Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006118.1 Hibiscus syriacus cultivar Beakdansim tig00014512_pilon, whole genome shotgun sequence
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: 107123
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:12098 original size:8 final size:8
Alignment explanation
Indices: 12066--12152 Score: 80
Period size: 8 Copynumber: 11.5 Consensus size: 8
12056 GCTTGAAGAA
*
12066 AAAAAAGG
1 AAAAAATG
*
12074 AACAAAT-
1 AAAAAATG
12081 AAAAAGATG
1 AAAAA-ATG
12090 AAAAAATG
1 AAAAAATG
12098 AAAAAATG
1 AAAAAATG
*
12106 AAAAAGA-A
1 AAAAA-ATG
12114 AAAAAATG
1 AAAAAATG
12122 -AAAAATG
1 AAAAAATG
12129 AAAAAA-G
1 AAAAAATG
12136 ---AAATG
1 AAAAAATG
12141 AAAAAATG
1 AAAAAATG
12149 AAAA
1 AAAA
12153 GAGAAAAAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
7 13 0.20
8 42 0.65
9 6 0.09
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:12104 original size:24 final size:25
Alignment explanation
Indices: 12066--12161 Score: 101
Period size: 24 Copynumber: 3.9 Consensus size: 25
12056 GCTTGAAGAA
* *
12066 AAAAAAGGAACAAAT-AAAAAGATG
1 AAAAAATGAAAAAATGAAAAAGATG
*
12090 AAAAAATGAAAAAATGAAAAAGA-A
1 AAAAAATGAAAAAATGAAAAAGATG
12114 AAAAAATG-AAAAATGAAAAAAGAAATG
1 AAAAAATGAAAAAATG-AAAAAG--ATG
*
12141 AAAAAATGAAAAGA-GAAAAAG
1 AAAAAATGAAAAAATGAAAAAG
12162 GAGGGTTTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
23 7 0.11
24 27 0.44
25 7 0.11
26 7 0.11
27 9 0.15
28 4 0.07
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (25 bp):
AAAAAATGAAAAAATGAAAAAGATG
Found at i:12147 original size:20 final size:19
Alignment explanation
Indices: 12101--12158 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
12091 AAAAATGAAA
12101 AAATGAAAAA-G-AAAAA-
1 AAATGAAAAATGAAAAAAG
12117 AAATGAAAAATGAAAAAAG
1 AAATGAAAAATGAAAAAAG
*
12136 AAATGAAAAAATGAAAAGAG
1 AAATG-AAAAATGAAAAAAG
12156 AAA
1 AAA
12159 AAGGAGGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 10 0.27
17 1 0.03
18 5 0.14
19 5 0.14
20 16 0.43
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (19 bp):
AAATGAAAAATGAAAAAAG
Found at i:13649 original size:334 final size:334
Alignment explanation
Indices: 13035--13690 Score: 1010
Period size: 334 Copynumber: 2.0 Consensus size: 334
13025 TTGATCAACA
*
13035 TTTCCAATGAAGAGTTTATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
* *
13100 AAGAGCCTATTCGACCTATCACTCGATTCATGGCGTTTCGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
*
13165 TCAACATTTCCAGAGAATAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
131 TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
* * *
13230 GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGGGATGGATTAAAATTTCCAATGGAGAGTTC
196 GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
* * * *
13295 ATAATAAGAAGAATTCATCCAACGA-GAGAGAATAATTTCATAATGAGAAAAACTTGTCCAACTT
261 ATAATAAGAAGAACTCATCCAAAGAGGA-AGAAGAAGTTCATAATGAGAAAAACTTGTCCAACTT
13359 CGCATTAGTG
325 CGCATTAGTG
*
13369 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
** * * *
13434 AAGAGTTTGTTCGACCTATCACTCGATTTACGGCATTTTGAATCAGTGACACCTCGCTTGAGGGA
66 AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
** * * *
13499 TTGACATTTCTA-ATTAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGGGAAAGTTCATAATG
131 TCAACATTTCCAGA-GAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
* * * * *
13563 AGAAGAACTTGTTCCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTGAAGAGTT
195 AGAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTT
* * *
13628 CATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
260 CATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTCCAAC
13691 CTTGGTTTGA
Statistics
Matches: 290, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
333 1 0.00
334 287 0.99
335 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (334 bp):
TTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCCTATTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAGGGA
TCAACATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGA
GAAGAACTTGTTCCTTTCAAATCCATCAAAGAAAGAGATGGATCAAAATTTCCAATGAAGAGTTC
ATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTCCAACTTC
GCATTAGTG
Found at i:13687 original size:20 final size:20
Alignment explanation
Indices: 13624--13688 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
13614 TTCAGTGAAG
13624 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
13644 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
13663 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
13683 TGTTCA
1 AGTTCA
13689 ACCTTGGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:13751 original size:117 final size:114
Alignment explanation
Indices: 13514--13806 Score: 399
Period size: 117 Copynumber: 2.6 Consensus size: 114
13504 ATTTCTAATT
*
13514 AAGAGTTCATAATGAGAAGAACTCGTCCTAAAG-GG--G-A-AAGTTCATAATGAGAAGAACTTG
1 AAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
13574 TT---CCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
65 TTCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
13621 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
** * * * *
13686 TCAACCTTGGTTTGATTTCATCACAGAAGGAGGTGGATCAACATTTTCAGTG
66 TCAACC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
13738 AAGAGTTCATAATGAGAAGAACTCATCCAACA-A-GAGAGAAGAAGTTCATAATGAGAAGAACTT
1 AAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGA-AGAAGAAGTTCATAATGAGAAGAACTT
13801 GTTCAA
64 GTTCAA
13807 TCCAACGCTT
Statistics
Matches: 166, Mismatches: 7, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
106 4 0.02
107 29 0.17
109 1 0.01
110 1 0.01
111 25 0.15
114 2 0.01
115 1 0.01
116 2 0.01
117 100 0.60
118 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (114 bp):
AAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTTCAGTG
Found at i:18611 original size:156 final size:156
Alignment explanation
Indices: 18338--18810 Score: 569
Period size: 156 Copynumber: 3.0 Consensus size: 156
18328 ATATTATCGA
*
18338 TGAATCCGCAAAG-TTTTAGGCTAACATAAGCGCACATAGACCCACGTCAATAGTCATAGCAGAG
1 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAG-GCC-CG-C----GTCATAGCAGAG
18402 CTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTT
59 CTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTT
* *
18467 CGGGTCATAGTAGATATTGTTGGTGAATATCTG
124 CGGGTCATAGTAGATATTGTCGATGAATATCTG
* *
18500 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCACACATAGGCCCGCGTCATAGCAGAGCTTCTGA
1 TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTGA
* * *
18565 AGGTTTGTTGAATCATTATGTATTCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCCGGTCA
66 AGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCGGGTCA
*
18630 TAGTCGATATTGTCGATGAATATCTG
131 TAGTAGATATTGTCGATGAATATCTG
* * * * * * * * ** * * *
18656 TGAATCTGCAGAGTTTCT-GGATATA-TTAAGTGGAAATAGGCTTGTGTCTTGGCAGAGCTTGTG
1 TGAATCCGCAAAGTTTTTAGGCTA-ACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTG
* * * *
18719 AAGGTTTGTTGAATCATTACATATGCCATTGATTCTTGTGGCTGAATTTTATGTTCTTCCGGG-C
65 AAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCGGGTC
18783 TATAGTCA-ATGTATTGTCGATGAATATC
130 -ATAGT-AGA--TATTGTCGATGAATATC
18811 CTAGAAATCT
Statistics
Matches: 273, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
154 1 0.00
155 93 0.34
156 119 0.44
157 17 0.06
160 1 0.00
161 2 0.01
162 15 0.05
163 25 0.09
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (156 bp):
TGAATCCGCAAAGTTTTTAGGCTAACATAAGCGCACATAGGCCCGCGTCATAGCAGAGCTTGTGA
AGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTATGTTCTTTCGGGTCA
TAGTAGATATTGTCGATGAATATCTG
Found at i:18788 original size:155 final size:149
Alignment explanation
Indices: 18394--18966 Score: 548
Period size: 156 Copynumber: 3.7 Consensus size: 149
18384 TCAATAGTCA
18394 TAGCAGAGCTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTA
1 TAGCAGAGCTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTA
* * * * *
18459 TGTTCTTTCGGGTCATAGTAGATATTGTTGGTGAATATCTGTGAATCCGCAAAGTTTTTAGGCTA
66 TGTTCTTCCGGGT-ATAGTCGATATTGTCGATGAATATCTGTGAATCTGC-AAG-TTTT-GG-TA
* * ** * *
18524 ACATAAGCA-CACATAGGCCCGCGTCA
126 A-TTAAG-AGGA-ATAGGCTTGTGTCT
* * *
18550 TAGCAGAGCTTCTGAAGGTTTGTTGAATCATTATGTATTCCATTGATTCTTGTTGCTGAATATTA
1 TAGCAGAGCTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTA
18615 TGTTCTTTCC-GGTCATAGTCGATATTGTCGATGAATATCTGTGAATCTGCAGAGTTTCTGGATA
66 TGTTC-TTCCGGGT-ATAGTCGATATTGTCGATGAATATCTGTGAATCTGCA-AGTTT-TGG-TA
*
18679 TATTAAGTGGAAATAGGCTTGTGTCT
126 -ATTAAGAGG-AATAGGCTTGTGTCT
* * * *
18705 TGGCAGAGCTTGTGAAGGTTTGTTGAATCATTACATATGCCATTGATTCTTGTGGCTGAATTTTA
1 TAGCAGAGCTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTA
* * * *
18770 TGTTCTTCCGGGCTATAGTCAATGTATTGTCGATGAATATCCTAG-AAATCTGGAAGTTTAGGTA
66 TGTTCTTCCGGG-TATAGTCGA--TATTGTCGATGAATAT-CT-GTGAATCTGCAAGTTTTGGTA
18834 GATTAAGAGG-A-A-G-TTGTGTCT
126 -ATTAAGAGGAATAGGCTTGTGTCT
* *
18855 TAGCAGAACTTGTGAAGGGGTTTTTTTTTTGGAATCATTATATATGCCATTGATTCTTGTTGCTG
1 TAGCAGAGCTTGTGAA--GG----TTTGTT-GAATCATTATATATGCCATTGATTCTTGTTGCTG
* * ** * *
18920 AATTTTATGTTATTTTGGGTTTAGTGGATATATTGTCGATGAATATC
59 AATATTATGTTCTTCCGGGTATAGTCG--ATATTGTCGATGAATATC
18967 CGCAAATCCA
Statistics
Matches: 356, Mismatches: 40, Indels: 43
0.81 0.09 0.10
Matches are distributed among these distances:
150 22 0.06
151 1 0.00
152 3 0.01
153 1 0.00
154 4 0.01
155 105 0.29
156 137 0.38
157 72 0.20
158 10 0.03
159 1 0.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (149 bp):
TAGCAGAGCTTGTGAAGGTTTGTTGAATCATTATATATGCCATTGATTCTTGTTGCTGAATATTA
TGTTCTTCCGGGTATAGTCGATATTGTCGATGAATATCTGTGAATCTGCAAGTTTTGGTAATTAA
GAGGAATAGGCTTGTGTCT
Found at i:37206 original size:40 final size:41
Alignment explanation
Indices: 37147--37250 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 41
37137 CTGGAAATGT
* * * * *
37147 TGATCCACCTCCTTCTGTGATGATTGAGC-CAA-GGTGATGC
1 TGATCCAACTCCTTATGTGATGACTG-GCGAAATGATGATGC
* *
37187 TGATCCAACTCCTTATGTGAGGGACTGGCGAAATGATTATGC
1 TGATCCAACTCCTTATGTGA-TGACTGGCGAAATGATGATGC
37229 TGATCCAACTCCTTATGTGATG
1 TGATCCAACTCCTTATGTGATG
37251 GACAAGCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 20 0.38
41 7 0.13
42 26 0.49
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (41 bp):
TGATCCAACTCCTTATGTGATGACTGGCGAAATGATGATGC
Found at i:37485 original size:240 final size:235
Alignment explanation
Indices: 37061--37623 Score: 834
Period size: 240 Copynumber: 2.4 Consensus size: 235
37051 ATGGAATCAC
* * *
37061 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTTTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCATTA
* * *
37126 TGAACTCTCAACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTGATGCTGAT
66 TAAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTGAT
*
37191 CCAACTCCTTATGTGAGGGACTGGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
131 CCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
*
37256 GCAAAAGTCGGTGATGTTCCAATTCCTTATGCGATGGAAACAA
196 GCAAAAGTCGGTGATGTTCCAACTCCTTATGCGAT-G-AA-AA
* *
37299 GCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCGGATGAGTTCTTCTCAT
1 -C-AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCAT
* * * *
37364 TATTAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGATCTAAGGTAATGTTG
64 TATAAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTG
* *
37429 ATCCATCTCCTTATGTGAGGGACTAGCTAAATGATTATGCTGATCCAACTCCTTATGTGATGGAC
129 ATCCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGAC
* *
37494 GAGCAAAAGTCGGTGTTGTTCCAACTCCTTATGCGATGAAAA
194 AAGCAAAAGTCGGTGATGTTCCAACTCCTTATGCGATGAAAA
*
37536 CAA-GCT-AA-AA-TTCTTCTCATTATGAACTTCGTT-TCCCTT-ATCGGATGAGTTATTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCT-CCTTCATCGGATGAGTTATTCTCAT
37595 TATAAACTCTCCACTGGAAA-GATTGATCC
64 TATAAACTCTCCACTGGAAATG-TTGATCC
37624 CTCGAGTGAG
Statistics
Matches: 301, Mismatches: 19, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
230 1 0.00
231 65 0.22
232 8 0.03
233 2 0.01
234 2 0.01
235 2 0.01
236 1 0.00
237 2 0.01
238 2 0.01
239 2 0.01
240 214 0.71
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (235 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCGGATGAGTTATTCTCATTA
TAAACTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGATTGAGCCAAGGTAATGCTGAT
CCAACTCCTTATGTGAGGGACTAGCGAAATGATTATGCTGATCCAACTCCTTATGTGATGGACAA
GCAAAAGTCGGTGATGTTCCAACTCCTTATGCGATGAAAA
Found at i:37888 original size:136 final size:135
Alignment explanation
Indices: 37546--38035 Score: 655
Period size: 139 Copynumber: 3.6 Consensus size: 135
37536 CAAGCTAAAA
* * *
37546 TTCTTCTCATTATGAACTTCGTT-TCCCTTATCGGATGAGTTATTCTCATTATAAACTCTCCACT
1 TTCTTCTCATTATGAACTTC-TTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
*
37610 GGAAA-GATTGATCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGACGAATCGAGCTAA
65 GGAAATG-TTGATCCCTCGAGTGAGGTGTTGCTGATTCAA---CATATGTGATGAATCGAG-TAA
37674 GGTTGAACAAG
125 GGTTGAACAAG
*
37685 TTCTTATCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
* ** ** * * * * *
37750 GAAATGTTGATCCCTCGAGTGAAGCATCACTGATTCGA-A-ATGTCATAAATCGAGTGATAGATC
66 GAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACATATGTGATGAATCGAGT-A-AGGTT
37813 GAACAAG
129 GAACAAG
*
37820 CTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
1 TTCTTCTCATTATGAACTTCTTCTCCCTC-ATCGGATGAGTTCTTCTCATTATGAACTCTCCACT
*
37885 GGAAATGTTGATCCCTCGAGTGAGGTGTTGCTAATTCAACTCCATATGTGATGAATCGAGTTAAG
65 GGAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAA---CATATGTGATGAATCGAG-TAAG
37950 GTTGAACAAG
126 GTTGAACAAG
* * *
37960 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTCTTCTCATTATGAACTCTCCATTT
1 TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
38025 GAAATGTTGAT
66 GAAATGTTGAT
38036 TGGTTCATCT
Statistics
Matches: 308, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
133 1 0.00
134 13 0.04
135 38 0.12
136 67 0.22
138 2 0.01
139 132 0.43
140 40 0.13
141 14 0.05
142 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (135 bp):
TTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTCCACTG
GAAATGTTGATCCCTCGAGTGAGGTGTTGCTGATTCAACATATGTGATGAATCGAGTAAGGTTGA
ACAAG
Found at i:38626 original size:18 final size:18
Alignment explanation
Indices: 38605--38654 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
38595 GTTGCGAGAG
38605 CAGTCTTCATTGC-TAGAT
1 CAGTCTTCATT-CTTAGAT
38623 CAGTCTTCATTCTTAGAT
1 CAGTCTTCATTCTTAGAT
38641 CAGTCTTCATTCTT
1 CAGTCTTCATTCTT
38655 TTCCTGGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (18 bp):
CAGTCTTCATTCTTAGAT
Found at i:38884 original size:50 final size:50
Alignment explanation
Indices: 38794--38935 Score: 160
Period size: 54 Copynumber: 2.7 Consensus size: 50
38784 ATTTACAGTT
* **
38794 ATCAAGAACCCCTAAAATTAGGCTTAACTTCTCTCAAAAATTCA-AAAAAA
1 ATCAAGAACCCCTAAAATTAGGCTTAATTTCT-TTGAAAATTCATAAAAAA
** * *
38844 ATCAAGAACCCCTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAAC
1 ATCAAGAACCCCT-AAAATTAGGCTTAATTTCTTTGAAAATTCA--TAAAAAA
38897 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAA
1 ATCAAG-AACCCCT-AAAATTAGGCTTAATTTCTTTGAA
38936 CGTTCATTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
50 22 0.29
51 16 0.21
53 10 0.13
54 29 0.38
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (50 bp):
ATCAAGAACCCCTAAAATTAGGCTTAATTTCTTTGAAAATTCATAAAAAA
Found at i:39026 original size:53 final size:53
Alignment explanation
Indices: 38855--39363 Score: 464
Period size: 54 Copynumber: 9.6 Consensus size: 53
38845 TCAAGAACCC
* * * * **
38855 CTGAAAACCAGGCTTAATTTCTTTGAAAATTCATTTGAAAACATCAAGAAACCC
1 CTGAAAATCAGACTTAATTTCTTT-AAAACTCATTTGAAATCATCAAGAAACTT
* * * * ** *
38909 CTAAAAATTAGGCTTAATTTCTTT-GAACGTTCATTTGAGAAAAATCAGGAAACTT
1 CTGAAAATCAGACTTAATTTCTTTAAAAC--TCATTTGA-AATCATCAAGAAACTT
* * *
38964 -TCGAAAATCAGACTTAATTTCTTTAAAACACATTTGAAAGCGTCAAGAAACTT
1 CT-GAAAATCAGACTTAATTTCTTTAAAACTCATTTGAAATCATCAAGAAACTT
* * *
39017 CTAAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCATGAAACTT
1 CTGAAAATCAGACTTAATTTCTTT-AAAACTCATTTGAAATCATCAAGAAACTT
* * * *
39071 CTGAAAATCAGACTTAGTTTCGTTGAAACTTATTTGAAATCATCAAG-AACTT
1 CTGAAAATCAGACTTAATTTCTTTAAAACTCATTTGAAATCATCAAGAAACTT
* *
39123 CTGAAAATCAGACTT-ATTTCTTTAAAACTCACTTGAAAATCATCATGAAACTT
1 CTGAAAATCAGACTTAATTTCTTTAAAACTCATTTG-AAATCATCAAGAAACTT
* * * *
39176 TTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAA-AAACTT
1 CTGAAAATCAGACTTAATTTC-TTTAAAACTCATTTGAAATCATCAAGAAACTT
* * * *
39229 CTG-AAATAAGACTTAGTTTCTTTAAAAGAACTCATTTAAAATGATCAAGAAACTT
1 CTGAAAATCAGACTTAATTTCTTT--AA-AACTCATTTGAAATCATCAAGAAACTT
* * ** *
39284 -TCGAAAATCGGAATT-ATTTCTAAAAAACTCATTTGAAAATCGTCAAG-AACTT
1 CT-GAAAATCAGACTTAATTTCTTTAAAACTCATTTG-AAATCATCAAGAAACTT
* *
39336 ATG-AAA-CAGACTTAGTTTCTTTAAAACT
1 CTGAAAATCAGACTTAATTTCTTTAAAACT
39364 AATAAAAAAT
Statistics
Matches: 374, Mismatches: 61, Indels: 43
0.78 0.13 0.09
Matches are distributed among these distances:
50 5 0.01
51 31 0.08
52 63 0.17
53 93 0.25
54 116 0.31
55 55 0.15
56 11 0.03
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (53 bp):
CTGAAAATCAGACTTAATTTCTTTAAAACTCATTTGAAATCATCAAGAAACTT
Found at i:39228 original size:106 final size:106
Alignment explanation
Indices: 38856--39363 Score: 489
Period size: 106 Copynumber: 4.8 Consensus size: 106
38846 CAAGAACCCC
* * * ** * *
38856 TGAAAACCAGGCTTAATTTCTTTGAAAA-TTCATTTGAAAACATCAAGAAACCCCTAAAAATTAG
1 TGAAAATCAGACTTAATTTC-TTGAAAACTT-ATTTGAAATCATCAA-AAACTTCTGAAAATCAG
* * * * *
38920 GCTTAATTTCTTT-GAACGTTCATTTGAGAAA-AATCAGGAAACTTT
63 ACTTAGTTTCTTTAAAAC--TCATTTGA-AAATCATCATGAAACTTT
* * ** * * *
38965 CGAAAATCAGACTTAATTTCTTTAAAACACATTTGAAAGCGTCAAGAAACTTCTAAAAATCAGAC
1 TGAAAATCAGACTTAATTTCTTGAAAACTTATTTGAAATCATCAA-AAACTTCTGAAAATCAGAC
*
39030 TTAGTTTCTTTAAAAACTCATTTG-AAATCATCATGAAACTTC
65 TTAGTTTCTTT-AAAACTCATTTGAAAATCATCATGAAACTTT
* *
39072 TGAAAATCAGACTTAGTTTCGTTG-AAACTTATTTGAAATCATCAAGAACTTCTGAAAATCAGAC
1 TGAAAATCAGACTTAATTTC-TTGAAAACTTATTTGAAATCATCAAAAACTTCTGAAAATCAGAC
*
39136 TTA-TTTCTTTAAAACTCACTTGAAAATCATCATGAAACTTT
65 TTAGTTTCTTTAAAACTCATTTGAAAATCATCATGAAACTTT
* *
39177 TGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAAAACTTCTG-AAATAAGAC
1 TGAAAATCAGACTTAATTTC-TTGAAAACTTATTTGAAATCATCAAAAACTTCTGAAAATCAGAC
* *
39241 TTAGTTTCTTTAAAAGAACTCATTT-AAAATGATCAAGAAACTTT
65 TTAGTTTCTTT--AA-AACTCATTTGAAAATCATCATGAAACTTT
* * * ** * * * *
39285 CGAAAATCGGAATT-ATTTCTAAAAAACTCATTTGAAAATCGTCAAGAACTTATG-AAA-CAGAC
1 TGAAAATCAGACTTAATTTCTTGAAAACTTATTTG-AAATCATCAAAAACTTCTGAAAATCAGAC
39347 TTAGTTTCTTTAAAACT
65 TTAGTTTCTTTAAAACT
39364 AATAAAAAAT
Statistics
Matches: 342, Mismatches: 45, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
103 4 0.01
104 13 0.04
105 58 0.17
106 86 0.25
107 69 0.20
108 84 0.25
109 25 0.07
110 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (106 bp):
TGAAAATCAGACTTAATTTCTTGAAAACTTATTTGAAATCATCAAAAACTTCTGAAAATCAGACT
TAGTTTCTTTAAAACTCATTTGAAAATCATCATGAAACTTT
Found at i:40194 original size:156 final size:155
Alignment explanation
Indices: 39882--40195 Score: 610
Period size: 156 Copynumber: 2.0 Consensus size: 155
39872 AATTCAATGG
39882 TTCTATCAGAACAGTGAGATAAGCTCTTCTTGTCCTCATATTCTGCCCTTGGCACTCCCAAACGC
1 TTCTATCAGAACAGTGAGATAAGCTCTTCTTGTCCTCATATTCTGCCCTTGGCACTCCCAAACGC
39947 GAAGCTCATTCACCATGTATTTTTTTATTTGATCATGTATCTTAGCAGATCTGGTTTGGTAATGC
66 GAAGCTCATTCACCATGTATTTTTTTATTTGATCATGTATCTTAGCAGATCTGGTTTGGTAATGC
40012 CCCAATGTGGGTACTTGTGGCTTTT
131 CCCAATGTGGGTACTTGTGGCTTTT
40037 TTCTATCAGAAACAGTGAGATAAGCTCTTCTTGTCCTCATATTCTGCCCTTGGCACTCCCAAACG
1 TTCTATCAG-AACAGTGAGATAAGCTCTTCTTGTCCTCATATTCTGCCCTTGGCACTCCCAAACG
40102 CGAAGCTCATTCACCATGTATTTTTTTATTTGATCATGTATCTTAGCAAGATCTGGTTTGGTAAT
65 CGAAGCTCATTCACCATGTATTTTTTTATTTGATCATGTATCTTAGC-AGATCTGGTTTGGTAAT
40167 GCCCCAATGTGGGTACTTGTGGCTTTT
129 GCCCCAATGTGGGTACTTGTGGCTTTT
40194 TT
1 TT
40196 TGCCAAAATC
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 9 0.06
156 102 0.65
157 46 0.29
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (155 bp):
TTCTATCAGAACAGTGAGATAAGCTCTTCTTGTCCTCATATTCTGCCCTTGGCACTCCCAAACGC
GAAGCTCATTCACCATGTATTTTTTTATTTGATCATGTATCTTAGCAGATCTGGTTTGGTAATGC
CCCAATGTGGGTACTTGTGGCTTTT
Found at i:41457 original size:23 final size:23
Alignment explanation
Indices: 41418--41473 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
41408 TGTAAAAAAG
41418 AAAAAAAAT-AAGAAAA-TAGATA
1 AAAAAAAATAAAGAAAATTAG-TA
*
41440 AAAAAAAATAAATGAAATTTAGTA
1 AAAAAAAATAAA-GAAAATTAGTA
41464 AAAAAAAATA
1 AAAAAAAATA
41474 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 9 0.30
23 2 0.07
24 16 0.53
25 3 0.10
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (23 bp):
AAAAAAAATAAAGAAAATTAGTA
Found at i:41489 original size:24 final size:23
Alignment explanation
Indices: 41418--41500 Score: 64
Period size: 24 Copynumber: 3.6 Consensus size: 23
41408 TGTAAAAAAG
*
41418 AAAAAAAAT-AA-GAAAATAGATA
1 AAAAAAAATAAATG-AAATATATA
*
41440 AAAAAAAATAAATGAAATTTAGTA
1 AAAAAAAATAAATGAAATATA-TA
*
41464 AAAAAAAATATATAT-ATATATATA
1 AAAAAAAATA-A-ATGAAATATATA
* *
41488 AACAAAAACAAAT
1 AAAAAAAATAAAT
41501 TAATAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 11 0.22
23 8 0.16
24 23 0.46
25 6 0.12
26 2 0.04
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (23 bp):
AAAAAAAATAAATGAAATATATA
Found at i:42798 original size:34 final size:35
Alignment explanation
Indices: 42746--42946 Score: 118
Period size: 35 Copynumber: 5.6 Consensus size: 35
42736 TTTTCAAAGC
42746 TATATATTATATAG-TTTTCAAAAATG-ATTTTAAAAA
1 TATATA-TATA-AGTTTTTC-AAAATGTATTTTAAAAA
*
42782 TATA-ATATAAGTTTTTCAAAATGTTTTTTAAAACTA
1 TATATATATAAGTTTTTCAAAATGTATTTTAAAA--A
* *
42818 TATATTATATAAATTTTTCAAAAATGTTTTTTTAAAAA
1 TATA-TATATAAGTTTTTC-AAAATG-TATTTTAAAAA
* *
42856 CTATACAT-T-A-TATTTTCAAAATG-ATTTCAAAAA
1 -TATATATATAAGT-TTTTCAAAATGTATTTTAAAAA
**
42889 TATATATTATATA-ACTTTCAAAATG--TTTTAAAACTTA
1 TATATA-TATA-AGTTTTTCAAAATGTATTTTAAAA---A
*
42926 TATATGTATAAG-TTTTCAAAA
1 TATATATATAAGTTTTTCAAAA
42947 ACATTAACTA
Statistics
Matches: 136, Mismatches: 11, Indels: 37
0.74 0.06 0.20
Matches are distributed among these distances:
32 5 0.04
33 17 0.12
34 25 0.18
35 27 0.20
36 20 0.15
37 7 0.05
38 15 0.11
39 10 0.07
40 10 0.07
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATATAAGTTTTTCAAAATGTATTTTAAAAA
Found at i:42866 original size:41 final size:38
Alignment explanation
Indices: 42786--42868 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 38
42776 TAAAAATATA
* *
42786 ATATAAGTTTTTCAAAATGTTTTTTAAAACTATATATT
1 ATATAAATTTTTCAAAATGTTTTTTAAAACTATACATT
42824 ATATAAATTTTTCAAAAATGTTTTTTTAAAAACTATACATT
1 ATATAAATTTTTC-AAAATG-TTTTTT-AAAACTATACATT
42865 ATAT
1 ATAT
42869 TTTCAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 12 0.30
39 6 0.15
40 6 0.15
41 16 0.40
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (38 bp):
ATATAAATTTTTCAAAATGTTTTTTAAAACTATACATT
Found at i:43360 original size:9 final size:9
Alignment explanation
Indices: 43333--43458 Score: 78
Period size: 10 Copynumber: 13.3 Consensus size: 9
43323 GATCTGTTTA
43333 TTTCTTTTT
1 TTTCTTTTT
43342 TTAATC-TTTT
1 TT--TCTTTTT
43352 TTTCTTTTT
1 TTTCTTTTT
*
43361 CTTCTATTTT
1 TTTCT-TTTT
43371 TTCTCTTTCTTT
1 TT-TC-TT-TTT
*
43383 TTTCTCTTT
1 TTTCTTTTT
43392 TTTCTATTTT
1 TTTCT-TTTT
*
43402 TTTCTGTGTT
1 TTTCT-TTTT
*
43412 TCTCTTTTT
1 TTTCTTTTT
*
43421 TTTCCTTTCT
1 TTT-CTTTTT
*
43431 TTT-TTTCT
1 TTTCTTTTT
43439 TTT-TTTTT
1 TTTCTTTTT
* *
43447 TGTGTTTTT
1 TTTCTTTTT
43456 TTT
1 TTT
43459 TATATCTTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
8 16 0.17
9 30 0.32
10 35 0.37
11 7 0.07
12 6 0.06
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:43391 original size:41 final size:40
Alignment explanation
Indices: 43346--43453 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 40
43336 CTTTTTTTAA
* *
43346 TCTTTTTTTCTTTTTCTTCTATTTTTTCTCTTTCTTTTT-TC
1 TCTTTTTTTCTTTTTCTTCT-GTGTTTCTCTTT-TTTTTCTC
* *
43387 TC-TTTTTTCTATTTTTTTCTGTGTTTCTCTTTTTTTTCCTT
1 TCTTTTTTTCT-TTTTCTTCTGTGTTTCTCTTTTTTTT-CTC
* *
43428 TCTTTTTTTCTTTTTTTTTTGTGTTT
1 TCTTTTTTTCTTTTTCTTCTGTGTTT
43454 TTTTTTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
39 5 0.09
40 18 0.31
41 27 0.47
42 8 0.14
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (40 bp):
TCTTTTTTTCTTTTTCTTCTGTGTTTCTCTTTTTTTTCTC
Found at i:43393 original size:50 final size:50
Alignment explanation
Indices: 43333--43442 Score: 136
Period size: 50 Copynumber: 2.2 Consensus size: 50
43323 GATCTGTTTA
* *
43333 TTTCTTTTTTTAATCTTTTTTTCT-T-TTTCTTCTATTTTTTCTCTTTCTTT
1 TTTCTCTTTTTAATATTTTTTTCTGTGTTTC-TCTATTTTTTC-CTTTCTTT
** *
43383 TTTCTCTTTTTTCTATTTTTTTCTGTGTTTCTCTTTTTTTTCCTTTCTTT
1 TTTCTCTTTTTAATATTTTTTTCTGTGTTTCTCTATTTTTTCCTTTCTTT
43433 TTT-TCTTTTT
1 TTTCTCTTTTT
43443 TTTTTGTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
49 7 0.13
50 31 0.58
51 11 0.21
52 4 0.08
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (50 bp):
TTTCTCTTTTTAATATTTTTTTCTGTGTTTCTCTATTTTTTCCTTTCTTT
Found at i:43422 original size:18 final size:16
Alignment explanation
Indices: 43346--43442 Score: 83
Period size: 18 Copynumber: 5.9 Consensus size: 16
43336 CTTTTTTTAA
43346 TCTTTTTTTCTTTTTC
1 TCTTTTTTTCTTTTTC
*
43362 TTCTATTTTTTCTCTTTC
1 -TCT-TTTTTTCTTTTTC
*
43380 T-TTTTTCTCTTTTTTC
1 TCTTTTTTTC-TTTTTC
*
43396 TATTTTTTTCTGTGTTTC
1 TCTTTTTTTCT-T-TTTC
**
43414 TCTTTTTTT-TCCTT-
1 TCTTTTTTTCTTTTTC
43428 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
43443 TTTTTGTGTT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
14 9 0.14
15 11 0.17
16 8 0.12
17 13 0.20
18 24 0.37
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (16 bp):
TCTTTTTTTCTTTTTC
Found at i:43433 original size:11 final size:11
Alignment explanation
Indices: 43348--43445 Score: 58
Period size: 11 Copynumber: 8.5 Consensus size: 11
43338 TTTTTTAATC
43348 TTTTTT-TCTT
1 TTTTTTCTCTT
* *
43358 TTTCTTCTATT
1 TTTTTTCTCTT
*
43369 TTTTCTCT-TT
1 TTTTTTCTCTT
43379 CTTTTTTCTCTT
1 -TTTTTTCTCTT
* *
43391 TTTTCTATTTTTT
1 TTTT-T-TCTCTT
43404 TCTGTGTTTCTCTT
1 T-T-T-TTTCTCTT
43418 TTTTTTC-CTT
1 TTTTTTCTCTT
*
43428 TCTTTTTTTCTT
1 T-TTTTTCTCTT
43440 TTTTTT
1 TTTTTT
43446 TTGTGTTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
10 11 0.16
11 34 0.50
12 8 0.12
13 6 0.09
14 6 0.09
15 2 0.03
16 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:43435 original size:13 final size:11
Alignment explanation
Indices: 43350--43459 Score: 69
Period size: 12 Copynumber: 8.9 Consensus size: 11
43340 TTTTAATCTT
43350 TTTTTCTTTTTC
1 TTTTT-TTTTTC
43362 TTCTATTTTTTCTC
1 TT-T-TTTTTT-TC
43376 TTTCTTTTTTCTC
1 TTT-TTTTTT-TC
43389 TTTTTTCTATTT-
1 TTTTTT-T-TTTC
*
43401 TTTTCTGTGTTTC
1 TTTT-T-TTTTTC
*
43414 TCTTTTTTTTCC
1 T-TTTTTTTTTC
43426 TTTCTTTTTTTC
1 TTT-TTTTTTTC
*
43438 TTTTTTTTTTG
1 TTTTTTTTTTC
43449 TGTTTTTTTTT
1 T-TTTTTTTTT
43460 ATATCTTTTC
Statistics
Matches: 81, Mismatches: 6, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
11 10 0.12
12 36 0.44
13 23 0.28
14 12 0.15
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:43474 original size:51 final size:51
Alignment explanation
Indices: 43367--43478 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
43357 TTTTCTTCTA
* *
43367 TTTTTTCTCTTTCTTTTTTCTCTTTTTTCTATTTTTTTCTGTGTTTCTCTT
1 TTTTTTCTCTTTCTTTTTTCTCTTTTTTCTATTTTTTTCTGTATATCTCTT
* * * *
43418 TTTTTTC-CTTTCTTTTTT-TCTTTTTTTTTTGTGTTTTTTTTTATATCT-TT
1 TTTTTTCTCTTTCTTTTTTCTCTTTTTTCTAT-T-TTTTTCTGTATATCTCTT
43468 TCTTTTTCTCT
1 T-TTTTTCTCT
43479 CTATGTTGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
49 10 0.20
50 15 0.29
51 24 0.47
52 2 0.04
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.79
Consensus pattern (51 bp):
TTTTTTCTCTTTCTTTTTTCTCTTTTTTCTATTTTTTTCTGTATATCTCTT
Found at i:49285 original size:15 final size:15
Alignment explanation
Indices: 49265--49295 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
49255 CAGACTAAAT
49265 TACATCAATCCAAAC
1 TACATCAATCCAAAC
49280 TACATCAATCCAAAC
1 TACATCAATCCAAAC
49295 T
1 T
49296 CTTAGACCAT
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:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (15 bp):
TACATCAATCCAAAC
Found at i:54355 original size:17 final size:14
Alignment explanation
Indices: 54316--54361 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
54306 TTTTTTATTG
54316 AAAAACCGAACCGA
1 AAAAACCGAACCGA
*
54330 AAAACCCGAACCGTTAA
1 AAAAACCGAACCG---A
54347 AAAAACCGAACCGA
1 AAAAACCGAACCGA
54361 A
1 A
54362 CCGAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 14 0.52
17 13 0.48
ACGTcount: A:0.54, C:0.28, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAACCGAACCGA
Found at i:57607 original size:20 final size:20
Alignment explanation
Indices: 57582--57621 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
57572 TTTGAGAATA
57582 TGCAAATAGTGAATAGGCTT
1 TGCAAATAGTGAATAGGCTT
57602 TGCAAATAGTGAATAGGCTT
1 TGCAAATAGTGAATAGGCTT
57622 GACGAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
TGCAAATAGTGAATAGGCTT
Found at i:57990 original size:20 final size:20
Alignment explanation
Indices: 57941--57988 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
57931 AAATTCAACA
57941 TGAGGATTTCTATTCACTCC
1 TGAGGATTTCTATTCACTCC
57961 TGAGGATTTCTATTCACTCC
1 TGAGGATTTCTATTCACTCC
57981 TGA-GATTT
1 TGAGGATTT
57989 TCAGTTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (20 bp):
TGAGGATTTCTATTCACTCC
Found at i:60670 original size:28 final size:28
Alignment explanation
Indices: 60601--60689 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 28
60591 GCCAAGACCA
* *
60601 TCTAGGGATTTATGTAAATGAAAATGCT
1 TCTACGGATTAATGTAAATGAAAATGCT
60629 TCTTCGACGGATTAATGTAAATGAAAATGCT
1 TC-T--ACGGATTAATGTAAATGAAAATGCT
* *
60660 TCTACGGATTAATGTAAGTGGAAATGCT
1 TCTACGGATTAATGTAAATGAAAATGCT
60688 TC
1 TC
60690 ACACATTTGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
28 27 0.50
29 1 0.02
30 1 0.02
31 25 0.46
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (28 bp):
TCTACGGATTAATGTAAATGAAAATGCT
Found at i:63294 original size:59 final size:60
Alignment explanation
Indices: 63184--63316 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 60
63174 AGTCGATAAC
*
63184 CATTTTGTAACTTTTAATAGTTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
1 CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
* * * * *
63244 TATTTTGTAATTTTTAATAATTGAAG-ACTCAACAAAACAATA-CACTATAGTCAAATGAT
1 CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCAC-ATAGTCAAAGGAT
63303 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
63317 ACCCTATTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
58 3 0.05
59 34 0.54
60 26 0.41
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.34
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATTGAAGAACCCAACAAAACAACATCACATAGTCAAAGGAT
Found at i:65803 original size:21 final size:21
Alignment explanation
Indices: 65773--65815 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
65763 ACAAGTTTAA
*
65773 AAATAGGGAAAAGAAGATGGC
1 AAATAAGGAAAAGAAGATGGC
65794 AAATAAGGAAAAGAAGATGGC
1 AAATAAGGAAAAGAAGATGGC
65815 A
1 A
65816 TTGGGCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.30, T:0.09
Consensus pattern (21 bp):
AAATAAGGAAAAGAAGATGGC
Found at i:67278 original size:2 final size:2
Alignment explanation
Indices: 67273--67297 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
67263 CTAAAGTGTG
67273 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
67298 TACTATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68706 original size:27 final size:27
Alignment explanation
Indices: 68668--68721 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
68658 TGGATACACC
68668 CTAGATAGAAGATAAAACAGATTAATT
1 CTAGATAGAAGATAAAACAGATTAATT
*
68695 CTAGATAGAAGATAAAAGAGATTAATT
1 CTAGATAGAAGATAAAACAGATTAATT
68722 TAGTATCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (27 bp):
CTAGATAGAAGATAAAACAGATTAATT
Found at i:71541 original size:5 final size:5
Alignment explanation
Indices: 71531--71555 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
71521 TAAATTATTA
71531 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
71556 GGTACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:86618 original size:15 final size:15
Alignment explanation
Indices: 86598--86627 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
86588 TTCCTTTATA
86598 AATATTCATGGTTAG
1 AATATTCATGGTTAG
86613 AATATTCATGGTTAG
1 AATATTCATGGTTAG
86628 TAAATTACAG
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:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
AATATTCATGGTTAG
Found at i:88194 original size:16 final size:17
Alignment explanation
Indices: 88164--88196 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
88154 TAATAAGTAT
*
88164 TAAAAAATAGTAATAAA
1 TAAAAAATAGAAATAAA
88181 TAAAAAA-AGAAATAAA
1 TAAAAAATAGAAATAAA
88197 AGAAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAAAATAGAAATAAA
Found at i:88287 original size:22 final size:22
Alignment explanation
Indices: 88246--88295 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
88236 ATATATATAT
88246 AAATAAAAAATAAAGTATAAAT-G
1 AAATAAAAAATAAAG-AT-AATGG
88269 AAATAAAAAATAATA-ATAATGG
1 AAATAAAAAATAA-AGATAATGG
88291 AAATA
1 AAATA
88296 TAAGTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 13 0.52
24 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (22 bp):
AAATAAAAAATAAAGATAATGG
Found at i:88813 original size:35 final size:35
Alignment explanation
Indices: 88769--88837 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
88759 TAAAAAAACC
*
88769 TATTTTAGACTAGTATTTGAGTCCTAATCCAACTA
1 TATTCTAGACTAGTATTTGAGTCCTAATCCAACTA
88804 TATTCTAGACTAGTATTTGAGTCCTAATCCAACT
1 TATTCTAGACTAGTATTTGAGTCCTAATCCAACT
88838 CTTCTTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (35 bp):
TATTCTAGACTAGTATTTGAGTCCTAATCCAACTA
Found at i:89509 original size:106 final size:106
Alignment explanation
Indices: 89324--89540 Score: 290
Period size: 106 Copynumber: 2.0 Consensus size: 106
89314 TACGTTGCTC
* * *
89324 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGACTCTGAAACTGGGAAATTGTTTGTTGACA
** * *
89389 GTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
89430 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGACTCTGAAACTGGGAAATTGTTTGTTGACA
* *
89495 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
*
89536 TGAGT
1 CGAGT
89541 GTTGAGCATG
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTGAAAATGACTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
Found at i:89743 original size:106 final size:106
Alignment explanation
Indices: 89605--89851 Score: 289
Period size: 106 Copynumber: 2.3 Consensus size: 106
89595 GTATTGCTCC
* * *
89605 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTATT-AACA
1 GAGTCCAATATCATCCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTGAA-A
* * *
89669 GCCAATCGCCCCTTCGTCGTGAAGTTGAGCTTGTACTGTCTT
65 ACCAATCACCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
* * *
89711 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTTTGAAACTGGGAAATTGTTCATTGAAAA
1 GAGTCCAATATCATCCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTGAAAA
* * * ** *
89776 CCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAATCACCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
* * *
89817 GAGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT--C-CAATATCATCCGTCGTGAAGTTGAAAT
89852 CGCGGATGGC
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
106 92 0.79
107 2 0.02
108 1 0.01
109 22 0.19
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCATCCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTCATTGAAAA
CCAATCACCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
Found at i:89789 original size:280 final size:281
Alignment explanation
Indices: 89272--89821 Score: 834
Period size: 280 Copynumber: 2.0 Consensus size: 281
89262 TGAGCCTGAG
* *
89272 AATTGGATATCCTTCGTCATGAAATTGAAATCCAATGTAAGTTACGTTGCTCCGAGTCCAATATC
1 AATTGGATATCCTTCATCATGAAATTGAAATCCAATGTAAGTTACATTGCTCCGAGTCCAATATC
* * * * *
89337 CTCCGTCGTGAAGTTGAAAATGGCTTTGGAACTGGGAAATTGTTTGTTGACAGTCAGTCGCCCCT
66 CTCCGTCGTGAAGTTGAAAATGGCTCTGGAACTGGGAAATTGTTTATTAACAGCCAATCGCCCCT
** * *
89402 TCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGAC
131 TCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGAC
* * ** * *
89467 TCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTT
196 TCTGAAACTGGGAAATTGTTCATTGAAAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTT
*
89532 GTCTTGAGTGTTGAGCATGGT
261 GTCTCGAGTGTTGAGCATGGT
* * **
89553 AATTGGATATCCTTCATCTTGAAGTTGAAATCCAA-GTAAGTTGTATTGCTCCGAGTCCAATATC
1 AATTGGATATCCTTCATCATGAAATTGAAATCCAATGTAAGTTACATTGCTCCGAGTCCAATATC
*
89617 CTCCGTCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTATTAACAGCCAATCGCCCCT
66 CTCCGTCGTGAAGTTGAAAATGGCTCTGGAACTGGGAAATTGTTTATTAACAGCCAATCGCCCCT
* *
89682 TCG-TCGTGAAGTTGAGCTTGTACTGTCTTGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGG
131 TCGCT-GTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGA
* *
89746 CTTTGAAACTGGGAAATTGTTCATTGAAAACCAGTCATCCCTTCGTTGTGAAGTTGAACTTGTGT
195 CTCTGAAACTGGGAAATTGTTCATTGAAAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGT
89811 TGTCTCGAGTG
260 TGTCTCGAGTG
89822 GCACGATATC
Statistics
Matches: 241, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
279 1 0.00
280 208 0.86
281 32 0.13
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (281 bp):
AATTGGATATCCTTCATCATGAAATTGAAATCCAATGTAAGTTACATTGCTCCGAGTCCAATATC
CTCCGTCGTGAAGTTGAAAATGGCTCTGGAACTGGGAAATTGTTTATTAACAGCCAATCGCCCCT
TCGCTGTGAAGTTGAGCTTGTACTGTCTCGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGAC
TCTGAAACTGGGAAATTGTTCATTGAAAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTT
GTCTCGAGTGTTGAGCATGGT
Found at i:94379 original size:31 final size:30
Alignment explanation
Indices: 94341--94412 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
94331 AGAGTCGAGG
*
94341 GTTTACCTA-TATCTTTCGAGACATATGGACA
1 GTTTACCTAGT-TC-TTCGAGACATATGGAAA
* *
94372 GTTTACCTAGGTTCTTCGGGACCTATGGAAA
1 GTTTACCTA-GTTCTTCGAGACATATGGAAA
94403 GTTTACCTAG
1 GTTTACCTAG
94413 GTTCGTCGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 32 0.89
32 2 0.06
33 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (30 bp):
GTTTACCTAGTTCTTCGAGACATATGGAAA
Found at i:94413 original size:31 final size:31
Alignment explanation
Indices: 94355--94436 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
94345 ACCTATATCT
* *
94355 TTCGAGACATATGGACAGTTTACCTAGGTTC
1 TTCGGGACCTATGGACAGTTTACCTAGGTTC
*
94386 TTCGGGACCTATGGAAAGTTTACCTAGGTTC
1 TTCGGGACCTATGGACAGTTTACCTAGGTTC
* *
94417 GTCGGGAGCTATGGACAGTT
1 TTCGGGACCTATGGACAGTT
94437 GTCGAGGTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (31 bp):
TTCGGGACCTATGGACAGTTTACCTAGGTTC
Found at i:98589 original size:31 final size:31
Alignment explanation
Indices: 98501--98596 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
98491 AGAGTCGAGG
* * *
98501 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGCTC-TTCGGGACCTATGGACA
*
98532 ATTTACCTAGGCTCTTCGGGACCTATGGACA
1 GTTTACCTAGGCTCTTCGGGACCTATGGACA
* *
98563 GTTTACCTAGGTTCGTT-GGGAGCTATGGACA
1 GTTTACCTAGGCTC-TTCGGGACCTATGGACA
98594 GTT
1 GTT
98597 GCCGAGGTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 52 0.93
32 4 0.07
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (31 bp):
GTTTACCTAGGCTCTTCGGGACCTATGGACA
Found at i:104590 original size:20 final size:20
Alignment explanation
Indices: 104538--104590 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
104528 TAAACAAGGT
104538 ATAAAAAAATAATAGTAATA
1 ATAAAAAAATAATAGTAATA
104558 ATAAGTATTAAAA-AATAGTAATAA
1 ATAA--A--AAAATAATAGTAAT-A
104582 ATAAAAAAA
1 ATAAAAAAA
104591 GAAATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
20 8 0.29
22 2 0.07
23 9 0.32
24 9 0.32
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.25
Consensus pattern (20 bp):
ATAAAAAAATAATAGTAATA
Found at i:104653 original size:34 final size:33
Alignment explanation
Indices: 104609--104702 Score: 82
Period size: 34 Copynumber: 2.7 Consensus size: 33
104599 AAAGAATATG
104609 AAAATCAAAGTAAATATATATATATATATATAATA
1 AAAAT-AAAGTAAATATATATATATATA-ATAATA
* * * *
104644 AAAATAAAGTATAATGAAATA-AAAAATAATAATG
1 AAAATAAAGTA-AAT-ATATATATATATAATAATA
* *
104678 GAAATAAAGTAAACATATATGATAT
1 AAAATAAAGTAAATATATAT-ATAT
104703 TAGTAGGAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
32 4 0.09
33 2 0.04
34 23 0.50
35 13 0.28
36 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (33 bp):
AAAATAAAGTAAATATATATATATATAATAATA
Found at i:105194 original size:35 final size:35
Alignment explanation
Indices: 105155--105226 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
105145 TAAAAAAAAC
*
105155 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
*
105190 CTATTCTAGATTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
105225 CT
1 CT
105227 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTCTAGACTAGTATTTGAGTCCTAATCCAACT
Found at i:106301 original size:28 final size:29
Alignment explanation
Indices: 106237--106304 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
106227 AGTTAGTAAA
* * * *
106237 AAATAATAATAATAATAATATACAAAAGT
1 AAATAAAAATAATAATAAAAGACAAAAAT
106266 AAAT-AAAATAATAATAAAAGA-AAAAAT
1 AAATAAAAATAATAATAAAAGACAAAAAT
*
106293 GAATAAAAATAA
1 AAATAAAAATAA
106305 AAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 8 0.24
28 21 0.64
29 4 0.12
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (29 bp):
AAATAAAAATAATAATAAAAGACAAAAAT
Done.