Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 60 of 240
Found at i:19801796 original size:28 final size:28
Alignment explanation
Indices: 19801764--19801889 Score: 171
Period size: 28 Copynumber: 4.5 Consensus size: 28
19801754 TTTAATAAGT
** * *
19801764 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
19801792 TCGCACACTTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
19801820 TCTCACACTTAGCGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
19801848 TCGCACACTTAGTGCTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
19801876 TCGCACACTTAGTG
1 TCGCACACTTAGTG
19801890 TCGAAAGTCA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 85 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:19804541 original size:21 final size:20
Alignment explanation
Indices: 19804517--19804556 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
19804507 GATAAGTATA
19804517 TTTTTTATTTT-GATTATTTTC
1 TTTTTT-TTTTCGATT-TTTTC
19804538 TTTTTTTTTTCGATTTTTT
1 TTTTTTTTTTCGATTTTTT
19804557 AGGCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTTCGATTTTTTC
Found at i:19809360 original size:21 final size:23
Alignment explanation
Indices: 19809334--19809378 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
19809324 AAAGGGTATC
*
19809334 TACAAATTAA-ATC-TCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
19809355 TACAAAATAATATCTTCTAAGAT
1 TACAAAATAATATCTTCTAAGAT
19809378 T
1 T
19809379 GCATATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 9 0.43
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (23 bp):
TACAAAATAATATCTTCTAAGAT
Found at i:19809394 original size:19 final size:19
Alignment explanation
Indices: 19809370--19809481 Score: 170
Period size: 19 Copynumber: 5.9 Consensus size: 19
19809360 AATAATATCT
19809370 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
19809389 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
19809408 TCTAAAATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
19809427 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
19809446 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
19809465 TCTAAGATTGCATATCA
1 TCTAAGATTGCATATCA
19809482 CTGAAGATTA
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:19809418 original size:38 final size:38
Alignment explanation
Indices: 19809370--19809473 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
19809360 AATAATATCT
19809370 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
* *
19809408 TCTAAAATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
19809446 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
19809474 GCATATCACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:19814692 original size:22 final size:21
Alignment explanation
Indices: 19814650--19814697 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
19814640 AAATTACTAA
*
19814650 CAACTAAATTAATAATGGATC
1 CAACTAAATTAATAATAGATC
**
19814671 CAACTAAAGTTAATTTTAGATC
1 CAACTAAA-TTAATAATAGATC
19814693 CAACT
1 CAACT
19814698 GCATCTCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (21 bp):
CAACTAAATTAATAATAGATC
Found at i:19818228 original size:39 final size:39
Alignment explanation
Indices: 19818169--19818247 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
19818159 TACTAATAAA
* * *
19818169 TTGCTTTTATTGATCCATATAGATATCAATGATGGATAG
1 TTGCTTTTATTAATCAATATAGATATCAATGATCGATAG
19818208 TTGCTTTTATTAATCAATATAGATATCAATGATCGATAG
1 TTGCTTTTATTAATCAATATAGATATCAATGATCGATAG
19818247 T
1 T
19818248 AAAACATTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (39 bp):
TTGCTTTTATTAATCAATATAGATATCAATGATCGATAG
Found at i:19824430 original size:30 final size:29
Alignment explanation
Indices: 19824386--19824449 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
19824376 TAGAGGATTC
* *
19824386 ATTTTTTCTCACTTTATCTATTTTTTTGAA
1 ATTTTTTCTCACTTTATCTAATTTTTAG-A
*
19824416 ATTTTTATCT-ACTTTATTTAATTTTTAGA
1 ATTTTT-TCTCACTTTATCTAATTTTTAGA
19824445 ATTTT
1 ATTTT
19824450 CTAAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 6 0.20
30 21 0.70
31 3 0.10
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.64
Consensus pattern (29 bp):
ATTTTTTCTCACTTTATCTAATTTTTAGA
Found at i:19825159 original size:5 final size:5
Alignment explanation
Indices: 19825149--19825177 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
19825139 TATCTTGTAA
19825149 AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGAT
19825178 ATGACATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:19836769 original size:91 final size:91
Alignment explanation
Indices: 19836614--19836785 Score: 292
Period size: 91 Copynumber: 1.9 Consensus size: 91
19836604 GTATAAGATA
*
19836614 AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAATCCAAAA
1 AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAAA
*
19836679 TTCCCCAAAATTCACAGAATTCCCTT
66 TTCCCCAAAACTCACAGAATTCCCTT
* *
19836705 AAGATAATCTCAACAAATAAA-TCTGAAATCTCGAAAGAACAAAGTACTCTAACTAAAACCCAAA
1 AAGATAATCTCAACAAATAAACCCT-AAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAA
19836769 ATTCCCCAAAACTCACA
65 ATTCCCCAAAACTCACA
19836786 AAACTCTCTT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 2 0.03
91 74 0.97
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.20
Consensus pattern (91 bp):
AAGATAATCTCAACAAATAAACCCTAAATCTCGAAAGAACAAAGTACTCTAAATAAAACCCAAAA
TTCCCCAAAACTCACAGAATTCCCTT
Found at i:19838010 original size:4 final size:4
Alignment explanation
Indices: 19838001--19838032 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
19837991 TTAAGCCATG
19838001 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
19838033 TGCATGCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:19838363 original size:6 final size:6
Alignment explanation
Indices: 19838352--19838377 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19838342 TTGCATCACC
19838352 CTGTCT CTGTCT CTGTCT CTGTCT CT
1 CTGTCT CTGTCT CTGTCT CTGTCT CT
19838378 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:19843907 original size:22 final size:23
Alignment explanation
Indices: 19843878--19843952 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
19843868 ACTAACCCTT
* *
19843878 TCTCAAATTTCATCTCATTTTCC
1 TCTCAAATTTCATCTCAATTTAC
*
19843901 TCT-AAATTTCCTCTCAATTTAC
1 TCTCAAATTTCATCTCAATTTAC
* *
19843923 TCTCAAATTCCTTC-CAAATTT-C
1 TCTCAAATTTCATCTC-AATTTAC
19843945 TCTCAAAT
1 TCTCAAAT
19843953 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:19843951 original size:11 final size:11
Alignment explanation
Indices: 19843878--19843952 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
19843868 ACTAACCCTT
19843878 TCTCAAATTTC
1 TCTCAAATTTC
*
19843889 ATCTC-ATTTTC
1 -TCTCAAATTTC
19843900 -CTCTAAATTTCC
1 TCTC-AAATTT-C
19843912 TCTC-AATTTAC
1 TCTCAAATTT-C
*
19843923 TCTCAAATTCC
1 TCTCAAATTTC
19843934 T-TCCAAATTTC
1 TCT-CAAATTTC
19843945 TCTCAAAT
1 TCTCAAAT
19843953 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:19845156 original size:7 final size:7
Alignment explanation
Indices: 19845144--19845176 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
19845134 TAGCCGATTG
19845144 GTATTTA
1 GTATTTA
19845151 GTATTTA
1 GTATTTA
19845158 GTATTTA
1 GTATTTA
19845165 GTATTTA
1 GTATTTA
19845172 GTATT
1 GTATT
19845177 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:19845854 original size:18 final size:18
Alignment explanation
Indices: 19845827--19845866 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19845817 CAGGTGCGTT
* *
19845827 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
19845845 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
19845863 TCCT
1 TCCT
19845867 TTTTTGAGTC
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:19846435 original size:15 final size:13
Alignment explanation
Indices: 19846409--19846468 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 13
19846399 TTAATTGACA
*
19846409 AACCTTAAACCCTT
1 AACCTAAAACCC-T
19846423 AACCTAAAAACCCT
1 AACCT-AAAACCCT
19846437 AACCCT-AAACCCTT
1 AA-CCTAAAACCC-T
19846451 AACCTGAAAACCCT
1 AACCT-AAAACCCT
19846465 AACC
1 AACC
19846469 CTTAACTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 9 0.22
14 16 0.40
15 15 0.38
ACGTcount: A:0.42, C:0.38, G:0.02, T:0.18
Consensus pattern (13 bp):
AACCTAAAACCCT
Found at i:19846449 original size:28 final size:28
Alignment explanation
Indices: 19846409--19846470 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
19846399 TTAATTGACA
*
19846409 AACCTTAAACCCTTAACCTAAAAACCCT
1 AACCCTAAACCCTTAACCTAAAAACCCT
*
19846437 AACCCTAAACCCTTAACCTGAAAACCCT
1 AACCCTAAACCCTTAACCTAAAAACCCT
19846465 AACCCT
1 AACCCT
19846471 TAACTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.39, G:0.02, T:0.19
Consensus pattern (28 bp):
AACCCTAAACCCTTAACCTAAAAACCCT
Found at i:19846489 original size:43 final size:43
Alignment explanation
Indices: 19846437--19847209 Score: 618
Period size: 43 Copynumber: 18.0 Consensus size: 43
19846427 TAAAAACCCT
* *
19846437 AACCCTAAACCCTTAACCTGAAAACCCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
19846480 AACCATAAACCCTTAACCTAAAAACCATAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * * * *
19846524 AACCCTAACCCTTAACCCTTAACTTAAAAATCATAAACTCTTAACCTACA
1 AACCCT-A-----AACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
*
19846574 AACTCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * * *
19846617 AATCATAAAGCCTTAACTTAAAAACTCTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * **
19846660 AACCCTAAATCCTTAACTTAAAAACCGTAACCCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
** * ** * * *
19846703 AATTCTAAACCCTTAACTTTAAAACTGTAACCTTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * *
19846746 AACCCT-AACACC-TAATTTAAAAACACTAACCTTTAACCTAAA
1 AACCCTAAAC-CCTTAACTTAAAAACCCTAACCCTTAACTTAAA
19846788 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * *
19846831 AACCATAAACCCTTAACTT-AAAACCCTAAACTCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
19846874 AACCCT-AACTCTTAACTT-AAAACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* *
19846916 AACCCTTAA--CTTAA--AAACCCTAAACCCTTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAA----AAACCC-TAACCCTTAACTTAAA
* * **
19846960 AACCCTAAACCCTTAACTTAAAAACCATAACTCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *** * *
19847003 AACCCTAAACCCTTAACTTTAAAATAATAACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* ***
19847046 AACCAT-AACCCTTAACTTAAAAATTATAAACCCTTAAGC-T---
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAA-CTTAAA
*
19847086 -A----AAACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * *** ** * *
19847125 AACCCTAAACCATTAACTTTAAAATTGTAAATCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
19847168 AACCCT-AACACTTAACTTTAAAACCCTAACCCTAAACTTAAA
1 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
19847210 TATAATTTGA
Statistics
Matches: 599, Mismatches: 96, Indels: 71
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.00
36 28 0.05
39 1 0.00
40 2 0.00
41 7 0.01
42 133 0.22
43 280 0.47
44 101 0.17
45 2 0.00
46 5 0.01
48 2 0.00
50 37 0.06
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (43 bp):
AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
Found at i:19846589 original size:21 final size:22
Alignment explanation
Indices: 19846437--19847209 Score: 636
Period size: 22 Copynumber: 36.0 Consensus size: 22
19846427 TAAAAACCCT
* *
19846437 AACCCTAAACCCTTAACCTGAA
1 AACCCTAAACCCTTAACTTAAA
19846459 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19846480 AACCATAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846502 AACCATAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19846524 AACCCTAACCCTTAACCCTTAACTTAAA
1 AACCCT-A-----AACCCTTAACTTAAA
* * * * *
19846552 AATCATAAACTCTTAACCTACA
1 AACCCTAAACCCTTAACTTAAA
*
19846574 AACTCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19846595 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* * *
19846617 AATCATAAAGCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846639 AACTCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846660 AACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* **
19846682 AACCGT-AACCCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAA
** *
19846703 AATTCTAAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
** * * *
19846725 AACTGT-AACCTTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846746 AACCCT-AACACC-TAATTTAAA
1 AACCCTAAAC-CCTTAACTTAAA
* * *
19846767 AACACT-AACCTTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
19846788 AACCCT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19846809 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846831 AACCATAAACCCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
* *
19846852 AACCCTAAACTCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19846874 AACCCT-AACTCTTAACTT-AA
1 AACCCTAAACCCTTAACTTAAA
*
19846894 AACCCTAAACCCTTAACCTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19846916 AACCCTTAA--CTTAA--AAACCCTA
1 AACCCTAAACCCTTAACTTAA----A
*
19846938 AACCCTTAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19846960 AACCCTAAACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* * **
19846982 AACCAT-AACTCTTAAAATAAA
1 AACCCTAAACCCTTAACTTAAA
*
19847003 AACCCTAAACCCTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*** * *
19847025 AATAAT-AACCCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
*
19847046 AACCAT-AACCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
***
19847067 AATTATAAACCCTTAAGC-T-AA
1 AACCCTAAACCCTTAA-CTTAAA
19847088 AACCCT------T-AACTTAAA
1 AACCCTAAACCCTTAACTTAAA
*
19847103 AACCCTAAATCCTTAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19847125 AACCCTAAACCATTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*** * * *
19847147 AATTGTAAA-TCTTAAATAAAA
1 AACCCTAAACCCTTAACTTAAA
* *
19847168 AACCCT-AACACTTAACTTTAA
1 AACCCTAAACCCTTAACTTAAA
*
19847189 AACCCT-AACCCTAAACTTAAA
1 AACCCTAAACCCTTAACTTAAA
19847210 TATAATTTGA
Statistics
Matches: 603, Mismatches: 111, Indels: 75
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.00
14 3 0.00
15 9 0.01
18 2 0.00
20 16 0.03
21 264 0.44
22 279 0.46
23 2 0.00
24 5 0.01
26 2 0.00
27 1 0.00
28 19 0.03
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (22 bp):
AACCCTAAACCCTTAACTTAAA
Found at i:19846795 original size:128 final size:128
Alignment explanation
Indices: 19846437--19847082 Score: 468
Period size: 128 Copynumber: 5.0 Consensus size: 128
19846427 TAAAAACCCT
* * * * * *
19846437 AACCCTAAACCCTTAACCTGAAAACCCT-AACCCTTAACTTAAAAACCATAA-ACCCTTAACCTA
1 AACCATAAACCCTTAA-CTTAAAACCCTAAACTCTTAACATAAAAACCCTAACA-CC-TAACTTA
* * * *
19846500 AAAAC-CATAAACCCTTAACTTAAAAACCCTAACCCTTAACCCTTAACTTAAAAATCATAAACTC
63 AAAACAC-T-AACCCTTAACCT--AAA----AACCC-TAACCCTTAACTTAAAAACCCTAAACCC
** *
19846564 TTAACCTACA
119 TTAAAATAAA
* * * *
19846574 AACTC-T-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAATCATAA-AGCCTTAACTT
1 AAC-CATAAACCCTTAACTT-AAAACCCTAAACTCTTAACATAAAAACCCTAACA-CC-TAACTT
* * * *
19846636 AAAAACTCTAACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAAAACCGT-AACCCTTAAAAT
62 AAAAACACTAACCCTTAACCTAAAAACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAAAAT
19846700 AAA
126 AAA
* ** * *
19846703 AATTC-TAAACCCTTAACTTTAAAACTGTAACCT-TTAA-ATAAAAAACCCTAACACCTAATTTA
1 AA-CCATAAACCCTTAAC-TTAAAACCCTAAACTCTTAACAT-AAAAACCCTAACACCTAACTTA
* **
19846765 AAAACACTAACCTTTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
63 AAAACACTAACCCTTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAATAA
19846830 A
128 A
* * *
19846831 AACCATAAACCCTTAACTTAAAACCCTAAACTCTTAACCTAAAAACCCTAACTCTTAACTT-AAA
1 AACCATAAACCCTTAACTTAAAACCCTAAACTCTTAACATAAAAACCCTAACACCTAACTTAAAA
*
19846895 ACCCTAAACCCTTAACCT--AAA----AACCCTTAACTTAAAAACCCTAAACCCTTAACCCTTAA
66 ACACT-AACCCTTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAA-----AA
19846954 CTTAAA
125 --TAAA
* * * *
19846960 AACCCTAAACCCTTAACTTAAAAACC-ATAACTCTTAAAATAAAAACCCTAA-ACCCTTAACTTT
1 AACCATAAACCCTTAACTTAAAACCCTA-AACTCTTAACATAAAAACCCTAACA-CC-TAACTTA
* * * * ***
19847023 AAAATAATAACCCTTAA-ATAAAAAACCATAACCCTTAACTTAAAAATTATAAACCCTTAA
63 AAAACACTAACCCTTAACCT-AAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAA
19847083 GCTAAAACCC
Statistics
Matches: 424, Mismatches: 52, Indels: 67
0.78 0.10 0.12
Matches are distributed among these distances:
122 31 0.07
126 3 0.01
127 39 0.09
128 94 0.22
129 83 0.20
130 58 0.14
131 7 0.02
132 3 0.01
134 3 0.01
135 2 0.00
136 57 0.13
137 42 0.10
138 2 0.00
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (128 bp):
AACCATAAACCCTTAACTTAAAACCCTAAACTCTTAACATAAAAACCCTAACACCTAACTTAAAA
ACACTAACCCTTAACCTAAAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAAAATAAA
Found at i:19846951 original size:29 final size:29
Alignment explanation
Indices: 19846916--19846976 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
19846906 TTAACCTAAA
19846916 AACCCTTAACTTAAAAACCCTAAACCCTT
1 AACCCTTAACTTAAAAACCCTAAACCCTT
19846945 AACCCTTAACTTAAAAACCCTAAACCCTT
1 AACCCTTAACTTAAAAACCCTAAACCCTT
19846974 AAC
1 AAC
19846977 TTAAAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.23
Consensus pattern (29 bp):
AACCCTTAACTTAAAAACCCTAAACCCTT
Found at i:19846984 original size:15 final size:15
Alignment explanation
Indices: 19846900--19846965 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
19846890 TTAAAACCCT
*
19846900 AAACCCTTAACCTAA
1 AAACCCTTAACTTAA
19846915 AAACCCTTAACTTAA
1 AAACCCTTAACTTAA
*
19846930 AAACCCTAAACCCTT--
1 AAACCCTTAA--CTTAA
19846945 -AACCCTTAACTTAA
1 AAACCCTTAACTTAA
19846959 AAACCCT
1 AAACCCT
19846966 AAACCCTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 3 0.07
14 8 0.19
15 29 0.67
17 3 0.07
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCCTTAACTTAA
Found at i:19847125 original size:36 final size:37
Alignment explanation
Indices: 19847052--19847130 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 37
19847042 AAAAAACCAT
**
19847052 AACCCTTAACTTAAAAATTATAAACCCTTAAGCT-AA
1 AACCCTTAACTTAAAAACCATAAACCCTTAAGCTAAA
* *
19847088 AACCCTTAACTTAAAAACCCTAAATCCTTAA-CTTAAA
1 AACCCTTAACTTAAAAACCATAAACCCTTAAGC-TAAA
19847125 AACCCT
1 AACCCT
19847131 AAACCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 1 0.03
36 28 0.76
37 8 0.22
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.27
Consensus pattern (37 bp):
AACCCTTAACTTAAAAACCATAAACCCTTAAGCTAAA
Found at i:19847134 original size:58 final size:57
Alignment explanation
Indices: 19847031--19847140 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 57
19847021 TTAAAATAAT
** *
19847031 AACCCTTAAATAAAAAACCATAACCCTTAACTTAAAAATTATAAACCCTTAAGCTAA
1 AACCCTTAAATAAAAAACCATAACCCTTAACTTAAAAACCATAAACCATTAAGCTAA
* * * * *
19847088 AACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAAAACCCTAAACCATTAA
1 AACCCTTAAATAAAAAACCAT-AACCCTTAACTTAAAAACCATAAACCATTAA
19847141 CTTTAAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
57 18 0.41
58 26 0.59
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (57 bp):
AACCCTTAAATAAAAAACCATAACCCTTAACTTAAAAACCATAAACCATTAAGCTAA
Found at i:19847146 original size:122 final size:121
Alignment explanation
Indices: 19846966--19847190 Score: 333
Period size: 122 Copynumber: 1.9 Consensus size: 121
19846956 TAAAAACCCT
* *
19846966 AAACCCTTAACTTAAAAACCATAACTCTTAAAATAAAAACCCTAAACCCTTAACTTTAAAATAAT
1 AAACCCTTAACTTAAAAACCATAAATCTTAAAATAAAAACCCTAAACCATTAACTTTAAAATAAT
* *
19847031 AACCCTTAAATAAAAAACCATAACCCTTAACTTAAAAATTATAAACCCTTAAGCTA
66 AAACCTTAAATAAAAAACCATAACACTTAACTTAAAAATTATAAACCCTTAAGCTA
* ** **
19847087 AAACCCTTAACTTAAAAACCCTAAATCCTTAACTTAAAAACCCTAAACCATTAACTTTAAAATTG
1 AAACCCTTAACTTAAAAACCATAAAT-CTTAAAATAAAAACCCTAAACCATTAACTTTAAAATAA
* * *
19847152 TAAATCTTAAATAAAAAACCCTAACACTTAACTTTAAAA
65 TAAACCTTAAATAAAAAACCATAACACTTAACTTAAAAA
19847191 CCCTAACCCT
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
121 24 0.26
122 67 0.74
ACGTcount: A:0.50, C:0.23, G:0.01, T:0.27
Consensus pattern (121 bp):
AAACCCTTAACTTAAAAACCATAAATCTTAAAATAAAAACCCTAAACCATTAACTTTAAAATAAT
AAACCTTAAATAAAAAACCATAACACTTAACTTAAAAATTATAAACCCTTAAGCTA
Found at i:19850641 original size:126 final size:125
Alignment explanation
Indices: 19850369--19850811 Score: 565
Period size: 126 Copynumber: 3.5 Consensus size: 125
19850359 CCCAAACATG
* *
19850369 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAACATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
* * * * *** * *
19850434 TAGAAGC--GATTTTATACTATTTACTTAGAAATACCAAGTCGAAATTATTTTTCCAGGAC
66 TTGCAGCTTG-TTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
19850493 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
* *
19850557 CTTGCAGCATTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAT
65 CTTGCAGC-TTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
19850619 CTACTGTAGCAAATGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
* *
19850683 CTTGCAGCGCTT-TTTTATACTATTTGCTCAGAAACGTTAACTCGAAATTATTTTTTTAGGAC
65 CTTGCA--GCTTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * * * * *
19850745 CTACTGTAGCAAAAGCGCGTACAC-ATGGGCACGACTTCAAAAATCCTTCTCATAAATCATCCTA
1 CTACTGTAGCAAAAGCGCGTCCACGA-GGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTA
19850809 CTT
65 CTT
19850812 TAATTTTATC
Statistics
Matches: 282, Mismatches: 29, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
123 2 0.01
124 65 0.23
126 208 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:19850957 original size:10 final size:9
Alignment explanation
Indices: 19850935--19850972 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
19850925 TTTTTTCTCC
19850935 AAAAACCCT
1 AAAAACCCT
*
19850944 AAAAATCCT
1 AAAAACCCT
19850953 AAAAACCCT
1 AAAAACCCT
*
19850962 AAAAAACCT
1 AAAAACCCT
19850971 AA
1 AA
19850973 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:19850958 original size:18 final size:18
Alignment explanation
Indices: 19850935--19850972 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
19850925 TTTTTTCTCC
*
19850935 AAAAACCCTAAAAATCCT
1 AAAAACCCTAAAAAACCT
19850953 AAAAACCCTAAAAAACCT
1 AAAAACCCTAAAAAACCT
19850971 AA
1 AA
19850973 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:19851105 original size:40 final size:40
Alignment explanation
Indices: 19851061--19851139 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
19851051 TGACGTAGAC
* * * *
19851061 ACAAATCGCGTTTACGTGGACGCGATTTTCTGCCACGTCA
1 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTCA
19851101 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTC
1 ACAAAACGCGTTGACGTGGACGCGATTTGCTGACACGTC
19851140 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:19851521 original size:16 final size:16
Alignment explanation
Indices: 19851500--19851551 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
19851490 TTCTTTTAAT
19851500 TTTATTTAAATTTTTA
1 TTTATTTAAATTTTTA
**
19851516 TTTATTTTTATTTTTA
1 TTTATTTAAATTTTTA
19851532 TAATT-TTTAAATTATTTA
1 T--TTATTTAAATT-TTTA
19851550 TT
1 TT
19851552 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:19852018 original size:23 final size:23
Alignment explanation
Indices: 19851983--19852039 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
19851973 AAATAAATAT
*
19851983 TTTATATTTAAAATAATTAATAAA
1 TTTATA-TAAAAATAATTAATAAA
* **
19852007 TTTATATAAAAATTATTTTTAAA
1 TTTATATAAAAATAATTAATAAA
19852030 TATTATATAA
1 T-TTATATAA
19852040 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:19852035 original size:24 final size:23
Alignment explanation
Indices: 19852003--19852048 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
19851993 AAATAATTAA
19852003 TAAATTTATATAAAAATTATTTT
1 TAAATTTATATAAAAATTATTTT
* *
19852026 TAAATATTATATAACATTTATTT
1 TAAAT-TTATATAAAAATTATTT
19852049 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:19853044 original size:12 final size:12
Alignment explanation
Indices: 19853027--19853052 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19853017 TCTTAATTAA
19853027 TTCCTAAATATT
1 TTCCTAAATATT
19853039 TTCCTAAATATT
1 TTCCTAAATATT
19853051 TT
1 TT
19853053 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:19870317 original size:46 final size:46
Alignment explanation
Indices: 19870265--19870416 Score: 205
Period size: 46 Copynumber: 3.1 Consensus size: 46
19870255 GAACCAGAAG
19870265 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTAA
1 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTAA
19870311 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTGCAGAACCAGAAA
1 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATT-----------AA
19870368 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTAA
1 ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTAA
19870414 ATT
1 ATT
19870417 GATTCTTAGA
Statistics
Matches: 95, Mismatches: 0, Indels: 22
0.81 0.00 0.19
Matches are distributed among these distances:
46 49 0.52
57 46 0.48
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (46 bp):
ATTCTTTAATTTAAAGGATTCTCATTTGTTGCTTGTTCTCAATTAA
Found at i:19872984 original size:7 final size:7
Alignment explanation
Indices: 19872972--19873023 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
19872962 CAGAGAGAGA
19872972 GAGCATG
1 GAGCATG
19872979 GAGCATG
1 GAGCATG
19872986 GAGCATG
1 GAGCATG
19872993 GAGCATG
1 GAGCATG
*
19873000 GAGCACG
1 GAGCATG
*
19873007 GAGCACG
1 GAGCATG
19873014 GAGCATG
1 GAGCATG
19873021 GAG
1 GAG
19873024 GGCGTTAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.29, C:0.17, G:0.44, T:0.10
Consensus pattern (7 bp):
GAGCATG
Found at i:19873255 original size:22 final size:21
Alignment explanation
Indices: 19873225--19873266 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19873215 AAAGTATTAT
* *
19873225 TTTAGTTTTTACTATTTTTTAC
1 TTTAATTTTTAAT-TTTTTTAC
19873247 TTTAATTTTTAATTTTTTTA
1 TTTAATTTTTAATTTTTTTA
19873267 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:19877771 original size:17 final size:17
Alignment explanation
Indices: 19877749--19877782 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19877739 AATAGCAAGC
*
19877749 AAAAAAAGGGAAAAAAG
1 AAAAAAACGGAAAAAAG
*
19877766 AAAAAAACGGAGAAAAG
1 AAAAAAACGGAAAAAAG
19877783 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:19878561 original size:3 final size:3
Alignment explanation
Indices: 19878553--19878653 Score: 80
Period size: 3 Copynumber: 33.7 Consensus size: 3
19878543 TATTTTAGTT
* * * * *
19878553 TTA TTA TTA TTA TTA TTA TTA ATG CTG TTA -TA TT- GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
19878599 CTGTA TTA TTA TTA GTA TTA TTA TTT TTA TTT TTA TTG CTA TTA TTA
1 -T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19878646 TTA TTA TT
1 TTA TTA TT
19878654 TCAATACATA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
2 3 0.04
3 70 0.91
4 2 0.03
5 2 0.03
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19878847 original size:25 final size:23
Alignment explanation
Indices: 19878792--19878847 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
19878782 TATATATACG
19878792 TATATACATTTATATTTTTATAA
1 TATATACATTTATATTTTTATAA
19878815 TATTTATACATTT-TCCATATTTTATAA
1 TA--TATACATTTAT--AT-TTTTATAA
19878842 TATATA
1 TATATA
19878848 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:19885575 original size:19 final size:19
Alignment explanation
Indices: 19885553--19885592 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
19885543 TAAAAAAAAC
*
19885553 AGAGAAGAACAAAAAAGAG
1 AGAGAAAAACAAAAAAGAG
* *
19885572 AGAGAAAAAGAAAAAGGAG
1 AGAGAAAAACAAAAAAGAG
19885591 AG
1 AG
19885593 GCCAAGGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (19 bp):
AGAGAAAAACAAAAAAGAG
Found at i:19887316 original size:45 final size:43
Alignment explanation
Indices: 19887130--19887316 Score: 127
Period size: 45 Copynumber: 4.3 Consensus size: 43
19887120 GACAAAAGAA
* * *
19887130 ACCA-ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAAA
1 ACCAGATCTTATCTCCCTGAAGTTGCAGTAGAGT-GATTAAAAC
* * * * * *
19887173 ATACAGATCTTATCT-TCTGAGGTTGCAG-AGAGCAGA-TCATA-
1 A-CCAGATCTTATCTCCCTGAAGTTGCAGTAGAG-TGATTAAAAC
* * *
19887214 TCTAG-TCTTA-CTTCCCTGAAGTTGCAGTGGAGTAGATTAAAAC
1 ACCAGATCTTATC-TCCCTGAAGTTGCAGTAGAGT-GATTAAAAC
* *
19887257 ATCCAAATCATATCTCCCTGAAGTTGCAGTAGAGTGTATTAAAAC
1 A-CCAGATCTTATCTCCCTGAAGTTGCAGTAGAGTG-ATTAAAAC
19887302 ACACAGATCTTATCT
1 AC-CAGATCTTATCT
19887317 TTCTGAGGTT
Statistics
Matches: 106, Mismatches: 24, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
38 1 0.01
39 6 0.06
40 13 0.12
41 5 0.05
42 6 0.06
43 6 0.06
44 17 0.16
45 51 0.48
46 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
ACCAGATCTTATCTCCCTGAAGTTGCAGTAGAGTGATTAAAAC
Found at i:19887370 original size:130 final size:130
Alignment explanation
Indices: 19887133--19887554 Score: 595
Period size: 130 Copynumber: 3.3 Consensus size: 130
19887123 AAAAGAAACC
*
19887133 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAAAATACAGATCTTATC-TTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
19887197 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
66 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
* * * *
19887262 AATCATATCTCCCTGAAGTTGCAGTAGAGTGTATTAAAACACACAGATCTTATCTTTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
* * *
19887327 GTAGAGCGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCATCCA
66 GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
** * * *
19887392 AATCCTATCTCTTTGAAGTGGCAGTGGAGTGGATTAAAACATTCAGATCTTATTTTTCTGAGGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
* ** *
19887457 ACAGAGAGCAGATC-TCATCTAGTCTTA-TCTCCCTGAAGTTGCAGTGGAACAGA-CAAAGGA-A
66 GCAGAGAGCAGATCAT-ATCTAGTCTTACT-TCCCTGAAGTTGCAGTGGAGTAGATTAAA--ACA
*
19887518 ACC-
127 TCCA
*
19887521 AATCCTATCTCCCTGATGTTGCAGTGGAGTGGAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
19887555 CGAAGCACTA
Statistics
Matches: 259, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
129 84 0.32
130 175 0.68
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (130 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATACAGATCTTATCTTTCTGAGGTT
GCAGAGAGCAGATCATATCTAGTCTTACTTCCCTGAAGTTGCAGTGGAGTAGATTAAAACATCCA
Found at i:19888790 original size:3 final size:3
Alignment explanation
Indices: 19888782--19888873 Score: 71
Period size: 3 Copynumber: 30.7 Consensus size: 3
19888772 TATTTTAGTT
* * *
19888782 TTA TTA TTA TTA TTA ATA TTG TTA -TA TT- GTA TTA TTA TTA CTGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -T-TA
* * * * * *
19888827 TTA 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 TTA TT
19888874 TCAATACATA
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
2 3 0.04
3 61 0.90
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:19888829 original size:39 final size:39
Alignment explanation
Indices: 19888786--19888873 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
19888776 TTAGTTTTAT
*
19888786 TATTATTATTAATATTGTTATATTGTATTATTATTACT-G
1 TATTATTATTAATATTATTAT-TTGTATTATTATTACTAG
* * * *
19888825 TATTATTATTAGTATTATTATTTTTATTTTTATTGCTAG
1 TATTATTATTAATATTATTATTTGTATTATTATTACTAG
19888864 TATTATTATT
1 TATTATTATT
19888874 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):
TATTATTATTAATATTATTATTTGTATTATTATTACTAG
Found at i:19889066 original size:25 final size:23
Alignment explanation
Indices: 19889011--19889066 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
19889001 TATATATACG
19889011 TATATACATTTATATTTTTATAA
1 TATATACATTTATATTTTTATAA
19889034 TATTTATACATTT-TCCATATTTTATAA
1 TA--TATACATTTAT--AT-TTTTATAA
19889061 TATATA
1 TATATA
19889067 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:19889411 original size:21 final size:21
Alignment explanation
Indices: 19889373--19889412 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19889363 TCTTTGTTGT
*
19889373 TGTTTTGTTTGGTGTATTTCA
1 TGTTTTGTTTGGTATATTTCA
* *
19889394 TGTTTTTTTTTGTATATTT
1 TGTTTTGTTTGGTATATTT
19889413 ATACATATCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.03, G:0.17, T:0.70
Consensus pattern (21 bp):
TGTTTTGTTTGGTATATTTCA
Found at i:19890323 original size:30 final size:30
Alignment explanation
Indices: 19890268--19890324 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19890258 TTTATAATAT
* *
19890268 TAAAAATATATATGTATATTTAAAAATTAA
1 TAAAAATATATATGTATAATAAAAAATTAA
19890298 TAAAAATATATAATG-ATAATAAAAAAT
1 TAAAAATATAT-ATGTATAATAAAAAAT
19890325 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:19897313 original size:21 final size:21
Alignment explanation
Indices: 19897284--19897323 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19897274 TACCCTTTTT
* *
19897284 TTATGTTTTAACTTTTATTCA
1 TTATATTTTAACATTTATTCA
19897305 TTATATTTTAACATTTATT
1 TTATATTTTAACATTTATT
19897324 AAATAATTTA
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:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTATATTTTAACATTTATTCA
Found at i:19903328 original size:28 final size:27
Alignment explanation
Indices: 19903272--19903327 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
19903262 AATATCCTAC
19903272 TTAATTAATTACTAATAAATTTTATTT
1 TTAATTAATTACTAATAAATTTTATTT
* *
19903299 TTAATTTAATTACTAGT-ATTTTTATTT
1 TTAA-TTAATTACTAATAAATTTTATTT
19903326 TT
1 TT
19903328 TTTTAAAAAA
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:19904220 original size:21 final size:21
Alignment explanation
Indices: 19904194--19904234 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19904184 ATCCGTTTTC
19904194 TATGTT-TATAATAGATTATAT
1 TATGTTATAT-ATAGATTATAT
*
19904215 TATGTTATATATATATTATA
1 TATGTTATATATAGATTATA
19904235 ATTTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TATGTTATATATAGATTATAT
Found at i:19915497 original size:22 final size:19
Alignment explanation
Indices: 19915467--19915510 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
19915457 GCTAAGGGTT
19915467 TTAAAGACTCAATTTAGGATAA
1 TTAAAGACT-AA-TTA-GATAA
*
19915489 TTAATGACTAATTAGATAA
1 TTAAAGACTAATTAGATAA
19915508 TTA
1 TTA
19915511 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:19924004 original size:40 final size:40
Alignment explanation
Indices: 19923952--19924181 Score: 318
Period size: 40 Copynumber: 5.8 Consensus size: 40
19923942 ATAACCACAA
* * * *
19923952 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19923992 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCATCTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
19924032 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
19924072 GCACTAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* * *
19924112 GCACAAATGCCTTCAGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
19924152 GCATAAATGCCTTCGGGACTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
19924182 GTATTCAAAT
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 168 0.98
41 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:19926843 original size:25 final size:26
Alignment explanation
Indices: 19926772--19926872 Score: 125
Period size: 26 Copynumber: 3.9 Consensus size: 26
19926762 ACATATTTTC
*
19926772 TCAAAATTTTACTAGGGGTAAAATTG
1 TCAAAATTTTACTAGGGGTAAAATCG
* *
19926798 TCAAAATTTTA-TTGAGAGTAAAATCG
1 TCAAAATTTTACTAG-GGGTAAAATCG
* *
19926824 TTAAAA-TTTATTAGGGGTAAAATCG
1 TCAAAATTTTACTAGGGGTAAAATCG
*
19926849 TCAAAATTTTACTAGGGATAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
19926873 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:19926871 original size:51 final size:52
Alignment explanation
Indices: 19926774--19926872 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
19926764 ATATTTTCTC
* *
19926774 AAAATTTTACTAGGGGTAAAATTGTCAAAATTTTATTGAGAGTAAAATCGTT
1 AAAATTTTACTAGGGGTAAAATCGTCAAAATTTTATAGAGAGTAAAATCGTT
* *
19926826 AAAA-TTTATTAGGGGTAAAATCGTCAAAATTTTACTAGGGA-TAAAAT
1 AAAATTTTACTAGGGGTAAAATCGTCAAAATTTTA-TAGAGAGTAAAAT
19926873 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:19928215 original size:6 final size:7
Alignment explanation
Indices: 19928202--19928232 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
19928192 TAAAAATTAC
19928202 CAAAAAA
1 CAAAAAA
19928209 C-AAAAA
1 CAAAAAA
19928215 CAAAAAA
1 CAAAAAA
19928222 CAAAAAA
1 CAAAAAA
19928229 CAAA
1 CAAA
19928233 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:19935434 original size:9 final size:9
Alignment explanation
Indices: 19935417--19935453 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
19935407 TGAGTTTTCG
19935417 AATTCGAAT
1 AATTCGAAT
*
19935426 AACTCGAAT
1 AATTCGAAT
19935435 AATTCGAAT
1 AATTCGAAT
19935444 AATTCGAAT
1 AATTCGAAT
19935453 A
1 A
19935454 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:19939122 original size:44 final size:44
Alignment explanation
Indices: 19939069--19939155 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
19939059 GTAGGTTAAA
*
19939069 TAATATTAAAATAATCTACACTAATCAGAATTTAAGTGAGAAAT
1 TAATATTAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAT
* * *
19939113 TAATATTAAAATAACCTACACTAATCAGAGTTTCAGTGGGAAA
1 TAATATTAAAATAACCTACACTAATCAGAATTTAAGTGAGAAA
19939156 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:19941414 original size:25 final size:25
Alignment explanation
Indices: 19941309--19941421 Score: 158
Period size: 25 Copynumber: 4.6 Consensus size: 25
19941299 ATACATGTAT
*
19941309 GCTCATACGAGCT--GTAAACGGGAA
1 GCTCATACGAGCTGAGT-ATCGGGAA
*
19941333 GCTCATGCGAGCTGAGTATCGGGAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19941358 GCTCATGCGAGCTGAGTATCGGGAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19941383 GCTCATACGAGCTGAGTATCGGAAA
1 GCTCATACGAGCTGAGTATCGGGAA
*
19941408 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
19941422 TTGTGTGTCC
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
24 12 0.15
25 68 0.83
26 2 0.02
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.19
Consensus pattern (25 bp):
GCTCATACGAGCTGAGTATCGGGAA
Found at i:19943791 original size:44 final size:44
Alignment explanation
Indices: 19943727--19943817 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
19943717 GTAGGTCAAA
*
19943727 TAATATTAAACTAACCTACACTAATCAAAGTTTAAGTGGGAAAT
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
* *
19943771 TAATATTAAAATAACTTACACTAATCAGAGTTTAAGTGGGAAAT
1 TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
19943815 TAA
1 TAA
19943818 AAATATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAAAGTTTAAGTGGGAAAT
Found at i:19946952 original size:19 final size:19
Alignment explanation
Indices: 19946930--19946966 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19946920 ACCACTGTCA
19946930 TCCACCGTAATAAAATTTG
1 TCCACCGTAATAAAATTTG
* *
19946949 TCCACTGTAATCAAATTT
1 TCCACCGTAATAAAATTT
19946967 TTTATTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (19 bp):
TCCACCGTAATAAAATTTG
Found at i:19954318 original size:24 final size:24
Alignment explanation
Indices: 19954271--19954321 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
19954261 AAGGAGCCTA
* *
19954271 TAACGGGTAGCTCTAAAGAGCAAT
1 TAACGGGTAGCTCCAAAGACCAAT
* *
19954295 TAACGGGTAGCTCCGAATACCAAT
1 TAACGGGTAGCTCCAAAGACCAAT
19954319 TAA
1 TAA
19954322 TGGGAAGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGACCAAT
Found at i:19958801 original size:41 final size:41
Alignment explanation
Indices: 19958756--19958932 Score: 135
Period size: 41 Copynumber: 4.3 Consensus size: 41
19958746 CAGATTTACT
**
19958756 GGCACTTCA-CCTGATAGGCTTATAGTTTAATTCAGTTCACC
1 GGCACTT-AGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
* * *
19958797 GGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACC
1 GGCACTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
* * * * * * *
19958838 GGCACTTAGCTTGCTAGACGTATAGTCC-GATTCAATTCACA
1 GGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACC
* * * * * * *
19958879 GGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCATC
1 GGCACTTAGCCTGATAGGCTTATAG-CCTAATTCAGTTCACC
19958920 GGCACTTAGCCTG
1 GGCACTTAGCCTG
19958933 CTAGACGTAT
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
40 1 0.01
41 115 0.97
42 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (41 bp):
GGCACTTAGCCTGATAGGCTTATAGCCTAATTCAGTTCACC
Found at i:19958933 original size:41 final size:41
Alignment explanation
Indices: 19958785--19958946 Score: 227
Period size: 41 Copynumber: 4.0 Consensus size: 41
19958775 TTATAGTTTA
* * * *
19958785 ATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTGTAG-CCTG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCC-G
* *
19958826 ATTCAGTTCACCGGCACTTAGCTTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
* *
19958867 ATTCAATTCACAGGCATTTAGCCTGCTAGACGTATAGTCCG
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
*
19958908 ATTCAATTCATCGGCACTTAGCCTGCTAGACGTATAGTC
1 ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTC
19958947 TGAATAATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 107 0.98
42 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
ATTCAATTCACCGGCACTTAGCCTGCTAGACGTATAGTCCG
Found at i:19958959 original size:82 final size:82
Alignment explanation
Indices: 19958791--19958964 Score: 217
Period size: 82 Copynumber: 2.1 Consensus size: 82
19958781 TTTAATTCAG
* * * * * *
19958791 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCAGTTCACCGGCACTTAGCTTGCTAGA
1 TTCACAGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
*
19958856 CGTATAGTCCGATTCAA
66 CGTATAGTCCGAATCAA
* *
19958873 TTCACAGGCATTTAGCCTGCTAGACGTATAGTCC-GATTCAATTCATCGGCACTTAGCCTGCTAG
1 TTCACAGGCACTTAGCCTGCTAGACGTATAG-CCTGATTCAATTCACCGGCACTTAGCCTGCTAG
*
19958937 ACGTATAGTCTGAAT-AA
65 ACGTATAGTCCGAATCAA
*
19958954 TTTCACTGGCA
1 -TTCACAGGCA
19958965 ATAAATCCGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 2 0.03
82 75 0.95
83 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (82 bp):
TTCACAGGCACTTAGCCTGCTAGACGTATAGCCTGATTCAATTCACCGGCACTTAGCCTGCTAGA
CGTATAGTCCGAATCAA
Found at i:19960618 original size:13 final size:13
Alignment explanation
Indices: 19960600--19960624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19960590 CAATCAAATG
19960600 CACACAAAATAAA
1 CACACAAAATAAA
19960613 CACACAAAATAA
1 CACACAAAATAA
19960625 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:19962615 original size:39 final size:38
Alignment explanation
Indices: 19962542--19962616 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
19962532 AATTAATTAT
*
19962542 AATTTAAGTTTATATATTTGATATATCATAATATTAATG
1 AATTTAAGTTTATATATTTCATATAT-ATAATATTAATG
* *
19962581 AATTTGAGTTTATATATATTCCATATAT-TTATATTA
1 AATTTAAGTTTATATAT-TT-CATATATATAATATTA
19962617 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:19962660 original size:9 final size:9
Alignment explanation
Indices: 19962637--19962677 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
19962627 TACTTAATAA
19962637 ATTATTTTT
1 ATTATTTTT
* *
19962646 AATATTGTT
1 ATTATTTTT
19962655 ATTATTTTT
1 ATTATTTTT
*
19962664 AGTATTTTT
1 ATTATTTTT
19962673 ATTAT
1 ATTAT
19962678 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:19962660 original size:18 final size:18
Alignment explanation
Indices: 19962637--19962677 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19962627 TACTTAATAA
19962637 ATTATTTTTAATATTGTT
1 ATTATTTTTAATATTGTT
* *
19962655 ATTATTTTTAGTATTTTT
1 ATTATTTTTAATATTGTT
19962673 ATTAT
1 ATTAT
19962678 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:19967653 original size:5 final size:5
Alignment explanation
Indices: 19967645--19967671 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19967635 AAAGTAAAAT
19967645 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
19967672 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:19979211 original size:25 final size:25
Alignment explanation
Indices: 19979176--19979246 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
19979166 ACACACCACA
*
19979176 GCTCTCTTGAGCTTCCCGATACTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* * *
19979201 GCTCTCATGAGCTTCTCAATATTTG
1 GCTCTCATGAGCTTCCCGATACTTG
* *
19979226 GCT-TGCAAGAGCTTCCTGATA
1 GCTCT-CATGAGCTTCCCGATA
19979247 TACAGCTCGT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATACTTG
Found at i:19979278 original size:25 final size:25
Alignment explanation
Indices: 19979234--19979320 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
19979224 TGGCTTGCAA
* * *
19979234 GAGCTTCCTGATATACAGCTCGTAT
1 GAGCTTCCCGTTATATAGCTCGTAT
**
19979259 GAGCTTCCCGTTACT-TAGCTTATAT
1 GAGCTTCCCGTTA-TATAGCTCGTAT
* * * *
19979284 GAGCTTCCTGTTATATGGCTCGAAA
1 GAGCTTCCCGTTATATAGCTCGTAT
19979309 GAGCTTCCCGTT
1 GAGCTTCCCGTT
19979321 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:19982078 original size:42 final size:42
Alignment explanation
Indices: 19982030--19982136 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 42
19982020 TTGCGATTTA
*
19982030 CGTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATATGAGTT
1 CGTGTAAGACCA-GTCTGGGACAGT-GACATCGATATATGAGTT
* * * *
19982072 CGTGTAAGACCCAGCCGGGGACAGTGACATCGATATTTGATTT
1 CGTGTAAGA-CCAGTCTGGGACAGTGACATCGATATATGAGTT
*
19982115 CATGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCA-GTCTGGGAC
19982137 GTTGCCATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
42 26 0.49
43 27 0.51
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (42 bp):
CGTGTAAGACCAGTCTGGGACAGTGACATCGATATATGAGTT
Found at i:19983469 original size:35 final size:35
Alignment explanation
Indices: 19983425--19983493 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
19983415 GATTGTTTTA
19983425 GTACATATCTAATTGGTAAATGATGAATATGATTG
1 GTACATATCTAATTGGTAAATGATGAATATGATTG
*
19983460 GTACTTATCTAATTGGTAAATGATGAATATGATT
1 GTACATATCTAATTGGTAAATGATGAATATGATT
19983494 TAAATATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (35 bp):
GTACATATCTAATTGGTAAATGATGAATATGATTG
Found at i:19984698 original size:26 final size:27
Alignment explanation
Indices: 19984648--19984698 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
19984638 AGTTAATAAA
* *
19984648 TTCTCTTTGAGTTTTTTTTTCAAGAAT
1 TTCTCTTTGAGTTTCTTTTACAAGAAT
*
19984675 TTCTC-TTGAGTTTCTTTTAGAAGA
1 TTCTCTTTGAGTTTCTTTTACAAGA
19984699 GTTTTAATAA
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:19985450 original size:29 final size:29
Alignment explanation
Indices: 19985422--19985477 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
19985412 GAAATTATAT
*
19985422 TTTTTATCA-TTTTTAAATTTTAAAAATA
1 TTTTTATAATTTTTTAAATTTTAAAAATA
* *
19985450 TTTTTATAATTTTTTGAATTTTTAAAAT
1 TTTTTATAATTTTTTAAATTTTAAAAAT
19985478 TTAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTATAATTTTTTAAATTTTAAAAATA
Found at i:19985457 original size:37 final size:36
Alignment explanation
Indices: 19985393--19985485 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 36
19985383 GTAATTAATT
* *
19985393 AATTTTAAAATTTTAAAAAGAAATTAT-ATTTTTT-
1 AATTTTTAAATTTTAAAAATAAATTATAATTTTTTG
**
19985427 ATCATTTTTAAATTTTAAAAATATTTTTATAATTTTTTG
1 A--ATTTTTAAATTTTAAAAATA-AATTATAATTTTTTG
*
19985466 AATTTTTAAAATTTAAAAAT
1 AATTTTTAAATTTTAAAAAT
19985486 TTAATTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
34 1 0.02
36 18 0.37
37 22 0.45
38 7 0.14
39 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (36 bp):
AATTTTTAAATTTTAAAAATAAATTATAATTTTTTG
Found at i:19988674 original size:21 final size:21
Alignment explanation
Indices: 19988649--19988688 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19988639 AACTATGCGA
19988649 GTCAAAATAGGTATGCTGGTG
1 GTCAAAATAGGTATGCTGGTG
* *
19988670 GTCAAAATTGGTGTGCTGG
1 GTCAAAATAGGTATGCTGG
19988689 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:19992696 original size:7 final size:7
Alignment explanation
Indices: 19992684--19992715 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
19992674 ATAATTAAAT
19992684 TATTTTA
1 TATTTTA
19992691 TATTTTA
1 TATTTTA
19992698 TATTTTA
1 TATTTTA
19992705 TATTTTA
1 TATTTTA
19992712 TATT
1 TATT
19992716 AATAATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:19995463 original size:16 final size:16
Alignment explanation
Indices: 19995442--19995510 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
19995432 TTTGGTTCGC
19995442 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19995458 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19995474 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
19995491 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19995507 TGTA
1 TGTA
19995511 ATAGCTAATC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:19995488 original size:33 final size:32
Alignment explanation
Indices: 19995442--19995510 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
19995432 TTTGGTTCGC
19995442 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
19995474 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
19995507 TGTA
1 TGTA
19995511 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.17
33 30 0.83
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:19995574 original size:44 final size:45
Alignment explanation
Indices: 19995491--19995581 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
19995481 GGATTAGAGG
* * *
19995491 TGTATTGGATTAGAGGTGTAATAGCTAATCTACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
**
19995536 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
19995580 TG
1 TG
19995582 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
Found at i:19995596 original size:39 final size:43
Alignment explanation
Indices: 19995491--19995604 Score: 128
Period size: 45 Copynumber: 2.7 Consensus size: 43
19995481 GGATTAGAGG
* *
19995491 TGTATTGGATTAGAGGTGTAATAGCTAATCTACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTT--A
* **
19995536 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTTA
19995576 TG-AATGGAATAGAGGTGTAATAGCATAAT
1 TGTAATGGAATAGAGGTGTAATAGC-TAAT
19995605 GGAAAAAACT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 20 0.33
40 2 0.03
41 4 0.07
43 1 0.02
44 13 0.21
45 21 0.34
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTTA
Found at i:19995767 original size:18 final size:17
Alignment explanation
Indices: 19995746--19995780 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19995736 TTATTATTAA
*
19995746 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19995764 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19995781 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19995827 original size:61 final size:61
Alignment explanation
Indices: 19995761--19995948 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
19995751 TTTTAATTAA
*
19995761 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCGAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * *
19995822 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCAT
*
19995881 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
19995942 AATATAT
1 AATATAT
19995949 GATACTATAA
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
58 2 0.02
59 30 0.32
60 23 0.24
61 37 0.39
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
Found at i:19995894 original size:14 final size:15
Alignment explanation
Indices: 19995845--19995896 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
19995835 ATAAAATATA
19995845 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
19995860 TATTAAATATATTAT
1 AATTAAATATATTAT
19995875 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
19995888 AATTTAATA
1 AATTAAATA
19995897 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:19995942 original size:120 final size:121
Alignment explanation
Indices: 19995729--19996021 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 121
19995719 ATCATATTTA
19995729 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
19995794 TATTCTTATATGAATTTACTCGAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
19995849 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
19995914 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
19995970 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
19996022 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 162 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:19996068 original size:101 final size:93
Alignment explanation
Indices: 19995962--19996244 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
19995952 ACTATAAAAG
* * * *
19995962 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
19996026 ATAATTATAACTAATAAATTATCTTATATGAATTTGT
62 -T--CT-TAA-TAATAAATTATCTTATATGAATTTAT
* *
19996063 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
19996126 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* *
19996154 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
19996217 AATAATAAAATGT-TCTTATATGAATTTA
66 AATAAT-AAAT-TATCTTATATGAATTTA
19996245 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
91 88 0.54
92 21 0.13
93 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTATCTTATATGAATTTAT
Found at i:19996091 original size:26 final size:28
Alignment explanation
Indices: 19996062--19996122 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
19996052 TATGAATTTG
*
19996062 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
19996088 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
19996116 TAAAATT
1 TATAATT
19996123 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:19996120 original size:47 final size:46
Alignment explanation
Indices: 19996069--19996212 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
19996059 TTGTATAATT
19996069 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
19996116 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
19996160 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
19996207 TAAAAT
1 TAAAAT
19996213 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:19996132 original size:91 final size:90
Alignment explanation
Indices: 19996037--19996244 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
19996027 TAATTATAAC
* * * *
19996037 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
19996102 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
19996128 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
19996193 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
19996219 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
19996245 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:19996204 original size:44 final size:43
Alignment explanation
Indices: 19996062--19996204 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
19996052 TATGAATTTG
* *
19996062 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
19996106 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
19996153 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
19996197 TATAATTT
1 TATAATTT
19996205 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:19996219 original size:47 final size:47
Alignment explanation
Indices: 19996087--19996225 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
19996077 TTATTATTAC
* *
19996087 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
19996134 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
19996178 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
19996225 A
1 A
19996226 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:19998561 original size:104 final size:104
Alignment explanation
Indices: 19998424--19998645 Score: 293
Period size: 104 Copynumber: 2.1 Consensus size: 104
19998414 ATCAGGCACC
* * * * * *
19998424 AACCACTAAGTTAAATACTCGAGTTTATGCGAAAATTACAG-ATCAAAAACAAACTCCTGCTACA
1 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGA-AGAATCAAAAACAAACTCATGCTACA
* * * *
19998488 ATGTAAGAGCTTTGATTCATTATTTACATGAAAATTTTTA
65 ATGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
* * *
19998528 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGATGAATCAAAATCAAACTCATTCTACAA
1 AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGAAGAATCAAAAACAAACTCATGCTACAA
19998593 TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
66 TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
* *
19998632 AGCCTCTAAATTTA
1 AACCTCTAAGTTTA
19998646 CAACACATTG
Statistics
Matches: 102, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
103 1 0.01
104 101 0.99
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (104 bp):
AACCTCTAAGTTTAATACTCAAGTTTAAGCGAAAATGAAGAATCAAAAACAAACTCATGCTACAA
TGTAAGAGCTTTGATTCATTACTTACAAGAAAATCTTGA
Found at i:20001221 original size:21 final size:23
Alignment explanation
Indices: 20001190--20001235 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
20001180 AAAATGCTAT
* *
20001190 AAATACTTATA-AAATTTGTAAA
1 AAATACTTATAGAAAATTATAAA
20001212 AAATA-TTATAGAAAATTATAAA
1 AAATACTTATAGAAAATTATAAA
20001234 AA
1 AA
20001236 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATACTTATAGAAAATTATAAA
Found at i:20001241 original size:8 final size:9
Alignment explanation
Indices: 20001124--20001334 Score: 79
Period size: 9 Copynumber: 22.1 Consensus size: 9
20001114 CTAGAAAATA
20001124 AAAAATTAT
1 AAAAATTAT
*
20001133 AAAAATAATAA
1 AAAAAT--TAT
20001144 AAAAATTAT
1 AAAAATTAT
* * *
20001153 TAGAATTAC
1 AAAAATTAT
**
20001162 AAAAAAAAT
1 AAAAATTAT
*
20001171 CAAAATTAT
1 AAAAATTAT
20001180 -AAAATGCTAT
1 AAAAAT--TAT
*
20001190 AAATACTTAT
1 AAA-AATTAT
* *
20001200 AAAATTTGTAA
1 AAAA-AT-TAT
20001211 AAAATATTAT
1 AAAA-ATTAT
20001221 AGAAAATTAT
1 A-AAAATTAT
*
20001231 AAAAATTTAA
1 AAAAA-TTAT
20001241 AAAAATTA-
1 AAAAATTAT
*
20001249 AAAAATAAT
1 AAAAATTAT
20001258 AAAAATGT-T
1 AAAAAT-TAT
20001267 ATAAAA-TAT
1 A-AAAATTAT
* *
20001276 AAAAGCTTAC
1 AAAA-ATTAT
* *
20001286 AAGAATTTT
1 AAAAATTAT
*
20001295 AAAAATATAGA
1 AAAAAT-TA-T
*
20001306 AAAAAATAT
1 AAAAATTAT
20001315 AGAAAATTAT
1 A-AAAATTAT
*
20001325 AAAAAATAT
1 AAAAATTAT
20001334 A
1 A
20001335 TATATTTTAA
Statistics
Matches: 149, Mismatches: 34, Indels: 38
0.67 0.15 0.17
Matches are distributed among these distances:
8 16 0.11
9 58 0.39
10 47 0.32
11 26 0.17
12 2 0.01
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20001312 original size:12 final size:12
Alignment explanation
Indices: 20001295--20001320 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20001285 CAAGAATTTT
20001295 AAAAATATAGAA
1 AAAAATATAGAA
20001307 AAAAATATAGAA
1 AAAAATATAGAA
20001319 AA
1 AA
20001321 TTATAAAAAA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAATATAGAA
Found at i:20001350 original size:29 final size:26
Alignment explanation
Indices: 20001317--20001378 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
20001307 AAAAATATAG
*
20001317 AAAATTATAAAAAATATATATATTTTAAT
1 AAAATTAT-AAAAAT-TATATA-TTCAAT
* *
20001346 AAAATTCTAGAAATTATATATTCAAT
1 AAAATTATAAAAATTATATATTCAAT
20001372 AAAATTA
1 AAAATTA
20001379 ATTGTTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 11 0.38
27 6 0.21
28 5 0.17
29 7 0.24
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATTATAAAAATTATATATTCAAT
Found at i:20001575 original size:18 final size:18
Alignment explanation
Indices: 20001553--20001588 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20001543 GCCCGGCCTA
20001553 TTTTTAATTAAAATTAAAT
1 TTTTTAA-TAAAATTAAAT
*
20001572 TTTTTGATAAAATTAAA
1 TTTTTAATAAAATTAAA
20001589 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:20001622 original size:16 final size:16
Alignment explanation
Indices: 20001585--20001624 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
20001575 TTGATAAAAT
* *
20001585 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
20001601 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
20001617 TAAAATTA
1 TAAAATTA
20001625 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:20001654 original size:59 final size:63
Alignment explanation
Indices: 20001591--20001727 Score: 153
Period size: 66 Copynumber: 2.2 Consensus size: 63
20001581 AAATTAAAAC
*
20001591 TAATTGTTATTAAAAT-T-A-A-TTG-TTAGTAAAATTATCAAATTTTTAATTGT-TAATTGTAT
1 TAATTGTTATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTGTATAATTG--T
**
20001650 TAATTGTTGTAACAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTGTACTAATTG
1 TAATTG-T-TATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTGTA-TAATTG
20001715 T
63 T
20001716 TAATTG-TATTAA
1 TAATTGTTATTAA
20001728 TTGTTGTAAC
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
59 6 0.09
60 1 0.02
61 7 0.11
62 1 0.02
63 5 0.08
64 1 0.02
65 3 0.05
66 34 0.53
68 6 0.09
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (63 bp):
TAATTGTTATTAAAATCTAACATTTGATTAGTAAAATTATCAAATTATTAATTGTATAATTGT
Found at i:20001683 original size:66 final size:72
Alignment explanation
Indices: 20001613--20001758 Score: 223
Period size: 75 Copynumber: 2.1 Consensus size: 72
20001603 AAATTAATTG
20001613 TTAGTAAAATTATC-AA-A-T-TT-T-TAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAA
1 TTAGTAAAATTATCAAATATTATTGTATAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAA
20001672 CATTTGA
66 CATTTGA
20001679 TTAGTAAAATTATCAAATTATTAATTGTACTAATTGTTAATTGTATTAATTGTTGTAACAAAATC
1 TTAGTAAAATTATCAAA-TATT-ATTGTA-TAATTGTTAATTGTATTAATTGTTGTAACAAAATC
20001744 TAACATTTGA
63 TAACATTTGA
20001754 TTAGT
1 TTAGT
20001759 TTGCATTTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
66 14 0.20
67 2 0.03
69 1 0.01
70 1 0.01
72 2 0.03
73 1 0.01
75 50 0.70
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (72 bp):
TTAGTAAAATTATCAAATATTATTGTATAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAA
CATTTGA
Found at i:20001718 original size:16 final size:16
Alignment explanation
Indices: 20001694--20001732 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
20001684 AAAATTATCA
*
20001694 AATTATTAATTGTACT
1 AATTGTTAATTGTACT
*
20001710 AATTGTTAATTGTATT
1 AATTGTTAATTGTACT
20001726 AATTGTT
1 AATTGTT
20001733 GTAACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (16 bp):
AATTGTTAATTGTACT
Found at i:20005230 original size:43 final size:42
Alignment explanation
Indices: 20005203--20005538 Score: 431
Period size: 43 Copynumber: 7.9 Consensus size: 42
20005193 TTTATAAAAA
*
20005203 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-TTTTCCCAC
* *
20005246 AAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-TTTTCCCAC
* **
20005289 AAAAGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCTGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-TTTTCCCAC
* * * *
20005332 AAACACTGCTAAAGTCCAAGACCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCG-TTTTCCCAC
* * *
20005375 AAACACTGCTAAAGACCAAGACCTTTAGCGGCATTTTCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTT-CCCAC
* * * *
20005418 AATCGCCGTTAAAGACCAAGACCTTTAGCGTCACTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGC-GTTTTCCCAC
* *
20005461 AAACACCGCTAAAGACCAAGACC-TTAGCGGCGCTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTCCCAC
*
20005502 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCATTTT
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTT
20005539 TTTAAAAACA
Statistics
Matches: 262, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
41 30 0.11
42 22 0.08
43 206 0.79
44 4 0.02
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTCCCAC
Found at i:20005343 original size:129 final size:129
Alignment explanation
Indices: 20005203--20005538 Score: 491
Period size: 129 Copynumber: 2.6 Consensus size: 129
20005193 TTTATAAAAA
* *
20005203 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGCAAATGCCGCTAAAGACCAAGAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAAGAC
* ** **
20005268 CTTTAGCGGCGCTTTTCCCGCA-AA-AGCCGCTAAAGACCAAGACCTTTAGCGGCGTTTTTCCTG
66 CTTTAGCGGC-ATTTTCCC-CACAATAGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCCA
20005331 C
129 C
* * * *
20005332 AAACACTGCTAAAGTCCAAGACCTTTAGCGGCGCTTTTCCCGCAAACACTGCTAAAGACCAAGAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAAGAC
* * *
20005397 CTTTAGCGGCATTTTCCCCACAATCGCCGTTAAAGACCAAGACCTTTAGCGTCACTTTTCCCAC
66 CTTTAGCGGCATTTTCCCCACAATAGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCCAC
*
20005461 AAACACCGCTAAAGACCAAGACC-TTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGACCAAGAC
1 AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAAGAC
20005524 CTTTAGCGGCATTTT
66 CTTTAGCGGCATTTT
20005539 TTTAAAAACA
Statistics
Matches: 186, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
127 44 0.24
128 19 0.10
129 123 0.66
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (129 bp):
AAACACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGACCAAGAC
CTTTAGCGGCATTTTCCCCACAATAGCCGCTAAAGACCAAGACCTTTAGCGGCACTTTTCCCAC
Found at i:20006008 original size:66 final size:66
Alignment explanation
Indices: 20005897--20006066 Score: 227
Period size: 66 Copynumber: 2.6 Consensus size: 66
20005887 CTCGCCGCAG
* * * *
20005897 CCTCTGCTTCTCTCGCTG-TCGCATCTGCTTTAAGCTGCAACTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCT-GCATCTACTTTAAGTTGTAACTGGAGTTCTTCATATCTTT-GTT
20005960 GAA
64 GAA
* *
20005963 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAACTGGAGTTCTTCATATCTTTGTTGA
20006028 A
66 A
* * *
20006029 CCTCAGCTTCTCTCGATGCTGCCTCCACTTTAAGTTGT
1 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGT
20006067 GTAATTTGCT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
66 88 0.95
67 5 0.05
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTACTTTAAGTTGTAACTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:20009255 original size:16 final size:16
Alignment explanation
Indices: 20009236--20009275 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20009226 TATATATGAG
20009236 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
20009252 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
20009268 TTATGTAA
1 TTATGTAA
20009276 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:20009485 original size:17 final size:17
Alignment explanation
Indices: 20009463--20009501 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20009453 ACTTTCATAA
20009463 TATTATTCGT-ATAACAT
1 TATTATTC-TAATAACAT
20009480 TATTATTCTAATAACAT
1 TATTATTCTAATAACAT
20009497 T-TTAT
1 TATTAT
20009502 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:20009547 original size:12 final size:12
Alignment explanation
Indices: 20009530--20009554 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20009520 TAGGATAGTG
20009530 AAAATTATGAAC
1 AAAATTATGAAC
20009542 AAAATTATGAAC
1 AAAATTATGAAC
20009554 A
1 A
20009555 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:20010712 original size:20 final size:19
Alignment explanation
Indices: 20010689--20010731 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
20010679 AAATTTTAGT
20010689 TTTTTTATTTCATTT-TTATA
1 TTTTTTATTT--TTTCTTATA
20010709 TTTTTTATTTTTTCTTATA
1 TTTTTTATTTTTTCTTATA
20010728 TTTT
1 TTTT
20010732 GATCCTATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.41
20 10 0.45
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTATTTTTTCTTATA
Found at i:20011352 original size:7 final size:7
Alignment explanation
Indices: 20011340--20011436 Score: 95
Period size: 7 Copynumber: 12.9 Consensus size: 7
20011330 AAGCAACCAT
20011340 CCCTAAC
1 CCCTAAC
20011347 CCCTAAC
1 CCCTAAC
20011354 CCCTAAATCC
1 CCCT-AA--C
*
20011364 CCCTAAA
1 CCCTAAC
*
20011371 CCCTAAAT
1 CCCT-AAC
20011379 CCCTAAC
1 CCCTAAC
20011386 CCCTAAC
1 CCCTAAC
20011393 CCCTAAATC
1 CCCT-AA-C
20011402 CCCTAAC
1 CCCTAAC
*
20011409 CCCTAAAT
1 CCCT-AAC
*
20011417 CTCTAAC
1 CCCTAAC
20011424 CCCTAAC
1 CCCTAAC
20011431 CCCTAA
1 CCCTAA
20011437 TCCATACCCC
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
7 47 0.62
8 17 0.22
9 7 0.09
10 5 0.07
ACGTcount: A:0.32, C:0.49, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:20011384 original size:15 final size:15
Alignment explanation
Indices: 20011338--20011429 Score: 82
Period size: 15 Copynumber: 6.0 Consensus size: 15
20011328 CTAAGCAACC
20011338 ATCCCTAACCCCT-A
1 ATCCCTAACCCCTAA
*
20011352 ACCCCTAAATCCCCCTAA
1 ATCCCT-AA--CCCCTAA
*
20011370 A-CCCTAAATCCCT-A
1 ATCCCT-AACCCCTAA
*
20011384 ACCCCTAACCCCTAA
1 ATCCCTAACCCCTAA
20011399 ATCCCCTAACCCCTAA
1 AT-CCCTAACCCCTAA
*
20011415 ATCTCTAACCCCTAA
1 ATCCCTAACCCCTAA
20011430 CCCCTAATCC
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
14 13 0.20
15 24 0.36
16 15 0.23
17 12 0.18
18 2 0.03
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCCCTAACCCCTAA
Found at i:20011414 original size:38 final size:39
Alignment explanation
Indices: 20011338--20011436 Score: 173
Period size: 38 Copynumber: 2.6 Consensus size: 39
20011328 CTAAGCAACC
20011338 ATCCCTAACCCCTAACCCCTAAATCCCCCTAAACCCTAA
1 ATCCCTAACCCCTAACCCCTAAATCCCCCTAAACCCTAA
*
20011377 ATCCCTAACCCCTAACCCCTAAAT-CCCCTAACCCCTAA
1 ATCCCTAACCCCTAACCCCTAAATCCCCCTAAACCCTAA
*
20011415 ATCTCTAACCCCTAACCCCTAA
1 ATCCCTAACCCCTAACCCCTAA
20011437 TCCATACCCC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
38 34 0.59
39 24 0.41
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.19
Consensus pattern (39 bp):
ATCCCTAACCCCTAACCCCTAAATCCCCCTAAACCCTAA
Found at i:20012272 original size:24 final size:24
Alignment explanation
Indices: 20012226--20012272 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
20012216 ATAGTATTTT
*
20012226 AATTTTTCCATGTGATTTATTTCA
1 AATTTTTCAATGTGATTTATTTCA
*
20012250 AATTATTTCAATGTTATTT-TTTC
1 AATT-TTTCAATGTGATTTATTTC
20012273 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:20012404 original size:41 final size:42
Alignment explanation
Indices: 20012359--20012525 Score: 128
Period size: 41 Copynumber: 4.0 Consensus size: 42
20012349 AATATTTTTT
* * * *
20012359 GCGGCGCTTC-CACAAAAATGCCGTTAAAACCCCTAACATTA
1 GCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCCTAACATTA
* * * *
20012400 GCGGCGCTTCTCAAAAAAACGCTGCTAAAAATCTTAACTTTA
1 GCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCCTAACATTA
* ** * * *
20012442 GCGGCGCTTAT-TTAAAAACGCCACTAAAAGA-CCAAACGTTA
1 GCGGCGCTTCTCAAAAAAACGCCGCTAAAA-ACCCTAACATTA
* * *
20012483 GCGGCGC-T-TCAAAGAAAACGCCGTTAAATACCTTAACATTA
1 GCGGCGCTTCTCAAA-AAAACGCCGCTAAAAACCCTAACATTA
20012524 GC
1 GC
20012526 AGCGATTGAT
Statistics
Matches: 97, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 59 0.61
42 34 0.35
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.22
Consensus pattern (42 bp):
GCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCCTAACATTA
Found at i:20012539 original size:82 final size:83
Alignment explanation
Indices: 20012397--20012552 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 83
20012387 ACCCCTAACA
* * * * *
20012397 TTAGCGGCGCTTCTCAAAAAAACGCTGCTAAAAATCTTAACTTTAGCGGCGCTTATTTAAAAACG
1 TTAGCGGCGCTTCTCAAAAAAACGCCGCTAAAAACCTTAACATTAGCAGCGATTATTTAAAAACG
20012462 CCACTAAAAGACCAAACG
66 CCACTAAAAGACCAAACG
* *
20012480 TTAGCGGCGC-T-TCAAAGAAAACGCCGTTAAATACCTTAACATTAGCAGCGATTGA-TTAAAAA
1 TTAGCGGCGCTTCTCAAA-AAAACGCCGCTAAAAACCTTAACATTAGCAGCGATT-ATTTAAAAA
20012542 CGCCACTAAAA
64 CGCCACTAAAA
20012553 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:20019126 original size:19 final size:17
Alignment explanation
Indices: 20019102--20019152 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 17
20019092 AGGGTGAGGC
20019102 ATAAAAGTTTAGGGGGAAA
1 ATAAAAGTTTAGGGGG--A
*
20019121 ATAAAAAGTTT-TGGGGA
1 AT-AAAAGTTTAGGGGGA
20019138 ATAAAAGTTTGAGGG
1 ATAAAAGTTT-AGGG
20019153 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:20019524 original size:9 final size:9
Alignment explanation
Indices: 20019510--20019546 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
20019500 TATAGTTTGA
20019510 TATTCGAAT
1 TATTCGAAT
20019519 TATTCGAAT
1 TATTCGAAT
*
20019528 TATTCGAGT
1 TATTCGAAT
20019537 TATTCGAAT
1 TATTCGAAT
20019546 T
1 T
20019547 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:20021878 original size:25 final size:25
Alignment explanation
Indices: 20021818--20021942 Score: 109
Period size: 25 Copynumber: 5.1 Consensus size: 25
20021808 CAGCTCTTAT
*
20021818 GAGCGTCCCG-TTATATGGCTCTTCG
1 GAGCTTCCCGATTA-ATGGCTCTTCG
20021843 AGAGCTTCCCGATTAATGGCTCTTCG
1 -GAGCTTCCCGATTAATGGCTCTTCG
*
20021869 GAGCTTCCCGA-T-ATGGCTCATT-T
1 GAGCTTCCCGATTAATGGCTC-TTCG
* * * *
20021892 GAACTTCCTGA-TATATGGCTATCCG
1 GAGCTTCCCGATTA-ATGGCTCTTCG
*
20021917 AAGCTTCCCG-TTAATGGCTCTTCG
1 GAGCTTCCCGATTAATGGCTCTTCG
20021941 GA
1 GA
20021943 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:20021959 original size:48 final size:48
Alignment explanation
Indices: 20021823--20021959 Score: 109
Period size: 48 Copynumber: 2.8 Consensus size: 48
20021813 CTTATGAGCG
* * * * * * *
20021823 TCCCGTTATATGGCTCTTCGAGAGCTTCCCGATTAATGGCTCTTCGGAGCT
1 TCCCGTTA-ATGGCTCTTCG-GAAC-TACCTATTATTGGCTATCCGAAGCT
* * *
20021874 TCCCGAT-ATGGCTCATT-TGAACTTCCTGA-TATATGGCTATCCGAAGCT
1 TCCCGTTAATGGCTC-TTCGGAACTACCT-ATTAT-TGGCTATCCGAAGCT
20021922 TCCCGTTAATGGCTCTTCGGAACTACCTATTATTGGCT
1 TCCCGTTAATGGCTCTTCGGAACTACCTATTATTGGCT
20021960 CGCACGAGCT
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
Done.