Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 16 of 218
Found at i:5647284 original size:46 final size:46
Alignment explanation
Indices: 5647234--5647357 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 46
5647224 CCCCACTCAG
* * * *
5647234 ATTTCCCCAATTTCATTTCCCTAATTTCCCATTTCCTATTCCCCCA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCATATTCCCCCA
** * * *
5647280 ATTTCTTCGATTTAATTTCCCCAATTTCCCAATTCATTTTCCCCTA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCATATTCCCCCA
5647326 ATTTCCCCGATTTCATTTCCCCAATTTCCCAA
1 ATTTCCCCGATTTCATTTCCCCAATTTCCCAA
5647358 CTGACCTGTC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (46 bp):
ATTTCCCCGATTTCATTTCCCCAATTTCCCAATTCATATTCCCCCA
Found at i:5647499 original size:13 final size:12
Alignment explanation
Indices: 5647466--5647499 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
5647456 GGTCATATTC
5647466 TTTTGTTGGCAT
1 TTTTGTTGGCAT
5647478 TTTTGTTGGCAT
1 TTTTGTTGGCAT
5647490 TTTTGCTTGG
1 TTTTG-TTGG
5647500 GCCGTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.06, C:0.09, G:0.26, T:0.59
Consensus pattern (12 bp):
TTTTGTTGGCAT
Found at i:5649374 original size:34 final size:34
Alignment explanation
Indices: 5649334--5649398 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
5649324 TACTATTAAC
* *
5649334 TTTTTAAATTTTAAACATAATTCTTTATTTTATA
1 TTTTTAAATATTAAACATAATTATTTATTTTATA
* *
5649368 TTTTTAAATATTATATATAATTATTTATTTT
1 TTTTTAAATATTAAACATAATTATTTATTTT
5649399 TAAATATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (34 bp):
TTTTTAAATATTAAACATAATTATTTATTTTATA
Found at i:5649428 original size:29 final size:27
Alignment explanation
Indices: 5649360--5649428 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
5649350 ATAATTCTTT
*
5649360 ATTTTATATTTTTAAATATTATATATA
1 ATTTTATATTTTTAAATATTATATAAA
5649387 ATTATT-TATTTTTAAATATTATACATAAA
1 ATT-TTATATTTTTAAATATTAT--ATAAA
*
5649416 ATTTTAAATTTTT
1 ATTTTATATTTTT
5649429 TTACATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 19 0.53
28 4 0.11
29 13 0.36
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATTTTTAAATATTATATAAA
Found at i:5649537 original size:9 final size:9
Alignment explanation
Indices: 5649523--5649646 Score: 55
Period size: 9 Copynumber: 13.8 Consensus size: 9
5649513 ACTAATTTCC
5649523 ACATAACAT
1 ACATAACAT
5649532 ACATAAC-T
1 ACATAACAT
5649540 CACATAACAT
1 -ACATAACAT
*
5649550 ACATAACTT
1 ACATAACAT
5649559 A-ATAACTTAT
1 ACATAAC--AT
* *
5649569 ATATATCAT
1 ACATAACAT
*
5649578 A-ACTCAACTT
1 ACA-T-AACAT
*
5649588 ACATAACTT
1 ACATAACAT
5649597 ACAT-A-AT
1 ACATAACAT
5649604 ACATAA-AT
1 ACATAACAT
* *
5649612 ATATATCAT
1 ACATAACAT
* *
5649621 ATCGTAACTT
1 A-CATAACAT
5649631 ACATAAC-T
1 ACATAACAT
5649639 CACATAAC
1 -ACATAAC
5649647 TTATGTATAT
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
7 5 0.06
8 16 0.18
9 51 0.57
10 13 0.14
11 5 0.06
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACATAACAT
Found at i:5649545 original size:18 final size:18
Alignment explanation
Indices: 5649522--5649557 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5649512 TACTAATTTC
5649522 CACATAACATACATAACT
1 CACATAACATACATAACT
5649540 CACATAACATACATAACT
1 CACATAACATACATAACT
5649558 TAATAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (18 bp):
CACATAACATACATAACT
Found at i:5649600 original size:47 final size:45
Alignment explanation
Indices: 5649535--5649718 Score: 149
Period size: 43 Copynumber: 4.3 Consensus size: 45
5649525 ATAACATACA
* *
5649535 TAACTCACATAACATACATAACTTA-ATAACTTATATATATCATAAC-
1 TAACTTACATAACTTACATAACTTACATAA---ATATATATCATAACG
*
5649581 TCAACTTACATAACTTACATAA--TACATAAATATATATCATATCG
1 T-AACTTACATAACTTACATAACTTACATAAATATATATCATAACG
* * * *
5649625 TAACTTACATAACTCACATAAC-T---T--ATGTATATCATATCA
1 TAACTTACATAACTTACATAACTTACATAAATATATATCATAACG
* * *
5649664 TAACTTACATAACTTGCATAA--TACATAAATATATATCATATCA
1 TAACTTACATAACTTACATAACTTACATAAATATATATCATAACG
*
5649707 TAAGTTACATAA
1 TAACTTACATAA
5649719 TTTAATTATA
Statistics
Matches: 119, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
38 1 0.01
39 32 0.27
41 2 0.02
43 57 0.48
44 2 0.02
45 2 0.02
46 5 0.04
47 18 0.15
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (45 bp):
TAACTTACATAACTTACATAACTTACATAAATATATATCATAACG
Found at i:5649630 original size:43 final size:43
Alignment explanation
Indices: 5649567--5649718 Score: 197
Period size: 43 Copynumber: 3.6 Consensus size: 43
5649557 TTAATAACTT
*
5649567 ATATATATCATAAC-TCAACTTACATAACTTACATAATACATAA
1 ATATATATCATATCAT-AACTTACATAACTTACATAATACATAA
* * *
5649610 ATATATATCATATCGTAACTTACATAACTCACAT-A-AC-T-T
1 ATATATATCATATCATAACTTACATAACTTACATAATACATAA
* *
5649649 ATGTATATCATATCATAACTTACATAACTTGCATAATACATAA
1 ATATATATCATATCATAACTTACATAACTTACATAATACATAA
*
5649692 ATATATATCATATCATAAGTTACATAA
1 ATATATATCATATCATAACTTACATAA
5649719 TTTAATTATA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 30 0.32
40 2 0.02
41 4 0.04
42 2 0.02
43 55 0.59
44 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (43 bp):
ATATATATCATATCATAACTTACATAACTTACATAATACATAA
Found at i:5649659 original size:82 final size:81
Alignment explanation
Indices: 5649542--5649718 Score: 266
Period size: 82 Copynumber: 2.2 Consensus size: 81
5649532 ACATAACTCA
* *
5649542 CATAACATACATAACTTAATAACTTATATATATCATAAC-TCAACTTACATAACTTACATAATAC
1 CATAACTTACATAACTCAATAACTTATATATATCATAACAT-AACTTACATAACTTACATAATAC
5649606 ATAAATATATATCATAT
65 ATAAATATATATCATAT
* * * *
5649623 CGTAACTTACATAACTCACATAACTTATGTATATCATATCATAACTTACATAACTTGCATAATAC
1 CATAACTTACATAACTCA-ATAACTTATATATATCATAACATAACTTACATAACTTACATAATAC
5649688 ATAAATATATATCATAT
65 ATAAATATATATCATAT
*
5649705 CATAAGTTACATAA
1 CATAACTTACATAA
5649719 TTTAATTATA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
81 15 0.17
82 70 0.81
83 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (81 bp):
CATAACTTACATAACTCAATAACTTATATATATCATAACATAACTTACATAACTTACATAATACA
TAAATATATATCATAT
Found at i:5649668 original size:39 final size:37
Alignment explanation
Indices: 5649589--5649718 Score: 131
Period size: 39 Copynumber: 3.4 Consensus size: 37
5649579 ACTCAACTTA
5649589 CATAACTTACATAA-TACATAA--ATATATATCATAT
1 CATAACTTACATAACTACATAACTATATATATCATAT
* *
5649623 CGTAACTTACATAACTCACATAACTTATGTATATCATAT
1 CATAACTTACATAACT-ACATAAC-TATATATATCATAT
*
5649662 CATAACTTACATAACTTGCATAATACATAAATATATATCATAT
1 CATAACTTACATAAC-TACAT-A-AC-T--ATATATATCATAT
*
5649705 CATAAGTTACATAA
1 CATAACTTACATAA
5649719 TTTAATTATA
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
34 13 0.16
35 1 0.01
36 6 0.08
39 29 0.37
40 2 0.03
41 3 0.04
43 25 0.32
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (37 bp):
CATAACTTACATAACTACATAACTATATATATCATAT
Found at i:5655233 original size:21 final size:21
Alignment explanation
Indices: 5655209--5655258 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5655199 CTACAACTTA
5655209 AAGCAAAGGCAGCAACGAGGG
1 AAGCAAAGGCAGCAACGAGGG
*
5655230 AAGCAGAGGCAGCAACGAGGG
1 AAGCAAAGGCAGCAACGAGGG
5655251 AAGCAAAG
1 AAGCAAAG
5655259 CAGAGTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.38, T:0.00
Consensus pattern (21 bp):
AAGCAAAGGCAGCAACGAGGG
Found at i:5655622 original size:43 final size:42
Alignment explanation
Indices: 5655569--5655730 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 42
5655559 AAAGCGTCGT
*
5655569 TAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGA
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGT-A
* * * *
5655612 TAAAAACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTACTA
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTT-GTA
* * *
5655655 GAAAAGCGCCGCTAAAGGTCCTGTTCTTTAGCGGCATTTGCTA
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTG-TA
*
5655698 CAAAAGCGCCGCTAAAGATCATGTTCTTTAGCG
1 TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCG
5655731 ATGTTTTTGT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
43 101 0.99
44 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (42 bp):
TAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTGTA
Found at i:5655715 original size:86 final size:86
Alignment explanation
Indices: 5655570--5655729 Score: 277
Period size: 86 Copynumber: 1.9 Consensus size: 86
5655560 AAGCGTCGTT
*
5655570 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGATAAAAACGCCGCTAAAGATCATG
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGACAAAAACGCCGCTAAAGATCATG
5655635 TTCTTTAGCAGCGTTTACTAG
66 TTCTTTAGCAGCGTTTACTAG
* *
5655656 AAAAGCGCCGCTAAAGGTCCTGTTCTTTAGCGGCATTTGCT-ACAAAAGCGCCGCTAAAGATCAT
1 AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTG-TGACAAAAACGCCGCTAAAGATCAT
5655720 GTTCTTTAGC
65 GTTCTTTAGC
5655730 GATGTTTTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
86 69 0.99
87 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (86 bp):
AAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGACAAAAACGCCGCTAAAGATCATG
TTCTTTAGCAGCGTTTACTAG
Found at i:5657163 original size:23 final size:23
Alignment explanation
Indices: 5657133--5657180 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5657123 AGAATACCAA
5657133 AAGAAAGTTGATTAACTTTTATT
1 AAGAAAGTTGATTAACTTTTATT
5657156 AAGAAAGTTGATTAACTTTTATT
1 AAGAAAGTTGATTAACTTTTATT
5657179 AA
1 AA
5657181 ATCAACCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (23 bp):
AAGAAAGTTGATTAACTTTTATT
Found at i:5659746 original size:28 final size:28
Alignment explanation
Indices: 5659715--5659782 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
5659705 ATCTTTTTTT
*
5659715 ATATATTTCATAATTTT-TATATACCTAC
1 ATATATTTCAT-ATTTTATACATACCTAC
* *
5659743 ATATA-TACATATTTTAATACATACTTAC
1 ATATATTTCATATTTT-ATACATACCTAC
5659771 ATATACTTTCAT
1 ATATA-TTTCAT
5659783 GTATAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.16
27 4 0.12
28 19 0.59
30 4 0.12
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATATTTCATATTTTATACATACCTAC
Found at i:5660248 original size:18 final size:18
Alignment explanation
Indices: 5660207--5660245 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5660197 TTATTTTATT
*
5660207 TTTATTTTTATAATTTTA
1 TTTATTTTCATAATTTTA
*
5660225 TTTATTTTCATTATTGTTA
1 TTTATTTTCATAATT-TTA
5660244 TT
1 TT
5660246 ATTGTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTCATAATTTTA
Found at i:5672912 original size:20 final size:20
Alignment explanation
Indices: 5672889--5672928 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5672879 TTCAATTCAA
* *
5672889 TATTCTAATTTTATTTTATT
1 TATTCTAATGTTATATTATT
*
5672909 TATTTTAATGTTATATTATT
1 TATTCTAATGTTATATTATT
5672929 CTATGGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TATTCTAATGTTATATTATT
Found at i:5678224 original size:10 final size:10
Alignment explanation
Indices: 5678209--5678235 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5678199 TATATATTTA
5678209 ATTATTTCAC
1 ATTATTTCAC
5678219 ATTATTTCAC
1 ATTATTTCAC
5678229 ATTATTT
1 ATTATTT
5678236 TTACAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTATTTCAC
Found at i:5684372 original size:12 final size:13
Alignment explanation
Indices: 5684355--5684391 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
5684345 GAACCGGACA
5684355 CGAACCGAA-CTC
1 CGAACCGAAGCTC
5684367 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
5684379 CGAACCGTAGCTC
1 CGAACCGAAGCTC
5684392 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:5692568 original size:38 final size:38
Alignment explanation
Indices: 5692526--5692598 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
5692516 CCCTACTGAT
5692526 TACATGTTAAGCATGTCT-ACTGCTAGTGTTGAATTAAA
1 TACATGTTAAGCATGT-TGACTGCTAGTGTTGAATTAAA
5692564 TACATGTTAAGCATGTTGACTGCTAGTGTTGAATT
1 TACATGTTAAGCATGTTGACTGCTAGTGTTGAATT
5692599 GTTCTATTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (38 bp):
TACATGTTAAGCATGTTGACTGCTAGTGTTGAATTAAA
Found at i:5705263 original size:12 final size:12
Alignment explanation
Indices: 5705212--5705250 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5705202 CTCTCTTAAC
5705212 AAAAATTTCAAAA
1 AAAAATTTC-AAA
*
5705225 AAAAAATTCAAA
1 AAAAATTTCAAA
*
5705237 AAAATTTTCAAA
1 AAAAATTTCAAA
5705249 AA
1 AA
5705251 TTCAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATTTCAAA
Found at i:5713228 original size:19 final size:19
Alignment explanation
Indices: 5713203--5713294 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
5713193 AATCTTCAGG
*
5713203 GATATGCAATCTTAGACAT
1 GATATGCAATCTTAGATAT
*
5713222 TATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
5713241 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5713260 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5713279 GATATACAATCTTAGA
1 GATATGCAATCTTAGA
5713295 AGATATGATT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5713931 original size:26 final size:26
Alignment explanation
Indices: 5713854--5713931 Score: 61
Period size: 26 Copynumber: 2.9 Consensus size: 26
5713844 TTTTTAAGTT
* *
5713854 TATATATATAATTATTA-TTTTTATGATT
1 TATATATAT-ATTA-TACTTTATAT-ATG
* *
5713882 TATATATTTATTA-CCTTATATATATG
1 TATATATATATTATACTT-TATATATG
*
5713908 TATATATATATTATACTTTCTATA
1 TATATATATATTATACTTTATATA
5713932 CATATTTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 21 0.52
27 11 0.28
28 8 0.20
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (26 bp):
TATATATATATTATACTTTATATATG
Found at i:5713936 original size:20 final size:20
Alignment explanation
Indices: 5713908--5713956 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5713898 TATATATATG
* *
5713908 TATATATATATTATACTTTC
1 TATATATATATTATAATTTA
* *
5713928 TATACATATTTTATAATTTA
1 TATATATATATTATAATTTA
5713948 TATATATAT
1 TATATATAT
5713957 GTAATCATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATATATTATAATTTA
Found at i:5713949 original size:48 final size:46
Alignment explanation
Indices: 5713897--5714052 Score: 147
Period size: 46 Copynumber: 3.2 Consensus size: 46
5713887 ATTTATTACC
5713897 TTATATATATGTATATATATATTATACTTTCTATACATATTTTATAAT
1 TTATATATAT-TATATATATATTATACTTTCTAT-CATATTTTATAAT
* *
5713945 TTATATATA-TATGTA-ATCATTAT-CTTTATGATCTATATATTTATTAACT
1 TTATATATATTATATATAT-ATTATACTTTCT-ATC-ATAT-TTTA-TAA-T
5713994 TATATATATATATACGTATATATATTATACTTTCTATCCATATTTTATAAT
1 T-TATATATAT-TA--TATATATATTATACTTTCTAT-CATATTTTATAAT
*
5714045 TTCTATAT
1 TTATATAT
5714053 GTATATTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 26
0.74 0.04 0.22
Matches are distributed among these distances:
45 8 0.09
46 16 0.18
47 4 0.04
48 12 0.13
49 2 0.02
50 14 0.16
51 2 0.02
52 5 0.06
53 4 0.04
54 14 0.16
55 8 0.09
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (46 bp):
TTATATATATTATATATATATTATACTTTCTATCATATTTTATAAT
Found at i:5713952 original size:50 final size:49
Alignment explanation
Indices: 5713898--5714052 Score: 158
Period size: 48 Copynumber: 3.1 Consensus size: 49
5713888 TTTATTACCT
5713898 TATATATATGTATATATATATTATACTTTCTATACATATTTTATAATTTA
1 TATATATATGTATATATATATTATACTTTCTAT-CATATTTTATAATTTA
* * *
5713948 TATATATATG--TA-AT-CATTAT-CTTTATGATCTATATATTTATTAACTTA
1 TATATATATGTATATATATATTATACTTTCT-ATC-ATAT-TTTA-TAATTTA
* *
5713996 TATATATATATACGTATATATATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATGTA--TATATATATTATACTTTCTAT-CATATTTTATAATTTA
5714048 TATAT
1 TATAT
5714053 GTATATTTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
45 6 0.07
46 11 0.13
47 6 0.07
48 17 0.20
50 10 0.12
52 12 0.14
53 6 0.07
54 11 0.13
55 6 0.07
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (49 bp):
TATATATATGTATATATATATTATACTTTCTATCATATTTTATAATTTA
Found at i:5713967 original size:96 final size:99
Alignment explanation
Indices: 5713854--5714058 Score: 299
Period size: 100 Copynumber: 2.1 Consensus size: 99
5713844 TTTTTAAGTT
* * * *
5713854 TATATATATAATTATTATTTTTATGATTTATATATTTATT-ACCT-TATATATATGTA-TATATA
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATATACTATATA
5713916 TATTATACTTTCTATACATATTTTATAATTTATA
66 TATTATACTTTCTATACATATTTTATAATTTATA
* *
5713950 TATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATATACGTATAT
1 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATATAC-TATAT
* *
5714015 ATATTATACTTTCTATCCATATTTTATAATTTCTA
65 ATATTATACTTTCTATACATATTTTATAATTTATA
*
5714050 TATGTATAT
1 TATATATAT
5714059 TTTTTTATTC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 36 0.38
97 3 0.03
98 11 0.12
100 45 0.47
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (99 bp):
TATATATATAATCATTATCTTTATGATCTATATATTTATTAACCTATATATATATATACTATATA
TATTATACTTTCTATACATATTTTATAATTTATA
Found at i:5714013 original size:14 final size:15
Alignment explanation
Indices: 5713980--5714023 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
5713970 TTATGATCTA
* *
5713980 TATATTTATTA-ACT
1 TATATATATTATACG
5713994 TATATATATATATACG
1 TATATATAT-TATACG
5714010 TATATATATTATAC
1 TATATATATTATAC
5714024 TTTCTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 8 0.31
15 7 0.27
16 11 0.42
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (15 bp):
TATATATATTATACG
Found at i:5714036 original size:20 final size:20
Alignment explanation
Indices: 5714013--5714050 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5714003 ATATACGTAT
*
5714013 ATATATTATACTTTCTATCC
1 ATATATTATAATTTCTATCC
*
5714033 ATATTTTATAATTTCTAT
1 ATATATTATAATTTCTAT
5714051 ATGTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATAATTTCTATCC
Found at i:5721054 original size:57 final size:57
Alignment explanation
Indices: 5720943--5721090 Score: 190
Period size: 57 Copynumber: 2.5 Consensus size: 57
5720933 AATTGACGGT
5720943 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGAT-C--T-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
5721006 AAAAAGATCTAGCCCGAACGGGTGATCT-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
* * *
5721062 AAAATGGATTTAGCCCGGACGGGTAATCT
1 AAAA-AGATCTAGCCCGGACGGGTGATCT
5721091 GAATTAGGGT
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
56 5 0.06
57 47 0.59
59 1 0.01
61 1 0.01
62 20 0.25
63 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCTCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:5723380 original size:44 final size:45
Alignment explanation
Indices: 5723332--5723513 Score: 113
Period size: 44 Copynumber: 4.1 Consensus size: 45
5723322 AGATCTTATT
5723332 TCCCTAAG-CAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
1 TCCCTAAGTCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
* * * * *** ** * *
5723376 TCCCTATAGTTA-TAGTGGAGTACATTGAAGCCAG-TAATTCTACT
1 TCCCTA-AGTCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
** * ** * ** * * *
5723420 TCCCT-AGTCAACAATGGAATAGATTGAAGATTTCAGATATTATC
1 TCCCTAAGTCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
*
5723464 TCCCTAAG-CAGTAGTGGAGCAGATCGAAGATGGCGGATTTTTCC
1 TCCCTAAGTCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
5723508 TCCCTA
1 TCCCTA
5723514 TGGTTACAGT
Statistics
Matches: 95, Mismatches: 38, Indels: 10
0.66 0.27 0.07
Matches are distributed among these distances:
42 4 0.04
43 14 0.15
44 56 0.59
45 20 0.21
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (45 bp):
TCCCTAAGTCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACC
Found at i:5723812 original size:44 final size:45
Alignment explanation
Indices: 5723763--5724197 Score: 125
Period size: 44 Copynumber: 9.9 Consensus size: 45
5723753 GAAGATGGCG
*
5723763 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTA
* *** * * * **
5723808 -ATTTTACTTCCCTG-GACAACAGTGGAATAGATTAAAGATTTTA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTA
* * * ** * * * * *
5723851 GGTCTTATCTCCCTAAGCAG-T--AGTGGAGCAGATCGAAGATGGCA
1 GATTTTACCTCCCT--GTGGTTACAGTGGAGTACATTGAAGATAGTA
*
5723895 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTA
* * *** * * *
5723940 -ATTCTACTTCCCTG-GACAACAGTGGAATAGATTGAAGAT-TTCA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGT-A
* * ** * * *
5723983 GATCTTATCTCCCTAAGCAG-TA-A-TGGAGCAGATCGAAGAT-G-A
1 GATTTTACCTCCCT--GTGGTTACAGTGGAGTACATTGAAGATAGTA
* **
5724025 CGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
1 --GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTA
* * *** * * *
5724072 -ATTCTACTTCCCTG-GACAACAGTGGAATAGATTGAAGAT-TTCA
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGT-A
* * ** * * * * **
5724115 GATCTTATCTCCCTAAGCAG-T--AGTGGAGCAGATCGAAGATGGCG
1 GATTTTACCTCCCT--GTGGTTACAGTGGAGTACATTGAAGATAGTA
*
5724159 GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG
1 GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAG
5724198 CCAGTAATTC
Statistics
Matches: 267, Mismatches: 95, Indels: 56
0.64 0.23 0.13
Matches are distributed among these distances:
42 9 0.03
43 62 0.23
44 146 0.55
45 44 0.16
46 5 0.02
47 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (45 bp):
GATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGATAGTA
Found at i:5724522 original size:132 final size:132
Alignment explanation
Indices: 5723217--5724507 Score: 2147
Period size: 132 Copynumber: 9.8 Consensus size: 132
5723207 TTGACAGCGA
*
5723217 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAATGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
5723282 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTTAGATCTTATTTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5723347 GG
131 GG
* * *
5723349 AGCAGATCGAAGATGGCGGATTTTACCTCCCTATAGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
5723414 TCTACTTCCCTAGTCAACAATGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5723479 GG
131 GG
* *
5723481 AGCAGATCGAAGATGGCGGATTTTTCCTCCCTATGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
5723546 TCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAACCGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5723611 GG
131 GG
* * *
5723613 AGCAGATCGAAGATGTCGGATTTTACCTCCCTGTAGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
5723678 TCTACTTCCCTGGACAATAGTGGAATAGATTAAAGATTTCATG-TCTTATCTCCCTAAGCAGTAG
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCA-GATCTTATCTCCCTAAGCAGTAG
5723742 TGG
130 TGG
*
5723745 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
5723810 TTTACTTCCCTGGACAACAGTGGAATAGATTAAAGATTTTAGGTCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5723875 GG
131 GG
* *
5723877 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
5723942 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAAT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5724007 GG
131 GG
* *
5724009 AGCAGATCGAAGATGACGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
5724074 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5724139 GG
131 GG
*
5724141 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
5724206 TCTACTTCCCTGGACAACAGTGGAATAGGTTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAAT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5724271 GG
131 GG
* * *
5724273 AGCAGATCGAAGATGACAGATTTTACCTCCCTGTAGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
5724338 TCTACTTCCCTGGACAACGGTGGAATATATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
5724403 GG
131 GG
* *
5724405 AGCATATCGAAAATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA-
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
5724469 TCATA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 TC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
5724508 GTAAGTCCTA
Statistics
Matches: 1086, Mismatches: 69, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
131 4 0.00
132 1081 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:5724858 original size:19 final size:19
Alignment explanation
Indices: 5724834--5724925 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
5724824 AATCTTCAGG
5724834 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5724853 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
5724872 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
5724891 GACATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
**
5724910 GATATATAATCTTAGA
1 GATATGCAATCTTAGA
5724926 AGATATGATT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5724884 original size:38 final size:38
Alignment explanation
Indices: 5724841--5724932 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 38
5724831 AGGGATATGC
5724841 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
* * *
5724879 AATCTTAGATATGACATGCAATTTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
5724917 AATCTTAGA-A-GATATG
1 AATCTTAGATATGATATG
5724933 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 5 0.10
37 1 0.02
38 44 0.88
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:5724931 original size:22 final size:23
Alignment explanation
Indices: 5724904--5724948 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5724894 ATGCAATTTT
5724904 AGATATGA-TATATAATCTTAGA
1 AGATATGATTATATAATCTTAGA
* *
5724926 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATATAATCTTAGA
5724949 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (23 bp):
AGATATGATTATATAATCTTAGA
Found at i:5724958 original size:22 final size:23
Alignment explanation
Indices: 5724916--5724958 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5724906 ATATGATATA
*
5724916 TAATCTTAGAAGATATGATTTTG
1 TAATCTTAGAAGATATAATTTTG
*
5724939 TAATCTTAG-AGATTTAATTT
1 TAATCTTAGAAGATATAATTT
5724959 GTAGATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (23 bp):
TAATCTTAGAAGATATAATTTTG
Found at i:5725530 original size:16 final size:17
Alignment explanation
Indices: 5725511--5725553 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
5725501 TTTTTATGAT
5725511 TTATATATTTAT-TACC
1 TTATATATTTATGTACC
* *
5725527 TTATATATATATGTACG
1 TTATATATTTATGTACC
5725544 TATATATATT
1 T-TATATATT
5725554 ATACTTTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (17 bp):
TTATATATTTATGTACC
Found at i:5725570 original size:20 final size:20
Alignment explanation
Indices: 5725547--5725592 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5725537 ATGTACGTAT
*
5725547 ATATATTATACTTTCTATAC
1 ATATATTATAATTTCTATAC
* *
5725567 ATATTTTATAATTTCTATAT
1 ATATATTATAATTTCTATAC
5725587 ATATAT
1 ATATAT
5725593 ATGTAATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATTATAATTTCTATAC
Found at i:5725605 original size:104 final size:105
Alignment explanation
Indices: 5725482--5725698 Score: 364
Period size: 104 Copynumber: 2.1 Consensus size: 105
5725472 TTTTTAAGTT
* * * *
5725482 TATATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATATGTACG-TA
1 TATATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGATA
5725546 TATATATTATACTTTCTATACATATTTTATAATTTCTATA
66 TATATATTATACTTTCTATACATATTTTATAATTTCTATA
5725586 TATATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGTAT
1 TATATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACG-AT
*
5725651 ATATATATTATACTTTCTATCCATATTTTATAATTTCTATA
65 ATATATATTATACTTTCTATACATATTTTATAATTTCTATA
*
5725692 TGTATAT
1 TATATAT
5725699 TTTTCTTTAT
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 58 0.55
106 47 0.45
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (105 bp):
TATATATATGTAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATATGTACGATA
TATATATTATACTTTCTATACATATTTTATAATTTCTATA
Found at i:5725637 original size:16 final size:16
Alignment explanation
Indices: 5725616--5725665 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5725606 CTTTATGATC
*
5725616 TATATATTTATTAACT
1 TATATATATATTAACT
*
5725632 TATATATATATGT-ACG
1 TATATATATAT-TAACT
5725648 TATATATATATTATACT
1 TATATATATATTA-ACT
5725665 T
1 T
5725666 TCTATCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 1 0.04
16 23 0.82
17 4 0.14
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (16 bp):
TATATATATATTAACT
Found at i:5725676 original size:20 final size:20
Alignment explanation
Indices: 5725653--5725690 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5725643 GTACGTATAT
*
5725653 ATATATTATACTTTCTATCC
1 ATATATTATAATTTCTATCC
*
5725673 ATATTTTATAATTTCTAT
1 ATATATTATAATTTCTAT
5725691 ATGTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATTATAATTTCTATCC
Found at i:5725698 original size:56 final size:56
Alignment explanation
Indices: 5725528--5725698 Score: 175
Period size: 56 Copynumber: 3.2 Consensus size: 56
5725518 TTTATTACCT
*
5725528 TATATATATATGTACG--TATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATATGTACGTATATATATATTATACTTTCTATCCATATTTTATAATTTC
* * * * *
5725582 TATATATATA--TA--TGTA-AT-CATTAT-CTTTATGATCTATATATTTATTAA-CT-
1 TATATATATATGTACGTATATATATATTATACTTTCT-ATCCATAT-TTTA-TAATTTC
5725632 TATATATATATGTACGTATATATATATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATATGTACGTATATATATATTATACTTTCTATCCATATTTTATAATTTC
*
5725688 TATATGTATAT
1 TATATATATAT
5725699 TTTTCTTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
49 5 0.05
50 21 0.23
51 7 0.08
52 9 0.10
54 16 0.17
55 7 0.08
56 22 0.24
57 5 0.05
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (56 bp):
TATATATATATGTACGTATATATATATTATACTTTCTATCCATATTTTATAATTTC
Found at i:5752514 original size:142 final size:142
Alignment explanation
Indices: 5752258--5752967 Score: 1105
Period size: 142 Copynumber: 5.0 Consensus size: 142
5752248 TCTTTATGGG
** * * * *
5752258 AATTCACCAATTCCTTCCCTACGTAAGCATTGGTTTCAAGTTCATTTCATTTAGAACCGACCACA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
** * * * * * *
5752323 TAGTTTAAGGACTGTCTTAAGTAATGGTTACAGTAAACCCCTGTTTGCAAGTTATGTCCAAATGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
5752388 GGCCTAGATTTC
131 GGCCTAGATTTC
* *
5752400 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCATTTAGAAGCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
** * ** *
5752465 TAGTTCGAGGACTATCTTAAGTAACAGTTACAATAAAACCTTGTTTGCAAGTTATATCCAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
5752530 GGCCTAGATTTC
131 GGCCTAGATTTC
5752542 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
* * * * *
5752607 TAGTTCGAGGAACATCTTAAGTAATGGTTACATTAAGCCCTTGTTTGCAAGTTATGTACAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
5752672 GGCCTAGATTTC
131 GGCCTAGATTTC
*
5752684 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGCTCATTTCACTTAGAACCGACAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
*
5752749 TAGTTAGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
5752814 GGCCTAGATTTC
131 GGCCTAGATTTC
* * *
5752826 AATTCACTGATTCCTTCCCTAAGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACGGATAATA
1 AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
* * *
5752891 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTAATGCCCAAATGT
66 TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
5752956 GGCCTAGATTTC
131 GGCCTAGATTTC
5752968 CTCACTTAAT
Statistics
Matches: 526, Mismatches: 42, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 526 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (142 bp):
AATTCACTGATTCCTTCCCTACGTAAGCATCGGTTTCAAGTTCATTTCACTTAGAACCGACAATA
TAGTTCGAGGACCGTCTTAAGTAACGGTTACAATAAGCCCTTGTTTGCAAGTTATGTCCAAGTGT
GGCCTAGATTTC
Found at i:5755742 original size:19 final size:19
Alignment explanation
Indices: 5755705--5755751 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5755695 TTATTACAAT
* *
5755705 TATTATTTTGATGACATTTT
1 TATT-TTTTCATGACATTTA
5755725 TATCTTTTTCATGA-ATTTA
1 TAT-TTTTTCATGACATTTA
5755744 TATTTTTT
1 TATTTTTT
5755752 ATAGAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 11 0.46
21 1 0.04
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (19 bp):
TATTTTTTCATGACATTTA
Found at i:5769870 original size:69 final size:69
Alignment explanation
Indices: 5769776--5770403 Score: 554
Period size: 69 Copynumber: 9.1 Consensus size: 69
5769766 ATTATCGTCG
* * * *
5769776 GTAAAAATAAGGTTCGCAGGCGAAGAGCCGTAGCCTCTAAAATAGTTAGCGAGAGAAAAGTTCCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
5769841 AGCT
66 AGCT
* * * *
5769845 GTAAAAATAAGGTTTGTAGGTGAAGAGCCGCAGCCTCTAAAATAGTTAGCAAGAGCAAAGCTCTC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
*
5769910 AACT
66 AGCT
* * * * * * * * *
5769914 GTGAAAACAAGGTTCATAAGCGAAGAGCCGCAGCTTCTAAAACAGTTAGTGAGAGTAAAGCTTCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
*
5769979 AACT
66 AGCT
* * * * * * **
5769983 GTAAAAACAAGGTTTGTAGGCAAAGAGTCACAACCTCTAAAATAGTTAAAGAGAGCAAAGCTCCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
*
5770048 AGGT
66 AGCT
** ** ** *** * * * * * * * *
5770052 GTGGAAATAAAATTCACAAAAGAAAAGTCGCAGCCTCTAAAACAGTTAGCTAAAGCTAAGTTTCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
5770117 AGCT
66 AGCT
* ** * * * * *
5770121 GTAAAAACAAGGTTCACAGGTGAAGAGTCGTAGCCTCTAAAACAGTTAGCGAGAGTAAAGCTCCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
*
5770186 AGTT
66 AGCT
* * * * * * *
5770190 GTGAAAATAAGGTTTGTAGGTGAAGAGCTGCAACCTCTAAACTAGTTAGCGAGAGCGAAGCTCCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
5770255 AGCT
66 AGCT
* * * * * * * *
5770259 GTAAAAATAAGGTTTGTAGGCAAAGAGCCGTAGACTCTAAAACAGTTAGCGAGAGTAAAACTCTC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
**
5770324 AATT
66 AGCT
* * * * * *
5770328 GTAAAAACAAAGTTCGCAGGCGAAGAGCCACGGCTTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
1 GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
*
5770393 AGTT
66 AGCT
5770397 GTAAAAA
1 GTAAAAA
5770404 CAAAGTTTAC
Statistics
Matches: 436, Mismatches: 123, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
69 436 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (69 bp):
GTAAAAATAAGGTTCGTAGGCGAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGCAAAGCTCCC
AGCT
Found at i:5784593 original size:135 final size:136
Alignment explanation
Indices: 5784342--5784605 Score: 372
Period size: 135 Copynumber: 1.9 Consensus size: 136
5784332 GCATGTCATG
* *
5784342 TGTATCTCACGCTAACATACATTGATTATTTTTTATCAGTAAAAATGGATGAAATTTTAACAAAA
1 TGTATCTCACGCTAACATACATTGACTATTTTTTACCAGTAAAAATGGATGAAATTTTAACAAAA
* * **
5784407 TGGACTAGTTTGCTCTTTGATCAAACGTATAAGGACTAAAATGCCTATTTTTTT-AGTAGAATGG
66 TGAACTAGTTTGCCCTTTGATCAAACGTATAAAAACTAAAATGCCTATTTTTTTGAGTAGAATGG
5784471 ACAACA
131 ACAACA
* * **
5784477 TGTATCTCATGCTAACATACGTTGACTATTTTTTACCAGTAAAAATGGATGATTTTTTAACAAAA
1 TGTATCTCACGCTAACATACATTGACTATTTTTTACCAGTAAAAATGGATGAAATTTTAACAAAA
* **
5784542 T-AACTAGTTTGCCCTTTGATCTAACGTATAAAAACTAAGCTGTCC-ATTTTTTTTGAGTAGAAT
66 TGAACTAGTTTGCCCTTTGATCAAACGTATAAAAACTAAAATG-CCTA-TTTTTTTGAGTAGAAT
5784605 G
129 G
5784606 AATTAAATGC
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
134 35 0.31
135 69 0.61
136 9 0.08
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (136 bp):
TGTATCTCACGCTAACATACATTGACTATTTTTTACCAGTAAAAATGGATGAAATTTTAACAAAA
TGAACTAGTTTGCCCTTTGATCAAACGTATAAAAACTAAAATGCCTATTTTTTTGAGTAGAATGG
ACAACA
Found at i:5798424 original size:51 final size:51
Alignment explanation
Indices: 5798369--5798485 Score: 209
Period size: 51 Copynumber: 2.3 Consensus size: 51
5798359 GGGATCACAT
5798369 TTATCACTTGTCACTTGTC-CTTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCAC-TGATCAGATAAGTGTAGCTAAAGCTACCAC
*
5798420 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAT
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
5798471 TTATCACTTGTCACT
1 TTATCACTTGTCACT
5798486 GATCAGAAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
51 63 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:5800074 original size:23 final size:23
Alignment explanation
Indices: 5800054--5800146 Score: 125
Period size: 23 Copynumber: 4.0 Consensus size: 23
5800044 GCCACACTAT
5800054 TATCTAGCCGAAGCTACCACTGA
1 TATCTAGCCGAAGCTACCACTGA
5800077 TA-CGTAGCCGAAGCTACCACTGA
1 TATC-TAGCCGAAGCTACCACTGA
* * *
5800100 TATGTAGCCGTAGCTACCACTAA
1 TATCTAGCCGAAGCTACCACTGA
* *
5800123 AATGTAGCCGAAGCTACCACTGA
1 TATCTAGCCGAAGCTACCACTGA
5800146 T
1 T
5800147 CAATAACACT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 60 0.98
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (23 bp):
TATCTAGCCGAAGCTACCACTGA
Found at i:5800130 original size:46 final size:46
Alignment explanation
Indices: 5800058--5800146 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
5800048 CACTATTATC
* *
5800058 TAGCCGAAGCTACCACTGATACGTAGCCGAAGCTACCACTGATATG
1 TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGATATG
* *
5800104 TAGCCGTAGCTACCACTAAAATGTAGCCGAAGCTACCACTGAT
1 TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGAT
5800147 CAATAACACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTAAAACGTAGCCGAAGCTACCACTGATATG
Found at i:5806830 original size:2 final size:2
Alignment explanation
Indices: 5806823--5806867 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5806813 GAGAAATTAT
5806823 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5806865 TC T
1 TC T
5806868 TCTGTTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5809246 original size:6 final size:6
Alignment explanation
Indices: 5809235--5809444 Score: 170
Period size: 6 Copynumber: 35.0 Consensus size: 6
5809225 CATTTTTGTC
* * *
5809235 ATTATT ATTATT ATTATT ATTATT ATTATT ATCATT ATCATT ATCATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * * * *
5809283 ATTATT ATTATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * * * * *
5809331 ATTATT ATAATT AATATT AATATT ACTATT TTTATT ATTACT ATTACT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * * * ** *
5809379 ATTACTT -TTATT ATTACT AATATT TTTATT TTTATT TTTACC ACTATT
1 ATTA-TT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* *
5809427 ATTATC ATTATT TTTATT
1 ATTATT ATTATT ATTATT
5809445 TTTAAACTGT
Statistics
Matches: 174, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
5 2 0.01
6 171 0.98
7 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTATT
Found at i:5809574 original size:6 final size:6
Alignment explanation
Indices: 5809563--5809625 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
5809553 AGTTTGTTTA
* * *
5809563 TATTTT TATTTT TA-TTT TATTTT GT-TTCT TA-TTT TGTTTT TATTCT
1 TATTTT TATTTT TATTTT TATTTT -TATTTT TATTTT TATTTT TATTTT
*
5809609 TATTATT CATTTT TATT
1 TATT-TT TATTTT TATT
5809626 ACATGTTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
5 9 0.20
6 30 0.68
7 5 0.11
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:5809582 original size:11 final size:11
Alignment explanation
Indices: 5809566--5809642 Score: 59
Period size: 11 Copynumber: 6.7 Consensus size: 11
5809556 TTGTTTATAT
5809566 TTTTATTTTTA
1 TTTTATTTTTA
5809577 TTTTATTTTGT-
1 TTTTATTTT-TA
5809588 TTCTTATTTTGT-
1 TT-TTATTTT-TA
*
5809600 TTTTATTCTTA
1 TTTTATTTTTA
5809611 TTATTCATTTTTA
1 TT-TT-ATTTTTA
** *
5809624 TTACATGTTTA
1 TTTTATTTTTA
5809635 TTTTATTT
1 TTTTATTT
5809643 CAACATTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
10 1 0.02
11 30 0.57
12 14 0.26
13 8 0.15
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:5809585 original size:17 final size:17
Alignment explanation
Indices: 5809563--5809625 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
5809553 AGTTTGTTTA
*
5809563 TATTTTTATTTTTATTT
1 TATTTTTATTCTTATTT
5809580 TATTTTGT-TTCTTATTT
1 TATTTT-TATTCTTATTT
*
5809597 TGTTTTTATTCTTATTAT
1 TATTTTTATTCTTATT-T
5809615 TCATTTTTATT
1 T-ATTTTTATT
5809626 ACATGTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 1 0.03
17 27 0.69
18 3 0.08
19 8 0.21
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTATTCTTATTT
Found at i:5809585 original size:40 final size:41
Alignment explanation
Indices: 5809541--5809621 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 41
5809531 TTACTTACTC
* *
5809541 ATTTT-TTTAATTAGTTTGTTTATATTTTTATT-TTTATTTT
1 ATTTTGTTT-ATTAGTTTGTTTATATTCTTATTATTCATTTT
* * *
5809581 ATTTTGTTTCTTATTTTGTTTTTATTCTTATTATTCATTTT
1 ATTTTGTTTATTAGTTTGTTTATATTCTTATTATTCATTTT
5809622 TATTACATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
40 24 0.71
41 10 0.29
ACGTcount: A:0.17, C:0.04, G:0.05, T:0.74
Consensus pattern (41 bp):
ATTTTGTTTATTAGTTTGTTTATATTCTTATTATTCATTTT
Found at i:5810866 original size:27 final size:27
Alignment explanation
Indices: 5810827--5810902 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
5810817 TAGTATTGGC
5810827 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
* *
5810854 GCCTACCTAGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
5810881 GCCTATCTGGGAGGCGCCAATG
1 GCCTATCTGGGAGGCGCCAATG
5810903 CTCTGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.17, C:0.25, G:0.38, T:0.20
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:5810943 original size:19 final size:19
Alignment explanation
Indices: 5810919--5810959 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5810909 TTTTTTCAGG
* *
5810919 TTTAGGGTTATGCTGTAAA
1 TTTAGGATTATGCTATAAA
*
5810938 TTTAGGATTATGTTATAAA
1 TTTAGGATTATGCTATAAA
5810957 TTT
1 TTT
5810960 TTGTGTTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (19 bp):
TTTAGGATTATGCTATAAA
Found at i:5811103 original size:21 final size:22
Alignment explanation
Indices: 5811069--5811109 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5811059 ACAAATTAAT
5811069 TATAAAATAATTACAATATTCA
1 TATAAAATAATTACAATATTCA
5811091 TATAAAA-AATTACAATATT
1 TATAAAATAATTACAATATT
5811110 ACAATATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAAAATAATTACAATATTCA
Found at i:5811202 original size:19 final size:19
Alignment explanation
Indices: 5811170--5811221 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
5811160 TTTCATACAA
5811170 ATTAT-TTA-AAATTTAAG
1 ATTATGTTATAAATTTAAG
*
5811187 ATTATGTTATAAATTTAGG
1 ATTATGTTATAAATTTAAG
5811206 ATTATGTTATAAATTT
1 ATTATGTTATAAATTT
5811222 TTGTGTTTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 5 0.16
18 3 0.09
19 24 0.75
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
ATTATGTTATAAATTTAAG
Found at i:5811366 original size:21 final size:22
Alignment explanation
Indices: 5811329--5811369 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5811319 ACAAATTAAT
*
5811329 TATAAAATAATTTCAATATTCA
1 TATAAAATAATTACAATATTCA
5811351 TATAAAA-AATTACAATATT
1 TATAAAATAATTACAATATT
5811370 ACAATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
TATAAAATAATTACAATATTCA
Found at i:5811397 original size:260 final size:262
Alignment explanation
Indices: 5810934--5811426 Score: 927
Period size: 260 Copynumber: 1.9 Consensus size: 262
5810924 GGTTATGCTG
5810934 TAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTATTAGTAAT
1 TAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTATTAGTAAT
5810999 AAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTACTAACAAA
66 AAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTACTAACAAA
5811064 TTAATTATAAAATAATTACAATATTCATATAAAAAATTACAATATTACAATATATCCCGACATTA
131 TTAATTATAAAATAATTACAATATTCATATAAAAAATTACAATATTACAATATATCCCGACATTA
* * *
5811129 CAATATTCATACAAAATTTCAATATTACAATTTTCATACAAATTATTTAAAATTTAAGATTATGT
196 CAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAAAATTTAAGATTATGT
5811194 TA
261 TA
*
5811196 TAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTTAATTTATTAGTAAT
1 TAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTATTAGTAAT
5811261 AAATTACAAAATTACTAATAAG-T-TACTAATAAATTTATAACATAATCCTAAATTACTAACAAA
66 AAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTACTAACAAA
*
5811324 TTAATTATAAAATAATTTCAATATTCATATAAAAAATTACAATATTACAATATATCCCGACATTA
131 TTAATTATAAAATAATTACAATATTCATATAAAAAATTACAATATTACAATATATCCCGACATTA
5811389 CAATATTCACACAAAATTACAATATTACAATATTCATA
196 CAATATTCACACAAAATTACAATATTACAATATTCATA
5811427 TAAAATTGCA
Statistics
Matches: 226, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
260 139 0.62
261 1 0.00
262 86 0.38
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (262 bp):
TAAATTTAGGATTATGTTATAAATTTTTGTGTTTGTAATTATTTAAAATTCAATTTATTAGTAAT
AAATTACAAAATTACTAATAAGTTATACTAATAAATTTATAACATAATCCTAAATTACTAACAAA
TTAATTATAAAATAATTACAATATTCATATAAAAAATTACAATATTACAATATATCCCGACATTA
CAATATTCACACAAAATTACAATATTACAATATTCATACAAATTATTTAAAATTTAAGATTATGT
TA
Found at i:5811421 original size:27 final size:27
Alignment explanation
Indices: 5811385--5811441 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
5811375 ATATCCCGAC
5811385 ATTACAATATTCACACAAAATTACAAT
1 ATTACAATATTCACACAAAATTACAAT
* * *
5811412 ATTACAATATTCATATAAAATTGCAAT
1 ATTACAATATTCACACAAAATTACAAT
5811439 ATT
1 ATT
5811442 TTTTTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCACACAAAATTACAAT
Found at i:5811507 original size:22 final size:22
Alignment explanation
Indices: 5811482--5811568 Score: 120
Period size: 22 Copynumber: 3.7 Consensus size: 22
5811472 TCTATATTTA
5811482 GTATGAATATTGTAATTTTTTT
1 GTATGAATATTGTAATTTTTTT
5811504 GTATGAATATTGTAATATTATAATTTT
1 GTATGAATATTGT-A-ATT-T--TTTT
*
5811531 GTATGAATATTGTAAATTTTTT
1 GTATGAATATTGTAATTTTTTT
5811553 GTATGAATATTGTAAT
1 GTATGAATATTGTAAT
5811569 GTCGGGATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
22 32 0.55
23 1 0.02
24 4 0.07
25 3 0.05
26 1 0.02
27 17 0.29
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
GTATGAATATTGTAATTTTTTT
Found at i:5811536 original size:49 final size:48
Alignment explanation
Indices: 5811475--5811615 Score: 173
Period size: 49 Copynumber: 2.9 Consensus size: 48
5811465 TAGATTATCT
* *
5811475 ATATTTAGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATAT-T
1 ATATTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGTAATATGG
*
5811523 ATAATTTTGTATGAATATTGTAAATTTTTTGTATGAATATTGTAATGTCGGG
1 AT-ATTTTGTATGAATATTGT-AATTTTTTGTATGAATATTGTAATAT--GG
*
5811575 ATATATTG--T-AATATTGTAATTTTTTGTATGAATATTGTAAT
1 ATATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAAT
5811616 TATTTTATAA
Statistics
Matches: 84, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
47 24 0.29
48 10 0.12
49 41 0.49
50 2 0.02
51 5 0.06
52 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (48 bp):
ATATTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATATGG
Found at i:5811780 original size:27 final size:27
Alignment explanation
Indices: 5811749--5811815 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
5811739 TAACATAAAT
5811749 TTCATTGGCGCCTCTCTATAAGGCACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
*
5811776 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATAAGGCACC
5811803 TTCATTGGCGCCT
1 TTCATTGGCGCCT
5811816 ACATGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.15, C:0.33, G:0.21, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATAAGGCACC
Found at i:5816995 original size:3 final size:3
Alignment explanation
Indices: 5816987--5817038 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
5816977 AGGCAATTAT
5816987 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A CATTA AT- ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA
5817031 ATA ATA AT
1 ATA ATA AT
5817039 GAGGAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.11
3 37 0.84
4 1 0.02
5 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5817941 original size:12 final size:12
Alignment explanation
Indices: 5817914--5817946 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
5817904 CCGAAGGTGA
5817914 GTTTTTATTTAT
1 GTTTTTATTTAT
5817926 -TTTTTATTTAT
1 GTTTTTATTTAT
5817937 GTTTTTATTT
1 GTTTTTATTT
5817947 CGGATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (12 bp):
GTTTTTATTTAT
Found at i:5821394 original size:3 final size:3
Alignment explanation
Indices: 5821386--5821412 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5821376 GAAGTCTAGA
5821386 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
5821413 TAGTATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5827934 original size:20 final size:20
Alignment explanation
Indices: 5827882--5827934 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
5827872 CATCTCGTAT
*
5827882 TTTTTTTGATAATCCCTCATA
1 TTTTTTT-ATACTCCCTCATA
* * * *
5827903 ATTTTGTGTACTCCCTCATG
1 TTTTTTTATACTCCCTCATA
5827923 TTTTTTTATACT
1 TTTTTTTATACT
5827935 TTTCTCATAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTTTTTATACTCCCTCATA
Found at i:5829406 original size:13 final size:13
Alignment explanation
Indices: 5829388--5829412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5829378 AAGTTTAATA
5829388 ACTAAAATGAATG
1 ACTAAAATGAATG
5829401 ACTAAAATGAAT
1 ACTAAAATGAAT
5829413 TTTATTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
ACTAAAATGAATG
Found at i:5837016 original size:29 final size:29
Alignment explanation
Indices: 5836983--5837043 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
5836973 TAATTGCACA
*
5836983 ATTACACTAATTATTACAACAT-TCGTAAT
1 ATTACACAAATTATTACAA-ATCTCGTAAT
5837012 ATTACACAAATTATTACAAATCTCGTAAT
1 ATTACACAAATTATTACAAATCTCGTAAT
5837041 ATT
1 ATT
5837044 TTGTGTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 2 0.07
29 28 0.93
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (29 bp):
ATTACACAAATTATTACAAATCTCGTAAT
Found at i:5842764 original size:4 final size:4
Alignment explanation
Indices: 5842755--5842781 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5842745 ATATATTACC
5842755 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
5842782 AAGAAATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:5843222 original size:20 final size:21
Alignment explanation
Indices: 5843180--5843224 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
5843170 CGGACTCGCC
5843180 AATTTTTTTAATAAATACCAAA
1 AATTTTTTTAATAAATA-CAAA
5843202 AATTTATTTTAA-AAATA-AAA
1 AATTT-TTTTAATAAATACAAA
5843222 AAT
1 AAT
5843225 AAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
22 10 0.45
23 6 0.27
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTTTTTAATAAATACAAA
Found at i:5843228 original size:26 final size:26
Alignment explanation
Indices: 5843207--5843264 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
5843197 CCAAAAATTT
5843207 ATTTTAAAAATAAAAAATAAAAAATA
1 ATTTTAAAAATAAAAAATAAAAAATA
*
5843233 ATTTTAAAATTAAAAAATAAAAAA-A
1 ATTTTAAAAATAAAAAATAAAAAATA
5843258 ATATTTA
1 AT-TTTA
5843265 TTATATTTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATA
Found at i:5844144 original size:11 final size:11
Alignment explanation
Indices: 5844128--5844166 Score: 50
Period size: 9 Copynumber: 3.9 Consensus size: 11
5844118 ATTACTTGAA
5844128 TATAATATATT
1 TATAATATATT
5844139 TATAATA-ATT
1 TATAATATATT
5844149 TA-AATATA-T
1 TATAATATATT
5844158 TAT-ATATAT
1 TATAATATAT
5844167 AAACTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
9 12 0.48
10 6 0.24
11 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATATATT
Found at i:5844408 original size:17 final size:17
Alignment explanation
Indices: 5844385--5844423 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5844375 ATGAAAATGA
5844385 AAAATATT-ATATAAAT
1 AAAATATTAATATAAAT
*
5844401 ACAAATATTAATATTAAT
1 A-AAATATTAATATAAAT
5844419 AAAAT
1 AAAAT
5844424 GACTAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.55
18 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATATTAATATAAAT
Found at i:5844906 original size:30 final size:29
Alignment explanation
Indices: 5844872--5844946 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
5844862 TGTAATTAGT
*
5844872 AATTAATGTTAATATTATTGAA-TAAAATAA
1 AATT-ATGTTAAT-TAATTGAACTAAAATAA
* *
5844902 AATTATATTAATTAATTGAACTTAACATAA
1 AATTATGTTAATTAATTGAAC-TAAAATAA
*
5844932 AATTCATGTCAATTA
1 AATT-ATGTTAATTA
5844947 TAAGTGTGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.19
29 7 0.19
30 15 0.41
31 8 0.22
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (29 bp):
AATTATGTTAATTAATTGAACTAAAATAA
Found at i:5848435 original size:18 final size:18
Alignment explanation
Indices: 5848412--5848451 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
5848402 TATTTAATCT
5848412 TGAGTGTATTATTTTCTG
1 TGAGTGTATTATTTTCTG
5848430 TGAGTGTATTATTTTCTG
1 TGAGTGTATTATTTTCTG
5848448 TGAG
1 TGAG
5848452 AGACAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.53
Consensus pattern (18 bp):
TGAGTGTATTATTTTCTG
Found at i:5854950 original size:13 final size:13
Alignment explanation
Indices: 5854929--5854979 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
5854919 ACACTCAAAA
5854929 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
5854942 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
5854955 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
5854968 TTCTCAAAAGCA
1 TTCTCAAAAGCA
5854980 ATGAAGAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:5855430 original size:39 final size:39
Alignment explanation
Indices: 5855358--5855433 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
5855348 TAGCAAAATA
* * *
5855358 AATAATAAAATAAAAGTCATACAATATGTAAATAATAAT
1 AATAATAAAATAAAAGTAATACAATAGGGAAATAATAAT
** *
5855397 AATAATAAAATAGTAGTAATATAATAGGGAAATAATA
1 AATAATAAAATAAAAGTAATACAATAGGGAAATAATA
5855434 GCAAAACAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (39 bp):
AATAATAAAATAAAAGTAATACAATAGGGAAATAATAAT
Found at i:5857032 original size:16 final size:18
Alignment explanation
Indices: 5857005--5857040 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5856995 TCAAAATCGG
5857005 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
5857022 ATTGA-AAAATTAATTTA
1 ATTGAGAAAATTAATTTA
5857039 AT
1 AT
5857041 AAATAATGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:5857117 original size:45 final size:45
Alignment explanation
Indices: 5857045--5857137 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 45
5857035 TTTAATAAAT
* * * * *
5857045 AATGTCTATTTTGATAAATAGAGAAACATGCACTGGGTTAGATTG
1 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGATTAGATTG
*
5857090 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGATTATATTG
1 AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGATTAGATTG
5857135 AAT
1 AAT
5857138 TATAAAGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
AATGTCTATTTTGAGAAAAAGAAAAACATGCACTAGATTAGATTG
Found at i:5859693 original size:21 final size:21
Alignment explanation
Indices: 5859667--5859726 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
5859657 GGTGAATCAT
* * *
5859667 CTCTTATGAGCTTTTGTTCAG
1 CTCTTATGAGCTTCTGTTAAA
*
5859688 CTCTTACGAGCTTCTGTTAAA
1 CTCTTATGAGCTTCTGTTAAA
*
5859709 CTCTTATAAGCTTCTGTT
1 CTCTTATGAGCTTCTGTT
5859727 GGCATATTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTAAA
Found at i:5863893 original size:77 final size:77
Alignment explanation
Indices: 5863765--5863914 Score: 239
Period size: 77 Copynumber: 1.9 Consensus size: 77
5863755 CATTCCCTAA
* *
5863765 TTCCAACAAGGATTGTGTTCGGTTTAGTTGAAATTAGAGTCAAGTAAAAATGTACAATGATATTA
1 TTCCAACAAGGATTGAGTTCGGTTTAATTGAAATTAGAGTCAAGTAAAAATGTACAATGATATTA
*
5863830 ACTAAAAGATAG
66 AATAAAAGATAG
* *
5863842 TTCCAACAAGGATTGAG-TCAGGTTTAATTGAAATTAGAGTTAAGTAGAAATGTACAATGATATT
1 TTCCAACAAGGATTGAGTTC-GGTTTAATTGAAATTAGAGTCAAGTAAAAATGTACAATGATATT
5863906 AAATAAAAG
65 AAATAAAAG
5863915 GGTAGGGTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
76 2 0.03
77 65 0.97
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (77 bp):
TTCCAACAAGGATTGAGTTCGGTTTAATTGAAATTAGAGTCAAGTAAAAATGTACAATGATATTA
AATAAAAGATAG
Found at i:5865244 original size:33 final size:33
Alignment explanation
Indices: 5865176--5865434 Score: 206
Period size: 33 Copynumber: 7.5 Consensus size: 33
5865166 TATAAAGGGA
*
5865176 GTTGCTAAGTGCTGATT-CCC---TCA-AGG-G
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
5865203 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
* *
5865236 GTTGCTAAGTGCTGATTCCACCGTAACTTGAATGTGAAATGG
1 GTTGCTAAGTGCTGATTCC-CCG-AA--T-CAT-TG--GT-G
* *
5865278 GTTGCTAAGTGCTGATTCTCCGAATCATTGGCG
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
5865311 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
* ** *
5865344 GTTGCTAAGTGCTAATTCCACCCTATCTTTGAATGTGAAAGGG
1 GTTGCTAAGTGCTGATTCC-CCGAATC-----AT-TG---GTG
* *
5865387 GTTGCTAAGTGCTGATTCCCCGAATCACTAGTG
1 GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
5865420 GTTGCTAAGTGCTGA
1 GTTGCTAAGTGCTGA
5865435 ATCCACCAAG
Statistics
Matches: 188, Mismatches: 19, Indels: 44
0.75 0.08 0.18
Matches are distributed among these distances:
27 17 0.09
28 3 0.02
31 3 0.02
32 2 0.01
33 87 0.46
34 8 0.04
35 2 0.01
36 3 0.02
37 4 0.02
38 3 0.02
39 4 0.02
40 4 0.02
41 4 0.02
42 24 0.13
43 20 0.11
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GTTGCTAAGTGCTGATTCCCCGAATCATTGGTG
Found at i:5865345 original size:108 final size:106
Alignment explanation
Indices: 5865169--5865434 Score: 387
Period size: 108 Copynumber: 2.5 Consensus size: 106
5865159 CACTGAATAT
*
5865169 AAAGGGAGTTGCTAAGTGCTGATTCCC---TCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCAT
1 AAAGGG-GTTGCTAAGTGCTGATTCCCGAATCATGGGGTTGCTAAGTGCTGATTCCCCGAATCAT
* *
5865231 TGGTGGTTGCTAAGTGCTGATTCCACCGTAAC-TTGAATGTG
65 TGGTGGTTGCTAAGTGCTAATTCCACCCTAACTTTGAATGTG
*
5865272 AAATGGGTTGCTAAGTGCTGATTCTCCGAATCATTGGCGGTTGCTAAGTGCTGATTCCCCGAATC
1 AAAGGGGTTGCTAAGTGCTGATTC-CCGAATCA-TGG-GGTTGCTAAGTGCTGATTCCCCGAATC
*
5865337 ATTGGTGGTTGCTAAGTGCTAATTCCACCCTATCTTTGAATGTG
63 ATTGGTGGTTGCTAAGTGCTAATTCCACCCTAACTTTGAATGTG
*
5865381 AAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGGTTGCTAAGTGCTGA
1 AAAGGGGTTGCTAAGTGCTGATT-CCCGAATCA-T-GGGGTTGCTAAGTGCTGA
5865435 ATCCACCAAG
Statistics
Matches: 146, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
102 18 0.12
103 7 0.05
106 3 0.02
107 2 0.01
108 58 0.40
109 56 0.38
110 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (106 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCGAATCATGGGGTTGCTAAGTGCTGATTCCCCGAATCATT
GGTGGTTGCTAAGTGCTAATTCCACCCTAACTTTGAATGTG
Found at i:5870294 original size:140 final size:141
Alignment explanation
Indices: 5869990--5870412 Score: 794
Period size: 140 Copynumber: 3.0 Consensus size: 141
5869980 AAAACATAAA
* *
5869990 AACCACTTAAATCTGGTTTCATTATCATATAATCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
*
5870055 GCTTATCCTAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
66 GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
*
5870120 CAAGAGATCGT
131 CAAGAGATCAT
5870131 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
5870196 GCTTATCCAAGAAAGAAT-AGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
66 GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
*
5870260 CTAGAGATCAT
131 CAAGAGATCAT
5870271 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
1 AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
5870336 GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
66 GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
5870401 CAAGAGATCAT
131 CAAGAGATCAT
5870412 A
1 A
5870413 TGGTTTTTAA
Statistics
Matches: 275, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
140 138 0.50
141 137 0.50
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (141 bp):
AACCACTTAAATCTGGTTTCATTGTCATATAAGCATTTGAAGCTCTTTTCTAAAAGACATACAAG
GCTTATCCAAGAAAGAATGAGTGAGAGTCTGGATTAAGAATTTTATCACATAGGATGAAGTTCAC
CAAGAGATCAT
Found at i:5872659 original size:62 final size:62
Alignment explanation
Indices: 5872562--5872685 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
5872552 AAACTGGGAT
5872562 AATTTAATAAAAATGAAGTTTCAACATATATTACATGTGAACCCTAGACTCCACAATTCACC
1 AATTTAATAAAAATGAAGTTTCAACATATATTACATGTGAACCCTAGACTCCACAATTCACC
5872624 AATTTAATAAAAATGAAGTTTCAACATATATTACATGTGAACCCTAGACTCCACAATTCACC
1 AATTTAATAAAAATGAAGTTTCAACATATATTACATGTGAACCCTAGACTCCACAATTCACC
5872686 GTGCCGTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (62 bp):
AATTTAATAAAAATGAAGTTTCAACATATATTACATGTGAACCCTAGACTCCACAATTCACC
Found at i:5873124 original size:6 final size:6
Alignment explanation
Indices: 5873113--5873141 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5873103 TTTCAGAAGT
5873113 TTGAAA TTGAAA TTGAAA TTGAAA TTGAA
1 TTGAAA TTGAAA TTGAAA TTGAAA TTGAA
5873142 GCAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
TTGAAA
Found at i:5886049 original size:22 final size:22
Alignment explanation
Indices: 5886021--5886067 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
5886011 TATGGTCACA
5886021 ATGCCCTGGCCACCTATAACCT
1 ATGCCCTGGCCACCTATAACCT
5886043 ATGCCCTGGCCACCTATAACCT
1 ATGCCCTGGCCACCTATAACCT
5886065 ATG
1 ATG
5886068 AGATGTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
ATGCCCTGGCCACCTATAACCT
Found at i:5887658 original size:22 final size:23
Alignment explanation
Indices: 5887606--5887663 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
5887596 TTTAGAAAAT
*
5887606 TTATTTCTTATAAATAAATTATA
1 TTATTTTTTATAAATAAATTATA
** *
5887629 GCACTTTTTATAAATAAA-TATA
1 TTATTTTTTATAAATAAATTATA
5887651 TTATTTTTTATAA
1 TTATTTTTTATAA
5887664 TATATAGGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTTTTATAAATAAATTATA
Found at i:5887849 original size:88 final size:88
Alignment explanation
Indices: 5887683--5887950 Score: 303
Period size: 88 Copynumber: 3.1 Consensus size: 88
5887673 TTAAGGGTGT
* * * **
5887683 AAAAAGCCCTCAAACTTTTTC-AAAAAAGTAATTAAGCCCCTGCTTTTTTTTTCTGTTCAATTGG
1 AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCATTTTTTTAC-ACTCAATTGG
* * *
5887747 ATACTTGAACTTTCAAAATGCATT
65 GTACTTGAAATTTCAAAATGCATA
* * * *
5887771 AAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTATGCCCCTAC-TTTTTTTGCACTCAGTTGG
1 AAAAAG-CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCATTTTTTTACACTCAATTGG
5887835 GTACTTGAAATTTCAAAATGCATA
65 GTACTTGAAATTTCAAAATGCATA
* ** * *
5887859 AAAAAGGCCCTCTAA--TTTAAAAAAAAAGCAATTAAGTCCCTGCATTTTTTTACACTCAATTGA
1 AAAAA-GCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCATTTTTTTACACTCAATTGG
*
5887922 GTACTTG-AATTGTCAAAACGCATA
65 GTACTTGAAATT-TCAAAATGCATA
5887946 AAAAA
1 AAAAA
5887951 AAGCTTTTTG
Statistics
Matches: 155, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
86 27 0.17
87 39 0.25
88 46 0.30
89 24 0.15
90 19 0.12
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (88 bp):
AAAAAGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCATTTTTTTACACTCAATTGGG
TACTTGAAATTTCAAAATGCATA
Found at i:5888172 original size:19 final size:19
Alignment explanation
Indices: 5888157--5888195 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5888147 TTGTAAAATT
5888157 TTATAAAAAT-CATAAAAAA
1 TTAT-AAAATGCATAAAAAA
5888176 TTATAAAATGCATAAAAAA
1 TTATAAAATGCATAAAAAA
5888195 T
1 T
5888196 GCCCTTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (19 bp):
TTATAAAATGCATAAAAAA
Found at i:5888475 original size:9 final size:9
Alignment explanation
Indices: 5888365--5888477 Score: 50
Period size: 9 Copynumber: 12.0 Consensus size: 9
5888355 TATTGGTACG
*
5888365 ATAATTCTT
1 ATAATTTTT
5888374 ATAATTTTT
1 ATAATTTTT
*
5888383 AGGAA-TTTT
1 A-TAATTTTT
*
5888392 ATATTTCTTT
1 ATAATT-TTT
* *
5888402 ACATTTTTT
1 ATAATTTTT
5888411 AATAATTTTTT
1 -ATAA-TTTTT
*
5888422 CATGATTTTT
1 -ATAATTTTT
**
5888432 ATAAAAGTTT
1 AT-AATTTTT
*
5888442 ACAATTGTTT
1 ATAATT-TTT
5888452 AT-ATTTTT
1 ATAATTTTT
**
5888460 ACGATTTTT
1 ATAATTTTT
5888469 ATAATTTTT
1 ATAATTTTT
5888478 TTTCTAATTT
Statistics
Matches: 77, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
8 5 0.06
9 38 0.49
10 26 0.34
11 8 0.10
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (9 bp):
ATAATTTTT
Found at i:5888844 original size:90 final size:89
Alignment explanation
Indices: 5888657--5888835 Score: 211
Period size: 90 Copynumber: 2.0 Consensus size: 89
5888647 TGGTCAAAGG
** *
5888657 GCATTTTTGATGCATTTTGGCATATCAAGTACCCAATTGAGGGGAAAAAAATAGGGGCTTAATTG
1 GCATTTTTGATGCATTTTGGCATATCAAGTACCCAATTGAGGAAAAAAAAAGAGGGGCTTAATTG
* *
5888722 TTTTTTTTTTAAAAAAAGTTTGAGA
66 -TGTTTTTTTAAAAAAAGTTGGAGA
* *
5888747 GCATTTTTTATGCATTTTGGCAGT-TCAAGTACCCAATTGAGTTAAAAAAAAAGAGCAGCGGCTT
1 GCATTTTTGATGCATTTTGGCA-TATCAAGTACCCAATTGAG-GAAAAAAAAAGAG--G-GGCTT
*
5888811 AATTG-GTTTTTTT-GAAAAAGTTGGA
61 AATTGTGTTTTTTTAAAAAAAGTTGGA
5888836 AGGCTTTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
90 38 0.50
91 20 0.26
92 7 0.09
93 1 0.01
94 10 0.13
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (89 bp):
GCATTTTTGATGCATTTTGGCATATCAAGTACCCAATTGAGGAAAAAAAAAGAGGGGCTTAATTG
TGTTTTTTTAAAAAAAGTTGGAGA
Found at i:5889191 original size:20 final size:20
Alignment explanation
Indices: 5889158--5889195 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5889148 ACGGTATAGT
5889158 TAATGGTTGATTAATTAAAC
1 TAATGGTTGATTAATTAAAC
5889178 TAAT-GTTGATTTAATTAA
1 TAATGGTTGA-TTAATTAA
5889196 CAAAAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (20 bp):
TAATGGTTGATTAATTAAAC
Found at i:5892920 original size:40 final size:40
Alignment explanation
Indices: 5892846--5892965 Score: 113
Period size: 40 Copynumber: 3.0 Consensus size: 40
5892836 ACACGGTTCA
* *
5892846 TGCCACGTCAGCAAATCGCGTCCT-A-GGGGGCGCGATTTCC
1 TGCCACGTCAGCAAATCGCG--CTGACGTGGACGCGATTTCC
* *
5892886 TTCCACGTCAGCAAATCGCGCTGACGTGGACGCGATGT-C
1 TGCCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCC
* *
5892925 TGACACGT-ACCCTAACATCGCGCTGACGTGGACGCGATTTC
1 TGCCACGTCA-GC-AA-ATCGCGCTGACGTGGACGCGATTTC
5892966 GCGAAAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
38 3 0.05
39 9 0.14
40 31 0.47
41 23 0.35
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.21
Consensus pattern (40 bp):
TGCCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCC
Found at i:5895407 original size:18 final size:19
Alignment explanation
Indices: 5895379--5895415 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5895369 TAGTTAAGTA
5895379 AAAAAATATATAAAAAATT
1 AAAAAATATATAAAAAATT
*
5895398 AAAAAA-ATATAGAAAATT
1 AAAAAATATATAAAAAATT
5895416 TACTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAAATATATAAAAAATT
Found at i:5896458 original size:17 final size:16
Alignment explanation
Indices: 5896419--5896461 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5896409 CCAAAAATAA
*
5896419 AATATAAAAAATTATG
1 AATATAAAAAAATATG
*
5896435 -TTATAAAAATAATATG
1 AATATAAAAA-AATATG
5896451 AATATAAAAAA
1 AATATAAAAAA
5896462 CTACTAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AATATAAAAAAATATG
Found at i:5901585 original size:10 final size:8
Alignment explanation
Indices: 5901555--5901588 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
5901545 ATTTAGTATC
5901555 TTAAAAAT
1 TTAAAAAT
5901563 TTAAAAAT
1 TTAAAAAT
5901571 TTAAAAACTT
1 TTAAAAA--T
5901581 TTAAAAAT
1 TTAAAAAT
5901589 AAAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAAAT
Found at i:5901746 original size:11 final size:11
Alignment explanation
Indices: 5901730--5901762 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5901720 CTCACAAATA
5901730 AGATTTAAACT
1 AGATTTAAACT
5901741 AGATTTAAACT
1 AGATTTAAACT
*
5901752 AGATTCAAACT
1 AGATTTAAACT
5901763 TTTCCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (11 bp):
AGATTTAAACT
Found at i:5902700 original size:7 final size:7
Alignment explanation
Indices: 5902666--5902690 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5902656 AATTAACCGA
5902666 AATAAAT
1 AATAAAT
5902673 AATAAAT
1 AATAAAT
5902680 AATAAAT
1 AATAAAT
5902687 AATA
1 AATA
5902691 TATATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:5910060 original size:12 final size:12
Alignment explanation
Indices: 5910026--5910062 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5910016 CGTGCAAAGC
*
5910026 AAAACGAAAACG
1 AAAACGAAAATG
5910038 AAAACGAAAATG
1 AAAACGAAAATG
*
5910050 AAAATGAAAATG
1 AAAACGAAAATG
5910062 A
1 A
5910063 CGTGGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAACGAAAATG
Found at i:5910062 original size:6 final size:6
Alignment explanation
Indices: 5910026--5910059 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5910016 CGTGCAAAGC
* *
5910026 AAAACG AAAACG AAAACG AAAATG AAAATG AAAA
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAA
5910060 TGACGTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.71, C:0.09, G:0.15, T:0.06
Consensus pattern (6 bp):
AAAACG
Found at i:5913890 original size:27 final size:27
Alignment explanation
Indices: 5913849--5913902 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5913839 AATGAAGGTG
*
5913849 TTAGAATATAGACATCTACATTTATAT
1 TTAGAATATAAACATCTACATTTATAT
5913876 TTAGAATATAAACATCTACATTTATAT
1 TTAGAATATAAACATCTACATTTATAT
5913903 ATTTGTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (27 bp):
TTAGAATATAAACATCTACATTTATAT
Found at i:5914803 original size:11 final size:11
Alignment explanation
Indices: 5914789--5914831 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5914779 AGTTAAATAT
5914789 TATTTTATTAA
1 TATTTTATTAA
5914800 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
5914813 TA-TTTATTAG
1 TATTTTATTAA
5914823 TATTTTATT
1 TATTTTATT
5914832 TAGAAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5914818 original size:23 final size:23
Alignment explanation
Indices: 5914792--5914835 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5914782 TAAATATTAT
5914792 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
5914815 TTTATTAGTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
5914836 AAATTGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:5916959 original size:31 final size:32
Alignment explanation
Indices: 5916923--5916987 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
5916913 CTTAGATAAT
*
5916923 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
5916954 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
5916986 TT
1 TT
5916988 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATCACTC
Found at i:5917545 original size:8 final size:8
Alignment explanation
Indices: 5917534--5917600 Score: 50
Period size: 8 Copynumber: 8.6 Consensus size: 8
5917524 ATAAAAGCAA
5917534 AAAAAAAG
1 AAAAAAAG
5917542 AAAAAAA-
1 AAAAAAAG
* **
5917549 AACAGCA-
1 AAAAAAAG
5917556 AAAAAAAG
1 AAAAAAAG
*
5917564 CAAAAAACG
1 -AAAAAAAG
* *
5917573 CAAAAGA-
1 AAAAAAAG
5917580 AAAAAAAG
1 AAAAAAAG
5917588 AAAAAAAG
1 AAAAAAAG
5917596 AAAAA
1 AAAAA
5917601 GCAAAAAGCG
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
7 13 0.30
8 24 0.55
9 7 0.16
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5917545 original size:10 final size:10
Alignment explanation
Indices: 5917526--5917600 Score: 53
Period size: 11 Copynumber: 7.0 Consensus size: 10
5917516 TTCTTTAAAT
5917526 AAAAGCAAAAA
1 AAAAG-AAAAA
5917537 AAAAGAAAAAA
1 AAAAG-AAAAA
*
5917548 AAACAGCAAAA
1 AAA-AGAAAAA
*
5917559 AAAAG-CAAA
1 AAAAGAAAAA
*
5917568 AAACGCAAAAGA
1 AAAAG-AAAA-A
*
5917580 AAAAAAAGAAA
1 AAAAGAA-AAA
5917591 AAAAGAAAAA
1 AAAAGAAAAA
5917601 GCAAAAAGCG
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
9 7 0.14
10 5 0.10
11 31 0.61
12 8 0.16
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:5917555 original size:23 final size:23
Alignment explanation
Indices: 5917529--5917594 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
5917519 TTTAAATAAA
5917529 AGCAAAAAAAAAGAAAAAAAAAC
1 AGCAAAAAAAAAGAAAAAAAAAC
* **
5917552 AGC-AAAAAAAAGCAAAAAACGC
1 AGCAAAAAAAAAGAAAAAAAAAC
**
5917574 AAAAGAAAAAAAAGAAAAAAA
1 AGCA-AAAAAAAAGAAAAAAA
5917595 GAAAAAGCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 17 0.49
23 3 0.09
24 15 0.43
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (23 bp):
AGCAAAAAAAAAGAAAAAAAAAC
Found at i:5917599 original size:22 final size:23
Alignment explanation
Indices: 5917526--5917607 Score: 96
Period size: 23 Copynumber: 3.5 Consensus size: 23
5917516 TTCTTTAAAT
5917526 AAAAGCAAAAAAAAAGAAAAAAA-
1 AAAAGC-AAAAAAAAGAAAAAAAG
* *
5917549 AACAGCAAAAAAAAGCAAAAAACG
1 AAAAGCAAAAAAAAG-AAAAAAAG
5917573 CAAAAG-AAAAAAAAGAAAAAAAG
1 -AAAAGCAAAAAAAAGAAAAAAAG
5917596 AAAAAGCAAAAA
1 -AAAAGCAAAAA
5917608 GCGCAAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.18
23 23 0.46
24 14 0.28
25 4 0.08
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (23 bp):
AAAAGCAAAAAAAAGAAAAAAAG
Found at i:5917600 original size:38 final size:37
Alignment explanation
Indices: 5917537--5917621 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
5917527 AAAGCAAAAA
**
5917537 AAAAGAAAAAAAAACAGCAAAAAAAAGCAAAAAACGC
1 AAAAGAAAAAAAAACAAAAAAAAAAAGCAAAAAACGC
*
5917574 AAAAGAAAAAAAAGA-AAAAAAGAAAAAGCAAAAAGCGC
1 AAAAGAAAAAAAA-ACAAAAAA-AAAAAGCAAAAAACGC
5917612 AAAA-AAAAAA
1 AAAAGAAAAAA
5917622 GTTGCCTACC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 23 0.53
38 20 0.47
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (37 bp):
AAAAGAAAAAAAAACAAAAAAAAAAAGCAAAAAACGC
Found at i:5920797 original size:31 final size:32
Alignment explanation
Indices: 5920761--5920825 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
5920751 CTTAGATAAT
*
5920761 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
5920792 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATCACTC
5920824 TT
1 TT
5920826 GTAATTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATCACTC
Found at i:5924495 original size:17 final size:18
Alignment explanation
Indices: 5924462--5924497 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5924452 AACTTGATGA
5924462 AAAACATATAGTCTTTCC
1 AAAACATATAGTCTTTCC
*
5924480 AAAACATAT-TTCTTTCC
1 AAAACATATAGTCTTTCC
5924497 A
1 A
5924498 CATTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAACATATAGTCTTTCC
Found at i:5927018 original size:124 final size:124
Alignment explanation
Indices: 5926798--5927045 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
5926788 GGTATGTATT
5926798 TAATATGTATATATTAAAATTTAAAAATATTTTTGAAAGATTATATTTTTATACCATCATGCTTT
1 TAATATGTATATATTAAAATTTAAAAATATTTTTGAAAGATTATATTTTTATACCATCATGCTTT
5926863 CTTCGAATACATATAGTATTCAAGTGGAAGCAATCTACTAAGCTAAAGCGGTCAAAAAA
66 CTTCGAATACATATAGTATTCAAGTGGAAGCAATCTACTAAGCTAAAGCGGTCAAAAAA
*
5926922 TAATATGTATATATTAAAATTTAAAAATATTTTTTAAAGATTATATTTTTATACCATCATGCTTT
1 TAATATGTATATATTAAAATTTAAAAATATTTTTGAAAGATTATATTTTTATACCATCATGCTTT
5926987 CTTCGAATACATATAGTATTCAAGTGGAAGCAATCTACTAAGCTAAAGCGGTCAAAAAA
66 CTTCGAATACATATAGTATTCAAGTGGAAGCAATCTACTAAGCTAAAGCGGTCAAAAAA
5927046 ACAACCAACG
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (124 bp):
TAATATGTATATATTAAAATTTAAAAATATTTTTGAAAGATTATATTTTTATACCATCATGCTTT
CTTCGAATACATATAGTATTCAAGTGGAAGCAATCTACTAAGCTAAAGCGGTCAAAAAA
Found at i:5938235 original size:11 final size:11
Alignment explanation
Indices: 5938221--5938245 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5938211 ATATTCAGCC
5938221 AATATTAAAAT
1 AATATTAAAAT
5938232 AATATTAAAAT
1 AATATTAAAAT
5938243 AAT
1 AAT
5938246 GAATTAATAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:5940713 original size:17 final size:17
Alignment explanation
Indices: 5940691--5940723 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5940681 TAGTATGAGG
*
5940691 TTGAGAAAATGATTTAA
1 TTGAGAAAATAATTTAA
5940708 TTGAGAAAATAATTTA
1 TTGAGAAAATAATTTA
5940724 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:5945675 original size:33 final size:33
Alignment explanation
Indices: 5945637--5945711 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
5945627 CTACTGTTAA
5945637 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
1 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
* * * * *
5945670 TCCTCCATCAGCATTGGTGCCGCCTATCGTCAG
1 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
5945703 CCCTCCACC
1 CCCTCCACC
5945712 CCACCTGAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (33 bp):
CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
Done.