Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 67 of 226
Found at i:25699974 original size:35 final size:35
Alignment explanation
Indices: 25699919--25700010 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
25699909 TTGAAAACAC
** *
25699919 GAAAACACGAAAAAAATTTTAAACACGGGAATTTTT
1 GAAAACAC-AAAAATTTTTTAAACACGAGAATTTTT
**
25699955 GAAAACACAAAAATTTTTTATTCACGAGAATTTTT
1 GAAAACACAAAAATTTTTTAAACACGAGAATTTTT
** *
25699990 G-AAACACGGAATTTTTTTAAA
1 GAAAACACAAAAATTTTTTAAA
25700011 GAAAGGAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
34 15 0.33
35 23 0.50
36 8 0.17
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.32
Consensus pattern (35 bp):
GAAAACACAAAAATTTTTTAAACACGAGAATTTTT
Found at i:25699997 original size:17 final size:17
Alignment explanation
Indices: 25699935--25700005 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
25699925 ACGAAAAAAA
*
25699935 TTTT-AAACACGGGAAT
1 TTTTGAAACACGAGAAT
* *
25699951 TTTTGAAAACACAAAAAT
1 TTTTG-AAACACGAGAAT
* **
25699969 TTTTTATTCACGAGAAT
1 TTTTGAAACACGAGAAT
25699986 TTTTGAAACACG-GAAT
1 TTTTGAAACACGAGAAT
25700002 TTTT
1 TTTT
25700006 TTAAAGAAAG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 12 0.29
17 17 0.40
18 13 0.31
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (17 bp):
TTTTGAAACACGAGAAT
Found at i:25700255 original size:20 final size:20
Alignment explanation
Indices: 25700226--25700263 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25700216 GGGATTCTAA
25700226 TAAAACACGAGAATTTTTAT
1 TAAAACACGAGAATTTTTAT
* *
25700246 TAAAATACGAGGATTTTT
1 TAAAACACGAGAATTTTT
25700264 GAATATTTTT
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:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (20 bp):
TAAAACACGAGAATTTTTAT
Found at i:25700733 original size:21 final size:20
Alignment explanation
Indices: 25700700--25700755 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
25700690 CTACTTTTTA
*
25700700 TTTTCTT-TTTTTCTTTCTT
1 TTTTCTTCTTTTTCTTTCTC
25700719 TTTTCTCTCTTTTTCTTTCTC
1 TTTTCT-TCTTTTTCTTTCTC
* *
25700740 CTTTCTTCTTCTTCTT
1 TTTTCTTCTTTTTCTT
25700756 CTTCCCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 16 0.50
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTCTTTTTCTTTCTC
Found at i:25700739 original size:12 final size:12
Alignment explanation
Indices: 25700701--25700749 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
25700691 TACTTTTTAT
*
25700701 TTTCTTTTTTTC
1 TTTCTCTTTTTC
25700713 TTTCT-TTTTTC
1 TTTCTCTTTTTC
25700724 --TCTCTTTTTC
1 TTTCTCTTTTTC
25700734 TTTCTCCTTTCTTC
1 TTTCT-CTTT-TTC
25700748 TT
1 TT
25700750 CTTCTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.09
10 6 0.19
11 6 0.19
12 8 0.25
13 4 0.12
14 5 0.16
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:25701548 original size:29 final size:28
Alignment explanation
Indices: 25701467--25701542 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
25701457 GGCCAAAACA
*
25701467 TAATTTTAAGAAAGTTTAGGGGTCAAAGTG
1 TAATTTT-AGAAAGTTTAAGGGTCAAA-TG
* * *
25701497 CAATTGTGAGAAAGTCTAAGGGTCGAAATG
1 TAATT-TTAGAAAGTTTAAGGGTC-AAATG
25701527 TAATTTTAGAAAGTTT
1 TAATTTTAGAAAGTTT
25701543 TTGGGTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 9 0.24
30 24 0.65
31 4 0.11
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (28 bp):
TAATTTTAGAAAGTTTAAGGGTCAAATG
Found at i:25705431 original size:19 final size:21
Alignment explanation
Indices: 25705402--25705446 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
25705392 TCTCTCTCAA
25705402 CAAAAATTACAAA-TAATTTT
1 CAAAAATTACAAAGTAATTTT
25705422 CAAAAA-TACAAAGTAATTTT
1 CAAAAATTACAAAGTAATTTT
*
25705442 TAAAA
1 CAAAA
25705447 TTTCAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (21 bp):
CAAAAATTACAAAGTAATTTT
Found at i:25705453 original size:20 final size:19
Alignment explanation
Indices: 25705404--25705454 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
25705394 TCTCTCAACA
25705404 AAAATTACAAATAATTTTC
1 AAAATTACAAATAATTTTC
* *
25705423 AAAAATACAAAGTAATTTTT
1 AAAATTACAAA-TAATTTTC
*
25705443 AAAATTTCAAAT
1 AAAATTACAAAT
25705455 TTTATATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTACAAATAATTTTC
Found at i:25705481 original size:18 final size:18
Alignment explanation
Indices: 25705460--25705516 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
25705450 CAAATTTTAT
25705460 ATTTTTAAAAAATTATAA
1 ATTTTTAAAAAATTATAA
25705478 ATTTTTAAAAAAAATTATAA
1 ATTTTT--AAAAAATTATAA
*
25705498 ATTTTTAAAAAATTCTAA
1 ATTTTTAAAAAATTATAA
25705516 A
1 A
25705517 GAATATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 18 0.50
20 18 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTTTAAAAAATTATAA
Found at i:25705491 original size:20 final size:20
Alignment explanation
Indices: 25705466--25705509 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
25705456 TTATATTTTT
25705466 AAAAAATTATAAATTTTTAA
1 AAAAAATTATAAATTTTTAA
25705486 AAAAAATTATAAATTTTTAA
1 AAAAAATTATAAATTTTTAA
25705506 AAAA
1 AAAA
25705510 TTCTAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTATAAATTTTTAA
Found at i:25705754 original size:15 final size:16
Alignment explanation
Indices: 25705734--25705767 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25705724 TTAACTCGAA
25705734 CAATTCCACTC-ATTT
1 CAATTCCACTCGATTT
*
25705749 CAATTCGACTCGATTT
1 CAATTCCACTCGATTT
25705765 CAA
1 CAA
25705768 ATCGAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (16 bp):
CAATTCCACTCGATTT
Found at i:25705766 original size:16 final size:15
Alignment explanation
Indices: 25705734--25705772 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
25705724 TTAACTCGAA
*
25705734 CAATTCCACTCATTT
1 CAATTCGACTCATTT
25705749 CAATTCGACTCGATTT
1 CAATTCGACTC-ATTT
*
25705765 CAAATCGA
1 CAATTCGA
25705773 GTTAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (15 bp):
CAATTCGACTCATTT
Found at i:25710687 original size:25 final size:25
Alignment explanation
Indices: 25710641--25710688 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
25710631 AATTTTTGAA
* *
25710641 ATTGATGATGATTTTTTGTTTTTCC
1 ATTGATGATGATCTTGTGTTTTTCC
25710666 ATTGATGAT-ATCTTGTGATTTTT
1 ATTGATGATGATCTTGTG-TTTTT
25710689 GTTGTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (25 bp):
ATTGATGATGATCTTGTGTTTTTCC
Found at i:25711438 original size:41 final size:42
Alignment explanation
Indices: 25711331--25711450 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 42
25711321 GATGTATGTT
* **
25711331 TTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGTGT
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGTAA
*
25711373 TTACGTATAAGACCATGTCTGGGACATTGGCATCG-TATT-TAA
1 TT-CGTGTAAGACCATGTCTGGGACATTGGCATCGAT-TTGTAA
* * *
25711415 TTCGTGGAAGACCCTGTCTGGGACAGTGGCATCGAT
1 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
25711451 ATGTGATTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 28 0.42
42 7 0.10
43 32 0.48
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCATCGATTTGTAA
Found at i:25714275 original size:17 final size:17
Alignment explanation
Indices: 25714253--25714286 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
25714243 GCATAAATGA
25714253 GATGGAAACTATAAAAC
1 GATGGAAACTATAAAAC
25714270 GATGGAAACTATAAAAC
1 GATGGAAACTATAAAAC
25714287 TTATACCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
GATGGAAACTATAAAAC
Found at i:25714713 original size:3 final size:3
Alignment explanation
Indices: 25714705--25714729 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25714695 CGTTTGTATC
25714705 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
25714730 TTATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:25719754 original size:27 final size:27
Alignment explanation
Indices: 25719723--25719785 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
25719713 CAAATCTACC
*
25719723 TTCTACTATTCAAATTTAA-CATTTAAT
1 TTCTACTATTC-AATTTAAGCATTAAAT
25719750 TTCTA-TACTTCAATTTAAGCATTAAAT
1 TTCTACTA-TTCAATTTAAGCATTAAAT
*
25719777 CTCT-CTATT
1 TTCTACTATT
25719786 GTTAAAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (27 bp):
TTCTACTATTCAATTTAAGCATTAAAT
Found at i:25720208 original size:15 final size:16
Alignment explanation
Indices: 25720184--25720217 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25720174 CAAATGAATT
25720184 ATTAAGAAATATAAAA
1 ATTAAGAAATATAAAA
*
25720200 ATTAA-AAATATATAA
1 ATTAAGAAATATAAAA
25720215 ATT
1 ATT
25720218 GGTCCAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTAAGAAATATAAAA
Found at i:25722424 original size:20 final size:21
Alignment explanation
Indices: 25722396--25722434 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25722386 GTGCATGGGT
*
25722396 GCAATTTC-AGCTTTACAACA
1 GCAAGTTCAAGCTTTACAACA
*
25722416 GCAAGTTCAATCTTTACAA
1 GCAAGTTCAAGCTTTACAA
25722435 GCTGAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (21 bp):
GCAAGTTCAAGCTTTACAACA
Found at i:25727701 original size:50 final size:50
Alignment explanation
Indices: 25727641--25727754 Score: 156
Period size: 50 Copynumber: 2.3 Consensus size: 50
25727631 ACAGAGAGTC
* * * *
25727641 CACCACAAAGGTTTTACAGAGAGCTCGCCACAAAGGCTTTATAGAATATT
1 CACCATAAAGGCTTTACAGAGAACTCGCCACAAAGGCTTTACAGAATATT
* * * *
25727691 CGCCATAAAGGCTTTATAGAGAATTCGCCACAAAGGTTTTACAGAATATT
1 CACCATAAAGGCTTTACAGAGAACTCGCCACAAAGGCTTTACAGAATATT
25727741 CACCATAAAGGCTT
1 CACCATAAAGGCTT
25727755 GGTTTGGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (50 bp):
CACCATAAAGGCTTTACAGAGAACTCGCCACAAAGGCTTTACAGAATATT
Found at i:25727722 original size:75 final size:76
Alignment explanation
Indices: 25727577--25727735 Score: 203
Period size: 75 Copynumber: 2.1 Consensus size: 76
25727567 CCAAAAATCC
* * * *
25727577 TTTATAGAGAGTTCGCCACAAAAGGCTTTACAAAATATTTGCCACAAAGACTTAACAGAGAGTCC
1 TTTACAGAGAGCTCGCCACAAAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCC
25727642 ACCACAAAGGT
66 ACCACAAAGGT
* * * * * * *
25727653 TTTACAGAGAGCTCGCCAC-AAAGGCTTTATAGAATATTCGCCATAAAGGCTTTATAGAGAATTC
1 TTTACAGAGAGCTCGCCACAAAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCC
*
25727717 GCCACAAAGGT
66 ACCACAAAGGT
25727728 TTTACAGA
1 TTTACAGA
25727736 ATATTCACCA
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 54 0.76
76 17 0.24
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (76 bp):
TTTACAGAGAGCTCGCCACAAAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCC
ACCACAAAGGT
Found at i:25727741 original size:25 final size:25
Alignment explanation
Indices: 25727576--25727754 Score: 139
Period size: 25 Copynumber: 7.1 Consensus size: 25
25727566 GCCAAAAATC
* *
25727576 CTTTATAGAGAGTTCGCCACAAAAGG
1 CTTTACAGAGAATTCGCCAC-AAAGG
* * *
25727602 CTTTACA-AAATATTTGCCACAAAGA
1 CTTTACAGAGA-ATTCGCCACAAAGG
* * * *
25727627 CTTAACAGAGAGTCCACCACAAAGG
1 CTTTACAGAGAATTCGCCACAAAGG
* **
25727652 TTTTACAGAGAGCTCGCCACAAAGG
1 CTTTACAGAGAATTCGCCACAAAGG
* *
25727677 CTTTATAGA-ATATTCGCCATAAAGG
1 CTTTACAGAGA-ATTCGCCACAAAGG
*
25727702 CTTTATAGAGAATTCGCCACAAAGG
1 CTTTACAGAGAATTCGCCACAAAGG
* * *
25727727 TTTTACAGA-ATATTCACCATAAAGG
1 CTTTACAGAGA-ATTCGCCACAAAGG
25727752 CTT
1 CTT
25727755 GGTTTGGTTT
Statistics
Matches: 120, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
24 2 0.02
25 102 0.85
26 16 0.13
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (25 bp):
CTTTACAGAGAATTCGCCACAAAGG
Found at i:25727751 original size:75 final size:75
Alignment explanation
Indices: 25727592--25727754 Score: 175
Period size: 75 Copynumber: 2.2 Consensus size: 75
25727582 AGAGAGTTCG
* *
25727592 CCACAAAAGGCTTTACAAAATATTTGCCACAAAGACTTAACAGAGAGTCCACCACAAAGGTTTTA
1 CCAC-AAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCCACCACAAAGGTTTTA
* *
25727657 CAGAGAGCTCG
65 CAGAGAACTCA
* * * * * * * *
25727668 CCACAAAGGCTTTATAGAATATTCGCCATAAAGGCTTTATAGAGAATTCGCCACAAAGGTTTTAC
1 CCACAAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCCACCACAAAGGTTTTAC
*
25727733 AGA-ATATTCA
66 AGAGA-ACTCA
*
25727743 CCATAAAGGCTT
1 CCACAAAGGCTT
25727755 GGTTTGGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
74 1 0.01
75 67 0.93
76 4 0.06
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (75 bp):
CCACAAAGGCTTTACAAAATATTCGCCACAAAGACTTAACAGAGAATCCACCACAAAGGTTTTAC
AGAGAACTCA
Found at i:25730641 original size:39 final size:40
Alignment explanation
Indices: 25730598--25730685 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
25730588 CGAATTATGG
* * *
25730598 AATACTGGATATTGTTTTG-ATTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGTTATGCA-TAATGCAGTGAATTGTGAA
*
25730637 AATACTGAATATTGTTATGCATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
*
25730677 ATTACTGAA
1 AATACTGAA
25730686 GTAAAGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 21 0.50
40 21 0.50
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (40 bp):
AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
Found at i:25730959 original size:45 final size:45
Alignment explanation
Indices: 25730887--25731037 Score: 230
Period size: 45 Copynumber: 3.3 Consensus size: 45
25730877 ATGTGCCGAC
* *
25730887 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* *
25730932 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
25730977 TACTGTTACTGTTACAGGTTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
25731022 TACTGTTACTGATTAC
1 TACTGTTACTG-TTAC
25731038 TGTATACTGG
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
45 93 0.96
46 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:25735908 original size:17 final size:18
Alignment explanation
Indices: 25735882--25735916 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
25735872 CCATTAGTCA
25735882 AAATGAAATAA-TATTTT
1 AAATGAAATAATTATTTT
*
25735899 AAATGCAATAATTATTTT
1 AAATGAAATAATTATTTT
25735917 TTTTGGGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATGAAATAATTATTTT
Found at i:25742233 original size:2 final size:2
Alignment explanation
Indices: 25742226--25742252 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
25742216 CTAAAAACAA
25742226 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
25742253 GCTGACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25743280 original size:37 final size:39
Alignment explanation
Indices: 25743170--25743263 Score: 107
Period size: 38 Copynumber: 2.6 Consensus size: 39
25743160 GAAAATCATA
*
25743170 AAAAAAAT-TAAAAAT-TAT-AAAA-TATT-GAAGTG-C
1 AAAAAAATATAAAAATATATAAAAACTATTAGAAATGAC
25743203 --AAAAATATAAAAATATATAAAAACTATTAGAAATGAC
1 AAAAAAATATAAAAATATATAAAAACTATTAGAAATGAC
*
25743240 AAAAAAATAT-ATAATATATAAAAA
1 AAAAAAATATAAAAATATATAAAAA
25743264 TAGTTCAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
31 6 0.12
32 7 0.14
33 3 0.06
34 4 0.08
35 4 0.08
36 5 0.10
37 1 0.02
38 13 0.25
39 8 0.16
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (39 bp):
AAAAAAATATAAAAATATATAAAAACTATTAGAAATGAC
Found at i:25743399 original size:20 final size:21
Alignment explanation
Indices: 25743374--25743422 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
25743364 TTATATATAT
25743374 AAAATTATTAAAAATA-TTAA
1 AAAATTATTAAAAATATTTAA
* *
25743394 AAAATTAAT-GAAATATTTAA
1 AAAATTATTAAAAATATTTAA
25743414 AAAA-TATTA
1 AAAATTATTA
25743423 TAAGAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATTATTAAAAATATTTAA
Found at i:25743918 original size:19 final size:18
Alignment explanation
Indices: 25743896--25743935 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
25743886 TCAATTTTAA
25743896 ATAATTATTAATATTTTTT
1 ATAATTATTAAT-TTTTTT
*
25743915 ATAATTTTTAATTTTTTT
1 ATAATTATTAATTTTTTT
25743933 ATA
1 ATA
25743936 GTTTGAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATAATTATTAATTTTTTT
Found at i:25744039 original size:10 final size:10
Alignment explanation
Indices: 25744024--25744060 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
25744014 ATTCAAGATG
25744024 TAATTTTTAT
1 TAATTTTTAT
25744034 TAATTTTT-T
1 TAATTTTTAT
25744043 TAATTATTTAT
1 TAATT-TTTAT
25744054 T-ATTTTT
1 TAATTTTT
25744061 GAAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.36
10 14 0.56
11 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TAATTTTTAT
Found at i:25744058 original size:19 final size:19
Alignment explanation
Indices: 25744024--25744060 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
25744014 ATTCAAGATG
25744024 TAATTTTTATTAATTTTTT
1 TAATTTTTATTAATTTTTT
25744043 TAATTATTTATT-ATTTTT
1 TAATT-TTTATTAATTTTT
25744061 GAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TAATTTTTATTAATTTTTT
Found at i:25744842 original size:15 final size:15
Alignment explanation
Indices: 25744822--25744851 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25744812 ATTTAGTATG
25744822 GGATAATCTTGTTGT
1 GGATAATCTTGTTGT
25744837 GGATAATCTTGTTGT
1 GGATAATCTTGTTGT
25744852 TTAATGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (15 bp):
GGATAATCTTGTTGT
Found at i:25745054 original size:30 final size:30
Alignment explanation
Indices: 25745020--25745081 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
25745010 GAAAAAAGTA
25745020 TACCACATCAATAATAATAAATATTAAATT
1 TACCACATCAATAATAATAAATATTAAATT
25745050 TACCACATCAATAATAATAAATATTAAATT
1 TACCACATCAATAATAATAAATATTAAATT
25745080 TA
1 TA
25745082 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
TACCACATCAATAATAATAAATATTAAATT
Found at i:25746420 original size:17 final size:18
Alignment explanation
Indices: 25746393--25746426 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25746383 CAAACACCCT
25746393 TGTAGGCCCACACGCCCG
1 TGTAGGCCCACACGCCCG
25746411 TGTA-GCCCACACGCCC
1 TGTAGGCCCACACGCCC
25746427 ATTCTGGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.12
Consensus pattern (18 bp):
TGTAGGCCCACACGCCCG
Found at i:25748159 original size:10 final size:10
Alignment explanation
Indices: 25748144--25748200 Score: 50
Period size: 10 Copynumber: 6.1 Consensus size: 10
25748134 GATTCGTTTC
25748144 AATTTTTTAT
1 AATTTTTTAT
**
25748154 AATTTTAAAT
1 AATTTTTTAT
* *
25748164 AATTATTAAT
1 AATTTTTTAT
25748174 -A-TTTTTAT
1 AATTTTTTAT
25748182 AA-TTTTTA-
1 AATTTTTTAT
25748190 AATTTTTTAT
1 AATTTTTTAT
25748200 A
1 A
25748201 GTTTAGAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.18
9 14 0.37
10 17 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:25748197 original size:18 final size:18
Alignment explanation
Indices: 25748147--25748200 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
25748137 TCGTTTCAAT
**
25748147 TTTTTATAATTTTAAATAA
1 TTTTTA-AATTTTTTATAA
*
25748166 TTATT-AATATTTTTATAA
1 TTTTTAAAT-TTTTTATAA
25748184 TTTTTAAATTTTTTATA
1 TTTTTAAATTTTTTATA
25748201 GTTTAGAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 19 0.66
19 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTTTTTATAA
Found at i:25748198 original size:9 final size:9
Alignment explanation
Indices: 25748147--25748196 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
25748137 TCGTTTCAAT
25748147 TTTTTATAA
1 TTTTTATAA
*
25748156 TTTTAAATAA
1 TTTT-TATAA
*
25748166 TTATTA-ATA
1 TTTTTATA-A
25748175 TTTTTATAA
1 TTTTTATAA
25748184 TTTTTA-AA
1 TTTTTATAA
25748192 TTTTT
1 TTTTT
25748197 TATAGTTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
8 8 0.24
9 18 0.53
10 8 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:25755665 original size:11 final size:11
Alignment explanation
Indices: 25755643--25755674 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25755633 ACAATATCCA
25755643 AACAATA-A-T
1 AACAATATAGT
25755652 AACAATATAGT
1 AACAATATAGT
25755663 AACAATATAGT
1 AACAATATAGT
25755674 A
1 A
25755675 GTGAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 7 0.33
10 1 0.05
11 13 0.62
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.25
Consensus pattern (11 bp):
AACAATATAGT
Found at i:25755727 original size:20 final size:20
Alignment explanation
Indices: 25755702--25755746 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
25755692 TAATGAAAAA
25755702 AAAAACAACAAGAAAATAAT
1 AAAAACAACAAGAAAATAAT
*
25755722 AAAAACAACAAGAAAATAGT
1 AAAAACAACAAGAAAATAAT
25755742 AAAAA
1 AAAAA
25755747 TACAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.76, C:0.09, G:0.07, T:0.09
Consensus pattern (20 bp):
AAAAACAACAAGAAAATAAT
Found at i:25755739 original size:17 final size:17
Alignment explanation
Indices: 25755696--25755739 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
25755686 GTAAAATAAT
*
25755696 GAAAAAAAAAACAACAA
1 GAAAATAAAAACAACAA
25755713 GAAAATAATAAAAACAACAA
1 G--AA-AATAAAAACAACAA
25755733 GAAAATA
1 GAAAATA
25755740 GTAAAAATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.22
18 2 0.09
19 2 0.09
20 14 0.61
ACGTcount: A:0.77, C:0.09, G:0.07, T:0.07
Consensus pattern (17 bp):
GAAAATAAAAACAACAA
Found at i:25757053 original size:60 final size:60
Alignment explanation
Indices: 25756924--25757072 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 60
25756914 TTGACAACTT
* * * * * *
25756924 TTCCCAAATTTAGGCCTGAACTTTTTATTGGTTCAAGTTAAGCCCTGAACTTAACAATTG
1 TTCCCACATTGAGGCTTAAACTTTTTTTTGGTCCAAGTTAAGCCCTGAACTTAACAATTG
* * * *
25756984 TTCCCACATTGAGG-TGTAAACTTTTTTTTTGTCCAAGTTAGGCCCTGGACTTAGCAATTG
1 TTCCCACATTGAGGCT-TAAACTTTTTTTTGGTCCAAGTTAAGCCCTGAACTTAACAATTG
*** * *
25757044 TTTTTACATTGGGGCTTAAAATTTTTTTT
1 TTCCCACATTGAGGCTTAAACTTTTTTTT
25757073 CCAAGTTATT
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
60 71 0.99
61 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (60 bp):
TTCCCACATTGAGGCTTAAACTTTTTTTTGGTCCAAGTTAAGCCCTGAACTTAACAATTG
Found at i:25765041 original size:8 final size:9
Alignment explanation
Indices: 25765019--25765135 Score: 62
Period size: 10 Copynumber: 12.2 Consensus size: 9
25765009 CCAAAAATTT
25765019 ATTTTAAAA
1 ATTTTAAAA
25765028 ATTTTAAAA
1 ATTTTAAAA
*
25765037 ATTTAAAAAA
1 ATTT-TAAAA
25765047 GTATTTTAAAA
1 --ATTTTAAAA
*
25765058 ATATTTTAAA
1 AT-TTTAAAA
25765068 A--TTAAAA
1 ATTTTAAAA
*
25765075 TATTTTAAATTT
1 -ATTTTAAA--A
*
25765087 TTTTTAAAAA
1 ATTTT-AAAA
25765097 GTATTTTAAAA
1 --ATTTTAAAA
*
25765108 ATATTTTAAA
1 AT-TTTAAAA
25765118 A-TTTAAAA
1 ATTTTAAAA
25765126 A-TTTAAAA
1 ATTTTAAAA
25765134 AT
1 AT
25765136 AAATATATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
7 5 0.06
8 16 0.19
9 17 0.20
10 23 0.27
11 12 0.14
12 11 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:25765046 original size:31 final size:31
Alignment explanation
Indices: 25765011--25765079 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
25765001 ATAAAATACC
25765011 AAAAATTTATTTTAAAAAT-TTTAAAAATTTA
1 AAAAATTTATTTTAAAAATATTTAAAAA-TTA
* *
25765042 AAAAA-GTATTTTAAAAATATTTTAAAATTA
1 AAAAATTTATTTTAAAAATATTTAAAAATTA
*
25765072 AAATATTT
1 AAAAATTT
25765080 TAAATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
AAAAATTTATTTTAAAAATATTTAAAAATTA
Found at i:25765062 original size:11 final size:11
Alignment explanation
Indices: 25765018--25765118 Score: 78
Period size: 11 Copynumber: 9.9 Consensus size: 11
25765008 ACCAAAAATT
25765018 TATTTT-AAAA
1 TATTTTAAAAA
25765028 -ATTTT-AAAA
1 TATTTTAAAAA
*
25765037 -ATTTAAAAAA
1 TATTTTAAAAA
25765047 GTATTTTAAAAA
1 -TATTTTAAAAA
25765059 TATTTT--AAA
1 TATTTTAAAAA
25765068 -A--TT-AAAA
1 TATTTTAAAAA
**
25765075 TATTTTAAATT
1 TATTTTAAAAA
*
25765086 TTTTTTAAAAA
1 TATTTTAAAAA
25765097 GTATTTTAAAAA
1 -TATTTTAAAAA
25765109 TATTTTAAAA
1 TATTTTAAAA
25765119 TTTAAAAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 17
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 2 0.03
9 16 0.22
10 6 0.08
11 26 0.35
12 19 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:25765091 original size:27 final size:28
Alignment explanation
Indices: 25765018--25765136 Score: 98
Period size: 30 Copynumber: 4.5 Consensus size: 28
25765008 ACCAAAAATT
*
25765018 TATTTTAAAAAT-TTTAAAAATTTAAAAAAG
1 TATTTTAAAAATATTTTAAAA-TT--AAAAG
25765048 TATTTTAAAAATATTTTAAAATTAAAA-
1 TATTTTAAAAATATTTTAAAATTAAAAG
*
25765075 TATTTT--AAAT-TTTT---TTTAAAAAG
1 TATTTTAAAAATATTTTAAAATT-AAAAG
25765098 TATTTTAAAAATATTTTAAAATTTAAAA-
1 TATTTTAAAAATATTTTAAAA-TTAAAAG
25765126 -A-TTTAAAAATA
1 TATTTTAAAAATA
25765137 AATATATTTA
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
21 2 0.03
22 4 0.05
23 6 0.08
24 4 0.05
25 8 0.11
26 14 0.18
27 7 0.09
28 4 0.05
29 4 0.05
30 16 0.21
31 7 0.09
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TATTTTAAAAATATTTTAAAATTAAAAG
Found at i:25767378 original size:28 final size:28
Alignment explanation
Indices: 25767333--25767386 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
25767323 AGATTCAGGA
*
25767333 TTTGGGTTCAGAACTTAAGGTTTAGGGT
1 TTTGGATTCAGAACTTAAGGTTTAGGGT
**
25767361 TTTGGATTCAGAGTTTAAGGTTTAGG
1 TTTGGATTCAGAACTTAAGGTTTAGG
25767387 TTCAAGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.41
Consensus pattern (28 bp):
TTTGGATTCAGAACTTAAGGTTTAGGGT
Found at i:25771948 original size:11 final size:11
Alignment explanation
Indices: 25771934--25771973 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
25771924 TTATTTACGT
*
25771934 TTATCAAATTA
1 TTATTAAATTA
*
25771945 TTATTTAAATAA
1 TTA-TTAAATTA
25771957 TTATTAAATTA
1 TTATTAAATTA
25771968 TTATTA
1 TTATTA
25771974 TTATTGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TTATTAAATTA
Found at i:25772447 original size:37 final size:36
Alignment explanation
Indices: 25772401--25772662 Score: 230
Period size: 37 Copynumber: 7.1 Consensus size: 36
25772391 GTCAAGGTCG
* *
25772401 ACCTTTAAAAAAGGTTGAGATAGACCCGTCTAAGGTA
1 ACCTTT-AAAAAGGTTGAGATAGACCTGTCTAAGGCA
*
25772438 ACCTTTAAAAAAGGTT-AGGATAGACCTGTCTAAGACA
1 ACCTTT-AAAAAGGTTGA-GATAGACCTGTCTAAGGCA
**
25772475 ACC-TTAAAAAGGCCG-GCATAGACCTTGTCTAAGGCA
1 ACCTTTAAAAAGGTTGAG-ATAGACC-TGTCTAAGGCA
* ** ** *
25772511 GCCTTTAAAAAAATTTGAGACGGAGCC-GTCTATGGCA
1 ACCTTT-AAAAAGGTTGAGATAGA-CCTGTCTAAGGCA
* *
25772548 ACC-TTAAAAAGGTTGGGATAGAATCTTGTCTAAGGCA
1 ACCTTTAAAAAGGTTGAGATAG-A-CCTGTCTAAGGCA
* *
25772585 ACCCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCA
1 ACCTTTAAAAAGGTTGAGATAGACC-TGTCTAAGGCA
**
25772622 ACCTTTAAAAAGGTTGAGATAGAGCC-GTCTAATACA
1 ACCTTTAAAAAGGTTGAGATAGA-CCTGTCTAAGGCA
25772658 ACCTT
1 ACCTT
25772663 AGTAGAAGAT
Statistics
Matches: 184, Mismatches: 28, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
34 1 0.01
35 25 0.14
36 33 0.18
37 93 0.51
38 29 0.16
39 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24
Consensus pattern (36 bp):
ACCTTTAAAAAGGTTGAGATAGACCTGTCTAAGGCA
Found at i:25772529 original size:110 final size:111
Alignment explanation
Indices: 25772401--25772663 Score: 336
Period size: 110 Copynumber: 2.4 Consensus size: 111
25772391 GTCAAGGTCG
* *
25772401 ACCTTTAAAAAAGGTTGAGATAGACCCGTCTAAGGTAACCTTTAAAAAAGGTTAGGATAG-A-CC
1 ACCTTTAAAAAAGGTTGAGATAGAGCCGTCTAAGGCAACC-TT-AAAAAGGTTAGGATAGAATCC
25772464 TGTCTAAGACAA-CCTTAAAAAGGCCGGCATAGACCTTGTCTAAGGCA
64 TGTCTAAGACAACCCTTAAAAAGGCCGGCATAGACCTTGTCTAAGGCA
* ** ** * * *
25772511 GCCTTTAAAAAAATTTGAGACGGAGCCGTCTATGGCAACCTTAAAAAGGTTGGGATAGAATCTTG
1 ACCTTTAAAAAAGGTTGAGATAGAGCCGTCTAAGGCAACCTTAAAAAGGTTAGGATAGAATCCTG
* ** *
25772576 TCTAAGGCAACCCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCA
66 TCTAAGACAACCCTTAAAAAGGCCGGCATAGACCTTGTCTAAGGCA
**
25772622 ACCTTT-AAAAAGGTTGAGATAGAGCCGTCTAATACAACCTTA
1 ACCTTTAAAAAAGGTTGAGATAGAGCCGTCTAAGGCAACCTTA
25772664 GTAGAAGATC
Statistics
Matches: 128, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
108 15 0.12
109 3 0.02
110 73 0.57
111 37 0.29
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (111 bp):
ACCTTTAAAAAAGGTTGAGATAGAGCCGTCTAAGGCAACCTTAAAAAGGTTAGGATAGAATCCTG
TCTAAGACAACCCTTAAAAAGGCCGGCATAGACCTTGTCTAAGGCA
Found at i:25772616 original size:74 final size:74
Alignment explanation
Indices: 25772408--25772644 Score: 250
Period size: 73 Copynumber: 3.2 Consensus size: 74
25772398 TCGACCTTTA
* * * *
25772408 AAAAAGGTTGAGATAG-ACC-CGTCTAAGGTAACCTTTAAAAAAGGTTAGGATAGACCTGTCTAA
1 AAAAAGGTTGGGATAGAACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACCTGTCTAA
*
25772471 GACAACCTT
66 GGCAACCTT
** * * ** * **
25772480 AAAAAGGCCGGCATAG-ACCTTGTCTAAGGCAGCCTTTAAAAAAATTTGAGACGGAGCC-GTCTA
1 AAAAAGGTTGGGATAGAACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGA-CCTGTCTA
*
25772543 TGGCAACCTT
65 AGGCAACCTT
* *
25772553 AAAAAGGTTGGGATAGAATCTTGTCTAAGGCAACCCTT-AAAAAGGTTGGGATAGACCTTGTCTA
1 AAAAAGGTTGGGATAGAACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACC-TGTCTA
25772617 AGGCAACCTTT
65 AGGCAACC-TT
*
25772628 AAAAAGGTTGAGATAGA
1 AAAAAGGTTGGGATAGA
25772645 GCCGTCTAAT
Statistics
Matches: 131, Mismatches: 28, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
72 17 0.13
73 64 0.49
74 32 0.24
75 18 0.14
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (74 bp):
AAAAAGGTTGGGATAGAACCTTGTCTAAGGCAACCTTTAAAAAAGGTTGGGATAGACCTGTCTAA
GGCAACCTT
Found at i:25778936 original size:7 final size:7
Alignment explanation
Indices: 25778924--25778959 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
25778914 ATAAAAGGAC
25778924 ATAATAA
1 ATAATAA
25778931 ATAATAA
1 ATAATAA
25778938 ATAATAA
1 ATAATAA
25778945 ATAATAA
1 ATAATAA
25778952 ATAATAA
1 ATAATAA
25778959 A
1 A
25778960 ATCATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATAATAA
Found at i:25779693 original size:11 final size:10
Alignment explanation
Indices: 25779669--25779702 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
25779659 AAAGTACATT
*
25779669 TATATATATA
1 TATATATGTA
25779679 TATATATGCTA
1 TATATATG-TA
25779690 TATATATGTA
1 TATATATGTA
25779700 TAT
1 TAT
25779703 TTTAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (10 bp):
TATATATGTA
Found at i:25779859 original size:27 final size:25
Alignment explanation
Indices: 25779807--25779863 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
25779797 GTGCTTTTTC
25779807 TTTTGATCTGTTTTGCTCTTTTTATT
1 TTTTGATCTGTTTT-CTCTTTTTATT
*
25779833 ATTTTGAATCTGTTTT-TTTTTTCTATT
1 -TTTTG-ATCTGTTTTCTCTTTT-TATT
25779860 TTTT
1 TTTT
25779864 CATTCCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.33
27 9 0.33
28 9 0.33
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.72
Consensus pattern (25 bp):
TTTTGATCTGTTTTCTCTTTTTATT
Found at i:25789812 original size:37 final size:37
Alignment explanation
Indices: 25789770--25789846 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
25789760 TTTTGTATTA
*
25789770 AGAGTTAGATTATATTTTGTCGTTTTTATTTAAAAAT
1 AGAGTTAGATTATATTTTATCGTTTTTATTTAAAAAT
25789807 AGAGTTAGATTATATTTTATCGTTTTTATTTAAAAAT
1 AGAGTTAGATTATATTTTATCGTTTTTATTTAAAAAT
25789844 AGA
1 AGA
25789847 CAAATTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (37 bp):
AGAGTTAGATTATATTTTATCGTTTTTATTTAAAAAT
Found at i:25797705 original size:16 final size:18
Alignment explanation
Indices: 25797684--25797716 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25797674 GAAACAAAAA
25797684 TATCAT-TT-TTATTTTT
1 TATCATATTATTATTTTT
25797700 TATCATATTATTATTTT
1 TATCATATTATTATTTT
25797717 GGTGTCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (18 bp):
TATCATATTATTATTTTT
Found at i:25800190 original size:21 final size:23
Alignment explanation
Indices: 25800139--25800194 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
25800129 TACCATTTCA
*
25800139 TATAATAAA-TAATTTAAAATGAT
1 TATAAAAAATTAA-TTAAAATGAT
25800162 TATAAAAAATTAATTAAAAT-AT
1 TATAAAAAATTAATTAAAATGAT
25800184 T-TAAAAAATTA
1 TATAAAAAATTA
25800195 CAATCTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 10 0.32
22 3 0.10
23 15 0.48
24 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TATAAAAAATTAATTAAAATGAT
Found at i:25818124 original size:48 final size:47
Alignment explanation
Indices: 25818072--25818231 Score: 131
Period size: 48 Copynumber: 3.3 Consensus size: 47
25818062 AGCCACAGCG
* *
25818072 GCGAATCTCACTACTAGTGATGCAGCGGAGCAGATTGAAGCTACAAC
1 GCGAATCTCACTTCTAGAGATGCAGCGGAGCAGATTGAAGCTACAAC
** * **** ** *
25818119 AGCGAATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAAC
1 -GCGAATCTCAC-TTCTAGAGA-TGCAGCGGAGCAGATTGAAGCTACAAC
* * *
25818169 GACGAATCTTACTTCTGGCGATGCAGCGGAGCAGATTGAAGCTACAAC
1 G-CGAATCTCACTTCTAGAGATGCAGCGGAGCAGATTGAAGCTACAAC
*
25818217 GGCAAATCTCACTTC
1 -GCGAATCTCACTTC
25818232 CCAGACATTG
Statistics
Matches: 82, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
48 42 0.51
49 11 0.13
50 29 0.35
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (47 bp):
GCGAATCTCACTTCTAGAGATGCAGCGGAGCAGATTGAAGCTACAAC
Found at i:25818168 original size:50 final size:48
Alignment explanation
Indices: 25818026--25818281 Score: 190
Period size: 50 Copynumber: 5.2 Consensus size: 48
25818016 CTGACAGCGG
* *
25818026 ATCTCACTTCCCCGACACTGCAATTTAAAAGATCGAAGCCACAGCGGCGA
1 ATCTCACTT-CCCGACA-TGCAATTTAAAAGATTGAAGCCACAACGGCGA
* ** ** **** ** * *
25818076 ATCTCACTACTAGTGATGCAGCGGAGCAGATTGAAGCTACAACAGCGA
1 ATCTCACTTCCCGACATGCAATTTAAAAGATTGAAGCCACAACGGCGA
*
25818124 ATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGACGA
1 ATCTCAC-TTCCCGACA-TGCAATTTAAAAGATTGAAGCCACAACGGCGA
* * * **** ** * *
25818174 ATCTTACTT-CTGGCGATGCAGCGGAGCAGATTGAAGCTACAACGGCAA
1 ATCTCACTTCCCGAC-ATGCAATTTAAAAGATTGAAGCCACAACGGCGA
25818222 ATCTCACTTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
1 ATCTCACTTCCC-GACA-TGCAATTTAAAAGATTGAAGCCACAACGGCGA
*
25818272 ATCTTACTTC
1 ATCTCACTTC
25818282 TGGCAATGTA
Statistics
Matches: 147, Mismatches: 53, Indels: 12
0.69 0.25 0.06
Matches are distributed among these distances:
48 63 0.43
49 12 0.08
50 72 0.49
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (48 bp):
ATCTCACTTCCCGACATGCAATTTAAAAGATTGAAGCCACAACGGCGA
Found at i:25818192 original size:98 final size:98
Alignment explanation
Indices: 25818019--25818350 Score: 461
Period size: 98 Copynumber: 3.4 Consensus size: 98
25818009 TCCTGCACTG
* * * * * *
25818019 ACAGCGGATCTCACTTCCCCGACACTGCAATTTAAAAGATCGAAGCCACAGCGGCGAATCTCACT
1 ACAGCGAATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACT
* * *
25818084 ACTAGTGATGCAGCGGAGCAGATTGAAGCTACA
66 TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
*
25818117 ACAGCGAATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGACGAATCTTACT
1 ACAGCGAATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACT
25818182 TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
66 TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
* *
25818215 ACGGCAAATCTCAC-TTCCCAGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTAC
1 ACAGCGAATCTCACTTTCCC-GACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTAC
* * *
25818279 TTCTGGCAATGTAGC-GAGAAGATTGAAAGCTACA
65 TTCTGGCGATGCAGCGGAGCAGATTG-AAGCTACA
* * *
25818313 ACAGCCGAATCTCATTTTCTCGATATTGCAATTTAAAA
1 ACAG-CGAATCTCACTTTCCCGACATTGCAATTTAAAA
25818351 AGATCAAAAG
Statistics
Matches: 209, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
97 14 0.07
98 167 0.80
99 24 0.11
100 4 0.02
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (98 bp):
ACAGCGAATCTCACTTTCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACT
TCTGGCGATGCAGCGGAGCAGATTGAAGCTACA
Found at i:25819766 original size:2 final size:2
Alignment explanation
Indices: 25819761--25819797 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25819751 CATATATACG
25819761 TA TA TA 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 TA TA TA T
25819798 TTCAACTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25821612 original size:19 final size:18
Alignment explanation
Indices: 25821580--25821615 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25821570 ATAAGTATGT
25821580 AAAACTTCAAAAATTTTA
1 AAAACTTCAAAAATTTTA
*
25821598 AAAACTTTCATAAATTTT
1 AAAAC-TTCAAAAATTTT
25821616 TTAAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAACTTCAAAAATTTTA
Found at i:25821769 original size:24 final size:23
Alignment explanation
Indices: 25821720--25821773 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
25821710 AATTTTAGGG
*
25821720 TTTTTTTTTGCATTTTTAAATGA
1 TTTTTTTTTGCATTTTTAAAGGA
*
25821743 TTTTTATTTTGTATTTTT-AAGGA
1 TTTTT-TTTTGCATTTTTAAAGGA
*
25821766 ATTTTTTT
1 TTTTTTTT
25821774 AGTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 13 0.48
24 11 0.41
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTGCATTTTTAAAGGA
Found at i:25821770 original size:23 final size:24
Alignment explanation
Indices: 25821720--25821770 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
25821710 AATTTTAGGG
* * *
25821720 TTTTTTTTTGCATTTTTAAATGAT
1 TTTTATTTTGCATTTTTAAAGGAA
*
25821744 TTTTATTTTGTATTTTT-AAGGAA
1 TTTTATTTTGCATTTTTAAAGGAA
25821767 TTTT
1 TTTT
25821771 TTTAGTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.67
Consensus pattern (24 bp):
TTTTATTTTGCATTTTTAAAGGAA
Found at i:25824989 original size:31 final size:32
Alignment explanation
Indices: 25824935--25825018 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 32
25824925 GCTCCAATTT
25824935 TTTTAAAATTTTTTAAAAAAATTCTCATTAAAC
1 TTTT-AAATTTTTTAAAAAAATTCTCATTAAAC
* * *
25824968 TTTTAAATTTTTT-AAATAATTCTTATTAAAG
1 TTTTAAATTTTTTAAAAAAATTCTCATTAAAC
*
25824999 TCTTAAA-TTTTTAAAAAAAT
1 TTTTAAATTTTTTAAAAAAAT
25825019 CTTACTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 5 0.11
31 27 0.60
32 9 0.20
33 4 0.09
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (32 bp):
TTTTAAATTTTTTAAAAAAATTCTCATTAAAC
Found at i:25825984 original size:2 final size:2
Alignment explanation
Indices: 25825973--25826011 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
25825963 ATTCTCTCTT
* *
25825973 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25826012 CTTTTACTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25830393 original size:2 final size:2
Alignment explanation
Indices: 25830386--25830427 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
25830376 TATTTGGCTC
25830386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25830427 A
1 A
25830428 ACAGCCCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25835328 original size:27 final size:29
Alignment explanation
Indices: 25835307--25835360 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
25835297 AAATAATATT
*
25835307 TAAAATATA-ATA-AAATACAATACAATA
1 TAAAATATATATATAAACACAATACAATA
25835334 TAAAATATATATATAAACACAATACAA
1 TAAAATATATATATAAACACAATACAA
25835361 GTTTATACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (29 bp):
TAAAATATATATATAAACACAATACAATA
Found at i:25836375 original size:17 final size:16
Alignment explanation
Indices: 25836345--25836378 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25836335 TTTTCTTTAA
25836345 AAAAAATTAAATTTTT
1 AAAAAATTAAATTTTT
*
25836361 AAAAAATATATATTTTT
1 AAAAAAT-TAAATTTTT
25836378 A
1 A
25836379 GTGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAAATTAAATTTTT
Found at i:25850672 original size:24 final size:24
Alignment explanation
Indices: 25850645--25850724 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
25850635 TTCCTAATAT
25850645 TGGCTCACTTAAACTTCCCGTTA-A
1 TGGCTCAC-TAAACTTCCCGTTACA
* *
25850669 TGGCTCTACGAAACTTCCCATTACA
1 TGGCTC-ACTAAACTTCCCGTTACA
* * ** *
25850694 TGACTCACATGAGTTTCCCGTTATA
1 TGGCTCAC-TAAACTTCCCGTTACA
25850719 TGGCTC
1 TGGCTC
25850725 GAAACAGCTT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.33
Consensus pattern (24 bp):
TGGCTCACTAAACTTCCCGTTACA
Found at i:25852885 original size:15 final size:15
Alignment explanation
Indices: 25852865--25852895 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25852855 CAAGGGCTTT
25852865 AAACTGCGGCCCGTG
1 AAACTGCGGCCCGTG
25852880 AAACTGCGGCCCGTG
1 AAACTGCGGCCCGTG
25852895 A
1 A
25852896 CATTCTCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.13
Consensus pattern (15 bp):
AAACTGCGGCCCGTG
Found at i:25863172 original size:2 final size:2
Alignment explanation
Indices: 25863165--25863212 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
25863155 TGGATTGTTT
25863165 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
25863207 TA TA TA
1 TA TA TA
25863213 AACTTAACAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25863266 original size:31 final size:31
Alignment explanation
Indices: 25863228--25863293 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
25863218 AACAACCTAG
*
25863228 TGACTTAAATAAAAATTTTCAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
* * *
25863259 TGACTTAAATGAATACTTTCAAATAGTTCAG
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
25863290 TGAC
1 TGAC
25863294 CATTTTATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAA
Found at i:25878715 original size:6 final size:6
Alignment explanation
Indices: 25878706--25878733 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
25878696 AAACATGGCA
25878706 ATGGTG ATGGTG ATGGTG ATGGTG ATGG
1 ATGGTG ATGGTG ATGGTG ATGGTG ATGG
25878734 ATCAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
ATGGTG
Found at i:25879451 original size:3 final size:3
Alignment explanation
Indices: 25879443--25879472 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25879433 AGCTGAAACA
*
25879443 AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25879473 CTTTGAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:25889597 original size:23 final size:23
Alignment explanation
Indices: 25889567--25889617 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
25889557 ATTGACTTAT
25889567 TTTTTAAAAA-TTAGTTATTTTTA
1 TTTTTAAAAATTTAGTTA-TTTTA
25889590 TTTTTAAAAATTTAGTTATTTTA
1 TTTTTAAAAATTTAGTTATTTTA
25889613 TTTTT
1 TTTTT
25889618 TACATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TTTTTAAAAATTTAGTTATTTTA
Found at i:25889618 original size:24 final size:23
Alignment explanation
Indices: 25889563--25889619 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 23
25889553 TCCCATTGAC
25889563 TTATTTTTTAAAAATTAGTTATT
1 TTATTTTTTAAAAATTAGTTATT
25889586 TT-TATTTTTAAAAATTTAGTTATT
1 TTAT-TTTTTAAAAA-TTAGTTATT
25889610 TTATTTTTTA
1 TTATTTTTTA
25889620 CATTTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.03
23 12 0.39
24 17 0.55
25 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (23 bp):
TTATTTTTTAAAAATTAGTTATT
Found at i:25890452 original size:25 final size:26
Alignment explanation
Indices: 25890416--25890469 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
25890406 AAATTCTAAA
*
25890416 TATTATAGAAT-ATTTTTATAATTTT
1 TATTATAGAATAATTTTTATAATCTT
25890441 TATTATTA-AATAATTTTTATAATCTT
1 TATTA-TAGAATAATTTTTATAATCTT
25890467 TAT
1 TAT
25890470 GCTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTATAGAATAATTTTTATAATCTT
Found at i:25891961 original size:21 final size:21
Alignment explanation
Indices: 25891932--25891972 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25891922 GGATCAACTT
* *
25891932 TTACTAGCTTATGTTCAGCTC
1 TTACGAGCTTATATTCAGCTC
*
25891953 TTACGAGCTTCTATTCAGCT
1 TTACGAGCTTATATTCAGCT
25891973 TTCAAGCTTC
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:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (21 bp):
TTACGAGCTTATATTCAGCTC
Found at i:25902166 original size:20 final size:20
Alignment explanation
Indices: 25902129--25902175 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
25902119 AACATAATAC
*
25902129 AAAAT-TATAATTAATTATA
1 AAAATATATAAATAATTATA
*
25902148 AAAATATATAAATATTTATA
1 AAAATATATAAATAATTATA
25902168 AATAATAT
1 AA-AATAT
25902176 GTTTAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATATAAATAATTATA
Found at i:25908157 original size:21 final size:21
Alignment explanation
Indices: 25908131--25908174 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
25908121 CACACTTTTG
*
25908131 ATGCTTCAGCATTTGTTGGTA
1 ATGCTTCAGCATTTGTAGGTA
*
25908152 ATGCTTTAGCATTTGTAGGTA
1 ATGCTTCAGCATTTGTAGGTA
25908173 AT
1 AT
25908175 CAGGCACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (21 bp):
ATGCTTCAGCATTTGTAGGTA
Found at i:25908757 original size:34 final size:35
Alignment explanation
Indices: 25908706--25908791 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
25908696 TTTAAAAAAG
** * *
25908706 AATTAAATTAGATTTTAGGGGGTTTAAA-CAAATA
1 AATTAAATTAGGGTTTAGGAGGTTTAAAGAAAATA
* *
25908740 AATTAAATTAGGGTTTA-GAGTTTTAAAGAAAATT
1 AATTAAATTAGGGTTTAGGAGGTTTAAAGAAAATA
25908774 AATTAAATTAGGGTTTAG
1 AATTAAATTAGGGTTTAG
25908792 TTTTTTGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 8 0.18
34 36 0.82
ACGTcount: A:0.43, C:0.01, G:0.19, T:0.37
Consensus pattern (35 bp):
AATTAAATTAGGGTTTAGGAGGTTTAAAGAAAATA
Found at i:25909116 original size:126 final size:126
Alignment explanation
Indices: 25908900--25909540 Score: 853
Period size: 126 Copynumber: 5.1 Consensus size: 126
25908890 ATTTTTCTTA
* * * *
25908900 TACAGTAGTTTCTGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAACGCTT
1 TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
* * *
25908965 CAAGCAGGATGCACTATCAACAAAATTACTGAAAAAAGCTCCCACGTGGACAATTTTTTTTC
66 CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGAC-ATTCTTTTTC
* *
25909027 TACAGTAGTTCCTG-AAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGGTT
1 TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
* * * *
25909091 CAAGTAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCCCACGTAGG-CTTTTTTTTTC
66 CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGT-GGACATTCTTTTTC
* * * * * *
25909152 TATAGTAGTTCCTGAAAAAATAATTTTTAAAAGATGGTTCTGAAAAAATAGTGTAAAAAATGCTT
1 TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
* * *
25909217 CAAACAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCATGTGGACACTCTTTTTC
66 CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACATTCTTTTTC
* * * *
25909278 TATAGTAATTTCTGAAAAAATAATATTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
1 TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
* * * ** *
25909343 TAAGCAAGATGCACTGCCAGCAAAATTACTGAAAAAAAGCTTTCACGTAGACATTCTTTTTC
66 CAAGCAGGATGCACTGTCAGCAAAATTACTG-AAAAAAGCTCCCACGTGGACATTCTTTTTC
* * *
25909405 TACAGTAGTGCTTGAAAAAATAATTTTGAGAAGACGGTTAT--AAAAAT-GTGTCAAAAACGCTT
1 TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
* * **
25909467 CAAGCAGGATGCACTGTTAGTAAAATTACT-ACAAAAAGCTCCCACGTGGACGCTCTTTTTC
66 CAAGCAGGATGCACTGTCAGCAAAATTACTGA-AAAAAGCTCCCACGTGGACATTCTTTTTC
25909528 TACAGTAGTTCCT
1 TACAGTAGTTCCT
25909541 ACTTTGCCTT
Statistics
Matches: 447, Mismatches: 62, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
122 1 0.00
123 35 0.08
124 40 0.09
125 30 0.07
126 267 0.60
127 74 0.17
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCTT
CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACATTCTTTTTC
Found at i:25913080 original size:18 final size:18
Alignment explanation
Indices: 25913039--25913081 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
25913029 GACTTGAAAA
* **
25913039 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGACT
*
25913057 AAGATACATATAAGGACT
1 AGGATACATATAAGGACT
25913075 AGGATAC
1 AGGATAC
25913082 GTATCTGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGACT
Found at i:25914564 original size:26 final size:24
Alignment explanation
Indices: 25914522--25914593 Score: 63
Period size: 26 Copynumber: 2.9 Consensus size: 24
25914512 GCTGTTATAA
* * *
25914522 AAAATTATAAAATAAAATTTAATT
1 AAAATTACAAAATAAAAATTAAAT
25914546 AAAATTACATAAATAAAAAATTAAAT
1 AAAATTACA-AAAT-AAAAATTAAAT
* * **
25914572 AATATTAAAAAATTGAAATTAA
1 AAAATTACAAAATAAAAATTAA
25914594 CCCTTACCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 15 0.38
25 8 0.21
26 16 0.41
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (24 bp):
AAAATTACAAAATAAAAATTAAAT
Found at i:25914565 original size:16 final size:18
Alignment explanation
Indices: 25914546--25914590 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
25914536 AAATTTAATT
*
25914546 AAAATTACATAA-A-TAA
1 AAAATTAAATAATATTAA
25914562 AAAATTAAATAATATTAA
1 AAAATTAAATAATATTAA
25914580 AAAATTGAAAT
1 AAAATT-AAAT
25914591 TAACCCTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 9 0.36
19 4 0.16
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATTAAATAATATTAA
Found at i:25924312 original size:17 final size:17
Alignment explanation
Indices: 25924286--25924321 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25924276 ATTAAAGAAG
* *
25924286 GTGTTTGATATTGGTAT
1 GTGTTCGATATAGGTAT
25924303 GTGTTCGATATAGGTAT
1 GTGTTCGATATAGGTAT
25924320 GT
1 GT
25924322 TCAAATTTCT
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:0.19, C:0.03, G:0.31, T:0.47
Consensus pattern (17 bp):
GTGTTCGATATAGGTAT
Found at i:25928156 original size:19 final size:19
Alignment explanation
Indices: 25928132--25928176 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
25928122 TTTTTTTTGA
25928132 AAAGAAATA-CATAAAATAC
1 AAAGAAATAGCA-AAAATAC
*
25928151 AAAGAAAAAGCAAAAATAC
1 AAAGAAATAGCAAAAATAC
25928170 AAA-AAAT
1 AAAGAAAT
25928177 TGTCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (19 bp):
AAAGAAATAGCAAAAATAC
Found at i:25934174 original size:11 final size:12
Alignment explanation
Indices: 25934155--25934187 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
25934145 AGAGGTTTAT
25934155 ATGTAAAAAAAA
1 ATGTAAAAAAAA
25934167 AT-TAAAAAAAA
1 ATGTAAAAAAAA
*
25934178 GTGTAAAAAA
1 ATGTAAAAAA
25934188 TCAATTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (12 bp):
ATGTAAAAAAAA
Found at i:25934437 original size:10 final size:10
Alignment explanation
Indices: 25934359--25934544 Score: 77
Period size: 10 Copynumber: 19.0 Consensus size: 10
25934349 AATTTTTTTC
25934359 TTATAAAAAA
1 TTATAAAAAA
* *
25934369 TAATTAAAAA
1 TTATAAAAAA
*
25934379 TCATAAAAAA
1 TTATAAAAAA
25934389 --ATACAAAAA
1 TTATA-AAAAA
* *
25934398 TTGT--TAAA
1 TTATAAAAAA
*
25934406 -TATTAAAAA
1 TTATAAAAAA
* *
25934415 -TATGAAAAT
1 TTATAAAAAA
25934424 TTATAAAAAA
1 TTATAAAAAA
25934434 TTATAAAACATA
1 TTATAAAA-A-A
**
25934446 TT-TAAAATT
1 TTATAAAAAA
25934455 TTATAAAAAAA
1 TTAT-AAAAAA
*
25934466 TTATTAAAAA
1 TTATAAAAAA
*
25934476 TTCTATAAAAA
1 TTATA-AAAAA
*
25934487 TCAT-AAAAA
1 TTATAAAAAA
*
25934496 GTATAAAAAA
1 TTATAAAAAA
* * *
25934506 GTAT-TAAGA
1 TTATAAAAAA
* *
25934515 TTGACACAAAA
1 TT-ATAAAAAA
25934526 TTAT-AAAAA
1 TTATAAAAAA
25934535 TTATAAAAAA
1 TTATAAAAAA
25934545 AATCACAAAA
Statistics
Matches: 130, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
7 2 0.02
8 6 0.05
9 36 0.28
10 56 0.43
11 27 0.21
12 3 0.02
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:25934464 original size:23 final size:23
Alignment explanation
Indices: 25934438--25934491 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
25934428 AAAAAATTAT
* *
25934438 AAAACATATTTAAAATTTTATAA
1 AAAACATATTAAAAATTCTATAA
25934461 AAAA-ATTATTAAAAATTCTATAA
1 AAAACA-TATTAAAAATTCTATAA
*
25934484 AAATCATA
1 AAAACATA
25934492 AAAAGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAACATATTAAAAATTCTATAA
Found at i:25934486 original size:12 final size:11
Alignment explanation
Indices: 25934419--25934486 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
25934409 TAAAAATATG
25934419 AAAATTTATAA
1 AAAATTTATAA
25934430 AAAA-TTATAA
1 AAAATTTATAA
*
25934440 AACATATT-T-A
1 AAAAT-TTATAA
*
25934450 AAATTTTATAA
1 AAAATTTATAA
* *
25934461 AAAAATTATTA
1 AAAATTTATAA
25934472 AAAATTCTATAA
1 AAAATT-TATAA
25934484 AAA
1 AAA
25934487 TCATAAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 14 0.32
11 19 0.43
12 9 0.20
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:25934542 original size:8 final size:9
Alignment explanation
Indices: 25934409--25934543 Score: 65
Period size: 9 Copynumber: 13.7 Consensus size: 9
25934399 TGTTAAATAT
25934409 TAAAAA-TA
1 TAAAAATTA
*
25934417 TGAAAATTTA
1 T-AAAAATTA
25934427 TAAAAAATTA
1 T-AAAAATTA
*
25934437 TAAAACATATT
1 TAAAA-AT-TA
*
25934448 TAAAATTTTA
1 TAAAA-ATTA
25934458 TAAAAAAATTA
1 T--AAAAATTA
25934469 TTAAAAATTCTA
1 -TAAAAA-T-TA
*
25934481 TAAAAATCA
1 TAAAAATTA
*
25934490 TAAAAAGTA
1 TAAAAATTA
*
25934499 TAAAAAAGTA
1 T-AAAAATTA
* *
25934509 TTAAGATTGA
1 TAAAAATT-A
*
25934519 CACAAAATTA
1 TA-AAAATTA
25934529 TAAAAATTA
1 TAAAAATTA
25934538 TAAAAA
1 TAAAAA
25934544 AAATCACAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 34 0.35
10 33 0.34
11 22 0.23
12 7 0.07
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:25934882 original size:30 final size:30
Alignment explanation
Indices: 25934833--25934912 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
25934823 TTTTTAAAAA
25934833 ATTAAAAATACTTAAAATAAAAAAAAACAT
1 ATTAAAAATACTTAAAATAAAAAAAAACAT
* * *
25934863 ATTAGAAAT-CTTAAAAATAATAAAAAA-TT
1 ATTAAAAATACTT-AAAATAAAAAAAAACAT
* * *
25934892 GTAAAAAATACTAAAAATAAA
1 ATTAAAAATACTTAAAATAAA
25934913 TAAGAGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (30 bp):
ATTAAAAATACTTAAAATAAAAAAAAACAT
Found at i:25935092 original size:20 final size:21
Alignment explanation
Indices: 25935059--25935097 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
25935049 CTAATTAATT
*
25935059 AATTTTTTACATTTTTAAGGG
1 AATTTTTTACATTTATAAGGG
*
25935080 AATTTTTT-TATTTATAAG
1 AATTTTTTACATTTATAAG
25935098 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (21 bp):
AATTTTTTACATTTATAAGGG
Found at i:25939219 original size:27 final size:29
Alignment explanation
Indices: 25939181--25939248 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
25939171 AATAAACACC
*
25939181 AAAAATTTATTTTAAAAAT-AAAAAATAA
1 AAAAATATATTTTAAAAATAAAAAAATAA
**
25939209 AAAAA-ATATTTTAAATTTAAAAAAATAA
1 AAAAATATATTTTAAAAATAAAAAAATAA
25939237 AAAAATATATTT
1 AAAAATATATTT
25939249 ATTATATTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.29
28 19 0.54
29 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAAATATATTTTAAAAATAAAAAAATAA
Found at i:25942286 original size:9 final size:9
Alignment explanation
Indices: 25942272--25942338 Score: 93
Period size: 9 Copynumber: 7.4 Consensus size: 9
25942262 TTTGGTTAAA
25942272 AATTAACCG
1 AATTAACCG
25942281 AATTAACCG
1 AATTAACCG
25942290 AATT-ACCTG
1 AATTAACC-G
25942299 AATTAACCG
1 AATTAACCG
25942308 AATTAACCG
1 AATTAACCG
*
25942317 GATT-ACCTG
1 AATTAACC-G
25942326 AATTAACCG
1 AATTAACCG
25942335 AATT
1 AATT
25942339 GAATCACTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
8 6 0.12
9 40 0.77
10 6 0.12
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:25942305 original size:27 final size:27
Alignment explanation
Indices: 25942272--25942338 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
25942262 TTTGGTTAAA
25942272 AATTAACCGAATTAACCGAATTACCTG
1 AATTAACCGAATTAACCGAATTACCTG
*
25942299 AATTAACCGAATTAACCGGATTACCTG
1 AATTAACCGAATTAACCGAATTACCTG
25942326 AATTAACCGAATT
1 AATTAACCGAATT
25942339 GAATCACTAC
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:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTAACCGAATTACCTG
Found at i:25945384 original size:22 final size:21
Alignment explanation
Indices: 25945354--25945398 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
25945344 ACACCAAAAC
*
25945354 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
25945376 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
25945397 AG
1 AG
25945399 CGCCGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:25945601 original size:42 final size:43
Alignment explanation
Indices: 25945555--25945646 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
25945545 AGACTCAGAC
*
25945555 CTTTAGCAGCGCTTTAGTG-GAAGCGCCGCTAAAGATTAGGGT
1 CTTTAGCAGCGCTTTAGCGAGAAGCGCCGCTAAAGATTAGGGT
* * * *
25945597 CTTTAGCAGTGTTTTTGCGAGAAGCGTCGCTAAAGATTAGGGT
1 CTTTAGCAGCGCTTTAGCGAGAAGCGCCGCTAAAGATTAGGGT
25945640 CTTTAGC
1 CTTTAGC
25945647 GGCACTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 15 0.34
43 29 0.66
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
CTTTAGCAGCGCTTTAGCGAGAAGCGCCGCTAAAGATTAGGGT
Found at i:25945675 original size:43 final size:43
Alignment explanation
Indices: 25945639--25945975 Score: 388
Period size: 43 Copynumber: 7.8 Consensus size: 43
25945629 AAGATTAGGG
*
25945639 TCTTTAGCGGCACTTTTCCCACAAACGCCGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
*
25945682 T-TTGTAGCGGCGCTTTTCCCACAAATGCCGCAAAAGACCCTGA
1 TCTT-TAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
* * *
25945725 TCTGTAGCGGTGCTTTTCCCACAAACGCTGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
* * *
25945768 TCTGTAGCGGCGCTTTTCCCACAAATGCTGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
* *** * * * **
25945811 TCTGTAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCAAA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
** * * *
25945854 TCTTTAGCGGCGCTTCCCCCACAAACACCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
* * * *
25945897 TCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
** * *
25945940 TCTTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAG
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAG
25945976 GCCAACACCT
Statistics
Matches: 254, Mismatches: 38, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
42 2 0.01
43 251 0.99
44 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
Found at i:25945988 original size:43 final size:43
Alignment explanation
Indices: 25945876--25946017 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
25945866 CTTCCCCCAC
* ** * * *
25945876 AAACACCGCTAAAGACCATGATCTTTAGTGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAACACCTTTAGTGGCGCTTTTTACAA
*** * *
25945919 AAACGCCGCTAAAGACCCTTATCTTTAGCGGCGC-TTTTATCAA
1 AAACGCCGCTAAAGACCAACACCTTTAGTGGCGCTTTTTA-CAA
* * *
25945962 AAACGCCGCTAAAGGCCAACACCTTTAGTGGCGTTTTTTAAAA
1 AAACGCCGCTAAAGACCAACACCTTTAGTGGCGCTTTTTACAA
*
25946005 AAACGCCACTAAA
1 AAACGCCGCTAAA
25946018 TTTGGCAGAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 4 0.05
43 73 0.89
44 5 0.06
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAACACCTTTAGTGGCGCTTTTTACAA
Found at i:25946000 original size:86 final size:86
Alignment explanation
Indices: 25945829--25946017 Score: 216
Period size: 86 Copynumber: 2.2 Consensus size: 86
25945819 GGCGCTTCGA
* *
25945829 CCACAAACGCCACTAAAGAACCAAATCTTTAGCGGCGCTTCCCCCACAAACACCGCTAAAGACCA
1 CCACAAACGCCACTAAAGAACCAAATCTTTAGCGGCGCTTCCACCAAAAACACCGCTAAAGACCA
** *
25945894 TGATCTTTAGTGGCGCTTTTT
66 ACACCTTTAGTGGCGCTTTTT
* * ** ** * * *
25945915 CCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTTATCAAAAACGCCGCTAAAGGCCA
1 CCACAAACGCCACTAAAGAACCAAATCTTTAGCGGCGCTTCCACCAAAAACACCGCTAAAGACCA
*
25945980 ACACCTTTAGTGGCGTTTTTT
66 ACACCTTTAGTGGCGCTTTTT
** *
25946001 AAAAAAACGCCACTAAA
1 CCACAAACGCCACTAAA
25946018 TTTGGCAGAT
Statistics
Matches: 84, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (86 bp):
CCACAAACGCCACTAAAGAACCAAATCTTTAGCGGCGCTTCCACCAAAAACACCGCTAAAGACCA
ACACCTTTAGTGGCGCTTTTT
Found at i:25946017 original size:129 final size:129
Alignment explanation
Indices: 25945643--25946017 Score: 288
Period size: 129 Copynumber: 2.9 Consensus size: 129
25945633 TTAGGGTCTT
* * *** * *
25945643 TAGCGGCACTTTTCCCACAAACGCCGCAAAAGACCCTGATTTGTAGCGGCGCTTTTCCCACAAAT
1 TAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTGTAGCGGCGCTTCGACCAAAAAC
* * * ** * * * * * ** * *
25945708 GCCGCAAAAGACCCTGATCTGTAGCGGTGCTTTTCCC--ACAAACGCTGCAAAAGACCCTGATCT
66 GCCACTAAAGAACCAAACCTTTAGCGGCGC--TTCCCAAAAAAACACCACTAAAGACCATGATCT
25945771 G
129 G
* * *
25945772 TAGCGGCGCTTTTCCCACAAATGCTGCAAAAGACCCTGATCTGTAGCGGCGCTTCGACCACAAAC
1 TAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTGTAGCGGCGCTTCGACCAAAAAC
* ** * * *
25945837 GCCACTAAAGAACCAAATCTTTAGCGGCGCTTCCCCCACAAACACCGCTAAAGACCATGATCTT
66 GCCACTAAAGAACCAAACCTTTAGCGGCGCTTCCCAAAAAAACACCACTAAAGACCATGATCTG
* * * * * ** *
25945901 TAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTTATCAAAAAC
1 TAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTGTAGCGGCGCTTCGACCAAAAAC
* * * * *** *
25945966 GCCGCTAAAG-GCCAACACCTTTAGTGGCGTTTTTTAAAAAAACGCCACTAAA
66 GCCACTAAAGAACCAA-ACCTTTAGCGGCGCTTCCCAAAAAAACACCACTAAA
25946018 TTTGGCAGAT
Statistics
Matches: 199, Mismatches: 44, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
127 5 0.03
128 4 0.02
129 190 0.95
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (129 bp):
TAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGATCTGTAGCGGCGCTTCGACCAAAAAC
GCCACTAAAGAACCAAACCTTTAGCGGCGCTTCCCAAAAAAACACCACTAAAGACCATGATCTG
Found at i:25946375 original size:21 final size:21
Alignment explanation
Indices: 25946326--25946376 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
25946316 TTGACGCTGC
* *
25946326 TCTGCTTCCCTCGCTGCAGCT
1 TCTGCTTCCATCGCTACAGCT
* * *
25946347 TTTACTTCCATCGCTATAGCT
1 TCTGCTTCCATCGCTACAGCT
25946368 TCTGCTTCC
1 TCTGCTTCC
25946377 CTTGCTGCAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.37, G:0.14, T:0.39
Consensus pattern (21 bp):
TCTGCTTCCATCGCTACAGCT
Found at i:25946429 original size:21 final size:21
Alignment explanation
Indices: 25946368--25946437 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
25946358 CGCTATAGCT
* *
25946368 TCTGCTTCCCTTGCTGCAGCC
1 TCTGCTTCTCTTGCTGCCGCC
* * * *
25946389 TGTACTTCTCTCGTTGCCGCC
1 TCTGCTTCTCTTGCTGCCGCC
* *
25946410 TCTGCTTCTCTTGCTACCGCA
1 TCTGCTTCTCTTGCTGCCGCC
25946431 TCTGCTT
1 TCTGCTT
25946438 TAAGCTGCTG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.06, C:0.39, G:0.17, T:0.39
Consensus pattern (21 bp):
TCTGCTTCTCTTGCTGCCGCC
Found at i:25946498 original size:66 final size:66
Alignment explanation
Indices: 25946408--25946573 Score: 210
Period size: 66 Copynumber: 2.5 Consensus size: 66
25946398 CTCGTTGCCG
* * * *
25946408 CCTCTGCTTCTCTTGCTACCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
25946471 GAA
64 GAA
* *
25946474 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
25946539 A
66 A
* * * *
25946540 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
25946574 TTGTGTAATT
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 1 0.01
66 83 0.94
67 4 0.05
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:25952093 original size:15 final size:16
Alignment explanation
Indices: 25952063--25952425 Score: 162
Period size: 16 Copynumber: 22.6 Consensus size: 16
25952053 AATTGCACGG
25952063 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
25952079 GTAAGTTAT-TATTAT
1 GTAAGTTATGTATTAT
*
25952094 GTAAGTTATGTAAGTAAT
1 GTAAGTTATGT-A-TTAT
25952112 GT-A-TTATGTATGTTAT
1 GTAAGTTATGTA--TTAT
**
25952128 GTATA-ACATGTA--AT
1 GTA-AGTTATGTATTAT
*
25952142 -TAAGTTATGTAAGTTGT
1 GTAAGTTATGT-A-TTAT
*
25952159 GT-A-TAATGTTAGTTAT
1 GTAAGTTATG-TA-TTAT
**
25952175 CAAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
25952191 GTAAGTTATTTAAGTTAT
1 GTAAGTTATGT-A-TTAT
*
25952209 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
*
25952225 GTAAGTTATGTAAGTTGT
1 GTAAGTTATGT-A-TTAT
25952243 GT-A-TTATGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
* *
25952259 GTAGGAGGCTATGTATGTTAA
1 GTA--A-GTTATGTA--TTAT
*
25952280 GTAAGTCATGTATTAT
1 GTAAGTTATGTATTAT
*
25952296 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
*
25952312 GTAAG---T-TATCA-
1 GTAAGTTATGTATTAT
25952323 --AAGTTATGTATTAT
1 GTAAGTTATGTATTAT
* *
25952337 GTAAGTTATTTAAGTCAT
1 GTAAGTTATGT-A-TTAT
*
25952355 GTAAGTTGTGTATTAT
1 GTAAGTTATGTATTAT
25952371 GTAAGTTATGTAGTCTAT
1 GTAAGTTATGTA-T-TAT
25952389 GT-A-TTATGTA--A-
1 GTAAGTTATGTATTAT
*
25952400 GTTA-TTATGTTATTAT
1 GTAAGTTATG-TATTAT
25952416 GTAAGTTATG
1 GTAAGTTATG
25952426 CAAGTTTATA
Statistics
Matches: 269, Mismatches: 36, Indels: 83
0.69 0.09 0.21
Matches are distributed among these distances:
9 3 0.01
11 2 0.01
12 13 0.05
13 13 0.05
14 3 0.01
15 17 0.06
16 125 0.46
17 21 0.08
18 57 0.21
19 2 0.01
20 1 0.00
21 12 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:25952102 original size:9 final size:9
Alignment explanation
Indices: 25952063--25952431 Score: 227
Period size: 9 Copynumber: 42.8 Consensus size: 9
25952053 AATTGCACGG
25952063 GTAAGTTAT
1 GTAAGTTAT
25952072 GT-A-TTAT
1 GTAAGTTAT
25952079 GTAAGTTAT
1 GTAAGTTAT
25952088 -T-A-TTAT
1 GTAAGTTAT
25952094 GTAAGTTAT
1 GTAAGTTAT
*
25952103 GTAAGTAAT
1 GTAAGTTAT
25952112 GT-A-TTAT
1 GTAAGTTAT
*
25952119 GTATGTTAT
1 GTAAGTTAT
*
25952128 GTATAACATGTAAT
1 G--T-A-A-GTTAT
25952142 -TAAGTTAT
1 GTAAGTTAT
*
25952150 GTAAGTTGT
1 GTAAGTTAT
*
25952159 GT-A-TAAT
1 GTAAGTTAT
*
25952166 GTTAGTTAT
1 GTAAGTTAT
**
25952175 CAAAGTTAT
1 GTAAGTTAT
25952184 GT-A-TTAT
1 GTAAGTTAT
25952191 GTAAGTTAT
1 GTAAGTTAT
*
25952200 TTAAGTTAT
1 GTAAGTTAT
*
25952209 GTAAGTTGT
1 GTAAGTTAT
25952218 GT-A-TTAT
1 GTAAGTTAT
25952225 GTAAGTTAT
1 GTAAGTTAT
*
25952234 GTAAGTTGT
1 GTAAGTTAT
25952243 GT-A-TTAT
1 GTAAGTTAT
25952250 GTAAGTTAT
1 GTAAGTTAT
*
25952259 GTAGGAGGCTAT
1 GTA--A-GTTAT
* *
25952271 GTATGTTAA
1 GTAAGTTAT
*
25952280 GTAAGTCAT
1 GTAAGTTAT
25952289 GT-A-TTAT
1 GTAAGTTAT
*
25952296 GTAAGTTGT
1 GTAAGTTAT
25952305 GT-A-TTAT
1 GTAAGTTAT
25952312 GTAAGTTAT
1 GTAAGTTAT
**
25952321 CAAAGTTAT
1 GTAAGTTAT
25952330 GT-A-TTAT
1 GTAAGTTAT
25952337 GTAAGTTAT
1 GTAAGTTAT
* *
25952346 TTAAGTCAT
1 GTAAGTTAT
*
25952355 GTAAGTTGT
1 GTAAGTTAT
25952364 GT-A-TTAT
1 GTAAGTTAT
25952371 GTAAGTTAT
1 GTAAGTTAT
25952380 GT-AGTCTAT
1 GTAAGT-TAT
25952389 GT-A-TTAT
1 GTAAGTTAT
25952396 GTAAGTTAT
1 GTAAGTTAT
*
25952405 -TATGTTATTAT
1 GTAAG---TTAT
25952416 GTAAGTTAT
1 GTAAGTTAT
*
25952425 GCAAGTT
1 GTAAGTT
25952432 TATATATAAG
Statistics
Matches: 277, Mismatches: 44, Indels: 78
0.69 0.11 0.20
Matches are distributed among these distances:
6 4 0.01
7 59 0.21
8 33 0.12
9 158 0.57
10 1 0.00
11 7 0.03
12 11 0.04
14 4 0.01
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:25952212 original size:59 final size:59
Alignment explanation
Indices: 25952141--25952258 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
25952131 TAACATGTAA
*
25952141 TTAAGTTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTAT
1 TTAAGTTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAGTTAT
* ** *
25952200 TTAAGTTATGTAAGTTGTGTATTATGTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 TTAAGTTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAGTTAT
25952259 GTAGGAGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (59 bp):
TTAAGTTATGTAAGTTGTGTATAATGTAAGTTATCAAAGTTATGTATTATGTAAGTTAT
Found at i:25952239 original size:34 final size:34
Alignment explanation
Indices: 25952063--25952412 Score: 205
Period size: 34 Copynumber: 10.3 Consensus size: 34
25952053 AATTGCACGG
25952063 GTAAGTTATGT-A-TTATGTAAGTTAT-T-A-TTAT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
* *
25952094 GTAAGTTATGTAAGTAATGTATTATGTATGTTAT
1 GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* * *
25952128 GTATAACATGTAAT-TAAGTTATGTAAGTTGTGT-A-TAAT
1 G--T-A-A-GTTATGTAAGTTATGT-A-TTATGTAAGTTAT
* **
25952166 GTTAGTTATCAAAGTTATGTATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* *
25952200 TTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* *
25952234 GTAAGTTGTGT-A-TTATGTAAGTTATGTAGGAGGCTAT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTA--A-GTTAT
* * * *
25952271 GTATGTTAAGTAAGTCATGTATTATGTAAGTTGT
1 GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
**
25952305 GT-A-TTATGTAAGTTATCAAAGTTATGT-A-TTAT
1 GTAAGTTATGTAAGTTAT-GTA-TTATGTAAGTTAT
* * *
25952337 GTAAGTTATTTAAGTCATGTAAGTTGTGT-A-TTAT
1 GTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
25952371 GTAAGTTATGT-AGTCTATGTATTATGTAAGTTAT
1 GTAAGTTATGTAAGT-TATGTATTATGTAAGTTAT
*
25952405 -TATGTTAT
1 GTAAGTTAT
25952413 TATGTAAGTT
Statistics
Matches: 247, Mismatches: 42, Indels: 58
0.71 0.12 0.17
Matches are distributed among these distances:
31 15 0.06
32 34 0.14
33 28 0.11
34 115 0.47
35 1 0.00
36 3 0.01
37 20 0.08
38 16 0.06
39 10 0.04
40 5 0.02
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (34 bp):
GTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
Found at i:25952320 original size:25 final size:24
Alignment explanation
Indices: 25952066--25952425 Score: 214
Period size: 25 Copynumber: 15.0 Consensus size: 24
25952056 TGCACGGGTA
25952066 AGTTATGTATTATGTAAGTTAT-T
1 AGTTATGTATTATGTAAGTTATGT
*
25952089 A-TTATGTAAGTTATGTAAGTAATGT
1 AGTTATGT-A-TTATGTAAGTTATGT
**
25952114 A-TTATGTATGTTATGTATA-ACATGT
1 AGTTATGTA--TTATGTA-AGTTATGT
* * *
25952139 AATTAAG--TTATGTAAGTTGTGT
1 AGTTATGTATTATGTAAGTTATGT
* **
25952161 A-TAATGTTAGTTATCAAAGTTATGT
1 AGTTATG-TA-TTATGTAAGTTATGT
*
25952186 A-TTATGTAAGTTATTTAAGTTATGT
1 AGTTATGT-A-TTATGTAAGTTATGT
*
25952211 AAGTTGTGTATTATGTAAGTTATGT
1 -AGTTATGTATTATGTAAGTTATGT
*
25952236 AAGTTGTGTATTATGTAAGTTATGT
1 -AGTTATGTATTATGTAAGTTATGT
* ** * *
25952261 AG-GA-G-GCTATGTATGTTAAGT
1 AGTTATGTATTATGTAAGTTATGT
* *
25952282 AAGTCATGTATTATGTAAGTTGTGT
1 -AGTTATGTATTATGTAAGTTATGT
**
25952307 A-TTATGTAAGTTATCAAAGTTATGT
1 AGTTATGT-A-TTATGTAAGTTATGT
* *
25952332 A-TTATGTAAGTTATTTAAGTCATGT
1 AGTTATGT-A-TTATGTAAGTTATGT
*
25952357 AAGTTGTGTATTATGTAAGTTATGT
1 -AGTTATGTATTATGTAAGTTATGT
25952382 AGTCTATGTATTATGTAAGTTAT-T
1 AGT-TATGTATTATGTAAGTTATGT
*
25952406 A--TGT-TATTATGTAAGTTATG
1 AGTTATGTATTATGTAAGTTATG
25952426 CAAGTTTATA
Statistics
Matches: 272, Mismatches: 41, Indels: 50
0.75 0.11 0.14
Matches are distributed among these distances:
20 15 0.06
21 18 0.07
22 20 0.07
23 8 0.03
24 24 0.09
25 168 0.62
26 9 0.03
27 10 0.04
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (24 bp):
AGTTATGTATTATGTAAGTTATGT
Found at i:25952415 original size:20 final size:19
Alignment explanation
Indices: 25952326--25952424 Score: 71
Period size: 20 Copynumber: 5.1 Consensus size: 19
25952316 GTTATCAAAG
25952326 TTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
* * *
25952345 TTTAAGTCATGTAAGT-TGTGTA
1 -TTATGT-AT-TATGTAAGT-TA
25952367 TTATGTAAGTTATGT-AG-T-
1 TTATGT-A-TTATGTAAGTTA
*
25952385 CTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
25952404 TTATGTTATTATGTAAGTTA
1 TTATG-TATTATGTAAGTTA
25952424 T
1 T
25952425 GCAAGTTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
16 6 0.10
17 3 0.05
18 6 0.10
19 5 0.08
20 20 0.32
21 15 0.24
22 7 0.11
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTATTATGTAAGTTA
Found at i:25952620 original size:121 final size:121
Alignment explanation
Indices: 25952478--25952888 Score: 675
Period size: 121 Copynumber: 3.4 Consensus size: 121
25952468 TATGTATCTT
* * * * *
25952478 ATTTATAATTATTTTTAAAATTATAAAATTCATT-TCTAATAAAATTGAAATGTAGGATATATAT
1 ATTTACAATTATTTTTAAAATTATAAAATTTATTGAC-AATAAAATTGAAATATAGGTTATATAT
* *
25952542 CCATATCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAAT
65 CCATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAAC
25952599 ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATATC
1 ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATATC
* *
25952664 CATACCATATATGGGGTGATATATTAAAAATATATGTTTTAATATTTAAAAATAAC
66 CATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAAC
25952720 ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATATC
1 ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATATC
*
25952785 CATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAATTAAC
66 CATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAAC
** *
25952841 ATTTAC-ATTATTTTTAAAATTATAAAAAATATTTAC-ATAAAATTGAAA
1 ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAA
25952889 ATNNNNNNNN
Statistics
Matches: 274, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
119 12 0.04
120 27 0.10
121 234 0.85
122 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (121 bp):
ATTTACAATTATTTTTAAAATTATAAAATTTATTGACAATAAAATTGAAATATAGGTTATATATC
CATACCATATATGGGGTAATATATTAAAAATATAGGTTTTAATATTTAAAAATAAC
Found at i:25955394 original size:2 final size:2
Alignment explanation
Indices: 25955387--25955412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25955377 AAGTAATTAC
25955387 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
25955413 AAATATCGAA
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:25955983 original size:7 final size:7
Alignment explanation
Indices: 25955971--25956094 Score: 65
Period size: 7 Copynumber: 17.0 Consensus size: 7
25955961 CTTAATTGAC
25955971 ACCCTAA
1 ACCCTAA
25955978 ACCCTAA
1 ACCCTAA
25955985 ATCCCT-A
1 A-CCCTAA
*
25955992 ACCCTTA
1 ACCCTAA
25955999 ACCCTTAA
1 ACCC-TAA
*
25956007 ATCTCCTAG
1 A-C-CCTAA
*
25956016 CCCCTAA
1 ACCCTAA
*
25956023 ATTCCTAA
1 A-CCCTAA
*
25956031 CCCCT-A
1 ACCCTAA
25956037 ACTCCTAA
1 AC-CCTAA
*
25956045 CCCCTAA
1 ACCCTAA
25956052 ATCCCTAA
1 A-CCCTAA
*
25956060 CCCCTAA
1 ACCCTAA
*
25956067 CCCCTAA
1 ACCCTAA
*
25956074 ACCTTATA
1 ACCCTA-A
*
25956082 TCCC-AA
1 ACCCTAA
25956088 ACCCTAA
1 ACCCTAA
25956095 TAATCATATA
Statistics
Matches: 89, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
6 10 0.11
7 50 0.56
8 24 0.27
9 3 0.03
10 2 0.02
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.23
Consensus pattern (7 bp):
ACCCTAA
Found at i:25955992 original size:15 final size:15
Alignment explanation
Indices: 25955971--25956094 Score: 80
Period size: 14 Copynumber: 8.5 Consensus size: 15
25955961 CTTAATTGAC
25955971 ACCCTAAA-CCCTAA
1 ACCCTAAATCCCTAA
*
25955985 ATCCCT-AA-CCCTTA
1 A-CCCTAAATCCCTAA
*
25955999 ACCCTTAAATCTCCTAG
1 ACCC-TAAATC-CCTAA
* *
25956016 CCCCTAAATTCCTAA
1 ACCCTAAATCCCTAA
* *
25956031 CCCCTAACT-CCTAA
1 ACCCTAAATCCCTAA
*
25956045 CCCCTAAATCCCTAA
1 ACCCTAAATCCCTAA
* *
25956060 CCCCT-AACCCCTAA
1 ACCCTAAATCCCTAA
* *
25956074 ACCTTATATCCC-AA
1 ACCCTAAATCCCTAA
25956088 ACCCTAA
1 ACCCTAA
25956095 TAATCATATA
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
13 3 0.03
14 41 0.47
15 32 0.36
16 6 0.07
17 6 0.07
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.23
Consensus pattern (15 bp):
ACCCTAAATCCCTAA
Found at i:25956043 original size:29 final size:29
Alignment explanation
Indices: 25956009--25956091 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 29
25955999 ACCCTTAAAT
* *
25956009 CTCCTAGCCCCTAAATTCCTAACCCCTAA
1 CTCCTAACCCCTAAATCCCTAACCCCTAA
25956038 CTCCTAACCCCTAAATCCCTAACCCCTAA
1 CTCCTAACCCCTAAATCCCTAACCCCTAA
* * * * *
25956067 CCCCTAAACCTTATATCCCAAACCC
1 CTCCTAACCCCTAAATCCCTAACCC
25956092 TAATAATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.30, C:0.47, G:0.01, T:0.22
Consensus pattern (29 bp):
CTCCTAACCCCTAAATCCCTAACCCCTAA
Found at i:25956057 original size:22 final size:22
Alignment explanation
Indices: 25955972--25956074 Score: 109
Period size: 22 Copynumber: 4.6 Consensus size: 22
25955962 TTAATTGACA
*
25955972 CCCTAAACCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
* * *
25955994 CCTTAACCCTTAAATCTCCTAGC
1 CCCTAACCCCTAAATC-CCTAAC
** *
25956017 CCCTAAATTCCT-AACCCCTAAC
1 CCCT-AACCCCTAAATCCCTAAC
*
25956039 TCCTAACCCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
25956061 CCCTAACCCCTAAA
1 CCCTAACCCCTAAA
25956075 CCTTATATCC
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 5 0.08
22 43 0.68
23 11 0.17
24 4 0.06
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (22 bp):
CCCTAACCCCTAAATCCCTAAC
Found at i:25956090 original size:22 final size:22
Alignment explanation
Indices: 25955971--25956091 Score: 77
Period size: 22 Copynumber: 5.5 Consensus size: 22
25955961 CTTAATTGAC
*
25955971 ACCCTAAA-CCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
** *
25955992 ACCCTTAACCCTTAAATCTCCTA
1 ACCCCAAACCCCTAAATC-CCTA
* ** *
25956015 GCCCCTAAATTCCT-AACCCCTA
1 ACCCC-AAACCCCTAAATCCCTA
* *
25956037 ACTCCTAACCCCTAAATCCCTA
1 ACCCCAAACCCCTAAATCCCTA
* *
25956059 ACCCCTAACCCCTAAA-CCTTA
1 ACCCCAAACCCCTAAATCCCTA
*
25956080 TATCCCAAACCC
1 -ACCCCAAACCC
25956092 TAATAATCAT
Statistics
Matches: 76, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
21 16 0.21
22 46 0.61
23 10 0.13
24 4 0.05
ACGTcount: A:0.32, C:0.45, G:0.01, T:0.22
Consensus pattern (22 bp):
ACCCCAAACCCCTAAATCCCTA
Done.