Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008007.1 Hibiscus syriacus cultivar Beakdansim tig00110469_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: 1953294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:187528 original size:42 final size:42
Alignment explanation
Indices: 187478--187565 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
187468 AGATTAAATT
*
187478 ATGCCAACCTAAATGCCCCGAATTTCCAAAACCAAGATGCAG
1 ATGCCAACCTAAATGCCCCGAATGTCCAAAACCAAGATGCAG
**
187520 ATGCCAACCTAAATGCCCCGAATGTCTGAAACCAAGATGCAG
1 ATGCCAACCTAAATGCCCCGAATGTCCAAAACCAAGATGCAG
187562 ATGC
1 ATGC
187566 TGCAGGTGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (42 bp):
ATGCCAACCTAAATGCCCCGAATGTCCAAAACCAAGATGCAG
Found at i:189399 original size:19 final size:19
Alignment explanation
Indices: 189377--189413 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
189367 TTTATTAAAA
*
189377 AATAAATATTTAAAATTAC
1 AATAAAAATTTAAAATTAC
*
189396 AATAAAAATTTATAATTA
1 AATAAAAATTTAAAATTA
189414 TACGTGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAAAAATTTAAAATTAC
Found at i:198607 original size:25 final size:21
Alignment explanation
Indices: 198559--198601 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
198549 TACAAAGTTA
198559 AAAACAACTAACAAATTAATT
1 AAAACAACTAACAAATTAATT
198580 AAAACAACTAACAAATTAATT
1 AAAACAACTAACAAATTAATT
198601 A
1 A
198602 TTTAAACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAACAACTAACAAATTAATT
Found at i:200003 original size:16 final size:16
Alignment explanation
Indices: 199962--200021 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
199952 TATATATAAT
* *
199962 AAAT-ATAATAACGAA
1 AAATAATAATAAAGTA
*
199977 AAAAAATTAATAAAGTA
1 AAATAA-TAATAAAGTA
*
199994 AAATAATAATAATGTA
1 AAATAATAATAAAGTA
*
200010 ATATAAT-ATAAA
1 AAATAATAATAAA
200022 TACATGAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 7 0.19
16 16 0.44
17 13 0.36
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (16 bp):
AAATAATAATAAAGTA
Found at i:200270 original size:11 final size:11
Alignment explanation
Indices: 200188--200271 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
200178 TTATATACGT
*
200188 TAATAGTAAAA
1 TAATATTAAAA
*
200199 TAATAATAAATA
1 TAATATTAAA-A
200211 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
200224 TATATATATATAA
1 TA-ATAT-TAAAA
200237 TAACT-TTAAAA
1 TAA-TATTAAAA
*
200248 -AACATTAAAA
1 TAATATTAAAA
*
200258 TAATATTAGAA
1 TAATATTAAAA
200269 TAA
1 TAA
200272 AAATAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:200759 original size:35 final size:37
Alignment explanation
Indices: 200714--200788 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 37
200704 GTTTAAAATA
*
200714 TAGCAAAATTCTATCCTATTTTAG-GAG-TTGAATCC
1 TAGCAAAATTCTATCATATTTTAGAGAGTTTGAATCC
* *
200749 TAGCAGAATTCTATCATATTTTTGAGAGTTTGAATCC
1 TAGCAAAATTCTATCATATTTTAGAGAGTTTGAATCC
200786 TAG
1 TAG
200789 TAGGACGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 21 0.60
36 3 0.09
37 11 0.31
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (37 bp):
TAGCAAAATTCTATCATATTTTAGAGAGTTTGAATCC
Found at i:201560 original size:106 final size:104
Alignment explanation
Indices: 201249--202106 Score: 754
Period size: 98 Copynumber: 8.3 Consensus size: 104
201239 AATATTGTTC
* * * *** *
201249 CGAGTCCAATATCATCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-ATAGAAAATGTTTGTTGACA
** * *
201314 GTCAGCCG-CCCTTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 ACCAGCCGTCCC-TTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
201355 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-CG-AAAT-CTTGTTGACAAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATAGAAAATGTTTGTTGACAAC
*
201416 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* *
201455 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTAAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA--TAGAAAATGTTTGTTGACA
* *
201520 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** *
201561 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTCG
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAA-TAGAAAA--TGTTTG
*
201623 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
58 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
201670 C-AGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGT
1 CGA-GT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAAT-AGAAAATGTTTGT
201733 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * **
201779 CGAATCCAATATCCTTCGCTGTGAAATTGAGATTGGCTCCGAAAT------TGCTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATAGAAAATGTTTGTTGACAAC
* * *
201838 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * **
201877 TGGGTCTAATATCCTTCGCTGTGAAATTGAGATTGGCTCCGAAAT------TGTTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATAGAAAATGTTTGTTGACAAC
* * *
201936 CAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
201975 TGGGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGCCCTGAAACTGGGAAAT-TATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TAGAAAATGT-TTGTTGACA
*
202039 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
*
202080 CGAGTTCAATATCCTTCGCTGTGAAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGT
202107 CAAAATTGAC
Statistics
Matches: 642, Mismatches: 81, Indels: 59
0.82 0.10 0.08
Matches are distributed among these distances:
98 175 0.27
99 1 0.00
100 80 0.12
101 8 0.01
102 1 0.00
104 2 0.00
105 76 0.12
106 113 0.18
107 6 0.01
108 7 0.01
109 163 0.25
110 6 0.01
111 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATAGAAAATGTTTGTTGACAAC
CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
Found at i:201751 original size:218 final size:206
Alignment explanation
Indices: 201249--202106 Score: 737
Period size: 206 Copynumber: 4.1 Consensus size: 206
201239 AATATTGTTC
* * * **
201249 CGAGTCCAATATCATCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * * *
201314 GTCAGCCG-CCCTTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTG
66 ACCAGCCGTCCC-TTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTG
* ** *
201378 AAGTTGAAATTGACTCTGAACGAAATCTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAA
130 AAGTTGAAATCGACGATGAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAA
201443 CTTGTGTTGTCT
195 CTTGTGTTGTCT
* * *** *
201455 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTAAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
* *
201520 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCCTCCG-T
66 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTCCGCT
* *
201583 CGTGGAGTTGAAATCG-CGGATGAAACTGAAAAGTTGTTCGTTGACAACCAGCCGTCCCTTCGTT
127 -GTGAAGTTGAAATCGAC-GATG-AAC-G-AAA--TCTT-GTTGACAACCAGCCGTCCCTTCGTT
201647 GTGAAGTTGAACTTGTGTTGTCT
184 GTGAAGTTGAACTTGTGTTGTCT
* *
201670 C-AGGTAGCACGATATCCTCCGTCGTG-G-AGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTG
1 CGA-GT--C-CAATATCCTCCG-C-TGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTG
* * *
201732 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCG
60 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCG
* * * * * * ** * *
201797 CTGTGAAATTGAGATTG--GCT--CCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGA
125 CTGTGAAGTTGAAATCGACGATGAACGAAA-T-CTTGTTGACAACCAGCCGTCCCTTCGTTGTGA
* *
201858 AGTTGAGCTTGTGCTGTCT
188 AGTTGAACTTGTGTTGTCT
* * * * * * * * *
201877 TGGGTCTAATATCCTTCGCTGTGAAATTGAGATTGGCTC--------CGAAATTGTTTGTCGACA
1 CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * * * * * * * *
201934 GTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTCGCCGTGA
66 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
* * ** *
201999 AGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
131 AGTTGAAATCGACGATG-AAC---GAAA-TCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
202064 TGAACTTGTGTTGTCT
191 TGAACTTGTGTTGTCT
* * *
202080 CGAGTTCAATATCCTTCGCTGTGAAGT
1 CGAGTCCAATATCCTCCGCTGCGAAGT
202107 CAAAATTGAC
Statistics
Matches: 533, Mismatches: 86, Indels: 69
0.77 0.12 0.10
Matches are distributed among these distances:
196 81 0.15
198 2 0.00
201 1 0.00
202 2 0.00
203 67 0.13
204 27 0.05
205 1 0.00
206 90 0.17
207 49 0.09
208 8 0.02
209 25 0.05
210 4 0.01
211 1 0.00
212 3 0.01
213 2 0.00
214 4 0.01
215 70 0.13
216 2 0.00
217 2 0.00
218 88 0.17
219 2 0.00
220 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (206 bp):
CGAGTCCAATATCCTCCGCTGCGAAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTCCGCTGTGA
AGTTGAAATCGACGATGAACGAAATCTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAAC
TTGTGTTGTCT
Found at i:201855 original size:55 final size:53
Alignment explanation
Indices: 201791--201962 Score: 150
Period size: 55 Copynumber: 3.4 Consensus size: 53
201781 AATCCAATAT
201791 CCTTCGCTGTGAAATTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAATTGAGATTGGCTCCGAAATTG-TTGTCGACAGTCAG-CGCC
* * ** * * *
201846 CCTTCGCTGTGAAGTTGAGCTTGTGCT--G-TCTTG-GGTCTA-A-T-A----T
1 CCTTCGCTGTGAAATTGAGATTG-GCTCCGAAATTGTTGTCGACAGTCAGCGCC
201889 CCTTCGCTGTGAAATTGAGATTGGCTCCGAAATTGTTTGTCGACAGTCAGTCGCC
1 CCTTCGCTGTGAAATTGAGATTGGCTCCGAAATTG-TTGTCGACAGTCAG-CGCC
*
201944 CCTTCGCTGTGAAGTTGAG
1 CCTTCGCTGTGAAATTGAG
201963 CTTGTGTTGT
Statistics
Matches: 88, Mismatches: 15, Indels: 28
0.67 0.11 0.21
Matches are distributed among these distances:
42 3 0.03
43 21 0.24
44 1 0.01
45 3 0.03
47 4 0.05
48 2 0.02
49 2 0.02
50 2 0.02
51 4 0.05
53 3 0.03
54 1 0.01
55 39 0.44
56 3 0.03
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (53 bp):
CCTTCGCTGTGAAATTGAGATTGGCTCCGAAATTGTTGTCGACAGTCAGCGCC
Found at i:202748 original size:65 final size:65
Alignment explanation
Indices: 202644--202809 Score: 296
Period size: 65 Copynumber: 2.6 Consensus size: 65
202634 GACAAAATTT
*
202644 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
202709 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
202774 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
202810 TTGTTTCGAG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:202815 original size:102 final size:102
Alignment explanation
Indices: 202709--203166 Score: 781
Period size: 102 Copynumber: 4.5 Consensus size: 102
202699 TCAATGTTTA
* *
202709 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
202774 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
202811 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTCCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
202876 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
202913 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
202978 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
203015 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
203080 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
203117 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
203167 CTGTCTCAAG
Statistics
Matches: 334, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 334 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:202825 original size:37 final size:37
Alignment explanation
Indices: 202774--203184 Score: 251
Period size: 37 Copynumber: 11.9 Consensus size: 37
202764 TCAATGTTTA
* *
202774 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
202811 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
202847 CATTCCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
202875 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
202913 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
202949 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
202977 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
203015 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
203051 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
203079 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
203117 TGTTTAAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
203153 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
203185 TGGTGAGCAC
Statistics
Matches: 277, Mismatches: 58, Indels: 78
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 38 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 80 0.29
37 116 0.42
38 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:202899 original size:167 final size:169
Alignment explanation
Indices: 202609--202926 Score: 523
Period size: 167 Copynumber: 1.9 Consensus size: 169
202599 AAGATGATGC
*
202609 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
202674 GAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAACTCATTCCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
202739 GAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
202777 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* * *
202841 AAAATTCATTCCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAACTCATTCCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
**
202906 AAAATTTTGTTTCAAGGGAAA
131 AAAATTTCATTTCAAGGGAAA
202927 CTATCTCAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
167 116 0.84
168 22 0.16
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (169 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAACTCATTCCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:203088 original size:50 final size:50
Alignment explanation
Indices: 202932--203091 Score: 124
Period size: 50 Copynumber: 3.2 Consensus size: 50
202922 GGAAACTATC
* *
202932 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
* *** * ** * * * * *** * *
202982 TCAAGAGAAAC-TGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATC
1 TCAAGAGAGACAAAACTCATTTCA-AGGGAAATGT-TTTCAATGTTTA-TGTT
203034 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
203084 TCAAGAGA
1 TCAAGAGA
203092 AACTGTCTCA
Statistics
Matches: 72, Mismatches: 34, Indels: 8
0.63 0.30 0.07
Matches are distributed among these distances:
49 5 0.07
50 27 0.38
51 15 0.21
52 19 0.26
53 6 0.08
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (50 bp):
TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
Found at i:203163 original size:36 final size:36
Alignment explanation
Indices: 203080--203184 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
203070 TCAATGTTTA
* * * *
203080 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
*
203117 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
203153 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
203185 TGGTGAGCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:204067 original size:22 final size:22
Alignment explanation
Indices: 204042--204092 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
204032 TTGTGTTTGG
204042 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
204064 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
204086 TCAAAGG
1 TCAAAGG
204093 ATTGATGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:204724 original size:20 final size:21
Alignment explanation
Indices: 204701--204759 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
204691 TTTGTCCCCT
*
204701 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
204721 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
**
204742 TTTTTGCTTCTT-TTCTTT
1 TTTTTTATTCTTGTTCTTT
204760 TTTCTTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 21 0.66
21 11 0.34
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:204777 original size:22 final size:23
Alignment explanation
Indices: 204734--204776 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
204724 TTTGTTCTTG
*
204734 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
204757 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
204777 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:209203 original size:25 final size:26
Alignment explanation
Indices: 209151--209209 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
209141 AAATAAGAGT
* * *
209151 AAATGAAATAAAGAAAATAGAAGGAA
1 AAATAAAATAAAAAAAATAGAAGAAA
*
209177 AAATAAAATAAAAAAAAT-GATGAAA
1 AAATAAAATAAAAAAAATAGAAGAAA
*
209202 AACTAAAA
1 AAATAAAA
209210 GAAGAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 12 0.43
26 16 0.57
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.14
Consensus pattern (26 bp):
AAATAAAATAAAAAAAATAGAAGAAA
Found at i:209486 original size:21 final size:24
Alignment explanation
Indices: 209450--209509 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
209440 ATATATATAT
* *
209450 ATAATAAATATAATAACG-AAAA-A
1 ATAAT-AATGTAATAAAGTAAAATA
*
209473 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAATAAAGTAAAATA
209496 ATAATAATGTAATA
1 ATAATAATGTAATA
209510 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.32
22 7 0.23
23 3 0.10
24 11 0.35
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (24 bp):
ATAATAATGTAATAAAGTAAAATA
Found at i:209502 original size:16 final size:16
Alignment explanation
Indices: 209481--209518 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
209471 AAAAATAATT
209481 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
209497 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
209513 T-ATAAA
1 TAATAAA
209519 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:209765 original size:11 final size:11
Alignment explanation
Indices: 209685--209766 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
209675 TTATATACGT
*
209685 TAATAGTAAAA
1 TAATATTAAAA
*
209696 TAATAATAAATA
1 TAATATTAAA-A
209708 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
209721 T-ATATATATAA
1 TAATAT-TAAAA
209732 TAACT-TTAAAA
1 TAA-TATTAAAA
*
209743 -AACATTAAAA
1 TAATATTAAAA
*
209753 TAATATTAGAA
1 TAATATTAAAA
209764 TAA
1 TAA
209767 AAATAATTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 28 0.50
12 13 0.23
13 5 0.09
14 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:210225 original size:36 final size:36
Alignment explanation
Indices: 210185--210267 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
210175 GGATCCTATC
210185 TTTAGGAGTTTAAAACATAACAAAATTCTATCATAT
1 TTTAGGAGTTTAAAACATAACAAAATTCTATCATAT
* * * * *
210221 TTTAGGAG-TTGAATCCTAGCAGAATTCTATCATAT
1 TTTAGGAGTTTAAAACATAACAAAATTCTATCATAT
*
210256 TTTTGAGAGTTT
1 TTTAG-GAGTTT
210268 GAATCCTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
35 26 0.67
36 11 0.28
37 2 0.05
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTAGGAGTTTAAAACATAACAAAATTCTATCATAT
Found at i:210252 original size:35 final size:37
Alignment explanation
Indices: 210208--210276 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
210198 AACATAACAA
210208 AATTCTATCATATTTTAG-GAG-TTGAATCCTAGCAG
1 AATTCTATCATATTTTAGAGAGTTTGAATCCTAGCAG
*
210243 AATTCTATCATATTTTTGAGAGTTTGAATCCTAG
1 AATTCTATCATATTTTAGAGAGTTTGAATCCTAG
210277 TAGGACGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.55
36 3 0.10
37 11 0.35
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (37 bp):
AATTCTATCATATTTTAGAGAGTTTGAATCCTAGCAG
Found at i:216064 original size:27 final size:26
Alignment explanation
Indices: 215998--216064 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
215988 GTGAAGAAGA
*
215998 AAAAAAATAATAATAACCTAAAAGTAG
1 AAAAAAATAA-AATAACATAAAAGTAG
* *
216025 TTAAATAAA-AAAATAAGATAAAAGTAG
1 --AAAAAAATAAAATAACATAAAAGTAG
216052 AAAGAAAATAAAA
1 AAA-AAAATAAAA
216065 AGAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 3 0.09
26 3 0.09
27 18 0.56
28 2 0.06
29 6 0.19
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.18
Consensus pattern (26 bp):
AAAAAAATAAAATAACATAAAAGTAG
Found at i:216101 original size:23 final size:22
Alignment explanation
Indices: 216052--216104 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
216042 ATAAAAGTAG
216052 AAAG-AAAATAAAAAGAAAAAT
1 AAAGTAAAATAAAAAGAAAAAT
216073 -AA-TAAAATAAACAA-AAGAAAT
1 AAAGTAAAATAAA-AAGAA-AAAT
216094 AAAGTAAAATA
1 AAAGTAAAATA
216105 GAATGAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 12 0.44
21 6 0.22
22 2 0.07
23 7 0.26
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (22 bp):
AAAGTAAAATAAAAAGAAAAAT
Found at i:216227 original size:18 final size:18
Alignment explanation
Indices: 216206--216243 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
216196 AATATTAAGT
216206 AAAAAATAATA-AAATAA
1 AAAAAATAATAGAAATAA
*
216223 AAAAAATAATAGTAATAA
1 AAAAAATAATAGAAATAA
216241 AAA
1 AAA
216244 CCTAATACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAATAATAGAAATAA
Found at i:217886 original size:30 final size:30
Alignment explanation
Indices: 217852--217910 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
217842 ATGTAAATAC
* *
217852 ATTATATAATGTAACGACATTAAATGACAT
1 ATTATATAATGTAACAACATTAAAGGACAT
*
217882 ATTATATAATGTAATAACATTAAAGGACA
1 ATTATATAATGTAACAACATTAAAGGACA
217911 AAATTTGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.32
Consensus pattern (30 bp):
ATTATATAATGTAACAACATTAAAGGACAT
Found at i:219268 original size:31 final size:29
Alignment explanation
Indices: 219216--219291 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
219206 CTCAAAACTC
* *
219216 GTTTCAAGGGAAACTGATTCAAATATTTTGT
1 GTTTCAAGGGAAACTGATTC-AAT-GTTTAT
*
219247 GTTTCAAGGGAAAC-GTTTTCAATGTTTAT
1 GTTTCAAGGGAAACTG-ATTCAATGTTTAT
*
219276 GTTTCAAGAGAAACTG
1 GTTTCAAGGGAAACTG
219292 TCTCAAGGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 17 0.44
30 5 0.13
31 17 0.44
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (29 bp):
GTTTCAAGGGAAACTGATTCAATGTTTAT
Found at i:219326 original size:37 final size:37
Alignment explanation
Indices: 219275--219487 Score: 176
Period size: 37 Copynumber: 5.9 Consensus size: 37
219265 TCAATGTTTA
* * *
219275 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTT
*
219312 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTT
** * * **
219348 CATTTCAAGGGAAA-TGT-T---TC----CAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTT
* * *
219376 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTT
* *
219414 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATATTT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGA-CAAA-ATTT
* *
219453 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAAT
219488 CTTCTTTAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 26
0.74 0.13 0.14
Matches are distributed among these distances:
27 3 0.02
28 2 0.01
29 11 0.08
30 3 0.02
31 1 0.01
34 1 0.01
35 2 0.01
36 14 0.10
37 59 0.42
38 12 0.09
39 31 0.22
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTT
Found at i:219356 original size:102 final size:102
Alignment explanation
Indices: 219248--219448 Score: 357
Period size: 102 Copynumber: 2.0 Consensus size: 102
219238 ATATTTTGTG
*
219248 TTTCAAGGGAAACGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAACGTTTCCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
219313 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
219350 TTTCAAGGGAAATGTTTCCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAACGTTTCCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
* * *
219415 GTTTCAAGTGAAACTATCTCAAGCGAGATAAAAT
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
219449 ATTTTGTTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TTTCAAGGGAAACGTTTCCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:219467 original size:39 final size:39
Alignment explanation
Indices: 219377--219487 Score: 154
Period size: 39 Copynumber: 2.9 Consensus size: 39
219367 CCAATGTTTA
* * *
219377 TGTTTCAAGAGAAACTGTCTCAAGGGAGA-CAAA-ATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTT
*
219414 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTT
* *
219453 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAAT
219488 CTTCTTTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 26 0.39
38 3 0.05
39 37 0.56
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATATTT
Found at i:220850 original size:95 final size:95
Alignment explanation
Indices: 220645--220907 Score: 325
Period size: 95 Copynumber: 2.7 Consensus size: 95
220635 GGATAGCTGA
* * *
220645 ATCCATAAAGTC-AGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAA--TATCATTGTATAA
1 ATCCATAAAGCCGA-GGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCT-TTATTG--T--
* * * *
220707 ATATTATAATCACCTTTATTAGTCTAGTTGAATATT
60 ACATTATAATCACCTTTATCAGGCTAGCTGAATATT
*
220743 ATACATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACATTA
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACATTA
* *
220808 TAGTCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* * *
220838 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACAT-T
220903 ATAAT
65 ATAAT
220908 ATTATAATCT
Statistics
Matches: 146, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
95 89 0.61
96 5 0.03
97 1 0.01
98 44 0.30
99 6 0.04
100 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:225029 original size:5 final size:5
Alignment explanation
Indices: 225012--225120 Score: 73
Period size: 5 Copynumber: 21.6 Consensus size: 5
225002 GTAACTAAAT
* *
225012 AATAA AA-AA AATAA AATAC AATAA AAGTAGA AAAAA AATAAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AA-TA-A AATAA AAT-AA AATAA
* * * * * *
225059 AA-AT AATAA AAT-A AACAA AA-GA AATAA AGTAA AATAG AATGA AATAAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT-AA
225107 AATGAA AATAA AAT
1 AAT-AA AATAA AAT
225121 TTGAATCAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
4 13 0.16
5 47 0.59
6 17 0.21
7 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:225060 original size:33 final size:31
Alignment explanation
Indices: 225018--225119 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 31
225008 AAATAATAAA
225018 AAAAATAAAATACAATAAAAGTAGAAAAAAAAT
1 AAAAATAAAATACAATAAAA-TA-AAAAAAAAT
*
225051 AAAAATAAAA-ATAATAAAATAAACAAAAGAA-
1 AAAAATAAAATACAATAAAATAAA-AAAA-AAT
* * *
225082 ATAAAGTAAAATAGAATGAAATAAAAATGAAAAT
1 A-AAAATAAAATACAATAAAATAAAAA--AAAAT
225116 AAAA
1 AAAA
225120 TTTGAATCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
30 2 0.03
31 7 0.12
32 20 0.34
33 26 0.45
34 3 0.05
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (31 bp):
AAAAATAAAATACAATAAAATAAAAAAAAAT
Found at i:225071 original size:59 final size:59
Alignment explanation
Indices: 224980--225119 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 59
224970 GAAGAAGAAA
* * *
224980 AAATAATAATAAAAACCTAAAAGTAACT-AAATAATA-AAAA-AAATAAAATACAATAAAAGTAG
1 AAATAAAAATAAAAA--TAAAAATAA-TAAAATAA-ACAAAAGAAATAAAATAAAATAAAA-T-G
* *
225042 AAA-AAAAATAAAAATAAAAATAATAAAATAAACAAAAGAAATAAAGTAAAATAGAATG
1 AAATAAAAATAAAAATAAAAATAATAAAATAAACAAAAGAAATAAAATAAAATAAAATG
*
225100 AAATAAAAATGAAAATAAAA
1 AAATAAAAATAAAAATAAAA
225120 TTTGAATCAA
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
58 6 0.09
59 34 0.50
60 15 0.22
61 10 0.15
62 3 0.04
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (59 bp):
AAATAAAAATAAAAATAAAAATAATAAAATAAACAAAAGAAATAAAATAAAATAAAATG
Found at i:227287 original size:15 final size:13
Alignment explanation
Indices: 227267--227400 Score: 92
Period size: 13 Copynumber: 9.7 Consensus size: 13
227257 CCATCATTGT
227267 AAAATAAATATGAAA
1 AAAATAAA-AT-AAA
227282 AAAATAAAATAAA
1 AAAATAAAATAAA
*
227295 AAATATTAATATAATA
1 AAA-A-TAAAATAA-A
*
227311 ATAATAAAATAAA
1 AAAATAAAATAAA
*
227324 TAGAAT-AAATAAA
1 -AAAATAAAATAAA
* *
227337 GATAA-AAAAGAACA
1 -AAAATAAAATAA-A
*
227351 ATAATAAAATAAA
1 AAAATAAAATAAA
*
227364 AAAATGAAATAAA
1 AAAATAAAATAAA
*
227377 CGAAATAAAATAAAA
1 -AAAATAAAAT-AAA
227392 AAAATAAAA
1 AAAATAAAA
227401 AGGTTAAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
13 38 0.39
14 37 0.38
15 19 0.20
16 3 0.03
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:227290 original size:5 final size:5
Alignment explanation
Indices: 227266--227400 Score: 74
Period size: 5 Copynumber: 28.0 Consensus size: 5
227256 TCCATCATTG
* * * *
227266 TAAAA TAAATA TGAAA -AAAA TAAAA TAAAA -AATA T-TAA TATAA TAATAA
1 TAAAA TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA
* *
227315 TAAAA T-AAA TAGAA T-AAA TAAAGA TAAAA -AAGAA CAATAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TAAAA TAA-AA TAA-AA TAAAA
* **
227360 T-AAA -AAAA TGAAA T-AAA CGAAA TAAAA TAAAA -AAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
227401 AGGTTAAATT
Statistics
Matches: 102, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
4 30 0.29
5 52 0.51
6 20 0.20
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:227296 original size:14 final size:14
Alignment explanation
Indices: 227267--227400 Score: 94
Period size: 14 Copynumber: 9.6 Consensus size: 14
227257 CCATCATTGT
*
227267 AAAATAAATATGAAA
1 AAAATAAA-ATAAAA
227282 AAAATAAAATAAAA
1 AAAATAAAATAAAA
* * *
227296 AATATTAATATAATA
1 AA-AATAAAATAAAA
* *
227311 ATAATAAAATAAAT
1 AAAATAAAATAAAA
* *
227325 AGAAT-AAATAAAG
1 AAAATAAAATAAAA
* * *
227338 ATAA-AAAAGAACA
1 AAAATAAAATAAAA
*
227351 ATAATAAAAT-AAA
1 AAAATAAAATAAAA
* *
227364 AAAATGAAATAAAC
1 AAAATAAAATAAAA
*
227378 GAAATAAAATAAAA
1 AAAATAAAATAAAA
227392 AAAATAAAA
1 AAAATAAAA
227401 AGGTTAAATT
Statistics
Matches: 91, Mismatches: 24, Indels: 9
0.73 0.19 0.07
Matches are distributed among these distances:
13 29 0.32
14 44 0.48
15 18 0.20
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (14 bp):
AAAATAAAATAAAA
Found at i:227325 original size:9 final size:9
Alignment explanation
Indices: 227266--227399 Score: 85
Period size: 9 Copynumber: 14.0 Consensus size: 9
227256 TCCATCATTG
227266 TAAAATAAA
1 TAAAATAAA
*
227275 TATGAAAAAAA
1 TA--AAATAAA
227286 TAAAATAAA
1 TAAAATAAA
227295 -AAATATTAATA
1 TAAA-A-TAA-A
227306 TAATAAT-AA
1 TAA-AATAAA
227315 TAAAATAAA
1 TAAAATAAA
*
227324 TAGAATAAA
1 TAAAATAAA
227333 TAAAGATAAA
1 TAAA-ATAAA
* *
227343 AAAGAACAATAA
1 TAA-AA-TA-AA
227355 TAAAATAAA
1 TAAAATAAA
227364 -AAAATGAAA
1 TAAAAT-AAA
**
227373 TAAACGAAA
1 TAAAATAAA
227382 TAAAATAAA
1 TAAAATAAA
*
227391 AAAAATAAA
1 TAAAATAAA
227400 AAGGTTAAAT
Statistics
Matches: 98, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
8 11 0.11
9 49 0.50
10 16 0.16
11 14 0.14
12 7 0.07
13 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (9 bp):
TAAAATAAA
Found at i:227368 original size:48 final size:47
Alignment explanation
Indices: 227267--227393 Score: 132
Period size: 48 Copynumber: 2.6 Consensus size: 47
227257 CCATCATTGT
* ** *
227267 AAAATAAATATGAAAAAAATAAAATAAAAAATATTAATATAATAATAAT
1 AAAATAAATA-G-AAAAAATAAAATAAAAAAGAACAATATAATAATAAA
*
227316 AAAATAAATAGAATAAATAAAGATAAAAAAGAACAATAATAA-AATAAA
1 AAAATAAATAGAAAAAATAAA-ATAAAAAAGAACAAT-ATAATAATAAA
*
227364 AAAATGAAATA-AACGAAATAAAATAAAAAA
1 AAAAT-AAATAGAA-AAAATAAAATAAAAAA
227394 AATAAAAAGG
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
47 9 0.13
48 33 0.49
49 26 0.38
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (47 bp):
AAAATAAATAGAAAAAATAAAATAAAAAAGAACAATATAATAATAAA
Found at i:228954 original size:36 final size:36
Alignment explanation
Indices: 228914--229087 Score: 228
Period size: 38 Copynumber: 4.8 Consensus size: 36
228904 CTCGAAGGTC
*
228914 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
*
228950 TTTTGTGTTTCAAGAGAAACAATTTCAAAGTTTTTATT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAG-GTTT-TT
* *
228988 TTTTGTGTTTCAAGAGAAATATTTTCAAAGGGTTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAA-GGTTTTT
* * *
229025 TTTTGTATTTCAAGAGAAGCAATTTCAAA-G--ATT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
*
229058 TATTGTGTTTCAAGAGAAACAATTTCAAAG
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAG
229088 ATTGGTGTTT
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
33 28 0.23
35 1 0.01
36 29 0.24
37 30 0.25
38 32 0.26
39 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (36 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
Found at i:229060 original size:74 final size:73
Alignment explanation
Indices: 228914--229087 Score: 257
Period size: 75 Copynumber: 2.4 Consensus size: 73
228904 CTCGAAGGTC
*
228914 TTTTGTGTTTCAAGAGAAACATTTTCAAA-GGTTTTTTTTTGTGTTTCAAGAGAAACAATTTCAA
1 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGGTTTTTTTTTGTATTTCAAGAGAAACAATTTCAA
*
228978 AGTTTTTA
66 AGTATTTA
* *
228986 TTTTTTGTGTTTCAAGAGAAATATTTTCAAAGGGTTTTTTTTTGTATTTCAAGAGAAGCAATTTC
1 --TTTTGTGTTTCAAGAGAAACATTTTCAAAGGGTTTTTTTTTGTATTTCAAGAGAAACAATTTC
229051 AAAG-ATTTA
64 AAAGTATTTA
*
229060 --TTGTGTTTCAAGAGAAACAATTTCAAAG
1 TTTTGTGTTTCAAGAGAAACATTTTCAAAG
229088 ATTGGTGTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
70 26 0.28
74 32 0.34
75 35 0.38
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (73 bp):
TTTTGTGTTTCAAGAGAAACATTTTCAAAGGGTTTTTTTTTGTATTTCAAGAGAAACAATTTCAA
AGTATTTA
Found at i:229098 original size:30 final size:32
Alignment explanation
Indices: 229032--229106 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
229022 TTTTTTTGTA
* *
229032 TTTCAAGAGAAGCAATTTCAAAGATTTATTGTG
1 TTTCAAGAGAAACAATTTCAAAGA-TTATGGTG
229065 TTTCAAGAGAAACAATTTCAAAGA-T-TGGTG
1 TTTCAAGAGAAACAATTTCAAAGATTATGGTG
229095 TTTCAAGAGAAA
1 TTTCAAGAGAAA
229107 TTTTCTCGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 16 0.40
31 1 0.03
33 23 0.57
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (32 bp):
TTTCAAGAGAAACAATTTCAAAGATTATGGTG
Found at i:229180 original size:36 final size:36
Alignment explanation
Indices: 229093--229519 Score: 350
Period size: 36 Copynumber: 12.1 Consensus size: 36
229083 CAAAGATTGG
* * * *
229093 TGTTTCAAGAGAAATTTTCTCGAGAGTGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
229130 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
229166 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
229202 TAG-TTCAAAAAAAAACTGTCTTCGAGAGAGACGAAATT
1 T-GTTTC-AAGAGAAACTGTC-TCAAGAGAGACAAAATT
* * ** *
229240 TGTTTAAAGAAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
*
229269 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
229305 TGTTTCAAGAGAAACTATCTCAATAGAGAGAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
229342 AGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
229378 TGTTTCAAG-GAAAACAAAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
229407 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
229443 TGTTTTAAGATAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
229479 TGTTTTAAGAGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
229515 TGTTT
1 TGTTT
229520 TGAGTAAATT
Statistics
Matches: 311, Mismatches: 54, Indels: 51
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 34 0.11
30 3 0.01
31 2 0.01
32 4 0.01
33 4 0.01
34 1 0.00
35 3 0.01
36 161 0.52
37 78 0.25
38 19 0.06
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:229316 original size:139 final size:138
Alignment explanation
Indices: 229128--229519 Score: 581
Period size: 138 Copynumber: 2.8 Consensus size: 138
229118 GTGACAAAAC
*
229128 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTACAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
*
229193 GACAAAATTTAGTTCAAAAAAAAACTGTCTTCGAGAGAGACGAAATTTGTTTAAAGAAAAACAAA
66 GACAAAATTTAGTTCAAAAAAAAACTGTC-TCAAGAGAGACGAAATTTGTTTAAAGAAAAACAAA
229258 TTCAAAGAT
130 TTCAAAGAT
* *
229267 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAATAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * * * *
229332 GAGAAAACTTAGTTCCAAAAGAAAA-TGTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACAAA
66 GACAAAATTTAGTT-CAAAAAAAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGAAAAACAAA
229396 TTCAAAGAT
130 TTCAAAGAT
* * *
229405 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTTAAGATAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
** * * **
229470 GACAAAATTT-GTTTTAAGAGAAACTGTCTCAAGAGAGATAAAATTTGTTT
66 GACAAAATTTAGTTCAAAAAAAAACTGTCTCAAGAGAGACGAAATTTGTTT
229520 TGAGTAAATT
Statistics
Matches: 226, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
136 5 0.02
137 26 0.12
138 108 0.48
139 78 0.35
140 9 0.04
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTTAGTTCAAAAAAAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGAAAAACAAAT
TCAAAGAT
Found at i:229481 original size:101 final size:103
Alignment explanation
Indices: 229303--229492 Score: 240
Period size: 101 Copynumber: 1.9 Consensus size: 103
229293 AGAGACAAAA
* * *
229303 TTTGTTTCAAGAGAAACTATCTCAATAGAGAGAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAG
*
229368 AGACGAAATTTGTTTCAAG-GAAAACAAATTCAAAGAT
66 AGACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
* * * * ** * * *
229405 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-TTTGTTTTAAGATAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAG
*
229469 AGACAAAATTTGTTTTAAGAGAAA
66 AGACAAAATTTGTTTCAAGAGAAA
229493 CTGTCTCAAG
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 38 0.52
102 35 0.48
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (103 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGAG
AGACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
Found at i:230934 original size:84 final size:86
Alignment explanation
Indices: 230826--231050 Score: 292
Period size: 95 Copynumber: 2.5 Consensus size: 86
230816 GGCTACCTAA
* *
230826 ATACATAAAGCCGGAGCGTTTAACCAATTTCTCTAGAGGGACAACTTA-G-TATTATAATCACCT
1 ATACATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTATGATATTATAATCACCT
*
230889 TTATTAGGCTAGCTGAATATT
66 TTATCAGGCTAGCTGAATATT
*
230910 ATACATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAACTCATACTTTATTGTATATTA
1 ATACATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGG---A--CA-AC-TTA-TG-ATATTA
*
230975 TAATCACCTTTATCAGGCTAGCTGAATCTT
57 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
231005 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACT
1 ATACATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACT
231051 CAAGCTTTAT
Statistics
Matches: 122, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
84 37 0.30
87 1 0.01
88 1 0.01
89 4 0.03
90 4 0.03
91 3 0.02
92 1 0.01
93 1 0.01
95 70 0.57
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (86 bp):
ATACATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTTATGATATTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:231042 original size:95 final size:95
Alignment explanation
Indices: 230875--231072 Score: 326
Period size: 95 Copynumber: 2.1 Consensus size: 95
230865 GACAACTTAG
*
230875 TATTATAATCACCTTTATTAGGCTAGCTGAATATTATACATAAAGCCGGGGCATTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAGCTGAATATTATACATAAAGCCGGGGCATTTAACCAATTG
230940 CTCTAGAGGGACAACTCATA-CTTTATTGTA
66 CTCTAGAGGGACAACTCA-AGCTTTATTGTA
* * *
230970 TATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCTAGCTGAATATTATACATAAAGCCGGGGCATTTAACCAATTG
*
231035 CTTTAGAGGGACAACTCAAGCTTTATTGTA
66 CTCTAGAGGGACAACTCAAGCTTTATTGTA
231065 TATATATA
1 TAT-TATA
231073 TAATTATAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
94 1 0.01
95 91 0.95
96 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
TATTATAATCACCTTTATCAGGCTAGCTGAATATTATACATAAAGCCGGGGCATTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGTA
Found at i:235924 original size:13 final size:12
Alignment explanation
Indices: 235906--235961 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 12
235896 GCTTGTTTTC
235906 TCTTTTTGAATTT
1 TCTTTTTG-ATTT
*
235919 TCTTTTT-CTTT
1 TCTTTTTGATTT
235930 TCTTTTCTGATTT
1 TCTTTT-TGATTT
**
235943 TCTTTCTTTTTTT
1 TCTTT-TTGATTT
235956 TCTTTT
1 TCTTTT
235962 CTTTTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 9 0.25
12 2 0.06
13 24 0.67
14 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.77
Consensus pattern (12 bp):
TCTTTTTGATTT
Found at i:235930 original size:5 final size:5
Alignment explanation
Indices: 235916--235976 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
235906 TCTTTTTGAA
235916 TTTTC TTTTTC TTTTC TTTTC TGATTT- TCTTTC TTTT- TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC T--TTTC T-TTTC TTTTC TTTTC TTTTC
235963 TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTT
235977 TGCACTCCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
4 4 0.08
5 36 0.72
6 7 0.14
7 3 0.06
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:235935 original size:24 final size:26
Alignment explanation
Indices: 235906--235963 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
235896 GCTTGTTTTC
235906 TCTTTT-TGAATTTTC-TT-TTTCTTT
1 TCTTTTCTG-ATTTTCTTTCTTTCTTT
*
235930 TCTTTTCTGATTTTCTTTCTTTTTTT
1 TCTTTTCTGATTTTCTTTCTTTCTTT
235956 TCTTTTCT
1 TCTTTTCT
235964 TTTCTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 12 0.40
25 4 0.13
26 14 0.47
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (26 bp):
TCTTTTCTGATTTTCTTTCTTTCTTT
Found at i:235936 original size:31 final size:31
Alignment explanation
Indices: 235901--235968 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
235891 CCTTGGCTTG
*
235901 TTTTCTCTTTTTGAATT-TTCTTTTTCTTTTC
1 TTTTCTCATTTT-AATTCTTCTTTTTCTTTTC
* ** *
235932 TTTTCTGATTTTCTTTCTTTTTTTTCTTTTC
1 TTTTCTCATTTTAATTCTTCTTTTTCTTTTC
235963 TTTTCT
1 TTTTCT
235969 TTTCTTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTTCTCATTTTAATTCTTCTTTTTCTTTTC
Found at i:235943 original size:18 final size:18
Alignment explanation
Indices: 235922--235973 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
235912 TGAATTTTCT
235922 TTTTCTTTTCTTTTCTGA
1 TTTTCTTTTCTTTTCTGA
* **
235940 TTTTC-TTTCTTTTTTTTC
1 TTTTCTTTTC-TTTTCTGA
235958 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCT
235974 TTTTGCACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 4 0.14
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCTGA
Found at i:235963 original size:26 final size:25
Alignment explanation
Indices: 235901--235963 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 25
235891 CCTTGGCTTG
*
235901 TTTTCTCTTTT-TGAATTTTCTTTT
1 TTTTTTCTTTTCTGAATTTTCTTTT
*
235925 TCTTTTCTTTTCTG-ATTTTCTTTCTT
1 TTTTTTCTTTTCTGAATTTTC-TT-TT
235951 TTTTTTCTTTTCT
1 TTTTTTCTTTTCT
235964 TTTCTTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 15 0.45
25 4 0.12
26 14 0.42
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (25 bp):
TTTTTTCTTTTCTGAATTTTCTTTT
Found at i:241651 original size:30 final size:30
Alignment explanation
Indices: 241617--241675 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
241607 ATGTAAATAC
* * *
241617 ATTATATAATGTAATGATATTAAATGACAT
1 ATTATATAATGTAATAACATTAAAGGACAT
241647 ATTATATAATGTAATAACATTAAAGGACA
1 ATTATATAATGTAATAACATTAAAGGACA
241676 AAATTTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (30 bp):
ATTATATAATGTAATAACATTAAAGGACAT
Found at i:252874 original size:24 final size:24
Alignment explanation
Indices: 252841--252924 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
252831 ATAACATAAT
* *
252841 CAGGTAAAGTATCAGATCAAAATC
1 CAGGTCAAGTATCAGATCAGAATC
252865 CAGGTCAAGTATTCA-ATCAGAATC
1 CAGGTCAAGTA-TCAGATCAGAATC
* *
252889 CAAGTCAAGTATCCGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
252913 CAGGTCAGGTAT
1 CAGGTCAAGTAT
252925 TATAATAGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.04
24 47 0.90
25 3 0.06
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:255387 original size:13 final size:13
Alignment explanation
Indices: 255369--255397 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
255359 GGTCAACGCC
255369 GGTCAACGGGTCG
1 GGTCAACGGGTCG
255382 GGTCAACGGGTCG
1 GGTCAACGGGTCG
255395 GGT
1 GGT
255398 AGGGTAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:257523 original size:24 final size:23
Alignment explanation
Indices: 257506--257592 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 23
257496 ATCATAACAT
257506 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATC-A
257530 AATCCAGGTCAAGTATTCA-ATCA
1 AATCCAGGTCAAGTA-TCAGATCA
*
257553 GAATCCAGGTCAAGTATCCGATCA
1 -AATCCAGGTCAAGTATCAGATCA
*
257577 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
257593 TATAATAGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
23 18 0.31
24 37 0.64
25 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (23 bp):
AATCCAGGTCAAGTATCAGATCA
Found at i:257541 original size:12 final size:13
Alignment explanation
Indices: 257506--257587 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 13
257496 ATCATAACAT
257506 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
257519 TAT-CAGATCAA-
1 AATCCAGGTCAAG
257530 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
257543 TATTCA-ATC-AG
1 AATCCAGGTCAAG
257554 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
257567 TATCC-GATC-A-
1 AATCCAGGTCAAG
257577 AATCCAGGTCA
1 AATCCAGGTCA
257588 GGTATTATAA
Statistics
Matches: 49, Mismatches: 14, Indels: 13
0.64 0.18 0.17
Matches are distributed among these distances:
10 4 0.08
11 12 0.24
12 21 0.43
13 12 0.24
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:265130 original size:19 final size:19
Alignment explanation
Indices: 265108--265149 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
265098 TATTTTAACG
265108 ATTATAGGAAATTTGACTA
1 ATTATAGGAAATTTGACTA
265127 ATTATAGGAAATTTGACTA
1 ATTATAGGAAATTTGACTA
265146 ATTA
1 ATTA
265150 CGTGATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (19 bp):
ATTATAGGAAATTTGACTA
Found at i:272511 original size:23 final size:24
Alignment explanation
Indices: 272485--272553 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
272475 TCTGAATATC
* *
272485 TAAACGAATTTGTTCTTGAACAT-
1 TAAACGAATATGTTCATGAACATA
* * *
272508 TAAATGAACATGTTCACGAACATA
1 TAAACGAATATGTTCATGAACATA
*
272532 TAAACGAATATGTTCGTGAACA
1 TAAACGAATATGTTCATGAACA
272554 CCAAATGAAC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (24 bp):
TAAACGAATATGTTCATGAACATA
Found at i:272656 original size:35 final size:35
Alignment explanation
Indices: 272613--272712 Score: 128
Period size: 35 Copynumber: 2.9 Consensus size: 35
272603 AAAAAAAATT
** *
272613 AAACGAACACGAATACGAACATTTTAAAAATAAAC
1 AAACGAACAATAATATGAACATTTTAAAAATAAAC
* * * *
272648 AAATGAACAATAACATAAACATTTTAAAAATAAGC
1 AAACGAACAATAATATGAACATTTTAAAAATAAAC
*
272683 AAACGAACAATAATATGAAAATTTTAAAAA
1 AAACGAACAATAATATGAACATTTTAAAAA
272713 GACCAACAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (35 bp):
AAACGAACAATAATATGAACATTTTAAAAATAAAC
Found at i:277007 original size:159 final size:158
Alignment explanation
Indices: 276737--277099 Score: 514
Period size: 159 Copynumber: 2.3 Consensus size: 158
276727 CATGTTTTCA
* * * * *
276737 TTATTTCTTCAATTCCTCCTTCATTTTAAGT-TCATTTTTACCAAATTTGAACCATATGCTCTTA
1 TTATTTATTCAATTCCTCATTTATTTTAAGTCTCATTTTTACCAAATTTGAACCACATGCTCCTA
* * * ** *
276801 AATCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGGTAACAATTTTTTTATTTTTCAA
66 AACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAAATCTTTATTTTTCAA
276866 TTTAGTCCTTCAATTTTTCATAATCTCC
131 TTTAGTCCTTCAATTTTTCATAATCTCC
* * * **
276894 TTATTTATTCAATTCATCATTTATTTTTAGTCTCTTTTTTTACCAAATTTGAGTCACATGCTCCT
1 TTATTTATTCAATTCCTCATTTATTTTAAGTCTC-ATTTTTACCAAATTTGAACCACATGCTCCT
**
276959 AAACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAAATCTTTATTTTTTG
65 AAACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAAATCTTTATTTTTCA
* *
277024 ATTTAGTCCTTTAGTTTTTCATAATCTCC
130 ATTTAGTCCTTCAATTTTTCATAATCTCC
*
277053 TTATTTATTCAATTCCTCATTTATTTTAAGTC-CGTTTTTACCAAATT
1 TTATTTATTCAATTCCTCATTTATTTTAAGTCTCATTTTTACCAAATT
277100 CGAGCTATAT
Statistics
Matches: 181, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
157 39 0.22
158 3 0.02
159 139 0.77
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.49
Consensus pattern (158 bp):
TTATTTATTCAATTCCTCATTTATTTTAAGTCTCATTTTTACCAAATTTGAACCACATGCTCCTA
AACCATAATAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAAATCTTTATTTTTCAA
TTTAGTCCTTCAATTTTTCATAATCTCC
Found at i:277566 original size:2 final size:2
Alignment explanation
Indices: 277487--277548 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
277477 TCAAACTTAA
277487 AT AT AT AT AT 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 AT AT AT AT AT
277529 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
277549 TTTAATTTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:281815 original size:27 final size:27
Alignment explanation
Indices: 281777--281832 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
281767 AAAAACGGTG
281777 GCGAGAATCTGAAATACATGCACTTCA
1 GCGAGAATCTGAAATACATGCACTTCA
281804 GCGAGAATCTGAAATACATGCACTTCA
1 GCGAGAATCTGAAATACATGCACTTCA
281831 GC
1 GC
281833 AAAATACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (27 bp):
GCGAGAATCTGAAATACATGCACTTCA
Found at i:283073 original size:19 final size:19
Alignment explanation
Indices: 283033--283075 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
283023 AGATGAGTCC
* *
283033 TTTTAAAATAATTATTTGA
1 TTTTAAAATAAATATATGA
283052 TTTTCAAAATAAATATAT-A
1 TTTT-AAAATAAATATATGA
283071 TTTTA
1 TTTTA
283076 CCGAGATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.43
20 11 0.52
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTAAAATAAATATATGA
Found at i:292297 original size:11 final size:11
Alignment explanation
Indices: 292281--292307 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
292271 AGTACTTTAA
292281 TTATTATTATT
1 TTATTATTATT
292292 TTATTATTATT
1 TTATTATTATT
292303 TTATT
1 TTATT
292308 TTAGTCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTATTATT
Found at i:292517 original size:140 final size:139
Alignment explanation
Indices: 292373--292693 Score: 554
Period size: 140 Copynumber: 2.3 Consensus size: 139
292363 AAATTGACAA
292373 TCTTAAGATAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
1 TCTTAAG-TAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
292438 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
65 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
*
292503 ATGAGCAGTC
130 AGGAGCAGTC
292513 TCTTAAGGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
1 TCTTAA-GTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
292578 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
65 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
292643 AGGAGCAGTC
130 AGGAGCAGTC
* * * *
292653 T-TAAAGTAACTAGATGCCCTTTTCTGATATTTCTAAATAAA
1 TCTTAAGTAATTAGATGTCCTTTT-TGATATTT-TTAATAAA
292694 TAAATATTTT
Statistics
Matches: 173, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
138 16 0.09
139 11 0.06
140 145 0.84
141 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (139 bp):
TCTTAAGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAGT
TAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAAA
GGAGCAGTC
Found at i:292720 original size:31 final size:31
Alignment explanation
Indices: 292685--292744 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
292675 TCTGATATTT
292685 CTAAATAA-ATAAATATTTTA-TTTATAAAACC
1 CTAAA-AATATAAAT-TTTTACTTTATAAAACC
*
292716 CTAAAAATATACATTTTTACTTTATAAAA
1 CTAAAAATATAAATTTTTACTTTATAAAA
292745 ATTATTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (31 bp):
CTAAAAATATAAATTTTTACTTTATAAAACC
Found at i:294766 original size:20 final size:19
Alignment explanation
Indices: 294727--294781 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
294717 TCCTTGCATT
294727 TTTCATTTTGCATTTATAC
1 TTTCATTTTGCATTTATAC
* *
294746 TTTCATGTTTGCTTTTGTAC
1 TTTCAT-TTTGCATTTATAC
* *
294766 TATACAATTTGCATTT
1 T-TTCATTTTGCATTT
294782 TTTATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.21
20 20 0.69
21 3 0.10
ACGTcount: A:0.20, C:0.15, G:0.09, T:0.56
Consensus pattern (19 bp):
TTTCATTTTGCATTTATAC
Found at i:294818 original size:12 final size:12
Alignment explanation
Indices: 294801--294854 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
294791 ACATTCACAT
294801 ATTTACATTTGC
1 ATTTACATTTGC
294813 ATTTACATTTGC
1 ATTTACATTTGC
* *
294825 ATTTTTACGTTTGT
1 A--TTTACATTTGC
*
294839 ATTTACATTTTC
1 ATTTACATTTGC
294851 ATTT
1 ATTT
294855 TTACATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.71
14 10 0.29
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:294831 original size:26 final size:26
Alignment explanation
Indices: 294802--294860 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
294792 CATTCACATA
294802 TTTACATTTGCATTTACATTTGCATT
1 TTTACATTTGCATTTACATTTGCATT
* * *
294828 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTACATTTGCATT
294854 TTTACAT
1 TTTACAT
294861 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTGCATT
Found at i:296947 original size:2 final size:2
Alignment explanation
Indices: 296940--296986 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
296930 TTTATCCTTT
296940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296982 TA TA T
1 TA TA T
296987 CCTTTGTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:297318 original size:8 final size:7
Alignment explanation
Indices: 297307--297406 Score: 73
Period size: 7 Copynumber: 13.9 Consensus size: 7
297297 AAATCCAGAA
297307 AAAAAAGG
1 AAAAAA-G
297315 AAAAAAG
1 AAAAAAG
297322 AGGAAAAAAG
1 A---AAAAAG
297332 AAAAAAG
1 AAAAAAG
297339 --AAAAG
1 AAAAAAG
297344 AAAAAAG
1 AAAAAAG
297351 AAATAAAG
1 AAA-AAAG
297359 AAATAAAG
1 AAA-AAAG
*
297367 AAATAA-
1 AAAAAAG
*
297373 AAATAA-
1 AAAAAAG
*
297379 AAAAAAC
1 AAAAAAG
*
297386 AAAAAGG
1 AAAAAAG
297393 AAAAAAAG
1 -AAAAAAG
297401 AAAAAA
1 AAAAAA
297407 ATTGAATCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.06
6 11 0.14
7 29 0.37
8 27 0.34
10 7 0.09
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:297346 original size:19 final size:19
Alignment explanation
Indices: 297307--297361 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
297297 AAATCCAGAA
*
297307 AAAAAAGGAAAAAAG--AGG
1 AAAAAA-GAAAAAAGAAAAG
297325 AAAAAAGAAAAAAGAAAAG
1 AAAAAAGAAAAAAGAAAAG
297344 AAAAAAGAAATAAAGAAA
1 AAAAAAGAAA-AAAGAAA
297362 TAAAGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 12 0.36
20 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAAAG
Found at i:297368 original size:16 final size:15
Alignment explanation
Indices: 297314--297406 Score: 65
Period size: 15 Copynumber: 6.5 Consensus size: 15
297304 GAAAAAAAAG
*
297314 GAAAAAAGAGGAAAAAA
1 GAAAAAAGA--AATAAA
297331 GAAAAAAG--A-AAA
1 GAAAAAAGAAATAAA
297343 GAAAAAAGAAATAAA
1 GAAAAAAGAAATAAA
297358 GAAATAAAGAAAT-AA
1 GAAA-AAAGAAATAAA
*
297373 -AAATAA-AAA-AAA
1 GAAAAAAGAAATAAA
* * *
297385 CAAAAAGGAAAAAAA
1 GAAAAAAGAAATAAA
297400 GAAAAAA
1 GAAAAAA
297407 ATTGAATCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
12 16 0.25
13 7 0.11
14 7 0.11
15 17 0.27
16 8 0.13
17 8 0.13
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (15 bp):
GAAAAAAGAAATAAA
Found at i:297407 original size:8 final size:8
Alignment explanation
Indices: 297306--297407 Score: 74
Period size: 8 Copynumber: 12.9 Consensus size: 8
297296 AAAATCCAGA
297306 AAAAAAAGG
1 AAAAAAA-G
297315 AAAAAAGAG
1 AAAAAA-AG
*
297324 GAAAAAAG
1 AAAAAAAG
297332 -AAAAAAG
1 AAAAAAAG
297339 ---AAAAG
1 AAAAAAAG
297344 -AAAAAAG
1 AAAAAAAG
*
297351 AAATAAAG
1 AAAAAAAG
*
297359 AAATAAAG
1 AAAAAAAG
297367 AAATAAAA-
1 AAA-AAAAG
297375 ATAAAAAA-
1 A-AAAAAAG
297383 AACAAAAAGG
1 AA-AAAAA-G
297393 AAAAAAAG
1 AAAAAAAG
297401 AAAAAAA
1 AAAAAAA
297408 TTGAATCAAG
Statistics
Matches: 81, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
5 5 0.06
7 13 0.16
8 38 0.47
9 22 0.27
10 3 0.04
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:302617 original size:221 final size:223
Alignment explanation
Indices: 302234--302665 Score: 619
Period size: 221 Copynumber: 1.9 Consensus size: 223
302224 GATTCAAATC
302234 CATCATTCGATGGATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
1 CATCATTCGATGGATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
* *
302299 GAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAA
66 GAAGAAATTCATAATGAGAAGAACTTATTCAACTTTTCGCCTGAATTCATCATTCGATGGATCAA
* *
302364 CATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCT-GAA-GAAGAAGAAGTTCATAATGAGA
131 CATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATATAGAAGGAAGAAGAAGTTCATAATGAGA
302427 AGAACTTGTTCAACTTTCTGCTTGAATT
196 AGAACTTGTTCAACTTTCTGCTTGAATT
* *
302455 CATCATTCGATGGATCAGCATTTCCAGAGAA-AGTTCATAATGAGAAGAAC-CTATCTGAAG-AG
1 CATCATTCGATGGATCAACATTTCC-G-GAAGAGTTCATAATGAGAAGAACTC-ATCTGAAGAAA
* * *
302517 GAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTT-GCCTGAATTCATCACTT-GATGG
63 GAAGAAGAAATTCATAATGAGAAGAACTTATTCAA-CTTTTCGCCTGAATTCATCA-TTCGATGG
* *
302580 ATTAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCA
126 ATCAACATTTCCAG-GTAAAGTTCATAATGAGAAGAACTCATAT--AGAAGGAAGAAGAAGTTCA
**
302644 TAATGAGAAGTGCTTGTTCAAC
188 TAATGAGAAGAACTTGTTCAAC
302666 CTTTTTTTGA
Statistics
Matches: 188, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
221 112 0.60
222 36 0.19
223 3 0.02
224 3 0.02
225 34 0.18
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (223 bp):
CATCATTCGATGGATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAA
GAAGAAATTCATAATGAGAAGAACTTATTCAACTTTTCGCCTGAATTCATCATTCGATGGATCAA
CATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATATAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACTTTCTGCTTGAATT
Found at i:302684 original size:112 final size:111
Alignment explanation
Indices: 302234--302670 Score: 611
Period size: 112 Copynumber: 3.9 Consensus size: 111
302224 GATTCAAATC
*
302234 CATCATTCGATGGATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAACATTTCCAGGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
302298 AGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTCGCTTGAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATT
*
302346 CATCATTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCT---GAA-GA
1 CATCATTCGATGGATCAACATTTCCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
302407 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTCTGCTTGAATT
65 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTT-TGCTTGAATT
*
302455 CATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAAC-CTATCTGAAG-AGG
1 CATCATTCGATGGATCAACATTTCCAG-GAAAGTTCATAATGAGAAGAACTC-ATCTGAAGAAGG
* * * *
302518 AAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATT
64 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATT
* * *
302567 CATCACTT-GATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGG
1 CATCA-TTCGATGGATCAACATTTCCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
**
302631 AAGAAGAAGTTCATAATGAGAAGTGCTTGTTCAACCTTTT
64 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
302671 TTTGATGCTA
Statistics
Matches: 295, Mismatches: 17, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
108 1 0.00
109 97 0.33
110 5 0.02
111 1 0.00
112 118 0.40
113 72 0.24
114 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (111 bp):
CATCATTCGATGGATCAACATTTCCAGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTTGAATT
Found at i:302880 original size:196 final size:196
Alignment explanation
Indices: 302519--302937 Score: 558
Period size: 196 Copynumber: 2.1 Consensus size: 196
302509 CTGAAGAGGA
* * * * ** *
302519 AGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCATCACTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTAAATTCATCACCCGATGGATCA
* *
302584 ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATG
66 ACGTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATG
* ** * ** * *
302649 AGAAGTGCTTGTTCAACCTTTTTTTGATGCTATCACAGAAGGAAATAGATCAGTATCAGCATTTC
131 AGAAGAGCTTGTTCAACCTTTTCATAATGCTATCACAGAAGGAAATAGATCAACACCAACATTTC
302714 C
196 C
*
302715 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG-CTCAAATTCATCACCCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCT-AAATTCATCACCCGATGGATC
* * * *
302779 AGCGTTGCCAGAGAAAGTTCATAATGAGAAGAATTTATCTGAAGAA-GAAGAAGAAGTTCATAAT
65 AACGTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAAT
* *
302843 GAGAAGAGCTTGTTCAACCTTTTGCATAACT-CTATCACAGAAGGAGATAGATCAACACCAACTT
130 GAGAAGAGCTTGTTCAACCTTTT-CATAA-TGCTATCACAGAAGGAAATAGATCAACACCAACAT
302907 TTCC
193 TTCC
302911 AG-AGAAAGTTCATAATGAGAAGAACTT
1 AGAAG-AAGTTCATAATGAGAAGAACTT
302938 ATCTGAAGAG
Statistics
Matches: 194, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
195 44 0.23
196 149 0.77
197 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (196 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTAAATTCATCACCCGATGGATCA
ACGTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCAACCTTTTCATAATGCTATCACAGAAGGAAATAGATCAACACCAACATTTC
C
Found at i:305228 original size:140 final size:140
Alignment explanation
Indices: 305075--305431 Score: 514
Period size: 139 Copynumber: 2.6 Consensus size: 140
305065 GATTAGATAA
* * *
305075 TAATATTTGTTTATTTTAA-ATATCAAGAAATTGA-TA-ATCTTAAGGTAATTAGATGTCCTTTT
1 TAATATTTATTTATTTTAATAT-TAAAGAAA-TGAGCAGATCTTAAGGTAATTAGATGTCC-TTT
305137 TGATATTTTTAATAAAATATTATATTTAATTCACTCTTAGTTAATCATATGTTTAGAAAAAAATT
63 TGATATTTTTAATAAAATATTATATTTAATTCACTCTTAGTTAATCATATGTTTAGAAAAAAATT
305202 ATTATATTCTTAT
128 ATTATATTCTTAT
*
305215 TAATATTTATTTA--TTAATATTAAAGAAATGAGCAGTCTCTTAAGGTAATTAGATGTCCTTTTG
1 TAATATTTATTTATTTTAATATTAAAGAAATGAGCAG-ATCTTAAGGTAATTAGATGTCCTTTTG
305278 ATATTTTTAATAAAATATTATATTTAATTCACTCTTAGTTAATCATATGTTTAGAAAAAAATTAT
65 ATATTTTTAATAAAATATTATATTTAATTCACTCTTAGTTAATCATATGTTTAGAAAAAAATTAT
305343 TATATTCTTAT
130 TATATTCTTAT
* * * *
305354 TAATATTTATTTA--TTAATATTAAAGAAAGGAGCAG-TCTTAAAGTAACTAGATGCCCTTTTCT
1 TAATATTTATTTATTTTAATATTAAAGAAATGAGCAGATCTTAAGGTAATTAGATGTCC-TTT-T
*
305416 GATATTTCTAAATAAA
64 GATATTT-TTAATAAA
305432 TAAATATTTT
Statistics
Matches: 201, Mismatches: 9, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
137 21 0.10
138 15 0.07
139 125 0.62
140 40 0.20
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (140 bp):
TAATATTTATTTATTTTAATATTAAAGAAATGAGCAGATCTTAAGGTAATTAGATGTCCTTTTGA
TATTTTTAATAAAATATTATATTTAATTCACTCTTAGTTAATCATATGTTTAGAAAAAAATTATT
ATATTCTTAT
Found at i:305433 original size:139 final size:139
Alignment explanation
Indices: 305112--305431 Score: 554
Period size: 139 Copynumber: 2.3 Consensus size: 139
305102 AAATTGATAA
305112 TCTTAAGGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
1 TCTTAAGGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
305177 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
66 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
*
305242 ATGAGCAGTC
131 AGGAGCAG-C
305252 TCTTAAGGTAATTAGATGTCC-TTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
1 TCTTAAGGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
305316 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
66 TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
305381 AGGAGCAG-
131 AGGAGCAGC
* * * *
305389 TCTTAAAGTAACTAGATGCCCTTTTCTGATATTTCTAAATAAA
1 TCTTAAGGTAATTAGATGTCCTTTT-TGATATTT-TTAATAAA
305432 TAAATATTTT
Statistics
Matches: 172, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
137 18 0.10
138 3 0.02
139 123 0.72
140 28 0.16
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (139 bp):
TCTTAAGGTAATTAGATGTCCTTTTTGATATTTTTAATAAAATATTATATTTAATTCACTCTTAG
TTAATCATATGTTTAGAAAAAAATTATTATATTCTTATTAATATTTATTTATTAATATTAAAGAA
AGGAGCAGC
Found at i:305458 original size:31 final size:31
Alignment explanation
Indices: 305423--305482 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
305413 TCTGATATTT
305423 CTAAATAA-ATAAATATTTTA-TTTATAAAACC
1 CTAAA-AATATAAAT-TTTTACTTTATAAAACC
*
305454 CTAAAAATATACATTTTTACTTTATAAAA
1 CTAAAAATATAAATTTTTACTTTATAAAA
305483 ATTATTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (31 bp):
CTAAAAATATAAATTTTTACTTTATAAAACC
Found at i:310951 original size:20 final size:21
Alignment explanation
Indices: 310926--310986 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
310916 TTTTTGTGCA
*
310926 GAGGGAATCGATTCCCCC-AT
1 GAGGGAACCGATTCCCCCTAT
*
310946 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
310967 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
310987 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 17 0.47
21 2 0.06
22 1 0.03
23 16 0.44
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:313228 original size:13 final size:13
Alignment explanation
Indices: 313209--313277 Score: 85
Period size: 13 Copynumber: 5.6 Consensus size: 13
313199 AGGGGGAGAA
313209 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
*
313222 --GAGTGTGTTTT
1 AAGTGTGTGTTTT
313233 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
313246 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
313259 GAA---TGTGTTTT
1 -AAGTGTGTGTTTT
313270 AAGTGTGT
1 AAGTGTGT
313278 TTTAAAATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
10 2 0.04
11 18 0.38
13 26 0.54
14 2 0.04
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:313241 original size:24 final size:24
Alignment explanation
Indices: 313209--313282 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
313199 AGGGGGAGAA
*
313209 AAGTGTGTGTTTTGAGTGTGTTTT
1 AAGTGTGTGTTTTAAGTGTGTTTT
313233 AAGTGTGTGTTTTAAGTGTGTGTTT
1 AAGTGTGTGTTTTAAGTGTGT-TTT
* **
313258 -TGAATGTGTTTTAAGTGTGTTTT
1 AAGTGTGTGTTTTAAGTGTGTTTT
313281 AA
1 AA
313283 AATGATAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 3 0.07
24 37 0.86
25 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.53
Consensus pattern (24 bp):
AAGTGTGTGTTTTAAGTGTGTTTT
Found at i:313281 original size:11 final size:11
Alignment explanation
Indices: 313213--313282 Score: 79
Period size: 11 Copynumber: 6.0 Consensus size: 11
313203 GGAGAAAAGT
*
313213 GTGTGTTTTGA
1 GTGTGTTTTAA
313224 GTGTGTTTTAA
1 GTGTGTTTTAA
313235 GTGTGTGTTTTAA
1 --GTGTGTTTTAA
313248 GTGTGTGTTTTGAA
1 --GTGTGTTTT-AA
313262 -TGTGTTTTAA
1 GTGTGTTTTAA
313272 GTGTGTTTTAA
1 GTGTGTTTTAA
313283 AATGATAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
10 2 0.04
11 28 0.52
13 22 0.41
14 2 0.04
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.54
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:315106 original size:7 final size:7
Alignment explanation
Indices: 315096--315148 Score: 69
Period size: 7 Copynumber: 8.0 Consensus size: 7
315086 GGGAAAAATG
315096 AATAATA
1 AATAATA
315103 AATAATA
1 AATAATA
315110 AATAAT-
1 AATAATA
315116 AATAAT-
1 AATAATA
315122 AA-AATA
1 AATAATA
315128 AATAA-A
1 AATAATA
315134 TAATAATA
1 -AATAATA
315142 AATAATA
1 AATAATA
315149 TATTATCATT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 3 0.07
6 11 0.26
7 27 0.64
8 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:315109 original size:3 final size:3
Alignment explanation
Indices: 315096--315148 Score: 54
Period size: 3 Copynumber: 16.3 Consensus size: 3
315086 GGGAAAAATG
315096 AAT AAT AAAT AAT AAAT AAT AAT AAT AA- AAT AAAT AAAT AAT AAT AAAT
1 AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT
315145 AAT A
1 AAT A
315149 TATTATCATT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.04
3 27 0.60
4 16 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:315134 original size:22 final size:19
Alignment explanation
Indices: 315096--315148 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
315086 GGGAAAAATG
315096 AATAATAAATAATAAATAAT
1 AATAATAAA-AATAAATAAT
315116 AATAAT-AAAATAAATAAAT
1 AATAATAAAAATAAAT-AAT
315135 AATAATAAATAATA
1 AATAATAAA-AATA
315149 TATTATCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 11 0.37
20 8 0.27
21 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAATAAAAATAAATAAT
Found at i:315721 original size:33 final size:33
Alignment explanation
Indices: 315695--315761 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
315685 CAAATGCTTC
315695 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
315728 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
315761 G
1 G
315762 ATTTATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
Found at i:315840 original size:6 final size:6
Alignment explanation
Indices: 315815--315880 Score: 54
Period size: 5 Copynumber: 11.7 Consensus size: 6
315805 GGCCTGCAAA
* *
315815 AATAAT AA-AAT AA-AAA AATATT AATAAT AATAAT AATAAAT AA-ATAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AAT-AAT AATA-AT
315862 AAT-AT AATAA- AATAA- AATA
1 AATAAT AATAAT AATAAT AATA
315881 TTTTTATAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 24 0.47
6 22 0.43
7 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AATAAT
Found at i:315842 original size:3 final size:3
Alignment explanation
Indices: 315815--315880 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
315805 GGCCTGCAAA
* *
315815 AAT AAT AA- AAT AA- AAA AAT ATT AAT AAT AAT AAT AAT AAAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
315858 ATAT AAT -AT AAT AA- AAT AA- AAT A
1 A-AT AAT AAT AAT AAT AAT AAT AAT A
315881 TTTTTATAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
2 11 0.21
3 37 0.71
4 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:315843 original size:9 final size:9
Alignment explanation
Indices: 315815--315880 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 9
315805 GGCCTGCAAA
315815 AATAATAA-
1 AATAATAAT
*
315823 AATAA-AAA
1 AATAATAAT
*
315831 AATATTAAT
1 AATAATAAT
315840 AATAATAAT
1 AATAATAAT
315849 AATAAATAA-
1 AAT-AATAAT
315858 ATATAAT-AT
1 A-ATAATAAT
315867 AATAA-AAT
1 AATAATAAT
315875 AA-AATA
1 AATAATA
315881 TTTTTATAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
7 4 0.08
8 19 0.40
9 18 0.38
10 7 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AATAATAAT
Found at i:315853 original size:31 final size:30
Alignment explanation
Indices: 315815--315880 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
315805 GGCCTGCAAA
315815 AATAATAAAATAAA-AAAATATTAATAATAAT
1 AATAATAAAATAAATAAAATA-TAATAA-AAT
*
315846 AATAAT-AAATAAATATAATATAATAAAAT
1 AATAATAAAATAAATAAAATATAATAAAAT
315875 AA-AATA
1 AATAATA
315881 TTTTTATAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 3 0.09
29 5 0.16
30 13 0.41
31 11 0.34
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (30 bp):
AATAATAAAATAAATAAAATATAATAAAAT
Found at i:315865 original size:19 final size:19
Alignment explanation
Indices: 315841--315877 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
315831 AATATTAATA
315841 ATAATAATAAT-AAATAAAT
1 ATAAT-ATAATAAAATAAAT
315860 ATAATATAATAAAATAAA
1 ATAATATAATAAAATAAA
315878 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATATAATAAAATAAAT
Found at i:316790 original size:4 final size:4
Alignment explanation
Indices: 316781--316808 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
316771 CCAGAACATG
316781 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
316809 GAACAGATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:319667 original size:30 final size:30
Alignment explanation
Indices: 319616--319695 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
319606 CATCATTTTT
* * *
319616 TAATATTTTCGGTCA-TTTTTAGCGTCTAA
1 TAATGTTTTCGATCATTTTTTAGCGCCTAA
319645 TAATGTTTTCGATCATTTTTTAGCGCCTAA
1 TAATGTTTTCGATCATTTTTTAGCGCCTAA
** *
319675 TAATGTTCCCGTTCATTTTTT
1 TAATGTTTTCGATCATTTTTT
319696 CGAAAATCCG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 13 0.30
30 31 0.70
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.50
Consensus pattern (30 bp):
TAATGTTTTCGATCATTTTTTAGCGCCTAA
Found at i:323285 original size:29 final size:29
Alignment explanation
Indices: 323214--323288 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
323204 ATCAAATTAT
* *
323214 AAATTTTTAAAGTTTAGTGACCAAAGTATA
1 AAATTTTAAAAGTTAAGTGACCAAAG-ATA
323244 AAATTTTAAAAAGTTCAAG-GACCAAA-ATA
1 AAATTTT-AAAAGTT-AAGTGACCAAAGATA
323273 ATAATTTTAAAAGTTA
1 A-AATTTTAAAAGTTA
323289 CAATTGGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 1 0.03
29 11 0.28
30 13 0.32
31 13 0.32
32 2 0.05
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.33
Consensus pattern (29 bp):
AAATTTTAAAAGTTAAGTGACCAAAGATA
Found at i:324483 original size:65 final size:64
Alignment explanation
Indices: 324351--324506 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 64
324341 ACACCCTATT
* * * * * *
324351 TCGAATGCATTTTGTGTACCAATGCACAGTCATGCATCGATTCACTCTTGATTTTATTGAAATA
1 TCGAATTCATTTTATGTACCGATGCACAGTCATGCATCGATGCACTCTTGATCTTATTGAAACA
* *
324415 TCGAATTCATTTTATGTACCGATGCACA-TACCATGCATTGATGCACTCTTGGCTCTT-TTGAAA
1 TCGAATTCATTTTATGTACCGATGCACAGT--CATGCATCGATGCACTCTT-GATCTTATTGAAA
324478 CA
63 CA
*
324480 TCGAATGT-A-ATTAGTGTACCGATGCAC
1 TCGAAT-TCATTTTA-TGTACCGATGCAC
324507 CCCAAGTGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 28 0.36
65 44 0.56
66 5 0.06
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (64 bp):
TCGAATTCATTTTATGTACCGATGCACAGTCATGCATCGATGCACTCTTGATCTTATTGAAACA
Found at i:325964 original size:117 final size:118
Alignment explanation
Indices: 325820--326044 Score: 328
Period size: 117 Copynumber: 1.9 Consensus size: 118
325810 GCTAAAAATT
* *
325820 AACTTCTTTTGAAAGCTAAAATAGATTTGGAAAATCAAAATGAAATTTTGAAAAAGGAATTAGAG
1 AACTTCTTTAGAAAGCTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGAATTAGAG
* * *
325885 CTTTCAAAAATAAAA-TCTGAAAACTTTGAAAAATAAATTTTCAAATTAAACA
66 CTCTCAAAAATAAAATTCTGAAAACTTTGAAAAAGAAAATTTCAAATTAAACA
* * * *
325937 AACTTCTTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGA
1 AACTTCTT-TAGAAAGCTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGAATTAGA
* *
326001 GCTCTCAAAAATAAAATTTTGAAAGCTTTGAAAAAGAAAATTTC
65 GCTCTCAAAAATAAAATTCTGAAAACTTTGAAAAAGAAAATTTC
326045 GATTTGAAAG
Statistics
Matches: 95, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
117 67 0.71
118 28 0.29
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (118 bp):
AACTTCTTTAGAAAGCTAAAATAGATTTGGAAAATCAAAATGAAATATTGAAAAAGGAATTAGAG
CTCTCAAAAATAAAATTCTGAAAACTTTGAAAAAGAAAATTTCAAATTAAACA
Found at i:329917 original size:44 final size:44
Alignment explanation
Indices: 329854--329959 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
329844 TTTTGTGCAC
*
329854 TATGCATCGATACACTATGAAAGTGTACCGATGCAT-TCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCGATGCATGT-CTTGAA
* *
329898 TATGCATCGATCCACTATGAAGGTGCACCGATGCATGTCTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCGATGCATGTCTTGAA
*
329942 TGTGCATCGATACACTAT
1 TATGCATCGATACACTAT
329960 ACAATGCATC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
44 55 0.98
45 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGCACCGATGCATGTCTTGAA
Found at i:332735 original size:65 final size:64
Alignment explanation
Indices: 332612--332765 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 64
332602 ACCCTATTTA
* * * * *
332612 GAATGCATTTTGTGTACCAATGCACAGTCATGCATCGATGCACTCTTGATTTTATTGAAATATC
1 GAATTCATTTTATGTACCGATGCACAGTCATGCATCGATGCACTCTTGATCTTATTGAAACATC
* *
332676 GAATTCATTTTATGTACCGATGCACA-TACCATGCATTGATGCACTCTTGGCTCTT-TTGAAACA
1 GAATTCATTTTATGTACCGATGCACAGT--CATGCATCGATGCACTCTT-GATCTTATTGAAACA
332739 TC
63 TC
*
332741 GAATGT-A-ATTAGTGTACCGATGCAC
1 GAAT-TCATTTTA-TGTACCGATGCAC
332766 CCCAAGTGTA
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 26 0.34
65 45 0.58
66 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
GAATTCATTTTATGTACCGATGCACAGTCATGCATCGATGCACTCTTGATCTTATTGAAACATC
Found at i:333688 original size:29 final size:30
Alignment explanation
Indices: 333645--333709 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
333635 ACAAGCCTTA
**
333645 GAAAAATTCAGGGACC-ATTTTATAATTTTT
1 GAAAAATTCAGGGACCAATTCAATAA-TTTT
*
333675 GAAAAGTT-AGGGACCAATTCAATAATTTT
1 GAAAAATTCAGGGACCAATTCAATAATTTT
333704 GAAAAA
1 GAAAAA
333710 GTTGTGAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (30 bp):
GAAAAATTCAGGGACCAATTCAATAATTTT
Found at i:333710 original size:30 final size:31
Alignment explanation
Indices: 333645--333712 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
333635 ACAAGCCTTA
**
333645 GAAAAA-TTCAGGGACCATTTTATAATTTTT
1 GAAAAAGTTCAGGGACCATTCAATAATTTTT
333675 G-AAAAGTT-AGGGACCAATTCAATAA-TTTT
1 GAAAAAGTTCAGGGACC-ATTCAATAATTTTT
333704 GAAAAAGTT
1 GAAAAAGTT
333713 GTGAATGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (31 bp):
GAAAAAGTTCAGGGACCATTCAATAATTTTT
Found at i:334289 original size:23 final size:24
Alignment explanation
Indices: 334249--334294 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
334239 CATGACATTG
334249 TACATAGATGTTTTATACATCATA
1 TACATAGATGTTTTATACATCATA
334273 TACATAGAT-TTTTATACATCAT
1 TACATAGATGTTTTATACATCAT
334295 CAGAAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (24 bp):
TACATAGATGTTTTATACATCATA
Found at i:334775 original size:7 final size:7
Alignment explanation
Indices: 334763--334805 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
334753 TATATTGGGC
334763 TATGGTT
1 TATGGTT
334770 TATGGTT
1 TATGGTT
334777 TATGGTT
1 TATGGTT
* *
334784 TATAGTC
1 TATGGTT
*
334791 TATAGTT
1 TATGGTT
334798 TACTGGTT
1 TA-TGGTT
334806 AATGAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (7 bp):
TATGGTT
Found at i:335964 original size:157 final size:154
Alignment explanation
Indices: 335587--335964 Score: 474
Period size: 154 Copynumber: 2.4 Consensus size: 154
335577 CATGTTTTCA
* * * * **
335587 TTATTTCTTCAATTCCTCCTTCATTTTCAGCTCATTTTTACCAAATTTAAACCGCATGCTCCTAA
1 TTATTTCTTCAATTCCTCATTTATTTTAAG-TCATTTTTACCAAATTTGAGTCGCATGCTCCTAA
* * * *
335652 ATCATAGTAGAATACATGTGTACTTTCAATTCTTCTTTTTGGTAACAATTTTTATTTTTCAATTT
65 ACCATAATAGAATACATGTGTACTTTCAATTCTTCTTTTTGATAACAATTATTATTTTTCAATTT
335717 AGTCCTTCAATTTTTCATAATCTCC
130 AGTCCTTCAATTTTTCATAATCTCC
* * * *
335742 --ATTTATTTCAATTCGTCATTTATTTTAAGTCTTTTTTTACCAAATTTGAGTCACATGCTCCTA
1 TTATTT-CTTCAATTCCTCATTTATTTTAAGTC-ATTTTTACCAAATTTGAGTCGCATGCTCCTA
* **
335805 AACCATAATAGAATACGTGTGTACTTTCAATTCCTT-TTTTTGATAACAAATTCATTATTTTTTT
64 AACCATAATAGAATACATGTGTACTTTCAATT-CTTCTTTTTGATAAC-AATT-ATTATTTTTCA
*
335869 ATTTAGTCCTTTAATTTTTCATAATCTCC
126 ATTTAGTCCTTCAATTTTTCATAATCTCC
* * * *
335898 TTATTTCTTCAATTCCTCATTTATTTTAAGTTCGTTTTTACCAAATTTGAGTTGTATGCTCATAA
1 TTATTTCTTCAATTCCTCATTTATTTTAAG-TCATTTTTACCAAATTTGAGTCGCATGCTCCTAA
335963 AC
65 AC
335965 TATAGTATCA
Statistics
Matches: 190, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
153 6 0.03
154 84 0.44
155 7 0.04
156 36 0.19
157 51 0.27
158 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (154 bp):
TTATTTCTTCAATTCCTCATTTATTTTAAGTCATTTTTACCAAATTTGAGTCGCATGCTCCTAAA
CCATAATAGAATACATGTGTACTTTCAATTCTTCTTTTTGATAACAATTATTATTTTTCAATTTA
GTCCTTCAATTTTTCATAATCTCC
Found at i:336376 original size:33 final size:32
Alignment explanation
Indices: 336272--336378 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 32
336262 TAAACATATA
336272 ATAATATATTTTAATTTGAAATATTCAAAAG-AT
1 ATAAT-TATTTTAATTTGAAATATT-AAAAGTAT
* * * *
336305 AAAACTCATTTTAACTTTCAAA-CTT-AAA-TAT
1 ATAA-TTATTTTAA-TTTGAAATATTAAAAGTAT
336336 AT-ATTATTTTAATTTGAAATATATAAAAGTAT
1 ATAATTATTTTAATTTGAAATAT-TAAAAGTAT
336368 ATAATTATTTT
1 ATAATTATTTT
336379 TAATATTAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
28 6 0.10
29 9 0.16
30 2 0.03
31 9 0.16
32 5 0.09
33 20 0.34
34 7 0.12
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
ATAATTATTTTAATTTGAAATATTAAAAGTAT
Found at i:339549 original size:36 final size:36
Alignment explanation
Indices: 339435--339535 Score: 168
Period size: 35 Copynumber: 2.8 Consensus size: 36
339425 GACAACCAAT
*
339435 TTTGAAAAAATGGTTTTCAAAGTTTAGTAAATGTTTC
1 TTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
339472 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
339507 TTTGAAAAATGGTTTTTCAAAGTTTGGTA
1 TTTGAAAAATGG-TTTTCAAAGTTTGGTA
339536 GTTGTTTGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
35 34 0.56
36 7 0.11
37 20 0.33
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTTC
Found at i:344068 original size:21 final size:21
Alignment explanation
Indices: 344044--344104 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
344034 AACTTTGAAA
344044 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
344065 AAAT-GTTTT-----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
344079 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
344100 AAATG
1 AAATG
344105 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
20 8 0.26
21 10 0.32
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:344135 original size:37 final size:36
Alignment explanation
Indices: 344036--344144 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
344026 TGGCAACCAA
344036 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
344073 TTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
344108 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
344145 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 7 0.10
37 26 0.39
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:366827 original size:21 final size:21
Alignment explanation
Indices: 366801--366859 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
366791 GTCCGAGTTA
*
366801 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAACG
366822 CCCGCGACGGCCGCAATAACG
1 CCCGCGACGGCCGCAATAACG
* *
366843 CCCGCGACAGTCGCAAT
1 CCCGCGACGGCCGCAAT
366860 CACGGTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAACG
Found at i:367743 original size:21 final size:21
Alignment explanation
Indices: 367713--367752 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
367703 TAATTGTTAA
*
367713 AAATATTAATGTTTTAGGTGG
1 AAATAATAATGTTTTAGGTGG
367734 AAATAATAATGTTTTAGGT
1 AAATAATAATGTTTTAGGT
367753 AATTTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (21 bp):
AAATAATAATGTTTTAGGTGG
Found at i:374292 original size:20 final size:20
Alignment explanation
Indices: 374267--374313 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
374257 CATGTTTATA
*
374267 AAAGTAATCTACAAATAATG
1 AAAGTAATCTACAAAAAATG
*
374287 AAAGTAATCTGCAAAAAATG
1 AAAGTAATCTACAAAAAATG
374307 AAAGTAA
1 AAAGTAA
374314 CCGGCAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAGTAATCTACAAAAAATG
Found at i:374320 original size:20 final size:20
Alignment explanation
Indices: 374278--374321 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
374268 AAGTAATCTA
* * *
374278 CAAATAATGAAAGTAATCTG
1 CAAAAAATGAAAGTAACCGG
374298 CAAAAAATGAAAGTAACCGG
1 CAAAAAATGAAAGTAACCGG
374318 CAAA
1 CAAA
374322 GGGATAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (20 bp):
CAAAAAATGAAAGTAACCGG
Found at i:380022 original size:29 final size:29
Alignment explanation
Indices: 379984--380048 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
379974 AGCAAGGTAT
379984 GTCGCCATGCAGTAGGGACGACCTTATAG
1 GTCGCCATGCAGTAGGGACGACCTTATAG
* * * * *
380013 TTCGCCATGCAGTTGGGGCGACGTTGTAG
1 GTCGCCATGCAGTAGGGACGACCTTATAG
380042 GTCGCCA
1 GTCGCCA
380049 GGTGAATTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.23
Consensus pattern (29 bp):
GTCGCCATGCAGTAGGGACGACCTTATAG
Found at i:383244 original size:24 final size:22
Alignment explanation
Indices: 383210--383260 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
383200 AATTATATTA
383210 AATTATTTAATCATTATTAAAT
1 AATTATTTAATCATTATTAAAT
383232 AATTATTAGTAATCATTATTAAAT
1 AATTATT--TAATCATTATTAAAT
*
383256 TATTA
1 AATTA
383261 GTATCAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 7 0.27
24 19 0.73
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTATTTAATCATTATTAAAT
Found at i:383281 original size:33 final size:33
Alignment explanation
Indices: 383242--383314 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
383232 AATTATTAGT
* * *
383242 AATCATTATTAAATTATTAGTATCAAATCAATA
1 AATCATTACTAAATCATTACTATCAAATCAATA
*
383275 AATCATTACTAAATCATTACTATCAAATCATTA
1 AATCATTACTAAATCATTACTATCAAATCAATA
383308 AAT-ATTA
1 AATCATTA
383315 ATAATAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.38
Consensus pattern (33 bp):
AATCATTACTAAATCATTACTATCAAATCAATA
Done.