Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 144 of 218
Found at i:43873426 original size:25 final size:25
Alignment explanation
Indices: 43873398--43873487 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
43873388 CAGCTCTTAT
*
43873398 GAGCGTCCCGATATATGGCTCACAC
1 GAGCTTCCCGATATATGGCTCACAC
* * *
43873423 GAGCTTCCTGAT-TAATTGCTCTC-C
1 GAGCTTCCCGATAT-ATGGCTCACAC
* *
43873447 GGAGCTACCCGATAT-TGGCTCACAT
1 -GAGCTTCCCGATATATGGCTCACAC
43873472 GAGCTTCCCGA-ATATG
1 GAGCTTCCCGATATATG
43873488 AATTGACATC
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
23 2 0.04
24 20 0.40
25 27 0.54
26 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (25 bp):
GAGCTTCCCGATATATGGCTCACAC
Found at i:43874520 original size:12 final size:12
Alignment explanation
Indices: 43874511--43874543 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
43874501 TAGCACACAA
43874511 GCTGGGACACGG
1 GCTGGGACACGG
*
43874523 GTTGGGACACGG
1 GCTGGGACACGG
43874535 GCTGGGACA
1 GCTGGGACA
43874544 TGGTCGTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.48, T:0.12
Consensus pattern (12 bp):
GCTGGGACACGG
Found at i:43879743 original size:20 final size:20
Alignment explanation
Indices: 43879707--43879744 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43879697 TTTTTTAAAA
*
43879707 TAAATAAAAAAATTAAAATT
1 TAAATAAAAAAAATAAAATT
43879727 TAAA-AAAAAAACATAAAA
1 TAAATAAAAAAA-ATAAAA
43879745 AAATCAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAATAAAAAAAATAAAATT
Found at i:43880126 original size:42 final size:42
Alignment explanation
Indices: 43880067--43880149 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
43880057 GACCAGAGGC
*
43880067 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGCCAAGGAT
1 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGAT
* * *
43880109 ATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGACAAGGA
1 ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGA
43880150 CATCGCCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (42 bp):
ATGGGCGTGTGCCCAGGCCGTGTAAGCCACACAGACAAGGAT
Found at i:43880799 original size:17 final size:17
Alignment explanation
Indices: 43880759--43880802 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
43880749 GGTTTAGCCT
*
43880759 ACACCCATGTGTTCCAC
1 ACACCCGTGTGTTCCAC
43880776 ACACCCGTGTGTTCCAC
1 ACACCCGTGTGTTCCAC
43880793 ACACCCGTGT
1 ACACCCGTGT
43880803 CACCTACCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (17 bp):
ACACCCGTGTGTTCCAC
Found at i:43881356 original size:19 final size:18
Alignment explanation
Indices: 43881329--43881390 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
43881319 ACGAAGAATG
43881329 GAAAGTAAAACGAAAATAAA
1 GAAA-TAAAA-GAAAATAAA
43881349 GAAAT-AAAGAAAGAATAAA
1 GAAATAAAAG-AA-AATAAA
43881368 GAAAT-AAAGTAAAAATAAA
1 GAAATAAAAG--AAAATAAA
43881387 GAAA
1 GAAA
43881391 GAATGGAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.03
18 5 0.13
19 26 0.67
20 7 0.18
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.11
Consensus pattern (18 bp):
GAAATAAAAGAAAATAAA
Found at i:43881365 original size:11 final size:11
Alignment explanation
Indices: 43881346--43881394 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
43881336 AAACGAAAAT
43881346 AAAGAAATAAAG
1 AAAG-AATAAAG
43881358 AAAGAATAAAG
1 AAAGAATAAAG
43881369 --A-AATAAAG
1 AAAGAATAAAG
43881377 TAAA-AATAAAG
1 -AAAGAATAAAG
43881388 AAAGAAT
1 AAAGAAT
43881395 GGAGGAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 3 0.09
11 18 0.55
12 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.12
Consensus pattern (11 bp):
AAAGAATAAAG
Found at i:43881418 original size:23 final size:23
Alignment explanation
Indices: 43881392--43881465 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
43881382 ATAAAGAAAG
43881392 AATGGAGGAATGGTAAAAACATA
1 AATGGAGGAATGGTAAAAACATA
*
43881415 AATGGA--AA--GTAAAACGAAAATA
1 AATGGAGGAATGGT-AAA--AACATA
43881437 AATGGAGGAATGGTAAAAACATA
1 AATGGAGGAATGGTAAAAACATA
43881460 AATGGA
1 AATGGA
43881466 AAGTAAAACG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 2 0.05
22 11 0.26
23 17 0.40
24 2 0.05
25 3 0.07
26 2 0.05
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.16
Consensus pattern (23 bp):
AATGGAGGAATGGTAAAAACATA
Found at i:43881428 original size:19 final size:19
Alignment explanation
Indices: 43881404--43881473 Score: 68
Period size: 22 Copynumber: 3.3 Consensus size: 19
43881394 TGGAGGAATG
43881404 GTAAAAACATAAATGGAAA
1 GTAAAAACATAAATGGAAA
*
43881423 GTAAAACGAAAATAAATGGAGGAA
1 GT-AAA--AACATAAATGGA--AA
43881447 TGGTAAAAACATAAATGGAAA
1 --GTAAAAACATAAATGGAAA
43881468 GTAAAA
1 GTAAAA
43881474 CGAAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
19 8 0.19
20 3 0.07
21 2 0.05
22 11 0.26
23 11 0.26
24 2 0.05
25 3 0.07
26 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.20, T:0.16
Consensus pattern (19 bp):
GTAAAAACATAAATGGAAA
Found at i:43881445 original size:45 final size:45
Alignment explanation
Indices: 43881392--43881483 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
43881382 ATAAAGAAAG
43881392 AATGGAGGAATGGTAAAAACATAAATGGAAAGTAAAACGAAAATA
1 AATGGAGGAATGGTAAAAACATAAATGGAAAGTAAAACGAAAATA
43881437 AATGGAGGAATGGTAAAAACATAAATGGAAAGTAAAACGAAAATA
1 AATGGAGGAATGGTAAAAACATAAATGGAAAGTAAAACGAAAATA
43881482 AA
1 AA
43881484 GCAATATCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.59, C:0.04, G:0.22, T:0.15
Consensus pattern (45 bp):
AATGGAGGAATGGTAAAAACATAAATGGAAAGTAAAACGAAAATA
Found at i:43881466 original size:20 final size:20
Alignment explanation
Indices: 43881398--43881466 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
43881388 AAAGAATGGA
43881398 GGAATGGTAAAAACATAAAT
1 GGAATGGTAAAAACATAAAT
* *
43881418 GGAA-AGTAAAACGAAAATAAAT
1 GGAATGGT-AAA--AACATAAAT
43881440 GGAGGAATGGTAAAAACATAAAT
1 ---GGAATGGTAAAAACATAAAT
43881463 GGAA
1 GGAA
43881467 AGTAAAACGA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 2 0.05
20 11 0.29
22 8 0.21
23 8 0.21
25 7 0.18
26 2 0.05
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.16
Consensus pattern (20 bp):
GGAATGGTAAAAACATAAAT
Found at i:43883595 original size:14 final size:14
Alignment explanation
Indices: 43883555--43883597 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
43883545 AATAGTAAAC
43883555 AAAA-TTATTATAA
1 AAAATTTATTATAA
**
43883568 AAAATTTAAAATAA
1 AAAATTTATTATAA
*
43883582 AAAATTTCTTATAA
1 AAAATTTATTATAA
43883596 AA
1 AA
43883598 TTAAGGGGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTTATTATAA
Found at i:43891746 original size:20 final size:20
Alignment explanation
Indices: 43891704--43891744 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
43891694 TACAACACAA
*
43891704 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
43891724 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
43891743 TT
1 TT
43891745 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:43891934 original size:28 final size:28
Alignment explanation
Indices: 43891903--43891957 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
43891893 CCTATTAATC
43891903 AAAA-TTTACAATAATTTCTAAAATTTCT
1 AAAATTTTACAA-AATTTCTAAAATTTCT
**
43891931 AAAATTTTTTAAAATTTCTAAAATTTC
1 AAAATTTTACAAAATTTCTAAAATTTC
43891958 GACATGGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAATTTTACAAAATTTCTAAAATTTCT
Found at i:43891945 original size:10 final size:9
Alignment explanation
Indices: 43891915--43891957 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
43891905 AATTTACAAT
43891915 AATTTCTAA
1 AATTTCTAA
43891924 AATTTCTAA
1 AATTTCTAA
*
43891933 AATTTTTTAA
1 AA-TTTCTAA
43891943 AATTTCTAA
1 AATTTCTAA
43891952 AATTTC
1 AATTTC
43891958 GACATGGCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTTCTAA
Found at i:43892541 original size:76 final size:76
Alignment explanation
Indices: 43892415--43892558 Score: 191
Period size: 76 Copynumber: 1.9 Consensus size: 76
43892405 ATATATTTAA
* *
43892415 TAAATATTTAAGAGTCCAATTTACGGGAATAGAGTCTCAGGAATGTACTTTCCAACACCCCTGAC
1 TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTGAC
43892480 TATTGGGTTGT
66 TATTGGGTTGT
* * * * * **
43892491 TAAATATTTACGAGTCTAATTTATGGGGACGGAGTCTC-GAGAATGCACTTTCTGACACCCCTGA
1 TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAG-GAATGCACTTTCCAACACCCCTGA
43892555 CTAT
65 CTAT
43892559 CGAGTCGTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 1 0.02
76 57 0.98
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (76 bp):
TAAATATTTAAGAGTCCAATTTACGGGAACAGAGTCTCAGGAATGCACTTTCCAACACCCCTGAC
TATTGGGTTGT
Found at i:43899833 original size:24 final size:26
Alignment explanation
Indices: 43899799--43899850 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
43899789 GATTTCAGTC
43899799 AAAAACTCTAAA-TTTAAAAATATTA
1 AAAAACTCTAAATTTTAAAAATATTA
*
43899824 AAAAAC-CTAAATTTTAAAAATTTTA
1 AAAAACTCTAAATTTTAAAAATATTA
43899849 AA
1 AA
43899851 CCTAGAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAACTCTAAATTTTAAAAATATTA
Found at i:43904782 original size:24 final size:24
Alignment explanation
Indices: 43904767--43904818 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
43904757 AATCAAAGTC
43904767 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
* *
43904791 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATGCT
43904815 AAAT
1 AAAT
43904819 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:43905497 original size:17 final size:18
Alignment explanation
Indices: 43905475--43905515 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
43905465 TTATTAATTG
43905475 ATATT-TTTAAATAGTAT
1 ATATTCTTTAAATAGTAT
43905492 ATATTTCTTTAAATAGTAT
1 ATA-TTCTTTAAATAGTAT
43905511 ATATT
1 ATATT
43905516 AATTCTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 4 0.18
19 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (18 bp):
ATATTCTTTAAATAGTAT
Found at i:43905659 original size:29 final size:29
Alignment explanation
Indices: 43905617--43905673 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
43905607 ATTTGAACCA
**
43905617 CAAATAAAGTTTCATGTGTACAATTGCAC
1 CAAATAAAGTTTCATGTACACAATTGCAC
43905646 CAAATTAAAG-TTCATGTACACAATTGCA
1 CAAA-TAAAGTTTCATGTACACAATTGCA
43905674 TACTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (29 bp):
CAAATAAAGTTTCATGTACACAATTGCAC
Found at i:43911789 original size:14 final size:14
Alignment explanation
Indices: 43911770--43911808 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 14
43911760 TTTCTCATAT
43911770 ATTATTTATTTTAA
1 ATTATTTATTTTAA
43911784 ATTATTT-TTTT--
1 ATTATTTATTTTAA
43911795 ATTATTTATTTTAA
1 ATTATTTATTTTAA
43911809 GTTTTCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.32
12 4 0.18
13 4 0.18
14 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTATTTATTTTAA
Found at i:43911791 original size:29 final size:25
Alignment explanation
Indices: 43911737--43911808 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 25
43911727 AAATTTGTTA
43911737 TTTATTTATTTATTTTAAACCTTTTT
1 TTTA-TTATTTATTTTAAACCTTTTT
*
43911763 CTCATATATTATTTATTTTAAA-TTATTTT
1 -T--T-TATTATTTATTTTAAACCT-TTTT
43911792 TTTATTATTTATTTTAA
1 TTTATTATTTATTTTAA
43911809 GTTTTCCACA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 15 0.38
26 1 0.03
27 1 0.03
28 2 0.05
29 19 0.47
30 2 0.05
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTATTATTTATTTTAAACCTTTTT
Found at i:43911910 original size:52 final size:51
Alignment explanation
Indices: 43911742--43912131 Score: 239
Period size: 52 Copynumber: 7.6 Consensus size: 51
43911732 TGTTATTTAT
* * * *
43911742 TTATTTATTTTAAACCTT-TTTCTCATATATTATTTATTTTAAATTATTTTTTTA
1 TTATTTATTTTAAA--TTGTTT-T-ATATATTATTTATTTTAAACTGTTTATATA
* ** * * * * *
43911796 TTATTTATTTTAAGTT-TTCCACATATAATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAACTGTTT-ATA-TA
** *
43911848 TTATCCATTTTAAATT-TTTTATATATTATTTATTTTTAAACTGTCATATATA
1 TTATTTATTTTAAATTGTTTTATATATTATTTA-TTTTAAACTGT-TTATATA
* * * * *
43911900 TTATTTATTTTGAATTGTTTT-TTTA-TATATATCATTT--A-TTTTTAGTACA
1 TTATTTATTTTAAATTGTTTTATATATTATTTAT--TTTAAACTGTTTA-TATA
* *
43911949 TTATTTATTTTAAACTTCTTTTTACATATTATTTATTTTAAACT-TTT-TATA
1 TTATTTATTTTAAA-TT-GTTTTATATATTATTTATTTTAAACTGTTTATATA
* * * * *
43912000 -TA-TTATTTTAAATTGTCTTATATGTTATTTATTTTAAATTGCTTTGTCTA
1 TTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAACTG-TTTATATA
* * * * *
43912050 TTATTTATTTTAATTTGTTTTACATATTAGTTACTTTAAATTGTTT-TATA
1 TTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAACTGTTTATATA
* * * *
43912100 CTATTTACTTCAAATTGTTCTATATATTATTT
1 TTATTTATTTTAAATTGTTTTATATATTATTT
43912132 TGTTTCGTTT
Statistics
Matches: 261, Mismatches: 55, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
47 21 0.08
48 4 0.02
49 31 0.12
50 58 0.22
51 20 0.08
52 86 0.33
53 26 0.10
54 15 0.06
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (51 bp):
TTATTTATTTTAAATTGTTTTATATATTATTTATTTTAAACTGTTTATATA
Found at i:43911941 original size:18 final size:19
Alignment explanation
Indices: 43911920--43911960 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
43911910 TGAATTGTTT
*
43911920 TTTTATA-TATATCATTTA
1 TTTTATAGTACATCATTTA
*
43911938 TTTT-TAGTACATTATTTA
1 TTTTATAGTACATCATTTA
43911956 TTTTA
1 TTTTA
43911961 AACTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTATAGTACATCATTTA
Found at i:43912007 original size:21 final size:22
Alignment explanation
Indices: 43911981--43912132 Score: 67
Period size: 26 Copynumber: 6.3 Consensus size: 22
43911971 TACATATTAT
43911981 TTATTTTAAACTT-T-TTATATA
1 TTATTTTAAA-TTGTCTTATATA
43912002 TTATTTTAAATTGTCTTATATGTTA
1 TTATTTTAAATTGTCTTATA---TA
* *
43912027 TTTATTTTAAATTGCTTTGTCTATTA
1 -TTATTTTAAATTG-TCT-TATA-TA
* *
43912053 TTTATTTTAATTTGTTTTACATATTA
1 -TTATTTTAAATTGTCTT--ATA-TA
* *
43912079 GTTACTTTAAATTGTTTTATACTA
1 -TTATTTTAAATTGTCTTATA-TA
* *
43912103 TTTACTTCAAATTGT-TCTATATA
1 -TTATTTTAAATTGTCT-TATATA
43912126 TTATTTT
1 TTATTTT
43912133 GTTTCGTTTT
Statistics
Matches: 108, Mismatches: 12, Indels: 21
0.77 0.09 0.15
Matches are distributed among these distances:
20 2 0.02
21 11 0.10
22 10 0.09
23 3 0.03
24 23 0.21
25 5 0.05
26 49 0.45
27 2 0.02
28 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.61
Consensus pattern (22 bp):
TTATTTTAAATTGTCTTATATA
Found at i:43912114 original size:24 final size:23
Alignment explanation
Indices: 43912080--43912127 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
43912070 TACATATTAG
* *
43912080 TTACTTTAAATTGTTTTATACTAT
1 TTACTTCAAATTGTTCTATA-TAT
43912104 TTACTTCAAATTGTTCTATATAT
1 TTACTTCAAATTGTTCTATATAT
43912127 T
1 T
43912128 ATTTTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.56
Consensus pattern (23 bp):
TTACTTCAAATTGTTCTATATAT
Found at i:43921995 original size:19 final size:20
Alignment explanation
Indices: 43921953--43921988 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
43921943 GTTTTCAAAT
43921953 AATT-ATAAAAATATATTAA
1 AATTAATAAAAATATATTAA
43921972 AATTAATAAAAA-ATATT
1 AATTAATAAAAATATATT
43921989 CGAATTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTAATAAAAATATATTAA
Found at i:43922001 original size:21 final size:21
Alignment explanation
Indices: 43921956--43922002 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
43921946 TTCAAATAAT
43921956 TATAAAAATATATTAAAATTA
1 TATAAAAATATATTAAAATTA
**
43921977 -ATAAAAA-ATATTCGAATTA
1 TATAAAAATATATTAAAATTA
43921996 CTATAAA
1 -TATAAA
43922003 TATAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 7 0.32
21 5 0.23
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAAAAATATATTAAAATTA
Found at i:43922341 original size:8 final size:8
Alignment explanation
Indices: 43922323--43922356 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
43922313 TTAAGTTTAA
*
43922323 TTTTAAAT
1 TTTTATAT
43922331 TTTT-TAT
1 TTTTATAT
43922338 TTTTATAT
1 TTTTATAT
43922346 TTTTATAT
1 TTTTATAT
43922354 TTT
1 TTT
43922357 CTTATAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTATAT
Found at i:43922341 original size:15 final size:15
Alignment explanation
Indices: 43922318--43922356 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
43922308 TTAAATTAAG
*
43922318 TTTAATTTTAAATTT
1 TTTATTTTTAAATTT
*
43922333 TTTATTTTTATATTT
1 TTTATTTTTAAATTT
43922348 TTATATTTT
1 TT-TATTTT
43922357 CTTATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTTTAAATTT
Found at i:43932157 original size:3 final size:3
Alignment explanation
Indices: 43932149--43932179 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
43932139 GGTAAGCGTT
43932149 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43932180 AACTTTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43932638 original size:15 final size:14
Alignment explanation
Indices: 43932618--43932652 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
43932608 TGGAAATTTA
43932618 AAAAAAATAATATGT
1 AAAAAAATAAT-TGT
*
43932633 AAAAAAATAATTTT
1 AAAAAAATAATTGT
43932647 AAAAAA
1 AAAAAA
43932653 TGGGATGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AAAAAAATAATTGT
Found at i:43935502 original size:44 final size:43
Alignment explanation
Indices: 43935452--43935544 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 43
43935442 ATGTTGTGGA
* * * *
43935452 GTTTGTAGCTAGAAGCGTCGCAAAAGATCATGTTCTGTAGCAGC
1 GTTTGTAG-TAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
* * * *
43935496 GTTTGTAGTAAAAGTGCCACTAAAGATCATGTTCTATAGCGGT
1 GTTTGTAGTAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
43935539 GTTTGT
1 GTTTGT
43935545 GGGAAAACAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 33 0.80
44 8 0.20
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (43 bp):
GTTTGTAGTAAAAGCGCCACAAAAGATCATGTTCTATAGCAGC
Found at i:43939852 original size:42 final size:43
Alignment explanation
Indices: 43939786--43939907 Score: 124
Period size: 41 Copynumber: 2.9 Consensus size: 43
43939776 ATATTCGTGA
* * * *
43939786 CATTTATGAGAAAAACATCGCTATTGTTTTTAACCTTTTACAG
1 CATTTATGCGAAAAATACCACTATTGTTTTTAACCTTTTACAG
* * *
43939829 TATTTATGC-AAAAATGCCACTATTG-TTTT-ACCTTTTGCAG
1 CATTTATGCGAAAAATACCACTATTGTTTTTAACCTTTTACAG
* * *
43939869 CGTTTATGCGAAAAATACCGCTATTGTTATTATACCTTT
1 CATTTATGCGAAAAATACCACTATTGTTTTTA-ACCTTT
43939908 AGCGGCGTTT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
40 17 0.27
41 18 0.29
42 15 0.24
43 7 0.11
44 6 0.10
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (43 bp):
CATTTATGCGAAAAATACCACTATTGTTTTTAACCTTTTACAG
Found at i:43943360 original size:18 final size:18
Alignment explanation
Indices: 43943334--43943384 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
43943324 TAAAAGTAAC
43943334 TAAAAATAAAAACAAAAA
1 TAAAAATAAAAACAAAAA
* *
43943352 TAAACATAAAAAGAAAAA
1 TAAAAATAAAAACAAAAA
* *
43943370 GAAAAA-GAAAACAAA
1 TAAAAATAAAAACAAA
43943385 TAAACTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:43944848 original size:35 final size:36
Alignment explanation
Indices: 43944786--43944854 Score: 90
Period size: 35 Copynumber: 1.9 Consensus size: 36
43944776 CGCCTAAAAT
*
43944786 AATAAGAAATATTAAGCAAATTAAATAA-AATAAGA
1 AATAAGAAATATTAAGCAAATGAAATAATAATAAGA
43944821 AATAAGAAATGA-TAAGCAAA-GAGAATAATAATAA
1 AATAAGAAAT-ATTAAGCAAATGA-AATAATAATAA
43944855 TAAAAGAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 1 0.03
35 23 0.77
36 6 0.20
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (36 bp):
AATAAGAAATATTAAGCAAATGAAATAATAATAAGA
Found at i:43951354 original size:22 final size:25
Alignment explanation
Indices: 43951328--43951381 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
43951318 TTATAAATTC
43951328 AATTTAAAAG-ATA-TAAT-ACAAT
1 AATTTAAAAGCATATTAATAACAAT
*
43951350 AATTT-CAAGCATATTTAATAACAAT
1 AATTTAAAAGCATA-TTAATAACAAT
43951375 AATTTAA
1 AATTTAA
43951382 TTATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
24 4 0.16
25 10 0.40
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTTAAAAGCATATTAATAACAAT
Found at i:43963600 original size:19 final size:18
Alignment explanation
Indices: 43963574--43963617 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
43963564 AGATTCAATC
* *
43963574 GAAAAAGAAGAAGAATAA
1 GAAAAAGAAAAAGAAAAA
43963592 GAGAAAAGAAAAAGAAAAA
1 GA-AAAAGAAAAAGAAAAA
43963611 GAAAAAG
1 GAAAAAG
43963618 GAGAGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAAA
Found at i:43963614 original size:6 final size:6
Alignment explanation
Indices: 43963574--43963617 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
43963564 AGATTCAATC
* *
43963574 GAAAAA GAAGAA GAATAA GAGAAAA GAAAAA GAAAAA GAAAAA G
1 GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA GAAAAA GAAAAA G
43963618 GAGAGTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:43964626 original size:44 final size:45
Alignment explanation
Indices: 43964515--43964722 Score: 181
Period size: 45 Copynumber: 4.7 Consensus size: 45
43964505 TCATGGCGAA
* * * ***
43964515 TCTTATCTCCCTAAAGTTGTAGTGGAACAGATT-AAGGCCACTAA-
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGATTAC-AAG
* * * *
43964559 TCTTACCCCGCCTGAAGTTGCAGTGGGGCAGGTTGAA-ATTACAAG
1 TCTTATCTC-CCTAAAGTTGCAGTGGAGCAGGTTGAAGATTACAAG
* * ** * * *
43964604 TCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAACAAA
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGATTACAAG
* *
43964649 CCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGA-TACAAG
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGATTACAAG
* *
43964693 TCTTATCTCCCTAAATTTGCAGCGGAGCAG
1 TCTTATCTCCCTAAAGTTGCAGTGGAGCAG
43964723 ACTGAAAACA
Statistics
Matches: 126, Mismatches: 34, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
44 59 0.47
45 65 0.52
46 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (45 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTGAAGATTACAAG
Found at i:43964631 original size:89 final size:89
Alignment explanation
Indices: 43964515--43964725 Score: 246
Period size: 89 Copynumber: 2.4 Consensus size: 89
43964505 TCATGGCGAA
* * * * * * *
43964515 TCTTATCTCCCTAAAGTTGTAGTGGAACAGA-TTAAGGCCACTAATCTTACCCCGCCTGAAGTTG
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAACAAACCTTACCCC-CCTAAAGTTG
*
43964579 CAGTGGGGCAGGTTGAA-ATTACAAG
65 CAGTGGAGCAGGTTGAAGA-TACAAG
* * * *
43964604 TCTTATCTCCTTAAAGTTGCAGTGGAACAGACTAAAGATAACAAACCTTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAACAAACCTTACCCCCCTAAAGTTGC
*
43964669 AGTGGAGTAGGTTGAAGATACAAG
66 AGTGGAGCAGGTTGAAGATACAAG
* * *
43964693 TCTTATCTCCCTAAATTTGCAGCGGAGCAGACT
1 TCTTATCTCCCTAAAGTTGCAGTGGAACAGACT
43964726 GAAAACAGTG
Statistics
Matches: 103, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
89 88 0.85
90 15 0.15
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (89 bp):
TCTTATCTCCCTAAAGTTGCAGTGGAACAGACTAAAGACAACAAACCTTACCCCCCTAAAGTTGC
AGTGGAGCAGGTTGAAGATACAAG
Found at i:43964908 original size:143 final size:143
Alignment explanation
Indices: 43964645--43965246 Score: 757
Period size: 143 Copynumber: 4.2 Consensus size: 143
43964635 CTAAAGATAA
* * * * * ** * * *
43964645 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGATACAAGTCTTATCTCCCTAAATT
1 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGT
* *
43964710 TGCAGCGGAGCAGACTGAAA-ACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAA
66 TGCAGCAGAGCAGACT-AAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAA
43964774 GCTACAAATTATGG
130 GCTACAAATTATGG
* * *
43964788 CAAATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTGAAGT
1 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGT
* *
43964853 TGCAGCAGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCGTTGTAGTGGAACAGATTAAAG
66 TGCAGCAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAG
43964918 CTACAAATTATGG
131 CTACAAATTATGG
** *
43964931 CGGATCTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGT
1 CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGT
* * * * * *
43964996 TGCAGCGGAGCAAACTGAAGACAGCGAACCTTATTTCCCTGGTGTTGCAGTGGAATAGATTAAAG
66 TGCAGCAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAG
43965061 CTACAAATTATGG
131 CTACAAATTATGG
* * * *
43965074 -AAGATCTTATCTTCCTGAAGTTCCAGTGGAGTAGATTGAAGCCACCAACCTTATCTCCCTGAAG
1 CAA-ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAG
* * * * ** * * *
43965138 TTGCAACAGAGCAGACTAAAGATAGCGAGTCTTATTTCCCAGAAGTTGTAGTGGAACAGATTGAC
65 TTGCAGCAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAA
*
43965203 GCTATAAA-T-T-G
130 GCTACAAATTATGG
* *
43965214 CAGATCTTATC-TCTCTGAAGTTGCAGTAGAGCA
1 CAAATCTTATCTTC-CTGAAGTTGCAGTGGAGCA
43965247 TATCATATTA
Statistics
Matches: 400, Mismatches: 55, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
139 2 0.00
140 25 0.06
141 2 0.00
142 4 0.01
143 367 0.92
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (143 bp):
CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGT
TGCAGCAGAGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAG
CTACAAATTATGG
Found at i:43965031 original size:286 final size:283
Alignment explanation
Indices: 43964650--43965246 Score: 856
Period size: 286 Copynumber: 2.1 Consensus size: 283
43964640 GATAACAAAC
* * * * * *
43964650 CTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGATACAAGTCTTATCTCCCTAAATTTGCAG
1 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * *
43964715 CGGAGCAGACTGAAAACAGTGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
66 CGGAGCAAACTGAAAACAGCGAACCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
**
43964780 AATTATGGCAA-ATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCT
131 AATTATGG-AAGATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATCT
* * **
43964844 CCCTGAAGTTGCAGCAGAGCAGACTAAAGACAACGAATCTTATTTCCCTGGCGTTGTAGTGGAAC
195 CCCTGAAGTTGCAACAGAGCAGACTAAAGACAACGAATCTTATTTCCCAGAAGTTGTAGTGGAAC
*
43964909 AGATTAAAGCTACAAATTATGGCGGAT
260 AGATTAAAGCTACAAA-T-T-GCAGAT
* *
43964936 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGCAG
1 CTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
* * *
43965001 CGGAGCAAACTGAAGACAGCGAACCTTATTTCCCTGGTGTTGCAGTGGAATAGATTAAAGCTACA
66 CGGAGCAAACTGAAAACAGCGAACCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
* *
43965066 AATTATGGAAGATCTTATCTTCCTGAAGTTCCAGTGGAGTAGATTGAAGCCACCAACCTTATCTC
131 AATTATGGAAGATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATCTC
* * *
43965131 CCTGAAGTTGCAACAGAGCAGACTAAAGATAGCGAGTCTTATTTCCCAGAAGTTGTAGTGGAACA
196 CCTGAAGTTGCAACAGAGCAGACTAAAGACAACGAATCTTATTTCCCAGAAGTTGTAGTGGAACA
* * *
43965196 GATTGACGCTATAAATTGCAGAT
261 GATTAAAGCTACAAATTGCAGAT
* *
43965219 CTTATC-TCTCTGAAGTTGCAGTAGAGCA
1 CTTATCTTC-CTAAAGTTGCAGTGGAGCA
43965247 TATCATATTA
Statistics
Matches: 278, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
282 2 0.01
283 28 0.10
284 1 0.00
285 3 0.01
286 244 0.88
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (283 bp):
CTTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGACACAAGCCTTATCTCCCTAAAGTTGCAG
CGGAGCAAACTGAAAACAGCGAACCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACA
AATTATGGAAGATCTTATCTTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAACCTTATCTC
CCTGAAGTTGCAACAGAGCAGACTAAAGACAACGAATCTTATTTCCCAGAAGTTGTAGTGGAACA
GATTAAAGCTACAAATTGCAGAT
Found at i:43965320 original size:44 final size:45
Alignment explanation
Indices: 43965260--43965507 Score: 193
Period size: 44 Copynumber: 5.6 Consensus size: 45
43965250 CATATTAAAC
* * * * *
43965260 CTTATCTCTCTAAAGTTGCAGTGGTGCAG-GTCGAAGTTA-TAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAGTAAGT
* *
43965304 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAGCT-AGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAG-TAAGT
* * *
43965349 CTTATCTCCCTCAAGTTGCAGTGGAGCAGACTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAGT
* * * ** * *
43965394 CTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCA-CAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAGT
* * * * **
43965438 CTAATCTCCCTGAA-TATGTAGTGGAGCAGATTGTAGAT-GCGAGT
1 CTTATCTCCCTGAAGT-TGCAGTGGAGCAGACTGAAGATAGTAAGT
* * *
43965482 CTAATCTCCCTGAAGTTACAGAGGAG
1 CTTATCTCCCTGAAGTTGCAGTGGAG
43965508 TAGATCCAAA
Statistics
Matches: 167, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 88 0.53
45 77 0.46
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAGT
Found at i:43965357 original size:45 final size:45
Alignment explanation
Indices: 43965300--43965507 Score: 215
Period size: 45 Copynumber: 4.7 Consensus size: 45
43965290 TCGAAGTTAT
*
43965300 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAGC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGC
* * *
43965345 TAGTCTTATCTCCCTCAAGTTGCAGTGGAGCAGACTGAAGATAGC
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGC
* * * * *
43965390 AAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCCA-C
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGC
* * * * * *
43965434 AAATCTAATCTCCCTGAA-TATGTAGTGGAGCAGATTGTAGA-TGC
1 AAGTCTTATCTCCCTGAAGT-TGCAGTGGAGCAGACTGAAGACAGC
* * * *
43965478 GAGTCTAATCTCCCTGAAGTTACAGAGGAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAG
43965508 TAGATCCAAA
Statistics
Matches: 136, Mismatches: 24, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
43 1 0.01
44 58 0.43
45 77 0.57
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGC
Found at i:43965413 original size:90 final size:89
Alignment explanation
Indices: 43965260--43965423 Score: 222
Period size: 89 Copynumber: 1.8 Consensus size: 89
43965250 CATATTAAAC
* * * * * *
43965260 CTTATCTCTCTAAAGTTGCAGTGGTGCAGGTCGAAGTTATAAGTCTTATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGCTCGAAGATACAAATCTTATCTCCCTGAAGTTGCAG
*
43965325 TGGAGCAGACTAAAGACAGCTAGT
66 TAGAGCAGACTAAAGACAGCTAGT
* *
43965349 CTTATCTCCCTCAAGTTGCAGTGGAGCAGACT-GAAGATAGCAAATCTTATCTCTCTGAAGTTGC
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAG-CTCGAAGATA-CAAATCTTATCTCCCTGAAGTTGC
43965413 AGTAGAGCAGA
64 AGTAGAGCAGA
43965424 TTGAAGCCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
89 32 0.50
90 32 0.50
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (89 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGCTCGAAGATACAAATCTTATCTCCCTGAAGTTGCAG
TAGAGCAGACTAAAGACAGCTAGT
Found at i:43967135 original size:3 final size:3
Alignment explanation
Indices: 43967127--43967161 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
43967117 TAAACTTTAG
*
43967127 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
43967162 CATCATCATC
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:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43969038 original size:20 final size:22
Alignment explanation
Indices: 43969015--43969054 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
43969005 GGTGAGAACT
43969015 AAAA-GTTTAGGGAA-AAAATA
1 AAAATGTTTAGGGAATAAAATA
*
43969035 AAAATTTTTAGGGAATAAAA
1 AAAATGTTTAGGGAATAAAA
43969055 GTTTGAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.25
Consensus pattern (22 bp):
AAAATGTTTAGGGAATAAAATA
Found at i:43969520 original size:9 final size:9
Alignment explanation
Indices: 43969503--43969533 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43969493 TCGAGTTGAT
43969503 TCGAATAAC
1 TCGAATAAC
*
43969512 TCGATTAAC
1 TCGAATAAC
43969521 TCGAATAAC
1 TCGAATAAC
43969530 TCGA
1 TCGA
43969534 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43970400 original size:33 final size:33
Alignment explanation
Indices: 43970339--43970413 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 33
43970329 AATTAAAATA
43970339 TTAAAAAATATATATTTTTAATAATTTTTATAGTTT
1 TTAAAAAATATATATTTTTAATAATTTTT-TA--TT
*
43970375 TTAAAAAA-ATAT-TTTTT-ATAGTTTTTTATT
1 TTAAAAAATATATATTTTTAATAATTTTTTATT
43970405 TTAAAAAAT
1 TTAAAAAAT
43970414 TAATTAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 10 0.27
32 2 0.05
33 8 0.22
34 5 0.14
35 4 0.11
36 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (33 bp):
TTAAAAAATATATATTTTTAATAATTTTTTATT
Found at i:43970823 original size:24 final size:23
Alignment explanation
Indices: 43970779--43970841 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 23
43970769 TTAAAATATA
*
43970779 ATTAAATGAAAAATTTATATTAAT
1 ATTAAAT-AAAAAATTATATTAAT
*
43970803 ATTAAATAAAATAATTGTATTAAT
1 ATTAAATAAAA-AATTATATTAAT
43970827 ATTAAATAAATAAAT
1 ATTAAATAAA-AAAT
43970842 AAAATACTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 4 0.11
24 30 0.86
25 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (23 bp):
ATTAAATAAAAAATTATATTAAT
Found at i:43974422 original size:6 final size:6
Alignment explanation
Indices: 43974411--43974441 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
43974401 AGTTTTCTTC
43974411 AAAATG AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG A
43974442 CCTAGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:43976939 original size:92 final size:92
Alignment explanation
Indices: 43976782--43976961 Score: 281
Period size: 92 Copynumber: 2.0 Consensus size: 92
43976772 AGAAAGCAGG
* *
43976782 GAGAAAAGATAGAGGGAATTGAGAATAGGAGAGAATAAAGAAGAAAGTTGTATTAACAAAAATTG
1 GAGAAAAGATAGAAGGAATTGAGAAGAGGAGAGAATAAAGAAGAAAGTTGTATTAACAAAAATTG
* *
43976847 ATAGTTGTTTCCTCTCTCAACAGTAGA
66 ATAATTGTTTCCCCTCTCAACAGTAGA
* * *
43976874 GAGAAAAGATATAAGGAATTGAGAAGAGGAGAGAATAATGAAGGAAA-TTGTATTAACCAAAATT
1 GAGAAAAGATAGAAGGAATTGAGAAGAGGAGAGAATAAAGAA-GAAAGTTGTATTAACAAAAATT
43976938 GATAATTGTTTCCCCTCTCAACAG
65 GATAATTGTTTCCCCTCTCAACAG
43976962 CAGGTTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 76 0.95
93 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (92 bp):
GAGAAAAGATAGAAGGAATTGAGAAGAGGAGAGAATAAAGAAGAAAGTTGTATTAACAAAAATTG
ATAATTGTTTCCCCTCTCAACAGTAGA
Found at i:43979573 original size:22 final size:21
Alignment explanation
Indices: 43979548--43979593 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
43979538 ACTTTTTAAG
43979548 TTTT-TTATTTGTCCTTTATTTA
1 TTTTATTATTTGT--TTTATTTA
43979570 TTTTACTTATTTGTTTTATTTA
1 TTTTA-TTATTTGTTTTATTTA
43979592 TT
1 TT
43979594 GGTTTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTATTATTTGTTTTATTTA
Found at i:43979748 original size:7 final size:7
Alignment explanation
Indices: 43979736--43979760 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43979726 TAATATAAAA
43979736 ATTTAAT
1 ATTTAAT
43979743 ATTTAAT
1 ATTTAAT
43979750 ATTTAAT
1 ATTTAAT
43979757 ATTT
1 ATTT
43979761 TATTTTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:43983063 original size:29 final size:30
Alignment explanation
Indices: 43983030--43983131 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
43983020 CCTATGGCCA
*
43983030 GGTGATATGAACTTGAATCGCCCATGT-TG
1 GGTGATATGAACTCGAATCGCCCATGTCTG
* * **
43983059 GGTGATATGAACTCAAATCGCCAATGTCCA
1 GGTGATATGAACTCGAATCGCCCATGTCTG
*
43983089 GGTGATATGAACTCGTA-CTGCCCATGTCTG
1 GGTGATATGAACTCGAATC-GCCCATGTCTG
43983119 GGTGATATGAACT
1 GGTGATATGAACT
43983132 GCTCTGCGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.41
30 36 0.59
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (30 bp):
GGTGATATGAACTCGAATCGCCCATGTCTG
Found at i:43983090 original size:59 final size:60
Alignment explanation
Indices: 43982996--43983131 Score: 186
Period size: 59 Copynumber: 2.3 Consensus size: 60
43982986 CGGTTGTTGC
* * * *
43982996 TCTGGGTGAAATAAACTCAAACCGCCTATGGCCAGGTGATATGAACTTGAA-TCGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCAATGGCCAGGTGATATGAACTCGAACT-GCCCATG
* * *
43983056 T-TGGGTGATATGAACTCAAATCGCCAATGTCCAGGTGATATGAACTCGTACTGCCCATG
1 TCTGGGTGATATGAACTCAAACCGCCAATGGCCAGGTGATATGAACTCGAACTGCCCATG
43983115 TCTGGGTGATATGAACT
1 TCTGGGTGATATGAACT
43983132 GCTCTGCGAC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 50 0.75
60 17 0.25
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (60 bp):
TCTGGGTGATATGAACTCAAACCGCCAATGGCCAGGTGATATGAACTCGAACTGCCCATG
Found at i:43983116 original size:30 final size:30
Alignment explanation
Indices: 43983000--43983131 Score: 115
Period size: 30 Copynumber: 4.4 Consensus size: 30
43982990 TGTTGCTCTG
* * * * * *
43983000 GGTGAAATAAACTCAAACCGCCTATGGCCA
1 GGTGATATGAACTCGAATCGCCCATGTCCA
* **
43983030 GGTGATATGAACTTGAATCGCCCATGT-TG
1 GGTGATATGAACTCGAATCGCCCATGTCCA
* *
43983059 GGTGATATGAACTCAAATCGCCAATGTCCA
1 GGTGATATGAACTCGAATCGCCCATGTCCA
* **
43983089 GGTGATATGAACTCGTA-CTGCCCATGTCTG
1 GGTGATATGAACTCGAATC-GCCCATGTCCA
43983119 GGTGATATGAACT
1 GGTGATATGAACT
43983132 GCTCTGCGAC
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
29 25 0.31
30 56 0.69
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (30 bp):
GGTGATATGAACTCGAATCGCCCATGTCCA
Found at i:43985760 original size:21 final size:22
Alignment explanation
Indices: 43985734--43985791 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
43985724 GTGACTAGTT
43985734 TAATATATATTTTTTA-TTTTC
1 TAATATATATTTTTTACTTTTC
* *
43985755 TAATATA-AATTTTTACTTTTT
1 TAATATATATTTTTTACTTTTC
*
43985776 TAATATATATATTTTA
1 TAATATATATTTTTTA
43985792 AAAAGCCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 7 0.23
21 18 0.58
22 6 0.19
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATATATATTTTTTACTTTTC
Found at i:43985931 original size:20 final size:20
Alignment explanation
Indices: 43985892--43985932 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43985882 CAATAGAATT
* *
43985892 TTAAAAAAATTTGAATATCA
1 TTAAAAAAATTTAAAAATCA
*
43985912 TTAAAACAATTTAAAAATCA
1 TTAAAAAAATTTAAAAATCA
43985932 T
1 T
43985933 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAAAAATTTAAAAATCA
Found at i:43985984 original size:21 final size:20
Alignment explanation
Indices: 43985960--43986003 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
43985950 TAAAATTAAA
*
43985960 TAAATATATATTTAAAAATTT
1 TAAATATACATTT-AAAATTT
43985981 TAAAATATACATTTAAAATTT
1 T-AAATATACATTTAAAATTT
43986002 TA
1 TA
43986004 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 9 0.43
22 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATATACATTTAAAATTT
Found at i:43986080 original size:19 final size:19
Alignment explanation
Indices: 43986058--43986113 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
43986048 TTTTAAATGT
*
43986058 TTTATATTATTAAAAAATA
1 TTTAAATTATTAAAAAATA
43986077 TTTAAATTA--AAAAATATA
1 TTTAAATTATTAAAAA-ATA
43986095 TTTAAAATT-TTAAAAAATA
1 TTT-AAATTATTAAAAAATA
43986114 ATATTATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 16 0.50
20 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAATTATTAAAAAATA
Found at i:43986095 original size:18 final size:19
Alignment explanation
Indices: 43986069--43986123 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
43986059 TTATATTATT
43986069 AAAAA-ATATTTAAA-TTA
1 AAAAATATATTTAAATTTA
43986086 AAAAATATATTTAAAATTTTA
1 AAAAATATATTT-AAA-TTTA
43986107 AAAAATAATATTATAAA
1 AAAAAT-ATATT-TAAA
43986124 ACCTTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.16
18 6 0.19
19 3 0.09
21 9 0.28
22 8 0.25
23 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATATATTTAAATTTA
Found at i:43986252 original size:25 final size:25
Alignment explanation
Indices: 43986191--43986246 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
43986181 TAAATAAAGG
43986191 AAAAATAAAAAACTTAAAAAGTAAAT
1 AAAAA-AAAAAACTTAAAAAGTAAAT
* *
43986217 AAATAAAAAAACTTAAAACG-AAA-
1 AAAAAAAAAAACTTAAAAAGTAAAT
43986240 AAAAAAA
1 AAAAAAA
43986247 TGAAAAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.22
24 3 0.11
25 14 0.52
26 4 0.15
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAAACTTAAAAAGTAAAT
Found at i:43991391 original size:35 final size:34
Alignment explanation
Indices: 43991350--43991415 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
43991340 ATGTATATAT
*
43991350 ATGTATATGTTATAATAATAAATAA-AATGAATCTA
1 ATGTATATATTATAAT-AT-AATAATAATGAATCTA
43991385 ATGTATATATTATAATATAATAATAATGAAT
1 ATGTATATATTATAATATAATAATAATGAAT
43991416 GAAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 9 0.31
35 15 0.52
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.39
Consensus pattern (34 bp):
ATGTATATATTATAATATAATAATAATGAATCTA
Found at i:43992646 original size:19 final size:20
Alignment explanation
Indices: 43992617--43992660 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
43992607 TAAAGAGTAA
43992617 AAATG-AATATGAGA-TGA-G
1 AAATGAAATATGA-ATTGATG
43992635 AAATGAAATATGAATTGATG
1 AAATGAAATATGAATTGATG
43992655 AAATGA
1 AAATGA
43992661 GATGTGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.23, T:0.25
Consensus pattern (20 bp):
AAATGAAATATGAATTGATG
Found at i:43998576 original size:26 final size:29
Alignment explanation
Indices: 43998542--43998601 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
43998532 GCTCACAAAG
43998542 GAGCACGCAT-GGAG-TT-TTATCACAGA
1 GAGCACGCATAGGAGTTTATTATCACAGA
*
43998568 GAGCTCGCATAAGGAGTTTACTTATCACAGA
1 GAGCACGCAT-AGGAGTTTA-TTATCACAGA
43998599 GAG
1 GAG
43998602 TTTGCATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.32
28 4 0.14
29 2 0.07
31 13 0.46
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (29 bp):
GAGCACGCATAGGAGTTTATTATCACAGA
Found at i:44007183 original size:26 final size:26
Alignment explanation
Indices: 44007147--44007218 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
44007137 GGTTAAAAAA
44007147 TAACGCGATGTGATCAGTCACATCGC
1 TAACGCGATGTGATCAGTCACATCGC
44007173 TAACGCGATGTGATCAGTCACATCGC
1 TAACGCGATGTGATCAGTCACATCGC
44007199 TAACGCGATGTGATCAGTCA
1 TAACGCGATGTGATCAGTCA
44007219 TGGTCAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (26 bp):
TAACGCGATGTGATCAGTCACATCGC
Found at i:44008995 original size:27 final size:27
Alignment explanation
Indices: 44008959--44009036 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
44008949 GAATATAAAG
*
44008959 GGGGTTGCTAAGTGCTGATTCTCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
44008986 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
* *
44009013 GGGGTTGCTAATTGTTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
44009037 GATTCATTGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.17, C:0.23, G:0.29, T:0.31
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:44009052 original size:33 final size:33
Alignment explanation
Indices: 44008988--44009311 Score: 152
Period size: 33 Copynumber: 9.4 Consensus size: 33
44008978 TCTCCCAAGG
*
44008988 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
44009015 GGTTGCTAATTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
44009048 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
44009090 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
44009123 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
44009165 GGTTGCTAAGTACTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
* *
44009192 GGTTGCTAAGTGCTGTTTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * * *
44009225 GGTTGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
44009267 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
44009300 AGTTGCTAAGTG
1 GGTTGCTAAGTG
44009312 TTGAATCCAC
Statistics
Matches: 227, Mismatches: 29, Indels: 76
0.68 0.09 0.23
Matches are distributed among these distances:
27 40 0.18
28 2 0.01
30 1 0.00
31 3 0.01
32 4 0.02
33 68 0.30
34 10 0.04
35 3 0.01
36 4 0.02
37 8 0.04
38 8 0.04
39 5 0.02
40 2 0.01
41 8 0.04
42 61 0.27
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:44009107 original size:42 final size:41
Alignment explanation
Indices: 44009048--44009184 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 41
44009038 ATTCATTGGT
44009048 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* *
44009090 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
44009123 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
*
44009165 GGTTGCTAAGTACTGATTCC
1 GGTTGCTAAGTGCTGATTCC
44009185 CCCGAGGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 40 0.49
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:44009134 original size:75 final size:75
Alignment explanation
Indices: 44009011--44009186 Score: 307
Period size: 75 Copynumber: 2.3 Consensus size: 75
44009001 TGATTCCCCC
* * *
44009011 AAGGGGTTGCTAATTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
44009076 TTAAATGTGA
66 TTAAATGTGA
44009086 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
44009151 TTAAATGTGA
66 TTAAATGTGA
* *
44009161 AGGGGGTTGCTAAGTACTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
44009187 CGAGGGGTTG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 96 1.00
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:44009193 original size:102 final size:102
Alignment explanation
Indices: 44009087--44009288 Score: 350
Period size: 102 Copynumber: 2.0 Consensus size: 102
44009077 TAAATGTGAA
* * *
44009087 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCGTATCT
*
44009152 TAAATGTGAAGGGGGTTGCTAAGTACTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCCCG
*
44009189 AGGGGTTGCTAAGTGCTGTTTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCGTATCT
*
44009254 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCC
44009289 GACTCATTGG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCCCG
Found at i:44009282 original size:177 final size:177
Alignment explanation
Indices: 44008986--44009321 Score: 573
Period size: 177 Copynumber: 1.9 Consensus size: 177
44008976 ATTCTCCCAA
* * * *
44008986 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAATTGTTGATTCCCCGATTCATTGGTGGT
1 GGGGTTGCTAAGTACTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* *
44009051 TGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACT
66 TGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACT
* *
44009116 CATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAG
131 CATTGGTAGTTGCTAAGTGCTGAATCCACCGTATCTTAAATGTGAAG
* *
44009163 GGGGTTGCTAAGTACTGATTCCCCCGAGGGGTTGCTAAGTGCTGTTTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTACTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
44009228 TGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACT
66 TGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACT
*
44009293 CATTGGTAGTTGCTAAGTGTTGAATCCAC
131 CATTGGTAGTTGCTAAGTGCTGAATCCAC
44009322 TGATAACGGA
Statistics
Matches: 148, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
177 148 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (177 bp):
GGGGTTGCTAAGTACTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
TGCTAAATGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACT
CATTGGTAGTTGCTAAGTGCTGAATCCACCGTATCTTAAATGTGAAG
Found at i:44010767 original size:45 final size:47
Alignment explanation
Indices: 44010716--44010826 Score: 145
Period size: 49 Copynumber: 2.4 Consensus size: 47
44010706 TCCATATAGA
*
44010716 ATTACACTTCTTTTATTT-TATT-TTACAATAAGGTTTTTCAACCTT
1 ATTACACTTCTTTTATTTATATTATTACAATAAGGTATTTCAACCTT
* * * *
44010761 ATTACACTTCATCTATTTGATATTAATTAGAATCAGGTATTTCAACCTT
1 ATTACACTTCTTTTATTT-ATATT-ATTACAATAAGGTATTTCAACCTT
44010810 ATTACACTTCTTTTATT
1 ATTACACTTCTTTTATT
44010827 AGAATATGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 16 0.29
47 4 0.07
49 35 0.64
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (47 bp):
ATTACACTTCTTTTATTTATATTATTACAATAAGGTATTTCAACCTT
Found at i:44019412 original size:75 final size:75
Alignment explanation
Indices: 44019262--44019431 Score: 236
Period size: 76 Copynumber: 2.3 Consensus size: 75
44019252 GGAAAGGTTT
** *
44019262 ATAATTTAAATGAAATGAGAAAAAAATTTGTTTGAAATGAAATGGTACAAAATTTAAATGAAAAT
1 ATAATTTAAATGAAATGAGAAAAAAATTTCATTGAAATGAAATGGTACAAAAATTAAATGAAAAT
44019327 TGAAAGAAAG
66 TGAAAGAAAG
* * * *
44019337 ATAAATTTAAATGAAATGAGTAAAAATTTTCATTGAAATGAAATGAG-A-AAAAATTAAATTATA
1 AT-AATTTAAATGAAATGAGAAAAAAATTTCATTGAAATGAAATG-GTACAAAAATTAAATGAAA
*
44019400 TTTGAAAGAAAG
64 ATTGAAAGAAAG
44019412 ATAATTTAAATGAAATGAGA
1 ATAATTTAAATGAAATGAGA
44019432 GGCACTTTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
74 17 0.20
75 27 0.32
76 39 0.46
77 1 0.01
ACGTcount: A:0.55, C:0.01, G:0.15, T:0.29
Consensus pattern (75 bp):
ATAATTTAAATGAAATGAGAAAAAAATTTCATTGAAATGAAATGGTACAAAAATTAAATGAAAAT
TGAAAGAAAG
Found at i:44019639 original size:19 final size:19
Alignment explanation
Indices: 44019600--44019640 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
44019590 TGAATTGAGA
*
44019600 AAAAAATAAATTTAAATTG
1 AAAAAATAAATTTAAAGTG
44019619 AAAAAATATAATTT-AAGTG
1 AAAAAATA-AATTTAAAGTG
44019638 AAA
1 AAA
44019641 TGGAATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTTAAAGTG
Found at i:44019659 original size:12 final size:12
Alignment explanation
Indices: 44019636--44019665 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
44019626 ATAATTTAAG
44019636 TGAAAT-GGAAT
1 TGAAATGGGAAT
44019647 TGAAATGGGAAT
1 TGAAATGGGAAT
44019659 TGAAATG
1 TGAAATG
44019666 AAATTGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (12 bp):
TGAAATGGGAAT
Found at i:44019669 original size:5 final size:5
Alignment explanation
Indices: 44019636--44019714 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
44019626 ATAATTTAAG
* * * *
44019636 TGAAA TGGAAT TGAAA TGGGAAT TGAAA TGAAA TTGGAA TGAAA TAAAA
1 TGAAA T-GAAA TGAAA T--GAAA TGAAA TGAAA -TGAAA TGAAA TGAAA
* *
44019685 TTAAAA TGAAA TGAAAA TGAAA AGAAA TGA
1 -TGAAA TGAAA TG-AAA TGAAA TGAAA TGA
44019715 CTAATCTCCA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 36 0.62
6 18 0.31
7 4 0.07
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (5 bp):
TGAAA
Found at i:44019677 original size:11 final size:11
Alignment explanation
Indices: 44019636--44019712 Score: 66
Period size: 11 Copynumber: 7.0 Consensus size: 11
44019626 ATAATTTAAG
*
44019636 TGAAATGGAAT
1 TGAAATGAAAT
*
44019647 TGAAATGGGAAT
1 TGAAAT-GAAAT
44019659 TGAAATGAAAT
1 TGAAATGAAAT
*
44019670 TGGAATGAAA-
1 TGAAATGAAAT
* * *
44019680 TAAAATTAAAA
1 TGAAATGAAAT
*
44019691 TGAAATGAAAA
1 TGAAATGAAAT
*
44019702 TGAAAAGAAAT
1 TGAAATGAAAT
44019713 GACTAATCTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
10 7 0.13
11 37 0.67
12 11 0.20
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:44019680 original size:16 final size:16
Alignment explanation
Indices: 44019636--44019714 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
44019626 ATAATTTAAG
*
44019636 TGAAATGGAATTGAAAT
1 TGAAAT-GAAATGAAAT
* *
44019653 GGGAATTGAAATGAAAT
1 -TGAAATGAAATGAAAT
* *
44019670 TGGAATGAAATAAAAT
1 TGAAATGAAATGAAAT
* *
44019686 TAAAATGAAATGAAAA
1 TGAAATGAAATGAAAT
*
44019702 TGAAAAGAAATGA
1 TGAAATGAAATGA
44019715 CTAATCTCCA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 35 0.73
17 9 0.19
18 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.23
Consensus pattern (16 bp):
TGAAATGAAATGAAAT
Found at i:44021865 original size:106 final size:105
Alignment explanation
Indices: 44021675--44021930 Score: 340
Period size: 106 Copynumber: 2.4 Consensus size: 105
44021665 AATTTTTTTA
*
44021675 ATTTTTTTGGGTACTTGGTGGTGGCCATTGACAGGCTAACA-CA-AAAAAAAAGTTGATTTTTTT
1 ATTTTTTT--GTACTTGGTGGTGGCCATTGACAGG-T--CAGCATCAAAAAAAGTTGATTTTTTT
* * *
44021738 ATACTTGGTGGTGGCCATTGACAGGCTAACATA-AAAAAAAATTG
61 ATACTTGGTGGTAGACATTGACAGGCCAACATACAAAAAAAATTG
* * *
44021782 ATTTTTTTGTACTTGATGGTGGCCATTGACAGGTCAGCATCAAAAAAATTTGATTTATTTTTGTA
1 ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGTCAGCATCAAAAAAAGTTGA-TT-TTTTTATA
*
44021847 CTTGGTGGTAGATATTGACAGGCCAACATACAAAAAAAATTG
64 CTTGGTGGTAGACATTGACAGGCCAACATACAAAAAAAATTG
*
44021889 ATTTTTTT-TACTTGGTGGTGGCCATTGACAGGCCAGCATCAA
1 ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGTCAGCATCAA
44021931 TTTTTTTAAA
Statistics
Matches: 134, Mismatches: 10, Indels: 11
0.86 0.06 0.07
Matches are distributed among these distances:
102 2 0.01
103 2 0.01
104 12 0.09
105 26 0.19
106 65 0.49
107 27 0.20
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (105 bp):
ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGTCAGCATCAAAAAAAGTTGATTTTTTTATACT
TGGTGGTAGACATTGACAGGCCAACATACAAAAAAAATTG
Found at i:44021922 original size:52 final size:52
Alignment explanation
Indices: 44021675--44021923 Score: 329
Period size: 52 Copynumber: 4.7 Consensus size: 52
44021665 AATTTTTTTA
* *
44021675 ATTTTTTTGGGTACTTGGTGGTGGCCATTGACAGGCTAACACAAAAAAAAAGTTG
1 ATTTTTTT--GTACTTGGTGGTGGCCATTGACAGGCCAACATAAAAAAAAA-TTG
* *
44021730 ATTTTTTTATACTTGGTGGTGGCCATTGACAGGCTAACATAAAAAAAAATTG
1 ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACATAAAAAAAAATTG
* * * * *
44021782 ATTTTTTTGTACTTGATGGTGGCCATTGACAGGTCAGCATCAAAAAAATTTG
1 ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACATAAAAAAAAATTG
* **
44021834 ATTTATTTTTGTACTTGGTGGTAGATATTGACAGGCCAACATACAAAAAAAATTG
1 A-TT-TTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACATA-AAAAAAAATTG
44021889 ATTTTTTT-TACTTGGTGGTGGCCATTGACAGGCCA
1 ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCA
44021924 GCATCAATTT
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
52 73 0.43
53 46 0.27
54 33 0.19
55 19 0.11
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.35
Consensus pattern (52 bp):
ATTTTTTTGTACTTGGTGGTGGCCATTGACAGGCCAACATAAAAAAAAATTG
Found at i:44032061 original size:20 final size:19
Alignment explanation
Indices: 44032038--44032174 Score: 78
Period size: 20 Copynumber: 6.9 Consensus size: 19
44032028 ATGCACATTA
44032038 GTGCCCCTGTTTGCACTTT
1 GTGCCCCTGTTTGCACTTT
* ***
44032057 GGTGCCCTTAAATGCACATTT
1 -GTGCCCCTGTTTGCAC-TTT
* ****
44032078 GTGCCACTGAACACACATTT
1 GTGCCCCTGTTTGCAC-TTT
*
44032098 GTGCCCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
* * *
44032117 GGTACCCCTGTATACACTTT
1 -GTGCCCCTGTTTGCACTTT
44032137 AGTGTCCCC-GTTTGCACGTTT
1 -GTG-CCCCTGTTTGCAC-TTT
*
44032158 GTGCCCCTGTTCGCACT
1 GTGCCCCTGTTTGCACT
44032175 ACGATGCCCT
Statistics
Matches: 90, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
19 8 0.09
20 72 0.80
21 10 0.11
ACGTcount: A:0.15, C:0.31, G:0.20, T:0.34
Consensus pattern (19 bp):
GTGCCCCTGTTTGCACTTT
Found at i:44032159 original size:60 final size:60
Alignment explanation
Indices: 44032095--44032244 Score: 212
Period size: 60 Copynumber: 2.5 Consensus size: 60
44032085 TGAACACACA
* * * *
44032095 TTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACACTTTAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
** * *
44032155 TTTGTGCCCCTGTTCGCACTACGATGCCCTTGTAAACAATTCAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
*
44032215 TTTGTG-CCCTGTTCGCACTTTAGTGCCCCT
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCT
44032245 ATTCTGTATA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 19 0.25
60 58 0.75
ACGTcount: A:0.13, C:0.32, G:0.20, T:0.35
Consensus pattern (60 bp):
TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTAAACAATTCAGTGTCCCCGTTTGCACG
Found at i:44034315 original size:42 final size:43
Alignment explanation
Indices: 44034264--44034366 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
44034254 TTGAGATTTG
*
44034264 CATGTAAGACCATGTCTGAGACATTAGCATC-ATATATGATTA
1 CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
* * * * * * *
44034306 CATGTAAGACCCTGTTTGGGACAGTGGCATCGTTGTTTGATTA
1 CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
* *
44034349 CTTGTAAGACCACGTCTG
1 CATGTAAGACCATGTCTG
44034367 GGACGTTGGC
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
42 26 0.54
43 22 0.46
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCATGTCTGAGACAGTAGCATCGATATATGATTA
Found at i:44040383 original size:8 final size:8
Alignment explanation
Indices: 44040370--44040394 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44040360 TTTTTAATGA
44040370 TATTTTAT
1 TATTTTAT
44040378 TATTTTAT
1 TATTTTAT
44040386 TATTTTAT
1 TATTTTAT
44040394 T
1 T
44040395 TAGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:44046262 original size:44 final size:44
Alignment explanation
Indices: 44046191--44046332 Score: 205
Period size: 44 Copynumber: 3.2 Consensus size: 44
44046181 TATGTGATAT
* * *
44046191 CGTGTAAGACCACGTCTAGGACATTGGCATC-ATATTGAAATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-ATTGAGATTTA
* *
44046235 CGTGTAAGATCACGTCTGGGACGTTGGCATCGAATTTAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
*
44046279 CGTGTAAGACCACGTTTGGGACGTTGGCATCGAATTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
*
44046323 TGTGTAAGAC
1 CGTGTAAGAC
44046333 TCTGTCTGGG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 87 0.99
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
Found at i:44111294 original size:25 final size:25
Alignment explanation
Indices: 44111265--44111356 Score: 75
Period size: 25 Copynumber: 3.8 Consensus size: 25
44111255 CCTTAGCGCA
44111265 CTCTCTGATTAATAGCACATTAGTG
1 CTCTCTGATTAATAGCACATTAGTG
* * *
44111290 CTCTCCGATTATTAGCACATTTA-TA
1 CTCTCTGATTAATAGCACA-TTAGTG
* *
44111315 CTCTCTG--T-ATAACACTTTAGTG
1 CTCTCTGATTAATAGCACATTAGTG
* * *
44111337 TTCTCTGTTTAATAGTACAT
1 CTCTCTGATTAATAGCACAT
44111357 AAAAATACAC
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
21 3 0.06
22 12 0.24
23 1 0.02
24 1 0.02
25 30 0.60
26 3 0.06
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (25 bp):
CTCTCTGATTAATAGCACATTAGTG
Found at i:44114613 original size:17 final size:18
Alignment explanation
Indices: 44114585--44114620 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
44114575 GAATTGTAAA
44114585 TATTGAGAAATAAATTAT
1 TATTGAGAAATAAATTAT
*
44114603 TATTG-GAAATATATTAT
1 TATTGAGAAATAAATTAT
44114620 T
1 T
44114621 GAATTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
TATTGAGAAATAAATTAT
Found at i:44126824 original size:21 final size:22
Alignment explanation
Indices: 44126789--44126833 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
44126779 AGCTCTCATA
*
44126789 AATTTTTAGAAAATTATA-AATT
1 AATTGTTAGAAAATT-TAGAATT
44126811 AATTGTTA-AAAATTTAGAATT
1 AATTGTTAGAAAATTTAGAATT
44126832 AA
1 AA
44126834 AATTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 12 0.57
22 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
AATTGTTAGAAAATTTAGAATT
Found at i:44127574 original size:31 final size:31
Alignment explanation
Indices: 44127539--44127602 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
44127529 CCACGTAAAA
*
44127539 ATATATGGTACACTATTTTTAGAAAAAGTAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
44127570 ATATATGGTACACTATTTTTAGAAAAAATAT
1 ATATATGGTACACTATTTTTAGAAAAAATAT
44127601 AT
1 AT
44127603 GATAATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (31 bp):
ATATATGGTACACTATTTTTAGAAAAAATAT
Found at i:44131066 original size:23 final size:23
Alignment explanation
Indices: 44131042--44131086 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
44131032 TGATTTTTAT
44131042 TTTTTA-AAAAAATTAAAAATAA
1 TTTTTATAAAAAATTAAAAATAA
*
44131064 TTTTTATATAAAATTAAAAATAA
1 TTTTTATAAAAAATTAAAAATAA
44131087 AAGAGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTTATAAAAAATTAAAAATAA
Found at i:44133681 original size:42 final size:43
Alignment explanation
Indices: 44133635--44133715 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
44133625 TAAAAGTCAT
44133635 GACCTTTAGCGACG-CTTTCCCACAAACGCCGCTAAAGATTAC
1 GACCTTTAGCGACGTCTTTCCCACAAACGCCGCTAAAGATTAC
* * * *
44133677 GACCTTTAGCGGCGTTTTTTCCACAAATGCCGCTAAAGA
1 GACCTTTAGCGACGTCTTTCCCACAAACGCCGCTAAAGA
44133716 CAATGACGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 13 0.38
43 21 0.62
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
GACCTTTAGCGACGTCTTTCCCACAAACGCCGCTAAAGATTAC
Found at i:44135137 original size:15 final size:17
Alignment explanation
Indices: 44135117--44135154 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
44135107 GATAAGGAAA
44135117 AAAAATTAT-AAAT-AT
1 AAAAATTATAAAATAAT
*
44135132 AAAAATTCTAAAATAAT
1 AAAAATTATAAAATAAT
44135149 AAAAAT
1 AAAAAT
44135155 AAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATAAAATAAT
Found at i:44138080 original size:12 final size:12
Alignment explanation
Indices: 44138047--44138081 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
44138037 TAAAAGAGTA
*
44138047 TACAAACCAATC
1 TACAAACCAGTC
44138059 TACAAACCAGTC
1 TACAAACCAGTC
*
44138071 TACAATCCAGT
1 TACAAACCAGT
44138082 TTAAGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.31, G:0.06, T:0.20
Consensus pattern (12 bp):
TACAAACCAGTC
Found at i:44139900 original size:15 final size:16
Alignment explanation
Indices: 44139880--44139917 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
44139870 CCGACCCCTG
44139880 AATCCCTAAAC-CTTA
1 AATCCCTAAACTCTTA
44139895 AATCCCT-AACTCTTA
1 AATCCCTAAACTCTTA
44139910 AA-CCCTAA
1 AATCCCTAA
44139918 CATCTAACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCCCTAAACTCTTA
Found at i:44139917 original size:14 final size:15
Alignment explanation
Indices: 44139891--44139932 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
44139881 ATCCCTAAAC
44139891 CTTAAATCCCTAAC-T
1 CTTAAA-CCCTAACAT
44139906 CTTAAACCCTAACAT
1 CTTAAACCCTAACAT
*
44139921 C-TAACCCCTAAC
1 CTTAAACCCTAAC
44139933 CCCTAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (15 bp):
CTTAAACCCTAACAT
Found at i:44139987 original size:49 final size:51
Alignment explanation
Indices: 44139882--44139995 Score: 155
Period size: 49 Copynumber: 2.3 Consensus size: 51
44139872 GACCCCTGAA
* * *
44139882 TCCCTAAACCTTAAATCCCTAACTCTTAAACCCTAACATCTAACCCCTAAC
1 TCCCTAAACCTTAAATCCCTAACCCTTAAACCATAACATCTAACCCATAAC
*
44139933 -CCCTAAACCTTAAATCCC-AACCCTTAAACCATAATCA-CTAATCCAT-AC
1 TCCCTAAACCTTAAATCCCTAACCCTTAAACCATAA-CATCTAACCCATAAC
44139981 TCCCTAAACCTTAAA
1 TCCCTAAACCTTAAA
44139996 ATATGAACTC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
48 2 0.04
49 35 0.61
50 20 0.35
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (51 bp):
TCCCTAAACCTTAAATCCCTAACCCTTAAACCATAACATCTAACCCATAAC
Found at i:44140186 original size:23 final size:22
Alignment explanation
Indices: 44140160--44140218 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
44140150 CCTTAACACG
44140160 TCTAACCCCTAAACCCCTAACAT
1 TCTAACCCCTAAACCCCTAA-AT
*
44140183 TCTAACCCCTAAA-CCTTAAAT
1 TCTAACCCCTAAACCCCTAAAT
* *
44140204 CCTAACCCTTAAACC
1 TCTAACCCCTAAACC
44140219 ATAATCCCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.41
22 6 0.19
23 13 0.41
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.24
Consensus pattern (22 bp):
TCTAACCCCTAAACCCCTAAAT
Found at i:44140235 original size:15 final size:14
Alignment explanation
Indices: 44140213--44140260 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
44140203 TCCTAACCCT
44140213 TAAACCATAATCCC
1 TAAACCATAATCCC
* *
44140227 TAAACCCATACTCTC
1 TAAA-CCATAATCCC
* *
44140242 TAAACTAAAATCCC
1 TAAACCATAATCCC
44140256 TAAAC
1 TAAAC
44140261 TATAGTGATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:44140594 original size:41 final size:41
Alignment explanation
Indices: 44140533--44140727 Score: 273
Period size: 41 Copynumber: 4.8 Consensus size: 41
44140523 TAAAATGTTT
* *
44140533 TTAGCGGCGCTTCTTTAAAAATGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
*
44140574 TTAGCGGCGCTTATTCAAAAACGCCGCTAAAGACCAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
* *
44140615 ATAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGTA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
* * * **
44140656 TTAGTGGCGCTTATTTAAAAACGCCGCTAAAGAATAGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
* * *
44140697 TTAGCGGCGCTTCTTAAAAAACTCCACTAAA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
44140728 TCCCTAAAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 136 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCA
Found at i:44140827 original size:39 final size:41
Alignment explanation
Indices: 44140779--44140864 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 41
44140769 TTTGCGGCAC
* * * *
44140779 TTTTT-GAAAAACGCCGCTAATGCTC-ATTTTTAGCGGCG-
1 TTTTTAGAAAAACGCCACCAATCCTCGATCTTTAGCGGCGA
**
44140817 TTTTTAGAAAAGTGCCACCAATCCTCGATCTTTAGCGGCGA
1 TTTTTAGAAAAACGCCACCAATCCTCGATCTTTAGCGGCGA
44140858 TTTTTAG
1 TTTTTAG
44140865 GTAGCGCCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 5 0.13
39 15 0.38
40 12 0.31
41 7 0.18
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (41 bp):
TTTTTAGAAAAACGCCACCAATCCTCGATCTTTAGCGGCGA
Found at i:44144874 original size:44 final size:43
Alignment explanation
Indices: 44144848--44145276 Score: 230
Period size: 44 Copynumber: 9.7 Consensus size: 43
44144838 ATTTTAATTC
* *
44144848 GCTCCACTGCAACTTCAGGGAGATAGGATT-TGCAACTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAT-C-ACTTCAATCT
44144892 GCTCCACTGCAACTTCAGGGAGATAAGATTCA-CTATCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-ATC-A-CTTCAATCT
* * * *
44144937 ACTCCATTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTATCACTTCAATCT
* * ** *
44144981 GCTCCACTACAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTA-TCACTTCAATCT
* * *
44145025 ACTCCACTGCAACTTCAGAGAGATAAGA-T-TCGC--CAGGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTATCACTTCA--ATCT
* * * * * *
44145066 ACTCTACTACAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A--T-CA-CTTCAATCT
* * * * * *
44145117 GTTCCACTACAACTTTAGGAAAATAAGATT-TGCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAT-C-A-CTTCAATCT
** * * * *
44145162 ATTCTACTGCAACTTCAGGGAGATAAGACT-TCATTTCAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATTATCACTTCAATCT
* * ** *
44145204 ACT-CATTGCAACTTCAGGGAGAT-AGTATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAG-ATTA-TCACTTCAATCT
* * *
44145247 ACTCTACTACAACTTCAGGGAGATAAGATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT
44145277 TGTCATCTTC
Statistics
Matches: 299, Mismatches: 60, Indels: 52
0.73 0.15 0.13
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 53 0.18
42 8 0.03
43 14 0.05
44 119 0.40
45 70 0.23
46 2 0.01
48 1 0.00
49 2 0.01
51 26 0.09
53 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTATCACTTCAATCT
Found at i:44144974 original size:89 final size:88
Alignment explanation
Indices: 44144849--44145052 Score: 291
Period size: 89 Copynumber: 2.3 Consensus size: 88
44144839 TTTTAATTCG
* * * *
44144849 CTCCACTGCAACTTCAGGGAGATAGGATTTGCAACTTCAATTTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCAACTTCAATCTGCTCCACTACAACTTCAGGGAG
*
44144914 ATAAGATTCACTATCTTCAATCTA
66 ATAAGATT-ACTAGCTTCAATCTA
* *
44144938 CTCCATTGCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTACAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCAACTTCAATCTGCTCCACTACAACTTCAGGGAG
* * * *
44145003 ATAGGATTATTGGCTTTAATCTA
66 ATAAGATTACTAGCTTCAATCTA
*
44145026 CTCCACTGCAACTTCAGAGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
44145053 TTCGCCAGGA
Statistics
Matches: 102, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 36 0.35
89 66 0.65
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (88 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCAACTTCAATCTGCTCCACTACAACTTCAGGGAG
ATAAGATTACTAGCTTCAATCTA
Found at i:44145008 original size:133 final size:131
Alignment explanation
Indices: 44144840--44145278 Score: 380
Period size: 133 Copynumber: 3.3 Consensus size: 131
44144830 GATTCATCAT
* * * *
44144840 TTTAAT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTTGCAACTTCAATTTGCTCCACTGCAA
1 TTTAATCT-GCTCCACTACAACTTCAGGGAGATAAGATTTGCAACTTCAATCTACTCCACTGCAA
44144904 CTTCAGGGAGATAAGATTCACTATCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGACTTG
65 CTTCAGGGAGATAAGATTC-C-ATCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGACTTG
44144969 TAAC
128 TAAC
* * * *
44144973 TTCAATCTGCTCCACTACAACTTCAGGGAGATAGGATTATTG--GCTTTAATCTACTCCACTGCA
1 TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA-T-TTGCAACTTCAATCTACTCCACTGCA
* * * * * *
44145036 ACTTCAGAGAGATAAGATT-C-GC--CAGGATCTACTCTACTACAACTTCAGAGAGATAAGATCT
64 ACTTCAGGGAGATAAGATTCCATCTTCA--ATCTACTCCATTGCAACTTCAGGGAGATAAGA-CT
44145097 GTGATTTATAGC
126 -TG---TA-A-C
* * * * * * * *
44145109 TTTAATCTGTTCCACTACAACTTTAGGAAAATAAGATTTGCTATCTTCAGTCTATTCTACTGCAA
1 TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGC-AACTTCAATCTACTCCACTGCAA
*
44145174 CTTCAGGGAGATAAGACTT-CAT-TTCAATCCACT-CATTGCAACTTCAGGGAGAT-AGTA-TTA
65 CTTCAGGGAGATAAGA-TTCCATCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAG-ACTT-
* **
44145234 TTGGC
127 GTAAC
* *
44145239 TTTAATCTACTCTACTACAACTTCAGGGAGATAAGATTTG
1 TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTG
44145279 TCATCTTCTT
Statistics
Matches: 246, Mismatches: 39, Indels: 45
0.75 0.12 0.14
Matches are distributed among these distances:
127 2 0.01
129 29 0.12
130 37 0.15
131 3 0.01
132 1 0.00
133 67 0.27
134 8 0.03
135 6 0.02
136 33 0.13
137 49 0.20
138 9 0.04
140 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (131 bp):
TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCAACTTCAATCTACTCCACTGCAAC
TTCAGGGAGATAAGATTCCATCTTCAATCTACTCCATTGCAACTTCAGGGAGATAAGACTTGTAA
C
Found at i:44161599 original size:20 final size:19
Alignment explanation
Indices: 44161576--44161782 Score: 87
Period size: 20 Copynumber: 10.4 Consensus size: 19
44161566 ATGCACATTA
44161576 GTGCCCCTGTTTGCACTTT
1 GTGCCCCTGTTTGCACTTT
* ***
44161595 GGTGCCCTTAAATGCACATTT
1 -GTGCCCCTGTTTGCAC-TTT
* ****
44161616 GTGCCACTGAACACACATTT
1 GTGCCCCTGTTTGCAC-TTT
*
44161636 GTGCCCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
* * *
44161655 GGTACCCCTGTATACACTTT
1 -GTGCCCCTGTTTGCACTTT
44161675 AGTGTCCCC-GTTTGCACGTTT
1 -GTG-CCCCTGTTTGCAC-TTT
* **
44161696 GTGCCCCTGTTCGCACTACG
1 GTGCCCCTGTTTGCACT-TT
* * * * *
44161716 GTGCCCTTGTATACAATTCA
1 GTGCCCCTGTTTGCACTT-T
44161736 GTGTCCCC-GTTTGCACGTTT
1 GTG-CCCCTGTTTGCAC-TTT
*
44161756 GTG-CCCTGTTCGCACTTT
1 GTGCCCCTGTTTGCACTTT
44161774 AGTGCCCCT
1 -GTGCCCCT
44161783 ATTATGTATA
Statistics
Matches: 138, Mismatches: 37, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
18 6 0.04
19 18 0.13
20 99 0.72
21 15 0.11
ACGTcount: A:0.14, C:0.31, G:0.20, T:0.34
Consensus pattern (19 bp):
GTGCCCCTGTTTGCACTTT
Found at i:44161697 original size:60 final size:60
Alignment explanation
Indices: 44161633--44161782 Score: 230
Period size: 60 Copynumber: 2.5 Consensus size: 60
44161623 TGAACACACA
* * *
44161633 TTTGTGCCCCTGTTCGCACTTTGGTACCCCTGTATACACTTTAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTATACAATTCAGTGTCCCCGTTTGCACG
** *
44161693 TTTGTGCCCCTGTTCGCACTACGGTGCCCTTGTATACAATTCAGTGTCCCCGTTTGCACG
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTATACAATTCAGTGTCCCCGTTTGCACG
*
44161753 TTTGTG-CCCTGTTCGCACTTTAGTGCCCCT
1 TTTGTGCCCCTGTTCGCACTTTGGTGCCCCT
44161783 ATTATGTATA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 20 0.25
60 60 0.75
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.36
Consensus pattern (60 bp):
TTTGTGCCCCTGTTCGCACTTTGGTGCCCCTGTATACAATTCAGTGTCCCCGTTTGCACG
Found at i:44167471 original size:8 final size:8
Alignment explanation
Indices: 44167458--44167482 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
44167448 TTTTTAATGA
44167458 TATTTTAT
1 TATTTTAT
44167466 TATTTTAT
1 TATTTTAT
44167474 TATTTTAT
1 TATTTTAT
44167482 T
1 T
44167483 TAGCATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:44174394 original size:44 final size:44
Alignment explanation
Indices: 44174323--44174464 Score: 205
Period size: 44 Copynumber: 3.2 Consensus size: 44
44174313 TATGTGATAT
* * *
44174323 CGTGTAAGACCACGTCTAGGACATTGGCATC-ATATTGAAATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-ATTGAGATTTA
* *
44174367 CGTGTAAGATCACGTCTGGGACGTTGGCATCGAATTTAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
*
44174411 CGTGTAAGACCACGTTTGGGACGTTGGCATCGAATTGAGATTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
*
44174455 TGTGTAAGAC
1 CGTGTAAGAC
44174465 TCTGTCTGGG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 87 0.99
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGAGATTTA
Found at i:44176993 original size:100 final size:97
Alignment explanation
Indices: 44176749--44177033 Score: 279
Period size: 98 Copynumber: 2.8 Consensus size: 97
44176739 ACAACCAAGG
* * * ** *
44176749 TGGTGGAGCCATTCTTTATGACTCCACCAAAATAAAATATCATTTTTAAAATTTTTGGATTAAAA
1 TGGTGGCGCCATTCTTTATGA-TCCACC-AAATAAAATATTATTTTTTAAATTTTTAAATAAAAA
44176814 AACAACACATTTAAAAAAAATCCATACAGTACAC
64 AACAACACATTTAAAAAAAATCCATACAGTACAC
* * *
44176848 TGGTGGCGTCATTCTTTATAGCTCCACCAAATAAAA-ATTATTTTTTTAAATTTTAAAATAAAAA
1 TGGTGGCGCCATTCTTTAT-GATCCACCAAATAAAATATTA-TTTTTTAAATTTTTAAATAAAAA
* * * * * *
44176912 AATAATAGATTTAAAAATATAT-TATACATAGTATAC
64 AACAACACATTTAAAAA-AAATCCATAC--AGTACAC
* *
44176948 TGGTGGCGCCATTCTATATGGATCTACCAAATAAAATATTATTTTTTAAAATTTTTAAATTTGAA
1 TGGTGGCGCCATTCTTTAT-GATCCACCAAATAAAATATTATTTTTT-AAATTTTTAAA--T-AA
*
44177013 AAAAA-ACCACATTTAAAAAAA
61 AAAAACAACACATTTAAAAAAA
44177034 CCTTAGTAAT
Statistics
Matches: 151, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
97 3 0.02
98 44 0.29
99 26 0.17
100 44 0.29
101 14 0.09
102 1 0.01
103 12 0.08
104 7 0.05
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (97 bp):
TGGTGGCGCCATTCTTTATGATCCACCAAATAAAATATTATTTTTTAAATTTTTAAATAAAAAAA
CAACACATTTAAAAAAAATCCATACAGTACAC
Found at i:44177052 original size:100 final size:95
Alignment explanation
Indices: 44176749--44177060 Score: 268
Period size: 100 Copynumber: 3.1 Consensus size: 95
44176739 ACAACCAAGG
* * **
44176749 TGGTGGAGCCATTCTTTATGACTCCACCAAAATAAAATATCA-TTTTTAAAATTTTTGGATTAAA
1 TGGTGGCGCCATTCTTTATGA-TCCACC-AAATAAAATATTATTTTTTAAAATTTTTAAATTAAA
* * * *
44176813 AAACAACACATTTAAAAAAAATCCATACAGTACAC
64 AAA-AACACATTT-AAAAAAA-CCTTATAATAAAC
* * * * *
44176848 TGGTGGCGTCATTCTTTATAGCTCCACCAAATAAAA-ATTATTTTTTTAAATTTTAAAATAAAAA
1 TGGTGGCGCCATTCTTTAT-GATCCACCAAATAAAATATTATTTTTTAAAATTTTTAAATTAAAA
* * * **
44176912 AATAATAGATTTAAAAATATATTATACATAGTATAC
65 AA-AACACATTTAAAAAAACCTTATA-ATA--A-AC
* *
44176948 TGGTGGCGCCATTCTATATGGATCTACCAAATAAAATATTATTTTTTAAAATTTTTAAATTTGAA
1 TGGTGGCGCCATTCTTTAT-GATCCACCAAATAAAATATTATTTTTTAAAATTTTTAAA-TT-AA
*
44177013 AAAAAACCACATTTAAAAAAACCTTAGTAATAAAA
63 AAAAAA-CACATTTAAAAAAACCTTA-TAATAAAC
*
44177048 TGGTGGTGCCATT
1 TGGTGGCGCCATT
44177061 TAGAACGGCT
Statistics
Matches: 168, Mismatches: 34, Indels: 21
0.75 0.15 0.09
Matches are distributed among these distances:
96 3 0.02
97 11 0.07
98 35 0.21
99 23 0.14
100 47 0.28
101 21 0.12
102 3 0.02
103 23 0.14
104 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (95 bp):
TGGTGGCGCCATTCTTTATGATCCACCAAATAAAATATTATTTTTTAAAATTTTTAAATTAAAAA
AAACACATTTAAAAAAACCTTATAATAAAC
Found at i:44179891 original size:61 final size:62
Alignment explanation
Indices: 44179792--44179917 Score: 218
Period size: 61 Copynumber: 2.0 Consensus size: 62
44179782 TATTCTAAAT
44179792 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTAT-GGGTATGGGTCGA
1 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
* * *
44179853 TTTAATTATTATCTTATCTATGATGTTTCCTACGAAGTTCAAAATTATGGGGTATGGGTCGA
1 TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
44179915 TTT
1 TTT
44179918 CACTTCACAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 45 0.74
62 16 0.26
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (62 bp):
TTTAATTACTATCTTATCTATGATGTTTCATACAAAGTTCAAAATTATGGGGTATGGGTCGA
Found at i:44180515 original size:14 final size:13
Alignment explanation
Indices: 44180496--44180532 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
44180486 CTTGCGGTAG
44180496 GGTTTAGGGTTATT
1 GGTTTAGGGTTA-T
44180510 GGTTTAGGGTTAT
1 GGTTTAGGGTTAT
44180523 GG-TTAGGGTT
1 GGTTTAGGGTT
44180533 TTAGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 12 0.52
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.46
Consensus pattern (13 bp):
GGTTTAGGGTTAT
Found at i:44180786 original size:95 final size:94
Alignment explanation
Indices: 44180653--44180968 Score: 407
Period size: 94 Copynumber: 3.4 Consensus size: 94
44180643 TGTTTATTAT
44180653 TTTTTAAGAAAAAAT-TAATTAAATTAGGGTTT-AGGGTTACTTGAGTAATTTAATTAAAAAATT
1 TTTTTAAGAAAAAATCTAA-TAAATTAGGGTTTGAGGGTTACTTGAGTAATTTAATT-AAAAATT
44180716 TTAAAATCAGATTAGGATTTAGAGTTAAGGG
64 TTAAAATCAGATTAGGATTTAGAGTTAAGGG
* *
44180747 TCTTTAAGAAAAAAATCTAATAAACTAGGGTTTGA-GGTTACTTGAGTAATTTAATTAAAAATTT
1 TTTTTAAG-AAAAAATCTAATAAATTAGGGTTTGAGGGTTACTTGAGTAATTTAATTAAAAATTT
*
44180811 AAAAATCAGATTAGGATTTAGAGTTAAGGG
65 TAAAATCAGATTAGGATTTAGAGTTAAGGG
* * * * *
44180841 TTTTTCAGAAAAAATCAAATAAATTAGGG-TTCAGGGTTACTTGAGTAAATTAATTATAAA-TTT
1 TTTTTAAGAAAAAATCTAATAAATTAGGGTTTGAGGGTTACTTGAGTAATTTAATTAAAAATTTT
* * * *
44180904 ATAAT-AAATTA-G-TTTAGGGTTTAGGG
66 AAAATCAGATTAGGATTTAGAGTTAAGGG
* *
44180930 TTTTTAAGTAAAAACCTAAATAAATTAGGGTTTG-GGGTT
1 TTTTTAAGAAAAAATCT-AATAAATTAGGGTTTGAGGGTT
44180969 TACGGTTACT
Statistics
Matches: 196, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
89 25 0.13
90 18 0.09
91 7 0.04
92 9 0.05
93 43 0.22
94 50 0.26
95 40 0.20
96 4 0.02
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.37
Consensus pattern (94 bp):
TTTTTAAGAAAAAATCTAATAAATTAGGGTTTGAGGGTTACTTGAGTAATTTAATTAAAAATTTT
AAAATCAGATTAGGATTTAGAGTTAAGGG
Found at i:44181230 original size:126 final size:126
Alignment explanation
Indices: 44181005--44181290 Score: 473
Period size: 126 Copynumber: 2.3 Consensus size: 126
44180995 TAATTTAAAG
* * * * *
44181005 AAGCTCCGACGTGGACGCGCTTTTACTACAGTGGCTCCTGAGAAAGTAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* *
44181070 CTGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTAAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
44181131 AAGCTCCCACGTGGACGCGCTTTTGTTACAGTAGCTCCTGAAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
44181196 CTAAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 CTAAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
* *
44181257 AAGCTTCCACGTGGACGTGCTTTTGCTACAGTAG
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAG
44181291 TTGAACGTTA
Statistics
Matches: 148, Mismatches: 12, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
126 148 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
CTAAGCAAACAATGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
Found at i:44183859 original size:11 final size:11
Alignment explanation
Indices: 44183843--44183946 Score: 53
Period size: 11 Copynumber: 9.7 Consensus size: 11
44183833 TTAAATAGGG
44183843 ATTTGAGAGAA
1 ATTTGAGAGAA
*
44183854 ATTTGAAAGGAA
1 ATTTGAGA-GAA
44183866 A-TTGAGAGAA
1 ATTTGAGAGAA
* *
44183876 AATTGAGATTAA
1 ATTTGAGA-GAA
*
44183888 A--T-AG-G-G
1 ATTTGAGAGAA
44183894 ATTTGAGAGAA
1 ATTTGAGAGAA
*
44183905 ATTTGAAAGCAA
1 ATTTGAGAG-AA
44183917 A-TTGAGAGGAA
1 ATTTGAGA-GAA
44183928 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
44183939 ATTAGAGA
1 ATTTGAGA
44183947 AAGAATGATT
Statistics
Matches: 73, Mismatches: 9, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
6 1 0.01
8 1 0.01
9 4 0.05
10 6 0.08
11 45 0.62
12 16 0.22
ACGTcount: A:0.47, C:0.01, G:0.28, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:44183889 original size:22 final size:22
Alignment explanation
Indices: 44183845--44183948 Score: 75
Period size: 22 Copynumber: 4.5 Consensus size: 22
44183835 AAATAGGGAT
*
44183845 TTGAGAGAAATTTGAAAGGAAA
1 TTGAGAGAAAATTGAAAGGAAA
* *
44183867 TTGAGAGAAAATTGAGATTAAATAGGGAT
1 TTGAGAGAAAATT--G----AA-AGGAAA
* *
44183896 TTGAGAGAAATTTGAAAGCAAA
1 TTGAGAGAAAATTGAAAGGAAA
* *
44183918 TTGAGAGGAAATTGAGAGGAAA
1 TTGAGAGAAAATTGAAAGGAAA
44183940 TT-AGAGAAA
1 TTGAGAGAAA
44183949 GAATGATTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
21 6 0.10
22 35 0.56
23 2 0.03
24 1 0.02
27 1 0.02
28 2 0.03
29 16 0.25
ACGTcount: A:0.48, C:0.01, G:0.28, T:0.23
Consensus pattern (22 bp):
TTGAGAGAAAATTGAAAGGAAA
Found at i:44183889 original size:51 final size:51
Alignment explanation
Indices: 44183833--44183934 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
44183823 TAAAGCTCTT
*
44183833 TTAAATAGGGATTTGAGAGAAATTTGAAAGGAAATTGAGAGAAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGAAAATTGAGA
*
44183884 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGGAAATTGAGA
1 TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGAAAATTGAGA
44183935 GGAAATTAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.46, C:0.01, G:0.27, T:0.25
Consensus pattern (51 bp):
TTAAATAGGGATTTGAGAGAAATTTGAAAGCAAATTGAGAGAAAATTGAGA
Found at i:44184362 original size:9 final size:9
Alignment explanation
Indices: 44184348--44184395 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
44184338 TAAAAATTTT
44184348 ATTTTTATA
1 ATTTTTATA
*
44184357 ATTTTTATG
1 ATTTTTATA
*
44184366 ATTTTTATG
1 ATTTTTATA
44184375 ATTTTTA-A
1 ATTTTTATA
44184383 TATTTTTA-A
1 -ATTTTTATA
44184392 ATTT
1 ATTT
44184396 AAAAGCGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
8 4 0.11
9 32 0.89
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Done.