Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold194
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: 3945165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1023 characters in sequence are not A, C, G, or T
File 20 of 24
Found at i:3342121 original size:22 final size:23
Alignment explanation
Indices: 3342080--3342127 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
3342070 TTAAACATGA
3342080 ATGAAACATAATAAAAAAAATGC
1 ATGAAACATAATAAAAAAAATGC
3342103 ATGAAACATAAT-AAAAAAATGC
1 ATGAAACATAATAAAAAAAATGC
3342125 ATG
1 ATG
3342128 GTCAAAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (23 bp):
ATGAAACATAATAAAAAAAATGC
Found at i:3343062 original size:20 final size:20
Alignment explanation
Indices: 3343037--3343111 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3343027 AAAAAGACAT
*
3343037 AATATATCGATACATTGCAG
1 AATATATCGATACATTGCAA
3343057 AATATATCGATACATT-CATA
1 AATATATCGATACATTGCA-A
* * * *
3343077 CATGTATCGATATATTGAAA
1 AATATATCGATACATTGCAA
*
3343097 AATGTATCGATACAT
1 AATATATCGATACAT
3343112 CAGGGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.04
20 43 0.93
21 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (20 bp):
AATATATCGATACATTGCAA
Found at i:3343820 original size:28 final size:28
Alignment explanation
Indices: 3343674--3344820 Score: 1409
Period size: 28 Copynumber: 39.8 Consensus size: 28
3343664 TAAAAAAAAT
* *
3343674 GTGCCACTAACTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGACTTGTG--GGCTTTG-AAAGA
* *
3343705 GTTGGCACTGACACATGTGGGCTTTGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTG-AAAGA
** * * *
3343737 GTGTTACTGATTTGCGTGGGCTTTAAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
3343767 GTGCCACTGACTTGCGTGGGCTTTGAAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
* * **
3343797 ATGCCACTAACTCATGGGCTTTGAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
3343824 GATGCTACTGACTTGTGGGCTTTGAAAGA
1 G-TGCCACTGACTTGTGGGCTTTGAAAGA
* *
3343853 GTGCCATTGACTCGTGGGCTTTGAAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* * *
3343880 GGTACCACTAACTTGCGTGGGCTTTAAAAGGA
1 -GTGCCACTGACTT--GTGGGCTTTGAAA-GA
* * *
3343912 GTGCCATTGACTTGTGTGGGCTTTAAAAGG
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGA
3343942 GTGCCACTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* * * *
3343970 GTGCCACTGAATTGTGGGCTTCGCAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
3343998 GTGCCACTGACTTGTGGGCTCTGAAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
3344025 GGTGCCACTAACTTGTGGGCTTTGAAAGG
1 -GTGCCACTGACTTGTGGGCTTTGAAAGA
*
3344054 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
*
3344083 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
3344112 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
*
3344141 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
3344169 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
3344197 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
* *
3344226 GTGCCACTGATTTATGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
*
3344255 GTGCCACTGACTTGTAGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
* *
3344284 GTGCCACTGACTTGTGGACTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
3344312 GTGCCACTGACTTGTGGGCTTTGAAGGGA
1 GTGCCACTGACTTGTGGGCTTTGAA-AGA
* *
3344341 GTGCCACTGACTTGTGTGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
3344369 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
3344398 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
*
3344427 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
3344455 GTGCCACTGACTTATGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
3344483 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
* *
3344512 GTGCCACTGATTTATGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
3344541 GTGCCACTGACTTGTGGGCTTTGAAAGAA
1 GTGCCACTGACTTGTGGGCTTTGAAAG-A
*
3344570 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
3344598 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAA-GA
3344627 GTGCCACTGACTTGTGTGGGCTTTGAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGA
* * * * *
3344657 GTGCCACTGAATTATGGGCTTCGCAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
3344685 GTGCCACTGACTTGTGGGCTTCGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* * *
3344713 GTGCCACTAACTTGTGGGCTCTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* * *
3344741 GTGGCACTAACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
3344769 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
*
3344798 GTGCCACTGATTTGTGGGCTTTG
1 GTGCCACTGACTTGTGGGCTTTG
3344821 CAAGGGATGA
Statistics
Matches: 986, Mismatches: 100, Indels: 62
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.00
28 471 0.48
29 360 0.37
30 75 0.08
31 51 0.05
32 21 0.02
33 1 0.00
34 6 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGA
Found at i:3344166 original size:143 final size:143
Alignment explanation
Indices: 3343674--3344820 Score: 1558
Period size: 143 Copynumber: 8.0 Consensus size: 143
3343664 TAAAAAAAAT
* ** * * *
3343674 GTGCCACTAACTTGTGTAGGCTTTGAAAAAAGTTGGCACTGACACATGTGGGCTTTGAAAAGAGT
1 GTGCCACTGACTTGTG--GGCTTTGAAAGGAG-TGCCACTG--ACTTGTGGGCTTTG-AAAGGGT
** * * *
3343739 GTTACTGATTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTG-AAAGAATGCCA
60 GCCACTGACTT--GTGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCA
* * * *
3343803 CTAACTCATGGGCTTTGAAAGGA
121 CTGATTTATGGGCTTTGAAAAGA
* * * * *
3343826 -TGCTACTGACTTGTGGGCTTTGAAA-GAGTGCCATTGACTCGTGGGCTTTGAAAAGGTACCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * * *
3343889 AACTTGCGTGGGCTTTAAAAGGAGTGCCATTGACTTGTGTGGGCTTT-AAAAGGGTGCCACTGAC
66 GACTT--GTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGAT
*
3343953 TTGTGGGCTTTG-AAAGA
126 TTATGGGCTTTGAAAAGA
* * * * *
3343970 GTGCCACTGAATTGTGGGCTTCGCAAGG-GTGCCACTGACTTGTGGGCTCTGAAAAGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * *
3344034 AACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTG
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
3344099 GGCTTTGAAAAGA
131 GGCTTTGAAAAGA
3344112 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
3344177 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
*
3344242 GGCTTTGAAAGGA
131 GGCTTTGAAAAGA
* *
3344255 GTGCCACTGACTTGTAGGCTTTGAAAGGAGTGCCACTGACTTGTGGACTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* * * * *
3344320 GACTTGTGGGCTTTGAAGGGAGTGCCACTGACTTGTGTGCTTTG-AAAGGGTGCCACTGACTTGT
66 GACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTAT
3344384 GGGCTTTGAAAAGA
130 GGGCTTTGAAAAGA
3344398 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
3344463 GACTTATGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
*
3344528 GGCTTTGAAAGGA
131 GGCTTTGAAAAGA
*
3344541 GTGCCACTGACTTGTGGGCTTTGAAAGAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
*
3344606 GACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTG-AAAGAGTGCCACTGAATT
66 GACTTGTGGGCTTTGAAAGG-GTGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGATTT
* * *
3344670 ATGGGCTTCG-CAAGG
128 ATGGGCTTTGAAAAGA
* * * *
3344685 GTGCCACTGACTTGTGGGCTTCGAAAGG-GTGCCACTAACTTGTGGGCTCTGAAAGGGTGGCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
* *
3344749 AACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTG
66 GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
3344814 GGCTTTG
131 GGCTTTG
3344821 CAAGGGATGA
Statistics
Matches: 904, Mismatches: 76, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
140 21 0.02
141 54 0.06
142 72 0.08
143 480 0.53
144 93 0.10
145 139 0.15
146 13 0.01
147 7 0.01
148 2 0.00
149 10 0.01
151 13 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (143 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
GACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTATG
GGCTTTGAAAAGA
Found at i:3346061 original size:1 final size:1
Alignment explanation
Indices: 3346057--3346102 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
3346047 TTTTTTGCTA
* * * *
3346057 TTTTTTCTTTTTTTTTTGTTTTTTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3346103 GGGTGTAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:3346102 original size:20 final size:20
Alignment explanation
Indices: 3346046--3346103 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
3346036 GACCCTTCTA
* *
3346046 TTTTTTTGCTATTTTTTCTTT
1 TTTTTTTG-TTTTTTTTGTTT
3346067 TTTTTTTGTTTTTTTTGTTT
1 TTTTTTTGTTTTTTTTGTTT
3346087 TTTTTTTGTTTTTTTTG
1 TTTTTTTGTTTTTTTTG
3346104 GGTGTAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTTTTGTTT
Found at i:3346103 original size:9 final size:9
Alignment explanation
Indices: 3346046--3346103 Score: 62
Period size: 9 Copynumber: 5.9 Consensus size: 9
3346036 GACCCTTCTA
3346046 TTTTTTTGCT
1 TTTTTTTG-T
*
3346056 ATTTTTTCTTT
1 -TTTTTT-TGT
3346067 TTTTTTTGT
1 TTTTTTTGT
3346076 TTTTTTTGTTT
1 TTTTTTTG--T
3346087 TTTTTTTGT
1 TTTTTTTGT
3346096 TTTTTTTG
1 TTTTTTTG
3346104 GGTGTAAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 19 0.45
10 6 0.14
11 16 0.38
12 1 0.02
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:3358744 original size:22 final size:23
Alignment explanation
Indices: 3358703--3358750 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
3358693 TTAAAGATGA
3358703 ATGAAACATAATAAAAAAAATGC
1 ATGAAACATAATAAAAAAAATGC
3358726 ATGAAACATAAT-AAAAAAATGC
1 ATGAAACATAATAAAAAAAATGC
3358748 ATG
1 ATG
3358751 GTCAAAGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.19
Consensus pattern (23 bp):
ATGAAACATAATAAAAAAAATGC
Found at i:3359707 original size:20 final size:20
Alignment explanation
Indices: 3359660--3359734 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3359650 AAAAAGACAT
*
3359660 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3359679 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3359700 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3359720 AATGTATCGATACAT
1 AATGTATCGATACAT
3359735 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3359728 original size:40 final size:39
Alignment explanation
Indices: 3359657--3359734 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3359647 GGTAAAAAGA
* *
3359657 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3359696 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3359735 CAGGGTAAAA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3360027 original size:22 final size:22
Alignment explanation
Indices: 3360002--3360080 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
3359992 AATGTCGTAC
*
3360002 TCATATGTACATTTAGTTTTAG
1 TCATATGTACATTTACTTTTAG
*
3360024 TCATA--TATATTGT-CTTTTAG
1 TCATATGTACATT-TACTTTTAG
* ** *
3360044 TCATATATGTATTTACTTATAG
1 TCATATGTACATTTACTTTTAG
*
3360066 CCATATGTACATTTA
1 TCATATGTACATTTA
3360081 GATATATGGA
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 16 0.36
21 2 0.04
22 27 0.60
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.49
Consensus pattern (22 bp):
TCATATGTACATTTACTTTTAG
Found at i:3360388 original size:22 final size:22
Alignment explanation
Indices: 3360360--3360407 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3360350 TGGTAATAGT
3360360 CATATATACA-TTATGTTCTAGC
1 CATATATACATTTA-GTTCTAGC
*
3360382 CATATATACATTTAGTTCTAGT
1 CATATATACATTTAGTTCTAGC
3360404 CATA
1 CATA
3360408 CATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (22 bp):
CATATATACATTTAGTTCTAGC
Found at i:3360939 original size:22 final size:23
Alignment explanation
Indices: 3360909--3360955 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3360899 TATGTGTGTA
* *
3360909 TTAAGTTATAATTATATGTACAT
1 TTAAGTTATAATAATATATACAT
3360932 TTAA-TTATAATAATATATACAT
1 TTAAGTTATAATAATATATACAT
3360954 TT
1 TT
3360956 TGCTAAAGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAAGTTATAATAATATATACAT
Found at i:3367538 original size:52 final size:52
Alignment explanation
Indices: 3367405--3367545 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
3367395 TGAAAAGTTA
3367405 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
3367457 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
3367509 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
3367546 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:3367552 original size:13 final size:13
Alignment explanation
Indices: 3367534--3367558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3367524 CAAAAATCAG
3367534 TGTATCGATACAA
1 TGTATCGATACAA
3367547 TGTATCGATACA
1 TGTATCGATACA
3367559 TGTGAGTAAT
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:3367642 original size:13 final size:13
Alignment explanation
Indices: 3367624--3367648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3367614 CAAAAAAATA
3367624 TGTATCGATACAT
1 TGTATCGATACAT
3367637 TGTATCGATACA
1 TGTATCGATACA
3367649 ACATTTTATG
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:3367644 original size:33 final size:33
Alignment explanation
Indices: 3367602--3367668 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3367592 AGTAGCTTAA
3367602 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3367635 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3367668 A
1 A
3367669 AATCATTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3367747 original size:21 final size:21
Alignment explanation
Indices: 3367706--3367747 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3367696 GTTGGGACCT
*
3367706 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
3367727 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
3367748 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:3368654 original size:171 final size:172
Alignment explanation
Indices: 3368460--3368851 Score: 669
Period size: 171 Copynumber: 2.3 Consensus size: 172
3368450 TAGAGATGAT
*
3368460 GAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTG
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTG
*
3368525 ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTGAAGATGAGAAAAAAGATGT
66 ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGATGT
3368590 CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA-C
131 CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATC
* * *
3368631 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTG
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTG
*
3368696 ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGT
66 ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGATGT
*
3368761 CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
131 CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATC
* **
3368803 GAAAATGTGCCAATATGCTGATTCAAGGCCAGTTATATTGGACTTAAAG
1 GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
3368852 GTGCCAATGT
Statistics
Matches: 207, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
171 164 0.79
172 4 0.02
174 39 0.19
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.24
Consensus pattern (172 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTG
ATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGATGT
CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATC
Found at i:3368798 original size:55 final size:52
Alignment explanation
Indices: 3368738--3369706 Score: 732
Period size: 52 Copynumber: 20.0 Consensus size: 52
3368728 CGATATTGGG
* *
3368738 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
3368793 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGTTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
3368845 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3368888 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3368937 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3368980 CTTAAAGGTGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
3369032 CTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * **
3369081 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3369133 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3369176 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3369225 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3369268 CTTAAAGGTGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
3369320 CTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * **
3369369 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3369421 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3369464 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
3369513 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
3369556 CTTAAAGGTGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
3369608 CTTAAAGAT-G--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * *
3369657 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTG
3369707 GGCTTAGAGG
Statistics
Matches: 783, Mismatches: 71, Indels: 123
0.80 0.07 0.13
Matches are distributed among these distances:
43 224 0.29
44 6 0.01
46 3 0.00
48 3 0.00
49 251 0.32
50 3 0.00
51 6 0.01
52 271 0.35
53 5 0.01
54 1 0.00
55 10 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:3368998 original size:144 final size:144
Alignment explanation
Indices: 3368848--3369663 Score: 1119
Period size: 144 Copynumber: 5.7 Consensus size: 144
3368838 TATTGGACTT
* *
3368848 AAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3368913 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
3368978 GACTTAAAGGTGGA
131 GACTTAAAGGTGGA
* * *
3368992 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
*
3369057 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTT-AA-A--G-----GTGCCAATGTGCTGATTCAAGGCCA
* *
3369122 GCTATATTGGGC-T-----T---
122 GCTACATTGGACTTAAAGGTGGA
*
3369136 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3369201 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
3369266 GACTTAAAGGTGGA
131 GACTTAAAGGTGGA
* * *
3369280 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
*
3369345 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTT-AA-A--G-----GTGCCAATGTGCTGATTCAAGGCCA
* *
3369410 GCTATATTGGGC-T-----T---
122 GCTACATTGGACTTAAAGGTGGA
*
3369424 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
* *
3369489 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
3369554 GACTTAAAGGTGGA
131 GACTTAAAGGTGGA
* * *
3369568 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
3369633 TGAGTCAAGGCCAGCTACATTGGACTTAAAG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAG
3369664 ATGGAAAATG
Statistics
Matches: 593, Mismatches: 43, Indels: 72
0.84 0.06 0.10
Matches are distributed among these distances:
135 68 0.11
136 2 0.00
140 2 0.00
141 2 0.00
142 2 0.00
143 4 0.01
144 433 0.73
145 4 0.01
146 2 0.00
147 2 0.00
148 2 0.00
152 2 0.00
153 68 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (144 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
GACTTAAAGGTGGA
Found at i:3369225 original size:288 final size:288
Alignment explanation
Indices: 3368698--3369712 Score: 1859
Period size: 288 Copynumber: 3.5 Consensus size: 288
3368688 GAAAAGTGAT
* * * * * * *
3368698 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * *
3368763 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
60 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCA
* * *
3368828 AGGCCAGTTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAA
125 AGGCCAGCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
3368893 AGATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTG
190 AGATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTG
3368958 ATTCAAGGCCAGCTACATTGGACTTAAAGGTGGA
255 ATTCAAGGCCAGCTACATTGGACTTAAAGGTGGA
3368992 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
3369057 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
3369122 GCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
131 GCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
3369187 AGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
196 AGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
3369252 GGCCAGCTACATTGGACTTAAAGGTGGA
261 GGCCAGCTACATTGGACTTAAAGGTGGA
3369280 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
3369345 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
3369410 GCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
131 GCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
3369475 AGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
196 AGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
3369540 GGCCAGCTACATTGGACTTAAAGGTGGA
261 GGCCAGCTACATTGGACTTAAAGGTGGA
3369568 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
3369633 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
3369698 GCTATATTGGGCTTA
131 GCTATATTGGGCTTA
3369713 GAGGGGTTGC
Statistics
Matches: 708, Mismatches: 13, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
288 660 0.93
289 4 0.01
292 1 0.00
294 43 0.06
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (288 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
GCTATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA
AGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAA
GGCCAGCTACATTGGACTTAAAGGTGGA
Found at i:3369813 original size:32 final size:33
Alignment explanation
Indices: 3369717--3369809 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
3369707 GGCTTAGAGG
3369717 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
3369750 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
3369783 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
3369810 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:3369887 original size:34 final size:34
Alignment explanation
Indices: 3369816--3371009 Score: 872
Period size: 34 Copynumber: 37.0 Consensus size: 34
3369806 TTGGGAAGGA
*
3369816 AAAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
3369850 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
3369884 AAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
*
3369919 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
**
3369954 AAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGG
1 -AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
**
3369991 AAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAG
1 -AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
3370026 AAGAAG-GTGCCACGGAGTTGTGGGTTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* * * *
3370060 AAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGG
1 AAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AG
* *
3370099 AGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--G
3370133 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
3370167 AAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
*
3370201 AAAAAG-GTGCCACGGAGTTGTGGGC-TTAAACG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370233 -----G-GTGCCACGGAGTTGTGGAC-TTAAAGATG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
* *
3370262 AAAAA-AGTGCCACAGAATTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370295 -----G-GTGCCACGGAGTTGTGGAC-TTAAAGATG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-A-G
*
3370324 AAAAA-AGTGCCACGGAATTGTGGGCTTTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
3370357 -----G-GTGCCACGGAGTTGTGGACTTT--GAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * *
3370383 ACAAA-A-TGCCACTGAGTTGTGGACTTT-AAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * * *
3370414 GAAAAGA-TGCCACTGAGTCGTGGAC-TTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370446 -----G-GTGCCACGGAGTTGTGGGC-TTAGAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAG
*
3370474 AAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * * *
3370507 GAAAAGAGTGCCACAGAGTTGTGGGC-TTAGGAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAG
*
3370541 AAAAAGAGTGCCACAGAGTTGTGGGCTTT-----
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370570 AAAAAGAGTGCCACGGAGTCGTGGGCTTT--AAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
3370602 AAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* *
3370636 AAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
* *
3370670 AAGAAG-GTGCCACAGAGTTGTGGGCTTT-----
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370698 --AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-AG
3370733 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
3370768 AAAAAG-GTGCCACGGAGTTGTGGGCTTT----G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370797 ---AAGAGTGCCACGGAGTCGTGGGCTTT----G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* *
3370824 ---AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAA-AG
3370858 AAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
** * *
3370890 -ATGAG-GTGCCACGGAATTGTGGGCTGTAAAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
*
3370922 -----G-GTGCCACGGAGTTGTGGAC-TT-AAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
** *
3370948 -ATGAG-GTGCCACGGAATTGTGGGCTTT-AAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
* * * *
3370979 AAAAA-A-TGCCACTGAGTCGTGGACGTTAAAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
3371010 AGGTATTTGA
Statistics
Matches: 980, Mismatches: 80, Indels: 202
0.78 0.06 0.16
Matches are distributed among these distances:
26 12 0.01
27 116 0.12
28 58 0.06
29 30 0.03
30 56 0.06
31 53 0.05
32 42 0.04
33 103 0.11
34 249 0.25
35 79 0.08
36 76 0.08
37 91 0.09
38 10 0.01
39 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:3370177 original size:141 final size:137
Alignment explanation
Indices: 3369779--3370888 Score: 771
Period size: 128 Copynumber: 8.5 Consensus size: 137
3369769 GGGCTTTAGG
* *
3369779 AAGAGTTGCCACCGACTTGTGTGGGCTTTGGGAAGGAAAAAAGATGCCACGGAGTTGTGGACTTA
1 AAGAG-TGCCACCGA-GT-TGTGGGCTTT--AAAGGAAAAAAGATGCCACGGAGTTGTGGACTTA
*
3369844 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC
61 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC
3369909 TTTGAAAAGGAAA
126 TTTGAAAA-GAAA
* ** *
3369922 AAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAA
1 AAGAGTGCCACCGAGTTGTGGGCTTTAAA-GGAAAAAAGA-TGCCACGGAGTTGTGGAC-TT-AA
* * * * *
3369987 AAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGTT
62 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
*
3370052 TTGAAAAGAAG
127 TTGAAAAGAAA
* * *
3370063 AAG-GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTA
1 AAGAG-TGCCACCGA-GT-TGTGGGCTTTA--AAGGAAAAAAGATGCCACGGAGTTGTGGACTTA
*
3370127 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC
61 AAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGC
*
3370192 TTTAAAAAGAAA
126 TTTGAAAAGAAA
*
3370204 AAG-GTGCCACGGAGTTGTGGGC-TTAAACGG------G-TGCCACGGAGTTGTGGACTT-AAAG
1 AAGAGTGCCACCGAGTTGTGGGCTTTAAA-GGAAAAAAGATGCCACGGAGTTGTGGACTTAAAAG
* * * *
3370259 ATGAAAAA-AGTGCCACAGAATTGTGGGCTTTAAAAG-----GGTGCCACGGAGTTGTGGAC-TT
65 -GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTT
3370317 -AAAGATGAAA
129 GAAA-A-GAAA
* * *
3370327 AA-AGTGCCACGGAATTGTGGGCTTTAAAAGG------G-TGCCACGGAGTTGTGGACTT---TG
1 AAGAGTGCCACCGAGTTGTGGGCTTT-AAAGGAAAAAAGATGCCACGGAGTTGTGGACTTAAAAG
* * * * * * * * *
3370381 AGACAAA-A-TGCCACTGAGTTGTGGACTTTAAAGGAAAAGA-TGCCACTGAGTCGTGGAC-TT-
65 GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
3370441 AAAAG---
130 AAAAGAAA
* * *
3370446 --G-GTGCCACGGAGTTGTGGGC-TTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAA
1 AAGAGTGCCACCGAGTTGTGGGCTTTA-AAGGAAAAAAGA-TGCCACGGAGTTGTGGACTTAAAA
* * *
3370506 -GG-AAAAGAGTGCCACAGAGTTGTGGGC-TTAGGAGGAAAAAGAGTGCCACAGAGTTGTGGGCT
64 GGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTA-AAAGAAAAA-AGTGCCACGGAGTTGTGGGCT
3370568 TT------AAA
127 TTGAAAAGAAA
* * * * * *
3370573 AAGAGTGCCACGGAGTCGTGGGCTTT-AA-G-AAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAA
1 AAGAGTGCCACCGAGTTGTGGGCTTTAAAGGAAAAAAGATGCCACGGAGTTGTGGAC-TT-AAAA
* * * *
3370635 --GAAGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTT
64 GGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTT
3370697 T--------A
128 TGAAAAGAAA
* * * * *
3370699 AAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGAGTGCCACCGAGTTGTGGGCTTT-AAAGGA-AAAAAGA-TGCCACGGAGTTGTGGACTTAAA
** * * *
3370764 ACAGAAAAAG-GTGCCACGGAGTTGTGGGCTTT----G--AAGAGTGCCACGGAGTCGTGGGCTT
63 AGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTT
3370822 T-----G---
128 TGAAAAGAAA
* * * *
3370824 AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 AAGAGTGCCACCGAGTTGTGGGCTTT-AAAGGA-AAAAAGA-TGCCACGGAGTTGTGGACTTAAA
3370889 GATGAGGTGC
Statistics
Matches: 826, Mismatches: 81, Indels: 138
0.79 0.08 0.13
Matches are distributed among these distances:
115 1 0.00
116 6 0.01
117 18 0.02
120 22 0.03
121 10 0.01
122 5 0.01
123 62 0.08
124 49 0.06
125 92 0.11
126 50 0.06
127 19 0.02
128 97 0.12
129 47 0.06
130 23 0.03
131 9 0.01
132 44 0.05
135 2 0.00
136 2 0.00
137 3 0.00
138 9 0.01
139 11 0.01
140 34 0.04
141 91 0.11
142 79 0.10
143 31 0.04
144 8 0.01
145 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (137 bp):
AAGAGTGCCACCGAGTTGTGGGCTTTAAAGGAAAAAAGATGCCACGGAGTTGTGGACTTAAAAGG
GAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
AAAGAAA
Found at i:3370241 original size:61 final size:62
Alignment explanation
Indices: 3370106--3370977 Score: 470
Period size: 61 Copynumber: 13.9 Consensus size: 62
3370096 GGGAGAAAGA
* *
3370106 TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 TGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAG---
*
3370170 AAAG
61 --GG
*
3370174 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * * *
3370235 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
3370297 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
3370359 TGCCACGGAGTTGTGGACTTT---GAGACAAAA--TGCCACTGAGTTGTGGACTTT-AAAGGAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGA-AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGG---
3370418 AG
62 -G
* * * *
3370420 ATGCCACTGAGTCGTGGAC-TT-AAAAG-----GGTGCCACGGAGTTGTGGGCTTAGAAGGAAAA
1 -TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTT------TAAA
*
3370478 AGAG
59 AGGG
* * * *
3370482 TGCCACGGAGTTGTGGGC-TT-AGAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTT------TAAA
*
3370545 AGAG
59 AGGG
* *
3370549 TGCCACAGAGTTGTGGGCTTTAAAAAG----A-GTGCCACGGAGTCGTGGGCTTTAAGAAGAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAA-AAG--GG
* * * *
3370609 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT---AA-AAG-
3370674 AGG
61 -GG
* *
3370677 TGCCACAGAGTTGTGGGCTTT--AAAG----A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--AAA-AG--
3370735 AAAGAG
61 ---G-G
* * *
3370741 TGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-GAAGAG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
3370802 TGCCACGGAGTCGTGGGCTTT-----G-AAGA-GTGCCACAGAGTCGTGGGCTTTGAAAAGAGAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--AAA-AG--
3370860 AAAGAG
61 ---G-G
** * *
3370866 TGCCACGGAGTTGTGGGC-TT--AAAG-ATGAGGTGCCACGGAATTGTGGGCTGTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* ** *
3370924 TGCCACGGAGTTGTGGAC-TT--AAAG-ATGAGGTGCCACGGAATTGTGGGCTTTAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
3370978 GAAAAAATGC
Statistics
Matches: 678, Mismatches: 60, Indels: 142
0.77 0.07 0.16
Matches are distributed among these distances:
54 20 0.03
55 3 0.00
56 1 0.00
57 8 0.01
58 76 0.11
59 22 0.03
60 41 0.06
61 107 0.16
62 105 0.15
63 28 0.04
64 42 0.06
65 24 0.04
66 22 0.03
67 89 0.13
68 58 0.09
69 10 0.01
70 1 0.00
71 21 0.03
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (62 bp):
TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:3370302 original size:28 final size:28
Alignment explanation
Indices: 3370201--3370463 Score: 120
Period size: 28 Copynumber: 8.8 Consensus size: 28
3370191 CTTTAAAAAG
* * *
3370201 AAAAAGGTGCCACGGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
* *
3370228 AAACGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** * *
3370261 GAAAAAAGTGCCACAGAATTGTGGGCTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
3370290 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** *
3370323 GAAAAAAGTGCCACGGAATTGTGGGCTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
3370352 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
** * *
3370380 GAGACAA-AATGCCACTGAGTTGTGGACTTT
1 -A-A-AAGGGTGCCACGGAATTGTGGACTTT
* * *
3370410 -AAAGGAAAAGATGCCACTGAGTCGTGGAC-TT
1 AAAAGG----G-TGCCACGGAATTGTGGACTTT
*
3370441 AAAAGGGTGCCACGGAGTTGTGG
1 AAAAGGGTGCCACGGAATTGTGG
3370464 GCTTAGAAGG
Statistics
Matches: 183, Mismatches: 30, Indels: 46
0.71 0.12 0.18
Matches are distributed among these distances:
26 2 0.01
27 37 0.20
28 48 0.26
29 3 0.02
30 21 0.11
31 4 0.02
32 22 0.12
33 2 0.01
34 44 0.24
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.22
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAATTGTGGACTTT
Found at i:3370302 original size:62 final size:61
Alignment explanation
Indices: 3370106--3370977 Score: 391
Period size: 62 Copynumber: 13.9 Consensus size: 61
3370096 GGGAGAAAGA
* *
3370106 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-TGAAAAA-AGTGCCACGGAATTGTGGGCTTTAAAAG----
*
3370171 AAG
60 -GG
* * * * *
3370174 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGAC-TTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
*
3370235 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
3370297 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
** * * * *
3370359 TGCCACGGAGTTGTGGACTT-TGA-GACAAAA-TGCCACTGAGTTGTGGACTTT-AAAGGAAAAG
1 TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGG----G
* * * * *
3370420 ATGCCACTGAGTCGTGGACTTAAAA-G-----GGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAA
1 -TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTT------TAAAA
*
3370479 GAG
59 GGG
* * * * * * *
3370482 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTT------TAAAAG
*
3370547 AG
60 GG
* * * *
3370549 TGCCACAGAGTTGTGGGCTT----T-AAAAAGAGTGCCACGGAGTCGTGGGCTTTAAGAAGAAGG
1 TGCCACGGAGTTGTGGACTTAAAATGAAAAA-AGTGCCACGGAATTGTGGGCTTTAA-AAG--GG
* * * * * *
3370609 TGCCACAGAGTTGTGGGCTTTGAAAA-GAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAG
1 TGCCACGGAGTTGTGGAC-TT-AAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT---AA-AAG
3370673 AAGG
60 --GG
* * * * *
3370677 TGCCACAGAGTTGTGGGCTT----T--AAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAA
1 TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT--AAA-AG---
3370736 AAGAG
60 --G-G
* * * * *
3370741 TGCCACGGAGTTGTGGGCTTTAAACA-GAAAAAGGTGCCACGGAGTTGTGGGCTTT-GAAGAG
1 TGCCACGGAGTTGTGGAC-TTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
* * * * * *
3370802 TGCCACGGAGTCGTGGGCTT----TG--AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAA
1 TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTT--AAA-AG---
3370861 AAGAG
60 --G-G
* * *
3370866 TGCCACGGAGTTGTGGGCTTAAAGATG----AGGTGCCACGGAATTGTGGGCTGTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
*
3370924 TGCCACGGAGTTGTGGACTTAAAGATG----AGGTGCCACGGAATTGTGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAA-ATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAA
3370978 GAAAAAATGC
Statistics
Matches: 664, Mismatches: 73, Indels: 144
0.75 0.08 0.16
Matches are distributed among these distances:
54 22 0.03
56 1 0.00
57 8 0.01
58 76 0.11
59 26 0.04
60 32 0.05
61 105 0.16
62 113 0.17
63 25 0.04
64 40 0.06
65 25 0.04
66 14 0.02
67 93 0.14
68 52 0.08
69 8 0.01
71 24 0.04
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
Found at i:3370394 original size:283 final size:286
Alignment explanation
Indices: 3369817--3371009 Score: 999
Period size: 280 Copynumber: 4.1 Consensus size: 286
3369807 TGGGAAGGAA
*
3369817 AAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1 AAAAGATGCCACGGAGTCGTGGACTTAAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
3369881 AAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
64 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--AAAGG----AGAGTGCCACGGAGTTGTGGGC-
**
3369946 TTAAACG-GAAAAAAGAGTGCCACA-AAGTTGTGGGCTTTAAAAAGGAAAAAAGAGTGCCACAAA
122 TT-AA-GTG-AAAAAGAGTGCCACAGAA-TTGTGGGCTTTAAAAA-G-----AGAGTGCCACGGA
* *
3370009 GTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGTTTTGAAAAGAAGAAGGTTGCCAC
177 GTTGTGGGC-TTAAAAGAAGAAGGTGCCACGGAATTGTGGGCTTT--AAAGAAG-AGG-TGCCAC
* * * *
3370074 CGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGG
237 GGA-GT-TGTGGACTTT--GAA--GAGAAA-ATGCCACAGAGTTGTGGACTT-AAA-GG
* *
3370133 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAA
1 -AAAAGA-TGCCACGGAGTCGTGGAC-TTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
3370197 AAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACG-G-GTGCCACGGAGTTGTGGACTTAAAG
63 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAGAGTGCCACGGAGTTGTGGGCTT-AAG
*
3370259 ATGAAAAA-AGTGCCACAGAATTGTGGGCTTT-AAAAG-G-GTGCCACGGAGTTGTGGACTTAAA
127 -TGAAAAAGAGTGCCACAGAATTGTGGGCTTTAAAAAGAGAGTGCCACGGAGTTGTGGGCTTAAA
* *
3370320 GATGAAAAAAGTGCCACGGAATTGTGGGCTTT-AA-AAG-GGTGCCACGGAGTTGTGGACTTTG-
191 -A-GAAGAAGGTGCCACGGAATTGTGGGCTTTAAAGAAGAGGTGCCACGGAGTTGTGGACTTTGA
* *
3370381 AGACAAAATGCCACTGAGTTGTGGACTTTAAAGG
254 AGAGAAAATGCCACAGAGTTGTGGAC-TTAAAGG
* * *
3370415 AAAAGATGCCACTGAGTCGTGGACTTAAAAG-----G-GTGCCACGGAGTTGTGGGC-TTAGAAG
1 AAAAGATGCCACGGAGTCGTGGACTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
*
3370473 GAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAG
66 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTA-AAGG---AGAGTGCCACGGAGTTGTGGGCTTA-
* *
3370537 GAG-GAAAAAGAGTGCCACAGAGTTGTGGGCTTT-AAAA-AGAGTGCCACGGAGTCGTGGGCTT-
125 -AGTGAAAAAGAGTGCCACAGAATTGTGGGCTTTAAAAAGAGAGTGCCACGGAGTTGTGGGCTTA
* * * * *
3370598 TAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTT
189 AAAGAAGAAGGTGCCACGGAATTGTGGGCTTT--AAAGAAG-AGGTGCCACGGAGTTGTGGACTT
* *
3370663 TGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTAAA-G
251 TGAAGAGAA-AA--TGCCACAGAGTTGTGGAC-TTAAAGG
*
3370702 ---AG-TGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAAGATGCCACGGAGTCGTGGAC-TT--AAA-AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
* * *
3370763 AACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT---GAAGAGTGCCACGGAGTCGTGGGCTT---
62 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAGAGTGCCACGGAGTTGTGGGCTTAAG
* *
3370822 TG---AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGC
127 TGAAAAAGAGTGCCACAGAATTGTGGGCTTT-AAAA-AG----AGAGTGCCACGGAGTTGTGGGC
* *
3370884 TT-AAAGATG-AGGTGCCACGGAATTGTGGGCTGT-AA-AAG-GGTGCCACGGAGTTGTGGAC-T
186 TTAAAAGAAGAAGGTGCCACGGAATTGTGGGCTTTAAAGAAGAGGTGCCACGGAGTTGTGGACTT
* ** * * *
3370943 TAAAGATG-AGGTGCCACGGAATTGTGGGCTTTAAA-G
251 TGAAGA-GAAAATGCCACAGAGTTGTGGAC-TTAAAGG
* *
3370979 AAAAAATGCCACTGAGTCGTGGACGTTAAAA
1 AAAAGATGCCACGGAGTCGTGGAC-TTAAAA
3371010 AGGTATTTGA
Statistics
Matches: 753, Mismatches: 65, Indels: 155
0.77 0.07 0.16
Matches are distributed among these distances:
273 12 0.02
274 41 0.05
275 3 0.00
277 23 0.03
278 26 0.03
279 19 0.03
280 94 0.12
281 66 0.09
282 8 0.01
283 42 0.06
284 35 0.05
285 4 0.01
286 6 0.01
287 47 0.06
288 50 0.07
289 9 0.01
290 2 0.00
291 8 0.01
292 3 0.00
293 38 0.05
294 16 0.02
295 2 0.00
296 5 0.01
297 17 0.02
298 26 0.03
304 1 0.00
305 4 0.01
306 21 0.03
307 12 0.02
308 19 0.03
309 1 0.00
314 4 0.01
316 25 0.03
317 41 0.05
318 17 0.02
319 6 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (286 bp):
AAAAGATGCCACGGAGTCGTGGACTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAGAGTGCCACGGAGTTGTGGGCTTAAGTGAA
AAAGAGTGCCACAGAATTGTGGGCTTTAAAAAGAGAGTGCCACGGAGTTGTGGGCTTAAAAGAAG
AAGGTGCCACGGAATTGTGGGCTTTAAAGAAGAGGTGCCACGGAGTTGTGGACTTTGAAGAGAAA
ATGCCACAGAGTTGTGGACTTAAAGG
Found at i:3370582 original size:247 final size:247
Alignment explanation
Indices: 3369823--3371009 Score: 807
Period size: 283 Copynumber: 4.6 Consensus size: 247
3369813 GGAAAAAAGA
* * *
3369823 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTT---TGAGAAAAA-AGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
* *
3369888 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACG
62 GA-TGCCACAGAGTTGTGGGC-TT--------AAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-G
** *
3369953 GAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGC
116 G-AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGG--AAAAGAGTGCCACAGAGTTGTGGGC
* * * *
3370018 TTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGTTTTGAAAAGAAGAAGGTTGCCACCGACTTGTG
177 -TT--AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG-AAA-AAG-A-G-TGCCACGGA-AT-TG
*
3370083 TGGGCTTTAGGAAGGGAGAAAGA
232 TGGGCTTTA--AA---AG--AGG
* * *
3370106 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTT---TGAGAAAAA-AGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
* * *
3370171 AAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACG--
62 GA-TGCCACAGAGTTGTGGGC-TT-AAAAG----A-GTGCCACGGAGTTGTGGGCTTTAAAGGAA
* * * * *
3370233 ---G-GTGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTT--TA
119 AAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAGAGTGCCACAGAGTTGTGGGCTTAAGA
* *
3370291 AAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA-AGTGCCACGGAATTGTGGGCTTTAAA
183 AAAAGGTGCCACGGAGTTGTGGGCTT-----TGAAAAAGAGTGCCACGGAATTGTGGGCTTTAAA
3370355 AG-GG
243 AGAGG
* * * *
3370359 TGCCACGGAGTTGTGGACTTTGAGACAAAA-TGCCACTGAGTTGTGGACTTTAAAGGAAAAGATG
1 TGCCACGGAGTTGTGGACTTTGAGAAAAAAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAGATG
* * * *
3370423 CCACTGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCA
66 CCACAGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAGGAAAAAGAGTGCCA
*
3370487 CGGAGTTGTGGGC-TTAGAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAAAAAGAGTG
130 CGGAGTTGTGGGCTTTAAAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTA--A-GAAAAAG-GTG
* * *
3370551 CCACAGAGTTGTGGGCTTT-AAAAAGAGTGCCACGGAGTCGTGGGCTTTAAGAAGAAGG
191 CCACGGAGTTGTGGGCTTTGAAAAAGAGTGCCACGGAATTGTGGGCTTTAA-AAG-AGG
* * *
3370609 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGA
1 TGCCACGGAGTTGTGGACTTTGAGAA-AA-AA-GTGCCACAGAGTTGTGGGCTTT-AAAAGAA-A
* * *
3370674 AGGTGCCACAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAG
61 AGATGCCACAGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGGCTTT--AAAG-GAAAAAG
* * * *
3370739 AGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAG-GTGCCACGGAGTTGTGGGCTT-TG-AAGA
123 AGTGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAGAGTGCCACAGAGTTGTGGGCTTAAGAAAAA
* * * *
3370801 -GTGCCACGGAGTCGTGGGCTTTG---AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAA
187 GGTGCCACGGAGTTGTGGGCTTTGAAAAAGAGTGCCACGGAATTGTGGGCTTT--AAA-AG----
3370862 AGAG
245 AG-G
* ** ** * * * * *
3370866 TGCCACGGAGTTGTGGGCTTAAAG-ATGAGGTGCCACGGAATTGTGGGCTGTAAAAG----GGTG
1 TGCCACGGAGTTGTGGACTTTGAGAAAAAAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAGATG
* * *
3370926 CCACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTTTAAA-GAAAAA-A-TGC
66 CCACAGAGTTGTGGGCTTAAA-A-GA-GTGCCACGGAGTTGTGGGCTTTAAAGGAAAAAGAGTGC
* * * *
3370988 CACTGAGTCGTGGACGTTAAAA
128 CACGGAGTTGTGGGCTTTAAAA
3371010 AGGTATTTGA
Statistics
Matches: 773, Mismatches: 80, Indels: 142
0.78 0.08 0.14
Matches are distributed among these distances:
240 22 0.03
241 3 0.00
243 1 0.00
244 20 0.03
245 6 0.01
246 41 0.05
247 83 0.11
248 35 0.05
249 3 0.00
250 50 0.06
251 32 0.04
252 27 0.03
253 64 0.08
254 20 0.03
255 9 0.01
256 49 0.06
257 23 0.03
258 3 0.00
259 30 0.04
260 24 0.03
261 18 0.02
262 1 0.00
263 8 0.01
264 24 0.03
265 1 0.00
267 2 0.00
268 5 0.01
269 24 0.03
270 3 0.00
271 4 0.01
272 16 0.02
273 1 0.00
276 6 0.01
279 1 0.00
280 6 0.01
281 19 0.02
283 89 0.12
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (247 bp):
TGCCACGGAGTTGTGGACTTTGAGAAAAAAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAGATG
CCACAGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAAGAGTGCCAC
GGAGTTGTGGGCTTTAAAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAAGAAAAAGGTGCCACG
GAGTTGTGGGCTTTGAAAAAGAGTGCCACGGAATTGTGGGCTTTAAAAGAGG
Found at i:3370812 original size:27 final size:27
Alignment explanation
Indices: 3370774--3370852 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
3370764 ACAGAAAAAG
*
3370774 GTGCCACGGAGTTGTGGGCTTTGAAGA
1 GTGCCACGGAGTCGTGGGCTTTGAAGA
3370801 GTGCCACGGAGTCGTGGGCTTTGAAGA
1 GTGCCACGGAGTCGTGGGCTTTGAAGA
*
3370828 GTGCCACAGAGTCGTGGGCTTTGAA
1 GTGCCACGGAGTCGTGGGCTTTGAA
3370853 AAGAGAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.19, C:0.18, G:0.39, T:0.24
Consensus pattern (27 bp):
GTGCCACGGAGTCGTGGGCTTTGAAGA
Found at i:3370839 original size:98 final size:97
Alignment explanation
Indices: 3370441--3370885 Score: 419
Period size: 98 Copynumber: 4.6 Consensus size: 97
3370431 TCGTGGACTT
* * *
3370441 AAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTA-AAAGAAAAAG-GTGCCACGGAGTTGTGGGCTT---
* * **
3370505 AGGAAAAGAGTGCCACAGAGTTGTGGGC-TT-AGGAG-GA
61 -TG--AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGA
* *
3370542 AAAAGAGTGCCACAGAGTTGTGGGCTTT--AA-AAAGA-GTGCCACGGAGTCGTGGGCTTTAAGA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT--GA
*
3370603 AGAAGGTGCCACAGAGTTGTGGGCTTTG-AAA-AGA
64 AG-A-GTGCCACAGAGTCGTGGGCTTTGAAAAGAGA
* * * *
3370637 AGAAG-GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTAAA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
*
3370701 GAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGA
65 GAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGA
*
3370734 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
*
3370799 GAGTGCCACGGAGTCGTGGGCTTT-------G-
65 GAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGA
*
3370824 --AAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACAGAGTTGTGGGCTTT--AAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTT
3370886 AAAGATGAGG
Statistics
Matches: 300, Mismatches: 24, Indels: 50
0.80 0.06 0.13
Matches are distributed among these distances:
88 24 0.08
90 11 0.04
91 22 0.07
92 3 0.01
93 1 0.00
94 42 0.14
95 30 0.10
96 24 0.08
97 15 0.05
98 82 0.27
99 21 0.07
101 23 0.08
102 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.36, T:0.20
Consensus pattern (97 bp):
AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
AGTGCCACAGAGTCGTGGGCTTTGAAAAGAGA
Found at i:3370856 original size:125 final size:122
Alignment explanation
Indices: 3370234--3370984 Score: 547
Period size: 125 Copynumber: 6.0 Consensus size: 122
3370224 GCTTAAACGG
* * * * *
3370234 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGGTG
1 GTGCCACGGAGTTGTGGGCTTAAA-A-GAAAAAGGTGCCACAGAGTTGTGGGCTTT-GAAGAGTG
* * * * *
3370299 CCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTT-AAA-AG-----
63 CCACAGAGTTGTGGGCTT-----T--AAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGAGAAAAA
3370357 G-
121 GA
* ** * * *
3370358 GTGCCACGGAGTTGTGGACTT-TGAGACAAAA--TGCCACTGAGTTGTGGACTTTAAAGGAAAAG
1 GTGCCACGGAGTTGTGGGCTTAAAAGA-AAAAGGTGCCACAGAGTTGTGGGCTTT----GAAGAG
* * * * * * *
3370420 ATGCCACTGAGTCGTGGACTTAAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAG-GAAAAAGA
61 -TGCCACAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGAGAAAAAGA
* * *
3370481 GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAGAGTGCCACAGAGTTGTGGGCTTAGGAGGAAAAA
1 GTGCCACGGAGTTGTGGGCTTAAAAGAAAAAG-GTGCCACAGAGTTGTGGGCTT----TG---AA
*
3370546 GAGTGCCACAGAGTTGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGGCTTT---A-AGAAGAA
58 GAGTGCCACAGAGTTGTGGGCTTT--AAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGAGAAAAA
3370607 G-
121 GA
* *
3370608 GTGCCACAGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAG
1 GTGCCACGGAGTTGTGGGC-TT-AAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTT-----GAAG
3370673 AAGGTGCCACAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAA
59 -A-GTGCCACAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTT-AAAAGAGAAAAA
3370738 GA
121 GA
*
3370740 GTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAGTGC
1 GTGCCACGGAGTTGTGGGC-TTAAA-AGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAGTGC
* * * *
3370805 CACGGAGTCGTGGGCTTTGAAGAGTGCCACAGAGTCGTGGGCTTTGAAAAGAGAAAAAGA
64 CACAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTT-AAAAGAGAAAAAGA
** * * ** *
3370865 GTGCCACGGAGTTGTGGGCTT-AAAG-ATGAGGTGCCACGGAATTGTGGGCTGTAAAAGGGTGCC
1 GTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCT-TTGAAGAGTGCC
* * * * *
3370928 ACGGAGTTGTGGACTTAAAGATGAGGTGCCACGGAATTGTGGGCTTT-AAAGA-AAAAA
65 ACAGAGTTGTGGGCTTTAA-A-GA-GTGCCACGGAGTCGTGGGCTTTAAAAGAGAAAAA
3370985 TGCCACTGAG
Statistics
Matches: 522, Mismatches: 57, Indels: 98
0.77 0.08 0.14
Matches are distributed among these distances:
116 2 0.00
117 24 0.05
120 18 0.03
121 24 0.05
122 37 0.07
123 35 0.07
124 45 0.09
125 98 0.19
126 50 0.10
127 23 0.04
128 69 0.13
129 13 0.02
130 23 0.04
131 12 0.02
132 49 0.09
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (122 bp):
GTGCCACGGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAGTGCCA
CAGAGTTGTGGGCTTTAAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGAGAAAAAGA
Found at i:3370865 original size:27 final size:27
Alignment explanation
Indices: 3370809--3370866 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3370799 GAGTGCCACG
* * ** *
3370809 GAGTCGTGGGCTTTGAAGAGTGCCACA
1 GAGTCGTGGGCTTTGAAAAGAGAAAAA
3370836 GAGTCGTGGGCTTTGAAAAGAGAAAAA
1 GAGTCGTGGGCTTTGAAAAGAGAAAAA
3370863 GAGT
1 GAGT
3370867 GCCACGGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (27 bp):
GAGTCGTGGGCTTTGAAAAGAGAAAAA
Found at i:3370901 original size:30 final size:30
Alignment explanation
Indices: 3370865--3370979 Score: 164
Period size: 30 Copynumber: 3.9 Consensus size: 30
3370855 GAGAAAAAGA
*
3370865 GTGCCACGGAGTTGTGGGCTTAAAGATGAG
1 GTGCCACGGAATTGTGGGCTTAAAGATGAG
3370895 GTGCCACGGAATTGTGGGCTGTAAA-A-G-G
1 GTGCCACGGAATTGTGGGCT-TAAAGATGAG
* *
3370923 GTGCCACGGAGTTGTGGACTTAAAGATGAG
1 GTGCCACGGAATTGTGGGCTTAAAGATGAG
3370953 GTGCCACGGAATTGTGGGCTTTAAAGA
1 GTGCCACGGAATTGTGGGC-TTAAAGA
3370980 AAAAATGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.05
28 20 0.27
29 2 0.03
30 38 0.51
31 11 0.15
ACGTcount: A:0.25, C:0.14, G:0.37, T:0.23
Consensus pattern (30 bp):
GTGCCACGGAATTGTGGGCTTAAAGATGAG
Found at i:3379356 original size:52 final size:52
Alignment explanation
Indices: 3379223--3379363 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
3379213 TGAAAAGTTA
3379223 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
3379275 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
3379327 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
3379364 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:3379370 original size:13 final size:13
Alignment explanation
Indices: 3379352--3379376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3379342 CAAAAATCAG
3379352 TGTATCGATACAA
1 TGTATCGATACAA
3379365 TGTATCGATACA
1 TGTATCGATACA
3379377 TGTGAGTAAT
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:3379460 original size:13 final size:13
Alignment explanation
Indices: 3379442--3379466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3379432 CAAAAAAATA
3379442 TGTATCGATACAT
1 TGTATCGATACAT
3379455 TGTATCGATACA
1 TGTATCGATACA
3379467 ACATTTTATG
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:3379462 original size:33 final size:33
Alignment explanation
Indices: 3379420--3379486 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3379410 AGTAGCTTAA
3379420 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3379453 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3379486 A
1 A
3379487 AATCATTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3379565 original size:21 final size:21
Alignment explanation
Indices: 3379524--3379565 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3379514 GTTGGGACCT
*
3379524 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
3379545 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
3379566 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:3379880 original size:13 final size:13
Alignment explanation
Indices: 3379862--3379886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3379852 CAAAGATCCG
3379862 TGTATCGATACAA
1 TGTATCGATACAA
3379875 TGTATCGATACA
1 TGTATCGATACA
3379887 TTTGAGTATT
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:3379949 original size:13 final size:13
Alignment explanation
Indices: 3379931--3379982 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
3379921 AGCTTCGTAG
3379931 CGATACATTGTAT
1 CGATACATTGTAT
3379944 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
3379963 CGATACATTGTAT
1 CGATACATTGTAT
3379976 CGATACA
1 CGATACA
3379983 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:3380249 original size:479 final size:487
Alignment explanation
Indices: 3379278--3380268 Score: 1355
Period size: 495 Copynumber: 2.0 Consensus size: 487
3379268 AATTTGCCTG
*
3379278 CATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC
1 CATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC
*
3379343 AAAAATCAGTGTATCGATACAATGTATCGATACATGTGAGTAATGTATCGATACATTTTTTTTTG
66 AAAAATCAGTGTATCGATACAATGTATCGATACATGTGAGTAATGTATCGATACA-TTTTTCTTG
* *
3379408 GCAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATCGATACATTGTATCGATACAACATTT
130 GCAGTAGCTT--ATCGTAGCGATAC-----AATATGTATCGATACATTGTATCGAT--AACA--T
* *
3379473 TATGTATCGATACAAATCATTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATT
184 TATGTATCGATACAAATCATTGAAATTCAAAATTTTTAACCGTTAGGACCTTGTATCGATACATT
*
3379538 TTAACAATGTATCGATACATTTGGACAAAAATGTAATTTTTTCATCCTTTTTGCCTTCGAAACAC
249 CTAACAATGTATCGATACATTTGGACAAAAATGTAATTTTTTCATCCTTTTTGCCTTCGAAACAC
* * *
3379603 CCTATCTTGACTAGGGACGACGGGAAATGAATTCGAGCTTAACAAAAAGTTATAAAAATCTAAAA
314 CCTATCTCGACTAAGGACGACGGGAAATGAATTCGAGCATAACAAAAAGTTATAAAAATCTAAAA
*
3379668 AACCATTTTCGCCGGGCGCTGCTGGCGCCCGGCGAATTCGTCCCCACATAAGTCGAATCCTCCAC
379 AACCATTTTCGCCGGGCGCTACT----------GAA-TCGTCCCCACATAAGTCGAATCCTCCAC
*
3379733 CTACTAGCTAGGCTTCAAATTGTCGAAAATTGGCCCGGACAAAATGAAGTGTCTA
433 CTACTAGCTAGGCCTCAAATTGTCGAAAATTGGCCCGGACAAAATGAAGTGTCTA
*
3379788 CATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC
1 CATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC
* * * *
3379853 AAAGATCCGTGTATCGATACAATGTATCGATACATTTGAGTATTGTATCGATACA-TTTTCTTGG
66 AAAAATCAGTGTATCGATACAATGTATCGATACATGTGAGTAATGTATCGATACATTTTTCTTGG
3379917 CAGTAGC-T-TCGTAGCGATAC-AT-TGTATCGATACAAAACTTATGTATCGAT-ACA-T-TGTA
131 CAGTAGCTTATCGTAGCGATACAATATGTATCGATAC---A--T-TGTATCGATAACATTATGTA
* *
3379975 TCGATACAAATCGTTGAAATTCAAAA-TTTTAACCGTTAGGACCTTGTATGGATACATTCTAACA
190 TCGATACAAATCATTGAAATTCAAAATTTTTAACCGTTAGGACCTTGTATCGATACATTCTAACA
* *
3380039 ATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATTCTTTTTGCCTTCTG-AACACCCTAT
255 ATGTATCGATACATTTGGACAAAAATGTAATTTTTTCATCCTTTTTGCCTTC-GAAACACCCTAT
* * *
3380103 CTCGACTAAGGACGATGGGAAATGGATTCGGGCATAACAAAAAGTTATAAAAATCTAAAAAACCA
319 CTCGACTAAGGACGACGGGAAATGAATTCGAGCATAACAAAAAGTTATAAAAATCTAAAAAACCA
* *
3380168 TTTTCGCC-GG-GC-ACT-AA-CGTCCTCACATATGTCGAATCCTCCACCTACTAGCTAGGCCTC
384 TTTTCGCCGGGCGCTACTGAATCGTCCCCACATAAGTCGAATCCTCCACCTACTAGCTAGGCCTC
* *
3380228 AAATTGTCGAAAATTGGCCCGGACGAAATGAGGTGTCTA
449 AAATTGTCGAAAATTGGCCCGGACAAAATGAAGTGTCTA
3380267 CA
1 CA
3380269 ATATCCTTGT
Statistics
Matches: 446, Mismatches: 28, Indels: 45
0.86 0.05 0.09
Matches are distributed among these distances:
479 79 0.18
481 2 0.00
492 2 0.00
493 2 0.00
494 2 0.00
495 161 0.36
496 30 0.07
497 12 0.03
498 2 0.00
500 4 0.01
502 1 0.00
503 9 0.02
504 10 0.02
507 1 0.00
508 15 0.03
510 114 0.26
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (487 bp):
CATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC
AAAAATCAGTGTATCGATACAATGTATCGATACATGTGAGTAATGTATCGATACATTTTTCTTGG
CAGTAGCTTATCGTAGCGATACAATATGTATCGATACATTGTATCGATAACATTATGTATCGATA
CAAATCATTGAAATTCAAAATTTTTAACCGTTAGGACCTTGTATCGATACATTCTAACAATGTAT
CGATACATTTGGACAAAAATGTAATTTTTTCATCCTTTTTGCCTTCGAAACACCCTATCTCGACT
AAGGACGACGGGAAATGAATTCGAGCATAACAAAAAGTTATAAAAATCTAAAAAACCATTTTCGC
CGGGCGCTACTGAATCGTCCCCACATAAGTCGAATCCTCCACCTACTAGCTAGGCCTCAAATTGT
CGAAAATTGGCCCGGACAAAATGAAGTGTCTA
Found at i:3382833 original size:22 final size:22
Alignment explanation
Indices: 3382805--3382877 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
3382795 GTTTGAAAAT
3382805 AAATTTTTTATCAAGGGGGAGA
1 AAATTTTTTATCAAGGGGGAGA
*
3382827 AAATTTTTTATCAAGGGGGAAA
1 AAATTTTTTATCAAGGGGGAGA
*
3382849 AAATTTTTTATCAAGGGAGAG-
1 AAATTTTTTATCAAGGGGGAGA
3382870 AAATTTTT
1 AAATTTTT
3382878 AAACGAGAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 8 0.17
22 40 0.83
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (22 bp):
AAATTTTTTATCAAGGGGGAGA
Found at i:3383458 original size:20 final size:19
Alignment explanation
Indices: 3383435--3383507 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
3383425 CACACCTAGA
*
3383435 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
3383455 TGTATCGATATATGTTCAT
1 TGTATCGATACATGTTCAT
**
3383474 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
3383494 TGTATCGATACATG
1 TGTATCGATACATG
3383508 AAACTGGCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.35
20 29 0.63
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:3384111 original size:46 final size:46
Alignment explanation
Indices: 3384061--3384152 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
3384051 GAAAGACTTT
*
3384061 GAAAAACTATAAACAAGTTTTGTTCGCTTAAAAATACTCTAAAAAC
1 GAAAAACTATAAACAAGTTTTGTTCGCTTAAAAACACTCTAAAAAC
*
3384107 GAAAAACTGTAAACAAGTTTTGTTCGCTTAAAAACACTCTAAAAAC
1 GAAAAACTATAAACAAGTTTTGTTCGCTTAAAAACACTCTAAAAAC
3384153 ATGTTCTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (46 bp):
GAAAAACTATAAACAAGTTTTGTTCGCTTAAAAACACTCTAAAAAC
Found at i:3384409 original size:20 final size:19
Alignment explanation
Indices: 3384359--3384412 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
3384349 ACATTATGCT
**
3384359 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
***
3384378 TTGTAAAAATACATGCACAA
1 TTGTATCGATACATGCAC-A
3384398 TTGTATCGATACATG
1 TTGTATCGATACATG
3384413 AAACTGGCAG
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:3389402 original size:21 final size:21
Alignment explanation
Indices: 3389378--3389429 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
3389368 ACCATAAATA
*
3389378 AATGTACATACCAGTATAATT
1 AATGTACATACCAGTATAATG
*
3389399 AATGTACATACCATTATAATG
1 AATGTACATACCAGTATAATG
*
3389420 AATATACATA
1 AATGTACATA
3389430 TGACTATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (21 bp):
AATGTACATACCAGTATAATG
Found at i:3389794 original size:22 final size:22
Alignment explanation
Indices: 3389745--3389842 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
3389735 CAAGCATATA
* * * *
3389745 TAAATGTACATACCACCATAGC
1 TAAATATACATATCACTATAAC
*
3389767 AAAATATACATATCACTATAAC
1 TAAATATACATATCACTATAAC
* * *
3389789 TCAATATACATATTAATATAAC
1 TAAATATACATATCACTATAAC
*
3389811 TAAATATACATATGACTATAAC
1 TAAATATACATATCACTATAAC
* *
3389833 TTAATGTACA
1 TAAATATACA
3389843 CATAACCTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAATATACATATCACTATAAC
Found at i:3390299 original size:22 final size:22
Alignment explanation
Indices: 3390272--3390325 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3390262 TGAATTTCTA
3390272 ACTATAACTAAATGTACATATG
1 ACTATAACTAAATGTACATATG
* *
3390294 ATTATAACTTAATGTACATATG
1 ACTATAACTAAATGTACATATG
3390316 ACTATAACTA
1 ACTATAACTA
3390326 TAACTAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (22 bp):
ACTATAACTAAATGTACATATG
Found at i:3390302 original size:28 final size:28
Alignment explanation
Indices: 3390270--3390352 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 28
3390260 AATGAATTTC
3390270 TAACTATAACTAAATGTACATATGATTA
1 TAACTATAACTAAATGTACATATGATTA
*
3390298 TAAC--T---T-AATGTACATATGACTA
1 TAACTATAACTAAATGTACATATGATTA
* *
3390320 TAACTATAACTAATTGTATATATGATTA
1 TAACTATAACTAAATGTACATATGATTA
3390348 TAACT
1 TAACT
3390353 GGATGTACAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
22 19 0.42
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 22 0.49
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (28 bp):
TAACTATAACTAAATGTACATATGATTA
Found at i:3393965 original size:20 final size:19
Alignment explanation
Indices: 3393919--3393993 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
3393909 TTTTACCGAG
3393919 ATGTATCGATACATTTTTCG-
1 ATGTATCGATACA-TTTT-GA
* *
3393939 ATATATCGATACATGTATGA
1 ATGTATCGATACAT-TTTGA
* *
3393959 ATGTATCGATATATTCTTTA
1 ATGTATCGATACATT-TTGA
3393979 ATGTATCGATACATT
1 ATGTATCGATACATT
3393994 ATATCTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.07
20 42 0.93
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTGA
Found at i:3394925 original size:22 final size:22
Alignment explanation
Indices: 3394899--3394953 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
3394889 AGCCTTTGAC
3394899 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
3394921 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
3394943 CATGCATTTTT
1 CATGCATTTTT
3394954 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:3394960 original size:20 final size:21
Alignment explanation
Indices: 3394899--3394960 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3394889 AGCCTTTGAC
**
3394899 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
3394921 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
3394943 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
3394961 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:3397663 original size:29 final size:29
Alignment explanation
Indices: 3397630--3397685 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
3397620 GGATTAGGCA
3397630 GATCCATCAAACAATTACATGGGCAACTT
1 GATCCATCAAACAATTACATGGGCAACTT
3397659 GATCCATCAAACAATTACATGGGCAAC
1 GATCCATCAAACAATTACATGGGCAAC
3397686 CTTTGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (29 bp):
GATCCATCAAACAATTACATGGGCAACTT
Found at i:3399132 original size:1 final size:1
Alignment explanation
Indices: 3399128--3399152 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3399118 TAACCATCAG
3399128 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3399153 GCAGACAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3400658 original size:11 final size:11
Alignment explanation
Indices: 3400642--3400666 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3400632 TTTGAAGTAA
3400642 AAAATTTATTT
1 AAAATTTATTT
3400653 AAAATTTATTT
1 AAAATTTATTT
3400664 AAA
1 AAA
3400667 TAGTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTTATTT
Found at i:3401412 original size:2 final size:2
Alignment explanation
Indices: 3401405--3401435 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3401395 TAACAAATTC
*
3401405 AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3401436 AATTACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3402017 original size:26 final size:25
Alignment explanation
Indices: 3401970--3402018 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
3401960 TTGATACTTT
* *
3401970 AATAAATAATTGAAAATAATAATTA
1 AATAAATAATAGAAAAAAATAATTA
3401995 AATAAATAAATAGAAAAAAATAAT
1 AATAAAT-AATAGAAAAAAATAAT
3402019 GATAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
AATAAATAATAGAAAAAAATAATTA
Found at i:3402094 original size:2 final size:2
Alignment explanation
Indices: 3402087--3402128 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3402077 GATTTCGTGC
3402087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3402129 ACTTTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3402490 original size:20 final size:20
Alignment explanation
Indices: 3402461--3402503 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3402451 TAAAATCAAA
*
3402461 TAATATAAAAGTTAAATTTT
1 TAATAAAAAAGTTAAATTTT
* *
3402481 TAATAAAAAATTTAACTTTT
1 TAATAAAAAAGTTAAATTTT
3402501 TAA
1 TAA
3402504 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAATAAAAAAGTTAAATTTT
Found at i:3402851 original size:13 final size:12
Alignment explanation
Indices: 3402800--3402852 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3402790 ATATAATTAT
*
3402800 TTTATTTTTTAA
1 TTTATATTTTAA
3402812 TTTATATTTTAA
1 TTTATATTTTAA
3402824 TATTATATTTT--
1 T-TTATATTTTAA
*
3402835 TTTAATTTTTTAA
1 TTT-ATATTTTAA
3402848 TTTAT
1 TTTAT
3402853 CTCAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
10 2 0.06
11 7 0.20
12 14 0.40
13 12 0.34
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATATTTTAA
Found at i:3403501 original size:19 final size:19
Alignment explanation
Indices: 3403479--3403555 Score: 70
Period size: 19 Copynumber: 3.9 Consensus size: 19
3403469 ATATAATTAT
3403479 ATAATATAAATATAAAAAA
1 ATAATATAAATATAAAAAA
3403498 ATAAT-TAAAATATAATAAAA
1 ATAATAT-AAATATAA-AAAA
*
3403518 TATAA-AAAATATGATATAAAAA
1 -ATAATATAA-AT-ATA-AAAAA
3403540 ATAATATAAATA-AAAA
1 ATAATATAAATATAAAA
3403556 TATATAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
18 4 0.08
19 14 0.29
20 7 0.15
21 12 0.25
22 10 0.21
23 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (19 bp):
ATAATATAAATATAAAAAA
Found at i:3403501 original size:27 final size:27
Alignment explanation
Indices: 3403471--3403526 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
3403461 TTGACATTAT
3403471 ATAATT-ATATAATATAAATATAAAAAA
1 ATAATTAATATAATA-AAATATAAAAAA
3403498 ATAATTAAAATATAATAAAATATAAAAAA
1 ATAATT--AATATAATAAAATATAAAAAA
3403527 TATGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.23
29 12 0.46
30 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
ATAATTAATATAATAAAATATAAAAAA
Found at i:3403528 original size:14 final size:14
Alignment explanation
Indices: 3403481--3403557 Score: 50
Period size: 14 Copynumber: 5.3 Consensus size: 14
3403471 ATAATTATAT
3403481 AATATAAATATAAAA
1 AATA-AAATATAAAA
*
3403496 AA-ATAAT-TAAAATA
1 AATAAAATAT-AAA-A
3403510 TAATAAAATATAAAA
1 -AATAAAATATAAAA
**
3403525 AATATGATATAAAA
1 AATAAAATATAAAA
* *
3403539 AATAATATAAATAAA
1 AATAAAATATA-AAA
3403554 AATA
1 AATA
3403558 TATAAATTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 22 0.45
15 12 0.24
16 7 0.14
17 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.27
Consensus pattern (14 bp):
AATAAAATATAAAA
Found at i:3403546 original size:12 final size:12
Alignment explanation
Indices: 3403516--3403559 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
3403506 AATATAATAA
3403516 AATATAAAAAAT
1 AATATAAAAAAT
3403528 ATGATATAAAAAAT
1 A--ATATAAAAAAT
3403542 AATATAAATAAA-
1 AATATAAA-AAAT
3403554 AATATA
1 AATATA
3403560 TAAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 14 0.48
13 3 0.10
14 12 0.41
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AATATAAAAAAT
Found at i:3403560 original size:14 final size:14
Alignment explanation
Indices: 3403482--3403564 Score: 53
Period size: 16 Copynumber: 5.6 Consensus size: 14
3403472 TAATTATATA
3403482 ATATAAATATAAAA-
1 ATATAAATA-AAAAT
* *
3403496 AAAT-AATTAAAAT
1 ATATAAATAAAAAT
*
3403509 ATAATAAAATATAAAAA
1 AT-AT-AAATA-AAAAT
*
3403526 ATATGATATAAAAAAT
1 ATAT-AAAT-AAAAAT
3403542 AATATAAATAAAAAT
1 -ATATAAATAAAAAT
3403557 ATATAAAT
1 ATATAAAT
3403565 TTATTAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
12 4 0.08
13 4 0.08
14 13 0.25
15 6 0.11
16 15 0.28
17 11 0.21
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (14 bp):
ATATAAATAAAAAT
Found at i:3403604 original size:31 final size:33
Alignment explanation
Indices: 3403475--3403613 Score: 117
Period size: 31 Copynumber: 4.2 Consensus size: 33
3403465 CATTATATAA
* * *
3403475 TTATATAATATAAATATAAAAAAATAATTAAAAT
1 TTATATAATAAAAATATATAAATAT-ATTAAAAT
* * * * *
3403509 ATAATAAAATATAAAAAATAT-GATATA--AAAAA
1 -TTATATAATA-AAAATATATAAATATATTAAAAT
* *
3403541 TAATATAAATAAAAATATATAAATTTATTAAAAT
1 TTATAT-AATAAAAATATATAAATATATTAAAAT
3403575 TTATATAATAAAAATAT-T-AATATATTAAAAT
1 TTATATAATAAAAATATATAAATATATTAAAAT
3403606 TTATATAA
1 TTATATAA
3403614 ATATATAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
31 33 0.39
32 13 0.15
33 11 0.13
34 10 0.12
35 11 0.13
36 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
TTATATAATAAAAATATATAAATATATTAAAAT
Found at i:3403616 original size:20 final size:19
Alignment explanation
Indices: 3403552--3403619 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 19
3403542 AATATAAATA
* *
3403552 AAAATATATA-AATTTATT
1 AAAATTTATATAATATATT
3403570 AAAATTTATAT-A-ATA--
1 AAAATTTATATAATATATT
3403585 AAAA--TAT-TAATATATT
1 AAAATTTATATAATATATT
3403601 AAAATTTATATAAATATAT
1 AAAATTTATAT-AATATAT
3403620 AATATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
12 1 0.03
13 4 0.10
14 3 0.08
15 4 0.10
16 4 0.10
17 2 0.05
18 13 0.33
19 1 0.03
20 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTTATATAATATATT
Found at i:3403620 original size:10 final size:10
Alignment explanation
Indices: 3403477--3403620 Score: 56
Period size: 10 Copynumber: 14.7 Consensus size: 10
3403467 TTATATAATT
3403477 ATATAATATAA
1 ATAT-ATATAA
* *
3403488 ATATAAAAAA
1 ATATATATAA
3403498 ATA-AT-TAA
1 ATATATATAA
3403506 A-ATATAATAA
1 ATATAT-ATAA
*
3403516 A-ATATAAAAA
1 ATATAT-ATAA
3403526 ATATGATATAA
1 ATAT-ATATAA
3403537 A-A-A-AT-A
1 ATATATATAA
*
3403543 ATATAAATAA
1 ATATATATAA
*
3403553 AAATATATAA
1 ATATATATAA
*
3403563 ATTTAT-TAAA
1 ATATATAT-AA
*
3403573 ATTTATATAA
1 ATATATATAA
* * *
3403583 TAAAAATATTA
1 -ATATATATAA
3403594 ATATAT-TAAA
1 ATATATAT-AA
*
3403604 ATTTATATAA
1 ATATATATAA
3403614 ATATATA
1 ATATATA
3403621 ATATTTTAAA
Statistics
Matches: 100, Mismatches: 19, Indels: 29
0.68 0.13 0.20
Matches are distributed among these distances:
6 2 0.02
7 4 0.04
8 7 0.07
9 5 0.05
10 62 0.62
11 18 0.18
12 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (10 bp):
ATATATATAA
Found at i:3406647 original size:18 final size:19
Alignment explanation
Indices: 3406603--3406650 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
3406593 GAAATTTATT
3406603 TATTTAT-TTTTTAGAAAA
1 TATTTATATTTTTAGAAAA
*
3406621 TATTT-TATTTTTA-TAAA
1 TATTTATATTTTTAGAAAA
*
3406638 TTTTTATATTTTT
1 TATTTATATTTTT
3406651 TATGCCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTATATTTTTAGAAAA
Found at i:3406650 original size:19 final size:18
Alignment explanation
Indices: 3406605--3406653 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
3406595 AATTTATTTA
*
3406605 TTTATTTTTTAGAAAATAT
1 TTTATTTTTTA-TAAATAT
*
3406624 TTTA-TTTTTATAAATTT
1 TTTATTTTTTATAAATAT
3406641 TTATATTTTTTAT
1 TT-TATTTTTTAT
3406654 GCCAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 8 0.31
19 11 0.42
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTTTTATAAATAT
Found at i:3407075 original size:2 final size:2
Alignment explanation
Indices: 3407068--3407102 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3407058 CATTTACTTT
3407068 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
3407103 TAAATTTTCA
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:3408094 original size:3 final size:3
Alignment explanation
Indices: 3408080--3408119 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3408070 AAATTACGAG
*
3408080 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3408120 TAATATGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3408497 original size:2 final size:2
Alignment explanation
Indices: 3408490--3408539 Score: 50
Period size: 2 Copynumber: 25.5 Consensus size: 2
3408480 ACTAGTATGC
* * *
3408490 AT AT AT AT AT AT AT AT AT -T AGC AT AT A- AA AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
3408531 AT AT AT AT A
1 AT AT AT AT A
3408540 AATTATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.93
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3409139 original size:19 final size:18
Alignment explanation
Indices: 3409115--3409154 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3409105 TTTAATATAA
*
3409115 AATATTTTATATTAATATT
1 AATATTTTATAATAAT-TT
*
3409134 AATATTTTTTAATAATTT
1 AATATTTTATAATAATTT
3409152 AAT
1 AAT
3409155 TTAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTTTATAATAATTT
Found at i:3409142 original size:20 final size:20
Alignment explanation
Indices: 3409106--3409154 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3409096 AAATTACTAT
*
3409106 TTAATA-TAAAATATTTTATA
1 TTAATATTAATATATTTT-TA
3409126 TTAATATTAATAT-TTTTTA
1 TTAATATTAATATATTTTTA
*
3409145 ATAAT-TTAAT
1 TTAATATTAAT
3409155 TTAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
20 10 0.38
21 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATATTAATATATTTTTA
Found at i:3409606 original size:19 final size:19
Alignment explanation
Indices: 3409565--3409609 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3409555 ATCATATTTT
* *
3409565 TAATACTTAAATATTATAT
1 TAATACTTAAATATTAAAA
3409584 TAATA-TTAAATATTTAAAA
1 TAATACTTAAATA-TTAAAA
3409603 TAATACT
1 TAATACT
3409610 ATTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 14 0.64
20 1 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATACTTAAATATTAAAA
Found at i:3409682 original size:46 final size:47
Alignment explanation
Indices: 3409563--3409697 Score: 129
Period size: 46 Copynumber: 2.9 Consensus size: 47
3409553 TAATCATATT
*
3409563 TTTAATACTT-AAATATTATATTAATATTAAATATTTAAAATAATACTA
1 TTTAATA-TTAAAATATTATATTAATA-TAAATATTTAAAATAATAATA
* *
3409611 TTTATTATTAAAATATTA-ATT-ATATAAATATTTTAAAATTATAA-A
1 TTTAATATTAAAATATTATATTAATATAAATA-TTTAAAATAATAATA
* *
3409656 TATTAATA-TACAAT-TTATATTAATATAATTATGATTAAAATA
1 T-TTAATATTAAAATATTATATTAATATAAATAT--TTAAAATA
3409698 TTATTTTAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
44 3 0.04
45 17 0.23
46 27 0.37
47 12 0.16
48 14 0.19
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (47 bp):
TTTAATATTAAAATATTATATTAATATAAATATTTAAAATAATAATA
Found at i:3410396 original size:16 final size:16
Alignment explanation
Indices: 3410358--3410417 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
3410348 AAGCAACCCA
*
3410358 AACCC-AAAATAGCTCG
1 AACCCGAAAA-AGGTCG
* *
3410374 AATCCGATAAAGGTCG
1 AACCCGAAAAAGGTCG
* *
3410390 AACCCGAAAAAGTTCA
1 AACCCGAAAAAGGTCG
3410406 AACCCGAAAAAG
1 AACCCGAAAAAG
3410418 TTTGAATCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 33 0.92
17 3 0.08
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.12
Consensus pattern (16 bp):
AACCCGAAAAAGGTCG
Found at i:3410447 original size:16 final size:16
Alignment explanation
Indices: 3410428--3410476 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
3410418 TTTGAATCCA
*
3410428 AAAAAACCCGAACCTG
1 AAAAAACCCGAACCCG
* *
3410444 AAAAGATCCGAACCCG
1 AAAAAACCCGAACCCG
* *
3410460 AAAGAACCTGAACCCG
1 AAAAAACCCGAACCCG
3410476 A
1 A
3410477 GACTGACCCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.31, G:0.16, T:0.06
Consensus pattern (16 bp):
AAAAAACCCGAACCCG
Found at i:3412476 original size:387 final size:387
Alignment explanation
Indices: 3411762--3412537 Score: 1552
Period size: 387 Copynumber: 2.0 Consensus size: 387
3411752 ATATCCTTAT
3411762 AATAGTCTTCTCTAACTTCATCAAATATATATCCAACTCTGATCTATTTGAAGTAAACCAAGAAT
1 AATAGTCTTCTCTAACTTCATCAAATATATATCCAACTCTGATCTATTTGAAGTAAACCAAGAAT
3411827 CAAAATGACAAAAAGCCTACATTAACAAAATAAACAAAGTCGAATACCATATTGTGATAATAAAT
66 CAAAATGACAAAAAGCCTACATTAACAAAATAAACAAAGTCGAATACCATATTGTGATAATAAAT
3411892 ATAAAATAAAATAAAAGTTAAAAATAACTAAATATTAAATTTTTTAATTAATAATTTAATAAAAA
131 ATAAAATAAAATAAAAGTTAAAAATAACTAAATATTAAATTTTTTAATTAATAATTTAATAAAAA
3411957 TATAAACAAATATTACTTACTGCCATGTCTGGAGAAATTATTCTTTGATTACTTCTTTCAATATC
196 TATAAACAAATATTACTTACTGCCATGTCTGGAGAAATTATTCTTTGATTACTTCTTTCAATATC
3412022 ATTAGATGACGTAAATTGATGCTCCCCAAATTTACTTCGATACTCTTCAAAAAGTTTCTTCAATT
261 ATTAGATGACGTAAATTGATGCTCCCCAAATTTACTTCGATACTCTTCAAAAAGTTTCTTCAATT
3412087 GTTCAAGAATACCAACCCACTTATTTTCATATTGTGGTCCCAATTGTGAAAAAACATATTGC
326 GTTCAAGAATACCAACCCACTTATTTTCATATTGTGGTCCCAATTGTGAAAAAACATATTGC
3412149 AATAGTCTTCTCTAACTTCATCAAATATATATCCAACTCTGATCTATTTGAAGTAAACCAAGAAT
1 AATAGTCTTCTCTAACTTCATCAAATATATATCCAACTCTGATCTATTTGAAGTAAACCAAGAAT
3412214 CAAAATGACAAAAAGCCTACATTAACAAAATAAACAAAGTCGAATACCATATTGTGATAATAAAT
66 CAAAATGACAAAAAGCCTACATTAACAAAATAAACAAAGTCGAATACCATATTGTGATAATAAAT
3412279 ATAAAATAAAATAAAAGTTAAAAATAACTAAATATTAAATTTTTTAATTAATAATTTAATAAAAA
131 ATAAAATAAAATAAAAGTTAAAAATAACTAAATATTAAATTTTTTAATTAATAATTTAATAAAAA
3412344 TATAAACAAATATTACTTACTGCCATGTCTGGAGAAATTATTCTTTGATTACTTCTTTCAATATC
196 TATAAACAAATATTACTTACTGCCATGTCTGGAGAAATTATTCTTTGATTACTTCTTTCAATATC
3412409 ATTAGATGACGTAAATTGATGCTCCCCAAATTTACTTCGATACTCTTCAAAAAGTTTCTTCAATT
261 ATTAGATGACGTAAATTGATGCTCCCCAAATTTACTTCGATACTCTTCAAAAAGTTTCTTCAATT
3412474 GTTCAAGAATACCAACCCACTTATTTTCATATTGTGGTCCCAATTGTGAAAAAACATATTGC
326 GTTCAAGAATACCAACCCACTTATTTTCATATTGTGGTCCCAATTGTGAAAAAACATATTGC
3412536 AA
1 AA
3412538 CAGTTGCAAT
Statistics
Matches: 389, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
387 389 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (387 bp):
AATAGTCTTCTCTAACTTCATCAAATATATATCCAACTCTGATCTATTTGAAGTAAACCAAGAAT
CAAAATGACAAAAAGCCTACATTAACAAAATAAACAAAGTCGAATACCATATTGTGATAATAAAT
ATAAAATAAAATAAAAGTTAAAAATAACTAAATATTAAATTTTTTAATTAATAATTTAATAAAAA
TATAAACAAATATTACTTACTGCCATGTCTGGAGAAATTATTCTTTGATTACTTCTTTCAATATC
ATTAGATGACGTAAATTGATGCTCCCCAAATTTACTTCGATACTCTTCAAAAAGTTTCTTCAATT
GTTCAAGAATACCAACCCACTTATTTTCATATTGTGGTCCCAATTGTGAAAAAACATATTGC
Found at i:3416366 original size:52 final size:52
Alignment explanation
Indices: 3416298--3416416 Score: 211
Period size: 52 Copynumber: 2.3 Consensus size: 52
3416288 AAATTTATCA
* *
3416298 GCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCTT
1 GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
*
3416350 GCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCT
1 GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
3416402 GCATGTATCGATACA
1 GCATGTATCGATACA
3416417 AAGATCGGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
GCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCT
Found at i:3416429 original size:52 final size:52
Alignment explanation
Indices: 3416298--3416436 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 52
3416288 AAATTTATCA
* *
3416298 GCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCTT
1 GCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
*** *
3416350 GCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCT
1 GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
*
3416402 GCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 GCATGTATCGATACATAAGAT-AGTGTATCGATACA
3416437 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
GCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCT
Found at i:3416443 original size:13 final size:13
Alignment explanation
Indices: 3416425--3416449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3416415 CAAAGATCGG
3416425 TGTATCGATACAA
1 TGTATCGATACAA
3416438 TGTATCGATACA
1 TGTATCGATACA
3416450 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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3416531 original size:13 final size:13
Alignment explanation
Indices: 3416513--3416537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3416503 CAAAAAAATA
3416513 TGTATCGATACAT
1 TGTATCGATACAT
3416526 TGTATCGATACA
1 TGTATCGATACA
3416538 ACATTTTATG
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:3416533 original size:33 final size:33
Alignment explanation
Indices: 3416491--3416557 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3416481 AGTAGCTTAA
3416491 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3416524 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3416557 A
1 A
3416558 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3418572 original size:13 final size:13
Alignment explanation
Indices: 3418556--3418585 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3418546 TTTTTTAATA
3418556 TTTTAATTTATAT
1 TTTTAATTTATAT
*
3418569 TTTTAATTTCTAT
1 TTTTAATTTATAT
3418582 TTTT
1 TTTT
3418586 TATCTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTATAT
Found at i:3418793 original size:73 final size:73
Alignment explanation
Indices: 3418702--3418898 Score: 331
Period size: 73 Copynumber: 2.7 Consensus size: 73
3418692 TGGTTGGACC
* *
3418702 ATTAATTAATGATTTTTTATTTAGATTAAAATATGGAATAAATTTTTTATTTAGTTGGACTATTA
1 ATTAATTAATGATTTTTTATTTAGATTAAAATATGGAATAAATTTCTTATTTAGTTAGACTATTA
3418767 TATTTTTT
66 TATTTTTT
* *
3418775 ATTAATTAATAATTTTTTATTTAGATTAAAATATGGAATAAATTTCTTATTTGGTTAGACTATTA
1 ATTAATTAATGATTTTTTATTTAGATTAAAATATGGAATAAATTTCTTATTTAGTTAGACTATTA
*
3418840 TGTTTTTT
66 TATTTTTT
* *
3418848 ATGAATTAATGATTTTTTATTTAGATTAAAATATGAAATAAATTTCTTATT
1 ATTAATTAATGATTTTTTATTTAGATTAAAATATGGAATAAATTTCTTATT
3418899 AAACTTGAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 116 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (73 bp):
ATTAATTAATGATTTTTTATTTAGATTAAAATATGGAATAAATTTCTTATTTAGTTAGACTATTA
TATTTTTT
Found at i:3419178 original size:16 final size:16
Alignment explanation
Indices: 3419157--3419276 Score: 109
Period size: 16 Copynumber: 7.5 Consensus size: 16
3419147 TTCAAACCCA
3419157 AACCCGAATAAGCTCG
1 AACCCGAATAAGCTCG
*
3419173 AACCCGAATGA-CTTCG
1 AACCCGAATAAGC-TCG
* *
3419189 AACTCGAATGAGCTCG
1 AACCCGAATAAGCTCG
* * *
3419205 AATCCGAATAAGCCCA
1 AACCCGAATAAGCTCG
* *
3419221 AACTCGAATGAGCTCG
1 AACCCGAATAAGCTCG
3419237 AACCCGAATGAA-CTCG
1 AACCCGAAT-AAGCTCG
* * *
3419253 AACCCGAAAAAACCCG
1 AACCCGAATAAGCTCG
3419269 AACCCGAA
1 AACCCGAA
3419277 CGAACCTGAA
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
15 3 0.04
16 79 0.94
17 2 0.02
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.12
Consensus pattern (16 bp):
AACCCGAATAAGCTCG
Found at i:3419215 original size:48 final size:48
Alignment explanation
Indices: 3419157--3419276 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
3419147 TTCAAACCCA
* * *
3419157 AACCCGAATAAGCTCGAACCCGAATGA-CTTCGAACTCGAATGAGCTCG
1 AACCCGAATAAGCCCGAACCCGAATGAGC-TCGAACCCGAATGAACTCG
* * *
3419205 AATCCGAATAAGCCCAAACTCGAATGAGCTCGAACCCGAATGAACTCG
1 AACCCGAATAAGCCCGAACCCGAATGAGCTCGAACCCGAATGAACTCG
* *
3419253 AACCCGAAAAAACCCGAACCCGAA
1 AACCCGAATAAGCCCGAACCCGAA
3419277 CGAACCTGAA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 59 0.98
49 1 0.02
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.12
Consensus pattern (48 bp):
AACCCGAATAAGCCCGAACCCGAATGAGCTCGAACCCGAATGAACTCG
Found at i:3419282 original size:16 final size:16
Alignment explanation
Indices: 3419235--3419302 Score: 66
Period size: 16 Copynumber: 4.3 Consensus size: 16
3419225 CGAATGAGCT
* *
3419235 CGAACCCGAATGAACT
1 CGAACCCGAACGAACC
**
3419251 CGAACCCGAAAAAACC
1 CGAACCCGAACGAACC
3419267 CGAACCCGAACGAACC
1 CGAACCCGAACGAACC
* * *
3419283 TGAATCTGAAC-AACC
1 CGAACCCGAACGAACC
3419298 CGAAC
1 CGAAC
3419303 TCAAACAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 7 0.17
16 35 0.83
ACGTcount: A:0.41, C:0.35, G:0.16, T:0.07
Consensus pattern (16 bp):
CGAACCCGAACGAACC
Found at i:3419535 original size:20 final size:20
Alignment explanation
Indices: 3419510--3419547 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3419500 AAGAATTGAA
3419510 GAGGGATACAAGAGAGGAAT
1 GAGGGATACAAGAGAGGAAT
3419530 GAGGGATACAAGAGAGGA
1 GAGGGATACAAGAGAGGA
3419548 GGGAGCCTCT
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:0.45, C:0.05, G:0.42, T:0.08
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGAAT
Found at i:3419667 original size:28 final size:27
Alignment explanation
Indices: 3419628--3419698 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
3419618 AAACAAGCCT
* * *
3419628 CCATATTTGACAAATACAAAGGA-AACCG
1 CCATTTTTGACAAACACAAA--ATAACCA
3419656 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
3419683 CAATTTTTGACAAACA
1 CCATTTTTGACAAACA
3419699 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.50
28 18 0.47
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:3421620 original size:21 final size:22
Alignment explanation
Indices: 3421582--3421627 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3421572 ATCTGTTGAA
* **
3421582 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3421603 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3421625 ACT
1 ACT
3421628 TATCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:3424287 original size:24 final size:27
Alignment explanation
Indices: 3424214--3424284 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
3424204 AAACAAGCCT
* *
3424214 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
3424242 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
3424269 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
3424285 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:3424955 original size:20 final size:20
Alignment explanation
Indices: 3424927--3425001 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
3424917 TTTTACCCTG
3424927 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3424947 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3424967 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
3424987 ACGTATCGATACATT
1 ATGTATCGATACATT
3425002 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3424994 original size:40 final size:39
Alignment explanation
Indices: 3424927--3425004 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3424917 TTTTACCCTG
* * *
3424927 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAACATATCGATACAT-TATGA
* *
3424967 ATGTATCGATATATTCTACAACGTATCGATACATTATG
1 ATGTATCGATACATTCTACAACATATCGATACATTATG
3425005 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAACATATCGATACATTATGA
Found at i:3432264 original size:49 final size:49
Alignment explanation
Indices: 3432194--3432531 Score: 455
Period size: 49 Copynumber: 6.9 Consensus size: 49
3432184 GCACCTTTTC
*
3432194 CATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * * *
3432243 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
3432292 TATCTTTAAGTCCAATGTAGCTGGCCTCGACTCAGCACATTGGCA-CTT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * * *
3432340 GCACCATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
1 -CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
* *
3432389 TATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
* * *
3432438 CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTT
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT
*
3432489 CCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 -CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3432532 ACATCATTTT
Statistics
Matches: 247, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
48 39 0.16
49 168 0.68
51 2 0.01
52 38 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:3432483 original size:146 final size:148
Alignment explanation
Indices: 3432173--3432531 Score: 461
Period size: 146 Copynumber: 2.4 Consensus size: 148
3432163 GGTGGAAGAT
* * * *
3432173 TCAGCATATCGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGC
1 TCAGCACATCGGCACC-TTTCCACCATTAAGTCC-ATGTAGCTGGCCTTGAATCAGCACATTGGC
* * *
3432238 ACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGT
64 ACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
3432303 CCAATGTAGCTGGCCTCGAC
129 CCAATATAGCTGGCCTCGAA
* * * *
3432323 TCAGCACATTGGCA-C-TTGCACCATTAAGTCCATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 TCAGCACATCGGCACCTTTCCACCATTAAGTCCATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
3432386 CTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCC
66 CTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC
*
3432451 AATATAGCTGGCCTTGAA
131 AATATAGCTGGCCTCGAA
* * * *
3432469 TCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TCAGCACATCGGCACC-TTTCCACCATTAAG-TCCATGTAGCTGGCCTTGAATCAGCACATTG
3432532 ACATCATTTT
Statistics
Matches: 178, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
146 113 0.63
147 14 0.08
149 11 0.06
150 40 0.22
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (148 bp):
TCAGCACATCGGCACCTTTCCACCATTAAGTCCATGTAGCTGGCCTTGAATCAGCACATTGGCAC
CTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCC
AATATAGCTGGCCTCGAA
Found at i:3432571 original size:56 final size:53
Alignment explanation
Indices: 3432173--3432579 Score: 302
Period size: 49 Copynumber: 8.1 Consensus size: 53
3432163 GGTGGAAGAT
* * * *
3432173 TCAGCATATCGGCACCTTTTC-CATCTTTAAGTCCAATGTAGCTGGCCTTGAC
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * *
3432225 TCAGCACATTGGCACC---T-TCACCATTAAGTCCAATATAGCTGGCCTTGAA
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * * * *
3432274 TCAGCATATTGGCA-C-TTT-T-ATCTTTAAGTCCAATGTAGCTGGCCTCGAC
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * * *
3432323 TCAGCACATTGGCA-C--TT-GCACCATTAAGTCC-ATATAGCTGGCCTTGAA
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * * *
3432371 TCAGCATATTGGCACC--TT-T-ATCTTTAAGTCCAATGTAGCTGGCCTTGAC
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* *
3432420 TCAGCACATTGGCACC---T-TCATCTTTAAGTCCAATATAGCTGGCCTTGAA
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * *
3432469 TCAGCATATCGGCACCTTTTC-CATCTTTAAGTTCAATGTAGCTGGCCTTGAA
1 TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
* * * * * *
3432521 TCAGCACATTGACATCATTTTTCATCATCTTTAAGCCCAATATCGTTGGCCATGAA
1 TCAGCACATCGACA-C-CTTTTC-TCATCTTTAAGTCCAATATAGCTGGCCTTGAA
3432577 TCA
1 TCA
3432580 ACATATTGGC
Statistics
Matches: 298, Mismatches: 42, Indels: 26
0.81 0.11 0.07
Matches are distributed among these distances:
48 42 0.14
49 165 0.55
50 2 0.01
52 55 0.18
53 1 0.00
54 5 0.02
56 28 0.09
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (53 bp):
TCAGCACATCGACACCTTTTCTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
Found at i:3433416 original size:33 final size:33
Alignment explanation
Indices: 3433379--3433445 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3433369 TTCAACGATT
3433379 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3433412 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3433445 T
1 T
3433446 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:3433417 original size:13 final size:13
Alignment explanation
Indices: 3433399--3433423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3433389 CATAAAATGT
3433399 TGTATCGATACAA
1 TGTATCGATACAA
3433412 TGTATCGATACA
1 TGTATCGATACA
3433424 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:3433504 original size:13 final size:13
Alignment explanation
Indices: 3433486--3433510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3433476 ATTACTCAAA
3433486 TGTATCGATACAT
1 TGTATCGATACAT
3433499 TGTATCGATACA
1 TGTATCGATACA
3433511 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:3437752 original size:10 final size:10
Alignment explanation
Indices: 3437737--3437763 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3437727 TGCTAACTAA
3437737 GTTTTTGTTT
1 GTTTTTGTTT
3437747 GTTTTTGTTT
1 GTTTTTGTTT
3437757 GTTTTTG
1 GTTTTTG
3437764 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:3447458 original size:1 final size:1
Alignment explanation
Indices: 3447452--3447561 Score: 76
Period size: 1 Copynumber: 110.0 Consensus size: 1
3447442 GGCGTCCTCC
** * ** ** * * *
3447452 AAAAAAAAAAAAAAAAAATGAAAAAACAAAAAAAATGAATGAAAAAAAAACAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
3447517 AAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3447562 GGGGGTCCGG
Statistics
Matches: 80, Mismatches: 29, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:3447477 original size:17 final size:16
Alignment explanation
Indices: 3447452--3447561 Score: 98
Period size: 17 Copynumber: 6.7 Consensus size: 16
3447442 GGCGTCCTCC
3447452 AAAAAAAAAAA-AAAA
1 AAAAAAAAAAACAAAA
**
3447467 AAATGAAAAAACAAAA
1 AAAAAAAAAAACAAAA
* **
3447483 AAAATGAATGAA-AAAA
1 AAAA-AAAAAAACAAAA
*
3447499 AAACAAAAAAACAAAA
1 AAAAAAAAAAACAAAA
3447515 CAAAAAAAAAAACAAAA
1 -AAAAAAAAAAACAAAA
*
3447532 ACAATAAAAAAACAAACA
1 A-AAAAAAAAAACAAA-A
3447550 AAAACAAAAAAA
1 AAAA-AAAAAAA
3447562 GGGGGTCCGG
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
15 13 0.17
16 19 0.25
17 35 0.46
18 9 0.12
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAAACAAAA
Found at i:3447482 original size:21 final size:20
Alignment explanation
Indices: 3447452--3447553 Score: 89
Period size: 22 Copynumber: 4.8 Consensus size: 20
3447442 GGCGTCCTCC
3447452 AAAAAAAAAAAAAAAAAATG
1 AAAAAAAAAAAAAAAAAATG
**
3447472 AAAAAACAAAAAAAATGAATG
1 AAAAAA-AAAAAAAAAAAATG
**
3447493 AAAAAAAAACAAAAAAACAAAAC
1 -AAAAAAAA-AAAAAAA-AAATG
3447516 AAAAAAAAAAACAAAAACAAT-
1 AAAAAAAAAAA-AAAAA-AATG
3447537 AAAAAAACAAACAAAAA
1 AAAAAAA-AAA-AAAAA
3447554 CAAAAAAAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.09
21 25 0.37
22 33 0.49
23 3 0.04
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAAAATG
Found at i:3447556 original size:21 final size:20
Alignment explanation
Indices: 3447452--3447553 Score: 91
Period size: 21 Copynumber: 4.8 Consensus size: 20
3447442 GGCGTCCTCC
3447452 AAAAAAA-AAAAAAAAAAAT
1 AAAAAAACAAAAAAAAAAAT
* *
3447471 GAAAAAACAAAAAAAATGAATGAA
1 AAAAAAACAAAAAAAA--AA--AT
*
3447495 AAAAAAACAAAAAAACAAAAC
1 AAAAAAACAAAAAAA-AAAAT
3447516 AAAAAAA-AAAACAAAAACAAT
1 AAAAAAACAAAA-AAAAA-AAT
3447537 AAAAAAACAAACAAAAA
1 AAAAAAACAAA-AAAAA
3447554 CAAAAAAAGG
Statistics
Matches: 68, Mismatches: 5, Indels: 17
0.76 0.06 0.19
Matches are distributed among these distances:
19 6 0.09
20 14 0.21
21 20 0.29
22 9 0.13
23 3 0.04
24 15 0.22
25 1 0.01
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.04
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAAAAT
Found at i:3447561 original size:21 final size:21
Alignment explanation
Indices: 3447493--3447561 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
3447483 AAAATGAATG
3447493 AAAAAAAAAC-AA-AAAAACAA
1 AAAAAAAAACAAACAAAAAC-A
*
3447513 AACAAAAAAAAAAACAAAAACA
1 AA-AAAAAAACAAACAAAAACA
*
3447535 ATAAAAAAACAAACAAAAACA
1 AAAAAAAAACAAACAAAAACA
3447556 AAAAAA
1 AAAAAA
3447562 GGGGGTCCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 2 0.05
21 30 0.71
22 4 0.10
23 6 0.14
ACGTcount: A:0.87, C:0.12, G:0.00, T:0.01
Consensus pattern (21 bp):
AAAAAAAAACAAACAAAAACA
Found at i:3449044 original size:29 final size:28
Alignment explanation
Indices: 3449005--3449451 Score: 296
Period size: 29 Copynumber: 15.4 Consensus size: 28
3448995 TCACCCTTCA
* * *
3449005 AAAGTCCACAAGTCAGTGGTATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
* *
3449034 AAAGCCCACAAGTCGGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
* *
3449063 GAAAGCCCCACAAGTCAGTGGCAAC-CTTC
1 -AAAG-CCCACAAGTCAGTGGCATCTTTTC
* *
3449092 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTT-C
* *
3449122 GAAGCCCACAAGTCGGTGGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* * * *
3449150 CAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TC-TTTTC
* * * *
3449180 TTTTGTAAGCTCACAACTCTA-TAGCACTCTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCA-TCTTTTC
* *
3449214 --AGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTC
*
3449241 AAAAGCCCACAAGTCAGTGGCATATTTTTTC
1 -AAAGCCCACAAGTCAGTGGC--ATCTTTTC
* * *
3449272 AAAAGCCCACAAGTCAGTGGCAACCTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTC
* * * *
3449301 AAAG-CCACAAGTTAGTGGCACCCTGTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
3449328 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 -AAAGCCCACAAGTCAGTGGCAT-CTTTTC
* * *
3449358 AAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* *
3449386 AAAGCCCACAAGTCAGTGGCAAC--CTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* *
3449412 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTT-C
3449442 AAAGCCCACA
1 AAAGCCCACA
3449452 CAAGTCGGTG
Statistics
Matches: 339, Mismatches: 53, Indels: 51
0.77 0.12 0.12
Matches are distributed among these distances:
26 22 0.06
27 56 0.17
28 57 0.17
29 79 0.23
30 59 0.17
31 42 0.12
32 1 0.00
34 5 0.01
35 18 0.05
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:3449107 original size:27 final size:28
Alignment explanation
Indices: 3449064--3449117 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
3449054 ATTTTTTTCG
*
3449064 AAAGCCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCCACAAATCAGTGGCAACCTTC
*
3449092 AAAG-CCCACAAATCAGTGGCACCCTT
1 AAAGCCCCACAAATCAGTGGCAACCTT
3449118 TTCCGAAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.15
Consensus pattern (28 bp):
AAAGCCCCACAAATCAGTGGCAACCTTC
Found at i:3449168 original size:28 final size:30
Alignment explanation
Indices: 3449035--3449451 Score: 128
Period size: 30 Copynumber: 14.3 Consensus size: 30
3449025 ATTTTTTTCA
* * * *
3449035 AAGCCCACAAGTCGGTGGCA-TTTTTTTCG
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* *
3449064 AAAGCCCCACAAGTCAGTGGCAAC-C--TT-CA
1 -AAG-CCCACAAATCAGTGGC-ACTCTTTTCCG
*
3449093 AAGCCCACAAATCAGTGGCACCCTTTTCCG
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* *
3449123 AAGCCCACAAGTCGGTGGCA-TCTTTTCC-
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* * * *
3449151 AAGTCCACAACTCCGTGGCACTCTTTTTCTTTTG
1 AAGCCCACAAATCAGTGGCACTC-TTTTC---CG
* * *
3449185 TAAGCTCACAACTCTA-TAGCACTCTTTT-C-
1 -AAGCCCACAAATC-AGTGGCACTCTTTTCCG
* * * **
3449214 -AGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* * * **
3449243 AAGCCCACAAGTCAGTGGCATATTTTTTCAA
1 AAGCCCACAAATCAGTGGCA-CTCTTTTCCG
* **
3449274 AAGCCCACAAGTCAGTGGCAAC-C-TTT-AA
1 AAGCCCACAAATCAGTGGC-ACTCTTTTCCG
* * * * **
3449302 AAG-CCACAAGTTAGTGGCAC-CCTGTCAA
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* * * *
3449330 AAGCCCACAAGTCAGTGGCA-TATTTTTCA
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
* **
3449359 AAGCCCACAAGTCAGTGGCAAC-C-TTT-AA
1 AAGCCCACAAATCAGTGGC-ACTCTTTTCCG
* *
3449387 AAGCCCACAAGTCAGTGGCAAC-C---T-CA
1 AAGCCCACAAATCAGTGGC-ACTCTTTTCCG
* *
3449413 AAGCCCACAAATCAGTGGCACCCTTTTCCA
1 AAGCCCACAAATCAGTGGCACTCTTTTCCG
3449443 AAGCCCACA
1 AAGCCCACA
3449452 CAAGTCGGTG
Statistics
Matches: 314, Mismatches: 41, Indels: 64
0.75 0.10 0.15
Matches are distributed among these distances:
25 2 0.01
26 27 0.09
27 51 0.16
28 54 0.17
29 56 0.18
30 59 0.19
31 41 0.13
32 2 0.01
34 4 0.01
35 18 0.06
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (30 bp):
AAGCCCACAAATCAGTGGCACTCTTTTCCG
Found at i:3449446 original size:113 final size:116
Alignment explanation
Indices: 3449214--3449451 Score: 315
Period size: 113 Copynumber: 2.1 Consensus size: 116
3449204 CACTCTTTTC
* * **
3449214 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTTCAAAAGCC
1 AGCCCACAAGTCAGTGGCACACTTTTCAAAAGCCCACAAGTCAGTGGCATATCCTTTCAAAAGCC
* *
3449279 CACAAGTCAGTGGCAACCTTTAAAAGCCACAAGTTAGTGGCACCCTGTCAAA
66 CACAAGTCAGTGGCAACC-TTAAAAGCCACAAATCAGTGGCACCCTGTCAAA
* *
3449331 AGCCCACAAGTCAGTGGCATATTTTTC-AAAGCCCACAAGTCAGTGGCA-A-CCTTT-AAAAGCC
1 AGCCCACAAGTCAGTGGCACACTTTTCAAAAGCCCACAAGTCAGTGGCATATCCTTTCAAAAGCC
* * *
3449392 CACAAGTCAGTGGCAACC-TCAAAGCCCACAAATCAGTGGCACCCTTTTCCAA
66 CACAAGTCAGTGGCAACCTTAAAAG-CCACAAATCAGTGGCACCC-TGTCAAA
3449444 AGCCCACA
1 AGCCCACA
3449452 CAAGTCGGTG
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
111 5 0.05
112 17 0.16
113 38 0.35
114 3 0.03
115 1 0.01
116 21 0.19
117 23 0.21
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (116 bp):
AGCCCACAAGTCAGTGGCACACTTTTCAAAAGCCCACAAGTCAGTGGCATATCCTTTCAAAAGCC
CACAAGTCAGTGGCAACCTTAAAAGCCACAAATCAGTGGCACCCTGTCAAA
Found at i:3449479 original size:86 final size:85
Alignment explanation
Indices: 3449214--3449467 Score: 343
Period size: 85 Copynumber: 2.9 Consensus size: 85
3449204 CACTCTTTTC
*
3449214 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTTCAAAAGCC
1 AGCCCACAAGTTAGTGGCACCC--TTCAAAAGCCCACAAGTCAGTGGCATA--TTTTCCAAAGCC
3449279 CACAAGTCAGTGGCAACCTTTAAA
62 CACAAGTCAGTGGCAACCTTTAAA
*
3449303 AG-CCACAAGTTAGTGGCACCCTGTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAGCCCAC
1 AGCCCACAAGTTAGTGGCACCCT-TCAAAAGCCCACAAGTCAGTGGCATATTTTCCAAAGCCCAC
3449367 AAGTCAGTGGCAACCTTTAAA
65 AAGTCAGTGGCAACCTTTAAA
* * * **
3449388 AGCCCACAAGTCAGTGGCAACC-TC-AAAGCCCACAAATCAGTGGCACCCTTTTCCAAAGCCCAC
1 AGCCCACAAGTTAGTGGCACCCTTCAAAAGCCCACAAGTCAGTGGCA-TATTTTCCAAAG-CC-C
*
3449451 ACAAGTCGGTGGCAACC
63 ACAAGTCAGTGGCAACC
3449468 CTTCTAAGCC
Statistics
Matches: 151, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
83 20 0.13
84 11 0.07
85 38 0.25
86 35 0.23
87 26 0.17
88 19 0.13
89 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (85 bp):
AGCCCACAAGTTAGTGGCACCCTTCAAAAGCCCACAAGTCAGTGGCATATTTTCCAAAGCCCACA
AGTCAGTGGCAACCTTTAAA
Found at i:3449570 original size:48 final size:49
Alignment explanation
Indices: 3449467--3449700 Score: 293
Period size: 48 Copynumber: 4.8 Consensus size: 49
3449457 CGGTGGCAAC
* * *
3449467 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTA
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
3449517 TCTTTAAGTCCAATATAGCTGGCCTTG-ATCAGCATATTGGCACCTTCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
*
3449565 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG------CA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
3449608 CCTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATTGGCACCTTTTCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAAT--CAGCATATTGGCACC--TTCA
* * * *
3449661 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
3449701 ACATCCTTTT
Statistics
Matches: 162, Mismatches: 11, Indels: 21
0.84 0.06 0.11
Matches are distributed among these distances:
43 32 0.20
45 10 0.06
48 45 0.28
49 34 0.21
50 3 0.02
51 9 0.06
53 29 0.18
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
Found at i:3449624 original size:43 final size:44
Alignment explanation
Indices: 3449563--3449657 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 44
3449553 TTGGCACCTT
3449563 CACCTTTAAGTCCAATATAGCTGGCCTTGAAT-CAGCACATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATACAGCACATTGG
*
3449606 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATTGG
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAAT-ACAGCACATTGG
3449651 CACCTTT
1 CACCTTT
3449658 TCATCTTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 32 0.65
45 17 0.35
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (44 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATACAGCACATTGG
Found at i:3449633 original size:22 final size:22
Alignment explanation
Indices: 3449565--3449633 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
3449555 GGCACCTTCA
3449565 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
* * *
3449587 CCTTGAA-TCAGCACAT-TGGC--A
1 CCTTTAAGTC--CA-ATATAGCTGG
3449608 CCTTTAAGTCCAATATAGCTGG
1 CCTTTAAGTCCAATATAGCTGG
3449630 CCTT
1 CCTT
3449634 GAATCACAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
CCTTTAAGTCCAATATAGCTGG
Found at i:3449712 original size:53 final size:54
Alignment explanation
Indices: 3449609--3449745 Score: 154
Period size: 53 Copynumber: 2.5 Consensus size: 54
3449599 ACATTGGCAC
* *
3449609 CTTTAAGTCCAATATAGCTGGCCTTGAATCACAGCATATTGGCACC-TTT-TCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAAT-ACAGCACATTGACACCTTTTCTCAT
* *
3449662 CTTTAAGTTCAATGTAGCTGGCCTTGAAT-CAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATACAGCACATTGACA-CC-TTTTCTCAT
* * * *
3449717 CTTTAAGCCCAATATCGTTGGCCGTGAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAAT
3449746 CGACATATTG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
51 11 0.16
52 2 0.03
53 27 0.39
54 3 0.04
55 27 0.39
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (54 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATACAGCACATTGACACCTTTTCTCAT
Found at i:3452033 original size:15 final size:15
Alignment explanation
Indices: 3452010--3452052 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3452000 CCAAATCATA
*
3452010 GACAATAAACTAAAT
1 GACAATAAAATAAAT
*
3452025 GACATTAAAATAAAT
1 GACAATAAAATAAAT
*
3452040 GA-AATAACATAAA
1 GACAATAAAATAAA
3452053 AGTCCTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.21
Consensus pattern (15 bp):
GACAATAAAATAAAT
Done.