Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 5 of 22
Found at i:648457 original size:23 final size:22
Alignment explanation
Indices: 648431--648475 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
648421 CCACTCAATC
648431 GGAAAACCCACTTTGGTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTT
* **
648454 GGAAAGCCCCTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTT
648476 TTTTCGACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (22 bp):
GGAAAACCCCTTTGGTTTTTTT
Found at i:649275 original size:45 final size:48
Alignment explanation
Indices: 649174--649279 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 48
649164 AATGTGCCAT
* *
649174 TTCAAGGTCAGCGACATCGGGCTAAGGGAAAAGTGGACCAATGTGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAA-GGAAAAGTGGACCAATATGCTGA
* * * *
649223 CTCAAGGCCAGCGACATTGGGCTTA-GAAAGGT-G-CCAATATGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
649268 TTCAAGGCCAGC
1 TTCAAGGCCAGC
649280 AATATCGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 22 0.44
46 1 0.02
47 6 0.12
49 21 0.42
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (48 bp):
TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
Found at i:649368 original size:32 final size:32
Alignment explanation
Indices: 649312--649785 Score: 779
Period size: 32 Copynumber: 14.8 Consensus size: 32
649302 AAAATGGTGA
* ** **
649312 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
649344 TTTTAAATGGGTTGCCCCCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
649376 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
649408 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
649440 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
649472 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
649504 TTTGAAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
649535 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
649567 TTTGGAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
649599 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
649631 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
649663 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
649695 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
649727 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
649759 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
649786 AATTTAAAAG
Statistics
Matches: 420, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
31 30 0.07
32 390 0.93
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:649834 original size:27 final size:27
Alignment explanation
Indices: 649771--650509 Score: 1066
Period size: 27 Copynumber: 26.9 Consensus size: 27
649761 TGGAATGGGT
* * * *
649771 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
649798 ATGCCACGGAGTTGTGGACTTAAAAGGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
649826 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
649853 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
649881 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
649909 ATGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
649937 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
649965 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
649992 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
650020 TGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
650047 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
650074 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
650101 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
650128 ATGCCATGGAGTTATGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
*
650156 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
650184 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
650211 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
650238 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
**
650266 TGCCATAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
650293 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
650320 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
650347 TGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
650374 TACCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
650402 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
650429 TACCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
650457 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
650484 TGCCACAGAGTTATGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
650510 AAAATGCCAC
Statistics
Matches: 649, Mismatches: 51, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
27 369 0.57
28 280 0.43
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:649840 original size:55 final size:54
Alignment explanation
Indices: 649771--650509 Score: 1066
Period size: 55 Copynumber: 13.5 Consensus size: 54
649761 TGGAATGGGT
* * * * *
649771 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
649826 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
649881 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACAGAGTTGTGGACTAAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
*
649937 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * * * *
649992 TGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
650047 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
650101 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG
* *
650156 TGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGG
*
650211 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-G
**
650266 TGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
650320 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
650374 TACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* * *
650429 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
650484 TGCCACAGAGTTATGGACTTTAAAAG
1 TGCCACGGAGTTGTGGAC-TTAAAAG
650510 AAAATGCCAC
Statistics
Matches: 629, Mismatches: 45, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
54 150 0.24
55 416 0.66
56 63 0.10
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:650048 original size:82 final size:81
Alignment explanation
Indices: 649771--650533 Score: 1069
Period size: 82 Copynumber: 9.2 Consensus size: 81
649761 TGGAATGGGT
* * * * * *
649771 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
649836 TTGTGGACTTAAAAGGGA
65 TTGTGGACTTAAAA-GGA
649854 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACAGA
* *
649919 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGA
*
649937 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
*
650002 TTGTGGACTTAAAAAAGA
65 TTGTGGACTT-AAAAGGA
* * * *
650020 TGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
* *
650085 TGTGGTCTTAAAAGGG
66 TGTGGACTTAAAAGGA
* * *
650101 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAGTTATGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
650166 TTGTGGTA-TTAAAAGGAA
65 TTGTGG-ACTTAAAAGG-A
* *
650184 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
650249 TGTGGACTTAAAAGGAA
66 TGTGGACTTAAAAGG-A
**
650266 TGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
*
650331 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGA
* * *
650347 TGCCACGGAGTTGTGGACTAAAAAGGGTACCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAG
*
650412 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGA
* * *
650429 TACCACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
* *
650494 TTATGGACTTTAAAAGAAAA
65 TTGTGGAC-TTAAAAG--GA
* *
650514 TGCCACTGAGTCGTGGACTT
1 TGCCACGGAGTTGTGGACTT
650534 TGAAAAGGTC
Statistics
Matches: 618, Mismatches: 50, Indels: 23
0.89 0.07 0.03
Matches are distributed among these distances:
81 71 0.11
82 326 0.53
83 173 0.28
84 33 0.05
85 15 0.02
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
TGTGGACTTAAAAGGA
Found at i:658360 original size:11 final size:11
Alignment explanation
Indices: 658346--658386 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
658336 CATTTCATAT
658346 TTTTTTCTTTC
1 TTTTTTCTTTC
658357 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
658370 TTCTTTCTTTC
1 TTTTTTCTTTC
658381 TTTTTT
1 TTTTTT
658387 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:658768 original size:23 final size:22
Alignment explanation
Indices: 658742--658786 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
658732 CCACTCAATC
658742 GGAAAACCCACTTTGGTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTT
* **
658765 GGAAAGCCCCTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTT
658787 TTTTTTCGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (22 bp):
GGAAAACCCCTTTGGTTTTTTT
Found at i:661578 original size:20 final size:20
Alignment explanation
Indices: 661522--661579 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
661512 TTTATCTTTT
* * * *
661522 TTTAAGATTTGGGATTAGGG
1 TTTAAGATTAGAGTTTAGGA
* *
661542 TTTAATACTTAGTGTTTAGGA
1 TTTAAGA-TTAGAGTTTAGGA
661563 TTTAAGATTAGAGTTTA
1 TTTAAGATTAGAGTTTA
661580 TCATTTAGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (20 bp):
TTTAAGATTAGAGTTTAGGA
Found at i:661586 original size:27 final size:27
Alignment explanation
Indices: 661556--661613 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
661546 ATACTTAGTG
661556 TTTAGGATTTAAGATTAG-AGTTTATCA
1 TTTAGGATTTAAGATTAGTA-TTTATCA
* *
661583 TTTAGGGTTTAAGTTTAGTATTTATCA
1 TTTAGGATTTAAGATTAGTATTTATCA
661610 TTTA
1 TTTA
661614 AAGTTTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.50
Consensus pattern (27 bp):
TTTAGGATTTAAGATTAGTATTTATCA
Found at i:661619 original size:27 final size:27
Alignment explanation
Indices: 661563--661661 Score: 78
Period size: 27 Copynumber: 3.6 Consensus size: 27
661553 GTGTTTAGGA
* **
661563 TTTAAGATTAG-AGTTTATCATTTAGGG
1 TTTAAGTTTAGTA-TTTATCATTTAAAG
661590 TTTAAGTTTAGTATTTATCATTTAAAG
1 TTTAAGTTTAGTATTTATCATTTAAAG
* **
661617 TTTAAGGTTCA-TATTTAGGATTTAGAA-
1 TTTAA-GTTTAGTATTTATCATTTA-AAG
*
661644 TTTAAAGTTTAATATTTA
1 TTT-AAGTTTAGTATTTA
661662 GAGTTTATGA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 45 0.75
28 15 0.25
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (27 bp):
TTTAAGTTTAGTATTTATCATTTAAAG
Found at i:661668 original size:28 final size:29
Alignment explanation
Indices: 661627--661703 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 29
661617 TTTAAGGTTC
661627 ATATTTAG-GATTTAGAATTTAAAG-TTTA
1 ATATTTAGAG-TTTAGAATTTAAAGTTTTA
*
661655 ATATTTAGAGTTTATG-ATTTAAGGTTTTA
1 ATATTTAGAGTTTA-GAATTTAAAGTTTTA
* *
661684 A-ATTTAGAATTTAAAATTTA
1 ATATTTAGAGTTTAGAATTTA
661704 GATTTAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 35 0.83
29 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (29 bp):
ATATTTAGAGTTTAGAATTTAAAGTTTTA
Found at i:661704 original size:14 final size:14
Alignment explanation
Indices: 661629--661709 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
661619 TAAGGTTCAT
* *
661629 ATTTAGGATTTAGA
1 ATTTAGAATTTAAA
*
661643 ATTTA-AAGTTTAAT
1 ATTTAGAA-TTTAAA
* **
661657 ATTTAGAGTTTATG
1 ATTTAGAATTTAAA
* *
661671 ATTTA-AGGTTTTAA
1 ATTTAGA-ATTTAAA
661685 ATTTAGAATTTAAA
1 ATTTAGAATTTAAA
661699 ATTTAG-ATTTA
1 ATTTAGAATTTA
661710 GTATTATAGC
Statistics
Matches: 52, Mismatches: 11, Indels: 9
0.72 0.15 0.12
Matches are distributed among these distances:
13 7 0.13
14 43 0.83
15 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (14 bp):
ATTTAGAATTTAAA
Found at i:670236 original size:26 final size:27
Alignment explanation
Indices: 670207--670281 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 27
670197 AAAATTTCTT
*
670207 AAATAATTTTATAATTATTATTT-AAG
1 AAATAATTTTATAATTATTATTTCAAC
* * * *
670233 AAATCATTATATAAGTATGATTTCCAAC
1 AAATAATTTTATAATTATTATTT-CAAC
*
670261 AAATTATTTATATAATT-TTAT
1 AAATAATTT-TATAATTATTAT
670282 AATAATTCTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
26 19 0.51
28 12 0.32
29 6 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (27 bp):
AAATAATTTTATAATTATTATTTCAAC
Found at i:670990 original size:18 final size:19
Alignment explanation
Indices: 670955--670995 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
670945 GAAACTAACT
**
670955 AAAACTAGTTAACCATTAA
1 AAAACTAGTTAAAAATTAA
670974 AAAACTAG-TAAAAATTAA
1 AAAACTAGTTAAAAATTAA
670992 AAAA
1 AAAA
670996 AAAAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (19 bp):
AAAACTAGTTAAAAATTAA
Found at i:672260 original size:20 final size:18
Alignment explanation
Indices: 672231--672287 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
672221 TTTTATATTA
672231 ATATAAAATATTTTAAAT
1 ATATAAAATATTTTAAAT
* *
672249 ATAGTAATAATATAATAAAAT
1 ATA-TAA-AATAT-TTTAAAT
672270 ATATAAAATTATTTTAAA
1 ATATAAAA-TATTTTAAA
672288 AAATTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.10
19 9 0.29
20 11 0.35
21 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATAAAATATTTTAAAT
Found at i:672277 original size:9 final size:9
Alignment explanation
Indices: 672231--672278 Score: 51
Period size: 9 Copynumber: 5.0 Consensus size: 9
672221 TTTTATATTA
672231 ATATAAAAT
1 ATATAAAAT
* *
672240 ATTTTAAAT
1 ATATAAAAT
672249 ATAGTAATAAT
1 ATA-TAA-AAT
672260 ATAATAAAAT
1 AT-ATAAAAT
672270 ATATAAAAT
1 ATATAAAAT
672279 TATTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 16 0.50
10 7 0.22
11 8 0.25
12 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATATAAAAT
Found at i:680876 original size:2 final size:2
Alignment explanation
Indices: 680866--680905 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
680856 GGGAAAAAAA
680866 AG AG A- 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 AG AG AG A
680906 ACAGAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:683111 original size:3 final size:3
Alignment explanation
Indices: 683103--683137 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
683093 ACGAATCCAC
683103 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
683138 GTCTTCAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:683207 original size:18 final size:19
Alignment explanation
Indices: 683160--683207 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
683150 ATTTTTTTAT
683160 AATATATTATTTTAAATATA
1 AATATATT-TTTTAAATATA
* *
683180 TATAAAATTTTTTAAAT-TA
1 AAT-ATATTTTTTAAATATA
683199 AATATATTT
1 AATATATTT
683208 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 10 0.43
21 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATATTTTTTAAATATA
Found at i:684008 original size:29 final size:32
Alignment explanation
Indices: 683948--684008 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 32
683938 TGAATGGGTT
* * *
683948 TTTTAGATTCATATAAACATAATTTGCTTTTA
1 TTTTAAATTCATATAAACATAATATGCATTTA
683980 TTTTAAATT-ATA-AAACATAA-ATGCATTTA
1 TTTTAAATTCATATAAACATAATATGCATTTA
684009 ACTATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 7 0.27
30 8 0.31
31 3 0.12
32 8 0.31
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (32 bp):
TTTTAAATTCATATAAACATAATATGCATTTA
Found at i:684698 original size:22 final size:22
Alignment explanation
Indices: 684647--684698 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
684637 TATTCATATT
684647 TGTATATTTTATCTTATATTTA
1 TGTATATTTTATCTTATATTTA
*
684669 TGTAATATTTTAT-TTATTTTTA
1 TGT-ATATTTTATCTTATATTTA
684691 TGATATAT
1 TG-TATAT
684699 CAAGATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (22 bp):
TGTATATTTTATCTTATATTTA
Found at i:685056 original size:19 final size:19
Alignment explanation
Indices: 685032--685083 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
685022 CATATATGTG
685032 TTATTTTTATAAATTATAA
1 TTATTTTTATAAATTATAA
* *
685051 TTA-TTTTA-AAAATATTA
1 TTATTTTTATAAATTATAA
685068 TATATTTTTATAAATT
1 T-TATTTTTATAAATT
685084 TAAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 8 0.30
20 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTTTATAAATTATAA
Found at i:685090 original size:18 final size:18
Alignment explanation
Indices: 685033--685090 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
685023 ATATATGTGT
*
685033 TATTTTTATAAATTATAAT
1 TATTTTTATAAATT-TAAA
* *
685052 TA-TTTTAAAAATATTATA
1 TATTTTTATAAAT-TTAAA
685070 TATTTTTATAAATTTAAA
1 TATTTTTATAAATTTAAA
685088 TAT
1 TAT
685091 ATTAATAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTTATAAATTTAAA
Found at i:685098 original size:18 final size:18
Alignment explanation
Indices: 685033--685098 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
685023 ATATATGTGT
* *
685033 TATTTTTATAAATTATAAT
1 TATTTTAATAAATT-TAAA
*
685052 TATTTTAA-AAATATTATA
1 TATTTTAATAAAT-TTAAA
*
685070 TATTTTTATAAATTTAAA
1 TATTTTAATAAATTTAAA
*
685088 TATATTAATAA
1 TATTTTAATAA
685099 TTAATAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 26 0.68
19 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTAATAAATTTAAA
Found at i:685150 original size:19 final size:17
Alignment explanation
Indices: 685111--685152 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
685101 AATAAAAATA
*
685111 AATTTTAATATATTTAT
1 AATTTTTATATATTTAT
685128 -ATTTTTATATCATATTAT
1 AATTTTTATAT-AT-TTAT
685146 AATTTTT
1 AATTTTT
685153 TATGTCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 2 0.10
18 4 0.19
19 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTTATATATTTAT
Found at i:690921 original size:18 final size:18
Alignment explanation
Indices: 690888--690936 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
690878 GGAGACTGGC
* *
690888 GAAACTGTTGAGAGCAAA
1 GAAACTGCTGAAAGCAAA
**
690906 GAAACTGCTGAAAGCAGT
1 GAAACTGCTGAAAGCAAA
*
690924 GAAACTACTGAAA
1 GAAACTGCTGAAA
690937 CCAGATAGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.16
Consensus pattern (18 bp):
GAAACTGCTGAAAGCAAA
Found at i:691515 original size:90 final size:90
Alignment explanation
Indices: 691344--691512 Score: 293
Period size: 91 Copynumber: 1.9 Consensus size: 90
691334 TACAAAATCG
*
691344 AAACTTATAACTCATAAAATTTTTAACTTTTCAGTTTACAAAAATCGATATTCTCTCAAATATTT
1 AAACTTATAACTCATAAAATTTTTAACTTTTCAGTTTAAAAAAATCGATATTCTCTCAAATATTT
691409 AATGATATAACTTTAAAAAATATAA
66 AATGATATAACTTTAAAAAATATAA
* * *
691434 AAACTTATAACTCATAAAGTTTTTAACTTTTTAGTTTATAAAAAATCGATATTTTCTCAAATATT
1 AAACTTATAACTCATAAAATTTTTAACTTTTCAGTTTA-AAAAAATCGATATTCTCTCAAATATT
691499 TAATGATATAACTT
65 TAATGATATAACTT
691513 AAACAAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 36 0.49
91 38 0.51
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.41
Consensus pattern (90 bp):
AAACTTATAACTCATAAAATTTTTAACTTTTCAGTTTAAAAAAATCGATATTCTCTCAAATATTT
AATGATATAACTTTAAAAAATATAA
Found at i:692079 original size:30 final size:31
Alignment explanation
Indices: 692006--692084 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
691996 CAGGCCGGAA
* *
692006 TAAAAACCACTGTTTTTATCCGGTGGCATTG
1 TAAAAACCACTATTCTTATCCGGTGGCATTG
*
692037 TAAAAACCACTATTCTTATCCGGTGGTA-TG
1 TAAAAACCACTATTCTTATCCGGTGGCATTG
*
692067 -ACAAAACTACTATTCTTA
1 TA-AAAACCACTATTCTTA
692085 ATTGGTGGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 17 0.40
31 25 0.58
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (31 bp):
TAAAAACCACTATTCTTATCCGGTGGCATTG
Found at i:692476 original size:31 final size:30
Alignment explanation
Indices: 692426--692514 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
692416 CAGGCCGGAA
* * * *
692426 TAAAAACCATTGTTTTTATCCGGTGGCATTG
1 TAAAAACCACTATTCTTATCTGGTGGCA-TG
*
692457 TAAAAACCACTATTCTTATCTGGTGGTATG
1 TAAAAACCACTATTCTTATCTGGTGGCATG
* *
692487 -ACAAAACTACTATTCTTAACTGGTGGCA
1 TA-AAAACCACTATTCTTATCTGGTGGCA
692515 CGGTTTGAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.02
30 25 0.51
31 23 0.47
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (30 bp):
TAAAAACCACTATTCTTATCTGGTGGCATG
Found at i:692633 original size:420 final size:420
Alignment explanation
Indices: 691854--692696 Score: 1587
Period size: 420 Copynumber: 2.0 Consensus size: 420
691844 TTATTTACAA
691854 AATGAAGTTTATCACATAACCAAAACAATGTAGGATCACAAATTATTAGTTTTCATTAGTTTCCC
1 AATGAAGTTTATCACATAACCAAAACAATGTAGGATCACAAATTATTAGTTTTCATTAGTTTCCC
* *
691919 GTCCCGTAACATACTAAAACCACATTTAACCTCTATGGCATAGGTTAGAACAAAAACTACAATTC
66 GTCCCGTAACATACTAAAACCACATTTAACCTCTATAGAATAGGTTAGAACAAAAACTACAATTC
*
691984 TTATTGGTGGGACAGGCCGGAATAAAAACCACTGTTTTTATCCGGTGGCATTGTAAAAACCACTA
131 TTATTGGTGGCACAGGCCGGAATAAAAACCACTGTTTTTATCCGGTGGCATTGTAAAAACCACTA
*
692049 TTCTTATCCGGTGGTATGACAAAACTACTATTCTTAATTGGTGGCACAGTTTGAAACCGATTTTT
196 TTCTTATCCGGTGGTATGACAAAACTACTATTCTTAACTGGTGGCACAGTTTGAAACCGATTTTT
*
692114 AATCATAAAGTACATGTCGACATAGCCAATGTTTAACCCCCATCGACAGGGTTAGAGCATAGTCA
261 AATCATAAAGTACATGTCGACATAGCCAATGTTTAACCCCCATCGACAGGGTTAGAGCATAATCA
*
692179 TACTAGGAGACCAAAGAAAACAAAAGCCATTTTTAGATTACCTAGTTATACAAAAGCAGAAATCA
326 TACTAGGAGACCAAAGAAAACAAAAGCCATTTTTAGATTACCCAGTTATACAAAAGCAGAAATCA
692244 GATATTTCACAATCACATTGTTTACAAAAC
391 GATATTTCACAATCACATTGTTTACAAAAC
692274 AATGAAGTTTATCACATAACCAAAACAATGTAGGATCACAAATTATTAGTTTTCATTAGTTTCCC
1 AATGAAGTTTATCACATAACCAAAACAATGTAGGATCACAAATTATTAGTTTTCATTAGTTTCCC
692339 GTCCCGTAACATACTAAAACCACATTTAACCTCTATAGAATAGGTTAGAACAAAAACTACAATTC
66 GTCCCGTAACATACTAAAACCACATTTAACCTCTATAGAATAGGTTAGAACAAAAACTACAATTC
*
692404 TTATTGGTGGCACAGGCCGGAATAAAAACCATTGTTTTTATCCGGTGGCATTGTAAAAACCACTA
131 TTATTGGTGGCACAGGCCGGAATAAAAACCACTGTTTTTATCCGGTGGCATTGTAAAAACCACTA
* * *
692469 TTCTTATCTGGTGGTATGACAAAACTACTATTCTTAACTGGTGGCACGGTTTGAAACCGGTTTTT
196 TTCTTATCCGGTGGTATGACAAAACTACTATTCTTAACTGGTGGCACAGTTTGAAACCGATTTTT
692534 AATCATAAAGTACATGTCGACATAGCCAATGTTTAACCCCCATCGACAGGGTTAGAGCATAATCA
261 AATCATAAAGTACATGTCGACATAGCCAATGTTTAACCCCCATCGACAGGGTTAGAGCATAATCA
692599 TACTAGGAGACCAAAGAAAACAAAAGCCATTTTTAGATTACCCAGTTATACAAAAGCAGAAATCA
326 TACTAGGAGACCAAAGAAAACAAAAGCCATTTTTAGATTACCCAGTTATACAAAAGCAGAAATCA
*
692664 GATATTTCACAATCATATTGTTTACAAAAC
391 GATATTTCACAATCACATTGTTTACAAAAC
692694 AAT
1 AAT
692697 TGTATACAGA
Statistics
Matches: 412, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
420 412 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (420 bp):
AATGAAGTTTATCACATAACCAAAACAATGTAGGATCACAAATTATTAGTTTTCATTAGTTTCCC
GTCCCGTAACATACTAAAACCACATTTAACCTCTATAGAATAGGTTAGAACAAAAACTACAATTC
TTATTGGTGGCACAGGCCGGAATAAAAACCACTGTTTTTATCCGGTGGCATTGTAAAAACCACTA
TTCTTATCCGGTGGTATGACAAAACTACTATTCTTAACTGGTGGCACAGTTTGAAACCGATTTTT
AATCATAAAGTACATGTCGACATAGCCAATGTTTAACCCCCATCGACAGGGTTAGAGCATAATCA
TACTAGGAGACCAAAGAAAACAAAAGCCATTTTTAGATTACCCAGTTATACAAAAGCAGAAATCA
GATATTTCACAATCACATTGTTTACAAAAC
Found at i:697204 original size:31 final size:31
Alignment explanation
Indices: 697127--697218 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
697117 CGGTTTCAAG
*
697127 TCGTGCCACTGGTTAAGAATAGTGGTTTTTA
1 TCGTGCCACTGGATAAGAATAGTGGTTTTTA
* * * *
697158 CCATGCCACTAGATAAGAATAGTAGTTTTTA
1 TCGTGCCACTGGATAAGAATAGTGGTTTTTA
* *
697189 TCGTGCCA-TCGGATAAAAATAATGGTTTTT
1 TCGTGCCACT-GGATAAGAATAGTGGTTTTT
697219 GTTCTAACCC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (31 bp):
TCGTGCCACTGGATAAGAATAGTGGTTTTTA
Found at i:697247 original size:37 final size:38
Alignment explanation
Indices: 697190--697302 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
697180 TAGTTTTTAT
* * *
697190 CGTGCCATCGGATAAAAATAATGGTTTTTGTTCTAACC
1 CGTGCCATCAGATAAGAATAATAGTTTTTGTTCTAACC
*
697228 CGTGCCATC-GATAAGAATAATAGTTTTTGTTCTAAAC
1 CGTGCCATCAGATAAGAATAATAGTTTTTGTTCTAACC
* * * *
697265 CGTGGCACCAGATTAGAATAGTAGTTTTTGTTCTAACC
1 CGTGCCATCAGATAAGAATAATAGTTTTTGTTCTAACC
697303 TATATCACAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
37 32 0.48
38 34 0.52
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (38 bp):
CGTGCCATCAGATAAGAATAATAGTTTTTGTTCTAACC
Found at i:697292 original size:38 final size:37
Alignment explanation
Indices: 697190--697300 Score: 132
Period size: 37 Copynumber: 2.9 Consensus size: 37
697180 TAGTTTTTAT
* * * *
697190 CGTGCCATCGGATAAAAATAATGGTTTTTGTTCTAACC
1 CGTGCCA-CCGATAAGAATAATAGTTTTTGTTCTAAAC
*
697228 CGTGCCATCGATAAGAATAATAGTTTTTGTTCTAAAC
1 CGTGCCACCGATAAGAATAATAGTTTTTGTTCTAAAC
* * *
697265 CGTGGCACCAGATTAGAATAGTAGTTTTTGTTCTAA
1 CGTGCCACC-GATAAGAATAATAGTTTTTGTTCTAA
697301 CCTATATCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
37 32 0.51
38 31 0.49
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (37 bp):
CGTGCCACCGATAAGAATAATAGTTTTTGTTCTAAAC
Found at i:705103 original size:43 final size:42
Alignment explanation
Indices: 705048--705134 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 42
705038 AAAAATATAT
* * * * **
705048 ATTATAATAAATAATAAATAATTGAAATTTATATTTATATTAA
1 ATTATAAAAAATAATAAA-AAATAAAAATTATACCTATATTAA
*
705091 ATTATAAAAAATATTAAAAAATAAAAATTATACCTATATTAA
1 ATTATAAAAAATAATAAAAAATAAAAATTATACCTATATTAA
705133 AT
1 AT
705135 AATTATTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (42 bp):
ATTATAAAAAATAATAAAAAATAAAAATTATACCTATATTAA
Found at i:705114 original size:17 final size:17
Alignment explanation
Indices: 705084--705117 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
705074 ATTTATATTT
**
705084 ATATTAAATTATAAAAA
1 ATATTAAAAAATAAAAA
705101 ATATTAAAAAATAAAAA
1 ATATTAAAAAATAAAAA
705118 TTATACCTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATATTAAAAAATAAAAA
Found at i:705174 original size:14 final size:14
Alignment explanation
Indices: 705157--705186 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
705147 AATTATATTA
*
705157 AAAATAAAATTAAT
1 AAAATAAAATAAAT
705171 AAAATAAAATAAAT
1 AAAATAAAATAAAT
705185 AA
1 AA
705187 TTTTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:705531 original size:23 final size:23
Alignment explanation
Indices: 705489--705532 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
705479 GTATTTTTTT
*
705489 AAATAAAAGAAATTTTAATATAA
1 AAATAAAAGAAATTTAAATATAA
705512 AAATAAAA-AAATTATAAATAT
1 AAATAAAAGAAATT-TAAATAT
705533 TAATATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAAAAGAAATTTAAATATAA
Found at i:705571 original size:22 final size:22
Alignment explanation
Indices: 705546--705607 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 22
705536 TATTTAAATT
705546 TTAAAATAATTTTATAAATTAA
1 TTAAAATAATTTTATAAATTAA
*
705568 TTAAATTAATATATTTTGATAAATTTA
1 TT-AA--AATA-ATTTT-ATAAATTAA
705595 TTAAAA-AATTTTA
1 TTAAAATAATTTTA
705608 ATGGCCTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 1 0.03
22 7 0.21
23 3 0.09
24 2 0.06
25 4 0.12
26 7 0.21
27 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAAATAATTTTATAAATTAA
Found at i:705589 original size:27 final size:25
Alignment explanation
Indices: 705550--705599 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
705540 TAAATTTTAA
705550 AATAATTTTATAAATTAATTAAATT
1 AATAATTTTATAAATTAATTAAATT
*
705575 AATATATTTTGATAAATTTATTAAA
1 AATA-ATTTT-ATAAATTAATTAAA
705600 AAATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 5 0.23
27 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
AATAATTTTATAAATTAATTAAATT
Found at i:707502 original size:17 final size:17
Alignment explanation
Indices: 707482--707626 Score: 114
Period size: 17 Copynumber: 8.8 Consensus size: 17
707472 ATATTATATT
707482 TATATTTAATATTTTAA
1 TATATTTAATATTTTAA
*
707499 TATATTTAATAATTTATAT
1 TATATTTAAT-ATTT-TAA
707518 TATATTT-ATA--TT--
1 TATATTTAATATTTTAA
707530 TATATTTAATATTTTAA
1 TATATTTAATATTTTAA
* *
707547 TATATCTAATAATTTATAT
1 TATATTTAAT-ATTT-TAA
707566 TATATTT-ATA--TT--
1 TATATTTAATATTTTAA
707578 TATATTTAATATTTTAA
1 TATATTTAATATTTTAA
* *
707595 TATATCTAATAATTTATAT
1 TATATTTAAT-ATTT-TAA
707614 TATATTT-ATATTT
1 TATATTTAATATTT
707627 ATATTTATAT
Statistics
Matches: 105, Mismatches: 7, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
12 14 0.13
13 6 0.06
14 2 0.02
15 6 0.06
17 34 0.32
18 18 0.17
19 25 0.24
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATTTAATATTTTAA
Found at i:707517 original size:31 final size:32
Alignment explanation
Indices: 707479--707638 Score: 156
Period size: 31 Copynumber: 5.0 Consensus size: 32
707469 TACATATTAT
707479 ATTTATATTTAATATTT-TAATATATTTAATA
1 ATTTATATTTAATATTTATAATATATTTAATA
*
707510 ATTTATA-TT-ATATTTATATTTATATTTAATA
1 ATTTATATTTAATATTTATA-ATATATTTAATA
* *
707541 TTTTAATATATCTAATAATTTATATTATATTT-AT-
1 ATTT-ATAT-T-TAAT-ATTTATAATATATTTAATA
*
707575 ATTTATATTTAATATTT-TAATATATCTAATA
1 ATTTATATTTAATATTTATAATATATTTAATA
*
707606 ATTTATA-TT-ATATTTATATTTATATTTATATA
1 ATTTATATTTAATATTTATA-ATATATTTA-ATA
707638 A
1 A
707639 CTAATAAAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
29 20 0.18
30 14 0.13
31 39 0.36
32 8 0.07
33 4 0.04
34 4 0.04
35 3 0.03
36 10 0.09
37 7 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTATATTTAATATTTATAATATATTTAATA
Found at i:707627 original size:17 final size:17
Alignment explanation
Indices: 707472--707636 Score: 121
Period size: 18 Copynumber: 9.5 Consensus size: 17
707462 TTTAATATAC
707472 ATATTATATTTATATTT
1 ATATTATATTTATATTT
* *
707489 AATATTTTA-ATATATTT
1 -ATATTATATTTATATTT
707506 AATAATT-TATATTATATTT
1 -AT-ATTATAT-TTATATTT
707525 ATATTTATATTTAATATTT
1 ATA-TTATATTT-ATATTT
* *
707544 -TAATATATCTAATAATTT
1 ATATTATAT-TTAT-ATTT
707562 ATATTATATTTATATTT
1 ATATTATATTTATATTT
707579 ATATT-TA---ATATTT
1 ATATTATATTTATATTT
* *
707592 -TAATATATCTAATAATTT
1 ATATTATAT-TTAT-ATTT
707610 ATATTATATTTATATTT
1 ATATTATATTTATATTT
707627 ATATTTATAT
1 ATA-TTATAT
707637 AACTAATAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.03
13 8 0.07
16 2 0.02
17 38 0.32
18 39 0.32
19 30 0.25
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTATATTTATATTT
Found at i:707644 original size:48 final size:48
Alignment explanation
Indices: 707475--707633 Score: 309
Period size: 48 Copynumber: 3.3 Consensus size: 48
707465 AATATACATA
*
707475 TTATATTTATATTTAATATTTTAATATATTTAATAATTTATATTATAT
1 TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
707523 TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
1 TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
707571 TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
1 TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
707619 TTATATTTATATTTA
1 TTATATTTATATTTA
707634 TATAACTAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 110 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (48 bp):
TTATATTTATATTTAATATTTTAATATATCTAATAATTTATATTATAT
Found at i:707894 original size:2 final size:2
Alignment explanation
Indices: 707884--707923 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
707874 ATTAAAAGAC
*
707884 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
707924 TGAAGGTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:708190 original size:12 final size:11
Alignment explanation
Indices: 708171--708203 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
708161 TTTAGTTTGA
708171 TTTTTTTATAT
1 TTTTTTTATAT
708182 TTATTTTTA-AT
1 TT-TTTTTATAT
708193 TTTTTTTATAT
1 TTTTTTTATAT
708204 CTTTATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.30
11 8 0.40
12 6 0.30
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:708297 original size:18 final size:18
Alignment explanation
Indices: 708245--708298 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
708235 TATAATTGTA
*
708245 TTTAAGATA-TTATATA-
1 TTTAATATATTTATATAT
*
708261 TTTATATAAATTT-TAATAT
1 TTTA-ATATATTTAT-ATAT
708280 TTTAATATATTTATATAT
1 TTTAATATATTTATATAT
708298 T
1 T
708299 CGTATCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 4 0.13
17 4 0.13
18 17 0.57
19 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAATATATTTATATAT
Found at i:710245 original size:11 final size:14
Alignment explanation
Indices: 710210--710240 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
710200 TAAATTTATT
710210 TATTATTTAAATAA
1 TATTATTTAAATAA
710224 TATTATTTAAA-AA
1 TATTATTTAAATAA
710237 TATT
1 TATT
710241 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATTTAAATAA
Found at i:710735 original size:2 final size:2
Alignment explanation
Indices: 710728--710777 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
710718 TAGGTCTATT
* *
710728 TA TA TA TA T- TA AA 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
710769 TA TA TA TA T
1 TA TA TA TA T
710778 GGAAGGTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:711068 original size:11 final size:11
Alignment explanation
Indices: 711045--711091 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
711035 ATTTTTTAAA
*
711045 ATATTTTTA-T
1 ATATTTATATT
*
711055 ATATTTGTATT
1 ATATTTATATT
711066 ATATTTATATT
1 ATATTTATATT
*
711077 AATTTTTATATT
1 -ATATTTATATT
711089 ATA
1 ATA
711092 ATTACATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
10 8 0.26
11 13 0.42
12 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:711159 original size:10 final size:9
Alignment explanation
Indices: 711107--711225 Score: 59
Period size: 9 Copynumber: 13.0 Consensus size: 9
711097 ATTCAAAATA
711107 TTATATATT
1 TTATATATT
*
711116 TATATAAATT
1 T-TATATATT
**
711126 TT-TATACG
1 TTATATATT
711134 TTA-ATATT
1 TTATATATT
711142 TTATATATT
1 TTATATATT
711151 TTGATATA-T
1 TT-ATATATT
*
711160 TCATATATT
1 TTATATATT
* *
711169 TGTATCGT-CT
1 T-TAT-ATATT
711179 TTATATTATT
1 TTATA-TATT
*
711189 TTTTATATT
1 TTATATATT
*
711198 ATATTATATT
1 TTA-TATATT
711208 TTA-ATTATT
1 TTATA-TATT
*
711217 TTTTATATT
1 TTATATATT
711226 ATTTTTATAA
Statistics
Matches: 81, Mismatches: 17, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
8 17 0.21
9 32 0.40
10 31 0.38
11 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TTATATATT
Found at i:711195 original size:12 final size:12
Alignment explanation
Indices: 711178--711231 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
711168 TTGTATCGTC
711178 TTTATATTATTT
1 TTTATATTATTT
711190 TTTATATTATATT
1 TTTATATTAT-TT
*
711203 ATATTTTAATTATTT
1 -T-TTAT-ATTATTT
711218 TTTATATTATTT
1 TTTATATTATTT
711230 TT
1 TT
711232 ATAATATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 19 0.53
13 5 0.14
14 2 0.06
15 5 0.14
16 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:711199 original size:17 final size:16
Alignment explanation
Indices: 711179--711253 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
711169 TGTATCGTCT
*
711179 TTATATTATTTTTTATA
1 TTATATTATATTTTA-A
711196 TTATATTATATTTTAA
1 TTATATTATATTTTAA
* * *
711212 TTATTTTTTATATT-A
1 TTATATTATATTTTAA
* *
711227 TT-T-TTATAATATAA
1 TTATATTATATTTTAA
*
711241 TTATGTTATATTT
1 TTATATTATATTT
711254 AAAATTATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
13 5 0.11
14 4 0.09
15 4 0.09
16 18 0.40
17 14 0.31
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:711938 original size:27 final size:27
Alignment explanation
Indices: 711877--711938 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
711867 TTAAAAAATC
711877 TTATTT-AATAATTTAAAATTTTTATA
1 TTATTTAAATAATTTAAAATTTTTATA
**
711903 TTAGATAAATAA-TTAAAATTTTT-TAA
1 TTATTTAAATAATTTAAAATTTTTAT-A
711929 TTTATTTAAA
1 -TTATTTAAA
711939 ATTTAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 16 0.55
27 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTATTTAAATAATTTAAAATTTTTATA
Found at i:712246 original size:13 final size:13
Alignment explanation
Indices: 712228--712252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
712218 TGCCGACAAG
712228 ATTGCTTAATCAA
1 ATTGCTTAATCAA
712241 ATTGCTTAATCA
1 ATTGCTTAATCA
712253 TACAAGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTGCTTAATCAA
Found at i:712583 original size:25 final size:25
Alignment explanation
Indices: 712553--712600 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
712543 TAAATTTAAT
* *
712553 AATTTTATACATAATATAAAATAAA
1 AATTTTAAACAAAATATAAAATAAA
*
712578 AATTTTAAATAAAATATAAAATA
1 AATTTTAAACAAAATATAAAATA
712601 TTAAAATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTTTAAACAAAATATAAAATAAA
Found at i:712591 original size:18 final size:19
Alignment explanation
Indices: 712568--712605 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
712558 TATACATAAT
*
712568 ATAAAATA-AAAATTTTAA
1 ATAAAATATAAAATATTAA
712586 ATAAAATATAAAATATTAA
1 ATAAAATATAAAATATTAA
712605 A
1 A
712606 ATATGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAATATAAAATATTAA
Found at i:712607 original size:20 final size:18
Alignment explanation
Indices: 712568--712608 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
712558 TATACATAAT
*
712568 ATAAAATAAAAATTTTAA
1 ATAAAATAAAAATTTAAA
712586 ATAAAATATAAAATATTAAA
1 ATAAAATA-AAAAT-TTAAA
712606 ATA
1 ATA
712609 TGTAACACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAATAAAAATTTAAA
Found at i:712923 original size:29 final size:26
Alignment explanation
Indices: 712890--712965 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 26
712880 ATATATAATC
712890 AATAAATTAAATAATATTATTTTAATTAA
1 AATAAATTAAATAATATT-TTTTAA--AA
*
712919 AATAAAATTATAT-ATA-TTTTTAAAA
1 AAT-AAATTAAATAATATTTTTTAAAA
* *
712944 AATTAATAAAATAATATTTTTT
1 AATAAATTAAATAATATTTTTT
712966 TGTTTATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
24 6 0.15
25 8 0.20
26 5 0.12
27 6 0.15
28 1 0.03
29 6 0.15
30 8 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATAAATTAAATAATATTTTTTAAAA
Found at i:712992 original size:19 final size:19
Alignment explanation
Indices: 712968--713007 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
712958 TATTTTTTTG
712968 TTTATAAATTA-TATATAAA
1 TTTATAAATTATTA-ATAAA
*
712987 TTTATATATTATTAATAAA
1 TTTATAAATTATTAATAAA
713006 TT
1 TT
713008 AAATATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATAAATTATTAATAAA
Found at i:714344 original size:2 final size:2
Alignment explanation
Indices: 714337--714387 Score: 75
Period size: 2 Copynumber: 25.0 Consensus size: 2
714327 TCATATAAAC
* *
714337 AT AT AT AT AT AT AT AT AT AT AT AT GT TT CAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
714380 AT AT AT AT
1 AT AT AT AT
714388 GTTTTCATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 44 0.98
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:714369 original size:27 final size:27
Alignment explanation
Indices: 714339--714391 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
714329 ATATAAACAT
714339 ATATATATATATATATATATATGTTTC
1 ATATATATATATATATATATATGTTTC
714366 ATATATATATATATATATATATGTTT
1 ATATATATATATATATATATATGTTT
714392 TCATGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
ATATATATATATATATATATATGTTTC
Found at i:715252 original size:18 final size:18
Alignment explanation
Indices: 715231--715269 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
715221 TTCTTTAAAA
*
715231 TTACATTTTTAAATATTT
1 TTACATCTTTAAATATTT
*
715249 TTACATCTTTGAATATTT
1 TTACATCTTTAAATATTT
715267 TTA
1 TTA
715270 AGATGATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTACATCTTTAAATATTT
Found at i:717485 original size:15 final size:14
Alignment explanation
Indices: 717459--717510 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
717449 TTTTTAAAAG
717459 TAAAGTAAATTTAAT
1 TAAA-TAAATTTAAT
717474 TAAATAATATTTATAAT
1 TAAATAA-A-TT-TAAT
717491 TAAATTAAATTTAAT
1 TAAA-TAAATTTAAT
717506 TAAAT
1 TAAAT
717511 TTTATCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.12
15 13 0.39
16 4 0.12
17 9 0.27
18 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
TAAATAAATTTAAT
Found at i:717514 original size:11 final size:10
Alignment explanation
Indices: 717464--717512 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
717454 AAAAGTAAAG
717464 TAAATTTAAT
1 TAAATTTAAT
* *
717474 TAAATAATATT
1 TAAAT-TTAAT
*
717485 TATAATTAAAT
1 TA-AATTTAAT
717496 TAAATTTAAT
1 TAAATTTAAT
717506 TAAATTT
1 TAAATTT
717513 TATCAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 19 0.61
11 9 0.29
12 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:719382 original size:14 final size:16
Alignment explanation
Indices: 719358--719389 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
719348 TTGAAAAAAA
719358 TATATATTTAAT-TTT
1 TATATATTTAATATTT
719373 TATA-ATTTAATATTT
1 TATATATTTAATATTT
719388 TA
1 TA
719390 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATATATTTAATATTT
Found at i:719415 original size:36 final size:39
Alignment explanation
Indices: 719346--719423 Score: 119
Period size: 36 Copynumber: 2.1 Consensus size: 39
719336 TTACTTATTT
719346 TTTTGAAAAAAATATATATTTAATTTTTATAATTTAATA
1 TTTTGAAAAAAATATATATTTAATTTTTATAATTTAATA
719385 TTTT-AAAAAAAT-T-TA-TTAATTTTTATTAATTTAATA
1 TTTTGAAAAAAATATATATTTAATTTTTA-TAATTTAATA
719421 TTT
1 TTT
719424 ATAGTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
35 10 0.26
36 15 0.39
37 1 0.03
38 8 0.21
39 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (39 bp):
TTTTGAAAAAAATATATATTTAATTTTTATAATTTAATA
Found at i:722642 original size:2 final size:2
Alignment explanation
Indices: 722629--722658 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
722619 ATTAAAAGAC
*
722629 AT AT AC 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
722659 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:722903 original size:19 final size:19
Alignment explanation
Indices: 722842--722903 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
722832 TGCATGGATA
722842 TATTATTTT-TTAAAAAAATT
1 TATTATTTTATT--AAAAATT
* *
722862 TAAATATTTTATTAATTAA-T
1 T-ATTATTTTATTAA-AAATT
722882 TATTATTTTATTAAAAATT
1 TATTATTTTATTAAAAATT
722901 TAT
1 TAT
722904 AACTTCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 2 0.06
19 16 0.47
20 5 0.15
21 9 0.26
22 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATTTTATTAAAAATT
Found at i:723772 original size:21 final size:22
Alignment explanation
Indices: 723748--723794 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
723738 GAGTTAAAAT
*
723748 TAATTTTTAATAATATA-AACA
1 TAATTTTTAACAATATATAACA
723769 TAATTTTTAACAATATATTAACA
1 TAATTTTTAACAATATA-TAACA
723792 TAA
1 TAA
723795 CATTCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
23 7 0.30
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATTTTTAACAATATATAACA
Found at i:724152 original size:17 final size:18
Alignment explanation
Indices: 724127--724164 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
724117 AAAATAATAT
724127 AATAATTAATTT-ATAAA
1 AATAATTAATTTAATAAA
*
724144 AATATTTAATTTAATAAA
1 AATAATTAATTTAATAAA
724162 AAT
1 AAT
724165 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATTAATTTAATAAA
Found at i:724158 original size:29 final size:28
Alignment explanation
Indices: 724121--724175 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
724111 AAATTAAAAA
* *
724121 TAATATAATAATTAATTTATAAAAATATT
1 TAATATAATAA-AAATTTAAAAAAATATT
*
724150 TAATTTAATAAAAATTTAAAAAAATA
1 TAATATAATAAAAATTTAAAAAAATA
724176 AAAAAATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATATAATAAAAATTTAAAAAAATATT
Found at i:724735 original size:15 final size:16
Alignment explanation
Indices: 724715--724744 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
724705 TCAATTCAAT
724715 TAAAAAT-AAATAAAC
1 TAAAAATAAAATAAAC
724730 TAAAAATAAAATAAA
1 TAAAAATAAAATAAA
724745 AATATAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAAAATAAAATAAAC
Found at i:725269 original size:18 final size:18
Alignment explanation
Indices: 725231--725284 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
725221 TATATAACAA
* *
725231 AAAATAAAAAATA-AAAT
1 AAAATAAAAAATATTAAC
725248 AAAATAAAAAATATTAAC
1 AAAATAAAAAATATTAAC
*
725266 AAAAT-TAAAATATGTAAC
1 AAAATAAAAAATAT-TAAC
725284 A
1 A
725285 CTTTGATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAATAAAAAATATTAAC
Found at i:726834 original size:19 final size:20
Alignment explanation
Indices: 726810--726848 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
726800 TACAATCAGA
*
726810 TAATT-AAATAATATTATTT
1 TAATTAAAATAAAATTATTT
726829 TAATTAAAATAAAATTATTT
1 TAATTAAAATAAAATTATTT
726849 ATATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAAAATAAAATTATTT
Found at i:727138 original size:18 final size:18
Alignment explanation
Indices: 727104--727139 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
727094 TTTAGCGGGG
*
727104 TTTATATTAGATTTATTA
1 TTTATATTAGATGTATTA
*
727122 TTTATATTATATGTATTA
1 TTTATATTAGATGTATTA
727140 GTAATGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTATATTAGATGTATTA
Found at i:727242 original size:41 final size:43
Alignment explanation
Indices: 727181--727264 Score: 113
Period size: 41 Copynumber: 2.0 Consensus size: 43
727171 TTAATTAAAT
727181 AATAATATTTTAATTAAAATAAAATTA-ATTATATTTA-TATTTA
1 AATAATATTTTAATTAAAATAAAATTATA-TA-ATTTATTATTTA
*
727224 AATAAT-TTTTAA-TAAAATAATATTATATAATTTATTATTTA
1 AATAATATTTTAATTAAAATAAAATTATATAATTTATTATTTA
727265 TATATAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
40 5 0.13
41 20 0.53
42 7 0.18
43 6 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (43 bp):
AATAATATTTTAATTAAAATAAAATTATATAATTTATTATTTA
Found at i:728179 original size:28 final size:27
Alignment explanation
Indices: 728121--728185 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
728111 CTGATGACTT
** * *
728121 TTTATTTTTAAAATTTTTATAAATTTT
1 TTTATTTTTAAAATAATTATAAATATC
*
728148 TTTATTTATTAAAATAATTATTAATATC
1 TTTATTT-TTAAAATAATTATAAATATC
728176 TTTAATTTTT
1 TTT-ATTTTT
728186 TTAAATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 7 0.23
28 20 0.65
29 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTATTTTTAAAATAATTATAAATATC
Found at i:728261 original size:2 final size:2
Alignment explanation
Indices: 728254--728281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
728244 TCAATATTTC
728254 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
728282 TTGTGTTTTC
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:733536 original size:22 final size:21
Alignment explanation
Indices: 733496--733537 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
733486 ATTTTATTTA
*
733496 TAAATTTTGTAATATAATAAT
1 TAAATTTTGTAATAAAATAAT
*
733517 TAAATTTTATTAATAAAATAA
1 TAAATTTT-GTAATAAAATAA
733538 ATATATGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TAAATTTTGTAATAAAATAAT
Found at i:735243 original size:18 final size:19
Alignment explanation
Indices: 735202--735245 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
735192 AAAATGTGAT
* *
735202 ATAAAATAAGATAGATATA
1 ATAAAATAACATAGATACA
735221 A-AAAATAACAT-GATACA
1 ATAAAATAACATAGATACA
735238 ATAAAATA
1 ATAAAATA
735246 TGAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 15 0.68
19 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (19 bp):
ATAAAATAACATAGATACA
Found at i:735293 original size:20 final size:19
Alignment explanation
Indices: 735270--735332 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
735260 TATCAAAATC
735270 TATATAAATATATTTATTAA
1 TATATAAATAT-TTTATTAA
735290 TATATTAAA-ATTTATATTAA
1 TATA-TAAATATTT-TATTAA
735310 TATA-AAATATTTTA--AA
1 TATATAAATATTTTATTAA
735326 TATATAA
1 TATATAA
735333 TAATAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.15
17 2 0.05
18 5 0.13
19 6 0.15
20 16 0.41
21 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATAAATATTTTATTAA
Found at i:738213 original size:20 final size:20
Alignment explanation
Indices: 738182--738238 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
738172 TCTTCGAATC
*
738182 TTTTAAAGTATATATTTG-TAT
1 TTTTAAA-TATATATATGAT-T
738203 TTTTAAATATA-AGTATGATT
1 TTTTAAATATATA-TATGATT
738223 TTTTAAATATATATAT
1 TTTTAAATATATATAT
738239 ATATAAGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 22 0.69
21 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTTAAATATATATATGATT
Found at i:741727 original size:13 final size:15
Alignment explanation
Indices: 741702--741733 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
741692 TTAAATTTTC
741702 ATTTTTAACAAAA-A
1 ATTTTTAACAAAATA
741716 ATTTTTAA-AAAATA
1 ATTTTTAACAAAATA
741730 ATTT
1 ATTT
741734 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTTAACAAAATA
Found at i:744588 original size:2 final size:2
Alignment explanation
Indices: 744581--744615 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
744571 CTTCTACCCT
*
744581 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
744616 TGCCTAGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:745440 original size:15 final size:15
Alignment explanation
Indices: 745420--745452 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
745410 AATTTTAAAA
*
745420 ATTAAATATATTTAT
1 ATTAAATATATATAT
745435 ATTAAATATATATAT
1 ATTAAATATATATAT
745450 ATT
1 ATT
745453 CATATTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAAATATATATAT
Found at i:745906 original size:85 final size:85
Alignment explanation
Indices: 745804--746079 Score: 534
Period size: 85 Copynumber: 3.2 Consensus size: 85
745794 TTTGCAGACA
745804 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
745869 AATTGAACCTTCAAATAAATAT
66 AATTGAACCTTCAAAT-AA-AT
745891 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
745956 AATTGAACCTTCAAATAAAT
66 AATTGAACCTTCAAATAAAT
745976 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
746041 AATTGAACCTTCAAATAAAT
66 AATTGAACCTTCAAATAAAT
746061 ATATATATATATATATATA
1 ATATATATATATATATATA
746080 TTCATTCAAC
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
85 106 0.56
86 2 0.01
87 81 0.43
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (85 bp):
ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
AATTGAACCTTCAAATAAAT
Found at i:745914 original size:87 final size:87
Alignment explanation
Indices: 745804--746080 Score: 540
Period size: 87 Copynumber: 3.2 Consensus size: 87
745794 TTTGCAGACA
745804 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
745869 AATTGAACCTTCAAATAAATAT
66 AATTGAACCTTCAAATAAATAT
745891 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
745956 AATTGAACCTTCAAAT-AA-AT
66 AATTGAACCTTCAAATAAATAT
745976 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
1 ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
746041 AATTGAACCTTCAAATAAATAT
66 AATTGAACCTTCAAATAAATAT
746063 ATATATATATATATATAT
1 ATATATATATATATATAT
746081 TCATTCAACT
Statistics
Matches: 188, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
85 83 0.44
86 4 0.02
87 101 0.54
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (87 bp):
ATATATATATATATATATAAATTTAAAATTAAATAATCATCCTATAATTCTCATTTATTTCAATC
AATTGAACCTTCAAATAAATAT
Found at i:746186 original size:31 final size:31
Alignment explanation
Indices: 746145--746218 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 31
746135 TTGTCCAATC
746145 AAGATTCAATTGAATGAAAATAAAATGTTTGA
1 AAGATTCAATTGAATGAAAAT-AAATGTTTGA
* *
746177 AA-ATTCAATTAAATGAAAATAAATTTTTGA
1 AAGATTCAATTGAATGAAAATAAATGTTTGA
746207 AAGA-TCAATTGA
1 AAGATTCAATTGA
746219 TTGCAATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 18 0.47
31 18 0.47
32 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.32
Consensus pattern (31 bp):
AAGATTCAATTGAATGAAAATAAATGTTTGA
Found at i:746208 original size:30 final size:32
Alignment explanation
Indices: 746145--746216 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 32
746135 TTGTCCAATC
*
746145 AAGATTCAATTGAATGAAAATAAAATGTTTGA
1 AAGATTCAATTAAATGAAAATAAAATGTTTGA
*
746177 AA-ATTCAATTAAATGAAAAT-AAATTTTTGA
1 AAGATTCAATTAAATGAAAATAAAATGTTTGA
746207 AAGA-TCAATT
1 AAGATTCAATT
746217 GATTGCAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 17 0.46
31 18 0.49
32 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (32 bp):
AAGATTCAATTAAATGAAAATAAAATGTTTGA
Found at i:747331 original size:1 final size:1
Alignment explanation
Indices: 747327--747352 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
747317 GGAAAAAGGA
747327 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
747353 AAGGTAAAAT
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:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:753463 original size:24 final size:24
Alignment explanation
Indices: 753431--753487 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
753421 CTCCGGTGGT
** * *
753431 TGGCTGCTGCTGAGGCTGAGATTG
1 TGGCTGCTGCAAAGACTGAGACTG
753455 TGGCTGCTGCAAAGACTGAGACTG
1 TGGCTGCTGCAAAGACTGAGACTG
753479 TGGCTGCTG
1 TGGCTGCTG
753488 TAGTGGCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.19, G:0.39, T:0.26
Consensus pattern (24 bp):
TGGCTGCTGCAAAGACTGAGACTG
Found at i:753497 original size:24 final size:24
Alignment explanation
Indices: 753431--753499 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
753421 CTCCGGTGGT
*
753431 TGGCTGCTGCT-GAGGCTGAGATTG
1 TGGCTGCTG-TAGAGGCTGAGACTG
* * *
753455 TGGCTGCTGCAAAGACTGAGACTG
1 TGGCTGCTGTAGAGGCTGAGACTG
*
753479 TGGCTGCTGTAGTGGCTGAGA
1 TGGCTGCTGTAGAGGCTGAGA
753500 AGCAGGCCTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.39, T:0.26
Consensus pattern (24 bp):
TGGCTGCTGTAGAGGCTGAGACTG
Found at i:753893 original size:15 final size:15
Alignment explanation
Indices: 753873--753911 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
753863 CCCTGATGTG
753873 AAGCCACCAGATTTT
1 AAGCCACCAGATTTT
753888 AAGCCACCAGATTTT
1 AAGCCACCAGATTTT
*
753903 ACGCCACCA
1 AAGCCACCA
753912 TTCATAGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.21
Consensus pattern (15 bp):
AAGCCACCAGATTTT
Found at i:758134 original size:2 final size:2
Alignment explanation
Indices: 758129--758154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
758119 CCCCCAAAAA
758129 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
758155 GCCGAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:768298 original size:2 final size:2
Alignment explanation
Indices: 768291--768320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
768281 AAGAGTAAAT
768291 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
768321 TTTTAGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:768918 original size:20 final size:18
Alignment explanation
Indices: 768879--768919 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
768869 GTGGTATAAA
768879 TTTAATTAAATTTTTTAT
1 TTTAATTAAATTTTTTAT
*
768897 TTTAATATATATTTTATTAT
1 TTTAAT-TAAATTTT-TTAT
768917 TTT
1 TTT
768920 TGACTTGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAATTAAATTTTTTAT
Found at i:770930 original size:18 final size:18
Alignment explanation
Indices: 770909--770964 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
770899 ATTAAATGAA
*
770909 TAAATAATGTAAAATTTT
1 TAAATAATATAAAATTTT
* *
770927 TAAATAAAATAAAAATTTG
1 TAAATAATAT-AAAATTTT
* *
770946 TATATAATTTAAAATTTT
1 TAAATAATATAAAATTTT
770964 T
1 T
770965 CTAATAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (18 bp):
TAAATAATATAAAATTTT
Found at i:771890 original size:20 final size:19
Alignment explanation
Indices: 771865--771916 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
771855 TTTGTGGGCA
771865 TTTTAAAAAATATTTAGTTT
1 TTTTAAAAAATATTTA-TTT
**
771885 TTTT-AAAAATAAATATTT
1 TTTTAAAAAATATTTATTT
771903 TTTTAAAAAA-ATTT
1 TTTTAAAAAATATTT
771917 GAATATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 9 0.33
19 14 0.52
20 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTAAAAAATATTTATTT
Found at i:771892 original size:19 final size:18
Alignment explanation
Indices: 771865--771916 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
771855 TTTGTGGGCA
*
771865 TTTTAAAAAATATTTAGTT
1 TTTTTAAAAATATTTA-TT
**
771884 TTTTTAAAAATAAATATT
1 TTTTTAAAAATATTTATT
*
771902 TTTTTAAAAAAATTT
1 TTTTTAAAAATATTT
771917 GAATATATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTAAAAATATTTATT
Found at i:780759 original size:2 final size:2
Alignment explanation
Indices: 780752--780776 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
780742 CGATACTCCA
780752 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
780777 CACACACACA
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:781716 original size:5 final size:5
Alignment explanation
Indices: 781692--781729 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
781682 AAGCTGATAC
781692 ATATG TATAT- ATAT- ATATG ATATG ATATG ATATG ATAT
1 ATATG -ATATG ATATG ATATG ATATG ATATG ATATG ATAT
781730 TTGCATAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.26
5 19 0.61
6 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (5 bp):
ATATG
Found at i:784302 original size:21 final size:21
Alignment explanation
Indices: 784276--784339 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
784266 AGTGACAATG
784276 AAATTAAATATTATAATAATA
1 AAATTAAATATTATAATAATA
*
784297 AAATTAAATATTATAATGATA
1 AAATTAAATATTATAATAATA
784318 AAATTAAA-A-T-TAATAATA
1 AAATTAAATATTATAATAATA
784336 AAAT
1 AAAT
784340 ATATTTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 1 0.02
21 28 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATTAAATATTATAATAATA
Found at i:784519 original size:16 final size:16
Alignment explanation
Indices: 784470--784528 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
784460 GAAATTAATG
*
784470 AATAAAAATTTTATT-
1 AATAATAATTTTATTA
*
784485 AA-AATTATTTGTATGTTA
1 AATAATAATTT-TA--TTA
784503 AATAATAATTTTATTA
1 AATAATAATTTTATTA
*
784519 ATTAATAATT
1 AATAATAATT
784529 AAAAAATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 6 0.17
15 4 0.11
16 12 0.34
17 2 0.06
18 4 0.11
19 7 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
AATAATAATTTTATTA
Found at i:784671 original size:33 final size:30
Alignment explanation
Indices: 784600--784703 Score: 78
Period size: 28 Copynumber: 3.5 Consensus size: 30
784590 ATATATTTTT
* *
784600 AATAAATTCATATTAATTTTA-TA-ATATTA
1 AATAAATTTATATT-ATTTTATTATATAATA
**
784629 AA-ATTTTTATATTATTAGATTATTATATAA-A
1 AATAAATTTATATTATT---TTATTATATAATA
784660 AATAAAATTTATA-TA-TTTATTATATAATA
1 AAT-AAATTTATATTATTTTATTATATAATA
784689 AATAAATTT-TATTAT
1 AATAAATTTATATTAT
784704 ATATTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
27 5 0.08
28 27 0.46
29 6 0.10
30 3 0.05
31 6 0.10
32 5 0.08
33 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
AATAAATTTATATTATTTTATTATATAATA
Found at i:784679 original size:28 final size:30
Alignment explanation
Indices: 784640--784705 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 30
784630 AATTTTTATA
*
784640 TTATTAGA-TTATTATATAA-AAATAAAAT
1 TTATTATATTTATTATATAATAAATAAAAT
*
784668 TTA-TATATTTATTATATAATAAATAAATT
1 TTATTATATTTATTATATAATAAATAAAAT
784697 TTATTATAT
1 TTATTATAT
784706 ATTTATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 3 0.09
28 14 0.42
29 11 0.33
30 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TTATTATATTTATTATATAATAAATAAAAT
Found at i:784694 original size:35 final size:35
Alignment explanation
Indices: 784627--784694 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
784617 TTTATAATAT
* * *
784627 TAAAATTTTTATATTATTAGATTATTATATAAAAA
1 TAAAATTTATATATTATTAGATTAATAAATAAAAA
*
784662 TAAAATTTATATATTTATTATA-TAATAAATAAA
1 TAAAATTTATATA-TTATTAGATTAATAAATAAA
784695 TTTTATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.75
36 7 0.25
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
TAAAATTTATATATTATTAGATTAATAAATAAAAA
Found at i:785624 original size:2 final size:2
Alignment explanation
Indices: 785617--785649 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
785607 ACTCAAAACC
785617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
785650 GATCATATTA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:787796 original size:4 final size:4
Alignment explanation
Indices: 787787--787826 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
787777 TGCCTTCAGC
787787 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
787827 GTATGTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:790574 original size:14 final size:15
Alignment explanation
Indices: 790555--790593 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
790545 TGAATTATAA
790555 AATATATAAATA-TT
1 AATATATAAATATTT
*
790569 AATATAAAAATATTT
1 AATATATAAATATTT
790584 AATAATATAA
1 AAT-ATATAA
790594 TAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATAAATATTT
Found at i:790920 original size:20 final size:20
Alignment explanation
Indices: 790876--790912 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
790866 TGTATTCTTA
*
790876 TTATATTTATTATATTATCT
1 TTATATTTATTATAATATCT
790896 TTATATTTATTA-AATAT
1 TTATATTTATTATAATAT
790913 GTTATATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATATTTATTATAATATCT
Found at i:792202 original size:13 final size:13
Alignment explanation
Indices: 792170--792195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
792160 TATTTTTTAA
792170 AAAATATTTATAT
1 AAAATATTTATAT
792183 AAAATATTTATAT
1 AAAATATTTATAT
792196 CTAATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATATTTATAT
Found at i:794212 original size:11 final size:11
Alignment explanation
Indices: 794196--794237 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
794186 TCGAATTAAA
*
794196 TTAATTATTAT
1 TTAATTTTTAT
*
794207 TTAATTTTTTT
1 TTAATTTTTAT
794218 TTAATTTTTTAT
1 TTAA-TTTTTAT
794230 TTAATTTT
1 TTAATTTT
794238 GAATTCAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTAATTTTTAT
Found at i:794232 original size:12 final size:12
Alignment explanation
Indices: 794203--794237 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
794193 AAATTAATTA
794203 TTATTTAATTTT
1 TTATTTAATTTT
794215 TT-TTTAATTTT
1 TTATTTAATTTT
794226 TTATTTAATTTT
1 TTATTTAATTTT
794238 GAATTCAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTAATTTT
Found at i:794858 original size:3 final size:3
Alignment explanation
Indices: 794852--794900 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
794842 TTAAGTCACG
794852 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
794900 T
1 T
794901 TACTCGCCGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:795127 original size:25 final size:22
Alignment explanation
Indices: 795072--795127 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
795062 ATATTTTTTA
*
795072 TTTAAAT-TTAATTATAAAATT
1 TTTAAATATTAATTAAAAAATT
*
795093 TATAAATATTAATTAAAAGTAATTT
1 TTTAAATATTAATTAAAA--AA-TT
795118 TTTAAATATT
1 TTTAAATATT
795128 TTATCATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
24 2 0.07
25 11 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAATATTAATTAAAAAATT
Found at i:795468 original size:20 final size:20
Alignment explanation
Indices: 795443--795484 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
795433 TTTATTATAC
795443 TATTAAACTAAATA-TATATT
1 TATTAAA-TAAATATTATATT
*
795463 TATTAAATAATTATTATATT
1 TATTAAATAAATATTATATT
795483 TA
1 TA
795485 ATATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAATAAATATTATATT
Found at i:795786 original size:3 final size:3
Alignment explanation
Indices: 795780--795814 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
795770 ATGGTAACTT
*
795780 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
795815 TAATGTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:796167 original size:21 final size:21
Alignment explanation
Indices: 796143--796184 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
796133 ATATTTTATT
796143 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
*
796164 TAAATATTAATATATAATATA
1 TAAATATTAATATAAAATATA
796185 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:796431 original size:22 final size:22
Alignment explanation
Indices: 796379--796427 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
796369 CTGTTTGGAC
*
796379 TTAATTT-T-TTTTTTGTGATT
1 TTAATTTATATTTTTTGTGATA
796399 TTAATTTATATTTTTTG-GATA
1 TTAATTTATATTTTTTGTGATA
796420 TTAATTTA
1 TTAATTTA
796428 ATATATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 12 0.46
22 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (22 bp):
TTAATTTATATTTTTTGTGATA
Done.