Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 58 of 226
Found at i:19040361 original size:5 final size:5
Alignment explanation
Indices: 19040351--19040384 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
19040341 TATCTTGTAA
19040351 AGATT AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGATT AGAT
19040385 ATGACATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:19052059 original size:91 final size:91
Alignment explanation
Indices: 19051904--19052087 Score: 298
Period size: 91 Copynumber: 2.0 Consensus size: 91
19051894 GTATAAGATA
*
19051904 AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAATCCAAAA
1 AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAAA
* *
19051969 TTCCCCAAAATTCACAGAATTCCCTT
66 TTCCCCAAAACTCACAAAATTCCCTT
* *
19051995 AAGATAATCTCAACAAATAAA-TCTGAAATCTCGAAAGAACAAAGTACTCTAACTAAAACCCAAA
1 AAGATAATCTCAACAAATAAACCCT-AAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAA
*
19052059 ATTCCCCAAAACTCACAAAATTCTCTT
65 ATTCCCCAAAACTCACAAAATTCCCTT
19052086 AA
1 AA
19052088 TCTCATAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
90 2 0.02
91 84 0.98
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (91 bp):
AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAAA
TTCCCCAAAACTCACAAAATTCCCTT
Found at i:19053302 original size:4 final size:4
Alignment explanation
Indices: 19053285--19053316 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19053275 CATTTTAAGC
*
19053285 CATA CATA CGTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
19053317 TGCATGCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:19053646 original size:6 final size:6
Alignment explanation
Indices: 19053635--19053660 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19053625 TTGCATCACC
19053635 CTGTCT CTGTCT CTGTCT CTGTCT CT
1 CTGTCT CTGTCT CTGTCT CTGTCT CT
19053661 CGCTTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.15, T:0.50
Consensus pattern (6 bp):
CTGTCT
Found at i:19059189 original size:22 final size:23
Alignment explanation
Indices: 19059160--19059234 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
19059150 ACTAACCCTT
* *
19059160 TCTCAAATTTCATCTCATTTTCC
1 TCTCAAATTTCATCTCAATTTAC
*
19059183 TCT-AAATTTCCTCTCAATTTAC
1 TCTCAAATTTCATCTCAATTTAC
* *
19059205 TCTCAAATTCCTTC-CAAATTT-C
1 TCTCAAATTTCATCTC-AATTTAC
19059227 TCTCAAAT
1 TCTCAAAT
19059235 CAATATTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 29 0.64
23 16 0.36
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (23 bp):
TCTCAAATTTCATCTCAATTTAC
Found at i:19059233 original size:11 final size:11
Alignment explanation
Indices: 19059160--19059234 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
19059150 ACTAACCCTT
19059160 TCTCAAATTTC
1 TCTCAAATTTC
*
19059171 ATCTC-ATTTTC
1 -TCTCAAATTTC
19059182 -CTCTAAATTTCC
1 TCTC-AAATTT-C
19059194 TCTC-AATTTAC
1 TCTCAAATTT-C
*
19059205 TCTCAAATTCC
1 TCTCAAATTTC
19059216 T-TCCAAATTTC
1 TCT-CAAATTTC
19059227 TCTCAAAT
1 TCTCAAAT
19059235 CAATATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
9 3 0.06
10 1 0.02
11 34 0.67
12 10 0.20
13 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.44
Consensus pattern (11 bp):
TCTCAAATTTC
Found at i:19060438 original size:7 final size:7
Alignment explanation
Indices: 19060426--19060465 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
19060416 TAGCCGATTG
19060426 GTATTTA
1 GTATTTA
19060433 GTATTTA
1 GTATTTA
19060440 GTATTTA
1 GTATTTA
19060447 GTATTTA
1 GTATTTA
19060454 GTATTTA
1 GTATTTA
19060461 GTATT
1 GTATT
19060466 ATGTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:19061143 original size:18 final size:18
Alignment explanation
Indices: 19061116--19061155 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19061106 CAGGTGCGTT
* *
19061116 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
19061134 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
19061152 TCCT
1 TCCT
19061156 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:19061715 original size:14 final size:13
Alignment explanation
Indices: 19061698--19061762 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 13
19061688 TTAATTGACA
19061698 AACCTTAAACCCTT
1 AACCTTAAACCC-T
*
19061712 AACCTAAAAACCCT
1 AACCT-TAAACCCT
*
19061726 AACCCTAAACCCTT
1 AACCTTAAACCC-T
*
19061740 AACCTGAAAACCCT
1 AACCT-TAAACCCT
19061754 AACTCTTAA
1 AAC-CTTAA
19061763 CTTAAAAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 6 0.15
14 21 0.51
15 14 0.34
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.22
Consensus pattern (13 bp):
AACCTTAAACCCT
Found at i:19061724 original size:15 final size:14
Alignment explanation
Indices: 19061698--19061753 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
19061688 TTAATTGACA
*
19061698 AACCTTAAACCCTT
1 AACCTAAAACCCTT
19061712 AACCTAAAAACCC-T
1 AACCT-AAAACCCTT
19061726 AACCCT-AAACCCTT
1 AA-CCTAAAACCCTT
19061740 AACCTGAAAACCCT
1 AACCT-AAAACCCT
19061754 AACTCTTAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.25
14 11 0.31
15 16 0.44
ACGTcount: A:0.41, C:0.38, G:0.02, T:0.20
Consensus pattern (14 bp):
AACCTAAAACCCTT
Found at i:19061738 original size:28 final size:28
Alignment explanation
Indices: 19061698--19061756 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
19061688 TTAATTGACA
*
19061698 AACCTTAAACCCTTAACCTAAAAACCCT
1 AACCCTAAACCCTTAACCTAAAAACCCT
*
19061726 AACCCTAAACCCTTAACCTGAAAACCCT
1 AACCCTAAACCCTTAACCTAAAAACCCT
19061754 AAC
1 AAC
19061757 TCTTAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.19
Consensus pattern (28 bp):
AACCCTAAACCCTTAACCTAAAAACCCT
Found at i:19061778 original size:43 final size:43
Alignment explanation
Indices: 19061726--19062461 Score: 487
Period size: 43 Copynumber: 17.0 Consensus size: 43
19061716 TAAAAACCCT
* * * *
19061726 AACCCTAAACCCTTAACCTGAAAACCCTAACTCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
19061769 AACCATAAACCCTTAACCTAAAAACCATAAACCCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * * * * *
19061813 AACCCTAACCCTTAACCCTTAACTTAAAAATCATAAACTCTTAACCTACA
1 AA-CC--A---TAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
19061863 AACTC-T-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AAC-CATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
** * * *
19061906 AATTATAAAGCCTTAATTTAAAAACTCTAACCCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * **
19061949 AACCCTAAATCCTTAACTTAAAAACCATAACCCTTAAAATAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * ** * * *
19061992 AATTC-TAAACCCTTAACTTTAAAACTGTAACCTTTAAATAAAA
1 AA-CCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * *
19062035 AACCCT-AACACC-TAATTTAAAAACACTAACCTTTAACTTAAA
1 AACCATAAAC-CCTTAACTTAAAAACCCTAACCCTTAACTTAAA
*
19062077 AACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
19062121 AACCATAAACCCTTAACTT-AAAACCCTAAACCC-TAACTCTTAATTTAA
1 AACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAA--CTT-A---AA
* *
19062169 AACCCTAAACCCTTAACCT--AAA----AACCCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
19062206 AACCCTAACACTTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAAA
1 AA--C---CA-TAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* ** *
19062256 AACCAT-AACTCTTAAAATAAAAACCCTAAACCCTTAACTTTAA
1 AACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
** * *
19062299 AATAAT-AACCCTTAAATAAAAAACCCTAA-CCTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
**
19062340 AATTATAAACCCTTAAGC-T---AA----AACCCTTAACTTAAA
1 AACCATAAACCCTTAA-CTTAAAAACCCTAACCCTTAACTTAAA
* * * * *
19062376 AACCCTAAATCATTAACTTAAAAACCCTAAACCATTAACTTTAA
1 AACCATAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
*** * * * *
19062420 AATTGTAAA-TCTTAAATAAAAAACCCTAACACTTAACTTAAA
1 AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
19062462 TATAATTTGA
Statistics
Matches: 560, Mismatches: 85, Indels: 97
0.75 0.11 0.13
Matches are distributed among these distances:
35 3 0.01
36 24 0.04
37 4 0.01
39 5 0.01
40 1 0.00
41 19 0.03
42 68 0.12
43 260 0.46
44 91 0.16
45 8 0.01
47 4 0.01
48 20 0.04
49 1 0.00
50 52 0.09
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (43 bp):
AACCATAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
Found at i:19061806 original size:65 final size:64
Alignment explanation
Indices: 19061733--19062341 Score: 435
Period size: 65 Copynumber: 9.3 Consensus size: 64
19061723 CCTAACCCTA
* * *
19061733 AACCCTTAACCTGAAAACCCTAACTCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCAT
1 AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCAT
* * *
19061797 AAACCCTTAACTTAAAAACCCTAACCCTTAACCCTTAACTTAAAAATCATAAACTCTTAACCTAC
1 -AACCCTTAACTT--AAA----AACCC-TAACCCTTAACTTAAAAACCATAAACCCTTAACCTAA
19061862 AAACTC-T
58 AAAC-CAT
** * **
19061869 AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAATTATAAAGCCTTAATTTAAAAACTC-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAAC-CA
19061933 T
64 T
* ** *
19061934 AACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAAAACCAT-AACCCTTAAAATAAAAATTC-
1 AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAA-CCA
19061997 T
64 T
* ** * * * * **
19061998 AAACCCTTAACTTTAAAACTGTAACCTTTAAATAAAAAACCCT-AACACC-TAATTTAAAAA-CA
1 -AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAAC-CCTTAACCTAAAAACCA
19062060 CT
64 -T
* * *
19062062 AACCTTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCAT
1 AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCAT
*
19062127 AAACCCTTAACTT-AAAACCCTAAACCC-TAACTCTTAATTTAAAACCCTAAACCCTTAACCT--
1 -AACCCTTAACTTAAAAACCCT-AACCCTTAA--CTT-A---AAAACCATAAACCCTTAACCTAA
19062188 -AA--A-
58 AAACCAT
* **
19062191 AACCCTTAACTTAAAAACCCTAACACTTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAAA
1 AACCCTTAACTTAAAAA--C---C-C-TAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAA
19062256 AACCAT
59 AACCAT
* ** * ** * *
19062262 AACTCTTAAAATAAAAACCCTAAACCCTTAACTTTAAAATAAT-AACCCTTAA-ATAAAAAACCC
1 AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCATAAACCCTTAACCT-AAAAACCA
19062325 T
64 T
19062326 AA-CCTTAACTTAAAAA
1 AACCCTTAACTTAAAAA
19062342 TTATAAACCC
Statistics
Matches: 449, Mismatches: 53, Indels: 86
0.76 0.09 0.15
Matches are distributed among these distances:
62 1 0.00
63 41 0.09
64 93 0.21
65 179 0.40
66 18 0.04
67 5 0.01
68 3 0.01
69 8 0.02
70 27 0.06
71 35 0.08
72 38 0.08
73 1 0.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (64 bp):
AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCATAAACCCTTAACCTAAAAACCAT
Found at i:19061858 original size:29 final size:28
Alignment explanation
Indices: 19061798--19061858 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
19061788 AAAAACCATA
*
19061798 AACCCTTAACTTAAAAACCCTAACCCTT
1 AACCCTTAACTTAAAAACCATAACCCTT
* *
19061826 AACCCTTAACTTAAAAATCATAAACTCTT
1 AACCCTTAACTTAAAAACCAT-AACCCTT
19061855 AACC
1 AACC
19061859 TACAAACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (28 bp):
AACCCTTAACTTAAAAACCATAACCCTT
Found at i:19062118 original size:27 final size:22
Alignment explanation
Indices: 19061726--19062461 Score: 533
Period size: 22 Copynumber: 34.0 Consensus size: 22
19061716 TAAAAACCCT
* *
19061726 AACCCTAAACCCTTAACCTGAA
1 AACCCTAAACCCTTAACTTAAA
*
19061748 AACCCT-AACTCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19061769 AACCATAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19061791 AACCATAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19061813 AACCCTAACCCTTAACCCTTAACTTAAA
1 AACCCT-A-----AACCCTTAACTTAAA
* * * * *
19061841 AATCATAAACTCTTAACCTACA
1 AACCCTAAACCCTTAACTTAAA
*
19061863 AACTCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19061884 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*** * *
19061906 AATTATAAAGCCTTAATTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19061928 AACTCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19061949 AACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* **
19061971 AACCAT-AACCCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAA
** *
19061992 AATTCTAAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
** * * *
19062014 AACTGT-AACCTTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
19062035 AACCCT-AACACC-TAATTTAAA
1 AACCCTAAAC-CCTTAACTTAAA
* *
19062056 AACACT-AACCTTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19062077 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19062099 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19062121 AACCATAAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
19062142 AACCCTAAACCC-TAACTCTTAATTTAA
1 AACCCTAAACCCTTAA--CTT-A---AA
*
19062169 AACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19062191 AACCCTTAA--CTTAA---AAA
1 AACCCTAAACCCTTAACTTAAA
* *
19062208 CCCTAACACTTAACCCTTAACTTAAA
1 ----AACCCTAAACCCTTAACTTAAA
*
19062234 AACCCTAAACCCTTAATTTAAA
1 AACCCTAAACCCTTAACTTAAA
* * **
19062256 AACCAT-AACTCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAA
*
19062277 AACCCTAAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*** * *
19062299 AATAAT-AACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
19062320 AACCCT-AA-CCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
***
19062340 AATTATAAACCCTTAAGC-T-AA
1 AACCCTAAACCCTTAA-CTTAAA
19062361 AACCCT------T-AACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19062376 AACCCTAAATCATTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19062398 AACCCTAAACCATTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*** * * *
19062420 AATTGTAAA-TCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
19062441 AACCCT-AACACTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19062462 TATAATTTGA
Statistics
Matches: 563, Mismatches: 107, Indels: 89
0.74 0.14 0.12
Matches are distributed among these distances:
13 1 0.00
14 3 0.01
15 9 0.02
17 3 0.01
20 24 0.04
21 195 0.35
22 278 0.49
23 7 0.01
25 1 0.00
26 5 0.01
27 15 0.03
28 22 0.04
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:19062195 original size:15 final size:15
Alignment explanation
Indices: 19062175--19062244 Score: 74
Period size: 15 Copynumber: 4.8 Consensus size: 15
19062165 TTAAAACCCT
19062175 AAACCCTTAACCTAA
1 AAACCCTTAACCTAA
*
19062190 AAACCCTTAACTTAA
1 AAACCCTTAACCTAA
19062205 AAACCC-TAACACT--
1 AAACCCTTAAC-CTAA
* *
19062218 TAACCCTTAACTTAA
1 AAACCCTTAACCTAA
*
19062233 AAACCCTAAACC
1 AAACCCTTAACC
19062245 CTTAATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 6 0.14
14 8 0.18
15 30 0.68
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACCCTTAACCTAA
Found at i:19062355 original size:135 final size:134
Alignment explanation
Indices: 19062076--19062413 Score: 335
Period size: 135 Copynumber: 2.5 Consensus size: 134
19062066 TTTAACTTAA
* * *
19062076 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACTTA
1 AAACCCTTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAAATAA
** ****
19062141 AAACCCTAAACCCTAACTCTTAATTTAAAACCCTAAACCCTTAACCTAAAAACCCTTAACTTAAA
66 AAACCCTAAACCCTAACTCTTAAAATAAAACCCTAAACAAAAAACCT--AAACCCTTAACTTAAA
*
19062206 AACCCT
129 AACCAT
* * *
19062212 -AACACTTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAAAAACCAT-AACTCTTAAAATA
1 AAACCCTTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTT-AAATA
*
19062275 AAAACCCTAAACCCTTAACT-TTAAAATAATAACCCTTAAATAAAAAACCCT-AA-CCTTAACTT
65 AAAACCCTAAACCC-TAACTCTTAAAATAA-AACCC-TAAACAAAAAA-CCTAAACCCTTAACTT
**
19062337 AAAAATTAT
126 AAAAACCAT
* * * *
19062346 AAACCCTTAAGCTAAAACCCTTAACTTAAAAACCCTAAATCATTAACTTAAAAACCCTAAACCAT
1 AAACCC-T----T--AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCT
19062411 TAA
59 TAA
19062414 CTTTAAAATT
Statistics
Matches: 165, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
134 21 0.13
135 77 0.47
136 11 0.07
137 6 0.04
138 3 0.02
140 1 0.01
142 41 0.25
143 5 0.03
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (134 bp):
AAACCCTTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAAATAA
AAACCCTAAACCCTAACTCTTAAAATAAAACCCTAAACAAAAAACCTAAACCCTTAACTTAAAAA
CCAT
Found at i:19062434 original size:121 final size:121
Alignment explanation
Indices: 19062240--19062461 Score: 338
Period size: 121 Copynumber: 1.8 Consensus size: 121
19062230 TAAAAACCCT
* * *
19062240 AAACCCTTAATTTAAAAACCATAACTCTTAAAATAAAAACCCTAAACCCTTAACTTTAAAATAAT
1 AAACCCTTAACTTAAAAACCATAAATCTTAAAATAAAAACCCTAAACCATTAACTTTAAAATAAT
*
19062305 AACCCTTAAATAAAAAACCCTAAC-CTTAACTTAAAAATTATAAACCCTTAAGCTA
66 AAACCTTAAATAAAAAACCCTAACACTTAACTTAAAAATTATAAACCCTTAAGCTA
* ** **
19062360 AAACCCTTAACTTAAAAACCCTAAATCATTAACTTAAAAACCCTAAACCATTAACTTTAAAATTG
1 AAACCCTTAACTTAAAAACCATAAATC-TTAAAATAAAAACCCTAAACCATTAACTTTAAAATAA
*
19062425 TAAATCTTAAATAAAAAACCCTAACACTTAACTTAAA
65 TAAACCTTAAATAAAAAACCCTAACACTTAACTTAAA
19062462 TATAATTTGA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
120 24 0.27
121 55 0.61
122 11 0.12
ACGTcount: A:0.50, C:0.22, G:0.01, T:0.27
Consensus pattern (121 bp):
AAACCCTTAACTTAAAAACCATAAATCTTAAAATAAAAACCCTAAACCATTAACTTTAAAATAAT
AAACCTTAAATAAAAAACCCTAACACTTAACTTAAAAATTATAAACCCTTAAGCTA
Found at i:19065895 original size:126 final size:125
Alignment explanation
Indices: 19065623--19066065 Score: 574
Period size: 126 Copynumber: 3.5 Consensus size: 125
19065613 CCCAAACATG
* *
19065623 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAACATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
* * * * *** * *
19065688 TAGAAGC--GATTTTATACTATTTACTTAGAAATACCAAGTCGAAATTATTTTTCCAGGAC
66 TTGCAGCTTG-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
19065747 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
* *
19065811 CTTGCAGCATTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAT
65 CTTGCAGC-TTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
19065873 CTACTGTAGCAAATGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
*
19065937 CTTGCAGCGCTT-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTTAGGAC
65 CTTGCA--GCTTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * * * *
19065999 CTACTGTAGCAAAAGCGCGTACAC-ATGGGCACGACTTCAAAAATCCTTCTCATAAATCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCACGA-GGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTA
19066063 CTT
65 CTT
19066066 TAATTTTATC
Statistics
Matches: 283, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
123 2 0.01
124 65 0.23
126 209 0.74
127 5 0.02
128 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
TTGCAGCTTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:19066204 original size:10 final size:9
Alignment explanation
Indices: 19066182--19066219 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
19066172 TTTTTTCTCC
19066182 AAAAACCCT
1 AAAAACCCT
*
19066191 AAAAATCCT
1 AAAAACCCT
19066200 AAAAACCCT
1 AAAAACCCT
*
19066209 AAAAAACCT
1 AAAAACCCT
19066218 AA
1 AA
19066220 TGTGGGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAACCCT
Found at i:19066205 original size:18 final size:18
Alignment explanation
Indices: 19066182--19066219 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19066172 TTTTTTCTCC
*
19066182 AAAAACCCTAAAAATCCT
1 AAAAACCCTAAAAAACCT
19066200 AAAAACCCTAAAAAACCT
1 AAAAACCCTAAAAAACCT
19066218 AA
1 AA
19066220 TGTGGGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAACCCTAAAAAACCT
Found at i:19066352 original size:40 final size:40
Alignment explanation
Indices: 19066308--19066386 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
19066298 TGACGTAGAC
* * * *
19066308 ACAAATCGCGTTTACGTGGACGCGATTTTCTGCCACGTCA
1 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTCA
19066348 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTC
1 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTC
19066387 CCCTGACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTCA
Found at i:19066769 original size:16 final size:16
Alignment explanation
Indices: 19066748--19066799 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
19066738 TTCTTTTAAT
19066748 TTTATTTAAATTTTTA
1 TTTATTTAAATTTTTA
**
19066764 TTTATTTTTATTTTTA
1 TTTATTTAAATTTTTA
19066780 TAATT-TTTAAATTATTTA
1 T--TTATTTAAATT-TTTA
19066798 TT
1 TT
19066800 GATACAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 16 0.55
17 6 0.21
18 7 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTTAAATTTTTA
Found at i:19067266 original size:23 final size:23
Alignment explanation
Indices: 19067231--19067287 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
19067221 AAATAAATAT
*
19067231 TTTATATTTAAAATAATTAATAAA
1 TTTATA-TAAAAATAATTAATAAA
* **
19067255 TTTATATAAAAATTATTTTTAAA
1 TTTATATAAAAATAATTAATAAA
19067278 TATTATATAA
1 T-TTATATAA
19067288 CATTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATAAAAATAATTAATAAA
Found at i:19067283 original size:24 final size:23
Alignment explanation
Indices: 19067251--19067296 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
19067241 AAATAATTAA
19067251 TAAATTTATATAAAAATTATTTT
1 TAAATTTATATAAAAATTATTTT
* *
19067274 TAAATATTATATAACATTTATTT
1 TAAAT-TTATATAAAAATTATTT
19067297 ATTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTATATAAAAATTATTTT
Found at i:19068292 original size:12 final size:12
Alignment explanation
Indices: 19068275--19068300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19068265 TCTTAATTAA
19068275 TTCCTAAATATT
1 TTCCTAAATATT
19068287 TTCCTAAATATT
1 TTCCTAAATATT
19068299 TT
1 TT
19068301 AGAAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (12 bp):
TTCCTAAATATT
Found at i:19083151 original size:57 final size:57
Alignment explanation
Indices: 19083063--19083182 Score: 231
Period size: 57 Copynumber: 2.1 Consensus size: 57
19083053 ATGGACATTC
*
19083063 ATTAAAGAACCAGAAGATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCA
1 ATTAAAGAACCAGAAAATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCA
19083120 ATTAAAGAACCAGAAAATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCA
1 ATTAAAGAACCAGAAAATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCA
19083177 ATTAAA
1 ATTAAA
19083183 TTGATTCTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (57 bp):
ATTAAAGAACCAGAAAATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCA
Found at i:19085967 original size:22 final size:21
Alignment explanation
Indices: 19085937--19085978 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19085927 AAAGTATTAT
* *
19085937 TTTAGTTTTTACTATTTTTTAC
1 TTTAATTTTTAAT-TTTTTTAC
19085959 TTTAATTTTTAATTTTTTTA
1 TTTAATTTTTAATTTTTTTA
19085979 TCCCGACGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTAATTTTTAATTTTTTTAC
Found at i:19090522 original size:17 final size:17
Alignment explanation
Indices: 19090500--19090533 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19090490 AATAGCAAGC
*
19090500 AAAAAAAGGGAAAAAAG
1 AAAAAAACGGAAAAAAG
*
19090517 AAAAAAACGGAGAAAAG
1 AAAAAAACGGAAAAAAG
19090534 GTTGTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAAAAACGGAAAAAAG
Found at i:19091307 original size:3 final size:3
Alignment explanation
Indices: 19091299--19091420 Score: 131
Period size: 3 Copynumber: 40.7 Consensus size: 3
19091289 TATTTTAGTT
*
19091299 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
19091347 CTG TTA -TA TT- GTA TTA TTA TTA CTGTA TTA TTA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA
* * * *
19091392 TTT TTA TTT TTA TTG CTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19091421 TCAATACATA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
2 3 0.03
3 91 0.93
4 2 0.02
5 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:19091610 original size:25 final size:23
Alignment explanation
Indices: 19091555--19091610 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
19091545 TATATATACG
19091555 TATATACATTTATATTTTTATAA
1 TATATACATTTATATTTTTATAA
19091578 TATTTATACATTT-TCCATATTTTATAA
1 TA--TATACATTTAT--AT-TTTTATAA
19091605 TATATA
1 TATATA
19091611 TAGATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 2 0.07
24 1 0.04
25 13 0.46
26 2 0.07
27 10 0.36
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATACATTTATATTTTTATAA
Found at i:19098344 original size:22 final size:22
Alignment explanation
Indices: 19098310--19098352 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19098300 TACTTTTCTT
*
19098310 AAAAAAAACAGAGAAGAAGAAC
1 AAAAAAAACAGAGAAAAAGAAC
* *
19098332 AAAAAAGAGAGAGAAAAAGAA
1 AAAAAAAACAGAGAAAAAGAA
19098353 AAAGGAGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAAAAACAGAGAAAAAGAAC
Found at i:19098346 original size:19 final size:20
Alignment explanation
Indices: 19098312--19098361 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
19098302 CTTTTCTTAA
* *
19098312 AAAAAACAGAGAAGAAGAAC
1 AAAAAAGAGAGAAGAAAAAC
*
19098332 AAAAAAGAGAG-AGAAAAAG
1 AAAAAAGAGAGAAGAAAAAC
*
19098351 AAAAAGGAGAG
1 AAAAAAGAGAG
19098362 GCCAAGGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.70, C:0.04, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAGAAGAAAAAC
Found at i:19100085 original size:45 final size:45
Alignment explanation
Indices: 19099995--19100202 Score: 144
Period size: 45 Copynumber: 4.7 Consensus size: 45
19099985 TAGTCTTACT
*
19099995 TCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCAAATCATATC
1 TCCCTGAAGTTGCAGTAGAGTAGATTAAAACATCCAAATCATATC
* *
19100040 TCCCTGAAGTTGCAGTAGAGT-GTATTAAAACA-CACAGATCTTATC
1 TCCCTGAAGTTGCAGTAGAGTAG-ATTAAAACATC-CAAATCATATC
** * * * * * * * * *
19100085 TTTCTGAGGTTGTAG-AGCGCAGA-T--CATAT-CTAGTCTTA-C
1 TCCCTGAAGTTGCAGTAGAGTAGATTAAAACATCCAAATCATATC
* * *
19100124 TTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCATCCAAATCCTATC
1 -TCCCTGAAGTTGCAGTAGAGTAGATTAAAACATCCAAATCATATC
* * * *
19100170 TCCTTGAAGTGGCAGTGGAGTGGATTAAAACAT
1 TCCCTGAAGTTGCAGTAGAGTAGATTAAAACAT
19100203 TCAGATCTTA
Statistics
Matches: 121, Mismatches: 31, Indels: 22
0.70 0.18 0.13
Matches are distributed among these distances:
39 1 0.01
40 17 0.14
41 7 0.06
42 1 0.01
43 1 0.01
44 8 0.07
45 85 0.70
46 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (45 bp):
TCCCTGAAGTTGCAGTAGAGTAGATTAAAACATCCAAATCATATC
Found at i:19100139 original size:130 final size:130
Alignment explanation
Indices: 19099902--19100323 Score: 586
Period size: 130 Copynumber: 3.3 Consensus size: 130
19099892 AAAAGAAACC
* *
19099902 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAAAATACAGATCGTATC-TTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
19099966 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
66 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
* * * *
19100031 AATCATATCTCCCTGAAGTTGCAGTAGAGTGTATTAAAACACACAGATCTTATCTTTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
* * *
19100096 GTAGAGCGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCATCCA
66 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
* * * *
19100161 AATCCTATCTCCTTGAAGTGGCAGTGGAGTGGATTAAAACATTCAGATCTTATTTTTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
* ** *
19100226 ACAGAGAGCAGATC-TCATCTAGTCTTA-TCTCCCTGAAGTTGCAGTGGAACAGA-CAAAGGA-A
66 GCAGAGAGCAGATCAT-ATCTAGTCTTACT-TCCCTGAAGTTGCAGTGGAGTAGATTAAA--ACA
*
19100287 ACC-
127 TCCA
* *
19100290 AATCCAATCTCCCTGATGTTGCAGTGGAGTGGAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
19100324 CGAAGCACTA
Statistics
Matches: 259, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
129 83 0.32
130 176 0.68
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (130 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
Found at i:19101558 original size:3 final size:3
Alignment explanation
Indices: 19101550--19101638 Score: 65
Period size: 3 Copynumber: 29.7 Consensus size: 3
19101540 TATTTTAGTT
* * *
19101550 TTA TTA TTA TTA ATA TTG TTA -TA TT- GTA TTA TTA TTA CTGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA
* * * * * *
19101595 TTA TTA GTA TTA TTA TTT TTA TTT TTA TTG CTA GTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19101639 TCAATACATA
Statistics
Matches: 65, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
2 3 0.05
3 58 0.89
4 2 0.03
5 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19101632 original size:39 final size:39
Alignment explanation
Indices: 19101551--19101638 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
19101541 ATTTTAGTTT
*
19101551 TATTATTATTAATATTGTTATATTGTATTATTATTACTG
1 TATTATTATTAATATTATTATATTGTATTATTATTACTG
* * * *
19101590 TATTATTATTAGTATTATTAT-TTTTATTTTTATTGCTAG
1 TATTATTATTAATATTATTATATTGTATTATTATTACT-G
19101629 TATTATTATT
1 TATTATTATT
19101639 TCAATACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 13 0.30
39 30 0.70
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.62
Consensus pattern (39 bp):
TATTATTATTAATATTATTATATTGTATTATTATTACTG
Found at i:19101743 original size:11 final size:12
Alignment explanation
Indices: 19101716--19101748 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19101706 ATACATATAC
*
19101716 ATATTTTTTTAT
1 ATATTTTATTAT
19101728 ATATTTTATTAT
1 ATATTTTATTAT
19101740 -TATTTTATT
1 ATATTTTATT
19101749 TCCTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:19101832 original size:25 final size:23
Alignment explanation
Indices: 19101777--19101832 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
19101767 TATATATACG
19101777 TATATACATTTATATTTTTATAA
1 TATATACATTTATATTTTTATAA
19101800 TATTTATACATTT-TCCATATTTTATAA
1 TA--TATACATTTAT--AT-TTTTATAA
19101827 TATATA
1 TATATA
19101833 TAGATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 2 0.07
24 1 0.04
25 13 0.46
26 2 0.07
27 10 0.36
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
TATATACATTTATATTTTTATAA
Found at i:19103097 original size:30 final size:30
Alignment explanation
Indices: 19103042--19103098 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19103032 TTTATAATAT
* *
19103042 TAAAAATATATATGTATATTTAAAAATTAA
1 TAAAAATATATATGTATAATAAAAAATTAA
19103072 TAAAAATATATAATG-ATAATAAAAAAT
1 TAAAAATATAT-ATGTATAATAAAAAAT
19103099 ATAGTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAAATATATATGTATAATAAAAAATTAA
Found at i:19116113 original size:28 final size:27
Alignment explanation
Indices: 19116057--19116112 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
19116047 AATATCCTAC
19116057 TTAATTAATTACTAATAAATTTTATTT
1 TTAATTAATTACTAATAAATTTTATTT
* *
19116084 TTAATTTAATTACTAGT-ATTTTTATTT
1 TTAA-TTAATTACTAATAAATTTTATTT
19116111 TT
1 TT
19116113 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
TTAATTAATTACTAATAAATTTTATTT
Found at i:19128302 original size:22 final size:19
Alignment explanation
Indices: 19128272--19128315 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
19128262 GCTAAGGGTT
19128272 TTAAAGACTCAATTTAGGATAA
1 TTAAAGACT-AA-TTA-GATAA
*
19128294 TTAATGACTAATTAGATAA
1 TTAAAGACTAATTAGATAA
19128313 TTA
1 TTA
19128316 GGAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 3 0.14
21 2 0.10
22 8 0.38
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAAGACTAATTAGATAA
Found at i:19136794 original size:40 final size:40
Alignment explanation
Indices: 19136743--19136932 Score: 265
Period size: 40 Copynumber: 4.8 Consensus size: 40
19136733 ATAACCACAA
* * * *
19136743 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19136783 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19136823 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19136863 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
19136903 GCATAAATGCCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
19136933 GTATTCAAAT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 132 0.97
41 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:19139595 original size:25 final size:26
Alignment explanation
Indices: 19139524--19139624 Score: 125
Period size: 26 Copynumber: 3.9 Consensus size: 26
19139514 ACATATTTTC
*
19139524 TCAAAATTTTACTAGGGGTAAAATTG
1 TCAAAATTTTACTAGGGGTAAAATCG
* *
19139550 TCAAAATTTTA-TTGAGAGTAAAATCG
1 TCAAAATTTTACTAG-GGGTAAAATCG
* *
19139576 TTAAAA-TTTATTAGGGGTAAAATCG
1 TCAAAATTTTACTAGGGGTAAAATCG
*
19139601 TCAAAATTTTACTAGGGATAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
19139625 AGGGAAGAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
25 21 0.33
26 42 0.67
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCG
Found at i:19139623 original size:51 final size:52
Alignment explanation
Indices: 19139526--19139624 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
19139516 ATATTTTCTC
* *
19139526 AAAATTTTACTAGGGGTAAAATTGTCAAAATTTTATTGAGAGTAAAATCGTT
1 AAAATTTTACTAGGGGTAAAATCGTCAAAATTTTATAGAGAGTAAAATCGTT
* *
19139578 AAAA-TTTATTAGGGGTAAAATCGTCAAAATTTTACTAGGGA-TAAAAT
1 AAAATTTTACTAGGGGTAAAATCGTCAAAATTTTA-TAGAGAGTAAAAT
19139625 AGGGAAGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 34 0.81
52 8 0.19
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (52 bp):
AAAATTTTACTAGGGGTAAAATCGTCAAAATTTTATAGAGAGTAAAATCGTT
Found at i:19140967 original size:6 final size:7
Alignment explanation
Indices: 19140954--19140984 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
19140944 TAAAAATTAC
19140954 CAAAAAA
1 CAAAAAA
19140961 C-AAAAA
1 CAAAAAA
19140967 CAAAAAA
1 CAAAAAA
19140974 CAAAAAA
1 CAAAAAA
19140981 CAAA
1 CAAA
19140985 CTTAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:19142253 original size:20 final size:20
Alignment explanation
Indices: 19142228--19142277 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19142218 TGGCTTAAAA
19142228 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19142248 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19142265 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19142278 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:19146883 original size:20 final size:20
Alignment explanation
Indices: 19146858--19146907 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
19146848 TGGCTTAAAA
19146858 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
19146878 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
19146895 GTGGTAGTGGATT
1 TTGGTAGTGGATT
19146908 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:19153290 original size:9 final size:9
Alignment explanation
Indices: 19153273--19153309 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19153263 TGAGTTTTCG
19153273 AATTCGAAT
1 AATTCGAAT
*
19153282 AACTCGAAT
1 AATTCGAAT
19153291 AATTCGAAT
1 AATTCGAAT
19153300 AATTCGAAT
1 AATTCGAAT
19153309 A
1 A
19153310 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:19156986 original size:44 final size:44
Alignment explanation
Indices: 19156933--19157019 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
19156923 GTAGGTTAAA
*
19156933 TAATATTAAAATAATCTACACTAATCAGAATTTAAGTGAGAAAT
1 TAATATTAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAT
* * *
19156977 TAATATTAAAATAACCTACACTAATCAGAGTTTCAGTGGGAAA
1 TAATATTAAAATAACCTACACTAATCAGAATTTAAGTGAGAAA
19157020 CTAAAAACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAT
Found at i:19159223 original size:25 final size:25
Alignment explanation
Indices: 19159191--19159302 Score: 188
Period size: 25 Copynumber: 4.5 Consensus size: 25
19159181 GAGCTGTAAA
* *
19159191 CGGGAAGCTCATGCGAGCTGAATAA
1 CGGGAAGCTCATGCGAGCTGAGTAT
19159216 CGGGAAGCTCATGCGAGCTGAGTAT
1 CGGGAAGCTCATGCGAGCTGAGTAT
19159241 CGGGAAGCTCATGCGAGCTGAGTAT
1 CGGGAAGCTCATGCGAGCTGAGTAT
*
19159266 CGGGAAGCTCATACGAGCTGAGTAT
1 CGGGAAGCTCATGCGAGCTGAGTAT
*
19159291 CGGAAAGCTCAT
1 CGGGAAGCTCAT
19159303 AAGAGCTGTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 83 1.00
ACGTcount: A:0.28, C:0.21, G:0.33, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATGCGAGCTGAGTAT
Found at i:19159303 original size:25 final size:25
Alignment explanation
Indices: 19159173--19159310 Score: 181
Period size: 25 Copynumber: 5.6 Consensus size: 25
19159163 ATACATGTAT
*
19159173 GCTCATACGAGCT--GTAAACGGGAA
1 GCTCATACGAGCTGAGT-ATCGGGAA
* * *
19159197 GCTCATGCGAGCTGAATAACGGGAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19159222 GCTCATGCGAGCTGAGTATCGGGAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19159247 GCTCATGCGAGCTGAGTATCGGGAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19159272 GCTCATACGAGCTGAGTATCGGAAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19159297 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
19159311 TTGTGTGTCC
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
24 12 0.11
25 92 0.88
26 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCTGAGTATCGGGAA
Found at i:19161669 original size:44 final size:44
Alignment explanation
Indices: 19161619--19161709 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
19161609 GTAGGTCAAA
19161619 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
* *
19161663 TAATATTAAAATAACTTACACTAATCAGAGTTTAAGTGGGAAAT
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
19161707 TAA
1 TAA
19161710 AAATATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
Found at i:19170938 original size:167 final size:168
Alignment explanation
Indices: 19170609--19170941 Score: 452
Period size: 167 Copynumber: 2.0 Consensus size: 168
19170599 CATATCGTCC
* * * ** *
19170609 CTTATATGAGCCCTCAAGGCCCAAAACATACATTGGAAACAATTCGAGACTAAATTGGAAACTCA
1 CTTATATAAACCCTCAAGGCCCAAAACATACATTAGAAACAATTCGAGACTAAACCGAAAACTCA
** * * *
19170674 GAGAATTTTTTTGCAAAATCTCAAAATTTCTCTAAAGTACAGGAGACACATGCCCGAATGTCTAA
66 GAGAA-TTTTTCACAAAATCTCAAAATTTCTCTAAAGTACAGGAGACACATACCCGAATGGCGAA
19170739 GCCGTATGGCTCACACGGCCAAGTGACACACCCGTGTCT
130 GCCGTATGGCTCACACGGCCAAGTGACACACCCGTGTCT
* * *
19170778 CTTATATAAACCCTCGAGGCCCAAAACATATATTAGAAACAATTCGAGAGTAAACCGAAAACTCA
1 CTTATATAAACCCTCAAGGCCCAAAACATACATTAGAAACAATTCGAGACTAAACCGAAAACTCA
* * * * * *
19170843 GAGAA-TTTTCACAAAATCTTAAATTTTTTCTAAAGTATAGGGGACACATACCCGTATGGCGAAG
66 GAGAATTTTTCACAAAATCTCAAAATTTCTCTAAAGTACAGGAGACACATACCCGAATGGCGAAG
* *
19170907 CTGTGTGGCTCACACGGCCAAGTGACACACCCGTG
131 CCGTATGGCTCACACGGCCAAGTGACACACCCGTG
19170942 CCTCAGGCCG
Statistics
Matches: 142, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
167 81 0.57
169 61 0.43
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.23
Consensus pattern (168 bp):
CTTATATAAACCCTCAAGGCCCAAAACATACATTAGAAACAATTCGAGACTAAACCGAAAACTCA
GAGAATTTTTCACAAAATCTCAAAATTTCTCTAAAGTACAGGAGACACATACCCGAATGGCGAAG
CCGTATGGCTCACACGGCCAAGTGACACACCCGTGTCT
Found at i:19172203 original size:24 final size:24
Alignment explanation
Indices: 19172156--19172207 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
19172146 AAGGAGCCTA
* *
19172156 TAACGGGTAGCTCTAAAGAGCAAT
1 TAACGGGTAGCTCCAAAGACCAAT
* *
19172180 TAACGGGTAGCTCCGAATACCAAT
1 TAACGGGTAGCTCCAAAGACCAAT
19172204 TAAC
1 TAAC
19172208 AGGAAGCACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGACCAAT
Found at i:19176690 original size:41 final size:41
Alignment explanation
Indices: 19176645--19176821 Score: 153
Period size: 41 Copynumber: 4.3 Consensus size: 41
19176635 CAGATTTACT
**
19176645 GGCACTTCA-CCTGATAGGCTTATAGTTTAATTCAGTTCACC
1 GGCACTT-AGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
* * *
19176686 GGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACC
1 GGCACTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
* * * * *
19176727 GGCACTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCACC
1 GGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACC
* * * * * * *
19176768 GGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCATC
1 GGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACC
19176809 GGCACTTAGCCTG
1 GGCACTTAGCCTG
19176822 CTAGACGTAT
Statistics
Matches: 122, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 119 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
GGCACTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
Found at i:19176822 original size:41 final size:41
Alignment explanation
Indices: 19176674--19176835 Score: 245
Period size: 41 Copynumber: 4.0 Consensus size: 41
19176664 TTATAGTTTA
* * * *
19176674 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
*
19176715 ATTCAGTTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
19176756 ATTCAATTCACCGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
19176797 ATTCAATTCATCGGCACTTAGCCTGCTAGACGTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
19176836 TGAATAATTT
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
41 111 0.98
42 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:19176848 original size:82 final size:82
Alignment explanation
Indices: 19176680--19176853 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
19176670 TTTAATTCAG
* * * *
19176680 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
*
19176745 CGTATAGTCCGATTCAA
66 CGTATAGTCCGAATCAA
* *
19176762 TTCACCGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCATCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAATTCACCGGCACTTAGCCTGCTAG
*
19176826 ACGTATAGTCTGAAT-AA
65 ACGTATAGTCCGAATCAA
*
19176843 TTTCACTGGCA
1 -TTCACCGGCA
19176854 ATAAATCCGA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
81 2 0.02
82 77 0.95
83 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
CGTATAGTCCGAATCAA
Found at i:19178508 original size:13 final size:13
Alignment explanation
Indices: 19178490--19178514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19178480 CAATCAAATG
19178490 CACACAAAATAAA
1 CACACAAAATAAA
19178503 CACACAAAATAA
1 CACACAAAATAA
19178515 TATTAATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:19180516 original size:39 final size:38
Alignment explanation
Indices: 19180443--19180517 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
19180433 AATTAATTAT
*
19180443 AATTTAAGTTTATATATTTGATATATCATAATATTAATG
1 AATTTAAGTTTATATATTTCATATAT-ATAATATTAATG
* *
19180482 AATTTGAGTTTATATATATTCCATATAT-TTATATTA
1 AATTTAAGTTTATATAT-TT-CATATATATAATATTA
19180518 TAATATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 23 0.74
40 2 0.06
41 6 0.19
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (38 bp):
AATTTAAGTTTATATATTTCATATATATAATATTAATG
Found at i:19180561 original size:9 final size:9
Alignment explanation
Indices: 19180538--19180578 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
19180528 TACTTAATAA
19180538 ATTATTTTT
1 ATTATTTTT
* *
19180547 AATATTGTT
1 ATTATTTTT
19180556 ATTATTTTT
1 ATTATTTTT
*
19180565 AGTATTTTT
1 ATTATTTTT
19180574 ATTAT
1 ATTAT
19180579 AATTTAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
ATTATTTTT
Found at i:19180561 original size:18 final size:18
Alignment explanation
Indices: 19180538--19180578 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19180528 TACTTAATAA
19180538 ATTATTTTTAATATTGTT
1 ATTATTTTTAATATTGTT
* *
19180556 ATTATTTTTAGTATTTTT
1 ATTATTTTTAATATTGTT
19180574 ATTAT
1 ATTAT
19180579 AATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
ATTATTTTTAATATTGTT
Found at i:19185550 original size:5 final size:5
Alignment explanation
Indices: 19185542--19185568 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19185532 AAAGTAAAAT
19185542 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
19185569 TATGGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:19197111 original size:25 final size:25
Alignment explanation
Indices: 19197076--19197146 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
19197066 ACACACCACA
*
19197076 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* *
19197101 GCTCTCATGAGCTTCTCGATATTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* *
19197126 GCT-TACAAGAGCTTCCTGATA
1 GCTCT-CATGAGCTTCCCGATA
19197147 TACAGCTCGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:19197178 original size:25 final size:25
Alignment explanation
Indices: 19197134--19197220 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
19197124 TGGCTTACAA
* * *
19197134 GAGCTTCCTGATATACAGCTCGTAT
1 GAGCTTCCCGTTATATAGCTCGTAT
**
19197159 GAGCTTCCCGTTACT-TAGCTTATAT
1 GAGCTTCCCGTTA-TATAGCTCGTAT
* * * *
19197184 GAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCCGTTATATAGCTCGTAT
19197209 GAGCTTCCCGTT
1 GAGCTTCCCGTT
19197221 TGCATGCTTG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
24 1 0.02
25 46 0.96
26 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCGTAT
Found at i:19197205 original size:50 final size:50
Alignment explanation
Indices: 19197084--19197220 Score: 134
Period size: 50 Copynumber: 2.7 Consensus size: 50
19197074 CAGCTCTCTT
* * * * *
19197084 GAGCTTCCCGATACT-TGGCTC-TCATGAGCTTCTCGATATTTGGCTTACAA
1 GAGCTTCCTGATA-TATGGCTCGT-ATGAGCTTCCCGTTACTTAGCTTACAA
** * *
19197134 GAGCTTCCTGATATACAGCTCGTATGAGCTTCCCGTTACTTAGCTTATAT
1 GAGCTTCCTGATATATGGCTCGTATGAGCTTCCCGTTACTTAGCTTACAA
* * *
19197184 GAGCTTCCTGTTATATGGCTCGAAAGAGCTTCCCGTT
1 GAGCTTCCTGATATATGGCTCGTATGAGCTTCCCGTT
19197221 TGCATGCTTG
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
49 1 0.01
50 69 0.97
51 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (50 bp):
GAGCTTCCTGATATATGGCTCGTATGAGCTTCCCGTTACTTAGCTTACAA
Found at i:19198803 original size:13 final size:13
Alignment explanation
Indices: 19198785--19198809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19198775 GAATTTATAT
19198785 GTGTGAAAATTTC
1 GTGTGAAAATTTC
19198798 GTGTGAAAATTT
1 GTGTGAAAATTT
19198810 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:19199970 original size:44 final size:42
Alignment explanation
Indices: 19199907--19200081 Score: 183
Period size: 44 Copynumber: 4.0 Consensus size: 42
19199897 TTATGTTATA
19199907 ACATTGGCATCGATTTGCGATTTACGTGTAAGACCATGTCTGGG
1 ACATTGGCATCGATTT-CGATTT-CGTGTAAGACCATGTCTGGG
19199951 ACATTGGCATCGATTTGCGATTTACGTGTAAGACCATGTCTGGG
1 ACATTGGCATCGATTT-CGATTT-CGTGTAAGACCATGTCTGGG
* * * * *
19199995 ACATCGGCATCGTATAT-GAGTTCGTGTAAGACCCA-GCCGGGG
1 ACATTGGCATCG-ATTTCGATTTCGTGTAAGA-CCATGTCTGGG
* * * * *
19200037 ACAGTGACATCGATATTTGATTTCATGTAAGACCACGTCTGGG
1 ACATTGGCATCGAT-TTCGATTTCGTGTAAGACCATGTCTGGG
19200080 AC
1 AC
19200082 GTTGCCATTG
Statistics
Matches: 113, Mismatches: 13, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
41 2 0.02
42 27 0.24
43 26 0.23
44 55 0.49
45 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (42 bp):
ACATTGGCATCGATTTCGATTTCGTGTAAGACCATGTCTGGG
Found at i:19201406 original size:20 final size:20
Alignment explanation
Indices: 19201381--19201438 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
19201371 TACATATCTA
19201381 ATTGGTAAATGATGAATATG
1 ATTGGTAAATGATGAATATG
* *
19201401 ATTGGTACAT-AT--CTA--
1 ATTGGTAAATGATGAATATG
19201416 ATTGGTAAATGATGAATATG
1 ATTGGTAAATGATGAATATG
19201436 ATT
1 ATT
19201439 TAAATATGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 9 0.31
16 2 0.07
17 2 0.07
18 2 0.07
19 2 0.07
20 12 0.41
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTGGTAAATGATGAATATG
Found at i:19201409 original size:35 final size:35
Alignment explanation
Indices: 19201370--19201438 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
19201360 GATTGTTTTA
19201370 GTACATATCTAATTGGTAAATGATGAATATGATTG
1 GTACATATCTAATTGGTAAATGATGAATATGATTG
19201405 GTACATATCTAATTGGTAAATGATGAATATGATT
1 GTACATATCTAATTGGTAAATGATGAATATGATT
19201439 TAAATATGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (35 bp):
GTACATATCTAATTGGTAAATGATGAATATGATTG
Found at i:19202644 original size:26 final size:27
Alignment explanation
Indices: 19202594--19202644 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19202584 AGTTAATAAA
* *
19202594 TTCTCTTTGAGTTTTTTTTTCAAGAAT
1 TTCTCTTTGAGTTTCTTTTACAAGAAT
*
19202621 TTCTC-TTGAGTTTCTTTTAGAAGA
1 TTCTCTTTGAGTTTCTTTTACAAGA
19202645 GTTTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.55
Consensus pattern (27 bp):
TTCTCTTTGAGTTTCTTTTACAAGAAT
Found at i:19206615 original size:21 final size:21
Alignment explanation
Indices: 19206590--19206629 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19206580 AACTATGCGA
19206590 GTCAAAATAGGTATGCTGGTG
1 GTCAAAATAGGTATGCTGGTG
* *
19206611 GTCAAAATTGGTGTGCTGG
1 GTCAAAATAGGTATGCTGG
19206630 CATGCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.30
Consensus pattern (21 bp):
GTCAAAATAGGTATGCTGGTG
Found at i:19210638 original size:7 final size:7
Alignment explanation
Indices: 19210626--19210664 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
19210616 ATAATTAAAT
19210626 TATTTTA
1 TATTTTA
19210633 TATTTTA
1 TATTTTA
19210640 TATTTTA
1 TATTTTA
19210647 TATTTTA
1 TATTTTA
19210654 TATTTTA
1 TATTTTA
19210661 TATT
1 TATT
19210665 AATAATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:19210672 original size:21 final size:21
Alignment explanation
Indices: 19210626--19210673 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19210616 ATAATTAAAT
*
19210626 TATTTTATATTTTATATTTTA
1 TATTTTATATTTTATATTATA
19210647 TATTTTATATTTTATATTA-A
1 TATTTTATATTTTATATTATA
19210667 TAATTTT
1 T-ATTTT
19210674 TTAAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTTTATATTTTATATTATA
Found at i:19213101 original size:10 final size:10
Alignment explanation
Indices: 19213082--19213120 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
19213072 AAAAATTTAT
*
19213082 TTTTTTAATA
1 TTTTTAAATA
19213092 TTTTTAAATA
1 TTTTTAAATA
*
19213102 TATATTAAATA
1 T-TTTTAAATA
19213113 TTTTTAAA
1 TTTTTAAA
19213121 AAAAATATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTTAAATA
Found at i:19214717 original size:19 final size:19
Alignment explanation
Indices: 19214639--19214708 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
19214629 GGAAATGATT
* *
19214639 AAAATTAATAGAATTATAA
1 AAAATTATTAGAATAATAA
*
19214658 AATAATT-CTAGAA-AATAA
1 AA-AATTATTAGAATAATAA
* *
19214676 AAAATTATAAAAATAATAA
1 AAAATTATTAGAATAATAA
19214695 AAAATTATTAGAAT
1 AAAATTATTAGAAT
19214709 TACAAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
17 4 0.10
18 9 0.22
19 24 0.59
20 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATTATTAGAATAATAA
Found at i:19214803 original size:8 final size:9
Alignment explanation
Indices: 19214675--19214895 Score: 90
Period size: 10 Copynumber: 23.1 Consensus size: 9
19214665 CTAGAAAATA
19214675 AAAAATTAT
1 AAAAATTAT
*
19214684 AAAAATAAT
1 AAAAATTAT
19214693 AAAAAATTAT
1 -AAAAATTAT
* * *
19214703 TAGAATTACA
1 AAAAATTA-T
**
19214713 AAAAAAAAT
1 AAAAATTAT
*
19214722 CAAAATTAT
1 AAAAATTAT
19214731 -AAAATGCTAT
1 AAAAAT--TAT
*
19214741 AAATACTTAT
1 AAA-AATTAT
* *
19214751 AAAATTTGT
1 AAAAATTAT
19214760 AAAAAGTATTAT
1 -AAAA--ATTAT
19214772 AGAAAATTAT
1 A-AAAATTAT
19214782 AAAACAATTAT
1 -AAA-AATTAT
*
19214793 AAAAATTTAA
1 AAAAA-TTAT
19214803 AAAAATTA-
1 AAAAATTAT
*
19214811 AAAAATAAT
1 AAAAATTAT
19214820 AAAAATGT-T
1 AAAAAT-TAT
19214829 ATAAAA-TAT
1 A-AAAATTAT
* *
19214838 AAAAGCTTAC
1 AAAA-ATTAT
* *
19214848 AAGAATTTT
1 AAAAATTAT
*
19214857 AAAAATATAG
1 AAAAAT-TAT
*
19214867 AAAAAATAT
1 AAAAATTAT
19214876 AGAAAATTAT
1 A-AAAATTAT
*
19214886 AAAAAATAT
1 AAAAATTAT
19214895 A
1 A
19214896 TATATTTTTT
Statistics
Matches: 157, Mismatches: 34, Indels: 42
0.67 0.15 0.18
Matches are distributed among these distances:
8 16 0.10
9 57 0.36
10 66 0.42
11 10 0.06
12 8 0.05
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:19214803 original size:19 final size:20
Alignment explanation
Indices: 19214747--19214834 Score: 81
Period size: 19 Copynumber: 4.4 Consensus size: 20
19214737 CTATAAATAC
* * *
19214747 TTATAAAATTTGTAAAAAGTA
1 TTATAAAAATTATAAAAA-AA
*
19214768 TTATAGAAAATTATAAAACAA
1 TTATA-AAAATTATAAAAAAA
19214789 TTATAAAAATT-TAAAAAAA
1 TTATAAAAATTATAAAAAAA
* **
19214808 TTA-AAAAATAATAAAAATG
1 TTATAAAAATTATAAAAAAA
19214827 TTATAAAA
1 TTATAAAA
19214835 TATAAAAGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 6 0.11
19 19 0.34
20 10 0.18
21 11 0.20
22 10 0.18
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (20 bp):
TTATAAAAATTATAAAAAAA
Found at i:19214835 original size:27 final size:29
Alignment explanation
Indices: 19214774--19214841 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
19214764 AGTATTATAG
* *
19214774 AAAATTATAAAACAATTATAAAAATTTAA
1 AAAAATATAAAACAATAATAAAAATTTAA
19214803 AAAAAT-TAAAA-AATAATAAAAATGTT-A
1 AAAAATATAAAACAATAATAAAAAT-TTAA
*
19214830 TAAAATATAAAA
1 AAAAATATAAAA
19214842 GCTTACAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 17 0.50
28 12 0.35
29 5 0.15
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (29 bp):
AAAAATATAAAACAATAATAAAAATTTAA
Found at i:19214886 original size:21 final size:21
Alignment explanation
Indices: 19214857--19214897 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19214847 CAAGAATTTT
19214857 AAAAATATAGAAAAA-ATATAG
1 AAAAATATA-AAAAATATATAG
*
19214878 AAAATTATAAAAAATATATA
1 AAAAATATAAAAAATATATA
19214898 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAAATATAAAAAATATATAG
Found at i:19215138 original size:18 final size:18
Alignment explanation
Indices: 19215116--19215151 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19215106 GCCCGGCCTA
19215116 TTTTTAATTAAAATTAAAT
1 TTTTTAA-TAAAATTAAAT
*
19215135 TTTTTGATAAAATTAAA
1 TTTTTAATAAAATTAAA
19215152 ACTAATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTTAATAAAATTAAAT
Found at i:19215185 original size:16 final size:16
Alignment explanation
Indices: 19215148--19215187 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
19215138 TTGATAAAAT
* *
19215148 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
19215164 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
19215180 TAAAATTA
1 TAAAATTA
19215188 TCAAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:19215245 original size:23 final size:24
Alignment explanation
Indices: 19215219--19215267 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
19215209 GTATTAATTG
* *
19215219 TTGT-AACAAATTAGTTTGCATTT
1 TTGTAAACAAATAAGTTTACATTT
19215242 TTGTAAACAAATAAGTTTACATTT
1 TTGTAAACAAATAAGTTTACATTT
19215266 TT
1 TT
19215268 TTTATCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (24 bp):
TTGTAAACAAATAAGTTTACATTT
Found at i:19218724 original size:43 final size:43
Alignment explanation
Indices: 19218671--19219044 Score: 560
Period size: 43 Copynumber: 8.7 Consensus size: 43
19218661 TTATAGAAAA
*
19218671 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
*
19218714 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
*
19218757 AAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
*
19218800 AAAAGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
* *
19218843 AAACACTGCTAAA-ATCCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGA-CCAAGACCTTTAGCGGCGCTTTTCCCGC
* *
19218886 AAACACTGCTAAAGACCAAGACCTTTAGCGGCG-TTTTCCC-C
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
* * * *
19218927 ACAATCGCCGTTAAAGACCAAGACCTTTAGCGTCGCTTTTTCCAC
1 A-AA-CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
* *
19218972 AAACACCGCTAAAGACCAAGACC-TTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
19219013 AAACGCCGCTAAAGACCAAGACCTTTAGCGGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGC
19219045 ATTTTTTTAA
Statistics
Matches: 306, Mismatches: 18, Indels: 15
0.90 0.05 0.04
Matches are distributed among these distances:
41 31 0.10
42 27 0.09
43 237 0.77
44 9 0.03
45 2 0.01
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
Found at i:19219518 original size:66 final size:66
Alignment explanation
Indices: 19219407--19219576 Score: 234
Period size: 66 Copynumber: 2.6 Consensus size: 66
19219397 CTCACCGCAG
* * * * *
19219407 CCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA-CTTTCGTTG
1 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-GTTG
19219471 AA
65 AA
* *
19219473 CCTCAGCTTCTCTCGCTACTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTGA
19219538 A
66 A
* * *
19219539 CCTCAGCTTCTCTCGATGCTGCCTCCACTTTAAGTTGT
1 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGT
19219577 GTAATTTGCT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 88 0.96
67 4 0.04
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:19222767 original size:16 final size:16
Alignment explanation
Indices: 19222748--19222787 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
19222738 TATATATGAG
19222748 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
19222764 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
19222780 TTATGTAA
1 TTATGTAA
19222788 CCTTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:19222996 original size:17 final size:17
Alignment explanation
Indices: 19222974--19223012 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
19222964 ACTTTCATAA
19222974 TATTATTCGT-ATAACAT
1 TATTATTC-TAATAACAT
19222991 TATTATTCTAATAACAT
1 TATTATTCTAATAACAT
19223008 T-TTAT
1 TATTAT
19223013 CATTTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (17 bp):
TATTATTCTAATAACAT
Found at i:19223058 original size:12 final size:12
Alignment explanation
Indices: 19223041--19223065 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19223031 TAGGATAGTG
19223041 AAAATTATGAAC
1 AAAATTATGAAC
19223053 AAAATTATGAAC
1 AAAATTATGAAC
19223065 A
1 A
19223066 GTTTCAAACT
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATTATGAAC
Found at i:19224213 original size:9 final size:9
Alignment explanation
Indices: 19224201--19224250 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
19224191 AAATTATAAA
19224201 TTTTATTTT
1 TTTTATTTT
19224210 TTTTATTTCAT
1 TTTTATTT--T
*
19224221 TTTTATATT
1 TTTTATTTT
19224230 TTTTATTTT
1 TTTTATTTT
19224239 TTCTTATATTT
1 TT-TTAT-TTT
19224250 T
1 T
19224251 GATCCTATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 19 0.54
10 4 0.11
11 12 0.34
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTTT
Found at i:19224231 original size:19 final size:19
Alignment explanation
Indices: 19224203--19224250 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
19224193 ATTATAAATT
*
19224203 TTATTTTTTTTATTTCATTT-
1 TTATATTTTTTATTT--TTTC
19224223 TTATATTTTTTATTTTTTC
1 TTATATTTTTTATTTTTTC
19224242 TTATATTTT
1 TTATATTTT
19224251 GATCCTATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.12
19 9 0.35
20 14 0.54
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TTATATTTTTTATTTTTTC
Found at i:19224889 original size:7 final size:7
Alignment explanation
Indices: 19224877--19224944 Score: 55
Period size: 7 Copynumber: 9.0 Consensus size: 7
19224867 TACCCTTGAC
19224877 ACCCTAA
1 ACCCTAA
19224884 ACCCTAA
1 ACCCTAA
19224891 ATCCCTAA
1 A-CCCTAA
*
19224899 CCCCTAA
1 ACCCTAA
19224906 ATCCCCCTAA
1 A---CCCTAA
*
19224916 CCCCTAA
1 ACCCTAA
19224923 ATCCCTAA
1 A-CCCTAA
*
19224931 CCCCTAA
1 ACCCTAA
*
19224938 CCCCTAA
1 ACCCTAA
19224945 TCCATACCCC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 33 0.65
8 12 0.24
10 6 0.12
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.18
Consensus pattern (7 bp):
ACCCTAA
Found at i:19224898 original size:15 final size:15
Alignment explanation
Indices: 19224878--19224937 Score: 93
Period size: 15 Copynumber: 3.9 Consensus size: 15
19224868 ACCCTTGACA
*
19224878 CCCTAAACCCTAAAT
1 CCCTAACCCCTAAAT
19224893 CCCTAACCCCTAAAT
1 CCCTAACCCCTAAAT
19224908 CCCCCTAACCCCTAAAT
1 --CCCTAACCCCTAAAT
19224925 CCCTAACCCCTAA
1 CCCTAACCCCTAA
19224938 CCCCTAATCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
15 27 0.64
17 15 0.36
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.18
Consensus pattern (15 bp):
CCCTAACCCCTAAAT
Found at i:19224937 original size:22 final size:21
Alignment explanation
Indices: 19224909--19224957 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19224899 CCCCTAAATC
*
19224909 CCCCTAACCCCTAAATCCCTAA
1 CCCCTAACCCCT-AATCCATAA
*
19224931 CCCCTAACCCCTAATCCATAC
1 CCCCTAACCCCTAATCCATAA
19224952 CCCCTA
1 CCCCTA
19224958 CTCCTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (21 bp):
CCCCTAACCCCTAATCCATAA
Found at i:19225782 original size:24 final size:24
Alignment explanation
Indices: 19225736--19225782 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
19225726 ATAGTATTTT
*
19225736 AATTTTTCCATGTGATTTATTTCA
1 AATTTTTCAATGTGATTTATTTCA
*
19225760 AATTATTTCAATGTTATTT-TTTC
1 AATT-TTTCAATGTGATTTATTTC
19225783 TGAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (24 bp):
AATTTTTCAATGTGATTTATTTCA
Found at i:19225953 original size:42 final size:41
Alignment explanation
Indices: 19225869--19226035 Score: 122
Period size: 41 Copynumber: 4.0 Consensus size: 41
19225859 AATGTTTTTT
* * * *
19225869 GCGGCGCTTCCACAAAAATGCTGTTAAAACCCCTAACATTA
1 GCGGCGCTTCCAAAAAAACGCTGCTAAAAACCCTAACATTA
* * *
19225910 GCGGCGCTTCTCAAAAAAACGCTGCTAAAAATCTTAACTTTA
1 GCGGCGCTTC-CAAAAAAACGCTGCTAAAAACCCTAACATTA
**** ** * *
19225952 GCGGCGCTTATTTAAAAACGCCACTAAAAGA-CCAAACGTTA
1 GCGGCGCTTCCAAAAAAACGCTGCTAAAA-ACCCTAACATTA
* * * *
19225993 GCGGCGCTT-CAAAGAAAACGCCGTTAAATACCTTAACATTA
1 GCGGCGCTTCCAAA-AAAACGCTGCTAAAAACCCTAACATTA
19226034 GC
1 GC
19226036 AGCGATTGAT
Statistics
Matches: 97, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
40 2 0.02
41 61 0.63
42 34 0.35
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTCCAAAAAAACGCTGCTAAAAACCCTAACATTA
Found at i:19226049 original size:82 final size:83
Alignment explanation
Indices: 19225907--19226062 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 83
19225897 ACCCCTAACA
* * * * *
19225907 TTAGCGGCGCTTCTCAAAAAAACGCTGCTAAAAATCTTAACTTTAGCGGCGCTTATTTAAAAACG
1 TTAGCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCTTAACATTAGCAGCGATTATTTAAAAACG
19225972 CCACTAAAAGACCAAACG
66 CCACTAAAAGACCAAACG
* *
19225990 TTAGCGGCGC-T-TCAAAGAAAACGCCGTTAAATACCTTAACATTAGCAGCGATTGA-TTAAAAA
1 TTAGCGGCGCTTCTCAAA-AAAACGCCGCTAAAAACCTTAACATTAGCAGCGATT-ATTTAAAAA
19226052 CGCCACTAAAA
64 CGCCACTAAAA
19226063 CCCCCGACCA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
81 5 0.08
82 48 0.75
83 11 0.17
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (83 bp):
TTAGCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCTTAACATTAGCAGCGATTATTTAAAAACG
CCACTAAAAGACCAAACG
Found at i:19231350 original size:17 final size:17
Alignment explanation
Indices: 19231328--19231371 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
19231318 ATCCACTAAT
*
19231328 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
*
19231345 CCACTACCAACAACAAT
1 CCACTACCAACAACAAC
19231362 CCACTACCAA
1 CCACTACCAA
19231372 TTTTAAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.48, G:0.00, T:0.09
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:19235986 original size:17 final size:17
Alignment explanation
Indices: 19235964--19236007 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
19235954 ATCCACTAAT
*
19235964 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
*
19235981 CCACTACCAACAACAAT
1 CCACTACCAACAACAAC
19235998 CCACTACCAA
1 CCACTACCAA
19236008 TTTTAAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.48, G:0.00, T:0.09
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:19237698 original size:19 final size:17
Alignment explanation
Indices: 19237674--19237724 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 17
19237664 AGGGTGAGGC
19237674 ATAAAAGTTTAGGGGGAAA
1 ATAAAAGTTTAGGGGG--A
*
19237693 ATAAAAAGTTT-TGGGGA
1 AT-AAAAGTTTAGGGGGA
19237710 ATAAAAGTTTGAGGG
1 ATAAAAGTTT-AGGG
19237725 AAAGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.30
17 3 0.11
18 2 0.07
19 6 0.22
20 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.25
Consensus pattern (17 bp):
ATAAAAGTTTAGGGGGA
Found at i:19238095 original size:9 final size:9
Alignment explanation
Indices: 19238081--19238117 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19238071 TATAGTTTGA
19238081 TATTCGAAT
1 TATTCGAAT
19238090 TATTCGAAT
1 TATTCGAAT
*
19238099 TATTCGAGT
1 TATTCGAAT
19238108 TATTCGAAT
1 TATTCGAAT
19238117 T
1 T
19238118 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:19240449 original size:25 final size:25
Alignment explanation
Indices: 19240389--19240513 Score: 109
Period size: 25 Copynumber: 5.1 Consensus size: 25
19240379 CAGCTCTTAT
*
19240389 GAGCGTCCCG-TTATATGGCTCTTCG
1 GAGCTTCCCGATTA-ATGGCTCTTCG
19240414 AGAGCTTCCCGATTAATGGCTCTTCG
1 -GAGCTTCCCGATTAATGGCTCTTCG
*
19240440 GAGCTTCCCGA-T-ATGGCTCATT-T
1 GAGCTTCCCGATTAATGGCTC-TTCG
* * * *
19240463 GAACTTCCTGA-TATATGGCTATCCG
1 GAGCTTCCCGATTA-ATGGCTCTTCG
*
19240488 AAGCTTCCCG-TTAATGGCTCTTCG
1 GAGCTTCCCGATTAATGGCTCTTCG
19240512 GA
1 GA
19240514 ACTACCTATT
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
23 17 0.21
24 14 0.17
25 26 0.32
26 20 0.25
27 3 0.04
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGATTAATGGCTCTTCG
Found at i:19240530 original size:48 final size:48
Alignment explanation
Indices: 19240394--19240530 Score: 109
Period size: 48 Copynumber: 2.8 Consensus size: 48
19240384 CTTATGAGCG
* * * * * * *
19240394 TCCCGTTATATGGCTCTTCGAGAGCTTCCCGATTAATGGCTCTTCGGAGCT
1 TCCCGTTA-ATGGCTCTTCG-GAAC-TACCTATTATTGGCTATCCGAAGCT
* * *
19240445 TCCCGAT-ATGGCTCATT-TGAACTTCCTGA-TATATGGCTATCCGAAGCT
1 TCCCGTTAATGGCTC-TTCGGAACTACCT-ATTAT-TGGCTATCCGAAGCT
19240493 TCCCGTTAATGGCTCTTCGGAACTACCTATTATTGGCT
1 TCCCGTTAATGGCTCTTCGGAACTACCTATTATTGGCT
19240531 CACACGAGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
47 5 0.07
48 30 0.44
49 25 0.37
50 2 0.03
51 6 0.09
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.34
Consensus pattern (48 bp):
TCCCGTTAATGGCTCTTCGGAACTACCTATTATTGGCTATCCGAAGCT
Found at i:19241622 original size:18 final size:18
Alignment explanation
Indices: 19241599--19241645 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
19241589 GGTTAAAAAA
19241599 TAACCGAATTACCCT-AAT
1 TAACCGAATTA-CCTGAAT
19241617 TAACCGAATTACCTGAAT
1 TAACCGAATTACCTGAAT
*
19241635 TACCCGAATTA
1 TAACCGAATTA
19241646 TATGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (18 bp):
TAACCGAATTACCTGAAT
Found at i:19241626 original size:9 final size:9
Alignment explanation
Indices: 19241599--19241645 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
19241589 GGTTAAAAAA
19241599 TAACCGAAT
1 TAACCGAAT
* *
19241608 TACCCTAAT
1 TAACCGAAT
19241617 TAACCGAAT
1 TAACCGAAT
19241626 T-ACCTGAAT
1 TAACC-GAAT
*
19241635 TACCCGAAT
1 TAACCGAAT
19241644 TA
1 TA
19241646 TATGTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 3 0.10
9 26 0.84
10 2 0.06
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.28
Consensus pattern (9 bp):
TAACCGAAT
Found at i:19241675 original size:13 final size:13
Alignment explanation
Indices: 19241658--19241707 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
19241648 TGTTTTTTAT
*
19241658 TTTTATTTTTAGA
1 TTTTAGTTTTAGA
*
19241671 CTTTAGTTTTAG-
1 TTTTAGTTTTAGA
19241683 TTTTAGTTTTAGAA
1 TTTTAGTTTTAG-A
*
19241697 TTTTATTTTTA
1 TTTTAGTTTTA
19241708 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 11 0.35
13 10 0.32
14 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (13 bp):
TTTTAGTTTTAGA
Found at i:19241680 original size:19 final size:18
Alignment explanation
Indices: 19241653--19241707 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
19241643 TTATATGTTT
*
19241653 TTTATTTTTATTTTTAGAC
1 TTTAGTTTTATTTTTAG-C
* *
19241672 TTTAGTTTTAGTTTTAGT
1 TTTAGTTTTATTTTTAGC
19241690 TTTAGAATTTTATTTTTA
1 TTTAG--TTTTATTTTTA
19241708 TTTATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 15 0.50
20 10 0.33
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTAGTTTTATTTTTAGC
Found at i:19241758 original size:18 final size:18
Alignment explanation
Indices: 19241735--19241778 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
19241725 AATTTTTCTG
*
19241735 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
*
19241753 ATTGGGTCGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
19241771 CTTGGGTT
1 ATTGGGTT
19241779 TGGATTGAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.11, C:0.05, G:0.45, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:19243561 original size:199 final size:199
Alignment explanation
Indices: 19243221--19243620 Score: 739
Period size: 199 Copynumber: 2.0 Consensus size: 199
19243211 ATCAAAAATA
*
19243221 AGCTGGATAGTGTGGCTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
1 AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
19243286 GATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATAC
66 GATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATAC
19243351 TCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACACC
131 TCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACACC
19243416 AAAC
196 AAAC
*
19243420 AGCTGGATAGTGTGACTTGAGTGCCGACCTGATCATCCAACCTTCCAAGTATCTACAAAAAAAAT
1 AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAA-
*
19243485 A-ATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGTCAGTCTAACCAAAACACACCAGATA
65 AGATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATA
* *
19243549 CTCACACGAGCCAATCCAACTGAAACACATTAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
130 CTCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACAC
19243614 CAAAC
195 CAAAC
19243619 AG
1 AG
19243621 AGTATAACAT
Statistics
Matches: 195, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
199 194 0.99
200 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.14, T:0.21
Consensus pattern (199 bp):
AGCTGGATAGTGTGACTTGAGTGCCGACCCGATCATCCAACCTTCCAAGTATCTACAAAAAAAAA
GATTAACATAAGTAAGCTTTAAGTAGCTTAGTACATCGCCAGTCTAACCAAAACACACCAGATAC
TCACACGAGCCAATCCAACCGAAACACATCAATACTCAAAAGAGCTAGTCCCTTATAAACACACC
AAAC
Found at i:19243826 original size:2 final size:2
Alignment explanation
Indices: 19243819--19243844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19243809 ACAAAAATTA
19243819 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19243845 GTTTTACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19251515 original size:14 final size:14
Alignment explanation
Indices: 19251474--19251516 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
19251464 TAGCTAAGTA
*
19251474 AATTAATTGATTTTT
1 AATTAATTGA-ATTT
* *
19251489 AATTAAATAAATTT
1 AATTAATTGAATTT
19251503 AATTAATTGAATTT
1 AATTAATTGAATTT
19251517 TTTAAATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
AATTAATTGAATTT
Found at i:19252345 original size:43 final size:43
Alignment explanation
Indices: 19252262--19252551 Score: 442
Period size: 43 Copynumber: 6.8 Consensus size: 43
19252252 CGCTTTTTAA
*
19252262 GACCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTATAGATCAG
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
* *
19252304 GACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTATAGATCAA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
* * *
19252347 GACCTTTAGCGGTGC-TTTCCCAAAAACGCCGCTATAGATCAA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
19252389 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
* * *
19252432 GACCTTTAGCTGCGCTTTTCCTACAAACACCGCTATAGATC-G
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
**
19252474 GACCTTTAGCGGTACTTTTCCCACAAACGCCGCTATAGATCAG
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
**
19252517 GACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTA
1 GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
19252552 AAAGTGCCAT
Statistics
Matches: 224, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
42 91 0.41
43 133 0.59
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
GACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAG
Found at i:19252494 original size:128 final size:128
Alignment explanation
Indices: 19252260--19252551 Score: 464
Period size: 128 Copynumber: 2.3 Consensus size: 128
19252250 GGCGCTTTTT
*
19252260 AAGACCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTC
* *
19252324 TCACAAACGCCGCTATAGATCAAGACCTTTAGCGGTGCTTTCCCAAAAACGCCGCTATAGATC
66 TCACAAACACCGCTATAGATCAAGACCTTTAGCGGTACTTTCCCAAAAACGCCGCTATAGATC
*
19252387 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCTGCGCTTTTC
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTC
* *
19252452 -CTACAAACACCGCTATAGATC-GGACCTTTAGCGGTACTTTTCCCACAAACGCCGCTATAGATC
66 TC-ACAAACACCGCTATAGATCAAGACCTTTAGCGGTAC-TTTCCCAAAAACGCCGCTATAGATC
* **
19252515 AGGACCTTTAGCGGCGCTTTTTTCACAAACGCCGCTA
1 AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
19252552 AAAGTGCCAT
Statistics
Matches: 153, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
127 32 0.21
128 121 0.79
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (128 bp):
AAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTC
TCACAAACACCGCTATAGATCAAGACCTTTAGCGGTACTTTCCCAAAAACGCCGCTATAGATC
Found at i:19252551 original size:85 final size:85
Alignment explanation
Indices: 19252262--19252534 Score: 440
Period size: 85 Copynumber: 3.2 Consensus size: 85
19252252 CGCTTTTTAA
*
19252262 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCTCA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCA
*
19252327 CAAACGCCGCTATAGATCAA
66 CAAACGCCGCTATAGATCAG
* *
19252347 GACCTTTAGCGGTGCTTTCCCAAAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCA
1 GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCA
19252412 CAAACGCCGCTATAGATCAG
66 CAAACGCCGCTATAGATCAG
* * * * **
19252432 GACCTTTAGCTGCGCTTTTCCTACAAACACCGCTATAGATC-GGACCTTTAGCGGTACTTTTCCC
1 GACCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCC
19252496 ACAAACGCCGCTATAGATCAG
65 ACAAACGCCGCTATAGATCAG
19252517 GACCTTTAGCGGCGCTTT
1 GACCTTTAGCGGCGCTTT
19252535 TTTCACAAAC
Statistics
Matches: 174, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
84 3 0.02
85 149 0.86
86 22 0.13
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (85 bp):
GACCTTTAGCGGCGCTTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCA
CAAACGCCGCTATAGATCAG
Found at i:19252671 original size:13 final size:13
Alignment explanation
Indices: 19252653--19252699 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
19252643 ATAAAAGTAA
19252653 AATAAATTATAGT
1 AATAAATTATAGT
**
19252666 AATAAATT-TCAAC
1 AATAAATTAT-AGT
*
19252679 ATTAAATTATAGT
1 AATAAATTATAGT
19252692 AATAAATT
1 AATAAATT
19252700 TCAACATTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (13 bp):
AATAAATTATAGT
Found at i:19252686 original size:26 final size:26
Alignment explanation
Indices: 19252655--19252707 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
19252645 AAAAGTAAAA
19252655 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
19252681 TAAATTATAGTAATAAATTTCAACAT
1 TAAATTATAGTAATAAATTTCAACAT
19252707 T
1 T
19252708 CACCTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATTATAGTAATAAATTTCAACAT
Found at i:19252715 original size:26 final size:26
Alignment explanation
Indices: 19252655--19252726 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
19252645 AAAAGTAAAA
*
19252655 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
*
19252681 TAAATTATAGTAATAAATTTCAACAT
1 TAAACTATAGTAATAAATTTCAACAT
* * *
19252707 TCACCTATAATAAATAAATT
1 TAAACTATAGT-AATAAATT
19252727 AACATAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 33 0.80
27 8 0.20
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (26 bp):
TAAACTATAGTAATAAATTTCAACAT
Found at i:19253147 original size:21 final size:21
Alignment explanation
Indices: 19253084--19253138 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
19253074 TCTGCCTTCT
19253084 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
19253105 TTGAGTAACTACATGGCAATC
1 TTGAGTAACTACATGGCAATC
19253126 TTGAGTAACTACA
1 TTGAGTAACTACA
19253139 GTAGCATCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (21 bp):
TTGAGTAACTACATGGCAATC
Found at i:19253972 original size:48 final size:48
Alignment explanation
Indices: 19253890--19253983 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
19253880 TTCTTGGCTT
* *
19253890 TAAAAACGCCTAAGTCAGCCCAACTTCCACCAATAATGGATCCAACCG
1 TAAAAACGCCTAAGTCAGCCCAACTTCCAACAATAAAGGATCCAACCG
* *
19253938 TAAAAACGCCTAAGTCAGCTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCCAACTTC-CAACAATAAAGGATCCAAC
19253984 AGAATTCCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.40, C:0.30, G:0.13, T:0.17
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCCAACTTCCAACAATAAAGGATCCAACCG
Found at i:19256485 original size:48 final size:48
Alignment explanation
Indices: 19256403--19256496 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
19256393 TTCTTGGCTT
* * *
19256403 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATCCAACCG
1 TAAAAACGCCTAAGTCAACCTAACTTCCAACAATAAAGGATCCAACCG
*
19256451 TAAAAACGCCTAAGTCAA-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAACCT-AACTTC-CAACAATAAAGGATCCAAC
19256497 AGAATTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 4 0.10
48 36 0.90
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAACCTAACTTCCAACAATAAAGGATCCAACCG
Found at i:19258806 original size:57 final size:57
Alignment explanation
Indices: 19258693--19258806 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
19258683 CTCCACTCCA
* **
19258693 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
19258750 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
19258807 TCTTCAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Done.