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 114 of 120
Found at i:33164701 original size:29 final size:29
Alignment explanation
Indices: 33164577--33164749 Score: 149
Period size: 29 Copynumber: 5.8 Consensus size: 29
33164567 TTTGGAAGAC
*
33164577 CTAATTAAAATTTTT-AAAAATTATGGAGGAT
1 CTAATTAAAATTTTTAAAAAATT-T--AGGAG
* *
33164608 CTAATTAAAATCTTCT--AAAATTTTGGAAAG
1 CTAATTAAAAT-TTTTAAAAAATTTAGG--AG
* * * * *
33164638 CTTAGTGAGAATTTTCAAAAAAATT-GGAGG
1 C-TAATTAAAATTTTTAAAAAATTTAGGA-G
33164668 TCTAATTAAAATTTTTAAAAAATTTAGGAG
1 -CTAATTAAAATTTTTAAAAAATTTAGGAG
33164698 CTAATTAAAATTTTTAAAAAATTTAGGAG
1 CTAATTAAAATTTTTAAAAAATTTAGGAG
33164727 CTAATTAAAA-TTTTAAATAAATT
1 CTAATTAAAATTTTTAAA-AAATT
33164750 AACAAAAACT
Statistics
Matches: 118, Mismatches: 14, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
28 9 0.08
29 45 0.38
30 25 0.21
31 30 0.25
32 9 0.08
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.38
Consensus pattern (29 bp):
CTAATTAAAATTTTTAAAAAATTTAGGAG
Found at i:33165873 original size:2 final size:2
Alignment explanation
Indices: 33165868--33165896 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33165858 TTGAAAAAAG
33165868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33165897 AATTTTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33168382 original size:15 final size:16
Alignment explanation
Indices: 33168343--33168383 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
33168333 ATATATTAAG
33168343 TTATATAAATTTGAAAA
1 TTATATAAA-TTGAAAA
33168360 TTCA-ATAAA-TGAAAA
1 TT-ATATAAATTGAAAA
33168375 TTATATAAA
1 TTATATAAA
33168384 ATTAAACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
17 7 0.32
18 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
TTATATAAATTGAAAA
Found at i:33170849 original size:7 final size:7
Alignment explanation
Indices: 33170837--33170861 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33170827 AGTTGTTTCA
33170837 TATTTAG
1 TATTTAG
33170844 TATTTAG
1 TATTTAG
33170851 TATTTAG
1 TATTTAG
33170858 TATT
1 TATT
33170862 ATGTATATAA
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:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:33171751 original size:21 final size:22
Alignment explanation
Indices: 33171727--33171781 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
33171717 CTAACACCCA
33171727 CAACCACAATCCCT-GCCGGAG
1 CAACCACAATCCCTCGCCGGAG
*
33171748 CAACCACAA-CCATCGCCGGAG
1 CAACCACAATCCCTCGCCGGAG
*
33171769 CAACCAAAATCCC
1 CAACCACAATCCC
33171782 CACCGAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.35, C:0.44, G:0.15, T:0.07
Consensus pattern (22 bp):
CAACCACAATCCCTCGCCGGAG
Found at i:33171944 original size:24 final size:24
Alignment explanation
Indices: 33171917--33171972 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
33171907 CATTTAATAA
*
33171917 AATAAAAATTGTTTTTA-ATATTTT
1 AATAAAAATTATTTTTATAT-TTTT
*
33171941 AATAGTAAATTATTTTTATATTTTT
1 AATA-AAAATTATTTTTATATTTTT
33171966 AATAAAA
1 AATAAAA
33171973 TTTAAGTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.22
25 19 0.70
26 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
AATAAAAATTATTTTTATATTTTT
Found at i:33171956 original size:25 final size:25
Alignment explanation
Indices: 33171922--33171969 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33171912 AATAAAATAA
*
33171922 AAATTGTTTTTA-ATATTTTAATAGT
1 AAATTATTTTTATAT-TTTTAATAGT
33171947 AAATTATTTTTATATTTTTAATA
1 AAATTATTTTTATATTTTTAATA
33171970 AAATTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AAATTATTTTTATATTTTTAATAGT
Found at i:33174702 original size:125 final size:126
Alignment explanation
Indices: 33174500--33174805 Score: 404
Period size: 125 Copynumber: 2.4 Consensus size: 126
33174490 AAGCGTCACC
* *
33174500 ATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTCAAGAACTACTATAGAAAAAGAGCGTCCAT
1 ATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTCAAGAACTACTGTAGAAAAAGAGCGTCCAC
** *
33174565 GTAGGGGCTTTTTTCAGTGTTTTTGCTGACAGTGCATCCTGCTTGAAGAGTTTTTGACACT
66 GTAGGGGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGAGGTTTTGACACT
* * * *
33174626 ATTTGCTCGGAACCGTCTT-TTCAGAATTATTTTTT-AGGAACTACTGTAGAAAAAGAGCGTCCA
1 ATTTGTTCAGAACCGTCTTCTT-AAAATTATTTTTTCAAGAACTACTGTAGAAAAAGAGCGTCCA
* * * * * *
33174689 CGT-GGGAGTTTTTTTTAGTAATTTTGCTGACAGTGCATCTTGCTTGAAGTGGTTTTGGCATT
65 CGTAGGG-GCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGAGGTTTTGACACT
* *
33174751 ATCTT-TTCAGAATCATCTTCTTAAAATTATTTTTTCAAGAACTACTGTAGAAAAA
1 AT-TTGTTCAGAACCGTCTTCTTAAAATTATTTTTTCAAGAACTACTGTAGAAAAA
33174806 AAAAACAAAA
Statistics
Matches: 154, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
124 3 0.02
125 100 0.65
126 51 0.33
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (126 bp):
ATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTCAAGAACTACTGTAGAAAAAGAGCGTCCAC
GTAGGGGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTTGAAGAGGTTTTGACACT
Found at i:33174980 original size:69 final size:68
Alignment explanation
Indices: 33174882--33175015 Score: 191
Period size: 69 Copynumber: 2.0 Consensus size: 68
33174872 AGAAAAAACT
*
33174882 AAACCATAATTTAATTAATTTTCTTAAAAACCCTAAACCTTAATTTAATTAATTTAAACCCTAAA
1 AAACCATAATTTAATTAATTTTCTTAAAAACCCTAAACCTTAATTT-ATT-ACTTAAACCCTAAA
33174947 CCCAA
64 CCCAA
* * *
33174952 AAACC-TAATTTAATT-ATTTTTTTAAAAAACCTTAAACCTTAATTTATTCCTTAAACCCTAAAC
1 AAACCATAATTTAATTAATTTTCTT-AAAAACCCTAAACCTTAATTTATTACTTAAACCCTAAAC
33175015 C
65 C
33175016 ATAAATTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
67 14 0.24
68 10 0.17
69 30 0.51
70 5 0.08
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (68 bp):
AAACCATAATTTAATTAATTTTCTTAAAAACCCTAAACCTTAATTTATTACTTAAACCCTAAACC
CAA
Found at i:33174995 original size:34 final size:33
Alignment explanation
Indices: 33174874--33174997 Score: 96
Period size: 34 Copynumber: 3.7 Consensus size: 33
33174864 ATTATTTAAG
* *
33174874 AAAAAA-CTAAACCATAATTTAATTAATTTTCTT
1 AAAAAACCTAAACCTTAATTTAATT-ATTTTTTT
* *
33174907 AAAAACCCTAAACCTTAATTTAATTA---ATTT
1 AAAAAACCTAAACCTTAATTTAATTATTTTTTT
*
33174937 AAACCCTAAACCCAAAAACC-TAATTTAATTATTTTTTT
1 AAA----AAA-CC-TAAACCTTAATTTAATTATTTTTTT
33174975 AAAAAACCTTAAACCTTAATTTA
1 AAAAAACC-TAAACCTTAATTTA
33174998 TTCCTTAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
30 5 0.07
33 13 0.18
34 29 0.41
35 13 0.18
36 5 0.07
38 6 0.08
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (33 bp):
AAAAAACCTAAACCTTAATTTAATTATTTTTTT
Found at i:33175072 original size:15 final size:16
Alignment explanation
Indices: 33175039--33175072 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33175029 ACAAAACCTT
*
33175039 AACCCTAAATCCTAAA
1 AACCCTAAATCCAAAA
33175055 AACCCTAAA-CCAAAA
1 AACCCTAAATCCAAAA
33175070 AAC
1 AAC
33175073 TTTAGGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (16 bp):
AACCCTAAATCCAAAA
Found at i:33183098 original size:22 final size:23
Alignment explanation
Indices: 33183044--33183100 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
33183034 ATTCTTTTAA
33183044 AAATTATAAAAATATATATTATTT
1 AAATTAT-AAAATATATATTATTT
*
33183068 AAATGATAAAAT-TATATT-TTT
1 AAATTATAAAATATATATTATTT
*
33183089 ATTATTATAAAA
1 A-AATTATAAAA
33183101 ATTAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 5 0.17
24 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATTATAAAATATATATTATTT
Found at i:33186018 original size:54 final size:54
Alignment explanation
Indices: 33185954--33186061 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
33185944 ATTTCGAATT
* *
33185954 GTTATCAATGTCAACCATAGTTTATATGTTTCAGAAAATGAGATAATATGGTTA
1 GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
*
33186008 GTTATCAATGTCAACCATAGTTTGTATGATTCAGAAAATGAAATAATATGGTTA
1 GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
33186062 ACCATATGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (54 bp):
GTTATCAATGTCAACCATAGTTTATATGATTCAGAAAATGAAATAATATGGTTA
Found at i:33188179 original size:3 final size:3
Alignment explanation
Indices: 33188162--33188197 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
33188152 TCCATTATAC
*
33188162 ATT AAT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
33188198 AAGTTATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:33200417 original size:14 final size:14
Alignment explanation
Indices: 33200386--33200445 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
33200376 TAATTTTAGT
* **
33200386 ATATTTGATATATT
1 ATATTTTATATAAA
33200400 ATATTTTATATAAA
1 ATATTTTATATAAA
33200414 ATATTTT-T-TAAA
1 ATATTTTATATAAA
*
33200426 ATTGTTTTTATATAAA
1 A-T-ATTTTATATAAA
33200442 ATAT
1 ATAT
33200446 AATATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
12 5 0.14
13 2 0.05
14 23 0.62
15 2 0.05
16 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
ATATTTTATATAAA
Found at i:33200418 original size:28 final size:28
Alignment explanation
Indices: 33200386--33200445 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
33200376 TAATTTTAGT
*
33200386 ATATTTGAT-ATATTATATTTTATATAAA
1 ATATTTGATAAAATTAT-TTTTATATAAA
** *
33200414 ATATTTTTTAAAATTGTTTTTATATAAA
1 ATATTTGATAAAATTATTTTTATATAAA
33200442 ATAT
1 ATAT
33200446 AATATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
ATATTTGATAAAATTATTTTTATATAAA
Found at i:33209086 original size:17 final size:17
Alignment explanation
Indices: 33209060--33209101 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
33209050 GTTATTGTTG
*
33209060 TTATTTTTATTGTATTA
1 TTATTATTATTGTATTA
* *
33209077 TTATTATTATTTTATTG
1 TTATTATTATTGTATTA
33209094 TTATTATT
1 TTATTATT
33209102 TGAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
TTATTATTATTGTATTA
Found at i:33209101 original size:14 final size:14
Alignment explanation
Indices: 33209049--33209102 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
33209039 TTTTTACTAC
*
33209049 TGTTATTGTTGTTAT
1 TGTTATTATT-TTAT
* * *
33209064 TTTTATTGTATTAT
1 TGTTATTATTTTAT
*
33209078 TATTATTATTTTAT
1 TGTTATTATTTTAT
33209092 TGTTATTATTT
1 TGTTATTATTT
33209103 GAATATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 25 0.76
15 8 0.24
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (14 bp):
TGTTATTATTTTAT
Found at i:33209109 original size:22 final size:22
Alignment explanation
Indices: 33209064--33209113 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
33209054 TTGTTGTTAT
* *
33209064 TTTTATTGTATTATTATTATTA
1 TTTTATTGTATTATTATGAATA
33209086 TTTTATTGTTATTATT-TGAATA
1 TTTTATTG-TATTATTATGAATA
33209108 TTTTAT
1 TTTTAT
33209114 AACTCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTATTGTATTATTATGAATA
Found at i:33209686 original size:17 final size:17
Alignment explanation
Indices: 33209660--33209706 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
33209650 GGGTTGGGTC
*
33209660 AATCTGACCTGAGCCAA
1 AATCTTACCTGAGCCAA
33209677 AATCTTACCTGAGCCAA
1 AATCTTACCTGAGCCAA
*
33209694 AATCTTACTTGAG
1 AATCTTACCTGAG
33209707 GCTCATTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (17 bp):
AATCTTACCTGAGCCAA
Found at i:33210187 original size:18 final size:19
Alignment explanation
Indices: 33210147--33210188 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
33210137 AAAAAACCTG
33210147 AAAATTTTTAAAAGAATAT
1 AAAATTTTTAAAAGAATAT
*
33210166 -AAATTTTTATAA-AATAT
1 AAAATTTTTAAAAGAATAT
33210183 AAAATT
1 AAAATT
33210189 AAAACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTTTTAAAAGAATAT
Found at i:33219706 original size:21 final size:22
Alignment explanation
Indices: 33219665--33219706 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
33219655 TTATGAAAGA
33219665 AATTGGAAAATCTTGTGATGAT
1 AATTGGAAAATCTTGTGATGAT
33219687 AATTGGAATAAT-TT-TGATGA
1 AATTGGAA-AATCTTGTGATGA
33219707 AGAAGGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (22 bp):
AATTGGAAAATCTTGTGATGAT
Found at i:33219748 original size:12 final size:12
Alignment explanation
Indices: 33219716--33219749 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
33219706 AAGAAGGTGG
33219716 TGGTGGTTGTGA
1 TGGTGGTTGTGA
33219728 TGGAT-GTTGTGA
1 TGG-TGGTTGTGA
33219740 TGGTGGTTGT
1 TGGTGGTTGT
33219750 AAGGGGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.09, C:0.00, G:0.47, T:0.44
Consensus pattern (12 bp):
TGGTGGTTGTGA
Found at i:33225279 original size:42 final size:42
Alignment explanation
Indices: 33225202--33225323 Score: 190
Period size: 42 Copynumber: 2.8 Consensus size: 42
33225192 CGCCATTGTT
* *
33225202 GAGGCGCCAAAGAAAGTGGAAGAAGCCATTGTTGAGGCTCCAAAG
1 GAGGCCCCAAAGAAA---GAAGAAGTCATTGTTGAGGCTCCAAAG
*
33225247 GAGGCCCCAAAGAAAGCAGAAGTCATTGTTGAGGCTCCAAAG
1 GAGGCCCCAAAGAAAGAAGAAGTCATTGTTGAGGCTCCAAAG
33225289 GAGGCCCCAAAGAAAGAAGAAGTCATTGTTGAGGC
1 GAGGCCCCAAAGAAAGAAGAAGTCATTGTTGAGGC
33225324 AAAAACAATG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
42 59 0.81
45 14 0.19
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.14
Consensus pattern (42 bp):
GAGGCCCCAAAGAAAGAAGAAGTCATTGTTGAGGCTCCAAAG
Found at i:33225369 original size:3 final size:3
Alignment explanation
Indices: 33225361--33225386 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
33225351 AAAGAAAAAG
33225361 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
33225387 GGTTATTGTT
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:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:33226008 original size:23 final size:23
Alignment explanation
Indices: 33225965--33226009 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33225955 CCTAAAAGTT
* *
33225965 TAAAAATTTAAAACTTCAAGTAC
1 TAAAAATATAAAACTTAAAGTAC
33225988 TAAAAATGATAAAA-TTAAAGTA
1 TAAAAAT-ATAAAACTTAAAGTA
33226010 TATAGACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (23 bp):
TAAAAATATAAAACTTAAAGTAC
Found at i:33229987 original size:127 final size:124
Alignment explanation
Indices: 33229856--33230194 Score: 308
Period size: 124 Copynumber: 2.7 Consensus size: 124
33229846 CAAAATCCTA
* * ** * * *
33229856 AAACAACTAAAACAGAAAATTACATGATCTAAACCTGAATCAAGTTGTTATCTTTATACCTACAA
1 AAACAACTAAAACACAAAATTAAATGATCTAAACCCAAATCAAATT-CTACCTTTATACCTAC--
* * * * *
33229921 ACAACATTCACACTCAAACTTTGAACTACAAAAATATTCAAACTCGAAAATACTTGAACTTG
63 ACAACACTAACACTCAAACTCTAAACTACAAAAACATTCAAACTCGAAAATACTTGAACTTG
* * * *
33229983 AAACAATTAAAACCCAAAATTAAATGATCTAAACCCAAATCAAATTCTACCTTTATACTTACCCA
1 AAACAACTAAAACACAAAATTAAATGATCTAAACCCAAATCAAATTCTACCTTTATACCTACACA
* *** * *
33230048 ACACTAACACTCAAACTCTAAACTACAAAAACATTCAAAC-CAGAAAACACCCAAATTTA
66 ACACTAACACTCAAACTCTAAACTACAAAAACATTCAAACTC-GAAAATACTTGAACTTG
*** * * * **
33230107 AAACAACTAAATTTCAAAATTACATTATAC-AAACCCGAATCAAATTACTATATTTATACCTACA
1 AAACAACTAAAACACAAAATTAAATGAT-CTAAACCCAAATCAAATT-CTACCTTTATACCTACA
*
33230171 CAACACTCACA-TCCAAACTC-AAAC
64 CAACACTAACACT-CAAACTCTAAAC
33230195 AACTTAGCTG
Statistics
Matches: 174, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
123 1 0.01
124 90 0.52
125 31 0.18
126 13 0.07
127 39 0.22
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (124 bp):
AAACAACTAAAACACAAAATTAAATGATCTAAACCCAAATCAAATTCTACCTTTATACCTACACA
ACACTAACACTCAAACTCTAAACTACAAAAACATTCAAACTCGAAAATACTTGAACTTG
Found at i:33231173 original size:51 final size:52
Alignment explanation
Indices: 33231082--33231196 Score: 135
Period size: 51 Copynumber: 2.2 Consensus size: 52
33231072 ATATTACGAG
* * * *
33231082 CTAAATTTGTTAAATCAAGGCCAAATTGATAGAATATGTAAA-TGTTTGTGGG
1 CTAAATTTGTTAAATCAAGACCAAATTGACACAATATGTAAACT-TTTGTGGA
* * * *
33231134 TTAAATTTGTTAAA-CAATACCAATTTGACACAATGTGTAAACTTTTGTGGA
1 CTAAATTTGTTAAATCAAGACCAAATTGACACAATATGTAAACTTTTGTGGA
33231185 CTAAATTTGTTA
1 CTAAATTTGTTA
33231197 TTATACCAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
51 39 0.74
52 14 0.26
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (52 bp):
CTAAATTTGTTAAATCAAGACCAAATTGACACAATATGTAAACTTTTGTGGA
Found at i:33232651 original size:22 final size:22
Alignment explanation
Indices: 33232626--33232679 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
33232616 TTTATGTTTT
*
33232626 ATATATATTATTTTATTATATA
1 ATATATATTATTGTATTATATA
*
33232648 ATATAT-TATATTGTATTATATT
1 ATATATAT-TATTGTATTATATA
*
33232670 ATATAAATTA
1 ATATATATTA
33232680 AATAGATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATATTATTGTATTATATA
Found at i:33232658 original size:5 final size:5
Alignment explanation
Indices: 33232624--33232673 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
33232614 TTTTTATGTT
*
33232624 TTATA -TATA TTAT- TT-TA TTATA TAATATA TTATA TTGTA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
33232673 T
1 T
33232674 AAATTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 1 0.03
4 8 0.21
5 24 0.63
7 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:33232834 original size:15 final size:17
Alignment explanation
Indices: 33232816--33232847 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
33232806 CAGAATAGAA
33232816 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
33232831 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
33232848 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:33233539 original size:3 final size:3
Alignment explanation
Indices: 33233512--33233564 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
33233502 GTGATGTAAG
* * *
33233512 TAT TAA TAT TAG TAT TAA T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
33233559 TAT TAT
1 TAT TAT
33233565 GAGTGAGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 1 0.02
3 42 0.98
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:33233744 original size:21 final size:22
Alignment explanation
Indices: 33233719--33233770 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
33233709 AAATAATTAT
33233719 TGATTGAAATGTGAGAA-AT-TG
1 TGATTGAAAT-TGAGAATATATG
33233740 TGATTG-AATTGAGAATATATG
1 TGATTGAAATTGAGAATATATG
*
33233761 TGATTTAAAT
1 TGATTGAAAT
33233771 ACCCTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.22
20 5 0.19
21 13 0.48
22 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (22 bp):
TGATTGAAATTGAGAATATATG
Found at i:33233954 original size:37 final size:39
Alignment explanation
Indices: 33233895--33233990 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
33233885 CGGATAGATT
* * * *
33233895 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
33233932 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
33233971 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
33233991 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:33233974 original size:39 final size:38
Alignment explanation
Indices: 33233854--33233987 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 38
33233844 GACCTCGAGT
* * *
33233854 CGATGAGACACTGGGTGTCACAATATTTCTTCGGATA-GATT
1 CGATGAGACACTGGGTGTCA-ACTA-TTCTTC-GA-ACTATC
** ** * *
33233895 CGATGAGGTACTGGGTACCAACT-TTCTTCG-GCTTTGC
1 CGATGAGACACTGGGTGTCAACTATTCTTCGAACTAT-C
33233932 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGACACTGGGTGTCAACTATT-CTTCGAACTATC
*
33233971 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
33233988 CCATTCTGGT
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
36 1 0.01
37 20 0.28
38 8 0.11
39 22 0.31
40 5 0.07
41 16 0.22
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTATTCTTCGAACTATC
Found at i:33234747 original size:3 final size:3
Alignment explanation
Indices: 33234739--33234766 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
33234729 TATAAAATTT
33234739 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
33234767 GAGATGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:33236922 original size:12 final size:10
Alignment explanation
Indices: 33236906--33236947 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
33236896 AACCAAATGT
*
33236906 AATAAT-ATC
1 AATAATAATA
33236915 AATAATAATA
1 AATAATAATA
33236925 AGAGTAATAATA
1 A-A-TAATAATA
33236937 AATAATAATA
1 AATAATAATA
33236947 A
1 A
33236948 GTTAATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 6 0.21
10 12 0.41
11 2 0.07
12 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (10 bp):
AATAATAATA
Found at i:33236958 original size:22 final size:22
Alignment explanation
Indices: 33236904--33236948 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
33236894 ATAACCAAAT
33236904 GTAATAATATCAATAATAATAAGA
1 GTAATAATA--AATAATAATAAGA
33236928 GTAATAATAAATAATAATAAG
1 GTAATAATAAATAATAATAAG
33236949 TTAATTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (22 bp):
GTAATAATAAATAATAATAAGA
Found at i:33243251 original size:3 final size:3
Alignment explanation
Indices: 33243237--33243289 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
33243227 ATTAAAAGGG
*
33243237 AAT AAA AAT AAT AAT AA- AA- AAT AAT AA- AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33243282 AAT AAT AA
1 AAT AAT AA
33243290 AATCTAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 6 0.13
3 40 0.87
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:33244740 original size:43 final size:42
Alignment explanation
Indices: 33244648--33244780 Score: 155
Period size: 41 Copynumber: 3.2 Consensus size: 42
33244638 TTTTAGTCTG
** * *
33244648 CTCCACTGTAACTTCAGGGAGATAAGA-CTGGATGCGATCTA
1 CTCCACTACAACTTCAGAGAGATAAGATCTTGATGCGATCTA
*
33244689 CTCTACTACAACTTCAGAGAGATAAGATCTTTGATGCGATCTA
1 CTCCACTACAACTTCAGAGAGATAAGATC-TTGATGCGATCTA
** * *
33244732 CTCCACTACTGCTT-AGAGAGATAAGATC-TAATGCGATCTG
1 CTCCACTACAACTTCAGAGAGATAAGATCTTGATGCGATCTA
33244772 CTCCACTAC
1 CTCCACTAC
33244781 TGTTTAGGGA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 19 0.24
41 23 0.29
42 15 0.19
43 23 0.29
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
CTCCACTACAACTTCAGAGAGATAAGATCTTGATGCGATCTA
Found at i:33244766 original size:40 final size:40
Alignment explanation
Indices: 33244666--33244801 Score: 157
Period size: 40 Copynumber: 3.3 Consensus size: 40
33244656 TAACTTCAGG
* * **
33244666 GAGATAAGA-CTGGATGCGATCTACTCTACTACAACTTCAGA
1 GAGATAAGATCT-AATGCGATCTACTCCACTACTGCTT-AGA
*
33244707 GAGATAAGATCTTTGATGCGATCTACTCCACTACTGCTTAGA
1 GAGATAAGATC--TAATGCGATCTACTCCACTACTGCTTAGA
* * *
33244749 GAGATAAGATCTAATGCGATCTGCTCCACTACTGTTTAGG
1 GAGATAAGATCTAATGCGATCTACTCCACTACTGCTTAGA
33244789 GAGATAAGATCTA
1 GAGATAAGATCTA
33244802 CAATCTTCAA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
40 38 0.45
41 9 0.11
42 15 0.18
43 22 0.26
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (40 bp):
GAGATAAGATCTAATGCGATCTACTCCACTACTGCTTAGA
Found at i:33244824 original size:127 final size:124
Alignment explanation
Indices: 33244686--33245076 Score: 350
Period size: 127 Copynumber: 3.1 Consensus size: 124
33244676 TGGATGCGAT
* * * *
33244686 CTACTCTACTACAACTTCAGAGAGATAAGATCTTTGATGCGATCTACTCCACTACTGCTTAGAGA
1 CTACTCCACTAC-ACTTCAGAGAGATAAGAT-TTTGCTTCGATCTGCTCCACTACTGCTTAG-GA
*
33244751 GATAAGATCTAATGCGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATCTTCAAC
63 GATAAGATCTAATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
* * * *
33244813 CTACTCCACTACTAC-TCAGGGAGATAGGATTGGTTTCTTCTATCTGCTCCACTACTGCTTAGGG
1 CTACTCCACTAC-ACTTCAGAGAGATAAGATT--TTGCTTCGATCTGCTCCACTACTGCTTA-GG
* * * * * * * * *
33244877 AGATAAGATCTAATGCTTTAACCTACTCCATTGCTGCTCAGGGAGATAGGAT-T-C-GTGGCTTA
62 AGATAAGATCTAATGC---GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT--CTTC
*
33244939 AAT
122 AAC
* *
33244942 CTGCTTCC-TTACACTT--GA-AGATAAGATTTACTGTCTTCGATCTGCTCCACTACTGCTTAGG
1 CTAC-TCCACTACACTTCAGAGAGATAAGATTT--TG-CTTCGATCTGCTCCACTACTGCTTAGG
* *
33245003 AAGATAAG-TCTTGATACGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
62 -AGATAAGATC-TAATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
33245067 CTACTCCACT
1 CTACTCCACT
33245077 GCTACTTAGG
Statistics
Matches: 205, Mismatches: 40, Indels: 40
0.72 0.14 0.14
Matches are distributed among these distances:
124 30 0.15
125 11 0.05
126 28 0.14
127 91 0.44
128 4 0.02
129 13 0.06
130 28 0.14
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Consensus pattern (124 bp):
CTACTCCACTACACTTCAGAGAGATAAGATTTTGCTTCGATCTGCTCCACTACTGCTTAGGAGAT
AAGATCTAATGCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAAC
Found at i:33245107 original size:168 final size:168
Alignment explanation
Indices: 33244854--33245353 Score: 896
Period size: 168 Copynumber: 3.0 Consensus size: 168
33244844 GGTTTCTTCT
* *
33244854 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT--AATGCTTTAACCTACTCCATTGCTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT-CTTTAACCTACTCCACTGCTACTCA
33244917 GGGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGA
65 GGGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGA
*
33244982 TCTGCTCCACTACTGCTTAGGAAGATAAGTCTTGATACG
130 TCTGCTCCGCTACTGCTTAGGAAGATAAGTCTTGATACG
* *
33245021 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTACTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTACTCAG
33245086 GGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGAT
66 GGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGAT
*
33245151 CTGCTCCGCTACTGCTTAGGAAGATAAGTCTTAATACG
131 CTGCTCCGCTACTGCTTAGGAAGATAAGTCTTGATACG
*
33245189 ATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTACTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTACTCAG
*
33245254 GGAGATAGGATTCGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTTACTGTCTTCGAT
66 GGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGAT
*
33245319 CTGCTCCGCTACTGCTTAGGAAGATAAGACTTGAT
131 CTGCTCCGCTACTGCTTAGGAAGATAAGTCTTGAT
33245354 GTCTTTAACC
Statistics
Matches: 319, Mismatches: 12, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
167 34 0.11
168 282 0.88
169 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (168 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTACTCAG
GGAGATAGGATTCGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTTACTGTCTTCGAT
CTGCTCCGCTACTGCTTAGGAAGATAAGTCTTGATACG
Found at i:33245112 original size:127 final size:128
Alignment explanation
Indices: 33244727--33245178 Score: 358
Period size: 127 Copynumber: 3.6 Consensus size: 128
33244717 CTTTGATGCG
* * * *
33244727 ATCTACTCCACTACTGCTTA-GAGAGATAAGATC-TAATGCGATCTGCTCCACTACTGTTTAGGG
1 ATCTGCTCCACTACTGCTTAGGA-AGATAAGATCTTGATACGATCTGCTCCACTACTGCTTAGGG
* * * *
33244790 AGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAGGGAGATAGGATTGGTTTCTTCT
65 AGATAAGATCTACAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGATTCGTGTCTTCA
* * *** * * * * *
33244854 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTAATGCTTTAACCTACTCCATTGCTGCTCAGG
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCT--TGATACGATCTGCTCCACTACTGCTTAGG
* * * * * * * *
33244919 GAGATAGGAT-T-C-GTGGCTTAAATCTGCTTCC-TTAC-ACTT--GAAGATAAGATTTAC-TGT
64 GAGATAAGATCTACAAT--CTTCAACCTAC-TCCACTACTACTTAGGGAGATAGGA-TT-CGTGT
*
33244976 CTTCG
124 CTTCA
33244981 ATCTGCTCCACTACTGCTTAGGAAGATAAG-TCTTGATACGATCTGCTCCACTACTGCTTAGGGA
1 ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTTGATACGATCTGCTCCACTACTGCTTAGGGA
* * *
33245045 GATAAGATCTACAATCTTCAACCTACTCCACTGCTACTTAGGGAGATAGGATTCGTGGCTTAA
66 GATAAGATCTACAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGATTCGTGTCTTCA
* * * * * *
33245108 ATCTGCTTCC-TTAC-ACTT--GAAGATAAGATTTACTGTCTTCGATCTGCTCCGCTACTGCTTA
1 ATCTGC-TCCACTACTGCTTAGGAAGATAAGATCT--TG-ATACGATCTGCTCCACTACTGCTTA
*
33245169 GGAAGATAAG
62 GGGAGATAAG
33245179 TCTTAATACG
Statistics
Matches: 249, Mismatches: 54, Indels: 43
0.72 0.16 0.12
Matches are distributed among these distances:
124 41 0.16
125 13 0.05
126 20 0.08
127 86 0.35
128 47 0.19
129 12 0.05
130 30 0.12
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (128 bp):
ATCTGCTCCACTACTGCTTAGGAAGATAAGATCTTGATACGATCTGCTCCACTACTGCTTAGGGA
GATAAGATCTACAATCTTCAACCTACTCCACTACTACTTAGGGAGATAGGATTCGTGTCTTCA
Found at i:33245300 original size:84 final size:86
Alignment explanation
Indices: 33244767--33245304 Score: 365
Period size: 84 Copynumber: 6.4 Consensus size: 86
33244757 ATCTAATGCG
** *
33244767 ATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
1 ATCTGCTCCACTACTACTTA-GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
* ** **
33244832 GGAGATAGGATTGGTTTCTTCT
65 GGAGATAGGATTCGTGGCTTAA
* * * * * *
33244854 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT--AATGCTTTAACCTACTCCATTGCTGCTCA
1 ATCTGCTCCACTACTACTTA-GAAGATAAGATCTACAAT-CTTCAACCTACTCCACTACTACTCA
33244917 GGGAGATAGGATTCGTGGCTTAA
64 GGGAGATAGGATTCGTGGCTTAA
* * ** * * * * *
33244940 ATCTGCTTCC-TTAC-ACTT-GAAGATAAGATTTACTGTCTTCGATCTGCTCCACTACTGCTTAG
1 ATCTGC-TCCACTACTACTTAGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
* * * * *
33245002 GAAGATA--AGTC-TTG-ATACG
65 GGAGATAGGATTCGTGGCTTA-A
* * * *
33245021 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTACTTAG
1 ATCTGCTCCACTACTACTTA-GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
33245086 GGAGATAGGATTCGTGGCTTAA
65 GGAGATAGGATTCGTGGCTTAA
* * ** * * * * * *
33245108 ATCTGCTTCC-TTAC-ACTT-GAAGATAAGATTTACTGTCTTCGATCTGCTCCGCTACTGCTTAG
1 ATCTGC-TCCACTACTACTTAGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
* * *** *
33245170 GAAGATA--AGTC-T-TAATACG
65 GGAGATAGGATTCGTGGCTTA-A
** * * *
33245189 ATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTACTCAG
1 ATCTGCTCCACTACTACTTA-GAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAG
33245254 GGAGATAGGATTCGTGGCTTAA
65 GGAGATAGGATTCGTGGCTTAA
* **
33245276 ATCTGCTTCTTTAC-ACTT-GAAGATAAGAT
1 ATCTGCTCCACTACTACTTAGAAGATAAGAT
33245305 TTACTGTCTT
Statistics
Matches: 339, Mismatches: 89, Indels: 49
0.71 0.19 0.10
Matches are distributed among these distances:
80 10 0.03
81 21 0.06
82 11 0.03
83 11 0.03
84 154 0.45
85 7 0.02
86 59 0.17
87 59 0.17
88 7 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (86 bp):
ATCTGCTCCACTACTACTTAGAAGATAAGATCTACAATCTTCAACCTACTCCACTACTACTCAGG
GAGATAGGATTCGTGGCTTAA
Found at i:33245621 original size:86 final size:87
Alignment explanation
Indices: 33245355--33245638 Score: 500
Period size: 87 Copynumber: 3.3 Consensus size: 87
33245345 AGACTTGATG
33245355 TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
33245420 CGCAGGAAGGCAAGATCTGTTA
66 CGCAGGAAGGCAAGATCTGTTA
*
33245442 TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCCCTGTTAA
1 TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
*
33245507 CGCAGGAAGACAAGATCTGTTA
66 CGCAGGAAGGCAAGATCTGTTA
* *
33245529 TTTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGG-TTTGGTTTT-GGTCTGCTTCGCTGTTA
1 TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTT-GTTTTCGATCTGCTTCGCTGTTA
33245592 ACGCAGGAAGGCAAGATCTGTTA
65 ACGCAGGAAGGCAAGATCTGTTA
*
33245615 TCTTTAACCAGCTCCACTGTAACC
1 TCTTTAACCAGCTCCACTGCAACC
33245639 TCAAGGAGAT
Statistics
Matches: 188, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
86 62 0.33
87 126 0.67
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (87 bp):
TCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
CGCAGGAAGGCAAGATCTGTTA
Found at i:33245679 original size:46 final size:45
Alignment explanation
Indices: 33245626--33246126 Score: 282
Period size: 44 Copynumber: 11.5 Consensus size: 45
33245616 CTTTAACCAG
*
33245626 CTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTA
* *
33245672 CTCCACTGTAACCTCAGGGAGATAAGACCTG-A---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTA
* * * * ** * **
33245713 CTCTACTGTAACTTCAGAGAGATGAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATTCTTCGATCTA
* * * * *
33245757 CTCCACTGTAACTTCAGGGAGATAGGA--T-AGTGTCTTGGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTA
* * * * * *
33245800 CTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTA
*
33245844 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTCGATCTA
* *
33245890 CTCCACTGTAACCTCAGGGAGATAAGACCTG-A---TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTA
* * * * ** *
33245931 CTCTACTGTAACTTCAGAGAGATGAGATCCTTTATT-TT-AATC-A
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATTCTTCGATCTA
* ** * * *
33245974 GCTCCACTGTAACTTCAGGGAGATGGGA--T-AGTGTCTTGGATCTG
1 -CTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTCGATCTA
* * *
33246018 CTCCGCTGTAATCTCAGGGAGATAAGATCT-AA---TACGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTA
* * * ** * *
33246059 CTCTACTGTAACTTCAGAGAGATAAGATTCTTTATT-TT-AATCCA
1 CTCCACTGTAACCTCAGGGAGATAAGA-TCTGAATTCTTCGATCTA
*
33246103 CTCCACTGTAATCTCAGGGAGATA
1 CTCCACTGTAACCTCAGGGAGATA
33246127 GGATTACCAG
Statistics
Matches: 352, Mismatches: 76, Indels: 56
0.73 0.16 0.12
Matches are distributed among these distances:
40 2 0.01
41 93 0.26
42 11 0.03
43 56 0.16
44 117 0.33
45 6 0.02
46 66 0.19
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTCGATCTA
Found at i:33245798 original size:87 final size:87
Alignment explanation
Indices: 33245672--33245916 Score: 198
Period size: 87 Copynumber: 2.8 Consensus size: 87
33245662 CTTCGATCTA
* ** * *
33245672 CTCCACTGTAACCTCAGGGAGATAAGA-CCTG--ATGCGATCTACTCTACTGTAA-CTTCAGAGA
1 CTCCACTGTAACCTCAGGGAGATAGGATAGTGTCTTG-GATCTACTCCACTGTAATC-TCAGAGA
* * * *
33245733 GATGAGATC-CTTTATTTTAATCCG
64 GATAAGATCTC-TGACTTCAATCCG
* * * *
33245757 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGAGA
1 CTCCACTGTAACCTCAGGGAGATAGGATAGTGTCTTGGATCTACTCCACTGTAATCTCAGAGAGA
* *
33245822 TAAGATCTCTGGCTTCAATCTG
66 TAAGATCTCTGACTTCAATCCG
* * *
33245844 CTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGG-TCTACTCCACTGTAACCTCAG
1 CTCCACTGTAACCTCAGGGAGATAGGATAGTG----TCTT-GGATCTACTCCACTGTAATCTCAG
*
33245907 GGAGATAAGA
61 AGAGATAAGA
33245917 CCTGATGCGA
Statistics
Matches: 129, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
85 25 0.19
86 4 0.03
87 62 0.48
88 4 0.03
90 32 0.25
91 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (87 bp):
CTCCACTGTAACCTCAGGGAGATAGGATAGTGTCTTGGATCTACTCCACTGTAATCTCAGAGAGA
TAAGATCTCTGACTTCAATCCG
Found at i:33245868 original size:218 final size:218
Alignment explanation
Indices: 33245625--33246047 Score: 810
Period size: 218 Copynumber: 1.9 Consensus size: 218
33245615 TCTTTAACCA
33245625 GCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTCAGG
1 GCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTCAGG
33245690 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATC
66 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATC
*
33245755 CGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
131 AGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
33245820 GATAAGATCTCTGGCTTCAATCT
196 GATAAGATCTCTGGCTTCAATCT
* *
33245843 GCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGG
1 GCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTCAGG
33245908 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATC
66 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATC
*
33245973 AGCTCCACTGTAACTTCAGGGAGATGGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
131 AGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
33246038 GATAAGATCT
196 GATAAGATCT
33246048 AATACGATCT
Statistics
Matches: 201, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
218 201 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (218 bp):
GCTCCACTGTAACCTCAAGGAGATAAGATCTGAAATTCTTCGATCTACTCCACTGTAACCTCAGG
GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAATC
AGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
GATAAGATCTCTGGCTTCAATCT
Found at i:33246069 original size:128 final size:129
Alignment explanation
Indices: 33245844--33246176 Score: 390
Period size: 128 Copynumber: 2.6 Consensus size: 129
33245834 CTTCAATCTG
* * * * * * * *
33245844 CTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTACTCCACTGTAACCTCAGG
1 CTCCACTGTAATCTCAGGGAGATAGGAT-T-ACCA-GCTTCAGTCTGCTCCGCTGTAATCTCAGG
* * * *
33245908 GAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATGAGATCCTTTATTTTAAT-
63 GAGATAAGATCTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATC
33245972 CA
128 CA
* ** *
33245974 GCTCCACTGTAA-CTTCAGGGAGATGGGA-TA-GTGTCTT-GGATCTGCTCCGCTGTAATCTCAG
1 -CTCCACTGTAATC-TCAGGGAGATAGGATTACCAG-CTTCAG-TCTGCTCCGCTGTAATCTCAG
*
33246035 GGAGATAAGATCTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATTCTTTATTTTAAT
62 GGAGATAAGATCTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
33246100 CCA
127 CCA
**
33246103 CTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAGTCTGCTCCGCTGTAATCTCAATGAG
1 CTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAGTCTGCTCCGCTGTAATCTCAGGGAG
33246168 ATAAGATCT
66 ATAAGATCT
33246177 GATATTCTTC
Statistics
Matches: 175, Mismatches: 19, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
127 2 0.01
128 106 0.61
129 41 0.23
130 3 0.02
131 23 0.13
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
CTCCACTGTAATCTCAGGGAGATAGGATTACCAGCTTCAGTCTGCTCCGCTGTAATCTCAGGGAG
ATAAGATCTAATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCA
Found at i:33247886 original size:21 final size:21
Alignment explanation
Indices: 33247856--33247897 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33247846 TCATAAAATC
*
33247856 AAATTTAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
33247877 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
33247898 TATATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:33249691 original size:13 final size:13
Alignment explanation
Indices: 33249673--33249702 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
33249663 ACTAGATTGA
33249673 AAGCTATTATTAT
1 AAGCTATTATTAT
33249686 AAGCTATTATTAT
1 AAGCTATTATTAT
33249699 AAGC
1 AAGC
33249703 AAATTCAATC
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:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (13 bp):
AAGCTATTATTAT
Found at i:33254763 original size:41 final size:41
Alignment explanation
Indices: 33254707--33254809 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
33254697 TGATTCAGTA
* * * *
33254707 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
* * * *
33254748 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
*
33254789 CACCGGCATCAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
33254810 GCACATAGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATAT
Found at i:33254823 original size:41 final size:41
Alignment explanation
Indices: 33254747--33254824 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
33254737 CCGAAATGTA
* ** *
33254747 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATT
1 TCACCGGCATCAAGCCTGCTAGACACAAAGCCTGAATTATT
* *
33254788 TCACCGGCATCAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGGCATCAAGCCTGCTAGACACAAAGCCTGAAT
33254825 AACTGAGATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (41 bp):
TCACCGGCATCAAGCCTGCTAGACACAAAGCCTGAATTATT
Found at i:33255460 original size:21 final size:21
Alignment explanation
Indices: 33255430--33255471 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
33255420 TCATAAAATC
*
33255430 AAATTTAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
33255451 AAATTCAGCTTATAGAACATA
1 AAATTCAGCTTATAGAACATA
33255472 TATATATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTCAGCTTATAGAACATA
Found at i:33257827 original size:7 final size:7
Alignment explanation
Indices: 33257815--33257859 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
33257805 TTAGCCTCTC
33257815 CATTTTT
1 CATTTTT
33257822 CA-TTTT
1 CATTTTT
33257828 CATTTTT
1 CATTTTT
33257835 CATTTTT
1 CATTTTT
*
33257842 CA-TTCT
1 CATTTTT
33257848 CATTTTT
1 CATTTTT
33257855 C-TTTT
1 CATTTT
33257860 CTTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 15 0.44
7 19 0.56
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:33257833 original size:13 final size:13
Alignment explanation
Indices: 33257818--33257865 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
33257808 GCCTCTCCAT
33257818 TTTTCA-TTTTCA
1 TTTTCATTTTTCA
33257830 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
*
33257844 TTCTCATTTTTC-
1 TTTTCATTTTTCA
33257856 TTTTC-TTTTT
1 TTTTCATTTTT
33257866 TTTGACTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 5 0.16
12 4 0.12
13 17 0.53
14 6 0.19
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:33257838 original size:20 final size:20
Alignment explanation
Indices: 33257815--33257859 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
33257805 TTAGCCTCTC
*
33257815 CATTTTTCATTTTCATTTTT
1 CATTTTTCATTCTCATTTTT
33257835 CATTTTTCATTCTCATTTTT
1 CATTTTTCATTCTCATTTTT
33257855 C-TTTT
1 CATTTT
33257860 CTTTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (20 bp):
CATTTTTCATTCTCATTTTT
Found at i:33258793 original size:35 final size:36
Alignment explanation
Indices: 33258746--33258820 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
33258736 TAGATTTCTC
33258746 TTTTTTCATTCTTCTTTCT-TTTTCTTGATTTTGAT
1 TTTTTTCATTCTTCTTTCTGTTTTCTTGATTTTGAT
* * * *
33258781 TTTTTTCTTTCTTCTTTTTGTTTTTTTTATTTTGAT
1 TTTTTTCATTCTTCTTTCTGTTTTCTTGATTTTGAT
33258817 TTTT
1 TTTT
33258821 GATTTTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (36 bp):
TTTTTTCATTCTTCTTTCTGTTTTCTTGATTTTGAT
Found at i:33258813 original size:28 final size:29
Alignment explanation
Indices: 33258746--33258813 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
33258736 TAGATTTCTC
* *
33258746 TTTTTTCATTCTTCTTTCTTTTTCTTGAT
1 TTTTTTTATTTTTCTTTCTTTTTCTTGAT
**
33258775 TTTGATT-TTTTTCTTTCTTCTTT-TTG-T
1 TTTTTTTATTTTTCTTTCTT-TTTCTTGAT
33258802 TTTTTTTATTTT
1 TTTTTTTATTTT
33258814 GATTTTTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.19
28 18 0.58
29 7 0.23
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (29 bp):
TTTTTTTATTTTTCTTTCTTTTTCTTGAT
Found at i:33258819 original size:21 final size:21
Alignment explanation
Indices: 33258774--33258839 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
33258764 TTTTTCTTGA
*
33258774 TTTTGATTTTTTTCTTTCTTC-T
1 TTTTGA-TTTTTTCATT-TTCAT
* * *
33258796 TTTTGTTTTTTTTATTTTGAT
1 TTTTGATTTTTTCATTTTCAT
33258817 TTTTGATTTTTTCATTTTCAT
1 TTTTGATTTTTTCATTTTCAT
33258838 TT
1 TT
33258840 CATTTTGACT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.81
22 5 0.14
ACGTcount: A:0.09, C:0.08, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTGATTTTTTCATTTTCAT
Found at i:33265030 original size:124 final size:125
Alignment explanation
Indices: 33264664--33265032 Score: 347
Period size: 124 Copynumber: 2.9 Consensus size: 125
33264654 CTTTGAACTT
** * * *
33264664 AAAAAAACTCAAACTCGAAAAC-CTCCAAAATCACAAAACAACTAAAACCTAAAATTACATCATC
1 AAAAAAACTCAAACTCGAAAACAC-CC-AAA-CTTAAAACAACTAAATCCCAAAATTACATGATC
* * * * * * * *
33264728 TAAACTTGAATCAAGTTGTTATCTTTATAACTACACACAACACTCAGACTCAAACTTTGAACTAC
63 TAAACCTGAATCAAATTGCTATCTTTATACCT--ACACAACACTCACACTCAAACTCTCAACCAC
* * * * *
33264793 AAAAAAACTCAAACTCGAAAATACTCAAACTTAAAACAATTAAAAT-CCAAGATTAAATGATCTA
1 AAAAAAACTCAAACTCGAAAACACCCAAACTTAAAACAACT-AAATCCCAAAATTACATGATCTA
* * * * *
33264857 AACCCGAATCAAATT-CTACCTTTATACTTACCCAACACT-AGCACTCAAACTCTCAACCAT
65 AACCTGAATCAAATTGCTATCTTTATACCTACACAACACTCA-CACTCAAACTCTCAACCAC
* * * * **
33264917 AAAAACATTCAAAC-CAGAAAACACCCAAATTTAAAATAACTAAATCCCAAAATTACATGAAATA
1 AAAAAAACTCAAACTC-GAAAACACCCAAACTTAAAACAACTAAATCCCAAAATTACATGATCTA
33264981 AACCTGAATCAAATTGCTATC-TTATACCTACACAACACTCACA-TCCAAACTC
65 AACCTGAATCAAATTGCTATCTTTATACCTACACAACACTCACACT-CAAACTC
33265033 GAATAACTTA
Statistics
Matches: 194, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
123 7 0.04
124 108 0.56
125 5 0.03
126 10 0.05
127 35 0.18
128 6 0.03
129 22 0.11
130 1 0.01
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (125 bp):
AAAAAAACTCAAACTCGAAAACACCCAAACTTAAAACAACTAAATCCCAAAATTACATGATCTAA
ACCTGAATCAAATTGCTATCTTTATACCTACACAACACTCACACTCAAACTCTCAACCAC
Found at i:33268378 original size:62 final size:62
Alignment explanation
Indices: 33268304--33268429 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
33268294 GACCACCCTT
33268304 TCATCATTGCAACAGCAAGCACTGCTCTTATCGTGACTGCCTGTACCACTGGACTAAATGTA
1 TCATCATTGCAACAGCAAGCACTGCTCTTATCGTGACTGCCTGTACCACTGGACTAAATGTA
33268366 TCATCATTGCAACAGCAAGCACTGCTCTTATCGTGACTGCCTGTACCACTGGACTAAATGTA
1 TCATCATTGCAACAGCAAGCACTGCTCTTATCGTGACTGCCTGTACCACTGGACTAAATGTA
33268428 TC
1 TC
33268430 TCAAAAATCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (62 bp):
TCATCATTGCAACAGCAAGCACTGCTCTTATCGTGACTGCCTGTACCACTGGACTAAATGTA
Found at i:33278366 original size:19 final size:17
Alignment explanation
Indices: 33278339--33278383 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
33278329 AAATATTTAG
33278339 ATAAATAAAGAAAAAGAA
1 ATAAATAAA-AAAAAGAA
*
33278357 ATATAAT-AAAAAAAGTA
1 ATA-AATAAAAAAAAGAA
33278374 ATAAATAAAA
1 ATAAATAAAA
33278384 GGAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.12
17 13 0.54
18 5 0.21
19 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (17 bp):
ATAAATAAAAAAAAGAA
Found at i:33279007 original size:113 final size:107
Alignment explanation
Indices: 33278846--33279076 Score: 347
Period size: 113 Copynumber: 2.1 Consensus size: 107
33278836 TTAAAATTGC
* *
33278846 TTCATTTTTGCACTTAACCGAAAAAAAAAATTCTCTCCAAAACTGTCTTCCCTTTTCCAGATCAA
1 TTCA-TTTTGCACTTAACCAAAAAAAAAAATTCTCTCCAAAACCGTCTTCCCTTTTCCAGATCAA
* *
33278911 AGAGAAAGTGGTAAATTTCTTCTTTTTTTTTGACATTGTTTTTTTGG
65 AGAGAAAGGGGT-AATTT-TT-TTTTTTTTT-ACATTGTTTTTATGG
*
33278958 TTCATTTCTGCACTTATCCAAAAAAAAAAATTTCTCTCCAAAACCGTCTTCCCTTTTCCAGATCA
1 TTCATTT-TGCACTTAACCAAAAAAAAAAA-TTCTCTCCAAAACCGTCTTCCCTTTTCCAGATCA
33279023 AAGAGAAAGGGGTAATTTTTTTTTTTTTTACATTGTTTTTATGG
64 AAGAGAAAGGGGTAATTTTTTTTTTTTTTACATTGTTTTTATGG
33279067 TT-ATTTTGCA
1 TTCATTTTGCA
33279077 AGGAATCATG
Statistics
Matches: 112, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
107 4 0.04
108 4 0.04
109 16 0.14
110 9 0.08
111 5 0.04
112 29 0.26
113 45 0.40
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (107 bp):
TTCATTTTGCACTTAACCAAAAAAAAAAATTCTCTCCAAAACCGTCTTCCCTTTTCCAGATCAAA
GAGAAAGGGGTAATTTTTTTTTTTTTTACATTGTTTTTATGG
Found at i:33279445 original size:116 final size:116
Alignment explanation
Indices: 33279294--33279505 Score: 277
Period size: 116 Copynumber: 1.8 Consensus size: 116
33279284 GGGTAATTAA
* * * *
33279294 ATTCTTACAGATAAGCAAAATTTTACAACTCCTACTACT-TTTGAATTTTTTGGAC-GTTAGAAT
1 ATTCTTACAAATAAGCAAAATTTTACAAATCCTACTACTGCTT-AATTCTTTGGACAG-TAGAAT
*
33279357 ATTGCTA-TTTTTTTAATTTAATTTAATTAATTACTATATATATTTCTATAAAT
64 ATTACTACTTTTTTTAATTTAA-TTAATTAATTACTATATATATTTCTATAAAT
* * * *
33279410 ATTCTTGCAAATAAGGAAAATTTTACAAATGCTACTACTGCTTAATTCTTTGTACAGTAGAATAT
1 ATTCTTACAAATAAGCAAAATTTTACAAATCCTACTACTGCTTAATTCTTTGGACAGTAGAATAT
*
33279475 TACTATCTTTTTTTATTTTAATTAATTAATT
66 TACTA-CTTTTTTTAATTTAATTAATTAATT
33279506 TAATTTTTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
116 56 0.68
117 13 0.16
118 13 0.16
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (116 bp):
ATTCTTACAAATAAGCAAAATTTTACAAATCCTACTACTGCTTAATTCTTTGGACAGTAGAATAT
TACTACTTTTTTTAATTTAATTAATTAATTACTATATATATTTCTATAAAT
Found at i:33281159 original size:51 final size:52
Alignment explanation
Indices: 33281101--33281216 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 52
33281091 ATTGGTATAA
* * * * *
33281101 TAACAAATTTAGTCCTCAAA-ATTTTACACATTGTGTCAAATTGGTATTG-TT
1 TAACAAATTTAGCCCACAAACA-TTTACACATTCTATCAAATTGATATTGATT
* * * *
33281152 TAACAAATTTAACCCACAAACATTTACATATTCTATCAATTTGATCTTGATT
1 TAACAAATTTAGCCCACAAACATTTACACATTCTATCAAATTGATATTGATT
33281204 TAACAAATTTAGC
1 TAACAAATTTAGC
33281217 TTGTAACATT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
51 38 0.72
52 15 0.28
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (52 bp):
TAACAAATTTAGCCCACAAACATTTACACATTCTATCAAATTGATATTGATT
Found at i:33282322 original size:124 final size:125
Alignment explanation
Indices: 33282102--33282473 Score: 351
Period size: 124 Copynumber: 3.0 Consensus size: 125
33282092 AGTTTGGATG
* * *
33282102 TGAGTGTTGTGTAGGTATAAAGATAGCAATTTGATTCGGGTTTATATCATGTAATTTTGGGATTT
1 TGAGTGTTGGGTAGGTATAAAGATAGCAATTTGATTCGGGTTTAGATCATGTAATCTTGGGATTT
* * * *** * *
33282167 AGTTGTTTTAAATTTGGGTGTTTTTTTGTTTGAATGTTTTTATAGTTGAGAGTTTGAGTGC
66 AATTGTTTTAAATTTGAGTATTTTCGAGTTTGAATGTTTTTATAGTTCAAAGTTTGAGT-C
* * *
33282228 T-AGTGTTGGGTAAGTATAAAGGTAG-AATTTGATTCGGGTTTAGATCATTTAATCTT-GGATTT
1 TGAGTGTTGGGTAGGTATAAAGATAGCAATTTGATTCGGGTTTAGATCATGTAATCTTGGGA-TT
* * * *
33282290 TAATTGTTTTAAGTTTGAGTATTTTCGAGTTTGAGTTTTTTTGTAGTTCAAAGTTTGAGTC
65 TAATTGTTTTAAATTTGAGTATTTTCGAGTTTGAATGTTTTTATAGTTCAAAGTTTGAGTC
* * * ** * * *
33282351 TGAGTGTTGTGTGTAGGTATAAAAATAACAACTT-ATTCAAGTTTAGATCATGTAATTTTAGGTT
1 TGAGTGTTG-G-GTAGGTATAAAGATAGCAATTTGATTCGGGTTTAGATCATGTAATCTTGGGAT
* * * * * *
33282415 TTAGTTGTTTTGTGATTTTGGAG-GTTTTCGAGTTTGAGTTTTTTTA-AGTTCAAAGTTTG
64 TTAATTG-TTT-TAAATTT-GAGTATTTTCGAGTTTGAATGTTTTTATAGTTCAAAGTTTG
33282474 GGTGTAACTG
Statistics
Matches: 204, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
123 5 0.02
124 85 0.42
125 22 0.11
126 41 0.20
127 22 0.11
128 26 0.13
129 3 0.01
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (125 bp):
TGAGTGTTGGGTAGGTATAAAGATAGCAATTTGATTCGGGTTTAGATCATGTAATCTTGGGATTT
AATTGTTTTAAATTTGAGTATTTTCGAGTTTGAATGTTTTTATAGTTCAAAGTTTGAGTC
Found at i:33285626 original size:124 final size:125
Alignment explanation
Indices: 33285314--33285671 Score: 404
Period size: 124 Copynumber: 2.8 Consensus size: 125
33285304 CTTTGTACTT
** * *
33285314 AAAAAAACTCAAACTCGAAAAC-CTCCAAAATCCCAAAACAACTAAAACCTAAAATTACATGATC
1 AAAAAAACTCAAACTCGAAAACAC-CC-AAA-CTTAAAACAACTAAATCCCAAAATTACATGATC
** * * *
33285378 TAAACTTGAATTAAATT-TATCTTTATACCTACATACAACACTCAGACTCAAACTTTGAACTACA
63 TAAACCCGAATCAAATTCTATCTTTATACCTAC--ACAACACTCAGACTCAAACTCTCAACTACA
* * * * *
33285442 AAAAAAACTCAAACTCGAAAATACTCAAACTTAAAACAATTAAAAT-CCAAGATTAAATGATCTA
1 AAAAAAACTCAAACTCGAAAACACCCAAACTTAAAACAACT-AAATCCCAAAATTACATGATCTA
* * *
33285506 AACCCGAATCAAATTCTACCTTTATACCTACCCAACACT-AGCACTCAAACTCTCAACTA-T
65 AACCCGAATCAAATTCTATCTTTATACCTACACAACACTCAG-ACTCAAACTCTCAACTACA
* * * *
33285566 AAAAACATTCAAAC-CAGAAAACACCCAAATTTAAAACAACTAAATCCCAAAATTACATGATATA
1 AAAAAAACTCAAACTC-GAAAACACCCAAACTTAAAACAACTAAATCCCAAAATTACATGATCTA
33285630 AACCCGAATCAAATTGCTATCTTTATACCTACACAACACTCA
65 AACCCGAATCAAATT-CTATCTTTATACCTACACAACACTCA
33285672 CATCCAGACT
Statistics
Matches: 194, Mismatches: 28, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
123 5 0.03
124 65 0.34
125 44 0.23
126 37 0.19
127 20 0.10
128 22 0.11
129 1 0.01
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (125 bp):
AAAAAAACTCAAACTCGAAAACACCCAAACTTAAAACAACTAAATCCCAAAATTACATGATCTAA
ACCCGAATCAAATTCTATCTTTATACCTACACAACACTCAGACTCAAACTCTCAACTACA
Found at i:33287090 original size:19 final size:18
Alignment explanation
Indices: 33287063--33287103 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
33287053 TGTAATATTG
*
33287063 AATTTAATTAAATGCAATT
1 AATTAAATTAAATGCAA-T
*
33287082 AATTAAATTAATTGCAAT
1 AATTAAATTAAATGCAAT
33287100 AATT
1 AATT
33287104 TTTCTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (18 bp):
AATTAAATTAAATGCAAT
Found at i:33291642 original size:23 final size:23
Alignment explanation
Indices: 33291599--33291642 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
33291589 ATGTTTAAGT
**
33291599 TTAATATATTTTTAAGTTTATTA
1 TTAATATATTTTTAAAATTATTA
33291622 TTAATACTA-TTTTAAAATTAT
1 TTAATA-TATTTTTAAAATTAT
33291643 AATATAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATATTTTTAAAATTATTA
Found at i:33295042 original size:7 final size:8
Alignment explanation
Indices: 33295024--33295078 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
33295014 CTTTACAAAA
33295024 TTTTATAT
1 TTTTATAT
*
33295032 TTTTTTAT
1 TTTTATAT
33295040 TTTCTATAT
1 TTT-TATAT
33295049 ATTTTATAAT
1 -TTTTAT-AT
*
33295059 TTTTACAT
1 TTTTATAT
*
33295067 TTTTTTAT
1 TTTTATAT
33295075 TTTT
1 TTTT
33295079 TTCTAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
8 22 0.56
9 12 0.31
10 5 0.13
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTATAT
Found at i:33298054 original size:91 final size:90
Alignment explanation
Indices: 33297889--33298057 Score: 205
Period size: 91 Copynumber: 1.9 Consensus size: 90
33297879 ATATAGGTAT
* * * * *
33297889 GTATCCAACATGGGTACCGTTAGATTTTTCAAAGTTGTTCCATATATTTGGAAGATCATTGAAGT
1 GTATCAAACACGGGCACCGTTAGATTTTTCAAAGTTGTTCCACATATTTGGAAGATCATTGAAGA
33297954 TCATATCCCCATAATCAGGATGTAA
66 TCATATCCCCATAATCAGGATGTAA
* * * * * *
33297979 GTATCAAACACGGGCACGGTTAGATTTTTTACAAGTTTTTCCACCA-ATTTGGAAGGTCTTTTAA
1 GTATCAAACACGGGCACCGTTAGATTTTTCA-AAGTTGTTCCA-CATATTTGGAAGATCATTGAA
*
33298043 GATCATGTCCCCATA
64 GATCATATCCCCATA
33298058 TCCATGTGTC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
90 26 0.40
91 38 0.58
92 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (90 bp):
GTATCAAACACGGGCACCGTTAGATTTTTCAAAGTTGTTCCACATATTTGGAAGATCATTGAAGA
TCATATCCCCATAATCAGGATGTAA
Found at i:33303480 original size:11 final size:11
Alignment explanation
Indices: 33303452--33303483 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
33303442 TATTCGAACA
*
33303452 ATAATAACAAT
1 ATAATAGCAAT
33303463 ATAATAGCAAT
1 ATAATAGCAAT
33303474 ATAATAGCAA
1 ATAATAGCAA
33303484 AATTGTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.25
Consensus pattern (11 bp):
ATAATAGCAAT
Found at i:33303729 original size:17 final size:16
Alignment explanation
Indices: 33303702--33303733 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
33303692 GTCTTTCATG
33303702 CTTTAGTTTCTCTTTA
1 CTTTAGTTTCTCTTTA
33303718 CTTTATGTTTCTCTTT
1 CTTTA-GTTTCTCTTT
33303734 CAAGTGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.19, G:0.06, T:0.66
Consensus pattern (16 bp):
CTTTAGTTTCTCTTTA
Found at i:33312305 original size:20 final size:20
Alignment explanation
Indices: 33312282--33312324 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
33312272 GAAAATTGGG
*
33312282 TAATTTATGGAGAAAAATGA
1 TAATTTATGGAGAAAAAAGA
*
33312302 TAATTTATGGATAAAAAAGA
1 TAATTTATGGAGAAAAAAGA
33312322 TAA
1 TAA
33312325 GACCTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.30
Consensus pattern (20 bp):
TAATTTATGGAGAAAAAAGA
Found at i:33314897 original size:4 final size:4
Alignment explanation
Indices: 33314888--33314957 Score: 131
Period size: 4 Copynumber: 17.5 Consensus size: 4
33314878 CTACCACAGC
*
33314888 TACA TACA TACA TACA TACA TACA TACA TAAA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33314936 TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TA
33314958 TAAAGATTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:33315080 original size:12 final size:12
Alignment explanation
Indices: 33315063--33315105 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
33315053 CGGCCAGGTA
33315063 TGTATGTATATG
1 TGTATGTATATG
* *
33315075 TGTATGTAAATA
1 TGTATGTATATG
*
33315087 TGTATATATATG
1 TGTATGTATATG
*
33315099 TATATGT
1 TGTATGT
33315106 TTTTAGTATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (12 bp):
TGTATGTATATG
Found at i:33326221 original size:23 final size:23
Alignment explanation
Indices: 33326194--33326250 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
33326184 TGACCATTGA
33326194 CGTCCCGATGAGAAGAGATGCCT
1 CGTCCCGATGAGAAGAGATGCCT
*
33326217 CGTCCTGATGAGAAGAGATGCCT
1 CGTCCCGATGAGAAGAGATGCCT
*
33326240 CGTCCGGATGA
1 CGTCCCGATGA
33326251 CCCAATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.19
Consensus pattern (23 bp):
CGTCCCGATGAGAAGAGATGCCT
Found at i:33327944 original size:18 final size:18
Alignment explanation
Indices: 33327921--33327958 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
33327911 TATACTCTTT
33327921 ACGAAAACAATTTATCCA
1 ACGAAAACAATTTATCCA
33327939 ACGAAAACAATTTATCCA
1 ACGAAAACAATTTATCCA
33327957 AC
1 AC
33327959 TGTTTTGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.05, T:0.21
Consensus pattern (18 bp):
ACGAAAACAATTTATCCA
Found at i:33346933 original size:23 final size:26
Alignment explanation
Indices: 33346889--33346940 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 26
33346879 ACATGCAATC
33346889 AAAGTAAAATATAAAATTTTCCAAGAA
1 AAAGTAAAATATAAAA-TTTCCAAGAA
*
33346916 AAAGTAAAA-A-AAAA-TTCCCAGAA
1 AAAGTAAAATATAAAATTTCCAAGAA
33346939 AA
1 AA
33346941 CTGGTTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.42
25 4 0.17
26 1 0.04
27 9 0.38
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.19
Consensus pattern (26 bp):
AAAGTAAAATATAAAATTTCCAAGAA
Found at i:33349673 original size:49 final size:49
Alignment explanation
Indices: 33349601--33349694 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
33349591 CTCGATGTTT
* *
33349601 TCCTGGTTGATCCGCCTAAGCCTGCTC-TAGCTATATTTTGAATCAAGTC
1 TCCTGGTTGATCCACCTAAGCCTGCTCTTA-CTACATTTTGAATCAAGTC
*
33349650 TCCTGGTTGATCCACCTGAGCCTGCTCTTACTACATTTTGAATCA
1 TCCTGGTTGATCCACCTAAGCCTGCTCTTACTACATTTTGAATCA
33349695 GACTTGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 39 0.95
50 2 0.05
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (49 bp):
TCCTGGTTGATCCACCTAAGCCTGCTCTTACTACATTTTGAATCAAGTC
Found at i:33352266 original size:25 final size:24
Alignment explanation
Indices: 33352238--33352308 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 24
33352228 TATTTAATTC
*
33352238 AATTTTTTTAAATATTTGCTTTATT
1 AATTTTTTTAAATATTTG-TTTAAT
33352263 AATTTTTTTAATATAAATATTGTTTAAT
1 AATTTTTTTAA-AT--AT-TTGTTTAAT
*
33352291 AATTTTTTATAATTATTT
1 AATTTTTT-TAAATATTT
33352309 AAGATAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 13 0.33
26 4 0.10
28 16 0.41
29 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (24 bp):
AATTTTTTTAAATATTTGTTTAAT
Found at i:33352293 original size:28 final size:31
Alignment explanation
Indices: 33352246--33352303 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
33352236 TCAATTTTTT
*
33352246 TAAATATTTGCTTTATTAATTTTTT-TAATA
1 TAAATATTTGCTTTAATAATTTTTTATAATA
33352276 TAAATA-TTG-TTTAATAATTTTTTATAAT
1 TAAATATTTGCTTTAATAATTTTTTATAAT
33352304 TATTTAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 7 0.27
30 6 0.23
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (31 bp):
TAAATATTTGCTTTAATAATTTTTTATAATA
Found at i:33352944 original size:4 final size:4
Alignment explanation
Indices: 33352935--33352983 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
33352925 CATCATCCAG
33352935 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
33352983 G
1 G
33352984 CGTGCAAGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:33354742 original size:49 final size:49
Alignment explanation
Indices: 33354685--33354779 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
33354675 CTCGATGTTT
33354685 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGCC
1 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGCC
* *
33354734 TCCTGGTTGATCCACCTGAGCCTGCTCTTGCTACATTTTGAATCAG
1 TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAG
33354780 ACTTGATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.33
Consensus pattern (49 bp):
TCCTGGTTGATCCACCTAAGCCTGCTCTCGCTACATTTTGAATCAGGCC
Found at i:33361855 original size:15 final size:15
Alignment explanation
Indices: 33361835--33361865 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33361825 GTTATGTAAG
33361835 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
33361850 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
33361865 T
1 T
33361866 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:33366206 original size:15 final size:15
Alignment explanation
Indices: 33366186--33366216 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33366176 GTTATGTAAG
33366186 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
33366201 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
33366216 T
1 T
33366217 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:33373950 original size:20 final size:21
Alignment explanation
Indices: 33373913--33373962 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
33373903 ATATAATAAT
33373913 AATTATATTAAGAATTTTATTA
1 AATTATA-TAAGAATTTTATTA
33373935 AATTATATAA-AATTTTATTA
1 AATTATATAAGAATTTTATTA
33373955 AATTATAT
1 AATTATAT
33373963 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTATATAAGAATTTTATTA
Found at i:33373963 original size:10 final size:10
Alignment explanation
Indices: 33373913--33373963 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
33373903 ATATAATAAT
33373913 AATTATATTAA
1 AATTATATT-A
*
33373924 GAATTTTATTA
1 -AATTATATTA
*
33373935 AATTATATAA
1 AATTATATTA
*
33373945 AATTTTATTA
1 AATTATATTA
33373955 AATTATATT
1 AATTATATT
33373964 TAATAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
AATTATATTA
Found at i:33374234 original size:16 final size:16
Alignment explanation
Indices: 33374213--33374267 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
33374203 TGAATTACTG
*
33374213 ATTACAGCTTTATTCA
1 ATTACAGCTCTATTCA
*
33374229 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCA
33374245 ATTACAGCTCTATTTC-
1 ATTACAGCTCTA-TTCA
33374261 ATTACAG
1 ATTACAG
33374268 TGAACCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 32 0.91
17 3 0.09
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:33378534 original size:105 final size:101
Alignment explanation
Indices: 33378390--33378817 Score: 422
Period size: 90 Copynumber: 4.2 Consensus size: 101
33378380 TTATATAAAA
*
33378390 ATTACATAAAAAATCACAAAACACTAAACTGAACGCTAACAATTTATATAACCTAATCATAAATT
1 ATTAC-TAAAAAATCACAAAACACTAAACT-AACACTAACAA-TT-TATAACCTAATCATAAATT
* *
33378455 ACTAGCAAAATAACTATAAAATTAATTTTTAAAAAAATTTC
62 ACTAACAAAATAACTATAAAATT-ATTTTTAAAAAAATTAC
* *
33378496 ATTACTAAAAAGTCACGAAACACTAAACTAACCACTAAC-A---AT----T--T-AT--ATTACT
1 ATTACTAAAAAATCACAAAACACTAAACTAA-CACTAACAATTTATAACCTAATCATAAATTACT
**
33378548 AACAAAATAACTATAAAATTATTTTTTTTAAAAATTAC
65 AACAAAATAACTATAAAATTA-TTTTTAAAAAAATTAC
* *
33378586 ATTACTAAAAAATCACAAAACCCTAAACTAAACACTTACAATTTATAACCTAATCCCATAAATTA
1 ATTACTAAAAAATCACAAAACACTAAACT-AACACTAACAATTTATAACCTAAT--CATAAATTA
* *
33378651 CTAACAAAATAAATAACTATAACATTTTTTTTAAAAGAAATTAC
63 CTAAC---A-AAATAACTATAAAATTATTTTTAAAA-AAATTAC
* * *
33378695 ATTACTAAAAAAATAACAAAACAC--AA--AACGCTAACAATTTATAACCTAATCATAAACTACT
1 ATTACT-AAAAAATCACAAAACACTAAACTAACACTAACAATTTATAACCTAATCATAAATTACT
* *
33378756 AACAAATTAACTATAAAATTATTTTTAAAAAAAATTTAT
65 AACAAAATAACTATAAAATTATTTTT-AAAAAAA-TTAC
*
33378795 ATTACTAAAAACTCACAAAACAC
1 ATTACTAAAAAATCACAAAACAC
33378818 AACAATTTAT
Statistics
Matches: 270, Mismatches: 26, Indels: 59
0.76 0.07 0.17
Matches are distributed among these distances:
89 1 0.00
90 70 0.26
91 3 0.01
92 2 0.01
93 1 0.00
94 2 0.01
95 1 0.00
98 1 0.00
99 39 0.14
100 15 0.06
103 15 0.06
104 3 0.01
105 59 0.22
106 5 0.02
108 10 0.04
109 28 0.10
110 15 0.06
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (101 bp):
ATTACTAAAAAATCACAAAACACTAAACTAACACTAACAATTTATAACCTAATCATAAATTACTA
ACAAAATAACTATAAAATTATTTTTAAAAAAATTAC
Found at i:33378791 original size:99 final size:99
Alignment explanation
Indices: 33378544--33378819 Score: 311
Period size: 99 Copynumber: 2.7 Consensus size: 99
33378534 CAATTTATAT
* ***
33378544 TACTAACAAAATAACTATAAAATTATTTTTTTTAAAAATTACATTACTAAAAAATCACAAAACCC
1 TACTAACAAATTAACTATAAAATTATTTTTAAAAAAAATTACATTACTAAAAAATCACAAAA--C
* * *
33378609 TAAACTAAACACTTACAATTTATAACCTAATCCCATAAAT
64 ---ACAAAACACTAACAATTTATAACCTAAT-CCATAAAC
* * * *
33378649 TACTAACAAAATAAATAACTATAACATTTTTTTTAAAAGAAATTACATTACTAAAAAAATAACAA
1 TACTAAC-AAAT---TAACTATAAAATTATTTTTAAAAAAAATTACATTACT-AAAAAATCACAA
*
33378714 AACACAAAACGCTAACAATTTATAACCTAAT-CATAAAC
61 AACACAAAACACTAACAATTTATAACCTAATCCATAAAC
* *
33378752 TACTAACAAATTAACTATAAAATTATTTTTAAAAAAAATTTATATTACTAAAAACTCACAAAACA
1 TACTAACAAATTAACTATAAAATTATTTTTAAAAAAAA-TTACATTACTAAAAAATCACAAAACA
33378817 CAA
65 CAA
33378820 CAATTTATAA
Statistics
Matches: 147, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
99 41 0.28
100 9 0.06
102 4 0.03
103 13 0.09
105 32 0.22
106 3 0.02
108 1 0.01
109 31 0.21
110 13 0.09
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.30
Consensus pattern (99 bp):
TACTAACAAATTAACTATAAAATTATTTTTAAAAAAAATTACATTACTAAAAAATCACAAAACAC
AAAACACTAACAATTTATAACCTAATCCATAAAC
Found at i:33382020 original size:2 final size:2
Alignment explanation
Indices: 33382008--33382047 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
33381998 TTGATTTCAG
*
33382008 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33382048 GGAAACCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33382641 original size:3 final size:3
Alignment explanation
Indices: 33382635--33382722 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
33382625 ATTATTATTA
33382635 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
33382683 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
33382723 AATACCCAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:33385713 original size:33 final size:35
Alignment explanation
Indices: 33385656--33385726 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 35
33385646 TACTCTTTTG
* *
33385656 TTATGTTATGCTTGAAAGTTTTGTTAAGGGATTAC
1 TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
*
33385691 TTATGTT-TGCTT-AAAATTTTGTTAATGGACTAC
1 TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
33385724 TTA
1 TTA
33385727 CATTTATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 21 0.64
34 5 0.15
35 7 0.21
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (35 bp):
TTATGTTATGCTTGAAAATTTTGTTAAGGGACTAC
Found at i:33392538 original size:91 final size:91
Alignment explanation
Indices: 33392383--33392564 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
33392373 CGTGCCAATG
*
33392383 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGTTTAAATTTGTCAATTTTTG
1 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGTTTAAAGTTGTCAATTTTTG
33392448 AAACAAAATCTTTGGGCTATGATTGA
66 AAACAAAATCTTTGGGCTATGATTGA
*
33392474 AAAGTGGCCACTACGGTCATCACAATGACATAAAGCTTACTTGTGTTTAAAGTTGTCAATTTTTG
1 AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGTTTAAAGTTGTCAATTTTTG
33392539 AAACAAAATCTTTGGGCTATGATTGA
66 AAACAAAATCTTTGGGCTATGATTGA
33392565 TGCTGATATT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (91 bp):
AAAGTGGCCACTACGGTCATCACAACGACATAAAGCTTACTTGTGTTTAAAGTTGTCAATTTTTG
AAACAAAATCTTTGGGCTATGATTGA
Found at i:33397240 original size:18 final size:18
Alignment explanation
Indices: 33397217--33397298 Score: 72
Period size: 18 Copynumber: 5.0 Consensus size: 18
33397207 TAAAATTAAA
*
33397217 ATCATAAAAATATAGAAT
1 ATCATAAAAATATAAAAT
33397235 ATCATAAAAATATAAAAT
1 ATCATAAAAATATAAAAT
*
33397253 AT--TTAAAAT-TAAAA-
1 ATCATAAAAATATAAAAT
* *
33397267 AT-AT-AAAAGAGAAAA-
1 ATCATAAAAATATAAAAT
33397282 AT-ATAAAAATATAAAAT
1 ATCATAAAAATATAAAAT
33397299 TTATTATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.11
15 14 0.26
16 15 0.28
18 19 0.35
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
ATCATAAAAATATAAAAT
Found at i:33397251 original size:7 final size:7
Alignment explanation
Indices: 33397207--33397298 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
33397197 TTGTATTTTT
33397207 TAAAAT-
1 TAAAATA
33397213 TAAAATCA
1 TAAAAT-A
33397221 TAAAAATA
1 T-AAAATA
33397229 TAGAATATCA
1 TA-AA-AT-A
33397239 TAAAAATA
1 T-AAAATA
33397247 TAAAATA
1 TAAAATA
33397254 TTTAAAAT-
1 --TAAAATA
33397262 TAAAAATA
1 T-AAAATA
*
33397270 TAAAAGA
1 TAAAATA
*
33397277 GAAAAATA
1 -TAAAATA
33397285 TAAAAATA
1 T-AAAATA
33397293 TAAAAT
1 TAAAAT
33397299 TTATTATAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
6 7 0.10
7 22 0.32
8 20 0.29
9 15 0.22
10 4 0.06
11 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:33397251 original size:8 final size:8
Alignment explanation
Indices: 33397214--33397297 Score: 75
Period size: 8 Copynumber: 10.4 Consensus size: 8
33397204 TTTTAAAATT
33397214 AAAATCATA
1 AAAAT-ATA
33397223 AAAATATA
1 AAAATATA
*
33397231 GAATATCATA
1 -AAAAT-ATA
33397241 AAAATAT-
1 AAAATATA
*
33397248 AAAATATTT
1 AAAATA-TA
33397257 AAAAT-TA
1 AAAATATA
33397264 AAAATAT-
1 AAAATATA
* *
33397271 AAAAGAGA
1 AAAATATA
33397279 AAAATATA
1 AAAATATA
33397287 AAAATATA
1 AAAATATA
33397295 AAA
1 AAA
33397298 TTTATTATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
7 17 0.27
8 24 0.39
9 18 0.29
10 3 0.05
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (8 bp):
AAAATATA
Found at i:33397269 original size:23 final size:24
Alignment explanation
Indices: 33397238--33397298 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
33397228 ATAGAATATC
33397238 ATAAAAATATAAAATATTTAAAAT
1 ATAAAAATATAAAATATTTAAAAT
* **
33397262 -TAAAAATATAAAAGA-GAAAAAT
1 ATAAAAATATAAAATATTTAAAAT
33397284 ATAAAAATATAAAAT
1 ATAAAAATATAAAAT
33397299 TTATTATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (24 bp):
ATAAAAATATAAAATATTTAAAAT
Found at i:33397405 original size:30 final size:28
Alignment explanation
Indices: 33397347--33397406 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
33397337 TTAAAATAAT
*
33397347 AAAAATTAAAAATTATATAAATTATGAA
1 AAAAATTAAAAATTATATAAAATATGAA
* *
33397375 AAAAATTAACAATTTTATAAAAATATTGAA
1 AAAAATTAAAAATTATAT-AAAATA-TGAA
33397405 AA
1 AA
33397407 GTGCAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 16 0.59
29 5 0.19
30 6 0.22
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTAAAAATTATATAAAATATGAA
Found at i:33407534 original size:2 final size:2
Alignment explanation
Indices: 33407527--33407554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33407517 GAAAGGTCCC
33407527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33407555 CTTANNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33412537 original size:23 final size:24
Alignment explanation
Indices: 33412495--33412540 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
33412485 TCACGAACAA
33412495 ACTCATTTATTAGCTCGTTTATTG
1 ACTCATTTATTAGCTCGTTTATTG
*
33412519 ACTCATTTA-TGGCTCGTTTATT
1 ACTCATTTATTAGCTCGTTTATT
33412541 TATTAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (24 bp):
ACTCATTTATTAGCTCGTTTATTG
Found at i:33412665 original size:24 final size:23
Alignment explanation
Indices: 33412638--33412695 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
33412628 TTATTAACAT
*
33412638 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATCTTCAATTA-A
* **
33412662 TGTTCATGAACATCTTCGTTTAA
1 TGTTCGTGAACATCTTCAATTAA
33412685 TGTTCGTGAAC
1 TGTTCGTGAAC
33412696 GTATTCGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATCTTCAATTAA
Found at i:33412702 original size:23 final size:23
Alignment explanation
Indices: 33412638--33412708 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
33412628 TTATTAACAT
* *
33412638 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATATTCGATTA-A
* * *
33412662 TGTTCATGAACATCTTCGTTTAA
1 TGTTCGTGAACATATTCGATTAA
*
33412685 TGTTCGTGAACGTATTCGATTAA
1 TGTTCGTGAACATATTCGATTAA
33412708 T
1 T
33412709 TTAAATGAAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 21 0.54
24 18 0.46
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATATTCGATTAA
Found at i:33414259 original size:16 final size:18
Alignment explanation
Indices: 33414224--33414260 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33414214 TGCAATATGA
33414224 TTTTTACAATATTATTTC
1 TTTTTACAATATTATTTC
*
33414242 TTTTTATAAT-TT-TTTC
1 TTTTTACAATATTATTTC
33414258 TTT
1 TTT
33414261 AAATATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTACAATATTATTTC
Found at i:33424708 original size:21 final size:22
Alignment explanation
Indices: 33424682--33424728 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
33424672 CTCTGCTCAA
*
33424682 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
33424703 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
33424725 ACTC
1 ACTC
33424729 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:33433032 original size:17 final size:18
Alignment explanation
Indices: 33433012--33433051 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
33433002 TTTTATATTG
33433012 AATTGTGATTTATGTGA-
1 AATTGTGATTTATGTGAT
33433029 AATTGTGATTTATGTGAT
1 AATTGTGATTTATGTGAT
33433047 AATTG
1 AATTG
33433052 AGTATTGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (18 bp):
AATTGTGATTTATGTGAT
Found at i:33437791 original size:14 final size:15
Alignment explanation
Indices: 33437769--33437845 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
33437759 CAATCAAACA
33437769 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
33437783 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
33437798 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
33437818 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
33437832 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
33437846 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:33437810 original size:20 final size:20
Alignment explanation
Indices: 33437785--33437824 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33437775 AATATTTTCC
*
33437785 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
33437805 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
33437825 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:33437830 original size:34 final size:35
Alignment explanation
Indices: 33437773--33437839 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
33437763 CAAACACCAG
*
33437773 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
33437808 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
33437840 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:33441728 original size:9 final size:9
Alignment explanation
Indices: 33441714--33441738 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33441704 TTTTTTATTT
33441714 AAATTTTTA
1 AAATTTTTA
33441723 AAATTTTTA
1 AAATTTTTA
33441732 AAATTTT
1 AAATTTT
33441739 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AAATTTTTA
Found at i:33451817 original size:166 final size:166
Alignment explanation
Indices: 33451538--33451870 Score: 648
Period size: 166 Copynumber: 2.0 Consensus size: 166
33451528 AAATATCGAA
33451538 TCAATTTAAAATTGTACATGCATAAGAACCAAATTTATATCGATATATTCATTTTATAATTATAT
1 TCAATTTAAAATTGTACATGCATAAGAACCAAATTTATATCGATATATTCATTTTATAATTATAT
33451603 AAAAGTTTGAGTAAACTATTAGCTTTACCTGGTGAAATAAAATTTTTTTAAGTGAAATTAAATTA
66 AAAAGTTTGAGTAAACTATTAGCTTTACCTGGTGAAATAAAATTTTTTTAAGTGAAATTAAATTA
33451668 TATATTTTTACGATAGTAAAAATATAATTTTACTAT
131 TATATTTTTACGATAGTAAAAATATAATTTTACTAT
33451704 TCAATTTAAAATTGTACATGCATAAGAACCAAATTTATATCGATATATTCATTTTATAATTATAT
1 TCAATTTAAAATTGTACATGCATAAGAACCAAATTTATATCGATATATTCATTTTATAATTATAT
*
33451769 AAAAGTTTGAGTAAACTATTAGCTTTACCTGGTGAAATAAATTTTTTTTAAGTGAAATTAAATTA
66 AAAAGTTTGAGTAAACTATTAGCTTTACCTGGTGAAATAAAATTTTTTTAAGTGAAATTAAATTA
*
33451834 TATATTTTTATGATAGTAAAAATATAATTTTACTAT
131 TATATTTTTACGATAGTAAAAATATAATTTTACTAT
33451870 T
1 T
33451871 TTTAATATTT
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 165 1.00
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (166 bp):
TCAATTTAAAATTGTACATGCATAAGAACCAAATTTATATCGATATATTCATTTTATAATTATAT
AAAAGTTTGAGTAAACTATTAGCTTTACCTGGTGAAATAAAATTTTTTTAAGTGAAATTAAATTA
TATATTTTTACGATAGTAAAAATATAATTTTACTAT
Found at i:33451882 original size:17 final size:17
Alignment explanation
Indices: 33451859--33451899 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
33451849 GTAAAAATAT
33451859 AATTTTACTA-TTTT-TA
1 AATTTTA-TACTTTTATA
33451875 ATATTTTATACTTTTATA
1 A-ATTTTATACTTTTATA
33451893 AATTTTA
1 AATTTTA
33451900 AAAGATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTATACTTTTATA
Found at i:33453042 original size:19 final size:17
Alignment explanation
Indices: 33453020--33453055 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
33453010 TATTTTTTTG
33453020 TTATTGTATAACTTTTGTT
1 TTATTGT-TAA-TTTTGTT
33453039 TTATTGTTAATTTTGTT
1 TTATTGTTAATTTTGTT
33453056 ACTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTATTGTTAATTTTGTT
Found at i:33463157 original size:4 final size:4
Alignment explanation
Indices: 33463148--33463173 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33463138 TCTCAAATAT
33463148 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
33463174 GTATCTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:33463276 original size:13 final size:12
Alignment explanation
Indices: 33463258--33463306 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
33463248 TAAATTTTAG
33463258 TTTTTTTTA-TT
1 TTTTTTTTATTT
*
33463269 TCTTTTTTATTT
1 TTTTTTTTATTT
33463281 TTTTATTTTATTT
1 TTTT-TTTTATTT
* *
33463294 TTTCTTATATTT
1 TTTTTTTTATTT
33463306 T
1 T
33463307 GGTCCTATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 8 0.25
12 13 0.41
13 11 0.34
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTATTT
Found at i:33464498 original size:41 final size:41
Alignment explanation
Indices: 33464441--33464600 Score: 239
Period size: 41 Copynumber: 3.9 Consensus size: 41
33464431 TTTTATTATT
*
33464441 ATTAGCGGTGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
*
33464482 ATTAGCGGCGCTATTTCAAAAAAGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
33464523 ATTAGCGGCGCTATCTCAAAAACGCTGCTAAAGGACCGAGC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
33464564 ATTAGTGGCACTACTCCAAAAACGCCGCTAAAGGCCC
1 ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCC
33464601 CAAAAACTCA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTATTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:33464728 original size:40 final size:40
Alignment explanation
Indices: 33464675--33464769 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
33464665 AATTCTTATT
*
33464675 TTTAGCGGCGTTTTTCGAAAAGCGCCGCTAATGCTCGATC
1 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
* * * * *
33464715 TTTAGCTGTGTTTTTATAAAAGCGCCGCTAATGCTTGATT
1 TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
**
33464755 TTTAGTAGCGTTTTT
1 TTTAGCGGCGTTTTT
33464770 TATCCAAACG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (40 bp):
TTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCGATC
Done.