Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 5 of 30
Found at i:1674483 original size:31 final size:27
Alignment explanation
Indices: 1674423--1674486 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
1674413 CAATTTTTAA
* *
1674423 TTATAATTTATTTATTTTTAGTTGTTT
1 TTATAATTAATTTATTTTTAGTAGTTT
1674450 TTATAATTAATTTATTTTTAAGTGAGTTAT
1 TTATAATTAATTTATTTTT-AGT-AGTT-T
1674480 TT-TAATT
1 TTATAATT
1674487 TTATGTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.56
28 3 0.09
29 8 0.25
30 3 0.09
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (27 bp):
TTATAATTAATTTATTTTTAGTAGTTT
Found at i:1675862 original size:24 final size:25
Alignment explanation
Indices: 1675817--1675869 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1675807 CTCTAGGCAA
1675817 ACATATATATACATGCACACACACGC
1 ACATATATATACAT-CACACACACGC
* *
1675843 ACATATATATATAT-ATACACACGC
1 ACATATATATACATCACACACACGC
1675867 ACA
1 ACA
1675870 CACATACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 12 0.48
26 13 0.52
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (25 bp):
ACATATATATACATCACACACACGC
Found at i:1675863 original size:28 final size:28
Alignment explanation
Indices: 1675819--1675880 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1675809 CTAGGCAAAC
* *
1675819 ATATATATACATGCACACACACGCACAT
1 ATATATATACATACACACACACACACAT
* *
1675847 ATATATATATATACACACGCACACACAT
1 ATATATATACATACACACACACACACAT
*
1675875 ACATAT
1 ATATAT
1675881 CAATTCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (28 bp):
ATATATATACATACACACACACACACAT
Found at i:1675871 original size:26 final size:26
Alignment explanation
Indices: 1675817--1675880 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
1675807 CTCTAGGCAA
* * *
1675817 ACATATATATACATGCACACACACGC
1 ACATATATATATATACACACACACAC
* *
1675843 ACATATATATATATATACACACGCAC
1 ACATATATATATATACACACACACAC
* *
1675869 ACACATACATAT
1 ACATATATATAT
1675881 CAATTCTCTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (26 bp):
ACATATATATATATACACACACACAC
Found at i:1680807 original size:21 final size:20
Alignment explanation
Indices: 1680773--1680812 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1680763 TAATTTGAAA
*
1680773 TAAAATAATATAAAATTAAAC
1 TAAAATAACAT-AAATTAAAC
*
1680794 TAAAATAACCTAAATTAAA
1 TAAAATAACATAAATTAAA
1680813 TTACTCAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAATAACATAAATTAAAC
Found at i:1682355 original size:26 final size:26
Alignment explanation
Indices: 1682295--1682356 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1682285 ACCATATACC
*
1682295 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
1682321 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
1682347 CATCATCATC
1 CATCATCATC
1682357 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:1682649 original size:42 final size:42
Alignment explanation
Indices: 1682591--1682672 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1682581 ATGGAGGCAA
1682591 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
* *
1682633 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTC
1 CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTC
1682673 CAAATCAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
Found at i:1689088 original size:6 final size:6
Alignment explanation
Indices: 1689077--1689101 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1689067 CTTCCTTTTA
1689077 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
1689102 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1689093 original size:16 final size:16
Alignment explanation
Indices: 1689072--1689105 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1689062 ACTTACTTCC
1689072 TTTTATTTATTTTTAT
1 TTTTATTTATTTTTAT
1689088 TTTTATTT-TTATTTAT
1 TTTTATTTATT-TTTAT
1689104 TT
1 TT
1689106 AATTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTTATTTTTAT
Found at i:1689485 original size:8 final size:7
Alignment explanation
Indices: 1689462--1689509 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
1689452 TTTGGACTAT
1689462 CCATTAC
1 CCATTAC
1689469 CCATTAC
1 CCATTAC
1689476 CCACTTAC
1 CCA-TTAC
*
1689484 CCACTAGC
1 CCATTA-C
1689492 CCATTTAC
1 CCA-TTAC
1689500 CCATTAC
1 CCATTAC
1689507 CCA
1 CCA
1689510 ACAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 19 0.53
8 15 0.42
9 2 0.06
ACGTcount: A:0.27, C:0.46, G:0.02, T:0.25
Consensus pattern (7 bp):
CCATTAC
Found at i:1689499 original size:16 final size:15
Alignment explanation
Indices: 1689465--1689509 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1689455 GGACTATCCA
*
1689465 TTACCCATTACCCAC
1 TTACCCACTACCCAC
*
1689480 TTACCCACTAGCCCAT
1 TTACCCACTA-CCCAC
*
1689496 TTACCCATTACCCA
1 TTACCCACTACCCA
1689510 ACAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.27, C:0.44, G:0.02, T:0.27
Consensus pattern (15 bp):
TTACCCACTACCCAC
Found at i:1696653 original size:25 final size:24
Alignment explanation
Indices: 1696608--1696655 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1696598 ACAAATTATA
* *
1696608 TAAATTATAATTTATAGATATAAC
1 TAAATTAAAATTTATAAATATAAC
*
1696632 TAAATTGAAAATTTTTAAATATAA
1 TAAATT-AAAATTTATAAATATAA
1696656 ATTGATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAATTAAAATTTATAAATATAAC
Found at i:1697319 original size:23 final size:22
Alignment explanation
Indices: 1697276--1697319 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1697266 TAAACAAATT
*
1697276 CAAAATTGAAAAATCTCAAAAA
1 CAAAATTGAAAAATCTAAAAAA
* *
1697298 CAAATATTTAAAAATTTAAAAA
1 CAAA-ATTGAAAAATCTAAAAA
1697320 TATTTAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.25
Consensus pattern (22 bp):
CAAAATTGAAAAATCTAAAAAA
Found at i:1698348 original size:424 final size:420
Alignment explanation
Indices: 1697527--1698373 Score: 1587
Period size: 424 Copynumber: 2.0 Consensus size: 420
1697517 GGATAAGGAC
1697527 AAAGA-AAATTTGGTCCAACATTATTTGATGTAATGGATTGATGGAAACATGAATGGGAAGAAAT
1 AAAGAGAAATTTGGTCCAACATTATTTGATGTAATGGATTGATGGAAACATGAATGGGAAGAAAT
1697591 TGTTCCGATCACTATCAAACATTAATTAGCCACACATTGCTTATGAGTCTTATGACTTTAGTAAG
66 TGTTCCGATCACTATCAAACATTAATTAGCCACACATTGCTTATGAGTCTTATGACTTTAGTAAG
1697656 TAAACAAGGGTATATGAATGTGATATATGTGCTGTCGCATGTTATGGATAAAAGATTTAAGTTAT
131 TAAACAAGGGTATATGAATGTGATATATGTGCTGTCGCATGTTATGGATAAAAGATTTAAGTTAT
1697721 CATGATTTTATTATTCATTTATCTGCTTTTGAAGATAAAAAGATAGAAAAAAAGGTAAAATATTT
196 CATGATTTTATTATTCATTTATCTGCTTTTGAAGATAAAAAGATAGAAAAAAAGGTAAAATATTT
*
1697786 TAATTTTTTAAATATTAATAATTTAAAATTTTAAACGAGTCCATTAATTTTTGAAATGAATACTT
261 TAATTTTTTAAATATT-ATAAGTTAAAATTTTAAACGAGTCCATTAATTTTTGAAATGAATACTT
1697851 TATCTCAAAAATGCAAATATTATTAACAAAAATTAAAAAAATAAAATATTTTTTTATCATTTTTA
325 TATCTCAAAAATGCAAATATTATTAACAAAAATTAAAAAAATAAAATATTTTTTTATCATTTTTA
1697916 AAATTATTATTATTTTAAAAAAAAAATTAAAAA
390 AAATTATTATTATTTT--AAAAAAAATTAAAAA
1697949 AAAGAGNAAATTTGGTCCAACATTATTTGATGTAATGGATTGATGGAAACATGAATGGGAAGAAA
1 AAAGAG-AAATTTGGTCCAACATTATTTGATGTAATGGATTGATGGAAACATGAATGGGAAGAAA
1698014 TTGTTCCGATCACTATCAAACATTAATTAGCCACACATTGCTTATGAGTCTTATGACTTTAGTAA
65 TTGTTCCGATCACTATCAAACATTAATTAGCCACACATTGCTTATGAGTCTTATGACTTTAGTAA
1698079 GTAAACAAGGGTATATGAATGTGATATATGTGCTGTCGCATGTTATGGATAAAAGATTTAAGTTA
130 GTAAACAAGGGTATATGAATGTGATATATGTGCTGTCGCATGTTATGGATAAAAGATTTAAGTTA
1698144 TCATGATTTTATTATTCATTTATCTGCTTTTGAAGATAAAAAGATAGAAAAAAAGGTAAAATATT
195 TCATGATTTTATTATTCATTTATCTGCTTTTGAAGATAAAAAGATAGAAAAAAAGGTAAAATATT
*
1698209 TTAATTTTTTAAAT-TT-T-AGTTAAAATTTTAAAC-AGATCTATTAATTTTTGAAATGAATACT
260 TTAATTTTTTAAATATTATAAGTTAAAATTTTAAACGAG-TCCATTAATTTTTGAAATGAATACT
1698270 TTATCTCAAAAATGCAAATATTATTAACAAAAATTAAAAAAATAAAATATTTTTTTATCATTTTT
324 TTATCTCAAAAATGCAAATATTATTAACAAAAATTAAAAAAATAAAATATTTTTTTATCATTTTT
1698335 AAAAATTATTATTATTTTAAAAAAAATTAAAAA
389 -AAAATTATTATTATTTTAAAAAAAATTAAAAA
1698368 AAAGAG
1 AAAGAG
1698374 CACCAATCTC
Statistics
Matches: 419, Mismatches: 2, Indels: 11
0.97 0.00 0.03
Matches are distributed among these distances:
419 23 0.05
420 104 0.25
421 18 0.04
422 5 0.01
423 2 0.00
424 267 0.64
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (420 bp):
AAAGAGAAATTTGGTCCAACATTATTTGATGTAATGGATTGATGGAAACATGAATGGGAAGAAAT
TGTTCCGATCACTATCAAACATTAATTAGCCACACATTGCTTATGAGTCTTATGACTTTAGTAAG
TAAACAAGGGTATATGAATGTGATATATGTGCTGTCGCATGTTATGGATAAAAGATTTAAGTTAT
CATGATTTTATTATTCATTTATCTGCTTTTGAAGATAAAAAGATAGAAAAAAAGGTAAAATATTT
TAATTTTTTAAATATTATAAGTTAAAATTTTAAACGAGTCCATTAATTTTTGAAATGAATACTTT
ATCTCAAAAATGCAAATATTATTAACAAAAATTAAAAAAATAAAATATTTTTTTATCATTTTTAA
AATTATTATTATTTTAAAAAAAATTAAAAA
Found at i:1701988 original size:13 final size:13
Alignment explanation
Indices: 1701979--1702004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1701969 TCATTTTGTT
1701979 TTCATTTTTTCTG
1 TTCATTTTTTCTG
1701992 TTCATTTTTTCTG
1 TTCATTTTTTCTG
1702005 GAGCAGGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (13 bp):
TTCATTTTTTCTG
Found at i:1702305 original size:19 final size:19
Alignment explanation
Indices: 1702278--1702315 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1702268 CCATTTGACT
1702278 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
1702297 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
1702316 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:1713824 original size:14 final size:14
Alignment explanation
Indices: 1713805--1713831 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1713795 AAAAATTTGA
1713805 AAAAACCCTAGAAC
1 AAAAACCCTAGAAC
1713819 AAAAACCCTAGAA
1 AAAAACCCTAGAA
1713832 ATCCCTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAAACCCTAGAAC
Found at i:1714665 original size:11 final size:11
Alignment explanation
Indices: 1714628--1714676 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1714618 AATTAATTAG
*
1714628 AAATCATAAAA
1 AAATTATAAAA
*
1714639 TAATTATAATATA
1 AAATTATAA-A-A
*
1714652 AAATTTTAAAA
1 AAATTATAAAA
1714663 AAATTATAAAA
1 AAATTATAAAA
1714674 AAA
1 AAA
1714677 AAGTAGCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 21 0.68
12 2 0.06
13 8 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATTATAAAA
Found at i:1714818 original size:10 final size:11
Alignment explanation
Indices: 1714803--1714844 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
1714793 ATCCTCAATC
1714803 AAAAA-ATACA
1 AAAAATATACA
1714813 AAAAA-ATA-A
1 AAAAATATACA
*
1714822 AAAAATATAGA
1 AAAAATATACA
1714833 AAAAATATACA
1 AAAAATATACA
1714844 A
1 A
1714845 TGGTAAGGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 6 0.21
10 11 0.38
11 12 0.41
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAATATACA
Found at i:1716637 original size:20 final size:20
Alignment explanation
Indices: 1716587--1716639 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1716577 GTAAAGTATA
1716587 AAAAAATAATAAT-TAGAAAT
1 AAAAAATAA-AATATAGAAAT
* *
1716607 AAAATAGAAAATAT-GATAAT
1 AAAAAATAAAATATAGA-AAT
1716627 AAAAAATAAAATA
1 AAAAAATAAAATA
1716640 AAATGAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAAATAAAATATAGAAAT
Found at i:1716660 original size:27 final size:27
Alignment explanation
Indices: 1716589--1716671 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
1716579 AAAGTATAAA
1716589 AAAATAATAATTAGAAATAAAATAGAAAAT-
1 AAAATAATAATT--AAATAAAAT--AAAATG
** *
1716619 ATGATAATAA-AAAATAAAATAAAATG
1 AAAATAATAATTAAATAAAATAAAATG
*
1716645 AAAATAATAATTAAATAATA-AAAATG
1 AAAATAATAATTAAATAAAATAAAATG
1716671 A
1 A
1716672 CAAAAAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
25 5 0.11
26 15 0.34
27 16 0.36
30 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAATAATAATTAAATAAAATAAAATG
Found at i:1716668 original size:26 final size:26
Alignment explanation
Indices: 1716622--1716671 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1716612 AGAAAATATG
1716622 ATAATAAAAAATAAAATAAAATGAAA
1 ATAATAAAAAATAAAATAAAATGAAA
* *
1716648 ATAATAATTAAATAATA-AAAATGA
1 ATAATAA-AAAATAAAATAAAATGA
1716672 CAAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
ATAATAAAAAATAAAATAAAATGAAA
Found at i:1716734 original size:17 final size:17
Alignment explanation
Indices: 1716708--1716752 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1716698 TAGCATATAT
1716708 ATAT-GTTGCATCATGC
1 ATATCGTTGCATCATGC
1716724 ATATCGTTGCATCATGC
1 ATATCGTTGCATCATGC
*
1716741 ATATCATTGCAT
1 ATATCGTTGCAT
1716753 ATAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 4 0.15
17 23 0.85
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (17 bp):
ATATCGTTGCATCATGC
Found at i:1733307 original size:49 final size:49
Alignment explanation
Indices: 1733253--1733414 Score: 148
Period size: 49 Copynumber: 3.2 Consensus size: 49
1733243 CGAGCCTAAA
*
1733253 TCAAGTCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
1 TCAAGCCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
* * * * *
1733302 TCAAGTCTA-AGGATTTCAATTTTTTAAATCGAACCTACTT-TGAGATAGG
1 TCAAGCCTAGA-AATTTTAATTTTTAAAATCAAACCTA-TTGTGAGATAGG
* * ** * *
1733351 TCAAGCCTAGGAATCTTAATTTAAAAAAAAAATCAAACCTATTGTAAGATAAG
1 TCAAGCCTAGAAATTTTAATTT----TTAAAATCAAACCTATTGTGAGATAGG
1733404 TCAAGCCTAGA
1 TCAAGCCTAGA
1733415 TCAAGTCTAG
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
48 1 0.01
49 56 0.63
50 2 0.02
52 2 0.02
53 28 0.31
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (49 bp):
TCAAGCCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
Found at i:1733522 original size:60 final size:60
Alignment explanation
Indices: 1733379--1733690 Score: 213
Period size: 60 Copynumber: 5.4 Consensus size: 60
1733369 ATTTAAAAAA
* * * * ** * * * *
1733379 AAAATCAAACCTATTGTAAGATAAGTCAAGCCTAGATCAAGTCTAGAAATTTTAATATTT
1 AAAATCGAACCTGTTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAGATTTCAATTTTT
* * * *
1733439 AAAATCAAACTTCTTGTGAGATAGGTTGAGCCTAGGTTAAGTCTAGAGATTTCAATTTTT
1 AAAATCGAACCTGTTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAGATTTCAATTTTT
* * ** * **
1733499 CAAATCGAACCTGCTT-TGGGATAGGTCAAGCCTAGGT--A-TCT-TA-ATTT-AA---AA
1 AAAATCGAACCTG-TTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAGATTTCAATTTTT
* ** *
1733550 ACAAATC-ATACCTGTTGTGAGATAGGTTGAGCTTAAATCAAGTCCAG-GAATTTC-ATTTTT
1 A-AAATCGA-ACCTGTTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAG-ATTTCAATTTTT
* *
1733610 AAAATTGAACCTGTTGTGAGATAAGTTGAGCCTAGGTCAAGTCTA-AGAGTTTCAATTTTT
1 AAAATCGAACCTGTTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAGA-TTTCAATTTTT
* *
1733670 -AAATCGAACCTATTTTGAGAT
1 AAAATCGAACCTGTTGTGAGAT
1733691 GGATCGAACT
Statistics
Matches: 193, Mismatches: 41, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
51 3 0.02
52 25 0.13
54 3 0.02
55 6 0.03
56 1 0.01
57 8 0.04
58 2 0.01
59 59 0.31
60 84 0.44
61 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (60 bp):
AAAATCGAACCTGTTGTGAGATAGGTTGAGCCTAGGTCAAGTCTAGAGATTTCAATTTTT
Found at i:1733624 original size:59 final size:59
Alignment explanation
Indices: 1733559--1733690 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 59
1733549 AACAAATCAT
* * * *
1733559 ACCTGTTGTGAGATAGGTTGAGCTTAAATCAAGTCCAGGAATTTC-ATTTTTAAAATTGA
1 ACCTGTTGTGAGATAAGTTGAGCCTAAATCAAGTCCAAGAATTTCAATTTTT-AAATCGA
** * *
1733618 ACCTGTTGTGAGATAAGTTGAGCCTAGGTCAAGTCTAAGAGTTTCAATTTTTAAATCGA
1 ACCTGTTGTGAGATAAGTTGAGCCTAAATCAAGTCCAAGAATTTCAATTTTTAAATCGA
* *
1733677 ACCTATTTTGAGAT
1 ACCTGTTGTGAGAT
1733691 GGATCGAACT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 56 0.90
60 6 0.10
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (59 bp):
ACCTGTTGTGAGATAAGTTGAGCCTAAATCAAGTCCAAGAATTTCAATTTTTAAATCGA
Found at i:1734765 original size:20 final size:21
Alignment explanation
Indices: 1734720--1734766 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1734710 AGATGTCTAA
*
1734720 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
1734741 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
1734761 AATAAT
1 AATAAT
1734767 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:1735730 original size:13 final size:13
Alignment explanation
Indices: 1735712--1735736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1735702 TTTCAGAAAA
1735712 TTTATAAAATCAT
1 TTTATAAAATCAT
1735725 TTTATAAAATCA
1 TTTATAAAATCA
1735737 CAATTTTTCC
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:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:1740888 original size:19 final size:19
Alignment explanation
Indices: 1740864--1740901 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1740854 CTGCCAAACC
*
1740864 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
1740883 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
1740902 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:1745714 original size:391 final size:390
Alignment explanation
Indices: 1744932--1745727 Score: 964
Period size: 391 Copynumber: 2.0 Consensus size: 390
1744922 TAATACTAAC
* ** * *
1744932 AAAATTCAAATTGTATGCAAAGGGAAAAGAAAATAAAAAAAATGTAAATTGTTTGATTGATTCAT
1 AAAATTCAAACTGTATGCAAAGGGAAAAGAAAATAAAAAAAATAAAAATTATTTGATTGATTCAC
* * *
1744997 GAAAAAAGAGAATAGGAAAAAAGTTGAAAACCATGTGCAAAGGGAAAAAATAGAGTTGATGCTCT
66 GAAAAAAGAGAATAGGAAAAAAGGTGAAAACCATGTGCAAAGGGAAAAAATAGAGTTAACGCTCT
* * *
1745062 ATAGTTGCTATAGAAATTGAAAGCGTTAAAATAAGTCAAATCAAACAATTTAGGAAAGGATATAC
131 ATAGTTGCTATAGAAATTGAAAGAGTTAAAATAAGTCAAATCAAACAATTCAAGAAAGGATATAC
* * * * *
1745127 AACTGATTTTTCTGTCTTTGACATTAACTAACATAACTTTGAAAGCGTTGAAACACTTTGCACAC
196 AACTAATTTTTCTGTCTTTGACATTAACTAACATAACTTTGAAAGAGTTAAAACACTTCGCAAAC
* * *
1745192 ACGAATCTCACCTAATATCAAATTCAAAAAGTTAAATGTAAATGGTTTGATTGATTCACAGAAAA
261 AAGAATCTCACCTAATATCAAATTCAAAAAGCTAAATGTAAATGATTTGATTGATT-ACAGAAAA
* * *
1745257 AAAAAAGAATAGGAGAAAGAGTGAAAATCATGTGCAAAGAAAAAGAAAAGGCTAAAGGGCTTTAA
325 AAAAAAGAATAGGAGAAAGAGTGAAAACCATGTGCAAAGAAAAAAAAAAGACTAAAGGGCTTTAA
1745322 A
390 A
* *
1745323 AATATTCAAACTGTCTGCAAAGGGAAAAGAAGAA-AAAATAAGAA-AAAAATTATTTGATTGATT
1 AAAATTCAAACTGTATGCAAAGGGAAAAGAA-AATAAAA-AA-AATAAAAATTATTTGATTGATT
* * *
1745386 CACGGAAAAAGAGAATAGGAGAAAGGGTGAAAACCATGTGCAAAGAGGAAAAAA-A-AGTTAACG
63 CACGAAAAAAGAGAATAGGAAAAAAGGTGAAAACCATGTGCAAAG-GGAAAAAATAGAGTTAACG
* * * * * ** *
1745449 CTTTGTAGTTGCTATAGAAATTGGAAGAGTTAAGATAAGTCAAATCGAATGATTCAAGAGAGGAT
127 CTCTATAGTTGCTATAGAAATTGAAAGAGTTAAAATAAGTCAAATCAAACAATTCAAGAAAGGAT
* *
1745514 ATACAACTAATTTTTCTGTCTTT-ACATTAACTAGCATAGCTTTGAAAGAGTTAAAACACTTCGC
192 ATACAACTAATTTTTCTGTCTTTGACATTAACTAACATAACTTTGAAAGAGTTAAAACACTTCGC
* * * * * * *
1745578 AAACATAG-ATTTCACCTATTATCTAGTTCAAAATGCTAAATGTAAATTATTTTATTGATT-CA-
257 AAACA-AGAATCTCACCTAATATCAAATTCAAAAAGCTAAATGTAAATGATTTGATTGATTACAG
* * * * *
1745640 AAAAAAATAA-AATAGGAGAAAGGGTGAAAACCGTGTGTAAAGTAAAAAAAAAAAAAAGAACTGA
321 AAAAAAAAAAGAATAGGAGAAAGAGTGAAAACCATGTGCAAAG-----AAAAAAAAAAG-ACTAA
1745704 AGGG-TTTAAA
380 AGGGCTTTAAA
*
1745714 AAAATTCAAGCTGT
1 AAAATTCAAACTGT
1745728 GTTGTCAAAC
Statistics
Matches: 343, Mismatches: 51, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
386 28 0.08
387 9 0.03
388 2 0.01
390 83 0.24
391 143 0.42
392 68 0.20
393 10 0.03
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (390 bp):
AAAATTCAAACTGTATGCAAAGGGAAAAGAAAATAAAAAAAATAAAAATTATTTGATTGATTCAC
GAAAAAAGAGAATAGGAAAAAAGGTGAAAACCATGTGCAAAGGGAAAAAATAGAGTTAACGCTCT
ATAGTTGCTATAGAAATTGAAAGAGTTAAAATAAGTCAAATCAAACAATTCAAGAAAGGATATAC
AACTAATTTTTCTGTCTTTGACATTAACTAACATAACTTTGAAAGAGTTAAAACACTTCGCAAAC
AAGAATCTCACCTAATATCAAATTCAAAAAGCTAAATGTAAATGATTTGATTGATTACAGAAAAA
AAAAAGAATAGGAGAAAGAGTGAAAACCATGTGCAAAGAAAAAAAAAAGACTAAAGGGCTTTAAA
Found at i:1746341 original size:18 final size:18
Alignment explanation
Indices: 1746310--1746363 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1746300 AGGAAATGAA
1746310 AATAT-TTAAGTATTATTT
1 AATATATTAA-TATTATTT
1746328 AATATATTAATATTATTT
1 AATATATTAATATTATTT
*
1746346 AACTATAATAAATATTAT
1 AA-TAT-ATTAATATTAT
1746364 AAAGAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.47
19 7 0.22
20 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATATTAATATTATTT
Found at i:1746400 original size:44 final size:45
Alignment explanation
Indices: 1746338--1746430 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 45
1746328 AATATATTAA
* * *
1746338 TATTATTTAACTATAATAAATATTATAAAGAATA-TATTTAATAT
1 TATTATTTAACTAGAATAAACATAATAAAGAATATTATTTAATAT
* *
1746382 TATTATTTGAA-TAGAATAAACGTAATAAAGAATATTATTTAGTAT
1 TATTATTT-AACTAGAATAAACATAATAAAGAATATTATTTAATAT
1746427 TATT
1 TATT
1746431 TAAATTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 27 0.64
45 15 0.36
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.44
Consensus pattern (45 bp):
TATTATTTAACTAGAATAAACATAATAAAGAATATTATTTAATAT
Found at i:1750506 original size:851 final size:850
Alignment explanation
Indices: 1748865--1750566 Score: 3395
Period size: 851 Copynumber: 2.0 Consensus size: 850
1748855 AATTCGATTA
1748865 TATTTTAATTTATTTAAAAAATAATTTAGTTTAATCTGAACTTTATCATAATATTTTATTATTAG
1 TATTTTAATTTATTTAAAAAATAATTTAGTTTAATCTGAACTTTATCATAATATTTTATTATTAG
1748930 AGAGTATAAAAGTGGTAAGGATATATTTTGTCCTCAGAAAAGTTTCACACCTCCTATTTTGCAAA
66 AGAGTATAAAAGTGGTAAGGATATATTTTGTCCTCAGAAAAGTTTCACACCTCCTATTTTGCAAA
1748995 CTCATGAGGTTCATTTAAAAGCAGTCGGTGAGACATATACAGCCTATCCATTCAAATCTTATTGC
131 CTCATGAGGTTCATTTAAAAGCAGTCGGTGAGACATATACAGCCTATCCATTCAAATCTTATTGC
1749060 AAGTTGATATATAGATTTTCATTTATTTGCTTGATAGATTTTGTCTTTATCTTCTTAATTATTGT
196 AAGTTGATATATAGATTTTCATTTATTTGCTTGATAGATTTTGTCTTTATCTTCTTAATTATTGT
1749125 AATAAATTAGTCACGTTGTTGTTCAAAGCTAAAACCAATAGCACGAGGCCATCTATTTCTCCTTG
261 AATAAATTAGTCACGTTGTTGTTCAAAGCTAAAACCAATAGCACGAGGCCATCTATTTCTCCTTG
1749190 ACGGCATGTGATAAGTTGATTGCTACTTATGGTGAGCATTCGGCGTCGGATTCAGACATGTTATT
326 ACGGCATGTGATAAGTTGATTGCTACTTATGGTGAGCATTCGGCGTCGGATTCAGACATGTTATT
1749255 TTGGTGCCAACAAAAATTATATTTTATTTTATTCTTTTCCATAAGTATGTATTTCACTACATTTC
391 TTGGTGCCAACAAAAATTATATTTTATTTTATTCTTTTCCATAAGTATGTATTTCACTACATTTC
1749320 TTAATATAAAAAAATAATATATAAAATTTTTGGAGCCTAGAGATCCACCTTTGCGAGCAATAGTG
456 TTAATATAAAAAAATAATATATAAAATTTTTGGAGCCTAGAGATCCACCTTTGCGAGCAATAGTG
1749385 ATGGTATTTGATCTACGCATGAATACCTTTTTTTCTAAACATATAATATATTAATACAAATTGTG
521 ATGGTATTTGATCTACGCATGAATACCTTTTTTTCTAAACATATAATATATTAATACAAATTGTG
1749450 TTCGCCCACGAGAAAAAATTTATTCATACTTTATATGACTAATATCATAAAACCAACCATCAAGT
586 TTCGCCCACGAGAAAAAATTTATTCATACTTTATATGACTAATATCATAAAACCAACCATCAAGT
1749515 AAAGCCCTTTGATGACGTTAATCTAAGTTTTCTTTATATTTTAAACATCTATGTATATCACCAAA
651 AAAGCCCTTTGATGACGTTAATCTAAGTTTTCTTTATATTTTAAACATCTATGTATATCACCAAA
1749580 ACTTTATTCAATCTTATTGTTATAAGACTAAGTATAAATTATATAAATTATAGATTACAGATATA
716 ACTTTATTCAATCTTATTGTTATAAGACTAAGTATAAATTATATAAATTATAGATTACAGATATA
1749645 ACTAAATTGAAATTTTTTAAATATAAATTGTCAAATTGATTAATTGTTTCAAAGATAAGCTTAGA
781 ACTAAATTGAAATTTTTTAAATATAAATTGTCAAATTGATTAATTGTTTCAAAGATAAGCTTAGA
1749710 ATTTT
846 ATTTT
1749715 NTATTTTAATTTATTTAAAAAATAATTTAGTTTAATCTGAACTTTATCATAATATTTTATTATTA
1 -TATTTTAATTTATTTAAAAAATAATTTAGTTTAATCTGAACTTTATCATAATATTTTATTATTA
1749780 GAGAGTATAAAAGTGGTAAGGATATATTTTGTCCTCAGAAAAGTTTCACACCTCCTATTTTGCAA
65 GAGAGTATAAAAGTGGTAAGGATATATTTTGTCCTCAGAAAAGTTTCACACCTCCTATTTTGCAA
1749845 ACTCATGAGGTTCATTTAAAAGCAGTCGGTGAGACATATACAGCCTATCCATTCAAATCTTATTG
130 ACTCATGAGGTTCATTTAAAAGCAGTCGGTGAGACATATACAGCCTATCCATTCAAATCTTATTG
1749910 CAAGTTGATATATAGATTTTCATTTATTTGCTTGATAGATTTTGTCTTTATCTTCTTAATTATTG
195 CAAGTTGATATATAGATTTTCATTTATTTGCTTGATAGATTTTGTCTTTATCTTCTTAATTATTG
1749975 TAATAAATTAGTCACGTTGTTGTTCAAAGCTAAAACCAATAGCACGAGGCCATCTATTTCTCCTT
260 TAATAAATTAGTCACGTTGTTGTTCAAAGCTAAAACCAATAGCACGAGGCCATCTATTTCTCCTT
1750040 GACGGCATGTGATAAGTTGATTGCTACTTATGGTGAGCATTCGGCGTCGGATTCAGACATGTTAT
325 GACGGCATGTGATAAGTTGATTGCTACTTATGGTGAGCATTCGGCGTCGGATTCAGACATGTTAT
1750105 TTTGGTGCCAACAAAAATTATATTTTATTTTATTCTTTTCCATAAGTATGTATTTCACTACATTT
390 TTTGGTGCCAACAAAAATTATATTTTATTTTATTCTTTTCCATAAGTATGTATTTCACTACATTT
1750170 CTTAATATAAAAAAATAATATATAAAATTTTTGGAGCCTAGAGATCCACCTTTGCGAGCAATAGT
455 CTTAATATAAAAAAATAATATATAAAATTTTTGGAGCCTAGAGATCCACCTTTGCGAGCAATAGT
1750235 GATGGTATTTGATCTACGCATGAATACCTTTTTTTCTAAACATATAATATATTAATACAAATTGT
520 GATGGTATTTGATCTACGCATGAATACCTTTTTTTCTAAACATATAATATATTAATACAAATTGT
1750300 GTTCGCCCACGAGAAAAAATTTATTCATACTTTATATGACTAATATCATAAAACCAACCATCAAG
585 GTTCGCCCACGAGAAAAAATTTATTCATACTTTATATGACTAATATCATAAAACCAACCATCAAG
1750365 TAAAGCCCTTTGATGACGTTAATCTAAGTTTTCTTTATATTTTAAACATCTATGTATATCACCAA
650 TAAAGCCCTTTGATGACGTTAATCTAAGTTTTCTTTATATTTTAAACATCTATGTATATCACCAA
1750430 AACTTTATTCAATCTTATTGTTATAAGACTAAGTATAAATTATATAAATTATAGATTACAGATAT
715 AACTTTATTCAATCTTATTGTTATAAGACTAAGTATAAATTATATAAATTATAGATTACAGATAT
1750495 AACTAAATTGAAATTTTTTAAATATAAATTGTCAAATTGATTAATTGTTTCAAAGATAAGCTTAG
780 AACTAAATTGAAATTTTTTAAATATAAATTGTCAAATTGATTAATTGTTTCAAAGATAAGCTTAG
1750560 AATTTT
845 AATTTT
1750566 T
1 T
1750567 CTCATTATTG
Statistics
Matches: 851, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
850 1 0.00
851 850 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (850 bp):
TATTTTAATTTATTTAAAAAATAATTTAGTTTAATCTGAACTTTATCATAATATTTTATTATTAG
AGAGTATAAAAGTGGTAAGGATATATTTTGTCCTCAGAAAAGTTTCACACCTCCTATTTTGCAAA
CTCATGAGGTTCATTTAAAAGCAGTCGGTGAGACATATACAGCCTATCCATTCAAATCTTATTGC
AAGTTGATATATAGATTTTCATTTATTTGCTTGATAGATTTTGTCTTTATCTTCTTAATTATTGT
AATAAATTAGTCACGTTGTTGTTCAAAGCTAAAACCAATAGCACGAGGCCATCTATTTCTCCTTG
ACGGCATGTGATAAGTTGATTGCTACTTATGGTGAGCATTCGGCGTCGGATTCAGACATGTTATT
TTGGTGCCAACAAAAATTATATTTTATTTTATTCTTTTCCATAAGTATGTATTTCACTACATTTC
TTAATATAAAAAAATAATATATAAAATTTTTGGAGCCTAGAGATCCACCTTTGCGAGCAATAGTG
ATGGTATTTGATCTACGCATGAATACCTTTTTTTCTAAACATATAATATATTAATACAAATTGTG
TTCGCCCACGAGAAAAAATTTATTCATACTTTATATGACTAATATCATAAAACCAACCATCAAGT
AAAGCCCTTTGATGACGTTAATCTAAGTTTTCTTTATATTTTAAACATCTATGTATATCACCAAA
ACTTTATTCAATCTTATTGTTATAAGACTAAGTATAAATTATATAAATTATAGATTACAGATATA
ACTAAATTGAAATTTTTTAAATATAAATTGTCAAATTGATTAATTGTTTCAAAGATAAGCTTAGA
ATTTT
Found at i:1751528 original size:16 final size:15
Alignment explanation
Indices: 1751497--1751525 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1751487 AATATTTATA
1751497 ATTTTAAAAACATTT
1 ATTTTAAAAACATTT
1751512 ATTTTAAAAA-ATTT
1 ATTTTAAAAACATTT
1751526 TTAAACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTTAAAAACATTT
Found at i:1753086 original size:83 final size:83
Alignment explanation
Indices: 1752984--1753156 Score: 312
Period size: 83 Copynumber: 2.1 Consensus size: 83
1752974 TATAATCAGG
1752984 ATTAATTAAAAAATAATACATTGATGAAATTTTAA-AAAGCAATGTAACACTACAACTTATATTT
1 ATTAATTAAAAAATAATACATTGATGAAATTTTAAGAAA-CAATGTAACACTACAACTTATATTT
1753048 GAGAACTATATAATAATTT
65 GAGAACTATATAATAATTT
* *
1753067 ATTAATTAAAAAATGATACATTGATGAAATTTTAAGTAACAATGTAACACTACAACTTATATTTG
1 ATTAATTAAAAAATAATACATTGATGAAATTTTAAGAAACAATGTAACACTACAACTTATATTTG
1753132 AGAACTATATAATAATTT
66 AGAACTATATAATAATTT
1753150 ATTAATT
1 ATTAATT
1753157 TTTAAAGATT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
83 85 0.98
84 2 0.02
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (83 bp):
ATTAATTAAAAAATAATACATTGATGAAATTTTAAGAAACAATGTAACACTACAACTTATATTTG
AGAACTATATAATAATTT
Found at i:1753368 original size:16 final size:18
Alignment explanation
Indices: 1753343--1753380 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
1753333 TAAAAATGAA
1753343 ATAAATAAATAAATATAAAT
1 ATAAAT-AAT-AATATAAAT
1753363 ATAAATAATAATATAAAT
1 ATAAATAATAATATAAAT
1753381 TGAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATATAAAT
Found at i:1754163 original size:27 final size:26
Alignment explanation
Indices: 1754119--1754172 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1754109 ATGTGACAAT
*
1754119 AATATTTTTTTAACATGACGTATAAC
1 AATATTTTTTCAACATGACGTATAAC
* *
1754145 AATATTTGTTTCAACATGATGTGTAAC
1 AATATTT-TTTCAACATGACGTATAAC
1754172 A
1 A
1754173 TGTTTATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (26 bp):
AATATTTTTTCAACATGACGTATAAC
Found at i:1754203 original size:54 final size:55
Alignment explanation
Indices: 1754140--1754290 Score: 178
Period size: 57 Copynumber: 2.7 Consensus size: 55
1754130 AACATGACGT
* * * *
1754140 ATAACAATA-TTTGTTTCAACATGATGTGTAACATGTTTATGTACATAACGTATA
1 ATAATAATATTTTTTTTTAACATGACGTGTAACATGTTTATGTACATAACGTATA
* * * *
1754194 ATAATAATATTTCTTTTTTTAACATGACGTGTAACATGTTTTTGTATATGATGTATA
1 ATAATAATA-TT-TTTTTTTAACATGACGTGTAACATGTTTATGTACATAACGTATA
* *
1754251 ACAATAATATTTTTTTTTTAACATGACGTATAACATGTTT
1 ATAATAATA-TTTTTTTTTAACATGACGTGTAACATGTTT
1754291 TTATACATGG
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 8 0.10
56 28 0.33
57 48 0.57
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (55 bp):
ATAATAATATTTTTTTTTAACATGACGTGTAACATGTTTATGTACATAACGTATA
Found at i:1754291 original size:56 final size:57
Alignment explanation
Indices: 1754157--1754298 Score: 205
Period size: 57 Copynumber: 2.5 Consensus size: 57
1754147 TATTTGTTTC
* * *
1754157 AACATGATGTGTAACATGTTTATGTACATAACGTATAATAATAATATTTCTTTTTTT
1 AACATGACGTGTAACATGTTTTTGTACATAACGTATAACAATAATATTTCTTTTTTT
* * *
1754214 AACATGACGTGTAACATGTTTTTGTATATGATGTATAACAATAATATTT-TTTTTTT
1 AACATGACGTGTAACATGTTTTTGTACATAACGTATAACAATAATATTTCTTTTTTT
* *
1754270 AACATGACGTATAACATGTTTTTATACAT
1 AACATGACGTGTAACATGTTTTTGTACAT
1754299 GGCATGTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
56 33 0.43
57 43 0.57
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (57 bp):
AACATGACGTGTAACATGTTTTTGTACATAACGTATAACAATAATATTTCTTTTTTT
Found at i:1756802 original size:16 final size:16
Alignment explanation
Indices: 1756783--1756816 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1756773 GTTTGTGGCA
*
1756783 TTACGTGACTGAATAT
1 TTACATGACTGAATAT
*
1756799 TTACATGATTGAATAT
1 TTACATGACTGAATAT
1756815 TT
1 TT
1756817 GTTGAGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (16 bp):
TTACATGACTGAATAT
Found at i:1756862 original size:22 final size:22
Alignment explanation
Indices: 1756828--1756879 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1756818 TTGAGTATTG
*
1756828 CGTGACCTATTTGTAGGCATTA
1 CGTGACTTATTTGTAGGCATTA
* * *
1756850 CGTGACTTGTTTGTATGCATTG
1 CGTGACTTATTTGTAGGCATTA
1756872 CGTGACTT
1 CGTGACTT
1756880 TATCTACCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTGACTTATTTGTAGGCATTA
Found at i:1758503 original size:22 final size:22
Alignment explanation
Indices: 1758477--1758525 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1758467 TTCACCTATT
1758477 GTTTTGAGGCTTTG-GTTCACTA
1 GTTTTGAGGCTTTGCG-TCACTA
* * *
1758499 GTTTTTAGGGTTTGCGTGACTA
1 GTTTTGAGGCTTTGCGTCACTA
1758521 GTTTT
1 GTTTT
1758526 TATATATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.12, C:0.10, G:0.29, T:0.49
Consensus pattern (22 bp):
GTTTTGAGGCTTTGCGTCACTA
Found at i:1758535 original size:22 final size:22
Alignment explanation
Indices: 1758510--1758561 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1758500 TTTTTAGGGT
*
1758510 TTGCGTGA-CTAGTTTTTATATA
1 TTGCGTGACCT-GTTGTTATATA
1758532 TTGCGTGACCTGTTGTTATATA
1 TTGCGTGACCTGTTGTTATATA
1758554 TTGCGTGA
1 TTGCGTGA
1758562 AATTAGGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (22 bp):
TTGCGTGACCTGTTGTTATATA
Found at i:1758830 original size:181 final size:179
Alignment explanation
Indices: 1758531--1759082 Score: 676
Period size: 181 Copynumber: 3.0 Consensus size: 179
1758521 GTTTTTATAT
* * *
1758531 ATTGCGTGACCTGTTGTTATATATTGCGTGAAATTAGGCCATTACGTGACTGGCTATGTTGGCAT
1 ATTGCGTGA-CTGTTGTTATGTATTGCGTGACATTAGGCCATTACGTGACTGGTTATGTTGGCAT
* * * *
1758596 AATGTGTGTGAATATCACGTATTGAGTGACTTATTATTAAGTATTA-AGAGATTGGTGCTGTGTG
65 AATGTGAGTGGATATAACGCATTGAGTGACTTATTATTAAGTA-TAGAGAGATTGGTGCTGTGTG
*
1758660 ACTTGTGCAATTCACATCTTGTTTTGAGGCTTTTGTTCATTAGTTTTTTGGC
129 ACTTGTGCAATTCAC-TCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTTGGC
* * * * * *
1758712 ATTGCGTGACTGATTTTTATGTATTGCGTGACATTAGGCCAGTATGTGACTGATTTTGTTGTCAT
1 ATTGCGTGACTG-TTGTTATGTATTGCGTGACATTAGGCCATTACGTGACTGGTTATGTTGGCAT
* * * * *
1758777 AATGTGAGTGGGTATAAGGCATTGAGTGACTTGTTCTTAAGTATAGTGAGATTGGCAGTGC-GTG
65 AATGTGAGTGGATATAACGCATTGAGTGACTTATTATTAAGTATAGAGAGATT-G--GTGCTGTG
* * **
1758841 ATTGACTTGTGCAATTTATCTCTTGTTTTGAGGCTTTTGGTCACTAGTTTTTAAGC
127 --TGACTTGTGCAATTCA-CTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTTGGC
* *
1758897 ATTGCGTGACTTGTTGTTATGTATTGCGTGACATTGGGCCATTACGTGACTGGTTATATTGGCAT
1 ATTGCGTGAC-TGTTGTTATGTATTGCGTGACATTAGGCCATTACGTGACTGGTTATGTTGGCAT
* * * * * * * *
1758962 AATATGAGTGGATATTACGCATTGGGTGACTTATTATTAAGTATTGCGAGACTAGTGCTGCGTGA
65 AATGTGAGTGGATATAACGCATTGAGTGACTTATTATTAAGTATAGAGAGATTGGTGCTGTGTGA
*
1759027 CTTGTGCAATTCACGTCTTGTTTTAAGGCTTTTGTTCACTAGTTTTTTGGC
130 CTTGTGCAATTCAC-TCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTTGGC
1759078 ATTGC
1 ATTGC
1759083 ATGAATGTGT
Statistics
Matches: 312, Mismatches: 48, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
180 6 0.02
181 145 0.46
182 5 0.02
183 5 0.02
184 4 0.01
185 144 0.46
186 3 0.01
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (179 bp):
ATTGCGTGACTGTTGTTATGTATTGCGTGACATTAGGCCATTACGTGACTGGTTATGTTGGCATA
ATGTGAGTGGATATAACGCATTGAGTGACTTATTATTAAGTATAGAGAGATTGGTGCTGTGTGAC
TTGTGCAATTCACTCTTGTTTTGAGGCTTTTGTTCACTAGTTTTTTGGC
Found at i:1765691 original size:23 final size:23
Alignment explanation
Indices: 1765665--1765711 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1765655 TCAAGATACC
1765665 ATACGTACCTATCCATTAACCAA
1 ATACGTACCTATCCATTAACCAA
1765688 ATACGTACCTATCCATTAACCAA
1 ATACGTACCTATCCATTAACCAA
1765711 A
1 A
1765712 ACAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.30, G:0.04, T:0.26
Consensus pattern (23 bp):
ATACGTACCTATCCATTAACCAA
Found at i:1770402 original size:18 final size:19
Alignment explanation
Indices: 1770374--1770421 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1770364 AGAACGGGCA
*
1770374 AAAAGAATATTTTA-GAAT
1 AAAATAATATTTTATGAAT
*
1770392 AAAATATTATTTTATGAAT
1 AAAATAATATTTTATGAAT
1770411 AAAATAATATT
1 AAAATAATATT
1770422 AAAACATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATGAAT
Found at i:1772080 original size:2 final size:2
Alignment explanation
Indices: 1772026--1772064 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1772016 GATGATAAAA
*
1772026 AT AT AT AT AT TT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1772065 TTCAAGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1773288 original size:102 final size:103
Alignment explanation
Indices: 1773053--1773316 Score: 289
Period size: 102 Copynumber: 2.6 Consensus size: 103
1773043 TTTATTTGGC
* * * * *
1773053 ATTAGGTGCCTGAATATTTGTTGAGCATTGCATGAGTTCTTTATAGGCATTACGTGATTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
* * * * **
1773118 ATGTTGAGCATTGCGTGAGAGTTAATATGTGACTGAAT
66 ATATTGAACATTGCATGACAGGCAATATGTGACTGAAT
* ** *
1773156 ATTACCTGACTGAATATTTGTTGAATATTGCGTGAGTTTTTTATAGGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
* * ** *
1773221 TTATT-AACGTTGCATGACAGGCGTTACT-TGACTTAAT
66 ATATTGAACATTGCATGACAGGCAATA-TGTGACTGAAT
** * *
1773258 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTATTTGTAGGCATTGCGTGACT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACT
1773317 TTAGCTGCCT
Statistics
Matches: 133, Mismatches: 27, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
102 72 0.54
103 61 0.46
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (103 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTATTTATAGGCATTACGTGACTGAATAT
ATATTGAACATTGCATGACAGGCAATATGTGACTGAAT
Found at i:1773310 original size:22 final size:23
Alignment explanation
Indices: 1773272--1773315 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1773262 CGTGACTGAA
*
1773272 TATTTGTTGAGCATTGCGTGACC
1 TATTTGTAGAGCATTGCGTGACC
1773295 TATTTGTAG-GCATTGCGTGAC
1 TATTTGTAGAGCATTGCGTGAC
1773316 TTTAGCTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (23 bp):
TATTTGTAGAGCATTGCGTGACC
Found at i:1775876 original size:19 final size:19
Alignment explanation
Indices: 1775852--1775888 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1775842 CCATTTAACT
*
1775852 TATTGGAGTATGATTTGAA
1 TATTGGAGTATAATTTGAA
1775871 TATTGGAGTATAATTTGA
1 TATTGGAGTATAATTTGA
1775889 GGGTTTGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAA
Found at i:1776100 original size:28 final size:29
Alignment explanation
Indices: 1776053--1776113 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1776043 ATGCCAATGG
*
1776053 GTAATTTTTCAATTTTTGGGGCAAAAA-T
1 GTAATTTTTCAATTTATGGGGCAAAAAGT
* * *
1776081 GTAATTTTTGACTTTATGGGGGAAAAAGT
1 GTAATTTTTCAATTTATGGGGCAAAAAGT
1776110 GTAA
1 GTAA
1776114 ATTTCAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (29 bp):
GTAATTTTTCAATTTATGGGGCAAAAAGT
Found at i:1776107 original size:29 final size:28
Alignment explanation
Indices: 1776053--1776113 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1776043 ATGCCAATGG
* *
1776053 GTAATTTTTCAATTTTTGGGGCAAAAAT
1 GTAATTTTTCAATTTTGGGGGAAAAAAT
* * *
1776081 GTAATTTTTGACTTTATGGGGGAAAAAGT
1 GTAATTTTTCAATTT-TGGGGGAAAAAAT
1776110 GTAA
1 GTAA
1776114 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (28 bp):
GTAATTTTTCAATTTTGGGGGAAAAAAT
Found at i:1777275 original size:13 final size:13
Alignment explanation
Indices: 1777257--1777281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1777247 AGAGAAATTG
1777257 TGATTTTATAAAA
1 TGATTTTATAAAA
1777270 TGATTTTATAAA
1 TGATTTTATAAA
1777282 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1779481 original size:21 final size:23
Alignment explanation
Indices: 1779455--1779502 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1779445 TAGATACAAC
*
1779455 TAAATTGA-AATT-TTTTAAATA
1 TAAATTGATAATTATTTTAAAGA
1779476 TAAATTGATTAATTATTTTAAAGA
1 TAAATTGA-TAATTATTTTAAAGA
1779500 TAA
1 TAA
1779503 GTTTAGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
23 4 0.17
24 11 0.48
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TAAATTGATAATTATTTTAAAGA
Found at i:1780631 original size:21 final size:22
Alignment explanation
Indices: 1780602--1780645 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1780592 TTTGTTAAAT
1780602 TTTAGTTAAAATTTT-AAATGAA
1 TTTAGTT-AAATTTTGAAATGAA
*
1780624 TTTA-TTAATTTTTGAAATGAA
1 TTTAGTTAAATTTTGAAATGAA
1780645 T
1 T
1780646 ATTTTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (22 bp):
TTTAGTTAAATTTTGAAATGAA
Found at i:1780715 original size:22 final size:20
Alignment explanation
Indices: 1780689--1780740 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1780679 TTAAAAAAAT
*
1780689 AAAATATTTTTTATCAATTTTA
1 AAAATATTTATTAT--ATTTTA
1780711 AAAAT-TATTATTATATTTTA
1 AAAATAT-TTATTATATTTTA
*
1780731 AAAAAATTTA
1 AAAATATTTA
1780741 AAAAAAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.50
21 2 0.08
22 11 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATATTTATTATATTTTA
Found at i:1781928 original size:37 final size:38
Alignment explanation
Indices: 1781846--1781928 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 38
1781836 TAAAATCAAT
* *
1781846 AATTATAAAAAAATTATAACAAAATAATAATAACATCA
1 AATTATAATAAAATTATAACAAAATAATAATAACATAA
*
1781884 AA-TATAATAAAATT-TAAC-AAA-AATAACATACATAA
1 AATTATAATAAAATTATAACAAAATAATAATA-ACATAA
1781919 AATTCATAAT
1 AATT-ATAAT
1781929 CATATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
34 6 0.15
35 10 0.26
36 5 0.13
37 16 0.41
38 2 0.05
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (38 bp):
AATTATAATAAAATTATAACAAAATAATAATAACATAA
Found at i:1784319 original size:129 final size:129
Alignment explanation
Indices: 1784089--1784341 Score: 407
Period size: 129 Copynumber: 2.0 Consensus size: 129
1784079 GTGGCCCGAA
* * *
1784089 CGTGAGGTGCACTCAAATCATACCTCAGGAGATATTTCACCCAACATCTCCCCCCGGAGGTAAGT
1 CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCCCGGAGGTAAAT
*
1784154 ATATAATTGAGTTACCGTGCCCCTCTCATAGGCAGTCCACGGAAACCCCCACCACTGCAGTGAC
66 ATATAATTGAGTTACCGTGCCCCTATCATAGGCAGTCCACGGAAACCCCCACCACTGCAGTGAC
* * * * *
1784218 CGTGAGGTGCATTCAAATCTTACCTCAAGAGATACTTCATCCAGCATCTCCCTCCGGAGGTAAAT
1 CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCCCGGAGGTAAAT
* *
1784283 ATATAATTGGGTTACCGTGCCTCTATCATAGGCAGTCCACGGAAACCCCCACCACTGCA
66 ATATAATTGAGTTACCGTGCCCCTATCATAGGCAGTCCACGGAAACCCCCACCACTGCA
1784342 ATAACCATTT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 113 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (129 bp):
CGTGAGGTGCACTCAAATCATACCTCAAGAGATACTTCACCCAACATCTCCCCCCGGAGGTAAAT
ATATAATTGAGTTACCGTGCCCCTATCATAGGCAGTCCACGGAAACCCCCACCACTGCAGTGAC
Found at i:1785963 original size:29 final size:29
Alignment explanation
Indices: 1785899--1785960 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1785889 GTAAAATTTT
* * *
1785899 AAAAATTACACTTTTGCCCTCGTAAAGTG
1 AAAAATTACACTTTTACCCTCGAAAACTG
*
1785928 AAAAATTACATTTTTACCCTC-AAAACTG
1 AAAAATTACACTTTTACCCTCGAAAACTG
1785956 AAAAA
1 AAAAA
1785961 ATTCCCCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCTCGAAAACTG
Found at i:1786152 original size:19 final size:19
Alignment explanation
Indices: 1786128--1786165 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1786118 ACTTCTAAAC
*
1786128 CTCAAATCATATTCCAATA
1 CTCAAATCATACTCCAATA
1786147 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
1786166 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:1787024 original size:13 final size:13
Alignment explanation
Indices: 1787015--1787040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1787005 TCATTTTGTT
1787015 TTCATTTTTTCTG
1 TTCATTTTTTCTG
1787028 TTCATTTTTTCTG
1 TTCATTTTTTCTG
1787041 GAGCAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (13 bp):
TTCATTTTTTCTG
Found at i:1788178 original size:19 final size:19
Alignment explanation
Indices: 1788151--1788188 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1788141 CCATTTGACT
1788151 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
1788170 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
1788189 GTTAAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:1791631 original size:14 final size:14
Alignment explanation
Indices: 1791612--1791638 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1791602 AAAAATTTGA
1791612 AAAAACCCTAGAAC
1 AAAAACCCTAGAAC
1791626 AAAAACCCTAGAA
1 AAAAACCCTAGAA
1791639 ATCCTTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAAACCCTAGAAC
Found at i:1814888 original size:49 final size:49
Alignment explanation
Indices: 1814834--1814995 Score: 166
Period size: 49 Copynumber: 3.2 Consensus size: 49
1814824 CGAGCCTAAA
*
1814834 TCAAGTCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
1 TCAAGCCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
* * * * *
1814883 TCAAGTCTA-AGGATTTCAATTTTTCAAATCGAACCTACTT-TGAGATAGG
1 TCAAGCCTAGA-AATTTTAATTTTTAAAATCAAACCTA-TTGTGAGATAGG
* * **
1814932 TCAAGCCTAGGAATCTTAATTTAAAAAAAAAATCAAACCTATTGTGAGATAGG
1 TCAAGCCTAGAAATTTTAATTT----TTAAAATCAAACCTATTGTGAGATAGG
1814985 TCAAGCCTAGA
1 TCAAGCCTAGA
1814996 TCAAGTCTAG
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
48 1 0.01
49 56 0.62
50 2 0.02
52 2 0.02
53 30 0.33
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (49 bp):
TCAAGCCTAGAAATTTTAATTTTTAAAATCAAACCTATTGTGAGATAGG
Found at i:1815029 original size:60 final size:60
Alignment explanation
Indices: 1814960--1815114 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 60
1814950 ATTTAAAAAA
* *
1814960 AAAATCAAACCTATTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGAAATTTTAATATTT
1 AAAATCAAACCTCTTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATATTT
* ** * * * *
1815020 AAAATCAAACTTCTTGTGAGATAGGTTGAGCCTAGGTTAAGTCTAGAGATTTCAATTTTT
1 AAAATCAAACCTCTTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATATTT
* ** *
1815080 CAAATCGGACCTGCTT-TGGGATAGGTCAAGCCTAG
1 AAAATCAAACCT-CTTGTGAGATAGGTCAAGCCTAG
1815115 GTATCTTAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 75 0.96
61 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (60 bp):
AAAATCAAACCTCTTGTGAGATAGGTCAAGCCTAGATCAAGTCTAGAAATTTCAATATTT
Found at i:1815115 original size:60 final size:60
Alignment explanation
Indices: 1814879--1815116 Score: 165
Period size: 60 Copynumber: 4.1 Consensus size: 60
1814869 TATTGTGAGA
* * * * *
1814879 TAGGTCAAGTCTA-AGGATTTCAATTTTTCAAATCGAACCTACTT-TGAGATAGGTCAAGCC
1 TAGGTCAAGTCTAGA-AATTTCAATATTTAAAATC-AAACTGCTTGTGAGATAGGTCAAGCC
* *** *
1814939 TAGG--AA-TCT--TAATTT-AA-AAAAAAAATCAAACCT-ATTGTGAGATAGGTCAAGCC
1 TAGGTCAAGTCTAGAAATTTCAATATTTAAAATCAAA-CTGCTTGTGAGATAGGTCAAGCC
* * * **
1814992 TAGATCAAGTCTAGAAATTTTAATATTTAAAATCAAACTTCTTGTGAGATAGGTTGAGCC
1 TAGGTCAAGTCTAGAAATTTCAATATTTAAAATCAAACTGCTTGTGAGATAGGTCAAGCC
* * * * * * *
1815052 TAGGTTAAGTCTAGAGATTTCAATTTTTCAAATCGGACCTGCTT-TGGGATAGGTCAAGCC
1 TAGGTCAAGTCTAGAAATTTCAATATTTAAAATC-AAACTGCTTGTGAGATAGGTCAAGCC
1815112 TAGGT
1 TAGGT
1815117 ATCTTAATTT
Statistics
Matches: 138, Mismatches: 29, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
52 4 0.03
53 26 0.19
54 2 0.01
55 6 0.04
56 3 0.02
57 3 0.02
58 7 0.05
59 4 0.03
60 77 0.56
61 6 0.04
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (60 bp):
TAGGTCAAGTCTAGAAATTTCAATATTTAAAATCAAACTGCTTGTGAGATAGGTCAAGCC
Found at i:1815244 original size:59 final size:59
Alignment explanation
Indices: 1815140--1815271 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
1815130 AACAAATCAT
* * * ** *
1815140 ACCTGTTGTGAGATAGGTTGAGCTTAAATCAAGTCCGGGAATTTC-ATTTTTAAAATTGA
1 ACCTGTTGTGAGATAAGTCGAGCCTAAATCAAGTCCAAGAATTTCAATTTTT-AAATCGA
** * *
1815199 ACCTGTTGTGAGATAAGTCGAGCCTAGGTCAAGTCTAAGAGTTTCAATTTTTAAATCGA
1 ACCTGTTGTGAGATAAGTCGAGCCTAAATCAAGTCCAAGAATTTCAATTTTTAAATCGA
* *
1815258 ACCTATTTTGAGAT
1 ACCTGTTGTGAGAT
1815272 GGATCGAACT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 54 0.90
60 6 0.10
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (59 bp):
ACCTGTTGTGAGATAAGTCGAGCCTAAATCAAGTCCAAGAATTTCAATTTTTAAATCGA
Found at i:1816347 original size:20 final size:21
Alignment explanation
Indices: 1816302--1816348 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1816292 AGATGTCTAA
*
1816302 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
1816323 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
1816343 AATAAT
1 AATAAT
1816349 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:1817313 original size:13 final size:13
Alignment explanation
Indices: 1817295--1817319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1817285 TTTCAGAAAA
1817295 TTTATAAAATCAT
1 TTTATAAAATCAT
1817308 TTTATAAAATCA
1 TTTATAAAATCA
1817320 CAATTTTTCC
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:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:1820610 original size:14 final size:14
Alignment explanation
Indices: 1820591--1820633 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1820581 TTAACTCACC
1820591 TAAAATAATTAATT
1 TAAAATAATTAATT
*
1820605 TAAAATAATTAA-A
1 TAAAATAATTAATT
1820618 TAAAATATATTAATT
1 TAAAATA-ATTAATT
1820633 T
1 T
1820634 CTATGCATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 17 0.68
15 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAATAATTAATT
Found at i:1820665 original size:22 final size:23
Alignment explanation
Indices: 1820640--1820686 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1820630 ATTTCTATGC
1820640 ATTACTA-CAAAAATTAAGC-CAA
1 ATTACTATC-AAAATTAAGCTCAA
*
1820662 ATTATTATCAAAATTAAGCTCAA
1 ATTACTATCAAAATTAAGCTCAA
1820685 AT
1 AT
1820687 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (23 bp):
ATTACTATCAAAATTAAGCTCAA
Found at i:1823293 original size:20 final size:20
Alignment explanation
Indices: 1823236--1823298 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
1823226 TATATACCCA
* *
1823236 TCATCATCA-TCTCACCAAC
1 TCATCATCATTATCACCAGC
* * *
1823255 CCATTATCATCATCACCAGC
1 TCATCATCATTATCACCAGC
1823275 TCATCATCATTATCACCAGC
1 TCATCATCATTATCACCAGC
1823295 TCAT
1 TCAT
1823299 GCGTACTCCC
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 7 0.20
20 28 0.80
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.29
Consensus pattern (20 bp):
TCATCATCATTATCACCAGC
Found at i:1823371 original size:43 final size:43
Alignment explanation
Indices: 1823297--1823458 Score: 234
Period size: 43 Copynumber: 3.8 Consensus size: 43
1823287 TCACCAGCTC
* * *
1823297 ATGCGTACTCCCTACTCGCACATGGCTGGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCATCGGGTT
* *
1823340 ATGCACACTCCCTACTCGCACATAACCGGGTCATCATCGGGTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCATCGGGTT
* * *
1823383 ATGCGCACTCCCTACTCGCACATAGCCAGGTCATCCTCGGTTT
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCATCGGGTT
* *
1823426 ATGTGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAGCCGGGTCA
1823459 ACATAATTAC
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAGCCGGGTCATCATCGGGTT
Found at i:1844927 original size:21 final size:22
Alignment explanation
Indices: 1844901--1844942 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1844891 TTGGAATTAA
1844901 AAGTATCAAGA-CTTAGATCAT
1 AAGTATCAAGACCTTAGATCAT
*
1844922 AAGTATCAAGACCTTATATCA
1 AAGTATCAAGACCTTAGATCA
1844943 AACAAGCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
AAGTATCAAGACCTTAGATCAT
Found at i:1845452 original size:34 final size:34
Alignment explanation
Indices: 1845374--1845453 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 34
1845364 AAAGGTAGAG
* * *
1845374 AGGTTAGGCTTGCTCCTTGAAAAGGCATTGTAAA
1 AGGTTATGCTTGCTCCGTGAAAAAGCATTGTAAA
* * * *
1845408 AAGTTGTGCTTGCTCCCGTGAAAAAGCATTG-CAT
1 AGGTTATGCTTGCT-CCGTGAAAAAGCATTGTAAA
1845442 AGGTTATGCTTG
1 AGGTTATGCTTG
1845454 AGCCCAAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (34 bp):
AGGTTATGCTTGCTCCGTGAAAAAGCATTGTAAA
Found at i:1846018 original size:17 final size:17
Alignment explanation
Indices: 1845996--1846044 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
1845986 AAAGAATCGA
1845996 CTTTGCTTTGAATTTTG
1 CTTTGCTTTGAATTTTG
1846013 CTTTGCTTTGAATTTTG
1 CTTTGCTTTGAATTTTG
1846030 CTTTGCTTTGAATTT
1 CTTTGCTTTGAATTT
1846045 GAATGAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (17 bp):
CTTTGCTTTGAATTTTG
Found at i:1846257 original size:15 final size:15
Alignment explanation
Indices: 1846233--1846280 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1846223 CAATAATATG
1846233 TTACTACCTAAGGCA
1 TTACTACCTAAGGCA
* **
1846248 TTACTGCCTAAGGTG
1 TTACTACCTAAGGCA
*
1846263 TTACTATCTAAGGCA
1 TTACTACCTAAGGCA
1846278 TTA
1 TTA
1846281 TTGTTTAAGG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (15 bp):
TTACTACCTAAGGCA
Found at i:1846299 original size:30 final size:30
Alignment explanation
Indices: 1846232--1846302 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
1846222 ACAATAATAT
* *
1846232 GTTACTACCTAAGGCATTACTGCCTAAGGT
1 GTTACTATCTAAGGCATTACTGCCTAAGGA
* **
1846262 GTTACTATCTAAGGCATTATTGTTTAAGGA
1 GTTACTATCTAAGGCATTACTGCCTAAGGA
1846292 GTTACTATCTA
1 GTTACTATCTA
1846303 GGGCGGTACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (30 bp):
GTTACTATCTAAGGCATTACTGCCTAAGGA
Found at i:1846594 original size:37 final size:35
Alignment explanation
Indices: 1846551--1846657 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 35
1846541 ACTTCACGTA
**
1846551 AGAACAATTAAAAACAAAGTGAAGCAATATTTCATGT
1 AGAACAATT-AAAAC-AAGTGAAGCAATATTTCACAT
* *
1846588 AGAACAATTAAAACAAGTGAAACACACTACTTCACAT
1 AGAACAATTAAAACAAGTGAAGCA-A-TATTTCACAT
* *
1846625 AAAACAATTAAAACAAGTGAAGCATTATTTCAC
1 AGAACAATTAAAACAAGTGAAGCAATATTTCAC
1846658 GCATAACAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
35 16 0.27
36 6 0.10
37 38 0.63
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.22
Consensus pattern (35 bp):
AGAACAATTAAAACAAGTGAAGCAATATTTCACAT
Found at i:1852502 original size:235 final size:237
Alignment explanation
Indices: 1852044--1852514 Score: 766
Period size: 235 Copynumber: 2.0 Consensus size: 237
1852034 AAATAAGGTG
* * *
1852044 AGATTAACATGATGGGAGTTGTAAGGGTGAGAGCTGGTATCAGTGGAATGGGGCTTACATGTTTG
1 AGATTAACATGATGAGAGTAGTAAGGGTGAGAGCTGGTATCAATGGAATGGGGCTTACATGTTTG
* * *
1852109 AATGTGATTGTGATTTACAATTTAATGAAGGGTAATGAGTTGAATGGTGATGGTGCTAAAAGGTC
66 AATGTGATTGTGATTTACAATCTAATGAAGGGTAATGAGGTGAATGGTGACGGTGCTAAAAGGTC
* * * *
1852174 TAGACCTAGTTGGAATATAGAAAAGAAGAGCCAAGGAGCTAGTATTAAGGTAAAAGTTAAAACCA
131 TACACCTAGTCGGAATATAGAAAAGAAGAGCCAAGGAGCTAATATTAAGGTAAAAGTCAAAACCA
* *
1852239 AGATACATATCAAGGTTTGTGTAGAAGAGACATGAAAATAGA
196 AGATACATATCAAGGCTTGTGAAGAAGAGACATGAAAATAGA
*
1852281 AGATTAACATGATGAGAGTAGT-AGGG-GAGAGCTGGTATTAATGGAATGGGGCTTACATGTTTG
1 AGATTAACATGATGAGAGTAGTAAGGGTGAGAGCTGGTATCAATGGAATGGGGCTTACATGTTTG
*
1852344 AATGTGATTGTGATTTACAATCTAATGAGGGGTAATGAGGTGAATGGTGACGGTGCTAAAAGGTC
66 AATGTGATTGTGATTTACAATCTAATGAAGGGTAATGAGGTGAATGGTGACGGTGCTAAAAGGTC
*
1852409 TACACCTAGTCGGAATATAGAAAAGAAGAGCCAAGGAGTTAATATTAAGGTAAAAGTCAAAACCA
131 TACACCTAGTCGGAATATAGAAAAGAAGAGCCAAGGAGCTAATATTAAGGTAAAAGTCAAAACCA
* * *
1852474 AGATACGTGTCAGGGCTTGTGAAGAAGAGACATGAAAATAG
196 AGATACATATCAAGGCTTGTGAAGAAGAGACATGAAAATAG
1852515 GAGAAGATAT
Statistics
Matches: 216, Mismatches: 18, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
235 192 0.89
236 4 0.02
237 20 0.09
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (237 bp):
AGATTAACATGATGAGAGTAGTAAGGGTGAGAGCTGGTATCAATGGAATGGGGCTTACATGTTTG
AATGTGATTGTGATTTACAATCTAATGAAGGGTAATGAGGTGAATGGTGACGGTGCTAAAAGGTC
TACACCTAGTCGGAATATAGAAAAGAAGAGCCAAGGAGCTAATATTAAGGTAAAAGTCAAAACCA
AGATACATATCAAGGCTTGTGAAGAAGAGACATGAAAATAGA
Found at i:1852670 original size:127 final size:129
Alignment explanation
Indices: 1852483--1852726 Score: 411
Period size: 127 Copynumber: 1.9 Consensus size: 129
1852473 AAGATACGTG
* ***
1852483 TCAGGGCTTGTGAAGAAGAGACATGAAAATAGGAGAAGATATTCATGACGGGAGGGCATTGGAAG
1 TCAGGGCTTGTGAAGAAGAGACATGAAAATAGGAGAAGATATACATGACGGGAAAACATTGGAAG
1852548 TAATTGAAATTGGCCGATGAGGAGCTTGT-GAAGAACTTATGGAAATGGTGGAAGCCAGAATTA
66 TAATTGAAATTGGCCGATGAGGAGCTTGTCGAAGAACTTATGGAAATGGTGGAAGCCAGAATTA
* *
1852611 TCAGGGCTTGTGAAGAAGAGCCATG-AAATATGAGAAGATATACATGACGGGAAAACATTGGAAG
1 TCAGGGCTTGTGAAGAAGAGACATGAAAATAGGAGAAGATATACATGACGGGAAAACATTGGAAG
*
1852675 TAATTGAAATTGGCCGATGAGGAGCTTGTCGAGGAACTTATGGAAATGGTGG
66 TAATTGAAATTGGCCGATGAGGAGCTTGTCGAAGAACTTATGGAAATGGTGG
1852727 TAGCTGGAAT
Statistics
Matches: 108, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
127 63 0.58
128 45 0.42
ACGTcount: A:0.36, C:0.10, G:0.32, T:0.22
Consensus pattern (129 bp):
TCAGGGCTTGTGAAGAAGAGACATGAAAATAGGAGAAGATATACATGACGGGAAAACATTGGAAG
TAATTGAAATTGGCCGATGAGGAGCTTGTCGAAGAACTTATGGAAATGGTGGAAGCCAGAATTA
Found at i:1853402 original size:15 final size:15
Alignment explanation
Indices: 1853378--1853418 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1853368 TATTTATTTT
1853378 GTAATGTGATTACAA
1 GTAATGTGATTACAA
* *
1853393 GTAATATGATTGCAA
1 GTAATGTGATTACAA
*
1853408 GCAATGTGATT
1 GTAATGTGATT
1853419 GTAAAGAAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (15 bp):
GTAATGTGATTACAA
Found at i:1853659 original size:22 final size:21
Alignment explanation
Indices: 1853634--1853688 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
1853624 TCATATATTT
1853634 TATTTTTTATTATGCTTTT-ATA
1 TATTTTTTATTAT--TTTTAATA
*
1853656 TATTTTATTTTTATTTTTAATA
1 TATTTT-TTATTATTTTTAATA
1853678 TAATTTTTTAT
1 T-ATTTTTTAT
1853689 ATTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 4 0.14
22 13 0.46
23 11 0.39
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTTATTATTTTTAATA
Found at i:1853691 original size:27 final size:27
Alignment explanation
Indices: 1853658--1853713 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1853648 CTTTTATATA
*
1853658 TTTTAT-TTTTAT-TTTTAATATAATT
1 TTTTATATTATATATTTTAATATAATT
* *
1853683 TTTTATATTATATATTTTATTTTAATT
1 TTTTATATTATATATTTTAATATAATT
1853710 TTTT
1 TTTT
1853714 TTAAAAGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 5 0.19
27 15 0.58
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTATATTATATATTTTAATATAATT
Found at i:1853706 original size:32 final size:31
Alignment explanation
Indices: 1853609--1853716 Score: 98
Period size: 33 Copynumber: 3.4 Consensus size: 31
1853599 TCATTTCTTA
* *
1853609 AATATATTTTTAATATCATATATTTTATTTT
1 AATATATTTTTTATATTATATATTTTATTTT
* *
1853640 -TTATTATGCTTTTATATATTTTAT-TTTTATTTTT
1 AATA-TAT--TTTT-TATATTATATATTTTA-TTTT
1853674 AATATAATTTTTTATATTATATATTTTATTTT
1 AATAT-ATTTTTTATATTATATATTTTATTTT
1853706 AAT-T-TTTTTTA
1 AATATATTTTTTA
1853717 AAAGGCAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
29 7 0.11
30 2 0.03
31 4 0.06
32 16 0.25
33 18 0.29
34 12 0.19
35 4 0.06
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (31 bp):
AATATATTTTTTATATTATATATTTTATTTT
Found at i:1866294 original size:28 final size:27
Alignment explanation
Indices: 1866243--1866296 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1866233 GTGTCCTAGT
*
1866243 GGTGGAAAATTACAACTTTGCCCTTAG
1 GGTGGAAAATTACAACTTTACCCTTAG
* *
1866270 GGTGGCAAAATTACCATTTTACCCTTA
1 GGTGG-AAAATTACAACTTTACCCTTA
1866297 TACTCCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAACTTTACCCTTAG
Found at i:1866364 original size:19 final size:19
Alignment explanation
Indices: 1866340--1866377 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1866330 ACTTCTAAAC
1866340 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
1866359 CTCAAATCATGCTCCAATA
1 CTCAAATCATACTCCAATA
1866378 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:1874477 original size:54 final size:54
Alignment explanation
Indices: 1874408--1874513 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
1874398 ATGGTGATAT
* *
1874408 TGTCCGGCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAAATGGGA
*
1874462 TGTCTGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAAATGG
1 TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAAATGG
1874514 AATGATTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.19, C:0.13, G:0.42, T:0.26
Consensus pattern (54 bp):
TGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAAATGGGA
Found at i:1897995 original size:20 final size:21
Alignment explanation
Indices: 1897966--1898019 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1897956 AAGAATGTTT
1897966 TATCGATACATTTTC-AAATG
1 TATCGATACATTTTCTAAATG
* *
1897986 TATTGATACATTGTCTAAATG
1 TATCGATACATTTTCTAAATG
1898007 TATCGATACATTT
1 TATCGATACATTT
1898020 GAAATAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (21 bp):
TATCGATACATTTTCTAAATG
Found at i:1900078 original size:10 final size:12
Alignment explanation
Indices: 1900029--1900089 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 12
1900019 TTTTTGTCAT
*
1900029 TTATTATTATTTAA
1 TTATTATT-TTT-C
*
1900043 TTATTATTTTTA
1 TTATTATTTTTC
1900055 TTATCATATTTTTC
1 TTAT--TATTTTTC
1900069 -TATT-TTTTTC
1 TTATTATTTTTC
1900079 TTATTATTTTT
1 TTATTATTTTT
1900090 TTTGTAAGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.14
11 5 0.12
12 10 0.24
13 6 0.14
14 15 0.36
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTATTTTTC
Found at i:1900635 original size:16 final size:16
Alignment explanation
Indices: 1900616--1900664 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
1900606 TTTGTAGTTT
1900616 TTTTATTTATTATTTA
1 TTTTATTTATTATTTA
* **
1900632 TTTTATTTTTTATTGC
1 TTTTATTTATTATTTA
**
1900648 TACTATTTATTATTTA
1 TTTTATTTATTATTTA
1900664 T
1 T
1900665 CGCTATTATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTATTTATTATTTA
Found at i:1900658 original size:20 final size:20
Alignment explanation
Indices: 1900633--1900680 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1900623 TATTATTTAT
* *
1900633 TTTATTTTTTATTGCTACTA
1 TTTATTATTTATCGCTACTA
*
1900653 TTTATTATTTATCGCTATTA
1 TTTATTATTTATCGCTACTA
1900673 -TTATTATT
1 TTTATTATT
1900681 ATTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.23, C:0.08, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTATTATTTATCGCTACTA
Found at i:1900931 original size:17 final size:17
Alignment explanation
Indices: 1900887--1900933 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
1900877 TGCAAACATA
1900887 CTTTATTTAGCTATATAG
1 CTTTATTTA-CTATATAG
*
1900905 TTTTATTTTAC-ATATATG
1 CTTTA-TTTACTATATA-G
1900923 CTTTATTTACT
1 CTTTATTTACT
1900934 TAAGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (17 bp):
CTTTATTTACTATATAG
Found at i:1902266 original size:19 final size:19
Alignment explanation
Indices: 1902242--1902287 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1902232 ACTCGACTTA
1902242 ATTTATTTTTTTATTTTTT
1 ATTTATTTTTTTATTTTTT
1902261 ATTTA-TTTTTTATTTTTT
1 ATTTATTTTTTTATTTTTT
*
1902279 -TTTGTTTTT
1 ATTTATTTTT
1902288 GTGTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 17 0.68
19 5 0.20
ACGTcount: A:0.13, C:0.00, G:0.02, T:0.85
Consensus pattern (19 bp):
ATTTATTTTTTTATTTTTT
Found at i:1902320 original size:33 final size:33
Alignment explanation
Indices: 1902268--1902430 Score: 114
Period size: 37 Copynumber: 4.7 Consensus size: 33
1902258 TTTATTTATT
* *
1902268 TTTTATTTTTTTT-TGTTTTTGTGTTTTTTTTG
1 TTTTGTTTTTTTTGTTTTTTTGTGTTTTTTTTG
*
1902300 TTTTGTTTTTTTTGTTTTTTTGGTTTTTTTTTGTG
1 TTTTGTTTTTTTTGTTTTTTT-GTGTTTTTTT-TG
* * *
1902335 TTTTTGTTTTTGTTTTTTTTTGTTCTCTTCTTTTTTG
1 -TTTTGTTTTT-TTTGTTTTT-TTGTGTT-TTTTTTG
* * *
1902372 TTTT-TGTGTTTTGTTGATTTTGTGGTTTTTTTTTG
1 TTTTGTTTTTTTTGTT-TTTTTGT-G-TTTTTTTTG
* *
1902407 TTTCGTTTTTGTTTTGTTTGTTTG
1 TTTTG-TTTT-TTTTGTTTTTTTG
1902431 AAAGAAAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
32 12 0.12
33 6 0.06
34 17 0.17
35 17 0.17
36 16 0.16
37 19 0.19
38 14 0.14
ACGTcount: A:0.01, C:0.02, G:0.17, T:0.80
Consensus pattern (33 bp):
TTTTGTTTTTTTTGTTTTTTTGTGTTTTTTTTG
Found at i:1902320 original size:50 final size:49
Alignment explanation
Indices: 1902266--1902425 Score: 135
Period size: 52 Copynumber: 3.0 Consensus size: 49
1902256 TTTTTATTTA
*
1902266 TTTTTTATTTTTTTTTGTTTTTGTGTTTTTTTTGTTTTGTTTTTTTTGT
1 TTTTTTTTTTTTTTTTGTTTTTGTGTTTTTTTTGTTTTGTTTTTTTTGT
*
1902315 TTTTTTGGTTTTTTTTTGTGTTTTTGT-TTTTGTTTTTTTTTGTTCTCTTCTTT-T
1 TTTTTT--TTTTTTTTT-TGTTTTTGTGTTTT-TTTTGTTTTGTT-T-TT-TTTGT
* * * *
1902369 TTGTTTTTGTGTTTTGTTGATTTTGTGGTTTTTTTTTGTTTCGTTTTTGTTTTGT
1 TT-TTTTT-TTTTTTTTTGTTTTTGT-G-TTTTTTTTGTTTTG-TTTT-TTTTGT
1902424 TT
1 TT
1902426 GTTTGAAAGA
Statistics
Matches: 89, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
49 6 0.07
51 12 0.13
52 20 0.22
53 10 0.11
54 15 0.17
55 20 0.22
56 6 0.07
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.81
Consensus pattern (49 bp):
TTTTTTTTTTTTTTTTGTTTTTGTGTTTTTTTTGTTTTGTTTTTTTTGT
Found at i:1902368 original size:24 final size:22
Alignment explanation
Indices: 1902247--1902429 Score: 106
Period size: 22 Copynumber: 8.0 Consensus size: 22
1902237 ACTTAATTTA
* *
1902247 TTTTTTTATTTTTTATTTATTT-
1 TTTTTTTGTTTTTT-TTTGTTTC
* *
1902269 TTTATTTTTTTTTGTTTTTGTGT-
1 TTT-TTTTGTTTT-TTTTTGTTTC
*
1902292 TTTTTTTGTTTTGTTTTT-TTTG
1 TTTTTTTGTTTT-TTTTTGTTTC
*
1902314 TTTTTTTGGTTTTTTTTTGTGTTT
1 TTTTTTT-GTTTTTTTTTGT-TTC
1902338 TTGTTTTTGTTTTTTTTTGTTCTC
1 TT-TTTTTGTTTTTTTTTGTT-TC
**
1902362 TTCTTTTTTGTTTTTGTGTTTTGTTGA
1 -T-TTTTTTG-TTTT-T-TTTTGTTTC
* *
1902389 TTTTGTGGTTTTTTTTTGTTTC
1 TTTTTTTGTTTTTTTTTGTTTC
* *
1902411 -GTTTTTG-TTTTGTTTGTTT
1 TTTTTTTGTTTTTTTTTGTTT
1902430 GAAAGAAAAA
Statistics
Matches: 131, Mismatches: 17, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
20 11 0.08
21 6 0.05
22 36 0.27
23 24 0.18
24 23 0.18
25 17 0.13
26 6 0.05
27 1 0.01
28 7 0.05
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTTTGTTTC
Found at i:1902370 original size:1 final size:1
Alignment explanation
Indices: 1902247--1902355 Score: 74
Period size: 1 Copynumber: 109.0 Consensus size: 1
1902237 ACTTAATTTA
* * * * * * * * *
1902247 TTTTTTTATTTTTTATTTATTTTTTATTTTTTTTTGTTTTTGTGTTTTTTTTGTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * * *
1902312 TGTTTTTTTGGTTTTTTTTTGTGTTTTTGTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1902356 GTTCTCTTCT
Statistics
Matches: 78, Mismatches: 30, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.04, C:0.00, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:1902370 original size:74 final size:76
Alignment explanation
Indices: 1902267--1902425 Score: 193
Period size: 74 Copynumber: 2.1 Consensus size: 76
1902257 TTTTATTTAT
* * * * * * *
1902267 TTTTTATTTTTTTTTGTTTTTGTGTTTTTTTTGTTTTGT-TTTTTTTGTTTTTTTGGTTTTTTTT
1 TTTTTGTTTTTTTTTGTTTCTGTCTTTTTTGT-TTTTGTGTTTTGTTGATTTTGTGGTTTTTTTT
1902331 TG-T-GTTTTTG
65 TGTTCGTTTTTG
1902341 TTTTTGTTTTTTTTTGTTCTCT-TCTTTTTTGTTTTTGTGTTTTGTTGATTTTGTGGTTTTTTTT
1 TTTTTGTTTTTTTTTGTT-TCTGTCTTTTTTGTTTTTGTGTTTTGTTGATTTTGTGGTTTTTTTT
1902405 TGTTTCGTTTTTG
65 TG-TTCGTTTTTG
1902418 -TTTTGTTT
1 TTTTTGTTT
1902426 GTTTGAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
73 6 0.08
74 49 0.67
75 2 0.03
76 9 0.12
77 7 0.10
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.81
Consensus pattern (76 bp):
TTTTTGTTTTTTTTTGTTTCTGTCTTTTTTGTTTTTGTGTTTTGTTGATTTTGTGGTTTTTTTTT
GTTCGTTTTTG
Found at i:1902568 original size:40 final size:39
Alignment explanation
Indices: 1902460--1902583 Score: 146
Period size: 38 Copynumber: 3.2 Consensus size: 39
1902450 AGGTGCTACA
* * * *
1902460 AAAC-TTT-AAAATGAAACTCCCCAAAACTGAGGTAGCG
1 AAACTTTTAAAAATGAAACTCCTCAAAATTGAGGCAACG
* *
1902497 AAACTTCTAAAAATG-AACTCCTCAAAGTTGAGGCAACG
1 AAACTTTTAAAAATGAAACTCCTCAAAATTGAGGCAACG
*
1902535 AAACTTTTAAAAATGAAAACTCGTCAAAATTGAGGCAACG
1 AAACTTTTAAAAATG-AAACTCCTCAAAATTGAGGCAACG
1902575 AAACCTTTT
1 AAA-CTTTT
1902584 TTAAAAGTGA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
37 4 0.05
38 34 0.47
39 6 0.08
40 24 0.33
41 5 0.07
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (39 bp):
AAACTTTTAAAAATGAAACTCCTCAAAATTGAGGCAACG
Found at i:1902603 original size:41 final size:38
Alignment explanation
Indices: 1902460--1902636 Score: 142
Period size: 38 Copynumber: 4.5 Consensus size: 38
1902450 AGGTGCTACA
* ** * *
1902460 AAAC-TTT-AAAATGAAACTCCCCAAAACTGAGGTAGCG
1 AAACTTTTAAAAATG-AACTCCTCAAAGTTGAGGCAACG
*
1902497 AAACTTCTAAAAATGAACTCCTCAAAGTTGAGGCAACG
1 AAACTTTTAAAAATGAACTCCTCAAAGTTGAGGCAACG
* *
1902535 AAACTTTTAAAAATGAAAACTCGTCAAAATTGAGGCAACG
1 AAACTTTTAAAAATG--AACTCCTCAAAGTTGAGGCAACG
* * * * *
1902575 AAACCTTTTTTAAAAGTGAATTCTTCAAAGCTGAGGCAATG
1 AAA-C--TTTTAAAAATGAACTCCTCAAAGTTGAGGCAACG
*
1902616 ACACTTTTTAAAAAATGAACT
1 AAAC-TTTT-AAAAATGAACT
1902637 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
37 4 0.04
38 34 0.30
39 11 0.10
40 34 0.30
41 21 0.18
43 10 0.09
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (38 bp):
AAACTTTTAAAAATGAACTCCTCAAAGTTGAGGCAACG
Found at i:1903026 original size:38 final size:38
Alignment explanation
Indices: 1902892--1903040 Score: 217
Period size: 38 Copynumber: 3.8 Consensus size: 38
1902882 NNNNNNNNNN
*
1902892 GAACTCCTCAAAGCTGAGGCAACGAGACTTTTAAAAAT
1 GAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAAT
* *
1902930 GAACTCCTCAAAGCTGAGGCAACGGAACTTTAAAAAAAAT
1 GAACTCCTCAAAGCTGAGGCAACGAAACTTT--TAAAAAT
1902970 GAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAAT
1 GAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAAT
** *
1903008 GAACTCCTCAAAAATGAGGTAACGAAACCTTTT
1 GAACTCCTCAAAGCTGAGGCAACGAAA-CTTTT
1903041 TTCTTTTTTG
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
38 59 0.59
39 5 0.05
40 36 0.36
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (38 bp):
GAACTCCTCAAAGCTGAGGCAACGAAACTTTTAAAAAT
Found at i:1915289 original size:51 final size:54
Alignment explanation
Indices: 1915202--1915318 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 54
1915192 ATGTCATGGG
1915202 TTTTATTTA-TTATATATATATACATTTGAATCATTA-TT-ATCATTT-TTATT
1 TTTTATTTATTTATATATATATACATTTGAATCATTATTTGATCATTTATTATT
* * * * * *
1915252 TTTTATTTATTTATATATATGTATATTT-TACCTATTATTTGTTTATTTATTATT
1 TTTTATTTATTTATATATATATACATTTGAATC-ATTATTTGATCATTTATTATT
1915306 TTATTATTTATTT
1 TT-TTATTTATTT
1915319 TTTGAATGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 11 0.20
51 20 0.36
52 2 0.04
53 5 0.09
54 7 0.13
55 10 0.18
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (54 bp):
TTTTATTTATTTATATATATATACATTTGAATCATTATTTGATCATTTATTATT
Found at i:1915302 original size:15 final size:16
Alignment explanation
Indices: 1915284--1915322 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1915274 ATATTTTACC
1915284 TATTATTTGT-TTATT
1 TATTATTTGTATTATT
1915299 TATTATTT-TATTATT
1 TATTATTTGTATTATT
*
1915314 TATTTTTTG
1 TATTATTTG
1915323 AATGATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TATTATTTGTATTATT
Found at i:1920257 original size:38 final size:39
Alignment explanation
Indices: 1920159--1920264 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 39
1920149 CACTCCCGGC
*
1920159 TCATGTACATCCCCCCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * *
1920199 TCATGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CTA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
*
1920237 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
1920265 CGGGCACTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
38 28 0.47
39 3 0.05
40 28 0.47
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.21
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:1933397 original size:2 final size:2
Alignment explanation
Indices: 1933390--1933480 Score: 114
Period size: 2 Copynumber: 46.5 Consensus size: 2
1933380 TCTAGGCAAC
**
1933390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT NG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1933431 AC A- AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1933472 AC AT AT AT A
1 AT AT AT AT A
1933481 ATCTATTCTA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1935789 original size:8 final size:9
Alignment explanation
Indices: 1935761--1935792 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1935751 AGCAACAAGC
*
1935761 AAATTTGAA
1 AAATATGAA
1935770 AAATATGAA
1 AAATATGAA
1935779 AAATATGAA
1 AAATATGAA
1935788 AAATA
1 AAATA
1935793 CCCAAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (9 bp):
AAATATGAA
Found at i:1937059 original size:36 final size:36
Alignment explanation
Indices: 1937012--1937122 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 36
1937002 TTAACTCAGC
* *
1937012 TCATGTGCACTCCCACACAGCGCATAGCTAATATCG
1 TCATGTGCACTCCCACACAGCACATAGCTAATATCA
* * *
1937048 TCATGTGCACTCCCACACCGCACATAGTTATTATCA
1 TCATGTGCACTCCCACACAGCACATAGCTAATATCA
* *
1937084 TCATGTGCACTCCCACACCA-CACATAGTTATTATCA
1 TCATGTGCACTCCCACA-CAGCACATAGCTAATATCA
1937120 TCA
1 TCA
1937123 ACCTGAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 67 0.99
37 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (36 bp):
TCATGTGCACTCCCACACAGCACATAGCTAATATCA
Found at i:1947709 original size:34 final size:35
Alignment explanation
Indices: 1947659--1947728 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
1947649 TTTCACCAAG
* **
1947659 CTTTACAATAGCTTTTCA-AGGCTCGGCTAAAACC
1 CTTTACAATAGCTTTTCACAAGCTCAACTAAAACC
* *
1947693 CTTTACACTAGTTTTTCACAAGCTCAACTAAAACC
1 CTTTACAATAGCTTTTCACAAGCTCAACTAAAACC
1947728 C
1 C
1947729 CAAGTGGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (35 bp):
CTTTACAATAGCTTTTCACAAGCTCAACTAAAACC
Found at i:1949360 original size:26 final size:28
Alignment explanation
Indices: 1949321--1949373 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
1949311 AAATATAATT
*
1949321 AGCAAGAATCTAACTA-A-AAAAATTAG
1 AGCAAGAATATAACTAGAGAAAAATTAG
*
1949347 AGCAATAATATAACTAGAGAAAAATTA
1 AGCAAGAATATAACTAGAGAAAAATTA
1949374 ATTCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 1 0.04
28 8 0.35
ACGTcount: A:0.58, C:0.09, G:0.11, T:0.21
Consensus pattern (28 bp):
AGCAAGAATATAACTAGAGAAAAATTAG
Found at i:1950827 original size:15 final size:15
Alignment explanation
Indices: 1950807--1950844 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1950797 TATAAATTTC
1950807 AATCAATTAATTTAT
1 AATCAATTAATTTAT
1950822 AATCAATTAATTTAT
1 AATCAATTAATTTAT
1950837 AATCAATT
1 AATCAATT
1950845 CCATAGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (15 bp):
AATCAATTAATTTAT
Found at i:1952394 original size:2 final size:2
Alignment explanation
Indices: 1952387--1952414 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1952377 CTCCAATTAA
1952387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1952415 TTGATGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1956383 original size:13 final size:13
Alignment explanation
Indices: 1956365--1956389 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1956355 GGAGAAATTG
1956365 TGATTTTATAAAA
1 TGATTTTATAAAA
1956378 TGATTTTATAAA
1 TGATTTTATAAA
1956390 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:1957345 original size:20 final size:18
Alignment explanation
Indices: 1957308--1957350 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1957298 AAAAATAGAA
*
1957308 TATTTTATTGAATATTAT
1 TATTTTATTAAATATTAT
1957326 TATTTTATTCAAACTATTAT
1 TATTTTATT-AAA-TATTAT
*
1957346 AATTT
1 TATTT
1957351 CATTTCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTTATTAAATATTAT
Found at i:1958433 original size:24 final size:25
Alignment explanation
Indices: 1958406--1958454 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1958396 CAATGCTTGT
1958406 GATTTGTATATTTCTG-TTGGATTC
1 GATTTGTATATTTCTGTTTGGATTC
* * *
1958430 GATTTTTATTTTTTTGTTTGGATTC
1 GATTTGTATATTTCTGTTTGGATTC
1958455 TCTTCCCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.14, C:0.06, G:0.18, T:0.61
Consensus pattern (25 bp):
GATTTGTATATTTCTGTTTGGATTC
Found at i:1960640 original size:2 final size:2
Alignment explanation
Indices: 1960633--1960682 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1960623 NNNNNNNNNN
1960633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1960675 AT AT AT AT
1 AT AT AT AT
1960683 CTTTTCATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1960726 original size:30 final size:32
Alignment explanation
Indices: 1960683--1960741 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
1960673 ATATATATAT
1960683 CTTTTCATGATTGAATACATTTATTTTTCATA
1 CTTTTCATGATTGAATACATTTATTTTTCATA
**
1960715 CTTTT-AT-ATTGAATATTTTTATTTTTC
1 CTTTTCATGATTGAATACATTTATTTTTC
1960742 TTAGTGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.72
31 2 0.08
32 5 0.20
ACGTcount: A:0.25, C:0.10, G:0.05, T:0.59
Consensus pattern (32 bp):
CTTTTCATGATTGAATACATTTATTTTTCATA
Found at i:1966777 original size:42 final size:42
Alignment explanation
Indices: 1966711--1966799 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
1966701 TGTTGATTTG
1966711 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* * * *
1966753 GACCCGACTATGTGTGAGTGGGAGTGCACATTAGTCGTTGCT
1 GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1966795 GACCC
1 GACCC
1966800 AGCTATATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:1968671 original size:22 final size:22
Alignment explanation
Indices: 1968643--1968691 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1968633 CCTTCTTTCC
1968643 TTTTTTTTATTT-TCTTTACTTA
1 TTTTTTTTATTTCT-TTTACTTA
*
1968665 TTTTTTTTATTTCTTTTATTTA
1 TTTTTTTTATTTCTTTTACTTA
1968687 TTTTT
1 TTTTT
1968692 GCTTTTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTTTTATTTCTTTTACTTA
Found at i:1968681 original size:13 final size:13
Alignment explanation
Indices: 1968643--1968689 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
1968633 CCTTCTTTCC
1968643 TTTTT-TTTATTT
1 TTTTTATTTATTT
* *
1968655 TCTTTACTTATTT
1 TTTTTATTTATTT
*
1968668 TTTTTATTTCTTT
1 TTTTTATTTATTT
*
1968681 TATTTATTT
1 TTTTTATTT
1968690 TTGCTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATTTATTT
Done.