Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015273.1 Kokia drynarioides strain JFW-HI SEQ_130318, whole genome shotgun sequence
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: 423685
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 472 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:64 original size:23 final size:23
Alignment explanation
Indices: 34--130 Score: 142
Period size: 23 Copynumber: 4.2 Consensus size: 23
24 ACAAAGTACT
34 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
57 GAGCACACGAAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
*
82 GAG-ACACATAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
104 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
127 GAGC
1 GAGC
131 GCGCTAATGT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
22 7 0.10
23 40 0.60
24 13 0.19
25 7 0.10
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:107 original size:47 final size:45
Alignment explanation
Indices: 38--129 Score: 141
Period size: 47 Copynumber: 2.0 Consensus size: 45
28 AGTACTGAGC
38 ACACAAAGTGCTAATCAGAGAGCACACGA-AGTGCTAATAACAGAGAG
1 ACACAAAGTGCTAATCAGAGAGCACAC-ACAGTGCTAAT--CAGAGAG
*
85 ACACATAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAG
1 ACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAG
130 CGCGCTAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
45 7 0.16
46 1 0.02
47 35 0.81
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (45 bp):
ACACAAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAG
Found at i:10055 original size:60 final size:60
Alignment explanation
Indices: 9985--10106 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
9975 TAAATGCAAC
*
9985 TGTAAAATGGGGGAGGAAATGAATAATTGACACCACCTTGAACCATTGATATTCATATTA
1 TGTAAAATGGGGGAGGAAATGAATAAATGACACCACCTTGAACCATTGATATTCATATTA
*
10045 TGTAAAATGGGGGAGGAAATGAGTAAATGACACCACCTTGAACCATTGATATTCATATTA
1 TGTAAAATGGGGGAGGAAATGAATAAATGACACCACCTTGAACCATTGATATTCATATTA
10105 TG
1 TG
10107 GTTACTCTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (60 bp):
TGTAAAATGGGGGAGGAAATGAATAAATGACACCACCTTGAACCATTGATATTCATATTA
Found at i:14036 original size:31 final size:29
Alignment explanation
Indices: 13987--14051 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
13977 AATTTTCATC
13987 TATAAAATTACACAAAATC-TAAATTTATG
1 TATAAAATTACACAAAATCAT-AATTTATG
* *
14016 TATACAATTACACATTAAATCATAGTTTATG
1 TATAAAATTACACA--AAATCATAATTTATG
14047 TATAA
1 TATAA
14052 TTTTGAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 13 0.43
31 16 0.53
32 1 0.03
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (29 bp):
TATAAAATTACACAAAATCATAATTTATG
Found at i:15117 original size:5 final size:5
Alignment explanation
Indices: 15107--15140 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
15097 TAGTAATGTT
*
15107 TTATG TTATG TTATG TTACG TTATG TTATG TTAT
1 TTATG TTATG TTATG TTATG TTATG TTATG TTAT
15141 ATATTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (5 bp):
TTATG
Found at i:19013 original size:16 final size:19
Alignment explanation
Indices: 18973--19011 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
18963 AATAAAAAAA
18973 AAAATTATTTAGAATATTT
1 AAAATTATTTAGAATATTT
*
18992 AAAATT-TTTAAAAT-TTT
1 AAAATTATTTAGAATATTT
19009 AAA
1 AAA
19012 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAAATTATTTAGAATATTT
Found at i:19077 original size:30 final size:32
Alignment explanation
Indices: 19005--19086 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 32
18995 ATTTTTAAAA
*
19005 TTTTAAATTAATAA-AAAAATTTATATTTTAATT
1 TTTTAAA--AATAATAAAAAATTATATTTTAATT
*
19038 TCCTTAAAAATAATAAAAAATTA-A-TTTAATT
1 T-TTTAAAAATAATAAAAAATTATATTTTAATT
*
19069 TTTTAAAAATTATAAAAA
1 TTTTAAAAATAATAAAAA
19087 TATAAATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
30 15 0.35
31 8 0.19
32 6 0.14
33 9 0.21
34 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTAAAAATAATAAAAAATTATATTTTAATT
Found at i:20304 original size:150 final size:153
Alignment explanation
Indices: 20029--20341 Score: 580
Period size: 150 Copynumber: 2.1 Consensus size: 153
20019 ATATTAGTAT
20029 AAAT-AATATTTTACACTAATATAAATAAATTTCTCCCAAAACGAATATATATATATATATATAG
1 AAATAAATATTTTACACTAATATAAATAAATTTCTCCCAAAACG-A-ATATATATATATATATAG
20093 ATTTTTTTGGGTCTATAAAGGAATAGATATTATTTAAAACCAAAATTAAAGTGCTATTCAAAATA
64 ATTTTTTTGGGTCTATAAAGGAATAGATATTATTTAAAACCAAAATTAAAGTGCTATTCAAAATA
20158 TAGTTTATTTAATATGAAAAAGAAA
129 TAGTTTATTTAATATGAAAAAGAAA
20183 AAATAAATATTTTACACTAATATAAATAAATTTCTCCCAAAACG-A-ATATATATATATATAGA-
1 AAATAAATATTTTACACTAATATAAATAAATTTCTCCCAAAACGAATATATATATATATATAGAT
20245 TTTTTTGGGTCTATAAAGGAATAGATATTATTTAAAACCAAAATTAAAGTGCTATTCAAAATATA
66 TTTTTTGGGTCTATAAAGGAATAGATATTATTTAAAACCAAAATTAAAGTGCTATTCAAAATATA
20310 GTTTATTTAATATGAAAAAGAAA
131 GTTTATTTAATATGAAAAAGAAA
20333 AAATAAATA
1 AAATAAATA
20342 ATAAAAATAA
Statistics
Matches: 158, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
150 97 0.61
151 17 0.11
152 1 0.01
154 4 0.03
155 39 0.25
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (153 bp):
AAATAAATATTTTACACTAATATAAATAAATTTCTCCCAAAACGAATATATATATATATATAGAT
TTTTTTGGGTCTATAAAGGAATAGATATTATTTAAAACCAAAATTAAAGTGCTATTCAAAATATA
GTTTATTTAATATGAAAAAGAAA
Found at i:22676 original size:24 final size:25
Alignment explanation
Indices: 22618--22676 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
22608 AATTTATTAA
*
22618 TAAATATT-TATATTTGAAAGTATT
1 TAAATATTATTTATTTGAAAGTATT
*
22642 T-AAT-TTAATTTATTTGATA-TATT
1 TAAATATT-ATTTATTTGAAAGTATT
22665 TAAATATTATTT
1 TAAATATTATTT
22677 TTTAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 2 0.07
23 8 0.28
24 17 0.59
25 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (25 bp):
TAAATATTATTTATTTGAAAGTATT
Found at i:24664 original size:31 final size:31
Alignment explanation
Indices: 24614--24672 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
24604 ATCTTACTGA
*
24614 ACTTTTTATTTTTAATATATATT-TTAAATT
1 ACTTTTTATCTTTAATATATATTATTAAATT
*
24644 ACTTTATTATCTTTGATATATATTATTAA
1 ACTTT-TTATCTTTAATATATATTATTAA
24673 CCCTTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 16 0.64
32 4 0.16
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (31 bp):
ACTTTTTATCTTTAATATATATTATTAAATT
Found at i:29437 original size:96 final size:96
Alignment explanation
Indices: 29281--29454 Score: 253
Period size: 96 Copynumber: 1.8 Consensus size: 96
29271 TCGATTATCC
* **
29281 CGATTTGATGAAAGGTTGCACCTAGTAAGCTAAGGCGCAAATTTTCAAAATCAAAGAT-AAAGAA
1 CGATTTGAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAAATTTTCAAAATCAAAGATAAAAG-A
29345 ACATTGCCTCGATTAAGGGTATTTGATTATTT
65 ACATTGCCTCGATTAAGGGTATTTGATTATTT
* * *
29377 CGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCGAAACTCGAA-ATAAAAGA
1 CGATTTGAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAAATTTTC-AAAATCAAAGATAAAAGA
*
29441 ATATTGCCTCGATT
65 ACATTGCCTCGATT
29455 TTAAAGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
96 58 0.84
97 11 0.16
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
CGATTTGAAGAAAAATTGCACCTAGTAAGCTAAGGCGCAAATTTTCAAAATCAAAGATAAAAGAA
CATTGCCTCGATTAAGGGTATTTGATTATTT
Found at i:29752 original size:30 final size:29
Alignment explanation
Indices: 29713--30005 Score: 292
Period size: 29 Copynumber: 10.0 Consensus size: 29
29703 GAAAAATTCA
29713 GGGGT-AAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
29741 GGGGTCAAAAATGGGATTCTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
*
29770 AAGGGGTAAAAATGGAATTTTTGGAAGTTTT
1 --GGGGTAAAAATGGAATTTTTGGAAGTTTC
* * * * * *
29801 AGGGTCAAAATGGGATTTTTGAAATTTTG
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
29830 GGGGTAAAAATGGAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTC
**
29859 GAGATTAAAAATAGG-ATTTTTGGAAG-TTC
1 G-GGGTAAAAAT-GGAATTTTTGGAAGTTTC
*
29888 GGGGTCAAAAATGGGATTTTTGGAA-TTTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
* * *
29917 AAGAGTAAAAATGGAATTTTTGGAAGTTTT
1 -GGGGTAAAAATGGAATTTTTGGAAGTTTC
* *
29947 GAGGTCAAAAATGGGATTTTTGGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTC
*
29976 GGGGGTAAAAACGGAATTTTTGGATAGTTT
1 -GGGGTAAAAATGGAATTTTTGGA-AGTTT
30006 AGGGACCTTC
Statistics
Matches: 216, Mismatches: 33, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
28 9 0.04
29 111 0.51
30 85 0.39
31 11 0.05
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTC
Found at i:29775 original size:59 final size:60
Alignment explanation
Indices: 29712--30009 Score: 294
Period size: 59 Copynumber: 5.1 Consensus size: 60
29702 GGAAAAATTC
* *
29712 AGGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTCTTGGAAGTTCA
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCT
** * *
29771 AGGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC-AAAATGGGATTTTT-GAAATTTT
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCT
* * * * *
29829 GGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGATTAAAAATAGGATTTTTGGAAGTTC-
1 AGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCT
* * * *
29888 -GGGGTCAAAAATGGGATTTTTGGAA-TTTCAAGAGT-AAAAATGGAATTTTTGGAAGTT-T
1 AGGGGT-AAAAATGGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAGTTCT
* * * * *
29946 TGAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGGT-AAAAACGGAATTTTTGGATAGTT-T
1 AGGGGT-AAAAATGGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTTGGA-AGTTCT
30006 AGGG
1 AGGG
30010 ACCTTCAGGG
Statistics
Matches: 201, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
58 64 0.32
59 98 0.49
60 39 0.19
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (60 bp):
AGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCT
Found at i:29878 original size:88 final size:87
Alignment explanation
Indices: 29709--30009 Score: 295
Period size: 88 Copynumber: 3.4 Consensus size: 87
29699 TTTGGAAAAA
* * * * * *
29709 TTCAGGGGT-AAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTCTTGGAAG-TTCAA
1 TTCA-GGGTCAAAATGGGATTTTTGGAATTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTTCGA
*
29772 GGGGTAAAAATGGAATTTTTGGAAGT
64 -GGTTAAAAATGG-ATTTTTGGAAGT
* * * *
29798 TTTAGGGTCAAAATGGGATTTTTGAAATTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGA
1 TTCAGGGTCAAAATGGGATTTTTGGAATTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGG
29863 TTAAAAATAGGATTTTTGGAAG-
66 TTAAAAAT-GGATTTTTGGAAGT
* * * * *
29885 TTCGGGGTCAAAAATGGGATTTTTGGAATTTCAAGAGTAAAAATGGAATTTTTGGAAGTTTTGAG
1 TTCAGGGTC-AAAATGGGATTTTTGGAATTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAG
*
29950 GTCAAAAATGGGATTTTTGGAAG-
65 GTTAAAAAT-GGATTTTTGGAAGT
* * * * *
29973 TTCGGGGGTAAAAACGGAATTTTTGGATAGTTTAGGG
1 TTC-AGGGTCAAAATGGGATTTTTGGA-ATTTTAGGG
30010 ACCTTCAGGG
Statistics
Matches: 178, Mismatches: 28, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
87 7 0.04
88 128 0.72
89 43 0.24
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (87 bp):
TTCAGGGTCAAAATGGGATTTTTGGAATTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGG
TTAAAAATGGATTTTTGGAAGT
Found at i:31831 original size:19 final size:19
Alignment explanation
Indices: 31809--31847 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31799 TTCAAAATTT
31809 AAAATAAATTTAAGTTTAA
1 AAAATAAATTTAAGTTTAA
*
31828 AAAATTAATTTAAGTTTAA
1 AAAATAAATTTAAGTTTAA
31847 A
1 A
31848 TTTAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATAAATTTAAGTTTAA
Found at i:31835 original size:25 final size:25
Alignment explanation
Indices: 31797--31853 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
31787 GTTTAAAATT
* *
31797 ATTTCAAAATTTAAAATAAATTTAA
1 ATTTAAAAAATTAAAATAAATTTAA
* ** *
31822 GTTTAAAAAATTAATTTAAGTTTAA
1 ATTTAAAAAATTAAAATAAATTTAA
31847 ATTTAAA
1 ATTTAAA
31854 GTAAATTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTTAAAAAATTAAAATAAATTTAA
Found at i:40800 original size:30 final size:30
Alignment explanation
Indices: 40739--40803 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
40729 ACTTATTTTA
* **
40739 TTGTTAATTTTGTTATTATGTTAGAGGCAT
1 TTGTTAATTTTGTTATTATGTTAAAAACAT
*
40769 TTGTTAATTTTGTTATTATTTTAAAAACAT
1 TTGTTAATTTTGTTATTATGTTAAAAACAT
40799 TTGTT
1 TTGTT
40804 TGTTAAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATGTTAAAAACAT
Found at i:44729 original size:18 final size:19
Alignment explanation
Indices: 44693--44732 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
44683 TTATTTGGAC
44693 ATTATATAATTCTTATATT
1 ATTATATAATTCTTATATT
44712 ATTAT-TAATT-TTACTATT
1 ATTATATAATTCTTA-TATT
44730 ATT
1 ATT
44733 TTAGAGGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 3 0.15
18 12 0.60
19 5 0.25
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATAATTCTTATATT
Found at i:46871 original size:29 final size:28
Alignment explanation
Indices: 46839--46897 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
46829 CGTGTTTGCT
*
46839 ATATAAAAGTAGAGA-GATTAAATTTTTAA
1 ATATAAAAATAGA-ATGATTAAA-TTTTAA
*
46868 ATATAAAAATATAATGATTAAATTTTAA
1 ATATAAAAATAGAATGATTAAATTTTAA
46896 AT
1 AT
46898 TTACGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.37
Consensus pattern (28 bp):
ATATAAAAATAGAATGATTAAATTTTAA
Found at i:47518 original size:18 final size:17
Alignment explanation
Indices: 47495--47531 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
47485 TTTTTATAAA
47495 ATTATAAAAATATAAATT
1 ATTATAAAAATA-AAATT
*
47513 ATTATAATAATAAAATT
1 ATTATAAAAATAAAATT
47530 AT
1 AT
47532 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATAAAAATAAAATT
Found at i:49074 original size:2 final size:2
Alignment explanation
Indices: 49069--49101 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
49059 TATATATATA
49069 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
49102 AAGATTCTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:58707 original size:16 final size:17
Alignment explanation
Indices: 58686--58718 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58676 AATGTTAGAT
58686 CATATA-AATTTAAAAC
1 CATATATAATTTAAAAC
*
58702 CATATATATTTTAAAAC
1 CATATATAATTTAAAAC
58719 TTTAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (17 bp):
CATATATAATTTAAAAC
Found at i:58837 original size:17 final size:16
Alignment explanation
Indices: 58815--58846 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
58805 AAATTTTAAA
58815 AATTTTATATATTTTTT
1 AATTTTATAT-TTTTTT
58832 AATTTTATATTTTTT
1 AATTTTATATTTTTT
58847 AAAAAATATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
AATTTTATATTTTTTT
Found at i:58889 original size:19 final size:19
Alignment explanation
Indices: 58865--58908 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
58855 TAAATTTTAA
58865 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTG
*
58884 AATTTTGAAAATTATTTTG
1 AATTTTTAAAATTATTTTG
58903 -ATTTTT
1 AATTTTT
58909 TTTGTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:59140 original size:108 final size:108
Alignment explanation
Indices: 59001--59207 Score: 414
Period size: 108 Copynumber: 1.9 Consensus size: 108
58991 GTTATTGGAA
59001 TTATTTGAGTTATTTTAATTGTAAAAATTCAACTTGACTCGAAATTTCTTATTCGAGTTTACTCG
1 TTATTTGAGTTATTTTAATTGTAAAAATTCAACTTGACTCGAAATTTCTTATTCGAGTTTACTCG
59066 AATAATTTGAATAACTCGATTCAATTAACTTTTTCAAAATTTC
66 AATAATTTGAATAACTCGATTCAATTAACTTTTTCAAAATTTC
59109 TTATTTGAGTTATTTTAATTGTAAAAATTCAACTTGACTCGAAATTTCTTATTCGAGTTTACTCG
1 TTATTTGAGTTATTTTAATTGTAAAAATTCAACTTGACTCGAAATTTCTTATTCGAGTTTACTCG
59174 AATAATTTGAATAACTCGATTCAATTAACTTTTT
66 AATAATTTGAATAACTCGATTCAATTAACTTTTT
59208 TATAATCGAA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 99 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.45
Consensus pattern (108 bp):
TTATTTGAGTTATTTTAATTGTAAAAATTCAACTTGACTCGAAATTTCTTATTCGAGTTTACTCG
AATAATTTGAATAACTCGATTCAATTAACTTTTTCAAAATTTC
Found at i:60375 original size:22 final size:23
Alignment explanation
Indices: 60341--60384 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
60331 ATTTAATCCT
*
60341 TTAATAATTAT-AAATATATATTA
1 TTAATAATGATAAAAT-TATATTA
60364 TTAA-AATGATAAAATTATATT
1 TTAATAATGATAAAATTATATT
60385 TTTACTATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAATAATGATAAAATTATATTA
Found at i:76382 original size:5 final size:5
Alignment explanation
Indices: 76369--76399 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
76359 CAAAGAGAAT
*
76369 CAATT CAATA CAATA CAATA CAATA CAATA C
1 CAATA CAATA CAATA CAATA CAATA CAATA C
76400 TAATTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (5 bp):
CAATA
Found at i:77846 original size:18 final size:18
Alignment explanation
Indices: 77823--77857 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
77813 AATAATAGTA
*
77823 ATTAATTCAAACAATTAT
1 ATTAATTAAAACAATTAT
*
77841 ATTAATTAAAATAATTA
1 ATTAATTAAAACAATTA
77858 AATTGAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAATTAAAACAATTAT
Found at i:84191 original size:27 final size:27
Alignment explanation
Indices: 84139--84193 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
84129 TCCAACACTC
* **
84139 TTTTCAAAAACATTCTATTTTTTTAAA
1 TTTTAAAAAACATTCTATTTGGTTAAA
84166 TTTTAAAAAACGA-TCTATTTGGTTAAA
1 TTTTAAAAAAC-ATTCTATTTGGTTAAA
84193 T
1 T
84194 ATTTTTTCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTTAAAAAACATTCTATTTGGTTAAA
Found at i:87409 original size:4 final size:4
Alignment explanation
Indices: 87402--87475 Score: 62
Period size: 4 Copynumber: 18.2 Consensus size: 4
87392 AAATAAACGG
* * * *
87402 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAAG GAAT G-AA GAAG GAGAG
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GA-AA
*
87452 GAAA GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
87476 GTAATGTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
3 5 0.09
4 42 0.72
5 11 0.19
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:87421 original size:13 final size:13
Alignment explanation
Indices: 87403--87430 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
87393 AATAAACGGG
87403 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
87416 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
87429 AA
1 AA
87431 GGAAGGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:91464 original size:28 final size:27
Alignment explanation
Indices: 91421--91501 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 27
91411 CCTTAATCAA
91421 TCTAGTGTTTACAGTTTAGAGTTTTAAG
1 TCTAGTGTTTACAGTTTAG-GTTTTAAG
* *
91449 TCTAGTGTTTATAGTTTAGGGTTTCAAG
1 TCTAGTGTTTACAGTTTA-GGTTTTAAG
91477 TCTAAG-GTTTACAGTTTAGGTTTTA
1 TCT-AGTGTTTACAGTTTAGGTTTTA
91502 GGGTTTAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 6 0.13
28 38 0.81
29 3 0.06
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.47
Consensus pattern (27 bp):
TCTAGTGTTTACAGTTTAGGTTTTAAG
Found at i:91874 original size:45 final size:45
Alignment explanation
Indices: 91747--91880 Score: 180
Period size: 45 Copynumber: 3.0 Consensus size: 45
91737 AGGAGTAGAA
* ** *
91747 TATTGCGGTGGCTCGTCAAACTCA-GCTTGATATCCTTCCCTTAAG
1 TATTGCGGTGGCTCGTCAAACTGAGGC-TGATATCCTTGGCTTGAG
* * * *
91792 TATTGCGATGGCTCATCAAATTGAGGCTGATATCCTTGGGTTGAG
1 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAG
91837 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
1 TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGA
91881 TGAGCTATGC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
45 74 0.97
46 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (45 bp):
TATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTGAG
Found at i:91997 original size:18 final size:18
Alignment explanation
Indices: 91976--92012 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
91966 TGCTCTGGCA
* *
91976 CTAGTTGTGGTTCTGGGG
1 CTAGCTGTGGCTCTGGGG
91994 CTAGCTGTGGCTCTGGGG
1 CTAGCTGTGGCTCTGGGG
92012 C
1 C
92013 AGGAGCTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.19, G:0.43, T:0.32
Consensus pattern (18 bp):
CTAGCTGTGGCTCTGGGG
Found at i:93830 original size:16 final size:16
Alignment explanation
Indices: 93809--93858 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
93799 TGATGGGGAT
93809 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
93825 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
93840 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
93855 ATTA
1 ATTA
93859 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:98301 original size:57 final size:58
Alignment explanation
Indices: 98222--98353 Score: 194
Period size: 57 Copynumber: 2.2 Consensus size: 58
98212 TTGTTGTCCA
*
98222 AATTAAGTATAAAAGTATGATTCTAATGTTCAAATTGATATATAA-TTTTTTTGTTTT
1 AATTAAGTATATAAGTATGATTCTAATGTTCAAATTGATATATAATTTTTTTTGTTTT
* *
98279 AATTAAGTATATAAGTATGATTCTAATGTTTAATTTGATATATAATTTTTTTTTTTTGTTTT
1 AATTAAGTATATAAGTATGATTCTAATGTTCAAATTGATATATAA----TTTTTTTTGTTTT
98341 AATTAAGTATATA
1 AATTAAGTATATA
98354 TGCTTTTTGT
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
57 42 0.63
62 25 0.37
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (58 bp):
AATTAAGTATATAAGTATGATTCTAATGTTCAAATTGATATATAATTTTTTTTGTTTT
Found at i:98321 original size:31 final size:30
Alignment explanation
Indices: 98229--98323 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 30
98219 CCAAATTAAG
* *
98229 TATAAAAGTATGATTCTAATGTTCAAATTGA
1 TATATAAGTATGATTCTAATGTT-TAATTGA
* *
98260 TATATAA-T-T--TT-T-TTGTTTTAATTAA
1 TATATAAGTATGATTCTAATG-TTTAATTGA
98285 GTATATAAGTATGATTCTAATGTTTAATTTGA
1 -TATATAAGTATGATTCTAATGTTTAA-TTGA
98317 TATATAA
1 TATATAA
98324 TTTTTTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
25 7 0.14
26 10 0.20
27 3 0.06
28 1 0.02
29 1 0.02
30 3 0.06
31 19 0.39
32 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (30 bp):
TATATAAGTATGATTCTAATGTTTAATTGA
Found at i:98352 original size:31 final size:32
Alignment explanation
Indices: 98266--98353 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
98256 TTGATATATA
98266 ATTTTTTTGTTTTAATTAAGTATATAAGTATG
1 ATTTTTTTGTTTTAATTAAGTATATAAGTATG
* ** * * *
98298 ATTCTAATG-TTTAATT-TGATATATAA-TTTT
1 ATTTTTTTGTTTTAATTAAG-TATATAAGTATG
*
98328 TTTTTTTTGTTTTAATTAAGTATATA
1 ATTTTTTTGTTTTAATTAAGTATATA
98354 TGCTTTTTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
30 8 0.19
31 27 0.64
32 7 0.17
ACGTcount: A:0.31, C:0.01, G:0.09, T:0.59
Consensus pattern (32 bp):
ATTTTTTTGTTTTAATTAAGTATATAAGTATG
Found at i:104647 original size:18 final size:18
Alignment explanation
Indices: 104624--104659 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
104614 GACCCAGCAA
104624 TTAAAGAAAAAAGAATAT
1 TTAAAGAAAAAAGAATAT
* *
104642 TTAAAGAGAACAGAATAT
1 TTAAAGAAAAAAGAATAT
104660 AGGCGTTGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.14, T:0.22
Consensus pattern (18 bp):
TTAAAGAAAAAAGAATAT
Found at i:106956 original size:3 final size:3
Alignment explanation
Indices: 106950--106990 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
106940 AGAAGAAGAA
106950 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
106991 AGAAAAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:111011 original size:24 final size:24
Alignment explanation
Indices: 110984--111029 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
110974 TAATTTTAGA
* *
110984 TATTTTTAATATTATAATAAATAT
1 TATTATTAATATTAAAATAAATAT
* *
111008 TATTATTATTTTTAAAATAAAT
1 TATTATTAATATTAAAATAAAT
111030 TTAAATATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATTAATATTAAAATAAATAT
Found at i:121350 original size:22 final size:22
Alignment explanation
Indices: 121324--121383 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
121314 TAAAAATAAT
* * **
121324 AAAATTTTAATTTAATCTTTTA
1 AAAATTATAATTTAATATCGTA
* *
121346 AAAATTATATTTTACTATCGTA
1 AAAATTATAATTTAATATCGTA
121368 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
121384 TTCAACCCTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAATTATAATTTAATATCGTA
Found at i:124871 original size:30 final size:28
Alignment explanation
Indices: 124837--124934 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
124827 CAAAATTCTA
124837 ATTTTTACTCCGATTTTTTCAAAAATTACC
1 ATTTTTAC-CCGATTTTTTC-AAAATTACC
**
124867 A-TTTTACCATCGAACTTTTCAAAATT-CC
1 ATTTTTACC--CGATTTTTTCAAAATTACC
*
124895 ATTTTTGACCCTGATTTTTTTTAAAATTACC
1 ATTTTT-ACCC-GA-TTTTTTCAAAATTACC
124926 A-TTTTACCC
1 ATTTTTACCC
124935 CCTAACCTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
28 5 0.09
29 22 0.39
30 26 0.46
31 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (28 bp):
ATTTTTACCCGATTTTTTCAAAATTACC
Found at i:124949 original size:29 final size:29
Alignment explanation
Indices: 124917--125010 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
124907 GATTTTTTTT
*
124917 AAAATTACCATTTTACCCCCTAACCTTCC
1 AAAATTACCATTTTACCCCCTAACTTTCC
* **
124946 AAAAAATT-CCATTTTTA-GCCCTATTTTTCC
1 --AAAATTACCA-TTTTACCCCCTAACTTTCC
*
124976 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCCTAACTTTCC
125005 AAAATT
1 AAAATT
125011 CCTTTTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
28 11 0.21
29 18 0.35
30 12 0.23
31 11 0.21
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCTAACTTTCC
Found at i:124960 original size:30 final size:31
Alignment explanation
Indices: 124917--125008 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
124907 GATTTTTTTT
*
124917 AAAATTACCATTTTACCCCCTAACCTTCCAA
1 AAAATTACCATTTTACCCCCTAACTTTCCAA
* **
124948 AAAATT-CCATTTTTA-GCCCTATTTTTCC--
1 AAAATTACCA-TTTTACCCCCTAACTTTCCAA
*
124976 AAAATTACCATTTTACCCCCAAACTTTCCAA
1 AAAATTACCATTTTACCCCCTAACTTTCCAA
125007 AA
1 AA
125009 TTCCTTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
28 11 0.23
29 12 0.25
30 12 0.25
31 13 0.27
ACGTcount: A:0.35, C:0.30, G:0.01, T:0.34
Consensus pattern (31 bp):
AAAATTACCATTTTACCCCCTAACTTTCCAA
Found at i:125018 original size:29 final size:28
Alignment explanation
Indices: 124917--125017 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
124907 GATTTTTTTT
* *
124917 AAAATTACCATTTTACCCCCTAACCTTCC
1 AAAATT-CCTTTTTACCCCCTAACTTTCC
* **
124946 AAAAAATTCCATTTTTA-GCCCTATTTTTCC
1 --AAAATTCC-TTTTTACCCCCTAACTTTCC
* *
124976 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATT-CCTTTTTACCCCCTAACTTTCC
125005 AAAATTCCTTTTT
1 AAAATTCCTTTTT
125018 TTACCCTAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 17 0.30
29 17 0.30
30 11 0.20
31 11 0.20
ACGTcount: A:0.32, C:0.30, G:0.01, T:0.38
Consensus pattern (28 bp):
AAAATTCCTTTTTACCCCCTAACTTTCC
Found at i:125108 original size:30 final size:28
Alignment explanation
Indices: 124839--125214 Score: 85
Period size: 29 Copynumber: 12.8 Consensus size: 28
124829 AAATTCTAAT
*
124839 TTTTA-CTCCGATTTTTTCAAAAATTACCA
1 TTTTACCT-CGATTTTTCCAAAAATT-CCA
*
124868 TTTTACCATCGAACTTTT-C-AAAATTCCA
1 TTTTACC-TCG-ATTTTTCCAAAAATTCCA
***
124896 TTTTTGACC-CTGATTTTTTTTAAAATTACCA
1 -TTTT-ACCTC-GATTTTTCCAAAAATT-CCA
* * ***
124927 TTTTACCCCCTAACCTTCCAAAAAATTCCA
1 TTTTA-CCTCGATTTTTCC-AAAAATTCCA
*
124957 TTTTTAGCC-CTATTTTTCC-AAAATTACCA
1 -TTTTA-CCTCGATTTTTCCAAAAATT-CCA
* * ** *
124986 TTTTACCCCCAAACTTTCC-AAAATTCCTTT
1 TTTTA-CCTCGATTTTTCCAAAAATTCC--A
* * *
125016 TTTTACC-CTAATTTTTCAAAAAAAATACCA
1 TTTTACCTC-GATTTTTC--CAAAAATTCCA
** *
125046 TTTTATCCTCGA-ACTTCCTAAAATTCCAA
1 TTTTA-CCTCGATTTTTCCAAAAATTCC-A
125075 TTTTGACCTCGATTTTTCCAAAAATTACCA
1 TTTT-ACCTCGATTTTTCCAAAAATT-CCA
* ***
125105 TTTTACC-CTTAAACTTCCAAAAATTCCA
1 TTTTACCTC-GATTTTTCCAAAAATTCCA
*
125133 TTTTTGAACCT-GATTTTT-AAAAAATTACCA
1 -TTTT--ACCTCGATTTTTCCAAAAATT-CCA
** ** *
125163 TTTTACCCTTAAACTTT-CAAAAAATCCA
1 TTTTA-CCTCGATTTTTCCAAAAATTCCA
*
125191 TTTTTGACCTTGATTTTTCCAAAA
1 -TTTT-ACCTCGATTTTTCCAAAA
125215 TCATCATTTT
Statistics
Matches: 259, Mismatches: 50, Indels: 75
0.67 0.13 0.20
Matches are distributed among these distances:
27 1 0.00
28 42 0.16
29 104 0.40
30 73 0.28
31 31 0.12
32 8 0.03
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (28 bp):
TTTTACCTCGATTTTTCCAAAAATTCCA
Found at i:125137 original size:29 final size:29
Alignment explanation
Indices: 124917--125194 Score: 101
Period size: 29 Copynumber: 9.5 Consensus size: 29
124907 GATTTTTTTT
* *
124917 AAAATTACCATTTTACCCCCTAACCTTCCAA
1 AAAATTACCATTTTA-CCCTTAAACTTCC-A
***
124948 AAAATT-CCATTTTTAGCCC-TATTTTTCC-
1 AAAATTACCA-TTTTA-CCCTTAAACTTCCA
**
124976 AAAATTACCATTTTACCCCCAAACTTTCC-
1 AAAATTACCATTTTACCCTTAAAC-TTCCA
* ** *
125005 AAAATT-CCTTTTTTTACCC-TAATTTTTCAAA
1 AAAATTACC--ATTTTACCCTTAA-ACTTC-CA
* * ** *
125036 AAAAATACCATTTTATCCTCGAACTTCCT
1 AAAATTACCATTTTACCCTTAAACTTCCA
* ***
125065 AAAATT-CCAATTTTGA-CCTCGATTTTTCCA
1 AAAATTACC-ATTTT-ACCCT-TAAACTTCCA
125095 AAAATTACCATTTTACCCTTAAACTTCCA
1 AAAATTACCATTTTACCCTTAAACTTCCA
* * ** **
125124 AAAATT-CCATTTTTGAACC-TGATTTTTAA
1 AAAATTACCA-TTTT-ACCCTTAAACTTCCA
*
125153 AAAATTACCATTTTACCCTTAAACTTTCA
1 AAAATTACCATTTTACCCTTAAACTTCCA
*
125182 AAAAAT-CCATTTT
1 AAAATTACCATTTT
125195 TGACCTTGAT
Statistics
Matches: 182, Mismatches: 45, Indels: 43
0.67 0.17 0.16
Matches are distributed among these distances:
27 3 0.02
28 29 0.16
29 74 0.41
30 52 0.29
31 22 0.12
32 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTAAACTTCCA
Found at i:125156 original size:58 final size:58
Alignment explanation
Indices: 124851--125283 Score: 378
Period size: 59 Copynumber: 7.4 Consensus size: 58
124841 TTACTCCGAT
* * * *
124851 TTTTTCAAAAATTACCATTTTACCATCGAACTTTTC-AAAATTCCATTTTTGACCCTGA
1 TTTTTCAAAAATTACCATTTTACCCTCAAAC-TTCCAAAAATTCCATTTTTGAACCTGA
** * * *
124909 TTTTTTTTAAAATTACCATTTTACCCCCTAACCTTCCAAAAAATTCCATTTTT-AGCCCT-A
1 -TTTTTCAAAAATTACCATTTTACCCTC-AAACTTCC-AAAAATTCCATTTTTGA-ACCTGA
* * * * * *
124969 TTTTTCCAAAATTACCATTTTACCCCCAAACTTTCC-AAAATTCCTTTTTTTACCCTAA
1 TTTTTCAAAAATTACCATTTTACCCTCAAAC-TTCCAAAAATTCCATTTTTGAACCTGA
* * * * *
125027 TTTTTCAAAAAAAATACCATTTTATCCTCGAACTTCCTAAAATTCCAATTTTG-ACCTCGA
1 TTTTTC--AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGAACCT-GA
*
125087 TTTTTCCAAAAATTACCATTTTACCCTTAAACTTCCAAAAATTCCATTTTTGAACCTGA
1 TTTTT-CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGAACCTGA
* * * *
125146 TTTTTAAAAAATTACCATTTTACCCTTAAACTTTCAAAAAATCCATTTTTG-ACCTTGA
1 TTTTTCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGAACC-TGA
* * * * * *
125204 TTTTTCCAAAATCATCATTTTACCCTCGAA-TGTCTAAAAATCCCATTTTT-AACCCTGAA
1 TTTTTCAAAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTGAA-CCTG-A
* * *
125263 TCTTCCTAAAATTACCATTTT
1 TTTTTCAAAAATTACCATTTT
125284 GGCCCCCTCG
Statistics
Matches: 311, Mismatches: 45, Indels: 36
0.79 0.11 0.09
Matches are distributed among these distances:
57 21 0.07
58 98 0.32
59 127 0.41
60 46 0.15
61 19 0.06
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40
Consensus pattern (58 bp):
TTTTTCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTGAACCTGA
Found at i:125209 original size:29 final size:28
Alignment explanation
Indices: 125065--125215 Score: 101
Period size: 29 Copynumber: 5.2 Consensus size: 28
125055 CGAACTTCCT
*
125065 AAAATTCCAATTTTGACCTCGATTTTTCCA
1 AAAATTCC-ATTTTGACCTTGATTTTT-CA
* ** *
125095 AAAATTACCATTTT-ACCCTTAAACTTCCA
1 AAAATT-CCATTTTGA-CCTTGATTTTTCA
*
125124 AAAATTCCATTTTTGAACC-TGATTTTTAA
1 AAAATTCCA-TTTTG-ACCTTGATTTTTCA
* **
125153 AAAATTACCATTTT-ACCCTTAAACTTTCA
1 AAAATT-CCATTTTGA-CCTTGATTTTTCA
* *
125182 AAAAATCCATTTTTGACCTTGATTTTTCC
1 AAAATTCCA-TTTTGACCTTGATTTTTCA
125211 AAAAT
1 AAAAT
125216 CATCATTTTA
Statistics
Matches: 91, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
27 1 0.01
28 8 0.09
29 56 0.62
30 23 0.25
31 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (28 bp):
AAAATTCCATTTTGACCTTGATTTTTCA
Found at i:126400 original size:16 final size:17
Alignment explanation
Indices: 126367--126400 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
126357 GACCTACATG
*
126367 TTTTTCAAAACGGTTTT
1 TTTTTAAAAACGGTTTT
*
126384 TTTTTAAAAACTGTTTT
1 TTTTTAAAAACGGTTTT
126401 GTGGTGATCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTTTAAAAACGGTTTT
Found at i:137832 original size:193 final size:193
Alignment explanation
Indices: 137379--138170 Score: 995
Period size: 193 Copynumber: 4.1 Consensus size: 193
137369 GATTATCCAC
* *
137379 AAACAA-TGAGGCGGTCGTCTTCCTAATGAGATATAGAGAAGTATACCAACTCAAGGTTCAATAC
1 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAA--C-----TCAATAC
* * * * *
137443 GAGCTAATCTTTGAACCCCAGCTTCCTAATGAGATACTGAGAAGTAGGGCGAAGCAATAAAAAGG
59 GAACAAATCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGG
* * * *
137508 TAAGCTTCCTGATGAGATACGGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGGACAAAGAAGC
123 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGC
137573 GGATTG
188 GGATTG
*
137579 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAAAGAAGTATACCAACTCAATACGAACAAA
1 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATACGAACAAA
* *
137644 TCTTCGAACACCAGTTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCCT
66 TCTTCGAAC-CCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
*
137709 CCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTT-CTGATGAGGTACAGAGAAGCGGATTG
130 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTG
*
137772 AAACAAGTGAGGGGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATACGAACAAA
1 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATACGAACAAA
* *
137837 TCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATGAAAAGGTTAG---
66 TCTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
* **
137899 -C---T----T-CTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAAAAATGGATTG
130 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTG
** * * ** ** **
137954 AAACAAACGAGGCGGTTATCTTCTTAATGAGATACAGAGAAGTATATTAACTC-A-GGGCTCAAA
1 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATACGAACAAA
* * * *
138017 TCTTCGAATCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAATCAATAAAATGGTTAGCTT
66 TCTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
* * * * *
138082 CCTGATAAAATACTAAGAAGTGGACCAAATTCGCCTTCCTGATAAGGTACAGAGAAGCGGATTG
130 CCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTG
* *
138146 AAACAAGCGATGCGGTCATCTTCCT
1 AAACAAGTGAGGCGGTCATCTTCCT
138171 GACAAGATAC
Statistics
Matches: 524, Mismatches: 51, Indels: 42
0.85 0.08 0.07
Matches are distributed among these distances:
180 57 0.11
181 28 0.05
182 70 0.13
184 1 0.00
186 1 0.00
187 1 0.00
189 1 0.00
191 1 0.00
192 69 0.13
193 144 0.27
194 104 0.20
199 1 0.00
200 6 0.01
201 40 0.08
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (193 bp):
AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATACGAACAAA
TCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTTC
CTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTG
Found at i:138570 original size:6 final size:6
Alignment explanation
Indices: 138527--138583 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
138517 TCATTTTGGG
* *
138527 TTTAAA TTT-AA TTTAAG TTTAAA CTTTTAAA GTTTAAA TTTAAA -TTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA --TTTAAA -TTTAAA TTTAAA TTTAAA
138576 TTTAAA TT
1 TTTAAA TT
138584 GAATTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 9 0.21
6 21 0.50
7 6 0.14
8 6 0.14
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:138581 original size:11 final size:11
Alignment explanation
Indices: 138563--138588 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
138553 TTAAAGTTTA
138563 AATTTAAATTG
1 AATTTAAATTG
138574 AATTTAAATTG
1 AATTTAAATTG
138585 AATT
1 AATT
138589 AAAAAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
AATTTAAATTG
Found at i:140418 original size:29 final size:29
Alignment explanation
Indices: 140386--140841 Score: 124
Period size: 29 Copynumber: 15.5 Consensus size: 29
140376 CCAAAATTTA
140386 CAAAATTCCATTTTTTACCTCGATTTTTC
1 CAAAATTCCATTTTTTACCTCGATTTTTC
* **
140415 CAAAAATTACCA--TTTTACCCCCGAACTTTC
1 C-AAAATT-CCATTTTTTA-CCTCGATTTTTC
* * *
140445 CAAAATTTCA-TTTTTGCCAT-GATTTTTTA
1 CAAAATTCCATTTTTTACC-TCGA-TTTTTC
* *
140474 AAAAATTACCA--TTTTACCCTCGAGCTTTT-
1 CAAAATT-CCATTTTTTA-CCTCGA-TTTTTC
* * ** * *
140503 AAAAATTCAATTTTTGGCCCCTATTTTTC
1 CAAAATTCCATTTTTTACCTCGATTTTTC
* ** **
140532 CAAAAATTACCATTCTACACCT-GAACTTTC
1 C-AAAATT-CCATTTTTTACCTCGATTTTTC
* *
140562 CAAAATTCCATTTTTGACCCCGATTTTTC
1 CAAAATTCCATTTTTTACCTCGATTTTTC
* * * **
140591 CAAAAAATTACCATTTTAT-CCCCTA-ACTTC
1 C--AAAATT-CCATTTTTTACCTCGATTTTTC
*
140621 CTAAAATTCCATTTTTTACC-CCATTTTTTC
1 C-AAAATTCCATTTTTTACCTCGA-TTTTTC
** **
140651 CAAAAATTACCA-TTTTTACCCTTAAACTTTC
1 C-AAAATT-CCATTTTTTA-CCTCGATTTTTC
*
140682 CAAAATACC-TTTTTTACCTCGATTTTTC
1 CAAAATTCCATTTTTTACCTCGATTTTTC
* *
140710 CAAAATAAT-CA--TTTTACCCTCGA-ATGTC
1 CAAAAT--TCCATTTTTTA-CCTCGATTTTTC
* * * *
140738 TAAAAATCTCATTTTTGACCCCGATTTTTC
1 CAAAATTC-CATTTTTTACCTCGATTTTTC
* * *
140768 CAAAA-T-CATCATTTTACCCTCGA-ATGTC
1 CAAAATTCCAT-TTTTTA-CCTCGATTTTTC
* * * *
140796 TAAAAATCTCATTTTTTACCTCGAATCTTC
1 CAAAATTC-CATTTTTTACCTCGATTTTTC
140826 TCAAAATTACCATTTT
1 -CAAAATT-CCATTTT
140842 GCCCCCCCGA
Statistics
Matches: 307, Mismatches: 78, Indels: 82
0.66 0.17 0.18
Matches are distributed among these distances:
26 1 0.00
27 3 0.01
28 70 0.23
29 95 0.31
30 84 0.27
31 45 0.15
32 9 0.03
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
CAAAATTCCATTTTTTACCTCGATTTTTC
Found at i:140445 original size:30 final size:30
Alignment explanation
Indices: 140411--140686 Score: 124
Period size: 30 Copynumber: 9.3 Consensus size: 30
140401 TACCTCGATT
140411 TTTCCAAAAATTACCATTTTACCCCCGAAC
1 TTTCCAAAAATTACCATTTTACCCCCGAAC
* ** ** **
140441 TTTCC-AAAATT-TCATTTTTGCCATGATT
1 TTTCCAAAAATTACCATTTTACCCCCGAAC
** * *
140469 TTTTAAAAAATTACCATTTTACCCTCGAGC
1 TTTCCAAAAATTACCATTTTACCCCCGAAC
* * ** * **
140499 TTT-TAAAAATT-CAATTTTTGGCCCCTATT
1 TTTCCAAAAATTACCA-TTTTACCCCCGAAC
* * *
140528 TTTCCAAAAATTACCATTCTACACCTGAAC
1 TTTCCAAAAATTACCATTTTACCCCCGAAC
**
140558 TTTCC-AAAATT-CCATTTTTGA-CCCCGATT
1 TTTCCAAAAATTACCA-TTTT-ACCCCCGAAC
* *
140587 TTTCCAAAAAATTACCATTTTATCCCCTAAC
1 TTTCC-AAAAATTACCATTTTACCCCCGAAC
* **
140618 -TTCCTAAAATT-CCATTTTTTA-CCCC-ATTT
1 TTTCCAAAAATTACCA--TTTTACCCCCGA-AC
***
140647 TTTCCAAAAATTACCATTTTTACCCTTAAAC
1 TTTCCAAAAATTACCA-TTTTACCCCCGAAC
140678 TTTCCAAAA
1 TTTCCAAAA
140687 TACCTTTTTT
Statistics
Matches: 178, Mismatches: 50, Indels: 35
0.68 0.19 0.13
Matches are distributed among these distances:
28 22 0.12
29 58 0.33
30 63 0.35
31 31 0.17
32 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTCCAAAAATTACCATTTTACCCCCGAAC
Found at i:140459 original size:58 final size:58
Alignment explanation
Indices: 140353--140847 Score: 389
Period size: 58 Copynumber: 8.4 Consensus size: 58
140343 GTCCCTGAAC
* * * *
140353 TTTCCAAAAATTA-TATTTTTA-CCCCAAAATTTACAAAATTCCATTTTTTACCTCGATT
1 TTTCCAAAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCA-TTTTTACCTCGATT
* *
140411 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTCATTTTTGCCAT-GATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTACC-TCGATT
** * * ** * * * *
140469 TTTTAAAAAATTACCATTTTACCCTCGAGCTTTTAAAAATTCAATTTTTGGCCCCTATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTT-ACCTCGATT
* * * *
140528 TTTCCAAAAATTACCATTCTACACCTGAACTTTCCAAAATTCCATTTTTGACCCCGATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTT-ACCTCGATT
* * *
140587 TTTCCAAAAAATTACCATTTTATCCCCTAAC-TTCCTAAAATTCCATTTTTTACC-CCATTT
1 TTTCC-AAAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCA-TTTTTACCTCGA-TT
*** * *
140647 TTTCCAAAAATTACCATTTTTACCCTTAAACTTTCCAAAATACCTTTTTTACCTCGATT
1 TTTCCAAAAATTACCA-TTTTACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGATT
* * * * * * *
140706 TTTCC-AAAATAATCATTTTACCCTCGAA-TGTCTAAAAATCTCATTTTTGACCCCGATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CATTTTT-ACCTCGATT
* * * * * * *
140764 TTTCC-AAAATCATCATTTTACCCTCGAA-TGTCTAAAAATCTCATTTTTTACCTCGAAT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CA-TTTTTACCTCGATT
* *
140822 CTTCTC-AAAATTACCATTTTGCCCCC
1 TTTC-CAAAAATTACCATTTTACCCCC
140848 CCGAGTGACC
Statistics
Matches: 362, Mismatches: 59, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
56 8 0.02
57 17 0.05
58 138 0.38
59 132 0.36
60 58 0.16
61 9 0.02
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (58 bp):
TTTCCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGATT
Found at i:140687 original size:30 final size:30
Alignment explanation
Indices: 140345--140699 Score: 127
Period size: 29 Copynumber: 12.1 Consensus size: 30
140335 GCCTGGAGGT
* *
140345 CCCTGAACTTTCCAAAAATTA-TATTTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
* * *
140374 CCCCAAAATTTAC-AAAATT-CCATTTTTTA
1 CCCTAAACTTTCCAAAAATTACCA-TTTTTA
* **
140403 -CCTCGATTTTTCCAAAAATTACCA-TTTTA
1 CCCT-AAACTTTCCAAAAATTACCATTTTTA
** * *
140432 CCCCCGAACTTTCC-AAAATT-TCATTTTTG
1 -CCCTAAACTTTCCAAAAATTACCATTTTTA
* * ** **
140461 CCATGATTTTTTAAAAAATTACCA-TTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
* * * * *
140490 CCCTCGAGCTTT-TAAAAATT-CAATTTTTGGC
1 CCCT-AAACTTTCCAAAAATTACCATTTTT--A
** *
140521 CCCT-ATTTTTCCAAAAATTACCA-TTCTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
*
140549 CACCTGAACTTTCC-AAAATT-CCATTTTTGA
1 C-CCTAAACTTTCCAAAAATTACCATTTTT-A
** ** *
140579 CCCCGATTTTTCCAAAAAATTACCATTTTATC
1 CCCTAAACTTTCC-AAAAATTACCATTTT-TA
*
140611 CCCT-AAC-TTCCTAAAATT-CCATTTTTTA
1 CCCTAAACTTTCCAAAAATTACCA-TTTTTA
* ***
140639 CCCCATTTTTTCCAAAAATTACCATTTTTA
1 CCCTAAACTTTCCAAAAATTACCATTTTTA
*
140669 CCCTTAAACTTTCC-AAAA-TACCTTTTTTA
1 CCC-TAAACTTTCCAAAAATTACCATTTTTA
140698 CC
1 CC
140700 TCGATTTTTC
Statistics
Matches: 240, Mismatches: 57, Indels: 58
0.68 0.16 0.16
Matches are distributed among these distances:
28 31 0.13
29 106 0.44
30 65 0.27
31 27 0.11
32 10 0.04
33 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTACCATTTTTA
Found at i:143008 original size:39 final size:39
Alignment explanation
Indices: 142964--143099 Score: 159
Period size: 39 Copynumber: 3.5 Consensus size: 39
142954 AAATGTGATT
*
142964 TTTACAGTGTCA-TCGCCAGTTCAATATAG-CATTGCAGTG
1 TTTACAGTGTCACT-GCCAGTTCAGTAT-GTCATTGCAGTG
* * * * * *
143003 GTTACAGTATCACTACCAGTTTAGTAGGTCATTGTAGTG
1 TTTACAGTGTCACTGCCAGTTCAGTATGTCATTGCAGTG
*
143042 TTTACAGTGTCACTGCCAGTTCAGTATGTCATTGCAATG
1 TTTACAGTGTCACTGCCAGTTCAGTATGTCATTGCAGTG
*
143081 TTTACAGTGTCACTACCAG
1 TTTACAGTGTCACTGCCAG
143100 CTTAATATAT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.01
39 78 0.98
40 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (39 bp):
TTTACAGTGTCACTGCCAGTTCAGTATGTCATTGCAGTG
Found at i:144526 original size:21 final size:21
Alignment explanation
Indices: 144502--144561 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
144492 GTGTGCCTAG
144502 CAGGCTTCGTGCTGGTGTATT
1 CAGGCTTCGTGCTGGTGTATT
** *
144523 CAGGC-T-GTG-T-GCCTA-G
1 CAGGCTTCGTGCTGGTGTATT
144539 CAGGCTTCGTGCTGGTGTATT
1 CAGGCTTCGTGCTGGTGTATT
144560 CA
1 CA
144562 AGCTGTGTGT
Statistics
Matches: 28, Mismatches: 6, Indels: 10
0.64 0.14 0.23
Matches are distributed among these distances:
16 5 0.18
17 4 0.14
18 4 0.14
19 4 0.14
20 4 0.14
21 7 0.25
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.33
Consensus pattern (21 bp):
CAGGCTTCGTGCTGGTGTATT
Found at i:144532 original size:37 final size:37
Alignment explanation
Indices: 144482--144624 Score: 223
Period size: 37 Copynumber: 3.9 Consensus size: 37
144472 GTTTGCACAA
144482 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
1 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
144519 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
1 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
* * * *
144556 TATTCAAGCTGTGTGTCTAGCAGGTTTCGTGCCGGTG
1 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
* * *
144593 TATTCGGGCTTTGTGCCTAGCAGGCTTTGTGC
1 TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGC
144625 CGGTTATCCA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.11, C:0.21, G:0.34, T:0.34
Consensus pattern (37 bp):
TATTCAGGCTGTGTGCCTAGCAGGCTTCGTGCTGGTG
Found at i:147960 original size:12 final size:12
Alignment explanation
Indices: 147939--147991 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
147929 TCATTAACAT
*
147939 TGTTCGTGAATA
1 TGTTCATGAATA
147951 TGTTCATGAATA
1 TGTTCATGAATA
*
147963 TGTTCAAT-TATA
1 TGTTC-ATGAATA
* *
147975 TATTCATGAACA
1 TGTTCATGAATA
147987 TGTTC
1 TGTTC
147992 GTTTAATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (12 bp):
TGTTCATGAATA
Found at i:147967 original size:24 final size:23
Alignment explanation
Indices: 147928--148012 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
147918 TTGTTTATCA
* *
147928 TTCATTAACATTGTTCGTGAATATG
1 TTCATGAACA-TGTTCGT-TATATG
* * *
147953 TTCATGAATATGTTCAATTATATA
1 TTCATGAACATGTTC-GTTATATG
147977 TTCATGAACATGTTCGTT-TAATG
1 TTCATGAACATGTTCGTTAT-ATG
*
148000 TTCATGACCATGT
1 TTCATGAACATGT
148013 CATGTTTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.02
23 16 0.33
24 23 0.47
25 9 0.18
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (23 bp):
TTCATGAACATGTTCGTTATATG
Found at i:149463 original size:18 final size:18
Alignment explanation
Indices: 149440--149477 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
149430 TTTTTTAAAT
149440 AATTTTAAATAATTTTTG
1 AATTTTAAATAATTTTTG
**
149458 AATTTTTTATAATTTTTG
1 AATTTTAAATAATTTTTG
149476 AA
1 AA
149478 AACTTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
AATTTTAAATAATTTTTG
Found at i:150998 original size:29 final size:28
Alignment explanation
Indices: 150958--151099 Score: 121
Period size: 29 Copynumber: 5.0 Consensus size: 28
150948 TTTGAGGTCG
* *
150958 AAAATGG-GATTTTTGGAAATTTGGGAGC
1 AAAATGGTAATTTTTGGAAGTTTGGG-GC
* * *
150986 AAAATGGTAA-TTTTGGATGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGTTTG-GGGC
*
151014 AAAATGGTAATTTTTGGATGTTTGGGGGC
1 AAAATGGTAATTTTTGGAAGTTT-GGGGC
151043 AAAATGGTAA-TTTTGGATGAGTTTGGGGTC
1 AAAATGGTAATTTTTGGA--AGTTTGGGG-C
**
151073 AAAAT-GTAATTTTAAGAATGTTTGGGG
1 AAAATGGTAATTTTTGGAA-GTTTGGGG
151100 TTAAAAATGC
Statistics
Matches: 95, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
28 36 0.38
29 43 0.45
30 16 0.17
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGC
Found at i:151114 original size:59 final size:59
Alignment explanation
Indices: 151051--151343 Score: 199
Period size: 59 Copynumber: 5.0 Consensus size: 59
151041 GCAAAATGGT
**
151051 AATTTTGGATGAGTTT-GGGGTCAAAATGTAATTTTAAGAATGTTT-GGGGTTAAAAATGC
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAAGAA-GTTTAGGGGTT-AAAATGC
* * * ** ** * *
151110 AATTTTGGAAAAGTTT-GGGGTCAAACTATGATTTTGGGAAGTTTAAAGGTTTAAATGTG
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAAGAAGTTTAGGGGTTAAAATG-C
* * * * *
151169 ATTTTTGG--AAGTTTAGGGGTTAAAATGTAATTTTAAAGAAGTTTAGGAGTCAAAATGT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT-AAGAAGTTTAGGGGTTAAAATGC
* * * * * *
151227 AATTTTGGAAAAGTTTGGGGGTTAAAATGTAATTTTGGAGAAGTTTA--AGTATCAAATAGG
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT-AAGAAGTTTAGGGGT-TAAAAT-GC
* * * **
151287 ATTTTTGG-AAAGTTTAGGGGTAAAAATGTGATTTTTGAA-AAGTTTATAGGTTAAAAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGT-AATTTT-AAGAAGTTTAGGGGTTAAAAT
151344 ATAATTTTTG
Statistics
Matches: 185, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
57 6 0.03
58 34 0.18
59 89 0.48
60 54 0.29
61 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.38
Consensus pattern (59 bp):
AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAAGAAGTTTAGGGGTTAAAATGC
Found at i:151360 original size:30 final size:30
Alignment explanation
Indices: 151013--151360 Score: 209
Period size: 30 Copynumber: 11.8 Consensus size: 30
151003 TGTTCGAGGG
* *
151013 TAAAATGGTAATTTTTG-GATGTTT-GGGGG
1 TAAAAT-GTAATTTTTGAGAAGTTTAGGGGT
* *
151042 CAAAATGGTAATTTTGGATG-AGTTT-GGGGT
1 TAAAAT-GTAATTTTTGA-GAAGTTTAGGGGT
* *
151072 CAAAATGTAA-TTTTAAGAATGTTT-GGGGT
1 TAAAATGTAATTTTTGAGAA-GTTTAGGGGT
* * *
151101 TAAAAATGCAATTTTGGAAAAGTTT-GGGGT
1 T-AAAATGTAATTTTTGAGAAGTTTAGGGGT
* * * * * **
151131 CAAACTATGA-TTTTGGGAAGTTTAAAGGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
* *
151160 TTAAATGTGATTTTTG-GAAGTTTAGGGGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
** *
151189 TAAAATGTAATTTTAAAGAAGTTTAGGAGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
* * * *
151219 CAAAATGTAATTTTGGAAAAGTTTGGGGGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
* *
151249 TAAAATGTAATTTTGGAGAAGTTTA--AGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
* *
151277 ATCAAATAG-GATTTTTG-GAAAGTTTAGGGGT
1 -TAAAAT-GTAATTTTTGAG-AAGTTTAGGGGT
* * * **
151308 AAAAATGTGATTTTTGAAAAGTTTATAGGT
1 TAAAATGTAATTTTTGAGAAGTTTAGGGGT
* *
151338 TAAAATATAATTTTTGTGAAGTT
1 TAAAATGTAATTTTTGAGAAGTT
151361 CGAGGGCCTC
Statistics
Matches: 247, Mismatches: 56, Indels: 31
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.00
28 18 0.07
29 84 0.34
30 135 0.55
31 9 0.04
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (30 bp):
TAAAATGTAATTTTTGAGAAGTTTAGGGGT
Found at i:154785 original size:13 final size:13
Alignment explanation
Indices: 154767--154792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
154757 TGCCTAAGGT
154767 CACTAAACTATTA
1 CACTAAACTATTA
154780 CACTAAACTATTA
1 CACTAAACTATTA
154793 GTAAGTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
CACTAAACTATTA
Found at i:159390 original size:29 final size:29
Alignment explanation
Indices: 159358--159535 Score: 96
Period size: 29 Copynumber: 6.1 Consensus size: 29
159348 AAAATGTGAC
* * *
159358 TTTTAGAAATTTGAGGGCAAAATGGTAAT
1 TTTTAGAAGTTCGAGGGAAAAATGGTAAT
* * ** *
159387 TTTTGGATGCACGAGGGAAAAATGGTGAT
1 TTTTAGAAGTTCGAGGGAAAAATGGTAAT
*
159416 TTTTAGAAGTTCGAGGGGAAAAT-GTAAT
1 TTTTAGAAGTTCGAGGGAAAAATGGTAAT
* *
159444 TTTTGATAAGTTC-AGGGGTAAAAAT-GTTAT
1 TTTT-AGAAGTTCGA-GGG-AAAAATGGTAAT
* * * **
159474 TTTTGGAAGTAC-TGGTTAAAATGGTAAT
1 TTTTAGAAGTTCGAGGGAAAAATGGTAAT
* * * *
159502 TTTGGAAAAGTT-TAGGGTCAAAATGGTAAT
1 TTT-TAGAAGTTCGAGGG-AAAAATGGTAAT
159532 TTTT
1 TTTT
159536 GCATGTTCGG
Statistics
Matches: 110, Mismatches: 32, Indels: 14
0.71 0.21 0.09
Matches are distributed among these distances:
27 5 0.05
28 18 0.16
29 60 0.55
30 27 0.25
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTAGAAGTTCGAGGGAAAAATGGTAAT
Found at i:159527 original size:30 final size:29
Alignment explanation
Indices: 159434--159682 Score: 132
Period size: 30 Copynumber: 8.4 Consensus size: 29
159424 GTTCGAGGGG
* * *
159434 AAAATGTAATTTTTGATAAGTTCAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTCA-GGGTC
* * * *
159464 AAAATGTTATTTTTGG--AAGTAC-TGGTT
1 AAAATG-TAATTTTGGAAAAGTTCAGGGTC
*
159491 AAAATGGTAATTTTGGAAAAGTTTAGGGTC
1 AAAAT-GTAATTTTGGAAAAGTTCAGGGTC
* * * * *
159521 AAAATGGTAATTTTTG-CATGTTCGGGGGC
1 AAAAT-GTAATTTTGGAAAAGTTCAGGGTC
* * * *
159550 AAAAATGCAACTTTGGAAATGTTCAAGGTC
1 -AAAATGTAATTTTGGAAAAGTTCAGGGTC
** *
159580 AAAATGGTAATTTTGGAAAAGTTTGGGGGTT
1 AAAAT-GTAATTTTGGAAAAG-TTCAGGGTC
*
159611 AAAATATAATTTTTGG-AAAGTTCGAGGGTC
1 AAAATGTAA-TTTTGGAAAAGTTC-AGGGTC
* * * *
159641 ACAATGTGATTTTTGAGAAGTTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTC-AGGGTC
*
159671 -AAATGTGATTTT
1 AAAATGTAATTTT
159683 TAGACAAAAT
Statistics
Matches: 167, Mismatches: 40, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
27 16 0.10
28 1 0.01
29 47 0.28
30 80 0.48
31 23 0.14
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTCAGGGTC
Found at i:160819 original size:9 final size:10
Alignment explanation
Indices: 160806--160841 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
160796 CTCCTTTTAT
160806 TTATTTATT-
1 TTATTTATTA
160815 TTA-TTATTA
1 TTATTTATTA
160824 TTA-TTATTA
1 TTATTTATTA
160833 TTATTTATT
1 TTATTTATT
160842 GTTTTAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTTATTA
Found at i:165438 original size:31 final size:30
Alignment explanation
Indices: 165401--165486 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
165391 AAATGTGTAT
*
165401 AATTGAACCAGAATCAAAATTTTATATATAC
1 AATTGAACCA-AATCAAAATTTAATATATAC
* * * *
165432 ATTTGAATCAAAATCAATATTTAATATATAT
1 AATTGAA-CCAAATCAAAATTTAATATATAC
165463 AATT-ATACCAAATCAAAATTTAAT
1 AATTGA-ACCAAATCAAAATTTAAT
165487 TATCAAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
30 16 0.36
31 27 0.60
32 2 0.04
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.36
Consensus pattern (30 bp):
AATTGAACCAAATCAAAATTTAATATATAC
Found at i:165478 original size:30 final size:29
Alignment explanation
Indices: 165442--165499 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
165432 ATTTGAATCA
*
165442 AAATCAATATTTAATATAT-ATAATTATACC
1 AAATCAAAATTTAAT-TATCA-AATTATACC
165472 AAATCAAAATTTAATTATCAAATTATAC
1 AAATCAAAATTTAATTATCAAATTATAC
165500 ATTAAACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATCAAAATTTAATTATCAAATTATACC
Found at i:179297 original size:31 final size:31
Alignment explanation
Indices: 179261--179321 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
179251 ATAGTCACTA
* **
179261 AACTATTCGAAAGTTTTTATTTTAGTTATTG
1 AACTATTCAAAAGTTTTTATTCAAGTTATTG
179292 AACTATTCAAAAGTTTTTATTCAAGTTATT
1 AACTATTCAAAAGTTTTTATTCAAGTTATT
179322 AGGCTGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTTATTCAAGTTATTG
Found at i:180311 original size:23 final size:22
Alignment explanation
Indices: 180271--180327 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
180261 GGGTTTTCCT
* *
180271 TTTTTTTTCTCTTCATGCTT-TCA
1 TTTTTTTT-TATTGATGCTTGT-A
180294 TTATTTTTTTATTGATGCTTGTA
1 TT-TTTTTTTATTGATGCTTGTA
180317 TTTTTTTTTAT
1 TTTTTTTTTAT
180328 CCAATTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.30
23 14 0.47
24 7 0.23
ACGTcount: A:0.12, C:0.11, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTTTTTTTATTGATGCTTGTA
Found at i:186224 original size:15 final size:14
Alignment explanation
Indices: 186200--186238 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
186190 TGAATCGATT
* *
186200 TTTATATTTTATAT
1 TTTATTTTTTATAA
186214 TTTGATTTTTTATAA
1 TTT-ATTTTTTATAA
186229 TTTATTTTTT
1 TTTATTTTTT
186239 TTTAACCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTATTTTTTATAA
Found at i:187358 original size:20 final size:19
Alignment explanation
Indices: 187329--187368 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
187319 AAACATATGT
187329 TAATAGATATTTTAGTTTTA
1 TAATAGATATTTTA-TTTTA
*
187349 TAATATATATTTTATTTTA
1 TAATAGATATTTTATTTTA
187368 T
1 T
187369 TTTTTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TAATAGATATTTTATTTTA
Found at i:189845 original size:125 final size:124
Alignment explanation
Indices: 189604--189922 Score: 415
Period size: 125 Copynumber: 2.6 Consensus size: 124
189594 AGGATAGGTG
* ** * *
189604 TATGTACACAATTGAACCTTGTGTGGAACTCTTGTTGTATTTATGTAGAACTTCTAATGTTGATC
1 TATGTAAACAATTGAACCTTGTGTGGAACTCTTGTTGTATTTATACAGAACTTGTAATGTTGATA
* * * * * *
189669 GATAGTAATGATCTACTATGTTACTTGGACCAGGTATCAGGTGTATGTGTGGATACAAA
66 GATACTAATGATCTACCATGTTACATGAACCAGGAAACAGGTGTATGTGTGGATACAAA
* *
189728 TATGTAAACAATTGAACCTTGTGTTGAACTCTTGTTGTATTTTATACAGAACTGGTAATGTTGAT
1 TATGTAAACAATTGAACCTTGTGTGGAACTCTTGTTGTA-TTTATACAGAACTTGTAATGTTGAT
* * * * *
189793 AGATACTAATGTTTTACCATGTTACATGAACTAGGAAAC-GAGTGTATGTGTGGATACTAG
65 AGATACTAATGATCTACCATGTTACATGAACCAGGAAACAG-GTGTATGTGTGGATACAAA
* * *
189853 TATGTAAACAATTGAACCTTGTCTGGAATTCTTGTTGTAGTTTATACAGAACTTGTAATGTTAAT
1 TATGTAAACAATTGAACCTTGTGTGGAACTCTTGTTGTA-TTTATACAGAACTTGTAATGTTGAT
189918 AGATA
65 AGATA
189923 GTAGTATTAC
Statistics
Matches: 169, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
124 38 0.22
125 131 0.78
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (124 bp):
TATGTAAACAATTGAACCTTGTGTGGAACTCTTGTTGTATTTATACAGAACTTGTAATGTTGATA
GATACTAATGATCTACCATGTTACATGAACCAGGAAACAGGTGTATGTGTGGATACAAA
Found at i:191295 original size:25 final size:25
Alignment explanation
Indices: 191266--191313 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
191256 CATTTTATTT
*
191266 TTTATATATT-ATATATACAAATAAC
1 TTTATATATTCA-ATATAAAAATAAC
*
191291 TTTATTTATTCAATATAAAAATA
1 TTTATATATTCAATATAAAAATA
191314 TTTTGATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTATATATTCAATATAAAAATAAC
Found at i:191482 original size:126 final size:125
Alignment explanation
Indices: 191266--191491 Score: 280
Period size: 126 Copynumber: 1.8 Consensus size: 125
191256 CATTTTATTT
* * * *
191266 TTTATATATTATATATACAAATAACTTTATTTATTCAATATAAAAATATTTTGATATATTTATTT
1 TTTATATATTACATACACAAAGAACTTTATTTATTCAATATAAAAATAATTTGATATATTTATTT
* * * *
191331 TTTAAAAGATTATAATTGGATCAAAATTAAAGTTTTTTGTATAATATTGTATTATTTCATG
66 GTTAAAAGATAATAATTGAACCAAAATTAAA-TTTTTTGTATAATATTGTATTATTTCATG
*
191392 TTTATATATTACATACACAAAGAA-TTATATTTA-TCTAATATAAAAATAATTTGATTTATTTAT
1 TTTATATATTACATACACAAAGAACTT-TATTTATTC-AATATAAAAATAATTTGATATATTTAT
* *
191455 TTCGTT-ATAG-TCAATGATTGAACCAAAATTAAATTTT
64 TT-GTTAAAAGAT-AATAATTGAACCAAAATTAAATTTT
191492 CATGTACATA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
125 9 0.11
126 74 0.87
127 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (125 bp):
TTTATATATTACATACACAAAGAACTTTATTTATTCAATATAAAAATAATTTGATATATTTATTT
GTTAAAAGATAATAATTGAACCAAAATTAAATTTTTTGTATAATATTGTATTATTTCATG
Found at i:192856 original size:16 final size:16
Alignment explanation
Indices: 192819--192861 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
192809 TAATTTATTA
*
192819 AATAAAA-ACTATCTT
1 AATAAAATATTATCTT
*
192834 AATTAAAATATTATTTT
1 AA-TAAAATATTATCTT
192851 AATAAAATATT
1 AATAAAATATT
192862 TAGATTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 8 0.33
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:200471 original size:20 final size:20
Alignment explanation
Indices: 200446--200488 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
200436 TTACACATAC
200446 TAATAAAAATATTAAATTTT
1 TAATAAAAATATTAAATTTT
** *
200466 TAATAAATTTATTAATTTTT
1 TAATAAAAATATTAAATTTT
200486 TAA
1 TAA
200489 AATCAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATAAAAATATTAAATTTT
Found at i:205297 original size:2 final size:2
Alignment explanation
Indices: 205290--205344 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
205280 TTATTAAAAC
205290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205332 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
205345 CTTATTAAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:212860 original size:31 final size:31
Alignment explanation
Indices: 212823--212882 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
212813 GATAAGCATT
* *
212823 GATGCAATCGAGTTGGCTTGAGTAGCCTTGA
1 GATGCAATCGAATTGGCTTGAGAAGCCTTGA
212854 GATGCAATCGAATTGGCTTGAGAAGCCTT
1 GATGCAATCGAATTGGCTTGAGAAGCCTT
212883 TTGGCAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (31 bp):
GATGCAATCGAATTGGCTTGAGAAGCCTTGA
Found at i:221759 original size:23 final size:21
Alignment explanation
Indices: 221725--221766 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
221715 ATTTGTCCGG
221725 ACCCAACACTTTGTTCAAATTGA
1 ACCCAACACTTT-TT-AAATTGA
221748 ACCCAA-ATCTTTTTAAATT
1 ACCCAACA-CTTTTTAAATT
221767 TATTCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (21 bp):
ACCCAACACTTTTTAAATTGA
Found at i:221786 original size:17 final size:16
Alignment explanation
Indices: 221759--221815 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
221749 CCCAAATCTT
*
221759 TTTAAATTTATTCTAAA
1 TTTAAA-TTATTTTAAA
221776 TTTAGAATTATTTTAAA
1 TTTA-AATTATTTTAAA
221793 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTTTAAA
221810 TTTAAA
1 TTTAAA
221816 ATTTGAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 2 0.05
17 33 0.89
18 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:222551 original size:10 final size:10
Alignment explanation
Indices: 222536--222563 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
222526 GGTCGTAAGT
222536 ATAATAATTA
1 ATAATAATTA
222546 ATAATAATTA
1 ATAATAATTA
222556 ATAATAAT
1 ATAATAAT
222564 ATTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATAATTA
Found at i:223730 original size:28 final size:30
Alignment explanation
Indices: 223685--223767 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
223675 CCAAGGAGGT
*
223685 CCCCT-AACTTTCCAAAATTCCATTTTTTA
1 CCCCTAAACTTTCTAAAATTCCATTTTTTA
* **
223714 CTCC-AAA-TTT-TAAAAATTAGA-TTTTTA
1 CCCCTAAACTTTCT-AAAATTCCATTTTTTA
223741 CCCCTAAACTTTCTAAAATTCCATTTT
1 CCCCTAAACTTTCTAAAATTCCATTTT
223768 GACCTTGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
27 9 0.22
28 13 0.32
29 15 0.37
30 4 0.10
ACGTcount: A:0.33, C:0.24, G:0.01, T:0.42
Consensus pattern (30 bp):
CCCCTAAACTTTCTAAAATTCCATTTTTTA
Found at i:223816 original size:29 final size:29
Alignment explanation
Indices: 223690--223818 Score: 70
Period size: 28 Copynumber: 4.5 Consensus size: 29
223680 GAGGTCCCCT
* * * *
223690 AACTTTCCAAAATTCCATTTTTT-ACTCC
1 AACTTTTCAAAATTACATTTTTTCCCTCG
* * * * *
223718 AAATTTTAAAAATTAGATTTTTACCC-CTA
1 AACTTTTCAAAATTACATTTTTTCCCTC-G
* ** *
223747 AAC-TTTCTAAAATTCCA-TTTTGACCTTG
1 AACTTTTC-AAAATTACATTTTTTCCCTCG
223775 AA-TTTTCCAAAAATTACATTTTTTCCCTCG
1 AACTTTT-C-AAAATTACATTTTTTCCCTCG
223805 AACTTTTCAAAATT
1 AACTTTTCAAAATT
223819 TTTATCTCGA
Statistics
Matches: 72, Mismatches: 21, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
28 32 0.44
29 25 0.35
30 11 0.15
31 4 0.06
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (29 bp):
AACTTTTCAAAATTACATTTTTTCCCTCG
Found at i:223900 original size:83 final size:81
Alignment explanation
Indices: 223747--223900 Score: 211
Period size: 83 Copynumber: 1.9 Consensus size: 81
223737 TTTACCCCTA
* * * * * *
223747 AACTTTCTAAAATTCCATTTTGACCTTGAATTTTCCAAAAATTACATTTTTTCCCTCGAACTTTT
1 AACTTTCCAAAATTCCATTTTGACCTTAAAATTTCCAAAAATTACAATTTTACCCTCGAACTTCT
*
223812 CAAAATTTTTATCTCG
66 AAAAATTTTTATCTCG
223828 AACTTTCCAAAATTCCATTTTTGACCTTAAAATTTCCAAAAAATTACAATTTTACCCTCGAA-TA
1 AACTTTCCAAAATTCCA-TTTTGACCTTAAAATTTCC-AAAAATTACAATTTTACCCTCGAACT-
223892 TCTAAAAAT
63 TCTAAAAAT
223901 GCTATTTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
81 16 0.25
82 18 0.29
83 29 0.46
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (81 bp):
AACTTTCCAAAATTCCATTTTGACCTTAAAATTTCCAAAAATTACAATTTTACCCTCGAACTTCT
AAAAATTTTTATCTCG
Found at i:223984 original size:28 final size:30
Alignment explanation
Indices: 223926--223996 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
223916 GAACCTTTTG
* *
223926 AAAATTACTATTTTACCCCCAAAGCGTCC-
1 AAAATCACTATTTTACCCCCAAAGCATCCA
**
223955 AAAATCACTATTTTA-CCCCTGAGCATCCA
1 AAAATCACTATTTTACCCCCAAAGCATCCA
223984 AAAATCAC-ATTTT
1 AAAATCACTATTTT
223997 GACTCCGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAATCACTATTTTACCCCCAAAGCATCCA
Found at i:227017 original size:19 final size:18
Alignment explanation
Indices: 226980--227027 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
226970 TAAGTTTACT
* *
226980 TTTTTATAAATAATTATA
1 TTTTTATTAATTATTATA
226998 TTTTTATTAATTATTGATA
1 TTTTTATTAATTATT-ATA
*
227017 -TTATATTAATT
1 TTTTTATTAATT
227028 TACTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATTAATTATTATA
Found at i:230329 original size:19 final size:18
Alignment explanation
Indices: 230307--230362 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
230297 TTTTGAGCAA
230307 TTTAATTTTTTTTGTTCTT
1 TTTAATTTTTTTTGTT-TT
230326 TTTAACCTTTTTTTT-TTTT
1 TTTAA--TTTTTTTTGTTTT
* *
230345 TTTCATTCTTTTCTGTTT
1 TTTAATT-TTTTTTGTTT
230363 CTCTTTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 2 0.06
18 5 0.16
19 14 0.45
20 2 0.06
21 8 0.26
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTAATTTTTTTTGTTTT
Found at i:230684 original size:29 final size:30
Alignment explanation
Indices: 230651--230716 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
230641 ACTTGATACT
*
230651 TTTTTTTAATTTGATATATTATTTA-TTTA
1 TTTTTTTAATTTAATATATTATTTATTTTA
230680 TTTTTTTAATTTAATATATTATTTATTTTA
1 TTTTTTTAATTTAATATATTATTTATTTTA
*
230710 TTATTTT
1 TTTTTTT
230717 CACGTGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (30 bp):
TTTTTTTAATTTAATATATTATTTATTTTA
Found at i:230687 original size:12 final size:12
Alignment explanation
Indices: 230673--230715 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
230663 GATATATTAT
*
230673 TTATTTATTTTT
1 TTATTTATTTTA
* *
230685 TTAATTTAATATA
1 TT-ATTTATTTTA
230698 TTATTTATTTTA
1 TTATTTATTTTA
230710 TTATTT
1 TTATTT
230716 TCACGTGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:230733 original size:33 final size:29
Alignment explanation
Indices: 230664--230735 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 29
230654 TTTTAATTTG
* *
230664 ATATATTATTTATTTATTTTTTTAATTTA
1 ATATATTATTTATTTATTTTTTCAATGTA
*
230693 ATATATTATTTATTTTATTATTTTCACGTGTA
1 ATATATTATTTA-TTTATT-TTTTCA-ATGTA
230725 ATACTATTATT
1 ATA-TATTATT
230736 GGGTTATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 12 0.33
30 6 0.17
31 5 0.14
32 6 0.17
33 7 0.19
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (29 bp):
ATATATTATTTATTTATTTTTTCAATGTA
Found at i:231000 original size:31 final size:31
Alignment explanation
Indices: 230942--231000 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
230932 CATTAAGCCT
* *
230942 AAAAAGTGTCAAGTTTAGATACTAAATTTAA
1 AAAAAATGTCAAGTTTAGATACCAAATTTAA
230973 AAAAAATGTCAAGTTT-GAGTACCAAATT
1 AAAAAATGTCAAGTTTAGA-TACCAAATT
231001 GGACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (31 bp):
AAAAAATGTCAAGTTTAGATACCAAATTTAA
Found at i:231009 original size:31 final size:32
Alignment explanation
Indices: 230942--231011 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
230932 CATTAAGCCT
* *
230942 AAAAAGTGTCAAGTTTAGATACTAAATTTAAA
1 AAAAAGTGTCAAGTTTAGATACCAAATTGAAA
230974 AAAAA-TGTCAAGTTT-GAGTACCAAATTGGACAA
1 AAAAAGTGTCAAGTTTAGA-TACCAAATT-GA-AA
231007 AAAAA
1 AAAAA
231012 ATTTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 18 0.55
32 6 0.18
33 7 0.21
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTAGATACCAAATTGAAA
Found at i:240892 original size:3 final size:3
Alignment explanation
Indices: 240884--240916 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
240874 GGAAGAGAAT
240884 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
240917 TCTTATTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:246329 original size:230 final size:222
Alignment explanation
Indices: 245915--246791 Score: 939
Period size: 222 Copynumber: 3.9 Consensus size: 222
245905 GGTTTCCCAG
*
245915 TACAATGGTTTTGGTATTAGCTCTGTTATTGCATCGAAG-TTCCTGATATGCTCTTTCTTTTGGG
1 TACAATGGTTTTGGTATTAGCCCTGTTATTGCATCGAAGCTTCC-GATATGCTCTTTCTTTTGGG
* * * *
245979 ACTTTTTTTTACGGTTACATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATATGGAT
65 AATTTTTTTTATGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATCTGG--
* * ** ** * * *
246044 ATATAACTCTATTTGAGCCATGCGTATTACGATTGAATACTGTTGTTCAGGGTAGCTTAGTGGGT
128 ATATAACTCTATTTGAGCCATGCTTATTATGATCAAATACTGTTGTTTGGGGTAGCTTAATAGAT
* *
246109 GATAGTTCTGTTTTCGGTACGGTTTTTCCA
193 GATATTTCTGTTTTCGGTACGGTTTTGCCA
* *
246139 TACAATGGTTTTGGTATTAGCCCTGTGGCTGTTAGCGTATCGAAGTTTCCGATATGCTCTTTCTT
1 TACAATGGTTTTGGTATTAGCCCTGT---TATT-GC--ATCGAAGCTTCCGATATGCTCTTTCTT
* *
246204 TTGGGAATTCTTTTTTATGGTTATATGATATAATGATCTTTGGTTTCGTTTTTTCTTTGCATATA
60 TTGGGAATT-TTTTTTATGGTTATATGATATAATGATCTTTGGGTTCG-TTTTTCTTTGCCTATA
** *
246269 TCTGGATATAACTCTATTTGAGCCATGCTTACCATGATCAAATACAGTTGTTTGGGGTAGCTTAA
123 TCTGGATATAACTCTATTTGAGCCATGCTTATTATGATCAAATACTGTTGTTTGGGGTAGCTTAA
*
246334 TAGATGATATTTCTGTTTACGGTACGGTTTTGCCA
188 TAGATGATATTTCTGTTTTCGGTACGGTTTTGCCA
* * ** * *
246369 TGCAA------TGGTATTAACTTTGTTATTGCATCGAAGCTGCTGATATGCTCTTTCTTTTGGGA
1 TACAATGGTTTTGGTATTAGCCCTGTTATTGCATCGAAGCTTCCGATATGCTCTTTCTTTTGGGA
* *** *
246428 CTTTTTTTTATGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGTGGATTTCTGGATA
66 ATTTTTTTTATGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATCTGGATA
* * * * * *
246493 TAACTCTATTTGAGCCTTGCTTGTTACT-ATAAAATATTGTTGTTTGGGGAAGCTTAATTGATGA
131 TAACTCTATTTGAGCCATGCTTATTA-TGATCAAATACTGTTGTTTGGGGTAGCTTAATAGATGA
* * **
246557 TCTTTTTGTTTTCCCTACGGTTTTGCCA
195 TATTTCTGTTTTCGGTACGGTTTTGCCA
* * * * * *
246585 TGCAATGGTTTTGGTGTTAACCCTGTTATTGCATTGAAGCTTCCTATATGCTCTTTCTTTTAGG-
1 TACAATGGTTTTGGTATTAGCCCTGTTATTGCATCGAAGCTTCCGATATGCTCTTTCTTTTGGGA
* * * * *
246649 A-CTTTTTTATGGTTGACTATGATATAATGATCTATGGGTTCTTTTTTCTATGCCTATATCTAGA
66 ATTTTTTTTATGGTT-A-TATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATCTGGA
* * * * * ** **
246713 TATAATTCTATTCGAGCTATTCTTATTATGATCAACTTTTGTTGTTCCGGGTAGCTTAATCA-AT
129 TATAACTCTATTTGAGCCATGCTTATTATGATCAAATACTGTTGTTTGGGGTAGCTTAAT-AGAT
* *
246777 GATTTTTGTGTTTTC
193 GATATTTCTGTTTTC
246792 CATAAGGTTT
Statistics
Matches: 549, Mismatches: 84, Indels: 42
0.81 0.12 0.06
Matches are distributed among these distances:
216 101 0.18
217 38 0.07
218 32 0.06
220 14 0.03
221 5 0.01
222 145 0.26
224 37 0.07
227 3 0.01
228 2 0.00
230 114 0.21
231 39 0.07
232 19 0.03
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (222 bp):
TACAATGGTTTTGGTATTAGCCCTGTTATTGCATCGAAGCTTCCGATATGCTCTTTCTTTTGGGA
ATTTTTTTTATGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATCTGGATA
TAACTCTATTTGAGCCATGCTTATTATGATCAAATACTGTTGTTTGGGGTAGCTTAATAGATGAT
ATTTCTGTTTTCGGTACGGTTTTGCCA
Found at i:246578 original size:216 final size:217
Alignment explanation
Indices: 245925--246740 Score: 852
Period size: 230 Copynumber: 3.7 Consensus size: 217
245915 TACAATGGTT
* *
245925 TTGGTATTAGCTCTGTTATTGCATCGAAGTTCCTGATATGCTCTTTCTTTTGGGACTTTTTTTTA
1 TTGGTATTAACTCTGTTATTGCATCGAAGCTCCTGATATGCTCTTTCTTTTGGGACTTTTTTTTA
* * * *
245990 CGGTTACATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCCTATATATGGATATATAACTCTA
66 TGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCATATATCTGG--ATATAACTCTA
* * ** ** * * * *
246055 TTTGAGCCATGCGTATTACGATTGAATACTGTTGTTCAGGGTAGCTTAGTGGGTGATAGTTCTGT
129 TTTGAGCCATGCTTATTACTATAAAATACTGTTGTTTGGGGTAGCTTAATAGATGATATTTCTGT
* *
246120 TTTCGGTACGGTTTTTCCATACAA
194 TTTCGGTACGGTTTTGCCATGCAA
* * * *
246144 TGGTTTTGGTATTAGCCCTGTGGCTGTTAGCGTATCGAAGTTTCC-GATATGCTCTTTCTTTTGG
1 -----TTGGTATTAACTCTGT---TATT-GC--ATCGAAG-CTCCTGATATGCTCTTTCTTTTGG
* *
246208 GAATTCTTTTTTATGGTTATATGATATAATGATCTTTGGTTTCGTTTTTTCTTTGCATATATCTG
54 GACTT-TTTTTTATGGTTATATGATATAATGATCTTTGGGTTCG-TTTTTCTTTGCATATATCTG
** * *
246273 GATATAACTCTATTTGAGCCATGCTTACCA-TGATCAAATACAGTTGTTTGGGGTAGCTTAATAG
117 GATATAACTCTATTTGAGCCATGCTTATTACT-ATAAAATACTGTTGTTTGGGGTAGCTTAATAG
*
246337 ATGATATTTCTGTTTACGGTACGGTTTTGCCATGCAA
181 ATGATATTTCTGTTTTCGGTACGGTTTTGCCATGCAA
* *
246374 -TGGTATTAACTTTGTTATTGCATCGAAGCTGCTGATATGCTCTTTCTTTTGGGACTTTTTTTTA
1 TTGGTATTAACTCTGTTATTGCATCGAAGCTCCTGATATGCTCTTTCTTTTGGGACTTTTTTTTA
*** *
246438 TGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGTGGATTTCTGGATATAACTCTATT
66 TGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCATATATCTGGATATAACTCTATT
* * * * * * *
246503 TGAGCCTTGCTTGTTACTATAAAATATTGTTGTTTGGGGAAGCTTAATTGATGATCTTTTTGTTT
131 TGAGCCATGCTTATTACTATAAAATACTGTTGTTTGGGGTAGCTTAATAGATGATATTTCTGTTT
**
246568 TCCCTACGGTTTTGCCATGCAA
196 TCGGTACGGTTTTGCCATGCAA
* * * *
246590 TGGTTTTGGTGTTAACCCTGTTATTGCATTGAAGCTTCCT-ATATGCTCTTTCTTTTAGGAC--T
1 -----TTGGTATTAACTCTGTTATTGCATCGAAGC-TCCTGATATGCTCTTTCTTTTGGGACTTT
* * * * *
246652 TTTTTATGGTTGACTATGATATAATGATCTATGGGTTCTTTTTTCTATGCCTATATCTAGATATA
60 TTTTTATGGTT-A-TATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCATATATCTGGATATA
* * * *
246717 ATTCTATTCGAGCTATTCTTATTA
123 ACTCTATTTGAGCCATGCTTATTA
246741 TGATCAACTT
Statistics
Matches: 501, Mismatches: 70, Indels: 44
0.81 0.11 0.07
Matches are distributed among these distances:
216 101 0.20
217 40 0.08
218 30 0.06
220 14 0.03
221 4 0.01
222 106 0.21
223 3 0.01
224 27 0.05
227 3 0.01
228 2 0.00
230 113 0.23
231 39 0.08
232 19 0.04
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (217 bp):
TTGGTATTAACTCTGTTATTGCATCGAAGCTCCTGATATGCTCTTTCTTTTGGGACTTTTTTTTA
TGGTTATATGATATAATGATCTTTGGGTTCGTTTTTCTTTGCATATATCTGGATATAACTCTATT
TGAGCCATGCTTATTACTATAAAATACTGTTGTTTGGGGTAGCTTAATAGATGATATTTCTGTTT
TCGGTACGGTTTTGCCATGCAA
Found at i:249054 original size:23 final size:22
Alignment explanation
Indices: 249023--249073 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
249013 TGATAGAAAA
249023 TTTAT-TTTTAATATAATTTTT
1 TTTATATTTTAATATAATTTTT
* * *
249044 TTTCATATTTTGATTTACTTTTT
1 TTT-ATATTTTAATATAATTTTT
249067 TTTATAT
1 TTTATAT
249074 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 6 0.24
23 16 0.64
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATATTTTAATATAATTTTT
Found at i:263133 original size:30 final size:29
Alignment explanation
Indices: 263088--263162 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
263078 AAATTTGTTC
*
263088 AAAAT-AAATTTAATTGAGTTTATTTGAAA
1 AAAATCAAATTCAATTG-GTTTATTTGAAA
* *
263117 AAAATCAAATTCAATTGGTTTTTTTTAAA
1 AAAATCAAATTCAATTGGTTTATTTGAAA
*
263146 GAAATCAAATTCAATTG
1 AAAATCAAATTCAATTG
263163 TTGAAACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 31 0.76
30 10 0.24
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (29 bp):
AAAATCAAATTCAATTGGTTTATTTGAAA
Found at i:279594 original size:29 final size:29
Alignment explanation
Indices: 279521--279705 Score: 142
Period size: 29 Copynumber: 6.3 Consensus size: 29
279511 GGAAAAAACG
* *
279521 GGGTCAAAA-ATGAAGTTTTGGAGAA-TTTG
1 GGGTCAAAATAT-AA-TTTTGGAAAAGTTTA
* *
279550 GGGTTAAAATACAATTTTGGAAAAGTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTA
* * *
279579 GGGTAAAAATATAATTTTGGGAAAGTTTG
1 GGGTCAAAATATAATTTTGGAAAAGTTTA
* **
279608 GGGCATCAAAATGTGGTTTTGGAAAAGTTTA
1 GGG--TCAAAATATAATTTTGGAAAAGTTTA
* * * *
279639 GGGTCAAAATGTGACTTTGGGAAAGTTTA
1 GGGTCAAAATATAATTTTGGAAAAGTTTA
* * *
279668 GGGGTTAAAATACAATTTTGGAAAA-TTTT
1 -GGGTCAAAATATAATTTTGGAAAAGTTTA
279697 GGAGTCAAA
1 GG-GTCAAA
279706 GGCTGTAACA
Statistics
Matches: 125, Mismatches: 25, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
28 11 0.09
29 72 0.58
30 19 0.15
31 23 0.18
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATATAATTTTGGAAAAGTTTA
Found at i:283514 original size:30 final size:29
Alignment explanation
Indices: 283472--283742 Score: 194
Period size: 30 Copynumber: 9.1 Consensus size: 29
283462 ACTCGGGGGC
* * *
283472 AAAATGGTAATTTTTGCAAGTTTCGAGATCA
1 AAAATGG-AATTTTTGGAAGTTT-GGGGTCA
*
283503 AAAATGGAATTTTTAGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTT-GGGGTCA
* * * *
283532 AAAATGTAATTTTTGGAAATTTTGGGCTTA
1 AAAATGGAATTTTTGG-AAGTTTGGGGTCA
283562 AAAATGGAA-TTTTGGAAGTTTGGGGTC-
1 AAAATGGAATTTTTGGAAGTTTGGGGTCA
* * *
283589 AAAATGTAATTTTTGGAAATTTTAGGGTCAA
1 AAAATGGAATTTTTGG-AAGTTTGGGGTC-A
283620 AAAATGGAATTTTTGGAAGTTTAGGGGTC-
1 AAAATGGAATTTTTGGAAGTTT-GGGGTCA
* * * * *
283649 AAAATGTAATTTTTAGAAATTTTAGGGTTAA
1 AAAATGGAATTTTT-GGAAGTTT-GGGGTCA
**
283680 AAAATGGAA-TTTTGGAAAGTTTAATGGT-A
1 AAAATGGAATTTTTGG-AAGTTT-GGGGTCA
* * *
283709 AAAATGTAATTTTTAGAAAGTTTTAGGGTCA
1 AAAATGGAATTTTT-GGAAG-TTTGGGGTCA
283740 AAA
1 AAA
283743 TATAATTTTA
Statistics
Matches: 193, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
27 8 0.04
28 15 0.08
29 58 0.30
30 69 0.36
31 43 0.22
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTCA
Found at i:283529 original size:59 final size:57
Alignment explanation
Indices: 283466--283701 Score: 233
Period size: 59 Copynumber: 4.0 Consensus size: 57
283456 TTGGATACTC
* * *
283466 GGGGGCAAAATGGTAATTTTTGCAAGTTTCGAGATCAAAAATGGAATTTTTAGAAGTTT
1 GGGGGCAAAAT-GTAATTTTTGGAAATTT-GAGATCAAAAATGGAATTTTTGGAAGTTT
* * * *
283525 GGGGGTAAAAATGTAATTTTTGGAAATTTTGGGCTTAAAAATGGAA-TTTTGGAAGTTT
1 GGGGG-CAAAATGTAATTTTTGGAAA-TTTGAGATCAAAAATGGAATTTTTGGAAGTTT
* * *
283583 GGGGTCAAAATGTAATTTTTGGAAATTTTAGGGTCAAAAAATGGAATTTTTGGAAGTTT
1 GGGGGCAAAATGTAATTTTTGGAAATTTGA-GATC-AAAAATGGAATTTTTGGAAGTTT
* * * * *
283642 AGGGGTCAAAATGTAATTTTTAGAAATTTTAGGGTTAAAAAATGGAA-TTTTGGAAAGTTT
1 -GGGGGCAAAATGTAATTTTTGGAAA-TTT-GAGATCAAAAATGGAATTTTTGG-AAGTTT
283702 AATGGTAAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
56 3 0.02
57 21 0.14
58 25 0.17
59 48 0.32
60 48 0.32
61 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.36
Consensus pattern (57 bp):
GGGGGCAAAATGTAATTTTTGGAAATTTGAGATCAAAAATGGAATTTTTGGAAGTTT
Found at i:283535 original size:29 final size:30
Alignment explanation
Indices: 283502--283824 Score: 229
Period size: 30 Copynumber: 10.9 Consensus size: 30
283492 TTTCGAGATC
* *
283502 AAAAATGGAATTTTTAG-AAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAAGTTTAGGGGT
* * *
283531 AAAAATGTAATTTTTGGAAA-TTTTGGGCTT
1 AAAAATGGAATTTTTGGAAAGTTTAGGG-GT
283561 AAAAATGGAA-TTTTGG-AAGTTT-GGGGT
1 AAAAATGGAATTTTTGGAAAGTTTAGGGGT
* * *
283588 CAAAATGTAATTTTTGGAAATTTTA-GGGT
1 AAAAATGGAATTTTTGGAAAGTTTAGGGGT
283617 CAAAAAATGGAATTTTTGG-AAGTTTAGGGGT
1 --AAAAATGGAATTTTTGGAAAGTTTAGGGGT
* * * * *
283648 CAAAATGTAATTTTTAGAAATTTTAGGGTT
1 AAAAATGGAATTTTTGGAAAGTTTAGGGGT
**
283678 AAAAAATGGAA-TTTTGGAAAGTTTAATGGT
1 -AAAAATGGAATTTTTGGAAAGTTTAGGGGT
* *
283708 AAAAATGTAATTTTTAGAAAGTTTTA-GGGT
1 AAAAATGGAATTTTTGGAAAG-TTTAGGGGT
* ** *
283738 CAAAATATAA-TTTT-AAAGAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAA-AGTTTAGGGGT
* ** *
283767 TAAAATATAA-TTTTGGAGAAGTTTAAGGGT
1 AAAAATGGAATTTTTGGA-AAGTTTAGGGGT
* * ** *
283797 TAAATTATAATTTTTGGACAGTTTAGGG
1 AAAAATGGAATTTTTGGAAAGTTTAGGG
283825 ACCTTTAAGG
Statistics
Matches: 240, Mismatches: 36, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
27 9 0.04
28 17 0.07
29 85 0.35
30 90 0.38
31 39 0.16
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAAGTTTAGGGGT
Found at i:283668 original size:60 final size:59
Alignment explanation
Indices: 283502--283780 Score: 334
Period size: 60 Copynumber: 4.7 Consensus size: 59
283492 TTTCGAGATC
* * * *
283502 AAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAATTTT-GGG-CTT
1 AAAAATGGAA-TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAATTTTAGGGTC-A
* *
283561 AAAAATGGAATTTTGGAAGTTT-GGGGTCAAAATGTAATTTTTGGAAATTTTAGGGTCA
1 AAAAATGGAATTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAATTTTAGGGTCA
* *
283619 AAAAATGGAATTTTTGGAAGTTTAGGGGTCAAAATGTAATTTTTAGAAATTTTAGGGTTA
1 AAAAATGGAA-TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAATTTTAGGGTCA
**
283679 AAAAATGGAATTTTGGAAAGTTTAATGGTAAAAATGTAATTTTTAGAAAGTTTTAGGGTCA
1 AAAAATGGAATTTTGG-AAGTTTAGGGGTAAAAATGTAATTTTTAGAAA-TTTTAGGGTCA
* ** * *
283740 AAATAT--AATTTTAAAGAGTTTAGGGGTTAAAATATAATTTT
1 AAAAATGGAATTTTGGA-AGTTTAGGGGTAAAAATGTAATTTT
283781 GGAGAAGTTT
Statistics
Matches: 197, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
57 28 0.14
58 25 0.13
59 56 0.28
60 73 0.37
61 15 0.08
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (59 bp):
AAAAATGGAATTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAATTTTAGGGTCA
Found at i:283743 original size:30 final size:30
Alignment explanation
Indices: 283502--283824 Score: 228
Period size: 29 Copynumber: 11.0 Consensus size: 30
283492 TTTCGAGATC
* * **
283502 AAAAATGGAATTTTTAG-AAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGGT
283531 AAAAATGTAATTTTTGGAAA-TTTT-GGGCTT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGG--T
* *
283561 AAAAATGGAA-TTTTGG-AAG-TTTGGGGT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGGT
*
283588 CAAAATGTAATTTTTGGAAA-TTTTAGGGT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGGT
*
283617 CAAAAAATGGAATTTTTGG-AAG-TTTAGGGGT
1 --AAAAATGTAATTTTTGGAAAGTTTTA-GGGT
* *
283648 CAAAATGTAATTTTTAGAAA-TTTTAGGGTT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGG-T
* * *
283678 AAAAAATGGAA-TTTTGGAAAGTTTAATGGT
1 -AAAAATGTAATTTTTGGAAAGTTTTAGGGT
*
283708 AAAAATGTAATTTTTAGAAAGTTTTAGGGT
1 AAAAATGTAATTTTTGGAAAGTTTTAGGGT
* * *
283738 CAAAATATAA-TTTT--AAAGAGTTTAGGGGT
1 AAAAATGTAATTTTTGGAAAG-TTTTA-GGGT
* * *
283767 TAAAATATAA-TTTTGGAGAAGTTTAAGGGT
1 AAAAATGTAATTTTTGGA-AAGTTTTAGGGT
* * * *
283797 TAAATTATAATTTTTGGACAG-TTTAGGG
1 AAAAATGTAATTTTTGGAAAGTTTTAGGG
283825 ACCTTTAAGG
Statistics
Matches: 240, Mismatches: 30, Indels: 48
0.75 0.09 0.15
Matches are distributed among these distances:
27 13 0.05
28 18 0.08
29 89 0.37
30 73 0.30
31 44 0.18
32 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAAATGTAATTTTTGGAAAGTTTTAGGGT
Found at i:284996 original size:22 final size:22
Alignment explanation
Indices: 284962--285010 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
284952 TTCCCCCTTT
284962 TTAATAAATGTTATTATTATTA
1 TTAATAAATGTTATTATTATTA
284984 TTAA-AAATAGTTATTATTATTA
1 TTAATAAAT-GTTATTATTATTA
285006 TTAAT
1 TTAAT
285011 TATTATTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTAATAAATGTTATTATTATTA
Found at i:285763 original size:14 final size:15
Alignment explanation
Indices: 285740--285768 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
285730 AATTTGGACA
285740 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
285755 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
285769 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:285805 original size:6 final size:6
Alignment explanation
Indices: 285794--285854 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
285784 ATTTTGAAAA
* * *
285794 TAAATT TAAATT T-AATT TAAATT CAAATT TAAA-A TAAATC TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
285840 TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAA
285855 AGGGGCCCGG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:285812 original size:11 final size:11
Alignment explanation
Indices: 285796--285853 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
285786 TTTGAAAATA
285796 AATTTAAATTT
1 AATTTAAATTT
*
285807 AATTTAAATTCA
1 AATTTAAATT-T
* *
285819 AATTTAAAATA
1 AATTTAAATTT
*
285830 AATCTAAATTT
1 AATTTAAATTT
**
285841 AAAATAAATTT
1 AATTTAAATTT
285852 AA
1 AA
285854 AAGGGGCCCG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 30 0.77
12 9 0.23
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:285816 original size:17 final size:17
Alignment explanation
Indices: 285779--285854 Score: 98
Period size: 17 Copynumber: 4.4 Consensus size: 17
285769 ATAATAATCT
285779 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAAATAAA
**
285798 TTTAAATTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
285815 TTCAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
285832 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
285849 TTTAAA
1 TTTAAA
285855 AGGGGCCCGG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 40 0.82
18 3 0.06
19 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:285854 original size:11 final size:11
Alignment explanation
Indices: 285790--285855 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 11
285780 TTAAATTTTG
285790 AAAATAAATTT
1 AAAATAAATTT
* *
285801 AAATTTAATTT
1 AAAATAAATTT
*
285812 AAATTCAAATTT
1 AAAAT-AAATTT
285824 AAAATAAA--T
1 AAAATAAATTT
*
285833 ---CTAAATTT
1 AAAATAAATTT
285841 AAAATAAATTT
1 AAAATAAATTT
285852 AAAA
1 AAAA
285856 GGGGCCCGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 1 0.02
11 28 0.65
12 9 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:286518 original size:206 final size:206
Alignment explanation
Indices: 286152--286969 Score: 1136
Period size: 206 Copynumber: 4.0 Consensus size: 206
286142 GTCTGGTTTC
* * * ** *
286152 ATTGACTTGGCCTTCTTCTCAGTATCTCATGAGGAAGATGACCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
* * * * * * * *
286217 TCTCTATGTTTCATTAGGAAGACGAATTTGGTTCACTTCTCCGTATCTTATCAGGAAGCTAACCA
66 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
286282 TTTTATTTCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGTTGGGGTTCGAAGGTTTGCTCACA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
286347 TCGAGCGTGGG
196 TCGAGCGTGGG
* * * * * ** *
286358 CTTGATTTGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGATCGCGTCGTTTGTTTCTATCCGCT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
*
286423 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCT
66 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
286488 TTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
286553 TTGAGCGTGGG
196 TCGAGCGTGGG
* * * *
286564 TTTGATTTGGTCTTCTTCTCAGTATCTCATCTGGAAGGTGACCGCATCGCTTGTTTCAATCCGCT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
* *
286629 TCTCTGTATCTCATCAAGAAGACAAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
66 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
286694 TTTTATTGTTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGGTTTGCTCACA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
286759 TCGAGTGTGGG
196 TCGAGCGTGGG
* * * * * *
286770 ATTGATTTGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCTGTT
1 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
* * *
286835 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCCCAGTATCTCATCAGGAAGCTAACC-
66 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * *
286899 TTTTATTGCTTC-ACCCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCAAAGATTTGCTCAC
131 TTTTATTGCTTCGA-CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
286963 ATCGAGC
195 ATCGAGC
286970 CCTGAGTTGG
Statistics
Matches: 539, Mismatches: 72, Indels: 3
0.88 0.12 0.00
Matches are distributed among these distances:
204 1 0.00
205 61 0.11
206 477 0.88
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (206 bp):
ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCT
TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
TCGAGCGTGGG
Found at i:287069 original size:115 final size:114
Alignment explanation
Indices: 286877--287084 Score: 328
Period size: 115 Copynumber: 1.8 Consensus size: 114
286867 CCACTTCCCA
* *
286877 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCT
1 GTATATCATCAGGAAGCTAACATTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCT
286942 GGGATTCAAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
66 GGGATTCAAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
*
286991 GTATATCATCAGGAAGCTAATCATTTTATTGCTTCGA-CCTGCTTCTCAGTATCTCATCAGGAAG
1 GTATATCATCAGGAAGCTAA-CATTTTATTGCTTC-ACCCTGCTTCTCAGTATCTCATCAAGAAG
* * * *
287055 CTGGGGTTCGAAGATTTGCTCGCATTGAGC
64 CTGGGATTCAAAGATTTGCTCACATCGAGC
287085 GTGGGTTTGA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
114 19 0.22
115 65 0.76
116 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (114 bp):
GTATATCATCAGGAAGCTAACATTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAAGAAGCT
GGGATTCAAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCT
Found at i:288154 original size:46 final size:47
Alignment explanation
Indices: 288078--288167 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 47
288068 GTTCTAGGAA
*
288078 GCCCTTTACGGGTTTTCATCATGATCC-TTTTTTTTTTAGGCGAGAC
1 GCCCTTTACGGGTTTTCATCATAATCCTTTTTTTTTTTAGGCGAGAC
** *
288124 GCCCTTTGTGGGTTTTCATC-TCAATTCTTTTTTTTTTTAGGCGA
1 GCCCTTTACGGGTTTTCATCAT-AATCCTTTTTTTTTTTAGGCGA
288168 AGTATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.03
46 21 0.55
47 16 0.42
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (47 bp):
GCCCTTTACGGGTTTTCATCATAATCCTTTTTTTTTTTAGGCGAGAC
Found at i:293800 original size:3 final size:3
Alignment explanation
Indices: 293792--293846 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
293782 TTAATAAATG
** * *
293792 TTA TTA TTA TTA TTA TTA TTA TTA AAA ATA GTTA TTA TTA TTAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA
293839 TTA TTA TT
1 TTA TTA TT
293847 GATATAACAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
3 40 0.91
4 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:293828 original size:16 final size:16
Alignment explanation
Indices: 293806--293846 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
293796 TATTATTATT
293806 ATTATTATTAAAAATA
1 ATTATTATTAAAAATA
* **
293822 GTTATTATTATTAATA
1 ATTATTATTAAAAATA
293838 ATTATTATT
1 ATTATTATT
293847 GATATAACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTATTATTAAAAATA
Done.