Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 176 of 325
Found at i:55326489 original size:40 final size:40
Alignment explanation
Indices: 55326391--55326653 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
55326381 TCCTCGTTCA
* * * * *
55326391 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
55326430 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55326470 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55326510 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55326550 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
55326590 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
55326630 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55326654 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 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:55334404 original size:38 final size:40
Alignment explanation
Indices: 55334265--55334519 Score: 239
Period size: 39 Copynumber: 6.6 Consensus size: 40
55334255 TCCTCGTTCA
* * * *
55334265 AATGCCTTC-GGACATAGCCCGGTTTTAGTAACTC-CAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
55334302 ACATGCCTTTCGGGAC-TAACCCGGATTTAA-CACTCGCACAG
1 A-ATGCC-TTCGGGACTTAACCCGGATTTAATAACTCGCAC-G
*
55334343 ACTGCCTTCGGGACTTAA-CCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
55334382 AATGCCTTC-GGACTTAA-CCGGATTTAAT-ACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
55334419 AATGCCTTCGGGACTTAACCCGGA-TTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
55334458 AAGGCCTTC-GGATCTTAATCCGGA-TTATTCACTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCGCACG
* *
55334496 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55334520 CAGCATCAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
37 19 0.10
38 60 0.32
39 87 0.47
40 19 0.10
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:55334442 original size:77 final size:77
Alignment explanation
Indices: 55334265--55334519 Score: 265
Period size: 77 Copynumber: 3.3 Consensus size: 77
55334255 TCCTCGTTCA
* * *
55334265 AATGCCTTC-GGACATAGCCCGGTTTTAGTAACTC-CACACATGCCTTTCGGGAC-TAACCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACA-ATGCC-TTC-GGACTTAACCCGGA
*
55334327 TTTAACACTCGCACAG
63 TTTAATACTCGCAC-G
* *
55334343 ACTGCCTTCGGGACTTAA-CCGGATTTAATAACTCGCACGAATGCCTTCGGACTTAA-CCGGATT
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGACTTAACCCGGATT
55334406 TAATACTCGCACG
65 TAATACTCGCACG
* * *
55334419 AATGCCTTCGGGACTTAACCCGGA-TTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGA-
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGA-CTTAACCCGGAT
* *
55334482 TTATTCACTAGCAC-
64 TTAAT-ACTCGCACG
* *
55334496 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
55334520 CAGCATCAAT
Statistics
Matches: 154, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
76 41 0.27
77 58 0.38
78 40 0.26
79 14 0.09
80 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (77 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGACTTAACCCGGATTT
AATACTCGCACG
Found at i:55334454 original size:116 final size:117
Alignment explanation
Indices: 55334265--55334483 Score: 263
Period size: 116 Copynumber: 1.9 Consensus size: 117
55334255 TCCTCGTTCA
* * *
55334265 AATGCCTTCGGACATAGCCCGGTTTTAGTAACTCCACACATGCCTTTCGGGACTAACCCGGATTT
1 AATGCCTTCGGACATAGACCGGATTTAATAACTCCACACATGCCTTTCGGGACTAACCCGGATTT
**
55334330 AACACTCGCACAGACTGCCTTCGGGA-CTTAA-CCGGATTTAATAACTCGCACG
66 AACACTCGCACA-AAGGCCTTC-GGATCTTAATCCGGATTTAATAACTCGCACG
*
55334382 AATGCCTTCGGACTTA-ACCGGATTTAAT-ACTCGCACGA-ATGCC-TTCGGGACTTAACCCGGA
1 AATGCCTTCGGACATAGACCGGATTTAATAACTC-CAC-ACATGCCTTTCGGGAC-TAACCCGGA
**
55334443 -TTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGATT
63 TTTAACA-CTCGCACAAAGGCCTTCGGATCTTAATCCGGATT
55334484 ATTCACTAGC
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
114 3 0.03
115 28 0.32
116 41 0.47
117 16 0.18
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (117 bp):
AATGCCTTCGGACATAGACCGGATTTAATAACTCCACACATGCCTTTCGGGACTAACCCGGATTT
AACACTCGCACAAAGGCCTTCGGATCTTAATCCGGATTTAATAACTCGCACG
Found at i:55342194 original size:39 final size:39
Alignment explanation
Indices: 55342037--55342198 Score: 161
Period size: 39 Copynumber: 4.2 Consensus size: 39
55342027 ACCCAAGTAT
* * *
55342037 CTTCGGGATTTAGCCGGAGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTAGCCCG-GATATAGCAACTCGCACAAATGC
55342078 CTTCGGGTCTAGCCCGGATATAGCAA-T-GCACAAATGC
1 CTTCGGGTCTAGCCCGGATATAGCAACTCGCACAAATGC
* * * * *
55342115 CTTCCGGTCTTGGCCCGGATATAAC-ACTAGCATAAATGC
1 CTTCGGGTC-TAGCCCGGATATAGCAACTCGCACAAATGC
* * *
55342154 CTTCGGGACATAGCCCGGAT-TAGCAACTCGCACGATTGC
1 CTTCGGGTC-TAGCCCGGATATAGCAACTCGCACAAATGC
55342193 CTTCGG
1 CTTCGG
55342199 ATCTTAGTCG
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
37 19 0.19
38 18 0.18
39 50 0.50
40 7 0.07
41 7 0.07
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CTTCGGGTCTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:55351029 original size:27 final size:27
Alignment explanation
Indices: 55350969--55351138 Score: 198
Period size: 27 Copynumber: 6.3 Consensus size: 27
55350959 GGAAAAATGG
* * * *
55350969 TAATTTTACCCCACAAGGGTATCTCG-
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
55350995 TAATTCTACCCTATAGGGCTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* * *
55351022 TATTTCTACCCTACAAGGGTATTTCGG
1 TAATTCTACCCTACAGGGGTATTTCGA
* *
55351049 TAATTCTATCCTACGGGGGTATTTCGA
1 TAATTCTACCCTACAGGGGTATTTCGA
**
55351076 TAATTCTACCCTACAGGGGTATTTTAA
1 TAATTCTACCCTACAGGGGTATTTCGA
*
55351103 TAATTCTACCCTACAGGGGTATTTTGA
1 TAATTCTACCCTACAGGGGTATTTCGA
55351130 TAATTCTAC
1 TAATTCTAC
55351139 AACTTATCCA
Statistics
Matches: 123, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 20 0.16
27 103 0.84
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.36
Consensus pattern (27 bp):
TAATTCTACCCTACAGGGGTATTTCGA
Found at i:55353913 original size:43 final size:42
Alignment explanation
Indices: 55353832--55353915 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
55353822 TGTAAAACTA
* *
55353832 TGTCTGGGACATTAGCATCGTATTTGATTTAGTGTAAGACCC
1 TGTCTGGGACAGTAGCATCGTATTTGATTTAATGTAAGACCC
*
55353874 TGTCTGGGACAGTGGCATCGATATTTGA-TTACATGTAAGACC
1 TGTCTGGGACAGTAGCATCG-TATTTGATTTA-ATGTAAGACC
55353916 ACGTATGCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TGTCTGGGACAGTAGCATCGTATTTGATTTAATGTAAGACCC
Found at i:55357105 original size:6 final size:6
Alignment explanation
Indices: 55357087--55357180 Score: 77
Period size: 6 Copynumber: 15.3 Consensus size: 6
55357077 AAGAAACATT
*
55357087 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
55357136 ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA AGCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
55357181 GTGAATGCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.06
6 57 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.17
Consensus pattern (6 bp):
ATCAGA
Found at i:55357138 original size:31 final size:31
Alignment explanation
Indices: 55357101--55357180 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
55357091 GAACTAGAAT
* *
55357101 CAGAATCAGAATCAGAATCAGAATCAGGTGA
1 CAGAATCAAAATCAGAATCAGAATCAGGTAA
*
55357132 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAGAATCAGGTAA
*
55357163 CAGAATCAAAAGCAGAAT
1 CAGAATCAAAATCAGAAT
55357181 GTGAATGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAGAATCAGGTAA
Found at i:55357394 original size:67 final size:67
Alignment explanation
Indices: 55357283--55357436 Score: 263
Period size: 67 Copynumber: 2.3 Consensus size: 67
55357273 CACCACAGAA
* *
55357283 ATTGCAGCGAGGTTGCCAGATATTGTGACGAAGTCACCATAACAGATATAAGTGGCGAAGCCACC
1 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATAAGTGGCGAAGCCACC
55357348 AG
66 AG
* * *
55357350 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGTGAGGCCACC
1 ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATAAGTGGCGAAGCCACC
55357415 AG
66 AG
55357417 ATTGCAGCGAGGCTGCCAGA
1 ATTGCAGCGAGGCTGCCAGA
55357437 ACGCTTCCTC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 82 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (67 bp):
ATTGCAGCGAGGCTGCCAGATATTGTGACGAAGTCACCAGAACAGATATAAGTGGCGAAGCCACC
AG
Found at i:55357788 original size:81 final size:81
Alignment explanation
Indices: 55357666--55357905 Score: 324
Period size: 81 Copynumber: 3.0 Consensus size: 81
55357656 TAAAATGGTA
* *
55357666 ATTT-TACCCCACAAGGGTATCTC-AGTAATTCTACCCTACAGGGATATTTCAGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGA-TAATTCTACCCTACAGGGATATTTCAGTAATTCTACCC
55357729 TACAAGGGTATTTCGGT
65 TACAAGGGTATTTCGGT
*
55357746 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGATATTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGATATTTCAGTAATTCTACCCT
* * *
55357811 ATAGGGGTATTTTGGT
66 ACAAGGGTATTTCGGT
* * * * * * *
55357827 ATTTCTACCTTATAGGGGTATTTCGGTATTTCTACCCTACAAGGG-TATTTCGGTATTTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC-AGGGATATTTCAGTAATTCTACCC
55357891 TACAAGGGTATTTCG
65 TACAAGGGTATTTCG
55357906 ATAATTTTGT
Statistics
Matches: 140, Mismatches: 17, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
80 4 0.03
81 131 0.94
82 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGATATTTCAGTAATTCTACCCT
ACAAGGGTATTTCGGT
Found at i:55357905 original size:27 final size:27
Alignment explanation
Indices: 55357666--55357905 Score: 288
Period size: 27 Copynumber: 8.9 Consensus size: 27
55357656 TAAAATGGTA
* * *
55357666 ATTT-TACCCCACAAGGGTATCTCAGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* *
55357692 AATTCTACCCTAC-AGGGATATTTCAGT
1 ATTTCTACCCTACAAGGG-TATTTCGGT
*
55357719 AATTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
*
55357746 ATTTCTACCCTACAAGGGTATTTCGAT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* **
55357773 AATTCTACCCTAC-AGGGATATTTTAGT
1 ATTTCTACCCTACAAGGG-TATTTCGGT
* * * *
55357800 AATTCTACCCTATAGGGGTATTTTGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
* * *
55357827 ATTTCTACCTTATAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
55357854 ATTTCTACCCTACAAGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTATTTCGGT
55357881 ATTTCTACCCTACAAGGGTATTTCG
1 ATTTCTACCCTACAAGGGTATTTCG
55357906 ATAATTTTGT
Statistics
Matches: 190, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
26 11 0.06
27 172 0.91
28 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (27 bp):
ATTTCTACCCTACAAGGGTATTTCGGT
Found at i:55357937 original size:27 final size:27
Alignment explanation
Indices: 55357915--55358033 Score: 166
Period size: 27 Copynumber: 4.4 Consensus size: 27
55357905 GATAATTTTG
* **
55357915 TAAATCAAGGGTAAAATTGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
* *
55357942 TAAATCGAGCGTAAAACGGTAATTTTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
55357969 TAAATCGAGGGTGAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
55357996 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTA
*
55358023 CAAATCGAGGG
1 TAAATCGAGGG
55358034 CATTTTAGTA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGGTAATTCTA
Found at i:55360356 original size:28 final size:25
Alignment explanation
Indices: 55360306--55360364 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
55360296 AGCTATAAAT
55360306 GGTAAGCTCCTCCGAGCTTAATAAC
1 GGTAAGCTCCTCCGAGCTTAATAAC
*
55360331 GGTAAGCTCCTCCGAGCTTAATAAT
1 GGTAAGCTCCTCCGAGCTTAATAAC
*
55360356 AGTAAGCTC
1 GGTAAGCTC
55360365 ATGTAAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (25 bp):
GGTAAGCTCCTCCGAGCTTAATAAC
Found at i:55361286 original size:20 final size:20
Alignment explanation
Indices: 55361258--55361295 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55361248 AACTATCATG
*
55361258 TTTTCTTTATTTTATTAACC
1 TTTTATTTATTTTATTAACC
55361278 TTTTATTTATTTTATTAA
1 TTTTATTTATTTTATTAA
55361296 TAAAAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATTTATTTTATTAACC
Found at i:55367428 original size:17 final size:17
Alignment explanation
Indices: 55367408--55367443 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55367398 AAATCCTAGG
55367408 AAGCATGAAATGTTGAA
1 AAGCATGAAATGTTGAA
55367425 AAGCATGAAATGTTGAA
1 AAGCATGAAATGTTGAA
55367442 AA
1 AA
55367444 TGATTTAGGC
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:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (17 bp):
AAGCATGAAATGTTGAA
Found at i:55370024 original size:23 final size:22
Alignment explanation
Indices: 55369972--55370024 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55369962 TCCACGTCTT
*
55369972 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55369994 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55370017 TTTCTTTT
1 TTTCTTTT
55370025 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55373609 original size:28 final size:27
Alignment explanation
Indices: 55373570--55373636 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
55373560 AAATATGTAA
55373570 TAATTA-TAAAATAATTAAATTTTACT
1 TAATTATTAAAATAATTAAATTTTACT
* *
55373596 TCAATTATTAAAAT-TTTTAATTTTACT
1 T-AATTATTAAAATAATTAAATTTTACT
*
55373623 TAATT-TTATAATAA
1 TAATTATTAAAATAA
55373637 ATTTTGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 6 0.18
26 5 0.15
27 17 0.50
28 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATTATTAAAATAATTAAATTTTACT
Found at i:55375939 original size:47 final size:47
Alignment explanation
Indices: 55375881--55376007 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 47
55375871 CGCATCCATA
* *
55375881 ATGAACACGGAACACAACTCAAAGAGTTCGGATG-C-CATCATTCAT-
1 ATGAACTCGGAACACAACTCAAAGAGTTCGGATGCCTCATAATTC-TC
** * *
55375926 AGGTGAACTCGGAATGCAAATCAACGAGTTCGGATGCCTCATAATTCTC
1 A--TGAACTCGGAACACAACTCAAAGAGTTCGGATGCCTCATAATTCTC
* *
55375975 ATGAACTCGGACCACAACTCAATGAGTTCGGAT
1 ATGAACTCGGAACACAACTCAAAGAGTTCGGAT
55376008 CTCAATTTCC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.02
47 55 0.83
48 2 0.03
49 8 0.12
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (47 bp):
ATGAACTCGGAACACAACTCAAAGAGTTCGGATGCCTCATAATTCTC
Found at i:55380660 original size:42 final size:43
Alignment explanation
Indices: 55380601--55380711 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
55380591 ATAGGATCGC
* *
55380601 ACGGGTCACACAAGACGACTGTGGACTATTCTATTAAGGTTG-
1 ACGGGTCACACGAGACGACTGTGGACTATTCTATTAAGGTCGT
* * * *
55380643 ACGGGTCACACGAGACGATTGTGGACTGTTTTGTTAAGGTCGT
1 ACGGGTCACACGAGACGACTGTGGACTATTCTATTAAGGTCGT
* *
55380686 ACGGGTCGA-GCGAGACGACTATGGAC
1 ACGGGTC-ACACGAGACGACTGTGGAC
55380712 CTACTGACAG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 36 0.62
43 21 0.36
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (43 bp):
ACGGGTCACACGAGACGACTGTGGACTATTCTATTAAGGTCGT
Found at i:55380762 original size:22 final size:22
Alignment explanation
Indices: 55380737--55380822 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 22
55380727 AGCCACTTGA
55380737 TCTGATTATGGCTCTGTGCCAT
1 TCTGATTATGGCTCTGTGCCAT
** * *
55380759 TCTGAAGATGGCTTTGTTCCAT
1 TCTGATTATGGCTCTGTGCCAT
* * *
55380781 CCCGATTATGGCT-TCATGCCA-
1 TCTGATTATGGCTCT-GTGCCAT
*
55380802 TCTTGATCATGGCTCTGTGCC
1 TC-TGATTATGGCTCTGTGCC
55380823 TATCATATTA
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
21 2 0.04
22 44 0.94
23 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (22 bp):
TCTGATTATGGCTCTGTGCCAT
Found at i:55380889 original size:30 final size:32
Alignment explanation
Indices: 55380838--55380914 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 32
55380828 TATTACTGTT
* * *
55380838 ACTGATGGCTCTAT-ACCGATCATATTAC-CA
1 ACTGATGGCTCTGTGACAGATCATACTACACA
*
55380868 ACTGATGGCTCTGTGA-AGATCATACTACAGCT
1 ACTGATGGCTCTGTGACAGATCATACTACA-CA
*
55380900 ACTGATGGCTTTGTG
1 ACTGATGGCTCTGTG
55380915 CCTGTAACAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 23 0.59
31 1 0.03
32 15 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (32 bp):
ACTGATGGCTCTGTGACAGATCATACTACACA
Found at i:55383951 original size:21 final size:21
Alignment explanation
Indices: 55383922--55383962 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55383912 AACAAATTGA
* *
55383922 TAATTTGTTTTGTTATATATG
1 TAATATGTTTTGTTACATATG
*
55383943 TAATATGTTTTTTTACATAT
1 TAATATGTTTTGTTACATAT
55383963 ATTTATTTGT
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:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
TAATATGTTTTGTTACATATG
Found at i:55384250 original size:26 final size:26
Alignment explanation
Indices: 55384214--55384288 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
55384204 AGCCATTCTG
*
55384214 TTACTGGCAGCCTTCCTGTGATACTA
1 TTACTGGCAGCCTTGCTGTGATACTA
* * * *
55384240 TTACTGGCAGCCCTGCTATGTTTCTA
1 TTACTGGCAGCCTTGCTGTGATACTA
*
55384266 TTACTGGCAGCATTGCTGTGATA
1 TTACTGGCAGCCTTGCTGTGATA
55384289 TTGGTGTGCT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (26 bp):
TTACTGGCAGCCTTGCTGTGATACTA
Found at i:55392139 original size:29 final size:29
Alignment explanation
Indices: 55392076--55392143 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
55392066 TAATCAACCA
55392076 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
55392105 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
55392134 CGCACACTTA
1 CGCACACTTA
55392144 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:55392284 original size:29 final size:30
Alignment explanation
Indices: 55392245--55392323 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
55392235 CTTAATAATC
55392245 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
55392275 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
55392304 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
55392324 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:55400305 original size:29 final size:29
Alignment explanation
Indices: 55400242--55400309 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
55400232 TAATCAACCA
55400242 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
55400271 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
55400300 CGCACACTTA
1 CGCACACTTA
55400310 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:55400450 original size:29 final size:30
Alignment explanation
Indices: 55400411--55400489 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
55400401 CTTAATAATC
55400411 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
55400441 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
55400470 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
55400490 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:55409554 original size:19 final size:19
Alignment explanation
Indices: 55409519--55409556 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55409509 TTGCAATTTA
*
55409519 AATTTTTATTTTCTTTTCT
1 AATTTTTATTTTATTTTCT
55409538 AATTTTTCA-TTTATTTTCT
1 AATTTTT-ATTTTATTTTCT
55409557 CTTGACAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTATTTTATTTTCT
Found at i:55411806 original size:31 final size:31
Alignment explanation
Indices: 55411768--55411828 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
55411758 ACATTGAGAG
55411768 TATTTCTTACCTTTTTTTTCATGATATTAAA
1 TATTTCTTACCTTTTTTTTCATGATATTAAA
55411799 TATTTCTTACCTTTTTTTTCATGATATTAA
1 TATTTCTTACCTTTTTTTTCATGATATTAA
55411829 GTTATTAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.03, T:0.59
Consensus pattern (31 bp):
TATTTCTTACCTTTTTTTTCATGATATTAAA
Found at i:55422178 original size:18 final size:18
Alignment explanation
Indices: 55422141--55422178 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
55422131 TAAATGATGA
55422141 ATTTTAAATATTAGTTATT
1 ATTTTAAATATTA-TTATT
55422160 ATTTTAAATTATT-TTATT
1 ATTTTAAA-TATTATTATT
55422178 A
1 A
55422179 AGTGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
ATTTTAAATATTATTATT
Found at i:55424163 original size:56 final size:55
Alignment explanation
Indices: 55424076--55424206 Score: 190
Period size: 56 Copynumber: 2.4 Consensus size: 55
55424066 ACCATGGCAT
** * * * *
55424076 CGATATATGTGAACGAGTAAGACCATGTTTTATACGTTGGCATCGATATGTGACTT
1 CGATATATGTGTGCGAGTAAGACCAAGTTTTATAAGTTGGCATCAATATGTGAC-C
*
55424132 TGATATATGTGTGCGAGTAAGACCAAGTTTTATAAGTTGGCATCAATATGTGACC
1 CGATATATGTGTGCGAGTAAGACCAAGTTTTATAAGTTGGCATCAATATGTGACC
55424187 CGATATATGTGTGCGAGTAA
1 CGATATATGTGTGCGAGTAA
55424207 AACCCTATCT
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
55 19 0.28
56 48 0.72
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (55 bp):
CGATATATGTGTGCGAGTAAGACCAAGTTTTATAAGTTGGCATCAATATGTGACC
Found at i:55426624 original size:26 final size:26
Alignment explanation
Indices: 55426595--55426645 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
55426585 CCAGCACACC
*
55426595 AATATCGCAGCAAAGCTACCAGTAAT
1 AATAACGCAGCAAAGCTACCAGTAAT
* *
55426621 AATAACGCAGCATAGCTGCCAGTAA
1 AATAACGCAGCAAAGCTACCAGTAA
55426646 CAGTAAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (26 bp):
AATAACGCAGCAAAGCTACCAGTAAT
Found at i:55429188 original size:42 final size:42
Alignment explanation
Indices: 55429138--55429247 Score: 116
Period size: 44 Copynumber: 2.6 Consensus size: 42
55429128 TCGATGCATC
* *
55429138 TGTCCCAGACAGGGTCTTATACAAA-AACAGATACGATGCT-G
1 TGTCCCAGACACGGTCTTATACAAATAACAAAT-CGATGCTAG
* * **
55429179 ATGTCCCAGACATGGTCTTACACGTAAATTTCAAATCGATGCTAG
1 -TGTCCCAGACACGGTCTTATAC--AAATAACAAATCGATGCTAG
55429224 TGTCCCAGACACGGTCTTATACAA
1 TGTCCCAGACACGGTCTTATACAA
55429248 TAATCTAGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
42 22 0.39
44 30 0.53
45 5 0.09
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (42 bp):
TGTCCCAGACACGGTCTTATACAAATAACAAATCGATGCTAG
Found at i:55429232 original size:44 final size:43
Alignment explanation
Indices: 55429096--55429242 Score: 133
Period size: 42 Copynumber: 3.4 Consensus size: 43
55429086 CAATGCCAAC
* * *
55429096 GTCCCAGACATGGTCTTACATGT-AATTCAGTATCGATGC-ATCT
1 GTCCCAGACATGGTCTTACACGTAAATTCA-AATCGATGCTA-GT
* * ** *
55429139 GTCCCAGACAGGGTCTTATAC--AAAAACAGATACGATGCT-GAT
1 GTCCCAGACATGGTCTTACACGTAAATTCAAAT-CGATGCTAG-T
55429181 GTCCCAGACATGGTCTTACACGTAAATTTCAAATCGATGCTAGT
1 GTCCCAGACATGGTCTTACACGTAAA-TTCAAATCGATGCTAGT
*
55429225 GTCCCAGACACGGTCTTA
1 GTCCCAGACATGGTCTTA
55429243 TACAATAATC
Statistics
Matches: 83, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
41 2 0.02
42 30 0.36
43 18 0.22
44 28 0.34
45 5 0.06
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAAATTCAAATCGATGCTAGT
Found at i:55438359 original size:29 final size:28
Alignment explanation
Indices: 55438299--55438388 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 28
55438289 CACATACCTA
* *
55438299 TATATGGCCCACTACGCCTAA-TCACATT
1 TATATGGCCCATTA-GCCCAATTCACATT
55438327 TATATGGCCCATTAGTCCCAATTCACATT
1 TATATGGCCCATTAG-CCCAATTCACATT
*
55438356 TATATGGCCCATCAAGCCCAATTCACATT
1 TATATGGCCCAT-TAGCCCAATTCACATT
55438385 TATA
1 TATA
55438389 GTCATGCTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
27 1 0.02
28 17 0.30
29 36 0.64
30 2 0.04
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.31
Consensus pattern (28 bp):
TATATGGCCCATTAGCCCAATTCACATT
Found at i:55443161 original size:40 final size:39
Alignment explanation
Indices: 55443088--55443165 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
55443078 TGCTTATCTG
**
55443088 CTAAAATGGCACTTAGTGTGCGGTTCGAAATAGCTTCGA
1 CTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCGA
* * *
55443127 CTAAAACTGGCACTTGGTGTGCAATTTGAGATAGCTTCG
1 CTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCTTCG
55443166 GTTATATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 6 0.18
40 27 0.82
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (39 bp):
CTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCGA
Found at i:55453651 original size:93 final size:93
Alignment explanation
Indices: 55453539--55453710 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
55453529 CGCCCATAAG
*
55453539 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
55453603 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
55453632 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55453697 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
55453711 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:55453705 original size:46 final size:46
Alignment explanation
Indices: 55453532--55453707 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
55453522 TGTAACCCGC
* *
55453532 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
55453578 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
55453628 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
55453671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
55453708 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55467812 original size:45 final size:44
Alignment explanation
Indices: 55467748--55467929 Score: 181
Period size: 45 Copynumber: 4.0 Consensus size: 44
55467738 ATTAACCCGC
*
55467748 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGGCTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGCTTCGCAT
* * * *
55467793 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGC-CTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCTTCGC-A--T
* *
55467839 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGTTCGG-C-TTCGCAT
* * *
55467886 CCATAAGTGAACTCGGACTCAAC-CAACGAGTTCGGATGCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCTTCGCAT
55467929 C
1 C
55467930 ATCCTAGTGA
Statistics
Matches: 112, Mismatches: 16, Indels: 20
0.76 0.11 0.14
Matches are distributed among these distances:
43 8 0.07
44 5 0.04
45 45 0.40
46 18 0.16
47 30 0.27
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (44 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGCTTCGCAT
Found at i:55467918 original size:92 final size:92
Alignment explanation
Indices: 55467755--55467924 Score: 290
Period size: 92 Copynumber: 1.8 Consensus size: 92
55467745 CGCCCATAAG
55467755 CGAACTCGGACTCAACTCAACGAGCTCAGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCAGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
55467820 TGAGTTCGGATGCCTAGTTACATCTCA
66 CGAGTTCGGATGCCTAGTTACATCTCA
*
55467847 CGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAAC-C
1 CGAACTCGGACTCAACTCAACGAGCTCAGG-C-TTCGCATCCATAAGTGAACTCGGACTCAACTC
55467910 AACGAGTTCGGATGC
64 AACGAGTTCGGATGC
55467925 GCATCATCCT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
91 2 0.03
92 42 0.57
93 30 0.41
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGGCTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCA
Found at i:55475412 original size:93 final size:93
Alignment explanation
Indices: 55475300--55475471 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
55475290 CGCCCATAAG
55475300 CGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
*
55475364 AATGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
55475393 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55475458 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
55475472 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:55475468 original size:46 final size:46
Alignment explanation
Indices: 55475293--55475468 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
55475283 TGTAACCCGC
*
55475293 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * *
55475339 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
55475389 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
55475432 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
55475469 TGCTCAATCA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:55481245 original size:44 final size:43
Alignment explanation
Indices: 55481196--55481356 Score: 177
Period size: 44 Copynumber: 3.7 Consensus size: 43
55481186 TATGTGTTAT
55481196 CGTGTAAGACCATGTCTGGGACATTGGCATTGACTTATTATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATTGA-TTATTATTTA
* * *
55481240 TGTGTAAGACCATGTCTGAGACATTGGCATTGTATT-TGATTT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATTG-ATTATTATTTA
* * * *
55481282 CGTGTAAGACCCTGTTTGGGACAGTGGCATCGA-TATT-TGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATTGATTATTAT--TTA
* *
55481325 CATGTAAGACCACGTCTGGGACATTGGCATTG
1 CGTGTAAGACCATGTCTGGGACATTGGCATTG
55481357 TACTAGCTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
42 28 0.29
43 31 0.32
44 32 0.33
45 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATTGATTATTATTTA
Found at i:55481333 original size:43 final size:42
Alignment explanation
Indices: 55481198--55481354 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
55481188 TGTGTTATCG
* * * **
55481198 TGTAAGACCATGTCTGGGACATTGGCATTG-ACTTATTATTTATG
1 TGTAAGACCCTGTCTGGGACATTGGCATCGTA-TT-TGA-TTACA
* * * * *
55481242 TGTAAGACCATGTCTGAGACATTGGCATTGTATTTGATTTCG
1 TGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTACA
* *
55481284 TGTAAGACCCTGTTTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCCTGTCTGGGACATTGGCATCG-TATTTGATTACA
55481327 TGTAAGACCAC-GTCTGGGACATTGGCAT
1 TGTAAGACC-CTGTCTGGGACATTGGCAT
55481355 TGTACTAGCT
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 28 0.29
43 36 0.37
44 32 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (42 bp):
TGTAAGACCCTGTCTGGGACATTGGCATCGTATTTGATTACA
Found at i:55485932 original size:106 final size:105
Alignment explanation
Indices: 55485748--55485981 Score: 353
Period size: 106 Copynumber: 2.2 Consensus size: 105
55485738 TCCTCAATCA
* * *
55485748 GATTACCCATCCGGGCTAAATCCTTAAGCACCCATTTTCTTCGAGAGGCTCGATCACTCAAGGAA
1 GATTACCCATCCGGGCTAAATCCATAAGCACCCATATTCTTCGAGAGGCTCGATCACTCAAAGAA
*
55485813 CACCCATCCAGGCTAGATCCTTTCTATTTTCAGATCATCG
66 CACCCATCCAGGCTAAATCCTTTCTATTTTCAGATCATCG
*
55485853 GATTACCCATCCGGGCTAAATCCATAATGCACCCATATTCTTCG-GAAGGCTTGATCACTCAAAG
1 GATTACCCATCCGGGCTAAATCCATAA-GCACCCATATTCTTCGAG-AGGCTCGATCACTCAAAG
* * *
55485917 AACACCCGTTCAGGCTAAATCCTTTCTATTTTGAGATCATCG
64 AACACCCATCCAGGCTAAATCCTTTCTATTTTCAGATCATCG
**
55485959 GATTACCCATCCGAACTAAATCC
1 GATTACCCATCCGGGCTAAATCC
55485982 TTTTCAGCAA
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
105 27 0.23
106 90 0.77
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (105 bp):
GATTACCCATCCGGGCTAAATCCATAAGCACCCATATTCTTCGAGAGGCTCGATCACTCAAAGAA
CACCCATCCAGGCTAAATCCTTTCTATTTTCAGATCATCG
Found at i:55488928 original size:31 final size:31
Alignment explanation
Indices: 55488890--55488955 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
55488880 TCTAATTATG
*
55488890 TGTTCTTAATTCTTGTTTTAATATTCCAGGA
1 TGTTCTTAATTCTTATTTTAATATTCCAGGA
55488921 TGTTCTTAATTCTTATTTTAATATTCCAGGA
1 TGTTCTTAATTCTTATTTTAATATTCCAGGA
55488952 TGTT
1 TGTT
55488956 GATTCAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (31 bp):
TGTTCTTAATTCTTATTTTAATATTCCAGGA
Found at i:55490927 original size:28 final size:28
Alignment explanation
Indices: 55490887--55490994 Score: 153
Period size: 28 Copynumber: 3.9 Consensus size: 28
55490877 GTTAGAAGTA
* *
55490887 ATTGTGCCTGATGGACCATATGAATGTG
1 ATTGGGCCTGATGGGCCATATGAATGTG
* *
55490915 ATTGGGCCTGATGGGCCATGTGAATGAG
1 ATTGGGCCTGATGGGCCATATGAATGTG
**
55490943 ATTAAGCCTGATGGGCCATATGAATGTG
1 ATTGGGCCTGATGGGCCATATGAATGTG
*
55490971 ATTGGGCCTGATGGGCCATGTGAA
1 ATTGGGCCTGATGGGCCATATGAA
55490995 CGAGATTGCA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (28 bp):
ATTGGGCCTGATGGGCCATATGAATGTG
Found at i:55490978 original size:56 final size:56
Alignment explanation
Indices: 55490892--55491001 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
55490882 AAGTAATTGT
*
55490892 GCCTGATGGACCATATGAATGTGATTGGGCCTGATGGGCCATGTGAATGAGATTAA
1 GCCTGATGGACCATATGAATGTGATTGGGCCTGATGGGCCATGTGAACGAGATTAA
*
55490948 GCCTGATGGGCCATATGAATGTGATTGGGCCTGATGGGCCATGTGAACGAGATT
1 GCCTGATGGACCATATGAATGTGATTGGGCCTGATGGGCCATGTGAACGAGATT
55491002 GCACCTAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (56 bp):
GCCTGATGGACCATATGAATGTGATTGGGCCTGATGGGCCATGTGAACGAGATTAA
Found at i:55491457 original size:80 final size:80
Alignment explanation
Indices: 55491333--55491663 Score: 400
Period size: 80 Copynumber: 4.1 Consensus size: 80
55491323 GAAATTACTG
* * * * *
55491333 AAATACCCTCGATTTGTAAAATTACCGAAATACCC-CTAATTTGTGAAATTACCAAAACACCCTC
1 AAATACCCTCGATTTGTAAAATTATCGAAACACCCTC-AATTTGTAAAATTACCGAAATACCCTC
55491397 GATTGTAAAATTATCA
65 GATTGTAAAATTATCA
* * *
55491413 AAACACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTGAAATTATCGAAATACCCTCG
1 AAATACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATTACCGAAATACCCTCG
*
55491478 TGTTGTAAAATTATCA
66 -ATTGTAAAATTATCA
* * * *
55491494 AAATACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTATAAAATTACTGAAATACCCTCG
1 AAATACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATTACCGAAATACCCTCG
**
55491559 ATTTGTAAAATTATTG
66 A-TTGTAAAATTATCA
* * *
55491575 AAATA-CCTCGATTTGTAAAATTA-CTGAAACACCCTCGATTTGTAAAATTATCGAAATATCCT-
1 AAATACCCTCGATTTGTAAAATTATC-GAAACACCCTCAATTTGTAAAATTACCGAAATACCCTC
* *
55491637 TATAGTGTAAAATTATCG
65 GAT--TGTAAAATTATCA
55491655 AAATACCCT
1 AAATACCCT
55491664 TGTAGTGTAA
Statistics
Matches: 220, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
78 1 0.00
79 2 0.01
80 124 0.56
81 93 0.42
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (80 bp):
AAATACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATTACCGAAATACCCTCG
ATTGTAAAATTATCA
Found at i:55491675 original size:161 final size:161
Alignment explanation
Indices: 55491333--55491692 Score: 451
Period size: 161 Copynumber: 2.2 Consensus size: 161
55491323 GAAATTACTG
* * *
55491333 AAATACCCTCGATTTGTAAAATTACCGAAATACCCCTAATTTGTGAAATTACCAAAACACCCTCG
1 AAATACCCTCGATGTGTAAAATTACCGAAATACCCCTAATTTATAAAATTACCAAAACACCCTCG
*
55491398 ATTGTAAAATTATCAAAACACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTGAAATT
66 ATTGTAAAATTATCAAAACACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATT
*
55491463 ATCGAAATACCCTCGTGTTGTAAAATTATCA
131 ATCGAAATACCCTCATGTTGTAAAATTATCA
* * * ** *
55491494 AAATACCCTCGATTTGTAAAATTATCGAAATA-CCCTCGATTTATAAAATTACTGAAATACCCTC
1 AAATACCCTCGATGTGTAAAATTACCGAAATACCCCT-AATTTATAAAATTACCAAAACACCCTC
** * *
55491558 GATTTGTAAAATTATTGAAATA-CCTCGATTTGTAAAATTA-CTGAAACACCCTCGATTTGTAAA
65 GA-TTGTAAAATTATCAAAACACCCTCGATTTGTAAAATTATC-GAAACACCCTCAATTTGTAAA
* * *
55491621 ATTATCGAAATATCCTTATAG-TGTAAAATTATCG
128 ATTATCGAAATACCCTCAT-GTTGTAAAATTATCA
* * *
55491655 AAATACCCTTG-TAGTGTAAAATGACCGACATACCCCTA
1 AAATACCCTCGAT-GTGTAAAATTACCGAAATACCCCTA
55491693 TAGGATAAAA
Statistics
Matches: 171, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
160 6 0.04
161 144 0.84
162 21 0.12
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (161 bp):
AAATACCCTCGATGTGTAAAATTACCGAAATACCCCTAATTTATAAAATTACCAAAACACCCTCG
ATTGTAAAATTATCAAAACACCCTCGATTTGTAAAATTATCGAAACACCCTCAATTTGTAAAATT
ATCGAAATACCCTCATGTTGTAAAATTATCA
Found at i:55491676 original size:27 final size:27
Alignment explanation
Indices: 55491324--55491663 Score: 408
Period size: 27 Copynumber: 12.7 Consensus size: 27
55491314 TAATAAAAAG
55491324 AAATTA-CTGAAATACCCTCGATTTGTA
1 AAATTATC-GAAATACCCTCGATTTGTA
* * *
55491351 AAATTACCGAAATACCC-CTAATTTGTG
1 AAATTATCGAAATACCCTC-GATTTGTA
* * *
55491378 AAATTACCAAAACACCCTCGA-TTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
* *
55491404 AAATTATCAAAACACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
* * *
55491431 AAATTATCGAAACACCCTCAATTTGTG
1 AAATTATCGAAATACCCTCGATTTGTA
55491458 AAATTATCGAAATACCCTCG-TGTTGTA
1 AAATTATCGAAATACCCTCGAT-TTGTA
*
55491485 AAATTATCAAAATACCCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
55491512 AAATTATCGAAATACCCTCGATTTATA
1 AAATTATCGAAATACCCTCGATTTGTA
55491539 AAATTA-CTGAAATACCCTCGATTTGTA
1 AAATTATC-GAAATACCCTCGATTTGTA
*
55491566 AAATTATTGAAATA-CCTCGATTTGTA
1 AAATTATCGAAATACCCTCGATTTGTA
*
55491592 AAATTA-CTGAAACACCCTCGATTTGTA
1 AAATTATC-GAAATACCCTCGATTTGTA
* * *
55491619 AAATTATCGAAATATCCT-TATAGTGTA
1 AAATTATCGAAATACCCTCGAT-TTGTA
55491646 AAATTATCGAAATACCCT
1 AAATTATCGAAATACCCT
55491664 TGTAGTGTAA
Statistics
Matches: 276, Mismatches: 25, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
26 52 0.19
27 220 0.80
28 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGATTTGTA
Found at i:55491687 original size:27 final size:27
Alignment explanation
Indices: 55491400--55491703 Score: 155
Period size: 27 Copynumber: 11.3 Consensus size: 27
55491390 CACCCTCGAT
* * * *
55491400 TGTAAAATTATCAAAACACCCTCGAT-T
1 TGTAAAATTATCGAAATACCCT-TATAG
* * *
55491427 TGTAAAATTATCGAAACACCCTCA-ATT
1 TGTAAAATTATCGAAATACCCTTATA-G
* **
55491454 TGTGAAATTATCGAAATACCCTCGT-G
1 TGTAAAATTATCGAAATACCCTTATAG
* * *
55491480 TTGTAAAATTATCAAAATACCCTCGAT-T
1 -TGTAAAATTATCGAAATACCCT-TATAG
* *
55491508 TGTAAAATTATCGAAATACCCTCGAT-T
1 TGTAAAATTATCGAAATACCCT-TATAG
* * *
55491535 TATAAAATTA-CTGAAATACCCTCGAT-T
1 TGTAAAATTATC-GAAATACCCT-TATAG
* * *
55491562 TGTAAAATTATTGAAATA-CCTCGAT-T
1 TGTAAAATTATCGAAATACCCT-TATAG
* * *
55491588 TGTAAAATTA-CTGAAACACCCTCGAT-T
1 TGTAAAATTATC-GAAATACCCT-TATAG
*
55491615 TGTAAAATTATCGAAATATCCTTATAG
1 TGTAAAATTATCGAAATACCCTTATAG
*
55491642 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTATAG
* * * *
55491669 TGTAAAATGACCGACATACCCCTATAG
1 TGTAAAATTATCGAAATACCCTTATAG
55491696 -GATAAAAT
1 TG-TAAAAT
55491704 GATTGTTTTG
Statistics
Matches: 237, Mismatches: 28, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
26 28 0.12
27 207 0.87
28 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTTATAG
Found at i:55495343 original size:40 final size:40
Alignment explanation
Indices: 55495266--55495403 Score: 217
Period size: 40 Copynumber: 3.5 Consensus size: 40
55495256 AACCCAAGTA
* *
55495266 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
55495305 CCTTCGGGACTTAGCCCAGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55495345 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55495385 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55495404 TTATCATCCG
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 14 0.15
40 77 0.85
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55520980 original size:9 final size:9
Alignment explanation
Indices: 55520966--55520990 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55520956 TGGAATGGTT
55520966 AATTTAGTC
1 AATTTAGTC
55520975 AATTTAGTC
1 AATTTAGTC
55520984 AATTTAG
1 AATTTAG
55520991 CTTGAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (9 bp):
AATTTAGTC
Found at i:55531446 original size:47 final size:47
Alignment explanation
Indices: 55530723--55531439 Score: 1148
Period size: 47 Copynumber: 15.3 Consensus size: 47
55530713 ACAAGATATG
*
55530723 TATATGTGATAAGGCCTAATGGCCAATGCGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
55530770 TATATGTGACAAGGCCTAATGGCCGATGTGATGCATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55530817 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55530864 TATATGTGATAAAGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
55530911 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
55530958 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55531005 TATATGTGATAAAGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
55531052 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55531099 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * * *
55531146 TATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55531193 TATATGTGATAAGGCCTAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
55531240 TATATGTGACAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
*
55531287 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* ** * * *
55531334 TATATGAGATAATACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
55531381 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
55531428 TA-ATGTGATAAG
1 TATATGTGATAAG
55531440 TCCCGAAGGG
Statistics
Matches: 619, Mismatches: 51, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
46 10 0.02
47 609 0.98
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:55534451 original size:44 final size:45
Alignment explanation
Indices: 55534386--55534488 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 45
55534376 TTAAGAACTT
* * *
55534386 GCACACTTAGTG-CATAAATGTTTAGCCGAAGCTA-CAACGATATC
1 GCACACTTAGTGCCATAAATGTTAAACCAAAGCTATC-ACGATATC
* * **
55534430 GCACACTTAGTGCCAT-CATGTTAAACCAAAGTTATCTTGATATC
1 GCACACTTAGTGCCATAAATGTTAAACCAAAGCTATCACGATATC
55534474 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
55534489 CACATAACCG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 46 0.92
45 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (45 bp):
GCACACTTAGTGCCATAAATGTTAAACCAAAGCTATCACGATATC
Found at i:55550370 original size:90 final size:90
Alignment explanation
Indices: 55550213--55550377 Score: 215
Period size: 90 Copynumber: 1.8 Consensus size: 90
55550203 TGCCAAAGCC
* * * * * * * *
55550213 ATGTCCCCGATATGGTCTTACATAGGCCTACATATTGATGCCATATCCCAGATATGGTCTTATAT
1 ATGTCCCAGACATGGTCTTACAGAGACCTACATATCGATGCCATATCCCAGACATAGTCTTACAT
*
55550278 GAAGTCTCATGCCGGTGCCGATGCA
66 GAAATCTCATGCCGGTGCCGATGCA
* *
55550303 ATGTCCCAGACATGGTCTTACACGAGACCT-CATATCGGTGCCATGTCCCAGACATAGTCTTACA
1 ATGTCCCAGACATGGTCTTACA-GAGACCTACATATCGATGCCATATCCCAGACATAGTCTTACA
55550367 TGAAATCTCAT
65 TGAAATCTCAT
55550378 ATCAACACCA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
90 58 0.92
91 5 0.08
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (90 bp):
ATGTCCCAGACATGGTCTTACAGAGACCTACATATCGATGCCATATCCCAGACATAGTCTTACAT
GAAATCTCATGCCGGTGCCGATGCA
Found at i:55550394 original size:42 final size:42
Alignment explanation
Indices: 55550306--55550394 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
55550296 CGATGCAATG
* * **** *
55550306 TCCCAGACATGGTCTTACACGAGACCTCATATCGGTGCCATG
1 TCCCAGACATAGTCTTACACGAAACCTCATATCAACACCATA
* *
55550348 TCCCAGACATAGTCTTACATGAAATCTCATATCAACACCATA
1 TCCCAGACATAGTCTTACACGAAACCTCATATCAACACCATA
55550390 TCCCA
1 TCCCA
55550395 TATATGGTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.25
Consensus pattern (42 bp):
TCCCAGACATAGTCTTACACGAAACCTCATATCAACACCATA
Found at i:55551958 original size:31 final size:31
Alignment explanation
Indices: 55551922--55552000 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
55551912 TTTAACGGTT
*
55551922 ACTGGGCTGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
55551953 ACTGGGCCGAAGCCTTTTCATAAATCATATT
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
55551984 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
55552001 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:55552249 original size:26 final size:26
Alignment explanation
Indices: 55552206--55552343 Score: 199
Period size: 26 Copynumber: 5.3 Consensus size: 26
55552196 CTGGAGGCCT
55552206 AGCCTCTTTT-AAT-AACTGGGGCATA
1 AGCC-CTTTTCAATAAACTGGGGCATA
* **
55552231 AGTCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
55552257 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* *
55552283 AGCCCTTTTCGATAAACTGGGTCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
55552309 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
55552335 AGCCCTTTT
1 AGCCCTTTT
55552344 GCACTTCCTC
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
24 5 0.05
25 4 0.04
26 90 0.91
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:55553220 original size:27 final size:27
Alignment explanation
Indices: 55553141--55553227 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
55553131 TATTCGTCAT
* *
55553141 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
55553168 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
*
55553195 TTTACCCTACAGGGGCTTTACGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
55553222 TTTACC
1 TTTACC
55553228 TAATAGGCGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:55553311 original size:27 final size:27
Alignment explanation
Indices: 55553281--55553332 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
55553271 GTAAATCTAC
*
55553281 AAACTAATGGTATTT-CAGTAATTTTGT
1 AAACCAATGGTATTTCCA-TAATTTTGT
55553308 AAACCAATGGTATTTCCATAATTTT
1 AAACCAATGGTATTTCCATAATTTT
55553333 TAGAAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (27 bp):
AAACCAATGGTATTTCCATAATTTTGT
Found at i:55553401 original size:27 final size:27
Alignment explanation
Indices: 55553371--55553683 Score: 256
Period size: 27 Copynumber: 11.6 Consensus size: 27
55553361 TGTATATCAG
55553371 GGGTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAATTGA
* * *
55553398 GGGTATTTCGGTAATTTCACAAACT-A
1 GGGTATTTTGGTAATTTTACAAATTGA
*
55553424 GTGGTATTTTGGTAATTTTACAAACT-A
1 G-GGTATTTTGGTAATTTTACAAATTGA
55553451 GGAGTATTTTGGTAATTTTACAAATTGA
1 GG-GTATTTTGGTAATTTTACAAATTGA
***
55553479 GGGTATTTCT-GTAATTTTACAAACCAA
1 GGGTATTT-TGGTAATTTTACAAATTGA
* * *
55553506 GGGTATTTTAGCAATTTTACAAACT-A
1 GGGTATTTTGGTAATTTTACAAATTGA
** *
55553532 GGGTATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAATTGA
** *
55553559 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAATTGA
****** * *
55553586 GGGTAAAACAATAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATTGA
**** * * *
55553613 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAATTGA
* *
55553640 GGGTACTTTGGTAATTTTACAATTTGA
1 GGGTATTTTGGTAATTTTACAAATTGA
**
55553667 GGGTATTTCAGTAATTT
1 GGGTATTTTGGTAATTT
55553684 GGTAAACTAA
Statistics
Matches: 238, Mismatches: 42, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
26 24 0.10
27 210 0.88
28 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATTGA
Found at i:55553468 original size:81 final size:80
Alignment explanation
Indices: 55553371--55553575 Score: 304
Period size: 81 Copynumber: 2.5 Consensus size: 80
55553361 TGTATATCAG
* *
55553371 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAA-CTAGTGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAG-GGTATTTTA
*
55553435 GTAATTTTACAAACTA
65 GCAATTTTACAAACTA
* *
55553451 GGAGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTTACAAACCAAGGGTATTTTA
1 GG-GTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTA
55553516 GCAATTTTACAAACTA
65 GCAATTTTACAAACTA
** * *
55553532 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTT
55553576 TGTAAATCGA
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 39 0.35
81 71 0.63
82 3 0.03
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.42
Consensus pattern (80 bp):
GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTAG
CAATTTTACAAACTA
Found at i:55560313 original size:29 final size:29
Alignment explanation
Indices: 55560276--55560335 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
55560266 AATTCACATA
55560276 TTATAAACATAGAAAATAATTAAAATATT
1 TTATAAACATAGAAAATAATTAAAATATT
55560305 TTATAAACATAGAAAATAATTAAAATATT
1 TTATAAACATAGAAAATAATTAAAATATT
55560334 TT
1 TT
55560336 TTTGACTCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TTATAAACATAGAAAATAATTAAAATATT
Found at i:55560886 original size:19 final size:19
Alignment explanation
Indices: 55560862--55560901 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55560852 TGTGTCATCA
*
55560862 TAAATTCATAGGCATAACT
1 TAAATTCATAGACATAACT
**
55560881 TAAATTTGTAGACATAACT
1 TAAATTCATAGACATAACT
55560900 TA
1 TA
55560902 CACATTTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (19 bp):
TAAATTCATAGACATAACT
Found at i:55562881 original size:47 final size:47
Alignment explanation
Indices: 55562786--55562905 Score: 147
Period size: 47 Copynumber: 2.6 Consensus size: 47
55562776 GATAAGTACA
*
55562786 TATACCATGGCTCGTAGCCATATCAAGGTAACTTATCCCAGAGAACC
1 TATACCATGGCTCGTAGCCAAATCAAGGTAACTTATCCCAGAGAACC
* ***
55562833 TATACCATGGCTCGTAGACAAATCAAGGTAACTCT-TCTTTGA-ATACC
1 TATACCATGGCTCGTAGCCAAATCAAGGTAACT-TATCCCAGAGA-ACC
55562880 TATACCATGG-TCCGTAGCCAAATCAA
1 TATACCATGGCT-CGTAGCCAAATCAA
55562906 TGTATTATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
46 2 0.03
47 61 0.95
48 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (47 bp):
TATACCATGGCTCGTAGCCAAATCAAGGTAACTTATCCCAGAGAACC
Found at i:55573700 original size:27 final size:27
Alignment explanation
Indices: 55573662--55573716 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55573652 GAGGGTGTAT
55573662 CATTGATTTTCGTGGAAGTTGGGAGGA
1 CATTGATTTTCGTGGAAGTTGGGAGGA
55573689 CATTGATTTTCGTGGAAGTTGGGAGGA
1 CATTGATTTTCGTGGAAGTTGGGAGGA
55573716 C
1 C
55573717 TACCTACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.09, G:0.36, T:0.33
Consensus pattern (27 bp):
CATTGATTTTCGTGGAAGTTGGGAGGA
Found at i:55582213 original size:43 final size:43
Alignment explanation
Indices: 55582148--55582270 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
55582138 CTAGTATTGA
55582148 TCTGTTAAGGTTGCAC-AGGTCACACGAGACGACTGTGGACTAT
1 TCTGTTAAGGTTGCACGA-GTCACACGAGACGACTGTGGACTAT
*
55582191 TCTGTTAAGGTTGCACGAGTCACATGAGACGACTGTGGACTAT
1 TCTGTTAAGGTTGCACGAGTCACACGAGACGACTGTGGACTAT
* * * *
55582234 TCTATTAAGGTCGCACGGGTCGA-GCGAGACGACTGTG
1 TCTGTTAAGGTTGCACGAGTC-ACACGAGACGACTGTG
55582271 CACCTACCGA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 70 0.97
44 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (43 bp):
TCTGTTAAGGTTGCACGAGTCACACGAGACGACTGTGGACTAT
Found at i:55582353 original size:22 final size:21
Alignment explanation
Indices: 55582306--55582384 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
55582296 TGATCTGATT
*
55582306 ATGGCTCTGTGCCATTCTGAA
1 ATGGCTCTGTGCCATCCTGAA
*
55582327 GATGGCTCTGTGCCATCCCGATA
1 -ATGGCTCTGTGCCATCCTGA-A
** * *
55582350 ATGGCTCCATGCCATCTTGACC
1 ATGGCTCTGTGCCATCCTGA-A
55582372 ATGGCTCTGTGCC
1 ATGGCTCTGTGCC
55582385 GATATATTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 45 0.98
23 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.29
Consensus pattern (21 bp):
ATGGCTCTGTGCCATCCTGAA
Found at i:55582472 original size:32 final size:30
Alignment explanation
Indices: 55582372--55582485 Score: 97
Period size: 32 Copynumber: 3.7 Consensus size: 30
55582362 CATCTTGACC
* *
55582372 ATGGCTCTGTGCCGAT-ATATTACCATTACTA
1 ATGGCTTTGTACCGATCATATTACC--TACTA
* * * *
55582403 ATGGCTTTGTATCGATCATATTACCGATTG
1 ATGGCTTTGTACCGATCATATTACCTACTA
* *
55582433 ATGGCTTTGTGCCGATCATACTATAGCTACTA
1 ATGGCTTTGTACCGATCATA-T-TACCTACTA
*
55582465 ATGGCTTTGTACC-ATCCTATT
1 ATGGCTTTGTACCGATCATATT
55582486 TATAACTTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 21 0.32
31 19 0.29
32 25 0.38
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (30 bp):
ATGGCTTTGTACCGATCATATTACCTACTA
Found at i:55585718 original size:27 final size:27
Alignment explanation
Indices: 55585677--55585781 Score: 160
Period size: 27 Copynumber: 4.0 Consensus size: 27
55585667 ATTAAGACCT
*
55585677 CAGTTTGTAATATTACTGAAATACCCC
1 CAGTTTGTAAGATTACTGAAATACCCC
55585704 CAGTTTGTAAGATTACTGAAATACCCC
1 CAGTTTGTAAGATTACTGAAATACCCC
55585731 CAGTTTGTAAGATTACTG-AATA-CCC
1 CAGTTTGTAAGATTACTGAAATACCCC
* * *
55585756 CTGTTTGTAAAATTACCGAAATACCC
1 CAGTTTGTAAGATTACTGAAATACCC
55585782 TAGTCAGGTA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 18 0.25
26 8 0.11
27 46 0.64
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (27 bp):
CAGTTTGTAAGATTACTGAAATACCCC
Found at i:55585778 original size:52 final size:54
Alignment explanation
Indices: 55585677--55585781 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 54
55585667 ATTAAGACCT
* * *
55585677 CAGTTTGTAATATTACTGAAATACCCCCAGTTTGTAAGATTACTGAAATACCCC
1 CAGTTTGTAAGATTACTGAAATACCCCCAGTTTGTAAAATTACCGAAATACCCC
*
55585731 CAGTTTGTAAGATTACTG-AATA-CCCCTGTTTGTAAAATTACCGAAATACCC
1 CAGTTTGTAAGATTACTGAAATACCCCCAGTTTGTAAAATTACCGAAATACCC
55585782 TAGTCAGGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
52 26 0.55
53 4 0.09
54 17 0.36
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (54 bp):
CAGTTTGTAAGATTACTGAAATACCCCCAGTTTGTAAAATTACCGAAATACCCC
Found at i:55604672 original size:43 final size:43
Alignment explanation
Indices: 55604607--55604729 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
55604597 CTAGTATTGA
55604607 TCTGTTAAGGTTGCAC-AGGTCACACGAGACGACTGTGGACTAT
1 TCTGTTAAGGTTGCACGA-GTCACACGAGACGACTGTGGACTAT
*
55604650 TCTGTTAAGGTTGCACGAGTCACATGAGACGACTGTGGACTAT
1 TCTGTTAAGGTTGCACGAGTCACACGAGACGACTGTGGACTAT
* * * *
55604693 TCTATTAAGGTCGCACGGGTCGA-GCGAGACGACTGTG
1 TCTGTTAAGGTTGCACGAGTC-ACACGAGACGACTGTG
55604730 CACCTACCGA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
43 70 0.97
44 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (43 bp):
TCTGTTAAGGTTGCACGAGTCACACGAGACGACTGTGGACTAT
Found at i:55604812 original size:22 final size:21
Alignment explanation
Indices: 55604765--55604843 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
55604755 TGATCTGATT
*
55604765 ATGGCTCTGTGCCATTCTGAA
1 ATGGCTCTGTGCCATCCTGAA
*
55604786 GATGGCTCTGTGCCATCCCGATA
1 -ATGGCTCTGTGCCATCCTGA-A
** * *
55604809 ATGGCTCCATGCCATCTTGACC
1 ATGGCTCTGTGCCATCCTGA-A
55604831 ATGGCTCTGTGCC
1 ATGGCTCTGTGCC
55604844 GATATATTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
22 45 0.98
23 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.29
Consensus pattern (21 bp):
ATGGCTCTGTGCCATCCTGAA
Found at i:55604931 original size:32 final size:30
Alignment explanation
Indices: 55604831--55604944 Score: 97
Period size: 32 Copynumber: 3.7 Consensus size: 30
55604821 CATCTTGACC
* *
55604831 ATGGCTCTGTGCCGAT-ATATTACCATTACTA
1 ATGGCTTTGTACCGATCATATTACC--TACTA
* * * *
55604862 ATGGCTTTGTATCGATCATATTACCGATTG
1 ATGGCTTTGTACCGATCATATTACCTACTA
* *
55604892 ATGGCTTTGTGCCGATCATACTATAGCTACTA
1 ATGGCTTTGTACCGATCATA-T-TACCTACTA
*
55604924 ATGGCTTTGTACC-ATCCTATT
1 ATGGCTTTGTACCGATCATATT
55604945 TATAACTTAT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 21 0.32
31 19 0.29
32 25 0.38
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (30 bp):
ATGGCTTTGTACCGATCATATTACCTACTA
Found at i:55608192 original size:27 final size:27
Alignment explanation
Indices: 55608154--55608265 Score: 179
Period size: 27 Copynumber: 4.1 Consensus size: 27
55608144 GGTCATTAAG
* *
55608154 ACCCTCAGTTTGTAATATTACTGAAAT
1 ACCCCCAGTTTGTAAGATTACTGAAAT
55608181 ACCCCCAGTTTGTAAGATTACTGAAAT
1 ACCCCCAGTTTGTAAGATTACTGAAAT
55608208 ACCCCCAGTTTGTAAGATTACTGAAAT
1 ACCCCCAGTTTGTAAGATTACTGAAAT
* * *
55608235 ACCCCCTGTTTGTAAAATTACCGAAAT
1 ACCCCCAGTTTGTAAGATTACTGAAAT
55608262 ACCC
1 ACCC
55608266 TAGTCAGGTA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (27 bp):
ACCCCCAGTTTGTAAGATTACTGAAAT
Found at i:55608606 original size:43 final size:43
Alignment explanation
Indices: 55608554--55608636 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
55608544 CCAGTATTGA
*
55608554 TCTGTTAAGGTTGCACAGGTCGCA-CGAGACGACTGTGGACTAT
1 TCTGTTAAGGTCGCACAGGTCG-AGCGAGACGACTGTGGACTAT
*
55608597 TCTGTTAAGGTCGCACGGGTCGAGCGAGACGACTGTGGAC
1 TCTGTTAAGGTCGCACAGGTCGAGCGAGACGACTGTGGAC
55608637 CTACCGATGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 36 0.97
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.23
Consensus pattern (43 bp):
TCTGTTAAGGTCGCACAGGTCGAGCGAGACGACTGTGGACTAT
Found at i:55608803 original size:30 final size:31
Alignment explanation
Indices: 55608735--55608806 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
55608725 CATCTTGATC
*
55608735 ATGGCTCTGTACCGATCATATTACCGTTACTG
1 ATGGCTCTGTACCGATCATATTACCG-TACTA
* *
55608767 ATGGCTCTGTATCGATCATATTATCG-ACTA
1 ATGGCTCTGTACCGATCATATTACCGTACTA
55608797 ATGGCTCTGT
1 ATGGCTCTGT
55608807 GCCAGTCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 13 0.35
32 24 0.65
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (31 bp):
ATGGCTCTGTACCGATCATATTACCGTACTA
Found at i:55610626 original size:47 final size:47
Alignment explanation
Indices: 55610555--55610684 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 47
55610545 ACAATCGATA
*
55610555 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCAG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAG
* * * * *
55610602 AGTACCTATGCCATGGCCCATAGCCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAG
* * *
55610649 AATACCTATACCATGGCCTGTAGCCATATCAAGGTA
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
55610685 TTATTCGTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAG
Found at i:55621643 original size:46 final size:44
Alignment explanation
Indices: 55621576--55621749 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 44
55621566 TGTAACCCGC
*
55621576 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TT-GCAT
* *
55621622 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-CTTGCAT
* *** * *
55621668 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTGCAT
*
55621714 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
55621750 ATGCCCAAAT
Statistics
Matches: 107, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
44 1 0.01
45 30 0.28
46 45 0.42
47 28 0.26
48 2 0.02
49 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTGCAT
Found at i:55621741 original size:92 final size:93
Alignment explanation
Indices: 55621583--55621754 Score: 301
Period size: 92 Copynumber: 1.9 Consensus size: 93
55621573 CGCCCATAAG
* *
55621583 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
55621648 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
55621676 CGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
55621740 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
55621755 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 44 0.59
93 31 0.41
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:55624185 original size:15 final size:15
Alignment explanation
Indices: 55624138--55624214 Score: 83
Period size: 14 Copynumber: 5.4 Consensus size: 15
55624128 CAAAGATAAC
55624138 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
55624151 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
55624166 GAGAAATCCAGAATA
1 AAGAAATCCAGAATA
55624181 AAG-AATCCAGAATA
1 AAGAAATCCAGAATA
* *
55624195 AA-AGATCCAGGATA
1 AAGAAATCCAGAATA
55624209 AAGAAA
1 AAGAAA
55624215 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.11
14 27 0.51
15 19 0.36
16 1 0.02
ACGTcount: A:0.58, C:0.13, G:0.17, T:0.12
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55628589 original size:29 final size:29
Alignment explanation
Indices: 55628547--55628647 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
55628537 CATGAAATTG
55628547 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
55628576 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
55628605 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
55628633 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
55628648 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:55630325 original size:46 final size:45
Alignment explanation
Indices: 55630250--55630424 Score: 163
Period size: 46 Copynumber: 3.8 Consensus size: 45
55630240 TGTAACCCGC
* *
55630250 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
* * * *
55630296 CCATGAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTAGCAT
* *** * * * *
55630342 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
*
55630389 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
55630425 ATGCCCAAAT
Statistics
Matches: 102, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 67 0.66
47 32 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTAGCAT
Found at i:55630369 original size:93 final size:93
Alignment explanation
Indices: 55630257--55630429 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
55630247 CGCCCATAAG
* * * *
55630257 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
55630322 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * *
55630350 CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
55630415 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
55630430 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:55630444 original size:46 final size:46
Alignment explanation
Indices: 55630301--55630444 Score: 111
Period size: 46 Copynumber: 3.1 Consensus size: 46
55630291 CGCATCCATG
* * * *
55630301 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TATATC-CT
* * *
55630350 --CGAACTCGGACTCAACTCAACGAGTTC--A-G-ACATTTGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATAT--ATCC-T
*
55630393 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCT
55630440 AGTGA
1 AGTGA
55630445 CATGTCACTT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 5 0.07
44 1 0.01
45 1 0.01
46 31 0.42
47 25 0.34
48 5 0.07
49 1 0.01
50 3 0.04
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATATCCT
Found at i:55642197 original size:21 final size:22
Alignment explanation
Indices: 55642173--55642221 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 22
55642163 GATAAACGGT
55642173 CACATAATTGCAGA-AAACTAC
1 CACATAATTGCAGATAAACTAC
*
55642194 CACATAATTGCAGATAAACTGC
1 CACATAATTGCAGATAAACTAC
55642216 CACATA
1 CACATA
55642222 TCTTCCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (22 bp):
CACATAATTGCAGATAAACTAC
Found at i:55642218 original size:22 final size:22
Alignment explanation
Indices: 55642153--55642221 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
55642143 CAAGCCACCT
* *
55642153 CATAATTGTC-GATAAACGGTCA
1 CATAATTG-CAGATAAACTGCCA
*
55642175 CATAATTGCAGA-AAACTACCA
1 CATAATTGCAGATAAACTGCCA
55642196 CATAATTGCAGATAAACTGCCA
1 CATAATTGCAGATAAACTGCCA
55642218 CATA
1 CATA
55642222 TCTTCCTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (22 bp):
CATAATTGCAGATAAACTGCCA
Found at i:55642459 original size:17 final size:15
Alignment explanation
Indices: 55642424--55642483 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
55642414 ATGAGATCTA
55642424 CACATATATCAATAT
1 CACATATATCAATAT
*
55642439 CACATATATGCAATTT
1 CACATATAT-CAATAT
* *
55642455 GCACAAAAATCACA-AT
1 -CACATATATCA-ATAT
55642471 CACATAATATCAA
1 CACAT-ATATCAA
55642484 CATATCACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 14 0.40
16 13 0.37
17 8 0.23
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.27
Consensus pattern (15 bp):
CACATATATCAATAT
Found at i:55646962 original size:43 final size:43
Alignment explanation
Indices: 55646801--55646959 Score: 185
Period size: 43 Copynumber: 3.7 Consensus size: 43
55646791 GATTAATGAG
* * *
55646801 ATGTGATTATGTGTAAGACCATGTCTGGGACATTGGAATCATT
1 ATGTGATTACGTGTAAGACCATATCTGGGACATTGGCATCATT
* * *
55646844 ATATGATTACGTGTAAGACCATGTCTAGGACATTGGCATCATT
1 ATGTGATTACGTGTAAGACCATATCTGGGACATTGGCATCATT
* * * **
55646887 A-GTTGATTTCGTGTAAGACCATAGCTGGGATATTGGCATCGGT
1 ATG-TGATTACGTGTAAGACCATATCTGGGACATTGGCATCATT
* *
55646930 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTACGTGTAAGACCATATCTGGGA
55646960 TATGTCATTG
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
43 97 0.99
44 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATATCTGGGACATTGGCATCATT
Found at i:55650266 original size:40 final size:40
Alignment explanation
Indices: 55650244--55650446 Score: 352
Period size: 40 Copynumber: 5.1 Consensus size: 40
55650234 AGCCCGGATG
*
55650244 TAACAACCAGCACAAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
* *
55650284 TAGCAACCAGCATGAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
*
55650324 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGGAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
55650364 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
* *
55650404 TAACAACCAGCATGAATGCCTTCGGGACTTAACCCGGATA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
55650444 TAA
1 TAA
55650447 TCCTCAATTG
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 154 1.00
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (40 bp):
TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
Found at i:55654495 original size:11 final size:11
Alignment explanation
Indices: 55654469--55654522 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
55654459 TGTAAGTAAA
55654469 AAAAAACAATTC
1 AAAAAA-AATTC
55654481 -AAAAAAATTC
1 AAAAAAAATTC
55654491 AAAAAAAATTC
1 AAAAAAAATTC
55654502 AAAAAAAATTC
1 AAAAAAAATTC
*
55654513 AGAAAAAATT
1 AAAAAAAATT
55654523 TTTGAAACTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
10 5 0.12
11 35 0.88
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:55655100 original size:21 final size:21
Alignment explanation
Indices: 55655074--55655114 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55655064 GAGCAACGTG
* *
55655074 AAAGACCTCTTGAAGTAGTCA
1 AAAGACCTCCTCAAGTAGTCA
55655095 AAAGACCTCCTCAAGTAGTC
1 AAAGACCTCCTCAAGTAGTC
55655115 CAACCTAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAGACCTCCTCAAGTAGTCA
Found at i:55655770 original size:10 final size:11
Alignment explanation
Indices: 55655747--55655795 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
55655737 TTGTAAGTAA
55655747 AAAAAACAATTC
1 AAAAAA-AATTC
55655759 AAAAAAAA-TC
1 AAAAAAAATTC
55655769 AAAAAAAATTC
1 AAAAAAAATTC
55655780 AAAAAAAATTC
1 AAAAAAAATTC
55655791 AAAAA
1 AAAAA
55655796 TTTTTTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.28
11 20 0.56
12 6 0.17
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:55655772 original size:21 final size:22
Alignment explanation
Indices: 55655747--55655795 Score: 82
Period size: 21 Copynumber: 2.2 Consensus size: 22
55655737 TTGTAAGTAA
55655747 AAAAAACAATTCAAAAAAAA-TC
1 AAAAAA-AATTCAAAAAAAATTC
55655769 AAAAAAAATTCAAAAAAAATTC
1 AAAAAAAATTCAAAAAAAATTC
55655791 AAAAA
1 AAAAA
55655796 TTTTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAAAAATTCAAAAAAAATTC
Found at i:55656378 original size:21 final size:21
Alignment explanation
Indices: 55656352--55656392 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
55656342 GAGCAACGTG
* *
55656352 AAAGACCTCTTGAAGTAGTCA
1 AAAGACCTCCTCAAGTAGTCA
55656373 AAAGACCTCCTCAAGTAGTC
1 AAAGACCTCCTCAAGTAGTC
55656393 CAACCTAGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAGACCTCCTCAAGTAGTCA
Found at i:55657944 original size:16 final size:17
Alignment explanation
Indices: 55657925--55657961 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
55657915 AGAAGATTGT
*
55657925 AAAAAAATAA-AAGAAG
1 AAAAAAATAAGAAAAAG
55657941 AAAAAAATAAGAAAAAG
1 AAAAAAATAAGAAAAAG
55657958 AAAA
1 AAAA
55657962 CAAAAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (17 bp):
AAAAAAATAAGAAAAAG
Found at i:55670478 original size:33 final size:33
Alignment explanation
Indices: 55670436--55670501 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
55670426 TAAGTGTTTG
55670436 AAAATTTTTATATGTGATCGGTTTAGTCCCGAC
1 AAAATTTTTATATGTGATCGGTTTAGTCCCGAC
55670469 AAAATTTTTATATGTGATCGGTTTAGTCCCGAC
1 AAAATTTTTATATGTGATCGGTTTAGTCCCGAC
55670502 CCCTTTCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (33 bp):
AAAATTTTTATATGTGATCGGTTTAGTCCCGAC
Found at i:55673314 original size:23 final size:21
Alignment explanation
Indices: 55673267--55673307 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55673257 ATAATTGATT
55673267 TAAATTTTTATGATATAAAAA
1 TAAATTTTTATGATATAAAAA
*
55673288 TAAATATTTTAT-ATTTAAAA
1 TAAAT-TTTTATGATATAAAA
55673308 TAGTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATTTTTATGATATAAAAA
Found at i:55676795 original size:26 final size:25
Alignment explanation
Indices: 55676760--55676883 Score: 64
Period size: 26 Copynumber: 5.1 Consensus size: 25
55676750 AATTTTAAAG
*
55676760 TAAATAAAACGGTTTAAAATAAATAA
1 TAAATGAAAC-GTTTAAAATAAATAA
***
55676786 TAAATGAAACAACTATAAATAAATAA
1 TAAATGAAACGTTTA-AAATAAATAA
* * *
55676812 TACAAAGAAACAGTTTCAAATGAATAA
1 TA-AATGAAAC-GTTTAAAATAAATAA
** *
55676839 TGTATAAAAC--TTAAAATAAAT-A
1 TAAATGAAACGTTTAAAATAAATAA
*
55676861 -AAA--AAA-GCTTAAAATAAATAA
1 TAAATGAAACGTTTAAAATAAATAA
55676882 TA
1 TA
55676884 TAAAAAATTA
Statistics
Matches: 73, Mismatches: 18, Indels: 18
0.67 0.17 0.17
Matches are distributed among these distances:
19 3 0.04
20 11 0.15
21 2 0.03
22 2 0.03
23 9 0.12
25 2 0.03
26 26 0.36
27 17 0.23
28 1 0.01
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (25 bp):
TAAATGAAACGTTTAAAATAAATAA
Found at i:55676832 original size:27 final size:25
Alignment explanation
Indices: 55676766--55676839 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
55676756 AAAGTAAATA
* *
55676766 AAACGGTTTAAAATAAATAATAAATG
1 AAACAGTTT-AAATAAATAATAAAAG
* *
55676792 AAACAACTATAAATAAATAATACAAAG
1 AAAC-AGTTTAAATAAATAATA-AAAG
*
55676819 AAACAGTTTCAAATGAATAAT
1 AAACAGTTT-AAATAAATAAT
55676840 GTATAAAACT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.24
Consensus pattern (25 bp):
AAACAGTTTAAATAAATAATAAAAG
Found at i:55676873 original size:20 final size:19
Alignment explanation
Indices: 55676844--55676881 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
55676834 AATAATGTAT
55676844 AAAACTTAAAATAAATAAA
1 AAAACTTAAAATAAATAAA
55676863 AAAAGCTTAAAATAAATAA
1 AAAA-CTTAAAATAAATAA
55676882 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAACTTAAAATAAATAAA
Found at i:55676928 original size:26 final size:24
Alignment explanation
Indices: 55676852--55676928 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
55676842 ATAAAACTTA
* * *
55676852 AAATAAATAAAAAAAGCTTAAAAT
1 AAATAAATATAAAAAGATTAAATT
55676876 AAAT-AATATAAAAA-ATTAAACTT
1 AAATAAATATAAAAAGATTAAA-TT
*
55676899 -AATAACATATAAAACAGTTTAAATT
1 AAATAA-ATATAAAA-AGATTAAATT
55676924 AAATA
1 AAATA
55676929 CTTTATATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 8 0.19
23 11 0.26
24 12 0.28
25 3 0.07
26 9 0.21
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (24 bp):
AAATAAATATAAAAAGATTAAATT
Found at i:55677014 original size:28 final size:26
Alignment explanation
Indices: 55676952--55677209 Score: 105
Period size: 28 Copynumber: 9.5 Consensus size: 26
55676942 TTTTGAATAG
*
55676952 ATAATATATGAAAATAATTTAAAATAA
1 ATAATATAT-AAAATAATTTAAAACAA
* *
55676979 AGAGTATATAAAATATATTTTAAAACAA
1 ATAATATATAAAATA-A-TTTAAAACAA
* * * *
55677007 ATAATATATAGAA-AGTTCAAAATAA
1 ATAATATATAAAATAATTTAAAACAA
* **
55677032 ATAATA-ATAAAA-AGGAGTTTAGAATGA
1 ATAATATATAAAATA--A-TTTAAAACAA
* * *
55677059 TTAATGTATAAAATAA--TATAACTAA
1 ATAATATATAAAATAATTTAAAAC-AA
* * * *
55677084 ATAACATAAAAAATAACTTTTAAAATAG
1 ATAATATATAAAATAA--TTTAAAACAA
* *
55677112 ATAATATATATATAATAGTTTAAAATAA
1 ATAATATATA-A-AATAATTTAAAACAA
* * * *
55677140 AAAAGGTATCTAAAA-ATTTTCAAAATAA
1 ATAA--TATATAAAATAATTT-AAAACAA
* *
55677168 ATAATATATATAATAGTTTAAAACAA
1 ATAATATATAAAATAATTTAAAACAA
55677194 ATAATGTATATAAAAT
1 ATAA--TATATAAAAT
55677210 CTAAAATGAA
Statistics
Matches: 172, Mismatches: 39, Indels: 39
0.69 0.16 0.16
Matches are distributed among these distances:
24 10 0.06
25 27 0.16
26 23 0.13
27 29 0.17
28 67 0.39
29 7 0.04
30 9 0.05
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (26 bp):
ATAATATATAAAATAATTTAAAACAA
Found at i:55677195 original size:26 final size:26
Alignment explanation
Indices: 55676869--55677224 Score: 111
Period size: 26 Copynumber: 13.6 Consensus size: 26
55676859 TAAAAAAAGC
*
55676869 TTAAAATAAATAATATA-A-AA-A-A
1 TTAAAATAAATAATATATATAATAGT
* * * * *
55676891 TTAAACTTAATAACATATAAAACAGT
1 TTAAAATAAATAATATATATAATAGT
* * * *
55676917 TTAAATTAAATACTTTATATGAA-AAT
1 TTAAAATAAATAATATATAT-AATAGT
** * * *
55676943 TTTGAATAGATAATATATGAAAATAAT
1 TTAAAATAAATAATATAT-ATAATAGT
* * * *
55676970 TTAAAATAAAGAGTATATAAAATATATT
1 TTAAAATAAATAATATAT-ATA-ATAGT
* *
55676998 TTAAAACAAATAATATATAGAA-AGT
1 TTAAAATAAATAATATATATAATAGT
* * *
55677023 TCAAAATAAATAATA-ATAAAAAGGAGT
1 TTAAAATAAATAATATAT-ATAA-TAGT
* * * * * *
55677050 TTAGAATGATTAATGTATAAAATAAT
1 TTAAAATAAATAATATATATAATAGT
* * * * * *
55677076 AT-AACTAAATAACATAAAAAATAACTT
1 TTAAAATAAATAATATATATAAT-A-GT
*
55677103 TTAAAATAGATAATATATATATAATAGT
1 TTAAAATAAAT-A-ATATATATAATAGT
* * * *
55677131 TTAAAATAAAAAAGGTATCTA-AAAATT
1 TTAAAATAAATAA--TATATATAATAGT
55677158 TTCAAAATAAATAATATATATAATAGT
1 TT-AAAATAAATAATATATATAATAGT
* * *
55677185 TTAAAACAAATAATGTATATAA-AAT
1 TTAAAATAAATAATATATATAATAGT
* *
55677210 CTAAAATGAATAATA
1 TTAAAATAAATAATA
55677225 ATTTAAAACA
Statistics
Matches: 241, Mismatches: 72, Indels: 39
0.68 0.20 0.11
Matches are distributed among these distances:
22 14 0.06
23 1 0.00
24 4 0.02
25 45 0.19
26 59 0.24
27 56 0.23
28 52 0.22
29 2 0.01
30 8 0.03
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.33
Consensus pattern (26 bp):
TTAAAATAAATAATATATATAATAGT
Found at i:55677225 original size:54 final size:55
Alignment explanation
Indices: 55677104--55677226 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 55
55677094 AAATAACTTT
* * *
55677104 TAAAATAGATAAT-ATATATATAATAGTTTAAAATAAAAAAGGTATCTAAAAATTT
1 TAAAATA-ATAATAATATATATAATAGTTTAAAACAAAAAAGGTATATAAAAATTC
* *
55677159 TCAAAAT-A-AATAATATATATAATAGTTTAAAACAAATAATGTATAT-AAAA-TC
1 T-AAAATAATAATAATATATATAATAGTTTAAAACAAAAAAGGTATATAAAAATTC
55677211 TAAAATGAATAATAAT
1 TAAAAT-AATAATAAT
55677227 TTAAAACACA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
51 5 0.09
52 2 0.03
53 8 0.14
54 37 0.64
55 1 0.02
56 5 0.09
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (55 bp):
TAAAATAATAATAATATATATAATAGTTTAAAACAAAAAAGGTATATAAAAATTC
Found at i:55677266 original size:44 final size:42
Alignment explanation
Indices: 55677177--55677270 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 42
55677167 AATAATATAT
* * * * *
55677177 ATAATAGTTTAAAACAAATAATGTATATAAAATCTAAAATGA
1 ATAATAATTTAAAACAAATAATGTAAAAAAAAACTAAAATAA
* *
55677219 ATAATAATTTAAAACACATAGCATGTAAAAAAAAACTAAATTAA
1 ATAATAATTTAAAACAAATA--ATGTAAAAAAAAACTAAAATAA
55677263 ATAATAAT
1 ATAATAAT
55677271 AAAATGATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 18 0.42
44 25 0.58
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (42 bp):
ATAATAATTTAAAACAAATAATGTAAAAAAAAACTAAAATAA
Found at i:55678325 original size:14 final size:13
Alignment explanation
Indices: 55678306--55678361 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 13
55678296 TTACAACTCA
55678306 TTTGTTTTCTTCTT
1 TTTGTTTT-TTCTT
55678320 TTTGTTTTTT-TGT
1 TTTGTTTTTTCT-T
55678333 TGTTGTTTTTTCCTT
1 T-TTGTTTTTT-CTT
55678348 TGTTGTTTGTTTCT
1 T-TTGTTT-TTTCT
55678362 GTGTTGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 17 0.46
15 11 0.30
16 4 0.11
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (13 bp):
TTTGTTTTTTCTT
Found at i:55678342 original size:15 final size:15
Alignment explanation
Indices: 55678307--55678370 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 15
55678297 TACAACTCAT
55678307 TTGTTTTCTTCT-TT-
1 TTGTTTT-TTCTGTTG
55678321 TTGTTTTTT-TGTTG
1 TTGTTTTTTCTGTTG
55678335 TTGTTTTTTCCT-TTG
1 TTGTTTTTT-CTGTTG
55678350 TTGTTTGTTTCTG-TG
1 TTGTTT-TTTCTGTTG
55678365 TTGTTT
1 TTGTTT
55678371 GTACTGCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.02
13 4 0.09
14 16 0.36
15 19 0.43
16 4 0.09
ACGTcount: A:0.00, C:0.08, G:0.17, T:0.75
Consensus pattern (15 bp):
TTGTTTTTTCTGTTG
Found at i:55678738 original size:48 final size:48
Alignment explanation
Indices: 55678667--55678764 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
55678657 TGGATTTCAC
** *
55678667 AATAATTATGATTAATTGTGTAAACAAGATACTTAATGCTTGTCAGGT
1 AATAATTATGATTAATTACGTAAACAAGATACTTAATGCTTGTAAGGT
* *
55678715 AATAATTATGATTAATTACGTAAACGAGATATTTAATGCTTGTAAGGT
1 AATAATTATGATTAATTACGTAAACAAGATACTTAATGCTTGTAAGGT
55678763 AA
1 AA
55678765 ATAAATTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (48 bp):
AATAATTATGATTAATTACGTAAACAAGATACTTAATGCTTGTAAGGT
Found at i:55682741 original size:49 final size:49
Alignment explanation
Indices: 55682669--55682841 Score: 211
Period size: 49 Copynumber: 3.5 Consensus size: 49
55682659 CAGGTCACGT
*
55682669 TGTAGTACTAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCATG
* * * * * * *
55682718 TGTAGTACTAAGTGTAAGCTACTATGCGTACCCGATAACTTTGATCACGTG
1 TGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAA--TTGGTCGCATG
* * *
55682769 TGTAGTACTAAGTGCAGGCTGCTACGTGTACTGGATAATTGGTCGCATG
1 TGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCATG
* *
55682818 TGTAGTACTAAGTGTAGGCTACTA
1 TGTAGTACTAAGTGCAAGCTACTA
55682842 TGCGTACCAG
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 63 0.62
51 39 0.38
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (49 bp):
TGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCATG
Found at i:55682842 original size:100 final size:99
Alignment explanation
Indices: 55682663--55682860 Score: 324
Period size: 100 Copynumber: 2.0 Consensus size: 99
55682653 TATTGTCAGG
55682663 TCACGTTGTAGTACTAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTA
1 TCACGTTGTAGTACTAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTA
*
55682728 AGTGTAAGCTACTATGCGTACCCGATAACTTTGA
66 AGTGTAAGCTACTATGCGTACCAGATAACTTTGA
* * * *
55682762 TCACGTGTGTAGTACTAAGTGCAGGCTGCTACGTGTACTGGATAATTGGTCGCATGTGTAGTACT
1 TCACGT-TGTAGTACTAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACT
* *
55682827 AAGTGTAGGCTACTATGCGTACCAGATAGCTTTG
65 AAGTGTAAGCTACTATGCGTACCAGATAACTTTG
55682861 GCTACAAGTG
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 6 0.07
100 85 0.93
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (99 bp):
TCACGTTGTAGTACTAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTA
AGTGTAAGCTACTATGCGTACCAGATAACTTTGA
Found at i:55682884 original size:100 final size:100
Alignment explanation
Indices: 55682677--55682887 Score: 282
Period size: 100 Copynumber: 2.1 Consensus size: 100
55682667 GTTGTAGTAC
*
55682677 TAAGTGCAAGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGTAAGCTACTA
1 TAAGTGCAGGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGTAAGCTACTA
* * * *
55682742 TGCGTACCCGATAACTTTGATCACGTGTGTAGTAC
66 TGCGTACCAGATAACTTTGATCAAGTGTGTAGAAA
* * * *
55682777 TAAGTGCAGGCTGCTACGTGTACTGGATAATTGGTCGCATGTGTAGTACTAAGTGTAGGCTACTA
1 TAAGTGCAGGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGTAAGCTACTA
* *
55682842 TGCGTACCAGATAGCTTTGGCTACAAGTGTG-A-AAA
66 TGCGTACCAGATAACTTT-GAT-CAAGTGTGTAGAAA
*
55682877 TATGTGCAGGC
1 TAAGTGCAGGC
55682888 AACTGAGTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
100 87 0.90
101 3 0.03
102 7 0.07
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (100 bp):
TAAGTGCAGGCTACTACATGTACCGGATAATTGGTCGCATGTGTAGTACTAAGTGTAAGCTACTA
TGCGTACCAGATAACTTTGATCAAGTGTGTAGAAA
Found at i:55691861 original size:27 final size:27
Alignment explanation
Indices: 55691830--55691949 Score: 150
Period size: 27 Copynumber: 4.4 Consensus size: 27
55691820 TGGATAAGTT
55691830 GTAGAATTACCAAAATACCCCTGTAGG
1 GTAGAATTACCAAAATACCCCTGTAGG
* * *
55691857 ATAGAATTACCTAAATACCCTTGTAGG
1 GTAGAATTACCAAAATACCCCTGTAGG
* *
55691884 GTAGAAATACCAAAATACCCCTGTAAG
1 GTAGAATTACCAAAATACCCCTGTAGG
* * * *
55691911 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCAAAATACCCCTGTAGG
*
55691938 GTAAAATTACCA
1 GTAGAATTACCA
55691950 TTTTGCCCCT
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCAAAATACCCCTGTAGG
Found at i:55691960 original size:54 final size:54
Alignment explanation
Indices: 55691830--55691949 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
55691820 TGGATAAGTT
* *
55691830 GTAGAATTACCAAAATACCCCTGTAGGATAGAATTACCTAAATACCCTTGTAGG
1 GTAGAAATACCAAAATACCCCTGTAGGATAGAATTACCGAAATACCCTTGTAGG
* *
55691884 GTAGAAATACCAAAATACCCCTGTAAGG-TAGAATTACCGAGATACCCTTGTGGG
1 GTAGAAATACCAAAATACCCCTGT-AGGATAGAATTACCGAAATACCCTTGTAGG
55691938 GTA-AAATTACCA
1 GTAGAAA-TACCA
55691950 TTTTGCCCCT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
53 3 0.05
54 54 0.90
55 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (54 bp):
GTAGAAATACCAAAATACCCCTGTAGGATAGAATTACCGAAATACCCTTGTAGG
Found at i:55696969 original size:25 final size:26
Alignment explanation
Indices: 55696898--55696994 Score: 144
Period size: 26 Copynumber: 3.8 Consensus size: 26
55696888 GAGGAAGTGC
55696898 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
55696924 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
55696950 AAAAGGGCTT-TGCCCTAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
55696975 AAAAGGGCTT-TGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
55696995 ATTAAAGAGG
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
25 32 0.47
26 36 0.53
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:55696978 original size:51 final size:51
Alignment explanation
Indices: 55696898--55696994 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
55696888 GAGGAAGTGC
**
55696898 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTT-TGCCCCAGTTTATTG
* *
55696950 AAAAGGGCTT-TGCCCTAGTTTACCGAAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTT
55696995 ATTAAAGAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 9 0.22
51 22 0.54
52 10 0.24
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.30
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATTG
Found at i:55699287 original size:50 final size:50
Alignment explanation
Indices: 55699222--55699457 Score: 190
Period size: 50 Copynumber: 4.7 Consensus size: 50
55699212 ACTGAAGCTC
* * *
55699222 TCTGGTGCGCATAGTAGCCTGCACTTAGTACTGCACATGCGAAATATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGAAATATCAA
* * ** * ** * *
55699272 TCTGGTACACGTAGTAGCCTGCACTTAGTACGACACGCGTGACTTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGAAATATCAA
* * * *
55699322 TCTGATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATCGAAGT-T-AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACA--TG--CGAAATATCAA
* ** * * * **
55699374 -CAGGTATGCATAGTAGCCTGCACTTAATACTAAACATACGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGAAATATCAA
*
55699423 TCTGGTACACATAGTAGCCTGCACTTAGTATTACA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACA
55699458 GACGTGACTC
Statistics
Matches: 140, Mismatches: 39, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
47 4 0.03
48 1 0.01
49 3 0.02
50 99 0.71
51 28 0.20
52 2 0.01
54 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGAAATATCAA
Done.