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 146 of 196
Found at i:43277984 original size:18 final size:18
Alignment explanation
Indices: 43277951--43278003 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
43277941 ATTCACCTAA
*
43277951 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
43277970 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
43277988 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
43278004 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:43278130 original size:18 final size:18
Alignment explanation
Indices: 43278107--43278173 Score: 107
Period size: 18 Copynumber: 3.7 Consensus size: 18
43278097 GTAGTGATTC
43278107 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
43278125 AATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGGT
*
43278143 AATCCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
43278161 AATTTGGTTAATT
1 AATTCGGTTAATT
43278174 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:43278174 original size:9 final size:9
Alignment explanation
Indices: 43278107--43278173 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
43278097 GTAGTGATTC
43278107 AATTCGGTT
1 AATTCGGTT
*
43278116 AATTCGGGT
1 AATTCGGTT
43278125 AATTCGGTT
1 AATTCGGTT
* *
43278134 AATTTGGGT
1 AATTCGGTT
*
43278143 AATCCGGTT
1 AATTCGGTT
*
43278152 AATTCGGGT
1 AATTCGGTT
*
43278161 AATTTGGTT
1 AATTCGGTT
43278170 AATT
1 AATT
43278174 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:43291459 original size:32 final size:32
Alignment explanation
Indices: 43291412--43291490 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
43291402 GTTTGCCATT
*
43291412 TGAACTTGTTC-AAAAGTACCTAGTTGGTGCC
1 TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
43291443 T-ACACTTGTCCAAAAAGTACCTAGTTGGTGCT
1 TGA-ACTTGTCCAAAAAGTACCTAGTTGGTGCC
*
43291475 TGAACTTATCCAAAAA
1 TGAACTTGTCCAAAAA
43291491 ATTATATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 8 0.19
32 32 0.76
33 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
TGAACTTGTCCAAAAAGTACCTAGTTGGTGCC
Found at i:43294051 original size:32 final size:31
Alignment explanation
Indices: 43294013--43294076 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
43294003 ACACTTATTT
43294013 TCACCTATGCCGAATGCATACACATAAATATA
1 TCACCTATGCCGAATGCA-ACACATAAATATA
* *
43294045 TCACCTATGCCGAATGCAACATATATATATA
1 TCACCTATGCCGAATGCAACACATAAATATA
43294076 T
1 T
43294077 ATACATATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (31 bp):
TCACCTATGCCGAATGCAACACATAAATATA
Found at i:43294338 original size:41 final size:41
Alignment explanation
Indices: 43294293--43294489 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
43294283 ACCGGCTCTT
*
43294293 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
43294334 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
43294375 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
43294416 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
43294457 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
43294490 TAACGATAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 139 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:43295410 original size:28 final size:28
Alignment explanation
Indices: 43295378--43295431 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
43295368 CACACATTGC
*
43295378 ATTTA-TTTCACATTTTAGTCCCTAAAAA
1 ATTTATTTTCACAATTTAG-CCCTAAAAA
43295406 ATTTATTTTCACAATTTAGCCCTAAA
1 ATTTATTTTCACAATTTAGCCCTAAA
43295432 TACTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
ATTTATTTTCACAATTTAGCCCTAAAAA
Found at i:43296007 original size:12 final size:12
Alignment explanation
Indices: 43295990--43296014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43295980 ACACGAAAAT
43295990 TTCACACATAAA
1 TTCACACATAAA
43296002 TTCACACATAAA
1 TTCACACATAAA
43296014 T
1 T
43296015 AAACACACAA
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (12 bp):
TTCACACATAAA
Found at i:43301712 original size:32 final size:31
Alignment explanation
Indices: 43301674--43301736 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
43301664 ACACTTATTT
43301674 TCACCTATGCCGAATGCATACACATAAATATA
1 TCACCTATGCCGAATGCA-ACACATAAATATA
* *
43301706 TCACCTATGCCGAATGCAACATATATATATA
1 TCACCTATGCCGAATGCAACACATAAATATA
43301737 CATATCTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.27
Consensus pattern (31 bp):
TCACCTATGCCGAATGCAACACATAAATATA
Found at i:43302049 original size:48 final size:43
Alignment explanation
Indices: 43301951--43302151 Score: 279
Period size: 41 Copynumber: 4.7 Consensus size: 43
43301941 ACCGGCTCTT
*
43301951 AGCCTGCTAGACTTATAGTCCG-A-AATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
43301992 AGCCTGCTAGACTTATAGTCTGAATGTCACATGCTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAA--T-A-ATG-TGTCACCGGCATTA
43302040 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
43302081 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
* * *
43302122 AGCCTGCTAGACGTAAAGTCTGAATTATGT
1 AGCCTGCTAGACTTATAGTCTGAATAATGT
43302152 CACTAACGAT
Statistics
Matches: 146, Mismatches: 4, Indels: 19
0.86 0.02 0.11
Matches are distributed among these distances:
41 94 0.64
42 7 0.05
43 4 0.03
46 1 0.01
47 4 0.03
48 36 0.25
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
Found at i:43303707 original size:13 final size:13
Alignment explanation
Indices: 43303689--43303713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43303679 CCATCGAATG
43303689 CACACAAAATAAA
1 CACACAAAATAAA
43303702 CACACAAAATAA
1 CACACAAAATAA
43303714 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:43321046 original size:36 final size:36
Alignment explanation
Indices: 43321005--43321078 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
43320995 TAATTTTAAT
43321005 TTAATTTCCATCACCTAATGAATGCTGATAAATTTA
1 TTAATTTCCATCACCTAATGAATGCTGATAAATTTA
43321041 TTAATTTCCATCACCTAATGAATGCTGATAAATTTA
1 TTAATTTCCATCACCTAATGAATGCTGATAAATTTA
43321077 TT
1 TT
43321079 TCAGATGTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (36 bp):
TTAATTTCCATCACCTAATGAATGCTGATAAATTTA
Found at i:43345428 original size:18 final size:18
Alignment explanation
Indices: 43345405--43345447 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
43345395 TGATAATGTG
43345405 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
43345423 ACACTTTAAAATTGTATC
1 ACACTTTAAAATTGTATC
43345441 ACACTTT
1 ACACTTT
43345448 CACATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (18 bp):
ACACTTTAAAATTGTATC
Found at i:43354144 original size:34 final size:34
Alignment explanation
Indices: 43354108--43354174 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
43354098 TCTATTTCAA
* *
43354108 ATAAAAACATAAAAAGTATCATTTTTATTTAAAAAT
1 ATAAAAAAATAAAAA-T-TCAATTTTATTTAAAAAT
*
43354144 ATAAAAAAATTAAAATTCAATTTTATTTAAA
1 ATAAAAAAATAAAAATTCAATTTTATTTAAA
43354175 TCGAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 14 0.50
35 1 0.04
36 13 0.46
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAAAAAAATAAAAATTCAATTTTATTTAAAAAT
Found at i:43357485 original size:2 final size:2
Alignment explanation
Indices: 43357478--43357514 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43357468 TTTAGACATC
43357478 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
43357515 CACCTGCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:43364057 original size:41 final size:40
Alignment explanation
Indices: 43364012--43364149 Score: 195
Period size: 41 Copynumber: 3.4 Consensus size: 40
43364002 GATTCACCGG
* * *
43364012 CACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCATCGA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
*
43364053 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGG
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCA-CGA
* *
43364094 CACTTAGTCTGCTAGGTTTATAACCTGATTCAGATCACCA
1 CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
43364134 GCACTTAGCCTGCTAG
1 -CACTTAGCCTGCTAG
43364150 ACGTATAGTC
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 86 0.99
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (40 bp):
CACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACGA
Found at i:43367712 original size:57 final size:58
Alignment explanation
Indices: 43367620--43367728 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 58
43367610 AATATAGATT
* * * *
43367620 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTT-GGAATGCGACTC
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAG-TTGGGAATGCGACTC
*
43367678 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAGTTGGGAATG
1 CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATG
43367729 TGAAGTTGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 2 0.04
57 27 0.60
58 16 0.36
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (58 bp):
CGCGAACTGTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGTTGGGAATGCGACTC
Found at i:43367740 original size:57 final size:57
Alignment explanation
Indices: 43367620--43367751 Score: 144
Period size: 57 Copynumber: 2.3 Consensus size: 57
43367610 AATATAGATT
* * * *
43367620 CGCGAGCTGTTTTGTACTTGGGAAAATTTTGTAAAGTAATAAGCTTGGAATGCGACTC
1 CGCGAACT-TTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
* *
43367678 CGCGAACTTTTTTATACTT-GGAAAATTTTCTAAAGTAACAAG-TTGGGAATGTGAAGT-
1 CGCGAAC-TTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTT-GGAATGCG-ACTC
*
43367735 TGCGAACTTTTTATACT
1 CGCGAACTTTTTATACT
43367752 AGTAGAATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
56 12 0.19
57 34 0.53
58 17 0.27
59 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.36
Consensus pattern (57 bp):
CGCGAACTTTTTATACTTGGGAAAATTTTCTAAAGTAACAAGCTTGGAATGCGACTC
Found at i:43368043 original size:69 final size:69
Alignment explanation
Indices: 43367958--43368451 Score: 436
Period size: 69 Copynumber: 7.2 Consensus size: 69
43367948 TCTTTGCATA
* * * * * *
43367958 CGAGCCTTAATATGATAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTC
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTTTTC
*
43368022 GCTTG
65 GCCTG
* * * ** * *
43368027 TGAGCCTTAGTGTGATAGTTGGAAGCTTTGCTCTCGCTAACTGTATTGGAGACTGCGGCTCTTCG
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTTTTCG
43368092 CCTG
66 CCTG
* * * * *
43368096 CGAGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTT-
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCT-TTTC
43368160 GCCTG
65 GCCTG
* * * * *
43368165 CAAGCCATAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTAC-GACTCTTC
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAG-CTTTTC
43368229 GCCTG
65 GCCTG
* * * * * * * * * * *
43368234 CAAGCCTTAGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCG
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTTTTCG
43368299 CCTG
66 CCTG
* * * * * * * * * *
43368303 TGAGCCTTAGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGGCTGTAGCTCTTCA
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTTTTCG
43368368 CCTG
66 CCTG
* * * * * * * *
43368372 TGAGCCTTAGTTTAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCG
1 CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTTTTCG
* *
43368437 CTTA
66 CCTG
*
43368441 CGAGCTTTAGT
1 CGAGCCTTAGT
43368452 ATGACAGAAA
Statistics
Matches: 343, Mismatches: 77, Indels: 10
0.80 0.18 0.02
Matches are distributed among these distances:
68 3 0.01
69 336 0.98
70 4 0.01
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (69 bp):
CGAGCCTTAGTGTGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGTTGCAGCTTTTCG
CCTG
Found at i:43368201 original size:207 final size:207
Alignment explanation
Indices: 43367970--43368458 Score: 534
Period size: 207 Copynumber: 2.4 Consensus size: 207
43367960 AGCCTTAATA
* * * **
43367970 TGATAGTTGGGAGCTTTTCTCTCGCTAACTATTTTGGAGGCTGCGACTTTTCGCTTGTGAGCCTT
1 TGATAGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTT
* * * * *
43368035 AGTGTGATAGTTG-GAAGCTTTGCTCTCGCTAACTGTATTGGAGA-CTGCGGCTCTTCGCCTGCG
66 AGTGTGACAGCTGAGAA-CTTTGCTCTCGCTAACTAT-TTGGAAAGCTGCAGCTCTTCGCCTGCG
* * **
43368098 AGCCATAGTGTGACAGCTGAGAGCTTTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTTGCC
129 AGCCATAGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGGCTGCAGCTCTTCACC
43368163 TGCAAGCCATAGTG
194 TGCAAGCCATAGTG
* * * * * *
43368177 TGATAGTTGGGAGCTTTGCTCTCGCTAACTGTGTTAGAGGTTACGACTCTTCGCCTGCAAGCCTT
1 TGATAGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTT
* * * * * *
43368242 AGTGTGACAGCTGAGAACTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCGCCTGTGAG
66 AGTGTGACAGCTGAGAACTTTGCTCTCGCTAACTATTTGGAAAGCTGCAGCTCTTCGCCTGCGAG
* * * * * *
43368307 CCTTAGTGTGACAGTTGAGAGCTTTGCTCTAGTTAATTGTGTTGGAGGCTGTAGCTCTTCACCTG
131 CCATAGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGGCTGCAGCTCTTCACCTG
** * *
43368372 TGAGCCTTAGTT
196 CAAGCCATAGTG
* * * * * * *
43368384 TAATAGTTGGGAGCTTTACTTTCGCTAATTGTTTTGAAGGTTGC-AGCTTTTCGCTTACGAGCTT
1 TGATAGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGA-CTTTTCGCTTGCAAGCCT
*
43368448 TAGTATGACAG
65 TAGTGTGACAG
43368459 AAATGCTAGT
Statistics
Matches: 230, Mismatches: 49, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
206 6 0.03
207 221 0.96
208 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (207 bp):
TGATAGTTGGGAGCTTTACTCTCGCTAACTGTTTTGGAGGTTGCGACTTTTCGCTTGCAAGCCTT
AGTGTGACAGCTGAGAACTTTGCTCTCGCTAACTATTTGGAAAGCTGCAGCTCTTCGCCTGCGAG
CCATAGTGTGACAGCTGAGAGCTTTGCTCTAGCTAACTGTGCTGGAGGCTGCAGCTCTTCACCTG
CAAGCCATAGTG
Found at i:43368451 original size:138 final size:137
Alignment explanation
Indices: 43367920--43368458 Score: 483
Period size: 138 Copynumber: 3.9 Consensus size: 137
43367910 ATGACAACAT
* * * * * * * * * * * * *
43367920 TCTCACTAACTGTGTTGGACGATGTGGATCTTTGCATACGAGCCTTAATATGATAGTTGGGAGCT
1 TCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCGCCTGCGAGCCTTAGTGTGACAGCTGAGAGCT
* * * * * *
43367985 TTTCTCTCGCTAACTATTTTGGAGGCTGC-GACTTTTCGCTTGTGAGCCTTAGTGTGATAGTTGG
66 TTGCTCTCGCTAACTATTTTGAAGGTTGCAG-CTTTTCGCCTGCGAGCCTTAGTGTGACAGTTGG
43368049 AAGCTTTGC
130 -AGCTTTGC
* * ** *
43368058 TCTCGCTAACTGTATTGGAGACTGCGGCTCTTCGCCTGCGAGCCATAGTGTGACAGCTGAGAGCT
1 TCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCGCCTGCGAGCCTTAGTGTGACAGCTGAGAGCT
* ** * * * *
43368123 TTGCTCTCGCTAACTGTGCTGGAGGTTGCAGCTCTTT-GCCTGCAAGCCATAGTGTGATAGTTGG
66 TTGCTCTCGCTAACTATTTTGAAGGTTGCAGCT-TTTCGCCTGCGAGCCTTAGTGTGACAGTT-G
43368187 GAGCTTTGC
129 GAGCTTTGC
* * *
43368196 TCTCGCTAACTGTGTTAGAGG-T-TACGACTCTTCGCCTGCAAGCCTTAGTGTGACAGCTGAGAA
1 TCTCGCTAACTGTGTTGGAGGCTGTA-G-CTCTTCGCCTGCGAGCCTTAGTGTGACAGCTGAGAG
* * * *
43368259 CTTTGCTCTCGTTAACTATTTTGAAAGTTGCAGTTTTTCGCCTGTGAGCCTTAGTGTGACAGTTG
64 CTTTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCGCCTGCGAGCCTTAGTGTGACAGTTG
43368324 AGAGCTTTGC
129 -GAGCTTTGC
* * * * * * * * * *
43368334 TCTAGTTAATTGTGTTGGAGGCTGTAGCTCTTCACCTGTGAGCCTTAGTTTAATAGTTGGGAGCT
1 TCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCGCCTGCGAGCCTTAGTGTGACAGCTGAGAGCT
* * * * * * * *
43368399 TTACTTTCGCTAATTGTTTTGAAGGTTGCAGCTTTTCGCTTACGAGCTTTAGTATGACAG
66 TTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCGCCTGCGAGCCTTAGTGTGACAG
43368459 AAATGCTAGT
Statistics
Matches: 323, Mismatches: 69, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
137 6 0.02
138 307 0.95
139 8 0.02
140 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (137 bp):
TCTCGCTAACTGTGTTGGAGGCTGTAGCTCTTCGCCTGCGAGCCTTAGTGTGACAGCTGAGAGCT
TTGCTCTCGCTAACTATTTTGAAGGTTGCAGCTTTTCGCCTGCGAGCCTTAGTGTGACAGTTGGA
GCTTTGC
Found at i:43370415 original size:25 final size:24
Alignment explanation
Indices: 43370386--43370434 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
43370376 AAAATTAAAA
*
43370386 TAAAAGAA-AATGGAATAGATTATT
1 TAAAAAAAGAATGGAATAGA-TATT
*
43370410 TAAAAAAAGAGTGGAATAGATATT
1 TAAAAAAAGAATGGAATAGATATT
43370434 T
1 T
43370435 TATTAGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (24 bp):
TAAAAAAAGAATGGAATAGATATT
Found at i:43386157 original size:42 final size:42
Alignment explanation
Indices: 43386103--43386228 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 42
43386093 AAATATATAC
*
43386103 TCTCAATGTGGATTGAAA-TTTAGTTTAGTTAGCACGGTTGTT
1 TCTCAACGTGGATT-AAATTTTAGTTTAGTTAGCACGGTTGTT
* * * *
43386145 TCTTAACGTGGATTAAATTTTACTTTAGTTGGCACGGTTGAT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
* * *
43386187 TCTCAATGTGGATTAAATTTTAGTTTAGTTAACACGTTTGTT
1 TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
43386229 ATTATACTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 3 0.04
42 68 0.96
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (42 bp):
TCTCAACGTGGATTAAATTTTAGTTTAGTTAGCACGGTTGTT
Found at i:43388738 original size:22 final size:24
Alignment explanation
Indices: 43388713--43388756 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
43388703 CATAAAACTG
43388713 TTAAAG-ATTTTA-TGATTTTTCA
1 TTAAAGAATTTTAGTGATTTTTCA
* *
43388735 TTAATGAATTTTAGTTATTTTT
1 TTAAAGAATTTTAGTGATTTTT
43388757 TATGTTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 6 0.33
24 7 0.39
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (24 bp):
TTAAAGAATTTTAGTGATTTTTCA
Found at i:43389274 original size:25 final size:26
Alignment explanation
Indices: 43389241--43389289 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
43389231 TATGTTGTTT
43389241 TGAATTATTTTGA-ATTGAAATGTTGC
1 TGAATTA-TTTGACATTGAAATGTTGC
*
43389267 TGAA-TATTTGACATTGGAATGTT
1 TGAATTATTTGACATTGAAATGTT
43389290 AATTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (26 bp):
TGAATTATTTGACATTGAAATGTTGC
Found at i:43392081 original size:21 final size:22
Alignment explanation
Indices: 43392057--43392102 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
43392047 TACAATCGTT
43392057 CTGT-GGCAAAGGATGAATTGA
1 CTGTAGGCAAAGGATGAATTGA
*
43392078 CTGTAAATGCAAAGGATGAATTGA
1 CTGT--AGGCAAAGGATGAATTGA
43392102 C
1 C
43392103 AACAAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
24 17 0.81
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (22 bp):
CTGTAGGCAAAGGATGAATTGA
Found at i:43392109 original size:24 final size:24
Alignment explanation
Indices: 43392062--43392109 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43392052 TCGTTCTGTG
***
43392062 GCAAAGGATGAATTGACTGTAAAT
1 GCAAAGGATGAATTGACAACAAAT
43392086 GCAAAGGATGAATTGACAACAAAT
1 GCAAAGGATGAATTGACAACAAAT
43392110 TACCCAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (24 bp):
GCAAAGGATGAATTGACAACAAAT
Found at i:43392264 original size:42 final size:41
Alignment explanation
Indices: 43392194--43392308 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 41
43392184 TGTTAACTCA
* * *
43392194 TATGAGTTTCTGTTTAACCCTAATGGGTTTTCGTTCAGCTCT
1 TATGAGCTTC-GTTTAACCCTTATGGGTTTTCGTTCAGATCT
* *
43392236 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGATCT
1 TATGAGCTTC-GTTTAACCCTTATGGGTTTTCGTTCAGATCT
*
43392278 TATGAGCTTTCGTTCAACCCTTATGGGTTTT
1 TATGAGC-TTCGTTTAACCCTTATGGGTTTT
43392309 TGTTTAGTAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 60 0.95
43 3 0.05
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (41 bp):
TATGAGCTTCGTTTAACCCTTATGGGTTTTCGTTCAGATCT
Found at i:43392281 original size:21 final size:20
Alignment explanation
Indices: 43392194--43392307 Score: 68
Period size: 21 Copynumber: 5.5 Consensus size: 20
43392184 TGTTAACTCA
* *
43392194 TATGAGTTTCTGTTTAACCCT
1 TATGGGTTTC-GTTCAACCCT
* * *
43392215 AATGGGTTTTCGTTCAGCTCT
1 TATGGG-TTTCGTTCAACCCT
* * * *
43392236 TTTGAGCTTCAGTTTAACCCT
1 TATGGGTTTC-GTTCAACCCT
*
43392257 TATGGGTTTCCGTTCAGA-TCT
1 TATGGGTTT-CGTTCA-ACCCT
*
43392278 TATGAGCTTTCGTTCAACCCT
1 TATG-GGTTTCGTTCAACCCT
43392299 TATGGGTTT
1 TATGGGTTT
43392308 TTGTTTAGTA
Statistics
Matches: 67, Mismatches: 20, Indels: 13
0.67 0.20 0.13
Matches are distributed among these distances:
20 8 0.12
21 49 0.73
22 10 0.15
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (20 bp):
TATGGGTTTCGTTCAACCCT
Found at i:43392322 original size:42 final size:43
Alignment explanation
Indices: 43392194--43392328 Score: 145
Period size: 42 Copynumber: 3.2 Consensus size: 43
43392184 TGTTAACTCA
* *
43392194 TATGAG-TTTCTGTTTAACCCTAATGGGTTTTCGTTCAGCT-CT
1 TATGAGCTTTCAGTTTAACCCTTATGGGTTTTCGTTCAG-TACT
* *
43392236 TTTGAGC-TTCAGTTTAACCCTTATGGGTTTCCGTTCAG-ATCT
1 TATGAGCTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGTA-CT
* * *
43392278 TATGAGCTTTC-GTTCAACCCTTATGGGTTTTTGTTTAGTACT
1 TATGAGCTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGTACT
*
43392320 TATGTGCTT
1 TATGAGCTT
43392329 CTATTCAGCC
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
42 74 0.95
43 4 0.05
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (43 bp):
TATGAGCTTTCAGTTTAACCCTTATGGGTTTTCGTTCAGTACT
Found at i:43398844 original size:66 final size:66
Alignment explanation
Indices: 43398738--43398863 Score: 252
Period size: 66 Copynumber: 1.9 Consensus size: 66
43398728 CATTTCAGAG
43398738 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
43398803 T
66 T
43398804 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
43398864 TAATATAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.18
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:43399082 original size:57 final size:60
Alignment explanation
Indices: 43398985--43399132 Score: 196
Period size: 57 Copynumber: 2.5 Consensus size: 60
43398975 ACCCTAATTC
* * * *
43398985 GGATTACCCGTCCGGACTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
*
43399043 -GATCACCTGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
43399104 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
43399133 ACCGTCAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
56 6 0.08
57 43 0.56
60 1 0.01
61 1 0.01
62 20 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:43407261 original size:101 final size:101
Alignment explanation
Indices: 43407136--43407341 Score: 376
Period size: 101 Copynumber: 2.0 Consensus size: 101
43407126 ATCTTCTAAC
*
43407136 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGGGGTGGAAAAGCACTTTTTGACAGCACA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
43407201 AGCAATGCCAAACAATCAGCTTTAACATCAAATTAA
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
*
43407237 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCATA
1 TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
*
43407302 AACAATGCCAAACAATCAGCTTTAACATCAAATTAG
66 AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
43407338 TTTT
1 TTTT
43407342 TCAACCCAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (101 bp):
TTTTCACCACTAAGGTTTTGTTTAGCATTGCTCATAGAGGTGGAAAAGCACTTTTTGACAGCACA
AACAATGCCAAACAATCAGCTTTAACATCAAATTAA
Found at i:43414334 original size:21 final size:21
Alignment explanation
Indices: 43414295--43414335 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43414285 AATTTATTAT
**
43414295 TATATTTATAATTGTAATATA
1 TATATTTATAATTAAAATATA
*
43414316 TATATTTATTATTAAAATAT
1 TATATTTATAATTAAAATAT
43414336 TAATATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATTTATAATTAAAATATA
Found at i:43414341 original size:21 final size:21
Alignment explanation
Indices: 43414292--43414341 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
43414282 AAAAATTTAT
**
43414292 TATT-ATATTTATAATTGTAA
1 TATTAATATTTATAATTAAAA
*
43414312 TA-TATATATTTATTATTAAAA
1 TATTA-ATATTTATAATTAAAA
43414333 TATTAATAT
1 TATTAATAT
43414342 AAATAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 2 0.08
21 19 0.79
22 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTAATATTTATAATTAAAA
Found at i:43414403 original size:17 final size:19
Alignment explanation
Indices: 43414367--43414406 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
43414357 ATATATCAAG
43414367 AATATTATTTAAAATTTAAA
1 AATATTATTTAAAA-TTAAA
43414387 AATATTA-TTAAAA-TAAA
1 AATATTATTTAAAATTAAA
43414404 AAT
1 AAT
43414407 GTAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTATTTAAAATTAAA
Found at i:43414457 original size:26 final size:27
Alignment explanation
Indices: 43414428--43414479 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
43414418 TAATTTATTA
* *
43414428 AAATAATTCATTATAT-TATTAAATAT
1 AAATAATTAAATATATATATTAAATAT
*
43414454 AAATAATTAAATATGTATATTAAATA
1 AAATAATTAAATATATATATTAAATA
43414480 ATATTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATAATTAAATATATATATTAAATAT
Found at i:43414462 original size:22 final size:21
Alignment explanation
Indices: 43414422--43414462 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
43414412 ATTAAATAAT
* *
43414422 TTATTAAAATAATTCATTATA
1 TTATTAAAATAAATAATTATA
43414443 TTATTAAATATAAATAATTA
1 TTATTAAA-ATAAATAATTA
43414463 AATATGTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTAAAATAAATAATTATA
Found at i:43414505 original size:22 final size:22
Alignment explanation
Indices: 43414480--43414522 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
43414470 ATATTAAATA
43414480 ATATTAAAA-TTTATAATATTTG
1 ATATTAAAATTTTA-AATATTTG
*
43414502 ATATTAATATTTTAAATATTT
1 ATATTAAAATTTTAAATATTT
43414523 TCAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAAAATTTTAAATATTTG
Found at i:43421597 original size:14 final size:14
Alignment explanation
Indices: 43421578--43421605 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43421568 AAAAAAAGAA
43421578 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
43421592 AGGAAATAAAGTTT
1 AGGAAATAAAGTTT
43421606 CAAGATAAAT
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AGGAAATAAAGTTT
Found at i:43424325 original size:20 final size:21
Alignment explanation
Indices: 43424297--43424344 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
43424287 AATGGTTATA
* *
43424297 GAAAATAATTTTTA-AAAAAT
1 GAAATTAATTTTAATAAAAAT
43424317 GAAATTAATTTTAATAAAAAT
1 GAAATTAATTTTAATAAAAAT
43424338 GATAATT
1 GA-AATT
43424345 CCGGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (21 bp):
GAAATTAATTTTAATAAAAAT
Found at i:43426362 original size:20 final size:20
Alignment explanation
Indices: 43426337--43426375 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43426327 CGCCTATGTG
* *
43426337 AAGGAGGCATACGCCCGTGA
1 AAGGAGGCACACGACCGTGA
43426357 AAGGAGGCACACGACCGTG
1 AAGGAGGCACACGACCGTG
43426376 TGTCGATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.36, T:0.08
Consensus pattern (20 bp):
AAGGAGGCACACGACCGTGA
Found at i:43434607 original size:14 final size:14
Alignment explanation
Indices: 43434584--43434617 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
43434574 TGGTATGGTT
43434584 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
43434597 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
43434611 TTATAGG
1 TTATAGG
43434618 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:43434772 original size:22 final size:23
Alignment explanation
Indices: 43434747--43434790 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
43434737 GAGGAAAGTT
43434747 TAAAGAACATAAAA-GAAAAAAA
1 TAAAGAACATAAAACGAAAAAAA
** *
43434769 TAAATTACTTAAAACGAAAAAA
1 TAAAGAACATAAAACGAAAAAA
43434791 TATGGGGATC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (23 bp):
TAAAGAACATAAAACGAAAAAAA
Found at i:43436775 original size:27 final size:27
Alignment explanation
Indices: 43436711--43436775 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
43436701 TATTTTATTA
43436711 TTATTATTTATTTCTTTTTGGTCACTTT
1 TTATTATTT-TTTCTTTTTGGTCACTTT
* * *
43436739 CTATCT-TTTTTTCTTCTTT-TTCATTTT
1 TTAT-TATTTTTTCTT-TTTGGTCACTTT
43436766 TTATTATTTT
1 TTATTATTTT
43436776 GTTAATCGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.03
27 19 0.63
28 9 0.30
29 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (27 bp):
TTATTATTTTTTCTTTTTGGTCACTTT
Found at i:43441165 original size:29 final size:29
Alignment explanation
Indices: 43441133--43441195 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
43441123 TACAAAATAA
43441133 TTTCTATTTTTTTTATATTTTGTTAAAAT
1 TTTCTATTTTTTTTATATTTTGTTAAAAT
43441162 TTTCTATTTTTTTTATATTTTGTTAAAAT
1 TTTCTATTTTTTTTATATTTTGTTAAAAT
43441191 TTTCT
1 TTTCT
43441196 CATATGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (29 bp):
TTTCTATTTTTTTTATATTTTGTTAAAAT
Found at i:43455557 original size:26 final size:26
Alignment explanation
Indices: 43455490--43455551 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
43455480 CTTGTAAGTG
* *
43455490 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATATATGCTACGATA
* *
43455516 TTCTGAAAGTGATATATGTTACGATA
1 TTCTGAAACTGATATATGCTACGATA
43455542 TTCTGAAACT
1 TTCTGAAACT
43455552 ACTATAGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (26 bp):
TTCTGAAACTGATATATGCTACGATA
Found at i:43455780 original size:17 final size:17
Alignment explanation
Indices: 43455760--43455792 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43455750 TATATTTTTA
*
43455760 TTTTTAATTAAATATAC
1 TTTTTAATCAAATATAC
43455777 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
43455793 TATATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:43460537 original size:21 final size:21
Alignment explanation
Indices: 43460511--43460564 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
43460501 GGCGTAATCA
43460511 TAGGACTGAGGAGGCCACGTG
1 TAGGACTGAGGAGGCCACGTG
*
43460532 TAGGACTAAGGAGGCCACGTG
1 TAGGACTGAGGAGGCCACGTG
43460553 -AGAGACTGAGGA
1 TAG-GACTGAGGA
43460565 TGCGATGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.17, G:0.41, T:0.13
Consensus pattern (21 bp):
TAGGACTGAGGAGGCCACGTG
Found at i:43464336 original size:13 final size:13
Alignment explanation
Indices: 43464314--43464343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43464304 TCTTTAGGTA
*
43464314 TTTAATTGACTTG
1 TTTAACTGACTTG
43464327 TTTAACTGACTTG
1 TTTAACTGACTTG
43464340 TTTA
1 TTTA
43464344 GTTTGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAACTGACTTG
Found at i:43468034 original size:9 final size:9
Alignment explanation
Indices: 43468020--43468068 Score: 89
Period size: 9 Copynumber: 5.4 Consensus size: 9
43468010 TTTGGTTAAA
43468020 AATTAACCG
1 AATTAACCG
43468029 AATTAACCG
1 AATTAACCG
*
43468038 AATTACCCG
1 AATTAACCG
43468047 AATTAACCG
1 AATTAACCG
43468056 AATTAACCG
1 AATTAACCG
43468065 AATT
1 AATT
43468069 GAATCACTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:43468237 original size:18 final size:18
Alignment explanation
Indices: 43468214--43468267 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
43468204 AATTTTTATG
43468214 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
* *
43468232 ATTGGGTTGAGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
43468250 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
43468268 TTAGGTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.13, C:0.02, G:0.44, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:43469040 original size:30 final size:30
Alignment explanation
Indices: 43469004--43469067 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
43468994 ATTACATTCC
43469004 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
43469034 AATAATTCTAATAAGAATACAACATCCTTA
1 AATAATTCTAATAAGAATACAACATCCTTA
43469064 AATA
1 AATA
43469068 TTTGATAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (30 bp):
AATAATTCTAATAAGAATACAACATCCTTA
Found at i:43475262 original size:2 final size:2
Alignment explanation
Indices: 43475255--43475281 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43475245 CTCTTCCAGG
43475255 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
43475282 AATCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43478890 original size:20 final size:21
Alignment explanation
Indices: 43478858--43478901 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
43478848 CAATCACTTT
43478858 ATAATATAATTAAAAAATAAA
1 ATAATATAATTAAAAAATAAA
**
43478879 ATAATA-AATTAAGTAATAAA
1 ATAATATAATTAAAAAATAAA
43478899 ATA
1 ATA
43478902 TATTTATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAATATAATTAAAAAATAAA
Found at i:43480923 original size:21 final size:21
Alignment explanation
Indices: 43480899--43480938 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
43480889 TTTTAAATTT
43480899 TAAAAATTATTAAA-AAAATCA
1 TAAAAATTA-TAAACAAAATCA
43480920 TAAAAATTATAAACAAAAT
1 TAAAAATTATAAACAAAAT
43480939 TTATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAATTATAAACAAAATCA
Found at i:43481094 original size:13 final size:12
Alignment explanation
Indices: 43481068--43481100 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43481058 AATATAATTT
43481068 TAAATTTTTTTA
1 TAAATTTTTTTA
43481080 TAAATTTTGTTTA
1 TAAATTTT-TTTA
43481093 T-AATTTTT
1 TAAATTTTT
43481101 ATGGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 14 0.70
13 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TAAATTTTTTTA
Found at i:43485222 original size:4 final size:4
Alignment explanation
Indices: 43485213--43485238 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
43485203 AGATATTTTA
43485213 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
43485239 TTTATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:43495559 original size:41 final size:40
Alignment explanation
Indices: 43495495--43495652 Score: 124
Period size: 41 Copynumber: 3.8 Consensus size: 40
43495485 CTCAATGTTG
* **
43495495 CGCACACTAAATGCCATCGCATAG-CGGAAGCTATTATAATCT
1 CGCACACTAAGTGCC-TTACATAGTC-GAAGCTATT-TAATCT
* * * *
43495537 CGCACTCTAAGTGCCTTACATAGCCGAAGCTGTCTCAATCT
1 CGCACACTAAGTGCCTTACATAGTCGAAGCTAT-TTAATCT
* *
43495578 CACACACTAAGTGCCATATATATAGTCGAAGCTATTCTCAAT-T
1 CGCACACTAAGTGCC-T-TACATAGTCGAAGCTATT-T-AATCT
* *
43495621 -GCACACTAAGTGCCATAAATAGTCGAAGCTAT
1 CGCACACTAAGTGCCTTACATAGTCGAAGCTAT
43495653 CTCGAGTCGA
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
40 16 0.17
41 31 0.33
42 30 0.32
43 15 0.16
44 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
CGCACACTAAGTGCCTTACATAGTCGAAGCTATTTAATCT
Found at i:43495633 original size:42 final size:43
Alignment explanation
Indices: 43495495--43495652 Score: 152
Period size: 42 Copynumber: 3.8 Consensus size: 43
43495485 CTCAATGTTG
* *** *
43495495 CGCACACTAAATGCCATCGCATAG-CGGAAGCTATTAT-AATCT
1 CGCACACTAAGTGCCATATAATAGTC-GAAGCTATTCTCAATCT
* * *
43495537 CGCACTCTAAGTGCC-T-TACATAGCCGAAGCT-GTCTCAATCT
1 CGCACACTAAGTGCCATATA-ATAGTCGAAGCTATTCTCAATCT
*
43495578 CACACACTAAGTGCCATATATATAGTCGAAGCTATTCTCAAT-T
1 CGCACACTAAGTGCCATATA-ATAGTCGAAGCTATTCTCAATCT
43495621 -GCACACTAAGTGCCATA-AATAGTCGAAGCTAT
1 CGCACACTAAGTGCCATATAATAGTCGAAGCTAT
43495653 CTCGAGTCGA
Statistics
Matches: 98, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
40 16 0.16
41 30 0.31
42 31 0.32
43 14 0.14
44 7 0.07
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
CGCACACTAAGTGCCATATAATAGTCGAAGCTATTCTCAATCT
Found at i:43499643 original size:43 final size:42
Alignment explanation
Indices: 43499576--43499705 Score: 163
Period size: 43 Copynumber: 3.0 Consensus size: 42
43499566 CATAGGACCT
**
43499576 TCGATATGTGTTTTTGTGTAAGACCACGTCTGGGACGTCGGCA
1 TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACGT-GGCA
*
43499619 TCGACT-TGTGTTTACGTGTAAGACCATGTCTGGGACAGTGGCA
1 TCGA-TATGTGTTTACGTGTAAGACCACGTCTGGGAC-GTGGCA
* * *
43499662 TTGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACG-TGGCA
43499705 T
1 T
43499706 TGTACGAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
42 2 0.03
43 71 0.93
44 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.32
Consensus pattern (42 bp):
TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTGGCA
Found at i:43501035 original size:15 final size:14
Alignment explanation
Indices: 43501014--43501049 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
43501004 ATAATCCTTA
*
43501014 ATAATTATCTTAAT
1 ATAATTATCCTAAT
43501028 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
43501043 ATAATTA
1 ATAATTA
43501050 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:43511109 original size:19 final size:19
Alignment explanation
Indices: 43511085--43511122 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43511075 AAAGTTAAAA
43511085 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
43511104 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
43511123 GTGACGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:43520913 original size:7 final size:7
Alignment explanation
Indices: 43520897--43520931 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
43520887 AAATCAAATT
43520897 TAAT-AA
1 TAATAAA
43520903 TAATAAA
1 TAATAAA
43520910 TAATAAA
1 TAATAAA
43520917 TAATAAA
1 TAATAAA
43520924 TAAATAAA
1 T-AATAAA
43520932 AGGACTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 4 0.15
7 17 0.63
8 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TAATAAA
Found at i:43521245 original size:19 final size:19
Alignment explanation
Indices: 43521221--43521293 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
43521211 AATCATATCT
43521221 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
43521240 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
43521259 TCTAAGATTACAAATCATA
1 TCTAAGATTGCATATCATA
43521278 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
43521294 CTTGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:43521417 original size:14 final size:14
Alignment explanation
Indices: 43521398--43521424 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43521388 TTTGGACTTT
43521398 GTTTTATTATTTTG
1 GTTTTATTATTTTG
43521412 GTTTTATTATTTT
1 GTTTTATTATTTT
43521425 TTATGCGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (14 bp):
GTTTTATTATTTTG
Found at i:43522516 original size:17 final size:17
Alignment explanation
Indices: 43522494--43522531 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43522484 TTGGAAAACA
*
43522494 AGAAGGAAAATAATGAT
1 AGAAGGAAAAAAATGAT
*
43522511 AGAAGGAAAAAAATGGT
1 AGAAGGAAAAAAATGAT
43522528 AGAA
1 AGAA
43522532 AACTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (17 bp):
AGAAGGAAAAAAATGAT
Found at i:43532099 original size:26 final size:26
Alignment explanation
Indices: 43532038--43532098 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
43532028 TTTTTCTTTT
* * *
43532038 CCCCTAAAACTTTTGCTTCCACCAAA
1 CCCCAAAAATTTTTACTTCCACCAAA
*
43532064 CCCCAAAAATTTTTACTTCCTCCTAAA
1 CCCCAAAAATTTTTACTTCCACC-AAA
43532091 CCCCAAAA
1 CCCCAAAA
43532099 TCTTGTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.34, C:0.38, G:0.02, T:0.26
Consensus pattern (26 bp):
CCCCAAAAATTTTTACTTCCACCAAA
Found at i:43532446 original size:19 final size:19
Alignment explanation
Indices: 43532422--43532459 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43532412 AAAGTTAAAA
43532422 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
43532441 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
43532460 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:43540212 original size:21 final size:23
Alignment explanation
Indices: 43540186--43540230 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
43540176 GAAAGGTATC
*
43540186 TACAAATTA-AATC-TCTAATAT
1 TACAAAATAGAATCTTCTAATAT
*
43540207 TACAAAATAGTATCTTCTAATAT
1 TACAAAATAGAATCTTCTAATAT
43540230 T
1 T
43540231 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.40
Consensus pattern (23 bp):
TACAAAATAGAATCTTCTAATAT
Found at i:43541488 original size:17 final size:17
Alignment explanation
Indices: 43541466--43541503 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43541456 TTGGAAAACA
*
43541466 AGAAGGAAAATAATGAT
1 AGAAGGAAAAAAATGAT
*
43541483 AGAAGGAAAAAAATGGT
1 AGAAGGAAAAAAATGAT
43541500 AGAA
1 AGAA
43541504 AACTTTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.13
Consensus pattern (17 bp):
AGAAGGAAAAAAATGAT
Found at i:43551042 original size:27 final size:28
Alignment explanation
Indices: 43551012--43551073 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
43551002 TTTTTCTTTT
* *
43551012 CCCCTAAAACTTTTGCTTCCACC-AAAC
1 CCCCAAAAACTTTTACTTCCACCTAAAC
* *
43551039 CCCCAAAAATTTTTACTTCCTCCTAAA-
1 CCCCAAAAACTTTTACTTCCACCTAAAC
43551066 CCCCAAAA
1 CCCCAAAA
43551074 TCTTGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.34, C:0.39, G:0.02, T:0.26
Consensus pattern (28 bp):
CCCCAAAAACTTTTACTTCCACCTAAAC
Found at i:43551421 original size:19 final size:19
Alignment explanation
Indices: 43551397--43551434 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43551387 AAAGTTAAAA
43551397 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
43551416 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
43551435 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:43557389 original size:17 final size:18
Alignment explanation
Indices: 43557367--43557403 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43557357 TTTTGGGTTG
43557367 TGTGGG-CCACACGGGCA
1 TGTGGGCCCACACGGGCA
*
43557384 TGTGGGCCCACATGGGCA
1 TGTGGGCCCACACGGGCA
43557402 TG
1 TG
43557404 CAGCATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCA
Found at i:43559433 original size:22 final size:21
Alignment explanation
Indices: 43559407--43559452 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
43559397 ATAGAGACCA
43559407 CCATTCAGTGGTATCGCGATAT
1 CCATTCAG-GGTATCGCGATAT
**
43559429 CCATTTTGGGTATCGCGATAT
1 CCATTCAGGGTATCGCGATAT
43559450 CCA
1 CCA
43559453 CCTGCCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (21 bp):
CCATTCAGGGTATCGCGATAT
Found at i:43562986 original size:28 final size:28
Alignment explanation
Indices: 43562955--43563054 Score: 148
Period size: 28 Copynumber: 3.6 Consensus size: 28
43562945 GTAGCAGTCT
*
43562955 GGGCCTAAGCCCAATAAAGCAATAGTTG
1 GGGCCTTAGCCCAATAAAGCAATAGTTG
43562983 GGGCCTTAGCCCAATAAAGCAATAGTTG
1 GGGCCTTAGCCCAATAAAGCAATAGTTG
* * *
43563011 GGGCCTTAGCCCAATACAGTAACAG-TG
1 GGGCCTTAGCCCAATAAAGCAATAGTTG
43563038 TGGGCCTTAGCCCAATA
1 -GGGCCTTAGCCCAATA
43563055 CAGTAACAGT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 2 0.03
28 65 0.97
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (28 bp):
GGGCCTTAGCCCAATAAAGCAATAGTTG
Found at i:43563055 original size:28 final size:28
Alignment explanation
Indices: 43562940--43563064 Score: 146
Period size: 28 Copynumber: 4.5 Consensus size: 28
43562930 AGTATACAGC
* *
43562940 ATACAGTAGCAGTCT-GGGCCTAAGCCCA
1 ATACAGTAACAGT-TGGGGCCTTAGCCCA
* * *
43562968 ATAAAGCAATAGTTGGGGCCTTAGCCCA
1 ATACAGTAACAGTTGGGGCCTTAGCCCA
* * *
43562996 ATAAAGCAATAGTTGGGGCCTTAGCCCA
1 ATACAGTAACAGTTGGGGCCTTAGCCCA
43563024 ATACAGTAACAG-TGTGGGCCTTAGCCCA
1 ATACAGTAACAGTTG-GGGCCTTAGCCCA
43563052 ATACAGTAACAGT
1 ATACAGTAACAGT
43563065 ATAATGCAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
27 3 0.03
28 83 0.97
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
ATACAGTAACAGTTGGGGCCTTAGCCCA
Found at i:43563243 original size:26 final size:26
Alignment explanation
Indices: 43563175--43563245 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
43563165 AAATTGCAGC
* * * * *
43563175 AAAGTTGCCAGTAATAATGATGCAAC
1 AAAGCTGCCAGTAACAGTAATGCAAA
43563201 AAAGCTGCCAGTAACAGTAATGCAAA
1 AAAGCTGCCAGTAACAGTAATGCAAA
43563227 AAAGCTGCCAGTAACAGTA
1 AAAGCTGCCAGTAACAGTA
43563246 TATGTGGCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (26 bp):
AAAGCTGCCAGTAACAGTAATGCAAA
Found at i:43563442 original size:27 final size:27
Alignment explanation
Indices: 43563420--43563703 Score: 274
Period size: 27 Copynumber: 10.5 Consensus size: 27
43563410 AGGGGTATGA
* *
43563420 CAGTCATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * *
43563447 CGGTAATTTTACCCTTCCAAGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
43563474 CAGTAATCTTT-CCCTTTGAGGGTATTT
1 CAGTAAT-TTTACCCTTCGAGGGTATTT
* **
43563501 TAGTAATTTTA-CCTTTTAGGAGTATTT
1 CAGTAATTTTACCCTTCGAGG-GTATTT
*
43563528 C-GATAATTTTACCTTTCGAGGGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
*
43563555 CAGTAATTTTACCCATCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* *
43563582 TAGTAATTTTACCCTTCAAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
**
43563609 TGGTAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * *
43563636 C-GATAATTTTA-CTTATCAACGGTATTT
1 CAG-TAATTTTACCCT-TCGAGGGTATTT
* * *
43563663 TAGTAGTTTTACCCCATCGAGGGTATTT
1 CAGTAATTTTA-CCCTTCGAGGGTATTT
*
43563691 -GGTAATTTTACCC
1 CAGTAATTTTACCC
43563704 ACGAATCGTA
Statistics
Matches: 212, Mismatches: 34, Indels: 23
0.79 0.13 0.09
Matches are distributed among these distances:
26 18 0.08
27 172 0.81
28 21 0.10
29 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGAGGGTATTT
Found at i:43563552 original size:81 final size:80
Alignment explanation
Indices: 43563425--43563703 Score: 312
Period size: 81 Copynumber: 3.4 Consensus size: 80
43563415 TATGACAGTC
* * * *
43563425 ATTTTACCTTTCGAGGGTATTTCGGTAATTTTACCCTTCCAAGGTATTTCAGTAATCTTT-CCCT
1 ATTTTACCTTT-AAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAAT-TTTACCCA
*
43563489 TTGAGGGTATTTTAGTA
64 TCGAGGGTATTTTAGTA
* * *
43563506 ATTTTACCTTTTAGGAGTATTTCGATAATTTTACCTTTCGAGGGTATTTCAGTAATTTTACCCAT
1 ATTTTACCTTTAAGG-GTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCAT
43563571 CGAGGGTATTTTAGTA
65 CGAGGGTATTTTAGTA
* * **
43563587 ATTTTACCCTTCAAGGGTATTTTGGTAATTTTACCCTTCGAGGGTATTTC-GATAATTTTACTTA
1 ATTTTA-CCTTTAAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAG-TAATTTTACCCA
* *
43563651 TCAACGGTATTTTAGTA
64 TCGAGGGTATTTTAGTA
* * **
43563668 GTTTTACCCCATCGAGGGTATTT-GGTAATTTTACCC
1 ATTTTA--CCTTTAAGGGTATTTCGGTAATTTTACCC
43563704 ACGAATCGTA
Statistics
Matches: 174, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
80 7 0.04
81 146 0.84
82 21 0.12
ACGTcount: A:0.23, C:0.16, G:0.17, T:0.44
Consensus pattern (80 bp):
ATTTTACCTTTAAGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCCATC
GAGGGTATTTTAGTA
Found at i:43568582 original size:32 final size:32
Alignment explanation
Indices: 43568527--43568650 Score: 131
Period size: 32 Copynumber: 3.9 Consensus size: 32
43568517 ATAAGTACAT
* * * * * *
43568527 TAATATGATTGGAACAAAACCATCAATAGTAG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* *
43568559 TAATATGATCGGCATACAGCCATCAGTAATGG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* *
43568591 TAACATGATCGGCATAAAGCCATCAGTAACAG
1 TAATATGATCGGCATAAAGCCATCAGTAATAG
* * *
43568623 TAATATGATCGGTAAAAAACCATCAGTA
1 TAATATGATCGGCATAAAGCCATCAGTA
43568651 GCATCGCAGC
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 76 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (32 bp):
TAATATGATCGGCATAAAGCCATCAGTAATAG
Found at i:43568817 original size:24 final size:24
Alignment explanation
Indices: 43568790--43568868 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
43568780 TGCTCAGAAA
* *
43568790 CAGTCATACAAATCACAGATAATT
1 CAGTCATACAAATCACAGACAAAT
* *
43568814 CAGTTATACCAATCACAGACAAAT
1 CAGTCATACAAATCACAGACAAAT
** * *
43568838 CAGTCATTTACATCACGGACAAAT
1 CAGTCATACAAATCACAGACAAAT
*
43568862 CAATCAT
1 CAGTCAT
43568869 TTACACTCGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (24 bp):
CAGTCATACAAATCACAGACAAAT
Found at i:43568869 original size:24 final size:24
Alignment explanation
Indices: 43568825--43568873 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
43568815 AGTTATACCA
*
43568825 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
*
43568849 ATCACGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
43568873 A
1 A
43568874 CTCGAGGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:43568936 original size:27 final size:27
Alignment explanation
Indices: 43568906--43569212 Score: 218
Period size: 27 Copynumber: 11.4 Consensus size: 27
43568896 TACCCTCTAA
* * *
43568906 GGGTATTATGGTCATTTTAACTTACAG
1 GGGTATTACGGTCATTTTAACCTATAG
*
43568933 GGGTATTACGGTTATTTT--CTCTATAG
1 GGGTATTACGGTCATTTTAAC-CTATAG
*
43568959 GGTTATTACGGTCA-TTTAACCCTATAG
1 GGGTATTACGGTCATTTTAA-CCTATAG
* * * * *
43568986 GGGTACTACGATTATTTTACCCCATAG
1 GGGTATTACGGTCATTTTAACCTATAG
* * * * *
43569013 AGGCATTACGATCATTTTACCCTACAG
1 GGGTATTACGGTCATTTTAACCTATAG
** *
43569040 GGGTATTATAGTCA-TTTAACCCTATGG
1 GGGTATTACGGTCATTTTAA-CCTATAG
** *
43569067 GGGTATTACAATCATTTTACCCTATAG
1 GGGTATTACGGTCATTTTAACCTATAG
* *
43569094 GGGTATTACGATCA-TTTAACCCTATGG
1 GGGTATTACGGTCATTTTAA-CCTATAG
43569121 GGGTATTACGGTCA-TTTAACCCTAT-G
1 GGGTATTACGGTCATTTTAA-CCTATAG
* *
43569147 AGGGTATTATGGTCATTTT-ACCTTACAG
1 -GGGTATTACGGTCATTTTAACC-TATAG
* * *
43569175 AGGGCATTACGGTTA-TTTAACCCTATGG
1 -GGGTATTACGGTCATTTTAA-CCTATAG
43569203 GGGTATTACG
1 GGGTATTACG
43569213 ATTGTTTTAC
Statistics
Matches: 224, Mismatches: 42, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.02
26 27 0.12
27 162 0.72
28 29 0.13
29 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (27 bp):
GGGTATTACGGTCATTTTAACCTATAG
Found at i:43569035 original size:54 final size:54
Alignment explanation
Indices: 43568931--43569214 Score: 252
Period size: 54 Copynumber: 5.3 Consensus size: 54
43568921 TTTAACTTAC
* * * *
43568931 AGGGGTATTACGGTTATTTT-CTCTATAG-GGTTATTACGGTCATTTAACCCTAT
1 AGGGGTATTACGATCATTTTACCCTATAGAGG-CATTACGGTCATTTAACCCTAT
* * * * * *
43568984 AGGGGTACTACGATTATTTTACCCCATAGAGGCATTACGATCATTTTACCCTAC
1 AGGGGTATTACGATCATTTTACCCTATAGAGGCATTACGGTCATTTAACCCTAT
* * * * * ** *
43569038 AGGGGTATTA-TAGTCATTTAACCCTATGGGGGTATTACAATCATTTTACCCTAT
1 AGGGGTATTACGA-TCATTTTACCCTATAGAGGCATTACGGTCATTTAACCCTAT
* * * *
43569092 AGGGGTATTACGATCATTTAACCCTATGGGGGTATTACGGTCATTTAACCCTAT
1 AGGGGTATTACGATCATTTTACCCTATAGAGGCATTACGGTCATTTAACCCTAT
* * * * *
43569146 -GAGGGTATTATGGTCATTTTACCTTACAGAGGGCATTACGGTTATTTAACCCTAT
1 AG-GGGTATTACGATCATTTTACCCTATAGA-GGCATTACGGTCATTTAACCCTAT
*
43569201 GGGGGTATTACGAT
1 AGGGGTATTACGAT
43569215 TGTTTTACAA
Statistics
Matches: 191, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
53 20 0.10
54 135 0.71
55 35 0.18
56 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (54 bp):
AGGGGTATTACGATCATTTTACCCTATAGAGGCATTACGGTCATTTAACCCTAT
Found at i:43569070 original size:81 final size:81
Alignment explanation
Indices: 43568957--43569211 Score: 267
Period size: 81 Copynumber: 3.1 Consensus size: 81
43568947 TTTTCTCTAT
* * * * *
43568957 AGGGTTATTACGGTCATTTAACCCTATAGGGGTACTACGATTATTTTACCCCATAGAGGCATTAC
1 AGGGGTATTACAGTCATTTAACCCTATGGGGGTACTACAATCATTTTACCCCATAGAGGCATTAC
*
43569022 GATCATTTTACCCTAC
66 GATCATTTAACCCTAC
* * * * *
43569038 AGGGGTATTATAGTCATTTAACCCTATGGGGGTATTACAATCATTTTACCCTATAGGGGTATTAC
1 AGGGGTATTACAGTCATTTAACCCTATGGGGGTACTACAATCATTTTACCCCATAGAGGCATTAC
*
43569103 GATCATTTAACCCTAT
66 GATCATTTAACCCTAC
* * * * *** ** *
43569119 GGGGGTATTACGGTCATTTAACCCTATGAGGGTATTATGGTCATTTTACCTTACAGAGGGCATTA
1 AGGGGTATTACAGTCATTTAACCCTATGGGGGTACTACAATCATTTTACCCCATAGA-GGCATTA
* * *
43569184 CGGTTATTTAACCCTAT
65 CGATCATTTAACCCTAC
*
43569201 GGGGGTATTAC
1 AGGGGTATTAC
43569212 GATTGTTTTA
Statistics
Matches: 148, Mismatches: 25, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 116 0.78
82 32 0.22
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (81 bp):
AGGGGTATTACAGTCATTTAACCCTATGGGGGTACTACAATCATTTTACCCCATAGAGGCATTAC
GATCATTTAACCCTAC
Found at i:43570323 original size:24 final size:24
Alignment explanation
Indices: 43570296--43570344 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
43570286 AGTTATACCA
*
43570296 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
**
43570320 ATCATGGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
43570344 A
1 A
43570345 CTCGAGGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:43570411 original size:27 final size:27
Alignment explanation
Indices: 43570381--43570667 Score: 279
Period size: 27 Copynumber: 10.6 Consensus size: 27
43570371 CTCTAAGGAC
* *
43570381 ATTATGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
43570408 ATTATGGTTATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
43570435 ATTACGGTTATTTAACCCTATAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
43570462 ATTACGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** **
43570489 ATTATAGTCA-TTTATCCCTATGGGGGGT
1 ATTACGGTCATTTTA-CCCTA-CAGGGGT
43570517 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * **
43570544 ATTACGATCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
43570571 ATTACGGTTATTTAACCTTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
43570598 ATTACGGTCATTTTACCCTACTGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * **
43570625 AATACGGTTATTTAACCCTATTGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
43570652 ATTACAGTTATTTTAC
1 ATTACGGTCATTTTAC
43570668 AACCTTTTCG
Statistics
Matches: 218, Mismatches: 39, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 4 0.02
27 192 0.88
28 18 0.08
29 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:43570465 original size:54 final size:54
Alignment explanation
Indices: 43570403--43570656 Score: 312
Period size: 54 Copynumber: 4.7 Consensus size: 54
43570393 TTACCTTACA
* * * *
43570403 GGGGTATTATGGTTATTTTACCCTACAGGGGTATTACGGTTATTTAACCCTATA
1 GGGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCATTTAACCCTATG
* * ** *
43570457 AGGGTATTACGGTCATTTTACCCTATAGGGGTATTATAGTCATTTATCCCTATGG
1 GGGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCATTTAACCCTAT-G
* * *
43570512 GGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTAACCCTATG
1 GGGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCATTTAACCCTATG
* * *
43570566 GGGGTATTACGGTTATTTAACCTTATAGGGGTATTACGGTCATTTTACCCTACT-
1 GGGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCATTTAACCCTA-TG
* * * *
43570620 GGGGCAATACGGTTATTTAACCCTATTGGGGTATTAC
1 GGGGTATTACGGTTATTTTACCCTATAGGGGTATTAC
43570657 AGTTATTTTA
Statistics
Matches: 173, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 125 0.72
55 48 0.28
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.37
Consensus pattern (54 bp):
GGGGTATTACGGTTATTTTACCCTATAGGGGTATTACGGTCATTTAACCCTATG
Found at i:43570557 original size:109 final size:110
Alignment explanation
Indices: 43570387--43570623 Score: 320
Period size: 109 Copynumber: 2.2 Consensus size: 110
43570377 GGACATTATG
* * * * * *
43570387 GTCATTTTACCTTAC--AGGGGTATTATGGTTATTTTACCCTACAGGGGTATTACGGTTATTTAA
1 GTCATTTTACCCTACTGGGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTAA
* *
43570450 CCCTATAAGGGTATTACGGTCATTTTACCCTATAGGGGTATTATA
66 CCCTATAAGGGTATTACGGTCATTTAACCCTATAGGGGTATTACA
43570495 GTCA-TTTATCCCTA-TGGGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTA
1 GTCATTTTA-CCCTACTGGGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTA
** * * *
43570558 ACCCTATGGGGGTATTACGGTTATTTAACCTTATAGGGGTATTACG
65 ACCCTATAAGGGTATTACGGTCATTTAACCCTATAGGGGTATTACA
43570604 GTCATTTTACCCTACTGGGG
1 GTCATTTTACCCTACTGGGG
43570624 CAATACGGTT
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
107 4 0.04
108 8 0.07
109 90 0.81
110 9 0.08
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (110 bp):
GTCATTTTACCCTACTGGGGGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTAA
CCCTATAAGGGTATTACGGTCATTTAACCCTATAGGGGTATTACA
Found at i:43575416 original size:28 final size:28
Alignment explanation
Indices: 43575353--43575418 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
43575343 ATACAACATG
*
43575353 CAGTAGCAGTCTGGGCCTGAGCCCAATA
1 CAGTAACAGTCTGGGCCTGAGCCCAATA
** * *
43575381 CAACAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTCTGGGCCTGAGCCCAATA
43575409 CAGTAACAGT
1 CAGTAACAGT
43575419 ACAATGCAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.18
Consensus pattern (28 bp):
CAGTAACAGTCTGGGCCTGAGCCCAATA
Found at i:43575545 original size:23 final size:25
Alignment explanation
Indices: 43575519--43575569 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
43575509 CCAACACACC
43575519 AATATCGCAGCAAAGCTGCCAGTAAT
1 AATA-CGCAGCAAAGCTGCCAGTAAT
43575545 AATGACGCAGCAAAGCTGCCAGTAA
1 AAT-ACGCAGCAAAGCTGCCAGTAA
43575570 CAGTATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.16
Consensus pattern (25 bp):
AATACGCAGCAAAGCTGCCAGTAAT
Found at i:43575772 original size:27 final size:27
Alignment explanation
Indices: 43575742--43575800 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
43575732 AACTCCTAGA
*
43575742 GGTATAACAGTCATTTTACCCTATGGG
1 GGTATAACAGCCATTTTACCCTATGGG
*** *
43575769 GGTATTTTAGCCATTTTACCCTTTGGG
1 GGTATAACAGCCATTTTACCCTATGGG
43575796 GGTAT
1 GGTAT
43575801 TTCGATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (27 bp):
GGTATAACAGCCATTTTACCCTATGGG
Found at i:43575811 original size:27 final size:27
Alignment explanation
Indices: 43575781--43576112 Score: 382
Period size: 27 Copynumber: 12.3 Consensus size: 27
43575771 TATTTTAGCC
*
43575781 ATTTTACCCTTTGGGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
43575808 ATTTTACCC-TTGAGGGGTATTTCG-TA
1 ATTTTACCCTTTGA-GGGTATTTCGATA
* * *
43575834 ATCTTACCCTTTAAGGGTATTTCAATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* ** *
43575861 ATCTTACCCTTTTCGGGTATTTCGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* *
43575888 ATTTTACCCTTCGGGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * * *
43575915 ATTTTACCCTTCGAGGATATTTTGGTA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* * * *
43575942 AATTTAACCTTCGAGGGTATTT-TAGTA
1 ATTTTACCCTTTGAGGGTATTTCGA-TA
* * *
43575969 ATTTTACTCATTGAGGGTATTTTGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
43575996 ATTTTACCCTTTGAGGGCATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* *
43576023 GTTTTACCCTTTGAGGGTATTTCGATT
1 ATTTTACCCTTTGAGGGTATTTCGATA
*
43576050 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
* *
43576077 ATTTTACCCTTCGAGGTTATTTCGATA
1 ATTTTACCCTTTGAGGGTATTTCGATA
43576104 ATTTTACCC
1 ATTTTACCC
43576113 ACGAATCATA
Statistics
Matches: 261, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.08
27 238 0.91
28 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTTTGAGGGTATTTCGATA
Found at i:43579804 original size:42 final size:42
Alignment explanation
Indices: 43579737--43579831 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
43579727 TTTCGGTATA
* * *
43579737 GCACACTTGGTGCCCGTTATTCAACATCATCATTTTAATTTC
1 GCACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTC
* *
43579779 GCACACTTAGTGCCTATTATCCAACATCATTATTTTAATTTC
1 GCACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTC
*
43579821 ACACACTTAGT
1 GCACACTTAGT
43579832 TCCGTTCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.38
Consensus pattern (42 bp):
GCACACTTAGTGCCCATTATCCAACATCATCATTTTAATTTC
Found at i:43585420 original size:28 final size:29
Alignment explanation
Indices: 43585364--43585592 Score: 175
Period size: 29 Copynumber: 8.0 Consensus size: 29
43585354 TTTTTTGTAG
* *
43585364 AATAGTGGTAAAACTGTAAAATCT-AAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
43585392 AATAGTGG-AAAACTGTAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
43585420 AATAATGGC-AAATTATAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
** * *
43585448 ACCAGAGGCAAAACTGTAAAATTTAGG-AA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * *
43585477 AATTGTGGTAGAACTGTAAAAT-TGGGAAA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * ** *
43585506 AATAGTGGCAGAACTATAAAAGATGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
43585535 ACCTA-TGGCAAAATTGTAAAAT-TTGAAA
1 A-ATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
43585563 AATAGTGGCAGAACTATAAAATCTGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
43585592 A
1 A
43585593 TGGCGGTACA
Statistics
Matches: 156, Mismatches: 36, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
27 17 0.11
28 62 0.40
29 72 0.46
30 5 0.03
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTGGAAA
Found at i:43588647 original size:65 final size:65
Alignment explanation
Indices: 43588538--43588668 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
43588528 TTTTAAAAAT
* *
43588538 ATTACTTTCCATCTTGCTTGATAGACATGAGATACATTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
*
43588603 ATTAATTTCCTTCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
43588668 A
1 A
43588669 AGAACCTACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (65 bp):
ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
Found at i:43593146 original size:22 final size:23
Alignment explanation
Indices: 43593118--43593165 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
43593108 GTGATATGTC
*
43593118 AAAGTAAAGTAAAT-AAAAAGAA
1 AAAGTAAAATAAATAAAAAAGAA
**
43593140 AAAGTAAAATATTTAAAAAAGAA
1 AAAGTAAAATAAATAAAAAAGAA
43593163 AAA
1 AAA
43593166 ATCACTCCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAGTAAAATAAATAAAAAAGAA
Found at i:43593624 original size:13 final size:13
Alignment explanation
Indices: 43593593--43593630 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43593583 AATTTCAAGT
43593593 ATTGT-ATAAAAA
1 ATTGTGATAAAAA
43593605 ATATGTGATAAAAA
1 AT-TGTGATAAAAA
*
43593619 CTTGTGATAAAA
1 ATTGTGATAAAA
43593631 TTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 13 0.57
14 8 0.35
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (13 bp):
ATTGTGATAAAAA
Found at i:43593957 original size:42 final size:38
Alignment explanation
Indices: 43593868--43593967 Score: 112
Period size: 42 Copynumber: 2.5 Consensus size: 38
43593858 AACATTAAAA
* *
43593868 AATTATTTTAAAATAAAAAAATAAAAGAAAATATTTTT
1 AATTATTTTAAAATTAAAAAATAAAAAAAAATATTTTT
*
43593906 AAAGTATTTTAAAATTAAAAAATAAAAATAAAGAATATATATTT
1 -AATTATTTTAAAATTAAAAAAT-AAAA-AAA-AATAT-T-TTT
43593950 -ATTATTTTAAAATTAAAA
1 AATTATTTTAAAATTAAAA
43593968 TTATTTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
39 20 0.38
40 4 0.08
41 2 0.04
42 22 0.42
43 1 0.02
44 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (38 bp):
AATTATTTTAAAATTAAAAAATAAAAAAAAATATTTTT
Found at i:43593984 original size:17 final size:17
Alignment explanation
Indices: 43593950--43593984 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43593940 ATATATATTT
*
43593950 ATTATTTTAAAATTAAA
1 ATTATTTTAAAATAAAA
43593967 ATTATTTTAAAATAAAA
1 ATTATTTTAAAATAAAA
43593984 A
1 A
43593985 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTATTTTAAAATAAAA
Found at i:43594151 original size:17 final size:17
Alignment explanation
Indices: 43594129--43594165 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43594119 TTTTGTGATA
43594129 ATACTAGTAGAGTATAT
1 ATACTAGTAGAGTATAT
43594146 ATACTAGTAGAGTATAT
1 ATACTAGTAGAGTATAT
43594163 ATA
1 ATA
43594166 ACCCGTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (17 bp):
ATACTAGTAGAGTATAT
Found at i:43597983 original size:17 final size:18
Alignment explanation
Indices: 43597961--43597994 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43597951 TGTGGTTGGT
43597961 AGGAAA-AAAATGAAAAG
1 AGGAAAGAAAATGAAAAG
43597978 AGGAAAGAAAATGAAAA
1 AGGAAAGAAAATGAAAA
43597995 AAATGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (18 bp):
AGGAAAGAAAATGAAAAG
Found at i:43613713 original size:18 final size:19
Alignment explanation
Indices: 43613690--43613726 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
43613680 TTTTTAAAAA
43613690 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
43613708 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
43613727 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:43613727 original size:18 final size:18
Alignment explanation
Indices: 43613690--43613743 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
43613680 TTTTTAAAAA
43613690 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAA-TTT
43613708 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
* *
43613726 TAAAAATTATTTTGAATT
1 TATAAA-TATTTAGAATT
43613744 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:43615258 original size:30 final size:31
Alignment explanation
Indices: 43615187--43615317 Score: 119
Period size: 30 Copynumber: 4.4 Consensus size: 31
43615177 AAAAAAATAT
*
43615187 AAATTACA-TTTGGACCCCTAAATTTTCTTT
1 AAATTACATTTTGGACCCCTAAATTTTCTTA
* ** *
43615217 GAATTGTATTTTGGA-CCTTAAATTTTCTTA
1 AAATTACATTTTGGACCCCTAAATTTTCTTA
* * * * *
43615247 AAATTTCATTTT-GACCACTTAACTTTCTAA
1 AAATTACATTTTGGACCCCTAAATTTTCTTA
* *
43615277 AAATTAAATTTTGG-CCCC-ATATTTTCTTA
1 AAATTACATTTTGGACCCCTAAATTTTCTTA
43615306 AAATTACATTTT
1 AAATTACATTTT
43615318 TTCCCATAAA
Statistics
Matches: 77, Mismatches: 21, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
29 20 0.26
30 50 0.65
31 7 0.09
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (31 bp):
AAATTACATTTTGGACCCCTAAATTTTCTTA
Found at i:43616040 original size:19 final size:20
Alignment explanation
Indices: 43616007--43616052 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
43615997 TTGGGTTTTC
*
43616007 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGAAGAA
*
43616027 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGAAGAA
43616046 GAAAGAA
1 GAAAGAA
43616053 AATAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGAAGAA
Found at i:43616051 original size:16 final size:16
Alignment explanation
Indices: 43616009--43616054 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
43615999 GGGTTTTCGA
*
43616009 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
43616025 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
43616041 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
43616055 TAAAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:43616067 original size:19 final size:20
Alignment explanation
Indices: 43616015--43616073 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
43616005 TCGAAAGAAG
* * *
43616015 AAAAAAGTAGAAGGAAGAAGA
1 AAAAAAGAAGAAAGAA-AATA
43616036 AAAAGAAGAAGAAAGAAAATA
1 AAAA-AAGAAGAAAGAAAATA
43616057 AAAAAAG-AGAAA-AAAAT
1 AAAAAAGAAGAAAGAAAAT
43616074 TTAAATCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.15
19 5 0.15
20 3 0.09
21 11 0.32
22 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (20 bp):
AAAAAAGAAGAAAGAAAATA
Found at i:43616274 original size:17 final size:19
Alignment explanation
Indices: 43616252--43616294 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
43616242 AGGCCAACTA
*
43616252 CCAGGCCAG-CA-CAGCGC
1 CCAGGCCAGCCAGCAGCCC
*
43616269 CCAGGCGAGCCAGCAGCCC
1 CCAGGCCAGCCAGCAGCCC
43616288 CCAGGCC
1 CCAGGCC
43616295 CAGCGTAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.21, C:0.49, G:0.30, T:0.00
Consensus pattern (19 bp):
CCAGGCCAGCCAGCAGCCC
Found at i:43617037 original size:19 final size:18
Alignment explanation
Indices: 43616998--43617067 Score: 67
Period size: 19 Copynumber: 4.0 Consensus size: 18
43616988 TTTCAACAAT
43616998 TTTCGTG-TT-AAAAAAA
1 TTTCGTGTTTCAAAAAAA
43617014 -TTCGTGTTTCAAAAAAA
1 TTTCGTGTTTCAAAAAAA
* *
43617031 TTCTCGTGTTTC-ATAAAT
1 TT-TCGTGTTTCAAAAAAA
*
43617049 TTTTGTGTTTTCAAAAAAA
1 TTTCGTG-TTTCAAAAAAA
43617068 AATTCTCGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 6 0.14
16 2 0.05
17 11 0.26
18 11 0.26
19 13 0.30
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTCGTGTTTCAAAAAAA
Found at i:43617074 original size:39 final size:38
Alignment explanation
Indices: 43617009--43617102 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 38
43616999 TTCGTGTTAA
*
43617009 AAAAATTCGTG-TTTC--AAAAAAATTCTCGTG-TTTC
1 AAAATTTCGTGTTTTCAAAAAAAAATTCTCGTGCTTTC
* *
43617043 ATAAATTTTTGTGTTTTCAAAAAAAAATTCTCGTGCTTTG
1 A-AAA-TTTCGTGTTTTCAAAAAAAAATTCTCGTGCTTTC
43617083 AAAATTTCGTGTTTTCAAAA
1 AAAATTTCGTGTTTTCAAAA
43617103 GTTTTTGTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
34 1 0.02
35 3 0.06
36 5 0.10
37 4 0.08
38 15 0.30
39 18 0.36
40 4 0.08
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (38 bp):
AAAATTTCGTGTTTTCAAAAAAAAATTCTCGTGCTTTC
Found at i:43617128 original size:16 final size:17
Alignment explanation
Indices: 43617067--43617127 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
43617057 TTTCAAAAAA
*
43617067 AAATTCTCGTGCTTT-G
1 AAATTTTCGTGCTTTCG
* * *
43617083 AAAATTTCGTGTTTTCA
1 AAATTTTCGTGCTTTCG
*
43617100 AAAGTTTTTGTG-TTTCG
1 AAA-TTTTCGTGCTTTCG
43617117 AAATTTTCGTG
1 AAATTTTCGTG
43617128 TCTCAATAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 19 0.54
17 10 0.29
18 6 0.17
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (17 bp):
AAATTTTCGTGCTTTCG
Found at i:43617145 original size:34 final size:33
Alignment explanation
Indices: 43617065--43617148 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
43617055 GTTTTCAAAA
* *
43617065 AAAAATTCTCGTGCTTTGAAAATTTCGTGTTTTC
1 AAAAATTCTTGTG-TTTGAAAATTTCGTGTTCTC
* * *
43617099 AAAAGTTTTTGTGTTTCGAAATTTTCGTG-TCTC
1 AAAAATTCTTGTGTTT-GAAAATTTCGTGTTCTC
43617132 AATAAATTCTTGTGTTT
1 AA-AAATTCTTGTGTTT
43617149 TTTAAATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 8 0.20
34 33 0.80
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (33 bp):
AAAAATTCTTGTGTTTGAAAATTTCGTGTTCTC
Found at i:43625591 original size:75 final size:76
Alignment explanation
Indices: 43625378--43626044 Score: 743
Period size: 75 Copynumber: 8.7 Consensus size: 76
43625368 AGAATTATAT
43625378 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CT
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
*
43625442 ATACACCGAGGTA
65 AT-CACTGAGGTA
* *
43625455 TTTTTAATTTATGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
43625519 TC-CTAAGGTA
66 TCACTGAGGTA
*
43625529 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTAAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
43625594 TC-CTGAGGTA
66 TCACTGAGGTA
* * *
43625604 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
43625669 TC-CTGAGGTA
66 TCACTGAGGTA
* * * *
43625679 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGTCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
43625744 -CGCTGAGGTA
66 TCACTGAGGTA
* * *
43625754 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCTG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-T-
*
43625819 CA-CGCTGAGGTA
64 CATCACTGAGGTA
* * * * *
43625831 TTTTTTAATTTAT-TTTAAAAAAAATCAAATCAAAACCAACTTATAATGCGAGAGGTGAGTTGAG
1 -TTTTCAATTTCTGTTT-------TTCAAA--AAAATCAACTCATAATGCGAGAGGTGAGTTGAG
* *
43625895 ACTTGGG-CTATACACTGAGGTA
56 CCTCGGGTC-AT-CACTGAGGTA
* * * * *
43625917 TTTTTAATTTCTGTTTTTC--AAAAATCAACTTATATTGTGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
43625980 T-ATGCCGAGGTA
66 TCA--CTGAGGTA
* ** *
43625992 TTTTTCAATTTCTATTTTTC--AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
43626045 ACTTCGAATC
Statistics
Matches: 522, Mismatches: 44, Indels: 49
0.85 0.07 0.08
Matches are distributed among these distances:
73 1 0.00
74 24 0.05
75 299 0.57
76 89 0.17
77 33 0.06
78 10 0.02
79 2 0.00
83 1 0.00
84 6 0.01
85 11 0.02
86 46 0.09
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (76 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
TCACTGAGGTA
Found at i:43626235 original size:5 final size:5
Alignment explanation
Indices: 43626225--43626250 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43626215 TTCTTCGTGT
43626225 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
43626251 ATATATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:43626259 original size:15 final size:15
Alignment explanation
Indices: 43626225--43626258 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
43626215 TTCTTCGTGT
*
43626225 TTTTATTTTATTTTA
1 TTTTATTTTATTATA
43626240 TTTTATTTTATATATA
1 TTTTATTTTAT-TATA
43626256 TTT
1 TTT
43626259 AAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTTATTATA
Found at i:43626558 original size:29 final size:30
Alignment explanation
Indices: 43626470--43626569 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
43626460 ATTTTATTTG
* *
43626470 AATTATATTTTAGACCCTA-AACTTTTTT-AA
1 AATTACATTTT-GACCCCATAA-TTTTTTAAA
* * * *
43626500 AATTTCATTTTGACCCCTTAACTTTCTAAA
1 AATTACATTTTGACCCCATAATTTTTTAAA
*
43626530 AATTACATTTTGGCCCCAT-ATTTTTTAAA
1 AATTACATTTTGACCCCATAATTTTTTAAA
43626559 AATTACATTTT
1 AATTACATTTT
43626570 CCCTAGAAAC
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 28 0.49
30 29 0.51
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (30 bp):
AATTACATTTTGACCCCATAATTTTTTAAA
Found at i:43627259 original size:3 final size:3
Alignment explanation
Indices: 43627253--43627301 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
43627243 GGGTTTTCGA
*
43627253 AAG AAG AA- AA- AAG TAG AAGG AAG AAG AAG AAG AAG AAG AAAG AA-
1 AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG -AAG AAG
43627297 AAG AA
1 AAG AA
43627302 AAAAAAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 28 0.70
4 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:43627270 original size:10 final size:10
Alignment explanation
Indices: 43627252--43627316 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
43627242 AGGGTTTTCG
43627252 AAAGAAGAAA
1 AAAGAAGAAA
* *
43627262 AAAGTAGAAG
1 AAAGAAGAAA
*
43627272 GAAGAAGAAGA
1 AAAGAAGAA-A
43627283 AGAAGAAGAAAGA
1 A-AAGAAG-AA-A
43627296 AAAGAA-AAA
1 AAAGAAGAAA
43627305 AAAG-AGAAA
1 AAAGAAGAAA
43627314 AAA
1 AAA
43627317 ATTTAAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 11 0.24
10 17 0.38
12 11 0.24
13 5 0.11
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (10 bp):
AAAGAAGAAA
Done.