Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 141 of 204
Found at i:42660219 original size:42 final size:42
Alignment explanation
Indices: 42660159--42660385 Score: 282
Period size: 42 Copynumber: 5.5 Consensus size: 42
42660149 NNNNNNNNNN
42660159 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
* * * *
42660201 ACTTTACGTCTAGTAGGCTTAATGCCAGTGAAATAATTTCAG
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
*
42660243 ACTTTACGTTTAGCAGGCTTAATGCCGGTGAAACAATATCAG
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
* *
42660285 ACTTTACGTCTAGAAGGCTTAATGCCGGTGAAAC-ATTTCAG
1 ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
* * * * *
42660326 ACTATATGTCCAGCAGGC-TAAGTGCCGGTG-TACTGA-ATCAG
1 ACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAAAC-AATATCAG
* *
42660367 GCTTTAAGTCTAGCAGGCT
1 ACTTTACGTCTAGCAGGCT
42660386 AAGTGCCAAT
Statistics
Matches: 159, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
40 5 0.03
41 46 0.29
42 108 0.68
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
ACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATATCAG
Found at i:42660950 original size:2 final size:2
Alignment explanation
Indices: 42660943--42660973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42660933 ATATTATTTC
42660943 TA TA TA 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 TA TA TA T
42660974 TTCATTATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42661696 original size:6 final size:6
Alignment explanation
Indices: 42661685--42661716 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
42661675 TCAAACAATA
42661685 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT AT
42661717 AACTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:42662466 original size:23 final size:22
Alignment explanation
Indices: 42662417--42662466 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
42662407 AATTTTAAAA
42662417 TAAAATAAAATTGAATCAAATT
1 TAAAATAAAATTGAATCAAATT
*
42662439 T-AAATAAATTATTTAATC-AATT
1 TAAAATAAA--ATTGAATCAAATT
42662461 TAAAAT
1 TAAAAT
42662467 TATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAATAAAATTGAATCAAATT
Found at i:42662478 original size:18 final size:18
Alignment explanation
Indices: 42662444--42662489 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
42662434 AAATTTAAAT
42662444 AAATTATT-TAATCAATTTA
1 AAATTATTATAA-CAA-TTA
42662463 AAATTATTATAA-AATTA
1 AAATTATTATAACAATTA
42662480 ATAATTATTA
1 A-AATTATTA
42662490 GAAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 8 0.32
20 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTATAACAATTA
Found at i:42664396 original size:28 final size:28
Alignment explanation
Indices: 42664356--42664421 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
42664346 AACATGGAAA
42664356 TAAACCCTAAGCTATAGAGAAGAAGAAC
1 TAAACCCTAAGCTATAGAGAAGAAGAAC
42664384 TAAACCCTAAGCTATAGAGAAGAAGAAC
1 TAAACCCTAAGCTATAGAGAAGAAGAAC
42664412 TAAACCCTAA
1 TAAACCCTAA
42664422 AAGATTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (28 bp):
TAAACCCTAAGCTATAGAGAAGAAGAAC
Found at i:42666497 original size:61 final size:63
Alignment explanation
Indices: 42666424--42666555 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 63
42666414 AAATCCTTGC
* * * * *
42666424 TCATTTGCAAATGAATTCATTTT-T-CATTTTTATTTTTATTTCCATTTT-GATAAAATCACAT
1 TCATTT-CAAATGAATTCATTTTCTCCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAA
* *
42666485 TCATTTCTAAATGATTTCATTTTCTCCATTTTCATTTTCATTTTCATTTTGGAGAAAACCACAA
1 TCATTTC-AAATGAATTCATTTTCTCCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAA
42666549 TCATTTC
1 TCATTTC
42666556 CTGAATGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
60 1 0.02
61 20 0.33
62 1 0.02
63 21 0.35
64 17 0.28
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (63 bp):
TCATTTCAAATGAATTCATTTTCTCCATTTTCATTTTCATTTCCATTTTGGAGAAAACCACAA
Found at i:42668255 original size:16 final size:16
Alignment explanation
Indices: 42668234--42668264 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42668224 TTAACTATTA
*
42668234 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
42668250 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
42668265 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:42672152 original size:31 final size:30
Alignment explanation
Indices: 42672117--42672184 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
42672107 ATTCTAAAAA
42672117 TAATA-TTATTTTAATAGTTTAATATTAAATT
1 TAATACTTATTTTAATA-TTTAATATT-AATT
**
42672148 TAATACTTATTTTAATATTTTTTATTAATT
1 TAATACTTATTTTAATATTTAATATTAATT
42672178 TAATACT
1 TAATACT
42672185 AAAGTGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 11 0.32
31 12 0.35
32 11 0.32
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
TAATACTTATTTTAATATTTAATATTAATT
Found at i:42675748 original size:22 final size:22
Alignment explanation
Indices: 42675718--42675760 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42675708 ACACCAAAAC
*
42675718 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
42675740 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
42675761 AGCGCCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:42675996 original size:43 final size:43
Alignment explanation
Indices: 42675938--42676019 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
42675928 CGCTTTAGTG
* **
42675938 GAAGCGTCACTAAAGACCCTGATCTTTAGCGGCATTTTTGGGA
1 GAAGCGCCACTAAAGACCAGGATCTTTAGCGGCATTTTTGGGA
* * * *
42675981 GAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTT
1 GAAGCGCCACTAAAGACCAGGATCTTTAGCGGCATTTTT
42676020 TTCTCAAACG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (43 bp):
GAAGCGCCACTAAAGACCAGGATCTTTAGCGGCATTTTTGGGA
Found at i:42676054 original size:43 final size:43
Alignment explanation
Indices: 42676024--42676295 Score: 264
Period size: 43 Copynumber: 6.3 Consensus size: 43
42676014 GTTTTTTTCT
* * *
42676024 CAAACGCCGC-AATAGACCCTGATCTATAGCGGCGTTTTGACCA
1 CAAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTCACCA
* * * * * *
42676067 CAAACGCC-ATGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCT
1 CAAACGCCGCT-AAAGACCCTGATCTTTAGCGGCGCTTTCACCA
* *
42676110 CAAACGCCGC-AATAGACCCTGATCTATAGCAGCGC-TTCGACCA
1 CAAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTC-ACCA
* * * *
42676153 CAAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCA
1 CAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCACCA
* * **
42676196 CAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCA
1 CAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCACCA
* * *
42676239 CAAACGCCGCTAAAGACCCTTATCTTTAGCGGCACTTTGACCA
1 CAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCACCA
* *
42676282 AAAACGCCACTAAA
1 CAAACGCCGCTAAA
42676296 AGCCAACACC
Statistics
Matches: 184, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
42 5 0.03
43 172 0.93
44 7 0.04
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (43 bp):
CAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTCACCA
Found at i:42676223 original size:129 final size:129
Alignment explanation
Indices: 42676045--42676295 Score: 319
Period size: 129 Copynumber: 1.9 Consensus size: 129
42676035 ATAGACCCTG
* * *
42676045 ATCTATAGCGGCGTTTTGACCACAAACGCCATGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCT
1 ATCTATAGCGGCGCTTTCACCACAAACGCCATGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCA
* *
42676110 CAAACGCCGC-AATAGACCCTGATCTATAGCAGCGCTTCGACCACAAACGCCACTAAAGAACCTA
66 CAAACGCCGCTAA-AGACCCTGATCTATAGCAGCACTTCGACCAAAAACGCCACTAAAGAACCTA
* * * * **
42676174 ATCTTTAGCGGCGCTTTCCCCACAAACGCCGCT-AAAG-ACCATGATCTTTAGTGGCGCTTTTTC
1 ATCTATAGCGGCGCTTTCACCACAAACGCC-ATGAAAGAACC-TAATCTTTAGTGGCGCTTTCCC
* * * *
42676237 CACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAA
64 CACAAACGCCGCTAAAGACCCTGATCTATAGCAGCACTTCGACCAAAAACGCCACTAAA
42676296 AGCCAACACC
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
128 3 0.03
129 98 0.94
130 3 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (129 bp):
ATCTATAGCGGCGCTTTCACCACAAACGCCATGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCA
CAAACGCCGCTAAAGACCCTGATCTATAGCAGCACTTCGACCAAAAACGCCACTAAAGAACCTA
Found at i:42676231 original size:86 final size:86
Alignment explanation
Indices: 42676024--42676276 Score: 348
Period size: 86 Copynumber: 2.9 Consensus size: 86
42676014 GTTTTTTTCT
*
42676024 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGTTTTGACCACAAACGCCA-TGAAAGAACCTA
1 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACT-AAAGAACCTA
* *
42676088 ATCTTTAGTGGCGCTTTCCCCT
65 ATCTTTAGCGGCGCTTTCCCCA
* *
42676110 CAAACGCCGCAATAGACCCTGATCTATAGCAGCGCTTCGACCACAAACGCCACTAAAGAACCTAA
1 CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAA
42676175 TCTTTAGCGGCGCTTTCCCCA
66 TCTTTAGCGGCGCTTTCCCCA
* * * ** * * *
42676196 CAAACGCCGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTT
1 CAAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTA
*
42676260 ATCTTTAGCGGCACTTT
65 ATCTTTAGCGGCGCTTT
42676277 GACCAAAAAC
Statistics
Matches: 149, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
86 146 0.98
87 3 0.02
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (86 bp):
CAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAA
TCTTTAGCGGCGCTTTCCCCA
Found at i:42676287 original size:86 final size:85
Alignment explanation
Indices: 42676025--42676416 Score: 300
Period size: 86 Copynumber: 4.6 Consensus size: 85
42676015 TTTTTTTCTC
* * * *
42676025 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGTTTTGACCACAAACGCCA-TGAAAGAACCTA
1 AAACGCCGCTAA-AGACCATGATCTTTAGTGGCGTTTT-TCCACAAACGCCACT-AAAGAACCTA
* * * **
42676088 ATCTTTAGTGGCGCTTTCCCCTC
63 ATCTTTAGCGGCACTTTCACCAA
* * ** ***
42676111 AAACGCCGC-AATAGACCCTGATCTATAGCAGCGCTTCGACCACAAACGCCACTAAAGAACCTAA
1 AAACGCCGCTAA-AGACCATGATCTTTAGTGGCG-TTTTTCCACAAACGCCACTAAAGAACCTAA
* * *
42676175 TCTTTAGCGGCGCTTTCCCCAC
64 TCTTTAGCGGCACTTTCACCAA
* * *
42676197 AAACGCCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTAT
1 AAACGCCGCTAAAGACCATGATCTTTAGTGGCG-TTTTTCCACAAACGCCACTAAAGAACCTAAT
*
42676262 CTTTAGCGGCACTTTGACCAA
65 CTTTAGCGGCACTTTCACCAA
* ** * * * *
42676283 AAACGCCACTAAA-AGCCAACACCTTTAGTGGCGTTTTT----TAA--CCACTAAAGACCCTTAT
1 AAACGCCGCTAAAGA-CCATGATCTTTAGTGGCGTTTTTCCACAAACGCCACTAAAGAACCTAAT
*
42676341 CTTTAGCGGCACTTTGACCAA
65 CTTTAGCGGCACTTTCACCAA
* * ** * ** *
42676362 AAACGCCACTAAAGGCCAACACCTTTAGTGGCGTTTTTTTAAAAACGCCACTAAA
1 AAACGCCGCTAAAGACCATGATCTTTAGTGGCGTTTTTCCACAAACGCCACTAAA
42676417 TTTGGCAGAT
Statistics
Matches: 268, Mismatches: 27, Indels: 23
0.84 0.08 0.07
Matches are distributed among these distances:
79 73 0.27
81 2 0.01
83 2 0.01
85 14 0.05
86 172 0.64
87 5 0.02
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (85 bp):
AAACGCCGCTAAAGACCATGATCTTTAGTGGCGTTTTTCCACAAACGCCACTAAAGAACCTAATC
TTTAGCGGCACTTTCACCAA
Found at i:42676309 original size:43 final size:43
Alignment explanation
Indices: 42676262--42676389 Score: 101
Period size: 43 Copynumber: 3.1 Consensus size: 43
42676252 AGACCCTTAT
42676262 CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACAC
1 CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACAC
* * *** *** *
42676305 CTTTAGTGGC-GTTT----TTTAA--CCACT-AAAGACCCTTAT
1 CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAG-CCAACAC
*
42676341 CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAGGCCAACAC
1 CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACAC
42676384 CTTTAG
1 CTTTAG
42676390 TGGCGTTTTT
Statistics
Matches: 57, Mismatches: 19, Indels: 18
0.61 0.20 0.19
Matches are distributed among these distances:
35 4 0.07
36 17 0.30
37 3 0.05
38 2 0.04
41 2 0.04
42 3 0.05
43 23 0.40
44 3 0.05
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACAC
Found at i:42676380 original size:79 final size:79
Alignment explanation
Indices: 42676248--42676400 Score: 297
Period size: 79 Copynumber: 1.9 Consensus size: 79
42676238 ACAAACGCCG
42676248 CTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACACCTTTAGTG
1 CTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACACCTTTAGTG
42676313 GCGTTTTTTAACCA
66 GCGTTTTTTAACCA
*
42676327 CTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAAGGCCAACACCTTTAGTG
1 CTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACACCTTTAGTG
42676392 GCGTTTTTT
66 GCGTTTTTT
42676401 TAAAAACGCC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.27
Consensus pattern (79 bp):
CTAAAGACCCTTATCTTTAGCGGCACTTTGACCAAAAACGCCACTAAAAGCCAACACCTTTAGTG
GCGTTTTTTAACCA
Found at i:42676809 original size:42 final size:42
Alignment explanation
Indices: 42676723--42676815 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
42676713 TTTGACGCTG
* **
42676723 CTCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCACTTTAGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCACTGCAGC
* * * * *
42676765 CTCTGTTTCCCTCGCTGTAGCCTGTACTTCTCTCACTGCCGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCACTGCAGC
42676807 CTCTGCTTC
1 CTCTGCTTC
42676816 TCTTGCTACC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCACTGCAGC
Found at i:42676818 original size:21 final size:21
Alignment explanation
Indices: 42676723--42676815 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
42676713 TTTGACGCTG
*
42676723 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCACTGCAGC
**
42676744 CTCTGCTTCCCTCACTTTAGC
1 CTCTGCTTCCCTCACTGCAGC
* * *
42676765 CTCTGTTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCACTGCAGC
* * * *
42676786 CTGTACTTCTCTCACTGCCGC
1 CTCTGCTTCCCTCACTGCAGC
42676807 CTCTGCTTC
1 CTCTGCTTC
42676816 TCTTGCTACC
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTGCAGC
Found at i:42676900 original size:66 final size:66
Alignment explanation
Indices: 42676806--42676971 Score: 192
Period size: 66 Copynumber: 2.5 Consensus size: 66
42676796 CTCACTGCCG
* * * *
42676806 CCTCTGCTTCTCTTGCTACCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
42676869 GAA
64 GAA
* * *
42676872 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTTAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
42676937 A
66 A
* * * * *
42676938 CATCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
42676972 TTGTGTAATT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 1 0.01
66 80 0.94
67 4 0.05
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:42682436 original size:9 final size:9
Alignment explanation
Indices: 42682400--42682584 Score: 80
Period size: 9 Copynumber: 22.0 Consensus size: 9
42682390 AATTGCACGA
42682400 GTAAGTTAT
1 GTAAGTTAT
*
42682409 GT-A-TTGT
1 GTAAGTTAT
*
42682416 GTAAGCTAT
1 GTAAGTTAT
*
42682425 GTAAGTTGT
1 GTAAGTTAT
42682434 GT-A-TTAT
1 GTAAGTTAT
42682441 GTAAGTTAT
1 GTAAGTTAT
42682450 -T-A-TTAT
1 GTAAGTTAT
42682456 GCTTTAAGTTAT
1 G---TAAGTTAT
*
42682468 GTAAGTAAT
1 GTAAGTTAT
42682477 GT-A-TTAT
1 GTAAGTTAT
*
42682484 GTAAGTTGT
1 GTAAGTTAT
*
42682493 GT-A-TAAT
1 GTAAGTTAT
*
42682500 GTTAGTTAT
1 GTAAGTTAT
**
42682509 CAAAGTTAT
1 GTAAGTTAT
42682518 GT-A-TTAT
1 GTAAGTTAT
***
42682525 GTGTTTCTAT
1 GTAAGT-TAT
*
42682535 TTAAGTTAT
1 GTAAGTTAT
*
42682544 GTAAGTTGT
1 GTAAGTTAT
42682553 GT-A-TTAT
1 GTAAGTTAT
*
42682560 GTAAGTTGT
1 GTAAGTTAT
42682569 GT-A-TTAT
1 GTAAGTTAT
42682576 GTAAGTTAT
1 GTAAGTTAT
42682585 TAAAAATTGA
Statistics
Matches: 128, Mismatches: 27, Indels: 42
0.65 0.14 0.21
Matches are distributed among these distances:
6 4 0.03
7 36 0.28
8 14 0.11
9 62 0.48
10 6 0.05
11 1 0.01
12 5 0.04
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.49
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42682441 original size:16 final size:16
Alignment explanation
Indices: 42682422--42682584 Score: 89
Period size: 16 Copynumber: 10.8 Consensus size: 16
42682412 TTGTGTAAGC
*
42682422 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
42682438 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
*
42682453 TATGCT---TTAAG--T
1 TATG-TAAGTTATGTAT
*
42682465 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
42682481 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
42682497 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
*
42682515 TATGT-A-TTATGTGT
1 TATGTAAGTTATGTAT
* * *
42682529 T-TCT-ATTTAAG--T
1 TATGTAAGTTATGTAT
*
42682541 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
42682557 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
42682573 TATGTAAGTTAT
1 TATGTAAGTTAT
42682585 TAAAAATTGA
Statistics
Matches: 111, Mismatches: 22, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
11 1 0.01
12 7 0.06
13 8 0.07
14 13 0.12
15 7 0.06
16 68 0.61
17 2 0.02
18 5 0.05
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.50
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:42682742 original size:120 final size:121
Alignment explanation
Indices: 42682587--42682863 Score: 495
Period size: 120 Copynumber: 2.3 Consensus size: 121
42682577 TAAGTTATTA
* *
42682587 AAAATTGAAATGTAGGATATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
*
42682652 AATATTTAAAAATAACA-TTACAATTATTTTTAAAATTATAAAATTCATT-TCTAAT
66 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGAC-AAT
42682707 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
*
42682772 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTTATTGACAAT
66 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
42682828 AAAATTGAAATATAGGTTATATATCCATACCATATA
1 AAAATTGAAATATAGGTTATATATCCATACCATATA
42682864 GCTAAATTTT
Statistics
Matches: 151, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
120 80 0.53
121 70 0.46
122 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (121 bp):
AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
Found at i:42682883 original size:2 final size:2
Alignment explanation
Indices: 42682876--42682900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42682866 TAAATTTTTA
42682876 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 A
42682901 AAGTTTAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42682927 original size:18 final size:18
Alignment explanation
Indices: 42682904--42682992 Score: 92
Period size: 18 Copynumber: 4.8 Consensus size: 18
42682894 ATATATAAAG
42682904 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
42682922 TTTAAGTAATGTAAGTTATAA
1 TTTAAGTAATGTAA--TAT-A
**
42682943 TTTTTTGTAA-GTAATATA
1 -TTTAAGTAATGTAATATA
*
42682961 TTTAAGTAATGTAACATA
1 TTTAAGTAATGTAATATA
*
42682979 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
42682993 GTAAGTAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 11 0.19
18 30 0.51
19 3 0.05
20 3 0.05
21 5 0.08
22 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:42682973 original size:22 final size:22
Alignment explanation
Indices: 42682909--42683001 Score: 74
Period size: 22 Copynumber: 4.4 Consensus size: 22
42682899 TAAAGTTTAA
42682909 GTAATGTAATATATTTAAGTAAT
1 GTAA-GTAATATATTTAAGTAAT
* *
42682932 GTAAGTTATA-ATTT---T-TT
1 GTAAGTAATATATTTAAGTAAT
42682949 GTAAGTAATATATTTAAGTAAT
1 GTAAGTAATATATTTAAGTAAT
* *
42682971 GTAA--CATATTTTAGTAAGTAAT
1 GTAAGTAATATATT--TAAGTAAT
42682993 GTAAGTAAT
1 GTAAGTAAT
42683002 GTAATATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
17 10 0.19
18 5 0.09
20 6 0.11
21 5 0.09
22 22 0.41
23 4 0.07
24 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (22 bp):
GTAAGTAATATATTTAAGTAAT
Found at i:42683049 original size:13 final size:13
Alignment explanation
Indices: 42683033--42683124 Score: 80
Period size: 13 Copynumber: 6.9 Consensus size: 13
42683023 GTAAGTCATG
42683033 TATTTAAGTAATA
1 TATTTAAGTAATA
*
42683046 TATTTAATTCAAT-
1 TATTTAAGT-AATA
* * *
42683059 TCTAGTAAGTAATG
1 TAT-TTAAGTAATA
42683073 TATTTAAGTAATA
1 TATTTAAGTAATA
42683086 TATTTAAGTAA-A
1 TATTTAAGTAATA
* *
42683098 TTTTAGTAATTAATA
1 TATT--TAAGTAATA
42683113 TATTTAAGTAAT
1 TATTTAAGTAAT
42683125 GTAAGTTATA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
12 4 0.06
13 39 0.63
14 15 0.24
15 4 0.06
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:42683074 original size:40 final size:40
Alignment explanation
Indices: 42682978--42683124 Score: 181
Period size: 40 Copynumber: 3.7 Consensus size: 40
42682968 AATGTAACAT
** * *
42682978 ATTTTAGTAAGTAATGTAAGTAATGTAATATA--TACTTTA
1 ATTTTAGTAAGTAATGTATTTAA-GTAATATATTTAATTAA
* *
42683017 ATTTTAGTAAGTCATGTATTTAAGTAATATATTTAATTCA
1 ATTTTAGTAAGTAATGTATTTAAGTAATATATTTAATTAA
* *
42683057 ATTCTAGTAAGTAATGTATTTAAGTAATATATTTAAGTAA
1 ATTTTAGTAAGTAATGTATTTAAGTAATATATTTAATTAA
* *
42683097 ATTTTAGTAATTAATATATTTAAGTAAT
1 ATTTTAGTAAGTAATGTATTTAAGTAAT
42683125 GTAAGTTATA
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
38 8 0.09
39 20 0.21
40 66 0.70
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (40 bp):
ATTTTAGTAAGTAATGTATTTAAGTAATATATTTAATTAA
Found at i:42683190 original size:11 final size:11
Alignment explanation
Indices: 42683159--42683191 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
42683149 ATATATTAAT
42683159 AATTCATTGAC
1 AATTCATTGAC
42683170 -ATTCATTGAC
1 AATTCATTGAC
*
42683180 AATTCACTGAC
1 AATTCATTGAC
42683191 A
1 A
42683192 GTCAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.33
Consensus pattern (11 bp):
AATTCATTGAC
Found at i:42684919 original size:21 final size:20
Alignment explanation
Indices: 42684889--42684929 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
42684879 CCTAACTCCT
*
42684889 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
42684910 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
42684930 TAAATCCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:42685146 original size:25 final size:24
Alignment explanation
Indices: 42685094--42685148 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
42685084 ATTATATATG
* * *
42685094 AAATTATTTAATATATAAATTTAT
1 AAATTATTTAAAATATAAATTAAA
42685118 AAATATATTTAAAATATAAATTAAA
1 AAAT-TATTTAAAATATAAATTAAA
42685143 AAATTA
1 AAATTA
42685149 ATCTAAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTATTTAAAATATAAATTAAA
Found at i:42685241 original size:21 final size:22
Alignment explanation
Indices: 42685199--42685244 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
42685189 ATCCTAAATT
*
42685199 AACCATATATATATATACTCTA
1 AACCATATATATATAAACTCTA
42685221 AACCATATATAT-TAAACTCTA
1 AACCATATATATATAAACTCTA
42685242 AAC
1 AAC
42685245 TATAATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.33
Consensus pattern (22 bp):
AACCATATATATATAAACTCTA
Found at i:42685900 original size:41 final size:41
Alignment explanation
Indices: 42685840--42686120 Score: 341
Period size: 41 Copynumber: 6.8 Consensus size: 41
42685830 TTATTATTAC
* * *
42685840 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAA
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
* ** *
42685881 TACCGGCGCTTCTTTAAAAACGCCGCTAAAGATCTGAGCAT
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
* ** *
42685922 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGATCTGAGCAT
1 TAGCGGCGCTTCTTTAAAAACGCCGCT-AAAGGCCAGAGCAT
* * *
42685964 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
* *
42686005 TAGCGGCGCTT-TTTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGCCAGAGCAT
42686046 TAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGCCAGAGCAT
* * * *
42686087 TAGCGGCGTTTATTCAAAAACGTCGCTAAAGGCC
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCC
42686121 CCCAAAAATC
Statistics
Matches: 218, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
40 2 0.01
41 173 0.79
42 43 0.20
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (41 bp):
TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
Found at i:42686062 original size:124 final size:123
Alignment explanation
Indices: 42685840--42686116 Score: 378
Period size: 124 Copynumber: 2.2 Consensus size: 123
42685830 TTATTATTAC
* * * *
42685840 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTTCTTTAAAAACGCC
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAAGACACAGCAATACCGGCGCTTCTTTAAAAACGCC
* * *
42685905 GCTAAAGATCTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGATCTGAGCAT
66 GCTAAAGATCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCT-AAAGACCAGAGCAT
* * * *
42685964 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTT-TTTCAAAAACGC
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAAAGACACAGCAATACCGGCGCTTCTTT-AAAAACGC
* *
42686028 CGCTAAAAGA-CAGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGCAT
65 CGCT-AAAGATCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCAT
* *
42686087 TAGCGGCGTTTATTCAAAAACGTCGCTAAA
1 TAGCGGCGCTTATTCAAAAACGCCGCTAAA
42686117 GGCCCCCAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
123 41 0.30
124 90 0.66
125 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (123 bp):
TAGCGGCGCTTATTCAAAAACGCCGCTAAAAGACACAGCAATACCGGCGCTTCTTTAAAAACGCC
GCTAAAGATCAGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCAT
Found at i:42686083 original size:82 final size:82
Alignment explanation
Indices: 42685840--42686116 Score: 380
Period size: 82 Copynumber: 3.4 Consensus size: 82
42685830 TTATTATTAC
* * * * * *
42685840 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTTCTTT-AAAAACGC
1 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTT-TTTCAAAAACGC
*
42685904 CGCTAAA-GATCTGAGCAT
65 CGCTAAAGGA-CAGAGCAT
* * *
42685922 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGATCTGAGCATTAGCGGCGCTTCTTCAAAAACGC
1 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGA-CAGAGCATTAGCGGCGCTTTTTCAAAAACGC
*
42685987 CGCTAAAAGACAGAGCAT
65 CGCTAAAGGACAGAGCAT
42686005 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTTCAAAAACGCC
1 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTTCAAAAACGCC
*
42686070 GCTAAAGGCCAGAGCAT
66 GCTAAAGGACAGAGCAT
*
42686087 TAGCGGCG-TTTATTCAAAAACGTCGCTAAA
1 TAGCGGCGCTTT-TTCAAAAACGCCGCTAAA
42686117 GGCCCCCAAA
Statistics
Matches: 175, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
81 3 0.02
82 101 0.58
83 69 0.39
84 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (82 bp):
TAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGACAGAGCATTAGCGGCGCTTTTTCAAAAACGCC
GCTAAAGGACAGAGCAT
Found at i:42686281 original size:40 final size:40
Alignment explanation
Indices: 42686157--42686293 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 40
42686147 TGGCTTAGGC
** *
42686157 TTTTT-GCGGCGCTTTTCAGAAAA-CGCCGTTAATGCT-TA
1 TTTTTAGCGGCG-TTTTTTGAAAAGCGCCGCTAATGCTCTA
* *
42686195 TTTTTAGCGGCGTTTTTGGATAAGCGCCGCTAATGCTCTA
1 TTTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTA
** * *
42686235 CCTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTA
* *
42686275 TTTTTAGTGGCATTTTTTG
1 TTTTTAGCGGCGTTTTTTG
42686294 TCCAAACGCC
Statistics
Matches: 81, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 13 0.16
39 18 0.22
40 50 0.62
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTGAAAAGCGCCGCTAATGCTCTA
Found at i:42686304 original size:41 final size:39
Alignment explanation
Indices: 42686177--42686308 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 39
42686167 GCTTTTCAGA
* *
42686177 AAACGCCGTTAATGCT-TATTTTTAGCGGCGTTTTTGGAT
1 AAACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTTG-T
* **
42686216 AAGCGCCGCTAATGCTCTACCTTTAGCGGCGTTTTTT-T
1 AAACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTTGT
* * *
42686254 AAAAGCGCCGCTAATGCTCGATTTTTAGTGGCATTTTTTGT
1 -AAA-CGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTTGT
42686295 CCAAACGCCGCTAA
1 --AAACGCCGCTAA
42686309 AAACGCCGCT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 16 0.21
40 46 0.61
41 10 0.13
42 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (39 bp):
AAACGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTTGT
Found at i:42686314 original size:12 final size:12
Alignment explanation
Indices: 42686297--42686322 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42686287 TTTTTTGTCC
42686297 AAACGCCGCTAA
1 AAACGCCGCTAA
42686309 AAACGCCGCTAA
1 AAACGCCGCTAA
42686321 AA
1 AA
42686323 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:42697104 original size:19 final size:18
Alignment explanation
Indices: 42697069--42697120 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
42697059 TTTCTCATTA
42697069 AAAAATATATAAAAAATCAT
1 AAAAATAT-T-AAAAATCAT
*
42697089 TAAAATGATTAAAAATCAT
1 AAAAAT-ATTAAAAATCAT
42697108 AAAAATATTAAAA
1 AAAAATATTAAAA
42697121 TTTATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 7 0.24
19 14 0.48
20 6 0.21
21 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATATTAAAAATCAT
Found at i:42697110 original size:18 final size:19
Alignment explanation
Indices: 42697063--42697120 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 19
42697053 TTATAGTTTC
42697063 TCATTAAAAAATATATAAAAAA
1 TCATT-AAAAATAT-T-AAAAA
42697085 TCATT-AAAATGATTAAAAA
1 TCATTAAAAAT-ATTAAAAA
42697104 TCA-TAAAAATATTAAAA
1 TCATTAAAAATATTAAAA
42697121 TTTATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.24
19 13 0.38
20 6 0.18
21 2 0.06
22 5 0.15
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (19 bp):
TCATTAAAAATATTAAAAA
Found at i:42697137 original size:28 final size:28
Alignment explanation
Indices: 42697106--42697204 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
42697096 ATTAAAAATC
* * *
42697106 ATAAAAA-TATTAAAATTTATATAATATT
1 ATAAAAATTATAAAAACTTAT-CAATATT
42697134 ATAAAAATTATAAAAACTTATCAATATT
1 ATAAAAATTATAAAAACTTATCAATATT
* *
42697162 ATAAAAGTTATAACAAA-TTAT-AATTTT
1 ATAAAAATTATAA-AAACTTATCAATATT
*
42697189 TTATAAAATTAATAAA
1 ATA-AAAATT-ATAAA
42697205 CATATTTAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.12
28 35 0.58
29 18 0.30
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (28 bp):
ATAAAAATTATAAAAACTTATCAATATT
Found at i:42697144 original size:19 final size:18
Alignment explanation
Indices: 42697132--42697184 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
42697122 TTATATAATA
42697132 TTATAAAAATTATAAAAAC
1 TTATAAAAATTAT-AAAAC
* * *
42697151 TTATCAATATTATAAAAG
1 TTATAAAAATTATAAAAC
42697169 TTATAACAAATTATAA
1 TTATAA-AAATTATAA
42697185 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (18 bp):
TTATAAAAATTATAAAAC
Found at i:42697145 original size:9 final size:9
Alignment explanation
Indices: 42697065--42697184 Score: 82
Period size: 9 Copynumber: 12.8 Consensus size: 9
42697055 ATAGTTTCTC
42697065 ATTA-AAAA
1 ATTATAAAA
42697073 ATATATAAAAA
1 AT-TAT-AAAA
* *
42697084 ATCATTAAA
1 ATTATAAAA
*
42697093 ATGATTAAAA
1 ATTA-TAAAA
*
42697103 ATCATAAAA
1 ATTATAAAA
42697112 A-TATTAAAA
1 ATTA-TAAAA
* *
42697121 TTTATATAAT
1 ATTATA-AAA
42697131 ATTATAAAA
1 ATTATAAAA
42697140 ATTATAAAA
1 ATTATAAAA
* *
42697149 ACTTATCAAT
1 A-TTATAAAA
42697159 ATTATAAAA
1 ATTATAAAA
*
42697168 GTTATAACAA
1 ATTATAA-AA
42697178 ATTATAA
1 ATTATAA
42697185 TTTTTTATAA
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
8 3 0.03
9 45 0.52
10 33 0.38
11 6 0.07
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (9 bp):
ATTATAAAA
Found at i:42698099 original size:9 final size:9
Alignment explanation
Indices: 42698056--42698358 Score: 134
Period size: 9 Copynumber: 31.6 Consensus size: 9
42698046 TATATTTTTA
42698056 TTTATAATT
1 TTTATAATT
*
42698065 TATTAGAACTT
1 T-TTATAA-TT
* *
42698076 ATTATGATTT
1 TTTAT-AATT
*
42698086 TTTATAAGT
1 TTTATAATT
*
42698095 TTTATAAGTA
1 TTTATAA-TT
* *
42698105 ATGATAATT
1 TTTATAATT
42698114 TTTATAATT
1 TTTATAATT
42698123 TGTATGATAATT
1 T-T-T-ATAATT
42698135 TATTATAACTT
1 T-TTATAA-TT
*
42698146 TTTAGAATT
1 TTTATAATT
*
42698155 TTTATAAGCT
1 TTTATAA-TT
*
42698165 TTTATAATA
1 TTTATAATT
42698174 TTTATAAGTT
1 TTTATAA-TT
*
42698184 TTGATGAATT
1 TTTAT-AATT
*
42698194 CTTTATAAGT
1 -TTTATAATT
42698204 TTTA-AATT
1 TTTATAATT
42698212 TTT-TAAATAT
1 TTTAT-AAT-T
42698222 GTTT-TAA-T
1 -TTTATAATT
*
42698230 TTTATTATT
1 TTTATAATT
*
42698239 GTTATAATTATT
1 -TT-T-ATAATT
42698251 TTTATAATT
1 TTTATAATT
*
42698260 TATTAGAA-T
1 T-TTATAATT
*
42698269 TTTATAATG
1 TTTATAATT
*
42698278 TTTATAAGT
1 TTTATAATT
42698287 TTTATGAATTTT
1 TTTAT-AA--TT
42698299 TTTATAATT
1 TTTATAATT
42698308 TTTATAAGTT
1 TTTATAA-TT
* *
42698318 TATATAAAT
1 TTTATAATT
42698327 TTT-TAATAT
1 TTTATAAT-T
* *
42698336 TTTAT-GTAC
1 TTTATAAT-T
42698345 TTTATAATT
1 TTTATAATT
42698354 TTTAT
1 TTTAT
42698359 GAAAAATATA
Statistics
Matches: 223, Mismatches: 41, Indels: 60
0.69 0.13 0.19
Matches are distributed among these distances:
7 3 0.01
8 17 0.08
9 90 0.40
10 70 0.31
11 23 0.10
12 20 0.09
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.58
Consensus pattern (9 bp):
TTTATAATT
Found at i:42698200 original size:21 final size:19
Alignment explanation
Indices: 42698084--42698214 Score: 106
Period size: 19 Copynumber: 6.7 Consensus size: 19
42698074 TTATTATGAT
* *
42698084 TTTTTATAAGTTTTATAAG
1 TTTTGATAATTTTTATAAG
** *
42698103 TAATGATAATTTTTATAAT
1 TTTTGATAATTTTTATAAG
*
42698122 TTGTATGATAATTTATTATAAC
1 TT-T-TGATAATTT-TTATAAG
* *
42698144 TTTTTAGAATTTTTATAAG
1 TTTTGATAATTTTTATAAG
*
42698163 CTTTT-ATAATATTTATAAG
1 -TTTTGATAATTTTTATAAG
42698182 TTTTGATGAATTCTTTATAAG
1 TTTTGAT-AATT-TTTATAAG
42698203 TTTT-A-AATTTTT
1 TTTTGATAATTTTT
42698215 TAAATATGTT
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
17 3 0.03
18 8 0.09
19 35 0.38
20 15 0.16
21 22 0.24
22 8 0.09
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (19 bp):
TTTTGATAATTTTTATAAG
Found at i:42698260 original size:48 final size:48
Alignment explanation
Indices: 42698203--42698310 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 48
42698193 TCTTTATAAG
* *
42698203 TTTTA-AATTTTTTA-AATATGTTTTAAT-TTTATTA-TTGTTAT-AATTAT
1 TTTTATAATTTTTTAGAAT-T-TTATAATGTTTATAAGTT-TTATGAATT-T
*
42698250 TTTTATAATTTATTAGAATTTTATAATGTTTATAAGTTTTATGAATTT
1 TTTTATAATTTTTTAGAATTTTATAATGTTTATAAGTTTTATGAATTT
42698298 TTTTATAATTTTT
1 TTTTATAATTTTT
42698311 ATAAGTTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
47 11 0.21
48 32 0.62
49 9 0.17
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (48 bp):
TTTTATAATTTTTTAGAATTTTATAATGTTTATAAGTTTTATGAATTT
Found at i:42708777 original size:17 final size:17
Alignment explanation
Indices: 42708739--42708780 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
42708729 ACAGCATAGT
*
42708739 TTTTAATATATATTATA
1 TTTTAATATATAATATA
*
42708756 ATTTAATATA-AATATCA
1 TTTTAATATATAATAT-A
42708773 TTTTAATA
1 TTTTAATA
42708781 ATTTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTAATATATAATATA
Found at i:42709847 original size:12 final size:12
Alignment explanation
Indices: 42709830--42709903 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
42709820 CTCTTCATCT
42709830 TTCTTCTTCTCC
1 TTCTTCTTCTCC
*
42709842 TTCTTC-TCTTC
1 TTCTTCTTCTCC
*
42709853 TT-TCTCTTCACC
1 TTCT-TCTTCTCC
* *
42709865 TTCTACCTCATCC
1 TTCTTCTTC-TCC
*
42709878 TTCTTCATT-TCT
1 TTCTTC-TTCTCC
42709890 TTCTTCTTCTCC
1 TTCTTCTTCTCC
42709902 TT
1 TT
42709904 TGCCTCTTTG
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
10 1 0.02
11 10 0.22
12 26 0.57
13 8 0.17
14 1 0.02
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTTCTTCTCC
Found at i:42709940 original size:30 final size:31
Alignment explanation
Indices: 42709890--42710418 Score: 100
Period size: 30 Copynumber: 16.7 Consensus size: 31
42709880 CTTCATTTCT
*
42709890 TTCTTCTTC-TCCTTTGCCTCTTTGTCTCTC
1 TTCTTCTTCTTCCTTTCCCTCTTTGTCTCTC
* *
42709920 TTCTT-TTCTTTCTTTCCCTCTTCTAAT-TCTTC
1 TTCTTCTTCTTCCTTTCCCTCTT-T-GTCTC-TC
* * * * * *
42709952 ATCTTCTTCTACCTCATCCTTCTTTTTTTCT-
1 TTCTTCTTCTTCCT-TTCCCTCTTTGTCTCTC
* *
42709983 TTCTTCTTC-TCCTTTGCCTCTTTGTCTTTC
1 TTCTTCTTCTTCCTTTCCCTCTTTGTCTCTC
** *
42710013 TTCTT-TTCTTTATTTCCCTCTTCTAAT-TCTTC
1 TTCTTCTTCTTCCTTTCCCTCTT-T-GTCTC-TC
** * * *
42710045 AGCTTCTTCTACCTCATCCTTCTTCT-TCT-T-
1 TTCTTCTTCTTCCT-TTCCCTCTT-TGTCTCTC
* *
42710075 TTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTC
1 TTC-TTCTTCTTC-CTTTC-CCTCTTTGTCTCTC
** *
42710109 TTCTT-TTCTTTATTTCCCTCTTCTAAT-TCTTC
1 TTCTTCTTCTTCCTTTCCCTCTT-T-GTCTC-TC
* * * * *
42710141 ATCTTCATCTACCTCATCCTTCTTCT-TCT-T-
1 TTCTTCTTCTTCCT-TTCCCTCTT-TGTCTCTC
* *
42710171 TTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTC
1 TTC-TTCTTCTTC-CTTTC-CCTCTTTGTCTCTC
* *
42710205 TTCTT-TTCTTTCTTTCCCTCTTCTAAT-TCTTC
1 TTCTTCTTCTTCCTTTCCCTCTT-T-GTCTC-TC
* * * * *
42710237 ATCTTCTTCTACCTCATCCTTCTTCTTTTTTTCT-
1 TTCTTCTTCTTCCT-TTCC--C-TCTTTGTCTCTC
* *
42710271 TTCTTATTC-TCC-TTCGCCTCTTTGTCTTTC
1 TTCTTCTTCTTCCTTTC-CCTCTTTGTCTCTC
* * *
42710301 TTCTT-TTCTTTCTTTCCCCCTTCTAAT-TCTTC
1 TTCTTCTTCTTCCTTTCCCTCTT-T-GTCTC-TC
** * * * *
42710333 AGCTTCTTCTACCTCATCCTTCTTCT-TCTTTTC
1 TTCTTCTTCTTCCT-TTCCCTCTT-TGTC-TCTC
* *
42710366 TTTCTTCTTC-TCCTTTGCCTCTTTGTCTTTC
1 -TTCTTCTTCTTCCTTTCCCTCTTTGTCTCTC
*
42710397 TTCTT-TTCTTTCTTTCCCTCTT
1 TTCTTCTTCTTCCTTTCCCTCTT
42710419 CTAATTCTTC
Statistics
Matches: 354, Mismatches: 89, Indels: 112
0.64 0.16 0.20
Matches are distributed among these distances:
29 30 0.08
30 78 0.22
31 59 0.17
32 75 0.21
33 45 0.13
34 57 0.16
35 2 0.01
36 4 0.01
37 4 0.01
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (31 bp):
TTCTTCTTCTTCCTTTCCCTCTTTGTCTCTC
Found at i:42709957 original size:96 final size:93
Alignment explanation
Indices: 42709864--42710553 Score: 1007
Period size: 96 Copynumber: 7.3 Consensus size: 93
42709854 TTCTCTTCAC
* *
42709864 CTTCTACCTCATCCTTCTTCATTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTCTCTTCTTTTCT
1 CTTCTACCTCATCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
42709929 TTCTTTCCCTCTTCTAATTCTTCATCTT
66 TTCTTTCCCTCTTCTAATTCTTCATCTT
*
42709957 CTTCTACCTCATCCTTCTTTTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
1 CTTCTACCTCATCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
* *
42710022 TTATTTCCCTCTTCTAATTCTTCAGCTT
66 TTCTTTCCCTCTTCTAATTCTTCATCTT
*
42710050 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCAT-C--CTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
*
42710115 TCTTTATTTCCCTCTTCTAATTCTTCATCTT
63 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* *
42710146 CATCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTCGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCAT-C--CTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
42710211 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
63 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* *
42710242 CTTCTACCTCATCCTTCTTCTTTTTTTCTTTCTTATTCTCCTTCGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCATCCTTCTTC---TTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
* *
42710307 TCTTTCTTTCCCCCTTCTAATTCTTCAGCTT
63 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
42710338 CTTCTACCTCATCCTTCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
1 CTTCTACCTCAT-C--CTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTT
* *
42710403 TCTTTCTTTCCCTCTTCTAATTCTTCTTCAT
63 TCTTTCTTTCCCTCTTCTAATTCTTCATCTT
* * * * *
42710434 CTTCT-TCT-AT-C-TCATC-CTTC-TTCTTCTTCTCTTTTGCCTCTTTGTCCTTCTTCTTTTCT
1 CTTCTACCTCATCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
42710493 TTCTTTCCCTCTTCTAATTCTTCATCTTCAT
66 TTCTTTCCCTCTTCTAATTCTTCATC-T--T
*
42710524 CTTCTACCTCATCCTTCTTCTTCT-TTTCTT
1 CTTCTACCTCATCCTTCTTCTTTTCTTTCTT
42710554 TCTTTCCCTC
Statistics
Matches: 548, Mismatches: 31, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
87 62 0.11
88 3 0.01
89 4 0.01
90 7 0.01
91 2 0.00
92 2 0.00
93 108 0.20
94 7 0.01
95 9 0.02
96 336 0.61
97 1 0.00
99 7 0.01
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.58
Consensus pattern (93 bp):
CTTCTACCTCATCCTTCTTCTTTTCTTTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCT
TTCTTTCCCTCTTCTAATTCTTCATCTT
Found at i:42710084 original size:12 final size:12
Alignment explanation
Indices: 42710067--42710119 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
42710057 CTCATCCTTC
42710067 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
42710079 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
* *
42710092 TCGCCTCTTTGTCT
1 T-TCTTCTTT-TCT
42710106 TTCTTCTTTTCT
1 TTCTTCTTTTCT
42710118 TT
1 TT
42710120 ATTTCCCTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 13 0.41
13 11 0.34
14 8 0.25
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:42710180 original size:12 final size:12
Alignment explanation
Indices: 42710163--42710218 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
42710153 CTCATCCTTC
42710163 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
42710175 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
* *
42710188 TCGCCTCTTTGTCT
1 T-TCTTCTTT-TCT
42710202 TTCTTCTTTTCT
1 TTCTTCTTTTCT
42710214 TTCTT
1 TTCTT
42710219 TCCCTCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 16 0.46
13 11 0.31
14 8 0.23
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:42710357 original size:3 final size:3
Alignment explanation
Indices: 42710351--42710616 Score: 69
Period size: 3 Copynumber: 88.7 Consensus size: 3
42710341 CTACCTCATC
* * *
42710351 CTT CTT CTT CTT -TT CTTT CTT CTT CTC CTT -TG CCT CTT -TGT CTTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CT-T C-TT
* * * * *
42710396 CTT CTT -TT CTTT CTT -TC CCT CTT CTA ATT CTT CTT CAT CTT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* *
42710440 CTAT C-T CATC CTT CTT CTT CTT C-T CTT -TT GCCT CTT -TGT CCTT
1 CT-T CTT C-TT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CT-T -CTT
* * * * * *
42710483 CTT CTT -TT CTTT CTT -TC CCT CTT CTA ATT CTT CAT CTT CAT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * *
42710527 CTA CCT CATC CTT CTT CTT CTT -TT CTTT CTT -TC CCT CTT CTAT -TT
1 CTT CTT C-TT CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CT-T CTT
* *
42710572 CTT CAT CTT CTT CTA CTT -TAT CCTT CTT CTT -TT CTTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CT-T -CTT CTT CTT CTT C-TT CTT CTT CT
42710617 CCTTTGCCTT
Statistics
Matches: 185, Mismatches: 46, Indels: 64
0.63 0.16 0.22
Matches are distributed among these distances:
2 24 0.13
3 133 0.72
4 25 0.14
5 3 0.02
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:42710544 original size:87 final size:87
Alignment explanation
Indices: 42710367--42710554 Score: 313
Period size: 87 Copynumber: 2.2 Consensus size: 87
42710357 CTTCTTTTCT
* * *
42710367 TTCTTCTTCTCCTTTGCCTCTTTGTCTTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCTTC
1 TTCTTCTTCTCTTTTGCCTCTTTGTCCTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATC
* *
42710432 ATCTTCTTCTATCTCATCCTTC
66 ATCATCTTCTACCTCATCCTTC
42710454 TTCTTCTTCTCTTTTGCCTCTTTGTCCTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATC
1 TTCTTCTTCTCTTTTGCCTCTTTGTCCTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATC
*
42710519 TTCATCTTCTACCTCATCCTTC
66 ATCATCTTCTACCTCATCCTTC
*
42710541 TTCTTCTTTTCTTT
1 TTCTTCTTCTCTTT
42710555 CTTTCCCTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 94 1.00
ACGTcount: A:0.06, C:0.33, G:0.02, T:0.59
Consensus pattern (87 bp):
TTCTTCTTCTCTTTTGCCTCTTTGTCCTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATC
ATCATCTTCTACCTCATCCTTC
Found at i:42710586 original size:57 final size:59
Alignment explanation
Indices: 42710480--42710611 Score: 196
Period size: 60 Copynumber: 2.2 Consensus size: 59
42710470 CCTCTTTGTC
42710480 CTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTACCTCATCCTT
1 CTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTT-ATCTTCTACCTCATCCTT
* * *
42710540 CTTCTTCTTTTCTTTCTTTCCCTCTTCTATTTCTTCATC-T-TCTTCTACTTTATCCTT
1 CTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTATCTTCTACCTCATCCTT
*
42710597 CTTCTTTTCTTTCTT
1 CTTCTTCT-TTTCTT
42710612 CTTCTCCTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
57 22 0.33
58 6 0.09
59 1 0.01
60 38 0.57
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.60
Consensus pattern (59 bp):
CTTCTTCTTTTCTTTCTTTCCCTCTTCTAATTCTTCATCTTATCTTCTACCTCATCCTT
Found at i:42710612 original size:12 final size:12
Alignment explanation
Indices: 42710541--42710641 Score: 51
Period size: 12 Copynumber: 7.7 Consensus size: 12
42710531 CTCATCCTTC
42710541 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
42710553 TTCTTTCCCTCTTCTAT
1 TTC-TT--CT-TT-TCT
*
42710570 TTCTTCATCTTC-
1 TTCTTC-TTTTCT
* *
42710582 TTCTACTTTATCC
1 TTCTTCTTT-TCT
42710595 TTCTTCTTTTCT
1 TTCTTCTTTTCT
*
42710607 TTCTTCTTCTCCT
1 TTCTTCTT-TTCT
*
42710620 TTGCCTTCTTGTCT
1 TT--CTTCTTTTCT
42710634 TTCTTCTT
1 TTCTTCTT
42710642 CTCTGTCTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
11 2 0.03
12 26 0.38
13 16 0.24
14 6 0.09
15 9 0.13
16 4 0.06
17 5 0.07
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.63
Consensus pattern (12 bp):
TTCTTCTTTTCT
Found at i:42710614 original size:57 final size:59
Alignment explanation
Indices: 42710473--42710614 Score: 179
Period size: 57 Copynumber: 2.5 Consensus size: 59
42710463 TCTTTTGCCT
*
42710473 CTTTGTCCTTCTTCTTTTC--T-TTCTTTCCCTCTTCTAATTCTTCATCTTCATCTTCTA
1 CTTTATCCTTCTTCTTTTCTTTCTTCTTTCCCTCTTCTAATTCTTCATCTT-ATCTTCTA
* * * *
42710530 CCTCATCCTTCTTCTTCT-TTTCTTTCTTTCCCTCTTCTATTTCTTCATC-T-TCTTCTA
1 CTTTATCCTTCTTCTTTTCTTTC-TTCTTTCCCTCTTCTAATTCTTCATCTTATCTTCTA
42710587 CTTTATCCTTCTTCTTTTCTTTCTTCTT
1 CTTTATCCTTCTTCTTTTCTTTCTTCTT
42710615 CTCCTTTGCC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
57 41 0.57
58 5 0.07
59 1 0.01
60 25 0.35
ACGTcount: A:0.07, C:0.32, G:0.01, T:0.60
Consensus pattern (59 bp):
CTTTATCCTTCTTCTTTTCTTTCTTCTTTCCCTCTTCTAATTCTTCATCTTATCTTCTA
Found at i:42710840 original size:12 final size:13
Alignment explanation
Indices: 42710811--42710855 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
42710801 CTTCTCCTTG
42710811 TCTTTCTTCTTC-
1 TCTTTCTTCTTCA
*
42710823 TGTTTCTTC-TCA
1 TCTTTCTTCTTCA
42710835 TCTTTC-TCTTCA
1 TCTTTCTTCTTCA
42710847 TC-TTCTTCT
1 TCTTTCTTCT
42710856 CCCTCAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 7 0.25
12 21 0.75
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62
Consensus pattern (13 bp):
TCTTTCTTCTTCA
Found at i:42710913 original size:15 final size:15
Alignment explanation
Indices: 42710818--42710925 Score: 63
Period size: 14 Copynumber: 7.5 Consensus size: 15
42710808 TTGTCTTTCT
42710818 TCTTCTGTT-TCTTC-
1 TCTTCT-TTCTCTTCA
*
42710832 TCATCTTTCTCTTCA
1 TCTTCTTTCTCTTCA
*
42710847 TCTTC-TTCTCCCTCA
1 TCTTCTTTCT-CTTCA
* *
42710862 ACCTCTTTCTCCTT-A
1 TCTTCTTTCT-CTTCA
42710877 TGCTTCTTTC-CTT--
1 T-CTTCTTTCTCTTCA
*
42710890 TTTTC-TTCTTCTTC-
1 TCTTCTTTC-TCTTCA
42710904 TCTTCTTTCTCTTCA
1 TCTTCTTTCTCTTCA
42710919 TCTTCTT
1 TCTTCTT
42710926 CTACCACCTC
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 6 0.08
14 26 0.35
15 22 0.30
16 14 0.19
ACGTcount: A:0.06, C:0.34, G:0.02, T:0.58
Consensus pattern (15 bp):
TCTTCTTTCTCTTCA
Found at i:42711050 original size:25 final size:22
Alignment explanation
Indices: 42711013--42711069 Score: 55
Period size: 25 Copynumber: 2.5 Consensus size: 22
42711003 TTCTCATCAT
42711013 CTTCTTCAT-CTTTGTGCATCTTCTC
1 CTTCTTC-TCCTTT-TGC-TCTT-TC
*
42711038 CTTCTTCTCCTTTTTCTCTTTC
1 CTTCTTCTCCTTTTGCTCTTTC
42711060 CTT-TTCTCCT
1 CTTCTTCTCCT
42711070 CTTTATTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 7 0.23
22 5 0.17
23 4 0.13
24 3 0.10
25 11 0.37
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.58
Consensus pattern (22 bp):
CTTCTTCTCCTTTTGCTCTTTC
Found at i:42714336 original size:19 final size:18
Alignment explanation
Indices: 42714312--42714348 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
42714302 CATGAAAATA
42714312 TTAAAATAAATATCGATAC
1 TTAAAATAAATAT-GATAC
*
42714331 TTAAAATATATATGATAC
1 TTAAAATAAATATGATAC
42714349 CAATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAAAATAAATATGATAC
Found at i:42715319 original size:15 final size:16
Alignment explanation
Indices: 42715299--42715329 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
42715289 TAATTTGCTT
42715299 TATATAAAAA-TAATA
1 TATATAAAAATTAATA
42715314 TATATAAAAATTAATA
1 TATATAAAAATTAATA
42715330 CGGACAGGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TATATAAAAATTAATA
Found at i:42721755 original size:4 final size:4
Alignment explanation
Indices: 42721748--42721787 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
42721738 TTAATTTGTT
* *
42721748 TGTA TGTA TGTA TGTA TGTG TGTG TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
42721788 AATATATGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:42728589 original size:20 final size:20
Alignment explanation
Indices: 42728564--42728611 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
42728554 CTTAAAAGGG
*
42728564 ACTTCTA-CCGATACAAGTCC
1 ACTTCTATCC-ATACAAATCC
42728584 ACTTCTATCCATACAAATCC
1 ACTTCTATCCATACAAATCC
42728604 ACTTCTAT
1 ACTTCTAT
42728612 TTGTAACACC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (20 bp):
ACTTCTATCCATACAAATCC
Found at i:42729985 original size:20 final size:20
Alignment explanation
Indices: 42729960--42729999 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42729950 ACTTTAAAAT
*
42729960 CAAGTTAAAATTATTTTAAC
1 CAAGTTAAAATGATTTTAAC
42729980 CAAGTTAAAATGATTTTAAC
1 CAAGTTAAAATGATTTTAAC
42730000 AAATCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
CAAGTTAAAATGATTTTAAC
Found at i:42731175 original size:18 final size:18
Alignment explanation
Indices: 42731152--42731190 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
42731142 TCCTGGCACT
42731152 AAGTGCACATTGGCACAC
1 AAGTGCACATTGGCACAC
*
42731170 AAGTGCATATTGGCACAC
1 AAGTGCACATTGGCACAC
42731188 AAG
1 AAG
42731191 GTGTGTTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (18 bp):
AAGTGCACATTGGCACAC
Found at i:42732632 original size:21 final size:20
Alignment explanation
Indices: 42732600--42732638 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
42732590 AACCCTCAAG
*
42732600 ACTTTTTATTTCCCCCTTAA
1 ACTTTTTATTTCACCCTTAA
*
42732620 ACTTTTATTTTTCACCCTT
1 ACTTTT-TATTTCACCCTT
42732639 TACCCCAAAA
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:0.18, C:0.28, G:0.00, T:0.54
Consensus pattern (20 bp):
ACTTTTTATTTCACCCTTAA
Found at i:42733819 original size:14 final size:14
Alignment explanation
Indices: 42733802--42733847 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
42733792 TAAAAAAATG
42733802 TTATTAAATTATTA
1 TTATTAAATTATTA
* *
42733816 TTATTAAATTAGTG
1 TTATTAAATTATTA
42733830 TTATTAAATTATTA
1 TTATTAAATTATTA
42733844 TTAT
1 TTAT
42733848 ATTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (14 bp):
TTATTAAATTATTA
Found at i:42733986 original size:3 final size:3
Alignment explanation
Indices: 42733978--42734027 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
42733968 TATTAAAATA
*
42733978 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42734026 TA
1 TA
42734028 ACTAGGAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:42735241 original size:23 final size:22
Alignment explanation
Indices: 42735212--42735272 Score: 99
Period size: 21 Copynumber: 2.8 Consensus size: 22
42735202 NNNNNNNNNN
42735212 TGTGTCGTATATCAGGCACCTCG
1 TGTGTCGT-TATCAGGCACCTCG
42735235 TGTGTCG-TATCAGGCACCTCG
1 TGTGTCGTTATCAGGCACCTCG
42735256 TGTGTCGTT-TCAGGCAC
1 TGTGTCGTTATCAGGCAC
42735273 TTATGTGTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 29 0.78
22 1 0.03
23 7 0.19
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (22 bp):
TGTGTCGTTATCAGGCACCTCG
Found at i:42735245 original size:21 final size:21
Alignment explanation
Indices: 42735212--42735285 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
42735202 NNNNNNNNNN
42735212 TGTGTCGTATATCAGGCACCTCG
1 TGTGTCG--TATCAGGCACCTCG
42735235 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* **
42735256 TGTGTCGTTTCAGGCA-CTTA
1 TGTGTCGTATCAGGCACCTCG
42735276 TGTGTCGTAT
1 TGTGTCGTAT
42735286 ACTGATCAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
20 11 0.23
21 29 0.62
23 7 0.15
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:42739064 original size:25 final size:25
Alignment explanation
Indices: 42739008--42739081 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
42738998 GGTTACCAAT
* *
42739008 TTTAGCTCGTATGAGCTTATCG--A
1 TTTAGCTCGCATGAGCTTACCGTTA
42739031 TTCTCAGCTCGCATGAGCTTACCGTTA
1 TT-T-AGCTCGCATGAGCTTACCGTTA
* * *
42739058 TTTAGCTTGGAGGAGCTTACCGTT
1 TTTAGCTCGCATGAGCTTACCGTT
42739082 TACAGCTCGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
23 2 0.05
24 1 0.02
25 35 0.83
26 1 0.02
27 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (25 bp):
TTTAGCTCGCATGAGCTTACCGTTA
Found at i:42740495 original size:16 final size:16
Alignment explanation
Indices: 42740470--42740503 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42740460 ATGAATATAT
* *
42740470 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
42740486 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
42740502 AT
1 AT
42740504 TGAATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:42743864 original size:40 final size:39
Alignment explanation
Indices: 42743819--42743916 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 39
42743809 CACACCACAC
* *
42743819 AGAAGCTCATAAGATTTGATCCAACCGAAATATGC-CAAAT
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACA--CACAAAT
* * *
42743859 AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAAT
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACACAAAT
42743898 AGAAGCTCATAAGAGTTGA
1 AGAAGCTCATAAGAGTTGA
42743917 ACAGAAGCTC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.02
39 22 0.44
40 27 0.54
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (39 bp):
AGAAGCTCATAAGAGTTGATCCAACCGAAACACACAAAT
Found at i:42743952 original size:60 final size:60
Alignment explanation
Indices: 42743859--42744022 Score: 283
Period size: 60 Copynumber: 2.7 Consensus size: 60
42743849 TATGCCAAAT
42743859 AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAATAGAAGCTCATAAGAGTTGAAC
1 AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAATAGAAGCTCATAAGAGTTGAAC
*
42743919 AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAATAGAAGCTTATAAGAGTTGAAC
1 AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAATAGAAGCTCATAAGAGTTGAAC
* * *
42743979 AGAAGCTCATAAGAGCTGATCCACTCGAAACACGCCAAATAGAA
1 AGAAGCTCATAAGAGCTGGTCCACCCGAAACAC-ACAAATAGAA
42744023 AATATAACGT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
60 90 0.91
61 9 0.09
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (60 bp):
AGAAGCTCATAAGAGCTGGTCCACCCGAAACACACAAATAGAAGCTCATAAGAGTTGAAC
Found at i:42745630 original size:17 final size:15
Alignment explanation
Indices: 42745605--42745648 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
42745595 ATTATTTTTT
*
42745605 AAATCTATAAAATATAA
1 AAATATATAAAAT-T-A
*
42745622 AAATATATACAATTA
1 AAATATATAAAATTA
42745637 AAATATATAAAA
1 AAATATATAAAA
42745649 AGCTTATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.50
16 1 0.04
17 11 0.46
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATATAAAATTA
Found at i:42745818 original size:7 final size:9
Alignment explanation
Indices: 42745784--42745813 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42745774 TTCTTGAACT
42745784 TTTTAT-TA
1 TTTTATATA
42745792 TTTTATATA
1 TTTTATATA
42745801 TTTTATATA
1 TTTTATATA
42745810 TTTT
1 TTTT
42745814 TTATTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATATA
Found at i:42756065 original size:39 final size:39
Alignment explanation
Indices: 42756014--42756291 Score: 403
Period size: 39 Copynumber: 7.1 Consensus size: 39
42756004 TTTTCAATCA
*
42756014 CACCGGCACACAGCCTGCTAGGCATATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
**
42756053 CACCGGCACACAGTTTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
* ** * *
42756092 CACTGGCACACAGTTTGCTAGGCACATAACCTGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
* *
42756131 TACTGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
* * *
42756170 CACCGGTATACAGCTTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
* * * *
42756209 CACCGGCACACAGCCTACTAGGTATATAGCCTGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
42756248 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
1 CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
42756287 CACCG
1 CACCG
42756292 TATTTATATT
Statistics
Matches: 212, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 212 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (39 bp):
CACCGGCACACAGCCTGCTAGGCACATAGCCCGAATAAT
Found at i:42760502 original size:12 final size:12
Alignment explanation
Indices: 42760485--42760509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42760475 GGTATTCATT
42760485 CAGTTAACCGAC
1 CAGTTAACCGAC
42760497 CAGTTAACCGAC
1 CAGTTAACCGAC
42760509 C
1 C
42760510 CGAAATAACA
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:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGTTAACCGAC
Found at i:42760653 original size:9 final size:9
Alignment explanation
Indices: 42760640--42760735 Score: 131
Period size: 9 Copynumber: 10.7 Consensus size: 9
42760630 TTTGGTTAAA
*
42760640 AATTAACCA
1 AATTAACCG
42760649 AATTAACCG
1 AATTAACCG
42760658 AATTAACCG
1 AATTAACCG
42760667 AATTAACCG
1 AATTAACCG
*
42760676 AATTACCCG
1 AATTAACCG
42760685 AATT-ACTCG
1 AATTAAC-CG
*
42760694 AATTACCCG
1 AATTAACCG
42760703 AATTAACCG
1 AATTAACCG
*
42760712 AATTACCCG
1 AATTAACCG
*
42760721 AATTAACCA
1 AATTAACCG
42760730 AATTAA
1 AATTAA
42760736 GCAAATTGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
8 1 0.01
9 75 0.97
10 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:42760889 original size:18 final size:18
Alignment explanation
Indices: 42760849--42760892 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42760839 TAATTTTATG
**
42760849 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
42760867 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
42760885 CTTGGGTT
1 ATTGGGTT
42760893 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:42763818 original size:12 final size:12
Alignment explanation
Indices: 42763801--42763828 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42763791 CATCAAAAAC
42763801 ATTAAAATAAAT
1 ATTAAAATAAAT
42763813 ATTAAAATAAAT
1 ATTAAAATAAAT
42763825 ATTA
1 ATTA
42763829 CCGAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATTAAAATAAAT
Found at i:42765447 original size:26 final size:26
Alignment explanation
Indices: 42765386--42765447 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
42765376 TTATCGGTCA
* * *
42765386 ATTTATTTTTATTTCAATAGATCTTT
1 ATTTACTTTTATTCCAATACATCTTT
*
42765412 ATTTATTTTTATTCCAATACATCTTT
1 ATTTACTTTTATTCCAATACATCTTT
42765438 -TCTTACTTTT
1 AT-TTACTTTT
42765448 TCTTATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 1 0.03
26 31 0.97
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTACTTTTATTCCAATACATCTTT
Found at i:42765447 original size:27 final size:26
Alignment explanation
Indices: 42765386--42765437 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
42765376 TTATCGGTCA
* *
42765386 ATTTATTTTTATTTCAATAGATCTTT
1 ATTTATTTTTATTCCAATACATCTTT
42765412 ATTTATTTTTATTCCAATACATCTTT
1 ATTTATTTTTATTCCAATACATCTTT
42765438 TCTTACTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTATTTTTATTCCAATACATCTTT
Found at i:42765501 original size:16 final size:16
Alignment explanation
Indices: 42765480--42765511 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42765470 AGATTAGTTT
42765480 GATCTAATTTTAAGAA
1 GATCTAATTTTAAGAA
*
42765496 GATCTAATTTTTAGAA
1 GATCTAATTTTAAGAA
42765512 TTGTGAGACT
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:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (16 bp):
GATCTAATTTTAAGAA
Found at i:42766222 original size:2 final size:2
Alignment explanation
Indices: 42766215--42766239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42766205 TAATAATTTT
42766215 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
42766240 TTCACACCTA
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:42767995 original size:56 final size:56
Alignment explanation
Indices: 42767883--42767995 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
42767873 GAGCTCTCTA
* * * * * * ** *
42767883 ACTTGGGTCACATGGCCAAGCCAGACGCCCGTGTGCTAGGCCGTGTGAGTATACTG
1 ACTTAGGTCACACGGCCAAACCACACACCCGTGTGCTAGGCCATGTGAAAAAACTG
42767939 ACTTAGGTCACACGGCCAAACCACACACCCGTGTGCTAGGCCATGTGAAAAAACTG
1 ACTTAGGTCACACGGCCAAACCACACACCCGTGTGCTAGGCCATGTGAAAAAACTG
42767995 A
1 A
42767996 GCATACTGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.19
Consensus pattern (56 bp):
ACTTAGGTCACACGGCCAAACCACACACCCGTGTGCTAGGCCATGTGAAAAAACTG
Found at i:42768060 original size:15 final size:15
Alignment explanation
Indices: 42768040--42768077 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
42768030 GACACACGAC
42768040 TGTGTCACTTGGCCG
1 TGTGTCACTTGGCCG
42768055 TGTGTCACTTGGCCG
1 TGTGTCACTTGGCCG
42768070 TGTGTCAC
1 TGTGTCAC
42768078 ACACGACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.32, T:0.34
Consensus pattern (15 bp):
TGTGTCACTTGGCCG
Found at i:42768924 original size:21 final size:21
Alignment explanation
Indices: 42768881--42769053 Score: 188
Period size: 21 Copynumber: 8.3 Consensus size: 21
42768871 GTACATCGTT
*
42768881 AACAGAAGCTCGT-A-AGCTG
1 AACAGAAGCTCGTAAGAGCTA
*
42768900 AACAGAAGCTTGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
*
42768921 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
* * *
42768942 AATAGAAGCTCGAAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTA
* * * *
42768963 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTA
*
42768984 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTA
* * * *
42769005 AACAGAAACTAGTAAAAGTTA
1 AACAGAAGCTCGTAAGAGCTA
*
42769026 AATAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCGTAAGAGCTA
42769047 AACAGAA
1 AACAGAA
42769054 AGTAAAAAAT
Statistics
Matches: 125, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
19 12 0.10
20 1 0.01
21 112 0.90
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTA
Found at i:42769043 original size:84 final size:84
Alignment explanation
Indices: 42768898--42769054 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
42768888 GCTCGTAAGC
* * * *
42768898 TGAACAGAAGCTTGTAAGAGCTAAACAGAAGCTCATAAGAGCTAAATAGAAGCTCGAAAGAGCTG
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAAAGCTAAATAGAAGCTCGAAAGAGCTA
42768963 AACAGAAACTCATAAGAGT
66 AACAGAAACTCATAAGAGT
* * *
42768982 TGAACAGAAGCTCGTAAGAGCTGAACAGAAACT-AGTAAAAGTTAAATAGAAGCTCGTAAGAGCT
1 TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCA-TAAAAGCTAAATAGAAGCTCGAAAGAGCT
42769046 AAACAGAAA
65 AAACAGAAA
42769055 GTAAAAAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.02
84 64 0.98
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (84 bp):
TGAACAGAAGCTCGTAAGAGCTAAACAGAAACTCATAAAAGCTAAATAGAAGCTCGAAAGAGCTA
AACAGAAACTCATAAGAGT
Found at i:42776989 original size:25 final size:25
Alignment explanation
Indices: 42776960--42777072 Score: 113
Period size: 25 Copynumber: 4.6 Consensus size: 25
42776950 CTCCTCTAAA
* *
42776960 CTGAATAACAGTAAGCTCATGCAAG
1 CTGAATATCAGTAAGCTCATACAAG
* * * *
42776985 TTGAATAACGGTAAGCTCATGCAAG
1 CTGAATATCAGTAAGCTCATACAAG
* *
42777010 CTGAGTATTAGTAAGCTCATACAAG
1 CTGAATATCAGTAAGCTCATACAAG
*
42777035 CTGAGTATC-GATAAGCTCATACAAG
1 CTGAATATCAG-TAAGCTCATACAAG
*
42777060 TTGAA-ATCAGTAA
1 CTGAATATCAGTAA
42777073 CCCTAATGAC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
24 7 0.09
25 68 0.91
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (25 bp):
CTGAATATCAGTAAGCTCATACAAG
Found at i:42780033 original size:27 final size:27
Alignment explanation
Indices: 42779963--42780026 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
42779953 TACCCTTCCC
*
42779963 CAAAGTCAGTCTCCACATCAGTTACCA
1 CAAAGTCAGTCTCCACATCAGTCACCA
* *
42779990 CAGAGTCAGTCTCCACATCGGTCACCA
1 CAAAGTCAGTCTCCACATCAGTCACCA
42780017 CAAAGTCAGT
1 CAAAGTCAGT
42780027 ATTCACAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (27 bp):
CAAAGTCAGTCTCCACATCAGTCACCA
Found at i:42783074 original size:12 final size:12
Alignment explanation
Indices: 42783057--42783098 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
42783047 CTTGAAATTA
42783057 AATAAATAATGG
1 AATAAATAATGG
**
42783069 AATAAA-ACATTA
1 AATAAATA-ATGG
42783081 AATAAATAATGG
1 AATAAATAATGG
42783093 AATAAA
1 AATAAA
42783099 ACATACCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (12 bp):
AATAAATAATGG
Found at i:42783080 original size:24 final size:24
Alignment explanation
Indices: 42783053--42783102 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
42783043 GGTTCTTGAA
42783053 ATTAAATAAATAATGGAATAAAAC
1 ATTAAATAAATAATGGAATAAAAC
42783077 ATTAAATAAATAATGGAATAAAAC
1 ATTAAATAAATAATGGAATAAAAC
42783101 AT
1 AT
42783103 ACCTTACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (24 bp):
ATTAAATAAATAATGGAATAAAAC
Found at i:42785023 original size:7 final size:7
Alignment explanation
Indices: 42785011--42785037 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
42785001 AATCTTAGTA
42785011 TAACATT
1 TAACATT
42785018 TAACATT
1 TAACATT
42785025 TAACATT
1 TAACATT
42785032 TAACAT
1 TAACAT
42785038 GTTATGTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (7 bp):
TAACATT
Found at i:42787812 original size:21 final size:21
Alignment explanation
Indices: 42787788--42787828 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42787778 CTAATCTTAC
*
42787788 CGCTACAGTATCCAATCTCAT
1 CGCTACAGTAACCAATCTCAT
*
42787809 CGCTACAGTAACTAATCTCA
1 CGCTACAGTAACCAATCTCA
42787829 CTGCCACCGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (21 bp):
CGCTACAGTAACCAATCTCAT
Found at i:42791349 original size:28 final size:28
Alignment explanation
Indices: 42791328--42791388 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
42791318 AAATATATTA
*
42791328 AAAATATGAAAA-TAAAAAAAATTATAT
1 AAAATACGAAAACTAAAAAAAATTATAT
* *
42791355 AAATTACGAAAACT-AAAAAAATTATGAA
1 AAAATACGAAAACTAAAAAAAATTAT-AT
42791383 AAAATA
1 AAAATA
42791389 TTTAAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAATACGAAAACTAAAAAAAATTATAT
Found at i:42791672 original size:2 final size:2
Alignment explanation
Indices: 42791665--42791707 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42791655 CAACAGAGGC
42791665 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
42791707 T
1 T
42791708 CTTTAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42793928 original size:2 final size:2
Alignment explanation
Indices: 42793921--42793945 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42793911 AATACGTAGT
42793921 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
42793946 TTGATAAATC
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:42796074 original size:17 final size:18
Alignment explanation
Indices: 42796042--42796075 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42796032 AAAATAAAAA
42796042 TAATATTATATTCTTATT
1 TAATATTATATTCTTATT
*
42796060 TAATA-TATTTTCTTAT
1 TAATATTATATTCTTAT
42796076 CCAATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATATTATATTCTTATT
Found at i:42796084 original size:26 final size:27
Alignment explanation
Indices: 42796055--42796113 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
42796045 TATTATATTC
*
42796055 TTATTTAATAT-ATTTTCTTATCCAAT
1 TTATTTAATATGATTTTCTAATCCAAT
* *
42796081 TTATTTAATATGTTTTTCTAATTCAAT
1 TTATTTAATATGATTTTCTAATCCAAT
42796108 TTATTT
1 TTATTT
42796114 TTCAAGTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTTAATATGATTTTCTAATCCAAT
Found at i:42797279 original size:8 final size:8
Alignment explanation
Indices: 42797266--42797293 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42797256 GGGCGGCTAT
42797266 CATGCTGA
1 CATGCTGA
42797274 CATGCTGA
1 CATGCTGA
42797282 CATGCTGA
1 CATGCTGA
42797290 CATG
1 CATG
42797294 TCAAACTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (8 bp):
CATGCTGA
Found at i:42803835 original size:26 final size:26
Alignment explanation
Indices: 42803806--42803863 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
42803796 TAAGTGTTCT
42803806 GAAACTGATACATGCTATGATATTCC
1 GAAACTGATACATGCTATGATATTCC
* * * *
42803832 GAAATTGATATATGTTATGATATTCT
1 GAAACTGATACATGCTATGATATTCC
42803858 GAAACT
1 GAAACT
42803864 ACTGTAGGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (26 bp):
GAAACTGATACATGCTATGATATTCC
Found at i:42812095 original size:68 final size:69
Alignment explanation
Indices: 42811968--42812097 Score: 208
Period size: 68 Copynumber: 1.9 Consensus size: 69
42811958 ACACTTGATC
* *
42811968 ACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGAT
1 ACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAGAT
42812033 AATT
66 AATT
** *
42812037 ACTTTAATATTAAATTAATAAAATAC-TATCAAGATATTTATTAAATTTAATTTAATATTAA
1 ACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAA
42812098 AACTATTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
68 31 0.55
69 25 0.45
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (69 bp):
ACTTTAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAGAT
AATT
Found at i:42812113 original size:68 final size:69
Alignment explanation
Indices: 42811972--42812115 Score: 184
Period size: 68 Copynumber: 2.1 Consensus size: 69
42811962 TTGATCACTT
* * *
42811972 TAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAGATAATT
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAATAATT
***
42812037 ACTT
66 AAAA
** *
42812041 TAATATTAAATTAATAAAATAC-TATCAAGATATTTATTAAATTTAATTTAATATTAAAACT-AT
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAA-TAAT
42812104 TAAAA
65 TAAAA
42812109 TAATATT
1 TAATATT
42812116 GTTTTTGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
68 43 0.66
69 22 0.34
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (69 bp):
TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAAATAATT
AAAA
Found at i:42817266 original size:14 final size:14
Alignment explanation
Indices: 42817247--42817274 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42817237 ACCAGTGGAA
42817247 CTTGATGCCATACC
1 CTTGATGCCATACC
42817261 CTTGATGCCATACC
1 CTTGATGCCATACC
42817275 TTTGTACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (14 bp):
CTTGATGCCATACC
Found at i:42819430 original size:21 final size:20
Alignment explanation
Indices: 42819389--42819430 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
42819379 ATATTTGAGC
*
42819389 ATAAAATATATAATTTTTTT
1 ATAAAATATATAATATTTTT
*
42819409 ATAAAATATTATTATATTTTT
1 ATAAAATA-TATAATATTTTT
42819430 A
1 A
42819431 CCTTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAAATATATAATATTTTT
Found at i:42820576 original size:9 final size:9
Alignment explanation
Indices: 42820558--42820594 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42820548 TATAGTTTGA
*
42820558 TATTCTAAT
1 TATTCGAAT
42820567 TATTCGAAT
1 TATTCGAAT
*
42820576 TATTCGAGT
1 TATTCGAAT
42820585 TATTCGAAT
1 TATTCGAAT
42820594 T
1 T
42820595 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42825019 original size:157 final size:158
Alignment explanation
Indices: 42824728--42825039 Score: 500
Period size: 157 Copynumber: 2.0 Consensus size: 158
42824718 TCTTTCATCC
* * *
42824728 ATGGTCTTACTCATTATTCTTGGCTGTCATAGCATCTTACCATAAATCCCACGAGTGAGTCTGTA
1 ATGGTCTTACTCATTATACCTGGCTGTCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
* *
42824793 AATAGTATTATTTAATATTTATGAGTCAAATATAGTATAATATTAAAATTTTATGTGATAAATTT
66 AATAGTATTATTTAATATTTATGAGTCAAATATAGTATAATATTAAAATTTTATATAATAAATTT
42824858 TGTTAATTGAATGAATAATTAAGTACAA
131 TGTTAATTGAATGAATAATTAAGTACAA
* * *
42824886 ATGG-CTTACTCATTATACCTGGTTGTCATAGCATCTTACCACAAATTCCACGAGTGAGTTTGTA
1 ATGGTCTTACTCATTATACCTGGCTGTCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
* * * *
42824950 AATATTATTATTTAATATTTATGGGTCAAATATAGTATAATATTTAATTTTTATATAATAAATTT
66 AATAGTATTATTTAATATTTATGAGTCAAATATAGTATAATATTAAAATTTTATATAATAAATTT
*
42825015 TGTTAATTGAATGAATAGTTAAGTA
131 TGTTAATTGAATGAATAATTAAGTA
42825040 TAAGTGGTTT
Statistics
Matches: 141, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
157 137 0.97
158 4 0.03
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (158 bp):
ATGGTCTTACTCATTATACCTGGCTGTCATAGCATCTTACCACAAATCCCACGAGTGAGTCTGTA
AATAGTATTATTTAATATTTATGAGTCAAATATAGTATAATATTAAAATTTTATATAATAAATTT
TGTTAATTGAATGAATAATTAAGTACAA
Found at i:42826722 original size:13 final size:13
Alignment explanation
Indices: 42826704--42826792 Score: 90
Period size: 13 Copynumber: 6.6 Consensus size: 13
42826694 AGAAAAATAA
42826704 TATATGAAATGGT
1 TATATGAAATGGT
*
42826717 TATATGAACTGGT
1 TATATGAAATGGT
*
42826730 TATATGGAAAAAT-GA
1 TATAT-G--AAATGGT
*
42826745 TATATGAAATGGG
1 TATATGAAATGGT
* *
42826758 TATATGAAAATAGA
1 TATATG-AAATGGT
42826772 TATATGAAATGGT
1 TATATGAAATGGT
42826785 TATATGAA
1 TATATGAA
42826793 TCAGTTATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
12 4 0.06
13 37 0.59
14 13 0.21
15 6 0.10
16 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:42826774 original size:27 final size:27
Alignment explanation
Indices: 42826704--42826792 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
42826694 AGAAAAATAA
* * *
42826704 TATATG-AAATGGTTATATGAACTGGT
1 TATATGAAAATAGATATATGAAATGGT
*
42826730 TATATGGAAAA-ATGATATATGAAATGGG
1 TATAT-GAAAATA-GATATATGAAATGGT
42826758 TATATGAAAATAGATATATGAAATGGT
1 TATATGAAAATAGATATATGAAATGGT
42826785 TATATGAA
1 TATATGAA
42826793 TCAGTTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 5 0.09
27 28 0.52
28 21 0.39
ACGTcount: A:0.44, C:0.01, G:0.21, T:0.34
Consensus pattern (27 bp):
TATATGAAAATAGATATATGAAATGGT
Found at i:42826809 original size:68 final size:67
Alignment explanation
Indices: 42826697--42826833 Score: 197
Period size: 68 Copynumber: 2.0 Consensus size: 67
42826687 TTGGATGAGA
*
42826697 AAAATAATATATGAAATGGTTATATGAACTGGTTATATGGAAAAATGATATATGA-AATGGGTAT
1 AAAATAATATATGAAATGGTTATATGAACTAGTTATATGGAAAAATGATATAT-ATAATGGGTAT
42826761 ATG
65 ATG
* * *
42826764 AAAATAGATATATGAAATGGTTATATGAA-TCAGTTATATGTAAAAATGATATGTATAATGGTTA
1 AAAATA-ATATATGAAATGGTTATATGAACT-AGTTATATGGAAAAATGATATATATAATGGGTA
42826828 TATG
64 TATG
42826832 AA
1 AA
42826834 TCAGTTATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
67 8 0.13
68 55 0.87
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.34
Consensus pattern (67 bp):
AAAATAATATATGAAATGGTTATATGAACTAGTTATATGGAAAAATGATATATATAATGGGTATA
TG
Found at i:42826849 original size:68 final size:68
Alignment explanation
Indices: 42826698--42826861 Score: 194
Period size: 68 Copynumber: 2.4 Consensus size: 68
42826688 TGGATGAGAA
*
42826698 AAATA-ATATATGAAATGGTTATATGAA-CTGGTTATATGGAAAAATGATATATGAAATGGGTAT
1 AAATAGATATATGAAATGGTTATATGAATCTAGTTATATGGAAAAATGATATATGAAATGGGTAT
42826761 ATG
66 ATG
* * *
42826764 AAAATAGATATATGAAATGGTTATATGAATC-AGTTATATGTAAAAATGATATGT-ATAATGGTT
1 -AAATAGATATATGAAATGGTTATATGAATCTAGTTATATGGAAAAATGATATATGA-AATGGGT
42826827 ATATG
64 ATATG
* * *
42826832 -AATCAGTTATATGGAAATAGATATATGAAT
1 AAAT-AGATATAT-GAAATGGTTATATGAAT
42826862 AAAACATTGG
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
66 3 0.04
67 13 0.15
68 68 0.80
69 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.35
Consensus pattern (68 bp):
AAATAGATATATGAAATGGTTATATGAATCTAGTTATATGGAAAAATGATATATGAAATGGGTAT
ATG
Found at i:42827397 original size:25 final size:25
Alignment explanation
Indices: 42827369--42827418 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
42827359 AATCCTTAAT
*
42827369 GTTATTTTTGTTGGTTTGGTAATTG
1 GTTATTTTGGTTGGTTTGGTAATTG
42827394 GTTATTTTGGTTGGTTTGGTAATTG
1 GTTATTTTGGTTGGTTTGGTAATTG
42827419 ATGCCATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.58
Consensus pattern (25 bp):
GTTATTTTGGTTGGTTTGGTAATTG
Found at i:42839616 original size:2 final size:2
Alignment explanation
Indices: 42839611--42839643 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
42839601 TATAAAAAAA
42839611 AT AT AT 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 AT AT AT A
42839644 CATAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42840337 original size:23 final size:22
Alignment explanation
Indices: 42840294--42840351 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
42840284 AAAGGGTATC
* *
42840294 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
42840315 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
42840338 TGCATATCATATCT
1 TACAAATCATATCT
42840352 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:42840984 original size:44 final size:44
Alignment explanation
Indices: 42840878--42840999 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 44
42840868 ACCTGATACG
* * * *
42840878 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTTA
1 ATCTACTCCACTGCAACTTCAGAGAGATAAGATCTATGACTTCA
** * * * *
42840922 ATCTGTTCCATTGTAACTTCAGTGAGATAAGAT-TACTGGCTTCA
1 ATCTACTCCACTGCAACTTCAGAGAGATAAGATCTA-TGACTTCA
* *
42840966 ATCTACTCCACTGCAACTT-AGGGAGATAAAATCT
1 ATCTACTCCACTGCAACTTCAGAGAGATAAGATCT
42841000 GTAATTTTTA
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
43 13 0.22
44 47 0.78
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (44 bp):
ATCTACTCCACTGCAACTTCAGAGAGATAAGATCTATGACTTCA
Found at i:42841342 original size:44 final size:44
Alignment explanation
Indices: 42841279--42841662 Score: 585
Period size: 44 Copynumber: 8.8 Consensus size: 44
42841269 GATCTGCTCC
*
42841279 ATCTTCAACCTATTCCACTGCTGACCAGGGAAATAGGATTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
42841323 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
*
42841367 ATCTTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTT-ACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACA
*
42841411 ATCTTCAACCTATT-CACTGCTGACCAGGGAGATAGGACTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
*
42841454 ATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
* *
42841498 ATCTTCAACCTATTACACTGCTGTCCAGGGAGATAGGATTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
* * *
42841542 ATCTTAAACCTATTCCACTGCTAACTAGGGAGATAGGATTCACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
* * **
42841586 ATCTTCAACCTATTCCGCTACTGATTAGGGAGATAGGACTT-ACA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACA
* **
42841630 ATCTTGAACCTATTCCACTGCTTTCCAGGGAGA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGA
42841663 CAAGACTAAT
Statistics
Matches: 311, Mismatches: 25, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
42 1 0.00
43 39 0.13
44 267 0.86
45 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACA
Found at i:42841574 original size:175 final size:176
Alignment explanation
Indices: 42841279--42841662 Score: 601
Period size: 175 Copynumber: 2.2 Consensus size: 176
42841269 GATCTGCTCC
* *
42841279 ATCTTCAACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTCAACCTATTCCACTGC
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTACACTGC
* * *
42841344 TGACCAGGGAGATAGGATTCACAATCTTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTT-
66 TGACCAGGGAGATAGGATTCACAATCTTAAACCTATTCCACTGCTAACCAGGGAGATAGGA-TTC
*
42841408 ACAATCTTCAACCTATT-CACTGCTGACCAGGGAGATAGGACTCACA
130 ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACA
*
42841454 ATTTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTACACTGC
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTACACTGC
* *
42841519 TGTCCAGGGAGATAGGATTCACAATCTTAAACCTATTCCACTGCTAACTAGGGAGATAGGATTCA
66 TGACCAGGGAGATAGGATTCACAATCTTAAACCTATTCCACTGCTAACCAGGGAGATAGGATTCA
* ** *
42841584 CAATCTTCAACCTATTCCGCTACTGATTAGGGAGATAGGACTTACA
131 CAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACA
* **
42841630 ATCTTGAACCTATTCCACTGCTTTCCAGGGAGA
1 ATCTTCAACCTATTCCACTGCTGACCAGGGAGA
42841663 CAAGACTAAT
Statistics
Matches: 190, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
174 2 0.01
175 135 0.71
176 53 0.28
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (176 bp):
ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTACACTGC
TGACCAGGGAGATAGGATTCACAATCTTAAACCTATTCCACTGCTAACCAGGGAGATAGGATTCA
CAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACA
Found at i:42846185 original size:33 final size:33
Alignment explanation
Indices: 42846141--42846206 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
42846131 AAATGAATGC
* *
42846141 CTAAAGTGACGTTGATTTTGATTTAATTACATT
1 CTAAAGAGACGTTGATTCTGATTTAATTACATT
42846174 CTAAAGAGACGTTGATTCTGATTTAATTACATT
1 CTAAAGAGACGTTGATTCTGATTTAATTACATT
42846207 TAGAAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (33 bp):
CTAAAGAGACGTTGATTCTGATTTAATTACATT
Done.