Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1599
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1324113
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 103357 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:385553 original size:28 final size:28
Alignment explanation
Indices: 385521--385574 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
385511 ACAAAGTCAT
385521 TTATAAGACTAGTGGTGTGTAGACAAAG
1 TTATAAGACTAGTGGTGTGTAGACAAAG
** *
385549 TTATAAGTGTGGTGGTGTGTAGACAA
1 TTATAAGACTAGTGGTGTGTAGACAA
385575 GTTGGAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (28 bp):
TTATAAGACTAGTGGTGTGTAGACAAAG
Found at i:385617 original size:32 final size:32
Alignment explanation
Indices: 385580--385714 Score: 216
Period size: 32 Copynumber: 4.2 Consensus size: 32
385570 GACAAGTTGG
385580 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
* * *
385612 AGACAAAGTCATTTATATGTGTGGTGGTGTGT
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
385644 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
* * *
385676 AGACAAAGTCATTTATATGTGTGGTGGTGTGT
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
385708 AGACAAA
1 AGACAAA
385715 TTGAAGACAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 94 1.00
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.34
Consensus pattern (32 bp):
AGACAAAGTCATTTATAGGTGTAGTAGTGTGT
Found at i:385649 original size:64 final size:67
Alignment explanation
Indices: 385580--385778 Score: 278
Period size: 64 Copynumber: 2.9 Consensus size: 67
385570 GACAAGTTGG
385580 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGT-G-
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGTAGA
385643 T-
66 TA
385644 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGTGTA
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGT-G-GTGTA
385709 GACAAATTGA
64 G----A-T-A
* * *
385719 AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAAGTCATTTATATGTGTGGTGGT
1 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGT
385779 CTGGAACAAG
Statistics
Matches: 121, Mismatches: 3, Indels: 13
0.88 0.02 0.09
Matches are distributed among these distances:
64 57 0.47
65 1 0.01
66 4 0.03
67 1 0.01
73 3 0.02
74 1 0.01
75 54 0.45
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.35
Consensus pattern (67 bp):
AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGTAGA
TA
Found at i:385723 original size:75 final size:73
Alignment explanation
Indices: 385644--385827 Score: 260
Period size: 75 Copynumber: 2.5 Consensus size: 73
385634 GGTGGTGTGT
* * *
385644 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGTGTA
1 AGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTCTGGA
*
385709 GACAAATTGA
66 -AC-AAGTGA
* *
385719 AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTCTGGA
1 AGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTCTGGA
*
385784 ACAAGTGT
66 ACAAGTGA
* * *
385792 TGACAAAGTCATTTATAAGTGTAGAAGTTTGTAGAC
1 AGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGAC
385828 CAAGGAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 35 0.36
74 2 0.02
75 60 0.62
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.33
Consensus pattern (73 bp):
AGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTCTGGA
ACAAGTGA
Found at i:385724 original size:43 final size:43
Alignment explanation
Indices: 385676--385757 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
385666 AGTAGTGTGT
*
385676 AGACAAAGTCATTTATATGTGTGGTGGTGTGTAGACAAATTGA
1 AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAATTGA
385719 AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAA
1 AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAA
385758 GTCATTTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.30
Consensus pattern (43 bp):
AGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAATTGA
Found at i:385725 original size:139 final size:135
Alignment explanation
Indices: 385509--385778 Score: 414
Period size: 139 Copynumber: 2.0 Consensus size: 135
385499 AGACAAATGG
*
385509 AGACAAAGTCATTTATAAGACTAGTGGTGTGTAGACAAAGTTATAAGTGTGGTGGTGTGTAGACA
1 AGACAAAGTCATTTATAAGACTAGTAGTGTGTAGACAAAGTTATAAGTGTGGTGGTGTGTAGACA
* * *
385574 AGTTGGAGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGG
66 AATTGAAGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGG
385639 TGTGT
131 TGTGT
* ** *
385644 AGACAAAGTCATTTATAGGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGGTGTGTA
1 AGACAAAGTCATTTATAAGACTAGTAGTGTGTAGACAAAG----TTATAAGTGTGGTGGTGTGTA
* *
385709 GACAAATTGAAGACAAAGTCATTTATAAGTGTGGTGGTGTGTAGACAAAGTCATTTATATGTGTG
62 GACAAATTGAAGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTG
385774 GTGGT
127 GTGGT
385779 CTGGAACAAG
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
135 36 0.30
139 85 0.70
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (135 bp):
AGACAAAGTCATTTATAAGACTAGTAGTGTGTAGACAAAGTTATAAGTGTGGTGGTGTGTAGACA
AATTGAAGACAAAGTCATTTATAAGTGTAGTAGTGTGTAGACAAAGTCATTTATATGTGTGGTGG
TGTGT
Found at i:391104 original size:6 final size:6
Alignment explanation
Indices: 391090--391133 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
391080 ATTGGCATAC
* * *
391090 AATTGG AATTAG AATTAG AATAAG -ATTAG TATTAG AATTAG AAT
1 AATTAG AATTAG AATTAG AATTAG AATTAG AATTAG AATTAG AAT
391134 ACATGTACAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (6 bp):
AATTAG
Found at i:391991 original size:52 final size:52
Alignment explanation
Indices: 391933--392069 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
391923 GATACATAGG
* *
391933 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCTGCAGTCTCCAATACACTGA
1 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCTGCAGTCACCAATACACAGA
*** *
391985 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCTGCAGTCACTGTTACGCAGA
1 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCTGCAGTCACCAATACACAGA
392037 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCT
1 GAGATCAACGGTTCAGTCAGAAGCATGCTGTCT
392070 TGGTCATGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (52 bp):
GAGATCAACGGTTCAGTCAGAAGCATGCTGTCTGCAGTCACCAATACACAGA
Found at i:393270 original size:2 final size:2
Alignment explanation
Indices: 393263--393290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
393253 TAGTCATTTG
393263 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
393291 TTAAAATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:399332 original size:2 final size:2
Alignment explanation
Indices: 399325--399372 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
399315 GATTTATTTA
399325 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
399367 TG TG TG
1 TG TG TG
399373 CCTGAAAAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:409456 original size:35 final size:34
Alignment explanation
Indices: 409415--409597 Score: 92
Period size: 35 Copynumber: 5.4 Consensus size: 34
409405 GAAAAAGAAG
409415 TGTATCATATGATACAATATTGTATAAGATAATAT
1 TGTATCATATGATA-AATATTGTATAAGATAATAT
** * * * * *
409450 TGTATCATAACATATATCATTGTATCACAAAAAAT
1 TGTATCATATGATAAAT-ATTGTATAAGATAATAT
*
409485 TGTATCAT-TG----ATATTGT-TAAATATAATAT
1 TGTATCATATGATAAATATTGTAT-AAGATAATAT
* * * *
409514 TGTATCATATGATATGATATTGTATGATATGATAT
1 TGTATCATATGATA-AATATTGTATAAGATAATAT
* * * * *
409549 TGTGTAATATGATATACA-ATTTTATCAGATCATAT
1 TGTATCATATGATA-A-ATATTGTATAAGATAATAT
* *
409584 TGTGTTATATGATA
1 TGTATCATATGATA
409598 TGCTACAGTT
Statistics
Matches: 115, Mismatches: 23, Indels: 20
0.73 0.15 0.13
Matches are distributed among these distances:
28 1 0.01
29 19 0.17
30 4 0.03
34 2 0.02
35 87 0.76
36 2 0.02
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.43
Consensus pattern (34 bp):
TGTATCATATGATAAATATTGTATAAGATAATAT
Found at i:409523 original size:15 final size:15
Alignment explanation
Indices: 409430--409528 Score: 58
Period size: 15 Copynumber: 6.3 Consensus size: 15
409420 CATATGATAC
* *
409430 AATATTGTATAAGAT
1 AATATTGTATCATAT
409445 AATATTGTATCATAACAT
1 AATATTGTATCAT---AT
* *
409463 ATATCATTGTATCACAA
1 A-AT-ATTGTATCATAT
*
409480 AAAATTGTATCAT-T
1 AATATTGTATCATAT
* *
409494 GATATTGT-TAAATAT
1 AATATTGTAT-CATAT
409509 AATATTGTATCATAT
1 AATATTGTATCATAT
*
409524 GATAT
1 AATAT
409529 GATATTGTAT
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.13
15 36 0.57
16 2 0.03
17 2 0.03
18 3 0.05
19 2 0.03
20 9 0.14
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.41
Consensus pattern (15 bp):
AATATTGTATCATAT
Found at i:409533 original size:20 final size:20
Alignment explanation
Indices: 409505--409548 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
409495 ATATTGTTAA
409505 ATATAATATTGTATCATATG
1 ATATAATATTGTATCATATG
* *
409525 ATATGATATTGTATGATATG
1 ATATAATATTGTATCATATG
409545 ATAT
1 ATAT
409549 TGTGTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (20 bp):
ATATAATATTGTATCATATG
Found at i:409539 original size:15 final size:15
Alignment explanation
Indices: 409521--409563 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
409511 TATTGTATCA
409521 TATGATATGATATTG
1 TATGATATGATATTG
409536 TATGATATGATATTG
1 TATGATATGATATTG
* *
409551 TGTAATATGATAT
1 TATGATATGATAT
409564 ACAATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (15 bp):
TATGATATGATATTG
Found at i:410063 original size:18 final size:19
Alignment explanation
Indices: 410026--410063 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
410016 ATATAATGCC
*
410026 ATATCATATTTTAGGATACA
1 ATATCATATCTTA-GATACA
410046 ATATCATATCTT-GATACA
1 ATATCATATCTTAGATACA
410064 CTGTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATCATATCTTAGATACA
Found at i:429516 original size:2 final size:2
Alignment explanation
Indices: 429509--429552 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
429499 AGACTGCTCT
*
429509 GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
429551 GA
1 GA
429553 TTTCTGCTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:432043 original size:12 final size:12
Alignment explanation
Indices: 431912--432046 Score: 180
Period size: 12 Copynumber: 11.2 Consensus size: 12
431902 AGTCGGTCTA
*
431912 TCTATCTATCTA
1 TCTATCTATCTT
*
431924 TCTATCTATCTA
1 TCTATCTATCTT
*
431936 TCTATCTATCTA
1 TCTATCTATCTT
*
431948 TCTATCTATCTA
1 TCTATCTATCTT
*
431960 TCTATCTATCTA
1 TCTATCTATCTT
*
431972 TCTATCTATCTA
1 TCTATCTATCTT
*
431984 TCTATCTATCTA
1 TCTATCTATCTT
431996 TCTATCTATCTT
1 TCTATCTATCTT
*
432008 TCTATCTATCTA
1 TCTATCTATCTT
432020 TCTATCTATCTT
1 TCTATCTATCTT
* *
432032 TCTTTCTTTCTT
1 TCTATCTATCTT
432044 TCT
1 TCT
432047 CCTTCCATTC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 118 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (12 bp):
TCTATCTATCTT
Found at i:432046 original size:4 final size:4
Alignment explanation
Indices: 431908--432030 Score: 237
Period size: 4 Copynumber: 30.8 Consensus size: 4
431898 TTTAAGTCGG
431908 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
431956 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA
*
432004 TCTT TCTA TCTA TCTA TCTA TCTA TCT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCT
432031 TTCTTTCTTT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 117 1.00
ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51
Consensus pattern (4 bp):
TCTA
Found at i:438344 original size:25 final size:25
Alignment explanation
Indices: 438310--438484 Score: 296
Period size: 25 Copynumber: 7.0 Consensus size: 25
438300 ATGAACGCAC
*
438310 ACAAACAAGGTGTGGATCCGTTATT
1 ACAAACAAGGTGTGGATCCGTTCTT
438335 ACAAACAAGGTGTGGATCCGTTCTT
1 ACAAACAAGGTGTGGATCCGTTCTT
*
438360 ACAAACAAGGTGTGGATCCGTTCTC
1 ACAAACAAGGTGTGGATCCGTTCTT
*
438385 ACAAACAAGGTGTGGATCCGTTCTC
1 ACAAACAAGGTGTGGATCCGTTCTT
438410 ACAAACAAGGTGTGGATCCGTTCTT
1 ACAAACAAGGTGTGGATCCGTTCTT
* *
438435 ACAAACAAGGTGTGGATCCATTCTA
1 ACAAACAAGGTGTGGATCCGTTCTT
*
438460 ACAAACGAGGTGTGGATCCGTTCTT
1 ACAAACAAGGTGTGGATCCGTTCTT
438485 CGCTCATACA
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 142 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (25 bp):
ACAAACAAGGTGTGGATCCGTTCTT
Found at i:438628 original size:21 final size:21
Alignment explanation
Indices: 438602--438679 Score: 156
Period size: 21 Copynumber: 3.7 Consensus size: 21
438592 TTCCTAAACC
438602 ATCAAGAGATACATGAGATGT
1 ATCAAGAGATACATGAGATGT
438623 ATCAAGAGATACATGAGATGT
1 ATCAAGAGATACATGAGATGT
438644 ATCAAGAGATACATGAGATGT
1 ATCAAGAGATACATGAGATGT
438665 ATCAAGAGATACATG
1 ATCAAGAGATACATG
438680 TTATGAATTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (21 bp):
ATCAAGAGATACATGAGATGT
Found at i:439780 original size:4 final size:4
Alignment explanation
Indices: 439771--439822 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
439761 TACCCTTGTG
* * * *
439771 TGTC TGTC TGTC CGTC CGTC CGTC TGTC TGTC TGTC TGTC CGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
439819 TGTC
1 TGTC
439823 CGTCCGTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (4 bp):
TGTC
Found at i:439823 original size:12 final size:12
Alignment explanation
Indices: 439771--439826 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
439761 TACCCTTGTG
*
439771 TGTCTGTCTGTC
1 TGTCCGTCTGTC
* *
439783 CGTCCGTCCGTC
1 TGTCCGTCTGTC
*
439795 TGTCTGTCTGTC
1 TGTCCGTCTGTC
439807 TGTCCGTCTGTC
1 TGTCCGTCTGTC
439819 TGTCCGTC
1 TGTCCGTC
439827 CGTAACAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.00, C:0.34, G:0.25, T:0.41
Consensus pattern (12 bp):
TGTCCGTCTGTC
Found at i:440237 original size:166 final size:166
Alignment explanation
Indices: 439853--440976 Score: 1686
Period size: 166 Copynumber: 6.8 Consensus size: 166
439843 GTCGCATTTA
*
439853 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTAT-AGGCATGCCATA
* *
439917 TCGTGGGATATATTTTTGTACCAATCGGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTT
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TT
* *
439982 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * * *
440020 TCTCAGCAACTGTTTATCCCAGTTGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * *
440085 CGTGGGATATATTTTTGTACCTATCAGACGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
440150 TAGCAAAAATTTTCAAACAAA-TTTCTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTC-GTCAAAGAAT
*
440186 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* *
440251 CGTGGGATATATTTTTGTACCTATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
440316 TAGCAAAAATTTTCAAACAAA-TTTCTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTC-GTCAAAGAAT
*
440352 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* *
440417 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
*
440482 TTGCCAAAATTTT--AACAAA-TTTCTGTCAAAGAAT
131 TAGCCAAAATTTTCAAACAAATTTTC-GTCAAAGAAT
* *
440516 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACATTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * * *
440581 TGTGGGATATATTTTTGTATCAATCGGATGTCAACTTCCTGTTAAACGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* * *
440646 TAGCCAACATTTTCAAACAAATTTTCGTCAAACATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * * * *
440682 TCTCAGCAGCTATATATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * * *
440747 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATAATGACTTTGTTT-TTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
440811 TAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
* * *
440847 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
* * * * * * * *
440912 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
440977 GCATATTCAC
Statistics
Matches: 894, Mismatches: 57, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
164 153 0.17
165 154 0.17
166 468 0.52
167 118 0.13
168 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAAT
Found at i:440687 original size:330 final size:331
Alignment explanation
Indices: 439853--440976 Score: 1743
Period size: 330 Copynumber: 3.4 Consensus size: 331
439843 GTCGCATTTA
* *
439853 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
*
439918 CGTGGGATATATTTTTGTACCAATCGGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTA-TTT
* * * *
439983 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCCCAGTTGCTT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
*
440048 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCTATCAGA
195 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
*
440113 CGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCTGT
260 CGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCCAAAATTTT-AAACAAATTTCTGT
440178 CAAAGAAT
324 CAAAGAAT
* *
440186 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
* * *
440251 CGTGGGATATATTTTTGTACCTATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* *
440316 TAGCAAAAATTTTCAAACAAA-TTTCTGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTT
131 TAGCCAAAATTTTCAAACAAATTTTC-GTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTT
440380 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
195 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
*
440445 CGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTTGCCAAAATTTT-AACAAATTTCTGTC
260 CGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTAAACAAATTTCTGTC
440509 AAAGAAT
325 AAAGAAT
*
440516 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACATTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
* * * * *
440581 TGTGGGATATATTTTTGTATCAATCGGATGTCAACTTCCTGTTAAACGACGACTTTGTTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * * *
440646 TAGCCAACATTTTCAAACAAATTTTCGTCAAACATTTCTCAGCAGCTATATATCGCAGATGCTTG
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG
* * * * * * *
440711 AAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTATCAATCGGAC
196 AAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGAC
* * * *
440776 GTCAACTTCCTGTTAAATAATGACTTTGTTT-TTTTTAGCCAAAATTTTCAAACAAATTT-TCCT
261 GTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCCAAAATTTT-AAACAAATTTCT-GT
*
440839 CAAAGATT
324 CAAAGAAT
* *
440847 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
* * * * * * *
440912 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
440977 GCATATTCAC
Statistics
Matches: 731, Mismatches: 55, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
329 16 0.02
330 283 0.39
331 145 0.20
332 169 0.23
333 118 0.16
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (331 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATTTATCGCAGATGCTTG
AAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGAC
GTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCCAAAATTTTAAACAAATTTCTGTCA
AAGAAT
Found at i:440779 original size:496 final size:496
Alignment explanation
Indices: 439853--440976 Score: 1700
Period size: 496 Copynumber: 2.3 Consensus size: 496
439843 GTCGCATTTA
*
439853 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
*
439918 CGTGGGATATATTTTTGTACCAATCGGACATCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * *
439983 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTGTTTATCCCAGTTGCTT
130 TTAACCAAAATTTT-AAACAAATTTTCGTCAAAGAATTCTCAGCAACTATTTATCCCAGATGCTT
* *
440048 GAAATTTTTACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCTATCAGA
194 GAAATTTTAACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
*
440113 CGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCTGT
259 CGTCAACTTCCTGTCAAACGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCTGT
* * * *
440178 CAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCA
324 CAAACAATTCTCAGCAACTATATATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCA
* *
440243 TGCCATATCGTGGGATATATTTTTGTACCTATCAGACGTCAACTTCCTGTTAAATGACGACTTTG
389 TGCCATATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTTTG
*
440308 TTTATTTTTAGCAAAAATTTTCAAACAAA-TTTCTGTCAAAGAAT
454 TTT-TTTTTAGCAAAAATTTTCAAACAAATTTTC-CTCAAAGAAT
*
440352 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGT-TAGGCATGCCATAT
* * *
440417 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTCAAATGACGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* *
440482 TT-GCCAAAATTTT-AACAAA-TTTCTGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTT
130 TTAACCAAAATTTTAAACAAATTTTC-GTCAAAGAATTCTCAGCAACTATTTATCCCAGATGCTT
* * * * *
440544 GAAATTTTAACACATTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTATCAATCGGA
194 GAAATTTTAACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGA
* * * *
440609 TGTCAACTTCCTGTTAAACGACGACTTTGTTTATTTTTAGCCAACATTTTCAAACAAATTT-TCG
259 CGTCAACTTCCTGTCAAACGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCT-G
* * * *
440673 TCAAACATTTCTCAGCAGCTATATATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGC
323 TCAAACAATTCTCAGCAACTATATATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGC
* * * *
440738 ATGCCATATTGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTTAAATAATGACTTT
388 ATGCCATATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTTT
* *
440803 GTTTTTTTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT
453 GTTTTTTTTAGCAAAAATTTTCAAACAAATTTTCCTCAAAGAAT
* *
440847 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * * * * *
440912 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
440977 GCATATTCAC
Statistics
Matches: 567, Mismatches: 53, Indels: 14
0.89 0.08 0.02
Matches are distributed among these distances:
495 152 0.27
496 280 0.49
498 10 0.02
499 124 0.22
500 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (496 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAGGCATGCCATATC
GTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTTT
TAACCAAAATTTTAAACAAATTTTCGTCAAAGAATTCTCAGCAACTATTTATCCCAGATGCTTGA
AATTTTAACACAGTATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCAGACG
TCAACTTCCTGTCAAACGACGACTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTCTGTCA
AACAATTCTCAGCAACTATATATCGCAGATGCTTGAAATTTTAACACACTATTTGTATAGGCATG
CCATATCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATAACGACTTTGTT
TTTTTTAGCAAAAATTTTCAAACAAATTTTCCTCAAAGAAT
Found at i:449755 original size:1 final size:1
Alignment explanation
Indices: 449751--449784 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
449741 GGGGGCGGGA
449751 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
449785 TAGATCCGCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:450458 original size:2 final size:2
Alignment explanation
Indices: 450451--450485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
450441 TAAGAGGATT
450451 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
450486 GACTGGAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:450589 original size:19 final size:19
Alignment explanation
Indices: 450565--450609 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
450555 AGAAGGTTTA
*
450565 GGTACAGTGACATGTGCTC
1 GGTACAGTGACAGGTGCTC
*
450584 GGTACAGTGGCAGGTGCTC
1 GGTACAGTGACAGGTGCTC
450603 GGTACAG
1 GGTACAG
450610 GTAGGACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (19 bp):
GGTACAGTGACAGGTGCTC
Found at i:461723 original size:2 final size:2
Alignment explanation
Indices: 461716--461764 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
461706 ATAAATATTC
461716 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
461758 AG AG AG A
1 AG AG AG A
461765 TGTGCGATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:463840 original size:2 final size:2
Alignment explanation
Indices: 463833--463884 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
463823 AAAGACATAT
463833 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
463875 GA GA GA GA GA
1 GA GA GA GA GA
463885 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:477654 original size:2 final size:2
Alignment explanation
Indices: 477647--477690 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
477637 AGACCCATGA
477647 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
477689 TC
1 TC
477691 CTCCTTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:486585 original size:2 final size:2
Alignment explanation
Indices: 486578--486625 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
486568 TGTCTGTTGA
486578 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
486620 TC TC TC
1 TC TC TC
486626 CAATTTCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:488584 original size:2 final size:2
Alignment explanation
Indices: 488571--488617 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
488561 AATTTGAAAA
*
488571 CT CT CT CG CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
488613 CT CT C
1 CT CT C
488618 CTTTGTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.47
Consensus pattern (2 bp):
CT
Found at i:502108 original size:21 final size:21
Alignment explanation
Indices: 502079--502154 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
502069 TCATAATATC
* *
502079 TAATCATCTGACAAGTCAATA
1 TAATTATCTGACAAGTCAACA
*
502100 TAATTATCTGACAAGTCGACA
1 TAATTATCTGACAAGTCAACA
* * *
502121 TAATGATCTTACAAGTAAACA
1 TAATTATCTGACAAGTCAACA
*
502142 TAATTATTTGACA
1 TAATTATCTGACA
502155 GAAAAAATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (21 bp):
TAATTATCTGACAAGTCAACA
Found at i:502223 original size:21 final size:21
Alignment explanation
Indices: 502194--502309 Score: 124
Period size: 21 Copynumber: 5.5 Consensus size: 21
502184 CATATCATAA
502194 GTCGACTTGTCAGATAATGAT
1 GTCGACTTGTCAGATAATGAT
* * *
502215 GTTGACTTGTCAGGTAATTAT
1 GTCGACTTGTCAGATAATGAT
*
502236 GTCGACTTGTCAAATAATGAT
1 GTCGACTTGTCAGATAATGAT
* *
502257 GTCGACTTGTCAGATGATTAT
1 GTCGACTTGTCAGATAATGAT
* * * ** *
502278 GACAACTTGTCAAATCCTTAT
1 GTCGACTTGTCAGATAATGAT
502299 GTCGACTTGTC
1 GTCGACTTGTC
502310 CGAAAATATT
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 78 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
GTCGACTTGTCAGATAATGAT
Found at i:502241 original size:42 final size:42
Alignment explanation
Indices: 502194--502309 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 42
502184 CATATCATAA
* * *
502194 GTCGACTTGTCAGATAATGATGTTGACTTGTCAGGTAATTAT
1 GTCGACTTGTCAAATAATGATGTCGACTTGTCAGATAATTAT
*
502236 GTCGACTTGTCAAATAATGATGTCGACTTGTCAGATGATTAT
1 GTCGACTTGTCAAATAATGATGTCGACTTGTCAGATAATTAT
* * ** *
502278 GACAACTTGTCAAATCCTTATGTCGACTTGTC
1 GTCGACTTGTCAAATAATGATGTCGACTTGTC
502310 CGAAAATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (42 bp):
GTCGACTTGTCAAATAATGATGTCGACTTGTCAGATAATTAT
Found at i:502416 original size:21 final size:21
Alignment explanation
Indices: 502390--502480 Score: 112
Period size: 21 Copynumber: 4.4 Consensus size: 21
502380 TGTGAATAAG
502390 TGACAAGTCGACATAAAGATC
1 TGACAAGTCGACATAAAGATC
* * * **
502411 TAACAAGTCAATATAATTATC
1 TGACAAGTCGACATAAAGATC
*
502432 TGACAAGTCGACATCAAGATC
1 TGACAAGTCGACATAAAGATC
*
502453 TG-CAAGTCGACATAATGATC
1 TGACAAGTCGACATAAAGATC
502473 TGACAAGT
1 TGACAAGT
502481 GGTGGCAGAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 18 0.32
21 38 0.68
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (21 bp):
TGACAAGTCGACATAAAGATC
Found at i:502451 original size:42 final size:41
Alignment explanation
Indices: 502390--502480 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
502380 TGTGAATAAG
* *
502390 TGACAAGTCGACATAAAGATCTAACAAGTCAATATAATTATC
1 TGACAAGTCGACATAAAGATCT-ACAAGTCAACATAATGATC
* * *
502432 TGACAAGTCGACATCAAGATCTGCAAGTCGACATAATGATC
1 TGACAAGTCGACATAAAGATCTACAAGTCAACATAATGATC
502473 TGACAAGT
1 TGACAAGT
502481 GGTGGCAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (41 bp):
TGACAAGTCGACATAAAGATCTACAAGTCAACATAATGATC
Found at i:502715 original size:2 final size:2
Alignment explanation
Indices: 502708--502759 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
502698 TAGATAGGTA
502708 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
502750 AG AG AG AG AG
1 AG AG AG AG AG
502760 GGAGGGAGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:512876 original size:2 final size:2
Alignment explanation
Indices: 512869--512934 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
512859 CCAAGAAAGA
512869 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
512911 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
512935 TTTATCAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:513922 original size:26 final size:26
Alignment explanation
Indices: 513893--514029 Score: 76
Period size: 26 Copynumber: 5.2 Consensus size: 26
513883 ATGGTATAAG
513893 TGCCATGTTGTAAATTTTGTATTTAC
1 TGCCATGTTGTAAATTTTGTATTTAC
**** **** *
513919 TGCCACCCGGTAAATTCAAAATTTAGT
1 TGCCATGTTGTAAATTTTGTATTTA-C
*
513946 TGTCATGTTGTAAATTTTGTATTTAC
1 TGCCATGTTGTAAATTTTGTATTTAC
**** **** *
513972 TGCCACCCGGTAAATTCAAAATTTAGT
1 TGCCATGTTGTAAATTTTGTATTTA-C
*
513999 TGTCATGTTGTAAATTTTGTATTTAC
1 TGCCATGTTGTAAATTTTGTATTTAC
514025 TGCCA
1 TGCCA
514030 CCCGGTAAAT
Statistics
Matches: 69, Mismatches: 40, Indels: 4
0.61 0.35 0.04
Matches are distributed among these distances:
26 37 0.54
27 32 0.46
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (26 bp):
TGCCATGTTGTAAATTTTGTATTTAC
Found at i:513960 original size:27 final size:27
Alignment explanation
Indices: 513928--514014 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
513918 CTGCCACCCG
513928 GTAAATTCAAAATTTAGTTGTCATGTT
1 GTAAATTCAAAATTTAGTTGTCATGTT
**** * * ****
513955 GTAAATTTTGTATTTA-CTGCCACCCG
1 GTAAATTCAAAATTTAGTTGTCATGTT
513981 GTAAATTCAAAATTTAGTTGTCATGTT
1 GTAAATTCAAAATTTAGTTGTCATGTT
514008 GTAAATT
1 GTAAATT
514015 TTGTATTTAC
Statistics
Matches: 39, Mismatches: 20, Indels: 2
0.64 0.33 0.03
Matches are distributed among these distances:
26 16 0.41
27 23 0.59
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (27 bp):
GTAAATTCAAAATTTAGTTGTCATGTT
Found at i:513976 original size:53 final size:53
Alignment explanation
Indices: 513896--514049 Score: 308
Period size: 53 Copynumber: 2.9 Consensus size: 53
513886 GTATAAGTGC
513896 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
1 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
513949 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
1 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
514002 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTA
1 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTA
514050 NNNNNNNNNN
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 101 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (53 bp):
CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
Found at i:514022 original size:27 final size:27
Alignment explanation
Indices: 513939--514023 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 27
513929 TAAATTCAAA
513939 ATTTAGTTGTCATGTTGTAAATTTTGT
1 ATTTAGTTGTCATGTTGTAAATTTTGT
* * **** ****
513966 ATTTA-CTGCCACCCGGTAAATTCAAA
1 ATTTAGTTGTCATGTTGTAAATTTTGT
513992 ATTTAGTTGTCATGTTGTAAATTTTGT
1 ATTTAGTTGTCATGTTGTAAATTTTGT
514019 ATTTA
1 ATTTA
514024 CTGCCACCCG
Statistics
Matches: 37, Mismatches: 20, Indels: 2
0.63 0.34 0.03
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (27 bp):
ATTTAGTTGTCATGTTGTAAATTTTGT
Found at i:514048 original size:26 final size:26
Alignment explanation
Indices: 513913--514049 Score: 76
Period size: 26 Copynumber: 5.2 Consensus size: 26
513903 TAAATTTTGT
513913 ATTTACTGCCACCCGGTAAATTCAAA
1 ATTTACTGCCACCCGGTAAATTCAAA
* * **** ****
513939 ATTTAGTTGTCATGTTGTAAATTTTGT
1 ATTTA-CTGCCACCCGGTAAATTCAAA
513966 ATTTACTGCCACCCGGTAAATTCAAA
1 ATTTACTGCCACCCGGTAAATTCAAA
* * **** ****
513992 ATTTAGTTGTCATGTTGTAAATTTTGT
1 ATTTA-CTGCCACCCGGTAAATTCAAA
514019 ATTTACTGCCACCCGGTAAATTCAAA
1 ATTTACTGCCACCCGGTAAATTCAAA
514045 ATTTA
1 ATTTA
514050 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 40, Indels: 4
0.61 0.35 0.04
Matches are distributed among these distances:
26 37 0.54
27 32 0.46
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (26 bp):
ATTTACTGCCACCCGGTAAATTCAAA
Found at i:514358 original size:2 final size:2
Alignment explanation
Indices: 514351--514391 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
514341 NNNNNNNNNN
514351 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
514392 TTTATCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:515379 original size:26 final size:26
Alignment explanation
Indices: 515350--515433 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
515340 ATGGTATAAG
515350 TGCCATGTTGTAAATTTTGTATTTAC
1 TGCCATGTTGTAAATTTTGTATTTAC
**** **** *
515376 TGCCACCCGGTAAATTCAAAATTTAGT
1 TGCCATGTTGTAAATTTTGTATTTA-C
*
515403 TGTCATGTTGTAAATTTTGTATTTAC
1 TGCCATGTTGTAAATTTTGTATTTAC
515429 TGCCA
1 TGCCA
515434 CCCGGTAAAT
Statistics
Matches: 37, Mismatches: 20, Indels: 2
0.63 0.34 0.03
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (26 bp):
TGCCATGTTGTAAATTTTGTATTTAC
Found at i:515433 original size:53 final size:53
Alignment explanation
Indices: 515353--515453 Score: 202
Period size: 53 Copynumber: 1.9 Consensus size: 53
515343 GTATAAGTGC
515353 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
1 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
515406 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTA
1 CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTA
515454 CAACATGACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (53 bp):
CATGTTGTAAATTTTGTATTTACTGCCACCCGGTAAATTCAAAATTTAGTTGT
Found at i:515452 original size:26 final size:26
Alignment explanation
Indices: 515370--515454 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
515360 TAAATTTTGT
515370 ATTTACTGCCACCCGGTAAATTCAAA
1 ATTTACTGCCACCCGGTAAATTCAAA
* * **** ****
515396 ATTTAGTTGTCATGTTGTAAATTTTGT
1 ATTTA-CTGCCACCCGGTAAATTCAAA
515423 ATTTACTGCCACCCGGTAAATTCAAA
1 ATTTACTGCCACCCGGTAAATTCAAA
515449 ATTTAC
1 ATTTAC
515455 AACATGACAT
Statistics
Matches: 38, Mismatches: 20, Indels: 2
0.63 0.33 0.03
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (26 bp):
ATTTACTGCCACCCGGTAAATTCAAA
Found at i:520611 original size:15 final size:16
Alignment explanation
Indices: 520591--520622 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
520581 CTTCCACATT
520591 AATGTTTTCTTT-ATC
1 AATGTTTTCTTTCATC
520606 AATGTTTTCTTTCATC
1 AATGTTTTCTTTCATC
520622 A
1 A
520623 TTGGCGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (16 bp):
AATGTTTTCTTTCATC
Found at i:522510 original size:18 final size:18
Alignment explanation
Indices: 522475--522508 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
522465 TATAATGTCC
522475 GATAAAAGCTTATGAAAG
1 GATAAAAGCTTATGAAAG
*
522493 GATATAAGC-TATGAAA
1 GATAAAAGCTTATGAAA
522509 AGCAATAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (18 bp):
GATAAAAGCTTATGAAAG
Found at i:524745 original size:14 final size:13
Alignment explanation
Indices: 524726--524787 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 13
524716 AATTTAGATT
524726 TTATTTATCTGCTA
1 TTATTTATCTGC-A
* *
524740 TTATTTTTGTTGCA
1 TTATTTAT-CTGCA
524754 TTATTTATCTG--
1 TTATTTATCTGCA
*
524765 TT-TTTGT-TGCA
1 TTATTTATCTGCA
524776 TTATTTATCTGC
1 TTATTTATCTGC
524788 TTTTGATTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
9 2 0.05
10 4 0.11
11 4 0.11
12 4 0.11
13 5 0.14
14 15 0.41
15 3 0.08
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.61
Consensus pattern (13 bp):
TTATTTATCTGCA
Found at i:524768 original size:22 final size:22
Alignment explanation
Indices: 524743--524792 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
524733 TCTGCTATTA
524743 TTTTTGTTGCATTATTTATCTG
1 TTTTTGTTGCATTATTTATCTG
524765 TTTTTGTTGCATTATTTATCTG
1 TTTTTGTTGCATTATTTATCTG
*
524787 CTTTTG
1 TTTTTG
524793 ATTTTTGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTTTGTTGCATTATTTATCTG
Found at i:524820 original size:28 final size:29
Alignment explanation
Indices: 524765--524820 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
524755 TATTTATCTG
* **
524765 TTTTTGTTGCATTATTTATCTGCTTTTGA
1 TTTTTGTGGCATTATAGATCTGCTTTTGA
*
524794 TTTTTGTGGCATTATAGATGTG-TTTTG
1 TTTTTGTGGCATTATAGATCTGCTTTTG
524821 TTTACAGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.14, C:0.07, G:0.20, T:0.59
Consensus pattern (29 bp):
TTTTTGTGGCATTATAGATCTGCTTTTGA
Found at i:529889 original size:2 final size:2
Alignment explanation
Indices: 529884--529921 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
529874 ATGTGTGTGT
529884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
529922 TCATCAGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:537398 original size:25 final size:25
Alignment explanation
Indices: 537364--537413 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
537354 CAGGATTTTT
537364 GCTTGTTCTTCACATACCATACATC
1 GCTTGTTCTTCACATACCATACATC
537389 GCTTGTTCTTCACATACCATACATC
1 GCTTGTTCTTCACATACCATACATC
537414 AAGTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (25 bp):
GCTTGTTCTTCACATACCATACATC
Found at i:543399 original size:2 final size:2
Alignment explanation
Indices: 543392--543442 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
543382 TTGTATATGT
543392 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
543434 TC TC TC TC T
1 TC TC TC TC T
543443 TACGCATGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:553607 original size:13 final size:13
Alignment explanation
Indices: 553589--553613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
553579 AAGCTCCGGT
553589 TTTTTAATTTTAA
1 TTTTTAATTTTAA
553602 TTTTTAATTTTA
1 TTTTTAATTTTA
553614 GCAGCGTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATTTTAA
Found at i:584110 original size:23 final size:23
Alignment explanation
Indices: 584049--584121 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
584039 TGATATTACA
584049 GTTT-CGGGAGGGCAATATAACT
1 GTTTCCGGGAGGGCAATATAACT
* *
584071 ATTTCCTGTGA----AATATAACT
1 GTTTCC-GGGAGGGCAATATAACT
584091 GTTTCCGGGAGGGCAATATAACT
1 GTTTCCGGGAGGGCAATATAACT
584114 GTTTCCGG
1 GTTTCCGG
584122 TGTGATTCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
19 3 0.07
20 14 0.34
22 3 0.07
23 18 0.44
24 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (23 bp):
GTTTCCGGGAGGGCAATATAACT
Found at i:599848 original size:167 final size:167
Alignment explanation
Indices: 599430--600056 Score: 903
Period size: 165 Copynumber: 3.8 Consensus size: 167
599420 GTGAATATGC
* * * * * * *
599430 AAAATAAGCAA-AGTCGACATTTAACAGAAAGCTGGCATCCGTTTGGTACAGAAATATATCCCAC
1 AAAATAAGCAATA-TCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * *
599494 AATATGGTATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
65 GATATGGCATGCCTTAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
* **
599559 AAATCTTTGAG-GAAAATTTGCTTGAAAATTTT-GCCT-
130 AAATCTTTG-GCGAAAATTTGTTTGAAAATTTTGGTTTA
*
599595 AAAATAAACAGAGTA-C-TCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCA
1 AAAATAAGCA-A-TATCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCA
*
599658 CGATATGGCATGCCTTAACAAATAATGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
64 CGATATGGCATGCCTTAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA
599723 GAAATCTTTGGCGAAAATTTGTTTGAAAATTTTGGTTTA
129 GAAATCTTTGGCGAAAATTTGTTTGAAAATTTTGGTTTA
*
599762 AAAATAAGCAATATCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAATATCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
599827 ATATGGCATGCC-TATACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
66 ATATGGCATGCCTTA-ACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
* *
599891 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
130 AAATCTTTGGCGAAAATTTGTTTGAAAATTTTGGTTTA
* *
599929 AAAATAAGCAATGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTAC--TAATATATCCCACG
1 AAAATAAGCAATATCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * *
599992 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCCGAGA
66 ATATGGCATGCCTTAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
600057 TAAATGCGAC
Statistics
Matches: 422, Mismatches: 30, Indels: 20
0.89 0.06 0.04
Matches are distributed among these distances:
164 1 0.00
165 212 0.50
166 10 0.02
167 198 0.47
168 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (167 bp):
AAAATAAGCAATATCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTTAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGGCGAAAATTTGTTTGAAAATTTTGGTTTA
Found at i:600036 original size:332 final size:331
Alignment explanation
Indices: 599430--600056 Score: 974
Period size: 332 Copynumber: 1.9 Consensus size: 331
599420 GTGAATATGC
* * *
599430 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGTTTGGTACAGAAATATATCCCACA
1 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGACATCCGATTGGTACAAAAATATATCCCACA
*
599495 ATATGGTATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
*
599560 AATCTTTGAGGAAAATTTGCTTGAAAATTTTGCCTAAAATAAACAGAGTACTCATTTAACAGGAA
131 AATCTTTGACGAAAATTTGCTTGAAAATTTTGCCTAAAATAAACAGAGTACTCATTTAACAGGAA
*
599625 GTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTTAACAAATAATGTGTAA
196 GTTGACGTCCGATTGGTAC-AAAATATATCCCACGATATGGCATGCCTTAACAAACAATGTGTAA
*
599690 AAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGGCGAAAATTTGTTTGAAAATTT
260 AAATTTCAAGCATCTGCGATAAATAGCTGCCGAGAAATCTTTGGCGAAAATTTGTTTGAAAATTT
599755 TGGTTTA
325 TGGTTTA
* * * * *
599762 AAAATAAGCAATA-TCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCAC
1 AAAATAAGCAA-AGTCGACATTTAACAGAAAGCTGACATCCGATTGGTACAAAAATATATCCCAC
* * *
599826 GATATGGCATGCCTATACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
65 AATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG
* ** *
599891 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAAAAAATAAGCA-ATGT-CGTCATTTAAC
130 AAATCTTTGACGAAAATTTGCTTGAAAATTTTGCCT--AAAATAAACAGA-GTAC-TCATTTAAC
* *
599954 AGGAAGTTGACGTCCGATTGGTAC-TAATATATCCCACGATATGGCATGCCTTAACAAACACTGT
191 AGGAAGTTGACGTCCGATTGGTACAAAATATATCCCACGATATGGCATGCCTTAACAAACAATGT
*
600018 GTAAAAATTTCAAGCATCTGCGATAAATAGTTGCCGAGA
256 GTAAAAATTTCAAGCATCTGCGATAAATAGCTGCCGAGA
600057 TAAATGCGAC
Statistics
Matches: 268, Mismatches: 22, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
332 221 0.82
333 3 0.01
334 44 0.16
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (331 bp):
AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGACATCCGATTGGTACAAAAATATATCCCACA
ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
AATCTTTGACGAAAATTTGCTTGAAAATTTTGCCTAAAATAAACAGAGTACTCATTTAACAGGAA
GTTGACGTCCGATTGGTACAAAATATATCCCACGATATGGCATGCCTTAACAAACAATGTGTAAA
AATTTCAAGCATCTGCGATAAATAGCTGCCGAGAAATCTTTGGCGAAAATTTGTTTGAAAATTTT
GGTTTA
Found at i:611069 original size:9 final size:9
Alignment explanation
Indices: 611057--611090 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
611047 CTATCAGTCA
611057 TATCTATAC
1 TATCTATAC
611066 TATCTATAC
1 TATCTATAC
*
611075 TGTCTATAC
1 TATCTATAC
611084 TAT-TATA
1 TATCTATA
611091 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (9 bp):
TATCTATAC
Found at i:612199 original size:2 final size:2
Alignment explanation
Indices: 612194--612228 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
612184 TTTTTTAGCG
612194 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
612229 ACACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:614895 original size:163 final size:162
Alignment explanation
Indices: 614694--615087 Score: 569
Period size: 163 Copynumber: 2.4 Consensus size: 162
614684 TGGAGTAGCT
* * * * *
614694 ACATCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
* *
614759 ATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATTAACGTTTATCACTAAAAAAACAAACATTGA
66 ATTTCATCCAGGGAGTCAAAAAGTAGCAGAAAATTAACGTTTATCACT-AAAAAA-AAACATAGA
*
614824 TCCAAGAGCTCCTCTTATGATTTAATGGATAGAC
129 TCCAAGAACTCCTCTTATGATTTAATGGATAGAC
* *
614858 A-ATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTCAAAATTTAA
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
* **
614922 ATTTCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACGTTTATCACTTCAAAAAAACATAGATC
66 ATTTCATCCAGGGAGTCAAAAAGTAGCAGAAAATTAACGTTTATCACTAAAAAAAAACATAGATC
* *
614987 CTAGAACTCCTTTTATGATTTAATGGATAGAC
131 CAAGAACTCCTCTTATGATTTAATGGATAGAC
* * *
615019 ACATCATATCTTGGGATATGATAGGAACTGTTCCATAGATGTGCATTACA-GTTTTGAAAAA-TT
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATA-AGGTTTT-AAAAATTT
615082 AAATTT
64 AAATTT
615088 AACCCTGAGG
Statistics
Matches: 208, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
161 40 0.19
162 60 0.29
163 107 0.51
164 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (162 bp):
ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
ATTTCATCCAGGGAGTCAAAAAGTAGCAGAAAATTAACGTTTATCACTAAAAAAAAACATAGATC
CAAGAACTCCTCTTATGATTTAATGGATAGAC
Found at i:615285 original size:135 final size:135
Alignment explanation
Indices: 615135--615433 Score: 381
Period size: 134 Copynumber: 2.2 Consensus size: 135
615125 GATGCCCTTT
* * *
615135 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATTCATGCAC
1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAGGCAC
* * * * * *
615199 TTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTTGATGCCCCT
65 TTCCTGTTCAA-GGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCA
615264 TGACA-C
129 TGACATC
* *
615270 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC
1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC
* ** *
615334 TTGCTGTTTGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCTCCAT
65 TTCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCAT
615399 GACATC
130 GACATC
* **
615405 -AGAAACATTAATATATATGGTTAAGGGGT
1 AAGGAACAAGAATATATATGGTTAAGGGGT
615434 CATGATTATA
Statistics
Matches: 142, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
133 4 0.03
134 73 0.51
135 61 0.43
136 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT
TCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCATG
ACATC
Found at i:633370 original size:13 final size:13
Alignment explanation
Indices: 633352--633376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
633342 GCTATTGAAG
633352 GTTTTACATACAT
1 GTTTTACATACAT
633365 GTTTTACATACA
1 GTTTTACATACA
633377 GTACATGATA
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:0.08, T:0.44
Consensus pattern (13 bp):
GTTTTACATACAT
Found at i:641404 original size:12 final size:13
Alignment explanation
Indices: 641379--641409 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
641369 TTAAGAGAAC
*
641379 TTTTATTCATTTT
1 TTTTTTTCATTTT
641392 TTTTTTTCATTTT
1 TTTTTTTCATTTT
641405 TTTTT
1 TTTTT
641410 GTTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTCATTTT
Found at i:641428 original size:17 final size:17
Alignment explanation
Indices: 641408--641443 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
641398 TCATTTTTTT
641408 TTGTTTAAATATTCGTC
1 TTGTTTAAATATTCGTC
641425 TTGTTTAAATATTCGTC
1 TTGTTTAAATATTCGTC
641442 TT
1 TT
641444 AATTGTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (17 bp):
TTGTTTAAATATTCGTC
Found at i:642088 original size:3 final size:3
Alignment explanation
Indices: 642068--642107 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
642058 GAATGAATCT
* *
642068 ATG ATA ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
642108 AAGTAACTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:651112 original size:2 final size:2
Alignment explanation
Indices: 651105--651131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
651095 NNNNNNNNNN
651105 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
651132 GAAATGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:651721 original size:1 final size:1
Alignment explanation
Indices: 651683--651710 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
651673 GTAATTTTGT
651683 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
651711 CTGTGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:654887 original size:2 final size:2
Alignment explanation
Indices: 654880--654912 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
654870 ACAAACACAG
654880 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
654913 TACTAATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:656829 original size:21 final size:21
Alignment explanation
Indices: 656804--656852 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
656794 TCGTGTTAAC
* *
656804 CGTTTCGTGTGAATCGTGAAG
1 CGTTTCGTGTAAACCGTGAAG
**
656825 CGTTTCGTGTAAACCGTTTAG
1 CGTTTCGTGTAAACCGTGAAG
656846 CGTTTCG
1 CGTTTCG
656853 GACAAAGCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTGAAG
Found at i:658253 original size:32 final size:33
Alignment explanation
Indices: 658210--658286 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
658200 ATTGACCCGG
658210 GTTGAAAATTGACCC-GGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
*
658242 GTTGAATATTGACCCGGGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
658275 GTTGAAAATTGA
1 GTTGAAAATTGA
658287 GACCAAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 14 0.33
33 28 0.67
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (33 bp):
GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
Found at i:663787 original size:456 final size:456
Alignment explanation
Indices: 662934--664179 Score: 2329
Period size: 456 Copynumber: 2.7 Consensus size: 456
662924 NNNNNNNNNN
662934 TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGAG
1 TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGAG
662999 TGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTTG
66 TGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTTG
663064 TTTATATTTTCAATGTTGAAGAACAAATATCAAATTTAAACCTAAAATGAATGTGTTAAACGTTA
131 TTTATATTTTCAATGTTGAAGAACAAATATCAAATTTAAACCTAAAATGAATGTGTTAAACGTTA
663129 GAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTTT
196 GAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTTT
663194 TAATTGGTAAATTGAACCACATGTATTCCTTTTAAGGAATGATCGGCATGAAATATCATTGGTCA
261 TAATTGGTAAATTGAACCACATGTATTCCTTTTAAGGAATGATCGGCATGAAATATCATTGGTCA
663259 GCTCTGTTTAAATAATTTTTGCACCTTAATTCAAGCTGGGAATGTCTTTTCGGTGACTCCATCTT
326 GCTCTGTTTAAATAATTTTTGCACCTTAATTCAAGCTGGGAATGTCTTTTCGGTGACTCCATCTT
*
663324 TGGTATCCGAAAATTGCATCGTTCCTATTCTTAAAGGGGCATGGTCACGATTTTGGTCAAAAAA-
391 TGGTATCCGAAAAGTGCATCGTTCCTATTCTTAAAGGGGCATGGTCACGATTTTGGTCAAAAAAT
663388 A
456 A
663389 TTTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGA
1 -TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGA
663454 GTGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTT
65 GTGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTT
663519 GTTTATATTTTCAATGTTGAAGAACAAATATCAAATTTAAACCTAAAATGAATGTGTTAAACGTT
130 GTTTATATTTTCAATGTTGAAGAACAAATATCAAATTTAAACCTAAAATGAATGTGTTAAACGTT
663584 AGAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTT
195 AGAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTT
663649 TTAATTGGTAAATTGAACCACATGTATTCCTTTTAAGGAATGATCGGCATGAAATATCATTGGTC
260 TTAATTGGTAAATTGAACCACATGTATTCCTTTTAAGGAATGATCGGCATGAAATATCATTGGTC
663714 AGCTCTGTTTAAATAATTTTTGCACCTTAATTCAAGCTGGGAATGTCTTTTCGGTGACTCCATCT
325 AGCTCTGTTTAAATAATTTTTGCACCTTAATTCAAGCTGGGAATGTCTTTTCGGTGACTCCATCT
* * *
663779 TTGGTATCCTAATAGTGCATCGTTCCTATTCTTAAAGGGGCATGGTCACGATTTTGGTCAAAAAT
390 TTGGTATCCGAAAAGTGCATCGTTCCTATTCTTAAAGGGGCATGGTCACGATTTTGGTCAAAAAA
663844 TA
455 TA
* *
663846 TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAACAAGATTTGAG
1 TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGAG
663911 TGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTTG
66 TGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTTG
* * * *
663976 TTTA-CTTTTCAATGTTGAAGTACAAATTTTTAAATTTAAACCTAAAATGAATGTGTTAAACGTT
131 TTTATATTTTCAATGTTGAAGAACAAA-TATCAAATTTAAACCTAAAATGAATGTGTTAAACGTT
*
664040 AGAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTG-AAAAAG-GTTT
195 AGAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTT
*
664103 TTAATTGGTAAATTGAACCACAAGTATTCCTTTTAAAGGAATGATCGGCATGAAATATCATTGGT
260 TTAATTGGTAAATTGAACCACATGTATTCCTTTT-AAGGAATGATCGGCATGAAATATCATTGGT
664168 CAGCTCTGTTTA
324 CAGCTCTGTTTA
664180 TAAAATATAC
Statistics
Matches: 775, Mismatches: 12, Indels: 7
0.98 0.02 0.01
Matches are distributed among these distances:
454 36 0.05
455 68 0.09
456 670 0.86
457 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (456 bp):
TTTTTCCGATTTGAATAATTACAATGGTTTAGTGAGGCATTCTTAATAGGCAAAAAAAATTTGAG
TGTCATTTGTTGAGTTATAAGCGAGTTACAGAGCTTACAATACTTTAACTAAAACAAAGCTTTTG
TTTATATTTTCAATGTTGAAGAACAAATATCAAATTTAAACCTAAAATGAATGTGTTAAACGTTA
GAAACTGTTTATCTATGCTTAAAATGAATAAGAAGATAGAAAAATCAGCTTGAAAAAAGTTTTTT
TAATTGGTAAATTGAACCACATGTATTCCTTTTAAGGAATGATCGGCATGAAATATCATTGGTCA
GCTCTGTTTAAATAATTTTTGCACCTTAATTCAAGCTGGGAATGTCTTTTCGGTGACTCCATCTT
TGGTATCCGAAAAGTGCATCGTTCCTATTCTTAAAGGGGCATGGTCACGATTTTGGTCAAAAAAT
A
Found at i:665102 original size:16 final size:16
Alignment explanation
Indices: 665081--665135 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
665071 TGCTAGTAGG
* *
665081 CCTTCGGTCAAATGAA
1 CCTTCGATCTAATGAA
* *
665097 CCTTCGAACTATTGAA
1 CCTTCGATCTAATGAA
*
665113 CCTTCGATTTAATGAA
1 CCTTCGATCTAATGAA
665129 CCTTCGA
1 CCTTCGA
665136 GCCATTGGGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (16 bp):
CCTTCGATCTAATGAA
Found at i:684806 original size:1 final size:1
Alignment explanation
Indices: 684802--684829 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
684792 CTGATTTTGT
684802 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
684830 GGTGGAGGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:684987 original size:11 final size:10
Alignment explanation
Indices: 684963--685001 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
684953 TCCTGGATTA
684963 ATTGGGGTTC
1 ATTGGGGTTC
684973 ATTGGGGTATC
1 ATTGGGGT-TC
684984 ATTGGGGTTC
1 ATTGGGGTTC
684994 ATTGGGGT
1 ATTGGGGT
685002 AAAAAGACGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.13, C:0.08, G:0.41, T:0.38
Consensus pattern (10 bp):
ATTGGGGTTC
Found at i:684989 original size:21 final size:21
Alignment explanation
Indices: 684963--685002 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
684953 TCCTGGATTA
684963 ATTGGGGTTCATTGGGGTATC
1 ATTGGGGTTCATTGGGGTATC
684984 ATTGGGGTTCATTGGGGTA
1 ATTGGGGTTCATTGGGGTA
685003 AAAAGACGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.07, G:0.40, T:0.38
Consensus pattern (21 bp):
ATTGGGGTTCATTGGGGTATC
Found at i:701236 original size:2 final size:2
Alignment explanation
Indices: 701231--701264 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
701221 GGTTTTTTTA
701231 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
701265 CATGTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:702738 original size:185 final size:185
Alignment explanation
Indices: 702405--702743 Score: 525
Period size: 185 Copynumber: 1.8 Consensus size: 185
702395 AACGGAAACC
* * * * * *
702405 CTTTAAATGATGTTTTGGAGGAAACTCTTACAGGAGAGAACGTTTCTTAGCCCTTGTGATAAAGT
1 CTTTAAATGATGTTTCGGAGGAAACTCTTACAGAAGAAAACGATTCTTAACCCTAGTGATAAAGT
* *
702470 TGAAGGGTTGACTCTGTAACCGCGAGTAATATAAATCGAATATCATTTTAGTGGAAATTCTCAAA
66 TGAAAGGTTGACTCTGTAACCGCGAGTAATATAAATCGAATATCATTTCAGTGGAAATTCTCAAA
702535 TCAAAGTCTAAGTTTGGAATCTCTATCTTTTTTGTTATAAAACGAAACCCTTAAG
131 TCAAAGTCTAAGTTTGGAATCTCTATCTTTTTTGTTATAAAACGAAACCCTTAAG
* *
702590 CTTTAGATGATGTTTCGGAGGAAACTTTTACAGAAGAAAACGATTCTTAACCCTAGTGATAAAGT
1 CTTTAAATGATGTTTCGGAGGAAACTCTTACAGAAGAAAACGATTCTTAACCCTAGTGATAAAGT
** * **
702655 TGAAAGGTTGGTTCTGTAACCGCGAGTAATATAAATCGAATGTCATTTCAGTGGAAATTCTCGGA
66 TGAAAGGTTGACTCTGTAACCGCGAGTAATATAAATCGAATATCATTTCAGTGGAAATTCTCAAA
* *
702720 TCAATGTCTAATTTTGGAATCTCT
131 TCAAAGTCTAAGTTTGGAATCTCT
702744 CTTGGTTTTC
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
185 137 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (185 bp):
CTTTAAATGATGTTTCGGAGGAAACTCTTACAGAAGAAAACGATTCTTAACCCTAGTGATAAAGT
TGAAAGGTTGACTCTGTAACCGCGAGTAATATAAATCGAATATCATTTCAGTGGAAATTCTCAAA
TCAAAGTCTAAGTTTGGAATCTCTATCTTTTTTGTTATAAAACGAAACCCTTAAG
Found at i:704401 original size:18 final size:18
Alignment explanation
Indices: 704380--704417 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
704370 TAAACAGTCG
704380 TTCTATGTTAATGAGTAT
1 TTCTATGTTAATGAGTAT
*
704398 TTCTATGTTATTGAGTAT
1 TTCTATGTTAATGAGTAT
704416 TT
1 TT
704418 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.55
Consensus pattern (18 bp):
TTCTATGTTAATGAGTAT
Found at i:713527 original size:2 final size:2
Alignment explanation
Indices: 713520--713555 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
713510 ATAATCTCAA
*
713520 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
713556 AAATGACGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:718120 original size:36 final size:36
Alignment explanation
Indices: 718080--718153 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
718070 TGTCGCTGCC
718080 GTCGTGGACGGGCTAGTGGCTGGGCTTGTTTGTTCT
1 GTCGTGGACGGGCTAGTGGCTGGGCTTGTTTGTTCT
718116 GTCGTGGACGGGCTAGTGGCTGGGCTTGTTTGTTCT
1 GTCGTGGACGGGCTAGTGGCTGGGCTTGTTTGTTCT
718152 GT
1 GT
718154 ACTAGAGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.05, C:0.16, G:0.42, T:0.36
Consensus pattern (36 bp):
GTCGTGGACGGGCTAGTGGCTGGGCTTGTTTGTTCT
Found at i:747385 original size:2 final size:2
Alignment explanation
Indices: 747378--747412 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
747368 AATCCGTCTC
747378 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
747413 CGCATCAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:751792 original size:15 final size:15
Alignment explanation
Indices: 751772--751801 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
751762 AAATGCGTTT
751772 GATGTAATATTCATA
1 GATGTAATATTCATA
*
751787 GATGTAATTTTCATA
1 GATGTAATATTCATA
751802 AGAAAGGCGT
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:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (15 bp):
GATGTAATATTCATA
Found at i:752400 original size:40 final size:40
Alignment explanation
Indices: 752355--752440 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
752345 CGTTCATGCT
752355 GGAAGCTCAGATGACGGCCGACATATCCAGTGATCCAGGG
1 GGAAGCTCAGATGACGGCCGACATATCCAGTGATCCAGGG
*
752395 GGAAGCTCAGGTGACGGCCGACATATCCAGTGATCCAGGG
1 GGAAGCTCAGATGACGGCCGACATATCCAGTGATCCAGGG
752435 GGAAGC
1 GGAAGC
752441 AAACACAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.27, C:0.24, G:0.35, T:0.14
Consensus pattern (40 bp):
GGAAGCTCAGATGACGGCCGACATATCCAGTGATCCAGGG
Found at i:766235 original size:22 final size:23
Alignment explanation
Indices: 766205--766248 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
766195 AAAATCTACC
*
766205 AATTCAAATTGAAATTATCAAAA
1 AATTCAAATTGAAATTACCAAAA
*
766228 AATT-AAATTTAAATTACCAAA
1 AATTCAAATTGAAATTACCAAA
766249 TTTCTTTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
AATTCAAATTGAAATTACCAAAA
Found at i:770461 original size:7 final size:7
Alignment explanation
Indices: 770449--770515 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
770439 GAGAAGGATC
770449 ATTCGAG
1 ATTCGAG
770456 ATTCGAG
1 ATTCGAG
*
770463 ATTCGAA
1 ATTCGAG
*
770470 ATACGAG
1 ATTCGAG
*
770477 ATTCGAA
1 ATTCGAG
*
770484 ATACGAG
1 ATTCGAG
770491 ATTCGAG
1 ATTCGAG
*
770498 ATTCGAA
1 ATTCGAG
770505 ATTCGAG
1 ATTCGAG
770512 ATTC
1 ATTC
770516 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:784542 original size:18 final size:18
Alignment explanation
Indices: 784519--784556 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
784509 TTTTAAGGTT
*
784519 ATTAAAATAAAGATTATC
1 ATTAAAATAAAAATTATC
784537 ATTAAAATAAAAATTATC
1 ATTAAAATAAAAATTATC
784555 AT
1 AT
784557 GAAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (18 bp):
ATTAAAATAAAAATTATC
Found at i:789298 original size:2 final size:2
Alignment explanation
Indices: 789293--789346 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
789283 ACGCCCCCCC
* * *
789293 CT CT CT CT CT CT GT CT CT GT CT CT GT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
789335 CT CT CT CT CT CT
1 CT CT CT CT CT CT
789347 GGTCTGTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (2 bp):
CT
Found at i:790955 original size:11 final size:11
Alignment explanation
Indices: 790939--790968 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
790929 GATATACAAT
790939 CTTTAAGCCAC
1 CTTTAAGCCAC
*
790950 CTTTAAGTCAC
1 CTTTAAGCCAC
790961 CTTTAAGC
1 CTTTAAGC
790969 TTAAACTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:791476 original size:2 final size:2
Alignment explanation
Indices: 791469--791532 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
791459 TCGGTGAAAG
791469 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
791511 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
791533 AACTCAGTGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:794829 original size:2 final size:2
Alignment explanation
Indices: 794822--794885 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
794812 ACTCAAGATA
794822 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
794864 GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT
794886 NGAGGTAAAC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:795055 original size:2 final size:2
Alignment explanation
Indices: 795048--795118 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
795038 ACTCAAGATA
795048 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
795090 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
795119 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:795055 original size:226 final size:225
Alignment explanation
Indices: 794660--795112 Score: 897
Period size: 226 Copynumber: 2.0 Consensus size: 225
794650 TGAACTTACC
794660 TGAGGTAAACCACCCGGTTAAAAACCTCGGCCTTTGAGCTATCTTTAAGGAGAACTTAAAGATGG
1 TGAGGTAAACCACCCGGTTAAAAACCTCGGCCTTTGAGCTATCTTTAAGGAGAACTTAAAGATGG
794725 TCATTTATCCTGTGAATCTGCCATGGTATATTTAGACATACTGTATATTATGAAATCCCTGAAAA
66 TCATTTATCCTGTGAATCTGCCATGGTATATTTAGACATACTGTATATTATGAAATCCCTGAAAA
794790 TGTCCTATAAAGCTGTTTATCTACTCAAGATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
131 TGTCCTATAAAGCTGTTTATCTACTCAAGATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
794855 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
196 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
794885 TNGAGGTAAACCACCCGGTTAAAAACCTCGGCCTTTGAGCTATCTTTAAGGAGAACTTAAAGATG
1 T-GAGGTAAACCACCCGGTTAAAAACCTCGGCCTTTGAGCTATCTTTAAGGAGAACTTAAAGATG
794950 GTCATTTATCCTGTGAATCTGCCATGGTATATTTAGACATACTGTATATTATGAAATCCCTGAAA
65 GTCATTTATCCTGTGAATCTGCCATGGTATATTTAGACATACTGTATATTATGAAATCCCTGAAA
795015 ATGTCCTATAAAGCTGTTTATCTACTCAAGATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
130 ATGTCCTATAAAGCTGTTTATCTACTCAAGATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
795080 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
195 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
795111 TG
1 TG
795113 TGTGTGNNNN
Statistics
Matches: 227, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
225 2 0.01
226 225 0.99
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.37
Consensus pattern (225 bp):
TGAGGTAAACCACCCGGTTAAAAACCTCGGCCTTTGAGCTATCTTTAAGGAGAACTTAAAGATGG
TCATTTATCCTGTGAATCTGCCATGGTATATTTAGACATACTGTATATTATGAAATCCCTGAAAA
TGTCCTATAAAGCTGTTTATCTACTCAAGATAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
TGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
Found at i:800926 original size:8 final size:8
Alignment explanation
Indices: 800913--800961 Score: 71
Period size: 8 Copynumber: 6.1 Consensus size: 8
800903 TTGTCTGTAA
800913 TCCGTCTG
1 TCCGTCTG
*
800921 TCCGTCCG
1 TCCGTCTG
800929 TCCGTCTG
1 TCCGTCTG
*
800937 TCTGTCTG
1 TCCGTCTG
*
800945 TCTGTCTG
1 TCCGTCTG
800953 TCCGTCTG
1 TCCGTCTG
800961 T
1 T
800962 AAACTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.00, C:0.35, G:0.24, T:0.41
Consensus pattern (8 bp):
TCCGTCTG
Found at i:800929 original size:4 final size:4
Alignment explanation
Indices: 800916--800961 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
800906 TCTGTAATCC
* * * *
800916 GTCT GTCC GTCC GTCC GTCT GTCT GTCT GTCT GTCT GTCC GTCT GT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GT
800962 AAACTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (4 bp):
GTCT
Found at i:809256 original size:1 final size:1
Alignment explanation
Indices: 809245--809277 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
809235 TACTTACACC
*
809245 AAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
809278 TTGAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:822865 original size:179 final size:180
Alignment explanation
Indices: 822558--822950 Score: 743
Period size: 179 Copynumber: 2.2 Consensus size: 180
822548 NNNNNNNNNN
822558 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCT
1 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCT
822623 ACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGATGTGCATA
66 ACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGATGTGCATA
822688 TTGCTAGGATTTTGATTTCCGATAATTTATG-AAAAAATACCAGCTTTTG
131 TTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACCAGCTTTTG
822737 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCT
1 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCT
*
822802 ACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGGTGTGCATA
66 ACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGATGTGCATA
*
822867 TTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACTAGCTTTTG
131 TTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACCAGCTTTTG
* *
822917 AACTTAGTCATTTTTTGGCAAAATGTTGTATATA
1 AACTTAGTCATTTTTTGGCAAAATATTGCATATA
822951 CATGTAGGGT
Statistics
Matches: 209, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
179 160 0.77
180 49 0.23
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (180 bp):
AACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCT
ACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAGATGTGCATA
TTGCTAGGATTTTGATTTCCGATAATTTATGAAAAAAATACCAGCTTTTG
Found at i:824479 original size:436 final size:433
Alignment explanation
Indices: 823065--824549 Score: 1738
Period size: 435 Copynumber: 3.4 Consensus size: 433
823055 GTGTAATAGA
* * * * ** * * * * * *
823065 TTATAGAAGCAAATATGTTTATCTTACAGTTATGAAGCCAAGCAGTATAACGATTGTCTCATATG
1 TTATAGAAGCAAATGTGTTTATCCT-CAATTATGTATTCAAGCAATGTAATGATTTTATCATGTG
* * * * * * *
823130 TTACGTAATTAGGGGTTTTTAGAGGTCAAAAGTCCAAAACTTTGAACACCTATATCTCAAAAAGG
65 TTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGG
* * * * * *
823195 AAAAATATTTTAAAATGCAGTATAAAAGAAAAGATGCTCAAAATGATGTACTTAACAACATGCAA
130 AAAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATGTTC-TAACAAAATGCAA
** * * * * *
823260 CCTAAAAAATTTGGTTCAGCGGCCCCAATAAGGAGATAAGGGACCGGCCCTTAAAACATTCTGTC
194 CCTTCAAAATTTCGTTAAACGGCCCCTATAAGGAGATAAGGGACCGGCCCTTAAAACATTCTTTC
* * ** * * * * *
823325 TCAGATATCTAAAGAATAGTAACGAATTTCTGAACACTTCTTCAACAAAATGTCT-TAATAATCA
259 TCATATATCTCAAGAACGGTAACGAATTTCTAAACACTTGTTGAACAAAAT-T-TGTAAGAATTA
* * *
823389 AATGACCTTTCTTTTGATACCAAGAAAAAAGGGCT-GACCCTAATATTA-GGGACCTAAAGGGCT
322 AATGACCTTTCATTTGATATCAAG-AAAAAGGGCTGGACCCTAAAATTAGGGGACC-AAAGGGCT
* *
823452 CTAAAGTCTTTTA-CTCATAACTCTTTACCGAGGGATATTTTGT--AATAG
385 CTAAAGTCTTTTATCT-ATAACCCTTTACTGAGGGATATTTTGTGAAAT-G
* **
823500 ATTAAAGAAGCAAACATGTTTAT-CTCACAGTTATGTATTCAAGCAATGTAATGATTTTATCATG
1 -TTATAGAAGCAAATGTGTTTATCCTCA-A-TTATGTATTCAAGCAATGTAATGATTTTATCATG
* * *
823564 TGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGCCCAAAATTTCGATCATCCATATCTCAGAAA
63 TGTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAA
* *
823629 GGAAAAATATTTTGAAATGCAGTACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAA-AAATTTG
128 GGAAAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATGTTC-TAACAAA-ATG
* * * * *
823693 CAACCGTC-AAATTTCGTTAAACGCCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACTTTCT
191 CAACCTTCAAAATTTCGTTAAACGGCCCCTATAAGGAGATAAGGGACCGGCCCTTAAAACATTCT
* * * *
823757 TTCTCATATATCTCTAGAACGGTAACAAATTTCTAAACACTTGTTGAACAAAATTTGTGTAGAAG
256 TTCTCATATATCTCAAGAACGGTAACGAATTTCTAAACACTTGTTGAACAAAATTTGT-AAGAAT
* *
823822 TAAATGACCTTTTATTTGATATCAA-AAAAAGGGGCTGGCCCCTAAAATTAGGGGACCAAAGGGC
320 TAAATGACCTTTCATTTGATATCAAGAAAAA-GGGCTGGACCCTAAAATTAGGGGACCAAAGGGC
* * * * *
823886 TCTAAAATCTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATG
384 TCTAAAGTCTTTTATCTATAACCCTTTACTGAGGGATATTTTGTGAAATG
*
823936 TTATAGAAGCAAATGTGTTTAT-CTTATAGTTATGTATTCAAGCAATGTAATGATTTTATCATGT
1 TTATAGAAGCAAATGTGTTTATCCTCA-A-TTATGTATTCAAGCAATGTAATGATTTTATCATGT
*
824000 GCTACGTAATTAAGGGTTTTTAGGGG-CACAAAGTCCAAAATTTTGATCACCCATATCTCAGAAA
64 GTTACGTAATTAAGGGTTTTTAGGGGCCA-AAAGTCCAAAATTTTGATCACCCATATCTCAGAAA
* * * * ** *
824064 GGAAATAGATTTTGTAATGCAATACAGCAGAAAAGTTGTTCAAAATGATGTTCTCACAAAATGCA
128 GGAAAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATGTTCTAACAAAATGCA
* * * ** *
824129 ACCTTCAAAATCTCGTTAAACGGCCCCTATAAGGAGTTATGGGATTGGCCCTTAAAACCTTCTTT
193 ACCTTCAAAATTTCGTTAAACGGCCCCTATAAGGAGATAAGGGACCGGCCCTTAAAACATTCTTT
*
824194 CTCATATATCTCCAGAACGGTAACGAATTTCTAAACACTTGTTGAACAAAATTTGATAAGAATTA
258 CTCATATATCTCAAGAACGGTAACGAATTTCTAAACACTTGTTGAACAAAATTTG-TAAGAATTA
* * * * *
824259 AATAACCTTTCATTTAATATCAAGAAAAAGGGACTGGTCCCTAAAAGTAGGGGATCAAAGGGCTC
322 AATGACCTTTCATTTGATATCAAGAAAAAGGG-CTGGACCCTAAAATTAGGGGACCAAAGGGCTC
* * *
824324 TAAAGTATTTTATCTATAACCCTTGATTGAGGGATATTTTGTGAAATG
386 TAAAGTCTTTTATCTATAACCCTTTACTGAGGGATATTTTGTGAAATG
* * *
824372 TTATAGAAGCAAATGTGTTTATCCTGCAATTATGTA-TCAAAGCAATGTATTGGTTTTGTCATGT
1 TTATAGAAGCAAATGTGTTTATCCT-CAATTATGTATTC-AAGCAATGTAATGATTTTATCATGT
** * * *
824436 GTTTTGTAATTAGGGGTTTTCAGGGGCCAAAAGTCCCAAATTTTGATCACCCATATC-CAAGAAA
64 GTTACGTAATTAAGGGTTTTTAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTC-AGAAA
*
824500 GGTAAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATG
128 GGAAAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATG
824550 CAAAAGGGCT
Statistics
Matches: 898, Mismatches: 129, Indels: 44
0.84 0.12 0.04
Matches are distributed among these distances:
433 6 0.01
434 22 0.02
435 472 0.53
436 389 0.43
437 8 0.01
438 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (433 bp):
TTATAGAAGCAAATGTGTTTATCCTCAATTATGTATTCAAGCAATGTAATGATTTTATCATGTGT
TACGTAATTAAGGGTTTTTAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGA
AAAATATTTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATGTTCTAACAAAATGCAACC
TTCAAAATTTCGTTAAACGGCCCCTATAAGGAGATAAGGGACCGGCCCTTAAAACATTCTTTCTC
ATATATCTCAAGAACGGTAACGAATTTCTAAACACTTGTTGAACAAAATTTGTAAGAATTAAATG
ACCTTTCATTTGATATCAAGAAAAAGGGCTGGACCCTAAAATTAGGGGACCAAAGGGCTCTAAAG
TCTTTTATCTATAACCCTTTACTGAGGGATATTTTGTGAAATG
Found at i:824758 original size:237 final size:236
Alignment explanation
Indices: 824315--824785 Score: 694
Period size: 237 Copynumber: 2.0 Consensus size: 236
824305 GTAGGGGATC
824315 AAAGGGCTCTAAAGTATTTTATCTATAACCCTTGATTGAGGGATATTTTGTGAAATGTTATAGAA
1 AAAGGGCTCTAAAGTATTTTATCTATAACCCTTGATTGAGGGATATTTTGTGAAATGTTATAGAA
* * **** * **
824380 GCAAATGTGTTTATCCTGCAATTATGTATCAAAGCAATGTATTGGTTTTGTCATGTGTTTTGTAA
66 GCAAATGTGTTTATCATACAATTATGTATCAAAGCAATGTAAACATTTTATCATGTGTTACGTAA
** * * *
824445 TTAGGGGTTTTCAGGGGCCAAAAGTCCCAAATTTTGATCACCCATATCCAAGAAAGGTAAAATAT
131 TTAAAGGTTTTCAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCCAAGAAAGGAAAAAGAT
824510 TTTGAAATGCAGTACAAAAGAAAAGTTGTTCAAAATGATGCA
196 TTTGAAATGCAGTAC-AAAGAAAAGTTGTTCAAAATGATGCA
* ** *
824552 AAAGGGCTCTAAAGTCTTTTATCTATTGCCCTTTATTGAGGGATATTTTGTGAAATGTTATAGAA
1 AAAGGGCTCTAAAGTATTTTATCTATAACCCTTGATTGAGGGATATTTTGTGAAATGTTATAGAA
* *
824617 GCAAATGTGTTTATCATATAGTTATGTATCAAAGCAATGTAAACATTTTATCATGTGTTACGTAA
66 GCAAATGTGTTTATCATACAATTATGTATCAAAGCAATGTAAACATTTTATCATGTGTTACGTAA
824682 TTAAAGGTTTT-AGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTC-AGAAAGGAAATAAG
131 TTAAAGGTTTTCAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATC-CAAGAAAGGAAA-AAG
* * *
824745 ATTTTGTAATGCAGTACGAAGATAAGTTGTTCAAAATGATG
194 ATTTTGAAATGCAGTACAAAGAAAAGTTGTTCAAAATGATG
824786 TTCTCAACAA
Statistics
Matches: 209, Mismatches: 23, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
236 66 0.32
237 143 0.68
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (236 bp):
AAAGGGCTCTAAAGTATTTTATCTATAACCCTTGATTGAGGGATATTTTGTGAAATGTTATAGAA
GCAAATGTGTTTATCATACAATTATGTATCAAAGCAATGTAAACATTTTATCATGTGTTACGTAA
TTAAAGGTTTTCAGGGGCCAAAAGTCCAAAATTTTGATCACCCATATCCAAGAAAGGAAAAAGAT
TTTGAAATGCAGTACAAAGAAAAGTTGTTCAAAATGATGCA
Found at i:827306 original size:2 final size:2
Alignment explanation
Indices: 827299--827347 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
827289 ATACATGCAC
827299 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
827341 AG AG AG A
1 AG AG AG A
827348 TTGTCAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:830912 original size:441 final size:440
Alignment explanation
Indices: 830024--831378 Score: 2247
Period size: 441 Copynumber: 3.1 Consensus size: 440
830014 CCTATGTTCC
* * * *
830024 AAGTTTGAAGCCTTAATGTCAAAAGCTATCCAAGTTACCACCCAGACAAAATTCAATTA--TTTT
1 AAGTTTGAAGTCTTAATGTCAAAAGGTATCTAAGTTACCACCCAGACAAAATTTAATTATTTTTT
* *
830087 -T-AATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTAATCAATAGTACACCTCAGTGTA
66 CTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGTA
* **
830150 ATATAATTAATCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAAT
131 TTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAAT
830215 GAAGTTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAATTTTGGTAAGGT
196 GAAGTTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAATTTTGGTAAGGT
*
830280 TGAACTGGACTGTATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCTTG
261 TGAACTGGACTATATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCTTG
* *
830345 TGTTATGGTCCGGACTATATATTTTATAAAACGCTTGACCTTGAAGAAGATAATAAGTCAAGGTC
326 TGTTATGGTCCGGACTATATTTTTTATAAAACGCTTGACCTTGAAGAAGATAATAGGTCAAGGTC
*
830410 AAACATTTTGATAGCGTGCACTTCTTCTTAATACCATCTACCTACGTTAA
391 AAAAATTTTGATAGCGTGCACTTCTTCTTAATACCATCTACCTACGTTAA
*
830460 AAGTTTGAAGTCTTAATGTCAAAAGGTATCTAAGTTA-TACCCCAGACAAAATTTAATTATTTTT
1 AAGTTTGAAGTCTTAATGTCAAAAGGTATCTAAGTTACCA-CCCAGACAAAATTTAATTATTTTT
830524 TCTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGT
65 TCTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGT
830589 ATTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAA
130 ATTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAA
830654 TGAAGTTTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAATTTTGGTAAG
195 TGAAG-TTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAATTTTGGTAAG
830719 GTTGAACTGGACTATATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCT
259 GTTGAACTGGACTATATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCT
830784 TGTGTTATGGTCCGGACTATATTTTTTATAAAACGCTTGACCTTGAAGAAGATAATAGGTCAAGG
324 TGTGTTATGGTCCGGACTATATTTTTTATAAAACGCTTGACCTTGAAGAAGATAATAGGTCAAGG
* *
830849 TCAAAAATTTTGATAGCCTGCACTTTTTCTTAATACCATCTACCTACGTTAA
389 TCAAAAATTTTGATAGCGTGCACTTCTTCTTAATACCATCTACCTACGTTAA
*
830901 AAGTTTGAAGTCTTAATGTCAAAAGATATCTAAAG-TACCACCCAGACAAAATTTAATTATTTTT
1 AAGTTTGAAGTCTTAATGTCAAAAGGTATCT-AAGTTACCACCCAGACAAAATTTAATTATTTTT
830965 TCTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGT
65 TCTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGT
831030 ATTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAA
130 ATTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAA
* * * *
831095 TGAAGTTTTTTCTGATTTGACTTTGAAATAAAATTTTAAGGTCAAGGT-AAAAATTTTTGGTAAG
195 TGAAGTTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAA-TTTTGGTAAG
* * * * * *
831159 GTTCAACTGGACTATCTACCATCTATCTATGATACAAGTTAAAAGTTTGTATGTTTAAGGAATCT
259 GTTGAACTGGACTATATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCT
* ** * * *
831224 TGTGTTATAGTCCAAACTCTATTTTTTATAAAACGCTTGACCTTGAAAAAGAAAATAGGTCAAGG
324 TGTGTTATGGTCCGGACTATATTTTTTATAAAACGCTTGACCTTGAAGAAGATAATAGGTCAAGG
* * * * **
831289 TCAAAAATTTTGGTGGCGTGCACTTCTTCTCAATACCATCTACCTATGTTCT
389 TCAAAAATTTTGATAGCGTGCACTTCTTCTTAATACCATCTACCTACGTTAA
* * *
831341 AAGTTTGAAGTCTTTATGTCAAAGGGTATTTAAGTTAC
1 AAGTTTGAAGTCTTAATGTCAAAAGGTATCTAAGTTAC
831379 GGCTTGGACA
Statistics
Matches: 863, Mismatches: 46, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
435 1 0.00
436 52 0.06
438 4 0.00
439 9 0.01
440 367 0.43
441 426 0.49
442 4 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (440 bp):
AAGTTTGAAGTCTTAATGTCAAAAGGTATCTAAGTTACCACCCAGACAAAATTTAATTATTTTTT
CTCAAGTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATATTTATCAATAGTACACCTCAGTGTA
TTATAATTGTTCTTTGTGTAAAGTTTGAAGTCCTTCTGTCAAAGAATATTTAGGAGGTGAACAAT
GAAGTTTTTTCTAATTTGACCTTGAAATATAATTTTTAGGTCAAGGTCAAAAATTTTGGTAAGGT
TGAACTGGACTATATACCATCTATGTATGATACAAGTTAAAAGATTGTATGATTAAGGAGTCTTG
TGTTATGGTCCGGACTATATTTTTTATAAAACGCTTGACCTTGAAGAAGATAATAGGTCAAGGTC
AAAAATTTTGATAGCGTGCACTTCTTCTTAATACCATCTACCTACGTTAA
Found at i:833956 original size:30 final size:30
Alignment explanation
Indices: 833917--833980 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
833907 AAAAGATGAA
*
833917 AAAATCGAAT-ATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAAGTACGACTTAAC
*
833946 AAAATACGAATGATTTTAAGTACGACTTAAC
1 AAAAT-CGAATGATTCTAAGTACGACTTAAC
833977 AAAA
1 AAAA
833981 ACCTTTCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (30 bp):
AAAATCGAATGATTCTAAGTACGACTTAAC
Found at i:834762 original size:30 final size:30
Alignment explanation
Indices: 834723--834786 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
834713 AAAAGATGAA
*
834723 AAAATCGAAT-ATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAAGTACGACTTAAC
*
834752 AAAATACGAATGATTTTAAGTACGACTTAAC
1 AAAAT-CGAATGATTCTAAGTACGACTTAAC
834783 AAAA
1 AAAA
834787 ACCTTTCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 6 0.20
31 19 0.63
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (30 bp):
AAAATCGAATGATTCTAAGTACGACTTAAC
Found at i:839496 original size:17 final size:17
Alignment explanation
Indices: 839474--839514 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
839464 GACGTCACAT
839474 CCGGTTTTGAGATATAG
1 CCGGTTTTGAGATATAG
839491 CCGGTTTTGAGATATAG
1 CCGGTTTTGAGATATAG
839508 CC-GTTTT
1 CCGGTTTT
839515 ATCGATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.39
Consensus pattern (17 bp):
CCGGTTTTGAGATATAG
Found at i:841371 original size:1 final size:1
Alignment explanation
Indices: 841365--841390 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
841355 AAACGTTTTA
841365 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
841391 TCCTCGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:844669 original size:16 final size:16
Alignment explanation
Indices: 844648--844682 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
844638 ATATAACCCG
*
844648 GTAATTTGTGAAACTA
1 GTAATTTGTGAAAATA
844664 GTAATTTGTGAAAATA
1 GTAATTTGTGAAAATA
844680 GTA
1 GTA
844683 TTTTTAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATTTGTGAAAATA
Found at i:845324 original size:17 final size:17
Alignment explanation
Indices: 845298--845333 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
845288 AGATAAGATT
*
845298 TTCCGTTTTCCCTTCCG
1 TTCCGCTTTCCCTTCCG
*
845315 TTCCGCTTTCCGTTCCG
1 TTCCGCTTTCCCTTCCG
845332 TT
1 TT
845334 TTCCGTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.39, G:0.14, T:0.47
Consensus pattern (17 bp):
TTCCGCTTTCCCTTCCG
Found at i:845325 original size:12 final size:12
Alignment explanation
Indices: 845310--845340 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
845300 CCGTTTTCCC
845310 TTCCGTTCCGCT
1 TTCCGTTCCGCT
*
845322 TTCCGTTCCGTT
1 TTCCGTTCCGCT
845334 TTCCGTT
1 TTCCGTT
845341 GCGCGTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.35, G:0.16, T:0.48
Consensus pattern (12 bp):
TTCCGTTCCGCT
Found at i:847612 original size:157 final size:154
Alignment explanation
Indices: 847324--847791 Score: 534
Period size: 157 Copynumber: 3.0 Consensus size: 154
847314 CTCTACTACC
* * *
847324 ATATATATTTGTTAAAAACTAAATGCATGATTATGATGTTCATGAAGCCCTCTACCTAAATTATG
1 ATATATATTTGTTTAAAACTAAATGCACGATTATGATGTTCATG-AGCCCTCTACCAAAATTATG
* *
847389 AAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCCTATAGTTAA
65 AAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTA-GG-GGGACCAATATGGCCATATAGTTAA
847454 AATGTATTAAATCTTGGAAAATCTTCT
128 AATGTATTAAATCTTGGAAAATCTTCT
* * *
847481 ATATATATTTGTTTAAAACTAAATGCACGATTGTGATGTTCATGTGGCCCTCTACCAAAATTGTG
1 ATATATATTTGTTTAAAACTAAATGCACGATTATGATGTTCATG-AGCCCTCTACCAAAATTATG
** * * *
847546 AAATTCATGACCCCTGTATCAGGGGTTTAGGCTCTAGGAAGGGTACAAATATGGCCATATAGTAA
65 AAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGG--GGG-ACCAATATGGCCATATAGTTA
**** *
847611 AAATGTATTAAATCTT-CTCTA-C-TCC
127 AAATGTATTAAATCTTGGAAAATCTTCT
* * * * ** *
847636 A-ATACATGTG-TTAAACACTAAATGC-CTGGTTACGATGACCATGAGCCCTTCTACTAAAATTA
1 ATATATATTTGTTTAAA-ACTAAATGCAC-GATTATGATGTTCATGAGCCC-TCTACCAAAATTA
* * *
847698 TGAAATTCATGACCACTGGGTCAGGGGTTCAGGCTCAAGGGTGGAGCCAATATGGCCATATTGTT
63 TGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGG-GGA-CCAATATGGCCATATAGTT
847763 AAAATGTATTAAATCTTGGAAAATCTTCT
126 AAAATGTATTAAATCTTGGAAAATCTTCT
847792 CTTCTCTCAT
Statistics
Matches: 258, Mismatches: 43, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
152 2 0.01
153 45 0.17
154 74 0.29
155 4 0.02
156 5 0.02
157 95 0.37
158 33 0.13
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (154 bp):
ATATATATTTGTTTAAAACTAAATGCACGATTATGATGTTCATGAGCCCTCTACCAAAATTATGA
AATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGGGACCAATATGGCCATATAGTTAAAAT
GTATTAAATCTTGGAAAATCTTCT
Found at i:853776 original size:13 final size:13
Alignment explanation
Indices: 853760--853784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
853750 TCTTTGAACA
853760 ATGAACATGAAAC
1 ATGAACATGAAAC
853773 ATGAACATGAAA
1 ATGAACATGAAA
853785 AAATCAAATG
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:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
ATGAACATGAAAC
Found at i:860623 original size:166 final size:164
Alignment explanation
Indices: 860303--860633 Score: 418
Period size: 166 Copynumber: 2.0 Consensus size: 164
860293 GTGATTTTGC
** *
860303 AAGATTTTTAAAGATTTTCTCTTTATATTCCTATGTAGAAATTCATCCCCCATTGTGGCCCCACC
1 AAGATTTTTAAAGATTTTCTCCATATATTCCTATGTAGAAATTCATCCCCCATTGTGACCCCACC
* * * **
860368 CTACCCCAGACACTATGATTTGAACACACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAA
66 CTACCCCAGACACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATTACAA
* * *
860433 TTTGAACTTTCCTGGCCTAATAGTTTTTTAGAAG
131 TTTGAACTTTCCAGGCCGAATAGTTTTTGAGAAG
* *
860467 AAGATTTTTAAAGATTTTCTCCATATATTCCTATTTA-AAACTTGATCCTCCTC-TTGTGACCCC
1 AAGATTTTTAAAGATTTTCTCCATATATTCCTATGTAGAAA-TTCATCC-CC-CATTGTGACCCC
* * **
860530 TCCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCA-T
63 ACCCTA-CCCCAGACACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATT
*
860594 ACAAGTTT-AAGCTTTTCAGGCCGAATAGTTTTTGAGAAG
127 ACAA-TTTGAA-CTTTCCAGGCCGAATAGTTTTTGAGAAG
860633 A
1 A
860634 TTTTTGAAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
163 3 0.02
164 40 0.28
165 21 0.15
166 79 0.55
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (164 bp):
AAGATTTTTAAAGATTTTCTCCATATATTCCTATGTAGAAATTCATCCCCCATTGTGACCCCACC
CTACCCCAGACACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCCTCCATTACAA
TTTGAACTTTCCAGGCCGAATAGTTTTTGAGAAG
Found at i:868942 original size:2 final size:2
Alignment explanation
Indices: 868935--869007 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
868925 AACCCTCGTA
*
868935 CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
868977 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
869008 ATAAGAGACC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:873870 original size:99 final size:100
Alignment explanation
Indices: 873767--873966 Score: 384
Period size: 99 Copynumber: 2.0 Consensus size: 100
873757 CAGCTAACAT
*
873767 ACATATATGTTTGTACAGTGCTTTTAAAATGATGGATTGTGAGAAAAATGTGA-TTTTTTTATGT
1 ACATATATGTTTGTACAGTGCTTATAAAATGATGGATTGTGAGAAAAATGTGATTTTTTTTATGT
873831 TGATAATTATCGTTGAAATCAATTTCTTTACACAA
66 TGATAATTATCGTTGAAATCAATTTCTTTACACAA
873866 ACATATATGTTTGTACAGTGCTTATAAAATGATGGATTGTGAGAAAAATGTGATTTTTTTTATGT
1 ACATATATGTTTGTACAGTGCTTATAAAATGATGGATTGTGAGAAAAATGTGATTTTTTTTATGT
873931 TGATAATTATCGTTGAAATCAATTTCTTTACACAA
66 TGATAATTATCGTTGAAATCAATTTCTTTACACAA
873966 A
1 A
873967 TCTTCTTGTA
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
99 52 0.53
100 47 0.47
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (100 bp):
ACATATATGTTTGTACAGTGCTTATAAAATGATGGATTGTGAGAAAAATGTGATTTTTTTTATGT
TGATAATTATCGTTGAAATCAATTTCTTTACACAA
Found at i:874292 original size:15 final size:15
Alignment explanation
Indices: 874272--874302 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
874262 ATATTTCTCT
*
874272 TTTTTTATTTTTTTA
1 TTTTTTATCTTTTTA
874287 TTTTTTATCTTTTTA
1 TTTTTTATCTTTTTA
874302 T
1 T
874303 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTATCTTTTTA
Found at i:875703 original size:16 final size:16
Alignment explanation
Indices: 875678--875711 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
875668 ATTGAACAAC
875678 GAATACAGCTTCAGAT
1 GAATACAGCTTCAGAT
* *
875694 GAATATAGCTTCGGAT
1 GAATACAGCTTCAGAT
875710 GA
1 GA
875712 TGTTTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (16 bp):
GAATACAGCTTCAGAT
Found at i:886007 original size:2 final size:2
Alignment explanation
Indices: 885966--885999 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
885956 CTAGAACTGA
885966 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
886000 AACTCTCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:898138 original size:13 final size:13
Alignment explanation
Indices: 898120--898147 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
898110 TTTATAGACG
898120 TTGAAAAGATCTA
1 TTGAAAAGATCTA
898133 TTGAAAAGATCTA
1 TTGAAAAGATCTA
898146 TT
1 TT
898148 ATATTGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (13 bp):
TTGAAAAGATCTA
Done.