Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 14 of 438
Found at i:3795325 original size:22 final size:22
Alignment explanation
Indices: 3795297--3795349 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3795287 ATATGGTAGC
* *
3795297 AAAACAAAAATATAACAGCAGT
1 AAAACAAAAACATAACAGCAGG
*
3795319 AAAACAACAACATAACAGCAGG
1 AAAACAAAAACATAACAGCAGG
3795341 AAAA-AAAAA
1 AAAACAAAAA
3795350 GTCATGTGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.68, C:0.15, G:0.09, T:0.08
Consensus pattern (22 bp):
AAAACAAAAACATAACAGCAGG
Found at i:3798730 original size:179 final size:179
Alignment explanation
Indices: 3798430--3798789 Score: 648
Period size: 179 Copynumber: 2.0 Consensus size: 179
3798420 TCAAAGCATC
*
3798430 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCACAAGGACATAA
1 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCAAAAGGACATAA
3798495 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATGCAGAA
66 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATGCAGAA
* *
3798560 TGAACGGAACAAATTCAAAATCAAACCTATATCTATTGTGAAGAGACTA
131 TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
*
3798609 AATCATTAGCTTTGCATCTTCAAAACGTTTTTCCTAAAGGAAGAATTAAATGCAAAAGGACATAA
1 AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCAAAAGGACATAA
* *
3798674 ACTTCAAAAGAGATTCATCATTAAACATTAGATGCTTCCCTAGGTAATGGTGTAGAAATGCAGAA
66 ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATGCAGAA
* *
3798739 TGAACGGCACAAATTCAAGATCAAACCTATACCTATTATGAAGAGACTA
131 TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
3798788 AA
1 AA
3798790 GCCAGTCTAG
Statistics
Matches: 173, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
179 173 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (179 bp):
AATCATTAGCTTTGCATCTTCAAAACCTTTTTCCTAAAGGAAGAATTAAATGCAAAAGGACATAA
ACTTCAAAAGAGATTCATCATTAAACATTAAATGCTTCCCTAGATAATGGTGTAGAAATGCAGAA
TGAACGGAACAAATTCAAAATCAAACCTATACCTATTATGAAGAGACTA
Found at i:3799864 original size:18 final size:18
Alignment explanation
Indices: 3799841--3799884 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3799831 GATATTAGCA
3799841 GATGATCAAAA-CTATGGT
1 GATGATCAAAATC-ATGGT
**
3799859 GATGATCATCATCATGGT
1 GATGATCAAAATCATGGT
3799877 GATGATCA
1 GATGATCA
3799885 TCATGGAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GATGATCAAAATCATGGT
Found at i:3799879 original size:15 final size:15
Alignment explanation
Indices: 3799861--3799890 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3799851 ACTATGGTGA
3799861 TGATCATCATCATGG
1 TGATCATCATCATGG
*
3799876 TGATGATCATCATGG
1 TGATCATCATCATGG
3799891 AACAGAGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (15 bp):
TGATCATCATCATGG
Found at i:3799885 original size:18 final size:18
Alignment explanation
Indices: 3799854--3799888 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3799844 GATCAAAACT
3799854 ATGGTGATGATCATCATC
1 ATGGTGATGATCATCATC
3799872 ATGGTGATGATCATCAT
1 ATGGTGATGATCATCAT
3799889 GGAACAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (18 bp):
ATGGTGATGATCATCATC
Found at i:3802796 original size:2 final size:2
Alignment explanation
Indices: 3802791--3802816 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3802781 TGCACGTGTG
3802791 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3802817 ATTTAGCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3803375 original size:31 final size:32
Alignment explanation
Indices: 3803334--3803393 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
3803324 TAATCGACTC
*
3803334 TTTTTCAAAAAGTTGAAGGTCAAATTTAACTA
1 TTTTTCAAAAAGTTAAAGGTCAAATTTAACTA
*
3803366 TTTTT-AAAAAGTTAAAGGTTAAATTTAA
1 TTTTTCAAAAAGTTAAAGGTCAAATTTAA
3803394 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (32 bp):
TTTTTCAAAAAGTTAAAGGTCAAATTTAACTA
Found at i:3807729 original size:294 final size:286
Alignment explanation
Indices: 3807201--3807781 Score: 844
Period size: 294 Copynumber: 2.0 Consensus size: 286
3807191 CTGTGTTTTA
**
3807201 AGCCAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATTTAAAAAAATG
1 AGCCAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATCGAAAAAAATG
** **
3807266 AAGTAAGCCATCTGCTAGAATATTCCTTTGTGTTTGACCACATTGATGGACTGTCAAAAGCACTT
66 AAG-AAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAAAGCACTT
*
3807331 TGTATGTCAAGGACCACACTTGGTAATCAAATTCTTAGGTGGTAACTTCATAGTGTGTAAAACTC
130 TGTATGTCAAGGACCACACTTGGTAATCAAATTCTTAGGTGGCAACTTCATAGTGTGTAAAACTC
*
3807396 ATTATTGACCTAGGTAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTT
195 ATTATTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTT
* * *
3807461 TCATATGGGAGAGGGCATTTTTTGATG
260 CCATATAGGAGAGGGCATTTTTCGATG
*
3807488 AGCCAAGAATAACTAGTATTTAATAGGAGAAAACACCTCGGTATAAGAATTCATAAAGCTATCGA
1 AGCCAAGAATAACTAGTATTTAATAGGAG-AAA-A------TATAAGAATCCATAAAGCTATCGA
* *
3807553 AAAAAATG-A-AA-TCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAGA
58 AAAAAATGAAGAAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAA
* *
3807615 AGCACTTTGTATGTCAAGGACCACACTTGTTATTAATCAAATTCTTAGGTGGCAACTTCATGGTG
123 AGCACTTTGTATGTCAAGGACCACACTTG---GTAATCAAATTCTTAGGTGGCAACTTCATAGTG
* * * *
3807680 TGTAATACTCATTATTGACCTAGGAAGAATATATAAAAAGCTTTTAATGAGGCTAGTAACCGGGG
185 TGTAAAACTCATTATTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGG
*
3807745 TACATGATTTCCATATAGGCGAGGGCATTTTTCGATG
250 TACATGATTTCCATATAGGAGAGGGCATTTTTCGATG
3807782 GTAGTAATCT
Statistics
Matches: 262, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
287 29 0.11
288 3 0.01
289 1 0.00
291 74 0.28
292 2 0.01
294 124 0.47
295 29 0.11
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (286 bp):
AGCCAAGAATAACTAGTATTTAATAGGAGAAAATATAAGAATCCATAAAGCTATCGAAAAAAATG
AAGAAGCCATCTGCTAGAATATTCCTCGGTGCGTGACCACATTGATGGACTGTCAAAAGCACTTT
GTATGTCAAGGACCACACTTGGTAATCAAATTCTTAGGTGGCAACTTCATAGTGTGTAAAACTCA
TTATTGACCTAGGAAGAATATAAAAAAAACTTTTAATGAGGCTAGTAACCAGGGTACATGATTTC
CATATAGGAGAGGGCATTTTTCGATG
Found at i:3809836 original size:20 final size:18
Alignment explanation
Indices: 3809797--3809833 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3809787 TATAGTTTAC
*
3809797 TTTTTTATATAGTTAAAA
1 TTTTTTATATAATTAAAA
3809815 TTTTTTATATTAATTAAAA
1 TTTTTTATA-TAATTAAAA
3809834 ATTAAGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTTATATAATTAAAA
Found at i:3810683 original size:14 final size:14
Alignment explanation
Indices: 3810664--3810692 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3810654 TATATATTTA
3810664 AATTTTAAATGGTG
1 AATTTTAAATGGTG
3810678 AATTTTAAATGGTG
1 AATTTTAAATGGTG
3810692 A
1 A
3810693 TATAGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
AATTTTAAATGGTG
Found at i:3810990 original size:28 final size:28
Alignment explanation
Indices: 3810959--3811029 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
3810949 TTAAAAATTT
3810959 AAATATTAAAAATTTATTAAAATTA-AAA
1 AAATA-TAAAAATTTATTAAAATTATAAA
* *
3810987 AAATATATAAAATATA-TAGAATTATAAA
1 AAATATA-AAAATTTATTAAAATTATAAA
3811015 AAATA-AAAAATTTAT
1 AAATATAAAAATTTAT
3811030 AATGTTGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 7 0.19
27 10 0.27
28 20 0.54
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AAATATAAAAATTTATTAAAATTATAAA
Found at i:3811026 original size:17 final size:17
Alignment explanation
Indices: 3810951--3811031 Score: 56
Period size: 17 Copynumber: 4.6 Consensus size: 17
3810941 AATTTTAATT
* *
3810951 AAAAATT-TAAATATTA
1 AAAAATTATAAAAAATA
* * *
3810967 AAAATTTATTAAAATTAA
1 AAAAATTATAAAAAAT-A
*
3810985 AAAAATATATAAAATATA
1 AAAAAT-TATAAAAAATA
* *
3811003 TAGAATTATAAAAAATA
1 AAAAATTATAAAAAATA
3811020 AAAAATTTATAA
1 AAAAA-TTATAA
3811032 TGTTGTAAGA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
16 6 0.12
17 19 0.39
18 17 0.35
19 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (17 bp):
AAAAATTATAAAAAATA
Found at i:3812792 original size:12 final size:12
Alignment explanation
Indices: 3812777--3812802 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3812767 TTAAACATTT
3812777 TTAATATTATTA
1 TTAATATTATTA
3812789 TTAATATTATTA
1 TTAATATTATTA
3812801 TT
1 TT
3812803 TGGTAGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAATATTATTA
Found at i:3815052 original size:30 final size:30
Alignment explanation
Indices: 3815018--3815078 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
3815008 AAATTCTACC
3815018 TAAGGCTGTTCCAAATTAAAATGCTAAACT
1 TAAGGCTGTTCCAAATTAAAATGCTAAACT
3815048 TAAGGCTGTTCCAAATTAAAATGCTAAACT
1 TAAGGCTGTTCCAAATTAAAATGCTAAACT
3815078 T
1 T
3815079 GAGCCTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.31
Consensus pattern (30 bp):
TAAGGCTGTTCCAAATTAAAATGCTAAACT
Found at i:3816972 original size:61 final size:60
Alignment explanation
Indices: 3816905--3817024 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 60
3816895 TAAACATGTA
*
3816905 AATTAAAATTTATGTTTAAAACTATTTTCAATGTTTATAGTATTTTCAACTTTTTTTATTT
1 AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAA-TTTTTTTATTT
*
3816966 AATTAAAATTTATGTTAAAAATTATTTTCAATGTTTATAGTATTTTCAATTTTTTTATT
1 AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAATTTTTTTATT
3817025 ATTTAAATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 10 0.18
61 47 0.82
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (60 bp):
AATTAAAATTTATGTTAAAAACTATTTTCAATGTTTATAGTATTTTCAATTTTTTTATTT
Found at i:3817027 original size:18 final size:18
Alignment explanation
Indices: 3816986--3817028 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3816976 TATGTTAAAA
3816986 ATTATTTTCAATGTTTAT
1 ATTATTTTCAATGTTTAT
* * *
3817004 AGTATTTTCAATTTTTTT
1 ATTATTTTCAATGTTTAT
3817022 ATTATTT
1 ATTATTT
3817029 AAATTTGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTATTTTCAATGTTTAT
Found at i:3817577 original size:11 final size:11
Alignment explanation
Indices: 3817563--3817630 Score: 64
Period size: 11 Copynumber: 6.1 Consensus size: 11
3817553 ATTTTGCTGC
3817563 TATTTTATTAT
1 TATTTTATTAT
* *
3817574 TATTTAAATAT
1 TATTTTATTAT
* * * *
3817585 TGTATAATTTT
1 TATTTTATTAT
*
3817596 TATTTTATTGT
1 TATTTTATTAT
3817607 TAATTTTATTAT
1 T-ATTTTATTAT
3817619 TATTTTATTAT
1 TATTTTATTAT
3817630 T
1 T
3817631 TTATTGTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 35 0.78
12 10 0.22
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:3817604 original size:19 final size:19
Alignment explanation
Indices: 3817582--3817641 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
3817572 ATTATTTAAA
3817582 TATTGTATAATTTTTATT-T
1 TATTGTATAA-TTTTATTAT
3817601 TATTGT-TAATTTTATTAT
1 TATTGTATAATTTTATTAT
* * *
3817619 TATTTTATTATTTTATTGT
1 TATTGTATAATTTTATTAT
3817638 TATT
1 TATT
3817642 AATATTAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 7 0.19
18 9 0.25
19 20 0.56
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TATTGTATAATTTTATTAT
Found at i:3817640 original size:11 final size:11
Alignment explanation
Indices: 3817595--3817641 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
3817585 TGTATAATTT
3817595 TTATTTTATTG
1 TTATTTTATTG
*
3817606 TTAATTTTATTA
1 TT-ATTTTATTG
3817618 TTATTTTA---
1 TTATTTTATTG
3817626 TTATTTTATTG
1 TTATTTTATTG
3817637 TTATT
1 TTATT
3817642 AATATTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
8 8 0.26
11 13 0.42
12 10 0.32
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (11 bp):
TTATTTTATTG
Found at i:3820341 original size:13 final size:13
Alignment explanation
Indices: 3820323--3820350 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3820313 GGCTGTTATT
3820323 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3820336 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3820349 TA
1 TA
3820351 TTAAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:3824193 original size:41 final size:41
Alignment explanation
Indices: 3824148--3824265 Score: 105
Period size: 41 Copynumber: 3.1 Consensus size: 41
3824138 GAAGGTAATC
3824148 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
* * * * *
3824189 TTC-TTATAC-TT---TTC-TAC--TAT-GA-AGTTTAAT-T
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTT-GTGT
3824220 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
1 TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
3824261 TTCTT
1 TTCTT
3824266 ATACTTTTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 24
0.62 0.11 0.27
Matches are distributed among these distances:
31 9 0.16
32 7 0.13
33 4 0.07
35 2 0.04
36 6 0.11
37 2 0.04
39 4 0.07
40 7 0.13
41 14 0.25
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (41 bp):
TTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGT
Found at i:3824265 original size:72 final size:72
Alignment explanation
Indices: 3824143--3824292 Score: 282
Period size: 72 Copynumber: 2.1 Consensus size: 72
3824133 TTCTGGAAGG
*
3824143 TAATCTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
1 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
3824208 TGAAGTT
66 TGAAGTT
3824215 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
1 TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
3824280 TGAAGTT
66 TGAAGTT
*
3824287 TGATTT
1 TAATTT
3824293 AATTTTTTAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.18, C:0.14, G:0.13, T:0.55
Consensus pattern (72 bp):
TAATTTTCTTTATCCATTAGGTTCTTTCTGTTTCTAGAGTTTGTGTTTCTTATACTTTTCTACTA
TGAAGTT
Found at i:3828499 original size:15 final size:15
Alignment explanation
Indices: 3828479--3828512 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3828469 AGTTTAAATA
*
3828479 ATTTTTTTTAAATTT
1 ATTTTTTGTAAATTT
3828494 ATTTTTTGTAAATTT
1 ATTTTTTGTAAATTT
3828509 ATTT
1 ATTT
3828513 AATTGAACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTTTGTAAATTT
Found at i:3829840 original size:5 final size:5
Alignment explanation
Indices: 3829832--3829865 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
3829822 ACCACTAGAG
3829832 TTTTA TTTTA TTTTA TTTTTA TTTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTT
3829866 TTTAAAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:3829853 original size:11 final size:11
Alignment explanation
Indices: 3829832--3829860 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3829822 ACCACTAGAG
3829832 TTTTA-TTTTA
1 TTTTATTTTTA
3829842 TTTTATTTTTA
1 TTTTATTTTTA
3829853 TTTTATTT
1 TTTTATTT
3829861 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:3829867 original size:16 final size:16
Alignment explanation
Indices: 3829832--3829866 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3829822 ACCACTAGAG
3829832 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
3829848 TTTTATTTTA-TTTAT
1 TTTTATTTTATTTTAT
3829863 TTTT
1 TTTT
3829867 TTAAAGTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:3831429 original size:2 final size:2
Alignment explanation
Indices: 3831422--3831452 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3831412 ATTGCTAATT
3831422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3831453 TATTTCTCGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3831608 original size:15 final size:16
Alignment explanation
Indices: 3831573--3831610 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3831563 ATTTATCTAA
3831573 AATTACAAATATTTATT
1 AATTA-AAATATTTATT
3831590 -ATTAAAAT-TTTATT
1 AATTAAAATATTTATT
3831604 AATTAAA
1 AATTAAA
3831611 TACATAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
15 10 0.50
16 4 0.20
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAATATTTATT
Found at i:3832597 original size:18 final size:17
Alignment explanation
Indices: 3832561--3832596 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3832551 CTACATCAAC
3832561 AATTAAAAACTTTTTAA
1 AATTAAAAACTTTTTAA
* *
3832578 AATTTAAAATTTTTTAA
1 AATTAAAAACTTTTTAA
3832595 AA
1 AA
3832597 AGAGTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAAAAACTTTTTAA
Found at i:3844735 original size:23 final size:23
Alignment explanation
Indices: 3844687--3844735 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3844677 CTATTCGAAT
* * *
3844687 TTCGAGTTAATCGAATTGAGTTA
1 TTCGAGTCAATCGAATTAAGTAA
3844710 TTCGAGTCAACTCGAA-TAAGTAA
1 TTCGAGTCAA-TCGAATTAAGTAA
3844733 TTC
1 TTC
3844736 AAGTTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (23 bp):
TTCGAGTCAATCGAATTAAGTAA
Found at i:3850909 original size:14 final size:15
Alignment explanation
Indices: 3850890--3850923 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3850880 AAAAATAGAT
3850890 TTTTAATTAA-AAAA
1 TTTTAATTAATAAAA
3850904 TTTTAATTAATTAAAA
1 TTTTAATTAA-TAAAA
3850920 TTTT
1 TTTT
3850924 TTTGGTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAATTAATAAAA
Found at i:3851686 original size:17 final size:17
Alignment explanation
Indices: 3851666--3851699 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3851656 AGGTTTAGGT
3851666 TTAAATATTTTAATTAA
1 TTAAATATTTTAATTAA
*
3851683 TTAAATTTTTTAATTAA
1 TTAAATATTTTAATTAA
3851700 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATATTTTAATTAA
Found at i:3851896 original size:31 final size:29
Alignment explanation
Indices: 3851827--3851900 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
3851817 ACAAAATAAT
**
3851827 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGCCA
*
3851856 AACATAAGTGACTAAAATGTAACCTGAGCCA
1 AACATAAGTGACTAAAATGTAACAT--GCCA
*
3851887 AACAAAAGTGACTA
1 AACATAAGTGACTA
3851901 TTTTTATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGCCA
Found at i:3852063 original size:23 final size:23
Alignment explanation
Indices: 3852031--3852076 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
3852021 ATTTAATGTA
* *
3852031 TCTCCTGTGATTAGTTGAATTTT
1 TCTCCCGTGATTAATTGAATTTT
3852054 TCTCCCGTGATTAATTGAATTTT
1 TCTCCCGTGATTAATTGAATTTT
3852077 AAATATTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (23 bp):
TCTCCCGTGATTAATTGAATTTT
Found at i:3856728 original size:2 final size:2
Alignment explanation
Indices: 3856721--3856751 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3856711 AACATCAAAA
3856721 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
3856752 CAAGGCCTAA
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:3861703 original size:2 final size:2
Alignment explanation
Indices: 3861696--3861720 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3861686 TACCTTGGTG
3861696 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3861721 GTGGATTGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3866706 original size:5 final size:5
Alignment explanation
Indices: 3866692--3866726 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3866682 ATAAACAGCA
3866692 AAAAC AAAAAC AAAAC AAAAC AAAAC AAAA- AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
3866727 TCTTTTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3868439 original size:20 final size:21
Alignment explanation
Indices: 3868414--3868457 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3868404 TTGAACATGT
3868414 TTTTTAT-ATTTTTGT-AATAA
1 TTTTTATGATTTTT-TAAATAA
3868434 TTTTTATGATTTTTTAAATAA
1 TTTTTATGATTTTTTAAATAA
3868455 TTT
1 TTT
3868458 ATTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTTATGATTTTTTAAATAA
Found at i:3873321 original size:17 final size:17
Alignment explanation
Indices: 3873301--3873335 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3873291 ATTTTTTATA
3873301 TATAATTTAAAATATTT
1 TATAATTTAAAATATTT
3873318 TATAATTTAAAATATTT
1 TATAATTTAAAATATTT
3873335 T
1 T
3873336 TGAAAGTCAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATAATTTAAAATATTT
Found at i:3873326 original size:28 final size:28
Alignment explanation
Indices: 3873272--3873326 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3873262 TCTGAGATAG
**
3873272 ATATAATCAAAATATTTTAATTTTTTAT
1 ATATAATCAAAATATTTTAATAATTTAT
*
3873300 ATATAATTTAAAATATTTT-ATAATTTA
1 ATATAA-TCAAAATATTTTAATAATTTA
3873327 AAATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATATAATCAAAATATTTTAATAATTTAT
Found at i:3875226 original size:21 final size:20
Alignment explanation
Indices: 3875190--3875231 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3875180 TTTTTTTTTT
3875190 ATTTTGAATCCCGAATCTCAA
1 ATTTTGAATCCCGAATC-CAA
* *
3875211 ATTTTGAATTCGGAATCCAA
1 ATTTTGAATCCCGAATCCAA
3875231 A
1 A
3875232 ACCCCAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTTTGAATCCCGAATCCAA
Found at i:3875919 original size:19 final size:19
Alignment explanation
Indices: 3875883--3875933 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
3875873 TAAAATTCAA
*
3875883 AAAATTATAAAAACTATTTTT
1 AAAATTAT-AAAACTA-TTAT
*
3875904 AAAATT-TAAAATTATTAT
1 AAAATTATAAAACTATTAT
3875922 AAAATTATAAAA
1 AAAATTATAAAA
3875934 AATAAATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 11 0.41
20 1 0.04
21 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTATAAAACTATTAT
Found at i:3875926 original size:39 final size:38
Alignment explanation
Indices: 3875861--3875934 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
3875851 TTTAATTACT
3875861 TTTTTAAAATTTTAAAATTCAAAAAATTATAAAAACTA
1 TTTTTAAAATTTTAAAATTCAAAAAATTATAAAAACTA
3875899 TTTTTAAAA-TTTAAAATT-ATTATAAAATTATAAAAA
1 TTTTTAAAATTTTAAAATTCA--A-AAAATTATAAAAA
3875935 ATAAATAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 1 0.03
37 9 0.27
38 10 0.30
39 13 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (38 bp):
TTTTTAAAATTTTAAAATTCAAAAAATTATAAAAACTA
Found at i:3878023 original size:17 final size:16
Alignment explanation
Indices: 3877996--3878029 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3877986 AATTTTAATT
*
3877996 TATAAATAAATGAATC
1 TATAAATAAATCAATC
3878012 TATAACATAAATCAATC
1 TATAA-ATAAATCAATC
3878029 T
1 T
3878030 TCCACTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (16 bp):
TATAAATAAATCAATC
Found at i:3881499 original size:18 final size:18
Alignment explanation
Indices: 3881476--3881510 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3881466 TTCAACCTAA
3881476 ATTATCTT-TAATATTATT
1 ATTATCTTATAA-ATTATT
3881494 ATTATCTTATAAATTAT
1 ATTATCTTATAAATTAT
3881511 GGATGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATCTTATAAATTATT
Found at i:3885326 original size:125 final size:125
Alignment explanation
Indices: 3885099--3885343 Score: 427
Period size: 125 Copynumber: 2.0 Consensus size: 125
3885089 TTTTTACTAT
* * *
3885099 TTAAATACCGGATTCAGTCCGTAGTCCTAGTTATAACTAACTTGTCCAAATTTGATCTATCGTCG
1 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
* *
3885164 CAGCTATAACTGGCAAATGCTTAACCAAAGATGGATGTTTTTTCCCTGATTTGTCAGTAG
66 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTCAGTAG
* *
3885224 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATTGTTG
1 TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
3885289 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTC
66 CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTC
3885344 CCAAGTGTTT
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 113 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (125 bp):
TTAAATACCGGATTCAGTCCATAGTCCTAGCTATAACTAACTTGTCCAAAATTGATCTATCGTCG
CAGCTATAACCGGCAAATGCTTAACCAAAGATAGATGTTTTTTCCCTGATTTGTCAGTAG
Found at i:3892105 original size:6 final size:6
Alignment explanation
Indices: 3892094--3892134 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
3892084 AGAAAAACCC
*
3892094 TATTTT TATTTT TATTTT TATTTT TA-TTG TATTTT CTATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT -TATTT
3892135 ATGCACATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:3894654 original size:46 final size:47
Alignment explanation
Indices: 3894599--3894826 Score: 247
Period size: 47 Copynumber: 4.9 Consensus size: 47
3894589 TAGGATGGTT
3894599 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-C
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAC
* * *
3894645 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG--AC
* * *
3894691 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG--AC
*
3894738 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-C
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAC
* ** *
3894785 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3894827 GCGGGTTACA
Statistics
Matches: 163, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
43 4 0.02
45 2 0.01
46 71 0.44
47 80 0.49
48 2 0.01
50 4 0.02
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (47 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAC
Found at i:3894700 original size:27 final size:27
Alignment explanation
Indices: 3894670--3894748 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
3894660 TTGAGTTGAG
3894670 TCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAGTTCGTGAGATGTAACTAGGCA
** *
3894697 TCCGAACTCGT-TGA-GT---T--G-A
1 TCCGAGTTCGTGAGATGTAACTAGGCA
3894716 GTCCGAGTTCGTGAGATGTAACTAGGCA
1 -TCCGAGTTCGTGAGATGTAACTAGGCA
3894744 TCCGA
1 TCCGA
3894749 ACTCGTTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 18
0.61 0.10 0.30
Matches are distributed among these distances:
19 1 0.03
20 10 0.27
21 2 0.05
22 3 0.08
25 3 0.08
26 2 0.05
27 15 0.41
28 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (27 bp):
TCCGAGTTCGTGAGATGTAACTAGGCA
Found at i:3894719 original size:47 final size:47
Alignment explanation
Indices: 3894601--3894772 Score: 253
Period size: 47 Copynumber: 3.7 Consensus size: 47
3894591 GGATGGTTGA
* * *
3894601 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAG
*
3894647 GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
3894694 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
3894741 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
3894773 ACTTATGGAT
Statistics
Matches: 117, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 33 0.28
47 78 0.67
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3906051 original size:12 final size:13
Alignment explanation
Indices: 3906023--3906050 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3906013 CTTTTCATAC
3906023 TTTACTATAATTT
1 TTTACTATAATTT
3906036 TTTACTATAATTT
1 TTTACTATAATTT
3906049 TT
1 TT
3906051 AAATAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTACTATAATTT
Found at i:3906443 original size:16 final size:18
Alignment explanation
Indices: 3906410--3906447 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
3906400 GTTTAAATTT
3906410 TATTTTTCTTATAATTTAA
1 TATTTTTCTTAT-ATTTAA
3906429 TATTTTT-TTAT-TTTAA
1 TATTTTTCTTATATTTAA
3906445 TAT
1 TAT
3906448 AATATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTCTTATATTTAA
Found at i:3906445 original size:21 final size:21
Alignment explanation
Indices: 3906412--3906452 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3906402 TTAAATTTTA
* *
3906412 TTTTTCTTATAATTTAATATT
1 TTTTTATTATAATATAATATT
*
3906433 TTTTTATTTTAATATAATAT
1 TTTTTATTATAATATAATAT
3906453 ATATTTCATA
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:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATTATAATATAATATT
Found at i:3907980 original size:83 final size:84
Alignment explanation
Indices: 3907841--3907999 Score: 232
Period size: 83 Copynumber: 1.9 Consensus size: 84
3907831 TAGCTTCGCT
*
3907841 CCTATGTATGCTACGTTTTATCATAAATTTCAAAATTCTATTGGAAATGATTATGTGAACGCTTT
1 CCTATGTATGCTACGTTTTATCATAAATTTCAAAATTCTATTGGAAATGATTATGTGAACACTTT
3907906 GG-GACTTTAAATAGATCC
66 GGAGACTTTAAATAGATCC
* * * **
3907924 CCTATGTATGCTATGTTTTATCATGAGTTTTGAAATT-TCATTGGAAATGATTATGTGAACACTT
1 CCTATGTATGCTACGTTTTATCATAAATTTCAAAATTCT-ATTGGAAATGATTATGTGAACACTT
*
3907988 TGGAGGCTTTAA
65 TGGAGACTTTAA
3908000 TTTGTGAGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 59 0.88
84 7 0.10
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.40
Consensus pattern (84 bp):
CCTATGTATGCTACGTTTTATCATAAATTTCAAAATTCTATTGGAAATGATTATGTGAACACTTT
GGAGACTTTAAATAGATCC
Found at i:3911149 original size:46 final size:44
Alignment explanation
Indices: 3911045--3911152 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3911035 TGTCTTTGAC
** * * *
3911045 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3911089 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3911135 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3911153 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3918532 original size:46 final size:44
Alignment explanation
Indices: 3918428--3918535 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3918418 TGTCTTTGAC
** * * *
3918428 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3918472 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3918518 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3918536 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3925913 original size:46 final size:44
Alignment explanation
Indices: 3925809--3925916 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3925799 TGTCTTTGAC
** * * *
3925809 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3925853 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3925899 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3925917 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3932972 original size:46 final size:44
Alignment explanation
Indices: 3932868--3932975 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3932858 TGTCTTTGAC
** * * *
3932868 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3932912 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3932958 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3932976 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3940360 original size:46 final size:44
Alignment explanation
Indices: 3940256--3940363 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
3940246 TGTCTTTGAC
** * * *
3940256 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
3940300 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
3940346 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
3940364 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:3945404 original size:89 final size:89
Alignment explanation
Indices: 3945224--3945392 Score: 268
Period size: 89 Copynumber: 1.9 Consensus size: 89
3945214 AAGCTCAAGC
* *
3945224 TGAATAATTAATTCGTAAAACTAACTCGACTCACCATTAAACATGGTTTGCATAGATGGTACTCG
1 TGAATAATTAATTCGTAAAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTCG
3945289 AACATAGGTATATAAGCTCTAAAT
66 AACATAGGTATATAAGCTCTAAAT
* * *
3945313 TGAATATTTAATTCGTACAAAC-AATTCAACTCACGATTAAACATGGTTTACATAGATGGTACTC
1 TGAATAATTAATTCGTA-AAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTC
*
3945377 GAACGTAGGTATATAA
65 GAACATAGGTATATAA
3945393 CTTGACAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
89 69 0.95
90 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (89 bp):
TGAATAATTAATTCGTAAAACTAACTCAACTCACCATTAAACATGGTTTACATAGATGGTACTCG
AACATAGGTATATAAGCTCTAAAT
Found at i:3961035 original size:31 final size:31
Alignment explanation
Indices: 3960999--3961064 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3960989 CACGCACACG
3960999 GATGACTAAAACAAGTAGTTAAATACTGTAT
1 GATGACTAAAACAAGTAGTTAAATACTGTAT
3961030 GATGACTAAAACAAGTAGTTAAATACTGTAT
1 GATGACTAAAACAAGTAGTTAAATACTGTAT
3961061 GATG
1 GATG
3961065 TTCTTTGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (31 bp):
GATGACTAAAACAAGTAGTTAAATACTGTAT
Found at i:3969613 original size:26 final size:26
Alignment explanation
Indices: 3969584--3969639 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3969574 TGATACAAAT
3969584 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3969610 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3969636 TGAT
1 TGAT
3969640 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3971217 original size:22 final size:21
Alignment explanation
Indices: 3971190--3971230 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3971180 CATGTTTGAC
*
3971190 TGTTGTTATTTACTGCATGCCA
1 TGTTGTTATTAACTG-ATGCCA
3971212 TGTTGTTATTAACTGATGC
1 TGTTGTTATTAACTGATGC
3971231 ATGGGATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (21 bp):
TGTTGTTATTAACTGATGCCA
Found at i:3976457 original size:4 final size:4
Alignment explanation
Indices: 3976448--3976478 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
3976438 GAAGAAATTG
3976448 AAAC AAAC AAAC AAAC AAAC AAAC AAA- AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
3976479 TGAATCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:3977646 original size:3 final size:3
Alignment explanation
Indices: 3977638--3977668 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3977628 ACAGCCACAC
*
3977638 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3977669 TTCTCTCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3981153 original size:20 final size:19
Alignment explanation
Indices: 3981128--3981166 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3981118 AGGACATTTT
* *
3981128 CATTTGTTTTGAGATCATTA
1 CATTTGCTTTAAGAT-ATTA
3981148 CATTTGCTTTAAGATATTA
1 CATTTGCTTTAAGATATTA
3981167 TTAGTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (19 bp):
CATTTGCTTTAAGATATTA
Found at i:3984404 original size:71 final size:71
Alignment explanation
Indices: 3984320--3984483 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
3984310 CGATTTGTCT
3984320 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
3984385 CTTTCA
66 CTTTCA
* *
3984391 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
3984456 CTTTCA
66 CTTTCA
3984462 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
3984484 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:3984521 original size:71 final size:70
Alignment explanation
Indices: 3984320--3984517 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
3984310 CGATTTGTCT
* * * * *
3984320 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
3984385 CTTTCA
65 CTTTCA
* * * *
3984391 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
3984456 CTTTCA
65 CTTTCA
* *
3984462 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
3984518 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:3991962 original size:71 final size:71
Alignment explanation
Indices: 3991878--3992041 Score: 310
Period size: 71 Copynumber: 2.3 Consensus size: 71
3991868 CGATTTGTCT
3991878 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
3991943 CTTTCA
66 CTTTCA
* *
3991949 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
3992014 CTTTCA
66 CTTTCA
3992020 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
3992042 GATACATCTC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
CTTTCA
Found at i:3992079 original size:71 final size:70
Alignment explanation
Indices: 3991878--3992075 Score: 249
Period size: 71 Copynumber: 2.8 Consensus size: 70
3991868 CGATTTGTCT
* * * * *
3991878 CGTAGCTCTCTTGTCTACATGGTGTCCGTCACTTGGAATCACGCATGCGACCCAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
3991943 CTTTCA
65 CTTTCA
* * * *
3991949 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
3992014 CTTTCA
65 CTTTCA
* *
3992020 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
3992076 TACAGGGTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
68 22 0.19
69 1 0.01
70 1 0.01
71 94 0.80
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:3996011 original size:31 final size:31
Alignment explanation
Indices: 3995946--3996010 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
3995936 TTTCTTACAA
*
3995946 TTTTGGATAGTTAATTGAATTAAATGAAAAT
1 TTTTGAATAGTTAATTGAATTAAATGAAAAT
* *
3995977 TTTTGAATAGTTTAA-TG-ATTAAATTATAAT
1 TTTTGAATAG-TTAATTGAATTAAATGAAAAT
3996007 TTTT
1 TTTT
3996011 TTTAGTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 15 0.50
31 11 0.37
32 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (31 bp):
TTTTGAATAGTTAATTGAATTAAATGAAAAT
Found at i:4001623 original size:69 final size:69
Alignment explanation
Indices: 4001512--4001650 Score: 251
Period size: 69 Copynumber: 2.0 Consensus size: 69
4001502 CAAGACTCTA
* *
4001512 TCAGCCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTGATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGATGAAAATCCTACAGCCACTGTGATTCCTGTTTTGGAA
4001577 CCTG
66 CCTG
*
4001581 TCAGCCCTACCACAACTACAAAACCTGATGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAA
1 TCAGCCCTACCACAACTACAAAACCTGATGAAAATCCTACAGCCACTGTGATTCCTGTTTTGGAA
4001646 CCTG
66 CCTG
4001650 T
1 T
4001651 TTTTCCTATC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.26
Consensus pattern (69 bp):
TCAGCCCTACCACAACTACAAAACCTGATGAAAATCCTACAGCCACTGTGATTCCTGTTTTGGAA
CCTG
Found at i:4006826 original size:16 final size:17
Alignment explanation
Indices: 4006793--4006828 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4006783 TAAATTCACC
*
4006793 TAATTTAAACTCAAAAA
1 TAATTCAAACTCAAAAA
4006810 TAATTCAAACT-AAAAA
1 TAATTCAAACTCAAAAA
4006826 TAA
1 TAA
4006829 CATAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (17 bp):
TAATTCAAACTCAAAAA
Found at i:4011001 original size:2 final size:2
Alignment explanation
Indices: 4010994--4011018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4010984 GTGAAATTAT
4010994 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4011019 GGTAAAAATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4011343 original size:22 final size:21
Alignment explanation
Indices: 4011302--4011359 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
4011292 AAGACCTATT
**
4011302 AATATAATTACGATAATTTAGA
1 AATATAATTAAAATAATTTA-A
*
4011324 AATATAATTAAAATATTTTAA
1 AATATAATTAAAATAATTTAA
*
4011345 AATTAAAATTAAAAT
1 AA-TATAATTAAAAT
4011360 TTAAAGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (21 bp):
AATATAATTAAAATAATTTAA
Found at i:4016196 original size:31 final size:30
Alignment explanation
Indices: 4016110--4016196 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 30
4016100 TTGTAATTTG
*
4016110 ATACAT-AAACTTTAA-TTTGATGC-AATT
1 ATACATGAAACTTTAATTTTGATTCAAATT
* * *
4016137 ATACATATGAAACTTTGATTGTGGTTCAAATGT
1 ATAC--ATGAAACTTTAATTTTGATTCAAAT-T
*
4016170 ATACATGAAATTTTAATTTTGATTCAA
1 ATACATGAAACTTTAATTTTGATTCAA
4016197 TCATGCACAT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
27 4 0.09
29 2 0.04
30 8 0.17
31 24 0.52
32 3 0.07
33 5 0.11
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.41
Consensus pattern (30 bp):
ATACATGAAACTTTAATTTTGATTCAAATT
Found at i:4018133 original size:10 final size:10
Alignment explanation
Indices: 4018118--4018142 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4018108 GTAAGTTTGT
4018118 TAATTATTAA
1 TAATTATTAA
4018128 TAATTATTAA
1 TAATTATTAA
4018138 TAATT
1 TAATT
4018143 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TAATTATTAA
Found at i:4025950 original size:21 final size:21
Alignment explanation
Indices: 4025921--4025964 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4025911 TTTGATAAAG
4025921 TCCTGGTTAATACAATATTGA
1 TCCTGGTTAATACAATATTGA
*
4025942 TCCTTGTTAATACAATATTGA
1 TCCTGGTTAATACAATATTGA
4025963 TC
1 TC
4025965 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (21 bp):
TCCTGGTTAATACAATATTGA
Found at i:4033707 original size:46 final size:46
Alignment explanation
Indices: 4033654--4033829 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
4033644 TATTTGGGCA
4033654 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
4033700 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
4033745 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
4033793 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4033830 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 6 0.06
46 59 0.54
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:4033809 original size:93 final size:93
Alignment explanation
Indices: 4033650--4033822 Score: 303
Period size: 93 Copynumber: 1.9 Consensus size: 93
4033640 GGGATATTTG
* *
4033650 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
4033715 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
4033743 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGA
4033807 GTTGAGTCCGAGTTCG
65 GTTGAGTCCGAGTTCG
4033823 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 4 0.05
93 72 0.95
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:4047859 original size:2 final size:2
Alignment explanation
Indices: 4047852--4047877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4047842 CTTTAACTTC
4047852 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4047878 TACTTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4052829 original size:2 final size:2
Alignment explanation
Indices: 4052822--4052850 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4052812 GAAGAGATGC
4052822 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 A
4052851 AAGGTGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4056590 original size:3 final size:3
Alignment explanation
Indices: 4056584--4056636 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
4056574 AAAAAAAAAA
** *
4056584 AAT AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT TGT AAT AAT AAA
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4056629 AAT AAT AA
1 AAT AAT AA
4056637 GTCCGTTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:4063158 original size:14 final size:14
Alignment explanation
Indices: 4063139--4063167 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4063129 CCTAACAAAC
4063139 ATGTATATATATAT
1 ATGTATATATATAT
4063153 ATGTATATATATAT
1 ATGTATATATATAT
4063167 A
1 A
4063168 AACAAGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATGTATATATATAT
Found at i:4064283 original size:3 final size:3
Alignment explanation
Indices: 4064275--4064307 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4064265 ATGTTTATTT
4064275 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
4064308 ATGGAACAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:4064824 original size:20 final size:20
Alignment explanation
Indices: 4064796--4064837 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
4064786 CTGAATTGAG
4064796 TATAATTTGAGCATCCCAAT
1 TATAATTTGAGCATCCCAAT
*
4064816 TATAGTTTGAGCATCCCAAT
1 TATAATTTGAGCATCCCAAT
4064836 TA
1 TA
4064838 CTTGTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
TATAATTTGAGCATCCCAAT
Found at i:4065348 original size:13 final size:13
Alignment explanation
Indices: 4065312--4065356 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
4065302 TTCAGGCTTC
*
4065312 AAGATTTGGGTTT
1 AAGATTCGGGTTT
* *
4065325 AAGTTTGGGGTTT
1 AAGATTCGGGTTT
*
4065338 AAGATTCGGGTTC
1 AAGATTCGGGTTT
4065351 AAGATT
1 AAGATT
4065357 AAGAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.40
Consensus pattern (13 bp):
AAGATTCGGGTTT
Found at i:4074821 original size:5 final size:5
Alignment explanation
Indices: 4074808--4074859 Score: 65
Period size: 5 Copynumber: 11.0 Consensus size: 5
4074798 AGTATTAATA
* *
4074808 TATAG TATAT TATA- T-TAT TATAT TATAT TATAT TATAT TATA- TATAA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
4074855 TATAT
1 TATAT
4074860 AAAACATAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 2 0.05
4 6 0.14
5 34 0.81
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (5 bp):
TATAT
Found at i:4074826 original size:23 final size:23
Alignment explanation
Indices: 4074767--4074858 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
4074757 TATAAAAATA
*
4074767 TATATTATA-TATTATATTA-ACT
1 TATATTATATTATTATATTATA-G
*
4074789 TAATATT-TAAGTATTA-ATATATAG
1 T-ATATTAT-ATTATTATAT-TATAG
*
4074813 TATATTATATTATTATATTATAT
1 TATATTATATTATTATATTATAG
*
4074836 TATATTATATTATATATAATATA
1 TATATTATATTAT-TATATTATA
4074859 TAAAACATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
22 2 0.03
23 36 0.62
24 19 0.33
25 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTATATTATTATATTATAG
Found at i:4074843 original size:15 final size:14
Alignment explanation
Indices: 4074764--4074859 Score: 87
Period size: 13 Copynumber: 6.9 Consensus size: 14
4074754 TTATATAAAA
4074764 ATATATATTATA-T
1 ATATATATTATATT
4074777 AT-TATATTA-ACTT
1 ATATATATTATA-TT
4074790 A-ATAT-TTAAGTATT
1 ATATATATT-A-TATT
*
4074804 AATATATAGTATATT
1 -ATATATATTATATT
4074819 ATAT-TATTATATT
1 ATATATATTATATT
4074832 ATATTATATTATATT
1 ATA-TATATTATATT
*
4074847 ATATATAATATAT
1 ATATATATTATAT
4074860 AAAACATAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
11 1 0.01
12 9 0.13
13 19 0.28
14 16 0.23
15 18 0.26
16 5 0.07
17 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (14 bp):
ATATATATTATATT
Found at i:4074860 original size:7 final size:7
Alignment explanation
Indices: 4074763--4074861 Score: 53
Period size: 7 Copynumber: 14.3 Consensus size: 7
4074753 TTTATATAAA
4074763 AATATAT
1 AATATAT
*
4074770 ATTATAT
1 AATATAT
*
4074777 ATTATATT
1 AATATA-T
*
4074785 AA-CT-T
1 AATATAT
*
4074790 AATATTT
1 AATATAT
4074797 AAGTAT-T
1 AA-TATAT
4074804 AATATAT
1 AATATAT
*
4074811 AGTATAT
1 AATATAT
*
4074818 TATAT-T
1 AATATAT
*
4074824 ATTATAT
1 AATATAT
*
4074831 TATATTAT
1 AATA-TAT
*
4074839 ATTATAT
1 AATATAT
*
4074846 TATATAT
1 AATATAT
4074853 AATATAT
1 AATATAT
4074860 AA
1 AA
4074862 AACATAAGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 14
0.70 0.16 0.14
Matches are distributed among these distances:
5 3 0.04
6 8 0.12
7 48 0.70
8 10 0.14
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (7 bp):
AATATAT
Found at i:4076098 original size:22 final size:23
Alignment explanation
Indices: 4076037--4076102 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
4076027 GTACTATTAT
* * *
4076037 TAGCACGTTAAGTGCTCTCTGTT
1 TAGCACATTTAGTGCTCTCTGTA
*
4076060 TAGCACATCT-GTGCTCTCTGTA
1 TAGCACATTTAGTGCTCTCTGTA
*
4076082 TAGCAC-TTTAGTACTCTCTGT
1 TAGCACATTTAGTGCTCTCTGT
4076103 TCGTTTGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 2 0.06
22 27 0.75
23 7 0.19
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (23 bp):
TAGCACATTTAGTGCTCTCTGTA
Found at i:4079734 original size:50 final size:50
Alignment explanation
Indices: 4079597--4079745 Score: 246
Period size: 50 Copynumber: 3.0 Consensus size: 50
4079587 CCATGGAAAC
*
4079597 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACAAATGA
* * *
4079647 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACAAATGA
4079697 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAATGG-CAAATG
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAA-GGACAAATG
4079746 GCAAATGACA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 89 0.98
51 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATTAAGGACAAATGA
Found at i:4079997 original size:31 final size:31
Alignment explanation
Indices: 4079758--4079990 Score: 340
Period size: 31 Copynumber: 7.5 Consensus size: 31
4079748 AAATGACAAC
4079758 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
4079789 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
4079820 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
4079851 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
4079882 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* ** *
4079913 TGAAAAATGGTAGCACCAGCTACCTGATCAA
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
4079944 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
4079975 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
4079991 TGGCTACAAG
Statistics
Matches: 186, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 186 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:4080008 original size:7 final size:7
Alignment explanation
Indices: 4079996--4080024 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
4079986 AGCTTTGGCT
4079996 ACAAGTG
1 ACAAGTG
4080003 ACAAGTG
1 ACAAGTG
4080010 ACAAGTG
1 ACAAGTG
4080017 ACAAGTG
1 ACAAGTG
4080024 A
1 A
4080025 TTTTTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:4080131 original size:47 final size:47
Alignment explanation
Indices: 4080029--4080151 Score: 126
Period size: 47 Copynumber: 2.6 Consensus size: 47
4080019 AAGTGATTTT
*
4080029 TGTATAAGACCATATCTGGGATATAGCATCGTTGTGATATATGCTAC
1 TGTATAAGACCATATCTGGGATATAGCATCGTTGAGATATATGCTAC
* * *
4080076 TGTATAAGACCATATTTGGGATAT-GACATCAG-TGAGATATGTGATTAC
1 TGTATAAGACCATATCTGGGATATAG-CATC-GTTGAGATATATG-CTAC
* * * *
4080124 -GTGTAAGACCATAGCTGGGCTATGGCAT
1 TGTATAAGACCATATCTGGGATATAGCAT
4080152 TATTATGTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
46 1 0.02
47 58 0.91
48 5 0.08
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (47 bp):
TGTATAAGACCATATCTGGGATATAGCATCGTTGAGATATATGCTAC
Found at i:4086230 original size:3 final size:3
Alignment explanation
Indices: 4086222--4086256 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4086212 AAGGTTAGAG
4086222 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
4086257 TTGCTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4088326 original size:13 final size:13
Alignment explanation
Indices: 4088308--4088353 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
4088298 CTTGGTTAGA
4088308 TATTTATTTTATT
1 TATTTATTTTATT
4088321 TATTTATTTTAATT
1 TATTTATTTT-ATT
* *
4088335 AATTTATTTTGTT
1 TATTTATTTTATT
4088348 TATTTA
1 TATTTA
4088354 CTTAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:4091656 original size:15 final size:14
Alignment explanation
Indices: 4091619--4091670 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
4091609 AATTATAAAA
4091619 AATACATATTAAATT
1 AATA-ATATTAAATT
4091634 --TAATATTAAGA-T
1 AATAATATTAA-ATT
4091646 AATATATATTAAATT
1 AATA-ATATTAAATT
4091661 AATAATATTA
1 AATAATATTA
4091671 TTTGAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 8 0.25
13 3 0.09
14 9 0.28
15 12 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
AATAATATTAAATT
Found at i:4092221 original size:7 final size:7
Alignment explanation
Indices: 4092177--4092203 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4092167 ATGTTATTTT
4092177 AAAAATG
1 AAAAATG
4092184 AAAAATG
1 AAAAATG
4092191 AAAAATG
1 AAAAATG
4092198 AAAAAT
1 AAAAAT
4092204 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:4092235 original size:27 final size:27
Alignment explanation
Indices: 4092184--4092236 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
4092174 TTTAAAAATG
*
4092184 AAAAATGAAAAATGAAAAATATATTTT
1 AAAAATGAAAAATGAAAAAGATATTTT
4092211 AAAAAT-AAAAA-GAATAAAGATTATTT
1 AAAAATGAAAAATGAA-AAAGA-TATTT
4092237 AATAGAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.13
26 9 0.39
27 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (27 bp):
AAAAATGAAAAATGAAAAAGATATTTT
Found at i:4093815 original size:18 final size:19
Alignment explanation
Indices: 4093777--4093817 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
4093767 TGGTTCATGT
4093777 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
4093796 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
4093814 TTTC
1 TTTC
4093818 TCATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:4094007 original size:39 final size:39
Alignment explanation
Indices: 4093940--4094074 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
4093930 ACCAATATGG
* * * *
4093940 CACCCAGTGCCTCATCGG-ATAGTTCGAAGCAATATTTAA
1 CACCCAGTGCCTCATCGGTCTAG-CCGAAGAAATATTTGA
* * * *
4093979 CACCCAGTGTCTCATCGGTCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGGTCTAGCCGAAGAAATATTTGA
* * * * *
4094017 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG-GTCTAGCCGAAGAAATAT-TTGA
*
4094058 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4094075 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 17 0.23
39 36 0.49
40 4 0.05
41 16 0.22
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGTCTAGCCGAAGAAATATTTGA
Found at i:4094340 original size:18 final size:19
Alignment explanation
Indices: 4094314--4094352 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
4094304 TTTCAATTCA
4094314 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
4094333 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
4094351 AT
1 AT
4094353 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:4095664 original size:5 final size:5
Alignment explanation
Indices: 4095654--4095685 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
4095644 TTATGTTTAT
4095654 ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA AT
4095686 TAAAACATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:4096429 original size:21 final size:22
Alignment explanation
Indices: 4096396--4096436 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4096386 AAAAATATAT
* *
4096396 AAAATTATTAAATTTTAAAATA
1 AAAATTATAAAATTTCAAAATA
4096418 AAAATTA-AAAATTTCAAAA
1 AAAATTATAAAATTTCAAAA
4096437 ATAATATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTATAAAATTTCAAAATA
Found at i:4097167 original size:29 final size:31
Alignment explanation
Indices: 4097115--4097184 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
4097105 TAGTCTAATC
* *
4097115 TTTTTATAATTTTTAAAGAGTTAAATTA-AA
1 TTTTTATCATTTTTAAAGAGTTAAAGTACAA
*
4097145 TTTTTATCATTTTTAGAGA-TTAAAGTACAA
1 TTTTTATCATTTTTAAAGAGTTAAAGTACAA
4097175 -TTTTATCATT
1 TTTTTATCATT
4097185 ACTAATCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.51
Consensus pattern (31 bp):
TTTTTATCATTTTTAAAGAGTTAAAGTACAA
Found at i:4097298 original size:25 final size:25
Alignment explanation
Indices: 4097264--4097314 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
4097254 GGGTCACAAC
*
4097264 TATGTACTTGTATACCTGTTCAGCA
1 TATGTACTTGTATACCTATTCAGCA
*
4097289 TATGTACTTGTATACTTATTCAGCA
1 TATGTACTTGTATACCTATTCAGCA
4097314 T
1 T
4097315 TCAATTCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (25 bp):
TATGTACTTGTATACCTATTCAGCA
Found at i:4103318 original size:40 final size:40
Alignment explanation
Indices: 4103224--4103318 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 40
4103214 ACTGACTTGG
* **
4103224 AAATCAGCAGTTTC-ACAATTTATATGTAAGTAATTAGCAA
1 AAATCAGCAG-TTCAACAATTTATATGTAAGCAAGAAGCAA
** * *
4103264 AAATCAATAATTCAACAATTTATATGTGA-CACAGAAGCAA
1 AAATCAGCAGTTCAACAATTTATATGTAAGCA-AGAAGCAA
4103304 AAATCAGCAGTTCAA
1 AAATCAGCAGTTCAA
4103319 GTTCATGTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (40 bp):
AAATCAGCAGTTCAACAATTTATATGTAAGCAAGAAGCAA
Found at i:4106448 original size:114 final size:114
Alignment explanation
Indices: 4106317--4106760 Score: 673
Period size: 114 Copynumber: 3.9 Consensus size: 114
4106307 TTATAGTTGG
*
4106317 TTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTGTATTGTGA-TTTTTTTAGT
1 TTAGGTTATATAAATTGTTAATGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTAGT
4106381 AATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGA
66 AATATA-TTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGA
* *
4106431 TTAAGTTATATAAATTGTTAATGTTTAGTGGTTTAGTGGT-TTAGTGTATTGT-AATTTTTTTAG
1 TTAGGTTATATAAATTGTTAATGTTTAGTGGTTTAGT-GTATTAGTGTATTGTGATTTTTTTTAG
* *
4106494 TAATATATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAATA
65 TAATATA-TTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGA
* *
4106545 TTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTATATTGTGATTTTTTTTAGT
1 TTAGGTTATATAAATTGTTAATGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTAGT
* *
4106610 AATATATTTAAAAAAATATTTTTATAGTTATTTTATTAGTAATTTAAGA
66 AATATATTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGA
*
4106659 TTAGGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTATTAGTGTGTATTGTGATTTTTTT
1 TTAGGTTATATAAATTGTTAATGTTTAGTGGTTTA--GTGTATTA--GTGTATTGTGA-TTTTTT
* *
4106722 TTAGTAATGTATTTAAAAAAATAATTTTATAGTTATTTT
61 TTAGTAATATATTTAAAAAAATAATTTTATAGCTATTTT
4106761 GGGTTAGTAT
Statistics
Matches: 308, Mismatches: 13, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
112 22 0.07
113 3 0.01
114 211 0.69
115 19 0.06
116 10 0.03
117 43 0.14
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (114 bp):
TTAGGTTATATAAATTGTTAATGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTTAGT
AATATATTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAAGA
Found at i:4106847 original size:15 final size:16
Alignment explanation
Indices: 4106819--4106849 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4106809 GTGATTTTTC
4106819 AATGTAATTTTTATAT
1 AATGTAATTTTTATAT
4106835 AATGTAA-TTTTATAT
1 AATGTAATTTTTATAT
4106850 TATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
AATGTAATTTTTATAT
Found at i:4109592 original size:23 final size:23
Alignment explanation
Indices: 4109510--4109596 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
4109500 CCTGATCAGT
*
4109510 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
4109532 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
4109552 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
4109575 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
4109597 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:4109993 original size:15 final size:15
Alignment explanation
Indices: 4109968--4110025 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
4109958 TCATATATAT
4109968 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
4109984 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
4109999 AATAATTTCAATCAA
1 TATAAATTCAATCAA
4110014 TATAAATTCAAT
1 TATAAATTCAAT
4110026 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:4111304 original size:5 final size:5
Alignment explanation
Indices: 4111291--4111327 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
4111281 TTCTTTAGTT
4111291 TATATA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA T
4111328 TAAAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:4111363 original size:8 final size:8
Alignment explanation
Indices: 4111350--4111378 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
4111340 TATCTTTATT
4111350 ATATAATA
1 ATATAATA
4111358 ATATAATA
1 ATATAATA
4111366 ATATAATA
1 ATATAATA
4111374 ATATA
1 ATATA
4111379 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:4115042 original size:27 final size:27
Alignment explanation
Indices: 4115012--4115069 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4115002 CAAGAAGACA
* * *
4115012 CAACTAGTCGTGCCTGTCAGATAGGCT
1 CAACTAATCGAGCCTGTCAGATAGGCG
* *
4115039 CAACTAATTGAGCCTTTCAGATAGGCG
1 CAACTAATCGAGCCTGTCAGATAGGCG
4115066 CAAC
1 CAAC
4115070 ATGTATGTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (27 bp):
CAACTAATCGAGCCTGTCAGATAGGCG
Found at i:4115886 original size:5 final size:5
Alignment explanation
Indices: 4115876--4115927 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
4115866 TTTTCAAACC
4115876 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
4115926 TA
1 TA
4115928 GGATAAACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:4126721 original size:5 final size:5
Alignment explanation
Indices: 4126711--4126768 Score: 116
Period size: 5 Copynumber: 11.6 Consensus size: 5
4126701 AGTAATTAAA
4126711 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
4126761 ATAAT ATA
1 ATAAT ATA
4126769 GGGTAAATTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:4127641 original size:7 final size:7
Alignment explanation
Indices: 4127629--4127665 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
4127619 ACTTCTAATT
4127629 AAATATA
1 AAATATA
4127636 AAATATA
1 AAATATA
4127643 AAATATA
1 AAATATA
4127650 AAATATA
1 AAATATA
4127657 AAATATA
1 AAATATA
4127664 AA
1 AA
4127666 GTATTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAATATA
Found at i:4141741 original size:26 final size:24
Alignment explanation
Indices: 4141708--4141768 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 24
4141698 ATATTTCTTA
*
4141708 TTTTATTTAATATTAATATAATTATT
1 TTTTATTTAATAATAATAT-A-TATT
*
4141734 TTTTATTTACTAATAATATATATT
1 TTTTATTTAATAATAATATATATT
4141758 TTTTATTTAAT
1 TTTTATTTAAT
4141769 TAGATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 14 0.44
25 1 0.03
26 17 0.53
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATTTAATAATAATATATATT
Done.