Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 115 of 292
Found at i:34979590 original size:20 final size:20
Alignment explanation
Indices: 34979538--34979591 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
34979528 GCTGAAAGTA
*
34979538 AGCTCAATTGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
**
34979558 AGCTGAAACGAGCTCAAATG
1 AGCTGAATTGAGCTCAAATG
*
34979578 AGCTGAGTTGAGCT
1 AGCTGAATTGAGCT
34979592 GGACGGAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (20 bp):
AGCTGAATTGAGCTCAAATG
Found at i:34980749 original size:32 final size:33
Alignment explanation
Indices: 34980694--34980756 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
34980684 AATTCGGCCA
* * *
34980694 CCAGTAGCTTCATTTAATCCGTCAACTAGCAGC
1 CCAGCAGCTTCATTAAATCCGTCAACCAGCAGC
*
34980727 CCAGCAGCTT-ATTAAATTCGTCAACCAGCA
1 CCAGCAGCTTCATTAAATCCGTCAACCAGCA
34980757 TGCTCTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (33 bp):
CCAGCAGCTTCATTAAATCCGTCAACCAGCAGC
Found at i:34985136 original size:32 final size:32
Alignment explanation
Indices: 34985095--34985159 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
34985085 AGCTTGTCCA
34985095 TGTTCGGCTGCACCTTCATCCAAATAGTCACC
1 TGTTCGGCTGCACCTTCATCCAAATAGTCACC
34985127 TGTTCGGCTGCACCTTCATCCAAATAGTCACC
1 TGTTCGGCTGCACCTTCATCCAAATAGTCACC
34985159 T
1 T
34985160 TTATGGCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTTCGGCTGCACCTTCATCCAAATAGTCACC
Found at i:34985199 original size:11 final size:11
Alignment explanation
Indices: 34985185--34985212 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
34985175 GGGAGATGAA
34985185 TGAACAAGGTG
1 TGAACAAGGTG
34985196 TGAACAAGGTG
1 TGAACAAGGTG
34985207 TGAACA
1 TGAACA
34985213 TGTTGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (11 bp):
TGAACAAGGTG
Found at i:34992768 original size:13 final size:12
Alignment explanation
Indices: 34992751--34992795 Score: 81
Period size: 12 Copynumber: 3.7 Consensus size: 12
34992741 ATCGCTCTTT
34992751 TTTTTTTTCGAA
1 TTTTTTTTCGAA
34992763 TTTTTTTTCGAA
1 TTTTTTTTCGAA
34992775 TTTTTTTTCGAAA
1 TTTTTTTTCG-AA
34992788 TTTTTTTT
1 TTTTTTTT
34992796 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 22 0.69
13 10 0.31
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:34992802 original size:24 final size:24
Alignment explanation
Indices: 34992749--34992804 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
34992739 AAATCGCTCT
34992749 TTTTTTTTTTCGAATTTTTTTTCGA
1 TTTTTTTTTTCGAATTTTTTTTC-A
*
34992774 -ATTTTTTTTCGAAATTTTTTTT-A
1 TTTTTTTTTTCG-AATTTTTTTTCA
34992797 TTTTTTTT
1 TTTTTTTT
34992805 AACTTGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.59
25 10 0.37
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.75
Consensus pattern (24 bp):
TTTTTTTTTTCGAATTTTTTTTCA
Found at i:34993218 original size:14 final size:14
Alignment explanation
Indices: 34993171--34993218 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
34993161 GTACGAATGG
*
34993171 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
34993185 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
34993199 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
34993213 ATTGGT
1 AATGGT
34993219 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:34994492 original size:19 final size:19
Alignment explanation
Indices: 34994455--34994494 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
34994445 CGTGAGCTGA
*
34994455 TAATGAGCTGGTTCTGAGC
1 TAATGAGCTGGTTCGGAGC
34994474 TAATGAGCTGGTGT-GGAGC
1 TAATGAGCTGGT-TCGGAGC
34994493 TA
1 TA
34994495 CATGGGAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (19 bp):
TAATGAGCTGGTTCGGAGC
Found at i:34997239 original size:38 final size:38
Alignment explanation
Indices: 34997195--34997272 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
34997185 CAAATGGGGT
34997195 TAATGGTTTCTCATAAGTCTTTTTCAAATGGCCCTTCA
1 TAATGGTTTCTCATAAGTCTTTTTCAAATGGCCCTTCA
*
34997233 TAATGGTTTCTCGTAAGTCTTTTTCAAATGGCCCTTCA
1 TAATGGTTTCTCATAAGTCTTTTTCAAATGGCCCTTCA
34997271 TA
1 TA
34997273 CTTCGCATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (38 bp):
TAATGGTTTCTCATAAGTCTTTTTCAAATGGCCCTTCA
Found at i:34999010 original size:18 final size:18
Alignment explanation
Indices: 34998989--34999034 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
34998979 TCATACTCAC
34998989 TTTCTTTTTCAATTT-TCT
1 TTTCTTTTTCAATTTCT-T
**
34999007 TTTCTTGATCAATTTCTT
1 TTTCTTTTTCAATTTCTT
34999025 TTTCTTTTTC
1 TTTCTTTTTC
34999035 TTTTTCAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCTTTTTCAATTTCTT
Found at i:34999022 original size:24 final size:24
Alignment explanation
Indices: 34998995--34999057 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
34998985 TCACTTTCTT
*
34998995 TTTCAATTTTCTTTTCTTGATCAA
1 TTTCATTTTTCTTTTCTTGATCAA
**
34999019 TTTC-TTTTTCTTTTTCTTTTTCAA
1 TTTCATTTTTC-TTTTCTTGATCAA
34999043 TTTCATTTTTCTTTT
1 TTTCATTTTTCTTTT
34999058 TCTCACTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.15
24 23 0.68
25 6 0.18
ACGTcount: A:0.13, C:0.16, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTCATTTTTCTTTTCTTGATCAA
Found at i:34999038 original size:5 final size:6
Alignment explanation
Indices: 34999019--34999060 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
34999009 TCTTGATCAA
**
34999019 TTTCTT TTTCTT TTTCTT TTTCAA TTTCATT TTTCTT TTTCT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCT
34999061 CACTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:34999124 original size:33 final size:34
Alignment explanation
Indices: 34999051--34999124 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
34999041 AATTTCATTT
*
34999051 TTCTTTTTCTCACTTTCTTTTTGATCTCTTTCACA
1 TTCTTTTTCTCACTTTCTTTTT-ATCTCTTTCAAA
* *
34999086 CTCTTTTTCTCTCATTTCTTTTT-T-TCTTTCAAA
1 TTCTTTTTCTCAC-TTTCTTTTTATCTCTTTCAAA
34999119 TTCTTT
1 TTCTTT
34999125 CTCACATGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 13 0.38
34 1 0.03
35 11 0.32
36 9 0.26
ACGTcount: A:0.11, C:0.24, G:0.01, T:0.64
Consensus pattern (34 bp):
TTCTTTTTCTCACTTTCTTTTTATCTCTTTCAAA
Found at i:34999596 original size:22 final size:21
Alignment explanation
Indices: 34999563--34999604 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
34999553 TCAAACCTAC
34999563 ACAAGCATGCAAAATTTACACA
1 ACAAGCATGCAAAA-TTACACA
*
34999585 ACAAGGCA-GCAACATTACAC
1 ACAA-GCATGCAAAATTACAC
34999605 CACCATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
ACAAGCATGCAAAATTACACA
Found at i:35000177 original size:18 final size:18
Alignment explanation
Indices: 35000152--35000196 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
35000142 CTTTTTTAAT
35000152 TTTC-TTTTCTTGATCAA
1 TTTCTTTTTCTTGATCAA
** *
35000169 TTTCTTTTTCTTTTTCAC
1 TTTCTTTTTCTTGATCAA
35000187 TTTCTTTTTC
1 TTTCTTTTTC
35000197 AATCTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTCTTTTTCTTGATCAA
Found at i:35002721 original size:10 final size:10
Alignment explanation
Indices: 35002703--35002753 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
35002693 AAATGAAAAA
*
35002703 GAAATGAGCT
1 GAAACGAGCT
35002713 GAAACGAGCT
1 GAAACGAGCT
* *
35002723 AAAATCAAGCT
1 GAAA-CGAGCT
*
35002734 CAAACGAGCT
1 GAAACGAGCT
35002744 GAAACGAGCT
1 GAAACGAGCT
35002754 CAAGTGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (10 bp):
GAAACGAGCT
Found at i:35004755 original size:30 final size:30
Alignment explanation
Indices: 35004719--35004816 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
35004709 AGCTCACTCC
*
35004719 TAGCTCATATTCAGCTCACAAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
35004749 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* *
35004779 TAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
35004809 TAGCTCAT
1 TAGCTCAT
35004817 TTTAGTTTAA
Statistics
Matches: 51, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:35007979 original size:10 final size:10
Alignment explanation
Indices: 35007964--35008010 Score: 85
Period size: 10 Copynumber: 4.7 Consensus size: 10
35007954 GTTCGTAAGT
35007964 AAAAAAATTC
1 AAAAAAATTC
35007974 AAAAAAATTC
1 AAAAAAATTC
35007984 AAAAAAATTC
1 AAAAAAATTC
*
35007994 AAAAAAATTT
1 AAAAAAATTC
35008004 AAAAAAA
1 AAAAAAA
35008011 AGTGTGTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:35010925 original size:15 final size:15
Alignment explanation
Indices: 35010886--35010930 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
35010876 GAAGTCTAGA
*
35010886 ATAAGGAAATCCAAG
1 ATAAGGAAATCCATG
**
35010901 ATAAAAAAATCCATG
1 ATAAGGAAATCCATG
35010916 ATAAGGAAATTCCAT
1 ATAAGGAAA-TCCAT
35010931 TTACAGCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
ATAAGGAAATCCATG
Found at i:35019699 original size:30 final size:30
Alignment explanation
Indices: 35019623--35019708 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
35019613 TTCAGCTCAC
* *
35019623 GAGCTAAACCTTAGCTGAACTTCAGCTTAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTTAG
* *
35019653 GAG-TATAATCTCAGCTCAACTTTAGCTTAAG
1 GAGCTA-AACCTTAGCTCAACTTTAGCTT-AG
* *
35019684 G-GCTAAAGCTTAGCTC-ATTTTAGCT
1 GAGCTAAACCTTAGCTCAACTTTAGCT
35019709 CAAACTCGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 10 0.22
30 31 0.67
31 5 0.11
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (30 bp):
GAGCTAAACCTTAGCTCAACTTTAGCTTAG
Found at i:35024350 original size:30 final size:30
Alignment explanation
Indices: 35024265--35024352 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
35024255 TGAGCTAAAA
* *
35024265 TGAGCTAAGCTTTAGC-CCTTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCC-TAAGCTGAAGT
*
35024295 TGAGCTGAGATTATA-CTCCTAAGCTGAAGT
1 TGAGCTAAGATT-TAGCTCCTAAGCTGAAGT
* * *
35024325 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCCTAAGCTGAA
35024353 TATAAGCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 2 0.04
30 42 0.88
31 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCCTAAGCTGAAGT
Found at i:35024400 original size:30 final size:30
Alignment explanation
Indices: 35024366--35024433 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
35024356 AAGCTAGGAG
35024366 TGAGCTCGGTTTAGCTCAGACAAGTTGGAT
1 TGAGCTCGGTTTAGCTCAGACAAGTTGGAT
35024396 TGAGCTCGGTTTAGCTCAGACAAGTTGGAT
1 TGAGCTCGGTTTAGCTCAGACAAGTTGGAT
35024426 TGAGCTCG
1 TGAGCTCG
35024434 AATAAGCTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (30 bp):
TGAGCTCGGTTTAGCTCAGACAAGTTGGAT
Found at i:35024923 original size:13 final size:13
Alignment explanation
Indices: 35024905--35024939 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
35024895 GGCTGAACCT
35024905 ACATAATTAAATA
1 ACATAATTAAATA
35024918 ACATAATTAAATA
1 ACATAATTAAATA
*
35024931 AAATAATTA
1 ACATAATTA
35024940 TTCATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:35025204 original size:20 final size:19
Alignment explanation
Indices: 35025154--35025213 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 19
35025144 AATGTAAAAG
* *
35025154 AAATGAGCTGAAACGAGCT
1 AAATGAGCTCAAGCGAGCT
35025173 AAATTTGAGCTCAAGCGAGCT
1 AAA--TGAGCTCAAGCGAGCT
*
35025194 AAATCGAGCTCAAGTGAGCT
1 AAAT-GAGCTCAAGCGAGCT
35025214 GATTGGATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 4 0.11
20 14 0.40
21 17 0.49
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (19 bp):
AAATGAGCTCAAGCGAGCT
Found at i:35031795 original size:20 final size:20
Alignment explanation
Indices: 35031772--35031819 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
35031762 AGCTCCGTCT
35031772 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
35031792 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
35031812 AGCTCAAC
1 AGCTCAAC
35031820 CGAGCTGACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:35032053 original size:20 final size:21
Alignment explanation
Indices: 35032010--35032061 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
35032000 AGCTCCGTCC
*
35032010 AGCTCAAATCCAGCTTGTTCG
1 AGCTCAAATCCAACTTGTTCG
35032031 AGCTC-AATCCAACTTGCTT-G
1 AGCTCAAATCCAACTTG-TTCG
35032051 AGCT-AAA-CCAA
1 AGCTCAAATCCAA
35032062 GCTCACTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 17 0.61
21 7 0.25
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
AGCTCAAATCCAACTTGTTCG
Found at i:35033500 original size:30 final size:30
Alignment explanation
Indices: 35033414--35033501 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
35033404 CTAGCTTACT
* *
35033414 TTCAACTCACGAGCTAAACCTTAGCTCAAC
1 TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
* * ** *
35033444 TTCAGCTTAGGAG-TTTAGCCTCAGCTCAAC
1 TTCAGCTCACGAGCTAAAG-CTTAGCTCAAC
*
35033474 TTTAGCTCACGAGCTAAAGCTTAGCTCA
1 TTCAGCTCACGAGCTAAAGCTTAGCTCA
35033502 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 38 0.88
31 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
TTCAGCTCACGAGCTAAAGCTTAGCTCAAC
Found at i:35037355 original size:21 final size:21
Alignment explanation
Indices: 35037331--35037398 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
35037321 GATTTTGAAT
35037331 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
35037352 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
35037373 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
35037394 GAAAT
1 GAAAT
35037399 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:35037371 original size:42 final size:42
Alignment explanation
Indices: 35037309--35037405 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
35037299 AGATTATGAG
* * *
35037309 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
35037351 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
35037393 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
35037406 AAAGAAAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:35041660 original size:10 final size:10
Alignment explanation
Indices: 35041647--35041682 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
35041637 AGCTCAACAC
35041647 AGCTCATTTG
1 AGCTCATTTG
* *
35041657 AGCTCGTTTC
1 AGCTCATTTG
35041667 AGCTCATTTG
1 AGCTCATTTG
35041677 AGCTCA
1 AGCTCA
35041683 ATCGAGCTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (10 bp):
AGCTCATTTG
Found at i:35041660 original size:20 final size:20
Alignment explanation
Indices: 35041637--35041683 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35041627 AGCTCCGTCC
35041637 AGCTCAACACAGCTCATTTG
1 AGCTCAACACAGCTCATTTG
****
35041657 AGCTCGTTTCAGCTCATTTG
1 AGCTCAACACAGCTCATTTG
35041677 AGCTCAA
1 AGCTCAA
35041684 TCGAGCTTAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (20 bp):
AGCTCAACACAGCTCATTTG
Found at i:35041690 original size:20 final size:20
Alignment explanation
Indices: 35041646--35041690 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35041636 CAGCTCAACA
**
35041646 CAGCTCATTTGAGCTCGTTT
1 CAGCTCATTTGAGCTCGAAT
35041666 CAGCTCATTTGAGCTC-AAT
1 CAGCTCATTTGAGCTCGAAT
35041685 CGAGCT
1 C-AGCT
35041691 TACTTTCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (20 bp):
CAGCTCATTTGAGCTCGAAT
Found at i:35044547 original size:29 final size:29
Alignment explanation
Indices: 35044515--35044592 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
35044505 ATACCCTCCG
** *
35044515 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
35044544 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
35044573 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
35044593 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:35052421 original size:29 final size:29
Alignment explanation
Indices: 35052356--35052428 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
35052346 CCCTCGAGCT
** * * *
35052356 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
35052385 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
35052414 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
35052429 GATCTCGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:35055119 original size:29 final size:29
Alignment explanation
Indices: 35055087--35055164 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
35055077 ATACCCTCCG
* *
35055087 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
35055116 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
35055145 AGCACGCACACTTAGTGCCA
1 AGCTCGCACACCCAGTGCCA
35055165 CGATCTCGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCATATATTTCC
Found at i:35062483 original size:517 final size:521
Alignment explanation
Indices: 35061472--35062511 Score: 2052
Period size: 517 Copynumber: 2.0 Consensus size: 521
35061462 AACCGAGACC
35061472 ATCGCCGGTGTCGGACACGAGGGGTTAACGAGACAAATCCTCTTAAAGTACCGACCAATTTGGCA
1 ATCGCCGGTGTCGGACACGAGGGGTTAACGAGACAAATCCTCTTAAAGTACCGACCAATTTGGCA
35061537 TTTCTGGACAGGCTGGAAAACTGCGTCACCGTCGCCTTAAAAATCATATCTCGAGTTTCAAAACT
66 TTTCTGGACAGGCTGGAAAACTGCGTCACCGTCGCCTTAAAAATCATATCTCGAGTTTCAAAACT
35061602 CGGAAACTGGTTTCGTAAATTTTCCCTGAATTTAGACTCATATACCCATCCATGGATTTATTTTT
131 CGGAAACTGGTTTCGTAAATTTTCCCTGAATTTAGACTCATATACCCATCCATGGATTTATTTTT
35061667 AGAATTTTTGGTTGGGCCAATTGGTACAGTTTATTAGTTAAAGTCACCCATGTTACAGGGATCGA
196 AGAATTTTTGGTTGGGCCAATTGGTACAGTTTATTAGTTAAAGTCACCCATGTTACAGGGATCGA
35061732 CTGCTCTGACCTTCGCGCGTTACAACTTGAATATCTCTCTGTACAGGGCTTTAATACTGGTGCCG
261 CTGCTCTGACCTTCGCGCGTTACAACTTGAATATCTCTCTGTACAGGGCTTTAATACTGGTGCCG
35061797 TTTGTTTCTAATGAAACTAGACTCAAAATGGAATCTGTACATATAAGGCATGACTCCTAATTCTT
326 TTTGTTTCTAATGAAACTAGACTCAAAATGGAATCTGTACATATAAGGCATGACTCCTAATTCTT
35061862 TCTGGATAATTTATGGTAAATTTTCAAAGTCGCGACAGGGGACCCAGAAACCGTTCTGGCCCTGT
391 TCTGGATAATTTATGGTAAATTTTCAAAGTCGCGACAGGGGACCCAGAAACCGTTCTGGCCCTGT
35061927 CTCACGAGAACTTTAATATTTCTCAGTATACTGCTCATATGGTCGTTTCGTTTCGTCCATATAAA
456 CTCACGAGAACTTTAATATTTCTCAGTATACTGCTCATATGGTCGTTTCGTTTCGTCCATATAAA
35061992 A
521 A
35061993 ATCGCCGGTGTCGGACACGAGGGGTTAACGAGAC-AATCCTCTTAAAGTACCGACCAATTTGGCA
1 ATCGCCGGTGTCGGACACGAGGGGTTAACGAGACAAATCCTCTTAAAGTACCGACCAATTTGGCA
35062057 TTTCTGGACAGGCTGGAAAACTGCGTCACCGTCGCCTT-AAAATCATATCTCGAGTTTCAAAACT
66 TTTCTGGACAGGCTGGAAAACTGCGTCACCGTCGCCTTAAAAATCATATCTCGAGTTTCAAAACT
35062121 C-GAAACTGGTTTCGTAAATTTTCCCTGAATTTAGACTCATATACCCATCCATGGATTTATTTTT
131 CGGAAACTGGTTTCGTAAATTTTCCCTGAATTTAGACTCATATACCCATCCATGGATTTATTTTT
35062185 AGAATTTTTGGTTGGG-CAATTGGTACAGTTTATTAGTTAAAGTCACCCATGTTACAGGGATCGA
196 AGAATTTTTGGTTGGGCCAATTGGTACAGTTTATTAGTTAAAGTCACCCATGTTACAGGGATCGA
35062249 CTGCTCTGACCTTCGCGCGTTACAACTTGAATATCTCTCTGTACAGGGCTTTAATACTGGTGCCG
261 CTGCTCTGACCTTCGCGCGTTACAACTTGAATATCTCTCTGTACAGGGCTTTAATACTGGTGCCG
35062314 TTTGTTTCTAATGAAACTAGACTCAAAATGGAATCTGTACATATAAGGCATGACTCCTAATTCTT
326 TTTGTTTCTAATGAAACTAGACTCAAAATGGAATCTGTACATATAAGGCATGACTCCTAATTCTT
35062379 TCTGGATAATTTATGGTAAATTTTCAAAGTCGCGACAGGGGACCCAGAAACCGTTCTGGCCCTGT
391 TCTGGATAATTTATGGTAAATTTTCAAAGTCGCGACAGGGGACCCAGAAACCGTTCTGGCCCTGT
35062444 CTCACGAGAACTTTAATATTTCTCAGTATACTGCTCATATGGTCGTTTCGTTTCGTCCATATAAA
456 CTCACGAGAACTTTAATATTTCTCAGTATACTGCTCATATGGTCGTTTCGTTTCGTCCATATAAA
35062509 A
521 A
35062510 AT
1 AT
35062512 AGATTCATCA
Statistics
Matches: 519, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
517 311 0.60
518 79 0.15
519 27 0.05
520 68 0.13
521 34 0.07
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (521 bp):
ATCGCCGGTGTCGGACACGAGGGGTTAACGAGACAAATCCTCTTAAAGTACCGACCAATTTGGCA
TTTCTGGACAGGCTGGAAAACTGCGTCACCGTCGCCTTAAAAATCATATCTCGAGTTTCAAAACT
CGGAAACTGGTTTCGTAAATTTTCCCTGAATTTAGACTCATATACCCATCCATGGATTTATTTTT
AGAATTTTTGGTTGGGCCAATTGGTACAGTTTATTAGTTAAAGTCACCCATGTTACAGGGATCGA
CTGCTCTGACCTTCGCGCGTTACAACTTGAATATCTCTCTGTACAGGGCTTTAATACTGGTGCCG
TTTGTTTCTAATGAAACTAGACTCAAAATGGAATCTGTACATATAAGGCATGACTCCTAATTCTT
TCTGGATAATTTATGGTAAATTTTCAAAGTCGCGACAGGGGACCCAGAAACCGTTCTGGCCCTGT
CTCACGAGAACTTTAATATTTCTCAGTATACTGCTCATATGGTCGTTTCGTTTCGTCCATATAAA
A
Found at i:35063441 original size:29 final size:29
Alignment explanation
Indices: 35063409--35063486 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
35063399 ATACCCTCCG
** *
35063409 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
35063438 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
35063467 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
35063487 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:35071288 original size:29 final size:29
Alignment explanation
Indices: 35071256--35071316 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
35071246 ATACCCTCCG
* *
35071256 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
* **
35071285 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACCCAGTGCCATATATTTCC
35071314 AGC
1 AGC
35071317 AGCACACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACCCAGTGCCATATATTTCC
Found at i:35071330 original size:28 final size:29
Alignment explanation
Indices: 35071269--35071331 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
35071259 TCGCACACCC
* * *
35071269 AGTGCCGTATTTTTCCAGCTTGCACACTT
1 AGTGCCATATATTTCCAGCTAGCACACTT
35071298 AGTGCCATATATTTCCAGC-AGCACACTT
1 AGTGCCATATATTTCCAGCTAGCACACTT
35071326 AGTGCC
1 AGTGCC
35071332 GATCTCGTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCTAGCACACTT
Found at i:35074666 original size:12 final size:12
Alignment explanation
Indices: 35074649--35074704 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
35074639 CTCTCTCAAA
35074649 CTCTTTTTCATT
1 CTCTTTTTCATT
35074661 CTCTTTTTCAATT
1 CTCTTTTTC-ATT
*
35074674 -TCTTTTTCAAT
1 CTCTTTTTCATT
* *
35074685 CTCATTTTCACT
1 CTCTTTTTCATT
35074697 CTCTTTTT
1 CTCTTTTT
35074705 TTTCTTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.87
13 3 0.08
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:35074676 original size:36 final size:36
Alignment explanation
Indices: 35074636--35074704 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
35074626 TCAACTTCTT
* *
35074636 TTTCTCTCTCAAACTCTTTTTCATTCTCTTTTTCAA
1 TTTCTCTCTCAAACTCATTTTCACTCTCTTTTTCAA
* * *
35074672 TTTCTTTTTCAATCTCATTTTCACTCTCTTTTT
1 TTTCTCTCTCAAACTCATTTTCACTCTCTTTTT
35074705 TTTCTTTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.59
Consensus pattern (36 bp):
TTTCTCTCTCAAACTCATTTTCACTCTCTTTTTCAA
Found at i:35074677 original size:24 final size:24
Alignment explanation
Indices: 35074644--35074704 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
35074634 TTTTTCTCTC
* * *
35074644 TCAAACTCTTTTTCATTCTCTTTT
1 TCAATCTCTTTTTCAATCTCATTT
*
35074668 TCAATTTCTTTTTCAATCTCATTT
1 TCAATCTCTTTTTCAATCTCATTT
*
35074692 TCACTCTCTTTTT
1 TCAATCTCTTTTT
35074705 TTTCTTTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (24 bp):
TCAATCTCTTTTTCAATCTCATTT
Found at i:35075997 original size:30 final size:30
Alignment explanation
Indices: 35075975--35076059 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 30
35075965 GCTCATATTC
35075975 AGCTCACGAGCTAAACCTTAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
* * * * * *
35076005 AGCTTAGGAGTTTAATCTCAGCTCAACTTT
1 AGCTCACGAGCTAAACCTTAGCTCAACTTT
*
35076035 AGCTCACGAGCTAAAGCTTAGCTCA
1 AGCTCACGAGCTAAACCTTAGCTCA
35076060 TTTTAGTTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (30 bp):
AGCTCACGAGCTAAACCTTAGCTCAACTTT
Found at i:35083645 original size:55 final size:53
Alignment explanation
Indices: 35083558--35083767 Score: 217
Period size: 55 Copynumber: 3.9 Consensus size: 53
35083548 ATTAGGGTTT
* *
35083558 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATATCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * *
35083613 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATATCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
** * * *
35083668 AAAGG-TCCCATGTAAGATCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGC
1 -AAGGATATCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* * **
35083721 AAGGATATGATGTAAGACCATGTCAAGACATGGCAAAGGTAAGTTTC
1 AAGGATATCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC
35083768 AAAAGGATAC
Statistics
Matches: 125, Mismatches: 24, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
52 5 0.04
53 38 0.30
54 11 0.09
55 67 0.54
56 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGGATATCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:35083764 original size:108 final size:110
Alignment explanation
Indices: 35083565--35083765 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
35083555 TTTAAGGATA
35083565 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
**
35083630 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAAAGATAAGTTACTATAAGGCAAAGGTC
* * * *
35083675 CCATGTAAGATCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATATGATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAATCATGTAAG
*
35083737 ACCATGTCAAGACATGGCAAAGGTAAGTT
65 ACCATGTCAAGACATGGCAAAGATAAGTT
35083766 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
CCATGTCAAGACATGGCAAAGATAAGTTACTATAAGGCAAAGGTC
Found at i:35085734 original size:30 final size:30
Alignment explanation
Indices: 35085639--35085736 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
35085629 TTAAACTAAA
* *
35085639 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAA-T
* * * * * * *
35085670 -TGAGCTGAGATTAAACTCCTAAGTTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
* *
35085699 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
35085729 ATGAGCTA
1 ATGAGCTA
35085737 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 18, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAT
Found at i:35088041 original size:30 final size:30
Alignment explanation
Indices: 35087970--35088052 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
35087960 CTTTTGTTTC
* *
35087970 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
35088001 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
35088030 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
35088053 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:35088052 original size:18 final size:18
Alignment explanation
Indices: 35088003--35088058 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
35087993 CACTCTCAAA
* *
35088003 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
35088020 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
35088038 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
35088057 TT
1 TT
35088059 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:35088059 original size:12 final size:12
Alignment explanation
Indices: 35088028--35088052 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35088018 TTTTTCAATC
35088028 TCATTTTCTTTT
1 TCATTTTCTTTT
35088040 TCATTTTCTTTT
1 TCATTTTCTTTT
35088052 T
1 T
35088053 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:35089071 original size:13 final size:13
Alignment explanation
Indices: 35089053--35089085 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
35089043 CATTAAACAC
*
35089053 TTTTTTTTCAAAT
1 TTTTTTTTCAAAA
35089066 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
35089079 TTTTTTT
1 TTTTTTT
35089086 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:35089072 original size:14 final size:14
Alignment explanation
Indices: 35089053--35089085 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
35089043 CATTAAACAC
35089053 TTTTTTTTC-AAAT
1 TTTTTTTTCAAAAT
35089066 TTTTTTTTCAAAAT
1 TTTTTTTTCAAAAT
35089080 TTTTTT
1 TTTTTT
35089086 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTTTCAAAAT
Found at i:35089107 original size:11 final size:11
Alignment explanation
Indices: 35089079--35089107 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
35089069 TTTTTCAAAA
35089079 TTTTTTTGAAT
1 TTTTTTTGAAT
35089090 TTTTTTTGAAT
1 TTTTTTTGAAT
35089101 TTTTTTT
1 TTTTTTT
35089108 TGACTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:35089108 original size:12 final size:12
Alignment explanation
Indices: 35089053--35089110 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
35089043 CATTAAACAC
**
35089053 TTTTTTTTCAAA
1 TTTTTTTTTGAA
*
35089065 TTTTTTTTTCAA
1 TTTTTTTTTGAA
**
35089077 AATTTTTTTGAA
1 TTTTTTTTTGAA
35089089 -TTTTTTTTGAA
1 TTTTTTTTTGAA
35089100 TTTTTTTTTGA
1 TTTTTTTTTGA
35089111 CTTGTATAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:35090736 original size:30 final size:30
Alignment explanation
Indices: 35090702--35090784 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 30
35090692 TAAACTAAAA
* *
35090702 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
35090732 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
35090762 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGATTTAGCTCGTGAG
35090785 AATATGAGCT
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:35094803 original size:30 final size:30
Alignment explanation
Indices: 35094767--35094827 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35094757 TCCTTAACTC
35094767 AAACTTTAGAAAAATTACAATTTTACCCCT
1 AAACTTTAGAAAAATTACAATTTTACCCCT
* * * * *
35094797 AAACTTTTGCATATTTACACTTTTACCCCT
1 AAACTTTAGAAAAATTACAATTTTACCCCT
35094827 A
1 A
35094828 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTACCCCT
Found at i:35098766 original size:14 final size:15
Alignment explanation
Indices: 35098747--35098796 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
35098737 GCAATCCATT
*
35098747 AAAAGAGA-AAAAGA
1 AAAAGAGACAAAACA
*
35098761 AAAAGA-ACAAAATA
1 AAAAGAGACAAAACA
* *
35098775 AAAAGAAAGAAAACA
1 AAAAGAGACAAAACA
35098790 AAAAGAG
1 AAAAGAG
35098797 TGGAAAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 1 0.03
14 17 0.57
15 12 0.40
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAGAGACAAAACA
Found at i:35098779 original size:20 final size:20
Alignment explanation
Indices: 35098754--35098792 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35098744 ATTAAAAGAG
35098754 AAAAAGAAA-AAGAACAAAAT
1 AAAAAGAAAGAA-AACAAAAT
35098774 AAAAAGAAAGAAAACAAAA
1 AAAAAGAAAGAAAACAAAA
35098793 AGAGTGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAAAGAAAGAAAACAAAAT
Found at i:35102463 original size:5 final size:5
Alignment explanation
Indices: 35102453--35102508 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
35102443 AAGAGAAAAT
*
35102453 AAAGA AAAGA AAAGA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
35102499 AAAGA AAAGA
1 AAAGA AAAGA
35102509 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 30 0.68
6 9 0.20
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:35102476 original size:11 final size:10
Alignment explanation
Indices: 35102453--35102508 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 10
35102443 AAGAGAAAAT
35102453 AAAGAAAAGA
1 AAAGAAAAGA
35102463 AAAGAAAAGCA
1 AAAGAAAAG-A
*
35102474 AAAGAAGA-A
1 AAAGAAAAGA
35102483 AAAGAAAATGA
1 AAAGAAAA-GA
35102494 AATA-AAAAGA
1 AA-AGAAAAGA
35102504 AAAGA
1 AAAGA
35102509 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.23
10 14 0.36
11 15 0.38
12 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:35102588 original size:11 final size:12
Alignment explanation
Indices: 35102556--35102586 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35102546 TTGAGAGAAC
35102556 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35102568 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35102580 TTGAAAA
1 TTGAAAA
35102587 GCAAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:35102620 original size:12 final size:12
Alignment explanation
Indices: 35102605--35102638 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
35102595 AAAAGAAAAA
*
35102605 GAAAATGAGATT
1 GAAAAAGAGATT
35102617 GAAAAAGAGATT
1 GAAAAAGAGATT
35102629 GAAAAAGAGA
1 GAAAAAGAGA
35102639 ACGAAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:35102644 original size:12 final size:12
Alignment explanation
Indices: 35102593--35102645 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
35102583 AAAAGCAAAA
* *
35102593 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
35102605 GAAAATGAGATT
1 GAAAAAGAGAAT
*
35102617 GAAAAAGAGATT
1 GAAAAAGAGAAT
*
35102629 GAAAAAGAGAAC
1 GAAAAAGAGAAT
35102641 GAAAA
1 GAAAA
35102646 GAAATTTGAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:35102645 original size:42 final size:42
Alignment explanation
Indices: 35102589--35102680 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
35102579 TTTGAAAAGC
*
35102589 AAAAGAAAAAGAAAAAGAAA-ATGAGATTGAAAAAG-AGATTGA
1 AAAAGAAAAAG-AAAAGAAATATGAGAGTGAAAAAGAAGA-TGA
* * *
35102631 AAAAGAGAACGAAAAGAAATTTGAGAGTGAAAAAGAAGATGA
1 AAAAGAAAAAGAAAAGAAATATGAGAGTGAAAAAGAAGATGA
35102673 AAAAGAAA
1 AAAAGAAA
35102681 TTGAAACAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 8 0.19
42 32 0.74
43 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.11
Consensus pattern (42 bp):
AAAAGAAAAAGAAAAGAAATATGAGAGTGAAAAAGAAGATGA
Found at i:35102675 original size:30 final size:31
Alignment explanation
Indices: 35102623--35102682 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
35102613 GATTGAAAAA
*
35102623 GAGATTGAAAAAGAGAACG-AAAAGAAATTT
1 GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
*
35102653 GAGAGTGAAAAAGA-AGATGAAAAAGAAATT
1 GAGAGTGAAAAAGAGA-ACGAAAAAGAAATT
35102683 GAAACAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.58
31 10 0.38
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (31 bp):
GAGAGTGAAAAAGAGAACGAAAAAGAAATTT
Found at i:35104822 original size:30 final size:31
Alignment explanation
Indices: 35104788--35104884 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
35104778 AGCTCACTCC
*
35104788 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
35104818 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
35104848 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
35104878 TAGCTCA
1 TAGCTCA
35104885 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:35111121 original size:13 final size:13
Alignment explanation
Indices: 35111103--35111127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35111093 TGGTCATCAT
35111103 GGTGTGAACACAA
1 GGTGTGAACACAA
35111116 GGTGTGAACACA
1 GGTGTGAACACA
35111128 TGATCAATAC
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:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:35111696 original size:30 final size:30
Alignment explanation
Indices: 35111611--35111707 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35111601 TAAACTAAAA
* *
35111611 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
35111641 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
35111671 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
35111700 ATGAGCTA
1 -TGAGCTA
35111708 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:35113167 original size:14 final size:14
Alignment explanation
Indices: 35113120--35113167 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
35113110 GTACGAATGG
*
35113120 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
35113134 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
35113148 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
35113162 ATTGGT
1 AATGGT
35113168 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:35119866 original size:19 final size:19
Alignment explanation
Indices: 35119842--35119880 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
35119832 TTATACAAGT
35119842 TAAAAAAATATCGAAAAAAA
1 TAAAAAAA-ATCGAAAAAAA
35119862 TAAAAAAAATCGAAAAAAA
1 TAAAAAAAATCGAAAAAAA
35119881 GTGATTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (19 bp):
TAAAAAAAATCGAAAAAAA
Found at i:35136504 original size:18 final size:18
Alignment explanation
Indices: 35136481--35136530 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
35136471 GAAAGAAAAA
*
35136481 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
35136499 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
35136517 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
35136531 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:35136507 original size:24 final size:24
Alignment explanation
Indices: 35136474--35136555 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
35136464 AAGAAATGAA
35136474 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
35136498 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
35136522 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
35136546 AGAAAAAGAA
1 AGAAAAAGAA
35136556 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:35136569 original size:48 final size:48
Alignment explanation
Indices: 35136472--35136590 Score: 116
Period size: 48 Copynumber: 2.5 Consensus size: 48
35136462 CAAAGAAATG
* * * **
35136472 AAAGAAAAAGAAAAAGAGATTGAGAGTGAAAAAGAAAATGAGATTGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
* **
35136520 AAAGAGAATGAAAAAGAGTTTGAGAGAGAAAAAGAATGTGA-ACAAGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGA-AAGAA
* *
35136568 AAA-AGAGTGGAAAAAGAAATTGA
1 AAAGAGAAT-GAAAAAGAGATTGA
35136591 CATAAAAGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
47 5 0.09
48 53 0.91
ACGTcount: A:0.61, C:0.01, G:0.26, T:0.13
Consensus pattern (48 bp):
AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
Found at i:35136584 original size:18 final size:19
Alignment explanation
Indices: 35136548--35136586 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
35136538 TTTGAGAGAG
*
35136548 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
35136567 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
35136585 AA
1 AA
35136587 TTGACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:35138801 original size:30 final size:30
Alignment explanation
Indices: 35138767--35138863 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35138757 AGCTCACTCC
35138767 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
35138797 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
35138827 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
35138857 TAGCTCA
1 TAGCTCA
35138864 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:35141489 original size:19 final size:19
Alignment explanation
Indices: 35141466--35141503 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 19
35141456 TATACAGTTA
35141466 AAAAAAATATCGAAAAAAAT
1 AAAAAAA-ATCGAAAAAAAT
35141486 AAAAAAAATCGAAAAAAA
1 AAAAAAAATCGAAAAAAA
35141504 GTGATTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAAAAATCGAAAAAAAT
Found at i:35143418 original size:30 final size:30
Alignment explanation
Indices: 35143384--35143480 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
35143374 AGCTCACTCC
* *
35143384 TAGCTCATA-TTCAACTCATGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
35143414 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* *
35143444 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
35143474 TAGCTCA
1 TAGCTCA
35143481 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:35152986 original size:444 final size:445
Alignment explanation
Indices: 35151657--35152989 Score: 2501
Period size: 444 Copynumber: 3.0 Consensus size: 445
35151647 ATGAACATTT
*
35151657 GTTCTTGTAAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
35151722 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
35151787 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
* *
35151852 CGTTAAGTTCGTTTTCCATTCCCATCCTTCAAATTATTTTCTTGTTATTCCAAACTGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
* *
35151917 AATCATCATCCATCTTTGCTACTAAATCGAATCTATTACTAAATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
*
35151982 TGCTTACCCATATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 TGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
35152047 TGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
391 TGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
35152102 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
35152167 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
35152232 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGAGACTTCTTAGTGTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
*
35152297 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTTTTGTTATTCCAAACCGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
35152362 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACT-AATTCACCCTACTTTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
*
35152426 CGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 TGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
* *
35152491 TGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCAAGCCAGATCACATCA
391 TGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
*
35152546 GTTCTTGTGAGGTTGCTTCCTCTTATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
1 GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
35152611 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
66 AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
*
35152676 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTCTTGAATCATTCCTGA
131 TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
35152741 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
196 CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
35152806 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTAC-TTGAAACCTTC
261 AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
35152870 TGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
326 TGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
* *
35152935 CGACGATCGGGCAACTAAGTGAATTCGACTCATC-TACCCGGGCCGGATCACATCA
391 TGACGATCGGGCAACTAAGTGAATTCGACTCATCAT-CCCGAGCCGGATCACATCA
35152990 TTTGGTATTA
Statistics
Matches: 866, Mismatches: 20, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
443 1 0.00
444 560 0.65
445 305 0.35
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (445 bp):
GTTCTTGTGAGGTTGCTTCCTCTCATATCTCGTACAAGTTTCGAAAGACTTATCTGGCTTGTGCT
AGTGGCGTCAATCGTCTTGTTTGAACTTATCACCAATCTTGGTGTGGCGTTCACCTATCCATCTA
TCCATCTTTTCACCTTAACAATATAGGAACCGGGGTGACACTTCTTAGTGTTGAATCATTCCTGA
CGTTAAGTTCGTTTTCCATTCCCATCCTTCGAATTATTTTCTTGTTATTCCAAACCGAGCCATTT
AACCATCATCCATCTTTGCTACTAAATCGAACCTATTACTAAATTCACCCTACTTTGAAACCTTC
TGCTTACCCGTATCTTTTCATTCACTTCTAGTTCTAAAACCCGAAGCACGAACGACTCTCTCGAA
TGACGATCGGGCAACTAAGTGAATTCGACTCATCATCCCGAGCCGGATCACATCA
Found at i:35153868 original size:14 final size:14
Alignment explanation
Indices: 35153821--35153868 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
35153811 GTACGAATGG
*
35153821 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
35153835 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
35153849 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
35153863 ATTGGT
1 AATGGT
35153869 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:35160466 original size:14 final size:14
Alignment explanation
Indices: 35160419--35160466 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
35160409 GTACGAATGG
*
35160419 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
35160433 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
35160447 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
35160461 ATTGGT
1 AATGGT
35160467 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:35164727 original size:30 final size:30
Alignment explanation
Indices: 35164632--35164728 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
35164622 AGCTCACTCC
* *
35164632 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
35164662 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
* *
35164692 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
35164722 TAGCTCA
1 TAGCTCA
35164729 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:35167295 original size:6 final size:5
Alignment explanation
Indices: 35167271--35167333 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
35167261 AAGAGAAAAC
*
35167271 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
35167319 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
35167334 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:35167301 original size:12 final size:10
Alignment explanation
Indices: 35167271--35167333 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
35167261 AAGAGAAAAC
35167271 AAAGAAAAGA
1 AAAGAAAAGA
35167281 AAAGAAAAAGCA
1 AAAG-AAAAG-A
35167293 AAAGCAAAAGA
1 AAAG-AAAAGA
*
35167304 AGA-AAAAGA
1 AAAGAAAAGA
35167313 AAATGAAATA-A
1 AAA-GAAA-AGA
35167324 AAAGAAAAGA
1 AAAGAAAAGA
35167334 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:35167413 original size:11 final size:12
Alignment explanation
Indices: 35167381--35167411 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35167371 TTGAGAGAAC
35167381 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35167393 TTGAAAAAGCCT
1 TTGAAAAAGCCT
35167405 TTGAAAA
1 TTGAAAA
35167412 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:35167422 original size:12 final size:12
Alignment explanation
Indices: 35167414--35167500 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
35167404 TTTGAAAAGC
35167414 AAAAAGAAAATG
1 AAAAAGAAAATG
35167426 AAAAAGAAAATG
1 AAAAAGAAAATG
* ** *
35167438 AGATTGAAAAAG
1 AAAAAGAAAATG
*
35167450 AGAAAGAAAA-G
1 AAAAAGAAAATG
** * *
35167461 AAATTTGAGAGTG
1 AAA-AAGAAAATG
*
35167474 AAAAAGAAGATG
1 AAAAAGAAAATG
*
35167486 AAAAAGAAATTG
1 AAAAAGAAAATG
35167498 AAA
1 AAA
35167501 CAAAAGAAAC
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
11 3 0.05
12 48 0.87
13 4 0.07
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:35167435 original size:18 final size:18
Alignment explanation
Indices: 35167408--35167463 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
35167398 AAAGCCTTTG
35167408 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
35167427 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
*
35167445 AAAAGAGAAAGAAAA-GA
1 AAAAGAAAAAGAAAATGA
35167462 AA
1 AA
35167464 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:35167446 original size:24 final size:25
Alignment explanation
Indices: 35167419--35167488 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 25
35167409 AAAGCAAAAA
*
35167419 GAAAATGAAAAAGAAAATGAGA-TT
1 GAAAATGAAAAAGAAAATGAAATTT
* *
35167443 GAAAAAGAGAAAGAAAA-GAAATTT
1 GAAAATGAAAAAGAAAATGAAATTT
* * *
35167467 GAGAGTGAAAAAGAAGATGAAA
1 GAAAATGAAAAAGAAAATGAAA
35167489 AAGAAATTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 3 0.08
24 29 0.81
25 4 0.11
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (25 bp):
GAAAATGAAAAAGAAAATGAAATTT
Found at i:35167448 original size:30 final size:31
Alignment explanation
Indices: 35167414--35167495 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
35167404 TTTGAAAAGC
*
35167414 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
35167444 AAAAAGAGAAA-G-AAAAGAAATTTGAGAGTG
1 AAAAAGA-AAATGAAAAAGAAATATGAGAGTG
*
35167474 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
35167496 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 10 0.22
30 23 0.51
31 12 0.27
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:35169701 original size:30 final size:30
Alignment explanation
Indices: 35169606--35169702 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 30
35169596 AGCTCACTCC
* * *
35169606 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCA
* * ** *
35169636 TAGCTCAACTTCAGCAT-AGGAG-TTTAGCC
1 TAGCTCAACTTTAGC-TCACGAGCTAAAGCA
35169665 TCAGCTCAACTTTAGCTCACGAGCTAAAGCA
1 T-AGCTCAACTTTAGCTCACGAGCTAAAGCA
35169696 TAGCTCA
1 TAGCTCA
35169703 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
29 5 0.10
30 35 0.70
31 10 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCA
Found at i:35174169 original size:30 final size:30
Alignment explanation
Indices: 35174113--35174170 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
35174103 TAAACTCCTA
*
35174113 AGCTGAAGTTGAGCTAAGGTTTAGCTCGTG
1 AGCTGAAGTTGAGCTAAGGTTGAGCTCGTG
35174143 AGCTGAA-TATGAGCTAAGAG-TGAGCTCG
1 AGCTGAAGT-TGAGCTAAG-GTTGAGCTCG
35174171 GTTTAGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 1 0.04
30 23 0.92
31 1 0.04
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.26
Consensus pattern (30 bp):
AGCTGAAGTTGAGCTAAGGTTGAGCTCGTG
Found at i:35176406 original size:13 final size:12
Alignment explanation
Indices: 35176376--35176408 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35176366 CTCTTTAATC
35176376 TCTTTTTCAATA
1 TCTTTTTCAATA
35176388 TCTTTTTCAACT-
1 TCTTTTTCAA-TA
35176400 TCTTTTTCA
1 TCTTTTTCA
35176409 CTCTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (12 bp):
TCTTTTTCAATA
Found at i:35176455 original size:30 final size:30
Alignment explanation
Indices: 35176400--35176466 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
35176390 TTTTTCAACT
* *
35176400 TCTTTTTCACTCTCAAATTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAATTTCTTTTCATTC
* *
35176430 TCTTTTTCAATCTC-ATTTTCTTTTTCATTT
1 TCTTTTTCAATCTCAAATTTC-TTTTCATTC
35176460 TCTTTTT
1 TCTTTTT
35176467 GCTTTTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
TCTTTTTCAATCTCAAATTTCTTTTCATTC
Found at i:35176466 original size:18 final size:18
Alignment explanation
Indices: 35176417--35176472 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
35176407 CACTCTCAAA
* *
35176417 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
35176434 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
35176452 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
35176471 TT
1 TT
35176473 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:35176473 original size:12 final size:12
Alignment explanation
Indices: 35176442--35176466 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35176432 TTTTTCAATC
35176442 TCATTTTCTTTT
1 TCATTTTCTTTT
35176454 TCATTTTCTTTT
1 TCATTTTCTTTT
35176466 T
1 T
35176467 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:35176557 original size:5 final size:5
Alignment explanation
Indices: 35176547--35176603 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
35176537 CTCTTGCCTC
* * *
35176547 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
35176594 TCTTT TCTTT
1 TCTTT TCTTT
35176604 GTTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:35176579 original size:25 final size:25
Alignment explanation
Indices: 35176551--35176599 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
35176541 TGCCTCTCTT
*
35176551 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
35176576 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
35176600 CTTTGTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:35176604 original size:21 final size:20
Alignment explanation
Indices: 35176560--35176614 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
35176550 TTTCTTTTTA
35176560 TTTTG-TTTTCTTTTTCTTC
1 TTTTGTTTTTCTTTTTCTTC
*
35176579 TTTTGCTTTTTC-TTTTCTTT
1 TTTTG-TTTTTCTTTTTCTTC
35176599 TCTTTGTTTTCTCTTT
1 T-TTTGTTTT-TCTTT
35176615 ACAAGAATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 11 0.37
22 2 0.07
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTGTTTTTCTTTTTCTTC
Found at i:35181916 original size:30 final size:30
Alignment explanation
Indices: 35181880--35181976 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
35181870 AGCTCACTCC
35181880 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
35181910 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
35181940 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
35181970 TAGCTCA
1 TAGCTCA
35181977 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:35194367 original size:13 final size:12
Alignment explanation
Indices: 35194341--35194398 Score: 73
Period size: 13 Copynumber: 4.7 Consensus size: 12
35194331 ATACAAGTAT
35194341 AAAAAAATTC-A
1 AAAAAAATTCAA
35194352 AAAAAAATTCGAA
1 AAAAAAATTC-AA
35194365 AAAAAAATTCAA
1 AAAAAAATTCAA
*
35194377 AAAAAAGTTTCAA
1 AAAAAA-ATTCAA
35194390 AAAATAAAT
1 AAAA-AAAT
35194399 GATTTGTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
11 10 0.24
12 8 0.20
13 21 0.51
14 2 0.05
ACGTcount: A:0.71, C:0.07, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:35194391 original size:24 final size:23
Alignment explanation
Indices: 35194341--35194398 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 23
35194331 ATACAAGTAT
35194341 AAAAAAATTCAAAAAAAATTCGAA
1 AAAAAAATTCAAAAAAAATTC-AA
35194365 AAAAAAATTCAAAAAAAAGTTTCAA
1 AAAAAAATTCAAAAAAAA--TTCAA
35194390 AAAATAAAT
1 AAAA-AAAT
35194399 GATTTGTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 18 0.58
25 6 0.19
26 7 0.23
ACGTcount: A:0.71, C:0.07, G:0.03, T:0.19
Consensus pattern (23 bp):
AAAAAAATTCAAAAAAAATTCAA
Found at i:35197766 original size:68 final size:70
Alignment explanation
Indices: 35197694--35197891 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
35197684 ACACCCTGTA
* * * *
35197694 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
35197756 ATAAAT
65 ATAAAT
*
35197762 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
35197827 ATAAAT
65 ATAAAT
*
35197833 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
35197892 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:35197805 original size:41 final size:41
Alignment explanation
Indices: 35197760--35197877 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
35197750 TGAAAGATAA
35197760 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
35197801 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
35197831 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
35197872 ATGTAG
1 ATGTAG
35197878 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:35197817 original size:71 final size:71
Alignment explanation
Indices: 35197728--35197891 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
35197718 GAGATGTATC
35197728 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
35197793 AGGACA
66 AGGACA
35197799 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
35197864 AGGACA
66 AGGACA
35197870 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
35197892 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:35207584 original size:30 final size:30
Alignment explanation
Indices: 35207548--35207607 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
35207538 TTCCCGAGCC
*
35207548 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
35207578 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
35207608 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:35211356 original size:14 final size:14
Alignment explanation
Indices: 35211309--35211356 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
35211299 GTACGAATGG
*
35211309 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
35211323 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
35211337 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
35211351 ATTGGT
1 AATGGT
35211357 CTGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:35212016 original size:12 final size:12
Alignment explanation
Indices: 35211999--35212053 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
35211989 TATACAAGTT
35211999 AAAAAAATTCAA
1 AAAAAAATTCAA
35212011 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
35212023 AAAAAATTTGAA
1 AAAAAAATTCAA
* *
35212035 AAAAAAAATCAG
1 AAAAAAATTCAA
35212047 AAAAAAA
1 AAAAAAA
35212054 GAAAAAGAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:35212984 original size:5 final size:5
Alignment explanation
Indices: 35212974--35213030 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
35212964 AAGAGAAAAT
*
35212974 AAAGA AAAGA AAAGA AAAGGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAGA AAA-G-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
35213021 AAAGA AAAGA
1 AAAGA AAAGA
35213031 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:35213109 original size:11 final size:12
Alignment explanation
Indices: 35213078--35213108 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35213068 TTGAGAGAAC
35213078 TTGAAAAAGCCT
1 TTGAAAAAGCCT
*
35213090 TTGAAAAAGTCT
1 TTGAAAAAGCCT
35213102 TTGAAAA
1 TTGAAAA
35213109 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:35213119 original size:12 final size:12
Alignment explanation
Indices: 35213111--35213135 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35213101 TTTGAAAAGC
35213111 AAAAAGAAAATG
1 AAAAAGAAAATG
35213123 AAAAAGAAAATG
1 AAAAAGAAAATG
35213135 A
1 A
35213136 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:35213132 original size:18 final size:18
Alignment explanation
Indices: 35213105--35213160 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
35213095 AAAGTCTTTG
35213105 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
35213124 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
35213142 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
35213159 AA
1 AA
35213161 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:35213145 original size:30 final size:31
Alignment explanation
Indices: 35213111--35213192 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
35213101 TTTGAAAAGC
*
35213111 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
35213141 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
35213171 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
35213193 TGAAATAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:35215440 original size:30 final size:30
Alignment explanation
Indices: 35215406--35215503 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
35215396 AGCTCACTCC
35215406 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
35215436 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
35215466 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
35215496 TAGCTCAT
1 TAGCTCAT
35215504 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:35219041 original size:38 final size:38
Alignment explanation
Indices: 35218999--35219138 Score: 217
Period size: 38 Copynumber: 3.7 Consensus size: 38
35218989 GCTTAAAGGT
35218999 CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC
1 CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC
* *
35219037 CCGCAAGCTTCGTACTGGTATTATATCCGGGTTAAATC
1 CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC
* * *
35219075 CCACAGGCTTCGTGCTAGTATTATATCCGAGTTAAATC
1 CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC
* *
35219113 CTGCAGGCTTAGTGCTGGTATTATAT
1 CCGCAGGCTTCGTGCTGGTATTATAT
35219139 TCGAGCTTAA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 91 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (38 bp):
CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATC
Found at i:35219088 original size:76 final size:78
Alignment explanation
Indices: 35218989--35219159 Score: 231
Period size: 76 Copynumber: 2.2 Consensus size: 78
35218979 GTGTATCCAG
* * * *
35218989 GCTTAAAGGT-CCGCAGGCTTCGTGCTGGTATTATATCCGGGTTAAATCCCGCAAGCTTCGTACT
1 GCTTAAA-GTCCCACAGGCTTCGTGCTAGTATTATATCCGAGTTAAATCCCGCAAGCTTAGTACT
35219053 GGTATTATATCCG-
65 GGTATTATATCCGA
* * * *
35219066 GGTTAAA-TCCCACAGGCTTCGTGCTAGTATTATATCCGAGTTAAATCCTGCAGGCTTAGTGCTG
1 GCTTAAAGTCCCACAGGCTTCGTGCTAGTATTATATCCGAGTTAAATCCCGCAAGCTTAGTACTG
*
35219130 GTATTATATTCGA
66 GTATTATATCCGA
35219143 GCTTAAAGTCCCACAGG
1 GCTTAAAGTCCCACAGG
35219160 TTTTGTACTG
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
75 1 0.01
76 59 0.73
77 12 0.15
78 9 0.11
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (78 bp):
GCTTAAAGTCCCACAGGCTTCGTGCTAGTATTATATCCGAGTTAAATCCCGCAAGCTTAGTACTG
GTATTATATCCGA
Found at i:35229566 original size:15 final size:16
Alignment explanation
Indices: 35229546--35229577 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
35229536 GATATATGAA
35229546 TAATTATAT-TTTATT
1 TAATTATATGTTTATT
35229561 TAATTATATGTTTATT
1 TAATTATATGTTTATT
35229577 T
1 T
35229578 CTTTATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TAATTATATGTTTATT
Found at i:35231135 original size:29 final size:28
Alignment explanation
Indices: 35231069--35231162 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
35231059 AAGTCTACAT
* * *
35231069 ACATGCATATGGCCCACTAGGCCTAATC
1 ACATTCATATGGCCCATTAGGCCAAATC
* *
35231097 TCTTTCATATGGCCCATTAGGCCAAAATC
1 ACATTCATATGGCCCATTAGGCC-AAATC
* *
35231126 ACATTCATATGGCCTATTAGGCCCAATC
1 ACATTCATATGGCCCATTAGGCCAAATC
35231154 ACATTCATA
1 ACATTCATA
35231163 GTCATGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 32 0.57
29 24 0.43
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (28 bp):
ACATTCATATGGCCCATTAGGCCAAATC
Found at i:35233816 original size:11 final size:11
Alignment explanation
Indices: 35233781--35233820 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
35233771 ACATTTTAGC
35233781 AAAAAAATTCA
1 AAAAAAATTCA
** *
35233792 AAAAATTTTGA
1 AAAAAAATTCA
35233803 AAAAAAATTCA
1 AAAAAAATTCA
35233814 AAAAAAA
1 AAAAAAA
35233821 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:35237614 original size:30 final size:29
Alignment explanation
Indices: 35237519--35237615 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
35237509 AGCTCACTCC
* *
35237519 TAGCTC-ACTTTCAACTCACGAGATAAACCT
1 TAGCTCAACTTT-AGCTCACGAG-TAAAGCT
* * * **
35237549 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGTAAAG-CT
*
35237579 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAG-TAAAGCT
35237609 TAGCTCA
1 TAGCTCA
35237616 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (29 bp):
TAGCTCAACTTTAGCTCACGAGTAAAGCT
Found at i:35245400 original size:30 final size:30
Alignment explanation
Indices: 35245366--35245460 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
35245356 AGCTCACTCC
35245366 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
35245396 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* *
35245426 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
35245456 TAGCT
1 TAGCT
35245461 TATTTTAGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:35246597 original size:8 final size:8
Alignment explanation
Indices: 35246584--35246609 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35246574 TGGCGTTCAC
35246584 CTATCCAT
1 CTATCCAT
35246592 CTATCCAT
1 CTATCCAT
35246600 CTATCCAT
1 CTATCCAT
35246608 CT
1 CT
35246610 TTCACCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (8 bp):
CTATCCAT
Found at i:35248079 original size:6 final size:5
Alignment explanation
Indices: 35248055--35248111 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
35248045 AAGAGAAAAT
*
35248055 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
35248102 AAAGA AAAGA
1 AAAGA AAAGA
35248112 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Done.