Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 51 of 208
Found at i:19877019 original size:5 final size:5
Alignment explanation
Indices: 19877009--19877068 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
19876999 AACATGTTTC
* * *
19877009 TTTTA TTTTA TTTTTA TTCTTA TTTTTA ATTT- CTTCA -TTTA TTTTA
1 TTTTA TTTTA -TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA
19877055 TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT
19877069 TTGCTTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
4 5 0.11
5 28 0.61
6 11 0.24
7 2 0.04
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:19879109 original size:22 final size:22
Alignment explanation
Indices: 19879084--19879134 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
19879074 ACATATGCAC
* *
19879084 ATATATATATTAAGATATATGG
1 ATATATATAATAAGATATATAG
19879106 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATATAG
19879128 ATATATA
1 ATATATA
19879135 ACTAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
ATATATATAATAAGATATATAG
Found at i:19879135 original size:20 final size:21
Alignment explanation
Indices: 19879086--19879144 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
19879076 ATATGCACAT
* *
19879086 ATATATATTAAGATATATGGAT
1 ATATATAATAAGATATAT-GAG
19879108 ATATATAATAAGATATAT-AG
1 ATATATAATAAGATATATGAG
19879128 ATATATAACTAA-ATATA
1 ATATATAA-TAAGATATA
19879145 ATATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATAATAAGATATATGAG
Found at i:19880316 original size:21 final size:21
Alignment explanation
Indices: 19880277--19880316 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19880267 CAAGTGGGCA
**
19880277 TGGGCGGTGGTGGCAGGTGCT
1 TGGGCGGTGGCAGCAGGTGCT
*
19880298 TGGGCGGTGGCAGCTGGTG
1 TGGGCGGTGGCAGCAGGTG
19880317 TCAGACGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.57, T:0.23
Consensus pattern (21 bp):
TGGGCGGTGGCAGCAGGTGCT
Found at i:19880937 original size:95 final size:95
Alignment explanation
Indices: 19880718--19881001 Score: 487
Period size: 95 Copynumber: 3.0 Consensus size: 95
19880708 GTAATCTCCG
*
19880718 ATCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTAGTCAC
1 ATCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--C
19880783 AGGGAGGTAAAATCTGCCATCTTTGATCTTCA
64 AGGGAGGTAAAATCTGCCATCTTTGATCTTCA
* *
19880815 ATCTATTCCACTGTCAAATGCAAGGAGATAGAGTTATCGGCTTCAATGTACTCCGCTGTAGTCAG
1 ATCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
19880880 GGAGGTAAAATCTGCCATCTTTGATCTTCA
66 GGAGGTAAAATCTGCCATCTTTGATCTTCA
* *
19880910 ATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
1 ATCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
* *
19880975 GGAGATAAAATCTGCCATCTTCGATCT
66 GGAGGTAAAATCTGCCATCTTTGATCT
19881002 GCTTCGCTGC
Statistics
Matches: 178, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
95 119 0.67
97 59 0.33
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (95 bp):
ATCTATTCCACTGTCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAG
GGAGGTAAAATCTGCCATCTTTGATCTTCA
Found at i:19881156 original size:132 final size:132
Alignment explanation
Indices: 19881037--19881916 Score: 1494
Period size: 132 Copynumber: 6.7 Consensus size: 132
19881027 AAGATCTACA
* * *
19881037 ATCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTTGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
*
19881102 CAGTATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
19881167 CT
131 CT
*
19881169 ACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
*
19881234 CAATAAGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
19881299 CT
131 CT
*
19881301 ACCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
* *
19881366 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTG
66 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
19881431 CT
131 CT
* *
19881433 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTTGCGAT-TACTTCACCA
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGC-TTTCTGCGATCTACTTCGCCA
* * * * * *
19881497 CCAGTATGGGAAGACAAAATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGACCT
65 CCAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCT
19881562 GCT
130 GCT
*
19881565 ATCTTCGATCTACTTCACGCCAATACATGAAGACCAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
** *
19881630 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACCGGACCTG
66 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
19881695 CT
131 CT
19881697 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
* *
19881762 TAA-ATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
19881826 CT
131 CT
* * * *
19881828 ACCTTCGATCTACTTCACGCTAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTTGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
19881893 CAATATGGGAAGACAAGATCTGCA
66 CAATATGGGAAGACAAGATCTGCA
19881917 ATCTTCAATC
Statistics
Matches: 706, Mismatches: 39, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
131 131 0.19
132 566 0.80
133 9 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
CAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
CT
Found at i:19881968 original size:45 final size:45
Alignment explanation
Indices: 19881919--19882078 Score: 135
Period size: 45 Copynumber: 3.4 Consensus size: 45
19881909 GATCTGCAAT
*
19881919 CTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
* * * * * *
19881964 CTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCCATCTTTGAT
1 CTTCAATCTACTCCACTGCCAAAT-ACAGGGAGATAGAGT-T---ATC---G-G
* *
19882016 CTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
*
19882061 CTTCAATGTACTCCACTG
1 CTTCAATCTACTCCACTG
19882079 TGGTCAGGGA
Statistics
Matches: 87, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
43 2 0.02
44 12 0.14
45 34 0.39
46 1 0.01
48 3 0.03
49 3 0.03
51 1 0.01
52 18 0.21
53 11 0.13
54 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTTATCGG
Found at i:19882031 original size:97 final size:95
Alignment explanation
Indices: 19881917--19882112 Score: 338
Period size: 97 Copynumber: 2.0 Consensus size: 95
19881907 AAGATCTGCA
19881917 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
*
19881982 TAGTCACAGGGAGGTAAAATCTGCCATCTTTG
66 TAGT--CAGGGAGGTAAAATCTGCCATCTTCG
* *
19882014 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
*
19882079 TGGTCAGGGAGGTAAAATCTGCCATCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
19882109 ATCT
1 ATCT
19882113 GCTTCGCTGC
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 29 0.31
97 66 0.69
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCG
Found at i:19882166 original size:134 final size:134
Alignment explanation
Indices: 19882014--19882289 Score: 482
Period size: 134 Copynumber: 2.1 Consensus size: 134
19882004 GCCATCTTTG
*
19882014 ATCTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
19882079 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
19882144 TGCA-
131 TG-AT
*
19882148 ATCTTCAATCTATTCCACTGCCAAATATAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* * *
19882213 TTGTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTTTGCTGCCAAATACAGGAAAGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
19882278 TGAT
131 TGAT
19882282 ATCTTCAA
1 ATCTTCAA
19882290 CCAGCTCTGC
Statistics
Matches: 135, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
133 1 0.01
134 134 0.99
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (134 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
TGAT
Found at i:19882363 original size:86 final size:86
Alignment explanation
Indices: 19882237--19882586 Score: 547
Period size: 86 Copynumber: 4.1 Consensus size: 86
19882227 AAATTTGCCA
* * * * *
19882237 TCTTCGATCTGCTTTGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
19882302 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* *
19882324 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
19882389 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
19882410 TCTTCGATCTGTTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
19882475 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
19882496 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * *
19882561 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
19882582 TCTTC
1 TCTTC
19882587 AATTTTTACT
Statistics
Matches: 245, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 226 0.92
87 19 0.08
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:19882532 original size:42 final size:42
Alignment explanation
Indices: 19882312--19882532 Score: 98
Period size: 42 Copynumber: 5.2 Consensus size: 42
19882302 CAAACGAGAG
*
19882312 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGA
1 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * * * *
19882354 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA
* *
19882397 GTGGCAAGGTTTGTCTTCGATCTGTTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * * * *
19882440 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA
*
19882483 GTGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
19882526 AGGCAAG
1 AGGCAAG
19882533 ATCTGATAAC
Statistics
Matches: 120, Mismatches: 39, Indels: 40
0.60 0.20 0.20
Matches are distributed among these distances:
41 23 0.19
42 33 0.28
43 16 0.13
44 25 0.21
45 23 0.19
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (42 bp):
AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
Found at i:19883867 original size:25 final size:26
Alignment explanation
Indices: 19883811--19883867 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
19883801 ATGGCCTCTC
* *
19883811 CTTTTTTCACTCATTTTTCTTTTCTT
1 CTTTTTTCACTCAATTTTCTCTTCTT
*
19883837 C-TTTTTCA-TTAATTTTCTCTTCTT
1 CTTTTTTCACTCAATTTTCTCTTCTT
19883861 CTTTTTT
1 CTTTTTT
19883868 TTGTGAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 14 0.52
25 12 0.44
26 1 0.04
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (26 bp):
CTTTTTTCACTCAATTTTCTCTTCTT
Found at i:19886716 original size:19 final size:20
Alignment explanation
Indices: 19886692--19886735 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
19886682 CGTGAAAGTC
* *
19886692 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
19886711 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
19886731 -AATGC
1 TAATGC
19886736 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:19889054 original size:22 final size:22
Alignment explanation
Indices: 19889029--19889079 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
19889019 ACATATGCAC
* *
19889029 ATATATATATTAAGATATATGG
1 ATATATATAATAAGATATATAG
19889051 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATATAG
19889073 ATATATA
1 ATATATA
19889080 ACTAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
ATATATATAATAAGATATATAG
Found at i:19889080 original size:20 final size:21
Alignment explanation
Indices: 19889031--19889089 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
19889021 ATATGCACAT
* *
19889031 ATATATATTAAGATATATGGAT
1 ATATATAATAAGATATAT-GAG
19889053 ATATATAATAAGATATAT-AG
1 ATATATAATAAGATATATGAG
19889073 ATATATAACTAA-ATATA
1 ATATATAA-TAAGATATA
19889090 ATATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATAATAAGATATATGAG
Found at i:19890261 original size:21 final size:21
Alignment explanation
Indices: 19890222--19890261 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19890212 CAAGTGGGCA
**
19890222 TGGGCGGTGGTGGCAGGTGCT
1 TGGGCGGTGGCAGCAGGTGCT
*
19890243 TGGGCGGTGGCAGCTGGTG
1 TGGGCGGTGGCAGCAGGTG
19890262 TCAGACGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.57, T:0.23
Consensus pattern (21 bp):
TGGGCGGTGGCAGCAGGTGCT
Found at i:19892578 original size:25 final size:26
Alignment explanation
Indices: 19892540--19892590 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
19892530 TAATTATAGA
*
19892540 TATATATTGTCGAATTTG-ATTGTTT
1 TATATATTGCCGAATTTGAATTGTTT
19892565 TATATATTGCCGAATTTGAATTGTTT
1 TATATATTGCCGAATTTGAATTGTTT
19892591 ATAGTTATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.25, C:0.06, G:0.16, T:0.53
Consensus pattern (26 bp):
TATATATTGCCGAATTTGAATTGTTT
Found at i:19892599 original size:31 final size:31
Alignment explanation
Indices: 19892564--19893068 Score: 413
Period size: 31 Copynumber: 16.6 Consensus size: 31
19892554 TTTGATTGTT
* * * *
19892564 TTATATATTGCCGAATTTGAATTGTTTATAG
1 TTATACATTGCCGAAATTGAATTGTATATGG
* * *
19892595 TTATACATTGTCGAAATTGATTTGCATATGG
1 TTATACATTGCCGAAATTGAATTGTATATGG
* * * *
19892626 ATATA-AGTTGCCG-AATTGATTTGTACATGA
1 TTATACA-TTGCCGAAATTGAATTGTATATGG
*
19892656 TTATACATTGCTGAAATT-AATTTGTATATGG
1 TTATACATTGCCGAAATTGAA-TTGTATATGG
*
19892687 TTATACATTGCTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAAATTGAATTGTATATGG
*
19892718 ATATA-AGTTGCCG-AATTG-ATTCGTATATGG
1 TTATACA-TTGCCGAAATTGAATT-GTATATGG
* *
19892748 TTGTACATTGCTGAAATT-AATTTGTATATGG
1 TTATACATTGCCGAAATTGAA-TTGTATATGG
* **
19892779 TTATATATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAAATTGAATTGTATATGG
* * *
19892810 ATATA-AGTTGCCG-AATTGATTTGTATATGA
1 TTATACA-TTGCCGAAATTGAATTGTATATGG
* * * *
19892840 CTATACATTGCTGAAATTAAATTGTACATGG
1 TTATACATTGCCGAAATTGAATTGTATATGG
**
19892871 TTATACATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAAATTGAATTGTATATGG
*
19892902 ATATA-AGTTGCCG-AATTG-ATTCGTATATGG
1 TTATACA-TTGCCGAAATTGAATT-GTATATGG
* * *
19892932 TTATACATTGCTGAATTTG-ATT-TGTA---
1 TTATACATTGCCGAAATTGAATTGTATATGG
* * *
19892958 -TATACATTGCTGAACTT-TATTCGTATATGG
1 TTATACATTGCCGAAATTGAATT-GTATATGG
*
19892988 TTATACATTGTCG-AATTG-ATTCGTATATGG
1 TTATACATTGCCGAAATTGAATT-GTATATGG
* * *
19893018 TTATACATTGCCGAATTTGATTTGTATATGA
1 TTATACATTGCCGAAATTGAATTGTATATGG
*
19893049 TTATACATTGCCGAACTTGA
1 TTATACATTGCCGAAATTGA
19893069 TTGGTTTCGT
Statistics
Matches: 388, Mismatches: 57, Indels: 58
0.77 0.11 0.12
Matches are distributed among these distances:
25 19 0.05
27 3 0.01
29 9 0.02
30 122 0.31
31 227 0.59
32 8 0.02
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (31 bp):
TTATACATTGCCGAAATTGAATTGTATATGG
Found at i:19892665 original size:61 final size:61
Alignment explanation
Indices: 19892565--19893070 Score: 375
Period size: 61 Copynumber: 8.3 Consensus size: 61
19892555 TTGATTGTTT
* * * * *
19892565 TATATATTGCCGAATTTGAATTGTTTAT-AGTTATACATTGTCGAAATTGATTTGCATATGGA
1 TATACATTGCCGAAATTGATTTGTATATGA-TTATACATTG-CGAAATTGATTTGTATATGGA
* * *
19892627 TATA-AGTTGCCG-AATTGATTTGTACATGATTATACATTGCTGAAATTAATTTGTATATGGT
1 TATACA-TTGCCGAAATTGATTTGTATATGATTATACATTGC-GAAATTGATTTGTATATGGA
* * * *
19892688 TATACATTGCTGAAATTGAATTGTATATGGA-TATA-AGTTGCCG-AATTGATTCGTATATGGT
1 TATACATTGCCGAAATTGATTTGTATAT-GATTATACA-TTG-CGAAATTGATTTGTATATGGA
* * * * * * *
19892749 TGTACATTGCTGAAATTAATTTGTATATGGTTATATATTGTTGAAATTGAATTGTATATGGA
1 TATACATTGCCGAAATTGATTTGTATATGATTATACATTG-CGAAATTGATTTGTATATGGA
* * * * *
19892811 TATA-AGTTGCCG-AATTGATTTGTATATGACTATACATTGCTGAAATTAAATTGTACATGGT
1 TATACA-TTGCCGAAATTGATTTGTATATGATTATACATTGC-GAAATTGATTTGTATATGGA
** * * *
19892872 TATACATTGTTGAAATTGAATTGTATATGGA-TATA-AGTTGCCG-AATTGATTCGTATATGGT
1 TATACATTGCCGAAATTGATTTGTATAT-GATTATACA-TTG-CGAAATTGATTTGTATATGGA
* * * * * *
19892933 TATACATTGCTGAATTTGATTTG----T-A-TATACATTGCTGAACTTTATTCGTATATGGT
1 TATACATTGCCGAAATTGATTTGTATATGATTATACATTGC-GAAATTGATTTGTATATGGA
* * * *
19892989 TATACATTGTCG-AATTGATTCGTATATGGTTATACATTGCCGAATTTGATTTGTATAT-GA
1 TATACATTGCCGAAATTGATTTGTATATGATTATACATTG-CGAAATTGATTTGTATATGGA
*
19893049 TTATACATTGCCGAACTTGATT
1 -TATACATTGCCGAAATTGATT
19893071 GGTTTCGTGC
Statistics
Matches: 360, Mismatches: 54, Indels: 60
0.76 0.11 0.13
Matches are distributed among these distances:
54 1 0.00
55 17 0.05
56 27 0.08
57 1 0.00
59 1 0.00
60 3 0.01
61 216 0.60
62 88 0.24
63 6 0.02
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (61 bp):
TATACATTGCCGAAATTGATTTGTATATGATTATACATTGCGAAATTGATTTGTATATGGA
Found at i:19892692 original size:92 final size:92
Alignment explanation
Indices: 19892585--19893068 Score: 610
Period size: 92 Copynumber: 5.3 Consensus size: 92
19892575 CGAATTTGAA
* * * * *
19892585 TTGTTTATAGTTATACATTGTCGAAATTGATTTGCATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
* *
19892650 ACATGATTATACATTGCTGAAATTAAT
66 ATATGGTTATACATTGCTGAAATTAAT
19892677 TTGTATATGGTTATACATTG-CTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCG
1 TTGTATATGGTTATACATTGTC-GAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCG
*
19892741 TATATGGTTGTACATTGCTGAAATTAAT
65 TATATGGTTATACATTGCTGAAATTAAT
* * *
19892769 TTGTATATGGTTATATATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
** *
19892834 ATATGACTATACATTGCTGAAATTAAA
66 ATATGGTTATACATTGCTGAAATTAAT
* *
19892861 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
* *
19892926 ATATGGTTATACATTGCTGAATTTGAT
66 ATATGGTTATACATTGCTGAAATTAAT
* * * *
19892953 TTG--TA----TATACATTG-CTGAACTT-TATTCGTATATGGTTATACA-TTGTCGAATTGATT
1 TTGTATATGGTTATACATTGTC-GAAATTGAATT-GTATATGGATATA-AGTTGCCGAATTGATT
* * *
19893009 CGTATATGGTTATACATTGCCGAATTTGAT
63 CGTATATGGTTATACATTGCTGAAATTAAT
* * *
19893039 TTGTATATGATTATACATTGCCGAACTTGA
1 TTGTATATGGTTATACATTGTCGAAATTGA
19893069 TTGGTTTCGT
Statistics
Matches: 348, Mismatches: 31, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
85 3 0.01
86 71 0.20
87 1 0.00
88 2 0.01
90 1 0.00
91 1 0.00
92 268 0.77
93 1 0.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (92 bp):
TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
ATATGGTTATACATTGCTGAAATTAAT
Found at i:19892961 original size:25 final size:25
Alignment explanation
Indices: 19892933--19892985 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
19892923 CGTATATGGT
*
19892933 TATACATTGCTGAA-TTTGATTTGTA
1 TATACATTGCTGAACTTT-ATTCGTA
19892958 TATACATTGCTGAACTTTATTCGTA
1 TATACATTGCTGAACTTTATTCGTA
19892983 TAT
1 TAT
19892986 GGTTATACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.47
Consensus pattern (25 bp):
TATACATTGCTGAACTTTATTCGTA
Found at i:19893290 original size:44 final size:43
Alignment explanation
Indices: 19893179--19893382 Score: 268
Period size: 43 Copynumber: 4.8 Consensus size: 43
19893169 GGTGTGATTT
* * *
19893179 CGTGTAAGACCATATTTGGGACATCGGCATCGAAGTAAGGAAA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTAAGGAAA
*
19893222 CGTGTAAGACCATGTCTGGGACATTGGCATCAAAGTAAGGAAA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTAAGGAAA
*
19893265 CGTGTAAAGACCATGTCTGGGACATTGGCATCGAAGTAAGAAAA
1 CGTGT-AAGACCATGTCTGGGACATTGGCATCGAAGTAAGGAAA
* * * **
19893309 CGTGTAAGACCATGTCTGGGACATAGGCATCGTA-T-ATGATT
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTAAGGAAA
* * *
19893350 CGTATAAGACCCTGTCTGGGACATTAGCATCGA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGA
19893383 TATGCGTTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 30 0.21
42 1 0.01
43 71 0.50
44 41 0.29
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTAAGGAAA
Found at i:19893330 original size:87 final size:86
Alignment explanation
Indices: 19893179--19893339 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 86
19893169 GGTGTGATTT
* *
19893179 CGTGTAAGACCATATTTGGGACATCGGCATCGAAGTAAGGAAACGTGTAAGACCATGTCTGGGAC
1 CGTGTAAGACCATATCTGGGACATCGGCATCGAAGTAAGAAAACGTGTAAGACCATGTCTGGGAC
*
19893244 ATTGGCATCAAAGTAAGGAAA
66 ATAGGCATCAAAGTAAGGAAA
* *
19893265 CGTGTAAAGACCATGTCTGGGACATTGGCATCGAAGTAAGAAAACGTGTAAGACCATGTCTGGGA
1 CGTGT-AAGACCATATCTGGGACATCGGCATCGAAGTAAGAAAACGTGTAAGACCATGTCTGGGA
19893330 CATAGGCATC
65 CATAGGCATC
19893340 GTATATGATT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 5 0.07
87 64 0.93
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (86 bp):
CGTGTAAGACCATATCTGGGACATCGGCATCGAAGTAAGAAAACGTGTAAGACCATGTCTGGGAC
ATAGGCATCAAAGTAAGGAAA
Found at i:19893405 original size:84 final size:85
Alignment explanation
Indices: 19893184--19893382 Score: 231
Period size: 87 Copynumber: 2.3 Consensus size: 85
19893174 GATTTCGTGT
* * ** * * *
19893184 AAGACCATATTTGGGACATCGGCATCGAAGTAAGGAAACGTGTAAGACCATGTCTGGGACATTGG
1 AAGACCATGTCTGGGACATTAGCATCGAAGTAAGAAAACATGTAAGACCATGTCTGGGACATAGG
*
19893249 CATCAAAGTAAGGAAACGTGTA
66 CATC--AGTAAGGAAACGTATA
* *
19893271 AAGACCATGTCTGGGACATTGGCATCGAAGTAAGAAAACGTGTAAGACCATGTCTGGGACATAGG
1 AAGACCATGTCTGGGACATTAGCATCGAAGTAAGAAAACATGTAAGACCATGTCTGGGACATAGG
* **
19893336 CATC-GTATATGATTCGTAT-
66 CATCAGTA-AGGAAACGTATA
*
19893355 AAGACCCTGTCTGGGACATTAGCATCGA
1 AAGACCATGTCTGGGACATTAGCATCGA
19893383 TATGCGTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
84 29 0.29
85 7 0.07
87 64 0.64
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.23
Consensus pattern (85 bp):
AAGACCATGTCTGGGACATTAGCATCGAAGTAAGAAAACATGTAAGACCATGTCTGGGACATAGG
CATCAGTAAGGAAACGTATA
Found at i:19928649 original size:17 final size:17
Alignment explanation
Indices: 19928618--19928658 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19928608 ATGTGTACCA
*
19928618 ATAAATAATTTAAAAATG
1 ATAAA-AATTCAAAAATG
*
19928636 ATAAAAATTCAAAAATT
1 ATAAAAATTCAAAAATG
19928653 ATAAAA
1 ATAAAA
19928659 GTTAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAATTCAAAAATG
Found at i:19928668 original size:17 final size:16
Alignment explanation
Indices: 19928627--19928669 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
19928617 AATAAATAAT
*
19928627 TTAAAAATGATAAAAA
1 TTAAAAATTATAAAAA
*
19928643 TTCAAAAATTATAAAAG
1 TT-AAAAATTATAAAAA
19928660 TTAATAAATT
1 TTAA-AAATT
19928670 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (16 bp):
TTAAAAATTATAAAAA
Found at i:19928781 original size:22 final size:22
Alignment explanation
Indices: 19928751--19928800 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19928741 ATTGATAATC
19928751 AAATT-TTAAAAAATAAAAATT
1 AAATTATTAAAAAATAAAAATT
* *
19928772 AAATTATTAAAAACTAAAATTT
1 AAATTATTAAAAAATAAAAATT
*
19928794 ACATTAT
1 AAATTAT
19928801 AGATTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTATTAAAAAATAAAAATT
Found at i:19932504 original size:9 final size:9
Alignment explanation
Indices: 19932493--19932559 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
19932483 TTTGGTTAAA
*
19932493 AATTAACCA
1 AATTAACCG
19932502 AATTAACCG
1 AATTAACCG
19932511 AATTAACCG
1 AATTAACCG
*
19932520 AATTACCCG
1 AATTAACCG
*
19932529 AACTAACCG
1 AATTAACCG
*
19932538 AATTACCCG
1 AATTAACCG
*
19932547 AATTAACCA
1 AATTAACCG
19932556 AATT
1 AATT
19932560 GAATCATTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:19932516 original size:18 final size:18
Alignment explanation
Indices: 19932493--19932559 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
19932483 TTTGGTTAAA
*
19932493 AATTAACCAAATTAACCG
1 AATTAACCAAATTACCCG
*
19932511 AATTAACCGAATTACCCG
1 AATTAACCAAATTACCCG
* *
19932529 AACTAACCGAATTACCCG
1 AATTAACCAAATTACCCG
19932547 AATTAACCAAATT
1 AATTAACCAAATT
19932560 GAATCATTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (18 bp):
AATTAACCAAATTACCCG
Found at i:19943362 original size:31 final size:31
Alignment explanation
Indices: 19943303--19943367 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
19943293 TACAAAGCAA
*
19943303 TCATTGAACTATTCAAATTTTTTCATTTAAG
1 TCATTGAACTATTCAAAGTTTTTCATTTAAG
* *
19943334 TCATTGGACTAGTTGAAAGTTTTT-ATTTAAG
1 TCATTGAACTA-TTCAAAGTTTTTCATTTAAG
19943365 TCA
1 TCA
19943368 CTAGGCTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (31 bp):
TCATTGAACTATTCAAAGTTTTTCATTTAAG
Found at i:19948422 original size:16 final size:15
Alignment explanation
Indices: 19948401--19948430 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19948391 AGCAAGTCTT
19948401 TTTACTTTTTATTTAG
1 TTTACTTTTT-TTTAG
19948417 TTTACTTTTTTTTA
1 TTTACTTTTTTTTA
19948431 CGTGAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTACTTTTTTTTAG
Found at i:19949304 original size:20 final size:20
Alignment explanation
Indices: 19949279--19949328 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19949269 TGGCTTAAAA
19949279 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19949299 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19949316 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19949329 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19953943 original size:20 final size:20
Alignment explanation
Indices: 19953918--19953967 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19953908 TGGCTTAAAA
19953918 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19953938 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19953955 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19953968 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19956445 original size:23 final size:25
Alignment explanation
Indices: 19956391--19956445 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
19956381 TAAGTTCAAC
19956391 TTAATTAGTAAAATGTACTTCTTTTAA
1 TTAA-TAGTAAAA-GTACTTCTTTTAA
*
19956418 ATAATAGTAAAA-TA-TTCTTTTAA
1 TTAATAGTAAAAGTACTTCTTTTAA
19956441 TTAAT
1 TTAAT
19956446 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 13 0.50
24 2 0.08
26 8 0.31
27 3 0.12
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (25 bp):
TTAATAGTAAAAGTACTTCTTTTAA
Found at i:19959374 original size:18 final size:18
Alignment explanation
Indices: 19959351--19959385 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19959341 GATTAAAAAT
19959351 ATTTTTA-TAAAAGCAAAC
1 ATTTTTATTAAAA-CAAAC
19959369 ATTTTTATTAAAACAAA
1 ATTTTTATTAAAACAAA
19959386 TGACAGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (18 bp):
ATTTTTATTAAAACAAAC
Found at i:19960388 original size:25 final size:23
Alignment explanation
Indices: 19960360--19960408 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
19960350 AAATTATAAA
19960360 AATACACAATATTTAAAATATATAT
1 AATA-ACAA-ATTTAAAATATATAT
* *
19960385 AATAATAAGTTTAAAATATATAT
1 AATAACAAATTTAAAATATATAT
19960408 A
1 A
19960409 TTGTTGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 3 0.14
25 4 0.18
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AATAACAAATTTAAAATATATAT
Found at i:19962210 original size:12 final size:12
Alignment explanation
Indices: 19962193--19962217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19962183 GGTGTTCATT
19962193 CGGTTAACCGAC
1 CGGTTAACCGAC
19962205 CGGTTAACCGAC
1 CGGTTAACCGAC
19962217 C
1 C
19962218 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:19962392 original size:9 final size:9
Alignment explanation
Indices: 19962378--19962424 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
19962368 TTTGGTTAAA
19962378 AATTACCCG
1 AATTACCCG
19962387 AATTACCCG
1 AATTACCCG
*
19962396 AATTACTCG
1 AATTACCCG
*
19962405 AATTAACCG
1 AATTACCCG
*
19962414 AATTAACCG
1 AATTACCCG
19962423 AA
1 AA
19962425 AAATACCCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:19963044 original size:21 final size:21
Alignment explanation
Indices: 19962980--19963044 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
19962970 AGCGCGATTT
19962980 GCTTCCACGTCAGCAAATCGC
1 GCTTCCACGTCAGCAAATCGC
* ** **
19963001 G-TT-CACGTAAGCGTGAT-TT
1 GCTTCCACGTCAGC-AAATCGC
19963020 GCTTCCACGTCAGCAAATCGC
1 GCTTCCACGTCAGCAAATCGC
19963041 GCTT
1 GCTT
19963045 ACGTGGGCGC
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 9 0.30
20 8 0.27
21 13 0.43
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (21 bp):
GCTTCCACGTCAGCAAATCGC
Found at i:19963059 original size:40 final size:40
Alignment explanation
Indices: 19962952--19963101 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
19962942 CACGTGCGGC
* *
19962952 GCAAATCGCGTCCT-CGTAAGCGCGATTTGCTTCCACGTCA
1 GCAAATCGCG-CTTACGTGAGCGCGATTTGCTTCCACGTCA
* *
19962992 GCAAATCGCG-TTCACGTAAGCGTGATTTGCTTCCACGTCA
1 GCAAATCGCGCTT-ACGTGAGCGCGATTTGCTTCCACGTCA
* *
19963032 GCAAATCGCGCTTACGTGGGCGCGATTTG-TTGCCACGTAA
1 GCAAATCGCGCTTACGTGAGCGCGATTTGCTT-CCACGTCA
* * * *
19963072 G-TAATCGCGCTGACATGAACGCGATTTGCT
1 GCAAATCGCGCTTACGTGAGCGCGATTTGCT
19963102 GACACGTCTC
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 24 0.26
40 67 0.71
41 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.26
Consensus pattern (40 bp):
GCAAATCGCGCTTACGTGAGCGCGATTTGCTTCCACGTCA
Found at i:19964007 original size:67 final size:67
Alignment explanation
Indices: 19963855--19963984 Score: 208
Period size: 67 Copynumber: 1.9 Consensus size: 67
19963845 CTGAAAGCTC
* * *
19963855 TGTACC-AGCACCACCCTTTACTACTTTGCTTGCCATGTTTACTTCTTTTCTCATCTTTCCTCTG
1 TGTACCTA-CACCACCTTTTACTACTTCGCTTACCATGTTTACTTCTTTTCTCATCTTTCCTCTG
19963919 AGT
65 AGT
*
19963922 TGTACCTACACCACCTTTTACTGCTTCGCTTACCATGTTTACTTCTTTTCTCATCTTTCCTCT
1 TGTACCTACACCACCTTTTACTACTTCGCTTACCATGTTTACTTCTTTTCTCATCTTTCCTCT
19963985 TATTTTTCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 57 0.98
68 1 0.02
ACGTcount: A:0.15, C:0.32, G:0.08, T:0.45
Consensus pattern (67 bp):
TGTACCTACACCACCTTTTACTACTTCGCTTACCATGTTTACTTCTTTTCTCATCTTTCCTCTGA
GT
Found at i:19965725 original size:106 final size:109
Alignment explanation
Indices: 19965590--19966135 Score: 610
Period size: 106 Copynumber: 5.1 Consensus size: 109
19965580 ACGAAAAAGA
* * *
19965590 AAAAAAATGAAAAAAAAATTTTGATGCTGGCCTGTCAATGGCCGGCACCCAGTACATAGTA-AAA
1 AAAAAAAT-AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAA
19965654 AAAAAATTAT-TTTTTTTCGTGTCAGAATCAGATATAAAAATAC-
65 AAAAAATTATATTTTTTTCGTGTCAGAATCAGATATAAAAATACG
*
19965697 AAAAAAATAAAAAAAAATTTGGGTGCTGGACTGTCAATGGCCGGCACCCAGTACACAGTAC-AAA
1 AAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAA
* *
19965761 AAAAATT-TACTTTTTTCGTGTCA-AATCAGATATTAAAATACG
66 AAAAATTATATTTTTTTCGTGTCAGAATCAGATATAAAAATACG
* * * *
19965803 AAAAAAATAAATAAAAAAAATTTGAGTGCTGGCCTGTCAATGGCCGGCACTCAATATACAGTAC-
1 AAAAAAAT--A-AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
* *
19965867 AAAAAAAA--A-ATTTTTTTCGTTTCAGAATCAAATATAAAAATACGG
63 AAAAAAAATTATATTTTTTTCGTGTCAGAATCAGATATAAAAATAC-G
*
19965912 AAAAAAATAAAAAAAAATTGGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAA
1 AAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA-AA
** * * *
19965977 AAATATTTTTTTTATTTTTTTCTTGTCAGAATCAGATATAAATATACG
65 AAA-A--AATTATATTTTTTTCGTGTCAGAATCAGATATAAAAATACG
*
19966025 ---------AAAAAAAA-TTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGGA
1 AAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA--A
*** * *
19966080 AAATATTTTTTTTATTTTTTTCGTGTCAGAATCAGATATAATATATACG
64 AAA-A-AAATTATATTTTTTTCGTGTCAGAATCAGATATAA-AAATACG
19966129 AAAAAAA
1 AAAAAAA
19966136 ATTTAAAATT
Statistics
Matches: 381, Mismatches: 31, Indels: 50
0.82 0.07 0.11
Matches are distributed among these distances:
103 75 0.20
104 20 0.05
105 20 0.05
106 126 0.33
107 22 0.06
108 22 0.06
109 65 0.17
113 1 0.00
114 30 0.08
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (109 bp):
AAAAAAATAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAA
AAAAATTATATTTTTTTCGTGTCAGAATCAGATATAAAAATACG
Found at i:19965838 original size:215 final size:216
Alignment explanation
Indices: 19965590--19966031 Score: 628
Period size: 215 Copynumber: 2.0 Consensus size: 216
19965580 ACGAAAAAGA
* * * *
19965590 AAAAAAATGAAAAAAAAATTTTGATGCTGGCCTGTCAATGGCCGGCACCCAGTACATAGTA-AAA
1 AAAAAAATAAAAAAAAAAATTTGATGCTGGCCTGTCAATGGCCGGCACCCAATACACAGTACAAA
* *
19965654 AAAAAATTATTTTTTTTCGTGTCAGAATCAGATATAAAAATAC-AAAAAAATAAAAAAAAATTTG
66 AAAAAA--A-TTTTTTTCGTGTCAGAATCAAATATAAAAATACGAAAAAAATAAAAAAAAATTGG
19965718 GGTGCTGGACTGTCAATGGCCGGCACCCAGTACACAGTACA-AAAAA-A-ATTTACTTTTTTCGT
128 GGTGCTGGACTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATATTTACTTTTTTCGT
19965780 GTCA-AATCAGATATTAAA-ATACG
193 GTCAGAATCAGATA-TAAATATACG
* *
19965803 AAAAAAATAAATAAAAAAAATTTGAGTGCTGGCCTGTCAATGGCCGGCACTCAATATACAGTACA
1 AAAAAAATAAA-AAAAAAAATTTGA-TGCTGGCCTGTCAATGGCCGGCACCCAATACACAGTACA
*
19965868 AAAAAAAAATTTTTTTCGTTTCAGAATCAAATATAAAAATACGGAAAAAAATAAAAAAAAATTGG
64 AAAAAAAAATTTTTTTCGTGTCAGAATCAAATATAAAAATAC-GAAAAAAATAAAAAAAAATTGG
* * *
19965933 GGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATTTTTTTTATTTTTTT
128 GGTGCTGGACTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATA---TATTTACTTTTTT
*
19965998 CTTGTCAGAATCAGATATAAATATACG
190 CGTGTCAGAATCAGATATAAATATACG
19966025 AAAAAAA
1 AAAAAAA
19966032 ATTAGGTGCT
Statistics
Matches: 203, Mismatches: 13, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
213 41 0.20
214 13 0.06
215 93 0.46
216 14 0.07
217 1 0.00
221 20 0.10
222 21 0.10
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (216 bp):
AAAAAAATAAAAAAAAAAATTTGATGCTGGCCTGTCAATGGCCGGCACCCAATACACAGTACAAA
AAAAAAATTTTTTTCGTGTCAGAATCAAATATAAAAATACGAAAAAAATAAAAAAAAATTGGGGT
GCTGGACTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATATTTACTTTTTTCGTGTC
AGAATCAGATATAAATATACG
Found at i:19966057 original size:103 final size:105
Alignment explanation
Indices: 19965921--19966138 Score: 395
Period size: 103 Copynumber: 2.1 Consensus size: 105
19965911 GAAAAAAATA
*
19965921 AAAAAAAATTGGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATTTT
1 AAAAAAAATTGAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATTTT
*
19965986 TTTTATTTTTTTCTTGTCAGAATCAGATATAA-ATATACG
66 TTTTATTTTTTTCGTGTCAGAATCAGATATAATATATACG
*
19966025 AAAAAAAATT-AGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGGAAAATATTTT
1 AAAAAAAATTGAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATTTT
19966089 TTTTATTTTTTTCGTGTCAGAATCAGATATAATATATACG
66 TTTTATTTTTTTCGTGTCAGAATCAGATATAATATATACG
19966129 AAAAAAAATT
1 AAAAAAAATT
19966139 TAAAATTTTT
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 83 0.75
104 27 0.25
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (105 bp):
AAAAAAAATTGAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAGAAAAATATTTT
TTTTATTTTTTTCGTGTCAGAATCAGATATAATATATACG
Found at i:19968709 original size:14 final size:14
Alignment explanation
Indices: 19968687--19968737 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
19968677 ATTTCATTCA
*
19968687 ATCTTATTTATTAC
1 ATCTAATTTATTAC
* **
19968701 ATCTGATTTCCTAC
1 ATCTAATTTATTAC
19968715 ATCTAATTTATTAC
1 ATCTAATTTATTAC
19968729 ATCTAATTT
1 ATCTAATTT
19968738 TTTTTTCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.51
Consensus pattern (14 bp):
ATCTAATTTATTAC
Found at i:19968852 original size:87 final size:87
Alignment explanation
Indices: 19968673--19968868 Score: 229
Period size: 87 Copynumber: 2.3 Consensus size: 87
19968663 ATTGAATATC
* * * * *
19968673 ATTTATTTCATTCAATCTTATTTATTACATCTGATTTCCTACATCTAATTTATTACATCTAATTT
1 ATTTTTTTCATTCAATCTCATTTATTACATCTAATTTCCTACATCGAATTTACTACATCTAATTT
** * * **
19968738 TTTTTTCATTCAATAGTACCTTT
66 TTTGGTAAATC-ATAACACCTTT
**
19968761 -TTTTTTTCATTCAATCTCATTTATTACATCTAATTTCCTACATCGGGTTTACTACATCTAATTT
1 ATTTTTTTCATTCAATCTCATTTATTACATCTAATTTCCTACATCGAATTTACTACATCTAATTT
19968825 TTTGGGTAAATC-TAACACCTTT
66 TTT-GGTAAATCATAACACCTTT
19968847 A--TTTTTCATTCAATCTCATTTA
1 ATTTTTTTCATTCAATCTCATTTA
19968869 GTTCAATTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 21 0.23
86 8 0.09
87 60 0.65
88 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (87 bp):
ATTTTTTTCATTCAATCTCATTTATTACATCTAATTTCCTACATCGAATTTACTACATCTAATTT
TTTGGTAAATCATAACACCTTT
Found at i:19968907 original size:53 final size:52
Alignment explanation
Indices: 19968837--19969105 Score: 185
Period size: 53 Copynumber: 5.3 Consensus size: 52
19968827 TGGGTAAATC
* * * *
19968837 TAACACCTTTATTTTTCATTCAATCTCATTTAGTTCAATTTTTTTTCCTACATC
1 TAACA-CTTTTTTTTTCATTCAATCTCATTTA-TTCAATCTATTTTCCTACATA
*
19968891 TAACACTTTTTTTTTCATTCAATCTCATTTATT-ACATCTAATTTCCTACATA
1 TAACACTTTTTTTTTCATTCAATCTCATTTATTCA-ATCTATTTTCCTACATA
* * * * *
19968943 T-A-A---TTTATTACA-TCTAAT-TTA-TTACATCTAAT-TTTTTTCCTACATA
1 TAACACTTTTTTTTTCATTC-AATCTCATTTA-TTC-AATCTATTTTCCTACATA
* *
19968989 TAATAC----TTTTT-ATTCAATCTCATTTATT-ACATCTAATTTCCTACATA
1 TAACACTTTTTTTTTCATTCAATCTCATTTATTCA-ATCTATTTTCCTACATA
* * * *
19969036 TAATACCTTTTTTTTTCATTCAATCTCATTTATTTCAA-ATGTTTTCCTACATC
1 TAACA-CTTTTTTTTTCATTCAATCTCATTTA-TTCAATCTATTTTCCTACATA
*
19969089 TAACACCTTTTTTTTCA
1 TAACACTTTTTTTTTCA
19969106 AATTGTTTTT
Statistics
Matches: 171, Mismatches: 23, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
45 4 0.02
46 24 0.14
47 38 0.22
48 6 0.04
50 1 0.01
51 2 0.01
52 32 0.19
53 55 0.32
54 8 0.05
55 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (52 bp):
TAACACTTTTTTTTTCATTCAATCTCATTTATTCAATCTATTTTCCTACATA
Found at i:19968934 original size:14 final size:14
Alignment explanation
Indices: 19968912--19968976 Score: 94
Period size: 14 Copynumber: 4.6 Consensus size: 14
19968902 TTTTCATTCA
*
19968912 ATCTCATTTATTAC
1 ATCTAATTTATTAC
**
19968926 ATCTAATTTCCTAC
1 ATCTAATTTATTAC
*
19968940 ATATAATTTATTAC
1 ATCTAATTTATTAC
19968954 ATCTAATTTATTAC
1 ATCTAATTTATTAC
19968968 ATCTAATTT
1 ATCTAATTT
19968977 TTTTCCTACA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (14 bp):
ATCTAATTTATTAC
Found at i:19972236 original size:113 final size:111
Alignment explanation
Indices: 19972021--19972278 Score: 344
Period size: 99 Copynumber: 2.4 Consensus size: 111
19972011 TATATATGAT
*
19972021 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACTCAAAAATTTTTTTCGTATATTTATATCTGAT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTCGTATATTTATATCTGAT
19972086 TCTGACACGAAAAAAATAAAAAAAATATTTTCCTGTACTGTGTACTG
66 TCTGACACG-AAAAAATAAAAAAAATATTTTCCTGTACTGTGTACTG
**
19972133 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTTCGTATATTTATATCTGA
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-AATTTTTTTCGTATATTTATATCTGA
*
19972198 TTCTGACACG-------AAAAAAAATAATTT--T-T--T-TGTACTG
65 TTCTGACACGAAAAAATAAAAAAAATATTTTCCTGTACTGTGTACTG
* * *
19972232 TGTACTGGATGCCGGCCATTGACAGGCCAGCACCTAAAATTTTTTTT
1 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTT
19972279 TTATTTTTTT
Statistics
Matches: 138, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
98 8 0.06
99 43 0.31
100 1 0.01
102 1 0.01
103 1 0.01
105 13 0.09
112 37 0.27
113 34 0.25
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (111 bp):
TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAATTTTTTTCGTATATTTATATCTGAT
TCTGACACGAAAAAATAAAAAAAATATTTTCCTGTACTGTGTACTG
Found at i:19972357 original size:103 final size:105
Alignment explanation
Indices: 19972173--19972412 Score: 387
Period size: 103 Copynumber: 2.3 Consensus size: 105
19972163 CACCCAAATT
19972173 TTTTTTTTCGTATATTTATATCTGATTCTGACACGAAAAAAAATAATTTTTTTGTACTGTGTACT
1 TTTTTTTTCGTAT-TTTATATCTGATTCTGACACGAAAAAAAATAA---TTTTGTACTGTGTACT
*
19972238 GGATGCCGGCCATTGACAGGCCAGCACCTAAAATTTTTTTTTTA
62 GGATGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTA
*
19972282 -TTTTTTTCGTATTTTAATATCTGATTCTGACACGAAAAAAAA-AA-TTTGTACTGTGTACTGGG
1 TTTTTTTTCGTATTTT-ATATCTGATTCTGACACGAAAAAAAATAATTTTGTACTGTGTACTGGA
19972344 TGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTA
65 TGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTA
19972385 TTTTTTTTCGTATTTTTATATCTGATTC
1 TTTTTTTTCGTA-TTTTATATCTGATTC
19972413 GGGTGCCGGC
Statistics
Matches: 126, Mismatches: 2, Indels: 11
0.91 0.01 0.08
Matches are distributed among these distances:
103 57 0.45
104 22 0.17
105 4 0.03
107 5 0.04
108 38 0.30
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (105 bp):
TTTTTTTTCGTATTTTATATCTGATTCTGACACGAAAAAAAATAATTTTGTACTGTGTACTGGAT
GCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTA
Found at i:19974482 original size:16 final size:16
Alignment explanation
Indices: 19974461--19974495 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
19974451 TTAATCTAAT
* *
19974461 TTTAAATTTTTTTACC
1 TTTAAATTATTTTAAC
19974477 TTTAAATTATTTTAAC
1 TTTAAATTATTTTAAC
19974493 TTT
1 TTT
19974496 TCTATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAATTATTTTAAC
Found at i:19980945 original size:3 final size:3
Alignment explanation
Indices: 19980937--19980975 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19980927 CTTACATAGC
19980937 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19980976 GATATAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19986583 original size:40 final size:39
Alignment explanation
Indices: 19986534--19986647 Score: 113
Period size: 40 Copynumber: 2.8 Consensus size: 39
19986524 GTTTAGTTAT
*
19986534 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAAC
1 TAAT-ATTATT-TTAGTTAGTATTATTGTTAGTAAAAAAAC
* * * **
19986575 TAATATTATTATGGTTAGTTATTA-GGATTAGTAAAAACTC
1 TAATATTATTTTAGTTAG-TATTATTG-TTAGTAAAAAAAC
*
19986615 TAATTATTATTTTAGTTAGTATGATTGTTAGTA
1 TAA-TATTATTTTAGTTAGTATTATTGTTAGTA
19986648 TTTTTTTCCC
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
39 6 0.10
40 35 0.59
41 18 0.31
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (39 bp):
TAATATTATTTTAGTTAGTATTATTGTTAGTAAAAAAAC
Found at i:19987191 original size:152 final size:152
Alignment explanation
Indices: 19986645--19987758 Score: 1352
Period size: 152 Copynumber: 7.3 Consensus size: 152
19986635 ATGATTGTTA
19986645 GTATTTTTTTCCCGAATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACA
1 GTATTTTTTTCCCGAATTTTATTACTTT-AAAAAATATACTATTTTCTAATTTTATTATTTTACA
*
19986710 TTATTTTAGTACATTATGTTT-AAATTTTAAATAAATTTAGTATGTTTTTTAAATAAATTTTAAA
65 TTATTTTAGTACATTATGTTTGAAA-TTTAAATAAATTTAGTGTG-TTTTTAAATAAA-TTT--A
* * *
19986774 AAAAAACCCTTATTTTGGTCCTTTACTC
125 AAAAAACCCTTATTTCGGCCCTTTGCTC
* * *
19986802 GTA-TTTTTTCTCGAGTTTTATTACTTTAAAAAATATACGATTTTCT-ATTTTATTATTTTACAT
1 GTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
* *
19986865 TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTATTGTGTTTTTAAATAAATTAAAAAAAA
66 TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAATT-TAAAAAA
**
19986930 ACAATTATTTCGGCCCTTTGCTC
130 ACCCTTATTTCGGCCCTTTGCTC
* *
19986953 GTATTTTTTTCCTGAGTTTTATTACTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
1 GTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
* *
19987018 TATTTTAGTACATTATTTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAA-TT-GAAAAA
66 TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAATTTAAAAAAA
*
19987081 TCCTTATTTCGGCCCTTTGCTC
131 CCCTTATTTCGGCCCTTTGCTC
* *
19987103 GTA-TTTTTTCCCCAATTTTATTACTTTCAATAAAAATATATTATTTTC-ATATTTTATTATTTT
1 GTATTTTTTTCCCGAATTTTATTACTTT--A-AAAAATATACTATTTTCTA-ATTTTATTATTTT
* * * * * * * * *
19987166 ACTTTATTTTAATACATTATGTTTGAAATGT--ATTAGTTAATTCTTTTTTTAACA-AAATTTAG
62 ACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAA-ATAAATTTA-
*
19987228 TAAAAAACCCTTATTTCGGCCCTTTGTTC
125 -AAAAAACCCTTATTTCGGCCCTTTGCTC
* *
19987257 GTATTTTTTTCCCGAGTTTTATTACTTTAAAAAATATACTATTCTCTAATTTTATTATTTTACAT
1 GTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
19987322 TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTTAAA-AAATTTAAAAAA
66 TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTG-TTTTTAAATAAATTT-AAAAA
* * * *
19987386 AATCCTTATTTCGGTCTTTTACTC
129 AACCCTTATTTCGGCCCTTTGCTC
* * *
19987410 CTA-TTTTTTCCCAAATTTTATTACTTTCAATAAAA-ATATTATTTTCGT-ATTTTATTATTTTA
1 GTATTTTTTTCCCGAATTTTATTACTTT-AA-AAAATATACTATTTTC-TAATTTTATTATTTTA
* * * * * **
19987472 CTTTATTTTAGTACATTATGTTTGAAATGT--ATTAA-TTAAT-TCTTTTT-TTTAAATTTAGTA
63 CATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAATTTA--A
* * *
19987532 AAAAACCCTTATTTCGGTCATTTGTTC
126 AAAAACCCTTATTTCGGCCCTTTGCTC
* * *
19987559 GTATTTTTTTCTCGAATTTTATTACTTTTAAAATATATATTATTTTCTAATTTTATTATTTTACA
1 GTATTTTTTTCCCGAATTTTATTAC-TTTAAAAAATATACTATTTTCTAATTTTATTATTTTACA
* *
19987624 TTATTTTAGTACATTATGTTTAAAATTT--ATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAA
65 TTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAATTTAAAAAA
*
19987687 AGCCTTTATTTCGGCCCTTTGCTC
130 A-CCCTTATTTCGGCCCTTTGCTC
* *
19987711 GTATTTTTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATTTT
1 GTATTTTTTTCCCGAATTTTATTACTTT--A-AAAAATATACTATTTT
19987759 TTACATTATT
Statistics
Matches: 831, Mismatches: 90, Indels: 75
0.83 0.09 0.08
Matches are distributed among these distances:
147 1 0.00
148 11 0.01
149 52 0.06
150 127 0.15
151 52 0.06
152 224 0.27
153 171 0.21
154 117 0.14
155 51 0.06
156 22 0.03
157 3 0.00
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (152 bp):
GTATTTTTTTCCCGAATTTTATTACTTTAAAAAATATACTATTTTCTAATTTTATTATTTTACAT
TATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTAAATAAATTTAAAAAAA
CCCTTATTTCGGCCCTTTGCTC
Found at i:19987332 original size:457 final size:452
Alignment explanation
Indices: 19986645--19987756 Score: 1435
Period size: 457 Copynumber: 2.4 Consensus size: 452
19986635 ATGATTGTTA
*
19986645 GTATTTTTTTCCCGAATTTTATTACTTTAA-AAAAATATACTATTTTCTAATTTTATTATTTTAC
1 GTATTTTTTTCCCGAATTTTATTACTTTAATAAAAATATATTATTTTCTAATTTTATTATTTTAC
*
19986709 ATTATTTTAGTACATTATGTTTAAATTTTAAATAAATTTAGTATGTTTTTTAAATAAATTTTAAA
66 ATTATTTTAGTACATTATGTTTAAA-TTT--ATTAATTTAGTAT-TTTTTTAAATAAA-TTT--A
* * * *
19986774 AAAAAACCCTTATTTTGGTCCTTTACTCGTA-TTTTTTCTCGAGTTTTATTACTTTAAAAAATAT
124 AAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAGTTTTATTACTTTAAAAAATAT
* *
19986838 ACGATTTTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTA
189 ACTATTCTCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTA
* * * *
19986903 TTGTG-TTTTTAAATAAA-TTAAAAAAAAACAATTATTTCGGCCCTTTGCTCGTATTTTTTTCCT
254 GTGTGTTTTTTAAA-AAATTTAAAAAAAAAC-ATTATTTCGGCCCTTTACTCCTA-TTTTTTCCC
* *
19986966 GAGTTTTATTACTTT-AA-AAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTA
316 AAATTTTATTACTTTCAATAAAA-ATACTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTA
* * * *
19987028 CATTATTTTTGAAAT-T-TAAATAAATT-TAGTGTGTTTTTAAATAAATTGAAAAATCCTTATTT
379 CATTATGTTTGAAATGTATAAATAAATTCT--T-T-TTTTTAAATAAAGTAAAAAACCCTTATTT
*
19987090 CGGCCCTTTGCTC
440 CGGCCATTTGCTC
*
19987103 GTA-TTTTTTCCCCAATTTTATTACTTTCAATAAAAATATATTATTTTC-ATATTTTATTATTTT
1 GTATTTTTTTCCCGAATTTTATTACTTT-AATAAAAATATATTATTTTCTA-ATTTTATTATTTT
* * * * * * *
19987166 ACTTTATTTTAATACATTATGTTTGAAATGTATTAGTTAATTCTTTTTTTAACA-AAATTTAGTA
64 ACATTATTTTAGTACATTATGTTT-AAATTTATTAATTTAGTATTTTTTTAA-ATAAATTTA--A
*
19987230 AAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAGTTTTATTACTTTAAAAAATATA
125 AAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAGTTTTATTACTTTAAAAAATATA
19987295 CTATTCTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTA
190 CTATTCTCT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTA
* * * *
19987360 GTGTGTTTTTTAAAAAATTTAAAAAAAATCCTTATTTCGGTCTTTTACTCCTATTTTTTCCCAAA
254 GTGTGTTTTTTAAAAAATTTAAAAAAAAACATTATTTCGGCCCTTTACTCCTATTTTTTCCCAAA
* *
19987425 TTTTATTACTTTCAATAAAAATATTATTTTCGTATTTTATTATTTTACTTTATTTTAGTACATTA
319 TTTTATTACTTTCAATAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTA
* * ** *
19987490 TGTTTGAAATGTATTAATTAATTCTTTTTTTTAAATTTAGTAAAAAACCCTTATTTCGGTCATTT
384 TGTTTGAAATGTATAAATAAATTCTTTTTTTTAAATAAAGTAAAAAACCCTTATTTCGGCCATTT
*
19987555 GTTC
449 GCTC
*
19987559 GTATTTTTTTCTCGAATTTTATTACTTT--TAAAATATATATTATTTTCTAATTTTATTATTTTA
1 GTATTTTTTTCCCGAATTTTATTACTTTAATAAAA-ATATATTATTTTCTAATTTTATTATTTTA
* *
19987622 CATTATTTTAGTACATTATGTTTAAAATTTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAA
65 CATTATTTTAGTACATTATGTTT-AAATTTATTAATTTAGTATTTTTTTAAATAAATTTAAAAAA
* * *
19987687 AGCCTTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCAAATTTTATTACTTTCAATAAAAATATA
129 A-CCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAGTTTTATTACTTT--A-AAAAATATA
*
19987752 TTATT
190 CTATT
19987757 TTTTACATTA
Statistics
Matches: 573, Mismatches: 56, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
453 7 0.01
454 52 0.09
455 106 0.18
456 111 0.19
457 200 0.35
458 32 0.06
459 61 0.11
460 4 0.01
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (452 bp):
GTATTTTTTTCCCGAATTTTATTACTTTAATAAAAATATATTATTTTCTAATTTTATTATTTTAC
ATTATTTTAGTACATTATGTTTAAATTTATTAATTTAGTATTTTTTTAAATAAATTTAAAAAAAC
CCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAGTTTTATTACTTTAAAAAATATACTATTC
TCTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTT
TTTTAAAAAATTTAAAAAAAAACATTATTTCGGCCCTTTACTCCTATTTTTTCCCAAATTTTATT
ACTTTCAATAAAAATACTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGA
AATGTATAAATAAATTCTTTTTTTTAAATAAAGTAAAAAACCCTTATTTCGGCCATTTGCTC
Found at i:19987617 original size:16 final size:16
Alignment explanation
Indices: 19987573--19987621 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19987563 TTTTTTCTCG
19987573 AATTTTATTACTTTTAA
1 AATTTTATTA-TTTTAA
* **
19987590 AATATATATTATTTTCT
1 AAT-TTTATTATTTTAA
19987607 AATTTTATTATTTTA
1 AATTTTATTATTTTA
19987622 CATTATTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.38
17 10 0.38
18 6 0.23
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTATTATTTTAA
Found at i:19987631 original size:18 final size:18
Alignment explanation
Indices: 19987574--19987631 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
19987564 TTTTTCTCGA
* *
19987574 ATTTTATTACTTTTAAAAT
1 ATTTTATTA-TTTTACATT
* *
19987593 A-TATATTATTTT-C-TA
1 ATTTTATTATTTTACATT
19987608 ATTTTATTATTTTACATT
1 ATTTTATTATTTTACATT
19987626 ATTTTA
1 ATTTTA
19987632 GTACATTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.03
16 10 0.33
17 5 0.17
18 13 0.43
19 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATTATTTTACATT
Found at i:19987779 original size:140 final size:139
Alignment explanation
Indices: 19987611--19987878 Score: 355
Period size: 140 Copynumber: 1.9 Consensus size: 139
19987601 TTTTCTAATT
* *
19987611 TTATTATTTTACATTATTTTAGTACATTATGTTTAAAATTTATTAATT-TAGTGTGTTTTTAAAT
1 TTATTATTTTACATTATTTTAGTACATTATGTTTAAAATGTATTAATTAT-GTCTGTTTTT--AT
* * *
19987675 AAATTTA-AAAAAAGCCTTTATTTCGGCCCTTTGCTCGTATTTTTT-TCCCAAATTTTATTACTT
63 AAATTTAGAAAAAA-CCCTAACTTCGGCCCTTTGCTCGTATTTTTTCT-CCAAATTTTATTACTT
19987738 TCAATAAAAATATA
126 TCAATAAAAATATA
* * * *
19987752 TTATT-TTTTACATTATTTTAGTACATTATGTTTTAAATGTATTAATTATTTCTGTTTTTTTTAA
1 TTATTATTTTACATTATTTTAGTACATTATGTTTAAAATGTATTAATTATGTCTGTTTTTATAAA
* *
19987816 TTTAGTAAAAAACCCTAACTTCGGCCCTTTGTTCGTATTTTTTCTCCACATTTTATTACTTTC
66 TTTAG-AAAAAACCCTAACTTCGGCCCTTTGCTCGTATTTTTTCTCCAAATTTTATTACTTTC
19987879 GGTGAATATA
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
138 7 0.06
139 44 0.39
140 55 0.49
141 6 0.05
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (139 bp):
TTATTATTTTACATTATTTTAGTACATTATGTTTAAAATGTATTAATTATGTCTGTTTTTATAAA
TTTAGAAAAAACCCTAACTTCGGCCCTTTGCTCGTATTTTTTCTCCAAATTTTATTACTTTCAAT
AAAAATATA
Found at i:19988237 original size:4 final size:4
Alignment explanation
Indices: 19988228--19988280 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
19988218 CTCCTTTCCT
*
19988228 TTTC TTTC TTT- TTTC -TCC TTTC -TT- TTTC TTTC TTT- TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
19988271 TTTC TTTC TT
1 TTTC TTTC TT
19988281 CTCCTTTCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 12 0.29
4 30 0.71
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:19988243 original size:11 final size:11
Alignment explanation
Indices: 19988227--19988280 Score: 65
Period size: 11 Copynumber: 4.6 Consensus size: 11
19988217 TCTCCTTTCC
19988227 TTTTCTTTCTT
1 TTTTCTTTCTT
19988238 TTTTCTCCTT-TCT
1 TTTTCT--TTCT-T
19988251 TTTTCTTTCTT
1 TTTTCTTTCTT
19988262 TTTTCTTTCTT
1 TTTTCTTTCTT
19988273 TCTTTCTT
1 T-TTTCTT
19988281 CTCCTTTCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
11 21 0.55
12 8 0.21
13 9 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:19988243 original size:24 final size:24
Alignment explanation
Indices: 19988216--19988267 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
19988206 CCTCTTCTTC
19988216 TTCTCCTTTCCTTTTCTTTCTTTT
1 TTCTCCTTTCCTTTTCTTTCTTTT
*
19988240 TTCTCCTTTCTTTTTCTTTCTTTT
1 TTCTCCTTTCCTTTTCTTTCTTTT
19988264 TTCT
1 TTCT
19988268 TTCTTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (24 bp):
TTCTCCTTTCCTTTTCTTTCTTTT
Found at i:19988258 original size:10 final size:10
Alignment explanation
Indices: 19988221--19988273 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 10
19988211 TCTTCTTCTC
*
19988221 CTTTCCTTTT
1 CTTTCTTTTT
19988231 CTTTCTTTTTTCT
1 CTTTC--TTTT-T
19988244 CCTTTCTTTTT
1 -CTTTCTTTTT
19988255 CTTTCTTTTTT
1 CTTTC-TTTTT
19988266 CTTTCTTT
1 CTTTCTTT
19988274 CTTTCTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 13 0.35
11 11 0.30
12 7 0.19
13 1 0.03
14 5 0.14
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:19989624 original size:19 final size:20
Alignment explanation
Indices: 19989600--19989638 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19989590 GATTTTTACT
*
19989600 AAAATATTA-CAAAAAAATA
1 AAAATAATACCAAAAAAATA
*
19989619 AAAATAATACCAAAATAATA
1 AAAATAATACCAAAAAAATA
19989639 TAAACTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATACCAAAAAAATA
Found at i:19990045 original size:153 final size:152
Alignment explanation
Indices: 19989868--19990824 Score: 1278
Period size: 153 Copynumber: 6.3 Consensus size: 152
19989858 TTTTTTATTG
*
19989868 AAAGTAATAAAATCT-GGGAAAAAATACGAACAAACGGCCGAAATAAGAGTTTTTTTAAAATTTA
1 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTTAAAATTTA
*
19989932 TTTAAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAC
65 TTT-AAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
19989997 AATTAGAAAATAGTATATTTTTTA
129 AATTAGAAAATAGTATATTTTTTA
* *
19990021 AAAGTAATAAAATCTAGGG-AAAAATACGAACAAAGGGTCGAAATAAGGGTTTTTTACTAAATTT
1 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTA--AAATTT
* *
19990085 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAGTGTACTAAAATAATGTAAAATAATAA
64 ATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
** *
19990150 AATTAGAAAA-AAAATATTTTTATTG
129 AATTAGAAAATAGTATA-TTTT-TTA
**
19990175 AAAGTAATAAAAT-TAGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTTAATTTAT
1 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAAATTTAT
* *
19990239 TT-AAAAA-ACAGTAAATTAATATATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
66 TTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
19990302 GTAGAAAATAGTATATTTTTT-
131 TTAGAAAATAGTATATTTTTTA
* * *
19990323 AAAGTAATAAACTCTAGGGAAAAACATACGAACAAAGGGCTGAAATAAGGGTTTTTT-AAATTTA
1 AAAGTAATAAAATCTAGGGAAAAA-ATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAAATTTA
* *
19990387 TTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTATAATAATAAA
65 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
*
19990452 ATTAGAAAATAGTATATTTTTTT
130 ATTAGAAAATAGTATATTTTTTA
* * * * * *
19990475 AAAGCAATAAACTTTAGGGAAAAAATACGAACAAATGACCGAAATAAGAGTTTTTTAAAAATTTA
1 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTTAAAATTTA
* * *
19990540 TTTAAAAAA-A-ACTAAATTAATACATTTCAAATATGAGGTACTAAAATAATGTAAAATAATAAA
65 TTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
* * *
19990603 A-TACAAAAATAATATATTTTTATTG
130 ATTA-GAAAATAGTATA-TTTT-TTA
* *
19990628 AAAGTAATAAAATCT-GGGAAAAAAATACGAACAAAGGGCTGAAATAAAGATTTTTTT--AATTT
1 AAAGTAATAAAATCTAGGG-AAAAAATACGAACAAAGGGCCGAAAT-AAGGTTTTTTTAAAATTT
* * * *
19990690 ATTTAAAAAACACACTAAATTAATACGTTTAAAATATAATGTACTAAAATAATGTAAAATAAAAA
64 ATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
* * *
19990755 AATAAAAAAAATATTATATTTTTTA
129 AAT-TAGAAAATAGTATATTTTTTA
* * * *
19990780 AAAGTAATAAAAT-TCGAGAAAAAATACGAACAGAGGGCCAAAATA
1 AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATA
19990825 CGAACAATTG
Statistics
Matches: 720, Mismatches: 60, Indels: 51
0.87 0.07 0.06
Matches are distributed among these distances:
148 12 0.02
149 21 0.03
150 103 0.14
151 202 0.28
152 75 0.10
153 230 0.32
154 76 0.11
155 1 0.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (152 bp):
AAAGTAATAAAATCTAGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAAATTTAT
TTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
TTAGAAAATAGTATATTTTTTA
Found at i:19990431 original size:454 final size:457
Alignment explanation
Indices: 19989868--19990824 Score: 1411
Period size: 454 Copynumber: 2.1 Consensus size: 457
19989858 TTTTTTATTG
* *
19989868 AAAGTAATAAAATCTGGGAAAAAATACGAACAAACGGCCGAAATAAGAGTTTTTTTAAAATTTAT
1 AAAGTAATAAAATCTGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGGTTTTTTAAAATTTAT
*
19989933 TTAAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATACA
66 TTAAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
* **
19989998 ATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATCTAGGG-AAAAATACGAACAAAGGGTCGA
131 ATTAGAAAATAGTATATTTTTTAAAAGCAATAAAATCTAGGGAAAAAATACGAACAAAGGACCGA
* * *
19990062 AATAAGGGTTTTTTACTAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACAT-AGTG
196 AATAAGAGTTTTTTA-AAAATTTATTTAAAAAA-A-ACTAAATTAATACATTTCAAACATGAG-G
*
19990126 TACTAAAATAATGTAAAATAATAAAATTAGAAAAA-AA-ATATTTTTATTGAAAGTAATAAAAT-
257 TACTAAAATAATGTAAAATAATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATC
* * *
19990188 TAGGG-AAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTTTAATTTATTT-AAAAA-ACAG
321 T-GGGAAAAAAATACGAACAAAGGGCCGAAATAAAG-ATTTTTTTAATTTATTTAAAAAACACAC
* * * *
19990250 TAAATTAATATATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAAGT-AGAAAATAGT
384 TAAATTAATACATTTAAAACATAATGTACTAAAATAATGTAAAATAA-AAAAATAAAAAAATAGT
19990314 ATATTTTTT-
448 ATATTTTTTA
* *
19990323 AAAGTAATAAACTCTAGGGAAAAACATACGAACAAAGGGCTGAAATAAG-GGTTTTTT-AAATTT
1 AAAGTAATAAAATCT-GGGAAAAA-ATACGAACAAAGGGCCGAAATAAGAGGTTTTTTAAAATTT
* *
19990386 ATTT-AAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTATAATAATA
64 ATTTAAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
* * * *
19990450 AAATTAGAAAATAGTATATTTTTTTAAAGCAATAAACTTTAGGGAAAAAATACGAACAAATGACC
129 AAATTAGAAAATAGTATATTTTTTAAAAGCAATAAAATCTAGGGAAAAAATACGAACAAAGGACC
*
19990515 GAAATAAGAGTTTTTTAAAAATTTATTTAAAAAAAACTAAATTAATACATTTCAAATATGAGGTA
194 GAAATAAGAGTTTTTTAAAAATTTATTTAAAAAAAACTAAATTAATACATTTCAAACATGAGGTA
19990580 CTAAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCTGG
259 CTAAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCTGG
*
19990645 GAAAAAAATACGAACAAAGGGCTGAAATAAAGATTTTTTTAATTTATTTAAAAAACACACTAAAT
324 GAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTTAATTTATTTAAAAAACACACTAAAT
* * *
19990710 TAATACGTTTAAAATATAATGTACTAAAATAATGTAAAATAAAAAAATAAAAAAAATATTATATT
389 TAATACATTTAAAACATAATGTACTAAAATAATGTAAAATAAAAAAAT-AAAAAAATAGTATATT
19990775 TTTTA
453 TTTTA
* * *
19990780 AAAGTAATAAAAT-TCGAGAAAAAATACGAACAGAGGGCCAAAATA
1 AAAGTAATAAAATCT-GGGAAAAAATACGAACAAAGGGCCGAAATA
19990825 CGAACAATTG
Statistics
Matches: 453, Mismatches: 36, Indels: 26
0.88 0.07 0.05
Matches are distributed among these distances:
451 7 0.02
452 51 0.11
453 47 0.10
454 152 0.34
455 122 0.27
456 40 0.09
457 34 0.08
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (457 bp):
AAAGTAATAAAATCTGGGAAAAAATACGAACAAAGGGCCGAAATAAGAGGTTTTTTAAAATTTAT
TTAAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
ATTAGAAAATAGTATATTTTTTAAAAGCAATAAAATCTAGGGAAAAAATACGAACAAAGGACCGA
AATAAGAGTTTTTTAAAAATTTATTTAAAAAAAACTAAATTAATACATTTCAAACATGAGGTACT
AAAATAATGTAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATCTGGGA
AAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTTAATTTATTTAAAAAACACACTAAATTA
ATACATTTAAAACATAATGTACTAAAATAATGTAAAATAAAAAAATAAAAAAATAGTATATTTTT
TA
Found at i:20006099 original size:29 final size:31
Alignment explanation
Indices: 20006030--20006151 Score: 92
Period size: 31 Copynumber: 3.9 Consensus size: 31
20006020 AACATGTAAG
20006030 TATTT-AATTAATTTTTTAAATTTTTAAAAAATA
1 TATTTAAATT-ATTTTTTAAA-TTTT-AAAAATA
* *
20006063 TATATAAATTATTTTTTAAA-TTT-AAAATT
1 TATTTAAATTATTTTTTAAATTTTAAAAATA
** *
20006092 TATTTAAATTA-TTTAAAAATTATAAAAAATA
1 TATTTAAATTATTTTTTAAATT-TTAAAAATA
* * *
20006123 TATTTTTAA-TATTTTTAAAATTCTAAAAA
1 TA-TTTAAATTATTTTTTAAATTTTAAAAA
20006152 ATCAATTAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
28 6 0.08
29 16 0.22
30 1 0.01
31 17 0.24
32 14 0.19
33 14 0.19
34 4 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TATTTAAATTATTTTTTAAATTTTAAAAATA
Found at i:20006130 original size:50 final size:50
Alignment explanation
Indices: 20006030--20006136 Score: 130
Period size: 50 Copynumber: 2.1 Consensus size: 50
20006020 AACATGTAAG
*
20006030 TATTTAATTAATTTTTTAAATTTTTAAAAAATATATATAAATTATTTTTTAA
1 TATTTAA--AATTTTTTAAATTTTTAAAAAATATATAAAAATTATTTTTTAA
*
20006082 -ATTTAAAATTTATTTAAATTATTT-AAAAAT-TATAAAAAATATATTTTTAA
1 TATTTAAAATTT-TTTAAATT-TTTAAAAAATATATAAAAATTAT-TTTTTAA
20006132 TATTT
1 TATTT
20006137 TTAAAATTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
49 15 0.31
50 21 0.43
51 13 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (50 bp):
TATTTAAAATTTTTTAAATTTTTAAAAAATATATAAAAATTATTTTTTAA
Found at i:20008253 original size:18 final size:18
Alignment explanation
Indices: 20008230--20008264 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20008220 ATAAAATATG
20008230 CATAAAAAAATTAAAATA
1 CATAAAAAAATTAAAATA
*
20008248 CATAAATAAATTAAAAT
1 CATAAAAAAATTAAAAT
20008265 GGAAGTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
CATAAAAAAATTAAAATA
Found at i:20008525 original size:17 final size:18
Alignment explanation
Indices: 20008503--20008542 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
20008493 GTGATATTTT
20008503 AATTAAATATTT-TTTAA
1 AATTAAATATTTATTTAA
*
20008520 AATTAAATTTTTATTTAA
1 AATTAAATATTTATTTAA
*
20008538 TATTA
1 AATTA
20008543 TATTTACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTAAATATTTATTTAA
Found at i:20008542 original size:18 final size:17
Alignment explanation
Indices: 20008503--20008547 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
20008493 GTGATATTTT
*
20008503 AATTAAATATTTTTTAA
1 AATTAAATTTTTTTTAA
20008520 AATTAAATTTTTATTTAA
1 AATTAAATTTTT-TTTAA
* *
20008538 TATTATATTT
1 AATTAAATTT
20008548 ACAACTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTAAATTTTTTTTAA
Found at i:20011207 original size:37 final size:37
Alignment explanation
Indices: 20011164--20011240 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
20011154 TTTCCTCAAA
20011164 ATGCAATATTTTTAGGTATGTCCAAAGTTTCTTTCAT
1 ATGCAATATTTTTAGGTATGTCCAAAGTTTCTTTCAT
20011201 ATGCAATATTTTTAGGTATGTCCAAAGTTTCTTTCAT
1 ATGCAATATTTTTAGGTATGTCCAAAGTTTCTTTCAT
20011238 ATG
1 ATG
20011241 ATGCCAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.45
Consensus pattern (37 bp):
ATGCAATATTTTTAGGTATGTCCAAAGTTTCTTTCAT
Found at i:20016130 original size:24 final size:24
Alignment explanation
Indices: 20016096--20016141 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20016086 TATATGAAAT
* *
20016096 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
20016120 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
20016142 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:20030848 original size:3 final size:3
Alignment explanation
Indices: 20030842--20030887 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
20030832 TTTTAGTTTT
* *
20030842 TTA TTA TTA TTA TTA TTA TTA TTA TCA -TA TTA TATA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
20030887 T
1 T
20030888 ACTTACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.92
4 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:20032209 original size:18 final size:18
Alignment explanation
Indices: 20032186--20032236 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
20032176 GACAGTCTTG
*
20032186 ATTATATAATTATAAAAA
1 ATTATATAAATATAAAAA
20032204 ATTATATAAATATAAAAA
1 ATTATATAAATATAAAAA
* *
20032222 ATTAAAAAAATATAA
1 ATTATATAAATATAA
20032237 TAATATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTATATAAATATAAAAA
Found at i:20032239 original size:27 final size:27
Alignment explanation
Indices: 20032193--20032253 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 27
20032183 TTGATTATAT
20032193 AATTATAAAAAATTATATAA-ATATAAAA
1 AATTA-AAAAAATTATATAATAT-TAAAA
20032221 AATTAAAAAAA-TATAATAATATTAAAA
1 AATTAAAAAAATTAT-ATAATATTAAAA
20032248 AATTAA
1 AATTAA
20032254 TAATGATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.10
27 21 0.68
28 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AATTAAAAAAATTATATAATATTAAAA
Found at i:20032256 original size:20 final size:20
Alignment explanation
Indices: 20032222--20032286 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
20032212 AATATAAAAA
*
20032222 ATTAAAAAAAT-ATAATAAT
1 ATTAAAAAATTAATAATAAT
*
20032241 ATTAAAAAATTAATAATGAT
1 ATTAAAAAATTAATAATAAT
*
20032261 ATTAATTAAAATAAAATAATAAT
1 ATTAA--AAAAT-TAATAATAAT
20032284 ATT
1 ATT
20032287 TTCTTACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.26
20 12 0.32
22 5 0.13
23 11 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
ATTAAAAAATTAATAATAAT
Found at i:20032266 original size:26 final size:25
Alignment explanation
Indices: 20032206--20032285 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
20032196 TATAAAAAAT
* *
20032206 TATATAAATA-TAAAAAATTAAAAAAA
1 TATATTAATATTAAAAAATT--AATAA
*
20032232 TATAATAATATTAAAAAATTAATAA
1 TATATTAATATTAAAAAATTAATAA
* *
20032257 TGATATTAAT-TAAAATAAAATAATAA
1 T-ATATTAATATTAAA-AAATTAATAA
20032283 TAT
1 TAT
20032286 TTTCTTACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
25 11 0.24
26 25 0.56
27 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
TATATTAATATTAAAAAATTAATAA
Found at i:20032278 original size:23 final size:23
Alignment explanation
Indices: 20032221--20032286 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
20032211 AAATATAAAA
20032221 AATTAAAA-AAATATAATAATATT
1 AATTAAAATAAA-ATAATAATATT
* *
20032244 AA--AAAAT-TAATAATGATATT
1 AATTAAAATAAAATAATAATATT
20032264 AATTAAAATAAAATAATAATATT
1 AATTAAAATAAAATAATAATATT
20032287 TTCTTACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 12 0.34
21 5 0.14
22 5 0.14
23 13 0.37
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AATTAAAATAAAATAATAATATT
Found at i:20037505 original size:30 final size:31
Alignment explanation
Indices: 20037453--20037512 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
20037443 AGTTACAAAG
*
20037453 TGGTCACTCAATTATTCAATTTTTTCTTTTT
1 TGGTCACTCAACTATTCAATTTTTTCTTTTT
*
20037484 TGGTCAC-CAACTATTCGATTTTTTCTTTT
1 TGGTCACTCAACTATTCAATTTTTTCTTTT
20037513 GTAGTCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.18, C:0.18, G:0.08, T:0.55
Consensus pattern (31 bp):
TGGTCACTCAACTATTCAATTTTTTCTTTTT
Found at i:20052400 original size:18 final size:18
Alignment explanation
Indices: 20052377--20052413 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20052367 GCTGGGCAGT
* *
20052377 AGAAGAAGGAGAAGAGAA
1 AGAAGAAGAAAAAGAGAA
20052395 AGAAGAAGAAAAAGAGAA
1 AGAAGAAGAAAAAGAGAA
20052413 A
1 A
20052414 AAAAAATCTA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAAAGAGAA
Found at i:20054830 original size:13 final size:12
Alignment explanation
Indices: 20054794--20054835 Score: 61
Period size: 11 Copynumber: 3.6 Consensus size: 12
20054784 GTTGCAGTTG
20054794 AAAAATATTTT-
1 AAAAATATTTTA
20054805 AAAAATA-TTTA
1 AAAAATATTTTA
20054816 AAAAATAATTTTA
1 AAAAAT-ATTTTA
20054829 AAAAATA
1 AAAAATA
20054836 GTAAAATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.11
11 13 0.46
12 2 0.07
13 10 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAATATTTTA
Found at i:20054840 original size:23 final size:22
Alignment explanation
Indices: 20054794--20054841 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
20054784 GTTGCAGTTG
*
20054794 AAAAATATTTTAAAAATATTTA
1 AAAAATATTTTAAAAATATGTA
20054816 AAAAATAATTTTAAAAA-ATAGTA
1 AAAAAT-ATTTTAAAAATAT-GTA
20054839 AAA
1 AAA
20054842 TGTGCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAAATATTTTAAAAATATGTA
Found at i:20055159 original size:18 final size:20
Alignment explanation
Indices: 20055110--20055160 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
20055100 TAAAATAGTT
*
20055110 TAATATAATAATATATAAAA
1 TAATTTAATAATATATAAAA
*
20055130 TAATTCATATAA-ATA-AAAA
1 TAATTTA-ATAATATATAAAA
*
20055149 TATTTTAATAAT
1 TAATTTAATAAT
20055161 TTTTAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 4 0.16
19 9 0.36
20 8 0.32
21 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATTTAATAATATATAAAA
Found at i:20055689 original size:5 final size:6
Alignment explanation
Indices: 20055663--20055687 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20055653 AATCAGATCG
20055663 TTGTTT TTGTTT TTGTTT TTGTTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT T
20055688 GTGGTTGCAT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTGTTT
Found at i:20063149 original size:88 final size:90
Alignment explanation
Indices: 20063021--20063195 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 90
20063011 TATATCACTG
*
20063021 GTAAAAAGTTTTAAGGCATATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
1 GTAAAAAGTTTAAAGGCA-ATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
20063086 GAGTCTCTGGA-TTGATCTAGAAGCA
65 GAGTCTCTGGATTTGATCTAGAAGCA
* * * * ** *
20063111 GTAAAATGTTTAAAGGC-ATAAACGAGATGGAGATATGAATGTGAAAGTAGATAGATCATGGATG
1 GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
20063175 AGTCTCTGGATTTGATCTAGA
66 AGTCTCTGGATTTGATCTAGA
20063196 TTCAAGAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
88 51 0.67
89 10 0.13
90 15 0.20
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.26
Consensus pattern (90 bp):
GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
AGTCTCTGGATTTGATCTAGAAGCA
Found at i:20066521 original size:116 final size:116
Alignment explanation
Indices: 20066317--20066554 Score: 467
Period size: 116 Copynumber: 2.0 Consensus size: 116
20066307 TACCCACTTT
20066317 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
1 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
20066382 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
66 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
20066433 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
1 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
20066498 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
66 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
20066549 CTCTAC
1 C-CTAC
20066555 TCAAGTTGTG
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 117 0.97
117 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (116 bp):
CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
Found at i:20071133 original size:18 final size:18
Alignment explanation
Indices: 20071112--20071148 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20071102 TGTTATATAC
20071112 GAGTACCAACTTATTTCG
1 GAGTACCAACTTATTTCG
*
20071130 GAGTACTAACTTATTTCG
1 GAGTACCAACTTATTTCG
20071148 G
1 G
20071149 CGTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
GAGTACCAACTTATTTCG
Found at i:20079555 original size:22 final size:23
Alignment explanation
Indices: 20079527--20079577 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
20079517 ACAATAAAGA
*
20079527 TAAATAATATTTGTATT-AACAT
1 TAAATAATATTTATATTAAACAT
*
20079549 TAAATAATATTTATATTAAATAT
1 TAAATAATATTTATATTAAACAT
20079572 TAAATA
1 TAAATA
20079578 TTATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATAATATTTATATTAAACAT
Found at i:20079635 original size:63 final size:64
Alignment explanation
Indices: 20079523--20079644 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 64
20079513 AATTACAATA
* * *
20079523 AAGATAAATAATATTTGTATTAACATTAAATAATATTTATATTAAATA-TTAAATATTATCTTT
1 AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
* * * * * *
20079586 AAGATAAATATTATTTATCTTAATATTTAA-AATTTTTATTATCAGATATTTAAAAATTA
1 AAGATAAATAATATTTATATTAACATTAAATAATATTTA-TATCAAATATTTAAAAATTA
20079645 AAATCATAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
62 7 0.15
63 32 0.67
64 9 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (64 bp):
AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
Found at i:20079673 original size:18 final size:18
Alignment explanation
Indices: 20079652--20079710 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
20079642 TTAAAATCAT
20079652 AATTATGAATTAAATTTA
1 AATTATGAATTAAATTTA
* *
20079670 AATT-TTATTTAAAATTTTA
1 AATTATGAATT-AAA-TTTA
20079689 AATTATGAATTAAATTTA
1 AATTATGAATTAAATTTA
20079707 AATT
1 AATT
20079711 CAAAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 11 0.32
20 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTATGAATTAAATTTA
Found at i:20081626 original size:27 final size:27
Alignment explanation
Indices: 20081573--20081625 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
20081563 TTATAATTTT
20081573 TTTATTTACCAAAATATTATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
*
20081600 TTTATTTACTAAAATA-TATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
20081626 ACAAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTATTTACCAAAATATTATAAAAAAA
Found at i:20082296 original size:19 final size:18
Alignment explanation
Indices: 20082272--20082359 Score: 90
Period size: 18 Copynumber: 4.7 Consensus size: 18
20082262 TCTAATTAAG
20082272 TAATAATTCTATTTCAATT
1 TAATAA-TCTATTTCAATT
*
20082291 TAATAAACTATTCTCAA-T
1 TAATAATCTATT-TCAATT
*
20082309 TAATAACTCTATTTTAATT
1 TAATAA-TCTATTTCAATT
*
20082328 TAATAAACTATTCTC-ATT
1 TAATAATCTATT-TCAATT
20082346 TAATAACTCTATTT
1 TAATAA-TCTATTT
20082360 TCATTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
18 30 0.52
19 28 0.48
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATCTATTTCAATT
Found at i:20082314 original size:37 final size:37
Alignment explanation
Indices: 20082272--20082367 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
20082262 TCTAATTAAG
*
20082272 TAATAATTCTATTTCAATTTAATAAACTATTCTCAAT
1 TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
* *
20082309 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
20082346 TAATAACTCTATTTTC-ATTTAA
1 TAATAACTCTA-TTTCAATTTAA
20082368 AATATAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 51 0.94
38 3 0.06
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (37 bp):
TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
Found at i:20082363 original size:19 final size:18
Alignment explanation
Indices: 20082272--20082367 Score: 95
Period size: 19 Copynumber: 5.2 Consensus size: 18
20082262 TCTAATTAAG
20082272 TAATAATTCTA-TTTCAATT
1 TAATAA-TCTATTTTC-ATT
* * *
20082291 TAATAAACTATTCTCAAT
1 TAATAATCTATTTTCATT
*
20082309 TAATAACTCTATTTTAATT
1 TAATAA-TCTATTTTCATT
* *
20082328 TAATAAACTATTCTCATT
1 TAATAATCTATTTTCATT
20082346 TAATAACTCTATTTTCATT
1 TAATAA-TCTATTTTCATT
20082365 TAA
1 TAA
20082368 AATATAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
18 26 0.42
19 36 0.58
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATCTATTTTCATT
Found at i:20082535 original size:82 final size:82
Alignment explanation
Indices: 20082436--20082600 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
20082426 TTAATTAAAA
20082436 TAGTCTAACATGTTTATGTTAGAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTAGAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
20082501 TTTATGTTTCCATTATT
66 TTTATGTTTCCATTATT
*
20082518 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATGTTAGAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
*
20082583 TTTATGTTTCCGTTATT
66 TTTATGTTTCCATTATT
20082600 T
1 T
20082601 TTTTCTTTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (82 bp):
TAGTCTAACATGTTTATGTTAGAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
TTTATGTTTCCATTATT
Found at i:20083140 original size:27 final size:25
Alignment explanation
Indices: 20083110--20083168 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
20083100 TTTTTTATTT
20083110 TTTTAGTATATTTTGGTAAATAAAAAA
1 TTTTA-TATATTTT-GTAAATAAAAAA
*
20083137 TTTTATAATATTTTTTAAATAAAAAA
1 TTTTAT-ATATTTTGTAAATAAAAAA
*
20083163 ATTTAT
1 TTTTAT
20083169 TTTATTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 17 0.59
27 12 0.41
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTTATATATTTTGTAAATAAAAAA
Found at i:20083177 original size:27 final size:26
Alignment explanation
Indices: 20083117--20083177 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
20083107 TTTTTTTAGT
* *
20083117 ATATTTTGGTAAATAAAAAATTTTATA
1 ATATTTT-TTAAATAAAAAAATTTATA
*
20083144 ATATTTTTTAAATAAAAAAATTTATT
1 ATATTTTTTAAATAAAAAAATTTATA
*
20083170 TTATTTTT
1 ATATTTTT
20083178 GTTATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
ATATTTTTTAAATAAAAAAATTTATA
Found at i:20083182 original size:14 final size:13
Alignment explanation
Indices: 20083164--20083195 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
20083154 AATAAAAAAA
20083164 TTTATTTTATTTT
1 TTTATTTTATTTT
20083177 TGTTATTTTATTTT
1 T-TTATTTTATTTT
20083191 TTTAT
1 TTTAT
20083196 AATAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:20091373 original size:18 final size:17
Alignment explanation
Indices: 20091345--20091388 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
20091335 ATAATTTATT
20091345 TTTAAAAATACAATTAA
1 TTTAAAAATACAATTAA
* *
20091362 TTTAATAAATACTATTAT
1 TTTAA-AAATACAATTAA
20091380 TTTGAAAAA
1 TTT-AAAAA
20091389 AAATTATCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAAAATACAATTAA
Found at i:20093560 original size:17 final size:19
Alignment explanation
Indices: 20093525--20093562 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
20093515 TATGCATGGT
*
20093525 AAATAATAAAAAGTCAACA
1 AAATAATAAAAAGTAAACA
20093544 AAATAA-AAAAA-TAAACA
1 AAATAATAAAAAGTAAACA
20093561 AA
1 AA
20093563 CAAGAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (19 bp):
AAATAATAAAAAGTAAACA
Found at i:20094031 original size:24 final size:24
Alignment explanation
Indices: 20093986--20094031 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20093976 ATAATTTTAG
* *
20093986 ACATATATATTATAGTATATAAGC
1 ACATATATATAATAATATATAAGC
20094010 ACATATATATAAATAATA-ATAA
1 ACATATATAT-AATAATATATAA
20094032 TATAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (24 bp):
ACATATATATAATAATATATAAGC
Found at i:20095849 original size:43 final size:43
Alignment explanation
Indices: 20095784--20095940 Score: 165
Period size: 43 Copynumber: 3.6 Consensus size: 43
20095774 ATTTTAATCC
*
20095784 GCTCCACTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCT
1 GCTCCACTGTAATC-TCAAGGAGATAGGATAGTGTCTTCGATCT
* * * * *
20095827 GCTCCGCTGTAATCTCAAGGAGATAAGAT-CTGAAATTCTCCGGTCT
1 GCTCCACTGTAATCTCAAGGAGATAGGATAGTG----TCTTCGATCT
* *
20095873 ACTCCACTGTAACCTCAAGGAGATAGGATAGTGTCTTCGATCT
1 GCTCCACTGTAATCTCAAGGAGATAGGATAGTGTCTTCGATCT
* *
20095916 GCTCCGCTGTAATCTCAGGGAGATA
1 GCTCCACTGTAATCTCAAGGAGATA
20095941 AGATCTGAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
42 2 0.02
43 53 0.58
44 1 0.01
46 33 0.36
47 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAAGGAGATAGGATAGTGTCTTCGATCT
Found at i:20095890 original size:46 final size:46
Alignment explanation
Indices: 20095828--20095994 Score: 189
Period size: 46 Copynumber: 3.7 Consensus size: 46
20095818 CTTCGATCTG
* *
20095828 CTCCGCTGTAATCTCAAGGAGATAAGATCTGAAATTCTCCGGTCTA
1 CTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTCCGGTCTA
* * * * *
20095874 CTCCACTGTAACCTCAAGGAGATAGGA--T--AGTGTCTTCGATCTG
1 CTCCACTGTAACCTCAAGGAGATAAGATCTGAAAT-TCTCCGGTCTA
* * *
20095917 CTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTA
1 CTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTCCGGTCTA
* *
20095963 CTCCACTGTAACCTCAAGGAAATAAGACCTGA
1 CTCCACTGTAACCTCAAGGAGATAAGATCTGA
20095995 TGTGATCTTC
Statistics
Matches: 96, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 31 0.32
44 1 0.01
45 1 0.01
46 59 0.61
47 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (46 bp):
CTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTCCGGTCTA
Found at i:20095902 original size:89 final size:89
Alignment explanation
Indices: 20095785--20095982 Score: 369
Period size: 89 Copynumber: 2.2 Consensus size: 89
20095775 TTTTAATCCG
* *
20095785 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAAGGAGA
1 CTCCACTGTAACCTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAAGGAGA
20095850 TAAGATCTGAAATTCTCCGGTCTA
66 TAAGATCTGAAATTCTCCGGTCTA
*
20095874 CTCCACTGTAACCTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
1 CTCCACTGTAACCTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAAGGAGA
20095939 TAAGATCTGAAATTCTCCGGTCTA
66 TAAGATCTGAAATTCTCCGGTCTA
20095963 CTCCACTGTAACCTCAAGGA
1 CTCCACTGTAACCTCAAGGA
20095983 AATAAGACCT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 106 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (89 bp):
CTCCACTGTAACCTCAAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAAGGAGA
TAAGATCTGAAATTCTCCGGTCTA
Found at i:20096065 original size:39 final size:40
Alignment explanation
Indices: 20095912--20096160 Score: 126
Period size: 44 Copynumber: 5.9 Consensus size: 40
20095902 AGTGTCTTCG
* * *
20095912 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTCCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTT-T--A
* * * * * * * * *
20095958 GTCTACTCCACTGTAACCTCAAGGAAATAAGACCTGATGTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTTTA
* * *
20095999 ATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTTTA
* * *
20096038 ATCTGCTCC-CTTGTAATCTCAAGGAGATAGGATTACTATCTTTG
1 ATCTGCTCCAC-TGTAATCTCAGGGAGATAAGA-T-C--TCTTTA
* *
20096082 ATCTGCTCCGCTGTAATCTCAGGGTGATAAGATCTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT---TT-A
* *
20096126 ATCTGCTCCACTGTAACCTTAGGGAGATAAGATCT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
20096161 GAAATTCTTT
Statistics
Matches: 157, Mismatches: 33, Indels: 28
0.72 0.15 0.13
Matches are distributed among these distances:
38 1 0.01
39 25 0.16
40 6 0.04
41 27 0.17
42 1 0.01
43 4 0.03
44 64 0.41
45 1 0.01
46 28 0.18
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (40 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTTA
Found at i:20117818 original size:88 final size:90
Alignment explanation
Indices: 20117690--20117864 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 90
20117680 TATATCACTG
*
20117690 GTAAAAAGTTTTAAGGCATATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
1 GTAAAAAGTTTAAAGGCA-ATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
20117755 GAGTCTCTGGA-TTGATCTAGAAGCA
65 GAGTCTCTGGATTTGATCTAGAAGCA
* * * * ** *
20117780 GTAAAATGTTTAAAGGC-ATAAACGAGATGGAGATATGAATGTGAAAGTAGATAGATCATGGATG
1 GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
20117844 AGTCTCTGGATTTGATCTAGA
66 AGTCTCTGGATTTGATCTAGA
20117865 TTCAAGAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
88 51 0.67
89 10 0.13
90 15 0.20
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.26
Consensus pattern (90 bp):
GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
AGTCTCTGGATTTGATCTAGAAGCA
Found at i:20121176 original size:116 final size:116
Alignment explanation
Indices: 20120972--20121209 Score: 467
Period size: 116 Copynumber: 2.0 Consensus size: 116
20120962 TACCCACTTT
20120972 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
1 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
20121037 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
66 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
20121088 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
1 CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
20121153 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
66 AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
20121204 CTCTAC
1 C-CTAC
20121210 TCAAGTTGTG
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 117 0.97
117 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (116 bp):
CCTACGTTTAACTTCAAACTTGGTTATTTGTGTATGAGTTAGTATAAAGATTATCTAGTATAATA
AAAATGAAAAATATAATATTAAAATTTGAAAGCTTGGTTAGTCTTTCGAGC
Found at i:20125787 original size:18 final size:18
Alignment explanation
Indices: 20125766--20125802 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
20125756 TGTTATATAC
20125766 GAGTACCAACTTATTTCG
1 GAGTACCAACTTATTTCG
*
20125784 GAGTACTAACTTATTTCG
1 GAGTACCAACTTATTTCG
20125802 G
1 G
20125803 CGTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
GAGTACCAACTTATTTCG
Found at i:20134194 original size:22 final size:23
Alignment explanation
Indices: 20134166--20134216 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
20134156 ACAATAAAGA
*
20134166 TAAATAATATTTGTATT-AACAT
1 TAAATAATATTTATATTAAACAT
*
20134188 TAAATAATATTTATATTAAATAT
1 TAAATAATATTTATATTAAACAT
20134211 TAAATA
1 TAAATA
20134217 TTATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATAATATTTATATTAAACAT
Found at i:20134274 original size:63 final size:64
Alignment explanation
Indices: 20134162--20134283 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 64
20134152 AATTACAATA
* * *
20134162 AAGATAAATAATATTTGTATTAACATTAAATAATATTTATATTAAATA-TTAAATATTATCTTT
1 AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
* * * * * *
20134225 AAGATAAATATTATTTATCTTAATATTTAA-AATTTTTATTATCAGATATTTAAAAATTA
1 AAGATAAATAATATTTATATTAACATTAAATAATATTTA-TATCAAATATTTAAAAATTA
20134284 AAATCATAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
62 7 0.15
63 32 0.67
64 9 0.19
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (64 bp):
AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
Found at i:20134311 original size:6 final size:6
Alignment explanation
Indices: 20134300--20134361 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
20134290 TAATTATGAA
* *
20134300 TTAAAT TTAAAT TT-TAT TTAAAATT TTAAAT TATGAA- TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TT-AAA-T TTAAAT T-TAAAT TTAAAT TTAAAT
*
20134349 TCAAAT TTAAAT T
1 TTAAAT TTAAAT T
20134362 AGATTTAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
5 7 0.16
6 28 0.62
7 7 0.16
8 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:20134312 original size:18 final size:18
Alignment explanation
Indices: 20134291--20134349 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
20134281 TTAAAATCAT
20134291 AATTATGAATTAAATTTA
1 AATTATGAATTAAATTTA
* *
20134309 AATT-TTATTTAAAATTTTA
1 AATTATGAATT-AAA-TTTA
20134328 AATTATGAATTAAATTTA
1 AATTATGAATTAAATTTA
20134346 AATT
1 AATT
20134350 CAAATTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 11 0.32
20 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTATGAATTAAATTTA
Found at i:20134367 original size:11 final size:11
Alignment explanation
Indices: 20134298--20134374 Score: 64
Period size: 11 Copynumber: 6.5 Consensus size: 11
20134288 CATAATTATG
20134298 AATTAAATTTA
1 AATTAAATTTA
**
20134309 AATTTTATTTAA
1 AATTAAATTT-A
*
20134321 AATTTTAAATTATG
1 AA--TTAAATT-TA
20134335 AATTAAATTTA
1 AATTAAATTTA
20134346 AATTCAAATTTA
1 AATT-AAATTTA
*
20134358 AATTAGATTTA
1 AATTAAATTTA
*
20134369 AGTTAA
1 AATTAA
20134375 CTATATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
11 23 0.44
12 21 0.40
14 7 0.13
15 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:20136244 original size:27 final size:27
Alignment explanation
Indices: 20136191--20136243 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
20136181 TTATAATTTT
20136191 TTTATTTACCAAAATATTATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
*
20136218 TTTATTTACTAAAATA-TATAAAAAAA
1 TTTATTTACCAAAATATTATAAAAAAA
20136244 ACAAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTATTTACCAAAATATTATAAAAAAA
Found at i:20136903 original size:19 final size:18
Alignment explanation
Indices: 20136879--20136973 Score: 97
Period size: 18 Copynumber: 5.2 Consensus size: 18
20136869 TCTAATTAAG
20136879 TAATAATTCTATTTCAATT
1 TAATAA-TCTATTTCAATT
*
20136898 TAATAAACTATTCTCAA-T
1 TAATAATCTATT-TCAATT
*
20136916 TAATAACTCTATTTTAATT
1 TAATAA-TCTATTTCAATT
*
20136935 TAATAAACTATTCTC-ATT
1 TAATAATCTATT-TCAATT
20136953 TAATAACTCTATTTC-ATT
1 TAATAA-TCTATTTCAATT
20136971 TAA
1 TAA
20136974 AATATAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
18 37 0.57
19 28 0.43
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATAATCTATTTCAATT
Found at i:20136921 original size:37 final size:37
Alignment explanation
Indices: 20136879--20136973 Score: 156
Period size: 37 Copynumber: 2.6 Consensus size: 37
20136869 TCTAATTAAG
*
20136879 TAATAATTCTATTTCAATTTAATAAACTATTCTCAAT
1 TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
* *
20136916 TAATAACTCTATTTTAATTTAATAAACTATTCTCATT
1 TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
20136953 TAATAACTCTATTTC-ATTTAA
1 TAATAACTCTATTTCAATTTAA
20136974 AATATAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
36 6 0.11
37 48 0.89
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (37 bp):
TAATAACTCTATTTCAATTTAATAAACTATTCTCAAT
Found at i:20137176 original size:82 final size:79
Alignment explanation
Indices: 20137042--20137203 Score: 279
Period size: 82 Copynumber: 2.0 Consensus size: 79
20137032 TTAATTAAAA
20137042 TAGTCTAACATGTTTATGTAGAAGTTATTAAGATATATTAAATTTATAAATAGATAAAATAGTTT
1 TAGTCTAACATGTTTATGTAGAAGTTATTAAGATATATTAAATTTATAAATAGATAAAATAGTTT
20137107 ATGTTTCCATTATT
66 ATGTTTCCATTATT
*
20137121 TAGTCTAACATGTTTATGTTATAAGTCTATTAAGAATATATTAAATTTATAAATAGATAAAATAG
1 TAGTCTAACATGTTTATG-TAGAAGT-TATTAAG-ATATATTAAATTTATAAATAGATAAAATAG
*
20137186 TTTATGTTTCCGTTATT
63 TTTATGTTTCCATTATT
20137203 T
1 T
20137204 TTTTCTTTTT
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
79 18 0.23
80 6 0.08
81 7 0.09
82 47 0.60
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (79 bp):
TAGTCTAACATGTTTATGTAGAAGTTATTAAGATATATTAAATTTATAAATAGATAAAATAGTTT
ATGTTTCCATTATT
Found at i:20137748 original size:25 final size:26
Alignment explanation
Indices: 20137705--20137765 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
20137695 TTTTTTTAGT
*
20137705 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTT--TAAATAAAAAAAATTTATA
*
20137733 ATATTTTTAAAT-AAAAAAATTTATT
1 ATATTTTTAAATAAAAAAAATTTATA
*
20137758 TTATTTTT
1 ATATTTTT
20137766 GTTATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.60
26 5 0.17
28 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
ATATTTTTAAATAAAAAAAATTTATA
Found at i:20137770 original size:14 final size:14
Alignment explanation
Indices: 20137753--20137779 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20137743 ATAAAAAAAT
20137753 TTATTTTATTTTTG
1 TTATTTTATTTTTG
20137767 TTATTTTATTTTT
1 TTATTTTATTTTT
20137780 TATAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTATTTTATTTTTG
Found at i:20158811 original size:24 final size:24
Alignment explanation
Indices: 20158766--20158811 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20158756 ATAATTTTAG
* *
20158766 ACATATATATTATAGTATATAAGC
1 ACATATATATAATAATATATAAGC
20158790 ACATATATATAAATAATA-ATAA
1 ACATATATAT-AATAATATATAA
20158812 TATAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (24 bp):
ACATATATATAATAATATATAAGC
Done.