Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 177 of 211
Found at i:52661391 original size:10 final size:10
Alignment explanation
Indices: 52661370--52661399 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
52661360 GCTTCCACCG
52661370 ATCTCG-TCC
1 ATCTCGCTCC
52661379 ATCTCGCTCC
1 ATCTCGCTCC
52661389 ATCTCGCTCC
1 ATCTCGCTCC
52661399 A
1 A
52661400 GATTATCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.13, C:0.47, G:0.10, T:0.30
Consensus pattern (10 bp):
ATCTCGCTCC
Found at i:52668921 original size:17 final size:16
Alignment explanation
Indices: 52668890--52668923 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
52668880 AAATATTATG
52668890 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
52668906 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
52668923 A
1 A
52668924 CACCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:52678297 original size:5 final size:5
Alignment explanation
Indices: 52678289--52678316 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
52678279 ATATTATAAC
52678289 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
52678317 TATATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:52679678 original size:22 final size:22
Alignment explanation
Indices: 52679645--52679700 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
52679635 ATTTCCTCTC
52679645 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
*
52679668 AATTCTCTCAATTTCCTTCTAA
1 AATTCTCTCAATTTCCTTCCAA
52679690 AATTCTCTCAA
1 AATTCTCTCAA
52679701 ATCTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:52679729 original size:51 final size:51
Alignment explanation
Indices: 52679672--52679787 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
52679662 TTCCAAAATT
* *
52679672 CTCTCAATTTCCTTCTAAAATTCTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
52679723 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
52679774 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
52679788 TTTTAAAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:52685304 original size:22 final size:22
Alignment explanation
Indices: 52685288--52685332 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
52685278 TATAACATCA
52685288 ACCAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
*
52685310 ACTAAGACATGGCATAAAACAT
1 ACCAAGACATGGCATAAAACAT
52685332 A
1 A
52685333 TCAACATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (22 bp):
ACCAAGACATGGCATAAAACAT
Found at i:52685811 original size:41 final size:41
Alignment explanation
Indices: 52685698--52685837 Score: 167
Period size: 41 Copynumber: 3.4 Consensus size: 41
52685688 GTACAACTTA
* * *
52685698 CCTGATACAATACACCAGTACGAAGCCTGCTAAGC-TCAAAG
1 CCTGATATAATACACCAGCACGAAGCCTGCTAGGCAT-AAAG
* * *
52685739 CCTAATATAACACACC-GACACAAAGCCTGCTAGGCATAAAG
1 CCTGATATAATACACCAG-CACGAAGCCTGCTAGGCATAAAG
* *
52685780 CCTGATATAATACACCAGCGCGAAGCTTGCTAGGCATAAAG
1 CCTGATATAATACACCAGCACGAAGCCTGCTAGGCATAAAG
*
52685821 CCCGATATAATACACCA
1 CCTGATATAATACACCA
52685838 TAACATCACG
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 81 0.96
42 2 0.02
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (41 bp):
CCTGATATAATACACCAGCACGAAGCCTGCTAGGCATAAAG
Found at i:52686139 original size:45 final size:45
Alignment explanation
Indices: 52686090--52686214 Score: 153
Period size: 46 Copynumber: 2.8 Consensus size: 45
52686080 ATTTGATTTG
* *
52686090 TGATGCCATAGCGTCTTTCAGCTATGGACTTAC-ACGATAGAATCA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTA-GATAGAATCA
* * * * *
52686135 TGATGCCATATATGGCTTTCACCTATGGTCTGACTAGATAGAATCG
1 TGATGCCATA-ACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
*
52686181 TGATGCCATAACGTCTTTTAGCTATGGTCTTACT
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACT
52686215 CGTTTTTGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 29 0.44
46 36 0.55
47 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTAGATAGAATCA
Found at i:52686242 original size:45 final size:45
Alignment explanation
Indices: 52686184--52686299 Score: 108
Period size: 45 Copynumber: 2.6 Consensus size: 45
52686174 AGAATCGTGA
* * *
52686184 TGCCATA-ACGTCTTTTAGCTATGGTCTTACTCGTTTTTGCTATGG
1 TGCCATAGA-GTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
* * * * * * * *
52686229 TGCCATAGTGTCTTTCAACTTTGTTCTTATTTATTTCTGGTATAG
1 TGCCATAGAGTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
*
52686274 TGTCATAGAGTCTTTTAGCTATGGTC
1 TGCCATAGAGTCTTTTAGCTATGGTC
52686300 CTAATAATTT
Statistics
Matches: 53, Mismatches: 17, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (45 bp):
TGCCATAGAGTCTTTTAGCTATGGTCTTACTCATTTCTGCTATAG
Found at i:52695558 original size:41 final size:41
Alignment explanation
Indices: 52695497--52695597 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 41
52695487 CTACTAAGCT
* * * * *
52695497 CAAAGCCTAATATAACACAACGGCATGAAGCCTGCTAGGGA
1 CAAAGCCTGATATAATACAACAGCACGAAGCCTGCTAGGCA
*
52695538 CAAAGCCTGATATAATACAACAGCACGAAGCTTGCTAGGCA
1 CAAAGCCTGATATAATACAACAGCACGAAGCCTGCTAGGCA
*
52695579 TAAAGCCTGATATAATACA
1 CAAAGCCTGATATAATACA
52695598 CCACAACATC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
CAAAGCCTGATATAATACAACAGCACGAAGCCTGCTAGGCA
Found at i:52695875 original size:45 final size:45
Alignment explanation
Indices: 52695815--52695946 Score: 140
Period size: 45 Copynumber: 2.9 Consensus size: 45
52695805 TCGTGTTGTC
* * *
52695815 ATAGTTTCTTTCAACTATGGTCTTA-TTCGTTTGATTCATGATACA
1 ATAGTGTCTTTCAACTATGGTCTTACTT-GATTGAATCATGATACA
* * *
52695860 ATAGTGTCTTTCAACTATGCTCTTACTTGATTGAATCATGATGCC
1 ATAGTGTCTTTCAACTATGGTCTTACTTGATTGAATCATGATACA
** * * * *
52695905 ATAACGTCTTTCACCTATGGTCTTCCTAGATAGAATCATGAT
1 ATAGTGTCTTTCAACTATGGTCTTACTTGATTGAATCATGAT
52695947 GCCATAACGT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 71 0.97
46 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (45 bp):
ATAGTGTCTTTCAACTATGGTCTTACTTGATTGAATCATGATACA
Found at i:52695947 original size:45 final size:45
Alignment explanation
Indices: 52695865--52695962 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
52695855 ATACAATAGT
* *
52695865 GTCTTTCAACTATGCTCTTACTTGATTGAATCATGATGCCATAAC
1 GTCTTTCAACTATGCTCTTACTAGATAGAATCATGATGCCATAAC
* * *
52695910 GTCTTTCACCTATGGTCTTCCTAGATAGAATCATGATGCCATAAC
1 GTCTTTCAACTATGCTCTTACTAGATAGAATCATGATGCCATAAC
*
52695955 GTCCTTCA
1 GTCTTTCA
52695963 TCTCTTGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (45 bp):
GTCTTTCAACTATGCTCTTACTAGATAGAATCATGATGCCATAAC
Found at i:52701140 original size:88 final size:88
Alignment explanation
Indices: 52700969--52701146 Score: 205
Period size: 88 Copynumber: 2.0 Consensus size: 88
52700959 GGACCATGAG
*
52700969 CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAAACTGCTCCACTACAACCGAGG
1 CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAAACTGCTCCACTACAACCAAGG
* * * *
52701034 GAGGTAAGCCTTGTGTCTTTGAT
66 GAGGGAAGCCTAGGGTCTTCGAT
* * * * * * * **
52701057 CTACTTCGCTGTCGATGTAGGAATG-AAGGATCTGCTATCTTCAACCTGTTCTGCTACAACCAAG
1 CTACTTCACTGTCGATGCAGGAAGGCAA-GACCAGCTATCTTCAAACTGCTCCACTACAACCAAG
*
52701121 GGAGGGAAGGCTAGGGTCTTCGAT
65 GGAGGGAAGCCTAGGGTCTTCGAT
52701145 CT
1 CT
52701147 GCTCCACTAC
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
87 2 0.03
88 72 0.97
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (88 bp):
CTACTTCACTGTCGATGCAGGAAGGCAAGACCAGCTATCTTCAAACTGCTCCACTACAACCAAGG
GAGGGAAGCCTAGGGTCTTCGAT
Found at i:52701240 original size:44 final size:44
Alignment explanation
Indices: 52701193--52701453 Score: 324
Period size: 44 Copynumber: 5.9 Consensus size: 44
52701183 TTCAACCTGC
** * * *
52701193 TCCACTGCTACTCAGGGAGCTAGGACTTACAATCTTCTACCTAC
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* *
52701237 TCCACTACTGGTCAAGGAGCTAGGATTTACAATCTTCCACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* * * *
52701281 TCCACTGCTGGTCAAGGAGCTAGGTTTTATAATCTTCCGCCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* * * * *
52701325 TCCACTGTTGTTCAGGGAGCTAGGACTTATAGTCTTCCACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* * * *
52701369 TCTACTGCTAGTCAGGGAGCTAAGATTTACAATCTTCTACCTAT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
* *
52701413 TCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCCACC
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACC
52701454 GGTTTGTTCT
Statistics
Matches: 184, Mismatches: 33, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 184 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (44 bp):
TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTAT
Found at i:52701245 original size:88 final size:87
Alignment explanation
Indices: 52701148--52701453 Score: 315
Period size: 88 Copynumber: 3.5 Consensus size: 87
52701138 CTTCGATCTG
* * * * * ** *
52701148 CTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTGCTCCACTGCTACTCAGGGAGC
1 CTCCACTACTG-TTAGGGAGCTAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGC
*
52701213 TAGGACTTACAATCTTCTACCTA
65 TAGGATTTACAATCTTCTACCTA
* * * * *
52701236 CTCCACTACTGGTCAAGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCTGGTCAAGGAGC
1 CTCCACTACT-GTTAGGGAGCTAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGC
* * **
52701301 TAGGTTTTATAATCTTCCGCCTA
65 TAGGATTTACAATCTTCTACCTA
* ** * * *
52701324 TTCCACTGTTGTTCAGGGAGCTAGGACTTATAGTCTTCCACCTATTCTACTGCTAGTCAGGGAGC
1 CTCCACTACTGTT-AGGGAGCTAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGC
*
52701389 TAAGATTTACAATCTTCTACCTA
65 TAGGATTTACAATCTTCTACCTA
* * * *
52701412 TTCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCCACC
1 CTCCACTACT-GTTAGGGAGCTAGGATTTATAATCTTCCACC
52701454 GGTTTGTTCT
Statistics
Matches: 178, Mismatches: 37, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
87 2 0.01
88 173 0.97
89 3 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (87 bp):
CTCCACTACTGTTAGGGAGCTAGGATTTATAATCTTCCACCTATTCCACTGCTAGTCAGGGAGCT
AGGATTTACAATCTTCTACCTA
Found at i:52701361 original size:132 final size:132
Alignment explanation
Indices: 52701204--52701450 Score: 377
Period size: 132 Copynumber: 1.9 Consensus size: 132
52701194 CCACTGCTAC
* * *
52701204 TCAGGGAGCTAGGACTTACAATCTTCTACCTACTCCACTACTGGTCAAGGAGCTAGGATTTACAA
1 TCAGGGAGCTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAAGGAGCTAAGATTTACAA
*
52701269 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGTTTTATAATCTTCCGCCTATTCCACTGTT
66 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGTT
52701334 GT
131 GT
* * * * * *
52701336 TCAGGGAGCTAGGACTTATAGTCTTCCACCTATTCTACTGCTAGTCAGGGAGCTAAGATTTACAA
1 TCAGGGAGCTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAAGGAGCTAAGATTTACAA
* * *
52701401 TCTTCTACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTATAGTCTTCC
66 TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCC
52701451 ACCGGTTTGT
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
132 102 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (132 bp):
TCAGGGAGCTAGGACTTACAATCTTCCACCTACTCCACTACTAGTCAAGGAGCTAAGATTTACAA
TCTTCCACCTATTCCACTGCTGGTCAAGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGTT
GT
Found at i:52712659 original size:27 final size:30
Alignment explanation
Indices: 52712623--52712704 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 30
52712613 GAATATAAAG
52712623 GGGGTTGCTAAGTGCTGATTCCC-C-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCACTCATA
* * *
52712650 GGGGTTGCTAAGTGTTAATTCCCTGACTCATT
1 GGGGTTGCTAAGTGCTGATTCCC--ACTCATA
52712682 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
52712705 ACCGTATCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 21 0.48
30 1 0.02
31 2 0.05
32 2 0.05
33 18 0.41
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCACTCATA
Found at i:52712787 original size:102 final size:101
Alignment explanation
Indices: 52712611--52712953 Score: 474
Period size: 102 Copynumber: 3.4 Consensus size: 101
52712601 CCGGAGTACA
*
52712611 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTAATTCCCTGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATT-CCCCAAGGGGTTGCTAAGTGCTAATTCCCTGA
*
52712676 CTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
65 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * *
52712713 TTGAATATAAAGGGGGTTGCTAAGTGTTGATTCCCCTAAGGGGTTGCTAGGTGCTGATTCCCTGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCC-AAGGGGTTGCTAAGTGCTAATTCCCTGA
* * *
52712778 TTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATT
65 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * * * * *
52712815 TTAAATGTGAAGGGGGTTTCTAAGTGCTGATTCCCACAAGGGGTTGCTAAGTGCTCATTCCCCGA
1 TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCC-CAAGGGGTTGCTAAGTGCTAATTCCCTGA
52712880 ATCATTGGTGGTTGCTAAGTGCTGATTCCACCAG-ATC
65 ATCATTGGTGGTTGCTAAGTGCTGATTCCACC-GTATC
* *
52712917 TTTGAATGTGAAA-GGGGTTGCTAAGTGGTGATTCCCC
1 -TTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
52712954 GAATCACTGG
Statistics
Matches: 214, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
101 4 0.02
102 178 0.83
103 30 0.14
104 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (101 bp):
TTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAAGGGGTTGCTAAGTGCTAATTCCCTGAA
TCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
Found at i:52712864 original size:27 final size:30
Alignment explanation
Indices: 52712827--52712908 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 30
52712817 AAATGTGAAG
*
52712827 GGGGTTTCTAAGTGCTGATTCCC-A-CA-A
1 GGGGTTGCTAAGTGCTGATTCCCAATCATA
* *
52712854 GGGGTTGCTAAGTGCTCATTCCCCGAATCATT
1 GGGGTTGCTAAGTGCTGATT-CCC-AATCATA
52712886 GGTGGTTGCTAAGTGCTGATTCC
1 GG-GGTTGCTAAGTGCTGATTCC
52712909 ACCAGATCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
27 18 0.40
28 3 0.07
30 1 0.02
31 2 0.04
32 4 0.09
33 17 0.38
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (30 bp):
GGGGTTGCTAAGTGCTGATTCCCAATCATA
Found at i:52720305 original size:33 final size:33
Alignment explanation
Indices: 52720241--52720394 Score: 122
Period size: 33 Copynumber: 4.6 Consensus size: 33
52720231 ATATAAAGGG
*
52720241 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
52720268 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
52720301 GGTTGCTAAGTGCTGATCCCACCATATTTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-GA--TT-CAT-TG--GT
*
52720342 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
52720375 GGTTGCTAGGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52720395 ACCATATCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
27 21 0.21
31 2 0.02
32 2 0.02
33 38 0.38
34 2 0.02
35 3 0.03
36 2 0.02
37 3 0.03
38 2 0.02
39 3 0.03
40 2 0.02
41 20 0.20
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:52720445 original size:76 final size:74
Alignment explanation
Indices: 52720264--52720473 Score: 312
Period size: 74 Copynumber: 2.8 Consensus size: 74
52720254 TGATTCCCCC
* *
52720264 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATT
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
52720329 TTAAATGTG
66 TTAAATGTG
* *
52720338 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAGGTGCTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATAT-
*
52720403 TTTTAATGTG
65 TTTAAATGTG
* * * * *
52720413 AAAGTGGTTGCTAAGTGTTGATTCCCCGAATCACTGTTGGTTGCTAAGCGCTGAATCCACC
1 -AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACC
52720474 GATAACAGTT
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
74 60 0.49
75 9 0.07
76 53 0.43
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (74 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
TTAAATGTG
Found at i:52728005 original size:2 final size:2
Alignment explanation
Indices: 52727998--52728029 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52727988 ACAAGCAAAA
52727998 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52728030 CTCTCAATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52731744 original size:792 final size:791
Alignment explanation
Indices: 52730192--52731784 Score: 2884
Period size: 792 Copynumber: 2.0 Consensus size: 791
52730182 TATCCAACCT
*
52730192 CAACTCCTTACTATCGACATTCAGTACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
1 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
52730257 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
66 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
* * *
52730322 TCGAAACCATCCGCGCAACACAAAATCACCATAATTACCTCACAATCAACCTTCGCTCGATGCTC
131 TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
* *
52730387 GGTCAACCAATCCATCCTGAGGATAACATAGAACCCTTAGAACGGTAATTCTAAAAGATCTATAG
196 GGTCAACCAATCCATCCTGAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
52730452 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
261 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
*
52730517 CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAGGAATCCTTAACTTTCTAAC
326 CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAAGAATCCTTAACTTTCTAAC
52730582 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
391 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
*
52730647 GTAGCATGAAAGTACCCACGATGACATCCGTAGCCTCTCTTGTCTAAGGCTCTCTAACTGTGTAA
456 GTAGCATGAAAGTACCCACGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
* * *
52730712 ACTCTGGCTGGACCTTCATTACCATCGTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
521 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
*
52730777 TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGGTGCAGTAGCAACAACAATAGCAATACGTTGGT
586 TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGGTGCAGCAGCAACAACAATAGCAATACGTTGGT
* * *
52730842 CCATCAAGCCGAACCATAACTGCTCTTCTCGGACAATTACTAACATGATGCTTCATCGATCCGTA
651 CCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACATGATGCTTCATCGATCCGTA
*
52730907 AAGAAGATAAGTGCCACTCATCCTCCAACACTCACC-ATGATGATGACGACCACAATGCTCACAT
716 AAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGAT-A-GACGACCACAATGCTCACAT
52730971 AACAGCCATGTAA
779 AACAGCCATGTAA
*
52730984 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCTAGACCAACT
1 CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
52731049 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
66 TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
*
52731114 TCGAAACCATCCACGCAACACAAAATCACCATAATTGCCTCACAATAAACCTTCGCTCAATGCTC
131 TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
* *
52731179 GGTCAACCAATCCATCCTGAGGATAACATAAAACCCTTAAAATGGTAATTCTAAAAGATTTATAG
196 GGTCAACCAATCCATCCTGAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
52731244 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
261 GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
52731309 CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAAGAATCCTTAACTTTCTAAC
326 CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAAGAATCCTTAACTTTCTAAC
52731374 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
391 TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
* *
52731439 GTAGCATGAAAGTACCCGCGATGACATCCGTGGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
456 GTAGCATGAAAGTACCCACGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
52731504 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
521 ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCA-C
* *
52731569 ACATCTGTCAAGGCCCCTCCCTCGAGCCGAAACAGGTGCAGCAGCAACAACAATAGCAATAGGTT
585 -C-TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGGTGCAGCAGCAACAACAATAGCAATACGTT
52731634 GGTCCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACATGATGCTTCATCGATCC
648 GGTCCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACATGATGCTTCATCGATCC
*
52731699 GTAAAGAAGATAAATGCCATTCATCCTCCAACACTCACC-ATGATGACGACGACCACAATGCTCA
713 GTAAAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGAT-A-GACGACCACAATGCTCA
52731763 CATAACAGCCATGTAA
776 CATAACAGCCATGTAA
52731779 CAACTC
1 CAACTC
52731785 TTTGATCACT
Statistics
Matches: 772, Mismatches: 26, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
792 566 0.73
793 1 0.00
794 1 0.00
795 204 0.26
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (791 bp):
CAACTCCTTACTATCGACATTCAATACATAGGCTAGATAAGCTTCGTAACCTTTCCAGACCAACT
TCTCAGCTCTAAGCGAAGAAATCACATTAGAAAGCAACTCCAACTTCTCTCCAACAACAACAACT
TCGAAACCATCCACGCAACACAAAATCACCATAATTACCTCACAATAAACCTTCGCTCAATGCTC
GGTCAACCAATCCATCCTGAGGATAACATAAAACCCTTAAAACGGTAATTCTAAAAGATCTATAG
GAAACACTTGTCCCTAAACCATTAGAGAACAACGACGGTAAACCCAATCCACCACTACACTATCA
CCTAGAGGGCTCTTAATCATAACACCTAACCTAGATGTCTCTACAAGAATCCTTAACTTTCTAAC
TACATCACTCAGAATAAACGATCCCATAGCACCCGAATCAACTAAAGCTAAAAGAGGAAAAGATT
GTAGCATGAAAGTACCCACGATGACATCCGTAGCCTCTCTTATCTAAGGCTCTCTAACTGTGTAA
ACTCTGGCTGGACCTCCATTACCACCCTGAGCAATTTTACGCTAACCAACATCTCTACCACCACC
TCTGTCAAGGCCCCTCCCTCAAGCCGAAACAGGTGCAGCAGCAACAACAATAGCAATACGTTGGT
CCATCAAGCCGAACCACAACTGCTCTCCTCGGACAATAACTAACATGATGCTTCATCGATCCGTA
AAGAAGATAAATGCCACTCATCCTCCAACACTCACCAATGATAGACGACCACAATGCTCACATAA
CAGCCATGTAA
Found at i:52737819 original size:13 final size:14
Alignment explanation
Indices: 52737801--52737830 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52737791 AAGCCTAAGA
52737801 AAAGAA-AAAGACT
1 AAAGAATAAAGACT
52737814 AAAGAATAAAGACT
1 AAAGAATAAAGACT
52737828 AAA
1 AAA
52737831 TCTAACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (14 bp):
AAAGAATAAAGACT
Found at i:52739628 original size:132 final size:132
Alignment explanation
Indices: 52739391--52739659 Score: 520
Period size: 132 Copynumber: 2.0 Consensus size: 132
52739381 CTTTCAATTG
*
52739391 ATTTGCTCATTTCCGATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
*
52739456 TGTATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TATATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
52739521 AT
131 AT
52739523 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
1 ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
52739588 TATATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
66 TATATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
52739653 AT
131 AT
52739655 ATTTG
1 ATTTG
52739660 TTTTCATTTT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (132 bp):
ATTTGCTCATTTCCAATTAGACTAATGATATGTTTAGGTTCATCTACTAATACAAGTTGTCTTTC
TATATTACGATCTGACCACGTGAAACCGCTTAGTATTAGTTAAATACTAGATAACCAGTGAGCCC
AT
Found at i:52740684 original size:27 final size:27
Alignment explanation
Indices: 52740620--52740685 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
52740610 GGTCGAGGGC
*
52740620 CTGCCATAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
* * *
52740647 GTGGCAGAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGGCACCAAAGGTGCCA
52740674 CTGCCACAGGCG
1 CTGCCACAGGCG
52740686 ACATCCCAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.32, G:0.35, T:0.09
Consensus pattern (27 bp):
CTGCCACAGGCGGCACCAAAGGTGCCA
Found at i:52740762 original size:3 final size:3
Alignment explanation
Indices: 52740734--52740785 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
52740724 TGCACGAAAG
*
52740734 AGA AGAA AGA A-A AGGA A-A AG- AGA AGA AGA AGA AGA AGA AGA AAA
1 AGA AG-A AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
52740778 AGA AGA AG
1 AGA AGA AG
52740786 GGGAAGGAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 6 0.14
3 31 0.74
4 5 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52745917 original size:11 final size:11
Alignment explanation
Indices: 52745871--52745938 Score: 68
Period size: 11 Copynumber: 6.2 Consensus size: 11
52745861 TAAATCATTT
*
52745871 CTCTC-AATTT
1 CTCTCAAATTC
52745881 CTCTCTAATATT-
1 CTCTC-AA-ATTC
52745893 CTCTCAAATTC
1 CTCTCAAATTC
* *
52745904 CTCCCAATTTC
1 CTCTCAAATTC
*
52745915 CTCTCAAGTTC
1 CTCTCAAATTC
52745926 CTCTCAAATTC
1 CTCTCAAATTC
52745937 CT
1 CT
52745939 ATTTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
10 8 0.16
11 32 0.65
12 6 0.12
13 3 0.06
ACGTcount: A:0.22, C:0.35, G:0.01, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:52745990 original size:29 final size:28
Alignment explanation
Indices: 52745943--52745998 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
52745933 ATTCCTATTT
*
52745943 AAAAAAGTTTTAATTTTTTAATTATTTTTA
1 AAAAAAGTTTTAATATTTT-ATT-TTTTTA
52745973 AAAAAAGTTTTAA-ATTTTATTTTTTT
1 AAAAAAGTTTTAATATTTTATTTTTTT
52745999 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 5 0.20
28 3 0.12
29 4 0.16
30 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
AAAAAAGTTTTAATATTTTATTTTTTTA
Found at i:52747124 original size:7 final size:7
Alignment explanation
Indices: 52747112--52747137 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52747102 AAGTCGATTG
52747112 GTATTTA
1 GTATTTA
52747119 GTATTTA
1 GTATTTA
52747126 GTATTTA
1 GTATTTA
52747133 GTATT
1 GTATT
52747138 ATGTATTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:52747143 original size:7 final size:7
Alignment explanation
Indices: 52747133--52747164 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
52747123 TTAGTATTTA
52747133 GTATTAT
1 GTATTAT
*
52747140 GTATTGT
1 GTATTAT
52747147 GTATTAT
1 GTATTAT
52747154 GTATTAT
1 GTATTAT
52747161 GTAT
1 GTAT
52747165 ATAACTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (7 bp):
GTATTAT
Found at i:52747143 original size:14 final size:14
Alignment explanation
Indices: 52747112--52747158 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
52747102 AAGTCGATTG
52747112 GTATTTAGTATT-T
1 GTATTTAGTATTAT
52747125 AGTATTTAGTATTAT
1 -GTATTTAGTATTAT
52747140 GTATTGT-GTATTAT
1 GTATT-TAGTATTAT
52747154 GTATT
1 GTATT
52747159 ATGTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 29 0.94
15 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.17, T:0.57
Consensus pattern (14 bp):
GTATTTAGTATTAT
Found at i:52747828 original size:18 final size:18
Alignment explanation
Indices: 52747805--52747843 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52747795 ATGCCAGGTG
* *
52747805 TGTATCATAGCCCTTTTA
1 TGTATCATAACCCTTATA
*
52747823 TGTATCCTAACCCTTATA
1 TGTATCATAACCCTTATA
52747841 TGT
1 TGT
52747844 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (18 bp):
TGTATCATAACCCTTATA
Found at i:52749675 original size:126 final size:126
Alignment explanation
Indices: 52749381--52749791 Score: 664
Period size: 126 Copynumber: 3.3 Consensus size: 126
52749371 CATGCACTAT
* * * *
52749381 TGTAGCAAAAACGCATCCACGTGGGAGCTTCTTTCAATACT-TCTACTGACAAAACATCCTGCTT
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTAT-TGCTGACAAAACATCCTGCTT
* * *
52749445 AAAGCTTTTTTAACACTATTTGCTCAGAAACGTCTACTCAAAATTA-TTTTTCATGAGCTAC
65 AAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
*
52749506 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAACATCTTGCTTA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAACATCCTGCTTA
* * *
52749571 AAGCGTTTTTGACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTTAGGAGCTAC
66 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
* *
52749632 TGTAGCGAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAGCATCCTGCTTA
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAACATCCTGCTTA
52749697 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
66 AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
* *
52749758 TGTAGCAAAAGCGCGTCCACGTGAGAACTTCTTT
1 TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
52749792 AAATTAACAA
Statistics
Matches: 264, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
125 99 0.38
126 165 0.62
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (126 bp):
TGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTATTGCTGACAAAACATCCTGCTTA
AAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGAGCTAC
Found at i:52749988 original size:96 final size:96
Alignment explanation
Indices: 52749830--52750101 Score: 324
Period size: 96 Copynumber: 2.9 Consensus size: 96
52749820 CCTCAACCAC
* * * *
52749830 AAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTTA
1 AAACCCTAATTTATTTGA-TTTTTTCATAAAAACCATAAACACTAAACCCTAATCTAATTTTTTA
*
52749895 AAAATTTATAATTAATTTATTCAAGTAACCTT
65 AAAATTTATAATTAATTTACTCAAGTAACCTT
* * * *
52749927 GAACCCTAATTTATTTGATTTTTTCATAAAAACCTTTAACTCTAAACCCTAATCTAATTTTTTTA
1 AAACCCTAATTTATTTGATTTTTTCATAAAAACCATAAACACTAAACCCTAATCTAA-TTTTTTA
* *
52749992 AAAAATT-TAATTAAATTACTCAAGTAACCTT
65 AAAATTTATAATTAATTTACTCAAGTAACCTT
* * *
52750023 AAACCCTAATTTAATTT--TTTTCTT-A-AAAAACAATAAACACGAAA-CCTAATCTAA-TTTTG
1 AAACCCTAATTT-ATTTGATTTT-TTCATAAAAACCATAAACACTAAACCCTAATCTAATTTTTT
*
52750082 AAAATTTTATAATTAATTTA
64 AAAAATTTATAATTAATTTA
52750102 ATTGACAAAC
Statistics
Matches: 151, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
91 10 0.07
92 10 0.07
93 10 0.07
94 14 0.09
95 5 0.03
96 68 0.45
97 34 0.23
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (96 bp):
AAACCCTAATTTATTTGATTTTTTCATAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAA
AAATTTATAATTAATTTACTCAAGTAACCTT
Found at i:52752406 original size:18 final size:18
Alignment explanation
Indices: 52752383--52752419 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52752373 GGGGGAAGGA
*
52752383 GAGGCGGTTATGGTGGAG
1 GAGGCGGTGATGGTGGAG
*
52752401 GAGGCGGTGGTGGTGGAG
1 GAGGCGGTGATGGTGGAG
52752419 G
1 G
52752420 CGCCGGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.05, G:0.62, T:0.19
Consensus pattern (18 bp):
GAGGCGGTGATGGTGGAG
Found at i:52755640 original size:28 final size:28
Alignment explanation
Indices: 52755579--52755644 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
52755569 TTTTAGGATG
* * *
52755579 ATTTTTATTTTAATATTTATTTTTAATT
1 ATTTTTATTTAAATATTTATTTTAAAAT
52755607 ATTTTTATTTAAATA-TTATTTTAAAAT
1 ATTTTTATTTAAATATTTATTTTAAAAT
*
52755634 ATATTT-TTTAA
1 ATTTTTATTTAA
52755645 GAATTTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.15
27 15 0.44
28 14 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTTTATTTAAATATTTATTTTAAAAT
Found at i:52759203 original size:4 final size:4
Alignment explanation
Indices: 52759186--52759219 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
52759176 CAAATTATTT
52759186 TTAA TTATA TTAA TTAA TTAA TTAA TTAAA TTAA
1 TTAA TTA-A TTAA TTAA TTAA TTAA TT-AA TTAA
52759220 CATATTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:52759208 original size:17 final size:17
Alignment explanation
Indices: 52759186--52759219 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
52759176 CAAATTATTT
52759186 TTAATTATATT-AATTAA
1 TTAATTA-ATTAAATTAA
52759203 TTAATTAATTAAATTAA
1 TTAATTAATTAAATTAA
52759220 CATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAATTAAATTAA
Found at i:52767467 original size:44 final size:44
Alignment explanation
Indices: 52767404--52767561 Score: 199
Period size: 44 Copynumber: 3.4 Consensus size: 44
52767394 TACTTCTAAC
* *
52767404 CAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACGCTTATCTGAT
1 CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
52767448 CAGTGACAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGAT
1 CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
*
52767492 CAGTGACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGAT
1 CAGT-----G--ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
* *
52767543 CAGGGACAAGTGACAAGTG
1 CAGTGACAAGTGATAAGTG
52767562 ATAAATGTGA
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
44 58 0.58
46 1 0.01
49 1 0.01
51 40 0.40
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
CAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:52767508 original size:51 final size:51
Alignment explanation
Indices: 52767453--52767565 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
52767443 CTGATCAGTG
* *
52767453 ACAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
* *
52767504 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAGGGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
52767555 ACAAGTGATAA
1 ACAAGTGATAA
52767566 ATGTGATCCG
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
Found at i:52768718 original size:14 final size:14
Alignment explanation
Indices: 52768699--52768725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
52768689 GTTTCGTCAT
52768699 CGAATACGGGTTAC
1 CGAATACGGGTTAC
52768713 CGAATACGGGTTA
1 CGAATACGGGTTA
52768726 GGGGTGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (14 bp):
CGAATACGGGTTAC
Found at i:52776375 original size:16 final size:16
Alignment explanation
Indices: 52776354--52776387 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52776344 TAAATAAATT
*
52776354 AAAATAATAGACAATA
1 AAAATAAAAGACAATA
*
52776370 AAAATAAAAGATAATA
1 AAAATAAAAGACAATA
52776386 AA
1 AA
52776388 TCACGAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAAGACAATA
Found at i:52780142 original size:20 final size:20
Alignment explanation
Indices: 52780117--52780159 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
52780107 CTAAAATTGT
* *
52780117 AAATTGAGCCCAAGAGCCCA
1 AAATTGAGACCAAGACCCCA
*
52780137 AAATTGAGATCAAGACCCCA
1 AAATTGAGACCAAGACCCCA
52780157 AAA
1 AAA
52780160 ACTAGTCGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATTGAGACCAAGACCCCA
Found at i:52780490 original size:48 final size:52
Alignment explanation
Indices: 52780425--52780543 Score: 165
Period size: 48 Copynumber: 2.3 Consensus size: 52
52780415 AAAATAATGT
* *
52780425 TATTTTAATAGATTTAATATTAAATTAAATTTAATATTTATC-T-TA-AT-AG
1 TATTTTATTA-ATTTAATATTAAATTAAATTTAATATTTATCTTATAGATAAA
* *
52780474 TATTTTATTAATTTAATATTAAATTTAATTTAATGTTTATCTTATAGATAAA
1 TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGATAAA
52780526 TATTTTATTAATTTAATA
1 TATTTTATTAATTTAATA
52780544 ATATTTAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
48 29 0.47
49 10 0.16
50 2 0.03
51 2 0.03
52 19 0.31
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (52 bp):
TATTTTATTAATTTAATATTAAATTAAATTTAATATTTATCTTATAGATAAA
Found at i:52780503 original size:17 final size:17
Alignment explanation
Indices: 52780436--52780507 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
52780426 ATTTTAATAG
*
52780436 ATTTAATATTAAATTAA
1 ATTTAATATTAAATTTA
*
52780453 ATTTAATATT-TATCTTA
1 ATTTAATATTAAAT-TTA
* **
52780470 A--TAGTATTTTA-TTA
1 ATTTAATATTAAATTTA
52780484 ATTTAATATTAAATTTA
1 ATTTAATATTAAATTTA
52780501 ATTTAAT
1 ATTTAAT
52780508 GTTTATCTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.09
15 6 0.14
16 11 0.25
17 23 0.52
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
ATTTAATATTAAATTTA
Found at i:52780548 original size:19 final size:21
Alignment explanation
Indices: 52780524--52780575 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
52780514 CTTATAGATA
52780524 AATATTT-TATT-AATTTAAT
1 AATATTTATATTAAATTTAAT
52780543 AATATTTAATATTAAATTTAATCT
1 AATATTT-ATATTAAATTTAA--T
52780567 AATATTTAT
1 AATATTTAT
52780576 CTTGATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
21 4 0.14
22 7 0.25
23 2 0.07
24 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTTATATTAAATTTAAT
Found at i:52787727 original size:24 final size:24
Alignment explanation
Indices: 52787700--52787784 Score: 99
Period size: 24 Copynumber: 3.6 Consensus size: 24
52787690 TGTGGCAAGG
52787700 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
52787724 GAAATA-TAAATTAT--TTAT-TTATA-
1 GAAA-ACT---TTATCCTTATGTTATAT
52787747 GAAAACTTTATCCTTATGTTATAT
1 GAAAACTTTATCCTTATGTTATAT
52787771 GAAAACTTTATCCT
1 GAAAACTTTATCCT
52787785 AATTGTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
20 4 0.08
22 5 0.10
23 10 0.19
24 24 0.46
25 5 0.10
27 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.45
Consensus pattern (24 bp):
GAAAACTTTATCCTTATGTTATAT
Found at i:52787947 original size:159 final size:160
Alignment explanation
Indices: 52787622--52787931 Score: 419
Period size: 159 Copynumber: 1.9 Consensus size: 160
52787612 TCTAAAGGCA
*
52787622 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACCAAAATTCAAGATA
1 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACAAAAATTCAAGATA
* *
52787687 ATGTGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTATAGAAAA
66 ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
*** ** * * ** *
52787752 CTTTATCCTTATGTTATATGAAAACTTTAT
131 AGGTAAACTTATATAATACCAAAACTATAT
* *
52787782 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTTAAAGATG-CAATAAGACAAAAATTCAAGATA
1 CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACAAAAATTCAAGATA
* *
52787846 GTGGGTGGCAATGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAATGTTA
66 ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAA-G--A
52787911 AAAAGGTAAAC-TA-ATAATACC
128 AAAAGGTAAACTTATATAATACC
52787932 TTAATATATG
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
159 77 0.59
160 45 0.34
161 2 0.02
162 7 0.05
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (160 bp):
CCTAATTGTTGTTGTCTTTTTAAATGGGAGGTTCAAAGATGAAAATAAGACAAAAATTCAAGATA
ATGGGTGGCAAGGGAAAACTTTATCCTTATGTTATATGAAATATAAATTATTTATTTAAAGAAAA
AGGTAAACTTATATAATACCAAAACTATAT
Found at i:52792163 original size:15 final size:16
Alignment explanation
Indices: 52792145--52792178 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52792135 AAATTAAATT
52792145 AATTAA-CTAAATGAA
1 AATTAACCTAAATGAA
*
52792160 AATTAACCTAAATGCA
1 AATTAACCTAAATGAA
52792176 AAT
1 AAT
52792179 GAGATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGAA
Found at i:52796853 original size:43 final size:43
Alignment explanation
Indices: 52796792--52796952 Score: 202
Period size: 43 Copynumber: 3.8 Consensus size: 43
52796782 TATTGAATAA
* * *
52796792 AAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTTGATTATG
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
* *
52796835 AAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCACTAAATAT-
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
* * *
52796876 AAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTG
1 AAAGG-GGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
* *
52796920 AAAGGGGTTGCTATGTGCTGATTCC-TCGTATCA
1 AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCA
52796953 CTGAATTTAT
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
41 5 0.05
42 37 0.37
43 54 0.53
44 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCATTAATTATG
Found at i:52796886 original size:42 final size:42
Alignment explanation
Indices: 52796787--52796990 Score: 182
Period size: 43 Copynumber: 4.8 Consensus size: 42
52796777 GAATATATTG
* * ** *
52796787 AATAAAAAGGGGTTGCTAAGTGCTGATCCCACCGTATCTTTG
1 AATATAAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTA
*
52796829 ATTATGAAAGGGGTTGCTAAGTGCTGATTCC-CCGTATCACTA
1 AATAT-AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTA
*
52796871 AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATC-CTTA
1 AATATAAAGG-GGTTGCTAAGTGCTGATTCCACCGTATCAC-TA
* * * * *
52796914 ATTGTGAAAGGGGTTGCTATGTGCTGATTCC-TCGTATCACTG
1 AATAT-AAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTA
* * * *
52796956 AAT-TTATGGTGGTTGCTAAAGTGTTGAATCCACCG
1 AATATAAAGG-GGTTGCT-AAGTGCTGATTCCACCG
52796991 AGTAACGGAT
Statistics
Matches: 132, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
40 3 0.02
41 13 0.10
42 54 0.41
43 57 0.43
44 5 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
AATATAAAGGGGTTGCTAAGTGCTGATTCCACCGTATCACTA
Found at i:52796940 original size:85 final size:85
Alignment explanation
Indices: 52796787--52796991 Score: 270
Period size: 85 Copynumber: 2.4 Consensus size: 85
52796777 GAATATATTG
* * * * *
52796787 AATAAAAAGG-GGTTGCTAAGTGCTGATCCCACCGTATCTTTGATTATGAAAGGGGTTGCTAAGT
1 AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTATGAAAGGGGTTGCTAAGT
52796851 GCTGATTCCCCGTATCACTA
66 GCTGATTCCCCGTATCACTA
* *
52796871 AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGGGTTGCTATGT
1 AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTATGAAAGGGGTTGCTAAGT
* *
52796936 GCTGATTCCTCGTATCACTG
66 GCTGATTCCCCGTATCACTA
* * * *
52796956 AAT-TTATGGTGGTTGCTAAAGTGTTGAATCCACCGA
1 AATATAAAGGTGGTTGCT-AAGTGCTGATTCCACCGA
52796992 GTAACGGATA
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
84 21 0.20
85 85 0.80
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (85 bp):
AATATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTATGAAAGGGGTTGCTAAGT
GCTGATTCCCCGTATCACTA
Found at i:52799413 original size:23 final size:22
Alignment explanation
Indices: 52799370--52799413 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
52799360 TTTGTTTTTA
*
52799370 ACTTTAACTTTTATTTAAAAAT
1 ACTTTAACTTTTATATAAAAAT
* *
52799392 ACTTTAATTTGTTATATCAAAA
1 ACTTTAACTT-TTATATAAAAA
52799414 CATATTATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (22 bp):
ACTTTAACTTTTATATAAAAAT
Found at i:52811377 original size:33 final size:33
Alignment explanation
Indices: 52811335--52811405 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
52811325 ATGACATTCG
* *
52811335 CAGATATAGTCTGCTGAGAAAGTAAACACAGAA
1 CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
* * * *
52811368 TAGAGATAGTCCGTTGGGACAGTAAACACAGAA
1 CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
52811401 CAGAG
1 CAGAG
52811406 TAAGTTCGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (33 bp):
CAGAGATAGTCCGCTGAGAAAGTAAACACAGAA
Found at i:52811425 original size:33 final size:33
Alignment explanation
Indices: 52811355--52811428 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
52811345 CTGCTGAGAA
* *
52811355 AGTAAACACAGAATAGAGATAGTCCGTTGGGAC
1 AGTAAACACAGAACAGAGATAGTCCGTCGGGAC
* *
52811388 AGTAAACACAGAACAGAG-TAAGTTCGTCGGGAG
1 AGTAAACACAGAACAGAGAT-AGTCCGTCGGGAC
52811421 AGTAAACA
1 AGTAAACA
52811429 TGAGGTGAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16
Consensus pattern (33 bp):
AGTAAACACAGAACAGAGATAGTCCGTCGGGAC
Found at i:52813026 original size:29 final size:29
Alignment explanation
Indices: 52812966--52813054 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 29
52812956 CATAACAAAA
* * * *
52812966 CAACCACAAGGGCTTCCGCATATAACATATT
1 CAACCACAAAGGC-T-CACATATAATAGATT
52812997 CAACCACAAAGGCTCACATATAATAGATT
1 CAACCACAAAGGCTCACATATAATAGATT
** * * *
52813026 CTGCCACTATGGCTCACATATAATTGATT
1 CAACCACAAAGGCTCACATATAATAGATT
52813055 TCGCCACTAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 36 0.73
30 1 0.02
31 12 0.24
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (29 bp):
CAACCACAAAGGCTCACATATAATAGATT
Found at i:52813060 original size:29 final size:29
Alignment explanation
Indices: 52813007--52813077 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
52812997 CAACCACAAA
*
52813007 GGCTCACATATAATAGATTCTGCCACTAT
1 GGCTCACATATAATAGATTCTGCCACTAG
*
52813036 GGCTCACATATAATTGATT-TCGCCACTAG
1 GGCTCACATATAATAGATTCT-GCCACTAG
52813065 GGC-CTACATATAA
1 GGCTC-ACATATAA
52813078 CTCAATGTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (29 bp):
GGCTCACATATAATAGATTCTGCCACTAG
Found at i:52821130 original size:50 final size:50
Alignment explanation
Indices: 52821045--52821159 Score: 117
Period size: 50 Copynumber: 2.3 Consensus size: 50
52821035 ATTCATGTAT
* * * * * *
52821045 GCTCATACGAGCTATGAATCAGTATGCTCTCACGAGTTATGAATCAGG-AA
1 GCTCATACGAGCTGTAAATCAGGAAGCTCTCACGAGATATAAAT-AGGAAA
* *
52821095 GCTCATACGAGCTGTAAATCGGGAAGCTCAT-ACGAGATATAAATTGGAAA
1 GCTCATACGAGCTGTAAATCAGGAAGCTC-TCACGAGATATAAATAGGAAA
*
52821145 GCTCATACAAGCTGT
1 GCTCATACGAGCTGT
52821160 GGTGTGTCTG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.04
50 51 0.94
51 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (50 bp):
GCTCATACGAGCTGTAAATCAGGAAGCTCTCACGAGATATAAATAGGAAA
Found at i:52821137 original size:25 final size:25
Alignment explanation
Indices: 52821045--52821157 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
52821035 ATTCATGTAT
* * *
52821045 GCTCATACGAGCTATGAATCAGTAT
1 GCTCATACGAGCTATAAATCAGGAA
* *
52821070 GCTC-TCACGAGTTATGAATCAGGAA
1 GCTCAT-ACGAGCTATAAATCAGGAA
* *
52821095 GCTCATACGAGCTGTAAATCGGGAA
1 GCTCATACGAGCTATAAATCAGGAA
* *
52821120 GCTCATACGAGATATAAAT-TGGAAA
1 GCTCATACGAGCTATAAATCAGG-AA
*
52821145 GCTCATACAAGCT
1 GCTCATACGAGCT
52821158 GTGGTGTGTC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
24 3 0.04
25 69 0.95
26 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTATAAATCAGGAA
Found at i:52826461 original size:12 final size:12
Alignment explanation
Indices: 52826446--52826471 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52826436 TAGTTATATA
52826446 TATTTCTATAAT
1 TATTTCTATAAT
52826458 TATTTCTATAAT
1 TATTTCTATAAT
52826470 TA
1 TA
52826472 ATATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTCTATAAT
Found at i:52827466 original size:29 final size:29
Alignment explanation
Indices: 52827394--52827479 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
52827384 TTAAAACTAA
* *
52827394 ATTTTATTAGTTTTTAAT-AATTTTAAATT
1 ATTTTA-TATTTTTTTATAAATTTTAAATT
* *
52827423 CTTTTATATTCTTTTATAAATTTTAAATT
1 ATTTTATATTTTTTTATAAATTTTAAATT
* *
52827452 ATTTTCT-TTATTTTTATAATTATTTAAA
1 ATTTTATATT-TTTTTATAAAT-TTTAAA
52827480 AAATTATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.22
29 30 0.65
30 6 0.13
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTTATATTTTTTTATAAATTTTAAATT
Found at i:52830493 original size:3 final size:3
Alignment explanation
Indices: 52830485--52830514 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
52830475 TGTTTTCATA
52830485 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52830515 CTACCGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:52845762 original size:25 final size:26
Alignment explanation
Indices: 52845734--52845853 Score: 105
Period size: 24 Copynumber: 4.9 Consensus size: 26
52845724 TGAGTGTCTT
52845734 GATATATGGCTCTCCA-GAGCTTTTC
1 GATATATGGCTCTCCATGAGCTTTTC
* *
52845759 GATATATGGCT-TGCATGAGC-TTCC
1 GATATATGGCTCTCCATGAGCTTTTC
52845783 AGAT-TAATGGCTCTCCA-GAGCTTTTC
1 -GATAT-ATGGCTCTCCATGAGCTTTTC
* * *
52845809 GATAT-TTGCTC-ACATGAGCTTCTC
1 GATATATGGCTCTCCATGAGCTTTTC
*
52845833 GAT-TATGGCTCT-TATGAGCTT
1 GATATATGGCTCTCCATGAGCTT
52845854 CCCGTATATG
Statistics
Matches: 77, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
23 3 0.04
24 36 0.47
25 31 0.40
26 7 0.09
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (26 bp):
GATATATGGCTCTCCATGAGCTTTTC
Found at i:52845798 original size:50 final size:48
Alignment explanation
Indices: 52845738--52845844 Score: 153
Period size: 50 Copynumber: 2.2 Consensus size: 48
52845728 TGTCTTGATA
**
52845738 TATGGCTCTCCAGAGCTTTTCGATATATGGCTTGCATGAGCTTC-CAGAT
1 TATGGCTCTCCAGAGCTTTTCGATAT-TGGCTCACATGAGCTTCTC-GAT
*
52845787 TAATGGCTCTCCAGAGCTTTTCGATATTTGCTCACATGAGCTTCTCGAT
1 T-ATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCTTCTCGAT
52845836 TATGGCTCT
1 TATGGCTCT
52845845 TATGAGCTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
48 8 0.15
49 19 0.36
50 26 0.49
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (48 bp):
TATGGCTCTCCAGAGCTTTTCGATATTGGCTCACATGAGCTTCTCGAT
Found at i:52845863 original size:24 final size:25
Alignment explanation
Indices: 52845822--52845868 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
52845812 ATTTGCTCAC
*
52845822 ATGAGCTTCTCGATTATG-GCTCTT
1 ATGAGCTTCCCGATTATGTGCTCTT
52845846 ATGAGCTTCCCG-TATATGTGCTC
1 ATGAGCTTCCCGAT-TATGTGCTC
52845869 GAACAAGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 15 0.75
25 4 0.20
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGATTATGTGCTCTT
Found at i:52845868 original size:49 final size:49
Alignment explanation
Indices: 52845739--52845868 Score: 122
Period size: 50 Copynumber: 2.6 Consensus size: 49
52845729 GTCTTGATAT
** * **
52845739 ATGGCTCTCCAGAGCTTTTCGATATATGGCTTGCATGAGCTTCCAGATTA
1 ATGGCTCTCCAGAGCTTCCCGATATGT-GCTCACATGAGCTTCCAGATTA
** *
52845789 ATGGCTCTCCAGAGCTTTTCGATATTTGCTCACATGAGCTTCTC-GATT-
1 ATGGCTCTCCAGAGCTTCCCGATATGTGCTCACATGAGCTTC-CAGATTA
*
52845837 ATGGCTCT-TATGAGCTTCCCGTATATGTGCTC
1 ATGGCTCTCCA-GAGCTTCCCG-ATATGTGCTC
52845869 GAACAAGCAT
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.01
48 16 0.23
49 26 0.37
50 27 0.39
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (49 bp):
ATGGCTCTCCAGAGCTTCCCGATATGTGCTCACATGAGCTTCCAGATTA
Found at i:52849852 original size:50 final size:51
Alignment explanation
Indices: 52849777--52849912 Score: 177
Period size: 50 Copynumber: 2.7 Consensus size: 51
52849767 GTGAAGTTGC
*
52849777 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-ATG-A
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATA-GCA
* * * * *
52849827 TAGGTCGCATGTGTAGTACTGTGTGCAGGCTACTATGCGTACCGGATAGCT
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGCA
* *
52849878 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTA
1 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
52849913 TGTGAATCGA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
50 42 0.58
51 31 0.42
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (51 bp):
TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGCA
Found at i:52852689 original size:9 final size:9
Alignment explanation
Indices: 52852677--52852776 Score: 59
Period size: 8 Copynumber: 11.2 Consensus size: 9
52852667 TTATCTCATT
52852677 TTTTTATAA
1 TTTTTATAA
*
52852686 -TTTTAAAA
1 TTTTTATAA
52852694 TTTGTTATAA
1 TTT-TTATAA
**
52852704 CATTTAT-A
1 TTTTTATAA
*
52852712 TTTTTATGA
1 TTTTTATAA
52852721 TTTTTA-AA
1 TTTTTATAA
52852729 TTTTT-TAA
1 TTTTTATAA
52852737 TTAGTTTTATAA
1 -T--TTTTATAA
*
52852749 -TTTTA-GA
1 TTTTTATAA
*
52852756 TTTTTTTGAA
1 TTTTTAT-AA
52852766 TTTTTATAA
1 TTTTTATAA
52852775 TT
1 TT
52852777 ATAAATTTCC
Statistics
Matches: 69, Mismatches: 11, Indels: 22
0.68 0.11 0.22
Matches are distributed among these distances:
7 1 0.01
8 30 0.43
9 18 0.26
10 13 0.19
11 4 0.06
12 3 0.04
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52852761 original size:36 final size:38
Alignment explanation
Indices: 52852706--52852777 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
52852696 TGTTATAACA
*
52852706 TTTATATTTTTATGA-TTTTTAAATTTTT-TAATTAGT
1 TTTATAATTTTATGATTTTTTAAATTTTTATAATTAGT
*
52852742 TTTATAATTTTA-GATTTTTTTGAATTTTTATAATTA
1 TTTATAATTTTATGA-TTTTTTAAATTTTTATAATTA
52852778 TAAATTTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 2 0.06
36 11 0.35
37 12 0.39
38 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (38 bp):
TTTATAATTTTATGATTTTTTAAATTTTTATAATTAGT
Found at i:52853919 original size:9 final size:9
Alignment explanation
Indices: 52853902--52853938 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52853892 TGAGTTTTCG
52853902 AATTCGAAT
1 AATTCGAAT
*
52853911 AACTCGAAT
1 AATTCGAAT
52853920 AATTCGAAT
1 AATTCGAAT
52853929 AATTCGAAT
1 AATTCGAAT
52853938 A
1 A
52853939 TCAAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52854194 original size:30 final size:31
Alignment explanation
Indices: 52854158--52854217 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
52854148 AAACCTTTTA
*
52854158 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
*
52854188 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
52854218 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.42, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:52861021 original size:22 final size:22
Alignment explanation
Indices: 52860991--52861047 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
52860981 TTAATTTTCA
*
52860991 TATACATATATATATACCTTAT
1 TATAAATATATATATACCTTAT
* * *
52861013 TATAAATATCTTTATATCTTAT
1 TATAAATATATATATACCTTAT
**
52861035 TATGTATATATAT
1 TATAAATATATAT
52861048 CTATATCTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TATAAATATATATATACCTTAT
Found at i:52861042 original size:26 final size:25
Alignment explanation
Indices: 52861009--52861058 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
52860999 TATATATACC
*
52861009 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
52861034 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
52861059 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:52866229 original size:17 final size:18
Alignment explanation
Indices: 52866207--52866240 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
52866197 TCAAAAATAA
52866207 GAGAAAAA-AAAAGAAAG
1 GAGAAAAAGAAAAGAAAG
52866224 GAGAAAAAGAAAAGAAA
1 GAGAAAAAGAAAAGAAA
52866241 AAGGAGAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
GAGAAAAAGAAAAGAAAG
Found at i:52867050 original size:15 final size:15
Alignment explanation
Indices: 52867030--52867063 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
52867020 ACTTTGGATC
52867030 AAAAAAATG-AAAAT
1 AAAAAAATGAAAAAT
52867044 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
52867059 AAAAA
1 AAAAA
52867064 TAGAGAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:52868647 original size:132 final size:132
Alignment explanation
Indices: 52868478--52869702 Score: 2011
Period size: 132 Copynumber: 9.3 Consensus size: 132
52868468 AAGACACAAA
* *
52868478 CCTATCACCCTAAACAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTTACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* *
52868543 GGAGCAGATTGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCATATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52868608 GT
131 GT
* * *
52868610 CCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCATATTCTGTCACCCTAAGTAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* * * * * *
52868675 AGAGCAGATCAAAAATGGTGAATCTTATCTTCCCAATACAGTGGACAAGTAGATTTAAGACATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52868740 GT
131 GT
* *
52868742 CCTATCACCCTAAGCAGTAGTAGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCGGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
*
52868807 GGAGCAGATCGAAGATGGTGAATCTTATCTTTCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52868872 GT
131 GT
*
52868874 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTATGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
*
52868939 GGAGCAGATCGAAAATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52869004 GT
131 GT
* * *
52869006 CCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTATGTAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
*
52869071 GGAGCAGATCGAAGATTGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52869136 GT
131 GT
* * * * *
52869138 CCTATCACCCTAAGCAGTAGTGGATTAGGTTGAAGATTGCATATTCTATCACCCTATGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* *
52869203 GGAGCAGATCGAAGATGGTAAATCTTATCTTCCCAATATAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52869268 GT
131 GT
* *
52869270 CCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAAATTCTGTCACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
*
52869335 GGAGCAGATCGAAGATGGTGAATCATATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52869400 GT
131 GT
* *
52869402 CCTATCACCCTAAGCAATAGTGGAGTAGGTCGAAGATTGCAGATTTTGTCACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
*
52869467 GGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
52869532 GT
131 GT
* * *
52869534 CCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTCTGT-ATCCCTAAGCAGTAG
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAG
* * * * *
52869598 TAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCATATGTAAGCCATT
65 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
*
52869663 AGC
130 AGT
* * *
52869666 CCTATCACCTTAAGCAGTAGTGGAGCAGATCGAAGAT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
52869703 GGTGAATCTT
Statistics
Matches: 1023, Mismatches: 69, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
131 1 0.00
132 1022 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (132 bp):
CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GT
Found at i:52869544 original size:220 final size:219
Alignment explanation
Indices: 52869450--52869909 Score: 573
Period size: 220 Copynumber: 2.1 Consensus size: 219
52869440 GCAGATTTTG
52869450 TCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* * * *
52869515 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATGGTAGAATC
* * * * ** * * *
52869580 TGTATCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGGAG
131 TATATCCCCAAACAGTAGGAGAGCAGATCAAAGACCATGAATCCTATCTACCCAAAACAGTGGAG
*
52869645 AAGCATATGTAAGCCATTAGCCCTA
196 AAGCATACGTAAG-CATTAGCCCTA
* *
52869670 TCACCTTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* * *
52869735 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATGGTAGAATC
* * * * *** * * *
52869800 TGTCA-CCCTAAGCAGTAGTG-GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGG
131 TAT-ATCCCCAAACAGTAG-GAGAGCAGATCAAAGACCATGAATCCTATCTACCCAAAACAGTGG
* ** *
52869863 AGAAGCAGATTTAAGCCATTAGTCCTA
194 AGAAGCATACGTAAG-CATTAGCCCTA
52869890 TCACCCTAAGCAGTAGTGGA
1 TCACCCTAAGCAGTAGTGGA
52869910 ATAGGTCAAA
Statistics
Matches: 226, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
220 225 1.00
221 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (219 bp):
TCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATGGTAGAATC
TATATCCCCAAACAGTAGGAGAGCAGATCAAAGACCATGAATCCTATCTACCCAAAACAGTGGAG
AAGCATACGTAAGCATTAGCCCTA
Found at i:52869709 original size:352 final size:352
Alignment explanation
Indices: 52869318--52869986 Score: 1266
Period size: 352 Copynumber: 1.9 Consensus size: 352
52869308 GCAAATTCTG
52869318 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCATATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCATATCTTCCCAATACAGTGGAGAA
*
52869383 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAATAGTGGAGTAGGTCGAAGATTGCAGATTT
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAATAGTGGAGTAGGTCGAAGATTGCAGATTC
52869448 TGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAG
131 TGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAG
52869513 AAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGAT
196 AAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGAT
52869578 TCTGTATCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGG
261 TCTGTATCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGG
52869643 AGAAGCATATGTAAGCCATTAGCCCTA
326 AGAAGCATATGTAAGCCATTAGCCCTA
* *
52869670 TCACCTTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCATATCTTCCCAATACAGTGGAGAA
*
52869735 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAATAGTGGAGTAGGTCGAAGATTGCAGATTC
*
52869800 TGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAG
131 TGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAG
* *
52869865 AAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAATATTTTAGAT
196 AAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGAT
*
52869930 TCTGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA
261 TCTGTATCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA
52869987 GATAGTAGGG
Statistics
Matches: 309, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
352 309 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (352 bp):
TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCATATCTTCCCAATACAGTGGAGAA
GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAATAGTGGAGTAGGTCGAAGATTGCAGATTC
TGTCACCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTGGAG
AAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGAT
TCTGTATCCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGG
AGAAGCATATGTAAGCCATTAGCCCTA
Found at i:52869787 original size:88 final size:88
Alignment explanation
Indices: 52869585--52869790 Score: 331
Period size: 88 Copynumber: 2.3 Consensus size: 88
52869575 GATTCTGTAT
* * *
52869585 CCCTAAGCAGTAGTAGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCA
*
52869650 TATGTAAGCCATTAGCCCTATCA
66 GATGTAAGCCATTAGCCCTATCA
*
52869673 CCTTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCA
* *
52869738 GATTTAAGCCATTAGTCCTATCA
66 GATGTAAGCCATTAGCCCTATCA
* *
52869761 CCCTAAGCAGTAGTGGAGTAGGTCGAAGAT
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGAT
52869791 TGCAGATTCT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 108 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (88 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCA
GATGTAAGCCATTAGCCCTATCA
Found at i:52870008 original size:132 final size:132
Alignment explanation
Indices: 52869670--52869986 Score: 546
Period size: 132 Copynumber: 2.4 Consensus size: 132
52869660 ATTAGCCCTA
*
52869670 TCACCTTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* *
52869735 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTC
52869800 TG
131 TG
52869802 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
* **
52869867 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAATATTTTAGATTC
66 GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTC
52869932 TG
131 TG
* *
52869934 T-ATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA
1 TCA-CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
52869987 GATAGTAGGG
Statistics
Matches: 176, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
131 1 0.01
132 175 0.99
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (132 bp):
TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
GCAGATTTAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTC
TG
Found at i:52870718 original size:21 final size:20
Alignment explanation
Indices: 52870692--52870730 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52870682 ATGAACTCTA
*
52870692 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
52870713 TTTTCCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
52870731 TCTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:52870926 original size:14 final size:14
Alignment explanation
Indices: 52870907--52870934 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52870897 ACCCAGGGCT
52870907 GGAGTTCAGAAAGG
1 GGAGTTCAGAAAGG
52870921 GGAGTTCAGAAAGG
1 GGAGTTCAGAAAGG
52870935 CTAAAAATAG
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:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (14 bp):
GGAGTTCAGAAAGG
Found at i:52871661 original size:22 final size:22
Alignment explanation
Indices: 52871631--52871687 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
52871621 TTTATTTTCA
*
52871631 TATACATATATATATACCTTAT
1 TATAAATATATATATACCTTAT
* * *
52871653 TATAAATATCTTTATATCTTAT
1 TATAAATATATATATACCTTAT
**
52871675 TATGTATATATAT
1 TATAAATATATAT
52871688 CTATATCTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TATAAATATATATATACCTTAT
Found at i:52871682 original size:26 final size:25
Alignment explanation
Indices: 52871649--52871698 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
52871639 TATATATACC
*
52871649 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
52871674 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
52871699 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:52879590 original size:20 final size:20
Alignment explanation
Indices: 52879553--52879590 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52879543 ATGCCAAAAG
*
52879553 AAGCCACAAGGAAAAACAAA
1 AAGCCACAAGAAAAAACAAA
52879573 AAGCCACAA-AAAAGAACA
1 AAGCCACAAGAAAA-AACA
52879591 CACACAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.66, C:0.21, G:0.13, T:0.00
Consensus pattern (20 bp):
AAGCCACAAGAAAAAACAAA
Found at i:52881144 original size:21 final size:20
Alignment explanation
Indices: 52881113--52881169 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
52881103 TTCTCAATCC
52881113 AATATACATTTCAATATCACAAT
1 AATAT-CATTTCAAT-TCA-AAT
52881136 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATTCAAAT
*
52881154 CATATCATTTGCAATT
1 AATATCATTT-CAATT
52881170 TCCATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 3 0.10
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATCATTTCAATTCAAAT
Found at i:52882632 original size:23 final size:22
Alignment explanation
Indices: 52882589--52882632 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52882579 TTCTAAGTCG
52882589 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52882612 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52882633 TTACGGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52882674 original size:16 final size:16
Alignment explanation
Indices: 52882653--52882706 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
52882643 TTTAGTTCGC
52882653 TGTAATGGAATACAGG
1 TGTAATGGAATACAGG
* *
52882669 TGTAATGGAATAGAGC
1 TGTAATGGAATACAGG
*
52882685 TGTAATGGAATATAGG
1 TGTAATGGAATACAGG
*
52882701 CGTAAT
1 TGTAAT
52882707 AGTAATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATACAGG
Found at i:52883044 original size:119 final size:119
Alignment explanation
Indices: 52882895--52883570 Score: 1187
Period size: 119 Copynumber: 5.7 Consensus size: 119
52882885 TTATTATTAA
* * * *
52882895 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTCTATGAATTTACTGAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
52882960 AATACTATAAAA-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
65 AATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
52883014 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
52883079 AATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
65 AATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
52883134 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
* *
52883199 ATACTCTAAAATATAATTTAAAATAATTATTATTATATATAATTTAAT-AAAAT
66 ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
52883252 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
* *
52883317 ATACTCTAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
66 ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
52883371 ATATAATTTAATAAAATTCTTAATATATTTATTCTTATATGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
* *
52883436 ATACTATAAAATATAATTTAAAATAATAATTATTAAATGTAATTTAATAAAAAT
66 ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
52883490 ATATAATTTAATAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
52883555 ATACTATAAAA-ATAAT
66 ATACTATAAAATATAAT
52883571 ATATAATCTA
Statistics
Matches: 540, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
118 120 0.22
119 353 0.65
120 67 0.12
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (119 bp):
ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
Found at i:52883186 original size:55 final size:55
Alignment explanation
Indices: 52883120--52883542 Score: 268
Period size: 63 Copynumber: 7.2 Consensus size: 55
52883110 TATTAAATAT
52883120 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
1 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
* * * *
52883175 AATTTACTAAAATCATAATATATAATACTCTAA-AATATAAT-TTAAAATAATTATTATTATATA
1 AATTTA--ATAA--A-AATATATAAT--T-TAATAA-A-ATTCTTAATATAATTATTCTTAT-T-
52883238 T-
54 TG
*
52883239 AATTTAAT-AAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATG
1 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
* * * * * *
52883293 AATTTACTAAAATCATAATATATAATACTCTAA-AATATAAT-TTAAAATAATAATTATTAAATA
1 AATTTA--ATAA--A-AATATATAAT--T-TAATAA-A-ATTCTTAATATAATTATTCTT--ATT
52883356 T-
54 TG
* *
52883357 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATATTTATTCTTATATG
1 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
* * * * * * **
52883412 AATTTACT-AAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATTATTAAATG
1 AATTTAATAAAAAT-AT-ATA-AT-TTA--ATAAAAT-T--CTTAATATAATTATTCTTATTTG
* *
52883475 TAATTTAATAAAAATATATAATTTAATAAAATTATTAATATAATTATTCTTATATG
1 -AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
*
52883531 AATTTACTAAAA
1 AATTTAATAAAA
52883543 TCATAATATA
Statistics
Matches: 290, Mismatches: 36, Indels: 84
0.71 0.09 0.20
Matches are distributed among these distances:
53 1 0.00
54 17 0.06
55 49 0.17
56 42 0.14
57 9 0.03
58 13 0.04
59 20 0.07
60 28 0.10
61 4 0.01
62 12 0.04
63 59 0.20
64 26 0.09
65 10 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (55 bp):
AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTG
Found at i:52883193 original size:53 final size:53
Alignment explanation
Indices: 52883136--52883311 Score: 174
Period size: 55 Copynumber: 3.1 Consensus size: 53
52883126 ATAAAAATAT
52883136 ATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATC
1 ATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATC
* * * *
52883189 ATAATATATAATACTCTAAAATATAATTTAAAATAATTATTATTATATAT-AATTTAATAAAATA
1 ATAAT-T-T-A-A---TAAAAT-T--CTTAATATAATTATTCTTAT-T-TGAATTTACTAAAAT-
*
52883253 T
53 C
*
52883254 ATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATC
1 ATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATC
52883307 ATAAT
1 ATAAT
52883312 ATATAATACT
Statistics
Matches: 98, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
53 11 0.11
54 13 0.13
55 18 0.18
56 1 0.01
57 2 0.02
58 6 0.06
60 6 0.06
61 2 0.02
62 1 0.01
63 18 0.18
64 14 0.14
65 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (53 bp):
ATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATC
Found at i:52883223 original size:22 final size:23
Alignment explanation
Indices: 52883181--52883223 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52883171 TTTGAATTTA
*
52883181 CTAAAATCATAATATATAATACT
1 CTAAAATCATAATATAAAATACT
*
52883204 CTAAAAT-ATAATTTAAAATA
1 CTAAAATCATAATATAAAATA
52883224 ATTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (23 bp):
CTAAAATCATAATATAAAATACT
Found at i:52883275 original size:17 final size:17
Alignment explanation
Indices: 52883233--52883268 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52883223 AATTATTATT
52883233 ATATATAATTTAATAAA
1 ATATATAATTTAATAAA
52883250 ATATATAATTTAATAAA
1 ATATATAATTTAATAAA
52883267 AT
1 AT
52883269 TCTTAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATAATTTAATAAA
Found at i:52883312 original size:36 final size:35
Alignment explanation
Indices: 52883251--52883433 Score: 114
Period size: 36 Copynumber: 4.8 Consensus size: 35
52883241 TTTAATAAAA
*
52883251 TATATAATTTAATAAAATTCTTAATATAATTATTCT
1 TATATAATTTAATAAAA-TCATAATATAATTATTCT
* * *
52883287 TATATGAATTTACTAAAATCATAATATATAATACTCT
1 TATAT-AATTTAATAAAATCATAATATA-ATTATTCT
* * ***
52883324 AAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAA
1 --TATATAATTT--AATAA-AATCA-T-AATATAA-TT-AT--TCT
* *
52883370 TATATAATTTAATAAAATTCTTAATATATTTATTCT
1 TATATAATTTAATAAAA-TCATAATATAATTATTCT
*
52883406 TATATGAATTTACTAAAATCATAATATA
1 TATAT-AATTTAATAAAATCATAATATA
52883434 TAATACTATA
Statistics
Matches: 111, Mismatches: 21, Indels: 30
0.69 0.13 0.19
Matches are distributed among these distances:
36 28 0.25
37 28 0.25
38 7 0.06
39 6 0.05
40 10 0.09
41 7 0.06
42 8 0.07
43 7 0.06
44 10 0.09
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (35 bp):
TATATAATTTAATAAAATCATAATATAATTATTCT
Found at i:52883341 original size:22 final size:23
Alignment explanation
Indices: 52883299--52883341 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
52883289 TATGAATTTA
*
52883299 CTAAAATCATAATATATAATACT
1 CTAAAATCATAATATAAAATACT
*
52883322 CTAAAAT-ATAATTTAAAATA
1 CTAAAATCATAATATAAAATA
52883342 ATAATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (23 bp):
CTAAAATCATAATATAAAATACT
Found at i:52883342 original size:237 final size:238
Alignment explanation
Indices: 52882895--52883570 Score: 1187
Period size: 237 Copynumber: 2.8 Consensus size: 238
52882885 TTATTATTAA
* * * *
52882895 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTCTATGAATTTACTGAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
52882960 AATACTATAAAA-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
65 AATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA
*
52883024 ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAA
130 ATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAA
*
52883089 AATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
194 AATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
*
52883134 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATTTGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
* *
52883199 ATACTCTAAAATATAATTTAAAATAATTATTATTATATATAATTTAAT-AAAATATATAATTTAA
66 ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
*
52883263 TAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTCTAAAA
131 TAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
52883328 TATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
196 TATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
*
52883371 ATATAATTTAATAAAATTCTTAATATATTTATTCTTATATGAATTTACTAAAATCATAATATATA
1 ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
* *
52883436 ATACTATAAAATATAATTTAAAATAATAATTATTAAATGTAATTTAATAAAAATATATAATTTAA
66 ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
*
52883501 TAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
131 TAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
52883566 -ATAAT
196 TATAAT
52883571 ATATAATCTA
Statistics
Matches: 417, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
237 203 0.49
238 155 0.37
239 59 0.14
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (238 bp):
ATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATA
ATACTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
TAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
TATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAAT
Found at i:52883347 original size:13 final size:12
Alignment explanation
Indices: 52883323--52883363 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
52883313 TATAATACTC
52883323 TAAAATATAATT
1 TAAAATATAATT
52883335 TAAAATAATAATT
1 TAAAAT-ATAATT
*
52883348 ATTAAATATAATT
1 -TAAAATATAATT
52883361 TAA
1 TAA
52883364 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:52883430 original size:53 final size:53
Alignment explanation
Indices: 52883373--52883549 Score: 165
Period size: 56 Copynumber: 3.1 Consensus size: 53
52883363 ATAAAAATAT
* *
52883373 ATAATTTAATAAAATTCTTAATATATTTATTCTTATATGAATTTACTAAAATC
1 ATAATTTAATAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATC
* * * * *
52883426 ATAATATATAATACTATAAAATATAATTTAAAATAATAATTATTAAATGTAATTTAATAAAAATA
1 AT-A-AT-T--TA--ATAAAAT-T-A-TTAATATAATTATTCTTATATG-AATTTACT-AAAAT-
*
52883491 T
53 C
52883492 ATAATTTAATAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATC
1 ATAATTTAATAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATC
52883545 ATAAT
1 ATAAT
52883550 ATATAATACT
Statistics
Matches: 97, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
53 7 0.07
54 6 0.06
55 9 0.09
56 19 0.20
57 1 0.01
58 3 0.03
59 7 0.07
60 7 0.07
61 3 0.03
63 18 0.19
64 9 0.09
65 6 0.06
66 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (53 bp):
ATAATTTAATAAAATTATTAATATAATTATTCTTATATGAATTTACTAAAATC
Found at i:52883513 original size:17 final size:18
Alignment explanation
Indices: 52883475--52883518 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
52883465 TTATTAAATG
52883475 TAATTTAATAAAAATATA
1 TAATTTAATAAAAATATA
*
52883493 TAATTTAATAAAATTAT-
1 TAATTTAATAAAAATATA
*
52883510 TAATATAAT
1 TAATTTAAT
52883519 TATTCTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATTTAATAAAAATATA
Found at i:52883549 original size:356 final size:356
Alignment explanation
Indices: 52882895--52883570 Score: 1203
Period size: 356 Copynumber: 1.9 Consensus size: 356
52882885 TTATTATTAA
* *
52882895 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTCTATGAATTTACTGAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
52882960 AATACTATAAAAATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAA
66 AATACTATAAAAATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAA
52883025 TAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
131 TAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
* *
52883090 ATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTT
196 ATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATT
* *
52883155 AATATAATTATTCTTATTTGAATTTACTAAAATCATAATATATAATACTCTAAAATATAATTTAA
261 AATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAATTTAA
52883220 AATAATTATTATTATATATAATTTAATAAAAT
325 AATAATTATTATTATATATAATTTAATAAAAT
* *
52883252 ATATAATTTAATAAAATTCTTAATA-TAATTATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
52883316 AATACTCTAAAATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTA
66 AATACTATAAAA-ATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTA
**
52883381 ATAAAATTCTTAATA-TATTTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAA
130 ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAA
*
52883445 AATATAATTTAAAATAATAATTATTAAATGTAATTTAATAAAAATATATAATTTAATAAAATTAT
195 AATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTAT
52883510 TAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
260 TAATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAAT
52883571 ATATAATCTA
Statistics
Matches: 305, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
355 5 0.02
356 210 0.69
357 90 0.30
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (356 bp):
ATATAATTTAATAAAAATCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATACTATAAAAATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAA
TAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAA
ATATAATTTAAAATAATAATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATT
AATATAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAATTTAAA
ATAATTATTATTATATATAATTTAATAAAAT
Found at i:52883702 original size:19 final size:19
Alignment explanation
Indices: 52883640--52883709 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
52883630 TAGTGAAACA
52883640 AATAATTTAATTATTCTAC
1 AATAATTTAATTATTCTAC
** *
52883659 AATAA-AAAAATA-T-TAGC
1 AATAATTTAATTATTCTA-C
*
52883676 AGTAATTTAATTATTCTAC
1 AATAATTTAATTATTCTAC
52883695 AATAATTTAA-TATTC
1 AATAATTTAATTATTC
52883710 ATATATTAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 13 0.33
19 16 0.41
20 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (19 bp):
AATAATTTAATTATTCTAC
Found at i:52885025 original size:49 final size:50
Alignment explanation
Indices: 52884950--52885054 Score: 158
Period size: 49 Copynumber: 2.1 Consensus size: 50
52884940 GAAAAAAAAC
* * * * *
52884950 AAATTAAAATTAAGTTTAGTATCATGAATCAAAATG-TGAACACTTTATA
1 AAATTAAAATTAAGTTCAATAACATGAATCAAAAAGCTCAACACTTTATA
52884999 AAATTAAAATTAAGTTCAATAACATGAATCAAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATAACATGAATCAAAAAGCTCAACACTTTATA
52885049 AAATTA
1 AAATTA
52885055 TAACACATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 32 0.64
50 18 0.36
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (50 bp):
AAATTAAAATTAAGTTCAATAACATGAATCAAAAAGCTCAACACTTTATA
Found at i:52887419 original size:16 final size:16
Alignment explanation
Indices: 52887400--52887436 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
52887390 AATAAATTGG
52887400 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
52887416 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
52887432 AATAT
1 AATAT
52887437 ATAATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:52888599 original size:21 final size:21
Alignment explanation
Indices: 52888575--52888615 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
52888565 CATAAATAGA
52888575 AAACATCAACTTAATACAGAC
1 AAACATCAACTTAATACAGAC
52888596 AAACATCAACTTAATACAGA
1 AAACATCAACTTAATACAGA
52888616 AACCAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.20
Consensus pattern (21 bp):
AAACATCAACTTAATACAGAC
Found at i:52889593 original size:17 final size:18
Alignment explanation
Indices: 52889571--52889611 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
52889561 AAATAGAGAA
52889571 AAGAAAAGAAACG-TGAG
1 AAGAAAAGAAACGATGAG
52889588 AAGAAAAGAAACGTATGAG
1 AAGAAAAGAAACG-ATGAG
52889607 AAGAA
1 AAGAA
52889612 GAAGCAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
19 9 0.41
ACGTcount: A:0.61, C:0.05, G:0.27, T:0.07
Consensus pattern (18 bp):
AAGAAAAGAAACGATGAG
Found at i:52890053 original size:51 final size:49
Alignment explanation
Indices: 52889995--52890178 Score: 206
Period size: 51 Copynumber: 3.7 Consensus size: 49
52889985 TCAGTTCACA
* *
52889995 TAGTAGCCTACACATAGTACTACACATGTGAGCATTACCATCCGATACACG
1 TAGTAGCCTACACATAGTACTACACACGTGA-CA-TACCATCCGGTACACG
* * * * *
52890046 TAGTAGCCTACACATAGTACTACACACGTGATCGAAACTATCTGGTACGCA
1 TAGTAGCCTACACATAGTACTACACACGTGA-C-ATACCATCCGGTACACG
* * * * *
52890097 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTACACATAGTACTACACACGTGACATACCA-TCCGGTACACG
*
52890147 TAGTAGCCTGCACATAGTACTACACACGTGAC
1 TAGTAGCCTACACATAGTACTACACACGTGAC
52890179 CATCACTTTC
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 69 0.62
52 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (49 bp):
TAGTAGCCTACACATAGTACTACACACGTGACATACCATCCGGTACACG
Found at i:52890170 original size:101 final size:102
Alignment explanation
Indices: 52889993--52890177 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
52889983 GTTCAGTTCA
* *
52889993 CATAGTAGCCTACACATAGTACTACACATGTGAGCATTACCATCCGATACACGTAGTAGCCTACA
1 CATAGTAGCCTACACATAGTACTACACATGCGAGCACTACCATCCGATACACGTAGTAGCCTACA
52890058 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
66 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* * * *
52890095 CATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGCGAGCACTACCA-TCCGATACACGTAGTAGCCTAC
52890158 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
52890178 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.54
102 31 0.41
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (102 bp):
CATAGTAGCCTACACATAGTACTACACATGCGAGCACTACCATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:52899660 original size:25 final size:25
Alignment explanation
Indices: 52899632--52899702 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
52899622 TACTAGCTGT
* *
52899632 ATATCGGGAAGCTCTTGCGAGACAA
1 ATATCGGGAAGCTCATGAGAGACAA
*
52899657 ATATCGGGAAGCTCATGAGAGCCAA
1 ATATCGGGAAGCTCATGAGAGACAA
* *
52899682 GTATCGGGAAGCTCAAGAGAG
1 ATATCGGGAAGCTCATGAGAG
52899703 TTGTGGTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.31, T:0.17
Consensus pattern (25 bp):
ATATCGGGAAGCTCATGAGAGACAA
Found at i:52905521 original size:103 final size:102
Alignment explanation
Indices: 52905344--52905711 Score: 524
Period size: 104 Copynumber: 3.6 Consensus size: 102
52905334 AACCGTTGTT
* * *
52905344 GGTGGATTCCGCACTTAGC-ACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGG
1 GGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGGG
* * *
52905408 AATCAGCACTTAGCAACCCCCTTCACATTTCAGATGC
66 AATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
** ** **
52905445 GGTGGAATCAGCACTTAGCAACCACCAAATGGGTCGGGGAATCAGCACTTAGCAACCCCTCAAGG
1 GGTGGAATCAGCACTTAGCAACCACC-AATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGG
52905510 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATAC
65 GAATCAGCACTTAGCAACCCCC-TTCACATTTAAAATAC
* * **
52905549 GGTGGAATCAGCACTTAGCAACCACCAAT-AGGTAGGGGGAATCAGCACTTAGCAACCCCTCGGG
1 GGTGGAATCAGCACTTAGCAACCACCAATGA-AT-CGGGGAATCAGCACACAGCAACCCCTCGGG
52905613 GGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATAC
64 GGAATCAGCACTTAGCAACCCCCTT-CACATTTAAAATAC
*
52905653 GGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCT
1 GGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
52905712 TTATATGCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
101 17 0.07
102 6 0.03
103 83 0.35
104 133 0.55
105 1 0.00
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.18
Consensus pattern (102 bp):
GGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTCGGGGG
AATCAGCACTTAGCAACCCCCTTCACATTTAAAATAC
Found at i:52905636 original size:28 final size:27
Alignment explanation
Indices: 52905583--52905634 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
52905573 CCAATAGGTA
52905583 GGGGGAATCAGCACTTAGCAACCCCTC
1 GGGGGAATCAGCACTTAGCAACCCCTC
52905610 GGGGGAATCAGCACTTAGCAACCCC
1 GGGGGAATCAGCACTTAGCAACCCC
52905635 CTTCCACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (27 bp):
GGGGGAATCAGCACTTAGCAACCCCTC
Found at i:52906077 original size:31 final size:29
Alignment explanation
Indices: 52906038--52906102 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
52906028 TAATCCTCCA
52906038 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
52906068 CCCAGACTTTTGCATAATTACATTTTTGTC
1 CCCA-ACTTTTGAAAAATTACAATTTTGCC
52906098 CCCAA
1 CCCAA
52906103 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 27 0.90
31 2 0.07
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:52910026 original size:25 final size:25
Alignment explanation
Indices: 52909997--52910067 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
52909987 TACTAGCTGT
* *
52909997 ATATCGGGAAGCTCTTGCGAGACAA
1 ATATCGGGAAGCTCATGAGAGACAA
* *
52910022 ATATCGAGAAGCTCATGAGAGCCAA
1 ATATCGGGAAGCTCATGAGAGACAA
* *
52910047 GTATCGGGAAGCTCAAGAGAG
1 ATATCGGGAAGCTCATGAGAG
52910068 TTGTGGTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (25 bp):
ATATCGGGAAGCTCATGAGAGACAA
Found at i:52910037 original size:75 final size:75
Alignment explanation
Indices: 52909908--52910049 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 75
52909898 GTACATGCTG
* * * * *
52909908 CTCATACAAGCATGTAACCGGGAAGCTCCTCCGAGCCATATAACGGGAAGCTCATGTGAGCTAAG
1 CTCATACAAGCATGTAACCGGGAAGCTCCTCCGAGACAAATAACGAGAAGCTCATGAGAGCCAAG
52909973 TAAAGGGGAA
66 TAAAGGGGAA
* * * * *
52909983 CTCATACTAGC-TGTATATCGGGAAGCTCTTGCGAGACAAATATCGAGAAGCTCATGAGAGCCAA
1 CTCATACAAGCATGTA-ACCGGGAAGCTCCTCCGAGACAAATAACGAGAAGCTCATGAGAGCCAA
52910047 GTA
65 GTA
52910050 TCGGGAAGCT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
74 4 0.07
75 52 0.93
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (75 bp):
CTCATACAAGCATGTAACCGGGAAGCTCCTCCGAGACAAATAACGAGAAGCTCATGAGAGCCAAG
TAAAGGGGAA
Found at i:52925930 original size:11 final size:11
Alignment explanation
Indices: 52925892--52925924 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
52925882 AAAAAAATTA
52925892 AATTTTAAAAT
1 AATTTTAAAAT
52925903 AATTTTAAAAT
1 AATTTTAAAAT
52925914 AATTTTAAAAT
1 AATTTTAAAAT
52925925 TTTTTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:52938666 original size:3 final size:3
Alignment explanation
Indices: 52938652--52938724 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
52938642 AAAGGAAAGG
* * *
52938652 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AGGA AGA AAA AGGA AAA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA A-GA AGA
* *
52938699 AGA AAA AG- AGA AGG AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
52938725 GGGAGGGAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.04
3 50 0.88
4 5 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52938754 original size:55 final size:57
Alignment explanation
Indices: 52938636--52938754 Score: 124
Period size: 55 Copynumber: 2.2 Consensus size: 57
52938626 TGAAGGAGAA
* * * *
52938636 GAAAGAAAAGGAAAGGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGGAAGAAAAAG
1 GAAAAAAAAGAAAAAGAGAAGGAGAAGAAGAAGAAG-AGAAGAAGAAGGAAAAAAAAG
* *
52938694 G---AAAAAGAAAAAGAGAAGGAGAAGAAGAAG-AG-GGAG-GGAAGGAAAAAGAAAG
1 GAAAAAAAAGAAAAAGAGAAGGAGAAGAAGAAGAAGAGAAGAAGAAGGAAAAA-AAAG
52938746 GAAAAAAAA
1 GAAAAAAAA
52938755 TAAGGAAAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
51 9 0.18
52 8 0.16
54 2 0.04
55 31 0.61
58 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (57 bp):
GAAAAAAAAGAAAAAGAGAAGGAGAAGAAGAAGAAGAGAAGAAGAAGGAAAAAAAAG
Found at i:52939705 original size:315 final size:316
Alignment explanation
Indices: 52939000--52939854 Score: 1409
Period size: 315 Copynumber: 2.7 Consensus size: 316
52938990 ATACAAAAAG
** *
52939000 AAATAA-AAAA-ACGAAAATAGTATATTTACTGAAAGTAATAAAATCCGGAAAAAAAAAAGAAAA
1 AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCC-G---AAAATAAGAAAA
*
52939063 ATACGAATAAATGGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTA
62 ATACGAACAAATGGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTA
52939128 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTT
127 ATACATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTT
*
52939193 TAAAAGTAATAAAATCTA-AAAATAAGAAAAATACGAACAAATGGCCAAAATAAGGGGGTTTTAC
192 TAAAAGTAATAAAATC-AGAAAATAAG-AAAATA-GAACAAAGGGCCAAAATAAGGGGGTTTTAC
*
52939257 TAAATTTATATAAAACACACACTAAATTAATACATTTCAAACATTATGTACTAAAATAATATA
254 TAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTATGTACTAAAATAATATA
*
52939320 AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAAATAAGAAAAATAC
1 AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
52939385 GAACAAATGGCCAAAATAAGGGTTTTTTTTACTAAATTTATAT-AAAAAACACACTAAATTAATA
66 GAACAAATGGCCAAAATAAGGG-TTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATA
* *
52939449 CATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACAAAAATAGTATA-TTTTTAA
130 CATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTAA
* **
52939513 AAGTAATAAAATCAGAAAATAAGAAAAT-GAACAAAGGGCCAAAATAATGGTTTTTTACTAAATT
195 AAGTAATAAAATCAGAAAATAAGAAAATAGAACAAAGGGCCAAAATAAGGGGGTTTTACTAAATT
*
52939577 TATATAAAAAAACACACTAAATTAATATATTTCAAACATTATGTACTAAAATAATATA
260 TATAT-AAAAAACACACTAAATTAATACATTTCAAACATTATGTACTAAAATAATATA
* *
52939635 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGGAAAATAC
1 AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
* *
52939700 GAACAAAGGGCCAAAATAATGG-TTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
66 GAACAAATGGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
*
52939764 ATTTCAAACATTATGTACTAAAATAATATGAAATAATAAAATACGAAAATAATATATTTTTTAAA
131 ATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTAAA
*
52939829 AGTAATAAAATCTGAAAATAAGAAAA
196 AGTAATAAAATCAGAAAATAAGAAAA
52939855 ATATATTGAA
Statistics
Matches: 506, Mismatches: 22, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
313 19 0.04
314 112 0.22
315 165 0.33
316 6 0.01
317 28 0.06
318 112 0.22
319 20 0.04
320 6 0.01
321 4 0.01
322 34 0.07
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.29
Consensus pattern (316 bp):
AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
GAACAAATGGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
ATTTCAAACATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAATATATTTTTTAAA
AGTAATAAAATCAGAAAATAAGAAAATAGAACAAAGGGCCAAAATAAGGGGGTTTTACTAAATTT
ATATAAAAAACACACTAAATTAATACATTTCAAACATTATGTACTAAAATAATATA
Found at i:52939760 original size:159 final size:159
Alignment explanation
Indices: 52939000--52939857 Score: 1363
Period size: 159 Copynumber: 5.4 Consensus size: 159
52938990 ATACAAAAAG
** * *
52939000 AAATAA-AAAA-ACGAAAATAGTATATTTACTGAAAGTAATAAAATCCGGAAAAAAAAAAGAAAA
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCC-G---AAAATAAGAAAA
*
52939063 ATACGAATAAATGGCCAAAATAAGGGTTTTTTTACTAAATTTATATAAAAAAACACACTAAATTA
62 ATACGAACAAATGGCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAAACACACTAAATTA
52939128 ATACATTTCAAACATTATGTACTAAAATAATATA
126 ATACATTTCAAACATTATGTACTAAAATAATATA
* **
52939162 AAATAATAAAATACGAAAATAATATATTTTTTAAAAGTAATAAAATCTAAAAATAAGAAAAATAC
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATAC
** *
52939227 GAACAAATGGCCAAAATAAGGGGGTTTTACTAAATTTATAT-AAAACACACACTAAATTAATACA
66 GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACA
52939291 TTTCAAACATTATGTACTAAAATAATATA
131 TTTCAAACATTATGTACTAAAATAATATA
* *
52939320 AAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCAAAAATAAGAAAAATAC
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATAC
52939385 GAACAAATGGCCAAAATAAGGGTTTTTTTTACTAAATTTATAT-AAAAAACACACTAAATTAATA
66 GAACAAATGGCCAAAATAAGGG--TTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATA
52939449 CATTTCAAACATTATGTACTAAAATAATATA
129 CATTTCAAACATTATGTACTAAAATAATATA
* *
52939480 AAATAATAAAATACAAAAATAGTATA-TTTTTAAAAGTAATAAAATCAGAAAATAAG-AAAAT--
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATAC
* * *
52939541 GAACAAAGGGCCAAAATAATGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATATA
66 GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACA
52939606 TTTCAAACATTATGTACTAAAATAATATA
131 TTTCAAACATTATGTACTAAAATAATATA
* * *
52939635 AAATAATAAAATACAAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGGAAAATAC
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATAC
* *
52939700 GAACAAAGGGCCAAAATAATGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACA
66 GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACA
*
52939765 TTTCAAACATTATGTACTAAAATAATATG
131 TTTCAAACATTATGTACTAAAATAATATA
* *
52939794 AAATAATAAAATACGAAAATAATATATTTTTTAAAAGTAATAAAATCTGAAAATAAGAAAAATA
1 AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATA
52939858 TATTGAAATT
Statistics
Matches: 654, Mismatches: 33, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
154 19 0.03
155 77 0.12
156 48 0.07
157 5 0.01
158 140 0.21
159 195 0.30
160 129 0.20
162 6 0.01
163 4 0.01
164 31 0.05
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.29
Consensus pattern (159 bp):
AAATAATAAAATACGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATAC
GAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACA
TTTCAAACATTATGTACTAAAATAATATA
Found at i:52945192 original size:76 final size:76
Alignment explanation
Indices: 52945102--52945243 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 76
52945092 ATAACAGTTT
52945102 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAAAAATAATAACTAACAATAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAA
52945166 TATAGTGTAAAA
65 TATAGTGTAAAA
* * *** *
52945178 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
52945243 A
66 A
52945244 ATACTAGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 14 0.24
76 45 0.76
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAGTGTAAAA
Done.