Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold211
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: 2157208
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 20444 characters in sequence are not A, C, G, or T
File 5 of 15
Found at i:476642 original size:22 final size:24
Alignment explanation
Indices: 476617--476721 Score: 74
Period size: 27 Copynumber: 4.2 Consensus size: 24
476607 AATATAAATG
476617 TAAATTAAATATATAAATTTT-T-
1 TAAATTAAATATATAAATTTTATA
476639 TAAATTATAATAT-TAAATTTTATA
1 TAAATTA-AATATATAAATTTTATA
*
476663 TAAAATTAAAATATTTTAAATATTT-TA
1 T-AAATT-AAATA-TATAAAT-TTTATA
* * *
476690 TAATTTAATAAATATATAAATATAATA
1 TAA---ATTAAATATATAAATTTTATA
476717 TAAAT
1 TAAAT
476722 ATATAAATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
22 15 0.23
23 6 0.09
24 2 0.03
25 9 0.14
26 5 0.08
27 19 0.29
28 8 0.12
29 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATTAAATATATAAATTTTATA
Found at i:479716 original size:7 final size:7
Alignment explanation
Indices: 479716--479757 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
479706 AATATTTAAT
479716 AAATTTA
1 AAATTTA
479723 AAATTTA
1 AAATTTA
479730 AAATTTA
1 AAATTTA
479737 AAATTTA
1 AAATTTA
479744 AAATTTA
1 AAATTTA
*
479751 ATATTTA
1 AAATTTA
479758 CATATTTCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AAATTTA
Found at i:479764 original size:8 final size:7
Alignment explanation
Indices: 479704--479764 Score: 59
Period size: 7 Copynumber: 8.3 Consensus size: 7
479694 ATGTAATTAA
479704 TTAATAT
1 TTAATAT
479711 TTAATAAAT
1 TTAAT--AT
*
479720 TTAAAAT
1 TTAATAT
*
479727 TTAAAAT
1 TTAATAT
*
479734 TTAAAAT
1 TTAATAT
*
479741 TTAAAAT
1 TTAATAT
479748 TTAATAT
1 TTAATAT
479755 TTACATAT
1 TTA-ATAT
479763 TT
1 TT
479765 CTCATTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
7 37 0.76
8 6 0.12
9 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (7 bp):
TTAATAT
Found at i:479873 original size:2 final size:2
Alignment explanation
Indices: 479866--479895 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
479856 TGCAAGTGTA
479866 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
479896 TTTATTTTTT
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:480062 original size:3 final size:3
Alignment explanation
Indices: 480054--480089 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
480044 ACAAATATCA
480054 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
480090 TCACTTTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:480138 original size:13 final size:13
Alignment explanation
Indices: 480120--480164 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
480110 CATTAGTTGA
480120 AAAAAATATATTT
1 AAAAAATATATTT
*
480133 AAAAAATAT-TAT
1 AAAAAATATATTT
*
480145 AAAAAAGATATTT
1 AAAAAATATATTT
*
480158 TAAAAAT
1 AAAAAAT
480165 TTTTAAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AAAAAATATATTT
Found at i:481540 original size:2 final size:2
Alignment explanation
Indices: 481533--481559 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
481523 TCACATACGC
481533 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 T
481560 TTAAGAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:482035 original size:16 final size:16
Alignment explanation
Indices: 482014--482044 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
482004 ATATAAAATC
*
482014 AATAAAAATTATATAA
1 AATAAAAATAATATAA
482030 AATAAAAATAATATA
1 AATAAAAATAATATA
482045 TAATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATAATATAA
Found at i:482287 original size:17 final size:17
Alignment explanation
Indices: 482267--482306 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
482257 AAAAATTTTA
*
482267 AAATATATATTTATATT
1 AAATATAAATTTATATT
482284 AAATATAAATTTATATT
1 AAATATAAATTTATATT
*
482301 TAATAT
1 AAATAT
482307 TCTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATATAAATTTATATT
Found at i:482690 original size:11 final size:10
Alignment explanation
Indices: 482665--482750 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 10
482655 TTATAATCAT
482665 TATTTAATAA
1 TATTTAATAA
482675 T-TTTAATATA
1 TATTTAATA-A
482685 TATTTATATTAA
1 TATTTA-A-TAA
482697 TATTTATAATTAA
1 TA-TT-TAA-TAA
482710 TATTTAATGTAA
1 TATTTAA--TAA
482722 TTAATTGTAATAA
1 -T-ATT-TAATAA
482735 TATTT-ATAA
1 TATTTAATAA
*
482744 TGTTTAA
1 TATTTAA
482751 AATCTTAATA
Statistics
Matches: 63, Mismatches: 2, Indels: 22
0.72 0.02 0.25
Matches are distributed among these distances:
9 15 0.24
10 5 0.08
11 10 0.16
12 10 0.16
13 15 0.24
14 5 0.08
15 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (10 bp):
TATTTAATAA
Found at i:482696 original size:25 final size:25
Alignment explanation
Indices: 482664--482742 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
482654 ATTATAATCA
482664 TTAT-TTAATAATTTTAATATATAT
1 TTATATTAATAATTTTAATATATAT
482688 TTATATTAAT-ATTTATAAT-TAATAT
1 TTATATTAATAATTT-TAATAT-ATAT
*
482713 TTA-ATGTAATTAATTGTAATA-ATAT
1 TTATAT-TAA-TAATTTTAATATATAT
482738 TTATA
1 TTATA
482743 ATGTTTAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
24 11 0.24
25 26 0.57
26 6 0.13
27 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATATTAATAATTTTAATATATAT
Found at i:483447 original size:12 final size:12
Alignment explanation
Indices: 483426--483457 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
483416 AATTTCAAAA
*
483426 TTGGCGGCACAG
1 TTGGCAGCACAG
483438 TTGGCAGCACAG
1 TTGGCAGCACAG
483450 TTGGCAGC
1 TTGGCAGC
483458 CTTTGTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.25, G:0.38, T:0.19
Consensus pattern (12 bp):
TTGGCAGCACAG
Found at i:488344 original size:13 final size:14
Alignment explanation
Indices: 488326--488357 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
488316 TAATTTTAAT
488326 ATATTTTAT-ATTA
1 ATATTTTATAATTA
488339 ATA-TTTATAATTA
1 ATATTTTATAATTA
488352 ATATTT
1 ATATTT
488358 AATGTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 10 0.59
14 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTTATAATTA
Found at i:488358 original size:13 final size:13
Alignment explanation
Indices: 488330--488386 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
488320 TTTAATATAT
488330 TTTAT-ATTAATA
1 TTTATAATTAATA
488342 TTTATAATTAATA
1 TTTATAATTAATA
488355 -TT-TAATGTAATTA
1 TTTATAAT-TAA-TA
*
488368 ATTATAA-TAATA
1 TTTATAATTAATA
488380 TTTATAA
1 TTTATAA
488387 AATTTAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 4 0.10
12 18 0.46
13 12 0.31
14 2 0.05
15 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:488393 original size:25 final size:26
Alignment explanation
Indices: 488343--488390 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
488333 ATATTAATAT
**
488343 TTATAATTAATATTTAATGTAATTAA
1 TTATAATTAATATTTAATAAAATTAA
488369 TTATAA-TAATATTT-ATAAAATT
1 TTATAATTAATATTTAATAAAATT
488391 TAAAATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 8 0.40
26 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TTATAATTAATATTTAATAAAATTAA
Found at i:491691 original size:24 final size:24
Alignment explanation
Indices: 491664--491709 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
491654 AGGTTTTATT
**
491664 TTTGTGATTTAATTAATCATAATC
1 TTTGTGACGTAATTAATCATAATC
*
491688 TTTGTGACGTGATTAATCATAA
1 TTTGTGACGTAATTAATCATAA
491710 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.46
Consensus pattern (24 bp):
TTTGTGACGTAATTAATCATAATC
Found at i:491911 original size:25 final size:25
Alignment explanation
Indices: 491841--491931 Score: 94
Period size: 25 Copynumber: 3.5 Consensus size: 25
491831 CATTCACTCT
*
491841 TTTAGTTTTTCTCTTTACATTTTCATC
1 TTTAGTTTTT-TCTTTTCA-TTTCATC
* *
491868 TTTAGCCTTTTTT-TCTTCATTTCATT
1 TTTAG--TTTTTTCTTTTCATTTCATC
*
491894 TTTAGTTTTTTCTTTTCATTTCGTC
1 TTTAGTTTTTTCTTTTCATTTCATC
*
491919 TTTAGTCTTTTCT
1 TTTAGTTTTTTCT
491932 CTATAAATCC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
24 6 0.11
25 22 0.41
26 11 0.20
27 9 0.17
28 1 0.02
29 5 0.09
ACGTcount: A:0.11, C:0.18, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTAGTTTTTTCTTTTCATTTCATC
Found at i:491929 original size:51 final size:55
Alignment explanation
Indices: 491823--491929 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 55
491813 AAAAAGCTAG
491823 TTTTCTTCCATTCACTCTTTTAGTTTTTCTCTTTACATTTTCATCTTTAGCCTTT
1 TTTTCTTCCATTCACTCTTTTAGTTTTTCTCTTTACATTTTCATCTTTAGCCTTT
* * *
491878 TTTTCTT-CATTTCA-T-TTTTAGTTTTT-TCTTTTCA-TTTCGTCTTTAGTCTTT
1 TTTTCTTCCA-TTCACTCTTTTAGTTTTTCTCTTTACATTTTCATCTTTAGCCTTT
491929 T
1 T
491930 CTCTATAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 16 0.33
52 7 0.15
53 11 0.23
54 3 0.06
55 11 0.23
ACGTcount: A:0.11, C:0.20, G:0.05, T:0.64
Consensus pattern (55 bp):
TTTTCTTCCATTCACTCTTTTAGTTTTTCTCTTTACATTTTCATCTTTAGCCTTT
Found at i:500713 original size:20 final size:20
Alignment explanation
Indices: 500688--500764 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
500678 TCAAAAAGAT
500688 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
500708 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
500728 TGCATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
* *
500748 AAAATATATCGATACAT
1 AGAATGTATCGATACAT
500765 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:505171 original size:13 final size:13
Alignment explanation
Indices: 505153--505196 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
505143 AAATCTTCAC
505153 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
*
505166 TTTTTTTTT-TACCT
1 TTTTTTTTTCT--GT
505180 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
505193 TTTT
1 TTTT
505197 ACAATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 10 0.38
15 1 0.04
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTCTGT
Found at i:513427 original size:80 final size:80
Alignment explanation
Indices: 513273--513719 Score: 274
Period size: 80 Copynumber: 5.6 Consensus size: 80
513263 TAACCTATCA
* * * * *
513273 GGATACTCCAACCCCATTTTTACTTTCAAAATATCAAAATTTTCACCATCAAGGGTACTACAACT
1 GGATACTTCAACCCTATTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGGTACTACAACC
*
513338 CCATCATTTTT-TAGG
66 CCATCATTTTTGCA-G
* * * * *
513353 GGATACTTCAACCATATTTTTACTTCCAAAATATCAAATTTTTTACTAT-TAGGGATACTCCAAC
1 GGATACTTCAACCCTATTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGG-TACTACAAC
*
513417 CCCATTATTTTTGCAG
65 CCCATCATTTTTGCAG
* * * * * *
513433 GGATAC-TCTGACCCTGTTTTTACCTCCAAAATATCAAA-TTTTCATCAT--TGGGAATACTCCA
1 GGATACTTC-AACCCTATTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGG--TACTACA
* *
513494 ACCTCATCA-TTTTCCAG
63 ACCCCATCATTTTTGCAG
* ** * * **
513511 TGGATAC-TCAAACCC-AGTTTTTATTTTTAAAATATCGAA-TTTTCACCATCGAGTATACT-CA
1 -GGATACTTC-AACCCTA-TTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGGTACTACA
**
513572 ACCCCATCATTTTTTAAG
63 ACCCCATCATTTTTGCAG
* * * * * *
513590 GGATACTCTGACCTGACCTCGTTTTTACTTCCAAAATATTAAATTTTTCACCATCGAGGATAC-A
1 GGATACT-TCAAC---CCT-ATTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGGTACTA
* * *
513654 CTAATCCTATCATTTCTG-AG
61 C-AACCCCATCATTTTTGCAG
* * * *
513674 AGGATACTTCAA-CCTCGTTTTTACTTTCAAAATATTAAAATTTTCA
1 -GGATACTTCAACCCT-ATTTTTACTTCCAAAATATCAAATTTTTCA
513720 TCATGGGGAT
Statistics
Matches: 292, Mismatches: 55, Indels: 40
0.75 0.14 0.10
Matches are distributed among these distances:
78 26 0.09
79 78 0.27
80 125 0.43
81 2 0.01
82 2 0.01
83 17 0.06
84 23 0.08
85 19 0.07
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (80 bp):
GGATACTTCAACCCTATTTTTACTTCCAAAATATCAAATTTTTCACCATCAAGGGTACTACAACC
CCATCATTTTTGCAG
Found at i:513696 original size:242 final size:238
Alignment explanation
Indices: 513273--513767 Score: 529
Period size: 242 Copynumber: 2.1 Consensus size: 238
513263 TAACCTATCA
* * *
513273 GGATACTCCAACCCCATTTTTACTTTCAAAATATCAAAATTTTCACCATCAAGGGTACTACAACT
1 GGATACT-CAAACCCATTTTTACTTTCAAAATATCAAAATTTTCACCATCAAGGATACTACAACC
* * * *
513338 CCATCATTTTTTAGGGGATACTTCAACCATATTTTTACTTCCAAAATATCAAATTTTTTACTATT
65 CCATCATTTTTTAAGGGATACTTCAACCATATTTTTACTTCCAAAATATCAAATTTTTCACCATG
* * * * *
513403 AGGGATACTCCAACCCCATTATTTTTGCAGGGATACTCTGACCCTGTTTTTACCTCCAAAATA-T
130 AGGGATACACCAACCCCATCATTTCTGCAGGGATACTCTCAACCTGTTTTTACCTCCAAAATATT
* * * *
513467 CAAATTTTCATCATTGGGAATACTCCAACCTCATCATTTTCC-AGT
195 AAAATTTTCATCA-TGGGAATACTCCAACCTCACCA-TCTCCGAGG
* * * * *
513512 GGATACTCAAACCCAGTTTTTATTTTTAAAATATC-GAATTTTCACCATCGAGTATACT-CAACC
1 GGATACTCAAACCCA-TTTTTACTTTCAAAATATCAAAATTTTCACCATCAAGGATACTACAACC
* * *
513575 CCATCATTTTTTAAGGGATAC-TCTGACCTGACCTCGTTTTTACTTCCAAAATATTAAATTTTTC
65 CCATCATTTTTTAAGGGATACTTC-AACC--A--T-ATTTTTACTTCCAAAATATCAAATTTTTC
* * * * *
513639 ACCATCGA-GGATACACTAATCCTATCATTTCTG-AGAGGATACT-TCAACCTCGTTTTTACTTT
124 ACCAT-GAGGGATACACCAACCCCATCATTTCTGCAG-GGATACTCTCAACCT-GTTTTTACCTC
* *
513701 CAAAATATTAAAATTTTCATCATGGGGATACTCCAATCTCACCATCTCCGAGG
186 CAAAATATTAAAATTTTCATCATGGGAATACTCCAACCTCACCATCTCCGAGG
*
513754 GGATACTCCAACCC
1 GGATACTCAAACCC
513768 TAATTTTCAC
Statistics
Matches: 212, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
236 2 0.01
237 27 0.13
238 26 0.12
239 25 0.12
241 12 0.06
242 106 0.50
243 14 0.07
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (238 bp):
GGATACTCAAACCCATTTTTACTTTCAAAATATCAAAATTTTCACCATCAAGGATACTACAACCC
CATCATTTTTTAAGGGATACTTCAACCATATTTTTACTTCCAAAATATCAAATTTTTCACCATGA
GGGATACACCAACCCCATCATTTCTGCAGGGATACTCTCAACCTGTTTTTACCTCCAAAATATTA
AAATTTTCATCATGGGAATACTCCAACCTCACCATCTCCGAGG
Found at i:517540 original size:52 final size:52
Alignment explanation
Indices: 517478--517612 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 52
517468 ATTTAAGTGG
* * *
517478 ATGTATCGATACATTGAA-GAATGTATCAATACATTTGGGTCAAAAACCTAGA
1 ATGTATCGATACAAT-AATGAATATATCAATACATTTGGGTCAAAAACCAAGA
* *
517530 ATGTATCGATACAATAATGAATATATCGATACTTTTGGGTCAAAAACCAAGA
1 ATGTATCGATACAATAATGAATATATCAATACATTTGGGTCAAAAACCAAGA
* *
517582 ATGTATCGATACAATAA-AAATATATCGATAC
1 ATGTATCGATACAATAATGAATATATCAATAC
517613 GCTTTCTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 15 0.20
52 61 0.80
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACAATAATGAATATATCAATACATTTGGGTCAAAAACCAAGA
Found at i:518137 original size:14 final size:14
Alignment explanation
Indices: 518118--518144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
518108 AATATCATTT
518118 TTTGTTTGTTTGTA
1 TTTGTTTGTTTGTA
518132 TTTGTTTGTTTGT
1 TTTGTTTGTTTGT
518145 GGTGTAGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.00, G:0.22, T:0.74
Consensus pattern (14 bp):
TTTGTTTGTTTGTA
Found at i:519270 original size:22 final size:22
Alignment explanation
Indices: 519240--519283 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
519230 AAATAATAAT
*
519240 TTATCAAAAAGTAATTTATATC
1 TTATCAAAAAGTAAATTATATC
*
519262 TTATTAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
519284 ATGAGCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:522694 original size:23 final size:23
Alignment explanation
Indices: 522668--522727 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
522658 TTTTATAATA
* *
522668 GTATCATAATCTAATCAATAGTT
1 GTATCATATTCTAATCAATAGCT
522691 GTATCATATTCTAATCAATAGCT
1 GTATCATATTCTAATCAATAGCT
*
522714 ATATCATATTCTAA
1 GTATCATATTCTAA
522728 ACATAAGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (23 bp):
GTATCATATTCTAATCAATAGCT
Found at i:523456 original size:20 final size:19
Alignment explanation
Indices: 523404--523459 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
523394 TTAAAAAATA
*
523404 ATTTTATATAACAAAT-TA-
1 ATTTTATA-AATAAATATAG
*
523422 ATTTTATACATAAATATAG
1 ATTTTATAAATAAATATAG
523441 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
523460 TTAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 5 0.16
20 12 0.38
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:524813 original size:16 final size:16
Alignment explanation
Indices: 524792--524822 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
524782 TGTGATCTGA
524792 TTTTTTTTAAAATTTT
1 TTTTTTTTAAAATTTT
*
524808 TTTTTTTTAAGATTT
1 TTTTTTTTAAAATTT
524823 GGGTAGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTTTAAAATTTT
Found at i:524937 original size:28 final size:28
Alignment explanation
Indices: 524906--525037 Score: 197
Period size: 28 Copynumber: 4.9 Consensus size: 28
524896 ATTAATACTT
524906 ATATATTTTTATAATTAAATTTAAATAA
1 ATATATTTTTATAATTAAATTTAAATAA
*
524934 ATATATTTTTTATCATT---TTTAAATAA
1 ATATA-TTTTTATAATTAAATTTAAATAA
524960 ATATATTTTTATAATTAAATTTAAATAA
1 ATATATTTTTATAATTAAATTTAAATAA
524988 ATATATTTTTATAATTAAATTTAAATAA
1 ATATATTTTTATAATTAAATTTAAATAA
525016 ATATA--TTTA-AATT-AATTTAAAT
1 ATATATTTTTATAATTAAATTTAAAT
525038 TTTTAAAAAT
Statistics
Matches: 98, Mismatches: 2, Indels: 12
0.88 0.02 0.11
Matches are distributed among these distances:
24 9 0.09
25 14 0.14
26 18 0.18
28 47 0.48
29 10 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATATTTTTATAATTAAATTTAAATAA
Found at i:524967 original size:54 final size:54
Alignment explanation
Indices: 524906--525037 Score: 193
Period size: 54 Copynumber: 2.5 Consensus size: 54
524896 ATTAATACTT
*
524906 ATATATTTTTATAATTAAATTTAAATAAATATATTTTTTATCATT-TTTAAATAA
1 ATATATTTTTATAATTAAATTTAAATAAATATA-TTTTTATAATTATTTAAATAA
524960 ATATATTTTTATAATTAAATTTAAATAAATATATTTTTATAATTAAATTTAAATAA
1 ATATATTTTTATAATTAAATTTAAATAAATATATTTTTATAATT--ATTTAAATAA
525016 ATATA--TTTA-AATT-AATTTAAAT
1 ATATATTTTTATAATTAAATTTAAAT
525038 TTTTAAAAAT
Statistics
Matches: 74, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
52 9 0.12
53 14 0.19
54 37 0.50
56 14 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.52
Consensus pattern (54 bp):
ATATATTTTTATAATTAAATTTAAATAAATATATTTTTATAATTATTTAAATAA
Found at i:525015 original size:14 final size:14
Alignment explanation
Indices: 524951--525027 Score: 73
Period size: 14 Copynumber: 5.5 Consensus size: 14
524941 TTTTATCATT
*
524951 TTTAAATAAATATA
1 TTTAAATAAATAAA
** *
524965 TTTTTATAATTAAA
1 TTTAAATAAATAAA
*
524979 TTTAAATAAATATA
1 TTTAAATAAATAAA
** *
524993 TTTTTATAATTAAA
1 TTTAAATAAATAAA
*
525007 TTTAAATAAATATA
1 TTTAAATAAATAAA
525021 TTTAAAT
1 TTTAAAT
525028 TAATTTAAAT
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAAATAAATAAA
Found at i:525234 original size:24 final size:24
Alignment explanation
Indices: 525186--525234 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
525176 TAATTTAAAG
*
525186 TTTAAATTAATTAATTTATATATT
1 TTTAAATTAATTAATTTATAAATT
525210 TTTAAATATAA-T-ATTTAATAAATT
1 TTTAAAT-TAATTAATTT-ATAAATT
525234 T
1 T
525235 AAATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.18
24 15 0.68
25 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAATTAATTAATTTATAAATT
Found at i:525238 original size:22 final size:23
Alignment explanation
Indices: 525210--525252 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
525200 TTTATATATT
525210 TTTAAATATAATAT-TTAATAAA
1 TTTAAATATAATATCTTAATAAA
* *
525232 TTTAAATTTAATTTCTTAATA
1 TTTAAATATAATATCTTAATA
525253 TTTATAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAAATATAATATCTTAATAAA
Found at i:525240 original size:15 final size:16
Alignment explanation
Indices: 525192--525243 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
525182 AAAGTTTAAA
*
525192 TTAATTAATTTATATAT
1 TTAATAAATTTA-ATAT
* *
525209 TT-TTAAATATAATAT
1 TTAATAAATTTAATAT
525224 TTAATAAATTTAA-AT
1 TTAATAAATTTAATAT
525239 TTAAT
1 TTAAT
525244 TTCTTAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 13 0.45
16 14 0.48
17 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATAAATTTAATAT
Found at i:525558 original size:5 final size:5
Alignment explanation
Indices: 525548--525644 Score: 57
Period size: 5 Copynumber: 20.6 Consensus size: 5
525538 AATATTAAAC
* * *
525548 ATAAT AT-A- ATAAT ATGAT AT-AT TTAAT -TAAT ATAAAA ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT
* * * *
525595 A-AAT ATTAA- ATAAT ATATT AAAAT ATTAT -TAAT ATAAT AT-AT TTAAT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
525642 ATA
1 ATA
525645 TATTATATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
3 2 0.03
4 22 0.31
5 40 0.57
6 6 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:525561 original size:20 final size:19
Alignment explanation
Indices: 525536--525611 Score: 59
Period size: 19 Copynumber: 4.0 Consensus size: 19
525526 ATTTAAGTGG
*
525536 ATAATATTAAACATAATATA
1 ATAATA-TAAAAATAATATA
* * *
525556 ATAATAT-GATAT-ATTTA
1 ATAATATAAAAATAATATA
525573 ATTAATATAAAAATAATATA
1 A-TAATATAAAAATAATATA
*
525593 ATAA-ATATTAAATAATATA
1 ATAATATA-AAAATAATATA
525612 TTAAAATATT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.11
18 12 0.27
19 17 0.38
20 11 0.24
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
ATAATATAAAAATAATATA
Found at i:525615 original size:38 final size:36
Alignment explanation
Indices: 525537--525649 Score: 102
Period size: 38 Copynumber: 3.1 Consensus size: 36
525527 TTTAAGTGGA
* * * *
525537 TAATATTAAACATAATATAATAATATGATATATTTAAT
1 TAATA-TAAAAATAATATAATAATATTAAATATAT-AT
525575 TAATATAAAAATAATATAATAAATATTAAATAATATAT
1 TAATATAAAAATAATATAAT-AATATTAAAT-ATATAT
* ** * *
525613 TAAAATATTATTAATATAAT-ATATTTAATATATAT
1 TAATATAAAAATAATATAATAATATTAAATATATAT
525648 TA
1 TA
525650 TATTTAGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 8 0.12
36 8 0.12
37 14 0.22
38 31 0.48
39 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (36 bp):
TAATATAAAAATAATATAATAATATTAAATATATAT
Found at i:525648 original size:24 final size:23
Alignment explanation
Indices: 525564--525649 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 23
525554 TAATAATATG
525564 ATATATTTAAT-TA-ATATAAA-A
1 ATATATTTAATATATAT-TAAATA
* *
525585 ATA-ATATAATAAATATTAAATA
1 ATATATTTAATATATATTAAATA
*
525607 ATATA-TTAAAATATTATTAATATA
1 ATATATTTAATATA-TATTAA-ATA
525631 ATATATTTAATATATATTA
1 ATATATTTAATATATATTA
525650 TATTTAGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 6 0.12
21 8 0.15
22 11 0.21
23 7 0.13
24 13 0.25
25 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATTTAATATATATTAAATA
Found at i:525651 original size:16 final size:14
Alignment explanation
Indices: 525548--525655 Score: 68
Period size: 14 Copynumber: 7.9 Consensus size: 14
525538 AATATTAAAC
*
525548 ATAATATA-ATAAT
1 ATAATATATTTAAT
*
525561 ATGATATATTTAAT
1 ATAATATATTTAAT
**
525575 -TAATATAAAAATAAT
1 ATAATAT--ATTTAAT
*
525590 ATAATAAATATTAA-
1 ATAATATAT-TTAAT
*
525604 ATAATATA-TTAAA
1 ATAATATATTTAAT
525617 AT-AT-TA-TTAAT
1 ATAATATATTTAAT
525628 ATAATATATTTAAT
1 ATAATATATTTAAT
525642 ATATATTATATTTA
1 ATA-A-TATATTTA
525656 GTTTTAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
11 8 0.11
12 8 0.11
13 16 0.22
14 20 0.27
15 9 0.12
16 13 0.18
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (14 bp):
ATAATATATTTAAT
Found at i:526519 original size:17 final size:17
Alignment explanation
Indices: 526497--526529 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
526487 TAAATGTTAT
526497 TAATATAATATATTTAA
1 TAATATAATATATTTAA
*
526514 TAATATATTATATTTA
1 TAATATAATATATTTA
526530 TGTTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATATAATATATTTAA
Found at i:527810 original size:3 final size:3
Alignment explanation
Indices: 527802--527832 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
527792 GAATATAATT
*
527802 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
527833 GAGTAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:528180 original size:49 final size:52
Alignment explanation
Indices: 528127--528231 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 52
528117 ATATTAATAA
* *
528127 ATTATTTTATATA-TT-TTT-AATAAATTTAA-TATTTAAAATTTTAGTATAT
1 ATTATTTTATATATTTATTTAAAT-AATTTAATTAATTAAAAATTTAGTATAT
* *
528176 ATTATTTTATATATTTATTTAAATATTTTAATTAATTAAAAATTTAGTATTT
1 ATTATTTTATATATTTATTTAAATAATTTAATTAATTAAAAATTTAGTATAT
528228 ATTA
1 ATTA
528232 AATAAATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 13 0.27
50 2 0.04
51 9 0.19
52 24 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (52 bp):
ATTATTTTATATATTTATTTAAATAATTTAATTAATTAAAAATTTAGTATAT
Found at i:528245 original size:17 final size:17
Alignment explanation
Indices: 528223--528258 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
528213 AAAAATTTAG
528223 TATTTATTAAATAAATT
1 TATTTATTAAATAAATT
* *
528240 TATTTATTATATTAATT
1 TATTTATTAAATAAATT
528257 TA
1 TA
528259 AAATCAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTATTAAATAAATT
Found at i:528743 original size:20 final size:19
Alignment explanation
Indices: 528693--528746 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
528683 CCTTTACTTT
*
528693 TTTTTGAATATTTTTAATTA
1 TTTTT-AATATTTTTAATAA
* *
528713 TTATTATTATTTTTAATCAA
1 TTTTTAATATTTTTAAT-AA
528733 TTTTTAATATTTTT
1 TTTTTAATATTTTT
528747 TGTTTTGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTAATATTTTTAATAA
Found at i:528746 original size:9 final size:9
Alignment explanation
Indices: 528693--528746 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
528683 CCTTTACTTT
528693 TTTTTGAATA
1 TTTTT-AATA
528703 TTTTTAATTA
1 TTTTTAA-TA
* *
528713 TTATTATTA
1 TTTTTAATA
528722 TTTTTAATCAA
1 TTTTTAAT--A
528733 TTTTTAATA
1 TTTTTAATA
528742 TTTTT
1 TTTTT
528747 TGTTTTGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 16 0.43
10 12 0.32
11 9 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTAATA
Found at i:528760 original size:16 final size:15
Alignment explanation
Indices: 528732--528780 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
528722 TTTTTAATCA
*
528732 ATTTTTAAT-ATTTT
1 ATTTTTTATAATTTT
528746 -TTGTTTTGATAATTTT
1 ATT-TTTT-ATAATTTT
528762 ATTTTTTATAATTTT
1 ATTTTTTATAATTTT
528777 ATTT
1 ATTT
528781 AAAGCTCGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 14 0.47
16 9 0.30
17 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
ATTTTTTATAATTTT
Found at i:529325 original size:11 final size:12
Alignment explanation
Indices: 529264--529331 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
529254 ATATAATTAA
*
529264 AAATATTTTATTT
1 AAATATTAT-TTT
*
529277 AAAT-TTAATTAT
1 AAATATT-ATTTT
* *
529289 AAATATTAATAT
1 AAATATTATTTT
*
529301 AAA-AATATTTT
1 AAATATTATTTT
*
529312 TAATATTATTTT
1 AAATATTATTTT
529324 AAATATTA
1 AAATATTA
529332 ATATGATCTT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
11 7 0.16
12 29 0.67
13 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATATTATTTT
Found at i:530230 original size:21 final size:22
Alignment explanation
Indices: 530195--530242 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
530185 TAAATTGATT
* * *
530195 AAAAATTATTATATATATTTAA
1 AAAAAATATTATATAAAATTAA
530217 AAAAAATATT-TATAAAATTAA
1 AAAAAATATTATATAAAATTAA
530238 AAAAA
1 AAAAA
530243 TATGATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAATATTATATAAAATTAA
Found at i:538762 original size:18 final size:21
Alignment explanation
Indices: 538739--538791 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
538729 TAATGTATAG
538739 ATAACATAGTAGT-A-AA-TA
1 ATAACATAGTAGTAACAATTA
* *
538757 ATAACATGGTTGTAATCAATTA
1 ATAACATAGTAGTAA-CAATTA
538779 ATAACATAGTAGT
1 ATAACATAGTAGT
538792 TGACACTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
21 2 0.07
22 13 0.48
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (21 bp):
ATAACATAGTAGTAACAATTA
Found at i:539153 original size:13 final size:14
Alignment explanation
Indices: 539105--539153 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
539095 TTATTACATC
*
539105 AAATTAATTAATTAA
1 AAATT-ATTAATAAA
539120 AAATTATTAATAAA
1 AAATTATTAATAAA
**
539134 ATTTTATT-ATAAA
1 AAATTATTAATAAA
539147 AAATTAT
1 AAATTAT
539154 AAATTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
13 10 0.34
14 14 0.48
15 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATTATTAATAAA
Found at i:543793 original size:2 final size:2
Alignment explanation
Indices: 543786--543815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
543776 CTAGGTATGC
543786 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
543816 GCTACTTGGA
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:545322 original size:168 final size:166
Alignment explanation
Indices: 545121--545453 Score: 424
Period size: 166 Copynumber: 2.0 Consensus size: 166
545111 TTAATTTTTC
* *
545121 TTGAAATTTCTCTTTTTTTGAAAAACTGAGTTTTCTATTCCATAAATTTTTTTCGAAGGTATTTT
1 TTGAAATCTCTCTTTTTTTGAAAAACTGAGTTTTCTATTCCATAAA-TATTTTCGAAGG-ATTTT
* *** *
545186 CTTTGGTCTAAAATTTTTAAAATGT-ATCTAATAATGTTATTGAATTCCCATTAAATCAGTTTTG
64 CTTTGGTCTAAAATTTTTAAAAT-TAATCTAATAATATTACAAAACTCCCATTAAATCAGTTTTG
*
545250 -AAAATTTAATTCATTT-TCATAAGTTTTAAATTTTTTACT
128 TAAAATTCAATTCATTTGT--TAAGTTTTAAATTTTTTACT
* *
545289 TTGAAATCTCT-TTTTTCTTGAAAAA-TCGAGTTTTCTATTTCATAAATATTTTCGGAGGATTTT
1 TTGAAATCTCTCTTTTT-TTGAAAAACT-GAGTTTTCTATTCCATAAATATTTTCGAAGGATTTT
** *
545352 CTTTGGTCTAAAATTTTTAAAATTAATCTAATTTTATTACAAAACTCCCATTAAATTAGTTTTGT
64 CTTTGGTCTAAAATTTTTAAAATTAATCTAATAATATTACAAAACTCCCATTAAATCAGTTTTGT
* **
545417 AAAATTCAATTTATTTGTTATTTTTTAAATTTTTTAC
129 AAAATTCAATTCATTTGTTAAGTTTTAAATTTTTTAC
545454 GTATGATAAT
Statistics
Matches: 144, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
165 1 0.01
166 76 0.53
167 30 0.21
168 37 0.26
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (166 bp):
TTGAAATCTCTCTTTTTTTGAAAAACTGAGTTTTCTATTCCATAAATATTTTCGAAGGATTTTCT
TTGGTCTAAAATTTTTAAAATTAATCTAATAATATTACAAAACTCCCATTAAATCAGTTTTGTAA
AATTCAATTCATTTGTTAAGTTTTAAATTTTTTACT
Found at i:549583 original size:13 final size:12
Alignment explanation
Indices: 549561--549600 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
549551 GAAAAGCAAA
549561 AAAGAGAAAAAG
1 AAAGAGAAAAAG
*
549573 AAAGATAAAAAG
1 AAAGAGAAAAAG
549585 AAAGAGAAAAAAG
1 AAAGAG-AAAAAG
549598 AAA
1 AAA
549601 AAAGCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (12 bp):
AAAGAGAAAAAG
Found at i:549588 original size:16 final size:16
Alignment explanation
Indices: 549569--549612 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 16
549559 AAAAAGAGAA
549569 AAAGAAAGATAAAAAG
1 AAAGAAAGATAAAAAG
549585 AAAG--AGA-AAAAAG
1 AAAGAAAGATAAAAAG
549598 AAA-AAAGCATAAAAA
1 AAAGAAAG-ATAAAAA
549613 AGGATGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.38
14 5 0.21
15 1 0.04
16 9 0.38
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAGAAAGATAAAAAG
Found at i:553393 original size:13 final size:13
Alignment explanation
Indices: 553375--553400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
553365 TACAGCAAGT
553375 ATGTATCGATACA
1 ATGTATCGATACA
553388 ATGTATCGATACA
1 ATGTATCGATACA
553401 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:555646 original size:21 final size:21
Alignment explanation
Indices: 555613--555657 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
555603 TTGCAAGTTG
*
555613 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
555635 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
555655 AAA
1 AAA
555658 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:559584 original size:20 final size:21
Alignment explanation
Indices: 559505--559583 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
559495 AATGTCCAAA
*
559505 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
559525 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
559550 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
559570 TTGTATCGATACAT
1 ATGTATCGATACAT
559584 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:559588 original size:13 final size:13
Alignment explanation
Indices: 559570--559608 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
559560 ACATTTTTCT
559570 TTGTATCGATACA
1 TTGTATCGATACA
559583 TTGTATCGATACA
1 TTGTATCGATACA
*
559596 CTGTATCGATACA
1 TTGTATCGATACA
559609 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:562171 original size:13 final size:13
Alignment explanation
Indices: 562153--562178 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
562143 TACAGCAAGT
562153 ATGTATCGATACA
1 ATGTATCGATACA
562166 ATGTATCGATACA
1 ATGTATCGATACA
562179 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:563182 original size:32 final size:33
Alignment explanation
Indices: 563146--563207 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
563136 ATCAATTTTA
* *
563146 AAATTTTACAGTTTTAT-AATTAAATTAAAAAT
1 AAATTTTAAAGTTTTATAAATCAAATTAAAAAT
*
563178 AAATTTTAAATTTTTATAAATCAAATTAAA
1 AAATTTTAAAGTTTTATAAATCAAATTAAA
563208 TTACATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (33 bp):
AAATTTTAAAGTTTTATAAATCAAATTAAAAAT
Found at i:563596 original size:16 final size:16
Alignment explanation
Indices: 563575--563612 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
563565 CTTCGTAGAG
563575 GAGCTCTTTATATAAA
1 GAGCTCTTTATATAAA
*
563591 GAGCTCTTTATATAAG
1 GAGCTCTTTATATAAA
563607 GAGCTC
1 GAGCTC
563613 CTCCGCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (16 bp):
GAGCTCTTTATATAAA
Found at i:563836 original size:24 final size:22
Alignment explanation
Indices: 563816--563899 Score: 75
Period size: 23 Copynumber: 3.9 Consensus size: 22
563806 ATAAATTTCA
563816 TAAAAATATATTAAATTAATTT
1 TAAAAATATATTAAATTAATTT
* *
563838 TAAAAATAAAAATAAATTAGATTT
1 TAAAAAT-ATATTAAATTA-ATTT
* * *
563862 TAAAAATTTTTTAAATT-A-CT
1 TAAAAATATATTAAATTAATTT
*
563882 TAAAAAAAT-TTAAATTAA
1 TAAAAATATATTAAATTAA
563900 ATTAATATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
19 7 0.14
20 9 0.18
21 1 0.02
22 7 0.14
23 15 0.30
24 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (22 bp):
TAAAAATATATTAAATTAATTT
Found at i:564326 original size:21 final size:22
Alignment explanation
Indices: 564293--564349 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
564283 TTTTAAAAAA
* *
564293 TAAT-TAATATTTTAA-TTTAT
1 TAATATAATTTTTTAAGTTAAT
564313 TAATATAATTTTTTAAGTTAAT
1 TAATATAATTTTTTAAGTTAAT
*
564335 TAAGTATTATTTTTT
1 TAA-TATAATTTTTT
564350 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 7 0.23
23 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
TAATATAATTTTTTAAGTTAAT
Found at i:564393 original size:9 final size:9
Alignment explanation
Indices: 564379--564409 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
564369 ATATATTATT
564379 ATTTTTTAA
1 ATTTTTTAA
*
564388 ATTTTTAAA
1 ATTTTTTAA
564397 ATTTTTTAA
1 ATTTTTTAA
564406 ATTT
1 ATTT
564410 AATTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:565863 original size:13 final size:13
Alignment explanation
Indices: 565845--565870 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
565835 ATTTTTTTTG
565845 TGTATCGATACAT
1 TGTATCGATACAT
565858 TGTATCGATACAT
1 TGTATCGATACAT
565871 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:567146 original size:33 final size:33
Alignment explanation
Indices: 567109--567175 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
567099 TTCAACGATT
567109 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
567142 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
567175 T
1 T
567176 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:567147 original size:13 final size:13
Alignment explanation
Indices: 567129--567153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567119 CATAAAATGT
567129 TGTATCGATACAA
1 TGTATCGATACAA
567142 TGTATCGATACA
1 TGTATCGATACA
567154 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:567234 original size:13 final size:13
Alignment explanation
Indices: 567216--567240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
567206 ATTACTCAAA
567216 TGTATCGATACAT
1 TGTATCGATACAT
567229 TGTATCGATACA
1 TGTATCGATACA
567241 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:567342 original size:52 final size:52
Alignment explanation
Indices: 567249--567372 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
567239 CACTGATCTT
*
567249 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
567300 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
567352 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
567373 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:572005 original size:15 final size:14
Alignment explanation
Indices: 571973--572018 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
571963 ATCAATTTCA
*
571973 TATTTCATATTTTT
1 TATTTAATATTTTT
*
571987 TATTTATTATTTTT
1 TATTTAATATTTTT
572001 ATATTTAATATTTATT
1 -TATTTAATATTT-TT
572017 TA
1 TA
572019 ATATCAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.44
15 13 0.48
16 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTAATATTTTT
Found at i:572419 original size:13 final size:13
Alignment explanation
Indices: 572371--572419 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
572361 TAATAAATGT
* *
572371 TTTAATAATATTT
1 TTTAATATTATTA
*
572384 TTTAAAATTATTA
1 TTTAATATTATTA
572397 TATATAATATTATTA
1 T-T-TAATATTATTA
572412 TTTAATAT
1 TTTAATAT
572420 GTTAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 17 0.57
14 2 0.07
15 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTAATATTATTA
Found at i:572954 original size:20 final size:21
Alignment explanation
Indices: 572913--572957 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
572903 TTAAGAAGTT
*
572913 TATA-CAAAATTAATTATTAA
1 TATATCAAAATTAATTATAAA
*
572933 TATATCAAAATTTA-TATAAA
1 TATATCAAAATTAATTATAAA
572953 TATAT
1 TATAT
572958 AAATATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATCAAAATTAATTATAAA
Found at i:573425 original size:27 final size:27
Alignment explanation
Indices: 573363--573414 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
573353 TTCACATAAC
573363 ATAAAT-TATTAATATGTTAAAATTTAT
1 ATAAATATA-TAATATGTTAAAATTTAT
573390 ATAAATATATAATAT-TTAAAATTTA
1 ATAAATATATAATATGTTAAAATTTA
573415 ATTATGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 10 0.42
27 12 0.50
28 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
ATAAATATATAATATGTTAAAATTTAT
Found at i:573786 original size:32 final size:34
Alignment explanation
Indices: 573750--573813 Score: 98
Period size: 32 Copynumber: 1.9 Consensus size: 34
573740 CAAAAGTTTT
573750 AAATTTATATAAA-ATA-AATT-ATTAATATATTA
1 AAATTTATATAAATATATAATTCATTAA-ATATTA
573782 AAATTTATATAAATATATAATTCATTAAATAT
1 AAATTTATATAAATATATAATTCATTAAATAT
573814 GGTGATGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.45
33 3 0.10
34 8 0.28
35 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (34 bp):
AAATTTATATAAATATATAATTCATTAAATATTA
Found at i:574582 original size:2 final size:2
Alignment explanation
Indices: 574575--574608 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
574565 GATTAGATGT
574575 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
574609 GATAGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574622 original size:3 final size:3
Alignment explanation
Indices: 574614--574667 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
574604 ATATAGATAG
574614 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
574660 ATA ATA AT
1 ATA ATA AT
574668 TATTATTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:575082 original size:113 final size:113
Alignment explanation
Indices: 574947--575172 Score: 400
Period size: 113 Copynumber: 2.0 Consensus size: 113
574937 TCAGCCAATT
*
574947 GACTTGATTTTTTTCAACCATGATTTTATTACCAACGAGAAAAGTACAAATGCTTTCCTTTGTTA
1 GACTTGATTTTTTTCAACCATGATTTTATTACCAACGACAAAAGTACAAATGCTTTCCTTTGTTA
*
575012 CAAGAAAGAAAAATTTTAGGTAAATTTTACTAATAAAACAAAGCTCTCA
66 CAAGAAAGAAAAATTTTA-GTAAATTCTACTAATAAAACAAAGCTCTCA
575061 GACTTGATTTTTTT-AACCATGATTTTATTACCAACGACAAAAGTACAAATGCTTTCCTTTGTTA
1 GACTTGATTTTTTTCAACCATGATTTTATTACCAACGACAAAAGTACAAATGCTTTCCTTTGTTA
* *
575125 CATGAAAGAAAAATTTTAGTAAATTCTACTAATTAAACAAAGCTCTCA
66 CAAGAAAGAAAAATTTTAGTAAATTCTACTAATAAAACAAAGCTCTCA
575173 AGCAAAAAAA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
112 28 0.26
113 66 0.61
114 14 0.13
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (113 bp):
GACTTGATTTTTTTCAACCATGATTTTATTACCAACGACAAAAGTACAAATGCTTTCCTTTGTTA
CAAGAAAGAAAAATTTTAGTAAATTCTACTAATAAAACAAAGCTCTCA
Found at i:575441 original size:14 final size:14
Alignment explanation
Indices: 575422--575453 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
575412 GATAAAAATG
575422 TCATGTTGATAATA
1 TCATGTTGATAATA
*
575436 TCATGTTGGTAATA
1 TCATGTTGATAATA
575450 TCAT
1 TCAT
575454 ATCTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (14 bp):
TCATGTTGATAATA
Found at i:582398 original size:24 final size:24
Alignment explanation
Indices: 582353--582439 Score: 57
Period size: 27 Copynumber: 3.4 Consensus size: 24
582343 AGTCACAAAA
* * **
582353 TTTGACAAATAACATGCCACCATT
1 TTTGACAAATAAAAAGAAACCATT
582377 TTTGACAAATAAAAAGAAACCACTATT
1 TTTGACAAATAAAAAGAAA-C-C-ATT
* * *
582404 TTTTACAAACACAAAATAACCACCATT
1 TTTGACAAATA-AAAAGAA--ACCATT
582431 TTTGACAAA
1 TTTGACAAA
582440 CAAAGGATGG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
24 15 0.31
25 1 0.02
26 1 0.02
27 23 0.47
28 7 0.14
29 1 0.02
30 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.28
Consensus pattern (24 bp):
TTTGACAAATAAAAAGAAACCATT
Found at i:582411 original size:27 final size:27
Alignment explanation
Indices: 582369--582441 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
582359 AAATAACATG
*
582369 CCACCATTTTTGACAAATA-AAAAGAAA
1 CCACCATTTTTGACAAACACAAAA-AAA
* * *
582396 CCACTATTTTTTACAAACACAAAATAA
1 CCACCATTTTTGACAAACACAAAAAAA
582423 CCACCATTTTTGACAAACA
1 CCACCATTTTTGACAAACA
582442 AAGGATGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 35 0.90
28 4 0.10
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTGACAAACACAAAAAAA
Found at i:584302 original size:21 final size:22
Alignment explanation
Indices: 584264--584309 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
584254 TTCTGTTGAA
**
584264 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGTTGCGGAGTACT
584285 ACTCCACCTGTTGCGGAGTACT
1 ACTCCACCTGTTGCGGAGTACT
584307 ACT
1 ACT
584310 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGTTGCGGAGTACT
Found at i:586917 original size:27 final size:27
Alignment explanation
Indices: 586879--586946 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
586869 ACATGCTACC
* *
586879 ATTTTTTACAAATA-AAAAGAAACCACT
1 ATTTTTTACAAACACAAAA-AAACCACA
*
586906 ATTTTTTACAAACACAAAATAACCACA
1 ATTTTTTACAAACACAAAAAAACCACA
586933 ATTTTTTACAAACA
1 ATTTTTTACAAACA
586947 AAGGATGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (27 bp):
ATTTTTTACAAACACAAAAAAACCACA
Found at i:587947 original size:16 final size:15
Alignment explanation
Indices: 587915--587966 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 15
587905 GATAAATAAT
*
587915 TTTTAAAA-TTTATC
1 TTTTAAAACTATATC
587929 TTTTAAAACTATGATC
1 TTTTAAAACTAT-ATC
*
587945 TTTTAAAATTATAT-
1 TTTTAAAACTATATC
587959 TTTTAAAA
1 TTTTAAAA
587967 AGTTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 16 0.47
15 4 0.12
16 14 0.41
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTAAAACTATATC
Found at i:588018 original size:32 final size:32
Alignment explanation
Indices: 587971--588047 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
587961 TTAAAAAGTT
*
587971 TTAAAAATAACATTTATTTTTAATATTATAAA
1 TTAAAAATAAAATTTATTTTTAATATTATAAA
* *
588003 TTAAAGATAAAATTTATTTTTAATATTATTAAG
1 TTAAAAATAAAATTTATTTTTAATATTA-TAAA
*
588036 TTTAAAATAAAA
1 TTAAAAATAAAA
588048 AAATATTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 26 0.67
33 13 0.33
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (32 bp):
TTAAAAATAAAATTTATTTTTAATATTATAAA
Found at i:588055 original size:34 final size:32
Alignment explanation
Indices: 587985--588063 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
587975 AAATAACATT
**
587985 TATTTTTAATATTATAAATTAAAGATAAAATT
1 TATTTTTAATATTATAAATTAAAGATAAAAAA
*
588017 TATTTTTAATATTATTAAGTTTAAA-ATAAAAAAA
1 TATTTTTAATATTA-TAA-ATTAAAGAT-AAAAAA
*
588051 TATTTTTATTATT
1 TATTTTTAATATT
588064 TATCTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 14 0.35
33 5 0.12
34 21 0.52
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TATTTTTAATATTATAAATTAAAGATAAAAAA
Found at i:589068 original size:27 final size:27
Alignment explanation
Indices: 589007--589077 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
588997 AAACAAGCCT
* *
589007 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
589035 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
589062 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
589078 AGTGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:590999 original size:21 final size:22
Alignment explanation
Indices: 590961--591006 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
590951 ATCTGTTGAA
* **
590961 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
590982 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
591004 ACT
1 ACT
591007 TATCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:593619 original size:28 final size:27
Alignment explanation
Indices: 593580--593650 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
593570 AAACAAGCCT
* *
593580 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
*
593608 CCATTTTTGACAGACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
593635 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
593651 AATGGGTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:595231 original size:20 final size:20
Alignment explanation
Indices: 595206--595251 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
595196 ATGAATTGAC
*
595206 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
595226 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
595246 GAGGGA
1 GAGGGA
595252 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:597315 original size:21 final size:22
Alignment explanation
Indices: 597277--597322 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
597267 ATCTGTTGAA
* **
597277 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
597298 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
597320 ACT
1 ACT
597323 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:599800 original size:20 final size:20
Alignment explanation
Indices: 599786--599840 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
599776 AGGGATACAA
599786 GAGAGGGATGAGGGATGCTT
1 GAGAGGGATGAGGGATGCTT
599806 GAGAGGGATGAGGGATGCTT
1 GAGAGGGATGAGGGATGCTT
*
599826 GAGAGGGAGGAGGGA
1 GAGAGGGATGAGGGA
599841 GCCTCTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.04, G:0.55, T:0.15
Consensus pattern (20 bp):
GAGAGGGATGAGGGATGCTT
Found at i:601915 original size:75 final size:75
Alignment explanation
Indices: 601792--601943 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
601782 ATGAGTTAGG
601792 TATGCGTTAAGTTAAAGTTAATTAACCTCCTTATCTTTATGGATAGCCTTCTACATGAACATGAA
1 TATGCGTTAAGTTAAAGTTAATTAACCTCCTTATCTTTATGGATAGCCTTCTACATGAACATGAA
601857 GCTATAAATA
66 GCTATAAATA
601867 TATGCGTTAAGTTAAAGTTAATTAACCTCCTTATCTTTATGGATAGCCTTCTACATGAACATGAA
1 TATGCGTTAAGTTAAAGTTAATTAACCTCCTTATCTTTATGGATAGCCTTCTACATGAACATGAA
601932 GCTATAAATA
66 GCTATAAATA
601942 TA
1 TA
601944 GTTAGCATGG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (75 bp):
TATGCGTTAAGTTAAAGTTAATTAACCTCCTTATCTTTATGGATAGCCTTCTACATGAACATGAA
GCTATAAATA
Found at i:602097 original size:37 final size:37
Alignment explanation
Indices: 602017--602098 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 37
602007 AATAATTATT
**
602017 TTTAAAAAATAAAAAATTTATTTTTAAAAGTTTTATA
1 TTTAAAAAATAAAAAATTTATTTTTAAAAGTCATATA
** *
602054 AATAAAAAATTAAAAAA-TTATTTTTTAAAA-TCATATC
1 TTTAAAAAA-TAAAAAATTTA-TTTTTAAAAGTCATATA
602091 TTTAAAAA
1 TTTAAAAA
602099 GTTTTAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
37 20 0.56
38 16 0.44
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (37 bp):
TTTAAAAAATAAAAAATTTATTTTTAAAAGTCATATA
Found at i:605135 original size:2 final size:2
Alignment explanation
Indices: 605130--605165 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
605120 TAGATGTGTG
605130 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
605166 GTAAGGCGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:606549 original size:12 final size:13
Alignment explanation
Indices: 606534--606580 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
606524 ATTTTTTTAT
606534 TTATATATAAA-A
1 TTATATATAAATA
*
606546 TTATAAATACAATA
1 TTATATATA-AATA
606560 TT-TATATAAATA
1 TTATATATAAATA
*
606572 TTATGTATA
1 TTATATATA
606581 CTAATTATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 14 0.48
13 12 0.41
14 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
TTATATATAAATA
Found at i:606749 original size:20 final size:20
Alignment explanation
Indices: 606721--606773 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
606711 AATTAATATG
*
606721 TACATTATATTATA-TATAA
1 TACATTATATTATATTAAAA
606740 TACATCTATATTATATTAAAA
1 TACAT-TATATTATATTAAAA
*
606761 TATATTATATTAT
1 TACATTATATTAT
606774 GTTTTAGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 17 0.57
21 8 0.27
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
TACATTATATTATATTAAAA
Found at i:607063 original size:33 final size:33
Alignment explanation
Indices: 607021--607087 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
607011 AGTGTCTAAG
607021 TTAGGGTGAATCCAAAATCAATGGATCGGTAAT
1 TTAGGGTGAATCCAAAATCAATGGATCGGTAAT
607054 TTAGGGTGAATCCAAAATCAATGGATCGGTAAT
1 TTAGGGTGAATCCAAAATCAATGGATCGGTAAT
607087 T
1 T
607088 GTGGATATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (33 bp):
TTAGGGTGAATCCAAAATCAATGGATCGGTAAT
Found at i:609926 original size:22 final size:22
Alignment explanation
Indices: 609901--609945 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
609891 TGGACTTGGT
609901 TTTTCATTTCTTGTTTTCTTTC
1 TTTTCATTTCTTGTTTTCTTTC
* * * *
609923 TTTTCTTTTTTTTTTTTTTTTC
1 TTTTCATTTCTTGTTTTCTTTC
609945 T
1 T
609946 CAAATACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTCATTTCTTGTTTTCTTTC
Found at i:609927 original size:17 final size:17
Alignment explanation
Indices: 609902--609945 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
609892 GGACTTGGTT
*
609902 TTTCATTTCTTGTTTTC
1 TTTCTTTTCTTGTTTTC
* *
609919 TTTCTTTTCTTTTTTTT
1 TTTCTTTTCTTGTTTTC
*
609936 TTTTTTTTCT
1 TTTCTTTTCT
609946 CAAATACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTCTTTTCTTGTTTTC
Found at i:610349 original size:2 final size:2
Alignment explanation
Indices: 610342--610372 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
610332 ACCCATACAT
610342 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 T
610373 TCACCACTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:610548 original size:14 final size:16
Alignment explanation
Indices: 610519--610550 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
610509 ATGTTTTGAC
610519 ATTTTATAAAAGTATA
1 ATTTTATAAAAGTATA
610535 ATTTTA-AAAA-TATA
1 ATTTTATAAAAGTATA
610549 AT
1 AT
610551 AATATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 4 0.25
16 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTTTATAAAAGTATA
Found at i:616254 original size:14 final size:14
Alignment explanation
Indices: 616235--616287 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
616225 TGATAAATAA
616235 TTTTTAAAATTTAT
1 TTTTTAAAATTTAT
616249 TTTTTAAAATTTTGAT
1 TTTTTAAAA-TTT-AT
*
616265 CTTTTAAAA-TTAT
1 TTTTTAAAATTTAT
616278 ATTTTTAAAA
1 -TTTTTAAAA
616288 AGCTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.06
14 19 0.56
15 3 0.09
16 10 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATTTAT
Found at i:616742 original size:18 final size:17
Alignment explanation
Indices: 616716--616749 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
616706 TTTTTAATAT
*
616716 ATTATTTTAATATTAAAA
1 ATTAATTTAAT-TTAAAA
616734 ATTAATTTAATTTAAA
1 ATTAATTTAATTTAAA
616750 TTTGAAGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTAATTTAATTTAAAA
Found at i:617515 original size:68 final size:68
Alignment explanation
Indices: 617406--617535 Score: 242
Period size: 68 Copynumber: 1.9 Consensus size: 68
617396 TCTAAGGGTG
617406 ATCCACTGATTAATGATATCCCAACTACTCTAGCTAGCAAATTATTAAGTCTTTCTTCCAAATAC
1 ATCCACTGATTAATGATATCCCAACTACTCTAGCTAGCAAATTATTAAGTCTTTCTTCCAAATAC
617471 GTA
66 GTA
* *
617474 ATCCACTGATTAATGATATCCCAACTCCTCTGGCTAGCAAATTATTAAGTCTTTCTTCCAAA
1 ATCCACTGATTAATGATATCCCAACTACTCTAGCTAGCAAATTATTAAGTCTTTCTTCCAAA
617536 CACCTAATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (68 bp):
ATCCACTGATTAATGATATCCCAACTACTCTAGCTAGCAAATTATTAAGTCTTTCTTCCAAATAC
GTA
Found at i:619086 original size:36 final size:36
Alignment explanation
Indices: 619011--619087 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
619001 ATTATTTTTA
* *
619011 AAAAATAAAAAAATTATTTTTAAAATTTTTATATAT
1 AAAAATAAAAAAATTATTTTTAAAATCTATATATAT
* * *
619047 AAAAATTAAAAAATTATTTTTTAAAA-CTATATCTCT
1 AAAAATAAAAAAATTA-TTTTTAAAATCTATATATAT
619083 AAAAA
1 AAAAA
619088 GTTTTAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (36 bp):
AAAAATAAAAAAATTATTTTTAAAATCTATATATAT
Found at i:623095 original size:21 final size:21
Alignment explanation
Indices: 623077--623134 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
623067 CAGGTGTATA
623077 ATACTATTGATATTATGTACAT
1 ATACTATT-ATATTATGTACAT
*
623099 ATATTATTATATTATGTACAT
1 ATACTATTATATTATGTACAT
623120 ATACTATTATATTAT
1 ATACTATTATATTAT
623135 TATATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (21 bp):
ATACTATTATATTATGTACAT
Found at i:623680 original size:21 final size:20
Alignment explanation
Indices: 623647--623699 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
623637 AGTATGCTAT
*
623647 TATATTATAATATAAATGTA
1 TATATTATAATATAAATATA
* *
623667 TATAGTTATGATATATATATA
1 TATA-TTATAATATAAATATA
623688 TATATATATAAT
1 TATAT-TATAAT
623700 CTATATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (20 bp):
TATATTATAATATAAATATA
Found at i:623854 original size:18 final size:18
Alignment explanation
Indices: 623824--623872 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
623814 GGATAAGTAT
623824 ATTTATATT-ATTAGAGT-G
1 ATTTA-ATTAATTA-AGTCG
623842 ATTTAATTAATTAAGTCG
1 ATTTAATTAATTAAGTCG
*
623860 ATTAAATT-ATTAA
1 ATTTAATTAATTAA
623873 ATATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (18 bp):
ATTTAATTAATTAAGTCG
Found at i:626881 original size:6 final size:7
Alignment explanation
Indices: 626859--626890 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
626849 CGAAAGTCAC
626859 AAATTTT
1 AAATTTT
626866 AAATTTT
1 AAATTTT
*
626873 AAATTTA
1 AAATTTT
626880 AAATTTT
1 AAATTTT
626887 AAAT
1 AAAT
626891 CATAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:626900 original size:21 final size:21
Alignment explanation
Indices: 626859--626901 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
626849 CGAAAGTCAC
**
626859 AAATTTTAAATTTTAAATTTA
1 AAATTTTAAATCATAAATTTA
*
626880 AAATTTTAAATCATAATTTTA
1 AAATTTTAAATCATAAATTTA
626901 A
1 A
626902 TAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTTTAAATCATAAATTTA
Found at i:628230 original size:13 final size:13
Alignment explanation
Indices: 628212--628236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
628202 AGTCACAAAT
628212 TTTAAATTTTTAA
1 TTTAAATTTTTAA
628225 TTTAAATTTTTA
1 TTTAAATTTTTA
628237 TATCATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAAATTTTTAA
Found at i:628849 original size:67 final size:67
Alignment explanation
Indices: 628740--628867 Score: 211
Period size: 67 Copynumber: 1.9 Consensus size: 67
628730 ATAGCGCAAG
* * *
628740 CTAGCAAGAGGTAGGTCTAAGGGTGCTTCACTTATTATTGATAACACAACTACTCTAGCTAACAA
1 CTAGCAAGAGGTAGGTCTAAGGGTGCTCCACTTATTAATGATAACACAACGACTCTAGCTAACAA
628805 CT
66 CT
* *
628807 CTAGCAAGAGGTAGGTCTAAGTGTGCTCCACTTATTAATGATAACCCAACGACTCTAGCTA
1 CTAGCAAGAGGTAGGTCTAAGGGTGCTCCACTTATTAATGATAACACAACGACTCTAGCTA
628868 GCAAATTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 56 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (67 bp):
CTAGCAAGAGGTAGGTCTAAGGGTGCTCCACTTATTAATGATAACACAACGACTCTAGCTAACAA
CT
Found at i:630439 original size:21 final size:21
Alignment explanation
Indices: 630414--630466 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
630404 TATAGTCAAT
630414 AATTATTTTTAAAAAATAAAA
1 AATTATTTTTAAAAAATAAAA
*
630435 AATTATCTTTAAAAAATAAAA
1 AATTATTTTTAAAAAATAAAA
630456 AATTATTTTTA
1 AATTATTTTTA
630467 TAAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTATTTTTAAAAAATAAAA
Found at i:633621 original size:2 final size:2
Alignment explanation
Indices: 633616--633650 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
633606 TGTGTGTATG
633616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
633651 GTAAGGTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:634958 original size:25 final size:25
Alignment explanation
Indices: 634930--634980 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
634920 TAGTTTGTGT
634930 TTTTCAATCCTTATG-TTTCTAACGG
1 TTTTCAATCCTTATGCTTT-TAACGG
* *
634955 TTTTCAATCTTTGTGCTTTTAACGG
1 TTTTCAATCCTTATGCTTTTAACGG
634980 T
1 T
634981 AAGAAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.51
Consensus pattern (25 bp):
TTTTCAATCCTTATGCTTTTAACGG
Found at i:635032 original size:6 final size:6
Alignment explanation
Indices: 635011--635045 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
635001 GTTAATGTTG
* *
635011 AATATA TATTTA AATATA AATATA AATATA AATAT
1 AATATA AATATA AATATA AATATA AATATA AATAT
635046 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
AATATA
Found at i:635916 original size:26 final size:27
Alignment explanation
Indices: 635877--635928 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
635867 ATAACATAGG
635877 AAAAAAATTAAAATATAATAT-AACAT
1 AAAAAAATTAAAATATAATATGAACAT
*
635903 AAAAAAA-TATAAATATGATATGAACA
1 AAAAAAATTA-AAATATAATATGAACA
635929 CGATATGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 17 0.74
27 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAAATTAAAATATAATATGAACAT
Found at i:637024 original size:19 final size:19
Alignment explanation
Indices: 636997--637038 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
636987 TATCAGAATT
*
636997 TATATAAAATGAAT-TAATA
1 TATAAAAAAT-AATATAATA
*
637016 TATAAAAAATTATATAATA
1 TATAAAAAATAATATAATA
637035 TATA
1 TATA
637039 TATAATGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TATAAAAAATAATATAATA
Found at i:637026 original size:15 final size:15
Alignment explanation
Indices: 636991--637031 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
636981 CAAATATATC
636991 AGAATT-TATATAAA
1 AGAATTATATATAAA
637005 ATGAATTAATATATAAA
1 A-GAATT-ATATATAAA
637022 A-AATTATATA
1 AGAATTATATA
637032 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.25
15 9 0.38
17 9 0.38
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
AGAATTATATATAAA
Found at i:637126 original size:16 final size:17
Alignment explanation
Indices: 637107--637144 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
637097 CACAAATATA
637107 AAAAATTAAATAAAA-T
1 AAAAATTAAATAAAATT
*
637123 AAAAATTAAGTAAAATT
1 AAAAATTAAATAAAATT
637140 AAAAA
1 AAAAA
637145 AAAGGTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAATTAAATAAAATT
Done.