Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 21 of 24
Found at i:3178340 original size:19 final size:19
Alignment explanation
Indices: 3178316--3178439 Score: 98
Period size: 19 Copynumber: 6.6 Consensus size: 19
3178306 GCGATACATG
3178316 GTATCGATACAACACTTAT
1 GTATCGATACAACACTTAT
3178335 GTATCGAT---ACA--T-T
1 GTATCGATACAACACTTAT
* *
3178348 GTATCGATAAAACATTTAT
1 GTATCGATACAACACTTAT
* ** *
3178367 GTATTGATACAGTTACTATTT
1 GTATCGATACA-ACACT-TAT
3178388 GTATCGATACAACACTTAT
1 GTATCGATACAACACTTAT
* *
3178407 GTATCGATACAATTACTATTT
1 GTATCGATACAA-CACT-TAT
3178428 GTATCGATACAA
1 GTATCGATACAA
3178440 ATTGTTGAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
13 9 0.11
14 1 0.01
16 6 0.07
18 1 0.01
19 32 0.39
20 8 0.10
21 26 0.31
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
GTATCGATACAACACTTAT
Found at i:3178352 original size:32 final size:32
Alignment explanation
Indices: 3178307--3178417 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 32
3178297 AGCTTCGTAG
*
3178307 CGATACATGGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
3178339 CGATACATTGTATCGATAAAACATTTATGTATTGAT
1 CGATACATTGTATCGATACAACACTTATG---T-AT
*
3178375 ACAGTTACTATTTGTATCGATACAACACTTATGTAT
1 -C-GATAC-A-TTGTATCGATACAACACTTATGTAT
3178411 CGATACA
1 CGATACA
3178418 ATTACTATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
32 26 0.41
33 1 0.02
34 4 0.06
35 2 0.03
36 4 0.06
37 2 0.03
38 4 0.06
39 1 0.02
40 20 0.31
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:3178407 original size:40 final size:40
Alignment explanation
Indices: 3178346--3178439 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
3178336 TATCGATACA
* * * *
3178346 TTGTATCGATAAAACATTTATGTATTGATACAGTTACTAT
1 TTGTATCGATACAACACTTATGTATCGATACAATTACTAT
3178386 TTGTATCGATACAACACTTATGTATCGATACAATTACTAT
1 TTGTATCGATACAACACTTATGTATCGATACAATTACTAT
3178426 TTGTATCGATACAA
1 TTGTATCGATACAA
3178440 ATTGTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (40 bp):
TTGTATCGATACAACACTTATGTATCGATACAATTACTAT
Found at i:3178439 original size:21 final size:21
Alignment explanation
Indices: 3178366--3178439 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
3178356 AAAACATTTA
* *
3178366 TGTATTGATACAGTTACTATT
1 TGTATCGATACAATTACTATT
* *
3178387 TGTATCGATACAA-CACT-TA
1 TGTATCGATACAATTACTATT
3178406 TGTATCGATACAATTACTATT
1 TGTATCGATACAATTACTATT
3178427 TGTATCGATACAA
1 TGTATCGATACAA
3178440 ATTGTTGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 14 0.31
20 6 0.13
21 25 0.56
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATCGATACAATTACTATT
Found at i:3185125 original size:101 final size:99
Alignment explanation
Indices: 3184951--3185340 Score: 401
Period size: 101 Copynumber: 3.9 Consensus size: 99
3184941 AGATGCGAAG
* * * * * * * *
3184951 AATGACAATGTGCTGATTCATGGCCAGCGACATTAGATTTGAAGAAGAA--TGCCAATGTGCTGA
1 AATGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAAGGTGCCAATATGCTGA
** * * *
3185014 GACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAA
66 TTCAAGGCCAGCGATATTGGGCTTA--AATGATGAA
* * *
3185050 AATGCCAATATGCTGATTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGCCAATGTGCTGA
1 AATGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAAGGTGCCAATATGCTGA
* **
3185115 TTCAAGGCCAGCGATAGTGGTTTTAAAGATGATGAA
66 TTCAAGGCCAGCGATATTGGGCTT-AA-ATGATGAA
*** * *
3185151 GGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACGAAGGTACCAATATGC
1 AATGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGAT---GAAGGTGCCAATATGC
*
3185216 TGATTCAAGGCCAGCGATATTGGACTTAAA-GATGAA
63 TGATTCAAGGCCAGCGATATTGGGCTTAAATGATGAA
** * * * * *
3185252 GGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGGTGCCAATATGATGA
1 AATGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAAGGTGCCAATATGCTGA
3185316 TTCAAGGCCAGCGATATTGGGCTTA
66 TTCAAGGCCAGCGATATTGGGCTTA
3185341 TGCCAATGTA
Statistics
Matches: 249, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
97 40 0.16
99 40 0.16
100 1 0.00
101 126 0.51
102 2 0.01
103 2 0.01
104 38 0.15
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (99 bp):
AATGCCAATATGCTGATTCAAGGCCAACGACATTAGACTTAAAGATGAAGGTGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGGCTTAAATGATGAA
Found at i:3185171 original size:52 final size:49
Alignment explanation
Indices: 3185052--3185607 Score: 408
Period size: 49 Copynumber: 11.9 Consensus size: 49
3185042 ATGTTAAAAA
**
3185052 TGCCAATATGCTGATTCAAGGCCAACGATATCAGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * **
3185101 TGCCAATGTGCTGATTCAAGGCCAGCGATAGTGGTTTTAAAGATGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT-AA-A-GATGAAGG
* *
3185153 CGCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT---GAAGG
* *
3185205 TACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * *
3185254 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * *
3185302 TGCCAATATGATGATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * * * * *
3185341 TGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* *
3185389 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * * * * *
3185428 TGCCAA-AGTGTTGATTCAAGGCCAGCGACATTGGTCTGAGAGA-CAAGG
1 TGCCAATA-TGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* *
3185476 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T--A--
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
* * * *
3185515 TGCCAATGTGCTGATTCAAGGCC-ACTGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAAC-GATATTGGACTTAAAGATGAAGG
* *
3185564 TGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA-AAGA
3185608 AGACGCCACC
Statistics
Matches: 408, Mismatches: 55, Indels: 87
0.74 0.10 0.16
Matches are distributed among these distances:
38 2 0.00
39 92 0.23
40 2 0.00
41 3 0.01
45 1 0.00
46 2 0.00
47 3 0.01
48 98 0.24
49 109 0.27
50 9 0.02
51 3 0.01
52 84 0.21
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
Found at i:3185183 original size:153 final size:149
Alignment explanation
Indices: 3185001--3185340 Score: 421
Period size: 153 Copynumber: 2.3 Consensus size: 149
3184991 GAAGAAGAAT
* ** * ** *
3185001 GCCAATGTGCTGAGACAAGGCCAGCGACATTGGGCTT-AGGAATGTTAAAAATGCCAATATGCTG
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAG-ATGACAAAAATACCAATATGCTG
* *
3185065 ATTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGAT
65 ATTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGAC
* *
3185130 AGTGGTTTTAAAGATGATGAAGGC
130 AGTGGTCTT-AA-A-GA-CAAGGC
* * * **
3185154 GCCAATATGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGA
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGACAAAAATACCAATATGCTGA
* **
3185219 TTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACA
66 TTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACA
* *
3185284 TTGGTCTTAAAGACAAGGT
131 GTGGTCTTAAAGACAAGGC
* *
3185303 GCCAATATGATGATTCAAGGCCAGCGATATTGGGCTTA
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA
3185341 TGCCAATGTA
Statistics
Matches: 161, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
149 38 0.24
150 2 0.01
151 1 0.01
152 2 0.01
153 116 0.72
154 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (149 bp):
GCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGACAAAAATACCAATATGCTGA
TTCAAGGCCAACGATATCAGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAACGACA
GTGGTCTTAAAGACAAGGC
Found at i:3185356 original size:39 final size:39
Alignment explanation
Indices: 3185302--3185538 Score: 204
Period size: 39 Copynumber: 5.6 Consensus size: 39
3185292 AAAGACAAGG
* *
3185302 TGCCAATATGATGATTCAAGGCCAGCGATATTGGGCTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
* * *
3185341 TGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT-------A
*
3185387 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 --TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
* * * * *
3185428 TGCCAAAGTGTTGATTCAAGGCCAGCGACATTGGTCTGAGAGACAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCT-------TA
*
3185474 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 --TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
3185515 TGCCAATGTGCTGATTCAAGGCCA
1 TGCCAATGTGCTGATTCAAGGCCA
3185539 CTGACATTGG
Statistics
Matches: 158, Mismatches: 22, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
39 88 0.56
41 2 0.01
46 2 0.01
48 66 0.42
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (39 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
Found at i:3185404 original size:87 final size:87
Alignment explanation
Indices: 3185254--3185602 Score: 556
Period size: 87 Copynumber: 4.0 Consensus size: 87
3185244 AAGATGAAGG
* *
3185254 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGATGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
3185319 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
3185341 TGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
3185406 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * * *
3185428 TGCCAAAGTGTTGATTCAAGGCCAGCGACATTGGTCTGAGAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
3185493 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
*
3185515 TGCCAATGTGCTGATTCAAGGCCA-CTGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGC-GACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
* * * *
3185579 TCAAGACCAACAATATTGGACTTA
64 TCAAGGCCAGCGATATTGGGCTTA
3185603 GAAGAAGACG
Statistics
Matches: 243, Mismatches: 17, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
86 1 0.00
87 203 0.84
88 39 0.16
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:3185548 original size:39 final size:39
Alignment explanation
Indices: 3185476--3185553 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3185466 AGAGACAAGG
*
3185476 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA
* *
3185515 TGCCAATGTGCTGATTCAAGGCCA-CTGACATTGGTCTTA
1 TGCCAATATGCTGATTCAAGGCCAGC-GACATTGGGCTTA
3185554 AAGATAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA
Found at i:3185690 original size:28 final size:30
Alignment explanation
Indices: 3185624--3185718 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 30
3185614 CACCAACTTG
* ** *
3185624 TGTGGGCTTTTGAAAGGGTTG-CACCAACG
1 TGTGGGCTTTTGAAAGGGGTGCCACTGACT
* * * *
3185653 TATGTGCTTTTG-AA-GGTTGCCATTGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACTGACT
3185681 TGTGGGC-TTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACTGACT
3185710 TGTGGGCTT
1 TGTGGGCTT
3185719 AAAAGGAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
27 9 0.17
28 13 0.25
29 29 0.56
30 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.34, T:0.34
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAGGGGTGCCACTGACT
Found at i:3185763 original size:27 final size:27
Alignment explanation
Indices: 3185732--3185872 Score: 111
Period size: 27 Copynumber: 5.0 Consensus size: 27
3185722 AGGAAAAAAA
*
3185732 TGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
3185759 TGCCACAGAGTTATGGATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
** *
3185786 TGCCACTAAGTTGTGGACTTAAAGGGAAAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-------G
* *
3185820 TGTCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
3185847 TGCCCCAGAGTCGTGGACTTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG
3185873 AACAAGGAGT
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
27 66 0.75
34 22 0.25
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:3185934 original size:28 final size:28
Alignment explanation
Indices: 3185876--3185932 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
3185866 TAAAAGGAAC
* ** *
3185876 AAGGAGTGCCACGGAGTTGTGGGCTTAA
1 AAGGAGTGCCACGAAGTCATGGACTTAA
3185904 AAGG-GTGCCACGAAGTCATGGACTTAA
1 AAGGAGTGCCACGAAGTCATGGACTTAA
3185931 AA
1 AA
3185933 AGAAAAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19
Consensus pattern (28 bp):
AAGGAGTGCCACGAAGTCATGGACTTAA
Found at i:3185979 original size:33 final size:33
Alignment explanation
Indices: 3185902--3186427 Score: 499
Period size: 33 Copynumber: 16.8 Consensus size: 33
3185892 TTGTGGGCTT
* ** *
3185902 AAAAGGGTGCCACGAAGTCATGGACTTAAAA-AG
1 AAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGG
3185935 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
3185968 ATAAGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186001 AAAAGATGCCACGGAGTTGTGGACTTAAAA--G
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
3186032 ----GGTGCGACTGAGTTGTGGACTT-AAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186060 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA--G
1 AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGG
**
3186092 ----GGTGCCACGGAGTCATGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186121 ACAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
3186154 AAAAGATGCCATGGAGTTGTGGACTTAAAA--G
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*** *
3186185 ----GGTGCCATTAAGTTATGGACTT-AAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186213 AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA--G
1 -AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186246 ----GGTGCCACGGAGTCGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186275 ACAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
3186308 ACAAGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
* *
3186341 AAAAGATGCCACGGACTTGTGGACTTAAAA--G
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
*
3186372 ----GGTGCCACTGAGTTGTGGACTT-AAAGGG
1 AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
**
3186400 AAAAAGAGTGCCACGGAGTCATGGACTT
1 -AAAAG-GTGCCACGGAGTTGTGGACTT
3186428 TGAAGAAAAA
Statistics
Matches: 409, Mismatches: 46, Indels: 75
0.77 0.09 0.14
Matches are distributed among these distances:
26 9 0.02
27 101 0.25
28 5 0.01
29 2 0.00
31 3 0.01
32 25 0.06
33 224 0.55
34 37 0.09
35 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.20
Consensus pattern (33 bp):
AAAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:3186046 original size:60 final size:61
Alignment explanation
Indices: 3185752--3186153 Score: 462
Period size: 60 Copynumber: 6.6 Consensus size: 61
3185742 TTGTGGACTT
* * * * *
3185752 AAAAGGGTGCCACAGAGTTATGGATTTAAAAGGGTGCCACTA-AGTTGTGGACTT-AAAGGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC-AGAGTCGTGGACTTAAAAGGG
* * * *
3185812 AAAAAAAGTGTCACGGAGTTGTGGGCTTAAAAGGGTGCCCCAGAGTCGTGGACTTAAAA-GG
1 -AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTCGTGGACTTAAAAGGG
* * *
3185873 AACAAGGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCAC-GAAGTCATGGACTTAAAA-AG
1 AA-AA-GAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAG-AGTCGTGGACTTAAAAGGG
*
3185935 AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGGATAAGGTGCCACAGAGTTGTGGACTTAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAA--G----GGTGCCACAGAGTCGTGGACTTAAAAG
3185999 GG
60 GG
* * *
3186001 AAAAGA-TGCCACGGAGTTGTGGACTTAAAAGGGTGCGACTGAGTTGTGGACTT-AAAGGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTCGTGGACTTAAAAGGG
* * *
3186060 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTCATGGACTTAAAAGGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTCGTGGACTTAAAAGGG
*
3186121 ACAAG-GTGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
3186154 AAAAGATGCC
Statistics
Matches: 298, Mismatches: 27, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
59 36 0.12
60 93 0.31
61 61 0.20
62 54 0.18
64 1 0.00
65 22 0.07
66 31 0.10
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (61 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTCGTGGACTTAAAAGGG
Found at i:3186189 original size:60 final size:60
Alignment explanation
Indices: 3186125--3186427 Score: 376
Period size: 60 Copynumber: 4.9 Consensus size: 60
3186115 AAAGGGACAA
*
3186125 GGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGATGCCATGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGATGCCACGGAGTTGTGGACTTAAAAG
*** * *
3186185 GGTGCCATTAAGTTATGGACTT-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGG-AAAAGA-TGCCACGGAGTTGTGGACTTAAAAG
* * *
3186246 GGTGCCACGGAGTCGTGGACTTAAAAGGGACAAGGTGCCACGGAGTTGTGGACTTAAAAGGG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGATGCCACGGAGTTGTGGACTTAAAA--G
* *
3186308 ACAAGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAGATGCCACGGACTTGTGGACTTAAAAG
1 ----GGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGATGCCACGGAGTTGTGGACTTAAAAG
* **
3186372 GGTGCCACTGAGTTGTGGACTT-AAAGGGAAAAAGAGTGCCACGGAGTCATGGACTT
1 GGTGCCACGGAGTTGTGGACTTAAAAGGG-AAAAGA-TGCCACGGAGTTGTGGACTT
3186428 TGAAGAAAAA
Statistics
Matches: 209, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
59 12 0.06
60 74 0.35
61 61 0.29
62 7 0.03
64 1 0.00
66 54 0.26
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.20
Consensus pattern (60 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAGATGCCACGGAGTTGTGGACTTAAAAG
Found at i:3186462 original size:34 final size:34
Alignment explanation
Indices: 3186374--3186524 Score: 179
Period size: 34 Copynumber: 4.6 Consensus size: 34
3186364 CTTAAAAGGG
* * **
3186374 TGCCACTGAGTTGTGGAC-TTAAAGGGAAAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAAGA
* *
3186407 GTGCCACGGAGTCATGGACTTTGAAGAAAAAAAGA
1 -TGCCACTGAGTCGTGGACTTTGAAGAAAAAAAGA
*
3186442 TGCCACTGAGTCGTGGACTTTG-A-AAAAAATGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAAGA
3186474 TGCCACTGAGTCGTGGACTTTGAAG---AAAAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAAAAGA
*
3186505 TGCCACTAAGTCGTGGACTT
1 TGCCACTGAGTCGTGGACTT
3186525 AGAAAAGAGA
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
31 24 0.23
32 30 0.29
33 2 0.02
34 35 0.34
35 12 0.12
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (34 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAAAAGA
Found at i:3187216 original size:17 final size:20
Alignment explanation
Indices: 3187171--3187344 Score: 93
Period size: 20 Copynumber: 8.8 Consensus size: 20
3187161 TTTTCACAAT
3187171 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
3187191 TTATATCGATACATTG-T-A
1 TTGTATCGATACATTGTTCA
3187209 -TGTATCGATACATTCTGGGTTTACCCA
1 TTGTATCGATACA-T-T--G-TT---CA
* *
3187236 GATGTATCGATGCATT-TTGCA
1 -TTGTATCGATACATTGTT-CA
* *
3187257 TTGTATCGATACATTGCTCC
1 TTGTATCGATACATTGTTCA
3187277 TTGTATCGAT--A-----CA
1 TTGTATCGATACATTGTTCA
*
3187290 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
*
3187310 TTGTATCAATACATT-TTACA
1 TTGTATCGATACATTGTT-CA
*
3187330 ATGTATCGATACATT
1 TTGTATCGATACATT
3187345 CAGGCATTTT
Statistics
Matches: 120, Mismatches: 13, Indels: 42
0.69 0.07 0.24
Matches are distributed among these distances:
13 11 0.09
15 1 0.01
17 11 0.09
18 3 0.03
19 3 0.03
20 70 0.58
21 4 0.03
23 3 0.03
27 2 0.02
28 1 0.01
29 11 0.09
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:3187297 original size:33 final size:33
Alignment explanation
Indices: 3187255--3187324 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
3187245 ATGCATTTTG
* *
3187255 CATTGTATCGATACATTGCTCCTTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
3187288 CATTGTATCGATACATTGCTCATTGTATCAATA
1 CATTGTATCGATACATTGCTCATTGTATCAATA
3187321 CATT
1 CATT
3187325 TTACAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCAATA
Found at i:3187324 original size:13 final size:13
Alignment explanation
Indices: 3187277--3187305 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3187267 ACATTGCTCC
3187277 TTGTATCGATACA
1 TTGTATCGATACA
3187290 TTGTATCGATACA
1 TTGTATCGATACA
3187303 TTG
1 TTG
3187306 CTCATTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3189779 original size:28 final size:28
Alignment explanation
Indices: 3189747--3189823 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
3189737 ATTTTTCACA
* *
3189747 ATCGAGGGTACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
3189775 ATCGAGGATACTCCAACCCCGTTATTT-
1 ATCGAGGATACTCCAACCCCGTTATTTC
*
3189802 -TCGAGGAGATACTCTAACCCCG
1 ATCGA-G-GATACTCCAACCCCG
3189824 ATTTTATATC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 39 0.89
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:3189914 original size:51 final size:52
Alignment explanation
Indices: 3189809--3189925 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 52
3189799 TTTTCGAGGA
*
3189809 GATAC-TCTAACCCCGATTTTATATCTAAAAATATTGATTTCTCACAATCAGG
1 GATACTTC-AACCCCGACTTTATATCTAAAAATATTGATTTCTCACAATCAGG
* * * *
3189861 GATACTTCAACCCCGGCTTTATTTCT-AAAATATTGATTTCTCATAATCGGG
1 GATACTTCAACCCCGACTTTATATCTAAAAATATTGATTTCTCACAATCAGG
*
3189912 GATACTCCAACCCC
1 GATACTTCAACCCC
3189926 ATTATTTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
51 36 0.62
52 20 0.34
53 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (52 bp):
GATACTTCAACCCCGACTTTATATCTAAAAATATTGATTTCTCACAATCAGG
Found at i:3190111 original size:130 final size:130
Alignment explanation
Indices: 3189775--3190112 Score: 362
Period size: 130 Copynumber: 2.6 Consensus size: 130
3189765 TCGTTATTTC
* * * *
3189775 ATCGAGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCTAACCCCGATTTTATATCTAAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTC-AAAAA
* * * ** *
3189840 TATTGATTTCTCACAATCAGGGATACTTCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCAT
65 TATTAATTTCTCACAATCAGGGACACTTCAACCCCGGCCTTATTTCTAAAATATCAATTTCTCAC
3189905 A
130 A
* * ***
3189906 ATCGGGGATACTCCAACCCCATTATTTTC-ACGGGGATACTCCAATCCCGATTTTATTTTGGAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCCCGATTTTATTTCAAAAA
* * * ** *
3189970 CATCTATTTTCT-ATAATC-GAGGACACTTCAACCCTTGCCTTATTTCT-AAATCATCAATTTTT
65 TAT-TAATTTCTCACAATCAG-GGACACTTCAACCCCGGCCTTATTTCTAAAAT-ATCAATTTCT
3190032 CACA
127 CACA
* * *
3190036 ATTGGGGATTCTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG-TTATTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATT-TTATTTCAAAAA
3190100 TATTAAATTTCTC
65 TATT-AATTTCTC
3190113 GTCGGGAGAT
Statistics
Matches: 169, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
129 8 0.05
130 104 0.62
131 57 0.34
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCAAAAAT
ATTAATTTCTCACAATCAGGGACACTTCAACCCCGGCCTTATTTCTAAAATATCAATTTCTCACA
Found at i:3191581 original size:1 final size:1
Alignment explanation
Indices: 3191575--3191611 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
3191565 AAAGTGTTTG
**
3191575 AAAAAAAAAAAAAAAAATGAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3191612 TTTAAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:3191597 original size:19 final size:19
Alignment explanation
Indices: 3191573--3191610 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3191563 ATAAAGTGTT
3191573 TGAAAAAAAAAAAAAAAAA
1 TGAAAAAAAAAAAAAAAAA
3191592 TGAAAAAAAAAAAAAAAAA
1 TGAAAAAAAAAAAAAAAAA
3191611 ATTTAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.05, T:0.05
Consensus pattern (19 bp):
TGAAAAAAAAAAAAAAAAA
Found at i:3191600 original size:20 final size:20
Alignment explanation
Indices: 3191575--3191612 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3191565 AAAGTGTTTG
3191575 AAAAAAAAAAAAAAAAATGA
1 AAAAAAAAAAAAAAAAATGA
3191595 AAAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAT
3191613 TTAAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAATGA
Found at i:3191640 original size:21 final size:21
Alignment explanation
Indices: 3191616--3191672 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3191606 AAAAAATTTA
3191616 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3191637 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3191658 AATGTATCGATACAT
1 AATGTATCGATACAT
3191673 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3191752 original size:19 final size:19
Alignment explanation
Indices: 3191728--3191795 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3191718 AATTCAACAA
3191728 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3191747 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3191762 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3191779 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3191796 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3191767 original size:13 final size:13
Alignment explanation
Indices: 3191749--3191773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3191739 ACATAAGTTT
3191749 TGTATCGATACAA
1 TGTATCGATACAA
3191762 TGTATCGATACA
1 TGTATCGATACA
3191774 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3191771 original size:32 final size:32
Alignment explanation
Indices: 3191730--3191792 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3191720 TTCAACAATT
*
3191730 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3191762 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3191793 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3194529 original size:15 final size:15
Alignment explanation
Indices: 3194509--3194573 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
3194499 CCTTCTCTTC
3194509 AAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
3194524 AAAAAAAAAACAAA-
1 AAAAAAAAAAAAAAG
* *
3194538 AAAAACAAAACAAAG
1 AAAAAAAAAAAAAAG
* * *
3194553 AAAAAGAGAGAAAAG
1 AAAAAAAAAAAAAAG
3194568 AAAAAA
1 AAAAAA
3194574 CCTACTTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
14 13 0.31
15 29 0.69
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:3194573 original size:1 final size:1
Alignment explanation
Indices: 3194509--3194557 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
3194499 CCTTCTCTTC
* * * * *
3194509 AAAAAAAAAAAAAAGAAAAAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3194558 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.06, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:3195624 original size:55 final size:55
Alignment explanation
Indices: 3195539--3196326 Score: 1170
Period size: 55 Copynumber: 14.3 Consensus size: 55
3195529 TCCGCTTTTT
*
3195539 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3195594 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
3195649 AGTCCTCAAAGAGCAGGACACCTTTTAAATCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3195704 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3195759 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3195814 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
3195869 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-C
3195924 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3195979 AGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3196034 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
3196089 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
3196144 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
3196199 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
3196254 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
3196309 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
3196327 TACAATTTAT
Statistics
Matches: 687, Mismatches: 31, Indels: 30
0.92 0.04 0.04
Matches are distributed among these distances:
53 2 0.00
54 15 0.02
55 655 0.95
56 13 0.02
57 2 0.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:3196942 original size:18 final size:18
Alignment explanation
Indices: 3196919--3196956 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3196909 GATAAAGTGT
3196919 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
3196937 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
3196955 TT
1 TT
3196957 TAAATGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (18 bp):
TTGAAAAAAAAAAAAAAA
Found at i:3196983 original size:21 final size:21
Alignment explanation
Indices: 3196959--3197015 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3196949 AAAAAATTTA
3196959 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3196980 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3197001 AATGTATCGATACAT
1 AATGTATCGATACAT
3197016 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3197095 original size:19 final size:19
Alignment explanation
Indices: 3197071--3197138 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3197061 AATTCAACAA
3197071 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3197090 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3197105 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3197122 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3197139 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3197110 original size:13 final size:13
Alignment explanation
Indices: 3197092--3197116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3197082 ACATAAGTTT
3197092 TGTATCGATACAA
1 TGTATCGATACAA
3197105 TGTATCGATACA
1 TGTATCGATACA
3197117 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3197114 original size:32 final size:32
Alignment explanation
Indices: 3197073--3197135 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3197063 TTCAACAATT
*
3197073 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3197105 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3197136 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3197196 original size:13 final size:13
Alignment explanation
Indices: 3197178--3197203 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3197168 CATTTTTCTG
3197178 TGTATCGATACAT
1 TGTATCGATACAT
3197191 TGTATCGATACAT
1 TGTATCGATACAT
3197204 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3197200 original size:33 final size:33
Alignment explanation
Indices: 3197158--3197224 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3197148 GCCAAGGAAA
***
3197158 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3197191 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3197224 T
1 T
3197225 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3199738 original size:28 final size:27
Alignment explanation
Indices: 3199671--3199743 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3199661 CTTCACAATC
* *
3199671 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3199698 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3199726 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3199744 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3199788 original size:51 final size:51
Alignment explanation
Indices: 3199726--3199896 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
3199716 TTATTTCTGA
* * *
3199726 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3199777 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * * *
3199830 GGGGATACTCCAATTCCGATTTTATTTCTAAAAATACCAATTTTTTACAATC
1 GGGGATACTCCAACCCCGATTTTATTT-TCAAAATACCAATTTTTCATAATC
*
3199882 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3199897 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 36 0.38
52 18 0.19
53 30 0.31
54 12 0.12
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3199915 original size:28 final size:28
Alignment explanation
Indices: 3199879--3199960 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3199869 ATTTTTTACA
*
3199879 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3199907 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3199935 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3199961 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3201586 original size:22 final size:22
Alignment explanation
Indices: 3201556--3201618 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 22
3201546 ACTCTCTCTC
* *
3201556 TCTCTTTTTGTGTGTGTTTTTT
1 TCTCTTTTTTTATGTGTTTTTT
*
3201578 TGT-TTTTTTTATG-GTTTTTT
1 TCTCTTTTTTTATGTGTTTTTT
*
3201598 TCTCTTTTTTTTTGTGTTTTT
1 TCTCTTTTTTTATGTGTTTTT
3201619 ACTTGTGACT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.26
21 17 0.50
22 8 0.24
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (22 bp):
TCTCTTTTTTTATGTGTTTTTT
Found at i:3205270 original size:13 final size:13
Alignment explanation
Indices: 3205252--3205276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3205242 CATAAAGTGT
3205252 TGTATCGATACAA
1 TGTATCGATACAA
3205265 TGTATCGATACA
1 TGTATCGATACA
3205277 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3205274 original size:33 final size:33
Alignment explanation
Indices: 3205232--3205298 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3205222 TTCAACGATT
3205232 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
3205265 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3205298 T
1 T
3205299 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3205357 original size:13 final size:13
Alignment explanation
Indices: 3205339--3205363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3205329 ATTACTCAAA
3205339 TGTATCGATACAT
1 TGTATCGATACAT
3205352 TGTATCGATACA
1 TGTATCGATACA
3205364 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3205428 original size:52 final size:52
Alignment explanation
Indices: 3205352--3205552 Score: 330
Period size: 52 Copynumber: 3.9 Consensus size: 52
3205342 ATCGATACAT
* **
3205352 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * * **
3205404 AGTATCAATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
3205456 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
3205508 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
3205553 TCATATTTCG
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 136 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:3212158 original size:20 final size:20
Alignment explanation
Indices: 3212133--3212238 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
3212123 ATTTGCCTGC
3212133 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
3212153 ATGTATCGATACATCTGGGTAAAATTCATA
1 ATGTATCGATACAT-T--G----A---ATA
** *
3212183 GATGTATCGATACAAAGATTA
1 -ATGTATCGATACATTGAATA
3212204 ATGTATCGATACATT-AAGTA
1 ATGTATCGATACATTGAA-TA
3212224 ATGTATCGATACATT
1 ATGTATCGATACATT
3212239 TTCTTGGCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 24
0.69 0.06 0.24
Matches are distributed among these distances:
19 1 0.01
20 44 0.65
21 3 0.04
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
30 3 0.04
31 13 0.19
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:3212292 original size:19 final size:19
Alignment explanation
Indices: 3212268--3212331 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
3212258 AACGATACAT
3212268 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3212287 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
3212300 TGTATTGATACAACACTTA
1 TGTATCGATACAACACTTA
3212319 TGTATCGATACAA
1 TGTATCGATACAA
3212332 TTACTGTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.57
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:3212301 original size:32 final size:32
Alignment explanation
Indices: 3212255--3212330 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
3212245 GCAGTAGCTT
*
3212255 TGTAACGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
3212287 TGTATCGATACATTGTATTGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
3212319 TGTATCGATACA
1 TGTATCGATACA
3212331 ATTACTGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:3218352 original size:21 final size:21
Alignment explanation
Indices: 3218328--3218403 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3218318 TCTACAAATT
3218328 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
* * *
3218349 TGTATCAATACATA-AGTGAA
1 TGTATCGATACAAACAGTAAA
* * *
3218369 TGTATCGATAGATAC-TTGAAA
1 TGTATCGATACAAACAGT-AAA
3218390 TGTATCGATACAAA
1 TGTATCGATACAAA
3218404 ACCACTCTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 18 0.41
21 26 0.59
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:3218451 original size:20 final size:21
Alignment explanation
Indices: 3218426--3218482 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
3218416 TCTAGAAAGG
3218426 AAATGTATCGATACAT-ATGT-
1 AAATGTATCGATACATGAT-TA
* * *
3218446 AAATGTGTCGATGCATGCTTA
1 AAATGTATCGATACATGATTA
3218467 AAATGTATCGATACAT
1 AAATGTATCGATACAT
3218483 TTATCATAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
AAATGTATCGATACATGATTA
Found at i:3227361 original size:2 final size:2
Alignment explanation
Indices: 3227354--3227388 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3227344 AGGCATTATC
3227354 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 T
3227389 TCTAAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3228197 original size:20 final size:21
Alignment explanation
Indices: 3228155--3228205 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
3228145 TTCAACAATT
3228155 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
3228176 TGTATCGATAC-ATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
3228196 TGTATCGATA
1 TGTATCGATA
3228206 TATGCATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:3228215 original size:20 final size:21
Alignment explanation
Indices: 3228155--3228228 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
3228145 TTCAACAATT
* *
3228155 TGTATCGATACAATAAG-GCAA
1 TGTATCGATA-TATAAGTGAAA
*
3228176 TGTATCGATACATAAGTG-AA
1 TGTATCGATATATAAGTGAAA
*
3228196 TGTATCGATATATGCA-TGAAA
1 TGTATCGATATAT-AAGTGAAA
*
3228217 TGTATCAATATA
1 TGTATCGATATA
3228229 GGACCATGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 21 0.46
21 25 0.54
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.31
Consensus pattern (21 bp):
TGTATCGATATATAAGTGAAA
Found at i:3233660 original size:20 final size:20
Alignment explanation
Indices: 3233635--3233689 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
3233625 GTTGGGCTCA
3233635 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
*
3233655 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
3233675 ATGTATCGATACAAT
1 ATGTATCGATACAAT
3233690 ATATCGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:3233808 original size:20 final size:20
Alignment explanation
Indices: 3233783--3233841 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
3233773 CGATACAATA
3233783 TATCGATACTAAGCAATATG
1 TATCGATACTAAGCAATATG
3233803 TATCG--A-T-A-CAAT-T-
1 TATCGATACTAAGCAATATG
3233816 TATCGATACTAAGCAATATG
1 TATCGATACTAAGCAATATG
3233836 TATCGA
1 TATCGA
3233842 GACATCTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 5 0.16
16 2 0.06
17 2 0.06
18 5 0.16
19 1 0.03
20 11 0.34
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (20 bp):
TATCGATACTAAGCAATATG
Found at i:3233812 original size:33 final size:33
Alignment explanation
Indices: 3233751--3233841 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
3233741 TTTCAAGGTG
* *
3233751 TATCGATACTAAG-AACATCTATCGATACAATA
1 TATCGATACTAAGCAATATGTATCGATACAATA
*
3233783 TATCGATACTAAGCAATATGTATCGATACAATT
1 TATCGATACTAAGCAATATGTATCGATACAATA
3233816 TATCGATACTAAGCAATATGTATCGA
1 TATCGATACTAAGCAATATGTATCGA
3233842 GACATCTGGG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 13 0.24
33 42 0.76
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (33 bp):
TATCGATACTAAGCAATATGTATCGATACAATA
Found at i:3234801 original size:12 final size:12
Alignment explanation
Indices: 3234786--3234817 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3234776 CTTAGCATAC
*
3234786 GACTACTCCTAT
1 GACTAATCCTAT
3234798 GACTAATCCTAT
1 GACTAATCCTAT
3234810 GACTAATC
1 GACTAATC
3234818 ATCACTCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.31
Consensus pattern (12 bp):
GACTAATCCTAT
Found at i:3242522 original size:20 final size:20
Alignment explanation
Indices: 3242497--3242551 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3242487 GTTGGGCTCA
3242497 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
* *
3242517 ATGTATCGATATAATTCATC
1 ATGTATCGATACAATTCACC
3242537 ATGTATCGATACAAT
1 ATGTATCGATACAAT
3242552 GTATCGATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:3242555 original size:13 final size:13
Alignment explanation
Indices: 3242537--3242563 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3242527 ATAATTCATC
3242537 ATGTATCGATACA
1 ATGTATCGATACA
3242550 ATGTATCGATACA
1 ATGTATCGATACA
3242563 A
1 A
3242564 AGTGAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3242652 original size:31 final size:32
Alignment explanation
Indices: 3242611--3242674 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
3242601 AATTTCAAGG
3242611 TGTATCGATACTAAG-AACATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
* *
3242642 TGTATTGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
3242674 T
1 T
3242675 ATGGGTGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTATCGATACTAAGCAACATGTATCGATACA
Found at i:3245385 original size:80 final size:78
Alignment explanation
Indices: 3245268--3245491 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 78
3245258 TAAAAAGGGG
* *
3245268 TACTCCAACCCTCGTTTTCACTTTTAAAA-CATCAAATTTTTCATCTCTAAGGATACTCCAGCCC
1 TACTCCAACCC-CGTTTT-ACTTCTAAAAGC-T-AAATTTTTCATCTCTAAGGATACTCCAACCC
3245332 CACCATCT-TCGAAG-GA
62 CACCATCTCT-GAAGTGA
* *
3245348 TACTCCAACCCCGTTTGTACTTCTAAAATGCTAAAATTTTCATCTCTAGGGATACTCCAACCCCA
1 TACTCCAACCCCGTTT-TACTTCTAAAA-GCTAAATTTTTCATCTCTAAGGATACTCCAACCCCA
*
3245413 CCATCTCTGAGGTGA
64 CCATCTCTGAAGTGA
* * *
3245428 TACCCCAACCCTGTTTTTACTTCCAAAACGCTAAATTTTTCATCTCT-AGGATACTCCAACCCCA
1 TACTCCAACCCCG-TTTTACTTCTAAAA-GCTAAATTTTTCATCTCTAAGGATACTCCAACCCCA
3245492 TTTTTTACTT
Statistics
Matches: 127, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
79 69 0.54
80 54 0.43
81 4 0.03
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (78 bp):
TACTCCAACCCCGTTTTACTTCTAAAAGCTAAATTTTTCATCTCTAAGGATACTCCAACCCCACC
ATCTCTGAAGTGA
Found at i:3248208 original size:12 final size:11
Alignment explanation
Indices: 3248191--3248242 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
3248181 TTATAAATAA
3248191 TAAAATATATAT
1 TAAAAT-TATAT
3248203 TAAAATTAT-T
1 TAAAATTATAT
*
3248213 TACTAAATAATAAT
1 TA--AAATTAT-AT
3248227 TAAAATTATAT
1 TAAAATTATAT
3248238 TAAAA
1 TAAAA
3248243 GTTAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.09
11 10 0.29
12 18 0.53
14 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAATTATAT
Found at i:3249378 original size:10 final size:10
Alignment explanation
Indices: 3249363--3249387 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3249353 AACGGACTGT
3249363 TTTTTTTTTG
1 TTTTTTTTTG
3249373 TTTTTTTTTG
1 TTTTTTTTTG
3249383 TTTTT
1 TTTTT
3249388 AAATTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:3251551 original size:3 final size:3
Alignment explanation
Indices: 3251497--3251536 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3251487 TTTTTCATTT
3251497 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3251537 GAAAGAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3252043 original size:9 final size:9
Alignment explanation
Indices: 3252029--3252078 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
3252019 TTTTTATATG
3252029 ATATAAATT
1 ATATAAATT
3252038 ATAT-AATAT
1 ATATAAAT-T
3252047 ATATAAA-T
1 ATATAAATT
*
3252055 ATA-AAGATA
1 ATATAA-ATT
3252064 ATATAAATT
1 ATATAAATT
3252073 ATATAA
1 ATATAA
3252079 TTGAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
7 2 0.06
8 8 0.24
9 20 0.59
10 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATATAAATT
Found at i:3254376 original size:20 final size:19
Alignment explanation
Indices: 3254334--3254404 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
3254324 GTAACTCAGA
* *
3254334 GTATCGATACATTTAAAGAT
1 GTATCGATACATTTATA-TT
3254354 GTATCGATACATTGTATATT
1 GTATCGATACATT-TATATT
*
3254374 GTATCGATATATTT-TCATGT
1 GTATCGATACATTTAT-AT-T
3254394 GTATCGATACA
1 GTATCGATACA
3254405 AATGAGAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 37 0.84
21 3 0.07
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (19 bp):
GTATCGATACATTTATATT
Found at i:3262665 original size:7 final size:7
Alignment explanation
Indices: 3262655--3262698 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
3262645 GCCACGTGTT
3262655 CAAGTGC
1 CAAGTGC
3262662 CAAGTGC
1 CAAGTGC
3262669 CAAGTGC
1 CAAGTGC
3262676 CAAGTGC
1 CAAGTGC
3262683 CAAGTGC
1 CAAGTGC
3262690 CAAGTGC
1 CAAGTGC
3262697 CA
1 CA
3262699 TATAATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.14
Consensus pattern (7 bp):
CAAGTGC
Found at i:3263265 original size:33 final size:33
Alignment explanation
Indices: 3263228--3263294 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3263218 TTCAACGATT
3263228 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3263261 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3263294 T
1 T
3263295 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3263266 original size:13 final size:13
Alignment explanation
Indices: 3263248--3263272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3263238 CATAAAATGT
3263248 TGTATCGATACAA
1 TGTATCGATACAA
3263261 TGTATCGATACA
1 TGTATCGATACA
3263273 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3263459 original size:52 final size:52
Alignment explanation
Indices: 3263368--3263491 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
3263358 GATTGATCTT
*
3263368 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3263419 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3263471 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
3263492 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3271556 original size:7 final size:7
Alignment explanation
Indices: 3271544--3271573 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3271534 TTTGCACCTG
3271544 CAAGTGC
1 CAAGTGC
3271551 CAAGTGC
1 CAAGTGC
3271558 CAAGTGC
1 CAAGTGC
3271565 CAAGTGC
1 CAAGTGC
3271572 CA
1 CA
3271574 TATAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.27, T:0.13
Consensus pattern (7 bp):
CAAGTGC
Found at i:3272264 original size:14 final size:14
Alignment explanation
Indices: 3272245--3272278 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3272235 TTTCAGTGAT
3272245 ACACATGCAGGTGC
1 ACACATGCAGGTGC
3272259 ACACATGCAGGTGC
1 ACACATGCAGGTGC
3272273 ACACAT
1 ACACAT
3272279 ACATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (14 bp):
ACACATGCAGGTGC
Found at i:3275041 original size:21 final size:21
Alignment explanation
Indices: 3274978--3275043 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
3274968 TTGATTATAA
* * *
3274978 TATATAAATTTATATATTATTAA
1 TATATAAAATTATA-AATATT-T
3275001 TATATAAAA-TATAAATATTT
1 TATATAAAATTATAAATATTT
*
3275021 TATATAAAATTATAAGTATTT
1 TATATAAAATTATAAATATTT
3275042 TA
1 TA
3275044 GTAAATATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.24
21 17 0.45
22 4 0.11
23 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TATATAAAATTATAAATATTT
Found at i:3275072 original size:18 final size:16
Alignment explanation
Indices: 3275049--3275082 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
3275039 TTTTAGTAAA
3275049 TATTTTTTAATAAAAATT
1 TATTTTTT--TAAAAATT
3275067 TATTTTTTTAAAAATT
1 TATTTTTTTAAAAATT
3275083 ATAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTTTTTAAAAATT
Found at i:3278461 original size:28 final size:29
Alignment explanation
Indices: 3278415--3278472 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
3278405 TAAAATAGTA
3278415 ATATTCAAATGATACATAAA-AAATGAAT
1 ATATTCAAATGATACATAAATAAATGAAT
*
3278443 ATATTCAAAT-ATTATATAAATTAAATGAAT
1 ATATTCAAATGA-TACATAAA-TAAATGAAT
3278473 TCTTATTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.04
28 17 0.65
30 8 0.31
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (29 bp):
ATATTCAAATGATACATAAATAAATGAAT
Found at i:3278646 original size:28 final size:27
Alignment explanation
Indices: 3278615--3278683 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
3278605 TAAATTTTTA
*
3278615 TGAAAAAAATATTTATTTTTTTAACGTT
1 TGAAAAAAATATTTA-TTTTTTAAAGTT
** *
3278643 TGAAAATATTTACTTATTTTTTAAAGTT
1 TGAAAA-AAATATTTATTTTTTAAAGTT
3278671 TGAAAAATAATAT
1 TGAAAAA-AATAT
3278684 ATTTACTTTC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 1 0.03
28 25 0.78
29 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (27 bp):
TGAAAAAAATATTTATTTTTTAAAGTT
Found at i:3278677 original size:29 final size:26
Alignment explanation
Indices: 3278619--3278679 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
3278609 TTTTTATGAA
*
3278619 AAAAATATTTATTTTTTTAACGTTTG
1 AAAAATATTTATTTTTTTAAAGTTTG
3278645 -AAAATATTTACTTATTTTTTAAAGTTTG
1 AAAAATATTTA--T-TTTTTTAAAGTTTG
3278673 AAAAATA
1 AAAAATA
3278680 ATATATTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 10 0.33
27 1 0.03
28 13 0.43
29 6 0.20
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (26 bp):
AAAAATATTTATTTTTTTAAAGTTTG
Found at i:3278794 original size:15 final size:16
Alignment explanation
Indices: 3278774--3278805 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3278764 ATTTTCTATC
3278774 ATTTTTTACTTA-AAA
1 ATTTTTTACTTACAAA
3278789 ATTTTTTACTTACAAA
1 ATTTTTTACTTACAAA
3278805 A
1 A
3278806 AAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTTACTTACAAA
Found at i:3280586 original size:13 final size:13
Alignment explanation
Indices: 3280568--3280593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3280558 AATTTTTTTG
3280568 TGTATCGATACAT
1 TGTATCGATACAT
3280581 TGTATCGATACAT
1 TGTATCGATACAT
3280594 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3280591 original size:34 final size:32
Alignment explanation
Indices: 3280547--3280611 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
3280537 TACAAGCCAA
*
3280547 TGTATAGATACAATTTTTTTGTGTATCGATACAT
1 TGTATAGATAC-A-TATTTTGTGTATCGATACAT
*
3280581 TGTATCGATACATATTTTGTGTATCGATACA
1 TGTATAGATACATATTTTGTGTATCGATACA
3280612 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 18 0.62
33 1 0.03
34 10 0.34
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (32 bp):
TGTATAGATACATATTTTGTGTATCGATACAT
Found at i:3280716 original size:20 final size:20
Alignment explanation
Indices: 3280663--3280718 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3280653 ACATCTTTTT
*
3280663 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
3280683 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
3280702 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
3280719 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:3283160 original size:13 final size:13
Alignment explanation
Indices: 3283142--3283179 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3283132 ATAATCCCCC
3283142 TGTATCGATACAG
1 TGTATCGATACAG
*
3283155 TGTATCGATACAT
1 TGTATCGATACAG
3283168 TGTATCGATACA
1 TGTATCGATACA
3283180 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3285290 original size:15 final size:15
Alignment explanation
Indices: 3285254--3285291 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3285244 TTCATCAATT
* *
3285254 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
3285269 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
3285284 TCATTTTG
1 TCATTTTG
3285292 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:3289358 original size:21 final size:20
Alignment explanation
Indices: 3289333--3289385 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
3289323 TACAAGTCAA
*
3289333 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TATTTTG
3289354 TGTATCGATAC-ATATTTTG
1 TGTATCGATACAATATTTTG
3289373 TGTATCGATACAA
1 TGTATCGATACAA
3289386 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
20 2 0.07
21 11 0.37
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATATTTTG
Found at i:3289489 original size:20 final size:20
Alignment explanation
Indices: 3289436--3289491 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3289426 ACATCTTTTT
*
3289436 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
3289456 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
3289475 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
3289492 TAAGTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:3289971 original size:20 final size:20
Alignment explanation
Indices: 3289946--3289985 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3289936 TGAATATGTC
3289946 ATGTGATCAAAGTATCATGA
1 ATGTGATCAAAGTATCATGA
3289966 ATGTGATCAAAGTATCATGA
1 ATGTGATCAAAGTATCATGA
3289986 GTAAACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGTGATCAAAGTATCATGA
Found at i:3290220 original size:17 final size:18
Alignment explanation
Indices: 3290180--3290222 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3290170 TAAATTATCA
* *
3290180 TTATAATTTTTTTACTGT
1 TTATAAATTTTTTAATGT
*
3290198 TAATAAATTTTTTAAT-T
1 TTATAAATTTTTTAATGT
3290215 TTATAAAT
1 TTATAAAT
3290223 AAAAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATAAATTTTTTAATGT
Found at i:3290223 original size:21 final size:20
Alignment explanation
Indices: 3290199--3290245 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3290189 TTTTACTGTT
*
3290199 AATAAATTTTTTAATTTTATA
1 AATAAAATTTTT-ATTTTATA
*
3290220 AATAAAAATTTTTATTTTATT
1 AAT-AAAATTTTTATTTTATA
3290241 AATAA
1 AATAA
3290246 CTCTCATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAAAATTTTTATTTTATA
Found at i:3298213 original size:21 final size:20
Alignment explanation
Indices: 3298187--3298225 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
3298177 GTTGGGACCT
3298187 TGTATCGATACATTCTAGAAA
1 TGTATCGATACATT-TAGAAA
3298208 TGTATCGATACATTTAGA
1 TGTATCGATACATTTAGA
3298226 CAAAAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATTTAGAAA
Found at i:3306081 original size:20 final size:20
Alignment explanation
Indices: 3306053--3306127 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3306043 TCATACCCTG
3306053 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3306073 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3306093 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3306113 ATGTATCGATACATT
1 ATGTATCGATACATT
3306128 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3306120 original size:40 final size:39
Alignment explanation
Indices: 3306053--3306130 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3306043 TCATACCCTG
* *
3306053 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3306093 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3306131 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3307068 original size:23 final size:23
Alignment explanation
Indices: 3307038--3307093 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
3307028 AGCCTTTGAC
3307038 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3307061 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
3307083 CATGCATTTTT
1 CATGCATTTTT
3307094 AACATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:3307100 original size:20 final size:21
Alignment explanation
Indices: 3307046--3307100 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3307036 ACCATGCATT
**
3307046 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3307067 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3307089 -TTTTTAACATGT
1 TTTTTTAACATGT
3307101 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3314681 original size:27 final size:27
Alignment explanation
Indices: 3314604--3315397 Score: 1266
Period size: 27 Copynumber: 29.0 Consensus size: 27
3314594 TGGCATTTCT
*
3314604 TTTTGAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
3314632 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
3314660 TTTTAAATCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3314687 TTTTAAAGTCCACAACTCCGTGGCACTC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
3314715 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
3314743 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
** *
3314770 TTCAAAGTCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3314797 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
3314825 TTTTAAGTCCACAACTCTGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3314851 TTTCAAAGTCCACAACTCCGTGGCACCC
1 TTT-TAAGTCCACAACTCCGTGGCACCC
* * *
3314879 TTTTAAGTCCACAACTCCGTAGCGCTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3314906 TTTTAAAGTCCACAACTCCATGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
3314934 TCTTTAAGTCCACAACTCCGTGGCACCC
1 T-TTTAAGTCCACAACTCCGTGGCACCC
3314962 TCTTTAAGTCCACAACTCCGTGGCACCC
1 T-TTTAAGTCCACAACTCCGTGGCACCC
3314990 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3315017 TTTTAAGTCCGCAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
3315045 TTTTAAGTCCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
3315073 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
**
3315100 TTTTAAGTCCACAACTTTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3315127 TTTTAAGTCCACAACTCCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3315154 TTTTAAGTCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315181 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315208 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315235 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315262 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
3315290 TTTTAAGACCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315317 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3315344 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3315371 TTTTAAATCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3315398 ATTTCAAAGC
Statistics
Matches: 715, Mismatches: 43, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
26 5 0.01
27 444 0.62
28 263 0.37
29 3 0.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:3314815 original size:82 final size:81
Alignment explanation
Indices: 3314604--3315397 Score: 1266
Period size: 82 Copynumber: 9.7 Consensus size: 81
3314594 TGGCATTTCT
* * *
3314604 TTTTGAAGTCCACAACTCCGTGGCATCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAATC
1 TTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
3314669 CACAACTCCGTGGCACTC
64 CACAACTCCGTGGCACCC
*
3314687 TTTTAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 TTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3314752 CACAACTCCGTGGCACCC
64 CACAACTCCGTGGCACCC
** *
3314770 TTCAAAGTCCACAACTCCGTGGCACTCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
3314835 ACAACTCTGTGGCA-CC
65 ACAACTCCGTGGCACCC
* * * *
3314851 TTTCAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTAGCGCTCTTTTAAAGTC
1 TTT-TAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
*
3314916 CACAACTCCATGGCACCC
64 CACAACTCCGTGGCACCC
3314934 TCTTTAAGTCCACAACTCCGTGGCACCCTCTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 T-TTTAAGTCCACAACTCCGTGGCACCCT-TTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
3314999 CACAACTCCGTGGCACCC
64 CACAACTCCGTGGCACCC
* *
3315017 TTTTAAGTCCGCAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCTCTTTTAAGTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
3315082 CACAACTCCGTGGCACCC
64 CACAACTCCGTGGCACCC
** *
3315100 TTTTAAGTCCACAACTTTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
*
3315165 CAACTCCGTGGCACTC
66 CAACTCCGTGGCACCC
3315181 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
3315246 CAACTCCGTGGCACCC
66 CAACTCCGTGGCACCC
*
3315262 TTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
3315327 ACAACTCCGTGGCACCC
65 ACAACTCCGTGGCACCC
* *
3315344 TTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCC
3315398 ATTTCAAAGC
Statistics
Matches: 666, Mismatches: 37, Indels: 18
0.92 0.05 0.02
Matches are distributed among these distances:
81 183 0.27
82 271 0.41
83 183 0.27
84 29 0.04
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.27
Consensus pattern (81 bp):
TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA
CAACTCCGTGGCACCC
Found at i:3315435 original size:32 final size:32
Alignment explanation
Indices: 3315380--3316365 Score: 1650
Period size: 32 Copynumber: 30.8 Consensus size: 32
3315370 CTTTTAAATC
* *
3315380 CACAACTCCGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315411 CACAAGTCAGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315443 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315475 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315507 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315539 CACAAGTCGGTGGTAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3315571 CACAAGGCGGTGGCAACCTATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315603 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315635 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315667 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315699 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315731 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315763 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3315795 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3315827 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315859 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315891 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315923 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315955 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3315987 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3316019 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3316051 CACAAGCCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3316083 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3316115 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3316147 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
3316179 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
3316211 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
3316243 CACAAGTCAGTGGCAACCCATTCCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3316275 CACAAGTCGGTGGCAACTCATTTCAAAGCGCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
3316307 CACAAGTCGGTGGCAACCCATTTAAAAGCCTA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
3316339 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
3316366 TCACCATTTT
Statistics
Matches: 908, Mismatches: 46, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
31 12 0.01
32 896 0.99
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:3316876 original size:20 final size:20
Alignment explanation
Indices: 3316848--3316922 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3316838 TCATACCCTG
3316848 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3316868 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3316888 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3316908 ATGTATCGATACATT
1 ATGTATCGATACATT
3316923 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3316915 original size:40 final size:39
Alignment explanation
Indices: 3316848--3316925 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3316838 TCATACCCTG
* *
3316848 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3316888 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3316926 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3317865 original size:24 final size:24
Alignment explanation
Indices: 3317833--3317889 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
3317823 AGCCTTTGAC
3317833 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3317857 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3317879 CATGCATTTTT
1 CATGCATTTTT
3317890 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:3317896 original size:20 final size:21
Alignment explanation
Indices: 3317842--3317896 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3317832 CCATGCATTT
**
3317842 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3317863 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3317885 -TTTTTAACATGT
1 TTTTTTAACATGT
3317897 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3323870 original size:10 final size:10
Alignment explanation
Indices: 3323855--3323881 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3323845 TGCTAACTAA
3323855 GTTTTTGTTT
1 GTTTTTGTTT
3323865 GTTTTTGTTT
1 GTTTTTGTTT
3323875 GTTTTTG
1 GTTTTTG
3323882 CTTGATACAT
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:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:3333581 original size:1 final size:1
Alignment explanation
Indices: 3333575--3333692 Score: 110
Period size: 1 Copynumber: 118.0 Consensus size: 1
3333565 GGCGTCCTTC
** ** ** *
3333575 AAAAAAAAAAAAAAAACCAAAAAATGAAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
3333640 AAACAAAAGAAAAAAAAAACAAAAAACAATAAAAAAACAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3333693 GAGGGGTCCG
Statistics
Matches: 94, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:3333613 original size:34 final size:33
Alignment explanation
Indices: 3333574--3333692 Score: 141
Period size: 33 Copynumber: 3.5 Consensus size: 33
3333564 CGGCGTCCTT
* * *
3333574 CAAAAAAAAAAAAAAAACCAAAAAATGAAAAAC
1 CAAAAAAAAAAAAAAAAACAAAAAATAAAAAAA
*
3333607 CAAAAAAAAAAAAAAAAA-AAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAACAAAAAATAAAAAAA
3333639 CAAACAAAAGAAAAAAAAAACAAAAAACAATAAAAAAA
1 CAAA-AAAA-AAAAAAAAAAC--AAAA-AATAAAAAAA
*
3333677 CAAACAAAAAAAAAAA
1 CAAAAAAAAAAAAAAA
3333693 GAGGGGTCCG
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
32 15 0.20
33 21 0.28
34 10 0.14
36 8 0.11
37 7 0.09
38 13 0.18
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (33 bp):
CAAAAAAAAAAAAAAAAACAAAAAATAAAAAAA
Found at i:3333626 original size:38 final size:36
Alignment explanation
Indices: 3333575--3333692 Score: 157
Period size: 37 Copynumber: 3.2 Consensus size: 36
3333565 GGCGTCCTTC
* *
3333575 AAAAAAAAAAAAAAAACCAAAAAATGAAA-AACCAAAA
1 AAAAAAAAAAAAAAAAACAAAAAA--AAACAAACAAAA
*
3333612 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAACAAAA
1 AAAAAAAAAAAAAAAAACAAAAAAAAACAAACAAAA
*
3333648 GAAAAAAAAAACAAAAAACAATAAAAAAACAAACAAAA
1 -AAAAAAAAAAAAAAAAACAA-AAAAAAACAAACAAAA
3333686 AAAAAAA
1 AAAAAAA
3333693 GAGGGGTCCG
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 3 0.04
36 7 0.10
37 47 0.64
38 16 0.22
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (36 bp):
AAAAAAAAAAAAAAAAACAAAAAAAAACAAACAAAA
Found at i:3335207 original size:33 final size:33
Alignment explanation
Indices: 3335160--3335574 Score: 458
Period size: 33 Copynumber: 12.9 Consensus size: 33
3335150 AGTGGCATCT
3335160 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
*
3335194 TTTTAAAGCCCACAACTCCGTGGCAC-----CC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* * *
3335222 TTTT-AAGTCCATAACTCCGTGGCAC---TCT-
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
3335250 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
3335283 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
3335319 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
*
3335353 TTTTAAAGCCCACAACTCCGTGGCAC-----CC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
* * *
3335381 TTTT-AAGTCCATAACTCCGTGGCAC---TCT-
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
3335409 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
3335442 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
*
3335478 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTCC
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTTC
* * *
3335512 TTTTAAAGCCCACAACTCTGTGGCACCTTGTTCC
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTC
* *
3335546 TTTT-AAGTCCACAACTTCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTT
3335575 CACCCTTTCC
Statistics
Matches: 336, Mismatches: 22, Indels: 47
0.83 0.05 0.12
Matches are distributed among these distances:
27 38 0.11
28 18 0.05
29 38 0.11
32 4 0.01
33 138 0.41
34 35 0.10
36 19 0.06
37 46 0.14
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (33 bp):
TTTTAAAGCCCACAACTCCGTGGCACTTTTTTC
Found at i:3335280 original size:89 final size:92
Alignment explanation
Indices: 3335136--3335574 Score: 409
Period size: 89 Copynumber: 4.6 Consensus size: 92
3335126 TTACCCTTCA
* *
3335136 AAAGCCCACAAGTCAGTGGCA--TCT-TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTTCTCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
3335198 AAAGCCCACAACTCCGTGGCACCCTTTT
65 AAAGCCCACAACTCCGTGGCACCCTTTT
* *
3335226 -AAGTCCATAACTCCGTGGCAC-TCT-TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTA
1 AAAGCCCACAACTCCGTGGCACTTCTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTA
3335288 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 AAGCCCACAACTCCGTGGCA--------CCCTTTT
* *
3335323 CAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCAC-----CCTT
1 -AAAGCCCACAACTCCGTGGCAC--TTCTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTT
* * *
3335383 TT-AAGTCCATAACTCCGTGGCACTCTTTTT
63 TTAAAGCCCACAACTCCGTGGCAC-CCTTTT
*
3335413 AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAAGCCCACAACTCCGTGGCAC--TTCTCTTTTAAAGCCCACAACTCCGTGGCACT-TTTTT--C
3335478 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
61 TTTT-AAAGCCCACAACTCCGTGGCAC-----CCTTTT
* * * *
3335516 AAAGCCCACAACTCTGTGGCACCTTGTTCCTTTT-AAGTCCACAACTTCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCA-CTT-CT-CTTTTAAAGCCCACAACTCCGTGGCA-CTTT
3335575 CACCCTTTCC
Statistics
Matches: 297, Mismatches: 18, Indels: 55
0.80 0.05 0.15
Matches are distributed among these distances:
89 126 0.42
90 12 0.04
97 30 0.10
98 5 0.02
99 38 0.13
102 4 0.01
103 74 0.25
104 8 0.03
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (92 bp):
AAAGCCCACAACTCCGTGGCACTTCTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTA
AAGCCCACAACTCCGTGGCACCCTTTT
Found at i:3335361 original size:70 final size:68
Alignment explanation
Indices: 3335160--3335594 Score: 419
Period size: 70 Copynumber: 6.7 Consensus size: 68
3335150 AGTGGCATCT
*
3335160 TTTTCAAAGCCCACAACTCCGTGGCA-CTTTTT-TCTTTTAAAGCCCACAACTCCGTGGCAC---
1 TTTT-AAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTTT
*
3335220 --CC
65 TTTC
* * *
3335222 TTTT-AAGTCCATAACTCCGTGGCA-C----T-CTTTTTAAAGCCCACAACTCCGTGGCACTTTT
1 TTTTAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTTTT
3335280 TTC
66 TTC
3335283 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTT
1 TTTTAAAGCCCACAACTCCGTGGCA-TCTTTTTCCCTTTT-AAAGCCCACAACTCCGTGGCACTT
3335348 TTTTC
64 TTTTC
* *
3335353 TTTTAAAGCCCACAACTCCGTGGCA-------CCCTTTT-AAGTCCATAACTCCGTGGCAC---T
1 TTTTAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTTTT
*
3335407 CT-
66 TTC
*
3335409 TTTTAAAGCCCACAACTCCGTGGCA-CTTTTT-TCTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 TTTTAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACT-TT
3335472 TTTCCC
65 TTT--C
*
3335478 TTTTCAAAGCCCACAACTCCGTGGCA-CTTTTT-CCTTTTAAAGCCCACAACTCTGTGGCACCTT
1 TTTT-AAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCA-CTT
* *
3335541 GTTCC
64 TTTTC
* * ** *
3335546 TTTT-AAGTCCACAACTTCGTGGCATCTTTCACCCTTTCCAAAGCCCACA
1 TTTTAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTT-TAAAGCCCACA
3335595 CAAGTCGGTG
Statistics
Matches: 316, Mismatches: 24, Indels: 59
0.79 0.06 0.15
Matches are distributed among these distances:
56 52 0.16
57 2 0.01
60 38 0.12
61 10 0.03
62 48 0.15
64 1 0.00
66 20 0.06
67 4 0.01
68 11 0.03
69 19 0.06
70 109 0.34
71 2 0.01
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (68 bp):
TTTTAAAGCCCACAACTCCGTGGCATCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACTTTT
TTC
Found at i:3335449 original size:159 final size:159
Alignment explanation
Indices: 3335160--3335538 Score: 740
Period size: 159 Copynumber: 2.4 Consensus size: 159
3335150 AGTGGCATCT
3335160 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTT
1 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTT
3335225 TAAGTCCATAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
66 TAAGTCCATAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
3335290 GCCCACAACTCCGTGGCACTCTTTTTCCC
131 GCCCACAACTCCGTGGCACTCTTTTTCCC
3335319 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTT
1 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTT
3335384 TAAGTCCATAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
66 TAAGTCCATAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
3335449 GCCCACAACTCCGTGGCACTCTTTTTCCC
131 GCCCACAACTCCGTGGCACTCTTTTTCCC
* *
3335478 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCTGTGGCACC
1 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACC
3335539 TTGTTCCTTT
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 218 1.00
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.32
Consensus pattern (159 bp):
TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACCCTTT
TAAGTCCATAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
GCCCACAACTCCGTGGCACTCTTTTTCCC
Found at i:3335618 original size:33 final size:33
Alignment explanation
Indices: 3335581--3335643 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
3335571 CTTTCACCCT
3335581 TTCCAAAGCCCACACAAGTCGGTGGCAACCTTC
1 TTCCAAAGCCCACACAAGTCGGTGGCAACCTTC
3335614 TTCCAAAGCCCACACAAGTCGGTGGCAACC
1 TTCCAAAGCCCACACAAGTCGGTGGCAACC
3335644 CCTCTAAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.16
Consensus pattern (33 bp):
TTCCAAAGCCCACACAAGTCGGTGGCAACCTTC
Found at i:3335764 original size:49 final size:49
Alignment explanation
Indices: 3335648--3336633 Score: 1324
Period size: 49 Copynumber: 20.2 Consensus size: 49
3335638 GCAACCCCTC
* * *
3335648 TAAGCCCAATACAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC---TTCATCTT
* *
3335700 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3335749 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
3335801 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3335850 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3335899 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3335948 GAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG------CATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3335991 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
3336043 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336092 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3336141 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336190 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336239 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336288 GAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG------CATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3336331 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
3336383 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336432 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3336481 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3336530 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T-TT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3336573 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
3336622 TAAGTCCAATAT
1 TAAGTCCAATAT
3336634 CGCTAGCCGC
Statistics
Matches: 838, Mismatches: 69, Indels: 57
0.87 0.07 0.06
Matches are distributed among these distances:
43 118 0.14
44 1 0.00
45 1 0.00
48 1 0.00
49 541 0.65
50 6 0.01
51 2 0.00
52 168 0.20
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:3336030 original size:242 final size:238
Alignment explanation
Indices: 3335648--3336637 Score: 1334
Period size: 242 Copynumber: 4.1 Consensus size: 238
3335638 GCAACCCCTC
* * *
3335648 TAAGCCCAATA-CAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTTAAGTCCAATGT
1 TAAGTCCAATATC-GCTGGCCTTGAATCAGCACATTGGCACC---TTCATCTTTAAGTCCAATAT
*
3335712 AGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCA
62 AGCTGGCCTTGAATCAGCACATTGG-----TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCA
3335777 GCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC
122 GCATATTGGCACCTTTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA--
3335842 TTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
184 --CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * *
3335899 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
*
3335964 GGCCTTGACTCAGCACATTGG-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 GGCCTTGAATCAGCACATTGGTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
3336028 CACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTT
131 CACCTTTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----CATCTTT
3336093 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
191 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * *
3336141 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* *
3336206 GGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 GGCCTTGAATCAGCACATTGG-----TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
* *
3336271 ATTGGCA--TCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGG--CATCTTT
126 ATTGGCACCTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCTTT
* *
3336332 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
191 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTT
* * * *
3336383 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
* * * *
3336448 GGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
66 GGCCTTGAATCAGCACATTGG-----TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCAT
*
3336513 ATTGGCACC--TTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC-T-TTT
126 ATTGGCACCTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCTTT
* * * *
3336574 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
191 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
3336622 TAAGTCCAATATCGCT
1 TAAGTCCAATATCGCT
3336638 AGCCGCATAT
Statistics
Matches: 693, Mismatches: 32, Indels: 40
0.91 0.04 0.05
Matches are distributed among these distances:
239 63 0.09
240 2 0.00
241 3 0.00
242 452 0.65
243 1 0.00
244 1 0.00
245 42 0.06
246 3 0.00
248 88 0.13
251 37 0.05
252 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (238 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCT
GGCCTTGAATCAGCACATTGGTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
CACCTTTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCTTTAAGTC
CAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
Found at i:3336283 original size:340 final size:340
Alignment explanation
Indices: 3335648--3336631 Score: 1782
Period size: 340 Copynumber: 2.9 Consensus size: 340
3335638 GCAACCCCTC
* * *
3335648 TAAGCCCAATACAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCATCTTTAAGTCCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
*
3335713 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAG
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
*
3335778 CATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
131 CATATTGGCA--TCTT-CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
3335843 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAA
193 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAA
3335908 TATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGAC
258 TATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGAC
3335973 TCAGCACATTGGCATCTT
323 TCAGCACATTGGCATCTT
3335991 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
3336056 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
3336121 CATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
131 CATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
3336186 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATAT
196 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATAT
3336251 CGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCA
261 CGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCA
3336316 GCACATTGGCATCTT
326 GCACATTGGCATCTT
3336331 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
3336396 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
3336461 CATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
131 CATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
* * * *
3336526 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T-TTTAAGTCCAATGT
196 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATAT
* * * *
3336585 CGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAAT
261 CGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAAT
3336632 ATCGCTAGCC
Statistics
Matches: 628, Mismatches: 13, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
334 56 0.09
335 1 0.00
336 1 0.00
340 431 0.69
341 3 0.00
343 136 0.22
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (340 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
CATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCA
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATAT
CGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTGGCCTTGACTCA
GCACATTGGCATCTT
Found at i:3337388 original size:33 final size:33
Alignment explanation
Indices: 3337351--3337417 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3337341 TTCAACGATT
3337351 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3337384 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3337417 T
1 T
3337418 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3337389 original size:13 final size:13
Alignment explanation
Indices: 3337371--3337395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3337361 CATAAAATGT
3337371 TGTATCGATACAA
1 TGTATCGATACAA
3337384 TGTATCGATACA
1 TGTATCGATACA
3337396 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3337478 original size:13 final size:13
Alignment explanation
Indices: 3337460--3337484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3337450 ATTACTCACA
3337460 TGTATCGATACAT
1 TGTATCGATACAT
3337473 TGTATCGATACA
1 TGTATCGATACA
3337485 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3337621 original size:52 final size:52
Alignment explanation
Indices: 3337493--3337613 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
3337483 CACTGATCTT
*
3337493 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
3337545 TGTATCGATAAATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3337597 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3337614 ATAAATTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:3342636 original size:13 final size:13
Alignment explanation
Indices: 3342618--3342642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3342608 AAAAGATTAA
3342618 TGTATCGATACAG
1 TGTATCGATACAG
3342631 TGTATCGATACA
1 TGTATCGATACA
3342643 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Done.