Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005395.1 Kokia drynarioides strain JFW-HI SEQ_119400, 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: 224582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 46 characters in sequence are not A, C, G, or T
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 7--36 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 ATATAT
7 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
37 TTACATGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4830 original size:106 final size:106
Alignment explanation
Indices: 4743--4950 Score: 294
Period size: 106 Copynumber: 2.0 Consensus size: 106
4733 TTTACTGAAT
4743 ATAATTTAACGTAATTATAAATATTAATTATAATAATTTCGTTAAATATT-AAAACATGGAAATT
1 ATAATTTAACGTAATTATAAATATTAATTATAATAATTTCGTTAAATATTAAAAACATGGAAATT
* **
4807 AATATCCTTTTGAAAAAGATAAAATATTTTAATAAACCTTCC
66 AATATCCTTTTGAAAAAGAT-AAATAGTTTAATAAACCTAAC
* * * *
4849 ATAATTTAACGTAATTATAATTATTAATTATAATGATTTCTTTAAATATTAAAAACATGGAAGTT
1 ATAATTTAACGTAATTATAAATATTAATTATAATAATTTCGTTAAATATTAAAAACATGGAAATT
* *
4914 TATATCCTTTTGAAAAGGATATAAT-GTTTTAATAAAC
66 AATATCCTTTTGAAAAAGATA-AATAG-TTTAATAAAC
4951 TTTCCATATA
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
106 48 0.52
107 44 0.48
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (106 bp):
ATAATTTAACGTAATTATAAATATTAATTATAATAATTTCGTTAAATATTAAAAACATGGAAATT
AATATCCTTTTGAAAAAGATAAATAGTTTAATAAACCTAAC
Found at i:10964 original size:27 final size:27
Alignment explanation
Indices: 10909--11002 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
10899 GCTTGAGGAG
* * **
10909 TAATTTGACTCTAGCTCGAAATATTGT
1 TAATTTGACTCTGGCTCGAAAGAGCGT
*
10936 TAATTTGACTCTGGCTTGAAAGAGCGT
1 TAATTTGACTCTGGCTCGAAAGAGCGT
* * * * *
10963 TATTTTTATTCAGGCTCGAAGGAGCGT
1 TAATTTGACTCTGGCTCGAAAGAGCGT
* *
10990 TATTTTGATTCTG
1 TAATTTGACTCTG
11003 TCTCAAATGA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (27 bp):
TAATTTGACTCTGGCTCGAAAGAGCGT
Found at i:11056 original size:25 final size:25
Alignment explanation
Indices: 11026--11197 Score: 200
Period size: 25 Copynumber: 6.8 Consensus size: 25
11016 TTATTCTAAT
11026 TCTGGCTCGTAAGAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
*
11051 TCTGGCTCGTAAAAGCGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * * *
11076 TTTAGCTCGTTAGAGCGATATTCTA
1 TCTGGCTCGTAAGAGCGATATTCTG
*
11101 TCTGGCTCGTAAGAGTGATATTCTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * *
11126 TCTGGCTTGTAAGAACGATATTTTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * *
11151 TCTAGCTCGTAAGAGTGATATACTG
1 TCTGGCTCGTAAGAGCGATATTCTG
* * *
11176 AACTGGCTTGTAAGAGAGATAT
1 -TCTGGCTCGTAAGAGCGATAT
11198 CCTGACTAGA
Statistics
Matches: 121, Mismatches: 25, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
25 104 0.86
26 17 0.14
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTCTG
Found at i:11109 original size:75 final size:76
Alignment explanation
Indices: 11017--11197 Score: 233
Period size: 75 Copynumber: 2.4 Consensus size: 76
11007 AAATGAGAAT
* *
11017 TATTCTAATTCTGGCTCGTAAGAGCGATATTCTGTCTGGCTCGTAA-AAGCGATATTCTGTTTAG
1 TATTCTAA-TCTGGCTCGTAAGAGAGATATTCTGTCTGGCTCGTAAGAA-CGATATTCTGTCTAG
*
11081 CTCGTTAGAGCGA
64 CTCGTAAGAGCGA
* * *
11094 TATTCT-ATCTGGCTCGTAAGAGTGATATTCTGTCTGGCTTGTAAGAACGATATTTTGTCTAGCT
1 TATTCTAATCTGGCTCGTAAGAGAGATATTCTGTCTGGCTCGTAAGAACGATATTCTGTCTAGCT
*
11158 CGTAAGAGTGA
66 CGTAAGAGCGA
* *
11169 TATACTGAA-CTGGCTTGTAAGAGAGATAT
1 TATTCT-AATCTGGCTCGTAAGAGAGATAT
11198 CCTGACTAGA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
75 64 0.70
76 21 0.23
77 7 0.08
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (76 bp):
TATTCTAATCTGGCTCGTAAGAGAGATATTCTGTCTGGCTCGTAAGAACGATATTCTGTCTAGCT
CGTAAGAGCGA
Found at i:11211 original size:26 final size:26
Alignment explanation
Indices: 11159--11213 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
11149 TGTCTAGCTC
* *
11159 GTAAGAGTGATATACTGAACTGGCTT
1 GTAAGAGAGATATACTGAACTGACTT
*
11185 GTAAGAGAGATATCCTG-ACTAGACTT
1 GTAAGAGAGATATACTGAACT-GACTT
11211 GTA
1 GTA
11214 TGAGCTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (26 bp):
GTAAGAGAGATATACTGAACTGACTT
Found at i:12940 original size:24 final size:24
Alignment explanation
Indices: 12885--12967 Score: 112
Period size: 24 Copynumber: 3.4 Consensus size: 24
12875 CAGCTAATGC
* *
12885 ACGTTTATGCTCATCAGCCATTATAT
1 ACGTTTATGCTCGTCAGCCA--CTAT
*
12911 ATGTTTATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
12935 ACGTTTATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
*
12959 ATGTTTATG
1 ACGTTTATG
12968 ACTCATATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 34 0.65
26 18 0.35
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (24 bp):
ACGTTTATGCTCGTCAGCCACTAT
Found at i:28359 original size:133 final size:133
Alignment explanation
Indices: 28182--28445 Score: 440
Period size: 133 Copynumber: 2.0 Consensus size: 133
28172 AATAACTACA
* * *
28182 CAAAAGAGGTGTATGATGACATGTATGCTTCGGTGATCCGATCCAAGTAGTAACAAAAGTTCACA
1 CAAAAGAGGTGTATGATGACATGTATGCTTCAGTGATCCGATCCAAGAAGTAACAAAAGTCCACA
* * *
28247 AAATCTACAAAACAATTAAACAAGGTAAGTTTTTTGAAGATTTATCGTTCTTAGGAAGAGTTCAA
66 AAATCTACAAAACAATTAAACAAGGTAAGTTTATTGAAGATTTATCATTCTGAGGAAGAGTTCAA
28312 ACC
131 ACC
* *
28315 CAAAAGAGGTGTATGATGACGTGTATGC-TCTAGTGATCCTATCCAAGAAGTAACAAAAGTCCAC
1 CAAAAGAGGTGTATGATGACATGTATGCTTC-AGTGATCCGATCCAAGAAGTAACAAAAGTCCAC
28379 AAAATCTACAAAACAATTAAACAAGGTAAGTTTATTGAAGATTTATCATTCTGAGGAAGAGTTCA
65 AAAATCTACAAAACAATTAAACAAGGTAAGTTTATTGAAGATTTATCATTCTGAGGAAGAGTTCA
28444 AA
130 AA
28446 TATAATTCTC
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
132 2 0.02
133 120 0.98
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (133 bp):
CAAAAGAGGTGTATGATGACATGTATGCTTCAGTGATCCGATCCAAGAAGTAACAAAAGTCCACA
AAATCTACAAAACAATTAAACAAGGTAAGTTTATTGAAGATTTATCATTCTGAGGAAGAGTTCAA
ACC
Found at i:28520 original size:24 final size:24
Alignment explanation
Indices: 28493--28573 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
28483 CAGCTAATAC
*
28493 ACGTTTATGCTCGTCGGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
*
28517 ACGTATATGCTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
*
28541 ACGTTTATGTTCGTCAGCCACTAT
1 ACGTTTATGCTCGTCAGCCACTAT
*
28565 ATGTTTATG
1 ACGTTTATG
28574 ACTCATATAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (24 bp):
ACGTTTATGCTCGTCAGCCACTAT
Found at i:31189 original size:21 final size:21
Alignment explanation
Indices: 31163--31215 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
31153 CTCGATGTTA
31163 CGACGACCACGTCCGGTGTCG
1 CGACGACCACGTCCGGTGTCG
31184 CGACGACCACGTCCGGTGTCG
1 CGACGACCACGTCCGGTGTCG
*
31205 CGACAACCACG
1 CGACGACCACG
31216 CATCAAGGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.40, G:0.30, T:0.11
Consensus pattern (21 bp):
CGACGACCACGTCCGGTGTCG
Found at i:35045 original size:39 final size:39
Alignment explanation
Indices: 34984--35074 Score: 173
Period size: 39 Copynumber: 2.3 Consensus size: 39
34974 CTAACACTTG
34984 CATTGGAGTGTTTCCCCCTTGATAGTTCACAATACACCCA
1 CATTGGAGTG-TTCCCCCTTGATAGTTCACAATACACCCA
35024 CATTGGAGTGTTCCCCCTTGATAGTTCACAATACACCCA
1 CATTGGAGTGTTCCCCCTTGATAGTTCACAATACACCCA
35063 CATTGGAGTGTT
1 CATTGGAGTGTT
35075 TTAATTATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 41 0.80
40 10 0.20
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (39 bp):
CATTGGAGTGTTCCCCCTTGATAGTTCACAATACACCCA
Found at i:45817 original size:55 final size:55
Alignment explanation
Indices: 45749--45857 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
45739 AAGTTTAGGC
* * *
45749 ACAATTTAGGATATTCTCATGCAGCGAGCTATCAAATACGACGATAATTTTGGGT
1 ACAATTTAGGATATGCTCATGCAGCGAGCTATCAAATAAGACGACAATTTTGGGT
* * *
45804 ACAATTCTA-GATATGCTCATTCAGCGAGCTGTCAGATAAGACGACAATTTTGGG
1 ACAATT-TAGGATATGCTCATGCAGCGAGCTATCAAATAAGACGACAATTTTGGG
45858 CTTGCTCATG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
55 45 0.96
56 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (55 bp):
ACAATTTAGGATATGCTCATGCAGCGAGCTATCAAATAAGACGACAATTTTGGGT
Found at i:45949 original size:38 final size:38
Alignment explanation
Indices: 45895--45977 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
45885 GCAGCGACAT
*
45895 TTCTGAACATCATCATGCAGTGACAATTTTGGGCGCAA
1 TTCTGAACATCATCATGCAGTGACAATTCTGGGCGCAA
* * *
45933 TTCTGGACATCGTCATGTAGTGACAATTCTGGGCGCAA
1 TTCTGAACATCATCATGCAGTGACAATTCTGGGCGCAA
45971 TTCTGAA
1 TTCTGAA
45978 TAGACTCATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (38 bp):
TTCTGAACATCATCATGCAGTGACAATTCTGGGCGCAA
Found at i:45987 original size:38 final size:38
Alignment explanation
Indices: 45907--45995 Score: 119
Period size: 38 Copynumber: 2.3 Consensus size: 38
45897 CTGAACATCA
* * *
45907 TCATGCAGTGACAATTTTGGGCGCAATTCTGGACATCG
1 TCATGTAGTGACAATTCTGGGCGCAATTCTGGACATAG
45945 TCATGTAGTGACAATTCTGGGCGCAATTCT-GA-ATAG
1 TCATGTAGTGACAATTCTGGGCGCAATTCTGGACATAG
45981 ACTCATGTAGTGACA
1 --TCATGTAGTGACA
45996 TTAGTAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
36 3 0.07
37 2 0.04
38 41 0.89
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (38 bp):
TCATGTAGTGACAATTCTGGGCGCAATTCTGGACATAG
Found at i:47172 original size:21 final size:22
Alignment explanation
Indices: 47139--47185 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
47129 AAAGAACGAG
*
47139 AAATAAAGTAAAA-TAAAACCT
1 AAATAAAGAAAAACTAAAACCT
*
47160 AAATAGAGAAAAACTAAAACCT
1 AAATAAAGAAAAACTAAAACCT
47182 AAAT
1 AAAT
47186 GAAAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (22 bp):
AAATAAAGAAAAACTAAAACCT
Found at i:53683 original size:18 final size:18
Alignment explanation
Indices: 53652--53697 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
53642 GTAGATAAAC
53652 TAACAAAT-AAAATGCAA
1 TAACAAATAAAAATGCAA
*
53669 TGACAAATAAAAATGCAA
1 TAACAAATAAAAATGCAA
*
53687 TAACAACTAAA
1 TAACAAATAAA
53698 TAAAATGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (18 bp):
TAACAAATAAAAATGCAA
Found at i:53704 original size:21 final size:19
Alignment explanation
Indices: 53656--53706 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
53646 ATAAACTAAC
*
53656 AAATAAAATGCAATGACAA
1 AAATAAAATGCAATAACAA
*
53675 ATA-AAAATGCAATAACAA
1 AAATAAAATGCAATAACAA
53693 CTAAATAAAATGCA
1 --AAATAAAATGCA
53707 TGTAACTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
20 2 0.08
21 8 0.31
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.18
Consensus pattern (19 bp):
AAATAAAATGCAATAACAA
Found at i:53712 original size:22 final size:23
Alignment explanation
Indices: 53673--53718 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
53663 ATGCAATGAC
53673 AAATAAAAATGCAATAAC-AACT
1 AAATAAAAATGCAATAACTAACT
*
53695 AAAT-AAAATGCATGTAACTAACT
1 AAATAAAAATGCA-ATAACTAACT
53718 A
1 A
53719 CTGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.22
Consensus pattern (23 bp):
AAATAAAAATGCAATAACTAACT
Found at i:68338 original size:17 final size:17
Alignment explanation
Indices: 68316--68348 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
68306 TTTTTTCTTT
68316 TTTCTTTTATCTTTTTC
1 TTTCTTTTATCTTTTTC
*
68333 TTTCTTTTCTCTTTTT
1 TTTCTTTTATCTTTTT
68349 TTATGCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTATCTTTTTC
Found at i:82489 original size:29 final size:29
Alignment explanation
Indices: 82447--82505 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
82437 AAAAGATCAC
82447 TCAGCACGCACAAGTGATAAACATGGGTA
1 TCAGCACGCACAAGTGATAAACATGGGTA
82476 TCAGCACGCACAAGTGATAAACATGGGTA
1 TCAGCACGCACAAGTGATAAACATGGGTA
82505 T
1 T
82506 GTATTCGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (29 bp):
TCAGCACGCACAAGTGATAAACATGGGTA
Found at i:84178 original size:21 final size:21
Alignment explanation
Indices: 84149--84222 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
84139 AGATCTTAGT
84149 TTTCAAGTTTTAGTTTTATTTA
1 TTTC-AGTTTTAGTTTTATTTA
84171 TTTCAGTTTTAGTTTTATTTA
1 TTTCAGTTTTAGTTTTATTTA
*
84192 TTTCAGTTTTAGTTTTCTTTA
1 TTTCAGTTTTAGTTTTATTTA
84213 TTTCAGTTTT
1 TTTCAGTTTT
84223 TGAAACGAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 47 0.92
22 4 0.08
ACGTcount: A:0.18, C:0.07, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTCAGTTTTAGTTTTATTTA
Found at i:95758 original size:19 final size:20
Alignment explanation
Indices: 95734--95777 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
95724 AAATAGTTAA
95734 AAAAATCAAAAC-TTTATTT
1 AAAAATCAAAACTTTTATTT
** *
95753 AAAAATTTAAACTTTTCTTT
1 AAAAATCAAAACTTTTATTT
95773 AAAAA
1 AAAAA
95778 GACTGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATCAAAACTTTTATTT
Found at i:95907 original size:149 final size:148
Alignment explanation
Indices: 95533--96160 Score: 802
Period size: 148 Copynumber: 4.2 Consensus size: 148
95523 TTATTAAAAC
* * *
95533 AAAATCACTATTTTACTTCAAAATTAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAATCTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTT
* * * * * *
95598 TGTTTAAAAATTCAAGCTTTTTCTTTAAAATTACTAAAAAAACATATTTTATTTTTTTTAAAATC
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAAAACATATTTT-TATTTTTAAAAATA
* *
95663 T-ATCTTTCTTTCTTTTTTAATG
128 TAAACTTTC--TCTTTTTTAAAG
* * *
95685 AAAATCACTAATTTACTTAAAGATTC-AACTTTTATTTTGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
95749 ATTTAAAAATTTAAAC-TTTTCTTTAAAA-AGACTGAAAAAACATATTTTTACTTTTAAAAATAT
66 GTTTAAAAATTTAAACTTTTTCTTTAAAATA-ACT-AAAAAACATATTTTTATTTTTAAAAATAT
95812 AAACTTTCTCTTTTTTAAAG
129 AAACTTTCTCTTTTTTAAAG
* * * * *
95832 GAAATCACTATTTTACTTAAAAATTCAATCTTTTATTTCAAAATAGTTAAAAAAAATTAAAAGTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
* * *
95897 TGTTTAAAAATTTAAATTTTTTCTTTAAAATAACTAAAAAACAGA-TTTTATTTTTAAAAATATC
65 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATA
*
95961 AACTTTCTCATTTTTAAAG
130 AACTTTCTCTTTTTTAAAG
* * * * *
95980 AAAATTACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTTAAAAAATTAAAATTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* *
96045 GTTAAAAAAATTTAAACTTTTTCTTTAAAATAACTAAACAACATATTTTTATTTTTAAAAATATA
66 GTT-TAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATA
96110 AACTTTCTCTTTTTTAAAG
130 AACTTTCTCTTTTTTAAAG
** * *
96129 AAAAAAACTATTTT--TTAAAAAATCAAAATTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTT
96161 TATTAAAAAA
Statistics
Matches: 419, Mismatches: 49, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
147 67 0.16
148 144 0.34
149 121 0.29
150 46 0.11
151 19 0.05
152 22 0.05
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (148 bp):
AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTATTTTTAAAAATATAA
ACTTTCTCTTTTTTAAAG
Found at i:96156 original size:21 final size:19
Alignment explanation
Indices: 96119--96218 Score: 73
Period size: 20 Copynumber: 5.2 Consensus size: 19
96109 AAACTTTCTC
96119 TTTTTTAAAGAAA-AAAACT
1 TTTTTTAAA-AAACAAAACT
96138 ATTTTTTAAAAAATCAAAA-T
1 -TTTTTTAAAAAA-CAAAACT
96158 TTTTATTAAAAAACCAAAACT
1 TTTT-TTAAAAAA-CAAAACT
** * *
96179 TTTCCT-AAAATCAAACCAT
1 TTTTTTAAAAAACAAAAC-T
*
96198 TTTTTTTAAAAA-AAAACT
1 TTTTTTAAAAAACAAAACT
96216 TTT
1 TTT
96219 ATTTTAGCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
18 9 0.14
19 20 0.31
20 28 0.43
21 8 0.12
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (19 bp):
TTTTTTAAAAAACAAAACT
Found at i:96577 original size:3 final size:3
Alignment explanation
Indices: 96565--96605 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
96555 AATGAAACCC
96565 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
96606 GAAGAAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:96610 original size:3 final size:3
Alignment explanation
Indices: 96604--96638 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
96594 TAATAATAAT
96604 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
96639 TGAATGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:100262 original size:21 final size:21
Alignment explanation
Indices: 100237--100278 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
100227 AAAAGCTAAG
*
100237 AAATCTTCCTAGGACTTAGTC
1 AAATCTCCCTAGGACTTAGTC
*
100258 AAATCTCCCTATGACTTAGTC
1 AAATCTCCCTAGGACTTAGTC
100279 TTATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (21 bp):
AAATCTCCCTAGGACTTAGTC
Found at i:102362 original size:14 final size:14
Alignment explanation
Indices: 102343--102374 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
102333 CCTCCCGTGG
102343 GTACAATCCTCAAA
1 GTACAATCCTCAAA
102357 GTACAATCCTCAAA
1 GTACAATCCTCAAA
102371 GTAC
1 GTAC
102375 TTGTTACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (14 bp):
GTACAATCCTCAAA
Found at i:103982 original size:36 final size:36
Alignment explanation
Indices: 103935--104097 Score: 227
Period size: 36 Copynumber: 4.5 Consensus size: 36
103925 TCAAAGGAAG
103935 GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
1 GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
* *
103971 GCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
1 GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
* *
104007 GCATACGTCTCAATTAGAGCGTATTGCTATGATGTT
1 GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
** * * *
104043 GCATAAATCTCAATTAGAGCATATTACTATGAAGTT
1 GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
* *
104079 ACATACGTCTCGGTTAGAG
1 GCATACGTCTCGATTAGAG
104098 TGTATTGTTA
Statistics
Matches: 113, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 113 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (36 bp):
GCATACGTCTCGATTAGAGCATATTGCTATGATGTT
Found at i:104125 original size:72 final size:72
Alignment explanation
Indices: 103936--104134 Score: 193
Period size: 72 Copynumber: 2.8 Consensus size: 72
103926 CAAAGGAAGG
* * * * ** ** * *
103936 CATACGTCTCGATTAGAGCATATTGCTATGATGTTGCATACGTCTCGGTTAGAGCGTATTGCTAT
1 CATACGTCTCAATTAGAGCGTATTGCTAAGATGTTACATAAATCTCAATTAGAGCATATTACTAT
* *
104001 GATGTTG
66 GAAGTTA
* *
104008 CATACGTCTCAATTAGAGCGTATTGCTATGATGTTGCATAAATCTCAATTAGAGCATATTACTAT
1 CATACGTCTCAATTAGAGCGTATTGCTAAGATGTTACATAAATCTCAATTAGAGCATATTACTAT
104073 GAAGTTA
66 GAAGTTA
** * * * * *
104080 CATACGTCTCGGTTAGAGTGTATTGTTAAGAAT-TTACTTACATCTCGATTAGAGC
1 CATACGTCTCAATTAGAGCGTATTGCTAAG-ATGTTACATAAATCTCAATTAGAGC
104135 GTAATGCTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
72 105 0.98
73 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (72 bp):
CATACGTCTCAATTAGAGCGTATTGCTAAGATGTTACATAAATCTCAATTAGAGCATATTACTAT
GAAGTTA
Found at i:104131 original size:108 final size:108
Alignment explanation
Indices: 103942--104143 Score: 280
Period size: 108 Copynumber: 1.9 Consensus size: 108
103932 AAGGCATACG
* * * * *
103942 TCTCGATTAGAGCATATTGCTATGATGTTGCATACGTCTCGGTTAGAGCGTATTGCTATGATGTT
1 TCTCAATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTAAGATGTT
* * *
104007 GCATACGTCTCAATTAGAGCGTATTGCTATGATGTTGCATAAA
66 ACATACATCTCAATTAGAGCGTAATGCTATGATGTTGCATAAA
* *
104050 TCTCAATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGTGTATTGTTAAGAAT-T
1 TCTCAATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTAAG-ATGT
* *
104114 TACTTACATCTCGATTAGAGCGTAATGCTA
65 TACATACATCTCAATTAGAGCGTAATGCTA
104144 AGTGATCGCT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
108 79 0.98
109 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (108 bp):
TCTCAATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTAAGATGTT
ACATACATCTCAATTAGAGCGTAATGCTATGATGTTGCATAAA
Found at i:104168 original size:108 final size:108
Alignment explanation
Indices: 103935--104173 Score: 275
Period size: 108 Copynumber: 2.2 Consensus size: 108
103925 TCAAAGGAAG
* * * *
103935 GCATACGTCTCGATTAGAGCATATTGCTATGATGTTGCATACGTCTCGGTTAGAGCGTATTGCTA
1 GCATAAGTCTCGATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTA
* * * * * *
104000 TGATGTTGCATACGTCTCAATTAGAGCGTATTGCTATGATGTT
66 AGATGTTACATACATCTCAATTAGAGCGTAATGCTAAGATGTC
* * * *
104043 GCATAAATCTCAATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGTGTATTGTTA
1 GCATAAGTCTCGATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTA
* *
104108 AGAAT-TTACTTACATCTCGATTAGAGCGTAATGCTAAG-TGATC
66 AG-ATGTTACATACATCTCAATTAGAGCGTAATGCTAAGATG-TC
* * *
104151 GCTTATGTCTCGGTTAGAGCATA
1 GCATAAGTCTCGATTAGAGCATA
104174 AGGTCATTCT
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
107 2 0.02
108 104 0.96
109 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (108 bp):
GCATAAGTCTCGATTAGAGCATATTACTATGAAGTTACATACGTCTCGGTTAGAGCGTATTGCTA
AGATGTTACATACATCTCAATTAGAGCGTAATGCTAAGATGTC
Found at i:110701 original size:32 final size:32
Alignment explanation
Indices: 110665--110727 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
110655 ATATATTGTT
*
110665 ACATATACGCATGCTATATACTAAAAGTTAAC
1 ACATATAAGCATGCTATATACTAAAAGTTAAC
*
110697 ACATATAAGCATGCTATATACTAAAATTTAA
1 ACATATAAGCATGCTATATACTAAAAGTTAA
110728 AGATTCTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (32 bp):
ACATATAAGCATGCTATATACTAAAAGTTAAC
Found at i:113226 original size:23 final size:25
Alignment explanation
Indices: 113198--113244 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
113188 TTCCTTGTAA
113198 TTTAGG-TTTAGTTATTTT-CTTTC
1 TTTAGGTTTTAGTTATTTTACTTTC
113221 TTTAGGTTTTAGTTATTTTACTTT
1 TTTAGGTTTTAGTTATTTTACTTT
113245 TGTTTTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.15, C:0.06, G:0.13, T:0.66
Consensus pattern (25 bp):
TTTAGGTTTTAGTTATTTTACTTTC
Found at i:115468 original size:58 final size:58
Alignment explanation
Indices: 115377--115486 Score: 202
Period size: 58 Copynumber: 1.9 Consensus size: 58
115367 AGTCTTTGCC
*
115377 TTAGCCTTTGTAGTGGTTCTCTCCTTATACATTTTGATCTGGTTCATAGTTGTATTGT
1 TTAGCCTTTGTAGTAGTTCTCTCCTTATACATTTTGATCTGGTTCATAGTTGTATTGT
*
115435 TTAGCCTTTGTAGTAGTTCTCTCCTTATGCATTTTGATCTGGTTCATAGTTG
1 TTAGCCTTTGTAGTAGTTCTCTCCTTATACATTTTGATCTGGTTCATAGTTG
115487 GGTTGTTGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.15, C:0.16, G:0.19, T:0.49
Consensus pattern (58 bp):
TTAGCCTTTGTAGTAGTTCTCTCCTTATACATTTTGATCTGGTTCATAGTTGTATTGT
Found at i:116337 original size:29 final size:30
Alignment explanation
Indices: 116295--116353 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
116285 GAATTCAATC
*
116295 AAATCAAAATTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTGCACA
116325 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTGCACA
116354 TTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATACAATTGCACA
Found at i:116372 original size:31 final size:29
Alignment explanation
Indices: 116305--116374 Score: 97
Period size: 29 Copynumber: 2.3 Consensus size: 29
116295 AAATCAAAAT
*
116305 TTCATGTATACAATTGCACAAAATCAAAG
1 TTCATGTATACAATTGCACAAAACCAAAG
116334 TTCATGTATACAATTGCACATTAAACCATAA-
1 TTCATGTATACAATTGCACA--AAACCA-AAG
116365 TTCATGTATA
1 TTCATGTATA
116375 GTTTTGATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 20 0.54
31 15 0.41
32 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (29 bp):
TTCATGTATACAATTGCACAAAACCAAAG
Found at i:126433 original size:16 final size:16
Alignment explanation
Indices: 126410--126450 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
126400 GTCATGGCGT
*
126410 TAAATTTATTTTTTTT
1 TAAATTTATTTTTTTA
* *
126426 TCAATTTAATTTTTTA
1 TAAATTTATTTTTTTA
126442 TAAATTTAT
1 TAAATTTAT
126451 ATTATGATCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TAAATTTATTTTTTTA
Found at i:132479 original size:17 final size:18
Alignment explanation
Indices: 132459--132492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
132449 AATATAAATT
*
132459 TAAAAGTTAAA-AAAAGC
1 TAAAAATTAAATAAAAGC
132476 TAAAAATTAAATAAAAG
1 TAAAAATTAAATAAAAG
132493 ACAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.03, G:0.09, T:0.21
Consensus pattern (18 bp):
TAAAAATTAAATAAAAGC
Found at i:137656 original size:55 final size:55
Alignment explanation
Indices: 137582--137867 Score: 317
Period size: 55 Copynumber: 5.2 Consensus size: 55
137572 TTTAATTCAC
* * * *
137582 TTATAGCTTGAGTAGAGCTTTGGTTTGCTTACGTCTTGGTTAGAGCGTAAAGATA
1 TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
* * * * * *
137637 TTATAGCTTGGGTATAGCTTTGGTTTGCTTACGACTTGATTAGAGCGTAAAGTTA
1 TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
** * * *
137692 TTATAGCTCAGATAGAGCTTTGGATTGCTTATGTCTCGGTTAGAGCAG-AAGGCTA
1 TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGC-GTAAAGCTA
* * *
137747 TTATAGCTTGAGTAGAGCTTTGG-TTGCTTACGTCTCAGTTAGAGCGTAAAGTTA
1 TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
* * * * * *
137801 TTATAGCTCGGGTAAAGTTTTGGAGTGCTTACGTCTCAGTTAGAGCGTAAGGCTA
1 TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
137856 TT-TCAGCTTGGG
1 TTAT-AGCTTGGG
137868 AGGAGCAATG
Statistics
Matches: 195, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 45 0.23
55 148 0.76
56 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.36
Consensus pattern (55 bp):
TTATAGCTTGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
Found at i:137824 original size:109 final size:110
Alignment explanation
Indices: 137560--137865 Score: 361
Period size: 109 Copynumber: 2.8 Consensus size: 110
137550 TTACTTATAG
* * * * * *
137560 CTCAGTTAGAGCTTTAA-TTCACTTATAGCTTGAGTAGAGCTTTGGTTTGCTTACGTCTTGGTTA
1 CTCAGTTAGAGCGTAAAGTT-A-TTATAGCTCGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTA
* * * *
137624 GAGCGTAAAGATATTATAGCTTGGGTATAGCTTTGGTTTGCTTACGA
64 GAGCGTAAGGCTATTATAGCTTGAGTAGAGCTTTGGTTTGCTTACGA
* * * *
137671 CT-TGATTAGAGCGTAAAGTTATTATAGCTCAGATAGAGCTTTGGATTGCTTATGTCTCGGTTAG
1 CTCAG-TTAGAGCGTAAAGTTATTATAGCTCGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAG
*
137735 AGCAG-AAGGCTATTATAGCTTGAGTAGAGCTTTGG-TTGCTTACGT
65 AGC-GTAAGGCTATTATAGCTTGAGTAGAGCTTTGGTTTGCTTACGA
* * * *
137780 CTCAGTTAGAGCGTAAAGTTATTATAGCTCGGGTAAAGTTTTGGAGTGCTTACGTCTCAGTTAGA
1 CTCAGTTAGAGCGTAAAGTTATTATAGCTCGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGA
137845 GCGTAAGGCTATT-TCAGCTTG
66 GCGTAAGGCTATTAT-AGCTTG
137866 GGAGGAGCAA
Statistics
Matches: 166, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
108 2 0.01
109 81 0.49
110 67 0.40
111 14 0.08
112 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.37
Consensus pattern (110 bp):
CTCAGTTAGAGCGTAAAGTTATTATAGCTCGGGTAGAGCTTTGGATTGCTTACGTCTCGGTTAGA
GCGTAAGGCTATTATAGCTTGAGTAGAGCTTTGGTTTGCTTACGA
Found at i:139371 original size:127 final size:127
Alignment explanation
Indices: 139145--139378 Score: 346
Period size: 127 Copynumber: 1.8 Consensus size: 127
139135 GATACTACCA
* * * *
139145 ATGACAAAAAATAAAGCTAAAAATATGTTTTTCGATTTAATGGGACAGTGGTTCTTAGAGTTTAT
1 ATGACAAAAAATAAAGCTAAAAATATGTTTTTCGATTTAATAGGACAATAGTTCTCAGAGTTTAT
* *
139210 GAGAAATAATCTCATGACATCGTAACCTCCACCTCCTGTCACACAACTTACCGATATAATTG
66 GAGAAATAATCTCATGACATCATAACCTCCACCTCCTATCACACAACTTACCGATATAATTG
* * *
139272 ATGACATAAAATGAAGCTAAAAATATGTTTTTCGGTTTAATAGGACAATAGTTCTCAGAGTTTAT
1 ATGACAAAAAATAAAGCTAAAAATATGTTTTTCGATTTAATAGGACAATAGTTCTCAGAGTTTAT
*
139337 GAGAAATAATCTGAT-AGC-TCTATAACCTCCACCTCCTATCAC
66 GAGAAATAATCTCATGA-CATC-ATAACCTCCACCTCCTATCAC
139379 TTAACCTACC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
126 3 0.03
127 92 0.97
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (127 bp):
ATGACAAAAAATAAAGCTAAAAATATGTTTTTCGATTTAATAGGACAATAGTTCTCAGAGTTTAT
GAGAAATAATCTCATGACATCATAACCTCCACCTCCTATCACACAACTTACCGATATAATTG
Found at i:147045 original size:9 final size:9
Alignment explanation
Indices: 147031--147072 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
147021 ATTCAATACT
147031 TTAATTCGG
1 TTAATTCGG
147040 TTAATTCGGG
1 TTAATTC-GG
*
147050 TTAA-TCGA
1 TTAATTCGG
147058 TTAATTCGG
1 TTAATTCGG
*
147067 GTAATT
1 TTAATT
147073 TGTTCTACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 5 0.18
9 17 0.61
10 6 0.21
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (9 bp):
TTAATTCGG
Found at i:148622 original size:35 final size:35
Alignment explanation
Indices: 148563--148629 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
148553 AAAGTATGCT
148563 ATTATTTTGATTATGAGTCACATGTTAAGCATGAC
1 ATTATTTTGATTATGAGTCACATGTTAAGCATGAC
* * **
148598 ATTATTTTGATTTTGATTTTCATGTTAAGCAT
1 ATTATTTTGATTATGAGTCACATGTTAAGCAT
148630 ACCACTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (35 bp):
ATTATTTTGATTATGAGTCACATGTTAAGCATGAC
Found at i:148681 original size:46 final size:46
Alignment explanation
Indices: 148618--148770 Score: 227
Period size: 46 Copynumber: 3.3 Consensus size: 46
148608 TTTTGATTTT
* *
148618 CATGTTAAGCATACCACTGTATTAAACCGTAATAAGATCTGATTTG
1 CATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATCTGATTCG
* *
148664 CATGTTAAGCATGCCACTGTATTAAACCATAATAAGATCTTATTCG
1 CATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATCTGATTCG
* * *
148710 CATGTTAAACATGGCACTGTATTAAACCGTAATAAGATCTGATTCA
1 CATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATCTGATTCG
148756 CAT-TTAAAGCATGCC
1 CATGTT-AAGCATGCC
148771 TATTGAAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 2 0.02
46 93 0.98
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (46 bp):
CATGTTAAGCATGCCACTGTATTAAACCGTAATAAGATCTGATTCG
Found at i:152323 original size:16 final size:17
Alignment explanation
Indices: 152292--152326 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
152282 TAACAAAATG
152292 ATGCAGTGATAAAATAAA
1 ATGCAGTGAT-AAATAAA
152310 ATGCAGTGAT-AATAAA
1 ATGCAGTGATAAATAAA
152326 A
1 A
152327 AGCATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
ATGCAGTGATAAATAAA
Found at i:154963 original size:84 final size:81
Alignment explanation
Indices: 154822--155008 Score: 234
Period size: 84 Copynumber: 2.3 Consensus size: 81
154812 CCTTTAACAT
* * *
154822 AGATAACCACAAAAGCATCC-TAAACAAAAATAATCATAAAGACGTCCTTAAGCAAAGAAAACCA
1 AGATAACCAC-AAAGCATCCATAAACAAAAATAACCACAAAGACGTCCATAAGCAAAGAAAACCA
*
154886 CAAAGGCTTCCATAAGCAA
65 CAAAGGCATCCAT--GCAA
* * *
154905 AGATAACCACAAAGTCATCCATAAGA-AAAAATAACCACAAAGATGTCCATAAGCAAAGATAGCC
1 AGATAACCACAAAG-CATCCATAA-ACAAAAATAACCACAAAGACGTCCATAAGCAAAGAAAACC
*
154969 ACAAAGGCATCCATTCAA
64 ACAAAGGCATCCATGCAA
154987 AGATAACCACAAAGACATCCAT
1 AGATAACCACAAAG-CATCCAT
155009 TTAGATATAG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
82 28 0.30
83 15 0.16
84 48 0.52
85 1 0.01
ACGTcount: A:0.51, C:0.24, G:0.11, T:0.14
Consensus pattern (81 bp):
AGATAACCACAAAGCATCCATAAACAAAAATAACCACAAAGACGTCCATAAGCAAAGAAAACCAC
AAAGGCATCCATGCAA
Found at i:154996 original size:26 final size:27
Alignment explanation
Indices: 154822--155008 Score: 144
Period size: 28 Copynumber: 6.8 Consensus size: 27
154812 CCTTTAACAT
* *
154822 AGATAACCACAAAAGCATCC-TAAACAA
1 AGATAACCACAAAGGCATCCAT-AGCAA
* * * * * *
154849 AAATAATCATAAAGACGTCCTTAAGCAA
1 AGATAACCACAAAGGCATCCAT-AGCAA
* *
154877 AGAAAACCACAAAGGCTTCCATAAGCAA
1 AGATAACCACAAAGGCATCCAT-AGCAA
* *
154905 AGATAACCACAAAGTCATCCATAAGAAA
1 AGATAACCACAAAGGCATCCAT-AGCAA
* ***
154933 AAATAACCACAAAGATGTCCATAAGCAA
1 AGATAACCACAAAGGCATCCAT-AGCAA
* *
154961 AGATAGCCACAAAGGCATCCAT-TCAA
1 AGATAACCACAAAGGCATCCATAGCAA
*
154987 AGATAACCACAAAGACATCCAT
1 AGATAACCACAAAGGCATCCAT
155009 TTAGATATAG
Statistics
Matches: 128, Mismatches: 31, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
26 23 0.18
27 14 0.11
28 91 0.71
ACGTcount: A:0.51, C:0.24, G:0.11, T:0.14
Consensus pattern (27 bp):
AGATAACCACAAAGGCATCCATAGCAA
Found at i:155022 original size:26 final size:26
Alignment explanation
Indices: 154958--155026 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
154948 TGTCCATAAG
*
154958 CAAAGATAGCCACAAAGGCATCCATT
1 CAAAGATAGCCACAAAGACATCCATT
*
154984 CAAAGATAACCACAAAGACATCCATT
1 CAAAGATAGCCACAAAGACATCCATT
* * *
155010 TAGATATAGCCACAAAG
1 CAAAGATAGCCACAAAG
155027 GCGTCCTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.16
Consensus pattern (26 bp):
CAAAGATAGCCACAAAGACATCCATT
Found at i:155107 original size:57 final size:56
Alignment explanation
Indices: 155019--155203 Score: 161
Period size: 57 Copynumber: 3.4 Consensus size: 56
155009 TTAGATATAG
* * *
155019 CCACAAAGGCGTC-CTTT-ACAGAATTAGCCATAGAGGCTCACGATAATAGAATCAA
1 CCACAAAGGCCTCACTTTAACAGAATTAACCATAAAGGCTCACG-TAATAGAATCAA
* * * *
155074 CCACAAAGGCCTCACTTTAACAGATTTACCCATAAAGG----CGTAACAGAATCGA
1 CCACAAAGGCCTCACTTTAACAGAATTAACCATAAAGGCTCACGTAATAGAATCAA
* * * * *
155126 CCACAAAAG-CTCACTTTAACAGAATTAACCAAAAAGGCTTCACTTTAATAGAATTAG
1 CCACAAAGGCCTCACTTTAACAGAATTAACCATAAAGGC-TCAC-GTAATAGAATCAA
* *
155183 CCATAAAGGCTTCA-TTTAACA
1 CCACAAAGGCCTCACTTTAACA
155204 TAATCAGCCA
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
51 25 0.24
52 18 0.17
53 2 0.02
55 12 0.12
56 5 0.05
57 38 0.37
58 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (56 bp):
CCACAAAGGCCTCACTTTAACAGAATTAACCATAAAGGCTCACGTAATAGAATCAA
Found at i:155148 original size:51 final size:52
Alignment explanation
Indices: 155066--155163 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 52
155056 TCACGATAAT
* * * *
155066 AGAATCAACCACAAAGGCCTCACTTTAACAGATTTACCCATAAAGGCGTAAC
1 AGAATCAACCACAAAAGCCTCACTTTAACAGAATTAACCAAAAAGGCGTAAC
*
155118 AGAATCGACCACAAAAG-CTCACTTTAACAGAATTAACCAAAAAGGC
1 AGAATCAACCACAAAAGCCTCACTTTAACAGAATTAACCAAAAAGGC
155164 TTCACTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 26 0.63
52 15 0.37
ACGTcount: A:0.44, C:0.26, G:0.13, T:0.17
Consensus pattern (52 bp):
AGAATCAACCACAAAAGCCTCACTTTAACAGAATTAACCAAAAAGGCGTAAC
Found at i:155156 original size:28 final size:29
Alignment explanation
Indices: 155126--155256 Score: 144
Period size: 28 Copynumber: 4.6 Consensus size: 29
155116 ACAGAATCGA
*
155126 CCACAAAAGC-TCACTTTAACAGAATTAA
1 CCACAAAAGCTTCACTTTAACAGAATTAG
*
155154 CCA-AAAAGGCTTCACTTTAATAGAATTAG
1 CCACAAAA-GCTTCACTTTAACAGAATTAG
* * * *
155183 CCATAAAGGCTTCA-TTTAACATAATCAG
1 CCACAAAAGCTTCACTTTAACAGAATTAG
*
155211 CCACAAAAGCTTCACTTTAATAGAATTAG
1 CCACAAAAGCTTCACTTTAACAGAATTAG
* *
155240 CCA-TAAAGGTTCACTTT
1 CCACAAAAGCTTCACTTT
155257 TTCGAGAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
27 4 0.05
28 40 0.47
29 39 0.45
30 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.27
Consensus pattern (29 bp):
CCACAAAAGCTTCACTTTAACAGAATTAG
Found at i:155178 original size:29 final size:29
Alignment explanation
Indices: 155136--155256 Score: 149
Period size: 29 Copynumber: 4.2 Consensus size: 29
155126 CCACAAAAGC
*
155136 TCACTTTAACAGAATTAACCAAAAAGGCT
1 TCACTTTAACAGAATTAGCCAAAAAGGCT
* *
155165 TCACTTTAATAGAATTAGCCATAAAGGCT
1 TCACTTTAACAGAATTAGCCAAAAAGGCT
* *
155194 TCA-TTTAACATAATCAGCCACAAAA-GCT
1 TCACTTTAACAGAATTAGCCA-AAAAGGCT
* *
155222 TCACTTTAATAGAATTAGCCATAAAGG-T
1 TCACTTTAACAGAATTAGCCAAAAAGGCT
155250 TCACTTT
1 TCACTTT
155257 TTCGAGAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
28 31 0.40
29 47 0.60
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (29 bp):
TCACTTTAACAGAATTAGCCAAAAAGGCT
Found at i:155223 original size:57 final size:56
Alignment explanation
Indices: 155140--155252 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 56
155130 AAAAGCTCAC
*
155140 TTTAACAGAATTAACCAAAAAGGCTTCACTTTAATAGAATTAGCCATAAAGGCTTCA
1 TTTAACAGAATCAACCAAAAAGGCTTCACTTTAATAGAATTAGCCATAAAGG-TTCA
* *
155197 TTTAACATAATCAGCCACAAAA-GCTTCACTTTAATAGAATTAGCCATAAAGGTTCA
1 TTTAACAGAATCAACCA-AAAAGGCTTCACTTTAATAGAATTAGCCATAAAGGTTCA
155253 CTTTTTCGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
56 4 0.08
57 44 0.85
58 4 0.08
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (56 bp):
TTTAACAGAATCAACCAAAAAGGCTTCACTTTAATAGAATTAGCCATAAAGGTTCA
Found at i:155422 original size:56 final size:56
Alignment explanation
Indices: 155361--155578 Score: 305
Period size: 56 Copynumber: 3.9 Consensus size: 56
155351 TCATCTTCTT
** * * *
155361 CCATATGATGTAATAGCCATCATGACTAGGTCTTACGCTATATGATCTTCATTTTC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTTC
** * *
155417 CCATATGATATCATAGCCACCATGACCAAGTCTTACACTATATGGTCTTCA-TTTC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTTC
* *
155472 TCCATATGATGCCATAGCCACCATGAC-ACTGTCTTACACTATATGGTCTTCATTTCC
1 -CCATATGATGCCATAGCCACCATGACTA-GGTCTTACACTATATGGTCTTCATTTTC
155529 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTC
1 CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTC
155579 GATTACCATG
Statistics
Matches: 146, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
55 5 0.03
56 137 0.94
57 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (56 bp):
CCATATGATGCCATAGCCACCATGACTAGGTCTTACACTATATGGTCTTCATTTTC
Found at i:164947 original size:17 final size:18
Alignment explanation
Indices: 164927--164965 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
164917 GATTAATAAG
164927 ATAAAATA-ATTAAAATT
1 ATAAAATATATTAAAATT
*
164944 ATAAAATATTTTAAAATT
1 ATAAAATATATTAAAATT
164962 -TAAA
1 ATAAA
164966 GCTAATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAATATATTAAAATT
Found at i:167550 original size:33 final size:33
Alignment explanation
Indices: 167495--167559 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
167485 TGTAAATATT
* *
167495 TTAAAAATTAAATTCAAGATTTTAGT-TTTAATA
1 TTAAAAAATAAATTCAACATTTTA-TATTTAATA
* *
167528 TTAAAAAATAATTTTAACATTTTATATTTAAT
1 TTAAAAAATAAATTCAACATTTTATATTTAAT
167560 TTTTTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
TTAAAAAATAAATTCAACATTTTATATTTAATA
Found at i:168960 original size:29 final size:32
Alignment explanation
Indices: 168927--168997 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 32
168917 AATAGTTTAT
168927 ATTTTTATCATTTTTAAAAGA-TTAAA-T-TA
1 ATTTTTATCATTTTTAAAAGAGTTAAAGTGTA
* * * *
168956 ATTTTTTTTATTTTTAGAGGAGTTAAAGTGTA
1 ATTTTTATCATTTTTAAAAGAGTTAAAGTGTA
168988 A-TTTTATCAT
1 ATTTTTATCAT
168998 ATACTAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 17 0.52
30 5 0.15
31 8 0.24
32 3 0.09
ACGTcount: A:0.34, C:0.03, G:0.10, T:0.54
Consensus pattern (32 bp):
ATTTTTATCATTTTTAAAAGAGTTAAAGTGTA
Found at i:176820 original size:109 final size:108
Alignment explanation
Indices: 176690--176898 Score: 264
Period size: 109 Copynumber: 1.9 Consensus size: 108
176680 AAAAGACAAA
* *
176690 GAATATTTATCGATTTAAAATAGGATATTCGATTACTT-AGGTTCGAA-GAAAAATCATACTCAG
1 GAATATTTATCGATTTAAAATAGGATATTCAATTACTTAAGG-TC-AACGAAAAATCATACCCA-
* *
176753 TACGT-TTA-AGAATAATTTCTCGAGTTCCCTAAAATAAAAGAATATT
63 -ACATGTTAGAGAACAATTTCTCGAGTTCCCT-AAATAAAAGAATATT
* * * *
176799 GAATATTTGTCGATTTTAAATAGGATATTTAATTATTTAAGGTCAACGAAAAATCATACCCAACA
1 GAATATTTATCGATTTAAAATAGGATATTCAATTACTTAAGGTCAACGAAAAATCATACCCAACA
*
176864 TGTTAGAGCACAATTTCTCGAGTTCCCTAAATAAA
66 TGTTAGAGAACAATTTCTCGAGTTCCCTAAATAAA
176899 TAAACATTGC
Statistics
Matches: 87, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
107 3 0.03
108 12 0.14
109 69 0.79
110 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (108 bp):
GAATATTTATCGATTTAAAATAGGATATTCAATTACTTAAGGTCAACGAAAAATCATACCCAACA
TGTTAGAGAACAATTTCTCGAGTTCCCTAAATAAAAGAATATT
Found at i:178726 original size:24 final size:22
Alignment explanation
Indices: 178697--178741 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
178687 ACGACTTGAA
178697 TTTTAAAAAGTAAAGAGAATAAAT
1 TTTTAAAAA-TAAA-AGAATAAAT
*
178721 TTTTAAAAATAAAAGTATAAA
1 TTTTAAAAATAAAAGAATAAA
178742 AACCAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (22 bp):
TTTTAAAAATAAAAGAATAAAT
Found at i:178728 original size:23 final size:22
Alignment explanation
Indices: 178695--178741 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
178685 TAACGACTTG
*
178695 AATTTTAAAAAGTAAAGAGAATA
1 AATTTTAAAAAATAAA-AGAATA
* *
178718 AATTTTTAAAAATAAAAGTATA
1 AATTTTAAAAAATAAAAGAATA
178740 AA
1 AA
178742 AACCAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (22 bp):
AATTTTAAAAAATAAAAGAATA
Found at i:180643 original size:84 final size:84
Alignment explanation
Indices: 180507--180664 Score: 199
Period size: 84 Copynumber: 1.9 Consensus size: 84
180497 TATGTTATGG
* * * * * *
180507 ATTCTTCATAGCTCATGTGAGCAGCATCGTGTAACGGTTAATGTCCCGATTTATTGGATACCTTA
1 ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTAGATACCTTA
180572 CCGATGGCTTGTGTTACAA
66 CCGATGGCTTGTGTTACAA
* * * * * *
180591 ATTCTTCACAGCTCGTGTGAGTAGCATTATGTAGCGATTAATGTCTCAATTTACTAGATACCTTG
1 ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTAGATACCTTA
*
180656 TCGATGGCT
66 CCGATGGCT
180665 AAGATTTTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
84 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (84 bp):
ATTCTTCACAGCTCATGTGAGCAGCATCATGTAACGATTAATGTCCCAATTTACTAGATACCTTA
CCGATGGCTTGTGTTACAA
Found at i:180747 original size:26 final size:25
Alignment explanation
Indices: 180718--180772 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
180708 AACATCATTA
180718 ATTTTCGATTCACAGCTCGTGTGAGC
1 ATTTTC-ATTCACAGCTCGTGTGAGC
* *
180744 ATTTTTCATTCACATCTTGTGTGAGC
1 A-TTTTCATTCACAGCTCGTGTGAGC
180770 ATT
1 ATT
180773 ACTATCCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.08
26 19 0.73
27 5 0.19
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (25 bp):
ATTTTCATTCACAGCTCGTGTGAGC
Found at i:182744 original size:29 final size:29
Alignment explanation
Indices: 182712--182780 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
182702 AGAGACAACA
* *
182712 ACAAAGGCTTACCTTTCCATAGA-TTAGCC
1 ACAAAGGCTT-CCTTTCAAAAGAGTTAGCC
*
182741 ACAAAGGCTTCCTTTTAAAAGAGTTTAGCC
1 ACAAAGGCTTCCTTTCAAAAGAG-TTAGCC
182771 ACAAAGGCTT
1 ACAAAGGCTT
182781 TATTCATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 9 0.26
29 10 0.29
30 16 0.46
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (29 bp):
ACAAAGGCTTCCTTTCAAAAGAGTTAGCC
Found at i:185550 original size:17 final size:17
Alignment explanation
Indices: 185528--185561 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
185518 TACATATGCA
185528 TACATGCATTTCATTTT
1 TACATGCATTTCATTTT
185545 TACATGCATTTCATTTT
1 TACATGCATTTCATTTT
185562 GAGAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
TACATGCATTTCATTTT
Found at i:187487 original size:22 final size:22
Alignment explanation
Indices: 187443--187489 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
187433 ATTTTCTGCC
* *
187443 TCATTTTACAAATATCTTAAAT
1 TCATTTGACAAACATCTTAAAT
* *
187465 TCATTTGACAAACATTTTCAAT
1 TCATTTGACAAACATCTTAAAT
187487 TCA
1 TCA
187490 CACTTTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (22 bp):
TCATTTGACAAACATCTTAAAT
Found at i:187581 original size:27 final size:28
Alignment explanation
Indices: 187528--187582 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
187518 ATTTGTTCTT
* *
187528 TTGTTCAATTTGACAAATATTTTTATTC
1 TTGTCCAATTTGACAAATATTTCTATTC
187556 TTGTCCAA-TTGACAAA-ATGTTCTATTC
1 TTGTCCAATTTGACAAATAT-TTCTATTC
187583 ATTCATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 15 0.62
28 7 0.29
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (28 bp):
TTGTCCAATTTGACAAATATTTCTATTC
Found at i:190148 original size:45 final size:45
Alignment explanation
Indices: 190100--190353 Score: 241
Period size: 45 Copynumber: 5.7 Consensus size: 45
190090 TACACCACCG
* *
190100 TCCAATCTTTTACCCCTAGTCAAGAGGGTCAAATTAAAGCCATCG
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAAATTAAAGCCATCA
* * *
190145 TCCAATCTTTT-CCCCTTAG-CTAAGAGGGGTAGATTGAAGCCATCA
1 TCCAATCTTTTACCCC-TAGTC-AAGAGGGGCAAATTAAAGCCATCA
* * * ** *
190190 TCCAATCGTTTACCCCTAATCAAGAGGGGCAAATTGAAGATACCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAAATTAAAGCCATCA
*
190235 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAAG-CATCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAAATT-AAAGCCATCA
* * * * * *
190280 TCCAATCTCTTACCCCGA-TC-A-TGGGGCAGACTGAAGCCATCA
1 TCCAATCTTTTACCCCTAGTCAAGAGGGGCAAATTAAAGCCATCA
* * *
190322 TCCAATCTCTTAACCCTAAGTCAATAGGGGCA
1 TCCAATCTTTTACCCCT-AGTCAAGAGGGGCA
190354 GATTGAAGTT
Statistics
Matches: 173, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.02
42 29 0.17
43 2 0.01
44 9 0.05
45 116 0.67
46 14 0.08
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (45 bp):
TCCAATCTTTTACCCCTAGTCAAGAGGGGCAAATTAAAGCCATCA
Found at i:190808 original size:17 final size:17
Alignment explanation
Indices: 190788--190823 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
190778 ACCTAAGGAT
* *
190788 AAAATAAACCAAAATAA
1 AAAATAAAACAAAACAA
190805 AAAATAAAACAAAACAA
1 AAAATAAAACAAAACAA
190822 AA
1 AA
190824 GTCCATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (17 bp):
AAAATAAAACAAAACAA
Found at i:191744 original size:28 final size:28
Alignment explanation
Indices: 191728--191783 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
191718 GATAATTTGG
191728 GGTTAAAATGTAATTTTAGAAAGTTTAA
1 GGTTAAAATGTAATTTTAGAAAGTTTAA
*
191756 GGTTAAAATGTGATTTTAAGAAAGTTTA
1 GGTTAAAATGTAATTTT-AGAAAGTTTA
191784 GGGGCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (28 bp):
GGTTAAAATGTAATTTTAGAAAGTTTAA
Found at i:191800 original size:30 final size:28
Alignment explanation
Indices: 191740--191811 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 28
191730 TTAAAATGTA
* **
191740 ATTTTAGAAAGTTTAAGGTTAAAATGTG
1 ATTTTAGAAAGTTTAAGGCTAAAACATG
*
191768 ATTTTAAGAAAGTTTAGGGGCTAAAACATG
1 ATTTT-AGAAAGTTTA-AGGCTAAAACATG
*
191798 ATTTTTAGGAAGTT
1 A-TTTTAGAAAGTT
191812 CGAAGGTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.14
29 10 0.28
30 17 0.47
31 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (28 bp):
ATTTTAGAAAGTTTAAGGCTAAAACATG
Found at i:192904 original size:13 final size:13
Alignment explanation
Indices: 192888--192921 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
192878 AATGTTTAGT
192888 AATAAATAATAGC
1 AATAAATAATAGC
* *
192901 AATAAATTATAGT
1 AATAAATAATAGC
192914 AATAAATA
1 AATAAATA
192922 TATTAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (13 bp):
AATAAATAATAGC
Found at i:194008 original size:85 final size:85
Alignment explanation
Indices: 193854--194021 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
193844 AACTTCATCT
* *
193854 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTGTCTTAATCAACTTCTTTG
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTGTCTTAACCAACTTCTTTA
193919 TATCTCATCAGGAAGATGGA
66 TATCTCATCAGGAAGATGGA
* * * * * * * *
193939 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCACTTTATTG-CTTTGACCCACTTTTTT
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTGTC-TTAACCAACTTCTTT
194003 ATATCTCATCAGGAAGATG
65 ATATCTCATCAGGAAGATG
194022 AGGGCTTGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 71 0.99
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTGTCTTAACCAACTTCTTTA
TATCTCATCAGGAAGATGGA
Found at i:194219 original size:209 final size:209
Alignment explanation
Indices: 193854--194231 Score: 553
Period size: 209 Copynumber: 1.8 Consensus size: 209
193844 AACTTCATCT
* *
193854 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACTTCATTGTCTTAATCAACTTCTTTG
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACCTCATTATCTTAATCAACTTCTTTG
* *
193919 TATCTCATCAGGAAGATGGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGATCACTTTAT
66 TATCTCATCAGGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCACTTTAT
* * *
193984 TGCTTTGACCCACTTTTTTATATCTCATC-AGGAAGATGAGGGCTTGAAGTTTCACTCACATTGA
131 TGCTTCGACCCACTTCTCTATATCTCATCAAGG-AGATGAGGGCTTGAAGTTTCACTCACATTGA
194048 GCTTGGCTTCATTGA
195 GCTTGGCTTCATTGA
* * * * * * *
194063 TTTGGTCTACTTCTCTGTATCTTATCAGGAAGATGACCACCTCATTATTTTAATCCATTTCTTTG
1 TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACCTCATTATCTTAATCAACTTCTTTG
* * *
194128 TATCTCATCAGGAAGATGAATTTGGTCCACTTCTTTGTATCTCATTAGGAAGATGA-CTGCTTTA
66 TATCTCATCAGGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATC-ACTTTA
* *
194192 TTGCTTCGACCCTCTTCTCTGTATCTCATCAAGGAGATGA
130 TTGCTTCGACCCACTTCTCTATATCTCATCAAGGAGATGA
194232 CCACTTCATC
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
208 1 0.01
209 144 0.97
210 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (209 bp):
TTTGGTCCACTTCTCTATATCTCATCAGGAAGATAACCACCTCATTATCTTAATCAACTTCTTTG
TATCTCATCAGGAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATCACTTTAT
TGCTTCGACCCACTTCTCTATATCTCATCAAGGAGATGAGGGCTTGAAGTTTCACTCACATTGAG
CTTGGCTTCATTGA
Found at i:194306 original size:38 final size:38
Alignment explanation
Indices: 194261--194372 Score: 93
Period size: 40 Copynumber: 2.9 Consensus size: 38
194251 TTTCACTCTT
194261 CTCATGATCAGGGTAAGAGATTATATGTTTCAATATTCC
1 CTCATGAT-AGGGTAAGAGATTATATGTTTCAATATTCC
* * * * *
194300 C-CATGATTGGTGTAAGATACTTGTATGTCTTCGATTTTCC
1 CTCATGATAGG-GTAAGAGA-TTATATGT-TTCAATATTCC
* * *
194340 CTC-TGATTAGGGTAAAAGATTAGATGCTTCAAT
1 CTCATGA-TAGGGTAAGAGATTATATGTTTCAAT
194373 TTGCCCGGCG
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
37 2 0.04
38 18 0.32
39 13 0.23
40 19 0.34
41 4 0.07
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (38 bp):
CTCATGATAGGGTAAGAGATTATATGTTTCAATATTCC
Found at i:196519 original size:3 final size:3
Alignment explanation
Indices: 196511--196543 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
196501 GATCATCCCT
*
196511 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
196544 AATATCGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:199667 original size:12 final size:12
Alignment explanation
Indices: 199650--199681 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
199640 AATAGTAGAT
199650 TTTTTAATTTTA
1 TTTTTAATTTTA
199662 TTTTTAATTTTA
1 TTTTTAATTTTA
199674 -TTTTAATT
1 TTTTTAATT
199682 ATGCAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTAATTTTA
Found at i:201441 original size:9 final size:9
Alignment explanation
Indices: 201427--201453 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
201417 AAAGCATTTG
201427 GGAGCGAAA
1 GGAGCGAAA
201436 GGAGCGAAA
1 GGAGCGAAA
201445 GGAGCGAAA
1 GGAGCGAAA
201454 AACAAGCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.44, T:0.00
Consensus pattern (9 bp):
GGAGCGAAA
Found at i:205203 original size:29 final size:29
Alignment explanation
Indices: 205128--205290 Score: 143
Period size: 29 Copynumber: 5.7 Consensus size: 29
205118 AAAAATGAAG
* *
205128 TTTTA-GAGAATTTGGGGTTAAAATGTAA
1 TTTTAGGAAAATTTGGGGTTAAAATATAA
* *
205156 TGTT-GGAAAATTTTAGGGTTAAAATATAA
1 TTTTAGGAAAA-TTTGGGGTTAAAATATAA
* * *
205185 TTTTAGGAAAGTTTGGGGTCAAAATATGA
1 TTTTAGGAAAATTTGGGGTTAAAATATAA
** * * * *
205214 TTTTAAAAAAATGTGGGGTCAAAATGTGA
1 TTTTAGGAAAATTTGGGGTTAAAATATAA
* * *
205243 TTTTAGGTAAGTTTGGGG-TCAAATATAA
1 TTTTAGGAAAATTTGGGGTTAAAATATAA
205271 TTTTAGGAAAATTTAGGGGT
1 TTTTAGGAAAATTT-GGGGT
205291 GAAATTTAAA
Statistics
Matches: 105, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
28 25 0.24
29 75 0.71
30 5 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTTAGGAAAATTTGGGGTTAAAATATAA
Found at i:205290 original size:58 final size:58
Alignment explanation
Indices: 205138--205363 Score: 162
Period size: 58 Copynumber: 3.9 Consensus size: 58
205128 TTTTAGAGAA
* * * *
205138 TTTGGGGTTAAAATGTAATGTT-GGAAAATTTTA-GGGTTAAAATATAATTTTAGGAAAG
1 TTTGGGG-TCAAATATAATTTTAGGAAAA-TTTAGGGGTCAAAATATAATTTTAGGAAAG
* ** * * * *
205196 TTTGGGGTCAAAATATGATTTTAAAAAAATGT-GGGGTCAAAATGTGATTTTAGGTAAG
1 TTTGGGGTC-AAATATAATTTTAGGAAAATTTAGGGGTCAAAATATAATTTTAGGAAAG
* *
205254 TTTGGGGTCAAATATAATTTTAGGAAAATTTAGGGGT-GAAATTTAAATTTTTAGG-AAG
1 TTTGGGGTCAAATATAATTTTAGGAAAATTTAGGGGTCAAAATAT-AA-TTTTAGGAAAG
* * * *
205312 TTCGAGGGT-AAATTTTGAATTTTA--AAAAGTTTAAGGGTCAAAATATAGTTTT
1 TTTG-GGGTCAAA-TAT-AATTTTAGGAAAA-TTTAGGGGTCAAAATATAATTTT
205364 TAAACAAAAT
Statistics
Matches: 133, Mismatches: 24, Indels: 22
0.74 0.13 0.12
Matches are distributed among these distances:
57 24 0.18
58 71 0.53
59 26 0.20
60 12 0.09
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.38
Consensus pattern (58 bp):
TTTGGGGTCAAATATAATTTTAGGAAAATTTAGGGGTCAAAATATAATTTTAGGAAAG
Found at i:205295 original size:29 final size:28
Alignment explanation
Indices: 205128--205310 Score: 136
Period size: 29 Copynumber: 6.3 Consensus size: 28
205118 AAAAATGAAG
* *
205128 TTTTA-GAGAATTTGGGGTTAAAATGTAA
1 TTTTAGGAAAATTTGGGG-TAAAATATAA
* *
205156 TGTT-GGAAAATTTTAGGGTTAAAATATAA
1 TTTTAGGAAAA-TTT-GGGGTAAAATATAA
* *
205185 TTTTAGGAAAGTTTGGGGTCAAAATATGA
1 TTTTAGGAAAATTTGGGGT-AAAATATAA
** * * *
205214 TTTTAAAAAAATGTGGGGTCAAAATGTGA
1 TTTTAGGAAAATTTGGGGT-AAAATATAA
* * *
205243 TTTTAGGTAAGTTTGGGGTCAAATATAA
1 TTTTAGGAAAATTTGGGGTAAAATATAA
* *
205271 TTTTAGGAAAATTTAGGGGTGAAATTTAAA
1 TTTTAGGAAAATTT-GGGGTAAAATAT-AA
205301 TTTTTAGGAA
1 -TTTTAGGAA
205311 GTTCGAGGGT
Statistics
Matches: 122, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
28 29 0.24
29 74 0.61
30 10 0.08
31 9 0.07
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (28 bp):
TTTTAGGAAAATTTGGGGTAAAATATAA
Found at i:206424 original size:13 final size:13
Alignment explanation
Indices: 206408--206441 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
206398 AATGTTTAGT
206408 AATAAATAATAGC
1 AATAAATAATAGC
* *
206421 AATAAATGATAGT
1 AATAAATAATAGC
206434 AATAAATA
1 AATAAATA
206442 TATTAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.26
Consensus pattern (13 bp):
AATAAATAATAGC
Found at i:208747 original size:3 final size:3
Alignment explanation
Indices: 208739--208764 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
208729 AGCCTCATTG
208739 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
208765 TTGTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:213687 original size:14 final size:17
Alignment explanation
Indices: 213645--213678 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
213635 GAACTCAAAA
*
213645 ATCCATAACCCACTAAC
1 ATCCCTAACCCACTAAC
213662 ATCCCTAACCCACTAAC
1 ATCCCTAACCCACTAAC
213679 CCTAACCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (17 bp):
ATCCCTAACCCACTAAC
Found at i:214764 original size:98 final size:98
Alignment explanation
Indices: 214585--214771 Score: 293
Period size: 98 Copynumber: 1.9 Consensus size: 98
214575 TAATCGTGTG
* * *
214585 TCATGAGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTTGATAAAGAGAAGAATCACTC
1 TCATAAGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTAGATAAAGAGAAAAATCACTC
214650 ATTTCACAATATACTAGTTCAAATTCTATTTCT
66 ATTTCACAATATACTAGTTCAAATTCTATTTCT
* * *
214683 TCATAAGTTCACCCATATCTTAACAAGTTTAAGATTTGTTCGCTAGATAAAGAGAAAAATCACTC
1 TCATAAGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTAGATAAAGAGAAAAATCACTC
***
214748 ATTTCATTGTATACTAGTTCAAAT
66 ATTTCACAATATACTAGTTCAAAT
214772 CAATAAGATA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 80 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (98 bp):
TCATAAGTTAACCCATATCTTAACAAGTTCAAGATTCGTTCGCTAGATAAAGAGAAAAATCACTC
ATTTCACAATATACTAGTTCAAATTCTATTTCT
Found at i:219777 original size:18 final size:18
Alignment explanation
Indices: 219703--219802 Score: 57
Period size: 17 Copynumber: 5.7 Consensus size: 18
219693 AAAAATTTTA
*
219703 AAAATATATAAAAATAA-
1 AAAATATATAAAAAAAAT
* *
219720 AAAATATTATTGACAAAAAT
1 AAAATA-TA-TAAAAAAAAT
* **
219740 AATAATATAT--TAAATTT
1 AA-AATATATAAAAAAAAT
219757 AAAATATATAAAAAAAAT
1 AAAATATATAAAAAAAAT
* **
219775 -AAATATTTTTAAAAAAT
1 AAAATATATAAAAAAAAT
219792 AAAATA-ATAAA
1 AAAATATATAAA
219803 GTGAAATCTC
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
16 7 0.11
17 28 0.46
18 11 0.18
19 7 0.11
20 4 0.07
21 4 0.07
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (18 bp):
AAAATATATAAAAAAAAT
Found at i:219798 original size:54 final size:53
Alignment explanation
Indices: 219648--219802 Score: 160
Period size: 53 Copynumber: 2.9 Consensus size: 53
219638 TTCTAAAAAA
* * * *
219648 TAAAAAAATATAAAAATACATAAATA-TTTTGAAAATTACAATAATAAAAATTT
1 TAAAAATATATAAAAATAAATAAATATTTTTAAAAAATA-AATAATAAAAATTT
*
219701 TAAAAATATATAAAAATAAA-AAATATTATTGACAAAAAT-AATAATATATTAAA-TT
1 TAAAAATATATAAAAATAAATAAATATT-TTTA-AAAAATAAATAATA-A--AAATTT
219756 T-AAAATATATAAAAA-AAATAAATATTTTTAAAAAATAAAATAATAAA
1 TAAAAATATATAAAAATAAATAAATATTTTTAAAAAAT-AAATAATAAA
219803 GTGAAATCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
51 1 0.01
52 11 0.13
53 33 0.38
54 31 0.36
55 8 0.09
56 3 0.03
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (53 bp):
TAAAAATATATAAAAATAAATAAATATTTTTAAAAAATAAATAATAAAAATTT
Found at i:220218 original size:29 final size:30
Alignment explanation
Indices: 220128--220206 Score: 117
Period size: 30 Copynumber: 2.6 Consensus size: 30
220118 TTAAATTAAT
*
220128 AATGAT-AAAA-TTACATTTTAATCCCTCAAA
1 AATGATAAAAATTTA-ATTTTAA-CCCCCAAA
220158 AATGATAAAAATTTAATTTTAACCCCCAAA
1 AATGATAAAAATTTAATTTTAACCCCCAAA
220188 AATGATAAAAATTTAATTT
1 AATGATAAAAATTTAATTT
220207 AACTTTTTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 32 0.70
31 11 0.24
32 3 0.07
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (30 bp):
AATGATAAAAATTTAATTTTAACCCCCAAA
Found at i:221192 original size:7 final size:6
Alignment explanation
Indices: 221165--221199 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
221155 ATCGTGCATT
*
221165 AAATTA AAATTA AAATTA AAATTTA AAACTA AAAT
1 AAATTA AAATTA AAATTA AAA-TTA AAATTA AAAT
221200 CACAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:221192 original size:13 final size:13
Alignment explanation
Indices: 221165--221199 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
221155 ATCGTGCATT
221165 AAATTAAAA-TTA
1 AAATTAAAATTTA
221177 AAATTAAAATTTA
1 AAATTAAAATTTA
*
221190 AAACTAAAAT
1 AAATTAAAAT
221200 CACAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTAAAATTTA
Done.