Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold26
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: 1656043
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 334368 characters in sequence are not A, C, G, or T
File 6 of 8
Found at i:1182790 original size:51 final size:51
Alignment explanation
Indices: 1182685--1182799 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
1182675 TTTCTACGAA
* ** *
1182685 GATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTTCACAATCAAG
1 GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATCATCCACAATCAAG
** * *
1182736 GATACTCCAACCCCGGTTTTATTTCTAAAACACTGATCATCCACCATCAGG
1 GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATCATCCACAATCAAG
1182787 GATACTCCAACCC
1 GATACTCCAACCC
1182800 TGTTATTTCT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.29
Consensus pattern (51 bp):
GATACTCCAACCCCGGTTTTATTTCTAAAACACCAATCATCCACAATCAAG
Found at i:1182806 original size:130 final size:130
Alignment explanation
Indices: 1182571--1182844 Score: 320
Period size: 130 Copynumber: 2.1 Consensus size: 130
1182561 TCATTCATGT
* * * * *
1182571 TTTTATTTCTAAAATACCGATTTTCCATAATCAGGGATACTCCAATCCCGATTTTATTTTCAAAA
1 TTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAACCCCGATTTTATTTTCAAAA
** * *
1182636 CATCAATTTTTCACAATAAGGGATACTCCAACCCCATTATTTCT-ACGAAGATACTCCAACCTCG
66 CATCAATCATCCACAATAAGGGATACTCCAACCCCATTATTTCTGA-GAAGATACTCCAACCTCA
1182700 G
130 G
* *
1182701 TTTTATTTCTAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGGTTTTA-TTTCTAAA
1 TTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAACCCCGATTTTATTTTC-AAA
* * * ** **
1182765 ACA-CTGATCATCCACCATCAGGGATACTCCAACCCTGTTATTTCTGAGGGGATACTCCAACCTC
65 ACATC-AATCATCCACAATAAGGGATACTCCAACCCCATTATTTCTGAGAAGATACTCCAACCTC
*
1182829 AT
129 AG
*
1182831 TTTTATCTCTAAAA
1 TTTTATTTCTAAAA
1182845 TATTAAATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
129 5 0.04
130 115 0.95
131 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (130 bp):
TTTTATTTCTAAAACACCAATTTTCCACAATCAAGGATACTCCAACCCCGATTTTATTTTCAAAA
CATCAATCATCCACAATAAGGGATACTCCAACCCCATTATTTCTGAGAAGATACTCCAACCTCAG
Found at i:1185780 original size:12 final size:12
Alignment explanation
Indices: 1185763--1185803 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1185753 TTTACTACTA
1185763 TTTTGGTTGTTG
1 TTTTGGTTGTTG
*
1185775 TTTTGGTTGCTG
1 TTTTGGTTGTTG
*
1185787 TTTTTGCTTGTTG
1 -TTTTGGTTGTTG
1185800 TTTT
1 TTTT
1185804 ACTTCGACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.00, C:0.05, G:0.27, T:0.68
Consensus pattern (12 bp):
TTTTGGTTGTTG
Found at i:1185801 original size:13 final size:13
Alignment explanation
Indices: 1185763--1185803 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1185753 TTTACTACTA
1185763 TTTTGGTTGTTG-
1 TTTTGGTTGTTGT
*
1185775 TTTTGGTTGCTGT
1 TTTTGGTTGTTGT
*
1185788 TTTTGCTTGTTGT
1 TTTTGGTTGTTGT
1185801 TTT
1 TTT
1185804 ACTTCGACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.00, C:0.05, G:0.27, T:0.68
Consensus pattern (13 bp):
TTTTGGTTGTTGT
Found at i:1186220 original size:12 final size:12
Alignment explanation
Indices: 1186203--1186237 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1186193 TATAATTGTG
1186203 TCTTCATTGCTT
1 TCTTCATTGCTT
*
1186215 TCTTCATTACTT
1 TCTTCATTGCTT
*
1186227 TTTTCATTGCT
1 TCTTCATTGCT
1186238 GCCATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.23, G:0.06, T:0.60
Consensus pattern (12 bp):
TCTTCATTGCTT
Found at i:1186726 original size:8 final size:8
Alignment explanation
Indices: 1186715--1186759 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
1186705 TAATTATTAC
1186715 TATTTTAT
1 TATTTTAT
*
1186723 TATTATA-
1 TATTTTAT
1186730 T-TTTTAT
1 TATTTTAT
1186737 TATTTTAT
1 TATTTTAT
1186745 TATTTTTAT
1 TA-TTTTAT
1186754 TATTTT
1 TATTTT
1186760 TATTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 18 0.56
9 8 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:1186726 original size:14 final size:14
Alignment explanation
Indices: 1186707--1186769 Score: 65
Period size: 14 Copynumber: 4.2 Consensus size: 14
1186697 TAATTAATTA
1186707 ATTATTACTA-TTTT
1 ATTATTA-TATTTTT
1186721 ATTATTATATTTTT
1 ATTATTATATTTTT
1186735 ATTATTTTATTATTTTT
1 ATTA--TTA-TATTTTT
*
1186752 ATTATTTTTATTTTT
1 ATTA-TTATATTTTT
1186767 ATT
1 ATT
1186770 TTAGAATTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
13 2 0.05
14 15 0.34
15 10 0.23
16 6 0.14
17 11 0.25
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTATATTTTT
Found at i:1186739 original size:17 final size:16
Alignment explanation
Indices: 1186719--1186769 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 16
1186709 TATTACTATT
1186719 TTATTATTATATTTTTA
1 TTATT-TTATATTTTTA
1186736 TTATTTTATTATTTTTA
1 TTATTTTA-TATTTTTA
1186753 TTATTTT-TATTTTTA
1 TTATTTTATATTTTTA
1186768 TT
1 TT
1186770 TTAGAATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.30
16 3 0.09
17 20 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATATTTTTA
Found at i:1186742 original size:9 final size:9
Alignment explanation
Indices: 1186719--1186763 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1186709 TATTACTATT
*
1186719 TTATTATTA
1 TTATTTTTA
1186728 -TATTTTTA
1 TTATTTTTA
1186736 TTA-TTTTA
1 TTATTTTTA
1186744 TTATTTTTA
1 TTATTTTTA
1186753 TTATTTTTA
1 TTATTTTTA
1186762 TT
1 TT
1186764 TTTATTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 15 0.45
9 18 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1191501 original size:5 final size:5
Alignment explanation
Indices: 1191493--1191517 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1191483 TATATATACA
1191493 TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT
1191518 ATAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1191743 original size:4 final size:4
Alignment explanation
Indices: 1191734--1191759 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1191724 ATCACATCTC
1191734 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
1191760 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:1192442 original size:63 final size:63
Alignment explanation
Indices: 1192351--1192486 Score: 177
Period size: 63 Copynumber: 2.2 Consensus size: 63
1192341 TCAAAGCAAG
* ** *
1192351 TTTGGGTTTTTACTGATTATAAGAAAAATAA-AGGTTGCGGTTACTAAAGGG-AAAAAATTAGGT
1 TTTGGGTTTTTACTGATGATAAGAAAAATAAGA-GTTGCGACTACT-AAGGGAAAAAAAATAGGT
* * *
1192414 TTTGAGTTTTTACTGATGCTAAGGAAAATAAGAGTTGCGACTACTAAGGGAAAAAAAATAGGT
1 TTTGGGTTTTTACTGATGATAAGAAAAATAAGAGTTGCGACTACTAAGGGAAAAAAAATAGGT
1192477 TTTGGGTTTT
1 TTTGGGTTTT
1192487 AAGTGTATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 5 0.08
63 57 0.90
64 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (63 bp):
TTTGGGTTTTTACTGATGATAAGAAAAATAAGAGTTGCGACTACTAAGGGAAAAAAAATAGGT
Found at i:1193076 original size:16 final size:16
Alignment explanation
Indices: 1193043--1193089 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1193033 TCTGAACTCA
* *
1193043 AATAAGGCCAAACTCG
1 AATAGGGCCAAACCCG
*
1193059 AATAGGGCCGAACCCG
1 AATAGGGCCAAACCCG
*
1193075 AATAGGCCCAAACCC
1 AATAGGGCCAAACCC
1193090 AAAAGAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.32, G:0.21, T:0.09
Consensus pattern (16 bp):
AATAGGGCCAAACCCG
Found at i:1193384 original size:16 final size:16
Alignment explanation
Indices: 1193360--1193411 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1193350 TTACTCAAAA
*
1193360 TTTACTTTTTTATTTT
1 TTTAATTTTTTATTTT
*
1193376 TTTAA-TTTTAACTTTT
1 TTTAATTTTTTA-TTTT
*
1193392 TTTAATTATTTATTTT
1 TTTAATTTTTTATTTT
1193408 TTTA
1 TTTA
1193412 TAAAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTAATTTTTTATTTT
Found at i:1193810 original size:18 final size:18
Alignment explanation
Indices: 1193773--1193832 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
1193763 GTATTTTTTA
*
1193773 TTTAATAAAATAATAATTT
1 TTTAA-AAAATAATAGTTT
*
1193792 TTTAAAAAATTATAGTTTT
1 TTTAAAAAATAATAG-TTT
*
1193811 TTTAAAAAATGATAGTTT
1 TTTAAAAAATAATAGTTT
1193829 TTTA
1 TTTA
1193833 TTTGAGTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTAAAAAATAATAGTTT
Found at i:1193811 original size:19 final size:19
Alignment explanation
Indices: 1193789--1193831 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1193779 AAAATAATAA
*
1193789 TTTTTTAAAAAATTATAGT
1 TTTTTTAAAAAATGATAGT
1193808 TTTTTTAAAAAATGATAGT
1 TTTTTTAAAAAATGATAGT
1193827 TTTTT
1 TTTTT
1193832 ATTTGAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (19 bp):
TTTTTTAAAAAATGATAGT
Found at i:1195183 original size:32 final size:32
Alignment explanation
Indices: 1195142--1195205 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1195132 TTTTTTTGAA
1195142 GAGTAAGGTTAGAGTGTCCCCTCGGAGGAATG
1 GAGTAAGGTTAGAGTGTCCCCTCGGAGGAATG
*
1195174 GAGTAAGGTTAGAGTGTTCCCTCGGAGGAATG
1 GAGTAAGGTTAGAGTGTCCCCTCGGAGGAATG
1195206 AGATGGAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.38, T:0.23
Consensus pattern (32 bp):
GAGTAAGGTTAGAGTGTCCCCTCGGAGGAATG
Found at i:1195434 original size:97 final size:98
Alignment explanation
Indices: 1195254--1195440 Score: 220
Period size: 97 Copynumber: 1.9 Consensus size: 98
1195244 ATTTGATTTT
* *
1195254 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAGTGGGGATGGAGCTTCCCCAAAGGTAAAAT
1 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAATGGGGATGGAGCTTCCCCAAAGGAAAAAT
** * *
1195319 TATATTAAGGAAATTTTGATTTTTTAAAAGAAA
66 TATACGAAGAAAAATTTGATTTTTTAAAAGAAA
* * * * *
1195352 TCTT-AAAGAAGGGTTGGAATGTCCT-TTCGAAGGAATGGGGATGGCA-TTTCTCCAAA-GAAAA
1 TCTTAAAAGAAAGGTTAGAATGTCCTCTTAG-AGGAATGGGGATGG-AGCTTCCCCAAAGGAAAA
1195413 AGTTATACGAAGAAAAATTTGATTTTTT
64 A-TTATACGAAGAAAAATTTGATTTTTT
1195441 TGAAAAACGA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
96 8 0.11
97 62 0.83
98 5 0.07
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (98 bp):
TCTTAAAAGAAAGGTTAGAATGTCCTCTTAGAGGAATGGGGATGGAGCTTCCCCAAAGGAAAAAT
TATACGAAGAAAAATTTGATTTTTTAAAAGAAA
Found at i:1197721 original size:21 final size:20
Alignment explanation
Indices: 1197679--1197728 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1197669 CAGGTTAATA
* *
1197679 TATCGATACATAAGTGAATG
1 TATCGATATATAAATGAATG
1197699 TATCGATATATAAATGCAATG
1 TATCGATATATAAATG-AATG
1197720 TATCGATAT
1 TATCGATAT
1197729 TGGACCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TATCGATATATAAATGAATG
Found at i:1198605 original size:22 final size:22
Alignment explanation
Indices: 1198580--1198632 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1198570 CAAACTTGTC
*
1198580 ACTTTCATTTTCTATTTTAGCT
1 ACTTTCATCTTCTATTTTAGCT
*
1198602 ACTTTCATCTTCTGTTTTAGCT
1 ACTTTCATCTTCTATTTTAGCT
1198624 ACTTTCATC
1 ACTTTCATC
1198633 ATCTTAGTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.23, G:0.06, T:0.55
Consensus pattern (22 bp):
ACTTTCATCTTCTATTTTAGCT
Found at i:1201930 original size:70 final size:68
Alignment explanation
Indices: 1201856--1202197 Score: 227
Period size: 68 Copynumber: 5.0 Consensus size: 68
1201846 TAGGTGGGTA
* *
1201856 CCACAAGCTTGTGTGGGCTTTGAGAAAGAAAAAAA-GCGTCCTGCTCCCT-AGAGA-TTGAGGTA
1 CCACAAGCTTGTGTGGGCTTTGAG---GAAAAAAATGCATCCTGCTCCCTAAG-GACTAGA-GTA
1201918 GATAAGTG
61 GATAAGTG
* * * *
1201926 CCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCTTGCTTCTTAAGGACTAGAGTAGATAG
1 CCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCCTGCTCCCTAAGGACTAGAGTAGATAA
1201991 GTG
66 GTG
* * * * * * *
1201994 CCACAAGCTTGTGT-GGCGTTTAATGAAAAAAATACATCTTTCTCCTTAAGGACTAGAATAGATA
1 CCACAAGCTTGTGTGGGC-TTTGAGGAAAAAAATGCATCCTGCTCCCTAAGGACTAGAGTAGATA
*
1202058 GGTG
65 AGTG
* * * ***
1202062 CCACTAA-CTTGTG-GGAGCTTTGAAGAAGAAAAGATG--TCTTACTTTTTAAGGACTAGAGTAG
1 CCAC-AAGCTTGTGTGG-GCTTTGAGGAA-AAAA-ATGCATCCTGCTCCCTAAGGACTAGAGTAG
* *
1202123 ATAGGTT
62 ATAAGTG
* * * * * ** * *
1202130 CCACAAACTT-TATGGGCTTTGA-AAAAGAAAAGGCATCCTACTCTTTAAAGACTAAAGTAGATA
1 CCACAAGCTTGTGTGGGCTTTGAGGAAA-AAAATGCATCCTGCTCCCTAAGGACTAGAGTAGATA
*
1202193 GGTG
65 AGTG
1202197 C
1 C
1202198 TAGCAATTTA
Statistics
Matches: 230, Mismatches: 28, Indels: 31
0.80 0.10 0.11
Matches are distributed among these distances:
65 3 0.01
66 5 0.02
67 49 0.21
68 134 0.58
69 13 0.06
70 26 0.11
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.27
Consensus pattern (68 bp):
CCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCCTGCTCCCTAAGGACTAGAGTAGATAA
GTG
Found at i:1202000 original size:68 final size:68
Alignment explanation
Indices: 1201915--1202197 Score: 285
Period size: 68 Copynumber: 4.2 Consensus size: 68
1201905 AGAGATTGAG
* *
1201915 GTAGATAAGTGCCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCTTGCTTCTTAAGGACT
1 GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCTTACTTCTTAAGGACT
1201980 AGA
66 AGA
* * * * *
1201983 GTAGATAGGTGCCACAAGCTTGTGT-GGCGTTTAATGAAAAAAATACATCTTTCTCCTTAAGGAC
1 GTAGATAGGTGCCACAAGCTTGTGTGGGC-TTTGAGGAAAAAAATGCATCTTACTTCTTAAGGAC
1202047 TAGA
65 TAGA
* * *
1202051 ATAGATAGGTGCCACTAA-CTTGTG-GGAGCTTTGAAGAAGAAAAGATG--TCTTACTTTTTAAG
1 GTAGATAGGTGCCAC-AAGCTTGTGTGG-GCTTTGAGGAA-AAAA-ATGCATCTTACTTCTTAAG
1202112 GACTAGA
62 GACTAGA
* * * * * * *
1202119 GTAGATAGGTTCCACAAACTT-TATGGGCTTTGA-AAAAGAAAAGGCATCCTAC-TCTTTAAAGA
1 GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTGAGGAAA-AAAATGCATCTTACTTC-TTAAGGA
*
1202181 CTAAA
64 CTAGA
1202186 GTAGATAGGTGC
1 GTAGATAGGTGC
1202198 TAGCAATTTA
Statistics
Matches: 180, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
65 3 0.02
66 6 0.03
67 39 0.22
68 122 0.68
69 8 0.04
70 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (68 bp):
GTAGATAGGTGCCACAAGCTTGTGTGGGCTTTGAGGAAAAAAATGCATCTTACTTCTTAAGGACT
AGA
Found at i:1206957 original size:51 final size:51
Alignment explanation
Indices: 1206852--1206968 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
1206842 TTTTTACGGA
* * * ** *
1206852 GATACTCCAACCTCGGTTTTATTTTTAAAACACCAATTTTTCACAATCAAG
1 GATACTCCAACCCCGGTTTGATTTCTAAAACACCAATCATCCACAATCAAG
** * *
1206903 GATACTCCAACCCCGGTTTGATTTCTAAAACACTGATCATCCACCATCAGG
1 GATACTCCAACCCCGGTTTGATTTCTAAAACACCAATCATCCACAATCAAG
1206954 GATACTCCAACCCCG
1 GATACTCCAACCCCG
1206969 TTATTTCCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.30, G:0.11, T:0.28
Consensus pattern (51 bp):
GATACTCCAACCCCGGTTTGATTTCTAAAACACCAATCATCCACAATCAAG
Found at i:1206973 original size:130 final size:130
Alignment explanation
Indices: 1206738--1206995 Score: 313
Period size: 130 Copynumber: 2.0 Consensus size: 130
1206728 TCATTCATGT
* ** * * *
1206738 TTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAATCTCGATTTTATTTTCAAAA
1 TTTTATTTCTAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGATTTGATTTTCAAAA
** * ** *
1206803 CATCAATTTTCCACAATAAGGGATACTCCAACCCTATTATTTTTACGGAGATACTCCAACCTCGG
66 CATCAATCATCCACAATAAGGGATACTCCAACCCCATTATTTCCAAGGAGATACTCCAACCTCGG
* *
1206868 TTTTATTTTTAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGGTTTGA-TTTCTAAA
1 TTTTATTTCTAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGATTTGATTTTC-AAA
* * * * *
1206932 ACA-CTGATCATCCACCATCAGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCTC
65 ACATC-AATCATCCACAATAAGGGATACTCCAACCCCATTATTTCCAAGGAGATACTCCAACCTC
1206996 ATTTTTATCT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
129 5 0.05
130 102 0.95
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (130 bp):
TTTTATTTCTAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGATTTGATTTTCAAAA
CATCAATCATCCACAATAAGGGATACTCCAACCCCATTATTTCCAAGGAGATACTCCAACCTCGG
Found at i:1207501 original size:32 final size:33
Alignment explanation
Indices: 1207460--1207589 Score: 113
Period size: 35 Copynumber: 3.8 Consensus size: 33
1207450 AAAATCAAGA
*
1207460 AATATAAAAAAA-AAATGGGATGATGGGCATGG
1 AATATAAAAAAAGAAATGGAATGATGGGCATGG
**
1207492 AATATAAAAATGAAGGCATGGAATGATGGGCATGG
1 AATATAAAAA--AAGAAATGGAATGATGGGCATGG
* *
1207527 AATA-AAAAAATGAAGGCATAGAATGATGGGCATGG
1 AATATAAAAAAAGAA---ATGGAATGATGGGCATGG
**
1207562 AATA-AAAAATGAAGGCATGGAATGATGG
1 AATATAAAAA--AAGAAATGGAATGATGG
1207590 ATAAAAATGA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
32 12 0.15
34 18 0.23
35 47 0.59
37 2 0.03
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.18
Consensus pattern (33 bp):
AATATAAAAAAAGAAATGGAATGATGGGCATGG
Found at i:1207574 original size:34 final size:34
Alignment explanation
Indices: 1207474--1207589 Score: 196
Period size: 35 Copynumber: 3.4 Consensus size: 34
1207464 TAAAAAAAAA
*
1207474 ATGGGATGATGGGCATGGAATATAAAAATGAAGGC
1 ATGGAATGATGGGCATGGAATA-AAAAATGAAGGC
1207509 ATGGAATGATGGGCATGGAATAAAAAAATGAAGGC
1 ATGGAATGATGGGCATGGAAT-AAAAAATGAAGGC
*
1207544 ATAGAATGATGGGCATGGAATAAAAAATGAAGGC
1 ATGGAATGATGGGCATGGAATAAAAAATGAAGGC
1207578 ATGGAATGATGG
1 ATGGAATGATGG
1207590 ATAAAAATGA
Statistics
Matches: 77, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 24 0.31
35 52 0.68
36 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.19
Consensus pattern (34 bp):
ATGGAATGATGGGCATGGAATAAAAAATGAAGGC
Found at i:1208929 original size:79 final size:79
Alignment explanation
Indices: 1208839--1209096 Score: 480
Period size: 79 Copynumber: 3.3 Consensus size: 79
1208829 CCCGTTAATC
* *
1208839 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
1208904 ATCAATTTTTCATA
66 ATCAATTTTTCATA
1208918 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
1208983 ATCAATTTTTCATA
66 ATCAATTTTTCATA
* *
1208997 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATGTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
1209062 ATCAATTTTTCATA
66 ATCAATTTTTCATA
1209076 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1209097 GTTTTATTTC
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 175 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAAC
ATCAATTTTTCATA
Found at i:1209087 original size:130 final size:130
Alignment explanation
Indices: 1208949--1209224 Score: 471
Period size: 130 Copynumber: 2.1 Consensus size: 130
1208939 TTATTTCCGA
*
1208949 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
* *
1209014 CCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATC
66 CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATGTCTAAAACATCAATTTTTCATAATC
* * *
1209079 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
* *
1209144 CCCGTTATTTCCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAACATCAATTTTTCATAATC
66 CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATGTCTAAAACATCAATTTTTCATAATC
*
1209209 GGGGATACTTCAACCC
1 GGGGATACTCCAACCC
1209225 TGTTATTTCC
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 137 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (130 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATGTCTAAAACATCAATTTTTCATAATC
Found at i:1209109 original size:51 final size:51
Alignment explanation
Indices: 1209028--1209147 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
1209018 TTATTTCCGA
*
1209028 GGGGATACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCACAATC
* * *
1209079 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCACAATC
1209130 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1209148 TTATTTCCGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCACAATC
Found at i:1209232 original size:209 final size:209
Alignment explanation
Indices: 1208870--1209596 Score: 898
Period size: 209 Copynumber: 3.3 Consensus size: 209
1208860 TTATTTTCGA
* *
1208870 GGGGATACTCTAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
*
1208935 CCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATC
66 CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAACATCAATTTTTCATAATC
*
1209000 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATGTCTAAAACATC
131 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
*
1209065 AATTTTTCATAATC
196 AATTTTTTATAATC
* * *
1209079 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
*
1209144 CCCGTTATTTCCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAACATCAATTTTTCATAATC
66 CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAACATCAATTTTTCATAATC
* * **
1209209 GGGGATACTTCAACCCTGTTATTTCCGAGGGGATACTCCAACCCTAGTTTTATCTCTAAAACATC
131 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
1209274 AATTTTTTATAATC
196 AATTTTTTATAATC
* * * *
1209288 GGGGATACTCCAATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGGT-TTT--------AT-TTCTAA------------------AACATC
* *
1209353 AATTTTTCATAATCGGGGATACTCTAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTT
38 AATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTT
*
1209418 ATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACT
103 ATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACT
* *
1209483 CCAACCCCGGCTTTATTTCTAAAACATCAATTTTTTATAATC
168 CCAACCCCGGTTTTATCTCTAAAACATCAATTTTTTATAATC
** * * * ** *
1209525 GGGGATACTCTGACCCCGATTTTATTTTTTAGAACA-CCGTTTTTCCATAATCGGGGATACTCTA
1 GGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACATCAATTTTT-CATAATCGGGGATACTCCA
*
1209589 GCCCCGTT
64 ACCCCGTT
1209597 GTTATCTCTA
Statistics
Matches: 447, Mismatches: 41, Indels: 59
0.82 0.07 0.11
Matches are distributed among these distances:
209 220 0.49
210 33 0.07
218 2 0.00
219 4 0.01
228 3 0.01
229 1 0.00
236 3 0.01
237 181 0.40
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (209 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAACATCAATTTTTCATAATC
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATCTCTAAAACATC
AATTTTTTATAATC
Found at i:1209355 original size:288 final size:288
Alignment explanation
Indices: 1208839--1209384 Score: 966
Period size: 288 Copynumber: 1.9 Consensus size: 288
1208829 CCCGTTAATC
* * *
1208839 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAAC
*
1208904 ATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGC
66 ATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGC
*
1208969 TTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
131 TTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
1209034 ACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGGT
196 ACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGGT
1209099 TTTATTTCTAAAATATTAATTTTTCACA
261 TTTATTTCTAAAATATTAATTTTTCACA
*
1209127 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTAGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAAC
* * * *
1209192 ATCAATTTTTCATAATCGGGGATACTTCAACCCTGTTATTTCCGAGGGGATACTCCAACCCTAGT
66 ATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGC
* *
1209257 TTTATCTCTAAAACATCAATTTTTTATAATCGGGGATACTCCAATCCCGTTATTTCCGAGGGGAT
131 TTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
* *
1209322 ACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCTAACCCCG
196 ACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCG
1209385 TTATTTCCGA
Statistics
Matches: 244, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
288 244 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (288 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAAC
ATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGC
TTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGAT
ACTCCAACCCCGGTTTTATGTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGGT
TTTATTTCTAAAATATTAATTTTTCACA
Found at i:1209542 original size:79 final size:79
Alignment explanation
Indices: 1209079--1209534 Score: 750
Period size: 79 Copynumber: 5.8 Consensus size: 79
1209069 TTTCATAATC
* * * *
1209079 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1209144 CCCGTTATTTCCGA
66 CCCGTTATTTCCGA
* * *
1209158 GGGGATACTCCAACCCTAGCTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTTCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
*
1209223 CCTGTTATTTCCGA
66 CCCGTTATTTCCGA
* * * *
1209237 GGGGATACTCCAACCCTAGTTTTATCTCTAAAACATCAATTTTTTATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1209302 CCCGTTATTTCCGA
66 CCCGTTATTTCCGA
* *
1209316 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCTAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1209381 CCCGTTATTTCCGA
66 CCCGTTATTTCCGA
*
1209395 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1209460 CCCGTTATTTCCGA
66 CCCGTTATTTCCGA
* * *
1209474 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTTATAATCGGGGATACTC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTC
1209535 TGACCCCGAT
Statistics
Matches: 350, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 350 1.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTCCGA
Found at i:1209550 original size:51 final size:49
Alignment explanation
Indices: 1209474--1209620 Score: 125
Period size: 52 Copynumber: 2.8 Consensus size: 49
1209464 TTATTTCCGA
* * *
1209474 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTT-TATAATC
1 GGGGATACT-CTACCCC-GTTTTATTTCTAAAACA-CAATTTTTCCATAATC
* * **
1209525 GGGGATACTCTGACCCCGATTTTATTTTTTAGAACACCGTTTTTCCATAATC
1 GGGGATACTCT-ACCCCG-TTTTA-TTTCTAAAACACAATTTTTCCATAATC
* *
1209577 GGGGATACTCTAGCCCCGTTGTTATCTCTAAAATACTAATTTTT
1 GGGGATACTCTA-CCCCGTT-TTATTTCTAAAACAC-AATTTTT
1209621 TTCTCGTCGG
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
50 2 0.03
51 35 0.46
52 39 0.51
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (49 bp):
GGGGATACTCTACCCCGTTTTATTTCTAAAACACAATTTTTCCATAATC
Found at i:1212209 original size:849 final size:849
Alignment explanation
Indices: 1210566--1212265 Score: 3310
Period size: 849 Copynumber: 2.0 Consensus size: 849
1210556 ACGTCGCGAC
1210566 AATCACGATTATTCATCACTAATCGAAAATAATCATGAGACACACTTTGATCCTCTCTCCTTTTT
1 AATCACGATTATTCATCACTAATCGAAAATAATCATGAGACACACTTTGATCCTCTCTCCTTTTT
*
1210631 ATATATTTTTGTGCATTTATTTTGTGTGAATTTGTTCATTATTTTCTGTTTTACTAACATGTTTC
66 ATAAATTTTTGTGCATTTATTTTGTGTGAATTTGTTCATTATTTTCTGTTTTACTAACATGTTTC
1210696 CTTTCATAGGGACCTTGTGCATTCATGCTTTAAAAACTTTTTTAAGATCATGAAACGATATTTCG
131 CTTTCATAGGGACCTTGTGCATTCATGCTTTAAAAACTTTTTTAAGATCATGAAACGATATTTCG
1210761 TGTCAATATCTCTCCAGTGCTTGACAAGAAATATTTTATTTTTCCAAACCTAATCCGAAAACCTA
196 TGTCAATATCTCTCCAGTGCTTGACAAGAAATATTTTATTTTTCCAAACCTAATCCGAAAACCTA
1210826 TTCTATAAGAATCATCATGTTCCTCACTTATCCGAGGCACATAGCTGATATAAGTTTTTGTACTA
261 TTCTATAAGAATCATCATGTTCCTCACTTATCCGAGGCACATAGCTGATATAAGTTTTTGTACTA
*
1210891 AACTCGGATTTGTAGTTTTCACAAAACTTCATGCATTAGAGAGAATTATATCAAAATAATGGTAA
326 AACTCGGATTTGTAGTTTCCACAAAACTTCATGCATTAGAGAGAATTATATCAAAATAATGGTAA
1210956 AAAAATGGAACCAAAAAAATCGAGATTTAAGTGAGACACAGTTAGAAGGTACCAATTTCGGGCAT
391 AAAAATGGAACCAAAAAAATCGAGATTTAAGTGAGACACAGTTAGAAGGTACCAATTTCGGGCAT
*
1211021 CGTAGGGGCGCTAATCCTTCCCCATGCATAACCAACTCCCAAACCCAAACACGAATCTCCAAATT
456 CCTAGGGGCGCTAATCCTTCCCCATGCATAACCAACTCCCAAACCCAAACACGAATCTCCAAATT
*
1211086 ACATAGATCGCGGGATCGAAATTTTGAGTTTCGTAACTCGAGACATTGGTTTCAATAGGCATTCG
521 ACATAGATCGCGGGATCGAAATTTCGAGTTTCGTAACTCGAGACATTGGTTTCAATAGGCATTCG
1211151 ATCATGCTTAGCCCGAAATGATCGGTGGCAACTCCAAGTTCATGGTCATTTTATGGTGACCATAC
586 ATCATGCTTAGCCCGAAATGATCGGTGGCAACTCCAAGTTCATGGTCATTTTATGGTGACCATAC
1211216 GAGACTAGTAGGATATGTAATTCGTCCGATAGTCTTTCATCCCTTCATATTGACCATCATCATCT
651 GAGACTAGTAGGATATGTAATTCGTCCGATAGTCTTTCATCCCTTCATATTGACCATCATCATCT
*
1211281 TTTGTTTTAAGTCGAGCACGTTTTGGCCCTTTGGATCTTCTGAAGTACTTAAAATTCGAGCCACG
716 TTTGTTTTAAGTCGAGCACGTTTTGGCCCTTTGGATCTTCTGAAGTACTTAAAATCCGAGCCACG
1211346 TTGCGGTAGTAAGTTTTTATTATTCTTTCTTATGCCCTACTGAAAACCCAGAGGAACATAAAAGG
781 TTGCGGTAGTAAGTTTTTATTATTCTTTCTTATGCCCTACTGAAAACCCAGAGGAACATAAAAGG
1211411 TTTT
846 TTTT
*
1211415 AATCATGATTATTCATCACTAATCGAAAATAATCATGAGACACACTTTGATCCTCTCTCCTTTTT
1 AATCACGATTATTCATCACTAATCGAAAATAATCATGAGACACACTTTGATCCTCTCTCCTTTTT
*
1211480 ATAAATTTTTGTGCATTTATTTTGTGTGAATTTGTTCGTTATTTTCTGTTTTACTAACATGTTTC
66 ATAAATTTTTGTGCATTTATTTTGTGTGAATTTGTTCATTATTTTCTGTTTTACTAACATGTTTC
1211545 CTTTCATAGGGACCTTGTGCATTCATGCTTTAAAAACTTTTTTAAGATCATGAAACGATATTTCG
131 CTTTCATAGGGACCTTGTGCATTCATGCTTTAAAAACTTTTTTAAGATCATGAAACGATATTTCG
1211610 TGTCAATATCTCTCCAGTGCTTGACAAGAAATATTTTATTTTTCCAAACCTAATCCGAAAACCTA
196 TGTCAATATCTCTCCAGTGCTTGACAAGAAATATTTTATTTTTCCAAACCTAATCCGAAAACCTA
1211675 TTCTATAAGAATCATCATGTTCCTCACTTATCCGAGGCACATAGCTGATATAAGTTTTTGTACTA
261 TTCTATAAGAATCATCATGTTCCTCACTTATCCGAGGCACATAGCTGATATAAGTTTTTGTACTA
* *
1211740 AACTCGGATTTGTAGTTTCCACAAAACTTCATGCATTATAGGGAATTATATCAAAATAATGGTAA
326 AACTCGGATTTGTAGTTTCCACAAAACTTCATGCATTAGAGAGAATTATATCAAAATAATGGTAA
1211805 AAAAATGGAACCAAAAAAATCGAGATTTAAGTGAGACACAGTTAGAAGGTACCAATTTCGGGCAT
391 AAAAATGGAACCAAAAAAATCGAGATTTAAGTGAGACACAGTTAGAAGGTACCAATTTCGGGCAT
1211870 CCTAGGGGCGCTAATCCTTCCCCATGCATAACCAACTCCCAAACCCAAACACGAATCTCCAAATT
456 CCTAGGGGCGCTAATCCTTCCCCATGCATAACCAACTCCCAAACCCAAACACGAATCTCCAAATT
1211935 ACATAGATCGCGGGATCGAAATTTCGAGTTTCGTAACTCGAGACATTGGTTTCAATAGGCATTCG
521 ACATAGATCGCGGGATCGAAATTTCGAGTTTCGTAACTCGAGACATTGGTTTCAATAGGCATTCG
1212000 ATCATGCTTAGCCCGAAATGATCGGTGGCAACTCCAAGTTCATGGTCATTTTATGGTGACCATAC
586 ATCATGCTTAGCCCGAAATGATCGGTGGCAACTCCAAGTTCATGGTCATTTTATGGTGACCATAC
1212065 GAGACTAGTAGGATATGTAATTCGTCCGATAGTCTTTCATCCCTTCATATTGACCATCATCATCT
651 GAGACTAGTAGGATATGTAATTCGTCCGATAGTCTTTCATCCCTTCATATTGACCATCATCATCT
1212130 TTTGTTTTAAGTCGAGCACGTTTTGGCCCTTTGGATCTTCTGAAGTACTTAAAATCCGAGCCACG
716 TTTGTTTTAAGTCGAGCACGTTTTGGCCCTTTGGATCTTCTGAAGTACTTAAAATCCGAGCCACG
*
1212195 TTGCGGTAGTAAGTTTTTATTATTCTTTCTTATGCCCTGCTGAAAACCCAGAGGAACATAAAAGG
781 TTGCGGTAGTAAGTTTTTATTATTCTTTCTTATGCCCTACTGAAAACCCAGAGGAACATAAAAGG
1212260 TTTT
846 TTTT
1212264 AA
1 AA
1212266 AAGCCAAGTG
Statistics
Matches: 841, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
849 841 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (849 bp):
AATCACGATTATTCATCACTAATCGAAAATAATCATGAGACACACTTTGATCCTCTCTCCTTTTT
ATAAATTTTTGTGCATTTATTTTGTGTGAATTTGTTCATTATTTTCTGTTTTACTAACATGTTTC
CTTTCATAGGGACCTTGTGCATTCATGCTTTAAAAACTTTTTTAAGATCATGAAACGATATTTCG
TGTCAATATCTCTCCAGTGCTTGACAAGAAATATTTTATTTTTCCAAACCTAATCCGAAAACCTA
TTCTATAAGAATCATCATGTTCCTCACTTATCCGAGGCACATAGCTGATATAAGTTTTTGTACTA
AACTCGGATTTGTAGTTTCCACAAAACTTCATGCATTAGAGAGAATTATATCAAAATAATGGTAA
AAAAATGGAACCAAAAAAATCGAGATTTAAGTGAGACACAGTTAGAAGGTACCAATTTCGGGCAT
CCTAGGGGCGCTAATCCTTCCCCATGCATAACCAACTCCCAAACCCAAACACGAATCTCCAAATT
ACATAGATCGCGGGATCGAAATTTCGAGTTTCGTAACTCGAGACATTGGTTTCAATAGGCATTCG
ATCATGCTTAGCCCGAAATGATCGGTGGCAACTCCAAGTTCATGGTCATTTTATGGTGACCATAC
GAGACTAGTAGGATATGTAATTCGTCCGATAGTCTTTCATCCCTTCATATTGACCATCATCATCT
TTTGTTTTAAGTCGAGCACGTTTTGGCCCTTTGGATCTTCTGAAGTACTTAAAATCCGAGCCACG
TTGCGGTAGTAAGTTTTTATTATTCTTTCTTATGCCCTACTGAAAACCCAGAGGAACATAAAAGG
TTTT
Found at i:1214191 original size:12 final size:12
Alignment explanation
Indices: 1214174--1214214 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1214164 TTTGCTACTA
1214174 TTTTGGTTGTTG
1 TTTTGGTTGTTG
*
1214186 TTTTGGTTGCTG
1 TTTTGGTTGTTG
*
1214198 TTTTTGCTTGTTG
1 -TTTTGGTTGTTG
1214211 TTTT
1 TTTT
1214215 ACTTCGGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.00, C:0.05, G:0.27, T:0.68
Consensus pattern (12 bp):
TTTTGGTTGTTG
Found at i:1214212 original size:13 final size:13
Alignment explanation
Indices: 1214174--1214214 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1214164 TTTGCTACTA
1214174 TTTTGGTTGTTG-
1 TTTTGGTTGTTGT
*
1214186 TTTTGGTTGCTGT
1 TTTTGGTTGTTGT
*
1214199 TTTTGCTTGTTGT
1 TTTTGGTTGTTGT
1214212 TTT
1 TTT
1214215 ACTTCGGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.00, C:0.05, G:0.27, T:0.68
Consensus pattern (13 bp):
TTTTGGTTGTTGT
Found at i:1214629 original size:12 final size:12
Alignment explanation
Indices: 1214612--1214646 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1214602 TGCAATTGTG
1214612 TCTTCATTGCTT
1 TCTTCATTGCTT
*
1214624 TCTTCATTACTT
1 TCTTCATTGCTT
*
1214636 TTTTCATTGCT
1 TCTTCATTGCT
1214647 GCCATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.11, C:0.23, G:0.06, T:0.60
Consensus pattern (12 bp):
TCTTCATTGCTT
Found at i:1215138 original size:22 final size:23
Alignment explanation
Indices: 1215112--1215157 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1215102 TAATTAATAC
1215112 TATTTTATTA-TTATATTTTTAT
1 TATTTTATTATTTATATTTTTAT
*
1215134 TATTTTATTATTTTTATTTTTAT
1 TATTTTATTATTTATATTTTTAT
1215157 T
1 T
1215158 TTAGAATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTTTATTATTTATATTTTTAT
Found at i:1215152 original size:14 final size:13
Alignment explanation
Indices: 1215112--1215160 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
1215102 TAATTAATAC
*
1215112 TATTTTATTATTA
1 TATTTTATTATTT
1215125 TATTTTTATTATTT
1 TA-TTTTATTATTT
*
1215139 TATTATTTTTATTTT
1 TATT-TTATTA-TTT
1215154 TATTTTA
1 TATTTTA
1215161 GAATTAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 4 0.13
14 19 0.63
15 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:1217113 original size:21 final size:21
Alignment explanation
Indices: 1217075--1217114 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1217065 ATGGAATAAC
* **
1217075 GTTACCATTGCCCTCTGATAG
1 GTTACCATTACCAACTGATAG
1217096 GTTACCATTACCAACTGAT
1 GTTACCATTACCAACTGAT
1217115 CCCTCGCCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (21 bp):
GTTACCATTACCAACTGATAG
Found at i:1218036 original size:20 final size:18
Alignment explanation
Indices: 1218018--1218057 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1218008 ACAAAAACTA
1218018 TTTTATACCGTGTAAAAC
1 TTTTATACCGTGTAAAAC
1218036 TTTTATACCGTGTAAAA-
1 TTTTATACCGTGTAAAAC
1218053 TTTTA
1 TTTTA
1218058 AATTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTTATACCGTGTAAAAC
Found at i:1218845 original size:27 final size:27
Alignment explanation
Indices: 1218809--1218898 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
1218799 CCCTTTTTCC
* *
1218809 TTTTAAGTCCATAACTCTGTGGCATCT
1 TTTTAAGTCCATAACTCTGTGGCACCA
* * *
1218836 TTTTAAGTCCATAACTTTTTGGCACCC
1 TTTTAAGTCCATAACTCTGTGGCACCA
1218863 TTTTAAGTCCATAACTCTGTGGCACCA
1 TTTTAAGTCCATAACTCTGTGGCACCA
1218890 TTTTAAGTC
1 TTTTAAGTC
1218899 TATGCCTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (27 bp):
TTTTAAGTCCATAACTCTGTGGCACCA
Found at i:1219069 original size:65 final size:64
Alignment explanation
Indices: 1219014--1219141 Score: 167
Period size: 65 Copynumber: 2.0 Consensus size: 64
1219004 CACTTCATCA
* *
1219014 CTTCAAAAGCCCACACAAGTTGGT-AGC-A-C-CC-TCTAAAGCCCACACAAGTTGGTGGCAACC
1 CTTCAAAAGCCCACACAAGTCGGTGA-CAACCTCCTTCAAAAGCCCACACAAGTTGGTGGC-ACC
1219074 T
64 T
* *
1219075 CTTCTAAAGCCCACACAAGTCGGTGACAACCTCCTTCAAAAGCCCACACAAGTTGGTGGCATCT
1 CTTCAAAAGCCCACACAAGTCGGTGACAACCTCCTTCAAAAGCCCACACAAGTTGGTGGCACCT
1219139 CTT
1 CTT
1219142 TCTAAGCCCA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
61 23 0.40
62 2 0.03
63 1 0.02
64 8 0.14
65 24 0.41
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (64 bp):
CTTCAAAAGCCCACACAAGTCGGTGACAACCTCCTTCAAAAGCCCACACAAGTTGGTGGCACCT
Found at i:1219086 original size:32 final size:31
Alignment explanation
Indices: 1219014--1219151 Score: 165
Period size: 32 Copynumber: 4.4 Consensus size: 31
1219004 CACTTCATCA
* *
1219014 CTTCAAAAGCCCACACAAGTTGGTAGCACC-
1 CTTCTAAAGCCCACACAAGTTGGTGGCACCT
1219044 C-TCTAAAGCCCACACAAGTTGGTGGCAACCT
1 CTTCTAAAGCCCACACAAGTTGGTGGC-ACCT
* *
1219075 CTTCTAAAGCCCACACAAGTCGGTGACAACCT
1 CTTCTAAAGCCCACACAAGTTGGTGGC-ACCT
* *
1219107 CCTTCAAAAGCCCACACAAGTTGGTGGCATCT
1 -CTTCTAAAGCCCACACAAGTTGGTGGCACCT
1219139 CTTTCT-AAGCCCA
1 C-TTCTAAAGCCCA
1219152 ATGTCACTGG
Statistics
Matches: 94, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.24
30 4 0.04
31 9 0.10
32 34 0.36
33 24 0.26
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (31 bp):
CTTCTAAAGCCCACACAAGTTGGTGGCACCT
Found at i:1219266 original size:52 final size:52
Alignment explanation
Indices: 1219209--1219553 Score: 313
Period size: 52 Copynumber: 6.6 Consensus size: 52
1219199 ATTGCTAGTA
* * * * *
1219209 TTGAATCAGCATATTGACACCTTTGCCATCTTTAAGTCTAATGTCGCTAGCC
1 TTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCC
* * * * * * *
1219261 TTGAATCAACACATTGGCACCTTTTTC-TTTCTTAAGTCCGATATGGTTGGCC
1 TTGAATCAGCACATTGGCACCTTTGTCATCT-TTAAGTCCAATGTCGCTGGCC
* * * * *
1219313 TTGAATCAGCATATTGGCATCTTTGTCAT-TCCTAAGCCCAATGTCACTGGCC
1 TTGAATCAGCACATTGGCACCTTTGTCATCT-TTAAGTCCAATGTCGCTGGCC
* * * *
1219365 TTGAATCAGCACATTGGCA--TTCCTCTCATCCTCAAGTCCAATGTCGCTTGCC
1 TTGAATCAGCACATTGGCACCTT--TGTCATCTTTAAGTCCAATGTCGCTGGCC
* * * * *
1219417 TTGAATCAGCACCTTGGCACCTTTCTCATTTTTAAGTCCAATGTTGCTGACC
1 TTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCC
* * *
1219469 TTGAATCAGCACATTGGCACCTTTGTCATCTTCAAG-CCTAATATCGTTGGCC
1 TTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCC-AATGTCGCTGGCC
* * *
1219521 TTGAATCAACATATTGGCACCTTTATCACTCTT
1 TTGAATCAGCACATTGGCACCTTTGTCA-TCTT
1219554 CTCATCTTCA
Statistics
Matches: 235, Mismatches: 49, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
50 2 0.01
51 4 0.02
52 222 0.94
53 5 0.02
54 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.35
Consensus pattern (52 bp):
TTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGGCC
Found at i:1219328 original size:104 final size:101
Alignment explanation
Indices: 1219144--1219544 Score: 329
Period size: 104 Copynumber: 3.9 Consensus size: 101
1219134 CATCTCTTTC
* * * *
1219144 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCA-----CT-TTCTTAAGTCTAATATTG
1 TAAGTCCAATGTCGCT-GCCTTGAATCAGCACATTGGCACCTTTCTCTTCTTAAGTCCAATATGG
* * ** *
1219203 CTAGTATTGAATCAGCATATTGACACCTTTGCCATCTT
65 TTGGCCTTGAATCAGCATATTGGCACCTTTGCCAT-TT
* * * *
1219241 TAAGTCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTTTCTTTCTTAAGTCCGATATG
1 TAAGTCCAATGTCGCT-GCCTTGAATCAGCACATTGGCACCTTTCTC-TTCTTAAGTCCAATATG
* * *
1219306 GTTGGCCTTGAATCAGCATATTGGCATCTTTGTCATTCC
64 GTTGGCCTTGAATCAGCATATTGGCACCTTTGCCATT-T
* * * * *
1219345 TAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCA--TTCCTCTCATCCTCAAGTCCAATG
1 TAAGTCCAATGTCGCT-GCCTTGAATCAGCACATTGGCACCTT--TCTC-TTCTTAAGTCCAATA
* **
1219408 TCGCTT-GCCTTGAATCAGCACCTTGGCACCTTT-CTCATTTT
62 T-GGTTGGCCTTGAATCAGCATATTGGCACCTTTGC-CA-TTT
* * *
1219449 TAAGTCCAATGTTGCTGACCTTGAATCAGCACATTGGCACCTTTGTCATCTTCAAG-CCTAATAT
1 TAAGTCCAATGTCGCTG-CCTTGAATCAGCACATTGGCACCTTTCTCTTCTT-AAGTCC-AATAT
* *
1219513 CGTTGGCCTTGAATCAACATATTGGCACCTTT
63 GGTTGGCCTTGAATCAGCATATTGGCACCTTT
1219545 ATCACTCTTC
Statistics
Matches: 238, Mismatches: 47, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
97 34 0.14
102 3 0.01
103 8 0.03
104 186 0.78
105 5 0.02
106 2 0.01
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (101 bp):
TAAGTCCAATGTCGCTGCCTTGAATCAGCACATTGGCACCTTTCTCTTCTTAAGTCCAATATGGT
TGGCCTTGAATCAGCATATTGGCACCTTTGCCATTT
Found at i:1219420 original size:156 final size:156
Alignment explanation
Indices: 1219242--1219539 Score: 393
Period size: 156 Copynumber: 1.9 Consensus size: 156
1219232 TGCCATCTTT
* * *
1219242 AAGTCTAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTTTC-TTTCTTAAGTCCGATATG
1 AAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTCTCATTT-TTAAGTCCAATATG
* * * * *
1219306 GTTGGCCTTGAATCAGCATATTGGCATCTTTGTCATTCCT-AAGCCCAATGTCACTGGCCTTGAA
65 GCTGACCTTGAATCAGCACATTGGCACCTTTGTCA-TCCTCAAGCCCAATATCACTGGCCTTGAA
*
1219370 TCAGCACATTGGCATTCCTCTCATCCTC
129 TCAACACATTGGCATTCCTCTCATCCTC
* * * * *
1219398 AAGTCCAATGTCGCTTGCCTTGAATCAGCACCTTGGCACCTTTCTCATTTTTAAGTCCAATGTTG
1 AAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTCTCATTTTTAAGTCCAATATGG
* * **
1219463 CTGACCTTGAATCAGCACATTGGCACCTTTGTCATCTTCAAGCCTAATATCGTTGGCCTTGAATC
66 CTGACCTTGAATCAGCACATTGGCACCTTTGTCATCCTCAAGCCCAATATCACTGGCCTTGAATC
*
1219528 AACATATTGGCA
131 AACACATTGGCA
1219540 CCTTTATCAC
Statistics
Matches: 121, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
155 3 0.02
156 115 0.95
157 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.34
Consensus pattern (156 bp):
AAGTCCAATGTCGCTAGCCTTGAATCAACACATTGGCACCTTTCTCATTTTTAAGTCCAATATGG
CTGACCTTGAATCAGCACATTGGCACCTTTGTCATCCTCAAGCCCAATATCACTGGCCTTGAATC
AACACATTGGCATTCCTCTCATCCTC
Found at i:1220252 original size:13 final size:13
Alignment explanation
Indices: 1220234--1220259 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1220224 GCATAAGTTT
1220234 TGTATCAATACAA
1 TGTATCAATACAA
1220247 TGTATCAATACAA
1 TGTATCAATACAA
1220260 AACTACCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TGTATCAATACAA
Found at i:1220308 original size:20 final size:20
Alignment explanation
Indices: 1220283--1220361 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1220273 ACTGCCAAGG
1220283 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTACT
*
1220303 AAATGTACCGATACATGTTTAC-
1 AAATGTATCGATACA---TTACT
* *
1220325 AATTGTATCGATACATTTCT
1 AAATGTATCGATACATTACT
* * *
1220345 CATTATATCGATACATT
1 AAATGTATCGATACATT
1220362 CTAGGTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 3 0.06
20 29 0.59
22 13 0.27
23 4 0.08
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTACT
Found at i:1222530 original size:27 final size:27
Alignment explanation
Indices: 1222499--1222567 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
1222489 TTCCTTTATT
1222499 GGGGATACTCCAACCCTATTCTTTCGA
1 GGGGATACTCCAACCCTATTCTTTCGA
1222526 GGGGATACTCCAACCCTATTCTTTCGA
1 GGGGATACTCCAACCCTATTCTTTCGA
1222553 GGGGATACTCCAACC
1 GGGGATACTCCAACC
1222568 TCCTTTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.26
Consensus pattern (27 bp):
GGGGATACTCCAACCCTATTCTTTCGA
Found at i:1225668 original size:78 final size:79
Alignment explanation
Indices: 1225578--1225781 Score: 268
Period size: 79 Copynumber: 2.6 Consensus size: 79
1225568 GAAATAATAT
* * * * *
1225578 GGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGGAAATAAAACT-AGGGTGGAGTATC-C
1 GGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAACTAAGGGTGGAGTATCTC
*
1225641 TCTCGAAAATAACGG
66 -CTCGAAAACAACGG
* * * *
1225656 GGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTATAGAAATAAAACTAAGGTTGGAGTATCTC
1 GGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAACTAAGGGTGGAGTATCTC
*
1225721 CTCGAAAACAATGG
66 CTCGAAAACAACGG
* *
1225735 GGTTGGAGTATCCACGATGGTGGAAAATTGGCATTTTAGAAATAAAA
1 GGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAA
1225782 ACATGAATGA
Statistics
Matches: 108, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
78 41 0.38
79 66 0.61
80 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATGGTGGAAAATTGGTATTTTAGAAATAAAACTAAGGGTGGAGTATCTC
CTCGAAAACAACGG
Found at i:1228178 original size:50 final size:50
Alignment explanation
Indices: 1228124--1228230 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 50
1228114 AAAATGCTTG
* * * *
1228124 AATGTATCGATACATTGAGA-AATATATTAATATATCTAGGTAAAACCCTA
1 AATGTATCGATACAATGA-ATAATATATCAATACATCTAGGTAAAACCCAA
* *
1228174 AATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCAA
1 AATGTATCGATACAATGAATAATATATCAATACATCTAGGTAAAACCCAA
1228224 AATGTAT
1 AATGTAT
1228231 ATGAAGAATG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (50 bp):
AATGTATCGATACAATGAATAATATATCAATACATCTAGGTAAAACCCAA
Found at i:1234326 original size:55 final size:54
Alignment explanation
Indices: 1234244--1234551 Score: 361
Period size: 55 Copynumber: 5.6 Consensus size: 54
1234234 GCCACCAGGG
* * *
1234244 CATCATTACTTATAGTGACACCAAGTCATCCGAATTTTGATTGCCACCAAGGCAT
1 CATCATTGCTTATAGTGACACCAAGTCA-CCCAATTTTGATCGCCACCAAGGCAT
* * * *
1234299 CACCATGGCTTATAATGACGCCAAGTCACCCCAATTTTGATCGCCACCAAGGCAT
1 CATCATTGCTTATAGTGACACCAAGTCA-CCCAATTTTGATCGCCACCAAGGCAT
* * * *
1234354 CATTATTGCTTATGGTGACACCAAGTTACCCTAATTTTAATCGCCACCAAGGCAT
1 CATCATTGCTTATAGTGACACCAAGTCACCC-AATTTTGATCGCCACCAAGGCAT
* * *
1234409 CATCATTGCTTATAATGACATCAAGTCACTCCAATTCTGATCGCCACCAAGGCAT
1 CATCATTGCTTATAGTGACACCAAGTCAC-CCAATTTTGATCGCCACCAAGGCAT
* * * *
1234464 CATCATTACTTATAGTGACATCAAGTCACTCAAATTTTGATTGCCACCAAGGCAT
1 CATCATTGCTTATAGTGACACCAAGTCAC-CCAATTTTGATCGCCACCAAGGCAT
* *
1234519 TATCA---CTTATAGTGACATCAAGTCACTCCAATT
1 CATCATTGCTTATAGTGACACCAAGTCAC-CCAATT
1234552 CTGGCCGCCG
Statistics
Matches: 221, Mismatches: 30, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
52 27 0.12
54 3 0.01
55 189 0.86
56 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (54 bp):
CATCATTGCTTATAGTGACACCAAGTCACCCAATTTTGATCGCCACCAAGGCAT
Found at i:1234421 original size:110 final size:109
Alignment explanation
Indices: 1234231--1234554 Score: 406
Period size: 110 Copynumber: 3.0 Consensus size: 109
1234221 CGTTATCCTA
* * *
1234231 ATCGCCACCAGGGCATCATTA--CTTATAGTGACACCAAGTCATCCGAATTTTGATTGCCACCAA
1 ATCGCCACCAAGGCATCATTATTCTTATAGTGACACCAAGTCACCCAAATTTTGATTGCCACCAA
* * *
1234294 GGCATCACCATGGCTTATAATGACGCCAAGTCACCCCAATTTTG
66 GGCATCATCATGGCTTATAATGACACCAAGTCACCCCAATTCTG
* * * * *
1234338 ATCGCCACCAAGGCATCATTATTGCTTATGGTGACACCAAGTTACCCTAATTTTAATCGCCACCA
1 ATCGCCACCAAGGCATCATTATT-CTTATAGTGACACCAAGTCACCCAAATTTTGATTGCCACCA
* * *
1234403 AGGCATCATCATTGCTTATAATGACATCAAGTCACTCCAATTCTG
65 AGGCATCATCATGGCTTATAATGACACCAAGTCACCCCAATTCTG
* * *
1234448 ATCGCCACCAAGGCATCATCATTACTTATAGTGACATCAAGTCACTCAAATTTTGATTGCCACCA
1 ATCGCCACCAAGGCATCATTATT-CTTATAGTGACACCAAGTCACCCAAATTTTGATTGCCACCA
* * * *
1234513 AGGCATTATCA---CTTATAGTGACATCAAGTCACTCCAATTCTG
65 AGGCATCATCATGGCTTATAATGACACCAAGTCACCCCAATTCTG
1234555 GCCGCCGTCA
Statistics
Matches: 190, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
107 50 0.26
110 140 0.74
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (109 bp):
ATCGCCACCAAGGCATCATTATTCTTATAGTGACACCAAGTCACCCAAATTTTGATTGCCACCAA
GGCATCATCATGGCTTATAATGACACCAAGTCACCCCAATTCTG
Found at i:1240332 original size:2 final size:2
Alignment explanation
Indices: 1240321--1240358 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1240311 TCGAAAGCAT
1240321 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1240359 TAAGAAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1242855 original size:6 final size:7
Alignment explanation
Indices: 1242825--1242853 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1242815 TCTTAAAACA
1242825 TTTAA-T
1 TTTAATT
1242831 TTTAATT
1 TTTAATT
1242838 TTTAATT
1 TTTAATT
1242845 TTTAATT
1 TTTAATT
1242852 TT
1 TT
1242854 AAAATGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:1243452 original size:42 final size:47
Alignment explanation
Indices: 1243405--1243519 Score: 116
Period size: 47 Copynumber: 2.5 Consensus size: 47
1243395 TGAAATTTTT
**
1243405 TTTTATT-TTTAT-TAAATATGAA-TAATTTAT-TTATA-TTATTTA
1 TTTTATTATTTATATAAATAAAAATTAATTTATATTATATTTATTTA
* *
1243447 TTTTATTATTTATAATTAATAAAAATTATTTTATATTATATTTATTTA
1 TTTTATTATTTAT-ATAAATAAAAATTAATTTATATTATATTTATTTA
* *
1243495 TTTTA-TACTTAAATTAAATAAAAAT
1 TTTTATTATTTATA-TAAATAAAAAT
1243520 ATTTTTTATA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
42 7 0.12
43 5 0.08
45 7 0.12
46 8 0.14
47 20 0.34
48 12 0.20
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (47 bp):
TTTTATTATTTATATAAATAAAAATTAATTTATATTATATTTATTTA
Found at i:1243455 original size:12 final size:13
Alignment explanation
Indices: 1243429--1243459 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1243419 AATATGAATA
1243429 ATTTATTTATATT
1 ATTTATTTATATT
1243442 ATTTATTT-TATT
1 ATTTATTTATATT
1243454 ATTTAT
1 ATTTAT
1243460 AATTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTATTTATATT
Found at i:1243486 original size:47 final size:48
Alignment explanation
Indices: 1243430--1243534 Score: 137
Period size: 47 Copynumber: 2.2 Consensus size: 48
1243420 ATATGAATAA
*
1243430 TTTAT-TTATA-TTATTTATTTTATTATTTATAATT-AATAAAAAT-TAT
1 TTTATATTATATTTATTTATTTTA-TACTTA-AATTAAATAAAAATATAT
*
1243476 TTTATATTATATTTATTTATTTTATACTTAAATTAAATAAAAATATTT
1 TTTATATTATATTTATTTATTTTATACTTAAATTAAATAAAAATATAT
1243524 TTTATAATTAT
1 TTTAT-ATTAT
1243535 TAAATATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
46 9 0.17
47 19 0.37
48 19 0.37
49 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (48 bp):
TTTATATTATATTTATTTATTTTATACTTAAATTAAATAAAAATATAT
Found at i:1243823 original size:4 final size:4
Alignment explanation
Indices: 1243810--1243840 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1243800 CGCAAATAGT
1243810 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1243841 AACACTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:1244518 original size:34 final size:33
Alignment explanation
Indices: 1244474--1244576 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
1244464 TCAGCAACCA
1244474 CCACCCCCACAACCTCCACCTCCACCGCCACCG
1 CCACCCCCACAACCTCCACCTCCACCGCCACCG
1244507 CCACCCCCCACAACCTCCACCTCCACCGCCACCG
1 CCA-CCCCCACAACCTCCACCTCCACCGCCACCG
* * *
1244541 CCACCCCCACAACCTCCACCTGCACCACCGCCG
1 CCACCCCCACAACCTCCACCTCCACCGCCACCG
1244574 CCA
1 CCA
1244577 AATCTTCTGC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
33 33 0.50
34 33 0.50
ACGTcount: A:0.21, C:0.66, G:0.07, T:0.06
Consensus pattern (33 bp):
CCACCCCCACAACCTCCACCTCCACCGCCACCG
Found at i:1244561 original size:6 final size:6
Alignment explanation
Indices: 1244489--1244550 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
1244479 CCCACAACCT
* * * * *
1244489 CCACCT CCACCG CCACCG CCACC- CC-CCA CAACCT CCACCT CCACCG
1 CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG CCACCG
*
1244535 CCACCG CCACCC CCAC
1 CCACCG CCACCG CCAC
1244551 AACCTCCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
4 2 0.04
5 3 0.06
6 43 0.90
ACGTcount: A:0.19, C:0.69, G:0.06, T:0.05
Consensus pattern (6 bp):
CCACCG
Found at i:1244910 original size:3 final size:3
Alignment explanation
Indices: 1244902--1244938 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1244892 AGTTCTATAC
1244902 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1244939 GTTCTATTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1248741 original size:13 final size:13
Alignment explanation
Indices: 1248720--1248787 Score: 66
Period size: 13 Copynumber: 4.9 Consensus size: 13
1248710 TAAAATTGAA
1248720 TAAAATAAAAAAT
1 TAAAATAAAAAAT
*
1248733 TAAATTAAAAAAT
1 TAAAATAAAAAAT
*
1248746 TAAAAATAATAATAAA
1 T-AAAATAA-AA-AAT
1248762 T-AAATAAATAAAAT
1 TAAAAT-AA-AAAAT
1248776 TAAAATAAAAAA
1 TAAAATAAAAAA
1248788 ATTCAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
13 17 0.37
14 15 0.33
15 11 0.24
16 3 0.07
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAATAAAAAAT
Found at i:1248757 original size:30 final size:29
Alignment explanation
Indices: 1248709--1248788 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 29
1248699 TAAAGTAAAG
*
1248709 ATAAAATTGAATAA-AATAAAAAATTAAATTA
1 ATAAAATT-AA-AATAATAAAAAA-TAAATAA
*
1248740 A-AAAATTAAAAATAATAATAAATAAATAA
1 ATAAAATT-AAAATAATAAAAAATAAATAA
1248769 ATAAAATTAAAATAA-AAAAA
1 ATAAAATTAAAATAATAAAAA
1248789 TTCAAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.09
29 16 0.37
30 22 0.51
31 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (29 bp):
ATAAAATTAAAATAATAAAAAATAAATAA
Found at i:1249102 original size:29 final size:29
Alignment explanation
Indices: 1249043--1249102 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
1249033 CATATTGGTT
* *
1249043 TTTAAATTTTAAATTTTAAAATATTTTTA
1 TTTAAATTTTAAATTATAAAATATTTATA
1249072 TTTAAA-TTT-AATTATAAAATATATTAATA
1 TTTAAATTTTAAATTATAAAATAT-TT-ATA
1249101 TT
1 TT
1249103 AATAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.44
28 5 0.19
29 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTAAATTTTAAATTATAAAATATTTATA
Found at i:1252029 original size:87 final size:88
Alignment explanation
Indices: 1251919--1252362 Score: 380
Period size: 87 Copynumber: 5.2 Consensus size: 88
1251909 CAGAGTAGTA
* * * **
1251919 GGGATGGAGTTT--CTAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTTAGGAGTGAGGT
1 GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCAAGGT
*
1251982 TGGAGTGTCTCCTCGAAGGAAT-
66 TGGAGTGTCTCCTCGAAGGAGTG
* ** * *
1252004 GGGATGGAGTTTCCTCAAAGATAAAATTCCATAAAGGAAAATTTGATTTTTTTTAAGAG-AGAGG
1 GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCA-AGG
* ** *
1252068 TTGGAATGTCTTTTC-AGATGAGTG
65 TTGGAGTGTCTCCTCGA-AGGAGTG
* *
1252092 GGGATGGAGTTTCCCCAAAGGTAAAATTATATGAA--AGAA-TT--TTTTTTTGAAGAGCAAGGT
1 GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCAAGGT
* *
1252152 TAGAGTGTC-CTTTCGAAGGAGTG
66 TGGAGTGTCTC-CTCGAAGGAGTG
* * * * *
1252175 GGGATGGAATTTCCCCAGAGATAAAGTTATACGAAGGAAAA-TTGATTTTCTTGAAGAGCAAGGT
1 GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCAAGGT
* *
1252239 TAGAGTG--TCCTCGCAAAAGAGTG
66 TGGAGTGTCTCCTCG--AAGGAGTG
** * ** * * *
1252262 AAGATGGAATTTCCCCAAAGATAAAATTATACAAAGAAAAATTTAATTTTTTTGAAGAGTAAGGT
1 GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCAAGGT
* * *
1252327 TGGAATATC-CCTC-AGAGGAGAG
66 TGGAGTGTCTCCTCGA-AGGAGTG
*
1252349 GGGATGAAGTTTCC
1 GGGATGGAGTTTCC
1252363 TTTAAAATAA
Statistics
Matches: 290, Mismatches: 50, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
83 62 0.21
84 2 0.01
85 22 0.08
86 6 0.02
87 140 0.48
88 54 0.19
89 4 0.01
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.30
Consensus pattern (88 bp):
GGGATGGAGTTTCCCCAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGCAAGGT
TGGAGTGTCTCCTCGAAGGAGTG
Found at i:1252475 original size:35 final size:35
Alignment explanation
Indices: 1252436--1252507 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1252426 GATTTTAAAA
1252436 ATATAAAGTTGAAGATTTGTATAAGATATTTTTTT
1 ATATAAAGTTGAAGATTTGTATAAGATATTTTTTT
* *
1252471 ATATAAAGTTGAAGTTTTGTATAAGATGTTTTTTT
1 ATATAAAGTTGAAGATTTGTATAAGATATTTTTTT
1252506 AT
1 AT
1252508 CTTAAGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (35 bp):
ATATAAAGTTGAAGATTTGTATAAGATATTTTTTT
Found at i:1253487 original size:12 final size:12
Alignment explanation
Indices: 1253470--1253502 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1253460 AGTGAAAAAT
1253470 AAAGGTTTTTAG
1 AAAGGTTTTTAG
1253482 AAAGGTTTTTAG
1 AAAGGTTTTTAG
1253494 AAAGGTTTT
1 AAAGGTTTT
1253503 GGTGATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (12 bp):
AAAGGTTTTTAG
Found at i:1254552 original size:20 final size:21
Alignment explanation
Indices: 1254510--1254560 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1254500 TTTTACAATT
*
1254510 TGTATCGATACAACAAGTCAA
1 TGTATCGATACAACAAGTAAA
*
1254531 TGTATCGATAC-ATAAGTAAA
1 TGTATCGATACAACAAGTAAA
1254551 TGTATCGATA
1 TGTATCGATA
1254561 TATGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAACAAGTAAA
Found at i:1258854 original size:68 final size:69
Alignment explanation
Indices: 1258764--1259048 Score: 235
Period size: 68 Copynumber: 4.2 Consensus size: 69
1258754 AGGGATTAAG
* * *
1258764 GTAGATAGGTGCC-GCAAGCTTGTGTGGGCTTTGAGGAAAAAAATACGTC-TCACTCTTTGAGGA
1 GTAGATAGGTGCCAGCAAGCTTGTGTGAGCTTTGAAGAAAAAAAGACGTCAT-ACTCTTTGAGGA
*
1258827 CTGGA
65 CTAGA
** * * *
1258832 GTAGATAGGTGCCATTAA-CTTGTGTGAGCTTTGAAGAATAAAAGATGTCATGCTCTTTGAGGAC
1 GTAGATAGGTGCCAGCAAGCTTGTGTGAGCTTTGAAGAAAAAAAGACGTCATACTCTTTGAGGAC
1258896 TAGA
66 TAGA
* * * * * ** *
1258900 GTAGATAGGTGCCACCAA-CTT-TAT-AGGCTTTGAAGAAGAAAAGGCATCATACTCTTCAAAGA
1 GTAGATAGGTGCCAGCAAGCTTGTGTGA-GCTTTGAAGAAAAAAAGACGTCATACTCTTTGAGGA
1258962 CTAGA
65 CTAGA
* ** * * * * *
1258967 GTAGATAAGTGCCAGCAA-CTTGCATGAGCTTTGAA-AGAGAAGAGGCGTCCTACTCTTTAAGGA
1 GTAGATAGGTGCCAGCAAGCTTGTGTGAGCTTTGAAGA-AAAAAAGACGTCATACTCTTTGAGGA
* *
1259030 TTGGA
65 CTAGA
*
1259035 GTTGATAGGTGCCA
1 GTAGATAGGTGCCA
1259049 CCAACCTATA
Statistics
Matches: 179, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
66 1 0.01
67 55 0.31
68 119 0.66
69 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (69 bp):
GTAGATAGGTGCCAGCAAGCTTGTGTGAGCTTTGAAGAAAAAAAGACGTCATACTCTTTGAGGAC
TAGA
Found at i:1258964 original size:67 final size:68
Alignment explanation
Indices: 1258815--1259079 Score: 259
Period size: 68 Copynumber: 3.9 Consensus size: 68
1258805 AATACGTCTC
* * ** * * **
1258815 ACTCTTTGAGGACTGGAGTAGATAGGTGCCATTAACTTGTGTGAGCTTTG-AAGAATAAAAGATG
1 ACTCTTTAAGGACTAGAGTAGATAGGTGCCACCAACTTGTATGAGCTTTGAAAG-AGAAAAGGCG
1258879 TCAT
65 TCAT
* *
1258883 GCTCTTTGAGGACTAGAGTAGATAGGTGCCACCAACTT-TAT-AGGCTTTG-AAGAAGAAAAGGC
1 ACTCTTTAAGGACTAGAGTAGATAGGTGCCACCAACTTGTATGA-GCTTTGAAAG-AGAAAAGGC
*
1258945 ATCAT
64 GTCAT
* * * * * *
1258950 ACTCTTCAAAGACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAGAGAAGAGGCGT
1 ACTCTTTAAGGACTAGAGTAGATAGGTGCCACCAACTTGTATGAGCTTTGAAAGAGAAAAGGCGT
*
1259015 CCT
66 CAT
* * * * * *
1259018 ACTCTTTAAGGATTGGAGTTGATAGGTGCCACCAACCTATATGGGCTTTGAAAGAGAAAAGG
1 ACTCTTTAAGGACTAGAGTAGATAGGTGCCACCAACTTGTATGAGCTTTGAAAGAGAAAAGG
1259080 TTCTTTAAGG
Statistics
Matches: 162, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
66 1 0.01
67 54 0.33
68 103 0.64
69 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (68 bp):
ACTCTTTAAGGACTAGAGTAGATAGGTGCCACCAACTTGTATGAGCTTTGAAAGAGAAAAGGCGT
CAT
Found at i:1258971 original size:135 final size:136
Alignment explanation
Indices: 1258825--1259079 Score: 309
Period size: 135 Copynumber: 1.9 Consensus size: 136
1258815 ACTCTTTGAG
* * ** ** * * *
1258825 GACTGGAGTAGATAGGTGCCATTAACTTGTGTGAGCTTTG-AAGAATAAAAGATGTCATGCTCTT
1 GACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAG-AGAAAAGACGTCATACTCTT
* *
1258889 TGAGGACTAGAGTAGATAGGTGCCACCAA-CTTTATAGGCTTTG-AAGAAGAAAAGGCATCATAC
65 TAAGGACTAGAGTAGATAGGTGCCACCAACCTATATAGGCTTTGAAAG-AGAAAAGGCATCATAC
1258952 TCTTCAAA
129 TCTTCAAA
* * *
1258960 GACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAGAGAAGAGGCGTCCTACTCTTT
1 GACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAGAGAAAAGACGTCATACTCTTT
* * * *
1259025 AAGGATTGGAGTTGATAGGTGCCACCAACCTATATGGGCTTTGAAAGAGAAAAGG
66 AAGGACTAGAGTAGATAGGTGCCACCAACCTATATAGGCTTTGAAAGAGAAAAGG
1259080 TTCTTTAAGG
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
135 73 0.74
136 23 0.23
137 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (136 bp):
GACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAGAGAAAAGACGTCATACTCTTT
AAGGACTAGAGTAGATAGGTGCCACCAACCTATATAGGCTTTGAAAGAGAAAAGGCATCATACTC
TTCAAA
Found at i:1259210 original size:68 final size:67
Alignment explanation
Indices: 1259103--1259392 Score: 273
Period size: 68 Copynumber: 4.3 Consensus size: 67
1259093 AAAAAAAACA
* * * * *
1259103 TCATGCTCTTTGAAGATTGGAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAAAGGAAAAT
1 TCATGCTCTTTGAGGACTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAAG
*
1259168 GCA
65 GCG
* * * * * * *
1259171 TCATGTTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTATATGTGCTTTGAAATAGAAAAT
1 TCATGCTCTTTGAGGACTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GGAAAAG
*
1259236 GTG
65 GCG
* *
1259239 TCCTGCTCTTTGAGGACTGGAAG-AGATAGGTGCCACCAACTTGTGTAGGCTTTG-AAGGAGAAG
1 TCATGCTCTTTGAGGACT-GAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGA-AA-
*
1259302 AGGTG
63 AGGCG
* * * * * *
1259307 TCCTGTTCTTTGAGGACTGGAGTAGATAAGTGCCACCAATCTAT-T-TGGGTTTTGAAGGAGAAA
1 TCATGCTCTTTGAGGACTGAAGTAGATAGGTGCCACCAA-CT-TGTGTGGGCTTTGAAAG-GAAA
1259370 AGGCG
63 AGGCG
1259375 TCATGCTCTTTGAGGACT
1 TCATGCTCTTTGAGGACT
1259393 AGAGGAAAAT
Statistics
Matches: 185, Mismatches: 28, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
66 2 0.01
67 10 0.05
68 159 0.86
69 11 0.06
70 3 0.02
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (67 bp):
TCATGCTCTTTGAGGACTGAAGTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGG
CG
Found at i:1259269 original size:225 final size:224
Alignment explanation
Indices: 1258879--1259305 Score: 509
Period size: 225 Copynumber: 1.9 Consensus size: 224
1258869 ATAAAAGATG
*
1258879 TCATGCTCTTTGAGGACTAGAGTAGATAGGTGCCACCAACTTTATAGGCTTTGAAGAAGAAAAGG
1 TCATGCTCTTTGAAGACTAGAGTAGATAGGTGCCACCAACTTTATAGGCTTTGAAGAAGAAAAGG
* * *
1258944 CATCATACTCTTCAAAGACTAGAGTAGATAAGTGCCAGCAACTTGCATGAGCTTTGAAAGAGAAG
66 CATCATACTCTTCAAAGACTAGAGTAGATAAGTGCCACCAACTTACATGAGCTTTGAAAGAGAAA
* * *
1259009 AGGCGTCCTACTCTTTAAGGATTGGAGTTGATAGGTGCCACCAACCTATATGGGCTTTGAAAGAG
131 AGGCGTCCTACTCTTTAAGGACTGGAGTAGATAGGTGCCACCAACCTATATAGGCTTTGAAAGAG
1259074 AAAAGGTTCTTTAAGGACTAAAAAAAACA
196 AAAAGGTTCTTTAAGGACTAAAAAAAACA
* * * * *
1259103 TCATGCTCTTTGAAGATTGGAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAA-AAGGAAAA
1 TCATGCTCTTTGAAGACTAGAGTAGATAGGTGCCACCAACTT-TATAGGCTTTGAAGAA-GAAAA
* ** ** * * * * * *
1259167 TGCATCATGTTCTTTGAGGACT-GAAGTAGATAGGTGTCACCAACTTATATGTGCTTTGAAATAG
64 GGCATCATACTCTTCAAAGACTAG-AGTAGATAAGTGCCACCAACTTACATGAGCTTTGAAAGAG
* * * * * * *
1259231 AAAATGTGTCCTGCTCTTTGAGGACTGGAAG-AGATAGGTGCCACCAACTTGTGTAGGCTTTGAA
128 AAAAGGCGTCCTACTCTTTAAGGACTGG-AGTAGATAGGTGCCACCAACCTATATAGGCTTTGAA
* *
1259295 GGAGAAGAGGT
192 AGAGAAAAGGT
1259306 GTCCTGTTCT
Statistics
Matches: 167, Mismatches: 32, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
224 41 0.25
225 124 0.74
226 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (224 bp):
TCATGCTCTTTGAAGACTAGAGTAGATAGGTGCCACCAACTTTATAGGCTTTGAAGAAGAAAAGG
CATCATACTCTTCAAAGACTAGAGTAGATAAGTGCCACCAACTTACATGAGCTTTGAAAGAGAAA
AGGCGTCCTACTCTTTAAGGACTGGAGTAGATAGGTGCCACCAACCTATATAGGCTTTGAAAGAG
AAAAGGTTCTTTAAGGACTAAAAAAAACA
Found at i:1259361 original size:136 final size:135
Alignment explanation
Indices: 1259103--1259392 Score: 343
Period size: 136 Copynumber: 2.1 Consensus size: 135
1259093 AAAAAAAACA
* * * * *
1259103 TCATGCTCTTTGAAGATTGGAGTAGATAGGTGTCACCAACTTGTGTGGGCTTTGAAAAGGAAAAT
1 TCATGCTCTTTGAGGACTGGAGTAGATAGGTGCCACCAACTTGTGTAGGCTTTG-AAAGGAAAAG
* * * *
1259168 GCATCATGTTCTTTGAGGACTGAAGTAGATAGGTGTCACCAACTTATATGTGCTTTGAAATAGAA
65 GCATCATGTTCTTTGAGGACTGAAGTAGATAAGTGCCACCAACTTATATGGGCTTTGAAAGAGAA
* *
1259233 AATGTG
130 AAGGCG
*
1259239 TCCTGCTCTTTGAGGACTGGAAG-AGATAGGTGCCACCAACTTGTGTAGGCTTTG-AAGGAGAAG
1 TCATGCTCTTTGAGGACTGG-AGTAGATAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGA-AA-
** * * * * *
1259302 AGGTGTCCTGTTCTTTGAGGACTGGAGTAGATAAGTGCCACCAA-TCTATTTGGGTTTTGAAGGA
63 AGGCATCATGTTCTTTGAGGACTGAAGTAGATAAGTGCCACCAACT-TATATGGGCTTTGAAAGA
1259366 GAAAAGGCG
127 GAAAAGGCG
1259375 TCATGCTCTTTGAGGACT
1 TCATGCTCTTTGAGGACT
1259393 AGAGGAAAAT
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
134 5 0.04
135 3 0.02
136 120 0.92
137 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (135 bp):
TCATGCTCTTTGAGGACTGGAGTAGATAGGTGCCACCAACTTGTGTAGGCTTTGAAAGGAAAAGG
CATCATGTTCTTTGAGGACTGAAGTAGATAAGTGCCACCAACTTATATGGGCTTTGAAAGAGAAA
AGGCG
Found at i:1263937 original size:14 final size:14
Alignment explanation
Indices: 1263910--1263948 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1263900 TTGATTCTTA
1263910 TTCTTTTTTGTTTTT
1 TTCTTTTTT-TTTTT
1263925 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
*
1263939 TGCTTTTTTT
1 TTCTTTTTTT
1263949 AAGTGGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:1263937 original size:21 final size:22
Alignment explanation
Indices: 1263904--1263948 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1263894 CTTAAGTTGA
1263904 TTCTTATTCTTTTTTG-TTTTT
1 TTCTTATTCTTTTTTGCTTTTT
* *
1263925 TTCTTTTTTTTTTTTGCTTTTT
1 TTCTTATTCTTTTTTGCTTTTT
1263947 TT
1 TT
1263949 AAGTGGTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.84
Consensus pattern (22 bp):
TTCTTATTCTTTTTTGCTTTTT
Found at i:1275697 original size:35 final size:35
Alignment explanation
Indices: 1275646--1275716 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1275636 AGGTGTAGGG
* *
1275646 ATGGAGTATCCTCAAAGATAAAATTCCACGAAAGA
1 ATGGAGTATCCCCAAAGATAAAATTCCACAAAAGA
1275681 ATGGAGTATCCCCAAAGATAAAATTCCACAAAAGA
1 ATGGAGTATCCCCAAAGATAAAATTCCACAAAAGA
1275716 A
1 A
1275717 AATTTGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (35 bp):
ATGGAGTATCCCCAAAGATAAAATTCCACAAAAGA
Found at i:1275784 original size:122 final size:122
Alignment explanation
Indices: 1275558--1275792 Score: 312
Period size: 122 Copynumber: 1.9 Consensus size: 122
1275548 AAGTAGTAGA
* * * * ** * *
1275558 AATGGAGTTTCCCCAAAGATAAAATTATACGAAAGAATATTTTTTTTTTTTGAAGAGCGGTTTGG
1 AATGGAGTATCCCCAAAGATAAAATTACACAAAAGAATAATTTGATTTTTTAAAGAGCGGATTGG
* * *
1275623 AGTGTCCCTTCGGAGGTGTAGGGATGGAGTATCCTCAAAGATAAAATTCCACGAAAG
66 AGTGTCCCCTCGGAGGTGTAGGGATGGACTATCCCCAAAGATAAAATTCCACGAAAG
*
1275680 AATGGAGTATCCCCAAAGATAAAATTCCACAAAAGAA-AATTTGATTTTTTAAAGAGCGAGATTG
1 AATGGAGTATCCCCAAAGATAAAATTACACAAAAGAATAATTTGATTTTTTAAAGAGCG-GATTG
* *
1275744 GAGTGTCCCCTCGGGGGAT-TAGGGATGGACTTTCCCCAAAGATAAAATT
65 GAGTGTCCCCTCGGAGG-TGTAGGGATGGACTATCCCCAAAGATAAAATT
1275793 ATACAAAGAA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
121 17 0.18
122 79 0.81
123 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (122 bp):
AATGGAGTATCCCCAAAGATAAAATTACACAAAAGAATAATTTGATTTTTTAAAGAGCGGATTGG
AGTGTCCCCTCGGAGGTGTAGGGATGGACTATCCCCAAAGATAAAATTCCACGAAAG
Found at i:1275836 original size:87 final size:87
Alignment explanation
Indices: 1275689--1275991 Score: 290
Period size: 87 Copynumber: 3.5 Consensus size: 87
1275679 GAATGGAGTA
** * * *
1275689 TCCCCAAAGATAAAATTCCACAAA-AGAAAATTTGATTTTTTAAAGAGCGAGATTGGAGTGTCCC
1 TCCCCAAAGATAAAATTATACAAAGA-AAAATTTAATTTTTTAAAGAGTGAGGTTGGAGTGTCCC
* * *
1275753 CTCGGGGGATTAGGGATGGACTT
65 CTCGGAGGAGTAGGGATGGAATT
* * **
1275776 TCCCCAAAGATAAAATTATACAAAGAAAAATTTAATTTTTTAAAGAATGGGGTTATAGTGTCCCC
1 TCCCCAAAGATAAAATTATACAAAGAAAAATTTAATTTTTTAAAGAGTGAGGTTGGAGTGTCCCC
** *
1275841 TCAAAGGAGTGGGGATGGAATT
66 TCGGAGGAGTAGGGATGGAATT
* ** * * *
1275863 TCCCCAAAGATAAAGTTATATGAAGAAAATTTTGATTTTTTTTGAAA-AGTGAGGTTGGAATGTC
1 TCCCCAAAGATAAAATTATACAAAGAAAAATTT-A-ATTTTTT-AAAGAGTGAGGTTGGAGTGTC
* * *
1275927 CCCTTGGAGGAGTA-GGATAGAGTT
63 CCCTCGGAGGAGTAGGGATGGAATT
* * *
1275951 TCTCCAAAGATAAAATTATAAGAAAG-AAAATTTGATTTTTT
1 TCCCCAAAGATAAAATTAT-ACAAAGAAAAATTTAATTTTTT
1275992 TTGAAGAGCG
Statistics
Matches: 173, Mismatches: 38, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
86 6 0.03
87 99 0.57
88 33 0.19
89 32 0.18
90 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (87 bp):
TCCCCAAAGATAAAATTATACAAAGAAAAATTTAATTTTTTAAAGAGTGAGGTTGGAGTGTCCCC
TCGGAGGAGTAGGGATGGAATT
Found at i:1276025 original size:88 final size:87
Alignment explanation
Indices: 1275689--1276043 Score: 278
Period size: 87 Copynumber: 4.1 Consensus size: 87
1275679 GAATGGAGTA
** *
1275689 TCCCCAAAGATAAAATTCCACA-AAAGAAAATTTGA-TTTTTTAAAGAGCGAGATTGGAGTGTCC
1 TCCCCAAAGATAAAATTATA-AGAAAGAAAATTTGATTTTTTTAAAGAGCGAGATTGAAGTGTCC
* * * *
1275752 CCTCGGGGGATTAGGGATGGACTT
65 CCTCAGAGGAGTA-GGATGGAATT
* * ** * *
1275776 TCCCCAAAGATAAAATTAT-ACAAAGAAAAATTT-AATTTTTTAAAGAATGGGGTT-ATAGTGTC
1 TCCCCAAAGATAAAATTATAAGAAAG-AAAATTTGATTTTTTTAAAGAGCGAGATTGA-AGTGTC
* *
1275838 CCCTCAAAGGAGTGGGGATGGAATT
64 CCCTCAGAGGAGT-AGGATGGAATT
* * * *
1275863 TCCCCAAAGATAAAGTTATATG-AAGAAAATTTTGATTTTTTTTGAAA-AGTGAGGTTGGAA-TG
1 TCCCCAAAGATAAAATTATAAGAAAGAAAA-TTTGA-TTTTTTT-AAAGAGCGAGATT-GAAGTG
** * *
1275925 TCCCCTTGGAGGAGTAGGATAGAGTT
62 TCCCCTCAGAGGAGTAGGATGGAATT
* * * *
1275951 TCTCCAAAGATAAAATTATAAGAAAGAAAATTTGATTTTTTTTGAAGAGCGTGATTGAAGTGTTC
1 TCCCCAAAGATAAAATTATAAGAAAGAAAATTTGA-TTTTTTTAAAGAGCGAGATTGAAGTGTCC
* * *
1276016 TCTCAGAGGAGAGAGGA-GGAGTT
65 CCTCAGAGGAG-TAGGATGGAATT
1276039 TCCCC
1 TCCCC
1276044 CAAAATCGAA
Statistics
Matches: 213, Mismatches: 39, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
85 1 0.00
86 9 0.04
87 92 0.43
88 68 0.32
89 38 0.18
90 4 0.02
91 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (87 bp):
TCCCCAAAGATAAAATTATAAGAAAGAAAATTTGATTTTTTTAAAGAGCGAGATTGAAGTGTCCC
CTCAGAGGAGTAGGATGGAATT
Found at i:1280497 original size:18 final size:17
Alignment explanation
Indices: 1280473--1280513 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1280463 AACAAAAACT
* *
1280473 ATTTTATATCGTGTAAA
1 ATTTTATACCATGTAAA
1280490 ACTTTTATACCATGTAAA
1 A-TTTTATACCATGTAAA
1280508 ATTTTA
1 ATTTTA
1280514 AATTTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (17 bp):
ATTTTATACCATGTAAA
Found at i:1282666 original size:2 final size:2
Alignment explanation
Indices: 1282659--1282686 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1282649 CTTTTATGTA
1282659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1282687 CTTTCTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1283163 original size:3 final size:3
Alignment explanation
Indices: 1283155--1283179 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1283145 AGTTCTATAC
1283155 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1283180 GTTCTATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1286146 original size:20 final size:20
Alignment explanation
Indices: 1286109--1286156 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1286099 ATAGAATATG
*
1286109 AAATATATTAAAACATAAAA
1 AAATATATGAAAACATAAAA
*
1286129 AAATAATATGAAAA-ATAATCA
1 AAAT-ATATGAAAACATAA-AA
1286150 AAATATA
1 AAATATA
1286157 ACATAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATATATGAAAACATAAAA
Found at i:1286352 original size:22 final size:22
Alignment explanation
Indices: 1286314--1286355 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1286304 ATTTTTTCTT
*
1286314 TTTCTCTTTTTTCTTCTTTTCC
1 TTTCTCTTTTCTCTTCTTTTCC
1286336 TTTC-CTTTTCTCTTTCTTTT
1 TTTCTCTTTTCTC-TTCTTTT
1286356 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTCTCTTTTCTCTTCTTTTCC
Found at i:1287010 original size:18 final size:17
Alignment explanation
Indices: 1286962--1287023 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
1286952 GAAATCGAAT
*
1286962 AAAATAAAAAAAATTAA
1 AAAATAAAATAAATTAA
1286979 AAAATAATAATAAA-TAA
1 AAAATAA-AATAAATTAA
1286996 GAAAATAAAATTAAAATTAA
1 -AAAATAAAA-T-AAATTAA
1287016 AAAA-AAAA
1 AAAATAAAA
1287024 ACTCAAAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 12 0.31
18 17 0.44
19 7 0.18
20 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAAAATAAATTAA
Found at i:1291157 original size:87 final size:87
Alignment explanation
Indices: 1291047--1291461 Score: 366
Period size: 86 Copynumber: 4.8 Consensus size: 87
1291037 AGAGTAGTAA
* * **
1291047 GGATGGAGTTT--CTAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGTGGGGTT
1 GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAATTTGATTTTTTTGAAGAGTAAGGTT
*
1291110 GGAGTGTCCTCTCGAAGGAATG
66 GGAGTGTCCTTTCGAAGGAATG
* ** * * * *
1291132 GGATGGAGTTTCTCCAAAGATAAAATTCCACAAAGGAAAATTTGATTTTTTTTAAAAG-ATGGGT
1 GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAATTTGATTTTTTTGAAGAGTA-AGGT
* ** *
1291196 TGGAATGT-CTTTTTAGAGGAGTGG
65 TGGAGTGTCCTTTCGA-AGGAAT-G
* * * ** *
1291220 GGATGGAGTTTCCCCAAAGGTAAAATTATATG-A--AAGATTTTTTTTTTGTTGAAGAGCAAGGT
1 GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAATTTGATTTTT-TTGAAGAGTAAGGT
1291282 TGGAGTGTCCTTTCGAAGGAATGG
65 TGGAGTGTCCTTTCGAAGGAAT-G
* * * * *
1291306 GGATGGAATTTCCCCAGAGATAAAGTTATACGAAGGAAAA-TTGA-TTTCTTGAAGAGCAAGGTT
1 GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAATTTGATTTTTTTGAAGAGTAAGGTT
* *
1291369 GGAGTCTCCTTTCAGAA-GAGTG
66 GGAGTGTCCTTTC-GAAGGAATG
* * * * *
1291391 AAGATGAAATTTCCCCAAAGATAAAATTATACGAA-GAAAATTTTAATTTTTTTGAAGAGTGAGG
1 -GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAA-TTTGATTTTTTTGAAGAGTAAGG
*
1291455 TTAGAGT
64 TTGGAGT
1291462 ATCCCCTCGG
Statistics
Matches: 265, Mismatches: 49, Indels: 29
0.77 0.14 0.08
Matches are distributed among these distances:
85 28 0.11
86 114 0.43
87 71 0.27
88 49 0.18
89 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (87 bp):
GGATGGAGTTTCCCCAAAGATAAAATTATACGAAGGAAAATTTGATTTTTTTGAAGAGTAAGGTT
GGAGTGTCCTTTCGAAGGAATG
Found at i:1291245 original size:88 final size:87
Alignment explanation
Indices: 1291047--1291246 Score: 219
Period size: 87 Copynumber: 2.3 Consensus size: 87
1291037 AGAGTAGTAA
* ** ** *
1291047 GGATGGAGTTT--CTAAAGATAAAATTATATGAAGGAAAATTTGATTTTTTTGAAGAGTGGGGTT
1 GGATGGAGTTTCCCCAAAGATAAAATTCCACAAAGGAAAATTTGATTTTTTTGAAAAGTGGGGTT
* *
1291110 GGAGTGTCCTCTCGAAGGAATG
66 GGAATGTCCTCTAGAAGGAATG
* *
1291132 GGATGGAGTTTCTCCAAAGATAAAATTCCACAAAGGAAAATTTGATTTTTTTTAAAAGAT-GGGT
1 GGATGGAGTTTCCCCAAAGATAAAATTCCACAAAGGAAAATTTGATTTTTTTGAAAAG-TGGGGT
* * *
1291196 TGGAATGTCTTTTTAG-AGGAGTGG
65 TGGAATGTC-CTCTAGAAGGAAT-G
*
1291220 GGATGGAGTTTCCCCAAAGGTAAAATT
1 GGATGGAGTTTCCCCAAAGATAAAATT
1291247 ATATGAAAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 11 0.11
87 55 0.57
88 30 0.31
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (87 bp):
GGATGGAGTTTCCCCAAAGATAAAATTCCACAAAGGAAAATTTGATTTTTTTGAAAAGTGGGGTT
GGAATGTCCTCTAGAAGGAATG
Found at i:1291604 original size:34 final size:34
Alignment explanation
Indices: 1291566--1291633 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
1291556 GATTTTAAAA
1291566 ATATAAAGTTGAAGATTTGTATAAGACATTTTTT
1 ATATAAAGTTGAAGATTTGTATAAGACATTTTTT
*
1291600 ATATAAAGTTGAAGATTTGTATAAGATATTTTTT
1 ATATAAAGTTGAAGATTTGTATAAGACATTTTTT
1291634 TTTTATCTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.46
Consensus pattern (34 bp):
ATATAAAGTTGAAGATTTGTATAAGACATTTTTT
Found at i:1293675 original size:20 final size:21
Alignment explanation
Indices: 1293633--1293679 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1293623 TTTTACAATT
1293633 TGTATCGATACAACAAGTCAA
1 TGTATCGATACAACAAGTCAA
* *
1293654 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAACAAGTCAA
1293674 TGTATC
1 TGTATC
1293680 AATATATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAACAAGTCAA
Found at i:1293811 original size:20 final size:20
Alignment explanation
Indices: 1293745--1293798 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1293735 ATGAAAAAAT
*
1293745 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAATTAAA
** *
1293765 TGTATCGATACATGCTTGCAA
1 TGTATCGATACATAATT-AAA
1293786 TGTATCGATACAT
1 TGTATCGATACAT
1293799 TATTTATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAATTAAA
Found at i:1297864 original size:68 final size:68
Alignment explanation
Indices: 1297785--1298090 Score: 273
Period size: 68 Copynumber: 4.5 Consensus size: 68
1297775 AAGGATTAAG
* * * *
1297785 GTAGATAGGTGCC-GCAAGCTTGTGTGGGCTTTGACGAAAAAAATGCGTCTTACTTTTTGAGGAC
1 GTAGATAGGTGCCACCAA-CTTGTGTGGGCTTTGAAGAAAAAAATGCGTCATACTCTTTGAGGAC
*
1297849 TGGA
65 TAGA
** * *
1297853 GTAGATAGGTGCCATTAACTTGTGTGAGCTTTGAAGAATAAAAGAT--GTCATGCTCTTTGAGGA
1 GTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAGAA-AAAA-ATGCGTCATACTCTTTGAGGA
1297916 CTAGA
64 CTAGA
* * * * * **
1297921 GTAGATAGGTGCCACCAACTT-TATGGGCTTTGAAGAAGAAAAGGCGTCATGCTCTTCGAAAACT
1 GTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAGAAAAAAATGCGTCATACTCTTTGAGGACT
1297985 AGA
66 AGA
* * * * * * * *
1297988 GTAAATAAGTGCTAGCAACTTGTGTGAGCTTTGAA-AGAGAAGAGGCGTTC-TACTCTTTGAGGA
1 GTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAGA-AAAAAATGCG-TCATACTCTTTGAGGA
1298051 CTAGA
64 CTAGA
* * * *
1298056 GTAGATAGCTGCCACCAACCTATATGGGCTTTGAA
1 GTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAA
1298091 AGAGAAAAGG
Statistics
Matches: 193, Mismatches: 37, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
65 1 0.01
66 3 0.02
67 51 0.26
68 128 0.66
69 8 0.04
70 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (68 bp):
GTAGATAGGTGCCACCAACTTGTGTGGGCTTTGAAGAAAAAAATGCGTCATACTCTTTGAGGACT
AGA
Found at i:1297990 original size:135 final size:136
Alignment explanation
Indices: 1297851--1298101 Score: 339
Period size: 135 Copynumber: 1.9 Consensus size: 136
1297841 TTGAGGACTG
* * ** * * *
1297851 GAGTAGATAGGTGCCATTAACTTGTGTGAGCTTTG-AAGAATAAAAGATG-TCATGCTCTTTGAG
1 GAGTAAATAAGTGCCAGCAACTTGTGTGAGCTTTGAAAG-AGAAAAGACGTTC-TACTCTTTGAG
* *
1297914 GACTAGAGTAGATAGGTGCCACCAA-CTTTATGGGCTTTG-AAGAAGAAAAGGCGTCATGCTCTT
64 GACTAGAGTAGATAGCTGCCACCAACCTATATGGGCTTTGAAAG-AGAAAAGGCGTCATGCTCTT
1297977 CGAAAACTA
128 CGAAAACTA
* * *
1297986 GAGTAAATAAGTGCTAGCAACTTGTGTGAGCTTTGAAAGAGAAGAGGCGTTCTACTCTTTGAGGA
1 GAGTAAATAAGTGCCAGCAACTTGTGTGAGCTTTGAAAGAGAAAAGACGTTCTACTCTTTGAGGA
1298051 CTAGAGTAGATAGCTGCCACCAACCTATATGGGCTTTGAAAGAGAAAAGGC
66 CTAGAGTAGATAGCTGCCACCAACCTATATGGGCTTTGAAAGAGAAAAGGC
1298102 TCTTTAAGGA
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
135 70 0.70
136 27 0.27
137 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (136 bp):
GAGTAAATAAGTGCCAGCAACTTGTGTGAGCTTTGAAAGAGAAAAGACGTTCTACTCTTTGAGGA
CTAGAGTAGATAGCTGCCACCAACCTATATGGGCTTTGAAAGAGAAAAGGCGTCATGCTCTTCGA
AAACTA
Found at i:1298232 original size:68 final size:68
Alignment explanation
Indices: 1298138--1298331 Score: 189
Period size: 68 Copynumber: 2.9 Consensus size: 68
1298128 CTTAAAAAAA
* * * * * *
1298138 CATCATGCTCTTTGAAGATTGG-AGTAGAAAGGTATCACCAACTTGTGCAGGCTTTGAAAAAGAA
1 CATCATACTATTTGAGGACTGGAAGTAGATAGGTGTCACCAACTTGTG-AGGCTTTGAAAAAGAA
1298202 AATG
65 AATG
* * *
1298206 CATCATATTATTTGAGGACT-GAAGTAGATAGATGTCACCAACTTGT-ATGTGCTTTGAAATAGA
1 CATCATACTATTTGAGGACTGGAAGTAGATAGGTGTCACCAACTTGTGA-G-GCTTTGAAAAAGA
1298269 AAATG
64 AAATG
** * * * *
1298274 TGTCCTACTCTTTGAGGACTGGAAG-AGATAGGTGCCACCAACTTATGTAGGCTTTGAA
1 CATCATACTATTTGAGGACTGGAAGTAGATAGGTGTCACCAACTTGTG-AGGCTTTGAA
1298332 GGAGAAGAGG
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
66 1 0.01
67 2 0.02
68 94 0.91
69 5 0.05
70 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (68 bp):
CATCATACTATTTGAGGACTGGAAGTAGATAGGTGTCACCAACTTGTGAGGCTTTGAAAAAGAAA
ATG
Found at i:1298345 original size:68 final size:68
Alignment explanation
Indices: 1298216--1298429 Score: 247
Period size: 68 Copynumber: 3.1 Consensus size: 68
1298206 CATCATATTA
* * ** *
1298216 TTTGAGGACT-GAAGTAGATAGATGTCACCAACT-TGTATGTGCTTTGAAATAGAAAATGTGTCC
1 TTTGAGGACTGGAAGTAGATAGGTGCCACCAACTATGTA-G-GCTTTGAAGGAGAAAAGGTGTCC
1298279 TACTC
64 TACTC
*
1298284 TTTGAGGACTGGAAG-AGATAGGTGCCACCAACTTATGTAGGCTTTGAAGGAGAAGAGGTGTCCT
1 TTTGAGGACTGGAAGTAGATAGGTGCCACCAAC-TATGTAGGCTTTGAAGGAGAAAAGGTGTCCT
*
1298348 GCTC
65 ACTC
* * * * *
1298352 TTTGAGGACTGG-AGTAGATAAGTGCCACTAACCTATTTGGGTTTTGAAGGAGAAAAGGTGTCCT
1 TTTGAGGACTGGAAGTAGATAGGTGCCACCAA-CTATGTAGGCTTTGAAGGAGAAAAGGTGTCCT
*
1298416 ACTA
65 ACTC
1298420 TTTGAGGACT
1 TTTGAGGACT
1298430 AGAGGAAAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
67 2 0.02
68 113 0.90
69 7 0.06
70 4 0.03
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (68 bp):
TTTGAGGACTGGAAGTAGATAGGTGCCACCAACTATGTAGGCTTTGAAGGAGAAAAGGTGTCCTA
CTC
Found at i:1299957 original size:20 final size:20
Alignment explanation
Indices: 1299932--1299985 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1299922 GTACCACTAT
*
1299932 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
*
1299952 TTGTATTGATACATGATGAA
1 TTGTATCGATACATGATGAA
1299972 TTGTATCGATACAT
1 TTGTATCGATACAT
1299986 TGCTTCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:1301218 original size:20 final size:21
Alignment explanation
Indices: 1301179--1301218 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301169 CAGCCCTTAA
*
1301179 TCATGCATTTTTTACTATGTT
1 TCATGCATTTTTAACTATGTT
1301200 TCATGCATTTTTAAC-ATGT
1 TCATGCATTTTTAACTATGT
1301219 CTAACACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (21 bp):
TCATGCATTTTTAACTATGTT
Found at i:1304261 original size:12 final size:12
Alignment explanation
Indices: 1304227--1304266 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1304217 ATTCTTATTC
1304227 TTTTTTGTTT-T
1 TTTTTTGTTTGT
1304238 TTTCTTTG--TGT
1 TTT-TTTGTTTGT
1304249 TTTTTTGTTTGT
1 TTTTTTGTTTGT
1304261 TTTTTT
1 TTTTTT
1304267 TTTAAGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 5 0.20
11 7 0.28
12 13 0.52
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (12 bp):
TTTTTTGTTTGT
Found at i:1304268 original size:14 final size:14
Alignment explanation
Indices: 1304232--1304267 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1304222 TATTCTTTTT
1304232 TGTTTTTTTCTTTG
1 TGTTTTTTTCTTTG
*
1304246 TGTTTTTTTGTTTG
1 TGTTTTTTTCTTTG
1304260 T-TTTTTTT
1 TGTTTTTTT
1304268 TTAAGTGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (14 bp):
TGTTTTTTTCTTTG
Found at i:1316060 original size:35 final size:35
Alignment explanation
Indices: 1316014--1316081 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
1316004 AGTAGGGATG
1316014 GAGTATCCCCAAAGATAAAATTCCATAAAAGAATA
1 GAGTATCCCCAAAGATAAAATTCCATAAAAGAATA
*
1316049 GAGTATCCCCAAAGATAAAATTCCATGAAAGAA
1 GAGTATCCCCAAAGATAAAATTCCATAAAAGAA
1316082 AATTTGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (35 bp):
GAGTATCCCCAAAGATAAAATTCCATAAAAGAATA
Found at i:1316150 original size:122 final size:119
Alignment explanation
Indices: 1315930--1316157 Score: 294
Period size: 122 Copynumber: 1.9 Consensus size: 119
1315920 AGTAGAAATG
* * * * * * *
1315930 GAGTTTCCCCAAAGATAAAATTATACGAAGGAATATTTTTTTTTTAAGAGCGGGTTGGAGTGTCC
1 GAGTATCCCCAAAGATAAAATTACACGAAAGAAAATTTTTTTTTGAAGAGCGGATTGGAGTATCC
*
1315995 CCTCGGAGGAGTAGGGATGGAGTATCCCCAAAGATAAAATTCCATAAAAGAATA
66 CCTCGGAGGAGTAGGGATGGACTATCCCCAAAGATAAAATTCCATAAAAGAATA
* *
1316049 GAGTATCCCCAAAGATAAAATTCCATGAAAGAAAATTTGATTTTTTGAAGAGCGAGATTGGAGTA
1 GAGTATCCCCAAAGATAAAATTACACGAAAGAAAATTT--TTTTTTGAAGAGCG-GATTGGAGTA
* * * * *
1316114 TCCCCTTGGGGGATTAGGGATGGACTTTCCCTAAAGATAAAATT
63 TCCCCTCGGAGGAGTAGGGATGGACTATCCCCAAAGATAAAATT
1316158 ATACAAAGAA
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
119 32 0.35
121 13 0.14
122 46 0.51
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (119 bp):
GAGTATCCCCAAAGATAAAATTACACGAAAGAAAATTTTTTTTTGAAGAGCGGATTGGAGTATCC
CCTCGGAGGAGTAGGGATGGACTATCCCCAAAGATAAAATTCCATAAAAGAATA
Found at i:1318880 original size:15 final size:16
Alignment explanation
Indices: 1318851--1318884 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1318841 TTTAATACCA
*
1318851 AAATTTTATTGTTTTT
1 AAATTTAATTGTTTTT
1318867 AAATTTAATT-TTTTT
1 AAATTTAATTGTTTTT
1318882 AAA
1 AAA
1318885 AAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
AAATTTAATTGTTTTT
Found at i:1319743 original size:18 final size:18
Alignment explanation
Indices: 1319722--1319769 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1319712 AAGTGCCTCC
1319722 ACCTCCGCCTCCCCCGCA
1 ACCTCCGCCTCCCCCGCA
1319740 ACCTCCGCCTCCCCCGCA
1 ACCTCCGCCTCCCCCGCA
*
1319758 ACCTCCACCTCC
1 ACCTCCGCCTCC
1319770 ATCATCGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.67, G:0.08, T:0.12
Consensus pattern (18 bp):
ACCTCCGCCTCCCCCGCA
Found at i:1319758 original size:45 final size:42
Alignment explanation
Indices: 1319682--1319769 Score: 95
Period size: 45 Copynumber: 2.0 Consensus size: 42
1319672 CAGACGACGA
** *
1319682 CGCCGCCCCCACAACCTCCTTCACCCGCGCAAGTGCCTCCACCTC
1 CGCCGCCCCCACAACCTCCGCCACCCCCGCAA---CCTCCACCTC
* * *
1319727 CGCCTCCCCCGCAACCTCCGCCTCCCCCGCAACCTCCACCTC
1 CGCCGCCCCCACAACCTCCGCCACCCCCGCAACCTCCACCTC
1319769 C
1 C
1319770 ATCATCGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
42 11 0.30
45 26 0.70
ACGTcount: A:0.14, C:0.62, G:0.11, T:0.12
Consensus pattern (42 bp):
CGCCGCCCCCACAACCTCCGCCACCCCCGCAACCTCCACCTC
Found at i:1320895 original size:18 final size:17
Alignment explanation
Indices: 1320871--1320911 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1320861 AACAAAAACT
* *
1320871 ATTTTATATCGTGTAAA
1 ATTTTATACCATGTAAA
1320888 ACTTTTATACCATGTAAA
1 A-TTTTATACCATGTAAA
1320906 ATTTTA
1 ATTTTA
1320912 AATTTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (17 bp):
ATTTTATACCATGTAAA
Found at i:1323670 original size:27 final size:26
Alignment explanation
Indices: 1323623--1323675 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
1323613 AAATATTAAA
* *
1323623 TTATATTTTTAATGTATTTTTATTTAT
1 TTATATTATTAATGTAATTTT-TTTAT
1323650 TTATATTATTATAT-TAATTTTTTTAT
1 TTATATTATTA-ATGTAATTTTTTTAT
1323676 CATTTTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 16 0.70
28 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATATTATTAATGTAATTTTTTTAT
Found at i:1324549 original size:10 final size:10
Alignment explanation
Indices: 1324536--1324571 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1324526 ATTATTAAAT
1324536 ATTAATTTAA
1 ATTAATTTAA
*
1324546 ATTAAATTAA
1 ATTAATTTAA
*
1324556 ATTATTTTAA
1 ATTAATTTAA
1324566 ATTAAT
1 ATTAAT
1324572 AAAAAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:1324556 original size:47 final size:47
Alignment explanation
Indices: 1324463--1324557 Score: 106
Period size: 47 Copynumber: 2.0 Consensus size: 47
1324453 TTTTTTAATT
* * *
1324463 TAAAAATATTTTTATTAATATTTATTTATTTTATAATTAATTTTAAA
1 TAAAAATATTTTTATTAATATTAATTTAATTTATAATTAATATTAAA
*
1324510 TAAAATTATTTTTA-TAATTATTAAATATTAATTTA-AATTAA-ATTAAA
1 TAAAAATATTTTTATTAA-TATT-AAT-TTAATTTATAATTAATATTAAA
1324557 T
1 T
1324558 TATTTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
46 3 0.07
47 23 0.56
48 8 0.20
49 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (47 bp):
TAAAAATATTTTTATTAATATTAATTTAATTTATAATTAATATTAAA
Found at i:1325085 original size:30 final size:30
Alignment explanation
Indices: 1325039--1325168 Score: 145
Period size: 30 Copynumber: 4.3 Consensus size: 30
1325029 AGTACCACCA
* *
1325039 CCACCCCCACCCCCCACCGCCCCCGCAACCT
1 CCACCTCCA-CCCCCACCACCCCCGCAACCT
* *
1325070 CCACCTCCACCCCCACCCGCCCCCGCAATCT
1 CCACCTCCACCCCCA-CCACCCCCGCAACCT
* * *
1325101 CCACCTCCACCTCCGCCACCCCCACAACCT
1 CCACCTCCACCCCCACCACCCCCGCAACCT
* *
1325131 CCACCTCCACCTCCC-CCACCCCCGGAACCG
1 CCACCTCCACC-CCCACCACCCCCGCAACCT
1325161 CCACCTCC
1 CCACCTCC
1325169 GCCATCCTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
30 49 0.57
31 37 0.43
ACGTcount: A:0.17, C:0.69, G:0.06, T:0.08
Consensus pattern (30 bp):
CCACCTCCACCCCCACCACCCCCGCAACCT
Found at i:1325125 original size:15 final size:15
Alignment explanation
Indices: 1325101--1325153 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1325091 CCCGCAATCT
* *
1325101 CCACCTCCACCTCCG
1 CCACCCCCACCTCCC
** *
1325116 CCACCCCCACAACCT
1 CCACCCCCACCTCCC
*
1325131 CCACCTCCACCTCCC
1 CCACCCCCACCTCCC
1325146 CCACCCCC
1 CCACCCCC
1325154 GGAACCGCCA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.17, C:0.72, G:0.02, T:0.09
Consensus pattern (15 bp):
CCACCCCCACCTCCC
Found at i:1325134 original size:24 final size:24
Alignment explanation
Indices: 1325103--1325149 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1325093 CGCAATCTCC
*
1325103 ACCTCCACCTCCGCCACCCCCACA
1 ACCTCCACCTCCACCACCCCCACA
*
1325127 ACCTCCACCTCCACCTCCCCCAC
1 ACCTCCACCTCCACCACCCCCAC
1325150 CCCCGGAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.68, G:0.02, T:0.11
Consensus pattern (24 bp):
ACCTCCACCTCCACCACCCCCACA
Found at i:1325144 original size:12 final size:12
Alignment explanation
Indices: 1325066--1325144 Score: 50
Period size: 12 Copynumber: 6.5 Consensus size: 12
1325056 CGCCCCCGCA
1325066 ACCTCCACCTCC
1 ACCTCCACCTCC
* *
1325078 ACCCCCACCCGCC
1 ACCTCCA-CCTCC
* * * *
1325091 CCCGCAATCTCC
1 ACCTCCACCTCC
1325103 ACCTCCACCTCC
1 ACCTCCACCTCC
* * * * *
1325115 GCCACCCCCACA
1 ACCTCCACCTCC
1325127 ACCTCCACCTCC
1 ACCTCCACCTCC
1325139 ACCTCC
1 ACCTCC
1325145 CCCACCCCCG
Statistics
Matches: 45, Mismatches: 21, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
12 37 0.82
13 8 0.18
ACGTcount: A:0.18, C:0.67, G:0.04, T:0.11
Consensus pattern (12 bp):
ACCTCCACCTCC
Found at i:1328466 original size:17 final size:19
Alignment explanation
Indices: 1328446--1328491 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1328436 AATCTAAAAA
*
1328446 ATAAGTATA-AAA-ATATT
1 ATAAATATACAAACATATT
1328463 ATAAATATACAAACATATT
1 ATAAATATACAAACATATT
1328482 A-AAATATACA
1 ATAAATATACA
1328492 TAAAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.31
18 12 0.46
19 6 0.23
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAATATACAAACATATT
Found at i:1328501 original size:19 final size:20
Alignment explanation
Indices: 1328452--1328507 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1328442 AAAAATAAGT
1328452 ATAAAAATATTATAAATATAC
1 ATAAAAA-ATTATAAATATAC
* *
1328473 A-AACATATTA-AAATATAC
1 ATAAAAAATTATAAATATAC
*
1328491 ATAAAAAATTATTAATA
1 ATAAAAAATTATAAATA
1328508 CATAAGATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 9 0.32
19 11 0.39
20 7 0.25
21 1 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAAAAATTATAAATATAC
Found at i:1329130 original size:14 final size:14
Alignment explanation
Indices: 1329111--1329138 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1329101 GATAAGGATA
1329111 GAGAAAAATAAAAC
1 GAGAAAAATAAAAC
1329125 GAGAAAAATAAAAC
1 GAGAAAAATAAAAC
1329139 AACTAGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07
Consensus pattern (14 bp):
GAGAAAAATAAAAC
Found at i:1329591 original size:17 final size:17
Alignment explanation
Indices: 1329580--1329636 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
1329570 AAAAATTATA
1329580 TAAAATATAAAATAAAT
1 TAAAATATAAAATAAAT
1329597 TAAAATAT--AATAAA-
1 TAAAATATAAAATAAAT
1329611 -AATAATATAAAA-AAAT
1 TAA-AATATAAAATAAAT
*
1329627 CAAAATATAA
1 TAAAATATAA
1329637 CACAACTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 5 0.14
15 9 0.26
16 9 0.26
17 10 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATATAAAATAAAT
Found at i:1329596 original size:11 final size:11
Alignment explanation
Indices: 1329582--1329626 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
1329572 AAATTATATA
1329582 AAATATAAAAT
1 AAATATAAAAT
1329593 AAAT-TAAAAT
1 AAATATAAAAT
1329603 ATAATA-AAAAT
1 A-AATATAAAAT
1329614 -AATATAAAA-
1 AAATATAAAAT
1329623 AAAT
1 AAAT
1329627 CAAAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 4 0.13
10 14 0.47
11 12 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:1329605 original size:26 final size:27
Alignment explanation
Indices: 1329571--1329621 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1329561 AAAAATCCCA
1329571 AAAATTAT-ATAAAATATAAAATAAATT
1 AAAATTATAATAAAA-ATAAAATAAATT
*
1329598 AAAA-TATAATAAAAATAATATAAA
1 AAAATTATAATAAAAATAAAATAAA
1329622 AAAATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATTATAATAAAAATAAAATAAATT
Done.