Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 186 of 196
Found at i:54814516 original size:20 final size:21
Alignment explanation
Indices: 54814493--54814540 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
54814483 CTCATATTAG
*
54814493 ATATTAACATAACATA-GAAA
1 ATATTAACATAACAAATGAAA
* * *
54814513 ATATAAACCTAACAAATTAAA
1 ATATTAACATAACAAATGAAA
54814534 ATATTAA
1 ATATTAA
54814541 ATATATTTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
ATATTAACATAACAAATGAAA
Found at i:54816261 original size:72 final size:72
Alignment explanation
Indices: 54816136--54816306 Score: 258
Period size: 72 Copynumber: 2.4 Consensus size: 72
54816126 AAAATCATAT
* * *
54816136 ATAAACAACTATTGATAAAACTA-ATTTAATAAAAATAAGTAGAACATAAATTCAATATCTAAAG
1 ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
54816200 ACCAAAC
66 ACCAAAC
* *
54816207 ATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATCCAAA
1 ATAAACAACTATTGATAAAACTAGATTTA-ACAAAAATAAGTAGAACATAAATTCAATATCCAAA
54816271 AACCAAAC
65 AACCAAAC
*
54816279 ATAAATAACTATTGATAAAACTAG-TTTA
1 ATAAACAACTATTGATAAAACTAGATTTA
54816307 GCATTGTCAG
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
71 25 0.28
72 65 0.72
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTGATAAAACTAGATTTAACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:54818691 original size:23 final size:24
Alignment explanation
Indices: 54818643--54818695 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
54818633 TGGAGAAGAA
*
54818643 GAACAAAGAATAAGCACCAGCAGAG
1 GAACAAAGAACAAGCA-CAGCAGAG
*
54818668 GAACAAAGAACCAGCA-AGCAGAG
1 GAACAAAGAACAAGCACAGCAGAG
54818691 GAACA
1 GAACA
54818696 CCAGCACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
25 14 0.54
ACGTcount: A:0.53, C:0.21, G:0.25, T:0.02
Consensus pattern (24 bp):
GAACAAAGAACAAGCACAGCAGAG
Found at i:54818784 original size:14 final size:14
Alignment explanation
Indices: 54818765--54818794 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
54818755 GAACACCAGC
54818765 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
54818779 ACCAGCAGAGAAGA
1 ACCAGCAGAGAAGA
54818793 AC
1 AC
54818795 AAATGTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.27, T:0.00
Consensus pattern (14 bp):
ACCAGCAGAGAAGA
Found at i:54819446 original size:34 final size:35
Alignment explanation
Indices: 54819392--54819458 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54819382 CAAACAGCAG
* *
54819392 AAAATATTTTCTAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATTATTTTACAGAAAAGT
*
54819427 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATTATTTTACAGAAAA
54819459 CATTTTACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATTATTTTACAGAAAAGT
Found at i:54821361 original size:17 final size:18
Alignment explanation
Indices: 54821339--54821373 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54821329 GTTAGGGGTA
54821339 AAAAATCAT-GAATAAAT
1 AAAAATCATGGAATAAAT
*
54821356 AAAAATGATGGAATAAAT
1 AAAAATCATGGAATAAAT
54821374 TGAGAAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.03, G:0.11, T:0.23
Consensus pattern (18 bp):
AAAAATCATGGAATAAAT
Found at i:54823378 original size:22 final size:23
Alignment explanation
Indices: 54823324--54823379 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
54823314 TTGTCTCATA
54823324 ATTTTTATTTTTCAAAAAACATT
1 ATTTTTATTTTTCAAAAAACATT
* *
54823347 ATAATTT-TTTTT-AAAATACATT
1 AT-TTTTATTTTTCAAAAAACATT
54823369 -TTTTTATTTTT
1 ATTTTTATTTTT
54823380 ATTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.11
21 6 0.21
22 9 0.32
23 7 0.25
24 3 0.11
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTTTATTTTTCAAAAAACATT
Found at i:54826884 original size:13 final size:13
Alignment explanation
Indices: 54826866--54826897 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
54826856 ATACATATAT
54826866 TTGTAAAATCTAA
1 TTGTAAAATCTAA
54826879 TTGTAAAATCTAA
1 TTGTAAAATCTAA
54826892 TT-TAAA
1 TTGTAAA
54826898 TCAATTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (13 bp):
TTGTAAAATCTAA
Found at i:54832448 original size:41 final size:41
Alignment explanation
Indices: 54832373--54832453 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
54832363 AACTGGTTTG
* * *
54832373 TATTATTTATTTAATTGTGATTATTATCGCAAGTGCTACTA
1 TATTATTCATTTAATGGTGATTATTATCACAAGTGCTACTA
* *
54832414 TATTATTCATTTAATGGTGATTATTATTATAAGTGCTACT
1 TATTATTCATTTAATGGTGATTATTATCACAAGTGCTACT
54832454 CTAAATTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (41 bp):
TATTATTCATTTAATGGTGATTATTATCACAAGTGCTACTA
Found at i:54835560 original size:3 final size:3
Alignment explanation
Indices: 54835552--54835577 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54835542 AGGGAAAACA
54835552 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
54835578 AAGGCCACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54837384 original size:17 final size:17
Alignment explanation
Indices: 54837362--54837396 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
54837352 TTATCAAACA
*
54837362 ATTTAATTATACTTAAT
1 ATTTAATTATACGTAAT
*
54837379 ATTTAATTTTACGTAAT
1 ATTTAATTATACGTAAT
54837396 A
1 A
54837397 CACCAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAATTATACGTAAT
Found at i:54842892 original size:12 final size:12
Alignment explanation
Indices: 54842856--54842895 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
54842846 AAGATATGTA
54842856 TATGTATGCATG
1 TATGTATGCATG
* *
54842868 CATGCATGCATG
1 TATGTATGCATG
*
54842880 TATGTATGTATG
1 TATGTATGCATG
54842892 TATG
1 TATG
54842896 ATTGAATGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (12 bp):
TATGTATGCATG
Found at i:54855298 original size:18 final size:18
Alignment explanation
Indices: 54855258--54855300 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
54855248 GTTTAAAGTG
54855258 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
54855276 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
54855294 TAATTAA
1 TAATTAA
54855301 AAACCCATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:54858524 original size:13 final size:13
Alignment explanation
Indices: 54858506--54858537 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54858496 TTAGAATGAA
54858506 ATGAAATGAAATT
1 ATGAAATGAAATT
54858519 ATGAAAT-AAATT
1 ATGAAATGAAATT
54858531 -TGAAATG
1 ATGAAATG
54858538 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 5 0.28
13 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGAAATGAAATT
Found at i:54865575 original size:84 final size:84
Alignment explanation
Indices: 54865481--54865774 Score: 385
Period size: 84 Copynumber: 3.5 Consensus size: 84
54865471 CGTTTTGCGG
** * * *
54865481 AACATTAATTCAATCTTGCGGCGTTTTCTTAAAAAACATCACTACAATATTTTATTTCAGTAGAG
1 AACATTAATTCAATCTTGCGGCGTTTTCTTAAAAAACGCCACTATAATATTTTATTCCAATAGAG
*
54865546 AAACAGCGCCGCATTGGCA
66 AAACGGCGCCGCATTGGCA
* * *
54865565 AACATTAATTCACTCTTGCGGCGTTTTATTAAAAAACGCCACTATAAGATTTTATTCCAATAGAG
1 AACATTAATTCAATCTTGCGGCGTTTTCTTAAAAAACGCCACTATAATATTTTATTCCAATAGAG
*
54865630 AAACGGCGCCGAATTGGCA
66 AAACGGCGCCGCATTGGCA
* *
54865649 AACATTAATTCACTCTTGCGGCGTTTTCTTAAAAAACGCCACTATAATATTTTATTCCACTAGAG
1 AACATTAATTCAATCTTGCGGCGTTTTCTTAAAAAACGCCACTATAATATTTTATTCCAATAGAG
* * *
54865714 AAACGGTGCCGCTTTGCCA
66 AAACGGCGCCGCATTGGCA
** * *
54865733 AATTTTAA-TAAATCCTTGCGGCGTTTTCACT-AAAAACGCCAC
1 AACATTAATTCAAT-CTTGCGGCGTTTTC-TTAAAAAACGCCAC
54865775 AAAAAAAATC
Statistics
Matches: 186, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
83 3 0.02
84 182 0.98
85 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (84 bp):
AACATTAATTCAATCTTGCGGCGTTTTCTTAAAAAACGCCACTATAATATTTTATTCCAATAGAG
AAACGGCGCCGCATTGGCA
Found at i:54865843 original size:83 final size:83
Alignment explanation
Indices: 54865703--54865864 Score: 184
Period size: 83 Copynumber: 2.0 Consensus size: 83
54865693 TAATATTTTA
* ** ** *
54865703 TTCCACTAGAGAAACGGTGCCGCTTTGCCAAATTTTAATAAATCCTTGCGGCGTTTTCAC-TAAA
1 TTCCACTAGAGAAACGGTGCCGCTTTGACAAATTTTAATAAATAATAACGGCATTTTC-CGTAAA
54865767 AACGCCACAAAAAAAATCG
65 AACGCCACAAAAAAAATCG
* * * *
54865786 TTCCTCTAGATAAACGGTGCCGTTTTGACAAATTTTAA-AACATAATAATGGCATTTTCCGTAAA
1 TTCCACTAGAGAAACGGTGCCGCTTTGACAAATTTTAATAA-ATAATAACGGCATTTTCCGTAAA
* *
54865850 AATGCCACTAAAAAA
65 AACGCCACAAAAAAA
54865865 TTAAACTCCT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
82 3 0.05
83 62 0.95
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
TTCCACTAGAGAAACGGTGCCGCTTTGACAAATTTTAATAAATAATAACGGCATTTTCCGTAAAA
ACGCCACAAAAAAAATCG
Found at i:54866380 original size:81 final size:81
Alignment explanation
Indices: 54866275--54866433 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 81
54866265 CCTAACTCAG
* *
54866275 CCCCTAACCCCTAAACTTTATTTAATATATAAATT-AAAAACACTAATTAATCTAAACCCTAAAC
1 CCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAAC
54866339 CATAACCCAACCCAAA
66 CATAACCCAACCCAAA
* *
54866355 CCCCTAAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAGTTAGTCTAAACCATAAA
1 CCCCT-AACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAA
54866420 CCATAACCCAACCC
65 CCATAACCCAACCC
54866434 CAAATCCTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 5 0.07
81 29 0.40
82 39 0.53
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (81 bp):
CCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCATAAAC
CATAACCCAACCCAAA
Found at i:54866433 original size:100 final size:101
Alignment explanation
Indices: 54866341--54866761 Score: 458
Period size: 100 Copynumber: 4.1 Consensus size: 101
54866331 CCCTAAACCA
*
54866341 TAACCCAACC-CAAACCCCTAAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAGTT
1 TAACCCAACCTCAAACCCCT-AACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
* * *
54866405 AGTCTAAACCATAAACCATAACCCAACCCCAAATCCT
65 AATCTAAACCCTAAACCATAACCCAACCCCAAATCCC
* *
54866442 TAACCGGGCCCCTAACACTTAACCCATAACCCATAACCCCTAAAACTTATTTAATATATAAA-TA
1 TAA------CCC-AAC-C-T----CA-AACCCCTAACCCCTAAACCTTATTTAATATATAAATTA
* *
54866506 AAAAATACTAATTAATTTAAACCCTAAACCATAACCCAACCCCAAATCCC
52 AAAAACACTAATTAATCTAAACCCTAAACCATAACCCAACCCCAAATCCC
** **
54866556 TAACCCCAACCTTTAA-CCCTAACATCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
1 TAA-CCCAACCTCAAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
* *
54866620 AATCTAAACCCTAAATCATAA-CCGACCCCAAATCCC
65 AATCTAAACCCTAAACCATAACCCAACCCCAAATCCC
* * *
54866656 CAACCCGACCAT-TAACCCCTAACCCCTAAACCTTATTTAATATATAAATT-AAAAACACTAATT
1 TAACCCAACC-TCAAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATT
* * * *
54866719 AATCTAAATCCTAAACCATAACCCAATCCCTAACCCC
65 AATCTAAACCCTAAACCATAACCCAACCCCAAATCCC
54866756 TAACCC
1 TAACCC
54866762 CTAAACCTTA
Statistics
Matches: 272, Mismatches: 29, Indels: 39
0.80 0.09 0.11
Matches are distributed among these distances:
99 41 0.15
100 93 0.34
101 38 0.14
106 1 0.00
107 4 0.01
108 6 0.02
109 5 0.02
114 49 0.18
115 29 0.11
116 6 0.02
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (101 bp):
TAACCCAACCTCAAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTA
ATCTAAACCCTAAACCATAACCCAACCCCAAATCCC
Found at i:54866560 original size:114 final size:115
Alignment explanation
Indices: 54866347--54866660 Score: 342
Period size: 114 Copynumber: 2.9 Consensus size: 115
54866337 ACCATAACCC
* * * *
54866347 AACCCAAACCCCTAAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAGTTAGTCTAA
1 AACCCAAACCCATAAACCCCTAAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
*
54866412 ACCATAAACCATAACCCAACCCCAAATCCTTAACCGGGCCCCTAACACTT
66 ACCATAAACCATAACCCAACCCCAAATCCCTAACCGGGCCCCTAACACTT
* *
54866462 AACCCATAACCCAT-AACCCCTAAAACTTATTTAATATATAAA-TAAAAAATACTAATTAATTTA
1 AACCCA-AACCCATAAACCCCTAAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTA
*
54866525 AACCCTAAACCATAACCCAACCCCAAATCCCTAA-----CCCC-AAC-CTTT
65 AACCATAAACCATAACCCAACCCCAAATCCCTAACCGGGCCCCTAACAC-TT
* *
54866570 AACCCTAACATC-TAAA---C-----CTTATTTAATATATAAATTAAAAAACACTAATTAATCTA
1 AACCCAAAC-CCATAAACCCCTAAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTA
* * * *
54866626 AACCCTAAATCATAA-CCGACCCCAAATCCCCAACC
65 AACCATAAACCATAACCCAACCCCAAATCCCTAACC
54866661 CGACCATTAA
Statistics
Matches: 177, Mismatches: 15, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
100 33 0.19
101 33 0.19
105 1 0.01
107 5 0.03
108 13 0.07
109 4 0.02
114 49 0.28
115 33 0.19
116 6 0.03
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.23
Consensus pattern (115 bp):
AACCCAAACCCATAAACCCCTAAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTAA
ACCATAAACCATAACCCAACCCCAAATCCCTAACCGGGCCCCTAACACTT
Found at i:54866761 original size:81 final size:81
Alignment explanation
Indices: 54866668--54866822 Score: 292
Period size: 81 Copynumber: 1.9 Consensus size: 81
54866658 ACCCGACCAT
*
54866668 TAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAA
1 TAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAA
54866733 ACCATAACCCAATCCC
66 ACCATAACCCAATCCC
*
54866749 TAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACGCTAATTAATCTAAACCCTAA
1 TAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAA
54866814 ACCATAACC
66 ACCATAACC
54866823 TGACCCCAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.27
Consensus pattern (81 bp):
TAACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAA
ACCATAACCCAATCCC
Found at i:54866841 original size:81 final size:81
Alignment explanation
Indices: 54866669--54866846 Score: 275
Period size: 81 Copynumber: 2.2 Consensus size: 81
54866659 CCCGACCATT
* *
54866669 AACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAATCCTAAA
1 AACCCATAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAA
* *
54866734 CCATAACCCAATCCCT
66 CCATAACCCAACCCCA
* *
54866750 AACCCCTAACCCCTAAACCTTATTTAATATATAAATTAAAAACGCTAATTAATCTAAACCCTAAA
1 AACCCATAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAA
**
54866815 CCATAACCTGACCCCA
66 CCATAACCCAACCCCA
*
54866831 AATCCATAACCCCTAA
1 AACCCATAACCCCTAA
54866847 TATTTAACCG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 89 1.00
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (81 bp):
AACCCATAACCCCTAAACCTTATTTAATATATAAATTAAAAACACTAATTAATCTAAACCCTAAA
CCATAACCCAACCCCA
Found at i:54867736 original size:6 final size:6
Alignment explanation
Indices: 54867725--54867757 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
54867715 AACATTGCAA
54867725 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
54867758 TCATATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:54874713 original size:23 final size:23
Alignment explanation
Indices: 54874687--54874753 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 23
54874677 TTTTGAGCAA
54874687 TATATTTTAAGTCATGGTAACTT
1 TATATTTTAAGTCATGGTAACTT
* *
54874710 TATA----AAATCATGATCAA---
1 TATATTTTAAGTCATGGT-AACTT
54874727 TATATTTTAAGTCATGGTAACTT
1 TATATTTTAAGTCATGGTAACTT
54874750 TATA
1 TATA
54874754 AAAACATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 16
0.62 0.08 0.31
Matches are distributed among these distances:
17 4 0.12
19 8 0.25
20 4 0.12
21 8 0.25
23 8 0.25
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.43
Consensus pattern (23 bp):
TATATTTTAAGTCATGGTAACTT
Found at i:54876524 original size:27 final size:27
Alignment explanation
Indices: 54876459--54876528 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
54876449 CAAATTTTAG
* *
54876459 ATTGTTGGATTTTGATATATGTCTTGA
1 ATTGTTGGATATTGATATATGTCTTAA
* *
54876486 ATTGGTTAGATATTGAT-TATGTTTTAA
1 ATT-GTTGGATATTGATATATGTCTTAA
54876513 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
54876529 ATTGATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (27 bp):
ATTGTTGGATATTGATATATGTCTTAA
Found at i:54877930 original size:14 final size:14
Alignment explanation
Indices: 54877907--54877948 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
54877897 ACAGAAAAGT
*
54877907 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
54877921 AAATCATTTTACGG
1 AAAACATTTTACAG
54877935 AAAACATTTTACAG
1 AAAACATTTTACAG
54877949 CCAATCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:54877932 original size:34 final size:35
Alignment explanation
Indices: 54877872--54877938 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
54877862 CAAACACCAG
* *
54877872 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
54877907 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
54877939 CATTTTACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:54882403 original size:8 final size:8
Alignment explanation
Indices: 54882390--54882414 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54882380 AAAATGTATA
54882390 AAAATTTT
1 AAAATTTT
54882398 AAAATTTT
1 AAAATTTT
54882406 AAAATTTT
1 AAAATTTT
54882414 A
1 A
54882415 GTCGACTGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:54884352 original size:19 final size:18
Alignment explanation
Indices: 54884314--54884352 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
54884304 TAATAAAGTG
* *
54884314 TGTATAATAAAATTAAAA
1 TGTATAAAAAAATCAAAA
54884332 TGTATAAAAAAGATCAAAA
1 TGTATAAAAAA-ATCAAAA
54884351 TG
1 TG
54884353 AAGCTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (18 bp):
TGTATAAAAAAATCAAAA
Found at i:54886226 original size:34 final size:33
Alignment explanation
Indices: 54886188--54886286 Score: 86
Period size: 34 Copynumber: 3.2 Consensus size: 33
54886178 TAAACACAAC
*
54886188 AATTTATAACTTAATCCTAAATTACTAATAAATT
1 AATTTATAAC-TAATCCTAAATTACTAACAAATT
* * **
54886222 AATTT-TAA--AA---T-AATTACAAACACACA
1 AATTTATAACTAATCCTAAATTACTAACAAATT
54886248 AATTTATAACATAATCCTAAATTACTAACAAATT
1 AATTTATAAC-TAATCCTAAATTACTAACAAATT
54886282 AATTT
1 AATTT
54886287 TAAAATAATT
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
26 15 0.31
27 4 0.08
30 4 0.08
33 4 0.08
34 21 0.44
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (33 bp):
AATTTATAACTAATCCTAAATTACTAACAAATT
Found at i:54886263 original size:60 final size:60
Alignment explanation
Indices: 54886179--54886297 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
54886169 ATACTAAACT
* *
54886179 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
54886239 AAACAC-ACAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAAC-AATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
54886298 TAAAAAGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 2 0.04
60 54 0.96
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:54888066 original size:6 final size:6
Alignment explanation
Indices: 54888057--54888083 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
54888047 AAAACAAAAT
54888057 GCCAAA GCCAAA GCCAAA GCCAAA GCC
1 GCCAAA GCCAAA GCCAAA GCCAAA GCC
54888084 TGCCATTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:54916649 original size:17 final size:17
Alignment explanation
Indices: 54916627--54916660 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54916617 AACTGGCCCC
54916627 TAACAATAATTAAACCT
1 TAACAATAATTAAACCT
54916644 TAACAATAATTAAACCT
1 TAACAATAATTAAACCT
54916661 GCATTGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (17 bp):
TAACAATAATTAAACCT
Found at i:54916756 original size:16 final size:16
Alignment explanation
Indices: 54916737--54916767 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54916727 CAAAGAGTAC
*
54916737 AACAGAAGAAGAATAT
1 AACAGAAGAAAAATAT
54916753 AACAGAAGAAAAATA
1 AACAGAAGAAAAATA
54916768 ATAAATTAAT
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:0.68, C:0.06, G:0.16, T:0.10
Consensus pattern (16 bp):
AACAGAAGAAAAATAT
Found at i:54918756 original size:32 final size:30
Alignment explanation
Indices: 54918675--54918756 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 30
54918665 TTGGCCTCAA
*
54918675 TGTTCAATTTTGTACCT-AAA--TATTTTT
1 TGTTCAATTTGGTACCTGAAACTTATTTTT
* * * *
54918702 TATCCAATTAGGTACTTG-AACTTCATTTTTT
1 TGTTCAATTTGGTACCTGAAACTT-A-TTTTT
54918733 TGTTCAATTTGGTACCTGAAACTT
1 TGTTCAATTTGGTACCTGAAACTT
54918757 GGATATATAG
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
27 14 0.35
29 1 0.03
30 1 0.03
31 19 0.47
32 5 0.12
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (30 bp):
TGTTCAATTTGGTACCTGAAACTTATTTTT
Found at i:54932425 original size:23 final size:22
Alignment explanation
Indices: 54932399--54932442 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
54932389 AATTGACTAA
54932399 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
54932422 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
54932443 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:54932473 original size:38 final size:38
Alignment explanation
Indices: 54932430--54932511 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
54932420 AGGTGTGGAA
54932430 TTGAATTGAATAT-CGACTTAGAAA-TGAAAAAGTG-AATT
1 TTGAATTGAAT-TGCGA-TT-GAAAGTGAAAAAGTGAAATT
*
54932468 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAAATT
1 TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAAATT
*
54932506 ATGAAT
1 TTGAAT
54932512 ACATTTAGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 4 0.10
37 13 0.33
38 22 0.56
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (38 bp):
TTGAATTGAATTGCGATTGAAAGTGAAAAAGTGAAATT
Found at i:54934572 original size:50 final size:51
Alignment explanation
Indices: 54934447--54934639 Score: 205
Period size: 51 Copynumber: 3.7 Consensus size: 51
54934437 GATAATAACA
* ** *
54934447 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGT-TC-TCGTGATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATCGT-AAGG
* * *
54934498 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATC-TCA-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATCGTAAGG
* *
54934548 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGACCTCTC---ATCGTAAGG
54934602 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGA
54934640 TCTATTTACC
Statistics
Matches: 120, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
49 10 0.08
50 30 0.25
51 34 0.28
52 6 0.05
53 4 0.03
54 1 0.01
55 31 0.26
56 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGACCTCTCATCGTAAGG
Found at i:54934626 original size:55 final size:52
Alignment explanation
Indices: 54934447--54934639 Score: 211
Period size: 50 Copynumber: 3.7 Consensus size: 52
54934437 GATAATAACA
* **
54934447 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGA--T-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTC-TGATCTAGG
* * *
54934498 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTC--ATCTCA-G
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTGATCT-AGG
*
54934548 TGCCAACGCCATGTCCCAGACATGGTCTTACA-GGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-TGATC-T-AGG
54934602 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
54934640 TCTATTTACC
Statistics
Matches: 120, Mismatches: 11, Indels: 17
0.81 0.07 0.11
Matches are distributed among these distances:
47 1 0.01
49 11 0.09
50 34 0.28
51 33 0.28
52 3 0.03
53 2 0.02
54 1 0.01
55 31 0.26
56 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTGATCTAGG
Found at i:54934762 original size:13 final size:13
Alignment explanation
Indices: 54934744--54934770 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54934734 GATCATAATC
54934744 AAATAAATTCATA
1 AAATAAATTCATA
54934757 AAATAAATTCATA
1 AAATAAATTCATA
54934770 A
1 A
54934771 TTGCTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:54935017 original size:30 final size:30
Alignment explanation
Indices: 54934982--54935039 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54934972 CCTCGACTCT
*
54934982 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
54935012 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
54935040 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:54942115 original size:50 final size:50
Alignment explanation
Indices: 54941991--54942239 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
54941981 GATAATAACA
* * ** * *
54941991 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
54942042 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
54942092 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
54942142 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
54942197 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
54942240 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:54942169 original size:100 final size:104
Alignment explanation
Indices: 54941990--54942239 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
54941980 TGATAATAAC
**
54941990 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
54942055 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
54942092 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
54942155 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
54942197 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
54942240 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:54942355 original size:13 final size:13
Alignment explanation
Indices: 54942334--54942365 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54942324 GCTTGGATCA
*
54942334 TCATCAAATAAAT
1 TCATAAAATAAAT
54942347 TCATAAAATAAAT
1 TCATAAAATAAAT
54942360 TCATAA
1 TCATAA
54942366 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:54942612 original size:30 final size:30
Alignment explanation
Indices: 54942577--54942634 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54942567 CCTCGACTCT
*
54942577 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
54942607 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
54942635 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:54946032 original size:43 final size:42
Alignment explanation
Indices: 54945966--54946094 Score: 174
Period size: 43 Copynumber: 3.0 Consensus size: 42
54945956 ATAGGATTTC
54945966 CGATATGTGTTATCGTGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTGTTA-CGTGTAAGACCACGTCTGGGACGTTGGCAT
54946009 CGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGA-TATGTG-TTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCAT
*
54946052 CGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATGTG-TTACGTGTAAGACCACGTCTGGGACGTTGGCAT
54946095 TGTACGAGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
42 3 0.04
43 68 0.88
44 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (42 bp):
CGATATGTGTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:54946956 original size:23 final size:23
Alignment explanation
Indices: 54946929--54947281 Score: 148
Period size: 23 Copynumber: 15.2 Consensus size: 23
54946919 ATGAGTTGAA
*
54946929 CCAATTTGTTATATATATGCTGT
1 CCAATTTGTTATATAAATGCTGT
* * *
54946952 CCAATTT-TGATGCTTAAATGCTGC
1 CCAATTTGTTAT--ATAAATGCTGT
* *
54946976 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTATATAAATGCTGT
**
54946999 CCAA-TTGATGCT-TAAATGCTG-
1 CCAATTTG-TTATATAAATGCTGT
* *
54947020 CCTAATTTGTTACATATATGCTGT
1 CC-AATTTGTTATATAAATGCTGT
* * *
54947044 CTAATTT-TGATGCTTAAATGCTG-
1 CCAATTTGTTAT--ATAAATGCTGT
* *
54947067 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTATATAAATGCTGT
* * *
54947090 CCAATTT-TGATGCTTAAATGCTGC
1 CCAATTTGTTAT--ATAAATGCTGT
* *
54947114 CCAATTTGTTACATATATGCTGT
1 CCAATTTGTTATATAAATGCTGT
* * * *
54947137 CCAGTTTTGGTGTAAAAATGCTG-
1 CCA-ATTTGTTATATAAATGCTGT
** * * *
54947160 CTCAAACTGTTGTATATATGCTGC
1 C-CAATTTGTTATATAAATGCTGT
* * ** *
54947184 CCAAATTGTTGTATTTATGCTAT
1 CCAATTTGTTATATAAATGCTGT
* *
54947207 CCAAATTTTGGTGTGA-AAATGCTGT
1 CC-AA-TTTGTTAT-ATAAATGCTGT
* *
54947232 CTAATTTGGTATATAAATGCTGT
1 CCAATTTGTTATATAAATGCTGT
* * * *
54947255 CCAAATTGATGTATAAAAGCTGT
1 CCAATTTGTTATATAAATGCTGT
54947278 CCAA
1 CCAA
54947282 ATAGGGTAGA
Statistics
Matches: 243, Mismatches: 65, Indels: 44
0.69 0.18 0.12
Matches are distributed among these distances:
21 2 0.01
22 30 0.12
23 132 0.54
24 61 0.25
25 17 0.07
26 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (23 bp):
CCAATTTGTTATATAAATGCTGT
Found at i:54947160 original size:47 final size:47
Alignment explanation
Indices: 54946929--54947145 Score: 377
Period size: 47 Copynumber: 4.7 Consensus size: 47
54946919 ATGAGTTGAA
*
54946929 CCAATTTGTTATATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
54946976 CCAATTTGTTACATATATGCTGTCCAA--TTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
* *
54947021 CTAATTTGTTACATATATGCTGTCTAATTTTGATGCTTAAATGCTG-
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
54947067 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
1 CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
*
54947114 CCAATTTGTTACATATATGCTGTCCAGTTTTG
1 CCAATTTGTTACATATATGCTGTCCAATTTTG
54947146 GTGTAAAAAT
Statistics
Matches: 161, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
45 43 0.27
46 44 0.27
47 74 0.46
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (47 bp):
CCAATTTGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGC
Found at i:54947177 original size:47 final size:47
Alignment explanation
Indices: 54946935--54947187 Score: 280
Period size: 47 Copynumber: 5.4 Consensus size: 47
54946925 TGAACCAATT
* * **
54946935 TGTTATATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATT
1 TGTTACATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
* * **
54946982 TGTTACATATATGCTGTCCAA--TTGATGCTTAAATGCTGCCTAATT
1 TGTTACATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
* * **
54947027 TGTTACATATATGCTGTCTAATTTTGATGCTTAAATGCTG-CCAATT
1 TGTTACATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
* **
54947073 TGTTACATATATGCTGTCCAATTTTGATGCTTAAATGCTGCCCAATT
1 TGTTACATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
* * *
54947120 TGTTACATATATGCTGTCCAGTTTTGGTG-TAAAAATGCTGCTCAAAC
1 TGTTACATATATGCTGTCCAATTTTGATGCT-AAAATGCTGCCCAAAC
** *
54947167 TGTTGTATATATGCTGCCCAA
1 TGTTACATATATGCTGTCCAA
54947188 ATTGTTGTAT
Statistics
Matches: 187, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
45 43 0.23
46 45 0.24
47 99 0.53
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (47 bp):
TGTTACATATATGCTGTCCAATTTTGATGCTAAAATGCTGCCCAAAC
Found at i:54947228 original size:71 final size:69
Alignment explanation
Indices: 54947106--54947269 Score: 179
Period size: 71 Copynumber: 2.3 Consensus size: 69
54947096 TTGATGCTTA
* ** * *
54947106 AATGCTGCCCAATTTGTTACATATATGCTGTCCAGTTTTGGTGTAAAAATGCTGCTCAAACTGTT
1 AATGCTGCCCAAATTGTTGTATATATGCTATCCAATTTTGGTGTAAAAATGCTG-TCAAA-T-TT
54947171 -GTATAT
63 GGTATAT
* * *
54947177 -ATGCTGCCCAAATTGTTGTATTTATGCTATCCAAATTTTGGTGTGAAAATGCTGTCTAATTTGG
1 AATGCTGCCCAAATTGTTGTATATATGCTATCC-AATTTTGGTGTAAAAATGCTGTCAAATTTGG
54947241 TATAT
65 TATAT
* *
54947246 AAATGCTGTCCAAATTGATGTATA
1 -AATGCTGCCCAAATTGTTGTATA
54947270 AAAGCTGTCC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
68 2 0.03
69 7 0.09
70 31 0.40
71 38 0.49
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (69 bp):
AATGCTGCCCAAATTGTTGTATATATGCTATCCAATTTTGGTGTAAAAATGCTGTCAAATTTGGT
ATAT
Found at i:54953450 original size:17 final size:15
Alignment explanation
Indices: 54953412--54953450 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54953402 GTTTAGTCCC
54953412 TAGGGTTTTTTGGTT
1 TAGGGTTTTTTGGTT
*
54953427 TAAGGTTTTTTAGGGTT
1 TAGGGTTTTTT--GGTT
54953444 TAGGGTT
1 TAGGGTT
54953451 AGGATTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (15 bp):
TAGGGTTTTTTGGTT
Found at i:54953601 original size:34 final size:32
Alignment explanation
Indices: 54953537--54953627 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 32
54953527 TTTAAAAAAC
* *
54953537 AAATTATGGTTTAGTGTTTTTTAAAATTAATT
1 AAATTAGGGTTTAGAGTTTTTTAAAATTAATT
* *
54953569 AATTTGGGGTTTAGAGTTTTTAATAAAATTAATT
1 AAATTAGGGTTTAGAGTTTTT--TAAAATTAATT
**
54953603 AAATTAGGGTTTAGCTTTTTTTAAA
1 AAATTAGGGTTTAGAGTTTTTTAAA
54953628 TAACTTTGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
32 21 0.43
34 28 0.57
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.49
Consensus pattern (32 bp):
AAATTAGGGTTTAGAGTTTTTTAAAATTAATT
Found at i:54957227 original size:24 final size:24
Alignment explanation
Indices: 54957200--54957245 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54957190 GTTGCTCCGA
*
54957200 TTGTGGGTGTTGGGAGGATGACGG
1 TTGTGGGTGTTAGGAGGATGACGG
54957224 TTGTGGGTGTTAGGAGGATGAC
1 TTGTGGGTGTTAGGAGGATGAC
54957246 CCACATTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.50, T:0.30
Consensus pattern (24 bp):
TTGTGGGTGTTAGGAGGATGACGG
Found at i:54959183 original size:18 final size:18
Alignment explanation
Indices: 54959145--54959184 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
54959135 TTTGATTAAA
**
54959145 AATTAACCGAATTACTTG
1 AATTAACCGAATTACCCG
*
54959163 AATTATCCGAATTACCCG
1 AATTAACCGAATTACCCG
54959181 AATT
1 AATT
54959185 GAATCACTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:54959229 original size:37 final size:37
Alignment explanation
Indices: 54959183--54959257 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
54959173 ATTACCCGAA
* *
54959183 TTGAATCACTACATAATTAAAAATATTACATAAATCT
1 TTGAATCACTACATAATTAAAAACATTAAATAAATCT
*
54959220 TTGAATCACTACATAATTAAAAACATTAAATAATTCT
1 TTGAATCACTACATAATTAAAAACATTAAATAAATCT
54959257 T
1 T
54959258 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.36
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTAAATAAATCT
Found at i:54959436 original size:38 final size:39
Alignment explanation
Indices: 54959385--54959462 Score: 124
Period size: 38 Copynumber: 2.0 Consensus size: 39
54959375 ACTTAAGAGT
*
54959385 TAGACTTTAGTTTTA-TTTCTATTGTGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTT-TATTGGGTTGGGTAATTGGG
54959423 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
54959462 T
1 T
54959463 TGGGTTGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 23 0.62
39 14 0.38
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:54959461 original size:13 final size:13
Alignment explanation
Indices: 54959443--54959467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54959433 TTTTAGTTTT
54959443 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
54959456 ATTGGGTTGGGT
1 ATTGGGTTGGGT
54959468 TGGTAATTGG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:54959467 original size:18 final size:19
Alignment explanation
Indices: 54959444--54959493 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
54959434 TTTAGTTTTA
54959444 TTGGGTTGGGTAATTGGG-
1 TTGGGTTGGGTAATTGGGC
54959462 TTGGGTT-GGTAATTGGGC
1 TTGGGTTGGGTAATTGGGC
*
54959480 TT-GGTTGGATAATT
1 TTGGGTTGGGTAATT
54959494 TTATTTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.14, C:0.02, G:0.42, T:0.42
Consensus pattern (19 bp):
TTGGGTTGGGTAATTGGGC
Found at i:54959474 original size:17 final size:18
Alignment explanation
Indices: 54959444--54959493 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
54959434 TTTAGTTTTA
54959444 TTGGGTTGGGTAATTGGG-
1 TTGGGTT-GGTAATTGGGC
54959462 TTGGGTTGGTAATTGGGC
1 TTGGGTTGGTAATTGGGC
54959480 TT-GGTTGGATAATT
1 TTGGGTTGG-TAATT
54959494 TTATTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.14, C:0.02, G:0.42, T:0.42
Consensus pattern (18 bp):
TTGGGTTGGTAATTGGGC
Found at i:54960859 original size:29 final size:29
Alignment explanation
Indices: 54960798--54960860 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
54960788 GTTTAATGTG
* * ** * *
54960798 CAATTTTATACATGAACTTTGATTTTGTG
1 CAATTTTATACATGAAATTTAAACTTATC
54960827 CAATTTTATACATGAAATTTAAACTTATC
1 CAATTTTATACATGAAATTTAAACTTATC
54960856 CAATT
1 CAATT
54960861 CTCACAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (29 bp):
CAATTTTATACATGAAATTTAAACTTATC
Found at i:54969149 original size:9 final size:9
Alignment explanation
Indices: 54969135--54969160 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54969125 AAAAAAACTT
54969135 CATCATCTA
1 CATCATCTA
54969144 CATCATCTA
1 CATCATCTA
54969153 CATCATCT
1 CATCATCT
54969161 TTTCCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
CATCATCTA
Found at i:54973168 original size:43 final size:43
Alignment explanation
Indices: 54973120--54973205 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
54973110 TTTTCAAATT
54973120 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
1 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
54973163 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
1 AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
54973206 TTGAACTCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (43 bp):
AATTTATCTTGTTGGTTGTAAATTGTTACTGAGTTTCCAACTC
Found at i:54976208 original size:21 final size:21
Alignment explanation
Indices: 54976179--54976218 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54976169 AAATTTATAC
*
54976179 ATTTTTTTCAAAATATTTTAA
1 ATTTATTTCAAAATATTTTAA
* *
54976200 ATTTATTTCCACATATTTT
1 ATTTATTTCAAAATATTTT
54976219 TTATTATTTT
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:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTATTTCAAAATATTTTAA
Found at i:54979670 original size:53 final size:53
Alignment explanation
Indices: 54979613--54979715 Score: 138
Period size: 53 Copynumber: 1.9 Consensus size: 53
54979603 GATTTTCTTC
*
54979613 TCTATTGATTCATTATGGTATTC-TCCCATGATTCTTTGT-GTTTTTCTTTCTCT
1 TCTATTGATTCATTATGGT-TTCTTCCC-TGATTCTCTGTGGTTTTTCTTTCTCT
* * *
54979666 TCTATTGGTTCCTTCTGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
1 TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTC
54979716 CTATGTCTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
52 13 0.30
53 31 0.70
ACGTcount: A:0.09, C:0.21, G:0.14, T:0.56
Consensus pattern (53 bp):
TCTATTGATTCATTATGGTTTCTTCCCTGATTCTCTGTGGTTTTTCTTTCTCT
Found at i:54979878 original size:15 final size:15
Alignment explanation
Indices: 54979860--54979890 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
54979850 TGCAATTAGC
54979860 AAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAGA
*
54979875 AAAAATAAAAAAAGA
1 AAAAAAAAAAAAAGA
54979890 A
1 A
54979891 GAAGAAGAAG
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:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAAAGA
Found at i:54979892 original size:3 final size:3
Alignment explanation
Indices: 54979886--54979911 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54979876 AAAATAAAAA
54979886 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
54979912 AGAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:54990120 original size:7 final size:7
Alignment explanation
Indices: 54990097--54990137 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
54990087 TTACACAATA
54990097 ATCACCAT
1 ATCA-CAT
54990105 ATCCACAT
1 AT-CACAT
54990113 ATCACAT
1 ATCACAT
54990120 ATCACAT
1 ATCACAT
54990127 ATCACAT
1 ATCACAT
54990134 ATCA
1 ATCA
54990138 TGCATATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 23 0.72
8 7 0.22
9 2 0.06
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (7 bp):
ATCACAT
Found at i:54994609 original size:7 final size:7
Alignment explanation
Indices: 54994597--54994622 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54994587 TAAAAATTTA
54994597 AATATTC
1 AATATTC
54994604 AATATTC
1 AATATTC
54994611 AATATTC
1 AATATTC
54994618 AATAT
1 AATAT
54994623 GAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:55002396 original size:78 final size:78
Alignment explanation
Indices: 55002267--55002434 Score: 282
Period size: 78 Copynumber: 2.2 Consensus size: 78
55002257 GTCTTTGAAG
* *
55002267 AAATTAATTGATTAGCTTTAACATTTGGAGTTCCTGAACAGCCATTGGAGTGGACTTAGGAGTTG
1 AAATTAATTGATTAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
*
55002332 AGCTAAATGAATC
66 AGCTAAATAAATC
*
55002345 AAATTAATTGATTAGCTTGGACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
1 AAATTAATTGATTAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
*
55002410 AGCTGAATAAATC
66 AGCTAAATAAATC
*
55002423 AAATTACTTGAT
1 AAATTAATTGAT
55002435 CGGTCAATGG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (78 bp):
AAATTAATTGATTAGCTTGAACATTTGGAGTTCCCGAACAGCCATTGGAGTGGACTTAGGAGTTG
AGCTAAATAAATC
Found at i:55018394 original size:11 final size:10
Alignment explanation
Indices: 55018359--55018475 Score: 53
Period size: 11 Copynumber: 11.3 Consensus size: 10
55018349 CCATTTTTAT
55018359 TTTAAAAAT-
1 TTTAAAAATA
*
55018368 TTTTAAAA-A
1 TTTAAAAATA
*
55018377 TTAAAAAAGTA
1 TTTAAAAA-TA
55018388 TTTAAAAAATA
1 TTT-AAAAATA
*
55018399 TTTTAAAAAAA
1 -TTTAAAAATA
**
55018410 TAAAAAAAAGTA
1 T-TTAAAAA-TA
55018422 TTTTAAAAATA
1 -TTTAAAAATA
*
55018433 TTT-TAAA-A
1 TTTAAAAATA
*
55018441 TTTAAAAAAA
1 TTTAAAAATA
*
55018451 ATTAAAAAGTA
1 TTTAAAAA-TA
*
55018462 TGTAAAAAATA
1 T-TTAAAAATA
55018473 TTT
1 TTT
55018476 TAACATTAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 23
0.66 0.14 0.19
Matches are distributed among these distances:
8 4 0.05
9 19 0.24
10 13 0.16
11 22 0.28
12 20 0.25
13 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:55018446 original size:18 final size:18
Alignment explanation
Indices: 55018423--55018491 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
55018413 AAAAAAGTAT
55018423 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTTAAAA
* * *
55018441 TTTAAAAAAAATTAAAAA
1 TTTAAAAATATTTTAAAA
*
55018459 GTATGTAAAAAATATTTTAACA
1 -T-T-T-AAAAATATTTTAAAA
*
55018481 TTAAAAAATAT
1 TTTAAAAATAT
55018492 ATATATTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
18 23 0.59
19 1 0.03
20 2 0.05
21 2 0.05
22 11 0.28
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAA
Found at i:55018448 original size:40 final size:40
Alignment explanation
Indices: 55018378--55018490 Score: 123
Period size: 40 Copynumber: 3.0 Consensus size: 40
55018368 TTTTAAAAAT
*
55018378 TAAAAAAGTATTTAAAAAATATTTT---A--AAAAAATAA
1 TAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATAA
* *
55018413 -AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAA-AA
1 TAAAAAAGTATGTAAAAAATATTTTAAAA-TTAAAAAATAA
* *
55018452 TTAAAAAGTATGTAAAAAATATTTTAACATTAAAAAATA
1 TAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATA
55018491 TATATATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
34 23 0.35
37 1 0.02
39 10 0.15
40 31 0.48
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (40 bp):
TAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATAA
Found at i:55026840 original size:7 final size:7
Alignment explanation
Indices: 55026828--55027016 Score: 75
Period size: 7 Copynumber: 26.7 Consensus size: 7
55026818 ACTAATTAAT
55026828 CTAAACC
1 CTAAACC
55026835 CTAAACTC
1 CTAAAC-C
55026843 CT-AACC
1 CTAAACC
*
55026849 TCT-ATCTC
1 -CTAAAC-C
55026857 CTAAACC
1 CTAAACC
*
55026864 CTAAATC
1 CTAAACC
* *
55026871 ATAAAAC
1 CTAAACC
* *
55026878 ATAAAAC
1 CTAAACC
*
55026885 ATAAACC
1 CTAAACC
55026892 CTAAACC
1 CTAAACC
55026899 TCT-AACC
1 -CTAAACC
*
55026906 CTTAACC
1 CTAAACC
*
55026913 CTTAACC
1 CTAAACC
*
55026920 C-CAACC
1 CTAAACC
55026926 CTTAAACC
1 C-TAAACC
*
55026934 ATAAACC
1 CTAAACC
* *
55026941 ATAAATC
1 CTAAACC
*
55026948 ATAAACC
1 CTAAACC
* *
55026955 ATAATCC
1 CTAAACC
55026962 CTAAACC
1 CTAAACC
*
55026969 TTAAA--
1 CTAAACC
*
55026974 ATAGTAACTC
1 CTA--AAC-C
55026984 CTAAACC
1 CTAAACC
*
55026991 TTAAACC
1 CTAAACC
*
55026998 CTAAACT
1 CTAAACC
*
55027005 ATAAACC
1 CTAAACC
55027012 CTAAA
1 CTAAA
55027017 TTATAATGAT
Statistics
Matches: 145, Mismatches: 24, Indels: 26
0.74 0.12 0.13
Matches are distributed among these distances:
5 2 0.01
6 8 0.06
7 118 0.81
8 15 0.10
10 2 0.01
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:55027002 original size:14 final size:14
Alignment explanation
Indices: 55026983--55027022 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
55026973 AATAGTAACT
55026983 CCTAAACCT-TAAAC
1 CCTAAA-CTATAAAC
55026997 CCTAAACTATAAAC
1 CCTAAACTATAAAC
*
55027011 CCTAAATTATAA
1 CCTAAACTATAA
55027023 TGATAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 2 0.08
14 22 0.92
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (14 bp):
CCTAAACTATAAAC
Found at i:55027494 original size:40 final size:40
Alignment explanation
Indices: 55027403--55027554 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 40
55027393 CCGTTAATGG
* * *** *
55027403 TCGATCTATAGAGGCATTTTTCAAGAAGCGTTGCCAAAAC
1 TCGACCTATAGCGGCATTTTTCAAGAAGCACCGCCAAAGC
*
55027443 TCGACCTATAGCGGCGTTTTTCAAGAAGCACCGCCAAAGC
1 TCGACCTATAGCGGCATTTTTCAAGAAGCACCGCCAAAGC
* * * ** * *
55027483 TCGACCTATAGCGTCGTTTTTCATA-AGGTGCCGCTAATGC
1 TCGACCTATAGCGGCATTTTTCA-AGAAGCACCGCCAAAGC
* *
55027523 TCGATCTATAGCGGCATTTTTCAAAAAGCACC
1 TCGACCTATAGCGGCATTTTTCAAGAAGCACC
55027555 ACTAATGCCA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
39 1 0.01
40 89 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGACCTATAGCGGCATTTTTCAAGAAGCACCGCCAAAGC
Found at i:55027560 original size:40 final size:40
Alignment explanation
Indices: 55027373--55027562 Score: 137
Period size: 40 Copynumber: 4.8 Consensus size: 40
55027363 TAATATCTTT
* * ** * * *
55027373 GCGGCGTTTTTCAAAAGGTGCCGTTAATGGTCGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTCGACCTATA
* * *** * **
55027413 GAGGCATTTTTCAAGAAGCGTTGCCAAAACTCGACCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTCGACCTATA
* * * *
55027453 GCGGCGTTTTTCAAGAAGCACCGCCAAAGCTCGACCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTCGACCTATA
* * * * ** *
55027493 GCGTCGTTTTTCATAAGGTGCCGCTAATGCTCGATCTATA
1 GCGGCATTTTTCAAAAAGCACCGCTAATGCTCGACCTATA
*
55027533 GCGGCATTTTTCAAAAAGCACCACTAATGC
1 GCGGCATTTTTCAAAAAGCACCGCTAATGC
55027563 CACGGCATTG
Statistics
Matches: 115, Mismatches: 35, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (40 bp):
GCGGCATTTTTCAAAAAGCACCGCTAATGCTCGACCTATA
Found at i:55027717 original size:40 final size:40
Alignment explanation
Indices: 55027590--55027707 Score: 105
Period size: 40 Copynumber: 3.0 Consensus size: 40
55027580 TTTTTTTGCG
* * * * *
55027590 GCGTTTTTCAAAAAGCACCGCTAATA-CTCGACCTAGAGC-
1 GCGTTTTTAAAAAAGCGCCACTAA-AGCTCGATCTATAGCA
* * * * * *
55027629 GACATTTTTTAAGAAGCGCCGCTAATGCTTGATCTATAGCA
1 G-CGTTTTTAAAAAAGCGCCACTAAAGCTCGATCTATAGCA
55027670 GCGTTTTTAAAAAAGCGCCACTAAAGCTCGATCTATAG
1 GCGTTTTTAAAAAAGCGCCACTAAAGCTCGATCTATAG
55027708 TGGTGTTTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
39 1 0.02
40 60 0.97
41 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (40 bp):
GCGTTTTTAAAAAAGCGCCACTAAAGCTCGATCTATAGCA
Found at i:55027719 original size:134 final size:132
Alignment explanation
Indices: 55027453--55027696 Score: 312
Period size: 134 Copynumber: 1.8 Consensus size: 132
55027443 TCGACCTATA
* * * * *
55027453 GCGGCGTTTTTCAAGAAGCACCGCCAAAGCTCGACCTATAGCGTCGTTTTTCATAAGGTGCCGCT
1 GCGGCGTTTTTCAAAAAGCACCGCCAAAGCTCGACCTAGAGCGACATTTTT-ATAAGGCGCCGCT
* * * *
55027518 AATGCTCGATCTATAGCGGCATTTTTCAAAAAGCACCACTAATGCCACGGCATTGTGCTTAATTT
65 AATGCTCGATCTATAGCAGCATTTTTAAAAAAGCACCACTAAAGCCACGGCATAGTGCTT-ATTT
55027583 TTTT
129 TTTT
*
55027587 GCGGCGTTTTTCAAAAAGCACCGCTAATA-CTCGACCTAGAGCGACATTTTT-TAAGAAGCGCCG
1 GCGGCGTTTTTCAAAAAGCACCGCCAA-AGCTCGACCTAGAGCGACATTTTTATAAG--GCGCCG
* * *
55027650 CTAATGCTTGATCTATAGCAGCGTTTTTAAAAAAGCGCCACTAAAGC
63 CTAATGCTCGATCTATAGCAGCATTTTTAAAAAAGCACCACTAAAGC
55027697 TCGATCTATA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
132 4 0.04
134 90 0.95
135 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (132 bp):
GCGGCGTTTTTCAAAAAGCACCGCCAAAGCTCGACCTAGAGCGACATTTTTATAAGGCGCCGCTA
ATGCTCGATCTATAGCAGCATTTTTAAAAAAGCACCACTAAAGCCACGGCATAGTGCTTATTTTT
TT
Found at i:55030031 original size:7 final size:7
Alignment explanation
Indices: 55030010--55030050 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
55030000 TATATACAAA
*
55030010 GATACTT
1 GATATTT
55030017 GA-ATTT
1 GATATTT
55030023 GATATTT
1 GATATTT
55030030 GATATTT
1 GATATTT
55030037 GATATTT
1 GATATTT
55030044 GATATTT
1 GATATTT
55030051 ATTTGGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (7 bp):
GATATTT
Found at i:55033263 original size:56 final size:56
Alignment explanation
Indices: 55033196--55033307 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
55033186 TTCACATTTT
* *
55033196 TTATTGATAACAATATCGATACCGATTAAATTAATACTCAATCAACTACAACTCAA
1 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
*
55033252 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACCACTCAA
1 TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
55033308 AGCAAACAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (56 bp):
TTATTGATAACAATATCAATACCGATTAAATTAAGACTCAATCAACTACAACTCAA
Found at i:55037583 original size:19 final size:18
Alignment explanation
Indices: 55037544--55037585 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
55037534 GTTTAAGAAC
55037544 TTTTAAATTATTTTTACTA
1 TTTTAAATTATTTTTA-TA
55037563 TTTTAAATATAATTTTT-TA
1 TTTTAAAT-T-ATTTTTATA
55037582 TTTT
1 TTTT
55037586 TATATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 14 0.67
20 1 0.05
21 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAAATTATTTTTATA
Found at i:55038108 original size:7 final size:7
Alignment explanation
Indices: 55038091--55038122 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
55038081 TTATGCTTTT
55038091 GTAAC-G
1 GTAACGG
55038097 GTAACGG
1 GTAACGG
55038104 GTAACGG
1 GTAACGG
55038111 GTAACGG
1 GTAACGG
55038118 GTAAC
1 GTAAC
55038123 TAACATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.31, C:0.16, G:0.38, T:0.16
Consensus pattern (7 bp):
GTAACGG
Found at i:55042309 original size:25 final size:25
Alignment explanation
Indices: 55042281--55042361 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
55042271 TATGCTCATT
*
55042281 CGAGCTATGAATCGGTATGCTCTCA
1 CGAGCTATGAATCGGTAAGCTCTCA
* * *
55042306 CGAGTTTTGAATTGGTAAGCTCAT-A
1 CGAGCTATGAATCGGTAAGCTC-TCA
* *
55042331 CGAGTTGA-GAATCAGTAAGCTCTCA
1 CGAGCT-ATGAATCGGTAAGCTCTCA
*
55042356 TGAGCT
1 CGAGCT
55042362 GCAAATCGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 1 0.02
25 42 0.95
26 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (25 bp):
CGAGCTATGAATCGGTAAGCTCTCA
Found at i:55042385 original size:25 final size:25
Alignment explanation
Indices: 55042320--55042387 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
55042310 TTTTGAATTG
*
55042320 GTAAGCTCATACGAGTTGAGAATCA
1 GTAAGCTCATACGAGCTGAGAATCA
*
55042345 GTAAGCTC-TCATGAGCTGCA-AATC-
1 GTAAGCTCAT-ACGAGCTG-AGAATCA
55042369 GATAAGCTCATACGAGCTG
1 G-TAAGCTCATACGAGCTG
55042388 TGGTGTGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 2 0.06
25 32 0.89
26 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAGAATCA
Found at i:55049785 original size:18 final size:19
Alignment explanation
Indices: 55049762--55049799 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
55049752 AAAAAAGTAT
*
55049762 TTTAAAAA-TGTTTTAAAA
1 TTTAAAAAGTATTTTAAAA
55049780 TTTAAAAAGTATTTTAAAA
1 TTTAAAAAGTATTTTAAAA
55049799 T
1 T
55049800 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTAAAAAGTATTTTAAAA
Found at i:55049799 original size:29 final size:30
Alignment explanation
Indices: 55049738--55049816 Score: 115
Period size: 29 Copynumber: 2.6 Consensus size: 30
55049728 ACCCAAAATT
55049738 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAAAAAGTATTTTAAAAA
* *
55049770 TGTTTTAAAATTTAAAAAGTATTTT-AAAA
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
55049799 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
55049817 TAATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 20 0.47
30 12 0.28
31 6 0.14
32 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAGTATTTTAAAAA
Found at i:55049804 original size:10 final size:10
Alignment explanation
Indices: 55049754--55049809 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
55049744 AAAAATTAAA
55049754 AAAAGTATTTT
1 AAAA-TATTTT
55049765 AAAA-ATGTTT
1 AAAATAT-TTT
* *
55049775 TAAA-ATTTA
1 AAAATATTTT
55049784 AAAAGTATTTT
1 AAAA-TATTTT
55049795 AAAATATTTT
1 AAAATATTTT
55049805 AAAAT
1 AAAAT
55049810 TAAAAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 7 0.18
10 19 0.50
11 12 0.32
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:55049838 original size:41 final size:40
Alignment explanation
Indices: 55049783--55049866 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 40
55049773 TTTAAAATTT
55049783 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAATAATAAA
1 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAA-AATAAA
*
55049824 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAAATTAA
1 AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAAATAAA
55049864 AAA
1 AAA
55049867 TTAAATATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 8 0.19
41 34 0.81
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (40 bp):
AAAAAGTATTTTAAAATATTTTAAAATTAAAAAAAATAAA
Found at i:55050310 original size:25 final size:25
Alignment explanation
Indices: 55050249--55050316 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
55050239 ACATGCGTAT
* * * *
55050249 TCATTCGAGCTATGAATCAGTATGC
1 TCATACGAGCTGTGAATTAGTAAGC
*
55050274 TCTTACGAGCTGTGAATTAGTAAGC
1 TCATACGAGCTGTGAATTAGTAAGC
*
55050299 TCATACGAGCTGAGAATT
1 TCATACGAGCTGTGAATT
55050317 GGTAGCCTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (25 bp):
TCATACGAGCTGTGAATTAGTAAGC
Found at i:55052580 original size:27 final size:27
Alignment explanation
Indices: 55052550--55052602 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
55052540 TCTGTTCATC
*
55052550 CAGAGTACACCATAAAGGTTATTTTTT
1 CAGAGTACACCATAAAGGCTATTTTTT
* *
55052577 CAGAGTTCGCCATAAAGGCTATTTTT
1 CAGAGTACACCATAAAGGCTATTTTT
55052603 AGTTGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (27 bp):
CAGAGTACACCATAAAGGCTATTTTTT
Found at i:55053407 original size:11 final size:11
Alignment explanation
Indices: 55053391--55053415 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
55053381 TACATTTAGA
55053391 TTTAAGGAAGG
1 TTTAAGGAAGG
55053402 TTTAAGGAAGG
1 TTTAAGGAAGG
55053413 TTT
1 TTT
55053416 TAGTAGATAC
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:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (11 bp):
TTTAAGGAAGG
Found at i:55057225 original size:73 final size:73
Alignment explanation
Indices: 55057106--55057253 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
55057096 GTATGTTGGA
55057106 TTGACATTTTCATATGTTCTTGTTGGTCAATTTGGAAATGTGAAACATGCTTGATCTTCTTTAAG
1 TTGACATTTTCATATGTTCTTGTTGGTCAATTTGGAAATGTGAAACATGCTTGATCTTCTTTAAG
55057171 GCAATCAG
66 GCAATCAG
55057179 TTGACATTTTCATATGTTCTTGTTGGTCAATTTGGAAATGTGAAACATGCTTGATCTTCTTTAAG
1 TTGACATTTTCATATGTTCTTGTTGGTCAATTTGGAAATGTGAAACATGCTTGATCTTCTTTAAG
55057244 GCAATCAG
66 GCAATCAG
55057252 TT
1 TT
55057254 TTGTTATGGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.42
Consensus pattern (73 bp):
TTGACATTTTCATATGTTCTTGTTGGTCAATTTGGAAATGTGAAACATGCTTGATCTTCTTTAAG
GCAATCAG
Found at i:55068679 original size:18 final size:18
Alignment explanation
Indices: 55068640--55068679 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55068630 ATTTAGGGCT
* *
55068640 TTAAGTGAAAATATGGAT
1 TTAAGTGAAAATAGGGAG
*
55068658 TTAAGTTAAAATAGGGAG
1 TTAAGTGAAAATAGGGAG
55068676 TTAA
1 TTAA
55068680 ATTTAGTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.33
Consensus pattern (18 bp):
TTAAGTGAAAATAGGGAG
Found at i:55075575 original size:33 final size:34
Alignment explanation
Indices: 55075500--55075568 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
55075490 TCTTTGTCGA
*
55075500 ACTAATCAAATCAAAATATCAAGTTCCAGTTCAG
1 ACTAATCAAATCAAAATATCAAATTCCAGTTCAG
55075534 ACTAATCAAATC-AAATATCAAATTCCAGTTCAG
1 ACTAATCAAATCAAAATATCAAATTCCAGTTCAG
55075567 AC
1 AC
55075569 ATATCAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (34 bp):
ACTAATCAAATCAAAATATCAAATTCCAGTTCAG
Found at i:55079608 original size:26 final size:26
Alignment explanation
Indices: 55079579--55079773 Score: 92
Period size: 26 Copynumber: 7.8 Consensus size: 26
55079569 TTCTCTCTCA
55079579 AGCCATATAACAGGAAGCTCACAAAG
1 AGCCATATAACAGGAAGCTCACAAAG
55079605 AGCCAT-TAATC-GAGAAGCTCACAAAG
1 AGCCATATAA-CAG-GAAGCTCACAAAG
* * *
55079631 AGCC-TAT--CAGAAAGCTTATC--CG
1 AGCCATATAACAGGAAGCTCA-CAAAG
* * *
55079653 GGCTATATAACAGGAA-CTCACACAG
1 AGCCATATAACAGGAAGCTCACAAAG
* * *
55079678 AGCCATA-ATCAGGAAGTTCACAAAT
1 AGCCATATAACAGGAAGCTCACAAAG
* * * *
55079703 A-ACTTTTAATCAGGAAGCTCACGAAG
1 AGCCATATAA-CAGGAAGCTCACAAAG
* * * *
55079729 AGCC-TTTAAACGGGAAACTCACGAAG
1 AGCCATAT-AACAGGAAGCTCACAAAG
55079755 AGCCAT-TAATCAGG-AGCTC
1 AGCCATATAA-CAGGAAGCTC
55079774 CGGATAGCCA
Statistics
Matches: 126, Mismatches: 26, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
22 3 0.02
23 11 0.09
24 14 0.11
25 30 0.24
26 64 0.51
27 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (26 bp):
AGCCATATAACAGGAAGCTCACAAAG
Found at i:55087622 original size:15 final size:15
Alignment explanation
Indices: 55087602--55087631 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55087592 GTGAGTAATT
55087602 CGTGCTTACTTTTAC
1 CGTGCTTACTTTTAC
55087617 CGTGCTTACTTTTAC
1 CGTGCTTACTTTTAC
55087632 TGTCTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (15 bp):
CGTGCTTACTTTTAC
Found at i:55090952 original size:29 final size:30
Alignment explanation
Indices: 55090885--55090943 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55090875 TATGGTTTAA
55090885 TGTG-CAATTGTATATATGAATTTTGATTT
1 TGTGCCAATTGTATATATGAATTTTGATTT
**
55090914 TGTGTAAATT-TATATATGAAATTTTGATTT
1 TGTGCCAATTGTATATATG-AATTTTGATTT
55090944 GATCCAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.53
Consensus pattern (30 bp):
TGTGCCAATTGTATATATGAATTTTGATTT
Found at i:55099350 original size:3 final size:3
Alignment explanation
Indices: 55099342--55099375 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
55099332 GCTCAATTTT
55099342 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
55099376 AAGTACCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:55104139 original size:21 final size:20
Alignment explanation
Indices: 55104107--55104146 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
55104097 TCTATTATTC
*
55104107 TCTCTTGTTTATTATATAAT
1 TCTCTTGTTTATAATATAAT
55104127 TCTCTTAGTTTATAATATAA
1 TCTCTT-GTTTATAATATAA
55104147 CCTCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (20 bp):
TCTCTTGTTTATAATATAAT
Found at i:55106755 original size:14 final size:14
Alignment explanation
Indices: 55106736--55106767 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
55106726 TCCAATCACC
55106736 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
55106750 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
55106764 GGGC
1 GGGC
55106768 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:55113858 original size:22 final size:22
Alignment explanation
Indices: 55113818--55113864 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
55113808 TATAATAGTA
*
55113818 AAATGACAGCAAATCAACATCG
1 AAATGACAGCAAATCAACAACG
*
55113840 AAATGGCAGCAAAAT-AACAACG
1 AAATGACAGC-AAATCAACAACG
55113862 AAA
1 AAA
55113865 AAATTAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.55, C:0.19, G:0.15, T:0.11
Consensus pattern (22 bp):
AAATGACAGCAAATCAACAACG
Found at i:55113920 original size:19 final size:21
Alignment explanation
Indices: 55113896--55113934 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55113886 GGCCAGGCAT
55113896 AGGCT-AA-AAATCTTACCCC
1 AGGCTAAATAAATCTTACCCC
55113915 AGGCTAAATAAATCTTACCC
1 AGGCTAAATAAATCTTACCC
55113935 AAACCCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (21 bp):
AGGCTAAATAAATCTTACCCC
Found at i:55114484 original size:21 final size:21
Alignment explanation
Indices: 55114460--55114525 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
55114450 TATTAAAGTG
55114460 GTAATTTTTTATTTGAATATA
1 GTAATTTTTTATTTGAATATA
** *
55114481 GTAA-AATTAATATT-AA-AGT-
1 GTAATTTTTTAT-TTGAATA-TA
55114500 GCTAATTTTTTATTTGAATATA
1 G-TAATTTTTTATTTGAATATA
55114522 GTAA
1 GTAA
55114526 AAATTGAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
19 2 0.06
20 12 0.38
21 16 0.50
22 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (21 bp):
GTAATTTTTTATTTGAATATA
Found at i:55114530 original size:42 final size:41
Alignment explanation
Indices: 55114443--55114527 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
55114433 CCCTAAATTC
*
55114443 AAAA-TAATATTAAAGTGGTAATTTTTTATTTGAATATAGT
1 AAAATTAATATTAAAGTGCTAATTTTTTATTTGAATATAGT
55114483 AAAATTAATATTAAAGTGCTAATTTTTTATTTGAATATAGT
1 AAAATTAATATTAAAGTGCTAATTTTTTATTTGAATATAGT
55114524 AAAA
1 AAAA
55114528 ATTGAGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 39 0.91
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.44
Consensus pattern (41 bp):
AAAATTAATATTAAAGTGCTAATTTTTTATTTGAATATAGT
Found at i:55114538 original size:42 final size:41
Alignment explanation
Indices: 55114443--55114538 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
55114433 CCCTAAATTC
* *
55114443 AAAA-TAATATTAAAGTGGTAATTTTTTATTTGAATATAGT
1 AAAATTAAGATTAAAGTGCTAATTTTTTATTTGAATATAGT
*
55114483 AAAATTAATATTAAAGTGCTAATTTTTTATTTGAATATAGT
1 AAAATTAAGATTAAAGTGCTAATTTTTTATTTGAATATAGT
*
55114524 AAAAATTGAGATTAA
1 -AAAATTAAGATTAA
55114539 TTATCAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 4 0.08
41 35 0.69
42 12 0.24
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (41 bp):
AAAATTAAGATTAAAGTGCTAATTTTTTATTTGAATATAGT
Found at i:55120007 original size:16 final size:17
Alignment explanation
Indices: 55119974--55120007 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55119964 GGACACGTAT
55119974 CTAAGCTACAGTCAAGCC
1 CTAAGCTACAG-CAAGCC
55119992 CTAAGCTACA-CAAGCC
1 CTAAGCTACAGCAAGCC
55120008 AAGCTCTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (17 bp):
CTAAGCTACAGCAAGCC
Found at i:55129515 original size:20 final size:20
Alignment explanation
Indices: 55129487--55129525 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55129477 TTGGCCTTTT
* *
55129487 TGGACTTAGGGAGAGAAGTG
1 TGGACTTAGAGAGAAAAGTG
*
55129507 TGGATTTAGAGAGAAAAGT
1 TGGACTTAGAGAGAAAAGT
55129526 TGGGTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.38, T:0.23
Consensus pattern (20 bp):
TGGACTTAGAGAGAAAAGTG
Found at i:55130179 original size:29 final size:29
Alignment explanation
Indices: 55130118--55130179 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
55130108 TTTTAACGTT
* *
55130118 TTTTTCCATTCTCTTCTTTTCTCCCTTTG
1 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
55130147 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
1 TTTTTCCATTCTCTTCTTTTCTCCCTCTC
55130176 TTTT
1 TTTT
55130180 AATTTAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.03, C:0.32, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTCCATTCTCTTCTTTTCTCCCTCTC
Found at i:55135673 original size:20 final size:20
Alignment explanation
Indices: 55135645--55135683 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55135635 TTGGCCTTTT
* *
55135645 TGGACTTAGGGAGAGAAGTG
1 TGGACTTAGAGAGAAAAGTG
*
55135665 TGGATTTAGAGAGAAAAGT
1 TGGACTTAGAGAGAAAAGT
55135684 TGGGTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.38, T:0.23
Consensus pattern (20 bp):
TGGACTTAGAGAGAAAAGTG
Found at i:55137204 original size:23 final size:23
Alignment explanation
Indices: 55137178--55137253 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
55137168 ATAAGTGCCA
55137178 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55137201 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
55137224 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
55137247 CACTGAT
1 CACTGAT
55137254 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:55137353 original size:8 final size:8
Alignment explanation
Indices: 55137340--55137368 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
55137330 ACCCGGGACT
55137340 CACTGTAA
1 CACTGTAA
55137348 CACTGTAA
1 CACTGTAA
55137356 CACTGTAA
1 CACTGTAA
55137364 CACTG
1 CACTG
55137369 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:55137499 original size:18 final size:17
Alignment explanation
Indices: 55137473--55137511 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
55137463 ATTTTCCTTC
55137473 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
55137490 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
55137508 CACA
1 CACA
55137512 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:55138673 original size:15 final size:16
Alignment explanation
Indices: 55138653--55138687 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
55138643 TTTAATTTTC
55138653 AAAATTTCAAAAAAA-
1 AAAATTTCAAAAAAAT
*
55138668 AAAATTTTAAAAAAAT
1 AAAATTTCAAAAAAAT
55138684 AAAA
1 AAAA
55138688 ATTGCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTTCAAAAAAAT
Found at i:55138726 original size:30 final size:30
Alignment explanation
Indices: 55138686--55138787 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
55138676 AAAAAAATAA
* *
55138686 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* *
55138716 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* * *
55138746 AAATTTCACTTAGACCCCTAAACCTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
55138776 AAATTTCATTTT
1 AAATTTCATTTT
55138788 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 4 0.07
30 57 0.93
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:55139233 original size:14 final size:15
Alignment explanation
Indices: 55139207--55139246 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
55139197 ATCAAATAAA
55139207 GAAAAGAGAAGAGAG
1 GAAAAGAGAAGAGAG
*
55139222 GAAAAG-GAAGAGTG
1 GAAAAGAGAAGAGAG
55139236 G--AAGAGAAGAG
1 GAAAAGAGAAGAG
55139247 CCCGTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 3 0.13
13 6 0.26
14 8 0.35
15 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (15 bp):
GAAAAGAGAAGAGAG
Found at i:55139347 original size:11 final size:11
Alignment explanation
Indices: 55139323--55139394 Score: 76
Period size: 12 Copynumber: 6.2 Consensus size: 11
55139313 CGGCCCGAAG
55139323 AAGAGGAAGAAA
1 AAGA-GAAGAAA
55139335 AAGA-AAGGAAAA
1 AAGAGAA-G-AAA
55139347 AAGAGAAGAAAA
1 AAGAGAAG-AAA
55139359 AGAGAGAAGAAA
1 A-AGAGAAGAAA
55139371 AAGAGAAAGAAA
1 AAGAG-AAGAAA
55139383 AAGA-AAGAAA
1 AAGAGAAGAAA
55139393 AA
1 AA
55139395 AAGGAGAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.18
11 5 0.09
12 31 0.56
13 9 0.16
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAGAAGAAA
Found at i:55139347 original size:12 final size:11
Alignment explanation
Indices: 55139332--55139426 Score: 79
Period size: 12 Copynumber: 8.3 Consensus size: 11
55139322 GAAGAGGAAG
55139332 AAAAAGAAAGGA
1 AAAAAGAAA-GA
55139344 AAAAAGAGAAGA
1 AAAAAGA-AAGA
55139356 AAAAGAGAGAAGA
1 AAAA-AGA-AAGA
55139369 AAAAGAGAAAG-
1 AAAA-AGAAAGA
55139380 AAAAAGAAAGAA
1 AAAAAGAAAG-A
*
55139392 AAAAAGGAGAGA
1 AAAAA-GAAAGA
*
55139404 AAAAA-ATAG-
1 AAAAAGAAAGA
*
55139413 AAAAGGAAAGA
1 AAAAAGAAAGA
55139424 AAA
1 AAA
55139427 GAAAATAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
9 4 0.06
10 12 0.17
11 7 0.10
12 27 0.38
13 22 0.31
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:55139359 original size:13 final size:13
Alignment explanation
Indices: 55139332--55139414 Score: 79
Period size: 13 Copynumber: 6.8 Consensus size: 13
55139322 GAAGAGGAAG
*
55139332 AAAAAGA-AAGGA
1 AAAAAGAGAAGAA
55139344 AAAAAGAGAAGAA
1 AAAAAGAGAAGAA
*
55139357 AAAGAGAGAAG--
1 AAAAAGAGAAGAA
*
55139368 AAAAAGAGAA-AG
1 AAAAAGAGAAGAA
55139380 AAAAAGA-AAGAA
1 AAAAAGAGAAGAA
55139392 AAAAAG-GAGAGAA
1 AAAAAGAGA-AGAA
*
55139405 AAAAATAGAA
1 AAAAAGAGAA
55139415 AAGGAAAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 11 0.19
12 22 0.37
13 24 0.41
14 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (13 bp):
AAAAAGAGAAGAA
Found at i:55139408 original size:25 final size:23
Alignment explanation
Indices: 55139323--55139409 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 23
55139313 CGGCCCGAAG
* *
55139323 AAGAGGAAGAAAAAGAAAGGAAAA
1 AAGA-GAAAAAAAAGAAAGAAAAA
* *
55139347 AAGAGAAGAAAAAGAGAGAAGAAA
1 AAGAGAAAAAAAAGAAAGAA-AAA
55139371 AAGAGAAAGAAAAAGAAAGAAAAA
1 AAGAGAAA-AAAAAGAAAGAAAAA
55139395 AAGGAGAGAAAAAAA
1 AA-GAGA-AAAAAAA
55139410 TAGAAAAGGA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
23 14 0.25
24 19 0.35
25 20 0.36
26 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
AAGAGAAAAAAAAGAAAGAAAAA
Found at i:55139414 original size:23 final size:23
Alignment explanation
Indices: 55139326--55139416 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
55139316 CCCGAAGAAG
*
55139326 AGGA-AGAAAAAGAAAGGAAAAA
1 AGGAGAGAAAAAGAAAGAAAAAA
*
55139348 A-GAGAAGAAAAAGAGAGAAGAAAA
1 AGGAG-AGAAAAAGAAAGAA-AAAA
*
55139372 AGAGAAAGAAAAAGAAAGAAAAAA
1 AG-GAGAGAAAAAGAAAGAAAAAA
55139396 AGGAGAGAAAAA-AATAGAAAA
1 AGGAGAGAAAAAGAA-AGAAAA
55139417 GGAAAGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.03
22 3 0.05
23 27 0.47
24 11 0.19
25 13 0.22
26 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (23 bp):
AGGAGAGAAAAAGAAAGAAAAAA
Found at i:55139428 original size:38 final size:36
Alignment explanation
Indices: 55139332--55139431 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 36
55139322 GAAGAGGAAG
*
55139332 AAAA-AGAAAGGAAAAAAGAGAAGAAAAAGAGAGAAGA
1 AAAAGAGAAAGGAAAAAA-AGAA-AAAAAGAGAGAAAA
*
55139369 AAAAGAGAAAGAAAAAGAAAGAAAAAAAGGAGAGAAAA
1 AAAAGAGAAAGGAAAA-AAAGAAAAAAA-GAGAGAAAA
55139407 AAATAGA-AAAGGAAAGAAAAGAAAA
1 AAA-AGAGAAAGGAAA-AAAAGAAAA
55139432 TAAAAAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
37 9 0.16
38 40 0.73
39 6 0.11
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (36 bp):
AAAAGAGAAAGGAAAAAAAGAAAAAAAGAGAGAAAA
Done.