Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold158
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: 3161772
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 138004 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:2490060 original size:21 final size:19
Alignment explanation
Indices: 2490021--2490070 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
2490011 TTAAATATTG
*
2490021 TTATTATTAT-TATTTTTA
1 TTATTATTATATATTGTTA
2490039 TTATTATTATATGATATGTTA
1 TTATTATTATAT-AT-TGTTA
*
2490060 TTGTTATTATA
1 TTATTATTATA
2490071 CTTACATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 10 0.37
19 1 0.04
20 2 0.07
21 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (19 bp):
TTATTATTATATATTGTTA
Found at i:2492135 original size:12 final size:12
Alignment explanation
Indices: 2492118--2492142 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2492108 GTCTTATTCA
2492118 ACCTTTAGAGAC
1 ACCTTTAGAGAC
2492130 ACCTTTAGAGAC
1 ACCTTTAGAGAC
2492142 A
1 A
2492143 TGATTTTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACCTTTAGAGAC
Found at i:2496352 original size:23 final size:23
Alignment explanation
Indices: 2496322--2496370 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2496312 AACCCATATA
*
2496322 TATGCATGCTAATATACTATTAT
1 TATGCATGCCAATATACTATTAT
*
2496345 TATGCATGCCGATATACTATTAT
1 TATGCATGCCAATATACTATTAT
2496368 TAT
1 TAT
2496371 TCTTTTAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (23 bp):
TATGCATGCCAATATACTATTAT
Found at i:2496971 original size:86 final size:87
Alignment explanation
Indices: 2496877--2497082 Score: 203
Period size: 87 Copynumber: 2.4 Consensus size: 87
2496867 TCTTTTGCCG
*
2496877 CGCCACTATAGATGTGGCTCTTTAGCGGCGCTTACA-TACAAAACGCCACTATAGATCG-GCCTC
1 CGCCACTATAGATGTGGCTCTTTAGCGGCGCTTACACT-CAAAACGCCACTATAGAT-GTG-ATC
* *
2496940 TCTAGCGGCGCTTAT-C-CAAAAAA
63 TATAGCGGCGCTTATACAAAAAAAA
* * * *
2496963 CGCCACTATAGAGGGTGGGTCTATT--CTGGCGATTATACTCAAAACGCCACTATAGATGTGATC
1 CGCCACTATAGA-TGTGGCTCT-TTAGC-GGCGCTTACACTCAAAACGCCACTATAGATGTGATC
2497026 TATAGCGGCGCTTATACAAAAAAAA
63 TATAGCGGCGCTTATACAAAAAAAA
* * *
2497051 CG-CACTATAGCT-TGGGTTCTATAGCGGCGCTT
1 CGCCACTATAGATGT-GGCTCTTTAGCGGCGCTT
2497083 GTACGACAAA
Statistics
Matches: 98, Mismatches: 12, Indels: 20
0.75 0.09 0.15
Matches are distributed among these distances:
85 2 0.02
86 41 0.42
87 44 0.45
88 11 0.11
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (87 bp):
CGCCACTATAGATGTGGCTCTTTAGCGGCGCTTACACTCAAAACGCCACTATAGATGTGATCTAT
AGCGGCGCTTATACAAAAAAAA
Found at i:2497051 original size:44 final size:42
Alignment explanation
Indices: 2496877--2497148 Score: 181
Period size: 43 Copynumber: 6.3 Consensus size: 42
2496867 TCTTTTGCCG
* * * *
2496877 CGCCACTATAGATGTGGCTCTTTAGCGGCGCTTACATACAAAA
1 CGCCACTATAGATGT-GCTCTATAGCGGCGCTTATACAAAAAA
* *
2496920 CGCCACTATAGATCG-GCCTCTCTAGCGGCGCTTATCCAAAAAA
1 CGCCACTATAGAT-GTG-CTCTATAGCGGCGCTTATACAAAAAA
* * * * **
2496963 CGCCACTATAGAGGGTGGGTCTAT-TCTGGCGATTATACTCAAAA
1 CGCCACTATAGA-TGT-GCTCTATAGC-GGCGCTTATACAAAAAA
*
2497007 CGCCACTATAGATGTGATCTATAGCGGCGCTTATACAAAAAAAA
1 CGCCACTATAGATGTGCTCTATAGCGGCGCTTATAC--AAAAAA
* * * * * *
2497051 CG-CACTATAGCTTGGGTTCTATAGCGGCGCTTGTACGACAAA
1 CGCCACTATAG-ATGTGCTCTATAGCGGCGCTTATACAAAAAA
* * * * * ** * *
2497093 CGCCACTAGAGAGAGGGTTCTTTTCCGGTGCTTATACAAGAAA
1 CGCCACTATAGA-TGTGCTCTATAGCGGCGCTTATACAAAAAA
2497136 CGCCACTATAGAT
1 CGCCACTATAGAT
2497149 AGGGTTCTTC
Statistics
Matches: 180, Mismatches: 37, Indels: 25
0.74 0.15 0.10
Matches are distributed among these distances:
42 23 0.13
43 99 0.55
44 57 0.32
45 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (42 bp):
CGCCACTATAGATGTGCTCTATAGCGGCGCTTATACAAAAAA
Found at i:2497100 original size:43 final size:43
Alignment explanation
Indices: 2496877--2497362 Score: 169
Period size: 43 Copynumber: 11.3 Consensus size: 43
2496867 TCTTTTGCCG
* * *
2496877 CGCCACTATAGATGTGGCTCTTTAGCGGCGC-T-TACATACAAAA
1 CGCCACTATAGATG-GGATCTATAGCGGCGCTTATACA-AAAAAA
** * *
2496920 CGCCACTATAGATCGGCCTCTCTAGCGGCGCTTAT-CCAAAAAA
1 CGCCACTATAGAT-GGGATCTATAGCGGCGCTTATACAAAAAAA
* * **
2496963 CGCCACTATAGAGGGTGGG-TCTAT-TCTGGCGATTATAC-TCAAAA
1 CGCCACTATAGA---TGGGATCTATAGC-GGCGCTTATACAAAAAAA
*
2497007 CGCCACTATAGATGTGATCTATAGCGGCGCTTATACAAAAAAAA
1 CGCCACTATAGATGGGATCTATAGCGGCGCTTATAC-AAAAAAA
* * * * *
2497051 CG-CACTATAGCTTGGGTTCTATAGCGGCGCTTGTAC-GACAAA
1 CGCCACTATAG-ATGGGATCTATAGCGGCGCTTATACAAAAAAA
* * * * ** * *
2497093 CGCCACTAGAGAGAGGGTTCTTTTCCGGTGCTTATAC-AAGAAA
1 CGCCACTATAGA-TGGGATCTATAGCGGCGCTTATACAAAAAAA
* ** * *
2497136 CGCCACTATAGATAGGGTTCT-TCTCTAGCGC-T-T-CAATAGGAAA
1 CGCCACTATAGAT-GGGATCTATAGC-GGCGCTTATACAA-A-AAAA
* * * * ** * *
2497179 CGCCACGATAGATAAGGTTCTTTTCCGGCGCTTATGC-AAGAAA
1 CGCCACTATAGAT-GGGATCTATAGCGGCGCTTATACAAAAAAA
* * * * *
2497222 CGCCACGATAGATAGGGTTCTTTTGCGGCGCTTATAC-AAGAAA
1 CGCCACTATAGAT-GGGATCTATAGCGGCGCTTATACAAAAAAA
* * * * * *
2497265 CGCCACAATAGATAGGGTTCTTTTGCGACGCTTAGT-C-TAAAAA
1 CGCCACTATAGAT-GGGATCTATAGCGGCGCTTA-TACAAAAAAA
* * * * * *
2497308 CACCACTACAGACGGGGATCTTTCGCGGCGCTTATGCAAAAAAA
1 CGCCACTATAGA-TGGGATCTATAGCGGCGCTTATACAAAAAAA
* *
2497352 TGCCACAATAG
1 CGCCACTATAG
2497363 GCTGTGTTTT
Statistics
Matches: 354, Mismatches: 61, Indels: 55
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.00
41 5 0.01
42 26 0.07
43 239 0.68
44 75 0.21
45 6 0.02
46 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (43 bp):
CGCCACTATAGATGGGATCTATAGCGGCGCTTATACAAAAAAA
Found at i:2497143 original size:86 final size:85
Alignment explanation
Indices: 2497031--2497298 Score: 272
Period size: 86 Copynumber: 3.1 Consensus size: 85
2497021 TGATCTATAG
* * * * *
2497031 CGGCGCTTATACAAAAAAAACG-CACTATAGCTTGGGTTCTATAGCGGCGCTTGTACGACAAACG
1 CGGCGCTTATAC--AAGAAACGCCACTATAGATAGGGTTCT-TAGCGGCGCTTATACGAGAAACG
* * *
2497095 CCACTAGAGAGAGGGTTCTTTTC
63 CCACAATAGATAGGGTTCTTTTC
* ** *
2497118 CGGTGCTTATACAAGAAACGCCACTATAGATAGGGTTCTTCTCTAGCGCTTCAATA-G-GAAACG
1 CGGCGCTTATACAAGAAACGCCACTATAGATAGGGTTCTTAGC-GGCGCTT--ATACGAGAAACG
* *
2497181 CCACGATAGATAAGGTTCTTTTC
63 CCACAATAGATAGGGTTCTTTTC
* * * *
2497204 CGGCGCTTATGCAAGAAACGCCACGATAGATAGGGTTCTTTTGCGGCGCTTATACAAGAAACGCC
1 CGGCGCTTATACAAGAAACGCCACTATAGATAGGGTTC-TTAGCGGCGCTTATACGAGAAACGCC
*
2497269 ACAATAGATAGGGTTCTTTTG
65 ACAATAGATAGGGTTCTTTTC
*
2497290 CGACGCTTA
1 CGGCGCTTA
2497299 GTCTAAAAAC
Statistics
Matches: 150, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
84 3 0.02
85 9 0.06
86 121 0.81
87 15 0.10
88 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (85 bp):
CGGCGCTTATACAAGAAACGCCACTATAGATAGGGTTCTTAGCGGCGCTTATACGAGAAACGCCA
CAATAGATAGGGTTCTTTTC
Found at i:2497330 original size:86 final size:87
Alignment explanation
Indices: 2497175--2497362 Score: 211
Period size: 86 Copynumber: 2.2 Consensus size: 87
2497165 GCTTCAATAG
* * * * * *
2497175 GAAACGCCACGATAGATAAGGTTCTTTTCCGGCGCTTATGCAAGAAACGCCACGATAGATAGGGT
1 GAAACGCCACAATAGATAAGGTTCTTTTCCGACGCTTATGCAAGAAACACCACGACAGACAGGGA
*
2497240 TCTTTTGCGGCGCTTATAC-AA
66 TCTTTCGCGGCGCTTATACAAA
* * * *
2497261 GAAACGCCACAATAGATAGGGTTCTTTTGCGACGCTTA-GTCTAA-AAACACCACTACAGACGGG
1 GAAACGCCACAATAGATAAGGTTCTTTTCCGACGCTTATG-C-AAGAAACACCACGACAGACAGG
*
2497324 GATCTTTCGCGGCGCTTATGCAAA
64 GATCTTTCGCGGCGCTTATACAAA
* *
2497348 AAAATGCCACAATAG
1 GAAACGCCACAATAG
2497363 GCTGTGTTTT
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
85 1 0.01
86 67 0.79
87 17 0.20
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (87 bp):
GAAACGCCACAATAGATAAGGTTCTTTTCCGACGCTTATGCAAGAAACACCACGACAGACAGGGA
TCTTTCGCGGCGCTTATACAAA
Found at i:2497330 original size:129 final size:129
Alignment explanation
Indices: 2497090--2497346 Score: 297
Period size: 129 Copynumber: 2.0 Consensus size: 129
2497080 CTTGTACGAC
* * *
2497090 AAACGCCACTAGAGAGAGGGTTCTTTTCCGGTGCTTATACAAGAAACGCCACTATAGATAGGGTT
1 AAACGCCACGAGAGAGAGGGTTCTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTT
* * * * * *
2497155 CTTCTCTAGCGCTTCAATAGGAAACGCCACGATAGATAAGGTTCTTTTC-CGGCGCTTATGCAAG
66 CTTCTCGAGCGCTTCAATAGAAAACACCACGACAGACAAGGATC-TTTCGCGGCGCTTATGCAAG
* * *
2497219 AAACGCCACGATAGATAGGGTTCTTTTGCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTT
1 AAACGCCACGAGAGAGAGGGTTCTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTT
* * * **
2497284 CTTTTGCGA-CGCTT-AGTCTA-AAAACACCACTACAGACGGGGATCTTTCGCGGCGCTTATGCA
66 CTTCT-CGAGCGCTTCA--ATAGAAAACACCACGACAGACAAGGATCTTTCGCGGCGCTTATGCA
2497346 A
128 A
2497347 AAAAATGCCA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
128 5 0.05
129 98 0.92
130 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (129 bp):
AAACGCCACGAGAGAGAGGGTTCTTTTCCGGCGCTTATACAAGAAACGCCACAATAGATAGGGTT
CTTCTCGAGCGCTTCAATAGAAAACACCACGACAGACAAGGATCTTTCGCGGCGCTTATGCAAG
Found at i:2497735 original size:21 final size:21
Alignment explanation
Indices: 2497711--2497750 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2497701 CTCTAATTCC
*
2497711 CTCGCTGCAGCCTCTGCTTCT
1 CTCGCTGCAGCATCTGCTTCT
* *
2497732 CTCGTTGCTGCATCTGCTT
1 CTCGCTGCAGCATCTGCTT
2497751 TAAGCTGCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.38, G:0.20, T:0.38
Consensus pattern (21 bp):
CTCGCTGCAGCATCTGCTTCT
Found at i:2497816 original size:87 final size:87
Alignment explanation
Indices: 2497711--2497903 Score: 273
Period size: 87 Copynumber: 2.2 Consensus size: 87
2497701 CTCTAATTCC
* *
2497711 CTCGCTGCAGCCTCTGCTTCTCTCGTTGCTGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCAT
1 CTCGCTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCAT
*
2497775 A-CTTTCATTGAACCTCAGCTTCT
65 ATCTTT-ATTGAACCTCAACTTCT
* *
2497798 CTCGCTGCTGCCTTTGCTTCTCTCGTTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATA
1 CTCGCTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATA
*
2497863 TCTTTTTTGAACCTCAACTTCT
66 TCTTTATTGAACCTCAACTTCT
* * *
2497885 CTCGATGTTGCCTCCGCTT
1 CTCGCTGCTGCCTCTGCTT
2497904 TAAGTTGTGT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
86 1 0.01
87 89 0.95
88 4 0.04
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
CTCGCTGCTGCCTCTGCTTCTCTCGTTGCCGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATA
TCTTTATTGAACCTCAACTTCT
Found at i:2497836 original size:21 final size:21
Alignment explanation
Indices: 2497792--2497837 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2497782 TTGAACCTCA
* * *
2497792 GCTTCTCTCGCTGCTGCCTTT
1 GCTTCTCTCGCTGCCGCATCT
*
2497813 GCTTCTCTCGTTGCCGCATCT
1 GCTTCTCTCGCTGCCGCATCT
2497834 GCTT
1 GCTT
2497838 TAAGTTGTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (21 bp):
GCTTCTCTCGCTGCCGCATCT
Found at i:2503262 original size:23 final size:23
Alignment explanation
Indices: 2503198--2503265 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
2503188 TAAATTACGG
2503198 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
* *
2503221 TTAATTCA-TGTT-TATAATATGA-
1 TTACTTAAGTGTTCTA-AATA-GAT
*
2503243 TTACTGAAGTGTTCTAAATAGAT
1 TTACTTAAGTGTTCTAAATAGAT
2503266 ATAAATCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 16 0.46
24 2 0.06
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (23 bp):
TTACTTAAGTGTTCTAAATAGAT
Found at i:2507299 original size:2 final size:2
Alignment explanation
Indices: 2507292--2507318 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2507282 CATCACCAAA
2507292 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2507319 GTACACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2507621 original size:11 final size:11
Alignment explanation
Indices: 2507605--2507631 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2507595 TTACTCAACC
2507605 AGTAATATGAA
1 AGTAATATGAA
2507616 AGTAATATGAA
1 AGTAATATGAA
2507627 AGTAA
1 AGTAA
2507632 ATTAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.19, T:0.26
Consensus pattern (11 bp):
AGTAATATGAA
Found at i:2509375 original size:15 final size:14
Alignment explanation
Indices: 2509352--2509418 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
2509342 ATGACCGTTG
2509352 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
2509366 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
2509381 TAACCCTAAAT-T-
1 AAACCCTAAATCTC
* *
2509393 -AACCTTAAATCTT
1 AAACCCTAAATCTC
*
2509406 AAACCTTAAATCT
1 AAACCCTAAATCT
2509419 ATACCCCGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.20
12 1 0.02
13 1 0.02
14 22 0.49
15 12 0.27
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:2509973 original size:41 final size:41
Alignment explanation
Indices: 2509912--2510025 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
2509902 AAGGTAATAA
* *
2509912 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAA-AGCCGGAGG
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCC-GAGC
* * * *
2509953 ATTACTGGCGCTTAGATAAAAACGTCACTAAAGATCCGAGC
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCCGAGC
* * * *
2509994 ATTACCGACGCTTATACAAAATCGCCGCTAAA
1 ATTACCGGCGCTTAGATAAAAACGCCGCTAAA
2510026 TGCAAAGAGC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
41 56 0.95
42 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
ATTACCGGCGCTTAGATAAAAACGCCGCTAAAGAGCCGAGC
Found at i:2510065 original size:83 final size:82
Alignment explanation
Indices: 2509953--2510108 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 82
2509943 AAGCCGGAGG
* * * * *
2509953 ATTACTGGCGCTTAGATAAAAACGTCACTAAAGATCCGAGCATTACCGACGCTTATACAAAATCG
1 ATTACTGGCGCTCAGATAAAAACG-CACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATCA
2510018 CCGCTAAATGCAAAGAGC
65 CCGCTAAATGCAAAGAGC
* * * * *
2510036 ATTAGTGGCGCTCAGAATAAAACAC-CACTAAAGATGCAAGCATTAGCGGCGCTGAAATAAAATC
1 ATTACTGGCGCTCAG-ATAAAA-ACGCACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATC
2510100 ACCGCTAAA
64 ACCGCTAAA
2510109 GACCAGAGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
83 53 0.87
84 6 0.10
85 2 0.03
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (82 bp):
ATTACTGGCGCTCAGATAAAAACGCACTAAAGATCCAAGCATTACCGACGCTGAAACAAAATCAC
CGCTAAATGCAAAGAGC
Found at i:2510081 original size:41 final size:41
Alignment explanation
Indices: 2510033--2510110 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
2510023 AAATGCAAAG
*
2510033 AGCATTAGTGGCGCTCAGAATAAAA-CACCACTAAAGATGCA
1 AGCATTAGCGGCGCTCA-AATAAAATCACCACTAAAGATGCA
* *
2510074 AGCATTAGCGGCGCTGAAATAAAATCACCGCTAAAGA
1 AGCATTAGCGGCGCTCAAATAAAATCACCACTAAAGA
2510111 CCAGAGATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 7 0.21
41 26 0.79
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.17
Consensus pattern (41 bp):
AGCATTAGCGGCGCTCAAATAAAATCACCACTAAAGATGCA
Found at i:2511041 original size:2 final size:2
Alignment explanation
Indices: 2511034--2511059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2511024 CTACTGCCAC
2511034 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2511060 ACATCACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2523871 original size:44 final size:44
Alignment explanation
Indices: 2523821--2523910 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
2523811 AATTTTTCAT
2523821 TTTATAATATTCTTACTTGCTAAGCTAACGATAGAAGGAAGCAA
1 TTTATAATATTCTTACTTGCTAAGCTAACGATAGAAGGAAGCAA
2523865 TTTATAATATTCTTACTTGCTAAGCTAACGATAGAAGGAAGCAA
1 TTTATAATATTCTTACTTGCTAAGCTAACGATAGAAGGAAGCAA
2523909 TT
1 TT
2523911 AATGCATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (44 bp):
TTTATAATATTCTTACTTGCTAAGCTAACGATAGAAGGAAGCAA
Found at i:2527527 original size:15 final size:15
Alignment explanation
Indices: 2527507--2527537 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2527497 AATGTTGCAG
*
2527507 CTGATTTGGTCATAC
1 CTGATTTGGTAATAC
2527522 CTGATTTGGTAATAC
1 CTGATTTGGTAATAC
2527537 C
1 C
2527538 ATGTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
CTGATTTGGTAATAC
Found at i:2568857 original size:48 final size:48
Alignment explanation
Indices: 2568804--2568961 Score: 226
Period size: 48 Copynumber: 3.3 Consensus size: 48
2568794 AGGAGTTATC
* * * *
2568804 ACTTACTTATTTCAATACATAACATATATCACATACAAAGTTATTTTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
* * *
2568852 ACTTACTCATTTCAATACATAACAGATATCACATGCAGGGTCATATTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
* *
2568900 ACTTACTCATTTCAGTACATAACATATATCACATAGAGAGTCATATTA
1 ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
*
2568948 ACTTACTCTTTTCA
1 ACTTACTCATTTCA
2568962 TATCCTTCCT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (48 bp):
ACTTACTCATTTCAATACATAACATATATCACATACAGAGTCATATTA
Found at i:2576243 original size:9 final size:9
Alignment explanation
Indices: 2576229--2576256 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2576219 TACACATTAA
2576229 GGACAATGT
1 GGACAATGT
2576238 GGACAATGT
1 GGACAATGT
2576247 GGACAATGT
1 GGACAATGT
2576256 G
1 G
2576257 TTGACTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (9 bp):
GGACAATGT
Found at i:2578908 original size:76 final size:78
Alignment explanation
Indices: 2578819--2578993 Score: 195
Period size: 76 Copynumber: 2.3 Consensus size: 78
2578809 TTTTTTTAAT
* *
2578819 ATTTCCCCTCCAAAA-TTTTACTCTTCCATTAC-C-TTTC-CCTCAAAATTTTACTCTCTTAAAA
1 ATTTCCCCTCCAAAACTTTTACTC-T-C-TTACGCTTTTCTCCT-AAAATTTTACTCCCCTAAAA
*
2578880 ACCCTCAAAACTTTTTA
62 ACCCCCAAAACTTTTTA
*
2578897 ATTT-CCC-CCAAAACTTTTACTCTCTTCCGCTTTTCTCCTAAAATTTTACTCCCCTAAAAACCC
1 ATTTCCCCTCCAAAACTTTTACTCTCTTACGCTTTTCTCCTAAAATTTTACTCCCCTAAAAACCC
2578960 CCAAAACTTTTTA
66 CCAAAACTTTTTA
* * *
2578973 TTTTTCCCT--TAAACTTTTACT
1 ATTTCCCCTCCAAAACTTTTACT
2578994 TCTCACCCTT
Statistics
Matches: 85, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
74 3 0.04
75 2 0.02
76 59 0.69
77 17 0.20
78 4 0.05
ACGTcount: A:0.27, C:0.31, G:0.01, T:0.41
Consensus pattern (78 bp):
ATTTCCCCTCCAAAACTTTTACTCTCTTACGCTTTTCTCCTAAAATTTTACTCCCCTAAAAACCC
CCAAAACTTTTTA
Found at i:2579864 original size:28 final size:28
Alignment explanation
Indices: 2579832--2579889 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2579822 TTAATTATAA
2579832 GACAATTTTTTTCTTCATTTATATGATT
1 GACAATTTTTTTCTTCATTTATATGATT
2579860 GACAATTTTTTTCTTCATTTATATGATT
1 GACAATTTTTTTCTTCATTTATATGATT
2579888 GA
1 GA
2579890 TTTTAATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.55
Consensus pattern (28 bp):
GACAATTTTTTTCTTCATTTATATGATT
Found at i:2581786 original size:92 final size:86
Alignment explanation
Indices: 2581506--2581787 Score: 302
Period size: 90 Copynumber: 3.1 Consensus size: 86
2581496 TTAAGGATGT
** *
2581506 AAAAAGT-CTTCAAACATTTAAAAAAAGGAAGCAATTAAGCCC-CTATTTTTTTTACACTCAATT
1 AAAAAGTCCTTCAAAC-TTTTTAAAAA--AAGCAATTAAGCCCTTTATTTTTTTT-CACTCAATT
2581569 GGGTACTTGAACTTTCAAAATGCATC
62 GGGTACTTGAACTTTC-AAATGCATC
* * *
2581595 AAAAAGACCCTCAAACTTTTTAAAAAAATCCAATTAAGCCACTGCTTA-TTTTTTTCACTCAATT
1 AAAAAGTCCTTCAAACTTTTTAAAAAAA-GCAATTAAGCC-CT--TTATTTTTTTTCACTCAATT
2581659 GGGTACTTGAACTTTCGAAATGCATC
62 GGGTACTTGAACTTTC-AAATGCATC
* *
2581685 AAAAAGTCCTTCAAACTCTTTTCAGAAAAAGCAATTAAGCCCTTTAATTTTTTTTTGCACTTAAT
1 AAAAAGTCCTTCAAACT-TTTT-AAAAAAAGCAATTAAGCCCTTT-A-TTTTTTTT-CACTCAAT
*
2581750 TGGATACTTGAACTATT-AAATGCATC
61 TGGGTACTTGAACT-TTCAAATGCATC
2581776 AAAAAGGTCCTT
1 AAAAA-GTCCTT
2581788 TAACCGTTAA
Statistics
Matches: 166, Mismatches: 13, Indels: 25
0.81 0.06 0.12
Matches are distributed among these distances:
87 2 0.01
88 12 0.07
89 16 0.10
90 58 0.35
91 42 0.25
92 34 0.20
93 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (86 bp):
AAAAAGTCCTTCAAACTTTTTAAAAAAAGCAATTAAGCCCTTTATTTTTTTTCACTCAATTGGGT
ACTTGAACTTTCAAATGCATC
Found at i:2581950 original size:20 final size:21
Alignment explanation
Indices: 2581904--2581962 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
2581894 CAATAAAAGT
* *
2581904 TATAAAAATATTAAATATTAA
1 TATAAAAATTTTAAAAATTAA
*
2581925 TATAAAAATTTTAAAAATTTA
1 TATAAAAATTTTAAAAATTAA
*
2581946 T-TAAAAATTCTAAAAAT
1 TATAAAAATTTTAAAAAT
2581963 CATAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TATAAAAATTTTAAAAATTAA
Found at i:2582208 original size:20 final size:21
Alignment explanation
Indices: 2582180--2582223 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2582170 GGATTTTATA
*
2582180 TTTCTTTAC-ATTTTTTATAAT
1 TTTCTTTACAATTTTATA-AAT
2582201 TTTC-TTACAATTTTATAAAT
1 TTTCTTTACAATTTTATAAAT
2582221 TTT
1 TTT
2582224 TACCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTCTTTACAATTTTATAAAT
Found at i:2587530 original size:11 final size:11
Alignment explanation
Indices: 2587514--2587538 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2587504 GAGAATAGAA
2587514 GAAAGAATGAG
1 GAAAGAATGAG
2587525 GAAAGAATGAG
1 GAAAGAATGAG
2587536 GAA
1 GAA
2587539 GAAAGAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (11 bp):
GAAAGAATGAG
Found at i:2589257 original size:75 final size:75
Alignment explanation
Indices: 2589076--2589361 Score: 457
Period size: 75 Copynumber: 3.8 Consensus size: 75
2589066 TACCCGTTAT
* * * *
2589076 CGGTGGATTCAACACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCATTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
2589141 ATTCAAAGATA
66 ATT-TAAGATA
* *
2589152 CGGTGGAATCAGCACTTAGCAACCACCAATGATTAGGGGAATCATCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
2589217 ATTTAAGATA
66 ATTTAAGATA
* * *
2589227 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGAGGAATCAGTACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
2589292 ATTTAAGATA
66 ATTTAAGATA
*
2589302 CGGTGGAATCAGCATTTAGCAACCACCAATGATTC-GGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTT
2589362 GGAGGAATCA
Statistics
Matches: 194, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
74 23 0.12
75 109 0.56
76 62 0.32
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTTAAGATA
Found at i:2597481 original size:6 final size:6
Alignment explanation
Indices: 2597470--2597502 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2597460 AATATATATG
2597470 TTTTAT TTTTAT TTTTA- TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
2597503 TGTACAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:2597490 original size:11 final size:11
Alignment explanation
Indices: 2597470--2597501 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2597460 AATATATATG
2597470 TTTTATTTTTAT
1 TTTTA-TTTTAT
2597482 TTTTATTTTAT
1 TTTTATTTTAT
2597493 TTTTATTTT
1 TTTTATTTT
2597502 TTGTACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:2597492 original size:17 final size:17
Alignment explanation
Indices: 2597470--2597502 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2597460 AATATATATG
2597470 TTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTA
2597487 TTTTATTTTTATTTTT
1 TTTTATTTTTATTTTT
2597503 TGTACAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTATTTTTATTTTTA
Found at i:2597902 original size:28 final size:28
Alignment explanation
Indices: 2597870--2597941 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
2597860 CTGTAATCAC
2597870 TTAATATTTATATTACAATTATTTTCAA
1 TTAATATTTATATTACAATTATTTTCAA
2597898 TTAATATTTATATTACAATTATTTTCAA
1 TTAATATTTATATTACAATTATTTTCAA
*
2597926 -AAATATTTATATTACA
1 TTAATATTTATATTACA
2597942 CTAAGGCCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 15 0.35
28 28 0.65
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATATTTATATTACAATTATTTTCAA
Found at i:2599722 original size:19 final size:17
Alignment explanation
Indices: 2599698--2599741 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2599688 CAATGCATCA
*
2599698 AATAATTATACAAATTACC
1 AATAATAATAC-AATT-CC
*
2599717 AATAATAATTCAATTCC
1 AATAATAATACAATTCC
2599734 AATAATAA
1 AATAATAA
2599742 AACACACACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
19 9 0.39
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATACAATTCC
Found at i:2601217 original size:8 final size:8
Alignment explanation
Indices: 2601204--2601228 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2601194 ATATATACTA
2601204 AATAAAAT
1 AATAAAAT
2601212 AATAAAAT
1 AATAAAAT
2601220 AATAAAAT
1 AATAAAAT
2601228 A
1 A
2601229 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:2609399 original size:30 final size:31
Alignment explanation
Indices: 2609350--2609408 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2609340 CCAAAAAAAA
2609350 AATCAAAGTCAAAAGTAAAAAAGGAAAAATC
1 AATCAAAGTCAAAAGTAAAAAAGGAAAAATC
* * *
2609381 AATCAAAGTTAAAA-TAAAATATGAAAAA
1 AATCAAAGTCAAAAGTAAAAAAGGAAAAA
2609409 GAGAAAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.66, C:0.07, G:0.10, T:0.17
Consensus pattern (31 bp):
AATCAAAGTCAAAAGTAAAAAAGGAAAAATC
Found at i:2610288 original size:6 final size:7
Alignment explanation
Indices: 2610263--2610296 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
2610253 TTTTAGTCAA
2610263 AAAAATGG
1 AAAAAT-G
2610271 AAAAATG
1 AAAAATG
2610278 AAAAATG
1 AAAAATG
2610285 AAAAATG
1 AAAAATG
2610292 AAAAA
1 AAAAA
2610297 GTAAAATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:2611738 original size:44 final size:44
Alignment explanation
Indices: 2611663--2612033 Score: 223
Period size: 44 Copynumber: 8.5 Consensus size: 44
2611653 AGAATTTCAG
* *
2611663 ATCTTATATCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTAGTA
* * * *
2611707 ATCCTATCTCCTTGAGATTACAGTGGAGCAGATTAAA-ATAAAG-G
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCT--AGTA
* * * *
2611751 ATTTTATCTCTCTGA-AGTTACAGTAGAGTAGA-T--AGC-A-TCA
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAGCTAGT-A
* * ** * * *
2611791 GGTCTTATCTCCTTGAGATTACAGTGGAATAGATTGAAG-AATTTCAA
1 -ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTA-GT--A
* * *
2611838 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCTAGAA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTAGTA
** * *
2611882 ATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTAGTA
* * * * * *
2611926 ATCCTATTTCCCTGAGATTACAGTCGAGCAGATTAAA-ATAAATG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCT-AGTA
* * * *
2611970 ATCTTATCTCTCTGAAATTACAGTAGAGTAGA-T--AGC-A-TCA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTAGT-A
*
2612010 GGTCTTATCTCCCTGAGATTACAG
1 -ATCTTATCTCCCTGAGATTACAG
2612034 GTGCATAGAC
Statistics
Matches: 252, Mismatches: 55, Indels: 43
0.72 0.16 0.12
Matches are distributed among these distances:
39 2 0.01
40 1 0.00
41 46 0.18
42 2 0.01
43 4 0.02
44 159 0.63
45 2 0.01
46 34 0.13
47 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGCTAGTA
Found at i:2612051 original size:219 final size:219
Alignment explanation
Indices: 2611663--2612062 Score: 658
Period size: 219 Copynumber: 1.8 Consensus size: 219
2611653 AGAATTTCAG
* * *
2611663 ATCTTATATCCCTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATCCTATCTCCTTGAGATTAC
1 ATCTTATATCCCTGAGATTACAACGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTAC
* * *
2611728 AGTGGAGCAGATTAAAATAAAGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATAGCATCAGG
66 AGTCGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCAGG
* **
2611793 TCTTATCTCCTTGAGATTACAGTGGAATAGATTGAAGAATTTCAAATCTTATCTCCCTGAGGTTA
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAAATCTTATCTCCCTGAGGTTA
2611858 CAGTGGAGCAGATTGAAGCTAGAA
196 CAGTGGAGCAGATTGAAGCTAGAA
* * *
2611882 ATCTTATCTCCCTGAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATATCCCTGAGATTACAACGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTAC
*
2611947 AGTCGAGCAGATTAAAATAAATGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCAGG
66 AGTCGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCAGG
*
2612012 TCTTATCTCCCTGAGATTACAG-GTGCATAGACCGAAGAATTTCAAATCTTA
131 TCTTATCTCCCTGAGATTACAGTG-GAATAGACCGAAGAATTTCAAATCTTA
2612063 CTTCACAGGT
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
218 1 0.01
219 165 0.99
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (219 bp):
ATCTTATATCCCTGAGATTACAACGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTAC
AGTCGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAATTACAGTAGAGTAGATAGCATCAGG
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTTCAAATCTTATCTCCCTGAGGTTA
CAGTGGAGCAGATTGAAGCTAGAA
Found at i:2612129 original size:50 final size:50
Alignment explanation
Indices: 2612075--2613049 Score: 461
Period size: 50 Copynumber: 19.5 Consensus size: 50
2612065 TCACAGGTGA
* * *
2612075 TGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * * ** * *
2612125 TGCAGTTAAAAAGATTAAAGCTACAACAACGAATCTTAC-TCCCCAGGCAA
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCC-GACAT
* * * * * *
2612175 TGCAGTGGAACAGATTAAAACCACATCGGTGAATATTTCTTCCTCGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * * * * **
2612225 TGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTAC-TCCCC-AGGT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
* * *
2612273 GATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 --TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * * **
2612325 TGCAGTTAAAAAGATTAAAGCTACAACAACGAATCTTAC-TCCCC-A-AGT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACA-T
* * * **
2612373 GGTGTAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGTTTCCCCGACAT
1 --TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * * ** * **
2612425 TGCAGTTAAAAAGATTAAAGCTACAACAACGAATCTTAC-TCCCCAGGCGG
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCC-GACAT
* * *
2612475 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
* ** * * * * * ****
2612525 TGCTGTTAAAAAGACTAAAGCCATAGCGGCGAGTGC-TACTTCCCTGGTGG
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAAT-CTTACTTCCCCGACAT
* * * * * *
2612575 CGCAGTGGAGCAA-ATTAAGGCCACGA-CGGCGTATCTTGCTT-CTCGACAT
1 TGCAGTGGA-AAAGATTAAAGCCAC-ATCGGCGAATCTTACTTCCCCGACAT
** * * * * * * **
2612624 TGCAGTTTAAAAGACTAAAGCCATAGCGGCGAATCCTACTTCCCTGGCGG
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * ** * *
2612674 TGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTTCCTGACAT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
** * * * *
2612724 TGCAGTTAAAAAGATTAAAACCACATCAGCGAATCTTACTTCCCTGGCGA-
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGAC-AT
* * ** * * * * *
2612774 TACAGTAGAGCAGATTAAAGCCACGA-CGACGTATCTTGCTTCCCCAAAAT
1 TGCAGTGGAAAAGATTAAAGCCAC-ATCGGCGAATCTTACTTCCCCGACAT
* ** * * * * ** * *
2612824 TGCAATTAAAAAAGACTAAAGCCACAGCGGCGAGTGTTACTTCCTTGGCAA
1 TGC-AGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
* ** ** * *
2612875 TGCAGTCGAGCAGATTATGGCCACGA-CGGCGTATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCAC-ATCGGCGAATCTTACTTCCCCGACAT
** * * * * * * *
2612925 TGCAGTTAAAAAGACTAAAGCCACAGCGACGAGTGTTACTTCCCTGGAGA-
1 TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCC-CGACAT
* ** * *
2612975 TGCACTGGAGCAGATTAAAGCCACGAT-GGCGTATCTTGCTTCCCCGACAT
1 TGCAGTGGAAAAGATTAAAGCCAC-ATCGGCGAATCTTACTTCCCCGACAT
** * *
2613025 TGCAGTTAAAAAGACTAAAGACACA
1 TGCAGTGGAAAAGATTAAAGCCACA
2613050 GCATCGAGTG
Statistics
Matches: 647, Mismatches: 247, Indels: 63
0.68 0.26 0.07
Matches are distributed among these distances:
47 1 0.00
48 7 0.01
49 54 0.08
50 518 0.80
51 62 0.10
52 4 0.01
53 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
TGCAGTGGAAAAGATTAAAGCCACATCGGCGAATCTTACTTCCCCGACAT
Found at i:2612229 original size:100 final size:100
Alignment explanation
Indices: 2612056--2613133 Score: 1065
Period size: 100 Copynumber: 10.8 Consensus size: 100
2612046 AAGAATTTCA
* * *
2612056 AATCTTACTTCACAGGTGATGCAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
2612121 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * * * *
2612156 AATCTTACTCCCCAGGCAATGCAGTGGAACAGATTAAAACCACATCGGTGAATATTTCTTCCTCG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
2612221 ACATTGCAGTTAAAAAGATTAAAGCTACAACAGTG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* *
2612256 AATCTTACTCCCCAGGTGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
2612321 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * * * * *
2612356 AATCTTACTCCCCAAGTGGTGTAGTGGAATAGATTAAAGCCACATCGGTGAATCTTGTTTCCCCG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
2612421 ACATTGCAGTTAAAAAGATTAAAGCTACAACAACG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* *
2612456 AATCTTACTCCCCAGGCGGTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * * *
2612521 ACATTGCTGTTAAAAAGACTAAAGCCATAGCGGCG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * ** * * * * * *
2612556 AGTGC-TACTTCCCTGGTGGCGCAGTGGAGCAAATTAAGGCCACGA-CGGCGTATCTTGCTT-CT
1 AAT-CTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCC
* * * *
2612618 CGACATTGCAGTTTAAAAGACTAAAGCCATAGCGGCG
64 CGACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * * * * *
2612655 AATCCTACTTCCCTGGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTTCCTG
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
* * *
2612720 ACATTGCAGTTAAAAAGATTAAAACCACATCAGCG
66 ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * * ** *
2612755 AATCTTACTTCCCTGGCGATACAGTAGAGCAGATTAAAGCCACGA-CGACGTATCTTGCTTCCCC
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCC
* * * * *
2612819 AAAATTGCAATTAAAAAAGACTAAAGCCACAGCGGCG
65 GACATTGCAGTT-AAAAAGACTAAAGCCACAACAGCG
* * ** * * * ** * *
2612856 AGTGTTACTTCCTTGGCAATGCAGTCGAGCAGATTATGGCCACGA-CGGCGTATCTTGCTTCCCC
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCC
*
2612920 GACATTGCAGTTAAAAAGACTAAAGCCACAGC-GACG
65 GACATTGCAGTTAAAAAGACTAAAGCCACAACAG-CG
* * * * * * * *
2612956 AGTGTTACTTCCCTGGAGATGCACTGGAGCAGATTAAAGCCACGAT-GGCGTATCTTGCTTCCCC
1 AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCC
* * *
2613020 GACATTGCAGTTAAAAAGACTAAAGACACAGCATCG
65 GACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
* * * * * * * *
2613056 AGTGTTACTTCCCTA-GCGATGCAGTTGAGCAGATTAAAGCTACAACAGCGAATCTTGCTTCCCC
1 AATCTTACTTCCC-AGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCC
* **
2613120 AACATCACAGTTAA
65 GACATTGCAGTTAA
2613134 GCAAATTAAA
Statistics
Matches: 852, Mismatches: 114, Indels: 24
0.86 0.12 0.02
Matches are distributed among these distances:
98 2 0.00
99 86 0.10
100 677 0.79
101 87 0.10
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (100 bp):
AATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCG
ACATTGCAGTTAAAAAGACTAAAGCCACAACAGCG
Found at i:2613067 original size:50 final size:50
Alignment explanation
Indices: 2612913--2613068 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 50
2612903 GCGTATCTTG
2612913 CTTCCCCGACATTGCAGTTAAAAAGACTAAAGCCACAGCGA-CGAGTGTTA
1 CTTCCCCGACATTGCAGTTAAAAAGACTAAAGCCACAGC-ATCGAGTGTTA
* * * ** ** * * *
2612963 CTTCCCTGGAGA-TGCACTGGAGCAGATTAAAGCCAC-G-ATGGCGTA-TCTTG
1 CTTCCC-CGACATTGCAGTTAAAAAGACTAAAGCCACAGCAT--CG-AGTGTTA
*
2613013 CTTCCCCGACATTGCAGTTAAAAAGACTAAAGACACAGCATCGAGTGTTA
1 CTTCCCCGACATTGCAGTTAAAAAGACTAAAGCCACAGCATCGAGTGTTA
2613063 CTTCCC
1 CTTCCC
2613069 TAGCGATGCA
Statistics
Matches: 76, Mismatches: 21, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
47 1 0.01
49 5 0.07
50 63 0.83
51 5 0.07
52 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (50 bp):
CTTCCCCGACATTGCAGTTAAAAAGACTAAAGCCACAGCATCGAGTGTTA
Found at i:2613667 original size:22 final size:22
Alignment explanation
Indices: 2613639--2613681 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2613629 ACCTACACAT
* *
2613639 AAACAAACAGCAGAGAGCAAAG
1 AAACAAAAAGCAGACAGCAAAG
*
2613661 AAACAAAAAGGAGACAGCAAA
1 AAACAAAAAGCAGACAGCAAA
2613682 AAAAGAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.16, G:0.21, T:0.00
Consensus pattern (22 bp):
AAACAAAAAGCAGACAGCAAAG
Found at i:2620567 original size:30 final size:30
Alignment explanation
Indices: 2620531--2620681 Score: 151
Period size: 30 Copynumber: 5.1 Consensus size: 30
2620521 GACTATTGAA
*
2620531 TATGAAAAGGGATGGTTTCGACCATCGGTT
1 TATGAAAAGGGATGGTTTCGACCATCGATT
** *
2620561 TATGAAAAGGGATGGTGACGACCATCAATT
1 TATGAAAAGGGATGGTTTCGACCATCGATT
* * * * *
2620591 AATGAAAATGGATGATTTTGACCATTGATT
1 TATGAAAAGGGATGGTTTCGACCATCGATT
* * ** * *
2620621 TATGAAAAGGTACGGTGACAACCATTGATT
1 TATGAAAAGGGATGGTTTCGACCATCGATT
*
2620651 AATGAAAAGGGATGGTTTCGACCATCG-TT
1 TATGAAAAGGGATGGTTTCGACCATCGATT
2620680 TA
1 TA
2620682 GCATACTTTG
Statistics
Matches: 92, Mismatches: 29, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
29 3 0.03
30 89 0.97
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (30 bp):
TATGAAAAGGGATGGTTTCGACCATCGATT
Found at i:2620625 original size:60 final size:60
Alignment explanation
Indices: 2620532--2620681 Score: 203
Period size: 60 Copynumber: 2.5 Consensus size: 60
2620522 ACTATTGAAT
* * *
2620532 ATGAAAAGGGATGGTTTCGACCATCGGTTTATGAAAAGGGATGGTGACGACCATCAATTA
1 ATGAAAAGGGATGGTTTCGACCATCGATTTATGAAAAGGGACGGTGACAACCATCAATTA
* * * * * **
2620592 ATGAAAATGGATGATTTTGACCATTGATTTATGAAAAGGTACGGTGACAACCATTGATTA
1 ATGAAAAGGGATGGTTTCGACCATCGATTTATGAAAAGGGACGGTGACAACCATCAATTA
2620652 ATGAAAAGGGATGGTTTCGACCATCG-TTTA
1 ATGAAAAGGGATGGTTTCGACCATCGATTTA
2620682 GCATACTTTG
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 4 0.05
60 72 0.95
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (60 bp):
ATGAAAAGGGATGGTTTCGACCATCGATTTATGAAAAGGGACGGTGACAACCATCAATTA
Found at i:2625160 original size:38 final size:38
Alignment explanation
Indices: 2625109--2625264 Score: 312
Period size: 38 Copynumber: 4.1 Consensus size: 38
2625099 ACTTGCCTAA
2625109 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
1 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
2625147 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
1 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
2625185 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
1 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
2625223 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
1 ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
2625261 ACAA
1 ACAA
2625265 ACTGAGAAAC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 118 1.00
ACGTcount: A:0.33, C:0.34, G:0.05, T:0.28
Consensus pattern (38 bp):
ACAACCTCCCCTTTTGTCAATTCTTTGAACAAAACCAC
Found at i:2626578 original size:20 final size:21
Alignment explanation
Indices: 2626540--2626578 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2626530 TTATTTATGT
* *
2626540 TTTTTTCTCTTCTTCTTTTAA
1 TTTTTCCTCTTCTTATTTTAA
2626561 TTTTTCCTCTT-TTATTTT
1 TTTTTCCTCTTCTTATTTT
2626579 TGCCGATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTCCTCTTCTTATTTTAA
Found at i:2632496 original size:43 final size:42
Alignment explanation
Indices: 2632448--2632531 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
2632438 GGGTAAATCG
* *
2632448 AACAACCCATGTTTATCTTCTCCTCTTTTAAAATTATTTTTTC
1 AACAACCCAAGATTATCTTCTCCT-TTTTAAAATTATTTTTTC
* * *
2632491 AACAACTCAAGATTATCTTCTCCTTTTTTAAATTCTTTTTT
1 AACAACCCAAGATTATCTTCTCCTTTTTAAAATTATTTTTT
2632532 TTCTAGGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 15 0.42
43 21 0.58
ACGTcount: A:0.26, C:0.21, G:0.02, T:0.50
Consensus pattern (42 bp):
AACAACCCAAGATTATCTTCTCCTTTTTAAAATTATTTTTTC
Found at i:2633874 original size:125 final size:126
Alignment explanation
Indices: 2633725--2633976 Score: 488
Period size: 125 Copynumber: 2.0 Consensus size: 126
2633715 AAACGAGATT
2633725 TTATATCCCTTTTTAGGGTTTCTTAAAATTAAATAAATATATCAACGTTTTTTAAACAAAAAATT
1 TTATATCCCTTTTTAGGGTTTCTTAAAATTAAATAAATATATCAACGTTTTTTAAACAAAAAATT
2633790 ATAATTACACTAGTTATAAAAATGATTTCGATAAACTATATATTTATTTGAATTTATATAC
66 ATAATTACACTAGTTATAAAAATGATTTCGATAAACTATATATTTATTTGAATTTATATAC
2633851 TTATATCCC-TTTTAGGGTTTCTTAAAATTAAATAAATATATCAACGTTTTTTAAACAAAAAATT
1 TTATATCCCTTTTTAGGGTTTCTTAAAATTAAATAAATATATCAACGTTTTTTAAACAAAAAATT
*
2633915 ATAATTACACTAGTTATAAAAATGATTTCGGTAAACTATATATTTATTTGAATTTATATAC
66 ATAATTACACTAGTTATAAAAATGATTTCGATAAACTATATATTTATTTGAATTTATATAC
2633976 T
1 T
2633977 AACCAAATTC
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 116 0.93
126 9 0.07
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.43
Consensus pattern (126 bp):
TTATATCCCTTTTTAGGGTTTCTTAAAATTAAATAAATATATCAACGTTTTTTAAACAAAAAATT
ATAATTACACTAGTTATAAAAATGATTTCGATAAACTATATATTTATTTGAATTTATATAC
Found at i:2641164 original size:41 final size:41
Alignment explanation
Indices: 2641098--2641255 Score: 138
Period size: 41 Copynumber: 3.9 Consensus size: 41
2641088 TGCTTATTAA
* * * *
2641098 AATACACTGGCATAAAGCGTTCTAGGCACAAAGCCAT-ATAT
1 AATACACCGGCATGAAGCCTGCTAGGCACAAAGCC-TGATAT
* * * *
2641139 AATACACCGGCACGAAGCCTGCTAGGTATAAAGCCTGGTAT
1 AATACACCGGCATGAAGCCTGCTAGGCACAAAGCCTGATAT
** * * *
2641180 GGTACATCGGCATGAAGCCTGCTAGGCATAAAGCCTGCTAT
1 AATACACCGGCATGAAGCCTGCTAGGCACAAAGCCTGATAT
* * * * *
2641221 AATTCACTGGCATAAAGCCTGCTAGGGACAGAGCC
1 AATACACCGGCATGAAGCCTGCTAGGCACAAAGCC
2641256 CGAATATCAC
Statistics
Matches: 93, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 1 0.01
41 92 0.99
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (41 bp):
AATACACCGGCATGAAGCCTGCTAGGCACAAAGCCTGATAT
Found at i:2641213 original size:16 final size:16
Alignment explanation
Indices: 2641188--2641219 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2641178 ATGGTACATC
*
2641188 GGCATGAAGCCTGCTA
1 GGCATAAAGCCTGCTA
2641204 GGCATAAAGCCTGCTA
1 GGCATAAAGCCTGCTA
2641220 TAATTCACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (16 bp):
GGCATAAAGCCTGCTA
Found at i:2641419 original size:14 final size:15
Alignment explanation
Indices: 2641394--2641436 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
2641384 TCGACTATAA
2641394 ATATGAAAATTCATAC
1 ATAT-AAAATTCATAC
*
2641410 A-ATTAAATTCA-AC
1 ATATAAAATTCATAC
2641423 ATATAAAATTCATA
1 ATATAAAATTCATA
2641437 TACACTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 3 0.13
16 1 0.04
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (15 bp):
ATATAAAATTCATAC
Found at i:2646577 original size:9 final size:9
Alignment explanation
Indices: 2646563--2646728 Score: 168
Period size: 9 Copynumber: 18.9 Consensus size: 9
2646553 CAAGTATAAT
2646563 TAAGTTATG
1 TAAGTTATG
2646572 TAAGTTATG
1 TAAGTTATG
*
2646581 CAAGTTAT-
1 TAAGTTATG
*
2646589 TAAATTATG
1 TAAGTTATG
2646598 TATAAGTTATG
1 --TAAGTTATG
2646609 TAAGTTATG
1 TAAGTTATG
2646618 TAAGTTAT-
1 TAAGTTATG
2646626 TAAGTTATG
1 TAAGTTATG
2646635 TAAGTTAT-
1 TAAGTTATG
*
2646643 TAAATTATG
1 TAAGTTATG
2646652 TAAGTTATG
1 TAAGTTATG
*
2646661 TAAGTTCT-
1 TAAGTTATG
* *
2646669 TATA-TGATA
1 TA-AGTTATG
*
2646678 TATATTTATG
1 TA-AGTTATG
2646688 T-A-TTATG
1 TAAGTTATG
2646695 TAAGTTAT-
1 TAAGTTATG
2646703 TAAGTTATG
1 TAAGTTATG
2646712 TAAGTTATG
1 TAAGTTATG
*
2646721 TAAATTAT
1 TAAGTTAT
2646729 ATATTAATTT
Statistics
Matches: 134, Mismatches: 12, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.04
8 35 0.26
9 81 0.60
10 4 0.03
11 8 0.06
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:2646591 original size:26 final size:26
Alignment explanation
Indices: 2646561--2646728 Score: 173
Period size: 26 Copynumber: 6.4 Consensus size: 26
2646551 TACAAGTATA
* *
2646561 ATTAAGTTATGTAAGTTATGCAAGTT
1 ATTAAATTATGTAAGTTATGTAAGTT
2646587 ATTAAATTATGTATAAGTTATGTAAGTT
1 ATTAAATTATG--TAAGTTATGTAAGTT
*
2646615 ATGTAAGTTAT-TAAGTTATGTAAGTT
1 AT-TAAATTATGTAAGTTATGTAAGTT
2646641 ATTAAATTATGTAAGTTATGTAAGTT
1 ATTAAATTATGTAAGTTATGTAAGTT
* * * * *
2646667 CTTATATGATATATATTTATGT-A-TT
1 ATTAAATTATGTA-AGTTATGTAAGTT
*
2646692 ATGTAAGTTAT-TAAGTTATGTAAGTT
1 AT-TAAATTATGTAAGTTATGTAAGTT
2646718 ATGTAAATTAT
1 AT-TAAATTAT
2646729 ATATTAATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
24 7 0.06
25 13 0.11
26 69 0.58
27 7 0.06
28 16 0.13
29 7 0.06
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.47
Consensus pattern (26 bp):
ATTAAATTATGTAAGTTATGTAAGTT
Found at i:2646631 original size:17 final size:18
Alignment explanation
Indices: 2646563--2646728 Score: 168
Period size: 17 Copynumber: 9.4 Consensus size: 18
2646553 CAAGTATAAT
2646563 TAAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATG
* *
2646581 CAAGTTAT-TAAATTATG
1 TAAGTTATGTAAGTTATG
2646598 TATAAGTTATGTAAGTTATG
1 --TAAGTTATGTAAGTTATG
2646618 TAAGTTAT-TAAGTTATG
1 TAAGTTATGTAAGTTATG
*
2646635 TAAGTTAT-TAAATTATG
1 TAAGTTATGTAAGTTATG
*
2646652 TAAGTTATGTAAGTTCT-
1 TAAGTTATGTAAGTTATG
* * *
2646669 TATA-TGATATATATTTATG
1 TA-AGTTATGTA-AGTTATG
2646688 T-A-TTATGTAAGTTAT-
1 TAAGTTATGTAAGTTATG
2646703 TAAGTTATGTAAGTTATG
1 TAAGTTATGTAAGTTATG
*
2646721 TAAATTAT
1 TAAGTTAT
2646729 ATATTAATTT
Statistics
Matches: 123, Mismatches: 15, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.01
16 6 0.05
17 67 0.54
18 33 0.27
19 8 0.07
20 8 0.07
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (18 bp):
TAAGTTATGTAAGTTATG
Found at i:2647099 original size:28 final size:29
Alignment explanation
Indices: 2647067--2647131 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
2647057 ACTAAGTTCG
2647067 ATTTAATT-AATCAAAT-ATAAAATCGATA
1 ATTTAATTCAATCAAATCA-AAAATCGATA
*
2647095 ATTT-ATTCAATTAAATCAAAAATCGATA
1 ATTTAATTCAATCAAATCAAAAATCGATA
2647123 ATTT-ATTCA
1 ATTTAATTCA
2647132 CATTAAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.09
28 30 0.88
29 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTTAATTCAATCAAATCAAAAATCGATA
Found at i:2648659 original size:24 final size:24
Alignment explanation
Indices: 2648632--2648679 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2648622 AAAGTAATGC
2648632 TTAAAAATTAAACATAGAAACAAA
1 TTAAAAATTAAACATAGAAACAAA
2648656 TTAAAAATTAAACATAGAAACAAA
1 TTAAAAATTAAACATAGAAACAAA
2648680 AATGTAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (24 bp):
TTAAAAATTAAACATAGAAACAAA
Found at i:2648732 original size:13 final size:13
Alignment explanation
Indices: 2648714--2648738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2648704 GCGAAACTAA
2648714 CCGTGAATAGAGC
1 CCGTGAATAGAGC
2648727 CCGTGAATAGAG
1 CCGTGAATAGAG
2648739 GAAGCGGATG
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:0.32, C:0.20, G:0.32, T:0.16
Consensus pattern (13 bp):
CCGTGAATAGAGC
Found at i:2649319 original size:7 final size:7
Alignment explanation
Indices: 2649261--2649488 Score: 93
Period size: 7 Copynumber: 32.3 Consensus size: 7
2649251 GTTTTCAGTT
2649261 AACCCATA
1 AACCC-TA
*
2649269 AACACTA
1 AACCCTA
*
2649276 AACACTA
1 AACCCTA
2649283 AACCCTA
1 AACCCTA
* *
2649290 AGCCATA
1 AACCCTA
*
2649297 AACTCTA
1 AACCCTA
*
2649304 AGCCCCTA
1 A-ACCCTA
2649312 AACCCTA
1 AACCCTA
*
2649319 AAGCCTA
1 AACCCTA
*
2649326 AGCCCATA
1 AACCC-TA
*
2649334 ACCCCTA
1 AACCCTA
*
2649341 AATCCTA
1 AACCCTA
* * *
2649348 AGCTCTT
1 AACCCTA
2649355 AACCCTTA
1 AACCC-TA
*
2649363 ACCCCTA
1 AACCCTA
*
2649370 AACACTA
1 AACCCTA
*
2649377 AACACTA
1 AACCCTA
*
2649384 AACCATA
1 AACCCTA
2649391 AACCC-A
1 AACCCTA
*
2649397 CACCCTA
1 AACCCTA
*
2649404 AACCGTA
1 AACCCTA
* *
2649411 AGCACTA
1 AACCCTA
* *
2649418 AACTCTT
1 AACCCTA
* *
2649425 AACACAA
1 AACCCTA
* *
2649432 AATCATA
1 AACCCTA
*
2649439 AACCTTA
1 AACCCTA
**
2649446 AACTTTA
1 AACCCTA
2649453 AATCCC-A
1 AA-CCCTA
*
2649460 AACCATA
1 AACCCTA
*
2649467 AA-CTTA
1 AACCCTA
*
2649473 CACCCTA
1 AACCCTA
2649480 AACCCTA
1 AACCCTA
2649487 AA
1 AA
2649489 TATATACTAC
Statistics
Matches: 158, Mismatches: 55, Indels: 15
0.69 0.24 0.07
Matches are distributed among these distances:
6 11 0.07
7 126 0.80
8 21 0.13
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:2649320 original size:22 final size:22
Alignment explanation
Indices: 2649263--2649350 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
2649253 TTTCAGTTAA
* ** *
2649263 CCCATAAACACTAAACACTAAA
1 CCCATAAACCCTAAAGTCTAAG
* * *
2649285 CCC-TAAGCCATAAACTCTAAG
1 CCCATAAACCCTAAAGTCTAAG
* *
2649306 CCCCTAAACCCTAAAGCCTAAG
1 CCCATAAACCCTAAAGTCTAAG
*
2649328 CCCATAACCCCTAAA-TCCTAAG
1 CCCATAAACCCTAAAGT-CTAAG
2649350 C
1 C
2649351 TCTTAACCCT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.31
22 36 0.69
ACGTcount: A:0.41, C:0.38, G:0.06, T:0.16
Consensus pattern (22 bp):
CCCATAAACCCTAAAGTCTAAG
Found at i:2649357 original size:22 final size:22
Alignment explanation
Indices: 2649301--2649359 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
2649291 GCCATAAACT
* *
2649301 CTAAGCCCCTAAACCCTAAAGC
1 CTAAGCCCATAACCCCTAAAGC
*
2649323 CTAAGCCCATAACCCCTAAATC
1 CTAAGCCCATAACCCCTAAAGC
* *
2649345 CTAAGCTCTTAACCC
1 CTAAGCCCATAACCC
2649360 TTAACCCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.34, C:0.41, G:0.07, T:0.19
Consensus pattern (22 bp):
CTAAGCCCATAACCCCTAAAGC
Found at i:2649387 original size:29 final size:27
Alignment explanation
Indices: 2649280--2649391 Score: 75
Period size: 29 Copynumber: 3.9 Consensus size: 27
2649270 ACACTAAACA
* *
2649280 CTAAACCCTAAGCCATAAACTC-TAAGCCC
1 CTAAA-CCTAAACC-TAAACCCATAA-CCC
*
2649309 CTAAACCCTAAAGCCTAAGCCCATAACCC
1 CTAAA-CCTAAA-CCTAAACCCATAACCC
* * *
2649338 CTAAATCCTAAGCTCTTAACCCTTAACCC
1 CTAAA-CCTAAAC-CTAAACCCATAACCC
2649367 CTAAACACTAAACACTAAA-CCATAA
1 CTAAAC-CTAAAC-CTAAACCCATAA
2649392 ACCCACACCC
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
28 7 0.10
29 55 0.82
30 5 0.07
ACGTcount: A:0.40, C:0.37, G:0.04, T:0.19
Consensus pattern (27 bp):
CTAAACCTAAACCTAAACCCATAACCC
Found at i:2649488 original size:20 final size:22
Alignment explanation
Indices: 2649437--2649488 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
2649427 CACAAAATCA
*
2649437 TAAACCTTAAACTTTAAATCCC
1 TAAACCATAAACTTTAAATCCC
*
2649459 -AAACCATAAAC-TTACA-CCC
1 TAAACCATAAACTTTAAATCCC
*
2649478 TAAACCCTAAA
1 TAAACCATAAA
2649489 TATATACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (22 bp):
TAAACCATAAACTTTAAATCCC
Found at i:2650086 original size:40 final size:39
Alignment explanation
Indices: 2650040--2650130 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
2650030 TAATTTTTTT
*
2650040 GCGGCGCTTTTCTAAAAACACCGCTATATATCGAGAATTA
1 GCGGCGCTTTTC-AAAAACACCGCTATAGATCGAGAATTA
** ** *
2650080 GCGGCGCTTTGTCCCAAACGTCGCTATAGATCGAGCATTA
1 GCGGCGCTTT-TCAAAAACACCGCTATAGATCGAGAATTA
*
2650120 GCGGCACTTTT
1 GCGGCGCTTTT
2650131 TTTAAAGTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 1 0.02
40 40 0.93
41 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (39 bp):
GCGGCGCTTTTCAAAAACACCGCTATAGATCGAGAATTA
Found at i:2650120 original size:155 final size:148
Alignment explanation
Indices: 2649948--2650260 Score: 374
Period size: 148 Copynumber: 2.1 Consensus size: 148
2649938 AAAAATGCCA
* * * *
2649948 CTATAGATCTAGCATTAGCCGCGCTTTCTAAAAAGCATCGCTAATGCCACTGAAGCTCAATCTAA
1 CTATAGATCGAGCATTAGCCGCACTTTCTAAAAAGCACCGCTAATGCCACTAAAGCTCAATC---
* * * *
2650013 AACTACGGCGTTGTGATTAATTTTTTTGCGGCGCTTTTCTAAAAACACCGCTATATATCGAGAAT
63 -A--ACGGCATTGTGATTAATTTTTTT-CGGCGCTTTTATAAAAACACCGCTACATATCAAGAAT
*
2650078 TAGCGGCGCTTTGTCCCAAACGTCG
124 TAGCGGCGCTTTGTCCCAAACATCG
* * ** ** *
2650103 CTATAGATCGAGCATTAGCGGCACTTTTTTTAAAGTGCCGCTAATGCCACTAAATCTCAATCAAC
1 CTATAGATCGAGCATTAGCCGCACTTTCTAAAAAGCACCGCTAATGCCACTAAAGCTCAATCAAC
** *
2650168 GGCATTGTGATTAATTTTTTTCGGCGCTTTTATAAAAATGCCGCTACATATCAAGAATTAGCGGT
66 GGCATTGTGATTAATTTTTTTCGGCGCTTTTATAAAAACACCGCTACATATCAAGAATTAGCGGC
* *
2650233 GTTTTGTCCCAAGCATCG
131 GCTTTGTCCCAAACATCG
2650251 CTATAGATCG
1 CTATAGATCG
2650261 GGCACACTAA
Statistics
Matches: 137, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
148 63 0.46
149 22 0.16
151 1 0.01
155 51 0.37
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (148 bp):
CTATAGATCGAGCATTAGCCGCACTTTCTAAAAAGCACCGCTAATGCCACTAAAGCTCAATCAAC
GGCATTGTGATTAATTTTTTTCGGCGCTTTTATAAAAACACCGCTACATATCAAGAATTAGCGGC
GCTTTGTCCCAAACATCG
Found at i:2650408 original size:40 final size:40
Alignment explanation
Indices: 2650347--2650430 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
2650337 AAATGAGATT
*
2650347 TAGCGGCGTTTTTAAAGAAGCACCACTAATGCTCGATATA
1 TAGCGGCGTTTTTAAAGAAGCACCACTAATGCTCAATATA
* * *
2650387 TAGCGGTGTTTTT-CAGAAAGCACCACTAATGCTCAATCTA
1 TAGCGGCGTTTTTAAAG-AAGCACCACTAATGCTCAATATA
2650427 TAGC
1 TAGC
2650431 TGCATTTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.05
40 37 0.95
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (40 bp):
TAGCGGCGTTTTTAAAGAAGCACCACTAATGCTCAATATA
Found at i:2652556 original size:40 final size:40
Alignment explanation
Indices: 2652489--2652663 Score: 149
Period size: 40 Copynumber: 4.4 Consensus size: 40
2652479 CGGACGAGCG
* * * * **
2652489 ATACCTACTGAATCTTCTTATACGTATGCGCTTTCAAGAG
1 ATACCTACTGAATCTACTAAAATGTATGCGCTTTCAAGCC
* **
2652529 ATACCTACTGAATCTACTAAAATGTATGCGATTTTGAGCC
1 ATACCTACTGAATCTACTAAAATGTATGCGCTTTCAAGCC
* * *
2652569 ATGCCTACT-AGATCTACTAAACA--TATGCACTTTCGAGCC
1 ATACCTACTGA-ATCTACTAAA-ATGTATGCGCTTTCAAGCC
* * * * *
2652608 TTACCTATTGAATCTACTGAAATGTATGAGCTCTCAAGCC
1 ATACCTACTGAATCTACTAAAATGTATGCGCTTTCAAGCC
*
2652648 ATACCTACTAAATCTA
1 ATACCTACTGAATCTA
2652664 TTGAAAAGAA
Statistics
Matches: 106, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
38 1 0.01
39 29 0.27
40 75 0.71
41 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.32
Consensus pattern (40 bp):
ATACCTACTGAATCTACTAAAATGTATGCGCTTTCAAGCC
Found at i:2664601 original size:47 final size:47
Alignment explanation
Indices: 2664532--2664626 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
2664522 GCAGTCATGA
* *
2664532 TTCGACATAACCTCTCTGTGATTAACCCTTCATGTATTAAATCCTTT
1 TTCGACATAACCTCTCTGTGATTAACCCTTAATGTATAAAATCCTTT
*
2664579 TTCGACATAACCTCTCTTTGATTAACCCTTAATGTATAAAATCCTTT
1 TTCGACATAACCTCTCTGTGATTAACCCTTAATGTATAAAATCCTTT
2664626 T
1 T
2664627 GTCCTTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (47 bp):
TTCGACATAACCTCTCTGTGATTAACCCTTAATGTATAAAATCCTTT
Found at i:2665942 original size:45 final size:44
Alignment explanation
Indices: 2665890--2666071 Score: 215
Period size: 44 Copynumber: 4.1 Consensus size: 44
2665880 CTCGGATTAG
* *
2665890 ACCGGATATCCTTG-AATATAAAGGTTGTTGCTAAGTGCTGATTCC
1 ACCGGATATCCATGTAA-AT-AAGGTGGTTGCTAAGTGCTGATTCC
* *
2665935 ACCGGATATCCATGTAAGTAAGGTGGTTGCTAAGTTCTGATTCC
1 ACCGGATATCCATGTAAATAAGGTGGTTGCTAAGTGCTGATTCC
* * * *
2665979 ATCGGATTTCCATGTAAGTAAGGTGGTTGCTAATTGCTGATTCC
1 ACCGGATATCCATGTAAATAAGGTGGTTGCTAAGTGCTGATTCC
* * *
2666023 ACCGGATAACCTTG-AATATAAAGGTGGTTGCTAACTGCTGATTCC
1 ACCGGATATCCATGTAA-AT-AAGGTGGTTGCTAAGTGCTGATTCC
2666068 ACCG
1 ACCG
2666072 TGTAATTATT
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.02
44 74 0.62
45 42 0.35
46 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (44 bp):
ACCGGATATCCATGTAAATAAGGTGGTTGCTAAGTGCTGATTCC
Found at i:2665965 original size:44 final size:44
Alignment explanation
Indices: 2665910--2666071 Score: 218
Period size: 44 Copynumber: 3.7 Consensus size: 44
2665900 CTTGAATATA
*
2665910 AAGGTTGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGT
* * *
2665954 AAGGTGGTTGCTAAGTTCTGATTCCATCGGATTTCCATGTAAGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGT
* * * *
2665998 AAGGTGGTTGCTAATTGCTGATTCCACCGGATAACCTTG-AATAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAA-GT
*
2666042 AAAGGTGGTTGCTAACTGCTGATTCCACCG
1 -AAGGTGGTTGCTAAGTGCTGATTCCACCG
2666072 TGTAATTATT
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 2 0.02
44 74 0.71
45 28 0.27
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (44 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGGATATCCATGTAAGT
Found at i:2668731 original size:43 final size:43
Alignment explanation
Indices: 2668630--2668862 Score: 212
Period size: 43 Copynumber: 5.5 Consensus size: 43
2668620 TTCCCTGAGA
* * * * *
2668630 GGTTTCTAAGTGCTGATTCCCCGAAT-TATTGACTCT-AAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCT-TTGATTGTGAAAGGT
* *
2668672 GGTTGCTAAGTTCTGATTCCATCGTATCTTTTATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCA-CGTATCTTTGATTGTGAAAGGT
* * ** * *
2668715 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATAT-AAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCTTTGATTGTGAAAGGT
2668757 GGTTGCTAAGTGCTGATTCCACTGTATCTTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCAC-GTATCTTTGATTGTGAAAGGT
* * **
2668800 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATT-T--AAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCTTTG-ATTGTGAAAGGT
*
2668841 GGTTGCTAAGTGCTGAATCCAC
1 GGTTGCTAAGTGCTGATTCCAC
2668863 CGAGTAACGG
Statistics
Matches: 155, Mismatches: 28, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
40 4 0.03
41 24 0.15
42 56 0.36
43 60 0.39
44 11 0.07
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACGTATCTTTGATTGTGAAAGGT
Found at i:2668761 original size:42 final size:42
Alignment explanation
Indices: 2668630--2668856 Score: 226
Period size: 42 Copynumber: 5.4 Consensus size: 42
2668620 TTCCCTGAGA
* * * * *
2668630 GGTTTCTAAGTGCTGATTCCCCGAATTATTGACTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAAAGGT
* * * * *
2668672 GGTTGCTAAGTTCTGATTCCATCGTATCTTTTATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGAATGT-AAAGGT
* * *
2668715 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAAAGGT
* * *
2668757 GGTTGCTAAGTGCTGATTCCACTGTATCTTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGTATCATTGAATGT-AAAGGT
* * *
2668800 GGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-TTAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAAAGGT
2668841 GGTTGCTAAGTGCTGA
1 GGTTGCTAAGTGCTGA
2668857 ATCCACCGAG
Statistics
Matches: 149, Mismatches: 30, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
40 4 0.03
41 21 0.14
42 57 0.38
43 57 0.38
44 10 0.07
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.37
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGTATCATTGAATGTAAAGGT
Found at i:2668784 original size:85 final size:85
Alignment explanation
Indices: 2668630--2668862 Score: 344
Period size: 85 Copynumber: 2.7 Consensus size: 85
2668620 TTCCCTGAGA
* * * * * * *
2668630 GGTTTCTAAGTGCTGATTCCCCGAATTATTGACTCTAAAGGTGGTTGCTAAGTTCTGATTCCA-T
1 GGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATTCCACT
*
2668694 CGTATCTTTTATTGTGAAAGG
65 CGTATCTTTGATTGTGAAAGG
2668715 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACT
1 GGTTGCTATGTGCTGATTCCCCGTATCACTGAAT-TAAAGGTGGTTGCTAAGTGCTGATTCCACT
2668780 -GTATCTTTGATTGTGAAAGG
65 CGTATCTTTGATTGTGAAAGG
* *
2668800 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTAAGGTGGTTGCTAAGTGCTGAATCCAC
1 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCAC
2668863 CGAGTAACGG
Statistics
Matches: 136, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
84 27 0.20
85 108 0.79
86 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (85 bp):
GGTTGCTATGTGCTGATTCCCCGTATCACTGAATTAAAGGTGGTTGCTAAGTGCTGATTCCACTC
GTATCTTTGATTGTGAAAGG
Found at i:2694456 original size:42 final size:40
Alignment explanation
Indices: 2694410--2694606 Score: 169
Period size: 43 Copynumber: 4.7 Consensus size: 40
2694400 ATATTCAGTG
*
2694410 ATACGGGGAGTCAGCACTTAGCAACCCTATTCACAATCAAAA
1 ATACGGGGAATCAGCACTTAGCAACCCT-TT-ACAATCAAAA
* * * * *
2694452 ATACGGTAGAATCAGCACATAGCAACAACCTTTATATTCAACA
1 ATACGG-GGAATCAGCACTTAGCAAC--CCTTTACAATCAAAA
*
2694495 ATACGGGGAATCAGCACTTAGCAACCCTTTTCACAATCAAAG
1 ATACGGGGAATCAGCACTTAGCAACCC-TTT-ACAATCAAAA
* * * * * *
2694537 TTACGGTGGGATCAGCACATAGCAACCTCCTTTAGAGTCAATA
1 ATACGG-GGAATCAGCACTTAGCAA-C-CCTTTACAATCAAAA
**
2694580 ATTTGGGGAATCAGCACTTAGCAACCC
1 ATACGGGGAATCAGCACTTAGCAACCC
2694607 CTCGGGGAAT
Statistics
Matches: 123, Mismatches: 24, Indels: 18
0.75 0.15 0.11
Matches are distributed among these distances:
40 4 0.03
41 4 0.03
42 50 0.41
43 54 0.44
44 6 0.05
45 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (40 bp):
ATACGGGGAATCAGCACTTAGCAACCCTTTACAATCAAAA
Found at i:2694464 original size:85 final size:85
Alignment explanation
Indices: 2694375--2694606 Score: 302
Period size: 85 Copynumber: 2.7 Consensus size: 85
2694365 GGATTCAGTG
* * * * * *
2694375 GAATCAGAACTTAGTAACCACCTTTATATTCAGTGATACGGGGAGTCAGCACTTAGCAACCCTAT
1 GAATCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACTTAGCAACCCTAT
2694440 TCACAATCAAAAATACGGTA
66 TCACAATCAAAAATACGGTA
* * *
2694460 GAATCAGCACATAGCAACAACCTTTATATTCAACAATACGGGGAATCAGCACTTAGCAACCCTTT
1 GAATCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACTTAGCAACCCTAT
** *
2694525 TCACAATCAAAGTTACGGTG
66 TCACAATCAAAAATACGGTA
* * * * **
2694545 GGATCAGCACATAGCAACCTCCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAACCC
1 GAATCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACTTAGCAACCC
2694607 CTCGGGGAAT
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 127 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (85 bp):
GAATCAGCACATAGCAACCACCTTTATATTCAATAATACGGGGAATCAGCACTTAGCAACCCTAT
TCACAATCAAAAATACGGTA
Found at i:2694613 original size:26 final size:26
Alignment explanation
Indices: 2694584--2694634 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2694574 TCAATAATTT
2694584 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
2694610 GGGGAATCAGCACTTAGCAACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
2694635 TTTTATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:2697181 original size:20 final size:20
Alignment explanation
Indices: 2697143--2697181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2697133 TAAGGAAGCA
*
2697143 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGAAAGTG
*
2697163 AGTAAGTAAAGAAGAAAGT
1 AGTAAGTAAACAAGAAAGT
2697182 AAAGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGAAAGTG
Found at i:2698402 original size:27 final size:27
Alignment explanation
Indices: 2698372--2698434 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
2698362 ATTGAGCATG
*
2698372 CCACTAAGGCAATCCTTTCATAATTTT
1 CCACAAAGGCAATCCTTTCATAATTTT
*** * *
2698399 CCACAAAGGTTTTTCTTTCATGATTTT
1 CCACAAAGGCAATCCTTTCATAATTTT
2698426 CCACAAAGG
1 CCACAAAGG
2698435 TTTTTCTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (27 bp):
CCACAAAGGCAATCCTTTCATAATTTT
Found at i:2698466 original size:28 final size:27
Alignment explanation
Indices: 2698399--2698611 Score: 250
Period size: 27 Copynumber: 7.8 Consensus size: 27
2698389 TCATAATTTT
**
2698399 CCACAAAGGTTTTTCTTTCATGATTTT
1 CCACAAAGGTTTTTCTTTCATGATTCG
2698426 CCACAAAGGTTTTTCTTTCATGATTCG
1 CCACAAAGGTTTTTCTTTCATGATTCG
* * *
2698453 CCACAAAAGATTTTCTTTCATGATTCA
1 CCACAAAGGTTTTTCTTTCATGATTCG
* *
2698480 TCACAAAGGCTTTTCTTTCATGATTTCG
1 CCACAAAGGTTTTTCTTTCATGA-TTCG
* *
2698508 CCACAAAAGCTTTTCTTTCATGATTTCG
1 CCACAAAGGTTTTTCTTTCATGA-TTCG
2698536 CCACAAAGGTTTTTCTTTCATGATTCG
1 CCACAAAGGTTTTTCTTTCATGATTCG
* * *
2698563 CAACAAAGGATTTTT-TTTCTTGATTCA
1 CCACAAAGG-TTTTTCTTTCATGATTCG
* *
2698590 CCA-AAATGTCTATTCTTTCATG
1 CCACAAAGGT-TTTTCTTTCATG
2698612 GCGTGTTTAT
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
25 1 0.01
26 7 0.04
27 99 0.61
28 55 0.34
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (27 bp):
CCACAAAGGTTTTTCTTTCATGATTCG
Found at i:2704209 original size:18 final size:18
Alignment explanation
Indices: 2704186--2704220 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2704176 ATTTAAATTA
2704186 CGGTCGCGGCCGCGTTTT
1 CGGTCGCGGCCGCGTTTT
2704204 CGGTCGCGGCCGCGTTT
1 CGGTCGCGGCCGCGTTT
2704221 ATCGCGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.40, T:0.26
Consensus pattern (18 bp):
CGGTCGCGGCCGCGTTTT
Found at i:2704865 original size:20 final size:19
Alignment explanation
Indices: 2704821--2704867 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2704811 TGTACATTTG
* *
2704821 AAATTTTGTATATTTTTTT
1 AAATTTTGTATAATTTCTT
2704840 AGAATTTTGTAATAATTTCTT
1 A-AATTTTGT-ATAATTTCTT
2704861 AAATTTT
1 AAATTTT
2704868 TTGAAGTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 9 0.38
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (19 bp):
AAATTTTGTATAATTTCTT
Found at i:2706179 original size:16 final size:16
Alignment explanation
Indices: 2706158--2706191 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2706148 ATGATAATGA
2706158 TACAGTGTTGAAAATT
1 TACAGTGTTGAAAATT
2706174 TACAGTGTTGAAAATT
1 TACAGTGTTGAAAATT
2706190 TA
1 TA
2706192 TGGCCTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (16 bp):
TACAGTGTTGAAAATT
Found at i:2709501 original size:6 final size:6
Alignment explanation
Indices: 2709471--2709517 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
2709461 GAGAAGGTGA
* * * *
2709471 GGTGGC AGTGGC AGTGGC AGTGGC GGTGGC GCTGGC GGTGGC GGTGG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGG
2709518 TTAAATCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.06, C:0.17, G:0.60, T:0.17
Consensus pattern (6 bp):
GGTGGC
Found at i:2711200 original size:528 final size:528
Alignment explanation
Indices: 2710204--2711259 Score: 2112
Period size: 528 Copynumber: 2.0 Consensus size: 528
2710194 GTTTATTTTG
2710204 GGAAATAAAAAAATCAATGTGAGAGAGGCCCAAAACCCCTCATATAACATGAAGGGGGTGACATC
1 GGAAATAAAAAAATCAATGTGAGAGAGGCCCAAAACCCCTCATATAACATGAAGGGGGTGACATC
2710269 CCTAGTAAGAATACTAGGGTGTGTCATCCACCCCACTCCCAGTCTAAGTAGAAAGTTATATTTCT
66 CCTAGTAAGAATACTAGGGTGTGTCATCCACCCCACTCCCAGTCTAAGTAGAAAGTTATATTTCT
2710334 ATTTGAAATAAACCACTACAACTCAACAAAGACTCTAACTTCTCTTCTTATAAACAGATGGCACT
131 ATTTGAAATAAACCACTACAACTCAACAAAGACTCTAACTTCTCTTCTTATAAACAGATGGCACT
2710399 GATAGGGCATAGAAAAAACTTAAAGAGATTGTTACTTTACCGAAAAATAGAGAGAATTTATTCTC
196 GATAGGGCATAGAAAAAACTTAAAGAGATTGTTACTTTACCGAAAAATAGAGAGAATTTATTCTC
2710464 AACTATTAAATATATTCTTTTAAAATGACAATTCTACTAGTTTATATTAAAGAAGAGAGAATTTT
261 AACTATTAAATATATTCTTTTAAAATGACAATTCTACTAGTTTATATTAAAGAAGAGAGAATTTT
2710529 CATTTTCATCCCAAATAAAAAAGTGAAAACATTTTTTAATTTTGTGTTTCAGTTCAATTGGTTTG
326 CATTTTCATCCCAAATAAAAAAGTGAAAACATTTTTTAATTTTGTGTTTCAGTTCAATTGGTTTG
2710594 AGCCCACACTTAGAGCAATTTGTGGTACGAGAATAGCGAAGAAGATTGTTTGGTTGAAAGCCGGG
391 AGCCCACACTTAGAGCAATTTGTGGTACGAGAATAGCGAAGAAGATTGTTTGGTTGAAAGCCGGG
2710659 AACAACAAATGTTCACTAAGACAAAAACATATGTATAAATTCTGTTAGGGTTTATTGCTATAAAT
456 AACAACAAATGTTCACTAAGACAAAAACATATGTATAAATTCTGTTAGGGTTTATTGCTATAAAT
2710724 ATAAAAAA
521 ATAAAAAA
2710732 GGAAATAAAAAAATCAATGTGAGAGAGGCCCAAAACCCCTCATATAACATGAAGGGGGTGACATC
1 GGAAATAAAAAAATCAATGTGAGAGAGGCCCAAAACCCCTCATATAACATGAAGGGGGTGACATC
2710797 CCTAGTAAGAATACTAGGGTGTGTCATCCACCCCACTCCCAGTCTAAGTAGAAAGTTATATTTCT
66 CCTAGTAAGAATACTAGGGTGTGTCATCCACCCCACTCCCAGTCTAAGTAGAAAGTTATATTTCT
2710862 ATTTGAAATAAACCACTACAACTCAACAAAGACTCTAACTTCTCTTCTTATAAACAGATGGCACT
131 ATTTGAAATAAACCACTACAACTCAACAAAGACTCTAACTTCTCTTCTTATAAACAGATGGCACT
2710927 GATAGGGCATAGAAAAAACTTAAAGAGATTGTTACTTTACCGAAAAATAGAGAGAATTTATTCTC
196 GATAGGGCATAGAAAAAACTTAAAGAGATTGTTACTTTACCGAAAAATAGAGAGAATTTATTCTC
2710992 AACTATTAAATATATTCTTTTAAAATGACAATTCTACTAGTTTATATTAAAGAAGAGAGAATTTT
261 AACTATTAAATATATTCTTTTAAAATGACAATTCTACTAGTTTATATTAAAGAAGAGAGAATTTT
2711057 CATTTTCATCCCAAATAAAAAAGTGAAAACATTTTTTAATTTTGTGTTTCAGTTCAATTGGTTTG
326 CATTTTCATCCCAAATAAAAAAGTGAAAACATTTTTTAATTTTGTGTTTCAGTTCAATTGGTTTG
2711122 AGCCCACACTTAGAGCAATTTGTGGTACGAGAATAGCGAAGAAGATTGTTTGGTTGAAAGCCGGG
391 AGCCCACACTTAGAGCAATTTGTGGTACGAGAATAGCGAAGAAGATTGTTTGGTTGAAAGCCGGG
2711187 AACAACAAATGTTCACTAAGACAAAAACATATGTATAAATTCTGTTAGGGTTTATTGCTATAAAT
456 AACAACAAATGTTCACTAAGACAAAAACATATGTATAAATTCTGTTAGGGTTTATTGCTATAAAT
2711252 ATAAAAAA
521 ATAAAAAA
2711260 TTGGGTCGAT
Statistics
Matches: 528, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
528 528 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (528 bp):
GGAAATAAAAAAATCAATGTGAGAGAGGCCCAAAACCCCTCATATAACATGAAGGGGGTGACATC
CCTAGTAAGAATACTAGGGTGTGTCATCCACCCCACTCCCAGTCTAAGTAGAAAGTTATATTTCT
ATTTGAAATAAACCACTACAACTCAACAAAGACTCTAACTTCTCTTCTTATAAACAGATGGCACT
GATAGGGCATAGAAAAAACTTAAAGAGATTGTTACTTTACCGAAAAATAGAGAGAATTTATTCTC
AACTATTAAATATATTCTTTTAAAATGACAATTCTACTAGTTTATATTAAAGAAGAGAGAATTTT
CATTTTCATCCCAAATAAAAAAGTGAAAACATTTTTTAATTTTGTGTTTCAGTTCAATTGGTTTG
AGCCCACACTTAGAGCAATTTGTGGTACGAGAATAGCGAAGAAGATTGTTTGGTTGAAAGCCGGG
AACAACAAATGTTCACTAAGACAAAAACATATGTATAAATTCTGTTAGGGTTTATTGCTATAAAT
ATAAAAAA
Found at i:2712165 original size:20 final size:19
Alignment explanation
Indices: 2712118--2712165 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2712108 AAAATTGGAA
*
2712118 AATTAATTTTAAAGTAATT
1 AATTAATTTTAAAGTAAAT
*
2712137 AAATAATTTT-AAGTGAAAAT
1 AATTAATTTTAAAGT--AAAT
2712157 AATTAATTT
1 AATTAATTT
2712166 GGGTAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (19 bp):
AATTAATTTTAAAGTAAAT
Found at i:2712960 original size:22 final size:21
Alignment explanation
Indices: 2712913--2712952 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2712903 ATTGATTTAA
2712913 ATGTGAAATTGATGCTTAGTTT
1 ATGTGAAATTGAT-CTTAGTTT
*
2712935 ATGTGTAATTGAT-TTAGT
1 ATGTGAAATTGATCTTAGT
2712953 ATTGATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (21 bp):
ATGTGAAATTGATCTTAGTTT
Found at i:2714927 original size:24 final size:24
Alignment explanation
Indices: 2714899--2714977 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 24
2714889 GGACACACCA
2714899 CAGCTTGTATGAGCTTACCGATTT
1 CAGCTTGTATGAGCTTACCGATTT
* *
2714923 TAGCTTGTGA-GAGCATACCGATTCT
1 CAGCTTGT-ATGAGCTTACCGATT-T
* *
2714948 CAGCTCGTATGAGCTTGCCGATTT
1 CAGCTTGTATGAGCTTACCGATTT
2714972 CCAGCT
1 -CAGCT
2714978 CGCGAGAACA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 21 0.47
25 24 0.53
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.33
Consensus pattern (24 bp):
CAGCTTGTATGAGCTTACCGATTT
Found at i:2714961 original size:25 final size:24
Alignment explanation
Indices: 2714899--2715015 Score: 78
Period size: 25 Copynumber: 4.8 Consensus size: 24
2714889 GGACACACCA
* *
2714899 CAGCTTGTATGAGCTTACCGATTT
1 CAGCTCGTATGAGCATACCGATTT
* *
2714923 TAGCTTGTGA-GAGCATACCGATTCT
1 CAGCTCGT-ATGAGCATACCGATT-T
* *
2714948 CAGCTCGTATGAGCTTGCCGATTT
1 CAGCTCGTATGAGCATACCGATTT
* *
2714972 CCAGCTCGCGA-GAACATACCGA-TT
1 -CAGCTCG-TATGAGCATACCGATTT
*
2714996 CATAGCTCGTATGATCATAC
1 C--AGCTCGTATGAGCATAC
2715016 ATGTACATGA
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.01
24 24 0.33
25 47 0.64
26 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (24 bp):
CAGCTCGTATGAGCATACCGATTT
Found at i:2714971 original size:49 final size:51
Alignment explanation
Indices: 2714899--2715009 Score: 147
Period size: 50 Copynumber: 2.2 Consensus size: 51
2714889 GGACACACCA
* * * * *
2714899 CAGCTTGTATGAGCTTACCGATTT-TAGCTTGTGAGAGCATACCGATTC-T
1 CAGCTCGTATGAGCTTACCGATTTCCAGCTCGCGAGAACATACCGATTCAT
*
2714948 CAGCTCGTATGAGCTTGCCGATTTCCAGCTCGCGAGAACATACCGATTCAT
1 CAGCTCGTATGAGCTTACCGATTTCCAGCTCGCGAGAACATACCGATTCAT
2714999 -AGCTCGTATGA
1 CAGCTCGTATGA
2715010 TCATACATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
49 22 0.41
50 31 0.57
51 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (51 bp):
CAGCTCGTATGAGCTTACCGATTTCCAGCTCGCGAGAACATACCGATTCAT
Found at i:2718203 original size:23 final size:23
Alignment explanation
Indices: 2718177--2718222 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2718167 CTAAAATTGG
2718177 GTTAGTTTTACCATAGATGATAC
1 GTTAGTTTTACCATAGATGATAC
2718200 GTTAGTTTTACCATAGATGATAC
1 GTTAGTTTTACCATAGATGATAC
2718223 AATGACAAAA
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:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (23 bp):
GTTAGTTTTACCATAGATGATAC
Found at i:2765326 original size:26 final size:26
Alignment explanation
Indices: 2765294--2765362 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
2765284 CATTTCGACC
* *
2765294 CATAGCTCGTGTGAGTAGGCCCATTT
1 CATAGCTCGTGTGAGCAAGCCCATTT
*
2765320 GATAGCTCGTGTGAGCAAGCCCATTT
1 CATAGCTCGTGTGAGCAAGCCCATTT
*
2765346 CATAGCTTGTGTGAGCA
1 CATAGCTCGTGTGAGCA
2765363 GTATTGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (26 bp):
CATAGCTCGTGTGAGCAAGCCCATTT
Found at i:2769631 original size:16 final size:16
Alignment explanation
Indices: 2769610--2769641 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2769600 ATTTTGTTGC
*
2769610 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
2769626 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
2769642 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:2769926 original size:51 final size:51
Alignment explanation
Indices: 2769858--2770054 Score: 231
Period size: 51 Copynumber: 3.9 Consensus size: 51
2769848 ATTAATGATA
* *
2769858 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATGACTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATGACTAT
* * *
2769909 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGA--TTGAAGCTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATG-A-CTAT
* * * * *
2769960 CCGGTACGCATAGTAGCCTGCACATACTACTACACATGCGACCTATCA-T-T
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATGACTAT
* *
2770010 CTGGTACACATAGTAGCCGGCACATAGTACTACACACGTGACCAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
2770055 CACTTTCACT
Statistics
Matches: 122, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
49 4 0.03
50 39 0.32
51 77 0.63
53 1 0.01
54 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (51 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATGACTAT
Found at i:2770049 original size:101 final size:102
Alignment explanation
Indices: 2769866--2770050 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
2769856 TACCGGTTCA
* * * * *
2769866 CATAGTAGCCTGCACATAGTACTACACATGTGACCATGACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATACTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCGGCA
2769931 CATAGTACTACACACGTGATTGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATTGAAGCTATCCGGTACG
* *
2769968 CATAGTAGCCTGCACATACTACTACACATGCGACCTATCA-T-TCTGGTACACATAGTAGCCGGC
1 CATAGTAGCCTGCACATACTACTACACATGCGACC-ATCACTATCCGATACACATAGTAGCCGGC
2770031 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
2770051 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 38 0.51
102 34 0.45
103 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTGCACATACTACTACACATGCGACCATCACTATCCGATACACATAGTAGCCGGCA
CATAGTACTACACACGTGATTGAAGCTATCCGGTACG
Found at i:2770074 original size:101 final size:102
Alignment explanation
Indices: 2769858--2770050 Score: 273
Period size: 102 Copynumber: 1.9 Consensus size: 102
2769848 ATTAATGATA
* * * *
2769858 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATGACTATCCGATACACGTAGT
1 CCGGTTCACATAGTAGCCTGCACATACTACTACACATGCGACCATCACTATCCGATACACATAGT
* *
2769923 AGCCTGCACATAGTACTACACACGTGATTGAAGCTAT
66 AGCCGGCACATAGTACTACACACGTGAATGAAGCTAT
* * * *
2769960 CCGGTACGCATAGTAGCCTGCACATACTACTACACATGCGACCTATCA-T-TCTGGTACACATAG
1 CCGGTTCACATAGTAGCCTGCACATACTACTACACATGCGACC-ATCACTATCCGATACACATAG
2770023 TAGCCGGCACATAGTACTACACACGTGA
65 TAGCCGGCACATAGTACTACACACGTGA
2770051 CCATCACTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 38 0.47
102 40 0.49
103 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATACTACTACACATGCGACCATCACTATCCGATACACATAGT
AGCCGGCACATAGTACTACACACGTGAATGAAGCTAT
Found at i:2772914 original size:42 final size:42
Alignment explanation
Indices: 2772834--2772915 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
2772824 CGTTTTCTCA
* **
2772834 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
* *
2772876 ATGCCATAGCCCAGCTCTGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACA-TATGCACATAT
2772916 CACACCGATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATATGCACATATTG
Found at i:2775644 original size:287 final size:287
Alignment explanation
Indices: 2775123--2775694 Score: 939
Period size: 287 Copynumber: 2.0 Consensus size: 287
2775113 TTATATTTAA
*
2775123 ATTCAAAGCTGTCTAGTCGAGTTACAGTCACTAAATTATTTTTATCCAGAGCTACAGAGCTCTAA
1 ATTCAAAGCTGTCTAGTCGAGTTACAGTCACTAAATTATTTTTATCCAGAGCTACAGAGCTCCAA
* *
2775188 ATTAAGTTCCATTAATTTTCCACGAAACTACACTCACATATCTTCTTACCATAAAATTTTTAGAA
66 ATTAAGTTCCATTAATTTTCCACGAAACTACACTCACATATATTCTTACCATAAAATTTTCAGAA
* * *
2775253 TTTTTGGCTTAGCCAATTAGTACTGTATATTCTTTAAAGTCACCCCTATTTCATTGCTCAACATC
131 TTTTTAGCTTAGCCAATTAGTACAGTATATTCTTTAAAGTCACCCCTATTTCACTGCTCAACATC
* * *
2775318 TCTGACCTCTCTTCACTAAAAATGAATTATTTCATTGTACAGAATTCAGATGATATTTCCGTTTA
196 TCTGACCTCTCTTCACTAAAAATAAATTATCTCATTGTACAGAATTCAGATGATATTTCCGTGTA
2775383 TTTAATTTGAAAATAGACTCATTAAGG
261 TTTAATTTGAAAATAGACTCATTAAGG
* *
2775410 ATTCCAAGCTGTCTAGTCGAGTTATAGTCACTAAATTATTTTTATCCAGAGCTACAGAGCTCCAA
1 ATTCAAAGCTGTCTAGTCGAGTTACAGTCACTAAATTATTTTTATCCAGAGCTACAGAGCTCCAA
* * * *
2775475 ATTAAGTTTCGTTAATTTTCTC-CGAAACTAGACTCACATATATTCTTACCATAATATTTTCAGA
66 ATTAAGTTCCATTAATTTTC-CACGAAACTACACTCACATATATTCTTACCATAAAATTTTCAGA
* *
2775539 ATTTTTAGCTTATCCAATTAGTACAGTTTATTCTTTAAAGTCACCCCTATTTCACTGCTCAACAT
130 ATTTTTAGCTTAGCCAATTAGTACAGTATATTCTTTAAAGTCACCCCTATTTCACTGCTCAACAT
* *
2775604 CTCTGGCCTCTCTTCACTAAAAATAAATTATCTCATTGTACAGAATTTAGATGATATTTCCGTGT
195 CTCTGACCTCTCTTCACTAAAAATAAATTATCTCATTGTACAGAATTCAGATGATATTTCCGTGT
**
2775669 ATTTCTTTTGAAAATAGACTCATTAA
260 ATTTAATTTGAAAATAGACTCATTAA
2775695 ATATTCTAAG
Statistics
Matches: 263, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
287 262 1.00
288 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (287 bp):
ATTCAAAGCTGTCTAGTCGAGTTACAGTCACTAAATTATTTTTATCCAGAGCTACAGAGCTCCAA
ATTAAGTTCCATTAATTTTCCACGAAACTACACTCACATATATTCTTACCATAAAATTTTCAGAA
TTTTTAGCTTAGCCAATTAGTACAGTATATTCTTTAAAGTCACCCCTATTTCACTGCTCAACATC
TCTGACCTCTCTTCACTAAAAATAAATTATCTCATTGTACAGAATTCAGATGATATTTCCGTGTA
TTTAATTTGAAAATAGACTCATTAAGG
Found at i:2775998 original size:16 final size:16
Alignment explanation
Indices: 2775977--2776008 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2775967 GTTTCGTTGC
*
2775977 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
2775993 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
2776009 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:2776294 original size:51 final size:51
Alignment explanation
Indices: 2776226--2776422 Score: 213
Period size: 51 Copynumber: 3.9 Consensus size: 51
2776216 ATTAATGATA
* *
2776226 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATGACTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATGACTAT
* * *
2776277 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGA--TTGAAGCTAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATG-A-CTAT
* * * * * * *
2776328 TCGGTACGCATAGTAGCCTGCACATACTACTACAAATGCGACCTATCA-T-T
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATGACTAT
* *
2776378 CTGGTACACATAGTAGCCGGCACATAGTACTACACACGTGACCAT
1 CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
2776423 CACTTTCACT
Statistics
Matches: 118, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
49 4 0.03
50 37 0.31
51 75 0.64
53 1 0.01
54 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (51 bp):
CCGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACCATGACTAT
Found at i:2776401 original size:101 final size:102
Alignment explanation
Indices: 2776234--2776418 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 102
2776224 TACCGGTTCA
* * * * * *
2776234 CATAGTAGCCTGCACATAGTACTACACATGTGACCATGACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATACTACTACAAATGCGACCATCACTATCCGATACACATAGTAGCCGGCA
2776299 CATAGTACTACACACGTGATTGAAGCTATTCGGTACG
66 CATAGTACTACACACGTGATTGAAGCTATTCGGTACG
* *
2776336 CATAGTAGCCTGCACATACTACTACAAATGCGACCTATCA-T-TCTGGTACACATAGTAGCCGGC
1 CATAGTAGCCTGCACATACTACTACAAATGCGACC-ATCACTATCCGATACACATAGTAGCCGGC
2776399 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
2776419 CCATCACTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
101 38 0.51
102 33 0.45
103 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATACTACTACAAATGCGACCATCACTATCCGATACACATAGTAGCCGGCA
CATAGTACTACACACGTGATTGAAGCTATTCGGTACG
Found at i:2784315 original size:25 final size:25
Alignment explanation
Indices: 2784281--2784346 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
2784271 GCTCTGTGCC
* * **
2784281 TAGCAAGCTTTATGCTGGTGAATTA
1 TAGCAGGCTTTATGCCGGTGAACCA
* *
2784306 TAGCAGGCTTCATGCCGGTGTACCA
1 TAGCAGGCTTTATGCCGGTGAACCA
*
2784331 TATCAGGCTTTATGCC
1 TAGCAGGCTTTATGCC
2784347 TAGCAGGCTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (25 bp):
TAGCAGGCTTTATGCCGGTGAACCA
Found at i:2784365 original size:41 final size:41
Alignment explanation
Indices: 2784320--2784398 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
2784310 AGGCTTCATG
*
2784320 CCGGTGTACCATA-TCAGGCTTTATGCCTAGCAGGCTTTGCA
1 CCGGTGTACCATATTCA-GCTTTATGCCTAGAAGGCTTTGCA
* *
2784361 CCGGTGTATCATATTTAGCTTTATGCCTAGAAGGCTTT
1 CCGGTGTACCATATTCAGCTTTATGCCTAGAAGGCTTT
2784399 ATACCGATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
CCGGTGTACCATATTCAGCTTTATGCCTAGAAGGCTTTGCA
Found at i:2784422 original size:41 final size:41
Alignment explanation
Indices: 2784337--2784425 Score: 106
Period size: 41 Copynumber: 2.2 Consensus size: 41
2784327 ACCATATCAG
* * * * *
2784337 GCTTTATGCCTAGCAGGCTTTGCACCGGTGTATCATATTTA
1 GCTTTATGCCTAGAAGGCTTTACACCGATGTATCATAATAA
* **
2784378 GCTTTATGCCTAGAAGGCTTTATACCGATGTATTTTAATAA
1 GCTTTATGCCTAGAAGGCTTTACACCGATGTATCATAATAA
2784419 GCTTTAT
1 GCTTTAT
2784426 ACCTCACAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (41 bp):
GCTTTATGCCTAGAAGGCTTTACACCGATGTATCATAATAA
Found at i:2792498 original size:16 final size:16
Alignment explanation
Indices: 2792477--2792508 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2792467 CAGTGAGTTA
*
2792477 TAGCAGGCTTTATGCC
1 TAGCAGGCTTCATGCC
2792493 TAGCAGGCTTCATGCC
1 TAGCAGGCTTCATGCC
2792509 GGTGTACCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (16 bp):
TAGCAGGCTTCATGCC
Found at i:2792561 original size:41 final size:41
Alignment explanation
Indices: 2792441--2792596 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 41
2792431 GTGATATTCG
* * * * *
2792441 GGCTCTATGCCTAGCAGGCTTTATGCCAGTG-AGTTATAGCA
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTA-TCATATCA
*
2792482 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTACCATATCA
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTATCATATCA
* **
2792523 GGCTTTATGCCTAGTAGGCTTCATGCCGGTGTATCATATGT
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTATCATATCA
* * * *
2792564 GGCTTTGTG-CTAGAAGGCTTTATGCCGATGTAT
1 GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTAT
2792597 TTTCATAAGC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 21 0.21
41 78 0.78
42 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (41 bp):
GGCTTTATGCCTAGCAGGCTTCATGCCGGTGTATCATATCA
Found at i:2793517 original size:2 final size:2
Alignment explanation
Indices: 2793510--2793534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2793500 ATTGAAAGTT
2793510 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2793535 GTTATGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2795207 original size:12 final size:10
Alignment explanation
Indices: 2795177--2795228 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
2795167 AATATGAACA
*
2795177 TGATGAATTT
1 TGATTAATTT
*
2795187 TAATTAATTT
1 TGATTAATTT
2795197 TGTAGTTAATTT
1 TG-A-TTAATTT
2795209 TGATTAATTT
1 TGATTAATTT
2795219 TGATT-ATTT
1 TGATTAATTT
2795228 T
1 T
2795229 CAACAGATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 5 0.14
10 21 0.57
11 2 0.05
12 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (10 bp):
TGATTAATTT
Found at i:2798560 original size:23 final size:23
Alignment explanation
Indices: 2798530--2798576 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2798520 AAAGTAGACA
*
2798530 AAAAATTTTC-TCATAAAAGGAAC
1 AAAAATTTTCTTCA-AAAAGAAAC
2798553 AAAAATTTTCTTCAAAAAGAAAC
1 AAAAATTTTCTTCAAAAAGAAAC
2798576 A
1 A
2798577 CGCGTGGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (23 bp):
AAAAATTTTCTTCAAAAAGAAAC
Found at i:2803241 original size:18 final size:18
Alignment explanation
Indices: 2803218--2803253 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2803208 ATACATGCCT
2803218 TATATTGAGCTTATGAAA
1 TATATTGAGCTTATGAAA
2803236 TATATTGAGCTTATGAAA
1 TATATTGAGCTTATGAAA
2803254 CCTAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
TATATTGAGCTTATGAAA
Found at i:2804351 original size:25 final size:25
Alignment explanation
Indices: 2804304--2804354 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2804294 GAGTTCAATA
*
2804304 ATGAAACATATAATTTTAGCATATC
1 ATGAAACATATAATTTTAACATATC
*
2804329 ATGAAACATGT-ATTTGTAACATATC
1 ATGAAACATATAATTT-TAACATATC
2804354 A
1 A
2804355 AATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (25 bp):
ATGAAACATATAATTTTAACATATC
Found at i:2804609 original size:26 final size:26
Alignment explanation
Indices: 2804565--2804685 Score: 179
Period size: 26 Copynumber: 4.7 Consensus size: 26
2804555 TAACAGTATA
* * *
2804565 TGCTCACACAAGTTGTGAAATGGGCC
1 TGCTCACACGAGCTATGAAATGGGCC
*
2804591 TGCTCAAACGAGCTATGAAATGGGCC
1 TGCTCACACGAGCTATGAAATGGGCC
2804617 TGCTCACACGAGCTATGAAATGGGCC
1 TGCTCACACGAGCTATGAAATGGGCC
* * *
2804643 TGCTCACACGAGATATTAAATAGGCC
1 TGCTCACACGAGCTATGAAATGGGCC
2804669 TGCTCACACGAGCTATG
1 TGCTCACACGAGCTATG
2804686 GGTTGGGATG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 85 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAATGGGCC
Found at i:2811923 original size:44 final size:45
Alignment explanation
Indices: 2811843--2811947 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 45
2811833 TAACGGTAGA
* *
2811843 AGTAACAGTAACAGTAATAGTATTCAACACATAAAGTGTTGAATC
1 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGTCGAATC
* ** * *
2811888 TGTAACAGTAATGGTAA-AGTATTCGATACACAAAGTGTCGAATC
1 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGTCGAATC
2811932 AGTAACAGTAACAGTA
1 AGTAACAGTAACAGTA
2811948 GTCGGCATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 36 0.72
45 14 0.28
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (45 bp):
AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGTCGAATC
Found at i:2812191 original size:40 final size:40
Alignment explanation
Indices: 2812147--2812253 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
2812137 AATTCATTAC
* *
2812147 TTCAGTAA-TCTCACAGTTCAATGT-AGTACACATAACAATA
1 TTCAGTAACTC-CACAATTCAAT-TCAGTACACAAAACAATA
* *
2812187 TTCAGTAACTCCACAATTTAATTCAGTACTCAAAACAATA
1 TTCAGTAACTCCACAATTCAATTCAGTACACAAAACAATA
* * *
2812227 TTCAGT-ATTCCATAATTCAGTTCAGTA
1 TTCAGTAACTCCACAATTCAATTCAGTA
2812254 TCAGTCTCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
39 18 0.32
40 37 0.65
41 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (40 bp):
TTCAGTAACTCCACAATTCAATTCAGTACACAAAACAATA
Found at i:2812952 original size:11 final size:11
Alignment explanation
Indices: 2812938--2812962 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2812928 CCCTTTCTTC
2812938 TTTCTTTCCTT
1 TTTCTTTCCTT
2812949 TTTCTTTCCTT
1 TTTCTTTCCTT
2812960 TTT
1 TTT
2812963 GGGTCGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTCCTT
Found at i:2814841 original size:19 final size:19
Alignment explanation
Indices: 2814794--2814844 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2814784 ACTTGTTTTC
* *
2814794 TTTAATTTTGTTTAATTTAT
1 TTTAA-TTTGGTTAATTAAT
* *
2814814 GTTATTTTGGTTAATTAAT
1 TTTAATTTGGTTAATTAAT
2814833 TTTAATTTGGTT
1 TTTAATTTGGTT
2814845 CTTCGTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (19 bp):
TTTAATTTGGTTAATTAAT
Found at i:2815438 original size:20 final size:20
Alignment explanation
Indices: 2815377--2815444 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
2815367 CATCATACCG
*
2815377 AATTTCTAAG-TAATACCAA
1 AATTTCTAAGCAAATACCAA
* *** *
2815396 AATTTGTAA-CATGCACTAA
1 AATTTCTAAGCAAATACCAA
2815415 AATTTCTAAGCAAATACCAA
1 AATTTCTAAGCAAATACCAA
2815435 AATTTCTAAG
1 AATTTCTAAG
2815445 AGTATCTTGT
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (20 bp):
AATTTCTAAGCAAATACCAA
Found at i:2818029 original size:16 final size:16
Alignment explanation
Indices: 2818008--2818039 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2817998 ATTTTGTTGC
*
2818008 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
2818024 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
2818040 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:2818602 original size:30 final size:30
Alignment explanation
Indices: 2818566--2818622 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
2818556 GAAATTAAAC
2818566 TTTATTCCTTTTTCTTATGTTTTATGAAAA
1 TTTATTCCTTTTTCTTATGTTTTATGAAAA
2818596 TTTATTCCTTTTTCTTATGTTTTATGA
1 TTTATTCCTTTTTCTTATGTTTTATGA
2818623 CATGCTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTATTCCTTTTTCTTATGTTTTATGAAAA
Done.