Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 40 of 126
Found at i:11961973 original size:30 final size:31
Alignment explanation
Indices: 11961909--11961989 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 31
11961899 AAATCAAAAA
*
11961909 TAAAGTTTCAAGTATACATTTGAACCACAAT
1 TAAAGTTTCAAGTATACAATTGAACCACAAT
* * * *
11961940 TAAAGTTTCACGTGTATAATTGCACCA-AAT
1 TAAAGTTTCAAGTATACAATTGAACCACAAT
* *
11961970 TAAAGTCT-ATGTATACAATT
1 TAAAGTTTCAAGTATACAATT
11961990 ACACATTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 9 0.22
30 10 0.24
31 22 0.54
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (31 bp):
TAAAGTTTCAAGTATACAATTGAACCACAAT
Found at i:11982427 original size:23 final size:25
Alignment explanation
Indices: 11982395--11982442 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
11982385 GATTTCAAAA
11982395 AAAAACGTGCTA-A-AGTAGCAGAC
1 AAAAACGTGCTAGAGAGTAGCAGAC
*
11982418 AAAAAGGTGCTAGAGAGTAGCAGAC
1 AAAAACGTGCTAGAGAGTAGCAGAC
11982443 TTTGATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.46, C:0.15, G:0.27, T:0.12
Consensus pattern (25 bp):
AAAAACGTGCTAGAGAGTAGCAGAC
Found at i:11994544 original size:18 final size:18
Alignment explanation
Indices: 11994521--11994593 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
11994511 TAACAATATT
*
11994521 TTTTATAATTTTAAATAA
1 TTTTATAATTTTTAATAA
11994539 TTTTAT-ATTCATTT-ATAA
1 TTTTATAATT--TTTAATAA
* *
11994557 TTCTATAGTTTTTAATAA
1 TTTTATAATTTTTAATAA
11994575 TTTGTTATAATTTTTAATA
1 -TT-TTATAATTTTTAATA
11994594 GCTTTCATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.14
18 19 0.43
19 6 0.14
20 13 0.30
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTATAATTTTTAATAA
Found at i:12000587 original size:23 final size:23
Alignment explanation
Indices: 12000561--12000606 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12000551 CTTCTTAACT
12000561 AAGGATTTACTGCTTCCTTTTCA
1 AAGGATTTACTGCTTCCTTTTCA
12000584 AAGGATTTACTGCTTCCTTTTCA
1 AAGGATTTACTGCTTCCTTTTCA
12000607 TTACAGTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (23 bp):
AAGGATTTACTGCTTCCTTTTCA
Found at i:12003526 original size:36 final size:30
Alignment explanation
Indices: 12003452--12003538 Score: 147
Period size: 30 Copynumber: 2.9 Consensus size: 30
12003442 TGAGCAGGAA
12003452 TGATAAAGGGAAAGGGAAAATGGTTGATGC
1 TGATAAAGGGAAAGGGAAAATGGTTGATGC
* *
12003482 TGATAAAGGGAAAGGTAAAATGGTTTATGC
1 TGATAAAGGGAAAGGGAAAATGGTTGATGC
*
12003512 TGATAAAGGGAAAGGGAAACTGGTTGA
1 TGATAAAGGGAAAGGGAAAATGGTTGA
12003539 CACCATAGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.40, C:0.03, G:0.34, T:0.22
Consensus pattern (30 bp):
TGATAAAGGGAAAGGGAAAATGGTTGATGC
Found at i:12006677 original size:78 final size:79
Alignment explanation
Indices: 12006587--12006739 Score: 272
Period size: 78 Copynumber: 1.9 Consensus size: 79
12006577 CAATGAGTCA
* *
12006587 TGTCTCTTCATTAGGATCTGATGTAGTTGAAAAGGCATGACATTTCTCCTT-ATGAAGAATTATT
1 TGTCTCTTCATTAGGATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGAATTATT
12006651 GTATCCTTAACCTG
66 GTATCCTTAACCTG
*
12006665 TGTCTCTTCATTAGGATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTATT
1 TGTCTCTTCATTAGGATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGAATTATT
12006730 GTATCCTTAA
66 GTATCCTTAA
12006740 TGTGTTTATT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 49 0.69
79 22 0.31
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (79 bp):
TGTCTCTTCATTAGGATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGAATTATT
GTATCCTTAACCTG
Found at i:12007182 original size:48 final size:48
Alignment explanation
Indices: 12007129--12007237 Score: 166
Period size: 48 Copynumber: 2.3 Consensus size: 48
12007119 GCAGATCTTT
*
12007129 AAAGATGCATTTAACAAACA-AAACATTTAATGATGTAGATTATTAAAC
1 AAAGATGCATTTAACAAA-AGAAACATTTAATGATGCAGATTATTAAAC
* * *
12007177 AAAGATTCATTTAACAAAAGAAATATTTAATGATGCATATTATTAAAC
1 AAAGATGCATTTAACAAAAGAAACATTTAATGATGCAGATTATTAAAC
12007225 AAAGATGCATTTA
1 AAAGATGCATTTA
12007238 GCACATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (48 bp):
AAAGATGCATTTAACAAAAGAAACATTTAATGATGCAGATTATTAAAC
Found at i:12011822 original size:23 final size:23
Alignment explanation
Indices: 12011793--12012025 Score: 299
Period size: 23 Copynumber: 10.1 Consensus size: 23
12011783 ATATTAATTC
12011793 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
12011816 TTTAAGCACAAGTCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
12011839 ATTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
12011862 TTTTGAGCACAAATCATATTAATA
1 -TTTAAGCACAAATCACATTAATA
12011886 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
12011909 TTTGAGCACAAAT-AGTATTAATA
1 TTTAAGCACAAATCA-CATTAATA
*
12011932 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
12011955 CTTAAGCATAAGTCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
12011978 TTT-AGTCATAAATCATATTAATG
1 TTTAAG-CACAAATCACATTAATA
12012001 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
12012024 TT
1 TT
12012026 CTTAAACATT
Statistics
Matches: 181, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.02
23 156 0.86
24 22 0.12
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:12015022 original size:36 final size:36
Alignment explanation
Indices: 12014945--12015022 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
12014935 AATATAATTA
* **
12014945 GTCACATGGCATGAAGAACATGCCCACATATTTTCT
1 GTCACATGGCATGAAGAACATGACCACATATTCACT
*
12014981 GTCACATGGCATGAAGAACATTACCACATATTCACT
1 GTCACATGGCATGAAGAACATGACCACATATTCACT
*
12015017 TTCACA
1 GTCACA
12015023 ACAATCATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATGACCACATATTCACT
Found at i:12015157 original size:23 final size:23
Alignment explanation
Indices: 12015091--12015367 Score: 335
Period size: 23 Copynumber: 12.2 Consensus size: 23
12015081 CATCTTAATA
*
12015091 AAGCACAAATTACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * *
12015114 AATCATAAAT--CA-TAATGTTT
1 AAGCACAAATCACATTAATATTT
*
12015134 AAGCACAAACCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
12015157 AAGCATAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
*
12015180 GAGCACAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
**
12015203 AAGCACAAGCCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
12015226 AAGCATAAATCACCTTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
12015249 GAGCACAAATCATATTAATATTT
1 AAGCACAAATCACATTAATATTT
* *
12015272 AAGCATAAATCACATTAATACTT
1 AAGCACAAATCACATTAATATTT
* *
12015295 AAGCATAAGTCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
* * * *
12015318 AATCATAAATTATATTAATATTT
1 AAGCACAAATCACATTAATATTT
12015341 AAGCACAAATCACATTAATATTT
1 AAGCACAAATCACATTAATATTT
12015364 AAGC
1 AAGC
12015368 GTAGATATAA
Statistics
Matches: 213, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
20 14 0.07
21 2 0.01
22 2 0.01
23 195 0.92
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.34
Consensus pattern (23 bp):
AAGCACAAATCACATTAATATTT
Found at i:12018628 original size:15 final size:15
Alignment explanation
Indices: 12018608--12018639 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12018598 TCAGTTAGAT
12018608 ACCAAGTGTATCTAA
1 ACCAAGTGTATCTAA
12018623 ACCAAGTGTATCTAA
1 ACCAAGTGTATCTAA
12018638 AC
1 AC
12018640 TATCTCCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (15 bp):
ACCAAGTGTATCTAA
Found at i:12024006 original size:28 final size:28
Alignment explanation
Indices: 12023965--12024030 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
12023955 CATTTGAAAA
* * *
12023965 TTAAATT-TATTTTAATCTTAAATTTATT
1 TTAAATTCAATTTAAAT-TTAAATTTAAT
*
12023993 TTAAATTCAATTTAAATTTGAATTTAAT
1 TTAAATTCAATTTAAATTTAAATTTAAT
12024021 TTAAATTCAA
1 TTAAATTCAA
12024031 GGTTATTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (28 bp):
TTAAATTCAATTTAAATTTAAATTTAAT
Found at i:12024027 original size:11 final size:11
Alignment explanation
Indices: 12023962--12024024 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
12023952 AACCATTTGA
*
12023962 AAATTAAATTT
1 AAATTTAATTT
*
12023973 -ATTTTAATCTT
1 AAATTTAAT-TT
*
12023984 AAATTTATTTT
1 AAATTTAATTT
*
12023995 AAATTCAATTT
1 AAATTTAATTT
12024006 AAATTTGAATTT
1 AAATTT-AATTT
12024018 -AATTTAA
1 AAATTTAA
12024025 ATTCAAGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.19
11 23 0.55
12 11 0.26
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:12024044 original size:28 final size:27
Alignment explanation
Indices: 12023976--12024049 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 27
12023966 TAAATTTATT
* *
12023976 TTAATCTTAAATTTATTTTAAATTCAAT
1 TTAAT-TTAAATTTAATTTAAATTCAAG
*
12024004 TTAAATTTGAATTTAATTTAAATTCAAGG
1 TT-AATTTAAATTTAATTTAAATTCAA-G
12024033 TT-ATTATAAATTTAATT
1 TTAATT-TAAATTTAATT
12024050 AGAAAAGTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 31 0.79
29 5 0.13
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
TTAATTTAAATTTAATTTAAATTCAAG
Found at i:12024281 original size:20 final size:20
Alignment explanation
Indices: 12024258--12024316 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
12024248 CGTGCCTATG
*
12024258 CTGCTGGCCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
12024278 CTGCTGACCACCAGCTCCAT
1 CTGCTGACCACCAGCTCCAT
*
12024298 CTGCTGACCACCTGCTCCA
1 CTGCTGACCACCAGCTCCA
12024317 CCATGCCCTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.17, C:0.46, G:0.17, T:0.20
Consensus pattern (20 bp):
CTGCTGACCACCAGCTCCAT
Found at i:12025161 original size:30 final size:30
Alignment explanation
Indices: 12025109--12025167 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12025099 TTAAAAAAGG
* ** *
12025109 ATAATAATAAAAAGGGTTTGTTTTTAAAAA
1 ATAAAAATAAAAAGGGAATGTTTTGAAAAA
12025139 ATAAAAATAAAAAGGGAATGTTTTGAAAA
1 ATAAAAATAAAAAGGGAATGTTTTGAAAA
12025168 TCCCAGATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (30 bp):
ATAAAAATAAAAAGGGAATGTTTTGAAAAA
Found at i:12026030 original size:30 final size:30
Alignment explanation
Indices: 12025994--12026315 Score: 477
Period size: 30 Copynumber: 10.7 Consensus size: 30
12025984 AAATTATCCA
* * *
12025994 AAAATTACATTTCGACACTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
12026024 AAAATTATATTTTGACCCTAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCC
12026054 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
12026084 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
12026114 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
12026144 AAAATTATATTTTGACCCCAAAACTTCTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
12026174 AAAATTACATTTTGACCCCAAAGCTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
12026204 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
12026234 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
12026264 AAAATTACATTTTGACCTCAAAAAC-TTTCA
1 AAAATTACATTTTGACC-CCAAAACTTTTCC
12026294 AAAATTATCATTTT-ACCCCAAA
1 AAAATTA-CATTTTGACCCCAAA
12026316 CTTCCCTAAA
Statistics
Matches: 266, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
29 4 0.02
30 250 0.94
31 12 0.05
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:12026363 original size:57 final size:58
Alignment explanation
Indices: 12026294--12026427 Score: 182
Period size: 58 Copynumber: 2.3 Consensus size: 58
12026284 AAAACTTTCA
* * *
12026294 AAAATTATCATTTTACCCC-AAACTTCCCT-AAATCCCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTACCCCTAAA-TTCCCTAAAATCCCATTTTTAACCCCGATTACACC
** *
12026351 AAAATTACCATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCCGATTACACC
1 AAAATTACCATTTTACCCCTAAATTCCCTAAAATCCCATTTTTAACCCCGATTACACC
*
12026409 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
12026428 CGGGTATCCA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
57 22 0.32
58 46 0.68
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAATTCCCTAAAATCCCATTTTTAACCCCGATTACACC
Found at i:12026364 original size:30 final size:30
Alignment explanation
Indices: 12026328--12026422 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 30
12026318 TCCCTAAATC
12026328 CCATTTTTAACCCTGATTTCACCAAAATTA
1 CCATTTTTAACCCTGATTTCACCAAAATTA
* * * *
12026358 CCA-TTTTACCCCTAAATTT-TCTAAAATT-
1 CCATTTTTAACCCT-GATTTCACCAAAATTA
* *
12026386 CCATTTTTAACCCCGATTACACCAAAATTA
1 CCATTTTTAACCCTGATTTCACCAAAATTA
12026416 CCATTTT
1 CCATTTT
12026423 GCCCCCGGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.12
29 31 0.61
30 14 0.27
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (30 bp):
CCATTTTTAACCCTGATTTCACCAAAATTA
Found at i:12026448 original size:58 final size:58
Alignment explanation
Indices: 12026294--12026461 Score: 164
Period size: 58 Copynumber: 2.9 Consensus size: 58
12026284 AAAACTTTCA
* * *
12026294 AAAATTATCATTTTA-CCCCAAACT-TCCCT-AAATCCCATTTTTAACCCTGATTTCACC
1 AAAATTACCATTTTACCCCCAAA-TAT-CCTAAAATCCCATTTTTAACCCCGATTACACC
* * * *
12026351 AAAATTACCATTTTACCCCTAAATTTTCTAAAATTCCATTTTTAACCCCGATTACACC
1 AAAATTACCATTTTACCCCCAAATATCCTAAAATCCCATTTTTAACCCCGATTACACC
* *** * *
12026409 AAAATTACCATTTTGCCCCCGGGTATCC-ATAAGTCCCATTTTTTACCCCGATT
1 AAAATTACCATTTTACCCCCAAATATCCTA-AAATCCCATTTTTAACCCCGATT
12026462 TCATCATTTA
Statistics
Matches: 91, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
57 18 0.20
58 73 0.80
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCAAATATCCTAAAATCCCATTTTTAACCCCGATTACACC
Found at i:12036052 original size:18 final size:18
Alignment explanation
Indices: 12036024--12036069 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
12036014 AATGAAATTT
12036024 ATATGAAAATCCCTAAAA-G
1 ATAT-AAAATCCC-AAAAGG
*
12036043 ATTTAAAATCCCAAAAGG
1 ATATAAAATCCCAAAAGG
12036061 ATATAAAAT
1 ATATAAAAT
12036070 TTATCGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 17 0.71
19 3 0.12
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (18 bp):
ATATAAAATCCCAAAAGG
Found at i:12037742 original size:38 final size:39
Alignment explanation
Indices: 12037699--12037800 Score: 100
Period size: 40 Copynumber: 2.6 Consensus size: 39
12037689 TATAACAGTC
* *
12037699 TAAAAATTATTAAAATTTATAAATATTATTGA-ATACTA
1 TAAAAAATATTAAAATTTATAAATATTATTAATATACTA
* * * *
12037737 TAAAAAACTAGATAAAATATA-AAATATTGTTAATATATTA
1 TAAAAAA-TA-TTAAAATTTATAAATATTATTAATATACTA
*
12037777 TGAAAAATATTAAAATATTATAAA
1 TAAAAAATATTAAAAT-TTATAAA
12037801 AATATAGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
38 12 0.24
39 16 0.32
40 22 0.44
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (39 bp):
TAAAAAATATTAAAATTTATAAATATTATTAATATACTA
Found at i:12037794 original size:20 final size:20
Alignment explanation
Indices: 12037766--12037831 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
12037756 TAAAATATTG
*
12037766 TTAATATATTATGAAAAATA
1 TTAAAATATTATGAAAAATA
12037786 TTAAAATATTAT-AAAAATA
1 TTAAAATATTATGAAAAATA
*
12037805 -TAGAA-ATTATAGAAAAAT-
1 TTAAAATATTAT-GAAAAATA
*
12037823 TAAAAATAT
1 TTAAAATAT
12037832 AGAAAATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 5 0.13
18 4 0.11
19 16 0.42
20 13 0.34
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
TTAAAATATTATGAAAAATA
Found at i:12037843 original size:16 final size:17
Alignment explanation
Indices: 12037812--12037855 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
12037802 ATATAGAAAT
*
12037812 TATAGAAAAATTAAAAA
1 TATAGAAAAATCAAAAA
12037829 TATAG-AAAATCAAAAA
1 TATAGAAAAATCAAAAA
*
12037845 TTTTAGAAAAA
1 -TATAGAAAAA
12037856 ACCTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 10 0.43
17 9 0.39
18 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (17 bp):
TATAGAAAAATCAAAAA
Found at i:12054731 original size:29 final size:28
Alignment explanation
Indices: 12054691--12054793 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
12054681 ACCCGAGGGC
*
12054691 AAAATGGTAATTTTGGTGAAATCAAGGTT
1 AAAATGG-AATTTTGGTGAAATCGAGGTT
* * ** *
12054720 AAAAATGGAATTTTTGAGAGTTCGAGGGT
1 -AAAATGGAATTTTGGTGAAATCGAGGTT
*
12054749 AAAATGGGAATTTTTGGTGAAATCGGGGTT
1 AAAAT-GGAA-TTTTGGTGAAATCGAGGTT
*
12054779 GAAATGGAATTTTGG
1 AAAATGGAATTTTGG
12054794 AAGTTCGGGG
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 11 0.19
29 23 0.40
30 24 0.41
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGAGGTT
Found at i:12054818 original size:57 final size:59
Alignment explanation
Indices: 12054684--12054822 Score: 194
Period size: 58 Copynumber: 2.4 Consensus size: 59
12054674 TTTGGATACC
* *
12054684 CGAGGGCAAAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATGGAATTTTTGAGAGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAGAGTT
* ** *
12054742 CGAGGGTAAAATGGGAATTTTTGGTGAAATCGGGGTT-GAAATGGAATTTTGGA-AGTT
1 CGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAGAGTT
*
12054799 CGGGGGTAAAATGGTAATTTTTGG
1 CGAGGGTAAAATGGTAATTTTTGG
12054823 AAGTTTCGGG
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
57 26 0.36
58 29 0.40
59 17 0.24
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (59 bp):
CGAGGGTAAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTGGAGAGTT
Found at i:12054833 original size:29 final size:27
Alignment explanation
Indices: 12054721--12054833 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 27
12054711 ATCAAGGTTA
12054721 AAAATGGAATTTTT-GAGAGTTCGAGGGT
1 AAAATGGAATTTTTGGA-AGTTCG-GGGT
*
12054749 AAAATGGGAATTTTTGGTGAA-ATCGGGGTT
1 AAAAT-GGAATTTTT-G-GAAGTTCGGGG-T
*
12054779 GAAATGGAA-TTTTGGAAGTTCGGGGGT
1 AAAATGGAATTTTTGGAAGTTC-GGGGT
12054806 AAAATGGTAATTTTTGGAAGTTTCGGGG
1 AAAATGG-AATTTTTGGAAG-TTCGGGG
12054834 ACATATAAAT
Statistics
Matches: 71, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
26 3 0.04
27 10 0.14
28 15 0.21
29 29 0.41
30 11 0.15
31 1 0.01
32 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:12055208 original size:162 final size:162
Alignment explanation
Indices: 12054911--12055223 Score: 482
Period size: 162 Copynumber: 1.9 Consensus size: 162
12054901 GATTAGATTG
* *
12054911 TAAACCTTGAAAAACTCTTGGGCCAATTTTATAATTAAATAAGAGTTGATTTGGGGATTAAATTA
1 TAAACCTTGAAAAACTCTTGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGATTAAATTA
* * * *
12054976 AAACAAATTAAAAATGTCAGGGACTAAATGGATAAATAAGCCAAAAAGTGACACGTGGCAACCCC
66 AAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCAAAAAATGACACGTAGCAACCCC
12055041 TGGTGCAGTCAAACAGTCAAATGACTAATTTA
131 TGGTGCAGTCAAACAGTCAAATGACTAATTTA
* * *
12055073 TAAACCTTGAAAAATTGTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATTA
1 TAAACCTTGAAAAACTCTTGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGATTAAATTA
* * * *** *
12055138 AAACAAATTAAAAATATCGGGGACTAAATGAATAAATAAGTCAAAAAATGACATGTAGTTGCCTC
66 AAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCAAAAAATGACACGTAGCAACCCC
12055203 TGGTGCAGTCAAACAGTCAAA
131 TGGTGCAGTCAAACAGTCAAA
12055224 GGATTAAATT
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
162 135 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (162 bp):
TAAACCTTGAAAAACTCTTGGGCCAATTTTATAATTAAATAAAAGTTGATTTAGGGATTAAATTA
AAACAAATTAAAAATATCAGGGACTAAATGAATAAATAAGCCAAAAAATGACACGTAGCAACCCC
TGGTGCAGTCAAACAGTCAAATGACTAATTTA
Found at i:12055767 original size:15 final size:16
Alignment explanation
Indices: 12055735--12055767 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12055725 GGTTTTTTCG
*
12055735 AAACCCAGATCTGGGA
1 AAACCCAGATCTGAGA
12055751 AAACCCAGATCT-AGA
1 AAACCCAGATCTGAGA
12055766 AA
1 AA
12055768 TATTTTCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.12
Consensus pattern (16 bp):
AAACCCAGATCTGAGA
Found at i:12056816 original size:6 final size:6
Alignment explanation
Indices: 12056802--12056907 Score: 109
Period size: 6 Copynumber: 18.2 Consensus size: 6
12056792 AATGTTTAGT
* *
12056802 ATTTTA ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
12056851 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA
12056897 A--TAA ATTTAA A
1 ATTTAA ATTTAA A
12056908 ATCAATTTAA
Statistics
Matches: 86, Mismatches: 3, Indels: 22
0.77 0.03 0.20
Matches are distributed among these distances:
4 6 0.07
5 10 0.12
6 62 0.72
7 2 0.02
8 6 0.07
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:12056837 original size:11 final size:11
Alignment explanation
Indices: 12056804--12056917 Score: 94
Period size: 11 Copynumber: 10.5 Consensus size: 11
12056794 TGTTTAGTAT
*
12056804 TTTAATTTAAA
1 TTTAAATTAAA
12056815 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
12056827 TTTAAAGTAAA
1 TTTAAATTAAA
12056838 TTTAAA-T-AA
1 TTTAAATTAAA
12056847 -TTAAATTTAAA
1 TTTAAA-TTAAA
12056858 TTTAAGA-TAAA
1 TTTAA-ATTAAA
*
12056869 TTTAAATTTAA
1 TTTAAATTAAA
**
12056880 GATAAATTTAAA
1 TTTAAA-TTAAA
12056892 TTTAAA-TAAA
1 TTTAAATTAAA
* *
12056902 TTTAAAATCAA
1 TTTAAATTAAA
12056913 TTTAA
1 TTTAA
12056918 CTCCAAATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
8 5 0.06
9 2 0.02
10 13 0.15
11 41 0.48
12 23 0.27
13 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:12056909 original size:17 final size:16
Alignment explanation
Indices: 12056802--12056907 Score: 135
Period size: 17 Copynumber: 6.4 Consensus size: 16
12056792 AATGTTTAGT
*
12056802 ATTTTAATTTAAATTTAA
1 ATTTAAATTTAAA--TAA
12056820 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAA-TAA
*
12056837 ATTTAAA--TAATTAA
1 ATTTAAATTTAAATAA
12056851 ATTTAAATTTAAGATAA
1 ATTTAAATTTAA-ATAA
12056868 ATTTAAATTTAAGATAA
1 ATTTAAATTTAA-ATAA
12056885 ATTTAAATTTAAATAA
1 ATTTAAATTTAAATAA
12056901 ATTTAAA
1 ATTTAAA
12056908 ATCAATTTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
14 10 0.12
15 3 0.04
16 14 0.17
17 42 0.52
18 12 0.15
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:12056925 original size:27 final size:27
Alignment explanation
Indices: 12056871--12056925 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12056861 AAGATAAATT
* **
12056871 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
* *
12056898 TAAATTTAAAATCAATTTAACTCCAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
12056925 T
1 T
12056926 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCCAAA
Found at i:12057331 original size:76 final size:76
Alignment explanation
Indices: 12057205--12057790 Score: 866
Period size: 76 Copynumber: 7.8 Consensus size: 76
12057195 TGCTCTTTAG
* * *
12057205 AGAGATAAAGACTTGCTATCCAACTTTACTTTAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057270 ACTTCAATTTC
66 ACTTCAATTTC
* * *
12057281 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057346 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
12057357 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTTAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057422 ACTTCAATTTC
66 ACTTCAATTTC
* * *
12057433 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGG-AAAGATCTGGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057497 ACTTCAATTTTC
66 ACTTCAA-TTTC
* *
12057509 AGAGATAACGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057574 ACTTCAATTTC
66 ACTTCAATTTC
* * **
12057585 AAAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAAAATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057650 ACTTCAATTTC
66 ACTTCAATTTC
* * *
12057661 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAAAGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
12057719 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
12057730 AGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAAAAAT-TTGCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT
12057791 ATGGTCTGAT
Statistics
Matches: 470, Mismatches: 32, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
69 62 0.13
71 1 0.00
72 2 0.00
73 1 0.00
74 1 0.00
75 26 0.06
76 356 0.76
77 21 0.04
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:12057543 original size:39 final size:38
Alignment explanation
Indices: 12057269--12057768 Score: 169
Period size: 38 Copynumber: 13.3 Consensus size: 38
12057259 ATCTTGCTCT
* * * *
12057269 TACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* ** * *
12057307 TACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--C-TCT-
1 TACTTCAATTTC-AGA-GATA--AAGACTTGTTGTCCAACTC
* * * *
12057345 TACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* * ** * *
12057383 TACTTCAATTTTAAGAGGATAGGAAAAGATCTTG--C-TCT-
1 TACTTCAA-TTTCAGA-GATA--AAGACTTGTTGTCCAACTC
* *
12057421 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* *
12057459 TACTTCAATTTCAAGCGGATAGGAAAGA-TCTG--G--C-TCT-
1 TACTTCAATTTC-AG-AGAT---AAAGACT-TGTTGTCCAACTC
*
12057496 TACTTCAATTTTCAGAGATAACGACTTGTTGTCCAACTC
1 TACTTCAA-TTTCAGAGATAAAGACTTGTTGTCCAACTC
* ** * *
12057535 TACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--C-TCT-
1 TACTTCAATTTC-AGA-GATA--AAGACTTGTTGTCCAACTC
*
12057573 TACTTCAATTTCAAAGATAAAGACTTGTTGTCCAACTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* *** * *
12057611 TACTTCAATTTCA-AGAAAATAGGAAAAGATCT-TGC-TCT-
1 TACTTCAATTTCAGAGATAA-A-GACTTG-T-TGTCCAACTC
* *
12057649 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTC
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* ** * *
12057687 TACTTCAATTTCA-AAAGGATGAC--GTTG--C-TCT-
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
* * *
12057718 TACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTT
1 TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
12057756 TACTTCAATTTCA
1 TACTTCAATTTCA
12057769 AGCGGATAGG
Statistics
Matches: 337, Mismatches: 72, Indels: 106
0.65 0.14 0.21
Matches are distributed among these distances:
31 13 0.04
32 8 0.02
33 7 0.02
34 22 0.07
35 5 0.01
36 22 0.07
37 46 0.14
38 130 0.39
39 39 0.12
40 21 0.06
41 1 0.00
42 16 0.05
43 7 0.02
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAGAGATAAAGACTTGTTGTCCAACTC
Found at i:12069659 original size:29 final size:29
Alignment explanation
Indices: 12069578--12069842 Score: 103
Period size: 28 Copynumber: 9.0 Consensus size: 29
12069568 TAAGAAACGA
* *
12069578 TAAAATCGAGGTTGAAAATGGGACTTTTGG
1 TAAAATCGAGGTTTAAAAT-GGAATTTTGG
* * *
12069608 --ATACCGAGG-GTAAAATGGTAATTTTGG
1 TAAAATCGAGGTTTAAAATGG-AATTTTGG
*
12069635 TAAAATCGAGGTTTAAAATGGAATTTTTG
1 TAAAATCGAGGTTTAAAATGGAATTTTGG
* * ** ** *
12069664 -AGACTTTAGGGGTAAAATGGGAATTTTCAG
1 TAAAATCGAGGTTTAAAAT-GGAATTTT-GG
* * *
12069694 TGAAATCGGGGTTAAAAATGGAATTTTGG
1 TAAAATCGAGGTTTAAAATGGAATTTTGG
* ** **
12069723 -AATATTTAGGGGTAAAATGGTAATTTTGG
1 TAAAATCGAGGTTTAAAATGG-AATTTTGG
* * * *
12069752 TTGAAATTGGGGTTAAAAATGGAAATTTTGG
1 -TAAAATCGAGGTTTAAAATGG-AATTTTGG
** * *
12069783 --AGTTCGGGGTGTAAAATGGTAATTTTTTGG
1 TAAAATCGAGGTTTAAAATGG-AA--TTTTGG
* *
12069813 TTAAAATCGGGGTTAAAAATGGAATTTTGG
1 -TAAAATCGAGGTTTAAAATGGAATTTTGG
12069843 AAAGTTTAAG
Statistics
Matches: 168, Mismatches: 52, Indels: 30
0.67 0.21 0.12
Matches are distributed among these distances:
26 2 0.01
27 12 0.07
28 47 0.28
29 31 0.18
30 29 0.17
31 30 0.18
32 2 0.01
33 15 0.09
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAAATCGAGGTTTAAAATGGAATTTTGG
Found at i:12069731 original size:59 final size:58
Alignment explanation
Indices: 12069615--12069868 Score: 291
Period size: 59 Copynumber: 4.3 Consensus size: 58
12069605 TGGATACCGA
* * * *
12069615 GGGTAAAATGGTAATTTTGG-TAAAATCGAGGTTTAAAATGGAATTTTTGAGACTTTAG
1 GGGTAAAATGGTAATTTTGGTTAAAATCGGGGTTAAAAATGGAATTTTGGA-AATTTAG
* * *
12069673 GGGTAAAATGGGAATTTTCAG-TGAAATCGGGGTTAAAAATGGAATTTTGGAATATTTAG
1 GGGTAAAATGGTAATTTT-GGTTAAAATCGGGGTTAAAAATGGAATTTTGGAA-ATTTAG
* * * **
12069732 GGGTAAAATGGTAATTTTGGTTGAAATTGGGGTTAAAAATGGAAATTTTGG-AGTTCGG
1 GGGTAAAATGGTAATTTTGGTTAAAATCGGGGTTAAAAATGG-AATTTTGGAAATTTAG
12069790 GGTGTAAAATGGTAATTTTTTGGTTAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA-
1 GG-GTAAAATGGTAA--TTTTGGTTAAAATCGGGGTTAAAAATGGAATTTTGGAAA-TTTAG
*
12069851 AGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
12069869 AGAAGTTTTG
Statistics
Matches: 168, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
58 28 0.17
59 82 0.49
60 28 0.17
61 28 0.17
62 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGTTAAAATCGGGGTTAAAAATGGAATTTTGGAAATTTAG
Found at i:12070177 original size:162 final size:159
Alignment explanation
Indices: 12069939--12070277 Score: 489
Period size: 162 Copynumber: 2.1 Consensus size: 159
12069929 AAGCATCCAG
* * * * *
12069939 CAGTCAATGGATTAAATTGTAAATCTTGAAAAATTCTTGGGCCATTTATAATTAAATAAGAGTTG
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCATTTATAATTAAATAAAAGTTG
* *
12070004 ATTTGGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGGATAAATAAGCCAAAAAG
66 ATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAA-
*
12070069 TGACACGTGGCAACCCCTGGTGCAGTCAAA
130 TGACACGTAGCAACCCCTGGTGCAGTCAAA
* * *
12070099 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATTGTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCC-A-TTTATAATTAAATAAAAGT
* *
12070164 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCGGGGACTAAATGAATAAATAAGTCAAAA
64 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAA
* ** *
12070229 ATGACATGTAGCTGCCTCTGGTGCAGTCAAA
129 ATGACACGTAGCAACCCCTGGTGCAGTCAAA
*
12070260 CAGTCAAAGGATTAAATT
1 CAGTCAAAGGACTAAATT
12070278 GAAAACTACT
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
160 37 0.23
161 42 0.27
162 79 0.50
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (159 bp):
CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCATTTATAATTAAATAAAAGTTG
ATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAGGGACTAAATGAATAAATAAGCCAAAAAT
GACACGTAGCAACCCCTGGTGCAGTCAAA
Found at i:12071832 original size:6 final size:6
Alignment explanation
Indices: 12071818--12071906 Score: 98
Period size: 6 Copynumber: 15.2 Consensus size: 6
12071808 AATGTTTAGT
* *
12071818 ATTTTA ATTTAA ATTTAA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
12071867 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
12071907 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.07
5 7 0.10
6 53 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:12071872 original size:37 final size:37
Alignment explanation
Indices: 12071826--12071899 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
12071816 GTATTTTAAT
12071826 TTAAATTTAAATTTAA-ATTTAAA-GTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA--TAAATGTAAATTTAAATAA
*
12071863 TTAAATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
12071900 ATTTAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 4 0.12
37 29 0.85
38 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (37 bp):
TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
Found at i:12071908 original size:11 final size:11
Alignment explanation
Indices: 12071827--12071916 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
12071817 TATTTTAATT
*
12071827 TAAATTTAAATT
1 TAAATTTAAA-A
*
12071839 TAAATTTAAAG
1 TAAATTTAAAA
12071850 TAAATTTAAATAA
1 TAAATTT-AA-AA
*
12071863 TTAAATTTAAAT
1 -TAAATTTAAAA
* ** *
12071875 TTAAGATAAATT
1 TAAATTTAAA-A
12071887 TAAATTT-AAA
1 TAAATTTAAAA
12071897 TAAATTTAAAA
1 TAAATTTAAAA
*
12071908 TCAATTTAA
1 TAAATTTAA
12071917 CTCCAAATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
10 7 0.11
11 27 0.44
12 18 0.29
13 3 0.05
14 7 0.11
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:12071908 original size:17 final size:16
Alignment explanation
Indices: 12071818--12071906 Score: 110
Period size: 17 Copynumber: 5.4 Consensus size: 16
12071808 AATGTTTAGT
*
12071818 ATTTTAATTTAAATTTAA
1 ATTTAAATTTAAA--TAA
12071836 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAA-TAA
*
12071853 ATTTAAA--TAATTAA
1 ATTTAAATTTAAATAA
12071867 ATTTAAATTTAAGATAA
1 ATTTAAATTTAA-ATAA
12071884 ATTTAAATTTAAATAA
1 ATTTAAATTTAAATAA
12071900 ATTTAAA
1 ATTTAAA
12071907 ATCAATTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 14 0.22
17 25 0.39
18 12 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:12071924 original size:27 final size:27
Alignment explanation
Indices: 12071870--12071924 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
12071860 TAATTAAATT
* **
12071870 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
* *
12071897 TAAATTTAAAATCAATTTAACTCCAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
12071924 T
1 T
12071925 TAAAACAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCCAAA
Found at i:12074686 original size:19 final size:19
Alignment explanation
Indices: 12074662--12074724 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 19
12074652 TCTTGCCAAT
12074662 ATATATTTTTAAATTAAAA
1 ATATATTTTTAAATTAAAA
12074681 ATATA---TTAAATGTAAAA
1 ATATATTTTTAAAT-TAAAA
*
12074698 ATATGATTTTTTAA-TAAAA
1 ATAT-ATTTTTAAATTAAAA
12074717 AT-TATTTT
1 ATATATTTT
12074725 AAAGATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
16 6 0.16
17 14 0.37
18 2 0.05
19 12 0.32
21 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (19 bp):
ATATATTTTTAAATTAAAA
Found at i:12074735 original size:36 final size:37
Alignment explanation
Indices: 12074662--12074739 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 37
12074652 TCTTGCCAAT
12074662 ATAT-ATTTTTAAATTAAAAATATATTAAATGTAAAA
1 ATATGATTTTTAAATTAAAAATATATTAAATGTAAAA
* *
12074698 ATATGATTTTTTAA-TAAAAATTATTTTAAA-G-ATAAA
1 ATATGATTTTTAAATTAAAAA-TATATTAAATGTA-AAA
12074734 ATATGA
1 ATATGA
12074740 AATTGATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
35 1 0.03
36 20 0.54
37 16 0.43
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (37 bp):
ATATGATTTTTAAATTAAAAATATATTAAATGTAAAA
Found at i:12076425 original size:21 final size:21
Alignment explanation
Indices: 12076400--12076439 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12076390 ATAAATTATT
12076400 TTTTTCAAC-CGATTCAACTGA
1 TTTTT-AACTCGATTCAACTGA
*
12076421 TTTTTAACTCGGTTCAACT
1 TTTTTAACTCGATTCAACT
12076440 AATCTATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTTAACTCGATTCAACTGA
Found at i:12080591 original size:18 final size:18
Alignment explanation
Indices: 12080557--12080591 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12080547 TTGTTACCAT
* *
12080557 CTAAAGTTTAATTCTTTC
1 CTAAAGTTAAATGCTTTC
12080575 CTAAAGTTAAATGCTTT
1 CTAAAGTTAAATGCTTT
12080592 ATTTTGTTTC
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:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (18 bp):
CTAAAGTTAAATGCTTTC
Found at i:12090652 original size:41 final size:41
Alignment explanation
Indices: 12090607--12090691 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
12090597 TCTACCTAAG
12090607 CTTATGACATCCTACCACTTACCCTTGACTGCAAATAGGAT
1 CTTATGACATCCTACCACTTACCCTTGACTGCAAATAGGAT
12090648 CTTATGACATCCTACCACTTACCCTTGACTGCAAATAGGAT
1 CTTATGACATCCTACCACTTACCCTTGACTGCAAATAGGAT
12090689 CTT
1 CTT
12090692 GACACGTGGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (41 bp):
CTTATGACATCCTACCACTTACCCTTGACTGCAAATAGGAT
Found at i:12091216 original size:30 final size:31
Alignment explanation
Indices: 12091180--12091253 Score: 132
Period size: 30 Copynumber: 2.4 Consensus size: 31
12091170 CAAATGATTT
12091180 TAAAATTATTAAAATTATTTTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
*
12091210 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTAAAATAA
12091241 TAAAATTATTAAA
1 TAAAATTATTAAA
12091254 TAACTTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 28 0.67
31 14 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TAAAATTATTAAAATTATTTTTTTAAAATAA
Found at i:12092187 original size:29 final size:29
Alignment explanation
Indices: 12092145--12092213 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
12092135 CTGAGAGATA
12092145 GGAGATGATGAAGGAAGGAAAGAAACAAT
1 GGAGATGATGAAGGAAGGAAAGAAACAAT
12092174 GGAGATGATGAAGGAAGGAAAGAAACAAT
1 GGAGATGATGAAGGAAGGAAAGAAACAAT
12092203 GGAGATGATGA
1 GGAGATGATGA
12092214 TGATTTAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.49, C:0.03, G:0.36, T:0.12
Consensus pattern (29 bp):
GGAGATGATGAAGGAAGGAAAGAAACAAT
Found at i:12092289 original size:6 final size:7
Alignment explanation
Indices: 12092260--12092289 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12092250 GGAAGAAGAT
12092260 TTAGAAA
1 TTAGAAA
12092267 TTAGAAA
1 TTAGAAA
12092274 TTAGAAA
1 TTAGAAA
12092281 TTA-AAA
1 TTAGAAA
12092287 TTA
1 TTA
12092290 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (7 bp):
TTAGAAA
Found at i:12092335 original size:21 final size:23
Alignment explanation
Indices: 12092293--12092346 Score: 87
Period size: 21 Copynumber: 2.5 Consensus size: 23
12092283 AAAATTATTT
12092293 AATAATTTT-ATTATTTTAAAAA
1 AATAATTTTAATTATTTTAAAAA
12092315 AATAATTTTAATT-TTTT-AAAA
1 AATAATTTTAATTATTTTAAAAA
12092336 AATAATTTTAA
1 AATAATTTTAA
12092347 AATCATTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.48
22 13 0.42
23 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATAATTTTAATTATTTTAAAAA
Found at i:12093103 original size:56 final size:54
Alignment explanation
Indices: 12093017--12093158 Score: 178
Period size: 56 Copynumber: 2.6 Consensus size: 54
12093007 GAATCCAAGT
12093017 TAGGGACCAAATTTAGAAAATCTACCAAGTTTTGGAACTAATGTAAACAAAAAAAA
1 TAGGGACCAAA-TTAGAAAATCTACCAAGTTTTGGAACTAATGTAAAC-AAAAAAA
* * *
12093073 TAGGGACCAAATTAGGAAAATTTACCAAGTTTTGGGACTAATGTAGACAAAAAAA
1 TAGGGACCAAATTA-GAAAATCTACCAAGTTTTGGAACTAATGTAAACAAAAAAA
** * *
12093128 TAGGGGTCAAATTAAAATAAT-TATCAAGTTT
1 TAGGGACCAAATTAGAA-AATCTACCAAGTTT
12093159 AGGGACCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
54 11 0.14
55 25 0.32
56 41 0.53
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (54 bp):
TAGGGACCAAATTAGAAAATCTACCAAGTTTTGGAACTAATGTAAACAAAAAAA
Found at i:12094370 original size:30 final size:29
Alignment explanation
Indices: 12094305--12094362 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
12094295 GTCTAATATG
* *
12094305 CAATGTTATATATGAATTTTGATTTTGTA
1 CAATTTTATATATGAATGTTGATTTTGTA
*
12094334 CGATTTTATATATTGAATGTTGATTTTGT
1 CAATTTTATATA-TGAATGTTGATTTTGT
12094363 TTAATTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.53
Consensus pattern (29 bp):
CAATTTTATATATGAATGTTGATTTTGTA
Found at i:12097753 original size:49 final size:49
Alignment explanation
Indices: 12097687--12098055 Score: 198
Period size: 49 Copynumber: 7.7 Consensus size: 49
12097677 AGGTACAAGG
* *
12097687 TTCGCCGTTGTGACTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGA
* * * * * * **
12097736 TTCGCCGTCGTGGCTTAAATCC-CT-CCTTT-CATTTTCTGAGGTACAAGG-
1 TTCGCCGTTGCGGCTTAAA-CCTTTCCCTTTGTATCTTC-GTGGTA-TTGGA
* * * *
12097784 TTCGTCGTTGCGGCTTAAACCTTTCCC-TTGACATCTTCGTGGTGTTGAA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTG-TATCTTCGTGGTATTGGA
* * *
12097833 TTCGCCGTTGTGGCTTAAATCTTTCCC-TT-TATGCTTC-TGAGTTATAAGG-
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTAT-CTTCGTG-G-TAT-TGGA
* * * ** *
12097882 TTCTCCATTGCGACTTAAACCTTT-CCTTTGTATCTTCGTAATACTGGA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGA
* * *
12097930 TTCACCGTTGCGGCTTAAATCTTTCCC-TT-CATGCTTC-TAAGGTA-T--A
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTAT-CTTCGT--GGTATTGGA
* * * * * *
12097976 --AGCCTTTACGACTTAAACCTTTCCCTTTGTTATCTTTGTGGTACTGGA
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTG-TATCTTCGTGGTATTGGA
* *
12098024 TTCACCGTTGCGGCTTAAATCTTTCCCTTTGT
1 TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGT
12098056 GTAATGAAAC
Statistics
Matches: 236, Mismatches: 55, Indels: 58
0.68 0.16 0.17
Matches are distributed among these distances:
44 19 0.08
45 6 0.03
46 5 0.02
47 19 0.08
48 67 0.28
49 84 0.36
50 36 0.15
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (49 bp):
TTCGCCGTTGCGGCTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGA
Found at i:12097801 original size:97 final size:98
Alignment explanation
Indices: 12097670--12098049 Score: 393
Period size: 97 Copynumber: 3.9 Consensus size: 98
12097660 TTCTATTTGC
* * * *
12097670 GCTTTTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCTTTCCCTTTG-TATCTTCGTGGTATTG
1 GCTTCTGAGGTACAAGGTTC-TCGTTGCGACTTAAACCTTTCCCTTTGATATCTTCGTGGTACTG
* * * **
12097734 GATTCGCCGTCGTGGCTTAAATCCCTCCTTTCAT
65 GATTCACCGTTGCGGCTTAAATCTTTCCTTTCAT
* * * **
12097768 -TTTCTGAGGTACAAGGTTCGTCGTTGCGGCTTAAACCTTTCCC-TTGACATCTTCGTGGTGTTG
1 GCTTCTGAGGTACAAGGTTC-TCGTTGCGACTTAAACCTTTCCCTTTGATATCTTCGTGGTACTG
* * *
12097831 AATTCGCCGTTGTGGCTTAAATCTTTCCCTTT-AT
65 GATTCACCGTTGCGGCTTAAATCTTT-CCTTTCAT
* * * **
12097865 GCTTCTGAGTTATAAGGTTCTCCATTGCGACTTAAACCTTT-CCTTTG-TATCTTCGTAATACTG
1 GCTTCTGAGGTACAAGGTTCT-CGTTGCGACTTAAACCTTTCCCTTTGATATCTTCGTGGTACTG
*
12097928 GATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT
65 GATTCACCGTTGCGGCTTAAATCTTTCCTTTCAT
* * * * * *
12097962 GCTTCTAAGGTATAA-G--C-CTTTACGACTTAAACCTTTCCCTTTGTTATCTTTGTGGTACTGG
1 GCTTCTGAGGTACAAGGTTCTCGTTGCGACTTAAACCTTTCCCTTTGATATCTTCGTGGTACTGG
12098023 ATTCACCGTTGCGGCTTAAATCTTTCC
66 ATTCACCGTTGCGGCTTAAATCTTTCC
12098050 CTTTGTGTAA
Statistics
Matches: 242, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
92 17 0.07
93 6 0.02
94 42 0.17
96 8 0.03
97 128 0.53
98 41 0.17
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (98 bp):
GCTTCTGAGGTACAAGGTTCTCGTTGCGACTTAAACCTTTCCCTTTGATATCTTCGTGGTACTGG
ATTCACCGTTGCGGCTTAAATCTTTCCTTTCAT
Found at i:12111988 original size:3 final size:3
Alignment explanation
Indices: 12111980--12112005 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12111970 TGGTCTACTT
12111980 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
12112006 TTGCATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:12116069 original size:16 final size:17
Alignment explanation
Indices: 12116050--12116085 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12116040 AAAAAAATAG
12116050 TTTAT-TTAAAAATATT
1 TTTATCTTAAAAATATT
*
12116066 TTTATCTTAAAAGTATT
1 TTTATCTTAAAAATATT
12116083 TTT
1 TTT
12116086 TAAAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTATCTTAAAAATATT
Found at i:12116588 original size:22 final size:25
Alignment explanation
Indices: 12116523--12116583 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
12116513 CGGTCACGAT
12116523 AATTTTTAATAGTAAAAAAGGATGA
1 AATTTTTAATAGTAAAAAAGGATGA
12116548 AATTTTTAATAGTAAAAAAGGATGA
1 AATTTTTAATAGTAAAAAAGGATGA
12116573 AATTTTTAATA
1 AATTTTTAATA
12116584 AAAAATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (25 bp):
AATTTTTAATAGTAAAAAAGGATGA
Found at i:12120102 original size:43 final size:40
Alignment explanation
Indices: 12120054--12120132 Score: 122
Period size: 43 Copynumber: 1.9 Consensus size: 40
12120044 AATAAGACAA
12120054 ATTTTAAATTTAAATTTACTTTAAATTTTAAAATGTCCAATAC
1 ATTTTAAATTTAAATTTA-TTTAAA-TTTAAAA-GTCCAATAC
*
12120097 ATTTTAATTTTAAATTTATTTAAATTTAAAAGTCCA
1 ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCA
12120133 TTTACAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 5 0.14
41 7 0.20
42 6 0.17
43 17 0.49
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.48
Consensus pattern (40 bp):
ATTTTAAATTTAAATTTATTTAAATTTAAAAGTCCAATAC
Found at i:12121624 original size:30 final size:30
Alignment explanation
Indices: 12121552--12121802 Score: 172
Period size: 30 Copynumber: 8.5 Consensus size: 30
12121542 TTATTTTGTC
* **
12121552 TAAAAATCACA-TTTGACCCCAGAACTTC-
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* *
12121580 CAAAAATCACATTTTGACCCTTGAACTTCA
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* ** *
12121610 TAAAAATTATATTTT-ATCCCCCGAACTTCT
1 TAAAAATTACATTTTGA-CCCTTGAACTTCA
* * * *
12121640 TGAAAATTATATTTTGACCCTCGAACTTCG
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* * **
12121670 TAAAAATTACATTTTGACCATTAAACTTTG
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* * * *
12121700 CAAAAATTACATTCT-AACC-TAAACTTCA
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* * * * * **
12121728 CAAAAAATACATTTTAACCCCTAAACTTTG
1 TAAAAATTACATTTTGACCCTTGAACTTCA
* *
12121758 TAAAAATTACATTTTAACCCTCGAACTT-A
1 TAAAAATTACATTTTGACCCTTGAACTTCA
12121787 TTAAAAATTACATTTT
1 -TAAAAATTACATTTT
12121803 AACCTCGAAC
Statistics
Matches: 181, Mismatches: 35, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
28 30 0.17
29 21 0.12
30 129 0.71
31 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAAAATTACATTTTGACCCTTGAACTTCA
Found at i:12121697 original size:60 final size:58
Alignment explanation
Indices: 12121582--12121803 Score: 200
Period size: 60 Copynumber: 3.8 Consensus size: 58
12121572 AGAACTTCCA
* * * **
12121582 AAAATCACATTTTGACCCTTGAACTTCATAAAAATTATATTTTATCCCCCGAACTTCTTG
1 AAAATTACATTTTGACCCTCGAACTTCATAAAAATTACATTTTA-CCCCTAAACTT-TTG
* * **
12121642 AAAATTATATTTTGACCCTCGAACTTCGTAAAAATTACATTTTGACCATTAAAC-TTTG
1 AAAATTACATTTTGACCCTCGAACTTCATAAAAATTACATTTT-ACCCCTAAACTTTTG
* * * * * *
12121700 CAAAAATTACATTCT-AACCT-AAACTTCACAAAAAATACATTTTAACCCCTAAACTTTGTA
1 --AAAATTACATTTTGACCCTCGAACTTCATAAAAATTACATTTT-ACCCCTAAACTTT-TG
*
12121760 AAAATTACATTTTAACCCTCGAACTT-ATTAAAAATTACATTTTA
1 AAAATTACATTTTGACCCTCGAACTTCA-TAAAAATTACATTTTA
12121804 ACCTCGAACT
Statistics
Matches: 129, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
58 42 0.33
59 13 0.10
60 73 0.57
61 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAATTACATTTTGACCCTCGAACTTCATAAAAATTACATTTTACCCCTAAACTTTTG
Found at i:12121803 original size:30 final size:29
Alignment explanation
Indices: 12121581--12121831 Score: 177
Period size: 30 Copynumber: 8.5 Consensus size: 29
12121571 CAGAACTTCC
* * * *
12121581 AAAAATCACATTTTGACCCTTGAACTTCAT
1 AAAAATTACATTTTAACCCTCGAACTT-TT
* * *
12121611 AAAAATTATATTTTATCCCCCGAACTTCTT
1 AAAAATTACATTTTAACCCTCGAACTT-TT
* * * *
12121641 GAAAATTATATTTTGACCCTCGAACTTCGT
1 AAAAATTACATTTTAACCCTCGAACTT-TT
* * ** *
12121671 AAAAATTACATTTTGACCATTAAACTTTGC
1 AAAAATTACATTTTAACCCTCGAACTTT-T
* * **
12121701 AAAAATTACATTCTAA-CCT-AAACTTCAC
1 AAAAATTACATTTTAACCCTCGAACTT-TT
* *
12121729 AAAAAATACATTTTAACCC-CTAAACTTTGT
1 AAAAATTACATTTTAACCCTC-GAACTTT-T
12121759 AAAAATTACATTTTAACCCTCGAACTTATT
1 AAAAATTACATTTTAACCCTCGAACTT-TT
12121789 AAAAATTACATTTTAA-CCTCGAACTTTT
1 AAAAATTACATTTTAACCCTCGAACTTTT
* *
12121817 CCAAAATTGCATTTT
1 -AAAAATTACATTTT
12121832 TGACTCCCAA
Statistics
Matches: 181, Mismatches: 31, Indels: 19
0.78 0.13 0.08
Matches are distributed among these distances:
28 23 0.13
29 26 0.14
30 130 0.72
31 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTCGAACTTTT
Found at i:12121844 original size:148 final size:147
Alignment explanation
Indices: 12121574--12121860 Score: 321
Period size: 148 Copynumber: 1.9 Consensus size: 147
12121564 TTGACCCCAG
* * * * * *
12121574 AACTTCCAAAAATCACATTTTGACCCTTGAACTTCATAAAAATTATATTTTATCCCCCGAACTTC
1 AACTTCCAAAAATCACATTTTAACCCCTAAACTTCATAAAAATTACATTTTAACCCCCGAACTTA
* * * ** **
12121639 TTGAAAATTATATTTTGACCCTCGAACTTCGTAAAAATTACATTTTGACCATTAAACTTTGCAAA
66 TTAAAAATTACATTTTGAACCTCGAACTTCGTAAAAATTACATTTTGACCACCAAACTTCCCAAA
12121704 AATTACATTCTAACCTA
131 AATTACATTCTAACCTA
** *
12121721 AACTTCACAAAAAAT-ACATTTTAACCCCTAAACTTTGTAAAAATTACATTTTAACCCTCGAACT
1 AACTTC-C-AAAAATCACATTTTAACCCCTAAACTTCATAAAAATTACATTTTAACCCCCGAACT
* * *
12121785 TATTAAAAATTACATTTT-AACCTCGAACTT-TTCCAAAATTGCATTTTTGACTC-CCAAACTTC
64 TATTAAAAATTACATTTTGAACCTCGAACTTCGT-AAAAATTACA-TTTTGAC-CACCAAACTTC
*
12121847 CCCAAAATTACATT
126 CCAAAAATTACATT
12121861 TTGACTCCAA
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
146 1 0.01
147 25 0.22
148 82 0.71
149 7 0.06
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (147 bp):
AACTTCCAAAAATCACATTTTAACCCCTAAACTTCATAAAAATTACATTTTAACCCCCGAACTTA
TTAAAAATTACATTTTGAACCTCGAACTTCGTAAAAATTACATTTTGACCACCAAACTTCCCAAA
AATTACATTCTAACCTA
Found at i:12121865 original size:30 final size:30
Alignment explanation
Indices: 12121790--12121892 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 30
12121780 GAACTTATTA
* * * *
12121790 AAAATTACATTTTAAC-CTCGAACTTTTCC
1 AAAATTACATTTTGACTCCCAAACTTCTCC
* *
12121819 AAAATTGCATTTTTGACTCCCAAACTTCCCC
1 AAAATTACA-TTTTGACTCCCAAACTTCTCC
12121850 AAAATTACATTTTGACT-CCAAAC-TCATCC
1 AAAATTACATTTTGACTCCCAAACTTC-TCC
12121879 AAAATTACCATTTT
1 AAAATTA-CATTTT
12121893 ACCACCGAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 2 0.03
29 23 0.37
30 20 0.32
31 17 0.27
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACTCCCAAACTTCTCC
Found at i:12125131 original size:29 final size:29
Alignment explanation
Indices: 12125086--12125259 Score: 128
Period size: 29 Copynumber: 6.0 Consensus size: 29
12125076 GTCCTTTTAG
* * *
12125086 GAAAATTCA-AGGTAAAAACATGATTTTT
1 GAAAGTTCAGAGGGAAAAATATGATTTTT
* *
12125114 GAAAGTTCAG-GGGCAAAAATGTGATCTTT
1 GAAAGTTCAGAGGG-AAAAATATGATTTTT
*
12125143 GAAAGTTC-GAGGGTAAAAATATAATTTTT
1 GAAAGTTCAGAGGG-AAAAATATGATTTTT
* *
12125172 GGAAGTT-TGAGGGAAAAA-AGTGATTTTT
1 GAAAGTTCAGAGGGAAAAATA-TGATTTTT
* *
12125200 GGAAGTTC-GAGGGTAAAAATGTGATTTTT
1 GAAAGTTCAGAGGG-AAAAATATGATTTTT
* **
12125229 -ACGAAGTACAGAGGTCAAAATATGATTTTT
1 GA--AAGTTCAGAGGGAAAAATATGATTTTT
12125259 G
1 G
12125260 GATAGTTTAG
Statistics
Matches: 117, Mismatches: 17, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 35 0.30
29 59 0.50
30 18 0.15
31 4 0.03
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (29 bp):
GAAAGTTCAGAGGGAAAAATATGATTTTT
Found at i:12125216 original size:57 final size:58
Alignment explanation
Indices: 12125096--12125228 Score: 171
Period size: 57 Copynumber: 2.3 Consensus size: 58
12125086 GAAAATTCAA
* *
12125096 GGTAAAAACATGATTTTTGAAAGTTCAGGGGCAAAAATGTGATCTTTGAAAGTTCGAG
1 GGTAAAAATATGATTTTTGAAAGTTCAGGGGCAAAAAAGTGATCTTTGAAAGTTCGAG
* * * * *
12125154 GGTAAAAATATAATTTTTGGAAGTT-TGAGGG-AAAAAAGTGATTTTTGGAAGTTCGAG
1 GGTAAAAATATGATTTTTGAAAGTTCAG-GGGCAAAAAAGTGATCTTTGAAAGTTCGAG
*
12125211 GGTAAAAATGTGATTTTT
1 GGTAAAAATATGATTTTT
12125229 ACGAAGTACA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 40 0.62
58 25 0.38
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (58 bp):
GGTAAAAATATGATTTTTGAAAGTTCAGGGGCAAAAAAGTGATCTTTGAAAGTTCGAG
Found at i:12127039 original size:17 final size:17
Alignment explanation
Indices: 12126972--12127048 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
12126962 ATTAAATTTT
12126972 TAAATTTAAA-TCCAAAA
1 TAAATTTAAACT-CAAAA
12126989 TAAATTTAAACTCAAAA
1 TAAATTTAAACTCAAAA
* * *
12127006 TAAGTTTAAATTTAAAA
1 TAAATTTAAACTCAAAA
*
12127023 TAAATTTAAACTAAAAA
1 TAAATTTAAACTCAAAA
12127040 T-AATTTAAA
1 TAAATTTAAA
12127049 ATTTAAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 8 0.15
17 44 0.83
18 1 0.02
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (17 bp):
TAAATTTAAACTCAAAA
Found at i:12127051 original size:34 final size:34
Alignment explanation
Indices: 12126976--12127057 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
12126966 AATTTTTAAA
** *
12126976 TTTAAATCCAAAATAAATTTAAACTCAAAATAAG
1 TTTAAATTTAAAATAAATTTAAACTAAAAATAAG
12127010 TTTAAATTTAAAATAAATTTAAACTAAAAATAA-
1 TTTAAATTTAAAATAAATTTAAACTAAAAATAAG
12127043 TTTAAAATTTAAAAT
1 TTT-AAATTTAAAAT
12127058 TGGGTTTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.07
34 41 0.93
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAACTAAAAATAAG
Found at i:12127056 original size:17 final size:16
Alignment explanation
Indices: 12126974--12127057 Score: 78
Period size: 17 Copynumber: 5.0 Consensus size: 16
12126964 TAAATTTTTA
**
12126974 AATTTAAATCCAAAAT
1 AATTTAAATTTAAAAT
* *
12126990 AAATTTAAACTCAAAAT
1 -AATTTAAATTTAAAAT
12127007 AAGTTTAAATTTAAAAT
1 AA-TTTAAATTTAAAAT
* *
12127024 AAATTTAAACTAAAAAT
1 -AATTTAAATTTAAAAT
12127041 AATTTAAAATTTAAAAT
1 AATTT-AAATTTAAAAT
12127058 TGGGTTTTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
16 7 0.12
17 47 0.84
18 2 0.04
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:12137188 original size:39 final size:39
Alignment explanation
Indices: 12137140--12137747 Score: 244
Period size: 39 Copynumber: 15.7 Consensus size: 39
12137130 CAGTCATCTG
* ** *
12137140 ATCTTTTACCCCGAGCCTAAGGCAGATCATCATAAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * * ** *
12137179 ATCTCTTACCCCGAG-TTCGGGGCAGATTA-CAGCAATTCG
1 ATCTCTTACCCCGAGCCT-GGGGCAGATCACCA-TAAGCCA
* * *
12137218 ATCTCTTACCTCGAGCCTGAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * *** * ***
12137257 ATCTCTTACCCCGAGCTTGGGGTAGAT-TGTAGTCAGTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TAAGCCA
* * ** * *
12137296 ATCTTTTACCTCGAGCCT-GGATAGACCAACATAAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * * *
12137334 ATCTCTTACCCAGAGCCTGAGACAGATTACAGCCAT-A--CG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATAAGCCA
* * * * * *
12137373 ATCTTTTACCCTGAACCTAGGGCAAATCACCATCAA-ACA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCAT-AAGCCA
* * *
12137412 ATCTCTTACCCCGAG-CTTGGGCAGATTGAACCAT---CCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CACCATAAGCCA
* * * * *
12137449 ATCTTTTATCCCGAGCTTGAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * *
12137488 ATCTCTTACCCCAAGCTTAGGGCAGATCACCATCAA-CCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCAT-AAGCCA
* * * ** *
12137527 ATCTCTTACCCCGAGCTTAGGGCAGATTGCAAC-T-ATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CACCATAAGCCA
* * * * * *
12137566 ATCTCTTACCCCGAGCCTGAGGTAGATCATCATCAGTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * * * * *
12137605 ATCTCTTACCTCGAGCTTGGGGCAAATAACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
* * ** * ** *
12137644 ATCTCTTACCCCCAACCT-GGGCAGAT-TGCAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TAAGCCA
* * * *
12137682 ACCTTTTACCCC-AACCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCC-TGGGGCAGATCACCATAAGCCA
*
12137721 ATCTCTTACCCCGAGCCAGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
12137748 TGCAACCATC
Statistics
Matches: 424, Mismatches: 115, Indels: 60
0.71 0.19 0.10
Matches are distributed among these distances:
36 9 0.02
37 26 0.06
38 71 0.17
39 293 0.69
40 16 0.04
41 6 0.01
42 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
Found at i:12137201 original size:78 final size:78
Alignment explanation
Indices: 12137101--12137757 Score: 369
Period size: 78 Copynumber: 8.5 Consensus size: 78
12137091 GAAGATTCCG
* * ** * * *
12137101 ATCTCTTACCCCAATCAAGGGGCAAATCACAGTCATCTGATCTTTTACCCCGAGCCTAAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCTGATCTTTTACCCCGAGCCTAAGGCAGA
*
12137166 TCATCATAAGCCA
66 TCACCATAAGCCA
* * * *
12137179 ATCTCTTACCCCGAG-TTCGGGGCAGATTACAGCAAT-TCGATCTCTTACCTCGAGCCTGAGGCA
1 ATCTCTTACCCCGAGCTT-GGGGCAGATTACAGCCATCT-GATCTTTTACCCCGAGCCTAAGGCA
*
12137242 GATCACCATCAGCCA
64 GATCACCATAAGCCA
* ** * * *
12137257 ATCTCTTACCCCGAGCTTGGGGTAGATTGTAGTCAGT-TGATCTTTTACCTCGAGCCT--GGATA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCA-TCTGATCTTTTACCCCGAGCCTAAGG-CA
* *
12137319 GACCAACATAAGCCA
64 GATCACCATAAGCCA
* * * * * * * *
12137334 ATCTCTTACCCAGAGCCTGAGACAGATTACAGCCATAC-GATCTTTTACCCTGAACCTAGGGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCAT-CTGATCTTTTACCCCGAGCCTAAGGCAG
*
12137398 ATCACCATCAA-ACA
65 ATCACCAT-AAGCCA
* * * *
12137412 ATCTCTTACCCCGAGCTT-GGGCAGATTGA-A-CCATCCGATCTTTTATCCCGAGCTTGAGGCAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATT-ACAGCCATCTGATCTTTTACCCCGAGCCTAAGGCAG
*
12137474 ATCACCATCAGCCA
65 ATCACCATAAGCCA
* * * * * ** * * *
12137488 ATCTCTTACCCCAAGCTTAGGGCAGATCACCA-TCAACCAATCTCTTACCCCGAGCTTAGGGCAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTA-CAGCCATCTGATCTTTTACCCCGAGCCTAAGGCAG
* ** *
12137552 ATTGCAAC-T-ATTCG
65 A-T-CACCATAAGCCA
* * * * * * * * **
12137566 ATCTCTTACCCCGAGCCTGAGGTAGATCATCA-TCAGTC-GATCTCTTACCTCGAGCTTGGGGCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTA-CAGCCA-TCTGATCTTTTACCCCGAGCCTAAGGCA
* * * *
12137629 AATAACCATCAGTCA
64 GATCACCATAAGCCA
* * * * * * * **
12137644 ATCTCTTACCCCCAACCT-GGGCAGATTGCAGTCAT-TCGACCTTTTACCCC-AACCTTGGGGCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCT-GATCTTTTACCCCGAGCC-TAAGGCA
*
12137706 GATCACCATCAGCCA
64 GATCACCATAAGCCA
** * *
12137721 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAACCATC
1 ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATC
12137758 CAATATCTTA
Statistics
Matches: 453, Mismatches: 99, Indels: 53
0.75 0.16 0.09
Matches are distributed among these distances:
75 2 0.00
76 61 0.13
77 128 0.28
78 248 0.55
79 11 0.02
80 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCTGATCTTTTACCCCGAGCCTAAGGCAGA
TCACCATAAGCCA
Found at i:12137375 original size:155 final size:155
Alignment explanation
Indices: 12137138--12137498 Score: 394
Period size: 155 Copynumber: 2.3 Consensus size: 155
12137128 CACAGTCATC
* * * * * *
12137138 TGATCTTTTACCCCGAGCCTAAGGCAGATCATCATAAGCCAATCTCTTACCCCGAGTTCGGGGCA
1 TGATCTTTTACCCCGAGCCT-AGGCAGACCAACATAAGCCAATCTCTTACCCAGAGCTCGAGACA
* * * **
12137203 GATTACAGCAATTCGATCTCTTA-CCTCGAGCCT-GAGGCAGATCACCATCAGCCAATCTCTTAC
65 GATTACAGCAATACGATCTCTTACCCT-GAACCTAG-GGCAAATCACCATCAAACAATCTCTTAC
12137266 CCCGAGCTTGGGGTAGATTGTAGTCAGT
128 CCCGAGCTTGGGGTAGATTGTAGTCAGT
* *
12137294 TGATCTTTTACCTCGAGCCT-GGATAGACCAACATAAGCCAATCTCTTACCCAGAGC-CTGAGAC
1 TGATCTTTTACCCCGAGCCTAGG-CAGACCAACATAAGCCAATCTCTTACCCAGAGCTC-GAGAC
* *
12137357 AGATTACAGCCATACGATCTTTTACCCTGAACCTAGGGCAAATCACCATCAAACAATCTCTTACC
64 AGATTACAGCAATACGATCTCTTACCCTGAACCTAGGGCAAATCACCATCAAACAATCTCTTACC
* **
12137422 CCGAGCTT-GGGCAGATTG-AACCA-T
129 CCGAGCTTGGGGTAGATTGTAGTCAGT
* * * * * *
12137446 CCGATCTTTTATCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCC
1 -TGATCTTTTACCCCGAGCCT-AGGCAGACCAACATAAGCCAATCTCTTACCC
12137499 CAAGCTTAGG
Statistics
Matches: 172, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
152 1 0.01
153 19 0.11
154 36 0.21
155 93 0.54
156 23 0.13
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (155 bp):
TGATCTTTTACCCCGAGCCTAGGCAGACCAACATAAGCCAATCTCTTACCCAGAGCTCGAGACAG
ATTACAGCAATACGATCTCTTACCCTGAACCTAGGGCAAATCACCATCAAACAATCTCTTACCCC
GAGCTTGGGGTAGATTGTAGTCAGT
Found at i:12137613 original size:117 final size:116
Alignment explanation
Indices: 12137177--12137732 Score: 423
Period size: 116 Copynumber: 4.8 Consensus size: 116
12137167 CATCATAAGC
* * * * *
12137177 CAATCTCTTACCCCGAG-TTCGGGGCAGATTACAGCAATTCGATCTCTTACCTCGAGCCTGAGGC
1 CAATCTCTTACCCCGAGCTT--GGGCAGATTGCAACTATTCGATCTTTTACCCCGAGCCTGAGGC
* * * * *** **
12137241 AGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGAT-TGTAGTCAGT
64 AGATCACCATCAGCCAATCTCTTACCCCAAGCTTAGGGCAAATCACCA-TCAAA
** * * * ** * ** * * * *
12137294 TGATCTTTTACCTCGAGCCTGGATAGA--CCAACATAAGCCAATCTCTTACCCAGAGCCTGAGAC
1 CAATCTCTTACCCCGAGCTTGGGCAGATTGCAAC-T-ATTCGATCTTTTACCCCGAGCCTGAGGC
* * * *
12137357 AGATTACAGCCAT-A--CGATCTTTTACCCTGAA-CCTAGGGCAAATCACCATCAAA
64 AGA-T-CA-CCATCAGCCAATCTCTTACCC-CAAGCTTAGGGCAAATCACCATCAAA
* * * *
12137410 CAATCTCTTACCCCGAGCTTGGGCAGATTG-AACCATCCGATCTTTTATCCCGAGCTTGAGGCAG
1 CAATCTCTTACCCCGAGCTTGGGCAGATTGCAACTATTCGATCTTTTACCCCGAGCCTGAGGCAG
* *
12137474 ATCACCATCAGCCAATCTCTTACCCCAAGCTTAGGGCAGATCACCATCAAC
66 ATCACCATCAGCCAATCTCTTACCCCAAGCTTAGGGCAAATCACCATCAAA
* *
12137525 CAATCTCTTACCCCGAGCTTAGGGCAGATTGCAACTATTCGATCTCTTACCCCGAGCCTGAGGTA
1 CAATCTCTTACCCCGAGCTT-GGGCAGATTGCAACTATTCGATCTTTTACCCCGAGCCTGAGGCA
* * * * * * * **
12137590 GATCATCATCAGTCGATCTCTTACCTCGAGCTTGGGGCAAATAACCATCAGT
65 GATCACCATCAGCCAATCTCTTACCCCAAGCTTAGGGCAAATCACCATCAAA
* * * * * * *
12137642 CAATCTCTTACCCCCAACCTGGGCAGATTGC-AGTCATTCGACCTTTTACCCC-AACCTTGGGGC
1 CAATCTCTTACCCCGAGCTTGGGCAGATTGCAACT-ATTCGATCTTTTACCCCGAGCC-TGAGGC
12137705 AGATCACCATCAGCCAATCTCTTACCCC
64 AGATCACCATCAGCCAATCTCTTACCCC
12137733 GAGCCAGGGG
Statistics
Matches: 341, Mismatches: 80, Indels: 37
0.74 0.17 0.08
Matches are distributed among these distances:
112 4 0.01
113 3 0.01
114 6 0.02
115 79 0.23
116 136 0.40
117 105 0.31
118 4 0.01
119 4 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (116 bp):
CAATCTCTTACCCCGAGCTTGGGCAGATTGCAACTATTCGATCTTTTACCCCGAGCCTGAGGCAG
ATCACCATCAGCCAATCTCTTACCCCAAGCTTAGGGCAAATCACCATCAAA
Found at i:12138252 original size:17 final size:17
Alignment explanation
Indices: 12138221--12138287 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
12138211 ATTGAACCTA
12138221 ATTTTAAATTTTAAATTT
1 ATTTTAAA-TTTAAATTT
*
12138239 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
12138256 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
12138273 ATTTTGAATTTAAAT
1 ATTTTAAATTTAAAT
12138288 CTAAAATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:12140199 original size:30 final size:30
Alignment explanation
Indices: 12140158--12140403 Score: 170
Period size: 30 Copynumber: 8.3 Consensus size: 30
12140148 TGTTTTGTTT
* *
12140158 AAAAATTACATTTCAACCCCCGAACTTTCC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
* * *
12140188 AAAAATCACATTTTGACTCTCGAAC-TTCAC
1 AAAAATTACATTTTAACCCTCGAACTTTC-C
* * *
12140218 AAAAATTACATTTTGACCC-CTAAAC-TTCAA
1 AAAAATTACATTTTAACCCTC-GAACTTTC-C
**
12140248 AAAAATTACATTTTAACCCTCGAACTTAGC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
*
12140278 AAAAATTACATTTTAA-CCTAGAACTTTCC
1 AAAAATTACATTTTAACCCTCGAACTTTCC
* * *
12140307 -AAAATTGCATTTTTGACTCC-CAAACTTTCC
1 AAAAATTACA-TTTTAAC-CCTCGAACTTTCC
* * * * *
12140337 TAAAATTACATTTTGACTC-CAAACTCATCC
1 AAAAATTACATTTTAACCCTCGAACT-TTCC
* *
12140367 -AAAATTACCATTTT-ACCCCCGAAC-ATCC
1 AAAAATTA-CATTTTAACCCTCGAACTTTCC
12140395 AAAAATTAC
1 AAAAATTAC
12140404 TATATCCCCT
Statistics
Matches: 178, Mismatches: 26, Indels: 26
0.77 0.11 0.11
Matches are distributed among these distances:
28 13 0.07
29 43 0.24
30 110 0.62
31 12 0.07
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCGAACTTTCC
Found at i:12144862 original size:20 final size:21
Alignment explanation
Indices: 12144830--12144876 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
12144820 TCATTTTAGT
12144830 ATTT-TTATATTTTGGAA-AC
1 ATTTCTTATATTTTGGAAGAC
* * *
12144849 GTTTCTTATTTTTTTGAAGAC
1 ATTTCTTATATTTTGGAAGAC
12144870 ATTTCTT
1 ATTTCTT
12144877 GTAGTAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
ATTTCTTATATTTTGGAAGAC
Found at i:12148886 original size:43 final size:43
Alignment explanation
Indices: 12148833--12148918 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
12148823 GAAAGGTTTT
* * *
12148833 TTATAAGGGTTTTAACAAGA-AATGGATTTGTGTTTGTTTCGAA
1 TTATAAGGGTTTTAAAAAGATAA-GGATTTGTATTAGTTTCGAA
* *
12148876 TTATTAGGGTTTTAAAAAGATAAGGATTTTTATTAGTTTCGAA
1 TTATAAGGGTTTTAAAAAGATAAGGATTTGTATTAGTTTCGAA
12148919 ATTTTGGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.43
Consensus pattern (43 bp):
TTATAAGGGTTTTAAAAAGATAAGGATTTGTATTAGTTTCGAA
Found at i:12149296 original size:85 final size:85
Alignment explanation
Indices: 12149147--12149307 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 85
12149137 TGTTGATATT
* * * * *
12149147 ATATGGTTGATGACTGTTTGGATAGACATGGAGTTGACTGTTGGAGTTATATTTGCTGTTGTTCA
1 ATATGGCTCATGACTATTTGGATAGACATGGAGTTGACTGTTGGAGTTATATTTGCTATGGTTCA
*
12149212 TGTCTGTTTTTGTTTAAGTG
66 TGACTGTTTTTGTTTAAGTG
* * **
12149232 ATATGGCTCATGACTATTTGGATGGACATGGAGTTGAGTGTTGGAGTTATATTTTTTATGGTTCA
1 ATATGGCTCATGACTATTTGGATAGACATGGAGTTGACTGTTGGAGTTATATTTGCTATGGTTCA
12149297 TGACTGTTTTT
66 TGACTGTTTTT
12149308 ATTTTGTTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.45
Consensus pattern (85 bp):
ATATGGCTCATGACTATTTGGATAGACATGGAGTTGACTGTTGGAGTTATATTTGCTATGGTTCA
TGACTGTTTTTGTTTAAGTG
Found at i:12149580 original size:22 final size:20
Alignment explanation
Indices: 12149553--12149624 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 20
12149543 AAAAATTTTG
12149553 AAATATGCTAAAAATATGCATA
1 AAATATG-TAAAAATATG-ATA
12149575 AAATATG--AAAATATGA-A
1 AAATATGTAAAAATATGATA
*
12149592 AAATATGTAAAAAAATGTATAA
1 AAATATGTAAAAATATG-AT-A
12149614 AAATATG-AAAA
1 AAATATGTAAAA
12149625 TATTAGGCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
17 8 0.18
18 1 0.02
19 15 0.34
20 1 0.02
21 4 0.09
22 15 0.34
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (20 bp):
AAATATGTAAAAATATGATA
Found at i:12149587 original size:8 final size:9
Alignment explanation
Indices: 12149562--12149624 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 9
12149552 GAAATATGCT
12149562 AAAAATATG
1 AAAAATATG
12149571 CATAAAATATG
1 -A-AAAATATG
12149582 -AAAATATG
1 AAAAATATG
12149590 AAAAATATG
1 AAAAATATG
*
12149599 TAAAAAAATG
1 -AAAAATATG
12149609 TATAAAAATATG
1 ---AAAAATATG
12149621 AAAA
1 AAAA
12149625 TATTAGGCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 8 0.17
9 12 0.26
10 9 0.20
11 8 0.17
12 9 0.20
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (9 bp):
AAAAATATG
Found at i:12149597 original size:39 final size:39
Alignment explanation
Indices: 12149553--12149627 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
12149543 AAAAATTTTG
*
12149553 AAATATGCTAAAAATATGCAT-AAAATATGAAAATATGAA
1 AAATATG-TAAAAAAATGCATAAAAATATGAAAATATGAA
*
12149592 AAATATGTAAAAAAATGTATAAAAATATGAAAATAT
1 AAATATGTAAAAAAATGCATAAAAATATGAAAATAT
12149628 TAGGCATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 11 0.33
39 22 0.67
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.27
Consensus pattern (39 bp):
AAATATGTAAAAAAATGCATAAAAATATGAAAATATGAA
Found at i:12150078 original size:16 final size:16
Alignment explanation
Indices: 12150059--12150089 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12150049 CCAAGAAGGC
12150059 CAAAAAAGAAGAGGAT
1 CAAAAAAGAAGAGGAT
*
12150075 CAAAGAAGAAGAGGA
1 CAAAAAAGAAGAGGA
12150090 AGGAGATGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.29, T:0.03
Consensus pattern (16 bp):
CAAAAAAGAAGAGGAT
Found at i:12153393 original size:191 final size:192
Alignment explanation
Indices: 12153066--12153457 Score: 669
Period size: 191 Copynumber: 2.0 Consensus size: 192
12153056 AACTGAAAGG
* *
12153066 TACAAAAAGTGAGGGATCGTAACGTCCCTTCTCATCGGATAGACCTCCAAAAGGTAAGTGAAGAT
1 TACAAAAAGTGAGGGATCGTAACGTCCCTACTCATCGGAGAGACCTCCAAAAGGTAAGTGAAGAT
* * * *
12153131 AGTCACCAGACTCTTCAAGAGTTATGCGAATGGGTGTAACCATGAGATAAGAGAATATAGCAATA
66 AGTCACCAAACTCTTCAAGAGTTATGCGAATAGGTGAAACCATGAGATAAGAGAAGATAGCAATA
* *
12153196 ATGGTTTCTTCAGACTCGTCATGTTCGAGTGTGGTATTGAAAAA-AAAGCTCGAACAAGTTT
131 ATGGTTTCTTCAGACTCGTCATGTTCGAGCGTGGTATTGAAAAAGAAAGCTCGAACAAGGTT
* *
12153257 TAGAAAAAGTGAGGGATCGTAACGTCCCTACTCATCGGAGAGACCTCCGAAAGGTAAGTGAAGAT
1 TACAAAAAGTGAGGGATCGTAACGTCCCTACTCATCGGAGAGACCTCCAAAAGGTAAGTGAAGAT
* *
12153322 AGTCACCAAACTCTTCAAGAGTTATGCGAATAGGTGAAACCATGAGATAAGAGGAGATGGCAATA
66 AGTCACCAAACTCTTCAAGAGTTATGCGAATAGGTGAAACCATGAGATAAGAGAAGATAGCAATA
12153387 ATGGTTTCTTCAGACTCGTCATGTTCGAGCGTGGTATTGAAAAAGAAAGCTCGAACAAGGTT
131 ATGGTTTCTTCAGACTCGTCATGTTCGAGCGTGGTATTGAAAAAGAAAGCTCGAACAAGGTT
12153449 TACAAAAAG
1 TACAAAAAG
12153458 CGATTAAGAA
Statistics
Matches: 187, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
191 163 0.87
192 24 0.13
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (192 bp):
TACAAAAAGTGAGGGATCGTAACGTCCCTACTCATCGGAGAGACCTCCAAAAGGTAAGTGAAGAT
AGTCACCAAACTCTTCAAGAGTTATGCGAATAGGTGAAACCATGAGATAAGAGAAGATAGCAATA
ATGGTTTCTTCAGACTCGTCATGTTCGAGCGTGGTATTGAAAAAGAAAGCTCGAACAAGGTT
Found at i:12160474 original size:58 final size:59
Alignment explanation
Indices: 12160402--12160514 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
12160392 AATCATTTTA
12160402 ACTTGATTTAAAAATTG-TTTAAACTTTTCTAAGAGTTCAAGATAGGAGTTTAAAATTG
1 ACTTGATTTAAAAATTGTTTTAAACTTTTCTAAGAGTTCAAGATAGGAGTTTAAAATTG
* *
12160460 ACTTGATTTGAAAATTGTTTTAAACTTTTCTAAGAGTTCAAGATATGAGTTTAAA
1 ACTTGATTTAAAAATTGTTTTAAACTTTTCTAAGAGTTCAAGATAGGAGTTTAAA
12160515 TTTTACCTCT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 16 0.31
59 36 0.69
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (59 bp):
ACTTGATTTAAAAATTGTTTTAAACTTTTCTAAGAGTTCAAGATAGGAGTTTAAAATTG
Found at i:12164368 original size:16 final size:18
Alignment explanation
Indices: 12164349--12164391 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
12164339 TTAAATATTT
12164349 TAAAAAT-T-AAAATATA
1 TAAAAATGTAAAAATATA
12164365 TAAAAATGTAAAAATATA
1 TAAAAATGTAAAAATATA
12164383 TAAAAATGT
1 TAAAAATGT
12164392 TTAAAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 7 0.28
17 1 0.04
18 17 0.68
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAAAATGTAAAAATATA
Found at i:12173390 original size:16 final size:15
Alignment explanation
Indices: 12173360--12173388 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12173350 GTTGTGTCTT
12173360 TTTTTTAAATATTTA
1 TTTTTTAAATATTTA
12173375 TTTTTTAAATATTT
1 TTTTTTAAATATTT
12173389 TACTATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTAAATATTTA
Found at i:12174503 original size:6 final size:6
Alignment explanation
Indices: 12174492--12174520 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12174482 CTCTTTTCAT
12174492 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
12174521 CCCCCGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:12177197 original size:12 final size:13
Alignment explanation
Indices: 12177164--12177200 Score: 58
Period size: 12 Copynumber: 2.8 Consensus size: 13
12177154 CTTTAGACAA
12177164 TTAATTATTATCT
1 TTAATTATTATCT
12177177 TTAAATTATTA-CT
1 TT-AATTATTATCT
12177190 TTAATTATTAT
1 TTAATTATTAT
12177201 TTGGGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.36
13 6 0.27
14 8 0.36
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (13 bp):
TTAATTATTATCT
Found at i:12177469 original size:13 final size:13
Alignment explanation
Indices: 12177453--12177477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12177443 TAAATTTACG
12177453 TTATTTTTTTATT
1 TTATTTTTTTATT
12177466 TTATTTTTTTAT
1 TTATTTTTTTAT
12177478 AAGAAGAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTATTTTTTTATT
Found at i:12178293 original size:13 final size:12
Alignment explanation
Indices: 12178261--12178299 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
12178251 ACTTGATATA
*
12178261 TAATTATTAAAT
1 TAATTAATAAAT
12178273 TAAGTTAATAAAT
1 TAA-TTAATAAAT
12178286 CTAATTAATAAAT
1 -TAATTAATAAAT
12178299 T
1 T
12178300 TAAATTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 17 0.71
14 3 0.12
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (12 bp):
TAATTAATAAAT
Found at i:12187279 original size:21 final size:20
Alignment explanation
Indices: 12187242--12187287 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
12187232 GAAATATACC
*
12187242 CTCTCTTTCTTCTATCTCGTT
1 CTCTCTTTCTTCAATCTC-TT
12187263 CTCTC-TTCTCTCAATCTCTT
1 CTCTCTTTCT-TCAATCTCTT
12187283 C-CTCT
1 CTCTCT
12187288 AATTTCTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 7 0.32
21 12 0.55
ACGTcount: A:0.07, C:0.39, G:0.02, T:0.52
Consensus pattern (20 bp):
CTCTCTTTCTTCAATCTCTT
Found at i:12188229 original size:5 final size:5
Alignment explanation
Indices: 12188214--12188246 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
12188204 GAGGTCTATC
*
12188214 AGAAA ATAAA AGAAA AGAAA AGAAA AGAAA AGA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGA
12188247 CATGCCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AGAAA
Found at i:12191909 original size:29 final size:29
Alignment explanation
Indices: 12191832--12191899 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
12191822 ACATTTGTTT
*
12191832 TAATGTGGTATCTAAAATTTTAAAATGTC
1 TAATGTGGTATCTAAAGTTTTAAAATGTC
12191861 TAATGTGGTATCTAAAGTTTTAAAATGTC
1 TAATGTGGTATCTAAAGTTTTAAAATGTC
12191890 TAATGTGGTA
1 TAATGTGGTA
12191900 CTTGAAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (29 bp):
TAATGTGGTATCTAAAGTTTTAAAATGTC
Found at i:12197548 original size:465 final size:464
Alignment explanation
Indices: 12196291--12197693 Score: 2105
Period size: 468 Copynumber: 3.0 Consensus size: 464
12196281 GACAATCAAC
* * *
12196291 GTGTTATTCAAATCACGATCAATTGGGTTCCCAGCAAAGACCTGCTTAA-CCAGTCGCAAACTGA
1 GTGTTATTCAGATCACGATCAATTGGGTTCCCAGCAAAGACCTGCTTAACCCAGTCACAAACTGC
* * *
12196355 ATCCTCGACTGCGTCCCACTACCTCTAGAAAAAAAAGCACATGGAAACCATCACTTCCTAAGGCT
66 ATCC-CGACTGCGTCCCATTGCCTCTAGAAAAAAAAGCACATGAAAACCATCACTTCCTAAGGCT
** * *
12196420 TTTAGAAGTGCCATATCAAAAAGGGCTGCCTTAGTTTCAATATTGGATACTAGTTTACCCAAAAA
130 TTTAGAAGTGCCATATCAAAAAAAGCTGCCTTAATTTCAATATTGGACACTAGTTTACCC-AAAA
* * ** * * *
12196485 ACTGAGGTCTTCAACCTCAAGCTGAGGAAACCGACTTCT-AGGAAGACTACCACAAGGTCCCAGA
194 ATTGAGGTCTTTAGGCTCAAGCTGAGGGAACCGACTT-TGAGGAAGAGTACCACAAGGTCCCAAA
* *
12196549 TATTCCCCATAAAGATTTTGAAAGAATAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAAT
258 TATT-CCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAAT
* * * *
12196614 CCAATTGCCGTCAGAATTGTGAATAGCTGATATGCAATTACTCTTCTGTCGTTACAAGGTACGAG
322 CCAATTGCCGTCAGAATTGCGAATAGCTGATATGCGATTACTCTTCCGTCGTTGCAAGGTACGAG
* *
12196679 TATGGAAAAACTTAGCATTCCTATCCCCTAGTTTCAACCAGTCATAACGTGCTTTTTGTTTCCAA
387 TATGGAAAAACTTAGTATTCCTAT-CCCTAGTTTCAACCAGTCATAACGTGCTTTCTGTTTCCAA
*
12196744 ATGAGCTCTTTATG
451 AAGAGCTCTTTATG
* *
12196758 GTGTTATTCAGATCACGATCAATTAGGTTCCCAGCAAAGACCTGCTTAACCTAGTCACAAACTGC
1 GTGTTATTCAGATCACGATCAATTGGGTTCCCAGCAAAGACCTGCTTAACCCAGTCACAAACTGC
* *
12196823 ATCCCTGACTGTGTCCCATTGCCTCTAGAAAAAAAAGCACATGAAAACCATCACTTTCTAAGGCT
66 ATCCC-GACTGCGTCCCATTGCCTCTAGAAAAAAAAGCACATGAAAACCATCACTTCCTAAGGCT
* *
12196888 TTTAGAAGTGCCATATCAAAAAAAACTGCCTTAATTTCAATATTGGACACTAGTTTACCTAAAAA
130 TTTAGAAGTGCCATATCAAAAAAAGCTGCCTTAATTTCAATATTGGACACTAGTTTACC-CAAAA
* * *
12196953 ATTAAGGT-TTTCAGGCTCAAGCTGAGGGAACCAACTTCGAGGAAGAGTACCACAAGGTCCCAAA
194 ATTGAGGTCTTT-AGGCTCAAGCTGAGGGAACCGACTTTGAGGAAGAGTACCACAAGGTCCCAAA
*
12197017 TATTCCCTATAGAGATTTTGAAAGAACAAATTAGCCTCAAACTCAATGGCCTCTGAATCATAAAT
258 TATTCCC-ATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAAT
* * *
12197082 CCAATTGCCATCAGAATTGCAAATAGCTGATATGCGATTACTCTTCCGTCGTTGCACGGTACGAG
322 CCAATTGCCGTCAGAATTGCGAATAGCTGATATGCGATTACTCTTCCGTCGTTGCAAGGTACGAG
* * *
12197147 TATGAAAAAACTTAGTATTCCTATCCCTAGTTTGAACCAGTCATAACGTGCTTTCTATTTCCAAA
387 TATGGAAAAACTTAGTATTCCTATCCCTAGTTTCAACCAGTCATAACGTGCTTTCTGTTTCCAAA
12197212 AGAGCTCTTTATG
452 AGAGCTCTTTATG
* * * * *
12197225 GTGTTATTCAGATCACAATCACTTGGGTTCTCAACAAAGACCTTCTTAACCCAGTCACAAACTGC
1 GTGTTATTCAGATCACGATCAATTGGGTTCCCAGCAAAGACCTGCTTAACCCAGTCACAAACTGC
*
12197290 ATTCCCGACTGCGTCTCATTGCCTCTAG-AAAAAAAGCACATGAAAACCATCACTTCCTAAGGCT
66 A-TCCCGACTGCGTCCCATTGCCTCTAGAAAAAAAAGCACATGAAAACCATCACTTCCTAAGGCT
* *
12197354 TTTAGAAGTACCATATCAAAAAAAGCTGCCTTAATTTTAATATTGGACACTAGTTTACCCAAAAA
130 TTTAGAAGTGCCATATCAAAAAAAGCTGCCTTAATTTCAATATTGGACACTAGTTTACCCAAAAA
* * *
12197419 TTGAGGTCTTTAGGCTCAAACAGAGGGAACCGACTTTGAGGAAGAGTACCACAAGGTCCCAAATG
195 TTGAGGTCTTTAGGCTCAAGCTGAGGGAACCGACTTTGAGGAAGAGTACCACAAGGTCCCAAATA
*
12197484 TTCCTCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGACCTCTGAATCATAAATCC
260 TTCC-CATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATCC
* * * *
12197549 AATTGCTGTCAGAATTACGAATAGCTGATATGTGATTACTCGTCCGTCGTTGCAAGGTACGAGTA
324 AATTGCCGTCAGAATTGCGAATAGCTGATATGCGATTACTCTTCCGTCGTTGCAAGGTACGAGTA
* *
12197614 TGGAAAAACTTAGTATTCCTAT-CCTCAGTTTCAACTAGTCATAACGTGCTTTCTGTTTCCAAAG
389 TGGAAAAACTTAGTATTCCTATCCCT-AGTTTCAACCAGTCATAACGTGCTTTCTGTTTCCAAAA
* *
12197678 GATCTCTTCATG
453 GAGCTCTTTATG
12197690 GTGT
1 GTGT
12197694 AGAACGATGT
Statistics
Matches: 848, Mismatches: 78, Indels: 22
0.89 0.08 0.02
Matches are distributed among these distances:
464 3 0.00
465 248 0.29
466 95 0.11
467 182 0.21
468 320 0.38
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (464 bp):
GTGTTATTCAGATCACGATCAATTGGGTTCCCAGCAAAGACCTGCTTAACCCAGTCACAAACTGC
ATCCCGACTGCGTCCCATTGCCTCTAGAAAAAAAAGCACATGAAAACCATCACTTCCTAAGGCTT
TTAGAAGTGCCATATCAAAAAAAGCTGCCTTAATTTCAATATTGGACACTAGTTTACCCAAAAAT
TGAGGTCTTTAGGCTCAAGCTGAGGGAACCGACTTTGAGGAAGAGTACCACAAGGTCCCAAATAT
TCCCATAGAGATTTTGAAAGAACAAATTAGCCTCAGACTCAATGGCCTCTGAATCATAAATCCAA
TTGCCGTCAGAATTGCGAATAGCTGATATGCGATTACTCTTCCGTCGTTGCAAGGTACGAGTATG
GAAAAACTTAGTATTCCTATCCCTAGTTTCAACCAGTCATAACGTGCTTTCTGTTTCCAAAAGAG
CTCTTTATG
Found at i:12205819 original size:20 final size:19
Alignment explanation
Indices: 12205788--12205876 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 19
12205778 AATTAGAAAG
* *
12205788 AAAATATATAAAAAATTGT
1 AAAATTTATAAAAAATTAT
*
12205807 AAAATTT-TATAAAAATCGTAA
1 AAAATTTATA-AAAAAT--TAT
* *
12205828 AAAATATATAAAATA-TAT
1 AAAATTTATAAAAAATTAT
12205846 AGAAA--TATAAAAAATTAT
1 A-AAATTTATAAAAAATTAT
12205864 AAAATTTTATAAA
1 AAAA-TTTATAAA
12205877 GTCGTAAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
17 11 0.20
18 9 0.17
19 15 0.28
20 6 0.11
21 11 0.20
22 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATTTATAAAAAATTAT
Found at i:12205840 original size:9 final size:9
Alignment explanation
Indices: 12205828--12205868 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
12205818 AAAATCGTAA
12205828 AAAATATAT
1 AAAATATAT
12205837 AAAATATAT
1 AAAATATAT
*
12205846 AGAAATATAA
1 A-AAATATAT
12205856 AAAAT-TAT
1 AAAATATAT
12205864 AAAAT
1 AAAAT
12205869 TTTATAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:12205840 original size:10 final size:10
Alignment explanation
Indices: 12205788--12205867 Score: 62
Period size: 10 Copynumber: 8.3 Consensus size: 10
12205778 AATTAGAAAG
12205788 AAAATATATA
1 AAAATATATA
*
12205798 AAAA-ATTGTA
1 AAAATA-TATA
* *
12205808 AAATTTTATA
1 AAAATATATA
*
12205818 AAAATCGTA-A
1 AAAAT-ATATA
12205828 AAAATATAT-
1 AAAATATATA
12205837 AAAATATATA
1 AAAATATATA
*
12205847 GAAATATA-A
1 AAAATATATA
12205856 AAAAT-TATA
1 AAAATATATA
12205865 AAA
1 AAA
12205868 TTTTATAAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 2 0.04
9 21 0.38
10 30 0.55
11 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAATATATA
Found at i:12205854 original size:57 final size:58
Alignment explanation
Indices: 12205793--12205914 Score: 176
Period size: 57 Copynumber: 2.1 Consensus size: 58
12205783 GAAAGAAAAT
* * *
12205793 ATATAAAAAATTGTAAAATTTTATAAAAATCGTAA-AAAA-TATATAAAATATATAGAA
1 ATATAAAAAATTATAAAATTTTAT-AAAATCGTAAGAAAATTATACAAAATATAAAGAA
* *
12205850 ATATAAAAAATTATAAAATTTTATAAAGTCGTAAGAAAATTATACAAAATGTAAAGAA
1 ATATAAAAAATTATAAAATTTTATAAAATCGTAAGAAAATTATACAAAATATAAAGAA
12205908 ATATAAA
1 ATATAAA
12205915 TTTCCTAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 9 0.16
57 27 0.47
58 22 0.38
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (58 bp):
ATATAAAAAATTATAAAATTTTATAAAATCGTAAGAAAATTATACAAAATATAAAGAA
Found at i:12205891 original size:29 final size:28
Alignment explanation
Indices: 12205796--12205893 Score: 110
Period size: 29 Copynumber: 3.4 Consensus size: 28
12205786 AGAAAATATA
*
12205796 TAAAAAATTGTAAAATTTTATAAAAATCG
1 TAAAAAATTATAAAATTTTAT-AAAATCG
* *
12205825 TAAAAAATATATAAAA-TATATAGAAAT-A
1 TAAAAAAT-TATAAAATTTTATA-AAATCG
*
12205853 TAAAAAATTATAAAATTTTATAAAGTCG
1 TAAAAAATTATAAAATTTTATAAAATCG
12205881 TAAGAAAATTATA
1 TAA-AAAATTATA
12205894 CAAAATGTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 10 0.17
28 17 0.29
29 25 0.43
30 6 0.10
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (28 bp):
TAAAAAATTATAAAATTTTATAAAATCG
Found at i:12206105 original size:19 final size:18
Alignment explanation
Indices: 12206083--12206144 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
12206073 TTAAAGGGAC
12206083 TTTTTATACATTTTATAAT
1 TTTTTATA-ATTTTATAAT
* *
12206102 TTTTTATGATTTCTATAAA
1 TTTTTATAATTT-TATAAT
* * *
12206121 ATTTTATAATTTTTTTAT
1 TTTTTATAATTTTATAAT
12206139 TTTTTA
1 TTTTTA
12206145 CGATTTTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 12 0.35
19 22 0.65
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTATAATTTTATAAT
Found at i:12206142 original size:37 final size:38
Alignment explanation
Indices: 12206084--12206158 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
12206074 TAAAGGGACT
*
12206084 TTTTATACATTTTATAATTTTTTATGATTTCTATAAAA
1 TTTTATACATTTTATAATTTTTTACGATTTCTATAAAA
* * *
12206122 TTTTATA-ATTTTTTTATTTTTTACGATTTTTATAAAA
1 TTTTATACATTTTATAATTTTTTACGATTTCTATAAAA
12206159 AAAATTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (38 bp):
TTTTATACATTTTATAATTTTTTACGATTTCTATAAAA
Found at i:12206216 original size:18 final size:18
Alignment explanation
Indices: 12206193--12206242 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
12206183 TAACTTTTTT
12206193 ATATTTTTATTAAATTTA
1 ATATTTTTATTAAATTTA
12206211 ATATTTTT-TCTAAAATTTA
1 ATATTTTTAT-T-AAATTTA
*
12206230 TTATTTATTATTA
1 ATATTT-TTATTA
12206243 TTTATAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 1 0.04
18 9 0.33
19 13 0.48
20 3 0.11
21 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTTTATTAAATTTA
Found at i:12206217 original size:27 final size:27
Alignment explanation
Indices: 12206168--12206219 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
12206158 AAAAATTCCA
*
12206168 ATTTTTAATAAATTTTAACTTTTTTAT
1 ATTTTTAATAAATTTTAAATTTTTTAT
*
12206195 ATTTTTATTAAA-TTTAATATTTTTT
1 ATTTTTAATAAATTTTAA-ATTTTTT
12206220 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTTTTAATAAATTTTAAATTTTTTAT
Found at i:12210742 original size:9 final size:9
Alignment explanation
Indices: 12210730--12210761 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
12210720 CATAATAAAT
12210730 ATAATATTA
1 ATAATATTA
12210739 ATAATATTAA
1 ATAATATT-A
12210749 ATAATATTA
1 ATAATATTA
12210758 ATAA
1 ATAA
12210762 AACAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATTA
Found at i:12210753 original size:10 final size:10
Alignment explanation
Indices: 12210730--12210758 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12210720 CATAATAAAT
12210730 ATAATATT-A
1 ATAATATTAA
12210739 ATAATATTAA
1 ATAATATTAA
12210749 ATAATATTAA
1 ATAATATTAA
12210759 TAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAATATTAA
Found at i:12211902 original size:57 final size:57
Alignment explanation
Indices: 12211832--12211964 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 57
12211822 GAACGTCTTT
* * *
12211832 AAAATAACATTTTTGCCCCTAAACTTCCAAAAATCGCATTTTACCTC-AAACTTCTCA
1 AAAATTACATTTTTGCCCCTAAACTT-CAAAAATCACATTATACCTCTAAACTTCTCA
* * * * * * *
12211889 AAAATTACATTTTTACCCCTGAACTTCTACAATCACGTTATCCCTCTGAACTTCTCA
1 AAAATTACATTTTTGCCCCTAAACTTCAAAAATCACATTATACCTCTAAACTTCTCA
12211946 AAAATTACATTTTTGCCCC
1 AAAATTACATTTTTGCCCC
12211965 CGAACTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
56 14 0.22
57 50 0.78
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.34
Consensus pattern (57 bp):
AAAATTACATTTTTGCCCCTAAACTTCAAAAATCACATTATACCTCTAAACTTCTCA
Found at i:12211979 original size:29 final size:29
Alignment explanation
Indices: 12211936--12212017 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
12211926 TTATCCCTCT
*
12211936 GAACTTCTCAAAAATTACATTTTTGCCCCC
1 GAACTT-TCAAAAATTACATTTTGGCCCCC
*
12211966 GAACTTTTAAAAATTACATTTTGGCCCCC
1 GAACTTTCAAAAATTACATTTTGGCCCCC
*
12211995 GAA-TTTCCAAAATTACCATTTTG
1 GAACTTTCAAAAATTA-CATTTTG
12212018 CCTCGAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
28 10 0.21
29 31 0.66
30 6 0.13
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (29 bp):
GAACTTTCAAAAATTACATTTTGGCCCCC
Found at i:12212071 original size:29 final size:27
Alignment explanation
Indices: 12212000--12212074 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
12211990 CCCCCGAATT
12212000 TCCAAAATTACCATTTTGCCTCGAGCA
1 TCCAAAATTACCATTTTGCCTCGAGCA
*
12212027 TCCAAAATTACCATTTTGTCTTCG-GACA
1 TCCAAAATTACCATTTTG-CCTCGAG-CA
12212055 TCCAAAAGTTACCATTTTGC
1 TCCAAAA-TTACCATTTTGC
12212075 TCCCAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
27 19 0.43
28 14 0.32
29 11 0.25
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (27 bp):
TCCAAAATTACCATTTTGCCTCGAGCA
Found at i:12212087 original size:29 final size:30
Alignment explanation
Indices: 12212055--12212129 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
12212045 TCTTCGGACA
12212055 TCCAAAAGTTACCATTTT-G-CTCCCAAA-TT
1 TCCAAAAGTTA-CATTTTCGAC-CCCAAACTT
* *
12212084 TCCAAAAGTCACATTTTCGACCTCAAACTT
1 TCCAAAAGTTACATTTTCGACCCCAAACTT
12212114 TCCAAAA-TTACATTTT
1 TCCAAAAGTTACATTTT
12212130 AACCCTAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.15
29 24 0.60
30 10 0.25
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (30 bp):
TCCAAAAGTTACATTTTCGACCCCAAACTT
Found at i:12221406 original size:117 final size:117
Alignment explanation
Indices: 12221200--12221415 Score: 351
Period size: 117 Copynumber: 1.8 Consensus size: 117
12221190 AAGATTGAAG
* *
12221200 ATTCGATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCAAATCTCTTACCCCGATCATAGG
1 ATTCGATCTTTTACCCCAAGCCTAGGGCAAATCACCATCAGCAAATCTCTTACCCCGATCATAGG
* *
12221265 ACAGATTGTAGCCATTCGATCTCTTACGCCGAGCTAGGGGCAAATTGTAGCC
66 ACAGATTGCAGCCATTCGATCTCTTACCCCGAGCTAGGGGCAAATTGTAGCC
* * *
12221317 ATTCGATCTTTTACCCCAAGCCTAGGGCAAATCACCATCAGTAAATCTTTTACCCCGATCATGGG
1 ATTCGATCTTTTACCCCAAGCCTAGGGCAAATCACCATCAGCAAATCTCTTACCCCGATCATAGG
* *
12221382 GCAGATTGCAGCCATTTGATCTCTTACCCCGAGC
66 ACAGATTGCAGCCATTCGATCTCTTACCCCGAGC
12221416 CTGCGGTAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 90 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (117 bp):
ATTCGATCTTTTACCCCAAGCCTAGGGCAAATCACCATCAGCAAATCTCTTACCCCGATCATAGG
ACAGATTGCAGCCATTCGATCTCTTACCCCGAGCTAGGGGCAAATTGTAGCC
Found at i:12221409 original size:39 final size:39
Alignment explanation
Indices: 12221244--12221415 Score: 138
Period size: 39 Copynumber: 4.4 Consensus size: 39
12221234 CCATCAGCAA
* * *
12221244 ATCTCTTACCCCGATCATAGGACAGATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCATAGGGCAGATTGCAGCCATTCG
* * *
12221283 ATCTCTTACGCCGAGC-TAGGGGCAAATTGTAGCCATTCG
1 ATCTCTTACCCCGAGCATA-GGGCAGATTGCAGCCATTCG
* * * *
12221322 ATCTTTTACCCCAAGCCTAGGGCA-AAT-CA-CCA-TCAG
1 ATCTCTTACCCCGAGCATAGGGCAGATTGCAGCCATTC-G
* * * *
12221358 TAAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCATTTG
1 ---ATCTCTTACCCCGAGCATAGGGCAGATTGCAGCCATTCG
12221400 ATCTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
12221416 CTGCGGTAGA
Statistics
Matches: 106, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
35 2 0.02
36 4 0.04
37 1 0.01
38 4 0.04
39 84 0.79
40 4 0.04
41 2 0.02
42 4 0.04
43 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCATAGGGCAGATTGCAGCCATTCG
Found at i:12221409 original size:78 final size:78
Alignment explanation
Indices: 12221283--12222317 Score: 927
Period size: 78 Copynumber: 13.3 Consensus size: 78
12221273 TAGCCATTCG
* * * * * * *
12221283 ATCTCTTACGCCGAGC-TAGGGGCAAATTGTAGCCATTCGATCTTTTACCCCAAGCCTAGGGCAA
1 ATCTCTTACCCCGATCAT-GGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAG
*
12221347 ATCACCATCAGTAA
65 ATCACCATCAGCAA
* * * * * * *
12221361 ATCTTTTACCCCGATCATGGGGCAGATTGCAGCCATTTGATCTCTTACCCCGAGCCT-GCGGTAG
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAG-GGCAG
* *
12221425 ATCATCATCACCAA
65 ATCACCATCAGCAA
* * * * *
12221439 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTTTTATCCCATGCTT-GGAGCAG
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGG-GCAG
*
12221503 ATCACTATCAGCAA
65 ATCACCATCAGCAA
* * * * * * * * ** * * *
12221517 ATCTTTTATCTCGAGCCTGGGGCATATTGCAGCAATTTAATCTCTTACCCCGAGCTTAGGGTAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
* *
12221582 T-A--ATTAGTAA
66 TCACCATCAGCAA
* * * * * * *
12221592 ATCTCTTACCTCGAGCTTGGGGTAGATTGTAACCATTCGATCCTTTACCCCAAGCCT-GGGACAG
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGG-CAG
*
12221656 ATCACTATCAGCAA
65 ATCACCATCAGCAA
* * * *
12221670 ATCTCTTACCCCGATCATGGGGCAGATTACAACCATTCGATCTCTTACCCCGAGCTTAGGGGAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
* *
12221735 TCATCATCAACAA
66 TCACCATCAGCAA
* * * * * * *
12221748 ATCTCTTACCTCGAGCCTGGGACAAATTGTAACCATTCGATCTTTTACCCCAAGCTTAGGGTAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
*
12221813 TCACCATCAGTAA
66 TCACCATCAGCAA
* *
12221826 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCTAGCTTGGGGCAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
* *
12221891 TCATCATCAGTAA
66 TCACCATCAGCAA
* * * * * * * * * *
12221904 ATCTATTACCCCGAGCCTGGGGTAGATTACAACCATTCGGTCTTTTATCCCAAGCTTGGGGTAAA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
12221969 TCACCATCAGCAA
66 TCACCATCAGCAA
* * * * * * * *
12221982 ATCTCTTATCCCGATCATGGGGCAGATTGTAGCCATTCGATCTCTTACCCCTAGCCTAGAGCAAA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
**
12222047 TCATTATCAGCAA
66 TCACCATCAGCAA
* * * * ** * *
12222060 ATCTGTTACCCCGAGCTTGGGGCAGATTACAATTATTTGATCTTTTACCCCAAGCTTGGGGCAGA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
*
12222125 TCACCATCAACAA
66 TCACCATCAGCAA
* ** * * * *
12222138 ATCTCTTACCCCGATCATGAGGCAGATTGCAGTCATTGGATCTTTTACCTCGAGCTT-GAGGCAA
1 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAG-GGCAG
*
12222202 ATCACCATAAGCAA
65 ATCACCATCAGCAA
* * * * ** * *
12222216 ATCTCTTACTCCGAGTC-TGGGGCAGATTGTAGCTATTCGATCTTTTACCCTGAGCTTGGGGTAG
1 ATCTCTTACCCCGA-TCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAG
*
12222280 ATCACCATCAGCCA
65 ATCACCATCAGCAA
* * * *
12222294 GTCTTTTACTCCGATCATAGGGCA
1 ATCTCTTACCCCGATCATGGGGCA
12222318 AATGGCATTC
Statistics
Matches: 769, Mismatches: 175, Indels: 26
0.79 0.18 0.03
Matches are distributed among these distances:
74 3 0.00
75 53 0.07
76 1 0.00
77 6 0.01
78 697 0.91
79 9 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (78 bp):
ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCAAGCTTAGGGCAGA
TCACCATCAGCAA
Found at i:12221507 original size:156 final size:155
Alignment explanation
Indices: 12221283--12222317 Score: 1119
Period size: 156 Copynumber: 6.7 Consensus size: 155
12221273 TAGCCATTCG
* * * * *
12221283 ATCTCTTACGCCGAG-CTAGGGGCAAATTGTAGCCATTCGATCTTTTACCCCAAGCCTAGGGCAA
1 ATCTCTTACCCCGAGCCT-GGGGCAGATTGTAACCATTCGATCTTTTACCCCAAG-CTTGGGCAG
* * *
12221347 ATCACCATCAGTAAATCTTTTACCCCGATCATGGGGCAGATTGCAGCCATTTGATCTCTTACCCC
64 ATCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCC
* * *
12221412 GAGCCT-GCGGTAGATCATCATCACCAA
129 GAGCTTAG-GGCAGATCATCATCAGCAA
* * * *
12221439 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTCGATCTTTTATCCCATGCTTGGAGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTTGG-GCAGA
* * * * * * * * **
12221504 TCACTATCAGCAAATCTTTTATCTCGAGCCTGGGGCATATTGCAGCAATTTAATCTCTTACCCCG
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCG
* * *
12221569 AGCTTAGGGTAGAT-A--ATTAGTAA
130 AGCTTAGGGCAGATCATCATCAGCAA
* * * * *
12221592 ATCTCTTACCTCGAGCTTGGGGTAGATTGTAACCATTCGATCCTTTACCCCAAGCCTGGGACAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTTGGG-CAGA
* * *
12221657 TCACTATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTACAACCATTCGATCTCTTACCCCG
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCG
* *
12221722 AGCTTAGGGGAGATCATCATCAACAA
130 AGCTTAGGGCAGATCATCATCAGCAA
* * * *
12221748 ATCTCTTACCTCGAGCCTGGGACAAATTGTAACCATTCGATCTTTTACCCCAAGCTTAGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTT-GGGCAGA
* * * *
12221813 TCACCATCAGTAAATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTCGATCTTTTACCCCT
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCG
* *
12221878 AGCTTGGGGCAGATCATCATCAGTAA
130 AGCTTAGGGCAGATCATCATCAGCAA
* * ** * * * *
12221904 ATCTATTACCCCGAGCCTGGGGTAGATTACAACCATTCGGTCTTTTATCCCAAGCTTGGGGTAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTT-GGGCAGA
* * *
12221969 TCACCATCAGCAAATCTCTTATCCCGATCATGGGGCAGATTGTAGCCATTCGATCTCTTACCCCT
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCG
* * * *
12222034 AGCCTAGAGCAAATCATTATCAGCAA
130 AGCTTAGGGCAGATCATCATCAGCAA
* * ** ** *
12222060 ATCTGTTACCCCGAGCTTGGGGCAGATTACAATTATTTGATCTTTTACCCCAAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTT-GGGCAGA
* * * * * *
12222125 TCACCATCAACAAATCTCTTACCCCGATCATGAGGCAGATTGCAGTCATTGGATCTTTTACCTCG
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCG
* * *
12222190 AGCTT-GAGGCAAATCACCATAAGCAA
130 AGCTTAG-GGCAGATCATCATCAGCAA
* * * * ** *
12222216 ATCTCTTACTCCGAGTCTGGGGCAGATTGTAGCTATTCGATCTTTTACCCTGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTT-GGGCAGA
* * * * *
12222281 TCACCATCAGCCAGTCTTTTACTCCGATCATAGGGCA
65 TCACCATCAGCAAATCTCTTACCCCGATCATGGGGCA
12222318 AATGGCATTC
Statistics
Matches: 745, Mismatches: 125, Indels: 18
0.84 0.14 0.02
Matches are distributed among these distances:
152 1 0.00
153 128 0.17
154 1 0.00
155 6 0.01
156 603 0.81
157 6 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (155 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTGTAACCATTCGATCTTTTACCCCAAGCTTGGGCAGAT
CACCATCAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATTCGATCTCTTACCCCGA
GCTTAGGGCAGATCATCATCAGCAA
Found at i:12221696 original size:39 final size:39
Alignment explanation
Indices: 12221400--12222242 Score: 206
Period size: 39 Copynumber: 21.7 Consensus size: 39
12221390 CAGCCATTTG
* * * *
12221400 ATCTCTTACCCCGAGCCTGCGGTAGATCA-TCATCACCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACT-ATCATCAA
* * ** * * *
12221439 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
* * * *
12221478 ATCTTTTATCCC-ATGCTTGGAGCAGATCACTATCAGCAA
1 ATCTCTTACCCCGA-GCTTGGGGCAGATCACTATCATCAA
* * * * * ** * **
12221517 ATCTTTTATCTCGAGCCTGGGGCATATTGC-AGCAATTTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATC-ATCAA
* * *
12221556 ATCTCTTACCCCGAGCTTAGGGTAGAT-A--ATTAGT-AA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
* * ** * *
12221592 ATCTCTTACCTCGAGCTTGGGGTAGAT-TGTAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACT-ATCA-TCAA
* * * *
12221631 ATC-CTTTACCCCAAGCCTGGGACAGATCACTATCAGCAA
1 ATCTC-TTACCCCGAGCTTGGGGCAGATCACTATCATCAA
* * * * * *
12221670 ATCTCTTACCCCGATCATGGGGCAGATTACAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
*
12221709 ATCTCTTACCCCGAGCTTAGGGG-AGATCA-TCATCAACAA
1 ATCTCTTACCCCGAGCTT-GGGGCAGATCACT-ATCATCAA
* * * * ** * *
12221748 ATCTCTTACCTCGAGCCTGGGACAAAT-TGTAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACT-ATCA-TCAA
* * * * *
12221787 ATCTTTTACCCCAAGCTTAGGGTAGATCACCATCAGT-AA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
* * ** * * *
12221826 ATCTCTTACCCCGATCATGGGGCAGATTGCAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
* *
12221865 ATCTTTTACCCCTAGCTTGGGGCAGATCA-TCATCAGT-AA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACT-ATCA-TCAA
* * * * * * *
12221904 ATCTATTACCCCGAGCCTGGGGTAGATTACAACCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCA-TCAA
* * * * * * * *
12221943 GTCTTTTATCCCAAGCTTGGGGTAAATCACCATCAGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
* * * ** * *
12221982 ATCTCTTATCCCGATCATGGGGCAGAT-TGTAGCCATTC-G
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTA-TCA-TCAA
* * * * * * *
12222021 ATCTCTTACCCCTAGCCTAGAGCAAATCATTATCAGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
* * * * ***
12222060 ATCTGTTACCCCGAGCTTGGGGCAGATTACAATTATTTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
* * * *
12222099 ATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
* * * ** ***
12222138 ATCTCTTACCCCGATCATGAGGCAGATTGC-AGTCATTGG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTA-TCATCAA
* * * * * * *
12222177 ATCTTTTACCTCGAGCTTGAGGCAAATCACCATAAGCAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
*
12222216 ATCTCTTACTCCGAG-TCTGGGGCAGAT
1 ATCTCTTACCCCGAGCT-TGGGGCAGAT
12222243 TGTAGCTATT
Statistics
Matches: 554, Mismatches: 213, Indels: 74
0.66 0.25 0.09
Matches are distributed among these distances:
36 27 0.05
37 2 0.00
38 15 0.03
39 496 0.90
40 14 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACTATCATCAA
Found at i:12222825 original size:18 final size:17
Alignment explanation
Indices: 12222798--12222845 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
12222788 GACCCAAATG
12222798 AAACTTAAATTTATTTTT
1 AAACTTAAATTTA-TTTT
*
12222816 AAATTTAAATTTATTTT
1 AAACTTAAATTTATTTT
*
12222833 AAACTTAAGTTTA
1 AAACTTAAATTTA
12222846 AAATCATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (17 bp):
AAACTTAAATTTATTTT
Found at i:12223525 original size:9 final size:9
Alignment explanation
Indices: 12223513--12223544 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
12223503 CATAATAAAT
12223513 ATAATATTA
1 ATAATATTA
12223522 ATAATATTAA
1 ATAATATT-A
12223532 ATAATATTA
1 ATAATATTA
12223541 ATAA
1 ATAA
12223545 AACAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATTA
Found at i:12223536 original size:10 final size:10
Alignment explanation
Indices: 12223513--12223541 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12223503 CATAATAAAT
12223513 ATAATATT-A
1 ATAATATTAA
12223522 ATAATATTAA
1 ATAATATTAA
12223532 ATAATATTAA
1 ATAATATTAA
12223542 TAAAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATAATATTAA
Found at i:12224643 original size:29 final size:29
Alignment explanation
Indices: 12224590--12224901 Score: 189
Period size: 29 Copynumber: 10.8 Consensus size: 29
12224580 TAAAAATCAA
* * *
12224590 TTTTGACCCTCGAACTTCTCTAAAATTATAT
1 TTTTG-CCCTCAAACTTC-CAAAAATTACAT
* *
12224621 TTTTGCCCTCGAACATCCAAAAA-TAGCAT
1 TTTTGCCCTCAAACTTCCAAAAATTA-CAT
* * *
12224650 TTTTACCCT-AAATTTCTTAAAAATTACAT
1 TTTTGCCCTCAAACTTC-CAAAAATTACAT
*
12224679 TTTTATCCC-CAAACTTCC-AAAATTCACA-
1 TTTT-GCCCTCAAACTTCCAAAAATT-ACAT
*
12224707 TTTTGCCCCCAAACTTCTCAAAAATTACAT
1 TTTTGCCCTCAAACTTC-CAAAAATTACAT
*
12224737 TTTTGCCCTCAAACTTCCAAAAATCACAT
1 TTTTGCCCTCAAACTTCCAAAAATTACAT
* * *
12224766 TTTTACCCCCAAATTTCC-AAAATTACCA-
1 TTTTGCCCTCAAACTTCCAAAAATTA-CAT
* *
12224794 TTTTGCCC-CGAACATCC-AAAATTACCA-
1 TTTTGCCCTCAAACTTCCAAAAATTA-CAT
*** * *
12224821 TTTTGCCCTTGGACATCCAAAAGTTACCA-
1 TTTTGCCCTCAAACTTCCAAAAATTA-CAT
* * *
12224850 TTTTGCTCC-CAAATTTCCAAAAGTCACAT
1 TTTTGC-CCTCAAACTTCCAAAAATTACAT
* * *
12224879 TTTCGACCTTAAACTTTCCAAAA
1 TTTTGCCCTCAAAC-TTCCAAAA
12224902 TTGCTTTTTA
Statistics
Matches: 229, Mismatches: 35, Indels: 35
0.77 0.12 0.12
Matches are distributed among these distances:
27 27 0.12
28 48 0.21
29 95 0.41
30 54 0.24
31 5 0.02
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTTGCCCTCAAACTTCCAAAAATTACAT
Found at i:12224673 original size:58 final size:56
Alignment explanation
Indices: 12224581--12224814 Score: 208
Period size: 58 Copynumber: 4.1 Consensus size: 56
12224571 TAAATTATCT
* * * *
12224581 AAAAATCA-ATTTTGACCCTCGAACTTCTCT-AAAATTATATTTTTGCCCTCGAACATCC
1 AAAAATCACATTTTTACCC-C-AAATT-TCTAAAAATTACATTTTTGCCC-CAAACATCC
* * *
12224639 AAAAAT-AGCATTTTTACCCTAAATTTCTTAAAAATTACATTTTTATCCCCAAACTTCC
1 AAAAATCA-CATTTTTACCCCAAATTTC-TAAAAATTACATTTTT-GCCCCAAACATCC
* ** * *
12224697 AAAATTCACATTTTGCCCCCAAACTTCTCAAAAATTACATTTTTGCCCTCAAACTTCC
1 AAAAATCACATTTTTACCCCAAATTTCT-AAAAATTACATTTTTGCCC-CAAACATCC
* *
12224755 AAAAATCACATTTTTACCCCCAAATTTC-CAAAATTACCA-TTTTGCCCCGAACATCC
1 AAAAATCACATTTTTA-CCCCAAATTTCTAAAAATTA-CATTTTTGCCCCAAACATCC
12224811 AAAA
1 AAAA
12224815 TTACCATTTT
Statistics
Matches: 146, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
56 13 0.09
57 25 0.17
58 85 0.58
59 23 0.16
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (56 bp):
AAAAATCACATTTTTACCCCAAATTTCTAAAAATTACATTTTTGCCCCAAACATCC
Done.