Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 106 of 187
Found at i:31097114 original size:12 final size:12
Alignment explanation
Indices: 31097097--31097124 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31097087 ATTGTAGGTG
31097097 TTGTGTAATATA
1 TTGTGTAATATA
31097109 TTGTGTAATATA
1 TTGTGTAATATA
31097121 TTGT
1 TTGT
31097125 TATAACTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (12 bp):
TTGTGTAATATA
Found at i:31098718 original size:11 final size:11
Alignment explanation
Indices: 31098698--31098731 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31098688 AATTATGAAC
31098698 TTACCGTTTCA
1 TTACCGTTTCA
*
31098709 TTACCTTTTC-
1 TTACCGTTTCA
31098719 TTACCGTTTCA
1 TTACCGTTTCA
31098730 TT
1 TT
31098732 TGCATAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.53
Consensus pattern (11 bp):
TTACCGTTTCA
Found at i:31099221 original size:33 final size:33
Alignment explanation
Indices: 31099151--31099268 Score: 128
Period size: 33 Copynumber: 3.5 Consensus size: 33
31099141 ACATTGTCAG
* * * *
31099151 TCCAACCAAATACACCAGATGCTCACATGAGCCAA
1 TCCAACC-AACACACCA-ATGCTCATAAGAGCTAA
** * * *
31099186 TCCTTCCATCACTCCAATGCTCATAAGAGTTAA
1 TCCAACCAACACACCAATGCTCATAAGAGCTAA
31099219 TCCAACCAACACACCAATGCTCATAAGAGCTAA
1 TCCAACCAACACACCAATGCTCATAAGAGCTAA
*
31099252 TCTAACCAACACACCAA
1 TCCAACCAACACACCAA
31099269 ACATAGTGTA
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
33 57 0.84
34 6 0.09
35 5 0.07
ACGTcount: A:0.39, C:0.34, G:0.08, T:0.19
Consensus pattern (33 bp):
TCCAACCAACACACCAATGCTCATAAGAGCTAA
Found at i:31104872 original size:5 final size:5
Alignment explanation
Indices: 31104851--31104884 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
31104841 AGAATTACAA
*
31104851 TAAAT TAAAT AATAAT TAAAT TAAAT TAAAT TAA
1 TAAAT TAAAT TA-AAT TAAAT TAAAT TAAAT TAA
31104885 TTTCCAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAAAT
Found at i:31105560 original size:19 final size:18
Alignment explanation
Indices: 31105521--31105568 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
31105511 TAAAGTGGCT
31105521 CAATTTTACCTCTTGGTCA
1 CAATTTTACCTCTT-GTCA
31105540 CAATTTTACCTCTCT-TCCA
1 CAATTTTACCTCT-TGT-CA
31105559 CAATTTTACC
1 CAATTTTACC
31105569 AAATTAGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.04
19 25 0.93
20 1 0.04
ACGTcount: A:0.23, C:0.31, G:0.04, T:0.42
Consensus pattern (18 bp):
CAATTTTACCTCTTGTCA
Found at i:31106955 original size:26 final size:27
Alignment explanation
Indices: 31106926--31106976 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
31106916 AATAGATCAT
* *
31106926 ACATCA-TATCTTAAATATTCAAACAA
1 ACATCATTATCATAAAAATTCAAACAA
*
31106952 ACATGATTATCATAAAAATTCAAAC
1 ACATCATTATCATAAAAATTCAAAC
31106977 TTAAATCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (27 bp):
ACATCATTATCATAAAAATTCAAACAA
Found at i:31110438 original size:17 final size:17
Alignment explanation
Indices: 31110386--31110438 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
31110376 CTTATTCTTT
31110386 CACTCACAATACTTTTAA
1 CACTCACAATA-TTTTAA
* * *
31110404 CACTCGCCATGCTTTTAA
1 CACTCACAAT-ATTTTAA
*
31110422 CTCTCACAATATTTTAA
1 CACTCACAATATTTTAA
31110439 TTTTCTCGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (17 bp):
CACTCACAATATTTTAA
Found at i:31118132 original size:15 final size:17
Alignment explanation
Indices: 31118112--31118144 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31118102 AACAACTTAC
31118112 ACATGC-AA-TAACCAA
1 ACATGCAAAGTAACCAA
31118127 ACATGCAAAGTAACCAA
1 ACATGCAAAGTAACCAA
31118144 A
1 A
31118145 AAATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.55, C:0.24, G:0.09, T:0.12
Consensus pattern (17 bp):
ACATGCAAAGTAACCAA
Found at i:31119965 original size:23 final size:25
Alignment explanation
Indices: 31119918--31119965 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31119908 TAAATAAAAA
31119918 ATATTATATTAATATAATTTAATTAG
1 ATATTATATTAATAT-ATTTAATTAG
31119944 ATATT-TATTAATAT-TTTAATTA
1 ATATTATATTAATATATTTAATTA
31119966 AAAAATGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
25 9 0.41
26 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATATTATATTAATATATTTAATTAG
Found at i:31123952 original size:45 final size:45
Alignment explanation
Indices: 31123899--31124232 Score: 243
Period size: 45 Copynumber: 7.6 Consensus size: 45
31123889 TTAATCCGCC
* * *
31123899 CCACTGCAATTTTAGAGG-GATAAGACTTG-ATTTCTTGAGTCTGCT
1 CCACTGCAACTTCAG-GGAGATAAGACTCGCA-TTCTTGAGTCTGCT
*
31123944 CCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGAGTCTGCT
* * *
31123989 CCACTGCAACTTCAGGGAGATAAGACCCG-ATGC---AATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGAGTCTGCT
* * * * **
31124030 -CTCTGCAACTTCAGAGAGATAAGA-TCTGTGATT-TT-AATCCACT
1 CCACTGCAACTTCAGGGAGATAAGACTC-G-CATTCTTGAGTCTGCT
* * * * *
31124073 CTACTGCAACTTCAGGGAGATAGGA-T--TATTGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCGCATT--CTTGAGTCTGCT
* * *
31124117 CCACTACAACTTCAGGGAGATAAGATTCGTCA-TCTTCAGTCTGC-
1 CCACTGCAACTTCAGGGAGATAAGACTCG-CATTCTTGAGTCTGCT
* * * *
31124161 CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTTCTT-AGTCTGCT
1 C-CACTGCAACTTCAGGGA-GATAAGACTCGCATTCTTGAGTCTGCT
31124206 CCACTGCAACTTCAGGGAGATAAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
31124233 AGATGCGATC
Statistics
Matches: 235, Mismatches: 33, Indels: 43
0.76 0.11 0.14
Matches are distributed among these distances:
39 1 0.00
40 26 0.11
41 6 0.03
42 2 0.01
43 8 0.03
44 86 0.37
45 103 0.44
46 1 0.00
47 1 0.00
48 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGAGTCTGCT
Found at i:31124039 original size:40 final size:43
Alignment explanation
Indices: 31123938--31124358 Score: 159
Period size: 44 Copynumber: 9.7 Consensus size: 43
31123928 ATTTCTTGAG
* * **
31123938 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGC-T-AA
31123983 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCG-ATGC-AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGCTAA
* * * * * **
31124024 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCG-CATGCTAA
** * * **
31124067 TCCACTCTACTGCAACTTCAGGGAGATAGGA---TTATTGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCA-T-GC--TAA
* ** *
31124111 TCTGCTCCACTACAACTTCAGGGAGATAAGATTCGTCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCG-CATGC-T-AA
* * ** * * *
31124156 TCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTTCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACCCGCATGC-TAA
** *
31124200 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGCTAA
* * * * * * **
31124241 TCTGCT-CTCTGCAACTTTAGAGAGATAAGATCTGTGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCG-CATGCTAA
* * * * * ** *
31124284 TCCGCTCCACTACGACTTCAAGGAGATAGGATTACTGGC-T-TTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATA--A-GACCCGCATGCTAA
*
31124328 TCTGCTCCACTGCAGCTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
31124359 TTCGCCATCT
Statistics
Matches: 285, Mismatches: 66, Indels: 54
0.70 0.16 0.13
Matches are distributed among these distances:
40 47 0.16
41 14 0.05
42 5 0.02
43 14 0.05
44 130 0.46
45 70 0.25
46 1 0.00
47 3 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGCATGCTAA
Found at i:31124255 original size:217 final size:218
Alignment explanation
Indices: 31123931--31124375 Score: 680
Period size: 217 Copynumber: 2.0 Consensus size: 218
31123921 AGACTTGATT
* * *
31123931 TCTTGAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCATTCTTGGGTCTGCTCCACTGC
1 TCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCATTCTTGAGTCTGCTCCACTGC
*
31123996 AACTTCAGGGAGATAAGACCCGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGA
66 AACTTCAGGGAGATAAGACCAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGA
* * * *
31124061 TTTTAATCCACTCTACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTACAA
131 TTTTAATCCACTCCACTACAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCTCCACTACAA
*
31124126 CTTCAGGGAGATAAGATTCGTCA
196 CTTCAGGGAGATAAGATTCGCCA
* * *
31124149 TCTTCAGTCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTTCTT-AGTCTGCTCCACT
1 TCTTCAGTCTGCTC-CACTACAACTTCAGGGA-GATAAGACTCGCATTCTTGAGTCTGCTCCACT
* * *
31124211 GCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAAGATCTGT
64 GCAACTTCAGGGAGATAAGACCAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGT
* * *
31124276 GATTTTAATCCGCTCCACTACGACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCTCCACTGC
129 GATTTTAATCCACTCCACTACAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCTCCACTAC
*
31124341 AGCTTCAGGGAGATAAGATTCGCCA
194 AACTTCAGGGAGATAAGATTCGCCA
31124366 TCTTCAGTCT
1 TCTTCAGTCT
31124376 TTTAAATTGC
Statistics
Matches: 206, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
217 168 0.82
218 38 0.18
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (218 bp):
TCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTCGCATTCTTGAGTCTGCTCCACTGC
AACTTCAGGGAGATAAGACCAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGA
TTTTAATCCACTCCACTACAACTTCAAGGAGATAGGATTACTGGCTTTAATCTGCTCCACTACAA
CTTCAGGGAGATAAGATTCGCCA
Found at i:31124791 original size:88 final size:88
Alignment explanation
Indices: 31124637--31125841 Score: 2232
Period size: 88 Copynumber: 13.7 Consensus size: 88
31124627 GTTGTCAGTG
* ** * * *
31124637 CAGGAAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
*
31124702 TTTTAACCTGCTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31124725 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31124790 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31124813 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31124878 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31124901 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31124966 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31124989 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125054 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125077 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125142 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125165 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125230 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125253 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125318 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125341 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125406 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125429 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125494 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
*
31125517 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGCAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125582 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
** * * *
31125605 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
*
31125670 TTTTAACCTGCTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
31125693 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
31125758 TTTTAACCTACTCCGCTACAACC
66 TTTTAACCTACTCCGCTACAACC
* * * *
31125781 CAGGGAGGTAAGGTTGGTGTCTTCGATCTGCTTC-ACTGTCGGTGCAGGAAGGCAAGATCTG
1 CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGA-TGTCAGTGTAGGAAGGCAAGATCTG
31125842 TTATCTTCAC
Statistics
Matches: 1093, Mismatches: 23, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
87 1 0.00
88 1092 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (88 bp):
CAGGGAGGCAAGATTGGTGTCTTCGATCTGCTTCGATGTCAGTGTAGGAAGGCAAGATCTGCTAT
TTTTAACCTACTCCGCTACAACC
Found at i:31127192 original size:14 final size:15
Alignment explanation
Indices: 31127169--31127201 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31127159 ATTAACGTTT
31127169 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
31127183 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
31127198 TTCC
1 TTCC
31127202 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:31131024 original size:29 final size:30
Alignment explanation
Indices: 31130968--31131024 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
31130958 CCATTTCTAT
* *
31130968 TTTAGAAAAAAATAAAAATTAGTTGTCGAC
1 TTTAGAAAAAAACAAAAATTAGTAGTCGAC
31130998 TTTA-AAAAAAACAAAAATTGAG-AGTCG
1 TTTAGAAAAAAACAAAAATT-AGTAGTCG
31131025 CCACCAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (30 bp):
TTTAGAAAAAAACAAAAATTAGTAGTCGAC
Found at i:31132191 original size:95 final size:95
Alignment explanation
Indices: 31132082--31132271 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
31132072 TAAAAAGAAA
31132082 GGAAGATGAACAAAAAACAAAATAAGAACAAGCCACAGAAAATAAGAACGCAAGAGAAGGAGAAA
1 GGAAGATGAACAAAAAACAAAATAAGAACAAGCCACAGAAAATAAGAACGCAAGAGAAGGAGAAA
31132147 TTTGAGTGAATGCTCTTAAGAATTATTATT
66 TTTGAGTGAATGCTCTTAAGAATTATTATT
*
31132177 GGAAGATGAACAAAAAACAAAATAAGAACAAGCCACAGAAAATAAGAATGCAAGAGAAGGAGAAA
1 GGAAGATGAACAAAAAACAAAATAAGAACAAGCCACAGAAAATAAGAACGCAAGAGAAGGAGAAA
31132242 TTTGAGTGAATGCTCTTAAGAATTATTATT
66 TTTGAGTGAATGCTCTTAAGAATTATTATT
31132272 ACTTCAAACT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.52, C:0.10, G:0.20, T:0.18
Consensus pattern (95 bp):
GGAAGATGAACAAAAAACAAAATAAGAACAAGCCACAGAAAATAAGAACGCAAGAGAAGGAGAAA
TTTGAGTGAATGCTCTTAAGAATTATTATT
Found at i:31132436 original size:22 final size:22
Alignment explanation
Indices: 31132411--31132458 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31132401 TATAAATTAA
31132411 ATCTT-TAAGATTACAAAATCTT
1 ATCTTCTAAGATTAC-AAATCTT
* *
31132433 ATCTTCTAAGATTGCATATCTT
1 ATCTTCTAAGATTACAAATCTT
31132455 ATCT
1 ATCT
31132459 AAGATTGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (22 bp):
ATCTTCTAAGATTACAAATCTT
Found at i:31132798 original size:44 final size:45
Alignment explanation
Indices: 31132747--31132841 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
31132737 AGGCTCACTT
* *
31132747 TCTTCAACCTACTCCATTGCAACTTCAGGGAGATAAGATT-GATA
1 TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
* * * *
31132791 TCTTCAACCGGCTCCACTGTAACTTCAGGGAGATAAGGTTGGTTA
1 TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
31132836 TCTTCA
1 TCTTCA
31132842 GTCTTTAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 35 0.80
45 9 0.20
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TCTTCAACCGACTCCACTGCAACTTCAGGGAGATAAGATTGGATA
Found at i:31133287 original size:169 final size:167
Alignment explanation
Indices: 31132991--31133482 Score: 617
Period size: 169 Copynumber: 2.9 Consensus size: 167
31132981 TTTTTCAATT
* * * * *
31132991 TTAACGCCAAGGAGATGAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTACAACACCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* ** ** *
31133056 ACCAGATTTTCTACCTTTAGCCTTAATCAATTCCACTGTAATGCAAAAGAGATAGGATTCGCTGC
66 ACAAGATTCACTACCTTTAG-CTTAATCTGTTCCACTATAATGC-AAAGAGATAGGATTCGCTGC
31133121 CCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
129 CCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
** * * * *
31133160 TTAATGCCAGGGATATAAGATTCGCTGCCCT-ATGCTCTAATCTGCTCCGCTGCAACGCTAGGGA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCA-GCTTTAATCTGCTCCGCTGCAACACCAGGGA
* *
31133224 AACAAGATTCGCTACCTTTAGCTTCAATCTGTTCCACTATAATGTCAAAGAGTTAGGATTCGCTG
65 AACAAGATTCACTACCTTTAGCTT-AATCTGTTCCACTATAATG-CAAAGAGATAGGATTCGCTG
* * ** * *
31133289 TCCGCAGCTTTAATCTACTCAACCTCAGCTATTCCAAGTC
128 CCCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
* * * *
31133329 TTAACACCAGGGAGATAAGATTCGCTGCGCTCAGCTTTAGTTTACTCCGCTGCAACACCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
* * *
31133394 ATAAGATTCACTACCTTTAGCTTTAATCTGTTCCACTATAAGGCCAAATAGATAGGATTCGCTGC
66 ACAAGATTCACTACCTTTAGC-TTAATCTGTTCCACTATAATG-CAAAGAGATAGGATTCGCTGC
*
31133459 CCACAGTTTTAATCCGCTCCACTT
129 CCACAGCTTTAATCCGCTCCACTT
31133483 TAGCATTAAC
Statistics
Matches: 273, Mismatches: 45, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
168 4 0.01
169 265 0.97
170 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (167 bp):
TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACACCAGGGAA
ACAAGATTCACTACCTTTAGCTTAATCTGTTCCACTATAATGCAAAGAGATAGGATTCGCTGCCC
ACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
Found at i:31133766 original size:45 final size:46
Alignment explanation
Indices: 31133715--31133850 Score: 159
Period size: 45 Copynumber: 3.0 Consensus size: 46
31133705 CGTCGTTTTT
* * *
31133715 GATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCA
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
* ** **
31133761 G-TCTGCTCCGCTACCAATACAGGAAGACAAGATCTAATATCTTC-
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
* * *
31133805 GATCTACTTCACTGTCAATACAGGAAGATAAGATCTGCTATCTTCA
1 GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
31133851 ATTCACTCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
44 1 0.01
45 70 0.97
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (46 bp):
GATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGCTATCTTCA
Found at i:31135165 original size:6 final size:6
Alignment explanation
Indices: 31135126--31135156 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31135116 TTTTTTTCCA
31135126 TCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
31135157 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:31138594 original size:8 final size:8
Alignment explanation
Indices: 31138581--31138607 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31138571 AGTTGATTAA
31138581 TTAATGTC
1 TTAATGTC
31138589 TTAATGTC
1 TTAATGTC
31138597 TTAATGTC
1 TTAATGTC
31138605 TTA
1 TTA
31138608 CTTTAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (8 bp):
TTAATGTC
Found at i:31139192 original size:23 final size:23
Alignment explanation
Indices: 31139164--31139208 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
31139154 ATTCAAAATT
*
31139164 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
31139187 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
31139209 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:31139383 original size:24 final size:24
Alignment explanation
Indices: 31139321--31139556 Score: 139
Period size: 24 Copynumber: 10.0 Consensus size: 24
31139311 AAAAATTTTG
* *
31139321 ATGAT-AATTCTAAAATAATCATAC
1 ATGATAAATT-TAAAATAATAATAT
* ** *
31139345 GTGATAAATCCAAAATAATAGTAT
1 ATGATAAATTTAAAATAATAATAT
* *
31139369 ATAATAAATTT-AAA-AATATTA-
1 ATGATAAATTTAAAATAATAATAT
* *
31139390 ATGATAAATTTGAAATAGAT-ATAC
1 ATGATAAATTTAAAATA-ATAATAT
**
31139414 ATGATAAATTTAAAATAATGTTA-
1 ATGATAAATTTAAAATAATAATAT
** *
31139437 ACAATGAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAATAATAT
* * *
31139461 -TGATAAATTAAAAATAATAAAAC
1 ATGATAAATTTAAAATAATAATAT
*
31139484 ATGATAAATCTAAAATAATAATAT
1 ATGATAAATTTAAAATAATAATAT
** * * * *
31139508 ACAATACACTT-AGATAATATTA-
1 ATGATAAATTTAAAATAATAATAT
*
31139530 ATGATTAATTTAATAATAATAAGTAT
1 ATGATAAATTTAA-AATAATAA-TAT
31139556 A
1 A
31139557 AACATTCAAA
Statistics
Matches: 156, Mismatches: 44, Indels: 22
0.70 0.20 0.10
Matches are distributed among these distances:
21 10 0.06
22 15 0.10
23 53 0.34
24 72 0.46
25 5 0.03
26 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
ATGATAAATTTAAAATAATAATAT
Found at i:31139525 original size:70 final size:68
Alignment explanation
Indices: 31139306--31139551 Score: 201
Period size: 70 Copynumber: 3.5 Consensus size: 68
31139296 ACACATATAA
* * * * * * * *
31139306 AATTTAAAAATTTTGATGAT-AATTCTAAAATAATCATACGTGATAAATCCAAAATAATAGTATA
1 AATTTAATAATATTAATGATAAATT-AAAAATAATAATACATGATAAATCTAAAATAATAATATA
*
31139370 TAAT
65 CAAT
* ** * **
31139374 AAATTTAAAAATATTAATGATAAATTTGAAATAGAT-ATACATGATAAATTTAAAATAATGTTA-
1 -AATTTAATAATATTAATGATAAATTAAAAATA-ATAATACATGATAAATCTAAAATAATAATAT
31139437 ACAAT
64 ACAAT
* * *
31139442 GAATTTAAAATAATAATATTGATAAATTAAAAATAATAAAACATGATAAATCTAAAATAATAATA
1 -AATTT--AATAATATTAATGATAAATTAAAAATAATAATACATGATAAATCTAAAATAATAATA
31139507 TACAAT
63 TACAAT
* * *
31139513 ACACTTAGATAATATTAATGATTAATTTAATAATAATAA
1 A-ATTTA-ATAATATTAATGA-TAAATTAAAAATAATAA
31139552 GTATAAACAT
Statistics
Matches: 144, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
68 9 0.06
69 49 0.34
70 63 0.44
71 23 0.16
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (68 bp):
AATTTAATAATATTAATGATAAATTAAAAATAATAATACATGATAAATCTAAAATAATAATATAC
AAT
Found at i:31143202 original size:18 final size:18
Alignment explanation
Indices: 31143154--31143204 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
31143144 ATCCAAAACT
*
31143154 AATT-AAAATAATATAAA
1 AATTAAAAATAAAATAAA
*
31143171 ATATTATAATAATAAAATTAA
1 A-ATTA-AA-AATAAAATAAA
31143192 AATTAAAAATAAA
1 AATTAAAAATAAA
31143205 TAATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 1 0.04
18 9 0.32
19 2 0.07
20 6 0.21
21 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTAAAAATAAAATAAA
Found at i:31144791 original size:24 final size:25
Alignment explanation
Indices: 31144761--31144846 Score: 106
Period size: 25 Copynumber: 3.5 Consensus size: 25
31144751 AGTAAAAATT
31144761 TTATA-TTAATATAACGTATTAGAA
1 TTATATTTAATATAACGTATTAGAA
**
31144785 TTATATTTAATA-AAC-TAACAGCAA
1 TTATATTTAATATAACGTATTAG-AA
*
31144809 TTTTATATTAATATAACGTATTAGAA
1 TTATAT-TTAATATAACGTATTAGAA
31144835 TTATATTTAATA
1 TTATATTTAATA
31144847 ATCTAACAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.08
24 15 0.29
25 18 0.35
26 10 0.20
27 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (25 bp):
TTATATTTAATATAACGTATTAGAA
Found at i:31144816 original size:26 final size:24
Alignment explanation
Indices: 31144783--31144867 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
31144773 AACGTATTAG
31144783 AATTATATTTAATAAACTAACAGC
1 AATTATATTTAATAAACTAACAGC
* **
31144807 AATTTTATATTAATATAACGTATTAG-
1 AATTATAT-TTAATA-AAC-TAACAGC
*
31144833 AATTATATTTAATAATCTAACAGC
1 AATTATATTTAATAAACTAACAGC
*
31144857 AAATA-ATTTAA
1 AATTATATTTAA
31144868 AATTTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 10 0.20
24 13 0.27
25 12 0.24
26 10 0.20
27 4 0.08
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (24 bp):
AATTATATTTAATAAACTAACAGC
Found at i:31144819 original size:50 final size:50
Alignment explanation
Indices: 31144757--31144858 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
31144747 CCTTAGTAAA
31144757 AATTTTATATTAATATAACGTATTAGAATTATATTTAATAAACTAACAGC
1 AATTTTATATTAATATAACGTATTAGAATTATATTTAATAAACTAACAGC
*
31144807 AATTTTATATTAATATAACGTATTAGAATTATATTTAATAATCTAACAGC
1 AATTTTATATTAATATAACGTATTAGAATTATATTTAATAAACTAACAGC
31144857 AA
1 AA
31144859 ATAATTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (50 bp):
AATTTTATATTAATATAACGTATTAGAATTATATTTAATAAACTAACAGC
Found at i:31145451 original size:36 final size:36
Alignment explanation
Indices: 31145380--31145451 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
31145370 TCGGAAAAGC
* *
31145380 TGTTTTTACATATATTAATAAATTTATATTTTAAAT
1 TGTTTTTACATATATTAACAAATTTATATTATAAAT
31145416 TGTTTTTACATATA-TAACAATGATTTAT-TTATAAAT
1 TGTTTTTACATATATTAACAA--ATTTATATTATAAAT
31145452 AAATAAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 5 0.16
36 21 0.66
37 6 0.19
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (36 bp):
TGTTTTTACATATATTAACAAATTTATATTATAAAT
Found at i:31146689 original size:32 final size:32
Alignment explanation
Indices: 31146653--31146742 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
31146643 CAATTATTTC
31146653 AATATCCAACAAGCTTAAAACATAATAAATTA
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
31146685 AATATCCAACAAGCTTAAAACATAATAAATTC
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
31146717 AATATCTAACAAGCTTAAAACATAAT
1 AATATCCAACAAGCTTAAAACATAAT
31146743 CAATATCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (32 bp):
AATATCCAACAAGCTTAAAACATAATAAATTA
Found at i:31146749 original size:27 final size:30
Alignment explanation
Indices: 31146650--31146755 Score: 128
Period size: 32 Copynumber: 3.5 Consensus size: 30
31146640 TGTCAATTAT
31146650 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
31146682 TTAAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
31146714 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
31146742 -TCAATATCTAACAA
1 TTCAATATCCAACAA
31146756 ATTCAAGACA
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
27 14 0.20
28 2 0.03
29 2 0.03
32 53 0.75
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:31146766 original size:27 final size:27
Alignment explanation
Indices: 31146715--31146769 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
31146705 CATAATAAAT
*
31146715 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
31146742 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
31146769 T
1 T
31146770 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:31146777 original size:59 final size:62
Alignment explanation
Indices: 31146648--31146787 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 62
31146638 ATTGTCAATT
*
31146648 ATTTCAATATCCAACAAGCTTAAAACATAATAAATTAAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCCAACAAGCTTAAAAC--AATAAATTAAATATCCAACAAGATTAAAACATAATA
* * * * *
31146712 AATTCAATATCTAACAAGCTTAAAAC-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATT-AAAACATAATA
*
31146771 ATTTCAAAATCCAACAA
1 ATTTCAATATCCAACAA
31146788 ACTAAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 36 0.55
60 2 0.03
61 2 0.03
64 24 0.36
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (62 bp):
ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATTAAAACATAATA
Found at i:31149925 original size:17 final size:17
Alignment explanation
Indices: 31149903--31149955 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
31149893 TCTTCAACAG
31149903 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
31149920 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
*
31149933 ACAGATGCAAAATCTAA
1 ACAGATGCAAAATCCAA
31149950 ACAGAT
1 ACAGAT
31149956 TCTTCAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 9 0.31
15 6 0.21
17 14 0.48
ACGTcount: A:0.55, C:0.19, G:0.11, T:0.15
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:31149937 original size:30 final size:30
Alignment explanation
Indices: 31149898--31149956 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
31149888 AAGATTCTTC
*
31149898 AACAGACAGATGCAAAATCCAAACAGATTA
1 AACAAACAGATGCAAAATCCAAACAGATTA
*
31149928 AACAAACAGATGCAAAATCTAAACAGATT
1 AACAAACAGATGCAAAATCCAAACAGATT
31149957 CTTCAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (30 bp):
AACAAACAGATGCAAAATCCAAACAGATTA
Found at i:31150579 original size:9 final size:8
Alignment explanation
Indices: 31150502--31150637 Score: 69
Period size: 8 Copynumber: 15.6 Consensus size: 8
31150492 TAAACTTATA
31150502 AAAAGATAT
1 AAAA-ATAT
*
31150511 AAAAATCCT
1 AAAAAT-AT
*
31150520 AGAAAATAA
1 A-AAAATAT
31150529 AAAAATATT
1 AAAAATA-T
31150538 AGAGATAATAT
1 A-A-A-AATAT
**
31150549 AAACTTAT
1 AAAAATAT
31150557 AAAAATAT
1 AAAAATAT
31150565 AAAAAAATCAT
1 --AAAAAT-AT
31150576 AAAAATAT
1 AAAAATAT
31150584 AAAAACTTAT
1 AAAAA--TAT
31150594 AAAAATA-
1 AAAAATAT
*
31150601 ATAAAT-T
1 AAAAATAT
31150608 AAAAATAT
1 AAAAATAT
* * *
31150616 ATAATTAC
1 AAAAATAT
31150624 AAAAATTAT
1 AAAAA-TAT
31150633 AAAAA
1 AAAAA
31150638 AAATCATTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
7 10 0.10
8 35 0.36
9 22 0.23
10 21 0.22
11 5 0.05
12 4 0.04
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:31150602 original size:56 final size:56
Alignment explanation
Indices: 31150470--31150603 Score: 157
Period size: 56 Copynumber: 2.4 Consensus size: 56
31150460 TTTAAAATTT
* * *
31150470 TATAAAATATTA-AAAAATTATATAAACTTATAAAAAGATATAAAAATCCTAGAAAA
1 TATAAAA-ATTATAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
* * * *
31150526 TA-AAAAAATATTAGAGATAATATAAACTTATAAAAATATAAAAAAATCATA-AAAA
1 TATAAAAATTA-TAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
31150581 TATAAAAACTTATAAAAATAATA
1 TATAAAAA-TTATAAAAATAATA
31150604 AATTAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
54 3 0.05
55 10 0.16
56 49 0.77
57 2 0.03
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (56 bp):
TATAAAAATTATAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAGAAAA
Found at i:31150619 original size:18 final size:17
Alignment explanation
Indices: 31150556--31150616 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 17
31150546 TATAAACTTA
*
31150556 TAAAAATATAAAAAAAT
1 TAAAAATATAAATAAAT
*
31150573 CATAAAAATATAAA-AACT
1 --TAAAAATATAAATAAAT
31150591 TATAAAA-AT-AATAAAT
1 TA-AAAATATAAATAAAT
31150607 TAAAAATATA
1 TAAAAATATA
31150617 TAATTACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 4 0.11
18 3 0.08
19 12 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATATAAATAAAT
Found at i:31150635 original size:30 final size:32
Alignment explanation
Indices: 31150575--31150635 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
31150565 AAAAAAATCA
*
31150575 TAAAAATATAAAAACTTATAAAAATAATAAAT
1 TAAAAATATAAAAACTTACAAAAATAATAAAT
* *
31150607 TAAAAATAT-ATAA-TTACAAAAATTATAAA
1 TAAAAATATAAAAACTTACAAAAATAATAAA
31150636 AAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 3 0.12
32 9 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (32 bp):
TAAAAATATAAAAACTTACAAAAATAATAAAT
Found at i:31158732 original size:20 final size:19
Alignment explanation
Indices: 31158702--31158785 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
31158692 GATGTTAGAA
31158702 TATTAATTCTATTATATATT
1 TATT-ATTCTATTATATATT
31158722 TATCTATTCTATTATATA--
1 TAT-TATTCTATTATATATT
*
31158740 TA-TATTCTAATATATATT
1 TATTATTCTATTATATATT
31158758 AGTATTATT-T-TTATATTATT
1 --TATTATTCTATTATA-TATT
31158778 TATCTATT
1 TAT-TATT
31158786 TCTTATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 8 0.15
20 23 0.43
21 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTATTCTATTATATATT
Found at i:31158747 original size:16 final size:17
Alignment explanation
Indices: 31158707--31158756 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
31158697 TAGAATATTA
31158707 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
31158727 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
31158743 ATTCTAATATATAT
1 ATTCTATTATATAT
31158757 TAGTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:31160511 original size:18 final size:18
Alignment explanation
Indices: 31160490--31160526 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31160480 AATTCGACGC
* *
31160490 AGTGGATAAATTAGATAA
1 AGTGGAAAAATGAGATAA
31160508 AGTGGAAAAATGAGATAA
1 AGTGGAAAAATGAGATAA
31160526 A
1 A
31160527 CCAGCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
AGTGGAAAAATGAGATAA
Found at i:31179417 original size:13 final size:13
Alignment explanation
Indices: 31179401--31179425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31179391 TTTACTTTTT
31179401 CTTAGTTAATTTA
1 CTTAGTTAATTTA
31179414 CTTAGTTAATTT
1 CTTAGTTAATTT
31179426 TTAGTTTTTA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTAGTTAATTTA
Found at i:31183999 original size:25 final size:25
Alignment explanation
Indices: 31183965--31184014 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31183955 CTGACTTTGT
31183965 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
31183990 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
31184015 GAGGTACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
TATCTTAGACTTTGAAGTAGATAAA
Found at i:31186743 original size:21 final size:20
Alignment explanation
Indices: 31186717--31186755 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31186707 GTTTTGATGA
31186717 AGGTATAGATACCTTAGGCCT
1 AGGTATAGATACC-TAGGCCT
*
31186738 AGGTATCGATACCTAGGC
1 AGGTATAGATACCTAGGC
31186756 TTATATTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AGGTATAGATACCTAGGCCT
Found at i:31187604 original size:28 final size:30
Alignment explanation
Indices: 31187572--31187653 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 30
31187562 GGAAATAATG
31187572 ATAAGCACCAAAGTGCAAATTAATA-A-CA
1 ATAAGCACCAAAGTGCAAATTAATACAGCA
* **
31187600 ATAAGCATCAAAGTGCAAATTTTTACAGCA
1 ATAAGCACCAAAGTGCAAATTAATACAGCA
** *
31187630 ATAAGCACCATTGTGCAAAATAAT
1 ATAAGCACCAAAGTGCAAATTAAT
31187654 TCGATAAGCG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
28 22 0.51
29 1 0.02
30 20 0.47
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (30 bp):
ATAAGCACCAAAGTGCAAATTAATACAGCA
Found at i:31190383 original size:15 final size:16
Alignment explanation
Indices: 31190363--31190392 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31190353 TAACAACTAA
31190363 TATATAA-ATATATTT
1 TATATAATATATATTT
31190378 TATATAATATATATT
1 TATATAATATATATT
31190393 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:31191984 original size:3 final size:3
Alignment explanation
Indices: 31191976--31192001 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31191966 TGAGGATCCT
31191976 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
31192002 TCCTACAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31199639 original size:33 final size:33
Alignment explanation
Indices: 31199587--31199650 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
31199577 AACAAGCAGT
* * *
31199587 GACAGTCTGGGCCTGAGCCCTATTCAGTAACAG
1 GACAGTCTGGACCTGAGCCCAATACAGTAACAG
* *
31199620 GACAGTGTGGACCTTAGCCCAATACAGTAAC
1 GACAGTCTGGACCTGAGCCCAATACAGTAAC
31199651 GGTGTGGGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (33 bp):
GACAGTCTGGACCTGAGCCCAATACAGTAACAG
Found at i:31200220 original size:26 final size:27
Alignment explanation
Indices: 31200004--31200219 Score: 250
Period size: 27 Copynumber: 8.1 Consensus size: 27
31199994 TATAACAGTT
31200004 ATTTTA-CCTATGAGGGTATTTTAGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
31200030 ATTTTACCCTAT-AGAGGTATTTT-GATC
1 ATTTTACCCTATGAG-GGTATTTTAG-TC
* *
31200057 ATTTTACCCTATGAGGGTATTTAAGTT
1 ATTTTACCCTATGAGGGTATTTTAGTC
31200084 ATTTTACCCTAT-AGGGGTATTTTAGTC
1 ATTTTACCCTATGA-GGGTATTTTAGTC
* * *
31200111 ATTTTACCATATGAGAGTATTTCAGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
* **
31200138 ATTTTATCCTA--AGGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
31200163 ATTTTACCCTATGAGGGTATTTT-GATC
1 ATTTTACCCTATGAGGGTATTTTAG-TC
* *
31200190 A-TTTAACCTATGAGGGTATTTTGGTC
1 ATTTTACCCTATGAGGGTATTTTAGTC
31200216 ATTT
1 ATTT
31200220 ATTAACCTCT
Statistics
Matches: 164, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
25 22 0.13
26 34 0.21
27 104 0.63
28 4 0.02
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTATGAGGGTATTTTAGTC
Found at i:31200466 original size:19 final size:17
Alignment explanation
Indices: 31200425--31200467 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
31200415 CATCCGTGTG
31200425 GGGCCCACAAGCCCTTT
1 GGGCCCACAAGCCCTTT
* *
31200442 GAGCCCACACTGCCCATTT
1 GGGCCCACA-AGCCC-TTT
31200461 GGGCCCA
1 GGGCCCA
31200468 ACGTGGCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (17 bp):
GGGCCCACAAGCCCTTT
Found at i:31203062 original size:25 final size:25
Alignment explanation
Indices: 31203020--31203082 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
31203010 TTAAGTGTTT
* *
31203020 TCAGTATAGT-CTATCTATAGTAGTC
1 TCAGTATA-TACTACCTATAGCAGTC
*
31203045 TCAGTATATACTACCTATAGCAGTT
1 TCAGTATATACTACCTATAGCAGTC
*
31203070 TCAGGATATACTA
1 TCAGTATATACTA
31203083 TCAAAGACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (25 bp):
TCAGTATATACTACCTATAGCAGTC
Found at i:31203446 original size:18 final size:19
Alignment explanation
Indices: 31203425--31203463 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
31203415 TTTCAAAACA
31203425 TTATTC-ATTTACAAAT-TT
1 TTATTCAATTT-CAAATGTT
31203443 TTATTCAATTTCAAATGTT
1 TTATTCAATTTCAAATGTT
31203462 TT
1 TT
31203464 CTTATTACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (19 bp):
TTATTCAATTTCAAATGTT
Found at i:31208888 original size:30 final size:30
Alignment explanation
Indices: 31208845--31208904 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
31208835 GAGACAGTTT
* *
31208845 GAAAGCAGTTTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
31208875 GAAAGAAGATTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
31208905 TTGGGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (30 bp):
GAAAGAAGATTCAGATCGACAGAAATCTTA
Found at i:31210276 original size:16 final size:16
Alignment explanation
Indices: 31210255--31210286 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31210245 ATATTAGGGG
31210255 CAAAAGTGTAAATTTT
1 CAAAAGTGTAAATTTT
*
31210271 CAAAAGTGTGAATTTT
1 CAAAAGTGTAAATTTT
31210287 GGATTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
CAAAAGTGTAAATTTT
Found at i:31214349 original size:42 final size:43
Alignment explanation
Indices: 31214288--31214396 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 43
31214278 AATTTGAGAT
* *
31214288 TTACGTGTATGACCATGTCTGGGACATTGACATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * * *
31214330 TTACGTGTAAGACCCTGTCTTGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
*
31214373 TTACATGTAA-ACCATGTCTGGGAC
1 TTACGTGTAAGACCATGTCTGGGAC
31214397 GTTGGCATTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 42 0.74
43 15 0.26
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:31214403 original size:42 final size:42
Alignment explanation
Indices: 31214249--31214404 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
31214239 TGAGATATAG
* * * * *
31214249 TGTAAGACCACGTCTGGGACGTTAGCATC-AATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGTATAT--GA-TTACA
* * * *
31214293 TGTATGACCATGTCTGGGACATTGACATCGTATATGATTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATCGTATATGATTACA
* * *
31214335 TGTAAGACCCTGTCTTGGACAG-TGGCATCGTTATTTGATTACA
1 TGTAAGACCATGTCTGGGAC-GTTGGCATCG-TATATGATTACA
31214378 TGTAA-ACCATGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
31214405 TGTAGGAGCT
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 47 0.51
43 17 0.18
44 24 0.26
45 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCGTATATGATTACA
Found at i:31217978 original size:44 final size:44
Alignment explanation
Indices: 31217913--31217999 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
31217903 GTTGATAAAG
* *
31217913 TATGTAAGAATTGTCCGTTGATGATTCGAGATTCATGTTTTCCT
1 TATGTAAGAATTGTCCATTGATGATTCGAGAATCATGTTTTCCT
31217957 TATGTAAGAATTG-CTCATTGATGATTCGAGAATCATGTTTTCC
1 TATGTAAGAATTGTC-CATTGATGATTCGAGAATCATGTTTTCC
31218000 GACTGATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (44 bp):
TATGTAAGAATTGTCCATTGATGATTCGAGAATCATGTTTTCCT
Found at i:31221193 original size:13 final size:13
Alignment explanation
Indices: 31221175--31221199 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31221165 GAATTAAAAT
31221175 GTGTGAAAATTTC
1 GTGTGAAAATTTC
31221188 GTGTGAAAATTT
1 GTGTGAAAATTT
31221200 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:31222372 original size:42 final size:43
Alignment explanation
Indices: 31222306--31222408 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
31222296 GATTTGAGAT
* * *
31222306 TTACGTGTAAGATCATGTCAAGGACATTGGCATCG-TATATGA
1 TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
* * * *
31222348 TTACGTGTAAGACCCTATCTAGGACAGTGGCATTGTTATTTGA
1 TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
* *
31222391 TTACATGTAAGATCATAT
1 TTACGTGTAAGACCATAT
31222409 TTGGGACGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 29 0.58
43 21 0.42
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (43 bp):
TTACGTGTAAGACCATATCAAGGACAGTGGCATCGTTATATGA
Found at i:31222422 original size:43 final size:42
Alignment explanation
Indices: 31222265--31222428 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 42
31222255 ATATGAGAAT
* **
31222265 CGTGTAAGACCACGTCTAGGACGTTGGCATTG-ATTTGAGATTTA
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTT--GA-TTA
* * * * *
31222309 CGTGTAAGATCATGTCAAGGACATTGGCATCGTATATGATTA
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTTGATTA
* *
31222351 CGTGTAAGACCCTATCTAGGACAG-TGGCATTGTTATTTGATTA
1 CGTGTAAGATCATATCTAGGAC-GTTGGCATTG-TATTTGATTA
* * *
31222394 CATGTAAGATCATATTTGGGACGTTGGCATTGTAT
1 CGTGTAAGATCATATCTAGGACGTTGGCATTGTAT
31222429 GAGCTTTTTG
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 32 0.33
43 36 0.37
44 27 0.28
45 3 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
CGTGTAAGATCATATCTAGGACGTTGGCATTGTATTTGATTA
Found at i:31225617 original size:21 final size:21
Alignment explanation
Indices: 31225588--31225629 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31225578 ACGGAAATTG
*
31225588 AAAAGGTAAGACATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
* *
31225609 AAAATGTAACCCATTTTCCCT
1 AAAAGGTAACACATTTTCCCT
31225630 TGTTTTGGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAAGGTAACACATTTTCCCT
Found at i:31229421 original size:27 final size:27
Alignment explanation
Indices: 31229399--31229571 Score: 211
Period size: 27 Copynumber: 6.4 Consensus size: 27
31229389 AAGTATAACA
* *
31229399 GTCATTTTACCTTATGGGGGTATTTAG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
31229426 GTCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31229453 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31229480 ATCATTTTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
31229507 GTTATTTTACCATATGAGAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
31229534 GCCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
31229561 GTCATTTTACC
1 GTCATTTTACC
31229572 TATTTTGGGA
Statistics
Matches: 126, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 126 1.00
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:31232937 original size:27 final size:27
Alignment explanation
Indices: 31232880--31233050 Score: 256
Period size: 27 Copynumber: 6.4 Consensus size: 27
31232870 GGGTATAATA
31232880 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31232906 ATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
31232933 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31232960 GTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
31232987 GTCATTTTACCCTAT-GGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
31233013 GTCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
31233040 GTCATTTTACC
1 GTCATTTTACC
31233051 TATTTTGGGG
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
26 38 0.29
27 92 0.71
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:31232937 original size:53 final size:53
Alignment explanation
Indices: 31232880--31233050 Score: 288
Period size: 53 Copynumber: 3.2 Consensus size: 53
31232870 GGGTATAATA
* *
31232880 GTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
**
31232933 GTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCCTATG-GGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
*
31232987 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
31233040 GTCATTTTACC
1 GTCATTTTACC
31233051 TATTTTGGGG
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 61 0.55
54 49 0.45
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.44
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTG
Found at i:31238726 original size:41 final size:40
Alignment explanation
Indices: 31238573--31238715 Score: 198
Period size: 41 Copynumber: 3.5 Consensus size: 40
31238563 AGATAATTTA
31238573 GACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTC
1 GACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTC
* *
31238613 AAACTTTACGTCTAGAAGGCTTGATGCTGAG-GAAATGTTTC
1 -GACTTTACGTCTAGCAGGCTTGATGCTG-GTGAAATGTTTC
* * *
31238654 AGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATATTTC
1 -GACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTC
31238695 GTACTTTACGTCTAGCAGGCT
1 G-ACTTTACGTCTAGCAGGCT
31238716 AATTGTCGGT
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
40 2 0.02
41 88 0.97
42 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (40 bp):
GACTTTACGTCTAGCAGGCTTGATGCTGGTGAAATGTTTC
Found at i:31239788 original size:23 final size:22
Alignment explanation
Indices: 31239753--31239798 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
31239743 TGCTTACTTA
* *
31239753 TATTTATTTAAATTCATATATT
1 TATTTATTAAAATGCATATATT
31239775 TATTGTATTAAAATGCATATATT
1 TATT-TATTAAAATGCATATATT
31239798 T
1 T
31239799 TGATTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TATTTATTAAAATGCATATATT
Found at i:31241849 original size:41 final size:40
Alignment explanation
Indices: 31241782--31241861 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
31241772 AATACCGACC
*
31241782 TTTTCATTGATATCTTATTTGTATATCGTCCTTTTCAACA
1 TTTTCATTGATATCTTATTTGGATATCGTCCTTTTCAACA
31241822 TTTTCATTTGATATCCTT-TTTGGATATCGTCCTTTTCAAC
1 TTTTCA-TTGATAT-CTTATTTGGATATCGTCCTTTTCAAC
31241862 CTATTATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 6 0.16
41 28 0.76
42 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.53
Consensus pattern (40 bp):
TTTTCATTGATATCTTATTTGGATATCGTCCTTTTCAACA
Found at i:31242034 original size:70 final size:70
Alignment explanation
Indices: 31241918--31242054 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 70
31241908 TTCACCTGGC
* * **
31241918 GCTAGTCGGATAAACCAATGATAGGTGTGCTCTTTACTAGTCGGATAAACAT-ACAACATCTTGT
1 GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAAC-TGACAACATCTTGT
31241982 GCCAAT
65 GCCAAT
* * *
31241988 GCTAGTCGGATAAACCGAGGATAGGTGTGCCCTGCAGTAGTTGGATAAACTGACAACATCTTGTG
1 GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAACTGACAACATCTTGTG
31242053 CC
66 CC
31242055 CAGTTCTAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 1 0.02
70 58 0.98
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (70 bp):
GCTAGTCGGATAAACCAAGGATAGGTGTGCCCTGCACTAGTCGGATAAACTGACAACATCTTGTG
CCAAT
Found at i:31245092 original size:37 final size:36
Alignment explanation
Indices: 31245051--31245128 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 36
31245041 TTATTGATTA
*
31245051 GATTAGCTTTTAGGAGCGATTGGCGTGTTATCGAG-TG
1 GATTAGCTCTTAGGAGCGATTGGCGTGTT-TC-AGTTG
*
31245088 GATTAGCTCTTATGAGCGATTGGCGTGTTTCAGTTG
1 GATTAGCTCTTAGGAGCGATTGGCGTGTTTCAGTTG
31245124 GATTA
1 GATTA
31245129 CTTGTGTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 2 0.05
36 9 0.24
37 27 0.71
ACGTcount: A:0.19, C:0.12, G:0.32, T:0.37
Consensus pattern (36 bp):
GATTAGCTCTTAGGAGCGATTGGCGTGTTTCAGTTG
Found at i:31248832 original size:36 final size:36
Alignment explanation
Indices: 31248792--31248860 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
31248782 ATGTCATTCA
*
31248792 ATGGTTTAGCATTTGTTGTGAATCATCAAATGTGTG
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
31248828 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
31248861 ACACTGTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (36 bp):
ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
Found at i:31257233 original size:6 final size:6
Alignment explanation
Indices: 31257224--31257248 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31257214 TAAAGATGAA
31257224 GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG G
31257249 GGTTAGGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:31259124 original size:18 final size:18
Alignment explanation
Indices: 31259101--31259135 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31259091 GGCTTAGTAC
31259101 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
31259119 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
31259136 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:31268756 original size:44 final size:43
Alignment explanation
Indices: 31268706--31268818 Score: 120
Period size: 44 Copynumber: 2.6 Consensus size: 43
31268696 AAGGGTGAGA
*
31268706 AGTAAAATTTTAAGGGGAAAATAAAAAGTTTGGGGGGTTGATA-G
1 AGTAAAATTTT-AGGGGAAAGTAAAAAGTTTGGGGGGTTGA-AGG
*** *
31268750 AGTAAAATTTTAGAGGGAAAGTAAATTTTTTTGGGGGTTGAAGG
1 AGTAAAATTTTAG-GGGAAAGTAAAAAGTTTGGGGGGTTGAAGG
* *
31268794 AGTAAATTTTTGGGGGGAAAGTAAA
1 AGTAAAATTTT-AGGGGAAAGTAAA
31268819 GAGGTTCGGG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 3 0.05
44 55 0.93
45 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (43 bp):
AGTAAAATTTTAGGGGAAAGTAAAAAGTTTGGGGGGTTGAAGG
Found at i:31268818 original size:19 final size:19
Alignment explanation
Indices: 31268750--31268818 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 19
31268740 GGGTTGATAG
* * *
31268750 AGTAAAATTTTAGAGGGAA
1 AGTAAATTTTTGGGGGGAA
31268769 AGTAAATTTTTTTGGGGGTTGAA
1 AGTAAA--TTTTTGGGGG--GAA
31268792 GGAGTAAATTTTTGGGGGGAA
1 --AGTAAATTTTTGGGGGGAA
31268813 AGTAAA
1 AGTAAA
31268819 GAGGTTCGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
19 12 0.29
21 10 0.24
23 13 0.32
25 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (19 bp):
AGTAAATTTTTGGGGGGAA
Found at i:31270440 original size:20 final size:20
Alignment explanation
Indices: 31270415--31270456 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
31270405 TTTATGTTAG
31270415 TATATATTTATAATTGAAAA
1 TATATATTTATAATTGAAAA
*
31270435 TATATATTTATAGTTGAAAA
1 TATATATTTATAATTGAAAA
31270455 TA
1 TA
31270457 AGTTATTGAA
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:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TATATATTTATAATTGAAAA
Found at i:31270491 original size:3 final size:3
Alignment explanation
Indices: 31270483--31270534 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
31270473 TGTTGCTAAA
* * *
31270483 TAT TAT TAT GAT TAT TAT TAT CAT TAT TAT TAC TACT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT
31270529 TAT TAT
1 TAT TAT
31270535 GGTAATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:31274776 original size:37 final size:37
Alignment explanation
Indices: 31274726--31274804 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
31274716 TTATTACGAA
* *
31274726 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
31274763 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
31274800 GTCTT
1 GTCTT
31274805 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:31275001 original size:47 final size:47
Alignment explanation
Indices: 31274923--31275208 Score: 464
Period size: 47 Copynumber: 6.1 Consensus size: 47
31274913 CCCTTCGGGA
* * * * * * *
31274923 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
31274970 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31275017 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
31275064 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31275111 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31275158 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31275205 CTTA
1 CTTA
31275209 CTATCATTTC
Statistics
Matches: 222, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 222 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31283531 original size:139 final size:141
Alignment explanation
Indices: 31283335--31283636 Score: 410
Period size: 139 Copynumber: 2.2 Consensus size: 141
31283325 GATCCGTCAC
* * * *
31283335 CTTGGGTTGCCCGGCAACAATGACGATATACATTTACATAATACCATCTCAGATTGCCCAACAAC
1 CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
* * * *
31283400 GATGGCATTCTCAATCTGATTAATCTGTCA-CCTTGGTTTCCCGACAAAGATGACACACCGAGTA
66 GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
31283464 CAATCTACCAT
131 CAATCTACCAT
* * * *
31283475 TTTGGG-TGCCTGGCAACGATGACGCTATACATGTACATAATACCACCTCAGGTTGCCCGACAAC
1 CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
* * * * * *
31283539 GATGGCTTTCTCAATCTGATTAATTTGTCACCCTGGGCTACCCGACCAAGATGACTCACTAATTA
66 GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
31283604 CAATCTACCAT
131 CAATCTACCAT
* *
31283615 CCTGGGTTGCCTAGCAACGATG
1 CTTGGGTTGCCTGGCAACGATG
31283637 GTTATCAATC
Statistics
Matches: 139, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
139 79 0.57
140 46 0.33
141 14 0.10
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (141 bp):
CTTGGGTTGCCTGGCAACGATGACGATATACATGTACATAATACCACCTCAGATTGCCCAACAAC
GATGGCATTCTCAATCTGATTAATCTGTCACCCTGGGCTACCCGACAAAGATGACACACCAAGTA
CAATCTACCAT
Found at i:31288057 original size:19 final size:19
Alignment explanation
Indices: 31288031--31288069 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
31288021 AAATATAGAG
*
31288031 AAATTTGAGAG-AAATAAT
1 AAATTTGAAAGAAAATAAT
31288049 AAATATTGAAAGAAAATAAT
1 AAAT-TTGAAAGAAAATAAT
31288069 A
1 A
31288070 GGGGGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (19 bp):
AAATTTGAAAGAAAATAAT
Found at i:31290133 original size:41 final size:41
Alignment explanation
Indices: 31290088--31290168 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
31290078 TAACCTTTTT
31290088 GGCGAAGCATCCATCTTAGTTTTCTTGCTAGGCGGTTCAGG
1 GGCGAAGCATCCATCTTAGTTTTCTTGCTAGGCGGTTCAGG
*
31290129 GGCGAAGCATCCATCTTAGTTTTCTTGCTTGGCGGTTCAG
1 GGCGAAGCATCCATCTTAGTTTTCTTGCTAGGCGGTTCAG
31290169 CTGTTTTTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.33
Consensus pattern (41 bp):
GGCGAAGCATCCATCTTAGTTTTCTTGCTAGGCGGTTCAGG
Found at i:31290725 original size:27 final size:27
Alignment explanation
Indices: 31290694--31290748 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
31290684 AATGATCAAA
31290694 TCTGAAACACATTTTAGCAATGAATAG
1 TCTGAAACACATTTTAGCAATGAATAG
31290721 TCTGAAACACATTTTAGCAATGAATAG
1 TCTGAAACACATTTTAGCAATGAATAG
31290748 T
1 T
31290749 TACACAAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (27 bp):
TCTGAAACACATTTTAGCAATGAATAG
Found at i:31292625 original size:45 final size:45
Alignment explanation
Indices: 31292561--31292735 Score: 235
Period size: 45 Copynumber: 3.9 Consensus size: 45
31292551 CTTTCCTTTC
** * * *
31292561 TGGCTGTGCAGCCTTTTTGGAATGACTCTCATCAGGAACAGTCTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
* ** * *
31292606 TGGCTGTGCTGCCTTTTTGGATTGACTCTCATCAGGTATACTTTT
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
31292651 TGGCTGTGCAGCCTTTTCAG-ATCGACTCTCATCAGGTATACTCTT
1 TGGCTGTGCAGCCTTTTCAGAAT-GACTCTCATCAGGTATACTCTT
*
31292696 TGGCTGAGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
1 TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATA
31292736 GACCCACTTG
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.01
45 113 0.97
46 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (45 bp):
TGGCTGTGCAGCCTTTTCAGAATGACTCTCATCAGGTATACTCTT
Found at i:31293520 original size:47 final size:48
Alignment explanation
Indices: 31293463--31293558 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 48
31293453 ATTAAGGAGA
31293463 ATAAAGCAGTTATAACTTC-A-AAGAAGACATAACAGATTTTATTAAGC
1 ATAAAGCAGTTATAACTTCAAGAAGAAGACATAACAGATTTTA-TAAGC
* * *
31293510 ATAAATCAGTTGTAACTTCAATGAAGAAGGCATAACAGATTTTATAAGC
1 ATAAAGCAGTTATAACTTCAA-GAAGAAGACATAACAGATTTTATAAGC
31293559 CAACAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 17 0.40
48 1 0.02
49 5 0.12
50 20 0.47
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.28
Consensus pattern (48 bp):
ATAAAGCAGTTATAACTTCAAGAAGAAGACATAACAGATTTTATAAGC
Found at i:31295588 original size:94 final size:94
Alignment explanation
Indices: 31295427--31295619 Score: 377
Period size: 94 Copynumber: 2.1 Consensus size: 94
31295417 AAAAAGCATC
31295427 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
31295492 TAAGACAATCAGTCAGTGGTAGCATGATT
66 TAAGACAATCAGTCAGTGGTAGCATGATT
*
31295521 CACTAACGTGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
1 CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
31295586 TAAGACAATCAGTCAGTGGTAGCATGATT
66 TAAGACAATCAGTCAGTGGTAGCATGATT
31295615 CACTA
1 CACTA
31295620 GTCACGAAAC
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 98 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (94 bp):
CACTAACATGCACTAGCGTAAGGTAGAACACAAAGGATATTAAACTATTAGAGCACCTAAAATAT
TAAGACAATCAGTCAGTGGTAGCATGATT
Found at i:31300882 original size:24 final size:23
Alignment explanation
Indices: 31300840--31300899 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 23
31300830 ATTAAATTAT
31300840 AAATTTATTTATTAAATTATAAAATA
1 AAATTTA--TATTAAATTAT-AAATA
*
31300866 AAATTTATATTACATTATAAATA
1 AAATTTATATTAAATTATAAATA
31300889 AAATTTCATAT
1 AAATTT-ATAT
31300900 AATTATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 11 0.34
24 14 0.44
26 7 0.22
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATTTATATTAAATTATAAATA
Found at i:31301572 original size:13 final size:12
Alignment explanation
Indices: 31301536--31301577 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
31301526 ATCATATTTG
*
31301536 ATTTTTATATCA
1 ATTTTTATATAA
31301548 ATTTTT-TATAA
1 ATTTTTATATAA
31301559 ATTTATTATATAAA
1 ATTT-TTATAT-AA
31301573 ATTTT
1 ATTTT
31301578 CATCCATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 4 0.15
14 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTTTATATAA
Found at i:31301739 original size:14 final size:14
Alignment explanation
Indices: 31301719--31301757 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
31301709 TTATTTCATT
*
31301719 AAAAATGATTTCTG
1 AAAAATGATTTCTA
*
31301733 GAAAATGATTTCTA
1 AAAAATGATTTCTA
31301747 AAAAATGATTT
1 AAAAATGATTT
31301758 ACTTTTCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (14 bp):
AAAAATGATTTCTA
Found at i:31302238 original size:19 final size:19
Alignment explanation
Indices: 31302200--31302238 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31302190 TTATACTACA
**
31302200 AAATATTTATAATTGTAAT
1 AAATATTTATAATTAAAAT
*
31302219 AAATATTTATTATTAAAAT
1 AAATATTTATAATTAAAAT
31302238 A
1 A
31302239 TTAATGTTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATATTTATAATTAAAAT
Found at i:31302304 original size:16 final size:16
Alignment explanation
Indices: 31302273--31302309 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
31302263 ATGTGAATAA
31302273 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
31302289 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
31302305 TATTA
1 TATTA
31302310 AAATAAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:31302361 original size:22 final size:21
Alignment explanation
Indices: 31302321--31302373 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
31302311 AATAAGATTG
*
31302321 AAATATTAAA-TAATTTATTA
1 AAATAATAAATTAATTTATTA
31302341 AAATAATAAATTATATTTATTA
1 AAATAATAAATTA-ATTTATTA
* *
31302363 TATTAATAAAT
1 AAATAATAAAT
31302374 ATGAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 2 0.07
22 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAATAAATTAATTTATTA
Found at i:31320447 original size:106 final size:106
Alignment explanation
Indices: 31320291--31320485 Score: 275
Period size: 106 Copynumber: 1.8 Consensus size: 106
31320281 ATCCAAGGAA
*
31320291 ACAAAGAGAGTTAACACGAGCATAACAACAATAATTCCACTACAATGTAATCGAACCAAATATCA
1 ACAAAGAGAGTTAACACGAGCATAACAACAATAATACCACTACAATGTAATCGAACCAAATATCA
*
31320356 TAAAACTTGTACTCTGATTGGTTGATCTGATATCGGAGAAC
66 TAAAACTTGTACTCTGATCGGTTGATCTGATATCGGAGAAC
** ** * * * *
31320397 ACAAAGAGAGTTAACACGAGCATGTCAACGGTGAA-ACCACTGCAATGTAATTGAGCCAAATTTC
1 ACAAAGAGAGTTAACACGAGCATAACAACAAT-AATACCACTACAATGTAATCGAACCAAATATC
*
31320461 ATAAAATTTGTACTCTGATCGGTTG
65 ATAAAACTTGTACTCTGATCGGTTG
31320486 TTGCGACAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
106 75 0.97
107 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (106 bp):
ACAAAGAGAGTTAACACGAGCATAACAACAATAATACCACTACAATGTAATCGAACCAAATATCA
TAAAACTTGTACTCTGATCGGTTGATCTGATATCGGAGAAC
Found at i:31323181 original size:19 final size:19
Alignment explanation
Indices: 31323157--31323267 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
31323147 AATCATATCT
*
31323157 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
**
31323176 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
31323195 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
31323214 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
31323233 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
31323252 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
31323268 CCTGAAGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 83 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:31323204 original size:38 final size:38
Alignment explanation
Indices: 31323157--31323260 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
31323147 AATCATATCT
*
31323157 TCTAAGATTGTATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
31323195 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
31323233 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
31323261 GCATATCCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:31327508 original size:11 final size:11
Alignment explanation
Indices: 31327492--31327522 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
31327482 TTTAAGGTGA
31327492 GTAATGTAATT
1 GTAATGTAATT
31327503 GTAATGTAATT
1 GTAATGTAATT
*
31327514 GAAATGTAA
1 GTAATGTAA
31327523 AATGTTACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (11 bp):
GTAATGTAATT
Found at i:31330893 original size:16 final size:16
Alignment explanation
Indices: 31330872--31330904 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31330862 AGTCCTTGTA
31330872 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
31330888 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
31330904 A
1 A
31330905 ACAAAATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:31337485 original size:43 final size:43
Alignment explanation
Indices: 31337438--31337562 Score: 146
Period size: 43 Copynumber: 2.9 Consensus size: 43
31337428 TGTAATCTCG
*
31337438 TATCGATGCCAATAGCCCAGCCATGGTCTTACACGAAATCACA
1 TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
* * * *
31337481 TATCGATGTCAAT-GTCCCAGACATGGTCTTACATGAATTCTCA
1 TATCGATGCCAATAG-CCCAGACATGGTCTTACACGAAATCACA
* * * *
31337524 TATCGATGCC-ATATCCCAAATATGGTCTTACACGTAATC
1 TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATC
31337563 TCGGTAACCC
Statistics
Matches: 68, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 23 0.34
43 45 0.66
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TATCGATGCCAATAGCCCAGACATGGTCTTACACGAAATCACA
Found at i:31344845 original size:24 final size:24
Alignment explanation
Indices: 31344807--31344853 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31344797 AGACTGTGTG
*
31344807 CATTTTAAAATTTGGTTTTATTTT
1 CATTTTAAAATTTGGGTTTATTTT
31344831 CATTTATAAAA-TTGGGTTTATTT
1 CATTT-TAAAATTTGGGTTTATTT
31344854 AGGTTTGCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (24 bp):
CATTTTAAAATTTGGGTTTATTTT
Found at i:31345200 original size:87 final size:87
Alignment explanation
Indices: 31345049--31345661 Score: 959
Period size: 87 Copynumber: 7.1 Consensus size: 87
31345039 CCCGGGGCAT
* *
31345049 AACAGATTTAGACCATTAATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAATACGGCGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
31345114 TCATCTTCCCCAGGAGTAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
* * * *
31345136 AACATATTTAGACCATTAATCCCATCTCCCTAAGCAATAGTGGAGCGTATCGAAGACTGCGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
*
31345201 TCATCTTCCTCAGGAGTAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
* * *
31345223 AACGGATTTATACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGTGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
31345288 TCATCTTCCCCAGGAGTAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
* *
31345310 AACATATTTAGACCATTAATCCCATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
*
31345375 TCATCTTCCACAGGAGTAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
* * *
31345397 AACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTAGAGCGGATCGAAAACGGCGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
*
31345462 TCATCTTCCCTAGGAGTA-GG-
66 TCATCTTCCCCAGGAGTAGGGA
* *
31345482 ----GATTTAGACCATTAATCCCATCTCCCTAAACAATAGTGGAGCGGATCGAAGACGGCGAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
*
31345543 TCATCTTCCCCATGAGTAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
* * *
31345565 AACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCAAATC
1 AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
* *
31345630 TCATATTCCCCAGGAATAGGGA
66 TCATCTTCCCCAGGAGTAGGGA
31345652 AACAGATTTA
1 AACAGATTTA
31345662 AGCCACAAAT
Statistics
Matches: 478, Mismatches: 42, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
81 73 0.15
82 2 0.00
86 2 0.00
87 401 0.84
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (87 bp):
AACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATC
TCATCTTCCCCAGGAGTAGGGA
Found at i:31346441 original size:257 final size:258
Alignment explanation
Indices: 31345985--31346498 Score: 940
Period size: 257 Copynumber: 2.0 Consensus size: 258
31345975 ATACAAACTA
31345985 AACCCAATATAACTAGTCCAAATCAGCCTAGCCCAGACCCGATTACAATAGGATAGGAAGCCCTA
1 AACCCAATATAACTAGTCCAAATCAGCCTAGCCCAGACCCGATTACAATAGGATAGGAAGCCCTA
* * *
31346050 GTGTCAGCCCCAACCAGCGCCGCAGCAGACGTCCCCTCGCACCTAGCACCGCTCGCACGAGCCTC
66 GCGTCAGCCCCAACCAGCGCCGCAACAGACATCCCCTCGCACCTAGCACCGCTCGCACGAGCCTC
31346115 GTACGCGCGCCTTCGCCTCCGTACATGCCACATCCGCAACCTCTGCACACAGTACCTGCAAGAGA
131 GTACGCGCGCCTTCGCCTCCGTACATGCCACATCCGCAACCTCTGCACACAGTACCTGCAAGAGA
*
31346180 CGCACAAAGCGCAGCAGAAACAGACCACAAAACG-AAAGAGGCAGAAATCGGCAGAGAAAAGC
196 CGCACAAAGCGCAACAGAAACAGACCACAAAACGAAAAGAGGCAGAAATCGGCAGAGAAAAGC
*
31346242 AACCCAATATAACTAGTCCAAATCAGCCTAGCCCAGACCCGATTACAATAGGATGGGAAGCCCTA
1 AACCCAATATAACTAGTCCAAATCAGCCTAGCCCAGACCCGATTACAATAGGATAGGAAGCCCTA
* *
31346307 GCGTTAGCCCCAACCAGCGCCGCAACAGACATCCCCTCGCACGTAGCACCGCTCGCACGAGCCTC
66 GCGTCAGCCCCAACCAGCGCCGCAACAGACATCCCCTCGCACCTAGCACCGCTCGCACGAGCCTC
*
31346372 GTACGCGTGCCTTCGCCTCCGTACATGCCACATCCGCAACCTCTGCACACAGTACCTGCAAGAGA
131 GTACGCGCGCCTTCGCCTCCGTACATGCCACATCCGCAACCTCTGCACACAGTACCTGCAAGAGA
*
31346437 CGCACAAAGCGCAACAGAAACAGACCACAAAACGAAAAGAGGCAGAAATCGTCAGAGAAAAG
196 CGCACAAAGCGCAACAGAAACAGACCACAAAACGAAAAGAGGCAGAAATCGGCAGAGAAAAG
31346499 TAAAAAATAA
Statistics
Matches: 247, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
257 221 0.89
258 26 0.11
ACGTcount: A:0.32, C:0.35, G:0.21, T:0.12
Consensus pattern (258 bp):
AACCCAATATAACTAGTCCAAATCAGCCTAGCCCAGACCCGATTACAATAGGATAGGAAGCCCTA
GCGTCAGCCCCAACCAGCGCCGCAACAGACATCCCCTCGCACCTAGCACCGCTCGCACGAGCCTC
GTACGCGCGCCTTCGCCTCCGTACATGCCACATCCGCAACCTCTGCACACAGTACCTGCAAGAGA
CGCACAAAGCGCAACAGAAACAGACCACAAAACGAAAAGAGGCAGAAATCGGCAGAGAAAAGC
Found at i:31347011 original size:186 final size:185
Alignment explanation
Indices: 31346697--31347069 Score: 710
Period size: 186 Copynumber: 2.0 Consensus size: 185
31346687 GATTCTCTTA
31346697 GTGATAAACTAAATAGGAGTTTAAGTTTCGAGTTTACCTGCCTCGATGACCCAGCCGTCGTTCTG
1 GTGATAAACTAAATAGGAGTTTAAGTTTCGAGTTTACCTGCCTCGATGACCCAGCCGTCGTTCTG
31346762 GGTGGTGTCGCGGCCACCGGAAGAACCATGAATGGTTCTAACCCGAGAACGGCGCAAAAGGGGAG
66 GGTGGTGTCGCGGCCACCGGAAGAACCATGAATGGTTCTAACCCGAGAACGGCGCAAAAGGGGAG
31346827 AGGGGAAAACTACTATTCTATCTGTTTTTTTTGAAGAAGATCTGATTAGTTTTTAG
131 AGGGGAAAACTACTATTCTATCTG-TTTTTTTGAAGAAGATCTGATTAGTTTTTAG
* *
31346883 GTGATAAACTAAATAGGAGTTTAAGTTTCGAGTTTACCTGCCTCGATGACCCAGCTGTCGTTTTG
1 GTGATAAACTAAATAGGAGTTTAAGTTTCGAGTTTACCTGCCTCGATGACCCAGCCGTCGTTCTG
31346948 GGTGGTGTCGCGGCCACCGGAAGAACCATGAATGGTTCTAACCCGAGAACGGCGCAAAAGGGGAG
66 GGTGGTGTCGCGGCCACCGGAAGAACCATGAATGGTTCTAACCCGAGAACGGCGCAAAAGGGGAG
*
31347013 AGGGGAAAACTACTTTTCTATCTGTTTTTTTGAAGAAGATCTGATTAGTTTTTAG
131 AGGGGAAAACTACTATTCTATCTGTTTTTTTGAAGAAGATCTGATTAGTTTTTAG
31347068 GT
1 GT
31347070 TTTTTTTTTA
Statistics
Matches: 184, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 33 0.18
186 151 0.82
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (185 bp):
GTGATAAACTAAATAGGAGTTTAAGTTTCGAGTTTACCTGCCTCGATGACCCAGCCGTCGTTCTG
GGTGGTGTCGCGGCCACCGGAAGAACCATGAATGGTTCTAACCCGAGAACGGCGCAAAAGGGGAG
AGGGGAAAACTACTATTCTATCTGTTTTTTTGAAGAAGATCTGATTAGTTTTTAG
Found at i:31347360 original size:130 final size:130
Alignment explanation
Indices: 31347127--31347385 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 130
31347117 GCCGTTTGGA
*
31347127 GTCTGATCTGTGGCTCCGAAACGACGCCGTACTGACCTACATTGACCTTCAACCTGATAACCCGA
1 GTCTGATCTGTGGCTCCGAAACGACGCCGTACTGACCTACATTGACCTTCAACCCGATAACCCGA
*
31347192 CCTAGTGGGCGAAGGATCCGCGCGTTTTAAAGCCAAACGGGCTATTTGCGCTTTGGGTCCCTCTG
66 CCTAGTGGGCGAAGGATCCGCGCGTTTTAAAGCCAAACGGGCTATTTACGCTTTGGGTCCCTCTG
31347257 GTCTGATCTGTGGCTCCGAAACGACGCCGTACTGACCTACATTGACCTTCAACCCGATAACCCGA
1 GTCTGATCTGTGGCTCCGAAACGACGCCGTACTGACCTACATTGACCTTCAACCCGATAACCCGA
31347322 CCTAGTGGGCGAAGGATCCGCGCGTTTTAAAGCCAAACGGGCTATTTACGCTTTGGGTCCCTCT
66 CCTAGTGGGCGAAGGATCCGCGCGTTTTAAAGCCAAACGGGCTATTTACGCTTTGGGTCCCTCT
31347386 ACTTTTCTGG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 127 1.00
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (130 bp):
GTCTGATCTGTGGCTCCGAAACGACGCCGTACTGACCTACATTGACCTTCAACCCGATAACCCGA
CCTAGTGGGCGAAGGATCCGCGCGTTTTAAAGCCAAACGGGCTATTTACGCTTTGGGTCCCTCTG
Found at i:31360400 original size:87 final size:87
Alignment explanation
Indices: 31360254--31360796 Score: 924
Period size: 87 Copynumber: 6.2 Consensus size: 87
31360244 AAGATAGCAG
*
31360254 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360319 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
*
31360341 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360406 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
*
31360428 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360493 GGGAAACGGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
31360515 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACAGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360580 AGGAAACAGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* *
31360602 ATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360667 AGGAAACAGATTTAGACCATTA
66 GGGAAACAGATTTAGACCATTA
* * * *
31360689 ATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAATATGGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360754 GGGAAACAGATTTAGAACATTA
66 GGGAAACAGATTTAGACCATTA
*
31360776 ATCCCATCTCCCTAAGCAATA
1 ATCCTATCTCCCTAAGCAATA
31360797 TATGGCGAAT
Statistics
Matches: 440, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 440 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (87 bp):
ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
GGGAAACAGATTTAGACCATTA
Found at i:31360544 original size:174 final size:174
Alignment explanation
Indices: 31360254--31361529 Score: 1991
Period size: 174 Copynumber: 7.5 Consensus size: 174
31360244 AAGATAGCAG
*
31360254 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
*
31360319 GGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31360384 AATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
*
31360428 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* *
31360493 GGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACAGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
* * *
31360558 AATCTCATCTTCCTCAGGAGTAAGGAAACAGATTTAGACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
* *
31360602 ATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* * * *
31360667 AGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAATATGGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
* * *
31360732 AATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
* *
31360776 ATCCCATCTCCCTAAGCAATA-T-------AT-------GGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* * * *
31360826 GGGAAACAGATTTAGAACATTAATCCCATCTCCCTAAGCAATAGTGGAGCGTATCGAAGACTGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31360891 AATCTCATCTTCCTCAGGAGTAGGGAAACGGATTTAGACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
* * *
31360935 ATTCTATCTCCCTAAGAAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCACAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* *
31361000 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAATACGGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
* *
31361065 AATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTATACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
*
31361109 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGTGAATCTCATCTTCCCCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* *
31361174 GGGAAACATATTTAGACCATTAATCCCATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31361239 AATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
* * *
31361283 ATCCTATCTCCCTAAGCAATAGTAGAGCGGATCGAAAACGGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
* *
31361348 -GG-----GATTTAGACCATTAATCCCATCTCCCTAAACAATAGTGGAGCGGATCGAAGACGGCG
66 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31361407 AATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTA
131 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
* * * *
31361451 ATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGACGGCAAATCTCATATTCCCCAGGAATA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
31361516 GGGAAACAGATTTA
66 GGGAAACAGATTTA
31361530 AGCCACAAAT
Statistics
Matches: 1009, Mismatches: 72, Indels: 42
0.90 0.06 0.04
Matches are distributed among these distances:
159 139 0.14
160 1 0.00
166 2 0.00
167 2 0.00
168 157 0.16
169 2 0.00
173 3 0.00
174 703 0.70
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (174 bp):
ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTA
GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTA
Found at i:31360724 original size:261 final size:260
Alignment explanation
Indices: 31360254--31361529 Score: 1973
Period size: 261 Copynumber: 5.0 Consensus size: 260
31360244 AAGATAGCAG
*
31360254 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTT-CCCAGGAGTA
*
31360319 GGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
65 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31360384 AATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
130 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
* *
31360449 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATT
195 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATT
31360514 A
260 A
*
31360515 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACAGCGAATCTCATCTTCCTCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCC-CAGGAGTA
* *
31360580 AGGAAACAGATTTAGACCATTAATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAAGACGGCG
65 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
* * *
31360645 AATCTCATCTTCCTCAGGAGTAAGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
130 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
* * * * *
31360710 GTGGAGCAGATCGAATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATT
195 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATT
31360775 A
260 A
*
31360776 ATCCCATCTCCCTAAGCAATA-T-------AT-------GGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCC-AGGAGTA
* * * *
31360826 GGGAAACAGATTTAGAACATTAATCCCATCTCCCTAAGCAATAGTGGAGCGTATCGAAGACTGCG
65 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
* * *
31360891 AATCTCATCTTCCTCAGGAGTAGGGAAACGGATTTAGACCATTAATTCTATCTCCCTAAGAAATA
130 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
*
31360956 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCACAGGAGTAGGGAAACAGATTTAGACCATT
195 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATT
31361021 A
260 A
* *
31361022 ATCCTATCTCCCTGAGCAATAGTGGAGCGGATCGAATACGGCGAATCTCATCTTCCCCAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTT-CCCAGGAGTA
* *
31361087 GGGAAACAGATTTATACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGTG
65 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
** *
31361152 AATCTCATCTTCCCCAGGAGTAGGGAAACATATTTAGACCATTAATCCCATCTCCCTAAGCAATA
130 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
* *
31361217 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATT
195 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATT
31361282 A
260 A
* *
31361283 ATCCTATCTCCCTAAGCAATAGTAGAGCGGATCGAAAACGGCGAATCTCATCTTCCCTAGGAGTA
1 ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCC-AGGAGTA
* *
31361348 -GG-----GATTTAGACCATTAATCCCATCTCCCTAAACAATAGTGGAGCGGATCGAAGACGGCG
65 GGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCG
*
31361407 AATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
130 AATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATA
* * * *
31361472 GTGGAGCAGATCGAAGACGGCAAATCTCATATTCCCCAGGAATAGGGAAACAGATTTA
195 GTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTA
31361530 AGCCACAAAT
Statistics
Matches: 928, Mismatches: 68, Indels: 44
0.89 0.07 0.04
Matches are distributed among these distances:
245 1 0.00
246 222 0.24
247 1 0.00
253 2 0.00
254 2 0.00
255 166 0.18
260 8 0.01
261 523 0.56
262 3 0.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (260 bp):
ATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCAGGAGTAG
GGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGCAATAGTGGAGCGGATCGAAGACGGCGA
ATCTCATCTTCCCCAGGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGCAATAG
TGGAGCGGATCGAAGACGGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTA
Found at i:31360841 original size:72 final size:72
Alignment explanation
Indices: 31360724--31360868 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
31360714 AGCAGATCGA
31360724 ATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCT
1 ATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCT
31360789 AAGCAAT
66 AAGCAAT
31360796 ATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCT
1 ATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCT
31360861 AAGCAAT
66 AAGCAAT
31360868 A
1 A
31360869 GTGGAGCGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (72 bp):
ATATGGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCT
AAGCAAT
Found at i:31360947 original size:87 final size:87
Alignment explanation
Indices: 31360800--31361529 Score: 1157
Period size: 87 Copynumber: 8.5 Consensus size: 87
31360790 AGCAATATAT
* * *
31360800 GGCGAATCTCATCTTCCCTAGGAGTAGGGAAACAGATTTAGAACATTAATCCCATCTCCCTAAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
*
31360865 AATAGTGGAGCGTATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* * * * *
31360887 TGCGAATCTCATCTTCCTCAGGAGTAGGGAAACGGATTTAGACCATTAATTCTATCTCCCTAAGA
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
31360952 AATAGTGGAGCGGATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* *
31360974 GGCGAATCTCATCTTCCACAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTGAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
*
31361039 AATAGTGGAGCGGATCGAATAC
66 AATAGTGGAGCGGATCGAAGAC
*
31361061 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTATACCATTAATCCTATCTCCCTAAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
31361126 AATAGTGGAGCGGATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* * *
31361148 GGTGAATCTCATCTTCCCCAGGAGTAGGGAAACATATTTAGACCATTAATCCCATCTCCCTAAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
31361213 AATAGTGGAGCGGATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* *
31361235 GGCGAATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
* *
31361300 AATAGTAGAGCGGATCGAAAAC
66 AATAGTGGAGCGGATCGAAGAC
* * *
31361322 GGCGAATCTCATCTTCCCTAGGAGTA-GG-----GATTTAGACCATTAATCCCATCTCCCTAAAC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
31361381 AATAGTGGAGCGGATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* *
31361403 GGCGAATCTCATCTTCCCCATGAGTAGGGAAACGGATTTAGACCATTAATCCTATCTCCCTAAGC
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
*
31361468 AATAGTGGAGCAGATCGAAGAC
66 AATAGTGGAGCGGATCGAAGAC
* * *
31361490 GGCAAATCTCATATTCCCCAGGAATAGGGAAACAGATTTA
1 GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTA
31361530 AGCCACAAAT
Statistics
Matches: 590, Mismatches: 47, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
81 73 0.12
82 2 0.00
86 2 0.00
87 513 0.87
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (87 bp):
GGCGAATCTCATCTTCCCCAGGAGTAGGGAAACAGATTTAGACCATTAATCCTATCTCCCTAAGC
AATAGTGGAGCGGATCGAAGAC
Found at i:31365470 original size:22 final size:21
Alignment explanation
Indices: 31365426--31365470 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
31365416 ACTAAAATTG
*
31365426 AATTATAATTTTTTATATATT
1 AATTATAATTTTTTAGATATT
* *
31365447 AATTTTAATTTTTTTAGATTTT
1 AATTATAA-TTTTTTAGATATT
31365469 AA
1 AA
31365471 AAGGGGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTATAATTTTTTAGATATT
Found at i:31367803 original size:46 final size:44
Alignment explanation
Indices: 31367699--31367806 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
31367689 TGTCTTTAAC
** * * *
31367699 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
31367743 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
31367789 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
31367807 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:31368140 original size:4 final size:4
Alignment explanation
Indices: 31368131--31368162 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
31368121 CCTTTTTCTT
31368131 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
31368163 CTTCCTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:31368244 original size:15 final size:16
Alignment explanation
Indices: 31368212--31368258 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
31368202 GTTTCGTCTC
* *
31368212 TTCTATTCTGTTTCTT
1 TTCTATTCTTTTTTTT
31368228 TTCT-TTCTTTTTTTT
1 TTCTATTCTTTTTTTT
31368243 TTCTATTCTTTCTTTT
1 TTCTATTCTTT-TTTT
31368259 GTTTTATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 13 0.48
16 10 0.37
17 4 0.15
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (16 bp):
TTCTATTCTTTTTTTT
Found at i:31368245 original size:20 final size:21
Alignment explanation
Indices: 31368222--31368263 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
31368212 TTCTATTCTG
*
31368222 TTTCTTTTCTTTCTTTT-TTT
1 TTTCTATTCTTTCTTTTGTTT
31368242 TTTCTATTCTTTCTTTTGTTT
1 TTTCTATTCTTTCTTTTGTTT
31368263 T
1 T
31368264 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTCTATTCTTTCTTTTGTTT
Found at i:31368280 original size:5 final size:5
Alignment explanation
Indices: 31368267--31368339 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
31368257 TTGTTTTATG
31368267 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
31368315 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
31368340 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:31368292 original size:19 final size:19
Alignment explanation
Indices: 31368268--31368310 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
31368258 TGTTTTATGT
31368268 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
31368287 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
31368306 ATATA
1 ATATA
31368311 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:31368320 original size:24 final size:25
Alignment explanation
Indices: 31368274--31368338 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
31368264 ATGTATATAT
* *
31368274 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
31368298 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
31368323 TTACTATAATATAATA
1 ATAATATAATATAATA
31368339 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:31370914 original size:20 final size:20
Alignment explanation
Indices: 31370889--31370927 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31370879 TACTTATAAT
*
31370889 ATTTATTATTTTATAAAATC
1 ATTTATTATCTTATAAAATC
*
31370909 ATTTATTATCTTGTAAAAT
1 ATTTATTATCTTATAAAAT
31370928 AATATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTATTATCTTATAAAATC
Found at i:31371968 original size:17 final size:17
Alignment explanation
Indices: 31371943--31372004 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
31371933 ACACATTTAT
*
31371943 ATAATATTCATCATCAA
1 ATAACATTCATCATCAA
* *
31371960 ATAACATTCA-CTATTTAT
1 ATAACATTCATC-A-TCAA
*
31371978 ATAATATTCATCATCAA
1 ATAACATTCATCATCAA
31371995 ATAACATTCA
1 ATAACATTCA
31372005 CTTTAATTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
16 1 0.03
17 21 0.60
18 12 0.34
19 1 0.03
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAACATTCATCATCAA
Found at i:31371976 original size:35 final size:35
Alignment explanation
Indices: 31371937--31372006 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
31371927 AATAAAACAC
31371937 ATTTATATAATATTCATCATCAAATAACATTCACT
1 ATTTATATAATATTCATCATCAAATAACATTCACT
31371972 ATTTATATAATATTCATCATCAAATAACATTCACT
1 ATTTATATAATATTCATCATCAAATAACATTCACT
31372007 TTAATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (35 bp):
ATTTATATAATATTCATCATCAAATAACATTCACT
Done.