Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 102 of 770
Found at i:29525902 original size:19 final size:20
Alignment explanation
Indices: 29525870--29525910 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
29525860 TGAATAAATC
29525870 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
29525890 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
29525909 GA
1 GA
29525911 AAATGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:29529544 original size:10 final size:10
Alignment explanation
Indices: 29529529--29529555 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29529519 TTCGTAAGTA
29529529 AAAAAAATTC
1 AAAAAAATTC
29529539 AAAAAAATTC
1 AAAAAAATTC
29529549 AAAAAAA
1 AAAAAAA
29529556 AGTGTGTTAA
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:29530516 original size:15 final size:15
Alignment explanation
Indices: 29530478--29530525 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
29530468 AACATCATGT
29530478 AAAAGAAAAG-AAGA
1 AAAAGAAAAGAAAGA
* *
29530492 AAAGGCAAAAGAAATA
1 AAAAG-AAAAGAAAGA
*
29530508 AAAAGAAAAGAGAGA
1 AAAAGAAAAGAAAGA
29530523 AAA
1 AAA
29530526 TGAGAGGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 4 0.15
15 16 0.59
16 7 0.26
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAGAAAGA
Found at i:29530564 original size:12 final size:13
Alignment explanation
Indices: 29530549--29530578 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
29530539 AAAGAGCTCG
29530549 AAAAAGCCTTT-A
1 AAAAAGCCTTTGA
29530561 AAAAAGCCTTTGA
1 AAAAAGCCTTTGA
29530574 AAAAA
1 AAAAA
29530579 AAAGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (13 bp):
AAAAAGCCTTTGA
Found at i:29530588 original size:6 final size:6
Alignment explanation
Indices: 29530573--29530604 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
29530563 AAAGCCTTTG
29530573 AAAA-A AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
29530605 TGAGATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:29530622 original size:30 final size:30
Alignment explanation
Indices: 29530588--29530653 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
29530578 AAAAGAAAAA
* *
29530588 GAAAAAGAAAAAGAAAATGAGATTGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATTGAGAGT
** *
29530618 GAAAAAGAAATTGAAAAAGAGTTTGAGAGT
1 GAAAAAGAAAAAGAAAAAGAGATTGAGAGT
29530648 GAAAAA
1 GAAAAA
29530654 AGAGTGGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAAAAGAGATTGAGAGT
Found at i:29530643 original size:12 final size:12
Alignment explanation
Indices: 29530570--29530637 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
29530560 AAAAAAGCCT
29530570 TTGAAAAA-AAA
1 TTGAAAAAGAAA
*
29530581 -AGAAAAAGAAA
1 TTGAAAAAGAAA
**
29530592 AAGAAAAAGAAA
1 TTGAAAAAGAAA
* * ** *
29530604 ATGAGATTGAGA
1 TTGAAAAAGAAA
29530616 TTGAAAAAGAAA
1 TTGAAAAAGAAA
29530628 TTGAAAAAGA
1 TTGAAAAAGA
29530638 GTTTGAGAGT
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
10 6 0.14
11 3 0.07
12 35 0.80
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (12 bp):
TTGAAAAAGAAA
Found at i:29530674 original size:30 final size:30
Alignment explanation
Indices: 29530630--29530692 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
29530620 AAAAGAAATT
** * *
29530630 GAAAAAGAGTTTGAGAGTGAAA-AAAGAGTG
1 GAAAAAGAAATTGAGA-TAAAAGAAAGAGCG
29530660 GAAAAAGAAATTGAGATAAAAGAAAGAGCG
1 GAAAAAGAAATTGAGATAAAAGAAAGAGCG
29530690 GAA
1 GAA
29530693 GAAGTGAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.56, C:0.02, G:0.30, T:0.13
Consensus pattern (30 bp):
GAAAAAGAAATTGAGATAAAAGAAAGAGCG
Found at i:29532082 original size:3 final size:3
Alignment explanation
Indices: 29532011--29532073 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
29532001 AAATCGAAAC
29532011 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29532059 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
29532074 GCAATAATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29532630 original size:22 final size:22
Alignment explanation
Indices: 29532580--29532624 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29532570 ATAAGTTAAT
* * *
29532580 AATAAATTAAATTAAATTAAAA
1 AATAAAATAAAATAAAATAAAA
29532602 AATAAAATAAAATAAAATAAAA
1 AATAAAATAAAATAAAATAAAA
29532624 A
1 A
29532625 CAAAAAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
AATAAAATAAAATAAAATAAAA
Found at i:29533476 original size:268 final size:264
Alignment explanation
Indices: 29532991--29533576 Score: 737
Period size: 268 Copynumber: 2.2 Consensus size: 264
29532981 TTTCGTTTCA
* * ** *
29532991 ATCTGCTCCACTCCTGCTTAGGGAGATATGATCTGTAA-TTTCAAGCCTGCTCCACTGCTGCTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC-AGCCTTTTCCACTACTGCTCA
* *
29533055 GGGAGATAACGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATTTGTAATTT
65 GGGAGATAACGCTCACCGTCTTCAACCTGCTCCACTACTGCTTAGAGAGATAAGATTTGTAATTT
*
29533120 TCAGCCTGCTCCACTACTACTTAGGGAGATAAGGCTTACCATCTGCGATCTGCTCCACTACTACT
130 TCAGCCTGCTCCACTACTACTTAGGGAGATAAGGCTCACCATCTGCGATCTGCTCCACTACTACT
*
29533185 TAGGGAGATAAGATCTATAATTTTCAGCCTATTTCCCTACTACCTAGGGGGATAAGGCTCACCAT
195 TAGGGAGATAAGATCTATAATTTTCAACCTATTTCCCTACTACCTAGGGGGATAAGGCTCACCAT
29533250 CTTCG
260 CTTCG
* * *
29533255 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCC-TTACTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCT-TTTCCACTACTGCTCA
* * * * * * * * *
29533319 GGGGGATAAGGCTCATCGTCTTCAACCTTCTCCATTACTGCTTAGGGAGATAGGGTGTGTTTGTC
65 GGGAGATAACGCTCACCGTCTTCAACCTGCTCCACTACTGCTTAGAGAGATA---AG-ATTTGTA
* * * * * * *
29533384 ATTTTTAGCCTGTTTCC-CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTA
126 ATTTTCAGCCTG-CTCCACTACTACTTAGGGAGATAAGGCTCACCATCTGCGATCTGCTCCACTA
* * * * *
29533448 CTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTATTTCCCTACTGCTTAGGGGGATAAGGCTC
190 CTACTTAGGGAGATAAGATCTATAATTTTCAACCTATTTCCCTACTACCTAGGGGGATAAGGCTC
**
29533513 ACTGTCTTCG
255 ACCATCTTCG
* * *
29533523 ATCTGCTCCATTACTGCTTAGGGAGATAAGATCTATAATCTTCAGCCTGTTTCC
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCT-TTTCC
29533577 CGTCTTTGAT
Statistics
Matches: 275, Mismatches: 40, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
264 91 0.33
265 7 0.03
267 1 0.00
268 173 0.63
269 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (264 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTTTTCCACTACTGCTCAG
GGAGATAACGCTCACCGTCTTCAACCTGCTCCACTACTGCTTAGAGAGATAAGATTTGTAATTTT
CAGCCTGCTCCACTACTACTTAGGGAGATAAGGCTCACCATCTGCGATCTGCTCCACTACTACTT
AGGGAGATAAGATCTATAATTTTCAACCTATTTCCCTACTACCTAGGGGGATAAGGCTCACCATC
TTCG
Found at i:29533565 original size:44 final size:44
Alignment explanation
Indices: 29532993--29533565 Score: 224
Period size: 44 Copynumber: 12.9 Consensus size: 44
29532983 TCGTTTCAAT
* * * *
29532993 CTGCTCCACTCCTGCTTAGGGAGATATGATCTGTAAT-TTCAAGC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGA-C
* * * *** *
29533037 CTGCTCCACTGCTGCTCAGGGAGATAACGCTC-ACCGTCTTCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAA-GATCTATAATCTTCGAC
* * * *
29533081 CTGCTCCACTACTGCTTAGAGAGATAAGATTTGTAATTTTC-AGC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGA-C
* * * *
29533125 CTGCTCCACTACTACTTAGGGAGATAAG-GCT-TACCATCTGCGAT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATA--ATCTTCGAC
* *
29533169 CTGCTCCACTACTACTTAGGGAGATAAGATCTATAATTTTC-AGC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGA-C
** * * * * ** *
29533213 CTATTTCC-CTACTACCTAGGGGGATAAG-GCTCACCATCTTCGAT
1 CT-GCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCGAC
* * *
29533257 CTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTC-AGC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGA-C
** * * * ** *
29533301 CTATTTCC-TTACTGCTTAGGGGGATAAG-GCTCATCGTCTTCAAC
1 CT-GCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCGAC
* * * * * * ** **
29533345 CTTCTCCATTACTGCTTAGGGAGATAGGGTGTGTTTGTCATTTTTAGC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATC--TTCGA-C
* * * * *** *
29533393 CTGTTTCC-CTACTGCTTAGGGGGTTAAG-GCTCACCGTCTTCGAT
1 CTG-CTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCGAC
* * * *
29533437 CTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAAC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGAC
** * * * *
29533481 CTATTTCC-CTACTGCTTAGGGGGATAAG-GCTCACT-GTCTTCGAT
1 CT-GCTCCACTACTGCTTAGGGAGATAAGATCT-A-TAATCTTCGAC
*
29533525 CTGCTCCATTACTGCTTAGGGAGATAAGATCTATAATCTTC
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTC
29533566 AGCCTGTTTC
Statistics
Matches: 382, Mismatches: 114, Indels: 66
0.68 0.20 0.12
Matches are distributed among these distances:
42 2 0.01
43 25 0.07
44 289 0.76
45 35 0.09
46 2 0.01
47 7 0.02
48 19 0.05
49 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (44 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCGAC
Found at i:29533576 original size:88 final size:88
Alignment explanation
Indices: 29532991--29533577 Score: 712
Period size: 88 Copynumber: 6.6 Consensus size: 88
29532981 TTTCGTTTCA
* * * * *
29532991 ATCTGCTCCACTCCTGCTTAGGGAGATATGATCTGTAA-TTTCAAGCCTG-CTCCACTGCTGCTC
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTC-AGCCTGTTTCC-CTACTGCTT
* *
29533054 AGGGAGATAACGCTCACCGTCTTCG
64 AGGGGGATAAGGCTCACCGTCTTCG
* * * *
29533079 ATCTGCTCCACTACTGCTTAGAGAGATAAGATTTGTAATTTTCAGCCTG-CTCCACTACTACTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCC-CTACTGCTTA
* * * *
29533143 GGGAGATAAGGCTTACCATCTGCG
65 GGGGGATAAGGCTCACCGTCTTCG
* * * * *
29533167 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAATTTTCAGCCTATTTCCCTACTACCTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
*
29533232 GGGGATAAGGCTCACCATCTTCG
66 GGGGATAAGGCTCACCGTCTTCG
* * *
29533255 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATTTTCAGCCTATTTCCTTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
* *
29533320 GGGGATAAGGCTCATCGTCTTCA
66 GGGGATAAGGCTCACCGTCTTCG
* * * * * * * *
29533343 ACCTTCTCCATTACTGCTTAGGGAGATAGGGTGTGTTTGTCATTTTTAGCCTGTTTCCCTACTGC
1 ATCTGCTCCACTACTGCTTAGGGAGATA---AG-ATCTGTAATTTTCAGCCTGTTTCCCTACTGC
*
29533408 TTAGGGGGTTAAGGCTCACCGTCTTCG
62 TTAGGGGGATAAGGCTCACCGTCTTCG
* * *
29533435 ATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTATTTCCCTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
*
29533500 GGGGATAAGGCTCACTGTCTTCG
66 GGGGATAAGGCTCACCGTCTTCG
* * *
29533523 ATCTGCTCCATTACTGCTTAGGGAGATAAGATCTATAATCTTCAGCCTGTTTCCC
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCC
29533578 GTCTTTGATC
Statistics
Matches: 434, Mismatches: 59, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
88 351 0.81
89 8 0.02
91 1 0.00
92 74 0.17
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (88 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAGCCTGTTTCCCTACTGCTTAG
GGGGATAAGGCTCACCGTCTTCG
Found at i:29533698 original size:150 final size:150
Alignment explanation
Indices: 29533426--29533727 Score: 426
Period size: 150 Copynumber: 2.0 Consensus size: 150
29533416 TTAAGGCTCA
* * *
29533426 CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTATTTCCCT
1 CCGTCTTCGATCGGCTCCACTACTGCTTAGGGACATAAGATTTGTAATCTTCAACCTATTTCCCT
* ** * *
29533491 ACTGCTTAGGGGGATAAGGCTCACTGTCTTCGATCTGCTCCATTACTGCTTAGGGAGATAAGATC
66 ACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAAGGAGATAAGATC
29533556 TATAATCTTC-AGCCTGTTTC
131 TATAAT-TTCTAGCCTGTTTC
* * * * *
29533576 CCGTCTTTGATCGGGTCTACTACTGCTTAGGGACATAAGATTTGTAATCTTCAGCCTGTTTCCCT
1 CCGTCTTCGATCGGCTCCACTACTGCTTAGGGACATAAGATTTGTAATCTTCAACCTATTTCCCT
* * * *
29533641 ACTTCTTAGGGGGTTAAGGCTTACCGTCTTTGATCCACTCCACTACTGCTTAAGGAGATAAGATC
66 ACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAAGGAGATAAGATC
*
29533706 TGTAATTTCTAGCCTGTTTC
131 TATAATTTCTAGCCTGTTTC
29533726 CC
1 CC
29533728 TACTGCTTAG
Statistics
Matches: 133, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
149 3 0.02
150 130 0.98
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (150 bp):
CCGTCTTCGATCGGCTCCACTACTGCTTAGGGACATAAGATTTGTAATCTTCAACCTATTTCCCT
ACTGCTTAGGGGGATAAGGCTCACCGTCTTCGATCCACTCCACTACTGCTTAAGGAGATAAGATC
TATAATTTCTAGCCTGTTTC
Found at i:29533725 original size:88 final size:87
Alignment explanation
Indices: 29533576--29534358 Score: 931
Period size: 88 Copynumber: 9.0 Consensus size: 87
29533566 AGCCTGTTTC
* * * * *
29533576 CCGTCTTTGATCGGGTCTACTACTGCTTAGGGACATAAGATTTGTAATCTTCAGCCTGTTTCCCT
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTGTTTCCCT
* *
29533641 ACTTCTTAGGGGGTTAAGGCTTA
65 ACTGCTTAGGGGGTTAAGGCTCA
** *
29533664 CCGTCTTTGATCCACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTTTCCCT
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTC-AGCCTGTTTCCCT
* *
29533729 ACTGCTTAGGGCGTGAAGGCTCA
65 ACTGCTTAGGGGGTTAAGGCTCA
* **
29533752 CTGTCTTCT-ATCTGCTCCGTTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCCC
1 CCGTCTT-TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTT-CAGCCTGTTTCCC
29533816 TACTGCTTAGGGGGTTAAGGCTCA
64 TACTGCTTAGGGGGTTAAGGCTCA
* ** * * * *
29533840 CCGTCTTCGATCCACTCCACTACTGCTTAGAGAGATAGGATCTATGATCTTCAGCCT-TTTACCC
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTGTTT-CCC
29533904 TACTGCTTAGGGGGTTAAGGCTCA
64 TACTGCTTAGGGGGTTAAGGCTCA
* * * *
29533928 ----C---GATCTTCTCCACTACTGCTTAAGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCT
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTGTTTCCCT
*
29533986 ACTGCTTAGGGGGTGAAGGCTCA
65 ACTGCTTAGGGGGTTAAGGCTCA
* ** * *
29534009 CTGTCTTCT-ATCTGCTCCGTTACTGCTTAGGGAGATAAGATTTGTAATTTCTAGCCTGTTACCC
1 CCGTCTT-TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTC-AGCCTGTTTCCC
*
29534073 TACTGCTTAAGGGGTTAAGGCTCA
64 TACTGCTTAGGGGGTTAAGGCTCA
* * * ** * *
29534097 CTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGAT-AGAATCCATGATCTTCAGCCTGTTACCC
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAG-ATCTGTAAT-TTCAGCCTGTTTCCC
29534161 TACTGCTTAGGGGGTTAAGGCTCA
64 TACTGCTTAGGGGGTTAAGGCTCA
* * * *
29534185 CCGTCTTCGATCTGCTCCACTACTGCTTAGGAAGATAAGATCTGTAATTTTTAGCCTGTTACCCT
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTTCAGCCTGTTTCCCT
29534250 ACTGCTTAGGGGGTTAAGGCTCA
65 ACTGCTTAGGGGGTTAAGGCTCA
* * * *
29534273 CTGTCTTTGATCTGCTCCGCTGCTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTGTTTCCCT
1 CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TTCAGCCTGTTTCCCT
*
29534338 ACTACTTAGGGGGTTAAGGCT
65 ACTGCTTAGGGGGTTAAGGCT
29534359 AGTGAATTCT
Statistics
Matches: 602, Mismatches: 70, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
81 65 0.11
82 3 0.00
84 1 0.00
85 1 0.00
87 13 0.02
88 509 0.85
89 10 0.02
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (87 bp):
CCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCAGCCTGTTTCCCTA
CTGCTTAGGGGGTTAAGGCTCA
Found at i:29533820 original size:44 final size:44
Alignment explanation
Indices: 29533683--29533827 Score: 138
Period size: 44 Copynumber: 3.3 Consensus size: 44
29533673 ATCCACTCCA
*
29533683 CTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTTTCC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTCTAGCCTGTTTCC
* * * * *
29533727 CTACTGCTTAGGGCG-TGAAGGCTCACTGT--CTTCTA-TCTG-CTCC
1 CTACTGCTTAGGGAGAT-AA-GAT--CTGTAATTTCTAGCCTGTTTCC
* *
29533770 GTTACTGCTTAGGGAGATAAGATCTGTAATTTCCAGCCTGTTTCC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTCTAGCCTGTTTCC
29533815 CTACTGCTTAGGG
1 CTACTGCTTAGGG
29533828 GGTTAAGGCT
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
41 4 0.05
43 10 0.13
44 48 0.62
45 11 0.14
47 4 0.05
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTCTAGCCTGTTTCC
Found at i:29533933 original size:44 final size:43
Alignment explanation
Indices: 29533803--29533935 Score: 119
Period size: 44 Copynumber: 3.0 Consensus size: 43
29533793 CTGTAATTTC
29533803 CAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCG-TCTT
1 CAGCCT-TTTCCCTACTGCTTAGGGGGTTAAGGCTCA-CGATCTT
* ** * * * * *
29533847 CGATCC-ACTCCACTACTGCTTAGAGAGAT-AGGATCTATGATCTT
1 C-AGCCTTTTCC-CTACTGCTTAGGGGGTTAAGGCTC-ACGATCTT
29533891 CAGCCTTTTACCCTACTGCTTAGGGGGTTAAGGCTCACGATCTT
1 CAGCCTTTT-CCCTACTGCTTAGGGGGTTAAGGCTCACGATCTT
29533935 C
1 C
29533936 TCCACTACTG
Statistics
Matches: 66, Mismatches: 16, Indels: 14
0.69 0.17 0.15
Matches are distributed among these distances:
43 12 0.18
44 44 0.67
45 10 0.15
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (43 bp):
CAGCCTTTTCCCTACTGCTTAGGGGGTTAAGGCTCACGATCTT
Found at i:29534077 original size:44 final size:44
Alignment explanation
Indices: 29533940--29534081 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 44
29533930 ATCTTCTCCA
*
29533940 CTACTGCTTAAGGAGATAAGATTTGTAATTT-TCAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATTTGTAATTTCT-AGCCTGTTACC
* * * * * *
29533984 CTACTGCTTAGGG-GGTGAAGGCTCACTGT--CTTCTA-TCTGCT-CC
1 CTACTGCTTAGGGAGAT-AA-GAT--TTGTAATTTCTAGCCTGTTACC
*
29534027 GTTACTGCTTAGGGAGATAAGATTTGTAATTTCTAGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATTTGTAATTTCTAGCCTGTTACC
29534072 CTACTGCTTA
1 CTACTGCTTA
29534082 AGGGGTTAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
41 3 0.04
43 11 0.15
44 45 0.62
45 9 0.12
46 1 0.01
47 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATTTGTAATTTCTAGCCTGTTACC
Found at i:29534214 original size:44 final size:44
Alignment explanation
Indices: 29533984--29534304 Score: 160
Period size: 44 Copynumber: 7.3 Consensus size: 44
29533974 GCCTGTTACC
* * *
29533984 CTACTGCTTAGGGGGTGAAGGCTCACTGTCTTCTATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
* * * * * * * * *
29534028 TTACTGCTTAGGGAGATAA-GAT--TTGTAATTTCTAGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGGCTCACTGT--CTTCGA-TCTGCT-CCA
* *
29534072 CTACTGCTTAAGGGGTTAAGGCTCACTGTCTTCGATCCGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
* * ** * *
29534116 CTACTGCTTAGGGAGAT-AGAATC-CATGATCTTC-AGCCTGTTACC-
1 CTACTGCTTAGGGGGTTAAGGCTCAC-TG-TCTTCGA-TCTGCT-CCA
*
29534160 CTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
** * * * * * * * *
29534204 CTACTGCTTAGGAAGATAAGATCTGTAAT-TTTTAG-CCTGTTACC-
1 CTACTGCTTAGGGGGTTAAG-GCT-CACTGTCTTCGATCTGCT-CCA
* *
29534248 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTTGATCTGCTCCG
1 CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
*
29534292 CTGCTGCTTAGGG
1 CTACTGCTTAGGG
29534305 AGATAAGATC
Statistics
Matches: 198, Mismatches: 57, Indels: 44
0.66 0.19 0.15
Matches are distributed among these distances:
41 3 0.02
42 3 0.02
43 26 0.13
44 137 0.69
45 24 0.12
46 2 0.01
47 3 0.02
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCA
Found at i:29534249 original size:345 final size:347
Alignment explanation
Indices: 29533594--29534358 Score: 1049
Period size: 345 Copynumber: 2.2 Consensus size: 347
29533584 GATCGGGTCT
* *
29533594 ACTACTGCTTAGGGACATAAGATTTGTAATCTTCAGCCTGTTTCCCTACTTCTTAGGGGGTTAAG
1 ACTACTGCTTAGGGAGATAAGATTTGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAG
*
29533659 GCTTACCGTCTTTGATCCACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTT
66 GCTCACCGTCTTTGATCCACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTT
* * * **
29533724 TCCCTACTGCTTAGGGCGTGAAGGCTCACTGTCTTCTATCTGCTCCGTTACTGCTTAGGGAGATA
131 ACCCTACTGCTTAGGGCGTGAAGGCTCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATA
** *
29533789 AGATCTGTAATTTCCAGCCTGTTTCCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCCA
196 AGATCCATAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCCA
* * *
29533854 CTCCACTACTGCTTAGAGAGATAGGATCTATGATCTTCAGCCTTTTACCCTACTGCTTAGGGGGT
261 CTCCACTACTGCTTAGAGAGATAAGATCTATAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGT
*
29533919 TAAGGCTCA-C-GATCTTCTCC
326 TAAGGCTCATCTGATCTGCTCC
* * * * *
29533939 ACTACTGCTTAAGGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTGAAG
1 ACTACTGCTTAGGGAGATAAGATTTGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAG
* ** ** * *
29534004 GCTCACTGTCTTCT-ATCTGCTCCGTTACTGCTTAGGGAGATAAGATTTGTAATTTCTAGCCTGT
66 GCTCACCGTCTT-TGATCCACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGT
*
29534068 TACCCTACTGCTTAAGGG-GTTAAGGCTCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGA
130 TACCCTACTGCTT-AGGGCGTGAAGGCTCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGA
*
29534132 T-AGAATCCATGATCTT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGA
194 TAAG-ATCCATAAT-TTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGA
** * * *
29534195 TCTGCTCCACTACTGCTTAG-GAAGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAG
257 TCCACTCCACTACTGCTTAGAG-AGATAAGATCTATAATCTTCAGCCTGTTACCCTACTGCTTAG
29534259 GGGGTTAAGGCTCACTGTCTTTGATCTGCTCC
321 GGGGTTAAGGCTCA---TC--TGATCTGCTCC
* * * *
29534291 GCTGCTGCTTAGGGAGATAAGATCTGTAATCTTCAGTCTGTTTCCCTACTACTTAGGGGGTTAAG
1 ACTACTGCTTAGGGAGATAAGATTTGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAG
29534356 GCT
66 GCT
29534359 AGTGAATTCT
Statistics
Matches: 366, Mismatches: 42, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
344 3 0.01
345 287 0.78
346 7 0.02
349 1 0.00
352 68 0.19
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (347 bp):
ACTACTGCTTAGGGAGATAAGATTTGTAATCTTCAGCCTGTTTCCCTACTACTTAGGGGGTTAAG
GCTCACCGTCTTTGATCCACTCCACTACTGCTTAAGGAGATAAGATCTGTAATTTCTAGCCTGTT
ACCCTACTGCTTAGGGCGTGAAGGCTCACTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATA
AGATCCATAATTTCCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCCA
CTCCACTACTGCTTAGAGAGATAAGATCTATAATCTTCAGCCTGTTACCCTACTGCTTAGGGGGT
TAAGGCTCATCTGATCTGCTCC
Found at i:29534528 original size:64 final size:64
Alignment explanation
Indices: 29534427--29534554 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
29534417 TCATGTATCT
*
29534427 ATGCTTATGCCAAATAATTAAGATACTATGATCGAAATGAATCAAATACTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATACTATAATCGAAATGAATCAAATACTCCTAACTAGATGTG
* * * * * *
29534491 ATGCTTATGTCAAATAATTAGGATGCTATAATTGAAATGAATCTAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAAGATACTATAATCGAAATGAATCAAATACTCCTAACTAGATGTG
29534555 TTATGAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAAGATACTATAATCGAAATGAATCAAATACTCCTAACTAGATGTG
Found at i:29538820 original size:15 final size:14
Alignment explanation
Indices: 29538758--29538827 Score: 52
Period size: 15 Copynumber: 4.8 Consensus size: 14
29538748 TAAAGATAAC
* *
29538758 AAGAAAACCGAATA
1 AAGAAATCCAAATA
29538772 AAGAAATCCAAGATA
1 AAGAAATCCAA-ATA
* *
29538787 GAA-AAACCCAGAGTA
1 -AAGAAATCCA-AATA
29538802 AAGAAATCCATAATA
1 AAGAAATCCA-AATA
*
29538817 AAGAAACCCAA
1 AAGAAATCCAA
29538828 GATACAATAC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
14 12 0.27
15 29 0.66
16 3 0.07
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AAGAAATCCAAATA
Found at i:29540010 original size:12 final size:12
Alignment explanation
Indices: 29539995--29540024 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
29539985 GTTGTTTTCA
29539995 TTTTTGTTTCTT
1 TTTTTGTTTCTT
29540007 TTTTTGTTTCTT
1 TTTTTGTTTCTT
29540019 TCTTTT
1 T-TTTT
29540025 TGGTTGCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTGTTTCTT
Found at i:29540835 original size:12 final size:12
Alignment explanation
Indices: 29540820--29540844 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29540810 GATTCTAAGG
29540820 ATGATTATTTGT
1 ATGATTATTTGT
29540832 ATGATTATTTGT
1 ATGATTATTTGT
29540844 A
1 A
29540845 CGATATGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (12 bp):
ATGATTATTTGT
Found at i:29543881 original size:6 final size:6
Alignment explanation
Indices: 29543863--29543988 Score: 89
Period size: 6 Copynumber: 20.3 Consensus size: 6
29543853 AAGAAACATT
* *
29543863 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
29543912 ATTAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA
*
29543961 ATCAGGTA A-CAGA ATCAAAA ATCAGA AT
1 ATCA-G-A ATCAGA ATC-AGA ATCAGA AT
29543989 GTGAATGCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
5 6 0.06
6 71 0.76
7 14 0.15
8 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:29543919 original size:31 final size:31
Alignment explanation
Indices: 29543877--29543988 Score: 161
Period size: 31 Copynumber: 3.6 Consensus size: 31
29543867 GAACTAGAAT
* * *
29543877 CAGAATCAGAATCAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGAATCAGTATCAGGTAA
*
29543908 CAGAATTAGAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGTATCAGGTAA
*
29543939 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGAATCAGTATCAGGTAA
*
29543970 CAGAATCAAAAATCAGAAT
1 CAGAATC-AGAATCAGAAT
29543989 GTGAATGCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
31 63 0.85
32 11 0.15
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGAATCAGAATCAGAATCAGTATCAGGTAA
Found at i:29543944 original size:19 final size:19
Alignment explanation
Indices: 29543920--29543977 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
29543910 GAATTAGAAT
29543920 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
29543939 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
29543951 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
29543970 CAGAATCA
1 CAGAATCA
29543978 AAAATCAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:29544167 original size:27 final size:26
Alignment explanation
Indices: 29544125--29544202 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
29544115 GCTCAGTTAT
* * * *
29544125 CAGATATTGTGACAGAGTCACTAGATA
1 CAGATATTGTGGCAGAGCCACCAG-GA
29544152 CAGATATTGTGGCAGAGCCACCAGGA
1 CAGATATTGTGGCAGAGCCACCAGGA
* *
29544178 CAGATATTTGTGGCATAACCACCAG
1 CAGATA-TTGTGGCAGAGCCACCAG
29544203 AAATAGATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.16
27 37 0.84
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGGA
Found at i:29544413 original size:22 final size:21
Alignment explanation
Indices: 29544385--29544449 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
29544375 GCAAATACGT
29544385 TTGGCACACAACCATAATCAGG
1 TTGGCACA-AACCATAATCAGG
* *
29544407 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACA-AACCATAAT-CAGG
*
29544429 TTGACACAAAGCCATAATCAG
1 TTGGCACAAA-CCATAATCAG
29544450 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.09
22 29 0.85
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (21 bp):
TTGGCACAAACCATAATCAGG
Found at i:29544933 original size:27 final size:27
Alignment explanation
Indices: 29544903--29545205 Score: 361
Period size: 27 Copynumber: 11.2 Consensus size: 27
29544893 AGGTATCTCG
* * *
29544903 GTAATTCCACGCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTTC
* * *
29544930 GTAATTCTTCCATACAGGGGTATTTTG
1 GTAATTCTACCCTACAGGGGTATTTTC
*
29544957 GTAATTCTACCCTACAGGGGTA-TTGC
1 GTAATTCTACCCTACAGGGGTATTTTC
29544983 GATAATTCTACCCTACAGGGGTA-TTTC
1 G-TAATTCTACCCTACAGGGGTATTTTC
*
29545010 GATAATTCCACCCTACAGGGGTA-TTTC
1 G-TAATTCTACCCTACAGGGGTATTTTC
* *
29545037 GATAATTCTACCCTACAGGGGCATTTTG
1 G-TAATTCTACCCTACAGGGGTATTTTC
*
29545065 GTAATTCTACCCTACAGGGGTA-TTGC
1 GTAATTCTACCCTACAGGGGTATTTTC
*
29545091 GATAATTCTACCCTACAGGGGTA-TTGC
1 G-TAATTCTACCCTACAGGGGTATTTTC
*
29545118 GATAATTCTACCCTACAGGGGTA-TTGC
1 G-TAATTCTACCCTACAGGGGTATTTTC
29545145 GGTAATTCTACCCTACAGGGGTA-TTTC
1 -GTAATTCTACCCTACAGGGGTATTTTC
29545172 GGTAATTCTACCCTACAGGGGTA-TTTC
1 -GTAATTCTACCCTACAGGGGTATTTTC
29545199 AGTAATT
1 -GTAATT
29545206 TTGTAAATCG
Statistics
Matches: 253, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.02
27 242 0.96
28 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (27 bp):
GTAATTCTACCCTACAGGGGTATTTTC
Found at i:29545204 original size:54 final size:53
Alignment explanation
Indices: 29544877--29545205 Score: 426
Period size: 54 Copynumber: 6.1 Consensus size: 53
29544867 GGGCAAAATG
* * * * * * **
29544877 GTAATTTTACCCCACA-AGGTATCTCGGTAATTCCACGCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTA-TTGC
* * *
29544930 GTAATTCTTCCATACAGGGGTATTTTGGTAATTCTACCCTACAGGGGTATTGC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
* * *
29544983 GATAATTCTACCCTACAGGGGTATTTCGATAATTCCACCCTACAGGGGTATTTC
1 G-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
* *
29545037 GATAATTCTACCCTACAGGGGCATTTTGGTAATTCTACCCTACAGGGGTATTGC
1 G-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
* *
29545091 GATAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGGGGTATTGC
1 G-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
*
29545145 GGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 -GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
29545199 AGTAATT
1 -GTAATT
29545206 TTGTAAATCG
Statistics
Matches: 243, Mismatches: 30, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
53 15 0.06
54 227 0.93
55 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (53 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTGC
Found at i:29545220 original size:27 final size:27
Alignment explanation
Indices: 29545190--29545401 Score: 135
Period size: 27 Copynumber: 7.9 Consensus size: 27
29545180 TACCCTACAG
**
29545190 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
*** * * ** *
29545217 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
29545244 GGGTACTTT-GGTAATTTTACAAGTCGA
1 GGGTA-TTTCAGTAATTTTACAAATCGA
* **
29545271 GGGTATTTCAATAATTTTACAGGTCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
29545298 GGGTATTTTAGTAATTTCACAAATC-A
1 GGGTATTTCAGTAATTTTACAAATCGA
** *
29545324 GGGGTATTTTGGTAATTTTACAAA-CTA
1 -GGGTATTTCAGTAATTTTACAAATCGA
** * *
29545351 GGGGTATTTTGGTAATTTTATAAA-CAAA
1 -GGGTATTTCAGTAATTTTACAAATC-GA
*
29545379 GGGTATTTTAGTAATTTTACAAA
1 GGGTATTTCAGTAATTTTACAAA
29545402 CCAGGGGTAT
Statistics
Matches: 152, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
26 5 0.03
27 146 0.96
28 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACAAATCGA
Found at i:29545221 original size:81 final size:81
Alignment explanation
Indices: 29544901--29545198 Score: 445
Period size: 81 Copynumber: 3.7 Consensus size: 81
29544891 CAAGGTATCT
* * * * * * *
29544901 CGGTAATTCCACGCTACAGGGGTATTT-TAGTAATTCTTCCATACAGGGGTATTTTGGTAATTCT
1 CGGTAATTCTACCCTACAGGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTTCGATAATTCT
29544965 ACCCTACAGGGGTATTG
65 ACCCTACAGGGGTATTG
* *
29544982 CGATAATTCTACCCTACAGGGGTATTTCGATAATTCCACCCTACAGGGGTATTTCGATAATTCTA
1 CGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTA
* *
29545047 CCCTACAGGGGCATTT
66 CCCTACAGGGGTATTG
* * *
29545063 TGGTAATTCTACCCTACAGGGGTATTGCGATAATTCTACCCTACAGGGGTATTGCGATAATTCTA
1 CGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTA
29545128 CCCTACAGGGGTATTG
66 CCCTACAGGGGTATTG
*
29545144 CGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
1 CGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
29545199 AGTAATTTTG
Statistics
Matches: 194, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 193 0.99
82 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (81 bp):
CGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGATAATTCTA
CCCTACAGGGGTATTG
Found at i:29545340 original size:54 final size:54
Alignment explanation
Indices: 29545270--29545422 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 54
29545260 TTACAAGTCG
* * **
29545270 AGGGTATTTCAATAATTTTACAGGTCGA-GGGTATTTTAGTAATTTCACAAATC-A
1 AGGGTATTTTAGTAATTTTACA-AACGAGGGGTATTTTAGTAATTTCACAAA-CAA
* * * * * *
29545324 GGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACAA
1 AGGGTATTTTAGTAATTTTACAAACGAGGGGTATTTTAGTAATTTCACAAACAA
* *
29545378 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTT
1 AGGGTATTTTAGTAATTTTACAAACGAGGGGTATTTTAGTAATTT
29545423 GATAAACTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
53 3 0.04
54 81 0.96
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACGAGGGGTATTTTAGTAATTTCACAAACAA
Found at i:29545356 original size:81 final size:82
Alignment explanation
Indices: 29545237--29545431 Score: 225
Period size: 81 Copynumber: 2.4 Consensus size: 82
29545227 GTAATTCTGT
* * * * ** *
29545237 AAATCAAGGGTACTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAATAATTTTACAGGTC-GAGG
1 AAATCAGGGGTATTTTGGTAATTTTACAAACTAGAGGGTATTTCAATAATTTTACA-AACAAAGG
29545300 GTATTTTAGTAATTTCAC
65 GTATTTTAGTAATTTCAC
*** *
29545318 AAATCAGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTTATAAACAAAGGG
1 AAATCAGGGGTATTTTGGTAATTTTACAAACTAGAGGGTATTTCAATAATTTTACAAACAAAGGG
*
29545382 TATTTTAGTAATTTTAC
66 TATTTTAGTAATTTCAC
* * *
29545399 AAACCAGGGGTATTTTGGTAATTTGATAAACTA
1 AAATCAGGGGTATTTTGGTAATTTTACAAACTA
29545432 AAGTATTCTA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 1 0.01
81 92 0.95
82 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (82 bp):
AAATCAGGGGTATTTTGGTAATTTTACAAACTAGAGGGTATTTCAATAATTTTACAAACAAAGGG
TATTTTAGTAATTTCAC
Found at i:29545429 original size:27 final size:27
Alignment explanation
Indices: 29545298--29545422 Score: 178
Period size: 27 Copynumber: 4.6 Consensus size: 27
29545288 TACAGGTCGA
* * *
29545298 GGGTATTTTAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
29545325 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * *
29545352 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTACAAACCAG
*
29545379 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
29545406 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
29545423 GATAAACTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:29548045 original size:21 final size:23
Alignment explanation
Indices: 29547998--29548051 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
29547988 CATTCAAGAT
** *
29547998 AAAATAATATATAAAACTCTTTT
1 AAAATAATATATAAAACTAATTC
29548021 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTC
29548042 AAAAT-ATATA
1 AAAATAATATA
29548052 ATGGTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTC
Found at i:29548093 original size:99 final size:100
Alignment explanation
Indices: 29547955--29548153 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 100
29547945 GCGATCTAAA
*
29547955 GTATATAAAATAATTTTAAAAAAAATTAGTATCCATTCAAGATAAAATAATATATAAAACTCTTT
1 GTATATAAAATAATTTTAAAAAAAAATAGTATCCATTCAAGATAAAATAATATATAAAACTCTTT
29548020 TAAAATAATATATAAACAATTCAAAATATATAATG
66 TAAAATAATATATAAACAATTCAAAATATATAATG
*
29548055 GTATATAAAATAA-TTTAAAAAAAAATAGTATCCATTCAAGGTAAAATAATATATAAAACTCTTT
1 GTATATAAAATAATTTTAAAAAAAAATAGTATCCATTCAAGATAAAATAATATATAAAACTCTTT
29548119 TAAAATAATATATAAACAATTCAAAATATATAATG
66 TAAAATAATATATAAACAATTCAAAATATATAATG
29548154 TGTAAAAAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 84 0.87
100 13 0.13
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (100 bp):
GTATATAAAATAATTTTAAAAAAAAATAGTATCCATTCAAGATAAAATAATATATAAAACTCTTT
TAAAATAATATATAAACAATTCAAAATATATAATG
Found at i:29548104 original size:51 final size:50
Alignment explanation
Indices: 29547955--29548112 Score: 148
Period size: 49 Copynumber: 3.2 Consensus size: 50
29547945 GCGATCTAAA
*
29547955 GTATATAAAATAATTTTAAAAAAAATTAGTATCCATTCAAGATAAAATAA-
1 GTATATAAAATAA-TTTAAAAAAAAATAGTATCCATTCAAGATAAAATAAT
** * * * * * *
29548005 -TATATAAAACTCTTTTAAAATAATATA-TAAACAATTCAAAAT-ATATAAT
1 GTATATAAAA-TAATTTAAAAAAAAATAGT-ATCCATTCAAGATAAAATAAT
*
29548054 GGTATATAAAATAATTTAAAAAAAAATAGTATCCATTCAAGGTAAAATAA-
1 -GTATATAAAATAATTTAAAAAAAAATAGTATCCATTCAAGATAAAATAAT
29548104 -TATATAAAA
1 GTATATAAAA
29548113 CTCTTTTAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
48 15 0.18
49 30 0.36
50 23 0.28
51 15 0.18
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.32
Consensus pattern (50 bp):
GTATATAAAATAATTTAAAAAAAAATAGTATCCATTCAAGATAAAATAAT
Found at i:29548144 original size:21 final size:23
Alignment explanation
Indices: 29548097--29548150 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
29548087 CATTCAAGGT
** *
29548097 AAAATAATATATAAAACTCTTTT
1 AAAATAATATATAAAACTAATTC
29548120 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTC
29548141 AAAAT-ATATA
1 AAAATAATATA
29548151 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTC
Found at i:29548370 original size:15 final size:15
Alignment explanation
Indices: 29548346--29548464 Score: 58
Period size: 15 Copynumber: 8.1 Consensus size: 15
29548336 ATATAAATAG
*
29548346 AAATAAAAATATAAT
1 AAATAGAAATATAAT
29548361 AAATAGAAATATAAT
1 AAATAGAAATATAAT
29548376 -AATAGGAGAA-AT-AT
1 AAATA-GA-AATATAAT
29548390 AAATAGATAA-ATAA-
1 AAATAGA-AATATAAT
29548404 AAATTAGATAA-ATAAT
1 AAA-TAGA-AATATAAT
* * *
29548420 -AATAGTATTAGAAT
1 AAATAGAAATATAAT
* *
29548434 -AACA-AAATAAATAT
1 AAATAGAAATATA-AT
*
29548448 AAATAGAAACATAAT
1 AAATAGAAATATAAT
29548463 AA
1 AA
29548465 TAATAGCAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
13 5 0.06
14 27 0.33
15 43 0.52
16 7 0.09
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.25
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:29548392 original size:29 final size:28
Alignment explanation
Indices: 29548359--29548466 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 28
29548349 TAAAAATATA
*
29548359 ATAAATAGAAATATAATAATAGGAGAAAT
1 ATAAATAGAAATATAATAATA-GATAAAT
*
29548388 ATAAATAGATAA-ATAAAAATTAGATAAAT
1 ATAAATAGA-AATATAATAA-TAGATAAAT
* * * * *
29548417 A-ATAATAGTATTAGAATAACAAAATAAAT
1 ATA-AATAGAAATATAATAA-TAGATAAAT
*
29548446 ATAAATAGAAACATAATAATA
1 ATAAATAGAAATATAATAATA
29548467 ATAGCAATAA
Statistics
Matches: 60, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
28 3 0.05
29 52 0.87
30 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (28 bp):
ATAAATAGAAATATAATAATAGATAAAT
Found at i:29548394 original size:44 final size:44
Alignment explanation
Indices: 29548340--29548424 Score: 104
Period size: 44 Copynumber: 1.9 Consensus size: 44
29548330 ATTAGTATAT
29548340 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGGAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGGAG
* *
29548384 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATAG
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAG
29548425 TATTAGAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
44 26 0.72
45 5 0.14
46 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGGAG
Found at i:29552167 original size:43 final size:43
Alignment explanation
Indices: 29552047--29552205 Score: 148
Period size: 43 Copynumber: 3.7 Consensus size: 43
29552037 AGCTCGTACA
* * *
29552047 ATGCCAACGCCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAAATA-CG
* * *** *
29552090 ATGCCACTGTCCCAAATAAGGTCTTACAC-AAAATCAAATACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAAATACG
29552132 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCA-AA-TACG
*
29552176 ATGCCCACAT-T-CTAGACGTGGTCTTACACG
1 ATG-CCA-ATGTCCCAGACGTGGTCTTACACG
29552206 AAAACACATA
Statistics
Matches: 94, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 26 0.28
43 36 0.38
44 25 0.27
45 5 0.05
46 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCAAATACG
Found at i:29557688 original size:30 final size:30
Alignment explanation
Indices: 29557603--29557699 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
29557593 TAAACTAAAA
* *
29557603 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
29557633 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
29557663 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
29557692 ATGAGCTA
1 -TGAGCTA
29557700 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:29559951 original size:30 final size:30
Alignment explanation
Indices: 29559880--29559962 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
29559870 CTTTTGTTTC
* *
29559880 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
29559911 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
29559940 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
29559963 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:29559962 original size:18 final size:18
Alignment explanation
Indices: 29559913--29559968 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
29559903 CACTCTCAAA
* *
29559913 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
29559930 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
29559948 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
29559967 TT
1 TT
29559969 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:29559969 original size:12 final size:12
Alignment explanation
Indices: 29559938--29559962 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29559928 TTTTTCAATC
29559938 TCATTTTCTTTT
1 TCATTTTCTTTT
29559950 TCATTTTCTTTT
1 TCATTTTCTTTT
29559962 T
1 T
29559963 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:29560041 original size:5 final size:5
Alignment explanation
Indices: 29560031--29560087 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
29560021 CTCTTGCCTC
*
29560031 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
29560078 TCTTT TCTTT
1 TCTTT TCTTT
29560088 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:29560071 original size:15 final size:14
Alignment explanation
Indices: 29560031--29560087 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
29560021 CTCTTGCCTC
*
29560031 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
29560046 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
29560061 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
29560078 TCTTTTCTTT
1 TCTTTTCTTT
29560088 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:29560088 original size:21 final size:21
Alignment explanation
Indices: 29560031--29560098 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
29560021 CTCTTGCCTC
* *
29560031 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
29560052 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
29560073 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
29560093 CTCTTT
1 -TCTTT
29560099 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:29561012 original size:11 final size:11
Alignment explanation
Indices: 29561011--29561053 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
29561001 TTTCAATTTT
29561011 TTTTCTTTTCGAA
1 TTTT-TTTTC-AA
29561024 TTTTTTTTCAA
1 TTTTTTTTCAA
* *
29561035 ATTTTTTTAAA
1 TTTTTTTTCAA
29561046 TTTTTTTT
1 TTTTTTTT
29561054 TACTTGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 18 0.67
12 5 0.19
13 4 0.15
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:29561019 original size:16 final size:17
Alignment explanation
Indices: 29560995--29561032 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
29560985 CATTAAACAC
29560995 TTTTT-TTTTC-AATTT
1 TTTTTCTTTTCGAATTT
29561010 TTTTTCTTTTCGAATTT
1 TTTTTCTTTTCGAATTT
29561027 TTTTTC
1 TTTTTC
29561033 AAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTCTTTTCGAATTT
Found at i:29562814 original size:30 final size:30
Alignment explanation
Indices: 29562729--29562825 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
29562719 TAAACTAAAA
* *
29562729 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
29562759 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
29562789 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
29562818 ATGAGCTA
1 -TGAGCTA
29562826 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:29563065 original size:30 final size:30
Alignment explanation
Indices: 29563031--29563127 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
29563021 TAAACTAAAA
*
29563031 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29563061 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
29563091 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
29563121 TGAGCTA
1 TGAGCTA
29563128 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:29563262 original size:302 final size:301
Alignment explanation
Indices: 29562695--29563294 Score: 1051
Period size: 302 Copynumber: 2.0 Consensus size: 301
29562685 ATTTTTATTT
* *
29562695 AATGTATTAAAGACAAAACGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
1 AATGCATTAAAGAAAAAACGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
29562760 GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
66 GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
* *
29562825 AGGAGTGAGCTCGGTTTAGCTCAGGCAAGTTGGATTGAGCTCGAATAAGCTAGATTTGAGCTGGA
131 AGGAGTGAGCTCGGTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTAGAGTTGAGCTGGA
*
29562890 CGGAGCTCGTGGAGCTAGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTAACA
196 CGGAGCTCGTGGAGCTAGAAACGAGATGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTAACA
* * *
29562955 GACTTGTTCGATGAAGTTCGCGGGGCGTGCTCGTATCATCA
261 GACTTGCTCGATAAAGTTCGCGGGGCATGCTCGTATCATCA
*
29562996 AATGCATTAAAGAAAAAACCGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 AATGCATTAAAGAAAAAA-CGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
*
29563061 TGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGTTGAA-AGTGAG
65 TGAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATA-TGAG
29563125 CTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTAGAGTTGAGCTG
129 CTAGGAGTGAGCTCGGTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTAGAGTTGAGCTG
*
29563190 GACGGAGCTCGTGGAGCTAGAAACGAGATGGGATCAGCTTGCCAACATGTCATTGCTCGGCTTGA
194 GACGGAGCTCGTGGAGCTAGAAACGAGATGGGATCAGCTTGCCAACATGTCAATGCTCGGCTT-A
*
29563255 A-AGACTTGCTCGATAAAGTTTGCGGGGCATGCTCGTATCA
258 ACAGACTTGCTCGATAAAGTTCGCGGGGCATGCTCGTATCA
29563295 AAGTTAACCT
Statistics
Matches: 284, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
301 17 0.06
302 265 0.93
303 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (301 bp):
AATGCATTAAAGAAAAAACGAGTTTAAACTAAAATGAGCTAAGCTTTAGCTCGTGAGCTAAAGTT
GAGCTGAGGCTAAACTCCTAAGCTGAAGTTGAGCTAAGGTTTAGCTCGTGAGCTGAATATGAGCT
AGGAGTGAGCTCGGTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTAGAGTTGAGCTGGA
CGGAGCTCGTGGAGCTAGAAACGAGATGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTAACA
GACTTGCTCGATAAAGTTCGCGGGGCATGCTCGTATCATCA
Found at i:29564439 original size:30 final size:29
Alignment explanation
Indices: 29564405--29564500 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
29564395 AGCTCACTCC
29564405 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ATTCAGCTCACGAGCTAAACCT
* * * * * *
29564435 TAGCTCACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAATTCAGCTCACGAGCTAAACCT
* * *
29564464 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAA-TTCAGCTCACGAGCTAAACCT
29564494 TAGCTCA
1 TAGCTCA
29564501 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 22 0.44
30 28 0.56
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (29 bp):
TAGCTCAATTCAGCTCACGAGCTAAACCT
Found at i:29568080 original size:19 final size:19
Alignment explanation
Indices: 29568035--29568080 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
29568025 ATAAACACAC
*
29568035 AATTAATTAAAACATAACT
1 AATTAATAAAAACATAACT
*
29568054 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAA-CATAACT
29568072 AATTAATAA
1 AATTAATAA
29568081 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTAATAAAAACATAACT
Found at i:29568307 original size:10 final size:10
Alignment explanation
Indices: 29568294--29568330 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
29568284 GAGCTCGGTT
29568294 GAGCTGAAAC
1 GAGCTGAAAC
29568304 GAGCTGAAAC
1 GAGCTGAAAC
* *
29568314 GAGCTCAAAT
1 GAGCTGAAAC
29568324 GAGCTGA
1 GAGCTGA
29568331 GTTGAGCTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.14
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:29568337 original size:20 final size:20
Alignment explanation
Indices: 29568291--29568338 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
29568281 TGTGAGCTCG
*
29568291 GTTGAGCTGAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
29568311 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
29568331 GTTGAGCT
1 GTTGAGCT
29568339 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:29572649 original size:20 final size:20
Alignment explanation
Indices: 29572626--29572673 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29572616 AGCTCCGTCC
29572626 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
29572646 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
29572666 AGCTCAAC
1 AGCTCAAC
29572674 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:29575022 original size:24 final size:26
Alignment explanation
Indices: 29574958--29575023 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
29574948 CACAACTCTC
*
29574958 TTTCTTTTCTCTCATATTTTCTTCTT
1 TTTCTTCTCTCTCATATTTTCTTCTT
* *
29574984 TTTCTTCTTTTTCAT-TTTTACTT-TT
1 TTTCTTCTCTCTCATATTTT-CTTCTT
29575009 TTT-TTCTCTCTCATA
1 TTTCTTCTCTCTCATA
29575024 CATTCTGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 9 0.27
25 9 0.27
26 15 0.45
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTCTTCTCTCTCATATTTTCTTCTT
Found at i:29575405 original size:14 final size:14
Alignment explanation
Indices: 29575386--29575430 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29575376 AACTCATCTT
*
29575386 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
29575400 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
29575413 AATTTAATTTAATG
1 AGTTTAATTTAATG
29575427 AGTT
1 AGTT
29575431 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:29576445 original size:29 final size:29
Alignment explanation
Indices: 29576412--29576471 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29576402 ATAACCAAAC
*
29576412 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
29576441 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
29576470 CT
1 CT
29576472 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:29576464 original size:15 final size:15
Alignment explanation
Indices: 29576418--29576465 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29576408 AAACCTACAA
*
29576418 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
29576433 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
29576447 AAACTTCATATCCAT
1 AAACTTCATATCCAT
29576462 AAAC
1 AAAC
29576466 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:29581101 original size:15 final size:14
Alignment explanation
Indices: 29581078--29581118 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
29581068 TCTTGTTCTC
29581078 TCTCGTCTTTTTCAA
1 TCTC-TCTTTTTCAA
29581093 TCGTCTCTTTTTCAA
1 TC-TCTCTTTTTCAA
*
29581108 TCTCACTTTTT
1 TCTCTCTTTTT
29581119 ATTTCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 14 0.58
16 2 0.08
ACGTcount: A:0.12, C:0.27, G:0.05, T:0.56
Consensus pattern (14 bp):
TCTCTCTTTTTCAA
Found at i:29581211 original size:35 final size:37
Alignment explanation
Indices: 29581172--29581244 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 37
29581162 GCTCTTTTTC
*
29581172 TTTC-TTC-TCTCTTTCATTTTCTT-TTTCAATTT-ATT
1 TTTCTTTCATCTCTTT--TTTTCTTCTCTCAATTTCATT
29581207 TTTCTTTCATCTCTTTTTTTCTTCTCTCAATTTCATT
1 TTTCTTTCATCTCTTTTTTTCTTCTCTCAATTTCATT
29581244 T
1 T
29581245 GATATTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 11 0.33
36 11 0.33
37 11 0.33
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (37 bp):
TTTCTTTCATCTCTTTTTTTCTTCTCTCAATTTCATT
Found at i:29585947 original size:2 final size:2
Alignment explanation
Indices: 29585942--29585966 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29585932 AATTTTTTGG
29585942 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 A
29585967 CTTTGGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29592538 original size:17 final size:17
Alignment explanation
Indices: 29592501--29592540 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29592491 GAAAGACATG
*
29592501 GGTATGAGTCCAGCACG
1 GGTATGAGTCCAGCACA
**
29592518 GGTATGAGTCTGGCACA
1 GGTATGAGTCCAGCACA
29592535 GGTATG
1 GGTATG
29592541 TTAATCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (17 bp):
GGTATGAGTCCAGCACA
Found at i:29594184 original size:21 final size:20
Alignment explanation
Indices: 29594143--29594186 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
29594133 TTTCAATTGA
29594143 AATAATATATTTAAATTAATT
1 AATAATATATTTAAA-TAATT
29594164 AATAATAATATTATAAA-AATT
1 AATAAT-ATATT-TAAATAATT
29594185 AA
1 AA
29594187 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 12 0.57
22 5 0.24
23 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATATATTTAAATAATT
Found at i:29594385 original size:26 final size:26
Alignment explanation
Indices: 29594349--29594402 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
29594339 GAGTTTATGC
29594349 ATATTTGTAATTTTCTTTGGTAAACA
1 ATATTTGTAATTTTCTTTGGTAAACA
29594375 ATATTTGTAATTTTCTTTGGTAAACA
1 ATATTTGTAATTTTCTTTGGTAAACA
29594401 AT
1 AT
29594403 CTAATAAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.50
Consensus pattern (26 bp):
ATATTTGTAATTTTCTTTGGTAAACA
Found at i:29596619 original size:46 final size:46
Alignment explanation
Indices: 29596546--29596717 Score: 149
Period size: 46 Copynumber: 3.7 Consensus size: 46
29596536 GTTATTGTGA
* * *
29596546 GCTAGTGTAAGACCATGTCTAAGACATGGCATCGGATTGAGACGAGT
1 GCTAGTGTAAGACCATGTCTAGGACAT-GCATCGGATCGAGATGAGT
* *
29596593 GCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCA-CGAGATGTA-A
1 GCTAGTGTAAGACCATGTCTAGGACATGCATCGG--ATCGAGATG-AGT
* * *
29596639 GCCAGTGTAAGA-CATGTCTAGGACATGCATCGGCTACGAGATGTGT
1 GCTAGTGTAAGACCATGTCTAGGACATGCATCGGAT-CGAGATGAGT
** *
29596685 -C-AGTGTAAGATAATGTCTGGGACATGGCATCGG
1 GCTAGTGTAAGACCATGTCTAGGACAT-GCATCGG
29596718 TACAGATATG
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
44 9 0.09
45 20 0.19
46 62 0.59
47 14 0.13
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTAGGACATGCATCGGATCGAGATGAGT
Found at i:29596717 original size:92 final size:93
Alignment explanation
Indices: 29596549--29596717 Score: 229
Period size: 92 Copynumber: 1.8 Consensus size: 93
29596539 ATTGTGAGCT
* *
29596549 AGTGTAAGACCATGTCTAAGACATGGCATCGGATTGAGACGAGTGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACCATGTCTAAGACATGGCATCGGATCGAGACGAGTGCTAGTGTAAGAAATGTCTGG
29596614 GACATGCATCGGCCACGAGATGTAAGCC
66 GACATGCATCGGCCACGAGATGTAAGCC
* * * *
29596642 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCTACGAGATGTGT-C-AGTGTAAGATAATGTCT
1 AGTGTAAGACCATGTCTAAGACATGGCATCGGAT-CGAGACGAGTGCTAGTGTAAGA-AATGTCT
29596703 GGGACATGGCATCGG
64 GGGACAT-GCATCGG
29596718 TACAGATATG
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
90 9 0.13
91 22 0.33
92 27 0.40
93 9 0.13
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (93 bp):
AGTGTAAGACCATGTCTAAGACATGGCATCGGATCGAGACGAGTGCTAGTGTAAGAAATGTCTGG
GACATGCATCGGCCACGAGATGTAAGCC
Found at i:29602514 original size:46 final size:45
Alignment explanation
Indices: 29602464--29602634 Score: 164
Period size: 46 Copynumber: 3.7 Consensus size: 45
29602454 TGGGCATCCG
*
29602464 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCC
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
*** * * ** *
29602509 AAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGCATCC
1 -AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-AAACGTCC
* * * *
29602556 AGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
* *
29602601 GAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 -AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29602635 GCGGGTTACA
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
45 8 0.08
46 81 0.83
47 9 0.09
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC
Found at i:29602625 original size:92 final size:93
Alignment explanation
Indices: 29602456--29602626 Score: 263
Period size: 92 Copynumber: 1.8 Consensus size: 93
29602446 AGGATGTTTG
* * *
29602456 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCGTTGAG
29602521 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
29602549 GGCATCC-AGCTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCGTTGAG
*
29602613 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
29602627 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 63 0.90
93 7 0.10
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCAAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29605598 original size:47 final size:48
Alignment explanation
Indices: 29605474--29605657 Score: 209
Period size: 47 Copynumber: 3.9 Consensus size: 48
29605464 TATGGGTTAT
* *
29605474 TGTAAGCTAGTGTAAGACCATGTCTGGG-CATGGCATCGGCAC-GGATA
1 TGTAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGA
*
29605521 TGTGAGAGCTAGTGTAAGACCATGTTTGGGACAT-GCATCGGCCTCGAGA
1 TGT-A-AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA
* * ** *
29605570 TGTAAGCCAGTGTAAGACCATGTCTGGGACATGACATC-AACTTGATGGA
1 TGTAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGA--GA
29605619 TG--AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
29605658 ATTATACCCT
Statistics
Matches: 116, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
47 65 0.56
48 7 0.06
49 41 0.35
50 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
TGTAAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA
Found at i:29606939 original size:7 final size:7
Alignment explanation
Indices: 29606927--29606952 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29606917 AAATAGTATT
29606927 TAATATA
1 TAATATA
29606934 TAATATA
1 TAATATA
29606941 TAATATA
1 TAATATA
29606948 TAATA
1 TAATA
29606953 ACAAGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TAATATA
Found at i:29607347 original size:20 final size:20
Alignment explanation
Indices: 29607300--29607364 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
29607290 TATATGTAAA
*
29607300 AATAATATGTATAAATAA-AT
1 AATAATATATATAAA-AATAT
*
29607320 ATATAATATATGTAAAAATAT
1 A-ATAATATATATAAAAATAT
29607341 AATAATATATATAAAAATAAT
1 AATAATATATATAAAAAT-AT
29607362 AAT
1 AAT
29607365 TATGAGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AATAATATATATAAAAATAT
Found at i:29607481 original size:19 final size:19
Alignment explanation
Indices: 29607445--29607494 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29607435 GAAGTAAAAT
*
29607445 TAAAATAAA-ACA-AATAA
1 TAAAATAAATATAGAATAA
*
29607462 TAAAATATATATAGAATAA
1 TAAAATAAATATAGAATAA
29607481 TAAAATAAATATAG
1 TAAAATAAATATAG
29607495 GACTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 8 0.29
18 2 0.07
19 18 0.64
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
TAAAATAAATATAGAATAA
Found at i:29609176 original size:87 final size:82
Alignment explanation
Indices: 29609084--29609446 Score: 254
Period size: 83 Copynumber: 4.3 Consensus size: 82
29609074 GACAATACAG
* * *
29609084 AGATGCCAAATCATCTTAGATTTGCTTGAACGTAAGCACGTGAAAGCCAAATCAGCTTCGTCTTC
1 AGATGCCAAATCATCTTAGATCTGCTTG-A-G-AA-CACGTGAAAGCCAAATCAGCTACGTCGTC
29609149 GATTTGCTCCTTGTAAGCACA-A
62 GATTTGCTCCTTGTAA--ACATA
* * * ** * *
29609171 AGATGCCAAACCATCTTAGGTCTGTTTGAGAACATTTGAGAGCCAAATCTGCTACGTCGTCGATT
1 AGATGCCAAATCATCTTAGATCTGCTTGAGAACACGTGAAAGCCAAATCAGCTACGTCGTCGATT
* *
29609236 TGTTTCTTGTAAACATA
66 TGCTCCTTGTAAACATA
* * * * *
29609253 AGAATGCCAAATCATCTTGAGTTC-GTTTGAGAACATC-T-AAGAGTCC-AATCTGCTATGTCCT
1 AG-ATGCCAAATCATCTT-AGATCTGCTTGAGAACA-CGTGAA-AG-CCAAATCAGCTACGTCGT
* * * *
29609314 CGATTTGTTTCTTGTAAATACA
61 CGATTTGCTCCTTGTAAACATA
* * ** * * * *
29609336 AGAATGCCAAATCATCTT-GAGTTTGTTTGAGAACATTTGAGAGTCC-AATCTGCTATGTCCTCG
1 AG-ATGCCAAATCATCTTAGA-TCTGCTTGAGAACACGTGAAAG-CCAAATCAGCTACGTCGTCG
* *
29609399 ATTTGTTCCTTGTAAACACA
63 ATTTGCTCCTTGTAAACATA
*
29609419 AGAATACCAAATCATCTTAGATCTGCTT
1 AG-ATGCCAAATCATCTTAGATCTGCTT
29609447 CAGTATAAAC
Statistics
Matches: 236, Mismatches: 29, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
81 4 0.02
82 5 0.02
83 190 0.81
84 11 0.05
85 1 0.00
86 1 0.00
87 24 0.10
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (82 bp):
AGATGCCAAATCATCTTAGATCTGCTTGAGAACACGTGAAAGCCAAATCAGCTACGTCGTCGATT
TGCTCCTTGTAAACATA
Found at i:29609245 original size:83 final size:83
Alignment explanation
Indices: 29609133--29609443 Score: 387
Period size: 83 Copynumber: 3.7 Consensus size: 83
29609123 GTGAAAGCCA
* * * * * *
29609133 AATCAGCTTCGTCTTCGATTTGCTCCTTGTAAGCACAA-AGATGCCAAACCATCTTAGGTCTGTT
1 AATCTGCTACGTCCTCGATTTGTTCCTTGTAAACACAAGA-ATGCCAAATCATCTTAGGTCTGTT
29609197 TGAGAACATTTGAGAG-CC
65 TGAGAACATTTGAGAGTCC
* * * *
29609215 AAATCTGCTACGTCGTCGATTTGTTTCTTGTAAACATAAGAATGCCAAATCATCTTGAGTTC-GT
1 -AATCTGCTACGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTT-AGGTCTGT
* *
29609279 TTGAGAACATCTAAGAGTCC
64 TTGAGAACATTTGAGAGTCC
* * * *
29609299 AATCTGCTATGTCCTCGATTTGTTTCTTGTAAATACAAGAATGCCAAATCATCTT-GAGTTTGTT
1 AATCTGCTACGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTAG-GTCTGTT
29609363 TGAGAACATTTGAGAGTCC
65 TGAGAACATTTGAGAGTCC
* * *
29609382 AATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCAAATCATCTTAGATCTG
1 AATCTGCTACGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTAGGTCTG
29609444 CTTCAGTATA
Statistics
Matches: 198, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
81 1 0.01
82 1 0.01
83 188 0.95
84 8 0.04
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (83 bp):
AATCTGCTACGTCCTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTAGGTCTGTTT
GAGAACATTTGAGAGTCC
Found at i:29609614 original size:118 final size:119
Alignment explanation
Indices: 29609361--29609718 Score: 637
Period size: 119 Copynumber: 3.0 Consensus size: 119
29609351 CTTGAGTTTG
* *
29609361 TTTGAGAACATTTGAGAGTCCAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATAC
1 TTTGAGAACATTTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
*
29609426 CAAATCATCTTAGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
29609480 TTTGAGAACATTTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATTTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
*
29609545 C-AATCATCTTGGATCTGCTCCAGTATAAACATCTGAAAGCTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
* * * *
29609598 TTTGAGAACATCTGAGAGTCAAATTTTCTATGTCCTCAATTTGTTTCTTGTAAACACAAGAATAC
1 TTTGAGAACATTTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
29609663 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
66 CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
29609717 TT
1 TT
29609719 GCAGCCTATT
Statistics
Matches: 229, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
118 112 0.49
119 117 0.51
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (119 bp):
TTTGAGAACATTTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTTCTTGTAAACACAAGAATAC
CAAATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGCTAGATCTGCTATA
Found at i:29619290 original size:19 final size:19
Alignment explanation
Indices: 29619266--29619302 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
29619256 ACATCAATCC
*
29619266 ATAATATAATTAATATAGA
1 ATAATATAATAAATATAGA
29619285 ATAATATAATAAATATAG
1 ATAATATAATAAATATAG
29619303 GACTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
ATAATATAATAAATATAGA
Found at i:29623577 original size:64 final size:64
Alignment explanation
Indices: 29623496--29623678 Score: 201
Period size: 67 Copynumber: 2.8 Consensus size: 64
29623486 AGACATTATG
* *
29623496 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
29623560 ATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGA-TACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
29623625 AA
63 AA
* * * *
29623627 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAG
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAG
29623679 TCGAACTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.18
64 23 0.23
65 6 0.06
66 17 0.17
67 31 0.32
68 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:29623618 original size:67 final size:64
Alignment explanation
Indices: 29623472--29623647 Score: 185
Period size: 67 Copynumber: 2.7 Consensus size: 64
29623462 CATCATGTGT
* * * *
29623472 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ATGTAGCTAGGTCGCATGGGTGATACAATGAGGACACCATG
29623537 TAG
62 TAG
* * *
29623540 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGA-TACAA-TG-AGGACACCATGT
29623605 AG
63 AG
* *
29623607 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTG
1 ACAAGAGAGCTACGAGATATA-TGTAGCTAGGTCGCATGGGTG
29623648 GTACTAAGTG
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
64 22 0.24
65 6 0.06
66 19 0.20
67 31 0.33
68 15 0.16
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGGGTGATACAATGAGGACACCATGTAG
Found at i:29624748 original size:2 final size:2
Alignment explanation
Indices: 29624741--29624779 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29624731 TCATGACATG
29624741 TA 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 TA T
29624780 GACTAGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29627383 original size:16 final size:18
Alignment explanation
Indices: 29627364--29627396 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
29627354 CATACGAATT
29627364 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
29627380 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
29627397 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:29629371 original size:49 final size:49
Alignment explanation
Indices: 29629167--29629477 Score: 216
Period size: 49 Copynumber: 6.4 Consensus size: 49
29629157 TAGGGTAATA
* * ** * *
29629167 CATGTCTGGGGCATGGCATCGGCATGGATATGTGAGAG-CTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCTCAAT-TTTGATAGTC-AGTGTAAGAC
** **
29629217 CATGTCTGGGACAT-GCATTAG-CTACAA-GATG-T-GTCAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCT-CAATTTTGATAGTCAGTGTAAGAC
* ** * *
29629262 CATGTCTGGGGCATGGCATCGGCAC-GGATATGTGAGAG-CTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGC-CTCAAT-TTTGATAGTC-AGTGTAAGAC
*
29629312 CATGTCTGGGACAT-GCTGTCGGCCTCAATTTTGATAGTCAGTGTAAGAC
1 CATGTCTGGGACATGGC-ATCGGCCTCAATTTTGATAGTCAGTGTAAGAC
* * ** *
29629361 CATGTTTGGGACATGGCATC-GACTTGA--TGGATGAG-CTAGTGTAAGAC
1 CATGTCTGGGACATGGCATCGGCCTCAATTTTGAT-AGTC-AGTGTAAGAC
* * * *
29629408 CATGTATGGGACATGGCATCGACCTCAATTTTGATAGTTAGTGTAAAAC
1 CATGTCTGGGACATGGCATCGGCCTCAATTTTGATAGTCAGTGTAAGAC
*
29629457 CATGTCTGGAACATGGCATCG
1 CATGTCTGGGACATGGCATCG
29629478 ACTTGATGGA
Statistics
Matches: 202, Mismatches: 39, Indels: 41
0.72 0.14 0.15
Matches are distributed among these distances:
45 24 0.12
46 12 0.06
47 33 0.16
48 11 0.05
49 71 0.35
50 51 0.25
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (49 bp):
CATGTCTGGGACATGGCATCGGCCTCAATTTTGATAGTCAGTGTAAGAC
Found at i:29629418 original size:47 final size:46
Alignment explanation
Indices: 29629106--29629522 Score: 226
Period size: 47 Copynumber: 8.7 Consensus size: 46
29629096 GGTTATTGTG
** * *
29629106 AGCTAGTGTAAGACCAAATCTAGGACATGACATCGACATTAAGAT-GAGT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TT--GATGGA-T
* * * * * *
29629155 -GCTAGGGTAATA-CATGTCTGGGGCATGGCATCGGCATGGATATGTGAG
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTG--ATG-GAT
* **
29629203 AGCTAGTGTAAGACCATGTCTGGGACAT-GCATTAGCTACAAGAT-G-T
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCA-T--CGACTTGATGGAT
* * *
29629249 -G-TCAGTGTAAGACCATGTCTGGGGCATGGCATCGGCAC-GGATATGTGAG
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATC-G-ACTTG--ATG-GAT
* * ** *
29629298 AGCTAGTGTAAGACCATGTCTGGGACAT-GCTGTCGGCCTCAATTTTGAT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGC-ATC-GACTTGA--TGGAT
*
29629347 AG-TCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGATGGAT
1 AGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
* ** *
29629393 GAGCTAGTGTAAGACCATGTATGGGACATGGCATCGACCTCAATTTTGAT
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTGA--TGGAT
* * *
29629443 AGTTAGTGTAAAACCATGTCTGGAACATGGCATCGACTTGATGGAT
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
* * *
29629489 AAGCCAGTGAAAGACCATGTCTGGGACATAGCAT
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCAT
29629523 TGGCATTATA
Statistics
Matches: 284, Mismatches: 52, Indels: 66
0.71 0.13 0.16
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 28 0.10
46 13 0.05
47 82 0.29
48 24 0.08
49 81 0.29
50 49 0.17
51 2 0.01
52 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (46 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGAT
Found at i:29629422 original size:96 final size:96
Alignment explanation
Indices: 29629167--29629522 Score: 370
Period size: 96 Copynumber: 3.7 Consensus size: 96
29629157 TAGGGTAATA
* * *
29629167 CATGTCTGGGGCATGGCATCGGCATGGATATGTGA-GAGCTAGTGTAAGACCATGTCTGGGACAT
1 CATGTCTGGGACATGGCATCGAC-TTG--ATG-GATGAGCTAGTGTAAGACCATGTCTGGGACAT
* * **
29629231 -GCAT-TAGCTACAA-GATG-T-GTCAGTGTAAGAC
62 GGCATCGACCT-CAATTTTGATAGTCAGTGTAAGAC
* *
29629262 CATGTCTGGGGCATGGCATCGGCAC-GGATATGTGA-GAGCTAGTGTAAGACCATGTCTGGGACA
1 CATGTCTGGGACATGGCATC-G-ACTTG--ATG-GATGAGCTAGTGTAAGACCATGTCTGGGACA
* *
29629325 T-GCTGTCGGCCTCAATTTTGATAGTCAGTGTAAGAC
61 TGGC-ATCGACCTCAATTTTGATAGTCAGTGTAAGAC
* *
29629361 CATGTTTGGGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTATGGGACATGGCA
1 CATGTCTGGGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTCTGGGACATGGCA
* *
29629426 TCGACCTCAATTTTGATAGTTAGTGTAAAAC
66 TCGACCTCAATTTTGATAGTCAGTGTAAGAC
* * * * *
29629457 CATGTCTGGAACATGGCATCGACTTGATGGATAAGCCAGTGAAAGACCATGTCTGGGACATAGCA
1 CATGTCTGGGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTCTGGGACATGGCA
29629522 T
66 T
29629523 TGGCATTATA
Statistics
Matches: 229, Mismatches: 22, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
95 63 0.28
96 123 0.54
97 9 0.04
98 3 0.01
99 31 0.14
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (96 bp):
CATGTCTGGGACATGGCATCGACTTGATGGATGAGCTAGTGTAAGACCATGTCTGGGACATGGCA
TCGACCTCAATTTTGATAGTCAGTGTAAGAC
Found at i:29629478 original size:49 final size:49
Alignment explanation
Indices: 29629206--29629479 Score: 226
Period size: 49 Copynumber: 5.7 Consensus size: 49
29629196 ATGTGAGAGC
* * **
29629206 TAGTGTAAGACCATGTCTGGGACAT-GCAT-TAGCTACAA-GATG-T-GT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACCT-CAATTTTGATAGT
* * * ** * * *
29629251 CAGTGTAAGACCATGTCTGGGGCATGGCATCGGCAC-GGATATGTGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGAC-CTCAAT-TTTGATAGT
* *
29629301 TAGTGTAAGACCATGTCTGGGACAT-GCTGTCGGCCTCAATTTTGATAGT
1 TAGTGTAAGACCATGTCTGGGACATGGC-ATCGACCTCAATTTTGATAGT
* * ** * *
29629350 CAGTGTAAGACCATGTTTGGGACATGGCATCGA-CTTGA--TGGATGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCAATTTTGAT-AGT
*
29629397 TAGTGTAAGACCATGTATGGGACATGGCATCGACCTCAATTTTGATAGT
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCAATTTTGATAGT
* *
29629446 TAGTGTAAAACCATGTCTGGAACATGGCATCGAC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGAC
29629480 TTGATGGATA
Statistics
Matches: 179, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
45 23 0.13
46 9 0.05
47 33 0.18
48 9 0.05
49 68 0.38
50 37 0.21
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (49 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGACCTCAATTTTGATAGT
Found at i:29631941 original size:27 final size:27
Alignment explanation
Indices: 29631824--29631941 Score: 164
Period size: 27 Copynumber: 4.4 Consensus size: 27
29631814 TGGATAAGTT
*
29631824 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
29631851 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
29631878 GTAGAATTACTGAAATAACCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
29631905 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
29631932 GTAAAATTAC
1 GTAGAATTAC
29631942 GATTTTACCC
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:29632170 original size:2 final size:2
Alignment explanation
Indices: 29632163--29632190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29632153 GCTTCGCCAC
29632163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29632191 CTATTCTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29632245 original size:27 final size:27
Alignment explanation
Indices: 29632195--29632246 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29632185 ATATATCTAT
*
29632195 TCTGGTGACCTAGCCACAATATCTGTA
1 TCTGGTGACCTAGCCACAAAATCTGTA
* * *
29632222 TCTGGTGACTTCGTCACAAAATCTG
1 TCTGGTGACCTAGCCACAAAATCTG
29632247 GCAGCCTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (27 bp):
TCTGGTGACCTAGCCACAAAATCTGTA
Found at i:29637340 original size:28 final size:27
Alignment explanation
Indices: 29637279--29637348 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
29637269 ATAGTGAGTC
*
29637279 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
29637306 CGCACACTTAGTGCTATATGATCCAACT
1 CGCACACTTAGTGCTATATAAT-CAACT
29637334 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29637349 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29639914 original size:45 final size:45
Alignment explanation
Indices: 29639821--29639974 Score: 193
Period size: 45 Copynumber: 3.4 Consensus size: 45
29639811 GTGTTTCAGA
** **
29639821 GTAAGACCACGTCTGGGACGTTGGCATCGATCTAAT-TATTTTTGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATCT-ATGTGGTTACGT
* * *
29639866 GTAAGACCACGTTTGGGACGTTGGCATCGATCTATGTGGATACAT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATCTATGTGGTTACGT
* * *
29639911 GTAAGACCACGTCTAGGACATTGACATCGATCTATGTGGTTACGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATCTATGTGGTTACGT
*
29639956 GTAAGACCATGTCTGGGAC
1 GTAAGACCACGTCTGGGAC
29639975 ATCGACATCG
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
44 2 0.02
45 91 0.98
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (45 bp):
GTAAGACCACGTCTGGGACGTTGGCATCGATCTATGTGGTTACGT
Found at i:29646654 original size:15 final size:15
Alignment explanation
Indices: 29646634--29646681 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29646624 TCAAAGATGG
29646634 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
29646649 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
29646663 GTTTATGGATATAAA
1 GTTTATGGATATGAA
29646678 GTTT
1 GTTT
29646682 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:29646668 original size:14 final size:14
Alignment explanation
Indices: 29646628--29646671 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29646618 AAAGATTCAA
29646628 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
29646642 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
29646657 AGATGGGTTTATGG
1 AGATGGGTTTATGG
29646671 A
1 A
29646672 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:29646697 original size:29 final size:29
Alignment explanation
Indices: 29646628--29646687 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29646618 AAAGATTCAA
*
29646628 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
29646657 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
29646686 AG
1 AG
29646688 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:29647703 original size:14 final size:14
Alignment explanation
Indices: 29647661--29647705 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29647651 TTAAAGAAGC
29647661 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
29647675 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
29647688 AACTCATTTAATTA
1 AACTCATTAAATTA
29647702 AACT
1 AACT
29647706 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:29650546 original size:15 final size:15
Alignment explanation
Indices: 29650526--29650573 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
29650516 TCAAAGATGG
29650526 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
29650541 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
29650555 GTTTATGGATATAAA
1 GTTTATGGATATGAA
29650570 GTTT
1 GTTT
29650574 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:29650560 original size:14 final size:14
Alignment explanation
Indices: 29650520--29650563 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
29650510 AAGGATTCAA
29650520 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
29650534 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
29650549 AGATGGGTTTATGG
1 AGATGGGTTTATGG
29650563 A
1 A
29650564 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:29650589 original size:29 final size:29
Alignment explanation
Indices: 29650520--29650579 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29650510 AAGGATTCAA
*
29650520 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
29650549 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
29650578 AG
1 AG
29650580 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:29651600 original size:14 final size:14
Alignment explanation
Indices: 29651558--29651602 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
29651548 TTAAAGAAGC
29651558 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
29651572 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
29651585 AACTCATTTAATTA
1 AACTCATTAAATTA
29651599 AACT
1 AACT
29651603 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:29653416 original size:18 final size:17
Alignment explanation
Indices: 29653371--29653427 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
29653361 CATGTGAACC
*
29653371 AGAAAAGGAAATTGAAAA
1 AGAAAA-GAGATTGAAAA
*
29653389 AGAGAGAGAGATTGAAGAA
1 AGA-AAAGAGATTGAA-AA
29653408 AGAAAAGAGAGTGTGAAAA
1 AGAAAAGAGA-T-TGAAAA
29653427 A
1 A
29653428 AATAAGTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 17 0.53
19 11 0.34
20 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.11
Consensus pattern (17 bp):
AGAAAAGAGATTGAAAA
Found at i:29661030 original size:15 final size:16
Alignment explanation
Indices: 29661010--29661039 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29661000 TTCTTCAAAA
29661010 CTATTCATC-ATACTG
1 CTATTCATCAATACTG
29661025 CTATTCATCAATACT
1 CTATTCATCAATACT
29661040 TTTGCCGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.40
Consensus pattern (16 bp):
CTATTCATCAATACTG
Found at i:29662064 original size:28 final size:28
Alignment explanation
Indices: 29662032--29662100 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
29662022 GCGTAGATCA
29662032 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
29662060 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29662088 CGATA-TACCCCTA
1 CGAAATTACCCCTA
29662101 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:29668401 original size:20 final size:20
Alignment explanation
Indices: 29668376--29668413 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29668366 GTTTATTCGC
*
29668376 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
29668396 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
29668414 TTTGGATGTG
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:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:29670081 original size:27 final size:28
Alignment explanation
Indices: 29670035--29670102 Score: 113
Period size: 27 Copynumber: 2.5 Consensus size: 28
29670025 GCGTAGATCA
29670035 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
29670063 CGAAATTA-CCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
29670090 CGATA-TACCCCTA
1 CGAAATTACCCCTA
29670103 GGGTTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
26 2 0.05
27 28 0.74
28 8 0.21
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:29673312 original size:79 final size:77
Alignment explanation
Indices: 29673219--29673391 Score: 229
Period size: 79 Copynumber: 2.2 Consensus size: 77
29673209 GTTCAAAACA
* * * **
29673219 CCTTCGGACATAGCCCGGTTATGGTAACCCGCACAAATGCCTTCGGGACTTAACCCGGATATCAC
1 CCTTCGGGCTTAGCCCGGGTATCATAACCCGCACAAATGCCTTCGGG-CTTAACCCGGATATCAC
29673284 AACTCGCACAATTG
65 AACTCGCAC-ATTG
* * * * *
29673298 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCATA
1 CCTTCGGGCTTAGCCCGGGTATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCACA
*
29673363 GCTCGCACATTG
66 ACTCGCACATTG
29673375 CCTTCGGGCTTAGCCCG
1 CCTTCGGGCTTAGCCCG
29673392 ATATCACTCG
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
77 21 0.25
78 23 0.28
79 39 0.47
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (77 bp):
CCTTCGGGCTTAGCCCGGGTATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCACA
ACTCGCACATTG
Found at i:29673384 original size:38 final size:39
Alignment explanation
Indices: 29673248--29673397 Score: 232
Period size: 39 Copynumber: 3.9 Consensus size: 39
29673238 TATGGTAACC
* * * *
29673248 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
29673288 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
29673327 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
29673366 CGCAC-ATTGCCTTCGGGCTTAGCCC-GATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
29673398 CTCGAACATT
Statistics
Matches: 104, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
37 7 0.07
38 20 0.19
39 60 0.58
40 17 0.16
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:29680696 original size:40 final size:39
Alignment explanation
Indices: 29680652--29680833 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
29680642 GTTCAAAACA
* * ** * *
29680652 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
29680692 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
29680732 CCTTCGGGCTTAGCCCGGGTATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
29680771 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
29680810 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
29680834 CTCGAACATT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 89 0.69
40 40 0.31
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:29680763 original size:39 final size:39
Alignment explanation
Indices: 29680682--29680833 Score: 250
Period size: 39 Copynumber: 3.9 Consensus size: 39
29680672 TATGGTAACC
* * * *
29680682 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAGCT
*
29680722 CGCACAATTGCCTTCGGGCTTAGCCCGGGTATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
29680761 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
29680800 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
29680834 CTCGAACATT
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
Found at i:29687498 original size:49 final size:49
Alignment explanation
Indices: 29687421--29687526 Score: 185
Period size: 49 Copynumber: 2.2 Consensus size: 49
29687411 AGGCCATTTT
* *
29687421 TGGGCTATGTGGGCCATACAAGAGTGTGGACCTACATGGGCCTACAATA
1 TGGGCTATGTGGGCCATACAAGAGTGTGGACCCACATGGGCCCACAATA
*
29687470 TGGGTTATGTGGGCCATACAAGAGTGTGGACCCACATGGGCCCACAATA
1 TGGGCTATGTGGGCCATACAAGAGTGTGGACCCACATGGGCCCACAATA
29687519 TGGGCTAT
1 TGGGCTAT
29687527 AGGCCCATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (49 bp):
TGGGCTATGTGGGCCATACAAGAGTGTGGACCCACATGGGCCCACAATA
Found at i:29698145 original size:46 final size:44
Alignment explanation
Indices: 29698086--29698200 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
29698076 ACAGGACAGA
* *
29698086 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
29698132 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
29698176 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
29698201 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:29698181 original size:44 final size:45
Alignment explanation
Indices: 29698086--29698219 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
29698076 ACAGGACAGA
* *
29698086 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
29698132 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
29698176 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29698220 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:29704281 original size:46 final size:44
Alignment explanation
Indices: 29704222--29704336 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
29704212 ACAGGACAGA
* *
29704222 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
29704268 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
29704312 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
29704337 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:29704317 original size:44 final size:45
Alignment explanation
Indices: 29704222--29704355 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
29704212 ACAGGACAGA
* *
29704222 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
29704268 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
29704312 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29704356 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:29729634 original size:43 final size:43
Alignment explanation
Indices: 29729568--29729724 Score: 185
Period size: 43 Copynumber: 3.7 Consensus size: 43
29729558 AGCTCGTATA
*
29729568 ATGCCGACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
* * **
29729611 ATGCC-ACTGTCCCAAACAGGGTCTTACATAAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGACATGGTCTTACATGTAATCAAATATCG
* * *
29729653 ATGCCAACGTCCTAGACATGGTCTTACACGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGT-AATCA-AATATCG
*
29729697 ATGCCAACGTCCCAGGCATGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
29729725 CGATAACACA
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
42 25 0.26
43 42 0.44
44 29 0.30
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
Found at i:29756589 original size:29 final size:29
Alignment explanation
Indices: 29756495--29756589 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
29756485 TACTCGATCA
**
29756495 CGCACACTTAGTGCCATGTGATTT-AAGC-
1 CGCACACTTAGTGCCAT-ACATTTCAAGCT
* * * * *
29756523 CTGCACACATAGTGCCATATAGTCCAAACT
1 C-GCACACTTAGTGCCATACATTTCAAGCT
29756553 CGCACACTTAGTGCCATACATTTCAAGCT
1 CGCACACTTAGTGCCATACATTTCAAGCT
29756582 CGCACACT
1 CGCACACT
29756590 CAGTTCCAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
28 3 0.06
29 49 0.92
30 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACATTTCAAGCT
Done.