Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 66 of 228
Found at i:19694394 original size:6 final size:6
Alignment explanation
Indices: 19694383--19694440 Score: 109
Period size: 6 Copynumber: 9.8 Consensus size: 6
19694373 AAAGTGATAA
19694383 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
19694431 -AAAAG AAAAA
1 AAAAAG AAAAA
19694441 TGAGAGGCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:19695437 original size:21 final size:21
Alignment explanation
Indices: 19695412--19695455 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
19695402 ATCTTCAAGG
19695412 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
19695433 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
19695454 AT
1 AT
19695456 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:19695461 original size:19 final size:19
Alignment explanation
Indices: 19695411--19695466 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
19695401 AATCTTCAAG
19695411 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19695430 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
19695451 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
19695467 AGATATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:19695502 original size:21 final size:23
Alignment explanation
Indices: 19695455--19695502 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
19695445 AGATATGATA
*
19695455 TGTAATCTTAGAAGATATTATTT
1 TGTAATCTTAGAAGATATTAATT
19695478 TGTAATCTTAG-AGAT-TTAATT
1 TGTAATCTTAGAAGATATTAATT
19695499 TGTA
1 TGTA
19695503 GATACCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATTAATT
Found at i:19702823 original size:15 final size:15
Alignment explanation
Indices: 19702803--19702831 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19702793 GATTAAAATT
19702803 TTAAATAAACTAATC
1 TTAAATAAACTAATC
19702818 TTAAATAAACTAAT
1 TTAAATAAACTAAT
19702832 TTATGTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAAATAAACTAATC
Found at i:19708455 original size:159 final size:159
Alignment explanation
Indices: 19708166--19708483 Score: 521
Period size: 159 Copynumber: 2.0 Consensus size: 159
19708156 TACTCTTCAG
*
19708166 ACATGAACTTCAAAAATAAATAACTAAGTCACTTACCTAGCTTAATGAAGTTTAGAGGTAAATAA
1 ACATGAACTTCAAAAATAAATAACTAAGTCACTTACCTAGCTTAATAAAGTTTAGAGGTAAATAA
* * * * *
19708231 ACTAATGCAGATACCAGACATAAAGTGCAAAGGAACTCACCAGAATACTTTATTCAGAGCTTTAT
66 ACTAATGCAAATACCAGACACAAAGTACAAAGGAACTCACCAAAATACTTTATTCAGAACTTTAT
19708296 CTACTTTACTAGTTCTTTTCCTTTAGCAC
131 CTACTTTACTAGTTCTTTTCCTTTAGCAC
* * *
19708325 ACATGAACTTCAGAAATAAATAACTAAGTCACTTACCTGGCTTAATAAAGTTTAGAGGTAAATGA
1 ACATGAACTTCAAAAATAAATAACTAAGTCACTTACCTAGCTTAATAAAGTTTAGAGGTAAATAA
*
19708390 ACTAATGCAAATACCAGACACAAAGTATAAAGGAACTCACCAAAATACTTT-TCTCAGAACTTTA
66 ACTAATGCAAATACCAGACACAAAGTACAAAGGAACTCACCAAAATACTTTAT-TCAGAACTTTA
*
19708454 TCTACTTTACTGGTTCTTTTCCTTTAGCAC
130 TCTACTTTACTAGTTCTTTTCCTTTAGCAC
19708484 TGGGACCTTT
Statistics
Matches: 147, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
158 1 0.01
159 146 0.99
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.30
Consensus pattern (159 bp):
ACATGAACTTCAAAAATAAATAACTAAGTCACTTACCTAGCTTAATAAAGTTTAGAGGTAAATAA
ACTAATGCAAATACCAGACACAAAGTACAAAGGAACTCACCAAAATACTTTATTCAGAACTTTAT
CTACTTTACTAGTTCTTTTCCTTTAGCAC
Found at i:19711810 original size:21 final size:21
Alignment explanation
Indices: 19711784--19711845 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
19711774 CGGGTGGATT
* *
19711784 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTA
* * *
19711805 AGCTCTTTTGAGTTTCTATTA
1 AGCTCTTATGAGCTTCTGTTA
19711826 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
19711846 GACGATGTAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTA
Found at i:19719140 original size:13 final size:13
Alignment explanation
Indices: 19719122--19719146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19719112 ATAACATTGA
19719122 AATTAATTTAATT
1 AATTAATTTAATT
19719135 AATTAATTTAAT
1 AATTAATTTAAT
19719147 CTCCTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:19720471 original size:16 final size:17
Alignment explanation
Indices: 19720445--19720476 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19720435 TAATCCAAAA
19720445 TTTATGTTTTGGCATTT
1 TTTATGTTTTGGCATTT
19720462 TTTA-GTTTTGGCATT
1 TTTATGTTTTGGCATT
19720477 GCGATGGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.06, G:0.19, T:0.62
Consensus pattern (17 bp):
TTTATGTTTTGGCATTT
Found at i:19720906 original size:26 final size:26
Alignment explanation
Indices: 19720873--19720942 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
19720863 TTAATAGAAA
19720873 AAAAAATTTGTATATGGAATTACATT
1 AAAAAATTTGTATATGGAATTACATT
* *
19720899 CACAAATTTAAGTA-ATGGAATTACATT
1 AAAAAATTT--GTATATGGAATTACATT
*
19720926 AAAAAATTTGTTTATGG
1 AAAAAATTTGTATATGG
19720943 TTTTGATGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 2 0.06
26 11 0.31
27 20 0.56
28 3 0.08
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (26 bp):
AAAAAATTTGTATATGGAATTACATT
Found at i:19724583 original size:14 final size:14
Alignment explanation
Indices: 19724564--19724592 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19724554 AAATGTGGAC
19724564 ATATTCATGAAAGA
1 ATATTCATGAAAGA
19724578 ATATTCATGAAAGA
1 ATATTCATGAAAGA
19724592 A
1 A
19724593 GGTGTCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATATTCATGAAAGA
Found at i:19729132 original size:9 final size:9
Alignment explanation
Indices: 19729118--19729236 Score: 130
Period size: 9 Copynumber: 12.6 Consensus size: 9
19729108 TTTGGTTAAA
19729118 AATTACCCG
1 AATTACCCG
*
19729127 AATTACCTG
1 AATTACCCG
19729136 AATTACCCG
1 AATTACCCG
* *
19729145 AAAATTATCCA
1 --AATTACCCG
19729156 AATTACCCG
1 AATTACCCG
19729165 AATTACCCG
1 AATTACCCG
*
19729174 AAAATTACCCA
1 --AATTACCCG
19729185 AATTACCCG
1 AATTACCCG
19729194 AATTACCCG
1 AATTACCCG
**
19729203 AAGATTACCTA
1 -A-ATTACCCG
19729214 AATTACCCG
1 AATTACCCG
19729223 AATTACCCG
1 AATTACCCG
19729232 AATTA
1 AATTA
19729237 AATCACTACA
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
9 69 0.75
10 2 0.02
11 21 0.23
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:19729159 original size:20 final size:21
Alignment explanation
Indices: 19729116--19729224 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 21
19729106 TTTTTGGTTA
19729116 AAAATTACCCG--AATTA-CC
1 AAAATTACCCGAAAATTACCC
** *
19729134 TGAATTACCCGAAAATTATCC
1 AAAATTACCCGAAAATTACCC
19729155 -AAATTACCCG--AATTACCC
1 AAAATTACCCGAAAATTACCC
19729173 GAAAATTACCC--AAATTACCC
1 -AAAATTACCCGAAAATTACCC
* *
19729193 -GAATTACCCGAAGATTA-CC
1 AAAATTACCCGAAAATTACCC
*
19729212 TAAATTACCCGAA
1 AAAATTACCCGAA
19729225 TTACCCGAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
18 24 0.32
19 2 0.03
20 47 0.63
21 2 0.03
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (21 bp):
AAAATTACCCGAAAATTACCC
Found at i:19729159 original size:29 final size:29
Alignment explanation
Indices: 19729116--19729233 Score: 191
Period size: 29 Copynumber: 4.1 Consensus size: 29
19729106 TTTTTGGTTA
* *
19729116 AAAATTACCCGAATTACCTGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
*
19729145 AAAATTATCCAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
19729174 AAAATTACCCAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
* *
19729203 AAGATTACCTAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
19729232 AA
1 AA
19729234 TTAAATCACT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAATTACCCAAATTACCCGAATTACCCG
Found at i:19729227 original size:38 final size:36
Alignment explanation
Indices: 19729118--19729236 Score: 139
Period size: 38 Copynumber: 3.1 Consensus size: 36
19729108 TTTGGTTAAA
* * *
19729118 AATTACCCGAATTACCTGAATTACCCGAAAATTATCCA
1 AATTACCCGAATTACCTAAATTACCCG--AATTACCCG
* *
19729156 AATTACCCGAATTACCCGAAAATTACCCAAATTACCCG
1 AATTACCCGAATTA-CC-TAAATTACCCGAATTACCCG
19729194 AATTACCCGAAGATTACCTAAATTACCCGAATTACCCG
1 AATTACCCG-A-ATTACCTAAATTACCCGAATTACCCG
19729232 AATTA
1 AATTA
19729237 AATCACTACA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
38 53 0.76
39 5 0.07
40 12 0.17
ACGTcount: A:0.39, C:0.28, G:0.08, T:0.24
Consensus pattern (36 bp):
AATTACCCGAATTACCTAAATTACCCGAATTACCCG
Found at i:19729265 original size:17 final size:17
Alignment explanation
Indices: 19729243--19729340 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
19729233 ATTAAATCAC
19729243 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
19729260 TACATAAATATTTGAATCAC
1 TACAT--A-ATTAAAAACAT
*
19729280 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
19729297 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
19729317 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
19729334 TACATAA
1 TACATAA
19729341 GTCTTGAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 12
0.66 0.21 0.14
Matches are distributed among these distances:
17 31 0.54
18 1 0.02
19 1 0.02
20 24 0.42
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:19729341 original size:37 final size:37
Alignment explanation
Indices: 19729237--19729361 Score: 191
Period size: 37 Copynumber: 3.4 Consensus size: 37
19729227 ACCCGAATTA
* *
19729237 AATCACTACATAATTAAAAACATTACATAAATATTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
19729274 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
19729311 AATCACTACATAATTAAAAACATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAACATTACATAAGTCTTTG
*
19729347 AAATAAC-ACATAATT
1 -AATCACTACATAATT
19729362 GAAATGTAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
36 11 0.13
37 71 0.87
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (37 bp):
AATCACTACATAATTAAAAACATTACATAAGTCTTTG
Found at i:19729417 original size:24 final size:24
Alignment explanation
Indices: 19729390--19729448 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
19729380 ATTCTCGATT
19729390 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
19729414 TATATTCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
19729438 TATCTCCATTT
1 TATATCCATTT
19729449 GCATTAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:19736666 original size:24 final size:24
Alignment explanation
Indices: 19736628--19736878 Score: 150
Period size: 24 Copynumber: 10.8 Consensus size: 24
19736618 TGAATTGGAT
* *
19736628 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
19736653 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
19736677 AATTT-AAA-AAT--TTTATGAT-
1 AATTTAAAATAATAATATATGATA
* * **
19736696 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
19736721 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
19736745 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
19736766 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
19736790 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
19736813 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
19736836 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
19736860 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
19736879 CAGTACACTT
Statistics
Matches: 172, Mismatches: 37, Indels: 35
0.70 0.15 0.14
Matches are distributed among these distances:
19 4 0.02
20 4 0.02
21 14 0.08
22 18 0.10
23 45 0.26
24 74 0.43
25 13 0.08
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:19736792 original size:69 final size:68
Alignment explanation
Indices: 19736628--19736920 Score: 222
Period size: 70 Copynumber: 4.2 Consensus size: 68
19736618 TGAATTGGAT
* * * *
19736628 AATTTACAATAAATAATATATAATAAATTTGAAATAAT-A-ATACATATAAAATTTAAAAAT-TT
1 AATTTA-AAT-AATAATACATGATAAATCTAAAATAATAATATACA-AT-AAATTTAAAAATATT
*
19736690 TATGAT-
62 AATGATA
* * * * *
19736696 AATTCTAGAATAATCATACGTGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAA
1 AATT-TA-AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAAAAATATTAA
19736761 TGATA
64 TGATA
* ** * *
19736766 AATTTGAAATAGAT-ATACATGATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAAT
1 AATTT-AAATA-ATAATACATGATAAATCTAAAATAATAATATACAATAAATTT-AAA-AATATT
*
19736829 ATTGATA
62 AATGATA
* * * * * *
19736836 AATTACAAATAATAAAACATGATAAATCTAAAATAATAATATACAGTACACTTAGATAATATTAA
1 AATT-TAAATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTA-AAAATATTAA
*
19736901 TGATT
64 TGATA
19736906 AATTT-AATAATAATA
1 AATTTAAATAATAATA
19736921 AGCATAAACA
Statistics
Matches: 177, Mismatches: 35, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
68 54 0.31
69 46 0.26
70 69 0.39
71 8 0.05
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (68 bp):
AATTTAAATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAAAAATATTAATG
ATA
Found at i:19738031 original size:85 final size:84
Alignment explanation
Indices: 19737866--19738032 Score: 196
Period size: 83 Copynumber: 2.0 Consensus size: 84
19737856 GCGTTTACAA
* * * *
19737866 AAAAAACCGCCGCTAAAGATCATATTCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACCTG
1 AAAAAACCGCCGCTAAAGATCATATTCTTTAGCGGCGTTTTTTTCAAACGCCGCAAAAGAACATG
19737931 CTCTTTAACGGCGCTTTGT
66 CTCTTTAACGGCGCTTTGT
* * *
19737950 AAAAAA-CGTCGCTAGAGATCATAATT-TTTAGCGGCGCTTTTTTTACAAATGCCGCGAAAAGAA
1 AAAAAACCGCCGCTAAAGATCAT-ATTCTTTAGCGGCG-TTTTTTT-CAAACGCCGC-AAAAGAA
* *
19738013 -ATGTTCTTTAGCGGCGCTTT
62 CATGCTCTTTAACGGCGCTTT
19738033 TATACAAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
83 24 0.34
84 16 0.23
85 24 0.34
86 6 0.09
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (84 bp):
AAAAAACCGCCGCTAAAGATCATATTCTTTAGCGGCGTTTTTTTCAAACGCCGCAAAAGAACATG
CTCTTTAACGGCGCTTTGT
Found at i:19738439 original size:21 final size:21
Alignment explanation
Indices: 19738415--19738465 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
19738405 TTTCTTTGAA
19738415 CCTCTGCTTCCCTCGCTGTCG
1 CCTCTGCTTCCCTCGCTGTCG
19738436 CCTCTGCTTCCCTCGCTGTCG
1 CCTCTGCTTCCCTCGCTGTCG
19738457 CCTCTGCTT
1 CCTCTGCTT
19738466 TAAGTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGTCG
Found at i:19743143 original size:16 final size:17
Alignment explanation
Indices: 19743122--19743168 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
19743112 AATCCCTAAA
19743122 CCCTAACCCCTAAATC-
1 CCCTAACCCCTAAATCT
*
19743138 CCCTAACCCATAAATCT
1 CCCTAACCCCTAAATCT
* *
19743155 CTCTAACCTCTAAA
1 CCCTAACCCCTAAA
19743169 GCATAACACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.34, C:0.43, G:0.00, T:0.23
Consensus pattern (17 bp):
CCCTAACCCCTAAATCT
Found at i:19743563 original size:114 final size:114
Alignment explanation
Indices: 19743425--19743871 Score: 557
Period size: 114 Copynumber: 4.0 Consensus size: 114
19743415 TAAATTATTT
* *
19743425 TAAATCCCTGAGCATTAGCGGCGCTTT-TGTAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAA
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCT-TAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
* *
19743489 CGGCGTCGTTGGGTTTAGGTTTTTTTGCGGTGCTTTCCCAAAAACGCCGC
65 CGGCGTCGTTGGGCTTAGTTTTTTTTGCGGTGCTTTCCCAAAAACGCCGC
* * *
19743539 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCTCAAAAGCTTAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
*
19743604 GGCGTCGTT-GG----G-----TTT----AGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGTTTTTTTTGCGGTGCTTTCCCAAAAACGCCGC
* * * *
19743639 TAAAGCCCTAAGCATTAGCTGCCCTTTCTTAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * * * *
19743704 GACGCCGTTGGGCTTAGTTTTTTTTACGACT-TTTTCCCAAAAACACCGC
66 GGCGTCGTTGGGCTTAGTTTTTTTTGCG-GTGCTTTCCCAAAAACGCCGC
*
19743753 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * *
19743818 GGCGTTGTTGGGCTTAGTTTTTTTTTGCGGCGCTTTCCCAAAAATGCCGC
66 GGCGTCGTTGGGCTTAG-TTTTTTTTGCGGTGCTTTCCCAAAAACGCCGC
19743868 TAAA
1 TAAA
19743872 TCCCCGAAAG
Statistics
Matches: 283, Mismatches: 32, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
100 84 0.30
101 2 0.01
104 3 0.01
105 1 0.00
109 1 0.00
110 3 0.01
113 2 0.01
114 157 0.55
115 30 0.11
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGTTTTTTTTGCGGTGCTTTCCCAAAAACGCCGC
Found at i:19743694 original size:100 final size:100
Alignment explanation
Indices: 19743520--19743834 Score: 387
Period size: 100 Copynumber: 3.0 Consensus size: 100
19743510 TTTTTGCGGT
19743520 GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
1 GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
* * *
19743585 CCTCAAAAGCTTAGAAAACGGCGTCGTTGGGTTTA
66 CCACGAAAGCTCAGAAAACGGCGTCGTTGGGTTTA
* * * *
19743620 GCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCTGCCCTTTCTTAAAAATGCCGCTAAAT
1 GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
* * *
19743685 CCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGTTTTTTTTA
66 CCACGAAAGCTCAGAAAACGGCGTCGTT-GG----G-----TTTA
*
19743730 CGACTTTTTCCCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCT
1 -G-C--TTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCT
* *
19743795 AAATCCACGAAAGCTCAGAAAACGGCGTTGTTGGGCTTA
62 AAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGTTTA
19743834 G
1 G
19743835 TTTTTTTTTG
Statistics
Matches: 182, Mismatches: 19, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
100 84 0.46
101 2 0.01
103 1 0.01
104 3 0.02
105 1 0.01
109 1 0.01
110 4 0.02
111 1 0.01
112 1 0.01
113 2 0.01
114 82 0.45
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (100 bp):
GCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
CCACGAAAGCTCAGAAAACGGCGTCGTTGGGTTTA
Found at i:19743817 original size:214 final size:214
Alignment explanation
Indices: 19743425--19743834 Score: 617
Period size: 214 Copynumber: 1.9 Consensus size: 214
19743415 TAAATTATTT
* * * *
19743425 TAAATCCCTGAGCATTAGCGGCGCTTTTGTAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTAAGCATTAGCGGCCCTTTTGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* * * * * *
19743490 GGCGTCGTTGGGTTTAGGTTTTTTTGCGGTGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATT
66 GACGCCGTTGGGCTTAGGTTTTTTTACGCTGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCATT
* * *
19743555 AGCGGCGCTTTCTTAAAAACGCCGCTAAATCCTCAAAAGCTTAGAAAACGGCGTCGTTGGGTTTA
131 AGCGGCGCTTTCTTAAAAACGCCGCTAAATCCACAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
19743620 GCTTTCCCAAAAACGCCGC
196 GCTTTCCCAAAAACGCCGC
* *
19743639 TAAAGCCCTAAGCATTAGCTGCCCTTTCT-TAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAA
1 TAAAGCCCTAAGCATTAGCGGCCCTTT-TGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
* *
19743703 CGACGCCGTTGGGCTTAGTTTTTTTTACGACT-TTTTCCCAAAAACACCGCTAAAGCCCTGAGCA
65 CGACGCCGTTGGGCTTAGGTTTTTTTACG-CTGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCA
* *
19743767 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTTGTTGGGCT
129 TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCACAAAAGCTCAGAAAACGGCGTCGTTGGGCT
19743832 TAG
194 TAG
19743835 TTTTTTTTTG
Statistics
Matches: 175, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
214 173 0.99
215 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (214 bp):
TAAAGCCCTAAGCATTAGCGGCCCTTTTGTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GACGCCGTTGGGCTTAGGTTTTTTTACGCTGCTTTCCCAAAAACACCGCTAAAGCCCTGAGCATT
AGCGGCGCTTTCTTAAAAACGCCGCTAAATCCACAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
GCTTTCCCAAAAACGCCGC
Found at i:19743891 original size:74 final size:74
Alignment explanation
Indices: 19743770--19743908 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
19743760 CTGAGCATTA
** *
19743770 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
19743835 TTTTTTTTT
66 TTTTTTTTT
* * *
19743844 GCGGCGCTTTCCCAAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
19743909 GTTTATTTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (74 bp):
GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
TTTTTTTTT
Found at i:19743986 original size:188 final size:187
Alignment explanation
Indices: 19743669--19744058 Score: 512
Period size: 188 Copynumber: 2.1 Consensus size: 187
19743659 GCCCTTTCTT
* *
19743669 AAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGTTTTTTTTACGAC
1 AAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTATTTACGAC
** * * *
19743734 TTTTTCCCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAT
66 TTTTGACCAAAAACACAGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTGAAAAACACCGCTAAAT
* * * * *
19743799 CCACGAAAGCTCAGAAAACGGCGTTGTTGGGCTTAGTTTTTTTTTGCGGCGCTTTCCC
131 CCACGAAAGCTCAGAAAACGACGTCGTTGGACTTAG-ATTTTTTTGCGGCGCTTTACC
** * ** *
19743857 AAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTATTTGTGGC
1 AAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTATTTACGAC
* * * * * *
19743922 TTTTGAGCAAAAACGCAGCTAAAGTCCTGGGTATTAGCGGCGC-TTCTCGAAAAACACTGCTAAA
66 TTTTGACCAAAAACACAGCTAAAGCCCTGAGCATTAGCGGCGCTTTCT-GAAAAACACCGCTAAA
* * *
19743986 TCCTCGAAAGCTCAGAAAACGACGTCGTTGGACTTAGATTTTTTTGTGGCGCTTTAGC
130 TCCACGAAAGCTCAGAAAACGACGTCGTTGGACTTAGATTTTTTTGCGGCGCTTTACC
19744044 AAAAATGCCGCTAAA
1 AAAAATGCCGCTAAA
19744059 GTCCTGGGTA
Statistics
Matches: 174, Mismatches: 27, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
187 36 0.21
188 138 0.79
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (187 bp):
AAAAATGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTATTTACGAC
TTTTGACCAAAAACACAGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTGAAAAACACCGCTAAAT
CCACGAAAGCTCAGAAAACGACGTCGTTGGACTTAGATTTTTTTGCGGCGCTTTACC
Found at i:19744045 original size:114 final size:112
Alignment explanation
Indices: 19743864--19744164 Score: 406
Period size: 114 Copynumber: 2.6 Consensus size: 112
19743854 CCCAAAAATG
* * *
19743864 CCGCTAAATCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTATTTGTGGC-TTTTGA
1 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTT-GGCTTA-GTTTTTTTGTGGCGCTTT-A
* *
19743928 GCAAAAACGCAGCTAAAGTCCTGGGTATTAGCGGCGCTTCTCGAAAAACA
63 GCAAAAACGCAGCTAAAGTCCTGGGTATTAGCGGCGCCTCCCGAAAAACA
* * *
19743978 CTGCTAAATCCTCGAAAGCTCAGAAAACGACGTCGTTGGACTTAGATTTTTTTGTGGCGCTTTAG
1 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGG-CTTAG-TTTTTTTGTGGCGCTTTAG
* * *
19744043 CAAAAATGCCGCTAAAGTCCTGGGTATTAGCGGCGCCTCCCGAAAAACG
64 CAAAAACGCAGCTAAAGTCCTGGGTATTAGCGGCGCCTCCCGAAAAACA
* * **
19744092 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTTGGTTTTTTGTGGCGCTTCGGC
1 CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTT-GGCTTAGTTTTTTTGTGGCGCTTTAGC
19744157 AAAAACGC
65 AAAAACGC
19744165 TACTAAATCC
Statistics
Matches: 164, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
113 27 0.16
114 132 0.80
115 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (112 bp):
CCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGCTTAGTTTTTTTGTGGCGCTTTAGCA
AAAACGCAGCTAAAGTCCTGGGTATTAGCGGCGCCTCCCGAAAAACA
Found at i:19744318 original size:72 final size:72
Alignment explanation
Indices: 19744085--19744315 Score: 279
Period size: 72 Copynumber: 3.2 Consensus size: 72
19744075 GCGCCTCCCG
* *
19744085 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTAGGCTTTGGTTTTTTGTGGCG
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
19744150 C-TTCGGC
66 CTTTC-GC
** * * * * *
19744157 AAAAACGCTACTAAATCCGCTAAAGCTCAAAAAATGGCGTCGTTGGTCTTAGGGTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GGTTTTTTGTGGC
19744222 GCTTT-GTC
65 GCTTTCG-C
* * * *
19744230 AAAAACGCCGCT-AATGCCCCGAAAGCTCAGAAAACGACGTCGTTGGGATTAAGTATTTTGTGGC
1 AAAAACGCCGCTAAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGC
19744294 GCTTTCGC
65 GCTTTCGC
*
19744302 AAAATCGCCGCTAA
1 AAAAACGCCGCTAA
19744316 TGCTTATTTC
Statistics
Matches: 132, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
72 74 0.56
73 56 0.42
74 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (72 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCG
CTTTCGC
Found at i:19745425 original size:30 final size:30
Alignment explanation
Indices: 19745383--19745440 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
19745373 TCGGCCATTG
*
19745383 TTTGAACATTTTGAAAAGTTTA-GCCTTCT
1 TTTGAACATTTTGAAAAGATTAGGCCTTCT
* *
19745412 TTTGAGCACTTTTGTAAAGATTAGGCCTT
1 TTTGAACA-TTTTGAAAAGATTAGGCCTT
19745441 ATATGACAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 12 0.50
31 5 0.21
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTGAACATTTTGAAAAGATTAGGCCTTCT
Found at i:19754101 original size:16 final size:18
Alignment explanation
Indices: 19754080--19754113 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19754070 CTTTGAGAAG
19754080 CTCAAG-TC-TATTTTGA
1 CTCAAGCTCTTATTTTGA
19754096 CTCAAGCTCTTATTTTGA
1 CTCAAGCTCTTATTTTGA
19754114 TATAGCCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (18 bp):
CTCAAGCTCTTATTTTGA
Found at i:19762640 original size:17 final size:18
Alignment explanation
Indices: 19762614--19762658 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
19762604 GGGAAATCAG
19762614 TTTTATTTTAATAA-TTAT
1 TTTTATTTTAA-AACTTAT
19762632 TTTTA-TTTAAAACTTAT
1 TTTTATTTTAAAACTTAT
19762649 TTTTAGTTTT
1 TTTTA-TTTT
19762659 TTTTATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 5 0.21
19 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATTTTAAAACTTAT
Found at i:19763325 original size:12 final size:12
Alignment explanation
Indices: 19763308--19763335 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19763298 GGGGACACAC
19763308 GCCCGTGTCTCT
1 GCCCGTGTCTCT
19763320 GCCCGTGTCTCT
1 GCCCGTGTCTCT
19763332 GCCC
1 GCCC
19763336 AATTTGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.46, G:0.25, T:0.29
Consensus pattern (12 bp):
GCCCGTGTCTCT
Found at i:19764492 original size:25 final size:25
Alignment explanation
Indices: 19764475--19764536 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
19764465 AAGCTTGTAC
*
19764475 GAGCTGAATATCGGTAAGCTCATAT
1 GAGCTGAATATCGGTAAGCTCATAA
*
19764500 GAGCTGAGTATCGGTAAGCTCATAA
1 GAGCTGAATATCGGTAAGCTCATAA
19764525 GAGCTGAA-ATCG
1 GAGCTGAATATCG
19764537 ATAACCCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 4 0.12
25 30 0.88
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
GAGCTGAATATCGGTAAGCTCATAA
Found at i:19767788 original size:45 final size:46
Alignment explanation
Indices: 19767720--19767821 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 46
19767710 ATGATCAAGC
* *
19767720 ATCAC-TTGTC-CTTGATAAGATAAGTGTAGCT-AGGCAACCACTT
1 ATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCAACCACTT
* *
19767763 ATCACTTTGTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCAACCACTT
*
19767809 ATCACTTTATCAC
1 ATCACTTTGTCAC
19767822 CACTTATCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
43 5 0.10
44 5 0.10
45 19 0.37
46 22 0.43
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (46 bp):
ATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCAACCACTT
Found at i:19767857 original size:62 final size:62
Alignment explanation
Indices: 19767756--19767945 Score: 299
Period size: 62 Copynumber: 3.0 Consensus size: 62
19767746 TAGCTAGGCA
* *
19767756 ACCACTTATCACTTTGTCACTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
1 ACCACTTATCAC-TTGT-TCTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
* * *
19767820 ACCACTTATCACTTGTTCTTGATTAGATAAGTGTAGCTAAAGTTACCACTTATCACTTTGTC
1 ACCACTTATCACTTGTTCTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
* *
19767882 ACCACTTATCACTTGTTCCTAATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
1 ACCACTTATCACTTGTTCTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
19767944 AC
1 AC
19767946 TTGATCAGAT
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
62 100 0.86
63 4 0.03
64 12 0.10
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (62 bp):
ACCACTTATCACTTGTTCTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
Found at i:19767996 original size:45 final size:46
Alignment explanation
Indices: 19767882--19767999 Score: 170
Period size: 45 Copynumber: 2.6 Consensus size: 46
19767872 TCACTTTGTC
* *
19767882 ACCACTTATCAC-TTGT-TCCTAATCAGATAAGTGTAGCTAAAACT
1 ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAACT
* *
19767926 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
1 ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAACT
*
19767971 ATCACTTATCACTTTGTCACCTGATCAGA
1 ACCACTTATCACTTTGTCACCTGATCAGA
19768000 AGTACTCAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 12 0.18
45 35 0.53
46 19 0.29
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACCTGATCAGATAAGTGTAGCTAAAACT
Found at i:19768108 original size:19 final size:21
Alignment explanation
Indices: 19768068--19768114 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
19768058 TTTTATTCTC
19768068 ATTTCATCAATAAATATATAT
1 ATTTCATCAATAAATATATAT
*
19768089 ATTTCATC-ATACAT-TATAT
1 ATTTCATCAATAAATATATAT
*
19768108 AATTCAT
1 ATTTCAT
19768115 GAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATCAATAAATATATAT
Found at i:19775001 original size:21 final size:21
Alignment explanation
Indices: 19774976--19775018 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19774966 TACAAGAATC
* *
19774976 AATAAACGCACAAGTAGGCTT
1 AATAAACACACAAGTAAGCTT
19774997 AATAAACACACAAGTAAGCTT
1 AATAAACACACAAGTAAGCTT
19775018 A
1 A
19775019 TAGAAAGCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.19
Consensus pattern (21 bp):
AATAAACACACAAGTAAGCTT
Found at i:19775336 original size:43 final size:43
Alignment explanation
Indices: 19775288--19775400 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
19775278 TACGTATGAT
* * *
19775288 CACTTATCACTTGTCCTTGATCAGGTTAGTGTAGCTAGGCTAC
1 CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAAGCTAC
*
19775331 CACTTATCACTTGTTCC-TGATCAGATAAGTGTAGCTAAGCTAT
1 CACTTATCACTTG-TCCTTGATCAGATAAGTGTAGCTAAGCTAC
*
19775374 CACTTGTCACTTTGTCACTTGATCAGA
1 CACTTATCAC-TTGTC-CTTGATCAGA
19775401 AGTACTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
43 46 0.75
44 7 0.11
45 8 0.13
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (43 bp):
CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:19782475 original size:45 final size:46
Alignment explanation
Indices: 19782397--19782503 Score: 157
Period size: 46 Copynumber: 2.4 Consensus size: 46
19782387 TACATATGAT
*
19782397 CACTTATCAC-TTGTC-CTTAATAAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCTAC
* *
19782440 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCTAC
*
19782486 CACTTATCACTTTATCAC
1 CACTTATCACTTTGTCAC
19782504 CACTTATCAC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
43 10 0.18
44 5 0.09
45 19 0.33
46 23 0.40
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTAATAAGATAAGTGTAGCTAAAGCTAC
Found at i:19782537 original size:62 final size:62
Alignment explanation
Indices: 19782438--19782627 Score: 328
Period size: 62 Copynumber: 3.0 Consensus size: 62
19782428 TAGCTAGGCT
*
19782438 ACCACTTATCACTT-TGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
1 ACCACTTATCACTTGT-TC-C-TGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
*
19782502 ACCACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
1 ACCACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
19782564 ACCACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
1 ACCACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
19782626 AC
1 AC
19782628 TTGATCAGAT
Statistics
Matches: 122, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
62 104 0.85
63 1 0.01
64 16 0.13
65 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (62 bp):
ACCACTTATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
Found at i:19782667 original size:45 final size:46
Alignment explanation
Indices: 19782564--19782681 Score: 190
Period size: 45 Copynumber: 2.6 Consensus size: 46
19782554 TCACTTTGTC
19782564 ACCACTTATCAC-TTGTTC-C-TGATCAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAAGCT
19782608 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
*
19782653 ATCACTTATCACTTTGTCACTTGATCAGA
1 ACCACTTATCACTTTGTCACTTGATCAGA
19782682 AGTACTCAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
44 14 0.20
45 37 0.53
46 19 0.27
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCT
Found at i:19782790 original size:19 final size:21
Alignment explanation
Indices: 19782750--19782796 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
19782740 TTTTATTCTC
19782750 ATTTCATCAATAAATATATAT
1 ATTTCATCAATAAATATATAT
*
19782771 ATTTCATC-ATACAT-TATAT
1 ATTTCATCAATAAATATATAT
*
19782790 AATTCAT
1 ATTTCAT
19782797 GAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 5 0.21
21 8 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTCATCAATAAATATATAT
Found at i:19784910 original size:28 final size:26
Alignment explanation
Indices: 19784872--19784934 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
19784862 ATGGATAATA
*
19784872 AAAAAAATATTTTAAGTATCATTTATG
1 AAAAAAATATTTTAAGTATCAATT-TG
*
19784899 ATAAAAAATA-TTTAGGTATCAATTTG
1 A-AAAAAATATTTTAAGTATCAATTTG
19784925 AAAAAAATAT
1 AAAAAAATAT
19784935 GTAGCTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 8 0.25
26 3 0.09
27 13 0.41
28 8 0.25
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAAAATATTTTAAGTATCAATTTG
Found at i:19789398 original size:21 final size:21
Alignment explanation
Indices: 19789372--19789422 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
19789362 CTACAACTTA
* *
19789372 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
19789393 AAGCAGAGGTAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
*
19789414 AAGCTGAGG
1 AAGCAGAGG
19789423 TTCAACGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:19789423 original size:21 final size:21
Alignment explanation
Indices: 19789383--19789423 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19789373 AGCAGATGCG
19789383 GCAGCGAGAGAAGCAGAGGTA
1 GCAGCGAGAGAAGCAGAGGTA
*
19789404 GCAGCGAGAGAAGCTGAGGT
1 GCAGCGAGAGAAGCAGAGGT
19789424 TCAACGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGTA
Found at i:19789467 original size:87 final size:87
Alignment explanation
Indices: 19789321--19789503 Score: 248
Period size: 87 Copynumber: 2.1 Consensus size: 87
19789311 GAGGCAACAT
*
19789321 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGGCA
1 CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGAAGATGCGGCA
19789386 GCGAGAGAAGCAGAGG-TAGCAG
66 GCGAGAGAAGCAGAGGCT-GCAG
* * *
19789408 CGAGAGAAGCTGAGGTTCAACGAAAG-TATG-AGCAACTGCAGC-AGCAGCTTAAAGAAGATGCG
1 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAG-AACTCCAGCTA-CAACTTAAAGAAGATGCG
*
19789470 GCAGCGAGAGAAGCAGCGGCTGCAG
63 GCAGCGAGAGAAGCAGAGGCTGCAG
*
19789495 CGAGGGAAG
1 CGAGAGAAG
19789504 TAGAGGCTGC
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
86 3 0.03
87 78 0.91
88 5 0.06
ACGTcount: A:0.37, C:0.18, G:0.33, T:0.11
Consensus pattern (87 bp):
CGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTTAAAGAAGATGCGGCA
GCGAGAGAAGCAGAGGCTGCAG
Found at i:19789496 original size:21 final size:21
Alignment explanation
Indices: 19789470--19789515 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
19789460 AGAAGATGCG
*
19789470 GCAGCGAGAGAAGCAGCGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
19789491 GCAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
19789512 GCAG
1 GCAG
19789516 TGAGGGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.20, G:0.46, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:19789755 original size:14 final size:14
Alignment explanation
Indices: 19789736--19789765 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19789726 TTATATAGAT
19789736 TTGGTTAGATTTGG
1 TTGGTTAGATTTGG
*
19789750 TTGGTTGGATTTGG
1 TTGGTTAGATTTGG
19789764 TT
1 TT
19789766 TCTTCTGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.37, T:0.53
Consensus pattern (14 bp):
TTGGTTAGATTTGG
Found at i:19789896 original size:43 final size:43
Alignment explanation
Indices: 19789830--19790396 Score: 832
Period size: 43 Copynumber: 13.1 Consensus size: 43
19789820 AAAAATTAGC
* *
19789830 GGCGTTTTTTTGGATAAGCGCCGCTAAAGACCATCGTCTATAGT
1 GGCG-TTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19789874 GACATTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19789917 GGCGTTTTTCGGCTAAGCACCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19789960 GGCGTTTTTTGTCTAAGCGCCGCTAAAGACCATGGTGTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
19790003 GGCATTTTATGGCTAAGCGCCGCTAAAGACCATGGTGTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
19790046 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19790089 GGCGTTTTTTGTCTAAGCCCCGCTGAAA-ACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCT-AAAGACCATGGTCTATAGT
*
19790132 GGCGTTTTTTGGCTAAGCGTCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19790175 GGCGTTTTGTGGCTAAGCGCCGCTAAAGACCATGATCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19790218 GGCATTTTTCGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
19790261 GGTGTTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGC
1 GGCGTTTTTT-GGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
***** * *
19790305 GGCGTTGCAAAG-AAAACGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
19790347 GGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCTATAGC
1 GGCGTTTTTT-GGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
19790391 GGCGTT
1 GGCGTT
19790397 GCAAAGAAAA
Statistics
Matches: 467, Mismatches: 51, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
42 36 0.08
43 356 0.76
44 75 0.16
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (43 bp):
GGCGTTTTTTGGCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:19790338 original size:42 final size:42
Alignment explanation
Indices: 19790279--19790409 Score: 181
Period size: 42 Copynumber: 3.1 Consensus size: 42
19790269 TTAGGCTAAG
19790279 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTGCAAAGAAAA
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTGCAAAGAAAA
* *** * * *
19790321 CGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTAGGCTAAG
1 CGCCGCTAAAGACCATGGTCTATAGCGGCG-TTGCAAAG-AAAA
19790365 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTGCAAAGAAAA
1 CGCCGCTAAAGACCATGGTCTATAGCGGCGTTGCAAAGAAAA
19790407 CGC
1 CGC
19790410 TGCGAAAGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
42 34 0.47
43 8 0.11
44 31 0.42
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGGTCTATAGCGGCGTTGCAAAGAAAA
Found at i:19790452 original size:86 final size:86
Alignment explanation
Indices: 19790235--19790461 Score: 256
Period size: 86 Copynumber: 2.6 Consensus size: 86
19790225 TTCGGCTAAG
* * * * * ***
19790235 CGCCGCTAAAGACCATGGTCTATAGTGGTGTTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCT
1 CGCCGCGAAAGACCATGATCTATAGCGGCGTTTATTAGAAAAAGCGCCGCTAAAGACCATGGTCT
19790300 ATAGCGGCGTTGCAAAGAAAA
66 ATAGCGGCGTTGCAAAGAAAA
* * * * ***
19790321 CGCCGCTAAAGACCATGGTCTATAGTGGCGTTTTTTAGGCTAAGCGCCGCTAAAGACCATGGTCT
1 CGCCGCGAAAGACCATGATCTATAGCGGCGTTTATTAGAAAAAGCGCCGCTAAAGACCATGGTCT
19790386 ATAGCGGCGTTGCAAAGAAAA
66 ATAGCGGCGTTGCAAAGAAAA
* ** * * * *
19790407 CGCTGCGAAAGGTCTTGATCTTTAGCGGTGTTTATTATAAAAAGCGCCGCTAAAG
1 CGCCGCGAAAGACCATGATCTATAGCGGCGTTTATTAGAAAAAGCGCCGCTAAAG
19790462 TTACCGACGC
Statistics
Matches: 126, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 126 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (86 bp):
CGCCGCGAAAGACCATGATCTATAGCGGCGTTTATTAGAAAAAGCGCCGCTAAAGACCATGGTCT
ATAGCGGCGTTGCAAAGAAAA
Found at i:19792709 original size:27 final size:28
Alignment explanation
Indices: 19792648--19792726 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 28
19792638 AACACTTGCA
*
19792648 TCATAAACTCGAACCGC--GAACCTCAAAC
1 TCATAATCTCGAACC-CTTGAACC-CAAAC
19792676 TCATAATCT-GTAA-CCTTGAACCCAAAC
1 TCATAATCTCG-AACCCTTGAACCCAAAC
**
19792703 TTGTAATCTCGAACCCTTGAACCC
1 TCATAATCTCGAACCCTTGAACCC
19792727 TTGAACCCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 16 0.37
28 26 0.60
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.23
Consensus pattern (28 bp):
TCATAATCTCGAACCCTTGAACCCAAAC
Found at i:19792740 original size:7 final size:7
Alignment explanation
Indices: 19792713--19792759 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
19792703 TTGTAATCTC
19792713 GAACCCTT
1 GAACCC-T
19792721 GAACCCTT
1 GAACCC-T
19792729 GAACCCT
1 GAACCCT
19792736 GAA-CCT
1 GAACCCT
* *
19792742 AAACCTT
1 GAACCCT
19792749 GAACCCT
1 GAACCCT
19792756 GAAC
1 GAAC
19792760 TCAAAGCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 5 0.15
7 15 0.44
8 14 0.41
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (7 bp):
GAACCCT
Found at i:19793699 original size:23 final size:23
Alignment explanation
Indices: 19793669--19793716 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
19793659 ATTGTTCCTA
19793669 AGTCTTCCTGAAAAAGGTTTCAC
1 AGTCTTCCTGAAAAAGGTTTCAC
19793692 AGTCTTCCTGAAAAAGGTTTCAC
1 AGTCTTCCTGAAAAAGGTTTCAC
19793715 AG
1 AG
19793717 CGAGAGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (23 bp):
AGTCTTCCTGAAAAAGGTTTCAC
Found at i:19809741 original size:18 final size:18
Alignment explanation
Indices: 19809720--19809763 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
19809710 GTGATGAGAT
*
19809720 AAAAATAACTAAACAAAG
1 AAAAATAAATAAACAAAG
*
19809738 -AAAATAAATAAATAAAG
1 AAAAATAAATAAACAAAG
19809755 AAAAATAAA
1 AAAAATAAA
19809764 CAAATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAAATAAATAAACAAAG
Found at i:19809768 original size:18 final size:18
Alignment explanation
Indices: 19809720--19809768 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
19809710 GTGATGAGAT
*
19809720 AAAAAT-AACTAAACAAAG
1 AAAAATAAAC-AAATAAAG
*
19809738 -AAAATAAATAAATAAAG
1 AAAAATAAACAAATAAAG
19809755 AAAAATAAACAAAT
1 AAAAATAAACAAAT
19809769 GAAATAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAAATAAACAAATAAAG
Found at i:19809777 original size:17 final size:16
Alignment explanation
Indices: 19809722--19809777 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
19809712 GATGAGATAA
*
19809722 AAATAACTAAACAAAG
1 AAATAAATAAACAAAG
*
19809738 AAAATAAATAAATAAAG
1 -AAATAAATAAACAAAG
19809755 -AA-AAATAAACAAATG
1 AAATAAATAAACAAA-G
19809770 AAATAAAT
1 AAATAAAT
19809778 CAATAAACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.30
15 3 0.09
16 2 0.06
17 18 0.55
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.16
Consensus pattern (16 bp):
AAATAAATAAACAAAG
Found at i:19815153 original size:11 final size:11
Alignment explanation
Indices: 19815134--19815173 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
19815124 GACAAAGGAG
*
19815134 TCAGTATGTCT
1 TCAGGATGTCT
19815145 TCAGGATGTCT
1 TCAGGATGTCT
19815156 TCAGGGGATGTCT
1 TCA--GGATGTCT
19815169 TCAGG
1 TCAGG
19815174 GGTATGTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.17, C:0.17, G:0.30, T:0.35
Consensus pattern (11 bp):
TCAGGATGTCT
Found at i:19815166 original size:13 final size:13
Alignment explanation
Indices: 19815139--19815181 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
19815129 AGGAGTCAGT
19815139 ATGTCTTCA--GG
1 ATGTCTTCAGGGG
19815150 ATGTCTTCAGGGG
1 ATGTCTTCAGGGG
19815163 ATGTCTTCAGGGG
1 ATGTCTTCAGGGG
19815176 TATGTC
1 -ATGTC
19815182 GCGACACCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.31
13 15 0.52
14 5 0.17
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.35
Consensus pattern (13 bp):
ATGTCTTCAGGGG
Found at i:19828186 original size:13 final size:13
Alignment explanation
Indices: 19828168--19828192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19828158 TTATTAGTTG
19828168 TAAAAATTTATTT
1 TAAAAATTTATTT
19828181 TAAAAATTTATT
1 TAAAAATTTATT
19828193 CCCGAAACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAAATTTATTT
Found at i:19832984 original size:18 final size:18
Alignment explanation
Indices: 19832961--19832995 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19832951 CAAGAACAGG
19832961 AAGCATAAAAACAGTTTC
1 AAGCATAAAAACAGTTTC
* *
19832979 AAGCATGAAAATAGTTT
1 AAGCATAAAAACAGTTT
19832996 GGCACATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (18 bp):
AAGCATAAAAACAGTTTC
Found at i:19833194 original size:17 final size:18
Alignment explanation
Indices: 19833151--19833184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19833141 GACTAATGAC
*
19833151 TGACATTTTCTACTTTTG
1 TGACTTTTTCTACTTTTG
19833169 TGACTTTTTC-ACTTTT
1 TGACTTTTTCTACTTTT
19833185 TTGATGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.59
Consensus pattern (18 bp):
TGACTTTTTCTACTTTTG
Found at i:19838975 original size:486 final size:486
Alignment explanation
Indices: 19838062--19839036 Score: 1842
Period size: 486 Copynumber: 2.0 Consensus size: 486
19838052 ACAACTCCGT
19838062 CAAATATCTTAACTTTAATCGTTCCAACACCTGTAATTTTACACGAAGCATTATTTCCCATCAAA
1 CAAATATCTTAACTTTAATCGTTCCAACACCTGTAATTTTACACGAAGCATTATTTCCCATCAAA
19838127 ACAATACCTTCAAACACTGTTTCGTAAGTTGTAAACCAATCCCAATTGGGACTTATGTGGAAGGT
66 ACAATACCTTCAAACACTGTTTCGTAAGTTGTAAACCAATCCCAATTGGGACTTATGTGGAAGGT
19838192 GCAACCCGAATCAAGGATCCACTTCTCGCTCATATTAGAATTGTTGACAGAAACGACTAGAAATT
131 GCAACCCGAATCAAGGATCCACTTCTCGCTCATATTAGAATTGTTGACAGAAACGACTAGAAATT
*
19838257 CACCATCACTGTAGTATTCTACAACATCAGCTTCACTAGAATTTTTTAGTTGTTTTCCTTTTTGA
196 CACCATCACTGTAGTATTCTACAACATCAGCTTCACTAGAATTTTCTAGTTGTTTTCCTTTTTGA
*
19838322 TTTGCAACCTCCCTTTTGATCTTATTTTGTAGCTTATAGCACTCAAATTTAATGTTTCCTTTCTT
261 TTTGCAACCTCCCTTTTGATCTTATTCTGTAGCTTATAGCACTCAAATTTAATGTTTCCTTTCTT
*
19838387 CTTGCAGAAGTTACAAGTTTTACCTTTGTTTGAAGACTTCGATCTACCCTTAGATTTACTGTGAG
326 CTTGCAGAAGTTACAAGTTTTACCTTTGTTTGAAGACTTCGATCTACCCTTAGATTTACCGTGAG
* *
19838452 GATTCTGTTCTTGTGTCCTTCTATGATCATCATCAGTATTCTATTCTTGTCTCCCACAAACAATG
391 GATTCTGTTCCTGTGTCCTTCTATGATCATCATCAGTATTCTATTCTTGTCTCCCACAAACAATA
19838517 AGACTCTCTCCGTTAGAGTGGGGTTTAACCA
456 AGACTCTCTCCGTTAGAGTGGGGTTTAACCA
*
19838548 CAAATATCTTAACTTTAATCGTTCCAACACCTGTAATTTTACACGAAGTATTATTTCCCATCAAA
1 CAAATATCTTAACTTTAATCGTTCCAACACCTGTAATTTTACACGAAGCATTATTTCCCATCAAA
19838613 ACAATACCTTCAAACACTGTTTCGTAAGTTGTAAACCAATCCCAATTGGGACTTATGTGGAAGGT
66 ACAATACCTTCAAACACTGTTTCGTAAGTTGTAAACCAATCCCAATTGGGACTTATGTGGAAGGT
*
19838678 GCAACCCGAATCAAGGATCCACTTCTCGCTCATATTAGAATTGTTGACAGAAGCGACTAGAAATT
131 GCAACCCGAATCAAGGATCCACTTCTCGCTCATATTAGAATTGTTGACAGAAACGACTAGAAATT
*
19838743 CACCATCACTGTAGTCTTCTACAACATCAGCTTCACTAGAATTTTCTAGTTGTTTTCCTTTTTGA
196 CACCATCACTGTAGTATTCTACAACATCAGCTTCACTAGAATTTTCTAGTTGTTTTCCTTTTTGA
* * *
19838808 TTTGCAGCCTTCCTTTTGATCTTATTCTGTAGCTTATAGCACTCAAATTTAATGTTTCCTTTTTT
261 TTTGCAACCTCCCTTTTGATCTTATTCTGTAGCTTATAGCACTCAAATTTAATGTTTCCTTTCTT
19838873 CTTGCAGAAGTTACAAGTTTTACCTTTGTTTGAAGACTTCGATCTACCCTTAGATTTACCGTGAG
326 CTTGCAGAAGTTACAAGTTTTACCTTTGTTTGAAGACTTCGATCTACCCTTAGATTTACCGTGAG
*
19838938 GATTCTGTTCCTGTGTCCTTCTATGATCATTATCAGTATTCTATTCTTGTCTCCCACAAACAATA
391 GATTCTGTTCCTGTGTCCTTCTATGATCATCATCAGTATTCTATTCTTGTCTCCCACAAACAATA
19839003 AGACTCTCTCCGTTAGAGTGGGGTTTAACCA
456 AGACTCTCTCCGTTAGAGTGGGGTTTAACCA
19839034 CAA
1 CAA
19839037 GATGTTTTAT
Statistics
Matches: 477, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
486 477 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (486 bp):
CAAATATCTTAACTTTAATCGTTCCAACACCTGTAATTTTACACGAAGCATTATTTCCCATCAAA
ACAATACCTTCAAACACTGTTTCGTAAGTTGTAAACCAATCCCAATTGGGACTTATGTGGAAGGT
GCAACCCGAATCAAGGATCCACTTCTCGCTCATATTAGAATTGTTGACAGAAACGACTAGAAATT
CACCATCACTGTAGTATTCTACAACATCAGCTTCACTAGAATTTTCTAGTTGTTTTCCTTTTTGA
TTTGCAACCTCCCTTTTGATCTTATTCTGTAGCTTATAGCACTCAAATTTAATGTTTCCTTTCTT
CTTGCAGAAGTTACAAGTTTTACCTTTGTTTGAAGACTTCGATCTACCCTTAGATTTACCGTGAG
GATTCTGTTCCTGTGTCCTTCTATGATCATCATCAGTATTCTATTCTTGTCTCCCACAAACAATA
AGACTCTCTCCGTTAGAGTGGGGTTTAACCA
Found at i:19839779 original size:24 final size:24
Alignment explanation
Indices: 19839764--19839815 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19839754 AATCAAATTC
19839764 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
19839788 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
19839812 AAAT
1 AAAT
19839816 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:19844684 original size:18 final size:18
Alignment explanation
Indices: 19844652--19844695 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
19844642 TTGATAAAAT
19844652 ATTTATTTTATATTTTTA
1 ATTTATTTTATATTTTTA
19844670 ATTT-TTTTATGATTTTTA
1 ATTTATTTTAT-ATTTTTA
*
19844688 ATTAATTT
1 ATTTATTT
19844696 CTAACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
19 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTATTTTATATTTTTA
Found at i:19847164 original size:44 final size:44
Alignment explanation
Indices: 19847116--19847416 Score: 136
Period size: 44 Copynumber: 6.7 Consensus size: 44
19847106 TAATTGTTTT
*
19847116 AATCTGCTCCATTGCAACTTCAAGGAGATAGGATTAGTAGCTTC
1 AATCTGCTCCATTGCAACTTCAAGGAGATAAGATTAGTAGCTTC
* * * *
19847160 AATCTACTCCACTT-CACCTTC-AGCGAGATAAGATTGGTATCTTC
1 AATCTGCTCCA-TTGCAACTTCAAG-GAGATAAGATTAGTAGCTTC
* * * * *
19847204 -ATCCTGCTCCTTTGCAACTTTAGGGAGATAAGGTT--T-GATAT-
1 AAT-CTGCTCCATTGCAACTTCAAGGAGATAAGATTAGTAGCT-TC
* * * *
19847245 GATCTGCTCTACTGCAACTTC-AGAGAGATAAGATCTGTAATTTATAGCTTC
1 AATCTGCTCCATTGCAACTTCAAG-GAGATAAGA--T-T-A---GTAGCTTC
* * * * * *
19847296 AATCTGTTCTACTTG-AACTTCAGGGAAATAAGATTCACTATCTTC
1 AATCTGCTCCA-TTGCAACTTCAAGGAGATAAGATT-AGTAGCTTC
* * * * *
19847341 AATCTACTCCACTGCAACTTCAGGGAGATAAGACTT-GCAACTTC
1 AATCTGCTCCATTGCAACTTCAAGGAGATAAGA-TTAGTAGCTTC
* * * *
19847385 AACCTGTTCCACTGCAACTTCAGGGAGATAAG
1 AATCTGCTCCATTGCAACTTCAAGGAGATAAG
19847417 GTTTGCGATG
Statistics
Matches: 195, Mismatches: 39, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
40 1 0.01
41 23 0.12
42 4 0.02
43 7 0.04
44 91 0.47
45 34 0.17
46 2 0.01
48 2 0.01
49 1 0.01
50 2 0.01
51 25 0.13
52 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCATTGCAACTTCAAGGAGATAAGATTAGTAGCTTC
Found at i:19847452 original size:48 final size:45
Alignment explanation
Indices: 19847311--19847455 Score: 129
Period size: 44 Copynumber: 3.2 Consensus size: 45
19847301 GTTCTACTTG
* *
19847311 AACTTCAGGGAAATAAGA-TT-CACTATCTTCAATCTA-CTCCACTGC
1 AACTTCAGGGAGATAAGACTTGCA--ATCTTCAATCCATC-CCACTGC
* *
19847356 AACTTCAGGGAGATAAGACTTGCAA-CTTCAA-CCTGTTCCACTGC
1 AACTTCAGGGAGATAAGACTTGCAATCTTCAATCC-ATCCCACTGC
** *
19847400 AACTTCAGGGAGATAAGGTTTGCGATGATCTTCAATCCATCCCACTAC
1 AACTTCAGGGAGATAAGACTTGC-A--ATCTTCAATCCATCCCACTGC
19847448 AACTTCAG
1 AACTTCAG
19847456 AGGCATAGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
43 1 0.01
44 34 0.41
45 19 0.23
46 2 0.02
47 3 0.04
48 21 0.26
49 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
AACTTCAGGGAGATAAGACTTGCAATCTTCAATCCATCCCACTGC
Found at i:19854699 original size:22 final size:23
Alignment explanation
Indices: 19854674--19854718 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
19854664 AATATATAGG
19854674 AAAAC-TTAAAATAAATAATAAT
1 AAAACATTAAAATAAATAATAAT
*
19854696 AAAACAGTTTGAAATAAATAATA
1 AAAACA--TTAAAATAAATAATA
19854719 TTATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
25 14 0.74
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (23 bp):
AAAACATTAAAATAAATAATAAT
Found at i:19854794 original size:22 final size:23
Alignment explanation
Indices: 19854753--19854796 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
19854743 AAGTACAAAC
*
19854753 AATTTTAAAGGATATATATATAA
1 AATTTGAAAGGATATATATATAA
*
19854776 AATTTGAAA-GATATGTATATA
1 AATTTGAAAGGATATATATATA
19854797 TATAACAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (23 bp):
AATTTGAAAGGATATATATATAA
Found at i:19854863 original size:55 final size:54
Alignment explanation
Indices: 19854764--19854881 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 54
19854754 ATTTTAAAGG
* * *
19854764 ATATATATATAAAATTTGAAAGATATGTATATATATAACAGTTTACAATAAATA
1 ATATATAAATAAAATTTGAAAGATAAGTATATATATAACAGTTTAAAATAAATA
* *
19854818 ATATATAAATGAAAATTTTAAA-ATAAGTA-ATATGTAACATTGTTTAAAATAAATA
1 ATATATAAAT-AAAATTTGAAAGATAAGTATATATATAACA--GTTTAAAATAAATA
19854873 ATATATAAA
1 ATATATAAA
19854882 ACTTAAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
53 9 0.16
54 15 0.27
55 32 0.57
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (54 bp):
ATATATAAATAAAATTTGAAAGATAAGTATATATATAACAGTTTAAAATAAATA
Found at i:19856634 original size:21 final size:21
Alignment explanation
Indices: 19856596--19856635 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19856586 AGAGAAAAAT
*
19856596 TAAATAATATAATAATATTAA
1 TAAATAACATAATAATATTAA
19856617 TAAATAACAT-ATATATATT
1 TAAATAACATAATA-ATATT
19856636 TTTAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATAACATAATAATATTAA
Found at i:19861733 original size:25 final size:25
Alignment explanation
Indices: 19861705--19861756 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19861695 ATAAACAACT
19861705 AAATATGTTGTGAAAAAGATACTCC
1 AAATATGTTGTGAAAAAGATACTCC
19861730 AAATATGTTGTGAAAAAGATACTCC
1 AAATATGTTGTGAAAAAGATACTCC
19861755 AA
1 AA
19861757 CAAACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATATGTTGTGAAAAAGATACTCC
Found at i:19862831 original size:20 final size:23
Alignment explanation
Indices: 19862792--19862832 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
19862782 AATGCAATAT
19862792 TAAAATTGCTAACTAAAATGTCC
1 TAAAATTGCTAACTAAAATGTCC
19862815 TAAAA-TGC-AAC-AAAATGT
1 TAAAATTGCTAACTAAAATGT
19862833 ACTTAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (23 bp):
TAAAATTGCTAACTAAAATGTCC
Found at i:19864893 original size:26 final size:26
Alignment explanation
Indices: 19864855--19865005 Score: 153
Period size: 26 Copynumber: 5.8 Consensus size: 26
19864845 ACACGCTAAG
* *
19864855 AAATGGAAACCTTTGTGGCGTATCCA
1 AAATGGAAGCCTTTGTGGCATATCCA
*
19864881 AAATGGAAGCCTTTGTGGCATATCCG
1 AAATGGAAGCCTTTGTGGCATATCCA
* *
19864907 AAATAGAAGCCTTTGTGGCATATCTA
1 AAATGGAAGCCTTTGTGGCATATCCA
* **
19864933 AAATGGAAGCCTTCGTGGCATATCTG
1 AAATGGAAGCCTTTGTGGCATATCCA
* * * **
19864959 AAATAGAAG-CTTTCATGGTATATCTG
1 AAATGGAAGCCTTT-GTGGCATATCCA
19864985 AAATGGAAG-CTTTCGTGGCAT
1 AAATGGAAGCCTTT-GTGGCAT
19865006 TCTCTAAAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
25 3 0.03
26 105 0.97
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
AAATGGAAGCCTTTGTGGCATATCCA
Found at i:19864921 original size:52 final size:52
Alignment explanation
Indices: 19864854--19865005 Score: 189
Period size: 52 Copynumber: 2.9 Consensus size: 52
19864844 AACACGCTAA
* * * *
19864854 GAAATGGAAACCTTTGTGGCGTATCCAAAATGGAAGCCTTTGTGGCATATCC
1 GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
* *
19864906 GAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGCCTTCGTGGCATATCT
1 GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
* * ** *
19864958 GAAATAGAAG-CTTTCATGGTATATCTGAAATGGAAGCTTTCGTGGCAT
1 GAAATAGAAGCCTTT-GTGGCATATCCAAAATGGAAGCCTTCGTGGCAT
19865006 TCTCTAAAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 4 0.04
52 85 0.96
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (52 bp):
GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
Found at i:19864988 original size:78 final size:79
Alignment explanation
Indices: 19864855--19865015 Score: 184
Period size: 78 Copynumber: 2.1 Consensus size: 79
19864845 ACACGCTAAG
* * * *
19864855 AAATGGAAACCTTTGTGGCGTATCCAAAATGGAAGCCTTTGTGGCATATCCGAAATAGAAGCCTT
1 AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTTATGGCATATCCGAAATAGAAG-CTT
19864920 T-GTGGCA-TATCTA
65 TCGTGGCATTATCTA
* ** * * *
19864933 AAATGGAAGCCTTCGTGGCATATCTGAAATAGAAG-CTTTCATGGTATATCTGAAATGGAAGCTT
1 AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTT-ATGGCATATCCGAAATAGAAGCTT
*
19864997 TCGTGGCATTCTCTA
65 TCGTGGCATTATCTA
19865012 AAAT
1 AAAT
19865016 AATGGCCCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.12
78 52 0.75
79 9 0.13
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (79 bp):
AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTTATGGCATATCCGAAATAGAAGCTTT
CGTGGCATTATCTA
Found at i:19868862 original size:7 final size:7
Alignment explanation
Indices: 19868850--19868880 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19868840 TTTGGTTGTA
19868850 ATTGGAC
1 ATTGGAC
19868857 ATTGGAC
1 ATTGGAC
19868864 ATTGGAC
1 ATTGGAC
19868871 ATTGGAC
1 ATTGGAC
19868878 ATT
1 ATT
19868881 TTATTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (7 bp):
ATTGGAC
Found at i:19869168 original size:4 final size:4
Alignment explanation
Indices: 19869159--19869243 Score: 161
Period size: 4 Copynumber: 21.2 Consensus size: 4
19869149 GAATTTGGGG
19869159 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
19869207 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA CGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
19869244 ATGTTAATTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 79 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:19870103 original size:27 final size:27
Alignment explanation
Indices: 19870065--19870134 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
19870055 TGGTGTCACA
*
19870065 ACTATCTTATGTGGAAAGTCCGCCAAG
1 ACTATCTTATGTGGAAAGCCCGCCAAG
*
19870092 ACTATCTTATGTGAAAAGCCCGCCAAG
1 ACTATCTTATGTGGAAAGCCCGCCAAG
*
19870119 ACTATCTTTTGTGGAA
1 ACTATCTTATGTGGAA
19870135 GTCTGTGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (27 bp):
ACTATCTTATGTGGAAAGCCCGCCAAG
Found at i:19871893 original size:22 final size:22
Alignment explanation
Indices: 19871858--19871908 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19871848 ATATTAAAAC
* *
19871858 AATTATATAATTCATAAAGTGGA
1 AATTA-ATAATTCAAAAAATGGA
*
19871881 AATTAATTATTCAAAAAATGGA
1 AATTAATAATTCAAAAAATGGA
19871903 AATTAA
1 AATTAA
19871909 ATAAGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (22 bp):
AATTAATAATTCAAAAAATGGA
Found at i:19881757 original size:28 final size:29
Alignment explanation
Indices: 19881718--19881773 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
19881708 AATTAAAATT
*
19881718 ATTTTTTAATTATAATA-TATATTTTTAA
1 ATTTTTTAATTAAAATATTATATTTTTAA
19881746 ATTTATTT-ATTAAAATATTTATATTTTT
1 ATTT-TTTAATTAAAATA-TTATATTTTT
19881774 TTTACAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 3 0.12
30 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATTTTTTAATTAAAATATTATATTTTTAA
Found at i:19881784 original size:21 final size:22
Alignment explanation
Indices: 19881741--19881784 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19881731 AATATATATT
19881741 TTTAAATTTATTTATTAAAATA
1 TTTAAATTTATTTATTAAAATA
*
19881763 TTTATATTT-TTT-TTACAAATA
1 TTTAAATTTATTTATTA-AAATA
19881784 T
1 T
19881785 AAGATTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 3 0.15
21 9 0.45
22 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAAATTTATTTATTAAAATA
Found at i:19894893 original size:13 final size:13
Alignment explanation
Indices: 19894875--19894901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19894865 GAAGTAATCA
19894875 CACACGGGCGTGT
1 CACACGGGCGTGT
19894888 CACACGGGCGTGT
1 CACACGGGCGTGT
19894901 C
1 C
19894902 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:19918745 original size:25 final size:25
Alignment explanation
Indices: 19918717--19918768 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19918707 ATAAACAACT
19918717 AAATATGTTGTGAAAAAGATACTCC
1 AAATATGTTGTGAAAAAGATACTCC
19918742 AAATATGTTGTGAAAAAGATACTCC
1 AAATATGTTGTGAAAAAGATACTCC
19918767 AA
1 AA
19918769 CAAACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (25 bp):
AAATATGTTGTGAAAAAGATACTCC
Found at i:19919842 original size:20 final size:23
Alignment explanation
Indices: 19919803--19919843 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
19919793 AATGCAATAT
19919803 TAAAATTGCTAACTAAAATGTCC
1 TAAAATTGCTAACTAAAATGTCC
19919826 TAAAA-TGC-AAC-AAAATGT
1 TAAAATTGCTAACTAAAATGT
19919844 ACTTAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (23 bp):
TAAAATTGCTAACTAAAATGTCC
Found at i:19921906 original size:26 final size:26
Alignment explanation
Indices: 19921868--19922018 Score: 153
Period size: 26 Copynumber: 5.8 Consensus size: 26
19921858 ACACGCTAAG
* *
19921868 AAATGGAAACCTTTGTGGCGTATCCA
1 AAATGGAAGCCTTTGTGGCATATCCA
*
19921894 AAATGGAAGCCTTTGTGGCATATCCG
1 AAATGGAAGCCTTTGTGGCATATCCA
* *
19921920 AAATAGAAGCCTTTGTGGCATATCTA
1 AAATGGAAGCCTTTGTGGCATATCCA
* **
19921946 AAATGGAAGCCTTCGTGGCATATCTG
1 AAATGGAAGCCTTTGTGGCATATCCA
* * * **
19921972 AAATAGAAG-CTTTCATGGTATATCTG
1 AAATGGAAGCCTTT-GTGGCATATCCA
19921998 AAATGGAAG-CTTTCGTGGCAT
1 AAATGGAAGCCTTT-GTGGCAT
19922019 TCTCTAAAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
25 3 0.03
26 105 0.97
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (26 bp):
AAATGGAAGCCTTTGTGGCATATCCA
Found at i:19921934 original size:52 final size:52
Alignment explanation
Indices: 19921867--19922018 Score: 189
Period size: 52 Copynumber: 2.9 Consensus size: 52
19921857 AACACGCTAA
* * * *
19921867 GAAATGGAAACCTTTGTGGCGTATCCAAAATGGAAGCCTTTGTGGCATATCC
1 GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
* *
19921919 GAAATAGAAGCCTTTGTGGCATATCTAAAATGGAAGCCTTCGTGGCATATCT
1 GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
* * ** *
19921971 GAAATAGAAG-CTTTCATGGTATATCTGAAATGGAAGCTTTCGTGGCAT
1 GAAATAGAAGCCTTT-GTGGCATATCCAAAATGGAAGCCTTCGTGGCAT
19922019 TCTCTAAAAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 4 0.04
52 85 0.96
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.29
Consensus pattern (52 bp):
GAAATAGAAGCCTTTGTGGCATATCCAAAATGGAAGCCTTCGTGGCATATCC
Found at i:19922001 original size:78 final size:79
Alignment explanation
Indices: 19921868--19922028 Score: 184
Period size: 78 Copynumber: 2.1 Consensus size: 79
19921858 ACACGCTAAG
* * * *
19921868 AAATGGAAACCTTTGTGGCGTATCCAAAATGGAAGCCTTTGTGGCATATCCGAAATAGAAGCCTT
1 AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTTATGGCATATCCGAAATAGAAG-CTT
19921933 T-GTGGCA-TATCTA
65 TCGTGGCATTATCTA
* ** * * *
19921946 AAATGGAAGCCTTCGTGGCATATCTGAAATAGAAG-CTTTCATGGTATATCTGAAATGGAAGCTT
1 AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTT-ATGGCATATCCGAAATAGAAGCTT
*
19922010 TCGTGGCATTCTCTA
65 TCGTGGCATTATCTA
19922025 AAAT
1 AAAT
19922029 AATGGCCCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.12
78 52 0.75
79 9 0.13
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (79 bp):
AAATGGAAACCTTCGTGGCATATCCAAAATAGAAGCCTTTATGGCATATCCGAAATAGAAGCTTT
CGTGGCATTATCTA
Found at i:19925877 original size:7 final size:7
Alignment explanation
Indices: 19925865--19925895 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
19925855 TTTGGTTGTA
19925865 ATTGGAC
1 ATTGGAC
19925872 ATTGGAC
1 ATTGGAC
19925879 ATTGGAC
1 ATTGGAC
19925886 ATTGGAC
1 ATTGGAC
19925893 ATT
1 ATT
19925896 TTATTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (7 bp):
ATTGGAC
Found at i:19926183 original size:4 final size:4
Alignment explanation
Indices: 19926174--19926258 Score: 161
Period size: 4 Copynumber: 21.2 Consensus size: 4
19926164 GAATTTGGGG
19926174 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
19926222 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA CGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
19926259 ATGTTAATTA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 79 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:19927119 original size:27 final size:27
Alignment explanation
Indices: 19927081--19927150 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
19927071 TGGTGTCACA
*
19927081 ACTATCTTATGTGGAAAGTCCGCCAAG
1 ACTATCTTATGTGGAAAGCCCGCCAAG
*
19927108 ACTATCTTATGTGAAAAGCCCGCCAAG
1 ACTATCTTATGTGGAAAGCCCGCCAAG
*
19927135 ACTATCTTTTGTGGAA
1 ACTATCTTATGTGGAA
19927151 GTCTGTGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (27 bp):
ACTATCTTATGTGGAAAGCCCGCCAAG
Found at i:19939181 original size:15 final size:15
Alignment explanation
Indices: 19939150--19939198 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
19939140 TCCATATTAC
*
19939150 ATTTTTATATTATTT
1 ATTTTTATATTAATT
19939165 ATTTTTA-ATATAATT
1 ATTTTTATAT-TAATT
19939180 ATTCTTT-T-TTAATT
1 ATT-TTTATATTAATT
19939194 ATTTT
1 ATTTT
19939199 AAAAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 15 0.50
16 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTATATTAATT
Found at i:19939248 original size:17 final size:17
Alignment explanation
Indices: 19939226--19939258 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19939216 ATTAACCTAA
*
19939226 TTATTTTTATAAATAAC
1 TTATTTATATAAATAAC
19939243 TTATTTATATAAATAA
1 TTATTTATATAAATAA
19939259 AGAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATTTATATAAATAAC
Found at i:19943603 original size:27 final size:27
Alignment explanation
Indices: 19943573--19943634 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
19943563 CCTATCAGGT
**
19943573 AGGCGCCACTAATTGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
*
19943600 AGGCGCCATTAAAAGTGCCTCATAGGG
1 AGGCGCCACTAAAAGTGCCTCATAGGG
19943627 AGGCGCCA
1 AGGCGCCA
19943635 ATTGCATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.26, C:0.26, G:0.31, T:0.18
Consensus pattern (27 bp):
AGGCGCCACTAAAAGTGCCTCATAGGG
Found at i:19943795 original size:3 final size:3
Alignment explanation
Indices: 19943769--19943817 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
19943759 GACGGTAGAG
*
19943769 AGA AAA AGA AGA GAGA A-A AG- AGA AGA AG- AGA AGA AG- AGA AGA
1 AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
19943811 AGA AGA A
1 AGA AGA A
19943818 AGAAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 8 0.21
3 28 0.72
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19943826 original size:8 final size:8
Alignment explanation
Indices: 19943767--19943813 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
19943757 TGGACGGTAG
19943767 AGAGAA-A
1 AGAGAAGA
19943774 A-AGAAG-
1 AGAGAAGA
19943780 AGAGAA-A
1 AGAGAAGA
19943787 AGAGAAGA
1 AGAGAAGA
19943795 AGAGAAGA
1 AGAGAAGA
19943803 AGAGAAGA
1 AGAGAAGA
19943811 AGA
1 AGA
19943814 AGAAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 5 0.14
7 11 0.31
8 20 0.56
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (8 bp):
AGAGAAGA
Found at i:19943988 original size:21 final size:21
Alignment explanation
Indices: 19943963--19944144 Score: 175
Period size: 21 Copynumber: 9.0 Consensus size: 21
19943953 TGGATTAGTA
19943963 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
19943984 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
19944003 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* * *
19944024 ATTTTATAATTAATTTTGT-ATT
1 -TTTTGT-ATGAATATTGTAATT
* * * * *
19944046 TATAGTTTTGGAT-TAGT-A--
1 TTTTG-TATGAATATTGTAATT
*
19944064 TTTTGTATGAATATTGTCATT
1 TTTTGTATGAATATTGTAATT
*
19944085 TTTTGTATGAACATTGTAA--
1 TTTTGTATGAATATTGTAATT
19944104 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
19944125 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
19944145 ATTGTAATTT
Statistics
Matches: 131, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.04
18 6 0.05
19 38 0.29
20 4 0.03
21 60 0.46
22 9 0.07
23 9 0.07
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:19944017 original size:40 final size:39
Alignment explanation
Indices: 19943962--19944144 Score: 151
Period size: 40 Copynumber: 4.5 Consensus size: 39
19943952 TTGGATTAGT
19943962 ATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTAA-TTTTTGTATGAATATTGTA
* * *
19944002 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGT-
1 ATTTTGTATGAATATTGTAA-T-TTTTGT-ATGAATATTGTA
* * *
19944043 ATTTATAGTTTTGGAT-TAGT-A-TTTTGTATGAATATTGTCA
1 ATTT-T-G-TATGAATATTGTAATTTTTGTATGAATATTGT-A
* *
19944083 TTTTTTGTATGAACATTGTAA-TTTTGTATGAATATTGTA
1 -ATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTA
*
19944122 ATTTTTTGTATGAATATTATAAT
1 A--TTTTGTATGAATATTGTAAT
19944145 ATTGTAATTT
Statistics
Matches: 113, Mismatches: 17, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
38 13 0.12
39 10 0.09
40 58 0.51
41 12 0.11
42 11 0.10
43 4 0.04
44 5 0.04
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (39 bp):
ATTTTGTATGAATATTGTAATTTTTGTATGAATATTGTA
Found at i:19944062 original size:101 final size:101
Alignment explanation
Indices: 19943942--19944128 Score: 340
Period size: 101 Copynumber: 1.9 Consensus size: 101
19943932 ATGTTTAGTG
*
19943942 TTTATAGTTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTT
1 TTTATAGTTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAACATTGTAATTTT
19944007 GTATGAATATTGTAATTATTTTATAATTAATTTTGTA
66 GTATGAATATTGTAATT-TTTTATAATTAATTTTGTA
*
19944044 TTTATAG-TTTTGGATTAGTATTTTGTATGAATATTGTCATTTTTTGTATGAACATTGTAATTTT
1 TTTATAGTTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAACATTGTAATTTT
19944108 GTATGAATATTGTAATTTTTT
66 GTATGAATATTGTAATTTTTT
19944129 GTATGAATAT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
100 4 0.05
101 72 0.87
102 7 0.08
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (101 bp):
TTTATAGTTTTTGGATTAGTATTTTGTATGAATATTGTAATTTTTTGTATGAACATTGTAATTTT
GTATGAATATTGTAATTTTTTATAATTAATTTTGTA
Found at i:19944130 original size:29 final size:28
Alignment explanation
Indices: 19944113--19944173 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
19944103 ATTTTGTATG
19944113 AATATTGTAATTTTTTGTATGAATATTAT
1 AATATTGTAATTTTTTGTA-GAATATTAT
*
19944142 AATATTGTAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTTTGTA-GAATATTAT
19944171 AAT
1 AAT
19944174 TATTTTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (28 bp):
AATATTGTAATTTTTTGTAGAATATTAT
Found at i:19944239 original size:60 final size:60
Alignment explanation
Indices: 19944167--19944288 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 60
19944157 TGTATGAATA
* * *
19944167 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATT-ATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTA-AATTTAATTTATTAGTAATTTAGGATTAAT-CTATAAATTGTTGTGT
19944227 TTGTAATTATTTTAAATTTAATTTATTAGTAATTTAGGATTAATCTATAAATTGTTGTGT
1 TTGTAATTATTTTAAATTTAATTTATTAGTAATTTAGGATTAATCTATAAATTGTTGTGT
19944287 TT
1 TT
19944289 AGTTTAGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
59 2 0.04
60 53 0.93
61 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (60 bp):
TTGTAATTATTTTAAATTTAATTTATTAGTAATTTAGGATTAATCTATAAATTGTTGTGT
Found at i:19949670 original size:27 final size:27
Alignment explanation
Indices: 19949612--19949686 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
19949602 AGACTATTGA
* *
19949612 CGCCTCTCA-ATATGGCACCACTAATGG
1 CGCCTATCAGATA-GGCACCACCAATGG
*
19949639 CGCCTATCAGATAGGCACCACCATTGG
1 CGCCTATCAGATAGGCACCACCAATGG
* * * *
19949666 TGCCTCTGAGATAGGCGCCAC
1 CGCCTATCAGATAGGCACCAC
19949687 TACTTTGTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 37 0.93
28 3 0.08
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (27 bp):
CGCCTATCAGATAGGCACCACCAATGG
Found at i:19953263 original size:2 final size:2
Alignment explanation
Indices: 19953258--19953284 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19953248 AGAAAACATG
19953258 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
19953285 TGGAAGGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:19956831 original size:29 final size:29
Alignment explanation
Indices: 19956798--19956955 Score: 88
Period size: 29 Copynumber: 5.2 Consensus size: 29
19956788 AATACTCGCT
19956798 ACAAAGGCTTTCCTAACCAGTGTTGTGCC
1 ACAAAGGCTTTCCTAACCAGTGTTGTGCC
* * ** *
19956827 ACAAAGGCATTCCTTAATATCTAGTACT-CGCC
1 ACAAAGGCTTTCC-T-A-A-CCAGTGTTGTGCC
** *
19956859 ACAAAGGCTTTCCTGTCCAGAGTTGTGCC
1 ACAAAGGCTTTCCTAACCAGTGTTGTGCC
* **
19956888 ACAAAGGCATTCCGTAATATCCAGTACT-TGCC
1 ACAAAGGCTTTCC-T-A-A-CCAGTGTTGTGCC
**
19956920 ACAAAGGCTTTCCTGTCCA-TAGTTGTGCC
1 ACAAAGGCTTTCCTAACCAGT-GTTGTGCC
*
19956949 ATAAAGG
1 ACAAAGG
19956956 TATTCCTTAA
Statistics
Matches: 93, Mismatches: 25, Indels: 22
0.66 0.18 0.16
Matches are distributed among these distances:
27 1 0.01
28 8 0.09
29 37 0.40
30 2 0.02
31 3 0.03
32 32 0.34
33 10 0.11
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (29 bp):
ACAAAGGCTTTCCTAACCAGTGTTGTGCC
Found at i:19957146 original size:61 final size:61
Alignment explanation
Indices: 19956601--19957135 Score: 640
Period size: 61 Copynumber: 8.8 Consensus size: 61
19956591 TATACTTTGA
* * *
19956601 ATCCAGTACTCGCCACAAAGGCTTTCCTATCTAGAATTGTGCCAAAAAGGCATTCCTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * * * * * * * *
19956662 ATTCAATACTTGCCATAAAGGTTTTCTTGTCCAGAGTTGTGCCATAAAGGCTTTCCTCAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * * ** * *
19956723 ATCCAATACTCGCCACAAAGGCTTACCTATCTAGAGTTGTGTCGTAAAGACATTCTTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * *
19956784 ATCCAATACTCGCTACAAAGGCTTTCCTAACCAGTGTTGTGCCACAAAGGCATTCCTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * *
19956845 ATCTAGTACTCGCCACAAAGGCTTTCCTGTCCAGAGTTGTGCCACAAAGGCATTCCGTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * * *
19956906 ATCCAGTACTTGCCACAAAGGCTTTCCTGTCCATAGTTGTGCCATAAAGGTATTCCTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * * *
19956967 ATCCAGTACTCACCACAAAGGCTTTACTATCCAGAGTTGTGTCACAAAGGTATTCTTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * *
19957028 ATCTAGTACTCGCCACAAATGCTTTCTTATCCAGAGTTGTTCCACAAAGGCATTCCTTAAT
1 ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
* * * *
19957089 ATCCAGAACTCGCCACCAAGGCTTT-CTCATCCAGAGTTTTTCCACAA
1 ATCCAGTACTCGCCACAAAGGCTTTCCT-ATCCAGAGTTGTGCCACAA
19957136 GGCTTTTCCT
Statistics
Matches: 401, Mismatches: 72, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
60 1 0.00
61 400 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (61 bp):
ATCCAGTACTCGCCACAAAGGCTTTCCTATCCAGAGTTGTGCCACAAAGGCATTCCTTAAT
Found at i:19957469 original size:15 final size:16
Alignment explanation
Indices: 19957446--19957483 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
19957436 CCAGAGATAG
19957446 GCATAGACTCA-TCAT
1 GCATAGACTCACTCAT
*
19957461 GCATCGACTCACTCAT
1 GCATAGACTCACTCAT
19957477 G-ATAGAC
1 GCATAGAC
19957484 ACTTTTATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (16 bp):
GCATAGACTCACTCAT
Found at i:19989738 original size:23 final size:23
Alignment explanation
Indices: 19989712--19989756 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
19989702 ATGAGTGTTA
19989712 GAGGTTTATATCACTTGTTGTAT
1 GAGGTTTATATCACTTGTTGTAT
19989735 GAGGTTTATATCACTTGTTGTA
1 GAGGTTTATATCACTTGTTGTA
19989757 CGAGTTGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.47
Consensus pattern (23 bp):
GAGGTTTATATCACTTGTTGTAT
Found at i:20008076 original size:18 final size:18
Alignment explanation
Indices: 20008053--20008087 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20008043 ACGATGTGTC
20008053 AAACTATTTTCATGCTTG
1 AAACTATTTTCATGCTTG
*
20008071 AAACTATTTTGATGCTT
1 AAACTATTTTCATGCTT
20008088 CCTATTCTTG
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:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
AAACTATTTTCATGCTTG
Found at i:20041286 original size:10 final size:10
Alignment explanation
Indices: 20041273--20041311 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
20041263 CTGTGACTAA
*
20041273 ATGTGATTTT
1 ATGTGATTAT
20041283 ATGTGATTAT
1 ATGTGATTAT
* *
20041293 AGGTGCTTAT
1 ATGTGATTAT
20041303 ATGTGATTA
1 ATGTGATTA
20041312 ATACATGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:20043167 original size:69 final size:69
Alignment explanation
Indices: 20043085--20043225 Score: 264
Period size: 69 Copynumber: 2.0 Consensus size: 69
20043075 GTTTTTAGCA
*
20043085 TTACTTGGGATAAGAAATGATATAATTTTAGGGGTGTATCAACTCTAAAATATTTATTTTAACAC
1 TTACTTGGGATAAGAAATGATATAATTTTAGGGGTGTATCAACTCTAAAATATATATTTTAACAC
20043150 TCTT
66 TCTT
*
20043154 TTACTTGGGATAAGAAATGATATAATTTTAGGGGTGTATCAAGTCTAAAATATATATTTTAACAC
1 TTACTTGGGATAAGAAATGATATAATTTTAGGGGTGTATCAACTCTAAAATATATATTTTAACAC
20043219 TCTT
66 TCTT
20043223 TTA
1 TTA
20043226 TATACATTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.40
Consensus pattern (69 bp):
TTACTTGGGATAAGAAATGATATAATTTTAGGGGTGTATCAACTCTAAAATATATATTTTAACAC
TCTT
Found at i:20050107 original size:23 final size:23
Alignment explanation
Indices: 20050071--20050121 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
20050061 ACTGTTTAAA
* *
20050071 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
20050094 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
20050117 AGTAA
1 TGTAA
20050122 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:20052513 original size:23 final size:23
Alignment explanation
Indices: 20052487--20052530 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20052477 TTCTTACTGT
*
20052487 AGTAATTTTTAGGGTATTACAAC
1 AGTAATTTTTAGGATATTACAAC
20052510 AGTAATTTTTAGGATATTACA
1 AGTAATTTTTAGGATATTACA
20052531 TTAAAGCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (23 bp):
AGTAATTTTTAGGATATTACAAC
Found at i:20053295 original size:27 final size:26
Alignment explanation
Indices: 20053261--20053431 Score: 153
Period size: 27 Copynumber: 6.3 Consensus size: 26
20053251 AGGGTTATAA
20053261 CAGTCATTTTACCCTATGAGGGTATTT
1 CAGTCATTTTACCCT-TGAGGGTATTT
* * *
20053288 AAATCATTTTACCCTTCAGGGGTATTT
1 CAGTCATTTTACCCTTGA-GGGTATTT
** * **
20053315 TGGTCATTTTATCCTCCAGGGGTATTT
1 CAGTCATTTTACCCTTGA-GGGTATTT
* *
20053342 CAATCATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
**
20053369 TGGTCATTTTACCCTTCGAGGGTATTT
1 CAGTCATTTTACCCTT-GAGGGTATTT
*
20053396 CAGTCATTTTACTCTTTGAGGGTATTT
1 CAGTCATTTTAC-CCTTGAGGGTATTT
* *
20053423 TAGTTATTT
1 CAGTCATTT
20053432 GCCCACGAAT
Statistics
Matches: 118, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.02
27 112 0.95
28 4 0.03
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (26 bp):
CAGTCATTTTACCCTTGAGGGTATTT
Found at i:20053338 original size:54 final size:54
Alignment explanation
Indices: 20053263--20053423 Score: 216
Period size: 54 Copynumber: 3.0 Consensus size: 54
20053253 GGTTATAACA
** * *
20053263 GTCATTTTACCCTATGAGGGTATTTAAATCATTTTACCCTTCAGGGGTATTTTG
1 GTCATTTTACCCTCCGAGGGTATTTCAATCATTTTACCCTTCAAGGGTATTTTG
*
20053317 GTCATTTTATCCTCC-AGGGGTATTTCAATCATTTTACCCTTCAAGGGTATTTTG
1 GTCATTTTACCCTCCGA-GGGTATTTCAATCATTTTACCCTTCAAGGGTATTTTG
* * * **
20053371 GTCATTTTACCCTTCGAGGGTATTTCAGTCATTTTACTCTTTGAGGGTATTTT
1 GTCATTTTACCCTCCGAGGGTATTTCAATCATTTTACCCTTCAAGGGTATTTT
20053424 AGTTATTTGC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 92 0.98
55 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (54 bp):
GTCATTTTACCCTCCGAGGGTATTTCAATCATTTTACCCTTCAAGGGTATTTTG
Found at i:20053771 original size:27 final size:27
Alignment explanation
Indices: 20053736--20053797 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
20053726 CTAACTGATA
* *
20053736 GGCGACACCAAAGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTCCCATTCCCATG
* * * *
20053763 GGTGGCACCGATGGTCCCATTCCCATT
1 GGCGGCACCAAAGGTCCCATTCCCATG
20053790 GGCGGCAC
1 GGCGGCAC
20053798 TAGTCGTGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.19, C:0.34, G:0.29, T:0.18
Consensus pattern (27 bp):
GGCGGCACCAAAGGTCCCATTCCCATG
Found at i:20053895 original size:10 final size:10
Alignment explanation
Indices: 20053880--20053915 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
20053870 GTTGGTGCGA
20053880 AAAAAGAGAG
1 AAAAAGAGAG
20053890 AAAAAGAGAG
1 AAAAAGAGAG
*
20053900 AAAGAGAAGAG
1 AAAAAG-AGAG
20053911 AAAAA
1 AAAAA
20053916 AAGTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAAAAGAGAG
Found at i:20053899 original size:12 final size:11
Alignment explanation
Indices: 20053878--20053918 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
20053868 GAGTTGGTGC
20053878 GAAAAAAGAGA
1 GAAAAAAGAGA
20053889 G-AAAAAGAGA
1 GAAAAAAGAGA
20053899 GAAAGAGAAGAGA
1 GAAA-A-AAGAGA
20053912 -AAAAAAG
1 GAAAAAAG
20053919 TATTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 13 0.48
11 4 0.15
12 4 0.15
13 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAGA
Done.