Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:830985 original size:32 final size:32
Alignment explanation
Indices: 830929--831912 Score: 1336
Period size: 32 Copynumber: 31.8 Consensus size: 32
830919 AAAATGGTGA
* ** **
830929 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
830961 TTTTAAATGGGTTGCCCCCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
830993 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831025 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831057 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
831089 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831121 TTTGAAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831152 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
831184 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831216 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831248 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
831280 TTTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
831308 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
831338 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
831366 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
831396 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831424 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831456 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
831488 TTTGGAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831520 TTTGAAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831551 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
831583 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831615 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831647 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
831679 TTTGGAAT--GATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
831707 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
831737 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
831765 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
831795 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831823 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
831855 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
831887 TTTGGAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
831913 GATTTAAAAG
Statistics
Matches: 864, Mismatches: 70, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
28 126 0.15
29 6 0.01
30 130 0.15
31 75 0.09
32 527 0.61
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:831756 original size:399 final size:398
Alignment explanation
Indices: 831018--831903 Score: 1738
Period size: 399 Copynumber: 2.2 Consensus size: 398
831008 CACCGACTTG
831018 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
*
831083 GTGGGCTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
66 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
831148 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
131 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
831213 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
196 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT-GGTTGCCACCGACTTGTGTGG
831278 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
260 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
831343 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
325 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
831408 CCACTGACT
390 CCACTGACT
831417 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
831482 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
66 GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
831547 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
131 GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
831612 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGG
196 GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAAT-GGTTGCCACCGACTTGTGTGG
831677 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
260 GCTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGA
831742 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
325 AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATG
831807 CCACTGACT
390 CCACTGACT
831816 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
831881 GTGGGCTTTGGAATGGG-TGCCAC
66 GTGGGCTTTGGAATGGGTTGCCAC
831904 AGAGTTGTGG
Statistics
Matches: 486, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
398 6 0.01
399 480 0.99
ACGTcount: A:0.18, C:0.19, G:0.33, T:0.30
Consensus pattern (398 bp):
TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGT
GTGGGCTTTGGAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATGGGTGCCACCGACTTGTGT
GGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTG
GGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGTTGCCACCGACTTGTGTGGG
CTTTGGAATGATGCCACTAACTTGTGGGCTTTGAAATGGATTGCCACCGACTTGTGGGCTTTGAA
AGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACCAACTTGTGTGGACTTTGAAAAGATGC
CACTGACT
Found at i:831929 original size:27 final size:27
Alignment explanation
Indices: 831895--832496 Score: 1024
Period size: 27 Copynumber: 22.0 Consensus size: 27
831885 GCTTTGGAAT
* *
831895 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
831922 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
831949 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
831976 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832003 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
832031 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
832058 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
832085 GGGTGCCACGGAGTTGTGGACCTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
832112 GGGTGCCACGGAGTTGTGAACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832139 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
832167 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832194 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
832221 GGGATGCCACGGAGTTGTGAACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
832249 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
832277 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832304 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832331 GGGATGCCACGGAGTTGTGGACTTAAAAA
1 GGG-TGCCACGGAGTTGTGGACTT-AAAA
*
832360 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
832387 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
832414 GAATGCCACGGAGTTGTGGACTTGAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832441 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
832468 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
832496 G
1 G
832497 AAAATGTGAA
Statistics
Matches: 545, Mismatches: 24, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
27 387 0.71
28 152 0.28
29 6 0.01
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:832065 original size:82 final size:81
Alignment explanation
Indices: 831895--832496 Score: 1024
Period size: 82 Copynumber: 7.3 Consensus size: 81
831885 GCTTTGGAAT
* * *
831895 GGGTGCCACAGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
831960 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
831976 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
832041 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
832058 GAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACCTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
*
832123 AGTTGTGAACTTAAAA
66 AGTTGTGGACTTAAAA
832139 GGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
832204 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
832221 GGGATGCCACGGAGTTGTGAACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
832286 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
*
832304 GGGTGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAAGGATGCCAC
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTT-AAAAGGGTGCCAC
832369 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
* ** *
832387 GGGTGCCACAGAGTTGTGGACTTAAAAGAATGCCACGGAGTTGTGGACTTGAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
832452 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
832468 GGGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGGTGCCACGGAGTTGTGGAC-TTAAAAG
832497 AAAATGTGAA
Statistics
Matches: 496, Mismatches: 20, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
81 126 0.25
82 259 0.52
83 111 0.22
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:832527 original size:46 final size:46
Alignment explanation
Indices: 832455--832548 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
832445 GCCACGGAGT
* *
832455 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAAAA
1 TGTGAACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAA
832501 TGTGAACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAA
1 TGTGAACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAA
832547 TG
1 TG
832549 CCACTGAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.29, T:0.24
Consensus pattern (46 bp):
TGTGAACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAA
Found at i:832552 original size:30 final size:31
Alignment explanation
Indices: 832516--832573 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
832506 ACTTAAAAGG
*
832516 ATGCCACGGAGTTGTGGACTTT-AAAAGAAA
1 ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
*
832546 ATGCCACTGAGTCGTGGACTTTGAAAAG
1 ATGCCACGGAGTCGTGGACTTTGAAAAG
832574 GTCACAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
Found at i:839970 original size:2 final size:2
Alignment explanation
Indices: 839963--839993 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
839953 GATTTTCAAA
*
839963 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
839994 AATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:840393 original size:11 final size:11
Alignment explanation
Indices: 840377--840417 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
840367 ATTTCATATT
840377 TTTTTTCTTTC
1 TTTTTTCTTTC
840388 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
840401 TTCTTTCTTTC
1 TTTTTTCTTTC
840412 TTTTTT
1 TTTTTT
840418 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:840431 original size:24 final size:22
Alignment explanation
Indices: 840377--840431 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
840367 ATTTCATATT
**
840377 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
840399 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
840425 TTTTTTC
1 TTTTTTC
840432 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:840799 original size:24 final size:24
Alignment explanation
Indices: 840772--840819 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
840762 CCACTCAATC
840772 GGAAAACCCACTTTGATTTTTTTT
1 GGAAAACCCACTTTGATTTTTTTT
* * **
840796 GGAAAGCCCTCTTTTTTTTTTTTT
1 GGAAAACCCACTTTGATTTTTTTT
840820 TTTTTTTTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (24 bp):
GGAAAACCCACTTTGATTTTTTTT
Found at i:843208 original size:3 final size:3
Alignment explanation
Indices: 843200--843249 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
843190 AGTTTTAATT
843200 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
843248 AA
1 AA
843250 AGAGCCCATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:849503 original size:2 final size:2
Alignment explanation
Indices: 849496--849527 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
849486 TCAGCATGCA
849496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
849528 CTTGTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:850073 original size:31 final size:31
Alignment explanation
Indices: 850029--850114 Score: 145
Period size: 31 Copynumber: 2.7 Consensus size: 31
850019 AATTAATTTA
850029 ATTTATTATTTAATAATAAAAATAATATTTTT
1 ATTTA-TATTTAATAATAAAAATAATATTTTT
*
850061 ATTTATATTTAATAATAAAAGTAATATTTTT
1 ATTTATATTTAATAATAAAAATAATATTTTT
*
850092 ATTTATATTTAATTATAAAAATA
1 ATTTATATTTAATAATAAAAATA
850115 TATAAATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 46 0.90
32 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
ATTTATATTTAATAATAAAAATAATATTTTT
Found at i:850140 original size:11 final size:11
Alignment explanation
Indices: 850105--850165 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
850095 TATATTTAAT
850105 TATAAAAAT-A
1 TATAAAAATAA
*
850115 TATAAATATTAA
1 TATAAA-AATAA
850127 TATAAAAATAA
1 TATAAAAATAA
***
850138 TATTTTAATAA
1 TATAAAAATAA
850149 TATAATAAATAA
1 TATAA-AAATAA
850161 T-TAAA
1 TATAAA
850166 TAAATTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 7 0.17
11 20 0.50
12 13 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:850140 original size:23 final size:23
Alignment explanation
Indices: 850100--850167 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
850090 TTATTTATAT
850100 TTAATTATAAAAAT-ATATAAATA
1 TTAA-TATAAAAATAATATAAATA
**
850123 TTAATATAAAAATAATAT-TTTA
1 TTAATATAAAAATAATATAAATA
*
850145 ATAATATAATAAATAAT-TAAATA
1 TTAATATAA-AAATAATATAAATA
850168 AATTTTTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 20 0.54
23 17 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAATATAAAAATAATATAAATA
Found at i:850147 original size:25 final size:29
Alignment explanation
Indices: 850030--850175 Score: 114
Period size: 31 Copynumber: 5.1 Consensus size: 29
850020 ATTAATTTAA
850030 TTTAT-TATTTAATAATAAAAATAATATT
1 TTTATATATTTAATAATAAAAATAATATT
*
850058 TTTATTTATATTTAATAATAAAAGTAATATT
1 TTTA--TATATTTAATAATAAAAATAATATT
*
850089 TTTATTTATATTTAATTATAAAAAT-ATA--
1 TTTA--TATATTTAATAATAAAAATAATATT
*
850117 --TAAATA-TTAAT-ATAAAAATAATATT
1 TTTATATATTTAATAATAAAAATAATATT
* *
850142 TTAATA-ATATAATAAATAATTAAATAA-ATT
1 TTTATATATTTAAT-AATAA--AAATAATATT
850172 TTTA
1 TTTA
850176 AGTCAGCTTA
Statistics
Matches: 97, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
22 8 0.08
23 8 0.08
24 3 0.03
26 3 0.03
27 6 0.06
28 4 0.04
29 4 0.04
30 10 0.10
31 51 0.53
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
TTTATATATTTAATAATAAAAATAATATT
Found at i:860370 original size:18 final size:18
Alignment explanation
Indices: 860342--860399 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
860332 ATTATATTTA
860342 AAATATTTTATATTTATAT
1 AAAT-TTTTATATTTATAT
860361 AAATTTTTATATATTA-AT
1 AAATTTTTATAT-TTATAT
860379 -AA--TTTATA-TTATAT
1 AAATTTTTATATTTATAT
*
860393 AGATTTT
1 AAATTTT
860400 AAAAATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 3 0.09
14 2 0.06
15 7 0.21
17 4 0.12
18 10 0.30
19 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AAATTTTTATATTTATAT
Found at i:860926 original size:23 final size:23
Alignment explanation
Indices: 860900--860945 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
860890 AAATTACATC
*
860900 ATATAATA-AATATAAAATATAAA
1 ATATAATATAAT-TAAAAAATAAA
*
860923 ATATTATATAATTAAAAAATAAA
1 ATATAATATAATTAAAAAATAAA
860946 TTCGATCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAATATAATTAAAAAATAAA
Found at i:863885 original size:25 final size:26
Alignment explanation
Indices: 863857--863906 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
863847 ACTTAAATTT
863857 AATTATAATATTATTATAAA-AATAA
1 AATTATAATATTATTATAAATAATAA
* * *
863882 AATTTTCATATTATTTTAAATAATA
1 AATTATAATATTATTATAAATAATA
863907 TTATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTATAATATTATTATAAATAATAA
Found at i:864321 original size:19 final size:17
Alignment explanation
Indices: 864282--864322 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
864272 ATAATATTTT
*
864282 AATTTTATAAAAATTAT
1 AATTTTATAAAAATTAA
864299 AATTATTATAAATAATTAA
1 AATT-TTATAAA-AATTAA
864318 AATTT
1 AATTT
864323 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 8 0.38
19 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTATAAAAATTAA
Found at i:864326 original size:7 final size:7
Alignment explanation
Indices: 864314--864348 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
864304 TTATAAATAA
864314 TTAAAAT
1 TTAAAAT
864321 TTAAAAT
1 TTAAAAT
864328 TTAAAAT
1 TTAAAAT
864335 TTAAAAT
1 TTAAAAT
864342 TTAAAAT
1 TTAAAAT
864349 CTCACGATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAAAAT
Found at i:864901 original size:16 final size:17
Alignment explanation
Indices: 864882--864915 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
864872 GAATCAATTT
864882 ATTTATTAA-ATTTAAA
1 ATTTATTAATATTTAAA
*
864898 ATTTTTTAATATTTAAA
1 ATTTATTAATATTTAAA
864915 A
1 A
864916 AAATTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATTAATATTTAAA
Found at i:866102 original size:30 final size:30
Alignment explanation
Indices: 866066--866122 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
866056 ATTTTAATAA
866066 AATATGTTAATATAAATTTGACATATTAAT
1 AATATGTTAATATAAATTTGACATATTAAT
* * *
866096 AATATGTTTATTTAAATTTGATATATT
1 AATATGTTAATATAAATTTGACATATT
866123 TATGTATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (30 bp):
AATATGTTAATATAAATTTGACATATTAAT
Found at i:866466 original size:29 final size:27
Alignment explanation
Indices: 866405--866466 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 27
866395 TCCGTGTTCA
*
866405 TATTAGTTTTTATATTATATTATATTT
1 TATTAGTTTTTATATTATATTATAATT
*
866432 TAATTA-TTTTTTTATTATAAATTATAAATT
1 T-ATTAGTTTTTATATTAT--ATTAT-AATT
866462 TATTA
1 TATTA
866467 ACTTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
27 12 0.41
28 4 0.14
29 9 0.31
30 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TATTAGTTTTTATATTATATTATAATT
Found at i:868758 original size:22 final size:23
Alignment explanation
Indices: 868712--868763 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
868702 AAAAATATAA
868712 AATATTATTTTTATATTAATATTT
1 AATA-TATTTTTATATTAATATTT
868736 -ATATATTTTGTA-ATTAA-ATTTT
1 AATATATTTT-TATATTAATA-TTT
868758 AATATA
1 AATATA
868764 AATATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 14 0.56
23 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATATATTTTTATATTAATATTT
Found at i:870810 original size:18 final size:18
Alignment explanation
Indices: 870780--870815 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
870770 CAGTTTTACT
870780 TAAAAAATGATTTATTTAA
1 TAAAAAATGATTT-TTTAA
870799 TAAAAAAT-ATTTTTTAA
1 TAAAAAATGATTTTTTAA
870816 AATTTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAAAAATGATTTTTTAA
Found at i:871204 original size:27 final size:27
Alignment explanation
Indices: 871174--871251 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
871164 TATAATTTTA
871174 TTTAAAATATTTTATATTTATATAAAT
1 TTTAAAATATTTTATATTTATATAAAT
*
871201 TTTAATATATAATTT-T-TTTATATAAAT
1 TTTAA-A-ATATTTTATATTTATATAAAT
*
871228 TTTAAAATATTTATATATTCATAT
1 TTTAAAATATTT-TATATTTATAT
871252 CTTATTTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
25 5 0.12
26 2 0.05
27 22 0.51
28 8 0.19
29 6 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTAAAATATTTTATATTTATATAAAT
Found at i:871211 original size:14 final size:14
Alignment explanation
Indices: 871192--871237 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
871182 ATTTTATATT
871192 TATATAAATTTTAA
1 TATATAAATTTTAA
**
871206 TATAT-AATTTTTT
1 TATATAAATTTTAA
871219 TATATAAATTTTAA
1 TATATAAATTTTAA
*
871233 AATAT
1 TATAT
871238 TTATATATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:871303 original size:31 final size:31
Alignment explanation
Indices: 871161--871319 Score: 92
Period size: 31 Copynumber: 5.0 Consensus size: 31
871151 TATTATATCG
* *
871161 TATTATAATTTTATT-TAAAATATTTTATATT-
1 TATTTTAATTTT-TTATATAAT-TTTTATATTA
* * * *
871192 TATATAAATTTTAATATATAATTTTTTTATATA
1 TATTTTAATTTT-TTATATAATTTTTATAT-TA
* * * ** *
871225 AATTTTAAAATATTTATAT-ATTCATATCTTA
1 TATTTT-AATTTTTTATATAATTTTTATATTA
*
871256 T-TTTTATTATTTTTATATAATTTTTATATTA
1 TATTTTAAT-TTTTTATATAATTTTTATATTA
* *
871287 TATTTTAATTTTTTATATTATATTTAATATTA
1 TATTTTAATTTTTTATATAAT-TTTTATATTA
871319 T
1 T
871320 CAATTAATAT
Statistics
Matches: 94, Mismatches: 26, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
29 1 0.01
30 12 0.13
31 41 0.44
32 28 0.30
33 8 0.09
34 4 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TATTTTAATTTTTTATATAATTTTTATATTA
Found at i:871327 original size:32 final size:32
Alignment explanation
Indices: 871263--871338 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
871253 TTATTTTTAT
* *
871263 TATTTTTATATAATTTTTATATTATATTTTAA
1 TATTTTTATATAATTTTAATATTATATATTAA
*
871295 T-TTTTTATATTATATTTAATATTATCA-ATTAA
1 TATTTTTATATAAT-TTTAATATTAT-ATATTAA
*
871327 TATTTATATATA
1 TATTTTTATATA
871339 CTTGTGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 11 0.31
32 16 0.44
33 9 0.25
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTTTTATATAATTTTAATATTATATATTAA
Found at i:871568 original size:21 final size:23
Alignment explanation
Indices: 871535--871583 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
871525 TATTTAAATT
871535 ATTTT-AAATTTAAATT-ATTGA
1 ATTTTGAAATTTAAATTAATTGA
*
871556 ATTTTGAAA-TTAAATTAATTTA
1 ATTTTGAAATTTAAATTAATTGA
871578 ATTTTG
1 ATTTTG
871584 GATTAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (23 bp):
ATTTTGAAATTTAAATTAATTGA
Found at i:877311 original size:16 final size:16
Alignment explanation
Indices: 877292--877324 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
877282 AATTTGAGTT
*
877292 ATTTTAGGTTTGAATC
1 ATTTTAGATTTGAATC
877308 ATTTTAGATTTGAATC
1 ATTTTAGATTTGAATC
877324 A
1 A
877325 ATTAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (16 bp):
ATTTTAGATTTGAATC
Found at i:883427 original size:18 final size:18
Alignment explanation
Indices: 883360--883428 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 18
883350 AAGAAATATA
* *
883360 TTTTAAATTAATTATAAT
1 TTTTAAAATAATTAAAAT
* * ** *
883378 TATTAATATAAACATAAT
1 TTTTAAAATAATTAAAAT
* *
883396 TTTTAATAT-TTTAAAAT
1 TTTTAAAATAATTAAAAT
883413 TTTTAAAATAATTAAA
1 TTTTAAAATAATTAAA
883429 TAGATTTATG
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
17 12 0.32
18 26 0.68
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTAAAATAATTAAAAT
Found at i:884574 original size:34 final size:36
Alignment explanation
Indices: 884536--884621 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 36
884526 TATATTTTAA
* *
884536 TAATTTTTA-ATTATTATTCAAA-ATAAATATAATT
1 TAATTTATATATTATTATTAAAATATAAATATAATT
* *
884570 TAATTTATATTTTATTATTAAAATATAAATATTATTT
1 TAATTTATATATTATTATTAAAATATAAATA-TAATT
* *
884607 TAAATTATTTATTAT
1 TAATTTATATATTAT
884622 AGACATAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 8 0.19
35 11 0.26
36 7 0.17
37 16 0.38
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (36 bp):
TAATTTATATATTATTATTAAAATATAAATATAATT
Found at i:884616 original size:35 final size:34
Alignment explanation
Indices: 884546--884621 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
884536 TAATTTTTAA
* *
884546 TTATTATTCAAAATAAATATAATTTAATTTATATT
1 TTATTATTAAAAATAAATATAATTTAATATATA-T
*
884581 TTATTATTAAAATATAAATATTATTTTAA-AT-TAT
1 TTATTATTAAAA-ATAAATA-TAATTTAATATATAT
884615 TTATTAT
1 TTATTAT
884622 AGACATAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 8 0.22
35 13 0.36
36 8 0.22
37 7 0.19
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
TTATTATTAAAAATAAATATAATTTAATATATAT
Found at i:885004 original size:21 final size:20
Alignment explanation
Indices: 884963--885004 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
884953 TTGATGTATT
*
884963 AAAAAATTGATTCTTTGTAA
1 AAAAAATTGATCCTTTGTAA
884983 AAAAAATATCGATCCTTT-TAA
1 AAAAAAT-T-GATCCTTTGTAA
885004 A
1 A
885005 TATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (20 bp):
AAAAAATTGATCCTTTGTAA
Found at i:887288 original size:20 final size:21
Alignment explanation
Indices: 887257--887346 Score: 76
Period size: 21 Copynumber: 4.2 Consensus size: 21
887247 CATATTGATC
*
887257 TAAAAAT-CTATTTTATTATT
1 TAAAAATAATATTTTATTATT
* **
887277 T-AAAATAATATTTAAAAATT
1 TAAAAATAATATTTTATTATT
*
887297 TAAAAATTATATTATTATTTATAAT
1 TAAAAATAATATT-TTA-TTAT--T
*
887322 TAAAAATAATTTTTTATTATT
1 TAAAAATAATATTTTATTATT
887343 TAAA
1 TAAA
887347 TGGTAACTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
19 5 0.09
20 11 0.20
21 15 0.28
22 2 0.04
23 6 0.11
24 3 0.06
25 12 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAAATAATATTTTATTATT
Found at i:890849 original size:43 final size:43
Alignment explanation
Indices: 890788--890875 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
890778 TAATATGTTA
890788 TTAAATCAATCAATTCAAGTAGATTTTTCCTTTTCTATTTTTT
1 TTAAATCAATCAATTCAAGTAGATTTTTCCTTTTCTATTTTTT
*
890831 TTAAATCAATCAATTCAAGTAGATTTTTCTTTTTCTATTTTTT
1 TTAAATCAATCAATTCAAGTAGATTTTTCCTTTTCTATTTTTT
890874 TT
1 TT
890876 TTCAATGCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (43 bp):
TTAAATCAATCAATTCAAGTAGATTTTTCCTTTTCTATTTTTT
Found at i:892146 original size:21 final size:20
Alignment explanation
Indices: 892118--892156 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
892108 ATAATTATAT
892118 TTTAAAAAAATAAAAAATTA
1 TTTAAAAAAATAAAAAATTA
* *
892138 TTTATAAAATATTAAAAAT
1 TTTA-AAAAAATAAAAAAT
892157 ATAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TTTAAAAAAATAAAAAATTA
Found at i:896437 original size:11 final size:11
Alignment explanation
Indices: 896421--896487 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
896411 AAATACGATA
896421 ATATTTAATAT
1 ATATTTAATAT
896432 ATATTT-ATATT
1 ATATTTAATA-T
896443 ATATTT-ATAT
1 ATATTTAATAT
896453 AT-TTT-AT-T
1 ATATTTAATAT
896461 ATATTATAAT-T
1 ATATT-TAATAT
*
896472 AT-TTTAAAAT
1 ATATTTAATAT
896482 AT-TTTA
1 ATATTTA
896488 TATGTAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 16 0.32
11 21 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:896446 original size:15 final size:15
Alignment explanation
Indices: 896421--896566 Score: 50
Period size: 13 Copynumber: 10.3 Consensus size: 15
896411 AAATACGATA
896421 ATATTTA-ATATATAT
1 ATATTTATAT-TATAT
*
896436 TTATATTATATT-TAT
1 ATAT-TTATATTATAT
896451 ATATTT-TATTATATT
1 ATATTTATATTATA-T
* * *
896466 ATAATTATTTTA-AA
1 ATATTTATATTATAT
*
896480 ATATTTTATATGTAAAT
1 ATA-TTTATAT-TATAT
* *
896497 AAATTT-TAATATAT
1 ATATTTATATTATAT
* *
896511 AAATATAT-TTAT-T
1 ATATTTATATTATAT
*
896524 ATA-TCATATTATAT
1 ATATTTATATTATAT
896538 -T-TTTA-ATTAT-T
1 ATATTTATATTATAT
*
896549 TTATTTATA-TATAT
1 ATATTTATATTATAT
896563 -TATT
1 ATATT
896567 ATCAAGTTTA
Statistics
Matches: 98, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
11 1 0.01
12 8 0.08
13 25 0.26
14 22 0.22
15 24 0.24
16 13 0.13
17 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (15 bp):
ATATTTATATTATAT
Found at i:896465 original size:29 final size:30
Alignment explanation
Indices: 896420--896490 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
896410 TAAATACGAT
*
896420 AATATTTAATATATATT-TATATTATATTT-A
1 AATATTTTATATATATTATA-ATTAT-TTTAA
*
896450 TATATTTTAT-TATATTATAATTATTTTAA
1 AATATTTTATATATATTATAATTATTTTAA
896479 AATATTTTATAT
1 AATATTTTATAT
896491 GTAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 3 0.09
29 21 0.60
30 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
AATATTTTATATATATTATAATTATTTTAA
Found at i:896567 original size:21 final size:21
Alignment explanation
Indices: 896513--896568 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
896503 TAATATATAA
896513 ATATATTTATTATATCATATT
1 ATATATTTATTATATCATATT
* * *
896534 ATATTTTTAATTATTTTAT-TT
1 ATATATTT-ATTATATCATATT
896555 ATATATATTATTAT
1 ATATAT-TTATTAT
896569 CAAGTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTTATTATATCATATT
Found at i:896567 original size:33 final size:31
Alignment explanation
Indices: 896516--896600 Score: 77
Period size: 34 Copynumber: 2.7 Consensus size: 31
896506 TATATAAATA
*
896516 TATTTAT-TATATCATATTATATTTTTAATTATTT
1 TATTTATATATAT--TATTATATGTTTAA-TA-TT
*
896550 TATTTATATATATTATTATCAAGTTTAATATT
1 TATTTATATATATTATTAT-ATGTTTAATATT
*
896582 TA-TTATA-ATATAATTATAT
1 TATTTATATATATTATTATAT
896601 AATATAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
29 1 0.02
30 9 0.20
31 5 0.11
32 4 0.09
33 8 0.18
34 13 0.29
35 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (31 bp):
TATTTATATATATTATTATATGTTTAATATT
Found at i:896603 original size:13 final size:11
Alignment explanation
Indices: 896585--896665 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
896575 TAATATTTAT
896585 TATAATATAATTA
1 TATAATATAA--A
896598 TATAATATAAA
1 TATAATATAAA
*
896609 TATAATATTAA
1 TATAATATAAA
896620 -A-AAT-TAAA
1 TATAATATAAA
*
896628 -ATTTATATAAA
1 TA-TAATATAAA
*
896639 TA-AATAAATAA
1 TATAATATA-AA
896650 TAT-AT-TAAA
1 TATAATATAAA
896659 TATAATA
1 TATAATA
896666 ATAATTAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
8 4 0.07
9 8 0.15
10 10 0.19
11 21 0.39
12 1 0.02
13 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TATAATATAAA
Found at i:896612 original size:19 final size:18
Alignment explanation
Indices: 896588--896683 Score: 67
Period size: 17 Copynumber: 5.4 Consensus size: 18
896578 TATTTATTAT
896588 AATATAATTATATAATATA
1 AATATAATTATATAA-ATA
896607 AATATAA-TAT-TAAA-A
1 AATATAATTATATAAATA
* *
896622 ATTAAAATTTATATAAATA
1 AATATAA-TTATATAAATA
* *
896641 AATA-AATAATAT-ATTA
1 AATATAATTATATAAATA
* *
896657 AATATAATAATAATTAAAAA
1 AATATAATTAT-A-TAAATA
896677 AATATAA
1 AATATAA
896684 ACATCATTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
15 6 0.10
16 8 0.13
17 17 0.27
18 10 0.16
19 12 0.19
20 9 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATAATTATATAAATA
Found at i:896757 original size:20 final size:20
Alignment explanation
Indices: 896732--896818 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 20
896722 CGAATTTTTC
896732 AAATAAAATTATATAATAAA
1 AAATAAAATTATATAATAAA
* *
896752 AAATAAATATATATTTATTAAAA
1 AAATAAA-AT-TATATAAT-AAA
896775 AAATTAAAATT-TAT-ATAAA
1 AAA-TAAAATTATATAATAAA
*
896794 TAAATATAA-TA-ATAATTAAA
1 -AAATAAAATTATATAA-TAAA
896814 AAATA
1 AAATA
896819 TATAAACACC
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
18 3 0.06
19 13 0.24
20 15 0.28
21 4 0.07
22 7 0.13
23 8 0.15
24 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAATTATATAATAAA
Found at i:896778 original size:19 final size:20
Alignment explanation
Indices: 896751--896823 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
896741 TATATAATAA
896751 AAAATAAATAT-ATATTTATT
1 AAAA-AAATATAATATTTATT
*
896771 AAAAAAAT-TAAAATTTATAT
1 AAAAAAATATAATATTTAT-T
* * *
896791 AAATAAATATAATAATAATT
1 AAAAAAATATAATATTTATT
896811 AAAAAATATATAA
1 AAAAAA-ATATAA
896824 ACACCATTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.02
19 11 0.26
20 18 0.42
21 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAAATATAATATTTATT
Found at i:896810 original size:25 final size:23
Alignment explanation
Indices: 896733--896810 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
896723 GAATTTTTCA
896733 AATAAAATTATATAATAAAAAATA-
1 AATAAAATT-TAT-ATAAAAAATAT
*
896757 AATATATATTTAT-TAAAAAA-AT
1 AATA-AAATTTATATAAAAAATAT
896779 --TAAAATTTATATAAATAAATAT
1 AATAAAATTTATATAAA-AAATAT
896801 AATAATAATT
1 AATAA-AATT
896811 AAAAAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
19 7 0.16
20 6 0.14
21 4 0.09
22 9 0.20
24 10 0.23
25 8 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAAATTTATATAAAAAATAT
Found at i:897898 original size:64 final size:64
Alignment explanation
Indices: 897717--897916 Score: 280
Period size: 70 Copynumber: 3.1 Consensus size: 64
897707 TTAATTTTGA
*
897717 TTGTTTAAGTTTGATTGGAAATTTGGG-TCTTTCTACTTGTTTCAATGCTTAATTTAGATGGTG
1 TTGTTTCAGTTTGATTGGAAATTTGGGATCTTTCTACTTGTTTCAATGCTTAATTTAGATGGTG
897780 TTGTTTCAGTTTGATTGGTGATTGGAAATTT-GGATCTTTCTACTTGTTTCAATGCTTAATTTAG
1 TTGTTTCA----G-TT--TGATTGGAAATTTGGGATCTTTCTACTTGTTTCAATGCTTAATTTAG
897844 ATGGTG
59 ATGGTG
* * *
897850 TTGTTTCAGTTTGATTGGAAATTTGGGATATTTCTACTTGTTTCAATGCTTCATTTGGATGGT-
1 TTGTTTCAGTTTGATTGGAAATTTGGGATCTTTCTACTTGTTTCAATGCTTAATTTAGATGGTG
897913 TTGT
1 TTGT
897917 AGTTTTCTTT
Statistics
Matches: 124, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
63 24 0.19
64 35 0.28
65 2 0.02
66 1 0.01
67 1 0.01
68 2 0.02
69 2 0.02
70 57 0.46
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (64 bp):
TTGTTTCAGTTTGATTGGAAATTTGGGATCTTTCTACTTGTTTCAATGCTTAATTTAGATGGTG
Found at i:899012 original size:32 final size:32
Alignment explanation
Indices: 898976--899072 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
898966 TGATTGCAGT
898976 TGTTACAGAGTAACCAAATATGTGTAAATGCC
1 TGTTACAGAGTAACCAAATATGTGTAAATGCC
* * *
899008 TGTTA-TGA--AATCCATAGCATAT-TG--CA-G-T
1 TGTTACAGAGTAA-CCA-A--ATATGTGTAAATGCC
899036 TGTTACAGAGTAACCAAATATGTGTAAATGCC
1 TGTTACAGAGTAACCAAATATGTGTAAATGCC
899068 TGTTA
1 TGTTA
899073 TGAAATCCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 24
0.61 0.08 0.31
Matches are distributed among these distances:
27 4 0.09
28 7 0.15
29 6 0.13
30 8 0.17
31 6 0.13
32 12 0.26
33 4 0.09
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (32 bp):
TGTTACAGAGTAACCAAATATGTGTAAATGCC
Found at i:899061 original size:60 final size:60
Alignment explanation
Indices: 898968--899087 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
898958 AAGATATGTG
898968 ATTGCAGTTGTTACAGAGTAACCAAATATGTGTAAATGCCTGTTATGAAATCCATAGCAT
1 ATTGCAGTTGTTACAGAGTAACCAAATATGTGTAAATGCCTGTTATGAAATCCATAGCAT
899028 ATTGCAGTTGTTACAGAGTAACCAAATATGTGTAAATGCCTGTTATGAAATCCATAGCAT
1 ATTGCAGTTGTTACAGAGTAACCAAATATGTGTAAATGCCTGTTATGAAATCCATAGCAT
899088 GTAGCAAAGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (60 bp):
ATTGCAGTTGTTACAGAGTAACCAAATATGTGTAAATGCCTGTTATGAAATCCATAGCAT
Found at i:902365 original size:16 final size:15
Alignment explanation
Indices: 902339--902370 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
902329 TTTTAAAATA
902339 AAAATTATAAATATT
1 AAAATTATAAATATT
902354 AAAATTATTAAATATT
1 AAAATTA-TAAATATT
902370 A
1 A
902371 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:904569 original size:13 final size:13
Alignment explanation
Indices: 904551--904593 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
904541 CTAAAATTTA
904551 TAAAAAAATTAAT
1 TAAAAAAATTAAT
*
904564 TAAAAATAA-TATT
1 TAAAAA-AATTAAT
*
904577 TCAAAAAATTAAT
1 TAAAAAAATTAAT
904590 TAAA
1 TAAA
904594 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAAAATTAAT
Found at i:908237 original size:12 final size:12
Alignment explanation
Indices: 908196--908238 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
908186 GAAAGCTCAT
*
908196 ATAATTATTTAAA
1 ATAATT-TTAAAA
*
908209 ATAATATTAAAA
1 ATAATTTTAAAA
908221 A-AATTTTAAAA
1 ATAATTTTAAAA
908232 ATAATTT
1 ATAATTT
908239 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.38
12 11 0.42
13 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATTTTAAAA
Found at i:909407 original size:5 final size:5
Alignment explanation
Indices: 909397--909422 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
909387 ACATGATTGG
909397 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
909423 TTCTTGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:909947 original size:21 final size:21
Alignment explanation
Indices: 909906--909947 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
909896 AAAAAATATT
*
909906 TTTATATTAATAGTTATATAA
1 TTTATATTAATAGTTAAATAA
*
909927 TTTATAATTAA-ATTTAAATAA
1 TTTAT-ATTAATAGTTAAATAA
909948 AAATATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTATATTAATAGTTAAATAA
Found at i:909978 original size:19 final size:20
Alignment explanation
Indices: 909939--909978 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
909929 TATAATTAAA
*
909939 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAATATACTAT
*
909959 TTTAATTAAAAAT-TACTAT
1 TTTAAATAAAAATATACTAT
909978 T
1 T
909979 CAAATCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATAAAAATATACTAT
Found at i:910353 original size:2 final size:2
Alignment explanation
Indices: 910348--910379 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
910338 CACACACGTG
910348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
910380 GAAAGAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:913682 original size:22 final size:24
Alignment explanation
Indices: 913631--913698 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 24
913621 ATTTTTAACG
913631 TATTTTAATTT--ATTTATATTAT
1 TATTTTAATTTAAATTTATATTAT
* *
913653 TGTATTAATTTAAATTT-T-TTAT
1 TATTTTAATTTAAATTTATATTAT
*
913675 TATTTTAATAATTAAATTGATATT
1 TATTTTAAT--TTAAATTTATATT
913699 CAGTTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 20 0.57
23 1 0.03
24 11 0.31
25 1 0.03
26 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TATTTTAATTTAAATTTATATTAT
Found at i:913819 original size:2 final size:2
Alignment explanation
Indices: 913812--913855 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
913802 TGCATTTCTT
* *
913812 TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
913854 TA
1 TA
913856 AATGCTTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:914025 original size:2 final size:2
Alignment explanation
Indices: 914018--914042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
914008 TCTCAAAAGC
914018 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 A
914043 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:914047 original size:2 final size:2
Alignment explanation
Indices: 914042--914074 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
914032 ATATATATAT
914042 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 A
914075 TGAGGCAATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:914460 original size:24 final size:24
Alignment explanation
Indices: 914407--914453 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
914397 TAATAATTTA
*
914407 AAATAAAATATTAAAATAATATATG
1 AAAT-AAATATAAAAATAATATATG
*
914432 TAATAAATATAAAAATAATATA
1 AAATAAATATAAAAATAATATA
914454 ATAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATAAATATAAAAATAATATATG
Found at i:927395 original size:2 final size:2
Alignment explanation
Indices: 927388--927418 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
927378 TCATCTTTCC
927388 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
927419 TCACAATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:928584 original size:2 final size:2
Alignment explanation
Indices: 928577--928614 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
928567 TTAGCATTCA
928577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
928615 GGTCAAGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:934337 original size:18 final size:18
Alignment explanation
Indices: 934311--934353 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
934301 ATTAATTTTT
*
934311 TATTTAAATATAAAAATA
1 TATTAAAATATAAAAATA
* *
934329 TATTAAAATTTAAATATA
1 TATTAAAATATAAAAATA
*
934347 AATTAAA
1 TATTAAA
934354 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTAAAATATAAAAATA
Found at i:934391 original size:17 final size:17
Alignment explanation
Indices: 934371--934405 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
934361 TTATTAATTT
*
934371 AATCTTTTAATATAATA
1 AATCATTTAATATAATA
*
934388 AATCATTTAATTTAATA
1 AATCATTTAATATAATA
934405 A
1 A
934406 TAGTAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
AATCATTTAATATAATA
Found at i:934915 original size:13 final size:13
Alignment explanation
Indices: 934892--934923 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
934882 TTATATTATT
934892 TAAAT-TTAAATA
1 TAAATATTAAATA
934904 TAAATATTAAATA
1 TAAATATTAAATA
934917 TAAATAT
1 TAAATAT
934924 ATACTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATATTAAATA
Found at i:934959 original size:34 final size:34
Alignment explanation
Indices: 934920--935007 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
934910 TTAAATATAA
* *
934920 ATATATACTTAATATATTTAAT-TTTTTAATATTT
1 ATATATACTTAA-ATATTTAATATTATTAATAATT
* * *
934954 TTATATATTTAAAAATTT-ATATTATTAATAATT
1 ATATATACTTAAATATTTAATATTATTAATAATT
*
934987 ATACTATACATAAATATTTAA
1 ATA-TATACTTAAATATTTAA
935008 AAAAATTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
32 2 0.05
33 17 0.40
34 22 0.52
35 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (34 bp):
ATATATACTTAAATATTTAATATTATTAATAATT
Found at i:934964 original size:17 final size:17
Alignment explanation
Indices: 934907--934975 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
934897 TTAAATATAA
* **
934907 ATATTAAATATAAATAT
1 ATATTTAATATATTTAT
*
934924 ATACTTAATATATTTA-
1 ATATTTAATATATTTAT
* *
934940 ATTTTTTAATATTTTTAT
1 A-TATTTAATATATTTAT
*
934958 ATATTTAA-AAATTTAT
1 ATATTTAATATATTTAT
934974 AT
1 AT
934976 TATTAATAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
16 9 0.22
17 30 0.75
18 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTAATATATTTAT
Found at i:935930 original size:16 final size:17
Alignment explanation
Indices: 935898--935953 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
935888 AAAAAAATTT
935898 ATTTTACATAATTTTAA
1 ATTTTACATAATTTTAA
*
935915 ATTTTACA-ATTTTTAA
1 ATTTTACATAATTTTAA
935931 ATATTTATCAAATAATTTTAA
1 AT-TTTA-C--ATAATTTTAA
935952 AT
1 AT
935954 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 9 0.28
17 12 0.38
18 1 0.03
20 1 0.03
21 9 0.28
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTTACATAATTTTAA
Found at i:935959 original size:9 final size:9
Alignment explanation
Indices: 935897--935960 Score: 53
Period size: 9 Copynumber: 6.9 Consensus size: 9
935887 TAAAAAAATT
*
935897 TATTTTACA
1 TATTTTAAA
935906 TAATTTT-AA
1 T-ATTTTAAA
935915 -ATTTTACAA
1 TATTTTA-AA
935924 T-TTTTAAA
1 TATTTTAAA
935932 TATTTATCAAA
1 TATTT-T-AAA
935943 TAATTTTAAA
1 T-ATTTTAAA
935953 TATTTTAA
1 TATTTTAA
935961 TAATAAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
7 5 0.11
8 3 0.07
9 19 0.41
10 10 0.22
11 5 0.11
12 4 0.09
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (9 bp):
TATTTTAAA
Found at i:935965 original size:21 final size:21
Alignment explanation
Indices: 935925--935966 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
935915 ATTTTACAAT
*
935925 TTTTAAATATTTATCAAATAA
1 TTTTAAATATTTATAAAATAA
935946 TTTTAAATATTT-TAATAATAA
1 TTTTAAATATTTATAA-AATAA
935967 AATACATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAATATTTATAAAATAA
Found at i:936129 original size:29 final size:29
Alignment explanation
Indices: 936084--936146 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
936074 TCACAGGAGC
*
936084 AAAATGATATTAATTTAATAAATAATTTT
1 AAAATAATATTAATTTAATAAATAATTTT
* * *
936113 AAAATAATATTAGTTTAATAATTTATTTT
1 AAAATAATATTAATTTAATAAATAATTTT
936142 AAAAT
1 AAAAT
936147 TAAAAGTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (29 bp):
AAAATAATATTAATTTAATAAATAATTTT
Found at i:936622 original size:58 final size:59
Alignment explanation
Indices: 936546--936658 Score: 185
Period size: 58 Copynumber: 1.9 Consensus size: 59
936536 CCGATTATCC
* *
936546 TATATTTTTTTGCTAGTAATGAAGCTTCGAAGAAATTGTC-TCTGATTTGGAGAGGTAAA
1 TATATTTTTTTACCAGTAATGAAGCTTCGAAGAAATTGTCAT-TGATTTGGAGAGGTAAA
936605 TATA-TTTTTTACCAGTAATGAAGCTTCGAAGAAATTGTCATTGATTTGGAGAGG
1 TATATTTTTTTACCAGTAATGAAGCTTCGAAGAAATTGTCATTGATTTGGAGAGG
936659 CATGCATGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
58 46 0.90
59 5 0.10
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (59 bp):
TATATTTTTTTACCAGTAATGAAGCTTCGAAGAAATTGTCATTGATTTGGAGAGGTAAA
Found at i:936674 original size:2 final size:2
Alignment explanation
Indices: 936667--936693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
936657 GGCATGCATG
936667 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
936694 TAAATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:936718 original size:15 final size:15
Alignment explanation
Indices: 936695--936724 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
936685 TATATATATT
*
936695 AAATTTTAAATATAA
1 AAATATTAAATATAA
936710 AAATATTAAATATAA
1 AAATATTAAATATAA
936725 TATAAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATTAAATATAA
Found at i:936733 original size:22 final size:22
Alignment explanation
Indices: 936690--936733 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
936680 ATATATATAT
* *
936690 ATATTAAATTTTAAATATAAAA
1 ATATTAAATTATAAATAAAAAA
936712 ATATTAAA-TATAATATAAAAAA
1 ATATTAAATTATAA-ATAAAAAA
936734 TAATACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATTAAATTATAAATAAAAAA
Found at i:936771 original size:22 final size:22
Alignment explanation
Indices: 936745--936795 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
936735 AATACAATCA
* *
936745 TAAAATAAAT-ATATAAAATTTT
1 TAAAATAAATAAAAT-AAATTAT
*
936767 TAAAATTAATAAAATAAATTAT
1 TAAAATAAATAAAATAAATTAT
936789 TAAAATA
1 TAAAATA
936796 TAAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATAAAATAAATTAT
Found at i:936795 original size:18 final size:19
Alignment explanation
Indices: 936774--936821 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
936764 TTTTAAAATT
936774 AATAAAATAAATTAT-TAA
1 AATAAAATAAATTATATAA
*
936792 AATATAAA-AATTTATATAA
1 AATA-AAATAAATTATATAA
936811 ATATAAAATAA
1 A-ATAAAATAA
936822 TTTAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAATAAATTATATAA
Found at i:936841 original size:20 final size:20
Alignment explanation
Indices: 936791--936851 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
936781 TAAATTATTA
*
936791 AAATAT-AAA-AATTTATAT
1 AAATATAAAATAATTTAAAT
936809 AAATATAAAATAATTTAAAT
1 AAATATAAAATAATTTAAAT
*
936829 ATAAT-TAATATAA--TAAAT
1 A-AATATAAAATAATTTAAAT
936847 AAATA
1 AAATA
936852 AACGTCACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 3 0.08
20 16 0.43
21 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATATAAAATAATTTAAAT
Found at i:936845 original size:34 final size:32
Alignment explanation
Indices: 936702--936847 Score: 87
Period size: 34 Copynumber: 4.7 Consensus size: 32
936692 ATTAAATTTT
936702 AAATATAAAAATAT--TAAATATAATATAA--A
1 AAATATAAAAATATAATAAATATAA-ATAATTA
* * *
936731 AAATA-ATACA-ATCATAAA-ATAAAT-ATATA
1 AAATATAAAAATATAATAAATATAAATAAT-TA
* * *
936760 AAATTTTTAAAAT-TAATAAA-ATAAATTATTA
1 AAA-TATAAAAATATAATAAATATAAATAATTA
* *
936791 AAATATAAAAATTTATATAAATATAAAATAATTT
1 AAATATAAAAATATA-ATAAATAT-AAATAATTA
*
936825 AAATATAATTAATATAATAAATA
1 AAATATAA-AAATATAATAAATA
936848 AATAAACGTC
Statistics
Matches: 90, Mismatches: 13, Indels: 23
0.71 0.10 0.18
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 7 0.08
29 13 0.14
30 8 0.09
31 21 0.23
32 7 0.08
33 2 0.02
34 22 0.24
35 5 0.06
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AAATATAAAAATATAATAAATATAAATAATTA
Found at i:942285 original size:18 final size:18
Alignment explanation
Indices: 942262--942302 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
942252 TATTTATATA
*
942262 ATTTTTTATACGATTAAT
1 ATTTTTTATACAATTAAT
942280 ATTTTTTATACAATTAAT
1 ATTTTTTATACAATTAAT
942298 ATTTT
1 ATTTT
942303 AATAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTTTATACAATTAAT
Found at i:942531 original size:9 final size:10
Alignment explanation
Indices: 942495--942542 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 10
942485 TGTATAATCT
942495 ATATAAATAAA
1 ATATAAAT-AA
*
942506 ATATAAA-AT
1 ATATAAATAA
942515 ATAATAAATAA
1 AT-ATAAATAA
942526 AT-TAAATAA
1 ATATAAATAA
942535 ATATAAAT
1 ATATAAAT
942543 CGTATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 12 0.38
10 10 0.31
11 10 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATAAATAA
Found at i:943035 original size:29 final size:28
Alignment explanation
Indices: 942963--943036 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
942953 GAACTTAAAA
942963 AATTAATAAAAATATAAAAATATTTTTAT
1 AATTAATAAAAATA-AAAAATATTTTTAT
** *
942992 AATTTAATTTAAATAAAAGATATTTTTACT
1 AA-TTAATAAAAATAAAAAATATTTTTA-T
943022 -ATTAATAAATAATAA
1 AATTAATAAA-AATAA
943037 TGTAAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 6 0.16
29 20 0.54
30 11 0.30
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
AATTAATAAAAATAAAAAATATTTTTAT
Found at i:948169 original size:13 final size:13
Alignment explanation
Indices: 948151--948175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
948141 AATTTAATTT
948151 AATTTAAAATATA
1 AATTTAAAATATA
948164 AATTTAAAATAT
1 AATTTAAAATAT
948176 TATTAAATTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTAAAATATA
Found at i:948274 original size:15 final size:16
Alignment explanation
Indices: 948239--948278 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
948229 TTATAATTTT
*
948239 TAATTTATTTTTTAAA
1 TAATTTAATTTTTAAA
*
948255 AAATTTAATTTTT-AA
1 TAATTTAATTTTTAAA
948270 TAATTTAAT
1 TAATTTAAT
948279 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATTTAATTTTTAAA
Found at i:948342 original size:14 final size:13
Alignment explanation
Indices: 948323--948364 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
948313 TGATATTTTT
948323 TAATATTTATACTA
1 TAATATTTATA-TA
948337 TAATA-TTATATA
1 TAATATTTATATA
948349 T-ATATTTATATGA
1 TAATATTTATAT-A
948362 TAA
1 TAA
948365 AAATTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.12
12 9 0.36
13 7 0.28
14 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (13 bp):
TAATATTTATATA
Found at i:948752 original size:16 final size:16
Alignment explanation
Indices: 948725--948794 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 16
948715 ACTTGAACTC
*
948725 AAAATAAATTAAATTT
1 AAAATAATTTAAATTT
* * * *
948741 TAAATGATTTAAACTC
1 AAAATAATTTAAATTT
*
948757 GAAATAATTTAAATTT
1 AAAATAATTTAAATTT
*
948773 AAAATAATTTAAATTC
1 AAAATAATTTAAATTT
948789 AAAATA
1 AAAATA
948795 CTCAAACAAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:948756 original size:32 final size:32
Alignment explanation
Indices: 948720--948794 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
948710 CTTTAACTTG
* *
948720 AACTCAAAATAAATTAAATTTTAAATGATTTA
1 AACTCAAAATAAATTAAATTTAAAATAATTTA
* *
948752 AACTCGAAATAATTTAAATTTAAAATAATTTA
1 AACTCAAAATAAATTAAATTTAAAATAATTTA
*
948784 AATTCAAAATA
1 AACTCAAAATA
948795 CTCAAACAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (32 bp):
AACTCAAAATAAATTAAATTTAAAATAATTTA
Found at i:948979 original size:15 final size:16
Alignment explanation
Indices: 948949--948986 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
948939 GACTCGAACC
948949 TAAAATGAATTAAAAT
1 TAAAATGAATTAAAAT
*
948965 TAAAAT-AATTTAAAT
1 TAAAATGAATTAAAAT
948980 TCAAAAT
1 T-AAAAT
948987 TTTAAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (16 bp):
TAAAATGAATTAAAAT
Found at i:949768 original size:31 final size:31
Alignment explanation
Indices: 949692--949777 Score: 77
Period size: 32 Copynumber: 2.7 Consensus size: 31
949682 TATCTAATAA
* *
949692 TTATT-TTATAATATTATATTCTTAAATAAAAT
1 TTATTATTATATTATTA-ATT-TAAAATAAAAT
*
949724 TTATTGTTAATATTATTAATTTAAAATAAAAT
1 TTATTATT-ATATTATTAATTTAAAATAAAAT
* *
949756 TT-TTAATTATATTCTTATTTTA
1 TTATT-ATTATATTATTAATTTA
949778 TTTTTAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 14 0.30
32 19 0.41
33 5 0.11
34 8 0.17
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TTATTATTATATTATTAATTTAAAATAAAAT
Found at i:951004 original size:16 final size:16
Alignment explanation
Indices: 950983--951034 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
950973 TTTATAAAAT
950983 AATATATATTTAATAA
1 AATATATATTTAATAA
950999 AATATA-ATTT--TAA
1 AATATATATTTAATAA
*
951012 AATAAATA-TTAAGT-A
1 AATATATATTTAA-TAA
951027 AATATATA
1 AATATATA
951035 CATATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 12 0.40
16 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AATATATATTTAATAA
Found at i:956815 original size:17 final size:17
Alignment explanation
Indices: 956780--956825 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
956770 TCTAAAATCG
*
956780 AAATAATTT-AAATTTA
1 AAATAATTTAAAATTAA
956796 AAATAATTTAAAATTAA
1 AAATAATTTAAAATTAA
956813 AAATAATTTAAAA
1 AAATAATTTAAAA
956826 AATTAAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATAATTTAAAATTAA
Found at i:958647 original size:17 final size:18
Alignment explanation
Indices: 958625--958663 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
958615 AATAAAATCA
958625 AAATTTA-ATTTTTATTT
1 AAATTTATATTTTTATTT
*
958642 AAATTTATTTTTTTATTT
1 AAATTTATATTTTTATTT
958660 AAAT
1 AAAT
958664 CTTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
AAATTTATATTTTTATTT
Found at i:958695 original size:17 final size:17
Alignment explanation
Indices: 958656--958700 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
958646 TTATTTTTTT
* *
958656 ATTTAAAT-CTTTTTAA
1 ATTTAAATAATTTATAA
958672 ATATTAAATAATTTATAA
1 AT-TTAAATAATTTATAA
958690 ATTTAAATAAT
1 ATTTAAATAAT
958701 AACTTGATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 15 0.60
18 8 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATAATTTATAA
Found at i:959580 original size:18 final size:18
Alignment explanation
Indices: 959557--959601 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
959547 TTAAATTTTA
*
959557 AATATTATAAATTTGAAT
1 AATATTATAAATATGAAT
*
959575 AATATT-TAAATATGGAT
1 AATATTATAAATATGAAT
*
959592 ATTATTATAA
1 AATATTATAA
959602 CTATTCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
AATATTATAAATATGAAT
Found at i:959834 original size:21 final size:21
Alignment explanation
Indices: 959821--959874 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
959811 AATTTAAATT
959821 TAAATTTAAATAATAAATATA
1 TAAATTTAAATAATAAATATA
* *
959842 TAAATTTAATACGAAT-AATAAA
1 TAAATTTAA-A-TAATAAATATA
959864 TAAATTTAAAT
1 TAAATTTAAAT
959875 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 10 0.36
22 15 0.54
23 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATTTAAATAATAAATATA
Found at i:960324 original size:19 final size:17
Alignment explanation
Indices: 960300--960340 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
960290 AATTTATAAC
*
960300 ATTAATTATTATATTTTT
1 ATTAATTATT-GATTTTT
960318 AATTAATTATTGATTTTT
1 -ATTAATTATTGATTTTT
960336 ATTAA
1 ATTAA
960341 AATTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTAATTATTGATTTTT
Found at i:960569 original size:168 final size:167
Alignment explanation
Indices: 960315--960616 Score: 507
Period size: 168 Copynumber: 1.8 Consensus size: 167
960305 TTATTATATT
960315 TTTAATTAATTATTGATTTTTATTAAAATTAAAATATTAAGTAAATTTATTTATTTCTTAATTAA
1 TTTAATTAATTATTGATTTTTATTAAAATTAAAATATTAAGTAAATTTATTTATTTCTTAATTAA
* *
960380 CTCAGAATTCTTATCAATGTAAACTCTCCTTTATTGATATATCTTTTATTAGTATTAACTAATTT
66 CTAAGAATTCTTATCAATGTAAACTCTCCTTTATTGATATATCTTTTATTAATATTAACTAATTT
960445 TTTATTAAATTATAATTTATAGTATTAACTACTAGTC
131 TTTATTAAATTATAATTTATAGTATTAACTACTAGTC
**
960482 TTTAATTAATTAATTTTTTTTTATTAAAATTAAAATATTAAGT-AATCTTATTTATTTCTTAATT
1 TTTAATTAATT-ATTGATTTTTATTAAAATTAAAATATTAAGTAAAT-TTATTTATTTCTTAATT
* ** *
960546 AACTAAGAATTCTTATTAATGTAAACTCTTTTTTATTGATATATCTTTTATTAATGTTAACTAAT
64 AACTAAGAATTCTTATCAATGTAAACTCTCCTTTATTGATATATCTTTTATTAATATTAACTAAT
960611 TTTTTA
129 TTTTTA
960617 ATGAATTTTT
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
167 14 0.11
168 111 0.89
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.52
Consensus pattern (167 bp):
TTTAATTAATTATTGATTTTTATTAAAATTAAAATATTAAGTAAATTTATTTATTTCTTAATTAA
CTAAGAATTCTTATCAATGTAAACTCTCCTTTATTGATATATCTTTTATTAATATTAACTAATTT
TTTATTAAATTATAATTTATAGTATTAACTACTAGTC
Found at i:966571 original size:32 final size:31
Alignment explanation
Indices: 966534--966593 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
966524 CTCTTCACAT
966534 AAAATATTATAAAAAAATAATAAAAATAATAA
1 AAAATATTATAAAAAAATAA-AAAAATAATAA
* * *
966566 AAAATATTATATAATATTAAAAAAATAA
1 AAAATATTATAAAAAAATAAAAAAATAA
966594 ATATAATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 8 0.32
32 17 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (31 bp):
AAAATATTATAAAAAAATAAAAAAATAATAA
Found at i:966597 original size:20 final size:20
Alignment explanation
Indices: 966543--966602 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
966533 TAAAATATTA
*
966543 TAAAAAAAT-AATA-AAAAT
1 TAAAAAAATAAATATAATAT
* *
966561 AATAAAAAATATTATATAATAT
1 TA-AAAAAATA-AATATAATAT
966583 TAAAAAAATAAATATAATAT
1 TAAAAAAATAAATATAATAT
966603 GAATTTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 9 0.27
21 11 0.33
22 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAAATATAATAT
Found at i:966602 original size:25 final size:25
Alignment explanation
Indices: 966567--966618 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
966557 AAATAATAAA
*
966567 AAATATTATAT-AATATTAAAAAAAT
1 AAATATAATATGAAT-TTAAAAAAAT
*
966592 AAATATAATATGAATTTATAAAAAT
1 AAATATAATATGAATTTAAAAAAAT
966617 AA
1 AA
966619 CAAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATATAATATGAATTTAAAAAAAT
Found at i:968082 original size:5 final size:5
Alignment explanation
Indices: 968069--968138 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
968059 ATAAAAGTTT
* * * * *
968069 TTAAT TTAAA TTAAT TTGAT TTTAAA TTAAT TTAAA TTAAA TT-AA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TTAAA
* *
968119 ATAAT TTAAAA TTAAA TTAA
1 TTAAA TT-AAA TTAAA TTAA
968139 TTTTATTTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
4 4 0.08
5 40 0.78
6 7 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (5 bp):
TTAAA
Found at i:968094 original size:16 final size:15
Alignment explanation
Indices: 968068--968115 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
968058 AATAAAAGTT
968068 TTTAATTTAAATTAA
1 TTTAATTTAAATTAA
*
968083 TTTGATTTTAAATTAA
1 TTT-AATTTAAATTAA
*
968099 TTTAAATTAAATTAA
1 TTTAATTTAAATTAA
968114 TT
1 TT
968116 AAAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTAATTTAAATTAA
Found at i:968130 original size:25 final size:24
Alignment explanation
Indices: 968070--968140 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 24
968060 TAAAAGTTTT
* * *
968070 TAATTTAAATTAATTTGATTTTAAAT
1 TAATTTAAATTAAATT-A-ATTAAAA
968096 TAATTTAAATTAAATTAATTAAAA
1 TAATTTAAATTAAATTAATTAAAA
968120 TAATTTAAAATTAAATTAATT
1 TAATTT-AAATTAAATTAATT
968141 TTATTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 11 0.27
25 15 0.37
26 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
TAATTTAAATTAAATTAATTAAAA
Found at i:968616 original size:26 final size:24
Alignment explanation
Indices: 968580--968628 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
968570 ACTTAGATCA
*
968580 TTATTTATTTAATTAAATAATATT
1 TTATTTATTTAATTAAAAAATATT
968604 TTATTTAATTTTAATTAAAAAATAT
1 TTATTT-A-TTTAATTAAAAAATAT
968629 ATAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTTATTTAATTAAAAAATATT
Found at i:969815 original size:2 final size:2
Alignment explanation
Indices: 969808--969849 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
969798 AGCTTTTTAA
969808 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
969850 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:971430 original size:153 final size:153
Alignment explanation
Indices: 971196--971499 Score: 608
Period size: 153 Copynumber: 2.0 Consensus size: 153
971186 TTGAGTCATA
971196 TATCTCCCCCTGGTTGATGGTCTAGTGTATCTCCATTTGTCCTGAAAATAGTTCTCAAAGTTGTG
1 TATCTCCCCCTGGTTGATGGTCTAGTGTATCTCCATTTGTCCTGAAAATAGTTCTCAAAGTTGTG
971261 GTTTTATGGGCTGGCACATTAAATGTTGAAAAAGGATGGGTTTCTTATTAATTGTTACATTGGCT
66 GTTTTATGGGCTGGCACATTAAATGTTGAAAAAGGATGGGTTTCTTATTAATTGTTACATTGGCT
971326 TGCTGCGTGATTTCAACTTAGTG
131 TGCTGCGTGATTTCAACTTAGTG
971349 TATCTCCCCCTGGTTGATGGTCTAGTGTATCTCCATTTGTCCTGAAAATAGTTCTCAAAGTTGTG
1 TATCTCCCCCTGGTTGATGGTCTAGTGTATCTCCATTTGTCCTGAAAATAGTTCTCAAAGTTGTG
971414 GTTTTATGGGCTGGCACATTAAATGTTGAAAAAGGATGGGTTTCTTATTAATTGTTACATTGGCT
66 GTTTTATGGGCTGGCACATTAAATGTTGAAAAAGGATGGGTTTCTTATTAATTGTTACATTGGCT
971479 TGCTGCGTGATTTCAACTTAG
131 TGCTGCGTGATTTCAACTTAG
971500 ACGTCAATGT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (153 bp):
TATCTCCCCCTGGTTGATGGTCTAGTGTATCTCCATTTGTCCTGAAAATAGTTCTCAAAGTTGTG
GTTTTATGGGCTGGCACATTAAATGTTGAAAAAGGATGGGTTTCTTATTAATTGTTACATTGGCT
TGCTGCGTGATTTCAACTTAGTG
Found at i:974842 original size:2 final size:2
Alignment explanation
Indices: 974835--974872 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
974825 TGGGCTTTAC
974835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
974873 GTGAGAAAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:974977 original size:32 final size:34
Alignment explanation
Indices: 974941--975014 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
974931 AACGATACCG
974941 ATTAAAATATTATTT-ATTAAAAATAAA-AATAT
1 ATTAAAATATTATTTAATTAAAAATAAATAATAT
* * * * *
974973 ATTAATATATTTTTTAATTCAATATAAATAATTT
1 ATTAAAATATTATTTAATTAAAAATAAATAATAT
975007 ATTAAAAT
1 ATTAAAAT
975015 TTAAAAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 13 0.38
33 10 0.29
34 11 0.32
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
ATTAAAATATTATTTAATTAAAAATAAATAATAT
Found at i:975395 original size:14 final size:13
Alignment explanation
Indices: 975373--975407 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
975363 TAATATTTAA
975373 TAAATTTAATATT
1 TAAATTTAATATT
975386 TAAATCTTAATATT
1 TAAAT-TTAATATT
975400 TATAATTT
1 TA-AATTT
975408 TTTTTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAATTTAATATT
Found at i:976075 original size:13 final size:14
Alignment explanation
Indices: 976046--976089 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
976036 ATCTCAAAAT
976046 TTTTAAAAGATATAA
1 TTTTAAAA-ATATAA
976061 TTTTAAAAA-ATAA
1 TTTTAAAAATATAA
976074 TTGTTAAAAATA-AA
1 TT-TTAAAAATATAA
976088 TT
1 TT
976090 ATTATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.22
14 12 0.44
15 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:976119 original size:20 final size:21
Alignment explanation
Indices: 976077--976122 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
976067 AAAATAATTG
976077 TTAAAAATAAATTATTATATT
1 TTAAAAATAAATTATTATATT
*
976098 TTAAAAAT-AATTATTAGTTTT
1 TTAAAAATAAATTATTA-TATT
976119 TTAA
1 TTAA
976123 TTAAATAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAAAAATAAATTATTATATT
Found at i:976711 original size:29 final size:29
Alignment explanation
Indices: 976679--976749 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
976669 TAGCTTAAAA
976679 TAAAAAAATAATTTA-TAAATATTAAGATT
1 TAAAAAAATAATTTATTAAATATT-AGATT
** **
976708 T-AAAATTTAAATTTATTAAATATTATTTT
1 TAAAAAAAT-AATTTATTAAATATTAGATT
976737 TAAAAAAATAATT
1 TAAAAAAATAATT
976750 ACATGAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
28 5 0.15
29 15 0.45
30 13 0.39
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
TAAAAAAATAATTTATTAAATATTAGATT
Found at i:976717 original size:14 final size:15
Alignment explanation
Indices: 976688--976732 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
976678 ATAAAAAAAT
976688 AATTTATAAATATTA
1 AATTTATAAATATTA
976703 AGATTTA-AAAT-TTA
1 A-ATTTATAAATATTA
976717 AATTTATTAAATATTA
1 AATTTA-TAAATATTA
976733 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 9 0.35
16 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATTTATAAATATTA
Found at i:981353 original size:2 final size:2
Alignment explanation
Indices: 981348--981375 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
981338 TCCATTTTTA
981348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
981376 CTTTACTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:987918 original size:17 final size:18
Alignment explanation
Indices: 987879--987923 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
987869 TAAAATAATT
987879 ATAT-TAAATAAATATAAA
1 ATATGTAAA-AAATATAAA
*
987897 TTATGTAAAAAA-ATAAA
1 ATATGTAAAAAATATAAA
987914 ATATGTAAAA
1 ATATGTAAAA
987924 CTAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 14 0.58
18 6 0.25
19 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
ATATGTAAAAAATATAAA
Found at i:987929 original size:19 final size:19
Alignment explanation
Indices: 987864--987932 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
987854 AAATAAAGCC
* *
987864 TAAAATAAA-ATAATTATA
1 TAAAATAAATAAAATTATG
*
987882 TTAAATAAATATAAATTATG
1 TAAAATAAATA-AAATTATG
987902 TAAAA-AAATAAAA-TATG
1 TAAAATAAATAAAATTATG
987919 TAAAACTAAATAAA
1 TAAAA-TAAATAAA
987933 TTTTACATCG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 9 0.21
18 11 0.26
19 13 0.30
20 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAAATAAATAAAATTATG
Done.