Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 5 of 145
Found at i:1652265 original size:23 final size:23
Alignment explanation
Indices: 1652235--1652281 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1652225 GAGAGAAAGG
1652235 AGAAGAAGAGAAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
*
1652258 AGAAGAAGAGAAGAAGAGGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
1652281 A
1 A
1652282 AGAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAGAAGAAGAAGAAGA
Found at i:1652288 original size:17 final size:15
Alignment explanation
Indices: 1652237--1652289 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 15
1652227 GAGAAAGGAG
1652237 AAGAAGAGAAGAAG-
1 AAGAAGAGAAGAAGA
1652251 AAGAAGAAGAAGAAGA
1 AAGAAG-AGAAGAAGA
1652267 GAAGAAGAGGAAGAAAGA
1 -AAGAAGA-GAAG-AAGA
1652285 AAGAA
1 AAGAA
1652290 AAAATGTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.18
15 8 0.24
16 1 0.03
17 15 0.44
18 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAGAAGAGAAGAAGA
Found at i:1652289 original size:20 final size:19
Alignment explanation
Indices: 1652235--1652289 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1652225 GAGAGAAAGG
1652235 AGAAGAAGAGAAGAAGAAGA
1 AGAAGAAGA-AAGAAGAAGA
1652255 AGAAGAAGAAGAGAAGAAGA
1 AGAAGAAGAA-AGAAGAAGA
*
1652275 GGAAGAAAGAAAGAA
1 AGAAG-AAGAAAGAA
1652290 AAAATGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 26 0.81
21 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AGAAGAAGAAAGAAGAAGA
Found at i:1652448 original size:21 final size:21
Alignment explanation
Indices: 1652423--1652488 Score: 100
Period size: 19 Copynumber: 3.2 Consensus size: 21
1652413 TGGATTAGCA
*
1652423 TTTTGTATTAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1652444 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
1652463 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1652484 ATTTT
1 -TTTT
1652489 ATAATTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 19 0.46
21 18 0.44
22 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:1656561 original size:22 final size:21
Alignment explanation
Indices: 1656535--1656579 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1656525 CAAAAAAAAT
*
1656535 AAGAAGGAAGGAAGCAGAAGAA
1 AAGAAGGAAGGAA-AAGAAGAA
*
1656557 AAGAATGAAGGAAAAGAAGAA
1 AAGAAGGAAGGAAAAGAAGAA
1656578 AA
1 AA
1656580 AAATAAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.64, C:0.02, G:0.31, T:0.02
Consensus pattern (21 bp):
AAGAAGGAAGGAAAAGAAGAA
Found at i:1656580 original size:22 final size:22
Alignment explanation
Indices: 1656535--1656587 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1656525 CAAAAAAAAT
* *
1656535 AAGAAGGAAGGAAGCAGAAGAA
1 AAGAATGAAGGAAGAAGAAGAA
1656557 AAGAATGAAGGAA-AAGAAGAA
1 AAGAATGAAGGAAGAAGAAGAA
*
1656578 AAAAAT-AAGG
1 AAGAATGAAGG
1656588 TATTTTGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 12 0.43
22 12 0.43
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (22 bp):
AAGAATGAAGGAAGAAGAAGAA
Found at i:1658914 original size:27 final size:26
Alignment explanation
Indices: 1658875--1658937 Score: 108
Period size: 27 Copynumber: 2.4 Consensus size: 26
1658865 AAATTGTAAA
1658875 ATAAAAAAAATTATAATTTTATTTAC
1 ATAAAAAAAATTATAATTTTATTTAC
*
1658901 ATAAAAAACCATTATAATTTTATTTAC
1 ATAAAAAA-AATTATAATTTTATTTAC
1658928 ATAAAAAAAA
1 ATAAAAAAAA
1658938 ATAAGAACTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAAAAAAAATTATAATTTTATTTAC
Found at i:1659310 original size:6 final size:6
Alignment explanation
Indices: 1659280--1659332 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
1659270 AGAATGTGGT
* * * * *
1659280 TCTGTC TCTGGC ACTGGC ACTGGC TCTGGC TTTGGC TCTGGC TCTGGT
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1659328 TCTGG
1 TCTGG
1659333 TGCATAATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.04, C:0.28, G:0.32, T:0.36
Consensus pattern (6 bp):
TCTGGC
Found at i:1661064 original size:39 final size:38
Alignment explanation
Indices: 1661021--1661099 Score: 140
Period size: 39 Copynumber: 2.1 Consensus size: 38
1661011 AAAAAGTCAG
1661021 TTATAATTAAACTTTTAATAAAATGATTTTTAAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTT-AATTTTT
*
1661060 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1661098 TT
1 TT
1661100 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 9 0.23
39 30 0.77
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:1661547 original size:19 final size:19
Alignment explanation
Indices: 1661523--1661563 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1661513 TTTTTTCGGG
*
1661523 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
1661542 TTTAGGATTATGTTATAAA
1 TTTAGGATTATGTTATAAA
1661561 TTT
1 TTT
1661564 TTGTGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:1661716 original size:8 final size:8
Alignment explanation
Indices: 1661703--1661793 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
1661693 CATACAAAAA
1661703 ATTACAAT
1 ATTACAAT
1661711 ATTACAAT
1 ATTACAAT
* * *
1661719 ATATCCCGAC
1 AT-T-ACAAT
1661729 ATTACAAT
1 ATTACAAT
*
1661737 ATTCATACAAA
1 A-T--TACAAT
*
1661748 ATTATAAT
1 ATTACAAT
1661756 ATTACAAT
1 ATTACAAT
*
1661764 ATTTATACAAA
1 A--T-TACAAT
1661775 ATTACAAT
1 ATTACAAT
1661783 ATTACAAT
1 ATTACAAT
1661791 ATT
1 ATT
1661794 CACACAAAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
8 41 0.65
9 4 0.06
10 6 0.10
11 12 0.19
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.36
Consensus pattern (8 bp):
ATTACAAT
Found at i:1661765 original size:27 final size:26
Alignment explanation
Indices: 1661729--1661872 Score: 162
Period size: 27 Copynumber: 5.8 Consensus size: 26
1661719 ATATCCCGAC
1661729 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
1661756 ATTACAATATTTATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTA-AAT
*
1661783 ATTACAATATTCACAC-AAA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
* *
1661805 ATTGCAAAATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTA-AAT
1661832 ATTACAATATTCATAC--AA--AAA-
1 ATTACAATATTCATACAAAATTAAAT
1661853 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
1661873 AACTAATCCA
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.16
22 15 0.15
23 8 0.08
24 1 0.01
25 3 0.03
26 5 0.05
27 53 0.52
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATTAAAT
Found at i:1661800 original size:19 final size:19
Alignment explanation
Indices: 1661706--1661800 Score: 51
Period size: 19 Copynumber: 5.2 Consensus size: 19
1661696 ACAAAAAATT
1661706 ACAATATTACAATATATC-C
1 ACAATATTACAATAT-TCAC
* * *
1661725 -CGACATTACAATATTCAT
1 ACAATATTACAATATTCAC
* *
1661743 ACAAAATTATAATATT-AC
1 ACAATATTACAATATTCAC
* *
1661761 A-ATATTTATACAAAATT---
1 ACA-ATAT-TACAATATTCAC
1661778 ACAATATTACAATATTCAC
1 ACAATATTACAATATTCAC
1661797 ACAA
1 ACAA
1661801 AAAAATTGCA
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
16 8 0.15
17 7 0.13
18 17 0.31
19 23 0.42
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (19 bp):
ACAATATTACAATATTCAC
Found at i:1661833 original size:76 final size:73
Alignment explanation
Indices: 1661682--1661863 Score: 242
Period size: 76 Copynumber: 2.4 Consensus size: 73
1661672 TTATAAAATA
* * *
1661682 ATTACAATATTCATACAAAAAATTACAATATTACAATATATCCCGACATTACAATATTCATACAA
1 ATTACAATATTCATAC-AAAAATTACAATATTACAATATATCCCAAAATTACAAAATTCATACAA
1661747 AATTATAAT
65 AATTATAAT
* *
1661756 ATTACAATATTTATAC-AAAATTACAATATTACAATAT-TCACACAAAAAAATTGCAAAATTCAT
1 ATTACAATATTCATACAAAAATTACAATATTACAATATATC-C-C---AAAATTACAAAATTCAT
1661819 ACAAAATTATAAT
61 ACAAAATTATAAT
1661832 ATTACAATATTCATACAAAAAATTACAATATT
1 ATTACAATATTCATAC-AAAAATTACAATATT
1661864 CATACAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
71 2 0.02
72 22 0.23
73 1 0.01
74 15 0.16
76 41 0.43
78 14 0.15
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.32
Consensus pattern (73 bp):
ATTACAATATTCATACAAAAATTACAATATTACAATATATCCCAAAATTACAAAATTCATACAAA
ATTATAAT
Found at i:1661836 original size:49 final size:48
Alignment explanation
Indices: 1661756--1661872 Score: 171
Period size: 49 Copynumber: 2.4 Consensus size: 48
1661746 AAATTATAAT
* *
1661756 ATTACAATATTTATACAAAATTACAATATTACAATATTCACACAAAAAA
1 ATTACAAAATTCATACAAAATTACAATATTACAATATTCACAC-AAAAA
* * *
1661805 ATTGCAAAATTCATACAAAATTATAATATTACAATATTCATACAAAAA
1 ATTACAAAATTCATACAAAATTACAATATTACAATATTCACACAAAAA
*
1661853 ATTACAATATTCATACAAAA
1 ATTACAAAATTCATACAAAA
1661873 AACTAATCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
48 23 0.38
49 38 0.62
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (48 bp):
ATTACAAAATTCATACAAAATTACAATATTACAATATTCACACAAAAA
Found at i:1661858 original size:21 final size:22
Alignment explanation
Indices: 1661832--1661874 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
1661822 AAATTATAAT
1661832 ATTACAATATTCATAC-AAAAA
1 ATTACAATATTCATACAAAAAA
1661853 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATACAAAAAA
1661875 CTAATCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (22 bp):
ATTACAATATTCATACAAAAAA
Found at i:1664318 original size:60 final size:60
Alignment explanation
Indices: 1664191--1664319 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 60
1664181 TTTTGGTGCA
* * *
1664191 TGAACTTAGCTTTAAGGTTCAAATTGGTATCTAATATTTTTTTTTGGTTCAATTAAGTACT
1 TGAACTT-GCTTTAAGGTTCAAATTGGTATCTAATAATTTATTTTGGTCCAATTAAGTACT
* * *
1664252 TAAACTTGCCTTTAGGGTTCAATTTGGTA-CTTAA-AATTTATTTTGGTCCAATT-AGATACT
1 TGAACTTG-CTTTAAGGTTCAAATTGGTATC-TAATAATTTATTTTGGTCCAATTAAG-TACT
1664312 TGAACTTG
1 TGAACTTG
1664320 GCTTCTTAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
59 2 0.03
60 29 0.50
61 27 0.47
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (60 bp):
TGAACTTGCTTTAAGGTTCAAATTGGTATCTAATAATTTATTTTGGTCCAATTAAGTACT
Found at i:1671912 original size:22 final size:22
Alignment explanation
Indices: 1671886--1671938 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1671876 TAACATGACT
1671886 TTAAATAAAATATTAAATTCAA
1 TTAAATAAAATATTAAATTCAA
* * * *
1671908 TTAAACAGATTATTAAATTTAA
1 TTAAATAAAATATTAAATTCAA
1671930 --AAATAAAAT
1 TTAAATAAAAT
1671939 GAAATAGTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 6 0.25
22 18 0.75
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAATAAAATATTAAATTCAA
Found at i:1672028 original size:15 final size:15
Alignment explanation
Indices: 1671981--1672029 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1671971 ACCAAATTAC
*
1671981 AAAAAATTTAAATATA
1 AAAAAATTGAAA-ATA
* **
1671997 AAAAAATAGAATCTA
1 AAAAAATTGAAAATA
1672012 AAAAAATTGAAAATA
1 AAAAAATTGAAAATA
1672027 AAA
1 AAA
1672030 GCAAAATCAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (15 bp):
AAAAAATTGAAAATA
Found at i:1673173 original size:16 final size:15
Alignment explanation
Indices: 1673134--1673176 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1673124 AAAGTGCAGG
1673134 GATTAAAATATTAAC
1 GATTAAAATATTAAC
** *
1673149 TTTTCAAATATATAAC
1 GATTAAAATAT-TAAC
1673165 GATTAAAATATT
1 GATTAAAATATT
1673177 CCTTTTAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (15 bp):
GATTAAAATATTAAC
Found at i:1674061 original size:16 final size:16
Alignment explanation
Indices: 1674040--1674073 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1674030 TGCAAACCGT
* *
1674040 TTATTTTTATTTTTTA
1 TTATTTTCATTTTCTA
1674056 TTATTTTCATTTTCTA
1 TTATTTTCATTTTCTA
1674072 TT
1 TT
1674074 CTTTCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCATTTTCTA
Found at i:1675201 original size:27 final size:27
Alignment explanation
Indices: 1674909--1675224 Score: 388
Period size: 27 Copynumber: 11.7 Consensus size: 27
1674899 CCCCAAACTA
*
1674909 TTATAAAATAACTGTTATG-CCCTCATG
1 TTATAAAATGACTGTTATGCCCCT-ATG
** * *
1674936 TGGTAAAATAACTATTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* *
1674963 TTATAAAATAACGGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* *
1674990 TTATAAAATTACAGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
* * *
1675017 TTATAAAATAACTATTATGCCCTTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1675044 TTATAAAATGACTGTTATG-CCCTCACG
1 TTATAAAATGACTGTTATGCCCCT-ATG
** *
1675071 TGGTAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1675098 TTATAAAATGACGGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
1675125 TTATAAAATGACTGTTATGCCCCTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1675152 TTATAAAATGACTGTTATGCCCTTATG
1 TTATAAAATGACTGTTATGCCCCTATG
*
1675179 TTATAAAATAACTGTTATG-CCCTCATG
1 TTATAAAATGACTGTTATGCCCCT-ATG
**
1675206 TGGTAAAATGACTG-TATGC
1 TTATAAAATGACTGTTATGC
1675225 TTAATGCTAT
Statistics
Matches: 252, Mismatches: 32, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
26 10 0.04
27 234 0.93
28 8 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (27 bp):
TTATAAAATGACTGTTATGCCCCTATG
Found at i:1675552 original size:34 final size:32
Alignment explanation
Indices: 1675504--1675566 Score: 99
Period size: 34 Copynumber: 1.9 Consensus size: 32
1675494 TTATTGTCAC
1675504 TGTAATGGGATAAGGCCCACACTGATACTGATAT
1 TGTAATGGGATAAGGCCCA-ACTGA-ACTGATAT
*
1675538 TGTAATGGGCTAAGGCCCAACTGAACTGA
1 TGTAATGGGATAAGGCCCAACTGAACTGA
1675567 ACTGTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 5 0.18
33 5 0.18
34 18 0.64
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (32 bp):
TGTAATGGGATAAGGCCCAACTGAACTGATAT
Found at i:1679322 original size:22 final size:21
Alignment explanation
Indices: 1679283--1679323 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1679273 AATTTTAAAA
*
1679283 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAATTTTTTT
*
1679304 TATTTTTAAAATAAATTTTT
1 TATTTTTAAAATAATTTTTT
1679324 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTT
Found at i:1684045 original size:3 final size:3
Alignment explanation
Indices: 1684037--1684128 Score: 80
Period size: 3 Copynumber: 30.3 Consensus size: 3
1684027 CAATAACATA
** *
1684037 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TGT ACT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * *
1684086 GCCAT CAT AAT ATT AA- CAT AA- AAT AAT AAT AAT AAT AAT AAT A
1 --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1684129 TGTGTGATAC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
2 3 0.04
3 67 0.92
4 1 0.01
5 2 0.03
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1697022 original size:44 final size:44
Alignment explanation
Indices: 1696972--1697056 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
1696962 TCTTTACGAT
1696972 TTATCATAATTAATAGATTAAACATTGAAATTCAAATCACTGAC
1 TTATCATAATTAATAGATTAAACATTGAAATTCAAATCACTGAC
1697016 TTATCATAATTAATAGATTAAACATTGAAATTCAAATCACT
1 TTATCATAATTAATAGATTAAACATTGAAATTCAAATCACT
1697057 ATCGTATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (44 bp):
TTATCATAATTAATAGATTAAACATTGAAATTCAAATCACTGAC
Found at i:1697608 original size:16 final size:17
Alignment explanation
Indices: 1697571--1697609 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1697561 GATAAAAATT
1697571 TAATTTTATTATTTTAA
1 TAATTTTATTATTTTAA
*
1697588 T-ATTTTA-TATTTTTA
1 TAATTTTATTATTTTAA
1697603 TAATTTT
1 TAATTTT
1697610 TACTTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTTTATTATTTTAA
Found at i:1704577 original size:39 final size:39
Alignment explanation
Indices: 1704522--1704598 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1704512 TTTATTTTTA
*
1704522 AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATT
1 AAAAAAGTATTGTAAAAATATTTTAAAA-TTAAAAAAATT
*
1704562 AAAAAAGTA-TGTAAAAATATTTTTAAATTAAAAAAAT
1 AAAAAAGTATTGTAAAAATATTTTAAAATTAAAAAAAT
1704599 AAATATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 10 0.29
39 16 0.46
40 9 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (39 bp):
AAAAAAGTATTGTAAAAATATTTTAAAATTAAAAAAATT
Found at i:1704586 original size:40 final size:38
Alignment explanation
Indices: 1704522--1704598 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 38
1704512 TTTATTTTTA
*
1704522 AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATT
1 AAAAAAGTATTGTAAAAATATTTT-AAA-TTAAAAAAATT
1704562 AAAAAAGTA-TGTAAAAATATTTTTAAATTAAAAAAAT
1 AAAAAAGTATTGTAAAAATA-TTTTAAATTAAAAAAAT
1704599 AAATATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 10 0.29
39 12 0.34
40 13 0.37
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (38 bp):
AAAAAAGTATTGTAAAAATATTTTAAATTAAAAAAATT
Found at i:1706990 original size:76 final size:76
Alignment explanation
Indices: 1706909--1707332 Score: 356
Period size: 76 Copynumber: 5.6 Consensus size: 76
1706899 TACGGTCCAC
* * * * * * * *
1706909 TGATTTAATATCGTGACTTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
*
1706974 TTATAATCTGT
66 TTATGATCTGT
* * * * * *
1706985 TGATTTAAGATCGAGACCATCCGTTTTCTAACAGTTTGC-TGATTTAATATCGTAACTGTCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
* *
1707049 TTACGATCCGCT
66 TTATGATCTG-T
* * * *
1707061 T-ATCTAAGATCGCAACCTTCAGTTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTAACATT
1 TGATTTAAGATCGCGACCTTCAG-TTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATT
* *
1707125 TTTATGGT-TCGC
65 TTTATGATCT-GT
* * * * *
1707137 TGATTTAAGATCGTGACCTTCGGTTTTCTAACAATTTGCTTGATTTAATCTTGCGACTATCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
* * *
1707202 TTACGATCCGC
66 TTATGATCTGT
* * * * * * **
1707213 TAATTTAATATCGCAACCTTCAATTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTATCATTT
1 TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
*
1707278 TTATG-GCTTGT
66 TTATGATC-TGT
* * * * *
1707289 TGATTTAATAGCACAACCTT-TGATTTTCTAACAGTTTGC-TGATT
1 TGATTTAAGATCGCGACCTTCAG-TTTTCTAACAGTTTGCTTGATT
1707333 CACGATCACG
Statistics
Matches: 280, Mismatches: 60, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
75 52 0.19
76 185 0.66
77 43 0.15
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (76 bp):
TGATTTAAGATCGCGACCTTCAGTTTTCTAACAGTTTGCTTGATTTAATCTCGTGACTATCATTT
TTATGATCTGT
Found at i:1707308 original size:152 final size:149
Alignment explanation
Indices: 1706861--1707355 Score: 513
Period size: 152 Copynumber: 3.3 Consensus size: 149
1706851 TCATTTAAGA
* * * * * * * **
1706861 TAACAGTTTACTTGATTTAATATCGCGATTATCCTCTTTACGGTCCACTGATTTAATATCGTGAC
1 TAACAGTTTGC-TGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
* * * * **
1706926 TTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATTTTTATAATCTGTTGATTT
65 CTTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGT-TGTTGATTT
* *
1706991 AAGATCGAGACCATCCGTTTTC
129 AAGATC-AGACCTTCGGTTTTC
** * * * *
1707013 TAACAGTTTGCTGATTTAATATCGTAACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACC
1 TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAACC
* * * * *
1707078 TTCAGTTTTTCTAACAGTTTGCTTGATTTAATCTTGTGACTAACATTTTTATGGTTCGCTGATTT
66 TTCA-ATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGTT-GTTGATTT
*
1707143 AAGATCGTGACCTTCGGTTTTC
129 AAGATC-AGACCTTCGGTTTTC
* * *
1707165 TAACAATTTGCTTGATTTAATCTTGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
1 TAACAGTTTGC-TGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAAC
* **
1707230 CTTCAATTTTCTAATAGTTCGCTTGATTTAATCTCGCAACTATCATTTTTATGGCTTGTTGATTT
65 CTTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGG-TTGTTGATTT
* * * * *
1707295 AATAGCACAACCTTTGATTTTC
129 AAGATCA-GACCTTCGGTTTTC
* ** *
1707317 TAACAGTTTGCTGATTCACGATCACGACTATCATTTTTA
1 TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTA
1707356 AAGCTCGCTA
Statistics
Matches: 280, Mismatches: 58, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
151 67 0.24
152 161 0.57
153 52 0.19
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (149 bp):
TAACAGTTTGCTGATTTAATATCGCGACTATCATTTTTACGATCCGCTAATTTAATATCGCAACC
TTCAATTTTCTAACAGTTCGCTTGATTTAATCTCGTGACTATCATTTTTATGGTTGTTGATTTAA
GATCAGACCTTCGGTTTTC
Found at i:1707318 original size:228 final size:227
Alignment explanation
Indices: 1706908--1707332 Score: 489
Period size: 228 Copynumber: 1.9 Consensus size: 227
1706898 TTACGGTCCA
* * * * *
1706908 CTGATTTAATATCGTGACTTTCAATTTTTTAACAATTCGCTTGATTTAATCTCGTGACTGTCATT
1 CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
* * * * ** * *
1706973 TTTATAATCTGTTGATTTAAGATCGAGACCATCCGTTTTCTAACAGTTTGCTGATTTAATATCGT
66 TTTACAATCCGCTAATTTAAGATCGAGACCATCAATTTTCTAACAGTTCGCTGATTTAATATCGC
* * * *
1707038 AACTGTCATTTTTACGATCCGCTTATCTAAGATCGCAACCTTCAGTTTTTCTAACAGTTTGCTTG
131 AACTATCATTTTTACGATCCGCTTATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTGC-TG
1707103 ATTTAATCTTGTGACTAACATTTTTATGGTTCG
195 ATTTAATCTTGTGACTAACATTTTTATGGTTCG
** * *
1707136 CTGATTTAAGATCGTGACCTTCGGTTTTCTAACAATTTGCTTGATTTAATCTTGCGACTATCATT
1 CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
* * * * *
1707201 TTTACGATCCGCTAATTTAATATCGCA-ACCTTCAATTTTCTAATAGTTCGCTTGATTTAATCTC
66 TTTACAATCCGCTAATTTAAGATCG-AGACCATCAATTTTCTAACAGTTCGC-TGATTTAATATC
* * * * * *
1707265 GCAACTATCATTTTTATG-GCTTG-TTGATTTAATAGCACAACCTT-TGATTTTCTAACAGTTTG
129 GCAACTATCATTTTTACGATC-CGCTT-ATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTG
1707327 CTGATT
192 CTGATT
1707333 CACGATCACG
Statistics
Matches: 161, Mismatches: 32, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
227 5 0.03
228 114 0.71
229 42 0.26
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (227 bp):
CTGATTTAAGATCGTGACCTTCAATTTTCTAACAATTCGCTTGATTTAATCTCGCGACTATCATT
TTTACAATCCGCTAATTTAAGATCGAGACCATCAATTTTCTAACAGTTCGCTGATTTAATATCGC
AACTATCATTTTTACGATCCGCTTATCTAAGAGCACAACCTTCAGATTTTCTAACAGTTTGCTGA
TTTAATCTTGTGACTAACATTTTTATGGTTCG
Found at i:1707741 original size:18 final size:19
Alignment explanation
Indices: 1707715--1707752 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1707705 CTCTCTTTGT
* *
1707715 TTTTGAAATTTTAAA-ATA
1 TTTTAAAATTATAAATATA
1707733 TTTTAAAATTATAAATATA
1 TTTTAAAATTATAAATATA
1707752 T
1 T
1707753 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTTAAAATTATAAATATA
Found at i:1707754 original size:2 final size:2
Alignment explanation
Indices: 1707742--1707775 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1707732 ATTTTAAAAT
* *
1707742 TA TA AA TA TA TA TA TA TA TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1707776 CCTCATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1710193 original size:13 final size:13
Alignment explanation
Indices: 1710159--1710200 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1710149 AAAGTCAAAT
*
1710159 TAAATAA-AAAAT
1 TAAATAATAAAAA
1710171 TAAAATTAATAAAAA
1 T-AAA-TAATAAAAA
1710186 TAAATAATAAAAA
1 TAAATAATAAAAA
1710199 TA
1 TA
1710201 TATTGATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 6 0.23
15 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:1714080 original size:19 final size:20
Alignment explanation
Indices: 1714056--1714094 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
1714046 AAATTGGTTA
1714056 GTGTAATTTA-ATTTTTTTC
1 GTGTAATTTAGATTTTTTTC
1714075 GTGTAATTTAGTATTTTTTT
1 GTGTAATTTAG-ATTTTTTT
1714095 TTATAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.13, T:0.64
Consensus pattern (20 bp):
GTGTAATTTAGATTTTTTTC
Found at i:1715905 original size:15 final size:15
Alignment explanation
Indices: 1715849--1715906 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
1715839 CTTTATACTA
*
1715849 TAAAATATTTAGTAT
1 TAAAATATTTATTAT
* *
1715864 TAATATATTTATAATT
1 TAAAATATTTATTA-T
1715880 GTAATAAATATTTATTAT
1 -T-A-AAATATTTATTAT
1715898 TAAAATATT
1 TAAAATATT
1715907 AATATTGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 18 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATATTTATTAT
Found at i:1715970 original size:13 final size:14
Alignment explanation
Indices: 1715937--1715980 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
1715927 ATATGTGAAG
*
1715937 AATATTATT-TAAA
1 AATATTATTATTAA
*
1715950 AATATTATTTTTAA
1 AATATTATTATTAA
1715964 AAT-TTATTATTAA
1 AATATTATTATTAA
1715977 AATA
1 AATA
1715981 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:1715971 original size:16 final size:16
Alignment explanation
Indices: 1715939--1715978 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 16
1715929 ATGTGAAGAA
1715939 TATTATTTAAAAATAT
1 TATTATTTAAAAATAT
1715955 TATT-TTT-AAAAT-T
1 TATTATTTAAAAATAT
1715968 TATTA-TTAAAA
1 TATTATTTAAAA
1715979 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTATTTAAAAATAT
Found at i:1717013 original size:54 final size:54
Alignment explanation
Indices: 1716949--1717054 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
1716939 CCGTGTGACC
*
1716949 CAAGTCAGTGAGTTACACGGGCAGGGACACGAGCTGGGACACAATCATGTGTTT
1 CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
* * * * *
1717003 CAAGTCAGTGAGTTACACGGGCAGAGACATGGGTTGGGACACGATCGTGTGT
1 CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGT
1717055 CCCAACTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACACGGGCAGAGACACGAGCTGGGACACAATCATGTGTTT
Found at i:1717388 original size:48 final size:48
Alignment explanation
Indices: 1717329--1717421 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1717319 TCAAGAGGGA
*
1717329 ATAAATAGTGATAAGACTGTAGACAGTGGAAGACCAAGCTTAGCAATG
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
* * * *
1717377 ATAAATAGTGATAAGAGTGTAGGCACTGGAAGATCAAGTTTAGCA
1 ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCA
1717422 TTGCATAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.23
Consensus pattern (48 bp):
ATAAATAGTGATAAGACTGTAGACACTGGAAGACCAAGCTTAGCAATG
Found at i:1718401 original size:19 final size:21
Alignment explanation
Indices: 1718360--1718403 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1718350 AAGGTTCAAA
1718360 AATGATGTTAATTGCATTAATT
1 AATGATGTTAATTGCA-TAATT
1718382 AATGATGTTAA-TGC-TAATT
1 AATGATGTTAATTGCATAATT
1718401 AAT
1 AAT
1718404 CCAATTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
21 3 0.14
22 11 0.50
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (21 bp):
AATGATGTTAATTGCATAATT
Found at i:1720596 original size:26 final size:28
Alignment explanation
Indices: 1720530--1720604 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 28
1720520 TATAGATACG
*
1720530 TACATATATGTATGAATAAATTATAAAAAA
1 TACATATATGTAT--ATATATTATAAAAAA
* * *
1720560 TATACACATGTATATATATTA-AAAAAA
1 TACATATATGTATATATATTATAAAAAA
*
1720587 -ACATATATGTGTATATAT
1 TACATATATGTATATATAT
1720605 ATGACTACGA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 14 0.38
27 6 0.16
28 7 0.19
30 10 0.27
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (28 bp):
TACATATATGTATATATATTATAAAAAA
Found at i:1721595 original size:3 final size:3
Alignment explanation
Indices: 1721587--1721616 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1721577 TAATGGTAAT
1721587 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1721617 ATAACATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1725838 original size:17 final size:18
Alignment explanation
Indices: 1725818--1725855 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1725808 TTTTTTATAA
1725818 TTATTAAGTA-TTTTAAG
1 TTATTAAGTAGTTTTAAG
* *
1725835 TTATTTAGTAGTTTTATG
1 TTATTAAGTAGTTTTAAG
1725853 TTA
1 TTA
1725856 ACAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTATTAAGTAGTTTTAAG
Found at i:1738682 original size:35 final size:35
Alignment explanation
Indices: 1738642--1738790 Score: 110
Period size: 35 Copynumber: 4.2 Consensus size: 35
1738632 TTTATGTAAT
1738642 ATTTATATTGAGTATATAATTATTTTCATATTGAA
1 ATTTATATTGAGTATATAATTATTTTCATATTGAA
* * * *
1738677 ATTTAT-TTCGAATATAT-GTT-TTAT-ATATTTAA
1 ATTTATATT-GAGTATATAATTATTTTCATATTGAA
* * * **
1738709 ATTTATAATGGTTGTATTTTAATAATATGTTTTTTA-TGTAA
1 ATTTAT-ATTG-AGTA-TATAAT--TAT-TTTCATATTG-AA
1738750 ATTTATATTGAGTATATAATTATTTTCATATTGAA
1 ATTTATATTGAGTATATAATTATTTTCATATTGAA
1738785 ATTTAT
1 ATTTAT
1738791 TTCGAATATA
Statistics
Matches: 84, Mismatches: 17, Indels: 26
0.66 0.13 0.20
Matches are distributed among these distances:
32 13 0.15
33 4 0.05
34 7 0.08
35 28 0.33
36 6 0.07
38 6 0.07
39 4 0.05
40 6 0.07
41 10 0.12
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (35 bp):
ATTTATATTGAGTATATAATTATTTTCATATTGAA
Found at i:1738761 original size:108 final size:109
Alignment explanation
Indices: 1738631--1738848 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
1738621 ATTTAATATA
1738631 TTTTATGTAATATTTATATTGAGTATATAATTATTTTCATATTGAAATTTATTTCGAATATATGT
1 TTTTATGTAATATTTATATTGAGTATATAATTATTTTCATATTGAAATTTATTTCGAATATATGT
1738696 TTTATATATTTAAATTTATAATGGTTGTATTTTAATAATATGTT
66 TTTATATATTTAAATTTATAATGGTTGTATTTTAATAATATGTT
1738740 TTTTATGTAA-ATTTATATTGAGTATATAATTATTTTCATATTGAAATTTATTTCGAATATATGT
1 TTTTATGTAATATTTATATTGAGTATATAATTATTTTCATATTGAAATTTATTTCGAATATATGT
1738804 TTTATATATTTAAATTTATAATGGTTGTATTTTAATAATATGTT
66 TTTATATATTTAAATTTATAATGGTTGTATTTTAATAATATGTT
1738848 T
1 T
1738849 AAATTAAATT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 99 0.91
109 10 0.09
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (109 bp):
TTTTATGTAATATTTATATTGAGTATATAATTATTTTCATATTGAAATTTATTTCGAATATATGT
TTTATATATTTAAATTTATAATGGTTGTATTTTAATAATATGTT
Found at i:1739462 original size:16 final size:16
Alignment explanation
Indices: 1739380--1739462 Score: 62
Period size: 16 Copynumber: 5.2 Consensus size: 16
1739370 CTTAAACACT
1739380 AATGACCTAAACTCAA
1 AATGACCTAAACTCAA
* * *
1739396 AAT-AACTCAACCTTAA
1 AATGACCT-AAACTCAA
* *
1739412 AATGACATGAACTCAA
1 AATGACCTAAACTCAA
* *
1739428 ACTAACCTAAACT-AGA
1 AATGACCTAAACTCA-A
*
1739444 AATGATCTAAACTCAA
1 AATGACCTAAACTCAA
1739460 AAT
1 AAT
1739463 TCATATAAAT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
15 4 0.08
16 41 0.85
17 3 0.06
ACGTcount: A:0.51, C:0.22, G:0.06, T:0.22
Consensus pattern (16 bp):
AATGACCTAAACTCAA
Found at i:1748517 original size:23 final size:25
Alignment explanation
Indices: 1748479--1748547 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 25
1748469 AATATCATAT
* *
1748479 TTTATAAAAAAAATATAAAATAT-A
1 TTTATATAAAATATATAAAATATGA
* * *
1748503 TTTGTCT-AAATATATAAAATATGT
1 TTTATATAAAATATATAAAATATGA
1748527 TTTATATAAAATATATAAAAT
1 TTTATATAAAATATATAAAAT
1748548 CTAAAAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 14 0.39
24 9 0.25
25 13 0.36
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (25 bp):
TTTATATAAAATATATAAAATATGA
Found at i:1751676 original size:24 final size:25
Alignment explanation
Indices: 1751643--1751696 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
1751633 CCTTAGCGCT
* *
1751643 CTCTCTGATTATTAGCACGTTA-TG
1 CTCTCCGATTATTAGCACATTAGTG
1751667 CTCTCCGATTATTAGCACATTAGTG
1 CTCTCCGATTATTAGCACATTAGTG
1751692 CTCTC
1 CTCTC
1751697 TGTTTAGCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.74
25 7 0.26
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.39
Consensus pattern (25 bp):
CTCTCCGATTATTAGCACATTAGTG
Found at i:1751709 original size:22 final size:22
Alignment explanation
Indices: 1751678--1751742 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
1751668 TCTCCGATTA
1751678 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
1751700 TTAGCTCATTTGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* * * *
1751722 ATAACACTTTAGTGTTCTCTG
1 TTAGCACATTAGTGCTCTCTG
1751743 CTTAATAGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:1754367 original size:23 final size:23
Alignment explanation
Indices: 1754324--1754382 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1754314 AAAAATAGTG
*
1754324 AAATTATATATTAATACATAATA
1 AAATTATATATTAATACATAAAA
* * **
1754347 AATTTATATTTTAATTTATAAAA
1 AAATTATATATTAATACATAAAA
1754370 AAATTATA-ATTAA
1 AAATTATATATTAA
1754383 ATACTGACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATTATATATTAATACATAAAA
Found at i:1756727 original size:11 final size:11
Alignment explanation
Indices: 1756711--1756735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1756701 TGTTCCGTTG
1756711 GTTGTTCAATC
1 GTTGTTCAATC
1756722 GTTGTTCAATC
1 GTTGTTCAATC
1756733 GTT
1 GTT
1756736 CTTCGACCAT
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:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (11 bp):
GTTGTTCAATC
Found at i:1757106 original size:20 final size:20
Alignment explanation
Indices: 1757094--1757133 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1757084 CTGACTGCAC
1757094 TTACTGCTAACTGCTAAACT
1 TTACTGCTAACTGCTAAACT
1757114 TTACTGCTAACTGCTAAACT
1 TTACTGCTAACTGCTAAACT
1757134 AACCATACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (20 bp):
TTACTGCTAACTGCTAAACT
Found at i:1789031 original size:18 final size:18
Alignment explanation
Indices: 1789010--1789046 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1789000 TAAACCCTTA
*
1789010 AAAAATCCTAACCCTAAC
1 AAAAATCCTAAACCTAAC
1789028 AAAAATCCTAAACCTAAC
1 AAAAATCCTAAACCTAAC
1789046 A
1 A
1789047 TAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATCCTAAACCTAAC
Found at i:1789253 original size:35 final size:35
Alignment explanation
Indices: 1789214--1789285 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1789204 ATAAAAACAG
1789214 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1789249 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1 ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
1789284 AT
1 AT
1789286 GATTTGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.26
Consensus pattern (35 bp):
ATCCTAAAGCATTAGATAATAAATAAATATGAGAA
Found at i:1791099 original size:18 final size:19
Alignment explanation
Indices: 1791062--1791099 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1791052 TTTAAAATAA
* *
1791062 TATAAATTATAAATTATTT
1 TATAAAATATAAAATATTT
1791081 TATAAAATA-AAAATATTT
1 TATAAAATATAAAATATTT
1791099 T
1 T
1791100 TATCATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATAAAATATAAAATATTT
Found at i:1792447 original size:17 final size:18
Alignment explanation
Indices: 1792414--1792448 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1792404 AATTTGTGTA
*
1792414 TTGTTTTAATCATTTTTT
1 TTGTTTTAATAATTTTTT
1792432 TTGTTTTAA-AATTTTTT
1 TTGTTTTAATAATTTTTT
1792449 ATTTAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (18 bp):
TTGTTTTAATAATTTTTT
Found at i:1797934 original size:16 final size:16
Alignment explanation
Indices: 1797913--1797948 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1797903 TTTGGTTCGC
1797913 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAAG
*
1797929 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAAG
1797945 TGTA
1 TGTA
1797949 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAAG
Found at i:1798205 original size:18 final size:17
Alignment explanation
Indices: 1798184--1798218 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1798174 TTATTATTAA
*
1798184 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1798202 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1798219 TCTTGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1798362 original size:28 final size:27
Alignment explanation
Indices: 1798275--1798437 Score: 86
Period size: 26 Copynumber: 6.3 Consensus size: 27
1798265 ATGATACTAT
*
1798275 ATTATATAATTTAATATAATTTGAAATA
1 ATTATAT-ATTTAATATAATTTAAAATA
* *
1798303 ATTA-ATATTAAATATATTTTAATTAA-A
1 ATTATATATTTAATATAATTTAA--AATA
*
1798330 A-TATATGATTTAATAAAATTTAAAATA
1 ATTATAT-ATTTAATATAATTTAAAATA
*
1798357 ATTATA-A-CTAATA-AATTT----T-
1 ATTATATATTTAATATAATTTAAAATA
* *
1798376 CTTATATGAATTT-GTATAATTTAAAATA
1 ATTATAT--ATTTAATATAATTTAAAATA
1798404 ATTAT-TA-TTACATATAATTTAATAATA
1 ATTATATATTTA-ATATAATTTAA-AATA
1798431 A-TATATA
1 ATTATATA
1798438 ATTTCATAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 41
0.66 0.08 0.26
Matches are distributed among these distances:
19 5 0.05
20 1 0.01
22 3 0.03
23 6 0.06
24 7 0.07
25 6 0.06
26 31 0.30
27 17 0.17
28 27 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
ATTATATATTTAATATAATTTAAAATA
Found at i:1798400 original size:47 final size:46
Alignment explanation
Indices: 1798331--1798498 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
1798321 TTAATTAAAA
*
1798331 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
1798378 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
1798426 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
1798469 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
1798499 ATATTAAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 18 0.19
45 5 0.05
46 5 0.05
47 40 0.43
48 14 0.15
49 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:1798420 original size:26 final size:28
Alignment explanation
Indices: 1798390--1798450 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1798380 TATGAATTTG
*
1798390 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
1798416 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
1798444 TAAAATT
1 TATAATT
1798451 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:1823985 original size:20 final size:21
Alignment explanation
Indices: 1823949--1823987 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1823939 TTGTATTTTT
1823949 TATTTATAATATAATTATTAA
1 TATTTATAATATAATTATTAA
*
1823970 TATTTAT-ATTTAATTATT
1 TATTTATAATATAATTATT
1823988 TTATATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTATAATATAATTATTAA
Found at i:1825805 original size:2 final size:2
Alignment explanation
Indices: 1825798--1825822 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1825788 ACTTCTAAAA
1825798 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1825823 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1835496 original size:184 final size:183
Alignment explanation
Indices: 1835184--1835551 Score: 413
Period size: 184 Copynumber: 2.0 Consensus size: 183
1835174 TAATTGTAAC
* * * ***
1835184 AATTATTATTTATTATATTTTATTTCGGGACACTTAGACTTGAGTGTGGTGGTTCAAAAATATTT
1 AATTATTATTTATTATATTTCATTTCGGGACACTTAGACTTGAGTATAGTGCCCCAAAAATATTT
* * *
1835249 TTAAGATTTTCTGTGATACTTATAAAAATTATCATTTATTATAATTCAATTTCAAGGCACTTGAG
66 TTAAGATTTTCTGAGATACTTATAAAAATTATCATTGATTATAATTCAATTTCAAGACACTTGAG
* * * * * *
1835314 TTTGAGTATGGTGGTGCAAAAGTATTTTTAAAAATTTTT-AGGATAGCTATAAA
131 CTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGG-TAACTATAAA
* *
1835367 AATTATTGTTTATTATATTTCATTTTCGGTG-CACTTGAGA-TTGAGTATAGTGCCCCCAAAATA
1 AATTATTATTTATTATATTTCA-TTTCGG-GACACTT-AGACTTGAGTATAGTGCCCCAAAAATA
** * * * * * *
1835430 TTTTTAATTTTTTTTGAGATAAC-TGTAAAAATTATTATTGATTATATTTTATTTTCCAA-ACAC
63 TTTTTAAGATTTTCTGAGAT-ACTTATAAAAATTATCATTGATTATAATTCAATTT-CAAGACAC
*
1835493 TTGAGCTTAAGTATGGTGATGAAAAAATATTTTTAAAATTTTTTGAGGTAACTATAAA
126 TTGAGCTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGGTAACTATAAA
1835551 A
1 A
1835552 GGGCCACAAT
Statistics
Matches: 153, Mismatches: 26, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
183 20 0.13
184 121 0.79
185 12 0.08
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (183 bp):
AATTATTATTTATTATATTTCATTTCGGGACACTTAGACTTGAGTATAGTGCCCCAAAAATATTT
TTAAGATTTTCTGAGATACTTATAAAAATTATCATTGATTATAATTCAATTTCAAGACACTTGAG
CTTAAGTATGGTGATGAAAAAATATTTTTAAAAATTTTTGAGGTAACTATAAA
Found at i:1835535 original size:92 final size:92
Alignment explanation
Indices: 1835184--1835551 Score: 332
Period size: 92 Copynumber: 4.0 Consensus size: 92
1835174 TAATTGTAAC
* *** * *
1835184 AATTATTATTTATTATATTTTA-TTTCGGGACACTT-AGACTTGAGTGTGGTGGTTCAAAAATAT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAG-CTTGAGTATGGTGGTGCAAAAATAT
* * *
1835247 TTTTAAGATTTTCTGTGAT-ACTTATAAA
65 TTTTAAAATTTTTTGAGATAAC-TATAAA
* * * * * *
1835275 AATTATCATTTATTATAATTCAATTT-CAAGGCACTTGAGTTTGAGTATGGTGGTGCAAAAGTAT
1 AATTATTATTTATTATATTTCATTTTCCAA-ACACTTGAGCTTGAGTATGGTGGTGCAAAAATAT
* *
1835339 TTTTAAAAATTTTT-AGGATAGCTATAAA
65 TTTTAAAATTTTTTGA-GATAACTATAAA
* **** * * *** *
1835367 AATTATTGTTTATTATATTTCATTTTCGGTGCACTTGAGATTGAGTATAGTGCCCCCAAAATATT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
** *
1835432 TTTAATTTTTTTTGAGATAACTGTAAA
66 TTTAAAATTTTTTGAGATAACTATAAA
* * * * *
1835459 AATTATTATTGATTATATTTTATTTTCCAAACACTTGAGCTTAAGTATGGTGATGAAAAAATATT
1 AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
*
1835524 TTTAAAATTTTTTGAGGTAACTATAAA
66 TTTAAAATTTTTTGAGATAACTATAAA
1835551 A
1 A
1835552 GGGCCACAAT
Statistics
Matches: 216, Mismatches: 54, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
91 19 0.09
92 193 0.89
93 4 0.02
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (92 bp):
AATTATTATTTATTATATTTCATTTTCCAAACACTTGAGCTTGAGTATGGTGGTGCAAAAATATT
TTTAAAATTTTTTGAGATAACTATAAA
Found at i:1836349 original size:20 final size:20
Alignment explanation
Indices: 1836319--1836361 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1836309 AACTGATGAA
1836319 TTTTATAATTTT-TAAATAT
1 TTTTATAATTTTGTAAATAT
*
1836338 TTTTATTAATTTTGTGAATAT
1 TTTTA-TAATTTTGTAAATAT
1836359 TTT
1 TTT
1836362 AAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 7 0.33
21 9 0.43
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTATAATTTTGTAAATAT
Found at i:1836362 original size:20 final size:18
Alignment explanation
Indices: 1836318--1836362 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
1836308 GAACTGATGA
1836318 ATTTTATAATTTTTAAAT
1 ATTTTATAATTTTTAAAT
*
1836336 ATTTTTATTAATTTTGTGAAT
1 A-TTTTA-TAATTTT-TAAAT
1836357 ATTTTA
1 ATTTTA
1836363 AATATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 5 0.22
20 12 0.52
21 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTTTATAATTTTTAAAT
Found at i:1836990 original size:237 final size:238
Alignment explanation
Indices: 1836564--1837040 Score: 947
Period size: 237 Copynumber: 2.0 Consensus size: 238
1836554 TATAAATATA
1836564 TATAGGATTATTTGCATCAAACATTATAAATTTTAAATTGTTTAATTAAGTATAGTATCAATTAG
1 TATAGGATTATTTGCATCAAACATTATAAATTTTAAATTGTTTAATTAAGTATAGTATCAATTAG
1836629 ACACTTCAATCAATCCAAAGTCAGCTTAGACTTTAAATATCGGACTCGGATTTGAGTTAGCTTAC
66 ACACTTCAATCAATCCAAAGTCAGCTTAGACTTTAAATATCGGACTCGGATTTGAGTTAGCTTAC
1836694 AATTAATAATTGGATAGTTTGAATAAACATATTAAAGAAAACAAACAATATCATTAAAATTTTAG
131 AATTAATAATTGGATAGTTTGAATAAACATATTAAAGAAAACAAACAATATCATTAAAATTTTAG
1836759 AACTATTTCTTCTTTCTAACCTATCATATTAAAATTATTCATG
196 AACTATTTCTTCTTTCTAACCTATCATATTAAAATTATTCATG
1836802 TATAGGATTA-TTGCATCAAACATTATAAATTTTAAATTGTTTAATTAAGTATAGTATCAATTAG
1 TATAGGATTATTTGCATCAAACATTATAAATTTTAAATTGTTTAATTAAGTATAGTATCAATTAG
1836866 ACACTTCAATCAATCCAAAGTCAGCTTAGACTTTAAATATCGGACTCGGATTTGAGTTAGCTTAC
66 ACACTTCAATCAATCCAAAGTCAGCTTAGACTTTAAATATCGGACTCGGATTTGAGTTAGCTTAC
1836931 AATTAATAATTGGATAGTTTGAATAAACATATTAAAGAAAACAAACAATATCATTAAAATTTTAG
131 AATTAATAATTGGATAGTTTGAATAAACATATTAAAGAAAACAAACAATATCATTAAAATTTTAG
1836996 AACTATTTCTTCTTTCTAACCTATCATATTAAAATTATTCATG
196 AACTATTTCTTCTTTCTAACCTATCATATTAAAATTATTCATG
1837039 TA
1 TA
1837041 ATATTTATAA
Statistics
Matches: 239, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
237 229 0.96
238 10 0.04
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (238 bp):
TATAGGATTATTTGCATCAAACATTATAAATTTTAAATTGTTTAATTAAGTATAGTATCAATTAG
ACACTTCAATCAATCCAAAGTCAGCTTAGACTTTAAATATCGGACTCGGATTTGAGTTAGCTTAC
AATTAATAATTGGATAGTTTGAATAAACATATTAAAGAAAACAAACAATATCATTAAAATTTTAG
AACTATTTCTTCTTTCTAACCTATCATATTAAAATTATTCATG
Found at i:1837427 original size:18 final size:19
Alignment explanation
Indices: 1837393--1837430 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1837383 TTTCAATTTC
*
1837393 AATTAAATAAATTATTAAA
1 AATTAAATAAATAATTAAA
1837412 AATTAAA-AAATAATTAAA
1 AATTAAATAAATAATTAAA
1837430 A
1 A
1837431 TATCATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAATAAATAATTAAA
Found at i:1844153 original size:141 final size:141
Alignment explanation
Indices: 1843899--1844177 Score: 427
Period size: 141 Copynumber: 2.0 Consensus size: 141
1843889 TAAATAAGAA
** * * *
1843899 TAAGTTTGCATAGGTCCACGACCTCTATCAGTTTCGACTATTAGTAATGAAAGGGGCCTTTCGCC
1 TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTGTCGCC
* * * *
1843964 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTTTTTCTCTGGCAAGGGAGTAATATTTTGGGC
66 AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
1844029 TGAATCTATAC
131 TGAATCTATAC
1844040 TAAGTTTGTC-TAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTAGT-G
1 TAAGTTTG-CATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCT-GTCG
* *
1844103 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTGATCTTATGG
64 CCAAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGG
1844168 GCTGAATCTA
129 GCTGAATCTA
1844178 CGTTAGGAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 123 0.98
142 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (141 bp):
TAAGTTTGCATAGGTCCAAAACCCCTATCAGTTTCGACTATTAGTAATGAAAGGGACCTGTCGCC
AAGTTTATCCTAACTCCAAGCTTGAGGACAAGCTCTTTCTCTAGCAAGGGACTAATATTATGGGC
TGAATCTATAC
Found at i:1844629 original size:129 final size:133
Alignment explanation
Indices: 1844390--1844772 Score: 452
Period size: 129 Copynumber: 2.8 Consensus size: 133
1844380 CACGAACCCT
* ** *
1844390 ATCGGTTTTGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATTGTAACTCTGAGCTTGAG
1 ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAG
* * *
1844455 GACAAGCTCTTTCTCTAGCAAGGGAGTAAAATTATGCGCCAAATCTATAATAAGTTTGT-T-T-A
66 GACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTGTCA
1844517 -A-
131 GAC
* * * * *
1844518 GTCGGTTTCAACTATTAGTAATGGAAGGGACCTTTTGCCAAAGTTTATCCTAGCTCCGAGCTTGA
1 ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCC-AAGTTTATCCTAACTCCGAGCTTGA
*
1844583 GGACAAGCTCTTTCTCTAGTAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTAGG
65 GGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGT--G
1844648 TCCATGACCCC
128 T-CA-GA---C
* * * * *
1844659 TATCGGTTTCGACTATTAGTAACGAAAGGGACCTTTCACCAAGTTCATCTTAACTCCAAGCTTGA
1 -ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGA
* * * *
1844724 GGACAATCTTTTTCTCTAGCAAGGTAGTAATATTATCAGCCGAATCTAT
65 GGACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTAT
1844773 GTTAGGAAAG
Statistics
Matches: 213, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
128 34 0.16
129 77 0.36
130 1 0.00
133 1 0.00
135 1 0.00
137 1 0.00
141 65 0.31
142 33 0.15
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (133 bp):
ATCGGTTTCGACTATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAG
GACAAGCTCTTTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATAATAAGTTTGTGTGTCA
GAC
Found at i:1845220 original size:142 final size:141
Alignment explanation
Indices: 1844992--1845650 Score: 870
Period size: 142 Copynumber: 4.7 Consensus size: 141
1844982 AGTCTCGACG
1844992 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
** * * *
1845057 TCTAGCAAGGGAGTAATATTATGGGTTGAATCTATAATAAGCTTGTATGGGTCCACAACCCCTAT
66 TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
1845122 CGGTTTCAACT
131 CGGTTTCAACT
* * * * * * *
1845133 ATTAGCAATGGAAGGGACCTTTCACCATGTTTATCCTTAACTCTGAGCCTGAGGAAAAGCTCTTT
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCC-TAACTCCGAGCTTGAGGACAAGCTCTTT
* * *
1845198 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAACAAGTTTGTGTAGGTCCACGACCCATA
65 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTA
**
1845263 TCGGTTTTGAC-
130 TCGGTTTCAACT
* * *
1845274 --T--TAATG-AGGGGACCTTTCTCCAAGTTTATCCTAGCTCCGAGCTTGAGGACAAGCTCTTTC
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
* * *
1845334 TCTAGCAAGGGAGTGATATTATGGGCCGAATCTATAATAAGTTTGGGTAGGTCCACAACACCTAT
66 TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
1845399 CGGTTTCAACT
131 CGGTTTCAACT
1845410 ATTAGTAATGAAAAGGG-CCTTTCGCCAAGTTTATCCTAACTCCGAGAGCTTGAGGACAAGCTCT
1 ATTAGTAATG-AAAGGGACCTTTCGCCAAGTTTATCCTAACTCC--GAGCTTGAGGACAAGCTCT
* * **
1845474 TTCTCTAGCAAGGGAGTAATATTATGAGCCGAATCTATTATAAGTTTGTGTAGGTCCACAACCGT
63 TTCTCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCC
*
1845539 TATCGGTTTCGACT
128 TATCGGTTTCAACT
* * * * *
1845553 ATTAGTAA-CAAGGGGACCTTTCCCCAAGTTTATCCTAACTCC-ACGCTCGAGGACAAGTTCTTT
1 ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGA-GCTTGAGGACAAGCTCTTT
* * * *
1845616 CTCTAGCAAGGAAGTGA-CTTATGGGCTGAATCTAT
65 CTCTAGCAAGGGAGTAATATTATGGGCCGAATCTAT
1845651 GTTAGGAAAG
Statistics
Matches: 452, Mismatches: 54, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
135 92 0.20
136 22 0.05
137 4 0.01
138 1 0.00
139 17 0.04
140 37 0.08
141 61 0.13
142 120 0.27
143 98 0.22
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (141 bp):
ATTAGTAATGAAAGGGACCTTTCGCCAAGTTTATCCTAACTCCGAGCTTGAGGACAAGCTCTTTC
TCTAGCAAGGGAGTAATATTATGGGCCGAATCTATAATAAGTTTGTGTAGGTCCACAACCCCTAT
CGGTTTCAACT
Found at i:1866648 original size:18 final size:16
Alignment explanation
Indices: 1866627--1866661 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1866617 AAATATTATT
1866627 ATATTTAAATTAAATTAA
1 ATATTT-AATT-AATTAA
1866645 ATATTTAATTAATTAA
1 ATATTTAATTAATTAA
1866661 A
1 A
1866662 GTCAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTAATTAATTAA
Found at i:1875684 original size:151 final size:151
Alignment explanation
Indices: 1875473--1875772 Score: 345
Period size: 151 Copynumber: 2.0 Consensus size: 151
1875463 AATATACATG
* * ** * * *
1875473 CGAGGAATTATAAGTATCAAATTATTACATCATAGATTGTTCGAAGAATCACGAAATAGATCAAA
1 CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAATAGATCAAA
* * ** * * *
1875538 CATTAAAGTATAA-TTGAAATAAG-AATAGGTACACTTTAGTCTAAGGCCAACAAACTAAATTAA
66 CATTAAAGCACAACCAG-AATAAGAAAT-GGTACACTTTAGACTAAAGCCAACAAACTAAACTAA
*
1875601 CTTGACTAAAACCCGCACATGTT
129 CTTGACTAAAACCCACACATGTT
* * *
1875624 CGAGGAACTAAAAGTATCGAATTATTATAGAATGGATTGTCCAAAAAATCAC-AAAGTAGATCAA
1 CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAA-TAGATCAA
* * * * *
1875688 TCGTTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAATAAACTGAGCTAAC
65 ACATTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAACAAACTAAACTAAC
1875753 TTGACTAAAACCCACACATG
130 TTGACTAAAACCCACACATG
1875773 ACAATTGCAT
Statistics
Matches: 123, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
150 3 0.02
151 116 0.94
152 4 0.03
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (151 bp):
CGAGGAACTAAAAGTATCAAATTATTACAGAATAGATTGTCCAAAAAATCACGAAATAGATCAAA
CATTAAAGCACAACCAGAATAAGAAATGGTACACTTTAGACTAAAGCCAACAAACTAAACTAACT
TGACTAAAACCCACACATGTT
Found at i:1876496 original size:196 final size:197
Alignment explanation
Indices: 1876151--1876543 Score: 779
Period size: 196 Copynumber: 2.0 Consensus size: 197
1876141 CTTAACAATT
1876151 TTTAATATTTACATTATAGTAGTATTATATATTACTATAGATTTAATTTTATGTGTTATAAATAA
1 TTTAATATTTACATTATAGTAGTATTATATATTACTATAGATTTAATTTTATGTGTTATAAATAA
1876216 AAATAACATAATATAAAATGTTACAAACTTAAAAAATGGGTCGGGTCAAACCTGGCTCGGGCCTT
66 AAATAACATAATATAAAATGTTACAAACTTAAAAAATGGGTCGGGTCAAACCTGGCTCGGGCCTT
1876281 GAATGTTCAAGCACGAGCCCAATCCATTTTTTAAATGAGCCTAACTTTTTTGTCCAAACCCTCCC
131 GAATGTTCAAGCACGAGCCCAATCCATTTTTTAAATGAGCCTAACTTTTTTGTCCAAACCCTCCC
1876346 AA
196 AA
1876348 TTTAATATTT-CATTATAGTAGTATTATATATTACTATAGATTTAATTTTATGTGTTATAAATAA
1 TTTAATATTTACATTATAGTAGTATTATATATTACTATAGATTTAATTTTATGTGTTATAAATAA
1876412 AAATAACATAATATAAAATGTTACAAACTTAAAAAATGGGTCGGGTCAAACCTGGCTCGGGCCTT
66 AAATAACATAATATAAAATGTTACAAACTTAAAAAATGGGTCGGGTCAAACCTGGCTCGGGCCTT
1876477 GAATGTTCAAGCACGAGCCCAATCCATTTTTTAAATGAGCCTAACTTTTTTGTCCAAACCCTCCC
131 GAATGTTCAAGCACGAGCCCAATCCATTTTTTAAATGAGCCTAACTTTTTTGTCCAAACCCTCCC
1876542 AA
196 AA
1876544 ATTTCAAGTT
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
196 186 0.95
197 10 0.05
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (197 bp):
TTTAATATTTACATTATAGTAGTATTATATATTACTATAGATTTAATTTTATGTGTTATAAATAA
AAATAACATAATATAAAATGTTACAAACTTAAAAAATGGGTCGGGTCAAACCTGGCTCGGGCCTT
GAATGTTCAAGCACGAGCCCAATCCATTTTTTAAATGAGCCTAACTTTTTTGTCCAAACCCTCCC
AA
Found at i:1884972 original size:19 final size:20
Alignment explanation
Indices: 1884945--1884985 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1884935 CTTCATTCCA
* *
1884945 TTTATTTTATTAATA-ATTT
1 TTTAATTTAATAATATATTT
1884964 TTTAATTTAATAATATATTT
1 TTTAATTTAATAATATATTT
1884984 TT
1 TT
1884986 AAGTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAATTTAATAATATATTT
Found at i:1886576 original size:14 final size:15
Alignment explanation
Indices: 1886549--1886577 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1886539 GCTGGGATGA
1886549 AAATAAATTTTAATT
1 AAATAAATTTTAATT
1886564 AAATAAA-TTTAATT
1 AAATAAATTTTAATT
1886578 TGAACTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATAAATTTTAATT
Found at i:1895226 original size:11 final size:11
Alignment explanation
Indices: 1895212--1895242 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
1895202 TTTTATAAAT
1895212 ATTTTTTAATA
1 ATTTTTTAATA
1895223 A-TTTTTAATA
1 ATTTTTTAATA
1895233 ATTTTTTAAT
1 ATTTTTTAAT
1895243 CGAATCAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:1899818 original size:11 final size:11
Alignment explanation
Indices: 1899802--1899846 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
1899792 TAGTTATTTA
1899802 TAATAAAATAT
1 TAATAAAATAT
1899813 TAATAAAATAT
1 TAATAAAATAT
*
1899824 CTCATTAAAATAT
1 -T-AATAAAATAT
1899837 TAATAAAATA
1 TAATAAAATA
1899847 ATATTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 19 0.63
12 2 0.07
13 9 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:1902420 original size:19 final size:19
Alignment explanation
Indices: 1902384--1902451 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1902374 TCTCTCTCTA
*
1902384 CAAAA-ATTTAAAAAAATT
1 CAAAATATTTATAAAAATT
*
1902402 CAAAATAATTT-TTAAAATT
1 CAAAAT-ATTTATAAAAATT
*
1902421 TAAAATATTTATAAAAATT
1 CAAAATATTTATAAAAATT
*
1902440 CCAAA-ATTTATA
1 CAAAATATTTATA
1902452 TTTTTAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
18 16 0.39
19 21 0.51
20 4 0.10
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAATATTTATAAAAATT
Found at i:1902525 original size:9 final size:9
Alignment explanation
Indices: 1902385--1902526 Score: 56
Period size: 9 Copynumber: 14.7 Consensus size: 9
1902375 CTCTCTCTAC
1902385 AAAAATTTAA
1 AAAAATTT-A
*
1902395 AAAAATTCA
1 AAAAATTTA
*
1902404 AAATAATTTT
1 AAA-AATTTA
*
1902414 TAAAATTTA
1 AAAAATTTA
*
1902423 AAATATTTA
1 AAAAATTTA
*
1902432 TAAAAA-TTC
1 -AAAAATTTA
*
1902441 CAAAATTT-
1 AAAAATTTA
* **
1902449 ATATTTTTA
1 AAAAATTTA
1902458 AATAAA-TTA
1 AA-AAATTTA
1902467 TAAAAATTTCAAA
1 -AAAAATTT---A
1902480 AATAAATTCTA
1 AA-AAATT-TA
1902491 AAAAATATTA
1 AAAAAT-TTA
*
1902501 AAGAAAGTTAA
1 AA-AAA-TTTA
1902512 AAAAATTTA
1 AAAAATTTA
1902521 AAAAAT
1 AAAAAT
1902527 ATTCTAGAAT
Statistics
Matches: 98, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
8 8 0.08
9 36 0.37
10 33 0.34
11 11 0.11
12 3 0.03
13 6 0.06
14 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTTA
Found at i:1906737 original size:24 final size:24
Alignment explanation
Indices: 1906700--1906746 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1906690 TATATATACC
1906700 AATTCAATCAATA-TAAATTCAATA
1 AATTCAATCAATATTAAA-TCAATA
1906724 AATTC-ATCACATATTAAATCAAT
1 AATTCAATCA-ATATTAAATCAAT
1906747 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCAATCAATATTAAATCAATA
Found at i:1907579 original size:19 final size:20
Alignment explanation
Indices: 1907555--1907593 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1907545 ATTAATAAGC
1907555 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
1907574 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
1907594 CACATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:1913864 original size:3 final size:3
Alignment explanation
Indices: 1913856--1913892 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1913846 ATTTTAATCC
1913856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1913893 CCTTCTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1917196 original size:24 final size:22
Alignment explanation
Indices: 1917162--1917221 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1917152 AAAATACACA
*
1917162 TTTTTTATATATACGTTTTCATT
1 TTTTTTATATATACATTTTCA-T
*
1917185 TTTTTTATTATAAACATTTTCAT
1 TTTTTTA-TATATACATTTTCAT
*
1917208 TATTTTATATATAC
1 TTTTTTATATATAC
1917222 TTCATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 6 0.19
23 14 0.44
24 12 0.38
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTTTATATATACATTTTCAT
Found at i:1917227 original size:19 final size:20
Alignment explanation
Indices: 1917203--1917240 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1917193 TATAAACATT
1917203 TTCATTATTT-TATATATAC
1 TTCATTATTTATATATATAC
1917222 TTCATTATTTATATATATA
1 TTCATTATTTATATATATA
1917241 TTGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCATTATTTATATATATAC
Found at i:1919521 original size:24 final size:24
Alignment explanation
Indices: 1919489--1919538 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1919479 GAAAAGAAAA
1919489 GGAACGGTATTCTTTGTGATTAGG
1 GGAACGGTATTCTTTGTGATTAGG
1919513 GGAACGGTATTCTTTGTGATTAGG
1 GGAACGGTATTCTTTGTGATTAGG
1919537 GG
1 GG
1919539 GCCTATCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.36, T:0.36
Consensus pattern (24 bp):
GGAACGGTATTCTTTGTGATTAGG
Found at i:1919714 original size:232 final size:232
Alignment explanation
Indices: 1919308--1919746 Score: 788
Period size: 232 Copynumber: 1.9 Consensus size: 232
1919298 GGGTTGGACC
* *
1919308 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAATATCTTGGGTCTTGAATA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
1919373 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
*
1919438 ATCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
1919503 TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
196 TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
* *
1919540 CCTATCAGCCCCATTCCGTTGTCTTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
1 CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
* * * *
1919605 TCCAAATTCGAGATTTACCGTACACAAACAAATGTTGGGATATCTGAATCTCTTTATAAATTGTT
66 CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
*
1919670 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAATGGTATTCTT
131 ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
1919735 TGTGATTAGGGG
196 TGTGATTAGGGG
1919747 GCCTATAACT
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 197 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (232 bp):
CCTATCAGCCCCATTCCGTCGTCCTGGACACAATTGGTAAAGGCAAAAATCTTGGGTCTTGAACA
CCCAAATTCGAGATTTACCATACACAAACAAATGTTGGAATATCTGAATCTCCTTATAAATTGTT
ACCTTACCATATATAAGTTTGAGACCGAATACCACCATTAAGAAAAGAAAAGGAACGGTATTCTT
TGTGATTAGGGGAACGGTATTCTTTGTGATTAGGGGG
Found at i:1931246 original size:29 final size:29
Alignment explanation
Indices: 1931213--1931269 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1931203 TATTGTATGT
1931213 TTTTA-AAGGATT-AAATCAAAATTTTATCA
1 TTTTAGAAGG-TTAAAAT-AAAATTTTATCA
*
1931242 TTTTAGAAGGTTAAAATATAATTTTATC
1 TTTTAGAAGGTTAAAATAAAATTTTATC
1931270 TTTATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTAGAAGGTTAAAATAAAATTTTATCA
Found at i:1943031 original size:19 final size:18
Alignment explanation
Indices: 1943004--1943097 Score: 73
Period size: 19 Copynumber: 5.2 Consensus size: 18
1942994 CAGTGGAGGC
1943004 AAAAACAAAAAAACAAAA
1 AAAAACAAAAAAACAAAA
*
1943022 AAAAAGCAAAAAAGCAAAA
1 AAAAA-CAAAAAAACAAAA
* ** *
1943041 AAAATAAAAAAAAAGGAAG
1 AAAA-ACAAAAAAACAAAA
* * *
1943060 CAAAA-AAAAAGAGAAAA
1 AAAAACAAAAAAACAAAA
* *
1943077 CAAAAGAAAAAAACAAAA
1 AAAAACAAAAAAACAAAA
1943095 AAA
1 AAA
1943098 TAAAAAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
17 14 0.23
18 18 0.30
19 27 0.45
20 1 0.02
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.01
Consensus pattern (18 bp):
AAAAACAAAAAAACAAAA
Found at i:1943061 original size:32 final size:33
Alignment explanation
Indices: 1943002--1943066 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
1942992 TTCAGTGGAG
1943002 GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
1 GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
**
1943035 GCAAAAA-AAATAAAA-AAAAAGGAAGCAAAAAA
1 GCAAAAACAAA-AAAACAAAAAAAAAGCAAAAAA
1943067 AAAGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (33 bp):
GCAAAAACAAAAAAACAAAAAAAAAGCAAAAAA
Found at i:1943066 original size:17 final size:17
Alignment explanation
Indices: 1943005--1943104 Score: 71
Period size: 17 Copynumber: 5.8 Consensus size: 17
1942995 AGTGGAGGCA
*
1943005 AAAACAAAAAAACAAAAA
1 AAAACAAAAAAA-AAAAG
**
1943023 AAAAGCAAAAAAGCAAA-
1 AAAA-CAAAAAAAAAAAG
*
1943040 AAAA-ATAAAAAAAAAG
1 AAAACAAAAAAAAAAAG
* * *
1943056 GAAGCAAAAAAAAAGAG
1 AAAACAAAAAAAAAAAG
*
1943073 AAAACAAAAGAAAAAAAC
1 AAAACAAAA-AAAAAAAG
1943091 AAAA-AAATAAAAAA
1 AAAACAAA-AAAAAA
1943105 TAAAAAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
15 8 0.12
16 2 0.03
17 29 0.45
18 18 0.28
19 7 0.11
ACGTcount: A:0.83, C:0.07, G:0.08, T:0.02
Consensus pattern (17 bp):
AAAACAAAAAAAAAAAG
Found at i:1943103 original size:35 final size:33
Alignment explanation
Indices: 1943004--1943125 Score: 95
Period size: 35 Copynumber: 3.4 Consensus size: 33
1942994 CAGTGGAGGC
*
1943004 AAAAACAAAAAAACAAAAAAAAAGCAAAAAAGCAAA
1 AAAAAGAAAAAAACAAAAAAAAA--AAAAAAG-AAA
* *
1943040 AAAAATAAAAAAA-AAGGAAGCAAAAAAAAAGAGAAA
1 AAAAAGAAAAAAACAA--AA--AAAAAAAAAAAGAAA
1943076 ACAAAAGAAAAAAACAAAAAAATAAAAAATAA-AAA
1 A-AAAAGAAAAAAACAAAAAAA-AAAAAA-AAGAAA
*
1943111 ATAAGAGAAAAAAAC
1 A-AAAAGAAAAAAAC
1943126 CTCTACCGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
34 3 0.04
35 24 0.33
36 19 0.26
37 19 0.26
38 2 0.03
39 5 0.07
ACGTcount: A:0.82, C:0.07, G:0.08, T:0.03
Consensus pattern (33 bp):
AAAAAGAAAAAAACAAAAAAAAAAAAAAAGAAA
Found at i:1943123 original size:14 final size:13
Alignment explanation
Indices: 1943004--1943124 Score: 66
Period size: 14 Copynumber: 8.8 Consensus size: 13
1942994 CAGTGGAGGC
*
1943004 AAAAACAAAAAAAC
1 AAAAA-AAAAAAAT
1943018 AAAAAAAAAGCAAA-
1 AAAAAAAAA--AAAT
*
1943032 AAAGCAAAAAAAAT
1 AAA-AAAAAAAAAT
* *
1943046 AAAAAAAAAGGAAG
1 AAAAAAAAA-AAAT
* * *
1943060 CAAAAAAAAAGAG
1 AAAAAAAAAAAAT
*
1943073 AAAACAAAAGAAA-
1 AAAA-AAAAAAAAT
*
1943086 AAAACAAAAAAAT
1 AAAAAAAAAAAAT
1943099 AAAAAATAAAAAAT
1 AAAAAA-AAAAAAT
*
1943113 AAGAGAAAAAAA
1 AA-AAAAAAAAA
1943125 CCTCTACCGG
Statistics
Matches: 84, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.07
13 26 0.31
14 41 0.49
15 11 0.13
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAAAT
Found at i:1943124 original size:1 final size:1
Alignment explanation
Indices: 1943004--1943111 Score: 54
Period size: 1 Copynumber: 108.0 Consensus size: 1
1942994 CAGTGGAGGC
* * ** ** * ** **
1943004 AAAAACAAAAAAACAAAAAAAAAGCAAAAAAGCAAAAAAAATAAAAAAAAAGGAAGCAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1943069 AGAGAAAACAAAAGAAAAAAACAAAAAAATAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1943112 TAAGAGAAAA
Statistics
Matches: 76, Mismatches: 31, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.83, C:0.06, G:0.07, T:0.03
Consensus pattern (1 bp):
A
Found at i:1943568 original size:8 final size:8
Alignment explanation
Indices: 1943555--1943584 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1943545 AAAAGAAACA
1943555 AAAAAAAG
1 AAAAAAAG
1943563 AAAAAAAG
1 AAAAAAAG
1943571 AACAAAAAG
1 AA-AAAAAG
1943580 AAAAA
1 AAAAA
1943585 GGAGAGGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1946991 original size:82 final size:82
Alignment explanation
Indices: 1946828--1947724 Score: 1338
Period size: 82 Copynumber: 11.0 Consensus size: 82
1946818 NNNNNNNNNN
*
1946828 AGTAGCGGAGCAGACAGAACCACAGATCTTATCTCCCTAAGCAA-AGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1946892 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* * *
1946909 AGTAGCAGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1946974 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* * * * *
1946991 AATAGTGGAGCAGACAGAACCACTGATCTTATTTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
*
1947056 GTCTTATCTCCCTAAAC
66 GTCTTATCTCCCTAAGC
1947073 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1947138 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* * * * * * *
1947155 AGTAGCAGAGCAGACAGAACCACAGATATTATCTCCCTAAGCAGTAGCGGAGCAGA-CAGAACCA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATC-GCATCA
1947219 CAGATCTTATCTCCCTAAGC
65 -AG-TCTTATCTCCCTAAGC
* * * * * * *
1947239 AATAGTGGAGCAGATCATG--TCA-A-ATCTTATCTCCCTAAGCAGTAGCGAAGCAGATCGCATC
1 AGTAGCGGAGCGGA-CA-GAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATC
1947300 AAGTCTTATCTCCCTAAGC
64 AAGTCTTATCTCCCTAAGC
*
1947319 AGTAGCGGAGCGGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1947384 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* *
1947401 AGTAACGGAGCGGACAAAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
*
1947466 GTCTTATCTCCCTTAGC
66 GTCTTATCTCCCTAAGC
* * * * *
1947483 AGTAGTGGAGCGGACAAAACCACAGATCTTATCTCCTTAAGCAATAGTGGAGCAGACCACATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1947548 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* * * *
1947565 AATAGCGGAGCGGACAAAACCACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
1947630 GTCTTATCTCCCTAAGC
66 GTCTTATCTCCCTAAGC
* * *
1947647 AGTAGCGGAGCGGACAAAACCACAGACCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAA
1 AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
*
1947712 ATCTTATCTCCCT
66 GTCTTATCTCCCT
1947725 GAAGTTGCAG
Statistics
Matches: 744, Mismatches: 61, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
79 2 0.00
80 29 0.04
81 45 0.06
82 632 0.85
83 4 0.01
84 29 0.04
85 2 0.00
86 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (82 bp):
AGTAGCGGAGCGGACAGAACCACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAA
GTCTTATCTCCCTAAGC
Found at i:1950977 original size:57 final size:57
Alignment explanation
Indices: 1950889--1951136 Score: 313
Period size: 57 Copynumber: 4.4 Consensus size: 57
1950879 TTAATGTCCC
* * *
1950889 TTGCCACCAGAACTTGGACCTGAATTGG-GGTTGACAGCATCAGTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCACTAAATGCATGACCT
**
1950946 TTGCCTCCTTCACTTGGACCTGAATTGG-GGTTGACAGCATCAGC-AAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGG-TGACAGCATCA-CTAAATGCATGACCT
* * **
1951003 TTGCCTCCTGGACTTGGACCTGAGTTGGTGGTGACAGCATCACTATGTGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* * * *
1951060 TTGCCACCAGAACTTGGCCCTGAATTGGTGGTGACAGAATCACTAAATGCATGACCT
1 TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
* *
1951117 TTGCCTCCTGGACTAGGACC
1 TTGCCTCCTGAACTTGGACC
1951137 ACTGGTCTTG
Statistics
Matches: 165, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
56 1 0.01
57 162 0.98
58 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (57 bp):
TTGCCTCCTGAACTTGGACCTGAATTGGTGGTGACAGCATCACTAAATGCATGACCT
Found at i:1957061 original size:44 final size:42
Alignment explanation
Indices: 1956959--1957089 Score: 142
Period size: 43 Copynumber: 3.0 Consensus size: 42
1956949 AGCTCGTACA
*
1956959 ATGCCTACGTCCCAGACGAGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACGTCCCAGACGA-GTCTTACACGTAAATCAAATATCG
*
1957002 ATGCCACTGTCCCAGACAGAGTCTTACACGTAAATCTCAAT-TCG
1 ATGCCAC-GTCCCAGAC-GAGTCTTACACGTAAATC-AAATATCG
* *
1957046 ATGCCGACGTCCCAGACGTGGTCTTACACG-AAATCACATATCG
1 ATGCC-ACGTCCCAGACG-AGTCTTACACGTAAATCAAATATCG
1957089 A
1 A
1957090 AATCCTATGT
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.05
43 34 0.45
44 33 0.43
45 5 0.07
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (42 bp):
ATGCCACGTCCCAGACGAGTCTTACACGTAAATCAAATATCG
Found at i:1958834 original size:226 final size:227
Alignment explanation
Indices: 1958572--1959025 Score: 901
Period size: 226 Copynumber: 2.0 Consensus size: 227
1958562 TTATCATTTT
1958572 TATATATTTTAAAGATTTTTAAAGATTTTTTTTAATAATTTTATTTTTTAAACTTTTCTATAGTT
1 TATATATTTTAAAGATTTTTAAAGATTTTTTTTAATAATTTTATTTTTTAAACTTTTCTATAGTT
1958637 ATAAAAATTTGGAAATATATATATTTTCATAAATATTGTGATTTTTTTTTGAATTTTTTGGTTGG
66 ATAAAAATTTGGAAATATATATATTTTCATAAATATTGTGATTTTTTTTTGAATTTTTTGGTTGG
1958702 AATGGACTAATCTACACATTTTCGAAATTGTCAAGGACCCAACTGGTATTTGCATAAATTTGTTA
131 AATGGACTAATCTACACATTTTCGAAATTGTCAAGGACCCAACTGGTATTTGCATAAATTTGTTA
1958767 TACAAGTTATTCGAATTATTTGAGTTGTAAAA
196 TACAAGTTATTCGAATTATTTGAGTTGTAAAA
1958799 TATATATTTT-AAGATTTTTAAAGATTTTTTTTAATAATTTTATTTTTTAAACTTTTCTATAGTT
1 TATATATTTTAAAGATTTTTAAAGATTTTTTTTAATAATTTTATTTTTTAAACTTTTCTATAGTT
1958863 ATAAAAATTTGGAAATATATATATTTTCATAAATATTGTGATTTTTTTTTGAATTTTTTGGTTGG
66 ATAAAAATTTGGAAATATATATATTTTCATAAATATTGTGATTTTTTTTTGAATTTTTTGGTTGG
1958928 AATGGACTAATCTACACATTTTCGAAATTGTCAAGGACCCAACTGGTATTTGCATAAATTTGTTA
131 AATGGACTAATCTACACATTTTCGAAATTGTCAAGGACCCAACTGGTATTTGCATAAATTTGTTA
1958993 TACAAGTTATTCGAATTATTTGAGTTGTAAAA
196 TACAAGTTATTCGAATTATTTGAGTTGTAAAA
1959025 T
1 T
1959026 TCAACTTGAC
Statistics
Matches: 227, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 217 0.96
227 10 0.04
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (227 bp):
TATATATTTTAAAGATTTTTAAAGATTTTTTTTAATAATTTTATTTTTTAAACTTTTCTATAGTT
ATAAAAATTTGGAAATATATATATTTTCATAAATATTGTGATTTTTTTTTGAATTTTTTGGTTGG
AATGGACTAATCTACACATTTTCGAAATTGTCAAGGACCCAACTGGTATTTGCATAAATTTGTTA
TACAAGTTATTCGAATTATTTGAGTTGTAAAA
Found at i:1963328 original size:14 final size:14
Alignment explanation
Indices: 1963309--1963338 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1963299 ATGAGTTTGA
1963309 GTATGTTAAAACAC
1 GTATGTTAAAACAC
1963323 GTATGTTAAAACAC
1 GTATGTTAAAACAC
1963337 GT
1 GT
1963339 TTATCCTCCT
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:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (14 bp):
GTATGTTAAAACAC
Found at i:1976426 original size:23 final size:24
Alignment explanation
Indices: 1976400--1976446 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1976390 CCCTTCTCCT
1976400 CTCTGTTCTTTT-TTTTCTTTTTG
1 CTCTGTTCTTTTGTTTTCTTTTTG
* *
1976423 CTCTTTTTTTTTGTTTTCTTTTTG
1 CTCTGTTCTTTTGTTTTCTTTTTG
1976447 TTGTTGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (24 bp):
CTCTGTTCTTTTGTTTTCTTTTTG
Found at i:1993147 original size:3 final size:3
Alignment explanation
Indices: 1993139--1993168 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1993129 CGCTTTTATA
1993139 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1993169 TTCGAGTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:1995465 original size:23 final size:22
Alignment explanation
Indices: 1995422--1995479 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1995412 AAAGGGTATC
* *
1995422 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1995443 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1995466 TACATATCATATCT
1 TACAAATCATATCT
1995480 AAGATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1995473 original size:17 final size:17
Alignment explanation
Indices: 1995451--1995503 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 17
1995441 ATTACAAAAT
1995451 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
1995468 CATATCATATCTAAGATTA
1 CATATC-T-TCTAAGATTA
* *
1995487 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
1995504 TGTTTCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:1995482 original size:19 final size:20
Alignment explanation
Indices: 1995435--1995492 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
1995425 AAATTAAATC
*
1995435 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
1995458 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
1995477 TCTAAGATTACATATC
1 TCTAAGATTACATATC
1995493 CTCGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
22 7 0.21
23 11 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Found at i:2003219 original size:26 final size:26
Alignment explanation
Indices: 2003189--2003246 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
2003179 GAAATTAAAT
*
2003189 ATTTATT-TTACTTTAAAATAATATAA
1 ATTTATTATTA-TTTAAAATAAGATAA
*
2003215 ATTTAATTATTATTTAAATTAAGATAA
1 ATTT-ATTATTATTTAAAATAAGATAA
*
2003242 TTTTA
1 ATTTA
2003247 ACATGTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 5 0.19
27 19 0.70
28 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTATTATTATTTAAAATAAGATAA
Found at i:2003390 original size:16 final size:17
Alignment explanation
Indices: 2003369--2003402 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2003359 TGGTATAATA
2003369 TTAA-TTTTACTAAAAT
1 TTAATTTTTACTAAAAT
*
2003385 TTAATTTTTACTATAAT
1 TTAATTTTTACTAAAAT
2003402 T
1 T
2003403 ATGCACATAT
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:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATTTTTACTAAAAT
Found at i:2007044 original size:59 final size:59
Alignment explanation
Indices: 2006976--2007145 Score: 313
Period size: 59 Copynumber: 2.9 Consensus size: 59
2006966 TCAAGTTTGT
* *
2006976 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
2007035 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
2007094 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
2007146 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 108 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (59 bp):
TTTATTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:2007179 original size:16 final size:16
Alignment explanation
Indices: 2007158--2007189 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2007148 TAATTTGATT
*
2007158 ATTTTACTAACAATTA
1 ATTTTAATAACAATTA
2007174 ATTTTAATAACAATTA
1 ATTTTAATAACAATTA
2007190 GTTCTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTAATAACAATTA
Found at i:2008997 original size:57 final size:57
Alignment explanation
Indices: 2008851--2008965 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
2008841 ATTAATTATT
* *
2008851 ATAATTTAAATACTTTTATTATACATATATTATTAAATTAATTTATTTTATTGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
2008908 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
1 ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
2008965 A
1 A
2008966 ATTGTTAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.53
Consensus pattern (57 bp):
ATAATTTAAATAATTTTATTATACATATATTATTAAATTAATTTATTTTAATGTTAA
Found at i:2010742 original size:20 final size:20
Alignment explanation
Indices: 2010717--2010756 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2010707 AATATTTTCC
*
2010717 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2010737 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2010757 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2010762 original size:34 final size:34
Alignment explanation
Indices: 2010705--2010770 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
2010695 CAAACACCAG
*
2010705 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
2010740 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
2010771 ATATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:2018139 original size:17 final size:17
Alignment explanation
Indices: 2018117--2018156 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2018107 AAAAACTTAC
*
2018117 ATTAACCCGAACATAAA
1 ATTAACCCAAACATAAA
*
2018134 ATTAACCCAAACTTAAA
1 ATTAACCCAAACATAAA
2018151 A-TAACC
1 ATTAACC
2018157 GAATTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.20
Consensus pattern (17 bp):
ATTAACCCAAACATAAA
Found at i:2032506 original size:16 final size:16
Alignment explanation
Indices: 2032487--2032538 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
2032477 GGCATTTTTG
* *
2032487 GTTTGAATTATTTCGA
1 GTTTAAATTATTTCAA
*
2032503 GTTTAAATTGTTTCAA
1 GTTTAAATTATTTCAA
*
2032519 GTTTAAA-CATTTCAA
1 GTTTAAATTATTTCAA
*
2032534 ATTTA
1 GTTTA
2032539 TATTCTAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 10 0.33
16 20 0.67
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.48
Consensus pattern (16 bp):
GTTTAAATTATTTCAA
Found at i:2035948 original size:18 final size:18
Alignment explanation
Indices: 2035925--2035970 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2035915 TTTGTTCACA
* * *
2035925 GGTTTTGGTGTTGGGTGT
1 GGTTTTGGAGTTGGATGG
2035943 GGTTTTGGAGTTGGATGG
1 GGTTTTGGAGTTGGATGG
2035961 GGTTTTGGAG
1 GGTTTTGGAG
2035971 GTCTGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.07, C:0.00, G:0.50, T:0.43
Consensus pattern (18 bp):
GGTTTTGGAGTTGGATGG
Found at i:2039465 original size:76 final size:76
Alignment explanation
Indices: 2039329--2039717 Score: 751
Period size: 76 Copynumber: 5.1 Consensus size: 76
2039319 CCAGTTTTTA
* *
2039329 TAGTTTCCTTCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
1 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
2039394 TTTAGGTCCTC
66 TTTAGGTCCTC
2039405 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
1 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
2039470 TTTAGGTCCTC
66 TTTAGGTCCTC
2039481 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
1 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
2039546 TTTAGGTCCTC
66 TTTAGGTCCTC
2039557 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
1 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
2039622 TTTAGGTCCTC
66 TTTAGGTCCTC
*
2039633 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTTGAGACA
1 TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
2039698 TTTAGGTCCTC
66 TTTAGGTCCTC
2039709 TAGTGTCCT
1 TAGTGTCCT
2039718 TTTCATTCTA
Statistics
Matches: 310, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 310 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (76 bp):
TAGTGTCCTCCTTAAGAGCTCGGTGTTTTACGTATTTTTTATATATGACTATAAATCTCGAGACA
TTTAGGTCCTC
Found at i:2046979 original size:60 final size:63
Alignment explanation
Indices: 2046847--2046988 Score: 175
Period size: 60 Copynumber: 2.3 Consensus size: 63
2046837 TTTAGACAAA
* * *
2046847 AAAGCCAAGTTTAGGTACCTAATTGGACCAAGAAAAAAATCTTTAGGTACTAAATTAAACCTT
1 AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGGTACCAAATTAAACCTT
* * * *
2046910 AAAGTCAAGTTCAAGTACCTAATTAGACCAA-AAAAGAA-C-TT-GGATACCAAATTGAACCTT
1 AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGG-TACCAAATTAAACCTT
*
2046970 CAAGCCAAGTTCAGGTACC
1 AAAGCCAAGTTCAGGTACC
2046989 AAAATGTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 32 0.47
61 1 0.01
62 6 0.09
63 27 0.40
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (63 bp):
AAAGCCAAGTTCAGGTACCTAATTAGACCAAGAAAAAAATCTTTAGGTACCAAATTAAACCTT
Done.