Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 161 of 344
Found at i:53736639 original size:26 final size:26
Alignment explanation
Indices: 53736610--53736717 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
53736600 TGGTGCAAAT
53736610 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
53736636 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53736662 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
53736688 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53736714 TGAT
1 TGAT
53736718 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:53741414 original size:18 final size:19
Alignment explanation
Indices: 53741391--53741426 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53741381 TAAACTTGGC
*
53741391 AACATAA-TCATTTAATTT
1 AACATAATTCAATTAATTT
53741409 AACATAATTCAATTAATT
1 AACATAATTCAATTAATT
53741427 CACTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AACATAATTCAATTAATTT
Found at i:53741758 original size:30 final size:30
Alignment explanation
Indices: 53741724--53741784 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53741714 TCCTTAACTC
53741724 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
53741754 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
53741784 A
1 A
53741785 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:53745184 original size:26 final size:26
Alignment explanation
Indices: 53745155--53745262 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
53745145 TGGTACAAAT
*
53745155 TGATAATGGGTTCGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
53745181 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53745207 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
53745233 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
53745259 TGAT
1 TGAT
53745263 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:53757856 original size:22 final size:21
Alignment explanation
Indices: 53757831--53757890 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
53757821 TTTGAGTATT
53757831 GTGATTTATGCTTGAATGTTA
1 GTGATTTATGCTTGAATGTTA
* *
53757852 CGTGA-TTAT--ATGAGTGTT-
1 -GTGATTTATGCTTGAATGTTA
*
53757870 GTGATATATGCTTGAATGTTA
1 GTGATTTATGCTTGAATGTTA
53757891 TGTAATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 9
0.67 0.12 0.21
Matches are distributed among these distances:
17 4 0.14
18 3 0.10
19 7 0.24
20 7 0.24
21 4 0.14
22 4 0.14
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (21 bp):
GTGATTTATGCTTGAATGTTA
Found at i:53757880 original size:39 final size:39
Alignment explanation
Indices: 53757823--53757960 Score: 213
Period size: 39 Copynumber: 3.5 Consensus size: 39
53757813 AACATATTTT
* *
53757823 TGAGTATTGTGATTTATGCTTGAATGTTACGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
53757862 TGAGTGTTGTGATATATGCTTGAATGTTATGTAATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
53757901 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
53757940 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
53757961 AAAAGTGAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 90 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:53759575 original size:39 final size:39
Alignment explanation
Indices: 53759521--53759598 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
53759511 AATGTTTTTA
* * *
53759521 AGTATTGTGATATATGCTTG-AATGTTATGTGGTTATATG
1 AGTATCGTCATATATGC-TGAAATGTTATGTGATTATATG
53759560 AGTATCGTCATATATGCTGAAATGTTATGTGATTATATG
1 AGTATCGTCATATATGCTGAAATGTTATGTGATTATATG
53759599 TGTAATGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 33 0.94
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (39 bp):
AGTATCGTCATATATGCTGAAATGTTATGTGATTATATG
Found at i:53763303 original size:42 final size:42
Alignment explanation
Indices: 53763235--53763352 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
53763225 TGTAATCTCG
* *
53763235 TATCGATGCCAATAGCCCATCA-ATGGTCTTACA-AGAAGTCCCA
1 TATCGATGCC-ATATCCCA-AATATGGTCTTACACA-AAGTCCCA
**
53763278 TATCGATGCCATATCCCAAATATGGTCTTACACAAAGTCTTA
1 TATCGATGCCATATCCCAAATATGGTCTTACACAAAGTCCCA
*
53763320 TA-CTGATGCCATATCCCAGATATGGTCTTACAC
1 TATC-GATGCCATATCCCAAATATGGTCTTACAC
53763353 GTAGTCTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
41 2 0.03
42 54 0.81
43 11 0.16
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (42 bp):
TATCGATGCCATATCCCAAATATGGTCTTACACAAAGTCCCA
Found at i:53772680 original size:29 final size:27
Alignment explanation
Indices: 53772645--53772709 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
53772635 ATCTTTATTG
53772645 AATATAAAATACTATAAAAACTACTAAA
1 AATATAAAATACTATAAAAACT-CTAAA
* *
53772673 AATCATAATTATACTATATAAACTCTAAA
1 AAT-ATAA-AATACTATAAAAACTCTAAA
53772702 AATATAAA
1 AATATAAA
53772710 TTATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 7 0.22
29 12 0.38
30 13 0.41
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (27 bp):
AATATAAAATACTATAAAAACTCTAAA
Found at i:53772711 original size:29 final size:30
Alignment explanation
Indices: 53772645--53772713 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
53772635 ATCTTTATTG
53772645 AATATAAA--ATACTATAAAAACTACTAAA
1 AATATAAATTATACTATAAAAACTACTAAA
*
53772673 AATCAT-AATTATACTATATAAACT-CTAAA
1 AAT-ATAAATTATACTATAAAAACTACTAAA
53772702 AATATAAATTAT
1 AATATAAATTAT
53772714 TATTAAATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 7 0.19
29 16 0.44
30 13 0.36
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (30 bp):
AATATAAATTATACTATAAAAACTACTAAA
Found at i:53774807 original size:43 final size:43
Alignment explanation
Indices: 53774754--53775103 Score: 610
Period size: 43 Copynumber: 8.1 Consensus size: 43
53774744 CCGGCATTAC
* *
53774754 GCCTGTTAGGCACGAAGGCCCGAATACACATCACCGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
53774797 GCCTACTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
53774840 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
53774883 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
53774926 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
53774969 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
53775012 GCTTGCTAGGCACGAAGGCCCAAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
53775055 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
53775098 GCCTGC
1 GCCTGC
53775104 GGGATTTAAC
Statistics
Matches: 291, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 291 1.00
ACGTcount: A:0.31, C:0.34, G:0.24, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:53790485 original size:15 final size:15
Alignment explanation
Indices: 53790465--53790493 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53790455 CTAAACAAAC
53790465 AAAATAATAATAATA
1 AAAATAATAATAATA
53790480 AAAATAATAATAAT
1 AAAATAATAATAAT
53790494 GATAACATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAATAATAATA
Found at i:53792303 original size:20 final size:18
Alignment explanation
Indices: 53792260--53792309 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
53792250 GTTCGTATGA
* *
53792260 TTATATATTGTTTTAATG
1 TTATATATTGATCTAATG
53792278 TTATATATTGATCTATATG
1 TTATATATTGATCTA-ATG
*
53792297 TTAATATGTTGAT
1 TT-ATATATTGAT
53792310 TGCTATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 13 0.48
19 5 0.19
20 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (18 bp):
TTATATATTGATCTAATG
Found at i:53794503 original size:13 final size:13
Alignment explanation
Indices: 53794485--53794510 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53794475 TATAGGGGAC
53794485 ACATGGCCATGTG
1 ACATGGCCATGTG
53794498 ACATGGCCATGTG
1 ACATGGCCATGTG
53794511 TCACACAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
ACATGGCCATGTG
Found at i:53794670 original size:20 final size:22
Alignment explanation
Indices: 53794633--53794673 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
53794623 CCCTTAACCA
53794633 AAGCATATAAACATACCAATTG
1 AAGCATATAAACATACCAATTG
53794655 AAGCATA-AAACA-ACCAATT
1 AAGCATATAAACATACCAATT
53794674 CAATGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.54, C:0.20, G:0.07, T:0.20
Consensus pattern (22 bp):
AAGCATATAAACATACCAATTG
Found at i:53795348 original size:13 final size:13
Alignment explanation
Indices: 53795332--53795357 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53795322 ATTTTTCTCT
53795332 TATAAGCATTTCA
1 TATAAGCATTTCA
53795345 TATAAGCATTTCA
1 TATAAGCATTTCA
53795358 CTCAAATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TATAAGCATTTCA
Found at i:53802302 original size:42 final size:41
Alignment explanation
Indices: 53802245--53802457 Score: 257
Period size: 42 Copynumber: 5.1 Consensus size: 41
53802235 AAGAGCACAA
53802245 TCACTTAAGCTCACATAGGGAGCTTCG-TCGATACATAGCTTG
1 TCACTTAAGCTCACAT-GGGAGCTTCGCT-GATACATAGCTTG
* * * *
53802287 TCACCTAAGGTCACATGGGGAGCTTCGCTGATACACAACTTG
1 TCACTTAAGCTCACAT-GGGAGCTTCGCTGATACATAGCTTG
* * *
53802329 TCACTTAAGCTCACGAGGGGAGCTTCACTGATACATAGCTTA
1 TCACTTAAGCTCAC-ATGGGAGCTTCGCTGATACATAGCTTG
* ** * *
53802371 TCACTTAAGCTCACATGGAGAGCTTTGCTGATACGCAACTTA
1 TCACTTAAGCTCACATGG-GAGCTTCGCTGATACATAGCTTG
53802413 TCACTTAAGCTCACATGGAGAGCTTCGCTGATACATAGCTTG
1 TCACTTAAGCTCACATGG-GAGCTTCGCTGATACATAGCTTG
53802455 TCA
1 TCA
53802458 AATCATTTCT
Statistics
Matches: 145, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
41 3 0.02
42 140 0.97
43 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACTTAAGCTCACATGGGAGCTTCGCTGATACATAGCTTG
Found at i:53802338 original size:84 final size:83
Alignment explanation
Indices: 53802244--53802457 Score: 304
Period size: 84 Copynumber: 2.5 Consensus size: 83
53802234 GAAGAGCACA
* *
53802244 ATCACTTAAGCTCACATAGGGAGCTTCG-TCGATACATAGCTTGTCACCTAAGGTCACATGGGGA
1 ATCACTTAAGCTCACAT-GGGAGCTTCGCT-GATACATAGCTTGTCACCTAAGCTCACATGGAGA
53802308 GCTTCGCTGATACACAACTT
64 GCTTCGCTGATACACAACTT
* * * * *
53802328 GTCACTTAAGCTCACGAGGGGAGCTTCACTGATACATAGCTTATCACTTAAGCTCACATGGAGAG
1 ATCACTTAAGCTCAC-ATGGGAGCTTCGCTGATACATAGCTTGTCACCTAAGCTCACATGGAGAG
* *
53802393 CTTTGCTGATACGCAACTT
65 CTTCGCTGATACACAACTT
53802412 ATCACTTAAGCTCACATGGAGAGCTTCGCTGATACATAGCTTGTCA
1 ATCACTTAAGCTCACATGG-GAGCTTCGCTGATACATAGCTTGTCA
53802458 AATCATTTCT
Statistics
Matches: 114, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
83 3 0.03
84 109 0.96
85 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (83 bp):
ATCACTTAAGCTCACATGGGAGCTTCGCTGATACATAGCTTGTCACCTAAGCTCACATGGAGAGC
TTCGCTGATACACAACTT
Found at i:53807327 original size:46 final size:46
Alignment explanation
Indices: 53807276--53807445 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 46
53807266 GATGGTTGAG
*
53807276 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAA
* * *
53807322 TATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAA--A
*
53807367 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCGAA
1 --CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAA
** * *
53807415 CGCCCGAGCTCATTGAGTTGAGTCCGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC
53807446 GCTTATGGGC
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 57 0.54
47 30 0.29
48 4 0.04
50 5 0.05
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAA
Found at i:53807434 original size:93 final size:93
Alignment explanation
Indices: 53807275--53807446 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
53807265 GGATGGTTGA
* * * *
53807275 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATATCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAACACCCGAACTCATTGAGT
53807340 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
53807368 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAACACCCGAACTCATTGAGT
53807433 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
53807447 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCAAACACCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53810733 original size:68 final size:67
Alignment explanation
Indices: 53810567--53810742 Score: 159
Period size: 68 Copynumber: 2.6 Consensus size: 67
53810557 TAGTACCACT
* * *
53810567 CATGCGACCTAGC--CA-ATTTGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTCATTCAC-T-GAAT
53810629 CACA
64 CACA
* * *
53810633 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATTC-C-GT
1 CATGCGACCTAGCTACATATATATCT--CGTAGCTCTCTTGTCTACATGGTG-T-CATTCACTGA
53810695 ATCACA
62 ATCACA
*
53810701 CATGTGACCTAGCTACTATATAGTATCTCGTAGC-CTTCTTGT
1 CATGCGACCTAGCTAC-ATATA-TATCTCGTAGCTC-TCTTGT
53810743 AAACATGATG
Statistics
Matches: 92, Mismatches: 8, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
66 13 0.14
67 1 0.01
68 36 0.39
69 9 0.10
70 5 0.05
71 24 0.26
72 4 0.04
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (67 bp):
CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTCATTCACTGAATCA
CA
Found at i:53815501 original size:75 final size:75
Alignment explanation
Indices: 53815412--53815561 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
53815402 GTAAAATTAG
** * *
53815412 TGAATTTTGGAAAATCCTTAGTTGGGGGAAGCTAAGGTAGTGGAGTAGGCAATTGGGACTGAGGC
1 TGAATTTTGGAAAATCCTTAGTTGGGCAAAGCTAAGGTAATGGAGTAGGCAATTGGGACTGAGCC
53815477 AATCTAAATT
66 AATCTAAATT
53815487 TGAATTTTGGAAAATCCTTAGTTGGGCAAAGCTAAGGTAATGGAGTAGGCAATTGGGACTGAGCC
1 TGAATTTTGGAAAATCCTTAGTTGGGCAAAGCTAAGGTAATGGAGTAGGCAATTGGGACTGAGCC
*
53815552 ACTCTAAATT
66 AATCTAAATT
53815562 CTTGTGTTCC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.28
Consensus pattern (75 bp):
TGAATTTTGGAAAATCCTTAGTTGGGCAAAGCTAAGGTAATGGAGTAGGCAATTGGGACTGAGCC
AATCTAAATT
Found at i:53821749 original size:136 final size:138
Alignment explanation
Indices: 53821498--53821760 Score: 386
Period size: 136 Copynumber: 1.9 Consensus size: 138
53821488 AGAGAACATA
* * * *
53821498 AATAAAATTAATATATGAATTCCTTTCATACAAAATATTATTTGTATATATTTTACCAGATTTAT
1 AATAAAATTAATATATGAATTCCATTAATACAAAATATTATATGTATATATTTTACCAAATTTAT
* * * * *
53821563 TAATATTAATAGTTATATTAATTAATGTCGGTAAAAATATAAATGACATGGAAATTAATATTCTT
66 TAATATAAACAATTATATTAATTAATGTCGGTAAAAATATAAAAGACATGGAAAATAATATTCTT
53821628 TTGTAAAG
131 TTGTAAAG
* **
53821636 AATATAATTAATATATGAATTTGATTAATACAAAATATTA-AT-TATATATTTTACCAAATTTAT
1 AATAAAATTAATATATGAATTCCATTAATACAAAATATTATATGTATATATTTTACCAAATTTAT
* *
53821699 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAAATAATATT
66 TAATATAAACAATTATATTAATTAATGTCGGTAAAAATATAAAAGACATGGAAAATAATATT
53821761 AATTTTATAT
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
136 75 0.68
137 1 0.01
138 35 0.32
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (138 bp):
AATAAAATTAATATATGAATTCCATTAATACAAAATATTATATGTATATATTTTACCAAATTTAT
TAATATAAACAATTATATTAATTAATGTCGGTAAAAATATAAAAGACATGGAAAATAATATTCTT
TTGTAAAG
Found at i:53821784 original size:88 final size:86
Alignment explanation
Indices: 53821669--53821848 Score: 261
Period size: 88 Copynumber: 2.1 Consensus size: 86
53821659 ATTAATACAA
*
53821669 AATATTAATTATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCGGTCAA
1 AATATTAATTATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCAGTCAA
*
53821734 AATATAAAAGACATGGAAAAT
66 AATATAAAAGACATAGAAAAT
* * * * *
53821755 AATATTAATTTTATATATTTTATCGAATTTATTAATATAAACAGTTATATTAATTAGTTTTAGTC
1 AATATTAA--TTATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCAGTC
* *
53821820 AAAATATACAAGACATAGAAATT
64 AAAATATAAAAGACATAGAAAAT
53821843 AATATT
1 AATATT
53821849 CTTTTGGAAA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 8 0.10
88 75 0.90
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (86 bp):
AATATTAATTATATATTTTACCAAATTTATTAATATAAACAATTATATTAATTAATTTCAGTCAA
AATATAAAAGACATAGAAAAT
Found at i:53822287 original size:9 final size:9
Alignment explanation
Indices: 53822275--53822310 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
53822265 AAAACAGAGG
53822275 AAACAAAGT
1 AAACAAAGT
53822284 AAACAAAGT
1 AAACAAAGT
*
53822293 AAACGAAGT
1 AAACAAAGT
53822302 AAACAAAGT
1 AAACAAAGT
53822311 TTTAAGCAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.64, C:0.11, G:0.14, T:0.11
Consensus pattern (9 bp):
AAACAAAGT
Found at i:53822769 original size:37 final size:37
Alignment explanation
Indices: 53822719--53822826 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
53822709 ACCTTTAGCT
* * *
53822719 CGGACGAAATCTCCACACGAAGTTATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
53822756 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
* * *
53822793 CGGACATACTCTCCACACGTAGTCATTGGGTCTT
1 CGGACAAAATCTCCACACGTAGTCATCGGGTCTT
53822827 TAGAGCTCGG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (37 bp):
CGGACAAAATCTCCACACGTAGTCATCGGGTCTTACC
Found at i:53823023 original size:47 final size:47
Alignment explanation
Indices: 53822945--53823431 Score: 821
Period size: 47 Copynumber: 10.3 Consensus size: 47
53822935 CCCTTCGGGA
* * ** * * *
53822945 CTTATCACATTTATACACTTTCACATCCATCATGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53822992 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53823039 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53823086 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53823133 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53823180 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53823227 CTTATCACATGTATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53823274 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53823321 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
53823368 CTTATCACATATATATACACTTTCACATTAATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53823417 CTTATCACATATATA
1 CTTATCACATATATA
53823432 TATCCACATA
Statistics
Matches: 418, Mismatches: 20, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
47 374 0.89
49 44 0.11
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53823508 original size:48 final size:48
Alignment explanation
Indices: 53823435--53823737 Score: 453
Period size: 48 Copynumber: 6.3 Consensus size: 48
53823425 ATATATATAT
* * *
53823435 CCACATATACATATCTCATACATATTTCACATTCGCCATTTGGCTTTA
1 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
** * *
53823483 CCACATATACATATAACACATATATTTCACATTAGCCATTCGACTTTA
1 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
53823531 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
1 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
*
53823579 CACACATATACATATCTCATATATATTTCACATTAGCCATTCGACTTTA
1 C-CACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
* * *
53823628 CCACATATACATATCTCATACATATTTCACATTCGCCATTCGGCTTCA
1 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
* * *
53823676 CCACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTCA
1 CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
* *
53823724 CCACACATATATAT
1 CCACATATACATAT
53823738 ATTTATCTTG
Statistics
Matches: 232, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
48 185 0.80
49 47 0.20
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (48 bp):
CCACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTA
Found at i:53823630 original size:145 final size:146
Alignment explanation
Indices: 53823436--53823739 Score: 466
Period size: 145 Copynumber: 2.1 Consensus size: 146
53823426 TATATATATC
* * *
53823436 CACATATACATATCTCATACATATTTCACATTCGCCATTTGGCTTTACCACATATACATATAACA
1 CACATATACATATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATACATATAACA
* * * *
53823501 CATATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTCATATATATTTCACATTAG
66 CACATATTTCACATTAGCCATTCGACTTCACCACATATACATATCACACATATATTTCACATTAG
*
53823566 CCATTCGGCTTTA-CA
131 CCATTCGGCTTCACCA
* **
53823581 CACATATACATATCTCATATATATTTCACATTAGCCATTCGACTTTACCACATATACATATCTCA
1 CACATATACATATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATACATATAACA
* * *
53823646 TACATATTTCACATTCGCCATTCGGCTTCACCACATATACATATCACACATATATTTCACATTAG
66 CACATATTTCACATTAGCCATTCGACTTCACCACATATACATATCACACATATATTTCACATTAG
53823711 CCATTCGGCTTCACCA
131 CCATTCGGCTTCACCA
*
53823727 CACATATATATAT
1 CACATATACATAT
53823740 TTATCTTGGA
Statistics
Matches: 143, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
145 129 0.90
146 14 0.10
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (146 bp):
CACATATACATATCTCATACATATTTCACATTAGCCATTCGACTTTACCACATATACATATAACA
CACATATTTCACATTAGCCATTCGACTTCACCACATATACATATCACACATATATTTCACATTAG
CCATTCGGCTTCACCA
Found at i:53829436 original size:39 final size:39
Alignment explanation
Indices: 53829400--53829650 Score: 268
Period size: 39 Copynumber: 6.4 Consensus size: 39
53829390 TTATCAGGAT
* * * **
53829400 TACCAAAGTACAATAAGGGCATGTAAGTGTGTTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* *
53829439 TACCGAAGTACAACAGGGGCACATAAGTGCATTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* *
53829478 TACCGAAGTACAATAGGGGCACGTAAGTGCATTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* * *
53829517 TACCAAAATACAACACGGGCATGTAAGTGCATTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* * * **
53829556 TACCGAAGCACAACTGGGGCACGTAAGTTTATTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* * * * * *
53829595 TATCGAAGTATAATAAGGGCACGTATGTGCATTCAGGGG
1 TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
* * *
53829634 TATCGAAGTGCAACAGG
1 TACCAAAGTACAACAGG
53829651 TTTCTACTAA
Statistics
Matches: 177, Mismatches: 35, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 177 1.00
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (39 bp):
TACCAAAGTACAACAGGGGCACGTAAGTGCATTCAGGGG
Found at i:53829455 original size:19 final size:19
Alignment explanation
Indices: 53829433--53829496 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
53829423 TAAGTGTGTT
53829433 CAGGGGTACCGAAGTACAA
1 CAGGGGTACCGAAGTACAA
* ** * *
53829452 CAGGGGCACATAAGTGCATT
1 CAGGGGTACCGAAGTACA-A
53829472 CAGGGGTACCGAAGTACAA
1 CAGGGGTACCGAAGTACAA
*
53829491 TAGGGG
1 CAGGGG
53829497 CACGTAAGTG
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.33, C:0.19, G:0.34, T:0.14
Consensus pattern (19 bp):
CAGGGGTACCGAAGTACAA
Found at i:53829477 original size:20 final size:20
Alignment explanation
Indices: 53829452--53829516 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
53829442 CGAAGTACAA
53829452 CAGGGGCACATAAGTGCATT
1 CAGGGGCACATAAGTGCATT
* ** * *
53829472 CAGGGGTACCGAAGTACAAT
1 CAGGGGCACATAAGTGCATT
*
53829492 -AGGGGCACGTAAGTGCATT
1 CAGGGGCACATAAGTGCATT
53829511 CAGGGG
1 CAGGGG
53829517 TACCAAAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.17
Consensus pattern (20 bp):
CAGGGGCACATAAGTGCATT
Found at i:53829505 original size:19 final size:19
Alignment explanation
Indices: 53829444--53829505 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
53829434 AGGGGTACCG
* *
53829444 AAGTACAACAGGGGCACAT
1 AAGTACAATAGGGGCACGT
* * *
53829463 AAGTGCATTCAGGGGTACCG-
1 AAGTACAAT-AGGGGCA-CGT
53829483 AAGTACAATAGGGGCACGT
1 AAGTACAATAGGGGCACGT
53829502 AAGT
1 AAGT
53829506 GCATTCAGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 13 0.41
21 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (19 bp):
AAGTACAATAGGGGCACGT
Found at i:53829513 original size:78 final size:78
Alignment explanation
Indices: 53829400--53829642 Score: 308
Period size: 78 Copynumber: 3.1 Consensus size: 78
53829390 TTATCAGGAT
* * * * * *
53829400 TACCAAAGTACAATAAGGGCATGTAAGTGTGTTCAGGGGTACCGAAGTACAACAGGGGCACATAA
1 TACCGAAGTACAATAGGGGCACGTAAGTGTATTCAGGGGTACCGAAGTACAACAAGGGCACGTAA
53829465 GTGCATTCAGGGG
66 GTGCATTCAGGGG
* * * * *
53829478 TACCGAAGTACAATAGGGGCACGTAAGTGCATTCAGGGGTACCAAAATACAACACGGGCATGTAA
1 TACCGAAGTACAATAGGGGCACGTAAGTGTATTCAGGGGTACCGAAGTACAACAAGGGCACGTAA
53829543 GTGCATTCAGGGG
66 GTGCATTCAGGGG
* * * * *
53829556 TACCGAAGCACAACT-GGGGCACGTAAGTTTATTCAGGGGTATCGAAGTATAATAAGGGCACGTA
1 TACCGAAGTACAA-TAGGGGCACGTAAGTGTATTCAGGGGTACCGAAGTACAACAAGGGCACGTA
*
53829620 TGTGCATTCAGGGG
65 AGTGCATTCAGGGG
*
53829634 TATCGAAGT
1 TACCGAAGT
53829643 GCAACAGGTT
Statistics
Matches: 141, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
78 140 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (78 bp):
TACCGAAGTACAATAGGGGCACGTAAGTGTATTCAGGGGTACCGAAGTACAACAAGGGCACGTAA
GTGCATTCAGGGG
Found at i:53829648 original size:117 final size:117
Alignment explanation
Indices: 53829400--53829635 Score: 346
Period size: 117 Copynumber: 2.0 Consensus size: 117
53829390 TTATCAGGAT
* * * ** *
53829400 TACCAAAGTACAATAAGGGCATGTAAGTGTGTTCAGGGGTACCGAAGTACAACAGGGGCACATAA
1 TACCAAAATACAACACGGGCATGTAAGTGCATTCAGGGGTACCGAAGCACAACAGGGGCACATAA
*
53829465 GTGCATTCAGGGGTACCGAAGTACAATAGGGGCACGTAAGTGCATTCAGGGG
66 GTGCATTCAGGGGTACCGAAGTACAATAAGGGCACGTAAGTGCATTCAGGGG
* *
53829517 TACCAAAATACAACACGGGCATGTAAGTGCATTCAGGGGTACCGAAGCACAACTGGGGCACGTAA
1 TACCAAAATACAACACGGGCATGTAAGTGCATTCAGGGGTACCGAAGCACAACAGGGGCACATAA
** * * *
53829582 GTTTATTCAGGGGTATCGAAGTATAATAAGGGCACGTATGTGCATTCAGGGG
66 GTGCATTCAGGGGTACCGAAGTACAATAAGGGCACGTAAGTGCATTCAGGGG
53829634 TA
1 TA
53829636 TCGAAGTGCA
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
117 105 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (117 bp):
TACCAAAATACAACACGGGCATGTAAGTGCATTCAGGGGTACCGAAGCACAACAGGGGCACATAA
GTGCATTCAGGGGTACCGAAGTACAATAAGGGCACGTAAGTGCATTCAGGGG
Found at i:53833589 original size:29 final size:29
Alignment explanation
Indices: 53833550--53833628 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
53833540 CTTAATAATC
*
53833550 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
53833580 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
53833609 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
53833629 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:53841578 original size:29 final size:29
Alignment explanation
Indices: 53841536--53841610 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
53841526 TATAGTGGGT
* *
53841536 TCGCACACATAGTGCCATGTACTTT-AAAC
1 TCGCACACTTAGTGCCATGCA-TTTCAAAC
*
53841565 TCGCACACTTAGTGCCATGCATTTCAAGC
1 TCGCACACTTAGTGCCATGCATTTCAAAC
*
53841594 CCGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
53841611 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.07
29 38 0.93
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATGCATTTCAAAC
Found at i:53856148 original size:30 final size:29
Alignment explanation
Indices: 53856105--53856168 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
53856095 CAAGTAGCCG
*
53856105 AAGCTAGTTAAATCACACACTTAGTGCTA
1 AAGCTAGTTAAATCACACACTTAGTGCCA
*
53856134 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAG-TTAAATCACACACTTAGTGCCA
53856164 AAGCT
1 AAGCT
53856169 TCCGATTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.22
30 25 0.78
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (29 bp):
AAGCTAGTTAAATCACACACTTAGTGCCA
Found at i:53862219 original size:20 final size:20
Alignment explanation
Indices: 53862183--53862222 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53862173 AAACTGAACC
*
53862183 TAACCAAAATTTTCAAAACT
1 TAACCAAAATTTCCAAAACT
53862203 TAACC-AAATCTTCCAAAACT
1 TAACCAAAAT-TTCCAAAACT
53862223 GTTCAAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (20 bp):
TAACCAAAATTTCCAAAACT
Found at i:53870160 original size:48 final size:48
Alignment explanation
Indices: 53870075--53870336 Score: 250
Period size: 48 Copynumber: 5.5 Consensus size: 48
53870065 ACATGTGGAC
* * * * * ** *
53870075 GCCATATCCCAGATATGGTCTTATACGAAGC-CTCATATCGGTGCCTAT
1 GCCATGTCCCAGACATGGTCTTACAC-TAGCACACATATCAATGCCGAT
* *
53870123 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATTGCTGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGAT
* * * *
53870171 GCCATGTCCTAGACATGGTCTTACACTGGCACACATATTAAAGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGAT
* **
53870219 GCCATGTCCCAGACATGGTCTTACACT-GACACATATATCAACACCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAG-CACACATATCAATGCCGAT
* * *
53870267 GCCATGTCCTAGACATGGTCTTACACT-GC-CTC-TCGTC--TCGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTAGCACACAT-ATCAAT-GCCGAT
*
53870312 GCCATGTCCTAGACATGGTCTTACA
1 GCCATGTCCCAGACATGGTCTTACA
53870337 TGGGATCTTA
Statistics
Matches: 184, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
45 31 0.17
46 3 0.02
47 5 0.03
48 145 0.79
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAATGCCGAT
Found at i:53870223 original size:96 final size:93
Alignment explanation
Indices: 53870121--53870336 Score: 281
Period size: 96 Copynumber: 2.3 Consensus size: 93
53870111 ATCGGTGCCT
*** *
53870121 ATGCCATGTCCCAGACATGGTCTTACACT-AGCACACATATCATTGCTGATGCCATGTCCTAGAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CACACATATCAACACCGATGCCATGTCCTAGAC
*
53870185 ATGGTCTTACACTGGCACACATATTAAAGCCG
65 ATGGTCTTACACT-GC-CAC-TAGTAAAGCCG
*
53870217 ATGCCATGTCCCAGACATGGTCTTACACTGACACATATATCAACACCGATGCCATGTCCTAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGACACACATATCAACACCGATGCCATGTCCTAGACA
* * ***
53870282 TGGTCTTACACTGCCTCTCGTCTCGCCG
66 TGGTCTTACACTGCCACTAGTAAAGCCG
*
53870310 ATGCCATGTCCTAGACATGGTCTTACA
1 ATGCCATGTCCCAGACATGGTCTTACA
53870337 TGGGATCTTA
Statistics
Matches: 107, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
93 32 0.30
94 2 0.02
95 2 0.02
96 70 0.65
97 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (93 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACACACATATCAACACCGATGCCATGTCCTAGACA
TGGTCTTACACTGCCACTAGTAAAGCCG
Found at i:53878845 original size:48 final size:48
Alignment explanation
Indices: 53878789--53878934 Score: 211
Period size: 48 Copynumber: 3.0 Consensus size: 48
53878779 CACGATGTCT
* * * * * *
53878789 CATATCGATGCAAATGTCATATCCCAAATATGGTCTTACATGGGATCA
1 CATATCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCA
* *
53878837 CATGTCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCT
1 CATATCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCA
*
53878885 CATAACGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCA
1 CATATCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCA
53878933 CA
1 CA
53878935 CATAACCTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (48 bp):
CATATCGATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCA
Found at i:53881768 original size:40 final size:40
Alignment explanation
Indices: 53881690--53881907 Score: 282
Period size: 40 Copynumber: 5.5 Consensus size: 40
53881680 AAACCAAGTA
* **
53881690 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTTAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
53881729 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
53881769 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
53881809 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
53881849 CCTTCAGGG-CTTAGCCTGGA-ATTAGTCACTAGCACAAATG
1 CCTTC-GGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
* *
53881889 CCTTTGGGACTCAGCCCGG
1 CCTTCGGGACTTAGCCCGG
53881908 TTATTCATGC
Statistics
Matches: 159, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 18 0.11
40 138 0.87
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:53889974 original size:40 final size:40
Alignment explanation
Indices: 53889897--53890114 Score: 318
Period size: 40 Copynumber: 5.5 Consensus size: 40
53889887 AAACCAAGTA
* *
53889897 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
53889936 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
53889976 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
53890016 CCTTCGGGAGTTAGTCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
53890056 CCTTCGCGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCG-GGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
53890096 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
53890115 TTATCATCTG
Statistics
Matches: 164, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.10
40 145 0.88
41 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:53892134 original size:44 final size:41
Alignment explanation
Indices: 53892066--53892230 Score: 123
Period size: 43 Copynumber: 3.9 Consensus size: 41
53892056 TTCCAATATG
* * **
53892066 TGATTTAGTGTAAGATCACATCTGGGACATTGGCATCGATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATT
* * * *
53892107 TGAGATTTACGTGTAAGGCTATGTCTGGGACATCGGCATCACATT
1 T--GATTT-CGTGTAAGACCATGTCTGGGACATTGGCATC-GATT
* * *
53892152 TGATTTCGTGTGAGACCCTGTCTGGGACAGTGGCATCGATATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCG--ATT
* * * * **
53892195 TGAGTACATGTAAGACCACGTCTGGGATGTTGGCAT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCAT
53892231 TATACGAGCT
Statistics
Matches: 94, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 1 0.01
42 25 0.27
43 40 0.43
44 24 0.26
45 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATT
Found at i:53892958 original size:23 final size:22
Alignment explanation
Indices: 53892927--53892972 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
53892917 TTATGAATCA
* *
53892927 TATGTTTTGTTATGATTTTGGTT
1 TATGATTTGGTATG-TTTTGGTT
53892950 TATGATTTGGTATGTTTTGGTT
1 TATGATTTGGTATGTTTTGGTT
53892972 T
1 T
53892973 GAATATAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.63
Consensus pattern (22 bp):
TATGATTTGGTATGTTTTGGTT
Found at i:53893586 original size:27 final size:27
Alignment explanation
Indices: 53893556--53893608 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
53893546 TTTAGTCTCG
53893556 ACCTCTTTCTAAAGCACA-TTTAAGGTA
1 ACCTCTTTCTAAAGCA-AGTTTAAGGTA
53893583 ACCTCTTTCTAAAGCAAGTTTAAGGT
1 ACCTCTTTCTAAAGCAAGTTTAAGGT
53893609 CTTGTTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (27 bp):
ACCTCTTTCTAAAGCAAGTTTAAGGTA
Found at i:53899834 original size:27 final size:27
Alignment explanation
Indices: 53899803--53899908 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
53899793 TTTTTTTTAA
53899803 GATTCTCCACAAAGGCTTTCATTTCAT
1 GATTCTCCACAAAGGCTTTCATTTCAT
** * *
53899830 GATTCTTTATAAAGGTTTTCATTTCAT
1 GATTCTCCACAAAGGCTTTCATTTCAT
* *
53899857 GATT-TGCCACAAAAGCTTTCATTTTAT
1 GATTCT-CCACAAAGGCTTTCATTTCAT
* *
53899884 GATTTTCCACAAAGGCTCTCATTTC
1 GATTCTCCACAAAGGCTTTCATTTC
53899909 CTTTCCTGAT
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.97
28 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (27 bp):
GATTCTCCACAAAGGCTTTCATTTCAT
Found at i:53912172 original size:42 final size:44
Alignment explanation
Indices: 53912093--53912198 Score: 110
Period size: 42 Copynumber: 2.5 Consensus size: 44
53912083 CATCGACTTA
* *** *
53912093 TGATTTACGTGTAAGACCATGTCTGGGATGTTAGCATC-GTATT
1 TGATTTACGTGTAAGACCATGCCTGGGACAATAGCATCAATATT
* *
53912136 TGATTT-CGTGTAAGACCCTGCCTGGGACAATGGCATCAATATT
1 TGATTTACGTGTAAGACCATGCCTGGGACAATAGCATCAATATT
* *
53912179 TGA-TTACATGTAACACCATG
1 TGATTTACGTGTAAGACCATG
53912199 TTTGGGACGT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
42 27 0.53
43 24 0.47
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (44 bp):
TGATTTACGTGTAAGACCATGCCTGGGACAATAGCATCAATATT
Found at i:53917480 original size:641 final size:641
Alignment explanation
Indices: 53916259--53917545 Score: 2421
Period size: 641 Copynumber: 2.0 Consensus size: 641
53916249 AAGTGTAGCA
* *
53916259 AATGTGAATTCTGGTTATAAGAAGTCGATTTTATAGGCCATATTGTGTCAGCATCAGGTATCCAA
1 AATGTGAATTCTGGTTATAAGAAGTCGATTTTATAGGCCATATGGTGTCAGCATCAGATATCCAA
*
53916324 GTTGGTCTGAGCAAAATTTTAGCTATTTTGGATTGGAAGCCTCTGAGAAATGTCTCCGAAGTCTG
66 GTTGATCTGAGCAAAATTTTAGCTATTTTGGATTGGAAGCCTCTGAGAAATGTCTCCGAAGTCTG
53916389 CAATTTTCTGGGACTTGCCGGTTATTATAGGAGTTTTGTAAAAGGCTTTTTAATGATCACGACTC
131 CAATTTTCTGGGACTTGCCGGTTATTATAGGAGTTTTGTAAAAGGCTTTTTAATGATCACGACTC
**
53916454 CATTGATGAAACTACTTTAGAAAGATGTGAAATTTGATTGGTTTAAAAAGTGTCAGAAAAGCTTT
196 CATTGACAAAACTACTTTAGAAAGATGTGAAATTTGATTGGTTTAAAAAGTGTCAGAAAAGCTTT
* *
53916519 GATCAGTTGAAAGCTCTATTGACTGAAGCCCTAGTGTTAGTACAACCAGAATAGGGTAAAGAATT
261 GATCAGTTGAAAGCTCTATTAACTGAAGCCCCAGTGTTAGTACAACCAGAATAGGGTAAAGAATT
53916584 TGTGATCTACAGTGATGCTTCATTAAACTGTCTAGGATGTGTTTTGATGCTAGAAGACAAAGTCA
326 TGTGATCTACAGTGATGCTTCATTAAACTGTCTAGGATGTGTTTTGATGCTAGAAGACAAAGTCA
53916649 TTGCTTATGTTTTGAGACAGTTAAAGCCACATGAAAAGAACTAGCCGACGCATAACCTTGAGTTA
391 TTGCTTATGTTTTGAGACAGTTAAAGCCACATGAAAAGAACTAGCCGACGCATAACCTTGAGTTA
*
53916714 GCTGGGATTGTATTTGCTTTGAAGATTTGGCGCCACTATTGTTTTGGAGAGAAATGTCTCGTATA
456 GCTGCGATTGTATTTGCTTTGAAGATTTGGCGCCACTATTGTTTTGGAGAGAAATGTCTCGTATA
53916779 TTCTGATCATAAGAGTTTGAAATATCTGATGACTCAGAAAGATCTGAATCTGTGACAAAGAAGAC
521 TTCTGATCATAAGAGTTTGAAATATCTGATGACTCAGAAAGATCTGAATCTGTGACAAAGAAGAC
53916844 GACTAGAGTTACTGAAAGACTATGAGCTTGTTATTGATTATCATCCAGGAAAAGCT
586 GACTAGAGTTACTGAAAGACTATGAGCTTGTTATTGATTATCATCCAGGAAAAGCT
*
53916900 AATGTGAATTCTGGTTATAAGAAGTCGGTTTTATAGGCCATATGGTGTCAGCATCAGATATCCAA
1 AATGTGAATTCTGGTTATAAGAAGTCGATTTTATAGGCCATATGGTGTCAGCATCAGATATCCAA
53916965 GTTGATCTGAGCAAAATTTTAGCTATTTTGGATTGGAAGCCTCTGAGAAATGTCTCCGAAGTCTG
66 GTTGATCTGAGCAAAATTTTAGCTATTTTGGATTGGAAGCCTCTGAGAAATGTCTCCGAAGTCTG
* *
53917030 CAATTTTCTGGGACTTGCCGGTTATTATAGGAGTTTTGTAAAAGGCTTTTTGATGATCACGATTC
131 CAATTTTCTGGGACTTGCCGGTTATTATAGGAGTTTTGTAAAAGGCTTTTTAATGATCACGACTC
53917095 CATTGACAAAACTACTTTAGAAAGATGTGAAATTTGATTGGTTTAAAAAGTGTCAGAAAAGCTTT
196 CATTGACAAAACTACTTTAGAAAGATGTGAAATTTGATTGGTTTAAAAAGTGTCAGAAAAGCTTT
53917160 GATCAGTTGAAAGCTCTATTAACTGAAGCCCCAGTGTTAGTACAACCAGAATAGGGTAAAGAATT
261 GATCAGTTGAAAGCTCTATTAACTGAAGCCCCAGTGTTAGTACAACCAGAATAGGGTAAAGAATT
*
53917225 TGTGATCTACAGTGATGCTTCATTAAACTGTCTAGGATGTGTTTTGATGCTGGAAGACAAAGTCA
326 TGTGATCTACAGTGATGCTTCATTAAACTGTCTAGGATGTGTTTTGATGCTAGAAGACAAAGTCA
* *
53917290 TTGCTTATGTTTTGAGATAGTTAAAGCCACATGAAAAGAACTAGCCGACGCATGACCTTGAGTTA
391 TTGCTTATGTTTTGAGACAGTTAAAGCCACATGAAAAGAACTAGCCGACGCATAACCTTGAGTTA
53917355 GCTGCGATTGTATTTGCTTTGAAGATTTGGCGCCACTATTGTTTTGGAGAGAAATGTCTCGTATA
456 GCTGCGATTGTATTTGCTTTGAAGATTTGGCGCCACTATTGTTTTGGAGAGAAATGTCTCGTATA
53917420 TTCTGATCATAAGAGTTTGAAATATCTGATGACTCAGAAAGATCTGAATCTGTGACAAAGAAGAC
521 TTCTGATCATAAGAGTTTGAAATATCTGATGACTCAGAAAGATCTGAATCTGTGACAAAGAAGAC
** *
53917485 GACTAGAGTTACTGAAAGACTATGAGCTTGTTATTGATTATCATCTGGGAAAGGCT
586 GACTAGAGTTACTGAAAGACTATGAGCTTGTTATTGATTATCATCCAGGAAAAGCT
53917541 AATGT
1 AATGT
53917546 TGTTGCTGAT
Statistics
Matches: 629, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
641 629 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (641 bp):
AATGTGAATTCTGGTTATAAGAAGTCGATTTTATAGGCCATATGGTGTCAGCATCAGATATCCAA
GTTGATCTGAGCAAAATTTTAGCTATTTTGGATTGGAAGCCTCTGAGAAATGTCTCCGAAGTCTG
CAATTTTCTGGGACTTGCCGGTTATTATAGGAGTTTTGTAAAAGGCTTTTTAATGATCACGACTC
CATTGACAAAACTACTTTAGAAAGATGTGAAATTTGATTGGTTTAAAAAGTGTCAGAAAAGCTTT
GATCAGTTGAAAGCTCTATTAACTGAAGCCCCAGTGTTAGTACAACCAGAATAGGGTAAAGAATT
TGTGATCTACAGTGATGCTTCATTAAACTGTCTAGGATGTGTTTTGATGCTAGAAGACAAAGTCA
TTGCTTATGTTTTGAGACAGTTAAAGCCACATGAAAAGAACTAGCCGACGCATAACCTTGAGTTA
GCTGCGATTGTATTTGCTTTGAAGATTTGGCGCCACTATTGTTTTGGAGAGAAATGTCTCGTATA
TTCTGATCATAAGAGTTTGAAATATCTGATGACTCAGAAAGATCTGAATCTGTGACAAAGAAGAC
GACTAGAGTTACTGAAAGACTATGAGCTTGTTATTGATTATCATCCAGGAAAAGCT
Found at i:53920524 original size:43 final size:42
Alignment explanation
Indices: 53920367--53920529 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 42
53920357 TATGTGTTCT
* * **
53920367 CGTGTATGACAACGTCTGGGACGTTGGCATTGCCTTATGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATTGTATT-TGA-TTA
* * *
53920411 CGTGTAAGACCACGTCTGGGACGTTGCCATCGTATTTGATTT
1 CGTGTAAGACCACGTCTGGGACGTTGGCATTGTATTTGATTA
*
53920453 CGTGTAAGACC-CTGTCTAGGACAG-TGGCATTGATATTTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATTG-TATTTGATTA
*
53920496 CATGTAAGACCACGTCTAGGG-CGTTGGCATTGTA
1 CGTGTAAGACCACGTCT-GGGACGTTGGCATTGTA
53920530 CGAGCTTTCC
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 36 0.36
44 33 0.33
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATTGTATTTGATTA
Found at i:53924883 original size:43 final size:43
Alignment explanation
Indices: 53924829--53924996 Score: 266
Period size: 43 Copynumber: 3.9 Consensus size: 43
53924819 GTTGGTATTA
*
53924829 TATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
1 TATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
*
53924872 TATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGTCGGTGATGTG
1 TATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
*
53924915 TATTCAGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
* * *
53924958 TATTC-GTGCCTTCGTGCCTAGTAGGCGTAATGCCGGTGA
1 TATTCAG-GCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGA
53924997 AATGATATGT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 1 0.01
43 115 0.99
ACGTcount: A:0.13, C:0.23, G:0.33, T:0.31
Consensus pattern (43 bp):
TATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTG
Found at i:53924930 original size:86 final size:84
Alignment explanation
Indices: 53924808--53924983 Score: 264
Period size: 86 Copynumber: 2.1 Consensus size: 84
53924798 GATAAATCCC
* *
53924808 GCAGGCCTAGTGTTGGTATTATATTCGGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTGT
1 GCAGGCCTAGTGTCGGTATTATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTGT
53924873 ATTCAG-GCCTTCGTGCCTA
66 ATTC-GTGCCTTCGTGCCTA
* * *
53924892 GCAGGCTTAGTGTCGGTGATGTGTATTCAGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGT
1 GCAGGCCTAGTGTCGGT-AT-TATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGT
53924957 GTATTCGTGCCTTCGTGCCTA
64 GTATTCGTGCCTTCGTGCCTA
*
53924978 GTAGGC
1 GCAGGC
53924984 GTAATGCCGG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
84 15 0.18
85 3 0.04
86 65 0.78
ACGTcount: A:0.13, C:0.23, G:0.32, T:0.32
Consensus pattern (84 bp):
GCAGGCCTAGTGTCGGTATTATATTCAGGCCTTCGTGCCTAGCAGGCTTAGTGCCGGTGATGTGT
ATTCGTGCCTTCGTGCCTA
Found at i:53925387 original size:45 final size:44
Alignment explanation
Indices: 53925313--53925439 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 44
53925303 TTGACTTGAT
* **
53925313 TATTCGGGCCTTTGAG-CTAAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCT-AGCAGGCTATAATGCCGGTGAGA-AC
53925358 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGT--GAAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
* *
53925400 TGATATCGGGCC-TCGAGCCTAACAGGCGA-AATGCCGGTGA
1 T-AT-TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
53925440 TTTGAGAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
42 12 0.17
43 19 0.26
44 7 0.10
45 32 0.44
46 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (44 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
Found at i:53930315 original size:38 final size:38
Alignment explanation
Indices: 53930251--53930330 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
53930241 GATGTGTATT
* * * *
53930251 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTAGTATTATATC
* *
53930289 CGGGATAAATCCCGCAGTCCTAGTGCTAGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTAGTATTATATC
53930327 CGGG
1 CGGG
53930331 CCTTCGGGCC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTAGTATTATATC
Found at i:53930390 original size:27 final size:27
Alignment explanation
Indices: 53930352--53930410 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
53930342 AGCAGGCTTA
53930352 GTGCCGGTGATGTGTATTCGAGCCTTC
1 GTGCCGGTGATGTGTATTCGAGCCTTC
*
53930379 GTGCCGGTGATGTGTATTCGGGCCTTC
1 GTGCCGGTGATGTGTATTCGAGCCTTC
53930406 GTGCC
1 GTGCC
53930411 TAGCAAGCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (27 bp):
GTGCCGGTGATGTGTATTCGAGCCTTC
Found at i:53930403 original size:70 final size:70
Alignment explanation
Indices: 53930323--53930453 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
53930313 GCTAGTATTA
*
53930323 TATTCGGGCCTTCGGGCCTAGCAGGCTTAGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCGGTG
1 TATTCGGGCCTTCGGGCCTAGCAAGCTTAGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCGGTG
53930388 ATGTG
66 ATGTG
* *
53930393 TATTCGGGCCTTCGTGCCTAGCAAGCTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCC
1 TATTCGGGCCTTCGGGCCTAGCAAGCTTAGTGCCGGTGATGTGTATTCGAGCCTTCGTGCC
53930454 TAGCAGGCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (70 bp):
TATTCGGGCCTTCGGGCCTAGCAAGCTTAGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCGGTG
ATGTG
Found at i:53930436 original size:43 final size:43
Alignment explanation
Indices: 53930375--53930458 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
53930365 GTATTCGAGC
*
53930375 CTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAG
1 CTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAAG
53930418 CTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCA
1 CTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCA
53930459 GGCGTAATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.12, C:0.26, G:0.31, T:0.31
Consensus pattern (43 bp):
CTTCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAAG
Found at i:53930470 original size:43 final size:43
Alignment explanation
Indices: 53930380--53930474 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
53930370 CGAGCCTTCG
* * **
53930380 TGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAAGCTTCG
1 TGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAAGCGTAA
*
53930423 TGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAGGCGTAA
1 TGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAAGCGTAA
53930466 TGCCGGTGA
1 TGCCGGTGA
53930475 AATGATATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (43 bp):
TGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAAGCGTAA
Found at i:53930858 original size:45 final size:42
Alignment explanation
Indices: 53930791--53930898 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 42
53930781 TTGACTTGAT
* *
53930791 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGT--GA-AC
***
53930836 TATTCGGGCCTTCGAGCCTAGCAGGTTATAATGCCGGTGAAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
53930878 TGATATCGGGCC-TCGAGCCTA
1 T-AT-TCGGGCCTTCGAGCCTA
53930899 ACAGGCGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.05
43 13 0.23
44 7 0.12
45 33 0.59
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (42 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
Found at i:53938078 original size:33 final size:32
Alignment explanation
Indices: 53938025--53938096 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 32
53938015 GGCCCTGCCG
**
53938025 TGGTCTTTCATTCACATGCCATAACCCGGTTA
1 TGGTCTTTCATTCACATGCCATAACCCGACTA
* *
53938057 TGGTCTTGTTATTCA-ATTGCCATAGCCCGACTA
1 TGGTCTT-TCATTCACA-TGCCATAACCCGACTA
53938090 TGGTCTT
1 TGGTCTT
53938097 ATTTGGCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (32 bp):
TGGTCTTTCATTCACATGCCATAACCCGACTA
Found at i:53946570 original size:21 final size:21
Alignment explanation
Indices: 53946546--53946588 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
53946536 ACAACATCAT
53946546 TCACACACTTGACATAATAAG
1 TCACACACTTGACATAATAAG
53946567 TCACACACTTGACATAATAAG
1 TCACACACTTGACATAATAAG
53946588 T
1 T
53946589 AATCATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (21 bp):
TCACACACTTGACATAATAAG
Found at i:53954252 original size:38 final size:38
Alignment explanation
Indices: 53954210--53954418 Score: 166
Period size: 38 Copynumber: 5.0 Consensus size: 38
53954200 TTTCAAATTA
*
53954210 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
*
53954248 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
53954289 GAATCGATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
53954333 ACATGTATCAATATGTGTAATCGTGGTATATCCACTTAGAACCACATT
1 ACATG------TA----TAACCGTGGTATATCCACTTAGCACCACGTT
* *
53954381 ACACGTTTAACCGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
53954419 TTTCCATTAC
Statistics
Matches: 139, Mismatches: 15, Indels: 34
0.74 0.08 0.18
Matches are distributed among these distances:
38 62 0.45
39 1 0.01
40 2 0.01
41 2 0.01
42 2 0.01
43 1 0.01
44 2 0.01
45 3 0.02
46 3 0.02
47 28 0.20
48 33 0.24
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (38 bp):
ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:53954371 original size:48 final size:48
Alignment explanation
Indices: 53954250--53954383 Score: 189
Period size: 48 Copynumber: 2.8 Consensus size: 48
53954240 ACCACGTTAC
* *
53954250 ATGTTTAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCGAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
* * *
53954297 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
* * *
53954345 ATGTGTAATCGTGGTATATCCACTTAGAACCACATTACA
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACA
53954384 CGTTTAACCG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
47 34 0.45
48 42 0.55
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (48 bp):
ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAAT
Found at i:53961489 original size:16 final size:16
Alignment explanation
Indices: 53961468--53961498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53961458 CAATGGAATA
*
53961468 GAATAGGGTTGTAATG
1 GAATAGAGTTGTAATG
53961484 GAATAGAGTTGTAAT
1 GAATAGAGTTGTAAT
53961499 CAATAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATG
Found at i:53975121 original size:18 final size:18
Alignment explanation
Indices: 53975098--53975195 Score: 117
Period size: 18 Copynumber: 5.4 Consensus size: 18
53975088 ATATGAAAAC
*
53975098 AAAATAAACATGAAA-AGA
1 AAAATAAAAAT-AAACAGA
*
53975116 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
* *
53975134 AAAATAAACATAAAGAGA
1 AAAATAAAAATAAACAGA
*
53975152 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
*
53975170 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
*
53975188 AAGATAAA
1 AAAATAAA
53975196 TGGACTCAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
17 3 0.04
18 67 0.96
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAATAAAAATAAACAGA
Found at i:53975125 original size:12 final size:12
Alignment explanation
Indices: 53975098--53975195 Score: 106
Period size: 12 Copynumber: 8.2 Consensus size: 12
53975088 ATATGAAAAC
* *
53975098 AAAATAAACATG
1 AAAATAAAAATA
*
53975110 AAAAGAAAAATA
1 AAAATAAAAATA
*
53975122 AAAATAAACATA
1 AAAATAAAAATA
*
53975134 AAAATAAACATA
1 AAAATAAAAATA
* *
53975146 AAGAGAAAAATA
1 AAAATAAAAATA
*
53975158 AAAATAAACATA
1 AAAATAAAAATA
53975170 AAAATAAAAATA
1 AAAATAAAAATA
* *
53975182 AACATAAAGATA
1 AAAATAAAAATA
53975194 AA
1 AA
53975196 TGGACTCAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:53975138 original size:36 final size:36
Alignment explanation
Indices: 53975098--53975183 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
53975088 ATATGAAAAC
53975098 AAAATAAACATGAAA-AGAAAAATAAAAATAAACATA
1 AAAATAAACAT-AAAGAGAAAAATAAAAATAAACATA
53975134 AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
1 AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
*
53975170 AAAATAAAAATAAA
1 AAAATAAACATAAA
53975184 CATAAAGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 3 0.06
36 45 0.94
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (36 bp):
AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
Found at i:53976856 original size:21 final size:21
Alignment explanation
Indices: 53976822--53976884 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
53976812 ATGAAATAAC
*
53976822 AAAT-AAGAATTAAAGAAAGA
1 AAATAAAGAAATAAAGAAAGA
*
53976842 AAATAAAGAAATAAAGAATGA
1 AAATAAAGAAATAAAGAAAGA
*
53976863 AAATGAAACAAAAATAAAGAAA
1 AAAT--AA-AGAAATAAAGAAA
53976885 AAGTTAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 18 0.51
23 2 0.06
24 11 0.31
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.13
Consensus pattern (21 bp):
AAATAAAGAAATAAAGAAAGA
Found at i:53999080 original size:18 final size:18
Alignment explanation
Indices: 53999057--53999154 Score: 117
Period size: 18 Copynumber: 5.4 Consensus size: 18
53999047 ATATGAAAAC
*
53999057 AAAATAAACATGAAA-AGA
1 AAAATAAAAAT-AAACAGA
*
53999075 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
* *
53999093 AAAATAAACATAAAGAGA
1 AAAATAAAAATAAACAGA
*
53999111 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
*
53999129 AAAATAAAAATAAACATA
1 AAAATAAAAATAAACAGA
*
53999147 AAGATAAA
1 AAAATAAA
53999155 TGGACTCAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
17 3 0.04
18 67 0.96
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAATAAAAATAAACAGA
Found at i:53999084 original size:12 final size:12
Alignment explanation
Indices: 53999057--53999154 Score: 106
Period size: 12 Copynumber: 8.2 Consensus size: 12
53999047 ATATGAAAAC
* *
53999057 AAAATAAACATG
1 AAAATAAAAATA
*
53999069 AAAAGAAAAATA
1 AAAATAAAAATA
*
53999081 AAAATAAACATA
1 AAAATAAAAATA
*
53999093 AAAATAAACATA
1 AAAATAAAAATA
* *
53999105 AAGAGAAAAATA
1 AAAATAAAAATA
*
53999117 AAAATAAACATA
1 AAAATAAAAATA
53999129 AAAATAAAAATA
1 AAAATAAAAATA
* *
53999141 AACATAAAGATA
1 AAAATAAAAATA
53999153 AA
1 AA
53999155 TGGACTCAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:53999097 original size:36 final size:36
Alignment explanation
Indices: 53999057--53999142 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
53999047 ATATGAAAAC
53999057 AAAATAAACATGAAA-AGAAAAATAAAAATAAACATA
1 AAAATAAACAT-AAAGAGAAAAATAAAAATAAACATA
53999093 AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
1 AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
*
53999129 AAAATAAAAATAAA
1 AAAATAAACATAAA
53999143 CATAAAGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 3 0.06
36 45 0.94
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (36 bp):
AAAATAAACATAAAGAGAAAAATAAAAATAAACATA
Found at i:54000808 original size:21 final size:21
Alignment explanation
Indices: 54000774--54000836 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
54000764 ATGAAATAAC
*
54000774 AAAT-AAGAATTAAAGAAAGA
1 AAATAAAGAAATAAAGAAAGA
*
54000794 AAATAAAGAAATAAAGAATGA
1 AAATAAAGAAATAAAGAAAGA
*
54000815 AAATGAAACAAAAATAAAGAAA
1 AAAT--AA-AGAAATAAAGAAA
54000837 AAGTTAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 18 0.51
23 2 0.06
24 11 0.31
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.13
Consensus pattern (21 bp):
AAATAAAGAAATAAAGAAAGA
Found at i:54017830 original size:47 final size:47
Alignment explanation
Indices: 54017767--54018228 Score: 664
Period size: 47 Copynumber: 9.7 Consensus size: 47
54017757 CCCTTCGGGA
* * *
54017767 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
54017814 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
54017861 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
54017908 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
54017955 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
54018002 CTTATCTCATATATGCA-TGTTCCCATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
54018049 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
54018096 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
54018145 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
54018192 CTTATCACATATATATACACTTTCACATTCATCACAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACAT
54018229 CATGTACAGA
Statistics
Matches: 386, Mismatches: 23, Indels: 10
0.92 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 314 0.81
49 70 0.18
50 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:54019833 original size:79 final size:81
Alignment explanation
Indices: 54019662--54019846 Score: 200
Period size: 79 Copynumber: 2.3 Consensus size: 81
54019652 GCTACTCGTT
* * *
54019662 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCG
* *
54019726 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* * * **
54019743 CAATGCATTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-AGATCTTAGTCCG
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCG
* *
54019805 GATATCGTCACTTAGCA-
65 GATATAGTAAC-TAGCAC
54019822 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
54019847 CATCATTCGA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
78 2 0.02
79 57 0.66
80 24 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGG
ATATAGTAACTAGCAC
Found at i:54019846 original size:40 final size:40
Alignment explanation
Indices: 54019643--54019846 Score: 211
Period size: 40 Copynumber: 5.1 Consensus size: 40
54019633 CGGAATTTAA
** *
54019643 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
54019683 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54019723 CCGGATTTAGTAACTCGCACCAATGCATTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
54019762 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-AGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
54019802 CCGGATATCGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
54019842 CCGGA
1 CCGGA
54019847 CATCATTCGA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 31 0.23
40 92 0.68
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:54027785 original size:39 final size:40
Alignment explanation
Indices: 54027668--54027852 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
54027658 GCTACTCGTT
* *
54027668 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATT-TAGTAACTCGCA
* *
54027708 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATTTAGTAACTCGCA
* * *
54027748 CCAATGCCTTCGAG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGAGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
54027787 CAAATGCCTTC-AGATCTTAGTCCGGATATCGTCACTTAGCA
1 CAAATGCCTTCGAGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
54027828 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGAGACTTAGCCCGGA
54027853 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 77 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGAGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:54027836 original size:79 final size:80
Alignment explanation
Indices: 54027668--54027852 Score: 189
Period size: 79 Copynumber: 2.3 Consensus size: 80
54027658 GCTACTCGTT
* * * *
54027668 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGAGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGAGACTTAACCCG
* *
54027732 GATTTAGTAACTCGCAC
64 GATATAGTAACTAGCAC
* * **
54027749 CAATGCCTTCGAG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-AGATCTTAGTCCGG
1 CAAAGCCTTCGAGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCGG
* *
54027812 ATATCGTCACTTAGCA-
65 ATATAGTAAC-TAGCAC
*
54027828 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGAGACTTAGCCCGGA
54027853 CATCATTCGA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
78 2 0.02
79 57 0.66
80 24 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGAGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGGA
TATAGTAACTAGCAC
Found at i:54037888 original size:21 final size:20
Alignment explanation
Indices: 54037856--54037894 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54037846 TTATAATGAC
54037856 CACACGGACGTGTTGCCCTTT
1 CACACGGACGTG-TGCCCTTT
54037877 CACACAGG-CGTGTGCCCT
1 CACAC-GGACGTGTGCCCT
54037895 GTTTCAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 9 0.53
22 2 0.12
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (20 bp):
CACACGGACGTGTGCCCTTT
Found at i:54038172 original size:26 final size:26
Alignment explanation
Indices: 54038136--54038191 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
54038126 ACTGAGTAGG
54038136 CACTCAGTGGTATTTCTATAAACCAA
1 CACTCAGTGGTATTTCTATAAACCAA
54038162 CACTCAGTGGTATTTCTATAAACCAA
1 CACTCAGTGGTATTTCTATAAACCAA
54038188 CACT
1 CACT
54038192 TAAATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (26 bp):
CACTCAGTGGTATTTCTATAAACCAA
Found at i:54039812 original size:9 final size:9
Alignment explanation
Indices: 54039800--54039860 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
54039790 CTGCTGTTCT
*
54039800 TTTTGTTTC
1 TTTTATTTC
*
54039809 TTTTACTTC
1 TTTTATTTC
54039818 TTTT-TTTC
1 TTTTATTTC
54039826 TTTTATTTC
1 TTTTATTTC
54039835 -TTTAGTTTC
1 TTTTA-TTTC
54039844 TTTTATTTAC
1 TTTTATTT-C
54039854 -TTTATTT
1 TTTTATTT
54039861 TATTTACTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
8 11 0.24
9 29 0.64
10 5 0.11
ACGTcount: A:0.10, C:0.11, G:0.03, T:0.75
Consensus pattern (9 bp):
TTTTATTTC
Found at i:54039827 original size:17 final size:17
Alignment explanation
Indices: 54039800--54039848 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
54039790 CTGCTGTTCT
54039800 TTTTGTTTCTTTTACTTC
1 TTTT-TTTCTTTTACTTC
*
54039818 TTTTTTTCTTTTATTTC
1 TTTTTTTCTTTTACTTC
*
54039835 TTTAGTTTCTTTTA
1 TTT-TTTTCTTTTA
54039849 TTTACTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTTTTCTTTTACTTC
Found at i:54039861 original size:14 final size:14
Alignment explanation
Indices: 54039844--54039873 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54039834 CTTTAGTTTC
*
54039844 TTTTATTTACTTTA
1 TTTTATTTACTGTA
54039858 TTTTATTTACTGTA
1 TTTTATTTACTGTA
54039872 TT
1 TT
54039874 GTTTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTATTTACTGTA
Found at i:54046510 original size:44 final size:44
Alignment explanation
Indices: 54046462--54046551 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
54046452 TCGGATTAAA
54046462 TCGAAGT-AATAGTAACAGTACGACACACA-AGGTGCCTCATCGAC
1 TCGAAGTCAA-AGTAACAGTACGACACACATA-GTGCCTCATCGAC
* **
54046506 TCGAAGTCAAAGTAACAGTACGGCACTTATAGTGCCTCATCGAC
1 TCGAAGTCAAAGTAACAGTACGACACACATAGTGCCTCATCGAC
54046550 TC
1 TC
54046552 AAGGTCGAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 38 0.93
45 3 0.07
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (44 bp):
TCGAAGTCAAAGTAACAGTACGACACACATAGTGCCTCATCGAC
Found at i:54047437 original size:19 final size:19
Alignment explanation
Indices: 54047413--54047476 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
54047403 GGCTTCTGCT
54047413 GTTCTTTTTGTTTCTTTTA
1 GTTCTTTTTGTTTCTTTTA
*
54047432 GTTCTTTTTTTTTCTTTTA
1 GTTCTTTTTGTTTCTTTTA
* *
54047451 CTTC-TTTAGTTTCTTTTA
1 GTTCTTTTTGTTTCTTTTA
54047469 GTTACTTT
1 GTT-CTTT
54047477 ATTTTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
18 14 0.37
19 22 0.58
20 2 0.05
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.72
Consensus pattern (19 bp):
GTTCTTTTTGTTTCTTTTA
Found at i:54047468 original size:10 final size:10
Alignment explanation
Indices: 54047414--54047476 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 10
54047404 GCTTCTGCTG
*
54047414 TTCTTTTTGT
1 TTCTTTTAGT
54047424 TTCTTTTAG-
1 TTCTTTTAGT
**
54047433 TTCTTTTTTT
1 TTCTTTTAGT
*
54047443 TTCTTTTA-C
1 TTCTTTTAGT
54047452 TTC-TTTAGT
1 TTCTTTTAGT
54047461 TTCTTTTAGT
1 TTCTTTTAGT
*
54047471 TACTTT
1 TTCTTT
54047477 ATTTTATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 4 0.09
9 13 0.30
10 26 0.60
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.73
Consensus pattern (10 bp):
TTCTTTTAGT
Found at i:54047487 original size:14 final size:14
Alignment explanation
Indices: 54047464--54047493 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54047454 CTTTAGTTTC
54047464 TTTTAGTTACTTTA
1 TTTTAGTTACTTTA
*
54047478 TTTTATTTACTTTA
1 TTTTAGTTACTTTA
54047492 TT
1 TT
54047494 GTTTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTAGTTACTTTA
Found at i:54048362 original size:3 final size:3
Alignment explanation
Indices: 54048354--54048394 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
54048344 TTGCTAATGC
54048354 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54048395 AAACTTCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54054828 original size:18 final size:17
Alignment explanation
Indices: 54054801--54054834 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
54054791 CTACATCCAT
54054801 AAACAAAAAAAAAGGCC
1 AAACAAAAAAAAAGGCC
54054818 AAACAAAAAAAAAGGCC
1 AAACAAAAAAAAAGGCC
54054835 TCCTTAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.18, G:0.12, T:0.00
Consensus pattern (17 bp):
AAACAAAAAAAAAGGCC
Found at i:54057902 original size:22 final size:22
Alignment explanation
Indices: 54057877--54057953 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 22
54057867 AAACTTGCAA
54057877 ATATTAACTTAAAAAACTCATT
1 ATATTAACTTAAAAAACTCATT
* *
54057899 ATATTTAACATGAATGTATAATA-TAATT
1 ATA-TTAAC-TTAA---A-AA-ACTCATT
*
54057927 ATAATAACTTAAAAAACTCATT
1 ATATTAACTTAAAAAACTCATT
54057949 ATATT
1 ATATT
54057954 TAACATGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
21 1 0.02
22 13 0.32
23 6 0.15
24 3 0.07
26 3 0.07
27 5 0.12
28 9 0.22
29 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (22 bp):
ATATTAACTTAAAAAACTCATT
Found at i:54057956 original size:50 final size:50
Alignment explanation
Indices: 54057881--54057981 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
54057871 TTGCAAATAT
54057881 TAACTTAAAAAACTCATTATATTTAACATGAATGTATAATATAATTATAA
1 TAACTTAAAAAACTCATTATATTTAACATGAATGTATAATATAATTATAA
54057931 TAACTTAAAAAACTCATTATATTTAACATGAATGTATAATATAATTATAA
1 TAACTTAAAAAACTCATTATATTTAACATGAATGTATAATATAATTATAA
54057981 T
1 T
54057982 TAAAATTTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.39
Consensus pattern (50 bp):
TAACTTAAAAAACTCATTATATTTAACATGAATGTATAATATAATTATAA
Found at i:54057978 original size:28 final size:28
Alignment explanation
Indices: 54057896--54057984 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 28
54057886 TAAAAAACTC
54057896 ATTATATTTAACATGAATGTATAATATA
1 ATTATATTTAACATGAATGTATAATATA
* * *
54057924 ATTATA-ATAAC-TTAA---A-AA-ACTC
1 ATTATATTTAACATGAATGTATAATA-TA
54057946 ATTATATTTAACATGAATGTATAATATA
1 ATTATATTTAACATGAATGTATAATATA
*
54057974 ATTATAATTAA
1 ATTATATTTAA
54057985 AATTTAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
21 1 0.02
22 9 0.20
23 5 0.11
24 3 0.07
26 3 0.07
27 5 0.11
28 19 0.41
29 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (28 bp):
ATTATATTTAACATGAATGTATAATATA
Found at i:54059517 original size:30 final size:30
Alignment explanation
Indices: 54059460--54059517 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54059450 TAGGCACTTC
* *
54059460 CACACGGGTGAGCCACACACTCGTGTGTGA
1 CACACGGGTGAGCCACACACCCATGTGTGA
*
54059490 CACACGGGT-AGACCACACGCCCATGTGT
1 CACACGGGTGAG-CCACACACCCATGTGT
54059518 CATGGCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.16
Consensus pattern (30 bp):
CACACGGGTGAGCCACACACCCATGTGTGA
Found at i:54068691 original size:14 final size:14
Alignment explanation
Indices: 54068672--54068703 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
54068662 AGGTCATTTA
*
54068672 GCCCAACCAAATTG
1 GCCCAACCAAACTG
54068686 GCCCAACCAAACTG
1 GCCCAACCAAACTG
54068700 GCCC
1 GCCC
54068704 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.44, G:0.16, T:0.09
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:54073816 original size:14 final size:14
Alignment explanation
Indices: 54073797--54073828 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
54073787 AGGTCATTTA
*
54073797 GCCCAACCAAATTG
1 GCCCAACCAAACTG
54073811 GCCCAACCAAACTG
1 GCCCAACCAAACTG
54073825 GCCC
1 GCCC
54073829 GGTGATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.44, G:0.16, T:0.09
Consensus pattern (14 bp):
GCCCAACCAAACTG
Found at i:54074639 original size:17 final size:17
Alignment explanation
Indices: 54074616--54074654 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
54074606 AGTCCATTTA
54074616 ATTTTCAATTTATTTTT
1 ATTTTCAATTTATTTTT
* *
54074633 CTTTTCATTTTATTTTT
1 ATTTTCAATTTATTTTT
54074650 ATTTT
1 ATTTT
54074655 AGCATTTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTTCAATTTATTTTT
Found at i:54074686 original size:24 final size:24
Alignment explanation
Indices: 54074624--54074688 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
54074614 TAATTTTCAA
* * *
54074624 TTTATTTTTC-TTTTCATTTTATT
1 TTTATTTATCATTTTCTTTTTATC
* *
54074647 TTTATTTTAGCA-TTTCTTTTTGTC
1 TTTA-TTTATCATTTTCTTTTTATC
54074671 TTTATTTATCATTTTCTT
1 TTTATTTATCATTTTCTT
54074689 AAAATACTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTATTTATCATTTTCTTTTTATC
Found at i:54093177 original size:50 final size:50
Alignment explanation
Indices: 54093102--54093200 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
54093092 TTAATATATT
*
54093102 TTTGGCAATTAATTTTCAAGTCAGACAAGTGGCCCAATGGGTGATTGAAA
1 TTTGGCAATTAATTTTCAAGTCAGACAAGTGGCCCAATGAGTGATTGAAA
*
54093152 TTTGGGAATTAATTTTCAAGTCAGACAAGTGGCCCAATGAGTGATTGAA
1 TTTGGCAATTAATTTTCAAGTCAGACAAGTGGCCCAATGAGTGATTGAA
54093201 CTTGAAAACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (50 bp):
TTTGGCAATTAATTTTCAAGTCAGACAAGTGGCCCAATGAGTGATTGAAA
Found at i:54093372 original size:34 final size:34
Alignment explanation
Indices: 54093329--54093393 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
54093319 GTAACTGGCT
54093329 CGAACAGAACCGATAGAAATCGAACCAACTCACC
1 CGAACAGAACCGATAGAAATCGAACCAACTCACC
54093363 CGAACAGAACCGATAGAAATCGAACCAACTC
1 CGAACAGAACCGATAGAAATCGAACCAACTC
54093394 GAGTGTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.45, C:0.31, G:0.15, T:0.09
Consensus pattern (34 bp):
CGAACAGAACCGATAGAAATCGAACCAACTCACC
Found at i:54094201 original size:49 final size:50
Alignment explanation
Indices: 54094109--54094232 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 50
54094099 AGTGGCCCGG
* *
54094109 CAATGATGATTTTCACTAATTT-TATATTCTACCATCCCAGGTGGCGC-AA
1 CAATGATGGTTTTCAC-AATTTGCATATTCTACCATCCCAGGTGGCGCGAA
*** *
54094158 CAATGATGGTTTTCACAATTTGCATATTCTACCATCTTGGGTGGCTCGAA
1 CAATGATGGTTTTCACAATTTGCATATTCTACCATCCCAGGTGGCGCGAA
* **
54094208 -AATGATGGCTTTCACTGTTTGCATA
1 CAATGATGGTTTTCACAATTTGCATA
54094233 CTGTTTGCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 5 0.08
49 57 0.89
50 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (50 bp):
CAATGATGGTTTTCACAATTTGCATATTCTACCATCCCAGGTGGCGCGAA
Found at i:54096125 original size:16 final size:16
Alignment explanation
Indices: 54096104--54096136 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54096094 TATTATTTTC
*
54096104 TTATATATTATGAAAT
1 TTATATAATATGAAAT
54096120 TTATATAATATGAAAT
1 TTATATAATATGAAAT
54096136 T
1 T
54096137 GAAATATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TTATATAATATGAAAT
Found at i:54104521 original size:86 final size:85
Alignment explanation
Indices: 54104347--54104768 Score: 349
Period size: 86 Copynumber: 4.9 Consensus size: 85
54104337 TAAAATATTG
* ** * * *
54104347 GTGTGCCAGTATAGTTG-CTTTAGTTTATCT-ATTGATGCATTGTGTGTTCTAGTATAGTTACTT
1 GTGTGCCAATATAGTTGCCTCGA-TTTATCTGA-TGATGCATTATGTGTGCCAGTATAGTTACTT
* * *
54104410 CG-ATATACCTGATCATGTACTGT
64 CGTATAT-TC-GATGATGCACTGT
* * * * * * *
54104433 GTGTGTCAGTATAGTTGCCTCGATTTATCTGATGATGTACTGTGTGTGCTAGTATAGTTTCTTC-
1 GTGTGCCAATATAGTTGCCTCGATTTATCTGATGATGCATTATGTGTGCCAGTATAGTTACTTCG
* * * *
54104497 TTTTTTCGATAATGCACTGG
66 TATATTCGATGATGCACTGT
* *
54104517 GTGTGCCAATATAATTG-CTACTG-TTTATCAGATGATGCA-TAGTGTGTGCCAGTATAGTTACT
1 GTGTGCCAATATAGTTGCCT-C-GATTTATCTGATGATGCATTA-TGTGTGCCAGTATAGTTACT
54104579 TCGGTATATTCGATGATGCACTGT
63 TC-GTATATTCGATGATGCACTGT
* * ** * * * * * *
54104603 ATATGCCAATATAGTTGTTTCAATATATCTGATGATGTATTATGTATGCTAGTATGGTTACTTCG
1 GTGTGCCAATATAGTTGCCTCGATTTATCTGATGATGCATTATGTGTGCCAGTATAGTTACTTC-
* *
54104668 GTATATCCAATGATGCACTGT
65 GTATATTCGATGATGCACTGT
* * *
54104689 GTGTGTCAATATAGTTGCTTCGGTTTATC-GATGATGCATTATGTGTGCCAGTATAGTTACTTCG
1 GTGTGCCAATATAGTTGCCTCGATTTATCTGATGATGCATTATGTGTGCCAGTATAGTTACTTC-
54104753 GTATA-TCTGATGATGC
65 GTATATTC-GATGATGC
54104769 GTTACGAAGC
Statistics
Matches: 273, Mismatches: 51, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
83 3 0.01
84 60 0.22
85 45 0.16
86 158 0.58
87 7 0.03
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (85 bp):
GTGTGCCAATATAGTTGCCTCGATTTATCTGATGATGCATTATGTGTGCCAGTATAGTTACTTCG
TATATTCGATGATGCACTGT
Found at i:54104594 original size:43 final size:43
Alignment explanation
Indices: 54104347--54104768 Score: 316
Period size: 43 Copynumber: 9.9 Consensus size: 43
54104337 TAAAATATTG
** * *
54104347 GTGTGCCAGTATAGTTGCTTTAGTTTATCT-ATTGATGCATTGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGA-TGATGCACTGT
* * * * * * *
54104390 GTGTTCTAGTATAGTTACTTCGATATACCTGATCATGTACTGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
* * * * *
54104433 GTGTGTCAGTATAGTTGCCTCGATTTATCTGATGATGTACTGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
* * * * * * *
54104476 GTGTGCTAGTATAGTTTCTTC-TTTTTTC-GATAATGCACTGG
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
* * * * * *
54104517 GTGTGCCAATATAATTGCTACTGTTTATCAGATGATGCA-TAGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACT-GT
*
54104560 GTGTGCCAGTATAGTTACTTCGGTATAT-TCGATGATGCACTGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCT-GATGATGCACTGT
* * * * ** * * *
54104603 ATATGCCAATATAGTTGTTTCAATATATCTGATGATGTATTAT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
* * * * **
54104646 GTATGCTAGTATGGTTACTTCGGTATATCCAATGATGCACTGT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
* * * * *
54104689 GTGTGTCAATATAGTTGCTTCGGTTTATC-GATGATGCATTAT
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
*
54104731 GTGTGCCAGTATAGTTACTTCGGTATATCTGATGATGC
1 GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGC
54104769 GTTACGAAGC
Statistics
Matches: 290, Mismatches: 81, Indels: 16
0.75 0.21 0.04
Matches are distributed among these distances:
41 26 0.09
42 46 0.16
43 215 0.74
44 3 0.01
ACGTcount: A:0.23, C:0.14, G:0.22, T:0.41
Consensus pattern (43 bp):
GTGTGCCAGTATAGTTGCTTCGGTATATCTGATGATGCACTGT
Found at i:54104634 original size:170 final size:170
Alignment explanation
Indices: 54104346--54104768 Score: 456
Period size: 170 Copynumber: 2.5 Consensus size: 170
54104336 ATAAAATATT
* * *** * * * *
54104346 GGTGTGCCAGTATAGTTGCTTTAGTTTATCTATTGATGCATTGTGTGTTCTAGTATAGTTACTTC
1 GGTGTGCCAATATAATTGCTACGGTTTATCGA-TGATGCATAGTGTGTGCCAGTATAGTTACTTC
* * * * * * * * * * *
54104411 GATATACCTGATCATGTACTGTGTGTGTCAGTATAGTTGCCTCGATTTATCTGATGATGTACTGT
65 GGTATATCTGATGATGCACTGTATATGCCAATATAGTTGCCTCAATATATCTGATGATGTACTAT
* * * * * *
54104476 GTGTGCTAGTATAGTTTCTTC-TTTTTTCGATAATGCACTG
130 GTATGCTAGTATAGTTACTTCGTATATCCAATAATGCACTG
*
54104516 GGTGTGCCAATATAATTGCTACTGTTTATCAGATGATGCATAGTGTGTGCCAGTATAGTTACTTC
1 GGTGTGCCAATATAATTGCTACGGTTTATC-GATGATGCATAGTGTGTGCCAGTATAGTTACTTC
** *
54104581 GGTATAT-TCGATGATGCACTGTATATGCCAATATAGTTGTTTCAATATATCTGATGATGTATTA
65 GGTATATCT-GATGATGCACTGTATATGCCAATATAGTTGCCTCAATATATCTGATGATGTACTA
* *
54104645 TGTATGCTAGTATGGTTACTTCGGTATATCCAATGATGCACTG
129 TGTATGCTAGTATAGTTACTTC-GTATATCCAATAATGCACTG
* * * *
54104688 TGTGTGTCAATATAGTTGCTTCGGTTTATCGATGATGCATTA-TGTGTGCCAGTATAGTTACTTC
1 GGTGTGCCAATATAATTGCTACGGTTTATCGATGATGCA-TAGTGTGTGCCAGTATAGTTACTTC
54104752 GGTATATCTGATGATGC
65 GGTATATCTGATGATGC
54104769 GTTACGAAGC
Statistics
Matches: 211, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
169 1 0.00
170 121 0.57
171 47 0.22
172 42 0.20
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (170 bp):
GGTGTGCCAATATAATTGCTACGGTTTATCGATGATGCATAGTGTGTGCCAGTATAGTTACTTCG
GTATATCTGATGATGCACTGTATATGCCAATATAGTTGCCTCAATATATCTGATGATGTACTATG
TATGCTAGTATAGTTACTTCGTATATCCAATAATGCACTG
Found at i:54106991 original size:46 final size:46
Alignment explanation
Indices: 54106931--54107146 Score: 260
Period size: 46 Copynumber: 5.0 Consensus size: 46
54106921 TTTGACATGA
* * * * * *
54106931 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
54106977 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
54107023 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
54107069 TGCCATGGTATCTTT----CA-------AC-CATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
54107103 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
54107147 AGAGCACACT
Statistics
Matches: 150, Mismatches: 7, Indels: 26
0.82 0.04 0.14
Matches are distributed among these distances:
34 30 0.20
35 2 0.01
38 2 0.01
42 2 0.01
45 6 0.04
46 108 0.72
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:54107094 original size:34 final size:34
Alignment explanation
Indices: 54107054--54107124 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
54107044 TGGTCTTACA
54107054 CATTTCATATCAGGCTGCCATGGTATCTTTCAAC
1 CATTTCATATCAGGCTGCCATGGTATCTTTCAAC
54107088 CATTTCATATCAGGCTGCCATGGTATCTTTCAAC
1 CATTTCATATCAGGCTGCCATGGTATCTTTCAAC
54107122 CAT
1 CAT
54107125 GGTCTTACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (34 bp):
CATTTCATATCAGGCTGCCATGGTATCTTTCAAC
Found at i:54109626 original size:30 final size:30
Alignment explanation
Indices: 54109570--54109637 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
54109560 CACCCTTAAA
* *
54109570 ATATTTGCACTATTAGTCCTTCAATTTTTC
1 ATATTTACACTATTAATCCTTCAATTTTTC
* *
54109600 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAATTTTTC
54109629 AGTATTTAC
1 A-TATTTAC
54109638 TCTTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.49
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAATTTTTC
Found at i:54111509 original size:27 final size:25
Alignment explanation
Indices: 54111478--54111545 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 25
54111468 AAAATCACAA
54111478 AAAAAATTGTAAAATTTAAAATATTTAT
1 AAAAAATT-TAAAA-TTAAAATA-TTAT
*
54111506 AAAAAAATTCAAACATTAAAATATTAT
1 -AAAAAATTTAAA-ATTAAAATATTAT
54111533 -AAAAATTATAAAA
1 AAAAAATT-TAAAA
54111546 AAAATTCTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
25 8 0.23
26 3 0.09
27 4 0.11
28 11 0.31
29 9 0.26
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (25 bp):
AAAAAATTTAAAATTAAAATATTAT
Found at i:54111510 original size:28 final size:26
Alignment explanation
Indices: 54111477--54111537 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 26
54111467 AAAAATCACA
54111477 AAAAAAATTGTAAAATTTAAAATATTTAT
1 AAAAAAATT-TAAAA-TTAAAATA-TTAT
*
54111506 AAAAAAATTCAAACATTAAAATATTAT
1 AAAAAAATTTAAA-ATTAAAATATTAT
54111533 AAAAA
1 AAAAA
54111538 TTATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.30
28 11 0.37
29 10 0.33
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAAAAATTTAAAATTAAAATATTAT
Found at i:54113400 original size:27 final size:27
Alignment explanation
Indices: 54113360--54113435 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
54113350 GGCAAAACAA
** *
54113360 TCATTTTACCCTACAGGGGTATGTCAG
1 TCATTTTATACTACAAGGGTATGTCAG
* * *
54113387 TCATTTTATGCTACAAGGGTATTTCGG
1 TCATTTTATACTACAAGGGTATGTCAG
*
54113414 TAATTTTATACTACAAGGGTAT
1 TCATTTTATACTACAAGGGTAT
54113436 TTTGATAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (27 bp):
TCATTTTATACTACAAGGGTATGTCAG
Found at i:54113436 original size:27 final size:27
Alignment explanation
Indices: 54113370--54113448 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
54113360 TCATTTTACC
* * * * *
54113370 CTACAGGGGTATGTCAGTCATTTTATG
1 CTACAAGGGTATTTCGGTAATTTTATA
54113397 CTACAAGGGTATTTCGGTAATTTTATA
1 CTACAAGGGTATTTCGGTAATTTTATA
* *
54113424 CTACAAGGGTATTTTGATAATTTTA
1 CTACAAGGGTATTTCGGTAATTTTA
54113449 CAAATCGAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (27 bp):
CTACAAGGGTATTTCGGTAATTTTATA
Found at i:54113459 original size:27 final size:27
Alignment explanation
Indices: 54113429--54113823 Score: 293
Period size: 27 Copynumber: 14.7 Consensus size: 27
54113419 TTATACTACA
54113429 AGGGTATTTTGATAATTTTACAAATCG
1 AGGGTATTTTGATAATTTTACAAATCG
* *
54113456 AGGGTGTTTCGATAATTTTACAAATCG
1 AGGGTATTTTGATAATTTTACAAATCG
*
54113483 AGGGTATTTT-AGTAATTTTACAAGTCG
1 AGGGTATTTTGA-TAATTTTACAAATCG
* * * * *
54113510 AGGGTATTTCGGTAATTTAAAAAATTG
1 AGGGTATTTTGATAATTTTACAAATCG
* *
54113537 AGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTTGATAATTTTACAAATCG
* * * *
54113564 AGGGTGTTTCGGTAATTTTACAACTCG
1 AGGGTATTTTGATAATTTTACAAATCG
* * * *
54113591 ATGGT-GTTTCAGTAATTTTACAAATCA
1 AGGGTATTTTGA-TAATTTTACAAATCG
* * * *
54113618 AGGGT-GTTTCAGTAATTTCACAAATTG
1 AGGGTATTTTGA-TAATTTTACAAATCG
* * *
54113645 GGGGTA-TTTCAGTAATTTTACAAATTG
1 AGGGTATTTTGA-TAATTTTACAAATCG
* *
54113672 AGGGT-GTTTCAGTAATTTTACAAATCG
1 AGGGTATTTTGA-TAATTTTACAAATCG
* * * * *
54113699 ATGGT-GTTTCAGTAATTTTATAAATCA
1 AGGGTATTTTGA-TAATTTTACAAATCG
* * *
54113726 ATGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTTGATAATTTTACAAATCG
* *
54113753 AGGGTATTTCGGTAATTTTACAAA-CG
1 AGGGTATTTTGATAATTTTACAAATCG
* *
54113779 -GGAGTATTTTGGTAATTTTACAAACCG
1 AGG-GTATTTTGATAATTTTACAAATCG
* * *
54113806 GGGGTATTTCGGTAATTT
1 AGGGTATTTTGATAATTT
54113824 CTTTTTATTA
Statistics
Matches: 316, Mismatches: 43, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.01
26 25 0.08
27 285 0.90
28 4 0.01
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGTATTTTGATAATTTTACAAATCG
Found at i:54113460 original size:54 final size:56
Alignment explanation
Indices: 54113402--54113823 Score: 342
Period size: 54 Copynumber: 7.8 Consensus size: 56
54113392 TTATGCTACA
* * * *
54113402 AGGGTATTTCGGTAATTTTATACTA-CAAGGGTATTTTGA-TAATTTTACAAATCG
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * *
54113456 AGGGTGTTTCGATAATTTTACA-AATCGAGGGTATTTT-AGTAATTTTACAAGTCG
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * *
54113510 AGGGTATTTCGGTAA-TTTAAAAAATTGAGGGTATTTCG-GTAATTTTACAAATCG
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * *
54113564 AGGGTGTTTCGGTAATTTT--ACAACTCGATGGT-GTTTCAGTAATTTTACAAATCA
1 AGGGTGTTTCGGTAATTTTAAACAA-TCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * * * * *
54113618 AGGGTGTTTCAGTAATTTCACA-AATTGGGGGTA-TTTCAGTAATTTTACAAATTG
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * * * * *
54113672 AGGGTGTTTCAGTAATTTTACA-AATCGATGGT-GTTTCAGTAATTTTATAAATCA
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * *
54113726 ATGGTATTTCGGTAATTTTACA-AATCGAGGGTATTTCG-GTAATTTTACAAA-CG
1 AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
* * * * * *
54113779 -GGAGTATTTTGGTAATTTTACA-AACCGGGGGTATTTCG-GTAATTT
1 AGG-GTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTT
54113824 CTTTTTATTA
Statistics
Matches: 308, Mismatches: 47, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
52 1 0.00
53 52 0.17
54 247 0.80
55 7 0.02
56 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (56 bp):
AGGGTGTTTCGGTAATTTTAAACAATCGAGGGTATTTTGAGTAATTTTACAAATCG
Found at i:54113487 original size:81 final size:80
Alignment explanation
Indices: 54113402--54113823 Score: 342
Period size: 81 Copynumber: 5.2 Consensus size: 80
54113392 TTATGCTACA
* *
54113402 AGGGTATTTCGGTAATTTTATACTACAAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTCG
1 AGGGTATTTCGGTAATTTTA-AATACGAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTCG
54113467 ATAATTTTACAAATCG
65 ATAATTTTACAAATCG
** * * * * * *
54113483 AGGGTATTTTAGTAATTTTACAAGT-CGAGGGTATTTCGGTAATTTAAAAAATTGAGGGTATTTC
1 AGGGTATTTCGGTAATTTTA-AA-TACGAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTC
*
54113547 GGTAATTTTACAAATCG
64 GATAATTTTACAAATCG
* * * * *
54113564 AGGGTGTTTCGGTAATTTTACAACT-CGATGGT-GTTTCAGTAATTTTACAAATCAAGGGTGTTT
1 AGGGTATTTCGGTAATTTTA-AA-TACGAGGGTATTTTGA-TAATTTTACAAATCGAGGGTGTTT
* *
54113627 C-AGTAATTTCACAAATTG
63 CGA-TAATTTTACAAATCG
* * * * * *
54113645 GGGGTATTTCAGTAATTTTACAA-ATTGAGGGT-GTTTCAGTAATTTTACAAATCGATGGTGTTT
1 AGGGTATTTCGGTAATTTTA-AATA-CGAGGGTATTTTGA-TAATTTTACAAATCGAGGGTGTTT
* *
54113708 C-AGTAATTTTATAAATCA
63 CGA-TAATTTTACAAATCG
* * * *
54113726 ATGGTATTTCGGTAATTTTACAA-ATCGAGGGTATTTCGGTAATTTTACAAA-CG-GGAGTATTT
1 AGGGTATTTCGGTAATTTTA-AATA-CGAGGGTATTTTGATAATTTTACAAATCGAGG-GTGTTT
* * *
54113788 TGGTAATTTTACAAACCG
63 CGATAATTTTACAAATCG
*
54113806 GGGGTATTTCGGTAATTT
1 AGGGTATTTCGGTAATTT
54113824 CTTTTTATTA
Statistics
Matches: 276, Mismatches: 57, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
79 1 0.00
80 37 0.13
81 235 0.85
82 3 0.01
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (80 bp):
AGGGTATTTCGGTAATTTTAAATACGAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTCGA
TAATTTTACAAATCG
Found at i:54116997 original size:17 final size:19
Alignment explanation
Indices: 54116975--54117018 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54116965 ACAATAATAT
54116975 AAAATA-AT-GATATGTAC
1 AAAATATATAGATATGTAC
*
54116992 AAAATATATATATATGTAC
1 AAAATATATAGATATGTAC
*
54117011 ATAATATA
1 AAAATATA
54117019 GTTATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATATATAGATATGTAC
Found at i:54117831 original size:13 final size:13
Alignment explanation
Indices: 54117789--54117839 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
54117779 TGAATGTTCC
* *
54117789 TTTTTTGTTGTTT
1 TTTTTTGCTGATT
54117802 TTTTTTGCTGGAAATT
1 TTTTTTGCT-G--ATT
54117818 TTTTTTGCTGATT
1 TTTTTTGCTGATT
54117831 TTTTTTGCT
1 TTTTTTGCT
54117840 CTTTTTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 20 0.61
14 1 0.03
15 1 0.03
16 11 0.33
ACGTcount: A:0.08, C:0.06, G:0.16, T:0.71
Consensus pattern (13 bp):
TTTTTTGCTGATT
Found at i:54118094 original size:29 final size:29
Alignment explanation
Indices: 54118062--54118167 Score: 81
Period size: 30 Copynumber: 3.6 Consensus size: 29
54118052 GTAATTTTTA
*
54118062 GAAAATTTAGGGTTAAAGTGTAATTTAAG
1 GAAAATTTAGGGTTAAAGTGAAATTTAAG
* * * *
54118091 GAAAGTTAAGGGGTCT-AAGTAAAATTTAAA
1 GAAAATTTA-GGGT-TAAAGTGAAATTTAAG
* * *
54118121 GAAAGTTTAAGGGTCAAAATGAAATTT-AG
1 GAAAATTT-AGGGTTAAAGTGAAATTTAAG
*
54118150 GAAAAGTTTAGGGATAAA
1 GAAAA-TTTAGGGTTAAA
54118168 AATGCAATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
29 19 0.32
30 38 0.64
31 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.28
Consensus pattern (29 bp):
GAAAATTTAGGGTTAAAGTGAAATTTAAG
Found at i:54118146 original size:30 final size:30
Alignment explanation
Indices: 54118061--54118148 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
54118051 TGTAATTTTT
* * *
54118061 AGAAAATTT-AGGGTTAAAGTGTAATTTAA
1 AGAAAGTTTAAGGGTCAAAGTGAAATTTAA
* * *
54118090 GGAAAG-TTAAGGGGTCTAAGTAAAATTTAA
1 AGAAAGTTTAA-GGGTCAAAGTGAAATTTAA
*
54118120 AGAAAGTTTAAGGGTCAAAATGAAATTTA
1 AGAAAGTTTAAGGGTCAAAGTGAAATTTA
54118149 GGAAAAGTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
28 2 0.04
29 5 0.11
30 35 0.76
31 4 0.09
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (30 bp):
AGAAAGTTTAAGGGTCAAAGTGAAATTTAA
Found at i:54118205 original size:24 final size:24
Alignment explanation
Indices: 54118174--54118219 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
54118164 TAAAAATGCA
54118174 ATTTTTATTTTTTGAAAATTTTTT
1 ATTTTTATTTTTTGAAAATTTTTT
*
54118198 ATTTTTATTTTTTTAAAATTTT
1 ATTTTTATTTTTTGAAAATTTT
54118220 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTATTTTTTGAAAATTTTTT
Found at i:54118471 original size:10 final size:10
Alignment explanation
Indices: 54118456--54118615 Score: 63
Period size: 10 Copynumber: 16.5 Consensus size: 10
54118446 TGACATATGG
54118456 AAAAAATTAT
1 AAAAAATTAT
54118466 -AAAAA--AT
1 AAAAAATTAT
*
54118473 -AAAAATCA-
1 AAAAAATTAT
*
54118481 ATAAAAGTTAT
1 A-AAAAATTAT
54118492 -AAAAATTAT
1 AAAAAATTAT
* **
54118501 TAAATTTTAAT
1 AAAAAATT-AT
54118512 AAAAAA-TATT
1 AAAAAATTA-T
* *
54118522 TAAAATTTAT
1 AAAAAATTAT
* *
54118532 TA-AAATTAG
1 AAAAAATTAT
54118541 AAAAAAATTAT
1 A-AAAAATTAT
*
54118552 -AAAAATCAT
1 AAAAAATTAT
54118561 AAAAAA-TAT
1 AAAAAATTAT
*
54118570 AAAAAAATTGT
1 -AAAAAATTAT
* *
54118581 AGAATATTAT
1 AAAAAATTAT
*
54118591 -AAAAATCAT
1 AAAAAATTAT
54118600 AAACAAATTAT
1 AAA-AAATTAT
54118611 AAAAA
1 AAAAA
54118616 TGCATAAAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 32
0.66 0.14 0.19
Matches are distributed among these distances:
7 7 0.06
9 36 0.33
10 43 0.39
11 24 0.22
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Done.