Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 123 of 290
Found at i:41825427 original size:61 final size:61
Alignment explanation
Indices: 41825332--41825452 Score: 152
Period size: 61 Copynumber: 2.0 Consensus size: 61
41825322 TTTTAAAACT
* * * * * *
41825332 TTTAGAGTTATGACTAAATTGACAAATTTTATAAATATTGAGGGCTAAATTTATTGAATTC
1 TTTAGAATTATAACGAAAATGACAAATTTTATAAATATTAAGAGCTAAATTTATTGAATTC
* * * *
41825393 TTTAGAATTATAACGAAAATGACAAGTTTTATAAATGTTAAGAGTTAAATTTGTTGAATT
1 TTTAGAATTATAACGAAAATGACAAATTTTATAAATATTAAGAGCTAAATTTATTGAATT
41825453 TCTTGTATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (61 bp):
TTTAGAATTATAACGAAAATGACAAATTTTATAAATATTAAGAGCTAAATTTATTGAATTC
Found at i:41825789 original size:62 final size:62
Alignment explanation
Indices: 41825720--41825842 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
41825710 CCCAAATATA
41825720 AACCCAAACAAGGCCCAAACAAACAGAAACCCAAGGCTGTTGCTTGAGCCCTCGCGCCGCAC
1 AACCCAAACAAGGCCCAAACAAACAGAAACCCAAGGCTGTTGCTTGAGCCCTCGCGCCGCAC
* * *
41825782 AACCCAAACAAGGCCCAAACAGACAGAAACCCAAGGGTGTTGCTTGAGCCCTCGCGTCGCA
1 AACCCAAACAAGGCCCAAACAAACAGAAACCCAAGGCTGTTGCTTGAGCCCTCGCGCCGCA
41825843 TGCCTCTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.33, C:0.35, G:0.21, T:0.11
Consensus pattern (62 bp):
AACCCAAACAAGGCCCAAACAAACAGAAACCCAAGGCTGTTGCTTGAGCCCTCGCGCCGCAC
Found at i:41826737 original size:23 final size:23
Alignment explanation
Indices: 41826681--41826760 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
41826671 TTTGTTATTA
41826681 TTATTA-ATCTATTATTACTAT--T
1 TTATTATAT-TATT-TTACTATCAT
41826703 TTATT-T-TT-TTTTACTATCAT
1 TTATTATATTATTTTACTATCAT
* *
41826723 TT-TTTTAGTTATTTTCCTATCAT
1 TTATTATA-TTATTTTACTATCAT
41826746 TTATTATATTATTTT
1 TTATTATATTATTTT
41826761 TTTACACTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
18 7 0.15
19 4 0.08
20 5 0.10
21 1 0.02
22 7 0.15
23 20 0.42
24 4 0.08
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATATTATTTTACTATCAT
Found at i:41826788 original size:16 final size:15
Alignment explanation
Indices: 41826739--41826789 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41826729 AGTTATTTTC
*
41826739 CTATCATTTATTATA
1 CTATTATTTATTATA
* *
41826754 TTATT-TTT-TTACA
1 CTATTATTTATTATA
41826767 CTATTATTTATTATA
1 CTATTATTTATTATA
41826782 CTCATTAT
1 CT-ATTAT
41826790 ATCATTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 8 0.29
14 6 0.21
15 9 0.32
16 5 0.18
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (15 bp):
CTATTATTTATTATA
Found at i:41838480 original size:90 final size:91
Alignment explanation
Indices: 41838371--41838578 Score: 314
Period size: 90 Copynumber: 2.3 Consensus size: 91
41838361 CATACCAGAT
*
41838371 CTTATCTTCACTGAGCAGGAGTGAAGCAAATT-AAATTTTGG-CAAGTCTTATCTCCATGTATCG
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAATTCAAATTTTGGTCAA-TCTTATCTCCATGTATCG
*
41838434 GCAATGGAGCAGATTTCAGCCACCAGC
65 ACAATGGAGCAGATTTCAGCCACCAGC
* * * *
41838461 CTTATCTTCGCTGAGCAGGAGCGGAGC-AGTTCAAATTTTGGTGAATCTTATCTCCATGTATCGA
1 CTTATCTTCACTGAGCAGGAGTGGAGCAAATTCAAATTTTGGTCAATCTTATCTCCATGTATCGA
*
41838525 CAATGGAGTAGATTTCAGCCACCAGC
66 CAATGGAGCAGATTTCAGCCACCAGC
*
41838551 CTTATCTTCACTAAGCAGGAGTGGAGCA
1 CTTATCTTCACTGAGCAGGAGTGGAGCA
41838579 GGCTAAATAT
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
89 3 0.03
90 100 0.95
91 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (91 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAAATTCAAATTTTGGTCAATCTTATCTCCATGTATCGA
CAATGGAGCAGATTTCAGCCACCAGC
Found at i:41838600 original size:135 final size:135
Alignment explanation
Indices: 41838461--41838767 Score: 443
Period size: 135 Copynumber: 2.3 Consensus size: 135
41838451 AGCCACCAGC
** * * *
41838461 CTTATCTTCGCTGAGCAGGAGCGGAGCAGTTCAAATTTTGGTGAATCTTATCTCCATGTATCGAC
1 CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATATATCGAC
* * * * * *
41838526 AATGGAGTAGATTTCAGCCACCAGCCTTATCTTCACTAAGCAGGAGTGGAGCAGGCTAAATATAC
66 AATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATAC
41838591 CAGAT
131 CAGAT
*
41838596 CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATATATCGGC
1 CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATATATCGAC
* * *
41838661 AATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAAGAGTGGAGCAAGCTAAACATAC
66 AATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATAC
41838726 CAGAT
131 CAGAT
* ** *
41838731 TTTATCTTTACTGAGCAGGAGTAAAGCAGATCAAATT
1 CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATT
41838768 ACAGCAGATC
Statistics
Matches: 153, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
135 153 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (135 bp):
CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATATATCGAC
AATGGAGCAGATTCCAACCACCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATAC
CAGAT
Found at i:41838803 original size:135 final size:135
Alignment explanation
Indices: 41838461--41838803 Score: 316
Period size: 135 Copynumber: 2.5 Consensus size: 135
41838451 AGCCACCAGC
* ** * ** * ** * *
41838461 CTTATCTTCGCTGAGCAGGAGCGGAGCAGTTCAAATTTTGGTGAATCTTATCTCCATGTATC-GA
1 CTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATGAATCACATCTCCATATAGCAG-
* * * ** * * * *
41838525 CAATGGAGTAGATTTCAGCCACCAGCCTTATCTTCACTAAGCAGGAGTGGAGCAGGCTAAATATA
65 CAACGGAGCAGATTCCAATCATCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATA
41838590 CCAGAT
130 CCAGAT
* ** ** * *
41838596 CTTATCTTCGCTGAGCAGGAGCAAAGCAGATCAAATTTTGATGAATCTTATCTCCATATATCGGC
1 CTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATGAATCACATCTCCATATAGCAGC
* *
41838661 AATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAAGAGTGGAGCAAGCTAAACATAC
66 AACGGAGCAGATTCCAATCATCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATAC
41838726 CAGAT
131 CAGAT
* * * *
41838731 TTTATCTTTACTGAGCAGGAGTAAAGCAGATCAAATTACAGCA-G-ATCACATCTCCGTGA-AGC
1 CTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATT-CAG-ATGAATCACATCTCCAT-ATAGC
*
41838793 AGTAACGGAGC
63 AGCAACGGAGC
41838804 GTTTTGAAGC
Statistics
Matches: 177, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
135 172 0.97
136 4 0.02
137 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (135 bp):
CTTATCTTCACTGAGCAGGAGCAAAGCAGATCAAATTCAGATGAATCACATCTCCATATAGCAGC
AACGGAGCAGATTCCAATCATCAGCCTTATCTTCACTAAGCAAGAGTGGAGCAAGCTAAACATAC
CAGAT
Found at i:41840256 original size:14 final size:14
Alignment explanation
Indices: 41840237--41840266 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41840227 TTTTTTACCG
41840237 TTTACTACTATTAT
1 TTTACTACTATTAT
*
41840251 TTTACTATTATTAT
1 TTTACTACTATTAT
41840265 TT
1 TT
41840267 ATAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTACTACTATTAT
Found at i:41840410 original size:30 final size:32
Alignment explanation
Indices: 41840333--41840412 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 32
41840323 AGACTTACTA
*
41840333 TATTATT-TTTATTATTTTTATATACCATAGT
1 TATTATTATTTATTATTTTTATATACCATAAT
* ** * *
41840364 T-TTTTTATCGAATATTTTT-TATACTA-AAT
1 TATTATTATTTATTATTTTTATATACCATAAT
41840393 TATTATTATTTATTATTTTT
1 TATTATTATTTATTATTTTT
41840413 CACTTTCACT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
29 3 0.08
30 24 0.65
31 10 0.27
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.64
Consensus pattern (32 bp):
TATTATTATTTATTATTTTTATATACCATAAT
Found at i:41842978 original size:221 final size:220
Alignment explanation
Indices: 41842575--41843012 Score: 628
Period size: 221 Copynumber: 2.0 Consensus size: 220
41842565 AGAAACAATA
* * * * *
41842575 TATAACCTTTTAAAAAATCCAAGTTATATGGAGTTGGAAGCTTTGCTTTACGTTTGTGTTATGGT
1 TATAACCTTTTAAAAAATCCAAATTATATGAAGCTGAAAGCTTTGCTTTACGTTTATGTTATGGT
* * * *
41842640 TTTTTGTGCTATGAGATTTTGTACTTGATCTCTTATCTGCATGCATTTTGCTCCGAATTTGGAAT
66 CTTTTATGCTATGAGATTGTGTACTTGATCTCTTATCTGCATGCATTTTGCTCCAAATTTGGAAT
* * * * * *
41842705 AGTACTTAGTACTGACAGTTTGCTAATTCCTTATTTTTGCTTTTAGGTACGTTCACTGAGTGGAG
131 AGTACTTAGTACTGACAGTTTGCTAATTCCATATGTGTGCATTTAAGTACGTTCACTGAATGGAG
*
41842770 TGA-TCAAAGATATTGGAAACCCCTT
196 TGAGT-AAAGAGATTGGAAACCCCTT
* * * *
41842795 TATAGCCTTTTAAAAAAATGCAAATTATATGAAGCTGAAAGCTTTGCTTT-TGTTTTATGTTTTG
1 TATAACCTTTT-AAAAAATCCAAATTATATGAAGCTGAAAGCTTTGCTTTACG-TTTATGTTATG
* * *
41842859 GTCTTTTATGCTATGGGATTGTGTATTTGATCTCTTATTTGCATGCATTTTGCTCCAAATTTGGA
64 GTCTTTTATGCTATGAGATTGTGTACTTGATCTCTTATCTGCATGCATTTTGCTCCAAATTTGGA
41842924 ATAGTACTTAGTACTGACAGTTTGCTAATTCCATATGTGTGCATTTAAGTACGTTCACTGAATGG
129 ATAGTACTTAGTACTGACAGTTTGCTAATTCCATATGTGTGCATTTAAGTACGTTCACTGAATGG
41842989 AGTGAGTAAAGAGATTGGAAACCC
194 AGTGAGTAAAGAGATTGGAAACCC
41843013 TTCTTGGAAG
Statistics
Matches: 192, Mismatches: 23, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
220 11 0.06
221 180 0.94
222 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.41
Consensus pattern (220 bp):
TATAACCTTTTAAAAAATCCAAATTATATGAAGCTGAAAGCTTTGCTTTACGTTTATGTTATGGT
CTTTTATGCTATGAGATTGTGTACTTGATCTCTTATCTGCATGCATTTTGCTCCAAATTTGGAAT
AGTACTTAGTACTGACAGTTTGCTAATTCCATATGTGTGCATTTAAGTACGTTCACTGAATGGAG
TGAGTAAAGAGATTGGAAACCCCTT
Found at i:41849850 original size:22 final size:22
Alignment explanation
Indices: 41849825--41849871 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41849815 TTTTTGAATA
*
41849825 ATATATGCTAAACAAAAAAATT
1 ATATATGATAAACAAAAAAATT
* * *
41849847 ATATATGATACACAATAAATTT
1 ATATATGATAAACAAAAAAATT
41849869 ATA
1 ATA
41849872 AATTAATTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (22 bp):
ATATATGATAAACAAAAAAATT
Found at i:41855243 original size:9 final size:9
Alignment explanation
Indices: 41855227--41855261 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41855217 TTAATTGATA
41855227 AATTAATTT
1 AATTAATTT
*
41855236 AGTTAATTT
1 AATTAATTT
*
41855245 AATTAATTA
1 AATTAATTT
41855254 AATTAATT
1 AATTAATT
41855262 GATTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (9 bp):
AATTAATTT
Found at i:41855254 original size:13 final size:13
Alignment explanation
Indices: 41855225--41855269 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
41855215 GTTTAATTGA
*
41855225 TAAATTAATTTAGT
1 TAAATTAA-TTAAT
*
41855239 TAATTTAATTAAT
1 TAAATTAATTAAT
*
41855252 TAAATTAATTGAT
1 TAAATTAATTAAT
41855265 TAAAT
1 TAAAT
41855270 AAATAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 20 0.74
14 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (13 bp):
TAAATTAATTAAT
Found at i:41857805 original size:11 final size:11
Alignment explanation
Indices: 41857789--41857816 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
41857779 TTCTACAAAC
41857789 AAAAAAACATG
1 AAAAAAACATG
41857800 AAAAAAACATG
1 AAAAAAACATG
41857811 AAAAAA
1 AAAAAA
41857817 GAAAATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAACATG
Found at i:41858219 original size:25 final size:25
Alignment explanation
Indices: 41858191--41858265 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
41858181 AAATAGAGTT
41858191 AGATCTTCAAAATGATGATTATTTG
1 AGATCTTCAAAATGATGATTATTTG
* *
41858216 AGATCTTTTAAGAA--A-GGTTA--T-
1 AGATC-TTCAA-AATGATGATTATTTG
41858237 AGATCTTCAAAATGATGATTATTTG
1 AGATCTTCAAAATGATGATTATTTG
41858262 AGAT
1 AGAT
41858266 ATTTTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
19 2 0.05
20 4 0.11
21 6 0.16
22 5 0.13
24 5 0.13
25 10 0.26
26 4 0.11
27 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (25 bp):
AGATCTTCAAAATGATGATTATTTG
Found at i:41858246 original size:46 final size:46
Alignment explanation
Indices: 41858190--41858282 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
41858180 AAAATAGAGT
* *
41858190 TAGATCTTCAAAATGATGATTATTTGAGATCTTTTAAGAAAGGTTA
1 TAGATCTTCAAAATGATGATTATTTGAGATATTTTAAGAAAGATTA
*
41858236 TAGATCTTCAAAATGATGATTATTTGAGATATTTTAATAAAGATTA
1 TAGATCTTCAAAATGATGATTATTTGAGATATTTTAAGAAAGATTA
41858282 T
1 T
41858283 GAAAAAGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (46 bp):
TAGATCTTCAAAATGATGATTATTTGAGATATTTTAAGAAAGATTA
Found at i:41864728 original size:14 final size:15
Alignment explanation
Indices: 41864703--41864731 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41864693 AAAAACTTTA
41864703 ATTAAGTTAATTAAT
1 ATTAAGTTAATTAAT
41864718 ATTAA-TTAATTAAT
1 ATTAAGTTAATTAAT
41864732 GTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATTAAGTTAATTAAT
Found at i:41868060 original size:14 final size:14
Alignment explanation
Indices: 41868027--41868065 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41868017 TTCGCATTGT
*
41868027 ACAAAATTAA-TAA
1 ACAAATTTAACTAA
*
41868040 TCAAATTTAACTAA
1 ACAAATTTAACTAA
41868054 ACAAATTTAACT
1 ACAAATTTAACT
41868066 TTTAACTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATTTAACTAA
Found at i:41869922 original size:26 final size:26
Alignment explanation
Indices: 41869893--41869944 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
41869883 TTTAATTGCC
*
41869893 TTAATTATAGTTTCTTATTCTATAAA
1 TTAATTATAGTTTCTTAGTCTATAAA
*
41869919 TTAATTTTAGTTTCTTAGTCTATAAA
1 TTAATTATAGTTTCTTAGTCTATAAA
41869945 AATAGAACCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.54
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTATAAA
Found at i:41874533 original size:24 final size:24
Alignment explanation
Indices: 41874486--41874533 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41874476 ATTTTACACT
* *
41874486 AATAAAATTAGCACAATTTTTTTA
1 AATAAAATTAGCACAAATTGTTTA
*
41874510 AATAGAATTAGCACAAATTGTTTA
1 AATAAAATTAGCACAAATTGTTTA
41874534 TATCAATTTT
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:0.08, G:0.08, T:0.38
Consensus pattern (24 bp):
AATAAAATTAGCACAAATTGTTTA
Found at i:41874818 original size:24 final size:24
Alignment explanation
Indices: 41874791--41874842 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
41874781 CTATTTTATT
41874791 TATTTAT-TAATTTATT-AAATAATA
1 TATTTATATAATTT-TTAAAAT-ATA
*
41874815 TATTTTTATAATTTTTAAAATATA
1 TATTTATATAATTTTTAAAATATA
41874839 TATT
1 TATT
41874843 CTAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TATTTATATAATTTTTAAAATATA
Found at i:41874827 original size:25 final size:25
Alignment explanation
Indices: 41874793--41874842 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
41874783 ATTTTATTTA
41874793 TTTATTAATTTATT-AAATAATATATT
1 TTTATTAATTT-TTAAAAT-ATATATT
41874819 TTTA-TAATTTTTAAAATATATATT
1 TTTATTAATTTTTAAAATATATATT
41874843 CTAATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTATTAATTTTTAAAATATATATT
Found at i:41878452 original size:22 final size:21
Alignment explanation
Indices: 41878424--41878468 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
41878414 AAACTGTAAG
41878424 ATTAAAAATGTAGATTTTCGT
1 ATTAAAAATGTAGATTTTCGT
*
41878445 ATTAAAAATGTAGATTTTTGT
1 ATTAAAAATGTAGATTTTCGT
41878466 ATT
1 ATT
41878469 TATTTTGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (21 bp):
ATTAAAAATGTAGATTTTCGT
Found at i:41884925 original size:24 final size:24
Alignment explanation
Indices: 41884893--41884949 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
41884883 TCTTCTCCAT
41884893 GCCATAGCTGAAATTTCCATGCTC
1 GCCATAGCTGAAATTTCCATGCTC
41884917 GCCATAGCTGAAATTTCCATGCTC
1 GCCATAGCTGAAATTTCCATGCTC
*
41884941 ACCATAGCT
1 GCCATAGCT
41884950 AAGGTTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (24 bp):
GCCATAGCTGAAATTTCCATGCTC
Found at i:41888284 original size:17 final size:18
Alignment explanation
Indices: 41888257--41888299 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
41888247 AGTGAAATTT
41888257 ATATGAAAAT-CCAGAAGG
1 ATAT-AAAATCCCAGAAGG
* *
41888275 ATTTAAAATCCCTGAAGG
1 ATATAAAATCCCAGAAGG
41888293 ATATAAA
1 ATATAAA
41888300 GTTTCTCGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:41892091 original size:22 final size:22
Alignment explanation
Indices: 41892054--41892122 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
41892044 TCTTCGATTA
* *
41892054 TTAGCACATTAT-TGCTTTCCGT
1 TTAGCACATT-TGTGCTCTCTGT
41892076 TTAGCACATTTGTGCTCTCTGT
1 TTAGCACATTTGTGCTCTCTGT
*
41892098 ATAGCAC-TTTAGTGCTCTCTGT
1 TTAGCACATTT-GTGCTCTCTGT
41892120 TTA
1 TTA
41892123 ATAGTGCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.10
22 37 0.90
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.45
Consensus pattern (22 bp):
TTAGCACATTTGTGCTCTCTGT
Found at i:41892966 original size:22 final size:24
Alignment explanation
Indices: 41892920--41892968 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
41892910 TGTATCTGTT
*
41892920 TTTTCTAATTTATTAAATAATATA
1 TTTTATAATTTATTAAATAATATA
41892944 TTTTATAATTT-TTAAA-AATATA
1 TTTTATAATTTATTAAATAATATA
41892966 TTT
1 TTT
41892969 GCTAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 5 0.21
24 10 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATAATTTATTAAATAATATA
Found at i:41892974 original size:22 final size:24
Alignment explanation
Indices: 41892924--41892975 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
41892914 TCTGTTTTTT
*
41892924 CTAATTTATTAAATAATATATTTT
1 CTAATTTATTAAATAATATATTTG
*
41892948 ATAATTT-TTAAA-AATATATTTG
1 CTAATTTATTAAATAATATATTTG
41892970 CTAATT
1 CTAATT
41892976 AAATAAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.56
23 5 0.20
24 6 0.24
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
CTAATTTATTAAATAATATATTTG
Found at i:41893344 original size:12 final size:13
Alignment explanation
Indices: 41893323--41893351 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41893313 TTCAAGTCAT
41893323 TTTTCGTTTTTCA
1 TTTTCGTTTTTCA
41893336 TTTTC-TTTTTCA
1 TTTTCGTTTTTCA
41893348 TTTT
1 TTTT
41893352 GGAGAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.07, C:0.14, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTCGTTTTTCA
Found at i:41895550 original size:37 final size:36
Alignment explanation
Indices: 41895488--41895563 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
41895478 GATAATCATT
*
41895488 TTAATATTAAATTAATAAAATACTATTAAGATAAATA
1 TTAATATTAAATTAATAAAATACTATTAAAAT-AATA
*
41895525 TTAA-ATTAAATTTAATATCAA-ACTATTAAAATAATA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAATA
41895561 TTA
1 TTA
41895564 TTTTTGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:41895964 original size:24 final size:24
Alignment explanation
Indices: 41895915--41895961 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
41895905 AAATATCATA
***
41895915 TTAATTTTAATTGATTTGATTAAT
1 TTAATTTTAATTGATAAAATTAAT
41895939 TTAATTTTAATTGATCAAAATTA
1 TTAATTTTAATTGAT-AAAATTA
41895962 TTTTTTCCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
TTAATTTTAATTGATAAAATTAAT
Found at i:41904970 original size:41 final size:41
Alignment explanation
Indices: 41904920--41905004 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
41904910 GTTTTACCAA
*
41904920 AAACGCCGCTAAAAAATAGAGCAATAGC-G-GCTTTTTTGCTC
1 AAACACCGCTAAAAAATAGAGCAATAGCTGTG-TTTTTT-CTC
41904961 AAACACCGCTAAAAAATAGAGCAATAGCTGTGTTTTTTCTC
1 AAACACCGCTAAAAAATAGAGCAATAGCTGTGTTTTTTCTC
41905002 AAA
1 AAA
41905005 ACGCCATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
41 33 0.80
42 7 0.17
43 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (41 bp):
AAACACCGCTAAAAAATAGAGCAATAGCTGTGTTTTTTCTC
Found at i:41905015 original size:41 final size:40
Alignment explanation
Indices: 41904919--41905016 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 40
41904909 CGTTTTACCA
41904919 AAAACGCCGCTAAAAAATAGAGCAATAGCGGCTTTTTTGCTC
1 AAAACG-C-CTAAAAAATAGAGCAATAGCGGCTTTTTTGCTC
41904961 AAACAC-CGCTAAAAAATAGAGCAATAGCTGTG-TTTTTT-CTC
1 AAA-ACGC-CTAAAAAATAGAGCAATAGC-G-GCTTTTTTGCTC
41905002 AAAACGCCATAAAAA
1 AAAACGCC-TAAAAA
41905017 GTCATATAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
40 3 0.06
41 35 0.69
42 10 0.20
43 3 0.06
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (40 bp):
AAAACGCCTAAAAAATAGAGCAATAGCGGCTTTTTTGCTC
Found at i:41905213 original size:7 final size:7
Alignment explanation
Indices: 41905202--41905265 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
41905192 TTTATTTTTG
*
41905202 GGTTTAG
1 GGTTTAA
41905209 GGTTTAA
1 GGTTTAA
**
41905216 TATTTAA
1 GGTTTAA
41905223 GGTTTAA
1 GGTTTAA
* *
41905230 GGTCTAT
1 GGTTTAA
*
41905237 GGTTTAG
1 GGTTTAA
*
41905244 GGTTTTAT
1 GG-TTTAA
41905252 GGTTTAA
1 GGTTTAA
41905259 GGTTTAA
1 GGTTTAA
41905266 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:41905254 original size:15 final size:15
Alignment explanation
Indices: 41905218--41905268 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
41905208 GGGTTTAATA
*
41905218 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
41905232 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
41905247 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
41905262 TTAATGG
1 TTTATGG
41905269 CCATGGGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:41905737 original size:18 final size:16
Alignment explanation
Indices: 41905697--41905738 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
41905687 AGAGATAATA
41905697 TTAAATT-TAATATAT
1 TTAAATTATAATATAT
*
41905712 TAAAATTATGAATATAGT
1 TTAAATTAT-AATATA-T
41905730 TTAAATTAT
1 TTAAATTAT
41905739 TTAAGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 1 0.05
17 6 0.27
18 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (16 bp):
TTAAATTATAATATAT
Found at i:41909781 original size:31 final size:32
Alignment explanation
Indices: 41909743--41909814 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 32
41909733 TTACTGTATT
41909743 TTATTTATATTTA-TATTT-AATCTA-ATTTTTA
1 TTATTTAT-TTTAGT-TTTGAATCTATATTTTTA
*
41909774 TTATTTATTTTAGTTTTGATTCTATATTTTTA
1 TTATTTATTTTAGTTTTGAATCTATATTTTTA
41909806 TT-TTTATTT
1 TTATTTATTT
41909815 AATTTGATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 7 0.19
31 21 0.57
32 9 0.24
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (32 bp):
TTATTTATTTTAGTTTTGAATCTATATTTTTA
Found at i:41909790 original size:19 final size:19
Alignment explanation
Indices: 41909767--41909813 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
41909757 ATTTAATCTA
*
41909767 ATTTTTATTATTTA-TTTT
1 ATTTTTATTATATATTTTT
* *
41909785 AGTTTTGATTCTATATTTTT
1 A-TTTTTATTATATATTTTT
41909805 ATTTTTATT
1 ATTTTTATT
41909814 TAATTTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:41909842 original size:11 final size:11
Alignment explanation
Indices: 41909822--41909850 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41909812 TTTAATTTGA
41909822 TAAT-GAATTT
1 TAATAGAATTT
41909832 TAATAGAATTT
1 TAATAGAATTT
41909843 TAATAGAA
1 TAATAGAA
41909851 AATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (11 bp):
TAATAGAATTT
Found at i:41913009 original size:40 final size:40
Alignment explanation
Indices: 41912827--41913049 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 40
41912817 TCCTCGTTCA
* * * * *
41912827 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41912866 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41912906 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41912946 AATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
41912986 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41913026 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41913050 CAGCATTCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 37 0.23
40 116 0.72
41 8 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41913058 original size:41 final size:41
Alignment explanation
Indices: 41912981--41913058 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41912971 TTAATATCTC
* * *
41912981 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41913022 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41913059 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41920836 original size:40 final size:40
Alignment explanation
Indices: 41920738--41921000 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
41920728 TCCTCGTTCA
* * * * *
41920738 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41920777 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41920817 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41920857 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41920897 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41920937 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41920977 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41921001 CAGCATTCAA
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 37 0.19
40 155 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41923689 original size:8 final size:8
Alignment explanation
Indices: 41923676--41923702 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41923666 AAGTCGATTT
41923676 GGAGGTAA
1 GGAGGTAA
41923684 GGAGGTAA
1 GGAGGTAA
41923692 GGAGGTAA
1 GGAGGTAA
41923700 GGA
1 GGA
41923703 TTTTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.52, T:0.11
Consensus pattern (8 bp):
GGAGGTAA
Found at i:41925974 original size:4 final size:4
Alignment explanation
Indices: 41925965--41926008 Score: 52
Period size: 4 Copynumber: 10.2 Consensus size: 4
41925955 GTGCTAGAAG
*
41925965 AATA AATA AATAA AATA AATA AATA AATA ACATGA CATA AATA A
1 AATA AATA AAT-A AATA AATA AATA AATA A-AT-A AATA AATA A
41926009 TATTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 26 0.74
5 8 0.23
6 1 0.03
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:41925983 original size:13 final size:13
Alignment explanation
Indices: 41925965--41925991 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41925955 GTGCTAGAAG
41925965 AATAAATAAATAA
1 AATAAATAAATAA
41925978 AATAAATAAATAA
1 AATAAATAAATAA
41925991 A
1 A
41925992 TAACATGACA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAATAAATAA
Found at i:41925987 original size:17 final size:18
Alignment explanation
Indices: 41925965--41926008 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
41925955 GTGCTAGAAG
41925965 AATAAATAAATAAAAT-A
1 AATAAATAAATAAAATGA
*
41925982 AATAAATAAATAACATGA
1 AATAAATAAATAAAATGA
*
41926000 CATAAATAA
1 AATAAATAA
41926009 TATTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
AATAAATAAATAAAATGA
Found at i:41927744 original size:45 final size:45
Alignment explanation
Indices: 41927677--41928128 Score: 174
Period size: 45 Copynumber: 9.6 Consensus size: 45
41927667 TAACTTGTAG
* * *
41927677 CTTCAATCTGCCCCACTACAACTTCAGGGAAATGAGATTCGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
* * * * * *
41927722 CTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCG---C---TAT
* * ** *
41927773 CTTCAATCTGCTCTACTGCAACTTTAAAGAAATAAGATTTGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
* * * * * ** * **
41927818 CTTTAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCT-GGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
* *
41927862 CTTCAATCTGCTTCACTGCAACTTCA-GGAAGACAAGATTCGTCATAATTTGT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTCG-C-T-A----T
* * * *
41927914 AGCTTTAATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGCTGT
1 --CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
* * * * * ** * ** *
41927961 ATTCAGTCTGTTTCGCTAAAACTTCAGGGAGATAAGACCCGTAACTTGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCG---C---TAT
* *
41928012 CTTCAATCTACTCCACTGCAA-TGTCAGGGAAATAAGATTCGCTGT
1 CTTCAATCTGCTCCACTGCAACT-TCAGGGAAATAAGATTCGCTAT
* * *** * ** * **
41928057 CCTCAGTCTGCTCTGTTGCAACTTCAGGGAGATAAGGCT-GGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
*
41928101 CTTCAATCTGCTCCATTGCAACTTCAGG
1 CTTCAATCTGCTCCACTGCAACTTCAGG
41928129 AAGATGAGAT
Statistics
Matches: 288, Mismatches: 93, Indels: 53
0.66 0.21 0.12
Matches are distributed among these distances:
43 3 0.01
44 55 0.19
45 123 0.43
46 1 0.00
47 2 0.01
48 4 0.01
50 1 0.00
51 62 0.22
52 1 0.00
53 1 0.00
54 31 0.11
55 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCGCTAT
Found at i:41927854 original size:96 final size:96
Alignment explanation
Indices: 41927641--41927854 Score: 320
Period size: 96 Copynumber: 2.2 Consensus size: 96
41927631 GATTGACCTA
* * **
41927641 CTGCAACTTCAGAGAGATAAGATCCGTAACTTGTAGCTTCAATCTGCCCCACTACAACTTCAGGG
1 CTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCCCCACTACAACTTCAAAG
* *
41927706 AAATGAGATTCGCTATCTTCAGTCTGCTCCG
66 AAATAAGATTCGCTATCTTCAGTCTACTCCG
* * * *
41927737 CTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCTACTGCAACTTTAAAG
1 CTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCCCCACTACAACTTCAAAG
* *
41927802 AAATAAGATTTGCTATCTTTAGTCTACTCCG
66 AAATAAGATTCGCTATCTTCAGTCTACTCCG
41927833 CTGCAACTTCAGGGAGATAAGG
1 CTGCAACTTCAGGGAGATAAGG
41927855 CTGGTGGCTT
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (96 bp):
CTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCCCCACTACAACTTCAAAG
AAATAAGATTCGCTATCTTCAGTCTACTCCG
Found at i:41927986 original size:239 final size:239
Alignment explanation
Indices: 41927671--41928132 Score: 656
Period size: 239 Copynumber: 1.9 Consensus size: 239
41927661 GATCCGTAAC
* * *
41927671 TTGTAGCTTCAATCTGCCCCACTACAACTTCAGGGAAATGAGATTCGCTATCTTCAGTCTGCTCC
1 TTGTAGCTTCAATCTGCCCCACTACAACATCAGGGAAATAAGATTCGCTATATTCAGTCTGCTCC
** ** * * *
41927736 GCTGCAACTTCAGGGAGATAAGGTCCGTAACTTGTAGCTTCAATCTGCTCTACTGCAACT-TTAA
66 GCTAAAACTTCAGGGAGATAAGACCCGTAACTTGTAGCTTCAATCTACTCCACTGCAA-TGTCAA
* * *
41927800 AGAAATAAGATTTGCTATCTTTAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTT
130 AGAAATAAGATTCGCTATCCTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTT
*
41927865 CAATCTGCTTCACTGCAACTTCAGGAAGACAAGATTCGTCATAAT
195 CAATCTGCTCCACTGCAACTTCAGGAAGACAAGATTCGTCATAAT
* ** * * * *
41927910 TTGTAGCTTTAATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGCTGTATTCAGTCTGTTTC
1 TTGTAGCTTCAATCTGCCCCACTACAACATCAGGGAAATAAGATTCGCTATATTCAGTCTGCTCC
**
41927975 GCTAAAACTTCAGGGAGATAAGACCCGTAACTTGTAGCTTCAATCTACTCCACTGCAATGTCAGG
66 GCTAAAACTTCAGGGAGATAAGACCCGTAACTTGTAGCTTCAATCTACTCCACTGCAATGTCAAA
* * * *
41928040 GAAATAAGATTCGCTGTCCTCAGTCTGCTCTGTTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
131 GAAATAAGATTCGCTATCCTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
*
41928105 AATCTGCTCCATTGCAACTTCAGGAAGA
196 AATCTGCTCCACTGCAACTTCAGGAAGA
41928133 TGAGATTTAT
Statistics
Matches: 194, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
238 1 0.01
239 193 0.99
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (239 bp):
TTGTAGCTTCAATCTGCCCCACTACAACATCAGGGAAATAAGATTCGCTATATTCAGTCTGCTCC
GCTAAAACTTCAGGGAGATAAGACCCGTAACTTGTAGCTTCAATCTACTCCACTGCAATGTCAAA
GAAATAAGATTCGCTATCCTCAGTCTACTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTC
AATCTGCTCCACTGCAACTTCAGGAAGACAAGATTCGTCATAAT
Found at i:41928027 original size:96 final size:96
Alignment explanation
Indices: 41927910--41928092 Score: 251
Period size: 96 Copynumber: 1.9 Consensus size: 96
41927900 TCGTCATAAT
* ** * *
41927910 TTGTAGCTTTAATCTGTTCCACTGCAACATCAGGGAAATAAGATTCGCTGTATTCAGTCTG-TTT
1 TTGTAGCTTCAATCTACTCCACTGCAACATCAGGGAAATAAGATTCGCTGTACTCAGTCTGCTCT
41927974 CGCTAAAACTTCAGGGAGATAAGACCCGTAAC
66 -GCTAAAACTTCAGGGAGATAAGACCCGTAAC
** *
41928006 TTGTAGCTTCAATCTACTCCACTGCAATGTCAGGGAAATAAGATTCGCTGTCCTCAGTCTGCTCT
1 TTGTAGCTTCAATCTACTCCACTGCAACATCAGGGAAATAAGATTCGCTGTACTCAGTCTGCTCT
* **
41928071 GTTGCAACTTCAGGGAGATAAG
66 GCTAAAACTTCAGGGAGATAAG
41928093 GCTGGTGGCT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 73 0.97
97 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (96 bp):
TTGTAGCTTCAATCTACTCCACTGCAACATCAGGGAAATAAGATTCGCTGTACTCAGTCTGCTCT
GCTAAAACTTCAGGGAGATAAGACCCGTAAC
Found at i:41942237 original size:18 final size:17
Alignment explanation
Indices: 41942211--41942244 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
41942201 ATTTTATAGA
41942211 TTTTAATAATTATTATT
1 TTTTAATAATTATTATT
41942228 TTTTATATAATTATTAT
1 TTTTA-ATAATTATTAT
41942245 ACATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATAATTATTATT
Found at i:41942419 original size:11 final size:11
Alignment explanation
Indices: 41942403--41942428 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41942393 AGAATTATCA
41942403 TTTATTTTTAT
1 TTTATTTTTAT
41942414 TTTATTTTTAT
1 TTTATTTTTAT
41942425 TTTA
1 TTTA
41942429 AGTAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:41946740 original size:2 final size:2
Alignment explanation
Indices: 41946733--41946758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41946723 TTCATTAAGC
41946733 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41946759 CGTGAATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41951150 original size:4 final size:4
Alignment explanation
Indices: 41951127--41951179 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
41951117 ATGTTGAGAA
* ** *
41951127 AATT ATTT AATT AAGA AATT AATTT AGTT AATT AAATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AA-TT AATT AATT -AATT AATT AATT AATT
41951177 AAT
1 AAT
41951180 ATTTATTTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:41951161 original size:13 final size:13
Alignment explanation
Indices: 41951143--41951176 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
41951133 TTAATTAAGA
*
41951143 AATTAATTTAGTT
1 AATTAATTTAATT
*
41951156 AATTAAATTAATT
1 AATTAATTTAATT
41951169 AATTAATT
1 AATTAATT
41951177 AATATTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:41952995 original size:82 final size:82
Alignment explanation
Indices: 41952862--41953190 Score: 622
Period size: 82 Copynumber: 4.0 Consensus size: 82
41952852 CAATCATCAC
41952862 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
1 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
*
41952927 ATTTAATTTTTTTTCAC
66 ATTTAATTTTTTTTCAA
*
41952944 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCATTATCATGAAAATATATTCTTTTCT
1 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
41953009 ATTTAATTTTTTTTCAA
66 ATTTAATTTTTTTTCAA
*
41953026 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCATTATCATGAAAATATATTCTTTTCT
1 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
41953091 ATTTAATTTTTTTTCAA
66 ATTTAATTTTTTTTCAA
*
41953108 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTCTTCT
1 AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
41953173 ATTTAATTTTTTTTCAA
66 ATTTAATTTTTTTTCAA
41953190 A
1 A
41953191 CTTGTGCGCA
Statistics
Matches: 243, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 243 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (82 bp):
AATTTATAAATTATAAATATTTTAATATTTAAATTTAGCAATATCATGAAAATATATTCTTTTCT
ATTTAATTTTTTTTCAA
Found at i:41957944 original size:17 final size:17
Alignment explanation
Indices: 41957922--41957957 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
41957912 AAAATAAAAG
41957922 TAAAATCCATATAGAAC
1 TAAAATCCATATAGAAC
41957939 TAAAATCCATATAGAAC
1 TAAAATCCATATAGAAC
41957956 TA
1 TA
41957958 CACTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (17 bp):
TAAAATCCATATAGAAC
Found at i:41958199 original size:5 final size:5
Alignment explanation
Indices: 41958189--41958216 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41958179 TTGTGTGTTC
41958189 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41958217 CACACTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:41961877 original size:40 final size:40
Alignment explanation
Indices: 41961799--41961979 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
41961789 ACCCAAGTAT
* *
41961799 CTTCGGGATTTAG-CCGGATATAG-CAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * **
41961838 CTTCAGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
41961878 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41961918 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
41961958 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
41961980 CATCCGAATA
Statistics
Matches: 128, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 10 0.08
40 117 0.91
41 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41965996 original size:13 final size:13
Alignment explanation
Indices: 41965978--41966043 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
41965968 TAGATTTTTC
41965978 CTAAATATTATCA
1 CTAAATATTATCA
41965991 CTAAATA--ATC-
1 CTAAATATTATCA
41966001 CTAAATATTATCA
1 CTAAATATTATCA
*
41966014 CTAAATA--AT-T
1 CTAAATATTATCA
*
41966024 CTAAATATTATCT
1 CTAAATATTATCA
41966037 CTAAATA
1 CTAAATA
41966044 ATTCAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
10 14 0.30
11 5 0.11
12 5 0.11
13 22 0.48
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:41966046 original size:23 final size:23
Alignment explanation
Indices: 41965978--41966052 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
41965968 TAGATTTTTC
*
41965978 CTAAATATTATCACTAAATAATC
1 CTAAATATTATCACTAAATAATT
41966001 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
41966024 CTAAATATTATCTCTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
41966047 CAAAAT
1 CTAAAT
41966053 TTAAAAATCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:41966955 original size:18 final size:17
Alignment explanation
Indices: 41966922--41966956 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41966912 AAATTAAAAT
*
41966922 AAAATAAAAACTTTTAA
1 AAAATAAAAAATTTTAA
41966939 AAAATAAAAAATATTTAA
1 AAAATAAAAAAT-TTTAA
41966957 TAGTTCCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAAAATTTTAA
Found at i:41970637 original size:30 final size:30
Alignment explanation
Indices: 41970596--41970655 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
41970586 CATATCTTAT
41970596 TGAATTCAATAGAGAAGTTGAGTTCATCAA
1 TGAATTCAATAGAGAAGTTGAGTTCATCAA
*
41970626 TGAATTTAATAGAGAAGTTGAGTTCATCAA
1 TGAATTCAATAGAGAAGTTGAGTTCATCAA
41970656 CTATCCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
TGAATTCAATAGAGAAGTTGAGTTCATCAA
Found at i:41976070 original size:6 final size:6
Alignment explanation
Indices: 41976061--41976092 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
41976051 GATTTTTTCC
*
41976061 AAAATG AAAATA AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AA
41976093 GAAACAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:41976140 original size:63 final size:57
Alignment explanation
Indices: 41976073--41976201 Score: 190
Period size: 57 Copynumber: 2.3 Consensus size: 57
41976063 AATGAAAATA
** * *
41976073 AAAATGAAAATGAAAAT-GAAGAAA-CAAAATCATATGGAAATGATTATGGTTTTCTCC
1 AAAATGAAAATGAAAATAG-AGAAATGGAAA-CATTTGGAAATGATGATGGTTTTCTCC
41976130 AAAATGAAAATGAAAATAGAGAAATGGAAACATTTGGAAATGATGATGGTTTTCTCC
1 AAAATGAAAATGAAAATAGAGAAATGGAAACATTTGGAAATGATGATGGTTTTCTCC
41976187 AAAATGAAAATGAAA
1 AAAATGAAAATGAAA
41976202 CTGACTTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
57 62 0.94
58 4 0.06
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (57 bp):
AAAATGAAAATGAAAATAGAGAAATGGAAACATTTGGAAATGATGATGGTTTTCTCC
Found at i:41980224 original size:12 final size:12
Alignment explanation
Indices: 41980185--41980235 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
41980175 TCTCCTTTTG
41980185 TTTCACACAT-TT
1 TTTCACAC-TCTT
* **
41980197 TTTCGCACTCCC
1 TTTCACACTCTT
*
41980209 TTTCACATTCTT
1 TTTCACACTCTT
41980221 TTTCACACTCTT
1 TTTCACACTCTT
41980233 TTT
1 TTT
41980236 TTTATCTCAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 1 0.03
12 29 0.97
ACGTcount: A:0.16, C:0.31, G:0.02, T:0.51
Consensus pattern (12 bp):
TTTCACACTCTT
Found at i:41980255 original size:23 final size:20
Alignment explanation
Indices: 41980226--41980281 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
41980216 TTCTTTTTCA
41980226 CACTCTTTTTTTTATCTCATTTT
1 CACTCTTTTTTTT-TCT-A-TTT
41980249 CACTC-TTTTTTTTCTATTT
1 CACTCTTTTTTTTTCTATTT
*
41980268 CGCTCTTTTTTTTT
1 CACTCTTTTTTTTT
41980282 ACTTTTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 7 0.23
20 9 0.29
21 3 0.10
22 7 0.23
23 5 0.16
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (20 bp):
CACTCTTTTTTTTTCTATTT
Found at i:41980268 original size:19 final size:21
Alignment explanation
Indices: 41980226--41980280 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 21
41980216 TTCTTTTTCA
41980226 CACTCTTTTTTTTATCTCATTTT
1 CACTC-TTTTTTT-TCTCATTTT
41980249 CACTCTTTTTTTTCT-A-TTT
1 CACTCTTTTTTTTCTCATTTT
*
41980268 CGCTCTTTTTTTT
1 CACTCTTTTTTTT
41980281 TACTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 15 0.48
20 1 0.03
21 3 0.10
22 7 0.23
23 5 0.16
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (21 bp):
CACTCTTTTTTTTCTCATTTT
Found at i:41999924 original size:25 final size:25
Alignment explanation
Indices: 41999894--41999950 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
41999884 GGCTAGTGAA
* *
41999894 AGCATACCGATTTACAGCTCG-AGTG
1 AGCATACCAATTCACAGCTCGTA-TG
41999919 AGCATACCAATTCACAGCTCGTATG
1 AGCATACCAATTCACAGCTCGTATG
41999944 AGCATAC
1 AGCATAC
41999951 ATATACAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 28 0.97
26 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (25 bp):
AGCATACCAATTCACAGCTCGTATG
Found at i:42002638 original size:48 final size:46
Alignment explanation
Indices: 42002484--42002652 Score: 205
Period size: 46 Copynumber: 3.6 Consensus size: 46
42002474 TATGTGTGCT
* *
42002484 AGTGTAAGACATGTCTGGGACATGCATCCGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGAACATGCATCGGCCACATTATGAGAGCC
* **
42002530 AGTGTAAGACATGTCTGAAACATGCATCAACCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGAACATGCATCGGCCACATTATGAGAGCC
* * * * *
42002576 ACTGTAAGACATGTCTGGAACATGCATCGGCCTCGAGATAT-ACAAGCT
1 AGTGTAAGACATGTCTGGAACATGCATCGGCCAC-A-TTATGA-GAGCC
*
42002624 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGAACATGCATCG
42002653 ACATTGAGAC
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
46 71 0.67
47 2 0.02
48 33 0.31
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGAACATGCATCGGCCACATTATGAGAGCC
Found at i:42002681 original size:17 final size:17
Alignment explanation
Indices: 42002659--42002696 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
42002649 ATCGACATTG
42002659 AGACGAGAGGTAGTGTA
1 AGACGAGAGGTAGTGTA
42002676 AGACGAGAGGTAGTGTA
1 AGACGAGAGGTAGTGTA
42002693 AGAC
1 AGAC
42002697 ATGTCTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.08, G:0.39, T:0.16
Consensus pattern (17 bp):
AGACGAGAGGTAGTGTA
Found at i:42002855 original size:48 final size:49
Alignment explanation
Indices: 42002778--42002906 Score: 125
Period size: 49 Copynumber: 2.7 Consensus size: 49
42002768 TGTTGTGTGT
* * ** *
42002778 CAGTGTAAGATCTGTCTGGGACATGGCATCGAACT-GATATATGAGAGC
1 CAGTGTAAGACCTGTCTGCGACACCGCATCGAACTCGATATATGAAAGC
* ** * *
42002826 CAGTGTAAGACCTGTTTGCGACACCGCATCGGCCTCGGTATATGAAAGT
1 CAGTGTAAGACCTGTCTGCGACACCGCATCGAACTCGATATATGAAAGC
* * **
42002875 TAGTGTAAGACCTGTCTGGGACATGGCATCGA
1 CAGTGTAAGACCTGTCTGCGACACCGCATCGA
42002907 CTTTGATATG
Statistics
Matches: 64, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
48 28 0.44
49 36 0.56
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGCGACACCGCATCGAACTCGATATATGAAAGC
Found at i:42003385 original size:57 final size:57
Alignment explanation
Indices: 42003317--42003430 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 57
42003307 GTAGTTATTT
* * *
42003317 CATTATTTACATGCGACTTACTAAGCTTTATGATTACCTC-TTTCACTTTCCATTTTC
1 CATTATTTACATGCGACTGACAAAGATTTATGATTACCTCTTTTC-CTTTCCATTTTC
*
42003374 CATTATTTACATGCGACTGACAAAGATTTATGCTTACCTCTTTTCCTTTCCATTTTC
1 CATTATTTACATGCGACTGACAAAGATTTATGATTACCTCTTTTCCTTTCCATTTTC
42003431 TTTTAGTGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 48 0.92
58 4 0.08
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.45
Consensus pattern (57 bp):
CATTATTTACATGCGACTGACAAAGATTTATGATTACCTCTTTTCCTTTCCATTTTC
Found at i:42010610 original size:46 final size:46
Alignment explanation
Indices: 42010557--42010869 Score: 208
Period size: 46 Copynumber: 6.6 Consensus size: 46
42010547 TGATATGTGT
**
42010557 GCTAGTGTAAGACATGTCTGGGACATGCATCAGTGACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACACATTATGAGA
*
42010603 GCTAGTGTAAGACATGTCTGGGACATGCATCGGACACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACACATTATGAGA
* * * * * * * *
42010649 GCCAATGTAAGACATGTCTGGAACATGCATCGGTCTCAAGATAT-ACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGACAC-A-TTATGA-GA
* *
42010697 G-TGAGTGTAAGACATGTCTGGGATATGGCATC-GACACCGATAGATGAGA
1 GCT-AGTGTAAGACATGTCTGGGACAT-GCATCAGACA-C-AT-TATGAGA
* * * * *
42010746 GCCAGTGTAAGACCTGTCTGGGACACGGCATC-GACCTCGATATATGAAA
1 GCTAGTGTAAGACATGTCTGGGACA-TGCATCAGA-CAC-AT-TATGAGA
* ** **
42010795 G-TCAGTGTAAGACATGTCTGGGGCATGACAT-AGA-ATTTGATATGCTA
1 GCT-AGTGTAAGACATGTCTGGGACATG-CATCAGACACAT--TATGAGA
*
42010842 GCCAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGA-CATGTCTGGGACATG
42010870 GCGTCGGCAT
Statistics
Matches: 212, Mismatches: 38, Indels: 32
0.75 0.13 0.11
Matches are distributed among these distances:
46 76 0.36
47 18 0.08
48 42 0.20
49 74 0.35
50 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGACACATTATGAGA
Found at i:42010733 original size:94 final size:98
Alignment explanation
Indices: 42010606--42010821 Score: 264
Period size: 98 Copynumber: 2.2 Consensus size: 98
42010596 TATGAGAGCT
*
42010606 AGTGTAAGACATGTCTGGGACATGCATCGGACA-C-AT-TATGAGAGCCAATGTAAGACATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGACACCGATAGATGAGAGCCAATGTAAGACATGTCT
* ** *
42010668 GGAACA-TGCATCGGTCTCAAGATAT-ACAAGTG
66 GGAACACGGCATCGACCTCAAGATATGA-AAGTC
* * *
42010700 AGTGTAAGACATGTCTGGGATATGGCATC-GACACCGATAGATGAGAGCCAGTGTAAGACCTGTC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGACACCGATAGATGAGAGCCAATGTAAGACATGTC
* * *
42010764 TGGGACACGGCATCGACCTCGATATATGAAAGTC
65 TGGAACACGGCATCGACCTCAAGATATGAAAGTC
*
42010798 AGTGTAAGACATGTCTGGGGCATG
1 AGTGTAAGACATGTCTGGGACATG
42010822 ACATAGAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
94 26 0.25
95 6 0.06
96 2 0.02
97 29 0.28
98 39 0.38
99 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (98 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGACACCGATAGATGAGAGCCAATGTAAGACATGTCT
GGAACACGGCATCGACCTCAAGATATGAAAGTC
Found at i:42010756 original size:49 final size:49
Alignment explanation
Indices: 42010560--42010821 Score: 240
Period size: 46 Copynumber: 5.5 Consensus size: 49
42010550 TATGTGTGCT
* ** *
42010560 AGTGTAAGACATGTCTGGGACATGCATCAGTGA-C-AT-TATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGACACCGATATATGAGAGCC
42010606 AGTGTAAGACATGTCTGGGACATGCATCGGACA-C-AT-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGACACCGATATATGAGAGCC
* * * * * * **
42010652 AATGTAAGACATGTCTGGAACATGCATCGGTCTCAAGATATA-CA-AGTG
1 AGTGTAAGACATGTCTGGGACATGCATCGGACAC-CGATATATGAGAGCC
* *
42010700 AGTGTAAGACATGTCTGGGATATGGCATC-GACACCGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGACACCGATATATGAGAGCC
* * * *
42010749 AGTGTAAGACCTGTCTGGGACACGGCATC-GAC-CTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACA-TGCATCGGACAC-CGATATATGAGAGCC
*
42010798 AGTGTAAGACATGTCTGGGGCATG
1 AGTGTAAGACATGTCTGGGACATG
42010822 ACATAGAATT
Statistics
Matches: 176, Mismatches: 31, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
46 71 0.40
47 5 0.03
48 28 0.16
49 70 0.40
50 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGACACCGATATATGAGAGCC
Found at i:42010837 original size:49 final size:48
Alignment explanation
Indices: 42010560--42010871 Score: 223
Period size: 49 Copynumber: 6.5 Consensus size: 48
42010550 TATGTGTGCT
* * * *
42010560 AGTGTAAGACATGTCTGGGACAT-GCATC-AGT-GACATTATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGGCATCGAATCGATA-TATGAAAGCC
*
42010606 AGTGTAAGACATGTCTGGGACAT-GCATCGGACA-C-AT-TATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATC-GA-ATCGATATATGAAAGCC
* * ** * * **
42010652 AATGTAAGACATGTCTGGAACAT-GCATCGGTCTCAAGATAT-ACAAGTG
1 AGTGTAAGACATGTCTGGGACATGGCATC-GAATCGATATATGA-AAGCC
* * * *
42010700 AGTGTAAGACATGTCTGGGATATGGCATCGACACCGATAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGA-ATCGATATATGAAAGCC
* * * *
42010749 AGTGTAAGACCTGTCTGGGACACGGCATCGACCTCGATATATGAAAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGA-ATCGATATATGAAAGCC
* * * * **
42010798 AGTGTAAGACATGTCTGGGGCATGACATAGAAT--TTGATATGCTAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGAATCGAT-ATATGAAAGCC
42010845 AGTGTAAGACCATGTCTGGGACATGGC
1 AGTGTAAGA-CATGTCTGGGACATGGC
42010872 GTCGGCATCT
Statistics
Matches: 210, Mismatches: 43, Indels: 24
0.76 0.16 0.09
Matches are distributed among these distances:
46 67 0.32
47 19 0.09
48 44 0.21
49 79 0.38
50 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGAATCGATATATGAAAGCC
Found at i:42014017 original size:13 final size:13
Alignment explanation
Indices: 42013999--42014023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42013989 TGTTTTTGGG
42013999 TTGGTTTATTTTT
1 TTGGTTTATTTTT
42014012 TTGGTTTATTTT
1 TTGGTTTATTTT
42014024 GGATTGGGCT
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:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (13 bp):
TTGGTTTATTTTT
Found at i:42014185 original size:16 final size:16
Alignment explanation
Indices: 42014164--42014197 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
42014154 TATACTTTCA
42014164 TATCCTATAATCATAT
1 TATCCTATAATCATAT
42014180 TATCCTATAATCATAT
1 TATCCTATAATCATAT
42014196 TA
1 TA
42014198 AATTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
TATCCTATAATCATAT
Found at i:42017616 original size:19 final size:20
Alignment explanation
Indices: 42017592--42017634 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
42017582 TCAAAATATG
42017592 TTTAA-TATTATA-AATTTAT
1 TTTAATTATTATATAATTT-T
42017611 TTTAATTTATTATATAATTTT
1 TTTAA-TTATTATATAATTTT
42017632 TTT
1 TTT
42017635 TCTTGTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAATTATTATATAATTTT
Found at i:42020582 original size:26 final size:26
Alignment explanation
Indices: 42020546--42020598 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
42020536 AACTTCATGC
*
42020546 AGTCAAGGGTGCTGCCAAAGAAAACA
1 AGTCAAGGGTGCTACCAAAGAAAACA
42020572 AGTCAAGGGTGCTACCAAAGAAAACA
1 AGTCAAGGGTGCTACCAAAGAAAACA
42020598 A
1 A
42020599 CTTGCTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (26 bp):
AGTCAAGGGTGCTACCAAAGAAAACA
Found at i:42022136 original size:38 final size:39
Alignment explanation
Indices: 42022080--42022161 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
42022070 TCTTAGATTG
**
42022080 TGTGAAACCTATGCCTAAAAT-ATAATGACACATGACCA
1 TGTGAAACCTACACCTAAAATAATAATGACACATGACCA
* *
42022118 TGTGAAACCTACATCTAAAATAATAATGACACATGACCG
1 TGTGAAACCTACACCTAAAATAATAATGACACATGACCA
42022157 TGTGA
1 TGTGA
42022162 TAGCCTGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 18 0.46
39 21 0.54
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (39 bp):
TGTGAAACCTACACCTAAAATAATAATGACACATGACCA
Found at i:42053807 original size:24 final size:24
Alignment explanation
Indices: 42053769--42053854 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
42053759 GTCATAAGAG
* **
42053769 CCATAGTCGGAAAGTTCACAATGAA
1 CCATA-TCGGGAAGTTCACAAAAAA
* *
42053794 TCTTATCGGGAAGTTCACAAAAAA
1 CCATATCGGGAAGTTCACAAAAAA
* * *
42053818 CCATATCAGGAAGTTCACAAAGAG
1 CCATATCGGGAAGTTCACAAAAAA
*
42053842 CCATATTGGGAAG
1 CCATATCGGGAAG
42053855 CTTTAGATAG
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 46 0.94
25 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (24 bp):
CCATATCGGGAAGTTCACAAAAAA
Found at i:42057878 original size:37 final size:36
Alignment explanation
Indices: 42057802--42057904 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 36
42057792 TGTGAGTACG
* **
42057802 TGTAAGACCATAATTGGGCTATGGCATCATAATAACA
1 TGTAAGACCAT-ATTGGGATATGGCATTGTAATAACA
* **
42057839 TGTAAGACCATAGTTGGGATATGGCATTGTGATCCCA
1 TGTAAGACCATA-TTGGGATATGGCATTGTAATAACA
* *
42057876 TGTAAGACCATATCTAGGATATGGTATTG
1 TGTAAGACCATAT-TGGGATATGGCATTG
42057905 GCATCAATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
36 2 0.04
37 54 0.96
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (36 bp):
TGTAAGACCATATTGGGATATGGCATTGTAATAACA
Found at i:42064689 original size:13 final size:13
Alignment explanation
Indices: 42064671--42064695 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42064661 AGCTGAAAGC
42064671 GGTATTGATACCT
1 GGTATTGATACCT
42064684 GGTATTGATACC
1 GGTATTGATACC
42064696 GTTACCTATC
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:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (13 bp):
GGTATTGATACCT
Found at i:42071115 original size:43 final size:43
Alignment explanation
Indices: 42070982--42071119 Score: 138
Period size: 43 Copynumber: 3.3 Consensus size: 43
42070972 TATCCCGGAT
* * * * **
42070982 ATGGTCTTACATGTTATCACATGTCGATGCCTCTGTCCCAGAC
1 ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGAC
* * * *
42071025 AGGGTCTTACACG-AA--TCATATACGATACCAATGTCCTAAAC
1 ATGGTCTTACACGTAATCTCATAT-CGATGCCAATGTCCCAGAC
* *
42071066 ACGGTCTTACACGTAATCTCAAATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGAC
42071109 ATGGTCTTACA
1 ATGGTCTTACA
42071120 TGAACTCAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
40 4 0.05
41 26 0.35
42 3 0.04
43 37 0.49
44 5 0.07
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGAC
Found at i:42078746 original size:43 final size:42
Alignment explanation
Indices: 42078692--42078831 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 42
42078682 TATCCCAGAT
* * **
42078692 ATGGTTCTTACATGTTATCACATGTCGATGCCTTTGTCCCAAAC
1 ATGG-TCTTACACGTAATCACAT-TCGATGCCAATGTCCCAAAC
* * * *
42078736 AGGGTCTTACACG-AATCATATACAATGCCAATGTCCCAAAC
1 ATGGTCTTACACGTAATCACATTCGATGCCAATGTCCCAAAC
* * *
42078777 ATAGTCTTACACGTAATCTCATATCGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAT-TCGATGCCAATGTCCCAAAC
42078820 ATGGTCTTACAC
1 ATGGTCTTACAC
42078832 AAATTCGCCC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
41 27 0.35
42 12 0.15
43 36 0.46
44 3 0.04
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (42 bp):
ATGGTCTTACACGTAATCACATTCGATGCCAATGTCCCAAAC
Found at i:42080206 original size:21 final size:21
Alignment explanation
Indices: 42080169--42080211 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42080159 TTAGTTAAAT
*
42080169 AAATTAGATGTTGATATGTTC
1 AAATTAGATGTTGATATATTC
*
42080190 AAATT-GATGGTTTATATATTC
1 AAATTAGAT-GTTGATATATTC
42080211 A
1 A
42080212 TGTTAAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (21 bp):
AAATTAGATGTTGATATATTC
Found at i:42090703 original size:26 final size:26
Alignment explanation
Indices: 42090674--42090779 Score: 167
Period size: 26 Copynumber: 4.1 Consensus size: 26
42090664 ATACAAATTA
42090674 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
** * *
42090700 ATAATGAATTAGGTAAATATTACATG
1 ATAATGGGTTAGGTAAATGTTCCATG
42090726 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
*
42090752 ATAATGGTTTAGGTAAATGTTCCATG
1 ATAATGGGTTAGGTAAATGTTCCATG
42090778 AT
1 AT
42090780 GGGCATTTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
ATAATGGGTTAGGTAAATGTTCCATG
Found at i:42093588 original size:87 final size:86
Alignment explanation
Indices: 42093440--42093625 Score: 255
Period size: 87 Copynumber: 2.2 Consensus size: 86
42093430 TTATTTGAAA
* * ** * *
42093440 AAACGCCGCTAAAGGCCATGGCCTTTAGCGGCGCTTTTCCCACAAACACCTTTAAAGGTCATGGC
1 AAACGCCGCTAAAGGCCATGGCCTTTAACGGCGCCTTTCCCACAAACACCGCTAAAAGTCATAGC
*
42093505 CTTTAGCAGCGCTTTTTACCAC
66 CTTTAGCAGCAC-TTTTACCAC
* * *
42093527 AAACGCCGCTAAAGGTCATGGCCTTTAACGGTGCCTTTCCCACAAACGCCGCTAAAAGTCATAGC
1 AAACGCCGCTAAAGGCCATGGCCTTTAACGGCGCCTTTCCCACAAACACCGCTAAAAGTCATAGC
* *
42093592 CTTTAGCGGCACTTTTCCCAC
66 CTTTAGCAGCACTTTTACCAC
42093613 AAACGCCGCTAAA
1 AAACGCCGCTAAA
42093626 AGTAATGAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 21 0.24
87 66 0.76
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTAAAGGCCATGGCCTTTAACGGCGCCTTTCCCACAAACACCGCTAAAAGTCATAGC
CTTTAGCAGCACTTTTACCAC
Found at i:42093628 original size:43 final size:43
Alignment explanation
Indices: 42093440--42093625 Score: 255
Period size: 43 Copynumber: 4.3 Consensus size: 43
42093430 TTATTTGAAA
*
42093440 AAACGCCGCTAAAGGCCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
* ** * *
42093483 AAACACCTTTAAAGGTCATGGCCTTTAGCAGCGCTTTTTACCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGC-TTTTCCCAC
* * *
42093527 AAACGCCGCTAAAGGTCATGGCCTTTAACGGTGCCTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
* * *
42093570 AAACGCCGCTAAAAGTCATAGCCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
42093613 AAACGCCGCTAAA
1 AAACGCCGCTAAA
42093626 AGTAATGAAA
Statistics
Matches: 122, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 86 0.70
44 36 0.30
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:42093796 original size:19 final size:19
Alignment explanation
Indices: 42093751--42093797 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
42093741 ATCAAATTAA
*
42093751 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
42093770 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
42093789 AATAAAAAT
1 AATAAAAAT
42093798 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:42095858 original size:39 final size:39
Alignment explanation
Indices: 42095804--42095881 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
42095794 AATCAACTAA
*
42095804 CAAGCATAATGATAATGAGACACATAGCAGGGGAAAGAG
1 CAAGCATAATGATAATGAGACACATAGCAGAGGAAAGAG
42095843 CAAGCATAATGATAATGAGACACATAGCAGAGGAAAGAG
1 CAAGCATAATGATAATGAGACACATAGCAGAGGAAAGAG
42095882 TACAAACAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (39 bp):
CAAGCATAATGATAATGAGACACATAGCAGAGGAAAGAG
Found at i:42098693 original size:17 final size:18
Alignment explanation
Indices: 42098660--42098693 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42098650 TCTCTCTTAA
42098660 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
42098678 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
42098694 AAAACAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:42099532 original size:15 final size:15
Alignment explanation
Indices: 42099489--42099542 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
42099479 TATAAACTTT
* *
42099489 TAAT-CCTAGACCCC
1 TAATCCCTAAACCCA
42099503 TAA-CCCTTAAA-CCA
1 TAATCCC-TAAACCCA
42099517 TAATCCCTAAACCCA
1 TAATCCCTAAACCCA
*
42099532 TAATCCATAAA
1 TAATCCCTAAA
42099543 ACTTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.41, C:0.35, G:0.02, T:0.22
Consensus pattern (15 bp):
TAATCCCTAAACCCA
Found at i:42099539 original size:22 final size:21
Alignment explanation
Indices: 42099500--42099541 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
42099490 AATCCTAGAC
*
42099500 CCCTAACCCTTAAACCATAAT
1 CCCTAACCCATAAACCATAAT
*
42099521 CCCTAAACCCATAATCCATAA
1 CCCT-AACCCATAAACCATAA
42099542 AACTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.21
Consensus pattern (21 bp):
CCCTAACCCATAAACCATAAT
Found at i:42099903 original size:41 final size:41
Alignment explanation
Indices: 42099846--42100046 Score: 271
Period size: 41 Copynumber: 4.9 Consensus size: 41
42099836 GTTATATGAC
**
42099846 TTTTAGCGGCGTTTTACGGAAAGCGCCGCTAATGCT-TCGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GGT
* * *
42099887 TTTTAGCGGCGTTTTACCAATAGCGCCACGAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
42099928 TTTTAGCGGTGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * *
42099969 TTTTAGTGGCGTTTTACCAAAAGTGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
42100009 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT
42100047 ATGTTTTACA
Statistics
Matches: 142, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 36 0.25
41 105 0.74
42 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:42100581 original size:62 final size:62
Alignment explanation
Indices: 42100501--42100643 Score: 180
Period size: 62 Copynumber: 2.3 Consensus size: 62
42100491 CAAAGTATAA
* * *
42100501 GTACCACATTGGAGATTTTATGAAAGTACAAATACCAAATAATATACAAATT-AGTAGTTTAG
1 GTACCACATTGGACATTTTATGAAAATACAAATACCAAATAATACACAAATTGA-TAGTTTAG
* * * ** **
42100563 GTACCACATTGGATATTTTATGAAAATATAAGTTTCAAATAATACATTAATTGATAGTTTAG
1 GTACCACATTGGACATTTTATGAAAATACAAATACCAAATAATACACAAATTGATAGTTTAG
42100625 GTACCACATTGGACATTTT
1 GTACCACATTGGACATTTT
42100644 CAAGTACAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
62 69 0.99
63 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (62 bp):
GTACCACATTGGACATTTTATGAAAATACAAATACCAAATAATACACAAATTGATAGTTTAG
Found at i:42101180 original size:13 final size:13
Alignment explanation
Indices: 42101140--42101198 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
42101130 TATAATTCAG
42101140 TTATTAAATAAAA
1 TTATTAAATAAAA
*
42101153 CTTTGTTCAAA-AAAA
1 --TTATT-AAATAAAA
42101168 TTATTAAATAAAA
1 TTATTAAATAAAA
42101181 TTATT--ATAAAA
1 TTATTAAATAAAA
42101192 -TATTAAA
1 TTATTAAA
42101199 ATTTTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 4 0.11
11 6 0.16
12 4 0.11
13 13 0.34
15 8 0.21
16 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (13 bp):
TTATTAAATAAAA
Found at i:42103672 original size:87 final size:88
Alignment explanation
Indices: 42103491--42103699 Score: 221
Period size: 87 Copynumber: 2.4 Consensus size: 88
42103481 ATAATTAAAC
* *
42103491 CTTTTTTTTTGCATTCACTTGGGTAGTTGAATTTTCACAATGCATCAAAAAGGCCTTAAAACTTT
1 CTTTTTTTTTGCATTCAATTGGGTACTTGAATTTTCACAATGCATCAAAAAGGCCTTAAAAC-TT
** * *
42103556 TTTTTTAAAAGCACTTAAGCCCTA
65 TTTTCAAAAAACAATTAAGCCCTA
* * *
42103580 C--TTTTTTTGCATTCAATTGGGTACTTGAACTTTTGA-AATGCATC-AAAAGGCTTTCAAAC-T
1 CTTTTTTTTTGCATTCAATTGGGTACTTGAA-TTTTCACAATGCATCAAAAAGGCCTTAAAACTT
*
42103640 TTTTCAAAAAACAATTAAGTCCCTG
65 TTTTCAAAAAACAATTAAG-CCCTA
**
42103665 CTTTTTTTTTTTTGCCCTCAATTGGGTACTTGAAT
1 C---TTTTTTTTTGCATTCAATTGGGTACTTGAAT
42103700 CACCCTTAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
84 16 0.16
85 5 0.05
86 13 0.13
87 34 0.34
88 5 0.05
89 2 0.02
90 26 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (88 bp):
CTTTTTTTTTGCATTCAATTGGGTACTTGAATTTTCACAATGCATCAAAAAGGCCTTAAAACTTT
TTTCAAAAAACAATTAAGCCCTA
Found at i:42104212 original size:20 final size:20
Alignment explanation
Indices: 42104189--42104255 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
42104179 TTAAAGGGGC
42104189 TTTTTAATGCATTTTATAATT
1 TTTTTAATG-ATTTTATAATT
* *
42104210 TTTTTTATGATTTTATAA-A
1 TTTTTAATGATTTTATAATT
* **
42104229 ATTTTACAAAATTTTATAATT
1 TTTTTA-ATGATTTTATAATT
42104250 TTTTTA
1 TTTTTA
42104256 CGATTTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.11
20 19 0.53
21 13 0.36
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTAATGATTTTATAATT
Found at i:42104263 original size:20 final size:19
Alignment explanation
Indices: 42104199--42104267 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
42104189 TTTTTAATGC
*
42104199 ATTTTATAATTTTTTTTATG
1 ATTTTATAA-TTTTTTTACG
** *
42104219 ATTTTATAA-AATTTTACAAA
1 ATTTTATAATTTTTTTAC--G
42104239 ATTTTATAATTTTTTTACG
1 ATTTTATAATTTTTTTACG
42104258 ATTTTTATAA
1 A-TTTTATAA
42104268 AAAAATTCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 5 0.13
19 1 0.03
20 26 0.68
21 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTATAATTTTTTTACG
Found at i:42104312 original size:29 final size:29
Alignment explanation
Indices: 42104279--42104336 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
42104269 AAAATTCCTA
42104279 ATTTTTAA-T-AAATCTTAA-ATATTTTTAT
1 ATTTTTAATTAAAAT-TTAATA-ATTTTTAT
42104307 ATTTTTAATTAAAATTTAATAATTTTTAT
1 ATTTTTAATTAAAATTTAATAATTTTTAT
42104336 A
1 A
42104337 ACATTTATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 8 0.30
29 14 0.52
30 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTTTAATTAAAATTTAATAATTTTTAT
Found at i:42104676 original size:3 final size:3
Alignment explanation
Indices: 42104668--42104800 Score: 266
Period size: 3 Copynumber: 44.3 Consensus size: 3
42104658 ACCCTTAAGC
42104668 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42104716 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42104764 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42104801 ATCACAAGTT
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 130 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42105032 original size:42 final size:42
Alignment explanation
Indices: 42104984--42105236 Score: 506
Period size: 42 Copynumber: 6.0 Consensus size: 42
42104974 TTTATATTTA
42104984 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105026 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105068 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105110 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105152 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105194 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
1 TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
42105236 T
1 T
42105237 AAGTATAAAA
Statistics
Matches: 211, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 211 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (42 bp):
TTGTATTAATTTTAAAATTGAGTTATTACTTAAATAAAACTC
Found at i:42105995 original size:24 final size:26
Alignment explanation
Indices: 42105947--42105996 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
42105937 GTATTATTTG
42105947 GTACTTGTACTTTCATAAAATGTCTA
1 GTACTTGTACTTTCATAAAATGTCTA
42105973 GTACTTGTACTTT-A-AAAATGTCTA
1 GTACTTGTACTTTCATAAAATGTCTA
42105997 ATGTGATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (26 bp):
GTACTTGTACTTTCATAAAATGTCTA
Found at i:42106094 original size:178 final size:178
Alignment explanation
Indices: 42105795--42106131 Score: 507
Period size: 178 Copynumber: 1.9 Consensus size: 178
42105785 TTCGAATAAT
* * * * * *
42105795 GTACTTGTACTTTAAAAATGTCTAATGTGATACTTGAACTGTTAATTTTTATATTATTTGGGACT
1 GTACTTGTACTTTAAAAATGTCTAATGTGATACCTAAACTATCAATTTTGATATTATTTGGGACC
* * * * *
42105860 TGTACTTTCATAAAATGTCTGATGTGGTACTTGTACTTTAAAAATGTCCAATGTGGTACCTGAAC
66 TGTACTTTCATAAAATGTCTAATGTGATACTTATAATTTAAAAATGTCCAATGTGGTACCTAAAC
* *
42105925 TAATCAATTTGTGTATTATT-TGGTACTTGTACTTTCATAAAATGTCTA
131 T-ATCAATCTGTGTATTATTATAGTACTTGTACTTTCATAAAATGTCTA
*
42105973 GTACTTGTACTTTAAAAATGTCTAATGTGATACCTAAACTATCAA-TTTGAGTATTATTTGGTAC
1 GTACTTGTACTTTAAAAATGTCTAATGTGATACCTAAACTATCAATTTTGA-TATTATTTGGGAC
*
42106037 CTGTACTTTCATAAAATGTCTAATGTGATACTTATAATTTAAAAATGTTCAATGTGGTACCTAAA
65 CTGTACTTTCATAAAATGTCTAATGTGATACTTATAATTTAAAAATGTCCAATGTGGTACCTAAA
42106102 CTATCAATCTGTGTATTATTATAGTACTTG
130 CTATCAATCTGTGTATTATTATAGTACTTG
42106132 AAGTTAAGAC
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
177 21 0.15
178 121 0.85
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (178 bp):
GTACTTGTACTTTAAAAATGTCTAATGTGATACCTAAACTATCAATTTTGATATTATTTGGGACC
TGTACTTTCATAAAATGTCTAATGTGATACTTATAATTTAAAAATGTCCAATGTGGTACCTAAAC
TATCAATCTGTGTATTATTATAGTACTTGTACTTTCATAAAATGTCTA
Found at i:42106107 original size:91 final size:89
Alignment explanation
Indices: 42105794--42106131 Score: 416
Period size: 91 Copynumber: 3.8 Consensus size: 89
42105784 ATTCGAATAA
* * * * * * * *
42105794 TGTACTTGTACTTTAAAAATG-TCTAATGTGATACTTGAACTGTTAATTTTTATATTATTTGGGA
1 TGTACTTGTACTTTAAAAATGTTC-AATGTGGTACCTAAACTATCAATTTGTGTATTATTTGGTA
42105858 CTTGTACTTTCATAAAATGTCTGATG
65 CTTGTACTTTCATAAAATGTCT-ATG
* *
42105884 TGGTACTTGTACTTTAAAAATGTCCAATGTGGTACCTGAACTAATCAATTTGTGTATTATTTGGT
1 T-GTACTTGTACTTTAAAAATGTTCAATGTGGTACCTAAACT-ATCAATTTGTGTATTATTTGGT
42105949 ACTTGTACTTTCATAAAATGTCTA--
64 ACTTGTACTTTCATAAAATGTCTATG
* *
42105973 -GTACTTGTACTTTAAAAATG-TCTAATGTGATACCTAAACTATCAATTTGAGTATTATTTGGTA
1 TGTACTTGTACTTTAAAAATGTTC-AATGTGGTACCTAAACTATCAATTTGTGTATTATTTGGTA
*
42106036 CCTGTACTTTCATAAAATGTCTAATG
65 CTTGTACTTTCATAAAATGTCT-ATG
* * * *
42106062 TGATACTTATAATTTAAAAATGTTCAATGTGGTACCTAAACTATCAATCTGTGTATTATTATAGT
1 TG-TACTTGTACTTTAAAAATGTTCAATGTGGTACCTAAACTATCAATTTGTGTATTATT-TGGT
42106127 ACTTG
64 ACTTG
42106132 AAGTTAAGAC
Statistics
Matches: 217, Mismatches: 20, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
86 44 0.20
87 36 0.17
90 2 0.01
91 85 0.39
92 50 0.23
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (89 bp):
TGTACTTGTACTTTAAAAATGTTCAATGTGGTACCTAAACTATCAATTTGTGTATTATTTGGTAC
TTGTACTTTCATAAAATGTCTATG
Found at i:42106258 original size:13 final size:12
Alignment explanation
Indices: 42106235--42106271 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
42106225 GCATTATTTG
42106235 AAAAAGATAAATT
1 AAAAA-ATAAATT
42106248 AAAAAATTAAATT
1 AAAAAA-TAAATT
42106261 AAAAAATAAAT
1 AAAAAATAAAT
42106272 AGCTTGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAAAATAAATT
Found at i:42110277 original size:53 final size:50
Alignment explanation
Indices: 42110198--42110359 Score: 190
Period size: 53 Copynumber: 3.3 Consensus size: 50
42110188 TGATGGAAAA
* * *
42110198 GATGTGAAATATGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGATGT
1 GATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCG--GT
* *
42110250 GATGTGATAATGTGATTCCGTATAAGACCATACCTGGGATATGGCATCGGT
1 GATGTGAT-ATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
* * *
42110301 -A--TGATATGTGA-TCCGTATAAGACCATGGCGGGGCTATGGCTTCGGT
1 GATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
42110347 G-TGTGATATGTGA
1 GATGTGATATGTGA
42110360 CTATGTGTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
46 30 0.31
47 6 0.06
48 14 0.15
50 1 0.01
51 2 0.02
52 7 0.07
53 36 0.38
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (50 bp):
GATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
Found at i:42117818 original size:53 final size:52
Alignment explanation
Indices: 42117683--42117886 Score: 177
Period size: 52 Copynumber: 4.0 Consensus size: 52
42117673 TGATGGAAAA
* * * * * * * *
42117683 GATGTGATATGTGCTTCCGTATAAGACCATAGATAGGTTATGACATTGGTGC
1 GATGTGATATGTGATTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGT
* * * * *
42117735 AATGTGATACGTGTTTCCGTATAAAACCATAGCTGGGCTATGGTATCGGTGT
1 GATGTGATATGTGATTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGT
* *
42117787 GATGTGATAATGTGATTCCATATAAAACCATATCTGGGATATGGCATC-G-GT
1 GATGTGAT-ATGTGATTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGT
* * * * *
42117838 -A--TGATATGTGA-TCCGTATAAGACCATGGCGGGGCTATGGCTTCGGTGT
1 GATGTGATATGTGATTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGT
42117886 G
1 G
42117887 TAATATGTGA
Statistics
Matches: 123, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
46 25 0.20
47 7 0.06
48 6 0.05
50 1 0.01
51 2 0.02
52 49 0.40
53 33 0.27
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (52 bp):
GATGTGATATGTGATTCCGTATAAAACCATAGCTGGGATATGGCATCGGTGT
Found at i:42121528 original size:30 final size:30
Alignment explanation
Indices: 42121494--42121551 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42121484 ATTTTCGGAC
* *
42121494 CTAGGGGTAAAATGGTCATTTTGCAAAAGT
1 CTAGGGGCAAAATGGCCATTTTGCAAAAGT
*
42121524 CTAGGGGCAAAATGGCCATTTTGTAAAA
1 CTAGGGGCAAAATGGCCATTTTGCAAAA
42121552 TTTTAAATTG
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:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (30 bp):
CTAGGGGCAAAATGGCCATTTTGCAAAAGT
Found at i:42122084 original size:50 final size:50
Alignment explanation
Indices: 42121885--42122199 Score: 177
Period size: 50 Copynumber: 6.6 Consensus size: 50
42121875 TTTATATGCT
42121885 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC--ATTA--TGAGAGC-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGGA-TACGTGAGA-CTC
* * * * ** * *
42121931 AGTATAAGACCGTGTTTGGGATATGGCATCGGCATTGAGACGAGAG-CT-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATACGTGAGACTC
* * *
42121979 AATGTAAGA-CATGTCTGGGACAT-GCATCAGCTAC--AT--GATGTG--TC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGGATACG-TGAGACTC
* * ** *
42122023 AATGTAAGACCATGTCTAGGACATGGCATCGGCACGGATTTGTGGGACTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATACGTGAGACTC
* * * * *
42122073 GGTGTAAGACCATGTCGGGGACATGGCATCAGTACGGATACGTGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATACGTGAGACTC
* * * **
42122123 AGTGTAAGACTATGTTTGGGTCATGGCATC-G-ACTTA-ACGTGAGAGC-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATACGTGAGA-CTC
* *
42122170 AGTGTAAGACCATGTCTAGGACATAGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
42122200 AGCATTATAC
Statistics
Matches: 207, Mismatches: 43, Indels: 37
0.72 0.15 0.13
Matches are distributed among these distances:
43 2 0.01
44 11 0.05
45 16 0.08
46 22 0.11
47 61 0.29
48 22 0.11
49 3 0.01
50 70 0.34
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATACGTGAGACTC
Found at i:42123901 original size:14 final size:14
Alignment explanation
Indices: 42123882--42123911 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42123872 ATGTTAAAAT
42123882 AATAAATAAAATTA
1 AATAAATAAAATTA
42123896 AATAAATAAAATTA
1 AATAAATAAAATTA
42123910 AA
1 AA
42123912 AGAAAGAAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAATAAAATTA
Found at i:42124807 original size:30 final size:32
Alignment explanation
Indices: 42124747--42124809 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
42124737 CATTTATTTT
42124747 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
42124780 CACCTATGCCGAATGCAACATATATATATA
1 CACCTATGCCGAATGCAACACATAAATATA
42124810 CATATCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:42130683 original size:37 final size:37
Alignment explanation
Indices: 42130633--42130711 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42130623 TTATTACGAA
* * *
42130633 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
42130670 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
42130707 GTCTT
1 GTCTT
42130712 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42130901 original size:47 final size:47
Alignment explanation
Indices: 42130830--42131287 Score: 792
Period size: 47 Copynumber: 9.7 Consensus size: 47
42130820 CCCTTCGGGA
* * * * * * *
42130830 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
42130877 CCTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42130924 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42130971 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42131018 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42131065 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42131112 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
42131159 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
*
42131206 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
* * *
42131253 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
42131288 AGAATCCTAA
Statistics
Matches: 397, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
46 1 0.00
47 396 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
Found at i:42141209 original size:25 final size:25
Alignment explanation
Indices: 42141163--42141210 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42141153 GCGTTATGGA
* *
42141163 AAACAAGAAAGTCCGCCTAGACAAT
1 AAACAAGAAAGTCCACCAAGACAAT
*
42141188 AAACAAGAAAGTTCACCAAGACA
1 AAACAAGAAAGTCCACCAAGACA
42141211 TTTAGGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.10
Consensus pattern (25 bp):
AAACAAGAAAGTCCACCAAGACAAT
Found at i:42147574 original size:49 final size:49
Alignment explanation
Indices: 42147474--42147597 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
42147464 GATGCCGACA
* *
42147474 CCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCAAGGCCAATG
1 CCATGTCCCAGACA-GGTCTTACACTAGCTCTCATATAGCAAGGCCAATG
* * * * *
42147524 CCATGTCCCAGACAGGTCTTACACTAGCTCTCATCTATC-GGTGTCGATG
1 CCATGTCCCAGACAGGTCTTACACTAGCTCTCATATAGCAAG-GCCAATG
*
42147573 CCATGTCCCAGATAGGTCTTACACT
1 CCATGTCCCAGACAGGTCTTACACT
42147598 GACACAGCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.77
50 14 0.22
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.27
Consensus pattern (49 bp):
CCATGTCCCAGACAGGTCTTACACTAGCTCTCATATAGCAAGGCCAATG
Found at i:42147684 original size:48 final size:48
Alignment explanation
Indices: 42147626--42147740 Score: 149
Period size: 48 Copynumber: 2.4 Consensus size: 48
42147616 GCTATATCCA
* ** * * *
42147626 AGACAAGTCTTACACTAGCTTGTATATCGCGAGGCCGATGCATGTCCC
1 AGACATGTCTTACACTAGCTTAAATATCGCAAGACCAATGCATGTCCC
* * *
42147674 AGACATGTCTTACACTGGCTTAAATATCTCAAGATCAATGCATGTCCC
1 AGACATGTCTTACACTAGCTTAAATATCGCAAGACCAATGCATGTCCC
42147722 AGACATGTCTTACACTAGC
1 AGACATGTCTTACACTAGC
42147741 ACACATATCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (48 bp):
AGACATGTCTTACACTAGCTTAAATATCGCAAGACCAATGCATGTCCC
Done.