Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 182 of 210
Found at i:54031150 original size:22 final size:22
Alignment explanation
Indices: 54031125--54031174 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
54031115 AAATATGGAT
54031125 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
54031147 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
54031169 TTGAGA
1 TTGAGA
54031175 AATGATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.32, T:0.24
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:54033126 original size:11 final size:11
Alignment explanation
Indices: 54033110--54033136 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
54033100 ATGTTAGTTG
54033110 GTTTGCTCCTA
1 GTTTGCTCCTA
54033121 GTTTGCTCCTA
1 GTTTGCTCCTA
54033132 GTTTG
1 GTTTG
54033137 ATACATGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (11 bp):
GTTTGCTCCTA
Found at i:54060695 original size:21 final size:21
Alignment explanation
Indices: 54060648--54060741 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
54060638 ATGGTTCATG
* *
54060648 ATTTTTTTAGTATTTTAATAC
1 ATTTTTATAATATTTTAATAC
*
54060669 ATTTTTATAATATTTTAA-AT
1 ATTTTTATAATATTTTAATAC
* *
54060689 ATGTTTTATTA-ATTAT-ATA-
1 AT-TTTTATAATATTTTAATAC
54060708 ATTTATTAT-A-ATTTT--TAC
1 ATTT-TTATAATATTTTAATAC
54060726 ATCTTTTATAATATTT
1 AT-TTTTATAATATTT
54060742 ATATTTTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.03
18 13 0.22
19 10 0.17
20 12 0.20
21 23 0.38
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATAATATTTTAATAC
Found at i:54060750 original size:18 final size:18
Alignment explanation
Indices: 54060670--54060751 Score: 58
Period size: 18 Copynumber: 4.3 Consensus size: 18
54060660 TTTTAATACA
54060670 TTTTTATAATATTTTAAATAT
1 TTTTTATAATA-TTT--ATAT
* *
54060691 GTTTTATTAAT-TATATAAT
1 TTTTTA-TAATATTTAT-AT
* * *
54060710 TTATTATAATTTTTACAT
1 TTTTTATAATATTTATAT
*
54060728 CTTTTATAATATTTATAT
1 TTTTTATAATATTTATAT
54060746 TTTTTA
1 TTTTTA
54060752 AGTTTATATC
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
18 27 0.57
19 9 0.19
20 2 0.04
21 5 0.11
22 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTTTATAATATTTATAT
Found at i:54073487 original size:2 final size:2
Alignment explanation
Indices: 54073482--54073544 Score: 110
Period size: 2 Copynumber: 31.5 Consensus size: 2
54073472 TTTTTTTTCC
54073482 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
54073524 AT AT AT AT AT AT -T ACT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT A
54073545 AGATAATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54075730 original size:49 final size:50
Alignment explanation
Indices: 54075675--54075771 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 50
54075665 TTTATTTTCT
* * * *
54075675 CGATGCCATAGTCAAACTATGGTCTTACATGTAGTCACAT-ATCACATAC
1 CGATGCCATAGCCAAACTATGGTCTTACACGGAATCACATAATCACATAC
* *
54075724 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCAAACTATGGTCTTACACGGAATCACATAATCACAT
54075772 TTTCACATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
49 34 0.83
50 7 0.17
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (50 bp):
CGATGCCATAGCCAAACTATGGTCTTACACGGAATCACATAATCACATAC
Found at i:54087627 original size:30 final size:28
Alignment explanation
Indices: 54087555--54087627 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
54087545 ACTTTGTGAA
54087555 AAGAAAA-AAAATTATGAAAAAAAAAGAG
1 AAGAAAAGAAAA-TATGAAAAAAAAAGAG
*
54087583 AAGAAATGAGAAATAT-AAAAAAAAAGAG
1 AAGAAAAGA-AAATATGAAAAAAAAAGAG
54087611 AAAGAAGGAAGAAAATA
1 -AAGAA--AAGAAAATA
54087628 GGGGAAAGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 18 0.47
29 9 0.24
30 8 0.21
31 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.10
Consensus pattern (28 bp):
AAGAAAAGAAAATATGAAAAAAAAAGAG
Found at i:54094443 original size:27 final size:29
Alignment explanation
Indices: 54094394--54094457 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
54094384 TTTTTCATCT
* **
54094394 GAAGAAGATGAAGAGGTGACTTCTTCTGAG
1 GAAGAAGAAGAAGAGGT-ACTTCAACTGAG
54094424 GAAGAAGAAGAAG-GGT-CTTCAACTGAG
1 GAAGAAGAAGAAGAGGTACTTCAACTGAG
54094451 GAAGAAG
1 GAAGAAG
54094458 GTGAGGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.52
29 3 0.10
30 12 0.39
ACGTcount: A:0.39, C:0.09, G:0.34, T:0.17
Consensus pattern (29 bp):
GAAGAAGAAGAAGAGGTACTTCAACTGAG
Found at i:54098300 original size:2 final size:2
Alignment explanation
Indices: 54098293--54098321 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
54098283 TAATAAGAGC
54098293 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 T
54098322 GCATTAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54100335 original size:10 final size:10
Alignment explanation
Indices: 54100322--54100389 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
54100312 ATCATAAAAA
54100322 ATAAAAAATT
1 ATAAAAAATT
54100332 ATAAAAAGA-T
1 ATAAAAA-ATT
* *
54100342 ATTAAAATTT
1 ATAAAAAATT
* *
54100352 ATATAAACTT
1 ATAAAAAATT
*
54100362 AT-AAATATT
1 ATAAAAAATT
54100371 AT-AAAAA-T
1 ATAAAAAATT
54100379 ATAAAAAATT
1 ATAAAAAATT
54100389 A
1 A
54100390 ATGAAACCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
8 3 0.07
9 15 0.33
10 26 0.58
11 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:54103216 original size:18 final size:18
Alignment explanation
Indices: 54103173--54103216 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
54103163 AAATATAATA
*
54103173 AAAAG-AAATCAACAAAT
1 AAAAGTAAATAAACAAAT
54103190 AAAAGTAAATAAACAAAT
1 AAAAGTAAATAAACAAAT
*
54103208 AAAATTAAA
1 AAAAGTAAA
54103217 GCACTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAAGTAAATAAACAAAT
Found at i:54103310 original size:2 final size:2
Alignment explanation
Indices: 54103303--54103409 Score: 187
Period size: 2 Copynumber: 53.5 Consensus size: 2
54103293 TAAAATTATG
54103303 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
** *
54103345 GC AT GT 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
54103387 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
54103410 CGTACGCGCG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54103455 original size:14 final size:14
Alignment explanation
Indices: 54103436--54103470 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54103426 AGATAGAGAG
54103436 ATATATACATATGT
1 ATATATACATATGT
* *
54103450 ATATATGCGTATGT
1 ATATATACATATGT
54103464 ATATATA
1 ATATATA
54103471 TATTTTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (14 bp):
ATATATACATATGT
Found at i:54103692 original size:3 final size:3
Alignment explanation
Indices: 54103684--54103790 Score: 51
Period size: 3 Copynumber: 35.3 Consensus size: 3
54103674 AAACTATCAT
* * *
54103684 ATA ATA ATA AT- ATG ATGA ATA AAA ATG AT- ATAA ATA ATA ATA GA-A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA AT-A ATA ATA ATA -ATA
* * * * *
54103729 ATA ATA ATC ATA ATA ATA AAA GATA ATA ACA TTA A-A ATA ATGA AGA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA AT-A ATA
* *
54103775 AAA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
54103791 AAGTGTTAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
2 7 0.09
3 64 0.80
4 9 0.11
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:54103746 original size:15 final size:13
Alignment explanation
Indices: 54103682--54103757 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 13
54103672 CTAAACTATC
54103682 ATATAATAATAAT
1 ATATAATAATAAT
*
54103695 ATGATGAATAAAAAT
1 AT-AT-AATAATAAT
54103710 GATATAAATAATAAT
1 -ATAT-AATAATAAT
*
54103725 AGA-AATAATAAT
1 ATATAATAATAAT
* *
54103737 -CATAATAATAAA
1 ATATAATAATAAT
*
54103749 AGATAATAA
1 ATATAATAA
54103758 CATTAAAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
11 1 0.02
12 17 0.33
13 9 0.18
14 4 0.08
15 18 0.35
16 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:54105044 original size:22 final size:24
Alignment explanation
Indices: 54105019--54105063 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
54105009 TAATACATAA
*
54105019 AGATAAATA-AA-TGATTTATCTT
1 AGATAAATAGAAGTAATTTATCTT
54105041 AGATAAATAGAAGTAATTTATCT
1 AGATAAATAGAAGTAATTTATCT
54105064 CCTATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 9 0.45
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (24 bp):
AGATAAATAGAAGTAATTTATCTT
Found at i:54108407 original size:20 final size:20
Alignment explanation
Indices: 54108382--54108437 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
54108372 ATCATAAAAA
*
54108382 ATTAAAAATTATAAAAAGAT
1 ATTAAAAATTATAAAAACAT
* * *
54108402 ATTAAAATTTATATAAACTT
1 ATTAAAAATTATAAAAACAT
*
54108422 A-TAAATATTATAAAAA
1 ATTAAAAATTATAAAAA
54108438 TATAAAATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
ATTAAAAATTATAAAAACAT
Found at i:54108509 original size:9 final size:9
Alignment explanation
Indices: 54108497--54108550 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
54108487 CTTTAAAAAA
54108497 ATTAAAATT
1 ATTAAAATT
54108506 ATTAAAATT
1 ATTAAAATT
54108515 ATTAAAATT
1 ATTAAAATT
* *
54108524 GTATAAACTT
1 AT-TAAAATT
54108534 A-TAAATATT
1 ATTAAA-ATT
*
54108543 ATAAAAAT
1 ATTAAAAT
54108551 ATAAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
8 4 0.11
9 24 0.65
10 9 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
ATTAAAATT
Found at i:54108512 original size:18 final size:18
Alignment explanation
Indices: 54108489--54108523 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54108479 TTAGAATTCT
54108489 TTAAAAAAATTAAAATTA
1 TTAAAAAAATTAAAATTA
**
54108507 TTAAAATTATTAAAATT
1 TTAAAAAAATTAAAATT
54108524 GTATAAACTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAAAAATTAAAATTA
Found at i:54108605 original size:22 final size:21
Alignment explanation
Indices: 54108579--54108627 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
54108569 CTATTTAAAA
54108579 TAAAATACATATTAGAATTCT-T
1 TAAAATACATATTA-AATT-TAT
* *
54108601 TAAAAAATATATTAAATTTAT
1 TAAAATACATATTAAATTTAT
54108622 TAAAAT
1 TAAAAT
54108628 TGTATAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 12 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAATACATATTAAATTTAT
Found at i:54113758 original size:36 final size:34
Alignment explanation
Indices: 54113680--54113765 Score: 91
Period size: 36 Copynumber: 2.5 Consensus size: 34
54113670 CAAATGCCTC
* * *
54113680 TAAAATAATAGCAAAATTAATAATAAAATAAGAG
1 TAAAATAATACCAAAAATAATAATAAAATAAGAA
* * *
54113714 TTATATAATATCCAAAAAATAATAATAAAATAATAA
1 TAAAATAATA-CC-AAAAATAATAATAAAATAAGAA
*
54113750 TAAAATAATAGCAAAA
1 TAAAATAATACCAAAA
54113766 TAACATCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
34 12 0.29
35 2 0.05
36 27 0.66
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (34 bp):
TAAAATAATACCAAAAATAATAATAAAATAAGAA
Found at i:54113768 original size:11 final size:11
Alignment explanation
Indices: 54113729--54113759 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
54113719 TAATATCCAA
54113729 AAAATAATAAT
1 AAAATAATAAT
54113740 AAAATAATAAT
1 AAAATAATAAT
54113751 AAAATAATA
1 AAAATAATA
54113760 GCAAAATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:54113796 original size:21 final size:22
Alignment explanation
Indices: 54113759--54113813 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
54113749 ATAAAATAAT
* * *
54113759 AGCAAAATAACATCAAAATGGC
1 AGCAAAACAACAACAAAATAGC
54113781 AGC-AAACAACAACAAAATAGC
1 AGCAAAACAACAACAAAATAGC
54113802 AGCAAAACAACA
1 AGCAAAACAACA
54113814 GTGAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.60, C:0.22, G:0.11, T:0.07
Consensus pattern (22 bp):
AGCAAAACAACAACAAAATAGC
Found at i:54114166 original size:61 final size:62
Alignment explanation
Indices: 54114079--54114249 Score: 168
Period size: 61 Copynumber: 2.8 Consensus size: 62
54114069 AGGTTTGAAC
* * * * ** *
54114079 TTTTTTTGTCCAAATTAAGTCATGAACTTGA-CAGTTGTTCCCACATTGGGGCCTGAACCCT
1 TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAACCCT
* * ***
54114140 TTTTTTTGTCCAAGTTAGGCCTTGAACTT-AGCAAATGTTCCCACGTTGGGACTTGAATTTT
1 TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAACCCT
* * *
54114201 TTTTCTTTGGTCCAAGTTAGGCCTTAAACTTG-GCAACTGTTCTCACATT
1 TTTT-TTT-GTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATT
54114250 AGAATTTGAA
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
60 1 0.01
61 51 0.57
62 3 0.03
63 35 0.39
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (62 bp):
TTTTTTTGTCCAAGTTAGGCCTTGAACTTGAGCAAATGTTCCCACATTGGGACCTGAACCCT
Found at i:54114259 original size:63 final size:61
Alignment explanation
Indices: 54114139--54114267 Score: 159
Period size: 63 Copynumber: 2.1 Consensus size: 61
54114129 GCCTGAACCC
* * * * *
54114139 TTTTTTTTGTCCAAGTTAGGCCTTGAACTTAGCAAATGTTCCCACGTTGGGACTTGAATTT
1 TTTTTTTTGTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
* * * *
54114200 TTTTTCTTTGGTCCAAGTTAGGCCTTAAACTTGGCAACTGTTCTCACATTAGAATTTGAACTT
1 TTTTT-TTT-GTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
54114263 TTTTT
1 TTTTT
54114268 ATTCAAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 5 0.09
62 3 0.05
63 49 0.86
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (61 bp):
TTTTTTTTGTCCAAGTTAGGCCTTAAACTTAGCAAATGTTCCCACATTAGAACTTGAACTT
Found at i:54118263 original size:34 final size:35
Alignment explanation
Indices: 54118220--54118292 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 35
54118210 TTTCTTTCTT
* *
54118220 AATTTA-TTTTTTCCTAATGATAAATTTGGCCCTC
1 AATTTATTTTTTTCATAATGATAAATTTGACCCTC
*
54118254 AATTTATTTTTTTTCATAATGATAAATTTGACTCTC
1 AATTTA-TTTTTTTCATAATGATAAATTTGACCCTC
54118290 AAT
1 AAT
54118293 ATTTATACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 6 0.18
36 28 0.82
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (35 bp):
AATTTATTTTTTTCATAATGATAAATTTGACCCTC
Found at i:54121791 original size:3 final size:3
Alignment explanation
Indices: 54121783--54121811 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54121773 TCTTCAACTC
54121783 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
54121812 AAATCTCATG
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:54127243 original size:2 final size:2
Alignment explanation
Indices: 54127236--54127272 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54127226 NTACTAAGTA
54127236 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 A
54127273 AACTAAAAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54130103 original size:15 final size:16
Alignment explanation
Indices: 54130078--54130107 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54130068 TGTTTAGTTT
54130078 TTATATTTTAATTTAG
1 TTATATTTTAATTTAG
54130094 TTAT-TTTTAATTTA
1 TTATATTTTAATTTA
54130108 AAATTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTATATTTTAATTTAG
Found at i:54132631 original size:20 final size:18
Alignment explanation
Indices: 54132608--54132704 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 18
54132598 TTTCTCAATA
54132608 AAAATTTTAAAATGATTTT
1 AAAATTTTAAAAT-ATTTT
* *
54132627 CAAAAATTCAAAATAATTTT
1 -AAAATTTTAAAAT-ATTTT
*
54132647 TAAATTTTAAAATATTTAT
1 AAAATTTTAAAATATTT-T
*
54132666 AAAAATTCTAAAA-A-TTT
1 -AAAATTTTAAAATATTTT
* *
54132683 -ATATTTTAAAAAATTTAT
1 AAAATTTTAAAATATTT-T
54132701 AAAA
1 AAAA
54132705 ATTCTAAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
15 9 0.15
16 1 0.02
17 3 0.05
18 7 0.12
19 14 0.23
20 26 0.43
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
AAAATTTTAAAATATTTT
Found at i:54132699 original size:35 final size:36
Alignment explanation
Indices: 54132645--54132721 Score: 120
Period size: 35 Copynumber: 2.2 Consensus size: 36
54132635 CAAAATAATT
* *
54132645 TTTAAATTTTAAAATATTTATAAAAATTCTAAA-AA
1 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
54132680 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
1 TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
*
54132716 TATATA
1 TTTATA
54132722 GAGAAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 31 0.82
36 7 0.18
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (36 bp):
TTTATATTTTAAAAAATTTATAAAAATTCTAAAGAA
Found at i:54132704 original size:10 final size:10
Alignment explanation
Indices: 54132648--54132707 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
54132638 AATAATTTTT
54132648 AAATTT-TAA
1 AAATTTATAA
54132657 AATATTTATAA
1 AA-ATTTATAA
*
54132668 AAA-TTCTAA
1 AAATTTATAA
54132677 AAATTTAT--
1 AAATTTATAA
*
54132685 -ATTTTA-AA
1 AAATTTATAA
54132693 AAATTTATAA
1 AAATTTATAA
54132703 AAATT
1 AAATT
54132708 CTAAAGAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
7 5 0.12
9 15 0.38
10 15 0.38
11 5 0.12
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AAATTTATAA
Found at i:54136814 original size:44 final size:43
Alignment explanation
Indices: 54136719--54136844 Score: 148
Period size: 43 Copynumber: 2.9 Consensus size: 43
54136709 TCGTACAATG
* * * *
54136719 CCAATGTCCCAGACGTGGTCTTACATGTAAT-TAAATATCGATG
1 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAA-ATCGATA
* * *
54136762 CCACTGTCCTAGACAG-GGTTTTACACGAAAGTCTCAAATCGATA
1 CCAATGTCCCAGAC-GTGGTCTTACACGAAA-TCTCAAATCGATA
54136806 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATC
1 CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATC
54136845 AAAATCCTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
43 33 0.48
44 33 0.48
45 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
CCAATGTCCCAGACGTGGTCTTACACGAAATCTCAAATCGATA
Found at i:54144273 original size:19 final size:19
Alignment explanation
Indices: 54144246--54144289 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
54144236 TTAGCTTTTT
*
54144246 AGAGCTTAATCCGGGTTTA
1 AGAGTTTAATCCGGGTTTA
*
54144265 AGAGTTTAATCTGGGTTTA
1 AGAGTTTAATCCGGGTTTA
54144284 AGAGTT
1 AGAGTT
54144290 GATTTAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.36
Consensus pattern (19 bp):
AGAGTTTAATCCGGGTTTA
Found at i:54161699 original size:18 final size:19
Alignment explanation
Indices: 54161673--54161709 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54161663 CATAACTGGA
54161673 AAATCTAAAAA-AGGTTTT
1 AAATCTAAAAATAGGTTTT
*
54161691 AAATGTAAAAATAGGTTTT
1 AAATCTAAAAATAGGTTTT
54161710 CATAGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (19 bp):
AAATCTAAAAATAGGTTTT
Found at i:54164154 original size:12 final size:12
Alignment explanation
Indices: 54164139--54164187 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
54164129 TTCAGTTTCC
54164139 GGTTTGGTCTCT
1 GGTTTGGTCTCT
54164151 GGTTTGGTCTCCT
1 GGTTTGGTCT-CT
*
54164164 -GTTTGGCCTCT
1 GGTTTGGTCTCT
*
54164175 TGTTTGGTCTCT
1 GGTTTGGTCTCT
54164187 G
1 G
54164188 ATTTAGGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.31, T:0.49
Consensus pattern (12 bp):
GGTTTGGTCTCT
Found at i:54164167 original size:24 final size:24
Alignment explanation
Indices: 54164140--54164185 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54164130 TCAGTTTCCG
*
54164140 GTTTGGTCTCTGGTTTGGTCTCCT
1 GTTTGGCCTCTGGTTTGGTCTCCT
*
54164164 GTTTGGCCTCTTGTTTGGTCTC
1 GTTTGGCCTCTGGTTTGGTCTC
54164186 TGATTTAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.00, C:0.22, G:0.28, T:0.50
Consensus pattern (24 bp):
GTTTGGCCTCTGGTTTGGTCTCCT
Found at i:54165561 original size:18 final size:18
Alignment explanation
Indices: 54165522--54165568 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
54165512 TAACTTTCTT
* *
54165522 TATATATTCTTAAAAGAG
1 TATATATTTTTAAAAGAA
54165540 TATATATTTTTAAAA-ATA
1 TATATATTTTTAAAAGA-A
*
54165558 TATACATTTTT
1 TATATATTTTT
54165569 GAATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (18 bp):
TATATATTTTTAAAAGAA
Found at i:54166115 original size:13 final size:14
Alignment explanation
Indices: 54166097--54166125 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54166087 GTTTGAGATT
54166097 ATTATATTA-AAAA
1 ATTATATTATAAAA
54166110 ATTATATTATAAAA
1 ATTATATTATAAAA
54166124 AT
1 AT
54166126 AATTTATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATATTATAAAA
Found at i:54166119 original size:18 final size:18
Alignment explanation
Indices: 54166096--54166150 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
54166086 TGTTTGAGAT
54166096 TATTATATTAAAAAATTA
1 TATTATATTAAAAAATTA
54166114 TATTATA--AAAATAATT-
1 TATTATATTAAAA-AATTA
* *
54166130 TATGTATTTTATAAAATTA
1 TAT-TATATTAAAAAATTA
54166149 TA
1 TA
54166151 GCAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 7 0.23
17 7 0.23
18 11 0.37
19 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTATATTAAAAAATTA
Found at i:54166270 original size:14 final size:15
Alignment explanation
Indices: 54166235--54166272 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
54166225 TTTACATGTT
54166235 ATAAATTT-TTTATA
1 ATAAATTTATTTATA
*
54166249 ATATATTTATTTATA
1 ATAAATTTATTTATA
54166264 A-AAATTTAT
1 ATAAATTTAT
54166273 GATCAAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAATTTATTTATA
Found at i:54167088 original size:17 final size:18
Alignment explanation
Indices: 54167066--54167108 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54167056 GTTTAGAAAT
*
54167066 TATTTTTATCAT-ACTAA
1 TATTTTTATAATAACTAA
*
54167083 TATTTTTATAATAATTAA
1 TATTTTTATAATAACTAA
54167101 TATTTTTA
1 TATTTTTA
54167109 AAAATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTTATAATAACTAA
Found at i:54169548 original size:22 final size:24
Alignment explanation
Indices: 54169523--54169569 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
54169513 CACAAGATAT
54169523 AAAGAAACTT-AATAAA-A-CTTCG
1 AAAGAAA-TTAAATAAAGATCTTCG
54169545 AAAGAAATTAAATAAAGATCTTCG
1 AAAGAAATTAAATAAAGATCTTCG
54169569 A
1 A
54169570 TCTTGAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 13 0.59
23 1 0.05
24 6 0.27
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (24 bp):
AAAGAAATTAAATAAAGATCTTCG
Found at i:54173993 original size:18 final size:20
Alignment explanation
Indices: 54173959--54173995 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
54173949 GGTCCGCCCA
54173959 AAAAATAATAGAATTTGAAT
1 AAAAATAATAGAATTTGAAT
54173979 AAAAATAA-A-AATTTGAA
1 AAAAATAATAGAATTTGAA
54173996 AAATGTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (20 bp):
AAAAATAATAGAATTTGAAT
Found at i:54174163 original size:23 final size:24
Alignment explanation
Indices: 54174135--54174182 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
54174125 GTTTTGGTGC
*
54174135 TGTTATTTTTG-TGCTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
*
54174158 TGTTATTTTTGCTATTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
54174182 T
1 T
54174183 ATTTGTACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (24 bp):
TGTTATTTTTGCTACTGTTTTTGT
Found at i:54174181 original size:21 final size:22
Alignment explanation
Indices: 54174135--54174186 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
54174125 GTTTTGGTGC
*
54174135 TGTTATTTTTGTGCTGTTTTTGT
1 TGTTA-TTTTGTGCTATTTTTGT
54174158 TGTTATTTT-TGCTATTGTTT-T
1 TGTTATTTTGTGCTATT-TTTGT
54174179 TGTTATTT
1 TGTTATTT
54174187 GTACTGGCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 15 0.56
22 7 0.26
23 5 0.19
ACGTcount: A:0.08, C:0.04, G:0.17, T:0.71
Consensus pattern (22 bp):
TGTTATTTTGTGCTATTTTTGT
Found at i:54178703 original size:10 final size:11
Alignment explanation
Indices: 54178678--54178703 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54178668 TGATATCTCT
54178678 TTTTTTAAATA
1 TTTTTTAAATA
54178689 TTTTTTAAATA
1 TTTTTTAAATA
54178700 TTTT
1 TTTT
54178704 ACTATACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:54180763 original size:18 final size:18
Alignment explanation
Indices: 54180742--54180809 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 18
54180732 TTATAGATTT
54180742 TTTTTGAAATTTTTATAA
1 TTTTTGAAATTTTTATAA
* * *
54180760 TTTTTTTAAA-ATATATAA
1 -TTTTTGAAATTTTTATAA
* *
54180778 ATTTTGGAATTTTTATAAA
1 TTTTTGAAATTTTTAT-AA
54180797 TATTTTG-AATTTT
1 T-TTTTGAAATTTT
54180810 AAAAATTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
17 6 0.16
18 10 0.27
19 16 0.43
20 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTTGAAATTTTTATAA
Found at i:54180771 original size:20 final size:22
Alignment explanation
Indices: 54180730--54180771 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
54180720 TCTTTTTATA
*
54180730 TTTTATAGATTTTTTTTGAAAT
1 TTTTATAGATTTTTTTTAAAAT
54180752 TTTTATA-A-TTTTTTTAAAAT
1 TTTTATAGATTTTTTTTAAAAT
54180772 ATATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTTATAGATTTTTTTTAAAAT
Found at i:54180808 original size:19 final size:19
Alignment explanation
Indices: 54180773--54180827 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
54180763 TTTTAAAATA
*
54180773 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
54180791 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
54180809 TAAAAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
54180828 AATTTTTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.47
19 15 0.47
20 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:54180810 original size:18 final size:18
Alignment explanation
Indices: 54180773--54180827 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
54180763 TTTTAAAATA
*
54180773 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAA-TTT
54180791 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
*
54180809 TAAAAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
54180828 AATTTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:54180816 original size:36 final size:36
Alignment explanation
Indices: 54180743--54180816 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
54180733 TATAGATTTT
* * *
54180743 TTTTGAAATTTTTATAATTTTTTTAAAATATATAAA
1 TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
* * * *
54180779 TTTTGGAATTTTTATAAATATTTTGAATTTTAAAAA
1 TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
54180815 TT
1 TT
54180817 ATTTTGAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (36 bp):
TTTTGAAATTTTTATAAATATTTTAAAATATAAAAA
Found at i:54182563 original size:10 final size:11
Alignment explanation
Indices: 54182538--54182571 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
54182528 AAATAAATTG
*
54182538 AAGAAAAAAGA
1 AAGAAAGAAGA
54182549 AAGAAAGAA-A
1 AAGAAAGAAGA
54182559 AAGAAAGAAGA
1 AAGAAAGAAGA
54182570 AA
1 AA
54182572 AATGAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:54182581 original size:14 final size:13
Alignment explanation
Indices: 54182537--54182573 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
54182527 CAAATAAATT
54182537 GAAGAAAAAAGAAA
1 GAAG-AAAAAGAAA
54182551 GAAAGAAAAAGAAA
1 G-AAGAAAAAGAAA
54182565 GAAGAAAAA
1 GAAGAAAAA
54182574 TGAGAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 11 0.50
15 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAGAAA
Found at i:54185425 original size:36 final size:36
Alignment explanation
Indices: 54185379--54185487 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
54185369 GGTAGCTTTA
*
54185379 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
54185415 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
54185451 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
54185487 G
1 G
54185488 TTAGTCTTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:54185435 original size:21 final size:20
Alignment explanation
Indices: 54185407--54185472 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
54185397 AGTGAAAAAG
54185407 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
54185427 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
54185443 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
54185463 TGATCAAGTG
1 TGAT-AAGTG
54185473 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:54185446 original size:82 final size:84
Alignment explanation
Indices: 54185343--54185576 Score: 226
Period size: 82 Copynumber: 2.8 Consensus size: 84
54185333 TTTGAGTACT
* *
54185343 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC--TAGCTACACTTATCTGATCAAGTGAAAAAGT
54185408 GATAAGTG-C-TA-T-ACTTA
64 GATAAGTGTCTTACTAACTTA
*
54185425 TCTGATCAAGTGAAAAAGTGATAA---GT-GCTA--T--ACTTATCTGATCAAGTGACAAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
54185482 TAAGTGTTAGTCTTAGCTACACTTA
66 TAA--G-T-GTCTTA-CTA-ACTTA
* * * *
54185507 TCTAATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGAAAAAGTG
54185570 ATAAGTG
65 ATAAGTG
54185577 ATCATATGTA
Statistics
Matches: 125, Mismatches: 8, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
72 28 0.22
74 2 0.02
75 1 0.01
76 3 0.02
77 1 0.01
78 4 0.03
79 2 0.02
80 1 0.01
82 49 0.39
85 3 0.02
86 2 0.02
87 4 0.03
89 11 0.09
90 2 0.02
91 12 0.10
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (84 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
TAAGTGTCTTACTAACTTA
Found at i:54190108 original size:26 final size:26
Alignment explanation
Indices: 54190079--54190161 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
54190069 TATGAACACG
54190079 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
*
54190105 TGTGTA-T-CGATAGATG-ATGG-TCAC-A
1 TGTGTAGTACTA-AG-TGCA-GGCT-ACTA
*
54190130 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
54190156 TGTGTA
1 TGTGTA
54190162 CTGGATGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
24 2 0.04
25 18 0.40
26 23 0.51
27 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:54190155 original size:51 final size:50
Alignment explanation
Indices: 54190075--54190262 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 50
54190065 TACTTATGAA
* *
54190075 CACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTA-TCGATAGATGATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTCGATAGAT--TGGT
* * *
54190126 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGAT-GACTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTCGATAGA--TTGGT
* * * * * *
54190177 TACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTGGAAAGCTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTCGATAGATTGGT
* *
54190227 CACGTGTGTAGTACTATGTGTAGGCTACTACATGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
54190263 TCGGATGACA
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
50 36 0.30
51 77 0.65
52 5 0.04
53 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.32
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACTCGATAGATTGGT
Found at i:54190269 original size:101 final size:101
Alignment explanation
Indices: 54190076--54190271 Score: 252
Period size: 101 Copynumber: 1.9 Consensus size: 101
54190066 ACTTATGAAC
* * * *
54190076 ACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTATCGATAGATGATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGAAAGAT-ATGATCACATGTGTAGTACT
**
54190141 ATGTGCAGGCTACTATGTGTACTGGATGACTTTGGTT
65 ATGTGCAGGCTACTACATGTACTGGATGACTTTGGTT
* * * *
54190178 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGAACTGGAAAGCT-TGATCACGTGTGTAGTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAA-TCGAAAGATATGATCACATGTGTAGTACT
*
54190242 ATGTGTAGGCTACTACATGTA-TCGGATGAC
65 ATGTGCAGGCTACTACATGTACT-GGATGAC
54190272 AATGGTCACA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
100 1 0.01
101 42 0.52
102 32 0.40
103 6 0.07
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.32
Consensus pattern (101 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACTACGTGAATCGAAAGATATGATCACATGTGTAGTACTA
TGTGCAGGCTACTACATGTACTGGATGACTTTGGTT
Found at i:54190287 original size:16 final size:16
Alignment explanation
Indices: 54190266--54190297 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54190256 ACATGTATCG
54190266 GATGACAATGGTCACA
1 GATGACAATGGTCACA
54190282 GATGACAATGGTCACA
1 GATGACAATGGTCACA
54190298 TGGGTGGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (16 bp):
GATGACAATGGTCACA
Found at i:54192757 original size:19 final size:19
Alignment explanation
Indices: 54192734--54192776 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
54192724 ATTTTTATAA
54192734 TTTTTCA-TAAAAAATATT
1 TTTTTCATTAAAAAATATT
* *
54192752 TATTTTTATTAAAAATTATT
1 T-TTTTCATTAAAAAATATT
54192772 TTTTT
1 TTTTT
54192777 GAGTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTCATTAAAAAATATT
Found at i:54197821 original size:59 final size:59
Alignment explanation
Indices: 54197689--54197821 Score: 162
Period size: 62 Copynumber: 2.2 Consensus size: 59
54197679 TCCAAAAATA
* * * *
54197689 ATATTATTTTAAT-AGTTTAATATTTAATTTAATTTAATGTTTATCTTGCAGATAAACATT
1 ATATTATTTTAATAAGTTTAAAATTAAATTTAATCTAATATTTATCTT--AGATAAACATT
* *
54197749 ATATTATTTTAATAAGATTTAAAATTAAATTTAATCTATTATTTATCTT-GATAAATATT
1 ATATTATTTTAATAAG-TTTAAAATTAAATTTAATCTAATATTTATCTTAGATAAACATT
*
54197808 ATATTAATTTAATA
1 ATATTATTTTAATA
54197822 TTAAAGTGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 22 0.34
60 13 0.20
61 2 0.03
62 27 0.42
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (59 bp):
ATATTATTTTAATAAGTTTAAAATTAAATTTAATCTAATATTTATCTTAGATAAACATT
Found at i:54206848 original size:31 final size:31
Alignment explanation
Indices: 54206808--54206875 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
54206798 TTAATAGCCT
*
54206808 AGTGACTTAAATAAAAACTTCTGAATTGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
* * *
54206839 AGTGGCTTAAATGAAAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTCTGAATAGTTC
54206870 AGTGAC
1 AGTGAC
54206876 CATTTTGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.34
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTCTGAATAGTTC
Found at i:54208291 original size:3 final size:3
Alignment explanation
Indices: 54208285--54208327 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
54208275 AATAATGATG
*
54208285 ACA ACA ACA ACA ACA ACA ACA ACA ATA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
54208328 GAGTTGCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.02
Consensus pattern (3 bp):
ACA
Found at i:54209753 original size:27 final size:28
Alignment explanation
Indices: 54209702--54209760 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
54209692 TATATTATAT
* *
54209702 TATATTATTTTAATATTTAATATTTTTA
1 TATATTATTTTAATATTGAAAATTTTTA
*
54209730 TATATT-TTTTATTATTGAAAATTTTTA
1 TATATTATTTTAATATTGAAAATTTTTA
54209757 TATA
1 TATA
54209761 GTCATCTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TATATTATTTTAATATTGAAAATTTTTA
Found at i:54211866 original size:14 final size:14
Alignment explanation
Indices: 54211847--54211877 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
54211837 GGAATTGTTT
*
54211847 TAATCTAAATTTAC
1 TAATCTAAATTAAC
54211861 TAATCTAAATTAAC
1 TAATCTAAATTAAC
54211875 TAA
1 TAA
54211878 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:54214392 original size:12 final size:12
Alignment explanation
Indices: 54214344--54214401 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 12
54214334 GATAATAAAC
54214344 AAGAAATAAATAA
1 AAGAAATAAAT-A
*
54214357 AAGAAAATAACTAA
1 AAG-AAATAAAT-A
*
54214371 TAATAAATAAATA
1 -AAGAAATAAATA
*
54214384 GAGAAATAAATA
1 AAGAAATAAATA
54214396 AAGAAA
1 AAGAAA
54214402 GGAGGGCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 15 0.41
13 4 0.11
14 16 0.43
15 2 0.05
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (12 bp):
AAGAAATAAATA
Found at i:54218285 original size:16 final size:17
Alignment explanation
Indices: 54218266--54218307 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
54218256 TAAATGAAAT
*
54218266 TTTATTTAATTTTAGC-
1 TTTAATTAATTTTAGCA
54218282 TTTAAGTT-ATTTTAGCA
1 TTTAA-TTAATTTTAGCA
54218299 TTTAATTAA
1 TTTAATTAA
54218308 ATGGAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTAATTAATTTTAGCA
Found at i:54219794 original size:14 final size:14
Alignment explanation
Indices: 54219772--54219823 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
54219762 GATGCAAGGT
54219772 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
* *
54219785 TTTAAGGTTTAAGA
1 TTTAAGGTTTAGGG
*
54219799 TTTAAGATTTAGGG
1 TTTAAGGTTTAGGG
*
54219813 TTTGAGGTTTA
1 TTTAAGGTTTA
54219824 ATGTTCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.16
14 26 0.84
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:54219809 original size:28 final size:27
Alignment explanation
Indices: 54219772--54219824 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
54219762 GATGCAAGGT
54219772 TTTAAGTTTAGGGTTTAAGGTTTAAGA
1 TTTAAGTTTAGGGTTTAAGGTTTAAGA
*
54219799 TTTAAGATTTAGGGTTTGAGGTTTAA
1 TTTAAG-TTTAGGGTTTAAGGTTTAA
54219825 TGTTCAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (27 bp):
TTTAAGTTTAGGGTTTAAGGTTTAAGA
Found at i:54219823 original size:21 final size:21
Alignment explanation
Indices: 54219767--54219824 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
54219757 ATCAAGATGC
* *
54219767 AAGGTTTTAAG-TTTAGGGTTT
1 AAGG-TTTAAGATTTAAGATTT
54219788 AAGGTTTAAGATTTAAGATTT
1 AAGGTTTAAGATTTAAGATTT
* * *
54219809 AGGGTTTGAGGTTTAA
1 AAGGTTTAAGATTTAA
54219825 TGTTCAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (21 bp):
AAGGTTTAAGATTTAAGATTT
Found at i:54221363 original size:14 final size:16
Alignment explanation
Indices: 54221333--54221365 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54221323 AAAATCTTTC
54221333 AAAAATAAGAAATTAA
1 AAAAATAAGAAATTAA
54221349 AAAAATAA-AAA-TAA
1 AAAAATAAGAAATTAA
54221363 AAA
1 AAA
54221366 TAAAAGGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAATAAGAAATTAA
Found at i:54224615 original size:28 final size:30
Alignment explanation
Indices: 54224574--54224640 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
54224564 TTCTTATATA
*
54224574 TATTTTATTAAATAT-AAAAAAGTTAACAT
1 TATTTTATTAAATATAAAAAAACTTAACAT
54224603 TATTTT-TTAAATATAAAAAAACTTAACAT
1 TATTTTATTAAATATAAAAAAACTTAACAT
54224632 TATTTTATT
1 TATTTTATT
54224641 TAAACACATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 8 0.23
29 25 0.71
30 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (30 bp):
TATTTTATTAAATATAAAAAAACTTAACAT
Found at i:54229205 original size:19 final size:21
Alignment explanation
Indices: 54229145--54229199 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
54229135 ATTGTTGAGG
* *
54229145 ATATGCAGTTTTAGATATG--
1 ATATGCAATCTTAGATATGAT
54229164 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
54229185 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
54229200 AGATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:54229221 original size:23 final size:24
Alignment explanation
Indices: 54229157--54229222 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 24
54229147 ATGCAGTTTT
54229157 AGATATG--ATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
54229176 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
54229200 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
54229223 GATTTAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.17
21 12 0.30
23 12 0.30
24 9 0.22
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:54230156 original size:4 final size:4
Alignment explanation
Indices: 54230136--54230196 Score: 63
Period size: 4 Copynumber: 15.5 Consensus size: 4
54230126 GCTTTGCATG
* * *
54230136 TTAT TGAT TTA- TT-T TTAT TTAT TTAT TTAT TTAT TTAT TTGT TTGT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
54230182 TTGT TTAT ATTAT TT
1 TTAT TTAT -TTAT TT
54230197 CTATGCCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 4 0.08
4 42 0.84
5 4 0.08
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:54230244 original size:19 final size:20
Alignment explanation
Indices: 54230203--54230244 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
54230193 ATTTCTATGC
* *
54230203 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
54230223 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
54230242 CAT
1 CAT
54230245 CACATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:54233192 original size:2 final size:2
Alignment explanation
Indices: 54233176--54233207 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
54233166 GTTTTGATGC
54233176 TA TA T- TA TA -A 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
54233208 AACCACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54238210 original size:25 final size:27
Alignment explanation
Indices: 54238161--54238212 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
54238151 TATAAAGTTT
* *
54238161 AATTTATTAATAATTTATATGTTTTCC
1 AATTTATTAATAATGTACATGTTTTCC
54238188 AATTTA-TAAT-ATGTACATGTTTTCC
1 AATTTATTAATAATGTACATGTTTTCC
54238213 TTGTTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 4 0.17
27 6 0.26
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.52
Consensus pattern (27 bp):
AATTTATTAATAATGTACATGTTTTCC
Found at i:54242455 original size:14 final size:15
Alignment explanation
Indices: 54242436--54242464 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54242426 ATTATAAAAA
54242436 TTTAAAAAG-ATATT
1 TTTAAAAAGAATATT
54242450 TTTAAAAAGAATATT
1 TTTAAAAAGAATATT
54242465 AAAATTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTAAAAAGAATATT
Found at i:54245671 original size:26 final size:25
Alignment explanation
Indices: 54245615--54245672 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
54245605 CAAATATATG
54245615 TTAATTTCAAGAATTATGTAATGTTA
1 TTAA-TTCAAGAATTATGTAATGTTA
* * *
54245641 GTAATTCAAAGACTTATGTAATGTTT
1 TTAATTC-AAGAATTATGTAATGTTA
54245667 TTAATT
1 TTAATT
54245673 ATGTAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (25 bp):
TTAATTCAAGAATTATGTAATGTTA
Found at i:54245699 original size:9 final size:9
Alignment explanation
Indices: 54245685--54245733 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
54245675 GTAGTGATTC
54245685 AATTCGGTT
1 AATTCGGTT
54245694 AATTCGAG-T
1 AATTCG-GTT
*
54245703 AATTCAGTT
1 AATTCGGTT
*
54245712 AATTCGGAT
1 AATTCGGTT
54245721 AATTCGGTT
1 AATTCGGTT
54245730 AATT
1 AATT
54245734 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 32 0.94
10 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:54245712 original size:18 final size:18
Alignment explanation
Indices: 54245685--54245733 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
54245675 GTAGTGATTC
54245685 AATTCGGTTAATTC-GAGT
1 AATTCGGTTAATTCGGA-T
*
54245703 AATTCAGTTAATTCGGAT
1 AATTCGGTTAATTCGGAT
54245721 AATTCGGTTAATT
1 AATTCGGTTAATT
54245734 TTTAACCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (18 bp):
AATTCGGTTAATTCGGAT
Found at i:54246920 original size:18 final size:18
Alignment explanation
Indices: 54246801--54247112 Score: 187
Period size: 17 Copynumber: 17.4 Consensus size: 18
54246791 TCGAGAAAAA
54246801 AAATTGTTTTGAAAACACG
1 AAATT-TTTTGAAAACACG
54246820 AGAA--TTTT-AAAACA--
1 A-AATTTTTTGAAAACACG
** *
54246834 ATTTTTTTTGAAAACATGG
1 AAATTTTTTGAAAACA-CG
*
54246853 AAAATTTTT-AAAACACG
1 AAATTTTTTGAAAACACG
*
54246870 AGAA-TTTTAG-AAACACG
1 A-AATTTTTTGAAAACACG
* *
54246887 AAAATTCTT-AAAACACG
1 AAATTTTTTGAAAACACG
54246904 AAATTTTTTGAAAACACG
1 AAATTTTTTGAAAACACG
54246922 ATAA--TTTTG-AAACACGAG
1 A-AATTTTTTGAAAACAC--G
54246940 AAATTTTTTGAAAACAC-
1 AAATTTTTTGAAAACACG
* *
54246957 AATTTTTTTTTTG-AAACACA
1 AA---ATTTTTTGAAAACACG
* * *
54246977 AAAATGTTTG-AAACACA
1 AAATTTTTTGAAAACACG
*
54246994 AAAATTTTTGAAAACACGG
1 AAATTTTTTGAAAACAC-G
*
54247013 AAA-TTTGTG-AAACACG
1 AAATTTTTTGAAAACACG
54247029 AGAATTTTTTTGAAAACACG
1 A-AA-TTTTTTGAAAACACG
54247049 AAAATTTTTTGAAAACACGG
1 -AAATTTTTTGAAAACAC-G
54247069 AAA-TTTTTG-AAACACG
1 AAATTTTTTGAAAACACG
*
54247085 AAGAATTTTTTTAAAAACAC-
1 -A-AA-TTTTTTGAAAACACG
54247105 AAATTTTT
1 AAATTTTT
54247113 GATGCACCGG
Statistics
Matches: 238, Mismatches: 20, Indels: 72
0.72 0.06 0.22
Matches are distributed among these distances:
14 1 0.00
15 4 0.02
16 23 0.10
17 85 0.36
18 40 0.17
19 46 0.19
20 32 0.13
21 7 0.03
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (18 bp):
AAATTTTTTGAAAACACG
Found at i:54247048 original size:37 final size:37
Alignment explanation
Indices: 54246837--54247114 Score: 169
Period size: 36 Copynumber: 7.7 Consensus size: 37
54246827 TAAAACAATT
* * *
54246837 TTTTTTGAAAACATGGAAAATTTTT-AAAACACGAGAA
1 TTTTGTGAAAACACGG-AAATTTTTGAAAACACGAAAA
* * *
54246874 TTTT-AG-AAACACGAAAATTCTT-AAAACACG-AAA
1 TTTTGTGAAAACACGGAAATTTTTGAAAACACGAAAA
*
54246907 TTTTTTGAAAACAC-GATAA-TTTTG-AAACACGAGAAA
1 TTTTGTGAAAACACGGA-AATTTTTGAAAACACGA-AAA
* * *
54246943 TTTTTTGAAAACAC--AATTTTTTTTTTG-AAACACAAAAA
1 TTTTGTGAAAACACGGAA----ATTTTTGAAAACACGAAAA
* ** *
54246981 TGTT-TG-AAACACAAAAATTTTTGAAAACACGGAAA
1 TTTTGTGAAAACACGGAAATTTTTGAAAACACGAAAA
*
54247016 -TTTGTG-AAACACGAGAATTTTTTTGAAAACACGAAAA
1 TTTTGTGAAAACACG-GAA-ATTTTTGAAAACACGAAAA
*
54247053 TTTTTTGAAAACACGGAAATTTTTG-AAACACGAAGAA
1 TTTTGTGAAAACACGGAAATTTTTGAAAACACGAA-AA
* *
54247090 TTTTTTTAAAAACAC--AAATTTTTGA
1 -TTTTGTGAAAACACGGAAATTTTTGA
54247115 TGCACCGGAA
Statistics
Matches: 197, Mismatches: 22, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
33 6 0.03
34 36 0.18
35 32 0.16
36 44 0.22
37 31 0.16
38 29 0.15
39 19 0.10
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (37 bp):
TTTTGTGAAAACACGGAAATTTTTGAAAACACGAAAA
Found at i:54247065 original size:91 final size:88
Alignment explanation
Indices: 54246839--54247094 Score: 270
Period size: 90 Copynumber: 2.9 Consensus size: 88
54246829 AAACAATTTT
* * * * *
54246839 TTTTGAAAACATG-GAAAATTTTT-AAAACACGAGAA-TTTTAGAAACACGAAAATTCTTAAAAC
1 TTTTG-AAACACGAGAAATTTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATT-TTGAAAC
* *
54246901 ACGAAATTTTTTGAAAACACGATAA
64 ACAAAAATTTTTGAAAACACGATAA
** *
54246926 TTTTGAAACACGAGAAATTTTTTGAAAACAC-AATTTTTTTTTTGAAACACAAAAATGTTTGAAA
1 TTTTGAAACACGAGAAATTTTTTGAAAACACGAA--AATTTTTTGAAACACGAAAAT-TTTGAAA
54246990 CACAAAAATTTTTGAAAACACGGA-AA
63 CACAAAAATTTTTGAAAACAC-GATAA
* *
54247016 TTTGTGAAACACGAGAATTTTTTTGAAAACACGAAAATTTTTTGAAAACACGGAAATTTTTGAAA
1 TTT-TGAAACACGAGAAATTTTTTGAAAACACGAAAATTTTTTG-AAACAC-GAAAATTTTGAAA
*
54247081 CACGAAGAATTTTT
63 CAC-AAAAATTTTT
54247095 TTAAAAACAC
Statistics
Matches: 141, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
86 6 0.04
87 15 0.11
88 7 0.05
90 52 0.37
91 46 0.33
92 15 0.11
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (88 bp):
TTTTGAAACACGAGAAATTTTTTGAAAACACGAAAATTTTTTGAAACACGAAAATTTTGAAACAC
AAAAATTTTTGAAAACACGATAA
Found at i:54247111 original size:17 final size:18
Alignment explanation
Indices: 54246837--54247112 Score: 115
Period size: 19 Copynumber: 15.3 Consensus size: 18
54246827 TAAAACAATT
* *
54246837 TTTTTTGAAAACATGGAAA
1 TTTTTTAAAAACA-CGAAA
*
54246856 ATTTTT-AAAACACGAGAA
1 TTTTTTAAAAACACGA-AA
*
54246874 --TTTTAGAAACACGAAA
1 TTTTTTAAAAACACGAAA
* *
54246890 ATTCTT-AAAACACGAAA
1 TTTTTTAAAAACACGAAA
*
54246907 TTTTTTGAAAACACGATAA
1 TTTTTTAAAAACACGA-AA
* *
54246926 -TTTTGAAACACGA-GAAA
1 TTTTTTAAAAAC-ACGAAA
* *
54246943 TTTTTTGAAAACAC-AATTT
1 TTTTTTAAAAACACGAA--A
** *
54246962 TTTTTTTGAAACACAAAA
1 TTTTTTAAAAACACGAAA
* * * *
54246980 ATGTTT-GAAACACAAAA
1 TTTTTTAAAAACACGAAA
* *
54246997 ATTTTTGAAAACACGGAAA
1 TTTTTTAAAAACAC-GAAA
* *
54247016 -TTTGT-GAAACACGAGAA
1 TTTTTTAAAAACACGA-AA
*
54247033 TTTTTTTGAAAACACGAAAA
1 -TTTTTTAAAAACACG-AAA
*
54247053 TTTTTTGAAAACACGGAAA
1 TTTTTTAAAAACAC-GAAA
* * * *
54247072 TTTTTGAAACACGAAGAAT
1 TTTTTTAAAAAC-ACGAAA
54247091 TTTTTTAAAAACAC-AAA
1 TTTTTTAAAAACACGAAA
54247108 TTTTT
1 TTTTT
54247113 GATGCACCGG
Statistics
Matches: 201, Mismatches: 35, Indels: 44
0.72 0.12 0.16
Matches are distributed among these distances:
16 8 0.04
17 60 0.30
18 53 0.26
19 66 0.33
20 13 0.06
21 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTTAAAAACACGAAA
Found at i:54247196 original size:29 final size:30
Alignment explanation
Indices: 54247164--54247228 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
54247154 GAAATTTAAA
54247164 AAAAAAACA-AAAAATTTGTGAAAACATGG
1 AAAAAAACACAAAAATTTGTGAAAACATGG
*
54247193 AAAAAAACACGAAAATTTGTGAAAACATGG
1 AAAAAAACACAAAAATTTGTGAAAACATGG
54247223 AAAAAA
1 AAAAAA
54247229 TTTTAAACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.63, C:0.08, G:0.14, T:0.15
Consensus pattern (30 bp):
AAAAAAACACAAAAATTTGTGAAAACATGG
Found at i:54247282 original size:18 final size:18
Alignment explanation
Indices: 54247240--54247304 Score: 71
Period size: 17 Copynumber: 3.7 Consensus size: 18
54247230 TTTAAACACG
*
54247240 AATTTTTAAAAACAT-GA
1 AATTTTTGAAAACATGGA
*
54247257 AAATTTTGAAAACATGGA
1 AATTTTTGAAAACATGGA
* *
54247275 AATTTTTG-AAACAGGGG
1 AATTTTTGAAAACATGGA
54247292 AATATTTTGAAAA
1 AAT-TTTTGAAAA
54247305 AATGAATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 23 0.57
18 14 0.35
19 3 0.08
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (18 bp):
AATTTTTGAAAACATGGA
Found at i:54247286 original size:17 final size:17
Alignment explanation
Indices: 54247249--54247303 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
54247239 GAATTTTTAA
*
54247249 AAACAT-GAAAATTTTG
1 AAACATGGAAATTTTTG
54247265 AAAACATGGAAATTTTTG
1 -AAACATGGAAATTTTTG
* *
54247283 AAACAGGGGAATATTTTG
1 AAACATGGAAAT-TTTTG
54247301 AAA
1 AAA
54247304 AAATGAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (17 bp):
AAACATGGAAATTTTTG
Found at i:54247622 original size:17 final size:17
Alignment explanation
Indices: 54247602--54247641 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
54247592 TTGAAATTAC
54247602 TTAAAATAAAATAAAAA
1 TTAAAATAAAATAAAAA
* *
54247619 TTAAATTAAATTAAAAA
1 TTAAAATAAAATAAAAA
54247636 TATAAA
1 T-TAAA
54247642 TACAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAAATAAAATAAAAA
Found at i:54247808 original size:7 final size:7
Alignment explanation
Indices: 54247792--54247845 Score: 76
Period size: 7 Copynumber: 7.9 Consensus size: 7
54247782 TTGAACCCTT
54247792 TTTTTCTC
1 TTTTT-TC
54247800 TTTTTTC
1 TTTTTTC
*
54247807 TTCTTT-
1 TTTTTTC
54247813 TTTTTTC
1 TTTTTTC
54247820 TTTTTTC
1 TTTTTTC
54247827 -TTTTTC
1 TTTTTTC
54247833 TTTTTTC
1 TTTTTTC
54247840 TTTTTT
1 TTTTTT
54247846 TTCCTTCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
6 11 0.26
7 26 0.62
8 5 0.12
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:54247814 original size:20 final size:21
Alignment explanation
Indices: 54247791--54247860 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
54247781 ATTGAACCCT
54247791 TTTTTTCTCTTTTTTCTTCT-
1 TTTTTTCTCTTTTTTCTTCTA
* * *
54247811 TTTTTTTTCTTTTTTCTTTTTC
1 TTTTTTCTCTTTTTTC-TTCTA
*
54247833 TTTTTTCTTTTTTTTCCTTCTA
1 TTTTTTCTCTTTTTT-CTTCTA
54247855 TTTTTT
1 TTTTTT
54247861 TCCTCTCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 15 0.37
21 3 0.07
22 22 0.54
23 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTCTCTTTTTTCTTCTA
Found at i:54247818 original size:13 final size:13
Alignment explanation
Indices: 54247790--54247862 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 13
54247780 AATTGAACCC
54247790 TTTTTTTC-TCTT
1 TTTTTTTCTTCTT
* *
54247802 TTTTCTTCTTTTT
1 TTTTTTTCTTCTT
*
54247815 TTTTCTTTTTTCTT
1 TTTT-TTTCTTCTT
54247829 TTTCTTTT-TTCTT
1 TTT-TTTTCTTCTT
* *
54247842 TTTTTTCCTTCTA
1 TTTTTTTCTTCTT
54247855 TTTTTTTC
1 TTTTTTTC
54247863 CTCTCTTCTG
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
12 10 0.20
13 26 0.53
14 12 0.24
15 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:54247858 original size:14 final size:13
Alignment explanation
Indices: 54247795--54247869 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
54247785 AACCCTTTTT
*
54247795 TTCTCTTTTTT-C
1 TTCTTTTTTTTCC
*
54247807 TTCTTTTTTTTTC
1 TTCTTTTTTTTCC
* *
54247820 TTTTTTCTTTTTCTTTT
1 TTCTTT-TTTTTC---C
54247837 TTCTTTTTTTTCC
1 TTCTTTTTTTTCC
54247850 TTCTATTTTTTTCC
1 TTCT-TTTTTTTCC
54247864 TCTCTT
1 T-TCTT
54247870 CTGGGCCGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
12 10 0.20
13 10 0.20
14 16 0.32
15 3 0.06
16 6 0.12
17 5 0.10
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTTCC
Found at i:54248346 original size:25 final size:25
Alignment explanation
Indices: 54248318--54248365 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
54248308 CCTTTCTCCT
*
54248318 TCTTT-TCTTCTTTTTTCTTCTTTAC
1 TCTTTCTCTT-TTTTTTCCTCTTTAC
54248343 TCTTTCTCTTTTTTTTCCTCTTT
1 TCTTTCTCTTTTTTTTCCTCTTT
54248366 TGCTTGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (25 bp):
TCTTTCTCTTTTTTTTCCTCTTTAC
Found at i:54248400 original size:25 final size:26
Alignment explanation
Indices: 54248351--54248400 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
54248341 ACTCTTTCTC
*
54248351 TTTTTTTTCCTCTTTTGCTTGCTTGT
1 TTTTTTTTCCTCTTTTGCCTGCTTGT
* *
54248377 TTTTTTTTTCTTTTTTGCCT-CTTG
1 TTTTTTTTCCTCTTTTGCCTGCTTG
54248401 GTTGTTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.00, C:0.18, G:0.10, T:0.72
Consensus pattern (26 bp):
TTTTTTTTCCTCTTTTGCCTGCTTGT
Found at i:54248408 original size:26 final size:27
Alignment explanation
Indices: 54248352--54248408 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
54248342 CTCTTTCTCT
*
54248352 TTTTTTTCCTCTTTTGCTTGCTTGTT-
1 TTTTTTTCCTCTTTTGCCTGCTTGTTG
* *
54248378 TTTTTTTTCTTTTTTGCCT-CTTGGTTG
1 TTTTTTTCCTCTTTTGCCTGCTT-GTTG
54248405 TTTT
1 TTTT
54248409 GCTAGGTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.12
26 19 0.73
27 4 0.15
ACGTcount: A:0.00, C:0.16, G:0.12, T:0.72
Consensus pattern (27 bp):
TTTTTTTCCTCTTTTGCCTGCTTGTTG
Found at i:54248828 original size:31 final size:29
Alignment explanation
Indices: 54248728--54248839 Score: 120
Period size: 30 Copynumber: 3.8 Consensus size: 29
54248718 AAAACTTTTG
* * *
54248728 GGGTTAAAGTATAATTTTGAGAATATTTAA
1 GGGTTAAAATATAATTTTGA-AAAAGTTAA
* *
54248758 -GGTCAAAATGTAATTTT-AAAAAGTTAA
1 GGGTTAAAATATAATTTTGAAAAAGTTAA
* *
54248785 GGGTTAAAATATAATTTTGGAAAAATTTAG
1 GGGTTAAAATATAATTTT-GAAAAAGTTAA
54248815 GGGTTAAAAATATAATTTTGAAAAA
1 GGGTT-AAAATATAATTTTGAAAAA
54248840 AATTTTGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
27 7 0.10
28 16 0.23
29 14 0.20
30 19 0.28
31 13 0.19
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.36
Consensus pattern (29 bp):
GGGTTAAAATATAATTTTGAAAAAGTTAA
Found at i:54249677 original size:29 final size:29
Alignment explanation
Indices: 54249643--54249699 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
54249633 AATAAAAATC
*
54249643 ATAGGTTAAGAGCTTATTTAACCACAAAA
1 ATAGGTTAAGAGCTTATTTAAACACAAAA
* * *
54249672 ATAGGTTGAGTGCTTGTTTAAACACAAA
1 ATAGGTTAAGAGCTTATTTAAACACAAA
54249700 GTAGTGAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (29 bp):
ATAGGTTAAGAGCTTATTTAAACACAAAA
Found at i:54250688 original size:27 final size:27
Alignment explanation
Indices: 54250645--54250722 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
54250635 TAATATTGGA
* *
54250645 GCCTATCTCAGATGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
54250672 GCCTATCTGAGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
*
54250699 GCCTATCTGATAGGCGCCAATGGT
1 GCCTATCTGAGAGGCGCCAATGGT
54250723 ATTATTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:54250773 original size:14 final size:14
Alignment explanation
Indices: 54250756--54250792 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54250746 TCAAAAAATT
54250756 AATAAATACTGTTA
1 AATAAATACTGTTA
*
54250770 AATAAATATTGTTA
1 AATAAATACTGTTA
54250784 AATAAATAC
1 AATAAATAC
54250793 AAAATCAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (14 bp):
AATAAATACTGTTA
Found at i:54251015 original size:60 final size:60
Alignment explanation
Indices: 54250941--54251062 Score: 192
Period size: 60 Copynumber: 2.0 Consensus size: 60
54250931 ATACTAAACT
* * * *
54250941 AAACACAATAATTTATAACTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
54251001 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
54251061 AA
1 AA
54251063 TATTCATACA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 4 0.07
60 53 0.93
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:54251134 original size:42 final size:42
Alignment explanation
Indices: 54251056--54251364 Score: 190
Period size: 42 Copynumber: 7.5 Consensus size: 42
54251046 TTATAAAATA
*
54251056 ATTACAATATTCATACAAAAAATATTACAATATTCATACAAACAAT
1 ATTACAATATCCATAC---AAA-ATTACAATATTCATACAAACAAT
*
54251102 ATTATAATATCCATACAAAATTACAATATTCATACAAACAAT
1 ATTACAATATCCATACAAAATTACAATATTCATACAAACAAT
*
54251144 ATTACAATATTCATACAAAATTACAATATTCATAC--A-AA-
1 ATTACAATATCCATACAAAATTACAATATTCATACAAACAAT
* * * * *
54251182 A-TACTA-ATCCAAAACTATAAA-TACAAAATTAATTA-TAA-AAT
1 ATTACAATATCC-ATAC-A-AAATTACAATATTCA-TACAAACAAT
*
54251223 AATTACAATATTCATACAAAATTACAATATTCATACAAA-ATACT
1 -ATTACAATATCCATACAAAATTACAATATTCATACAAACA-A-T
* * ** *
54251267 AATCAAAAACTATAAATACAAAATT---A-ATT-ATA-AAA-TA-
1 -AT-TACAA-TATCCATACAAAATTACAATATTCATACAAACAAT
* *
54251304 ATTACAATATTCATAAAAAATTACAATATTCATACAAA-AA-
1 ATTACAATATCCATACAAAATTACAATATTCATACAAACAAT
* *
54251344 ATTACACTATTCATACAAAAT
1 ATTACAATATCCATACAAAAT
54251365 ACTAATCCAA
Statistics
Matches: 213, Mismatches: 28, Indels: 50
0.73 0.10 0.17
Matches are distributed among these distances:
34 12 0.06
35 3 0.01
36 5 0.02
37 8 0.04
38 14 0.07
39 11 0.05
40 30 0.14
41 8 0.04
42 73 0.34
43 12 0.06
44 7 0.03
45 3 0.01
46 27 0.13
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (42 bp):
ATTACAATATCCATACAAAATTACAATATTCATACAAACAAT
Found at i:54251237 original size:80 final size:80
Alignment explanation
Indices: 54251039--54251342 Score: 393
Period size: 80 Copynumber: 3.7 Consensus size: 80
54251029 AATTACTAAC
54251039 AAATTAATTATAAAATAATTACAATATTCATACAAAAAATATTACAATATTCATACAAACA-A-T
1 AAATTAATTATAAAATAATTACAATATTCATAC---AAA-ATTACAATATTCATACAAA-ATACT
* * **
54251102 -AT-TATAA-TATCCATACA
61 AATCAAAAACTATAAATACA
*
54251119 AAATTACAATATTCATACAAACAATATTACAATATTCATACAAAATTACAATATTCATACAAAAT
1 AAATT---A-ATT-ATA-AAA-TA-ATTACAATATTCATACAAAATTACAATATTCATACAAAAT
*
54251184 ACTAATCCAAAACTATAAATACA
58 ACTAATCAAAAACTATAAATACA
54251207 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCA
54251272 AAAACTATAAATACA
66 AAAACTATAAATACA
*
54251287 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAA
54251343 AATTACACTA
Statistics
Matches: 203, Mismatches: 8, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
80 122 0.60
81 1 0.00
82 3 0.01
83 5 0.02
84 26 0.13
85 8 0.04
86 5 0.02
87 4 0.02
88 29 0.14
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (80 bp):
AAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCA
AAAACTATAAATACA
Found at i:54251359 original size:21 final size:21
Alignment explanation
Indices: 54251050--54251262 Score: 169
Period size: 23 Copynumber: 10.2 Consensus size: 21
54251040 AATTAATTAT
54251050 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
54251072 AAAAAATATTACAATATTCATAC
1 -AAAAA-ATTACAATATTCATAC
* *
54251095 AAACAATATTATAATATCCATAC
1 AAA-AA-ATTACAATATTCATAC
54251118 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
54251137 AAACAATATTACAATATTCATAC
1 AAA-AA-ATTACAATATTCATAC
54251160 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
54251179 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * * *
54251197 TATAAA-TACAAAATTAATTAT
1 AAAAAATTACAATATTCA-TAC
54251218 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
54251240 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
54251259 AAAA
1 AAAA
54251263 TACTAATCAA
Statistics
Matches: 157, Mismatches: 18, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.02
18 7 0.04
19 51 0.32
20 14 0.09
21 10 0.06
22 10 0.06
23 62 0.39
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:54251367 original size:101 final size:101
Alignment explanation
Indices: 54251216--54251465 Score: 414
Period size: 101 Copynumber: 2.5 Consensus size: 101
54251206 AAAATTAATT
54251216 ATAAAATAATTACAATATTCATAC--AAAATTACAATATTCATACAAAATACTAATCAAAAACTA
1 ATAAAA-AATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCAAAAACTA
54251279 TAAATACAAAATTAATTATAAAATAATTACAATATTC
65 TAAATACAAAATTAATTATAAAATAATTACAATATTC
* *
54251316 ATAAAAAATTACAATATTCATACAAAAAATTACACTATTCATACAAAATACTAATCCAAAACTAT
1 ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCAAAAACTAT
*
54251381 AAATACAAAATTAATTATAAAATAATTATAATATTC
66 AAATACAAAATTAATTATAAAATAATTACAATATTC
* * * *
54251417 ATACAAAATTATAATATTCATACAAAAAGTTACAATATACATACAAAAT
1 ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAAT
54251466 TACCCATTGG
Statistics
Matches: 140, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
99 17 0.12
100 6 0.04
101 117 0.84
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (101 bp):
ATAAAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAATACTAATCAAAAACTAT
AAATACAAAATTAATTATAAAATAATTACAATATTC
Found at i:54251459 original size:21 final size:20
Alignment explanation
Indices: 54251055--54251468 Score: 218
Period size: 19 Copynumber: 20.3 Consensus size: 20
54251045 ATTATAAAAT
54251055 AATTACAATATTCATACAAAAA
1 AATTACAATATTCATAC--AAA
54251077 ATATTACAATATTCATACAAACA
1 A-ATTACAATATTCATAC-AA-A
* *
54251100 ATATTATAATATCCATAC-AA
1 A-ATTACAATATTCATACAAA
54251120 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC-AA-A
54251142 ATATTACAATATTCATAC-AA
1 A-ATTACAATATTCATACAAA
54251162 AATTACAATATTCATAC-AA
1 AATTACAATATTCATACAAA
* * * *
54251181 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-AAA
* * *
54251201 AA-TACAAAATTAATTATAAAA
1 AATTACAATATTCA-TA-CAAA
54251222 TAATTACAATATTCATAC-AA
1 -AATTACAATATTCATACAAA
54251242 AATTACAATATTCATAC-AA
1 AATTACAATATTCATACAAA
* *
54251261 AA-TAC--TAATCA-AAAACTA
1 AATTACAATATTCATACAA--A
* * * *
54251279 TAAATACAAAATTAATTATAAAA
1 -AATTACAATATTCA-TA-CAAA
54251302 TAATTACAATATTCATA-AAA
1 -AATTACAATATTCATACAAA
54251322 AATTACAATATTCATACAAAA
1 AATTACAATATTCATAC-AAA
*
54251343 AATTACACTATTCATAC-AA
1 AATTACAATATTCATACAAA
* * * *
54251362 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-AAA
* * *
54251382 AA-TACAAAATTAATTATAAAA
1 AATTACAATATTCA-TA-CAAA
*
54251403 TAATTATAATATTCATAC-AA
1 -AATTACAATATTCATACAAA
*
54251423 AATTATAATATTCATACAAA
1 AATTACAATATTCATACAAA
*
54251443 AAGTTACAATATACATAC-AA
1 AA-TTACAATATTCATACAAA
54251463 AATTAC
1 AATTAC
54251469 CCATTGGCGC
Statistics
Matches: 313, Mismatches: 43, Indels: 75
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.00
16 6 0.02
17 6 0.02
18 17 0.05
19 98 0.31
20 38 0.12
21 45 0.14
22 19 0.06
23 79 0.25
24 1 0.00
25 3 0.01
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTACAATATTCATACAAA
Found at i:54251514 original size:27 final size:27
Alignment explanation
Indices: 54251473--54251545 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
54251463 AATTACCCAT
*
54251473 TGGCGCCTCCCTATGAGGCATTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
* * *
54251500 TGGCACCTCCTTATGAGGCACTTTTGA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
54251527 TGGTGCCTCCCTATGAGGC
1 TGGCGCCTCCCTATGAGGC
54251546 GCCACCCGAC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACTTTTAA
Found at i:54252435 original size:14 final size:15
Alignment explanation
Indices: 54252416--54252446 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
54252406 ATAATAAAAT
54252416 AATAAAAATT-TAAA
1 AATAAAAATTATAAA
54252430 AATAAAAATTATAAA
1 AATAAAAATTATAAA
54252445 AA
1 AA
54252447 AAATCATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAATTATAAA
Found at i:54253791 original size:85 final size:85
Alignment explanation
Indices: 54253648--54253816 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
54253638 GTCATAAAAG
54253648 TATGAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGATTCCTCCTTATCATATTCGCCTGTA
1 TATGAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGATTCCTCCTTATCATATTCGCCTGTA
54253713 AAAATAGTCTTAGGGATAAA
66 AAAATAGTCTTAGGGATAAA
* **
54253733 TATGAGTCAAAAAGGTTGTTTGTTTGTTATGTAAA-GGAGATTCCTCCTTTTCATATTCGTTTGT
1 TATGAGTCAAAAAGGTTGTTTGTTTGTTATG-AAACGGAGATTCCTCCTTATCATATTCGCCTGT
54253797 AAAAATAGTCTTAGGGATAA
65 AAAAATAGTCTTAGGGATAA
54253817 GTCAAAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
85 77 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (85 bp):
TATGAGTCAAAAAGGTTGTTTGTTTGTTATGAAACGGAGATTCCTCCTTATCATATTCGCCTGTA
AAAATAGTCTTAGGGATAAA
Found at i:54255968 original size:42 final size:42
Alignment explanation
Indices: 54255909--54255994 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
54255899 TTTTATGAAC
* *
54255909 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCTGGTTGAAATT
1 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCCGCTTGAAATT
54255951 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCCGCTTGAAATT
1 GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCCGCTTGAAATT
54255993 GA
1 GA
54255995 CATTGCTGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (42 bp):
GAAAGAGAACTTTCTGTGGGTCCTTGCCCGCCGCTTGAAATT
Found at i:54262875 original size:23 final size:24
Alignment explanation
Indices: 54262821--54262874 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
54262811 ATGAAAATGG
54262821 AAAATTTTCTATTTAAGTCTATTT
1 AAAATTTTCTATTTAAGTCTATTT
*
54262845 AAAATTTTC-ATTTAAGT-TTTTT
1 AAAATTTTCTATTTAAGTCTATTT
*
54262867 AAAGTTTT
1 AAAATTTT
54262875 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 11 0.39
23 8 0.29
24 9 0.32
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (24 bp):
AAAATTTTCTATTTAAGTCTATTT
Found at i:54266307 original size:58 final size:58
Alignment explanation
Indices: 54266194--54266377 Score: 278
Period size: 59 Copynumber: 3.1 Consensus size: 58
54266184 TAAAATACCA
** *
54266194 AAAATATATTTTAAAAATAAAAAAAAGTATTTTAAAAATATTTTATAATTAAAAAATTTT
1 AAAA-ATATTTT-AAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTT
* *
54266254 AAAAATATTTTAAAATTTAAAAAATGTATTTTAAAATTATTTTAAAATTAAAAAATTGT
1 AAAAATATTTTAAAATTTAAAAAA-GTATTTTAAAAATATTTTAAAATTAAAAAATTTT
* *
54266313 AAAAATATTTTAAAATTTTAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTT
1 AAAAATATTTTAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTT
54266371 AAAAATA
1 AAAAATA
54266378 AATATATTTA
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
58 49 0.43
59 61 0.54
60 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (58 bp):
AAAAATATTTTAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTT
Found at i:54266344 original size:12 final size:11
Alignment explanation
Indices: 54266194--54266358 Score: 91
Period size: 11 Copynumber: 16.4 Consensus size: 11
54266184 TAAAATACCA
54266194 AAAATATATTTT
1 AAAA-ATATTTT
**
54266206 AAAAATA--AA
1 AAAAATATTTT
54266215 AAAAAGTATTTT
1 AAAAA-TATTTT
54266227 AAAAATATTTT
1 AAAAATATTTT
*
54266238 ----ATA-ATT
1 AAAAATATTTT
54266244 AAAAA-ATTTT
1 AAAAATATTTT
54266254 AAAAATATTTT
1 AAAAATATTTT
*
54266265 --AAA-ATTTA
1 AAAAATATTTT
54266273 AAAAATGTATTTT
1 AAAAA--TATTTT
*
54266286 AAAATTATTTT
1 AAAAATATTTT
54266297 --AAA-A--TT
1 AAAAATATTTT
*
54266303 AAAAA-ATTGT
1 AAAAATATTTT
54266313 AAAAATATTTT
1 AAAAATATTTT
54266324 --AAA-ATTTT
1 AAAAATATTTT
54266332 AAAAAGTATTTT
1 AAAAA-TATTTT
54266344 AAAAATATTTT
1 AAAAATATTTT
54266355 AAAA
1 AAAA
54266359 TTAAAAAAAT
Statistics
Matches: 118, Mismatches: 12, Indels: 47
0.67 0.07 0.27
Matches are distributed among these distances:
6 4 0.03
7 3 0.03
8 14 0.12
9 14 0.12
10 22 0.19
11 34 0.29
12 19 0.16
13 8 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:54266364 original size:17 final size:17
Alignment explanation
Indices: 54266342--54266386 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
54266332 AAAAAGTATT
54266342 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
54266359 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
54266375 ATAAATATATTT
1 TTAAAAATATTT
54266387 ATTATATCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:54266740 original size:94 final size:95
Alignment explanation
Indices: 54266642--54266945 Score: 344
Period size: 94 Copynumber: 3.0 Consensus size: 95
54266632 TGCCAACCGT
54266642 TGGCAGGCCACCA-CAATTTTTTTTTTACTTTTTTCGTATACTAATACCTGCTATTGACACGAAA
1 TGGCAGGCCACCACCAATTTTTTTTTTACTTTTTTCGTATACTAATACCTGCTATTGACACGAAA
*
54266706 AAAGTGAAAAAAAAAATTCCCCATAAAAGG
66 AAAGTGAAAAAAAAAATTCCCCAAAAAAGG
* * *
54266736 TGGCAGGCCACCACCAA-TTTTTTTTTACTTTTTTCGTATATTGATACCAGCTATTGACACGAAA
1 TGGCAGGCCACCACCAATTTTTTTTTTACTTTTTTCGTATACTAATACCTGCTATTGACACGAAA
*
54266800 AAAGTAAAAAAAAAAATTCTCCCCCCAAAAAAGATGG
66 AAAGTGAAAAAAAAAA-T-T--CCCC-AAAAA-A-GG
**
54266837 TGCCGGCCATTGGCAAGCCACCACCAAATTTTTTTTTTACTTTTTTTATATACTAATACCTGCTA
1 T---GG-CA---G---GCCACCACC-AATTTTTTTTTTACTTTTTTCGTATACTAATACCTGCTA
*
54266902 TTGACACGAAAAAAAGTG-AAAAAAAATTTCCCCAAAAAAGG
55 TTGACACG-AAAAAAGTGAAAAAAAAAATTCCCCAAAAAAGG
54266943 TGG
1 TGG
54266946 TGCCGACTAG
Statistics
Matches: 177, Mismatches: 12, Indels: 33
0.80 0.05 0.15
Matches are distributed among these distances:
94 72 0.41
95 4 0.02
96 1 0.01
98 4 0.02
99 4 0.02
100 1 0.01
101 3 0.02
103 2 0.01
104 2 0.01
105 2 0.01
106 3 0.02
107 1 0.01
108 6 0.03
109 4 0.02
111 10 0.06
112 3 0.02
113 47 0.27
114 8 0.05
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (95 bp):
TGGCAGGCCACCACCAATTTTTTTTTTACTTTTTTCGTATACTAATACCTGCTATTGACACGAAA
AAAGTGAAAAAAAAAATTCCCCAAAAAAGG
Found at i:54266904 original size:113 final size:107
Alignment explanation
Indices: 54266736--54266950 Score: 288
Period size: 113 Copynumber: 2.0 Consensus size: 107
54266726 CCATAAAAGG
* * * *
54266736 TGGCAGGCCACCACCAATTTTTTTTTACTTTTTTCGTATATTGATACCAGCTATTGACACG-AAA
1 TGGCAAGCCACCACCAATTTTTTTTTACTTTTTTCATATACTAATACCAGCTATTGACACGAAAA
54266800 AAAGTAAAAAAAAAAATTCTCCCCCCAAAAAAGATGGTGCCGGCCAT
66 AAAGT--AAAAAAAAATT-T--CCCCAAAAAAGATGGTGCCGGCCAT
* *
54266847 TGGCAAGCCACCACCAAATTTTTTTTTTACTTTTTTTATATACTAATACCTGCTATTGACACGAA
1 TGGCAAGCCACCACC-AA-TTTTTTTTTACTTTTTTCATATACTAATACCAGCTATTGACACGAA
* *
54266912 AAAAAGTGAAAAAAAATTTCCCCAAAAAAGGTGGTGCCG
64 AAAAAGTAAAAAAAAATTTCCCCAAAAAAGATGGTGCCG
54266951 ACTAGAGGCG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
109 19 0.20
111 15 0.16
112 12 0.13
113 39 0.42
114 8 0.09
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (107 bp):
TGGCAAGCCACCACCAATTTTTTTTTACTTTTTTCATATACTAATACCAGCTATTGACACGAAAA
AAAGTAAAAAAAAATTTCCCCAAAAAAGATGGTGCCGGCCAT
Found at i:54266926 original size:207 final size:200
Alignment explanation
Indices: 54266551--54266945 Score: 585
Period size: 207 Copynumber: 1.9 Consensus size: 200
54266541 TTTTTGGGGG
* *
54266551 AATTTTTTTTTACTTTTCTCGTATACTGATACCTGTTATTGACACGAAAAAAGTAAAAAAAAATT
1 AATTTTTTTTTACTTTTCTCGTATACTGATACCAGCTATTGACACGAAAAAAGTAAAAAAAAATT
* * * *
54266616 CTCACAAAAAAGGTGGTGCCAACCGTTGGCAGGCCACCACAATTTTTTTTTTACTTTTTTCGTAT
66 CTCACAAAAAAGATGGTGCCAACCATTGGCAAGCCACCACAATTTTTTTTTTACTTTTTTCATAT
*
54266681 ACTAATACCTGCTATTGACACGAAAAAAGTGAAAAAAAAAATTCCCCATAAAAGGTGGCAGGCCA
131 ACTAATACCTGCTATTGACACGAAAAAAGTGAAAAAAAAAATTCCCCAAAAAAGGTGGCAGGCCA
54266746 CCACC
196 CCACC
* *
54266751 AATTTTTTTTTACTTTTTTCGTATATTGATACCAGCTATTGACACGAAAAAAGTAAAAAAAAAAA
1 AATTTTTTTTTACTTTTCTCGTATACTGATACCAGCTATTGACACGAAAAAAGT--AAAAAAAAA
* **
54266816 TTCTCCCCCCAAAAAAGATGGTGCCGGCCATTGGCAAGCCACCACCAAATTTTTTTTTTACTTTT
64 TTCT---CACAAAAAAGATGGTGCCAACCATTGGCAAGCCACCA-C-AATTTTTTTTTTACTTTT
* *
54266881 TTTATATACTAATACCTGCTATTGACACGAAAAAAAGTG-AAAAAAAATTTCCCCAAAAAAGGTG
124 TTCATATACTAATACCTGCTATTGACACG-AAAAAAGTGAAAAAAAAAATTCCCCAAAAAAGGTG
54266945 G
188 G
54266946 TGCCGACTAG
Statistics
Matches: 173, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
200 50 0.29
202 13 0.08
205 31 0.18
206 1 0.01
207 69 0.40
208 9 0.05
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (200 bp):
AATTTTTTTTTACTTTTCTCGTATACTGATACCAGCTATTGACACGAAAAAAGTAAAAAAAAATT
CTCACAAAAAAGATGGTGCCAACCATTGGCAAGCCACCACAATTTTTTTTTTACTTTTTTCATAT
ACTAATACCTGCTATTGACACGAAAAAAGTGAAAAAAAAAATTCCCCAAAAAAGGTGGCAGGCCA
CCACC
Done.