Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold9
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: 3883850
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 144036 characters in sequence are not A, C, G, or T
File 22 of 24
Found at i:3428922 original size:184 final size:181
Alignment explanation
Indices: 3428454--3429105 Score: 901
Period size: 184 Copynumber: 3.5 Consensus size: 181
3428444 GAGTAGGGCG
* *
3428454 CCTTTCAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATG-CTTTTCCTTT
* *
3428519 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGCAGGATGCCTTTTCCTTTTAAA
65 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAA
* **
3428584 GCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAA-CAGGATGATTTTTTT
130 GCCCACACAAGTTGGTGGCACTTTTC-AGTCCTC-AAGAAGCAGGA-CA-CATTTT
*
3428639 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGC-TTTTCCTTT
* * *
3428704 TAAAGCCGACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGAATGCCTTTTCCTTTGAAA
65 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAA
*
3428769 GCCAACACAAGTTGGTGGCACTTTTCAGTCCTCAAGAAGCAGGACACATTTT
130 GCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGAAGCAGGACACATTTT
* * * * * *
3428821 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAATCTTCAAAGAGCTGGACGTCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTC-AGTCCTCAAAGAGCAGGATG-CTTTTCCT
* **
3428886 TTTAAAGCCCACATAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTA
63 TTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTA
* * * *
3428951 CAGCCCATACAAGTTGGTGGCACTTTTCAGTCCTCAAGAAGCAGGACGCCTTTT
128 AAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGAAGCAGGACACATTTT
* * * *
3429005 CCTTTTAAAGCCCACAGAAGTTGGTGGCACCTTCTAGTTCTCAAAAAGCAGGATGCTTTCTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCTTT-TCCTT
** * *
3429070 GCAAAACCCATACAAGTTGGTGGCACCTTCTAGTCC
64 TTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCC
3429106 CCAAGGAACA
Statistics
Matches: 418, Mismatches: 43, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
182 37 0.09
183 63 0.15
184 172 0.41
185 146 0.35
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (181 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTCCTTTT
AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAG
CCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAGAAGCAGGACACATTTT
Found at i:3429056 original size:245 final size:243
Alignment explanation
Indices: 3428454--3429119 Score: 847
Period size: 245 Copynumber: 2.7 Consensus size: 243
3428444 GAGTAGGGCG
* * *
3428454 CCTTTCAAAGCCCACACAAGCTAGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
*
3428519 TAAAGCCCACACAAGTTGGTGGCACCTTCTAG-TCTTCAAAGAGCAGGATGCCTTTTCCTTTTAA
66 TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTC-TCAAAAAGCAGGATG-CTTTTCCTTTTAA
* * *
3428583 AGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAACAGGATGATTTTTTTCCTTTCAAA
129 AGCCCACACAAGTTGGTGGCACTTTTCTAATCCTCAAAGAACAGGACGA-TCTTTTCCTTTCAAA
** *
3428648 GCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTT
193 GCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTT
* * * *
3428699 CTTTTTAAAGCCGACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGAATGCCTTTTCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTT
* * * * * **
3428764 TGAAAGCCAACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAGAAGCAGGACACATTTTCCTTTTA
65 TTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTTCTCAAAAAGCAGGATGC-TTTTCCTTTTA
* * * *
3428828 AAGCCCACACAAGTTGGTGGCACTTTTCTAATCTTCAAAGAGCTGGACG-TCTTTTCCTTTTAAA
128 AAGCCCACACAAGTTGGTGGCACTTTTCTAATCCTCAAAGAACAGGACGATCTTTTCCTTTCAAA
* *
3428892 GCCCACATAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACACCTTTT
193 GCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACACCTTTT
* * * *
3428944 CCTTTTACAGCCCATACAAGTTGGTGGCACTTTTCAGTCCTC-AAGAAGCAGGACGCCTTTTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAG-AGCAGGATGCCTTTTCCT
* **
3429008 TTTAAAGCCCACAGAAGTTGGTGGCACCTTCTAGTTCTCAAAAAGCAGGATGCTTTCTCCTTGCA
64 TTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTCTCAAAAAGCAGGATGCTTT-TCCTTTTA
* * * * * *
3429073 AAACCCATACAAGTTGGTGGCAC-CTTCTAGTCCCCAAGGAACAGGAC
128 AAGCCCACACAAGTTGGTGGCACTTTTCTAATCCTCAAAGAACAGGAC
3429120 CCATTTCATT
Statistics
Matches: 358, Mismatches: 54, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
244 60 0.17
245 171 0.48
246 126 0.35
247 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (243 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTT
TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTTCTCAAAAAGCAGGATGCTTTTCCTTTTAAAG
CCCACACAAGTTGGTGGCACTTTTCTAATCCTCAAAGAACAGGACGATCTTTTCCTTTCAAAGCC
CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTT
Found at i:3429118 original size:61 final size:61
Alignment explanation
Indices: 3428454--3429105 Score: 805
Period size: 61 Copynumber: 10.7 Consensus size: 61
3428444 GAGTAGGGCG
* * *
3428454 CCTTTCAAAGCCCACACAAGCTAGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
*
3428514 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * **
3428575 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAACAGGATGATTTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGATG--CCTTTT
* *
3428639 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
3428699 CTTTTTAAAGCCGACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGAATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * ** *
3428760 CCTTTGAAAGCCAACACAAGTTGGTGGCA-CTTTTCAGTCCTC-AAGAAGCAGGACACATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAG-AGCAGGATGCCTTTT
* * * * * *
3428821 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAATCTTCAAAGAGCTGGACGTCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * **
3428883 CCTTTTAAAGCCCACATAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * * *
3428944 CCTTTTACAGCCCATACAAGTTGGTGGCA-CTTTTCAGTCCTC-AAGAAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTCAAAG-AGCAGGATGCCTTTT
* * *
3429005 CCTTTTAAAGCCCACAGAAGTTGGTGGCACCTTCTAGTTCTCAAAAAGCAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-T
** * *
3429066 CCTTGCAAAACCCATACAAGTTGGTGGCACCTTCTAGTCC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCC
3429106 CCAAGGAACA
Statistics
Matches: 512, Mismatches: 65, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
60 85 0.17
61 293 0.57
62 92 0.18
63 9 0.02
64 33 0.06
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:3429801 original size:29 final size:30
Alignment explanation
Indices: 3429739--3429811 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 30
3429729 CATTGTTAAT
*
3429739 TGTATCGATACATTCTGAGTTTTACCCAGA
1 TGTATCGATACATTCTGAGGTTTACCCAGA
* *
3429769 TGTATTGATACATTCTG-GGTTTACCCATA
1 TGTATCGATACATTCTGAGGTTTACCCAGA
*
3429798 TGTATCGACACATT
1 TGTATCGATACATT
3429812 TTTTAATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (30 bp):
TGTATCGATACATTCTGAGGTTTACCCAGA
Found at i:3432378 original size:28 final size:27
Alignment explanation
Indices: 3432309--3432379 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
3432299 TTTCACAATC
*
3432309 GGGGATACTCCAACCCCGTTATTTCAT
1 GGGGATACTCCAACCCCGTTATTTCAA
**
3432336 CCGGATACTCCAACCCCGTTATTTCCAA
1 GGGGATACTCCAACCCCGTTATTT-CAA
3432364 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
3432380 TGGCTTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTATTTCAA
Found at i:3432595 original size:79 final size:80
Alignment explanation
Indices: 3432338--3432663 Score: 286
Period size: 79 Copynumber: 4.1 Consensus size: 80
3432328 TATTTCATCC
* * * ***
3432338 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTGGCTTTATTTCTAAAATATTGA
1 GGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGACTTTATTTCTAAAACACCAA
3432403 -TTTCTCACAATCAG
66 TTTTCTCACAATCAG
* *** * * * * *
3432417 GGATACTCCAACCTCGTTATTTTTGCGAGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCAA
1 GGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGACTTTATTTCTAAAACACCAA
*
3432482 TTTTC-CACAATCGG
66 TTTTCTCACAATCAG
* * *
3432496 GGATACTCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTT-TCAAAACACCA
1 GGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGACTTTATTTCT-AAAACACCA
* *
3432560 ATTTTCT-ATAATCAA
65 ATTTTCTCACAATCAG
*** * * * * * * **
3432575 GGATACTCCAACCTTATTA-TTTCTGAGCGGATACTCCAATCCTGATTTTATTTTTAGAACACTG
1 GGATACTCCAACCCCGTTATTTTC-AAGGGGATACTCCAACCCTGACTTTATTTCTAAAACACCA
* *
3432639 ATTTT-TCATAATCGG
65 ATTTTCTCACAATCAG
3432654 GGATACTCCA
1 GGATACTCCA
3432664 GCTCCGTTGT
Statistics
Matches: 203, Mismatches: 38, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
78 6 0.03
79 192 0.95
80 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (80 bp):
GGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCTGACTTTATTTCTAAAACACCAA
TTTTCTCACAATCAG
Found at i:3432626 original size:158 final size:158
Alignment explanation
Indices: 3432338--3432663 Score: 372
Period size: 158 Copynumber: 2.1 Consensus size: 158
3432328 TATTTCATCC
* * * ***
3432338 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCTGGCTTTATTTCTAAAATATTGA
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAA
* * * * *
3432403 TTTCTCACAATCAGGGATACTCCAACCTCGTTATTTTTGCGAGGATACTCCAACCCTGGCCTTAT
66 TTTCTCACAATCAAGGATACTCCAACCTCATTATTTCTGAGAGGATACTCCAACCCTGACCTTAT
3432468 TTCTA-AAGCA-TCAATTTTCCACAATCGG
131 TTCTAGAA-CACT-AATTTTCCACAATCGG
* * *
3432496 GGATACTCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCCGATTTTATTT-TCAAAACACCA
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCT-AAAACACCA
* * * * **
3432560 ATTT-TCTATAATCAAGGATACTCCAACCTTATTATTTCTGAGCGGATACTCCAATCCTGATTTT
65 ATTTCTC-ACAATCAAGGATACTCCAACCTCATTATTTCTGAGAGGATACTCCAACCCTGACCTT
* * * *
3432624 ATTTTTAGAACACTGATTTTTCATAATCGG
129 ATTTCTAGAACACTAATTTTCCACAATCGG
3432654 GGATACTCCA
1 GGATACTCCA
3432664 GCTCCGTTGT
Statistics
Matches: 140, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
157 3 0.02
158 134 0.96
159 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (158 bp):
GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGACTTTATTTCTAAAACACCAA
TTTCTCACAATCAAGGATACTCCAACCTCATTATTTCTGAGAGGATACTCCAACCCTGACCTTAT
TTCTAGAACACTAATTTTCCACAATCGG
Found at i:3437410 original size:3 final size:3
Alignment explanation
Indices: 3437402--3437429 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3437392 TCCGAGTCAA
3437402 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
3437430 TTTATCGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:3439153 original size:32 final size:33
Alignment explanation
Indices: 3439110--3439174 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
3439100 ACAATTGTGC
* *
3439110 ATGTATTGATACAATGAAT-ATATATCGATACA
1 ATGTATAGATACAAGGAATAATATATCGATACA
* *
3439142 ATGTATAGATACAAGGCATAATGTATCGATACA
1 ATGTATAGATACAAGGAATAATATATCGATACA
3439175 TTTGGATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (33 bp):
ATGTATAGATACAAGGAATAATATATCGATACA
Found at i:3441934 original size:13 final size:13
Alignment explanation
Indices: 3441916--3441942 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3441906 ACATTCTGTT
3441916 TTGTATCAATACA
1 TTGTATCAATACA
3441929 TTGTATCAATACA
1 TTGTATCAATACA
3441942 T
1 T
3441943 GTTTGCATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:3442027 original size:13 final size:13
Alignment explanation
Indices: 3442009--3442033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3441999 TACCACTATT
3442009 TGTATCGATACAA
1 TGTATCGATACAA
3442022 TGTATCGATACA
1 TGTATCGATACA
3442034 TGAAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3445595 original size:66 final size:64
Alignment explanation
Indices: 3445425--3445604 Score: 217
Period size: 59 Copynumber: 2.8 Consensus size: 64
3445415 TGGGCTTAAA
* * * *
3445425 AAAAGAAAAAGGAAAGGCATCCAGCTTTTTGAGGACTAAGAGGTGCCACCAACTTGCATGGGCTT
1 AAAAGAAAAAGG-AAGGCATCCA-CTCTTTGAGGACTAAAAGGTGCCACCAACTTACATGCGCTT
3445490 T
64 T
* * *
3445491 AAAA-AGAAA--AAGGCATCCA--GTTTGAGGACTAAAAGGTGCCACCAACTTACGTGCGCTTT
1 AAAAGAAAAAGGAAGGCATCCACTCTTTGAGGACTAAAAGGTGCCACCAACTTACATGCGCTTT
*
3445550 AAAAGAAAAAGGCAAGGCATCCTACTCTTTAAGGACTAAAAGGTGCCACCAACTT
1 AAAAGAAAAAGG-AAGGCATCC-ACTCTTTGAGGACTAAAAGGTGCCACCAACTT
3445605 TTGTAGACTT
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
59 39 0.40
60 4 0.04
62 10 0.10
63 9 0.09
64 1 0.01
65 4 0.04
66 31 0.32
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (64 bp):
AAAAGAAAAAGGAAGGCATCCACTCTTTGAGGACTAAAAGGTGCCACCAACTTACATGCGCTTT
Found at i:3445628 original size:31 final size:31
Alignment explanation
Indices: 3445593--3446941 Score: 1117
Period size: 31 Copynumber: 42.7 Consensus size: 31
3445583 GACTAAAAGG
* * * *
3445593 TGCCACCAACTTTTGTAGACTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
3445624 TGCCACCAACTTGTGTGGGCTTTAGGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * * *
3445655 TGCCACTGACTTGTGTAGACTTTATAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
3445686 TGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
*
3445719 TGCCACCGACTTGTGTAGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
3445750 TGCCACCGACTTGTGTGGGCTTTAG-AGAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAG-GGT
* *
3445781 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGT
** * * *
3445814 CACCACCTACTTGTGTGGACTTTATAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* ** *
3445845 TGCCACCAACTTGTGTGGGCTTTAGTTGTGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3445876 TGCCATCGACTTGTGTGGGATTTAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
3445907 T-CCACCGACTTGTGTGGGCTTTAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3445937 TTCCACCCACTTGTGTGGCCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** *
3445968 TGCCATTGACTTGTGTGGGCTTTTGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** *
3445999 TGCCACCGACTTGCATGGGCTTTAGAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** * **
3446030 TTTCACCAACTTGCATGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3446061 TACCACCAACTTATGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* * * *
3446094 TACCACCAACTTGTGTAGGCTTTAGAGAATGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* * * **
3446127 TGCCACCGGCTTGTGTGGACTTTTGCAA--AA
1 TGCCACCGACTTGTGTGGGCTTTAG-AAGGGT
*
3446157 TGCCACCGACTTGTGTGGGCTTTAGAGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
3446188 TTCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
** *
3446221 TGCCATTGACTTGTGTTGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* * * *
3446254 TGCCACCAACTTGTGTGGGCCTTAAAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * * *
3446285 TGCCACCAACTTGTATGGGCTTTAAAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3446316 TGCCACCGACTTATGTGGACTTTAGATGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* ***
3446347 TGGCACCGACTTGTGTGGGCTTTATTGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** * *
3446378 T-CCATTGACTTATGTGGGCTTCAAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTT--TAGAAGGGT
* * * *
3446410 TGCCATCGACTTATGTAGGCTTGAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTT--TAGAAGGGT
* * *
3446443 TGCCACCAACTTGTGTAGGCTTTAGAAGGAT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
3446474 AGCCACCGACTTGTGTAGGCTTTAGAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
** *
3446507 TGCCACTAACTTATGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** *
3446538 TG-CATTTGACTAGTGTGGGCTTTAGAAGGGT
1 TGCCA-CCGACTTGTGTGGGCTTTAGAAGGGT
* ** *
3446569 T-TCACCGACTTGTGTAAGCTTTAAAGAAGGGC
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
3446601 TGCC-CTCGACTTGTGTGGGCTTTAGAAGGGT
1 TGCCAC-CGACTTGTGTGGGCTTTAGAAGGGT
* * *
3446632 TGCCATCGACTTGTGTGGGTTTTAGATAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGA-AGGGT
** * * *
3446664 TGCCATTGAC-T-TCTAGACTTTAAGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT-A-GAAGGGT
* *
3446695 TGCTACCAACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
3446728 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
** * *
3446761 TGCCACTAACTTGTGTAGGCTTT---TGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
** * *
3446789 TGCCACTAACTAGTATGGGCTTTTGAGGAA-GGT
1 TGCCACCGACTTGTGTGGGC-TTT-A-GAAGGGT
* *
3446822 TGCCCCCGACTTGTGTGGGCTTTTGGGGAA-GGT
1 TGCCACCGACTTGTGTGGGC-TTT--AGAAGGGT
* * * *
3446855 TGCTACCGACTTGTATGCGCTTTAGAGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGT
* *
3446888 TGCCACCAACTTGTGTGGACTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
*
3446919 TGCCACTGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
3446942 TGAGAAAAAG
Statistics
Matches: 1074, Mismatches: 204, Indels: 80
0.79 0.15 0.06
Matches are distributed among these distances:
28 21 0.02
29 4 0.00
30 89 0.08
31 542 0.50
32 40 0.04
33 375 0.35
34 3 0.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Found at i:3445748 original size:64 final size:64
Alignment explanation
Indices: 3445593--3446941 Score: 1106
Period size: 64 Copynumber: 21.4 Consensus size: 64
3445583 GACTAAAAGG
* * * *
3445593 TGCCACCAACTTTTGTAGACTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG-G-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * * *
3445655 TGCCACTGACTTGTGTAGACTTTATAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* *
3445719 TGCCACCGACTTGTGTAGGCTTTAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG-A-GGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * ** * * *
3445781 TGCCACTGACTTGTGTGGGCTTTAGAAAAAGGTCACCACCTACTTGTGTGGACTTT--ATAAGGG
1 TGCCACCGACTTGTGTGGGCTTTAG--AAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3445844 T
64 T
* ** * * * *
3445845 TGCCACCAACTTGTGTGGGCTTTAGTTGTGTTGCCATCGACTTGTGTGGGATTTA-A-AAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * * *
3445907 T-CCACCGACTTGTGTGGGCTTTAAAAGGGTTTCCACCCACTTGTGTGGCCTTT--AGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
** * * **
3445968 TGCCATTGACTTGTGTGGGCTTTTGAAGGGTTGCCACCGACTTGCATGGGCTTTAGAG--GGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
** * ** * *
3446030 TTTCACCAACTTGCATGGGCTTTAGAAGGGTTACCACCAACTTATGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * * * ** * *
3446094 TACCACCAACTTGTGTAGGCTTTAGAGAATGGTTGCCACCGGCTTGTGTGGACTTTTGCA-AA--
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG-AGAAGG
*
3446156 -A
63 GT
* *
3446157 TGCCACCGACTTGTGTGGGCTTTAGAGGGGTTTCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
** * * *
3446221 TGCCATTGACTTGTGTTGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCCTTA-A-AAGAG
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446284 T
64 T
* * * * * * * *
3446285 TGCCACCAACTTGTATGGGCTTTAAAAGAGTTGCCACCGACTTATGTGGACTTT--AGATGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* *** *** * * *
3446347 TGGCACCGACTTGTGTGGGCTTTATTGGGGTT-CCATTGACTTATGTGGGCTTCAAAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * * * * *
3446410 TGCCATCGACTTATGTAGGCTTGAGAGAAGGGTTGCCACCAACTTGTGTAGGCTTT--AGAAGGA
1 TGCCACCGACTTGTGTGGGCTT--TAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446473 T
64 T
* * * * *
3446474 AGCCACCGACTTGTGTAGGCTTTAGAGAAAGGTTGCCACTAACTTATGTGGGCTTT--AGAAGGG
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446537 T
64 T
** * * * ** * *
3446538 TG-CATTTGACTAGTGTGGGCTTTAGAAGGGTT-TCACCGACTTGTGTAAGCTTTAAAGAAGGGC
1 TGCCA-CCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
* * * *
3446601 TGCC-CTCGACTTGTGTGGGCTTTAGAAGGGTTGCCATCGACTTGTGTGGGTTTTAGATAA-GGT
1 TGCCAC-CGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
** * * * *
3446664 TGCCATTGAC-T-TCTAGACTTTAAGGAAGGGTTGCTACCAACTTGTGTGGGCTTTAGAGAAGGG
1 TGCCACCGACTTGTGTGGGCTTT-A-GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446727 T
64 T
* * *
3446728 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACTAACTTGTGTAGGCTTT-----TGGG
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446788 T
64 T
** * * * * * *
3446789 TGCCACTAACTAGTATGGGCTTTTGAGGAA-GGTTGCCCCCGACTTGTGTGGGCTTTTGGGGAA-
1 TGCCACCGACTTGTGTGGGC-TTT-A-GAAGGGTTGCCACCAACTTGTGTGGGC-TTTAGAGAAG
3446852 GGT
62 GGT
* * * * *
3446855 TGCTACCGACTTGTATGCGCTTTAGAGAAAGGTTGCCACCAACTTGTGTGGACTTT--AGAAGGG
1 TGCCACCGACTTGTGTGGGCTTT--AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGG
3446918 T
64 T
*
3446919 TGCCACTGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
3446942 TGAGAAAAAG
Statistics
Matches: 1027, Mismatches: 206, Indels: 106
0.77 0.15 0.08
Matches are distributed among these distances:
60 2 0.00
61 158 0.15
62 270 0.26
63 127 0.12
64 305 0.30
65 17 0.02
66 146 0.14
67 2 0.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (64 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGT
Found at i:3446797 original size:28 final size:28
Alignment explanation
Indices: 3446757--3446813 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3446747 CTTTAGAGAA
* *
3446757 GGGTTGCCACTAACTTGTGTAGGCTTTT
1 GGGTTGCCACTAACTAGTATAGGCTTTT
*
3446785 GGGTTGCCACTAACTAGTATGGGCTTTT
1 GGGTTGCCACTAACTAGTATAGGCTTTT
3446813 G
1 G
3446814 AGGAAGGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.37
Consensus pattern (28 bp):
GGGTTGCCACTAACTAGTATAGGCTTTT
Found at i:3446823 original size:61 final size:61
Alignment explanation
Indices: 3446688--3446903 Score: 173
Period size: 66 Copynumber: 3.4 Consensus size: 61
3446678 AGACTTTAAG
* * * * * *
3446688 GAAGGGTTGCTACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 GAAGGGTTGCCACCAACTTGTGTAGGCTTT-----TGGGTTGCCACCAACTAGTATGGGCTTTAG
3446753 A
61 A
* * *
3446754 GAAGGGTTGCCACTAACTTGTGTAGGCTTTTGGGTTGCCACTAACTAGTATGGGCTTTTGA
1 GAAGGGTTGCCACCAACTTGTGTAGGCTTTTGGGTTGCCACCAACTAGTATGGGCTTTAGA
* * * * * * *
3446815 GGAA-GGTTGCCCCCGACTTGTGTGGGCTTTTGGGGAAGGTTGCTACCGACTTGTATGCGCTTTA
1 -GAAGGGTTGCCACCAACTTGTGTAGGCTTTT---G--GGTTGCCACCAACTAGTATGGGCTTTA
3446879 GA
60 GA
*
3446881 GAAAGGTTGCCACCAACTTGTGT
1 GAAGGGTTGCCACCAACTTGTGT
3446904 GGACTTTAGA
Statistics
Matches: 122, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
61 48 0.39
62 3 0.02
64 1 0.01
65 3 0.02
66 67 0.55
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (61 bp):
GAAGGGTTGCCACCAACTTGTGTAGGCTTTTGGGTTGCCACCAACTAGTATGGGCTTTAGA
Found at i:3446823 original size:127 final size:128
Alignment explanation
Indices: 3445616--3446941 Score: 1041
Period size: 127 Copynumber: 10.5 Consensus size: 128
3445606 TGTAGACTTT
* * *
3445616 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGGAGGGTTGCCACTGACTTGTGTAGACTTT-A-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA--AGGGTTGCCACTGACTTGTGTGGGCTTTGAG
* *
3445679 TAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTAGGCTTT--
64 GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
3445742 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGTTGCCACTGACTTGTGTGGGCTTT-AG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA-AG-GGTTGCCACTGACTTGTGTGGGCTTTGAG
* * ** * * * *
3445806 AAAAAGGTCACCACCTACTTGTGTGGACTTT--ATAAGGGTTGCCACCAACTTGTGTGGGCTTT-
64 -GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
3445868 -
128 G
** * * * *
3445868 AGTTGTGTTGCCATCGACTTGTGTGGGATTTAAAAGGGTT-CCACCGACTTGTGTGGGCTTT-A-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--AAGGGTTGCCACTGACTTGTGTGGGCTTTGAG
* * * * **
3445930 AAAGGGTTTCCACCCACTTGTGTGGCCTTT--AGAAGGGTTGCCATTGACTTGTGTGGGCTTT--
64 GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* ** ** ** **
3445991 TGAAGGGTTGCCACCGACTTGCATGGGCTTTAGAGGGGTTTTCACCAACTTGCATGGGCTTT-A-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA-A-GGGTTGCCACTGACTTGTGTGGGCTTTGAG
* * * * *
3446054 GAAGGGTTACCACCAACTTATGTGGGCTTTAGAGAAGGGTTACCACCAACTTGTGTAGGCTTTAG
64 GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * ** *
3446119 AGAATGGTTGCCACCGGCTTGTGTGGACTTTTGCAA--AATGCCACCGACTTGTGTGGGCTTT-A
1 AGAAGGGTTGCCACCGACTTGTGTGGGC-TTT--AAGGGTTGCCACTGACTTGTGTGGGCTTTGA
* * ** *
3446181 -GAGGGGTTTCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCATTGACTTGTGTTGGCTTTA
63 GGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
3446245 G
128 G
* * * ** *
3446246 AGAAGGGTTGCCACCAACTTGTGTGGGCCTTAAAAGAGTTGCCACCAACTTGTATGGGCTTT-A-
1 AGAAGGGTTGCCACCGACTTGTGTGGG-CTT-TAAGGGTTGCCACTGACTTGTGTGGGCTTTGAG
* * * * * * * *
3446309 AAAGAGTTGCCACCGACTTATGTGGACTTT--AGATGGGTTGGCACCGACTTGTGTGGGCTTTAT
64 GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* ** * * * *
3446372 TG--GGGTT-CCATTGACTTATGTGGGCTTCAAAGAAGGGTTGCCA-TCGACTTATGTAGGC-TT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTT----TAAGGGTTGCCACT-GACTTGTGTGGGCTTT
* * * *
3446432 GAGAGAAGGGTTGCCACCAACTTGTGTAGGCTTT--AGAAGGATAGCCACCGACTTGTGTAGGCT
61 GAG-GAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCT
3446495 TTAG
125 TTAG
* ** * * *
3446499 AGAAAGGTTGCCACTAACTTATGTGGGCTTTAGAAGGGTTG-CATTTGACTAGTGTGGGCTTT-A
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--AAGGGTTGCCA-CTGACTTGTGTGGGCTTTGA
* * ** * *
3446562 -GAAGGGTT-TCACCGACTTGTGTAAGCTTTAAAGAAGGGCTGCC-CTCGACTTGTGTGGGCTTT
63 GGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCAC-CGACTTGTGTGGGCTTT
3446624 --
127 AG
* * * * * * * *
3446624 AGAAGGGTTGCCATCGACTTGTGTGGGTTTTAGATAAGGTTGCCATTGAC-T-TCTAGACTTTAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--A-AGGGTTGCCACTGACTTGTGTGGGCTTTGA
*
3446687 GGAAGGGTTGCTACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
63 GGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
3446752 G
128 G
** * * * * *
3446753 AGAAGGGTTGCCACTAACTTGTGTAGGCTTT-TGGGTTGCCACTAACTAGTATGGGCTTTTGAGG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAAGGGTTGCCACTGACTTGTGTGGGC-TTTGAGG
* * * * * * *
3446817 AA-GGTTGCCCCCGACTTGTGTGGGCTTTTGGGGAA-GGTTGCTACCGACTTGTATGCGCTTTAG
65 AAGGGTTGCCACCAACTTGTGTGGGC-TTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3446880 AGAAAGGTTGCCACCAACTTGTGTGGACTTTAGAAGGGTTGCCACTGACTTGTGTGGGCTTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT--AAGGGTTGCCACTGACTTGTGTGGGCTTT
3446942 TGAGAAAAAG
Statistics
Matches: 969, Mismatches: 179, Indels: 101
0.78 0.14 0.08
Matches are distributed among these distances:
121 1 0.00
122 4 0.00
123 93 0.10
124 57 0.06
125 103 0.11
126 198 0.20
127 305 0.31
128 128 0.13
129 39 0.04
130 40 0.04
131 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (128 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAAGGGTTGCCACTGACTTGTGTGGGCTTTGAGGA
AGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:3447029 original size:62 final size:62
Alignment explanation
Indices: 3446927--3447079 Score: 202
Period size: 62 Copynumber: 2.4 Consensus size: 62
3446917 GTTGCCACTG
** *
3446927 ACTTGTGTGGGCTTTTGAGAAAA-AGAAAAGGTGTCCTGCTCTTTGAGGACTAAAAGGTGCTACC
1 ACTTGTGTGGGC-TTT-A-AAAAGA-AAAAGACGTCCTGCTCTTTGAGGACTAAAAGGTGCCACC
3446991 A
62 A
*
3446992 ACTTGTGTTGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCA
1 ACTTGTGTGGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCA
* *
3447054 ATTTGTGTGGGGTTT-AAAAGAAAAAG
1 ACTTGTGTGGGCTTTAAAAAGAAAAAG
3447080 GTGTCACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
61 11 0.14
62 53 0.66
63 2 0.03
64 3 0.04
65 11 0.14
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (62 bp):
ACTTGTGTGGGCTTTAAAAAGAAAAAGACGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCA
Found at i:3447187 original size:34 final size:34
Alignment explanation
Indices: 3447101--3447201 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 34
3447091 TTGTGGACTT
* *
3447101 AAAAGGGTGCCAC-GAAGTTGTGGACTGAAAAAGA
1 AAAAGGATGCCACAG-AGTTGTGGACTTAAAAAGA
***
3447135 AAAAGGATGCCTTGGAGTTGTGGACTTAAAAAGA
1 AAAAGGATGCCACAGAGTTGTGGACTTAAAAAGA
* *
3447169 AAAAGTG-TGTCACAGAGTTGTGGACCTAAAAAG
1 AAAAG-GATGCCACAGAGTTGTGGACTTAAAAAG
3447202 GGTGCCACGG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 54 0.96
35 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.30, T:0.20
Consensus pattern (34 bp):
AAAAGGATGCCACAGAGTTGTGGACTTAAAAAGA
Found at i:3447256 original size:95 final size:92
Alignment explanation
Indices: 3447069--3447256 Score: 227
Period size: 95 Copynumber: 2.0 Consensus size: 92
3447059 TGTGGGGTTT
*
3447069 AAAAGAAAAAGGTGTCACAAAATTGTGGACTTAAAAGGGTGCCACGAAGTTGTGGACTGAAAAAG
1 AAAAGAAAAAGGTGTCACAAAATTGTGGACTAAAAAGGGTGCCACGAAGTTGTGGAC--AAAAAG
* * * *
3447134 AAAAAGGATGCCTTGGAGTTGTGGACTTA
64 AAAAAAGATGCCTTGAAGTCGTAGACTTA
* * *
3447163 AAAAGAAAAAGTGTGTCACAGAGTTGTGGACCTAAAAAGGGTGCCACGGAGTTGTGGA-AAGAAA
1 AAAAGAAAAAG-GTGTCACAAAATTGTGGA-CTAAAAAGGGTGCCACGAAGTTGTGGACAA-AAA
3447227 GAAAACAAGATGCCATT-AAGTCGTAGACTT
63 GAAAA-AAGATGCC-TTGAAGTCGTAGACTT
3447257 TGAGAAGAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
93 2 0.02
94 19 0.23
95 33 0.41
96 27 0.33
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (92 bp):
AAAAGAAAAAGGTGTCACAAAATTGTGGACTAAAAAGGGTGCCACGAAGTTGTGGACAAAAAGAA
AAAAGATGCCTTGAAGTCGTAGACTTA
Found at i:3447270 original size:30 final size:29
Alignment explanation
Indices: 3447235--3447345 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
3447225 AAGAAAACAA
* * * *
3447235 GATGCCATTAAGTCGTAGACTTTGAGAAG
1 GATGCCACTAAGTCATGGACTTTAAGAAG
*
3447264 AAATGCCACTAAGTCATGGACTTTAAGAAG
1 -GATGCCACTAAGTCATGGACTTTAAGAAG
*
3447294 GGTGCCACTAAGTCATGGACTTTAAGAAG
1 GATGCCACTAAGTCATGGACTTTAAGAAG
* * *
3447323 GGTGCCACTAAGTCGTTGACTTT
1 GATGCCACTAAGTCATGGACTTT
3447346 TGGAAAAAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 48 0.67
30 24 0.33
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (29 bp):
GATGCCACTAAGTCATGGACTTTAAGAAG
Found at i:3447308 original size:29 final size:29
Alignment explanation
Indices: 3447267--3447345 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
3447257 TGAGAAGAAA
3447267 TGCCACTAAGTCATGGACTTTAAGAAGGG
1 TGCCACTAAGTCATGGACTTTAAGAAGGG
3447296 TGCCACTAAGTCATGGACTTTAAGAAGGG
1 TGCCACTAAGTCATGGACTTTAAGAAGGG
* *
3447325 TGCCACTAAGTCGTTGACTTT
1 TGCCACTAAGTCATGGACTTT
3447346 TGGAAAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (29 bp):
TGCCACTAAGTCATGGACTTTAAGAAGGG
Found at i:3454297 original size:21 final size:20
Alignment explanation
Indices: 3454250--3454303 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3454240 CATTTGAGAC
* **
3454250 ATGTATCGATACATTCACTT
1 ATGTATCGATACATGCACCA
3454270 ATGTATCGATACATGCACCA
1 ATGTATCGATACATGCACCA
3454290 ATTGTATCGATACA
1 A-TGTATCGATACA
3454304 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATGCACCA
Found at i:3456243 original size:156 final size:155
Alignment explanation
Indices: 3456063--3456465 Score: 488
Period size: 156 Copynumber: 2.6 Consensus size: 155
3456053 TTCAATGCTG
* *
3456063 AAGGTGGGTATTTAGCATAGGTTCATCCCATTTTACATCATTTTCAAGTCCTTTAGGGGTACC-G
1 AAGGTGGGTATTTAGGATAGGTTCATCCCATTTTACATC-TTTTTAAGTCCTTTAGGGGTACCAG
* * *
3456127 AGATGCTTTCACGTCAAAGGTATCCCCTAAGG-GTATTTTGGTAATTTTTTGAAATCAAGTCCTA
65 -GATGCTTTCACGTCAAAGGTAT-CCCTAAGGCGCATTTTGGTAATTTTTTAAAACCAAGTCCTA
*
3456191 AGTTGTCACCGGGTCCACTTTTATGCCA
128 AGTTGTCACCAGGTCCACTTTTATGCCA
*
3456219 AAGGTGGGTATTTAGGATATGTTCATCCCATTTTACATCCTTTTTAAGTCCTTTAGGGGTACCAG
1 AAGGTGGGTATTTAGGATAGGTTCATCCCATTTTACAT-CTTTTTAAGTCCTTTAGGGGTACCAG
* * * * * *
3456284 GATGCTTTTAAGTCAAAGGTATCCGTTAGGCGCATTTTGGTAATTTTTTAAAACCAAGTCTTAGG
65 GATGCTTTCACGTCAAAGGTATCCCTAAGGCGCATTTTGGTAATTTTTTAAAACCAAGTCCTAAG
* * * * * *
3456349 TTGTTACTAGGTTCGCTTTTATGTCG
130 TTGTCACCAGGTCCACTTTTATGCCA
* ** * * **
3456375 AAGGTGGGCATTTAGGATAGGTTCATCTTATCTCTA-ATCTTTTTAAGTCCTTTAGGGTTATTAG
1 AAGGTGGGTATTTAGGATAGGTTCATCCCAT-TTTACATCTTTTTAAGTCCTTTAGGGGTACCAG
* *
3456439 GATACTTTCACGTCAAAGGTATACCTA
65 GATGCTTTCACGTCAAAGGTATCCCTA
3456466 TAGGTGGGTA
Statistics
Matches: 210, Mismatches: 33, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
155 50 0.24
156 155 0.74
157 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (155 bp):
AAGGTGGGTATTTAGGATAGGTTCATCCCATTTTACATCTTTTTAAGTCCTTTAGGGGTACCAGG
ATGCTTTCACGTCAAAGGTATCCCTAAGGCGCATTTTGGTAATTTTTTAAAACCAAGTCCTAAGT
TGTCACCAGGTCCACTTTTATGCCA
Found at i:3458536 original size:20 final size:20
Alignment explanation
Indices: 3458511--3458570 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
3458501 TTTTACCTAG
* *
3458511 ATGTATGGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
3458531 ATGTATCGATACATATATGA
1 ATGTATCGATACATTTATCA
3458551 ATGTATCGATACATTCTATC
1 ATGTATCGATACATT-TATC
3458571 TTTTTACCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:3463037 original size:28 final size:28
Alignment explanation
Indices: 3462956--3463037 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
3462946 TTTTGGAGAT
*
3462956 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* *
3462984 AGTAACG-GGATTGGAGTATCCCCGATGA
1 AATAACGAGG-TTGGAGTATCCTCGATGA
3463012 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
3463038 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
26 4 0.09
27 3 0.07
28 36 0.80
29 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:3463180 original size:51 final size:51
Alignment explanation
Indices: 3463020--3463190 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
3463010 GAAATAACGA
* * *
3463020 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGA-AAATAAAATCGG
** * * * * *
3463072 AATTGGAGTATCCCCGATTAAAAGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
3463125 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
3463176 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
3463191 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 28 0.29
54 14 0.14
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:3463236 original size:27 final size:28
Alignment explanation
Indices: 3463173--3463248 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
3463163 AAAATAAAGT
*
3463173 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
3463201 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
3463228 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3463249 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:3463262 original size:212 final size:213
Alignment explanation
Indices: 3462964--3463356 Score: 542
Period size: 212 Copynumber: 1.8 Consensus size: 213
3462954 ATAATAACGA
* * * *
3462964 GGTTGGAGTGTTCCCTCGGAAGTAACGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
*
3463029 ATCCTCGATTGTGAAAAATT-G-G-TATTTTTAGAAATAAAATCGGAATTGGAGTATCCCCGATT
66 ATCCCCGATTGTGAAAAATTGGTGTTATTTTTAGAAATAAAATCGGAATTGGAGTATCCCCGATT
** * *
3463091 AAAAGAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGA
131 -AAAGA-AAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCGA
3463156 TATTTTGAAAATAAAGTCGG
194 TATTTTGAAAATAAAGTCGG
* * *
3463176 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* * * *
3463240 GTCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
66 ATCCCCGATTGTGAA-AAATTGGTGTTATTTTTAGAAATAAAATCGGAATTGGAGTATCCCCGAT
* * * * *
3463305 TATAGAAAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
130 TAAAGAAAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATT
3463357 GTGGAGAATT
Statistics
Matches: 156, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
211 28 0.18
212 47 0.30
213 39 0.25
214 5 0.03
215 37 0.24
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (213 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAATTGGTGTTATTTTTAGAAATAAAATCGGAATTGGAGTATCCCCGATT
AAAGAAAATTAATGTTGTGAAAATAAAACCGGAGTTGGAATATCCCCGATTATGAAAAATCGATA
TTTTGAAAATAAAGTCGG
Found at i:3465731 original size:13 final size:13
Alignment explanation
Indices: 3465713--3465737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3465703 CAAAGATCTG
3465713 TGTATCGATACAA
1 TGTATCGATACAA
3465726 TGTATCGATACA
1 TGTATCGATACA
3465738 CAGAAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3465801 original size:19 final size:18
Alignment explanation
Indices: 3465777--3465844 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3465767 CAGTAGCTAA
3465777 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3465796 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3465811 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3465828 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3465845 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3465817 original size:13 final size:13
Alignment explanation
Indices: 3465799--3465823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3465789 ACAATACTTA
3465799 TGTATCGATACAT
1 TGTATCGATACAT
3465812 TGTATCGATACA
1 TGTATCGATACA
3465824 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3465821 original size:32 final size:32
Alignment explanation
Indices: 3465780--3465842 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3465770 TAGCTAATTA
*
3465780 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3465812 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3465843 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3476693 original size:8 final size:8
Alignment explanation
Indices: 3476680--3476743 Score: 56
Period size: 8 Copynumber: 7.6 Consensus size: 8
3476670 CTTCGTAACA
*
3476680 AAAAAAAT
1 AAAAAAAC
3476688 AAAAAAAC
1 AAAAAAAC
*
3476696 AAAAAAAA
1 AAAAAAAC
*
3476704 ATTAAAAAAA
1 A--AAAAAAC
3476714 ACAAAAAAC
1 A-AAAAAAC
*
3476723 CAAAAAAC
1 AAAAAAAC
*
3476731 AAACAAAC
1 AAAAAAAC
3476739 AAAAA
1 AAAAA
3476744 TAGAAAGGTC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
8 32 0.70
9 6 0.13
10 8 0.17
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (8 bp):
AAAAAAAC
Found at i:3476701 original size:15 final size:15
Alignment explanation
Indices: 3476681--3476743 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
3476671 TTCGTAACAA
*
3476681 AAAAAATAAAAAAAC
1 AAAAAACAAAAAAAC
**
3476696 AAAAAA-AAATTAA-
1 AAAAAACAAAAAAAC
*
3476709 AAAAAACAAAAAACC
1 AAAAAACAAAAAAAC
*
3476724 AAAAAACAAACAAAC
1 AAAAAACAAAAAAAC
3476739 AAAAA
1 AAAAA
3476744 TAGAAAGGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.15
14 9 0.23
15 24 0.62
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.05
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:3476701 original size:19 final size:19
Alignment explanation
Indices: 3476679--3476743 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
3476669 CCTTCGTAAC
3476679 AAAAAAAATAAAAAAACAA
1 AAAAAAAATAAAAAAACAA
*
3476698 AAAAAAATTAAAAAAAACAA
1 AAAAAAAAT-AAAAAAACAA
* *
3476718 AAAACCAAA-AAACAAACAA
1 AAAA-AAAATAAAAAAACAA
3476737 ACAAAAA
1 A-AAAAA
3476744 TAGAAAGGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 19 0.50
20 17 0.45
21 2 0.05
ACGTcount: A:0.85, C:0.11, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAAAATAAAAAAACAA
Found at i:3476742 original size:28 final size:27
Alignment explanation
Indices: 3476676--3476743 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
3476666 AATCCTTCGT
*
3476676 AACAAAAAAAATAAAAAAACAAAAAAA
1 AACAAAAAAAACAAAAAAACAAAAAAA
* *
3476703 AATTAAAAAAAACAAAAAACCAAAAAACA
1 AA-CAAAAAAAACAAAAAAACAAAAAA-A
3476732 AACAAACAAAAA
1 AACAAA-AAAAA
3476744 TAGAAAGGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 24 0.71
29 8 0.24
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.04
Consensus pattern (27 bp):
AACAAAAAAAACAAAAAAACAAAAAAA
Found at i:3477680 original size:222 final size:222
Alignment explanation
Indices: 3477294--3477738 Score: 703
Period size: 222 Copynumber: 2.0 Consensus size: 222
3477284 TTCCTTGCTT
3477294 TCACAAGCCACATCTCAAGAAAAACCATTTCAAGCTAACTAAAGTCAACCTGTATATTCTATCAG
1 TCACAAGCCACATCTCAAGAAAAACCATTTCAAGCTAACTAAAGTCAACCTGTATATTCTATCAG
* *
3477359 AATCCTATCGAAACCAAAAAAATAGTCTCTAGATTGTTGACAATGCCTTCTAGTGTCAAGAAAAC
66 AATCCTATCGAAACCAAAAAAACAGTCTCTAGATTGTTGACAATGCCTTCGAGTGTCAAGAAAAC
3477424 AATTGAGCCTCAAAAGCCGAAAATGCAATCGTTCATATGTTTGAAAACAGACGAATGATTCAAGC
131 AATTGAGCCTCAAAAGCCGAAAATGCAATCGTTCATATGTTTGAAAACAGACGAATGATTCAAGC
*
3477489 TGTTCAAGCATCATATCCCCAATGGAG
196 TGTTCAAACATCATATCCCCAATGGAG
*
3477516 TCACAAGCCACATCTTAAGAAAAACCATTTCAAGCTAACTAAAGTCAACCTGTATATTCTATCCA
1 TCACAAGCCACATCTCAAGAAAAACCATTTCAAGCTAACTAAAGTCAACCTGTATATTCTAT-CA
* * * **
3477581 -AATCCTATCGAAACCAGAGAAACAGTCTCTAGATTGTTGACGATGCCTTCGAGTGTCGGGAAAA
65 GAATCCTATCGAAACCAAAAAAACAGTCTCTAGATTGTTGACAATGCCTTCGAGTGTCAAGAAAA
* ** * * * *
3477645 TAATTGAGCCTCTCAAGTCGAAAATGCGATCGTTCATATGTTTGAAAATAGATGAATGATTCAAG
130 CAATTGAGCCTCAAAAGCCGAAAATGCAATCGTTCATATGTTTGAAAACAGACGAATGATTCAAG
* * *
3477710 TTGTTCAAACATCATATCCCTAGTGGAG
195 CTGTTCAAACATCATATCCCCAATGGAG
3477738 T
1 T
3477739 TGTATAGTTT
Statistics
Matches: 203, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
222 201 0.99
223 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (222 bp):
TCACAAGCCACATCTCAAGAAAAACCATTTCAAGCTAACTAAAGTCAACCTGTATATTCTATCAG
AATCCTATCGAAACCAAAAAAACAGTCTCTAGATTGTTGACAATGCCTTCGAGTGTCAAGAAAAC
AATTGAGCCTCAAAAGCCGAAAATGCAATCGTTCATATGTTTGAAAACAGACGAATGATTCAAGC
TGTTCAAACATCATATCCCCAATGGAG
Found at i:3478189 original size:28 final size:28
Alignment explanation
Indices: 3478159--3479197 Score: 1215
Period size: 28 Copynumber: 36.5 Consensus size: 28
3478149 ATATGACCCT
*
3478159 TTTCAAAGCCCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478187 TTTCAATGCCCACAAGTCAGTGGCAAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC--ATCC
* * *
3478217 TTTTAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3478245 TTTCATACCCCACAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478273 TTTCAAAGCCCACAAGTTAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
3478301 TTTCAAAGCTCACAAATTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
3478329 TTTTCAAAGCCCACAAGTCAGTGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
* *
3478360 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478388 TTTCAAA-CCGCACAAGACAGTGGCATCC
1 TTTCAAAGCC-CACAAGTCAGTGGCATCC
* * *
3478416 TTTCAAAGCCTACAAATCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478444 TTTTCAAAGCCAACAAGTTAGTGGCATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
* *
3478475 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
3478503 TTTTAAA-CCTGACAAGACAGCTGGTATCC
1 TTTCAAAGCC-CACAAGTCAG-TGGCATCC
*
3478532 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478560 TTTCAAAGCCCACAAGTTAGTGGCATAC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478588 TTTCAAAGCCCACAAGTCAGTGGCATAC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478616 TTTCAAAGCCCACAAGTCAGTGGTATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478644 TTTCAAAGCCCACAAGTCAGTGGACACCC
1 TTTCAAAGCCCACAAGTCAGTGG-CATCC
* *
3478673 TTTTCAAAGCCCACAAGTTAGTGGTATACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCAT--CC
* *
3478704 TTTCAAAGCCCACAAGTCGGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478732 TTTCAAACCCCACAAGACAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478760 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3478788 TTCCAAAGCACACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478815 ATTTCGAAGCCCATAAGTCAGTGGCA-CC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3478843 ATTTCGAAGCCCATAAGTCAGTGGCATAC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478872 TTTCAAATCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478900 TTTTAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3478928 TTTCAAAGCCCACAAGTTAGCGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3478956 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3478984 TTTTAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
3479012 TTTCAAAGCCTAGAAGTCAATGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3479040 TTTCAAAGCCCACAAGTCAGTGGCATCA
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
3479068 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3479095 ATTTCAAAGCCTACAAGTTAGTGGCATCA
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3479124 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3479152 TTTCAAAGCCTACACAAGTCAGTGGTAACTCT
1 TTTCAAAGCC--CACAAGTCAGTGG-CA-TCC
3479184 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
3479198 CAAGTTAGCA
Statistics
Matches: 870, Mismatches: 116, Indels: 48
0.84 0.11 0.05
Matches are distributed among these distances:
27 6 0.01
28 641 0.74
29 71 0.08
30 133 0.15
31 7 0.01
32 12 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:3479342 original size:45 final size:47
Alignment explanation
Indices: 3479284--3479403 Score: 136
Period size: 49 Copynumber: 2.6 Consensus size: 47
3479274 AAGCTCGATA
* * *
3479284 TCGCTGATATTGAATCAGCATATTGG-CACCTTT-ATTAGCCCAATG
1 TCGCTGGTCTTGAATCAGCACATTGGCCACCTTTCATTAGCCCAATG
* *
3479329 TCGCTGGTCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGTCTTGAATCAGCACATTGG-CCACCTTT-CATTAGCCCAATG
* **
3479378 TCGCTGGCCTTGAATTGGCACATTGG
1 TCGCTGGTCTTGAATCAGCACATTGG
3479404 TACTCCTCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 23 0.37
47 6 0.10
49 34 0.54
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (47 bp):
TCGCTGGTCTTGAATCAGCACATTGGCCACCTTTCATTAGCCCAATG
Found at i:3480402 original size:50 final size:50
Alignment explanation
Indices: 3480326--3480502 Score: 146
Period size: 50 Copynumber: 3.7 Consensus size: 50
3480316 AAAGTCACAT
*
3480326 TTTTACTCAGATGTAT-AGATGA-ATTTTTCAATGTATCGATACATTATGTC
1 TTTTACCCAGATGTATCA-AT-ACATTTTTCAATGTATCGATACATTATGTC
* * *
3480376 TTTTACCCAGATGTATCGATACATTTTTCAGTTTATCGATACATGTATG--
1 TTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACAT-TATGTC
* * * * *
3480425 --------A-ATTTATCAATATATTCTTCAATGTATCGATACATTCTATC
1 TTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACATTATGTC
3480466 ATTTTACCCAGATGTATCAATACATTTTTCAATGTAT
1 -TTTTACCCAGATGTATCAATACATTTTTCAATGTAT
3480503 TAATACATCT
Statistics
Matches: 97, Mismatches: 15, Indels: 29
0.69 0.11 0.21
Matches are distributed among these distances:
39 2 0.02
40 28 0.29
41 1 0.01
49 1 0.01
50 38 0.39
51 27 0.28
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (50 bp):
TTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACATTATGTC
Found at i:3480414 original size:20 final size:20
Alignment explanation
Indices: 3480389--3480460 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
3480379 TACCCAGATG
*
3480389 TATCGATACATTTTTCAGTT
1 TATCGATACATTTTTCAATT
* * *
3480409 TATCGATACATGTATGAATT
1 TATCGATACATTTTTCAATT
* * * *
3480429 TATCAATATATTCTTCAATG
1 TATCGATACATTTTTCAATT
3480449 TATCGATACATT
1 TATCGATACATT
3480461 CTATCATTTT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (20 bp):
TATCGATACATTTTTCAATT
Found at i:3483989 original size:20 final size:20
Alignment explanation
Indices: 3483964--3484013 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3483954 AAAGAAAATA
* *
3483964 TATCGATACATTTTTCATTG
1 TATCGATACATTCTTCAATG
3483984 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
*
3484004 TATCAATACA
1 TATCGATACA
3484014 CGTCGGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:3488867 original size:81 final size:80
Alignment explanation
Indices: 3488703--3488959 Score: 265
Period size: 80 Copynumber: 3.2 Consensus size: 80
3488693 CAATTTTGGG
* ** * * * *
3488703 GGATATTCCAACCTTGTTTTTACTTTTAAAATACTAAAATTTTCAT-TTTAGGGATACTCCAACC
1 GGATACTCCAACCTCATTTTTACTTTTAAAACATTAAAATTTTCATATCTGGGGATACTCCAACC
* ** *
3488767 CCATTAACTCCGA-A
66 CCATCATTTCTGAGA
*
3488781 GGGATACTCCAACCTCATTTTTACTTTTAAAACATTAAATTTCTTCATATCTGGGGATACTCCAA
1 -GGATACTCCAACCTCATTTTTACTTTTAAAACATTAAAATT-TTCATATCTGGGGATACTCCAA
3488846 CCCCATCATTTCTGAGA
64 CCCCATCATTTCTGAGA
* *
3488863 GGATACTCCAACCAC-TTTTTA-TTTTCCAAAACATCAAAATTTT--TATCTGAGGGGATACTCC
1 GGATACTCCAACCTCATTTTTACTTTT--AAAACATTAAAATTTTCATATCT--GGGGATACTCC
* * *
3488924 AACACCACCATTTCTGAGG
62 AACCCCATCATTTCTGAGA
3488943 GGATACTCCAACCTCAT
1 GGATACTCCAACCTCAT
3488960 CAATTCTAAG
Statistics
Matches: 151, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
78 5 0.03
79 39 0.26
80 54 0.36
81 52 0.34
82 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (80 bp):
GGATACTCCAACCTCATTTTTACTTTTAAAACATTAAAATTTTCATATCTGGGGATACTCCAACC
CCATCATTTCTGAGA
Found at i:3488948 original size:28 final size:28
Alignment explanation
Indices: 3488908--3488986 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
3488898 AAAATTTTTA
*
3488908 TCTGAGGGGATACTCCAACACCACCATT
1 TCTGAGGGGATACTCCAACACCACCAAT
*
3488936 TCTGAGGGGATACTCCAAC-CTCATCAAT
1 TCTGAGGGGATACTCCAACAC-CACCAAT
* *
3488964 TCTAAGGAGATACTCCAACACCA
1 TCTGAGGGGATACTCCAACACCA
3488987 TTTTTACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 1 0.02
28 43 0.96
29 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (28 bp):
TCTGAGGGGATACTCCAACACCACCAAT
Found at i:3488961 original size:108 final size:109
Alignment explanation
Indices: 3488833--3489045 Score: 281
Period size: 109 Copynumber: 2.0 Consensus size: 109
3488823 CTTCATATCT
* * *
3488833 GGGGATACTCCAACCCCATCATTTCTGA-GAGGATACTCC-A-ACCACTTTTTATTTTCCAAAAC
1 GGGGATACTCCAACCCCATCAATTCTAAGGA-GATACTCCAACACCA-TTTTTA-CTTCCAAAAC
* * *
3488895 A-TCAAAATTTTTATCTGAGGGGATACTCCAACACCACCATTTCTGA
63 ATTAAAAATTTTCATCTCAGGGGATACTCCAACACCACCATTTCTGA
* *
3488941 GGGGATACTCCAACCTCATCAATTCTAAGGAGATACTCCAACACCATTTTTACTTCTAAAACATT
1 GGGGATACTCCAACCCCATCAATTCTAAGGAGATACTCCAACACCATTTTTACTTCCAAAACATT
* *
3489006 AAAAATTTTCATCTCAGTGGATACTCCAACCCCACCATTT
66 AAAAATTTTCATCTCAGGGGATACTCCAACACCACCATTT
3489046 TCAACCCTAC
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
108 42 0.46
109 45 0.49
110 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (109 bp):
GGGGATACTCCAACCCCATCAATTCTAAGGAGATACTCCAACACCATTTTTACTTCCAAAACATT
AAAAATTTTCATCTCAGGGGATACTCCAACACCACCATTTCTGA
Found at i:3489052 original size:15 final size:15
Alignment explanation
Indices: 3489032--3489064 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3489022 GTGGATACTC
3489032 CAACCCCACCATTTT
1 CAACCCCACCATTTT
*
3489047 CAACCCTACCATTTT
1 CAACCCCACCATTTT
3489062 CAA
1 CAA
3489065 AGGAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.27
Consensus pattern (15 bp):
CAACCCCACCATTTT
Found at i:3489152 original size:124 final size:124
Alignment explanation
Indices: 3488945--3489169 Score: 294
Period size: 124 Copynumber: 1.8 Consensus size: 124
3488935 TTCTGAGGGG
*
3488945 ATACTCCAACCTCATCAATTCTAAGGAGATACTCCAACACCATTTTTACTTCTAAAACATTAAAA
1 ATACTCCAACCTCATCAATTCCAAGGAGATACTCCAACACCATTTTTACTTCTAAAACATTAAAA
3489010 ATTTTCATCTCAGTGGATACTCCAACCCCACCATTTTCAACCCTACCATTTTCAAAGGA
66 ATTTTCATCTCAGTGGATACTCCAACCCCACCATTTTCAACCCTACCATTTTCAAAGGA
* * * * * * *
3489069 ATACTCCAACC-CTATCAATTCCGAGGGGATATTTCAACCCCGTTTTTACTTCTAAAACATT-GA
1 ATACTCCAACCTC-ATCAATTCCAAGGAGATACTCCAACACCATTTTTACTTCTAAAACATTAAA
* * * *
3489132 ATTTCTTCATCTCTAG-GGATACTCTAACCTCATCATTT
65 AATT-TTCATCTC-AGTGGATACTCCAACCCCACCATTT
3489170 CTGAGGGGAT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
123 5 0.06
124 79 0.92
125 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (124 bp):
ATACTCCAACCTCATCAATTCCAAGGAGATACTCCAACACCATTTTTACTTCTAAAACATTAAAA
ATTTTCATCTCAGTGGATACTCCAACCCCACCATTTTCAACCCTACCATTTTCAAAGGA
Found at i:3489199 original size:28 final size:28
Alignment explanation
Indices: 3489147--3489216 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
3489137 TTCATCTCTA
* * * * *
3489147 GGGATACTCTAACCTCATCATTTCTGAG
1 GGGATACTCCAACCACAACAATTCTAAG
3489175 GGGATACTCCAACCACAACAATTCTAAG
1 GGGATACTCCAACCACAACAATTCTAAG
* *
3489203 AGAATACTCCAACC
1 GGGATACTCCAACC
3489217 CTATTTTTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (28 bp):
GGGATACTCCAACCACAACAATTCTAAG
Found at i:3490560 original size:51 final size:52
Alignment explanation
Indices: 3490505--3490633 Score: 174
Period size: 51 Copynumber: 2.5 Consensus size: 52
3490495 AAAATGTATC
* *
3490505 GATACATTTTTCATTGTATCGATACATTCTGG-GTTTTAACCCCAATGCA-T
1 GATACATTATTCATTGTATCGATACATTCTGGTGTTTTAACCCAAATGCACT
* *
3490555 AGATACATTATTCATT-TATCGATACATTCTGGTTTTTTAACCCAAATGTACT
1 -GATACATTATTCATTGTATCGATACATTCTGGTGTTTTAACCCAAATGCACT
* *
3490607 GATACATTCTTCAATGTATCGATACAT
1 GATACATTATTCATTGTATCGATACAT
3490634 GTAGACAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 16 0.23
51 41 0.59
52 12 0.17
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (52 bp):
GATACATTATTCATTGTATCGATACATTCTGGTGTTTTAACCCAAATGCACT
Found at i:3495852 original size:20 final size:20
Alignment explanation
Indices: 3495827--3495925 Score: 100
Period size: 20 Copynumber: 5.7 Consensus size: 20
3495817 AAATTCCCAG
3495827 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
3495847 ATGTATCGAT------A-CA
1 ATGTATCGATACAAAGATCA
3495860 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
3495880 ATGTATCGAT------A-CA
1 ATGTATCGATACAAAGATCA
3495893 ATGTATCGATACAAAGATCA
1 ATGTATCGATACAAAGATCA
3495913 ATGTATCGATACA
1 ATGTATCGATACA
3495926 TTTCCTTGGC
Statistics
Matches: 65, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 24 0.37
14 2 0.03
19 2 0.03
20 37 0.57
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
ATGTATCGATACAAAGATCA
Found at i:3495863 original size:13 final size:13
Alignment explanation
Indices: 3495845--3495906 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 13
3495835 ATACAAAGAT
3495845 CAATGTATCGATA
1 CAATGTATCGATA
3495858 CAATGTATCGATA
1 CAATGTATCGATA
3495871 CAA---A--GAT-
1 CAATGTATCGATA
3495878 CAATGTATCGATA
1 CAATGTATCGATA
3495891 CAATGTATCGATA
1 CAATGTATCGATA
3495904 CAA
1 CAA
3495907 AGATCAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.07
8 3 0.07
10 2 0.05
12 3 0.07
13 32 0.74
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3495869 original size:33 final size:33
Alignment explanation
Indices: 3495827--3495925 Score: 198
Period size: 33 Copynumber: 3.0 Consensus size: 33
3495817 AAATTCCCAG
3495827 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
3495860 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
3495893 ATGTATCGATACAAAGATCAATGTATCGATACA
1 ATGTATCGATACAAAGATCAATGTATCGATACA
3495926 TTTCCTTGGC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCGATACA
Found at i:3495970 original size:13 final size:13
Alignment explanation
Indices: 3495952--3495977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3495942 CAGGGCAGCT
3495952 TTGTATCGATACA
1 TTGTATCGATACA
3495965 TTGTATCGATACA
1 TTGTATCGATACA
3495978 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3498343 original size:13 final size:13
Alignment explanation
Indices: 3498325--3498350 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3498315 CATGGGACAA
3498325 TGTATCGATACAT
1 TGTATCGATACAT
3498338 TGTATCGATACAT
1 TGTATCGATACAT
3498351 GAAGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3498347 original size:33 final size:33
Alignment explanation
Indices: 3498305--3498371 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3498295 CTGAGTGAAA
*
3498305 TGTATCGATACATG-GGACAATGTATCGATACAT
1 TGTATCGATACATGAAGA-AATGTATCGATACAT
*
3498338 TGTATCGATACATGAAGAATTGTATCGATACAT
1 TGTATCGATACATGAAGAAATGTATCGATACAT
3498371 T
1 T
3498372 ATTCCCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGAAGAAATGTATCGATACAT
Found at i:3499395 original size:15 final size:15
Alignment explanation
Indices: 3499377--3499408 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3499367 TGAGTCAACT
3499377 TCATCATTATCATCA
1 TCATCATTATCATCA
*
3499392 TCATCATTATCTTCA
1 TCATCATTATCATCA
3499407 TC
1 TC
3499409 GTCTTTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:3502525 original size:13 final size:13
Alignment explanation
Indices: 3502506--3502544 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3502496 ACTATTTATG
3502506 ATGTATCGATACA
1 ATGTATCGATACA
*
3502519 CTGTATCGATACA
1 ATGTATCGATACA
3502532 ATGTATCGATACA
1 ATGTATCGATACA
3502545 TGAATAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3502896 original size:53 final size:54
Alignment explanation
Indices: 3502832--3502949 Score: 202
Period size: 53 Copynumber: 2.2 Consensus size: 54
3502822 CTACTACCAA
* *
3502832 TGTATTGATACAAATTTGGCTACTGCCAATGACCTGTATCGATACATA-TTGTG
1 TGTATCGATACAAATTTGGCTACTGCCAATGACCTATATCGATACATATTTGTG
*
3502885 TGTATCGATACAAATTTGGCTACTGCCAATGTCCTATATCGATACATATTTGTG
1 TGTATCGATACAAATTTGGCTACTGCCAATGACCTATATCGATACATATTTGTG
3502939 TGTATCGATAC
1 TGTATCGATAC
3502950 TATGCAATCT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 45 0.74
54 16 0.26
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (54 bp):
TGTATCGATACAAATTTGGCTACTGCCAATGACCTATATCGATACATATTTGTG
Found at i:3503056 original size:21 final size:21
Alignment explanation
Indices: 3503030--3503070 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3503020 GTCAACCTTG
3503030 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
3503051 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
3503071 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:3503749 original size:13 final size:13
Alignment explanation
Indices: 3503731--3503755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3503721 CAATTCTTCT
3503731 TGTATCGATACAA
1 TGTATCGATACAA
3503744 TGTATCGATACA
1 TGTATCGATACA
3503756 TTATCCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3503849 original size:19 final size:20
Alignment explanation
Indices: 3503804--3503854 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3503794 CTACTAGTTT
* *
3503804 CATGTATCGATACAATTAGG
1 CATGTATCGATAAAATGAGG
*
3503824 TATGTATCGATAAAATGA-G
1 CATGTATCGATAAAATGAGG
3503843 CATGTATCGATA
1 CATGTATCGATA
3503855 CTAAGCATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
CATGTATCGATAAAATGAGG
Found at i:3507143 original size:72 final size:72
Alignment explanation
Indices: 3507024--3507159 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 72
3507014 TTCATGAATG
* * * * *
3507024 TTATTATGTACATTCATATACTTTAACTATATATGAATTTTAGTATTCATGAATTATGCACATAT
1 TTATTATGAACATTCATAAACTTTAACTATATATAAATTTAAGTATTCATGAATCATGCACATAT
3507089 ATAAATA
66 ATAAATA
* * * * * *
3507096 TTATTATGAACATTCATAAACTTTGATTATTTATAAATTTAATTATTCCTGAATCATGTACATA
1 TTATTATGAACATTCATAAACTTTAACTATATATAAATTTAAGTATTCATGAATCATGCACATA
3507160 CATGAATGCC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 53 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (72 bp):
TTATTATGAACATTCATAAACTTTAACTATATATAAATTTAAGTATTCATGAATCATGCACATAT
ATAAATA
Found at i:3512307 original size:20 final size:20
Alignment explanation
Indices: 3512282--3512321 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3512272 GATTGTAGAA
3512282 ATGAAATAAAGAGA-AAAAAG
1 ATGAAA-AAAGAGAGAAAAAG
*
3512302 ATGAAAAAAGTGAGAAAAAG
1 ATGAAAAAAGAGAGAAAAAG
3512322 TCCAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (20 bp):
ATGAAAAAAGAGAGAAAAAG
Found at i:3512729 original size:7 final size:7
Alignment explanation
Indices: 3512717--3512743 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3512707 CATAACATAT
3512717 TTAAATA
1 TTAAATA
3512724 TTAAATA
1 TTAAATA
3512731 TTAAATA
1 TTAAATA
3512738 TTAAAT
1 TTAAAT
3512744 TTTGAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAAATA
Found at i:3513162 original size:26 final size:25
Alignment explanation
Indices: 3513114--3513163 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3513104 TATATATTAT
*
3513114 TATTTATATAATAAAAATTATATAA
1 TATTTATATAATAAAAATAATATAA
3513139 TATTTATA-AATATAAAAGTAATATA
1 TATTTATATAATA-AAAA-TAATATA
3513164 TAATTGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 12 0.55
26 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
TATTTATATAATAAAAATAATATAA
Found at i:3515194 original size:2 final size:2
Alignment explanation
Indices: 3515187--3515216 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3515177 GTCAGTATGC
3515187 AT 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 AT
3515217 TTCTTTACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3519758 original size:18 final size:19
Alignment explanation
Indices: 3519732--3519773 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3519722 TGAGTGCTTA
* *
3519732 TTTTGAATAATTA-CATTT
1 TTTTAAATAATTATAATTT
*
3519750 TTTTAAATATTTATAATTT
1 TTTTAAATAATTATAATTT
3519769 TTTTA
1 TTTTA
3519774 TACTACAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTAAATAATTATAATTT
Found at i:3520592 original size:13 final size:13
Alignment explanation
Indices: 3520574--3520601 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3520564 AAGTCCAAAC
3520574 TTGAATGCTCCTA
1 TTGAATGCTCCTA
3520587 TTGAATGCTCCTA
1 TTGAATGCTCCTA
3520600 TT
1 TT
3520602 ATTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGAATGCTCCTA
Found at i:3524033 original size:138 final size:138
Alignment explanation
Indices: 3523785--3524063 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 138
3523775 CACTGTGCCT
*
3523785 TTCACAGCCGGTTCCAGGATTTCCTTCTGATGTGGAAAGTCAAAAAAACATCGCAACCAGGAAAA
1 TTCACAGCCGGTTCCAGGATTTCCTTCTGACGTGGAAAGTCAAAAAAACATCGCAACCAGGAAAA
3523850 AAAGACCTCAAGCGTTTAGATTTCCATCAAACCATTTAATTGAAGAAAGCTCTTGTTTAATTATA
66 AAAGACCTCAAGCGTTTAGATTTCCATCAAACCATTTAATTGAAGAAAGCTCTTGTTTAATTATA
3523915 AATTGCAA
131 AATTGCAA
*
3523923 TTCACAGCCGGTTCCAGGATTTCCTTCTGACGTGGAAAGTCAAAACAACATCGCAACCAGGAAAA
1 TTCACAGCCGGTTCCAGGATTTCCTTCTGACGTGGAAAGTCAAAAAAACATCGCAACCAGGAAAA
3523988 AAAGACCTCAAGCGTTTAGATTTCCATCAAACCATTTAATTGAAGAAAGCTCTTGTTTAATTATA
66 AAAGACCTCAAGCGTTTAGATTTCCATCAAACCATTTAATTGAAGAAAGCTCTTGTTTAATTATA
3524053 AATTGCAA
131 AATTGCAA
3524061 TTC
1 TTC
3524064 TCCAAACTTA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (138 bp):
TTCACAGCCGGTTCCAGGATTTCCTTCTGACGTGGAAAGTCAAAAAAACATCGCAACCAGGAAAA
AAAGACCTCAAGCGTTTAGATTTCCATCAAACCATTTAATTGAAGAAAGCTCTTGTTTAATTATA
AATTGCAA
Found at i:3528530 original size:156 final size:156
Alignment explanation
Indices: 3528141--3529457 Score: 1565
Period size: 156 Copynumber: 8.5 Consensus size: 156
3528131 TTAAGTTCAA
* * * * *
3528141 AAAAAATTACGAAAATACCCTTAGGGGATACCTTCGACATAAAAGTAT-TCGATACCACTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
* * * * * *
3528205 ACATAAAAAGGATTATAAAAGGGATAAACCTATCCTAAATATCCACCTTCGGCATAAAAGTGGAC
66 ACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
* * * * *
3528270 CCGGTTATAACCTAAGACTTGGTTTT
131 CCGGTGATAACCTAGGACTCGATTCT
* * * * *
3528296 AAAAAATTACG-AAATGCCCCTAGTGGATACTTTTGACGTGAAAGTATCTTGGTACCCCTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
* *
3528360 ACTTAAAAAGGACTATAAAATGAG-TGAATCTATCCTAAATACCCACATTCGGCATAAAAGCGGA
66 ACTTAAAAAGGACTATAAAA-GAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA
*
3528424 CCCGGTGATAACTTAGGACTCGATTCT
130 CCCGGTGATAACCTAGGACTCGATTCT
* * **
3528451 AAAAAAATACAAAAATACCCCTAGGGGATACCTTCGATATGAAAGTATCTCGGTACCCCTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
* * * * *
3528516 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCATAAATACCCACCTTCGGCATAAAAACAGAC
66 ACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
** * * *
3528581 CTAGTGATAACCTACGACTCAATTTT
131 CCGGTGATAACCTAGGACTCGATTCT
* * * * * *
3528607 AGAAAATTACGAAAATACTCCTAGGAGATACCTTTC-ACGTGAAAGTATCTTGGTACCCTTAAAA
1 AAAAAATTACGAAAATACCCCTAGGGGATACC-TTCGACGTGAAAGTATCTCGGTACCCCTAAAG
* * * *
3528671 AACTTAAAAAAGACTATAAAAG-GAATGAACCTATCCTAAATACCTACCTTCGGCATAAAAGCGA
65 GACTTAAAAAGGACTATAAAAGAG-ATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGG
* *
3528735 ACTCGGTGATAATCTAGGACTCGATTCT
129 ACCCGGTGATAACCTAGGACTCGATTCT
* * * * * * *
3528763 GAAAAATTATGAAAATACCCCTAAGAGATACCTTCGACGTGAAAGTATC-CTAGTGCCACTAAAG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTC-GGTACCCCTAAAG
* *
3528827 GACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCATCTTCGGCATAAAAGCGGA
65 GACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA
*
3528892 CCCGATGATAACCTAGGACTCGATTCT
130 CCCGGTGATAACCTAGGACTCGATTCT
* **** * * *
3528919 GAAAAATTACGAAAATGTTTCTAGGGGATACCTTCGACATGAAAGTATCTCAGTACCCTTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
* *
3528984 ACTTAAAAAGGACTATAAAATGA-ATGAACCTATCCTAAATACCCACATTTGGCATAAAAGCGGA
66 ACTTAAAAAGGACTATAAAA-GAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA
*
3529048 CCTGGTGATAACCTAGGACTCGATTCT
130 CCCGGTGATAACCTAGGACTCGATTCT
* * * ** * *
3529075 -AAAAATTACG-AAATACCCCTAAGGGATACCTTCAAC-TCGAAAGTATCCCAATAGCTCTAAAG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGT-GAAAGTATCTCGGTACCCCTAAAG
* * * ** *
3529137 GACTTAAAAAAGACTATAAAAGAGCTGAACTTATCCTAAATACCCACCTTTAGCATAAAAGCAGA
65 GACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGA
* * *
3529202 CCCGATGATAACTTAAGACTCGATTCT
130 CCCGGTGATAACCTAGGACTCGATTCT
* * *
3529229 AAAAAATTACGAAAATACCCCTGGGGGATACCTTCGACGTCAAAGTATCCCGGTACCCCTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
* * * * * * *
3529294 ACTTAAAAAGGACTATAAAAGGGATAAACCTATCCTAAATACCTACCTTCAGCTTAAAAACAGAC
66 ACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
* *
3529359 CCGGTGATAACCTAAGACTCGTTTCT
131 CCGGTGATAACCTAGGACTCGATTCT
* * * * * *
3529385 AAAAAATTATGAAAATACACCTAGGGGATACCTTTGACGTGATAGTATCCCGGTACCCCTAAAAG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
3529450 ACTTAAAA
66 ACTTAAAA
3529458 CTTATTCTAA
Statistics
Matches: 993, Mismatches: 153, Indels: 31
0.84 0.13 0.03
Matches are distributed among these distances:
153 3 0.00
154 147 0.15
155 133 0.13
156 703 0.71
157 7 0.01
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (156 bp):
AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAGG
ACTTAAAAAGGACTATAAAAGAGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
CCGGTGATAACCTAGGACTCGATTCT
Found at i:3528730 original size:312 final size:312
Alignment explanation
Indices: 3528141--3529643 Score: 1651
Period size: 312 Copynumber: 4.9 Consensus size: 312
3528131 TTAAGTTCAA
* * * *
3528141 AAAAAATTACGAAAATACCCTTAGGGGATACCTTCGACATAAAAGTAT-TCGATACCACTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACATGAAAGTATCCCGGTACCACTAAAGG
* * * * * **
3528205 ACATAAAAAGGATTATAAAAGGGATAAACCTATCCTAAATATCCACCTTCGGCATAAAAGTGGAC
66 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGAC
* * * * * * * * *
3528270 CCGGTTATAACCTAAGACTTGGTTTTAAAAAATTACG-AAATGCCCCTAGTGGATACTTTTGACG
131 CCGATGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACG
* * * *
3528334 TGAAAGTATCTTGGTACCCCTAAAGGACTTAAAAAGGACTATAAAATGAGTGAATCTATCCTAAA
196 TGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTAAA
*
3528399 TACCCACATTCGGCATAAAAGCGGACCCGGTGATAACTTAGGACTCGATTCT
261 TACCCACATTCGGCATAAAAGCGGACCCGGTGATAACCTAGGACTCGATTCT
* * * * *
3528451 AAAAAAATACAAAAATACCCCTAGGGGATACCTTCGATATGAAAGTATCTCGGTACCCCTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACATGAAAGTATCCCGGTACCACTAAAGG
* *
3528516 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCATAAATACCCACCTTCGGCATAAAAACAGA-
66 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGAC
* * * * * * *
3528580 CCTAGTGATAACCTACGACTCAATTTTAGAAAATTACGAAAATACTCCTAGGAGATACCTTTC-A
131 CCGA-TGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACC-TTCGA
* * ** *
3528644 CGTGAAAGTATCTTGGTACCCTTAAAAAACTTAAAAAAGACTATAAAAGGAATGAACCTATCCTA
194 CGTGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTA
* * * * *
3528709 AATACCTACCTTCGGCATAAAAGCGAACTCGGTGATAATCTAGGACTCGATTCT
259 AATACCCACATTCGGCATAAAAGCGGACCCGGTGATAACCTAGGACTCGATTCT
* * * * * ** *
3528763 GAAAAATTATGAAAATACCCCTAAGAGATACCTTCGACGTGAAAGTATCCTAGTGCCACTAAAGG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACATGAAAGTATCCCGGTACCACTAAAGG
* * *
3528828 ACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCATCTTCGGCATAAAAGCGGAC
66 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGAC
* * **** *
3528893 CCGATGATAACCTAGGACTCGATTCTGAAAAATTACGAAAATGTTTCTAGGGGATACCTTCGACA
131 CCGATGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACG
* * *
3528958 TGAAAGTATCTCAGTACCCTTAAAGGACTTAAAAAGGACTATAAAATGAATGAACCTATCCTAAA
196 TGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTAAA
* *
3529023 TACCCACATTTGGCATAAAAGCGGACCTGGTGATAACCTAGGACTCGATTCT
261 TACCCACATTCGGCATAAAAGCGGACCCGGTGATAACCTAGGACTCGATTCT
* * ** * *
3529075 -AAAAATTACG-AAATACCCCTAAGGGATACCTTCAAC-TCGAAAGTATCCCAATAGCTCTAAAG
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACAT-GAAAGTATCCCGGTACCACTAAAG
* * * **
3529137 GACTTAAAAAAGACTATAAAAGAGCTGAACTTATCCTAAATACCCACCTTTAGCATAAAAGCAGA
65 GACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGA
* *
3529202 CCCGATGATAACTTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTGGGGGATACCTTCGAC
130 CCCGATGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACCTTCGAC
* * * *
3529267 GTCAAAGTATCCCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGGATAAACCTATCCTAA
195 GTGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTAA
* * * * * * * *
3529332 ATACCTACCTTCAGCTTAAAAACAGACCCGGTGATAACCTAAGACTCGTTTCT
260 ATACCCACATTCGGCATAAAAGCGGACCCGGTGATAACCTAGGACTCGATTCT
* * * * *
3529385 AAAAAATTATGAAAATACACCTAGGGGATACCTTTGACGTGATAGTATCCCGGTACC-C------
1 AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACATGAAAGTATCCCGGTACCACTAAAGG
* * * **
3529443 -C-T--AAAAGACT-T---A---A--AACTTATTCTAAATACCCACCTTCGACATAAAAGTGGAC
66 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGAC
* * * * * * * *
3529495 CCGGTGATAACTTAGGACTTGATTCTAAAAAATTACAAAAATGCCCTTAAGGGATACCTTCGACG
131 CCGATGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACG
* ** * * * * *
3529560 TAAAAGTATCTTAGTATCCCTAAAAGACTTAAAAA-GACTATAAAAGGGATGAACTTATTCTAAA
196 TGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTAAA
*
3529624 TACACACATT-GGCATTAAAA
261 TACCCACATTCGGCA-TAAAA
3529644 TGGACCCAAT
Statistics
Matches: 1017, Mismatches: 165, Indels: 41
0.83 0.13 0.03
Matches are distributed among these distances:
290 2 0.00
291 38 0.04
292 119 0.12
297 1 0.00
300 1 0.00
301 8 0.01
303 1 0.00
304 1 0.00
309 1 0.00
310 302 0.30
311 118 0.12
312 419 0.41
313 6 0.01
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (312 bp):
AAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACATGAAAGTATCCCGGTACCACTAAAGG
ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCAGAC
CCGATGATAACCTAAGACTCGATTCTAAAAAATTACGAAAATACCCCTAGGGGATACCTTCGACG
TGAAAGTATCTCGGTACCCCTAAAGGACTTAAAAAGGACTATAAAAGGAATGAACCTATCCTAAA
TACCCACATTCGGCATAAAAGCGGACCCGGTGATAACCTAGGACTCGATTCT
Found at i:3530632 original size:31 final size:31
Alignment explanation
Indices: 3530594--3530678 Score: 161
Period size: 31 Copynumber: 2.7 Consensus size: 31
3530584 AATTCATAAA
3530594 ATATGTCTAAAATTCATGAAATACCCCTTCC
1 ATATGTCTAAAATTCATGAAATACCCCTTCC
*
3530625 ATATGTCTAAAATTCGTGAAATACCCCTTCC
1 ATATGTCTAAAATTCATGAAATACCCCTTCC
3530656 ATATGTCTAAAATTCATGAAATA
1 ATATGTCTAAAATTCATGAAATA
3530679 TCTTTTGCGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (31 bp):
ATATGTCTAAAATTCATGAAATACCCCTTCC
Found at i:3531214 original size:16 final size:16
Alignment explanation
Indices: 3531191--3531231 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3531181 TTTACACCCA
3531191 AAAAAAAAACAAAAA-
1 AAAAAAAAACAAAAAC
3531206 AATAAAAAAACAAAAAC
1 AA-AAAAAAACAAAAAC
3531223 AAAAAAAAA
1 AAAAAAAAA
3531232 AAACCAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.02
Consensus pattern (16 bp):
AAAAAAAAACAAAAAC
Found at i:3531243 original size:14 final size:14
Alignment explanation
Indices: 3531190--3531256 Score: 64
Period size: 14 Copynumber: 4.9 Consensus size: 14
3531180 CTTTACACCC
*
3531190 AAAAA-AAAAACAA
1 AAAAACAAAAAAAA
* *
3531203 AAAAATAAAAAAAC
1 AAAAACAAAAAAAA
3531217 AAAAACAAAAAAAA
1 AAAAACAAAAAAAA
* *
3531231 AAAACCAAGAAAAA
1 AAAAACAAAAAAAA
* *
3531245 AATAGCAAAAAA
1 AAAAACAAAAAA
3531257 TAGAAAGGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
13 5 0.11
14 39 0.89
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (14 bp):
AAAAACAAAAAAAA
Found at i:3531243 original size:22 final size:22
Alignment explanation
Indices: 3531190--3531234 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3531180 CTTTACACCC
3531190 AAAAA-AAAAACAAAAAAATAA
1 AAAAACAAAAACAAAAAAATAA
3531211 AAAAACAAAAACAAAAAAA-AA
1 AAAAACAAAAACAAAAAAATAA
3531232 AAA
1 AAA
3531235 CCAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAACAAAAACAAAAAAATAA
Found at i:3531246 original size:1 final size:1
Alignment explanation
Indices: 3531190--3531234 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
3531180 CTTTACACCC
* * * *
3531190 AAAAAAAAAACAAAAAAATAAAAAAACAAAAACAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3531235 CCAAGAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:3532511 original size:28 final size:28
Alignment explanation
Indices: 3532477--3532970 Score: 600
Period size: 28 Copynumber: 17.5 Consensus size: 28
3532467 CGTTCATCTC
* *
3532477 TTCAAAGCTCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3532505 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
3532534 TTCAAAGCCCATACGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3532562 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3532590 TTCAAAGCCCACAAGTTAGTGACACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* * *
3532619 TTCAAAGCCCATAGGTCAATGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
3532647 TTCAAAGCCCATAAGTCAATGGTA-CTTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
3532675 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3532703 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
3532731 TTTAAAGCCAACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
*
3532760 TTCAAAGCCCACAATTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
3532788 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
3532816 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3532844 TTTAAAGCCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
3532872 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
3532900 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
3532928 TTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CA-TCCT
3532958 TTCAAAGCCCACA
1 TTCAAAGCCCACA
3532971 CGAGTCGGTG
Statistics
Matches: 409, Mismatches: 45, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
27 5 0.01
28 316 0.77
29 73 0.18
30 15 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:3532620 original size:85 final size:85
Alignment explanation
Indices: 3532477--3532970 Score: 645
Period size: 85 Copynumber: 5.8 Consensus size: 85
3532467 CGTTCATCTC
* * * *
3532477 TTCAAAGCTCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
* * * *
3532542 CCATACGTTAGTGGCATCCT
66 CCACAAGTCAGTGGCACCCT
* *
3532562 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGACACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
* * * *
3532627 CCATAGGTCAATGGCATCCT
66 CCACAAGTCAGTGGCACCCT
* * * ** * *
3532647 TTCAAAGCCCATAAGTCAATGGTACTTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
3532711 CCACAAGTCAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* * * *
3532731 TTTAAAGCCAACAAGTCAGTGGCACTCTTTTCAAAGCCCACAA-TTCAGTGGCA-TCCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTT-AGTGGCACTCTTTTCAAA
*
3532794 GCCCACAAGTCAGTGGCACCTT
64 GCCCACAAGTCAGTGGCACCCT
* * * *
3532816 TTCAAAGCCCACAAGTTAGTGGCATCTTTTTAAAGCCCACAAGTTAGTGGCAC-CTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
3532880 CCACAAGTCAGTGGCACCCT
66 CCACAAGTCAGTGGCACCCT
* *
3532900 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGCTAGTGGTAACTCTTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGG-CACTCTTTTCAAAG
3532965 CCCACA
65 CCCACA
3532971 CGAGTCGGTG
Statistics
Matches: 362, Mismatches: 41, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
84 145 0.40
85 201 0.56
86 16 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
CCACAAGTCAGTGGCACCCT
Found at i:3532732 original size:141 final size:142
Alignment explanation
Indices: 3532477--3532970 Score: 735
Period size: 141 Copynumber: 3.5 Consensus size: 142
3532467 CGTTCATCTC
* *
3532477 TTCAAAGCTCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
3532542 CCATACGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTT
66 CCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTC
*
3532607 AGTGACACTCTT
131 AGTGGCACTCTT
* * * * * *
3532619 TTCAAAGCCCATAGGTCAATGGCATCCTTTCAAAGCCCATAAGTCAATGGTACT-TTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * * *
3532683 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCAACAAGTC
66 CCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTC
3532748 AGTGGCACTCTT
131 AGTGGCACTCTT
*
3532760 TTCAAAGCCCACAATTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
3532824 CCACAAGTTAGTGGCATCTTTTTAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTC
66 CCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTC
*
3532889 AGTGGCAC-CCT
131 AGTGGCACTCTT
* *
3532900 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC-AGTGG-CACTCTTTTCAAA
3532964 GCCCACA
64 GCCCACA
3532971 CGAGTCGGTG
Statistics
Matches: 314, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
139 1 0.00
140 48 0.15
141 203 0.65
142 62 0.20
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (142 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTC
AGTGGCACTCTT
Found at i:3541106 original size:20 final size:21
Alignment explanation
Indices: 3541075--3541113 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3541065 AGATCAAAAT
3541075 CCTAGAAAGTATCGATACAGG
1 CCTAGAAAGTATCGATACAGG
3541096 CCTAG-AAGTATCGATACA
1 CCTAGAAAGTATCGATACA
3541114 TATTACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAGG
Found at i:3541126 original size:20 final size:19
Alignment explanation
Indices: 3541103--3541140 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
3541093 AGGCCTAGAA
3541103 GTATCGATACATATTACATT
1 GTATCGATACATA-TACATT
3541123 GTATCGATACATATACAT
1 GTATCGATACATATACAT
3541141 AAAACTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATACATT
Found at i:3541207 original size:13 final size:13
Alignment explanation
Indices: 3541189--3541213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3541179 TACATGGGAC
3541189 ATTGTATCGATAT
1 ATTGTATCGATAT
3541202 ATTGTATCGATA
1 ATTGTATCGATA
3541214 CATAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGTATCGATAT
Found at i:3542645 original size:13 final size:13
Alignment explanation
Indices: 3542609--3542645 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3542599 ACTTACTCAA
* *
3542609 TATCGATATAGTG
1 TATCGATACATTG
3542622 TATCGATACATTG
1 TATCGATACATTG
3542635 TATCGATACAT
1 TATCGATACAT
3542646 GGTCAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:3550584 original size:34 final size:35
Alignment explanation
Indices: 3550533--3550674 Score: 180
Period size: 34 Copynumber: 4.0 Consensus size: 35
3550523 TGCTATAACA
3550533 AAAAAGGGGAGAAATATTTTGA-AAATAAATTTGT
1 AAAAAGGGGAGAAATATTTTGAGAAATAAATTTGT
* * *
3550567 AAAAGGGGGAGAGATATTTTGAGAAATAAACTTGTTTT
1 AAAAAGGGGAGAAATATTTTGAGAAATAAA--T-TTGT
3550605 ATAAAAGGGGAGAAATATTTTGA-AAATAAATTTGT
1 A-AAAAGGGGAGAAATATTTTGAGAAATAAATTTGT
* * *
3550640 AAAAGGGGGAGAGATATTTTGAGAAATAAACTTGT
1 AAAAAGGGGAGAAATATTTTGAGAAATAAATTTGT
3550675 TTTATAAAAG
Statistics
Matches: 93, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
34 39 0.42
35 22 0.24
36 1 0.01
37 1 0.01
38 11 0.12
39 19 0.20
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (35 bp):
AAAAAGGGGAGAAATATTTTGAGAAATAAATTTGT
Found at i:3550701 original size:73 final size:73
Alignment explanation
Indices: 3550534--3550697 Score: 312
Period size: 73 Copynumber: 2.3 Consensus size: 73
3550524 GCTATAACAA
3550534 AAAAGGGGAGAAATATTTTGAAAATAAATTTGTAAAAGGGGGAGAGATATTTTGAGAAATAAACT
1 AAAAGGGGAGAAATATTTTGAAAATAAATTTGTAAAAGGGGGAGAGATATTTTGAGAAATAAACT
3550599 TGTTTTAT
66 TGTTTTAT
3550607 AAAAGGGGAGAAATATTTTGAAAATAAATTTGTAAAAGGGGGAGAGATATTTTGAGAAATAAACT
1 AAAAGGGGAGAAATATTTTGAAAATAAATTTGTAAAAGGGGGAGAGATATTTTGAGAAATAAACT
3550672 TGTTTTAT
66 TGTTTTAT
*
3550680 AAAAGGGGA-AATTATTTT
1 AAAAGGGGAGAAATATTTT
3550698 TGAAGATTAT
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
72 8 0.09
73 82 0.91
ACGTcount: A:0.44, C:0.01, G:0.23, T:0.32
Consensus pattern (73 bp):
AAAAGGGGAGAAATATTTTGAAAATAAATTTGTAAAAGGGGGAGAGATATTTTGAGAAATAAACT
TGTTTTAT
Found at i:3550708 original size:13 final size:13
Alignment explanation
Indices: 3550690--3550714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3550680 AAAAGGGGAA
3550690 ATTATTTTTGAAG
1 ATTATTTTTGAAG
3550703 ATTATTTTTGAA
1 ATTATTTTTGAA
3550715 ACAAAAAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTATTTTTGAAG
Found at i:3553429 original size:85 final size:85
Alignment explanation
Indices: 3553312--3553669 Score: 410
Period size: 84 Copynumber: 4.2 Consensus size: 85
3553302 GAGCTGACAG
* * *
3553312 GTAAACAATGAGATGAAGGTTGACC-AGAGACTAAGTTGACAGGTCACCATAAGGATAATAGGTT
1 GTAAACAATG-GATGAAGGTTGACCGAG-GACTAAGCTGACAGGTCACCATAAGGGTAATGGGTT
3553376 TACTAAGGACTAA-CTCGATAG-
64 TACTAAGGACTAAGC-CGATAGA
* *
3553397 GTAAACAATGGATGAAGGGTTGACCGAGGACTACGCTGACAGGCCACCATAAGGGTAATGGGTTT
1 GTAAACAATGGATGAA-GGTTGACCGAGGACTAAGCTGACAGGTCACCATAAGGGTAATGGGTTT
*
3553462 A-TCAGGGACTAAGCC-A-ACGA
65 ACT-AAGGACTAAGCCGATA-GA
* * * * * * *
3553482 GTAAACAATGGATGAAGGTTGATCGGAGG-TTGAGCTGATAGGTTACCAGAAAGGTAATGGGTTT
1 GTAAACAATGGATGAAGGTTGA-CCGAGGACTAAGCTGACAGGTCACCATAAGGGTAATGGGTTT
**
3553546 ACCGAGGACTAAGCCGAT-GA
65 ACTAAGGACTAAGCCGATAGA
* * * *
3553566 GTAAACAATGGATGAAGGTTGACCGAAGACTGAGTTGATAGGTCACCATAAGGGTAATGGGTTTA
1 GTAAACAATGGATGAAGGTTGACCGAGGACTAAGCTGACAGGTCACCATAAGGGTAATGGGTTTA
*
3553631 CTAGGGACTAAGCCGAT-GA
66 CTAAGGACTAAGCCGATAGA
3553650 GTAAACAATGGATGAAGGTT
1 GTAAACAATGGATGAAGGTT
3553670 ACTTAGCTAA
Statistics
Matches: 234, Mismatches: 28, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
83 5 0.02
84 144 0.62
85 82 0.35
86 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.22
Consensus pattern (85 bp):
GTAAACAATGGATGAAGGTTGACCGAGGACTAAGCTGACAGGTCACCATAAGGGTAATGGGTTTA
CTAAGGACTAAGCCGATAGA
Found at i:3553731 original size:76 final size:77
Alignment explanation
Indices: 3553605--3553747 Score: 200
Period size: 76 Copynumber: 1.9 Consensus size: 77
3553595 CTGAGTTGAT
* ** * *
3553605 AGGTCACCATAAGGGTAATGGGTTTACTAGGGACTAAGCCGATGAGTAAACAATG-GATGAAGGT
1 AGGTCACCATAAGGGTAATGGGTTTACCAGGGACTAAGCAAAAGAGTAAACAATGAGATGAAAGT
3553669 TACTTAGCTAAC
66 TACTTAGCTAAC
* *
3553681 AGGTCCCCATAAGGGTAATGGGTTTACCGGGGACTAAGCTAAAAG-GTAAACAATGAGATGAAAG
1 AGGTCACCATAAGGGTAATGGGTTTACCAGGGACTAAGC-AAAAGAGTAAACAATGAGATGAAAG
3553745 TTA
65 TTA
3553748 TTTCCCGAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
76 46 0.79
77 12 0.21
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (77 bp):
AGGTCACCATAAGGGTAATGGGTTTACCAGGGACTAAGCAAAAGAGTAAACAATGAGATGAAAGT
TACTTAGCTAAC
Found at i:3553902 original size:42 final size:42
Alignment explanation
Indices: 3553846--3554033 Score: 145
Period size: 42 Copynumber: 4.5 Consensus size: 42
3553836 CATGGGTTTG
* *
3553846 AGCCGAT-AGCCAGACAAAGAATGAAGAAGTCTCCCAAGTCTA
1 AGCCGATGAG-CAGACAAAGAATAAAAAAGTCTCCCAAGTCTA
* * *
3553888 AGCCGACGAGCAGACAAA-AGATAAAAAAGTCT--CATGGTTTA
1 AGCCGATGAGCAGACAAAGA-ATAAAAAAGTCTCCCA-AGTCTA
* * *
3553929 AGCCGATGGGTAGACAAAAGAA-AAAAAAGTCTCCCGAGTCTA
1 AGCCGATGAGCAGAC-AAAGAATAAAAAAGTCTCCCAAGTCTA
* * * * *
3553971 AGCTGATGAGTAGATGAAAG-ATAAAGAAGTCTCCCAGGTCTA
1 AGCCGATGAGCAGA-CAAAGAATAAAAAAGTCTCCCAAGTCTA
* * *
3554013 AGCGGATGGGCAAACAAAGAA
1 AGCCGATGAGCAGACAAAGAA
3554034 AGGATAAAGA
Statistics
Matches: 114, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
40 2 0.02
41 32 0.28
42 76 0.67
43 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (42 bp):
AGCCGATGAGCAGACAAAGAATAAAAAAGTCTCCCAAGTCTA
Found at i:3553969 original size:83 final size:84
Alignment explanation
Indices: 3553824--3554003 Score: 220
Period size: 83 Copynumber: 2.2 Consensus size: 84
3553814 AGGATGATTA
* * *
3553824 ATAAAGAAGTCTCATGGGTTTGAGCCGATAGCCAGACAAAGAATGAAGAAGTCTCCCAAGTCTAA
1 ATAAAGAAGTCTCATGGGTTTAAGCCGATAGCCAGACAAAGAATAAAAAAGTCTCCCAAGTCTAA
3553889 GCCGACGAGCAGACAAAAG
66 GCCGACGAGCAGACAAAAG
* * ** *
3553908 ATAAAAAAGTCTCAT-GGTTTAAGCCGATGGGTAGACAAAAGAA-AAAAAAGTCTCCCGAGTCTA
1 ATAAAGAAGTCTCATGGGTTTAAGCCGATAGCCAGAC-AAAGAATAAAAAAGTCTCCCAAGTCTA
* * * **
3553971 AGCTGATGAGTAGATGAAAG
65 AGCCGACGAGCAGACAAAAG
3553991 ATAAAGAAGTCTC
1 ATAAAGAAGTCTC
3554004 CCAGGTCTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
83 61 0.75
84 20 0.25
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (84 bp):
ATAAAGAAGTCTCATGGGTTTAAGCCGATAGCCAGACAAAGAATAAAAAAGTCTCCCAAGTCTAA
GCCGACGAGCAGACAAAAG
Found at i:3554032 original size:83 final size:83
Alignment explanation
Indices: 3553872--3554034 Score: 195
Period size: 83 Copynumber: 2.0 Consensus size: 83
3553862 AAGAATGAAG
*
3553872 AAGTCTCCCAAGTCTAAGCCGACGAGCAGACAAAAGATAAAAAAGTCTCATGGTTTAAGCCGATG
1 AAGTCTCCCAAGTCTAAGCCGACGAGCAGACAAAAGATAAAAAAGTCTCATGGTCTAAGCCGATG
* *
3553937 GGTAGACAAAAGAAAAAA
66 GGCAAACAAAAGAAAAAA
* * * * ** * *
3553955 AAGTCTCCCGAGTCTAAGCTGATGAGTAGATGAAAGATAAAGAAGTCTCCCA-GGTCTAAGCGGA
1 AAGTCTCCCAAGTCTAAGCCGACGAGCAGACAAAAGATAAAAAAGTCT--CATGGTCTAAGCCGA
3554019 TGGGCAAAC-AAAGAAA
64 TGGGCAAACAAAAGAAA
3554035 GGATAAAGAA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
83 48 0.72
84 17 0.25
85 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.17
Consensus pattern (83 bp):
AAGTCTCCCAAGTCTAAGCCGACGAGCAGACAAAAGATAAAAAAGTCTCATGGTCTAAGCCGATG
GGCAAACAAAAGAAAAAA
Found at i:3554098 original size:42 final size:41
Alignment explanation
Indices: 3553899--3554178 Score: 163
Period size: 42 Copynumber: 6.5 Consensus size: 41
3553889 GCCGACGAGC
* *
3553899 AGACAAAAGATAAAAAAGTCTCAT-GGTTTAAGCCGATGGGT
1 AGACAAAAGAT-AAAAAGTCTCATAGGTCTAAGCTGATGGGT
* ** *
3553940 AGACAAAAGAAAAAAAAGTCTC-CCGAGTCTAAGCTGATGAGT
1 AGACAAAAG-ATAAAAAGTCTCATAG-GTCTAAGCTGATGGGT
** ** * *
3553982 AGATGAAAGATAAAGAAGTCTCCCAGGTCTAAGCGGATGGGC
1 AGACAAAAGATAAA-AAGTCTCATAGGTCTAAGCTGATGGGT
* *
3554024 AAACAAAGAAAGGATAAAGAAGGTCTCCTAGGTCTAAGCTGATGGGT
1 AGAC--A-AAA-GATAAA-AA-GTCTCATAGGTCTAAGCTGATGGGT
* * **
3554071 AGA-AAATAGATGAAAAAGTCTCATAGGTCTGAGCCGACAGGT
1 AGACAAA-AGAT-AAAAAGTCTCATAGGTCTAAGCTGATGGGT
* * ***
3554113 AGACAAAGAGATAACGAAGTCTC-TCGGGTCTAAGCTGACAAGT
1 AGACAAA-AGATAA-AAAGTCTCAT-AGGTCTAAGCTGATGGGT
*
3554156 AGACAAAGGATAAAGAAGGTCTC
1 AGACAAAAGATAAA-AA-GTCTC
3554179 TCGGGTCTAG
Statistics
Matches: 190, Mismatches: 32, Indels: 32
0.75 0.13 0.13
Matches are distributed among these distances:
41 24 0.13
42 76 0.40
43 49 0.26
44 5 0.03
45 3 0.02
46 9 0.05
47 24 0.13
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.18
Consensus pattern (41 bp):
AGACAAAAGATAAAAAGTCTCATAGGTCTAAGCTGATGGGT
Found at i:3554143 original size:43 final size:43
Alignment explanation
Indices: 3554096--3554579 Score: 172
Period size: 43 Copynumber: 11.3 Consensus size: 43
3554086 AAGTCTCATA
* * *
3554096 GGTCTGAGCCGACAGGTAGACAAAGAGATAACGAA-GTCTCTCG
1 GGTCTAAGCCGACAAGTAGACAAAG-GATAAAGAAGGTCTCTCG
*
3554139 GGTCTAAGCTGACAAGTAGACAAAGGATAAAGAAGGTCTCTCG
1 GGTCTAAGCCGACAAGTAGACAAAGGATAAAGAAGGTCTCTCG
** ** * * * *
3554182 GGTCT-AGCTAATGAGCAGACGAAA-GATAAAGGA-GTATCCCG
1 GGTCTAAGCCGACAAGTAGAC-AAAGGATAAAGAAGGTCTCTCG
* ** * * *
3554223 GGTCTAAGTCGATGGGCAAACAAAGAAAGGATAAAGAAGGTCTTTCG
1 GGTCTAAGCCGA----CAAGTAGACAAAGGATAAAGAAGGTCTCTCG
* * * *
3554270 GGTCTAAGCCGACAAGCAGAAAAAAGATGAAGAA-GTCTC-CTG
1 GGTCTAAGCCGACAAGTAGACAAAGGATAAAGAAGGTCTCTC-G
* * * ** * *
3554312 AGTTTGAGCCGATGA-TAAGATAAAAAGATAAAGAA-GTCTCTCG
1 GGTCTAAGCCGACAAGT-AGA-CAAAGGATAAAGAAGGTCTCTCG
* * * *** * *
3554355 GATTTAAGCTGATGGGTAGAAAAAGGATAAAGAAGGTCTCCCG
1 GGTCTAAGCCGACAAGTAGACAAAGGATAAAGAAGGTCTCTCG
* ** * *
3554398 GGTCTAAGCCAACGGGTAGA-AAAGAGATGAA-AA-GTTTC-CTG
1 GGTCTAAGCCGACAAGTAGACAAAG-GATAAAGAAGGTCTCTC-G
* ** * * *
3554439 GGTCTGAGCCGA-TGGACAGACAAAGGATAAAGAAGGTCTCCCA
1 GGTCTAAGCCGACAAG-TAGACAAAGGATAAAGAAGGTCTCTCG
* *** * * *
3554482 GGTCTAAGCTGATGGGTAGACAATGAGATGAAGAA-GTCTGC-CA
1 GGTCTAAGCCGACAAGTAGACAAAG-GATAAAGAAGGTCT-CTCG
* * * * * *
3554525 GGTCTAAACCAACGAGCAGATAAAGGATAAAAAAGGTCTCCTC-
1 GGTCTAAGCCGACAAGTAGACAAAGGATAAAGAAGGTCT-CTCG
3554568 GGTCTAAGCCGA
1 GGTCTAAGCCGA
3554580 TGGGAAGACA
Statistics
Matches: 337, Mismatches: 77, Indels: 54
0.72 0.16 0.12
Matches are distributed among these distances:
40 3 0.01
41 35 0.10
42 80 0.24
43 173 0.51
44 15 0.04
45 3 0.01
46 12 0.04
47 16 0.05
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (43 bp):
GGTCTAAGCCGACAAGTAGACAAAGGATAAAGAAGGTCTCTCG
Found at i:3554229 original size:216 final size:214
Alignment explanation
Indices: 3553938--3554520 Score: 601
Period size: 216 Copynumber: 2.7 Consensus size: 214
3553928 AAGCCGATGG
* * * * * *
3553938 GTAGACAAAAGA-AAAAAAAGTCTCCCGAGTCTAAGCTGATGAGTAGATGAAAGATAAAGAAGTC
1 GTAGACAAAGGATAAAGAAGGTCTCCCGGGTCTAAGCTAATGAGTAGA-GAAAGATAAAG-AGTA
*
3554002 TCCCAGGTCTAAGCGGATGGGCAAACAAAGAAAGGATAAAGAAGGTCTCCTAGGTCTAAGCTGAT
64 TCCCGGGTCTAAGC-GATGGGCAAACAAAGAAAGGATAAAGAAGGTCTCCTAGGTCTAAGCTGAT
* * * *
3554067 GGGTAGAAAATAGATGAAAAAGTCTCAT-AGGTCTGAGCCGACAGGT-AGACAAAGAGATAACGA
128 GGGTAGAAAATAGATGAAGAAGTCTCATGA-GTCTGAGCCGA-AGATAAGACAAAAAGATAAAGA
*
3554130 AGTCTCTCGGGTCTAAGCTGACAA
191 AGTCTCTCGGATCTAAGCTGACAA
* *
3554154 GTAGACAAAGGATAAAGAAGGTCTCTCGGGTCT-AGCTAATGAGCAGACGAAAGATAAAGGAGTA
1 GTAGACAAAGGATAAAGAAGGTCTCCCGGGTCTAAGCTAATGAGTAGA-GAAAGATAAA-GAGTA
* * *
3554218 TCCCGGGTCTAAGTCGATGGGCAAACAAAGAAAGGATAAAGAAGGTCT-TTCGGGTCTAAGCCGA
64 TCCCGGGTCTAAG-CGATGGGCAAACAAAGAAAGGATAAAGAAGGTCTCCT-AGGTCTAAGCTGA
*** * * * * * *
3554282 CAAGCAGAAAAAAGATGAAGAAGTCTCCTGAGTTTGAGCCGATGATAAGATAAAAAGATAAAGAA
127 TGGGTAGAAAATAGATGAAGAAGTCTCATGAGTCTGAGCCGAAGATAAGACAAAAAGATAAAGAA
* ***
3554347 GTCTCTCGGATTTAAGCTGATGG
192 GTCTCTCGGATCTAAGCTGACAA
* * * * * *
3554370 GTAGAAAAAGGATAAAGAAGGTCTCCCGGGTCTAAGCCAACGGGTAGAAAAGAGATGAAA-AGTT
1 GTAGACAAAGGATAAAGAAGGTCTCCCGGGTCTAAGCTAATGAGTAGAGAA-AGAT-AAAGAGTA
* * * * *
3554434 TCCTGGGTCTGAGCCGAT-GG---ACAGACAAAGGATAAAGAAGGTCTCCCAGGTCTAAGCTGAT
64 TCCCGGGTCTAAG-CGATGGGCAAACAAAGAAAGGATAAAGAAGGTCTCCTAGGTCTAAGCTGAT
*
3554495 GGGTAGACAATGAGATGAAGAAGTCT
128 GGGTAGAAAAT-AGATGAAGAAGTCT
3554521 GCCAGGTCTA
Statistics
Matches: 302, Mismatches: 54, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
212 39 0.13
213 14 0.05
215 5 0.02
216 208 0.69
217 33 0.11
218 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (214 bp):
GTAGACAAAGGATAAAGAAGGTCTCCCGGGTCTAAGCTAATGAGTAGAGAAAGATAAAGAGTATC
CCGGGTCTAAGCGATGGGCAAACAAAGAAAGGATAAAGAAGGTCTCCTAGGTCTAAGCTGATGGG
TAGAAAATAGATGAAGAAGTCTCATGAGTCTGAGCCGAAGATAAGACAAAAAGATAAAGAAGTCT
CTCGGATCTAAGCTGACAA
Found at i:3554529 original size:127 final size:125
Alignment explanation
Indices: 3554248--3554601 Score: 336
Period size: 127 Copynumber: 2.8 Consensus size: 125
3554238 GCAAACAAAG
** * * * * * *
3554248 AAAGGATAAAGAAGGTCTTTCGGGTCTAAGCCGACAAGCAGAAAAAAGATGAAGAAGTCTCCTGA
1 AAAGGATAAAGAAGGTCTCCCAGGTCTAAACCAACGAGCAGAAAAGAGATGAA-AAGTCTCCTGG
* * * * * *
3554313 GTTTGAGCCGATGATAAGATAAAAAGATAAAGAAGTCTCTCGGATTTAAGCTGATGGGTAGAA
65 GTCTGAGCCGATG-GAAGA-CAAAGGATAAAGAAGTCTCCCGGATCTAAGCTGATGGGTAGAA
* * * * *
3554376 AAAGGATAAAGAAGGTCTCCCGGGTCTAAGCCAACGGGTAGAAAAGAGATGAAAAGTTTCCTGGG
1 AAAGGATAAAGAAGGTCTCCCAGGTCTAAACCAACGAGCAGAAAAGAGATGAAAAGTCTCCTGGG
*
3554441 TCTGAGCCGATGGACAGACAAAGGATAAAGAAGGTCTCCCAGG-TCTAAGCTGATGGGTAGAC
66 TCTGAGCCGATGGA-AGACAAAGGATAAAGAA-GTCTCCC-GGATCTAAGCTGATGGGTAGAA
* * * *
3554503 AATGAGATGAAGAA-GTCTGCCAGGTCTAAACCAACGAGCAGATAAAG-GATAAAAAAGGTCTCC
1 AAAG-GATAAAGAAGGTCTCCCAGGTCTAAACCAACGAGCAGA-AAAGAGAT-GAAAA-GTCTCC
* * *
3554566 TCGGTCTAAGCCGATGGGAAGACAAAGAGATGAAGA
62 TGGGTCTGAGCCGAT-GGAAGACAAAG-GATAAAGA
3554602 TTAGAATAAG
Statistics
Matches: 189, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
126 13 0.07
127 76 0.40
128 64 0.34
129 26 0.14
130 10 0.05
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (125 bp):
AAAGGATAAAGAAGGTCTCCCAGGTCTAAACCAACGAGCAGAAAAGAGATGAAAAGTCTCCTGGG
TCTGAGCCGATGGAAGACAAAGGATAAAGAAGTCTCCCGGATCTAAGCTGATGGGTAGAA
Found at i:3554564 original size:86 final size:85
Alignment explanation
Indices: 3554376--3554601 Score: 262
Period size: 86 Copynumber: 2.6 Consensus size: 85
3554366 ATGGGTAGAA
* * * *
3554376 AAAGGATAAAGAAGGTCTCCCGGGTCTAAGCCAACGGGTAGA-AAAGAGATGAA-AAGTTTCCTG
1 AAAGGATAAAGAAGGTCTCCC-GGTCTAAGCCGATGGGTAGACAAAGAGATGAAGAAGTTGCCTA
* * * *
3554439 GGTCTGAGCCGATGGACAGAC
65 GGTCTAAACCAACGGACAGAC
* *
3554460 AAAGGATAAAGAAGGTCTCCCAGGTCTAAGCTGATGGGTAGACAATGAGATGAAGAAGTCTGCC-
1 AAAGGATAAAGAAGGTCTCCC-GGTCTAAGCCGATGGGTAGACAAAGAGATGAAGAAGT-TGCCT
*
3554524 AGGTCTAAACCAAC-GAGCAGAT
64 AGGTCTAAACCAACGGA-CAGAC
* *
3554546 AAAGGATAAAAAAGGTCTCCTCGGTCTAAGCCGATGGGAAGACAAAGAGATGAAGA
1 AAAGGATAAAGAAGGTCTCC-CGGTCTAAGCCGATGGGTAGACAAAGAGATGAAGA
3554602 TTAGAATAAG
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
84 38 0.31
85 12 0.10
86 67 0.55
87 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (85 bp):
AAAGGATAAAGAAGGTCTCCCGGTCTAAGCCGATGGGTAGACAAAGAGATGAAGAAGTTGCCTAG
GTCTAAACCAACGGACAGAC
Found at i:3555038 original size:78 final size:77
Alignment explanation
Indices: 3554954--3555413 Score: 457
Period size: 78 Copynumber: 5.9 Consensus size: 77
3554944 TTGGAAACAT
* * * * *
3554954 GTGGGAAGTGTCCCTCATGGCCATGTGATACATCAATACCATTTAGTATTTGAGAAGGAGGGATA
1 GTGGGAAGTG-CCCTCTTGGCCATGTGATGCATCAATATCATCTAGTATTTGAGAATGAGGGATA
*
3555019 TGATTGGAAGCGT
65 TGATTGGAAGCGA
* * *
3555032 GTGGGAAGTGCCCCTCTTAGCCATATGATGCATCAATATCATCTAGTATTTAAGAATGAGGGATA
1 GTGGGAAGTG-CCCTCTTGGCCATGTGATGCATCAATATCATCTAGTATTTGAGAATGAGGGATA
* *
3555097 TGACTGGAAGTGA
65 TGATTGGAAGCGA
* * ** * *
3555110 GTGGGAAATGCTCTTCTTGGCCATGTGATATATCAATATCATCTAGTGCTTCG-G-A-GA--GAT
1 GTGGGAAGTGC-CCTCTTGGCCATGTGATGCATCAATATCATCTAGT-ATTTGAGAATGAGGGAT
*
3555170 ATGATTGGAAGTGA
64 ATGATTGGAAGCGA
* * *
3555184 GTGGGAGGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTTGAGAATAAGGGATA
1 GTGGGAAGTG-CCCTCTTGGCCATGTGATGCATCAATATCATCTAGTATTTGAGAATGAGGGATA
*
3555249 TGATTGGAAACGA
65 TGATTGGAAGCGA
* * * * * *
3555262 GTAGGAGGTGTCCCTTTTAGCCATGTGATGCATAAATATCATTTAGTATTTGAGAATGAGGGATA
1 GTGGGAAGTG-CCCTCTTGGCCATGTGATGCATCAATATCATCTAGTATTTGAGAATGAGGGATA
* * * **
3555327 CGTTTGTAAGTAA
65 TGATTGGAAGCGA
* * * *
3555340 GTGGGAAGTGCCCTTTTTGGCCATGTGATGCATCAATATCCTCTAGGGATTAGATGAA--AGGGA
1 GTGGGAAGTGCCC-TCTTGGCCATGTGATGCATCAATATCATCTA-GTATTTGA-GAATGAGGGA
3555403 TATGATTGGAA
63 TATGATTGGAA
3555414 ATATGCGGGC
Statistics
Matches: 314, Mismatches: 57, Indels: 22
0.80 0.15 0.06
Matches are distributed among these distances:
73 3 0.01
74 57 0.18
75 2 0.01
76 3 0.01
77 5 0.02
78 233 0.74
79 8 0.03
80 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (77 bp):
GTGGGAAGTGCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTATTTGAGAATGAGGGATAT
GATTGGAAGCGA
Found at i:3555284 original size:230 final size:230
Alignment explanation
Indices: 3554954--3555385 Score: 594
Period size: 230 Copynumber: 1.9 Consensus size: 230
3554944 TTGGAAACAT
* * *
3554954 GTGGGAAGTGTCCCTCATGGCCATGTGATACATCAATACCATTTAGTATTTGAGAAGGAGGGATA
1 GTGGGAAGTGCCCCTCATGGCCATGTGATACATCAATACCATCTAGTATTTGAGAAGAAGGGATA
* * * *
3555019 TGATTGGAAGCGTGTGGGAAGTGCCCCTCTTAGCCATATGATGCATCAATATCATCTAGTATTTA
66 TGATTGGAAACGAGTAGGAAGTGCCCCTCTTAGCCATATGATGCATAAATATCATCTAGTATTTA
* * * *
3555084 AGAATGAGGGATATGACTGGAAGTGAGTGGGAAATGCTCTTCTTGGCCATGTGATATATCAATAT
131 AGAATGAGGGATACGACTGGAAGTAAGTGGGAAATGCCCTTCTTGGCCATGTGATACATCAATAT
3555149 CATCTAGTGCTTCGGAGAGATATGATTGGAAGTGA
196 CATCTAGTGCTTCGGAGAGATATGATTGGAAGTGA
* * * * * *
3555184 GTGGGAGGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTTGAGAATAAGGGATA
1 GTGGGAAGTGCCCCTCATGGCCATGTGATACATCAATACCATCTAGTATTTGAGAAGAAGGGATA
* * * * * *
3555249 TGATTGGAAACGAGTAGGAGGTGTCCCTTTTAGCCATGTGATGCATAAATATCATTTAGTATTTG
66 TGATTGGAAACGAGTAGGAAGTGCCCCTCTTAGCCATATGATGCATAAATATCATCTAGTATTTA
** * * * *
3555314 AGAATGAGGGATACGTTTGTAAGTAAGTGGGAAGTGCCCTTTTTGGCCATGTGATGCATCAATAT
131 AGAATGAGGGATACGACTGGAAGTAAGTGGGAAATGCCCTTCTTGGCCATGTGATACATCAATAT
*
3555379 CCTCTAG
196 CATCTAG
3555386 GGATTAGATG
Statistics
Matches: 172, Mismatches: 30, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
230 172 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (230 bp):
GTGGGAAGTGCCCCTCATGGCCATGTGATACATCAATACCATCTAGTATTTGAGAAGAAGGGATA
TGATTGGAAACGAGTAGGAAGTGCCCCTCTTAGCCATATGATGCATAAATATCATCTAGTATTTA
AGAATGAGGGATACGACTGGAAGTAAGTGGGAAATGCCCTTCTTGGCCATGTGATACATCAATAT
CATCTAGTGCTTCGGAGAGATATGATTGGAAGTGA
Found at i:3555300 original size:152 final size:150
Alignment explanation
Indices: 3554973--3555414 Score: 420
Period size: 152 Copynumber: 2.9 Consensus size: 150
3554963 GTCCCTCATG
* * * * * *
3554973 GCCATGTGATACATCAATACCATTTAGTATTTGAGAAGGAGGGATATGATTGGAAGCGTGTGGGA
1 GCCATGTGATACATAAATATCATCTAGTATTCG-G-A-GA--GATATGATTGGAAGTGAGTGGGA
* * * * *
3555038 AGTGCCCCTCTTAGCCATATGATGCATCAATATCATCTAGTATTTAAGAATGAGGGATATGACTG
61 AGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTT-AGAATAAGGGATATGATTG
** * * *
3555103 GAAGTGAGTGGGAAATGCTCTTCTTG
125 GAAACGAGTAGGAAATGCCCTTCTTA
* * * *
3555129 GCCATGTGATATATCAATATCATCTAGTGCTTCGGAGAGATATGATTGGAAGTGAGTGGGAGGTG
1 GCCATGTGATACATAAATATCATCTAGT-ATTCGGAGAGATATGATTGGAAGTGAGTGGGAAGTG
3555194 CCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTTGAGAATAAGGGATATGATTGGAAA
65 CCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTT-AGAATAAGGGATATGATTGGAAA
**
3555259 CGAGTAGGAGGTGTCCCTT-TTA
129 CGAGTAGGAAATG-CCCTTCTTA
* * * * * * *
3555281 GCCATGTGATGCATAAATATCATTTAGTATTTGAGAATGAGGGATACGTTTGTAAGTAAGTGGGA
1 GCCATGTGATACATAAATATCATCTAGTATTCG-G-A-GA--GATATGATTGGAAGTGAGTGGGA
* * * * *
3555346 AGTGCCCTTTTTGGCCATGTGATGCATCAATATCCTCTAGGGATTAG-ATGAAAGGGATATGATT
61 AGTGCCCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTTAGAAT--AAGGGATATGATT
3555410 GGAAA
124 GGAAA
3555415 TATGCGGGCT
Statistics
Matches: 240, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
151 3 0.01
152 118 0.49
153 5 0.02
154 6 0.03
155 3 0.01
156 102 0.43
157 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.30
Consensus pattern (150 bp):
GCCATGTGATACATAAATATCATCTAGTATTCGGAGAGATATGATTGGAAGTGAGTGGGAAGTGC
CCCTCTTGGCCATGTGATGCATCAATATCATCTAGTGTTTAGAATAAGGGATATGATTGGAAACG
AGTAGGAAATGCCCTTCTTA
Found at i:3556055 original size:68 final size:68
Alignment explanation
Indices: 3555976--3556114 Score: 188
Period size: 68 Copynumber: 2.0 Consensus size: 68
3555966 AATGATGTAA
* * *** * * *
3555976 ATGCAAGCATCAATAAAATGGCGGATGCATGTGGAATGATGCAAATACTATTATTATCTAAAATG
1 ATGCAAACATCAATAAAAGGGAAAATGCATATGGAATAATGCAAATACTAATATTATCTAAAATG
3556041 CAG
66 CAG
*
3556044 ATGCAAACATCAATAAAAGGGAAAATGCATATGGAATAATGCAAATACTAATGTTATCTAAAATG
1 ATGCAAACATCAATAAAAGGGAAAATGCATATGGAATAATGCAAATACTAATATTATCTAAAATG
*
3556109 TAG
66 CAG
3556112 ATG
1 ATG
3556115 TAGGTGAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.26
Consensus pattern (68 bp):
ATGCAAACATCAATAAAAGGGAAAATGCATATGGAATAATGCAAATACTAATATTATCTAAAATG
CAG
Found at i:3559614 original size:24 final size:24
Alignment explanation
Indices: 3559587--3559633 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3559577 AAATGACTAT
*
3559587 TTACTTGGAATCGCCACCTATCTG
1 TTACTTGGAATCGCCACCAATCTG
*
3559611 TTACTTGGAGTCGCCACCAATCT
1 TTACTTGGAATCGCCACCAATCT
3559634 ATTTTGGCTG
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:0.21, C:0.30, G:0.17, T:0.32
Consensus pattern (24 bp):
TTACTTGGAATCGCCACCAATCTG
Found at i:3560885 original size:156 final size:156
Alignment explanation
Indices: 3560493--3561203 Score: 764
Period size: 156 Copynumber: 4.6 Consensus size: 156
3560483 GGCTAAGTTA
* * * * *
3560493 AAAAAATTACAAAAATGCCTCTAAGGGATACCTTCGATGT-AGAAGTA-CTCGATACCCCTAAAG
1 AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGA-AAGTATCCCGGTACCCCTAAAG
* * * *
3560556 GACATAAAAAAGATTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAA-GAA
65 GACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAA
* * * * *
3560620 GACCTGGTTATAACTTAAGACTCGGA-TCT
130 -TCC-GATGATAACCTAGGACTC-GATTCT
** * * * * * *
3560649 AAAAAATTATGAAAATACCCTTAGGAGAAACTTTTGATGTGAAAGTATCTCGGTACCCCTAAAGG
1 AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGGTACCCCTAAAGG
* * * *
3560714 ATTTGAAAAGGACTATAAAAGGGGTGAACCTATCCTAAATACCCACCTTTGGCATAAAAACGAAT
66 ACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAAT
* * *
3560779 TCGATGATAACCTAGGACTTGGTTCT
131 CCGATGATAACCTAGGACTCGATTCT
* * * * * * *
3560805 ATAAAATTACTAAAATGCCCCTAGGGGATACCTTTGAAGTGAAAGTATCCCGGTATCCCTAAAAG
1 AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGGTACCCCTAAAGG
* * * ** *
3560870 ACTTAAAAAAGACTATAAAAGGGATGAAGCTATCCTAAATACCCACCTTCAGCATAAAAGTGGAT
66 ACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAAT
* * *
3560935 CCGGTGATAACTTGGGACTCGATTCT
131 CCGATGATAACCTAGGACTCGATTCT
* * * *
3560961 AAAAAATTACAAAAATATCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGATGCCTCTAAAGG
1 AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGGTACCCCTAAAGG
* * ** * * *
3561026 ACTTGAAAAGGACTATAAAAGGTATGAACCTATCCTAAATACCCACCTTCGATATAAAAGCGCAC
66 ACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAAT
* * *
3561091 CCAATGATAACCTAGGACTCTATTTT
131 CCGATGATAACCTAGGACTCGATTCT
* * * * * *
3561117 AAAAAATTACAAAAATACTCTTAGGAGATACCTTCGATATAAAACTATCCCGGTACCCCTAAAGG
1 AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGGTACCCCTAAAGG
*
3561182 GCTTAAAAAGGACTATAAAAGG
66 ACTTAAAAAGGACTATAAAAGG
3561204 ACCAAATTGT
Statistics
Matches: 459, Mismatches: 92, Indels: 8
0.82 0.16 0.01
Matches are distributed among these distances:
155 1 0.00
156 383 0.83
157 72 0.16
158 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (156 bp):
AAAAAATTACAAAAATACCCCTAGGGGATACCTTCGATGTGAAAGTATCCCGGTACCCCTAAAGG
ACTTAAAAAGGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAACGAAT
CCGATGATAACCTAGGACTCGATTCT
Found at i:3561060 original size:312 final size:312
Alignment explanation
Indices: 3560493--3561203 Score: 851
Period size: 312 Copynumber: 2.3 Consensus size: 312
3560483 GGCTAAGTTA
* * * * *
3560493 AAAAAATTACAAAAATGCCTCTAAGGGATACCTTCGATGTAGAAGTA-CTCGATACCCCTAAAGG
1 AAAAAATTACAAAAATGCCCCTAGGGGATACCTTCGAAGTA-AAGTATCCCGGTACCCCTAAAGG
* * **
3560557 ACATAAAAAAGATTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGCATAAAAAGAAGA
65 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAAGAAGA
* ** * *
3560622 CCTGGTTATAACTTAAGACTCGGATCTAAAAAATTATGAAAATACCCTTAGGAGAAACTTTTGAT
130 CCTGGTGATAACTTAAGACTCGGATCTAAAAAATTACAAAAATACCCTTAGGAGAAACCTTCGAT
* * * *
3560687 GTGAAAGTATCTCGGTACCCCTAAAGGATTTGAAAAGGACTATAAAAGGGGTGAACCTATCCTAA
195 GTGAAAGTATCCCGATACCCCTAAAGGACTTGAAAAGGACTATAAAAGGGATGAACCTATCCTAA
* * ** * *
3560752 ATACCCACCTTTGGCATAAAAACGAATTCGATGATAACCTAGGACT-TGGTTCT
260 ATACCCACCTTCGACATAAAAACGAACCCAATGATAACCTAGGACTCT-ATTCT
* * * * *
3560805 ATAAAATTACTAAAATGCCCCTAGGGGATACCTTTGAAGTGAAAGTATCCCGGTATCCCTAAAAG
1 AAAAAATTACAAAAATGCCCCTAGGGGATACCTTCGAAGT-AAAGTATCCCGGTACCCCTAAAGG
* **
3560870 ACTTAAAAAAGACTATAAAAGGGATGAAGCTATCCTAAATACCCACCTTCAGCAT-AAAAGTGGA
65 ACTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAAGAAGA
** * *
3560934 TCC-GGTGATAACTTGGGACTC-GATTCTAAAAAATTACAAAAATATCCC-TAGGGGATACCTTC
130 -CCTGGTGATAACTTAAGACTCGGA-TCTAAAAAATTACAAAAATA-CCCTTAGGAGAAACCTTC
* * *
3560996 GATGTGAAAGTATCCCGATGCCTCTAAAGGACTTGAAAAGGACTATAAAAGGTATGAACCTATCC
192 GATGTGAAAGTATCCCGATACCCCTAAAGGACTTGAAAAGGACTATAAAAGGGATGAACCTATCC
* * * *
3561061 TAAATACCCACCTTCGATATAAAAGCGCACCCAATGATAACCTAGGACTCTATTTT
257 TAAATACCCACCTTCGACATAAAAACGAACCCAATGATAACCTAGGACTCTATTCT
* * * * *
3561117 AAAAAATTACAAAAATACTCTTAGGAGATACCTTCGATA-TAAAACTATCCCGGTACCCCTAAAG
1 AAAAAATTACAAAAATGCCCCTAGGGGATACCTTCGA-AGT-AAAGTATCCCGGTACCCCTAAAG
* *
3561181 GGCTTAAAAAGGACTATAAAAGG
64 GACTTAAAAAAGACTATAAAAGG
3561204 ACCAAATTGT
Statistics
Matches: 336, Mismatches: 56, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
311 2 0.01
312 263 0.78
313 71 0.21
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (312 bp):
AAAAAATTACAAAAATGCCCCTAGGGGATACCTTCGAAGTAAAGTATCCCGGTACCCCTAAAGGA
CTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTCAGCATAAAAAGAAGAC
CTGGTGATAACTTAAGACTCGGATCTAAAAAATTACAAAAATACCCTTAGGAGAAACCTTCGATG
TGAAAGTATCCCGATACCCCTAAAGGACTTGAAAAGGACTATAAAAGGGATGAACCTATCCTAAA
TACCCACCTTCGACATAAAAACGAACCCAATGATAACCTAGGACTCTATTCT
Found at i:3561883 original size:165 final size:167
Alignment explanation
Indices: 3561596--3561995 Score: 510
Period size: 165 Copynumber: 2.4 Consensus size: 167
3561586 AAATATTATG
* * * * *
3561596 AATTTTAAAAA-TAAAAACCCATG-AAAA-CCATCTTAAAAA-ATTTACGGAGTAGAAAACTCCG
1 AATTTTAAAAATTAAAAA-CCAAGAAAAATCCCTC-CAAAAACATTTACGGAGTAAAAAACTCAG
* *** *
3561657 CATTTCAAAAATAGGAGACTTTCAAGGAAAAAATTCAAAAACTCATGAAAATTAATGAATTTTTG
64 TATTTTGGAAATAGGAGACTTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTG
3561722 AAAA-ATAATTTAATATGAATTAAATAATAATATTTCATA
129 AAAACA-AATTTAATATGAATTAAATAATAATATTTCATA
* * * *
3561761 AATTTTAAAAATTAAAAATCAAGAAAAATCCC-CCCAAAACATTTACGGAGTAAAAAATTCTGTA
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAACATTTACGGAGTAAAAAACTCAGTA
** *
3561825 TTTTGGAAATAAGG-GACTTTCAAGGAAAAAA-TCAAAGTCTCATGAAACTGAATGAATTTTTGA
66 TTTTGGAAAT-AGGAGACTTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGA
* * * *
3561888 AAACAGATTTACTATGACTTAAATAATAATATTTGATA
130 AAACAAATTTAATATGAATTAAATAATAATATTTCATA
*
3561926 AATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAACATTTACGGAGTAGAAAACTCAGTA
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAACATTTACGGAGTAAAAAACTCAGTA
3561991 TTTTG
66 TTTTG
3561996 AAAACAAGAG
Statistics
Matches: 203, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
165 109 0.54
166 89 0.44
167 5 0.02
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (167 bp):
AATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCAAAAACATTTACGGAGTAAAAAACTCAGTA
TTTTGGAAATAGGAGACTTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATGAATTTTTGAA
AACAAATTTAATATGAATTAAATAATAATATTTCATA
Found at i:3562088 original size:166 final size:163
Alignment explanation
Indices: 3561630--3562057 Score: 407
Period size: 166 Copynumber: 2.6 Consensus size: 163
3561620 AAACCATCTT
* * * ** * * ** *
3561630 AAAAA-ATTTACGGAGTAGAAAACTCCGCATTTCAAAAATAGGAGACTTTCAAGGAAAAAATTCA
1 AAAAACATTTACGGAGTAAAAAACTCAGTATTTTGAAAACAAGAGAAATTCAAAGAAAAAA-TCA
* * * * * * *
3561694 AAAACTCATGAAAATTAATGAATTTTTGAAAA-ATAATTTAATATGAATTAAATAATAATATTTC
65 AAGACTCA-GAAAATCAAAGAATTTTTGAAAACA-GATTTACTACG-ATTAAATAATAATATTTG
*
3561758 ATAAATTTTAAAAATTAAAAATCAAGAAAAATCCCCC
127 ATAAATTTTAAAAATTAAAAACCAAGAAAAATCCCCC
* * * * * * ** *
3561795 CAAAACATTTACGGAGTAAAAAATTCTGTATTTTGGAAATAAGGGACTTTCAAGGAAAAAATCAA
1 AAAAACATTTACGGAGTAAAAAACTCAGTATTTTGAAAACAAGAGAAATTCAAAGAAAAAATCAA
* * * * *
3561860 AGTCTCATGAAACTGAATGAATTTTTGAAAACAGATTTACTATGACTTAAATAATAATATTTGAT
66 AGACTCA-GAAAATCAAAGAATTTTTGAAAACAGATTTACTACGA-TTAAATAATAATATTTGAT
3561925 AAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCC
129 AAATTTTAAAAATTAAAAACCAAGAAAAATCCC-CC
* *
3561961 AAAAACATTTACGGAGTAGAAAACTCAGTATTTTGAAAACAAGAGAAATTCTAAAG-AAAAATTA
1 AAAAACATTTACGGAGTAAAAAACTCAGTATTTTGAAAACAAGAGAAATTC-AAAGAAAAAATCA
*
3562025 ATA-ACTCA-AAATATACAAAGAATTTTTTAAAAC
65 A-AGACTCAGAAA-AT-CAAAGAATTTTTGAAAAC
3562058 TAATTTGATG
Statistics
Matches: 221, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
164 4 0.02
165 95 0.43
166 118 0.53
167 4 0.02
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (163 bp):
AAAAACATTTACGGAGTAAAAAACTCAGTATTTTGAAAACAAGAGAAATTCAAAGAAAAAATCAA
AGACTCAGAAAATCAAAGAATTTTTGAAAACAGATTTACTACGATTAAATAATAATATTTGATAA
ATTTTAAAAATTAAAAACCAAGAAAAATCCCCC
Found at i:3564207 original size:20 final size:20
Alignment explanation
Indices: 3564138--3564210 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3564128 GCCAAGGAAA
** *
3564138 TGTATCGATACATTAATAAA
1 TGTATCGATACATTTCTAAT
*
3564158 TGTATCGATACATGCTTCAAAT
1 TGTATCGATACAT--TTCTAAT
* *
3564180 TTTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTAAT
3564200 TGTATCGATAC
1 TGTATCGATAC
3564211 TGTGAGCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 28 0.65
22 15 0.35
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTCTAAT
Found at i:3565027 original size:13 final size:13
Alignment explanation
Indices: 3565009--3565034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3564999 CTATTTATGA
3565009 TGTATCGATACAC
1 TGTATCGATACAC
3565022 TGTATCGATACAC
1 TGTATCGATACAC
3565035 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3565151 original size:21 final size:22
Alignment explanation
Indices: 3565121--3565176 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
3565111 ACAGTGACCT
3565121 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3565143 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3565164 ATGAACAGTGATG
1 ATGAACAGTGATG
3565177 AATAGTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:3565183 original size:10 final size:10
Alignment explanation
Indices: 3565164--3565193 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3565154 GTATCGATAC
3565164 ATGAACAGTG
1 ATGAACAGTG
*
3565174 ATGAATAGTG
1 ATGAACAGTG
3565184 ATGAACAGTG
1 ATGAACAGTG
3565194 GAAAATGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:3565293 original size:53 final size:53
Alignment explanation
Indices: 3565219--3565355 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
3565209 CTACTTCCAA
* *
3565219 TGTATCGATACATATTTTGTGTATCGATACAGATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
3565272 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
3565325 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATA-TTGTGTGTATCGATAC
3565356 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 64 0.80
54 16 0.20
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:3565388 original size:20 final size:20
Alignment explanation
Indices: 3565325--3565395 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3565315 GCCAATGTCC
**
3565325 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
3565345 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
3565365 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
3565385 TGTATCGATAC
1 TGTATCGATAC
3565396 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:3565461 original size:21 final size:21
Alignment explanation
Indices: 3565435--3565475 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3565425 GTCAACCTTG
3565435 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
3565456 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
3565476 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:3566339 original size:79 final size:79
Alignment explanation
Indices: 3566169--3566351 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 79
3566159 TATGTACCTC
* * *
3566169 TTTCTGAGGGGATACTCCAACCCCATTTTTATTTCCAAAATATTACCATTTTCATCTCGAGGATA
1 TTTCCGAGGGGATACTCCAACCCCATTTTTATTTCCAAAATATTACCATTTTCATATCAAGGATA
*
3566234 CTCCAACCCCTTTA
66 CTCCAACCCCATTA
** * * * * * *
3566248 TTTTTGAAGGGATACTCTAACCTCGTTTTTATTTCTAAAATA-T-CGATTTTTCACTATCAAGGA
1 TTTCCGAGGGGATACTCCAACCCCATTTTTATTTCCAAAATATTACCA-TTTTCA-TATCAAGGA
3566311 TACTCCAACCCCATTA
64 TACTCCAACCCCATTA
* *
3566327 TTTCCGTGGGGATACTCGAACCCCA
1 TTTCCGAGGGGATACTCCAACCCCA
3566352 ACTTTTACCA
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
77 2 0.02
78 7 0.08
79 76 0.89
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTCCGAGGGGATACTCCAACCCCATTTTTATTTCCAAAATATTACCATTTTCATATCAAGGATA
CTCCAACCCCATTA
Found at i:3568513 original size:13 final size:13
Alignment explanation
Indices: 3568495--3568520 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3568485 CAATTTTTGG
3568495 TGTATCGATACAT
1 TGTATCGATACAT
3568508 TGTATCGATACAT
1 TGTATCGATACAT
3568521 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3568532 original size:32 final size:33
Alignment explanation
Indices: 3568475--3568538 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3568465 TACAAGCCAA
**
3568475 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
3568508 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
3568539 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:3568545 original size:19 final size:18
Alignment explanation
Indices: 3568475--3568545 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
3568465 TACAAGCCAA
3568475 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
3568495 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
3568508 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
3568527 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
3568546 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:3570109 original size:13 final size:13
Alignment explanation
Indices: 3570091--3570116 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3570081 ATAATCACCC
3570091 TGTATCGATACAA
1 TGTATCGATACAA
3570104 TGTATCGATACAA
1 TGTATCGATACAA
3570117 AGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3572205 original size:15 final size:15
Alignment explanation
Indices: 3572185--3572215 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3572175 ATTTCGTTTG
*
3572185 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3572200 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3572215 G
1 G
3572216 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3574047 original size:21 final size:21
Alignment explanation
Indices: 3574018--3574062 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3574008 AAGTTTTTAT
*
3574018 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3574038 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3574060 TTT
1 TTT
3574063 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Done.