Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 18 of 345
Found at i:5405808 original size:22 final size:22
Alignment explanation
Indices: 5405733--5405808 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
5405723 TACATATTTC
5405733 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
5405755 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
5405779 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
5405802 ATCACAT
1 ATCACAT
5405809 ACATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:5405881 original size:25 final size:25
Alignment explanation
Indices: 5405802--5405881 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
5405792 ATTCGGCCTT
* **
5405802 ATCACATACATGCATGTTCACATTC
1 ATCACATATATGCACATTCACATTC
* * *
5405827 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATGCACATTC-ACATTC
*
5405849 ATCTCATATATGCACATTCACATTC
1 ATCACATATATGCACATTCACATTC
5405874 ATCACATA
1 ATCACATA
5405882 AAATCCTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
22 9 0.23
23 6 0.15
24 5 0.13
25 19 0.49
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (25 bp):
ATCACATATATGCACATTCACATTC
Found at i:5414306 original size:29 final size:29
Alignment explanation
Indices: 5414248--5414306 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5414238 AATACATAAA
* * *
5414248 ATATATATAAAATATATAAAAGAATTAGT
1 ATATATAAAAAATATATAAAAAAATGAGT
5414277 ATATATAAAAAATATA-AAATAAAATGAGT
1 ATATATAAAAAATATATAAA-AAAATGAGT
5414306 A
1 A
5414307 ATTGTTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (29 bp):
ATATATAAAAAATATATAAAAAAATGAGT
Found at i:5414664 original size:14 final size:15
Alignment explanation
Indices: 5414647--5414719 Score: 51
Period size: 17 Copynumber: 4.7 Consensus size: 15
5414637 ATGATAGATA
5414647 ATATATAAAAAT-AT
1 ATATATAAAAATAAT
* **
5414661 ATATA-ATAAATTTT
1 ATATATAAAAATAAT
*
5414675 ATACAATAAAATATAAT
1 ATA-TATAAAA-ATAAT
5414692 ATATATAGGAAAATAAT
1 ATATATA--AAAATAAT
5414709 ATATGATAAAA
1 ATAT-ATAAAA
5414720 GATTTTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
13 5 0.11
14 9 0.20
15 1 0.02
16 9 0.20
17 15 0.33
18 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (15 bp):
ATATATAAAAATAAT
Found at i:5414783 original size:21 final size:23
Alignment explanation
Indices: 5414747--5414798 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
5414737 TGGTATTTTT
5414747 AATAATAATAAAT-AAATTATAAA
1 AATAATAATAAATAAAATT-TAAA
5414770 AATAA-AAT-AATAAAATTTAAA
1 AATAATAATAAATAAAATTTAAA
5414791 AATAATAA
1 AATAATAA
5414799 AGAAAGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.44
22 10 0.37
23 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AATAATAATAAATAAAATTTAAA
Found at i:5424914 original size:41 final size:42
Alignment explanation
Indices: 5424744--5424917 Score: 205
Period size: 41 Copynumber: 4.2 Consensus size: 42
5424734 TGTAAAACAT
* **
5424744 AGAGCAATAGCGGCG-TTTTACCAAAAACGCCGCTAAAAA-C
1 AGAGCATTAGCGGCGCTTTTAGAAAAAACGCCGCTAAAAACC
* * *
5424784 AGAGCAATAGCGGC-ATTTTAGTAAAAAACGCCTCTAAAAACC
1 AGAGCATTAGCGGCGCTTTTAG-AAAAAACGCCGCTAAAAACC
** * *
5424826 AGAGCATTAGCGGCGCTTTTA-TTAAAACGCTGCTAAAAACT
1 AGAGCATTAGCGGCGCTTTTAGAAAAAACGCCGCTAAAAACC
*
5424867 AGAGCATTAGCGGCGCTTTT-GGAAAAACGCCGCTAAAAACC
1 AGAGCATTAGCGGCGCTTTTAGAAAAAACGCCGCTAAAAACC
5424908 AGAGCATTAG
1 AGAGCATTAG
5424918 TTTGGAAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
40 19 0.17
41 77 0.67
42 14 0.12
43 5 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (42 bp):
AGAGCATTAGCGGCGCTTTTAGAAAAAACGCCGCTAAAAACC
Found at i:5424914 original size:82 final size:82
Alignment explanation
Indices: 5424744--5424917 Score: 228
Period size: 82 Copynumber: 2.1 Consensus size: 82
5424734 TGTAAAACAT
*
5424744 AGAGCAATAGCGGCGTTTTACCAAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTTAGTAAA
1 AGAGCATTAGCGGCGTTTTACCAAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTTAGTAAA
*
5424809 AAACGCCTCTAAAAACC
66 AAACGCCGCTAAAAACC
** * * *
5424826 AGAGCATTAGCGGCGCTTTTA-TTAAAACGCTGCTAAAAACTAGAGCATTAGCGGCGCTTTT-G-
1 AGAGCATTAGCGGCG-TTTTACCAAAAACGCCGCTAAAAAC-AGAGCAATAGCGGC-ATTTTAGT
*
5424888 GAAAAACGCCGCTAAAAACC
63 AAAAAACGCCGCTAAAAACC
5424908 AGAGCATTAG
1 AGAGCATTAG
5424918 TTTGGAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
82 58 0.72
83 19 0.23
84 4 0.05
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (82 bp):
AGAGCATTAGCGGCGTTTTACCAAAAACGCCGCTAAAAACAGAGCAATAGCGGCATTTTAGTAAA
AAACGCCGCTAAAAACC
Found at i:5425139 original size:31 final size:32
Alignment explanation
Indices: 5425101--5425161 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
5425091 TATTATTATA
*
5425101 GTTTAAGGTTTATGATTTAA-GATGGTTTAGG
1 GTTTAAGGTTTATGAGTTAACGATGGTTTAGG
*
5425132 GTTTAAGGTTTATGAGTTAACTATGGTTTA
1 GTTTAAGGTTTATGAGTTAACGATGGTTTA
5425162 AGATATATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (32 bp):
GTTTAAGGTTTATGAGTTAACGATGGTTTAGG
Found at i:5425174 original size:32 final size:31
Alignment explanation
Indices: 5425104--5425175 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 31
5425094 TATTATAGTT
* * * *
5425104 TAAGGTTTATGATTTAAGATGGTTTAGGGTT
1 TAAGGTTTATGAGTTAAGATGGTTTAAGATA
*
5425135 TAAGGTTTATGAGTTAACTATGGTTTAAGATA
1 TAAGGTTTATGAGTTAA-GATGGTTTAAGATA
*
5425167 TATGGTTTA
1 TAAGGTTTA
5425176 GGGTTTAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 16 0.47
32 18 0.53
ACGTcount: A:0.29, C:0.01, G:0.25, T:0.44
Consensus pattern (31 bp):
TAAGGTTTATGAGTTAAGATGGTTTAAGATA
Found at i:5425962 original size:3 final size:3
Alignment explanation
Indices: 5425954--5425985 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5425944 CATTTTAGTA
5425954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5425986 AAGAGGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5431635 original size:19 final size:19
Alignment explanation
Indices: 5431613--5431653 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5431603 TTTATTAATA
5431613 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
5431631 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
5431650 TTTT
1 TTTT
5431654 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:5431999 original size:42 final size:43
Alignment explanation
Indices: 5431944--5432087 Score: 159
Period size: 45 Copynumber: 3.3 Consensus size: 43
5431934 GTTTTTGAAA
* *
5431944 AAAGCGCCGCTAAAAGTACAGGTCTATAGGGGCGTTTTTTTAC
1 AAAGAGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTTAC
* * *
5431987 -AAGAGCCGCT-AAAGTTCTTGGTCTATAGCAGCGATTTTTTTAC
1 AAAGAGCCGCTAAAAGTAC-AGGTCTATAGCGGCG-TTTTTTTAC
*
5432030 AAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTATA-
1 -AAAGAGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTT-TAC
* *
5432074 AAAGCGCCACTAAA
1 AAAGAGCCGCTAAA
5432088 GGTCCTGGTC
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
41 6 0.07
42 21 0.25
43 22 0.26
44 6 0.07
45 24 0.28
46 6 0.07
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (43 bp):
AAAGAGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTTAC
Found at i:5432098 original size:43 final size:43
Alignment explanation
Indices: 5431931--5432087 Score: 183
Period size: 43 Copynumber: 3.6 Consensus size: 43
5431921 GACATTTAGT
* * *
5431931 GGCGTTTTTGAAAAAAGCGCCGCTAAAAGTACAGGTCTATAGG
1 GGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTATAGC
* * * *
5431974 GGCGTTTTTT-TACAAGAGCCGCT-AAAGTTCTTGGTCTATAGC
1 GGCGTTTTTTATAAAAGCGCCGCTAAAAGTAC-AGGTCTATAGC
* *
5432016 AGCGATTTTTTTACAAAAGCGCCGCTAAAAGTACAGGTCTATAGC
1 GGCG--TTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTATAGC
*
5432061 GGCGTTTTTTATAAAAGCGCCACTAAA
1 GGCGTTTTTTATAAAAGCGCCGCTAAA
5432088 GGTCCTGGTC
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 6 0.06
42 22 0.24
43 30 0.32
44 6 0.06
45 23 0.25
46 6 0.06
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
GGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTATAGC
Found at i:5435838 original size:29 final size:29
Alignment explanation
Indices: 5435786--5435855 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5435776 AAACGTACAA
*
5435786 ACATACAAAGTAA-TAATTAAATAATGCATG
1 ACATACAAA--AAGTAATAAAATAATGCATG
*
5435816 ATATACAAAAAGTAATAAAATAATGCATG
1 ACATACAAAAAGTAATAAAATAATGCATG
5435845 ACATACAAAAA
1 ACATACAAAAA
5435856 AGAGTACTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.06
29 26 0.72
30 8 0.22
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.23
Consensus pattern (29 bp):
ACATACAAAAAGTAATAAAATAATGCATG
Found at i:5436483 original size:3 final size:3
Alignment explanation
Indices: 5436475--5436555 Score: 53
Period size: 3 Copynumber: 27.0 Consensus size: 3
5436465 CAAGTAAGAT
* *
5436475 ATA ATA AT- ATA A-A ATA ATA AT- GTA A-A ATA ATA ATA ATA ATA ATTT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * *
5436520 GTGA ACA ATA AGA TATA ATAA ATA ATA ATA ATA ATA
1 AT-A ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA
5436556 TATATAGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
2 7 0.12
3 47 0.78
4 6 0.10
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5436493 original size:13 final size:13
Alignment explanation
Indices: 5436475--5436509 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5436465 CAAGTAAGAT
5436475 ATAATAATATAAA
1 ATAATAATATAAA
*
5436488 ATAATAATGTAAA
1 ATAATAATATAAA
5436501 ATAATAATA
1 ATAATAATA
5436510 ATAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAATAATATAAA
Found at i:5437547 original size:20 final size:21
Alignment explanation
Indices: 5437511--5437550 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5437501 TCTGCTGAAA
5437511 TCTTTTTATTTTATTTTAGTT
1 TCTTTTTATTTTATTTTAGTT
5437532 TCTTTTT-TTTGT-TTTTAGT
1 TCTTTTTATTT-TATTTTAGT
5437551 ATCTGCTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (21 bp):
TCTTTTTATTTTATTTTAGTT
Found at i:5438650 original size:210 final size:210
Alignment explanation
Indices: 5438208--5439186 Score: 1384
Period size: 210 Copynumber: 4.7 Consensus size: 210
5438198 AAATCTGCTT
* * * * * *
5438208 CTTCGATTTGTTCTTTGACAATACAGAGATGACAAATCATCTTAAATTTGCTTCATCATAAGCTC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * * ** * * * *
5438273 GTGTAAA-CTAAATCAGCTATGTCTTCGATTTGCTCCTTG--TAAGCACA-AG-GAT--G-CCAA
66 ATG-AAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAA-TACAGAGAGATAAGATC-T
* * * * * * *
5438330 ATCATCTTGGATCTTGTTTCAGTC-TAATCGTCTGAAGGTCAGATCTGCTATGTATATG-CTCTC
128 GTCATCTTGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCT-TC
* ** * * *
5438393 TATTGAAGTAGAGATGCTAGA
190 CATCAAAGTGGAAATGCCAGA
5438414 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
5438479 ATGAAAGTCAAATCAGCTATATCTTCGATCTGCTCCCCACCGAATACAGAGAGATAAGATCTGTC
66 ATGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
* *
5438544 ATCTTGGATCTGGTTCAACGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCTTCCATCAA
131 ATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCTTCCATCAA
5438609 AGTGGAAATGCCAGA
196 AGTGGAAATGCCAGA
* *
5438624 CTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * * *
5438689 GTGAAAGCCAAATCAGCTATTTCTTCGATTTGTTCCCCGCTGAATACAGAGAGATAAGATCTGTC
66 ATGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
*
5438754 ATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATTTGCTATGTGTCTGCCTTCCATCAA
131 ATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCTTCCATCAA
*
5438819 AGTGGAAATGCCAAA
196 AGTGGAAATGCCAGA
5438834 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
5438899 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATATAGAGAGATAAGATCTGTC
66 ATGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
* **
5438964 ATCTTGGATCTGCTTCAGCGTAAAAATCTGAAGGTGAGATCTGCTATGTGTCTGCCCCCCATCAA
131 ATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCTTCCATCAA
*
5439029 AATGGAAATGCCAGA
196 AGTGGAAATGCCAGA
*
5439044 CTTCGATTTGTTCTCTGACAATACAGAGACGACGAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
5439109 ATGAAAGCCAAATCAACTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
66 ATGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
5439174 ATCTTGGATCTGC
131 ATCTTGGATCTGC
5439187 CCCGATAAAG
Statistics
Matches: 701, Mismatches: 62, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
205 3 0.00
206 86 0.12
207 3 0.00
208 4 0.01
209 4 0.01
210 585 0.83
211 15 0.02
212 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (210 bp):
CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
ATGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCCGAATACAGAGAGATAAGATCTGTC
ATCTTGGATCTGCTTCAGCGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGCCTTCCATCAA
AGTGGAAATGCCAGA
Found at i:5447269 original size:15 final size:15
Alignment explanation
Indices: 5447227--5447276 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
5447217 ATAACTTTGA
*
5447227 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
5447241 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
5447256 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
5447270 ATGCAAA
1 ATGCAAA
5447277 AAAGAATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:5450760 original size:29 final size:29
Alignment explanation
Indices: 5450708--5450777 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
5450698 AAACGTACAA
*
5450708 ACATACAAAGTAA-TAATTAAATAATGCATG
1 ACATACAAA--AAGTAATAAAATAATGCATG
*
5450738 ATATACAAAAAGTAATAAAATAATGCATG
1 ACATACAAAAAGTAATAAAATAATGCATG
5450767 ACATACAAAAA
1 ACATACAAAAA
5450778 AGAGTACTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.06
29 26 0.72
30 8 0.22
ACGTcount: A:0.59, C:0.10, G:0.09, T:0.23
Consensus pattern (29 bp):
ACATACAAAAAGTAATAAAATAATGCATG
Found at i:5450869 original size:2 final size:2
Alignment explanation
Indices: 5450864--5450894 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5450854 GATATATGCA
5450864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5450895 AATGAGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5451428 original size:13 final size:13
Alignment explanation
Indices: 5451410--5451444 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5451400 CAAGTAAGAT
5451410 ATAATAATATAAA
1 ATAATAATATAAA
*
5451423 ATAATAATGTAAA
1 ATAATAATATAAA
5451436 ATAATAATA
1 ATAATAATA
5451445 ATAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAATAATATAAA
Found at i:5454202 original size:97 final size:96
Alignment explanation
Indices: 5454092--5454404 Score: 278
Period size: 97 Copynumber: 3.2 Consensus size: 96
5454082 TCATACATAA
* *
5454092 TTCTTAATGTTACACGTATTTGTGAAAATCGATTGTATAATTGATTTGATTTCTATGGTTCAAAT
1 TTCTTAATATTACACGTGTTTGTGAAAATCGATTGTATAATTGATTTGATTT-TATGGTTCAAAT
*
5454157 ACAAATCATATTCTTCATTTATTCTTATGCAC
65 ACAAATCATATTCTTCATTTATTCTTATGCAG
* * * * *
5454189 CTCTTAATATTACATGTGTTT-TGCAAATATCGATAT-TGTAATTTATTT-AATTTATGGGATTC
1 TTCTTAATATTACACGTGTTTGTG-AAA-ATCGAT-TGTATAATTGATTTGATTTTAT-GG-TTC
* * * **
5454251 AAATATAAAT--TACTGTCTTCATTTAATCATATGTTG
61 AAATACAAATCATA-T-TCTTCATTTATTCTTATGCAG
* * * * *
5454287 TTCTCAATATTATAGGTGCTTGTGAAAATCGATCGTATAATTGATTTGATTTT-TAGAGTTCAAA
1 TTCTTAATATTACACGTGTTTGTGAAAATCGATTGTATAATTGATTTGATTTTAT-G-GTTCAAA
** * **
5454351 TGGAAACCATCGTCTTCATTTATTCTTATGCAG
64 TACAAATCATATTCTTCATTTATTCTTATGCAG
*
5454384 TTCTTAATATTACACATGTTT
1 TTCTTAATATTACACGTGTTT
5454405 TGCGATATGA
Statistics
Matches: 166, Mismatches: 37, Indels: 26
0.72 0.16 0.11
Matches are distributed among these distances:
96 7 0.04
97 87 0.52
98 68 0.41
99 4 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (96 bp):
TTCTTAATATTACACGTGTTTGTGAAAATCGATTGTATAATTGATTTGATTTTATGGTTCAAATA
CAAATCATATTCTTCATTTATTCTTATGCAG
Found at i:5454327 original size:195 final size:193
Alignment explanation
Indices: 5453993--5454456 Score: 523
Period size: 195 Copynumber: 2.4 Consensus size: 193
5453983 TCATTAAATT
* * * * * * *
5453993 TTATGCGCTTCTTAATATTGCATGTGCTTTGAAAAGATCTATCTTATAATTTATTTAA-TT-T--
1 TTATGCACTTCTTAATATTACATGTGTTTTGCAAATATCGATATTATAATTTATTTAATTTATGG
* * *
5454054 -ATTCAAATATAAATTAGTCTTCATTAATTCATACATAATTCTTAATGTTACACGTATTTGTGAA
66 GATTCAAATATAAATTAGTCTTCATTAATTCATACATAATTCTCAATATTACACGTACTTGTGAA
* * *
5454118 AATCGATTGTATAATTGATTTGATTTCTATG-GTTCAAATACAAATCATATTCTTCATTTATTC
131 AATCGATCGTATAATTGATTTGATTTCTA-GAGTTCAAATACAAACCATAGTCTTCATTTATTC
* *
5454181 TTATGCACCTCTTAATATTACATGTGTTTTGCAAATATCGATATTGTAATTTATTTAATTTATGG
1 TTATGCACTTCTTAATATTACATGTGTTTTGCAAATATCGATATTATAATTTATTTAATTTATGG
** ** * * *
5454246 GATTCAAATATAAATTACTGTCTTCATTTAA-TCATATGTTGTTCTCAATATTATAGGTGCTTGT
66 GATTCAAATATAAATTA--GTCTTCA-TTAATTCATACATAATTCTCAATATTACACGTACTTGT
* ** *
5454310 GAAAATCGATCGTATAATTGATTTGATTTTTAGAGTTCAAATGGAAACCATCGTCTTCATTTATT
128 GAAAATCGATCGTATAATTGATTTGATTTCTAGAGTTCAAATACAAACCATAGTCTTCATTTATT
5454375 C
193 C
* ** * * *
5454376 TTATGCAGTTCTTAATATTACACATGTTTTGC-GATAT-GAATATTATAGTTTATTTATTTTATG
1 TTATGCACTTCTTAATATTACATGTGTTTTGCAAATATCG-ATATTATAATTTATTTAATTTATG
*
5454439 GGATTCAAATAAAAATTA
65 GGATTCAAATATAAATTA
5454457 TTGTGGTCAT
Statistics
Matches: 231, Mismatches: 35, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
188 49 0.21
189 2 0.01
190 1 0.00
193 17 0.07
194 43 0.19
195 115 0.50
196 4 0.02
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (193 bp):
TTATGCACTTCTTAATATTACATGTGTTTTGCAAATATCGATATTATAATTTATTTAATTTATGG
GATTCAAATATAAATTAGTCTTCATTAATTCATACATAATTCTCAATATTACACGTACTTGTGAA
AATCGATCGTATAATTGATTTGATTTCTAGAGTTCAAATACAAACCATAGTCTTCATTTATTC
Found at i:5455815 original size:80 final size:80
Alignment explanation
Indices: 5455682--5455842 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 80
5455672 CTTGAGATAG
*
5455682 ATTCTTTTTTCGTGGCTCATCAGCATGTTCTTCAGATATTTCATGTGCAAAAGATGATAGTTTAT
1 ATTCTTTTTCCGTGGCTCATCAGCATGTTCTTCAGATATTTCATGTGCAAAAGATGATAGTTTAT
5455747 TAGAGAGAGATGTCA
66 TAGAGAGAGATGTCA
*
5455762 ATTCTTTTTCCGTGGCTCATCAGCATGTTCTTCAGATATTTCATGTTCAAAAGATGATAGTTTAT
1 ATTCTTTTTCCGTGGCTCATCAGCATGTTCTTCAGATATTTCATGTGCAAAAGATGATAGTTTAT
5455827 TAGAGAGAGATGTCA
66 TAGAGAGAGATGTCA
5455842 A
1 A
5455843 CTGCTGCTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (80 bp):
ATTCTTTTTCCGTGGCTCATCAGCATGTTCTTCAGATATTTCATGTGCAAAAGATGATAGTTTAT
TAGAGAGAGATGTCA
Found at i:5457671 original size:21 final size:21
Alignment explanation
Indices: 5457625--5457671 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5457615 TCAAATTACT
* *
5457625 ACTAACAAGCTAACAACTCCT
1 ACTAACAAGCTAACAAATCCC
5457646 ACTAACAAGCTAACAAATCCC
1 ACTAACAAGCTAACAAATCCC
*
5457667 CCTAA
1 ACTAA
5457672 GACTTAGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (21 bp):
ACTAACAAGCTAACAAATCCC
Found at i:5459746 original size:6 final size:6
Alignment explanation
Indices: 5459735--5459786 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
5459725 GAAAAAAAGG
*
5459735 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATACGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
5459783 ATAT
1 ATAT
5459787 AATATACCTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:5460885 original size:98 final size:96
Alignment explanation
Indices: 5460780--5461087 Score: 284
Period size: 98 Copynumber: 3.2 Consensus size: 96
5460770 TACAATTATT
* *
5460780 AATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATCTATGA-AATTCAAATATA
1 AATATTACACGTGTTTTGC-AAGATCGATATTATAATTTATTTAAT-TAT-ACAATTCAAATACA
5460844 AATTATTGTCATCATTTATTCATATGTAGTTCTC
63 AATTATTGTCATCATTTATTCATATGTAGTTCTC
* * * * * *
5460878 AATATTACACATGTTTGTG-AAGATCGAT-TGTATAATTGATTTGATTTTTAGAGTTCAAATACA
1 AATATTACACGTGTTT-TGCAAGATCGATAT-TATAATTTATTT-AATTATACAATTCAAATACA
** * * * * *
5460941 AACCATCGTCTTTATTTATTCTTATGCAGTTCTC
63 AATTATTGTCATCATTTATTCATATGTAGTTCTC
* * * * *
5460975 AATATTACACGTGTTTTGTCAATATCAATCA-TATAGTTTATTTAATTTATACGATTCAAATAGA
1 AATATTACACGTGTTTTG-CAAGATCGAT-ATTATAATTTATTTAA-TTATACAATTCAAATACA
* * *
5461039 AATTATTGTCATCATTCATTCATACGTAGTTCTTT
63 AATTATTGTCATCATTTATTCATATGTAGTTC-TC
5461074 AA-ATTACACGTGTT
1 AATATTACACGTGTT
5461088 CGTGCAAACA
Statistics
Matches: 165, Mismatches: 35, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
96 4 0.02
97 74 0.45
98 82 0.50
99 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (96 bp):
AATATTACACGTGTTTTGCAAGATCGATATTATAATTTATTTAATTATACAATTCAAATACAAAT
TATTGTCATCATTTATTCATATGTAGTTCTC
Found at i:5461082 original size:195 final size:196
Alignment explanation
Indices: 5460378--5461087 Score: 751
Period size: 195 Copynumber: 3.6 Consensus size: 196
5460368 TAATTATCTG
* ** *** * *
5460378 TTCTTAATATTACATGTG-TTTAAAAAGAACAATATTATAATTTATTTGATTTATGGGATTCAAA
1 TTCTTAATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATTTATGAGATTCAAA
** * * *
5460442 TATAAATTATTGTGTTCATTCATTCATACACAATTCTTT-ATGTTACA-A-GTAGTTGTGAAGAT
66 TATAAATTATTGTCATCATTCATTCATACGCAGTTCTTTAATATTACACATGT--TTGTGAAGAT
* * *
5460504 TGATCAG-AAAATTGATTTGAGTTTTAGTGTTAAAATACAAGCCATCGTCTTCATTTATTCTTAT
129 TGAT-TGTATAATTGATTTGATTTTTAGTGTTAAAATACAAGCCATCGTCTTCATTTATTCTTAT
5460568 ACAA
193 ACAA
* *
5460572 TTCTTAATATTACACGTGTTTTGCGAAGATGGATATTATAATTTATTTAATTTATGAGTTTCAAA
1 TTCTTAATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATTTATGAGATTCAAA
* * * *
5460637 TATAAATTATTATCATCATGT-ATTCATATGCAGTTATGCAAGTTTTAATGTTACACATATTTGT
66 TATAAATTATTGTCATCAT-TCATTCATACGCAG-T-T-C----TTTAATATTACACATGTTTGT
* * * * * *
5460701 TAAGATTG-TTCCTATAATTGATTTGATTTCTAGTGTTAAAATACATGCCATAGTCTTCATTTGT
123 GAAGATTGATT-GTATAATTGATTTGATTTTTAGTGTTAAAATACAAGCCATCGTCTTCATTTAT
5460765 TCTTATACAA
187 TCTTATACAA
* * *
5460775 TTATTAATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATCTATGAAATTCAAA
1 TTCTTAATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATTTATGAGATTCAAA
* * * * *
5460840 TATAAATTATTGTCATCATTTATTCATATGTAGTTC-TCAATATTACACATGTTTGTGAAGATCG
66 TATAAATTATTGTCATCATTCATTCATACGCAGTTCTTTAATATTACACATGTTTGTGAAGATTG
* * * * *
5460904 ATTGTATAATTGATTTGATTTTTAGAGTTCAAATACAAACCATCGTCTTTATTTATTCTTATGCA
131 ATTGTATAATTGATTTGATTTTTAGTGTTAAAATACAAGCCATCGTCTTCATTTATTCTTATACA
*
5460969 G
196 A
* * ** *
5460970 TTCTCAATATTACACGTGTTTTGTC-AATATCAATCA-TATAGTTTATTTAATTTAT-ACGATTC
1 TTCTTAATATTACACGTGTTTTG-CAAAGATGGAT-ATTATAATTTATTTAATTTATGA-GATTC
* * *
5461032 AAATAGAAATTATTGTCATCATTCATTCATACGTAGTTCTTTAA-ATTACACGTGTT
63 AAATATAAATTATTGTCATCATTCATTCATACGCAGTTCTTTAATATTACACATGTT
5461088 CGTGCAAACA
Statistics
Matches: 434, Mismatches: 62, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
194 18 0.04
195 232 0.53
196 9 0.02
197 1 0.00
198 1 0.00
200 1 0.00
201 1 0.00
202 6 0.01
203 163 0.38
204 1 0.00
205 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (196 bp):
TTCTTAATATTACACGTGTTTTGCAAAGATGGATATTATAATTTATTTAATTTATGAGATTCAAA
TATAAATTATTGTCATCATTCATTCATACGCAGTTCTTTAATATTACACATGTTTGTGAAGATTG
ATTGTATAATTGATTTGATTTTTAGTGTTAAAATACAAGCCATCGTCTTCATTTATTCTTATACA
A
Found at i:5461995 original size:14 final size:14
Alignment explanation
Indices: 5461976--5462018 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5461966 ATTTGTAACG
5461976 TTATTTGGTAACAT
1 TTATTTGGTAACAT
* * *
5461990 TTATTT-TTAATAG
1 TTATTTGGTAACAT
5462003 TTATTTGGTAACAT
1 TTATTTGGTAACAT
5462017 TT
1 TT
5462019 TCTTTTAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (14 bp):
TTATTTGGTAACAT
Found at i:5462005 original size:27 final size:27
Alignment explanation
Indices: 5461975--5462027 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5461965 CATTTGTAAC
5461975 GTTATTTGGTAACATTTAT-TTTTAATA
1 GTTATTTGGTAACATTT-TCTTTTAATA
5462002 GTTATTTGGTAACATTTTCTTTTAAT
1 GTTATTTGGTAACATTTTCTTTTAAT
5462028 TTGTAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (27 bp):
GTTATTTGGTAACATTTTCTTTTAATA
Found at i:5467591 original size:27 final size:26
Alignment explanation
Indices: 5467554--5467668 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
5467544 AGCATGGCTG
* *
5467554 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
5467580 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
5467608 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
5467635 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
5467662 CCAGAAC
1 CCAGAAC
5467669 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:5467618 original size:54 final size:54
Alignment explanation
Indices: 5467554--5467668 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
5467544 AGCATGGCTG
*
5467554 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
5467608 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
5467662 CCAGAAC
1 CCAGAAC
5467669 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:5469257 original size:26 final size:26
Alignment explanation
Indices: 5469228--5469333 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
5469218 ATACAAAAGA
5469228 CATGAAACATTTACCTAACCCATTAT
1 CATGAAACATTTACCTAACCCATTAT
5469254 CATGAAACATTTACCTAACCCATTAT
1 CATGAAACATTTACCTAACCCATTAT
* *
5469280 CATGAAGCATTTACCTAACCTATTAT
1 CATGAAACATTTACCTAACCCATTAT
*
5469306 CATTG-AACATTTACCTAACCTATTAT
1 CA-TGAAACATTTACCTAACCCATTAT
5469332 CA
1 CA
5469334 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 74 0.97
27 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
CATGAAACATTTACCTAACCCATTAT
Found at i:5473378 original size:27 final size:26
Alignment explanation
Indices: 5473317--5473427 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 26
5473307 TGGCTGCCAA
* *
5473317 AACAGATAATGTGACAGAGTCACCAG
1 AACAGATAATGTGGCAGAGCCACCAG
*
5473343 ATACTGATAATCGTGGCAGAGCCACCAG
1 A-ACAGATAAT-GTGGCAGAGCCACCAG
5473371 AACAGATATATGTGGCAGAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
* * *
5473398 ATCAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-ATGTGGCAGAGCCACCAG
5473425 AAC
1 AAC
5473428 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.01
27 56 0.76
28 17 0.23
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
AACAGATAATGTGGCAGAGCCACCAG
Found at i:5473420 original size:54 final size:54
Alignment explanation
Indices: 5473317--5473427 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
5473307 TGGCTGCCAA
* *
5473317 AACAGATAATGTGACAGAGTCACCAGATACTGATAATCGTGGCAGAGCCACCAG
1 AACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAG
* * * *
5473371 AACAGATATATGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAG
5473425 AAC
1 AAC
5473428 GCTTCCTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
AACAGATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCACCAG
Found at i:5475046 original size:26 final size:26
Alignment explanation
Indices: 5475010--5475093 Score: 143
Period size: 26 Copynumber: 3.2 Consensus size: 26
5475000 CATGAAATTC
*
5475010 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
5475036 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
5475062 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCTA
5475088 TTATCA
1 TTATCA
5475094 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
26 54 0.96
27 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:5479238 original size:195 final size:195
Alignment explanation
Indices: 5478995--5479350 Score: 479
Period size: 195 Copynumber: 1.8 Consensus size: 195
5478985 TTGATCGGAC
* * * *
5478995 AATTGATTTGTGTTTTAGTGTTAAAATACAGACTATAGTATTCATTTATTCTTATGCAATTCTTA
1 AATTGATTTGTGTTTTAGAGCTAAAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTTA
** *
5479060 ATATTACACGTGTTTTG-CGAAGATGGAT-ACTATAATTTATTTAATTGATGA-GATTCAAATAT
66 ATATTACACGTGTTTTGTC-AAGATCAATCA-TATAATTTATTTAATTGAT-ACGATTCAAATAG
* *
5479122 AAATTATTATTGTCATGT-ATTCATATGTAGTTCTCAATATTACTCTTGTTTGTGAAGATCGATT
128 AAATTATTATCGTCAT-TCATTCATACGTAGTTCTCAATATTACTCTTGTTTGTGAAGATCGATT
5479186 GTAT
192 GTAT
* * * *
5479190 AATTGATTTGAT-TTTTAGAGCTCAAATACAAACTATCGTCTGCATTTATTCTTATGCAGTTCTT
1 AATTGATTTG-TGTTTTAGAGCTAAAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTT
* * * *
5479254 AATATTACATGTGTTTTGTCAATATCAATCATATAGTTTATTTAATTTATACGATTCAAATAGAA
65 AATATTACACGTGTTTTGTCAAGATCAATCATATAATTTATTTAATTGATACGATTCAAATAGAA
5479319 ATTATTATCGTCATTCATTCATACGTAGTTCT
130 ATTATTATCGTCATTCATTCATACGTAGTTCT
5479351 TTAAATTACA
Statistics
Matches: 139, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
194 2 0.01
195 134 0.96
196 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (195 bp):
AATTGATTTGTGTTTTAGAGCTAAAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTTA
ATATTACACGTGTTTTGTCAAGATCAATCATATAATTTATTTAATTGATACGATTCAAATAGAAA
TTATTATCGTCATTCATTCATACGTAGTTCTCAATATTACTCTTGTTTGTGAAGATCGATTGTAT
Found at i:5479269 original size:97 final size:96
Alignment explanation
Indices: 5478995--5479269 Score: 243
Period size: 97 Copynumber: 2.8 Consensus size: 96
5478985 TTGATCGGAC
* * * * *
5478995 AATTGATTTG-TGTTTTAGTGTTAAAATACAGACTATAGTATTCATTTATTCTTATGCAATTCTT
1 AATTGATTTGAT-TTTTAGAGTTCAAATACAAACTATAGT-TGCATTTATTCTTATGCAGTTCTT
* *
5479059 AATATTACACGTGTTTTGCGAAGATGGATACTAT
64 AATATTACATGTG-TTTGCGAAGATCGATACTAT
* * ** * * * * *
5479093 AATTTATTTAATTGAT-GAGATTCAAATATAAATTATTA-TTGTCATGTATTCATATGTAGTTCT
1 AATTGATTTGATTTTTAGAG-TTCAAATACAAACTA-TAGTTG-CATTTATTCTTATGCAGTTCT
* * * **
5479156 CAATATTAC-TCTTGTTTGTGAAGATCGATTGTAT
63 TAATATTACAT-GTGTTTGCGAAGATCGATACTAT
* *
5479190 AATTGATTTGATTTTTAGAGCTCAAATACAAACTATCGTCTGCATTTATTCTTATGCAGTTCTTA
1 AATTGATTTGATTTTTAGAGTTCAAATACAAACTATAGT-TGCATTTATTCTTATGCAGTTCTTA
5479255 ATATTACATGTGTTT
65 ATATTACATGTGTTT
5479270 TGTCAATATC
Statistics
Matches: 134, Mismatches: 34, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
96 1 0.01
97 75 0.56
98 55 0.41
99 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (96 bp):
AATTGATTTGATTTTTAGAGTTCAAATACAAACTATAGTTGCATTTATTCTTATGCAGTTCTTAA
TATTACATGTGTTTGCGAAGATCGATACTAT
Found at i:5479350 original size:98 final size:95
Alignment explanation
Indices: 5479040--5479424 Score: 280
Period size: 97 Copynumber: 3.9 Consensus size: 95
5479030 TAGTATTCAT
* * * *
5479040 TTATTCTTATGCAATTCTTAATATTACACGTGTTTTG-CGAAGATGGATACTATAATTTATTTAA
1 TTATTCATATGTAGTTCTTAATATTACACGTGTTTTGTC-AAGATCGATA-TATAATTTATTTAA
* * *
5479104 TTGATGAGATTCAAATATAAATTATTATTGTCA
64 TTTAT-AGATTCAAATACAAATTATTATCGTCA
* * * * * * *
5479137 TGTATTCATATGTAGTTCTCAATATTACTCTTG-TTTGTGAAGATCGATTGTATAATTGATTTGA
1 T-TATTCATATGTAGTTCTTAATATTACACGTGTTTTGTCAAGATCGA-TATATAATTTATTTAA
* * * **
5479201 TTTTTAGAGCTCAAATACAAACTATCGTC-TGCA
64 TTTATAGA-TTCAAATACAAATTATTATCGT-CA
* * * * * *
5479234 TTTATTCTTATGCAGTTCTTAATATTACATGTGTTTTGTCAATATCAATCATATAGTTTATTTAA
1 -TTATTCATATGTAGTTCTTAATATTACACGTGTTTTGTCAAGATCGAT-ATATAATTTATTTAA
*
5479299 TTTATACGATTCAAATAGAAATTATTATCGTCA
64 TTTATA-GATTCAAATACAAATTATTATCGTCA
* * * * * *
5479332 TTCATTCATACGTAGTTCTTTAA-ATTACACGTG-TTCGTGCAA-A-CAAATTTCAAAATTTATA
1 TT-ATTCATATGTAGTTC-TTAATATTACACGTGTTTTGT-CAAGATC-GATAT-ATAATTTATT
5479393 TAATTTATAGGATTCAAATACAAATTAATTAT
61 TAATTTATA-GATTCAAATACAAATT-ATTAT
5479425 TATCGTGGTT
Statistics
Matches: 223, Mismatches: 49, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
96 6 0.03
97 110 0.49
98 100 0.45
99 7 0.03
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (95 bp):
TTATTCATATGTAGTTCTTAATATTACACGTGTTTTGTCAAGATCGATATATAATTTATTTAATT
TATAGATTCAAATACAAATTATTATCGTCA
Found at i:5479412 original size:195 final size:195
Alignment explanation
Indices: 5479018--5479416 Score: 429
Period size: 195 Copynumber: 2.0 Consensus size: 195
5479008 TTTAGTGTTA
* *
5479018 AAATACAGACTATAGTATTCATTTATTCTTATGCAATTCTTAATATTACACGTGTTTTGCGAAGA
1 AAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTTAATATTACACGTGTTTTGCGAAGA
** * * *
5479083 TGGATACTATAATTTATTTAATTGATGAGATTCAAATATAAATTATTATTGTCATGTATTCATAT
66 TCAATACTATAATTTATTTAATTGATGAGATTCAAATAGAAATTATTATCGTCATGTATTCATAC
* * * * * * * *
5479148 GTAGTTCTCAATATTACTCTTGTTTGTGAAGATCGATTGTATAATTGATTTGATTTTTAGAGCTC
131 GTAGTTCTCAATATTACACGTGTTCGTGAAGATCAATTGTAAAATTGATATAATTTATAGAGCTC
* * * * *
5479213 AAATACAAACTATCGTCTGCATTTATTCTTATGCAGTTCTTAATATTACATGTGTTTTGTC-AAT
1 AAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTTAATATTACACGTGTTTTG-CGAAG
* *
5479277 ATCAAT-CATATAGTTTATTTAATTTAT-ACGATTCAAATAGAAATTATTATCGTCAT-TCATTC
65 ATCAATAC-TATAATTTATTTAATTGATGA-GATTCAAATAGAAATTATTATCGTCATGT-ATTC
* *
5479339 ATACGTAGTTCTTTAA-ATTACACGTGTTCGTGCAA-A-CAAATT-TCAAAATTTATATAATTTA
127 ATACGTAGTTC-TCAATATTACACGTGTTCGTG-AAGATC-AATTGT-AAAATTGATATAATTTA
*
5479400 TAG-GATTC
188 TAGAG-CTC
5479408 AAATACAAA
1 AAATACAAA
5479417 TTAATTATTA
Statistics
Matches: 170, Mismatches: 25, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
194 6 0.04
195 158 0.93
196 6 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (195 bp):
AAATACAAACTATAGTATGCATTTATTCTTATGCAATTCTTAATATTACACGTGTTTTGCGAAGA
TCAATACTATAATTTATTTAATTGATGAGATTCAAATAGAAATTATTATCGTCATGTATTCATAC
GTAGTTCTCAATATTACACGTGTTCGTGAAGATCAATTGTAAAATTGATATAATTTATAGAGCTC
Found at i:5480272 original size:14 final size:14
Alignment explanation
Indices: 5480253--5480295 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5480243 ATTTGTAACG
5480253 TTATTTGGTAACAT
1 TTATTTGGTAACAT
* * *
5480267 TTATTT-TTAATAG
1 TTATTTGGTAACAT
5480280 TTATTTGGTAACAT
1 TTATTTGGTAACAT
5480294 TT
1 TT
5480296 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (14 bp):
TTATTTGGTAACAT
Found at i:5480282 original size:27 final size:27
Alignment explanation
Indices: 5480252--5480304 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5480242 CATTTGTAAC
5480252 GTTATTTGGTAACATTTATTTTTAATA
1 GTTATTTGGTAACATTTATTTTTAATA
*
5480279 GTTATTTGGTAACATTTTTTTTTAAT
1 GTTATTTGGTAACATTTATTTTTAAT
5480305 TTGTAACGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.58
Consensus pattern (27 bp):
GTTATTTGGTAACATTTATTTTTAATA
Found at i:5482408 original size:98 final size:97
Alignment explanation
Indices: 5482081--5482413 Score: 244
Period size: 97 Copynumber: 3.4 Consensus size: 97
5482071 CAAAGAGTAT
* * * * *
5482081 TATAATTGATTTGATTTTTAGTGTTAAAATACAAATGATAGTCTTCATTTATTCTTATGCATACA
1 TATAATTTATTTAATTTATAG-ATTAAAATACAAATCATAGTCTTCATTTATTCTTATG----CA
* * *
5482146 GTTCTTAATATTACACGTGTTTTG-CGAAAATGGAT-A
61 GTTCTCAATATTACACGTGTTTTGTC-AATATCGATCA
* * * * * * * * *
5482182 TTATAATTTATTTAATTCACAAGATTCAAATATAAATTATTA-TCGTCATGTATTCATATGTAGT
1 -TATAATTTATTTAATTTA-TAGATTAAAATACAAATCA-TAGTCTTCATTTATTCTTATGCAGT
** * *
5482246 AATCAATATTACTCAG-G-TTTGTGAATATCGATCA
63 TCTCAATATTACAC-GTGTTTTGTCAATATCGATCA
* ** * * * *
5482280 TATAATTGATTTGGTTTTTAGAGTTCAAATACAAACCATCGTCTTCATTTATTCTTATGCAGTTC
1 TATAATTTATTTAATTTATAGA-TTAAAATACAAATCATAGTCTTCATTTATTCTTATGCAGTTC
*
5482345 TCAATATTACACGTGTTTTGTCAATATCAATCA
65 TCAATATTACACGTGTTTTGTCAATATCGATCA
* *
5482378 TATAGTTTATTTAATTTATAGGATTAAAATAGAAAT
1 TATAATTTATTTAATTTATA-GATTAAAATACAAAT
5482414 TATGGTCGTC
Statistics
Matches: 174, Mismatches: 47, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
96 5 0.03
97 66 0.38
98 55 0.32
99 3 0.02
102 41 0.24
103 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (97 bp):
TATAATTTATTTAATTTATAGATTAAAATACAAATCATAGTCTTCATTTATTCTTATGCAGTTCT
CAATATTACACGTGTTTTGTCAATATCGATCA
Found at i:5482434 original size:195 final size:195
Alignment explanation
Indices: 5482081--5482440 Score: 458
Period size: 195 Copynumber: 1.8 Consensus size: 195
5482071 CAAAGAGTAT
* **
5482081 TATAATTGATTTGATTTTTAGTGTTAAAATACAAATGATAGTCTTCATTTATTCTTATGCATACA
1 TATAATTGATTTGATTTTTAGAGTTAAAATACAAACCATAGTCTTCATTTATTCTTATG---ACA
* ** *
5482146 GTTCTTAATATTACACGTGTTTTGCGAAAATGGATATTATAATTTATTTAATTCACAAGATTCAA
63 GTTCTCAATATTACACGTGTTTTGCGAAAATCAATATTATAATTTATTTAATTCACAAGATTAAA
* *
5482211 ATATAAATTATTATCGTCATGTATTCATATGTAGTAATCAATATTACTCAGGTTTGTGAATATCG
128 ATAGAAATTATGATCGTCA-GTATTCATATGTAGTAATCAATATTACTCAGGTTTGTGAATATCG
5482276 ATCA
192 ATCA
* * *
5482280 TATAATTGATTTGGTTTTTAGAGTTCAAATACAAACCATCGTCTTCATTTATTCTTATG-CAGTT
1 TATAATTGATTTGATTTTTAGAGTTAAAATACAAACCATAGTCTTCATTTATTCTTATGACAGTT
* * * * *
5482344 CTCAATATTACACGTGTTTTGTC-AATATCAATCA-TATAGTTTATTTAATTTATAGGATTAAAA
66 CTCAATATTACACGTGTTTTG-CGAAAATCAAT-ATTATAATTTATTTAATTCACAAGATTAAAA
*
5482407 TAGAAATTATGGTCGTC-GCTCATTCATATGTAGT
129 TAGAAATTATGATCGTCAG-T-ATTCATATGTAGT
5482441 TCTTTAAATT
Statistics
Matches: 139, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
193 1 0.01
194 1 0.01
195 82 0.59
196 2 0.01
199 53 0.38
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (195 bp):
TATAATTGATTTGATTTTTAGAGTTAAAATACAAACCATAGTCTTCATTTATTCTTATGACAGTT
CTCAATATTACACGTGTTTTGCGAAAATCAATATTATAATTTATTTAATTCACAAGATTAAAATA
GAAATTATGATCGTCAGTATTCATATGTAGTAATCAATATTACTCAGGTTTGTGAATATCGATCA
Found at i:5483715 original size:26 final size:30
Alignment explanation
Indices: 5483671--5483729 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
5483661 GACATATATG
*
5483671 AAAATATACGCATATCATA-AT-TATTAAA
1 AAAATATACACATATCATATATGTATTAAA
5483699 AAAATATACACA-A-CATATATGGTATTAAA
1 AAAATATACACATATCATATAT-GTATTAAA
5483728 AA
1 AA
5483730 TAGTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.15
27 3 0.11
28 11 0.41
29 9 0.33
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (30 bp):
AAAATATACACATATCATATATGTATTAAA
Found at i:5483830 original size:17 final size:18
Alignment explanation
Indices: 5483794--5483830 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5483784 ATAATAGTAA
5483794 TAATAAAATGCTAATAAG
1 TAATAAAATGCTAATAAG
5483812 TAAT-AAATG-TAATATAG
1 TAATAAAATGCTAATA-AG
5483829 TA
1 TA
5483831 CTAGAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
TAATAAAATGCTAATAAG
Found at i:5484177 original size:25 final size:24
Alignment explanation
Indices: 5484147--5484199 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
5484137 TAACGATAAT
*
5484147 ATAACAATAATAGTAATAAAAAATA
1 ATAACAATAATAGAAATAAAAAA-A
*
5484172 ATAACAGTAATAGAAATAAAAAAA
1 ATAACAATAATAGAAATAAAAAAA
5484196 ATAA
1 ATAA
5484200 AAAAAAAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
ATAACAATAATAGAAATAAAAAAA
Found at i:5484240 original size:3 final size:3
Alignment explanation
Indices: 5484234--5484368 Score: 64
Period size: 3 Copynumber: 45.7 Consensus size: 3
5484224 TGACACTGAC
* * * * * * *
5484234 AAT AAT ACT AAT AAT AAC AAT -AT ATT AAT AAT ACT GAT -AT ATT CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5484280 AAT AAT AAT AAT AAT AGT -AT AAAT AAC AAT CAT -AT AAGT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA-T AAT AAT
** * * *
5484325 AAT AGG GAT AAT AAT AAT AAT AGT AAT AAT -TT GAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
5484369 AAAAGGCAAA
Statistics
Matches: 94, Mismatches: 30, Indels: 16
0.67 0.21 0.11
Matches are distributed among these distances:
2 8 0.09
3 81 0.86
4 5 0.05
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5484264 original size:17 final size:17
Alignment explanation
Indices: 5484232--5484289 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5484222 ACTGACACTG
*
5484232 ACAATAATACTAATAATA
1 ACAAT-ATATTAATAATA
5484250 ACAATATATTAATAAT-
1 ACAATATATTAATAATA
* *
5484266 ACTGATATATTCATAATA
1 AC-AATATATTAATAATA
*
5484284 ATAATA
1 ACAATA
5484290 ATAATAGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 2 0.06
17 25 0.76
18 6 0.18
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (17 bp):
ACAATATATTAATAATA
Found at i:5485898 original size:42 final size:44
Alignment explanation
Indices: 5485791--5485910 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 44
5485781 TATTTGATTT
* *
5485791 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCA
1 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAACA
** * * * *
5485835 TTGATCTGTTTCCCTACTGCTTA-GGGGTTTA-GATCTGTAAAC-
1 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCT-TGTAAACA
*
5485877 TCAACCTGTTACCCTACTGCTTAGGGGATTAAGG
1 TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGG
5485911 TTTGAAAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
42 21 0.36
43 18 0.31
44 20 0.34
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (44 bp):
TCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTAAACA
Found at i:5485962 original size:86 final size:86
Alignment explanation
Indices: 5485790--5486001 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 86
5485780 ATATTTGATT
** *
5485790 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGATCTGTTTCCCTACTGC
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAAT-ATTGATCTGTTACCCTACTGC
** * *
5485855 TTAGGGGTTTAGATCTGTAAAC
65 TTAGGGAATAAGATCTATAAAC
* * * *
5485877 -TCAACCTGTTACCCTACTGCTTAGGGGATTAAGGTTTGAAA-ATTTGGGT-TGTTACCCTATTG
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATA-TT-GATCTGTTACCCTACTG
*
5485939 CTTAGGGCAATAATATCTATAAAC
64 CTTAGGG-AATAAGATCTATAAAC
* * * *
5485963 TTCAGCTTGTTACCCTACTGTTTAGGGGGTTAAAGCTTG
1 TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTG
5486002 GTGGTTTGAA
Statistics
Matches: 103, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
84 1 0.01
85 20 0.19
86 50 0.49
87 32 0.31
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (86 bp):
TTCAACCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATATTGATCTGTTACCCTACTGCT
TAGGGAATAAGATCTATAAAC
Found at i:5486461 original size:43 final size:44
Alignment explanation
Indices: 5486394--5486480 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
5486384 GGAGACGAAA
* *
5486394 TCTGTAATTTTCAGCCTATTACCCTACTGCTTAAGGGG-TTAAGG
1 TCTGTAAATTTCAACCTATTACCCTACTGCTT-AGGGGTTTAAGG
*
5486438 TCTGTAAATTT-AACCTGTTACCCTACTGCTTAGGGGTTTAAGG
1 TCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGTTTAAGG
5486481 CTTGGTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 5 0.13
43 24 0.62
44 10 0.26
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (44 bp):
TCTGTAAATTTCAACCTATTACCCTACTGCTTAGGGGTTTAAGG
Found at i:5498964 original size:27 final size:31
Alignment explanation
Indices: 5498919--5498978 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
5498909 GACATATATG
*
5498919 AAAATATACGCATATCATA-AT-TATTAAAA
1 AAAATATACACATATCATATATGTATTAAAA
5498948 AAAATATACACA-A-CATATATGGTATTAAAA
1 AAAATATACACATATCATATAT-GTATTAAAA
5498978 A
1 A
5498979 TAGTTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 11 0.41
30 9 0.33
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (31 bp):
AAAATATACACATATCATATATGTATTAAAA
Found at i:5499079 original size:17 final size:18
Alignment explanation
Indices: 5499043--5499079 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5499033 ATAATAGTAA
5499043 TAATAAAATGCTAATAAG
1 TAATAAAATGCTAATAAG
5499061 TAAT-AAATG-TAATATAG
1 TAATAAAATGCTAATA-AG
5499078 TA
1 TA
5499080 CTAGAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.32
Consensus pattern (18 bp):
TAATAAAATGCTAATAAG
Found at i:5499370 original size:3 final size:3
Alignment explanation
Indices: 5499364--5499524 Score: 61
Period size: 3 Copynumber: 55.3 Consensus size: 3
5499354 TTGCATTAAC
* * * * * *
5499364 AAT AAT AAT AGT AAG AAT AAT AAC GAT AAT -AT AAC AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5499411 AA- AA- AAT AAT AAC AGT AAT AGA- AAT AAT AAA AAT AAA AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * * *
5499453 AA- AAGGT AACG AA- AAT AAT ACT AAT AAT AAC AAT -AT ATT AAT AAT
1 AAT AA--T AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5499498 ACT GAT -AT ATT CAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5499525 GTAGAATAAC
Statistics
Matches: 113, Mismatches: 35, Indels: 20
0.67 0.21 0.12
Matches are distributed among these distances:
2 17 0.15
3 91 0.81
4 3 0.03
5 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:5499427 original size:19 final size:18
Alignment explanation
Indices: 5499399--5499452 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
5499389 ATAATATAAC
*
5499399 AATAATAGTAATAAAAAAT
1 AATAACAGTAAT-AAAAAT
*
5499418 AATAACAGTAATAGAAAT
1 AATAACAGTAATAAAAAT
5499436 AATAA-A--AATAAAAAT
1 AATAACAGTAATAAAAAT
5499451 AA
1 AA
5499453 AAAAGGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 10 0.31
17 1 0.03
18 10 0.31
19 11 0.34
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AATAACAGTAATAAAAAT
Found at i:5499496 original size:17 final size:17
Alignment explanation
Indices: 5499474--5499521 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5499464 AAAATAATAC
5499474 TAATAATAACAATATAT
1 TAATAATAACAATATAT
*
5499491 TAATAAT-ACTGATATAT
1 TAATAATAAC-AATATAT
* *
5499508 TCATAATAATAATA
1 TAATAATAACAATA
5499522 ATAGTAGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 22 0.88
18 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (17 bp):
TAATAATAACAATATAT
Found at i:5501478 original size:28 final size:27
Alignment explanation
Indices: 5501415--5501467 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5501405 CTAATTCTTC
5501415 ATTTTAATGATTATTTTCGAATTTTTG
1 ATTTTAATGATTATTTTCGAATTTTTG
*
5501442 ATTTTAATGATTATTTTTGAATTTTT
1 ATTTTAATGATTATTTTCGAATTTTT
5501468 TTTTGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.62
Consensus pattern (27 bp):
ATTTTAATGATTATTTTCGAATTTTTG
Found at i:5504029 original size:98 final size:97
Alignment explanation
Indices: 5503885--5504177 Score: 256
Period size: 98 Copynumber: 3.0 Consensus size: 97
5503875 TTACATGTAG
* * * * * * * *
5503885 TTGTGAAGATTGATGGGATAATTGATTTGAGTTTT-AGTGTTAAAATACAAACCATAGCCTTCAT
1 TTGTGAAGATAGATTGTATAATTAATTT-AATTTTGAGAGTTCAAATACAAACCATAGTCTTCAT
*
5503949 TTATTCTTATGCAATTCTTAATATTACACATG-
65 TTATTCTTATGCAGTTCTTAATATTACACATGT
* * ** *
5503981 TTGTTCGAAGATGGATAT-TATAATTAATTTAATTTATGAGA-TTCAAATATAAATTATTA-TCG
1 TTG-T-GAAGATAGAT-TGTATAATTAATTTAATTT-TGAGAGTTCAAATACAAACCA-TAGTCT
* * * * * * *
5504043 TCATGTATTCATATGTAGTTATCAATATTACTCGTGT
61 TCATTTATTCTTATGCAGTTCTTAATATTACACATGT
* * * *
5504080 TTGTGAAGATAGATTGTATAATTGATTTGATTTTTAGAGTTCAAATACAAACCATCGTCTTCATT
1 TTGTGAAGATAGATTGTATAATTAATTTAATTTTGAGAGTTCAAATACAAACCATAGTCTTCATT
*
5504145 T-TTCTTATACAGTTCTTAATATTACACATGT
66 TATTCTTATGCAGTTCTTAATATTACACATGT
5504176 TT
1 TT
5504178 TGTCAATATC
Statistics
Matches: 150, Mismatches: 37, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
96 34 0.23
97 48 0.32
98 61 0.41
99 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (97 bp):
TTGTGAAGATAGATTGTATAATTAATTTAATTTTGAGAGTTCAAATACAAACCATAGTCTTCATT
TATTCTTATGCAGTTCTTAATATTACACATGT
Found at i:5504144 original size:195 final size:193
Alignment explanation
Indices: 5503885--5504255 Score: 489
Period size: 194 Copynumber: 1.9 Consensus size: 193
5503875 TTACATGTAG
* *
5503885 TTGTGAAGATTGATGGGATAATTGATTTGAGTTTTAGTGTTAAAATACAAACCATAGCCTTCATT
1 TTGTGAAGATAGATGGGATAATTGATTTGAGTTTTAGAGTTAAAATACAAACCATAGCCTTCATT
* **
5503950 TATTCTTATGCAATTCTTAATATTACACATGTTGT-TCGAAGATGGAT-ATTATAATTAATTTAA
66 T-TTCTTATACAATTCTTAATATTACACATGTTGTGTC-AAGATCAATCA-TATAATTAATTTAA
*
5504013 TTTATGA-GATTCAAATATAAATTATTATCGTCATGT-ATTCATATGTAGTTATCAATATTACTC
128 TTTAT-ACGATTCAAATAGAAATTATTATCGTCAT-TCATTCAT-TGTAGTTATCAATATTACTC
5504076 GTGT
190 GTGT
* * * * * *
5504080 TTGTGAAGATAGATTGTATAATTGATTTGATTTTTAGAGTTCAAATACAAACCATCGTCTTCATT
1 TTGTGAAGATAGATGGGATAATTGATTTGAGTTTTAGAGTTAAAATACAAACCATAGCCTTCATT
* * * * *
5504145 TTTCTTATACAGTTCTTAATATTACACATGTTTTGTCAATATCAATCATATAGTTTATTTAATTT
66 TTTCTTATACAATTCTTAATATTACACATGTTGTGTCAAGATCAATCATATAATTAATTTAATTT
* *
5504210 ATACGATTCAAATAGAAATTATTGTCGTTATTCATTCATTGTAGTT
131 ATACGATTCAAATAGAAATTATTATCGTCATTCATTCATTGTAGTT
5504256 CTTTAAATTA
Statistics
Matches: 153, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
193 9 0.06
194 83 0.54
195 61 0.40
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (193 bp):
TTGTGAAGATAGATGGGATAATTGATTTGAGTTTTAGAGTTAAAATACAAACCATAGCCTTCATT
TTTCTTATACAATTCTTAATATTACACATGTTGTGTCAAGATCAATCATATAATTAATTTAATTT
ATACGATTCAAATAGAAATTATTATCGTCATTCATTCATTGTAGTTATCAATATTACTCGTGT
Found at i:5504703 original size:12 final size:12
Alignment explanation
Indices: 5504686--5504710 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5504676 CTAATAATAT
5504686 TAGCAATTAACG
1 TAGCAATTAACG
5504698 TAGCAATTAACG
1 TAGCAATTAACG
5504710 T
1 T
5504711 TAATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TAGCAATTAACG
Found at i:5505577 original size:17 final size:16
Alignment explanation
Indices: 5505553--5505586 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5505543 TGATTTTTTG
*
5505553 AAATTAATTGAAAAAT
1 AAATTAATTAAAAAAT
5505569 AAATGTAATTAAAAAAT
1 AAAT-TAATTAAAAAAT
5505586 A
1 A
5505587 TATTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATTAATTAAAAAAT
Found at i:5518994 original size:34 final size:34
Alignment explanation
Indices: 5518950--5519017 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
5518940 GCACATTTGA
*
5518950 ACAGTCTTGGGCCTAAGCCCTTTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATTTCAGTA-CAGTG
*
5518985 ACAGT-TTGGGCCTTAGCCCATTTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATTTCAGTACAGTG
5519018 TCAACAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 5 0.16
34 21 0.68
35 5 0.16
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATTTCAGTACAGTG
Found at i:5521389 original size:61 final size:60
Alignment explanation
Indices: 5521268--5521395 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 60
5521258 GTGGGAAATC
* * * *
5521268 AACACGGCTAGACTTTCCTACACGGGTACACCACACGCTCGTGTAGTGTTAGCAGTCTCT
1 AACACGGCTAGACTTTCCTACACGGGTACACCACACGCTCGTGTACTATTAACAGACTCT
*
5521328 AACACGGCCTAGAC-TTCCTTACACGGGTAGACCACACGAC-CGTGT-CTATTCAACAGACTCT
1 AACACGG-CTAGACTTTCC-TACACGGGTACACCACACG-CTCGTGTACTATT-AACAGACTCT
5521389 AACACGG
1 AACACGG
5521396 TTTGAAGCAC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
60 14 0.24
61 44 0.75
62 1 0.02
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (60 bp):
AACACGGCTAGACTTTCCTACACGGGTACACCACACGCTCGTGTACTATTAACAGACTCT
Found at i:5522246 original size:13 final size:13
Alignment explanation
Indices: 5522228--5522253 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5522218 CTGTGCATTC
5522228 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
5522241 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
5522254 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:5529659 original size:48 final size:48
Alignment explanation
Indices: 5529598--5530069 Score: 768
Period size: 48 Copynumber: 9.8 Consensus size: 48
5529588 ATATACACAC
* *
5529598 ATCTCCTACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
5529646 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCGCATATACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
5529694 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCGCATATACAA
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
5529742 ATCTCAT-TCATATTTCACACTAGCCATTCGGCTTTACCGCATATACAT
1 ATCTCATAT-ATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
5529790 ATCTCATATATATTTCACACTAGCCATTCGACTTTACCACATAAACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
5529838 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
5529886 ATCTCAAACATATTTCACACTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
5529934 ATCTCAT-TCATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATAT-ATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
5529982 ATCTCATACATATTTCACATTAGCCATTCAGCTTTACCACATATACAT
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
5530030 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCAC
1 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCAC
5530070 GCACATATAT
Statistics
Matches: 399, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
47 1 0.00
48 397 0.99
49 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:5531880 original size:14 final size:14
Alignment explanation
Indices: 5531861--5531890 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5531851 AAGTTGATTT
5531861 TTGAGAATTAAAAA
1 TTGAGAATTAAAAA
5531875 TTGAGAATTAAAAA
1 TTGAGAATTAAAAA
5531889 TT
1 TT
5531891 TTTAGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (14 bp):
TTGAGAATTAAAAA
Found at i:5532385 original size:17 final size:17
Alignment explanation
Indices: 5532363--5532397 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5532353 TTGTTCTTAC
5532363 AAAATATATATATACAT
1 AAAATATATATATACAT
5532380 AAAATATATATATACAT
1 AAAATATATATATACAT
5532397 A
1 A
5532398 CTTACATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATATATATACAT
Found at i:5533313 original size:61 final size:61
Alignment explanation
Indices: 5533195--5533317 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
5533185 GTAGGAAATC
* * * *
5533195 AACACGGCCTGGACTTCCCTACACGGGTACACCACACGCCCGTGTAGTGTTAGCAGACTCT
1 AACACGGCCTGGACTTCCCTACACGGGTACACCACACGACCGTGTACTATTAACAGACTCT
* *
5533256 AACACGGCCTGGACTTCCTTACACGGGTAGACCACACGACCGTGT-CTATTCAACAGACTCT
1 AACACGGCCTGGACTTCCCTACACGGGTACACCACACGACCGTGTACTATT-AACAGACTCT
5533317 A
1 A
5533318 CCATGGTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 3 0.05
61 52 0.95
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.20
Consensus pattern (61 bp):
AACACGGCCTGGACTTCCCTACACGGGTACACCACACGACCGTGTACTATTAACAGACTCT
Found at i:5544673 original size:13 final size:13
Alignment explanation
Indices: 5544655--5544680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5544645 CTGTGCATTC
5544655 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
5544668 TTAGTTTAGTTAA
1 TTAGTTTAGTTAA
5544681 AACAAATCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTAGTTAA
Found at i:5547954 original size:39 final size:40
Alignment explanation
Indices: 5547837--5548060 Score: 262
Period size: 39 Copynumber: 5.7 Consensus size: 40
5547827 GCTACTCGTT
* *
5547837 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
5547877 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
5547917 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
5547956 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
** * * *
5547995 CAAATGCCTTC-GGATCTTAGTACGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
5548036 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5548061 CATCATTCAA
Statistics
Matches: 162, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.46
40 73 0.45
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:5548014 original size:79 final size:79
Alignment explanation
Indices: 5547837--5548060 Score: 265
Period size: 79 Copynumber: 2.8 Consensus size: 79
5547827 GCTACTCGTT
* * *
5547837 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
5547902 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * *
5547917 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
5547980 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
** * * * *
5547995 CAAATGCCTTCGGATCTTAGTACGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCG
5548059 GA
64 GA
5548061 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
78 36 0.29
79 57 0.46
80 31 0.25
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
ATTAGTAACTCGCA
Found at i:5552683 original size:23 final size:25
Alignment explanation
Indices: 5552638--5552687 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 25
5552628 AGGATATTAC
5552638 AGCTGGCAACCCCTTTAAGTCCGTAG
1 AGCTGGCAACCCC-TTAAGTCCGTAG
5552664 AGCTGGCAA-CCC-TAAGTCCGTAG
1 AGCTGGCAACCCCTTAAGTCCGTAG
5552687 A
1 A
5552688 CTCAACTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 12 0.50
25 3 0.12
26 9 0.38
ACGTcount: A:0.26, C:0.30, G:0.24, T:0.20
Consensus pattern (25 bp):
AGCTGGCAACCCCTTAAGTCCGTAG
Found at i:5554089 original size:40 final size:38
Alignment explanation
Indices: 5554024--5554103 Score: 124
Period size: 40 Copynumber: 2.1 Consensus size: 38
5554014 CAGTAGCCCC
*
5554024 ATGTTTTCGATTCAGTCACTGGGGGCTTATTTGCCCTT
1 ATGTTTTCGATTCAGTCACTGGGGGCTTATTTGACCTT
*
5554062 ATGTTTTCGGATTCTGTCAACTGGGGGCTTATTTGACCTT
1 ATGTTTTC-GATTCAGTC-ACTGGGGGCTTATTTGACCTT
5554102 AT
1 AT
5554104 TTGGTCAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 8 0.21
39 8 0.21
40 22 0.58
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (38 bp):
ATGTTTTCGATTCAGTCACTGGGGGCTTATTTGACCTT
Found at i:5556102 original size:40 final size:40
Alignment explanation
Indices: 5555820--5556102 Score: 328
Period size: 40 Copynumber: 7.1 Consensus size: 40
5555810 CGGAATTTAA
** *
5555820 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5555860 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
5555900 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5555940 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5555979 CCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5556018 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
5556058 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5556098 CCGGA
1 CCGGA
5556103 CATCATTCAA
Statistics
Matches: 218, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 72 0.33
40 132 0.61
41 12 0.06
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5558555 original size:16 final size:17
Alignment explanation
Indices: 5558534--5558583 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
5558524 AGCTTATTTC
5558534 ATTAAATAATA-AAAAA
1 ATTAAATAATATAAAAA
*
5558550 ATTAAA-AATATAATAA
1 ATTAAATAATATAAAAA
* *
5558566 ATCAAATACATTTAAAAA
1 ATTAAATA-ATATAAAAA
5558584 CATAAAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 1 0.04
18 7 0.26
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTAAATAATATAAAAA
Found at i:5565547 original size:29 final size:30
Alignment explanation
Indices: 5565510--5565568 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
5565500 TTGGTTTTAG
*
5565510 TGTGTAATTATATACAT-AAACTTTAATTT
1 TGTGCAATTATATACATCAAACTTTAATTT
* *
5565539 TGTGCAATTTTATACATCAAATTTTAATTT
1 TGTGCAATTATATACATCAAACTTTAATTT
5565569 GATCTAACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (30 bp):
TGTGCAATTATATACATCAAACTTTAATTT
Found at i:5565609 original size:21 final size:21
Alignment explanation
Indices: 5565580--5565620 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5565570 ATCTAACTCT
*
5565580 CACAAATCTGGTTAAAAAAAA
1 CACAAATCTAGTTAAAAAAAA
* *
5565601 CACATATCTAGTTAAGAAAA
1 CACAAATCTAGTTAAAAAAA
5565621 TATGGGTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (21 bp):
CACAAATCTAGTTAAAAAAAA
Found at i:5565707 original size:17 final size:17
Alignment explanation
Indices: 5565687--5565747 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5565677 TGAAAGAGTA
5565687 TTTGTACTATATATTAG
1 TTTGTACTATATATTAG
* * * *
5565704 TTTGTATTTTGAAGGAGTTAA
1 TTTGTACTAT--A-TA-TTAG
5565725 TTTGTACTATATATTAG
1 TTTGTACTATATATTAG
5565742 TTTGTA
1 TTTGTA
5565748 TTCCCGTGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 17 0.53
18 1 0.03
19 2 0.06
20 1 0.03
21 11 0.34
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (17 bp):
TTTGTACTATATATTAG
Found at i:5565762 original size:43 final size:38
Alignment explanation
Indices: 5565674--5565749 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
5565664 ATTTTTATTG
*
5565674 TTTTGAAAGAG-T-ATTTGTACTATATATTAGTTTGTA
1 TTTTGAAGGAGTTAATTTGTACTATATATTAGTTTGTA
5565710 TTTTGAAGGAGTTAATTTGTACTATATATTAGTTTGTA
1 TTTTGAAGGAGTTAATTTGTACTATATATTAGTTTGTA
5565748 TT
1 TT
5565750 CCCGTGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 10 0.27
37 1 0.03
38 26 0.70
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (38 bp):
TTTTGAAGGAGTTAATTTGTACTATATATTAGTTTGTA
Found at i:5568443 original size:22 final size:22
Alignment explanation
Indices: 5568415--5568536 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
5568405 TTCCACATCC
5568415 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
5568437 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
5568461 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
5568484 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
5568508 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
5568531 ATCACA
1 ATCACA
5568537 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:5568612 original size:49 final size:47
Alignment explanation
Indices: 5568387--5569034 Score: 912
Period size: 47 Copynumber: 13.6 Consensus size: 47
5568377 CCCTTCGGGA
* * *
5568387 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
5568434 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5568481 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
5568528 CTTATCACACATACACA-TGTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
*
5568575 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
5568624 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCTATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5568671 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
5568718 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
5568767 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5568814 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
5568861 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
5568910 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
5568959 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
5569008 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
5569035 TATTCAAATA
Statistics
Matches: 555, Mismatches: 34, Indels: 24
0.91 0.06 0.04
Matches are distributed among these distances:
46 3 0.01
47 327 0.59
49 222 0.40
50 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:5568643 original size:143 final size:143
Alignment explanation
Indices: 5568408--5569034 Score: 1050
Period size: 143 Copynumber: 4.4 Consensus size: 143
5568398 TATACACTTC
*
5568408 CACATCCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACATTG
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
5568471 GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
5568536 ACATACACATGTT
131 ACATACACATGTT
*
5568549 CACATTCATCACATTGGTCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
* *
5568614 GTCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCTATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
5568679 ACATACACATGTT
131 ACATACACATGTT
5568692 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
5568757 GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
66 GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
5568822 ACATACACATGTT
131 ACATACACATGTT
*
5568835 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATCG
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
* * * *
5568900 GCCATTAGGCCTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTAGGCCTTAT
66 GCCATTCGGCCTTATCTC--ATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGCCTTAT
* *
5568964 CACATATATATACACT-TT
128 CAC--ACATACACA-TGTT
*
5568982 CACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATT
5569035 TATTCAAATA
Statistics
Matches: 463, Mismatches: 15, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
141 32 0.07
143 325 0.70
145 62 0.13
146 1 0.00
147 42 0.09
148 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.34
Consensus pattern (143 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACATTG
GCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCAC
ACATACACATGTT
Found at i:5568937 original size:40 final size:42
Alignment explanation
Indices: 5568892--5569033 Score: 130
Period size: 49 Copynumber: 3.1 Consensus size: 42
5568882 TTCACATTCA
5568892 TCACAT-C-GGCCATTAGGCCTTATCACATATATATACACTT
1 TCACATACTGGCCATTAGGCCTTATCACATATATATACACTT
5568932 TCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTT
1 T--CA--CAT-AC--TGGCCATTAGGCCTTATCACATATATATACACTT
5568981 TCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACACTT
1 T--CA--CAT-AC--TGGCCATTAGGCCTTATCACATATATATACACTT
5569028 TCACAT
1 TCACAT
5569034 TTATTCAAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 15
0.86 0.00 0.14
Matches are distributed among these distances:
40 1 0.01
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 1 0.01
47 13 0.14
49 68 0.73
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.34
Consensus pattern (42 bp):
TCACATACTGGCCATTAGGCCTTATCACATATATATACACTT
Found at i:5571580 original size:16 final size:15
Alignment explanation
Indices: 5571554--5571588 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5571544 TGATGTGAAT
5571554 AATATAAAATATTAA
1 AATATAAAATATTAA
*
5571569 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
5571585 AATA
1 AATA
5571589 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:5571776 original size:20 final size:21
Alignment explanation
Indices: 5571734--5571776 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
5571724 CTTTTTTTAG
* *
5571734 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
5571755 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
5571775 AA
1 AA
5571777 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:5572463 original size:11 final size:11
Alignment explanation
Indices: 5572447--5572471 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5572437 GTTTTGTATA
5572447 TATATTTTTAT
1 TATATTTTTAT
5572458 TATATTTTTAT
1 TATATTTTTAT
5572469 TAT
1 TAT
5572472 GATGTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:5572825 original size:18 final size:18
Alignment explanation
Indices: 5572802--5572848 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5572792 TAGGTTTTTC
*
5572802 TTTTTTTTTGGTGTTAGG
1 TTTTTTTTTGGAGTTAGG
**
5572820 TTTTTTTGGGGAGTTAGG
1 TTTTTTTTTGGAGTTAGG
5572838 TTTTTTTTTGG
1 TTTTTTTTTGG
5572849 GAGGCTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.06, C:0.00, G:0.30, T:0.64
Consensus pattern (18 bp):
TTTTTTTTTGGAGTTAGG
Found at i:5572850 original size:19 final size:19
Alignment explanation
Indices: 5572802--5572851 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
5572792 TAGGTTTTTC
*
5572802 TTTTTTTTT-GGTGTTAGG
1 TTTTTTTTTGGGAGTTAGG
*
5572820 -TTTTTTTGGGGAGTTAGG
1 TTTTTTTTTGGGAGTTAGG
5572838 TTTTTTTTTGGGAG
1 TTTTTTTTTGGGAG
5572852 GCTTAATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 12 0.44
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.60
Consensus pattern (19 bp):
TTTTTTTTTGGGAGTTAGG
Found at i:5573710 original size:78 final size:75
Alignment explanation
Indices: 5573584--5573836 Score: 251
Period size: 77 Copynumber: 3.3 Consensus size: 75
5573574 GAAACTTAAC
* ** *
5573584 TTGAAAAGCAGATTTTGAAAATACCT-CGATATGTGACTCAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCCG-TGTGTGACTCAAGGCTCAACTCACCTCTCGCAATA
5573648 TGAGTTGATTT
65 TGAGTTGATTT
* * *
5573659 TTGAAAAATATAAATTGAAAAAAATACCTCCGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCA
1 TTGAAAAACAGAAATTG---AAAATACCTCCGTGTGTGA-CTCAAGGCTCAACTCACCTCTCGCA
5573723 ATATGAGTTGATTTTT
62 ATATGAGTTGA--TTT
* ** * * *
5573739 TTGAAAGACAGAAATTGAAAATAGTTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCCGTGTGTGA-CTCAAGGCTCAACTCACCTCTCGCAATA
*
5573803 TGAGTCGATTTTT
65 TGAGTTGA--TTT
**
5573816 TTGAAAGGCAGAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
5573837 ATGGAAATTG
Statistics
Matches: 151, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
75 12 0.08
76 2 0.01
77 69 0.46
78 45 0.30
79 6 0.04
80 17 0.11
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAATACCTCCGTGTGTGACTCAAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTT
Found at i:5573806 original size:77 final size:78
Alignment explanation
Indices: 5573616--5573836 Score: 272
Period size: 77 Copynumber: 2.9 Consensus size: 78
5573606 ACCTCGATAT
* * *
5573616 GTGA-CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAAATTGAA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG--
* * *
5573678 AAAAATACCTCCGTGT
64 -AAAATACCTCAGCGC
* *
5573694 GTGATCTGAA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
**
5573758 AATAGTTCAGCGC
66 AATACCTCAGCGC
* *
5573771 GTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTTTGAAAGGCAGAAATTGAA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
5573835 AA
66 AA
5573837 ATGGAAATTG
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
76 2 0.02
77 69 0.55
78 34 0.27
79 4 0.03
80 17 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (78 bp):
GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
AATACCTCAGCGC
Found at i:5573962 original size:73 final size:75
Alignment explanation
Indices: 5573840--5574000 Score: 220
Period size: 73 Copynumber: 2.1 Consensus size: 75
5573830 TTGAAAAATG
* * *
5573840 GAAATTGAAAATACCTCGGCGTATGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGA-TT
1 GAAATTGAAAATACCTCGGCG-ATGACCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTT
5573904 TTTTGACAA-CA
65 TTTTGA-AAGCA
* * *
5573915 GAAATTGAAATTACCTCGGC-ATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTT
1 GAAATTGAAAATACCTCGGCGATGACCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTT
5573979 TTTGAAAGGCA
66 TTTGAAA-GCA
5573990 GAAATTGAAAA
1 GAAATTGAAAA
5574001 ACGAAAATTG
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
73 37 0.49
74 8 0.11
75 31 0.41
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (75 bp):
GAAATTGAAAATACCTCGGCGATGACCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTT
TTTGAAAGCA
Found at i:5573985 original size:164 final size:165
Alignment explanation
Indices: 5573679--5574150 Score: 723
Period size: 164 Copynumber: 2.8 Consensus size: 165
5573669 TAAATTGAAA
* * * * * * *
5573679 AAAATACCTCCGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAC
* ** *
5573744 AGACAGAAATTGAAAATAGTTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAATTACCTC-G-GCGTG-TCCTAAGGCTCAACTCACCTCTCGCAATATGAGT
* *
5573808 CGATTTTTTTGAAAGGCAGAAATTGAAAAATGGAAATTG
127 CGATTTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
*
5573847 AAAATACCTCGGCGTATGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGA-TTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAC
*
5573911 AACAGAAATTGAAATTACCTCGGCATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
66 AACAGAAATTGAAATTACCTCGGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
5573976 TTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
131 TTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
*
5574011 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTGCAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAC
* * *
5574076 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACAGAAATTGAAATTACCTCGGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
5574141 TTTTTTGAAA
131 TTTTTTGAAA
5574151 ATACCTCAGC
Statistics
Matches: 281, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
163 2 0.01
164 124 0.44
165 81 0.29
166 17 0.06
167 9 0.03
168 48 0.17
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (165 bp):
AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATTTTTTTGAC
AACAGAAATTGAAATTACCTCGGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGAT
TTTTTTGAAAGGCAGAAATTGAAAAACGAAAATTG
Found at i:5574069 original size:91 final size:88
Alignment explanation
Indices: 5573916--5574089 Score: 242
Period size: 91 Copynumber: 1.9 Consensus size: 88
5573906 TTGACAACAG
* *
5573916 AAATTGAAATTACCTCGGCATGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTT
1 AAATTGAAAATACCTCGGCATGTCCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTTTT
5573981 TGA-AAGGCAGAAATTGAAAAACGA
66 TGACAA--CAGAAATTGAAAAACGA
* * * * *
5574005 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCGGCATGT--CCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTT
5574070 TTTGACAACAGAAATTGAAA
64 TTTGACAACAGAAATTGAAA
5574090 TTACCTCAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
89 21 0.28
90 12 0.16
91 40 0.53
92 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (88 bp):
AAATTGAAAATACCTCGGCATGTCCTAAGGCTCAACTCACCTCTCGCAATACGAGTCGATTTTTT
TGACAACAGAAATTGAAAAACGA
Found at i:5574130 original size:74 final size:75
Alignment explanation
Indices: 5574005--5574148 Score: 227
Period size: 74 Copynumber: 1.9 Consensus size: 75
5573995 TGAAAAACGA
* * *
5574005 AAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTGCAATACGAGTTGATTTT
1 AAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
5574070 TTTGACAACAG
65 TTTGACAACAG
* *
5574081 AAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT
5574145 TTGA
66 TTGA
5574149 AAATACCTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 42 0.67
76 21 0.33
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (75 bp):
AAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT
TTGACAACAG
Found at i:5574179 original size:61 final size:61
Alignment explanation
Indices: 5574084--5574205 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
5574074 ACAACAGAAA
* *
5574084 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5574145 TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
5574206 GAAACATACG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (61 bp):
TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
Found at i:5574254 original size:137 final size:136
Alignment explanation
Indices: 5574008--5574281 Score: 381
Period size: 137 Copynumber: 2.0 Consensus size: 136
5573998 AAAACGAAAA
* * * * **
5574008 TTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCTCTTGCAATACGAGTTGATTTTTTT
1 TTGAAAATACCTCAGCGCGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGA
* * * *
5574073 GACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
65 AACAACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATT
*
5574138 GATTTTT
130 GAATTTT
*
5574145 TTGAAAATACCTCAGCGCGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
1 TTGAAAATACCTCAGCGCGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGAA
*
5574209 ACATACGAAAAATTGACAA-TACTTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAA
66 ACA-AC-AAAAATTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAA
5574273 TTGAATTTT
128 TTGAATTTT
5574282 GAAATAAAAC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
135 41 0.34
136 2 0.02
137 76 0.63
138 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (136 bp):
TTGAAAATACCTCAGCGCGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTGAA
ACAACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTG
AATTTT
Found at i:5574282 original size:76 final size:76
Alignment explanation
Indices: 5574145--5574285 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 76
5574135 GTTGATTTTT
* * *
5574145 TTGAAAATACCTCAGCGCGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGAATTTTGAAA
5574210 CATACGAAAAA
66 CATACGAAAAA
* * *
5574221 TTGACAATACTTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGAATTTTGAAA
1 TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGAATTTTGAAA
5574286 TAAAACATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (76 bp):
TTGAAAATACCTCAGCGCGTCCCGAGGCTCAACTCACCTCTCGCAATATGAATTGAATTTTGAAA
CATACGAAAAA
Found at i:5584213 original size:16 final size:15
Alignment explanation
Indices: 5584187--5584221 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5584177 TGATGTGAAT
5584187 AATATAAAATATTAA
1 AATATAAAATATTAA
*
5584202 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
5584218 AATA
1 AATA
5584222 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:5584409 original size:20 final size:21
Alignment explanation
Indices: 5584367--5584409 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
5584357 CTTTTTTTAG
* *
5584367 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
5584388 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
5584408 AA
1 AA
5584410 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:5584626 original size:11 final size:11
Alignment explanation
Indices: 5584610--5584639 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5584600 TAACATTAAG
5584610 AATATATATAT
1 AATATATATAT
*
5584621 AATATAAATAT
1 AATATATATAT
5584632 AATATATA
1 AATATATA
5584640 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:5585103 original size:11 final size:12
Alignment explanation
Indices: 5585061--5585112 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
5585051 CCGGAAAAGG
5585061 TATTTTTT-TTA
1 TATTTTTTATTA
*
5585072 TATTTGTTTTGTATA
1 TA-TT-TTTTAT-TA
5585087 TATATTTTTATTA
1 TAT-TTTTTATTA
5585100 TATTTTTTATTA
1 TATTTTTTATTA
5585112 T
1 T
5585113 GATGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 2 0.06
12 12 0.34
13 9 0.26
14 7 0.20
15 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (12 bp):
TATTTTTTATTA
Found at i:5585456 original size:24 final size:25
Alignment explanation
Indices: 5585429--5585480 Score: 88
Period size: 24 Copynumber: 2.1 Consensus size: 25
5585419 TTTTTTGGGG
5585429 GGGTTAGGTTTTTCT-TTTTTTTTT
1 GGGTTAGGTTTTTCTCTTTTTTTTT
*
5585453 GGGTTAGGTTTTTTTCTTTTTTTTT
1 GGGTTAGGTTTTTCTCTTTTTTTTT
5585478 GGG
1 GGG
5585481 GGGGTTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.04, C:0.04, G:0.25, T:0.67
Consensus pattern (25 bp):
GGGTTAGGTTTTTCTCTTTTTTTTT
Found at i:5585486 original size:24 final size:26
Alignment explanation
Indices: 5585417--5585499 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
5585407 GGTTTCTTGG
5585417 TTTTTTTTGGGGGGGTTAGGTTTTTCTT
1 TTTTTTTTGGGGGGGTT--GTTTTTCTT
**
5585445 TTTTTTTTGGGTTAGGTT-TTTTTC-T
1 TTTTTTTTGGG-GGGGTTGTTTTTCTT
*
5585470 TTTTTTTTGGGGGGGTTAGGTTTT-TT
1 TTTTTTTTGGGGGGGTT-GTTTTTCTT
5585496 TTTT
1 TTTT
5585500 GGGAGGCTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
24 4 0.09
25 12 0.26
26 15 0.33
28 11 0.24
29 4 0.09
ACGTcount: A:0.04, C:0.02, G:0.28, T:0.66
Consensus pattern (26 bp):
TTTTTTTTGGGGGGGTTGTTTTTCTT
Found at i:5587433 original size:28 final size:26
Alignment explanation
Indices: 5587385--5587436 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
5587375 TCAATTGCAA
*
5587385 ATATTATTTTTGTAATAATTTTTATG
1 ATATTATTTTTGTAACAATTTTTATG
*
5587411 ATATTAGTTTTTGTTTACAATTTTTA
1 ATATTA-TTTTTG-TAACAATTTTTA
5587437 AAGATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 6 0.27
28 10 0.45
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (26 bp):
ATATTATTTTTGTAACAATTTTTATG
Found at i:5587848 original size:16 final size:14
Alignment explanation
Indices: 5587823--5587870 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
5587813 TTTGTACTTA
5587823 ATAA-TTTAATATT
1 ATAATTTTAATATT
5587836 CATTAATTTTAATATT
1 -A-TAATTTTAATATT
5587852 ATAATTTTAA-ATT
1 ATAATTTTAATATT
*
5587865 TTAATT
1 ATAATT
5587871 CAAAAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 8 0.26
14 10 0.32
15 4 0.13
16 9 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
ATAATTTTAATATT
Found at i:5589656 original size:15 final size:15
Alignment explanation
Indices: 5589616--5589659 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5589606 TATTAAAAAA
* *
5589616 AATGATAGTAATAGT
1 AATGATAATAATATT
5589631 AATGATAATAATATT
1 AATGATAATAATATT
* *
5589646 AATGGTGATAATAT
1 AATGATAATAATAT
5589660 AAATAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (15 bp):
AATGATAATAATATT
Found at i:5589860 original size:12 final size:15
Alignment explanation
Indices: 5589829--5589863 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5589819 ATAATAGTAG
5589829 TAATAGTAATAGAAA
1 TAATAGTAATAGAAA
* *
5589844 TAATAGTAAAAAAAA
1 TAATAGTAATAGAAA
5589859 TAATA
1 TAATA
5589864 CTCACTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAATAGTAATAGAAA
Found at i:5590025 original size:88 final size:88
Alignment explanation
Indices: 5589864--5590663 Score: 827
Period size: 88 Copynumber: 9.0 Consensus size: 88
5589854 AAAAATAATA
* * * * * * * * * *
5589864 CTCACTGTCTTCGATCTGTTCCCCTACTGTTTAGGGTGATAGGATCTGTAATCTCCAGACTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
*
5589929 CCCTACTGCTTAGGGAGTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* * * * ** **
5589952 CTAACCGTATTTGATCTACTCCACTATTGCTTAGGGAGGTAAGATCTAAAATTTCCAGCCTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
5590017 CCCTACTGCTTA-GGGGTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* ** * * ** * * *
5590039 CTTACTATCTTCGATCTACTCTGCTACTACTTGGGGAGACAAGATCTGTAATTTCTAGCCTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
*
5590104 CCCTACTACTTAGGGGGTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* * ** * * * * * *
5590127 CTCACCTTCTTCGATCTTTTCCCCTACTGCTTAGAGTGATAAGATCTATAATCTT-CAGCCTATT
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAAT-TTCCAGCCTGTT
*
5590191 ACCCTACTACTTAGGGGGTTAAGG
65 ACCCTACTGCTTAGGGGGTTAAGG
* * *
5590215 CTCACCGTCTTTGATCTGCTCTACTACTGCTTAGGGAGACAAGATCGGTAATTTTCAGCCTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
* *
5590280 CCCTACTGCTTAGAGGTTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* ** * * * *
5590303 CTTACTATCTTTGATCTGCTCCACTATTGCTTAGGGAGATAAGATCTGAAATTTCCAGCCTATTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
* *
5590368 TCCTACTACTTAGGGGGTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* * * **
5590391 CTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCGGTAATTT-TTGCCTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
5590455 CCCTACTACTTACTGCTTAGGGGGTTAAGG
66 --C--C--C-TACTGCTTAGGGGGTTAAGG
* * * * * **
5590485 CTCACCGTCTTCGATCTGTTCCACTACTACTTAGGGAGGCAAGATCGGTAATTTTTAGCCTGTTA
1 CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
5590550 CCCTACTGCTTAGGGGGTTAAGG
66 CCCTACTGCTTAGGGGGTTAAGG
* * * *
5590573 CTAACCGT-TTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGATCTGTAATCTTTCAGCCTG-
1 CTCACCGTCTTT-GATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAAT-TTCCAGCCTGT
*
5590636 TACCCTACTGCTTAGGGGGTAAAGG
64 TACCCTACTGCTTAGGGGGTTAAGG
5590661 CTC
1 CTC
5590664 GTGAATTCAC
Statistics
Matches: 594, Mismatches: 105, Indels: 26
0.82 0.14 0.04
Matches are distributed among these distances:
87 81 0.14
88 417 0.70
89 12 0.02
91 2 0.00
93 2 0.00
94 71 0.12
95 9 0.02
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (88 bp):
CTCACCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAGCCTGTTA
CCCTACTGCTTAGGGGGTTAAGG
Found at i:5590152 original size:44 final size:44
Alignment explanation
Indices: 5590101--5590231 Score: 113
Period size: 44 Copynumber: 3.0 Consensus size: 44
5590091 TTCTAGCCTG
* *
5590101 TTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTCGATCTT
1 TTACCCTACTACTTAGGGGGTTAAGGCTCACCATCTTCGATCTA
* * * * * * ** *
5590145 TTCCCCTACTGCTTAGAGTGATAA-GATCTATAATCTTC-AGCCTA
1 TTACCCTACTACTTAGGGGGTTAAGGCTC-ACCATCTTCGA-TCTA
* *
5590189 TTACCCTACTACTTAGGGGGTTAAGGCTCACCGTCTTTGATCT
1 TTACCCTACTACTTAGGGGGTTAAGGCTCACCATCTTCGATCT
5590232 GCTCTACTAC
Statistics
Matches: 61, Mismatches: 22, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
43 4 0.07
44 53 0.87
45 4 0.07
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (44 bp):
TTACCCTACTACTTAGGGGGTTAAGGCTCACCATCTTCGATCTA
Found at i:5590832 original size:64 final size:64
Alignment explanation
Indices: 5590731--5590858 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
5590721 TCATGTATCT
* *
5590731 ATGCTTATGCCAAATAATTAGGATATTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
* * *
5590795 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCCAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
5590859 TTATGAATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATACTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
Found at i:5601816 original size:20 final size:20
Alignment explanation
Indices: 5601791--5601836 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5601781 GTTGGGCCTT
5601791 GCCCATATT-AACACAGTTGG
1 GCCCATATTCAACACAGTT-G
*
5601811 GCCCAT-TTCAATACAGTTG
1 GCCCATATTCAACACAGTTG
5601830 GCCCATA
1 GCCCATA
5601837 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
GCCCATATTCAACACAGTTG
Found at i:5601845 original size:19 final size:20
Alignment explanation
Indices: 5601803--5601846 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5601793 CCATATTAAC
** *
5601803 ACAGTTGGGCCCATTTCAAT
1 ACAGTTGGGCCCATAACAAA
5601823 ACAGTT-GGCCCATAACAAA
1 ACAGTTGGGCCCATAACAAA
5601842 ACAGT
1 ACAGT
5601847 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ACAGTTGGGCCCATAACAAA
Found at i:5604606 original size:34 final size:35
Alignment explanation
Indices: 5604548--5604619 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
5604538 CGTATCCTAG
*
5604548 CTACAGTCTCAGTCTTCTAAAGTTTTCAGT-TTTCC
1 CTACAGTCTCAGTCTTCTAAAG-TTTCAGTATTACC
* *
5604583 CTACTGTCTCAGT-TTCTACAGTTTCAGTATTACC
1 CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
5604617 CTA
1 CTA
5604620 ACTACAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 14 0.42
35 12 0.36
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (35 bp):
CTACAGTCTCAGTCTTCTAAAGTTTCAGTATTACC
Found at i:5609323 original size:15 final size:15
Alignment explanation
Indices: 5609283--5609326 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5609273 ATTATTAAAA
* *
5609283 AATGATAGTAATAGT
1 AATGATAATAATATT
5609298 AATGATAATAATATT
1 AATGATAATAATATT
* *
5609313 AATGGTGATAATAT
1 AATGATAATAATAT
5609327 AAATAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (15 bp):
AATGATAATAATATT
Found at i:5609457 original size:3 final size:3
Alignment explanation
Indices: 5609451--5609801 Score: 117
Period size: 3 Copynumber: 117.7 Consensus size: 3
5609441 AAAAAAAACT
* * * * * *
5609451 ATA ATA ATA TTA AT- ATA ATA GTG ATA AGA ACA GTA -TA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * ** *
5609497 GTA GTA ATA GTA ATA GA-A ATA ATA GTA ACA AAA ATA ATA CCA ATG
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
5609542 GTA ATA ATA ATA ATA ATA ATA CTA ATA ATG ATA GTA GTA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * * * * *
5609587 ATG GTA ATA ATG ATA ATA A-A AAA ATA GTA ATA ATA GT- ATG TTA GATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * * * * * * * *
5609634 ATA GTA GTA AAA AAA ATA ATA GTA AGA ATA ATT ACA AAA ATTG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * * * * * * * *
5609680 GTG ATA ATAA ATA A-A GTG ATA ATA ATA CTT ATG TTA ATA GTA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
5609725 AAA ATA ATA ATA GTA ATA ATA ATA ATGA A-A ATA GTGA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA
5609770 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5609802 GATGATGATG
Statistics
Matches: 245, Mismatches: 87, Indels: 32
0.67 0.24 0.09
Matches are distributed among these distances:
2 14 0.06
3 221 0.90
4 10 0.04
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5609965 original size:29 final size:30
Alignment explanation
Indices: 5609933--5609991 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
5609923 TTTGGTTTAG
5609933 TGTGTAATTATATACAT-AAACTTTAATTT
1 TGTGTAATTATATACATCAAACTTTAATTT
* *
5609962 TGTGTAATTTTATACATCAAATTTTAATTT
1 TGTGTAATTATATACATCAAACTTTAATTT
5609992 GATCTAACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (30 bp):
TGTGTAATTATATACATCAAACTTTAATTT
Found at i:5610130 original size:17 final size:17
Alignment explanation
Indices: 5610110--5610170 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5610100 TGAAATAGTA
5610110 TTTGTACTATATATTAG
1 TTTGTACTATATATTAG
* * * *
5610127 TTTGTATTTTGAAGGAGTTAA
1 TTTGTACTAT--A-TA-TTAG
5610148 TTTGTACTATATATTAG
1 TTTGTACTATATATTAG
5610165 TTTGTA
1 TTTGTA
5610171 TTCCCGTGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 17 0.53
18 1 0.03
19 2 0.06
20 1 0.03
21 11 0.34
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (17 bp):
TTTGTACTATATATTAG
Found at i:5610137 original size:36 final size:38
Alignment explanation
Indices: 5610097--5610172 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
5610087 ATTTTTGTTG
*
5610097 TTTTGAAATAG-T-ATTTGTACTATATATTAGTTTGTA
1 TTTTGAAAGAGTTAATTTGTACTATATATTAGTTTGTA
*
5610133 TTTTGAAGGAGTTAATTTGTACTATATATTAGTTTGTA
1 TTTTGAAAGAGTTAATTTGTACTATATATTAGTTTGTA
5610171 TT
1 TT
5610173 CCCGTGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 9 0.25
37 1 0.03
38 26 0.72
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTGAAAGAGTTAATTTGTACTATATATTAGTTTGTA
Done.