Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 175 of 770
Found at i:52308551 original size:2 final size:2
Alignment explanation
Indices: 52308546--52308577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52308536 TCTCTCTCTC
52308546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52308578 ATACTTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52312871 original size:44 final size:44
Alignment explanation
Indices: 52312723--52312979 Score: 196
Period size: 44 Copynumber: 5.8 Consensus size: 44
52312713 ATCATTAAAG
* * ** * *
52312723 CAAATCCTATCTCCCTGAAATTGCAGTGGAGCGGATTGAA-ACCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGA-TA
* * * *
52312767 CAAATCTTATCTCCCTAAAGTTGCAGAGGAGTAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATA
* *
52312811 CAGATATTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATA
* * * * * *
52312855 GCAAACCTTATC-CCCTGAAGTTACAGTGGGGTAGGTTGAAGTTA
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATA
* * * * * ** *
52312899 CGAGTCCTATCTCCTTGAAGTTGTAGTGGAACAGA-CTAAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATC-GAAGATA
* * *
52312943 GCAAATCTTATTTCCCTGAAGTTACAGTGGAATAGAT
1 -CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGAT
52312980 TAAAGCTACA
Statistics
Matches: 163, Mismatches: 44, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
43 7 0.04
44 121 0.74
45 35 0.21
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATA
Found at i:52312894 original size:88 final size:88
Alignment explanation
Indices: 52312729--52312980 Score: 260
Period size: 88 Copynumber: 2.9 Consensus size: 88
52312719 AAAGCAAATC
* * * * * *
52312729 CTATCTCCCTGAAATTGCAGTGGAGCGGATTGAA-ACCA-CAAATCTTATCTCCCTAAAGTTGCA
1 CTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGA-TAGCAAATCTTATC-CCCTGAAGTTACA
*
52312792 GAGGAGTAGATTGAAGTTAC-AGATA
64 GTGGAGTAGATTGAAGTTACGAG-TA
* * *
52312817 TTATCTCCCTGAAGTTGCAGTGGAGTAGATCGAAGATAGCAAACCTTATCCCCTGAAGTTACAGT
1 CTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATAGCAAATCTTATCCCCTGAAGTTACAGT
* * *
52312882 GGGGTAGGTTGAAGTTACGAGTC
66 GGAGTAGATTGAAGTTACGAGTA
* * * * *
52312905 CTATCTCCTTGAAGTTGTAGTGGAACAGA-CTAAAGATAGCAAATCTTATTTCCCTGAAGTTACA
1 CTATCTCCCTGAAGTTGCAGTGGAGCAGATC-GAAGATAGCAAATCTTA-TCCCCTGAAGTTACA
*
52312969 GTGGAATAGATT
64 GTGGAGTAGATT
52312981 AAAGCTACAA
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
87 1 0.01
88 98 0.73
89 36 0.27
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (88 bp):
CTATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATAGCAAATCTTATCCCCTGAAGTTACAGT
GGAGTAGATTGAAGTTACGAGTA
Found at i:52313288 original size:31 final size:32
Alignment explanation
Indices: 52313252--52313323 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
52313242 TTGCTGGTCC
52313252 AATTTGGTACATAAACTTGACA-ATTTTTCCT
1 AATTTGGTACATAAACTTGACACATTTTTCCT
* * * * *
52313283 AATTTGGAACTTCAACTTGACACTTTTTTCTT
1 AATTTGGTACATAAACTTGACACATTTTTCCT
52313315 AATTTGGTA
1 AATTTGGTA
52313324 TTTCATCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 19 0.56
32 15 0.44
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (32 bp):
AATTTGGTACATAAACTTGACACATTTTTCCT
Found at i:52320949 original size:20 final size:22
Alignment explanation
Indices: 52320920--52320977 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
52320910 AAAAAGTATC
52320920 AATA-TTATATATTT-AT-ATA
1 AATATTTATATATTTAATCATA
52320939 AATATTTATATATTTAAATCATA
1 AATATTTATATATTT-AATCATA
*
52320962 ATTATTTTATATATTT
1 AATA-TTTATATATTT
52320978 TATTTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 10 0.30
22 2 0.06
23 6 0.18
24 11 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATTTATATATTTAATCATA
Found at i:52321468 original size:2 final size:2
Alignment explanation
Indices: 52321461--52321488 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52321451 TAACTCAATA
52321461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52321489 TGAATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52325971 original size:14 final size:14
Alignment explanation
Indices: 52325952--52325979 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52325942 ACAACAATGT
52325952 TCATATCAATTAAA
1 TCATATCAATTAAA
52325966 TCATATCAATTAAA
1 TCATATCAATTAAA
52325980 CTAAGACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
TCATATCAATTAAA
Found at i:52332053 original size:14 final size:14
Alignment explanation
Indices: 52332036--52332087 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
52332026 ATTGCGTTAA
52332036 ATATATTATTTTAT
1 ATATATTATTTTAT
* *
52332050 ATATAATATTTTCAG
1 ATATATTATTTT-AT
52332065 AT-TATTATTTT-T
1 ATATATTATTTTAT
52332077 ATATATTATTT
1 ATATATTATTT
52332088 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 2 0.06
13 8 0.25
14 19 0.59
15 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
ATATATTATTTTAT
Found at i:52333806 original size:31 final size:31
Alignment explanation
Indices: 52333770--52333849 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
52333760 CTAATATAAG
* *
52333770 TTAGCTTGTGTGAGTAAC-CTTGATATAAATT
1 TTAGCTTGTGTAAGCAACTC-TGATATAAATT
*
52333801 TTAGCTTGTGTAAGCAACTCTGATAT-AATG
1 TTAGCTTGTGTAAGCAACTCTGATATAAATT
* *
52333831 TCAACTTGTGTAAGCAACT
1 TTAGCTTGTGTAAGCAACT
52333850 TAATCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 20 0.47
31 22 0.51
32 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (31 bp):
TTAGCTTGTGTAAGCAACTCTGATATAAATT
Found at i:52335356 original size:21 final size:21
Alignment explanation
Indices: 52335306--52335359 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
52335296 TATCCCCTCC
*
52335306 ACATGGGCATGTGTAGCCTTT
1 ACATGGGCGTGTGTAGCCTTT
* *
52335327 ACATAGGCGTGTGTGGCCTTT
1 ACATGGGCGTGTGTAGCCTTT
52335348 ACATGGGCGTGT
1 ACATGGGCGTGT
52335360 AGACCCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (21 bp):
ACATGGGCGTGTGTAGCCTTT
Found at i:52339208 original size:46 final size:46
Alignment explanation
Indices: 52339155--52339330 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
52339145 TATTTGGGCA
52339155 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
52339201 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
52339248 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
52339294 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52339331 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:52339310 original size:93 final size:93
Alignment explanation
Indices: 52339151--52339322 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
52339141 GGGATATTTG
* *
52339151 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
52339216 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
52339244 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
52339309 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
52339323 ACTTATGGGC
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:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:52342075 original size:2 final size:2
Alignment explanation
Indices: 52342068--52342105 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52342058 CATAAGTACG
52342068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52342106 ATGGTGTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52342211 original size:22 final size:22
Alignment explanation
Indices: 52342137--52342211 Score: 55
Period size: 22 Copynumber: 3.3 Consensus size: 22
52342127 GTAGTATCAG
*
52342137 AAATATACGT-ACAATAGTATAA
1 AAATATACATAACAAT-GTATAA
* *
52342159 AAGATATATAACTAACAATAT-TAA
1 AA-ATATA-CA-TAACAATGTATAA
*
52342183 AGTATATACATAACAATGTATAA
1 A-AATATACATAACAATGTATAA
52342206 AAATAT
1 AAATAT
52342212 GATATTAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 14 0.35
23 10 0.25
24 9 0.22
25 2 0.05
26 5 0.12
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.29
Consensus pattern (22 bp):
AAATATACATAACAATGTATAA
Found at i:52342249 original size:2 final size:2
Alignment explanation
Indices: 52342244--52342280 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
52342234 AGTAATATGA
52342244 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52342281 GTATTAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52342270 original size:21 final size:21
Alignment explanation
Indices: 52342244--52342286 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
52342234 AGTAATATGA
52342244 ATATATATATATATATA-TATT
1 ATATATATATA-ATATAGTATT
52342265 ATATATATATAATATAGTATT
1 ATATATATATAATATAGTATT
52342286 A
1 A
52342287 GAATGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATATATATATAATATAGTATT
Found at i:52352219 original size:12 final size:12
Alignment explanation
Indices: 52352178--52352219 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
52352168 CTAAATATAA
52352178 ATGAATGAAATT
1 ATGAATGAAATT
*
52352190 ATCAAT-AAATT
1 ATGAATGAAATT
* *
52352201 TTGAATGATATT
1 ATGAATGAAATT
52352213 ATGAATG
1 ATGAATG
52352220 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (12 bp):
ATGAATGAAATT
Found at i:52358232 original size:94 final size:93
Alignment explanation
Indices: 52358048--52358283 Score: 278
Period size: 94 Copynumber: 2.5 Consensus size: 93
52358038 TGTTATAACT
* * *
52358048 GAACTATGGTCTTACACATGTAACCCCATGTTTAATGTCATGGCAACTACCCTATGTTTACTATC
1 GAACTAAGGTCTTACACATGTAACCCCATGTTTAATGTCATGGAAACTACCCCATGTTTACTATC
* * * * *
52358113 ACTACAGATTCTACATGTTACCATAGTC
66 ACGACAAACTCCACATGTTACCATAGCC
* * *
52358141 GAGA-TAAGG-CGTTACACAAGTAACCCCATGTTTAATGTCCTGGTAAACTACCCCGTGTTTACT
1 GA-ACTAAGGTC-TTACACATGTAACCCCATGTTTAATGTCATGG-AAACTACCCCATGTTTACT
* * **
52358204 ATCCCGCCAAACTCCACATGTTTTCATAGCC
63 ATCACGACAAACTCCACATGTTACCATAGCC
*
52358235 GAACTAAGGTCTTACACATGTAACCCCATGTTTAATGTCTTGGAGAACT
1 GAACTAAGGTCTTACACATGTAACCCCATGTTTAATGTCATGGA-AACT
52358284 CTCTTGATTT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
92 1 0.01
93 38 0.32
94 80 0.67
95 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (93 bp):
GAACTAAGGTCTTACACATGTAACCCCATGTTTAATGTCATGGAAACTACCCCATGTTTACTATC
ACGACAAACTCCACATGTTACCATAGCC
Found at i:52364109 original size:25 final size:25
Alignment explanation
Indices: 52364081--52364128 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52364071 TTATACCATG
* * *
52364081 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
52364106 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52364129 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:52364231 original size:20 final size:20
Alignment explanation
Indices: 52364171--52364231 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
52364161 ATAAATATGG
*
52364171 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
52364191 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52364211 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52364231 T
1 T
52364232 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:52364308 original size:24 final size:24
Alignment explanation
Indices: 52364281--52364423 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
52364271 GAGGAAGTGA
52364281 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52364305 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52364329 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
52364352 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
52364376 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
52364400 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52364424 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:52364374 original size:47 final size:47
Alignment explanation
Indices: 52364281--52364423 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
52364271 GAGGAAGTGA
52364281 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
52364329 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
52364376 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
52364424 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:52364397 original size:71 final size:72
Alignment explanation
Indices: 52364281--52364424 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
52364271 GAGGAAGTGA
*
52364281 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
52364344 CCAGTTAT
65 CCAGTTAT
** * *
52364352 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
52364417 CAGTTAT
66 CAGTTAT
52364424 A
1 A
52364425 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:52364674 original size:30 final size:31
Alignment explanation
Indices: 52364614--52364676 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
52364604 CGTTTACAGT
52364614 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
52364645 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52364675 AA
1 AA
52364677 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52372224 original size:25 final size:25
Alignment explanation
Indices: 52372196--52372243 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52372186 TTATACCATG
* * *
52372196 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
52372221 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52372244 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:52372346 original size:20 final size:20
Alignment explanation
Indices: 52372286--52372346 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
52372276 ATAAATATGG
*
52372286 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
52372306 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52372326 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
52372346 T
1 T
52372347 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:52372423 original size:24 final size:24
Alignment explanation
Indices: 52372396--52372538 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
52372386 GAGGAAGTGA
52372396 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52372420 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52372444 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
52372467 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
52372491 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
52372515 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52372539 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:52372489 original size:47 final size:47
Alignment explanation
Indices: 52372396--52372538 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
52372386 GAGGAAGTGA
52372396 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
52372444 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
52372491 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
52372539 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:52372512 original size:71 final size:72
Alignment explanation
Indices: 52372396--52372539 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
52372386 GAGGAAGTGA
*
52372396 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
52372459 CCAGTTAT
65 CCAGTTAT
** * *
52372467 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
52372532 CAGTTAT
66 CAGTTAT
52372539 A
1 A
52372540 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:52372790 original size:30 final size:31
Alignment explanation
Indices: 52372730--52372792 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
52372720 CGTTTACAGT
52372730 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
52372761 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52372791 AA
1 AA
52372793 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52380501 original size:17 final size:18
Alignment explanation
Indices: 52380467--52380508 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
52380457 TTTTTTAAAA
*
52380467 TTCTTTTTTCATTGATTT
1 TTCTTTTTTCATTCATTT
*
52380485 TTCTTTTTT-TTTCATTT
1 TTCTTTTTTCATTCATTT
*
52380502 TACTTTT
1 TTCTTTT
52380509 GTAGGTCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (18 bp):
TTCTTTTTTCATTCATTT
Found at i:52384204 original size:52 final size:52
Alignment explanation
Indices: 52384086--52384290 Score: 218
Period size: 52 Copynumber: 3.9 Consensus size: 52
52384076 CACATATCAT
* * *
52384086 ACCGATGCCATATCCCAGATATGGTCTTATAC-GGAGGCACATTATCAC-AT-C
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGA-ACACA-TATCACAATGC
* * * *
52384137 AAACCGATGCTATAGCCCAGCCATGGTCTTATATGGGAATACATATCACAATGC
1 --ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACAATGC
* **
52384191 ACCGATGCCATAGCCTAGCTATGGTCTTATACGGGTGCACATATCACAATGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACAATGC
** * * *
52384243 ACTAATGCCATAGCCCAACTATGGTCTTATACAGGCACACATATCACA
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACA
52384291 TCTATTCTGT
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
52 92 0.72
53 32 0.25
54 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (52 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACAATGC
Found at i:52384287 original size:104 final size:104
Alignment explanation
Indices: 52384086--52384290 Score: 245
Period size: 104 Copynumber: 2.0 Consensus size: 104
52384076 CACATATCAT
* * *
52384086 ACCGATGCCATATCCCAGATATGGTCTTATACGGAGGCACATTATCACATCAAACCGATGCTATA
1 ACCGATGCCATAGCCCAGATATGGTCTTATACGGAGGCACATTATCACATC-AACCAATGCCATA
* ** *
52384151 GCCCAGCCATGGTCTTATATGGGAATACATATCACAATGC
65 GCCCAACCATGGTCTTATACAGGAACACATATCACAATGC
* * *
52384191 ACCGATGCCATAGCCTAGCTATGGTCTTATACGG-GTGCACA-TATCACAATGC-ACTAATGCCA
1 ACCGATGCCATAGCCCAGATATGGTCTTATACGGAG-GCACATTATCAC-AT-CAACCAATGCCA
* *
52384253 TAGCCCAACTATGGTCTTATACAGGCACACATATCACA
63 TAGCCCAACCATGGTCTTATACAGGAACACATATCACA
52384291 TCTATTCTGT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
104 46 0.54
105 38 0.45
106 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (104 bp):
ACCGATGCCATAGCCCAGATATGGTCTTATACGGAGGCACATTATCACATCAACCAATGCCATAG
CCCAACCATGGTCTTATACAGGAACACATATCACAATGC
Found at i:52386469 original size:57 final size:58
Alignment explanation
Indices: 52386350--52386472 Score: 151
Period size: 57 Copynumber: 2.1 Consensus size: 58
52386340 TTACATAAAG
* * * * * * *
52386350 GATTTAGCCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTATAGATAG
1 GATTTAGCCCGAACGGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTAGAAACAA
*
52386408 GATTTAGCCCGAACGGGTAATCCTGAT-TAAGCTCT-TATGAGCATATGTTAGAAACAA
1 GATTTAGCCCGAACGGGTAATCCTGATATAAGCCCTCT-TGAGCATATGTTAGAAACAA
52386465 GATTTAGC
1 GATTTAGC
52386473 TTGGACAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 1 0.02
57 31 0.55
58 24 0.43
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (58 bp):
GATTTAGCCCGAACGGGTAATCCTGATATAAGCCCTCTTGAGCATATGTTAGAAACAA
Found at i:52399444 original size:22 final size:24
Alignment explanation
Indices: 52399414--52399463 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
52399404 ACAGATACGC
*
52399414 GAATTTCC-ACCCAAACACA-CCA
1 GAATGTCCAACCCAAACACACCCA
52399436 GAATGTCCAACCCAAACACACCCA
1 GAATGTCCAACCCAAACACACCCA
52399460 GAAT
1 GAAT
52399464 ATTTTAAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
23 11 0.44
24 7 0.28
ACGTcount: A:0.42, C:0.38, G:0.08, T:0.12
Consensus pattern (24 bp):
GAATGTCCAACCCAAACACACCCA
Found at i:52400529 original size:14 final size:14
Alignment explanation
Indices: 52400505--52400537 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
52400495 TCCCTGCTTC
52400505 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
52400520 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
52400533 GTTTC
1 GTTTC
52400538 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:52400893 original size:21 final size:20
Alignment explanation
Indices: 52400869--52400937 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
52400859 AATGCTAATA
52400869 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
52400890 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
52400909 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
52400930 ATAATAAT
1 ATAATAAT
52400938 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:52415639 original size:27 final size:26
Alignment explanation
Indices: 52415577--52415718 Score: 149
Period size: 27 Copynumber: 5.3 Consensus size: 26
52415567 AGCATGGCTG
* *
52415577 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
* *
52415603 CTAGATACAGATAATCGTGGCAGGGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
52415631 CTAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
52415658 CCAGATCAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
52415685 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
52415712 CCAGAAC
1 CCAGAAC
52415719 GCTTCCTCCA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
26 4 0.04
27 83 0.81
28 16 0.16
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:52415668 original size:54 final size:55
Alignment explanation
Indices: 52415577--52415716 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 55
52415567 AGCATGGCTG
* * * *
52415577 CCAGAACAGATA-ATGTGACAGAGTCACTAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
52415631 CTAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
52415685 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
52415717 ACGCTTCCTC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 57 0.77
55 17 0.23
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.19
Consensus pattern (55 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:52417337 original size:26 final size:26
Alignment explanation
Indices: 52417306--52417413 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
52417296 TGAAATGCCC
*
52417306 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
52417332 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
52417358 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
52417384 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52417410 ATCA
1 ATCA
52417414 ATTTGCATCA
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:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52421287 original size:2 final size:2
Alignment explanation
Indices: 52421280--52421315 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52421270 AATGAAGAAA
52421280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52421316 TTCATGGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52422242 original size:26 final size:26
Alignment explanation
Indices: 52422213--52422320 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
52422203 TGGTACAAAT
*
52422213 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
**
52422239 TGATAATGAATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
52422265 TGATAATGGGTTAGGTAAATATTCCG
1 TGATAATGGGTTAGGTAAATATTCCA
* *
52422291 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
52422317 TGAT
1 TGAT
52422321 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:52424605 original size:20 final size:20
Alignment explanation
Indices: 52424580--52424619 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
52424570 TGCACAGCTT
52424580 CCATTCACTTTAACCTATAA
1 CCATTCACTTTAACCTATAA
52424600 CCATTCACTTTAACCTATAA
1 CCATTCACTTTAACCTATAA
52424620 TGAAATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (20 bp):
CCATTCACTTTAACCTATAA
Found at i:52425323 original size:33 final size:34
Alignment explanation
Indices: 52425283--52425349 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
52425273 ATGTAATAAT
* * *
52425283 TATATATACATAATATGGTA-TTAAGAATATATA
1 TATATATACACAATATAGTATTTAAAAATATATA
*
52425316 TATATATATACAATATAGTATTTAAAAATATATA
1 TATATATACACAATATAGTATTTAAAAATATATA
52425350 CATAAGATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (34 bp):
TATATATACACAATATAGTATTTAAAAATATATA
Found at i:52425365 original size:24 final size:23
Alignment explanation
Indices: 52425338--52425398 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
52425328 ATATAGTATT
52425338 TAAAAATATATACAT-AAGATGGTA
1 TAAAAATATATACATGAA-AT-GTA
*
52425362 TAAAAATATGTACATGGAAATGTA
1 TAAAAATATATACAT-GAAATGTA
52425386 TAAGAAATATATA
1 TAA-AAATATATA
52425399 TAATTAGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 20 0.62
25 10 0.31
26 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (23 bp):
TAAAAATATATACATGAAATGTA
Found at i:52425538 original size:2 final size:2
Alignment explanation
Indices: 52425533--52425559 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52425523 ACACACACAC
52425533 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52425560 AATAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52425580 original size:23 final size:22
Alignment explanation
Indices: 52425553--52425648 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 22
52425543 ATATATATAT
52425553 ATATATAAATAATAGTATTAGAA
1 ATATATAAATAATAGTATTA-AA
* * *
52425576 ATATACATATAATAGTATAAAA
1 ATATATAAATAATAGTATTAAA
* * *
52425598 ATATGTAACTAATAATATTAAA
1 ATATATAAATAATAGTATTAAA
*
52425620 ATATATATAATAACA-TA-TAAA
1 ATATATA-AATAATAGTATTAAA
*
52425641 AAATATAA
1 ATATATAA
52425649 TATTGAAAAC
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 26 0.44
23 22 0.37
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATATAAATAATAGTATTAAA
Found at i:52425611 original size:45 final size:44
Alignment explanation
Indices: 52425553--52425648 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
52425543 ATATATATAT
* *
52425553 ATATATAAATAATAGTATTAGAAATATACAT-ATAATAGTATAAAA
1 ATATATAAATAATAATATTA-AAATATACATAATAACA-TATAAAA
* * *
52425598 ATATGTAACTAATAATATTAAAATATATATAATAACATATAAAA
1 ATATATAAATAATAATATTAAAATATACATAATAACATATAAAA
52425642 A-ATATAA
1 ATATATAA
52425649 TATTGAAAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
43 5 0.11
44 17 0.39
45 22 0.50
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (44 bp):
ATATATAAATAATAATATTAAAATATACATAATAACATATAAAA
Found at i:52425896 original size:3 final size:3
Alignment explanation
Indices: 52425882--52426041 Score: 57
Period size: 3 Copynumber: 53.3 Consensus size: 3
52425872 ATGCATACAC
* *
52425882 TAA TAT TAA TAA TAA TAA TAA -AA CTAGA -AA TAA TAA TAA TTAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA -TAA TAA
* * * ** * *
52425928 TAA TAA TACG TTA GAA -AA TAA TTAA T-A TGT TAA TAA AAA TAA TAG
1 TAA TAA TA-A TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
52425973 TAA TGGA -AA TAA TAC TAA CAG TAA TAA TAA -AGA TAA TAA TAGA -AA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA
* *
52426018 TAA -AA TAA TAG TAA TAA TAT TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
52426042 TATATGTAAA
Statistics
Matches: 113, Mismatches: 28, Indels: 32
0.65 0.16 0.18
Matches are distributed among these distances:
2 12 0.11
3 90 0.80
4 10 0.09
5 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:52425931 original size:16 final size:16
Alignment explanation
Indices: 52425894--52425935 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
52425884 ATATTAATAA
52425894 TAATAATAA-AACTAG
1 TAATAATAATAACTAG
* *
52425909 AAATAATAATAATTAG
1 TAATAATAATAACTAG
52425925 TAATAATAATA
1 TAATAATAATA
52425936 CGTTAGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (16 bp):
TAATAATAATAACTAG
Found at i:52429119 original size:18 final size:18
Alignment explanation
Indices: 52429091--52429134 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
52429081 AGTAAAATTT
*
52429091 ATATGAAAATCCCTGAAGG
1 ATAT-AAAATCCCAGAAGG
* *
52429110 ATTTAAAATCTCAGAAGG
1 ATATAAAATCCCAGAAGG
52429128 ATATAAA
1 ATATAAA
52429135 GTTTATCGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:52430937 original size:29 final size:27
Alignment explanation
Indices: 52430874--52430940 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
52430864 TTTTTCATAT
* **
52430874 ATTTAGAATTTAATCTTTTTATTTTTA
1 ATTTAAAATTTAATCCATTTATTTTTA
52430901 ATTCTTAAAATTTAATCCATTTACTTTTTA
1 A-T-TTAAAATTTAATCCATTTA-TTTTTA
52430931 GATTTAAAAT
1 -ATTTAAAAT
52430941 ACAAATGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.03
28 1 0.03
29 23 0.70
30 7 0.21
31 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (27 bp):
ATTTAAAATTTAATCCATTTATTTTTA
Found at i:52431679 original size:20 final size:20
Alignment explanation
Indices: 52431654--52431694 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52431644 AGAACTTGGG
52431654 TTCGAAACTAAAAATTTCTC
1 TTCGAAACTAAAAATTTCTC
52431674 TTCGAAACTAAAAATTTCTC
1 TTCGAAACTAAAAATTTCTC
52431694 T
1 T
52431695 CTCAGGCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (20 bp):
TTCGAAACTAAAAATTTCTC
Found at i:52431896 original size:2 final size:2
Alignment explanation
Indices: 52431889--52431931 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
52431879 GAGTTTACTT
*
52431889 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52431931 T
1 T
52431932 TAATAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52432665 original size:3 final size:3
Alignment explanation
Indices: 52432657--52432685 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52432647 TTGAAGAATG
52432657 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
52432686 CTTACCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:52434079 original size:18 final size:18
Alignment explanation
Indices: 52434032--52434084 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
52434022 ATGCAACAAT
*
52434032 AATTAAATAAATAATTAA
1 AATTATATAAATAATTAA
* * *
52434050 AATTTTAAAAATATTTAA
1 AATTATATAAATAATTAA
52434068 AATTATATAAATTAATT
1 AATTATATAAA-TAATT
52434085 CAATTGTTGA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATATAAATAATTAA
Found at i:52443163 original size:2 final size:2
Alignment explanation
Indices: 52443156--52443183 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52443146 AATTAAAACA
52443156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52443184 TCATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52445035 original size:2 final size:2
Alignment explanation
Indices: 52445028--52445062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52445018 TTCTCAAATG
52445028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52445063 GTTCATATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52451851 original size:21 final size:21
Alignment explanation
Indices: 52451822--52451865 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52451812 TTAGTCCCAT
52451822 TAAGCATGGGTATAGAATTTA
1 TAAGCATGGGTATAGAATTTA
*
52451843 TAAGTATGGGTATAGAATTTA
1 TAAGCATGGGTATAGAATTTA
52451864 TA
1 TA
52451866 TTGGCAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (21 bp):
TAAGCATGGGTATAGAATTTA
Found at i:52458022 original size:28 final size:29
Alignment explanation
Indices: 52457969--52458023 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
52457959 ACCTCTAAAG
**
52457969 GGACCTTATAACAAATTTTATTAGTTTGC
1 GGACCTTATAACAAATTTTACCAGTTTGC
52457998 GGACCTTATAAC-AATTTTACCAGTTT
1 GGACCTTATAACAAATTTTACCAGTTT
52458024 TTGGGGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (29 bp):
GGACCTTATAACAAATTTTACCAGTTTGC
Found at i:52459805 original size:25 final size:26
Alignment explanation
Indices: 52459777--52459832 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
52459767 TTTACAAATT
*
52459777 ATATTTAAATTA-AATAAT-AAAATAA
1 ATATATAAATTATAATAATGAAAA-AA
* *
52459802 ATATATAACTTATAATTATGAAAAAA
1 ATATATAAATTATAATAATGAAAAAA
52459828 ATATA
1 ATATA
52459833 AATAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 10 0.38
26 12 0.46
27 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
ATATATAAATTATAATAATGAAAAAA
Found at i:52460348 original size:24 final size:23
Alignment explanation
Indices: 52460300--52460348 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
52460290 AAACATTCAT
* *
52460300 TTGAGTTTTTTTTTATTATTTAA
1 TTGAGTTTTTTTATATTATTAAA
52460323 TTGAGTTTATTTTATATCTA-TAAA
1 TTGAGTTT-TTTTATAT-TATTAAA
52460347 TT
1 TT
52460349 TATATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
24 12 0.55
25 2 0.09
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (23 bp):
TTGAGTTTTTTTATATTATTAAA
Found at i:52460639 original size:15 final size:15
Alignment explanation
Indices: 52460619--52460670 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
52460609 ACTACAAAAC
52460619 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
52460634 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
52460653 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
52460668 ATT
1 ATT
52460671 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:52460765 original size:22 final size:22
Alignment explanation
Indices: 52460740--52460785 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52460730 TAAAATTAAA
52460740 ATATTAAATAAT-TTAATAAATT
1 ATATT-AATAATATTAATAAATT
* *
52460762 ATATTAATTATATTAATAATTT
1 ATATTAATAATATTAATAAATT
52460784 AT
1 AT
52460786 TATATGACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATAATATTAATAAATT
Found at i:52460870 original size:9 final size:9
Alignment explanation
Indices: 52460853--52460882 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
52460843 ATTTTATATT
52460853 AATATTTTTA
1 AATA-TTTTA
52460863 AATATTTTA
1 AATATTTTA
52460872 AATATTTTA
1 AATATTTTA
52460881 AA
1 AA
52460883 AATAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATTTTA
Found at i:52461166 original size:16 final size:13
Alignment explanation
Indices: 52461136--52461173 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
52461126 TTTCGAAGAA
52461136 TATTATTTAAATT
1 TATTATTTAAATT
52461149 TATTATTTAAACTT
1 TATTATTTAAA-TT
*
52461163 T-TTATTAAAAT
1 TATTATTTAAAT
52461174 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 19 0.83
14 3 0.13
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTTAAATT
Found at i:52467307 original size:2 final size:2
Alignment explanation
Indices: 52467300--52467326 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52467290 AGGATTTTTA
52467300 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52467327 ATTTAGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52472781 original size:26 final size:26
Alignment explanation
Indices: 52472745--52472828 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
52472735 TGATACAAAT
52472745 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
52472771 TGATGATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
52472797 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
52472823 TGATAA
1 TGATAA
52472829 GAATTTCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:52478558 original size:25 final size:25
Alignment explanation
Indices: 52478524--52478682 Score: 273
Period size: 25 Copynumber: 6.2 Consensus size: 25
52478514 TGATACAAAT
52478524 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
52478549 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
52478575 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
52478600 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
*
52478625 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
52478651 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
52478677 TGATAA
1 TGATAA
52478683 GAATTTCATG
Statistics
Matches: 131, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
25 70 0.53
26 61 0.47
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:52478584 original size:51 final size:50
Alignment explanation
Indices: 52478524--52478682 Score: 273
Period size: 51 Copynumber: 3.1 Consensus size: 50
52478514 TGATACAAAT
52478524 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTT-CA
52478575 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCA
* *
52478625 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAATAGGTTAGGTAAATG-TTCA
52478677 TGATAA
1 TGATAA
52478683 GAATTTCATG
Statistics
Matches: 104, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
50 22 0.21
51 72 0.69
52 10 0.10
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (50 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCA
Found at i:52478611 original size:76 final size:77
Alignment explanation
Indices: 52478524--52478682 Score: 284
Period size: 76 Copynumber: 2.1 Consensus size: 77
52478514 TGATACAAAT
52478524 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAG
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAG
52478589 GTAAATG-TTCA
66 GTAAATGTTTCA
* * *
52478600 TGATAATAGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAG
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAG
52478665 GTAAATGTTTCA
66 GTAAATGTTTCA
52478677 TGATAA
1 TGATAA
52478683 GAATTTCATG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 69 0.87
77 10 0.13
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (77 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCATGATAATAGGTTAG
GTAAATGTTTCA
Found at i:52482507 original size:42 final size:43
Alignment explanation
Indices: 52482438--52482523 Score: 156
Period size: 42 Copynumber: 2.0 Consensus size: 43
52482428 AAAGTAGTGT
52482438 TATGTTTCCTCTTTTTTCTTCTTTAGACTCTGACGCTGAATTA
1 TATGTTTCCTCTTTTTTCTTCTTTAGACTCTGACGCTGAATTA
*
52482481 TATGTTTCCTC-TTTTTCTTCTTTAGACTCTGACGTTGAATTA
1 TATGTTTCCTCTTTTTTCTTCTTTAGACTCTGACGCTGAATTA
52482523 T
1 T
52482524 CTACTTGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 31 0.74
43 11 0.26
ACGTcount: A:0.16, C:0.20, G:0.12, T:0.52
Consensus pattern (43 bp):
TATGTTTCCTCTTTTTTCTTCTTTAGACTCTGACGCTGAATTA
Found at i:52488119 original size:47 final size:48
Alignment explanation
Indices: 52488065--52488287 Score: 233
Period size: 46 Copynumber: 4.8 Consensus size: 48
52488055 AGGGTGAATT
* * *
52488065 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTG-G
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTG
* * * **
52488112 GCCGATGCCATGTCCC-AACATGGTCTTACACTAGCTCTCGTCTCAAT-
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAT-TGTG
* * *
52488159 G-CGATG-CATGTCCCAGAGATGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTG
* * * *
52488205 GCCAATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCCTATCGTG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTG
* * *
52488253 GCTGATG-CATGTCCCAGACATGGACTTACACTGGC
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGC
52488288 ACACATATCA
Statistics
Matches: 143, Mismatches: 27, Indels: 12
0.79 0.15 0.07
Matches are distributed among these distances:
45 9 0.06
46 50 0.35
47 45 0.31
48 39 0.27
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTG
Found at i:52490478 original size:40 final size:39
Alignment explanation
Indices: 52490310--52490480 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
52490300 AGAAATTGAA
* *
52490310 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
52490350 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
52490390 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
52490430 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
52490470 TGATATCCGGG
1 TGATATCCGGG
52490481 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:52498576 original size:40 final size:39
Alignment explanation
Indices: 52498408--52498578 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
52498398 AGAAATTGAA
* *
52498408 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
52498448 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
52498488 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
52498528 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
52498568 TGATATCCGGG
1 TGATATCCGGG
52498579 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:52503594 original size:40 final size:40
Alignment explanation
Indices: 52503539--52503783 Score: 356
Period size: 40 Copynumber: 6.2 Consensus size: 40
52503529 CGGATGATAA
*
52503539 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCC
*
52503579 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCC
*
52503619 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
*
52503659 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
52503699 CGAAGGCATTTGTGCGAGCT-ACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCC
* * *
52503739 CGAAGGCATTTGAGCGAGT-AGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTGA-CTATATCCGGGCTAAGTCC
52503778 CGAAGG
1 CGAAGG
52503784 TACTTGGTTT
Statistics
Matches: 197, Mismatches: 5, Indels: 7
0.94 0.02 0.03
Matches are distributed among these distances:
39 16 0.08
40 179 0.91
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
Found at i:52511914 original size:40 final size:40
Alignment explanation
Indices: 52511850--52512053 Score: 308
Period size: 40 Copynumber: 5.2 Consensus size: 40
52511840 CGGATGATAA
* *
52511850 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
52511890 CGAAGGCATTTGTGCGAGTTACTA-ATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
52511929 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
52511969 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
52512009 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
52512048 CGAAGG
1 CGAAGG
52512054 TACTTGGTTT
Statistics
Matches: 156, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 54 0.35
40 102 0.65
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:52511981 original size:79 final size:80
Alignment explanation
Indices: 52511850--52512053 Score: 308
Period size: 79 Copynumber: 2.6 Consensus size: 80
52511840 CGGATGATAA
* * *
52511850 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTA
52511914 -ATCCGGGCTAAGTCC
65 TATCCGGGCTAAGTCC
52511929 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAT
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAT
52511994 ATCCGGGCTAAGTCC
66 ATCCGGGCTAAGTCC
* * *
52512009 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCGAAGG
52512054 TACTTGGTTT
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
79 75 0.65
80 41 0.35
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTAT
ATCCGGGCTAAGTCC
Found at i:52517540 original size:25 final size:25
Alignment explanation
Indices: 52517506--52517557 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
52517496 CAGCATCTTC
52517506 GCGGGCGCGAATGGTGTATGTCCTT
1 GCGGGCGCGAATGGTGTATGTCCTT
52517531 GCGGGCGCGAATGGTGTATGTCCTT
1 GCGGGCGCGAATGGTGTATGTCCTT
52517556 GC
1 GC
52517558 AGGCACTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.40, T:0.27
Consensus pattern (25 bp):
GCGGGCGCGAATGGTGTATGTCCTT
Found at i:52520769 original size:79 final size:80
Alignment explanation
Indices: 52520668--52520850 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 80
52520658 ACGACTCGCT
** * * *
52520668 CAAATGCCTTCGGGACGAAGCCCGATTATAGTGACTCGCCCGAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC-
*
52520732 GGCT-TAGTAACTT-GCA
63 GGATATAGTAACTTAGCA
* **
52520748 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
52520812 ATATAGTCACTTAGCA
65 ATATAGTAACTTAGCA
52520828 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
52520851 GACATCATTC
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
78 6 0.07
79 49 0.56
80 33 0.38
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGGA
TATAGTAACTTAGCA
Found at i:52520782 original size:39 final size:40
Alignment explanation
Indices: 52520668--52520852 Score: 171
Period size: 40 Copynumber: 4.7 Consensus size: 40
52520658 ACGACTCGCT
** * * *
52520668 CAAATGCCTTCGGGACGAAGCCC-GATTATAGTGACTCGCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTTGCA
* * **
52520708 CGAATGCCTTCGGGACTTAACCCGGGCTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* *
52520748 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
* * * * *
52520787 CGAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTT-GCA
52520828 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52520853 CATCATTCGA
Statistics
Matches: 115, Mismatches: 25, Indels: 10
0.77 0.17 0.07
Matches are distributed among these distances:
38 2 0.02
39 30 0.26
40 72 0.63
41 11 0.10
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
Found at i:52523092 original size:29 final size:29
Alignment explanation
Indices: 52523055--52523157 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
52523045 ATGAATGTGA
*
52523055 TTGGGCCTAACGGGCCATATAAATGTAAT
1 TTGGGCCTAATGGGCCATATAAATGTAAT
*** *
52523084 TTGGGCCTAATGGGCCATATACGGGTGAT
1 TTGGGCCTAATGGGCCATATAAATGTAAT
* *
52523113 TTGGGCCTAATGGGCCATATGAATATAA-
1 TTGGGCCTAATGGGCCATATAAATGTAAT
*
52523141 TTGGGCTTAATGGGCCA
1 TTGGGCCTAATGGGCCA
52523158 GATACAGGTA
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 16 0.26
29 46 0.74
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATAAATGTAAT
Found at i:52523153 original size:28 final size:28
Alignment explanation
Indices: 52523043--52523157 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 28
52523033 GTGAGCATGA
* * *
52523043 ATATGAATGTGATTGGGCCTAACGGGCC
1 ATATGAATATAATTGGGCCTAATGGGCC
* *
52523071 ATATAAATGTAATTTGGGCCTAATGGGCC
1 ATATGAATATAA-TTGGGCCTAATGGGCC
**
52523100 ATATACGGGTGAT--TTGGGCCTAATGGGCC
1 ATAT--GAAT-ATAATTGGGCCTAATGGGCC
*
52523129 ATATGAATATAATTGGGCTTAATGGGCC
1 ATATGAATATAATTGGGCCTAATGGGCC
52523157 A
1 A
52523158 GATACAGGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.03
27 2 0.03
28 26 0.37
29 39 0.55
31 1 0.01
32 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (28 bp):
ATATGAATATAATTGGGCCTAATGGGCC
Found at i:52523153 original size:57 final size:57
Alignment explanation
Indices: 52523051--52523162 Score: 163
Period size: 58 Copynumber: 2.0 Consensus size: 57
52523041 GAATATGAAT
* *
52523051 GTGATTGGGCCTAACGGGCCATATAAATGTAATTTGGGCCTAATGGGCCATATACGG
1 GTGATTGGGCCTAACGGGCCATATAAATATAATTTGGGCCTAATGGGCCAGATACGG
* * *
52523108 GTGATTTGGGCCTAATGGGCCATATGAATATAA-TTGGGCTTAATGGGCCAGATAC
1 GTGA-TTGGGCCTAACGGGCCATATAAATATAATTTGGGCCTAATGGGCCAGATAC
52523163 AGGTATGTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 24 0.49
58 25 0.51
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (57 bp):
GTGATTGGGCCTAACGGGCCATATAAATATAATTTGGGCCTAATGGGCCAGATACGG
Found at i:52530401 original size:46 final size:45
Alignment explanation
Indices: 52530261--52530561 Score: 190
Period size: 46 Copynumber: 6.6 Consensus size: 45
52530251 GTGTCGATGC
* * * **
52530261 CATGTCCCAGACAGGTCTTACACTGAC-ACATGTAACCGT-GCTAACG
1 CATGTCCCAGACATGTCTTACACTGGCTACATCT---CGTAGCCGACG
*
52530307 CATGTCCCAGACATGTCTTACACTAGC-ACATCTCGTAGCCGACG
1 CATGTCCCAGACATGTCTTACACTGGCTACATCTCGTAGCCGACG
* *
52530351 CATGTCCCAAACATGT-TTGACACTGGCTAACATCTCG-AGGCCGATG
1 CATGTCCCAGACATGTCTT-ACACTGGCT-ACATCTCGTA-GCCGACG
* * ** * * *
52530397 CATGTCCCAGACATGTCTTACACTGGCTCTCATATTATGGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCT-ACATCTCGTAGCCGACG
* * * *
52530443 CATGTCCCAGACATGTCTTACACTAGCCCT-CGTCTC-AATGCCGATG
1 CATGTCCCAGACATGTCTTACACT-G-GCTACATCTCGTA-GCCGACG
* * * *
52530489 CCATGT-CCAGACATGGTCTTACACTAGCTATCATAAT-GTGGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTA-CAT-CTCGTAGCCGACG
*
52530536 CATGT-CCAGACATGTCTTACAATGGC
1 CATGTCCCAGACATGTCTTACACTGGC
52530562 ACACAAATCT
Statistics
Matches: 207, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
43 5 0.02
44 27 0.13
45 14 0.07
46 131 0.63
47 27 0.13
48 3 0.01
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTACATCTCGTAGCCGACG
Found at i:52530512 original size:47 final size:46
Alignment explanation
Indices: 52530306--52530556 Score: 194
Period size: 46 Copynumber: 5.5 Consensus size: 46
52530296 CCGTGCTAAC
* * ** * *
52530306 GCATGTCCCAGACATGTCTTACACTAG--CACATCTCGTAGCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGCCCTCATATAATGGCCGAT
* * *** * *
52530350 GCATGTCCCAAACATGT-TTGACACTGGCTAACATCTCGA-GGCCGAT
1 GCATGTCCCAGACATGTCTT-ACACTAGCCCTCATAT-AATGGCCGAT
* * * *
52530396 GCATGTCCCAGACATGTCTTACACTGGCTCTCATATTATGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCCTCATATAATGGCCGAT
* *
52530442 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAAT-GCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCCTCATAT-AATGGCCGAT
** *
52530488 GCCATGT-CCAGACATGGTCTTACACTAGCTATCATA-ATGTGGCCGAT
1 G-CATGTCCCAGACAT-GTCTTACACTAGCCCTCATATA-ATGGCCGAT
52530535 GCATGT-CCAGACATGTCTTACA
1 GCATGTCCCAGACATGTCTTACA
52530557 ATGGCACACA
Statistics
Matches: 172, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.01
44 22 0.13
45 10 0.06
46 106 0.62
47 32 0.19
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTAGCCCTCATATAATGGCCGAT
Found at i:52530590 original size:93 final size:92
Alignment explanation
Indices: 52530392--52530573 Score: 217
Period size: 93 Copynumber: 2.0 Consensus size: 92
52530382 ATCTCGAGGC
* * * *
52530392 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATATTATGGCTGATGCATGTCCCAGAC
1 CGATGCCATGT-CCAGACATGGTCTTACACTAGCTATCATAATATGGCCGATGCATGTCCCAGAC
* ***
52530455 ATGTCTTACACTAGCCCTCGTCTCAATG
65 ATGTCTTACAATAGCCCAAATCTCAATG
*
52530483 CCGATGCCATGTCCAGACATGGTCTTACACTAGCTATCATAATGTGGCCGATGCATGT-CCAGAC
1 -CGATGCCATGTCCAGACATGGTCTTACACTAGCTATCATAATATGGCCGATGCATGTCCCAGAC
*
52530547 ATGTCTTACAATGGCACACAAATCTCA
65 ATGTCTTACAATAGC-C-CAAATCTCA
52530574 TGTATTTCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
92 32 0.42
93 38 0.50
94 6 0.08
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (92 bp):
CGATGCCATGTCCAGACATGGTCTTACACTAGCTATCATAATATGGCCGATGCATGTCCCAGACA
TGTCTTACAATAGCCCAAATCTCAATG
Found at i:52536431 original size:48 final size:48
Alignment explanation
Indices: 52536360--52536640 Score: 294
Period size: 48 Copynumber: 5.9 Consensus size: 48
52536350 GGTGAATTGT
* * * *
52536360 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
** * * * *
52536408 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTTCGTCTTAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
* * ** * *
52536456 C-ATGCCATGTCCTAGACATGGTCTTACACTGGCTCTTATAATGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
* * * ** *
52536503 CGATGCCATGTCTCAAACATGGTCTTACACTAGCGCACATATCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
* * * * *
52536551 CGATGCCATGTCCCAGACATGGTCTTGCACTAGCTCTCTTATCGTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
* *
52536599 CGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATAT
52536641 CACCGAAATG
Statistics
Matches: 187, Mismatches: 45, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
47 37 0.20
48 150 0.80
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATATTGAGGC
Found at i:52536604 original size:96 final size:95
Alignment explanation
Indices: 52536360--52536642 Score: 347
Period size: 95 Copynumber: 3.0 Consensus size: 95
52536350 GGTGAATTGT
* * * *
52536360 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGT-TGAGGCCGATGCCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-T-TATGTGGCCGATGCCATGTCCCAG
*** * * *
52536424 ACATGGTCTTACACTAGCTTTCGTCTTAATGC
64 ACATGGTCTTACACTAGCACACATATCAATGC
* * *
52536456 C-ATGCCATGTCCTAGACATGGTCTTACACTGGCTCT-TATAATGTGGCCGATGCCATGTCTCAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCT-T-ATGTGGCCGATGCCATGTCCCAG
*
52536519 ACATGGTCTTACACTAGCGCACATATCAATGC
64 ACATGGTCTTACACTAGCACACATATCAATGC
* *
52536551 CGATGCCATGTCCCAGACATGGTCTTGCACTAGCTCTCTTATCGTGGCCGATGCCATGTCCCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTTAT-GTGGCCGATGCCATGTCCCAGA
*
52536616 CATGGTCTTACACTGGCACACATATCA
65 CATGGTCTTACACTAGCACACATATCA
52536643 CCGAAATGTC
Statistics
Matches: 161, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.01
95 79 0.49
96 79 0.49
97 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (95 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTTATGTGGCCGATGCCATGTCCCAGAC
ATGGTCTTACACTAGCACACATATCAATGC
Found at i:52540035 original size:22 final size:23
Alignment explanation
Indices: 52539989--52540093 Score: 85
Period size: 23 Copynumber: 4.6 Consensus size: 23
52539979 CTAAGCCAAT
** * *
52539989 AAACGGTAAGCTCAATTGAGCTG
1 AAACGGTAAGCTCCCTAGAGATG
*
52540012 -AACGGTAAGCTCCGTAGAGATG
1 AAACGGTAAGCTCCCTAGAGATG
*
52540034 AAATGGTAAGC-CCCTA-AGGAATG
1 AAACGGTAAGCTCCCTAGA-G-ATG
52540057 AAACGGTAAGC-CCCTA-AGGAATG
1 AAACGGTAAGCTCCCTAGA-G-ATG
52540080 AAACGGTAAGCTCC
1 AAACGGTAAGCTCC
52540094 GAAGATTTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 23 0.32
23 45 0.63
24 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (23 bp):
AAACGGTAAGCTCCCTAGAGATG
Found at i:52540057 original size:23 final size:23
Alignment explanation
Indices: 52540031--52540090 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
52540021 CTCCGTAGAG
*
52540031 ATGAAATGGTAAGCCCCTAAGGA
1 ATGAAACGGTAAGCCCCTAAGGA
52540054 ATGAAACGGTAAGCCCCTAAGGA
1 ATGAAACGGTAAGCCCCTAAGGA
52540077 ATGAAACGGTAAGC
1 ATGAAACGGTAAGC
52540091 TCCGAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.40, C:0.18, G:0.27, T:0.15
Consensus pattern (23 bp):
ATGAAACGGTAAGCCCCTAAGGA
Found at i:52540104 original size:23 final size:23
Alignment explanation
Indices: 52540012--52540114 Score: 104
Period size: 23 Copynumber: 4.5 Consensus size: 23
52540002 AATTGAGCTG
*
52540012 AACGGTAAGCTCCGTA-GAGATGA
1 AACGGTAAGCTCCGAAGGA-ATGA
* * *
52540035 AATGGTAAGCCCCTAAGGAATGA
1 AACGGTAAGCTCCGAAGGAATGA
* *
52540058 AACGGTAAGCCCCTAAGGAATGA
1 AACGGTAAGCTCCGAAGGAATGA
*
52540081 AACGGTAAGCTCCGAA-GATTTG-
1 AACGGTAAGCTCCGAAGGA-ATGA
52540103 AACGGTAAGCTC
1 AACGGTAAGCTC
52540115 ATAAAAACTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
22 14 0.20
23 54 0.77
24 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (23 bp):
AACGGTAAGCTCCGAAGGAATGA
Found at i:52542913 original size:21 final size:23
Alignment explanation
Indices: 52542887--52542931 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
52542877 CTTGGCAGGT
52542887 GGATATCACAATACC-C-AAAGG
1 GGATATCACAATACCACTAAAGG
52542908 GGATATCACAATACCACTAAAGG
1 GGATATCACAATACCACTAAAGG
52542931 G
1 G
52542932 AATCTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 15 0.68
22 1 0.05
23 6 0.27
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (23 bp):
GGATATCACAATACCACTAAAGG
Found at i:52549636 original size:57 final size:58
Alignment explanation
Indices: 52549570--52549687 Score: 202
Period size: 57 Copynumber: 2.1 Consensus size: 58
52549560 ATTGATTTTC
* *
52549570 AATTTTCAATTTTTAGACTACTAAGTTCTATATATT-TGCTTTAAATAGGTATTGAGT
1 AATTTTCAATTTTTAGACTACTAAGGTCTATATATTATACTTTAAATAGGTATTGAGT
*
52549627 AATTTTCAATTTTTAGACTATTAAGGTCTATATATTATACTTTAAATAGGTATTGAGT
1 AATTTTCAATTTTTAGACTACTAAGGTCTATATATTATACTTTAAATAGGTATTGAGT
52549685 AAT
1 AAT
52549688 CAAATATACC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 34 0.60
58 23 0.40
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.47
Consensus pattern (58 bp):
AATTTTCAATTTTTAGACTACTAAGGTCTATATATTATACTTTAAATAGGTATTGAGT
Found at i:52551195 original size:16 final size:16
Alignment explanation
Indices: 52551171--52551207 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
52551161 TTGCGACATA
*
52551171 GACATTAGGGTGTCAC
1 GACACTAGGGTGTCAC
52551187 GACACTAGGGTGTCAC
1 GACACTAGGGTGTCAC
52551203 GACAC
1 GACAC
52551208 CGGCCCAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (16 bp):
GACACTAGGGTGTCAC
Found at i:52552130 original size:34 final size:34
Alignment explanation
Indices: 52552084--52552152 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
52552074 AAAGTATGAG
*
52552084 TCCTTATGTGGTAATTAGACAATAAATGGTGTTA
1 TCCTTATATGGTAATTAGACAATAAATGGTGTTA
*
52552118 TCCTTATATGGTAATTAGACCATAAATGGTGTTA
1 TCCTTATATGGTAATTAGACAATAAATGGTGTTA
52552152 T
1 T
52552153 TAGATGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (34 bp):
TCCTTATATGGTAATTAGACAATAAATGGTGTTA
Found at i:52556732 original size:19 final size:19
Alignment explanation
Indices: 52556708--52556744 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52556698 TGAAAATGTG
52556708 TAAGTTATGCCTACGAATT
1 TAAGTTATGCCTACGAATT
*
52556727 TAAGTTATGCCTATGAAT
1 TAAGTTATGCCTACGAAT
52556745 CTATGCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
TAAGTTATGCCTACGAATT
Found at i:52561839 original size:42 final size:43
Alignment explanation
Indices: 52561780--52561879 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
52561770 TAAAAAGTTA
* *
52561780 AGGCACACGCCCGTGGCCAGAGGCCAT-TTCTCCACACAACTG
1 AGGCACACGCCCGTGGCCAGAGACCATGCTCTCCACACAACTG
*
52561822 AGGCACACGCCCGTGGCCAGAGACCGTGCTCTCCACACAACTG
1 AGGCACACGCCCGTGGCCAGAGACCATGCTCTCCACACAACTG
* *
52561865 AGACACACGGCCGTG
1 AGGCACACGCCCGTG
52561880 TCTCTGCCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
42 25 0.48
43 27 0.52
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (43 bp):
AGGCACACGCCCGTGGCCAGAGACCATGCTCTCCACACAACTG
Found at i:52564552 original size:40 final size:40
Alignment explanation
Indices: 52564495--52564681 Score: 179
Period size: 39 Copynumber: 4.7 Consensus size: 40
52564485 TCGAATGATG
52564495 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACC-AT
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGC-AAGTGACCAAT
* * *
52564534 ATCCGGGCTAAGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACCAAT
* * *
52564575 TCCGGGCT-AGATCCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACCAAT
* * * * * *
52564614 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACCAAT
*
52564653 TCCGGGTTAAG-TCCCGAAGGCATTTGTGC
1 TCCGGGCTAAGAT-CCGAAGGCATTTGTGC
52564682 GAGTTGCTAT
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
39 74 0.56
40 49 0.37
41 10 0.08
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGATCCGAAGGCATTTGTGCAAGTGACCAAT
Found at i:52564682 original size:40 final size:40
Alignment explanation
Indices: 52564495--52564718 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
52564485 TCGAATGATG
* * * *
52564495 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
52564535 TCCGGGCTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
52564575 TCCGGGCT-AGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
52564614 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
52564653 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
52564694 -CCGGGCTATGTCCCGAAGGAATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
52564719 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 74 0.45
40 81 0.49
41 10 0.06
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:52564682 original size:79 final size:80
Alignment explanation
Indices: 52564495--52564712 Score: 275
Period size: 79 Copynumber: 2.8 Consensus size: 80
52564485 TCGAATGATG
* * * *
52564495 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGGCTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAGACCCGAAGGCATT
* *
52564559 TGTGCGAGTTACTAAT
65 GGTGCGAGTTACTAAA
52564575 TCCGGGCT-AGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGACCCGAAGGCAT
52564636 TGGTGCGAGTTACTAAA
64 TGGTGCGAGTTACTAAA
* * * * *
52564653 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATAACCGGGCTATGTCCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGACCCGAAGG
52564713 AATTTGAACG
Statistics
Matches: 121, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
78 34 0.28
79 62 0.51
80 25 0.21
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGACCCGAAGGCATTG
GTGCGAGTTACTAAA
Found at i:52564740 original size:79 final size:79
Alignment explanation
Indices: 52564495--52564751 Score: 211
Period size: 79 Copynumber: 3.3 Consensus size: 79
52564485 TCGAATGATG
* * * * * * *
52564495 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCCGGGCTAAGATCCGAAGGCAT
1 TCCGGGTTAAATCCCGAAGGCATTTGTGC-GAGTTACTAATA-CCGGGCTAAG-CCCGAAGGAAT
* ** *
52564558 TTGTGCGAGTTACTAAT
63 TGGAACGAGTTACTAAA
* * * *
52564575 TCCGGGCTAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGG
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGAATTGG
**
52564639 TGCGAGTTACTAAA
66 AACGAGTTACTAAA
* * *
52564653 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTGCT-ATAACCGGGCTATGTCCCGAAGGAATT
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGAATT
* *
52564717 TGAACGAG-TAGCTATA
64 GGAACGAGTTA-CTAAA
*
52564733 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAATCCCGAAGG
52564752 TACGTGATTC
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
78 36 0.24
79 71 0.48
80 42 0.28
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGAATTGG
AACGAGTTACTAAA
Found at i:52566529 original size:48 final size:46
Alignment explanation
Indices: 52566501--52566624 Score: 212
Period size: 46 Copynumber: 2.7 Consensus size: 46
52566491 ATCTCAAGGT
52566501 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTAATGC
* *
52566547 CGATGCATCTTCCAGACATGTCTTACACTAGCTCTCATCTTAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTAATGC
* *
52566593 CGATGCATGTCCTAGACATGTCTTGCACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
52566625 ACACATATCA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTAATGC
Found at i:52570238 original size:28 final size:27
Alignment explanation
Indices: 52570175--52570244 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
52570165 ATAGTGAGTC
52570175 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
52570202 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
52570230 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52570245 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:52577878 original size:28 final size:27
Alignment explanation
Indices: 52577815--52577884 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
52577805 ATAGTGAGTC
52577815 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
52577842 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
52577870 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52577885 GTACAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:52589918 original size:2 final size:2
Alignment explanation
Indices: 52589913--52589943 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52589903 GCAATTTTCT
52589913 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52589944 TTCAATTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:52595302 original size:11 final size:11
Alignment explanation
Indices: 52595286--52595311 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52595276 AGACACTTGC
52595286 TCAAATGGTAT
1 TCAAATGGTAT
52595297 TCAAATGGTAT
1 TCAAATGGTAT
52595308 TCAA
1 TCAA
52595312 CTGCAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (11 bp):
TCAAATGGTAT
Found at i:52597462 original size:2 final size:2
Alignment explanation
Indices: 52597455--52598017 Score: 247
Period size: 2 Copynumber: 292.5 Consensus size: 2
52597445 GTGAAAATAA
* *
52597455 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AA AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
52597496 GG AG AG GG AG AG GG AG -G GG AG AG AG AG AG TG -G TAG AG -G GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG
* * * * * *
52597536 AG AG -G GG AG AG GG GG AG GG AG AG A- AG -G AG AG GG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
52597575 GG AG A- AG AG AG TG GG AG AG GG GG AG AG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * *
52597616 AG -G GG GG AG AG AG AG AG AG GG AG AG A- AG -G AG TG GG AT AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * *
52597655 TG -G AG AG AG AG AG GG AG AG GG AG AG AG AA AG AG AG TG TG TG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * * * *
52597696 TG TG TG TG AG -G GG AG AG AG AG TG AG AG AG GG AA AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * *
52597737 AG AG TG GG AG AG AG AG AG AG -G A- AG AG AG AG AG AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
52597777 AG AG AG AG AG AG AG GG AG -G AG -G CAG AG AG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG
* * * * *
52597818 AG GG AG AG AG AT AG AG AG AG AG A- AG -G AG AG GG AG GG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * * * *
52597858 AG AG AG AG -G GG AA AG GG GG AA AG GG GG AG GG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
52597899 AG AG AG AG AG GG AG GG AG GG AG AG GG AG AG AG AG AG AG -G A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * * * * *
52597939 AG GG GG AG GG GG AG GG AG -G AG AG -G GG GG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
52597979 GG AG AG AG GG GG AG AG AG GG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52598018 AAAGAGATGA
Statistics
Matches: 428, Mismatches: 107, Indels: 52
0.73 0.18 0.09
Matches are distributed among these distances:
1 24 0.06
2 402 0.94
3 2 0.00
ACGTcount: A:0.38, C:0.00, G:0.59, T:0.03
Consensus pattern (2 bp):
AG
Found at i:52597593 original size:47 final size:46
Alignment explanation
Indices: 52597456--52598012 Score: 179
Period size: 49 Copynumber: 11.8 Consensus size: 46
52597446 TGAAAATAAA
* * * * *
52597456 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGAAAGGGGAGAGGGA
1 GAGAGAGA-AG-GAGAGAGAGAG-GGGGGAGAGAGAGAGGGGAGAGGGG
* * * * *
52597505 GAGGGAG-GGGAGAGAGAGA-GTGGTAGAGGGGAGAGGGGAGAGGGG
1 GAGAGAGAAGGAGAGAGAGAGGGGGGAGA-GAGAGAGGGGAGAGGGG
*
52597550 GAGGGAGAGAAGGAGAGGGAGA-GGGGGAGA-AGAGAGTGGGAGAGGGG
1 GA--GAGAGAAGGAGAGAGAGAGGGGGGAGAGAGAGAG-GGGAGAGGGG
* **
52597597 GAGAGAGAGGGAGAGAGAGAGGGGGGAGAGAGAGAGAGGGAGAGAAG
1 GAGAGAGAAGGAGAGAGAGAGGGGGGAGAGAGAGAG-GGGAGAGGGG
* * **
52597644 GAGTGGGATAGTGGAGAGAGAGAGGGAGAGG-GAGAGAGA-AAGAGAGTGTGTG
1 GAGAGAGA-A--GGAGAGAGAGAGGG-G-GGAGAGAGAGAGGGGAGAG-G-G-G
* * * * * * * *
52597696 TGTGTGTG-AGGGGAGAGAGAGTGAGAGAGGGAAAGAGAGGGAGAGTGGG
1 -GAGAGAGAAGGAGAGAGAGAG-GGGGGAGAGAGAGAG-GGGAGAG-GGG
* * * *
52597745 AGAGAGAGAGAGGA-AGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGGGAG
1 -GAGAGAGA-AGGAGAGAGAGAG-GGGGGAGAGAGAGAG-GGGAGAGGG-G
* * *
52597795 GAG-GCAG-AGAGAGAGAGAGAGGGAGGGAGAGAGATAGAGAGAGAGAAGGA
1 GAGAG-AGAAG-GAGAGAGAGAGGG-GGGAGAGAG--AGAG-GGGAGAGGGG
* ** ** * * *
52597845 GAGGGAGGGGGAGAGAGAGAGGGGAAAGGGGGAAAGGGG-GAGGGAG
1 GAGAGAGAAGGAGAGAGAGAGGGGGGAGAGAGAGAGGGGAGAGGG-G
* *
52597891 G-GAGAG-A-GAGAGAGAGAGGGAGGGAG-G-GAGA-GGGAGAGAGA
1 GAGAGAGAAGGAGAGAGAGAGGG-GGGAGAGAGAGAGGGGAGAGGGG
* *
52597932 GAGAG-GAAGG-G-G-GAGGGGGAGGGAG-GAGAGGGGGGAGAGAGAGG
1 GAGAGAGAAGGAGAGAGAGAGGG-GGGAGAGAGAGAGGGGAGAG-G-GG
* * *
52597976 GAGGGAGAGAGG-GGGAGAGAGGGAGAGAGAGAGAGAG
1 GAGAGAGA-AGGAGAGAGAGAGGG-GGGAGAGAGAGAG
52598013 AGAGAAAAGA
Statistics
Matches: 389, Mismatches: 73, Indels: 92
0.70 0.13 0.17
Matches are distributed among these distances:
40 13 0.03
41 9 0.02
42 19 0.05
43 15 0.04
44 13 0.03
45 43 0.11
46 30 0.08
47 43 0.11
48 32 0.08
49 67 0.17
50 62 0.16
51 35 0.09
52 3 0.01
53 5 0.01
ACGTcount: A:0.37, C:0.00, G:0.60, T:0.03
Consensus pattern (46 bp):
GAGAGAGAAGGAGAGAGAGAGGGGGGAGAGAGAGAGGGGAGAGGGG
Found at i:52598331 original size:29 final size:28
Alignment explanation
Indices: 52598282--52598336 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
52598272 TACTATTAGA
*
52598282 TATATTTATAATATATGTTACTAAATTAT
1 TATATTTATAATATATATTAC-AAATTAT
*
52598311 TATATTTA-ATTATAATATTACAAATT
1 TATATTTATAATAT-ATATTACAAATT
52598337 TCAAGATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATTTATAATATATATTACAAATTAT
Found at i:52598500 original size:28 final size:29
Alignment explanation
Indices: 52598451--52598507 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
52598441 ATTTAATAAC
52598451 TATTGTATTAAAATATGATTAA-AATATT
1 TATTGTATTAAAATATGATTAATAATATT
* * **
52598479 TATTTTATTAAATTATTTTTAATAATATT
1 TATTGTATTAAAATATGATTAATAATATT
52598508 CTTATTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TATTGTATTAAAATATGATTAATAATATT
Found at i:52598706 original size:16 final size:16
Alignment explanation
Indices: 52598685--52598740 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
52598675 TGAATTACTG
*
52598685 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
*
52598701 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCA
*
52598717 ATTACAGCTCTATTTA
1 ATTACAGCTCTATTCA
52598733 ATTACAGC
1 ATTACAGC
52598741 CTTATTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:52598746 original size:16 final size:16
Alignment explanation
Indices: 52598685--52598755 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
52598675 TGAATTACTG
**
52598685 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTTA
* *
52598701 ATTACAACTCTATTCA
1 ATTACAGCTCTATTTA
52598717 ATTACAGCTCTATTTA
1 ATTACAGCTCTATTTA
*
52598733 ATTACAGC-CTTATTTC
1 ATTACAGCTC-TATTTA
52598749 ATTACAG
1 ATTACAG
52598756 TGAACCAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
15 1 0.02
16 48 0.98
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTTA
Found at i:52602349 original size:38 final size:38
Alignment explanation
Indices: 52602298--52602373 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
52602288 TCGTGCCGAA
*
52602298 GGTCGTAGCAATAGTCGTGCCCATGACTCCAATCTTAC
1 GGTCGTAGCAATAGTCGTGCCCATGACTCCAATATTAC
*
52602336 GGTCGTAGCAATAGTTGTGCCCATGACTCCAATATTAC
1 GGTCGTAGCAATAGTCGTGCCCATGACTCCAATATTAC
52602374 CTGCAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (38 bp):
GGTCGTAGCAATAGTCGTGCCCATGACTCCAATATTAC
Found at i:52603336 original size:16 final size:15
Alignment explanation
Indices: 52603315--52603361 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
52603305 CTAATTTAAT
52603315 ATAAAATCAAAAATAA
1 ATAAAAT-AAAAATAA
52603331 ATAAAAATAAAAATAA
1 AT-AAAATAAAAATAA
52603347 ATAAAAT-AAAATAA
1 ATAAAATAAAAATAA
52603361 A
1 A
52603362 ATTTTCCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.27
15 5 0.17
16 12 0.40
17 5 0.17
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAATAAAAATAA
Found at i:52603363 original size:10 final size:11
Alignment explanation
Indices: 52603315--52603363 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
52603305 CTAATTTAAT
52603315 ATAAAATCAAAA
1 ATAAAAT-AAAA
52603327 AT-AAATAAAA
1 ATAAAATAAAA
*
52603337 ATAAAA-ATAA
1 ATAAAATAAAA
52603347 ATAAAAT-AAA
1 ATAAAATAAAA
52603357 ATAAAAT
1 ATAAAAT
52603364 TTTCCTAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 24 0.73
11 7 0.21
12 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:52604032 original size:84 final size:84
Alignment explanation
Indices: 52603891--52604057 Score: 298
Period size: 84 Copynumber: 2.0 Consensus size: 84
52603881 CGTAAGGCAA
* *
52603891 GACGTGCCAACCGTAGAACGATAATGGATTTAACAATATTTGTCCCTGTCCTACTCCATTGCCAA
1 GACGTGCCAACCGTAGAACAATAATGGATTTAACAATATTTATCCCTGTCCTACTCCATTGCCAA
52603956 TCCCTAAAAACAATTGCAG
66 TCCCTAAAAACAATTGCAG
*
52603975 GACGTGCCAACCGTAGAACAATAATGGATTTAATAATATTTATCCCTGTCCTACTCCATTGCCAA
1 GACGTGCCAACCGTAGAACAATAATGGATTTAACAATATTTATCCCTGTCCTACTCCATTGCCAA
*
52604040 TCCCTAAATACAATTGCA
66 TCCCTAAAAACAATTGCA
52604058 CATACAGAAG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (84 bp):
GACGTGCCAACCGTAGAACAATAATGGATTTAACAATATTTATCCCTGTCCTACTCCATTGCCAA
TCCCTAAAAACAATTGCAG
Found at i:52607296 original size:18 final size:18
Alignment explanation
Indices: 52607254--52607302 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
52607244 AAATTTGAGA
52607254 ATAAA-AAATAA-AAATC
1 ATAAATAAATAAGAAATC
52607270 ATAAATAAATAAGAAAT-
1 ATAAATAAATAAGAAATC
*
52607287 ATAAATTAAAAAAGAA
1 ATAAA-TAAATAAGAA
52607303 CAAAGTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.17
17 11 0.38
18 13 0.45
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAATAAATAAGAAATC
Found at i:52620638 original size:75 final size:75
Alignment explanation
Indices: 52620550--52620709 Score: 200
Period size: 75 Copynumber: 2.1 Consensus size: 75
52620540 ACTAGCTTGG
* * * *
52620550 TAAACCGACAAATATAATGGTGTGCCCAGCACTAGTCAAATAAA-CTGACAAGGGTTGCACCCAG
1 TAAACCGACAAATATAATGATGTGCCCAGCACTAGTCAAATAAATC-AACAAAGATTGCACCCAG
*
52620614 CGCTAGTCCAA
65 CACTAGTCCAA
* * * *
52620625 TAAACTGATAAATATAATGATGTGCCTAGCACTAGTCGAATAAATCAACAAAGATTGCACCCAGC
1 TAAACCGACAAATATAATGATGTGCCCAGCACTAGTCAAATAAATCAACAAAGATTGCACCCAGC
52620690 ACTAGT-CAGA
66 ACTAGTCCA-A
52620700 T-AACCGACAA
1 TAAACCGACAA
52620710 TAATTGTGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
74 9 0.12
75 62 0.86
76 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (75 bp):
TAAACCGACAAATATAATGATGTGCCCAGCACTAGTCAAATAAATCAACAAAGATTGCACCCAGC
ACTAGTCCAA
Found at i:52623870 original size:48 final size:47
Alignment explanation
Indices: 52623799--52623977 Score: 250
Period size: 48 Copynumber: 3.7 Consensus size: 47
52623789 ATGGAAACAG
* * * * * **
52623799 TATGTGATCCCGTATAAGACCATGTTTGGAACATGGCATCAGCATCAT
1 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGT
52623847 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGT
1 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGT
*
52623895 TATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACATTGT
1 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG-CATTGT
*
52623943 TACGTGAGCCAGTGTAAGACCATGTCTGGGACATG
1 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATG
52623978 ACATTGGCAT
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 1 0.01
48 118 0.99
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (47 bp):
TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGT
Done.