Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold136
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: 1085849
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 50585 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:2826 original size:12 final size:12
Alignment explanation
Indices: 2795--2857 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
2785 AATCAACATT
*
2795 TCCAGGCATGCC
1 TCCAGGCATACC
* * *
2807 ACCCGGCATGCC
1 TCCAGGCATACC
2819 TCCAGGCATACC
1 TCCAGGCATACC
2831 TCCAGGCATACC
1 TCCAGGCATACC
2843 TCCAGGCATACC
1 TCCAGGCATACC
2855 TCC
1 TCC
2858 GGGAAAACCC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.16
Consensus pattern (12 bp):
TCCAGGCATACC
Found at i:2827 original size:24 final size:24
Alignment explanation
Indices: 2795--2881 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
2785 AATCAACATT
* * *
2795 TCCAGGCATGCCACCCGGCATGCC
1 TCCAGGCATACCACCAGGCATACC
*
2819 TCCAGGCATACCTCCAGGCATACC
1 TCCAGGCATACCACCAGGCATACC
* * * *
2843 TCCAGGCATACCTCCGGGAAAACC
1 TCCAGGCATACCACCAGGCATACC
* *
2867 CCCAGGCATTCCACC
1 TCCAGGCATACCACC
2882 TGGAAACCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.23, C:0.44, G:0.20, T:0.14
Consensus pattern (24 bp):
TCCAGGCATACCACCAGGCATACC
Found at i:2851 original size:36 final size:36
Alignment explanation
Indices: 2795--2881 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
2785 AATCAACATT
* * * * *
2795 TCCAGGCATGCCACCCGGCATGCCTCCAGGCATACC
1 TCCAGGCATACCACCAGGCATACCTCCAGGAAAACC
* *
2831 TCCAGGCATACCTCCAGGCATACCTCCGGGAAAACC
1 TCCAGGCATACCACCAGGCATACCTCCAGGAAAACC
* *
2867 CCCAGGCATTCCACC
1 TCCAGGCATACCACC
2882 TGGAAACCCA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.23, C:0.44, G:0.20, T:0.14
Consensus pattern (36 bp):
TCCAGGCATACCACCAGGCATACCTCCAGGAAAACC
Found at i:2886 original size:24 final size:24
Alignment explanation
Indices: 2844--2899 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
2834 AGGCATACCT
*
2844 CCAGGCATACCTCCGGGAAAACCC-
1 CCAGGCATACCACCGGG-AAACCCA
* *
2868 CCAGGCATTCCACCTGGAAACCCA
1 CCAGGCATACCACCGGGAAACCCA
2892 CCAGGCAT
1 CCAGGCAT
2900 GCCTCCAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.29, C:0.41, G:0.20, T:0.11
Consensus pattern (24 bp):
CCAGGCATACCACCGGGAAACCCA
Found at i:4003 original size:21 final size:21
Alignment explanation
Indices: 3962--4004 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3952 CGAAGCAACT
** *
3962 GAATCATTCTATCAAATATAA
1 GAATCATTCTAAAAAAGATAA
3983 GAATCATTCTAAAAAAGATAA
1 GAATCATTCTAAAAAAGATAA
4004 G
1 G
4005 GAATGCATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (21 bp):
GAATCATTCTAAAAAAGATAA
Found at i:9086 original size:39 final size:39
Alignment explanation
Indices: 9041--9240 Score: 195
Period size: 39 Copynumber: 5.1 Consensus size: 39
9031 AATAAAAATA
* *
9041 CGGTGATTATTCAAGCTAAATGCCTAGTAGGCTTTATGC
1 CGGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGC
* * * ** *
9080 CAGTGATTATTCAGGCTAAGTGCTTAGCAGATTTTGTGC
1 CGGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGC
* *
9119 TGGTGATTATTCAGGCTAAATGCCTAGCAAGCTTTATGC
1 CGGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGC
* * * *
9158 CGGTGATTATTCGGGCTAAGTGCCTAGTAGGCTTTGTGC
1 CGGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGC
* * *** * *
9197 CTGTGATTTTTC-GGCCTTTGTGCCTAGCAGGCTGTGTGC
1 CGGTGATTATTCAGG-CTAAATGCCTAGCAGGCTTTATGC
9236 CGGTG
1 CGGTG
9241 TATTGGAAGT
Statistics
Matches: 131, Mismatches: 29, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
38 2 0.02
39 129 0.98
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.34
Consensus pattern (39 bp):
CGGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGC
Found at i:9221 original size:78 final size:78
Alignment explanation
Indices: 9042--9240 Score: 231
Period size: 78 Copynumber: 2.6 Consensus size: 78
9032 ATAAAAATAC
* * * *
9042 GGTGATTATTCAAGCTAAATGCCTAGTAGGCTTTATGCCAGTGATTATTCAGGCTAAGTGCTTAG
1 GGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGCCGGTGATTATTCAGGCTAAGTGCCTAG
*
9107 CAGATTTTGTGCT
66 CAGACTTTGTGCT
* *
9120 GGTGATTATTCAGGCTAAATGCCTAGCAAGCTTTATGCCGGTGATTATTCGGGCTAAGTGCCTAG
1 GGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGCCGGTGATTATTCAGGCTAAGTGCCTAG
* *
9185 TAGGCTTTGTGCCT
66 CAGACTTTGTG-CT
* *** * *
9199 -GTGATTTTTC-GGCCTTTGTGCCTAGCAGGCTGTGTGCCGGTG
1 GGTGATTATTCAGG-CTAAATGCCTAGCAGGCTTTATGCCGGTG
9241 TATTGGAAGT
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
77 2 0.02
78 99 0.96
79 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (78 bp):
GGTGATTATTCAGGCTAAATGCCTAGCAGGCTTTATGCCGGTGATTATTCAGGCTAAGTGCCTAG
CAGACTTTGTGCT
Found at i:12964 original size:168 final size:169
Alignment explanation
Indices: 12685--13007 Score: 594
Period size: 168 Copynumber: 1.9 Consensus size: 169
12675 AGTAAAAATA
* * * *
12685 AATAATAATTATAGGAAAATTAAAATGTTTTTTTTTTCAAATTTATTAGCTAAGCTATAAACTCG
1 AATAATAATAATAGGAAAATTAAAATGATATTTTTTTCAAATTTAGTAGCTAAGCTATAAACTCG
*
12750 AGAAATAAATTATTAAAAACCAAGATTACGAGATTTGGTAAAACAGTCGTGATAAATGCACCAAG
66 AGAAATAAATTATTAAAAACCAAGATTACGAGATTTGGTAAAACAGTCGTGATAAATGCACCAAA
12815 TAAGTTCCCAGGAAAGAGAGGTGAGAAATAAATAATAAT
131 TAAGTTCCCAGGAAAGAGAGGTGAGAAATAAATAATAAT
12854 AATAATAATAATAGGAAAATTAAAAT-ATATTTTTTTCAAATTTAGTAGCTAAGCTATAAACTCG
1 AATAATAATAATAGGAAAATTAAAATGATATTTTTTTCAAATTTAGTAGCTAAGCTATAAACTCG
12918 AGAAATAAATTATTAAAAACCAAGATTACGAGATTTGGTAAAACAGTCGTGATAAATGCACCAAA
66 AGAAATAAATTATTAAAAACCAAGATTACGAGATTTGGTAAAACAGTCGTGATAAATGCACCAAA
12983 TAAGTTCCCAGGAAAGAGAGGTGAG
131 TAAGTTCCCAGGAAAGAGAGGTGAG
13008 TCACAATGGA
Statistics
Matches: 149, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
168 124 0.83
169 25 0.17
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (169 bp):
AATAATAATAATAGGAAAATTAAAATGATATTTTTTTCAAATTTAGTAGCTAAGCTATAAACTCG
AGAAATAAATTATTAAAAACCAAGATTACGAGATTTGGTAAAACAGTCGTGATAAATGCACCAAA
TAAGTTCCCAGGAAAGAGAGGTGAGAAATAAATAATAAT
Found at i:16266 original size:46 final size:48
Alignment explanation
Indices: 16203--16430 Score: 369
Period size: 47 Copynumber: 4.9 Consensus size: 48
16193 CAAAGTGTGT
*
16203 AAAGTAGGCATGGTATTTCAATAAAGAAAACCATACTGAGTTG-T-AA
1 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTTGTTGAA
* *
16249 AAAGTAGGTATGATATTTCAATAAAGAAAACTATACTGAGTTG-TG-A
1 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTTGTTGAA
16295 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAG-TGTTGAA
1 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTTGTTGAA
*
16342 AAAGTAAGTATGGTATTTCAATAAAGAAAACCATACTGAG-TGTTGAA
1 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTTGTTGAA
*
16389 AAAGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
1 AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTT
16431 ATAGTATTGT
Statistics
Matches: 170, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
45 2 0.01
46 82 0.48
47 85 0.50
48 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (48 bp):
AAAGTAGGTATGGTATTTCAATAAAGAAAACCATACTGAGTTGTTGAA
Found at i:20168 original size:12 final size:12
Alignment explanation
Indices: 20147--20228 Score: 60
Period size: 12 Copynumber: 6.8 Consensus size: 12
20137 AAAAACGAAA
*
20147 TGATTAAAAACT
1 TGATGAAAAACT
* *
20159 TGATGGAAAATT
1 TGATGAAAAACT
*
20171 TTATGAAAAGACT
1 TGATGAAAA-ACT
20184 TGATGAAAAACT
1 TGATGAAAAACT
* *
20196 TTA-AAAAGAACT
1 TGATGAAA-AACT
* *
20208 TGCTGCAAAACT
1 TGATGAAAAACT
20220 TGAT-AAAAA
1 TGATGAAAAA
20229 AATTGGTAAT
Statistics
Matches: 52, Mismatches: 15, Indels: 7
0.70 0.20 0.09
Matches are distributed among these distances:
11 7 0.13
12 33 0.63
13 12 0.23
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:20188 original size:25 final size:24
Alignment explanation
Indices: 20152--20229 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
20142 CGAAATGATT
* *
20152 AAAAACTTGATGGAAAATTTTATG
1 AAAAACTTGATGAAAAACTTTATG
*
20176 AAAAGACTTGATGAAAAACTTTA-A
1 AAAA-ACTTGATGAAAAACTTTATG
* * * *
20200 AAAGAACTTGCTGCAAAACTTGATA
1 AAA-AACTTGATGAAAAACTTTATG
20225 AAAAA
1 AAAAA
20230 ATTGGTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 24 0.53
25 21 0.47
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (24 bp):
AAAAACTTGATGAAAAACTTTATG
Found at i:20208 original size:24 final size:25
Alignment explanation
Indices: 20155--20220 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
20145 AATGATTAAA
* *
20155 AACTTGATGGAAAATTTTATGAAAAG
1 AACTTGATGAAAAACTTTA-GAAAAG
20181 -ACTTGATGAAAAACTTTA-AAAAG
1 AACTTGATGAAAAACTTTAGAAAAG
* *
20204 AACTTGCTGCAAAACTT
1 AACTTGATGAAAAACTT
20221 GATAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.14
24 14 0.40
25 16 0.46
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (25 bp):
AACTTGATGAAAAACTTTAGAAAAG
Found at i:20229 original size:12 final size:12
Alignment explanation
Indices: 20147--20276 Score: 55
Period size: 12 Copynumber: 10.2 Consensus size: 12
20137 AAAAACGAAA
*
20147 TGATTAAAAACT
1 TGATAAAAAACT
** *
20159 TGATGGAAAATT
1 TGATAAAAAACT
* *
20171 TTATGAAAAGACT
1 TGAT-AAAAAACT
*
20184 TGATGAAAAACT
1 TGATAAAAAACT
*
20196 TTA-AAAAGAACT
1 TGATAAAA-AACT
* **
20208 TGCTGCAAAACT
1 TGATAAAAAACT
*
20220 TGATAAAAAAAT
1 TGATAAAAAACT
*
20232 TGGTAATTTAAAACT
1 TGATAA---AAAACT
20247 TGATAAAAGAACT
1 TGATAAAA-AACT
*
20260 AGATGAAAAATACT
1 TGAT-AAAAA-ACT
20274 TGA
1 TGA
20277 AGAAAGAAAA
Statistics
Matches: 83, Mismatches: 26, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
11 3 0.04
12 44 0.53
13 17 0.20
14 9 0.11
15 10 0.12
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (12 bp):
TGATAAAAAACT
Found at i:20293 original size:19 final size:19
Alignment explanation
Indices: 20265--20302 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20255 GAACTAGATG
*
20265 AAAAATACTTGAA-GAAAGA
1 AAAAACACTT-AATGAAAGA
20284 AAAAACACTTAATGAAAGA
1 AAAAACACTTAATGAAAGA
20303 CTTAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (19 bp):
AAAAACACTTAATGAAAGA
Found at i:24154 original size:21 final size:21
Alignment explanation
Indices: 24130--24182 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
24120 CGCTGTTTCT
* *
24130 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
24151 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
24172 AATCTCACCGC
1 AATCTCACCGC
24183 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:28371 original size:18 final size:18
Alignment explanation
Indices: 28345--28381 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28335 TAAAATATGT
*
28345 AATTGAAAACCCAATTAA
1 AATTGAAAACCAAATTAA
*
28363 AATTTAAAACCAAATTAA
1 AATTGAAAACCAAATTAA
28381 A
1 A
28382 GGCCTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTGAAAACCAAATTAA
Found at i:28659 original size:28 final size:28
Alignment explanation
Indices: 28619--28707 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 28
28609 TATACAGTAT
*
28619 CAGT-ATAATGTGGGCCTTAGCCCATTA
1 CAGTAATAATGTGGGCCTTAGCCCAATA
*
28646 CAGTAATAGTGTGGGCCTTAGCCCAATA
1 CAGTAATAATGTGGGCCTTAGCCCAATA
* * * *
28674 CAGTAACAATATGGGCCTTTGCCTAATA
1 CAGTAATAATGTGGGCCTTAGCCCAATA
*
28702 TAGTAA
1 CAGTAA
28708 ACATTACAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 4 0.08
28 49 0.92
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (28 bp):
CAGTAATAATGTGGGCCTTAGCCCAATA
Found at i:29142 original size:54 final size:54
Alignment explanation
Indices: 29060--29231 Score: 222
Period size: 54 Copynumber: 3.2 Consensus size: 54
29050 CCAATTCTAA
* * * * *
29060 GGGTATATTAGTCATTTTA-CCTTATGAGGGTGTTTTGGTCATATTACCTTTCGG
1 GGGTATTTTGGTCATTATACCCTT-TGAGGGTATTTTGGTCATTTTACCTTTCGG
*
29114 GGGTATTTTGGTCATTATACCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGA
1 GGGTATTTTGGTCATTATACCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGG
* * *
29168 AGGTATTTTGGTCATTATACCCTTCGGGGGTATTTTGGTCATTTTACCTTTTC-G
1 GGGTATTTTGGTCATTATACCCTTTGAGGGTATTTTGGTCATTTTACC-TTTCGG
*
29222 GGTTATTTTG
1 GGGTATTTTG
29232 ATAATTTGCG
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
54 96 0.92
55 8 0.08
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (54 bp):
GGGTATTTTGGTCATTATACCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGG
Found at i:29228 original size:27 final size:27
Alignment explanation
Indices: 29059--29231 Score: 199
Period size: 27 Copynumber: 6.4 Consensus size: 27
29049 TCCAATTCTA
* *
29059 AGGGTATATTAGTCATTTTACCTTAT-G
1 AGGGTATTTTGGTCATTTTACCTT-TCG
* *
29086 AGGGTGTTTTGGTCATATTACCTTTCG
1 AGGGTATTTTGGTCATTTTACCTTTCG
* *
29113 GGGGTATTTTGGTCATTATACCCTTT-G
1 AGGGTATTTTGGTCATTTTA-CCTTTCG
29140 AGGGTATTTTGGTCATTTTACCTTTCG
1 AGGGTATTTTGGTCATTTTACCTTTCG
* * *
29167 AAGGTATTTTGGTCATTATACCCTTCG
1 AGGGTATTTTGGTCATTTTACCTTTCG
*
29194 GGGGTATTTTGGTCATTTTACCTTTTCG
1 AGGGTATTTTGGTCATTTTACC-TTTCG
*
29222 -GGTTATTTTG
1 AGGGTATTTTG
29232 ATAATTTGCG
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 6 0.05
27 109 0.88
28 9 0.07
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (27 bp):
AGGGTATTTTGGTCATTTTACCTTTCG
Found at i:29231 original size:81 final size:81
Alignment explanation
Indices: 29059--29215 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 81
29049 TCCAATTCTA
* * * * *
29059 AGGGTATATTAGTCATTTTACCTTATGAGGGTGTTTTGGTCATATTACCTTTCGGGGGTATTTTG
1 AGGGTATTTTGGTCATTTTACCTTATGAAGGTATTTTGGTCATATTACCCTTCGGGGGTATTTTG
29124 GTCATTATACCCTTTG
66 GTCATTATACCCTTTG
29140 AGGGTATTTTGGTCATTTTACCTT-TCGAAGGTATTTTGGTCAT-TATACCCTTCGGGGGTATTT
1 AGGGTATTTTGGTCATTTTACCTTAT-GAAGGTATTTTGGTCATAT-TACCCTTCGGGGGTATTT
*
29203 TGGTCATTTTACC
64 TGGTCATTATACC
29216 TTTTCGGGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 2 0.03
81 66 0.97
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.45
Consensus pattern (81 bp):
AGGGTATTTTGGTCATTTTACCTTATGAAGGTATTTTGGTCATATTACCCTTCGGGGGTATTTTG
GTCATTATACCCTTTG
Found at i:32725 original size:120 final size:121
Alignment explanation
Indices: 32580--32821 Score: 477
Period size: 120 Copynumber: 2.0 Consensus size: 121
32570 TGAATAGGTG
32580 AAGAATTATGATGGACTAAATTGCAATTTTACTAAATTAAGTGATGACTCAAGGATGAAAATTTA
1 AAGAATTATGATGGACTAAATTGCAATTTTACTAAATTAAGTGATGACTCAAGGATGAAAATTTA
32645 AAAGATCATAAACGGAAAAAATGGTCAATTAGAAAGAGAGAGAACTCTAGAAGGCA
66 AAAGATCATAAACGGAAAAAATGGTCAATTAGAAAGAGAGAGAACTCTAGAAGGCA
32701 AAGAATTA-GATGGACTAAATTGCAATTTTACTAAATTAAGTGATGACTCAAGGATGAAAATTTA
1 AAGAATTATGATGGACTAAATTGCAATTTTACTAAATTAAGTGATGACTCAAGGATGAAAATTTA
32765 AAAGATCATAAACGGAAAAAATGGTCAATTAGAAAGAGAGAGAACTCTAGAAGGCA
66 AAAGATCATAAACGGAAAAAATGGTCAATTAGAAAGAGAGAGAACTCTAGAAGGCA
32821 A
1 A
32822 TGATGATATA
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 113 0.93
121 8 0.07
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (121 bp):
AAGAATTATGATGGACTAAATTGCAATTTTACTAAATTAAGTGATGACTCAAGGATGAAAATTTA
AAAGATCATAAACGGAAAAAATGGTCAATTAGAAAGAGAGAGAACTCTAGAAGGCA
Found at i:35830 original size:28 final size:28
Alignment explanation
Indices: 35798--35851 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
35788 CACCAAAAAA
* *
35798 TGTAGAAATTGAATTACATGTTAATTTT
1 TGTAGAAATTGAATTAAAGGTTAATTTT
35826 TGTAGAAATTGAATTAAAGGTTAATT
1 TGTAGAAATTGAATTAAAGGTTAATT
35852 AAAGTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.43
Consensus pattern (28 bp):
TGTAGAAATTGAATTAAAGGTTAATTTT
Found at i:36373 original size:12 final size:12
Alignment explanation
Indices: 36356--36382 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
36346 AATAGTAGAC
36356 TTATAGATAATA
1 TTATAGATAATA
36368 TTATAGATAATA
1 TTATAGATAATA
36380 TTA
1 TTA
36383 CATATAAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (12 bp):
TTATAGATAATA
Found at i:37321 original size:68 final size:68
Alignment explanation
Indices: 37237--37388 Score: 232
Period size: 68 Copynumber: 2.2 Consensus size: 68
37227 GATAACACCG
** * *
37237 TAACTGGGTTATGGCACTATAAACGTAAGACTGTGGTTGGACCATGGTAGTGTTTATATGTAAGA
1 TAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAGTGCTTATATGTAAGA
37302 CCA
66 CCA
*
37305 TAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGCTTATATGTAAGA
1 TAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAGTGCTTATATGTAAGA
37370 CCA
66 CCA
* * *
37373 TAGCTAGGCTATGGCA
1 TAACTGGGTTATGGCA
37389 TTTTGATGAT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 76 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (68 bp):
TAACTGGGTTATGGCACTATAAACGTAAGACCATGGTTGGACCATGGCAGTGCTTATATGTAAGA
CCA
Found at i:37455 original size:24 final size:24
Alignment explanation
Indices: 37427--37477 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
37417 TGGCACTACG
37427 AATGTAAAGGATGAATTGACGAAA
1 AATGTAAAGGATGAATTGACGAAA
*
37451 AATGTAAAGGATGAATTGACGACA
1 AATGTAAAGGATGAATTGACGAAA
37475 AAT
1 AAT
37478 TACCCAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.22
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGAAA
Found at i:43997 original size:68 final size:68
Alignment explanation
Indices: 43925--44144 Score: 153
Period size: 68 Copynumber: 3.1 Consensus size: 68
43915 TATACACAAC
43925 ATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATTTATATTAGTATATAT
1 ATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATTTATATTAGTATATAT
43990 TTA
66 TTA
** ** * * * * **
43993 ATATTTT-TTTTGTATAAAATTGATAGT-TA-ATTTTTTTATTTTATATCAACT-TTGACATATA
1 ATATTTTGAATTG-AT---A-TGATA-TCTATATAATATCAATCTA-A--AA-TATT-ATTTATA
* ***
44054 TATA-TTTATACACAA
55 T-TAGTATATA-TTTA
44069 CATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATTTATATTAGTATATA
1 -ATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATTTATATTAGTATATA
44134 TTTA
65 TTTA
44138 ATATTTT
1 ATATTTT
44145 TTTTGTATAA
Statistics
Matches: 105, Mismatches: 28, Indels: 38
0.61 0.16 0.22
Matches are distributed among these distances:
67 3 0.03
68 16 0.15
69 3 0.03
70 12 0.11
71 13 0.12
72 9 0.09
73 9 0.09
74 13 0.12
75 12 0.11
76 3 0.03
77 9 0.09
78 3 0.03
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (68 bp):
ATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATTTATATTAGTATATAT
TTA
Found at i:44089 original size:145 final size:145
Alignment explanation
Indices: 43910--44200 Score: 573
Period size: 145 Copynumber: 2.0 Consensus size: 145
43900 ATTTATTAAG
43910 ATATTTATACACAACATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATT
1 ATATTTATACACAACATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATT
43975 TATATTAGTATATATTTAATATTTTTTTTGTATAAAATTGATAGTTAATTTTTTTATTTTATATC
66 TATATTAGTATATATTTAATATTTTTTTTGTATAAAATTGATAGTTAATTTTTTTATTTTATATC
*
44040 AACTTTGACATATAT
131 AAATTTGACATATAT
44055 ATATTTATACACAACATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATT
1 ATATTTATACACAACATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATT
44120 TATATTAGTATATATTTAATATTTTTTTTGTATAAAATTGATAGTTAATTTTTTTATTTTATATC
66 TATATTAGTATATATTTAATATTTTTTTTGTATAAAATTGATAGTTAATTTTTTTATTTTATATC
44185 AAATTTGACATATAT
131 AAATTTGACATATAT
44200 A
1 A
44201 ATCTAGATTA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.50
Consensus pattern (145 bp):
ATATTTATACACAACATATTTTGAATTGATATGATATCTATATAATATCAATCTAAAATATTATT
TATATTAGTATATATTTAATATTTTTTTTGTATAAAATTGATAGTTAATTTTTTTATTTTATATC
AAATTTGACATATAT
Found at i:45508 original size:16 final size:16
Alignment explanation
Indices: 45487--45551 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
45477 TTCGCTGTAT
45487 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
45503 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
45519 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
45535 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
45551 T
1 T
45552 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:55459 original size:38 final size:38
Alignment explanation
Indices: 55416--55492 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
55406 AAATAGTGAT
55416 AATAAGAAAAGTGATCGTGTGATTGAAATTCCAAGTTA
1 AATAAGAAAAGTGATCGTGTGATTGAAATTCCAAGTTA
55454 AATAAGAAAAGTGATCGTGTGATTGAAATTCCAAGTTA
1 AATAAGAAAAGTGATCGTGTGATTGAAATTCCAAGTTA
55492 A
1 A
55493 CTTGCATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.29
Consensus pattern (38 bp):
AATAAGAAAAGTGATCGTGTGATTGAAATTCCAAGTTA
Found at i:57011 original size:20 final size:20
Alignment explanation
Indices: 56988--57040 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
56978 TAGGGGCATA
56988 GTATCGATACTTAGAGTAAG
1 GTATCGATACTTAGAGTAAG
* * * *
57008 GTATTGATACGTCGAGTAGG
1 GTATCGATACTTAGAGTAAG
57028 GTATCGATACTTA
1 GTATCGATACTTA
57041 TGATTTAATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (20 bp):
GTATCGATACTTAGAGTAAG
Found at i:62860 original size:41 final size:41
Alignment explanation
Indices: 62815--62941 Score: 102
Period size: 41 Copynumber: 3.1 Consensus size: 41
62805 ATCTTTTACA
62815 CATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATT
1 CATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATT
* * * * * * * * *
62856 CATAATTTCTATGACGATTTAC-CCCAAGTTG-AGTCT-ACCA-A
1 CATAACTTGTTTTA--A-CTCCTCCCATGTTGTAATCTCA-CATT
62897 CATAACTTG-TTTAACTCCTCCCATGTTGTAATCTCACATT
1 CATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATT
62937 CATAA
1 CATAA
62942 TTTCTATGAC
Statistics
Matches: 60, Mismatches: 18, Indels: 17
0.63 0.19 0.18
Matches are distributed among these distances:
37 2 0.03
38 9 0.15
39 6 0.10
40 8 0.13
41 18 0.30
42 6 0.10
43 9 0.15
44 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.37
Consensus pattern (41 bp):
CATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATT
Found at i:62917 original size:81 final size:82
Alignment explanation
Indices: 62814--62978 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 82
62804 AATCTTTTAC
62814 ACATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATTCATAATTTCTATGACGATTTACC
1 ACATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATTCATAATTTCTATGACGATTTACC
62879 CCAAGTTGAGTCTACCA
66 CCAAGTTGAGTCTACCA
62896 ACATAACTTG-TTTAACTCCTCCCATGTTGTAATCTCACATTCATAATTTCTATGACGATTTACC
1 ACATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATTCATAATTTCTATGACGATTTACC
62960 CCAAGTTGAGTCTACCA
66 CCAAGTTGAGTCTACCA
62977 AC
1 AC
62979 TTAATGCATA
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 73 0.88
82 10 0.12
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (82 bp):
ACATAACTTGTTTTAACTCCTCCCATGTTGTAATCTCACATTCATAATTTCTATGACGATTTACC
CCAAGTTGAGTCTACCA
Found at i:67291 original size:14 final size:14
Alignment explanation
Indices: 67245--67293 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
67235 TTGAATATGT
67245 AATTTTATTCAT-A
1 AATTTTATTCATGA
*
67258 AATTTTGATTTCATGC
1 AATTTT-A-TTCATGA
*
67274 AATTTTATACATGA
1 AATTTTATTCATGA
67288 AATTTT
1 AATTTT
67294 TTTCGATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.20
14 12 0.40
15 6 0.20
16 6 0.20
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (14 bp):
AATTTTATTCATGA
Found at i:67584 original size:21 final size:21
Alignment explanation
Indices: 67560--67602 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
67550 TTTTATGTTT
* *
67560 ATATATTACACATAAAAATAA
1 ATATATTAAAAATAAAAATAA
*
67581 ATATATTAAAAATAAATATAA
1 ATATATTAAAAATAAAAATAA
67602 A
1 A
67603 AATTGATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATATTAAAAATAAAAATAA
Found at i:67592 original size:15 final size:15
Alignment explanation
Indices: 67572--67600 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
67562 ATATTACACA
67572 TAAAAATAAATATAT
1 TAAAAATAAATATAT
67587 TAAAAATAAATATA
1 TAAAAATAAATATA
67601 AAAATTGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATAAATATAT
Found at i:67670 original size:31 final size:31
Alignment explanation
Indices: 67635--67693 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
67625 ATGTGTATGG
* * *
67635 TTAAATAAAAATTAAAATTTTATGTATACAT
1 TTAAACAAAAATCAAAATTTTAGGTATACAT
* *
67666 TTAAACCATAATCAAAATTTTAGGTATA
1 TTAAACAAAAATCAAAATTTTAGGTATA
67694 TAATTGCATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (31 bp):
TTAAACAAAAATCAAAATTTTAGGTATACAT
Found at i:69410 original size:8 final size:8
Alignment explanation
Indices: 69397--69458 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
69387 GTAAAAGAAT
69397 TATAAAAA
1 TATAAAAA
69405 TAT-AAAA
1 TATAAAAA
69412 TATAAAAA
1 TATAAAAA
**
69420 TATTAAATT
1 TA-TAAAAA
69429 TAATAAAAA
1 T-ATAAAAA
69438 TATAAAAA
1 TATAAAAA
*
69446 TATTTAAAA
1 TA-TAAAAA
69455 TATA
1 TATA
69459 TTATAAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 7 0.16
8 19 0.43
9 17 0.39
10 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TATAAAAA
Found at i:69504 original size:20 final size:19
Alignment explanation
Indices: 69463--69518 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
69453 AATATATTAT
*
69463 AAATTAGAAAAAAT-TATA-
1 AAATTATAAAAAATGTA-AG
* *
69481 AAATTTTATAAAATCGTAAG
1 AAATTATAAAAAAT-GTAAG
69501 AAATTATAAAAAATGTAA
1 AAATTATAAAAAATGTAA
69519 AGCAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
18 11 0.37
19 5 0.17
20 14 0.47
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (19 bp):
AAATTATAAAAAATGTAAG
Found at i:69809 original size:200 final size:202
Alignment explanation
Indices: 69576--69941 Score: 478
Period size: 200 Copynumber: 1.8 Consensus size: 202
69566 GAAGCGTTTC
* * *
69576 ATAATTTTTCTATAACTTTTATTGATTTTTATTTTTTGTCATTTTTCGCCACATGTCATGCTGTG
1 ATAATTTTTCTATAACTTTTATTGATTTTTATTTTTTATCATTTTTCACCACATGTCATGCCGTG
* *
69641 -CTGTAACACG-TGATGACTTTAACTGGAAAAAAAAC-TAGGGTC-GTTAATTTTAATGGTC-AG
66 ACTGTAACACGTTG-TGACTTTAA-TGG--AAAAAACTTAGGGGCGGTTAATTTTAATGGTCAAC
* * * *
69701 TGGTTAAAGTTAATGGTTAAAG-GATCTTTTTGATGCATTTTATAAAAAAAAATTCTAATTTTTA
127 T-ATTAAAGTTAATGGTAAAAGAGCT-TTTTTGATACATTTTATAAAAAAAAATTCTAATTTTTA
69765 ATTTTTTAATTTA
190 ATTTTTTAATTTA
* * **
69778 ATAA-TTTT-TATAACTTTTATTGATTTTTATTTTTTATCCTTTTTTATTACATGTCATGCCGTG
1 ATAATTTTTCTATAACTTTTATTGATTTTTATTTTTTATCATTTTTCACCACATGTCATGCCGTG
* * *
69841 ATTGTGACACGTTGTGACTTTAATTGAAAAAACTTAGGGGCGGTTAATTTTAATGGTCAACTATT
66 ACTGTAACACGTTGTGACTTTAATGGAAAAAACTTAGGGGCGGTTAATTTTAATGGTCAACTATT
69906 AAAGTTAATGGTAAAAGAGCTTTTTTGATACATTTT
131 AAAGTTAATGGTAAAAGAGCTTTTTTGATACATTTT
69942 GGCAATTCAA
Statistics
Matches: 142, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
198 7 0.05
199 6 0.04
200 98 0.69
201 25 0.18
202 6 0.04
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.46
Consensus pattern (202 bp):
ATAATTTTTCTATAACTTTTATTGATTTTTATTTTTTATCATTTTTCACCACATGTCATGCCGTG
ACTGTAACACGTTGTGACTTTAATGGAAAAAACTTAGGGGCGGTTAATTTTAATGGTCAACTATT
AAAGTTAATGGTAAAAGAGCTTTTTTGATACATTTTATAAAAAAAAATTCTAATTTTTAATTTTT
TAATTTA
Found at i:78209 original size:21 final size:21
Alignment explanation
Indices: 78180--78222 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
78170 TTATTAATAA
*
78180 GACTGAGTCCTAAGGAGATTT
1 GACTAAGTCCTAAGGAGATTT
*
78201 GACTAAGTCCTAGGGAGATTT
1 GACTAAGTCCTAAGGAGATTT
78222 G
1 G
78223 TTAGCTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (21 bp):
GACTAAGTCCTAAGGAGATTT
Found at i:78244 original size:21 final size:21
Alignment explanation
Indices: 78220--78262 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
78210 CTAGGGAGAT
* *
78220 TTGTTAGCTTGTTAGTAGGAG
1 TTGTTAGATTGTTAATAGGAG
78241 TTGTTAGATTGTTAATAGGAG
1 TTGTTAGATTGTTAATAGGAG
78262 T
1 T
78263 AGAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.30, T:0.44
Consensus pattern (21 bp):
TTGTTAGATTGTTAATAGGAG
Found at i:83994 original size:13 final size:13
Alignment explanation
Indices: 83976--84000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
83966 TCCAAAGAAA
83976 ATTTGGAAATTTG
1 ATTTGGAAATTTG
83989 ATTTGGAAATTT
1 ATTTGGAAATTT
84001 TCCTAAACAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
ATTTGGAAATTTG
Found at i:84391 original size:24 final size:25
Alignment explanation
Indices: 84350--84396 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
84340 CCATGTAACG
*
84350 GGAAGCTCATAAGTGCC-ATAATTA
1 GGAAGCTCATAAGAGCCAATAATTA
*
84374 GGAAGCTCATGAGAGCCAATAAT
1 GGAAGCTCATAAGAGCCAATAAT
84397 GGGTAGCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (25 bp):
GGAAGCTCATAAGAGCCAATAATTA
Found at i:84438 original size:24 final size:24
Alignment explanation
Indices: 84337--84440 Score: 68
Period size: 24 Copynumber: 4.3 Consensus size: 24
84327 AAGCTCCTGT
**
84337 GAGCCATGTAACGGGAAGCTCATAA
1 GAGCCAT-TAACGGGAAGCTCCGAA
* ** *
84362 GTGCCA-TAATTAGGAAGCTCATG-A
1 GAGCCATTAA-CGGGAAGCTC-CGAA
* * *
84386 GAGCCAATAATGGGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
*
84410 GAGCCATTAACGGGAAGCTCCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
*
84434 TAGCCAT
1 GAGCCAT
84441 ATATCAAGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
23 4 0.07
24 49 0.80
25 8 0.13
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:87402 original size:42 final size:43
Alignment explanation
Indices: 87356--87476 Score: 138
Period size: 42 Copynumber: 2.9 Consensus size: 43
87346 ACTCATATGA
* * *
87356 GTTTCAGTTCAACTCTTTTGAGCTTTTGTTTAACCCTAAT-GG
1 GTTTCAGTTCAGCTCTTATGAGCTTCTGTTTAACCCTAATAGG
* * * * *
87398 GTTTCAGTTTAGCTCTTCTGAGCTTCAGATTAACCCTTATAGG
1 GTTTCAGTTCAGCTCTTATGAGCTTCTGTTTAACCCTAATAGG
* *
87441 TTTTC-GTTCAGCTCCTATGAGCTTCTGTTTAACCCT
1 GTTTCAGTTCAGCTCTTATGAGCTTCTGTTTAACCCT
87477 TACATGTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 59 0.91
43 6 0.09
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.43
Consensus pattern (43 bp):
GTTTCAGTTCAGCTCTTATGAGCTTCTGTTTAACCCTAATAGG
Found at i:87477 original size:42 final size:42
Alignment explanation
Indices: 87374--87490 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
87364 TCAACTCTTT
* * * * * *
87374 TGAGCTTTTGTTTAACCCTAAT-GGGTTTCAGTTTAGCTCTTC
1 TGAGCTTCTGTTTAACCCTTATAGGTTTTC-GTTCAGCTCCTA
* *
87416 TGAGCTTCAGATTAACCCTTATAGGTTTTCGTTCAGCTCCTA
1 TGAGCTTCTGTTTAACCCTTATAGGTTTTCGTTCAGCTCCTA
* *
87458 TGAGCTTCTGTTTAACCCTTACATGTTTTCGTT
1 TGAGCTTCTGTTTAACCCTTATAGGTTTTCGTT
87491 TAGTACTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
42 56 0.90
43 6 0.10
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TGAGCTTCTGTTTAACCCTTATAGGTTTTCGTTCAGCTCCTA
Found at i:88353 original size:29 final size:29
Alignment explanation
Indices: 88320--88379 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
88310 TGGCCGTATG
*
88320 ACCCCTACACCTTGCATATGGCCTAGCAC
1 ACCCCTACACCTTGCATACGGCCTAGCAC
88349 ACCCCTACACCTTGCATACGGCCTAGCAC
1 ACCCCTACACCTTGCATACGGCCTAGCAC
88378 AC
1 AC
88380 GGGCATGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.43, G:0.13, T:0.18
Consensus pattern (29 bp):
ACCCCTACACCTTGCATACGGCCTAGCAC
Found at i:88941 original size:13 final size:14
Alignment explanation
Indices: 88918--88949 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
88908 ATTTAAAATC
88918 TAACA-TTCATTTA
1 TAACATTTCATTTA
88931 -AACATTTCATTTA
1 TAACATTTCATTTA
88944 TAACAT
1 TAACAT
88950 AGAATACTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (14 bp):
TAACATTTCATTTA
Found at i:96963 original size:27 final size:26
Alignment explanation
Indices: 96925--96988 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 26
96915 TTTATCGAGG
*
96925 TTATTAGTTTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATA-T
* *
96952 TTATTAATTTATTGATAAATTAATAT
1 TTATTAATTTATCGATAAATGAATAT
96978 TTATTAATTTA
1 TTATTAATTTA
96989 GAGAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATGAATAT
Found at i:97819 original size:24 final size:24
Alignment explanation
Indices: 97757--97808 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
97747 TTTCTAGAAG
* * *
97757 ATTTAGTACTTATGAGTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
97781 ATTTAGTATTTATTAGCATAATAT
1 ATTTAGTATTTATTAGCATAATAT
97805 ATTT
1 ATTT
97809 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Found at i:102268 original size:24 final size:24
Alignment explanation
Indices: 102240--102291 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
102230 TTTCTAGAAG
* *
102240 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
102264 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
102288 ATTT
1 ATTT
102292 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:123346 original size:2 final size:2
Alignment explanation
Indices: 123341--123393 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
123331 TGTTTTTCAT
123341 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
123382 GA GA GA GA GA GA
1 GA GA GA GA GA GA
123394 TAAAAAACAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:124895 original size:2 final size:2
Alignment explanation
Indices: 124888--124919 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
124878 NNNNNNNATA
124888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124920 GAGTAAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:126034 original size:22 final size:22
Alignment explanation
Indices: 126009--126086 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
125999 ATAATAAGGG
126009 AAAAAATAAAATAAGATAAATA
1 AAAAAATAAAATAAGATAAATA
*
126031 AAAAAATAAAACAAGCCAATTAAATA
1 AAAAAATAAAATAAG---A-TAAATA
*
126057 AAAAGAA-ATAATAA-ATAAATA
1 AAAA-AATAAAATAAGATAAATA
*
126078 AACAAATAA
1 AAAAAATAA
126087 GAACTAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 15 0.33
25 1 0.02
26 15 0.33
27 2 0.04
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (22 bp):
AAAAAATAAAATAAGATAAATA
Found at i:129142 original size:14 final size:15
Alignment explanation
Indices: 129108--129146 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
129098 TGGGTTGAGA
*
129108 AAATTATTTAATTGGT
1 AAATTAATTAATT-GT
129124 AAATTAATTAATT-T
1 AAATTAATTAATTGT
129138 AAATTAATT
1 AAATTAATT
129147 TAATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
AAATTAATTAATTGT
Found at i:139885 original size:18 final size:19
Alignment explanation
Indices: 139862--139898 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
139852 AGCAACGATC
*
139862 TCAAAAA-TGTAAAAATTA
1 TCAAAAACTGAAAAAATTA
139880 TCAAAAACTGAAAAAATTA
1 TCAAAAACTGAAAAAATTA
139899 CATAGCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (19 bp):
TCAAAAACTGAAAAAATTA
Found at i:140087 original size:20 final size:21
Alignment explanation
Indices: 140052--140090 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
140042 TCAAAATAAC
*
140052 TTTTATAATTCAATATACACA
1 TTTTATAATACAATATACACA
140073 TTTTAT-ATACAATATACA
1 TTTTATAATACAATATACA
140091 TAACCATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTTATAATACAATATACACA
Found at i:145318 original size:13 final size:13
Alignment explanation
Indices: 145300--145325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
145290 TTAAATGAAC
145300 AAAAATAAAATAA
1 AAAAATAAAATAA
145313 AAAAATAAAATAA
1 AAAAATAAAATAA
145326 TGTACTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:150738 original size:25 final size:26
Alignment explanation
Indices: 150678--150738 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
150668 ATTTTTTAAA
* *
150678 AAATTTTAAATTTAACTAAAAAATTT
1 AAATATTAAATTTAACTAAAAAATAT
* *
150704 AAAAAATAAA-TTAAC-AAAAATATAT
1 AAATATTAAATTTAACTAAAAA-ATAT
150729 AAATATTAAA
1 AAATATTAAA
150739 AGTAAAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 5 0.18
25 16 0.57
26 7 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATTAAATTTAACTAAAAAATAT
Found at i:151920 original size:16 final size:16
Alignment explanation
Indices: 151899--151931 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
151889 TAAAATAAGC
151899 TTAAAAAAGAAT-TAAA
1 TTAAAAAA-AATATAAA
151915 TTAAAAAAAATATAAA
1 TTAAAAAAAATATAAA
151931 T
1 T
151932 GTTAGATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
TTAAAAAAAATATAAA
Found at i:152929 original size:6 final size:6
Alignment explanation
Indices: 152918--152958 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
152908 GGTTATTGGT
*
152918 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAAGG TTAGG
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGG
152959 TTTTTGGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.46, T:0.34
Consensus pattern (6 bp):
TTAGGG
Found at i:153643 original size:126 final size:126
Alignment explanation
Indices: 153418--153697 Score: 452
Period size: 126 Copynumber: 2.2 Consensus size: 126
153408 TAATTTAAAG
** * *
153418 AAGCTCCCACATGGACGCGCTTTTGCTACAGTGGCTCCTGAGAAAATAATTTCGAGTAGACGTTT
1 AAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* * *
153483 CTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAA
66 ATGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAATACTGAAAA
* * *
153544 AAGCTTCCATGTGGACGCGCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTTGAGTAGACGTTT
1 AAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
* *
153609 ATGAGTAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAATACTGAAAG
66 ATGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAATACTGAAAA
153670 AAGCTCCCATGTGGACGCGCTTTTGCTA
1 AAGCTCCCATGTGGACGCGCTTTTGCTA
153698 TAGTGGCGCA
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 141 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (126 bp):
AAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTT
ATGAGCAAACAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAATACTGAAAA
Found at i:156880 original size:11 final size:11
Alignment explanation
Indices: 156864--156916 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
156854 TTAAATAGGG
156864 ATTTGAGAGAA
1 ATTTGAGAGAA
*
156875 ATTTGAAAGAA
1 ATTTGAGAGAA
*
156886 AATTGAGAGCAA
1 ATTTGAGAG-AA
156898 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
156909 ATTAGAGA
1 ATTTGAGA
156917 AAGGATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 26 0.74
12 9 0.26
ACGTcount: A:0.49, C:0.02, G:0.26, T:0.23
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:156916 original size:23 final size:22
Alignment explanation
Indices: 156866--156918 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
156856 AAATAGGGAT
156866 TTGAGAGAAATTTGAAAGAAAA
1 TTGAGAGAAATTTGAAAGAAAA
* *
156888 TTGAGAGCAAA-TTGAGAGGAAA
1 TTGAGAG-AAATTTGAAAGAAAA
156910 TT-AGAGAAA
1 TTGAGAGAAA
156919 GGATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 4 0.14
22 18 0.64
23 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (22 bp):
TTGAGAGAAATTTGAAAGAAAA
Found at i:160509 original size:46 final size:47
Alignment explanation
Indices: 160443--160536 Score: 181
Period size: 46 Copynumber: 2.0 Consensus size: 47
160433 AATAATATAT
160443 ATATTATATAAAGTATTTTCAAATAAAATATATAATATTAAAGTTTA
1 ATATTATATAAAGTATTTTCAAATAAAATATATAATATTAAAGTTTA
160490 ATATTATAT-AAGTATTTTCAAATAAAATATATAATATTAAAGTTTA
1 ATATTATATAAAGTATTTTCAAATAAAATATATAATATTAAAGTTTA
160536 A
1 A
160537 AGTTATCTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 38 0.81
47 9 0.19
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (47 bp):
ATATTATATAAAGTATTTTCAAATAAAATATATAATATTAAAGTTTA
Found at i:162348 original size:23 final size:23
Alignment explanation
Indices: 162319--162380 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
162309 GCCCGGCCCG
* *
162319 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAATTAAAATTAAAACTAA
*
162342 TTTTTAAATAAAATTAAAACTAA
1 TTTTTAATTAAAATTAAAACTAA
*
162365 TTGTT-ATTAAAATTAA
1 TTTTTAATTAAAATTAA
162381 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 10 0.29
23 24 0.71
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTTAATTAAAATTAAAACTAA
Found at i:162393 original size:16 final size:16
Alignment explanation
Indices: 162356--162395 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
162346 TAAATAAAAT
* *
162356 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
162372 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
162388 TAAAATTA
1 TAAAATTA
162396 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:162623 original size:22 final size:24
Alignment explanation
Indices: 162583--162626 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
162573 AAATAAACTT
162583 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
162607 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
162627 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:163171 original size:14 final size:13
Alignment explanation
Indices: 163149--163294 Score: 63
Period size: 12 Copynumber: 11.2 Consensus size: 13
163139 AAGTGTTTTC
*
163149 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
163163 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
163177 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
163189 TTAATTACCAAGTTTT
1 TT--TCATCAAG-TTT
* *
163205 TTTTATTAAG-TT
1 TTTCATCAAGTTT
*
163217 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
*
163231 TTT--T-AAG-CT
1 TTTCATCAAGTTT
*
163240 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
163253 TTTCAT-AAATTT
1 TTTCATCAAGTTT
* *
163265 TTCCATTAAGTTT
1 TTTCATCAAGTTT
*
163278 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
163293 TT
1 TT
163295 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 14, Indels: 27
0.72 0.10 0.19
Matches are distributed among these distances:
9 4 0.04
11 4 0.04
12 25 0.24
13 25 0.24
14 24 0.23
15 17 0.16
16 5 0.05
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:163246 original size:23 final size:22
Alignment explanation
Indices: 163210--163255 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
163200 GTTTTTTTTA
163210 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAG-TCTTT
163233 TTAAGCTTTT-CATCAAGTCTTT
1 TTAAG-TTTTGCATCAAGTCTTT
163255 T
1 T
163256 CATAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (22 bp):
TTAAGTTTTGCATCAAGTCTTT
Found at i:163302 original size:13 final size:12
Alignment explanation
Indices: 163203--163307 Score: 63
Period size: 12 Copynumber: 8.3 Consensus size: 12
163193 TTACCAAGTT
*
163203 TTTTTTATTAAG
1 TTTTTCATTAAG
* *
163215 TTTTGCATCAAG
1 TTTTTCATTAAG
163227 TTCTTT--TTAAG
1 TT-TTTCATTAAG
* *
163238 CTTTTCATCAAG
1 TTTTTCATTAAG
*
163250 TCTTTTCA-TAAA
1 T-TTTTCATTAAG
163262 TTTTTCCATTAAG
1 TTTTT-CATTAAG
163275 TTTTTAATCATTAAG
1 -TTTT--TCATTAAG
163290 TTTTTCAATTAAG
1 TTTTTC-ATTAAG
163303 CTTTT
1 -TTTT
163308 ATCTCTTGCA
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
10 3 0.04
11 9 0.13
12 22 0.31
13 17 0.24
14 12 0.17
15 7 0.10
16 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (12 bp):
TTTTTCATTAAG
Found at i:166031 original size:20 final size:20
Alignment explanation
Indices: 165997--166038 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
165987 AACTATTTAA
** *
165997 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
166017 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
166037 AT
1 AT
166039 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:171006 original size:20 final size:20
Alignment explanation
Indices: 170972--171013 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
170962 AACTATTTAA
** *
170972 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
170992 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
171012 AT
1 AT
171014 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:176382 original size:50 final size:50
Alignment explanation
Indices: 176242--176518 Score: 358
Period size: 50 Copynumber: 5.4 Consensus size: 50
176232 ATGAAAATAT
*
176242 TCTGGGACATGGCGTTGGCACCGAGATGAAAGGTCCCATGTAAGACCATG
1 TCTGGGACATGGCGTTGGCACCGATATGAAAGGTCCCATGTAAGACCATG
* *
176292 TCTGGGACATGGCATTGGCATCCTTGAGATCATGAAAGGTCTCATGTAAGACCATG
1 TCTGGGACATGGCGTTGGCA-CC----GAT-ATGAAAGGTCCCATGTAAGACCATG
176348 TCTGGGACATGGCGTTGGCACCGATATGAAAGGTCCCATGTAAGACCATG
1 TCTGGGACATGGCGTTGGCACCGATATGAAAGGTCCCATGTAAGACCATG
* * *
176398 TCTGGGACATGGCGTTGGCATCGAGATGAGAGGTCCC-TGGTAAGACCATG
1 TCTGGGACATGGCGTTGGCACCGATATGAAAGGTCCCAT-GTAAGACCATG
* * * * **
176448 TCTAGGACATGGCATGGGCAACGATATGAGAACATCCCATGTAAGACCATG
1 TCTGGGACATGGCGTTGGCACCGATATGA-AAGGTCCCATGTAAGACCATG
*
176499 TCTGGGACATGGCTTTGGCA
1 TCTGGGACATGGCGTTGGCA
176519 TGTTATTATC
Statistics
Matches: 199, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
49 1 0.01
50 112 0.56
51 38 0.19
52 1 0.01
55 4 0.02
56 43 0.22
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TCTGGGACATGGCGTTGGCACCGATATGAAAGGTCCCATGTAAGACCATG
Found at i:179735 original size:127 final size:127
Alignment explanation
Indices: 179562--179835 Score: 512
Period size: 127 Copynumber: 2.1 Consensus size: 127
179552 TCAGACAGAG
*
179562 GAATTATCTGATGTGATTTTAGTGATGACAGCTCAGGGGTGTGTCAGAAAAGGGTACGATGTTTA
1 GAATTTTCTGATGTG--TTTAGTGATGACAGCTCAGGGGTGTGTCAGAAAAGGGTACGATGTTTA
179627 TTTGGCATATGTGTTGGATACTAAGGTATCTGAGTCAAATATACAAGCAGTGCCAGTTGTATGT
64 TTTGGCATATGTGTTGGATACTAAGGTATCTGAGTCAAATATACAAGCAGTGCCAGTTGTATGT
179691 GAATTTTCTGATGTGTTTAGTGATGACAGCTCAGGGGTGTGTCAGAAAAGGGTACGATGTTTATT
1 GAATTTTCTGATGTGTTTAGTGATGACAGCTCAGGGGTGTGTCAGAAAAGGGTACGATGTTTATT
*
179756 TGGCATATGTGTTGGATACTAAGGTATCTGTGTCAAATATACAAGCAGTGCCAGTTGTATGT
66 TGGCATATGTGTTGGATACTAAGGTATCTGAGTCAAATATACAAGCAGTGCCAGTTGTATGT
179818 GAATTTTCTGATGTGTTT
1 GAATTTTCTGATGTGTTT
179836 CCAGAGGAGT
Statistics
Matches: 143, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
127 129 0.90
129 14 0.10
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (127 bp):
GAATTTTCTGATGTGTTTAGTGATGACAGCTCAGGGGTGTGTCAGAAAAGGGTACGATGTTTATT
TGGCATATGTGTTGGATACTAAGGTATCTGAGTCAAATATACAAGCAGTGCCAGTTGTATGT
Found at i:183531 original size:56 final size:56
Alignment explanation
Indices: 183440--183644 Score: 298
Period size: 56 Copynumber: 3.8 Consensus size: 56
183430 ATTTGGGTAA
183440 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
*
183496 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
* * *
183552 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGAATTGGCA----T--GAT-ATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
* *
183601 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
183645 GTTATTATCA
Statistics
Matches: 139, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
49 5 0.04
50 38 0.27
52 1 0.01
56 95 0.68
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (56 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
Found at i:183643 original size:112 final size:108
Alignment explanation
Indices: 183440--183644 Score: 290
Period size: 106 Copynumber: 1.9 Consensus size: 108
183430 ATTTGGGTAA
* **
183440 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCA--C-T-AGATCATGAGACATCCC
183505 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
62 ATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
* *
183552 AGAGGTCCCATGTAAGACTATGTCTGGGACATGGAATTGGCA-T-GAT-ATGAGAACATCCCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCACTAGATCATGAG-ACATCCCATG
*
183614 TAAGACCATGTCTGGGACATGGCTTTGGCAT
65 TAAGACCATGTCTGGGACATGGCATTGGCAT
183645 GTTATTATCA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
105 5 0.06
106 41 0.48
108 1 0.01
112 39 0.45
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (108 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCACTAGATCATGAGACATCCCATGT
AAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
Found at i:186882 original size:15 final size:15
Alignment explanation
Indices: 186851--186896 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
186841 AATATCTCAT
186851 TTTATTTAAAA-ATAA
1 TTTATTTAAAATA-AA
186866 TTTATTTAAAATAAA
1 TTTATTTAAAATAAA
186881 TTT-TTAGTAAAATAAA
1 TTTATT--TAAAATAAA
186897 ATTTTATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.07
15 16 0.57
16 10 0.36
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTTATTTAAAATAAA
Found at i:186893 original size:16 final size:16
Alignment explanation
Indices: 186872--186902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
186862 ATAATTTATT
*
186872 TAAAATAAATTTTTAG
1 TAAAATAAAATTTTAG
186888 TAAAATAAAATTTTA
1 TAAAATAAAATTTTA
186903 TAATTTGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATAAAATTTTAG
Found at i:187928 original size:25 final size:26
Alignment explanation
Indices: 187900--187956 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
187890 ATATAAACAC
187900 AATTTTTAATAT-ATATTT-ATTATTT
1 AATTTTTAATATAAT-TTTAATTATTT
**
187925 AATTTAAAATATAATTTTAATTATTT
1 AATTTTTAATATAATTTTAATTATTT
187951 -ATTTTT
1 AATTTTT
187957 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
AATTTTTAATATAATTTTAATTATTT
Found at i:187943 original size:36 final size:37
Alignment explanation
Indices: 187880--187954 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 37
187870 ACCCATAAAA
*
187880 TTATTATTTAATATAAACACAATTTTTAA-TATATAT
1 TTATTATTTAATATAAACACAAATTTTAATTATATAT
* * *
187916 TTATTATTTAATTTAAA-ATATAATTTTAATTATTTAT
1 TTATTATTTAATATAAACACA-AATTTTAATTATATAT
187953 TT
1 TT
187955 TTNNNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.06
36 23 0.70
37 8 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (37 bp):
TTATTATTTAATATAAACACAAATTTTAATTATATAT
Found at i:191083 original size:75 final size:75
Alignment explanation
Indices: 190959--191099 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
190949 TGCTTTCCAA
* * * *
190959 TGGTTTTCCCCTGGATTGCTTGTGAATCTACTTAAATTGCTCACGGTGAAAGTAATATCTGGTCT
1 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
191024 AGTACAGCAG
66 AGTACAGCAG
*
191034 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCGCAGTGAAAGCAATATCTGGTCT
1 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
191099 A
66 A
191100 AAATAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (75 bp):
TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
AGTACAGCAG
Found at i:195080 original size:75 final size:75
Alignment explanation
Indices: 194956--195096 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 75
194946 TGCTTTCCAA
* * * *
194956 TGGTTTTCCCCTGGATTGCTTGTGAATCTACTTAAATTGCTCACGGTGAAAGTAATATCTGGTCT
1 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
195021 AGTACAGCAG
66 AGTACAGCAG
*
195031 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCGCAGTGAAAGCAATATCTGGTCT
1 TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
195096 A
66 A
195097 AAATAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (75 bp):
TGGTTTTCCCCTAGATTGCTTGTGAATCTACTTAAACTGCTCACAGTGAAAGCAATATCTGGTCT
AGTACAGCAG
Found at i:201292 original size:28 final size:28
Alignment explanation
Indices: 201251--201318 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
201241 AATAAAAAAT
201251 TAAAAT-A-CTAATTAAACTAATT-ATCC
1 TAAAATAACCTAATTAAACTAATTAAT-C
*
201277 TAAAATAACCTAATTAAATTAATTAATC
1 TAAAATAACCTAATTAAACTAATTAATC
*
201305 TAAAATAACTTAAT
1 TAAAATAACCTAAT
201319 GAGATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 6 0.16
27 1 0.03
28 28 0.76
29 2 0.05
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAATAACCTAATTAAACTAATTAATC
Found at i:209072 original size:17 final size:17
Alignment explanation
Indices: 209050--209093 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
209040 CTTAAAGAAG
209050 ACTCATAATATTGGCGT
1 ACTCATAATATTGGCGT
209067 ACTCATAATATTGGCGT
1 ACTCATAATATTGGCGT
*
209084 ACTCTTAATA
1 ACTCATAATA
209094 CTTCCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (17 bp):
ACTCATAATATTGGCGT
Found at i:209790 original size:29 final size:29
Alignment explanation
Indices: 209748--209812 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
209738 ACAGCAACAT
**
209748 GTGGCATGCCATGTGTATTTCACATTAAC
1 GTGGCATGCCATGTGTACCTCACATTAAC
209777 GTGGCATGCCATGTGTACCTCACATTAAC
1 GTGGCATGCCATGTGTACCTCACATTAAC
*
209806 ATGGCAT
1 GTGGCAT
209813 TTTTGCTACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (29 bp):
GTGGCATGCCATGTGTACCTCACATTAAC
Found at i:209996 original size:20 final size:19
Alignment explanation
Indices: 209956--210065 Score: 61
Period size: 20 Copynumber: 5.7 Consensus size: 19
209946 TAATAATAAG
209956 AATTATTTTAAAATATAGAA
1 AATTA-TTTAAAATATAGAA
*
209976 AATTATTTAAAATGATTGAA
1 AATTATTTAAAAT-ATAGAA
* * * *
209996 ATTTA-TAAAAAAATTATAA
1 AATTATTTAAAATA-TAGAA
210015 AA-TATTTAAAAATTAATA-AA
1 AATTATTT-AAAA-T-ATAGAA
210035 AA-TATTTAAAA-ATA-AA
1 AATTATTTAAAATATAGAA
*
210051 TATTAATTTAAAATA
1 AATT-ATTTAAAATA
210066 AATAACTAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.08
17 1 0.01
18 11 0.15
19 23 0.32
20 27 0.38
21 2 0.03
22 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTATTTAAAATATAGAA
Found at i:210588 original size:15 final size:16
Alignment explanation
Indices: 210540--210586 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
210530 TAGATATGAT
210540 TTTTTAAATAATTATTTA
1 TTTTTAAAT-ATT-TTTA
*
210558 TTTTT-AGTATTTTTA
1 TTTTTAAATATTTTTA
210573 TTTTTAAATATTTT
1 TTTTTAAATATTTT
210587 ATGTGACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 9 0.35
16 10 0.38
17 2 0.08
18 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTTAAATATTTTTA
Found at i:212579 original size:9 final size:9
Alignment explanation
Indices: 212561--212591 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
212551 TTTGGTTAAA
212561 AATTAACCG
1 AATTAACCG
*
212570 AATTATCCG
1 AATTAACCG
212579 AATTAACCG
1 AATTAACCG
212588 AATT
1 AATT
212592 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:214254 original size:22 final size:22
Alignment explanation
Indices: 214229--214270 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
214219 AATAATGTAA
*
214229 AATGACATGCATATATGGAAAG
1 AATGACACGCATATATGGAAAG
214251 AATGACACGCATATATGGAA
1 AATGACACGCATATATGGAA
214271 CGATTAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (22 bp):
AATGACACGCATATATGGAAAG
Found at i:215792 original size:2 final size:2
Alignment explanation
Indices: 215752--215777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
215742 GATGTCTTCC
215752 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
215778 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215832 original size:2 final size:2
Alignment explanation
Indices: 215825--215852 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
215815 NNNNNNTTCC
215825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
215853 TTCATTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:221349 original size:3 final size:3
Alignment explanation
Indices: 221343--221369 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
221333 ATTGATATTG
221343 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
221370 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:221492 original size:68 final size:68
Alignment explanation
Indices: 221383--221610 Score: 438
Period size: 68 Copynumber: 3.4 Consensus size: 68
221373 TATTATTATT
221383 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
1 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
221448 ATC
66 ATC
221451 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
1 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
221516 ATC
66 ATC
*
221519 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAA
1 ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
221584 ATC
66 ATC
*
221587 ATAATTAGGTAGCTACAAAATCAT
1 ATAATTAGATAGCTACAAAATCAT
221611 ACATAAATTA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 158 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (68 bp):
ATAATTAGATAGCTACAAAATCATTTCATCTCTAATATTGCTAGTTCTAAAGGGAAACTCTCGAG
ATC
Found at i:221670 original size:28 final size:28
Alignment explanation
Indices: 221629--221684 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
221619 TAGACTCAGT
*
221629 ACCTTGCTTTTCGATTTCCATGTCTGAA
1 ACCTTGCTTGTCGATTTCCATGTCTGAA
221657 ACCTTGCTTGTCGATTTCCATGTCTGAA
1 ACCTTGCTTGTCGATTTCCATGTCTGAA
221685 CCAACCTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (28 bp):
ACCTTGCTTGTCGATTTCCATGTCTGAA
Found at i:226586 original size:41 final size:42
Alignment explanation
Indices: 226514--226608 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
226504 TTTTTAAAAG
* * * * *
226514 TTAGTGGCGTTTTATGTAAAACGGCGCTAAAGGTTATGGCCT
1 TTAGCGGCGTTTTATCTAAAACGGCCCTAAAGGTCATGACCT
*
226556 TTAGCGGCGCTTTTATCT-AAAC-GCCCTAAAGGTCATGATCT
1 TTAGCGGCG-TTTTATCTAAAACGGCCCTAAAGGTCATGACCT
226597 TTAGCGGCGTTT
1 TTAGCGGCGTTT
226609 GTAGGTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 3 0.07
41 24 0.52
42 12 0.26
43 7 0.15
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
TTAGCGGCGTTTTATCTAAAACGGCCCTAAAGGTCATGACCT
Found at i:226677 original size:43 final size:43
Alignment explanation
Indices: 226577--226677 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
226567 TTTATCTAAA
* *
226577 CGCC-CTAAAGGTCATGATCTTTAGCGGCGTTTGTAGGTAAAG
1 CGCCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTAGGAAAAG
** * * *
226619 CATCGTTAAAAGTCATGATCTGTAGTGGCGTTTGT-GGAAGAAG
1 CGCCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTAGGAA-AAG
226662 CGCCGCTAAAGGTCAT
1 CGCCGCTAAAGGTCAT
226678 TTATTTCTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
42 5 0.11
43 41 0.89
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (43 bp):
CGCCGCTAAAGGTCATGATCTGTAGCGGCGTTTGTAGGAAAAG
Found at i:233288 original size:24 final size:23
Alignment explanation
Indices: 233261--233311 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
233251 CATTAATTAT
*
233261 TATAGATTGAATTTAATTTATGTG
1 TATAGATGGAATTTAATTTA-GTG
*
233285 TATATATGGAATTTAATTTAGTG
1 TATAGATGGAATTTAATTTAGTG
233308 TATA
1 TATA
233312 TATGTGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (23 bp):
TATAGATGGAATTTAATTTAGTG
Found at i:233312 original size:23 final size:24
Alignment explanation
Indices: 233269--233315 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
233259 ATTATAGATT
233269 GAATTTAATTTATGTGTATATATG
1 GAATTTAATTTATGTGTATATATG
233293 GAATTTAATTTA-GTGTATATATG
1 GAATTTAATTTATGTGTATATATG
233316 TGATTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (24 bp):
GAATTTAATTTATGTGTATATATG
Found at i:236250 original size:21 final size:21
Alignment explanation
Indices: 236226--236265 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
236216 TACCTTTCTA
236226 AAGTTAAAA-GTCAAAACTATT
1 AAGTTAAAATG-CAAAACTATT
236247 AAGTTAAAATGCAAAACTA
1 AAGTTAAAATGCAAAACTA
236266 CGTTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (21 bp):
AAGTTAAAATGCAAAACTATT
Found at i:242275 original size:95 final size:97
Alignment explanation
Indices: 241999--242268 Score: 413
Period size: 97 Copynumber: 2.8 Consensus size: 97
241989 TATATATAAA
* * *
241999 CTTTTAACTAATTTATAAATAATTTACTCAAGTAACCCTAAACCCTAATTT-TTTTATTTTTTCC
1 CTTTTAA-AAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCC
242063 TTAAAACCCTAAACACTAAACCCCAATCTAATT
65 TTAAAACCCTAAACACTAAACCCCAATCTAATT
242096 CTTTTAAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAA-TTTTTCC
1 CTTTT-AAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCC
*
242160 TTAAAAACCCTAAACACTAAACCCTAATCTAATT
65 TT-AAAACCCTAAACACTAAACCCCAATCTAATT
* * * *
242194 -TTTT-AAAATTTATAATTAATTTAATTAAGAAACCCTAAACCCTTATTTATTTAATTTTTTCCT
1 CTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCT
242257 TAAAACCCTAAA
66 TAAAACCCTAAA
242269 ATCTAAAAAC
Statistics
Matches: 161, Mismatches: 8, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
95 57 0.35
96 9 0.06
97 59 0.37
98 36 0.22
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.40
Consensus pattern (97 bp):
CTTTTAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTTCCT
TAAAACCCTAAACACTAAACCCCAATCTAATT
Found at i:245894 original size:7 final size:7
Alignment explanation
Indices: 245882--245921 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
245872 CAGTAAAAGA
245882 ATGAGTG
1 ATGAGTG
245889 ATGAGTG
1 ATGAGTG
245896 ATGAGTG
1 ATGAGTG
245903 ATGAGTG
1 ATGAGTG
245910 ATGAGTG
1 ATGAGTG
245917 ATGAG
1 ATGAG
245922 CACCACCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.28
Consensus pattern (7 bp):
ATGAGTG
Found at i:256236 original size:32 final size:30
Alignment explanation
Indices: 256196--256281 Score: 84
Period size: 32 Copynumber: 2.8 Consensus size: 30
256186 AAAGAAGTAC
256196 AAGA-AAATAAAAATAAAACAAAACAACTAAG
1 AAGAGAAATAAAAATAAAACAAAACAA--AAG
* * *
256227 AAGAGAAATAAACATAAAAGAAAAGAAAAG
1 AAGAGAAATAAAAATAAAACAAAACAAAAG
* *
256257 AAAAGAAAACTAAAAAGAAAACAAA
1 AAGAG-AAA-TAAAAATAAAACAAA
256282 TAAAATAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
30 7 0.16
31 7 0.16
32 31 0.69
ACGTcount: A:0.76, C:0.07, G:0.10, T:0.07
Consensus pattern (30 bp):
AAGAGAAATAAAAATAAAACAAAACAAAAG
Found at i:264473 original size:2 final size:2
Alignment explanation
Indices: 264468--264496 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
264458 AATGAAGCAA
264468 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
264497 GTATTCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:268088 original size:45 final size:45
Alignment explanation
Indices: 268037--268122 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
268027 CGAAGCTTTG
*
268037 GGTACCCTAAATCCGAATCCCATTGACGCGGTCACAATTTCTGAA
1 GGTACCCCAAATCCGAATCCCATTGACGCGGTCACAATTTCTGAA
* *
268082 GGTACCCCAAATCCGAATCCCATTGACGTGTTCACAATTTC
1 GGTACCCCAAATCCGAATCCCATTGACGCGGTCACAATTTC
268123 AGATGATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (45 bp):
GGTACCCCAAATCCGAATCCCATTGACGCGGTCACAATTTCTGAA
Found at i:268340 original size:93 final size:90
Alignment explanation
Indices: 268184--268367 Score: 323
Period size: 93 Copynumber: 2.0 Consensus size: 90
268174 ACCCCACAAA
* *
268184 AGGGTCGTGGCTGTCCGGGATTTTCCTACTCCAACAAAGTTTCAAACTCCGTGCTCTGAAGGTCA
1 AGGGTCGTGGCTGTCAGGGATTTTCCTACTCCAACAAAGTTTCAAACTCCATGCTCTGAAGGTCA
268249 ATACTCTAGCCCCAGTTATGATGAG
66 ATACTCTAGCCCCAGTTATGATGAG
268274 AGGGTCGTGGCTGTCAGGGATTTTCCTACTCCACCAACAAAGTTTCAAACTCCATGCTCTGAAGG
1 AGGGTCGTGGCTGTCAGGGATTTTCCTACT---CCAACAAAGTTTCAAACTCCATGCTCTGAAGG
268339 TCAATACTCTAGCCCCAGTTATGATGAG
63 TCAATACTCTAGCCCCAGTTATGATGAG
268367 A
1 A
268368 AAAAACTTGA
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
90 29 0.33
93 60 0.67
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (90 bp):
AGGGTCGTGGCTGTCAGGGATTTTCCTACTCCAACAAAGTTTCAAACTCCATGCTCTGAAGGTCA
ATACTCTAGCCCCAGTTATGATGAG
Found at i:270261 original size:28 final size:29
Alignment explanation
Indices: 270208--270262 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
270198 ACAAATTTAC
270208 AATTTAATCCTTATATCTTTACTTTTAGA
1 AATTTAATCCTTATATCTTTACTTTTAGA
*
270237 AATTTAATCTCTT-TAT-TTTTCTTTTA
1 AATTTAATC-CTTATATCTTTACTTTTA
270263 ACTTGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 12 0.50
30 3 0.12
ACGTcount: A:0.27, C:0.13, G:0.02, T:0.58
Consensus pattern (29 bp):
AATTTAATCCTTATATCTTTACTTTTAGA
Found at i:270448 original size:23 final size:23
Alignment explanation
Indices: 270422--270466 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
270412 CTATGTTAAT
270422 TGAAATCTGAAAAATTA-AAAGAC
1 TGAAATCT-AAAAATTATAAAGAC
* *
270445 TGAATTCTAAAATTTATAAAGA
1 TGAAATCTAAAAATTATAAAGA
270467 GTTCAGGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (23 bp):
TGAAATCTAAAAATTATAAAGAC
Found at i:274318 original size:27 final size:27
Alignment explanation
Indices: 274256--274306 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
274246 CTTTTAATGT
274256 TTATTATAACATATTAATATATTATAC
1 TTATTATAACATATTAATATATTATAC
274283 TTATTATAACAT-TT-ATATATTATA
1 TTATTATAACATATTAATATATTATA
274307 TTAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.42
26 2 0.08
27 12 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTATAACATATTAATATATTATAC
Found at i:282596 original size:27 final size:27
Alignment explanation
Indices: 282534--282584 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
282524 CTTTTAATGT
282534 TTATTATAACATATTAATATATTATAC
1 TTATTATAACATATTAATATATTATAC
282561 TTATTATAACAT-TT-ATATATTATA
1 TTATTATAACATATTAATATATTATA
282585 TTAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.42
26 2 0.08
27 12 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTATAACATATTAATATATTATAC
Found at i:283406 original size:38 final size:37
Alignment explanation
Indices: 283355--283462 Score: 171
Period size: 38 Copynumber: 2.9 Consensus size: 37
283345 TATGACTCAT
* *
283355 ATAACAAACAAACTTACTTTTTTAACTCATACTTTCAC
1 ATAACAAACAAACTTACTTTTATGACTCATACTTT-AC
*
283393 ATAACAAACAAACTTACTTTTATGACTCATAGATTTAC
1 ATAACAAACAAACTTACTTTTATGACTCATA-CTTTAC
283431 ATAACAAACAAACTTACTTTTATGACTCATAC
1 ATAACAAACAAACTTACTTTTATGACTCATAC
283463 AAAATAGTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
38 62 0.95
39 3 0.05
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (37 bp):
ATAACAAACAAACTTACTTTTATGACTCATACTTTAC
Found at i:284206 original size:5 final size:5
Alignment explanation
Indices: 284196--284235 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
284186 GAAGAATATT
*
284196 TTTAA TTTAA TTTAA TTTAA TTTAA TTT-A TTTAT TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
284236 ATTATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (5 bp):
TTTAA
Found at i:284216 original size:15 final size:14
Alignment explanation
Indices: 284196--284240 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
284186 GAAGAATATT
284196 TTTAATTTAATTTAA
1 TTTAATTTAATTT-A
284211 TTTAATTTAATTTA
1 TTTAATTTAATTTA
*
284225 TTTATTTTAATATTA
1 TTTAATTTAAT-TTA
284240 T
1 T
284241 ATTATCCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATTTAATTTA
Found at i:284465 original size:221 final size:222
Alignment explanation
Indices: 284187--284661 Score: 886
Period size: 221 Copynumber: 2.1 Consensus size: 222
284177 TCACTTAATG
* *
284187 AAGAATATTTTTAATTT-AATTTAAT--TTAATTTAATTTATTTATTTTAATATTATATTATCCT
1 AAGAAT-TTTATAATTTAAATTCAATACTTAA-TTAATTTATTTATTTTAATATTATATTATCCT
284249 ATTAAAAATTTACATCTAAAATTTGATTTTTGCATAGAAGAGAGTGGAATGTTTTAAAATTTAAG
64 ATTAAAAATTTACATCTAAAATTTGATTTTTGCATAGAAGAGAGTGGAATGTTTTAAAATTTAAG
284314 GAAAAAATGTAGAATTTTAATTTTTTATAATTTAAAATCTATTTTTATCAAACTATATAATTATA
129 GAAAAAATGTAGAATTTTAATTTTTTATAATTTAAAATCTATTTTTATCAAACTATATAATTATA
284379 TTTCATAATTAATTTTAAGTATTAGATCA
194 TTTCATAATTAATTTTAAGTATTAGATCA
284408 AAGAATTTTATAATTTAAATTCAATACTTAATTAATTTATTT-TTTTAATATTATATTATCCTAT
1 AAGAATTTTATAATTTAAATTCAATACTTAATTAATTTATTTATTTTAATATTATATTATCCTAT
284472 TAAAAATTTACATCTAAAATTTGATTTTTGCATAGAAGAGAGTGGAATGTTTTAAAATTTAAGGA
66 TAAAAATTTACATCTAAAATTTGATTTTTGCATAGAAGAGAGTGGAATGTTTTAAAATTTAAGGA
284537 AAAAATGTAGAATTTTAATTTTTTATAATTTAAAATCTATTTTTATCAAACTATATAATTATATT
131 AAAAATGTAGAATTTTAATTTTTTATAATTTAAAATCTATTTTTATCAAACTATATAATTATATT
284602 TCATAATTAATTTTAAGTATTAGATCA
196 TCATAATTAATTTTAAGTATTAGATCA
284629 AAGAATTTTATAATTTAAATTCAATACTTAATT
1 AAGAATTTTATAATTTAAATTCAATACTTAATT
284662 TTTCAACATT
Statistics
Matches: 249, Mismatches: 2, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
220 9 0.04
221 225 0.90
222 11 0.04
223 4 0.02
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (222 bp):
AAGAATTTTATAATTTAAATTCAATACTTAATTAATTTATTTATTTTAATATTATATTATCCTAT
TAAAAATTTACATCTAAAATTTGATTTTTGCATAGAAGAGAGTGGAATGTTTTAAAATTTAAGGA
AAAAATGTAGAATTTTAATTTTTTATAATTTAAAATCTATTTTTATCAAACTATATAATTATATT
TCATAATTAATTTTAAGTATTAGATCA
Found at i:284678 original size:15 final size:15
Alignment explanation
Indices: 284648--284697 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
284638 ATAATTTAAA
*
284648 TTCAATACTTAATTT
1 TTCAACACTTAATTT
* *
284663 TTCAACATTTATTTT
1 TTCAACACTTAATTT
*
284678 TTCAGCACTTAATTT
1 TTCAACACTTAATTT
284693 TTCAA
1 TTCAA
284698 TTTATCAAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:286875 original size:30 final size:30
Alignment explanation
Indices: 286836--286896 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
286826 AGAAGAATCT
* *
286836 CCAACAACCTTTACAAATGGTTCTAATCAA
1 CCAACAACCTTCACAAATGGTTCTAACCAA
*
286866 CCAATAACCTTCACAAATGGTTCTAACCAA
1 CCAACAACCTTCACAAATGGTTCTAACCAA
286896 C
1 C
286897 TCCTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.30, G:0.07, T:0.25
Consensus pattern (30 bp):
CCAACAACCTTCACAAATGGTTCTAACCAA
Found at i:314629 original size:58 final size:60
Alignment explanation
Indices: 314514--314632 Score: 215
Period size: 58 Copynumber: 2.0 Consensus size: 60
314504 GCCTTATATT
314514 AGAAGGCCTATATTACCCTTAAGTAAAAAAAATAAAAACATTACTACTTCCATGCTCAAA
1 AGAAGGCCTATATTACCCTTAAGTAAAAAAAATAAAAACATTACTACTTCCATGCTCAAA
*
314574 AGAAGGCCTATATTACGCTTAAGT-AAAAAAAT-AAAACATTACTACTTCCATGCTCAAA
1 AGAAGGCCTATATTACCCTTAAGTAAAAAAAATAAAAACATTACTACTTCCATGCTCAAA
314632 A
1 A
314633 ACAAGGGTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 27 0.47
59 8 0.14
60 23 0.40
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.25
Consensus pattern (60 bp):
AGAAGGCCTATATTACCCTTAAGTAAAAAAAATAAAAACATTACTACTTCCATGCTCAAA
Found at i:317286 original size:96 final size:96
Alignment explanation
Indices: 317122--317312 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 96
317112 GTGAACGGTA
317122 AGTGTTTAGAATCACTGCTTGTAGTCACGATTCATAGTGTTAAATGGAAGCTTAGGAGTAGCCTA
1 AGTGTTTAGAATCACTGCTTGTAGTCACGATTCATAGTGTTAAATGGAAGCTTAGGAGTAGCCTA
317187 AACCCCTACTCTAAGTTCTGAGTGTAAACTG
66 AACCCCTACTCTAAGTTCTGAGTGTAAACTG
*
317218 AGTGTTTAGAATCACTGCTTGTAGTCACGATTCATAGTGTTAAATGGGAGCTTAGGAGTAGCCTA
1 AGTGTTTAGAATCACTGCTTGTAGTCACGATTCATAGTGTTAAATGGAAGCTTAGGAGTAGCCTA
317283 AACCCCTACTCTAAGTTCTGAGTGTAAACT
66 AACCCCTACTCTAAGTTCTGAGTGTAAACT
317313 TTCTTATTCC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (96 bp):
AGTGTTTAGAATCACTGCTTGTAGTCACGATTCATAGTGTTAAATGGAAGCTTAGGAGTAGCCTA
AACCCCTACTCTAAGTTCTGAGTGTAAACTG
Found at i:318683 original size:35 final size:35
Alignment explanation
Indices: 318613--318742 Score: 109
Period size: 35 Copynumber: 3.7 Consensus size: 35
318603 TTACAGTAGG
* * * * *
318613 CATGCTTAACATGCGAATTAGAATAAAAAACATGA
1 CATGCTTAACATGCGAATCAAAATCAGAAATATGA
* *
318648 CATGTTTAACATGCGAATCATAATCAGAAATATGA
1 CATGCTTAACATGCGAATCAAAATCAGAAATATGA
* * *
318683 CATACTTAACATACGAATCAGAACATCAG-AATATTAA
1 CATGCTTAACATGCGAATCA-AA-ATCAGAAATA-TGA
* **
318720 CATGTTTAACATGTAAATCAAAA
1 CATGCTTAACATGCGAATCAAAA
318743 CATCAATAAC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
35 47 0.62
36 7 0.09
37 22 0.29
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (35 bp):
CATGCTTAACATGCGAATCAAAATCAGAAATATGA
Found at i:326757 original size:28 final size:27
Alignment explanation
Indices: 326693--326757 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
326683 TATTCAGTAT
*
326693 CAGTACAGTGTGAGCCTTAGCCCAATA
1 CAGTACAGTGTGAGCCTAAGCCCAATA
* * *
326720 TAGAAACAGTGTGGGCCTAAGCCCAATA
1 CAG-TACAGTGTGAGCCTAAGCCCAATA
326748 CAGTATCAGT
1 CAGTA-CAGT
326758 ATGATGCAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (27 bp):
CAGTACAGTGTGAGCCTAAGCCCAATA
Done.