Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 2 of 106
Found at i:104754 original size:124 final size:124
Alignment explanation
Indices: 104529--105144 Score: 917
Period size: 124 Copynumber: 5.0 Consensus size: 124
104519 GTCTAGGAGT
* *
104529 ATTTAC-TTTTCAAAGT--TCGCTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTTCGT-T
1 ATTTACTTTTTCAAAGTCGT-GGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-TCGTGT
* * * *
104590 GCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
* * * *
104651 ATTTACTTTTTCAAAGT-TTGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTCCGT-T
1 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-T-CGTGT
104714 GCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
64 GCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
*
104775 ATTTACTTTCT-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTG
1 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT-GTG
*
104839 CCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
65 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
* * *
104899 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGGTG
1 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT-GTG
104964 CCTCTGTTTAGAGGAGCAATTTACTTTTT-CAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
65 CCTCTGTTTAGAGGAGCAATTTA-TTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
*
105024 ATTTAC-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT-GTG
* * * *
105088 CCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGA
65 CCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGA
105145 ACTTCGGCAA
Statistics
Matches: 462, Mismatches: 23, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
122 9 0.02
123 58 0.13
124 279 0.60
125 111 0.24
126 5 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (124 bp):
ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGTGC
CTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
Found at i:105159 original size:1 final size:1
Alignment explanation
Indices: 105153--105273 Score: 107
Period size: 1 Copynumber: 121.0 Consensus size: 1
105143 GAACTTCGGC
* * * * *
105153 AAAAAAAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAAAACAAAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *** ** *
105218 ACAAAAAACAAAAAACAAAAAACAAAAATTTAAAAAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
105274 TGTTGAGTTG
Statistics
Matches: 95, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 95 1.00
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:105172 original size:14 final size:14
Alignment explanation
Indices: 105153--105273 Score: 122
Period size: 14 Copynumber: 8.7 Consensus size: 14
105143 GAACTTCGGC
105153 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
105167 AAAAAAAAACAAA-A
1 AAAAAAAAA-AAACA
*
105181 AAAACAAAAAAA-A
1 AAAAAAAAAAAACA
*
105194 AACAAAAAAAAA-A
1 AAAAAAAAAAAACA
*
105207 TAAAAAAAAAAACA
1 AAAAAAAAAAAACA
*
105221 AAAAACAAAAAACA
1 AAAAAAAAAAAACA
* ***
105235 AAAAACAAAAATTT
1 AAAAAAAAAAAACA
*
105249 AAAAAAAAAAATCA
1 AAAAAAAAAAAACA
105263 AAAAATAAAAA
1 AAAAA-AAAAA
105274 TGTTGAGTTG
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
13 25 0.27
14 58 0.64
15 8 0.09
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:105271 original size:20 final size:19
Alignment explanation
Indices: 105154--105273 Score: 131
Period size: 18 Copynumber: 6.3 Consensus size: 19
105144 AACTTCGGCA
105154 AAAAAAAAAAACAAAAAA-
1 AAAAAAAAAAACAAAAAAT
*
105172 AAAACAAAAAAA-ACAAAA-
1 AAAA-AAAAAAACAAAAAAT
*
105190 AAAAAACAAAA-AAAAAAT
1 AAAAAAAAAAACAAAAAAT
*
105208 AAAAAAAAAAACAAAAAACA
1 AAAAAAAAAAACAAAAAA-T
*
105228 AAAAACAAAAAACAAAAATTT
1 AAAAA-AAAAAACAAAAA-AT
105249 AAAAAAAAAAATCAAAAAAT
1 AAAAAAAAAAA-CAAAAAAT
105269 AAAAA
1 AAAAA
105274 TGTTGAGTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
17 11 0.13
18 23 0.26
19 13 0.15
20 17 0.20
21 23 0.26
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAAAAAAACAAAAAAT
Found at i:106190 original size:19 final size:20
Alignment explanation
Indices: 106166--106211 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
106156 TCCGGCCAAC
106166 TTCCGGCGA-AATTTCCAGA
1 TTCCGGCGATAATTTCCAGA
*
106185 TTCCGGCGATATTTTCCAGA
1 TTCCGGCGATAATTTCCAGA
*
106205 ATCCGGC
1 TTCCGGC
106212 ACCGGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (20 bp):
TTCCGGCGATAATTTCCAGA
Found at i:106562 original size:12 final size:11
Alignment explanation
Indices: 106524--106565 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
106514 CCGCTCCAGG
106524 TTTT-TTTTTT
1 TTTTATTTTTT
106534 TTTTATTTCTTT
1 TTTTATTT-TTT
*
106546 GTTTATTTTATT
1 TTTTATTTT-TT
106558 TTTTATTT
1 TTTTATTT
106566 ATTAGATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 19 0.70
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.86
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:106695 original size:59 final size:59
Alignment explanation
Indices: 106631--106996 Score: 463
Period size: 60 Copynumber: 6.1 Consensus size: 59
106621 AAATAAAAAT
106631 AAAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAA
1 AAAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AGAA
106693 AAATAAATTTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
1 AAA-AAA-TTCC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
* * * * *
106755 ATAAATTTCC--AAAAAATATTTTTGGGGAAGAGTTGAAAGTATCAATTTTCCTCAGAA
1 AAAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
* * * *
106812 ATAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC-TCGAA
1 AAAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
* *
106870 AATCAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAA
1 AA--AAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
* * * *
106930 AATCGAAATTTCC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTACAA
1 AA---AAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
106991 AAAAAA
1 AAAAAA
106997 ATCATTATTT
Statistics
Matches: 272, Mismatches: 22, Indels: 24
0.86 0.07 0.08
Matches are distributed among these distances:
57 53 0.19
58 7 0.03
59 39 0.14
60 99 0.36
61 13 0.05
62 9 0.03
63 3 0.01
64 4 0.01
65 45 0.17
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (59 bp):
AAAAAATTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
Found at i:108946 original size:29 final size:29
Alignment explanation
Indices: 108914--108999 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
108904 ATTGAATTAC
108914 TAAATGCAAATAAATAAAAACTAAAA-AAT
1 TAAAT-CAAATAAATAAAAACTAAAATAAT
*
108943 TAAAATAAAATAAA-ATAAAACTTAAAATAAT
1 T-AAATCAAATAAATA-AAAAC-TAAAATAAT
* *
108974 GAAATCAAA-AAATCAAAAAATAAAAT
1 TAAATCAAATAAAT-AAAAACTAAAAT
109000 GAAAAAGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
28 1 0.02
29 22 0.47
30 20 0.43
31 4 0.09
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (29 bp):
TAAATCAAATAAATAAAAACTAAAATAAT
Found at i:108958 original size:10 final size:11
Alignment explanation
Indices: 108938--108972 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
108928 TAAAAACTAA
108938 AAAATTAAAAT
1 AAAATTAAAAT
108949 AAAA-TAAAAT
1 AAAATTAAAAT
108959 AAAACTTAAAAT
1 AAAA-TTAAAAT
108971 AA
1 AA
108973 TGAAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 4 0.18
12 8 0.36
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:108999 original size:21 final size:20
Alignment explanation
Indices: 108949--109005 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
108939 AAATTAAAAT
* *
108949 AAAATAAAAT-AAAACTTAA
1 AAAATAAAATAAAAAATCAA
*
108968 AATAATGAAATCAAAAAATCAA
1 AA-AATAAAAT-AAAAAATCAA
108990 AAAATAAAATGAAAAA
1 AAAATAAAAT-AAAAA
109006 GGAAAAGGGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.07
20 7 0.23
21 12 0.40
22 9 0.30
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.18
Consensus pattern (20 bp):
AAAATAAAATAAAAAATCAA
Found at i:109884 original size:3 final size:3
Alignment explanation
Indices: 109878--110042 Score: 108
Period size: 3 Copynumber: 59.7 Consensus size: 3
109868 AGAAGAAAAC
* * *
109878 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA GT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
109925 A-A AT- ATA AT- ACA AT- ATT ATA CT- ATA GTA CTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
109968 ATA ATA ATA AT- ATA CT- ATA AT- ATA CT- ATA ATA A-A AT- ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* *
110011 AT- ATA AT- ATA AT- ATA AAA ATA ATA CTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
110043 GAAAGTCAAT
Statistics
Matches: 124, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
2 25 0.20
3 96 0.77
4 3 0.02
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:109939 original size:10 final size:10
Alignment explanation
Indices: 109878--110040 Score: 98
Period size: 10 Copynumber: 15.1 Consensus size: 10
109868 AGAAGAAAAC
109878 ATAATAATAAT
1 ATAAT-ATAAT
109889 AATAATAATAAT
1 -ATAAT-ATAAT
109901 AATAATAGTAAT
1 -ATAATA-TAAT
109913 AGTAATAGT-AT
1 A-TAATA-TAAT
*
109924 AAAATATAAT
1 ATAATATAAT
* *
109934 ACAATATTAT
1 ATAATATAAT
*
109944 ACT-ATAGTACT
1 A-TAATA-TAAT
109955 AATAATAATAAT
1 -ATAAT-ATAAT
109967 AATAATAATAAT
1 -ATAAT-ATAAT
*
109979 ATACTATAAT
1 ATAATATAAT
*
109989 ATACTATAAT
1 ATAATATAAT
*
109999 AAAATATAAT
1 ATAATATAAT
110009 -TAATATAAT
1 ATAATATAAT
*
110018 ATAATATAAAA
1 ATAATAT-AAT
110029 ATAATACTAAT
1 ATAATA-TAAT
110040 A
1 A
110041 ATGAAAGTCA
Statistics
Matches: 127, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
9 9 0.07
10 47 0.37
11 23 0.18
12 47 0.37
13 1 0.01
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAATATAAT
Found at i:113034 original size:19 final size:18
Alignment explanation
Indices: 113012--113113 Score: 73
Period size: 19 Copynumber: 5.3 Consensus size: 18
113002 GTCAAGGAAG
*
113012 AAAAGAACAAAAGAG-AA
1 AAAAAAACAAAAGAGAAA
* *
113029 AAAAAATCTATCAAGAGAAA
1 AAAAAAAC-A-AAAGAGAAA
*
113049 AACAAAAAAAAAAGAGAAA
1 AA-AAAAACAAAAGAGAAA
*
113068 AAAAAGGAA-AAATAGCAAAAA
1 AAAAA--AACAAA-AG-AGAAA
113089 AAAAAAACAAAAAGAGAAA
1 AAAAAAAC-AAAAGAGAAA
113108 AAAAAA
1 AAAAAA
113114 TCTATCATGA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
17 6 0.09
18 4 0.06
19 30 0.45
20 11 0.16
21 16 0.24
ACGTcount: A:0.78, C:0.06, G:0.12, T:0.04
Consensus pattern (18 bp):
AAAAAAACAAAAGAGAAA
Found at i:113127 original size:38 final size:37
Alignment explanation
Indices: 113012--113127 Score: 96
Period size: 40 Copynumber: 3.0 Consensus size: 37
113002 GTCAAGGAAG
*
113012 AAAAGAAC-AAAAGAG-AAAAAAAATCTATCAAGAGAAA
1 AAAAAAACAAAAAGAGAAAAAAAAATCTATC-AGA-AAA
***
113049 AACAAAAA-AAAAAGAGAAAAAAAAGGAAAAAT-AGCAAAAA
1 AA-AAAAACAAAAAGAGAAAAAAAA--ATCTATCAG--AAAA
113089 AAAAAAACAAAAAGAGAAAAAAAAATCTATCATGAAAA
1 AAAAAAACAAAAAGAGAAAAAAAAATCTATCA-GAAAA
113127 A
1 A
113128 GATGAAAGAG
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
37 2 0.03
38 19 0.31
39 15 0.24
40 22 0.35
41 4 0.06
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.07
Consensus pattern (37 bp):
AAAAAAACAAAAAGAGAAAAAAAAATCTATCAGAAAA
Found at i:113312 original size:31 final size:31
Alignment explanation
Indices: 113274--113334 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
113264 ATGATACAAG
113274 ATAAGATTTAAGTCC-AGTTTAGCTAGCACCA
1 ATAAGATTTAAG-CCTAGTTTAGCTAGCACCA
* *
113305 ATAAGATTTAAGCCTATTTTAGCTTGCACC
1 ATAAGATTTAAGCCTAGTTTAGCTAGCACC
113335 GATGAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (31 bp):
ATAAGATTTAAGCCTAGTTTAGCTAGCACCA
Found at i:113539 original size:52 final size:51
Alignment explanation
Indices: 113446--113543 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
113436 TAGCTGATAC
*
113446 TTTAAGCCTAGATTAGTTGGCACACAAACCCAAATTAGTTGGCACCTAAAT
1 TTTAAGCCTAGATTAGCTGGCACACAAACCCAAATTAGTTGGCACCTAAAT
* * *
113497 TTTAAGCCTAGTTTAGCTGGCA-ATTTAAACCCATATTAGTTGGCACC
1 TTTAAGCCTAGATTAGCTGGCACA--CAAACCCAAATTAGTTGGCACC
113544 CTAACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
50 1 0.02
51 20 0.49
52 20 0.49
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (51 bp):
TTTAAGCCTAGATTAGCTGGCACACAAACCCAAATTAGTTGGCACCTAAAT
Found at i:113566 original size:74 final size:74
Alignment explanation
Indices: 113396--113609 Score: 178
Period size: 74 Copynumber: 2.9 Consensus size: 74
113386 TAGCTATCAC
* * * * * * * *
113396 CAAATCCAAATTAACTGACA-CTCAAACTTTAAGCCCAGTTTAGCTGATACTTTAAGCCTAGATT
1 CAAACCCAAATTAGCTAACACCT-AAAATTTAAGCCCAGTTTAGCTGACAATTTAAACCCAGATT
113460 AGTTGGCACA
65 AGTTGGCACA
* ** * * * *
113470 CAAACCCAAATTAGTTGGCACCTAAATTTTAAGCCTAGTTTAGCTGGCAATTTAAACCCATATTA
1 CAAACCCAAATTAGCTAACACCTAAAATTTAAGCCCAGTTTAGCTGACAATTTAAACCCAGATTA
*
113535 GTTGGCACC
66 GTTGGCACA
* * * ** * * * * *
113544 CTAACTCAAATTTGCTAACACCTAAAATTTAAATCCAATTTAACTGACATTTTAAGCCCAAATTA
1 CAAACCCAAATTAGCTAACACCTAAAATTTAAGCCCAGTTTAGCTGACAATTTAAACCCAGATTA
113609 G
66 G
113610 CTAGTTTTAA
Statistics
Matches: 110, Mismatches: 29, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
74 108 0.98
75 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.30
Consensus pattern (74 bp):
CAAACCCAAATTAGCTAACACCTAAAATTTAAGCCCAGTTTAGCTGACAATTTAAACCCAGATTA
GTTGGCACA
Found at i:113642 original size:23 final size:23
Alignment explanation
Indices: 113615--113713 Score: 99
Period size: 23 Copynumber: 4.0 Consensus size: 23
113605 ATTAGCTAGT
* * *
113615 TTTAAACCTAGTTTAGTTAGCAC
1 TTTAAGCCTAGATTAGTTGGCAC
113638 TTTAAGCCTAGATTAGTTGGCAC
1 TTTAAGCCTAGATTAGTTGGCAC
* *
113661 CTTAAGCCCAGATTAGTTGGCACTC
1 TTTAAGCCTAGATTAGTTGGCA--C
113686 AAATTTTAAGCCTAGATTAGTTGGCAC
1 ----TTTAAGCCTAGATTAGTTGGCAC
113713 T
1 T
113714 CTAATTTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
23 41 0.65
25 1 0.02
27 1 0.02
29 20 0.32
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (23 bp):
TTTAAGCCTAGATTAGTTGGCAC
Found at i:113704 original size:29 final size:28
Alignment explanation
Indices: 113638--113723 Score: 110
Period size: 29 Copynumber: 3.2 Consensus size: 28
113628 TAGTTAGCAC
113638 TTTAAGCCTAGATTAGTTGGCAC-C---
1 TTTAAGCCTAGATTAGTTGGCACTCAAT
*
113662 -TTAAGCCCAGATTAGTTGGCACTCAAAT
1 TTTAAGCCTAGATTAGTTGGCACTC-AAT
113690 TTTAAGCCTAGATTAGTTGGCACTCTAAT
1 TTTAAGCCTAGATTAGTTGGCACTC-AAT
113719 TTTAA
1 TTTAA
113724 ACTTAGCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
23 21 0.40
24 1 0.02
29 31 0.58
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (28 bp):
TTTAAGCCTAGATTAGTTGGCACTCAAT
Found at i:113734 original size:29 final size:29
Alignment explanation
Indices: 113670--113734 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
113660 CCTTAAGCCC
*
113670 AGATTAGTTGGCACTCAAATTTTAAGCCT
1 AGATTAGTTGGCACTCAAATTTTAAACCT
* *
113699 AGATTAGTTGGCACTCTAATTTTAAACTT
1 AGATTAGTTGGCACTCAAATTTTAAACCT
*
113728 AGCTTAG
1 AGATTAG
113735 CTAACACTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (29 bp):
AGATTAGTTGGCACTCAAATTTTAAACCT
Found at i:113780 original size:23 final size:21
Alignment explanation
Indices: 113752--113809 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
113742 TTCAAGCTAG
113752 ATTAGCTGGCACCTTAAGCCCAA
1 ATTAGCTGGCACC--AAGCCCAA
* *
113775 ATTAGCTAGCATCCAAGCCCAT
1 ATTAGCTGGCA-CCAAGCCCAA
*
113797 ATTAGTTGGCACC
1 ATTAGCTGGCACC
113810 GACAAGATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 16 0.53
23 10 0.33
24 2 0.07
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
ATTAGCTGGCACCAAGCCCAA
Found at i:114550 original size:102 final size:102
Alignment explanation
Indices: 114363--114587 Score: 267
Period size: 102 Copynumber: 2.2 Consensus size: 102
114353 ATCTACTTTA
* * * ** * *
114363 ATGTCAAGATTTTTAAGACATTC-AGGTATAGTCTCTAAGTCCTATGAGTAGAATGCTTAAATTT
1 ATGTCAAGATTTGTAAAACCTTCGA-GTATAGTCTCTAAGTCCTACAAGCAAAATGCTTAAATTT
* *
114427 TAAAAGTTTCAAGGCCTTTTTTTAGAGGAGCATTTATAG
65 TAAAAGTTTCAAGACC-TTTTTTAGAGAAGCATTTATAG
* *
114466 ATGT-AAGATTTGTAAAACCTTCGAGTATAGTCTCTAAGTCCTCCAAGCAAAATGTTTAAATTTT
1 ATGTCAAGATTTGTAAAACCTTCGAGTATAGTCTCTAAGTCCTACAAGCAAAATGCTTAAATTTT
* *
114530 AAAA-TTTCAAGACCTCTTTTTAGAGAAGTATTTGTAG
66 AAAAGTTTCAAGACCT-TTTTTAGAGAAGCATTTATAG
* *
114567 GTGTCAAGATTTGTAAGACCT
1 ATGTCAAGATTTGTAAAACCT
114588 CCGGATGTAG
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
100 1 0.01
101 30 0.29
102 68 0.65
103 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (102 bp):
ATGTCAAGATTTGTAAAACCTTCGAGTATAGTCTCTAAGTCCTACAAGCAAAATGCTTAAATTTT
AAAAGTTTCAAGACCTTTTTTAGAGAAGCATTTATAG
Found at i:114610 original size:102 final size:102
Alignment explanation
Indices: 114414--114610 Score: 245
Period size: 102 Copynumber: 1.9 Consensus size: 102
114404 CTATGAGTAG
* * *
114414 AATGCTTAAATTTTAAAAGTTTCAAGGCCTTTTTTTAGAGGAGCATTTATAGATGTAAGATTTGT
1 AATGCTTAAATTTTAAAAGTTTCAAGACCTCTTTTTAGAGAAGCATTTATAGATGTAAGATTTGT
* ** *
114479 AAAACCTTCGAGTATAGTCTCTAAGTCCTCCAAGCAA
66 AAAACCTCCGAGTATAGTAACTAACTCCTCCAAGCAA
* * * *
114516 AATGTTTAAATTTTAAAA-TTTCAAGACCTCTTTTTAGAGAAGTATTTGTAGGTGTCAAGATTTG
1 AATGCTTAAATTTTAAAAGTTTCAAGACCTCTTTTTAGAGAAGCATTTATAGATGT-AAGATTTG
* *
114580 TAAGACCTCCG-GATGTAGTAACTAACTCCTC
65 TAAAACCTCCGAG-TATAGTAACTAACTCCTC
114611 TGGGCAAGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
101 32 0.40
102 48 0.60
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (102 bp):
AATGCTTAAATTTTAAAAGTTTCAAGACCTCTTTTTAGAGAAGCATTTATAGATGTAAGATTTGT
AAAACCTCCGAGTATAGTAACTAACTCCTCCAAGCAA
Found at i:114769 original size:45 final size:45
Alignment explanation
Indices: 114713--114828 Score: 171
Period size: 45 Copynumber: 2.6 Consensus size: 45
114703 ATATTTTAAA
* *
114713 ATTTT-AAAGTTGTGTAGCCTCTAATTAGAGGAACTTTTAAATTT
1 ATTTTCAAAGTTGTGAAGCCTCTAATTAGAGAAACTTTTAAATTT
* * *
114757 ATTTTCAAAGTTGTGGAGTCTCTAATTATAGAAACTTTTAAATTT
1 ATTTTCAAAGTTGTGAAGCCTCTAATTAGAGAAACTTTTAAATTT
114802 ATTTTCAAAAGTTGTGAAGCCTCTAAT
1 ATTTTC-AAAGTTGTGAAGCCTCTAAT
114829 AAAAGAGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 5 0.08
45 41 0.64
46 18 0.28
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (45 bp):
ATTTTCAAAGTTGTGAAGCCTCTAATTAGAGAAACTTTTAAATTT
Found at i:114876 original size:21 final size:19
Alignment explanation
Indices: 114850--114895 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
114840 TCAAAAATTC
*
114850 AAAAAACCCAAAAAAGTTAA
1 AAAAAAACCAAAAAAG-TAA
*
114870 ACAAAAAATCAAAAAAGTAA
1 A-AAAAAACCAAAAAAGTAA
114890 AAAAAA
1 AAAAAA
114896 TAGAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 5 0.22
21 13 0.57
ACGTcount: A:0.76, C:0.11, G:0.04, T:0.09
Consensus pattern (19 bp):
AAAAAAACCAAAAAAGTAA
Found at i:114890 original size:20 final size:20
Alignment explanation
Indices: 114858--114912 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 20
114848 TCAAAAAACC
114858 CAAAAAAGTTAAACAAAAAAT
1 CAAAAAAGTTAAA-AAAAAAT
114879 CAAAAAAG-T-AAAAAAAAT
1 CAAAAAAGTTAAAAAAAAAT
*
114897 -AGAAAA-TTAAAAAAAA
1 CAAAAAAGTTAAAAAAAA
114913 TTTGAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.19
18 14 0.45
19 2 0.06
20 1 0.03
21 8 0.26
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (20 bp):
CAAAAAAGTTAAAAAAAAAT
Found at i:114902 original size:17 final size:18
Alignment explanation
Indices: 114858--114913 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 18
114848 TCAAAAAACC
114858 CAAAAAAGTTAAACAAAAAAT
1 CAAAAAAG-T-AA-AAAAAAT
114879 CAAAAAAGTAAAAAAAAT
1 CAAAAAAGTAAAAAAAAT
* *
114897 -AGAAAATTAAAAAAAAT
1 CAAAAAAGTAAAAAAAAT
114914 TTGAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 15 0.45
18 7 0.21
19 2 0.06
20 1 0.03
21 8 0.24
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (18 bp):
CAAAAAAGTAAAAAAAAT
Found at i:116764 original size:15 final size:14
Alignment explanation
Indices: 116746--116835 Score: 54
Period size: 15 Copynumber: 5.9 Consensus size: 14
116736 GTAAAAAATG
116746 TATAAAAATAAGAAA
1 TATAAAAATAA-AAA
* *
116761 TATATAAATAATAA
1 TATAAAAATAAAAA
116775 TATAAACAATATAATAA
1 TATAAA-AATA-AA-AA
* *
116792 TAATAATAATAATAA
1 T-ATAAAAATAAAAA
* *
116807 TAATAATAATAATAA
1 T-ATAAAAATAAAAA
*
116822 TAATAATAATAAAA
1 T-ATAAAAATAAAA
116836 TGAAAATCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
14 7 0.11
15 44 0.69
16 2 0.03
17 7 0.11
18 4 0.06
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (14 bp):
TATAAAAATAAAAA
Found at i:116766 original size:17 final size:18
Alignment explanation
Indices: 116741--116774 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
116731 TATAGGTAAA
*
116741 AAATGTATAAA-AATAAG
1 AAATATATAAATAATAAG
116758 AAATATATAAATAATAA
1 AAATATATAAATAATAA
116775 TATAAACAAT
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:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATATATAAATAATAAG
Found at i:116775 original size:3 final size:3
Alignment explanation
Indices: 116767--116833 Score: 102
Period size: 3 Copynumber: 22.7 Consensus size: 3
116757 GAAATATATA
*
116767 AAT AAT AAT -AT AAAC AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
116811 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
116834 AATGAAAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 54 0.92
4 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:117001 original size:3 final size:3
Alignment explanation
Indices: 116995--117040 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
116985 TAAAATGTAA
116995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
117041 GAAATGATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:119217 original size:25 final size:24
Alignment explanation
Indices: 119189--119248 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
119179 TACTTAAAAA
119189 TTAAAATATTAATATTAAA-AGTCTT
1 TTAAAATATTAATATTAAATA-T-TT
* * *
119214 TTAATATTTTAATTTTAAATATTT
1 TTAAAATATTAATATTAAATATTT
*
119238 TTATAATATTA
1 TTAAAATATTA
119249 TTCAAGTAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 10 0.36
25 17 0.61
26 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAAATATTAATATTAAATATTT
Found at i:119415 original size:15 final size:15
Alignment explanation
Indices: 119376--119408 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
119366 ATTAAAAGTC
119376 TTTT-AATATTTTAA
1 TTTTAAATATTTTAA
*
119390 TTTTAAATATTTTTA
1 TTTTAAATATTTTAA
119405 TTTT
1 TTTT
119409 GTATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAAATATTTTAA
Found at i:119439 original size:164 final size:160
Alignment explanation
Indices: 119141--119440 Score: 381
Period size: 164 Copynumber: 1.8 Consensus size: 160
119131 AACCTGACCC
* * * *
119141 AAAATATTATTATCTTAATAAATAATATGTTTTAATTTTACTTAAAAATTAAAATATTAATATTA
1 AAAATATTATTATATTAATAAATAATATGTTTTAATTTTAATTAAAAATTAAAATATAAACATTA
* * * *
119206 AAAGTCTTTTAATATTTTAATTTTAAATATTTTTATAATATTATTCAAGTAAGACTTTGAACATA
66 AAAGTCTTTTAATATTTTAATTTTAAATATTTTTATAATATTATTAAAATAAAAATTT----ATA
119271 ATATTTTAAACTTAAACTTGATTTGATTCGACTT
127 ATATTTTAAACTTAAACTTGATTTGATTCGACTT
**
119305 AAAATATTATTATATTAATAAA-AATAT-TTTATTTTATTTAATTAAAAATTAAAATATAAACAT
1 AAAATATTATTATATTAATAAATAATATGTTT-TAAT-TTTAATTAAAAATTAAAATATAAACAT
*
119368 TAAAAGTCTTTTAATATTTTAATTTTAAATATTTTTATTTTGTATATTATTAAACATAAAAATTT
64 TAAAAGTCTTTTAATATTTTAATTTTAAATATTTTTA---T-AATATTATTAAA-ATAAAAATTT
119433 -TAATATTT
124 ATAATATTT
119441 CAATAATAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
162 3 0.03
163 7 0.06
164 90 0.76
167 1 0.01
168 10 0.08
169 7 0.06
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.48
Consensus pattern (160 bp):
AAAATATTATTATATTAATAAATAATATGTTTTAATTTTAATTAAAAATTAAAATATAAACATTA
AAAGTCTTTTAATATTTTAATTTTAAATATTTTTATAATATTATTAAAATAAAAATTTATAATAT
TTTAAACTTAAACTTGATTTGATTCGACTT
Found at i:119717 original size:21 final size:21
Alignment explanation
Indices: 119693--119760 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
119683 TACTCTCAAT
*
119693 ATAAATGTTAATATTTTAATA
1 ATAAATATTAATATTTTAATA
*
119714 ATAAATATTACTATTTTAATATTA
1 ATAAATATTAATATTTT-A-A-TA
*
119738 ATAAA-AATAATATTTTAATA
1 ATAAATATTAATATTTTAATA
119758 ATA
1 ATA
119761 GTAATACTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.12
21 16 0.40
22 2 0.05
23 10 0.25
24 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
ATAAATATTAATATTTTAATA
Found at i:119759 original size:20 final size:20
Alignment explanation
Indices: 119701--119775 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
119691 ATATAAATGT
*
119701 TAATATTTTAATAATAAATAT
1 TAATATTTTAATAATAAA-AA
*
119722 TACTATTTTAATATTAATAAAAA
1 TAATATTTT-A-A-TAATAAAAA
**
119745 TAATATTTTAATAATAGTAA
1 TAATATTTTAATAATAAAAA
*
119765 TACTATTTTAA
1 TAATATTTTAA
119776 ATATTTGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 17 0.38
21 9 0.20
22 2 0.04
23 10 0.22
24 7 0.16
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (20 bp):
TAATATTTTAATAATAAAAA
Found at i:119923 original size:24 final size:24
Alignment explanation
Indices: 119874--119928 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
119864 TATTAAATGT
*
119874 TATTAAAATATAATTATTCTTGAA
1 TATTAAAATATAATTATACTTGAA
* *
119898 TATTAATAATTTAA-TATACTTTAA
1 TATTAA-AATATAATTATACTTGAA
*
119922 TAATAAA
1 TATTAAA
119929 TAGTTTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.73
25 6 0.23
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (24 bp):
TATTAAAATATAATTATACTTGAA
Found at i:134504 original size:19 final size:20
Alignment explanation
Indices: 134477--134514 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
134467 ATTTCATTAA
*
134477 AATAAATTC-TTAAAATTTT
1 AATAAATTCACTAAAATTTT
*
134496 AATATATTCACTAAAATTT
1 AATAAATTCACTAAAATTT
134515 AAAAAATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAAATTCACTAAAATTTT
Found at i:137462 original size:158 final size:158
Alignment explanation
Indices: 137182--137807 Score: 802
Period size: 158 Copynumber: 4.0 Consensus size: 158
137172 TTAAATACGC
* * ** * *
137182 AATAGTTTTCACCTTTCATAAATTCATTGCATCCCATTACAT-ACAAAACACTATCTAGTTCAAT
1 AATAGTTTTCACCTTTCACAAAGTCATTGCATCTTAATAC-TCATAAAACACTATCTAGTTCAAT
* *
137246 ATTGAATTTCTTACAATGTTTAAGCTTTCAATTACTATAAAGATAGTTCATCAACAATCATC-AT
65 ACTGAATTTCTTACAATGTTTAGGCTTTCAATTACTATAAAGATAGTTCATCAACAATCA-CAAT
137310 ATACAACCAGAATCACAAAGCAAAATACAT
129 ATACAACCAGAATCACAAAGCAAAATACAT
*
137340 AATAGTTTTCACCTTTCACAAAGTCATTGCATCTTAATACTCATAAAATACTATCTAGTTCAATA
1 AATAGTTTTCACCTTTCACAAAGTCATTGCATCTTAATACTCATAAAACACTATCTAGTTCAATA
* *
137405 CTAAATTT-TCTACAATGTTTAGGCTTTCAATTACTATAAAGATAGTTTATCAACAATCTA-AAT
66 CTGAATTTCT-TACAATGTTTAGGCTTTCAATTACTATAAAGATAGTTCATCAACAATC-ACAAT
* * * * *
137468 ATATAGCTAGAAGT-ACAAAACAAAATACGT
129 ATACAACCAGAA-TCACAAAGCAAAATACAT
* * * * **
137498 AATAGTTTTCACCTTTCACAAAATCATTGCATCTAAACACACATAAAACACTATCTAAATCAATA
1 AATAGTTTTCACCTTTCACAAAGTCATTGCATCTTAATACTCATAAAACACTATCTAGTTCAATA
* *
137563 CTGAATTTCTTACAATGTTTATGTTTTCAATTACTATTAAA-ATAGTTCATCAACAATCACAATA
66 CTGAATTTCTTACAATGTTTAGGCTTTCAATTACTA-TAAAGATAGTTCATCAACAATCACAATA
* * * * *
137627 TACAATCAAAATCACAAAGCAACATATAC
130 TACAACCAGAATCACAAAGCAAAATACAT
* *
137656 AATAGTTTTCACCTTTCATAAAGTCATTGCAT-TTCAATA-TACATAAAACACTATCTAGTTTAA
1 AATAGTTTTCACCTTTCACAAAGTCATTGCATCTT-AATACT-CATAAAACACTATCTAGTTCAA
* *
137719 TATTGAATTT-TCTACAATGTTTAGGCTTTCAATTACTATAAAAATAGTTCATCAACAATCACAA
64 TACTGAATTTCT-TACAATGTTTAGGCTTTCAATTACTATAAAGATAGTTCATCAACAATCACAA
*
137783 TATACAACTAGAATCACAAAGCAAA
128 TATACAACCAGAATCACAAAGCAAA
137808 TAATAGGGTA
Statistics
Matches: 403, Mismatches: 52, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
157 10 0.02
158 386 0.96
159 7 0.02
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (158 bp):
AATAGTTTTCACCTTTCACAAAGTCATTGCATCTTAATACTCATAAAACACTATCTAGTTCAATA
CTGAATTTCTTACAATGTTTAGGCTTTCAATTACTATAAAGATAGTTCATCAACAATCACAATAT
ACAACCAGAATCACAAAGCAAAATACAT
Found at i:137747 original size:316 final size:316
Alignment explanation
Indices: 137174--137795 Score: 912
Period size: 316 Copynumber: 2.0 Consensus size: 316
137164 TTTGATTATT
* * * ** *
137174 AAATACGCAATAGTTTTCACCTTTCATAAATTCATTGCATCCCATTACATACAAAACACTATCTA
1 AAATACGCAATAGTTTTCACCTTTCACAAAATCATTGCATCCAAACACACACAAAACACTATCTA
** *
137239 GTTCAATATTGAATTTCTTACAATGTTTAAGCTTTCAATTACTATAAAGATAGTTCATCAACAAT
66 AATCAATACTGAATTTCTTACAATGTTTAAGCTTTCAATTACTATAAAGATAGTTCATCAACAAT
* *
137304 CATCATATACAACCAGAATCACAAAGCAAAATACATAATAGTTTTCACCTTTCACAAAGTCATTG
131 CATCATATACAACCAAAATCACAAAGCAAAATACACAATAGTTTTCACCTTTCACAAAGTCATTG
*
137369 CATCTTAATACTCATAAAATACTATCTAGTTCAATACTAAATTTTCTACAATGTTTAGGCTTTCA
196 CATCTTAATACTCATAAAACACTATCTAGTTCAATACTAAATTTTCTACAATGTTTAGGCTTTCA
* * * *
137434 ATTACTATAAAGATAGTTTATCAACAATCTA-AATATATAGCTAGAAGTACAAAACA
261 ATTACTATAAAAATAGTTCATCAACAATC-ACAATATACAACTAGAAGTACAAAACA
* * *
137490 AAATACGTAATAGTTTTCACCTTTCACAAAATCATTGCATCTAAACACACATAAAACACTATCTA
1 AAATACGCAATAGTTTTCACCTTTCACAAAATCATTGCATCCAAACACACACAAAACACTATCTA
* *
137555 AATCAATACTGAATTTCTTACAATGTTTATGTTTTCAATTACTATTAAA-ATAGTTCATCAACAA
66 AATCAATACTGAATTTCTTACAATGTTTAAGCTTTCAATTACTA-TAAAGATAGTTCATCAACAA
* * * *
137619 TCA-CAATATACAATCAAAATCACAAAGCAACATATACAATAGTTTTCACCTTTCATAAAGTCAT
130 TCATC-ATATACAACCAAAATCACAAAGCAAAATACACAATAGTTTTCACCTTTCACAAAGTCAT
* * *
137683 TGCAT-TTCAATA-TACATAAAACACTATCTAGTTTAATATTGAATTTTCTACAATGTTTAGGCT
194 TGCATCTT-AATACT-CATAAAACACTATCTAGTTCAATACTAAATTTTCTACAATGTTTAGGCT
137746 TTCAATTACTATAAAAATAGTTCATCAACAATCACAATATACAACTAGAA
257 TTCAATTACTATAAAAATAGTTCATCAACAATCACAATATACAACTAGAA
137796 TCACAAAGCA
Statistics
Matches: 273, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
315 5 0.02
316 264 0.97
317 4 0.01
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (316 bp):
AAATACGCAATAGTTTTCACCTTTCACAAAATCATTGCATCCAAACACACACAAAACACTATCTA
AATCAATACTGAATTTCTTACAATGTTTAAGCTTTCAATTACTATAAAGATAGTTCATCAACAAT
CATCATATACAACCAAAATCACAAAGCAAAATACACAATAGTTTTCACCTTTCACAAAGTCATTG
CATCTTAATACTCATAAAACACTATCTAGTTCAATACTAAATTTTCTACAATGTTTAGGCTTTCA
ATTACTATAAAAATAGTTCATCAACAATCACAATATACAACTAGAAGTACAAAACA
Found at i:141981 original size:20 final size:19
Alignment explanation
Indices: 141942--141981 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
141932 TTTAATAATG
**
141942 AATAAATATTAATTTTTTA
1 AATAAATATTAAAATTTTA
141961 AATAAATATATAAAATTTTA
1 AATAAATAT-TAAAATTTTA
141981 A
1 A
141982 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAATATTAAAATTTTA
Found at i:142043 original size:31 final size:31
Alignment explanation
Indices: 141995--142057 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
141985 TTTAAAAAAA
* *
141995 TTTACTAATGAAATAATATTATATATTTTAT
1 TTTACTAATAAAATAATATTATATAATTTAT
* *
142026 TTTATTAATAAAATAATATTATGTAATTTAT
1 TTTACTAATAAAATAATATTATATAATTTAT
142057 T
1 T
142058 AATAACGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
TTTACTAATAAAATAATATTATATAATTTAT
Found at i:148528 original size:15 final size:15
Alignment explanation
Indices: 148508--148539 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
148498 ACCCTTGAAA
148508 TTTCATAAATTACAG
1 TTTCATAAATTACAG
148523 TTTCATAAATTACAG
1 TTTCATAAATTACAG
148538 TT
1 TT
148540 GAATTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
TTTCATAAATTACAG
Found at i:153520 original size:23 final size:23
Alignment explanation
Indices: 153494--153542 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
153484 TAATTACTAT
153494 TTTTTAAAATATA-TAATAATTAA
1 TTTTTAAAATA-ACTAATAATTAA
*
153517 TTTTTATAATAACTAATAATTAA
1 TTTTTAAAATAACTAATAATTAA
153540 TTT
1 TTT
153543 AATAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTTAAAATAACTAATAATTAA
Found at i:154374 original size:62 final size:62
Alignment explanation
Indices: 154298--154442 Score: 163
Period size: 62 Copynumber: 2.3 Consensus size: 62
154288 AATAATACTC
* * **
154298 TAAAAAATGCCTTAAATAAT-ATGGTTT-AAAAAA-TTAAAAAGTATTATTTAAAGTATTT-TTT
1 TAAAAAACGTCTTAAATAATCAT--TTTAAAAAAATTTAAAAA--ATTATTTAAAGTATTTCTAG
154359 A
62 A
* *
154360 TCAAAAACGTCTTAAATAATCCTTTTAAAAAAATTTAAAAAATTATTTAAAGTATTTCTAGA
1 TAAAAAACGTCTTAAATAATCATTTTAAAAAAATTTAAAAAATTATTTAAAGTATTTCTAGA
*
154422 TAAAAAACGTCTAAAATAATC
1 TAAAAAACGTCTTAAATAATC
154443 TTCTGATACA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
61 19 0.27
62 44 0.62
63 8 0.11
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.37
Consensus pattern (62 bp):
TAAAAAACGTCTTAAATAATCATTTTAAAAAAATTTAAAAAATTATTTAAAGTATTTCTAGA
Found at i:154414 original size:61 final size:62
Alignment explanation
Indices: 154325--154442 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
154315 AATATGGTTT
** * *
154325 AAAAAATTAAAAAGTATTATTTAAAGTATTT-TTTATCAAAAACGTCTTAAATAATCCTTTTA
1 AAAAAATTAAAAAG-ATTATTTAAAGTATTTCTAGATAAAAAACGTCTAAAATAATCCTTTTA
154387 AAAAAATTTAAAAA-ATTATTTAAAGTATTTCTAGATAAAAAACGTCTAAAATAATC
1 AAAAAA-TTAAAAAGATTATTTAAAGTATTTCTAGATAAAAAACGTCTAAAATAATC
154443 TTCTGATACA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
61 16 0.32
62 27 0.54
63 7 0.14
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (62 bp):
AAAAAATTAAAAAGATTATTTAAAGTATTTCTAGATAAAAAACGTCTAAAATAATCCTTTTA
Found at i:154533 original size:63 final size:63
Alignment explanation
Indices: 154399--154633 Score: 228
Period size: 63 Copynumber: 3.8 Consensus size: 63
154389 AAAATTTAAA
* * ** * * * *
154399 AAATTATTTAA-AGTATTTCTAGATAAAAAACGTCTAAAATAATCTTCTGATACATTTTAAACG
1 AAATTATTTAAGA-TATTTTTGGATAAAAAATATCTTAAATAATCTCCTGATATATTTTAAAGG
* * * * * * *
154462 AAACTATTTAAGACATTTTTTGA-ACAAAAATGTCTCAAATAATCTCCTTATATTTTTTAAAGG
1 AAATTATTTAAGATATTTTTGGATA-AAAAATATCTTAAATAATCTCCTGATATATTTTAAAGG
* * * *
154525 ATATTATTTACGATATTTTTGGATAAAAAATACCTTAAA-ATTACT-CTGATATATTTTAAAGG
1 AAATTATTTAAGATATTTTTGGATAAAAAATATCTTAAATAAT-CTCCTGATATATTTTAAAGG
*
154587 AAATTATTTAAGGTATTTTTGGATAAAAAATATCTTAAATAAT-TCCT
1 AAATTATTTAAGATATTTTTGGATAAAAAATATCTTAAATAATCTCCT
154634 CTCGTATTTT
Statistics
Matches: 139, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
61 1 0.01
62 55 0.40
63 81 0.58
64 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (63 bp):
AAATTATTTAAGATATTTTTGGATAAAAAATATCTTAAATAATCTCCTGATATATTTTAAAGG
Found at i:156749 original size:17 final size:18
Alignment explanation
Indices: 156717--156750 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
156707 ATATTTTATT
156717 AATTAAAATAATAAAAAA
1 AATTAAAATAATAAAAAA
*
156735 AATTTAAAT-ATAAAAA
1 AATTAAAATAATAAAAA
156751 CTCGATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAATAATAAAAAA
Found at i:157896 original size:14 final size:14
Alignment explanation
Indices: 157858--157896 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
157848 AGTACAAATA
157858 ATATAAATATAATT
1 ATATAAATATAATT
* * *
157872 AAATTATTATAATT
1 ATATAAATATAATT
157886 ATATAAATATA
1 ATATAAATATA
157897 TATGTGAATT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAAATATAATT
Found at i:161364 original size:15 final size:16
Alignment explanation
Indices: 161334--161372 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
161324 ATCTCTTAGA
*
161334 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
161350 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
*
161365 ATTTTAAA
1 ATTATAAA
161373 ACAATATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:166348 original size:14 final size:14
Alignment explanation
Indices: 166318--166346 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
166308 AGATTCTCTT
166318 AATATTTTTAAATA
1 AATATTTTTAAATA
166332 AATATTTTT-AATA
1 AATATTTTTAAATA
166345 AA
1 AA
166347 ATTATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTTTAAATA
Found at i:166980 original size:25 final size:24
Alignment explanation
Indices: 166952--167010 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
166942 AGTTAAGTAT
* *
166952 TAAATAATTTTTTTATTTAATAAAA
1 TAAATAATTTTATTATATAAT-AAA
*
166977 TAAATAAAATTTATTATATAATAAA
1 TAAAT-AATTTTATTATATAATAAA
*
167002 TTAATAATT
1 TAAATAATT
167011 GGAGATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 3 0.11
25 12 0.43
26 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATAATTTTATTATATAATAAA
Found at i:173949 original size:19 final size:18
Alignment explanation
Indices: 173921--173956 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
173911 AATGGGACCT
*
173921 TGTTATTAATAGTGGTATA
1 TGTTAATAAT-GTGGTATA
173940 TGTTAATAATGTGGTAT
1 TGTTAATAATGTGGTAT
173957 GGCAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTAATAATGTGGTATA
Found at i:174170 original size:21 final size:22
Alignment explanation
Indices: 174146--174189 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
174136 AGAAAAGAAT
174146 AAAC-TAACTTGACCATCTTAA
1 AAACTTAACTTGACCATCTTAA
174167 AAACTATTAACTTGACCATCTTA
1 AAAC--TTAACTTGACCATCTTA
174190 CTAGTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
24 16 0.80
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (22 bp):
AAACTTAACTTGACCATCTTAA
Found at i:175026 original size:18 final size:18
Alignment explanation
Indices: 175003--175062 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
174993 AATTTTACCG
175003 TCACCATCATTTTCAATC
1 TCACCATCATTTTCAATC
*
175021 TCACCA-C-TTATTCATATG
1 TCACCATCATT-TTCA-ATC
*
175039 TCACCGTCATTTTCAATC
1 TCACCATCATTTTCAATC
175057 TCACCA
1 TCACCA
175063 CTTATTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 20 0.59
19 5 0.15
20 2 0.06
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (18 bp):
TCACCATCATTTTCAATC
Found at i:175049 original size:36 final size:36
Alignment explanation
Indices: 175002--175074 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
174992 TAATTTTACC
175002 GTCACCATCATTTTCAATCTCACCACTTATTCATAT
1 GTCACCATCATTTTCAATCTCACCACTTATTCATAT
*
175038 GTCACCGTCATTTTCAATCTCACCACTTATTCATAT
1 GTCACCATCATTTTCAATCTCACCACTTATTCATAT
175074 G
1 G
175075 ATTCTCACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.30, G:0.05, T:0.38
Consensus pattern (36 bp):
GTCACCATCATTTTCAATCTCACCACTTATTCATAT
Found at i:175080 original size:22 final size:22
Alignment explanation
Indices: 175055--175126 Score: 90
Period size: 22 Copynumber: 3.1 Consensus size: 22
175045 TCATTTTCAA
*
175055 TCTCACCACTTATTCATATGAT
1 TCTCACCAATTATTCATATGAT
175077 TCTCACCATTTATTATTCATATGAT
1 TCTCACCA---ATTATTCATATGAT
* *
175102 TCTCACCATTTATTCAAATGAT
1 TCTCACCAATTATTCATATGAT
175124 TCT
1 TCT
175127 AAGTCCGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 23 0.52
25 21 0.48
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (22 bp):
TCTCACCAATTATTCATATGAT
Found at i:175098 original size:25 final size:25
Alignment explanation
Indices: 175064--175115 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
175054 ATCTCACCAC
175064 TTATTCATATGATTCTCACCATTTA
1 TTATTCATATGATTCTCACCATTTA
175089 TTATTCATATGATTCTCACCATTTA
1 TTATTCATATGATTCTCACCATTTA
175114 TT
1 TT
175116 CAAATGATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.19, G:0.04, T:0.50
Consensus pattern (25 bp):
TTATTCATATGATTCTCACCATTTA
Found at i:182029 original size:26 final size:27
Alignment explanation
Indices: 181978--182031 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
181968 GGTTGGCGGT
*
181978 GGCGGAGACTGATGGAGGAGGAGGAAA
1 GGCGGAGACTGAAGGAGGAGGAGGAAA
*
182005 GGCGGAGA-TGAAGGTGGA-GAGGGAAA
1 GGCGGAGACTGAAGGAGGAGGA-GGAAA
182031 G
1 G
182032 TGTTGGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.58
27 8 0.33
ACGTcount: A:0.33, C:0.06, G:0.54, T:0.07
Consensus pattern (27 bp):
GGCGGAGACTGAAGGAGGAGGAGGAAA
Found at i:182643 original size:21 final size:21
Alignment explanation
Indices: 182599--182644 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
182589 GATATTTTTT
* *
182599 ATTTTTAATTGTTTTAATATA
1 ATTTTTAATTATTTAAATATA
182620 ATTTTTAATATATTTAAATA-A
1 ATTTTTAAT-TATTTAAATATA
182641 ATTT
1 ATTT
182645 ATATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTTTAATTATTTAAATATA
Found at i:182690 original size:18 final size:18
Alignment explanation
Indices: 182669--182711 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
182659 TATTTTATTT
182669 TATAAAATT-TAAAATATA
1 TATAAAATTATAAAA-ATA
182687 TATAAAAATTAATAAAAATA
1 TAT-AAAATT-ATAAAAATA
182707 TATAA
1 TATAA
182712 TTCAGTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 8 0.36
20 6 0.27
21 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAATTATAAAAATA
Found at i:184122 original size:20 final size:21
Alignment explanation
Indices: 184086--184137 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
184076 TCTGAAATTA
184086 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
184108 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
184129 AT-AAATATT
1 ATAAAATATT
184138 TAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:184128 original size:21 final size:22
Alignment explanation
Indices: 184086--184137 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
184076 TCTGAAATTA
184086 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
184108 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
184129 AT-AAATATT
1 ATAAAATATT
184138 TAAATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:184130 original size:14 final size:14
Alignment explanation
Indices: 184122--184161 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
184112 AATATTATTT
184122 TTTAAATATAAATA
1 TTTAAATATAAATA
184136 TTTAAATATATAATTA
1 TTTAAATATA-AA-TA
*
184152 TATAAATATA
1 TTTAAATATA
184162 TATAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAAATATAAATA
Found at i:184143 original size:8 final size:8
Alignment explanation
Indices: 184127--184163 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
184117 TATTTTTTAA
184127 ATATAAAT
1 ATATAAAT
*
184135 ATTTAAAT
1 ATATAAAT
*
184143 ATATAATT
1 ATATAAAT
184151 ATATAAAT
1 ATATAAAT
184159 ATATA
1 ATATA
184164 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAAAT
Found at i:184170 original size:14 final size:14
Alignment explanation
Indices: 184124--184171 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
184114 TATTATTTTT
* *
184124 TAAATATAAATATT
1 TAAATATATATATA
184138 TAAATATATAATTATA
1 TAAATATAT-A-TATA
*
184154 TAAATATATATAAA
1 TAAATATATATATA
184168 TAAA
1 TAAA
184172 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATATATATA
Found at i:188656 original size:2 final size:2
Alignment explanation
Indices: 188649--188678 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
188639 CGACAATGGC
188649 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
188679 TGTACTGATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196561 original size:2 final size:2
Alignment explanation
Indices: 196554--196597 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
196544 ATGGCAATGA
* * *
196554 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT 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
196596 AT
1 AT
196598 TGTACTGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203193 original size:15 final size:15
Alignment explanation
Indices: 203173--203202 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
203163 ATTGTTGTGC
203173 ATCACTATGTATTTT
1 ATCACTATGTATTTT
203188 ATCACTATGTATTTT
1 ATCACTATGTATTTT
203203 TTCTGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATCACTATGTATTTT
Found at i:203534 original size:23 final size:23
Alignment explanation
Indices: 203508--203556 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
203498 TAAAATTAAT
203508 AGAAAAAAAAAGATA-AAAACAAA
1 AGAAAAAAAAA-ATATAAAACAAA
*
203531 AGAAAAAAAGAATATAAAACAAA
1 AGAAAAAAAAAATATAAAACAAA
203554 AGA
1 AGA
203557 CAAATAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.06
Consensus pattern (23 bp):
AGAAAAAAAAAATATAAAACAAA
Found at i:206790 original size:18 final size:18
Alignment explanation
Indices: 206767--206805 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
206757 CAGAAGATTT
206767 AAAATTGAAATTTAAGAA
1 AAAATTGAAATTTAAGAA
* *
206785 AAAATTTAATTTTAAGAA
1 AAAATTGAAATTTAAGAA
206803 AAA
1 AAA
206806 TTTTATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAAATTGAAATTTAAGAA
Found at i:206810 original size:18 final size:19
Alignment explanation
Indices: 206777--206815 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
206767 AAAATTGAAA
206777 TTTAAGAAAAAATTTA-AT
1 TTTAAGAAAAAATTTATAT
*
206795 TTTAAGAAAAATTTTATAT
1 TTTAAGAAAAAATTTATAT
206814 TT
1 TT
206816 CAATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTAAGAAAAAATTTATAT
Found at i:206981 original size:112 final size:112
Alignment explanation
Indices: 206842--207113 Score: 290
Period size: 112 Copynumber: 2.4 Consensus size: 112
206832 TTTTTGTAAT
* * * *
206842 TTTTTTGTCTTAAGTAAATATTAATATTTCAACTTTTTTCTTAAATTTCAAAATT-ATTTCGTTT
1 TTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAAATTTCAAAATTGATTTCGTTT
*
206906 TAAAAAGGAAAA-TAGATATT-TCCACTTT-TCTCTC-AAATTTTGAAATTA
66 T---AAGGAAAAGTAGATATTAT-AACTTTCTC-CTCAAAATTTTGAAATTA
* ** * *
206954 TTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTT-TAAAAATTTTTAAATTGTTTTTGTT
1 TTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTTCT-TAAATTTCAAAATTGATTTCGTT
* *
207018 TTAGGGAAAAGTTGATATTATAACTTTCTCCTCAAAATTTTGAAATTA
65 TTAAGGAAAAGTAGATATTATAACTTTCTCCTCAAAATTTTGAAATTA
* *
207066 TTTTTCT-TTCTAA-GAAAAATTGATATCTCAACTTTTTTCTTAACATTT
1 TTTTT-TGTTTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAA-ATTT
207114 TAAGAAATAT
Statistics
Matches: 136, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
110 7 0.05
111 42 0.31
112 78 0.57
113 9 0.07
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (112 bp):
TTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAAATTTCAAAATTGATTTCGTTT
TAAGGAAAAGTAGATATTATAACTTTCTCCTCAAAATTTTGAAATTA
Found at i:207114 original size:56 final size:53
Alignment explanation
Indices: 206794--207114 Score: 227
Period size: 56 Copynumber: 5.8 Consensus size: 53
206784 AAAAATTTAA
* * *
206794 TTTTAAGAAAAATTTTATATTTCAA-TTTCTTTATCAAATTTTTGTAATT-TTTTT
1 TTTTAAGAAAAA-TTGATATTTCAACTTT-TTTCTCAAA-TTTTGAAATTATTTTT
* * * * **
206848 GTCTTAAGTAAATATTAATATTTCAACTTTTTTCTTAAATTTCAAAATTATTTCGTT
1 -TTTTAAG-AAAAATTGATATTTCAACTTTTTTCTCAAATTTTGAAATTATTT--TT
** * * * *
206905 TTAAAAAGGAAAATAGATATTTCCACTTTTCTCTCAAATTTTGAAATTATTTTTT
1 TT-TTAAGAAAAATTGATATTTCAACTTTTTTCTCAAATTTTGAAATTA-TTTTT
* * *
206960 GTTTTAAGGAAAAATTGATATTTCAACTTTTTT-TAAAAATTTTTAAATTGTTTTT
1 -TTTTAA-GAAAAATTGATATTTCAACTTTTTTCT-CAAATTTTGAAATTATTTTT
* * * *
207015 GTTTTAGGGAAAAGTTGATATTAT-AACTTTCTCCTCAAAATTTTGAAATTATTTTT
1 -TTTTA-AGAAAAATTGATATT-TCAACTTTTTTCTC-AAATTTTGAAATTATTTTT
* *
207071 CTTTCTAAGAAAAATTGATATCTCAACTTTTTTCTTAACATTTT
1 -TTT-TAAGAAAAATTGATATTTCAACTTTTTTCTCAA-ATTTT
207115 AAGAAATATT
Statistics
Matches: 206, Mismatches: 43, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
54 7 0.03
55 66 0.32
56 123 0.60
57 10 0.05
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (53 bp):
TTTTAAGAAAAATTGATATTTCAACTTTTTTCTCAAATTTTGAAATTATTTTT
Found at i:207137 original size:111 final size:110
Alignment explanation
Indices: 206932--207134 Score: 259
Period size: 112 Copynumber: 1.8 Consensus size: 110
206922 TATTTCCACT
* *
206932 TTTCTCTCAAATTTTGAAATTATTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTTTAAA
1 TTTCTCTCAAATTTTGAAATTATTTTTTGTTCTAAGGAAAAATTGATATCTCAACTTTTTTTAAA
* * * * *
206997 AATTTTTAAATTGTTTTTGTTTTAGGGAAAAGTTGATATTATAAC
66 AATTTTAAAAATGATTTTCTTTGAGGGAAAAGTTGATATTATAAC
207042 TTTCTCCTCAAAATTTTGAAATTATTTTTCT-TTCTAA-GAAAAATTGATATCTCAACTTTTTTC
1 TTTCT-CTC-AAATTTTGAAATTATTTTT-TGTTCTAAGGAAAAATTGATATCTCAACTTTTTT-
* *
207105 TTAACATTTTAAGAAAT-ATTTTCTTTGAGG
62 TAAAAATTTTAA-AAATGATTTTCTTTGAGG
207135 AAAGATTAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
110 5 0.06
111 27 0.34
112 43 0.54
113 4 0.05
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (110 bp):
TTTCTCTCAAATTTTGAAATTATTTTTTGTTCTAAGGAAAAATTGATATCTCAACTTTTTTTAAA
AATTTTAAAAATGATTTTCTTTGAGGGAAAAGTTGATATTATAAC
Found at i:207157 original size:111 final size:111
Alignment explanation
Indices: 206931--207158 Score: 245
Period size: 112 Copynumber: 2.1 Consensus size: 111
206921 ATATTTCCAC
* *
206931 TTTTCT-CTCAAATTTTGAAATTATTTTTTGTTTTAAGGAAAAATTGATATTTCAACTTTTTTTA
1 TTTTCTCCTCAAATTTTGAAATTATTTTTTGTTCTAAGGAAAAATTGATATCTCAACTTTTTTTA
* * * * * * *
206995 AAAATTTTTAAATTGTTTTTGTTTTAGGGAAAAGTTGATATTATAA
66 AAAATTTTAAAAATGATTTTCTTTGAGGGAAAAGTTAATATTACAA
*
207041 CTTTCTCCTCAAAATTTTGAAATTATTTTTCT-TTCTAA-GAAAAATTGATATCTCAACTTTTTT
1 TTTTCTCCTC-AAATTTTGAAATTATTTTT-TGTTCTAAGGAAAAATTGATATCTCAACTTTTTT
* *
207104 CTTAACATTTTAAGAAAT-ATTTTCTTTGA-GG-AAAGATTAATACTT-CAA
64 -TAAAAATTTTAA-AAATGATTTTCTTTGAGGGAAAAG-TTAATA-TTACAA
207152 TTTTCTC
1 TTTTCTC
207159 TTTAATTTTC
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
110 9 0.09
111 42 0.43
112 43 0.44
113 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (111 bp):
TTTTCTCCTCAAATTTTGAAATTATTTTTTGTTCTAAGGAAAAATTGATATCTCAACTTTTTTTA
AAAATTTTAAAAATGATTTTCTTTGAGGGAAAAGTTAATATTACAA
Found at i:208887 original size:21 final size:23
Alignment explanation
Indices: 208851--208893 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
208841 AAAAATTACC
*
208851 TGGAGGTTTTAGAAAAT-GATAT
1 TGGAGGTTTTACAAAATCGATAT
208873 TGGAGGTTTT-CAAAATCGATA
1 TGGAGGTTTTACAAAATCGATA
208894 CTATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (23 bp):
TGGAGGTTTTACAAAATCGATAT
Found at i:209097 original size:18 final size:18
Alignment explanation
Indices: 209048--209122 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 18
209038 AAAAATAGGC
* *
209048 AATGAATGCAATACATAA
1 AATGAATGAAATGCATAA
* **
209066 AATGTATGTGATGCATAA
1 AATGAATGAAATGCATAA
* *
209084 AATGCATGAAATGCATAC
1 AATGAATGAAATGCATAA
* *
209102 AACGAATGCAATGCATAA
1 AATGAATGAAATGCATAA
209120 AAT
1 AAT
209123 CAATACCATA
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (18 bp):
AATGAATGAAATGCATAA
Found at i:210023 original size:6 final size:6
Alignment explanation
Indices: 210007--210057 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
209997 TAACTTTATT
*
210007 AATAT- AATATA AATATA AATAT- -ATAAA AATA-A ATATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA A-ATATA AATATA
210052 AATATA
1 AATATA
210058 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
4 3 0.08
5 7 0.17
6 28 0.70
7 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:210030 original size:14 final size:14
Alignment explanation
Indices: 210013--210069 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
210003 TATTAATATA
*
210013 ATATAAATATAAAT
1 ATATAAAAATAAAT
210027 ATATAAAAATAAAT
1 ATATAAAAATAAAT
*
210041 ATATAAATATAAAT
1 ATATAAAAATAAAT
210055 ATATAAAAATAAAT
1 ATATAAAAATAAAT
210069 A
1 A
210070 AATCCTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAAAAATAAAT
Found at i:210032 original size:8 final size:8
Alignment explanation
Indices: 210019--210069 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
210009 TATAATATAA
210019 ATATAAAT
1 ATATAAAT
210027 ATATAAA-
1 ATATAAAT
210034 A-ATAAAT
1 ATATAAAT
210041 ATAT-AA-
1 ATATAAAT
210047 ATATAAAT
1 ATATAAAT
210055 ATATAAA-
1 ATATAAAT
210062 A-ATAAAT
1 ATATAAAT
210069 A
1 A
210070 AATCCTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
6 14 0.37
7 8 0.21
8 16 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATATAAAT
Found at i:210045 original size:28 final size:28
Alignment explanation
Indices: 210013--210069 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
210003 TATTAATATA
210013 ATATAAATATAAATATATAAAAATAAAT
1 ATATAAATATAAATATATAAAAATAAAT
210041 ATATAAATATAAATATATAAAAATAAAT
1 ATATAAATATAAATATATAAAAATAAAT
210069 A
1 A
210070 AATCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (28 bp):
ATATAAATATAAATATATAAAAATAAAT
Found at i:217113 original size:27 final size:27
Alignment explanation
Indices: 217054--217116 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
217044 GATTGTTTCT
*
217054 GTCTTTTTTTTTTTATTTCTACAAAAT
1 GTCTTTTTTTTTTTATTTCTACAAAAA
*
217081 GGCTTTATTTTTTTT-TTT-TACAAAAA
1 GTCTTT-TTTTTTTTATTTCTACAAAAA
217107 GCTCTTTTTT
1 G-TCTTTTTT
217117 AAAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 11 0.35
27 12 0.39
28 8 0.26
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (27 bp):
GTCTTTTTTTTTTTATTTCTACAAAAA
Found at i:217231 original size:23 final size:23
Alignment explanation
Indices: 217198--217243 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
217188 AAGCTTGCTG
217198 GGATTCAAATCTCAGATTTTCAA
1 GGATTCAAATCTCAGATTTTCAA
* **
217221 GGATTCGAATCTCATTTTTTCAA
1 GGATTCAAATCTCAGATTTTCAA
217244 CTGACGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (23 bp):
GGATTCAAATCTCAGATTTTCAA
Found at i:217399 original size:4 final size:4
Alignment explanation
Indices: 217392--217417 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
217382 AAAGAAGAAA
217392 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
217418 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:217421 original size:3 final size:3
Alignment explanation
Indices: 217413--217439 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
217403 TAAATAAATA
217413 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
217440 TAAAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:223683 original size:2 final size:2
Alignment explanation
Indices: 223644--223670 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
223634 GGTTCGATAA
223644 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
223671 AATTTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:226000 original size:14 final size:14
Alignment explanation
Indices: 225942--225994 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
225932 CCATTGATAT
225942 TATTTCTTTAAAAAA
1 TATTT-TTTAAAAAA
**
225957 TATCTAATT-AAAAA
1 TAT-TTTTTAAAAAA
*
225971 TTTTTTTTAAAAAA
1 TATTTTTTAAAAAA
225985 TATTTTTTAA
1 TATTTTTTAA
225995 TCAATAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.10
14 21 0.70
15 5 0.17
16 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTTTTTAAAAAA
Found at i:226081 original size:21 final size:21
Alignment explanation
Indices: 226048--226087 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
226038 GATTATTTAT
* * *
226048 TAAATATAGAAAATAAAAAAA
1 TAAAAATAAAAAAGAAAAAAA
226069 TAAAAATAAAAAAGAAAAA
1 TAAAAATAAAAAAGAAAAA
226088 TGGAAAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (21 bp):
TAAAAATAAAAAAGAAAAAAA
Found at i:229546 original size:22 final size:23
Alignment explanation
Indices: 229521--229565 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
229511 TGAAATTGAG
229521 TCAA-TGTCAAGCAAAT-GTTAAA
1 TCAATTGTC-AGCAAATGGTTAAA
*
229543 TCAATTGTCAGCCAATGGTTAAA
1 TCAATTGTCAGCAAATGGTTAAA
229566 CATCTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (23 bp):
TCAATTGTCAGCAAATGGTTAAA
Found at i:236942 original size:2 final size:2
Alignment explanation
Indices: 236937--236966 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
236927 AAAGAACCCC
236937 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
236967 AGGCGTGCAA
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):
GA
Found at i:239735 original size:30 final size:31
Alignment explanation
Indices: 239700--239759 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
239690 ATATGTTAAA
*
239700 CCTTAAATATCTATTCTT-AC-TTAATTGAAT
1 CCTTAAACATCTATT-TTCACTTTAATTGAAT
*
239730 CCTTAAACATTTATTTTCACTTTAATTGAA
1 CCTTAAACATCTATTTTCACTTTAATTGAA
239760 CTCTCAAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 15 0.58
31 9 0.35
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (31 bp):
CCTTAAACATCTATTTTCACTTTAATTGAAT
Found at i:240929 original size:14 final size:15
Alignment explanation
Indices: 240906--240938 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
240896 TTTTGAAAAA
240906 AAATTC-AAAAAATT
1 AAATTCAAAAAAATT
*
240920 AAATTTAAAAAAATT
1 AAATTCAAAAAAATT
240935 AAAT
1 AAAT
240939 ATGATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTCAAAAAAATT
Found at i:240956 original size:16 final size:16
Alignment explanation
Indices: 240935--240970 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
240925 TAAAAAAATT
240935 AAATATGATCTTTAAA
1 AAATATGATCTTTAAA
*
240951 AAATATGATTTTTAAA
1 AAATATGATCTTTAAA
240967 AAAT
1 AAAT
240971 TAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATATGATCTTTAAA
Found at i:242359 original size:24 final size:24
Alignment explanation
Indices: 242332--242379 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
242322 AATAATAATT
242332 ATTATTATAATTACAATTAAAAAA
1 ATTATTATAATTACAATTAAAAAA
**
242356 ATTATTATAATTTTAATTAAAAAA
1 ATTATTATAATTACAATTAAAAAA
242380 TTCATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTATTATAATTACAATTAAAAAA
Found at i:242391 original size:24 final size:24
Alignment explanation
Indices: 242346--242392 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
242336 TTATAATTAC
* *
242346 AATTAAAAAAATTATTATAATTTT
1 AATTAAAAAAATTATAAAAATTTT
242370 AATT-AAAAAATTCATAAAAATTT
1 AATTAAAAAAATT-ATAAAAATTT
242393 ATATGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTAAAAAAATTATAAAAATTTT
Found at i:242425 original size:16 final size:17
Alignment explanation
Indices: 242383--242425 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
242373 TAAAAAATTC
*
242383 ATAAAAATTTATATGAA
1 ATAAATATTTATATGAA
242400 ATAAAT-TTTAT-TGAA
1 ATAAATATTTATATGAA
*
242415 ATTAATATTTA
1 ATAAATATTTA
242426 AATTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (17 bp):
ATAAATATTTATATGAA
Found at i:251508 original size:17 final size:16
Alignment explanation
Indices: 251478--251510 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
251468 AAAATTTATT
251478 AATTATATTATAATTA
1 AATTATATTATAATTA
251494 AATTATATATATAATTA
1 AATTATAT-TATAATTA
251511 TTACTTGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATATTATAATTA
Found at i:257500 original size:19 final size:19
Alignment explanation
Indices: 257463--257500 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
257453 AATTGTAATT
*
257463 TATAATTAAAATAATAAAA
1 TATAATTAAAATAAGAAAA
257482 TATATATTAAAAT-AGAAAA
1 TATA-ATTAAAATAAGAAAA
257501 AGCTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TATAATTAAAATAAGAAAA
Found at i:258999 original size:57 final size:58
Alignment explanation
Indices: 258858--258978 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 58
258848 TCAAAAACCC
* *
258858 TTTTTTA-AAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATA
1 TTTTTTAGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA
258915 TTTTTTAGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA
1 TTTTTTAGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA
258973 TTTTTT
1 TTTTTT
258979 TTTAGATTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 7 0.11
58 54 0.89
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (58 bp):
TTTTTTAGAAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATA
Found at i:259049 original size:8 final size:8
Alignment explanation
Indices: 259026--259093 Score: 57
Period size: 8 Copynumber: 7.8 Consensus size: 8
259016 AATAAAAGTG
259026 AAAATAAA
1 AAAATAAA
259034 AAAATAAA
1 AAAATAAA
259042 AAAATAAA
1 AAAATAAA
259050 GAAAAGTAAA
1 -AAAA-TAAA
259060 ACAAA-AATA
1 A-AAATAA-A
259069 AAAATGAAA
1 AAAAT-AAA
259078 TAAAGATAAA
1 -AAA-ATAAA
*
259088 AGAATA
1 AAAATA
259094 TTAAATAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
8 24 0.47
9 10 0.20
10 15 0.29
11 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:260114 original size:6 final size:6
Alignment explanation
Indices: 260103--260205 Score: 79
Period size: 6 Copynumber: 16.8 Consensus size: 6
260093 AATACCTAAG
* * * *
260103 ATAAAA ATAAAA GAAAAAA ATATATA A-AAAA ATAATA AT-AAA ATAGAA
1 ATAAAA ATAAAA -ATAAAA ATA-AAA ATAAAA ATAAAA ATAAAA ATAAAA
*
260151 AT-AAA ATAAAA ATGTAAAA TACAAAAA ATAAAA ATAAAA ATAAAA AT-AAA
1 ATAAAA ATAAAA A--TAAAA -A-TAAAA ATAAAA ATAAAA ATAAAA ATAAAA
260201 ATAAA
1 ATAAA
260206 GAAAAAAAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
5 16 0.21
6 42 0.55
7 9 0.12
8 9 0.12
9 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:260179 original size:27 final size:26
Alignment explanation
Indices: 260103--260215 Score: 92
Period size: 28 Copynumber: 4.3 Consensus size: 26
260093 AATACCTAAG
*
260103 ATAAAAATAAAAGA-AAAA-AATATATA
1 ATAAAAATAAAA-ATAAAATAA-ATAAA
*
260129 A-AAAAATAATAATAAAATAGAAATAAA
1 ATAAAAATAAAAATAAAAT--AAATAAA
*
260156 ATAAAAATGTAAAATACAAA-AAATAAAA
1 ATAAAAAT-AAAAATA-AAATAAAT-AAA
*
260184 ATAAAAATAAAAATAAAATAAAGAAA
1 ATAAAAATAAAAATAAAATAAATAAA
260210 A-AAAAA
1 ATAAAAA
260216 GAACATAGAC
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
24 1 0.01
25 18 0.25
26 8 0.11
27 18 0.25
28 19 0.26
29 5 0.07
30 3 0.04
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.17
Consensus pattern (26 bp):
ATAAAAATAAAAATAAAATAAATAAA
Found at i:260182 original size:75 final size:77
Alignment explanation
Indices: 260050--260198 Score: 182
Period size: 75 Copynumber: 2.0 Consensus size: 77
260040 ATTAACAGGA
* * ** *
260050 AAAAAAATAATAATAAAGATATATACATATTAATAAATAAGTAAATACCTAAGATAAAAATAAAA
1 AAAAAAATAATAATAAAGATAGATACATATAAATAAATAAGTAAATACAAAAAATAAAAATAAAA
260115 GAAAAAAATATAT
66 -AAAAAAATATAT
260128 AAAAAAATAATAATAAA-ATAGA-A-ATA-AAATAAA-AATGTAAAATACAAAAAATAAAAATAA
1 AAAAAAATAATAATAAAGATAGATACATATAAATAAATAA-GT-AAATACAAAAAATAAAAATAA
*
260188 AAATAAAAATA
64 AAAAAAAAATA
260199 AAATAAAGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
73 2 0.03
74 16 0.25
75 23 0.37
76 1 0.02
77 4 0.06
78 17 0.27
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (77 bp):
AAAAAAATAATAATAAAGATAGATACATATAAATAAATAAGTAAATACAAAAAATAAAAATAAAA
AAAAAAATATAT
Found at i:260204 original size:11 final size:11
Alignment explanation
Indices: 260103--260205 Score: 97
Period size: 11 Copynumber: 9.5 Consensus size: 11
260093 AATACCTAAG
260103 ATAAAAATAAA
1 ATAAAAATAAA
* *
260114 AGAAAAA-AAT
1 ATAAAAATAAA
*
260124 ATATAAA-AAA
1 ATAAAAATAAA
*
260134 ATAATAATAAA
1 ATAAAAATAAA
*
260145 ATAGAAATAAA
1 ATAAAAATAAA
260156 ATAAAAATGTAAA
1 ATAAAAA--TAAA
*
260169 AT-ACAA-AAA
1 ATAAAAATAAA
260178 ATAAAAATAAAA
1 ATAAAAAT-AAA
260190 ATAAAAATAAA
1 ATAAAAATAAA
260201 ATAAA
1 ATAAA
260206 GAAAAAAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
9 5 0.07
10 17 0.23
11 32 0.43
12 14 0.19
13 6 0.08
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:260378 original size:8 final size:7
Alignment explanation
Indices: 260368--260393 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
260358 ACCTTTTACT
260368 TTTTTTA
1 TTTTTTA
260375 TTTTTTA
1 TTTTTTA
260382 TTTTTTA
1 TTTTTTA
260389 TTTTT
1 TTTTT
260394 GATCAAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:260449 original size:43 final size:42
Alignment explanation
Indices: 260401--260766 Score: 255
Period size: 41 Copynumber: 8.8 Consensus size: 42
260391 TTTGATCAAA
* * * * *
260401 GCTCCTCTAAGCAGATGCTTAACGATTTTGAGAAACATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGA-AAAAATAAATG
260444 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
* * * *
260486 GCTCCTCTAATCAGAGGCACCACGACTTTTG-AAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAAATAAATG
* * * * ** *
260528 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAATGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
* * * * * *
260569 GCTCATCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
* * * * * * *
260610 ACTCCTCTAAACAGAGGCACCACGATTTTG-AAAATTAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
* * * * *
260651 GCTCCTCTAAAT-AGAGGCACCATGACTTTG-AAAAGTAAATT
1 GCTCCTCT-AATCAGAGGCTCAACGACTTTGAAAAAATAAATG
* * * *
260692 GCTCTTCTAAACAGAGG--CAACGGAACTTTG-AAAAGTAAATT
1 GCTCCTCTAATCAGAGGCTCAAC-G-ACTTTGAAAAAATAAATG
* * *
260733 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA
260767 GTAAATTGCG
Statistics
Matches: 285, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.01
40 3 0.01
41 172 0.60
42 74 0.26
43 34 0.12
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (42 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAATAAATG
Found at i:260578 original size:41 final size:41
Alignment explanation
Indices: 260438--260775 Score: 482
Period size: 41 Copynumber: 8.2 Consensus size: 41
260428 TTGAGAAACA
* * * * *
260438 TAAATGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAA
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAG
* *
260480 TAAATGGCTCCTCTAATCAGAGGCACCACGACTTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAG
* *
260522 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAATG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
*
260563 TAAATTGCTCATCTAAACAGAGGCACCACGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
* * *
260604 TAAATTACTCCTCTAAACAGAGGCACCACGATTTTGAAAAT
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
* *
260645 TAAATTGCTCCTCTAAATAGAGGCACCATGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
*
260686 TAAATTGCTCTTCTAAACAGAGGCA--ACGGAACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCAC-G-ACTTTGAAAAG
260727 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
1 TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
260768 TAAATTGC
1 TAAATTGC
260776 GCCTTGATAA
Statistics
Matches: 268, Mismatches: 23, Indels: 11
0.89 0.08 0.04
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 195 0.73
42 65 0.24
43 6 0.02
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
TAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAG
Found at i:270520 original size:57 final size:58
Alignment explanation
Indices: 270465--270695 Score: 333
Period size: 58 Copynumber: 4.0 Consensus size: 58
270455 CCCTTTTTTG
* *
270465 AAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCAAAATTATTTTTTAG
1 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAATTATTTTTTAA
***
270523 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTTTCAAAA--ACTTTTTTAA
1 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAATTA-TTTTTTAA
* *
270580 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATCT-TTTTTTTA
1 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCC-C-CAAAAT-TATTTTTTAA
*
270640 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
1 AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAATTATTTTTT
270696 TTAGATTTAT
Statistics
Matches: 154, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
56 1 0.01
57 47 0.31
58 53 0.34
59 5 0.03
60 48 0.31
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (58 bp):
AAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAATTATTTTTTAA
Found at i:270526 original size:15 final size:16
Alignment explanation
Indices: 270508--270542 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
270498 ACTTTTCCCC
*
270508 AAAA-TTATTTTTTAG
1 AAAATTTATTTTTAAG
270523 AAAATTTATTTTTAAG
1 AAAATTTATTTTTAAG
270539 AAAA
1 AAAA
270543 ATTGATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (16 bp):
AAAATTTATTTTTAAG
Found at i:270765 original size:8 final size:8
Alignment explanation
Indices: 270742--270809 Score: 57
Period size: 8 Copynumber: 7.8 Consensus size: 8
270732 AATAAAAGTG
270742 AAAATAAA
1 AAAATAAA
270750 AAAATAAA
1 AAAATAAA
270758 AAAATAAA
1 AAAATAAA
270766 GAAAAGTAAA
1 -AAAA-TAAA
270776 ACAAA-AATA
1 A-AAATAA-A
270785 AAAATGAAA
1 AAAAT-AAA
270794 TAAAGATAAA
1 -AAA-ATAAA
*
270804 AGAATA
1 AAAATA
270810 TTAAATAAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
8 24 0.47
9 10 0.20
10 15 0.29
11 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.13
Consensus pattern (8 bp):
AAAATAAA
Found at i:271439 original size:26 final size:26
Alignment explanation
Indices: 271380--271432 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
271370 ACCGGAATCT
* *
271380 AAAAATTT-TCCAAAAATTTCCAAAA
1 AAAAATTTCACCAAAAATCTCCAAAA
271405 AAAAATTTCACCAAAAATCTCCAAAA
1 AAAAATTTCACCAAAAATCTCCAAAA
271431 AA
1 AA
271433 TTTTTTCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (26 bp):
AAAAATTTCACCAAAAATCTCCAAAA
Found at i:271917 original size:18 final size:18
Alignment explanation
Indices: 271839--271942 Score: 74
Period size: 17 Copynumber: 5.9 Consensus size: 18
271829 AATACCTAAG
*
271839 ATAAAAAT-AAAAGAAAA
1 ATAAAAATAAAAATAAAA
* * * *
271856 A-AAATATATAAACAATA
1 ATAAAAATAAAAATAAAA
*
271873 ATAATAAT-AAAATAAAA
1 ATAAAAATAAAAATAAAA
*
271890 ATGTAAAATACAAAA-AAAA
1 AT-AAAAATA-AAAATAAAA
* *
271909 ATAACAATAAAAATAACA
1 ATAAAAATAAAAATAAAA
271927 ATAAAAAT-AAAATAAA
1 ATAAAAATAAAAATAAA
271943 GAAAAAAAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.08
17 27 0.42
18 23 0.35
19 6 0.09
20 4 0.06
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (18 bp):
ATAAAAATAAAAATAAAA
Found at i:271949 original size:11 final size:12
Alignment explanation
Indices: 271908--271956 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
271898 TACAAAAAAA
271908 AATAACAATAAA-
1 AATAA-AATAAAG
271920 AATAACAATAAA-
1 AATAA-AATAAAG
271932 AATAAAATAAAG
1 AATAAAATAAAG
*
271944 AA-AAAAAAAAG
1 AATAAAATAAAG
271955 AA
1 AA
271957 CATAGACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
11 16 0.46
12 19 0.54
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.12
Consensus pattern (12 bp):
AATAAAATAAAG
Found at i:271953 original size:6 final size:6
Alignment explanation
Indices: 271839--271942 Score: 74
Period size: 6 Copynumber: 17.8 Consensus size: 6
271829 AATACCTAAG
* * * * * *
271839 ATAAAA AT-AAA AGAAAA A-AAAT ATATAA ACAATA ATAATA AT-AAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
271884 ATAAAA ATGTAAA ATACAAA A-AAAA ATAACA ATAAAA ATAACA ATAAAA
1 ATAAAA AT-AAAA ATA-AAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
271933 AT-AAA ATAAA
1 ATAAAA ATAAA
271943 GAAAAAAAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
5 21 0.28
6 46 0.61
7 9 0.12
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:275230 original size:22 final size:22
Alignment explanation
Indices: 275203--275261 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
275193 TTATTATAAG
*
275203 AAAAATTAAGAAAAATTTGAAA
1 AAAAATTAAGAAAAAGTTGAAA
* *
275225 AAAAATGAATAAAAAAGTTGAAA
1 AAAAATTAA-GAAAAAGTTGAAA
*
275248 AGAAGATTAAGAAA
1 A-AAAATTAAGAAA
275262 TAGTGGGTCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 8 0.28
23 15 0.52
24 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19
Consensus pattern (22 bp):
AAAAATTAAGAAAAAGTTGAAA
Found at i:275993 original size:56 final size:58
Alignment explanation
Indices: 275889--275997 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 58
275879 GAAAACCTAA
* *
275889 TCTTTGTACAATAATTTTTTTTCAATAAAAGATCACATTTCTAGTTTAAAAAAGGTAG
1 TCTTTGTAAAATAATTTTTTTTCAATAAAAGACCACATTTCTAGTTTAAAAAAGGTAG
* *
275947 TCTTTGTAAAATAA-TTTTTTT-AATTACAA-ACCACATTTCTATTTTAAAAAA
1 TCTTTGTAAAATAATTTTTTTTCAA-TAAAAGACCACATTTCTAGTTTAAAAAA
275998 TGACCACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
56 22 0.48
57 11 0.24
58 13 0.28
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.43
Consensus pattern (58 bp):
TCTTTGTAAAATAATTTTTTTTCAATAAAAGACCACATTTCTAGTTTAAAAAAGGTAG
Found at i:276003 original size:24 final size:24
Alignment explanation
Indices: 275976--276021 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
275966 TTAATTACAA
*
275976 ACCACATTTCTATTTTAAAAAATG
1 ACCACATTTCTAGTTTAAAAAATG
276000 ACCACATTTCTAGTTTAAAAAA
1 ACCACATTTCTAGTTTAAAAAA
276022 AGTAGACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.35
Consensus pattern (24 bp):
ACCACATTTCTAGTTTAAAAAATG
Found at i:276008 original size:80 final size:81
Alignment explanation
Indices: 275922--276078 Score: 280
Period size: 80 Copynumber: 2.0 Consensus size: 81
275912 AATAAAAGAT
* *
275922 CACATTTCTAGTTTAAAAAAGGTAGTCTTTGTAAAATAATTTTTTTAATTACAAACCACA-TTTC
1 CACATTTCTAGTTTAAAAAAAGTAGACTTTGTAAAATAATTTTTTTAATTACAAACCACATTTTC
275986 TATTTTAAAAAATGAC
66 TATTTTAAAAAATGAC
*
276002 CACATTTCTAGTTTAAAAAAAGTAGACTTTGTACAATAATTTTTTTAATTACAAACCACATTTTC
1 CACATTTCTAGTTTAAAAAAAGTAGACTTTGTAAAATAATTTTTTTAATTACAAACCACATTTTC
276067 TATTTTAAAAAA
66 TATTTTAAAAAA
276079 CATAGTCTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 57 0.78
81 16 0.22
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (81 bp):
CACATTTCTAGTTTAAAAAAAGTAGACTTTGTAAAATAATTTTTTTAATTACAAACCACATTTTC
TATTTTAAAAAATGAC
Found at i:276090 original size:57 final size:56
Alignment explanation
Indices: 276000--276215 Score: 231
Period size: 57 Copynumber: 3.7 Consensus size: 56
275990 TTAAAAAATG
* *
276000 ACCACATTTCTAGTTTAAAAAA-AGTAGACTTTGTACAAT-AATTTTTTTAATTACAA
1 ACCACATTTCTATTTTAAAAAATA-TAGTCTTTGTACAATAAATTTTTTTAATTA-AA
* *
276056 ACCACATTTTCTATTTTAAAAAACATAGTCTTTGTATAATAAATTTTTTTAATTAAA
1 ACCACA-TTTCTATTTTAAAAAATATAGTCTTTGTACAATAAATTTTTTTAATTAAA
* * * * * *
276113 GACTATATTT-TCACTTTAAAAAATGTAATCTTTGTATAATAAAATTTTTTATTCAATTAAAA
1 -ACCACATTTCT-ATTTTAAAAAATATAGTCTTTGTACAAT-AAA-TTTTT-TT-AATT-AAA
276175 ACCACATTTCTATTTTAAAAAATATAGTCTTTGTACAATAA
1 ACCACATTTCTATTTTAAAAAATATAGTCTTTGTACAATAA
276216 TATCAAATGG
Statistics
Matches: 134, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
56 7 0.05
57 57 0.43
58 22 0.16
59 5 0.04
60 4 0.03
61 35 0.26
62 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (56 bp):
ACCACATTTCTATTTTAAAAAATATAGTCTTTGTACAATAAATTTTTTTAATTAAA
Done.