Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold414
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: 2018024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:481720 original size:11 final size:10
Alignment explanation
Indices: 481699--481737 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
481689 GGAAAAGAGA
481699 AAAACAAAAAC
1 AAAA-AAAAAC
481710 AAAAAAGAAAC
1 AAAAAA-AAAC
*
481721 AAAAAAAAAG
1 AAAAAAAAAC
481731 AAAAAAA
1 AAAAAAA
481738 CAAAGGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 12 0.46
11 14 0.54
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:481722 original size:17 final size:18
Alignment explanation
Indices: 481691--481741 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
481681 AAATCAAAGG
*
481691 AAAAGAGAAAAACAAAAA
1 AAAAGAAAAAAACAAAAA
* *
481709 CAAA-AAAGAAACAAAAA
1 AAAAGAAAAAAACAAAAA
481726 AAAAGAAAAAAACAAA
1 AAAAGAAAAAAACAAA
481742 GGAAAGAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAACAAAAA
Found at i:481749 original size:17 final size:15
Alignment explanation
Indices: 481704--481741 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
481694 AGAGAAAAAC
481704 AAAAACAAAAAAGAA
1 AAAAACAAAAAAGAA
*
481719 ACAAA-AAAAAAGAA
1 AAAAACAAAAAAGAA
481733 AAAAACAAA
1 AAAAACAAA
481742 GGAAAGAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAGAA
Found at i:482964 original size:22 final size:22
Alignment explanation
Indices: 482936--482980 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
482926 ATTTCATCAT
482936 TGATAGTTCTCTATGTATCTAA
1 TGATAGTTCTCTATGTATCTAA
*
482958 TGATAGTTCTTTATGTATCTAA
1 TGATAGTTCTCTATGTATCTAA
482980 T
1 T
482981 ATTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (22 bp):
TGATAGTTCTCTATGTATCTAA
Found at i:483994 original size:13 final size:13
Alignment explanation
Indices: 483951--483997 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
483941 CGGTTTTTGT
*
483951 TTCATATATTTCT
1 TTCATATATTTCA
483964 TTCATATATTT-A
1 TTCATATATTTCA
483976 --CAATATATTTCA
1 TTC-ATATATTTCA
483988 TTCATATATT
1 TTCATATATT
483998 CATATTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
10 1 0.03
11 8 0.28
12 1 0.03
13 18 0.62
14 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (13 bp):
TTCATATATTTCA
Found at i:495428 original size:2 final size:2
Alignment explanation
Indices: 495421--495450 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
495411 GCTTAGACAA
*
495421 AT AT AT AT AC 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
495451 TTGTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:496443 original size:14 final size:14
Alignment explanation
Indices: 496404--496445 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
496394 TTTTCTAGTA
*
496404 AATTTATAATTTA-
1 AATTTTTAATTTAT
*
496417 AATTTTAATATTTAT
1 AATTTTTA-ATTTAT
496432 AATTTTTAATTTAT
1 AATTTTTAATTTAT
496446 CGTATTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 11 0.46
15 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTTAATTTAT
Found at i:497851 original size:27 final size:25
Alignment explanation
Indices: 497821--497873 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 25
497811 TTATTATATT
497821 TTATTATAATTATAAATATAATAAATA
1 TTATTATAA-T-TAAATATAATAAATA
*
497848 TTATTATAATTAATTATAATAAATA
1 TTATTATAATTAAATATAATAAATA
497873 T
1 T
497874 CAACTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.60
26 1 0.04
27 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATTATAATTAAATATAATAAATA
Found at i:504628 original size:38 final size:37
Alignment explanation
Indices: 504557--504655 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 37
504547 AATTTTTATT
* ** *
504557 AATT-ATAAACATTTAATATGAAT-AATCTGAATGGA
1 AATTAATAAAAATTTAATCCGAATGAATCTAAATGGA
*
504592 TATTAAGTAAAAATTTAATCCGAATGAATCTAAATGGA
1 AATTAA-TAAAAATTTAATCCGAATGAATCTAAATGGA
**
504630 AATTAATATGAA--TAATCCGAATGAAT
1 AATTAATAAAAATTTAATCCGAATGAAT
504656 AATCTGAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
35 17 0.32
36 1 0.02
37 19 0.36
38 16 0.30
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.32
Consensus pattern (37 bp):
AATTAATAAAAATTTAATCCGAATGAATCTAAATGGA
Found at i:504660 original size:38 final size:40
Alignment explanation
Indices: 504574--504667 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 40
504564 AACATTTAAT
*
504574 ATGAATAATCTGAATGGATATTAAGTAAAAATTTAATCCGA
1 ATGAATAATCTGAATGGAAATTAAGTAAAAA-TTAATCCGA
* **
504615 ATG---AATCTAAATGGAAATTAA-TATGAA-TAATCCGA
1 ATGAATAATCTGAATGGAAATTAAGTAAAAATTAATCCGA
504650 ATGAATAATCTGAATGGA
1 ATGAATAATCTGAATGGA
504668 TCGAGAGTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
35 11 0.24
37 4 0.09
38 27 0.60
41 3 0.07
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (40 bp):
ATGAATAATCTGAATGGAAATTAAGTAAAAATTAATCCGA
Found at i:507653 original size:107 final size:108
Alignment explanation
Indices: 507508--507712 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 108
507498 AAAAAAAAAT
** * *
507508 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGATTGGAGTATCCCCGAGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* *
507573 TTTTGG-AATAAAGCCGGGGTTAGAGTATCCCCTCGGAAGTAA
66 TTTTGGAAATAAAACCGGAGTTAGAGTATCCCCTCGGAAGTAA
* * * * * ***
507615 CGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTAT
1 CGGGATTGGAGTATCCCCGAGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* *
507680 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
66 TTTTGGAAATAAAACCGGAGTTAGAGTATCCCC
507713 GATTAAAGGT
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
107 59 0.73
108 22 0.27
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (108 bp):
CGGGATTGGAGTATCCCCGAGAAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTTTGGAAATAAAACCGGAGTTAGAGTATCCCCTCGGAAGTAA
Found at i:507710 original size:52 final size:51
Alignment explanation
Indices: 507646--508032 Score: 273
Period size: 52 Copynumber: 7.4 Consensus size: 51
507636 AAAATAACGA
* * * *
507646 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAATCGG
* * ** * *
507698 AGTTGGAGTATCCCCGATTAAAGGTAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * *
507750 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * *
507802 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
** * * *** * *
507853 GGTTGGAGTATCCCC---TCGGAAATAACGGGGTTGGAGTATCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TTAGTGT-TTTGGA-AATAAAATCGG
* * *
507907 GGTTGGAGTATCCCCGATTGTAAAGAAATTGGTGTTTTTTTGGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAA-AAATTAGTG---TTTT-GGAAATAAAATCGG
* *
507963 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAATCGG
* *
508014 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
508033 GTGGAGAATT
Statistics
Matches: 261, Mismatches: 53, Indels: 43
0.73 0.15 0.12
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 69 0.26
52 104 0.40
53 9 0.03
54 23 0.09
55 18 0.07
56 25 0.10
57 5 0.02
58 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:507856 original size:263 final size:264
Alignment explanation
Indices: 507536--508037 Score: 789
Period size: 263 Copynumber: 1.9 Consensus size: 264
507526 TCGAAAATAA
*
507536 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTTGGAATAAAGCCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTTGGAATAAAGCCGGGGTTAGAGTAT
* *
507601 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATAAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAAATAACGGGGTTGGAGTAT-CCCGAT-AAATAACGAGGTTGGAGTATCCCCGATTG
* *
507666 TGAA-AAATT-G-GTATTTTT-GGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGTAAAT
129 TAAAGAAATTGGTGTATTTTTGGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAAT
* * *
507727 TGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
193 TAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCA
507792 ATAAAAC
258 ATAAAAC
* * *
507799 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTTGG-AATAAAGCCGGGGTTAGAGTA
* * *
507863 TCCCCTCGGAAATAACGGGGTTGGAGTATCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
65 TCCCCTCGGAAATAACGGGGTTGGAGTATCCCGATAAATAACGAGGTTGGAGTATCCCCGATTGT
* *
507928 AAAGAAATTGGTGTTTTTTTGGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTA
130 AAAGAAATTGGTGTATTTTTGGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTA
507993 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
195 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
508038 GAATTGGGAA
Statistics
Matches: 218, Mismatches: 16, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
261 28 0.13
262 17 0.08
263 82 0.38
264 56 0.26
265 35 0.16
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (264 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATCAATATTTTTGGAATAAAGCCGGGGTTAGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCGATAAATAACGAGGTTGGAGTATCCCCGATTGTA
AAGAAATTGGTGTATTTTTGGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAG
TGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
AAAC
Found at i:507877 original size:31 final size:28
Alignment explanation
Indices: 507850--507921 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 28
507840 GAAATAAAGT
507850 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
* *
507878 CGGGGTTGGAGTATCCCGAT--G-ATTAA
1 CGGGGTTGGAGTATCCC-CTCGGAAATAA
507904 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
507922 GATTGTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 21 0.52
27 1 0.03
28 17 0.43
29 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAA
Found at i:507975 original size:56 final size:51
Alignment explanation
Indices: 507908--508034 Score: 164
Period size: 51 Copynumber: 2.4 Consensus size: 51
507898 GATTAACGGG
* *
507908 GTTGGAGTATCCCCGATTGTAAAGAAATTGGTGTTTTTTTGGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAA-AAATTAGTG---TTTT-GAAAATAAAATCGGA
* *
507964 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTGAAAATAAAATCGGA
*
508015 GTTGGAATATCCCCGATTGT
1 GTTGGAGTATCCCCGATTGT
508035 GGAGAATTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
51 32 0.49
52 4 0.06
55 8 0.12
56 21 0.32
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:510418 original size:13 final size:13
Alignment explanation
Indices: 510400--510425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
510390 ACAAAGATCC
510400 ATGTATCGATACA
1 ATGTATCGATACA
510413 ATGTATCGATACA
1 ATGTATCGATACA
510426 CAGAAAAATG
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:510437 original size:33 final size:33
Alignment explanation
Indices: 510379--510445 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
510369 AAAATTTCCA
*** *
510379 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
*
510412 AATGTATCGATACACAGAAAAATGTATCAATAC
1 AATGTATCGATACAAAGAAAAATGTATCAATAC
510445 A
1 A
510446 TTTCCTTAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCAATAC
Found at i:510560 original size:21 final size:21
Alignment explanation
Indices: 510536--510612 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
510526 GTTTGGACCC
* *
510536 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
* *
510557 TGTATCAATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
510578 TGCATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
510599 TGTATCGATACATT
1 TGTATCGATACATT
510613 TGGATAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 3 0.06
21 44 0.94
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:512182 original size:23 final size:25
Alignment explanation
Indices: 512134--512184 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
512124 CCACATCGTC
512134 AAAACGACACAAAAAAAAAACCGAAA
1 AAAACGACACAAAAAAAAAA-CGAAA
512160 AAAACGA-A-AAAAAGAAAAA-GAAA
1 AAAACGACACAAAAA-AAAAACGAAA
512183 AA
1 AA
512185 GGAGGGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.25
24 5 0.21
25 6 0.25
26 7 0.29
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAACGACACAAAAAAAAAACGAAA
Found at i:518621 original size:168 final size:168
Alignment explanation
Indices: 518289--518622 Score: 433
Period size: 167 Copynumber: 2.0 Consensus size: 168
518279 AAATTCTAGC
* *
518289 TAAAAACAACGTTTTTAATTATTTTGGAAAATGAATTTAAAGTTTTTGGATATAATAATTAAATT
1 TAAAAACAACGTTTTTAATTATTTTGGAAAATGAATTTAAAGTTTTCGGACATAATAATTAAATT
* * * *
518354 AATATATAGTTGATGTAATGATTTAATTTTTAAATAAATAAATTTAAAGTAAAACTTTTATTATT
66 AATATATAATTAATATAATGATTCAATTTTTAAATAAATAAATTTAAAGTAAAACTTTTATTATT
* * * **
518419 ATAATAATTATATAAAATTTCTGTTAAATTAAGACAGT
131 ATAAAAATCATACAAAATTTCTAATAAATTAAGACAGT
* *
518457 TAAAAACAATGTTTTTAATTGA-TTTGGAAAATGAATTTAAAG-TTTCGGACATTATAATTAAAT
1 TAAAAACAACGTTTTTAATT-ATTTTGGAAAATGAATTTAAAGTTTTCGGACATAATAATTAAAT
* * * *
518520 TAGTTTATAATTAATATAATGATTCAATTTTTAAGTAAATAAATTTAAAATTAAAA-TTTTATTA
65 TAATATATAATTAATATAATGATTCAATTTTTAAATAAATAAATTT-AAAGTAAAACTTTTATTA
* *
518584 TTATAACAAATCATACAAGATTTGC-AATAATTTAAGACA
129 TTATAA-AAATCATACAAAATTT-CTAATAAATTAAGACA
518623 AAATATAAAA
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
167 71 0.50
168 70 0.49
169 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (168 bp):
TAAAAACAACGTTTTTAATTATTTTGGAAAATGAATTTAAAGTTTTCGGACATAATAATTAAATT
AATATATAATTAATATAATGATTCAATTTTTAAATAAATAAATTTAAAGTAAAACTTTTATTATT
ATAAAAATCATACAAAATTTCTAATAAATTAAGACAGT
Found at i:520242 original size:30 final size:30
Alignment explanation
Indices: 520206--520264 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
520196 AGATGGGAAA
*
520206 CATAGAGATGTACAATGACCTCTGGATTTT
1 CATAGAGATGTACAATGACCTCTAGATTTT
520236 CATAGAGATGTACAATGACCTCTAGATTT
1 CATAGAGATGTACAATGACCTCTAGATTT
520265 CACTTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (30 bp):
CATAGAGATGTACAATGACCTCTAGATTTT
Found at i:522897 original size:49 final size:51
Alignment explanation
Indices: 522844--522956 Score: 176
Period size: 50 Copynumber: 2.3 Consensus size: 51
522834 ATTTACCTGC
* * * *
522844 ATGTATCAATACATTTGGGT-AAAATCTAGAATGTATCGATACAATGAA-G
1 ATGTATCGATACATCTGGGTAAAAACCTAGAATGTATCGATACAATGAATA
522893 ATGTATCGATACATCTGGGTAAAAACCTAGAATGTATCGATACAATGAATA
1 ATGTATCGATACATCTGGGTAAAAACCTAGAATGTATCGATACAATGAATA
522944 ATGTATCGATACA
1 ATGTATCGATACA
522957 AATAGTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 18 0.31
50 27 0.47
51 13 0.22
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATCTGGGTAAAAACCTAGAATGTATCGATACAATGAATA
Found at i:522965 original size:50 final size:50
Alignment explanation
Indices: 522864--522967 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 50
522854 ACATTTGGGT
* * ** *
522864 AAAATCTAGAATGTATCGATACAATGAAGATGTATCGATACATCTGGGTA
1 AAAACCTAGAATGTATCGATACAATGAAAATGTATCGATACAAATGAGTA
522914 AAAACCTAGAATGTATCGATACAATGAATAATGTATCGATACAAAT-AGTA
1 AAAACCTAGAATGTATCGATACAATGAA-AATGTATCGATACAAATGAGTA
522964 AAAA
1 AAAA
522968 TTTGAAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 34 0.71
51 14 0.29
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (50 bp):
AAAACCTAGAATGTATCGATACAATGAAAATGTATCGATACAAATGAGTA
Found at i:523488 original size:11 final size:11
Alignment explanation
Indices: 523472--523508 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
523462 TTATTACTTT
523472 TTATTTATAAA
1 TTATTTATAAA
* *
523483 TTATTTTTAAT
1 TTATTTATAAA
523494 TTATTTATAAA
1 TTATTTATAAA
523505 TTAT
1 TTAT
523509 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:523743 original size:298 final size:297
Alignment explanation
Indices: 523352--524003 Score: 1038
Period size: 298 Copynumber: 2.2 Consensus size: 297
523342 TACATATATT
* *
523352 ATTTTTCAGTAATGACTTAAATGCGAGCTTTT-TTTATCTGTAAAATGACCAAGAAAAAATTTAT
1 ATTTTTCAGTAATGACTTAAATACGAG-TTTTCTTTATCTGTAAAATGACTAAGAAAAAATTTAT
*
523416 TGTACATATATTATTTTTATTAAAATTAATTAATATTGTGCATGTATTATTACTTTTTATTTATA
65 TGTACATATATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATA
523481 AATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
130 AATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
* **
523546 ATGTATTATTTTTATAATTGATAGAACTTAAATTTATCTTAGCCAACAATATTTTACTTTTTTCG
195 ATATATTATTTTTATAATTGATAGAACTTAAATTTATCTTAGCCAACAATAAATTACTTTTTTCG
* *
523611 ATAACGACTTATTTTGGATTTACAGACGCACACATTTC
260 ATAACGACTTATTTCGGATTTACAAACGCACACATTTC
* * * *
523649 ATTTTTCGGTAACGACTTAAATAAGAGTTTTCCTTTATCTGTAAAATAACTAAGAAAAAATTTAT
1 ATTTTTCAGTAATGACTTAAATACGAGTTTT-CTTTATCTGTAAAATGACTAAGAAAAAATTTAT
* * * *
523714 TGTACATGTATTATTTTTATTAAAATTAATTAATTTTGTGCATGCGTTATTATTTTTTATTTATA
65 TGTACATATATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATA
*
523779 AATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTGC
130 AATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTAC
* * *
523844 ATATATTATTTTTGTAATTGATAGAACTTAAATTTATGTTAGCCAATAATAAATTACTTTTTTCG
195 ATATATTATTTTTATAATTGATAGAACTTAAATTTATCTTAGCCAACAATAAATTACTTTTTTCG
* *
523909 ATAACGACTTATTTCGGATTTACAAATGCACACATTTT
260 ATAACGACTTATTTCGGATTTACAAACGCACACATTTC
* * *
523947 ATTTTTTAGTAATAACTTAAATACGAGCTTTCTTTTATCTGTAAAATGACTAA-AAAA
1 ATTTTTCAGTAATGACTTAAATACGAGTTTTC-TTTATCTGTAAAATGACTAAGAAAA
524004 TTTTTTTCTC
Statistics
Matches: 323, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
296 4 0.01
297 28 0.09
298 291 0.90
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (297 bp):
ATTTTTCAGTAATGACTTAAATACGAGTTTTCTTTATCTGTAAAATGACTAAGAAAAAATTTATT
GTACATATATTATTTTTATTAAAATTAATTAATATTGTGCATGCATTATTACTTTTTATTTATAA
ATTATTTTTAATTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAATATTGTACA
TATATTATTTTTATAATTGATAGAACTTAAATTTATCTTAGCCAACAATAAATTACTTTTTTCGA
TAACGACTTATTTCGGATTTACAAACGCACACATTTC
Found at i:523784 original size:11 final size:11
Alignment explanation
Indices: 523770--523806 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
523760 TTATTATTTT
523770 TTATTTATAAA
1 TTATTTATAAA
* *
523781 TTATTTTTAAT
1 TTATTTATAAA
523792 TTATTTATAAA
1 TTATTTATAAA
523803 TTAT
1 TTAT
523807 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:527554 original size:31 final size:31
Alignment explanation
Indices: 527494--527554 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
527484 TTTAAAACAG
* *
527494 AATCTATGCATTAGTCCATTTTTCTAATTTC
1 AATCCATGCATTAGTCCATTTTACTAATTTC
*
527525 AATCCATGCATTAGTCTATTCTTAC-AATTT
1 AATCCATGCATTAGTCCATT-TTACTAATTT
527555 GGCATTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.46
Consensus pattern (31 bp):
AATCCATGCATTAGTCCATTTTACTAATTTC
Found at i:527960 original size:126 final size:125
Alignment explanation
Indices: 527777--528080 Score: 443
Period size: 126 Copynumber: 2.4 Consensus size: 125
527767 AAAAAATTTA
*
527777 TTTTTTAAAATAAAAAATATTAAATAAAA-AATAAAAAGTATTTATTATTATTATTTTTTAATAA
1 TTTTTTAAAATAAAAAAT-TT---TAAAATAA-AAAAAGT-TTT-TTATTATAATTTTTTAATAA
* * *
527841 AATTAAAAATAATATTTAATTAAGTTTAAAAAA-TTACATTAACAAATTAAAATATTAATTATTA
59 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTA
527905 TG
124 TG
*
527907 TTTTTATAAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAA-TTTTTAATACAATAA
1 TTTTT-T-AAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTTAATAAAATAA
527971 AAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
64 AAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
* *
528033 TTTTTTAAAATAAAAAATTTTAAATTAAAAAAGGTTTTTTATTATAAT
1 TTTTTTAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAAT
528081 AATATTTTTT
Statistics
Matches: 162, Mismatches: 7, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
124 39 0.24
125 42 0.26
126 44 0.27
127 3 0.02
128 12 0.07
129 2 0.01
130 5 0.03
131 3 0.02
132 12 0.07
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (125 bp):
TTTTTTAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTTAATAAAATAAAA
AATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
Found at i:527988 original size:125 final size:124
Alignment explanation
Indices: 527777--528080 Score: 441
Period size: 125 Copynumber: 2.4 Consensus size: 124
527767 AAAAAATTTA
*
527777 TTTTTTAAAATAAAAAATATTAAATAAAA-AATAAAAAGTATTTATTATTATTATTTTTTAATAA
1 TTTTTTAAAATAAAAAAT-TT---TAAAATAA-AAAAAGT-TTT-TTATTA-TAATTTTTAATAA
* * *
527841 AATTAAAAATAATATTTAATTAAGTTTAAAAAA-TTACATTAACAAATTAAAATATTAATTATTA
58 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTA
527905 TG
123 TG
*
527907 TTTTTATAAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTAATACAATAAA
1 TTTTT-T-AAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAA
527972 AAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
64 AAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
* *
528033 TTTTTTAAAATAAAAAATTTTAAATTAAAAAAGGTTTTTTATTATAAT
1 TTTTTTAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAAT
528081 AATATTTTTT
Statistics
Matches: 163, Mismatches: 7, Indels: 14
0.89 0.04 0.08
Matches are distributed among these distances:
124 40 0.25
125 44 0.27
126 42 0.26
127 3 0.02
128 12 0.07
129 2 0.01
130 5 0.03
131 3 0.02
132 12 0.07
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (124 bp):
TTTTTTAAAATAAAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAAAA
ATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAAGTAAAATATTAATTAGTATG
Found at i:528062 original size:14 final size:15
Alignment explanation
Indices: 528035--528064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
528025 TTAGTATGTT
528035 TTTTAAAATAAAAAA
1 TTTTAAAATAAAAAA
*
528050 TTTTAAATTAAAAAA
1 TTTTAAAATAAAAAA
528065 GGTTTTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTTAAAATAAAAAA
Found at i:528505 original size:110 final size:114
Alignment explanation
Indices: 528385--528661 Score: 363
Period size: 118 Copynumber: 2.4 Consensus size: 114
528375 AAATATTATT
528385 TTTTAATTTATTAATGTAAATTTTTAAACTTAATTAAATATTATTTTT-ATTTTATTAAAAAATA
1 TTTTAATTTATTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATA
*
528449 ATAATAA-AAA-ATTCT-TTTT-A-TTTTTA-TAAAAACATAATAATTAATA
66 ACAATAATAAACATTCTATTTTAATTTTTTATTAAAAA-AT--TAATTAATA
*
528495 TTTTAATTTATTAATGTAATTTTTTTAAAC-TAATTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTATTAATGTAA-ATTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
* *
528559 AACAATAATAAACCCTTTTTATTTTAATTTTTTATTTTAAAAAATTAATTAATA
65 AACAATAATAAA--CATTCTATTTTAATTTTTTA--TTAAAAAATTAATTAATA
* *
528613 TTTTAATTTATTAATATAAATTTTTTAAAATTAATTAAATATTATTTTT
1 TTTTAATTTATTAATGTAAA-TTTTTAAACTTAATTAAATATTATTTTT
528662 TATTAAAAAT
Statistics
Matches: 146, Mismatches: 7, Indels: 19
0.85 0.04 0.11
Matches are distributed among these distances:
110 37 0.25
111 31 0.21
112 3 0.02
115 3 0.02
116 4 0.03
117 1 0.01
118 41 0.28
119 18 0.12
120 2 0.01
121 6 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (114 bp):
TTTTAATTTATTAATGTAAATTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAATA
ACAATAATAAACATTCTATTTTAATTTTTTATTAAAAAATTAATTAATA
Found at i:528592 original size:13 final size:13
Alignment explanation
Indices: 528574--528598 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
528564 TAATAAACCC
528574 TTTTTATTTTAAT
1 TTTTTATTTTAAT
528587 TTTTTATTTTAA
1 TTTTTATTTTAA
528599 AAAATTAATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:528616 original size:20 final size:20
Alignment explanation
Indices: 528591--528655 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
528581 TTTAATTTTT
528591 TATTTTAAAAAATTAATTAA
1 TATTTTAAAAAATTAATTAA
***
528611 TATTTTAATTTATTAATATAA
1 TATTTTAAAAAATTAAT-TAA
**
528632 -ATTTTTTAAAATTAATTAAA
1 TATTTTAAAAAATTAATT-AA
528652 TATT
1 TATT
528656 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.79
21 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTTAAAAAATTAATTAA
Found at i:528649 original size:24 final size:24
Alignment explanation
Indices: 528617--528663 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
528607 TTAATATTTT
*
528617 AATTTATT-AATATAAATTTTTTAA
1 AATTAATTAAATAT-AATTTTTTAA
*
528641 AATTAATTAAATATTATTTTTTA
1 AATTAATTAAATATAATTTTTTA
528664 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AATTAATTAAATATAATTTTTTAA
Found at i:528683 original size:6 final size:7
Alignment explanation
Indices: 528663--528688 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
528653 ATTATTTTTT
528663 ATTAAAA
1 ATTAAAA
528670 ATTAAAA
1 ATTAAAA
528677 ATTAAAA
1 ATTAAAA
528684 ATTAA
1 ATTAA
528689 TACATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATTAAAA
Found at i:528721 original size:110 final size:110
Alignment explanation
Indices: 528385--528721 Score: 242
Period size: 110 Copynumber: 3.0 Consensus size: 110
528375 AAATATTATT
* *
528385 TTTTAATTTATTAATGTAAA-TTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATA
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTA---TT-TTTTATTAAAAATTA
* * * ** *** *
528449 ATAATAAAAAATT-CT-TTTTATT-TTTA-TAAAAACATAATAATTAATA
62 AAAATTAAAAATTAATACATTATTATTTATTAAAATTTTAA-ATTTAATA
* * * **
528495 TTTTAATTTATTAATGT-AATTTTTTTAAACTAATTAAATATTATTTTTAATT--TTATTAAAAA
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTAAAAATTAAAAA
* * * * ***
528557 ATAACAA-TAATAAACCCTTTTTATTTTAATTTTTTATTTTAAAAAATTAATTAATA
66 TTAAAAATTAAT--A-CATTATTA-TTT-A-TTAAAATTTT---AAA-T--TTAATA
*
528613 TTTTAATTTATTAATATAAATTTTTTAAAATTAATTAAATATTATTTTTTATTAAAAATTAAAAA
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTAAAAATTAAAAA
528678 TTAAAAATTAATACATTATTATTTATTAAAATTTTAAATTTAAT
66 TTAAAAATTAATACATTATTATTTATTAAAATTTTAAATTTAAT
528722 TAATTTATAA
Statistics
Matches: 171, Mismatches: 35, Indels: 42
0.69 0.14 0.17
Matches are distributed among these distances:
103 1 0.01
104 11 0.06
106 6 0.04
107 2 0.01
108 4 0.02
109 2 0.01
110 45 0.26
111 1 0.01
112 1 0.01
113 6 0.04
115 1 0.01
116 9 0.05
117 1 0.01
118 25 0.15
119 38 0.22
120 1 0.01
121 13 0.08
122 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (110 bp):
TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTAAAAATTAAAAA
TTAAAAATTAATACATTATTATTTATTAAAATTTTAAATTTAATA
Found at i:528726 original size:118 final size:113
Alignment explanation
Indices: 528385--528725 Score: 345
Period size: 119 Copynumber: 3.0 Consensus size: 113
528375 AAATATTATT
*
528385 TTTTAATTTATTAATGTAAA-TTTTTAAACTTAATTAAATATTA-TTTTTATTTTATTAAAAAAT
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAAAT
* * * * ***
528448 AATAATAAAAAATTCTT-TTTATTTTTATAAAAACATAA-TAATTAATA
66 AAAAATAATACATTATTATTTATTTTTATTTTAA-ATAATTAATTAATA
* * *
528495 TTTTAATTTATTAATGT-AATTTTTTTAAACTAATTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAAAT
* * * *
528559 AACAATAATAAACCCTTTTTATTTTAATTTTTTATTTTAAAAAATTAATTAATA
66 AAAAATAAT--A-CATTATTA-TTT-A-TTTTTATTTTAAATAATTAATTAATA
* **
528613 TTTTAATTTATTAATATAAATTTTTTAAAATTAATTAAATATTATTTTTTATTAAAAATTAAAAA
1 TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATT--TTATTAAAAA
* ***
528678 TTAAAAATTAATACATTATTATTTATTAAAATTTTAAAT--TTAATTAAT
64 ATAAAAA-TAATACATTATTATTTATTTTTATTTTAAATAATTAATTAAT
528726 TTATAAAAAA
Statistics
Matches: 190, Mismatches: 27, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
109 2 0.01
110 37 0.19
111 26 0.14
113 1 0.01
114 13 0.07
116 13 0.07
117 5 0.03
118 37 0.19
119 38 0.20
120 1 0.01
121 13 0.07
122 4 0.02
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (113 bp):
TTTTAATTTATTAATGTAAATTTTTTAAAATTAATTAAATATTATTTTTTATTTTATTAAAAAAT
AAAAATAATACATTATTATTTATTTTTATTTTAAATAATTAATTAATA
Found at i:530056 original size:36 final size:38
Alignment explanation
Indices: 530004--530080 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
529994 TTTATTAATT
530004 TTTTAATATAATTTTAATTATTATTTAAC-A-AATATAA
1 TTTTAATATAATTTTAATTATT-TTTAACGACAATATAA
*
530041 TTTTAATA-AATTTTAATTATTTTTAGCGACAATATAA
1 TTTTAATATAATTTTAATTATTTTTAACGACAATATAA
530078 TTT
1 TTT
530081 ATTTATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 5 0.14
36 14 0.38
37 18 0.49
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.52
Consensus pattern (38 bp):
TTTTAATATAATTTTAATTATTTTTAACGACAATATAA
Found at i:530309 original size:24 final size:21
Alignment explanation
Indices: 530259--530299 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
530249 ATCTTATCGT
**
530259 TATAATAATTAATTCAATTAC
1 TATAATAATTAATTTTATTAC
530280 TATAATAATTAATTTTATTA
1 TATAATAATTAATTTTATTA
530300 TCATCATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TATAATAATTAATTTTATTAC
Found at i:531856 original size:18 final size:20
Alignment explanation
Indices: 531835--531875 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
531825 TTTATATGAT
531835 ATATACTAA-AAATATAA-A
1 ATATACTAAGAAATATAATA
**
531853 ATATTTTAAGAAATATAATA
1 ATATACTAAGAAATATAATA
531873 ATA
1 ATA
531876 ATTTTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATACTAAGAAATATAATA
Found at i:531868 original size:19 final size:21
Alignment explanation
Indices: 531844--531882 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
531834 TATATACTAA
531844 AAATATAA-AAT-ATTTTAAG
1 AAATATAATAATAATTTTAAG
531863 AAATATAATAATAATTTTAA
1 AAATATAATAATAATTTTAA
531883 AAGATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAATATAATAATAATTTTAAG
Found at i:532071 original size:2 final size:2
Alignment explanation
Indices: 532066--532120 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
532056 ACACACACAC
*
532066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
*
532109 AT AT AC AT AT AT
1 AT AT AT AT AT AT
532121 CAACTTTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 47 0.98
3 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:532800 original size:29 final size:30
Alignment explanation
Indices: 532747--532805 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
532737 TAATAGATGA
532747 AAATTAGTTTTTTTGTTTAATTTTTGGGCT
1 AAATTAGTTTTTTTGTTTAATTTTTGGGCT
532777 AAATTAGTTTTTTTGTTGT-A-TTTTGGGCT
1 AAATTAGTTTTTTTGTT-TAATTTTTGGGCT
532806 TCAAATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 9 0.32
30 18 0.64
31 1 0.04
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.59
Consensus pattern (30 bp):
AAATTAGTTTTTTTGTTTAATTTTTGGGCT
Found at i:537151 original size:17 final size:17
Alignment explanation
Indices: 537131--537177 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
537121 TAAGAGTACT
537131 TAAAATATAAATTTTA-A
1 TAAAA-ATAAATTTTATA
* *
537148 TAAAAATAAAATTTATT
1 TAAAAATAAATTTTATA
537165 TAAAAAATAAATT
1 T-AAAAATAAATT
537178 AAAATTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATAAATTTTATA
Found at i:537169 original size:16 final size:18
Alignment explanation
Indices: 537130--537177 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
537120 TTAAGAGTAC
537130 TTAAAATATAAATTTTAA
1 TTAAAATATAAATTTTAA
* *
537148 -TAAAA-ATAAAATTTAT
1 TTAAAATATAAATTTTAA
*
537164 TTAAAAAATAAATT
1 TTAAAATATAAATT
537178 AAAATTTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 9 0.36
17 10 0.40
18 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATATAAATTTTAA
Found at i:537250 original size:18 final size:18
Alignment explanation
Indices: 537227--537266 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
537217 TTAATTTTTA
537227 ATTAA-TTATATAATATAT
1 ATTAATTTATAT-ATATAT
*
537245 ATTAATTTATATTTATAT
1 ATTAATTTATATATATAT
537263 ATTA
1 ATTA
537267 TATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTAATTTATATATATAT
Found at i:537278 original size:25 final size:25
Alignment explanation
Indices: 537218--537282 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
537208 TTGACTCATT
*
537218 TAATTTTTAATTAATTATATAATATA
1 TAATTTTTTA-TAATTATATAATATA
* * *
537244 T-ATTAATTTATATTTATATATTATA
1 TAATT-TTTTATAATTATATAATATA
537269 TAATTTTTTATAAT
1 TAATTTTTTATAAT
537283 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
25 24 0.77
26 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TAATTTTTTATAATTATATAATATA
Found at i:541578 original size:2 final size:2
Alignment explanation
Indices: 541571--541599 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
541561 TTTTTACCTT
541571 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
541600 TACAAAAGAA
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:542045 original size:20 final size:21
Alignment explanation
Indices: 542020--542059 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
542010 CACCGGAATG
*
542020 AATTATAAT-TATAATAAAAT
1 AATTATAATATAAAATAAAAT
*
542040 AATTATTATATAAAATAAAA
1 AATTATAATATAAAATAAAA
542060 ATAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTATAATATAAAATAAAAT
Found at i:542054 original size:16 final size:15
Alignment explanation
Indices: 542024--542077 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
542014 GGAATGAATT
542024 ATAATTA-TAATAAA
1 ATAATTATTAATAAA
542038 ATAATTATTATATAAA
1 ATAATTATTA-ATAAA
** *
542054 ATAAAAATAAAATAAA
1 ATAATTAT-TAATAAA
542070 ATAATTAT
1 ATAATTAT
542078 GTCATAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 22 0.69
17 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATTATTAATAAA
Found at i:544534 original size:16 final size:16
Alignment explanation
Indices: 544509--544539 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
544499 AACACTAACA
*
544509 TAACATTGAAAACAAC
1 TAACACTGAAAACAAC
544525 TAACACTGAAAACAA
1 TAACACTGAAAACAA
544540 TTTAATTCTC
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:0.58, C:0.19, G:0.06, T:0.16
Consensus pattern (16 bp):
TAACACTGAAAACAAC
Found at i:551478 original size:11 final size:10
Alignment explanation
Indices: 551459--551492 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
551449 TGAAATATTT
551459 TTTATTTTTA
1 TTTATTTTTA
551469 TTTAATTTTTA
1 TTT-ATTTTTA
*
551480 ATTATTTTTA
1 TTTATTTTTA
551490 TTT
1 TTT
551493 TTTATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:551728 original size:29 final size:29
Alignment explanation
Indices: 551696--551760 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
551686 AAAATACTAT
* *
551696 ATATTAATTATAAATTTTTTTT-AAAATCA
1 ATATAAATTAT-AATTTTTTTTCAAAACCA
*
551725 ATATAAATTATTATTTTTTTTCAAAACCA
1 ATATAAATTATAATTTTTTTTCAAAACCA
551754 ATATAAA
1 ATATAAA
551761 CTAAACTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATAAATTATAATTTTTTTTCAAAACCA
Found at i:553461 original size:14 final size:14
Alignment explanation
Indices: 553413--553480 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
553403 ATCAATCAAA
553413 TATTATTTAAT-TAT
1 TATT-TTTAATATAT
* *
553427 TA-TTTTAAAATTT
1 TATTTTTAATATAT
*
553440 TATATTTAATATAT
1 TATTTTTAATATAT
* *
553454 TATTTTTATTATAA
1 TATTTTTAATATAT
**
553468 TAAATTTAATATA
1 TATTTTTAATATA
553481 AATAATATAT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 5 0.12
13 5 0.12
14 31 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTAATATAT
Found at i:554159 original size:16 final size:16
Alignment explanation
Indices: 554138--554171 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
554128 ATATAGAAAA
554138 TTAAATTTAAAATTAT
1 TTAAATTTAAAATTAT
*
554154 TTAAATTTATAATTAT
1 TTAAATTTAAAATTAT
554170 TT
1 TT
554172 TTATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAATTTAAAATTAT
Found at i:554258 original size:2 final size:2
Alignment explanation
Indices: 554253--554281 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
554243 GGTAAAAATT
554253 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
554282 GAGAGAGAAT
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:556718 original size:22 final size:22
Alignment explanation
Indices: 556693--556734 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
556683 TACTGAGACG
*
556693 CTGTAAAGTGCTAACTTGATAA
1 CTGTAAAGTGCCAACTTGATAA
*
556715 CTGTAAGGTGCCAACTTGAT
1 CTGTAAAGTGCCAACTTGAT
556735 TCATATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (22 bp):
CTGTAAAGTGCCAACTTGATAA
Found at i:558128 original size:6 final size:6
Alignment explanation
Indices: 558113--558146 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
558103 AAAAATTAGT
*
558113 AAAAGC AAAAGA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
558147 AAAGGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:558627 original size:24 final size:25
Alignment explanation
Indices: 558600--558646 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
558590 CAAACATAAC
* *
558600 TAACCAAAA-TAAAGATAGAAAGCA
1 TAACAAAAATTAAAAATAGAAAGCA
558624 TAACAAAAATTAAAAATAGAAAG
1 TAACAAAAATTAAAAATAGAAAG
558647 TGTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.66, C:0.09, G:0.11, T:0.15
Consensus pattern (25 bp):
TAACAAAAATTAAAAATAGAAAGCA
Found at i:570620 original size:15 final size:15
Alignment explanation
Indices: 570600--570644 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 15
570590 AAATAAAAAT
570600 AATTAAAAATTATTA
1 AATTAAAAATTATTA
570615 AATTAAAAATTATTTTA
1 AATTAAAAATTA--TTA
*
570632 AAATAAAAATTAT
1 AATTAAAAATTAT
570645 ATTTATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAAAATTATTA
Found at i:570638 original size:17 final size:17
Alignment explanation
Indices: 570603--570649 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
570593 TAAAAATAAT
*
570603 TAAAAATTA--TTAAAT
1 TAAAAATTATTTTAAAA
570618 TAAAAATTATTTTAAAA
1 TAAAAATTATTTTAAAA
570635 TAAAAATTATATTTA
1 TAAAAATTAT-TTTA
570650 TATTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 9 0.32
17 15 0.54
18 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAAATTATTTTAAAA
Found at i:570671 original size:27 final size:28
Alignment explanation
Indices: 570641--570695 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
570631 AAAATAAAAA
570641 TTATATTTATATT-ATTTAT-GTAATTAT
1 TTATATTTA-ATTAATTTATAGTAATTAT
* *
570668 TTATTTTTAATTAATTTATATTAATTAT
1 TTATATTTAATTAATTTATAGTAATTAT
570696 ATAACAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 14 0.58
28 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TTATATTTAATTAATTTATAGTAATTAT
Found at i:573275 original size:20 final size:19
Alignment explanation
Indices: 573250--573298 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
573240 TACAAGCCAA
**
573250 TGTATCGATATAATTTTTTG
1 TGTATCGATA-AATACTTTG
*
573270 TGTATCGATACATACTTTG
1 TGTATCGATAAATACTTTG
573289 TGTATCGATA
1 TGTATCGATA
573299 CAAGTTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (19 bp):
TGTATCGATAAATACTTTG
Found at i:574003 original size:39 final size:40
Alignment explanation
Indices: 573928--574018 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 40
573918 TTTTCTTTCT
**
573928 CCCTTAATTAAAGTAATTTTAACAAATTTGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTTACACATTCTCC
* * *
573968 CCCTTAA-T-AAGATAATTTTAGCAAATTTACGCATTCTTC
1 CCCTTAATTAAAG-TAATTTTAACAAATTTACACATTCTCC
* *
574007 CCTTTTATTAAA
1 CCCTTAATTAAA
574019 AAAAATCTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
38 3 0.07
39 28 0.68
40 8 0.20
41 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (40 bp):
CCCTTAATTAAAGTAATTTTAACAAATTTACACATTCTCC
Found at i:576495 original size:84 final size:84
Alignment explanation
Indices: 576340--576504 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
576330 CATTTTCCAC
* * * * *
576340 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTATTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTACTTTTAAAAGAATTATTCTCTAAAC
576405 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
576424 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTT-CTTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCACTTAATTTACTTTTAAAAGAAT-T-ATTCTCTA
* * *
576486 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
576505 TTCTTTGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 53 0.78
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCACTTAATTTACTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:578566 original size:20 final size:20
Alignment explanation
Indices: 578541--578592 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
578531 TACAAGCCAA
**
578541 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
578561 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
578580 TGTATCGATACAA
1 TGTATCGATACAA
578593 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:581163 original size:13 final size:14
Alignment explanation
Indices: 581140--581168 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
581130 GACTTCTCAA
581140 TTGAGTTATATCTT
1 TTGAGTTATATCTT
581154 TTGA-TTATATCTT
1 TTGAGTTATATCTT
581167 TT
1 TT
581169 AGTGGTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (14 bp):
TTGAGTTATATCTT
Found at i:581831 original size:17 final size:17
Alignment explanation
Indices: 581811--581843 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
581801 GTAATATTTA
581811 GCTAAAGTGAATCTTAG
1 GCTAAAGTGAATCTTAG
*
581828 GCTAAGGTGAATCTTA
1 GCTAAAGTGAATCTTA
581844 CTTAGGGTGA
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:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (17 bp):
GCTAAAGTGAATCTTAG
Found at i:581914 original size:15 final size:16
Alignment explanation
Indices: 581874--581918 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
581864 AAAGTGACAT
* *
581874 TTGGCTAAGATGAGAC
1 TTGGCTAAGGTGAAAC
581890 TTGTGCTAAGGT-AAAC
1 TTG-GCTAAGGTGAAAC
581906 TTGGCTAAGGTGA
1 TTGGCTAAGGTGA
581919 TTTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 7 0.28
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (16 bp):
TTGGCTAAGGTGAAAC
Found at i:585409 original size:52 final size:52
Alignment explanation
Indices: 585339--585459 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
585329 GAAAATTTAT
*
585339 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
585391 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
585443 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
585460 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:585472 original size:52 final size:51
Alignment explanation
Indices: 585339--585479 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
585329 GAAAATTTAT
585339 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
585391 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
585443 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
585480 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:585486 original size:13 final size:13
Alignment explanation
Indices: 585468--585492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
585458 CAAAGATCAG
585468 TGTATCGATACAA
1 TGTATCGATACAA
585481 TGTATCGATACA
1 TGTATCGATACA
585493 TGTGAGTAAT
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:585575 original size:13 final size:13
Alignment explanation
Indices: 585557--585581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
585547 CAAAAAAATA
585557 TGTATCGATACAT
1 TGTATCGATACAT
585570 TGTATCGATACA
1 TGTATCGATACA
585582 ACATTTTATG
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:585577 original size:33 final size:33
Alignment explanation
Indices: 585535--585601 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
585525 AGTAGCTTAA
585535 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
585568 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
585601 A
1 A
585602 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:586620 original size:43 final size:45
Alignment explanation
Indices: 586559--586692 Score: 191
Period size: 43 Copynumber: 2.9 Consensus size: 45
586549 GATGGAAAAT
586559 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
* *
586602 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-ATG-A
*
586650 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
586693 AATGATGATG
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 37 0.46
44 2 0.03
45 1 0.01
46 1 0.01
47 1 0.01
48 3 0.04
49 35 0.44
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
Found at i:586658 original size:49 final size:49
Alignment explanation
Indices: 586516--586702 Score: 233
Period size: 49 Copynumber: 3.9 Consensus size: 49
586506 GATGTCAACG
* *
586516 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
586568 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
586611 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
586660 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATG
586703 AGAAGAGTGA
Statistics
Matches: 119, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
43 36 0.30
44 2 0.02
45 1 0.01
46 1 0.01
48 2 0.02
49 46 0.39
50 1 0.01
51 2 0.02
52 28 0.24
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:586689 original size:92 final size:94
Alignment explanation
Indices: 586515--586692 Score: 306
Period size: 92 Copynumber: 1.9 Consensus size: 94
586505 GGATGTCAAC
586515 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GTGCCAATATGCTGATTCAAG
*
586580 GCCAGCTATATTGGACTTAAAGGTGCCAAT
65 GCCAGCGATATTGGACTTAAAGGTGCCAAT
* *
586610 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA-TGCCAATATGCTGATTCAAGG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
586673 CCAGCGATATTGGACTTAAA
66 CCAGCGATATTGGACTTAAA
586693 AATGATGATG
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
92 40 0.50
94 4 0.05
95 36 0.45
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (94 bp):
GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
CCAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:586852 original size:266 final size:266
Alignment explanation
Indices: 586378--586956 Score: 1070
Period size: 266 Copynumber: 2.2 Consensus size: 266
586368 TTTTAGAGAT
* * *
586378 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATCAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATCAGAAAA
586443 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATGGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATGGGGCCTAAAGATGAGAAAAAGGA
586508 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
*
586573 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
196 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
586638 CTTAAA
261 CTTAAA
* * *
586644 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAGA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATCAGAAAA
* *
586709 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATGGGGCCTAAAGATGAGAAAAAGGA
586774 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
586839 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
196 ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
586904 CTTAAA
261 CTTAAA
586910 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATA-TGGACTTAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
586957 TGGTGCAAGT
Statistics
Matches: 304, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
265 9 0.03
266 295 0.97
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (266 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATCAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATGGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTG
ATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
CTTAAA
Found at i:586924 original size:49 final size:49
Alignment explanation
Indices: 586782--587344 Score: 634
Period size: 49 Copynumber: 11.6 Consensus size: 49
586772 GATGTCAACG
* *
586782 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
586834 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
586877 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
586926 TGCTGATTCAAGGCCAGCGATA-TGGACTTAATGGTGCAAG-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGATGCCAATA
* *
586974 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-AAAAGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA-TGCCAATA
* * * * * *
587023 TGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
587072 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
587121 TGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
587170 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
587219 TGCTGATTCAAGGCCAACGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
587262 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
587314 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
587345 GAGGGGTTGC
Statistics
Matches: 432, Mismatches: 59, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
43 69 0.16
44 5 0.01
45 2 0.00
46 2 0.00
47 4 0.01
48 42 0.10
49 238 0.55
50 3 0.01
51 3 0.01
52 64 0.15
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:587106 original size:98 final size:98
Alignment explanation
Indices: 586781--587344 Score: 827
Period size: 98 Copynumber: 5.8 Consensus size: 98
586771 GGATGTCAAC
* *
586781 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT--AAAA-GTGCCAATATGCTGATTCAAG
586846 GCCAGCTATATTGGACTT-A-----AAGGTGCCAAT
63 GCCAGCTATATTGGACTTAATGGTGAAGGTGCCAAT
*
586876 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAG-TGCCAATATGCTGATTCAAGGC
*
586940 CAGCGATA-TGGACTTAATGGTGCAA-GTGCCAAT
65 CAGCTATATTGGACTTAATGGTG-AAGGTGCCAAT
586973 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCC
*
587038 AGCTATATTGGGCTTAATGGTGAAGGTGCCAAT
66 AGCTATATTGGACTTAATGGTGAAGGTGCCAAT
*
587071 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCC
587136 AGCTATATTGGACTTAATGGTGAAGGTGCCAAT
66 AGCTATATTGGACTTAATGGTGAAGGTGCCAAT
* *
587169 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GATGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAG-TGCCAATATGCTGATTCAAGGC
* *
587233 CAACGATATTGGACTT-A-----AAGGTGCCAAT
65 CAGCTATATTGGACTTAATGGTGAAGGTGCCAAT
*
587261 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT--AAAA-GTGCCAATATGCTGATTCAAG
*
587326 GCCAGCTATATTGGGCTTA
63 GCCAGCTATATTGGACTTA
587345 GAGGGGTTGC
Statistics
Matches: 433, Mismatches: 19, Indels: 33
0.89 0.04 0.07
Matches are distributed among these distances:
91 8 0.02
92 79 0.18
95 71 0.16
96 1 0.00
97 79 0.18
98 195 0.45
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (98 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAAGTGCCAATATGCTGATTCAAGGCC
AGCTATATTGGACTTAATGGTGAAGGTGCCAAT
Found at i:587418 original size:34 final size:34
Alignment explanation
Indices: 587346--587479 Score: 199
Period size: 34 Copynumber: 4.1 Consensus size: 34
587336 TTGGGCTTAG
*
587346 AGGGGTTGCCACCGACTTGTGTGGGCTTT---G-
1 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
* *
587376 -GGG-TTGCCACCAACTTGTGTGGGCTTTGGAGA
1 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
587408 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
1 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
587442 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
1 AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
587476 AGGG
1 AGGG
587480 AGAAAGATGC
Statistics
Matches: 95, Mismatches: 3, Indels: 8
0.90 0.03 0.08
Matches are distributed among these distances:
28 23 0.24
29 3 0.03
31 1 0.01
33 3 0.03
34 65 0.68
ACGTcount: A:0.16, C:0.18, G:0.38, T:0.28
Consensus pattern (34 bp):
AGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGA
Found at i:587513 original size:34 final size:36
Alignment explanation
Indices: 587461--588128 Score: 395
Period size: 34 Copynumber: 19.4 Consensus size: 36
587451 CACCGACTTG
*
587461 TGTGGGCTTTAGAGAAGGGAGAAAGA-TGCCACGGAGT
1 TGTGGGCTTTA-A-AAGGGAAAAAGAGTGCCACGGAGT
* *
587498 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGATT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
587533 TGTGGGCTTTAAAA--GAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
587566 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
587603 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
* **
587637 TGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*** ** * *
587674 TGTAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGT
1 TGT-GG-GCTTTA-A---AAGGG------AA-AAAGA-GTGCCACGGAGT
* **
587724 TGTGGGCTTTGAAAAGGAAAAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAAGG--GAAAAAGAGTGCCACGGAGT
*
587763 TGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
587796 TGTGGGCTTTGAAAA--GAAGAAG-GTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
587830 TGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
587864 TGTGGGCTTT---------AAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* * *
587891 CGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
587928 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
*
587962 TGTGGGC-TT-AAA-CG-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* ** * * *
587989 TGTGGAC-TT-AAAGATAAAAAAAGTGCCACAGAAT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
588023 TGTGGGCTTTAAAA--G-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
588051 TGTGGAC-TTAAAA-GGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
*
588084 TGTGGGCTTT-AAA--GAAAAA-A-TGCCACTGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
588115 CGTGGACTTTAAAA
1 TGTGGGCTTTAAAA
588129 AGGTATTTGA
Statistics
Matches: 519, Mismatches: 52, Indels: 125
0.75 0.07 0.18
Matches are distributed among these distances:
26 3 0.01
27 51 0.10
28 17 0.03
31 19 0.04
32 11 0.02
33 66 0.13
34 150 0.29
35 36 0.07
36 30 0.06
37 69 0.13
38 7 0.01
39 24 0.05
40 4 0.01
41 2 0.00
42 3 0.01
45 2 0.00
48 5 0.01
49 6 0.01
50 14 0.03
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (36 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
Found at i:587592 original size:70 final size:70
Alignment explanation
Indices: 587482--587668 Score: 297
Period size: 71 Copynumber: 2.7 Consensus size: 70
587472 GAGAAGGGAG
* *
587482 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGATTTGTGGGCTTTAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
587546 -AGAAA
65 CAGAAA
587551 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
587616 CAGAAA
65 CAGAAA
* *
587622 AAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCAC
1 AAAGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCAC
587669 AAAGTTGTAG
Statistics
Matches: 110, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
68 17 0.15
69 6 0.05
70 38 0.35
71 49 0.45
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (70 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAC
AGAAA
Found at i:587663 original size:71 final size:69
Alignment explanation
Indices: 587482--588128 Score: 330
Period size: 61 Copynumber: 10.0 Consensus size: 69
587472 GAGAAGGGAG
* * *
587482 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGATTTGTGGGCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
587546 AGAA
66 AGAA
*
587550 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
587615 ACAGAA
65 A-AGAA
* ** * ***
587621 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGTTGTAGG-TGCCA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
587685 CAG--
65 AAGAA
* * ****** ** * *
587688 --AGTTG---TGG-GCTT-T-AAAAGAAAAAGGTGCCACAGAGT---T-------GTGGGCTTTG
1 AAAGGTGCCACGGAG-TTGTGGGCTTTAAAAGG-GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
587735 AAAAGGAAAAA
63 AAAA-G---AA
** *
587746 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTTGA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
587808 AAAGAA
64 AAAGAA
* * *
587814 GAAGGTGCCACAGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTT-A
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
587875 AAG--
65 AAGAA
* * *
587878 --A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
587940 ACAGAA
65 A-AGAA
* *
587946 AAAGGTGCCACGGAGTTGTGGGC-TT-AAA-CG-----G-GTGCCACGGAGTTGTGGAC-TTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
588001 GATAAA
66 -A-GAA
* * * *
588007 AAAAGTGCCACAGAATTGTGGGCTTTAAAA--G-----G-GTGCCACGGAGTTGTGGAC-TTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
588063 AGGAA
66 A-GAA
* * * *
588068 CAAGGTGCCACGGAGTTGTGGGCTTT-AAA--GAAAAA-A-TGCCACTGAGTCGTGGACTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
588128 A
66 A
588129 AGGTATTTGA
Statistics
Matches: 457, Mismatches: 69, Indels: 109
0.72 0.11 0.17
Matches are distributed among these distances:
50 4 0.01
51 1 0.00
52 2 0.00
53 1 0.00
59 6 0.01
60 19 0.04
61 93 0.20
62 36 0.08
63 12 0.03
64 39 0.09
65 14 0.03
66 10 0.02
67 22 0.05
68 61 0.13
69 4 0.01
70 43 0.09
71 76 0.17
72 14 0.03
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (69 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AGAA
Found at i:587714 original size:33 final size:33
Alignment explanation
Indices: 587677--588128 Score: 415
Period size: 34 Copynumber: 13.8 Consensus size: 33
587667 ACAAAGTTGT
*
587677 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
587710 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAAAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAA-G---AAAA
** *
587748 AGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
587782 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
* *
587816 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
587850 AGGTGCCACGGAGTTGTGGGCTTT-AAAG----
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
587878 A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTT--AAA-AGAAAA
*
587913 AGAGTGCCGCGGAGTTGTGGGCTTTAAACAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAA-AGAAAA
*
587948 AGGTGCCACGGAGTTGTGGGC-TTAAACG----
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* *
587976 -GGTGCCACGGAGTTGTGGAC-TTAAAGATAAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAA-A-GAAAA
* * *
588009 AAGTGCCACAGAATTGTGGGCTTTAAAAG----
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* *
588038 -GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA-GAAAA
588070 AGGTGCCACGGAGTTGTGGGCTTT-AAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* * * *
588102 A-ATGCCACTGAGTCGTGGACTTTAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA
588129 AGGTATTTGA
Statistics
Matches: 356, Mismatches: 30, Indels: 67
0.79 0.07 0.15
Matches are distributed among these distances:
27 51 0.14
28 18 0.05
30 2 0.01
31 20 0.06
32 13 0.04
33 71 0.20
34 111 0.31
35 18 0.05
37 21 0.06
38 10 0.03
39 21 0.06
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (33 bp):
AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
Found at i:587739 original size:87 final size:89
Alignment explanation
Indices: 587591--587765 Score: 282
Period size: 87 Copynumber: 2.0 Consensus size: 89
587581 GGGAAAAAGA
* * *
587591 GTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGG-G
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAA
*
587655 AAAGAGAGTGCCACAAAGTTGTAG
66 AAAAAGAGTGCCACAAAGTTGTAG
*
587679 GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGG-A
587743 AAAAAAGAGTGCCACAAAGTTGT
65 AAAAAAGAGTGCCACAAAGTTGT
587766 GGGCTTTAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
87 35 0.44
88 24 0.30
89 21 0.26
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (89 bp):
GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAAGGAA
AAAAAGAGTGCCACAAAGTTGTAG
Found at i:587796 original size:72 final size:67
Alignment explanation
Indices: 587677--588130 Score: 400
Period size: 61 Copynumber: 6.9 Consensus size: 67
587667 ACAAAGTTGT
* *
587677 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-
587742 AAAAAA
64 --AAAA
*
587748 AGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
1 AG-GTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
*
587813 AGA
65 AAA
587816 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAAG-
1 AGGTGCCACAGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGA
587878 ---
65 AAA
* * * *
587878 A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGTTGTGGGCTTT-AAA
1 AGGTGCCACAGAGTTGTGGGCTTT--AAA-AGAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAA
587941 CAGAAAA
62 -AGAAAA
* * * *
587948 AGGTGCCACGGAGTTGTGGGC-TT--AA-ACG--GGTGCCACGGAGTTGTGGAC-TT-AAAGATA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAA-A-G
588005 AAAA
64 AAAA
* * *
588009 AAGTGCCACAGAATTGTGGGCTTT--AA-AAG--GGTGCCACGGAGTTGTGGAC-TT-AAAAGGA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GA
*
588067 ACA
65 AAA
* ** * * * *
588070 AGGTGCCACGGAGTTGTGGGCTTT-AAAGAA-AAAATGCCACTGAGTCGTGGACTTTAAAAAG
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
588131 GTATTTGAAG
Statistics
Matches: 332, Mismatches: 31, Indels: 46
0.81 0.08 0.11
Matches are distributed among these distances:
60 6 0.02
61 84 0.25
62 38 0.11
63 9 0.03
64 38 0.11
65 6 0.02
66 11 0.03
67 21 0.06
68 38 0.11
70 3 0.01
71 21 0.06
72 57 0.17
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (67 bp):
AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
AA
Found at i:587896 original size:61 final size:64
Alignment explanation
Indices: 587818--587940 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
587808 AAAGAAGAAG
* *
587818 GTGCCACAGAGTTGTGGGCTTTG-AAA-AGAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAAGA
1 GTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGA
* *
587879 GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGTTGTGGGCTTTAAA
1 GTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
587941 CAGAAAAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 21 0.38
62 3 0.05
63 7 0.13
64 24 0.44
ACGTcount: A:0.28, C:0.14, G:0.37, T:0.22
Consensus pattern (64 bp):
GTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGA
Found at i:587955 original size:98 final size:94
Alignment explanation
Indices: 587679--588130 Score: 413
Period size: 95 Copynumber: 4.6 Consensus size: 94
587669 AAAGTTGTAG
*
587679 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAA-G---
**
587744 AAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
62 AAAAAG-GTGCCACGGAGTTGTGGGCTTT---A-AAG-A
*
587783 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
1 -GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
*
587848 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGA
64 AAAGGTGCCACGGAGTTGTGGGCTTTAAAGA
* * *
587879 GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGTTGTGGGCTTT-AAACA
1 GTGCCACGGAGTTGTGGGCTTT--AAA-AGAAAAAG-GTGCCACAGAGTTGTGGGCTTTGAAA-A
*
587943 GAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGG
61 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-GA
* * * *
587977 GTGCCACGGAGTTGTGGAC-TTAAAGATAAAAAAAGTGCCACAGAATTGTGGGCTTT-AAAAG--
1 GTGCCACGGAGTTGTGGGCTTTAAA-A-GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAA
* *
588038 ---GGTGCCACGGAGTTGTGGACTTAAAAGGAACAA
64 AAAGGTGCCACGGAGTTGTGGGCTTTAAA-G----A
* * * * *
588071 GGTGCCACGGAGTTGTGGGCTTT-AAAGAAAAA-ATGCCACTGAGTCGTGGACTTTAAAAAG
1 -GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAG
588131 GTATTTGAAG
Statistics
Matches: 302, Mismatches: 30, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
89 19 0.06
90 5 0.02
92 17 0.06
93 10 0.03
94 3 0.01
95 68 0.23
96 11 0.04
97 20 0.07
98 65 0.22
101 20 0.07
102 5 0.02
105 22 0.07
106 37 0.12
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (94 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAA
AGGTGCCACGGAGTTGTGGGCTTTAAAGA
Found at i:587982 original size:193 final size:192
Alignment explanation
Indices: 587482--588128 Score: 539
Period size: 193 Copynumber: 3.3 Consensus size: 192
587472 GAGAAGGGAG
* * *
587482 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGATTTGTGGGCTTTAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
587545 AAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
66 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTT---AA---AAAGAG-GTGCCACGGAGTTGTGGGC
* **
587610 TTT-AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAA-AGAGAGTGCCACAAAG
124 TTTGAAA-AG-AAAAGGTGCCACAGAGTTGTGGGCTTT-AAAA--GAAGA-AG-GTGCCACGGAG
587673 -T-T--G---T
182 TTGTGGGCTTT
* *
587677 --AG-GTGCCACAGAGTTGTGGGCTTT-AAA-AGAAAAAG-GTGCCACAGAGTTGTGGGCTTTGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-A
**
587736 AAAGGAAAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGG
65 AAA-G---AAAAAG-GTGCCACGGAGTTGTGGGCTTT-AAA-AAG-AGGTGCCACGGAGTTGTGG
587801 GCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTG
122 GCTTTGAAAAGAA-AAGGTGCCACAGAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTG
587866 TGGGCTTT
185 TGGGCTTT
* *
587874 AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCGCGGAGTTGTGGGCTTTA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* * *
587939 AACAGAAAAAGGTGCCACGGAGTTGTGGGC-TT-AAACG-GGTGCCACGGAGTTGTGGACTTAAA
65 AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGGTGCCACGGAGTTGTGGGCTT--T
* *
588001 GATAAA-AAAA-GTGCCACAGAATTGTGGGCTTT--AA-AAG--GGTGCCACGGAGTTGTGGACT
127 GA-AAAGAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCT
*
588059 TA
191 TT
* * *
588061 AAAGGAACAAGGTGCCACGGAGTTGTGGGCTTT--AA-AGAAAAA-A-TGCCACTGAGTCGTGGA
1 AAA-G----A-GTGCCACGGAGTTGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGG
588121 CTTTAAAA
60 CTTTAAAA
588129 AGGTATTTGA
Statistics
Matches: 385, Mismatches: 30, Indels: 83
0.77 0.06 0.17
Matches are distributed among these distances:
186 1 0.00
187 44 0.11
188 2 0.01
189 10 0.03
190 13 0.03
191 26 0.07
192 17 0.04
193 139 0.36
194 10 0.03
195 9 0.02
196 10 0.03
197 21 0.05
198 2 0.01
199 19 0.05
200 26 0.07
202 3 0.01
203 12 0.03
204 21 0.05
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (192 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAGGTGCCACGGAGTTGTGGGCTTTGAAA
AGAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:587987 original size:27 final size:27
Alignment explanation
Indices: 587949--588000 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
587939 AACAGAAAAA
*
587949 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAACG
587976 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
588001 GATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAACG
Found at i:588061 original size:27 final size:28
Alignment explanation
Indices: 588011--588065 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
588001 GATAAAAAAA
*
588011 GTGCCACAGAATTGTGGGCTTTAAAAGG
1 GTGCCACAGAATTGTGGACTTTAAAAGG
* *
588039 GTGCCACGGAGTTGTGGAC-TTAAAAGG
1 GTGCCACAGAATTGTGGACTTTAAAAGG
588066 AACAAGGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (28 bp):
GTGCCACAGAATTGTGGACTTTAAAAGG
Found at i:588125 original size:31 final size:33
Alignment explanation
Indices: 588040--588127 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 33
588030 TTTAAAAGGG
* **
588040 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTTAAAGGAACAAAA
*
588073 TGCCACGGAGTTGTGGGCTTTAAA-GAA-AAAA
1 TGCCACGGAGTTGTGGACTTTAAAGGAACAAAA
* *
588104 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACGGAGTTGTGGACTTTAAA
588128 AAGGTATTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 23 0.48
32 3 0.06
33 22 0.46
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (33 bp):
TGCCACGGAGTTGTGGACTTTAAAGGAACAAAA
Found at i:589082 original size:16 final size:16
Alignment explanation
Indices: 589058--589089 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
589048 TTTTCCTCTC
*
589058 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
589074 TTTTGTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
589090 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:589339 original size:8 final size:8
Alignment explanation
Indices: 589326--589377 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
589316 GCCTTTGCAC
589326 TTTTTT-T
1 TTTTTTGT
589333 TTTTTT-T
1 TTTTTTGT
*
589340 TTTTGTGTT
1 TTTTTTG-T
589349 TTTTTTGT
1 TTTTTTGT
*
589357 TTGTTTGT
1 TTTTTTGT
*
589365 TTGTTTGT
1 TTTTTTGT
589373 TTTTT
1 TTTTT
589378 CCATCACCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
7 12 0.31
8 20 0.51
9 7 0.18
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
TTTTTTGT
Found at i:589341 original size:12 final size:12
Alignment explanation
Indices: 589326--589377 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
589316 GCCTTTGCAC
*
589326 TTTTTTT-TTTT
1 TTTTTTTGTTTG
*
589337 TTTTTTTGTGT-
1 TTTTTTTGTTTG
589348 TTTTTTTGTTTG
1 TTTTTTTGTTTG
*
589360 TTTGTTTGTTTG
1 TTTTTTTGTTTG
589372 TTTTTT
1 TTTTTT
589378 CCATCACCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
11 17 0.49
12 18 0.51
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:589352 original size:15 final size:15
Alignment explanation
Indices: 589332--589374 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
589322 GCACTTTTTT
*
589332 TTTTTTTTTTTTGTG
1 TTTTTTTTGTTTGTG
589347 TTTTTTTTGTTTGT-
1 TTTTTTTTGTTTGTG
589361 TTGTTTGTTTGTTT
1 TT-TTT-TTTGTTT
589375 TTTCCATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 2 0.08
15 16 0.64
16 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (15 bp):
TTTTTTTTGTTTGTG
Found at i:596362 original size:52 final size:52
Alignment explanation
Indices: 596292--596412 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
596282 GAAAATTTAT
*
596292 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
596344 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
596396 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
596413 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:596425 original size:52 final size:51
Alignment explanation
Indices: 596292--596432 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
596282 GAAAATTTAT
596292 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
596344 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
596396 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
596433 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:596439 original size:13 final size:13
Alignment explanation
Indices: 596421--596445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
596411 CAAAGATCAG
596421 TGTATCGATACAA
1 TGTATCGATACAA
596434 TGTATCGATACA
1 TGTATCGATACA
596446 TGTGAGTAAT
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:596528 original size:13 final size:13
Alignment explanation
Indices: 596510--596534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
596500 CAAAAAAATA
596510 TGTATCGATACAT
1 TGTATCGATACAT
596523 TGTATCGATACA
1 TGTATCGATACA
596535 ACATTTTATG
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:596530 original size:33 final size:33
Alignment explanation
Indices: 596488--596554 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
596478 AGTAGCTTAA
596488 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
596521 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
596554 A
1 A
596555 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:599683 original size:31 final size:31
Alignment explanation
Indices: 599648--599707 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
599638 CTAGTAGTTC
599648 TAGTTAT-TCAAGACCAAAAATATAGTTGCCT
1 TAGTTATCTCAA-ACCAAAAATATAGTTGCCT
* *
599679 TAGTTATCTGAAACTAAAAATATAGTTGC
1 TAGTTATCTCAAACCAAAAATATAGTTGC
599708 TGCCTTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (31 bp):
TAGTTATCTCAAACCAAAAATATAGTTGCCT
Found at i:600137 original size:11 final size:12
Alignment explanation
Indices: 600113--600167 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 12
600103 ATTTGACGTA
600113 TAAATTTTTAAT
1 TAAATTTTTAAT
600125 TAAATTTTTATTAT
1 TAAATTTTTA--AT
600139 TAATATTTTTAAT
1 TAA-ATTTTTAAT
**
600152 TACTCTTTTTAAT
1 TA-AATTTTTAAT
600165 TAA
1 TAA
600168 CTAAATTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 10 0.28
13 14 0.39
14 5 0.14
15 7 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTTAAT
Found at i:600454 original size:23 final size:21
Alignment explanation
Indices: 600421--600480 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
600411 ACTTAGTAGA
600421 AAAAAAGAAAAAAAAG-ATAC
1 AAAAAAGAAAAAAAAGCATAC
600441 AAACATAAAGAAAAAGAAAGCATAC
1 -AA-A-AAAGAAAAA-AAAGCATAC
*
600466 GAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
600481 TTGGAAGACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 5 0.15
22 10 0.29
23 10 0.29
24 5 0.15
25 4 0.12
ACGTcount: A:0.77, C:0.07, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAGCATAC
Found at i:608822 original size:52 final size:52
Alignment explanation
Indices: 608743--608854 Score: 145
Period size: 52 Copynumber: 2.2 Consensus size: 52
608733 CATGCATATG
* * * *
608743 TCGATACATTAAAGAACGTATCGATACATTTGGGTTAAAAACCCA-AAATGTA
1 TCGATACAATAAAGAACGTATCAATACATTTGAGTCAAAAACCCAGAAA-GTA
* * *
608795 TCGATACAATGAAGAATGTATTAATACATTTGAGTCAAAAACCCAGAAAGTA
1 TCGATACAATAAAGAACGTATCAATACATTTGAGTCAAAAACCCAGAAAGTA
608847 TCGATACA
1 TCGATACA
608855 TTTTTTTACC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
52 49 0.94
53 3 0.06
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (52 bp):
TCGATACAATAAAGAACGTATCAATACATTTGAGTCAAAAACCCAGAAAGTA
Found at i:608999 original size:91 final size:92
Alignment explanation
Indices: 608844--609037 Score: 336
Period size: 91 Copynumber: 2.1 Consensus size: 92
608834 AACCCAGAAA
* *
608844 GTATCGATACATTTTTTTACCAGAATGTAAAATTTTGCCTGCATAGTCCTGTATAGATACATTTC
1 GTATCGATACATTTTCTTACCAGAATGTAAAATTTTGCCTGCATAGTCCTATATAGATACATTTC
**
608909 AAGCATGTATTGATACATTCACTTA-T
66 AAGCATGTATCAATACATTCACTTATT
608935 GTATCGATACATTTTCTTACCAGAATGTAAAATTTTGCCTGCATAGTCCTATATAGATACATTTC
1 GTATCGATACATTTTCTTACCAGAATGTAAAATTTTGCCTGCATAGTCCTATATAGATACATTTC
*
609000 AAGCATGTATCAATACATTCATTTATT
66 AAGCATGTATCAATACATTCACTTATT
609027 GTATCGATACA
1 GTATCGATACA
609038 AATTGTACAA
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 85 0.88
92 12 0.12
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (92 bp):
GTATCGATACATTTTCTTACCAGAATGTAAAATTTTGCCTGCATAGTCCTATATAGATACATTTC
AAGCATGTATCAATACATTCACTTATT
Found at i:613259 original size:439 final size:439
Alignment explanation
Indices: 612441--613315 Score: 1741
Period size: 439 Copynumber: 2.0 Consensus size: 439
612431 TAAAGTCCTA
612441 TATTAGAAAAATGTGCTTAGCATGAGGAAATCTCATGTGTGAGAGAAACAATTAAAAGTTTCAAA
1 TATTAGAAAAATGTGCTTAGCATGAGGAAATCTCATGTGTGAGAGAAACAATTAAAAGTTTCAAA
612506 CTCGTAAGAAGCTTCCGAGAAACATCTTTATGGGAGAAATATTCATGAATGAAAAATTCAAAATA
66 CTCGTAAGAAGCTTCCGAGAAACATCTTTATGGGAGAAATATTCATGAATGAAAAATTCAAAATA
612571 AACTTAAGTATTAAAAAGTTGAAATAAAAGCATTTGATTGAAAGTGCACAAAAATTTTGAAAACC
131 AACTTAAGTATTAAAAAGTTGAAATAAAAGCATTTGATTGAAAGTGCACAAAAATTTTGAAAACC
612636 CTAAACTTGAAAATTTTATAAAAAGGAAACTCGCGATACTATCTGAAATTGAAAATTAATTAATT
196 CTAAACTTGAAAATTTTATAAAAAGGAAACTCGCGATACTATCTGAAATTGAAAATTAATTAATT
612701 AATTTTACAACTGGATATCTTGTGATATAAATGTCAATACAAACTTTTTCTCATAAGTTCTTGAT
261 AATTTTACAACTGGATATCTTGTGATATAAATGTCAATACAAACTTTTTCTCATAAGTTCTTGAT
612766 TTTTCAGAGTAAGTATTAGTATAAACTGCACTATTATCGATAAAATATACGATAATCAATTTGCA
326 TTTTCAGAGTAAGTATTAGTATAAACTGCACTATTATCGATAAAATATACGATAATCAATTTGCA
612831 TGATTAACGAAAATAGTTTTGAAAAATTTTTAAAAATGAAAAACTTATG
391 TGATTAACGAAAATAGTTTTGAAAAATTTTTAAAAATGAAAAACTTATG
612880 TATTAGAAAAATGTGCTTAGCATGAGGAAATCTCATGTGTGAGAGAAACAATTAAAAGTTTCAAA
1 TATTAGAAAAATGTGCTTAGCATGAGGAAATCTCATGTGTGAGAGAAACAATTAAAAGTTTCAAA
612945 CTCGTAAGAAGCTTCCGAGAAACATCTTTATGGGAGAAATATTCATGAATGAAAAATTCAAAATA
66 CTCGTAAGAAGCTTCCGAGAAACATCTTTATGGGAGAAATATTCATGAATGAAAAATTCAAAATA
613010 AACTTAAGTATTAAAAAGTTGAAATAAAAGCATTTGATTGAAAGTGCACAAAAATTTTGAAAACC
131 AACTTAAGTATTAAAAAGTTGAAATAAAAGCATTTGATTGAAAGTGCACAAAAATTTTGAAAACC
*
613075 CTAAACTTGAAAATTTTATAAAAAGGAAACTCGCGATACTGTCTGAAATTGAAAATTAATTAATT
196 CTAAACTTGAAAATTTTATAAAAAGGAAACTCGCGATACTATCTGAAATTGAAAATTAATTAATT
613140 AATTTTACAACTGGATATCTTGTGATATAAATGTCAATACAAACTTTTTCTCATAAGTTCTTGAT
261 AATTTTACAACTGGATATCTTGTGATATAAATGTCAATACAAACTTTTTCTCATAAGTTCTTGAT
613205 TTTTCAGAGTAAGTATTAGTATAAACTGCACTATTATCGATAAAATATACGATAATCAATTTGCA
326 TTTTCAGAGTAAGTATTAGTATAAACTGCACTATTATCGATAAAATATACGATAATCAATTTGCA
613270 TGATTAACGAAAATAGTTTTGAAAAATTTTTAAAAATGAAAAACTT
391 TGATTAACGAAAATAGTTTTGAAAAATTTTTAAAAATGAAAAACTT
613316 GACCATGATA
Statistics
Matches: 435, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
439 435 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (439 bp):
TATTAGAAAAATGTGCTTAGCATGAGGAAATCTCATGTGTGAGAGAAACAATTAAAAGTTTCAAA
CTCGTAAGAAGCTTCCGAGAAACATCTTTATGGGAGAAATATTCATGAATGAAAAATTCAAAATA
AACTTAAGTATTAAAAAGTTGAAATAAAAGCATTTGATTGAAAGTGCACAAAAATTTTGAAAACC
CTAAACTTGAAAATTTTATAAAAAGGAAACTCGCGATACTATCTGAAATTGAAAATTAATTAATT
AATTTTACAACTGGATATCTTGTGATATAAATGTCAATACAAACTTTTTCTCATAAGTTCTTGAT
TTTTCAGAGTAAGTATTAGTATAAACTGCACTATTATCGATAAAATATACGATAATCAATTTGCA
TGATTAACGAAAATAGTTTTGAAAAATTTTTAAAAATGAAAAACTTATG
Found at i:614766 original size:19 final size:20
Alignment explanation
Indices: 614723--614776 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
614713 CACATCCAGA
* *
614723 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
*
614743 TGTATCGATACATGCT-CAT
1 TGTATCGATACATGATGCAT
614762 TGTATCGATACATGA
1 TGTATCGATACATGA
614777 AACTGGTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:614849 original size:20 final size:19
Alignment explanation
Indices: 614805--614855 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
614795 TAAGTGAAAT
* **
614805 GTATCGATACATGGACATT
1 GTATCGATACATGGAAAAA
614824 GTATCGATACATGGTAAAAA
1 GTATCGATACATGG-AAAAA
614844 GTATCGATACAT
1 GTATCGATACAT
614856 TGTGCCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACATGGAAAAA
Found at i:618578 original size:10 final size:10
Alignment explanation
Indices: 618563--618594 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
618553 AAAATAAGCA
618563 TCCATAGAGC
1 TCCATAGAGC
618573 TCCATAGAGC
1 TCCATAGAGC
618583 TCCATAGAGC
1 TCCATAGAGC
618593 TC
1 TC
618595 GACAATCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (10 bp):
TCCATAGAGC
Found at i:627965 original size:9 final size:8
Alignment explanation
Indices: 627932--627969 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
627922 TTGTGCTGTA
*
627932 ATCATGAC
1 ATCATAAC
627940 ATCATAAC
1 ATCATAAC
627948 ATCATAAC
1 ATCATAAC
627956 ATCAATAAC
1 ATC-ATAAC
627965 ATCAT
1 ATCAT
627970 TATTTGCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (8 bp):
ATCATAAC
Found at i:628140 original size:31 final size:32
Alignment explanation
Indices: 628069--628225 Score: 124
Period size: 31 Copynumber: 4.9 Consensus size: 32
628059 TTCAAATACC
** **
628069 TTCTTAAAGTCCATGACTCAGTGGCAATCTCT
1 TTCTTAAAGTCCACAACTCAGTGGCACCCTCT
*
628101 TT-TTAAAGTCCACAACTCAGTGGCA-TCT-T
1 TTCTTAAAGTCCACAACTCAGTGGCACCCTCT
* *
628130 TTCTTCAAAGTTCACAACTCTGTGGCACCCT-T
1 TTCTT-AAAGTCCACAACTCAGTGGCACCCTCT
* * *
628162 TTCCCTTTTAAAGCCCACAACTCCGTGGCACCCTGT
1 TT--C--TTAAAGTCCACAACTCAGTGGCACCCTCT
* * *
628198 TCCTTTAAGTCCACAACTCCGTGGCACC
1 TTCTTAAAGTCCACAACTCAGTGGCACC
628226 ATTTTAAGTC
Statistics
Matches: 106, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
29 3 0.03
30 5 0.05
31 40 0.38
32 30 0.28
34 2 0.02
35 22 0.21
36 4 0.04
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (32 bp):
TTCTTAAAGTCCACAACTCAGTGGCACCCTCT
Found at i:628269 original size:33 final size:33
Alignment explanation
Indices: 628096--628374 Score: 159
Period size: 33 Copynumber: 8.6 Consensus size: 33
628086 TCAGTGGCAA
* * * *
628096 TCTCTTTTTAAAGTCCACAACTCAGTGGCATCTT
1 TCTCCTTTT-AAGTCCACAACTCCGTGGAACCTT
** * * *
628130 T-T-CTTCAAAGTTCACAACTCTGTGGCACCCTT
1 TCTCCTTTTAAGTCCACAACTCCGTGG-AACCTT
* * *
628162 T-TCCCTTTTAAAGCCCACAACTCCGTGGCACCCTG
1 TCT-CCTTTT-AAGTCCACAACTCCGTGG-AACCTT
628197 T-TCC-TTTAAGTCCACAACTCCGTGG---C--
1 TCTCCTTTTAAGTCCACAACTCCGTGGAACCTT
* * * *
628223 AC-CATTTTAAGTCCACAACTCCATGGAATCTT
1 TCTCCTTTTAAGTCCACAACTCCGTGGAACCTT
* * * *
628255 TTTCCTTTTAAGTCCACGACTCTGTGGCACCCTT
1 TCTCCTTTTAAGTCCACAACTCCGTGG-AACCTT
* * *
628289 TCCCCTTTTAAAGCCCACAACTCCGTGGCACCTT
1 TCTCCTTTT-AAGTCCACAACTCCGTGGAACCTT
* * *
628323 GT-TCCTTTTAAGTCCACAACTTCGTGGCATCTT
1 -TCTCCTTTTAAGTCCACAACTCCGTGGAACCTT
*
628356 TCTCCTTTTAAGCCCACAA
1 TCTCCTTTTAAGTCCACAA
628375 GTTAGTGGCA
Statistics
Matches: 191, Mismatches: 38, Indels: 33
0.73 0.15 0.13
Matches are distributed among these distances:
26 1 0.01
27 20 0.10
28 1 0.01
30 1 0.01
31 16 0.08
32 25 0.13
33 61 0.32
34 27 0.14
35 39 0.20
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
TCTCCTTTTAAGTCCACAACTCCGTGGAACCTT
Found at i:628295 original size:127 final size:127
Alignment explanation
Indices: 628101--628351 Score: 382
Period size: 127 Copynumber: 2.0 Consensus size: 127
628091 GGCAATCTCT
* * *
628101 TTTTAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTTCACAACTCTGTGGCACCCTTTTCC
1 TTTTAAAGTCCACAACTCAGTGGAATCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTCCC
628166 CTTTTAAAGCCCACAACTCCGTGGCACCCTGTTCC-TTTAAGTCCACAACTCCGTGGCACCA
66 CTTTTAAAGCCCACAACTCCGTGGCACCCTGTTCCTTTTAAGTCCACAACTCCGTGGCACCA
** *
628227 TTTT-AAGTCCACAACTCCA-TGGAATCTTTTTCCTTTTAAGTCCACGACTCTGTGGCACCCTTT
1 TTTTAAAGTCCACAACT-CAGTGGAATC-TTTT-CTTCAAAGTCCACAACTCTGTGGCACCCTTT
* *
628290 CCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
63 CCCCTTTTAAAGCCCACAACTCCGTGGCACCCTGTTCCTTTTAAGTCCACAACTCCGTGGCA
628352 TCTTTCTCCT
Statistics
Matches: 113, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
125 18 0.16
126 10 0.09
127 63 0.56
128 22 0.19
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.32
Consensus pattern (127 bp):
TTTTAAAGTCCACAACTCAGTGGAATCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTCCC
CTTTTAAAGCCCACAACTCCGTGGCACCCTGTTCCTTTTAAGTCCACAACTCCGTGGCACCA
Found at i:628350 original size:68 final size:66
Alignment explanation
Indices: 628137--628374 Score: 240
Period size: 68 Copynumber: 3.7 Consensus size: 66
628127 CTTTTCTTCA
* * * * *
628137 AAGTTCACAACTCTGTGGCACCCTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCCTGTTCC-
1 AAGTCCACAACTCTGTGGCA-CCTTTCCCCTTTT-AAGCCCACAACTCCATGGAACCTTGTTCCT
628201 TTT
64 TTT
* * * * *
628204 AAGTCCACAACTCCGTGGCA------CCATTTTAAGTCCACAACTCCATGGAATCTTTTTCCTTT
1 AAGTCCACAACTCTGTGGCACCTTTCCCCTTTTAAGCCCACAACTCCATGGAACCTTGTTCCTTT
628263 T
66 T
* * *
628264 AAGTCCACGACTCTGTGGCACCCTTTCCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
1 AAGTCCACAACTCTGTGGCA-CCTTTCCCCTTTT-AAGCCCACAACTCCATGGAACCTTGTTCCT
628329 TTT
64 TTT
* *
628332 AAGTCCACAACT-TCGTGGCATCTTTCTCCTTTTAAGCCCACAA
1 AAGTCCACAACTCT-GTGGCACCTTTCCCCTTTTAAGCCCACAA
628375 GTTAGTGGCA
Statistics
Matches: 141, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
59 23 0.16
60 27 0.19
66 10 0.07
67 36 0.26
68 45 0.32
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (66 bp):
AAGTCCACAACTCTGTGGCACCTTTCCCCTTTTAAGCCCACAACTCCATGGAACCTTGTTCCTTT
T
Found at i:628401 original size:28 final size:30
Alignment explanation
Indices: 628365--628441 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 30
628355 TTCTCCTTTT
* *
628365 AAGCCCACAAGTTAGTGGCAA-CC-TTCAA
1 AAGCACACAAGTTGGTGGCAACCCTTTCAA
*
628393 AAGCACACAAGTTGGT-ACAACCCTTTCAA
1 AAGCACACAAGTTGGTGGCAACCCTTTCAA
628422 AAGTCCACACAAGTTGGTGG
1 AAG--CACACAAGTTGGTGG
628442 TGTCTTCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 16 0.40
29 8 0.20
31 13 0.32
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (30 bp):
AAGCACACAAGTTGGTGGCAACCCTTTCAA
Found at i:628546 original size:21 final size:21
Alignment explanation
Indices: 628522--628589 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
628512 ATGTCGCTGG
628522 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** *
628543 CCTTTAAGTCCAATATCGTTGG--
1 CCTTGAA-T-CAGCA-CATTGGCA
*
628565 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCACATTGGCA
628586 CCTT
1 CCTT
628590 TTCTTTAAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 3 0.09
21 11 0.33
22 7 0.21
23 3 0.09
24 5 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:628663 original size:49 final size:49
Alignment explanation
Indices: 628450--629141 Score: 659
Period size: 52 Copynumber: 13.9 Consensus size: 49
628440 GGTGTCTTCT
* * * * * *
628450 TTTAAGCCCAAAATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT-G-GCATCT-TCATC
* *
628502 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * * *
628545 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTT-TTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
*
628593 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
*
628642 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-TCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAT-C--T-TCATC
* ** *
628694 TTTAAGTCCAATGTCATTGGCCTTGAATCAGCACATTGGCATTTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
** ** * *
628743 TTTAAGTCCGGTATCATTGGCCTTGAATCAGCATATTGGCACCTTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATC
* *
628795 TTTAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* *
628844 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---TCTTCATC
* *
628896 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
** * *
628945 TTTAAGTCCAATATCATTGGTCCTTGAATTAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGG-CCTTGAATCAGCACATTGGCATCTTCATC
* * * * ** * * *
628995 CTTAAGTCCAATATCGTTGACCTTGAATCAACGTATTGGCATTTTTAAC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * ** *
629044 ATTCCTAAGCCCAATGTCGCTGGCCTTGCCTCAGCACATTGGCAT-TT-TTC
1 -TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * * *
629094 TTCAAGTCTAAATGTCGCTGG-CTATGAATCAGCACATTGTCATTCTTC
1 TTTAAGTC-CAATATCGCTGGCCT-TGAATCAGCACATTGGCA-TCTTC
629142 GCATCTTCGA
Statistics
Matches: 536, Mismatches: 77, Indels: 55
0.80 0.12 0.08
Matches are distributed among these distances:
43 38 0.07
45 1 0.00
47 6 0.01
48 69 0.13
49 176 0.33
50 50 0.09
51 4 0.01
52 191 0.36
53 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
Found at i:628741 original size:101 final size:101
Alignment explanation
Indices: 628450--629141 Score: 819
Period size: 101 Copynumber: 7.0 Consensus size: 101
628440 GGTGTCTTCT
* * * ** *
628450 TTTAAGCCCAAAATCGCTAGCCTTGAATCAGCATATTGGTGCCTTTGTCATCTTTAAGACCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
628515 TCGCTGGCCTTGAATCAGCACATTGGCA----C--C
66 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
*
628545 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC-TT-T--TCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
628606 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
66 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
*
628642 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
** *
628707 TCATTGGCCTTGAATCAGCACATTGGCATTTTCATC
66 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
** ** *
628743 TTTAAGTCCGGTATCATTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
*
628808 TCGTTGGCCTTGAATCAGCACATTGGCATCTTCATC
66 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
*
628844 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
*
628909 TCGCTGGCCTTGAATCAGTACATTGGCATCTTCATC
66 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
** * * *
628945 TTTAAGTCCAATATCATTGGTCCTTGAATTAGCACATTGGCACC--T-TCATCCTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGG-CCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
* * * * ** * * *
629007 ATCGTTGACCTTGAATCAACGTATTGGCATTTTTAAC
65 GTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* * ** * * *
629044 ATTCCTAAGCCCAATGTCGCTGGCCTTGCCTCAGCACATTGGCA--TTT-T--TCTTCAAGTCTA
1 -TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTC-C
*
629104 AATGTCGCTGG-CTATGAATCAGCACATTGTCATTCTTC
62 AATGTCGCTGGCCT-TGAATCAGCACATTGGCA-TCTTC
629142 GCATCTTCGA
Statistics
Matches: 517, Mismatches: 61, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
91 42 0.08
93 1 0.00
94 2 0.00
95 38 0.07
97 42 0.08
98 2 0.00
99 54 0.10
100 24 0.05
101 277 0.54
102 35 0.07
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (101 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
Done.