Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 62 of 128
Found at i:19834086 original size:9 final size:9
Alignment explanation
Indices: 19834011--19834349 Score: 190
Period size: 9 Copynumber: 38.7 Consensus size: 9
19834001 ATCTTGCATA
19834011 ATAACTTAC
1 ATAACTTAC
*
19834020 ATAACATAC
1 ATAACTTAC
*
19834029 ATAA--TAT
1 ATAACTTAC
* *
19834036 AGAATTTAC
1 ATAACTTAC
**
19834045 ATAAAATAC
1 ATAACTTAC
19834054 --AACTTAC
1 ATAACTTAC
*
19834061 ATATCTTAC
1 ATAACTTAC
19834070 ATAA--TAC
1 ATAACTTAC
19834077 ATAACTTAC
1 ATAACTTAC
19834086 ATAA--TAC
1 ATAACTTAC
19834093 A-ACACTTAC
1 ATA-ACTTAC
* *
19834102 ACAACTTAA
1 ATAACTTAC
*
19834111 ATAACTTAT
1 ATAACTTAC
*
19834120 ATAACTTGC
1 ATAACTTAC
*
19834129 ATAACTTAT
1 ATAACTTAC
*
19834138 ATAA-TAAC
1 ATAACTTAC
*
19834146 ATAA-TAAC
1 ATAACTTAC
*
19834154 -TAACATAC
1 ATAACTTAC
19834162 AATATA-TTAAC
1 -ATA-ACTT-AC
* *
19834173 ATATA-TAAT
1 ATA-ACTTAC
* *
19834182 GTAACTTGC
1 ATAACTTAC
*
19834191 ATAACTTAT
1 ATAACTTAC
*
19834200 ATAA-TAAC
1 ATAACTTAC
*
19834208 ATAA-TAAC
1 ATAACTTAC
19834216 -TAACATAGTAC
1 ATAAC-T--TAC
** * *
19834227 ATTGCCTAA
1 ATAACTTAC
19834236 ATAACTTAC
1 ATAACTTAC
19834245 ATAACTTAC
1 ATAACTTAC
* *
19834254 ATAAATTAA
1 ATAACTTAC
19834263 ATAACTTAC
1 ATAACTTAC
19834272 ATAACTTAC
1 ATAACTTAC
*
19834281 ATAAGTTAC
1 ATAACTTAC
* *
19834290 ATAAATTAA
1 ATAACTTAC
19834299 ATAACTTAC
1 ATAACTTAC
19834308 ATAACTTAC
1 ATAACTTAC
19834317 ATAACTTAC
1 ATAACTTAC
* *
19834326 ATAAATTAA
1 ATAACTTAC
19834335 ATAACTTAC
1 ATAACTTAC
19834344 ATAACT
1 ATAACT
19834350 CATTTATGGT
Statistics
Matches: 253, Mismatches: 56, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
6 1 0.00
7 28 0.11
8 23 0.09
9 184 0.73
10 10 0.04
11 5 0.02
12 2 0.01
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:19834282 original size:36 final size:36
Alignment explanation
Indices: 19834236--19834349 Score: 219
Period size: 36 Copynumber: 3.2 Consensus size: 36
19834226 CATTGCCTAA
19834236 ATAACTTACATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACATAAATTAAATAACTTAC
*
19834272 ATAACTTACATAAGTTACATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACATAAATTAAATAACTTAC
19834308 ATAACTTACATAACTTACATAAATTAAATAACTTAC
1 ATAACTTACATAACTTACATAAATTAAATAACTTAC
19834344 ATAACT
1 ATAACT
19834350 CATTTATGGT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (36 bp):
ATAACTTACATAACTTACATAAATTAAATAACTTAC
Found at i:19834371 original size:26 final size:26
Alignment explanation
Indices: 19834335--19834390 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
19834325 CATAAATTAA
*
19834335 ATAACTTACATAACTCATTTATGGTT
1 ATAAATTACATAACTCATTTATGGTT
19834361 ATAAATTACATAACTCATTTATGGTT
1 ATAAATTACATAACTCATTTATGGTT
19834387 ATAA
1 ATAA
19834391 CTGGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (26 bp):
ATAAATTACATAACTCATTTATGGTT
Found at i:19839495 original size:3 final size:3
Alignment explanation
Indices: 19839446--19839484 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19839436 NNNNNNNNNN
19839446 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19839485 GCACATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19841310 original size:111 final size:111
Alignment explanation
Indices: 19841116--19841315 Score: 337
Period size: 111 Copynumber: 1.8 Consensus size: 111
19841106 GAGGTAAAAC
* *
19841116 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCACTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTTATTTTAATCCACTCCACTG
19841181 TAATCTCAGGGAGATAGGATTACTAGATAAGATTTCTGGCTTTAAT
66 TAATCTCAGGGAGATAGGATTACTAGATAAGATTTCTGGCTTTAAT
* ** *
19841227 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTTATTTTAATCCGTTCTACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTTATTTTAATCCACTCCACTG
*
19841292 TAATCTTAGGGAGATAGGATTACT
66 TAATCTCAGGGAGATAGGATTACT
19841316 GGCTTCAATC
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 82 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (111 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCCTTTATTTTAATCCACTCCACTG
TAATCTCAGGGAGATAGGATTACTAGATAAGATTTCTGGCTTTAAT
Found at i:19841464 original size:142 final size:142
Alignment explanation
Indices: 19841205--19841497 Score: 469
Period size: 142 Copynumber: 2.1 Consensus size: 142
19841195 TAGGATTACT
* *
19841205 AGATAAGATTTCTGGCTTTAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGACCC
1 AGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCC
*** * * **
19841270 TTTATTTTAATCCGTTCTACTGTAATCTTAGGGAGATAGGATTACTGGCTTCAATCTGCTCCGCT
66 TTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCT
*
19841335 GTAATTTCAGGG
131 GTAATCTCAGGG
*
19841347 AGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC
1 AGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCC
*
19841412 TTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATTGGATTACTAACTTCAATCTGCTCCGCT
66 TTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCT
*
19841477 TTAATCTCAGGG
131 GTAATCTCAGGG
19841489 AGATAAGAT
1 AGATAAGAT
19841498 CTGAAATTCT
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
142 138 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (142 bp):
AGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGACCC
TTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCT
GTAATCTCAGGG
Found at i:19841690 original size:129 final size:129
Alignment explanation
Indices: 19841512--19843346 Score: 3575
Period size: 129 Copynumber: 14.2 Consensus size: 129
19841502 AATTCTTCGG
* * * * * * *
19841512 TCTGTTCCACTGTAATCTCAGAGCA-ATAAGACCTGGA-GCGATCTACTCTACTGTAACTTCAGA
1 TCTGCTCCGCTGTAATCTCAG-GGAGATAAGACCT-GATACGCTCTTCTCTATTGTAACTTCAGA
19841575 GAGATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCA
64 GAGATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCA
19841640 A
129 A
19841641 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19841706 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19841770 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19841835 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19841899 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19841964 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842028 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842093 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842157 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842222 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842286 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842351 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842415 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842480 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842544 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842609 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842673 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842738 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842802 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842867 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19842931 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19842996 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19843060 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19843125 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19843189 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
19843254 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
66 GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
19843318 TCTGCTCCGCTGTAATCTCAGGGAGATAA
1 TCTGCTCCGCTGTAATCTCAGGGAGATAA
19843347 TATCTGAAAT
Statistics
Matches: 1697, Mismatches: 7, Indels: 4
0.99 0.00 0.00
Matches are distributed among these distances:
128 4 0.00
129 1693 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (129 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATACGCTCTTCTCTATTGTAACTTCAGAGA
GATAAGATCCTTTATTTTAATCAACTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAA
Found at i:19843650 original size:44 final size:44
Alignment explanation
Indices: 19843513--19843650 Score: 106
Period size: 44 Copynumber: 3.2 Consensus size: 44
19843503 TAATGCAGGA
* *
19843513 AGGCAAGATCTACTATCTTCAATCAGCTCCACTATAACCGATG-G
1 AGGCAAGATCTGCTATCTTCAATCAGCTCCACAATAACCGA-GAG
* * * * * ** *
19843557 AGACAAGGCTTTG-T-T-TTCAATCTGCTTCGTAATTAACGCAAGA-
1 AGGCAA-GATCTGCTATCTTCAATCAGCTCCACAA-TAAC-CGAGAG
*
19843600 AGGCAAGATCTGCTATCTTCAATCAGCTCCACCATAACCGAGAG
1 AGGCAAGATCTGCTATCTTCAATCAGCTCCACAATAACCGAGAG
19843644 AGGCAAG
1 AGGCAAG
19843651 GTTTGTGTCT
Statistics
Matches: 67, Mismatches: 19, Indels: 16
0.66 0.19 0.16
Matches are distributed among these distances:
42 16 0.24
43 16 0.24
44 20 0.30
45 15 0.22
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAATCAGCTCCACAATAACCGAGAG
Found at i:19843718 original size:88 final size:88
Alignment explanation
Indices: 19843460--19843937 Score: 520
Period size: 88 Copynumber: 5.5 Consensus size: 88
19843450 CAGCTTCACG
* * * *
19843460 CAACCGATG-GAGGCAAGGCTTTGT-T-TTCGATCTACTCCGTTGTTAATGCAGGAAGGCAAGAT
1 CAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGAT
** * *
19843522 CTACTATCTTCAATCAGCTCCA-CTA
64 CTGTTGTCTTCAACCAGCTCCATC-A
* * * * ** * * *
19843547 TAACCGATG-GAGACAAGGCTTTGT-T-TTCAATCTGCTTCGTAATTAACGCAAGAAGGCAAGAT
1 CAACCGA-GAGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGAT
* * * *
19843609 CTGCTATCTTCAATCAGCTCCACCA
64 CTGTTGTCTTCAACCAGCTCCATCA
* *
19843634 TAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGTAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCT
*
19843699 GTTGTCTTTAACCAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
* * * * * * *
19843722 CAACTGAGAGAGGCAAGGTTTGTGTCTTTGAACTGCTACGCTGTCAATACAGGAAGGCAGGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCT
*
19843787 GTTGTCTTTAACCAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
* * * * *
19843810 CAACCGAGGGAGGCAAAGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGTACGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCT
*
19843875 TTTGTCTTCAACCAGCTCCATCA
66 GTTGTCTTCAACCAGCTCCATCA
19843898 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCG
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCG
19843938 NNNNNNNNNN
Statistics
Matches: 340, Mismatches: 47, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
86 6 0.02
87 91 0.27
88 243 0.71
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (88 bp):
CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCT
GTTGTCTTCAACCAGCTCCATCA
Found at i:19845714 original size:14 final size:14
Alignment explanation
Indices: 19845695--19845724 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19845685 TGACCTCTCC
*
19845695 TTTTCTTTTTCTTT
1 TTTTCTCTTTCTTT
19845709 TTTTCTCTTTCTTT
1 TTTTCTCTTTCTTT
19845723 TT
1 TT
19845725 CCCCTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTCTTTCTTT
Found at i:19847902 original size:19 final size:20
Alignment explanation
Indices: 19847873--19847921 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
19847863 CACTTCGTGA
* *
19847873 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
19847892 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
19847912 AAATG-AATGC
1 AAATGTAATGC
19847922 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:19848969 original size:13 final size:13
Alignment explanation
Indices: 19848951--19848975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19848941 GATTTGATTT
19848951 TATTAAAACAATA
1 TATTAAAACAATA
19848964 TATTAAAACAAT
1 TATTAAAACAAT
19848976 GCTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
TATTAAAACAATA
Found at i:19849362 original size:108 final size:108
Alignment explanation
Indices: 19849195--19849569 Score: 696
Period size: 108 Copynumber: 3.5 Consensus size: 108
19849185 AATTTGGCTA
* * *
19849195 AACGTGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
19849260 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
19849303 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
19849368 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
19849411 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
19849476 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
* * *
19849519 AAAGAGAAATCGAAACACAATACCTTAGGGCACGTTCCTCGAATTTCCAAA
1 AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAA
19849570 NNNNNNNNNN
Statistics
Matches: 261, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 261 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (108 bp):
AACGAGAAATCGAAACCCAATACCTTAGGGCACATTCCTCGAATTTCCAAACGCAAAATATTGCC
TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
Found at i:19853506 original size:3 final size:3
Alignment explanation
Indices: 19853457--19853495 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19853447 NNNNNNNNNN
19853457 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19853496 GCACATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19854247 original size:17 final size:17
Alignment explanation
Indices: 19854210--19854248 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
19854200 AAATAAATCG
* *
19854210 GAAATAAAAAAAATTGT
1 GAAATAAAAAAAATAGA
19854227 GAAATAAAAAAAATAGA
1 GAAATAAAAAAAATAGA
19854244 GAAAT
1 GAAAT
19854249 CAAGTGGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.18
Consensus pattern (17 bp):
GAAATAAAAAAAATAGA
Found at i:19857181 original size:21 final size:21
Alignment explanation
Indices: 19857157--19857207 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
19857147 CTACAACTTA
*
19857157 AAGCAGAGGCAGCAGCGAGGG
1 AAGCAGAGGCAGCAGCGAGAG
*
19857178 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
19857199 AAGCAGAGG
1 AAGCAGAGG
19857208 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.45, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:19857851 original size:42 final size:42
Alignment explanation
Indices: 19857787--19857882 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
19857777 NNNNNNNNNN
19857787 CCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCG
1 CCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCG
* *
19857829 CCGCGAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCG
1 CCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCG
*
19857871 CCTCTAAAGAAC
1 CCGCTAAAGAAC
19857883 TTTTTGTTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
CCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTCTAAGCG
Found at i:19860503 original size:20 final size:20
Alignment explanation
Indices: 19860471--19860533 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 20
19860461 ATATTATAAA
19860471 AAAAATAT-A-AATTATTAT
1 AAAAATATGATAATTATTAT
*
19860489 AAAAATATGATAATTATAAT
1 AAAAATATGATAATTATTAT
* *
19860509 AATAAT-TGATAATTAGTA-
1 AAAAATATGATAATTATTAT
19860527 AAAAATA
1 AAAAATA
19860534 CTAACAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 13 0.35
19 11 0.30
20 13 0.35
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAAATATGATAATTATTAT
Found at i:19860504 original size:17 final size:19
Alignment explanation
Indices: 19860484--19860530 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
19860474 AATATAAATT
19860484 ATTATAAAAAT-A-TGATA
1 ATTATAAAAATAATTGATA
*
19860501 ATTATAATAATAATTGATA
1 ATTATAAAAATAATTGATA
19860520 ATTAGTAAAAA
1 ATTA-TAAAAA
19860531 ATACTAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 9 0.36
20 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (19 bp):
ATTATAAAAATAATTGATA
Found at i:19863364 original size:21 final size:21
Alignment explanation
Indices: 19863338--19863392 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
19863328 AACAGCGGTG
*
19863338 GCGGTGAGATTAGTTACTATA
1 GCGGTGAGATTAGGTACTATA
* * *
19863359 GCGGTGAGATTGGGTATTGTA
1 GCGGTGAGATTAGGTACTATA
*
19863380 GCAGTGAGATTAG
1 GCGGTGAGATTAG
19863393 AAATAGCGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.36, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTATA
Found at i:19863571 original size:12 final size:12
Alignment explanation
Indices: 19863556--19863609 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
19863546 TTTATTAATT
19863556 TATTTAATAAAA
1 TATTTAATAAAA
*
19863568 TATTAAATAAAA
1 TATTTAATAAAA
* *
19863580 TAGTAAATATAAA
1 TATTTAATA-AAA
19863593 T-TTATAATAAAA
1 TATT-TAATAAAA
19863605 TATTT
1 TATTT
19863610 TTTCCTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
TATTTAATAAAA
Found at i:19863645 original size:22 final size:22
Alignment explanation
Indices: 19863620--19863663 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19863610 TTTCCTTTAG
*
19863620 CCATCAACGTTTTCTATTTTTT
1 CCATCAAAGTTTTCTATTTTTT
* *
19863642 CCATCAAAGTTTTTTTTTTTTT
1 CCATCAAAGTTTTCTATTTTTT
19863664 ACTTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.59
Consensus pattern (22 bp):
CCATCAAAGTTTTCTATTTTTT
Found at i:19885021 original size:393 final size:387
Alignment explanation
Indices: 19884298--19885074 Score: 1293
Period size: 393 Copynumber: 2.0 Consensus size: 387
19884288 AATCTGCTTA
* *
19884298 TTGCTAATGGAATTGGCCAACTTTTTGATATCCTTCATTTTGCACAACAATGATGTCTCCGCAGT
1 TTGCTAATAGAATTGGCCAACTTTTCGATATCCTTCATTTTGCACAACAATGATGTCTCCGCAGT
* * ***
19884363 CATTGCTTCGCTTTCTACTTTGGTTTTGTCCTTCCTTATCTTGTTGGTCCTTGCCTCCTTCATTG
66 CATTGCTTCGCTTTCTACTTTGGTTTTGTCCTTCCTTATCATGCTGGTCCCCACCTCCTTCATTG
* * ** * *
19884428 TCGGCGTATCTTTACTATGAGTCATTCTTTCAATAGACGCTTCTTTGATTGGGCCCTTATTTTCC
131 TCAGCGTATCTTTACCATGAGTCATTCTTTCAATAGACGCTTCAATGATCGGGCCCCTATTTTCC
*
19884493 AAGATCTCTTCATCTTCACGGGGCACAATACCTTTCTGTTGGCACAGTAGCATCACCAACAATAG
196 AAGATCTCTTCATCTTCACAGGGCACAATACCTTTCTGTTGGCACAGTAGCATCACCAACAATAG
* *
19884558 GAAAACCAAAATTCAATTTTGCCTTGCGGCGTAGTCAGTAATTTCTTGGTGGACTATTATGTCAA
261 GAAAACCAAAATTCAATTTTGCCTTGCAGCGTAGTCAGTAATTTCTTGGTGGACTATTATATCAA
* *
19884623 CATCAATCTTTCTACCCTTGACAATTGAATGTATCAGACACATTCTATCAAAGTTGACTATG
326 CATCAATCTTTCTACCCTCGACAATCGAATGTATCAGACACATTCTATCAAAGTTGACTATG
* *
19884685 TTGCTAATAGAATTGGCCAACTTTTCGATATCCTTTATTTTGCACAACAATGATGTCTCTGCAGT
1 TTGCTAATAGAATTGGCCAACTTTTCGATATCCTTCATTTTGCACAACAATGATGTCTCCGCAGT
*
19884750 CAAGTTTACTGCTTCGCTTTCTACTTTGGTTTTGTCCTTCCTTGTCATGCTGGTCCCCACCTCCT
66 C-A---T--TGCTTCGCTTTCTACTTTGGTTTTGTCCTTCCTTATCATGCTGGTCCCCACCTCCT
19884815 TCATTGTCAGCGTATCTTTACCATGAGTCATTCTTTCAATAGACGCTTCAATGATCGGGCCCCTA
125 TCATTGTCAGCGTATCTTTACCATGAGTCATTCTTTCAATAGACGCTTCAATGATCGGGCCCCTA
19884880 TTTTCCAAGATCTCTTCATCTTCACAGGGCACAATACCTTTCTGTTGGCACAGTAGCATCACCAA
190 TTTTCCAAGATCTCTTCATCTTCACAGGGCACAATACCTTTCTGTTGGCACAGTAGCATCACCAA
19884945 CAATAGGAAAACCAAAATTCAATTTTGCCTTGCAGCGTAGTCAGTAATTTCTTGGTGGACTATTA
255 CAATAGGAAAACCAAAATTCAATTTTGCCTTGCAGCGTAGTCAGTAATTTCTTGGTGGACTATTA
* *
19885010 TATCGACATCAATCTTTCTGCCCTCGACAATCGAATGTATCAGACACATTCTATCAAAGTTGACT
320 TATCAACATCAATCTTTCTACCCTCGACAATCGAATGTATCAGACACATTCTATCAAAGTTGACT
19885075 GTGGTGCTGT
Statistics
Matches: 361, Mismatches: 23, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
387 62 0.17
388 1 0.00
391 1 0.00
393 297 0.82
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (387 bp):
TTGCTAATAGAATTGGCCAACTTTTCGATATCCTTCATTTTGCACAACAATGATGTCTCCGCAGT
CATTGCTTCGCTTTCTACTTTGGTTTTGTCCTTCCTTATCATGCTGGTCCCCACCTCCTTCATTG
TCAGCGTATCTTTACCATGAGTCATTCTTTCAATAGACGCTTCAATGATCGGGCCCCTATTTTCC
AAGATCTCTTCATCTTCACAGGGCACAATACCTTTCTGTTGGCACAGTAGCATCACCAACAATAG
GAAAACCAAAATTCAATTTTGCCTTGCAGCGTAGTCAGTAATTTCTTGGTGGACTATTATATCAA
CATCAATCTTTCTACCCTCGACAATCGAATGTATCAGACACATTCTATCAAAGTTGACTATG
Found at i:19889092 original size:30 final size:30
Alignment explanation
Indices: 19889057--19889115 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
19889047 TATGGGGTAG
19889057 TAAAGCTCCTAGGATCTTTTATTTTGGGGT
1 TAAAGCTCCTAGGATCTTTTATTTTGGGGT
19889087 TAAAGCTCCTAGGATCTTTTATTTTGGGG
1 TAAAGCTCCTAGGATCTTTTATTTTGGGG
19889116 GCAACTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (30 bp):
TAAAGCTCCTAGGATCTTTTATTTTGGGGT
Found at i:19898177 original size:30 final size:30
Alignment explanation
Indices: 19898143--19898205 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
19898133 TAGTATTAAG
19898143 ATAATTTCAAGCCATATAAGTAATATATGA
1 ATAATTTCAAGCCATATAAGTAATATATGA
* * *
19898173 ATAATTTGAAGTCATATAAGTAATATATTA
1 ATAATTTCAAGCCATATAAGTAATATATGA
19898203 ATA
1 ATA
19898206 TACTTGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (30 bp):
ATAATTTCAAGCCATATAAGTAATATATGA
Found at i:19899052 original size:14 final size:14
Alignment explanation
Indices: 19899005--19899052 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
19898995 AGGAATCTTT
19899005 ATTATATTAACTTA
1 ATTATATTAACTTA
*
19899019 ATTAAATTAATCTTA
1 ATTATATTAA-CTTA
19899034 ATTATATTAACTTA
1 ATTATATTAACTTA
19899048 ATTAT
1 ATTAT
19899053 TCATTAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTATATTAACTTA
Found at i:19900997 original size:20 final size:21
Alignment explanation
Indices: 19900973--19901043 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 21
19900963 AGATTAAATT
*
19900973 TAATATTAAATTTATTAAA-T
1 TAATATTAAATTTATTAAAGA
*
19900993 TAATA-GAATATTTATCTACAAGA
1 TAATATTAA-ATTTAT-TA-AAGA
19901016 TAATATTAAATTTATTAAA-A
1 TAATATTAAATTTATTAAAGA
19901036 TAATATTA
1 TAATATTA
19901044 TTTTTGGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.05
20 20 0.47
21 4 0.09
22 4 0.09
23 11 0.26
24 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
TAATATTAAATTTATTAAAGA
Found at i:19905400 original size:13 final size:13
Alignment explanation
Indices: 19905382--19905406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19905372 GCTCCTACTG
19905382 ATAAAACATGCTT
1 ATAAAACATGCTT
19905395 ATAAAACATGCT
1 ATAAAACATGCT
19905407 AGGGATAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (13 bp):
ATAAAACATGCTT
Found at i:19906962 original size:27 final size:26
Alignment explanation
Indices: 19906932--19906996 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
19906922 TTTAATAGTA
*
19906932 ACAGTACAGTGTGGGCCTTAGCCCAAT
1 ACAGTACAGTGT-GGCCTAAGCCCAAT
* * *
19906959 ACAGAAATAGTGTGTCCTAAGCCCAAT
1 ACAG-TACAGTGTGGCCTAAGCCCAAT
19906986 ACAGTATCAGT
1 ACAGTA-CAGT
19906997 ATGGTGCAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 23 0.77
28 6 0.20
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (26 bp):
ACAGTACAGTGTGGCCTAAGCCCAAT
Found at i:19907168 original size:22 final size:22
Alignment explanation
Indices: 19907143--19907189 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19907133 CTAAGAGCCG
*
19907143 TAAACATG-ATAGCTATAAGCTA
1 TAAACA-GAATAGCTACAAGCTA
*
19907165 TAAACAGAATGGCTACAAGCTA
1 TAAACAGAATAGCTACAAGCTA
19907187 TAA
1 TAA
19907190 GTATAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (22 bp):
TAAACAGAATAGCTACAAGCTA
Found at i:19907271 original size:32 final size:32
Alignment explanation
Indices: 19907211--19907445 Score: 353
Period size: 32 Copynumber: 7.3 Consensus size: 32
19907201 TAATTGGGAC
* * * * * *
19907211 AGCCATCAGTAGCAGTGATATGACCGGCATAC
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
* *
19907243 ATCCATCAGTAACGGTAATACGATCGGCACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
*
19907275 AGCCATCAGTAACGGTAATATGATCGACACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
*
19907307 AGCCATCAGTAACGGTAATATGATTGGCACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
19907339 AGCCATCAGTAACGGTAATATGATCGGCACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
*
19907371 ATCCATCAGTAACGGTAATATGATCGGCACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
*
19907403 AGCTATCAGTAACGGTAATATGATCGGCACAA
1 AGCCATCAGTAACGGTAATATGATCGGCACAA
*
19907435 AGCCATTAGTA
1 AGCCATCAGTA
19907446 GCATCGCAGC
Statistics
Matches: 184, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 184 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (32 bp):
AGCCATCAGTAACGGTAATATGATCGGCACAA
Found at i:19907648 original size:24 final size:23
Alignment explanation
Indices: 19907616--19907698 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
19907606 GCCATGCTCA
*
19907616 AAATTAATCATTCAAATCACAGAC
1 AAATCAATCATTCAAA-CACAGAC
* * *
19907640 AAATAAATCATACCAAACATAGAC
1 AAATCAATCAT-TCAAACACAGAC
* * *
19907664 AAATCAGTCATTTAACCACAGAC
1 AAATCAATCATTCAAACACAGAC
19907687 AAATCAATCATT
1 AAATCAATCATT
19907699 TGACCTCGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 19 0.40
24 25 0.52
25 4 0.08
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATCAATCATTCAAACACAGAC
Found at i:19907772 original size:27 final size:27
Alignment explanation
Indices: 19907723--19908104 Score: 532
Period size: 27 Copynumber: 14.2 Consensus size: 27
19907713 AAAATAATCA
*
19907723 TTTAACCTACA-GGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19907749 TTTACCCTATAGGGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
19907776 TCTACCCTATAGGGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19907803 TCTACCCTACAGGGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19907830 TTTACCCTAAAGGGGTATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
19907857 TTTACCTTACAGGGGTATTACAGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19907884 TTTACCCTACAGGGGTATTACAGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19907911 TTTACCCTACAGGGGTATTACGGTGAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* * *
19907938 TTTAACCTACAGGGGTATTACAGTTAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* * * * *
19907965 TTTACCCTATAAGGGCATTATGTTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
19907992 TTTACCCTAGAGGGGTATTACGATCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
*
19908019 TTTACCCTACAGGGGTATTACTGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
19908046 TTTACCCTACAAGGGCATTACGGTCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
* *
19908073 TTAACCCTACAGGGGTATTACGATCAT
1 TTTACCCTACAGGGGTATTACGGTCAT
19908100 TTTAC
1 TTTAC
19908105 AACCTTTCTG
Statistics
Matches: 316, Mismatches: 39, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
26 9 0.03
27 307 0.97
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
TTTACCCTACAGGGGTATTACGGTCAT
Found at i:19926155 original size:20 final size:20
Alignment explanation
Indices: 19926126--19926167 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
19926116 AAGTACGAAT
19926126 AGGGGCACGTATGTGCAATC
1 AGGGGCACGTATGTGCAATC
*
19926146 AGGGGTACGTATGTGCAATC
1 AGGGGCACGTATGTGCAATC
19926166 AG
1 AG
19926168 TGTATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (20 bp):
AGGGGCACGTATGTGCAATC
Found at i:19939444 original size:25 final size:25
Alignment explanation
Indices: 19939416--19939464 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
19939406 ACGAATTTTC
19939416 TCAAAA-TTTATCGGGGGTAAAATTA
1 TCAAAATTTTA-CGGGGGTAAAATTA
*
19939441 TCAAAATTTTACTGGGGTAAAATT
1 TCAAAATTTTACGGGGGTAAAATT
19939465 GGGATGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (25 bp):
TCAAAATTTTACGGGGGTAAAATTA
Found at i:19959984 original size:76 final size:76
Alignment explanation
Indices: 19959838--19959989 Score: 198
Period size: 76 Copynumber: 2.0 Consensus size: 76
19959828 TGGCATTGTA
** * * *
19959838 GTACATCATCGGATAAATCGAAAGAAATATATTGGCACACATTGTGCATCGTCAGACAACCCGAA
1 GTACATCATCGGATAAATCGAAAGAAATATACCGGCACACACTGTGCATCATCAGACAACCCAAA
*
19959903 GCAATTATACT
66 ACAATTATACT
* * * *
19959914 GTACATCATTGGATAAATCGAAAGAAATATACCGGCACATACTGTGTATCATC-GAACAAGCCAA
1 GTACATCATCGGATAAATCGAAAGAAATATACCGGCACACACTGTGCATCATCAG-ACAACCCAA
19959978 AACAATTATACT
65 AACAATTATACT
19959990 AACACGCGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 1 0.02
76 64 0.98
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (76 bp):
GTACATCATCGGATAAATCGAAAGAAATATACCGGCACACACTGTGCATCATCAGACAACCCAAA
ACAATTATACT
Found at i:19969104 original size:16 final size:16
Alignment explanation
Indices: 19969073--19969105 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19969063 AAATATTATA
*
19969073 TATTTTTTATACTTTT
1 TATTTTTTAAACTTTT
19969089 TATTTTTTAAA-TTTT
1 TATTTTTTAAACTTTT
19969104 TA
1 TA
19969106 AACAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTTAAACTTTT
Found at i:19979041 original size:44 final size:45
Alignment explanation
Indices: 19978967--19979064 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
19978957 TACTATGTGA
* *
19978967 ACCGGGTACCATTGACTATAAAGGTGGTTGCAATGTGCTGATTCC
1 ACCGAGTATCATTGACTATAAAGGTGGTTGCAATGTGCTGATTCC
* *
19979012 ACCGAGTATCATTGATTAT-AAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAGTATCATTGACTATAAAGGTGGTTGCAATGTGCTGATTCC
*
19979056 ACCGTGTAT
1 ACCGAGTAT
19979065 TTGTTATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (45 bp):
ACCGAGTATCATTGACTATAAAGGTGGTTGCAATGTGCTGATTCC
Found at i:19982316 original size:2 final size:2
Alignment explanation
Indices: 19982309--19982336 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19982299 AGAAGGAGGA
19982309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19982337 GAATATTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19987555 original size:91 final size:90
Alignment explanation
Indices: 19987378--19987556 Score: 243
Period size: 91 Copynumber: 2.0 Consensus size: 90
19987368 GTGGCAGGTG
* * *
19987378 AATACACTATCAGTAGTTGTGAATACACAATGGGTTTGTAGATAAAAGCTACTAGTAAAAGTTGT
1 AATACACTATCAATAGTTGTGAATACACAATGGGTTTGCAGATAAAAACTACTAGT-AAAGTTGT
* *
19987443 GGGTAAACCACCAGTGCTTGCAAGTT
65 GGATAAACCACCACTGCTTGCAAGTT
* * *
19987469 AATACACTGTCAATAGGTTGTGAATACATAATGGTTTTGCAGATAAAAACTACTAGT-AAGTTTG
1 AATACACTATCAATA-GTTGTGAATACACAATGGGTTTGCAGATAAAAACTACTAGTAAAG-TTG
*
19987533 TGGATAAACCACCACTGTTTGCAA
64 TGGATAAACCACCACTGCTTGCAA
19987557 ATAAATTGCC
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
90 3 0.04
91 37 0.48
92 37 0.48
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (90 bp):
AATACACTATCAATAGTTGTGAATACACAATGGGTTTGCAGATAAAAACTACTAGTAAAGTTGTG
GATAAACCACCACTGCTTGCAAGTT
Found at i:19989978 original size:22 final size:22
Alignment explanation
Indices: 19989950--19990009 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
19989940 ATTAGCACGA
19989950 TAGTGCTTTCTGTTTAACACAT
1 TAGTGCTTTCTGTTTAACACAT
* * *
19989972 TAGTGCTATCTGATTAGCACAT
1 TAGTGCTTTCTGTTTAACACAT
19989994 TAGTGCTCTT-TGTTTA
1 TAGTGCT-TTCTGTTTA
19990010 GCACCTAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.45
Consensus pattern (22 bp):
TAGTGCTTTCTGTTTAACACAT
Found at i:19990010 original size:22 final size:21
Alignment explanation
Indices: 19989941--19990013 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 21
19989931 CTCTGATTCA
19989941 TTAGCACGA-TAGTGCTTTCTGT
1 TTAGCAC-ATTAGTGCTTT-TGT
* * *
19989963 TTAACACATTAGTGCTATCTGA
1 TTAGCACATTAGTGCT-TTTGT
19989985 TTAGCACATTAGTGCTCTTTGT
1 TTAGCACATTAGTGCT-TTTGT
19990007 TTAGCAC
1 TTAGCAC
19990014 CTAGGTGCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.02
22 40 0.95
23 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (21 bp):
TTAGCACATTAGTGCTTTTGT
Found at i:19990022 original size:44 final size:44
Alignment explanation
Indices: 19989940--19990027 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
19989930 TCTCTGATTC
*
19989940 ATTAGCACGATAGTGCTTTCTGTTTAACACATTAGTGCTATCTG
1 ATTAGCACGATAGTGCTTTCTGTTTAACACACTAGTGCTATCTG
* *
19989984 ATTAGCAC-ATTAGTGCTCTT-TGTTTAGCAC-CTAGGTGCTCTCTG
1 ATTAGCACGA-TAGTGCT-TTCTGTTTAACACACTA-GTGCTATCTG
19990028 TTCTGTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
43 3 0.08
44 33 0.87
45 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (44 bp):
ATTAGCACGATAGTGCTTTCTGTTTAACACACTAGTGCTATCTG
Found at i:19991297 original size:27 final size:25
Alignment explanation
Indices: 19991259--19991326 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
19991249 CATCCCGACC
*
19991259 CATATCTCGTGTGAGCAGGCCAATATT
1 CATAACTCGTGTGAGCA--CCAATATT
***
19991286 CATAACTCGTGT-AGCATTTATATT
1 CATAACTCGTGTGAGCACCAATATT
*
19991310 CATAGCTCGTGTGAGCA
1 CATAACTCGTGTGAGCA
19991327 ACTCTATCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 16 0.46
25 4 0.11
26 4 0.11
27 11 0.31
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (25 bp):
CATAACTCGTGTGAGCACCAATATT
Found at i:19994227 original size:29 final size:29
Alignment explanation
Indices: 19994195--19994261 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
19994185 ATCGATTATG
*
19994195 AAAAGGGATGGTGACGACCATCAACTACA
1 AAAAGGGATGGTAACGACCATCAACTACA
* *
19994224 AAAAGGGATGGTAACGATCATCAACTACG
1 AAAAGGGATGGTAACGACCATCAACTACA
19994253 AAAAGGGAT
1 AAAAGGGAT
19994262 AGCTTCAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.15
Consensus pattern (29 bp):
AAAAGGGATGGTAACGACCATCAACTACA
Found at i:20002018 original size:29 final size:29
Alignment explanation
Indices: 20001928--20002098 Score: 159
Period size: 29 Copynumber: 5.9 Consensus size: 29
20001918 AGACATCGAA
*
20001928 TATGAAAAGGGATGGTGACAACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
20001957 TATCAAAAGGGATGGTGACGACCATCAAC
1 TATGAAAAGGGATGGTGACGACCATCAAC
*
20001986 TATGAAAAGGGATGGTGACGACCATCGGA-
1 TATGAAAAGGGATGGTGACGACCATC-AAC
* * * * * *
20002015 TATGAAACGGGATAGCT-TCGACTATCGAT
1 TATGAAAAGGGAT-GGTGACGACCATCAAC
* **
20002044 TATGAAAAGAGATTCT-AGCGACCATCAAC
1 TATGAAAAGGGATGGTGA-CGACCATCAAC
* * *
20002073 TATTAATAGGGATGGTGATGACCATC
1 TATGAAAAGGGATGGTGACGACCATC
20002099 GTGATTCCAC
Statistics
Matches: 116, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.03
29 108 0.93
30 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCAAC
Found at i:20012483 original size:18 final size:17
Alignment explanation
Indices: 20012443--20012486 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
20012433 AAAAAAAATG
20012443 TTTTGAAATTGAATAAT
1 TTTTGAAATTGAATAAT
20012460 TATTTGTAAA-TGAATAAT
1 T-TTTG-AAATTGAATAAT
20012478 ATTTTGAAA
1 -TTTTGAAA
20012487 ACGAACGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (17 bp):
TTTTGAAATTGAATAAT
Found at i:20031321 original size:107 final size:106
Alignment explanation
Indices: 20031116--20031421 Score: 441
Period size: 107 Copynumber: 2.9 Consensus size: 106
20031106 AAGTTAAGAA
* *
20031116 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGTACATTCTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTC-CTCGAAT
* * ** *
20031181 TTCCAAACGCAAAACATTACCTCGTTTTGAAAGTTCAAAAAG
65 TTCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
* *
20031223 GATATTTGGCTATTTGGTCGAACGAGGAATCGAAACCCAGCACGTTAGGGCACACTTCCTCGATT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACA-TTCCTCGAAT
* *
20031288 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAG
65 TTCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
* * * * *
20031330 GATATTTGGCTATTTGGCCAAACGAGTAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC-ATTCCTCGAAT
20031395 TTCCAAACGCAAAATATTGCCTTATTT
65 TTCCAAACGCAAAATATTGCCTTATTT
20031422 AGAAAAAATT
Statistics
Matches: 179, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 176 0.98
108 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (106 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTCCTCGAATT
TCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
Found at i:20033523 original size:84 final size:84
Alignment explanation
Indices: 20033430--20033923 Score: 331
Period size: 84 Copynumber: 5.8 Consensus size: 84
20033420 CTTCTGTCTA
* *
20033430 CTCCACTACTGCTTAGGGAGATAAGACTTGGTGCTATCTGCTCCACTACTGCTTAGGGAGATAAA
1 CTCCACTACTGCTTAGGGAGATAAGACTTGCTGCTATCTGCTCCACTACTGCTTAGGGAGATAAG
* *
20033495 ATCTACAATCTTCGACCTA
66 ATCTACAATCTTCGATCTG
* * * * *
20033514 CTCCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGTGAGA
1 CTCCACTACTGCTTAGGGAGATAAGACTTG----CTGCTATCTGCTCCACTACTGCTTAGGGAGA
** *
20033579 TAAGA-CT-TGA--TGCGATCTG
62 TAAGATCTACAATCTTCGATCTG
* * * * * * *
20033598 CTCCACTACTGCTTAGGGAGATAAAATCTGTAAGCTTCGACCTACTCCACTACTGCTTAAGAAGA
1 CTCCACTACTGCTTAGGGAGATAAGA-CT-T--GCTGCTATCTGCTCCACTACTGCTTAGGGAGA
* ** * *
20033663 TAGGA-CTTGATTTCCTTTG-TCTG
62 TAAGATCTACA-AT-CTTCGATCTG
** * * * *
20033686 CTCTGCTACTGCTTAGGGAGATAAGACTTGATGCGATCTGCTCCACTGCTGCTTAAGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAGACTTGCTGCTATCTGCTCCACTACTGCTTAGGGAGATAAG
*
20033751 ATCTACAATCTTCGACCTG
66 ATCTACAATCTTCGATCTG
* * * * * * *
20033770 CTCCGCTAATGCTTAGCGAGATAGGAC-TGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGA
1 CTCCACTACTGCTTAGGGAGATAAGACTTGCT-GC-T--ATCTGCTCCACTACTGCTTAGGGAGA
** * *
20033834 TAAGAT-TCACCGTCTTCGATTTT
62 TAAGATCT-ACAATCTTCGATCTG
* ** *
20033857 CTCCACTACTGCTTAGGGAGATAGGATCTACCAT-CTTTGACCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGA-CTTGC-TGC--T-ATCTGCTCCACTACTGCTTAGGGAG
20033921 ATA
61 ATA
20033924 GGACTGGATA
Statistics
Matches: 318, Mismatches: 68, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
83 7 0.02
84 146 0.46
85 5 0.02
86 4 0.01
87 65 0.20
88 86 0.27
89 4 0.01
90 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (84 bp):
CTCCACTACTGCTTAGGGAGATAAGACTTGCTGCTATCTGCTCCACTACTGCTTAGGGAGATAAG
ATCTACAATCTTCGATCTG
Found at i:20033586 original size:128 final size:128
Alignment explanation
Indices: 20033324--20033928 Score: 695
Period size: 128 Copynumber: 4.7 Consensus size: 128
20033314 CAGGATTGGT
** **
20033324 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACGGT-TTTAATCC-GC
1 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGA-CCTGC
* * * *
20033387 TCCACT-GTAACTTCAGGAAGATAGGA-TTGGTTTCTTCTGTCTACTCCACTACTGCTTAGGGAG
65 TCCACTACT-GCTT-AGGAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAG
20033450 A
128 A
* * * *
20033451 TAAGACTTGGTGCTATCTGCTCCACTACTGCTTAGGGAGATAAAATCTACAATCTTCGACCTACT
1 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCT
*
20033516 CCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGTGAGA
66 CCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGA
* ** * *
20033579 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAAGCTTCGACCTACT
1 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCT
* **
20033644 CCACTACTGCTTAAGAAGATAGGACTTGATTTCCTT-TGTCTGCTCTGCTACTGCTTAGGGAGA
66 CCACTACTGCTTAGGAAGATAGGACTTGATTT-CTTCTGTCTGCTCCACTACTGCTTAGGGAGA
* *
20033707 TAAGACTTGATGCGATCTGCTCCACTGCTGCTTAAGGAGATAAGATCTACAATCTTCGACCTGCT
1 TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCT
* * * ** *** * *
20033772 CCGCTAATGCTTAGCG-AGATAGGAC-TGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGA
66 CCACTACTGCTTAG-GAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGA
* * * * * * *
20033834 TAAGA-TTCACCGTCTTCGATTTTCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGAC
1 TAAGACTT----G-ATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGAC
*
20033898 CTGCTCCACTACTGCTTAGGGAGATAGGACT
61 CTGCTCCACTACTGCTTAGGAAGATAGGACT
20033929 GGATAAGATG
Statistics
Matches: 412, Mismatches: 52, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
126 5 0.01
127 91 0.22
128 241 0.58
129 5 0.01
130 2 0.00
131 68 0.17
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (128 bp):
TAAGACTTGATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTGCT
CCACTACTGCTTAGGAAGATAGGACTTGATTTCTTCTGTCTGCTCCACTACTGCTTAGGGAGA
Found at i:20033716 original size:44 final size:45
Alignment explanation
Indices: 20033337--20033928 Score: 261
Period size: 44 Copynumber: 13.8 Consensus size: 45
20033327 GACTTGATGC
** *
20033337 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-TCT-A-CGGTTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGATTTGCTTT
* * * * * * *
20033380 AATCCGCTCCACT-GTAACTTCAGGAAGATAGGA-TTGGTTT-CTTCT
1 GATCTGCTCCACTACT-GCTT-AGGGAGATAAGACTTGATTTGCTT-T
* *
20033425 G-TCTACTCCACTACTGCTTAGGGAGATAAGACTTG--GTGC--T
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
* ** * *
20033465 -ATCTGCTCCACTACTGCTTAGGGAGATAAAATCTACA-AT-CTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATTTGCTTT
* * * *
20033508 GACCTACTCCACTACTGCTTAGGAAGATAGGACTTGATTT-CTTCT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTT-T
*
20033553 G-TCTGCTCCACTACTGCTTAGTGAGATAAGACTTGA--TGC---
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
* ** *
20033592 GATCTGCTCCACTACTGCTTAGGGAGATAA-AATCTG-TAAGCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGATTTGCTTT
* * * * * *
20033636 GACCTACTCCACTACTGCTTAAGAAGATAGGACTTGATTTCCTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
**
20033681 G-TCTGCTCTGCTACTGCTTAGGGAGATAAGACTTGA--TGC---
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
* * ** * *
20033720 GATCTGCTCCACTGCTGCTTAAGGAGATAAGATCTACA-AT-CTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGA-CTTGATTTGCTTT
* * * * * * * *
20033764 GACCTGCTCCGCTAATGCTTAGCGAGATAGGAC-TG-GTGGCTTA
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
* * * * ** *
20033807 AATCTGCTTCACTACTGCTTAGGAAGATAAGA-TTCA-CCGTCTTC
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTG-CTTT
* * * **
20033851 GATTTTCTCCACTACTGCTTAGGGAGATAGGA-TCT-ACCAT-CTTT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACT-TGA-TTTGCTTT
* *
20033895 GACCTGCTCCACTACTGCTTAGGGAGATAGGACT
1 GATCTGCTCCACTACTGCTTAGGGAGATAAGACT
20033929 GGATAAGATG
Statistics
Matches: 407, Mismatches: 101, Indels: 80
0.69 0.17 0.14
Matches are distributed among these distances:
39 4 0.01
40 84 0.21
41 9 0.02
42 7 0.02
43 60 0.15
44 231 0.57
45 12 0.03
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (45 bp):
GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATTTGCTTT
Found at i:20034276 original size:24 final size:24
Alignment explanation
Indices: 20034244--20034299 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
20034234 GATTGCCCCT
*
20034244 ACTGTAATCTTCAAAGTTTAA-TCC
1 ACTGTAATCTT-AAAGGTTAAGTCC
*
20034268 ACTGTAATCTTTAAGGTTAAGTCC
1 ACTGTAATCTTAAAGGTTAAGTCC
20034292 ACTGTAAT
1 ACTGTAAT
20034300 TTTGGGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (24 bp):
ACTGTAATCTTAAAGGTTAAGTCC
Found at i:20045773 original size:107 final size:106
Alignment explanation
Indices: 20045568--20045873 Score: 434
Period size: 107 Copynumber: 2.9 Consensus size: 106
20045558 AAGTTAAGAA
* *
20045568 GATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCA-CATTCTATCGAA
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAGC-TT-TCTCGAA
* ** *
20045632 TTTCCAAACGCAAAACATTGCCTCGTTTTGAAAGTTCAAAAAG
64 TTTCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
* *
20045675 GATATTTGGCTATTTGGTCGAACGAGGAATCGAAACCCAGCACGTTAGGGCAGGCTTTCTCGATT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCA-GCTTTCTCGAAT
* * *
20045740 TTCCAAACGCGAAATATTGTCTTATTTTAAAAGTTTAAAAAG
65 TTCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
* * * *
20045782 GATATTTGGCTATTTGGCCAAACGAGTAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGAAT
1 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCA-GCTTTCTCGAAT
20045847 TTCCAAACGCAAAATATTGCCTTATTT
65 TTCCAAACGCAAAATATTGCCTTATTT
20045874 AGAAAAAATT
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 175 0.98
108 2 0.01
109 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (106 bp):
GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAGCTTTCTCGAATT
TCCAAACGCAAAATATTGCCTTATTTTAAAAGTTCAAAAAG
Found at i:20049209 original size:37 final size:37
Alignment explanation
Indices: 20049159--20049235 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
20049149 CATTAGATTA
20049159 AGATAAGCAATAAGCAGAGAGGTGAAAAATATAAATC
1 AGATAAGCAATAAGCAGAGAGGTGAAAAATATAAATC
20049196 AGATAAGCAATAAGCAGAGAGGTGAAAAATATAAATC
1 AGATAAGCAATAAGCAGAGAGGTGAAAAATATAAATC
20049233 AGA
1 AGA
20049236 GGAGGGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.55, C:0.08, G:0.22, T:0.16
Consensus pattern (37 bp):
AGATAAGCAATAAGCAGAGAGGTGAAAAATATAAATC
Found at i:20050175 original size:33 final size:34
Alignment explanation
Indices: 20050123--20050187 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
20050113 ATTTACAAAT
**
20050123 TATAAAAAAATATTTTAAAAAATT-AAAAGAAAGA
1 TATAAAAAAATATCAT-AAAAATTCAAAAGAAAGA
20050157 TATAAAAAAAT-TCATAAAAATTCAAAAGAAA
1 TATAAAAAAATATCATAAAAATTCAAAAGAAA
20050188 TTAGCATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 7 0.25
33 10 0.36
34 11 0.39
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (34 bp):
TATAAAAAAATATCATAAAAATTCAAAAGAAAGA
Found at i:20055117 original size:21 final size:21
Alignment explanation
Indices: 20055082--20055121 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20055072 ATTTGTTCGT
20055082 AAAATGTGTAAAATACATGATG
1 AAAATGTGTAAAATA-ATGATG
*
20055104 AAAAT-TGTGAAATAATGA
1 AAAATGTGTAAAATAATGA
20055122 ATTGTATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAATGTGTAAAATAATGATG
Found at i:20055751 original size:26 final size:26
Alignment explanation
Indices: 20055690--20055752 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
20055680 TCTGACCCAT
* * *
20055690 AGCTCGTGTGAGCAGACCCATTTTAC
1 AGCTCGTGTGAACAAACCCATTTCAC
* *
20055716 AGCGCTTGTGAACAAACCCATTTCAC
1 AGCTCGTGTGAACAAACCCATTTCAC
20055742 AGCTCGTGTGA
1 AGCTCGTGTGA
20055753 GCAACGATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (26 bp):
AGCTCGTGTGAACAAACCCATTTCAC
Found at i:20066208 original size:37 final size:38
Alignment explanation
Indices: 20066139--20066211 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
20066129 ATGTGTGGAA
* * *
20066139 TTGAATTGAATATTGACTTGAAAATGACAAAGTGAATT
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
*
20066177 TTGAATTAAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAA
20066212 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (38 bp):
TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:20070669 original size:93 final size:92
Alignment explanation
Indices: 20070494--20070693 Score: 242
Period size: 93 Copynumber: 2.2 Consensus size: 92
20070484 TGCTAGTTTG
** * * *
20070494 CTCATAAGAGCAATTTCAACCGATAACACGCCAAATGCACATAGTGTAAAGCCCTTAGGCTAAAT
1 CTCATAAGAGTTATTTCAACCGATAACACGCCAAATACACATAGTGCAAAGCCCATAGGCTAAAT
*
20070559 ATTCTCCCTCAAGAACAC-GTCAGATTC
66 ATTCTCCCTCAAGAACACACT-AGATTC
* * *
20070586 CTCATAAGAGTTATTTCCAACTGATAACATGCCAGATACACATAGTGCAAAGCCCATAGGCTAAA
1 CTCATAAGAGTTATTT-CAACCGATAACACGCCAAATACACATAGTGCAAAGCCCATAGGCTAAA
** *
20070651 TATTCTCCC-CCCGTAACACACTAGATTG
65 TATTCTCCCTCAAG-AACACACTAGATTC
*
20070679 CTCATAAAAGTTATT
1 CTCATAAGAGTTATT
20070694 AACACACCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
92 16 0.17
93 75 0.82
94 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (92 bp):
CTCATAAGAGTTATTTCAACCGATAACACGCCAAATACACATAGTGCAAAGCCCATAGGCTAAAT
ATTCTCCCTCAAGAACACACTAGATTC
Found at i:20071821 original size:27 final size:27
Alignment explanation
Indices: 20071767--20071822 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
20071757 TACACCCAGT
* *
20071767 AAAATTTTGACGATTTTAATCCCGATA
1 AAAATTTTGACGATTTTAACCCCAATA
*
20071794 AAAATTTTGATGATTTT-ACCCCTAATA
1 AAAATTTTGACGATTTTAACCCC-AATA
20071821 AA
1 AA
20071823 GTTTTGAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (27 bp):
AAAATTTTGACGATTTTAACCCCAATA
Found at i:20071990 original size:6 final size:6
Alignment explanation
Indices: 20071974--20072038 Score: 112
Period size: 6 Copynumber: 10.8 Consensus size: 6
20071964 GCAAATGAAT
* *
20071974 CATTTC AATTTT CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
20072022 CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTT
20072039 TTTGGAAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.52
Consensus pattern (6 bp):
CATTTC
Found at i:20075276 original size:7 final size:8
Alignment explanation
Indices: 20075257--20075285 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
20075247 TTATATTTAT
20075257 TTTTTGAA
1 TTTTTGAA
20075265 TTTTTGAA
1 TTTTTGAA
20075273 TTTTTGAA
1 TTTTTGAA
20075281 TTTTT
1 TTTTT
20075286 CTAGTTTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (8 bp):
TTTTTGAA
Found at i:20078607 original size:64 final size:63
Alignment explanation
Indices: 20078506--20078632 Score: 218
Period size: 64 Copynumber: 2.0 Consensus size: 63
20078496 ATAGAGCTCA
* *
20078506 ATCAAAAGATTGCACAATAAACAATAATTTTCGTGTCTAATAAAAATAAATAATACTCTTCAGG
1 ATCAAAAGATTGCACAATAAACAATAATCTTCATGTCTAA-AAAAATAAATAATACTCTTCAGG
*
20078570 ATCAAAAGATTGCACAATAAACAATAATCTTCATGTCTAAAAAAATAAATAGTACTCTTCAGG
1 ATCAAAAGATTGCACAATAAACAATAATCTTCATGTCTAAAAAAATAAATAATACTCTTCAGG
20078633 TCTAAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 22 0.37
64 38 0.63
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.28
Consensus pattern (63 bp):
ATCAAAAGATTGCACAATAAACAATAATCTTCATGTCTAAAAAAATAAATAATACTCTTCAGG
Found at i:20078617 original size:28 final size:28
Alignment explanation
Indices: 20078585--20078642 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
20078575 AAGATTGCAC
*
20078585 AATAAACAATAATCTTCATGTCTAAAAA
1 AATAAACAATAATCTTCAGGTCTAAAAA
* * *
20078613 AATAAATAGTACTCTTCAGGTCTAAAAA
1 AATAAACAATAATCTTCAGGTCTAAAAA
20078641 AA
1 AA
20078643 GAACTGGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (28 bp):
AATAAACAATAATCTTCAGGTCTAAAAA
Found at i:20080552 original size:1 final size:1
Alignment explanation
Indices: 20080546--20080573 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
20080536 CTGCAAAATC
20080546 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
20080574 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20083106 original size:20 final size:20
Alignment explanation
Indices: 20083070--20083108 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20083060 CAGAAATCTC
*
20083070 TCTTTTCTCTCTGTTCTTCT
1 TCTTTTCTCTCTCTTCTTCT
20083090 TCTTTTCTCTAC-CTTCTTC
1 TCTTTTCTCT-CTCTTCTTC
20083109 CTATCTCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (20 bp):
TCTTTTCTCTCTCTTCTTCT
Found at i:20089228 original size:61 final size:61
Alignment explanation
Indices: 20089150--20089267 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 61
20089140 TAAAAGAAAT
* * * * *
20089150 AATAAATTGAGCTCTTAATATTTACAAAA-TTGATCATTTTATTTCTAATTCTAAAAAATTC
1 AATAAATTGAGCCCTTAATATTTACAAAACCT-ATCAATTTATTCCTAACTCTAAAAAATTC
20089211 AATAAATTTG-GCCCTTAATATTTACAAAACCTATCAATTTATTCCTAACTCTAAAAA
1 AATAAA-TTGAGCCCTTAATATTTACAAAACCTATCAATTTATTCCTAACTCTAAAAA
20089268 TTAAAAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 46 0.92
62 4 0.08
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (61 bp):
AATAAATTGAGCCCTTAATATTTACAAAACCTATCAATTTATTCCTAACTCTAAAAAATTC
Found at i:20099030 original size:29 final size:29
Alignment explanation
Indices: 20098985--20099043 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
20098975 TAAAACACTC
*
20098985 AACCCATCTCATAAAAATTA-TTTCTTTAG
1 AACCCATCCCATAAAAATTAGTTT-TTTAG
*
20099014 AACCCATCCCATCAAAATTAGTTTTTTAG
1 AACCCATCCCATAAAAATTAGTTTTTTAG
20099043 A
1 A
20099044 TATTATCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (29 bp):
AACCCATCCCATAAAAATTAGTTTTTTAG
Found at i:20099139 original size:17 final size:17
Alignment explanation
Indices: 20099107--20099140 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20099097 CTAAAATCCT
20099107 AAACACTTAAAATTAAA
1 AAACACTTAAAATTAAA
20099124 AAAC-CTTAAAACTTAAA
1 AAACACTTAAAA-TTAAA
20099141 TATTAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (17 bp):
AAACACTTAAAATTAAA
Found at i:20101353 original size:38 final size:38
Alignment explanation
Indices: 20101310--20101395 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
20101300 GGATTGGTTG
*
20101310 GAAATGGTTATCTACAGGCTCTTCA-AAGTGACACCATCA
1 GAAATGGTTATATACAGGCTCTTCAGAA-TGACACCAT-A
20101349 -AAATGGTTATATACAGGCTCTTCAGAATGACACCATA
1 GAAATGGTTATATACAGGCTCTTCAGAATGACACCATA
20101386 GAAATGGTTA
1 GAAATGGTTA
20101396 CCTATAAGCT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
37 1 0.02
38 41 0.93
39 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (38 bp):
GAAATGGTTATATACAGGCTCTTCAGAATGACACCATA
Found at i:20117411 original size:134 final size:133
Alignment explanation
Indices: 20117165--20117433 Score: 441
Period size: 134 Copynumber: 2.0 Consensus size: 133
20117155 AATAAAATGG
*
20117165 ATAAATTAGTTTATGTATGTTAGATTAAAGAGCAAATTAAAATTTTTTGTTAAAAAGTTTATCAA
1 ATAAATTAGTTTATGTATGTTAGATTAAAGAGCAAATTAAAATTTTTTGCTAAAAAGTTTATCAA
* *
20117230 ATTGTACTGTTAAAAATTGGCGTGATTGATGGTATAATCGGCTAGTGATGTGATGTGCCATGTGT
66 ATTATACTGTTAAAAATTGGCGTGATTGATGGTATAATCGGCCAGTGATGTGATGTGCC--GTGT
20117295 ATTTT
129 ATTTT
* * *
20117300 ATAAATTAGTTTATGTTTGTTAGATTAAAGAGCAAATT-AATTTTTTTGCTAAAAAGTTTATGAA
1 ATAAATTAGTTTATGTATGTTAGATTAAAGAGCAAATTAAAATTTTTTGCTAAAAAGTTTATCAA
* *
20117364 ATTATACTGTTAAAAATTGGTGTGATTGATGGTATAATCGGCCAGTGATGTGATGTGTCGTGTAT
66 ATTATACTGTTAAAAATTGGCGTGATTGATGGTATAATCGGCCAGTGATGTGATGTGCCGTGTAT
20117429 TTT
131 TTT
20117432 AT
1 AT
20117434 GTTGATATAT
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
132 11 0.09
134 78 0.62
135 37 0.29
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.42
Consensus pattern (133 bp):
ATAAATTAGTTTATGTATGTTAGATTAAAGAGCAAATTAAAATTTTTTGCTAAAAAGTTTATCAA
ATTATACTGTTAAAAATTGGCGTGATTGATGGTATAATCGGCCAGTGATGTGATGTGCCGTGTAT
TTT
Found at i:20118196 original size:31 final size:31
Alignment explanation
Indices: 20118158--20118217 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20118148 CAACCTAGTG
**
20118158 ACTTAAATAAAAATATTTGAATAATTCAATA
1 ACTTAAATAAAAATATTCAAATAATTCAATA
20118189 ACTTAAATAAAAATATTCAAATAATTCAA
1 ACTTAAATAAAAATATTCAAATAATTCAA
20118218 CGACTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (31 bp):
ACTTAAATAAAAATATTCAAATAATTCAATA
Found at i:20120467 original size:16 final size:15
Alignment explanation
Indices: 20120435--20120476 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
20120425 ATAAAGGATT
20120435 TAATTGAAGT-G-CA
1 TAATTGAAGTAGACA
20120448 TAATTGAAGTAGAACA
1 TAATTGAAGTAG-ACA
*
20120464 TAATTGGAGTAGA
1 TAATTGAAGTAGA
20120477 GGTCCTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 1 0.04
16 13 0.52
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.29
Consensus pattern (15 bp):
TAATTGAAGTAGACA
Found at i:20125863 original size:14 final size:14
Alignment explanation
Indices: 20125844--20125871 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20125834 TAAAAGTTAA
20125844 TTTAATAATTCATT
1 TTTAATAATTCATT
20125858 TTTAATAATTCATT
1 TTTAATAATTCATT
20125872 AATAAATTGG
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:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:20126342 original size:19 final size:19
Alignment explanation
Indices: 20126320--20126357 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20126310 TCAATCATCC
20126320 CTCATCTCATCA-TCTCTCA
1 CTCAT-TCATCATTCTCTCA
20126339 CTCATTCATCATTCTCTCA
1 CTCATTCATCATTCTCTCA
20126358 ACTCTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATTCATCATTCTCTCA
Found at i:20135702 original size:39 final size:39
Alignment explanation
Indices: 20135648--20135726 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
20135638 CTACATTATA
20135648 AGCCAGTACCATCTTTTTAAAATTATCCTAATTTTTTGC
1 AGCCAGTACCATCTTTTTAAAATTATCCTAATTTTTTGC
20135687 AGCCAGTACCATCTTTTTAAAATTATCCTAATTTTTTGC
1 AGCCAGTACCATCTTTTTAAAATTATCCTAATTTTTTGC
20135726 A
1 A
20135727 CCTATCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (39 bp):
AGCCAGTACCATCTTTTTAAAATTATCCTAATTTTTTGC
Found at i:20135861 original size:3 final size:3
Alignment explanation
Indices: 20135853--20135941 Score: 178
Period size: 3 Copynumber: 29.7 Consensus size: 3
20135843 TCAAGAGCTT
20135853 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
20135901 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
20135942 AGAAAGAGTG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:20146565 original size:19 final size:19
Alignment explanation
Indices: 20146541--20146581 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
20146531 AAGTTATAAG
20146541 TATGTGATAGTTATGCATA
1 TATGTGATAGTTATGCATA
20146560 TATGTGATAGTTATGCATA
1 TATGTGATAGTTATGCATA
20146579 TAT
1 TAT
20146582 AGACATGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (19 bp):
TATGTGATAGTTATGCATA
Found at i:20151059 original size:17 final size:18
Alignment explanation
Indices: 20151027--20151061 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20151017 CTATGATGTT
*
20151027 CGCCTGTGTGGGCCCACA
1 CGCCTATGTGGGCCCACA
20151045 CGCCTATGT-GGCCCACA
1 CGCCTATGTGGGCCCACA
20151062 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.40, G:0.29, T:0.17
Consensus pattern (18 bp):
CGCCTATGTGGGCCCACA
Found at i:20156312 original size:25 final size:25
Alignment explanation
Indices: 20156253--20156314 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
20156243 TATAGTCTAT
* * *
20156253 CTATAGTAGTCTCAGTATATACTAC
1 CTATAGCAGTTTCAGGATATACTAC
20156278 CTATAGCAGTTTCAGGATATACTA-
1 CTATAGCAGTTTCAGGATATACTAC
*
20156302 TTATAGACAGTTT
1 CTATAG-CAGTTT
20156315 TAGCTTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (25 bp):
CTATAGCAGTTTCAGGATATACTAC
Found at i:20156654 original size:18 final size:19
Alignment explanation
Indices: 20156631--20156679 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
20156621 AATCATGTCG
20156631 TTCATTTCAAAAAT-ATTA
1 TTCATTTCAAAAATCATTA
* *
20156649 TTCATTT-ACAAATCGTTA
1 TTCATTTCAAAAATCATTA
20156667 TTCAATTTCAAAA
1 TTC-ATTTCAAAA
20156680 TGTTTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 5 0.20
18 13 0.52
19 4 0.16
20 3 0.12
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (19 bp):
TTCATTTCAAAAATCATTA
Found at i:20159340 original size:25 final size:29
Alignment explanation
Indices: 20159292--20159355 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
20159282 AGATGGCTAT
*
20159292 TTTTTTATGTTCATGTTCATACCA-A-TT-G
1 TTTTTT-T-TTCATGTTCACACCATATTTAG
20159320 TTTTTTTTTCA-GTTCACACCATATTTAG
1 TTTTTTTTTCATGTTCACACCATATTTAG
20159348 TTTTTTTT
1 TTTTTTTT
20159356 AAGTTTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.28
26 5 0.16
27 3 0.09
28 15 0.47
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.59
Consensus pattern (29 bp):
TTTTTTTTTCATGTTCACACCATATTTAG
Found at i:20168772 original size:27 final size:27
Alignment explanation
Indices: 20168741--20168793 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
20168731 TAAAAGCAGC
*
20168741 TAAAATAAAAGTTTTTCATTTAATTTT
1 TAAAATAAAAGTTTTTAATTTAATTTT
20168768 TAAAATAAAAGTTTTTAATTTAATTT
1 TAAAATAAAAGTTTTTAATTTAATTT
20168794 AATTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
TAAAATAAAAGTTTTTAATTTAATTTT
Found at i:20169654 original size:25 final size:26
Alignment explanation
Indices: 20169600--20169655 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
20169590 TTTCTCCTAA
* *
20169600 ATTTTAATTTTATTTAATTATTTGAT
1 ATTTTAATTTTATTAAATTATTTCAT
20169626 -TTTTCAA-TTTATTAAATTA-TTCAT
1 ATTTT-AATTTTATTAAATTATTTCAT
20169650 ATTTTA
1 ATTTTA
20169656 TGCAAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
24 5 0.19
25 19 0.73
26 2 0.08
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTAATTTTATTAAATTATTTCAT
Found at i:20174864 original size:25 final size:25
Alignment explanation
Indices: 20174836--20174893 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
20174826 ATGCTCATTT
* * *
20174836 GAGCTGTAGATCGGTATGCTCTCAC
1 GAGCTATAAATCGATATGCTCTCAC
*
20174861 GAGCTATAAATCGATATTCTCTCAC
1 GAGCTATAAATCGATATGCTCTCAC
*
20174886 GAGATATA
1 GAGCTATA
20174894 GAGCATCCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (25 bp):
GAGCTATAAATCGATATGCTCTCAC
Found at i:20179366 original size:75 final size:75
Alignment explanation
Indices: 20179077--20179359 Score: 359
Period size: 75 Copynumber: 3.8 Consensus size: 75
20179067 CGTTGGGCGT
* * *
20179077 AACTTTCATCAGTTTATCTGACTAGTGCTAGGCACACCATTATATTTGTTGGTTTATCCGATTAG
1 AACTTTCATCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTCGGTTTATCCGACTAG
* *
20179142 CGCTGGGTGC
66 CGCTAGGAGC
* * *
20179152 AATTTTCTTCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTTGGTTTATCCGACTAG
1 AACTTTCATCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTCGGTTTATCCGACTAG
* *
20179217 CGTTAGGCGC
66 CGCTAGGAGC
* * * * * * *
20179227 AACTTTCATTAGTTTATCTGACTAATGTTGCGCACAACATTTTATCTGTCGGTTTATCCGACTAG
1 AACTTTCATCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTCGGTTTATCCGACTAG
*
20179292 CACTAGGAGC
66 CGCTAGGAGC
* * * * *
20179302 AACTTTCATCAATTTATCTTACTAGTGTTGGGCACATCATTATATATGTCGGTTTATC
1 AACTTTCATCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTCGGTTTATC
20179360 TAACTAGTGC
Statistics
Matches: 180, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 180 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (75 bp):
AACTTTCATCAGTTTATCTGACTAGTGCTGGGCACACCATTATATTTGTCGGTTTATCCGACTAG
CGCTAGGAGC
Found at i:20179366 original size:150 final size:149
Alignment explanation
Indices: 20179044--20179366 Score: 396
Period size: 150 Copynumber: 2.2 Consensus size: 149
20179034 TGTATAATGA
* * * * *
20179044 ATATTGTCAGTTTATCTTACTAGCGTTGGGCGTAACTTTCATCAGTTTATCTGACTAGTGCTAGG
1 ATATTGTCGGTTTATCTAACTAGCGTTAGGCGCAACTTTCATCAGTTTATCTGACTAATGCTAGG
* * * * * * * * * *
20179109 CACACCATTATATTTGTTGGTTTATCCGATTAGCGCTGGGTGCAATTTTCTTCAGTTTATCTGAC
66 CACAACATTATATCTGTCGGTTTATCCGACTAGCACTAGGAGCAACTTTCATCAATTTATCTGAC
20179174 TAGTGCTGGGCACACCATT
131 TAGTGCTGGGCACACCATT
* ** * *
20179193 ATATTTGTTGGTTTATCCGACTAGCGTTAGGCGCAACTTTCATTAGTTTATCTGACTAATG-TTG
1 ATA-TTGTCGGTTTATCTAACTAGCGTTAGGCGCAACTTTCATCAGTTTATCTGACTAATGCTAG
* *
20179257 CGCACAACATTTTATCTGTCGGTTTATCCGACTAGCACTAGGAGCAACTTTCATCAATTTATCTT
65 -GCACAACATTATATCTGTCGGTTTATCCGACTAGCACTAGGAGCAACTTTCATCAATTTATCTG
* *
20179322 ACTAGTGTTGGGCACATCATT
129 ACTAGTGCTGGGCACACCATT
20179343 ATATATGTCGGTTTATCTAACTAG
1 ATAT-TGTCGGTTTATCTAACTAG
20179367 TGCAGGGTGT
Statistics
Matches: 145, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
149 6 0.04
150 139 0.96
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (149 bp):
ATATTGTCGGTTTATCTAACTAGCGTTAGGCGCAACTTTCATCAGTTTATCTGACTAATGCTAGG
CACAACATTATATCTGTCGGTTTATCCGACTAGCACTAGGAGCAACTTTCATCAATTTATCTGAC
TAGTGCTGGGCACACCATT
Found at i:20184861 original size:67 final size:66
Alignment explanation
Indices: 20184728--20184861 Score: 198
Period size: 67 Copynumber: 2.0 Consensus size: 66
20184718 TTAACAAAAA
20184728 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTTCTTCAAAAAACATGGTTGCTGCCAT
1 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTTCTTCAAAAAACATGGTTGCT-CCAT
20184793 TT
65 TT
* * * *
20184795 TTTTTCTCTCATTTTCTCTCTTTCCAAACACCATTTTTCTTCTTCAAAACATATGGTTGGCT-CA
1 TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTT-TTCTTCAAAAAACATGGTT-GCTCCA
20184859 TTT
64 TTT
20184862 CATCTACAAG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
67 41 0.67
68 17 0.28
69 3 0.05
ACGTcount: A:0.20, C:0.26, G:0.07, T:0.47
Consensus pattern (66 bp):
TTTTTCTCTCATTTTCTCTCTTGCCAAACACCACTTTTTTCTTCAAAAAACATGGTTGCTCCATT
T
Found at i:20198413 original size:162 final size:164
Alignment explanation
Indices: 20198144--20198469 Score: 629
Period size: 162 Copynumber: 2.0 Consensus size: 164
20198134 ATAATCGTTT
*
20198144 TATTTTTCTTTTATAAACAACCAAGGCTAATGTGAAGAAGCTAAAAAAAAAAAAAAAGCTTACAG
1 TATTTTTCTTTTAAAAACAACCAAGGCTAATGTGAAGAAGCTAAAAAAAAAAAAAAAGCTTACAG
20198209 AACCGAGAAAAAGATAAACAAGAATAGCCTAGCGAAAGCTAAATGTATCTGATACTGTTAGCCGC
66 AACCGAGAAAAAGATAAACAAGAATAGCCTAGCGAAAGCTAAATGTATCTGATACTGTTAGCCGC
20198274 CACTCTTGTTTCGAATGAAGTTTTGTGAAGGTTA
131 CACTCTTGTTTCGAATGAAGTTTTGTGAAGGTTA
20198308 TATTTTTC-TTTAAAAACAACCAAGGCTAATGTGAAGAAGCT-AAAAAAAAAAAAAAGCTTACAG
1 TATTTTTCTTTTAAAAACAACCAAGGCTAATGTGAAGAAGCTAAAAAAAAAAAAAAAGCTTACAG
20198371 AACCGAGAAAAAGATAAACAAGAATAGCCTAGCGAAAGCTAAATGTATCTGATACTGTTAGCCGC
66 AACCGAGAAAAAGATAAACAAGAATAGCCTAGCGAAAGCTAAATGTATCTGATACTGTTAGCCGC
20198436 CACTCTTGTTTCGAATGAAGTTTTGTGAAGGTTA
131 CACTCTTGTTTCGAATGAAGTTTTGTGAAGGTTA
20198470 AAAGTTGATG
Statistics
Matches: 161, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
162 121 0.75
163 32 0.20
164 8 0.05
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (164 bp):
TATTTTTCTTTTAAAAACAACCAAGGCTAATGTGAAGAAGCTAAAAAAAAAAAAAAAGCTTACAG
AACCGAGAAAAAGATAAACAAGAATAGCCTAGCGAAAGCTAAATGTATCTGATACTGTTAGCCGC
CACTCTTGTTTCGAATGAAGTTTTGTGAAGGTTA
Found at i:20201306 original size:14 final size:14
Alignment explanation
Indices: 20201287--20201324 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
20201277 AGATAATTAT
20201287 TAGATTAAATTTAA
1 TAGATTAAATTTAA
20201301 TAGATTAAATTTAA
1 TAGATTAAATTTAA
20201315 T--ATTAAATTT
1 TAGATTAAATTT
20201325 TATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
TAGATTAAATTTAA
Found at i:20201421 original size:25 final size:25
Alignment explanation
Indices: 20201367--20201421 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
20201357 AAACATTAAA
*
20201367 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
20201392 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
20201416 TATTAA
1 T-TTAA
20201422 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:20201467 original size:37 final size:36
Alignment explanation
Indices: 20201398--20201469 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
20201388 TCACTTTAAT
*
20201398 ATTAAATTAATAAAATACTATTAAGATAAGTATTAC
1 ATTAAATTAATAAAATACTATTAAAATAAGTATTAC
20201434 ATTAAATTTAATATTAAATA-TATTAAAAT-AGTATTA
1 ATTAAA-TTAATA--AAATACTATTAAAATAAGTATTA
20201470 GTTTTGGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 6 0.19
37 13 0.41
38 8 0.25
39 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (36 bp):
ATTAAATTAATAAAATACTATTAAAATAAGTATTAC
Found at i:20207732 original size:40 final size:38
Alignment explanation
Indices: 20207688--20207764 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
20207678 TTAAAATTAT
* * *
20207688 TTATATTAAAAAAATTACCATAAATATAATAAATATTTTA
1 TTATATGAAAAAAA-TA-AATAAATATAATAAAGATTTTA
*
20207728 TTATATGAAAAACATAAATAAATATAATAAAGATTTT
1 TTATATGAAAAAAATAAATAAATATAATAAAGATTTT
20207765 TATTNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 19 0.58
39 2 0.06
40 12 0.36
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (38 bp):
TTATATGAAAAAAATAAATAAATATAATAAAGATTTTA
Found at i:20235703 original size:12 final size:12
Alignment explanation
Indices: 20235663--20235712 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
20235653 TAAGTCTAAG
20235663 AAAATAACAATA
1 AAAATAACAATA
*
20235675 AAAAGAAC--TA
1 AAAATAACAATA
20235685 AAAATAACAATA
1 AAAATAACAATA
*
20235697 AACATAA-ACATA
1 AAAATAACA-ATA
20235709 AAAA
1 AAAA
20235713 AAGAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
12 21 0.68
ACGTcount: A:0.74, C:0.10, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:20236400 original size:13 final size:13
Alignment explanation
Indices: 20236382--20236407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20236372 ATGCCCATGT
20236382 GCTAGTTCCAACG
1 GCTAGTTCCAACG
20236395 GCTAGTTCCAACG
1 GCTAGTTCCAACG
20236408 AAAATATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
GCTAGTTCCAACG
Found at i:20237065 original size:24 final size:24
Alignment explanation
Indices: 20237020--20237072 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
20237010 TCCAAGCTGT
20237020 ATAATGGGAAGCTCATAAGAGCC-
1 ATAATGGGAAGCTCATAAGAGCCA
* **
20237043 ATAATCGGGAAGCTTATGCGAGCCA
1 ATAAT-GGGAAGCTCATAAGAGCCA
20237068 ATAAT
1 ATAAT
20237073 AGGTAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 15 0.60
25 5 0.20
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (24 bp):
ATAATGGGAAGCTCATAAGAGCCA
Found at i:20237194 original size:26 final size:25
Alignment explanation
Indices: 20237158--20237240 Score: 103
Period size: 26 Copynumber: 3.2 Consensus size: 25
20237148 AAAGCACCGG
* *
20237158 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCTTTAAT-GGGAAGCTCACAA
20237184 AGAGCCTTTAATTGGGAAGCTCACAA
1 AGAGCCTTTAA-TGGGAAGCTCACAA
* *
20237210 AGAGCCATATAATGGGACGCTCACAA
1 AGAGCC-TTTAATGGGAAGCTCACAA
20237236 AGAGC
1 AGAGC
20237241 TGCGGTATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 46 0.90
27 5 0.10
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (25 bp):
AGAGCCTTTAATGGGAAGCTCACAA
Found at i:20239970 original size:21 final size:21
Alignment explanation
Indices: 20239946--20240001 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
20239936 GAAAATACAT
*
20239946 AAGAAATAATATAATAACTAA
1 AAGAAATAAAATAATAACTAA
* *
20239967 AAGAAATAAAATAA-CAGTAA
1 AAGAAATAAAATAATAACTAA
20239987 AA-AAATAAAATAATA
1 AAGAAATAAAATAATA
20240002 TGAAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.20
Consensus pattern (21 bp):
AAGAAATAAAATAATAACTAA
Found at i:20239979 original size:18 final size:18
Alignment explanation
Indices: 20239932--20240034 Score: 72
Period size: 18 Copynumber: 5.7 Consensus size: 18
20239922 AGTTAAAATT
*
20239932 AAAAGAAAAT-ACATAAGA
1 AAAATAAAATAACATAA-A
*
20239950 AATAATATAATAAC-TAAA
1 AA-AATAAAATAACATAAA
20239968 AGAAATAAAATAACAGTAAA
1 A-AAATAAAATAACA-TAAA
* *
20239988 AAAATAAAATAATAT-GA
1 AAAATAAAATAACATAAA
*
20240005 AAAATAAATACTAA-A-AAC
1 AAAATAAA-A-TAACATAAA
20240023 AAAATAAAATAA
1 AAAATAAAATAA
20240035 GGACAAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
16 3 0.04
17 10 0.14
18 25 0.36
19 25 0.36
20 7 0.10
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATAAAATAACATAAA
Found at i:20240042 original size:16 final size:16
Alignment explanation
Indices: 20240021--20240051 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20240011 AATACTAAAA
20240021 ACAAAATAAAATAAGG
1 ACAAAATAAAATAAGG
20240037 ACAAAATAAAATAAG
1 ACAAAATAAAATAAG
20240052 TCAGAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (16 bp):
ACAAAATAAAATAAGG
Found at i:20248510 original size:13 final size:13
Alignment explanation
Indices: 20248458--20248510 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
20248448 ATAGTAACGA
*
20248458 ATAAATGAAGAAG
1 ATAAATTAAGAAG
20248471 ATAAATTAAGAA-
1 ATAAATTAAGAAG
*
20248483 ATAAAAAAATAAGAAG
1 AT---AAATTAAGAAG
20248499 ATAAATTAAGAA
1 ATAAATTAAGAA
20248511 ATTTTTTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
12 2 0.06
13 20 0.61
15 9 0.27
16 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (13 bp):
ATAAATTAAGAAG
Found at i:20252582 original size:3 final size:3
Alignment explanation
Indices: 20252574--20252622 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
20252564 AATTTTGTTA
20252574 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20252622 T
1 T
20252623 TGTGTCTGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20253056 original size:3 final size:3
Alignment explanation
Indices: 20253048--20253079 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20253038 NNNNNNNNNN
20253048 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20253080 TGTGTCTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20255391 original size:16 final size:17
Alignment explanation
Indices: 20255357--20255392 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20255347 GTTTGCTTCT
*
20255357 CTGCTGTTTGTTGTGGG
1 CTGCTGTTGGTTGTGGG
20255374 CTGCTGTTGGTT-TGGG
1 CTGCTGTTGGTTGTGGG
20255390 CTG
1 CTG
20255393 GGTTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.00, C:0.14, G:0.42, T:0.44
Consensus pattern (17 bp):
CTGCTGTTGGTTGTGGG
Found at i:20256018 original size:138 final size:138
Alignment explanation
Indices: 20255860--20256127 Score: 394
Period size: 138 Copynumber: 1.9 Consensus size: 138
20255850 TTCAATATGA
* * * * *
20255860 TCTGCTCTACTGCGACTTCAGAGAGATAAGA-TCTGTTATGGTAGATTTAATCCGACCTACTGCA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACT-TGTTATGGTACATTTAATCCGACCGACTACA
* * * *
20255924 ACTTCAGAGGTATAGGATTCATCGTTTTAATTCGCTCCATTGCAACTTCAGGGAGATAGGATTAG
65 ACTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAAATAGGATTAG
20255989 TAGCTTCAG
130 TAGCTTCAG
* * *
20255998 TCTGCTCCACTGCAATTTCAGGGAGATAAGACTTGTTATGGTACATTTGATCCGACCGACTACAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTTATGGTACATTTAATCCGACCGACTACAA
* *
20256063 CTTTAGAGGTATAGGATTCATCATTTTAATCCGCTCCGCTGCAACTTCAGGGAAATAGGATTAGT
66 CTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAAATAGGATTAGT
20256128 GGTTTCACTG
Statistics
Matches: 115, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 114 0.99
139 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (138 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTTATGGTACATTTAATCCGACCGACTACAA
CTTCAGAGGTATAGGATTCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAAATAGGATTAGT
AGCTTCAG
Found at i:20269197 original size:28 final size:28
Alignment explanation
Indices: 20269145--20269198 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
20269135 AACGTGCGGT
* * * *
20269145 GCTGGGGCATTGGGTAGAGGTGTGCAGC
1 GCTGAGGCATTGGGCAAAGGCGTGCAGC
20269173 GCTGAGGCATTGGGCAAAGGCGTGCA
1 GCTGAGGCATTGGGCAAAGGCGTGCA
20269199 ACGCCTTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.46, T:0.19
Consensus pattern (28 bp):
GCTGAGGCATTGGGCAAAGGCGTGCAGC
Found at i:20269253 original size:16 final size:17
Alignment explanation
Indices: 20269219--20269253 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20269209 GTTTGCTTCT
*
20269219 CTGCTGTTTGTTGTGGG
1 CTGCTGTTGGTTGTGGG
20269236 CTGCTGTTGGTT-TGGG
1 CTGCTGTTGGTTGTGGG
20269252 CT
1 CT
20269254 AGGGTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.00, C:0.14, G:0.40, T:0.46
Consensus pattern (17 bp):
CTGCTGTTGGTTGTGGG
Found at i:20269270 original size:18 final size:18
Alignment explanation
Indices: 20269247--20269294 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
20269237 TGCTGTTGGT
20269247 TTGGGCTAGGGTTATTAA
1 TTGGGCTAGGGTTATTAA
* **
20269265 TTGGGCTTGGGTTATTGT
1 TTGGGCTAGGGTTATTAA
20269283 TTGGGCTAGGGT
1 TTGGGCTAGGGT
20269295 AACAATTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.06, G:0.40, T:0.42
Consensus pattern (18 bp):
TTGGGCTAGGGTTATTAA
Found at i:20269913 original size:28 final size:28
Alignment explanation
Indices: 20269861--20269914 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
20269851 AACGTGCGGT
* * * *
20269861 GCTGGGGCATTGGGTAGAGGTGTGCAGC
1 GCTGAGGCATTGGGCAAAGGCGTGCAGC
20269889 GCTGAGGCATTGGGCAAAGGCGTGCA
1 GCTGAGGCATTGGGCAAAGGCGTGCA
20269915 ACGCCTTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.46, T:0.19
Consensus pattern (28 bp):
GCTGAGGCATTGGGCAAAGGCGTGCAGC
Found at i:20269967 original size:716 final size:716
Alignment explanation
Indices: 20268594--20270025 Score: 2839
Period size: 716 Copynumber: 2.0 Consensus size: 716
20268584 GAAAAGAAAG
20268594 AAAAAAGTTGCAAACCCTATTTCTTAAAAATATAGAGGGCCTTCAAATTTCTCTCTCGCAACCCC
1 AAAAAAGTTGCAAACCCTATTTCTTAAAAATATAGAGGGCCTTCAAATTTCTCTCTCGCAACCCC
20268659 CCAAATTCGGCTGATTGGGCCGCCGTCTGCACAGTCGTGGCTGATGGCCGGCGTCGAGCAATGAC
66 CCAAATTCGGCTGATTGGGCCGCCGTCTGCACAGTCGTGGCTGATGGCCGGCGTCGAGCAATGAC
20268724 GTTTCTGATCAGCGCGTTGAAACGCGTTCAAAGGCCAAAACTTTAGAACAGGGAAACAAGGAGAA
131 GTTTCTGATCAGCGCGTTGAAACGCGTTCAAAGGCCAAAACTTTAGAACAGGGAAACAAGGAGAA
20268789 AAAAAAGGTCCTAGGCTTTTCCTTTTTATTTCCTTGCTGATTATTTTAAAATAGGTTTGTAAAAA
196 AAAAAAGGTCCTAGGCTTTTCCTTTTTATTTCCTTGCTGATTATTTTAAAATAGGTTTGTAAAAA
20268854 ATAAATGAATAAATAAATAAAAAGAAAAACAAAGAGAAAACAGTTAAAATCAACCTTTTAAAATT
261 ATAAATGAATAAATAAATAAAAAGAAAAACAAAGAGAAAACAGTTAAAATCAACCTTTTAAAATT
20268919 TCATTTTCTACTTTCCGATTTACTATTGTGCGTAAAAACTTTACAAAGATAAGATCTAGGCCTTT
326 TCATTTTCTACTTTCCGATTTACTATTGTGCGTAAAAACTTTACAAAGATAAGATCTAGGCCTTT
20268984 ATAGACGGATACAACTACTAATTTTTTTTTCTTTATCTGCCTATATTTACTGCCATTACTGTTAG
391 ATAGACGGATACAACTACTAATTTTTTTTTCTTTATCTGCCTATATTTACTGCCATTACTGTTAG
20269049 CATGTTTCTTCGTTGTTGCATTCAATTCTTTGCAAGGGTTTCGAGGCCCACGGTGGTGGCAGAGG
456 CATGTTTCTTCGTTGTTGCATTCAATTCTTTGCAAGGGTTTCGAGGCCCACGGTGGTGGCAGAGG
20269114 CATGCGCGAGGGGGCTGGTAGAACGTGCGGTGCTGGGGCATTGGGTAGAGGTGTGCAGCGCTGAG
521 CATGCGCGAGGGGGCTGGTAGAACGTGCGGTGCTGGGGCATTGGGTAGAGGTGTGCAGCGCTGAG
20269179 GCATTGGGCAAAGGCGTGCAACGCCTTAGGGTTTGCTTCTCTGCTGTTTGTTGTGGGCTGCTGTT
586 GCATTGGGCAAAGGCGTGCAACGCCTTAGGGTTTGCTTCTCTGCTGTTTGTTGTGGGCTGCTGTT
20269244 GGTTTGGGCTAGGGTTATTAATTGGGCTTGGGTTATTGTTTGGGCTAGGGTAACAATTAGGTTAG
651 GGTTTGGGCTAGGGTTATTAATTGGGCTTGGGTTATTGTTTGGGCTAGGGTAACAATTAGGTTAG
20269309 T
716 T
20269310 AAAAAAGTTGCAAACCCTATTTCTTAAAAATATAGAGGGCCTTCAAATTTCTCTCTCGCAACCCC
1 AAAAAAGTTGCAAACCCTATTTCTTAAAAATATAGAGGGCCTTCAAATTTCTCTCTCGCAACCCC
20269375 CCAAATTCGGCTGATTGGGCCGCCGTCTGCACAGTCGTGGCTGATGGCCGGCGTCGAGCAATGAC
66 CCAAATTCGGCTGATTGGGCCGCCGTCTGCACAGTCGTGGCTGATGGCCGGCGTCGAGCAATGAC
20269440 GTTTCTGATCAGCGCGTTGAAACGCGTTCAAAGGCCAAAACTTTAGAACAGGGAAACAAGGAGAA
131 GTTTCTGATCAGCGCGTTGAAACGCGTTCAAAGGCCAAAACTTTAGAACAGGGAAACAAGGAGAA
20269505 AAAAAAGGTCCTAGGCTTTTCCTTTTTATTTCCTTGCTGATTATTTTAAAATAGGTTTGTAAAAA
196 AAAAAAGGTCCTAGGCTTTTCCTTTTTATTTCCTTGCTGATTATTTTAAAATAGGTTTGTAAAAA
20269570 ATAAATGAATAAATAAATAAAAAGAAAAACAAAGAGAAAACAGTTAAAATCAACCTTTTAAAATT
261 ATAAATGAATAAATAAATAAAAAGAAAAACAAAGAGAAAACAGTTAAAATCAACCTTTTAAAATT
20269635 TCATTTTCTACTTTCCGATTTACTATTGTGCGTAAAAACTTTACAAAGATAAGATCTAGGCCTTT
326 TCATTTTCTACTTTCCGATTTACTATTGTGCGTAAAAACTTTACAAAGATAAGATCTAGGCCTTT
20269700 ATAGACGGATACAACTACTAATTTTTTTTTCTTTATCTGCCTATATTTACTGCCATTACTGTTAG
391 ATAGACGGATACAACTACTAATTTTTTTTTCTTTATCTGCCTATATTTACTGCCATTACTGTTAG
*
20269765 CATGTTTCTTCGTTGTTGCATTCAATTCTTTGCAAGGGTTTCGAGGCCGACGGTGGTGGCAGAGG
456 CATGTTTCTTCGTTGTTGCATTCAATTCTTTGCAAGGGTTTCGAGGCCCACGGTGGTGGCAGAGG
20269830 CATGCGCGAGGGGGCTGGTAGAACGTGCGGTGCTGGGGCATTGGGTAGAGGTGTGCAGCGCTGAG
521 CATGCGCGAGGGGGCTGGTAGAACGTGCGGTGCTGGGGCATTGGGTAGAGGTGTGCAGCGCTGAG
20269895 GCATTGGGCAAAGGCGTGCAACGCCTTAGGGTTTTGCTTCTC-GCTGTTTGTTGTGGGCTGCTGT
586 GCATTGGGCAAAGGCGTGCAACGCCTTAGGG-TTTGCTTCTCTGCTGTTTGTTGTGGGCTGCTGT
20269959 TGGTTTGGGCTAGGGTTATTAATTGGGCTTGGGTTATTGTTTGGGCTAGGGTAACAATTAGGTTA
650 TGGTTTGGGCTAGGGTTATTAATTGGGCTTGGGTTATTGTTTGGGCTAGGGTAACAATTAGGTTA
20270024 GT
715 GT
20270026 TTGTTTAATT
Statistics
Matches: 714, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
716 704 0.99
717 10 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (716 bp):
AAAAAAGTTGCAAACCCTATTTCTTAAAAATATAGAGGGCCTTCAAATTTCTCTCTCGCAACCCC
CCAAATTCGGCTGATTGGGCCGCCGTCTGCACAGTCGTGGCTGATGGCCGGCGTCGAGCAATGAC
GTTTCTGATCAGCGCGTTGAAACGCGTTCAAAGGCCAAAACTTTAGAACAGGGAAACAAGGAGAA
AAAAAAGGTCCTAGGCTTTTCCTTTTTATTTCCTTGCTGATTATTTTAAAATAGGTTTGTAAAAA
ATAAATGAATAAATAAATAAAAAGAAAAACAAAGAGAAAACAGTTAAAATCAACCTTTTAAAATT
TCATTTTCTACTTTCCGATTTACTATTGTGCGTAAAAACTTTACAAAGATAAGATCTAGGCCTTT
ATAGACGGATACAACTACTAATTTTTTTTTCTTTATCTGCCTATATTTACTGCCATTACTGTTAG
CATGTTTCTTCGTTGTTGCATTCAATTCTTTGCAAGGGTTTCGAGGCCCACGGTGGTGGCAGAGG
CATGCGCGAGGGGGCTGGTAGAACGTGCGGTGCTGGGGCATTGGGTAGAGGTGTGCAGCGCTGAG
GCATTGGGCAAAGGCGTGCAACGCCTTAGGGTTTGCTTCTCTGCTGTTTGTTGTGGGCTGCTGTT
GGTTTGGGCTAGGGTTATTAATTGGGCTTGGGTTATTGTTTGGGCTAGGGTAACAATTAGGTTAG
T
Found at i:20269969 original size:16 final size:17
Alignment explanation
Indices: 20269937--20269969 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20269927 TTTGCTTCTC
*
20269937 GCTGTTTGTTGTGGGCT
1 GCTGTTGGTTGTGGGCT
20269954 GCTGTTGGTT-TGGGCT
1 GCTGTTGGTTGTGGGCT
20269970 AGGGTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.12, G:0.42, T:0.45
Consensus pattern (17 bp):
GCTGTTGGTTGTGGGCT
Found at i:20269986 original size:18 final size:18
Alignment explanation
Indices: 20269963--20270010 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
20269953 TGCTGTTGGT
20269963 TTGGGCTAGGGTTATTAA
1 TTGGGCTAGGGTTATTAA
* **
20269981 TTGGGCTTGGGTTATTGT
1 TTGGGCTAGGGTTATTAA
20269999 TTGGGCTAGGGT
1 TTGGGCTAGGGT
20270011 AACAATTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.12, C:0.06, G:0.40, T:0.42
Consensus pattern (18 bp):
TTGGGCTAGGGTTATTAA
Found at i:20271189 original size:37 final size:37
Alignment explanation
Indices: 20271141--20271239 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 37
20271131 TTAAACATGT
*
20271141 TTTATTGA-TTTTATAAATATTT-TAAAATTTAT-TAGAA
1 TTTATTAATTTTTAT-AATATTTAT-AAATTTATAT-GAA
20271178 TTTATTAATTTTTATAATATTTATAAATTTATATGAA
1 TTTATTAATTTTTATAATATTTATAAATTTATATGAA
*
20271215 TTTTAATACATATTTT-TAATATTTA
1 -TTTATTA-AT-TTTTATAATATTTA
20271240 AGAATTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
37 25 0.46
38 14 0.26
39 11 0.20
40 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (37 bp):
TTTATTAATTTTTATAATATTTATAAATTTATATGAA
Found at i:20271200 original size:29 final size:28
Alignment explanation
Indices: 20271182--20271256 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 28
20271172 TTAGAATTTA
20271182 TTAATTTTTATAATATTTA-TAAATTTA
1 TTAATTTTTATAATATTTATTAAATTTA
*
20271209 TATGAATTTTAATACATATTT-TTAATATTTA
1 T-T-AATTTTTATA-ATATTTATTAA-ATTTA
**
20271240 AGAATTTTTAT-ATATTT
1 TTAATTTTTATAATATTT
20271257 TATTTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
27 7 0.18
28 1 0.03
29 17 0.44
30 9 0.23
31 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (28 bp):
TTAATTTTTATAATATTTATTAAATTTA
Found at i:20271246 original size:39 final size:36
Alignment explanation
Indices: 20271149--20271246 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 36
20271139 GTTTTATTGA
*
20271149 TTTTATAAATATTTTAAAATTTATTAGAATTTATTAAT
1 TTTTAT-AATA-TTTAAAATTTATTAGAATTTAATAAT
20271187 TTTTATAATATTTATAAATTTA-TATGAATTTTAATACAT
1 TTTTATAATATTTA-AAATTTATTA-GAA-TTTAATA-AT
20271226 ATTTT-TAATATTTAAGAATTT
1 -TTTTATAATATTTAA-AATTT
20271247 TTATATATTT
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
36 6 0.11
37 14 0.26
38 13 0.25
39 16 0.30
40 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
TTTTATAATATTTAAAATTTATTAGAATTTAATAAT
Found at i:20275143 original size:4 final size:4
Alignment explanation
Indices: 20275134--20275164 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
20275124 TTTATTTCAG
*
20275134 TAAA TAAA TAAG TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
20275165 CATATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:20276483 original size:95 final size:94
Alignment explanation
Indices: 20276240--20276504 Score: 289
Period size: 94 Copynumber: 2.8 Consensus size: 94
20276230 CTAGGGAGAT
* * * *
20276240 AAGATTCGCCGTCGTGGCTTCAAT-TTGCTCCGCTACAACGCCAGGGAAATAAGATTCGCCATTG
1 AAGATTCGCCGTCGTAGCTTCAATCTT-CTCCACTACAACGCCAGGGGAATAAGATTCGCCGTTG
* ** *
20276304 CGGCTTCAATCTTTGCAATGTTGGGGAAAT
65 CGACTTCAATCTTCACAATGTTGGGGAAAC
* * * * * * * *
20276334 GAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTACATCACCAGAGGAATAAGATTCACCGTTGC
1 AAGATTCGCCGTCGTAGCTTCAATCTTCTCCACTACAACGCCAGGGGAATAAGATTCGCCGTTGC
20276399 GACTTCAATCTTCACAATGTTGGGGTAAAC
66 GACTTCAATCTTCACAATGTTGGGG-AAAC
* * ** * *
20276429 AAGATTCACCGTCGTAGCTTCAATCTTTTCCACTACCCCGCCAGGGGAGTAAGATTCGTCGTTGC
1 AAGATTCGCCGTCGTAGCTTCAATCTTCTCCACTACAACGCCAGGGGAATAAGATTCGCCGTTGC
* *
20276494 AACTTTAATCT
66 GACTTCAATCT
20276505 GCTCCACTGC
Statistics
Matches: 138, Mismatches: 31, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
94 73 0.53
95 65 0.47
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (94 bp):
AAGATTCGCCGTCGTAGCTTCAATCTTCTCCACTACAACGCCAGGGGAATAAGATTCGCCGTTGC
GACTTCAATCTTCACAATGTTGGGGAAAC
Found at i:20276685 original size:50 final size:50
Alignment explanation
Indices: 20276582--20276701 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 50
20276572 TCCAAGCCTT
* * *
20276582 AACGCCAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTAC
1 AACGCCAAGGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTAC
* * * ** * *
20276632 AACGCCAAGGAAATAAGACTCGCCGTTGTGGCTTTAATCTTTTCCATTGC
1 AACGCCAAGGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTAC
* *
20276682 AACGTCAAGGCGATAAGACT
1 AACGCCAAGGAGATAAGACT
20276702 AATGTCTTCG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (50 bp):
AACGCCAAGGAGATAAGACTCGCCGTCGTGGCTTCAATCTGCTCCACTAC
Found at i:20276832 original size:87 final size:88
Alignment explanation
Indices: 20276706--20276874 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 88
20276696 AAGACTAATG
* * *
20276706 TCTTCGATCTACTTCACTGCCAGCACAGGAAGGCGAGATCTGCTA-CTTCAACGTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
20276770 TGCTCAAGGAGACAAGGCTGGTA
66 TGCTCAAGGAGACAAGGCTGGTA
* *
20276793 TCTTCGATCTACTTCACTGCCAATACAGGAAGACGAGATCTGCTATTTTCAACCTACTCCACTGC
1 TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
* *
20276858 TGCTCAGGGAGATAAGG
66 TGCTCAAGGAGACAAGG
20276875 TTATCGTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 42 0.57
88 32 0.43
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (88 bp):
TCTTCGATCTACTTCACTGCCAACACAGGAAGACGAGATCTGCTATCTTCAACCTACTCCACTGC
TGCTCAAGGAGACAAGGCTGGTA
Found at i:20280602 original size:28 final size:28
Alignment explanation
Indices: 20280550--20280603 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
20280540 AACGTGCGGT
* * * *
20280550 GCTGGGGCATTGGGTAGAGGTGTGCAGC
1 GCTGAGGCATTGGGCAAAGGCGTGCAGC
20280578 GCTGAGGCATTGGGCAAAGGCGTGCA
1 GCTGAGGCATTGGGCAAAGGCGTGCA
20280604 ACGCCTTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.46, T:0.19
Consensus pattern (28 bp):
GCTGAGGCATTGGGCAAAGGCGTGCAGC
Done.