Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 40 of 120
Found at i:10821351 original size:24 final size:26
Alignment explanation
Indices: 10821320--10821378 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
10821310 AAATAAATAA
*
10821320 AAAATACTAAA-CTTGGTTTAAG-TT
1 AAAATACTAAAGCTTAGTTTAAGTTT
*
10821344 AAAATACTAAAGCTTAGTTTATGTTT
1 AAAATACTAAAGCTTAGTTTAAGTTT
10821370 ATAAATACT
1 A-AAATACT
10821379 CATGATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 11 0.37
25 9 0.30
26 3 0.10
27 7 0.23
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (26 bp):
AAAATACTAAAGCTTAGTTTAAGTTT
Found at i:10822493 original size:13 final size:14
Alignment explanation
Indices: 10822475--10822507 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10822465 GAATGTTGGC
*
10822475 ATTATCTT-CATAA
1 ATTATCTTGAATAA
10822488 ATTATCTTGAATAA
1 ATTATCTTGAATAA
10822502 ATTATC
1 ATTATC
10822508 CCAATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTATCTTGAATAA
Found at i:10822669 original size:15 final size:15
Alignment explanation
Indices: 10822649--10822680 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10822639 CATCACTTAG
10822649 GATTTCTGTGATTAA
1 GATTTCTGTGATTAA
10822664 GATTTCTGTGATTAA
1 GATTTCTGTGATTAA
10822679 GA
1 GA
10822681 GAAAAGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (15 bp):
GATTTCTGTGATTAA
Found at i:10823828 original size:18 final size:18
Alignment explanation
Indices: 10823790--10823828 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
10823780 TTTGAGCATT
**
10823790 TATGTATTATTTTGCTTC
1 TATGTATTATTTTGCAAC
10823808 TATGTATTATTTTGCAAC
1 TATGTATTATTTTGCAAC
10823826 TAT
1 TAT
10823829 TTCTCTTCAT
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:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (18 bp):
TATGTATTATTTTGCAAC
Found at i:10825445 original size:23 final size:23
Alignment explanation
Indices: 10825417--10825460 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10825407 AGTAAATAAT
*
10825417 AAATATTTAAAATGAATAATGCG
1 AAATATTCAAAATGAATAATGCG
*
10825440 AAATATTCAAAATTAATAATG
1 AAATATTCAAAATGAATAATG
10825461 TACAATTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (23 bp):
AAATATTCAAAATGAATAATGCG
Found at i:10825636 original size:26 final size:26
Alignment explanation
Indices: 10825607--10825656 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
10825597 AAATAACATA
* *
10825607 GAAAGCAATTTAAA-TAGGTAATATAT
1 GAAA-CAAGTTAAAGTAGCTAATATAT
10825633 GAAACAAGTTAAAGTAGCTAATAT
1 GAAACAAGTTAAAGTAGCTAATAT
10825657 CAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (26 bp):
GAAACAAGTTAAAGTAGCTAATATAT
Found at i:10827495 original size:44 final size:44
Alignment explanation
Indices: 10827445--10827884 Score: 167
Period size: 44 Copynumber: 9.6 Consensus size: 44
10827435 ATTTTAATCC
* **
10827445 GCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-GTAGCTTCAACCT
* * * *
10827489 GTTCCACTGTAACTTCAGGGAAATAAGACTTGTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
* * * *
10827533 GCCCCACTGCAACTTCAGGGGGATAAGACTCT-CAACTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACT-TGTAGCTTCAACCT
* * * * * * * * *
10827577 GCCCCACTACAAATTCGGGGAGATGAG-GTT-T-GATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCT-TCAACCT
* * ** *
10827618 GCTCTATTGCAACTTCAGAAAGATAAGATCTGTAATGTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-C--T--TG--TAGCTTCAACCT
** * * * **
10827669 ATTCCACTGCTACTTCAGGGAAATAAGA-TTCGTTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAGCTTCAACCT
* *
10827714 CCTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTACTCTACTGCAACT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TA-G--CT--TC-A----ACCT
* * **
10827769 GCCCCACTGCAACTTCAGGGGGATAAGGTTTGTTA-CTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAACCT
* * * * ** * * **
10827813 TCTCTACTGTAACTTCAGAGAGATAAGGTTTGTGGCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
*
10827857 GCTCCACTGCAACTTCAAGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
10827885 TTCGCCATGA
Statistics
Matches: 290, Mismatches: 79, Indels: 54
0.69 0.19 0.13
Matches are distributed among these distances:
41 22 0.08
42 2 0.01
43 2 0.01
44 148 0.51
45 42 0.14
46 3 0.01
47 2 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 29 0.10
55 31 0.11
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAACCT
Found at i:10836156 original size:14 final size:14
Alignment explanation
Indices: 10836133--10836168 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
10836123 GATAAGATAT
10836133 AATACAAATGAATG
1 AATACAAATGAATG
*
10836147 AATGCAAATGAATG
1 AATACAAATGAATG
10836161 AATACAAA
1 AATACAAA
10836169 AAGAGGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.19
Consensus pattern (14 bp):
AATACAAATGAATG
Found at i:10841321 original size:30 final size:32
Alignment explanation
Indices: 10841270--10841331 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
10841260 AATTTTTCGA
*
10841270 ATAAGGATTAATTTGTTAAATTAGT-AAAAAT
1 ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
* *
10841301 ATAAGGATT-TTTTGTGAAATTATTGAAAAAT
1 ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
10841332 GGGTTGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (32 bp):
ATAAGGATTAATTTGTGAAATTAGTGAAAAAT
Found at i:10841910 original size:25 final size:26
Alignment explanation
Indices: 10841882--10841999 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 26
10841872 ATCCCAATAT
*
10841882 TTGGCTCTCACGAGCTTCCTGG-TAC
1 TTGGCTCTCACGAGCTTCCTGGATAA
10841907 TTGGCTCTCACGAGCTT-CTGGATAA
1 TTGGCTCTCACGAGCTTCCTGGATAA
* * * *
10841932 TTAGCTCTAATGAGCTTCC-CGATTAA
1 TTGGCTCTCACGAGCTTCCTGGA-TAA
** * *
10841958 -TGGCTCTCTTGAGCTTCC-CGATAT
1 TTGGCTCTCACGAGCTTCCTGGATAA
* *
10841982 TTGGCTCGCATGAGCTTC
1 TTGGCTCTCACGAGCTTC
10842000 TTGATTTACA
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
24 6 0.08
25 68 0.87
26 4 0.05
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (26 bp):
TTGGCTCTCACGAGCTTCCTGGATAA
Found at i:10844470 original size:11 final size:11
Alignment explanation
Indices: 10844454--10844511 Score: 55
Period size: 11 Copynumber: 5.3 Consensus size: 11
10844444 TATTTAAAAT
10844454 AAAATATTTTA
1 AAAATATTTTA
10844465 AAAATATTTTA
1 AAAATATTTTA
* ***
10844476 AAATTA-AAAA
1 AAAATATTTTA
*
10844486 AATAACATTTTA
1 AA-AATATTTTA
10844498 AAAATATTTTA
1 AAAATATTTTA
10844509 AAA
1 AAA
10844512 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
10 3 0.09
11 29 0.83
12 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:10844470 original size:16 final size:14
Alignment explanation
Indices: 10844439--10844484 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
10844429 ATTAATAATT
10844439 TAAAATATTTAAAA
1 TAAAATATTTAAAA
*
10844453 TAAAATATTTTAAA
1 TAAAATATTTAAAA
*
10844467 -AATAT-TTTAAAA
1 TAAAATATTTAAAA
10844479 TTAAAA
1 -TAAAA
10844485 AAATAACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 6 0.23
13 4 0.15
14 16 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATATTTAAAA
Found at i:10844476 original size:35 final size:35
Alignment explanation
Indices: 10844432--10844523 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 35
10844422 AAAATTTATT
* * *
10844432 AATAATTTAAAATATTTAAAATAA-AATATTTTAAA
1 AATATTTTAAAATA-TTAAAAAAATAACATTTTAAA
10844467 AATATTTT-AAA-ATTAAAAAAATAACATTTTAAA
1 AATATTTTAAAATATTAAAAAAATAACATTTTAAA
10844500 AATATTTT-AAA-ATTAAAAAAATAA
1 AATATTTTAAAATATTAAAAAAATAA
10844524 ATATATTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
32 8 0.15
33 35 0.66
34 3 0.06
35 7 0.13
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (35 bp):
AATATTTTAAAATATTAAAAAAATAACATTTTAAA
Found at i:10844501 original size:33 final size:33
Alignment explanation
Indices: 10844459--10844523 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
10844449 AAAATAAAAT
10844459 ATTTTAAAAATATTTTAAAATTAAAAAAATAAC
1 ATTTTAAAAATATTTTAAAATTAAAAAAATAAC
10844492 ATTTTAAAAATATTTTAAAATTAAAAAAATAA
1 ATTTTAAAAATATTTTAAAATTAAAAAAATAA
10844524 ATATATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
ATTTTAAAAATATTTTAAAATTAAAAAAATAAC
Found at i:10844521 original size:52 final size:51
Alignment explanation
Indices: 10844467--10844580 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 51
10844457 ATATTTTAAA
*
10844467 AATATTTTAAAATTAAAAAAATAACATTTTAAAAATATTTTAAAATTAAAAAAAT
1 AATATATT-AAATTAAAAAAAT---ATTTTAAAAATATTTTAAAATTAAAAAAAT
* * *
10844522 AAATATATTTAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAATA-
1 -AATATATTAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAT
10844573 AATATATT
1 AATATATT
10844581 TATTATATCG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
50 8 0.15
52 28 0.52
55 11 0.20
56 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (51 bp):
AATATATTAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAT
Found at i:10844522 original size:19 final size:18
Alignment explanation
Indices: 10844464--10844519 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
10844454 AAAATATTTT
10844464 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
* *
10844482 AAAAA-A---TAACATTTT
1 AAAAATATTTTAA-AATTA
10844497 AAAAATATTTTAAAATTA
1 AAAAATATTTTAAAATTA
10844515 AAAAA
1 AAAAA
10844520 ATAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 1 0.03
17 1 0.03
18 13 0.45
19 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATATTTTAAAATTA
Found at i:10844876 original size:21 final size:21
Alignment explanation
Indices: 10844842--10844882 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10844832 AATTATTTAT
*
10844842 TTTTTAGTTTATAAT-ATTAA
1 TTTTTAGTTGATAATCATTAA
10844862 TTTTTAGTGTGATAATCATTA
1 TTTTTAGT-TGATAATCATTA
10844883 TTATTATTTN
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (21 bp):
TTTTTAGTTGATAATCATTAA
Found at i:10846734 original size:23 final size:21
Alignment explanation
Indices: 10846697--10846756 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
10846687 GGCCCGGCCC
10846697 ATTT-TTTTAACAAATACCAAAAA
1 ATTTATTTTAA-AAATA--AAAAA
10846720 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
*
10846742 A-GTATTTTAAAAATA
1 ATTTATTTTAAAAATA
10846757 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 6 0.18
23 7 0.21
24 8 0.24
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:10846758 original size:11 final size:11
Alignment explanation
Indices: 10846738--10846804 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
10846728 TAAAAATTAA
10846738 AAAAAGTATTTT
1 AAAAA-TATTTT
10846750 AAAAATATTTT
1 AAAAATATTTT
10846761 --AAA-A--TT
1 AAAAATATTTT
* *
10846767 AAAAAAAATTT
1 AAAAATATTTT
10846778 AAAAAGTATTTT
1 AAAAA-TATTTT
*
10846790 TAAAATATTTT
1 AAAAATATTTT
10846801 AAAA
1 AAAA
10846805 TTAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 4 0.09
11 22 0.49
12 13 0.29
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:10846770 original size:17 final size:17
Alignment explanation
Indices: 10846748--10846781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10846738 AAAAAGTATT
* *
10846748 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
10846765 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
10846782 AGTATTTTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:10846784 original size:40 final size:40
Alignment explanation
Indices: 10846729--10846859 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 40
10846719 AATTTATTTT
10846729 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* *
10846770 AAAAATTTAAAAAGTATTTTTAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
10846810 AAATAA-TAAAAAAGTAAATCAATTTTAAAAATATTTTAAAATTAAA
1 AAA-AATTAAAAAAG----T--ATTTTAAAAATATTTTAAAATTAAA
10846856 AAAA
1 AAAA
10846860 TAAATATATT
Statistics
Matches: 79, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
40 41 0.52
41 9 0.11
44 1 0.01
45 1 0.01
46 27 0.34
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:10846990 original size:32 final size:35
Alignment explanation
Indices: 10846937--10847008 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 35
10846927 GTTTTCTAAA
** *
10846937 CGGGCCTCATTTTTTTGCCAAA-GC-C-CATATTT
1 CGGGCCTCATTTTTTACCCAAACCCTCACATATTT
10846969 CGGGCCT-ATATTTTTACCCAAACCCTCACATATTT
1 CGGGCCTCAT-TTTTTACCCAAACCCTCACATATTT
10847004 CGGGC
1 CGGGC
10847009 AGGCCGTCGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 2 0.06
32 17 0.52
33 1 0.03
34 1 0.03
35 12 0.36
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (35 bp):
CGGGCCTCATTTTTTACCCAAACCCTCACATATTT
Found at i:10854367 original size:138 final size:138
Alignment explanation
Indices: 10854131--10854382 Score: 387
Period size: 138 Copynumber: 1.8 Consensus size: 138
10854121 ATCTTATGAT
* * * * *
10854131 GGTAACACACTTACAAAGTCATTGGTTAAGAAGTTGATTAGCAGTTTCGTGATAGTATATAATAA
1 GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
* *
10854196 TGAAGAGTTCAATCATGATACTTTAGTGGAATGACTTCATGACTAAATAATACTGTAACGAATAT
66 TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATAATACTGTAACGAATAT
10854261 CCTATTAG
131 CCTATTAG
* * * * *
10854269 GGTAATACAATTACAAAGTCACTGGCTGAGAAGTTGATAAGTAGTTTTGTGATAGGGTATAATAA
1 GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
*
10854334 TGGAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATA
66 TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATA
10854383 CTGTTATAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 101 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (138 bp):
GGTAACACAATTACAAAGTCACTGGCTAAGAAGTTGATAAGCAGTTTCGTGATAGGATATAATAA
TGAAGAGCTCAATCATGATACTTTAGTGAAATGACTTCATGACTAAATAATACTGTAACGAATAT
CCTATTAG
Found at i:10854799 original size:22 final size:21
Alignment explanation
Indices: 10854774--10854821 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
10854764 CCTTAATAGA
10854774 AATTAAAATGAATAGAGAAAAT
1 AATTAAAATG-ATAGAGAAAAT
** *
10854796 AATTTAATTTGATAGAGAAATT
1 AA-TTAAAATGATAGAGAAAAT
10854818 AATT
1 AATT
10854822 TAGTTAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.09
22 14 0.64
23 6 0.27
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTAAAATGATAGAGAAAAT
Found at i:10856924 original size:17 final size:18
Alignment explanation
Indices: 10856891--10856930 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
10856881 CATAAACAAC
*
10856891 ATAAACTTGATAAAATAA
1 ATAAACATGATAAAATAA
10856909 ATAAACATGA-AAAATAA
1 ATAAACATGATAAAATAA
10856926 ATAAA
1 ATAAA
10856931 GAGTAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (18 bp):
ATAAACATGATAAAATAA
Found at i:10859537 original size:41 final size:41
Alignment explanation
Indices: 10859491--10859573 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
10859481 TCGAACCTAA
* ** *
10859491 AAATTCTTATTTTACCCTTATACCTGAAACAACCTTAAATC
1 AAATTCTCATTTTACCCTTATACCCAAAACAACCCTAAATC
10859532 AAATTCTCATTTTACCCTTATACCCAAAACAACCCTAAATC
1 AAATTCTCATTTTACCCTTATACCCAAAACAACCCTAAATC
10859573 A
1 A
10859574 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.33
Consensus pattern (41 bp):
AAATTCTCATTTTACCCTTATACCCAAAACAACCCTAAATC
Found at i:10865016 original size:43 final size:42
Alignment explanation
Indices: 10864981--10865070 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
10864971 TCTTACATAT
*
10864981 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATA-CGATGCCAATGTCCCAGACAGGGTCTTACACGA
* * *
10865024 AGTCATATACGATGCCAATGTCCCAGACATGGTCTTACACGTA
1 AATCAAATACGATGCCAATGTCCCAGACAGGGTCTTACACG-A
10865067 AATC
1 AATC
10865071 TCAGGTTGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 30 0.73
43 11 0.27
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
AATCAAATACGATGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:10867883 original size:14 final size:14
Alignment explanation
Indices: 10867864--10867895 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
10867854 TGTTAATTTT
10867864 AAAGCTTATTAGAG
1 AAAGCTTATTAGAG
*
10867878 AAAGCTTATTAGCG
1 AAAGCTTATTAGAG
10867892 AAAG
1 AAAG
10867896 AGCATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (14 bp):
AAAGCTTATTAGAG
Found at i:10869061 original size:10 final size:10
Alignment explanation
Indices: 10869035--10869075 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
10869025 ATTAAAATAC
*
10869035 AATAATTTGCA
1 AATAATTT-AA
10869046 AA-AATTTAA
1 AATAATTTAA
10869055 AATAATTTAA
1 AATAATTTAA
10869065 AATAATTTAA
1 AATAATTTAA
10869075 A
1 A
10869076 GAATGTCAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 3 0.11
10 23 0.82
11 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AATAATTTAA
Found at i:10870771 original size:18 final size:18
Alignment explanation
Indices: 10870748--10870784 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10870738 ACCAAACAAA
10870748 AAGGGTAAGTACATGGTC
1 AAGGGTAAGTACATGGTC
10870766 AAGGGTAAGTACATGGTC
1 AAGGGTAAGTACATGGTC
10870784 A
1 A
10870785 TTTTTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (18 bp):
AAGGGTAAGTACATGGTC
Found at i:10871241 original size:17 final size:17
Alignment explanation
Indices: 10871200--10871245 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
10871190 TTTGACAAGA
*
10871200 AAAATAAATGAAAAATCTT
1 AAAATAAA--AAAAATCCT
10871219 AGAAATAAAAAAAATCCT
1 A-AAATAAAAAAAATCCT
10871237 AAAATAAAA
1 AAAATAAAA
10871246 TTTAAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 8 0.32
18 9 0.36
19 1 0.04
20 7 0.28
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (17 bp):
AAAATAAAAAAAATCCT
Found at i:10888692 original size:24 final size:24
Alignment explanation
Indices: 10888660--10888707 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
10888650 AGTAGAATTA
*
10888660 AAGAGCCAACGACGTCCCCGTGAT
1 AAGAGCCAACGACGTCCCCATGAT
10888684 AAGAGCCAACGACGTCCCCATGAT
1 AAGAGCCAACGACGTCCCCATGAT
10888708 GAATCCTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.23, T:0.12
Consensus pattern (24 bp):
AAGAGCCAACGACGTCCCCATGAT
Found at i:10890115 original size:27 final size:27
Alignment explanation
Indices: 10890055--10890108 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
10890045 TCCTTTCTTT
* *
10890055 AGAGTTTGTCATACGTACTATTCCTTC
1 AGAGTTCGTCACACGTACTATTCCTTC
10890082 AGAGTTCGTCACACGTACTATTCCTTC
1 AGAGTTCGTCACACGTACTATTCCTTC
10890109 CAAGTTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (27 bp):
AGAGTTCGTCACACGTACTATTCCTTC
Found at i:10890218 original size:53 final size:53
Alignment explanation
Indices: 10890123--10890298 Score: 282
Period size: 53 Copynumber: 3.3 Consensus size: 53
10890113 TTCACCATGT
* * * *
10890123 ATATCATCCTTTCATGGTTT-CCATACTTATCATTCTTCAAAGTTAGCCAAAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
*
10890175 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAACCATAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
* *
10890228 ATATTATTCTTTTAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
1 ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
10890281 ATATCATTCTTTCAGGGT
1 ATATCATTCTTTCAGGGT
10890299 CCGCCACAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 18 0.16
53 95 0.84
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (53 bp):
ATATCATTCTTTCAGGGTTTGCCATACTTACCATTCTTCAAAGTTAGCCATAC
Found at i:10890304 original size:27 final size:27
Alignment explanation
Indices: 10890123--10890298 Score: 144
Period size: 26 Copynumber: 6.7 Consensus size: 27
10890113 TTCACCATGT
* * *
10890123 ATATCATCCTTTCATGGTT-TCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* ** *
10890149 TTATCATTC-TTCAAAGTTAGCCAAAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
*
10890175 ATATCATTCTTTCAGGGTTTGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * ** *
10890202 TTACCATTC-TTCAAAGTTAACCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * *
10890228 ATATTATTCTTTTAGGGTTTGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
* * **
10890255 TTACCATTC-TTCAAAGTTAGCCATAC
1 ATATCATTCTTTCAGGGTTAGCCATAC
10890281 ATATCATTCTTTCAGGGT
1 ATATCATTCTTTCAGGGT
10890299 CCGCCACAAA
Statistics
Matches: 110, Mismatches: 36, Indels: 7
0.72 0.24 0.05
Matches are distributed among these distances:
25 7 0.06
26 59 0.54
27 44 0.40
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (27 bp):
ATATCATTCTTTCAGGGTTAGCCATAC
Found at i:10895635 original size:60 final size:61
Alignment explanation
Indices: 10895560--10895674 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 61
10895550 TTCTGAGAAC
* *
10895560 TTCAAATCGTCACTCCTAAAATTTTGGGGAGCACTCTTCTCTTGAATCT-GGTTTTGGAAG
1 TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTTTGGAAG
* *
10895620 TTCAAATCGTTACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGATTCTCGGTTT
1 TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTT
10895675 GTACTTTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 45 0.90
61 5 0.10
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (61 bp):
TTCAAATCGTCACTCCCAAAATTTTGGGGAGCACCCTTCTCTTGAATCTCGGTTTTGGAAG
Found at i:10898832 original size:101 final size:99
Alignment explanation
Indices: 10898692--10898884 Score: 260
Period size: 101 Copynumber: 1.9 Consensus size: 99
10898682 TGAATTGACG
** * * *
10898692 GATAAGACCATAACTGGGTTATGGCACTATGAACATAAGACCATGGTTGGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATG--C
*
10898757 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
64 ATATGTAAGACCATAGCTGGACTATGGCATTCTGAT
** * *
10898793 GATAAGACCATAACTGGGTTATGGCACTACAAATGTAAGACCATGGTAGGGCCATGGCAATGCAT
1 GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATGCAT
* *
10898858 GTGTAAGACCATAGTTGGACTATGGCA
66 ATGTAAGACCATAGCTGGACTATGGCA
10898885 CAAAAAGAAC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 26 0.32
101 54 0.68
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (99 bp):
GATAAGACCATAACTGGGTTATGGCACTACAAACATAAGACCATGGTAGGACCATGACAATGCAT
ATGTAAGACCATAGCTGGACTATGGCATTCTGAT
Found at i:10898883 original size:33 final size:33
Alignment explanation
Indices: 10898760--10898884 Score: 103
Period size: 33 Copynumber: 3.8 Consensus size: 33
10898750 AGTGTTTATA
*
10898760 TGTAAGACCATAGCTGGGCTATGGC-ATTC-TG
1 TGTAAGACCATAGCTGGGCTATGGCAATACATG
* * * **
10898791 ATGATAAGACCATAACTGGGTTATGGCACTACAAA
1 -TG-TAAGACCATAGCTGGGCTATGGCAATACATG
* * *
10898826 TGTAAGACCAT-GGTAGGGCCATGGCAATGCATG
1 TGTAAGACCATAGCT-GGGCTATGGCAATACATG
* *
10898859 TGTAAGACCATAGTTGGACTATGGCA
1 TGTAAGACCATAGCTGGGCTATGGCA
10898885 CAAAAAGAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
32 3 0.04
33 62 0.87
34 6 0.08
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (33 bp):
TGTAAGACCATAGCTGGGCTATGGCAATACATG
Found at i:10904977 original size:5 final size:5
Alignment explanation
Indices: 10904960--10904991 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
10904950 CCACTTTTTT
10904960 GGCCC GAGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC G-GCCC GGCCC GGCCC GGCCC GGCCC G
10904992 ATATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.56, G:0.41, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:10905055 original size:36 final size:36
Alignment explanation
Indices: 10905006--10905086 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
10904996 AATAAATATA
*
10905006 TTTATTTTTTAATTTTAAAATATTTTTAAAATATTTT
1 TTTA-TTTTTAATTTTAAAATATTTTTAAAATACTTT
10905043 TTTATTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTATTTTTAATTTTAAAATATTTTTAAAATACTTT
*
10905079 TTAATTTT
1 TTTATTTT
10905087 AAATAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 38 0.90
37 4 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (36 bp):
TTTATTTTTAATTTTAAAATATTTTTAAAATACTTT
Found at i:10905081 original size:12 final size:11
Alignment explanation
Indices: 10905018--10905082 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
10905008 TATTTTTTAA
10905018 TTTTAAAATAT
1 TTTTAAAATAT
10905029 TTTTAAAATATTT
1 TTTTAAAATA--T
*** *
10905042 TTTTATTTTTAA
1 TTTTA-AAATAT
10905054 TTTTAAAATAT
1 TTTTAAAATAT
10905065 TTTTAAAATACT
1 TTTTAAAATA-T
10905077 TTTTAA
1 TTTTAA
10905083 TTTTAAATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 22 0.52
12 12 0.29
13 6 0.14
14 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:10907336 original size:17 final size:17
Alignment explanation
Indices: 10907314--10907360 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
10907304 CCATTATGAT
*
10907314 TTTAAAATTATTTTTAA
1 TTTAAAATTATTTATAA
*
10907331 TTTAAAAATATATTATAA
1 TTTAAAATTAT-TTATAA
*
10907349 TTTTAAATTATT
1 TTTAAAATTATT
10907361 ATATTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATTATTTATAA
Found at i:10907349 original size:18 final size:18
Alignment explanation
Indices: 10907314--10907368 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
10907304 CCATTATGAT
* *
10907314 TTTAAAATTAT-TTTTAA
1 TTTAAAAATATATTATAA
10907331 TTTAAAAATATATTATAA
1 TTTAAAAATATATTATAA
* *
10907349 TTT-TAAAT-TATTATAT
1 TTTAAAAATATATTATAA
10907365 TTTA
1 TTTA
10907369 TTAATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 10 0.31
17 14 0.44
18 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAAATATATTATAA
Found at i:10910358 original size:43 final size:43
Alignment explanation
Indices: 10910264--10910350 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
10910254 ATGAAGGCAG
* * *
10910264 GATATGATATGTTACAAGATATGTTTCGATATGAATCTGATAT
1 GATATGATATGTTACAAGAAATGTTCCGAAATGAATCTGATAT
* *
10910307 GATATGATATG-TATAAGAAATGTTCCGAAATGGAGTCTGATAT
1 GATATGATATGTTACAAGAAATGTTCCGAAAT-GAATCTGATAT
10910350 G
1 G
10910351 CTTTGATACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 16 0.42
43 22 0.58
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (43 bp):
GATATGATATGTTACAAGAAATGTTCCGAAATGAATCTGATAT
Found at i:10911258 original size:13 final size:13
Alignment explanation
Indices: 10911240--10911295 Score: 85
Period size: 13 Copynumber: 4.2 Consensus size: 13
10911230 CATACTCATC
10911240 TAGGAAGTAATCA
1 TAGGAAGTAATCA
*
10911253 TAGGAAGTACTCA
1 TAGGAAGTAATCA
10911266 TCTAGGAAGTAATCA
1 --TAGGAAGTAATCA
10911281 TAGGAAGTAATCA
1 TAGGAAGTAATCA
10911294 TA
1 TA
10911296 CTCTTTCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
13 27 0.69
15 12 0.31
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (13 bp):
TAGGAAGTAATCA
Found at i:10911272 original size:28 final size:28
Alignment explanation
Indices: 10911232--10911294 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
10911222 GTGCCAACCA
10911232 TACTCATCTAGGAAGTAATCATAGGAAG
1 TACTCATCTAGGAAGTAATCATAGGAAG
10911260 TACTCATCTAGGAAGTAATCATAGGAAG
1 TACTCATCTAGGAAGTAATCATAGGAAG
*
10911288 TAATCAT
1 TACTCAT
10911295 ACTCTTTCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (28 bp):
TACTCATCTAGGAAGTAATCATAGGAAG
Found at i:10911941 original size:43 final size:43
Alignment explanation
Indices: 10911884--10912067 Score: 219
Period size: 43 Copynumber: 4.3 Consensus size: 43
10911874 TTTTTCACAT
10911884 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
* ** *
10911927 ACACGCCGCTAAAGAGCATGACC-TTAGCAACGAC-TTCATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCG-CTTTTATCAC
* * * * *
10911969 AAACACCGCTAAAGAACATGATCTTTAGTGGCACTTTTATCAC
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
* * * *
10912012 AAATGCTGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATTAT
1 AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
*
10912055 AAACGCTGCTAAA
1 AAACGCCGCTAAA
10912068 AGTACCGTTC
Statistics
Matches: 115, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
42 34 0.30
43 81 0.70
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAGCATGACCTTTAGCGGCGCTTTTATCAC
Found at i:10918960 original size:31 final size:31
Alignment explanation
Indices: 10918867--10918962 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
10918857 GGCAAATTAC
*
10918867 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
10918898 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
10918930 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
10918961 AA
1 AA
10918963 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:10924209 original size:100 final size:101
Alignment explanation
Indices: 10924077--10924293 Score: 285
Period size: 100 Copynumber: 2.2 Consensus size: 101
10924067 TAGAGTTGCA
** * * *
10924077 ATCATAAATCGGTGAACTCTTAATGAATTGTTCATGAT-AGTAAATCAATGAACCGAAGTTGTGA
1 ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCA-TAAATCAATGAACAGAAGTTGTGA
* ** *
10924141 TCGT-AAATCAGTGAGCTTCAAAAGATGACAGCTGTG
65 TAGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
*
10924177 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
* * *
10924242 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTG
66 AGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
*
10924278 ATCGTAAATCAATGAA
1 ATCATAAATCAATGAA
10924294 TTATTTCAAG
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
100 59 0.58
101 42 0.42
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (101 bp):
ATCATAAATCAATGAACTCTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
AGTAAAATCAACGAGCTTCAAAAAATGACAGCTGTG
Found at i:10924317 original size:100 final size:98
Alignment explanation
Indices: 10924117--10924328 Score: 239
Period size: 101 Copynumber: 2.1 Consensus size: 98
10924107 TTCATGATAG
* * ** *
10924117 TAAATCAATGAACCGAAGTTGTGATCGTAAATCAGTGAGCTTCAAAAGATGACAGCTGTGATCAT
1 TAAATCAATGAACAGAAGTTGTGATAGTAAATCAACGAGCTTCAAAAAATGACAGCTGTGATCAT
* *
10924182 AAATCAATGAACTGTTAATAAAGTGTTCATGATCA
66 AAATCAATGAACTATT-ATAAAGAGTTCA-GATCA
* * * *
10924217 TAAATCAATGAACAGAAGTTGTGATAGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCG
1 TAAATCAATGAACAGAAGTTGTGATAGT-AAATCAACGAGCTTCAAAAAATGACAGCTGTGATCA
* *
10924282 TAAATCAATGAATTATT-TCAAGGGAGTTGCA-ATCA
65 TAAATCAATGAACTATTAT-AA-AGAGTT-CAGATCA
10924317 TAAATCAATGAA
1 TAAATCAATGAA
10924329 ATCTTCATGA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
99 1 0.01
100 44 0.46
101 48 0.51
102 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (98 bp):
TAAATCAATGAACAGAAGTTGTGATAGTAAATCAACGAGCTTCAAAAAATGACAGCTGTGATCAT
AAATCAATGAACTATTATAAAGAGTTCAGATCA
Found at i:10924449 original size:134 final size:136
Alignment explanation
Indices: 10924177--10924456 Score: 402
Period size: 136 Copynumber: 2.1 Consensus size: 136
10924167 GACAGCTGTG
* * * * * * * *
10924177 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
* * *
10924242 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAATGAATTATTTCAAGGGA
66 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
10924307 GTTGCA
131 GTTGCA
* *
10924313 ATCATAAATCAATGAAATCTTCATGAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
1 ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
* * *
10924378 CGT-AAATTAACGAGCTTT-AAAGATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAATGGA
66 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
10924441 GTTGCA
131 GTTGCA
10924447 ATCATAAATC
1 ATCATAAATC
10924457 GACAAACTCT
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
134 56 0.44
135 15 0.12
136 57 0.45
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (136 bp):
ATCATAAATCAATGAAATCTTAATAAACTGCTCATCATCATAAATCAATAAACAAAAATTGTGAT
AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
GTTGCA
Found at i:10924507 original size:98 final size:98
Alignment explanation
Indices: 10924405--10924619 Score: 250
Period size: 98 Copynumber: 2.2 Consensus size: 98
10924395 TAAAGATGAC
* *
10924405 AGTTGTGATCGTAAATCAAAGAACTATTTAAATGGAGTTGCAATCATAAATCGACAAACTCTTAA
1 AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
* * * * *
10924470 TGAAGTGTTCACGGTCGTAAATTAATGAATTGA
66 TGAAATGTTCACGATCATAAATCAATGAACTGA
** * * * ** ** *
10924503 AGTTGTGATCATAAATCAGTGACCTGTTTAAAAGGATTTGTGATTGTAAATCGACGAACTCTTAA
1 AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
* *
10924568 TGAAATGTTCATGATCATATATCAATGAACTGA
66 TGAAATGTTCACGATCATAAATCAATGAACTGA
*
10924601 AGTTGTTATCATAAATCAA
1 AGTTGTGATCATAAATCAA
10924620 CGAGCTTTAA
Statistics
Matches: 96, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (98 bp):
AGTTGTGATCATAAATCAAAGAACTATTTAAAAGGAGTTGCAATCATAAATCGACAAACTCTTAA
TGAAATGTTCACGATCATAAATCAATGAACTGA
Found at i:10924509 original size:134 final size:135
Alignment explanation
Indices: 10924177--10924518 Score: 411
Period size: 134 Copynumber: 2.5 Consensus size: 135
10924167 GACAGCTGTG
** * * *
10924177 ATCATAAATCAATGAACTGTTAATAAAGTGTTCATGATCATAAATCAATGAACAGAAGTTGTGAT
1 ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
* * * *
10924242 AGTAAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAATGAATTATTTCAAGGGA
66 CGT-AAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGA
10924307 GTTGCA
130 GTTGCA
* * * * * * *
10924313 ATCATAAATCAATGAAA-TCTTCATGAACTGCTCATC-ATCATAAATCAATAAACAAAAATTGTG
1 ATCATAAATCAA-CAAACTCTTAATGAAGTGTTCA-CGATCATAAATCAATGAACAGAAGTTGTG
* *
10924376 ATCGTAAATTAACGAGCTTT-AAAGATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAATGG
64 ATCGTAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGG
10924440 AGTTGCA
129 AGTTGCA
* * * * **
10924447 ATCATAAATCGACAAACTCTTAATGAAGTGTTCACGGTCGTAAATTAATGAATTGAAGTTGTGAT
1 ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
*
10924512 CATAAAT
66 CGTAAAT
10924519 CAGTGACCTG
Statistics
Matches: 171, Mismatches: 31, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
133 4 0.02
134 98 0.57
135 15 0.09
136 52 0.30
137 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (135 bp):
ATCATAAATCAACAAACTCTTAATGAAGTGTTCACGATCATAAATCAATGAACAGAAGTTGTGAT
CGTAAATTAACGAGCTTTAAAAAATGACAGTTGTGATCGTAAATCAAAGAACTATTTAAAGGGAG
TTGCA
Found at i:10924776 original size:133 final size:134
Alignment explanation
Indices: 10924559--10924866 Score: 349
Period size: 133 Copynumber: 2.3 Consensus size: 134
10924549 TAAATCGACG
* * *
10924559 AACTCTTAATGAAATGTTCATGATCATATATCAATGAACTGAAGTTGTTATCATAAATCAACGAG
1 AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTAAAGTTG-TATCATAAATCAACGAA
* *
10924624 CTTTAAAAATGACAGTTGTGATCGTAAATCA-ATGAATTGTTTAAATGGAGTTGCGATCATAAAT
65 CTTTAAAAATGACAGTTGTGATCGTAAATCAGA-GAACTGTTTAAATGAAGTTGCGATCATAAAT
10924688 AAAAAA
129 AAAAAA
* *
10924694 AACTCTTACTGAAGTGTTCATGATCATA-AGTCAATAAA-TCAAAGTTG-ATCATAAATCAACGA
1 AACTCTTAATGAAATGTTCATGATCATATA-TCAATAAACT-AAAGTTGTATCATAAATCAACGA
* * * ** *
10924756 ATTTTAAAAATGGCAGTTGTGATCGTAAATTAGAGAACTGTTTAAATGAAGTTATGATCGT--AT
64 ACTTTAAAAATGACAGTTGTGATCGTAAATCAGAGAACTGTTTAAATGAAGTTGCGATCATAAAT
** **
10924819 ACCGACG
129 A-AAAAA
* * *
10924826 AACTCTTAATGAAATGTTCATGATCGTAAATCAACAAACTA
1 AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTA
10924867 TAAAAATTCC
Statistics
Matches: 146, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
131 3 0.02
132 34 0.23
133 67 0.46
134 3 0.02
135 39 0.27
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (134 bp):
AACTCTTAATGAAATGTTCATGATCATATATCAATAAACTAAAGTTGTATCATAAATCAACGAAC
TTTAAAAATGACAGTTGTGATCGTAAATCAGAGAACTGTTTAAATGAAGTTGCGATCATAAATAA
AAAA
Found at i:10924930 original size:107 final size:107
Alignment explanation
Indices: 10924739--10924963 Score: 315
Period size: 107 Copynumber: 2.1 Consensus size: 107
10924729 AAATCAAAGT
* * * * * *
10924739 TGATCATAAATCAACGAATTTTAAAAATGGCAGTTGTGATCGTAAATTAGAGAACTGTTTAAATG
1 TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
* * *
10924804 AAGTTATGATCGTATACCGACGAACTCTTAATGAAATGTTCA
66 AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
* * * *
10924846 TGATCGTAAATCAACAAACTATAAAAATTCCATTTGTGATTGTAAATCAGCGAACTGTTTAAATG
1 TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
* *
10924911 GAGTTATGATCATAAACCGACAAACTCTTAATGAAGTGTTCA
66 AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
10924953 TGATCGTAAAT
1 TGATCGTAAAT
10924964 TAATGAACTG
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (107 bp):
TGATCGTAAATCAACAAACTATAAAAATGCCAGTTGTGATCGTAAATCAGAGAACTGTTTAAATG
AAGTTATGATCATAAACCGACAAACTCTTAATGAAATGTTCA
Found at i:10930694 original size:29 final size:29
Alignment explanation
Indices: 10930617--10930695 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
10930607 ACAGTCCATC
* * *
10930617 TGGCCTACAAGGCCTGACACATGATCGTG
1 TGGCCCACAAGGCCTGGCACATGACCGTG
* * *
10930646 TGGCTCA-AATGGTCTAGCACATGACCGTG
1 TGGCCCACAA-GGCCTGGCACATGACCGTG
*
10930675 TGGCCCACACGGCCTGGCACA
1 TGGCCCACAAGGCCTGGCACA
10930696 CGTTCATGTG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
28 2 0.05
29 35 0.92
30 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.28, T:0.19
Consensus pattern (29 bp):
TGGCCCACAAGGCCTGGCACATGACCGTG
Found at i:10935778 original size:13 final size:13
Alignment explanation
Indices: 10935760--10935797 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
10935750 ATGGTAACAA
10935760 GAAATGTTTA-AGT
1 GAAATGTTTATA-T
*
10935773 GAAATGGTTATAT
1 GAAATGTTTATAT
10935786 GAAATGTTTATA
1 GAAATGTTTATA
10935798 AGGATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (13 bp):
GAAATGTTTATAT
Found at i:10935779 original size:26 final size:26
Alignment explanation
Indices: 10935736--10935795 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
10935726 AATTATATGT
* **
10935736 AATGTGTAAGTGTTATGGTAACAAGA
1 AATGTTTAAGTGAAATGGTAACAAGA
* * *
10935762 AATGTTTAAGTGAAATGGTTATATGA
1 AATGTTTAAGTGAAATGGTAACAAGA
10935788 AATGTTTA
1 AATGTTTA
10935796 TAAGGATATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
AATGTTTAAGTGAAATGGTAACAAGA
Found at i:10936586 original size:13 final size:13
Alignment explanation
Indices: 10936568--10936597 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
10936558 TATTGATTAG
10936568 TTGAAATGACATT
1 TTGAAATGACATT
10936581 TTGAAATGACATT
1 TTGAAATGACATT
10936594 TTGA
1 TTGA
10936598 TGTGTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGAAATGACATT
Found at i:10942335 original size:81 final size:79
Alignment explanation
Indices: 10942224--10942542 Score: 422
Period size: 81 Copynumber: 4.0 Consensus size: 79
10942214 GGTATAACAG
* *
10942224 TCATTTTACCCTATAGGGGTATTTTAGTCATTTTACCCTATGGGTGTATTTTGGTCATTTTATCC
1 TCATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGGG-GTATTTTGGTCATTTTACCC
10942289 TATAGGGGTATTTCGA
64 TATAGGGGTATTTCGA
* * * *
10942305 TCATTTTACCCTATGGGGTTATTTTGGTCATTTTACCCTATGGGGTTATTTTAGTTATTTTAACA
1 TCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCCTATGGGG-TATTTTGGTCATTTTACCC
* *
10942370 TATGGGGGTATTTCGG
64 TATAGGGGTATTTCGA
* *
10942386 TCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCCTATGAGGGTATTTCGATCATTTTACCC
1 TCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCCTATG-GGGTATTTTGGTCATTTTACCC
* *
10942451 TGTGGGGGTATTTCGA
64 TATAGGGGTATTTCGA
* * * * *
10942467 TCATTTTACCCTATGAGGTATTTCGGTTATTTTACCCTATGAGGTATTTTGGTTATTTTACCCTA
1 TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTA
*
10942532 TAAGGGTATTT
66 TAGGGGTATTT
10942543 TGGTTATTAT
Statistics
Matches: 209, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
79 28 0.13
80 28 0.13
81 147 0.70
82 6 0.03
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.45
Consensus pattern (79 bp):
TCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTA
TAGGGGTATTTCGA
Found at i:10942547 original size:27 final size:27
Alignment explanation
Indices: 10942223--10942555 Score: 382
Period size: 27 Copynumber: 12.4 Consensus size: 27
10942213 GGGTATAACA
* *
10942223 GTCATTTTACCCTATAGGGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
*
10942250 GTCATTTTACCCTATGGGTGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
10942277 GTCATTTTATCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
10942304 ATCATTTTACCCTATGGGGTTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
10942331 GTCATTTTACCCTATGGGGTTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTTG
* * * *
10942358 GTTATTTTAACATATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
*
10942385 GTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
10942412 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
10942439 ATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* * *
10942466 ATCATTTTACCCTAT-GAGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
10942492 GTTATTTTACCCTAT-GAGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* **
10942518 GTTATTTTACCCTATAAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTG
* *
10942545 GTTATTATACC
1 GTCATTTTACC
10942556 TATTTTGGGG
Statistics
Matches: 268, Mismatches: 37, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 48 0.18
27 220 0.82
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTTG
Found at i:10945257 original size:17 final size:18
Alignment explanation
Indices: 10945224--10945258 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10945214 GGTTATCAAA
10945224 TATTTTGTTCATTTTTTT
1 TATTTTGTTCATTTTTTT
*
10945242 TATTTT-TTCCTTTTTTT
1 TATTTTGTTCATTTTTTT
10945259 ACTTTTCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (18 bp):
TATTTTGTTCATTTTTTT
Found at i:10951766 original size:7 final size:7
Alignment explanation
Indices: 10951749--10951789 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
10951739 AGCTTCAGTG
10951749 GGGTATTA
1 GGGT-TTA
10951757 GGGTTTA
1 GGGTTTA
10951764 GGGTTTA
1 GGGTTTA
10951771 GGGTTTA
1 GGGTTTA
*
10951778 AGGTTTA
1 GGGTTTA
*
10951785 AGGTT
1 GGGTT
10951790 CAGTGGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 28 0.88
8 4 0.12
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:10954642 original size:22 final size:22
Alignment explanation
Indices: 10954577--10954643 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
10954567 TTTATTGTTC
*
10954577 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
10954599 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
10954621 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
10954643 A
1 A
10954644 TAGGTTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:10958337 original size:18 final size:18
Alignment explanation
Indices: 10958298--10958393 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 18
10958288 AATTAGAAAA
**
10958298 AAAAATAT-AAAAATCAT
1 AAAAATATAAAAAATTGT
10958315 AAAAAATATAAAAAATTGT
1 -AAAAATATAAAAAATTGT
* * * *
10958334 AAAATTTTATAAAATCGT
1 AAAAATATAAAAAATTGT
* *
10958352 AAAAAATTTAAAAAAATATGG
1 -AAAAATAT-AAAAAAT-TGT
*
10958373 AAAAATA-AAAAAATTAT
1 AAAAATATAAAAAATTGT
10958390 AAAA
1 AAAA
10958394 TTTTATAAAG
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
17 5 0.08
18 29 0.48
19 14 0.23
20 12 0.20
21 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAAATTGT
Found at i:10958366 original size:56 final size:55
Alignment explanation
Indices: 10958297--10958440 Score: 166
Period size: 56 Copynumber: 2.5 Consensus size: 55
10958287 AAATTAGAAA
* *
10958297 AAAAAATAT-AAAAATCATAAAAAATATAAAAAATTGTAAAATTTTATAAAATCGT
1 AAAAAATTTAAAAAAT-ATAAAAAATATAAAAAATTATAAAATTTTATAAAATCGT
* *
10958352 AAAAAATTTAAAAAAATATGGAAAAATA-AAAAAATTATAAAATTTTATAAAGTCGT
1 AAAAAATTT-AAAAAATAT-AAAAAATATAAAAAATTATAAAATTTTATAAAATCGT
* *
10958408 AAGAAAATTATACAAAATGTAAAGAAATATAAA
1 AA-AAAATT-TAAAAAATATAAA-AAATATAAA
10958441 TTTTGTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
55 8 0.11
56 32 0.43
57 31 0.41
58 4 0.05
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (55 bp):
AAAAAATTTAAAAAATATAAAAAATATAAAAAATTATAAAATTTTATAAAATCGT
Found at i:10958393 original size:10 final size:10
Alignment explanation
Indices: 10958286--10958393 Score: 57
Period size: 10 Copynumber: 11.2 Consensus size: 10
10958276 CAAATTTATT
*
10958286 AAAATTAGAA
1 AAAATTATAA
**
10958296 AAAAAAATATA
1 AAAATTATA-A
*
10958307 AAAATCATAA
1 AAAATTATAA
10958317 AAAA-TATAA
1 AAAATTATAA
*
10958326 AAAATTGT--
1 AAAATTATAA
* *
10958334 AAAATTTTAT
1 AAAATTATAA
**
10958344 AAAATCGTAA
1 AAAATTATAA
10958354 AAAATT-TAA
1 AAAATTATAA
* *
10958363 AAAAATATGGA
1 AAAATTAT-AA
10958374 AAAA-TA-AA
1 AAAATTATAA
10958382 AAAATTATAA
1 AAAATTATAA
10958392 AA
1 AA
10958394 TTTTATAAAG
Statistics
Matches: 75, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
8 12 0.16
9 18 0.24
10 32 0.43
11 13 0.17
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.25
Consensus pattern (10 bp):
AAAATTATAA
Found at i:10958632 original size:19 final size:19
Alignment explanation
Indices: 10958610--10958700 Score: 64
Period size: 19 Copynumber: 4.9 Consensus size: 19
10958600 TTTTTTTATG
10958610 ATTTTTATAAAATTTTACA
1 ATTTTTATAAAATTTTACA
* * **
10958629 ATTTTTTTTATTTTTTACA
1 ATTTTTATAAAATTTTACA
* *
10958648 GTTTTTATAAAAATTT-CTA
1 ATTTTTATAAAATTTTAC-A
*
10958667 ATTTTTA-ATCAATTTTA-A
1 ATTTTTATA-AAATTTTACA
*
10958685 ATTTTT-TAAATTTTTA
1 ATTTTTATAAAATTTTA
10958701 TTAAATTTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.11
18 10 0.19
19 37 0.70
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAAATTTTACA
Found at i:10958696 original size:27 final size:28
Alignment explanation
Indices: 10958666--10958718 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
10958656 AAAAATTTCT
* *
10958666 AATTTTTAATCAATTTTA-AATTTTTTA
1 AATTTTTAATAAATTTAATAATTTTTTA
*
10958693 AATTTTTATTAAATTTAATAATTTTT
1 AATTTTTAATAAATTTAATAATTTTT
10958719 CCAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
AATTTTTAATAAATTTAATAATTTTTTA
Found at i:10958718 original size:20 final size:20
Alignment explanation
Indices: 10958681--10958718 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10958671 TTAATCAATT
**
10958681 TTAAATTTTTTAAATTTTTA
1 TTAAATTTAATAAATTTTTA
10958701 TTAAATTTAAT-AATTTTT
1 TTAAATTTAATAAATTTTT
10958719 CCAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAAATTTAATAAATTTTTA
Found at i:10958942 original size:90 final size:88
Alignment explanation
Indices: 10958775--10958975 Score: 210
Period size: 90 Copynumber: 2.2 Consensus size: 88
10958765 TAATAAGAGT
* *
10958775 AGGGGCTTAATTGC-TTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTGAAAGTTCAAT
1 AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTAAAAGTTCAAG
*
10958839 TACCCAATTGAGTG-AAAAAAAG
66 TACCAAATTGAGTGAAAAAAAAG
* * * * *
10958861 CAGGGGCTTAATTGCTTTTTTTG-AAGAAGTTTAAGGGGTTTTTTTTTGATGTATTTTAAAAGTT
1 -AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAA--GG-ATCTTTTTGATGCATTTTAAAAGTT
***
10958925 CAAGTGTTAAATTGAGTGCAAAAAAAAAG
62 CAAGTACCAAATTGAGTG--AAAAAAAAG
*
10958954 AGGGGCTTAATTGTATTTTTTT
1 AGGGGCTTAATTG-CTTTTTTT
10958976 TTAAATTGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
87 23 0.24
88 7 0.07
89 2 0.02
90 34 0.36
92 13 0.14
93 15 0.16
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.40
Consensus pattern (88 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAAAATTTAAGGATCTTTTTGATGCATTTTAAAAGTTCAAG
TACCAAATTGAGTGAAAAAAAAG
Found at i:10960497 original size:2 final size:2
Alignment explanation
Indices: 10960490--10960515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10960480 CATTATACAA
10960490 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
10960516 GTAATACAAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10966753 original size:361 final size:362
Alignment explanation
Indices: 10966074--10967174 Score: 1582
Period size: 361 Copynumber: 3.0 Consensus size: 362
10966064 GAGTTTAAAT
** *
10966074 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCCATGGTTAGTGTTGTTTGGACTGGTAGTTGTAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * *
10966139 GGTCATCTAGATGGCAAAATTTAACTATCCATATAGAAGGCAAATTGTCTTAAGAGATGTGCTTT
66 GGCCATCTAGATGGCAGAATTTAGCTATCC-------AGG-AAATTGTCTTAAGAGATGTGCTTT
* * *
10966204 TGCCAAAATGTCATATGAGGGGGAGGGGGGATTAGCCACCTAAATTGCATCAGGATTGCTTTAAC
123 TGCCAAAACGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAAC
*
10966269 ATATGTAAAATTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
188 ATATGTAAAAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
* * * *
10966334 CAAACACGTAGCGGGCGATTTGATATG-GTTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGA
253 CAAACACTTAGAGGGTGATTTGATGTGAG-TTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGA
* *
10966398 ATTTGTTTTTCTGATATTTTTATTAAATTATTTTAAAAATGTATTA
317 ATTTGTTTTTATGATATTTTTATTAAATGATTTTAAAAATGTATTA
* *
10966444 AAGCTTTGAAAATGTTTTAAAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGCAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * *
10966509 GGCCATCTAAATGGTAGAATTTAGCTATCCA-GAAATTGTCTTAAGAGATGTACTTTTGCCAAAA
66 GGCCATCTAGATGGCAGAATTTAGCTATCCAGGAAATTGTCTTAAGAGATGTGCTTTTGCCAAAA
** * * * * *
10966573 CGTCATTTGAACGGGAGGGGGGAATAGTCACGTAAATTGCATCAAGATTGCTTCAACGTATGTAA
131 CGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAACATATGTAA
*
10966638 AAGTGTGTTAATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATCCAAACACT
196 AAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATCCAAACACT
*
10966703 TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTGGAAAAGGTTGGAATTTGTTTT
261 TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAATTTGTTTT
10966768 TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
326 TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
*
10966805 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGTTGGTAGTTGTAG
1 AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
* * * * *
10966870 GGCCATCTAGATGGCGGAGTTTAGCTATCTAGATGGAGGGCATATTGTCTTCAGAAATGTGCTTT
66 GGCCATCTAGATGGCAGAATTTAGCTATC--CA-GGA----A-ATTGTCTTAAGAGATGTGCTTT
* * * * *
10966935 TACCAAAACGTCATTTG-GGGGGAGGGGGGAATAACCACTTGAATTGCATCAGGATTGTTTTAAC
123 TGCCAAAACGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAAC
* * *
10966999 ATATGTAAAAGTGTGTTGATTGTATTTTAATTTATCGGATGTCCATTTTATGTAATTGTCATATC
188 ATATGTAAAAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATC
* *
10967064 CAAACACTT--AGGGTGATTTGATGTGATTTTTAAAATGTCTTTGAGCCTTAGAAAATGTTGGAA
253 CAAACACTTAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAA
* *
10967127 TTTATTTTTATGATATTTTTATTAAATGATTTTAAAACTGTATTA
318 TTTGTTTTTATGATATTTTTATTAAATGATTTTAAAAATGTATTA
10967172 AAG
1 AAG
10967175 TTGTTTAAAT
Statistics
Matches: 660, Mismatches: 61, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
361 329 0.50
362 2 0.00
363 2 0.00
365 2 0.00
367 97 0.15
369 108 0.16
370 120 0.18
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (362 bp):
AAGCTTTGAAAATGTTTTAGAAATGAAGTGTCTTTGGTTAGTGTTGTTTGGGCTGGTAGTTGTAG
GGCCATCTAGATGGCAGAATTTAGCTATCCAGGAAATTGTCTTAAGAGATGTGCTTTTGCCAAAA
CGTCATTTGAGGGGGAGGGGGGAATAGCCACCTAAATTGCATCAGGATTGCTTTAACATATGTAA
AAGTGTGTTGATTGCATTTTAATTTATCGAAAGTCCATTTTATGTAATTGTCATATCCAAACACT
TAGAGGGTGATTTGATGTGAGTTTTAAAATGTCTTTGAGCCTTAGAAAAGGTTGGAATTTGTTTT
TATGATATTTTTATTAAATGATTTTAAAAATGTATTA
Found at i:10969241 original size:25 final size:25
Alignment explanation
Indices: 10969203--10969250 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
10969193 CCAATATCGC
*
10969203 AGCAAGGCTACCAGCAACAGTATTG
1 AGCAAAGCTACCAGCAACAGTATTG
* * *
10969228 AGCAAAGCTGCCAGTAATAGTAT
1 AGCAAAGCTACCAGCAACAGTAT
10969251 ACTTCCTCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (25 bp):
AGCAAAGCTACCAGCAACAGTATTG
Found at i:10969441 original size:27 final size:27
Alignment explanation
Indices: 10969411--10969550 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 27
10969401 AGAATAACAG
10969411 TCATTTTACCCTATGGGGGTATTTTGA
1 TCATTTTACCCTATGGGGGTATTTTGA
* ** * *
10969438 TCATTTTACTCTATAAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTTGA
* *
10969465 TCATTTTATCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTTGA
*
10969492 TCATTTTACCCTGTGGGGGTATTTT-A
1 TCATTTTACCCTATGGGGGTATTTTGA
*
10969518 GTCATTTTACCCTATGGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTTGA
10969546 TCATT
1 TCATT
10969551 CATTGACCTC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
27 95 0.99
28 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTTGA
Found at i:10969478 original size:54 final size:54
Alignment explanation
Indices: 10969408--10969550 Score: 205
Period size: 54 Copynumber: 2.6 Consensus size: 54
10969398 AGGAGAATAA
*
10969408 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACTCTATAAGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
* * * * **
10969462 CGGTCATTTTATCCTATGGGGGTATTTTGGTCATTTTACCCTGTGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
* *
10969516 TAGTCATTTTACCCTATGGGGGTATTTCGATCATT
1 CAGTCATTTTACCCTATGGGGGTATTTTGATCATT
10969551 CATTGACCTC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.44
Consensus pattern (54 bp):
CAGTCATTTTACCCTATGGGGGTATTTTGATCATTTTACCCTATAAGGGTATTT
Found at i:10971392 original size:37 final size:37
Alignment explanation
Indices: 10971342--10971438 Score: 167
Period size: 37 Copynumber: 2.6 Consensus size: 37
10971332 CTGTTTCAAT
* *
10971342 GTTGCGAGCTTAACTTAGCTAACTCAAATAATTTGAG
1 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
10971379 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
1 GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
*
10971416 GTTGCGAGCTTAACTCAACTAAC
1 GTTGCGAGCTTAACTCAGCTAAC
10971439 CTTTAATCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (37 bp):
GTTGCGAGCTTAACTCAGCTAACTCAAATAATTGGAG
Found at i:10981480 original size:3 final size:3
Alignment explanation
Indices: 10981472--10981498 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10981462 ATCTATCCTT
10981472 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
10981499 CAAGTTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10981535 original size:65 final size:65
Alignment explanation
Indices: 10981431--10981562 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
10981421 GTGTTTTTGG
10981431 TTACAAGTTAACCGAGAGTTCCTTACGGCAAATCTATCCTTTTATTATTATTATTATTATTATTA
1 TTACAAGTTAACCGAGAGTTCCTTACGGCAAATCTATCCTTTTATTATTATTATTATTATTATTA
10981496 TTACAAGTTAACCGAGAGTTCCTTACGGCAAATCTATCCTTTTATTATTATTATTATTATTATTA
1 TTACAAGTTAACCGAGAGTTCCTTACGGCAAATCTATCCTTTTATTATTATTATTATTATTATTA
10981561 TT
1 TT
10981563 TAACTAATTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (65 bp):
TTACAAGTTAACCGAGAGTTCCTTACGGCAAATCTATCCTTTTATTATTATTATTATTATTATTA
Found at i:10981545 original size:3 final size:3
Alignment explanation
Indices: 10981537--10981562 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10981527 ATCTATCCTT
10981537 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
10981563 TAACTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:10987368 original size:31 final size:31
Alignment explanation
Indices: 10987330--10987390 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
10987320 AGATAATTTT
* *
10987330 AAAGAGTTTTGTTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTACGATTCAATTACTCTTG
10987361 AAAGAGTTTTATTACGATTCAATTACTCTT
1 AAAGAGTTTTATTACGATTCAATTACTCTT
10987391 CTAATTTGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (31 bp):
AAAGAGTTTTATTACGATTCAATTACTCTTG
Found at i:10998943 original size:31 final size:31
Alignment explanation
Indices: 10998869--10998943 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
10998859 TTCTTTAAAG
* * *
10998869 GTGTATGATTGAATCAAAATTAAAATTTTAT
1 GTGTATAATTGAACCAAAATCAAAATTTTAT
* * * *
10998900 GTATACATTTGAACCACAATCAAAATTTTAT
1 GTGTATAATTGAACCAAAATCAAAATTTTAT
10998931 GTGTATAATTGAA
1 GTGTATAATTGAA
10998944 TTGAACCAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (31 bp):
GTGTATAATTGAACCAAAATCAAAATTTTAT
Found at i:11004950 original size:17 final size:17
Alignment explanation
Indices: 11004928--11004960 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11004918 TCTCAGATTT
*
11004928 TGATACTCATATCTTTC
1 TGATACCCATATCTTTC
11004945 TGATACCCATATCTTT
1 TGATACCCATATCTTT
11004961 GACTTTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:11006040 original size:31 final size:32
Alignment explanation
Indices: 11006002--11006064 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
11005992 AGGCAAATTA
*
11006002 CAAGAGTAATTG-AATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
11006033 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
1 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
11006065 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAAATCCTAATAAAAATCTTT
Found at i:11010610 original size:13 final size:13
Alignment explanation
Indices: 11010592--11010621 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11010582 GGTAGGCAAC
*
11010592 TTTTTTTTGCGGT
1 TTTTTTTTGCGCT
11010605 TTTTTTTTGCGCT
1 TTTTTTTTGCGCT
11010618 TTTT
1 TTTT
11010622 GCTCTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.17, T:0.73
Consensus pattern (13 bp):
TTTTTTTTGCGCT
Found at i:11011253 original size:31 final size:32
Alignment explanation
Indices: 11011215--11011277 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
11011205 AGGCAAATTA
*
11011215 CAAGAGTAATTG-AATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
11011246 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
1 CAAGAGTAATTGAAATCCTAATAAAAATCTTT
11011278 AAAATTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAAATCCTAATAAAAATCTTT
Found at i:11013101 original size:23 final size:23
Alignment explanation
Indices: 11013075--11013118 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
11013065 GCACGCCTCA
*
11013075 ACCTTTTTTTTTCCTTTCTTCCC
1 ACCTTTTTTATTCCTTTCTTCCC
11013098 ACCTTTTTTATTCCTTTCTTC
1 ACCTTTTTTATTCCTTTCTTC
11013119 TTTCTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (23 bp):
ACCTTTTTTATTCCTTTCTTCCC
Found at i:11015589 original size:26 final size:27
Alignment explanation
Indices: 11015509--11015591 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 27
11015499 GTTTTGATAG
11015509 TTGTAAATTTGATAAGTTATATCATAT
1 TTGTAAATTTGATAAGTTATATCATAT
*
11015536 TTGTAATTTTGA-AA-TTATAT-ATAT
1 TTGTAAATTTGATAAGTTATATCATAT
11015560 TTGTAAATTTGATAAGTTATATCATA-
1 TTGTAAATTTGATAAGTTATATCATAT
11015586 TTGTAA
1 TTGTAA
11015592 TTATGAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.29
25 8 0.16
26 14 0.27
27 14 0.27
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.49
Consensus pattern (27 bp):
TTGTAAATTTGATAAGTTATATCATAT
Found at i:11015606 original size:26 final size:24
Alignment explanation
Indices: 11015509--11015607 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 24
11015499 GTTTTGATAG
*
11015509 TTGTAAATTTGATAAGTTATATCATA
1 TTGT-AATTTGA-AATTTATATCATA
11015535 TTTGTAATTTTGAAA-TTATAT-ATA
1 -TTGTAA-TTTGAAATTTATATCATA
*
11015559 TTTGTAAATTTGATAAGTTATATCATA
1 -TTGT-AATTTGA-AATTTATATCATA
11015586 TTGTAATTATGAAATTGTATAT
1 TTGTAATT-TGAAATT-TATAT
11015608 ATTTGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
24 13 0.20
25 17 0.27
26 22 0.34
27 12 0.19
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.49
Consensus pattern (24 bp):
TTGTAATTTGAAATTTATATCATA
Found at i:11015611 original size:50 final size:51
Alignment explanation
Indices: 11015509--11015613 Score: 185
Period size: 50 Copynumber: 2.1 Consensus size: 51
11015499 GTTTTGATAG
*
11015509 TTGTAAATTTGATAAGTTATATCATATTTGTAATTTTGAAATTATATATAT
1 TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
*
11015560 TTGTAAATTTGATAAGTTATATCATA-TTGTAATTATGAAATTGTATATAT
1 TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
11015610 TTGT
1 TTGT
11015614 TGAAGAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 26 0.50
51 26 0.50
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (51 bp):
TTGTAAATTTGATAAGTTATATCATATTTGTAATTATGAAATTATATATAT
Found at i:11022618 original size:12 final size:11
Alignment explanation
Indices: 11022597--11022711 Score: 70
Period size: 11 Copynumber: 11.1 Consensus size: 11
11022587 AATTAAAAAG
11022597 AATATTTTAAA
1 AATATTTTAAA
*
11022608 AATATTTT--T
1 AATATTTTAAA
11022617 AA-A--TTAAA
1 AATATTTTAAA
*
11022625 AAAATTTTACAA
1 AATATTTTA-AA
*
11022637 AGTATTTTAAA
1 AATATTTTAAA
11022648 AATATTTT--A
1 AATATTTTAAA
11022657 AA-A--TTAAA
1 AATATTTTAAA
* *
11022665 AAAATTTAAAAA
1 AATATTT-TAAA
11022677 AAGTATTTTAAA
1 AA-TATTTTAAA
*
11022689 AGTATTTTAAA
1 AATATTTTAAA
*
11022700 AGTATTTTAAA
1 AATATTTTAAA
11022711 A
1 A
11022712 TTAAAAAATA
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
6 4 0.05
8 7 0.09
9 7 0.09
11 42 0.51
12 18 0.22
13 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (11 bp):
AATATTTTAAA
Found at i:11022630 original size:40 final size:41
Alignment explanation
Indices: 11022589--11022700 Score: 158
Period size: 40 Copynumber: 2.8 Consensus size: 41
11022579 ATTTCACAAA
*
11022589 TTAAAAAGAATATTTTAAAAATATTTTTAAATTAAAAAAATT
1 TTAAAAAGAATATTTTAAAAATATTTTAAAATTAAAAAAA-T
*
11022631 TTACAAAG--TATTTTAAAAATATTTTAAAATTAAAAAAAT
1 TTAAAAAGAATATTTTAAAAATATTTTAAAATTAAAAAAAT
*
11022670 TTAAAAA-AAGTATTTTAAAAGTATTTTAAAA
1 TTAAAAAGAA-TATTTTAAAAATATTTTAAAA
11022701 GTATTTTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
39 7 0.11
40 29 0.46
41 20 0.32
42 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (41 bp):
TTAAAAAGAATATTTTAAAAATATTTTAAAATTAAAAAAAT
Found at i:11022736 original size:52 final size:53
Alignment explanation
Indices: 11022622--11022736 Score: 164
Period size: 52 Copynumber: 2.2 Consensus size: 53
11022612 TTTTTAAATT
**
11022622 AAAAAA-ATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTTAA
1 AAAAAATATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
* *
11022674 AAAAAGTATTTTA-AAAGTATTTTAAAAGTATTTTAAAATT-AAAAAATAAAA
1 AAAAAATATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
11022725 AATAAAATATTT
1 AA-AAAATATTT
11022737 ATTATTAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
51 11 0.20
52 39 0.70
53 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (53 bp):
AAAAAATATTTTACAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATAAAA
Found at i:11024103 original size:3 final size:3
Alignment explanation
Indices: 11024095--11024120 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11024085 CTGTTGTCAT
11024095 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
11024121 TCATCATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:11024188 original size:3 final size:3
Alignment explanation
Indices: 11024182--11024212 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11024172 CCACCACCAC
*
11024182 CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
11024213 GTTGCCGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:11024252 original size:66 final size:66
Alignment explanation
Indices: 11024057--11024253 Score: 342
Period size: 66 Copynumber: 3.0 Consensus size: 66
11024047 ACATTCTAGA
* * *
11024057 ATCATCATCATCACCATCATCATCGTCT-CTGTTGTCATCACCACCACCACCACCACCACCACCA
1 ATCATCATCATCACCATCATCATCGT-TGCCGATGTCATCACCACCACCACCACCACCACCATCA
11024121 TC
65 TC
11024123 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
1 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
11024188 C
66 C
*
11024189 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCATCATCAT
1 ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
11024254 TTGCTTGTAT
Statistics
Matches: 126, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
65 1 0.01
66 125 0.99
ACGTcount: A:0.28, C:0.44, G:0.06, T:0.22
Consensus pattern (66 bp):
ATCATCATCATCACCATCATCATCGTTGCCGATGTCATCACCACCACCACCACCACCACCATCAT
C
Found at i:11026506 original size:21 final size:21
Alignment explanation
Indices: 11026397--11026506 Score: 96
Period size: 21 Copynumber: 5.2 Consensus size: 21
11026387 TAATAGCATG
* * *
11026397 GGTTTGTACATAGTATAACAT
1 GGTTTGCATATAGTATAACAA
** *
11026418 GGTTCACATATAGTATAATAA
1 GGTTTGCATATAGTATAACAA
*
11026439 GGTTCT-CATATAGTATAATAA
1 GGTT-TGCATATAGTATAACAA
* * *
11026460 GTTTTGCATATAATATAACAT
1 GGTTTGCATATAGTATAACAA
* *
11026481 GGTTTGCATATGGTATAACAG
1 GGTTTGCATATAGTATAACAA
11026502 GGTTT
1 GGTTT
11026507 TTAGAATACA
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 71 0.99
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (21 bp):
GGTTTGCATATAGTATAACAA
Found at i:11027889 original size:21 final size:21
Alignment explanation
Indices: 11027863--11027902 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11027853 TGCATTTGAA
* *
11027863 ACAAAAGGGTGTGGTACCTAG
1 ACAAAAAGGTGTGATACCTAG
11027884 ACAAAAAGGTGTGATACCT
1 ACAAAAAGGTGTGATACCT
11027903 CTATGTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
ACAAAAAGGTGTGATACCTAG
Found at i:11042357 original size:5 final size:5
Alignment explanation
Indices: 11042347--11042406 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
11042337 CATTCATTCT
*
11042347 TTTTA TTTTA TTTTA TTTT- TATTTA TTTGA TTATT- TGTTTA TCATTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TT-TTA T-TTTA T--TTTA
11042395 TTTTA TTTTA TT
1 TTTTA TTTTA TT
11042407 CCTTTATTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 1 0.02
5 36 0.78
6 4 0.09
7 5 0.11
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:11042373 original size:20 final size:22
Alignment explanation
Indices: 11042348--11042406 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
11042338 ATTCATTCTT
11042348 TTTATTTTATTTTATTTT-T-A
1 TTTATTTTATTTTATTTTATCA
*
11042368 TTTATTTGATTATT-TGTTTATCA
1 TTTATTTTATT-TTAT-TTTATCA
11042391 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
11042407 CCTTTATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 4 0.12
23 12 0.38
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTATTTTATTTTATTTTATCA
Found at i:11051457 original size:31 final size:31
Alignment explanation
Indices: 11051422--11051526 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
11051412 AACATTAAAT
*
11051422 TTAATTTAATATTTATCTTGATAATATTTTC
1 TTAATTTAATATTTATCTTGATAATATTTTA
* * * **
11051453 TTAATTTAATATTAAT-GTGA-GATATTAAA
1 TTAATTTAATATTTATCTTGATAATATTTTA
* *
11051482 TGTGATTTAATATTTATCTTGATAGTATTTTA
1 T-TAATTTAATATTTATCTTGATAATATTTTA
11051514 TTAATTTAATATT
1 TTAATTTAATATT
11051527 ATGTGAATAA
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
29 6 0.11
30 16 0.28
31 29 0.51
32 6 0.11
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTTGATAATATTTTA
Found at i:11051493 original size:61 final size:60
Alignment explanation
Indices: 11051415--11051532 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 60
11051405 CAAATTTAAC
* *
11051415 ATTAAATTTAATTTAATATTTATCTTGATAATATTTTCTTAATTTAATATTAATGTGAGAT
1 ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATT-ATGTGAGAT
* *
11051476 ATTAAATGTGATTTAATATTTATCTTGATAGTATTTTATTAATTTAATATTATGTGA
1 ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTATGTGA
11051533 ATAATTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 6 0.11
61 47 0.89
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (60 bp):
ATTAAATGTAATTTAATATTTATCTTGATAATATTTTATTAATTTAATATTATGTGAGAT
Found at i:11054005 original size:274 final size:274
Alignment explanation
Indices: 11053505--11054054 Score: 1010
Period size: 274 Copynumber: 2.0 Consensus size: 274
11053495 TTTTATATGG
* *
11053505 ATTTTACTTATGCAGCCTATACCGTACCGCTAGGCCCAGAGGTCTCCGCACCCCTAGTTACAACC
1 ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
*
11053570 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGTAACCTTTGCCCTCATAGATCCCC
66 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
* *
11053635 TTTCTTGCCTATTGTATTTTATTTTAACATGAATTTGGGTTACACAATTTCTAACATAAACCATA
131 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
* *
11053700 CATTCAACTTAGGAAATTGCATCATAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
196 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
*
11053765 AAAACTTTCCAAAT
261 AAAACTTGCCAAAT
*
11053779 ATTTTGCTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
1 ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
*
11053844 CTAGTCCAATATTTTGCTTATTATGGATCTACGATGGACTGCAACCTTTGCCCTCATAGATCCCC
66 CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
11053909 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
131 TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
11053974 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
196 CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
11054039 AAAACTTGCCAAAT
261 AAAACTTGCCAAAT
11054053 AT
1 AT
11054055 ACTCAACATA
Statistics
Matches: 266, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
274 266 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (274 bp):
ATTTTACTTATGCAGCCTATACCGTACCGCAAGGCCCAGAGGTCCCCGCACCCCTAGTTACAACC
CTAGTCCAATATTTTGCTTATTATGGATCTAAGATGGACTGCAACCTTTGCCCTCATAGATCCCC
TATCTTGCCTATTGTATTTTATTTTAACAGGAATTTGGGTTACACAATTTCTAACATAAACCATA
CATTAAACTTAGGAAATTGCATCACAAATCCAAATCAAAAGTATTTCAAAGTCCCAAAATAAGCC
AAAACTTGCCAAAT
Found at i:11056028 original size:18 final size:18
Alignment explanation
Indices: 11055996--11056042 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
11055986 CTTCATGTTA
*
11055996 ATTTTTTAAAATTTTAAT
1 ATTTTTTAAATTTTTAAT
* *
11056014 TTTTTTTAAATTTTTTAT
1 ATTTTTTAAATTTTTAAT
*
11056032 AATTTTTAAAT
1 ATTTTTTAAAT
11056043 ATTTGATGAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTAAATTTTTAAT
Found at i:11057074 original size:19 final size:20
Alignment explanation
Indices: 11057042--11057080 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11057032 TACTCTTAAA
* *
11057042 AAAGAATTAGAATATAATTT
1 AAAGAATTAAAATAGAATTT
11057062 AAAG-ATTAAAATAGAATTT
1 AAAGAATTAAAATAGAATTT
11057081 TTTTTGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAGAATTAAAATAGAATTT
Found at i:11057652 original size:30 final size:30
Alignment explanation
Indices: 11057618--11057680 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
11057608 GCATTTTTCC
*
11057618 TTTCTCATATCA-ACAC-TTTCTTTCTTTCTT
1 TTTCTCAT-TCACACACATGTC-TTCTTTCTT
11057648 TTTCTCATTCACTACACATGTCTTCTTTCTT
1 TTTCTCATTCAC-ACACATGTCTTCTTTCTT
11057679 TT
1 TT
11057681 CCATTTGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 8 0.28
31 15 0.52
32 3 0.10
ACGTcount: A:0.16, C:0.27, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTCTCATTCACACACATGTCTTCTTTCTT
Found at i:11064405 original size:14 final size:14
Alignment explanation
Indices: 11064386--11064425 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11064376 TTGATTGCCA
11064386 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
11064400 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
11064414 GGAAAATGTTTT
1 GTAAAATGTTTT
11064426 ACATTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:11064433 original size:20 final size:20
Alignment explanation
Indices: 11064408--11064447 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11064398 CCGTAAAATG
*
11064408 ATTTCTGGAAAATGTTTTAC
1 ATTTCTGGAAAATGATTTAC
*
11064428 ATTTCTGTAAAATGATTTAC
1 ATTTCTGGAAAATGATTTAC
11064448 TGGAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTTCTGGAAAATGATTTAC
Found at i:11064443 original size:34 final size:35
Alignment explanation
Indices: 11064395--11064460 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
11064385 AGTAAAATGT
*
11064395 TTTCCGTAAAATGATTT-CTGGAAAATGTTTTACA
1 TTTCCGTAAAATGATTTACTGGAAAATATTTTACA
*
11064429 TTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTCCGTAAAATGATTTACTGGAAAATATTTT
11064461 CTGATGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (35 bp):
TTTCCGTAAAATGATTTACTGGAAAATATTTTACA
Found at i:11065284 original size:47 final size:47
Alignment explanation
Indices: 11065215--11065307 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
11065205 TGGAGTGAAT
11065215 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
1 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
11065262 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAG
1 CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAG
11065308 TTCAGACAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.24
Consensus pattern (47 bp):
CCCTTGCGATTAGTGGCTCTCACTGAAACTCCTGATGAAAGCAGAGC
Found at i:11072750 original size:20 final size:20
Alignment explanation
Indices: 11072725--11072768 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
11072715 CTAAACTTTT
11072725 AATCCAACACTTTACAATTC
1 AATCCAACACTTTACAATTC
*
11072745 AATCCAACACTTTACAATTG
1 AATCCAACACTTTACAATTC
11072765 AATC
1 AATC
11072769 AAACCCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.30
Consensus pattern (20 bp):
AATCCAACACTTTACAATTC
Found at i:11072850 original size:17 final size:17
Alignment explanation
Indices: 11072828--11072860 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11072818 TTTAAATAAA
11072828 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
11072845 TAAATAAATTTCTCAA
1 TAAATAAATTTCTCAA
11072861 CCCAATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:11074971 original size:21 final size:22
Alignment explanation
Indices: 11074947--11074987 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
11074937 CTATTAATTA
11074947 ATTTATTATTGTT-TTATTACT
1 ATTTATTATTGTTATTATTACT
11074968 ATTTATTATTGTTATTATTA
1 ATTTATTATTGTTATTATTA
11074988 TACTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (22 bp):
ATTTATTATTGTTATTATTACT
Found at i:11080583 original size:21 final size:21
Alignment explanation
Indices: 11080559--11080604 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11080549 ATTATGTTCA
*
11080559 AAAACGAAAA-GATGAAAAATG
1 AAAACGAAAATGA-AAAAAATG
*
11080580 AAAATGAAAATGAAAAAAATG
1 AAAACGAAAATGAAAAAAATG
11080601 AAAA
1 AAAA
11080605 GTAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (21 bp):
AAAACGAAAATGAAAAAAATG
Found at i:11081968 original size:87 final size:87
Alignment explanation
Indices: 11081833--11082423 Score: 879
Period size: 87 Copynumber: 6.9 Consensus size: 87
11081823 AAACGAAACT
* *
11081833 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCAGCATTAACAGT
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
11081898 GAAACAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * *
11081920 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATCTTGCCTTCCTACATTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
11081985 GAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
*
11082007 TTGCCTCCATCGGTTGCA---GAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTACATTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
11082069 AAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * *
11082091 TTGCCTTCATCGGTT---GTAGAGTTGGTTAAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
11082153 GAAGCAGATCGAAAACAAAACC
66 GAAGCAGATCGAAAACAAAGCC
* *
11082175 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGCCTTCCTGCGTTAACAGC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
*
11082240 AAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * * *
11082262 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAACAAATCTTGCCTTCTTGCGTTAACAAC
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
11082327 GAAGCAGATCGAAAACAAAGCC
66 GAAGCAGATCGAAAACAAAGCC
* * * * * ** *
11082349 TTGCCTCCATCGGTTGCAGTGAAGCTTGTTAAAGATAACAGATCTTACCCTCCTGCATCGACAGT
1 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
11082414 GAAGCAGATC
66 GAAGCAGATC
11082424 AAAGATTACA
Statistics
Matches: 460, Mismatches: 38, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
84 153 0.33
87 307 0.67
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (87 bp):
TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGC
GAAGCAGATCGAAAACAAAGCC
Found at i:11081970 original size:44 final size:44
Alignment explanation
Indices: 11081833--11081971 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
11081823 AAACGAAACT
* *
11081833 TTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATC
1 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
* * * * * * * ** * * *
11081877 TTGCCTTCCAGC-ATTAACAGTGAAACAGATCGAAAACA-AAG-CC
1 TTGCCTT-CATCGGTT-GCAGTGGAGCTGGTTAAAAATAGCAGATC
11081920 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
1 TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
11081964 TTGCCTTC
1 TTGCCTTC
11081972 CTACATTAAC
Statistics
Matches: 64, Mismatches: 26, Indels: 10
0.64 0.26 0.10
Matches are distributed among these distances:
42 17 0.27
43 12 0.19
44 19 0.30
45 16 0.25
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
TTGCCTTCATCGGTTGCAGTGGAGCTGGTTAAAAATAGCAGATC
Found at i:11082523 original size:44 final size:44
Alignment explanation
Indices: 11082474--11082682 Score: 142
Period size: 44 Copynumber: 4.8 Consensus size: 44
11082464 GTTGGAAATT
* *
11082474 ACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGTAGACTG-AGAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AA
** *
11082518 ACAAGTCTTATC-CCCTTGAAGTCACAGTGGGGCAGACTGAAGAA
1 ACAAGTCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACTGAAGAA
* * * * * ***
11082562 GCAAATCTTATCTCCCTGAGGTTGCAGTAGAGCAGATTGAATTCG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GAA
* * * * *
11082607 ATAA-TCCTATCTCCCTGAAGTTGTAGTGGAGCGGA-TTAA-AA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA
* * *
11082648 TA-TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
1 -ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA
11082683 TATCGCATCA
Statistics
Matches: 126, Mismatches: 32, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 30 0.24
44 87 0.69
45 7 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAA
Found at i:11088398 original size:41 final size:41
Alignment explanation
Indices: 11088349--11088430 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
11088339 ATGCACATAG
11088349 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
1 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
11088390 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
1 ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
11088431 CATATAGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (41 bp):
ACAAAAATACTACACTTAGGGCACCAGATCTGACACATTCA
Found at i:11094289 original size:27 final size:26
Alignment explanation
Indices: 11094259--11094317 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
11094249 AATTTGGGTT
11094259 ATATTAATGAAA-TATGCCATTTTTTTA
1 ATATTAA-GAAATTA-GCCATTTTTTTA
*
11094286 ATATTTAAGAAATTAGCCCTTTTTTTA
1 ATA-TTAAGAAATTAGCCATTTTTTTA
11094313 ATATT
1 ATATT
11094318 TATTAGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 21 0.72
28 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (26 bp):
ATATTAAGAAATTAGCCATTTTTTTA
Found at i:11095613 original size:35 final size:35
Alignment explanation
Indices: 11095566--11095657 Score: 105
Period size: 35 Copynumber: 2.6 Consensus size: 35
11095556 ACATGCAATT
* * *
11095566 TTATCTCGGGATTCCCAAGTTCCAGTGTTTAAAAA
1 TTATCTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
** * *
11095601 TTATCCTA-GGATTGTCTGGTTCCAGTGTCTAAAAC
1 TTAT-CTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
11095636 TTATCTAGGGATTCCCAGGTTC
1 TTATCTAGGGATTCCCAGGTTC
11095658 TGACAAGGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
34 3 0.07
35 40 0.89
36 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (35 bp):
TTATCTAGGGATTCCCAGGTTCCAGTGTCTAAAAA
Done.