Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 162 of 290
Found at i:52300093 original size:45 final size:45
Alignment explanation
Indices: 52300025--52300143 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 45
52300015 CAGCACTAAA
52300025 CAGT-ATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
* *
52300069 CAGTGATTTGCAGTAGAGTTGCCAGTATAATAGGCTTAGAGCCAT
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
* * *
52300114 CAGTGTTTTGTAGCAGAGCTGCTAGTATAA
1 CAGTGATTTGCAGCAGAGCTGCCAGTATAA
52300144 AACACTTCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
44 4 0.06
45 63 0.94
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
CAGTGATTTGCAGCAGAGCTGCCAGTATAATAGGCTTAGAGCCAT
Found at i:52300333 original size:27 final size:27
Alignment explanation
Indices: 52300298--52300463 Score: 143
Period size: 27 Copynumber: 6.1 Consensus size: 27
52300288 TACATCACAT
* * *
52300298 AGGGCAAAACAGTAATCTTACCATATA
1 AGGGAAAAACAGTCATTTTACCATATA
* * *
52300325 AGGGAAAAACAATCATTTCACCACATA
1 AGGGAAAAACAGTCATTTTACCATATA
* * *
52300352 AAGGAAAAATAGTTATTTTACCATATA
1 AGGGAAAAACAGTCATTTTACCATATA
*
52300379 AGGGTAAAACAGTCATTTTACCATATA
1 AGGGAAAAACAGTCATTTTACCATATA
* * * * * *
52300406 AAGGCAAAACAATCATTTTTCAACATA
1 AGGGAAAAACAGTCATTTTACCATATA
* * * * *
52300433 AGGGTAATATAGTCATTTTATCACATA
1 AGGGAAAAACAGTCATTTTACCATATA
52300460 AGGG
1 AGGG
52300464 CTCTAGGTAA
Statistics
Matches: 109, Mismatches: 30, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 109 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (27 bp):
AGGGAAAAACAGTCATTTTACCATATA
Found at i:52300424 original size:54 final size:54
Alignment explanation
Indices: 52300300--52300460 Score: 178
Period size: 54 Copynumber: 3.0 Consensus size: 54
52300290 CATCACATAG
* * * *
52300300 GGCAAAACAGTAATCTTACCATATAAGGGAAAAACAATCATTTCACCACATAAA
1 GGCAAAACAGTAATTTTACCATATAAGGGTAAAACAGTCATTTTACCACATAAA
* * * *
52300354 GGAAAAATAGTTATTTTACCATATAAGGGTAAAACAGTCATTTTACCATATAAA
1 GGCAAAACAGTAATTTTACCATATAAGGGTAAAACAGTCATTTTACCACATAAA
* * * * * * * *
52300408 GGCAAAACAATCATTTTTCAACATAAGGGTAATATAGTCATTTTATCACATAA
1 GGCAAAACAGTAATTTTACCATATAAGGGTAAAACAGTCATTTTACCACATAA
52300461 GGGCTCTAGG
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (54 bp):
GGCAAAACAGTAATTTTACCATATAAGGGTAAAACAGTCATTTTACCACATAAA
Found at i:52300432 original size:81 final size:81
Alignment explanation
Indices: 52300293--52300464 Score: 211
Period size: 81 Copynumber: 2.1 Consensus size: 81
52300283 ATATTTACAT
* *
52300293 CACAT-AGGGCAAAACAGTAATCTTACCATATAAGGGAAAAACAATCATTTCACCACATAAAGGA
1 CACATAAGGGCAAAACAGTAATCTTACCATATAAAGGAAAAACAATCATTTCACAACATAAAGGA
*
52300357 AAAATAGTTATTTTAC
66 AAAATAGTCATTTTAC
* * * * * ** * *
52300373 CATATAAGGGTAAAACAGTCATTTTACCATATAAAGGCAAAACAATCATTTTTCAACATAAGGGT
1 CACATAAGGGCAAAACAGTAATCTTACCATATAAAGGAAAAACAATCATTTCACAACATAAAGGA
* *
52300438 AATATAGTCATTTTAT
66 AAAATAGTCATTTTAC
52300454 CACATAAGGGC
1 CACATAAGGGC
52300465 TCTAGGTAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
80 4 0.05
81 71 0.95
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (81 bp):
CACATAAGGGCAAAACAGTAATCTTACCATATAAAGGAAAAACAATCATTTCACAACATAAAGGA
AAAATAGTCATTTTAC
Found at i:52300851 original size:18 final size:18
Alignment explanation
Indices: 52300828--52300863 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52300818 ACACCTGCTA
52300828 GGATACTAGGTACGCAAC
1 GGATACTAGGTACGCAAC
52300846 GGATACTAGGTACGCAAC
1 GGATACTAGGTACGCAAC
52300864 TCTTTCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (18 bp):
GGATACTAGGTACGCAAC
Found at i:52305989 original size:31 final size:31
Alignment explanation
Indices: 52305951--52306014 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
52305941 CCTTTTCATG
52305951 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** * *
52305982 TTTCATATTTCATATTATTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52306013 TT
1 TT
52306015 ATTATAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52306330 original size:26 final size:25
Alignment explanation
Indices: 52306222--52306329 Score: 132
Period size: 25 Copynumber: 4.4 Consensus size: 25
52306212 CTGGAGGCTT
*
52306222 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTGATAAACTGGGGCAAA
*
52306246 AGCCCTTTTGATAAACTAGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
*
52306271 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTGATAAACTGGGGCAAA
* *
52306296 AGCCCTTTTCGGTAAACTGGGGC-AT
1 AGCCCTTTT-GATAAACTGGGGCAAA
52306321 AGCCCTTTT
1 AGCCCTTTT
52306330 TGCACTTCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.09
24 12 0.16
25 44 0.59
26 11 0.15
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (25 bp):
AGCCCTTTTGATAAACTGGGGCAAA
Found at i:52306400 original size:20 final size:20
Alignment explanation
Indices: 52306377--52306424 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
52306367 TTATGAATAC
* *
52306377 ATCATGTGCATATCATA-CA
1 ATCATGTACACATCATATCA
52306396 TATCATGTACACATCATATCA
1 -ATCATGTACACATCATATCA
52306417 ATCATGTA
1 ATCATGTA
52306425 TATCAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (20 bp):
ATCATGTACACATCATATCA
Found at i:52313403 original size:40 final size:40
Alignment explanation
Indices: 52313356--52313529 Score: 226
Period size: 40 Copynumber: 4.3 Consensus size: 40
52313346 CTCGCACAAG
* * * *
52313356 GCCTTCGGGTCTTAGTCCGG-ATATGGTCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAAT
*
52313396 GCCTTCGGGACTTAGCCCGG-ATATAGTAACTCGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTAGCACAAAT
* *
52313436 GCCTTCGGGACTTAGCCCGGAATTAGTAACTCGTACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
* *
52313476 GCCTTCGGGACTTAGCCCGGAATTAATCACTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
*
52313516 GTCTTCGGGACTTA
1 GCCTTCGGGACTTA
52313530 ACCCCGTTAG
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
40 120 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGAATTAGTAACTAGCACAAAT
Found at i:52321490 original size:38 final size:38
Alignment explanation
Indices: 52321439--52321646 Score: 191
Period size: 38 Copynumber: 5.4 Consensus size: 38
52321429 ACCCAAGTAT
*
52321439 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATAT-A-CACTCGCACAAATGC
* *
52321477 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATAT--ACACTCGCACAAATGC
*
52321517 CTTCGGGACTTAGCCCGGATAGTA-ACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATA-TACACTCGCACAAATGC
52321555 CTTCGGG--TTAGCCCGGAATAGTA-ACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGG-ATA-TACACTCGCACAAATGC
* * *
52321592 CTTC-GGACTTAGCCCGAAT-TAGTCACTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATA--CACTCGCACAAATGC
*
52321630 CTTCGGGACTTAGCCCG
1 CTTCGGGTCTTAGCCCG
52321647 TTGATCCAAT
Statistics
Matches: 149, Mismatches: 9, Indels: 23
0.82 0.05 0.13
Matches are distributed among these distances:
35 2 0.01
36 11 0.07
37 27 0.18
38 56 0.38
39 28 0.19
40 24 0.16
41 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.23
Consensus pattern (38 bp):
CTTCGGGTCTTAGCCCGGATATACACTCGCACAAATGC
Found at i:52321624 original size:75 final size:77
Alignment explanation
Indices: 52321475--52321646 Score: 242
Period size: 75 Copynumber: 2.2 Consensus size: 77
52321465 CTCGCACAAG
* * *
52321475 GCCTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAGT
1 GCCTTCGGG-CTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGAATAGT
*
52321540 AACTCGCACAAAT
65 AACTAGCACAAAT
*
52321553 GCCTTCGGG-TTAGCCCGGA-ATAGTAACTCGCACAAATGCCTTC-GGACTTAGCCCGAATTAGT
1 GCCTTCGGGCTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGAA-TAGT
*
52321615 CACTAGCACAAAT
65 AACTAGCACAAAT
52321628 GCCTTCGGGACTTAGCCCG
1 GCCTTCGGG-CTTAGCCCG
52321647 TTGATCCAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
74 13 0.15
75 45 0.53
76 10 0.12
77 8 0.09
78 9 0.11
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.23
Consensus pattern (77 bp):
GCCTTCGGGCTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGAATAGTA
ACTAGCACAAAT
Found at i:52325996 original size:47 final size:47
Alignment explanation
Indices: 52325879--52326225 Score: 552
Period size: 47 Copynumber: 7.4 Consensus size: 47
52325869 CCCTTCGGGA
* * * * * * *
52325879 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52325926 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52325972 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52326019 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52326066 CTTATCACACATATGCACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52326113 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52326160 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52326207 CTTATCACATATATACACT
1 CTTATCACATATATACACT
52326226 GTGTTGGCTG
Statistics
Matches: 282, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
46 38 0.13
47 244 0.87
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52330168 original size:20 final size:20
Alignment explanation
Indices: 52330139--52330183 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
52330129 ATCACATGTA
* *
52330139 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
52330159 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
52330179 TTCAT
1 TTCAT
52330184 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:52333424 original size:13 final size:13
Alignment explanation
Indices: 52333406--52333457 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
52333396 AGTTTGGAAA
52333406 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
52333419 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
52333432 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
52333445 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
52333457 T
1 T
52333458 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52334792 original size:13 final size:13
Alignment explanation
Indices: 52334774--52334825 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
52334764 AGTTTGGAAA
52334774 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
52334787 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
52334800 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
52334813 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
52334825 T
1 T
52334826 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52336160 original size:13 final size:13
Alignment explanation
Indices: 52336142--52336193 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
52336132 AGTTTGGAAA
52336142 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
52336155 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
52336168 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
52336181 T-CTTTTGAAAAG
1 TGCTTTTGAAAAG
52336193 T
1 T
52336194 TTAGTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.37
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52343109 original size:12 final size:12
Alignment explanation
Indices: 52343087--52343124 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
52343077 GTGCGTTTCT
52343087 AAAAT-AAAATG
1 AAAATAAAAATG
52343098 AAAATAAAAATG
1 AAAATAAAAATG
52343110 AAAAATGAAAAATG
1 -AAAAT-AAAAATG
52343124 A
1 A
52343125 TCCATTAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 6 0.25
13 6 0.25
14 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:52343121 original size:8 final size:7
Alignment explanation
Indices: 52343092--52343124 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
52343082 TTTCTAAAAT
52343092 AAAATG-
1 AAAATGA
52343098 AAAAT-A
1 AAAATGA
52343104 AAAATGA
1 AAAATGA
52343111 AAAATGA
1 AAAATGA
52343118 AAAATGA
1 AAAATGA
52343125 TCCATTAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
AAAATGA
Found at i:52349130 original size:47 final size:47
Alignment explanation
Indices: 52349077--52349252 Score: 173
Period size: 47 Copynumber: 3.8 Consensus size: 47
52349067 CACCCATAAG
* *
52349077 CGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCA
1 CGAACTCAGACTCAACTCAACGAGCTCAGATGCCCAGTTACATCTCA
* * * *
52349124 CGAACTCAGACTCAACTCAATGAGTTCAGA-G----GTTCGCATCCATAA
1 CGAACTCAGACTCAACTCAACGAGCTCAGATGCCCAGTT-ACAT-C-TCA
* * * *
52349169 GTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCA
1 -CGAACTCAGACTCAACTCAACGAGCTCAGATGCCCAGTTACATCTCA
* *
52349217 CGAACTCGGACTCAACTCAACGAGTTCAGATGCCCA
1 CGAACTCAGACTCAACTCAACGAGCTCAGATGCCCA
52349253 AATATCTGAA
Statistics
Matches: 103, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 1 0.01
45 2 0.02
46 26 0.25
47 59 0.57
48 2 0.02
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (47 bp):
CGAACTCAGACTCAACTCAACGAGCTCAGATGCCCAGTTACATCTCA
Found at i:52349185 original size:93 final size:93
Alignment explanation
Indices: 52349070--52349246 Score: 300
Period size: 93 Copynumber: 1.9 Consensus size: 93
52349060 TGTAACCCAC
52349070 CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
1 CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
*
52349135 TCAACTCAATGAGTTCAGAGGTTCGCAT
66 TCAACTCAACGAGTTCAGAGGTTCGCAT
* * * * *
52349163 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCACGAACTCGGAC
1 CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
52349228 TCAACTCAACGAGTTCAGA
66 TCAACTCAACGAGTTCAGA
52349247 TGCCCAAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (93 bp):
CCATAAGCGAACTCAGACTCAACTCAACAAGCTCGGATGCCCAGTTACATCTCACGAACTCAGAC
TCAACTCAACGAGTTCAGAGGTTCGCAT
Found at i:52352132 original size:17 final size:17
Alignment explanation
Indices: 52352096--52352150 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
52352086 AACAATCTGT
52352096 AGAAAAATCAAAAGAAAAAG
1 AGAAAAA-C-AAA-AAAAAG
52352116 AGAAAAACAAAAAAAAG
1 AGAAAAACAAAAAAAAG
* * *
52352133 TGAAAAAGAAAAGAAAG
1 AGAAAAACAAAAAAAAG
52352150 A
1 A
52352151 AAGGAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 20 0.65
18 3 0.10
19 1 0.03
20 7 0.23
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (17 bp):
AGAAAAACAAAAAAAAG
Found at i:52360491 original size:26 final size:26
Alignment explanation
Indices: 52360448--52360508 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
52360438 TATCCAAAGC
* * *
52360448 TCCTGATTAAAGGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCATGAACT
** *
52360474 TCCTGATTAAAATTTCTTTATGAACT
1 TCCTGATTAAAAGCTCTTCATGAACT
52360500 TCCTGATTA
1 TCCTGATTA
52360509 TGTCTCTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCATGAACT
Found at i:52360525 original size:24 final size:24
Alignment explanation
Indices: 52360468--52360526 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
52360458 AGGCTCTTCG
*
52360468 TGAGCTTCCTGATTAAAATTTCTTTA
1 TGAGCTTCCTGATT--AATGTCTTTA
*
52360494 TGAACTTCCTGATT-ATGTCTCTTA
1 TGAGCTTCCTGATTAATGTCT-TTA
52360518 TGAGCTTCC
1 TGAGCTTCC
52360527 GTTATATAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
26 13 0.45
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (24 bp):
TGAGCTTCCTGATTAATGTCTTTA
Found at i:52374327 original size:68 final size:68
Alignment explanation
Indices: 52374255--52374408 Score: 308
Period size: 68 Copynumber: 2.3 Consensus size: 68
52374245 GGATACATCC
52374255 CACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTA
1 CACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTA
52374320 TCA
66 TCA
52374323 CACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTA
1 CACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTA
52374388 TCA
66 TCA
52374391 CACATGTGACCTAGCTAC
1 CACATGTGACCTAGCTAC
52374409 TATATAGTAT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 86 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (68 bp):
CACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCCCGTA
TCA
Found at i:52383538 original size:26 final size:26
Alignment explanation
Indices: 52383509--52383561 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
52383499 TAATATATTT
* *
52383509 TCGTAAAAATTTTACCATGGGTAAAA
1 TCGTAAAAATTCTACCAAGGGTAAAA
* *
52383535 TCGTCATAATTCTACCAAGGGTAAAA
1 TCGTAAAAATTCTACCAAGGGTAAAA
52383561 T
1 T
52383562 TGGGATGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (26 bp):
TCGTAAAAATTCTACCAAGGGTAAAA
Found at i:52385474 original size:38 final size:38
Alignment explanation
Indices: 52385430--52385505 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
52385420 GGTGCAAGTA
52385430 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
1 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
52385468 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
1 TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
52385506 CGAATATCGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (38 bp):
TACACTATCATTGACAAGTAATAAAGTGATAAGTATAT
Found at i:52391814 original size:43 final size:43
Alignment explanation
Indices: 52391724--52391838 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
52391714 TATCGAGATG
* *
52391724 TGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTACTG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTACTA
* **
52391767 TGATTACATGTAAGACCATGTCTGGGATATTGGCATCT-TTGTA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCAT-TGTACTA
*** *
52391810 TGATTTTGTGTAAGACCCTGTCTGGGACA
1 TGATTACATGTAAGACCATGTCTGGGACA
52391839 GCGGCATCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 60 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTACTA
Found at i:52392891 original size:34 final size:34
Alignment explanation
Indices: 52392834--52392900 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
52392824 CAAGTATCAG
**
52392834 TGTGGACCTTAGCCCATAGCAGTAGTAGTATTAA
1 TGTGGACCTTAGCCCATAGCAGTAACAGTATTAA
*
52392868 TGTGGGCCTTAGCCCATTA-CAGTAACAGTATTA
1 TGTGGACCTTAGCCCA-TAGCAGTAACAGTATTA
52392901 GTAATGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (34 bp):
TGTGGACCTTAGCCCATAGCAGTAACAGTATTAA
Found at i:52400652 original size:34 final size:34
Alignment explanation
Indices: 52400580--52400657 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
52400570 AGTAATAGAC
* * **
52400580 CAGTATCAGTGTGGGCCTTAGCCCAAAGCAGTTG
1 CAGTATCAATGTAGGCCTTAGCCCAAAGCAGTAA
*
52400614 CAGTATCAATGTAGGCCTTAGCCCATTAG-AGTAA
1 CAGTATCAATGTAGGCCTTAGCCCA-AAGCAGTAA
52400648 CAGTATCAAT
1 CAGTATCAAT
52400658 AATGCAACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 36 0.95
35 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (34 bp):
CAGTATCAATGTAGGCCTTAGCCCAAAGCAGTAA
Found at i:52404080 original size:46 final size:45
Alignment explanation
Indices: 52404013--52404188 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 45
52404003 TGTAACCCGC
52404013 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTT-GCAT
*
52404059 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTGCAT
* * * * * * *
52404109 CTC-TCGAACTCAAACTCGGACTCAACTCAATGAGTTCAGACATTTGCAT
1 C-CAT--AAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-GTTGCAT
52404158 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
52404189 TTCGTTTGCC
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
46 57 0.53
47 3 0.03
48 2 0.02
49 9 0.08
50 6 0.06
51 4 0.04
52 3 0.03
53 24 0.22
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTGCAT
Found at i:52406654 original size:27 final size:26
Alignment explanation
Indices: 52406616--52406675 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
52406606 ACACATATAT
* *
52406616 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
52406642 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
52406669 ATATCTG
1 ATATCTG
52406676 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:52416972 original size:62 final size:62
Alignment explanation
Indices: 52416875--52416998 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
52416865 TATCTTTGAA
*
52416875 AACACAGTAGCACCTTTCAACTGATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
1 AACACAGTAGCACCTTTCAACTAATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
52416937 AACACAGTAGCACCTTTCAACTAATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
1 AACACAGTAGCACCTTTCAACTAATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
52416999 CTTTATATTC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (62 bp):
AACACAGTAGCACCTTTCAACTAATCGAATAAGTCATCAATTCAAGGCAGAGGATATTTGTT
Found at i:52421617 original size:30 final size:30
Alignment explanation
Indices: 52421583--52421643 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52421573 TCTTTAACTC
52421583 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52421613 AAACTTTTGCATACTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52421643 A
1 A
52421644 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:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52423945 original size:43 final size:44
Alignment explanation
Indices: 52423894--52424031 Score: 124
Period size: 43 Copynumber: 3.2 Consensus size: 44
52423884 GTCTCGGACG
* * *
52423894 TGGTCTTACATGTAATTCA-ATATCGATGCCTCTGTCCCAGATA
1 TGGTCTTACATGTAAATCACATATCGATGCCTATGTCCCAGACA
* * * *
52423937 -GGATCTTACACG-AAATCAGATAT-GATGTCGATGTCCCAGACA
1 TGG-TCTTACATGTAAATCACATATCGATGCCTATGTCCCAGACA
* * *
52423979 TGGTCTTATATGTAAATCACA-ATCGAGGCCTGTGTCCCAGACA
1 TGGTCTTACATGTAAATCACATATCGATGCCTATGTCCCAGACA
* *
52424022 CGCTCTTACA
1 TGGTCTTACA
52424032 CGATGTCTAA
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
42 31 0.42
43 43 0.58
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
TGGTCTTACATGTAAATCACATATCGATGCCTATGTCCCAGACA
Found at i:52428740 original size:13 final size:13
Alignment explanation
Indices: 52428724--52428749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52428714 AATCAATTAG
52428724 GTTAAACAAAATA
1 GTTAAACAAAATA
52428737 GTTAAACAAAATA
1 GTTAAACAAAATA
52428750 AAGGAGAATA
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
GTTAAACAAAATA
Found at i:52434531 original size:25 final size:24
Alignment explanation
Indices: 52434503--52434648 Score: 105
Period size: 25 Copynumber: 5.9 Consensus size: 24
52434493 CAAACCAAGA
*
52434503 CTTTATGGCGAGTTATCTGTAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGC
* * *
52434528 CTTTGTGGTGAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTATT-GTAAAGC
*
52434553 TTTTGTGGCGAGTTATTTGTAAAGC
1 CTTTGTGGCGAGTTA-TTGTAAAGC
* * ***
52434578 CTTTGTGGTGAATTATCAAAAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGC
* * *
52434603 CTTTGTGGCAAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTATT-GTAAAGC
* *
52434628 CTTTGTGGTGAATTATT-TAAA
1 CTTTGTGGCGAGTTATTGTAAA
52434649 AATTCTTTGT
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 89 0.93
26 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (24 bp):
CTTTGTGGCGAGTTATTGTAAAGC
Found at i:52434565 original size:50 final size:49
Alignment explanation
Indices: 52434503--52434660 Score: 199
Period size: 50 Copynumber: 3.2 Consensus size: 49
52434493 CAAACCAAGA
* *
52434503 CTTTATGGCGAGTTATCTGTAAAGCCTTTGTGGTGAATTATTAGAAAAGC
1 CTTTGTGGCGAGTTAT-TGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
* *
52434553 TTTTGTGGCGAGTTATTTGTAAAGCCTTTGTGGTGAATTATCAAAAAAGC
1 CTTTGTGGCGAGTTA-TTGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
* * * * **
52434603 CTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGTGAATTATTTAAAAATT
1 CTTTGTGGCGAGTTATT-GTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
52434653 CTTTGTGG
1 CTTTGTGG
52434661 TGTATTGTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 2 0.02
50 91 0.97
51 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (49 bp):
CTTTGTGGCGAGTTATTGTAAAGCCTTTGTGGTGAATTATTAAAAAAGC
Found at i:52434650 original size:25 final size:25
Alignment explanation
Indices: 52434523--52434662 Score: 149
Period size: 25 Copynumber: 5.6 Consensus size: 25
52434513 AGTTATCTGT
52434523 AAAGCCTTTGTGGTGAATTA-TTAGA
1 AAAGCCTTTGTGGTGAATTATTTA-A
* * * **
52434548 AAAGCTTTTGTGGCGAGTTATTTGT
1 AAAGCCTTTGTGGTGAATTATTTAA
**
52434573 AAAGCCTTTGTGGTGAATTATCAAA
1 AAAGCCTTTGTGGTGAATTATTTAA
**
52434598 AAAGCCTTTGTGGCAAATTA-TTAGA
1 AAAGCCTTTGTGGTGAATTATTTA-A
52434623 AAAGCCTTTGTGGTGAATTATTTAA
1 AAAGCCTTTGTGGTGAATTATTTAA
**
52434648 AAATTCTTTGTGGTG
1 AAAGCCTTTGTGGTG
52434663 TATTGTATGG
Statistics
Matches: 92, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
24 1 0.01
25 86 0.93
26 5 0.05
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (25 bp):
AAAGCCTTTGTGGTGAATTATTTAA
Found at i:52434677 original size:75 final size:75
Alignment explanation
Indices: 52434523--52434662 Score: 199
Period size: 75 Copynumber: 1.9 Consensus size: 75
52434513 AGTTATCTGT
** * * **
52434523 AAAGCCTTTGTGGTGAATTATTAGAAAAGCTTTTGTGGCGAGTTATTTGTAAAGCCTTTGTGGTG
1 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
52434588 AATTATCAAA
66 AATTATCAAA
* **
52434598 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGTGAATTATTTAAAAATTCTTTGTGGTG
1 AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
52434663 TATTGTATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (75 bp):
AAAGCCTTTGTGGCAAATTATTAGAAAAGCCTTTGTGGCGAATTATTTAAAAAGCCTTTGTGGTG
AATTATCAAA
Found at i:52436363 original size:46 final size:46
Alignment explanation
Indices: 52436313--52436485 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
52436303 TGGTTGAGCA
52436313 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
52436359 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
52436404 CATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
52436452 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
52436486 GGGCGGGTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52436469 original size:93 final size:93
Alignment explanation
Indices: 52436310--52436480 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
52436300 GGATGGTTGA
* * *
52436310 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52436375 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
52436403 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52436468 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
52436481 ACTTAGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAATTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52442787 original size:46 final size:46
Alignment explanation
Indices: 52442731--52442899 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 46
52442721 TGAGCATCCA
52442731 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * * * * *
52442777 AACTCATTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* *
52442824 AACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* *
52442870 AGCTCGTTGAGTTGAGCCCGAGTTCACTTA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTA
52442900 GGGGCGGGTT
Statistics
Matches: 97, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 53 0.55
47 26 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:52442883 original size:93 final size:93
Alignment explanation
Indices: 52442724--52442894 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
52442714 GGATGGTTGA
*
52442724 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCATTGAGT
*
52442789 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGCCCGAGTTCGTGAAATGTAACTAG
* * *
52442817 GCATCCAAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCATTGAGT
52442882 TGAGCCCGAGTTC
66 TGAGCCCGAGTTC
52442895 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCATTGAGT
TGAGCCCGAGTTCGTGAAATGTAACTAG
Found at i:52446564 original size:22 final size:22
Alignment explanation
Indices: 52446539--52446581 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52446529 CATCTCAAAT
*
52446539 CAAACCACAATATACCAACTTC
1 CAAACAACAATATACCAACTTC
* *
52446561 CAAACAATAATATTCCAACTT
1 CAAACAACAATATACCAACTT
52446582 ACAACTATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (22 bp):
CAAACAACAATATACCAACTTC
Found at i:52447373 original size:43 final size:43
Alignment explanation
Indices: 52447227--52447376 Score: 176
Period size: 43 Copynumber: 3.5 Consensus size: 43
52447217 TATCCCATAT
* * * * *
52447227 ATGGTCTTACATGTTATCA-TATATCGATGTCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATA-CGATGCCAATGTCCCAGAC
* * * *
52447270 AAGGTCTTATACGAAATCATAATACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
* *
52447313 ATGGTCTTACACATAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
*
52447356 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACACGTAATCACA
52447377 TCTCGGTAAC
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 87 0.97
44 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACGATGCCAATGTCCCAGAC
Found at i:52468601 original size:15 final size:15
Alignment explanation
Indices: 52468581--52468610 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52468571 CAACACTTGT
52468581 GCCGAAACCACAAAA
1 GCCGAAACCACAAAA
*
52468596 GCCGAAACCTCAAAA
1 GCCGAAACCACAAAA
52468611 AATACATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.33, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCGAAACCACAAAA
Found at i:52475738 original size:15 final size:15
Alignment explanation
Indices: 52475718--52475764 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
52475708 ATCTAAACAT
52475718 ATTCAAATTAAGTTC
1 ATTCAAATTAAGTTC
*
52475733 ATTCAAA--CA--T-
1 ATTCAAATTAAGTTC
52475743 ATTCAAATTAAGTTC
1 ATTCAAATTAAGTTC
52475758 ATTCAAA
1 ATTCAAA
52475765 CATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 7 0.28
11 1 0.04
12 1 0.04
13 1 0.04
14 1 0.04
15 14 0.56
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (15 bp):
ATTCAAATTAAGTTC
Found at i:52475740 original size:25 final size:25
Alignment explanation
Indices: 52475712--52475770 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
52475702 TTCTTGATCT
52475712 AAACATATTCAAATTAAGTTCATTC
1 AAACATATTCAAATTAAGTTCATTC
52475737 AAACATATTCAAATTAAGTTCATTC
1 AAACATATTCAAATTAAGTTCATTC
52475762 AAACATATT
1 AAACATATT
52475771 TTCATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (25 bp):
AAACATATTCAAATTAAGTTCATTC
Found at i:52479552 original size:79 final size:79
Alignment explanation
Indices: 52479421--52479581 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
52479411 TATTTTTTAG
52479421 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
1 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
52479486 TTCATGAAGAAGCT
66 TTCATGAAGAAGCT
*
52479500 AAATTCAATCTAGCAAGAATATTTCATAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
1 AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
52479565 TTCATGAAGAAGCT
66 TTCATGAAGAAGCT
52479579 AAA
1 AAA
52479582 GACAGTGTCA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.17
Consensus pattern (79 bp):
AAATTCAATCTAGCAAGAATATTTCAAAAAGAAAAAAAAGGAAAAAACTAAGGCAAGAAGACAGC
TTCATGAAGAAGCT
Found at i:52490416 original size:79 final size:80
Alignment explanation
Indices: 52490318--52490500 Score: 221
Period size: 79 Copynumber: 2.3 Consensus size: 80
52490308 TCCTCGTTCA
* *
52490318 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
52490381 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
* **
52490398 AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
52490462 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
52490477 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
52490501 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:52490500 original size:40 final size:40
Alignment explanation
Indices: 52490316--52490500 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
52490306 GCTCCTCGTT
* *
52490316 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
52490356 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
52490396 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
52490435 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
52490476 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52490501 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 79 0.64
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:52492652 original size:40 final size:40
Alignment explanation
Indices: 52492608--52492829 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
52492598 GCTCCTCGTT
* *
52492608 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
52492648 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
52492688 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* *
52492727 CAAATGCCTTC-GG-CTTAGTCCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
52492764 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
52492805 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52492830 CATCATTCAA
Statistics
Matches: 162, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 25 0.15
38 12 0.07
39 44 0.27
40 70 0.43
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:52492816 original size:77 final size:78
Alignment explanation
Indices: 52492608--52492829 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 78
52492598 GCTCCTCGTT
* * * *
52492608 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTAGCACAAATGCCTTC-GGACTTAACCCG
52492672 GATTTAGTAACTCGCA
63 GATTTAGTAACTCGCA
* **
52492688 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG-CTTAGTCCGGA-
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCACAAATGCCTTCGGACTTAACCCGGAT
*
52492751 TTAGTATCTCGCA
66 TTAGTAACTCGCA
* * * *
52492764 CAAATGCCTTCGGATCTTAGTCCGG-ATATGGTCA-CTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGG-GCTTAGCCCGGAAT-TAGT-ATC-TAGCACAAATGCCTTC-GGACTTAACC
52492826 CGGA
61 CGGA
52492830 CATCATTCAA
Statistics
Matches: 124, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
76 27 0.22
77 28 0.23
78 13 0.10
79 41 0.33
80 15 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTAGCACAAATGCCTTCGGACTTAACCCGGAT
TTAGTAACTCGCA
Found at i:52500862 original size:40 final size:40
Alignment explanation
Indices: 52500638--52500862 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
52500628 GCTCCTCGTT
* *
52500638 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
52500678 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
52500718 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
52500758 CCAATGCCTTCAGG-CTTAGCCC-GAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
52500797 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
52500838 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52500863 CATCATTCAA
Statistics
Matches: 161, Mismatches: 18, Indels: 12
0.84 0.09 0.06
Matches are distributed among these distances:
38 4 0.02
39 28 0.17
40 115 0.71
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:52507634 original size:53 final size:54
Alignment explanation
Indices: 52507557--52507758 Score: 190
Period size: 53 Copynumber: 3.7 Consensus size: 54
52507547 CTTTTTAAAC
* * * *
52507557 TTACCATTGCCATGTCTTGACATGGTCTTACGTGGCATCCTTGCCTTAT-GAAG
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* * * * * ** * *
52507610 TCACCATTGCCACGCCTTGGCATGGTCTTACATGGGATATTTGCCTTATCGTAG
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* * * * * * *
52507664 TTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAAAAC
1 -TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
* *
52507719 TTACCAATGCCATGCCTTGGCATGGTCTTACTTGGTATCC
1 TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC
52507759 CTAAACCCTA
Statistics
Matches: 116, Mismatches: 31, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
53 41 0.35
54 37 0.32
55 38 0.33
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.36
Consensus pattern (54 bp):
TTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAAG
Found at i:52511926 original size:30 final size:30
Alignment explanation
Indices: 52511890--52511950 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52511880 CACGGGTTGG
* *
52511890 CACATGGGCATGTGGCCTGCCCGTGTGGAT
1 CACATGGGCATGTGCCCAGCCCGTGTGGAT
* *
52511920 CACATGGGCGTGTGCCCAGCTCGTGTGGAT
1 CACATGGGCATGTGCCCAGCCCGTGTGGAT
52511950 C
1 C
52511951 CTGAAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (30 bp):
CACATGGGCATGTGCCCAGCCCGTGTGGAT
Found at i:52513659 original size:49 final size:48
Alignment explanation
Indices: 52513605--52513723 Score: 143
Period size: 49 Copynumber: 2.5 Consensus size: 48
52513595 TCGATGCCGA
* **
52513605 GTCCCAGACAGGTCTTACACTAACTT-TCATAT-ATCGAGGGTAATGCCAT
1 GTCCCAGACAGGTCTTACACTAACTTGT-ATATCCT-GAGGCCAATG-CAT
* *
52513654 GTCCCAGACAGGTCTTACACTAGCTTGTATATCCTGAGGCCGATGCAT
1 GTCCCAGACAGGTCTTACACTAACTTGTATATCCTGAGGCCAATGCAT
*
52513702 GTCCCAGACATGTCTTACACTA
1 GTCCCAGACAGGTCTTACACTA
52513724 GCTCTCGTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
48 24 0.39
49 36 0.58
50 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
GTCCCAGACAGGTCTTACACTAACTTGTATATCCTGAGGCCAATGCAT
Found at i:52516310 original size:40 final size:40
Alignment explanation
Indices: 52516257--52516456 Score: 235
Period size: 40 Copynumber: 5.0 Consensus size: 40
52516247 AATTCAACCA
* * *
52516257 GATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGCCCG
1 GATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
52516297 GTTATAGTAACTCGCACAAATGCCTCCGGGACTTAGCCCG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* * *
52516337 GATATAGTAACTCGCACGAATGCCTTCAGGACTTAGCACG
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* * * *
52516377 GATATAATAACTCGCACAATTGCCTTCAGG-CTTAGCCCA
1 GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
52516416 GA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 GATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
52516456 G
1 G
52516457 TTATCATCCG
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 31 0.23
40 104 0.76
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
GATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:52519397 original size:42 final size:42
Alignment explanation
Indices: 52519279--52519407 Score: 168
Period size: 42 Copynumber: 3.0 Consensus size: 42
52519269 CATATAGTAC
* * **
52519279 CATACCAATGCCATATCCCAGATATGGTCTTACATGGGATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAAATCT
* * *
52519321 CATATCTATGCCAATAGCCCAGCTATGGTCTTACACGAAATCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACGAAATCT
* *
52519364 CATATCAATTCCATATCCCAGATATGGTCTTACACGTAATCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAAATCT
52519406 CA
1 CA
52519408 ACTAACCCTA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 39 0.53
43 35 0.47
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.29
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACGAAATCT
Found at i:52533929 original size:57 final size:57
Alignment explanation
Indices: 52533841--52533955 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
52533831 ACAAATCTAA
52533841 GATAGAAATAATTATTTTATTATCATTTTAAGGTATATGGCATGATTTCATGATTGT
1 GATAGAAATAATTATTTTATTATCATTTTAAGGTATATGGCATGATTTCATGATTGT
* *
52533898 GATAGAAATAATTATTTTATTATCATTTTAAGGTATATGTCATGATTTCGTGATTGT
1 GATAGAAATAATTATTTTATTATCATTTTAAGGTATATGGCATGATTTCATGATTGT
52533955 G
1 G
52533956 TGAAAATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (57 bp):
GATAGAAATAATTATTTTATTATCATTTTAAGGTATATGGCATGATTTCATGATTGT
Found at i:52537755 original size:19 final size:21
Alignment explanation
Indices: 52537733--52537780 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
52537723 AAGTAAAATT
52537733 AAATTAAT-CAA-ATTAGTAA
1 AAATTAATACAATATTAGTAA
**
52537752 AAATTAATACAATATTTTTAA
1 AAATTAATACAATATTAGTAA
52537773 AAATTAAT
1 AAATTAAT
52537781 TTTTAAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 3 0.12
21 14 0.56
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTAATACAATATTAGTAA
Found at i:52539520 original size:19 final size:17
Alignment explanation
Indices: 52539472--52539520 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
52539462 CATATTGCGG
*
52539472 GCCCATGTGAGCCAACAC
1 GCCCATATG-GCCAACAC
*
52539490 GCCCGTATGGCCAACAC
1 GCCCATATGGCCAACAC
52539507 GACCCATAATGGCC
1 G-CCCAT-ATGGCC
52539521 TTGGTCGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.27, C:0.39, G:0.22, T:0.12
Consensus pattern (17 bp):
GCCCATATGGCCAACAC
Found at i:52558947 original size:33 final size:33
Alignment explanation
Indices: 52558877--52558965 Score: 135
Period size: 33 Copynumber: 2.6 Consensus size: 33
52558867 TTTCAGTTAG
52558877 GGGCCTTAGCCCATTTTCAGTAACAGCAGCAGTCT
1 GGGCCTTAGCCCA-TTTCAGT-ACAGCAGCAGTCT
*
52558912 GGGCCTGAGCCCATTTCAGTACAG-AGGCAGTCT
1 GGGCCTTAGCCCATTTCAGTACAGCA-GCAGTCT
52558945 GGGCCTTAGCCCATTTCAGTA
1 GGGCCTTAGCCCATTTCAGTA
52558966 TAGTATGCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 1 0.02
33 31 0.61
34 7 0.14
35 12 0.24
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (33 bp):
GGGCCTTAGCCCATTTCAGTACAGCAGCAGTCT
Found at i:52559404 original size:30 final size:30
Alignment explanation
Indices: 52559368--52559435 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
52559358 TCAGTGATAA
52559368 TGGGCCTACAACCCATATTGCGGGCCCATG
1 TGGGCCTACAACCCATATTGCGGGCCCATG
*
52559398 TGGGCCTACAACCCATATTGCGGGCCTATG
1 TGGGCCTACAACCCATATTGCGGGCCCATG
52559428 TGGGCCTA
1 TGGGCCTA
52559436 TACTCTCATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.19, C:0.31, G:0.28, T:0.22
Consensus pattern (30 bp):
TGGGCCTACAACCCATATTGCGGGCCCATG
Found at i:52573860 original size:43 final size:42
Alignment explanation
Indices: 52573812--52573975 Score: 181
Period size: 43 Copynumber: 3.9 Consensus size: 42
52573802 ATCGAGATGT
52573812 GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
* *
52573854 AGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATTAATT-
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATTA-T-ATTG
* * * *
52573898 GATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATTGATA-TG
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATT-ATATTG
* * *
52573940 TGATAACATGTAAGACCATATCTGGGATA-TGGCATT
1 -GATTACATGTAAGACCATGTCTGGGACATTGGCATT
52573976 GTATGAGCTT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 90 0.87
44 2 0.02
45 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATTATATTG
Found at i:52575526 original size:29 final size:29
Alignment explanation
Indices: 52575464--52575553 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
52575454 CACATACCTG
* * *
52575464 TATATGGGCCACTAGGCCC-AATCATATT
1 TATATGGCCCATTAGGCCCAAATCACATT
52575492 TATATGGCCCATTAGGCCCAAATCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
* * * * *
52575521 TTTATGGTCCATCAAGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
52575550 TATA
1 TATA
52575554 GTCATGCTCA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 17 0.33
29 35 0.67
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:52578834 original size:43 final size:42
Alignment explanation
Indices: 52578764--52578880 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
52578754 ACGTAGTACT
*
52578764 GTACCAATGCCACAT-CCCAGATATGGTCTTACATG-TGATCTC
1 GTACCAATGCCA-ATACCCAGATATGGTCTTACATGAAG-TCTC
* *
52578806 GTACCAATGCCAATAGCCCAGCTATGGTCTTAGATGAAGTCTC
1 GTACCAATGCCAATA-CCCAGATATGGTCTTACATGAAGTCTC
* * *
52578849 ATATCGATGCC-ATATCCCAGATATGGTCTTAC
1 GTACCAATGCCAATA-CCCAGATATGGTCTTAC
52578881 GCGTAATCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
41 2 0.03
42 30 0.48
43 30 0.48
44 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (42 bp):
GTACCAATGCCAATACCCAGATATGGTCTTACATGAAGTCTC
Found at i:52584658 original size:30 final size:30
Alignment explanation
Indices: 52584615--52584672 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
52584605 TTAATACGAG
52584615 CTTTGGCAAAATTACA-TTTTTGCCCCTAAA
1 CTTTGGCAAAATTACACTTTTT-CCCCTAAA
* *
52584645 CTTTTGCATAATTACACTTTTTCCCCTA
1 CTTTGGCAAAATTACACTTTTTCCCCTA
52584673 TGCTCGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.26, C:0.26, G:0.07, T:0.41
Consensus pattern (30 bp):
CTTTGGCAAAATTACACTTTTTCCCCTAAA
Found at i:52590471 original size:21 final size:21
Alignment explanation
Indices: 52590447--52590488 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52590437 TCATCAGATC
*
52590447 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
52590468 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
52590489 AGGTGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:52594427 original size:49 final size:50
Alignment explanation
Indices: 52594355--52594452 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 50
52594345 TTTAATATGT
52594355 TTAGTTTAATTAATTCAATTGTTTT-AATTTTCTTTAGTTGCGTAAATAC
1 TTAGTTTAATTAATTCAATTGTTTTGAATTTTCTTTAGTTGCGTAAATAC
*
52594404 TTAGTTTAATTAATT-AAGTTGTTTTGAATTTTCTTTAGTTGCTTAAATA
1 TTAGTTTAATTAATTCAA-TTGTTTTGAATTTTCTTTAGTTGCGTAAATA
52594453 ATTTCGGCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 2 0.04
49 22 0.48
50 22 0.48
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (50 bp):
TTAGTTTAATTAATTCAATTGTTTTGAATTTTCTTTAGTTGCGTAAATAC
Found at i:52597703 original size:18 final size:18
Alignment explanation
Indices: 52597680--52597726 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
52597670 AGAGACTGTG
* *
52597680 GAAAAAGAAAAAGAACAA
1 GAAAAATAAAAAGAAAAA
*
52597698 GAAAAATAAAGAGAAAAA
1 GAAAAATAAAAAGAAAAA
*
52597716 TAAAAATAAAA
1 GAAAAATAAAA
52597727 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (18 bp):
GAAAAATAAAAAGAAAAA
Found at i:52597726 original size:5 final size:5
Alignment explanation
Indices: 52597712--52597741 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
52597702 AATAAAGAGA
52597712 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
52597742 AGGAAAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52606942 original size:16 final size:16
Alignment explanation
Indices: 52606921--52606953 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52606911 CAGCCATTTT
52606921 GCCCTGAAGAATTGGA
1 GCCCTGAAGAATTGGA
*
52606937 GCCCTGAAGATTTGGA
1 GCCCTGAAGAATTGGA
52606953 G
1 G
52606954 ACACCATTTG
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:0.27, C:0.18, G:0.33, T:0.21
Consensus pattern (16 bp):
GCCCTGAAGAATTGGA
Found at i:52612608 original size:46 final size:46
Alignment explanation
Indices: 52612558--52612721 Score: 158
Period size: 46 Copynumber: 3.5 Consensus size: 46
52612548 GCATCCGAAC
52612558 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAAG
1 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAAG
* * * * * *
52612604 TCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATCCGAAC
1 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCAAAG
* **
52612651 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCGAG
1 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAAG
52612696 CTCGTTGAGTTGAGTCCGAGTTCACT
1 -TCGTTGAGTTGAGTCCGAGTTCACT
52612722 CAGGGGCGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 6 0.06
46 47 0.50
47 27 0.29
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAAG
Found at i:52612707 original size:93 final size:93
Alignment explanation
Indices: 52612548--52612718 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
52612538 GGATGGTTGA
*
52612548 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCAAAGTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAAGTCGTTGAGT
52612613 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
**
52612641 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAAG-TCGTTGAG
52612705 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
52612719 ACTCAGGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 4 0.05
93 70 0.95
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCAAAGTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52616910 original size:46 final size:45
Alignment explanation
Indices: 52616737--52616907 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
52616727 ATGTAACCTG
* * *
52616737 TCCATAAGTGAACTCGGACTCAACTCAACGACCTCGGGCATTCGTA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTC-CA
*
52616783 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-ATGCCTA
1 TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCC-A
* *** *
52616827 GTTACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACA
1 --TCCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTC-CA
* *
52616876 TCCAAAAGTGAACTCGTACTCAACTCAACGAG
1 TCCATAAGTGAACTCGGACTCAACTCAACGAG
52616908 TTCAGATGCC
Statistics
Matches: 102, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
44 4 0.04
45 1 0.01
46 61 0.60
47 29 0.28
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (45 bp):
TCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCCA
Found at i:52619098 original size:25 final size:25
Alignment explanation
Indices: 52619070--52619142 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
52619060 AGGTGCCATC
52619070 TGTATGCTAGACTGGTAGCTATTAT
1 TGTATGCTAGACTGGTAGCTATTAT
* * * *
52619095 TGTAAGC-A-A-AGGT-GCCA-T-C
1 TGTATGCTAGACTGGTAGCTATTAT
52619114 TGTATGCTAGACTGGTAGCTATTAT
1 TGTATGCTAGACTGGTAGCTATTAT
52619139 TGTA
1 TGTA
52619143 AGCAAACTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 6 0.18
20 2 0.06
21 4 0.12
22 6 0.18
23 4 0.12
24 2 0.06
25 10 0.29
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (25 bp):
TGTATGCTAGACTGGTAGCTATTAT
Found at i:52619122 original size:44 final size:44
Alignment explanation
Indices: 52619059--52619148 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
52619049 AGTGCTTCGT
52619059 AAGGTGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCA
1 AAGGTGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCA
52619103 AAGGTGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCA
1 AAGGTGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCA
52619147 AA
1 AA
52619149 CTCTGGTAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
AAGGTGCCATCTGTATGCTAGACTGGTAGCTATTATTGTAAGCA
Found at i:52620752 original size:12 final size:12
Alignment explanation
Indices: 52620735--52620764 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
52620725 CCAGAGATGT
52620735 TCATCATGTTCC
1 TCATCATGTTCC
52620747 TCATCATGTTCC
1 TCATCATGTTCC
52620759 TCATCA
1 TCATCA
52620765 GTCCTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
TCATCATGTTCC
Found at i:52628650 original size:18 final size:19
Alignment explanation
Indices: 52628601--52628650 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
52628591 ATAATTTTGA
*
52628601 CATTTAATATG-TTTCAGT
1 CATTTAATATGCTATCAGT
* *
52628619 CTAATTAATTTGCTAT-AGT
1 C-ATTTAATATGCTATCAGT
52628638 CATTTAATATGCT
1 CATTTAATATGCT
52628651 TAATTATGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 11 0.44
19 12 0.48
20 2 0.08
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (19 bp):
CATTTAATATGCTATCAGT
Found at i:52632194 original size:46 final size:46
Alignment explanation
Indices: 52632064--52632279 Score: 185
Period size: 46 Copynumber: 4.7 Consensus size: 46
52632054 AACCGTCCCA
* *
52632064 ATGCTATGTCCCAGACATGGTCTTACACTAACACATC-T-T-GTA-GCCG
1 ATGC-ATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTCTCG-AGGCTG
* *
52632110 ATGCATGTCCCAGACATGTCTTATACTAGTTTA-T-GTCTCGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTAG--CACTCGTCTCGAGGCTG
* * * *
52632156 ATGCATGTCCCAAACATGTCTTACACTAGCACTCGTCTCAATGCCG
1 ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAGGCTG
* * * * *
52632202 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCTG
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGT-CTCGAGGCTG
52632250 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
52632280 TCACACAAAT
Statistics
Matches: 139, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 13 0.09
45 16 0.12
46 60 0.43
47 27 0.19
48 22 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAGGCTG
Found at i:52632225 original size:94 final size:90
Alignment explanation
Indices: 52632064--52632279 Score: 240
Period size: 94 Copynumber: 2.3 Consensus size: 90
52632054 AACCGTCCCA
* **
52632064 ATGCTATGTCCCAGACATGGTCTTACACTAACACATCTTGTAGCCGATGCATGTCCCAGACATGT
1 ATGC-ATGTCCCAGACAT-GTCTTACACTAGCACATCTTCAAGCCGATGCATGTCCCAGACATGT
* * **
52632129 CTTATACTAG-T-TTATGTCTCGAGGCTG
64 CTTACACTAGCTCTCAT-AAT-GAGGCTG
*
52632156 ATGCATGTCCCAAACATGTCTTACACTAGCAC-TCGTCTCAATGCCGATGCCATGTCCCAGACAT
1 ATGCATGTCCCAGACATGTCTTACACTAGCACATC-T-TCAA-GCCGATG-CATGTCCCAGACAT
* *
52632220 GGTCTTACACTGGCTCTCATAATGTGGCTG
62 -GTCTTACACTAGCTCTCATAATGAGGCTG
52632250 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
52632280 TCACACAAAT
Statistics
Matches: 106, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
89 2 0.02
90 15 0.14
91 14 0.13
92 11 0.10
93 14 0.13
94 45 0.42
95 2 0.02
96 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (90 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCACATCTTCAAGCCGATGCATGTCCCAGACATGTCT
TACACTAGCTCTCATAATGAGGCTG
Found at i:52639013 original size:40 final size:40
Alignment explanation
Indices: 52638955--52639136 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
52638945 TTCGAATGAC
*
52638955 ATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACTAT
1 ATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACTAT
* * *
52638995 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CTAT
1 ATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACTAT
* * * *
52639035 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTAT
1 ATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACTAT
*
52639075 ATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACCAT
1 ATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACTAT
* *
52639115 ATCCAGGCTAAGACCCGAAGGC
1 ATCCGGGCTAAGATCCGAAGGC
52639137 CTTGTGCGAG
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 117 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACTAT
Found at i:52639093 original size:80 final size:79
Alignment explanation
Indices: 52638955--52639172 Score: 262
Period size: 80 Copynumber: 2.7 Consensus size: 79
52638945 TTCGAATGAC
* * * *
52638955 ATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGCAT
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAG-TCCCGAAGGCAT
* *
52639019 TTGTGCGAGTTG-CTAT
64 TTATGCGAG-TGACCAT
*
52639035 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGC-TTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCATT
*
52639100 TATGCTAGTGACCAT
65 TATGCGAGTGACCAT
* * * * *
52639115 ATCCAGGCTAAGACCCGAAGGCCTTGTGCGAGTGGTTATATCC-GGCTAAATCCCGAAG
1 ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAG
52639173 ATACTTGGGT
Statistics
Matches: 121, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
78 14 0.12
79 20 0.17
80 87 0.72
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGACCCGAAGGCTTTGTGCTAGTGATTATATCCGGGCTAAGTCCCGAAGGCATTT
ATGCGAGTGACCAT
Found at i:52643074 original size:20 final size:20
Alignment explanation
Indices: 52643032--52643074 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
52643022 ATGTCCCAAA
*
52643032 CATGGTCTTACACTAGCTGT
1 CATGGTCTTACACTAGCTAT
*
52643052 CATGGTCTTACACTGGCTAT
1 CATGGTCTTACACTAGCTAT
52643072 CAT
1 CAT
52643075 CTTCGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (20 bp):
CATGGTCTTACACTAGCTAT
Found at i:52643157 original size:50 final size:49
Alignment explanation
Indices: 52643093--52643220 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 49
52643083 CTTATGCCAA
* *
52643093 GTCCCAAACATGGTCTTACACTAGCTCTCACATAACCAT-CCCGATGTCAT
1 GTCCCAGACATGGTCTTACACTAGCTCTCACATAA-CATGCCCGAT-ACAT
** *
52643143 GTCCCAGACATGGTCTTACACTAGCTCT--CATAATGTGGCCGATACAT
1 GTCCCAGACATGGTCTTACACTAGCTCTCACATAACATGCCCGATACAT
*
52643190 GTCCCAGACAT-GTCTTACACTAGCTCACACA
1 GTCCCAGACATGGTCTTACACTAGCTCTCACA
52643221 AATGACCCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
46 15 0.22
47 15 0.22
48 12 0.17
50 27 0.39
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (49 bp):
GTCCCAGACATGGTCTTACACTAGCTCTCACATAACATGCCCGATACAT
Found at i:52645511 original size:19 final size:19
Alignment explanation
Indices: 52645475--52645511 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52645465 GATGAAAAGG
*
52645475 ATGATAGATAAAAAAAATT
1 ATGATAGAGAAAAAAAATT
*
52645494 ATGATAGAGAAAAGAAAT
1 ATGATAGAGAAAAAAAAT
52645512 ATCAAGACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (19 bp):
ATGATAGAGAAAAAAAATT
Found at i:52646099 original size:16 final size:17
Alignment explanation
Indices: 52646053--52646101 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 17
52646043 TGATTTTTTT
*
52646053 TATTTTGTTATATTAGA
1 TATTTTTTTATATTAGA
**
52646070 TAAATTTTTA-ATTA-A
1 TATTTTTTTATATTAGA
52646085 TATTTTTTTATATTAGA
1 TATTTTTTTATATTAGA
52646102 AAATATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTTTTTATATTAGA
Found at i:52655061 original size:26 final size:27
Alignment explanation
Indices: 52655000--52655119 Score: 111
Period size: 26 Copynumber: 4.5 Consensus size: 27
52654990 TGAAAGTTTG
** *
52655000 AAATAAATAATATACAGAAA-AAGTTTA
1 AAATAAATAATATGTA-AAATAAATTTA
*
52655027 AAATGAATAATATGTAAAAT-AATTTA
1 AAATAAATAATATGTAAAATAAATTTA
* * * *
52655053 AGATAAATAATATAT-AAATGAGTTTA
1 AAATAAATAATATGTAAAATAAATTTA
**
52655079 AAATAAATGTTATGTAAAAATAAATTTA
1 AAATAAATAATATGT-AAAATAAATTTA
52655107 AAATAAATAATAT
1 AAATAAATAATAT
52655120 ACAAGACATT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
25 4 0.05
26 36 0.49
27 13 0.18
28 20 0.27
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (27 bp):
AAATAAATAATATGTAAAATAAATTTA
Found at i:52655093 original size:52 final size:55
Alignment explanation
Indices: 52655000--52655122 Score: 162
Period size: 52 Copynumber: 2.3 Consensus size: 55
52654990 TGAAAGTTTG
*
52655000 AAATAAATAATATACAGAAAAAGTTTAAAATGAATAATATGT-AAAAT-AATTTA
1 AAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAATAAATTTA
* * ** **
52655053 AGATAAATAATATATA-AATGAGTTTAAAATAAATGTTATGTAAAAATAAATTTA
1 AAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAATAAATTTA
52655107 AAATAAATAATATACA
1 AAATAAATAATATACA
52655123 AGACATTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
52 20 0.34
53 19 0.32
54 20 0.34
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (55 bp):
AAATAAATAATATACAGAAAAAGTTTAAAATAAATAATATGTAAAAATAAATTTA
Found at i:52656510 original size:15 final size:16
Alignment explanation
Indices: 52656490--52656519 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52656480 CGGAGGTACG
52656490 TTTTATTATT-TTTCT
1 TTTTATTATTATTTCT
52656505 TTTTATTATTATTTC
1 TTTTATTATTATTTC
52656520 GTGAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTATTATTTCT
Found at i:52657358 original size:44 final size:44
Alignment explanation
Indices: 52657274--52657358 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
52657264 ATTTGATAAT
* * *
52657274 TTCAACCTACTCCATTGCATCTTCATGGAGATGAGGTTTGCGAC
1 TTCAACCTACTCCACTGCAACTTCATGGAGATGAGATTTGCGAC
* * *
52657318 TTCAATCTGCTCCACTGCAACTTCA-GGCAGATTAGATTTGC
1 TTCAACCTACTCCACTGCAACTTCATGG-AGATGAGATTTGC
52657359 CATGGTAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.06
44 32 0.94
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (44 bp):
TTCAACCTACTCCACTGCAACTTCATGGAGATGAGATTTGCGAC
Found at i:52657581 original size:44 final size:44
Alignment explanation
Indices: 52657498--52657582 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
52657488 AAGATCTGTA
* * **
52657498 ACTTCGATCTACTCCTCTACAACTTCAAGGAGATGAGATTCACG
1 ACTTCAATCTACTCCACTACAACTTCAAGGAGACAAGATTCACG
* *
52657542 ACTTCAATCTGCTCCACTACAACTTCAGGGAGACAAGATTC
1 ACTTCAATCTACTCCACTACAACTTCAAGGAGACAAGATTC
52657583 GCCATTGTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (44 bp):
ACTTCAATCTACTCCACTACAACTTCAAGGAGACAAGATTCACG
Found at i:52668692 original size:27 final size:27
Alignment explanation
Indices: 52668657--52668780 Score: 99
Period size: 26 Copynumber: 4.6 Consensus size: 27
52668647 CGAAAGTTTG
52668657 AAATAAATAATATACAAAAAAAATTTA
1 AAATAAATAATATACAAAAAAAATTTA
* ** *
52668684 AAATGAATAATAT-GTAAAATAATTTA
1 AAATAAATAATATACAAAAAAAATTTA
* * ** *
52668710 AGATAAATAATATA-TAAATGAGTTTA
1 AAATAAATAATATACAAAAAAAATTTA
** ** *
52668736 AAATAAATGTTATGTAAAAAGAAACTTA
1 AAATAAATAATATACAAAAA-AAATTTA
52668764 AAATAAATAATATACAA
1 AAATAAATAATATACAA
52668781 GACATTTAAG
Statistics
Matches: 72, Mismatches: 22, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
26 40 0.56
27 15 0.21
28 17 0.24
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.30
Consensus pattern (27 bp):
AAATAAATAATATACAAAAAAAATTTA
Found at i:52670164 original size:14 final size:14
Alignment explanation
Indices: 52670145--52670172 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52670135 CGGAGGTACG
52670145 TTTTATTATTATTT
1 TTTTATTATTATTT
52670159 TTTTATTATTATTT
1 TTTTATTATTATTT
52670173 CGTGAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTATTATTT
Found at i:52671704 original size:93 final size:93
Alignment explanation
Indices: 52671591--52671762 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
52671581 CGCCCATAAG
* *
52671591 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52671656 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
52671684 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52671749 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
52671763 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:52671759 original size:46 final size:46
Alignment explanation
Indices: 52671584--52671759 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
52671574 TGTAACCCGC
* * *
52671584 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
52671630 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
52671680 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
52671723 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
52671760 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:52677269 original size:17 final size:19
Alignment explanation
Indices: 52677249--52677290 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
52677239 TATATAATAC
52677249 TAAAAATTC-TTAA-AATT-
1 TAAAAA-TCATTAAGAATTA
52677266 TAAAAATCATTAAGAATTA
1 TAAAAATCATTAAGAATTA
52677285 TAAAAA
1 TAAAAA
52677291 ATCGATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 10 0.45
18 4 0.18
19 6 0.27
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAATCATTAAGAATTA
Found at i:52677384 original size:10 final size:10
Alignment explanation
Indices: 52677369--52677401 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
52677359 AAAAATACAT
52677369 AAATAATTTA
1 AAATAATTTA
52677379 AAATAATTTTA
1 AAATAA-TTTA
52677390 AAA-AATTTA
1 AAATAATTTA
52677399 AAA
1 AAA
52677402 ACTATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 8 0.36
11 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATAATTTA
Found at i:52677933 original size:35 final size:35
Alignment explanation
Indices: 52677888--52677959 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
52677878 AAAAATTCTT
*
52677888 TAACACATATGCATGTGGGAATTATATATTTAGAA
1 TAACAAATATGCATGTGGGAATTATATATTTAGAA
52677923 TAACAAATATGCATGTGGGAATTATATATTTAGAA
1 TAACAAATATGCATGTGGGAATTATATATTTAGAA
52677958 TA
1 TA
52677960 TAGGGGTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (35 bp):
TAACAAATATGCATGTGGGAATTATATATTTAGAA
Found at i:52678073 original size:17 final size:20
Alignment explanation
Indices: 52678044--52678087 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
52678034 AATATGTATA
*
52678044 ATATT-AATATAAA-A-ATT
1 ATATTAAATATAAATACATC
52678061 ATATTAAAT-TAAATACATC
1 ATATTAAATATAAATACATC
52678080 ATATTAAA
1 ATATTAAA
52678088 AATACTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 4 0.17
19 10 0.43
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATTAAATATAAATACATC
Found at i:52684299 original size:56 final size:56
Alignment explanation
Indices: 52684213--52684388 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
52684203 ACAAGGGATG
*
52684213 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
52684269 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
52684325 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
52684381 ATGGGCAA
1 ATGGGCAA
52684389 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:52685888 original size:47 final size:47
Alignment explanation
Indices: 52685834--52686478 Score: 840
Period size: 47 Copynumber: 13.6 Consensus size: 47
52685824 TATTTGAATA
* *
52685834 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52685881 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
52685928 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC-ATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
52685974 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
52686023 AATGTGAAAGTG--TATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686068 AATGTGAAA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686114 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52686161 AATGTGAACA-TGTGTATGTGTGATGAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52686208 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGACCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686255 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686302 AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGA--AA---G----TGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686358 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
52686405 AATGTGAAAGTGTATATATGTGATAAGGCTGGATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
52686452 GATGTGGAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
52686479 TCCCGAAGGG
Statistics
Matches: 549, Mismatches: 31, Indels: 36
0.89 0.05 0.06
Matches are distributed among these distances:
44 2 0.00
45 41 0.07
46 60 0.11
47 357 0.65
48 26 0.05
49 21 0.04
54 1 0.00
55 1 0.00
56 40 0.07
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:52686307 original size:9 final size:9
Alignment explanation
Indices: 52686293--52686317 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52686283 CCGAATGGCC
52686293 AATGTGATG
1 AATGTGATG
52686302 AATGTGATG
1 AATGTGATG
52686311 AATGTGA
1 AATGTGA
52686318 ACATGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (9 bp):
AATGTGATG
Found at i:52686307 original size:103 final size:103
Alignment explanation
Indices: 52686199--52686411 Score: 417
Period size: 103 Copynumber: 2.1 Consensus size: 103
52686189 CCGAATGGCC
52686199 AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAC
52686264 ATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
66 ATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
*
52686302 AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC
1 AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAC
52686367 ATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
66 ATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
52686405 AATGTGA
1 AATGTGA
52686412 AAGTGTATAT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (103 bp):
AATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGACCAATGTGATGAATGTGAAC
ATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
Found at i:52686309 original size:150 final size:139
Alignment explanation
Indices: 52685834--52686466 Score: 853
Period size: 150 Copynumber: 4.5 Consensus size: 139
52685824 TATTTGAATA
* * * *
52685834 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA-TGTGTATG
* * * * *
52685899 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
65 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA-TGCATATATGAGATAAGGCCGAATGG
52685964 CC-ATGTGATG
129 CCAATGTGATG
52685974 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA-GTGTAT
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGTGTAT
52686038 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGCATATATGAGATAAGGCCGAATGG
64 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGCATATATGAGATAAGGCCGAATGG
52686103 CCAATGTGATG
129 CCAATGTGATG
* *
52686114 AATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTAT
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-ATGTGTAT
* ** * *
52686178 GTGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATG
64 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-ATGCATATATGAGATAAGGCCGAATG
*
52686243 ACCAATGTGATG
128 GCCAATGTGATG
* *
52686255 AATGTGAACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGATGAATGTGAA
1 AATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCC---------AATGTGATGAATGTGAA
52686319 CATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAA
56 -ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-ATGCATATATGAGATAA
52686384 GGCCGAATGGCCAATGTGATG
119 GGCCGAATGGCCAATGTGATG
* * * *
52686405 AATGTGAAAGTGTATATATGTGATAAGGCTGGATGGCCAATGTGATGGATGTGGAA-GTGTAT
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGTGTAT
52686467 AAATGTGATA
Statistics
Matches: 443, Mismatches: 33, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
138 41 0.09
139 32 0.07
140 115 0.26
141 83 0.19
142 42 0.09
149 1 0.00
150 129 0.29
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (139 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGTGTATGT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGCATATATGAGATAAGGCCGAATGGCC
AATGTGATG
Found at i:52691285 original size:46 final size:46
Alignment explanation
Indices: 52691218--52691343 Score: 234
Period size: 46 Copynumber: 2.7 Consensus size: 46
52691208 TGTAACCCGC
52691218 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
52691264 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
52691310 CCATAAGTGAACTCAGACTCAACTCAACGAGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC
52691344 CGATGCCTAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:52695503 original size:96 final size:97
Alignment explanation
Indices: 52695338--52695530 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 97
52695328 AAGGAGGAAT
* *
52695338 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGGGTTTCCG
1 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
52695403 ATGTCCAATTAAACATCCAAATAGAG-AGAAA
66 ATGTCCAATTAAACATCCAAATAGAGAAGAAA
** * *
52695434 ACAATTGAGTTATCACCTTTTGTGCAATGTTATTGGTGTAGTTTAGAAGATCATAAGAGTTTCCA
1 ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
* *
52695499 ATGTCCAATTAAATATCCAACTAGAGAAGAAA
66 ATGTCCAATTAAACATCCAAATAGAGAAGAAA
52695531 GTAAGTATGA
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
96 83 0.94
97 5 0.06
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (97 bp):
ACAATTGAGCGATCACCTTTTGTGCAATGTTATTGGTGTAGTTCAAAAGATCATAAGAGTTTCCA
ATGTCCAATTAAACATCCAAATAGAGAAGAAA
Found at i:52698476 original size:43 final size:42
Alignment explanation
Indices: 52698424--52698605 Score: 136
Period size: 43 Copynumber: 4.3 Consensus size: 42
52698414 TCTGGCACTG
*
52698424 TAGTGCATCATCGGATAAATCGAATGAAATATTGTGGCACACA
1 TAGTGCATCATCGGATAAA-CGAATGAAATATTCTGGCACACA
* * * * * * *
52698467 TAGTGCATCATCAGATAAGC-CATAGAAATAATACTTGCATACG
1 TAGTGCATCATCGGATAAACGAAT-GAAAT-ATTCTGGCACACA
* * * * **
52698510 TAGTGCATCATTGGATTAACCGAA-GTAATAATGCTGGCACGTA
1 TAGTGCATCATCGGA-TAAACGAATGAAAT-ATTCTGGCACACA
* * *
52698553 -AGTGCATCATCGGATATACAAAAGAAAATATTCTGGCACACA
1 TAGTGCATCATCGGATAAACGAATG-AAATATTCTGGCACACA
52698595 TAGTGCATCAT
1 TAGTGCATCAT
52698606 TGATTAAACC
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
41 7 0.07
42 30 0.29
43 63 0.60
44 4 0.04
45 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (42 bp):
TAGTGCATCATCGGATAAACGAATGAAATATTCTGGCACACA
Found at i:52700586 original size:17 final size:18
Alignment explanation
Indices: 52700564--52700599 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
52700554 ATACTGGGCC
52700564 GTGTGGGCC-ACACGGGT
1 GTGTGGGCCTACACGGGT
52700581 GTGTGGGCCTACACGGGT
1 GTGTGGGCCTACACGGGT
52700599 G
1 G
52700600 AACCACACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (18 bp):
GTGTGGGCCTACACGGGT
Found at i:52702424 original size:20 final size:21
Alignment explanation
Indices: 52702401--52702440 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
52702391 AGTTTTATTT
52702401 AATTAAATAA-AGGTTAATTA
1 AATTAAATAACAGGTTAATTA
* *
52702421 AATTAATTAACATGTTAATT
1 AATTAAATAACAGGTTAATT
52702441 TAGCTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (21 bp):
AATTAAATAACAGGTTAATTA
Found at i:52702740 original size:24 final size:24
Alignment explanation
Indices: 52702708--52702765 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
52702698 ATAATTATTC
* *
52702708 ATGAGGTAATTATATAATGCTTGT
1 ATGAGGTAAGTATATAAAGCTTGT
*
52702732 ATGAGGTAAGTGTATAAAGCTTGT
1 ATGAGGTAAGTATATAAAGCTTGT
*
52702756 ATGAGTTAAG
1 ATGAGGTAAG
52702766 ATAAGATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (24 bp):
ATGAGGTAAGTATATAAAGCTTGT
Found at i:52704592 original size:22 final size:24
Alignment explanation
Indices: 52704558--52704602 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
52704548 AATCCAAATA
*
52704558 ATTAACATCTTTAA-CT-ATTTTG
1 ATTAAAATCTTTAATCTAATTTTG
*
52704580 ATTAAAATTTTTAATCTAATTTT
1 ATTAAAATCTTTAATCTAATTTT
52704603 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTAAAATCTTTAATCTAATTTTG
Found at i:52704610 original size:24 final size:22
Alignment explanation
Indices: 52704567--52704610 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
52704557 AATTAACATC
* *
52704567 TTTAACTATTTTGATTAAAATT
1 TTTAACTATTTTAATAAAAATT
52704589 TTTAATCTAATTTTAATAAAAA
1 TTTAA-CT-ATTTTAATAAAAA
52704611 ATATCATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 2 0.11
24 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAACTATTTTAATAAAAATT
Found at i:52706027 original size:19 final size:19
Alignment explanation
Indices: 52705971--52706063 Score: 68
Period size: 19 Copynumber: 5.0 Consensus size: 19
52705961 ATAAATTTAA
*
52705971 ATAATTTTATATACTTTTT
1 ATAATTTTATATAATTTTT
*
52705990 -T-ATTTTTTA-AATTGATTT
1 ATAATTTTATATAATT--TTT
*
52706008 ATAATTTTATATAGTTTTT
1 ATAATTTTATATAATTTTT
* *
52706027 ATAATTCTATAT-CTTTTT
1 ATAATTTTATATAATTTTT
* * *
52706045 ACATTTTTTTATAATTTTT
1 ATAATTTTATATAATTTTT
52706064 TTACTTTTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
16 3 0.05
17 7 0.12
18 17 0.30
19 20 0.35
20 7 0.12
21 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
ATAATTTTATATAATTTTT
Found at i:52706104 original size:9 final size:10
Alignment explanation
Indices: 52706083--52706118 Score: 56
Period size: 9 Copynumber: 3.6 Consensus size: 10
52706073 AAAAAATAAT
52706083 TTTTTAAATA
1 TTTTTAAATA
52706093 TTTTTAAA-A
1 TTTTTAAATA
52706102 TTTTTAAATA
1 TTTTTAAATA
52706112 GTTTTTA
1 -TTTTTA
52706119 TGATTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 9 0.38
11 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:52707911 original size:20 final size:19
Alignment explanation
Indices: 52707853--52707905 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
52707843 GAATCTATTG
* * *
52707853 TCTTTTTGTTTGAATCGAT
1 TCTTTTTTTTTAAATCAAT
*
52707872 TC-ATTTTTTTAAATCAAT
1 TCTTTTTTTTTAAATCAAT
52707890 TCTTTTTTATTTAAAT
1 TCTTTTTT-TTTAAAT
52707906 TGATTCAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 14 0.52
19 6 0.22
20 7 0.26
ACGTcount: A:0.25, C:0.09, G:0.06, T:0.60
Consensus pattern (19 bp):
TCTTTTTTTTTAAATCAAT
Found at i:52712056 original size:49 final size:49
Alignment explanation
Indices: 52711988--52712115 Score: 168
Period size: 49 Copynumber: 2.6 Consensus size: 49
52711978 ATCTAAGTTG
*
52711988 ATGCCATGTCCTAGACAGGTCTTACACTAACTTTCATATATCGAG-GCCA
1 ATGCCATGTCCTAGACAGGTCTTACACTAACTCTCATATATCG-GTGCCA
* * ** * * *
52712037 ATGCCATGTCCCAGGCAGGTCTTACACTGGCTCTCATCTATCGGTGTCG
1 ATGCCATGTCCTAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
52712086 ATGCCATGTCCTAGACAGGTCTTACACTAA
1 ATGCCATGTCCTAGACAGGTCTTACACTAA
52712116 TACATGTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.02
49 65 0.98
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (49 bp):
ATGCCATGTCCTAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
Found at i:52712164 original size:93 final size:93
Alignment explanation
Indices: 52711942--52712204 Score: 277
Period size: 93 Copynumber: 2.8 Consensus size: 93
52711932 CGATGCCGAT
* * *
52711942 GCCATGTTCCAAACATGGTCTTACACTGGCTCTCA-TATC-TAAGTTGATGCCATGTCCTAGACA
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATTATCGT--GTCGATGCCATGTCCTAGACA
* * *
52712005 GGTCTTACACTAACTTTCATATATCGAGGCCAAT
63 GGTCTTACACTAAC-TACATATA-C-AAGCCAAC
*
52712039 GCCATGTCCCAGGCAGGTCTTACACTGGCTCTCATCTATCGGTGTCGATGCCATGTCCTAGACAG
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCAT-TATC-GTGTCGATGCCATGTCCTAGACAG
* *
52712104 GTCTTACACTAA-TACATGTA-AAGCCGAC
64 GTCTTACACTAACTACATATACAAGCCAAC
* * * * *
52712132 GCCATGTCCCAGATAGGTCTTACACTGGCTCTCATAAT-GTGGCTAATG-CATGTCCTAGACATG
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATTATCGTGTC-GATGCCATGTCCTAGACAGG
52712195 TCTTACACTA
65 TCTTACACTA
52712205 GCACACATAT
Statistics
Matches: 146, Mismatches: 15, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
90 28 0.19
91 3 0.02
92 2 0.01
93 38 0.26
96 25 0.17
97 12 0.08
98 37 0.25
100 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (93 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATTATCGTGTCGATGCCATGTCCTAGACAGGT
CTTACACTAACTACATATACAAGCCAAC
Found at i:52712893 original size:20 final size:21
Alignment explanation
Indices: 52712868--52712907 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
52712858 ACAATTTTAA
*
52712868 TTATTTCACACA-TTTACAAC
1 TTATTTCACAAACTTTACAAC
*
52712888 TTATTTTACAAACTTTACAA
1 TTATTTCACAAACTTTACAA
52712908 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (21 bp):
TTATTTCACAAACTTTACAAC
Done.