Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 12 of 97
Found at i:5880628 original size:41 final size:41
Alignment explanation
Indices: 5880571--5880686 Score: 214
Period size: 41 Copynumber: 2.8 Consensus size: 41
5880561 AATTTAATCC
*
5880571 ATTGTTTGAAACCTTATGGTTGAGGATAAGGTAAATAATTT
1 ATTGTTTGAAACCTTATGGTCGAGGATAAGGTAAATAATTT
5880612 ATTGTTTGAAACCTTATGGTCGAGGATAAGGTAAATAATTT
1 ATTGTTTGAAACCTTATGGTCGAGGATAAGGTAAATAATTT
*
5880653 ATTGTTTGAAACCTTATGGTCGAGGGTAAGGTAA
1 ATTGTTTGAAACCTTATGGTCGAGGATAAGGTAA
5880687 CCAAATTGAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (41 bp):
ATTGTTTGAAACCTTATGGTCGAGGATAAGGTAAATAATTT
Found at i:5883239 original size:13 final size:13
Alignment explanation
Indices: 5883210--5883248 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
5883200 CTTCTTATTT
5883210 ATCTATAATT-T-
1 ATCTATAATTATA
*
5883221 ATCTATATTTATA
1 ATCTATAATTATA
5883234 ATCTATAATTATA
1 ATCTATAATTATA
5883247 AT
1 AT
5883249 ATACATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 14 0.58
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (13 bp):
ATCTATAATTATA
Found at i:5883478 original size:20 final size:20
Alignment explanation
Indices: 5883453--5883494 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5883443 AGAGCTATGC
5883453 TTATTTGAAAGATAAAAAAT
1 TTATTTGAAAGATAAAAAAT
* * *
5883473 TTATTTTAAATATAAAATAT
1 TTATTTGAAAGATAAAAAAT
5883493 TT
1 TT
5883495 TACAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTATTTGAAAGATAAAAAAT
Found at i:5889849 original size:20 final size:19
Alignment explanation
Indices: 5889824--5889906 Score: 66
Period size: 20 Copynumber: 4.4 Consensus size: 19
5889814 TAGTTCAGTT
5889824 TTTTTTTCATTTCAGCATAA
1 TTTTTTT-ATTTCAGCATAA
* * *
5889844 TTTTTTT-TCATCAGCTTGTA
1 TTTTTTTAT-TTCAGCAT-AA
*
5889864 TTTGTTTAGTTT-AGC-T-A
1 TTTTTTTA-TTTCAGCATAA
5889881 TTTTTTTATTTCAGCATAA
1 TTTTTTTATTTCAGCATAA
5889900 TTTTTTT
1 TTTTTTT
5889907 TCATCAACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
16 3 0.06
17 11 0.22
18 2 0.04
19 15 0.30
20 17 0.34
21 1 0.02
22 1 0.02
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTTTTATTTCAGCATAA
Found at i:5889849 original size:21 final size:20
Alignment explanation
Indices: 5889823--5889910 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
5889813 TTAGTTCAGT
5889823 TTTTTTTTCATTTCAGCATAA
1 TTTTTTTTCATTTCAGC-TAA
**
5889844 TTTTTTTTCA--TCAGCTTG
1 TTTTTTTTCATTTCAGCTAA
*
5889862 TATTTGTTT-AGTTT-AGCT-A
1 T-TTTTTTTCA-TTTCAGCTAA
5889881 -TTTTTTT-ATTTCAGCATAA
1 TTTTTTTTCATTTCAGC-TAA
5889900 TTTTTTTTCAT
1 TTTTTTTTCAT
5889911 CAACTTGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
16 3 0.06
17 10 0.19
18 4 0.08
19 12 0.23
20 11 0.21
21 13 0.25
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.61
Consensus pattern (20 bp):
TTTTTTTTCATTTCAGCTAA
Found at i:5889895 original size:56 final size:56
Alignment explanation
Indices: 5889809--5889932 Score: 205
Period size: 56 Copynumber: 2.2 Consensus size: 56
5889799 ATAAAAATAG
* *
5889809 TTGTTTAGTTCAGTTTTTTTTTCATTTCAGCATAATTTTTTTTCATCAGCTTGTAT
1 TTGTTTAGTTCAGTATTTTTTTCATTTCAGCATAATTTTTTTTCATCAACTTGTAT
*
5889865 TTGTTTAGTTTAGCTATTTTTTT-ATTTCAGCATAATTTTTTTTCATCAACTTGTAT
1 TTGTTTAGTTCAG-TATTTTTTTCATTTCAGCATAATTTTTTTTCATCAACTTGTAT
5889921 TTGTTTAGTTCA
1 TTGTTTAGTTCA
5889933 ACTTGTGAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 55 0.87
57 8 0.13
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.59
Consensus pattern (56 bp):
TTGTTTAGTTCAGTATTTTTTTCATTTCAGCATAATTTTTTTTCATCAACTTGTAT
Found at i:5890133 original size:42 final size:42
Alignment explanation
Indices: 5890050--5890133 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
5890040 TCTCCTCAAT
* * *
5890050 ATTAATTTTTTTAATAAAATATCTCCTCGTTAAATTTTTTGC
1 ATTAATTTTTTTAATAAAATATCTCCTCGTCAAAATATTTGC
*
5890092 ATTAATTTTTTTAATAAAATATCT-CTGGTACAAAATATTTGC
1 ATTAATTTTTTTAATAAAATATCTCCTCGT-CAAAATATTTGC
5890134 TCATCCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (42 bp):
ATTAATTTTTTTAATAAAATATCTCCTCGTCAAAATATTTGC
Found at i:5890289 original size:23 final size:24
Alignment explanation
Indices: 5890242--5890289 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5890232 TATTATCTAC
5890242 TCATTAATTTTATTTAGTTCAGCT
1 TCATTAATTTTATTTAGTTCAGCT
*
5890266 TCATTAATTTTGTTTA-TTCAGCT
1 TCATTAATTTTATTTAGTTCAGCT
5890289 T
1 T
5890290 GTAGAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (24 bp):
TCATTAATTTTATTTAGTTCAGCT
Found at i:5890729 original size:66 final size:66
Alignment explanation
Indices: 5890649--5890780 Score: 158
Period size: 66 Copynumber: 2.0 Consensus size: 66
5890639 TGGTAGCATC
** * * * * * *
5890649 ACTCAGCTTGAAGTGATTTCAAGT-TTTTTAAAATTTTGAATTTAAGAATGTTTATGTTTTATTA
1 ACTCAGCTCAAAGTGATTTCAAATGTTTTT-AAACTTCGAATTCAAGAATGTTTACGTTTAATTA
5890713 AA
65 AA
* *
5890715 ACTCAGCTCAAAGTGATTTCAAATGTTTTTACACTTCGAATTCGAGAATGTTTACGTTTAATTAA
1 ACTCAGCTCAAAGTGATTTCAAATGTTTTTAAACTTCGAATTCAAGAATGTTTACGTTTAATTAA
5890780 A
66 A
5890781 CGGATTCAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 50 0.91
67 5 0.09
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (66 bp):
ACTCAGCTCAAAGTGATTTCAAATGTTTTTAAACTTCGAATTCAAGAATGTTTACGTTTAATTAA
A
Found at i:5901919 original size:9 final size:9
Alignment explanation
Indices: 5901886--5901925 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
5901876 CACAAAAAAG
5901886 AAAAACAAA
1 AAAAACAAA
* *
5901895 AGAAAGAAA
1 AAAAACAAA
*
5901904 CAAAACAAA
1 AAAAACAAA
5901913 AAAAACAAA
1 AAAAACAAA
5901922 AAAA
1 AAAA
5901926 GGAAGAGGGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:5902215 original size:30 final size:30
Alignment explanation
Indices: 5902179--5902243 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
5902169 CTTTTATACC
*
5902179 CAGAGGAAGGAGGGCAAAACGGTGTCGTTT
1 CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
5902209 CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
1 CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
5902239 CAGAG
1 CAGAG
5902244 AGGCAAGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.15, G:0.40, T:0.14
Consensus pattern (30 bp):
CAGAGGAAGGAGGGCAAAACGGCGTCGTTT
Found at i:5914678 original size:2 final size:2
Alignment explanation
Indices: 5914671--5914723 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
5914661 CTTCCNTGGT
5914671 TA TA TA TA TA TA TA TA CTA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
5914713 TA TA TA TA TA T
1 TA TA TA TA TA T
5914724 TTGTGGAGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5940654 original size:15 final size:16
Alignment explanation
Indices: 5940634--5940675 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
5940624 AATGTATATA
5940634 TTATAA-TTAATAA-TT
1 TTATAAGTT-ATAATTT
5940649 TTATAAGTTATAATTT
1 TTATAAGTTATAATTT
5940665 TTATAACGTTA
1 TTATAA-GTTA
5940676 ACACAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.42
16 10 0.42
17 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (16 bp):
TTATAAGTTATAATTT
Found at i:5952459 original size:8 final size:8
Alignment explanation
Indices: 5952446--5952474 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
5952436 TACATAAATG
5952446 TATATGTA
1 TATATGTA
5952454 TATATGTA
1 TATATGTA
5952462 TATATGTA
1 TATATGTA
5952470 TATAT
1 TATAT
5952475 ACATACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
TATATGTA
Found at i:5952484 original size:20 final size:20
Alignment explanation
Indices: 5952413--5952487 Score: 55
Period size: 22 Copynumber: 3.8 Consensus size: 20
5952403 AAATACGCAC
* *
5952413 ATACACACATATGTGTAT-T
1 ATACATACATATATGTATAT
* *
5952432 -TATATACATAAATGTATATGT
1 ATACATACATATATGTATA--T
* **
5952453 ATATATGTATATATGTATAT
1 ATACATACATATATGTATAT
5952473 ATACATACATATATG
1 ATACATACATATATG
5952488 CCCATTCAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
18 13 0.31
20 13 0.31
21 1 0.02
22 15 0.36
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.41
Consensus pattern (20 bp):
ATACATACATATATGTATAT
Found at i:5972096 original size:2 final size:2
Alignment explanation
Indices: 5972089--5972118 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5972079 TTGGTCTAAC
5972089 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
5972119 CTAGAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5972185 original size:2 final size:2
Alignment explanation
Indices: 5972178--5972207 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5972168 NNNNNNNNAC
5972178 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
5972208 CTGAAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5975091 original size:2 final size:2
Alignment explanation
Indices: 5975086--5975125 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5975076 TGTGTGTGTG
5975086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5975126 AGTTGCATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5999382 original size:42 final size:42
Alignment explanation
Indices: 5999294--5999424 Score: 120
Period size: 42 Copynumber: 3.0 Consensus size: 42
5999284 CCCACCGCCT
* *
5999294 CCTGTTTACTCTCCACCTCCCCCTCCACCTTCACCTCCACCCCCACCA
1 CCTGTTTATTCTCCACCTCCCCCTCCA----C-CCT-CACCTCCACCA
5999342 CCTGTTTATTCTCCACCTCCCCCTCCACCCTCACCTCCACCA
1 CCTGTTTATTCTCCACCTCCCCCTCCACCCTCACCTCCACCA
** * * * *
5999384 CCAATTTATTCACCTCCACCACCC-CCGCCCTCACCTCCACC
1 CCTGTTTATTCTCCACCTCC-CCCTCCACCCTCACCTCCACC
5999425 TCCTTCACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
42 41 0.55
43 6 0.08
44 1 0.01
48 26 0.35
ACGTcount: A:0.16, C:0.59, G:0.02, T:0.23
Consensus pattern (42 bp):
CCTGTTTATTCTCCACCTCCCCCTCCACCCTCACCTCCACCA
Found at i:5999436 original size:18 final size:18
Alignment explanation
Indices: 5999415--5999452 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5999405 CCCCCGCCCT
* *
5999415 CACCTCCACCTCCTTCAC
1 CACCGCCACCTCCTCCAC
5999433 CACCGCCACCTCCTCCAC
1 CACCGCCACCTCCTCCAC
5999451 CA
1 CA
5999453 GTTTATTCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.63, G:0.03, T:0.16
Consensus pattern (18 bp):
CACCGCCACCTCCTCCAC
Found at i:5999477 original size:3 final size:3
Alignment explanation
Indices: 5999462--5999526 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
5999452 AGTTTATTCC
* * * * *
5999462 CCA CCA CCT CCA CCA CCA TCC- CCA CCC CCA CCA TCA CCT CCC CCA
1 CCA CCA CCA CCA CCA CCA -CCA CCA CCA CCA CCA CCA CCA CCA CCA
* *
5999507 CCT CCG CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CC
5999527 TACTTATCCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.22, C:0.69, G:0.02, T:0.08
Consensus pattern (3 bp):
CCA
Found at i:5999485 original size:21 final size:21
Alignment explanation
Indices: 5999459--5999521 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
5999449 ACCAGTTTAT
*
5999459 TCCCCACCACCTCCACCACCA
1 TCCCCACCACCACCACCACCA
* *
5999480 TCCCCACCCCCACCATCACC-
1 TCCCCACCACCACCACCACCA
* *
5999500 TCCCCCACCTCCGCCACCACCA
1 T-CCCCACCACCACCACCACCA
5999522 CCACCTACTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.21, C:0.68, G:0.02, T:0.10
Consensus pattern (21 bp):
TCCCCACCACCACCACCACCA
Found at i:5999494 original size:15 final size:15
Alignment explanation
Indices: 5999474--5999524 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
5999464 ACCACCTCCA
5999474 CCACCATCCCCACCC
1 CCACCATCCCCACCC
* *
5999489 CCACCATCACCTCCC
1 CCACCATCCCCACCC
*
5999504 CCACC-TCCGCCACCA
1 CCACCATCC-CCACCC
5999519 CCACCA
1 CCACCA
5999525 CCTACTTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 2 0.07
15 27 0.93
ACGTcount: A:0.22, C:0.69, G:0.02, T:0.08
Consensus pattern (15 bp):
CCACCATCCCCACCC
Found at i:5999718 original size:24 final size:24
Alignment explanation
Indices: 5999691--5999746 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5999681 CCCCATTATT
*
5999691 CACCGCCACCACCAC-TACACTCTC
1 CACCACCACCACCACATACAC-CTC
* *
5999715 CACCACCACCGCCACATTCACCTC
1 CACCACCACCACCACATACACCTC
5999739 CACCACCA
1 CACCACCA
5999747 ATTTATCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.27, C:0.59, G:0.04, T:0.11
Consensus pattern (24 bp):
CACCACCACCACCACATACACCTC
Found at i:5999741 original size:21 final size:21
Alignment explanation
Indices: 5999688--5999746 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
5999678 CCGCCCCATT
* *
5999688 ATTCACCGCCACCACCACTAC
1 ATTCACCACCACCACCACCAC
* * *
5999709 ACTCTCCACCACCACCGCCAC
1 ATTCACCACCACCACCACCAC
*
5999730 ATTCACCTCCACCACCA
1 ATTCACCACCACCACCA
5999747 ATTTATCCAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.56, G:0.03, T:0.14
Consensus pattern (21 bp):
ATTCACCACCACCACCACCAC
Found at i:6014341 original size:2 final size:2
Alignment explanation
Indices: 6014334--6014380 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
6014324 AGTAATTGTA
* *
6014334 CT CT CT CT CT CT CT CA AT CT CT CT C- CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6014375 CT CT CT
1 CT CT CT
6014381 TCTTCTTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.04, C:0.49, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:6015154 original size:2 final size:2
Alignment explanation
Indices: 6015149--6015185 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6015139 TCTCTCTCTC
6015149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6015186 CACCTAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6047102 original size:24 final size:24
Alignment explanation
Indices: 6047070--6047120 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
6047060 TTCTTTCATG
6047070 ACTTAATTTATCCACACTATTAGT
1 ACTTAATTTATCCACACTATTAGT
6047094 ACTTAATTTATCCACACTATTAGT
1 ACTTAATTTATCCACACTATTAGT
6047118 ACT
1 ACT
6047121 ACTTTCTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (24 bp):
ACTTAATTTATCCACACTATTAGT
Found at i:6057896 original size:21 final size:21
Alignment explanation
Indices: 6057870--6057909 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6057860 ATATGAGATT
6057870 GAGCCAAATATTAAAAAAAAG
1 GAGCCAAATATTAAAAAAAAG
* *
6057891 GAGCCAAATCTTAAGAAAA
1 GAGCCAAATATTAAAAAAA
6057910 TGTAGATTCT
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:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (21 bp):
GAGCCAAATATTAAAAAAAAG
Found at i:6060080 original size:16 final size:14
Alignment explanation
Indices: 6060043--6060085 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
6060033 TAATAGGACT
6060043 AACAAATATAATAAA
1 AACAAA-ATAATAAA
6060058 AACAAAATAATAATA
1 AACAAAATAATAA-A
6060073 AACTAAAATAATA
1 AAC-AAAATAATA
6060086 TTTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.27
15 10 0.38
16 9 0.35
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AACAAAATAATAAA
Found at i:6062235 original size:2 final size:2
Alignment explanation
Indices: 6062222--6062285 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
6062212 CTTCTCAATA
* * * * *
6062222 AT AT AC AT AT AT AT AT AT AT AC AT AT AT AC AT AT AT AC AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
6062264 AT AT AT GT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
6062286 CAAGAACAAT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6062239 original size:8 final size:8
Alignment explanation
Indices: 6062222--6062266 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
6062212 CTTCTCAATA
6062222 ATATACAT
1 ATATACAT
*
6062230 ATATATAT
1 ATATACAT
6062238 ATATACAT
1 ATATACAT
6062246 ATATACAT
1 ATATACAT
6062254 ATATACAT
1 ATATACAT
*
6062262 GTATA
1 ATATA
6062267 TATGTATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATACAT
Found at i:6062243 original size:16 final size:16
Alignment explanation
Indices: 6062222--6062285 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
6062212 CTTCTCAATA
6062222 ATATACATATATATAT
1 ATATACATATATATAT
*
6062238 ATATACATATATACAT
1 ATATACATATATATAT
*
6062254 ATATACATGTATATAT
1 ATATACATATATATAT
* * *
6062270 GTATATATGTATATAT
1 ATATACATATATATAT
6062286 CAAGAACAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (16 bp):
ATATACATATATATAT
Found at i:6066488 original size:21 final size:21
Alignment explanation
Indices: 6066462--6066506 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
6066452 TCAGCTTCAG
6066462 GTCTCTCTCCCAACACCCTCT
1 GTCTCTCTCCCAACACCCTCT
6066483 GTCTCTCTCCCAACACCCTCT
1 GTCTCTCTCCCAACACCCTCT
6066504 GTC
1 GTC
6066507 AGTCTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.51, G:0.07, T:0.29
Consensus pattern (21 bp):
GTCTCTCTCCCAACACCCTCT
Found at i:6082116 original size:42 final size:43
Alignment explanation
Indices: 6082063--6082171 Score: 114
Period size: 45 Copynumber: 2.5 Consensus size: 43
6082053 ATGAAAATAT
* *
6082063 TTAAATATTATTTCACTATAATAAATAGT-ATAAAGCATATTAC
1 TTAAATATTATTTCAATATAATAAAT-GTAATAAAGAATATTAC
*
6082106 TTAATATTATTATTTGAATATAATAAATGTAATAAAGAATATTA-
1 TTAA-A-TATTATTTCAATATAATAAATGTAATAAAGAATATTAC
* * * *
6082150 TTTAGTATTATTTAAATTTAAT
1 TTAAATATTATTTCAATATAAT
6082172 GAAGAATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
42 15 0.27
43 4 0.07
44 6 0.11
45 31 0.55
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (43 bp):
TTAAATATTATTTCAATATAATAAATGTAATAAAGAATATTAC
Found at i:6082128 original size:45 final size:45
Alignment explanation
Indices: 6082068--6082161 Score: 127
Period size: 45 Copynumber: 2.1 Consensus size: 45
6082058 AATATTTAAA
* *
6082068 TATTATTTCACTATAATAAATAGT-ATAAAGCATATTACTTAATAT
1 TATTATTTCAATATAATAAAT-GTAATAAAGAATATTACTTAATAT
* * *
6082113 TATTATTTGAATATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTTCAATATAATAAATGTAATAAAGAATATTACTTAATAT
6082158 TATT
1 TATT
6082162 TAAATTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 2 0.05
45 41 0.95
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (45 bp):
TATTATTTCAATATAATAAATGTAATAAAGAATATTACTTAATAT
Found at i:6082391 original size:63 final size:61
Alignment explanation
Indices: 6082323--6082451 Score: 134
Period size: 63 Copynumber: 2.0 Consensus size: 61
6082313 TTATTTTGAT
6082323 TTTATTGC-TCAGAATATTTTTATCTTTTAACAAAATAAATTCTTTAAATTTTAATAAAGAGTA
1 TTTATTGCTTCAGAATATTTTTATCTTTTAACAAAA-AAA-TCTTT-AATTTTAATAAAGAGTA
* * * * * * * *
6082386 TTTATTTCTTATCATAGTTTTTTTGTTTTTTAACTAAAAAATCTTTAATTTTAATAAAGGGTA
1 TTTATTGC-T-TCAGAATATTTTTATCTTTTAACAAAAAAATCTTTAATTTTAATAAAGAGTA
6082449 TTT
1 TTT
6082452 TTATCATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
63 26 0.47
64 5 0.09
65 3 0.05
66 21 0.38
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (61 bp):
TTTATTGCTTCAGAATATTTTTATCTTTTAACAAAAAAATCTTTAATTTTAATAAAGAGTA
Found at i:6084947 original size:37 final size:37
Alignment explanation
Indices: 6084905--6084979 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
6084895 TAATGGTGTG
6084905 TAGGGAGCACATACTTATTTACTTACTGAAGTTTTGT
1 TAGGGAGCACATACTTATTTACTTACTGAAGTTTTGT
6084942 TAGGGAGCACATACTTATTTACTTACTGAAGTTTTGT
1 TAGGGAGCACATACTTATTTACTTACTGAAGTTTTGT
6084979 T
1 T
6084980 GTGCATTGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (37 bp):
TAGGGAGCACATACTTATTTACTTACTGAAGTTTTGT
Found at i:6086021 original size:28 final size:28
Alignment explanation
Indices: 6085988--6086049 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
6085978 AAATATTCGA
6085988 TTAAAATAAATATATAAT-TAATGAATTT
1 TTAAAATAAAT-TATAATATAATGAATTT
* * * *
6086016 TTAAAATCAATTTTTATATAATTAATTT
1 TTAAAATAAATTATAATATAATGAATTT
6086044 TTAAAA
1 TTAAAA
6086050 ACTAATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAAAATAAATTATAATATAATGAATTT
Found at i:6086029 original size:13 final size:13
Alignment explanation
Indices: 6086011--6086049 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
6086001 ATAATTAATG
6086011 AATTTTTAAAATC
1 AATTTTTAAAATC
*
6086024 AATTTTTATATAATT
1 AATTTTTA-A-AATC
6086039 AATTTTTAAAA
1 AATTTTTAAAA
6086050 ACTAATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTTTTAAAATC
Found at i:6086044 original size:15 final size:14
Alignment explanation
Indices: 6086006--6086047 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
6085996 AATATATAAT
*
6086006 TAATGAATTTTTAA
1 TAATCAATTTTTAA
6086020 -AATCAATTTTTATA
1 TAATCAATTTTTA-A
*
6086034 TAATTAATTTTTAA
1 TAATCAATTTTTAA
6086048 AAACTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 11 0.46
14 2 0.08
15 11 0.46
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (14 bp):
TAATCAATTTTTAA
Found at i:6087699 original size:15 final size:15
Alignment explanation
Indices: 6087679--6087708 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6087669 AGAAAGGAAA
6087679 AGGGTTACTTTTGCC
1 AGGGTTACTTTTGCC
6087694 AGGGTTACTTTTGCC
1 AGGGTTACTTTTGCC
6087709 CATTTCCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (15 bp):
AGGGTTACTTTTGCC
Found at i:6089716 original size:50 final size:50
Alignment explanation
Indices: 6089641--6089744 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
6089631 TGTTTGCAAC
6089641 AAGAAAGTTATTACAAATAGTTACAGGAATGTCACCTCCCTTAACTCATA
1 AAGAAAGTTATTACAAATAGTTACAGGAATGTCACCTCCCTTAACTCATA
6089691 AAGAAAGTTATTACAAATAGTTACAGGAATGTCACCTCCCTTAACTCATA
1 AAGAAAGTTATTACAAATAGTTACAGGAATGTCACCTCCCTTAACTCATA
6089741 AAGA
1 AAGA
6089745 GAATGTTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (50 bp):
AAGAAAGTTATTACAAATAGTTACAGGAATGTCACCTCCCTTAACTCATA
Found at i:6089927 original size:16 final size:15
Alignment explanation
Indices: 6089886--6089928 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
6089876 GGAAGGTGAG
6089886 AGAAATAAAAAAGAAA
1 AGAAAT-AAAAAGAAA
* *
6089902 AGAGAGAAAAAGAAGA
1 AGAAATAAAAAGAA-A
6089918 AGAAATAAAAA
1 AGAAATAAAAA
6089929 ACAAGGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AGAAATAAAAAGAAA
Found at i:6099243 original size:2 final size:2
Alignment explanation
Indices: 6099238--6099270 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6099228 GTGTGTGTGT
6099238 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
6099271 TAGTGTACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6099313 original size:2 final size:2
Alignment explanation
Indices: 6099301--6099333 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
6099291 CCGTGTTGTN
6099301 AG AG TAG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6099334 TGTTGTACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
AG
Found at i:6099342 original size:63 final size:62
Alignment explanation
Indices: 6099230--6099362 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 62
6099220 GTGTGTGTGT
6099230 GTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTAGTGTACTCTACTCGTTTTCC
1 GTGT-TGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTAGTGTACTCTACTCGTTTTCC
*
6099293 GTGTTGTNAGAGTAGAGAGAGAGAGAGAGAGAGAGAGAGAGT-GTTGTACTCTACTCGTTTTCC
1 GTGTTGTGAGAG-AGAGAGAGAGAGAGAGAGAGAGAGAGAGTAG-TGTACTCTACTCGTTTTCC
6099356 GTGTTGT
1 GTGTTGT
6099363 ACCCTACTCG
Statistics
Matches: 67, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
62 8 0.12
63 59 0.88
ACGTcount: A:0.28, C:0.09, G:0.37, T:0.26
Consensus pattern (62 bp):
GTGTTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGTAGTGTACTCTACTCGTTTTCC
Found at i:6099363 original size:23 final size:23
Alignment explanation
Indices: 6099333--6099383 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
6099323 GAGAGAGAGA
*
6099333 GTGTTGTACTCTACTCGTTTTCC
1 GTGTTGTACCCTACTCGTTTTCC
6099356 GTGTTGTACCCTACTCGTTTTCC
1 GTGTTGTACCCTACTCGTTTTCC
6099379 GTGTT
1 GTGTT
6099384 CCAGGGCCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.08, C:0.25, G:0.20, T:0.47
Consensus pattern (23 bp):
GTGTTGTACCCTACTCGTTTTCC
Found at i:6102053 original size:2 final size:2
Alignment explanation
Indices: 6102046--6102077 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6102036 CGCTGATTAT
6102046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6102078 TCTTTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6108292 original size:19 final size:20
Alignment explanation
Indices: 6108247--6108292 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
6108237 ATTTAAAATG
*
6108247 ATTAATTATTATTTTATTAAA
1 ATTAA-TATGATTTTATTAAA
*
6108268 A-AAATATGATTTT-TTAAA
1 ATTAATATGATTTTATTAAA
6108286 ATTAATA
1 ATTAATA
6108293 CGTACCATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 2 0.10
21 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTAATATGATTTTATTAAA
Found at i:6118581 original size:17 final size:18
Alignment explanation
Indices: 6118533--6118581 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
6118523 TTCTAAATTT
6118533 TAAATATAAAAAATAAATC
1 TAAAT-TAAAAAATAAATC
*
6118552 TAAA-TAATCAAATAAA-C
1 TAAATTAA-AAAATAAATC
6118569 TAAATTAAAAAAT
1 TAAATTAAAAAAT
6118582 CGATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 12 0.46
18 10 0.38
19 4 0.15
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATTAAAAAATAAATC
Found at i:6127055 original size:40 final size:39
Alignment explanation
Indices: 6126967--6127057 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
6126957 GGAAAATTTA
* **
6126967 ATTTCTTTTCTTCCCTATAATATGTAAAGAAAATTCGAT
1 ATTTCTTTTCTTCCCCATAATATGTAAAGAAAATTAAAT
* *
6127006 ATTTTTTTTCTTCCCCATAATCTGTAAAAGAAAATTAAAT
1 ATTTCTTTTCTTCCCCATAATATGT-AAAGAAAATTAAAT
*
6127046 CTTTCTTTTCTT
1 ATTTCTTTTCTT
6127058 TTTATAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 22 0.50
40 22 0.50
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.47
Consensus pattern (39 bp):
ATTTCTTTTCTTCCCCATAATATGTAAAGAAAATTAAAT
Found at i:6127326 original size:22 final size:22
Alignment explanation
Indices: 6127284--6127327 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6127274 TTTTTAATTT
* *
6127284 TTTTAAAATTTGTAATTAATAA
1 TTTTAAAATTTGAAATAAATAA
6127306 TTTTAAATATTT-AAATAAATAA
1 TTTTAAA-ATTTGAAATAAATAA
6127328 AAATATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTAAAATTTGAAATAAATAA
Found at i:6127868 original size:38 final size:38
Alignment explanation
Indices: 6127817--6127893 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
6127807 ACACTTAACC
*
6127817 TAGATTTGAAGAACACCTTGCCTTACCTTGCCTTATCT
1 TAGATTTGAAGAACACCTTGCCTTAACTTGCCTTATCT
*
6127855 TAGATTTGAAGAACACCTTGCTTTAACTTGCCTTATCT
1 TAGATTTGAAGAACACCTTGCCTTAACTTGCCTTATCT
6127893 T
1 T
6127894 CTTCTTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.39
Consensus pattern (38 bp):
TAGATTTGAAGAACACCTTGCCTTAACTTGCCTTATCT
Found at i:6131445 original size:19 final size:18
Alignment explanation
Indices: 6131401--6131445 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
6131391 TTTGACTAAA
*
6131401 AATAAAATAAAATAAAAT
1 AATAAAATAAAATAAAAC
*
6131419 AATCAAAATAAAATAAAGC
1 AAT-AAAATAAAATAAAAC
6131438 ACATAAAA
1 A-ATAAAA
6131446 AATAAAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (18 bp):
AATAAAATAAAATAAAAC
Found at i:6131452 original size:5 final size:5
Alignment explanation
Indices: 6131399--6131435 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
6131389 AATTTGACTA
6131399 AAAAT AAAAT AAAAT AAAAT --AAT CAAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAA
6131436 GCACATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.10
5 23 0.79
6 3 0.10
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:6131467 original size:6 final size:6
Alignment explanation
Indices: 6131458--6131572 Score: 61
Period size: 6 Copynumber: 18.3 Consensus size: 6
6131448 TAAAACTCAT
* * * * * *
6131458 ATATAA ATATTAA NTATAA ATATTAAA ATTTTA ATATAT ATATAT ATATAT
1 ATATAA ATA-TAA ATATAA ATA-T-AA ATATAA ATATAA ATATAA ATATAA
* * * * *
6131509 ATATATA ATATAT ATATTA ATAATAA ATAT-A ATATATA TTATAT ATATAT
1 ATATA-A ATATAA ATATAA AT-ATAA ATATAA ATATA-A ATATAA ATATAA
*
6131559 ATATAT ATATAA AT
1 ATATAA ATATAA AT
6131573 GGTGTCTACA
Statistics
Matches: 86, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
5 5 0.06
6 55 0.64
7 22 0.26
8 4 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
ATATAA
Found at i:6131475 original size:13 final size:12
Alignment explanation
Indices: 6131458--6131572 Score: 66
Period size: 13 Copynumber: 9.7 Consensus size: 12
6131448 TAAAACTCAT
6131458 ATATAAATATTA
1 ATATAAATATTA
6131470 ANTATAAATA-T-
1 A-TATAAATATTA
*
6131481 -TA-AAATTTTA
1 ATATAAATATTA
*
6131491 ATATATATA-TA
1 ATATAAATATTA
*
6131502 TATATATATATATA
1 -ATATAAATAT-TA
*
6131516 ATATATATATTA
1 ATATAAATATTA
6131528 ATAATAAATA-TA
1 AT-ATAAATATTA
6131540 ATAT--ATATTA
1 ATATAAATATTA
*
6131550 TATATATATATATA
1 -ATATAAATAT-TA
6131564 TATATAAAT
1 -ATATAAAT
6131573 GGTGTCTACA
Statistics
Matches: 84, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
8 4 0.05
9 6 0.07
10 2 0.02
11 10 0.12
12 22 0.26
13 28 0.33
14 12 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATAAATATTA
Found at i:6131498 original size:2 final size:2
Alignment explanation
Indices: 6131491--6131569 Score: 107
Period size: 2 Copynumber: 42.5 Consensus size: 2
6131481 TAAAATTTTA
6131491 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6131530 A- AT AA AT AT A- AT AT AT AT -T 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
6131569 A
1 A
6131570 AATGGTGTCT
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6131520 original size:58 final size:56
Alignment explanation
Indices: 6131458--6131569 Score: 154
Period size: 56 Copynumber: 2.0 Consensus size: 56
6131448 TAAAACTCAT
*
6131458 ATATAAATATTAANT-ATAAATATTAAAATTTTAATATATATATATATATATATATATA
1 ATATAAATATTAA-TAATAAATA-TAAAA-TATAATATATATATATATATATATATATA
* * *
6131516 ATATATATATTAATAATAAATATAATATATATTATATATATATATATATATATA
1 ATATAAATATTAATAATAAATATAAAATATAATATATATATATATATATATATA
6131570 AATGGTGTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 25 0.51
57 5 0.10
58 19 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (56 bp):
ATATAAATATTAATAATAAATATAAAATATAATATATATATATATATATATATATA
Found at i:6143889 original size:2 final size:2
Alignment explanation
Indices: 6143884--6143911 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6143874 GTGTGTGTGT
6143884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
6143912 TCCTTTTCTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6156919 original size:22 final size:23
Alignment explanation
Indices: 6156875--6156925 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
6156865 TTTAAAAAAA
* * *
6156875 ATTAAATAATTTTTTATTCTTTT
1 ATTAATTAAATTTTTATTATTTT
6156898 ATTAATTAAATTTTTA-TATTTT
1 ATTAATTAAATTTTTATTATTTT
*
6156920 TTTAAT
1 ATTAAT
6156926 ATCAAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTAATTAAATTTTTATTATTTT
Found at i:6156932 original size:24 final size:24
Alignment explanation
Indices: 6156882--6156932 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
6156872 AAAATTAAAT
* *
6156882 AATTTTTTATTCTTTTATTAATTA
1 AATTTTTTATTCTTTTAATAATCA
*
6156906 AATTTTTATATTTTTTTAAT-ATCA
1 AATTTTT-TATTCTTTTAATAATCA
6156930 AAT
1 AAT
6156933 AGTGTTTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
AATTTTTTATTCTTTTAATAATCA
Found at i:6159386 original size:2 final size:2
Alignment explanation
Indices: 6159379--6159426 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6159369 CATTTTAATG
6159379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6159421 TA TA TA
1 TA TA TA
6159427 AAAGCCTTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6164132 original size:2 final size:2
Alignment explanation
Indices: 6164125--6164161 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6164115 CTCTATGAAT
6164125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6164162 GAATAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6164293 original size:16 final size:16
Alignment explanation
Indices: 6164269--6164303 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6164259 TCATTGAGAT
*
6164269 ATATTTAAATAAAATA
1 ATATATAAATAAAATA
*
6164285 ATATATAAATATAATA
1 ATATATAAATAAAATA
6164301 ATA
1 ATA
6164304 AAAAGACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATATAAATAAAATA
Found at i:6166788 original size:33 final size:33
Alignment explanation
Indices: 6166741--6166841 Score: 193
Period size: 33 Copynumber: 3.1 Consensus size: 33
6166731 GCCCCCTTAA
6166741 CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
1 CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
*
6166774 CGGCGCCCTCCACAACCGTTTCTTACTTTGCAT
1 CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
6166807 CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
1 CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
6166840 CG
1 CG
6166842 TTGTCCTTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.15, C:0.42, G:0.14, T:0.30
Consensus pattern (33 bp):
CGGCCCCCTCCACAACCGTTTCTTACTTTGCAT
Found at i:6187832 original size:2 final size:2
Alignment explanation
Indices: 6187820--6187868 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
6187810 NNNNNNNNAT
*
6187820 TA TA CA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6187861 TA TA TA TA
1 TA TA TA TA
6187869 AATGAAAGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6190862 original size:69 final size:69
Alignment explanation
Indices: 6190789--6190976 Score: 168
Period size: 69 Copynumber: 2.7 Consensus size: 69
6190779 TTAGTTACCT
* * *
6190789 GAATGTATCCATC-TTTTCCATTCATAAAGCCC-AGTGTGGAGG-TAATAATACCACAAGGTTTA
1 GAATGTACCCATCTTTTTCCATT-ATAAAGCCCGA-TGTGG-GGATAAGAATACCACAAGGTCTA
6190851 GTTGGAG-
63 GTTGG-GC
* * * * *
6190858 GAATGTGCCCATCTTTTTCCCTTTTAAAGCCCGATGTGGGGATAAGAATAGCACAGGGTCTAGTT
1 GAATGTACCCATCTTTTTCCATTATAAAGCCCGATGTGGGGATAAGAATACCACAAGGTCTAGTT
6190923 GGGC
66 GGGC
* * * * * ** *
6190927 GAATGTACTCTTTTTTTTCCCTCATAAAGCTTGGTGTGGGGATAAGAATA
1 GAATGTACCCATCTTTTTCCATTATAAAGCCCGATGTGGGGATAAGAATA
6190977 TCATAGGGAT
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
68 3 0.03
69 86 0.88
70 9 0.09
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (69 bp):
GAATGTACCCATCTTTTTCCATTATAAAGCCCGATGTGGGGATAAGAATACCACAAGGTCTAGTT
GGGC
Found at i:6200996 original size:133 final size:132
Alignment explanation
Indices: 6200758--6201022 Score: 521
Period size: 133 Copynumber: 2.0 Consensus size: 132
6200748 AAGAATTCAA
6200758 CTTCTGAGTTGTGGCTGGAGGGGCAGTAGTCTCGTTGCTGTGTGTCACAATGCTTGTGTAGATCT
1 CTTCTGAGTTGTGGCTGGAGGGGCAGTAGTCTCGTTGCTGTGTGTCACAATGCTTGTGTAGATCT
6200823 ATCATGTTCTTTGGATTTATATATGTTTCTTCTTTATATATAAATAACTATATATATATATATAT
66 ATCATGTTCTTTGGATTTATATATGTTTCTTCTTTATATATAAATAACTATATATATATATATAT
6200888 AT
131 AT
6200890 NCTTCTGAGTTGTGGCTGGAGGGGCAGTAGTCTCGTTGCTGTGTGTCACAATGCTTGTGTAGATC
1 -CTTCTGAGTTGTGGCTGGAGGGGCAGTAGTCTCGTTGCTGTGTGTCACAATGCTTGTGTAGATC
6200955 TATCATGTTCTTTGGATTTATATATGTTTCTTCTTTATATATAAATAACTATATATATATATATA
65 TATCATGTTCTTTGGATTTATATATGTTTCTTCTTTATATATAAATAACTATATATATATATATA
6201020 TAT
130 TAT
6201023 ATTCCTTTTG
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (132 bp):
CTTCTGAGTTGTGGCTGGAGGGGCAGTAGTCTCGTTGCTGTGTGTCACAATGCTTGTGTAGATCT
ATCATGTTCTTTGGATTTATATATGTTTCTTCTTTATATATAAATAACTATATATATATATATAT
AT
Found at i:6202966 original size:22 final size:23
Alignment explanation
Indices: 6202927--6202974 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6202917 TCTTTAATCC
*
6202927 AAAAAATTACAACGTAAAA-ATT
1 AAAAAAATACAACGTAAAATATT
* *
6202949 AAAAAAATATAACTTAAAATATT
1 AAAAAAATACAACGTAAAATATT
6202972 AAA
1 AAA
6202975 TCAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAAAATACAACGTAAAATATT
Found at i:6203629 original size:21 final size:21
Alignment explanation
Indices: 6203605--6203646 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6203595 GTAATATCAA
6203605 TTTTAAAAAAAAAATTTTTTT
1 TTTTAAAAAAAAAATTTTTTT
6203626 TTTTAAAAAAAAAATTTTTTT
1 TTTTAAAAAAAAAATTTTTTT
6203647 GACCTATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAAAAAAATTTTTTT
Found at i:6206368 original size:3 final size:3
Alignment explanation
Indices: 6206349--6206398 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
6206339 AAATTAAAAA
* *
6206349 ATT AGT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6206397 AT
1 AT
6206399 AGATTTATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:6211807 original size:64 final size:64
Alignment explanation
Indices: 6211697--6211820 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
6211687 CTGGATGAAA
* * * *
6211697 GCTAAATTCTAGTATCTAATAGTTGTTAGATGATCTAGCTTGGATTGCTATGGTAGATCGGAAC
1 GCTAAACTCTAGTATCTAATAGTTGTTAGATGATCTAACTTAGATTGCTATGCTAGATCGGAAC
* * *
6211761 GCTAAACTCTAGTATCTGATAGTTGTTATATTATCTAACTTAGATTGCTATGCTAGATCG
1 GCTAAACTCTAGTATCTAATAGTTGTTAGATGATCTAACTTAGATTGCTATGCTAGATCG
6211821 AAATTTTCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (64 bp):
GCTAAACTCTAGTATCTAATAGTTGTTAGATGATCTAACTTAGATTGCTATGCTAGATCGGAAC
Found at i:6218301 original size:18 final size:17
Alignment explanation
Indices: 6218273--6218317 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
6218263 ATATAATTGA
6218273 AATAAATAAATAAAAAT
1 AATAAATAAATAAAAAT
6218290 AATAATATAAATAAAAA-
1 AATAA-ATAAATAAAAAT
6218307 AATTAAATAAA
1 AA-TAAATAAA
6218318 AACTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AATAAATAAATAAAAAT
Found at i:6223982 original size:12 final size:12
Alignment explanation
Indices: 6223958--6224004 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
6223948 GCCAAACCTC
*
6223958 CCTCTACCCCTT
1 CCTCTTCCCCTT
*
6223970 CCTCTTCCTCTT
1 CCTCTTCCCCTT
6223982 CCTCTTCCCCTT
1 CCTCTTCCCCTT
*
6223994 CCCCTTCCCCT
1 CCTCTTCCCCT
6224005 CCCCCTTCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.02, C:0.60, G:0.00, T:0.38
Consensus pattern (12 bp):
CCTCTTCCCCTT
Found at i:6223988 original size:18 final size:18
Alignment explanation
Indices: 6223958--6224019 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
6223948 GCCAAACCTC
* *
6223958 CCTCTACCCCTTCCTCTT
1 CCTCTTCCCCTTCCCCTT
*
6223976 CCTCTTCCTCTTCCCCTT
1 CCTCTTCCCCTTCCCCTT
* *
6223994 CCCCTTCCCCTCCCCCTT
1 CCTCTTCCCCTTCCCCTT
6224012 CCT-TTCCC
1 CCTCTTCCC
6224020 TCCACGTTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 5 0.14
18 32 0.86
ACGTcount: A:0.02, C:0.61, G:0.00, T:0.37
Consensus pattern (18 bp):
CCTCTTCCCCTTCCCCTT
Found at i:6224002 original size:6 final size:6
Alignment explanation
Indices: 6223964--6224013 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
6223954 CCTCCCTCTA
* * * *
6223964 CCCCTT CCTCTT CCTCTT CCTCTT CCCCTT CCCCTT CCCCTC CCCCTT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
6224012 CC
1 CC
6224014 TTTCCCTCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CCCCTT
Found at i:6225831 original size:27 final size:26
Alignment explanation
Indices: 6225800--6225857 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
6225790 TCATTATGGA
*
6225800 AAATGAGATGCTGGAGAAAATATGTTT
1 AAATGAG-TGCTGGAAAAAATATGTTT
*
6225827 AAATGTGTGCTGGAAAAAATATGTTT
1 AAATGAGTGCTGGAAAAAATATGTTT
*
6225853 GAATG
1 AAATG
6225858 TGTGTTTCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (26 bp):
AAATGAGTGCTGGAAAAAATATGTTT
Found at i:6225837 original size:26 final size:26
Alignment explanation
Indices: 6225808--6225861 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
6225798 GAAAATGAGA
*
6225808 TGCTGGAGAAAATATGTTTAAATGTG
1 TGCTGGAAAAAATATGTTTAAATGTG
*
6225834 TGCTGGAAAAAATATGTTTGAATGTG
1 TGCTGGAAAAAATATGTTTAAATGTG
6225860 TG
1 TG
6225862 TTTCTGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (26 bp):
TGCTGGAAAAAATATGTTTAAATGTG
Found at i:6236797 original size:15 final size:15
Alignment explanation
Indices: 6236777--6236816 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6236767 GGATTCAGAG
6236777 AGAGAGAAAAAAAGA
1 AGAGAGAAAAAAAGA
* *
6236792 AGAGAGCAAAAGAGA
1 AGAGAGAAAAAAAGA
*
6236807 AAAGAGAAAA
1 AGAGAGAAAA
6236817 TGAAAGCAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (15 bp):
AGAGAGAAAAAAAGA
Found at i:6251856 original size:16 final size:15
Alignment explanation
Indices: 6251835--6251869 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6251825 TATATTTTAT
*
6251835 ATATAAATATACAAAA
1 ATATAAATA-AAAAAA
6251851 ATATAAATAAAAAAA
1 ATATAAATAAAAAAA
6251866 ATAT
1 ATAT
6251870 TATTACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
ATATAAATAAAAAAA
Found at i:6260578 original size:3 final size:3
Alignment explanation
Indices: 6260570--6260642 Score: 74
Period size: 3 Copynumber: 24.3 Consensus size: 3
6260560 CCTTCTCTTC
* * * * *
6260570 GCT GCT GCT GCT GCT GTT GCT GTT GCT GTT GCT GCT GCT GCT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * *
6260618 GTT GTT GTT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT G
6260643 AGCATGCCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.00, C:0.22, G:0.34, T:0.44
Consensus pattern (3 bp):
GCT
Found at i:6260610 original size:27 final size:27
Alignment explanation
Indices: 6260572--6260639 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
6260562 TTCTCTTCGC
6260572 TGCTGCTGCTGCTGTTGCTGTTGCTGT
1 TGCTGCTGCTGCTGTTGCTGTTGCTGT
* *
6260599 TGCTGCTGCTGCTGTTGTTGTTGTTGT
1 TGCTGCTGCTGCTGTTGCTGTTGCTGT
6260626 TGCTGCTGCTGCTG
1 TGCTGCTGCTGCTG
6260640 CTGAGCATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.00, C:0.21, G:0.34, T:0.46
Consensus pattern (27 bp):
TGCTGCTGCTGCTGTTGCTGTTGCTGT
Found at i:6264336 original size:49 final size:50
Alignment explanation
Indices: 6264242--6264355 Score: 151
Period size: 49 Copynumber: 2.3 Consensus size: 50
6264232 CTCTTATGAA
*
6264242 AAATAATAATTTTTAAAATTAAATTAAGATTTAATTATAA-ATTTTTAAT
1 AAATAATAATTTTTAAAATTAAATTAAGAATTAATTATAATATTTTTAAT
* * * *
6264291 ANATAATAATTTTTAAAATTAAATTAA-AATTATTTAATAATTTTTTTTAT
1 AAATAATAATTTTTAAAATTAAATTAAGAATTAATT-ATAATATTTTTAAT
*
6264341 AAATTATAATTTTTA
1 AAATAATAATTTTTA
6264356 TTAAAACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
48 6 0.11
49 30 0.54
50 20 0.36
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.50
Consensus pattern (50 bp):
AAATAATAATTTTTAAAATTAAATTAAGAATTAATTATAATATTTTTAAT
Found at i:6264360 original size:17 final size:17
Alignment explanation
Indices: 6264274--6264360 Score: 58
Period size: 17 Copynumber: 5.1 Consensus size: 17
6264264 ATTAAGATTT
6264274 AATTATAAATTTTTAATA
1 AATTAT-AATTTTTAATA
* *
6264292 NATAATAATTTTTAAAATTA
1 AATTATAATTTTT--AA-TA
*
6264312 AATTAAAATTATTTAAT-
1 AATTATAATT-TTTAATA
6264329 AATT-T--TTTTT-ATA
1 AATTATAATTTTTAATA
*
6264342 AATTATAATTTTTATTA
1 AATTATAATTTTTAATA
6264359 AA
1 AA
6264361 ACTATCATAG
Statistics
Matches: 53, Mismatches: 7, Indels: 19
0.67 0.09 0.24
Matches are distributed among these distances:
12 2 0.04
13 7 0.13
14 3 0.06
16 5 0.09
17 15 0.28
18 5 0.09
19 4 0.08
20 9 0.17
21 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATAATTTTTAATA
Found at i:6289744 original size:2 final size:2
Alignment explanation
Indices: 6289737--6289778 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6289727 ATTCAGCTTT
6289737 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6289779 CAAGGGAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6296691 original size:2 final size:2
Alignment explanation
Indices: 6296679--6296708 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
6296669 GTAGTGACAA
6296679 AT AT AT GAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
6296709 GTTGTTGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6304658 original size:14 final size:14
Alignment explanation
Indices: 6304639--6304668 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6304629 GTTCAAAAAT
6304639 TTATTATTTTTTTA
1 TTATTATTTTTTTA
6304653 TTATTATTTTTTTA
1 TTATTATTTTTTTA
6304667 TT
1 TT
6304669 TATATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TTATTATTTTTTTA
Found at i:6305070 original size:11 final size:11
Alignment explanation
Indices: 6305037--6305080 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
6305027 TCATTTATTG
6305037 TTATTATTTA-
1 TTATTATTTAT
6305047 TTATTATTTAT
1 TTATTATTTAT
6305058 TTATT-TTTCAT
1 TTATTATTT-AT
6305069 TTATTA-TTAT
1 TTATTATTTAT
6305079 TT
1 TT
6305081 TTTGATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 17 0.55
11 14 0.45
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:6305070 original size:25 final size:25
Alignment explanation
Indices: 6305042--6305090 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6305032 TATTGTTATT
6305042 ATTTATTATTATTTATTT-ATTTTTC
1 ATTTATTATTATTT-TTTGATTTTTC
6305067 ATTTATTATTATTTTTTGATTTTT
1 ATTTATTATTATTTTTTGATTTTT
6305091 TAATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (25 bp):
ATTTATTATTATTTTTTGATTTTTC
Found at i:6314835 original size:14 final size:13
Alignment explanation
Indices: 6314811--6314848 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
6314801 GCCATCCCCC
*
6314811 TTTTTTTTATTAA
1 TTTTTTATATTAA
6314824 TTTTTTAATATTAA
1 TTTTTT-ATATTAA
6314838 TTTTTTATATT
1 TTTTTTATATT
6314849 TTAGTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTTATATTAA
Found at i:6324101 original size:2 final size:2
Alignment explanation
Indices: 6324094--6324151 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
6324084 AAAGCTGCTA
*
6324094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA 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
*
6324135 AT AT AT A- AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
6324152 NNNNNNNNNN
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6324217 original size:2 final size:2
Alignment explanation
Indices: 6324210--6324254 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6324200 NNNNTAATAG
6324210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6324252 TA T
1 TA T
6324255 TGGATAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6328630 original size:6 final size:7
Alignment explanation
Indices: 6328613--6328640 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
6328603 TAATAGGAGA
6328613 AAAAAAT
1 AAAAAAT
6328620 AAAAAAT
1 AAAAAAT
6328627 AAAAAAT
1 AAAAAAT
6328634 AAAAAAT
1 AAAAAAT
6328641 TATAGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:6329544 original size:27 final size:28
Alignment explanation
Indices: 6329512--6329565 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
6329502 ATTAAACCCG
6329512 ATTCATCATAAAA-CCT-AACCCAATTCA
1 ATTCATCA-AAAACCCTAAACCCAATTCA
6329539 ATTCATCAAAAACCCTAAACCCAATTC
1 ATTCATCAAAAACCCTAAACCCAATTC
6329566 GACAAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.16
27 11 0.44
28 10 0.40
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (28 bp):
ATTCATCAAAAACCCTAAACCCAATTCA
Found at i:6329594 original size:23 final size:22
Alignment explanation
Indices: 6329537--6329611 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
6329527 TAACCCAATT
6329537 CAATTCATCAAAAACCCTAAACC
1 CAATTCA-CAAAAACCCTAAACC
*
6329560 CAATTCGACAAAAACCCTAAGCC
1 CAATTC-ACAAAAACCCTAAACC
* * * * * *
6329583 TAGTTCACCAAAACACTGAACT
1 CAATTCACAAAAACCCTAAACC
6329605 CAATTCA
1 CAATTCA
6329612 ATAAAAATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
22 16 0.39
23 24 0.59
24 1 0.02
ACGTcount: A:0.44, C:0.32, G:0.05, T:0.19
Consensus pattern (22 bp):
CAATTCACAAAAACCCTAAACC
Found at i:6329782 original size:20 final size:21
Alignment explanation
Indices: 6329759--6329806 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6329749 TCACCACACT
6329759 CTAAAATC-ATTCA-TGAAATC
1 CTAAAATCGATTCACT-AAATC
*
6329779 CTAAAACCGATTCACTAAATC
1 CTAAAATCGATTCACTAAATC
6329800 CTAAAAT
1 CTAAAAT
6329807 TAGTTCACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 16 0.67
22 1 0.04
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (21 bp):
CTAAAATCGATTCACTAAATC
Found at i:6329927 original size:21 final size:21
Alignment explanation
Indices: 6329903--6329947 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6329893 AAAAAAAGTT
* *
6329903 AAATTGATTTATCAAACCCTA
1 AAATCGATTCATCAAACCCTA
*
6329924 AAATCGATTCATCAACCCCTA
1 AAATCGATTCATCAAACCCTA
6329945 AAA
1 AAA
6329948 CTAGTTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATCGATTCATCAAACCCTA
Found at i:6329989 original size:63 final size:63
Alignment explanation
Indices: 6329846--6330013 Score: 153
Period size: 63 Copynumber: 2.7 Consensus size: 63
6329836 CATAAAATTA
* **
6329846 ATTCACTAAACCATAAAATCGGTTCACCAAAACCCTAAAACCTAGTTAAAAAAAGTTAAATTG
1 ATTCACTAAACCATAAAATCGATTCACCAAAACCCTAAAACCTAGTTAAAAAAAGTTAAACCG
* * * * * **
6329909 ATTTA-TCAAACCCTAAAATCGATTCATC-AACCCCTAAAA-CTAGTTTGAAAAACTTTAAAACC
1 ATTCACT-AAACCATAAAATCGATTCACCAAAACCCTAAAACCTAG-TTAAAAAAAGTT-AAACC
6329971 G
63 G
* * * *
6329972 ATTCACTAAACCTTAAAATTGGTTCACACAAAATCCTAAAAC
1 ATTCACTAAACCATAAAATCGATTCAC-CAAAACCCTAAAAC
6330014 AAATTCTTTA
Statistics
Matches: 81, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
61 4 0.05
62 20 0.25
63 46 0.57
64 2 0.02
65 9 0.11
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.26
Consensus pattern (63 bp):
ATTCACTAAACCATAAAATCGATTCACCAAAACCCTAAAACCTAGTTAAAAAAAGTTAAACCG
Found at i:6330080 original size:21 final size:21
Alignment explanation
Indices: 6330055--6330130 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 21
6330045 ACAAGTTTAC
6330055 AAAACCTTAAAATCAGTTCAT
1 AAAACCTTAAAATCAGTTCAT
* * * * *
6330076 GAAACCCT-AAACCAATTCAC
1 AAAACCTTAAAATCAGTTCAT
*
6330096 CAAACCTTAAAATC-GATTCACT
1 AAAACCTTAAAATCAG-TTCA-T
6330118 AAAACCTTAAAAT
1 AAAACCTTAAAAT
6330131 TAATTCCCTA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
20 15 0.37
21 14 0.34
22 12 0.29
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAACCTTAAAATCAGTTCAT
Found at i:6330124 original size:22 final size:21
Alignment explanation
Indices: 6330055--6330130 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
6330045 ACAAGTTTAC
6330055 AAAACCTTAAAATCAGTTCA-T
1 AAAACCTTAAAATCA-TTCACT
* * *
6330076 GAAACCCT-AAACCAATTCAC-
1 AAAACCTTAAAATC-ATTCACT
*
6330096 CAAACCTTAAAATCGATTCACT
1 AAAACCTTAAAATC-ATTCACT
6330118 AAAACCTTAAAAT
1 AAAACCTTAAAAT
6330131 TAATTCCCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
20 14 0.33
21 17 0.40
22 12 0.28
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAACCTTAAAATCATTCACT
Found at i:6330136 original size:22 final size:22
Alignment explanation
Indices: 6330055--6330142 Score: 83
Period size: 22 Copynumber: 4.1 Consensus size: 22
6330045 ACAAGTTTAC
*
6330055 AAAACCTTAAAATCAGTTCA-T
1 AAAACCTTAAAATCAATTCACT
* * *
6330076 GAAACCCT-AAACCAATTCAC-
1 AAAACCTTAAAATCAATTCACT
* *
6330096 CAAACCTTAAAATCGATTCACT
1 AAAACCTTAAAATCAATTCACT
* *
6330118 AAAACCTTAAAATTAATTCCCT
1 AAAACCTTAAAATCAATTCACT
6330140 AAA
1 AAA
6330143 CTTTTAAATC
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
20 15 0.29
21 16 0.31
22 21 0.40
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAACCTTAAAATCAATTCACT
Found at i:6334695 original size:4 final size:4
Alignment explanation
Indices: 6334688--6334715 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6334678 TTGCTCCTTC
6334688 GTTT GTTT GTTT GTTT GTTT GTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT
6334716 TTCCATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
GTTT
Found at i:6336339 original size:2 final size:2
Alignment explanation
Indices: 6336332--6336360 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6336322 CTGCAGGTAA
6336332 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
6336361 CAGTACTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6337669 original size:31 final size:31
Alignment explanation
Indices: 6337585--6337691 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
6337575 ATAAAAATAT
6337585 TTAAATAAATTTTTATAC-TTTTA--TT-AA
1 TTAAATAAATTTTTATACTTTTTATTTTGAA
*
6337612 GTTTAATCAAATTTTTATA-TTTTTATTTTGAA
1 -TTAAAT-AAATTTTTATACTTTTTATTTTGAA
* *
6337644 TCAAATAAATTTTTATACTTTTTATTTTGAG
1 TTAAATAAATTTTTATACTTTTTATTTTGAA
*
6337675 TTAAATAAGTTTTTATA
1 TTAAATAAATTTTTATA
6337692 ACTAATAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.07
29 16 0.24
30 11 0.16
31 33 0.49
32 2 0.03
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.56
Consensus pattern (31 bp):
TTAAATAAATTTTTATACTTTTTATTTTGAA
Found at i:6342538 original size:2 final size:2
Alignment explanation
Indices: 6342531--6342556 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6342521 TTGAAATACT
6342531 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6342557 AAGAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6342621 original size:53 final size:50
Alignment explanation
Indices: 6342531--6342629 Score: 155
Period size: 51 Copynumber: 1.9 Consensus size: 50
6342521 TTGAAATACT
6342531 TATATATATATATATATATATATATAAAGAAAAGGTAAGTAACAAAGAANC
1 TATATATATATATATATATATATATAAAGAAAAGGTAAGTAACAAAGAA-C
6342582 TATATATATATATATATATATATA-AAAGAAAAAAGGGTAAGTAACAAA
1 TATATATATATATATATATATATATAAAG--AAAA-GGTAAGTAACAAA
6342630 AAGAAATACC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
50 4 0.09
51 24 0.53
52 4 0.09
53 13 0.29
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (50 bp):
TATATATATATATATATATATATATAAAGAAAAGGTAAGTAACAAAGAAC
Found at i:6347515 original size:21 final size:21
Alignment explanation
Indices: 6347490--6347549 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
6347480 ATACTTATGA
6347490 AATTTATAAATTAAAATAAAT
1 AATTTATAAATTAAAATAAAT
* *
6347511 AATTTGTCAATT---ATAAAT
1 AATTTATAAATTAAAATAAAT
*
6347529 AATATA-ACAATTAAAATAAAT
1 AATTTATA-AATTAAAATAAAT
6347550 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 14 0.47
21 16 0.53
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTTATAAATTAAAATAAAT
Found at i:6348103 original size:20 final size:21
Alignment explanation
Indices: 6348056--6348103 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
6348046 ACAAAGAGTC
6348056 ATAAAAAAATTTTTGATAGGAG
1 ATAAAAAAATTTTTGATA-GAG
*
6348078 A-AAAAAAGATTTTTTATA-AG
1 ATAAAAAA-ATTTTTGATAGAG
6348098 ATAAAA
1 ATAAAA
6348104 TTATTAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 10 0.43
22 10 0.43
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (21 bp):
ATAAAAAAATTTTTGATAGAG
Found at i:6348103 original size:22 final size:21
Alignment explanation
Indices: 6348058--6348103 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
6348048 AAAGAGTCAT
*
6348058 AAAAAAATTTTTGATAGGAGA
1 AAAAAAATTTTTGATAAGAGA
* *
6348079 AAAAAAGATTTTTTATAAGATA
1 AAAAAA-ATTTTTGATAAGAGA
6348101 AAA
1 AAA
6348104 TTATTAAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (21 bp):
AAAAAAATTTTTGATAAGAGA
Found at i:6352777 original size:2 final size:2
Alignment explanation
Indices: 6352770--6352797 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6352760 TATCTTGTCA
6352770 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
6352798 GTTTAAATTC
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:6355211 original size:2 final size:2
Alignment explanation
Indices: 6355204--6355232 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6355194 TTGGTGAACC
6355204 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
6355233 ATTGAGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6362237 original size:20 final size:20
Alignment explanation
Indices: 6362208--6362248 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6362198 ATCAATGTAC
*
6362208 TATTAATATAAATACTATAA
1 TATTAATATAAATAATATAA
*
6362228 TATTACTATAAATAATATAA
1 TATTAATATAAATAATATAA
6362248 T
1 T
6362249 TCTAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTAATATAAATAATATAA
Found at i:6371321 original size:2 final size:2
Alignment explanation
Indices: 6371314--6371354 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6371304 AATGAAGATG
6371314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6371355 AAATATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6371365 original size:12 final size:14
Alignment explanation
Indices: 6371314--6371365 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
6371304 AATGAAGATG
*
6371314 ATATATATATATAT
1 ATATATATATATAA
*
6371328 ATATATATATATAT
1 ATATATATATATAA
6371342 ATATATATATATAA
1 ATATATATATATAA
6371356 A-ATATA-ATAT
1 ATATATATATAT
6371366 TAAAAGGAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
12 4 0.11
13 5 0.14
14 28 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:6371645 original size:3 final size:3
Alignment explanation
Indices: 6371637--6371673 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6371627 CAGATGTTTC
6371637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6371674 ATGAATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6384634 original size:3 final size:3
Alignment explanation
Indices: 6384626--6384654 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6384616 TCATAGCTGC
6384626 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
6384655 CCCTCGAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:6390412 original size:14 final size:12
Alignment explanation
Indices: 6390384--6390420 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 12
6390374 AAAATATTAA
6390384 TAATATAATTTT
1 TAATATAATTTT
6390396 TAATATCAATATTT
1 TAATAT-AAT-TTT
6390410 TAATATAATTT
1 TAATATAATTT
6390421 AATTACTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (12 bp):
TAATATAATTTT
Found at i:6390438 original size:15 final size:15
Alignment explanation
Indices: 6390353--6390449 Score: 59
Period size: 15 Copynumber: 6.9 Consensus size: 15
6390343 TTTTTTAAAT
*
6390353 ATTAATAAT-TTATA
1 ATTAATAATATTTTA
* *
6390367 ATTAATTAAAATATTA
1 ATTAA-TAATATTTTA
*
6390383 ATAATATAAT-TTTTA
1 ATTA-ATAATATTTTA
6390398 A-T-ATCAATATTTTA
1 ATTAAT-AATATTTTA
6390412 A-T-AT-A-A-TTTA
1 ATTAATAATATTTTA
*
6390422 ATTACTAATATTTTA
1 ATTAATAATATTTTA
6390437 ATTAATAATATTT
1 ATTAATAATATTT
6390450 AATGTCATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
10 5 0.08
11 2 0.03
12 4 0.06
13 4 0.06
14 15 0.23
15 24 0.38
16 9 0.14
17 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAATAATATTTTA
Done.