Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold172
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: 689488
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.18
Warning! 301009 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2824 original size:79 final size:80
Alignment explanation
Indices: 2723--2986 Score: 367
Period size: 79 Copynumber: 3.3 Consensus size: 80
2713 GCTACTCGTT
* * * **
2723 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
*
2786 AGATTTAGTAACTCGCA
64 GGATTTAGTAACTCGCA
2803 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
*
2867 ATTTAATAACTCGCA
66 ATTTAGTAACTCGCA
2882 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
* * * *
2946 ATATGGTCACTTAGCA
66 ATTTAGTAAC-TCGCA
2962 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
2987 CATCATTCAA
Statistics
Matches: 168, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
78 3 0.02
79 131 0.78
80 34 0.20
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
ATTTAGTAACTCGCA
Found at i:2986 original size:40 final size:40
Alignment explanation
Indices: 2704--2986 Score: 312
Period size: 40 Copynumber: 7.1 Consensus size: 40
2694 CGGAATTTAA
** *
2704 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
2744 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
2784 CCAGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
2823 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
2863 CCGGATTTAATAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
2902 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
2942 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
2982 CCGGA
1 CCGGA
2987 CATCATTCAA
Statistics
Matches: 205, Mismatches: 26, Indels: 24
0.80 0.10 0.09
Matches are distributed among these distances:
38 4 0.02
39 63 0.31
40 124 0.60
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5288 original size:18 final size:18
Alignment explanation
Indices: 5265--5322 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
5255 TGGAGAAATG
* *
5265 AAAGAAAAATACATTGAA
1 AAAGAAAAAGAAATTGAA
*
5283 AAAGAAAAAGAAATTGCA
1 AAAGAAAAAGAAATTGAA
* *
5301 AAAGAAAAGGGAATTGAA
1 AAAGAAAAAGAAATTGAA
5319 AAAG
1 AAAG
5323 TGAGTGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.66, C:0.03, G:0.19, T:0.12
Consensus pattern (18 bp):
AAAGAAAAAGAAATTGAA
Found at i:5321 original size:30 final size:29
Alignment explanation
Indices: 5286--5366 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
5276 CATTGAAAAA
*
5286 GAAAAAGAAATTGCAAAAG-AAAAGGGAATT
1 GAAAAAGAAATTG-AAAAGAAAAAGAG-ATT
** *
5316 GAAAAAGTGAGTGAAAAGGAAAAAGAGATT
1 GAAAAAGAAATTGAAAA-GAAAAAGAGATT
5346 GAAAAAGAAATTGAAAGAGAA
1 GAAAAAGAAATTGAAA-AGAA
5367 GAAAAAGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 4 0.10
30 30 0.73
31 7 0.17
ACGTcount: A:0.60, C:0.01, G:0.26, T:0.12
Consensus pattern (29 bp):
GAAAAAGAAATTGAAAAGAAAAAGAGATT
Found at i:5337 original size:18 final size:18
Alignment explanation
Indices: 5316--5355 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5306 AAAGGGAATT
* *
5316 GAAAAAGTGAGTGAAAAG
1 GAAAAAGAGAGTGAAAAA
*
5334 GAAAAAGAGATTGAAAAA
1 GAAAAAGAGAGTGAAAAA
5352 GAAA
1 GAAA
5356 TTGAAAGAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (18 bp):
GAAAAAGAGAGTGAAAAA
Found at i:18526 original size:17 final size:18
Alignment explanation
Indices: 18504--18539 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18494 AAAAAATCAG
*
18504 TAGAAAAAGTC-AAAAAA
1 TAGAAAAAGACGAAAAAA
18521 TAGAAAAAGACGAAAAAA
1 TAGAAAAAGACGAAAAAA
18539 T
1 T
18540 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (18 bp):
TAGAAAAAGACGAAAAAA
Found at i:27746 original size:330 final size:330
Alignment explanation
Indices: 27145--27807 Score: 1299
Period size: 330 Copynumber: 2.0 Consensus size: 330
27135 AACTTTGCCT
* *
27145 AAATCAGGGAAAGACTTTGTGGTTTACAATGATGCCTTATTGAATGATTTGGGTTGCGTTTTGAT
1 AAATCAGGGAAAGACTTTGTGGTTTACAACGATGCCTTATTGAATGATTTGGGTTGCATTTTGAT
*
27210 GCAAGACGGAAAAGTAATTCCATATGCCTCTCGCCAGCAAAAAACGCATGAAAGCAACTATCTGG
66 GCAAGACGGAAAAGTAATTCCATATGCCTCTCGCCAGCAAAAAACGCATGAAAGCAACTATCTAG
27275 CACATAATTTAGAGCAAGCCACTGTGGCTTTTGCTCGAAAGATCTTGAGGCACTATTTGATGTGG
131 CACATAATTTAGAGCAAGCCACTGTGGCTTTTGCTCGAAAGATCTTGAGGCACTATTTGATGTGG
27340 TTTTTTTCTCTAAAGATCTAAAGTCACTATTTGTATAGTGAAAAGTGACATATTTACACCATTCA
196 TTTTTTTCTCTAAAGATCTAAAGTCACTATTTGTATAGTGAAAAGTGACATATTTACACCATTCA
27405 TAAAAGTCTTAAATACCTCCTAACCCAAAAGGAGTTGAATTTGAGATAGCATCACTAGGCTGAAC
261 TAAAAGTCTTAAATACCTCCTAACCCAAAAGGAGTTGAATTTGAGATAGCATCACTAGGCTGAAC
27470 CATTA
326 CATTA
27475 AAATCAGGGAAAGACTTTGTGGTTTACAACGATGCCTTATTGAATGATTTGGGTTGCATTTTGAT
1 AAATCAGGGAAAGACTTTGTGGTTTACAACGATGCCTTATTGAATGATTTGGGTTGCATTTTGAT
27540 GCAAGACGGAAAAGTAATTCCATATGCCTCTCGCCAGCAAAAAACGCATGAAAGCAACTATCTAG
66 GCAAGACGGAAAAGTAATTCCATATGCCTCTCGCCAGCAAAAAACGCATGAAAGCAACTATCTAG
27605 CACATAATTTAGAGCAAGCCACTGTGGCTTTTGCTCGAAAGATCTTGAGGCACTATTTGATGTGG
131 CACATAATTTAGAGCAAGCCACTGTGGCTTTTGCTCGAAAGATCTTGAGGCACTATTTGATGTGG
27670 TTTTTTTCTCTAAAGATCTAAAGTCACTATTTGTATAGTGAAAAGTGACATATTTACACCATTCA
196 TTTTTTTCTCTAAAGATCTAAAGTCACTATTTGTATAGTGAAAAGTGACATATTTACACCATTCA
27735 TAAAAGTCTTAAATACCTCCTAACCCAAAAGGAGTTGAATTTGAGATAGCATCACTAGGCTGAAC
261 TAAAAGTCTTAAATACCTCCTAACCCAAAAGGAGTTGAATTTGAGATAGCATCACTAGGCTGAAC
27800 CATTA
326 CATTA
27805 AAA
1 AAA
27808 GATTATGATT
Statistics
Matches: 330, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
330 330 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (330 bp):
AAATCAGGGAAAGACTTTGTGGTTTACAACGATGCCTTATTGAATGATTTGGGTTGCATTTTGAT
GCAAGACGGAAAAGTAATTCCATATGCCTCTCGCCAGCAAAAAACGCATGAAAGCAACTATCTAG
CACATAATTTAGAGCAAGCCACTGTGGCTTTTGCTCGAAAGATCTTGAGGCACTATTTGATGTGG
TTTTTTTCTCTAAAGATCTAAAGTCACTATTTGTATAGTGAAAAGTGACATATTTACACCATTCA
TAAAAGTCTTAAATACCTCCTAACCCAAAAGGAGTTGAATTTGAGATAGCATCACTAGGCTGAAC
CATTA
Found at i:30248 original size:51 final size:51
Alignment explanation
Indices: 30125--30265 Score: 176
Period size: 51 Copynumber: 2.8 Consensus size: 51
30115 TATTATTCGA
* * * * * * *
30125 TACACGTAGTAGCCTTCACATAGTAATACACACCTAATC-AAACTTTTCGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAACCTTCCGG
* * *
30175 TTCACATAGTATCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAACCTTCCGG
*
30226 TACACATAGTAGCCTTCACATAGTACTACACATGTGACCA
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCA
30266 TTATCTATCG
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 31 0.41
51 45 0.59
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (51 bp):
TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAACCTTCCGG
Found at i:30281 original size:51 final size:51
Alignment explanation
Indices: 30122--30312 Score: 170
Period size: 51 Copynumber: 3.8 Consensus size: 51
30112 TATTATTATT
* * * * * * * *
30122 CGATACACGTAGTAGCCTTCACATAGTAATACACACCTAATC-AAACTTTT
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTC
* * *
30172 CGGTTCACATAGTATCCTGCACATAGTACTACACACGTGACCAAAACCTTC
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTC
* * * ** *
30223 CGGTACACATAGTAGCCTTCACATAGTACTACACATGTGACCATTATCTAT-
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCT-TC
* * * *
30274 CGATACACGTAGTAGTCTGCACTTAGTACTACAGACGTG
1 CGATACACATAGTAGCCTGCACATAGTACTACACACGTG
30313 TTTATAAGCA
Statistics
Matches: 114, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
50 33 0.29
51 80 0.70
52 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
CGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTC
Found at i:34909 original size:19 final size:20
Alignment explanation
Indices: 34874--34923 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
34864 AAAGAAAGAC
*
34874 AGAAAAATA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
34892 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
34912 AGAAAAAAGAGA
1 AG-AAAAAGAGA
34924 TTGAGAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 2 0.07
21 9 0.33
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:42782 original size:19 final size:19
Alignment explanation
Indices: 42703--42783 Score: 58
Period size: 19 Copynumber: 4.2 Consensus size: 19
42693 AACTCAAATG
*
42703 AAAGAAAAAGAAAATAATGAA
1 AAAGAAAAATAAAA-AAT-AA
* *
42724 AAAGAAAAA-AAGAAAGTGA
1 AAAGAAAAATAA-AAAATAA
* * *
42743 AAAGAACATTAGAAACA-AA
1 AAAGAAAAATA-AAAAATAA
42762 AAAGAAAAATAAAAAATAA
1 AAAGAAAAATAAAAAATAA
42781 AAA
1 AAA
42784 AAAGTTTGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
18 4 0.09
19 23 0.50
20 7 0.15
21 12 0.26
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAGAAAAATAAAAAATAA
Found at i:45139 original size:20 final size:20
Alignment explanation
Indices: 45116--45153 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
45106 TTAAGCTAAA
45116 ATTGAGCT-GAATTGAGCTCG
1 ATTGAGCTAG-ATTGAGCTCG
45136 ATTGAGCTAGATTGAGCT
1 ATTGAGCTAGATTGAGCT
45154 TTATTTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (20 bp):
ATTGAGCTAGATTGAGCTCG
Found at i:46934 original size:17 final size:18
Alignment explanation
Indices: 46912--46953 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
46902 TATCATATCC
*
46912 CTCATTTCTTT-TGCACT
1 CTCATTTCTTTCTGCAAT
*
46929 CTCATTTCTTTCTTCAAT
1 CTCATTTCTTTCTGCAAT
46947 CTCATTT
1 CTCATTT
46954 TCAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.14, C:0.29, G:0.02, T:0.55
Consensus pattern (18 bp):
CTCATTTCTTTCTGCAAT
Found at i:48072 original size:9 final size:10
Alignment explanation
Indices: 48043--48083 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
48033 ATCACGTACA
48043 AATTTTTGTTG
1 AATTTTT-TTG
48054 AAATTTTTTTG
1 -AATTTTTTTG
48065 AATTTTTTTG
1 AATTTTTTTG
48075 AATTTTTTT
1 AATTTTTTT
48084 TCACAATCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 3 0.10
12 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:48084 original size:11 final size:11
Alignment explanation
Indices: 48043--48084 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
48033 ATCACGTACA
*
48043 AATTTTTGTTG
1 AATTTTTTTTG
*
48054 AAATTTTTTTG
1 AATTTTTTTTG
48065 AA-TTTTTTTG
1 AATTTTTTTTG
48075 AATTTTTTTT
1 AATTTTTTTT
48085 CACAATCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:51777 original size:11 final size:11
Alignment explanation
Indices: 51745--51778 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
51735 TACGGTGTTG
*
51745 TCAAAAAAAAA
1 TCAAAAAAAAT
51756 TCAAAAAAAAT
1 TCAAAAAAAAT
*
51767 TGAAAAAAAAT
1 TCAAAAAAAAT
51778 T
1 T
51779 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (11 bp):
TCAAAAAAAAT
Found at i:52792 original size:21 final size:21
Alignment explanation
Indices: 52752--52810 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
52742 AATCTTGAAT
*
52752 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
52773 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
52794 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
52811 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:52802 original size:15 final size:14
Alignment explanation
Indices: 52763--52810 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
52753 AAATTGAGAG
52763 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
52777 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
52792 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
52807 AAGA
1 AAGA
52811 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:52866 original size:12 final size:12
Alignment explanation
Indices: 52849--52911 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
52839 AGTGAAAAGC
*
52849 AAAAAGAGATTG
1 AAAAAGAAATTG
52861 AAAAAGAAATTG
1 AAAAAGAAATTG
52873 AAAAAGAAA---
1 AAAAAGAAATTG
*
52882 AAAAAGAAAGAGTGG
1 AAAAAG-AA-A-TTG
52897 AAAAAGAAATTG
1 AAAAAGAAATTG
52909 AAA
1 AAA
52912 GAGAGCTTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 1 0.02
12 25 0.58
13 1 0.02
14 2 0.05
15 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:52913 original size:21 final size:21
Alignment explanation
Indices: 52851--52914 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 21
52841 TGAAAAGCAA
*
52851 AAAGAGATTGAAAAAGAAATTG
1 AAAGAG-TAGAAAAAGAAATTG
52873 AAA-A--AGAAAAA-AAA--G
1 AAAGAGTAGAAAAAGAAATTG
*
52888 AAAGAGTGGAAAAAGAAATTG
1 AAAGAGTAGAAAAAGAAATTG
52909 AAAGAG
1 AAAGAG
52915 AGCTTGAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 3 0.09
18 12 0.35
19 3 0.09
21 8 0.24
22 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (21 bp):
AAAGAGTAGAAAAAGAAATTG
Found at i:54604 original size:82 final size:82
Alignment explanation
Indices: 54453--54615 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 82
54443 TTGTGTCTGC
* * * *
54453 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
54518 GGAACGGCATTTAAAGA
66 GGAACGGCATTTAAAGA
* **
54535 AGGTCATTGAAATTTGGCTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGCA
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCA
* *
54599 TGGAACGGTATTTAAAG
65 AGGAACGGCATTTAAAG
54616 GGAAGTAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 41 0.58
83 30 0.42
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGGCATTTAAAGA
Found at i:59755 original size:6 final size:6
Alignment explanation
Indices: 59744--59803 Score: 75
Period size: 6 Copynumber: 10.0 Consensus size: 6
59734 AATGAAAGAG
** ** *
59744 AAGAAA AAGAAA AAGAAA GTGAAA AAGAAA AAGAAA AAGAAA TTGCAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
59792 AAGAAA AAGAAA
1 AAGAAA AAGAAA
59804 TCAAAAAAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:59776 original size:24 final size:23
Alignment explanation
Indices: 59744--59828 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 23
59734 AATGAAAGAG
59744 AAGAAAAAGAAAAAGAAAGTGAAA
1 AAGAAAAAGAAAAAGAAAGTG-AA
*
59768 AAGAAAAAGAAAAAGAAATTGCAA
1 AAGAAAAAGAAAAAGAAAGTG-AA
*
59792 AAGAAAAAGAAATCAAAAAAGTG-A
1 AAGAAAAAGAAA--AAGAAAGTGAA
*
59816 GAGAAAAAGAAAA
1 AAGAAAAAGAAAA
59829 TGAAGAAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 1 0.02
24 46 0.85
26 7 0.13
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (23 bp):
AAGAAAAAGAAAAAGAAAGTGAA
Found at i:59811 original size:18 final size:18
Alignment explanation
Indices: 59771--59812 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59761 AGTGAAAAAG
**
59771 AAAAAGAAAAAGAAATTG
1 AAAAAGAAAAAGAAATCA
*
59789 CAAAAGAAAAAGAAATCA
1 AAAAAGAAAAAGAAATCA
59807 AAAAAG
1 AAAAAG
59813 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.74, C:0.05, G:0.14, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAAGAAATCA
Found at i:59852 original size:13 final size:13
Alignment explanation
Indices: 59732--59854 Score: 58
Period size: 12 Copynumber: 9.2 Consensus size: 13
59722 CATTTTAATA
59732 AAAATGAAAGAGAAG
1 AAAATGAAA-A-AAG
*
59747 AAAAAG-AAAAAG
1 AAAATGAAAAAAG
*
59759 AAAGTG-AAAAAG
1 AAAATGAAAAAAG
*
59771 AAAAAG-AAAAAG
1 AAAATGAAAAAAG
* *
59783 AAATTG-CAAAAG
1 AAAATGAAAAAAG
*
59795 AAAAAGAAATCAAA-
1 AAAATGAAA--AAAG
*
59809 AAAGTGAGAGAAAAAG
1 AAAAT--GA-AAAAAG
59825 AAAATGAAGAAAAG
1 AAAATGAA-AAAAG
**
59839 AAAATTTAAAAAG
1 AAAATGAAAAAAG
59852 AAA
1 AAA
59855 TTGAGATTGA
Statistics
Matches: 84, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
12 36 0.43
13 11 0.13
14 18 0.21
15 11 0.13
16 6 0.07
17 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.08
Consensus pattern (13 bp):
AAAATGAAAAAAG
Found at i:62434 original size:25 final size:25
Alignment explanation
Indices: 62400--62469 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
62390 AATAAATTAG
*
62400 CATGCATGTTTCCTTGAATGTCATT
1 CATGCATGTTTCCTTTAATGTCATT
* *
62425 CATGCATGTTTCTTTTAATGTCGTT
1 CATGCATGTTTCCTTTAATGTCATT
*
62450 CATGCATGCTTCCTTTAATG
1 CATGCATGTTTCCTTTAATG
62470 CTCTCCTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.46
Consensus pattern (25 bp):
CATGCATGTTTCCTTTAATGTCATT
Found at i:62904 original size:20 final size:20
Alignment explanation
Indices: 62879--62920 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
62869 AATTTAAACC
62879 AAGCTCAAATGAGTTGAATT
1 AAGCTCAAATGAGTTGAATT
**
62899 AAGCTCATGTGAGTTGAATT
1 AAGCTCAAATGAGTTGAATT
62919 AA
1 AA
62921 AAATCATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
AAGCTCAAATGAGTTGAATT
Found at i:62929 original size:21 final size:20
Alignment explanation
Indices: 62888--62937 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
62878 CAAGCTCAAA
**
62888 TGAGTTGAATTAAGCTCATG
1 TGAGTTGAATTAAAATCATG
62908 TGAGTTGAATTAAAAATCATG
1 TGAGTTGAATT-AAAATCATG
*
62929 TGAGCTGAA
1 TGAGTTGAA
62938 CCAAGCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTAAAATCATG
Found at i:64967 original size:33 final size:33
Alignment explanation
Indices: 64906--64968 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
64896 GATTTCTCTC
* *
64906 TTCACTCATTTCTTTTGTAAACTTTCTTTCTTT
1 TTCACTCATTTCTTTTGCAAACTCTCTTTCTTT
*
64939 TTCACTCTATTTCTTTT-CAAGCTCTCTTTC
1 TTCACTC-ATTTCTTTTGCAAACTCTCTTTC
64969 AATTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 17 0.65
34 9 0.35
ACGTcount: A:0.14, C:0.25, G:0.03, T:0.57
Consensus pattern (33 bp):
TTCACTCATTTCTTTTGCAAACTCTCTTTCTTT
Found at i:64998 original size:14 final size:15
Alignment explanation
Indices: 64971--65000 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
64961 TCTCTTTCAA
64971 TTTCTTTTTCCACTC
1 TTTCTTTTTCCACTC
64986 TTTCTTTTT-CACTC
1 TTTCTTTTTCCACTC
65000 T
1 T
65001 CAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTCTTTTTCCACTC
Found at i:65091 original size:22 final size:23
Alignment explanation
Indices: 65057--65099 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
65047 TCAATCTCTT
65057 TTTCAATTTTC-TTTTCTTTTTC
1 TTTCAATTTTCTTTTTCTTTTTC
65079 TTTC-ATTTCTCTTTTTCTTTT
1 TTTCAATTT-TCTTTTTCTTTT
65100 GGTTTCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTCAATTTTCTTTTTCTTTTTC
Found at i:66044 original size:26 final size:26
Alignment explanation
Indices: 66007--66075 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
65997 CTTCACTCTC
* **
66007 TTTTTTTCGAATTTTTTTATTTA-TTA
1 TTTTTTTTGAATTTTTTT-TGAATTTA
66033 TTTTTTTTGAATTTTTTTTGAATTTA
1 TTTTTTTTGAATTTTTTTTGAATTTA
66059 TTTTTTTTGAATTTTTT
1 TTTTTTTTGAATTTTTT
66076 AATTCAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
25 2 0.05
26 37 0.95
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.75
Consensus pattern (26 bp):
TTTTTTTTGAATTTTTTTTGAATTTA
Found at i:66051 original size:15 final size:15
Alignment explanation
Indices: 66043--66072 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66033 TTTTTTTTGA
66043 ATTTTTTTTGAATTT
1 ATTTTTTTTGAATTT
66058 ATTTTTTTTGAATTT
1 ATTTTTTTTGAATTT
66073 TTTAATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
ATTTTTTTTGAATTT
Found at i:66075 original size:11 final size:11
Alignment explanation
Indices: 66032--66063 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
66022 TTTATTTATT
66032 ATTTTTTTTGA
1 ATTTTTTTTGA
66043 ATTTTTTTTGA
1 ATTTTTTTTGA
66054 ATTTATTTTT
1 ATTT-TTTTT
66064 TTTGAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (11 bp):
ATTTTTTTTGA
Found at i:79675 original size:20 final size:21
Alignment explanation
Indices: 79631--79676 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
79621 CAATGTGTAT
79631 TGTCTTAACCGAATTAATTAG
1 TGTCTTAACCGAATTAATTAG
**
79652 -GTCTTAACTTAATTAATT-G
1 TGTCTTAACCGAATTAATTAG
79671 TGTCTT
1 TGTCTT
79677 GTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (21 bp):
TGTCTTAACCGAATTAATTAG
Found at i:82868 original size:9 final size:9
Alignment explanation
Indices: 82854--82880 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
82844 ATTTCTTAGA
82854 CCAAGATTT
1 CCAAGATTT
82863 CCAAGATTT
1 CCAAGATTT
82872 CCAAGATTT
1 CCAAGATTT
82881 GAAATCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (9 bp):
CCAAGATTT
Found at i:90497 original size:23 final size:22
Alignment explanation
Indices: 90471--90521 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
90461 TTTAACTGAT
90471 TTTTTTTTGCTCACTTTTTTTT-C
1 TTTTTTTTGCT--CTTTTTTTTAC
90494 TTTTTTTTGCTCTTTTTTTTAC
1 TTTTTTTTGCTCTTTTTTTTAC
90516 TTTTTT
1 TTTTTT
90522 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.33
22 7 0.26
23 11 0.41
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTTTTTGCTCTTTTTTTTAC
Found at i:90500 original size:12 final size:12
Alignment explanation
Indices: 90471--90513 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
90461 TTTAACTGAT
90471 TTTTTTTTGCTC
1 TTTTTTTTGCTC
*
90483 ACTTTTTTT--TC
1 -TTTTTTTTGCTC
90494 TTTTTTTTGCTC
1 TTTTTTTTGCTC
90506 TTTTTTTT
1 TTTTTTTT
90514 ACTTTTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 10 0.38
13 7 0.27
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGCTC
Found at i:94761 original size:6 final size:6
Alignment explanation
Indices: 94724--94850 Score: 96
Period size: 6 Copynumber: 21.0 Consensus size: 6
94714 TAAATCTCAA
* * * ** **
94724 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCAA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** *
94775 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCTT TTTCTT TTTCAT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
**
94823 TTTC-- TTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
94851 CTTTTTTGTT
Statistics
Matches: 93, Mismatches: 24, Indels: 8
0.74 0.19 0.06
Matches are distributed among these distances:
4 4 0.04
6 77 0.83
7 9 0.10
8 3 0.03
ACGTcount: A:0.08, C:0.20, G:0.01, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:97190 original size:28 final size:28
Alignment explanation
Indices: 97124--97245 Score: 135
Period size: 28 Copynumber: 4.4 Consensus size: 28
97114 ATATTAAGTC
* *
97124 CGCACACTCA-TGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
97150 CCCACA-TTAAGTGCTACATAATCAAACT
1 CGCACACTT-AGTGCTACATAATCAAACT
97178 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
97206 CGCACACTTAGGTGCTGACA-ATTTAAACC
1 CGCACACTTA-GTGCT-ACATAATCAAACT
97235 CGCACACTTAG
1 CGCACACTTAG
97246 CGCCAATCTC
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.01
26 6 0.07
27 11 0.13
28 39 0.47
29 23 0.28
30 3 0.04
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:97242 original size:57 final size:55
Alignment explanation
Indices: 97123--97245 Score: 142
Period size: 57 Copynumber: 2.2 Consensus size: 55
97113 TATATTAAGT
* *
97123 CCGCACACTCA-TGCTATATAATCAACTCCCACATTAAGTGCTACATAATCAAAC
1 CCGCACACTTAGTGCTACATAATCAACTCCCACATTAAGTGCTACATAATCAAAC
* * * * *
97177 TCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGGTGCTGACA-ATTTAAAC
1 CCGCACACTTAGTGCTACATAATC-AACTCCCACA-TTAAGTGCT-ACATAATCAAAC
97234 CCGCACACTTAG
1 CCGCACACTTAG
97246 CGCCAATCTC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
54 9 0.16
55 11 0.19
56 9 0.16
57 25 0.44
58 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (55 bp):
CCGCACACTTAGTGCTACATAATCAACTCCCACATTAAGTGCTACATAATCAAAC
Found at i:105309 original size:28 final size:28
Alignment explanation
Indices: 105246--105396 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
105236 ATATTAAGTC
*
105246 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
105273 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
105301 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
105329 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
105357 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
105386 CGCACACTTAG
1 CGCACACTTAG
105397 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:109300 original size:30 final size:31
Alignment explanation
Indices: 109250--109309 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
109240 ACTTAATTTA
*
109250 ATGATGCTGACTTAAACTAACATGGGAGTTT
1 ATGATGCTGACTTAAACTAACATGGAAGTTT
109281 ATGATGCAT-ACTT-AACTAACATGGAAGTT
1 ATGATGC-TGACTTAAACTAACATGGAAGTT
109310 ACATAATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 15 0.56
31 11 0.41
32 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (31 bp):
ATGATGCTGACTTAAACTAACATGGAAGTTT
Found at i:109319 original size:31 final size:31
Alignment explanation
Indices: 109259--109321 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
109249 AATGATGCTG
* * *
109259 ACTTAAACTAACATGGGAGTTTATGATGCAT
1 ACTTAAACTAACATGGAAGTTCATAATGCAT
109290 ACTT-AACTAACATGGAAGTTACATAATGCAT
1 ACTTAAACTAACATGGAAGTT-CATAATGCAT
109321 A
1 A
109322 ACTTTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (31 bp):
ACTTAAACTAACATGGAAGTTCATAATGCAT
Found at i:111067 original size:18 final size:18
Alignment explanation
Indices: 111018--111074 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
111008 TTACTCAATA
111018 TCTTTTCTCTCTTCAA-TT
1 TCTTTTCTCT-TTCAATTT
* * *
111036 TCAATCTCTTTTTCAATTT
1 TC-TTTTCTCTTTCAATTT
111055 TCTTTTCTCTTTCACATTT
1 TCTTTTCTCTTTCA-ATTT
111074 T
1 T
111075 TGTTTACTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTTTCTCTTTCAATTT
Found at i:121570 original size:19 final size:19
Alignment explanation
Indices: 121546--121589 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
121536 TTTCCAACAC
121546 TTTTTTTTGAAGTTTAGTT
1 TTTTTTTTGAAGTTTAGTT
* *
121565 TTTTTTTTGAATTTTTGTT
1 TTTTTTTTGAAGTTTAGTT
121584 TTTTTT
1 TTTTTT
121590 CAATACTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (19 bp):
TTTTTTTTGAAGTTTAGTT
Found at i:123136 original size:50 final size:52
Alignment explanation
Indices: 123011--123141 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 52
123001 AAACTAAATG
* * *
123011 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
** * *
123063 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAACATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
123113 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
123142 CAAAACACAC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
50 32 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:129918 original size:16 final size:16
Alignment explanation
Indices: 129897--129930 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
129887 TATTGAGCCA
129897 TAATTAAACACTTAAT
1 TAATTAAACACTTAAT
**
129913 TAATTAAGTACTTAAT
1 TAATTAAACACTTAAT
129929 TA
1 TA
129931 GGAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
TAATTAAACACTTAAT
Found at i:130012 original size:17 final size:18
Alignment explanation
Indices: 129974--130017 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
129964 CCAAGTTTTT
*
129974 TTTAAC-AAATTAATTAA
1 TTTAACTAAATTAACTAA
*
129991 CTTAACTAAA-TAACTAA
1 TTTAACTAAATTAACTAA
130008 TTTAACTAAA
1 TTTAACTAAA
130018 GACAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAACTAAATTAACTAA
Found at i:136830 original size:105 final size:105
Alignment explanation
Indices: 136664--136860 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 105
136654 GTCTACCTCT
* * *
136664 AAGGGAAGTCAGTCCAACTCGGATTAGGACATCCATCGCATCAAGTCAATCCCAAAACTCAACTT
1 AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
* *
136729 CAGTTCTCAGTTCAACTTCAAGAGGAGTCGGTCCAACTCC
66 CAGTTATAAGTTCAACTTCAAGAGGAGTCGGTCCAACTCC
* * * ** * * *
136769 AAGGGTAGTGAGTCCAACTCGGATGAGAACATCGAGCTTATCGAGTCAATCCCATAGCTCAACTT
1 AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
* *
136834 CAGTTATAAGTTTAACTTCAAGTGGAG
66 CAGTTATAAGTTCAACTTCAAGAGGAG
136861 CCAATCCAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
105 77 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (105 bp):
AAGGGAAGTCAGTCCAACTCGGATGAGAACATCCAGCGCATCAAGTCAATCCCAAAACTCAACTT
CAGTTATAAGTTCAACTTCAAGAGGAGTCGGTCCAACTCC
Found at i:136935 original size:84 final size:84
Alignment explanation
Indices: 136781--136935 Score: 204
Period size: 84 Copynumber: 1.8 Consensus size: 84
136771 GGGTAGTGAG
* * * * *
136781 TCCAACTCGGATGAGAACATCGAGCTTATCGAGTCAATCCCATAGCTCAACTTCAGTTATAAGTT
1 TCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAGTT
*
136846 TAACTTCAAGTGGAGCCAA
66 CAACTTCAAGTGGAGCCAA
** * *
136865 TCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTTAGT
1 TCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATA-TAAGT
136929 TCAACTT
65 TCAACTT
136936 TAAGAGGGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
83 2 0.03
84 58 0.97
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (84 bp):
TCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGCTCAACTCCAGATATAAGTT
CAACTTCAAGTGGAGCCAA
Found at i:137177 original size:105 final size:105
Alignment explanation
Indices: 136865--137792 Score: 807
Period size: 105 Copynumber: 8.9 Consensus size: 105
136855 GTGGAGCCAA
* * * * * * * *
136865 TCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTTAGT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTA-TCAGT
** * * *
136929 TCAACTTTAAGAGGGGTCAGTCCTACTCCAAGGGTAATCAG
65 TCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
* * * * * *
136970 TCCAACTCGAATGAGTACATCCACCTCATTGAGTCTATCCCATAGCTCCACTTTAG-T-T-AGTT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
* * *
137032 CAACTCCAAGAAGAGTCAATCCAACTCCAAGGGTAGTGAG
66 CAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
* * * *
137072 TCCAACTCGGATAAGGACATACACCTCATCGAGTCAATCGCATAGTTCAACTTCAGTTATCAGTT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
* * * *
137137 CAACTCCAAGAGGAGTCATTCCAACTTCAAGGGTACTGAG
66 CAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
* * * * *
137177 TCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCTCATTT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
*
137242 CAACCCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
66 CAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
* ** * * * * * *
137282 TCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATTAGT
1 TCCAACTCGGATGAGGACATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGT
* * *
137346 TCAACTCCAAG-GGTAGTCAGTCCAACTCGGATGGG-A-ACA-
65 TCAACTCCAAGAGG-AGTCAGTCCAACTC-CAAGGGTAGTCAG
* * * * * * * * * *
137385 TCCACCTC--ATCGA-GTCAATCC-CAT-AGCTCAACTTCAGT--TATCAGTTCAACTCCAAGAG
1 TCCAACTCGGAT-GAGGAC-ATCCACCTCA--TCGA-GTCAATCCCAT-AGCTCAACTTC-AG-T
* * * * * * * * * *
137443 GAGTAAGTCCAACTCCAA-ATGTTA-TCATTTCAATTCCAAGGGGACTCAA
58 TA-TCAGTTCAACTCCAAGA-G-GAGTCAGTCCAACTCCAAGGGTAGTCAG
** * * *
137492 TCCAACTCCAATCAGGACATCCACCTCATCTAGTCAATCCCATAGCTCCACTTCAGTTATCAGTT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
* *
137557 CAACTCCAAGAGGATTCAGTCCAACTCCAAGGGTAGTTAG
66 CAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
137597 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATC-GAT
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAG-T
* *
137661 TCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAG
65 TCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
* * * * *
137702 TCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCCCATAGCTCAACTTCAATTACCAGTC
1 TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
* *
137767 CAACTCCAATG-GTAGTTAGTCCAACT
66 CAACTCCAA-GAGGAGTCAGTCCAACT
137793 TGGATGAGGA
Statistics
Matches: 661, Mismatches: 128, Indels: 68
0.77 0.15 0.08
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 97 0.15
103 14 0.02
104 12 0.02
105 478 0.72
106 13 0.02
107 13 0.02
108 16 0.02
109 8 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (105 bp):
TCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTT
CAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAG
Found at i:137271 original size:21 final size:21
Alignment explanation
Indices: 137242--137286 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
137232 GTTCTCATTT
137242 CAACCCCAAGAGG-AGTCAGTC
1 CAACCCCAAG-GGTAGTCAGTC
*
137263 CAACTCCAAGGGTAGTCAGTC
1 CAACCCCAAGGGTAGTCAGTC
137284 CAA
1 CAA
137287 TTCAAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.13
Consensus pattern (21 bp):
CAACCCCAAGGGTAGTCAGTC
Found at i:137341 original size:210 final size:208
Alignment explanation
Indices: 136882--137373 Score: 544
Period size: 207 Copynumber: 2.4 Consensus size: 208
136872 CGGATGAGGG
* * * * * * * ** *
136882 CATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCA-ATAGTTAGTTCAACTTTAAGAGGGGT
1 CATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTA-TCAGTTCAACTCCAAGAGGAGT
* * * * * ** *
136946 CAGTCCTACTCCAAGGGTAATCAGTCCAACTCGAATGAGTACATCCACCTCATTGAGTCTATCCC
65 CAGTCCAACTCCAAGGGTACT-AGTCCAACTCGGATGAGGACATCCAACTCATCAAGTCAATCCC
* * * * *
137011 ATAGCTCCACTTTAG-TT-AGTTCAACTCCAAGAAGAGTCAATCCAACTCCAAGGGTAGTGAGTC
129 ATAGCTCAACTTCAGTTTCAGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTC
**
137074 CAACTCGGATAAGGA
194 CAACTCAAATAAGGA
* * *
137089 CATACACCTCATCGAGTCAATCGCATAGTTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTC
1 CATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTC
* * *
137154 ATTCCAACTTCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAATCCCA
66 AGTCCAACTCCAAGGGTACT-AGTCCAACTCGGATGAGGACATCCAACTCATCAAGTCAATCCCA
* *
137219 TAGCTCAACTTCAGTTCTCATTTCAACCCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTC
130 TAGCTCAACTTCAGTT-TCAGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTC
* *
137284 CAATTCAAATAAGAA
194 CAACTCAAATAAGGA
* * * *
137299 CATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATTAGTTCAACTCCAAG-GGTAG
1 CATCCA-CCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-AG
137362 TCAGTCCAACTC
64 TCAGTCCAACTC
137374 GGATGGGAAC
Statistics
Matches: 234, Mismatches: 45, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
207 114 0.49
208 3 0.01
209 3 0.01
210 112 0.48
211 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (208 bp):
CATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTC
AGTCCAACTCCAAGGGTACTAGTCCAACTCGGATGAGGACATCCAACTCATCAAGTCAATCCCAT
AGCTCAACTTCAGTTTCAGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTCAGTCCA
ACTCAAATAAGGA
Found at i:137404 original size:84 final size:84
Alignment explanation
Indices: 137257--137462 Score: 272
Period size: 84 Copynumber: 2.4 Consensus size: 84
137247 CCAAGAGGAG
* * *
137257 TCAGTCCAACTCCAAGGGTAGTCAGTCCAATTCAAATAAGAACATCCAGCATATTGAGTCAATCC
1 TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCATATCGAGTCAATCC
*
137322 CATAGCTCGACTTCAGTTA
66 CATAGCTCAACTTCAGTTA
* ** ** *
137341 TTAGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATGGGAACATCCA-CCTCATCGAGTCAATC
1 TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCAT-ATCGAGTCAATC
137405 CCATAGCTCAACTTCAGTTA
65 CCATAGCTCAACTTCAGTTA
*
137425 TCAGTTCAACTCCAAGAGG-AGTAAGTCCAACTCCAAAT
1 TCAGTTCAACTCCAAG-GGTAGTCAGTCCAACT-CAAAT
137463 GTTATCATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
83 2 0.02
84 98 0.93
85 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (84 bp):
TCAGTTCAACTCCAAGGGTAGTCAGTCCAACTCAAATAAGAACATCCAGCATATCGAGTCAATCC
CATAGCTCAACTTCAGTTA
Found at i:137469 original size:42 final size:42
Alignment explanation
Indices: 137421--137502 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
137411 CTCAACTTCA
*
137421 GTTATCAGTTCAACTCCAAGAGGAGT-AAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGACTCAA-TCCAACTCCAAAT
* * *
137463 GTTATCATTTCAATTCCAAGGGGACTCAATCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAA
137503 TCAGGACATC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGACTCAATCCAACTCCAAAT
Found at i:137582 original size:420 final size:420
Alignment explanation
Indices: 137085--137880 Score: 1202
Period size: 420 Copynumber: 1.9 Consensus size: 420
137075 AACTCGGATA
* *
137085 AGGACATACACCTCATCGAGTCAATCGCATAGTTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
1 AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
* *
137150 AGTCATTCCAACTTCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
66 AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
* *
137215 CCCATAGCTCAACTTCAGTTCTC-ATTTCAACCCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGT
131 CCCATAGCTCAACTTCAGTTATCGA-TTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGT
* ** * * **
137279 CAGTCCAATTCAAATAAGAACATCCAGCAT-ATTGAGTCAATCCCATAGCTCGACTTCAGTTATT
195 CAGTCCAACTCAAATAAGAACATCCA-CATCATCCAGTCAATCCCATAGCTCAACTTCAATTACC
*
137343 AGTTCAACTCCAAGGGTAGTCAGTCCAACTCGGATG-GGAACATCCACCTCATCGAGTCAATCCC
259 AGTCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGG-ACATCCACCTCATCGAGTCAATCCC
*
137407 ATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATT
323 ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATT
137472 TCAATTCCAAGGGGACTCAATCCAACTCCAATC
388 TCAATTCCAAGGGGACTCAATCCAACTCCAATC
* * *
137505 AGGACATCCACCTCATCTAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCAACTCCAAGAGG
1 AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
* * * * * *
137570 ATTCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAAT
66 AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
* *
137635 CCCATAGCTCAACTTCAGTTATCGATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTT
131 CCCATAGCTCAACTTCAGTTATCGATTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTC
* * * *
137700 AGTCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCCCATAGCTCAACTTCAATTACCAG
196 AGTCCAACTCAAATAAGAACATCCACATCATCCAGTCAATCCCATAGCTCAACTTCAATTACCAG
* * * * * *
137765 TCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTCATA
261 TCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATA
* *
137830 GCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAA
326 GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
137881 GGGTAGTTAG
Statistics
Matches: 335, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
419 2 0.01
420 330 0.99
421 3 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (420 bp):
AGGACATACACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
AGTCAGTCCAACTCCAAGGGTACTGAGTCCAACTAGGATGAGGACATCCAACTCATCAAGTCAAT
CCCATAGCTCAACTTCAGTTATCGATTCAACCCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTC
AGTCCAACTCAAATAAGAACATCCACATCATCCAGTCAATCCCATAGCTCAACTTCAATTACCAG
TCCAACTCCAAGGGTAGTCAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATA
GCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAATGTTATCATTTCA
ATTCCAAGGGGACTCAATCCAACTCCAATC
Found at i:137598 original size:21 final size:21
Alignment explanation
Indices: 137551--137604 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
137541 ACTTCAGTTA
*
137551 TCAGTTCAACTCCAAGAGGAT
1 TCAGTCCAACTCCAAGAGGAT
137572 TCAGTCCAACTCCAAG-GGTAGT
1 TCAGTCCAACTCCAAGAGG-A-T
137594 T-AGTCCAACTC
1 TCAGTCCAACTC
137605 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAT
Found at i:137688 original size:21 final size:21
Alignment explanation
Indices: 137662--137709 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
137652 GTTATCGATT
137662 CAACTCCAAGAGG-AGCCAGTC
1 CAACTCCAAG-GGTAGCCAGTC
**
137683 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGCCAGTC
137704 CAACTC
1 CAACTC
137710 AGATGAGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (21 bp):
CAACTCCAAGGGTAGCCAGTC
Found at i:137770 original size:84 final size:84
Alignment explanation
Indices: 137677--137877 Score: 278
Period size: 84 Copynumber: 2.4 Consensus size: 84
137667 CCAAGAGGAG
137677 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCC
1 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCC
*
137742 CATAGCTCAACTTCAATTA
66 CATAGCTCAACCTCAATTA
* ** * * *
137761 CCAGTCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCT
1 CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCC
*
137826 CATAGCTCAACCTCAGTTA
66 CATAGCTCAACCTCAATTA
* * * *
137845 TCAGTTCAACTCTAAGAGG-AGTCAGTCCAACTC
1 CCAGTCCAACTCCAAG-GGTAGTTAGTCCAACTC
137878 CAAGGGTAGT
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 100 0.98
85 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (84 bp):
CCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCC
CATAGCTCAACCTCAATTA
Found at i:137812 original size:189 final size:189
Alignment explanation
Indices: 137573--137917 Score: 593
Period size: 189 Copynumber: 1.8 Consensus size: 189
137563 CAAGAGGATT
137573 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
*
137638 ATAGCTCAACTTCAGTTATC-GATTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAG
66 ATAGCTCAACCTCAGTTATCAG-TTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAG
137702 TCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCCCATAGCTCAACTTCAATTAC
130 TCCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCCCATAGCTCAACTTCAATTAC
* * * * *
137762 CAGTCCAACTCCAATGGTAGTTAGTCCAACTTGGATGAGGACGTCCACCTCATCTAGTCAATCTC
1 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
* *
137827 ATAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGT
66 ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGT
*
137892 CCAACTCGGATGAGGACATCCACCTC
131 CCAACTCAGATGAGGACATCCACCTC
137918 TAGCTCAACC
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
189 145 0.99
190 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (189 bp):
CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
ATAGCTCAACCTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTCCAACTCCAAGGGTAGTTAGT
CCAACTCAGATGAGGACATCCACCTCATCCAGTCAATCCCATAGCTCAACTTCAATTAC
Found at i:137878 original size:210 final size:203
Alignment explanation
Indices: 137242--137898 Score: 423
Period size: 210 Copynumber: 3.1 Consensus size: 203
137232 GTTCTCATTT
*
137242 CAACCCCAAGAGG-AGTCAGTCCAACTCCAAGGGTAGTCAGTCCAATTCAAATAAGAACATCCAG
1 CAACTCCAAG-GGTAGTCAGTCCAACTCCAAGGG-A-TCAGTCCAA-TC-AAT-AG-ACATCCA-
** * * * *
137306 CATATTGAGTCAATCCCATAGCTCGACTTCAGTTATTAGTTCAACTCCAAGGGTAGTCAGTCCAA
58 CATATCCAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAAGGTAGTTAGTCCAA
137371 CTCGGATG-GGAACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAAC
123 CTCGGATGAGG-ACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAAC
*
137435 TCCAAGAGGAGTAAGTC
187 TCCAAGAGGAGTCAGTC
* * * * * *
137452 CAACTCCAAATGTTA-TCATTTCAATTCCAAGGGGACTCAATCCAACTCCAATCAGGACATCCAC
1 CAACTCC-AAGGGTAGTCAGTCCAACTCCAA-GGGA-TCAGTCCAA-T-CAAT-A-GACATCCAC
* * *
137516 CTCATCTAGTCAATCCCATAGCTCCACTTCAGTTATCAGTTCAACTCCAAGAGG-A-TTCAGTCC
59 AT-ATCCAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAA-AGGTAGTT-AGTCC
* * * * * * * * *
137579 AACTCCAAGGGT-AGTTA-GTCCAACTCGGAT-GAG-GACAT-CC--ACCTCATCGAGTCAATCC
121 AACT-C--GGATGAG-GACATCCACCTC--ATCGAGTCA-ATCCCATAGCTCAAC--TTCAGT--
* * * ** *
137637 CAT-AGCTCAACTTC-AG-TTA-TC-GATT
175 TATCAGTTCAACTCCAAGAGGAGTCAG-TC
* *
137662 CAACTCCAAGAGG-AGCCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCAC
1 CAACTCCAAG-GGTAGTCAGTCCAACTCCAAGGG-A-TCAGTCCAA-TCA-AT-A-GACATCCAC
* * * * *
137726 CTCATCCAGTCAATCCCATAGCTCAACTTCAATTACCAGTCCAACTCCAATGGTAGTTAGTCCAA
59 AT-ATCCAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAAGGTAGTTAGTCCAA
* * * * *
137791 CTTGGATGAGGACGTCCACCTCATCTAGTCAATCTCATAGCTCAACCTCAGTTATCAGTTCAACT
123 CTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACT
*
137856 CTAAGAGGAGTCAGTC
188 CCAAGAGGAGTCAGTC
*
137872 CAACTCCAAGGGTAGTTAGTCCAACTC
1 CAACTCCAAGGGTAGTCAGTCCAACTC
137899 GGATGAGGAC
Statistics
Matches: 338, Mismatches: 69, Indels: 80
0.69 0.14 0.16
Matches are distributed among these distances:
206 4 0.01
207 16 0.05
208 18 0.05
209 17 0.05
210 229 0.68
211 15 0.04
212 16 0.05
213 19 0.06
214 4 0.01
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (203 bp):
CAACTCCAAGGGTAGTCAGTCCAACTCCAAGGGATCAGTCCAATCAATAGACATCCACATATCCA
GTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAAGGTAGTTAGTCCAACTCGGATG
AGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG
AGTCAGTC
Found at i:137892 original size:21 final size:21
Alignment explanation
Indices: 137845--137898 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
137835 ACCTCAGTTA
* *
137845 TCAGTTCAACTCTAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
137866 TCAGTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
137887 TTAGTCCAACTC
1 TCAGTCCAACTC
137899 GGATGAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:137927 original size:90 final size:90
Alignment explanation
Indices: 137828--138097 Score: 425
Period size: 90 Copynumber: 3.0 Consensus size: 90
137818 GTCAATCTCA
* *
137828 TAGCTCAACCTCAGTTATCAGTTCAACTCTAAGAGGAGTCAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
137893 CAACTCGGATGAGGACATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
*
137918 TAGCTCAACCTCAGTTATCAATTCAACTCCAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
1 TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
* *
137983 CAAATCGGATGAGGATATCCACCTC
66 CAACTCGGATGAGGACATCCACCTC
** * *
138008 TAGCTCAACCTCAGTTATCAATTCAACT-TCAAGAGGAGTTAGTCCTTCTCCAAGGGTAGTCAAT
1 TAGCTCAACCTCAGTTATCAATTCAACTCT-AAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGT
**
138072 CCAACTCAAATGAGGACATCCACCTC
65 CCAACTCGGATGAGGACATCCACCTC
138098 ATCTAGTCAA
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
90 165 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (90 bp):
TAGCTCAACCTCAGTTATCAATTCAACTCTAAGAGGAGTTAGTCCAACTCCAAGGGTAGTTAGTC
CAACTCGGATGAGGACATCCACCTC
Found at i:137966 original size:21 final size:21
Alignment explanation
Indices: 137941--137985 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
137931 GTTATCAATT
137941 CAACTCCAAGAGG-AGTTAGTC
1 CAACTCCAAG-GGTAGTTAGTC
137962 CAACTCCAAGGGTAGTTAGTC
1 CAACTCCAAGGGTAGTTAGTC
137983 CAA
1 CAA
137986 ATCGGATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
CAACTCCAAGGGTAGTTAGTC
Found at i:143440 original size:41 final size:40
Alignment explanation
Indices: 143355--143498 Score: 105
Period size: 41 Copynumber: 3.5 Consensus size: 40
143345 TTAGAATATT
* * * * * **
143355 GCCGCTAATGTTTGGGGTTTTAGCGACGTTTTTAGTTTTGC
1 GCCGCTAATG-CTCGGGTTTTAGCGGCGTTTATAGATAAGC
*
143396 GCCGCTAATGCTCGTGGTTTTAGCGGCGTTTCT-GATTCAA-C
1 GCCGCTAATGCTCG-GGTTTTAGCGGCGTTTATAGA-T-AAGC
* *
143437 GCCGGC-AAAGACTAGGGTTTTAGCGGCGTTTATAGATAAGC
1 GCC-GCTAATG-CTCGGGTTTTAGCGGCGTTTATAGATAAGC
*
143478 ACCGCTAATGCTCGGGGTTTT
1 GCCGCTAATGCTC-GGGTTTT
143499 TAGTGGAGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
40 9 0.11
41 65 0.80
42 7 0.09
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.34
Consensus pattern (40 bp):
GCCGCTAATGCTCGGGTTTTAGCGGCGTTTATAGATAAGC
Found at i:144146 original size:7 final size:7
Alignment explanation
Indices: 144134--144181 Score: 62
Period size: 7 Copynumber: 7.0 Consensus size: 7
144124 CTTGTATGGA
144134 TTTAGGG
1 TTTAGGG
*
144141 TTTAGGA
1 TTTAGGG
*
144148 TTTAAGG
1 TTTAGGG
144155 TTTAGGG
1 TTTAGGG
144162 TTTAGGG
1 TTTAGGG
*
144169 TTAAGGG
1 TTTAGGG
144176 -TTAGGG
1 TTTAGGG
144182 GTTAAAAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:144160 original size:21 final size:20
Alignment explanation
Indices: 144134--144181 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
144124 CTTGTATGGA
*
144134 TTTAGGGTTTAGGATTTAAGG
1 TTTAGGGTTTAGG-GTTAAGG
144155 TTTAGGGTTTAGGGTTAAGG
1 TTTAGGGTTTAGGGTTAAGG
*
144175 GTTAGGG
1 TTTAGGG
144182 GTTAAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTAAGG
Found at i:144184 original size:21 final size:21
Alignment explanation
Indices: 144135--144181 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
144125 TTGTATGGAT
* *
144135 TTAGGGTTTAGGATTTAAGGT
1 TTAGGGTTTAGGAGTTAAGGG
144156 TTAGGGTTTAGG-GTTAAGGG
1 TTAGGGTTTAGGAGTTAAGGG
144176 TTAGGG
1 TTAGGG
144182 GTTAAAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.38
Consensus pattern (21 bp):
TTAGGGTTTAGGAGTTAAGGG
Found at i:144462 original size:13 final size:14
Alignment explanation
Indices: 144444--144474 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
144434 GTGGACACTT
144444 GTTT-GGATTTAGG
1 GTTTGGGATTTAGG
144457 GTTTGGGATTTAGG
1 GTTTGGGATTTAGG
144471 GTTT
1 GTTT
144475 AGGGGTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (14 bp):
GTTTGGGATTTAGG
Found at i:145755 original size:336 final size:332
Alignment explanation
Indices: 144866--145996 Score: 1186
Period size: 336 Copynumber: 3.4 Consensus size: 332
144856 TAAGTAAAAC
* * * * * * * *
144866 AATTTTTAGTGGCGTGTTTAAAAAAAATGCCAGAACTGTGCATTGAAGCTTAATAAAACGGCGCA
1 AATTTTTACTGGCAT-TTTACAGAAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCC
* * * * * *
144931 GTTTCCGATTAGAACTTTAACA-ATTAGTGGCGTTTTTGTTA-AAAACACCGCTAATGCT-GAAG
65 GTTTCGGATTAGAACTTTAA-ATTTTAGTGGCG-CTTT-TTAGAAAACGCCGCAAATG-TACAAG
* * * * *
144993 TAATAGCGGCGTTTGTACAAGAAAT-GCCGCAAAAGTGACTTAAAATTTTGGCTGAACGACGCCG
126 CAATAGCGGCGTTTGT-CCAGAAATCGCCGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCG
* * * *
145057 TTTCTGTCCACAATTTTTAACTTAGTATTTTCTCTATATTAATTAAACGGCGCCGTTTATGTTAA
190 TTTCTGT--ACAGTTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGCGCCGTTTCTGTTAA
* * * * * * * * *
145122 TTTTTAGTGGCATTTGTTCAGGAAACGCCGCAAAAGTGACTTGAAATATTGGCTAAAAGTCGACA
253 TTTTT-GTGGCGTTT-TTCACGAAACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACG
* *
145187 TCTAACTTAAGCAAATT
316 TTTAGCTTAAGCAAATT
* * * * *
145204 AATTTTTAGTGGCATTTTAAAGGAAAACGCCAGAAATGTGCATTAAATCTTAACAAAACGGTGCC
1 AATTTTTACTGGCATTTTACA-GAAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCC
* * * *
145269 GTTTCGGATTAGAACCTT-AATTCTTTGTGGCGCTTCTTTAG-AAACGCCGCAAATATACAAGCT
65 GTTTCGGATTAGAACTTTAAATT-TTAGTGGCGCTT-TTTAGAAAACGCCGCAAATGTACAAGCA
* * *
145332 ATAGCGGCGTTTGTTCA-ATAAACGCCGCAAAAGTGTCTTAAAATTTT-TGGTAAACGACGCCGT
128 ATAGCGGCGTTTGTCCAGA-AATCGCCGCAAAAGTGTCTTAAAATTTTGT-CTAAACGACGCCGT
* * * *
145395 CTCTATACACGTTTTTATACTTAGCATTTTCTCTATATTAATTCAACGGCTCCATTTCTGTTAAT
191 TTCTGTACA-GTTTTTA-ACTTAGCATTTTCTCTATATTAATTCAACGGCGCCGTTTCTGTTAAT
** * * **
145460 TTCTTGTGGCGTTTTTACATAAAACGCTGCAAAAGTGACATAAAATATTGCCTAAACGGCTTCGT
254 TT-TTGTGGCGTTTTT-CACGAAACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGT
145525 TTAGCTTAAGCAAATT
317 TTAGCTTAAGCAAATT
*
145541 AATTTTTACTGGCATTTTAGCAGAAAACGCCAAAAATGTGC-TTAAAGCTTAATAAAACGGCGCC
1 AATTTTTACTGGCATTTTA-CAGAAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCC
145605 GTTTCGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAAT
65 GTTTCGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAAT
* * * * * *
145670 AGCGGCATTTGTCCAGGATTCACCGCAAAATTGTCTTAAAATTTTGTCTAAACGACGCCATTTCT
130 AGCGGCGTTTGTCCAGAAATCGCCGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCGTTTCT
* * *
145735 GTACTAGTTTTTTAACTTAGCATTTTCTCTAAATTAATCCAACGGCGCCGTTTCTCTTAATTTAT
195 GTAC-AG-TTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGCGCCGTTTCTGTTAATTT-T
* * * *
145800 AGTGGCGTTTTTGCACGAAACGCTGCAAAA-TGACTTAAAATATTGTCTAAACGACCCCGTTTTG
257 TGTGGCGTTTTT-CACGAAACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAG
*
145864 CTTAAGAAAATT
321 CTTAAGCAAATT
** * * * * * *
145876 AATTTTTACTACCGTTTTTACAGAAAATGCCAGAACTGTGCAATAAAGCTTAATTAAACGGTGCC
1 AATTTTTACTGGC-ATTTTACAGAAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCC
* * * ** *
145941 GTTTCAG-TTTGAACTTTAATTTTTAGTGGCATTTTTTTAAAAAACGCCGCAAATGT
65 GTTTCGGATTAGAACTTTAAATTTTAGTGGC-GCTTTTTAGAAAACGCCGCAAATGT
145997 TTCTTAAACT
Statistics
Matches: 668, Mismatches: 102, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
335 98 0.15
336 263 0.39
337 230 0.34
338 77 0.12
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (332 bp):
AATTTTTACTGGCATTTTACAGAAAACGCCAGAAATGTGCATTAAAGCTTAATAAAACGGCGCCG
TTTCGGATTAGAACTTTAAATTTTAGTGGCGCTTTTTAGAAAACGCCGCAAATGTACAAGCAATA
GCGGCGTTTGTCCAGAAATCGCCGCAAAAGTGTCTTAAAATTTTGTCTAAACGACGCCGTTTCTG
TACAGTTTTTAACTTAGCATTTTCTCTATATTAATTCAACGGCGCCGTTTCTGTTAATTTTTGTG
GCGTTTTTCACGAAACGCTGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGTTTAGCTTAA
GCAAATT
Found at i:147309 original size:13 final size:13
Alignment explanation
Indices: 147293--147356 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
147283 TGAAATATAT
*
147293 TACATAACTTAAA
1 TACATTACTTAAA
147306 TACATTACTTACTAA
1 TACATTACTTA--AA
147321 -A-ATTTACTTAAA
1 TACA-TTACTTAAA
*
147333 TATATTACTTAAA
1 TACATTACTTAAA
*
147346 TACATGACTTA
1 TACATTACTTA
147357 CTAAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 2 0.05
13 30 0.70
14 9 0.21
15 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (13 bp):
TACATTACTTAAA
Found at i:147312 original size:18 final size:17
Alignment explanation
Indices: 147271--147314 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
147261 TTACATTACT
*
147271 TACATTACTTACTGAAA
1 TACATTACTAACTGAAA
* *
147288 TATATTACATAACTTAAA
1 TACATTAC-TAACTGAAA
147306 TACATTACT
1 TACATTACT
147315 TACTAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (17 bp):
TACATTACTAACTGAAA
Found at i:147314 original size:31 final size:31
Alignment explanation
Indices: 147256--147314 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
147246 ATTTTCCGCT
* *
147256 ATATATTACATTACTTACATTACTTACTGAA
1 ATATATTACATAACTTACAATACTTACTGAA
147287 ATATATTACATAACTTA-AATACATTACT
1 ATATATTACATAACTTACAATAC-TTACT
147315 TACTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.41
Consensus pattern (31 bp):
ATATATTACATAACTTACAATACTTACTGAA
Found at i:147350 original size:40 final size:38
Alignment explanation
Indices: 147255--147402 Score: 140
Period size: 40 Copynumber: 3.9 Consensus size: 38
147245 TATTTTCCGC
** * *
147255 TATATATTACATTACTTACATTACTTACTGAAATAT-A-
1 TATATATTAC-TTAAATACATTACTTACTAAAATTTAAG
* * **
147292 T-TACATAACTTAAATACATTACTTACTAAAATTTACT
1 TATATATTACTTAAATACATTACTTACTAAAATTTAAG
*
147329 TAAATATATTACTTAAATACATGACTTACTAAAATTTAAG
1 T--ATATATTACTTAAATACATTACTTACTAAAATTTAAG
**
147369 TATATATTACATTACTTACATTACTTACTAAAAT
1 TATATATTAC-TTAAATACATTACTTACTAAAAT
147403 ATATTACATT
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
35 21 0.23
36 6 0.07
37 2 0.02
38 9 0.10
39 20 0.22
40 32 0.36
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (38 bp):
TATATATTACTTAAATACATTACTTACTAAAATTTAAG
Found at i:147414 original size:18 final size:18
Alignment explanation
Indices: 147388--147439 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
147378 CATTACTTAC
147388 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
* *
147405 ATTACATTACTTAAATGT
1 ATTACATTACTAAAATAT
*
147423 ATTAAATTACTTAAAAT
1 ATTACATTAC-TAAAAT
147440 TTATACATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:147682 original size:44 final size:44
Alignment explanation
Indices: 147619--147942 Score: 356
Period size: 44 Copynumber: 7.7 Consensus size: 44
147609 TAACATTTCT
*
147619 TACATAACTTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* *
147663 TACATAACATACGTAATACATAATACACAACTTAATTAAGATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
*
147707 TACATAACATACATAATACATAATACAC-A--TAACTTACATA--G
1 TACATAACATACATAATACATAATACACAACTTAA-TTA-ATATTA
* * *
147748 TACAT---A-AC-T-A-ACATTATACACAACTTACA-TACTA-CA
1 TACATAACATACATAATACATAATACACAACTTA-ATTAATATTA
** * * * *
147784 TTTATTACATA-A-CATACATTATACACAACTTAAATAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
*
147826 TACATAACGTACATAATACATAATACACAACTTAATTAATATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
* * *
147870 TACATAACGTACATAATACATAATACACAACTTGATTAAGATTA
1 TACATAACATACATAATACATAATACACAACTTAATTAATATTA
147914 TACATAACATACATAATACATAATACACA
1 TACATAACATACATAATACATAATACACA
147943 TAACTTACAT
Statistics
Matches: 239, Mismatches: 23, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
34 10 0.04
35 4 0.02
36 6 0.03
37 4 0.02
38 2 0.01
39 1 0.00
40 3 0.01
41 29 0.12
42 11 0.05
43 4 0.02
44 165 0.69
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.31
Consensus pattern (44 bp):
TACATAACATACATAATACATAATACACAACTTAATTAATATTA
Found at i:147752 original size:16 final size:15
Alignment explanation
Indices: 147733--147784 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
147723 TACATAATAC
147733 ACATAACTTACATAGT
1 ACATAACTTACATA-T
*
147749 ACATAACTAACATTAT
1 ACATAACTTACA-TAT
*
147765 ACACAACTTACATACT
1 ACATAACTTACATA-T
147781 ACAT
1 ACAT
147785 TTATTACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 26 0.87
17 2 0.07
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (15 bp):
ACATAACTTACATAT
Found at i:147753 original size:32 final size:32
Alignment explanation
Indices: 147707--147784 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
147697 ATTAAGATTA
147707 TACATAACATACATAA-T-ACATAATACACATAACT
1 TACAT-AC-TACATAACTAACATAATACAC--AACT
* *
147741 TACATAGTACATAACTAACATTATACACAACT
1 TACATACTACATAACTAACATAATACACAACT
147773 TACATACTACAT
1 TACATACTACAT
147785 TTATTACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 22 0.56
33 2 0.05
34 15 0.38
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (32 bp):
TACATACTACATAACTAACATAATACACAACT
Found at i:147959 original size:16 final size:15
Alignment explanation
Indices: 147940--148014 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 15
147930 TACATAATAC
147940 ACATAACTTACATAGT
1 ACATAACTTACATA-T
*
147956 ACATAACTAACATTAT
1 ACATAACTTACA-TAT
* *
147972 ACACAACTTACGTAACTT
1 ACATAACTTACAT-A--T
* *
147990 AAATAACGTACATAAT
1 ACATAACTTACAT-AT
148006 ACATAACTT
1 ACATAACTT
148015 TGATAACTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
15 1 0.02
16 30 0.67
17 2 0.04
18 12 0.27
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (15 bp):
ACATAACTTACATAT
Found at i:147968 original size:25 final size:25
Alignment explanation
Indices: 147827--147961 Score: 78
Period size: 25 Copynumber: 5.9 Consensus size: 25
147817 ATAATATTAT
*
147827 ACATAACGTACATAATACATAATAC
1 ACATAACATACATAATACATAATAC
* * *
147852 AC--AACTTA-AT--TA-ATATTAT
1 ACATAACATACATAATACATAATAC
*
147871 ACATAACGTACATAATACATAATAC
1 ACATAACATACATAATACATAATAC
** * * *
147896 AC--AAC-TTGAT--TA-AGATTAT
1 ACATAACATACATAATACATAATAC
147915 ACATAACATACATAATACATAATAC
1 ACATAACATACATAATACATAATAC
* *
147940 ACATAACTTACATAGTACATAA
1 ACATAACATACATAATACATAA
147962 CTAACATTAT
Statistics
Matches: 80, Mismatches: 18, Indels: 24
0.66 0.15 0.20
Matches are distributed among these distances:
19 13 0.16
20 4 0.05
21 8 0.10
22 10 0.12
23 8 0.10
24 4 0.05
25 33 0.41
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (25 bp):
ACATAACATACATAATACATAATAC
Found at i:148012 original size:25 final size:25
Alignment explanation
Indices: 147915--148049 Score: 79
Period size: 25 Copynumber: 5.4 Consensus size: 25
147905 TTAAGATTAT
147915 ACATAACATACATAATACATAA--TA
1 ACATAAC-TACATAATACATAACTTA
*
147939 CACATAACTTACATAGTACATAAC-TA
1 -ACATAAC-TACATAATACATAACTTA
* * *
147965 ACATTA-TACACAACTTACGTAACTTA
1 ACATAACTACATAA--TACATAACTTA
147991 A-ATAACGTACATAATACATAACTT-
1 ACATAAC-TACATAATACATAACTTA
** * *
148015 TGATAACTAACATTATACACAACTT-
1 ACATAACT-ACATAATACATAACTTA
148040 ACAT-ACTACA
1 ACATAACTACA
148050 ATTCTTACAT
Statistics
Matches: 88, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
23 8 0.09
24 4 0.05
25 65 0.74
26 5 0.06
27 6 0.07
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (25 bp):
ACATAACTACATAATACATAACTTA
Found at i:148027 original size:266 final size:266
Alignment explanation
Indices: 147751--148424 Score: 1249
Period size: 266 Copynumber: 2.5 Consensus size: 266
147741 TACATAGTAC
* *
147751 ATAACTAACATTATACACAACTTACATACTACATTTATTACATAACATACATTATACACAACTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
147816 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
* *
147881 CATAATACATAATACACAACTTGATTAAGATTATACATAACATACATAATACATAATACACATAA
131 CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
147946 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
196 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
148011 ACTTTG
261 ACTTTG
*
148017 ATAACTAACATTATACACAACTTACATACTACAATTCTTACATAACTTACATTATACACAACTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
148082 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
*
148147 CATAATACACAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
131 CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
*
148212 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAATGTACATAATACATA
196 CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
148277 ACTTTG
261 ACTTTG
* * *
148283 GTAACTAACATTATACACAACTTACATAATACATTTCTTACATAACTTTCATTATACACAACTTA
1 ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
148348 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
66 AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
*
148413 CCTAATACATAA
131 CATAATACATAA
148425 ATATATATCA
Statistics
Matches: 395, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
266 395 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (266 bp):
ATAACTAACATTATACACAACTTACATACTACATTTCTTACATAACTTACATTATACACAACTTA
AATAATATTATACATAACGTACATAATACATAATACACAACTTAATTAATATTATACATAACGTA
CATAATACATAATAAACAACTTAATTAAGATTATACATAACATACATAATACATAATACACATAA
CTTACATAGTACATAACTAACATTATACACAACTTACGTAACTTAAATAACGTACATAATACATA
ACTTTG
Found at i:148065 original size:9 final size:9
Alignment explanation
Indices: 147914--148068 Score: 59
Period size: 9 Copynumber: 18.6 Consensus size: 9
147904 ATTAAGATTA
*
147914 TACATAACA
1 TACATAACT
147923 TACATAA--
1 TACATAACT
147930 TACATAA-T
1 TACATAACT
*
147938 ACACATAACT
1 -TACATAACT
*
147948 TACAT-A-G
1 TACATAACT
147955 TACATAACT
1 TACATAACT
* *
147964 AACATTA--
1 TACATAACT
*
147971 TACACAACT
1 TACATAACT
*
147980 TACGTAACT
1 TACATAACT
* *
147989 TAAATAACG
1 TACATAACT
147998 TACATAA--
1 TACATAACT
148005 TACATAACT
1 TACATAACT
**
148014 TTGATAACT
1 TACATAACT
* *
148023 AACATTA--
1 TACATAACT
*
148030 TACACAACT
1 TACATAACT
148039 TACAT-AC-
1 TACATAACT
*
148046 TACA-ATTCT
1 TACATA-ACT
148055 TACATAACT
1 TACATAACT
148064 TACAT
1 TACAT
148069 TATACACAAC
Statistics
Matches: 104, Mismatches: 27, Indels: 30
0.65 0.17 0.19
Matches are distributed among these distances:
7 31 0.30
8 5 0.05
9 66 0.63
10 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (9 bp):
TACATAACT
Found at i:148081 original size:25 final size:25
Alignment explanation
Indices: 147955--148125 Score: 69
Period size: 25 Copynumber: 7.1 Consensus size: 25
147945 ACTTACATAG
*
147955 TACATAACTAACATTATACACAACT
1 TACATAACTTACATTATACACAACT
* * * *
147980 TACGTAACTTAAATAACGTACATAA--
1 TACATAACTTACATTA--TACACAACT
** * *
148005 TACATAACTTTGATAACTA-AC-ATT
1 TACATAACTTACATTA-TACACAACT
* *
148029 ATACACAACTTACA-TACTACA-ATTCT
1 -TACATAACTTACATTA-TACACA-ACT
148055 TACATAACTTACATTATACACAACT
1 TACATAACTTACATTATACACAACT
* * *
148080 TAAATAA--T--ATTATACATAACG
1 TACATAACTTACATTATACACAACT
*
148101 TACATAA--TACATAATACACAACT
1 TACATAACTTACATTATACACAACT
148124 TA
1 TA
148126 ATTAATATTA
Statistics
Matches: 109, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
21 18 0.17
22 1 0.01
23 14 0.13
24 6 0.06
25 60 0.55
26 4 0.04
27 6 0.06
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (25 bp):
TACATAACTTACATTATACACAACT
Found at i:148093 original size:21 final size:21
Alignment explanation
Indices: 148067--148153 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
148057 CATAACTTAC
*
148067 ATTATACACAACTTAAATAAT
1 ATTATACACAACGTAAATAAT
* *
148088 ATTATACATAACGTACATAAT
1 ATTATACACAACGTAAATAAT
* * *
148109 ACATAATACACAACTTAATTAAT
1 --ATTATACACAACGTAAATAAT
* *
148132 ATTATACATAACGTACATAAT
1 ATTATACACAACGTAAATAAT
148153 A
1 A
148154 CACAATAAAC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
21 35 0.69
23 16 0.31
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTATACACAACGTAAATAAT
Found at i:148122 original size:44 final size:44
Alignment explanation
Indices: 148055--148424 Score: 267
Period size: 44 Copynumber: 8.3 Consensus size: 44
148045 CTACAATTCT
* * *
148055 TACATAACTTACATTATACACAACTTAAATAATATTATACATAACG
1 TACATAA--TACATAATACACAACTTAATTAATATTATACATAACA
*
148101 TACATAATACATAATACACAACTTAATTAATATTATACATAACG
1 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
* * *
148145 TACATAATACACAATAAACAACTTAATTAAGATTATACATAACA
1 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
*
148189 TACATAATACATAATACAC-A--TAACTTACATA--GTACATAAC-
1 TACATAATACATAATACACAACTTAA-TTA-ATATTATACATAACA
* * ** * * *
148229 TAACATTATACACAACTTACGTAACTTAAATAATGTACATAATACATAACT
1 T-ACATAATACATAA--TACACAACTTAATTAA--T--ATTATACATAACA
*** * * ** *
148280 TTGGTAACTAACATTATACACAACTT-A--CATA--ATACATTTCT
1 TACATAA-T-ACATAATACACAACTTAATTAATATTATACATAACA
* * * *
148321 TACATAACTTTCATTATACACAACTTAAATAATATTATACATAACG
1 TACATAA--TACATAATACACAACTTAATTAATATTATACATAACA
*
148367 TACATAATACATAATACACAACTTAATTAATATTATACATAACG
1 TACATAATACATAATACACAACTTAATTAATATTATACATAACA
*
148411 TACCTAATACATAA
1 TACATAATACATAA
148425 ATATATATCA
Statistics
Matches: 261, Mismatches: 40, Indels: 48
0.75 0.11 0.14
Matches are distributed among these distances:
40 1 0.00
41 49 0.19
42 5 0.02
43 7 0.03
44 144 0.55
45 3 0.01
46 25 0.10
47 1 0.00
48 1 0.00
49 1 0.00
50 18 0.07
51 2 0.01
52 4 0.02
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.32
Consensus pattern (44 bp):
TACATAATACATAATACACAACTTAATTAATATTATACATAACA
Found at i:148225 original size:16 final size:16
Alignment explanation
Indices: 148206--148248 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
148196 TACATAATAC
148206 ACATAACTTACA-TAGT
1 ACATAACTTACATTA-T
*
148222 ACATAACTAACATTAT
1 ACATAACTTACATTAT
*
148238 ACACAACTTAC
1 ACATAACTTAC
148249 GTAACTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (16 bp):
ACATAACTTACATTAT
Found at i:148312 original size:41 final size:41
Alignment explanation
Indices: 148264--148354 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
148254 TTAAATAATG
***
148264 TACATAATACATAACTTTGGTAACTAACATTATACACAACT
1 TACATAATACATAACTTACATAACTAACATTATACACAACT
** **
148305 TACATAATACATTTCTTACATAACTTTCATTATACACAACT
1 TACATAATACATAACTTACATAACTAACATTATACACAACT
*
148346 TAAATAATA
1 TACATAATA
148355 TTATACATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (41 bp):
TACATAATACATAACTTACATAACTAACATTATACACAACT
Found at i:148347 original size:25 final size:23
Alignment explanation
Indices: 148319--148391 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 23
148309 TAATACATTT
148319 CTTACATAACTTTCATTATACACAA
1 CTTACATAA--TTCATTATACACAA
* *
148344 CTTAAATAA-T-ATTATACATAA
1 CTTACATAATTCATTATACACAA
* * *
148365 CGTACATAATACATAATACACAA
1 CTTACATAATTCATTATACACAA
148388 CTTA
1 CTTA
148392 ATTAATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 17 0.45
22 1 0.03
23 12 0.32
25 8 0.21
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (23 bp):
CTTACATAATTCATTATACACAA
Found at i:148359 original size:21 final size:21
Alignment explanation
Indices: 148333--148405 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
148323 CATAACTTTC
148333 ATTATACACAACTTAAATAAT
1 ATTATACACAACTTAAATAAT
* * *
148354 ATTATACATAACGTACATAAT
1 ATTATACACAACTTAAATAAT
* *
148375 ACATAATACACAACTTAATTAAT
1 --ATTATACACAACTTAAATAAT
148398 ATTATACA
1 ATTATACA
148406 TAACGTACCT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 25 0.61
23 16 0.39
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (21 bp):
ATTATACACAACTTAAATAAT
Found at i:151195 original size:21 final size:21
Alignment explanation
Indices: 151171--151211 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
151161 AGCAAAGGCT
*
151171 GTAGCGAGGGAAGCAGAGGTA
1 GTAGCGAGAGAAGCAGAGGTA
*
151192 GTAGCGAGAGAAGCTGAGGT
1 GTAGCGAGAGAAGCAGAGGT
151212 TCAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.46, T:0.12
Consensus pattern (21 bp):
GTAGCGAGAGAAGCAGAGGTA
Found at i:151683 original size:42 final size:41
Alignment explanation
Indices: 151636--151994 Score: 358
Period size: 42 Copynumber: 8.5 Consensus size: 41
151626 CACTAAAAAT
* * * * *
151636 CCTGATCTATAGCGGCATTTTTAAAAAGGCACCGCTAAAAGT
1 CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCT-AAAGC
* * * * *
151678 CCTGATCTATAGCAGCATTTTTAAAAAAAGTGCCGCTAAAGGT
1 CCTGATCTATAGCGGCGTTTGT-AAAAAAGCGCCGCTAAA-GC
* * *
151721 CTTGATCTATAGCGGCGTTTGTAAAAGAAGCGTCACTAAAGAC
1 CCTGATCTATAGCGGCGTTTGTAAAA-AAGCGCCGCTAAAG-C
* *
151764 CCTGATCTATAACGGCGTTTGTAAAAAAGTGCCGCTAAAGGC
1 CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAA-GC
*
151806 CCTGATCTATAGCGGCGTTTGTAAAAAAGTGCCGCTAAAGAC
1 CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAG-C
* *
151848 CCTGGTCTATAGCGGCGTTTGTAGAAAAAGCGACGCTAAAGAC
1 CCTGATCTATAGCGGCGTTTGTA-AAAAAGCGCCGCTAAAG-C
* * ** *
151891 ACTGCTCTATAGCGGCGTTTGTGGAGAAGCGCCGCTAAAGAC
1 CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAG-C
* ** * *
151933 CCTGATCTATAGCGGCATTTGTGGAGAAGCACCGCTAAAGAC
1 CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAG-C
*
151975 CCTGATCTATAGCGACGTTT
1 CCTGATCTATAGCGGCGTTT
151995 TTTCTATAAA
Statistics
Matches: 277, Mismatches: 33, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
41 1 0.00
42 173 0.62
43 103 0.37
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (41 bp):
CCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGC
Found at i:151727 original size:43 final size:42
Alignment explanation
Indices: 151572--151988 Score: 341
Period size: 42 Copynumber: 9.8 Consensus size: 42
151562 GTGGCGTTTA
* * ** *
151572 TAAAAAAATACCGCTAAAGGTCCTGAGATATAGTGGCATTTG
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* * ** *
151614 TGGAAAAAGTGCCACTAAAAATCCTGATCTATAGCGGCATTTT
1 T-AAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* ** * * *
151657 TAAAAAGGCACCGCTAAAAGTCCTGATCTATAGCAGCATTTT
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* *
151699 TAAAAAAAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTG
1 T-AAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* * * ** * *
151742 TAAAAGAAGCGTCACTAAAGACCCTGATCTATAACGGCGTTTG
1 TAAAA-AAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* *
151785 TAAAAAAGTGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTG
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
** * *
151827 TAAAAAAGTGCCGCTAAAGACCCTGGTCTATAGCGGCGTTTG
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
* * * * *
151869 TAGAAAAAGCGACGCTAAA-GACACTGCTCTATAGCGGCGTTTG
1 TA-AAAAAGTGCCGCTAAAGGTC-CTGATCTATAGCGGCATTTG
** * * **
151912 TGGAGAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTG
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
** * ** **
151954 TGGAGAAGCACCGCTAAAGACCCTGATCTATAGCG
1 TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCG
151989 ACGTTTTTTC
Statistics
Matches: 316, Mismatches: 53, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
42 180 0.57
43 136 0.43
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (42 bp):
TAAAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCATTTG
Found at i:151876 original size:85 final size:85
Alignment explanation
Indices: 151564--151994 Score: 427
Period size: 85 Copynumber: 5.1 Consensus size: 85
151554 TAAAATTAGT
* *** ** ** * * *
151564 GGCGTTTATAAAAAAATACCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGTGCCAC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCGC
* *
151629 TAAAAATCCTGATCTATAGC
66 TAAAGACCCTGATCTATAGC
* * * * * * * *
151649 GGCATTTTTAAAAAGGCACCGCTAAA-AGTCCTGATCTATAGCAGCATTTTTAAAAAAAGTGCCG
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGA-CCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCG
** *
151713 CTAAAGGTCTTGATCTATAGC
65 CTAAAGACCCTGATCTATAGC
* * * *
151734 GGCGTTTGTAAAAGAAGCGTCACTAAAGACCCTGATCTATAACGGCGTTTGTA-AAAAAGTGCCG
1 GGCGTTTGTAAAA-AAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCG
*
151798 CTAAAGGCCCTGATCTATAGC
65 CTAAAGACCCTGATCTATAGC
* * * * *
151819 GGCGTTTGTAAAAAAGTGCCGCTAAAGACCCTGGTCTATAGCGGCGTTTGTAGAAAAAGCGACGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCGC
* *
151884 TAAAGACACTGCTCTATAGC
66 TAAAGACCCTGATCTATAGC
** * * * **
151904 GGCGTTTGTGGAGAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGT-GGAGAAGCACCGC
1 GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCGC
151968 TAAAGACCCTGATCTATAGC
66 TAAAGACCCTGATCTATAGC
*
151988 GACGTTT
1 GGCGTTT
151995 TTTCTATAAA
Statistics
Matches: 289, Mismatches: 53, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
84 67 0.23
85 193 0.67
86 28 0.10
87 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (85 bp):
GGCGTTTGTAAAAAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTGTAGAAAAAGTGCCGC
TAAAGACCCTGATCTATAGC
Found at i:151888 original size:127 final size:127
Alignment explanation
Indices: 151572--151994 Score: 443
Period size: 127 Copynumber: 3.3 Consensus size: 127
151562 GTGGCGTTTA
* ** ** * * * * * * *
151572 TAAAAAAATACCGCTAAAGGTCCTGAGATATAGTGGCATTTGTGGAAAAAGTGCCACTAAAAATC
1 TAAAAAAGTACCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACACTAAAGACC
* * * * * * * *
151637 CTGATCTATAGCGGCATTTTTAAAAAGGCACCGCTAAAAGTCCTGATCTATAGCAGCATTTT
66 CTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCATTTG
* ** * *
151699 TAAAAAAAGTGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTA-AAAGAAGCGTCACTAAAGA
1 T-AAAAAAGTACCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAA-AAGCGACACTAAAGA
* * *
151763 CCCTGATCTATAACGGCGTTTGTAAAAAAGTGCCGCTAAAGGCCCTGATCTATAGCGGCGTTTG
64 CCCTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCATTTG
* * * *
151827 TAAAAAAGTGCCGCTAAAGACCCTGGTCTATAGCGGCGTTTGTAGAAAAAGCGACGCTAAAGACA
1 TAAAAAAGTACCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACACTAAAGACC
* ** * *
151892 CTGCTCTATAGCGGCGTTTGTGGAGAAGCGCCGCTAAAGACCCTGATCTATAGCGGCATTTG
66 CTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCATTTG
** * * *
151954 TGGAGAAGCACCGCTAAAGACCCTGATCTATAGCGACGTTT
1 TAAAAAAGTACCGCTAAAGACCCTGATCTATAGCGGCGTTT
151995 TTTCTATAAA
Statistics
Matches: 248, Mismatches: 45, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
127 145 0.58
128 103 0.42
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (127 bp):
TAAAAAAGTACCGCTAAAGACCCTGATCTATAGCGGCGTTTGTAGAAAAAGCGACACTAAAGACC
CTGATCTATAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGCCCTGATCTATAGCGGCATTTG
Found at i:156313 original size:15 final size:15
Alignment explanation
Indices: 156267--156305 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
156257 TATAAGTAAT
156267 AAAACATAGTAATTA
1 AAAACATAGTAATTA
*
156282 AAAA-ATAATTAATTA
1 AAAACAT-AGTAATTA
156297 AAAACATAG
1 AAAACATAG
156306 CTATTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.10
15 16 0.80
16 2 0.10
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:156523 original size:19 final size:20
Alignment explanation
Indices: 156499--156536 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
156489 TGAGCTGGTT
156499 GGAGCT-AAAATGAGCTAAG
1 GGAGCTGAAAATGAGCTAAG
*
156518 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAAATGAGCTAA
156537 AATAGCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAAATGAGCTAAG
Found at i:156872 original size:20 final size:20
Alignment explanation
Indices: 156849--156888 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
156839 TAGCTCTAAC
*
156849 CAGCTCATTTGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
156869 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
156889 TAGTTTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.33
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:163971 original size:11 final size:11
Alignment explanation
Indices: 163944--163984 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
163934 AGTTTCTTCG
163944 AAAAAATTTGA
1 AAAAAATTTGA
163955 ACAAAAATTTGA
1 A-AAAAATTTGA
**
163967 AAAAAATTCAA
1 AAAAAATTTGA
163978 AAAAAAT
1 AAAAAAT
163985 ATTTCCATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (11 bp):
AAAAAATTTGA
Found at i:168024 original size:21 final size:22
Alignment explanation
Indices: 167995--168045 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
167985 TCTCTCTCGC
*
167995 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
168016 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
168038 TTT-ATTTT
1 TTTCATTTT
168046 TCTCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:168051 original size:21 final size:21
Alignment explanation
Indices: 168007--168067 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
167997 TCCTTTTCGC
168007 CTTTTTCATTTTCATTTTCTT
1 CTTTTTCATTTTCATTTTCTT
168028 CTTTTTCACTTTT-ATTTT-TCT
1 CTTTTTCA-TTTTCATTTTCT-T
* * *
168049 CTTCTTCTTTTTCTTTTTC
1 CTTTTTCATTTTCATTTTC
168068 CTCACTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 24 0.73
22 4 0.12
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (21 bp):
CTTTTTCATTTTCATTTTCTT
Found at i:182248 original size:25 final size:25
Alignment explanation
Indices: 182214--182263 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
182204 AACCTTGCAG
182214 CTAAGGTGCATTGAATCTCAGTTAT
1 CTAAGGTGCATTGAATCTCAGTTAT
182239 CTAAGGTGCATTGAATCTCAGTTAT
1 CTAAGGTGCATTGAATCTCAGTTAT
182264 GAGCATCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (25 bp):
CTAAGGTGCATTGAATCTCAGTTAT
Found at i:187896 original size:15 final size:15
Alignment explanation
Indices: 187876--187906 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
187866 TGGCTATACC
187876 TAAGGAAACAATAGT
1 TAAGGAAACAATAGT
187891 TAAGGAAACAATAGT
1 TAAGGAAACAATAGT
187906 T
1 T
187907 CGCGGAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (15 bp):
TAAGGAAACAATAGT
Found at i:196336 original size:22 final size:21
Alignment explanation
Indices: 196305--196346 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
196295 CACATTTAAC
*
196305 ACTTAACTAAATTAATTAAAT
1 ACTTAACTAAATTAACTAAAT
196326 ACTTAAACTAAATTAACTAAA
1 ACTT-AACTAAATTAACTAAA
196347 ATTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
ACTTAACTAAATTAACTAAAT
Found at i:200077 original size:6 final size:6
Alignment explanation
Indices: 200068--200138 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
200058 CTCACTCTCA
* * * * * *
200068 TTTTCT TTTTCG ATTTCA TTTTCA TTTTCT TTTTCA TTTTCT TTTTCA
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
*
200116 ATTTCT TTTCTCGTT TTTTCT TT
1 TTTTCT TTT-TC--T TTTTCT TT
200139 ACAAGATAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
6 43 0.84
7 2 0.04
8 2 0.04
9 4 0.08
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTCT
Found at i:200084 original size:12 final size:12
Alignment explanation
Indices: 200065--200124 Score: 86
Period size: 12 Copynumber: 5.0 Consensus size: 12
200055 TTTCTCACTC
200065 TCATTTTCTTTT
1 TCATTTTCTTTT
*
200077 TCGA-TTTCATTT
1 TC-ATTTTCTTTT
200089 TCATTTTCTTTT
1 TCATTTTCTTTT
200101 TCATTTTCTTTT
1 TCATTTTCTTTT
*
200113 TCAATTTCTTTT
1 TCATTTTCTTTT
200125 CTCGTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 1 0.02
12 41 0.95
13 1 0.02
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.70
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:200991 original size:16 final size:16
Alignment explanation
Indices: 200970--201007 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
200960 TTCACTTCAT
200970 TTTTTTATAC-TCGAA
1 TTTTTTATACTTCGAA
*
200985 CTTTTTTTTACTTCGAA
1 -TTTTTTATACTTCGAA
201002 TTTTTT
1 TTTTTT
201008 CTATTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.18, C:0.13, G:0.05, T:0.63
Consensus pattern (16 bp):
TTTTTTATACTTCGAA
Found at i:200991 original size:17 final size:16
Alignment explanation
Indices: 200968--201007 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
200958 ACTTCACTTC
200968 ATTTTTTTATAC-TCGA
1 ATTTTTTT-TACTTCGA
200984 ACTTTTTTTTACTTCGA
1 A-TTTTTTTTACTTCGA
201001 ATTTTTT
1 ATTTTTT
201008 CTATTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTTTTTACTTCGA
Found at i:208255 original size:21 final size:23
Alignment explanation
Indices: 208210--208256 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
208200 TCACCTGCAA
* *
208210 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
208233 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
208254 TAA
1 TAA
208257 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:213544 original size:15 final size:15
Alignment explanation
Indices: 213524--213563 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
213514 GCTTGTTTTC
213524 TTTTTTTT-ACGAAT
1 TTTTTTTTCACGAAT
213538 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
213553 TTTTTTTTCAC
1 TTTTTTTTCAC
213564 AACTTGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:213620 original size:12 final size:12
Alignment explanation
Indices: 213603--213630 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
213593 TGGAAACTAA
213603 TTTTTTTCGATT
1 TTTTTTTCGATT
213615 TTTTTTTCGATT
1 TTTTTTTCGATT
213627 TTTT
1 TTTT
213631 CAATTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTCGATT
Found at i:215939 original size:20 final size:20
Alignment explanation
Indices: 215894--215940 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
215884 TAAAGCTAAG
*
215894 TTGAGCTCAAACGAGCTTAA
1 TTGAGCTCAAACGAACTTAA
*
215914 TTGAGCTCAAATGAAC-TAA
1 TTGAGCTCAAACGAACTTAA
215933 TTCGAGCT
1 TT-GAGCT
215941 AGATAGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TTGAGCTCAAACGAACTTAA
Found at i:224459 original size:30 final size:30
Alignment explanation
Indices: 224423--224495 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
224413 ACAAAGGAAA
224423 AAGAAAATCAAGATTCACTTTCTTGTTTTC
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
*
224453 AAGAAAATCAAGATTCACTTTCTTGTTTTT
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
224483 AAGAAAATCAAGA
1 AAGAAAATCAAGA
224496 AACCGAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
AAGAAAATCAAGATTCACTTTCTTGTTTTC
Found at i:529318 original size:10 final size:10
Alignment explanation
Indices: 529303--529345 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
529293 GTGTAAGTAT
529303 TTGAAAAAAA
1 TTGAAAAAAA
529313 TTGAAAAAAA
1 TTGAAAAAAA
529323 TT-AAAAAAA
1 TTGAAAAAAA
*
529332 TTTCAAAAAAA
1 -TTGAAAAAAA
529343 TTG
1 TTG
529346 TGAACGTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 7 0.23
10 16 0.53
11 7 0.23
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (10 bp):
TTGAAAAAAA
Found at i:529343 original size:11 final size:11
Alignment explanation
Indices: 529301--529349 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 11
529291 CGGTGTAAGT
529301 ATTTGAAAAAA
1 ATTTGAAAAAA
529312 A-TTGAAAAAA
1 ATTTGAAAAAA
529322 A-TT-AAAAAA
1 ATTTGAAAAAA
*
529331 ATTTCAAAAAA
1 ATTTGAAAAAA
529342 ATTGTGAA
1 ATT-TGAA
529350 CGTGATTGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 7 0.21
10 14 0.41
11 10 0.29
12 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (11 bp):
ATTTGAAAAAA
Found at i:530543 original size:17 final size:17
Alignment explanation
Indices: 530517--530557 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
530507 ATGAAAAAAC
530517 AAAAGAAAAAGAAAGTA
1 AAAAGAAAAAGAAAGTA
*
530534 AAAAGTAAAAGAAAGT-
1 AAAAGAAAAAGAAAGTA
530550 AAAAGAAA
1 AAAAGAAA
530558 GAAAAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAGAAAGTA
Found at i:530617 original size:18 final size:20
Alignment explanation
Indices: 530594--530640 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
530584 GCATGCGAGC
530594 AAGAAAAGAAAG-TTGAA-A
1 AAGAAAAGAAAGATTGAAGA
*
530612 AAGAAAA-AGAGATTGAAGA
1 AAGAAAAGAAAGATTGAAGA
530631 AAGAAAAGAA
1 AAGAAAAGAA
530641 CGTGTCCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 8 0.33
20 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.09
Consensus pattern (20 bp):
AAGAAAAGAAAGATTGAAGA
Found at i:530621 original size:19 final size:19
Alignment explanation
Indices: 530597--530637 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
530587 TGCGAGCAAG
530597 AAAAGAAAGTTGAA-AAAGA
1 AAAAGAAA-TTGAAGAAAGA
*
530616 AAAAGAGATTGAAGAAAGA
1 AAAAGAAATTGAAGAAAGA
530635 AAA
1 AAA
530638 GAACGTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10
Consensus pattern (19 bp):
AAAAGAAATTGAAGAAAGA
Found at i:532551 original size:10 final size:10
Alignment explanation
Indices: 532536--532591 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
532526 TGCAAAATAA
*
532536 AGCTCAATCC
1 AGCTCAATTC
532546 AGCTCAATTC
1 AGCTCAATTC
532556 AGCTCAATTC
1 AGCTCAATTC
* *
532566 GGCTCAA-TG
1 AGCTCAATTC
*
532575 AGCTCATTTC
1 AGCTCAATTC
532585 TAGCTCA
1 -AGCTCA
532592 CAAGCTCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
9 6 0.16
10 26 0.68
11 6 0.16
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (10 bp):
AGCTCAATTC
Done.