTTT
126 AAAATATAAACTTTC--TCTTTTTT
* * * * *
28431207 AATGAAAATCACTACTTTACTTAAAGATCCAAACTTTTATTTCGAAATAGTTTAAAAAATCAAAA
1 AAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
*
28431272 CATTGTTTAAAAATTTAAAC-TTTTCTTTAAAA-AGACTAAAAAAACATATTTTTATTTTT-AAA
66 CTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATA-ACT-AAAAAACATATTTTTATTTTTAAAA
* *
28431334 ATCTAAACTTTCCCTTTTTT
129 ATATAAACTTTCTCTTTTTT
* *
28431354 AAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCAAAATAGTTAAAAAAATTAAAA
1 AAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
* * * *
28431419 GTTTTTTTAAAAATTTAAA-TTTTT-TTTAAAATAACTAAAAAATAGA-TTTTATTTTTAAAAAT
66 CTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAAT
*
28431481 ATCAACTTTCTCTTTTTT
131 ATAAACTTTCTCTTTTTT
* * * *
28431499 AAAGAAAATTACTATTTTACTTAAAAATCCAAACTTTTACTTCGAAATAATTAAAAAAATCAAAA
1 AAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
*
28431564 CTTTGTTT-AAAATTTAAACTTTTTCTTTAAAATAACTAAATAACATATTTTTATTTTTAAAAAT
66 CTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAAT
28431628 ATAAACTTTCTCTTTTTT
131 ATAAACTTTCTCTTTTTT
*
28431646 AAAGAAAATCACTATTTT-CTTAAAAA-TCAAAATTTTTATTTCGAAAT
1 AAAGAAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTCGAAAT
28431693 TATTTCAAAA
Statistics
Matches: 435, Mismatches: 42, Indels: 26
0.86 0.08 0.05
Matches are distributed among these distances:
144 20 0.05
145 99 0.23
146 53 0.12
147 136 0.31
149 15 0.03
150 5 0.01
152 32 0.07
153 32 0.07
154 42 0.10
155 1 0.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (148 bp):
AAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA
CTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAAT
ATAAACTTTCTCTTTTTT
Found at i:28431450 original size:18 final size:19
Alignment explanation
Indices: 28431408--28431449 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
28431398 AAATAGTTAA
28431408 AAAAATTAAAAGTTTTTTT
1 AAAAATTAAAAGTTTTTTT
* *
28431427 AAAAATTTAAATTTTTTTT
1 AAAAATTAAAAGTTTTTTT
28431446 AAAA
1 AAAA
28431450 TAACTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAAATTAAAAGTTTTTTT
Found at i:28431590 original size:292 final size:299
Alignment explanation
Indices: 28431053--28431714 Score: 900
Period size: 292 Copynumber: 2.2 Consensus size: 299
28431043 CTTTTGATTA
* * *
28431053 AAAGAAAATTACTACTTTACTTTAAAATCAAAAATTTTATTTCGAAATAGTTTAAAAAAATCAAA
1 AAAGAAAATCACTATTTTACTTAAAAATCAAAAATTTTATTTCGAAATAGTTTAAAAAAATCAAA
* * * *
28431118 ACTTTGTTTAAAATTTTAAACTTTTTCTTTAAAATCACTAAAAAAACATATTTTTATTTTTTTTA
66 ACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACAGATTTTTA-TTTTTTAA
* * * *
28431183 AAATCTAAACTTTCTTTCTTTTTTAATGAAAATCACTACTTTACTTAAAGATCCAAACTTTTATT
130 AAATATAAACTTTC-TTCTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCCAAACTTTTACT
* *
28431248 TCGAAATAGTTTAAAAAATCAAAACATTGTTTAAAAATTTAAACTTTTCTTTAAAA-AGACTAAA
194 TCGAAATAATTAAAAAAATCAAAACATTGTTTAAAAATTTAAACTTTTCTTTAAAATA-ACT-AA
*
28431312 AAAACATATTTTTATTTTT-AAAATCTAAACTTTCCCTTTTTT
257 AAAACATATTTTTATTTTTAAAAATATAAACTTTCCCTTTTTT
* * *
28431354 AAAGAAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTCAAAATAG-TTAAAAAAATTAA
1 AAAGAAAATCACTATTTTACTTAAAAA-TCAAAAATTTTATTTCGAAATAGTTTAAAAAAATCAA
* * *
28431417 AAGTTTTTTTAAAAATTTAAA-TTTTT-TTTAAAATAACT-AAAAAATAGA-TTTTA-TTTTTAA
65 AACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACAGATTTTTATTTTTTAA
* * *
28431477 AAATATCAACTTTC-TCTTTTTTAAAGAAAATTACTATTTTACTTAAAAATCCAAACTTTTACTT
130 AAATATAAACTTTCTTCTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCCAAACTTTTACTT
* *
28431541 CGAAATAATTAAAAAAATCAAAACTTTGTTT-AAAATTTAAACTTTTTCTTTAAAATAACTAAAT
195 CGAAATAATTAAAAAAATCAAAACATTGTTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAA
*
28431605 AACATATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTT
259 AACATATTTTTATTTTTAAAAATATAAACTTTCCCTTTTTT
* * * *
28431646 AAAGAAAATCACTATTTT-CTTAAAAATCAAAATTTTTATTTCGAAATTA-TTTCAAAAAACCGA
1 AAAGAAAATCACTATTTTACTTAAAAATCAAAAATTTTATTTCGAAA-TAGTTTAAAAAAATCAA
28431709 AACTTT
65 AACTTT
28431715 TCCCAAAATC
Statistics
Matches: 321, Mismatches: 33, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
290 2 0.01
291 54 0.17
292 143 0.45
293 1 0.00
294 18 0.06
296 5 0.02
297 8 0.02
298 11 0.03
299 5 0.02
300 30 0.09
301 42 0.13
302 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (299 bp):
AAAGAAAATCACTATTTTACTTAAAAATCAAAAATTTTATTTCGAAATAGTTTAAAAAAATCAAA
ACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACAGATTTTTATTTTTTAAA
AATATAAACTTTCTTCTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCCAAACTTTTACTTC
GAAATAATTAAAAAAATCAAAACATTGTTTAAAAATTTAAACTTTTCTTTAAAATAACTAAAAAA
CATATTTTTATTTTTAAAAATATAAACTTTCCCTTTTTT
Found at i:28435739 original size:21 final size:21
Alignment explanation
Indices: 28435714--28435755 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28435704 AAAAGCTAAG
*
28435714 AAATCTTCCTAGGACTTAGTC
1 AAATCTCCCTAGGACTTAGTC
*
28435735 AAATCTCCCTATGACTTAGTC
1 AAATCTCCCTAGGACTTAGTC
28435756 TTATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATCTCCCTAGGACTTAGTC
Found at i:28439433 original size:36 final size:36
Alignment explanation
Indices: 28439382--28439554 Score: 202
Period size: 36 Copynumber: 4.8 Consensus size: 36
28439372 TCAAAGGAAG
* *
28439382 GCATACGTCTTGGTTAGAGCATATTGCTATGATGTT
1 GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
*
28439418 GCATACGTCTCGGTTAGAGAGTATTGCTATGATGTT
1 GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
* * *** * *
28439454 ACATATGTCTAAATTTGAGCGTATTGCTATAATGTT
1 GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
** **
28439490 GCATAAATCTCAATTAGAGCGTATTGCTATGATGTT
1 GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
* *
28439526 ACATACATCTCGGTTAGAGCGTATTGCTA
1 GCATACGTCTCGGTTAGAGCGTATTGCTA
28439555 AGAATTTATT
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 116 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (36 bp):
GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
Found at i:28439579 original size:36 final size:36
Alignment explanation
Indices: 28439395--28439584 Score: 159
Period size: 36 Copynumber: 5.3 Consensus size: 36
28439385 TACGTCTTGG
* * * * *
28439395 TTAGAGCATATTGCTATGATGTTGCATACGTCTCGG
1 TTAGAGCGTATTGCTAAGATGTTACATACATCTCGA
* * ** **
28439431 TTAGAGAGTATTGCTATGATGTTACATATGTCTAAA
1 TTAGAGCGTATTGCTAAGATGTTACATACATCTCGA
* * * *
28439467 TTTGAGCGTATTGCTATA-ATGTTGCATAAATCTCAA
1 TTAGAGCGTATTGCTA-AGATGTTACATACATCTCGA
* *
28439503 TTAGAGCGTATTGCTATGATGTTACATACATCTCGG
1 TTAGAGCGTATTGCTAAGATGTTACATACATCTCGA
** * *
28439539 TTAGAGCGTATTGCTAAGAAT-TTATTTACGTCTTGA
1 TTAGAGCGTATTGCTAAG-ATGTTACATACATCTCGA
28439575 TTAGAGCGTA
1 TTAGAGCGTA
28439585 ATGTTAAGTG
Statistics
Matches: 125, Mismatches: 26, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
36 123 0.98
37 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (36 bp):
TTAGAGCGTATTGCTAAGATGTTACATACATCTCGA
Found at i:28439615 original size:108 final size:108
Alignment explanation
Indices: 28439382--28439616 Score: 242
Period size: 108 Copynumber: 2.2 Consensus size: 108
28439372 TCAAAGGAAG
* * * *
28439382 GCATACGTCTTGGTTAGAGCATATTGCTATGATGTTGCATACGTCTCGGTTAGAGAGTATTGCTA
1 GCATAAGTCTCGGTTAGAGCATATTGCTATGATGTTACATACATCTCGGTTAGAGAGTATTGCTA
* * * * *
28439447 TGATGTTACATATGTCTAAATTTGAGCGTATTGCTATAATGTT
66 AGATGTTACATACGTCTAAATTAGAGCGTAATGCTATAATGTC
* ** * *
28439490 GCATAAATCTCAATTAGAGCGTATTGCTATGATGTTACATACATCTCGGTTAGAGCGTATTGCTA
1 GCATAAGTCTCGGTTAGAGCATATTGCTATGATGTTACATACATCTCGGTTAGAGAGTATTGCTA
** **
28439555 AGAAT-TTATTTACGTCTTGATTAGAGCGTAATG-T-TAAGTGATC
66 AG-ATGTTACATACGTCTAAATTAGAGCGTAATGCTATAA-TG-TC
* *
28439598 GCTTATGTCTCGGTTAGAG
1 GCATAAGTCTCGGTTAGAG
28439617 TATAAGGTCA
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
106 3 0.03
107 3 0.03
108 93 0.92
109 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (108 bp):
GCATAAGTCTCGGTTAGAGCATATTGCTATGATGTTACATACATCTCGGTTAGAGAGTATTGCTA
AGATGTTACATACGTCTAAATTAGAGCGTAATGCTATAATGTC
Found at i:28448644 original size:24 final size:24
Alignment explanation
Indices: 28448607--28448653 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28448597 TTCCTTGTAA
28448607 TTTAGGTTTAGTTATTTT-CTTTC
1 TTTAGGTTTAGTTATTTTACTTTC
28448630 TTTAGGTGTTAGTTATTTTACTTT
1 TTTAGGT-TTAGTTATTTTACTTT
28448654 TGTTTTATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 11 0.50
25 4 0.18
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (24 bp):
TTTAGGTTTAGTTATTTTACTTTC
Found at i:28450361 original size:11 final size:11
Alignment explanation
Indices: 28450345--28450383 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
28450335 TATGTCTTAG
28450345 CCTTCAATGCT
1 CCTTCAATGCT
28450356 CCTTCAATGCT
1 CCTTCAATGCT
28450367 CCTTCAATGCTT
1 CCTTCAATGC-T
28450379 CCTTC
1 CCTTC
28450384 TACCAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (11 bp):
CCTTCAATGCT
Done.