Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2178920 original size:61 final size:61
Alignment explanation
Indices: 2178788--2178922 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
2178778 CGCTATGTAA
* * * * * ** *
2178788 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCATTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
* * *
2178849 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT-CCAAT
2178911 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2178923 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:2179012 original size:21 final size:21
Alignment explanation
Indices: 2178972--2179012 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2178962 ATTGTATACC
**
2178972 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2178993 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2179013 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2197325 original size:2 final size:2
Alignment explanation
Indices: 2197318--2197358 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2197308 ATGCTAAATT
2197318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2197359 CTTATTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2198955 original size:39 final size:40
Alignment explanation
Indices: 2198901--2198992 Score: 152
Period size: 39 Copynumber: 2.3 Consensus size: 40
2198891 CAATCCAGAT
*
2198901 TATATATGTATATAATATTTTATA-TTTTTATATTAATTA
1 TATATATATATATAATATTTTATATTTTTTATATTAATTA
2198940 TATATATATATATAATATTTTATATTTTTTTATATTAATTA
1 TATATATATATATAATATTTTATA-TTTTTTATATTAATTA
2198981 TATATATA-ATAT
1 TATATATATATAT
2198993 TTTCGGGTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
39 23 0.46
40 4 0.08
41 23 0.46
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (40 bp):
TATATATATATATAATATTTTATATTTTTTATATTAATTA
Found at i:2199034 original size:32 final size:32
Alignment explanation
Indices: 2198985--2199066 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 32
2198975 TAATTATATA
2198985 TATAATATTTTCGGGTTCGGGTTCGGGTTTGAG
1 TATAATA-TTTCGGGTTCGGGTTCGGGTTTGAG
2199018 TATAATA--T----TTCGGGTTCGGGTTTGAG
1 TATAATATTTCGGGTTCGGGTTCGGGTTTGAG
2199044 TATAATATTTCGGG-TCGGGTTCG
1 TATAATATTTCGGGTTCGGGTTCG
2199067 AAGACGGCGC
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
26 25 0.58
28 1 0.02
30 1 0.02
31 9 0.21
33 7 0.16
ACGTcount: A:0.17, C:0.10, G:0.32, T:0.41
Consensus pattern (32 bp):
TATAATATTTCGGGTTCGGGTTCGGGTTTGAG
Found at i:2199036 original size:26 final size:26
Alignment explanation
Indices: 2199000--2199064 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
2198990 TATTTTCGGG
2199000 TTCGGGTTCGGGTTTGAGTATAATAT
1 TTCGGGTTCGGGTTTGAGTATAATAT
2199026 TTCGGGTTCGGGTTTGAGTATAATAT
1 TTCGGGTTCGGGTTTGAGTATAATAT
2199052 TTCGGG-TCGGGTT
1 TTCGGGTTCGGGTT
2199065 CGAAGACGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 7 0.18
26 32 0.82
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (26 bp):
TTCGGGTTCGGGTTTGAGTATAATAT
Found at i:2199678 original size:13 final size:14
Alignment explanation
Indices: 2199658--2199696 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
2199648 AAATTTTTAA
2199658 ATTAAAAAATATTG
1 ATTAAAAAATATTG
2199672 ATTAAAATAAAATATTG
1 ATT--AA-AAAATATTG
2199689 ATTAAAAA
1 ATTAAAAA
2199697 TTATGCAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.27
15 2 0.09
16 2 0.09
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
ATTAAAAAATATTG
Found at i:2199685 original size:17 final size:17
Alignment explanation
Indices: 2199663--2199695 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2199653 TTTAAATTAA
2199663 AAAATATTGATTAAAAT
1 AAAATATTGATTAAAAT
2199680 AAAATATTGATTAAAA
1 AAAATATTGATTAAAA
2199696 ATTATGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AAAATATTGATTAAAAT
Found at i:2200137 original size:502 final size:502
Alignment explanation
Indices: 2199195--2200189 Score: 1981
Period size: 502 Copynumber: 2.0 Consensus size: 502
2199185 AAGAGAAATC
2199195 TTATGCAGAAATGTGATTATTGTGTCCTATGTTCAAAGTTTAAACGATCTAGTTACTAGTCATGT
1 TTATGCAGAAATGTGATTATTGTGTCCTATGTTCAAAGTTTAAACGATCTAGTTACTAGTCATGT
2199260 GGATTGCATGGGCGGACCTATATGGCCCAGGAAGTAGCAAATGCATACCTATTTTTCTTAAAAAA
66 GGATTGCATGGGCGGACCTATATGGCCCAGGAAGTAGCAAATGCATACCTATTTTTCTTAAAAAA
2199325 ATATCAGCATTTAAACTTTGAACATAGGACACAATAATCACATTTCTGCATAAGATTTCTTGAGC
131 ATATCAGCATTTAAACTTTGAACATAGGACACAATAATCACATTTCTGCATAAGATTTCTTGAGC
2199390 TTTGTGCTCTTTGACGAGAGTAAGAAATCAATGTCAACCTTTTATTTTAAAAATTTAAATTAAAA
196 TTTGTGCTCTTTGACGAGAGTAAGAAATCAATGTCAACCTTTTATTTTAAAAATTTAAATTAAAA
2199455 AAATACTGATTAAAATAATATATCATTTTACCTTTTACAACAATTCATCTCGCCTTTTTTACTTT
261 AAATACTGATTAAAATAATATATCATTTTACCTTTTACAACAATTCATCTCGCCTTTTTTACTTT
2199520 CTCTCATTTTCCTTAAAAAAATATAAATATTTAATATATTATATTAAGAGTTAAAAATTATGCAC
326 CTCTCATTTTCCTTAAAAAAATATAAATATTTAATATATTATATTAAGAGTTAAAAATTATGCAC
2199585 ACATCTTTCTTGAGCTCTGTGCTCTTTAAGGTAGGTAATAAACCAATGTCAACCTTTTATTCTAA
391 ACATCTTTCTTGAGCTCTGTGCTCTTTAAGGTAGGTAATAAACCAATGTCAACCTTTTATTCTAA
2199650 ATTTTTAAATTAAAAAATATTGATTAAAATAAAATATTGATTAAAAA
456 ATTTTTAAATTAAAAAATATTGATTAAAATAAAATATTGATTAAAAA
2199697 TTATGCAGAAATGTGATTATTGTGTCCTATGTTCAAAGTTTAAACGATCTAGTTACTAGTCATGT
1 TTATGCAGAAATGTGATTATTGTGTCCTATGTTCAAAGTTTAAACGATCTAGTTACTAGTCATGT
2199762 GGATTGCATGGGCGGACCTATATGGCCCAGGAAGTAGCAAATGCATACCTATTTTTCTTAAAAAA
66 GGATTGCATGGGCGGACCTATATGGCCCAGGAAGTAGCAAATGCATACCTATTTTTCTTAAAAAA
2199827 ATATCAGCATTTAAACTTTGAACATAGGACACAATAATCACATTTCTGCATAAGATTTCTTGAGC
131 ATATCAGCATTTAAACTTTGAACATAGGACACAATAATCACATTTCTGCATAAGATTTCTTGAGC
2199892 TTTGTGCTCTTTGACGAGAGTAAGAAATCAATGTCAACCTTTTATTTTAAAAATTTAAATTAAAA
196 TTTGTGCTCTTTGACGAGAGTAAGAAATCAATGTCAACCTTTTATTTTAAAAATTTAAATTAAAA
2199957 AAATACTGATTAAAATAATATATCATTTTACCTTTTACAACAATTCATCTCGCCTTTTTTACTTT
261 AAATACTGATTAAAATAATATATCATTTTACCTTTTACAACAATTCATCTCGCCTTTTTTACTTT
2200022 CTCTCATTTTCCTTAAAAAAATATAAATATTTAATATATTATATTAAGAGTTAAAAATTATGCAC
326 CTCTCATTTTCCTTAAAAAAATATAAATATTTAATATATTATATTAAGAGTTAAAAATTATGCAC
2200087 ACATCTTTCTTGAGCTCTGTGCTCTTTAAGGTAGGTAATAAACCAATGTCAACCTTTTATTCTAA
391 ACATCTTTCTTGAGCTCTGTGCTCTTTAAGGTAGGTAATAAACCAATGTCAACCTTTTATTCTAA
*
2200152 ATTTTTAAATTAAAAAATATTGATTAAAATAATATATT
456 ATTTTTAAATTAAAAAATATTGATTAAAATAAAATATT
2200190 CTATTTTATA
Statistics
Matches: 492, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
502 492 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (502 bp):
TTATGCAGAAATGTGATTATTGTGTCCTATGTTCAAAGTTTAAACGATCTAGTTACTAGTCATGT
GGATTGCATGGGCGGACCTATATGGCCCAGGAAGTAGCAAATGCATACCTATTTTTCTTAAAAAA
ATATCAGCATTTAAACTTTGAACATAGGACACAATAATCACATTTCTGCATAAGATTTCTTGAGC
TTTGTGCTCTTTGACGAGAGTAAGAAATCAATGTCAACCTTTTATTTTAAAAATTTAAATTAAAA
AAATACTGATTAAAATAATATATCATTTTACCTTTTACAACAATTCATCTCGCCTTTTTTACTTT
CTCTCATTTTCCTTAAAAAAATATAAATATTTAATATATTATATTAAGAGTTAAAAATTATGCAC
ACATCTTTCTTGAGCTCTGTGCTCTTTAAGGTAGGTAATAAACCAATGTCAACCTTTTATTCTAA
ATTTTTAAATTAAAAAATATTGATTAAAATAAAATATTGATTAAAAA
Found at i:2212550 original size:2 final size:2
Alignment explanation
Indices: 2212543--2212571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2212533 AACAATTAAG
2212543 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2212572 TCATTTTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2213583 original size:219 final size:219
Alignment explanation
Indices: 2213204--2213641 Score: 790
Period size: 219 Copynumber: 2.0 Consensus size: 219
2213194 CTACGCAATA
*
2213204 ACGATAGTTAAAAAAAACCGTTAAGTAACATGTGATGTTTATATCTTTTTATAATATTTTTTCCA
1 ACGATAGTTAAAAAAAACCGTTAAGTAACATGTGATATTTATATCTTTTTATAATATTTTTTCCA
*
2213269 AAAAATCTTAATATTATTATTATTAAAAAAACAAATTTTACTGAAATTACAAAAAAGACTTGCAA
66 AAAAATCTTAATAATATTATTATTAAAAAAACAAATTTTACTGAAATTACAAAAAAGACTTGCAA
* *
2213334 TCCTAAAATCTCCCATTTCAACCATTACCAAATGTCATTATCGACCTTTTTCGTTATCGTCGGAG
131 TCCTAAAATCTCCCATTTCAACCATTACCAAATGTCATTATCGACCTTTTTCGTCATCGTCGAAG
2213399 GCCACTCACCCGTCGTCGACCATC
196 GCCACTCACCCGTCGTCGACCATC
*
2213423 ACGATAGTTAAAAAAAAAACCGTTAAGTGACATGTGATATTTATATCTTTTTATAAT-TTTTTTC
1 ACGATAGTT--AAAAAAAACCGTTAAGTAACATGTGATATTTATATCTTTTTATAATATTTTTTC
2213487 CAAAAAATCTTAATAATATTATTATT-AAAAAACAAATTTTACTGAAATTACAAAAAAGACTTGC
64 CAAAAAATCTTAATAATATTATTATTAAAAAAACAAATTTTACTGAAATTACAAAAAAGACTTGC
2213551 AATCCTAAAATCTCCCATTTCAACCATTACCAAATGTCATTATCGACCTTTTTCGTCATCGTCGA
129 AATCCTAAAATCTCCCATTTCAACCATTACCAAATGTCATTATCGACCTTTTTCGTCATCGTCGA
*
2213616 AGGCCACTCACCCGTCGTCGATCATC
194 AGGCCACTCACCCGTCGTCGACCATC
2213642 CCTCTTGTCG
Statistics
Matches: 211, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
219 135 0.64
220 32 0.15
221 44 0.21
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (219 bp):
ACGATAGTTAAAAAAAACCGTTAAGTAACATGTGATATTTATATCTTTTTATAATATTTTTTCCA
AAAAATCTTAATAATATTATTATTAAAAAAACAAATTTTACTGAAATTACAAAAAAGACTTGCAA
TCCTAAAATCTCCCATTTCAACCATTACCAAATGTCATTATCGACCTTTTTCGTCATCGTCGAAG
GCCACTCACCCGTCGTCGACCATC
Found at i:2213897 original size:16 final size:17
Alignment explanation
Indices: 2213868--2213900 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2213858 ATATTTTAAT
2213868 TTTTTAAAAGAATATTA
1 TTTTTAAAAGAATATTA
2213885 TTTTTAAAA-AATATTA
1 TTTTTAAAAGAATATTA
2213901 ACGCGACACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTTTAAAAGAATATTA
Found at i:2215644 original size:18 final size:15
Alignment explanation
Indices: 2215604--2215637 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2215594 TTTTGGGGTT
2215604 TATATTTTCTAATAA
1 TATATTTTCTAATAA
2215619 TATATTTTCTAATAA
1 TATATTTTCTAATAA
2215634 TATA
1 TATA
2215638 CTATTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTTTCTAATAA
Found at i:2221088 original size:51 final size:51
Alignment explanation
Indices: 2221009--2221118 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 51
2220999 CCTTCTTTTA
*
2221009 CTTAATTTTAATTAGAATGAATGTATTGCTTATCATTTTGGGTTTCAAGTG
1 CTTAATTTTAATTAGAATGAATGGATTGCTTATCATTTTGGGTTTCAAGTG
* *
2221060 TTTAATTTTAATTAGAATGAATGGATTGCTTATCATTTTGGGTTTTAAGTG
1 CTTAATTTTAATTAGAATGAATGGATTGCTTATCATTTTGGGTTTCAAGTG
2221111 CTTAATTT
1 CTTAATTT
2221119 GTGATTTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.49
Consensus pattern (51 bp):
CTTAATTTTAATTAGAATGAATGGATTGCTTATCATTTTGGGTTTCAAGTG
Found at i:2224067 original size:29 final size:29
Alignment explanation
Indices: 2224025--2224099 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
2224015 AACCCAACCA
**
2224025 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
2224054 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
2224083 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
2224100 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:2224105 original size:29 final size:29
Alignment explanation
Indices: 2224026--2224113 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
2224016 ACCCAACCAT
* * ****
2224026 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
2224055 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
2224084 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
2224113 A
1 A
2224114 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:2234188 original size:21 final size:18
Alignment explanation
Indices: 2234139--2234186 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
2234129 TGGCTTTTTG
2234139 TTCTTTAATAATTGAATT
1 TTCTTTAATAATTGAATT
2234157 TTCTTTAATAATTGAATT
1 TTCTTTAATAATTGAATT
2234175 TTCTTTAATAAT
1 TTCTTTAATAAT
2234187 AAAAAATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (18 bp):
TTCTTTAATAATTGAATT
Found at i:2239499 original size:19 final size:19
Alignment explanation
Indices: 2239475--2239513 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2239465 AAGTATAATT
2239475 ATATCATTTTTAAAATTTA
1 ATATCATTTTTAAAATTTA
2239494 ATATCATTTTTAAAATTTA
1 ATATCATTTTTAAAATTTA
2239513 A
1 A
2239514 GACTGATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATCATTTTTAAAATTTA
Found at i:2239523 original size:19 final size:19
Alignment explanation
Indices: 2239477--2239525 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2239467 GTATAATTAT
*
2239477 ATCATTTTTAAAATTTAAT
1 ATCATTTTTAAAATTTAAG
2239496 ATCATTTTTAAAATTTAAG
1 ATCATTTTTAAAATTTAAG
*
2239515 ACTGATTTTTA
1 A-TCATTTTTA
2239526 GGTATTATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (19 bp):
ATCATTTTTAAAATTTAAG
Found at i:2243755 original size:28 final size:26
Alignment explanation
Indices: 2243697--2243773 Score: 75
Period size: 26 Copynumber: 2.8 Consensus size: 26
2243687 TTTTATATGT
*
2243697 TTTCATTAT-AAATTTTATTGATAATTTA
1 TTTCATTTTAAAATTTTA-T-A-AATTTA
*
2243725 TTTACTTTTTTAAAATTTTATAAATTTA
1 TTT-C-ATTTTAAAATTTTATAAATTTA
*
2243753 TTTCATTTTAAATTTTTATAA
1 TTTCATTTTAAAATTTTATAA
2243774 GTTCAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 15 0.36
27 1 0.02
28 12 0.29
29 2 0.05
30 4 0.10
31 8 0.19
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (26 bp):
TTTCATTTTAAAATTTTATAAATTTA
Found at i:2247161 original size:20 final size:21
Alignment explanation
Indices: 2247136--2247177 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2247126 TTTGTTTATT
2247136 GCTGAATG-GAACCATTCAGC
1 GCTGAATGTGAACCATTCAGC
*
2247156 GCTGAATGTTGAACCGTTCAGC
1 GCTGAATG-TGAACCATTCAGC
2247178 ATTCAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
GCTGAATGTGAACCATTCAGC
Found at i:2248833 original size:200 final size:205
Alignment explanation
Indices: 2248457--2248849 Score: 519
Period size: 200 Copynumber: 1.9 Consensus size: 205
2248447 ATTTAATTCT
** * *
2248457 ATCAAATCGAATTAAATTCAGATTTTTTTTGTTATCCCTACCTAACATCTAATACGTTAAATAAA
1 ATCAAATCGAATTAAATTCAGA-TTTTTTCATCATCCCTACCTAACATCCAATACGTTAAATAAA
* * * * * * * *
2248522 GTGTAAGATTGAGGCGAGCCATCTACGATATCACCCAAATATTTTTTTTCTTTTTGTATAGTTTA
65 GCGTAAGACTGAGACAAACCATCTACGATATCACCCAAATA-TTATTTTCTTTTTATATACTTTA
* *
2248587 TAATTTATATAATAAATTGACACTGATCAAATTAGGTGATAATTAAATGAG-TTTTAAATGAATT
129 TAACTTATATAATAAATTGACACTGATCAAAATAGGTGATAATTAAATGAGTTTTTAAATGAATT
2248651 GAATTGAACCCA
194 GAATTGAACCCA
* * *
2248663 ATCAAATCGAATTGAATTTAGA-TTTTTCATCATCCC-ACCTAACATCCAATATGTTAAATAAAG
1 ATCAAATCGAATTAAATTCAGATTTTTTCATCATCCCTACCTAACATCCAATACGTTAAATAAAG
* * * *
2248726 CGTAAGACTGAGATAAATCGTCTACGATATCATCCAAATA-TATTTTC-TTTTATATACTTTATA
66 CGTAAGACTGAGACAAACCATCTACGATATCACCCAAATATTATTTTCTTTTTATATACTTTATA
*
2248789 ACTTATATAATAAATTGACA-TCGATCAAAATAGGTTATAATTAAATGAGTTTTTAAATGAA
131 ACTTATATAATAAATTGACACT-GATCAAAATAGGTGATAATTAAATGAGTTTTTAAATGAA
2248850 ATGCCATGCT
Statistics
Matches: 163, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
199 1 0.01
200 58 0.36
201 17 0.10
203 56 0.34
204 11 0.07
206 20 0.12
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (205 bp):
ATCAAATCGAATTAAATTCAGATTTTTTCATCATCCCTACCTAACATCCAATACGTTAAATAAAG
CGTAAGACTGAGACAAACCATCTACGATATCACCCAAATATTATTTTCTTTTTATATACTTTATA
ACTTATATAATAAATTGACACTGATCAAAATAGGTGATAATTAAATGAGTTTTTAAATGAATTGA
ATTGAACCCA
Found at i:2249375 original size:39 final size:39
Alignment explanation
Indices: 2249321--2249398 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
2249311 ACTGAGAAAG
* *
2249321 AATATATCAGCTTCTATACGTGAGAAGATGAAGGGAGTT
1 AATATATCAGCTTCTATACGAGAGAAGATGAAGGAAGTT
*
2249360 AATATATCAGCTTCTATATGAGAGAAGATGAAGGAAGTT
1 AATATATCAGCTTCTATACGAGAGAAGATGAAGGAAGTT
2249399 TTCATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.28
Consensus pattern (39 bp):
AATATATCAGCTTCTATACGAGAGAAGATGAAGGAAGTT
Found at i:2259529 original size:21 final size:23
Alignment explanation
Indices: 2259503--2259550 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
2259493 TGCCTGCAAT
2259503 ATTAGGTGCAACAATG-TT-AAA
1 ATTAGGTGCAACAATGTTTGAAA
*
2259524 ATTAGGTGCAATAATGTTTGAAA
1 ATTAGGTGCAACAATGTTTGAAA
2259547 ATTA
1 ATTA
2259551 AATGGGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTAGGTGCAACAATGTTTGAAA
Found at i:2274235 original size:20 final size:20
Alignment explanation
Indices: 2274210--2274357 Score: 172
Period size: 20 Copynumber: 7.3 Consensus size: 20
2274200 AATTGGGAAA
*
2274210 ATCGCAATACGATACTGACT
1 ATCGCAATGCGATACTGACT
2274230 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
2274250 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2274270 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
2274290 ATCGTAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
2274311 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
2274331 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
2274351 TTCGCAA
1 ATCGCAA
2274358 CACGATTTAC
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 96 0.86
21 12 0.11
22 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2274358 original size:20 final size:20
Alignment explanation
Indices: 2274312--2274364 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2274302 TAATACAAAA
* *
2274312 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2274332 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
2274352 TCGCAACACGATT
1 TCGCAACGCGATT
2274365 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2274918 original size:19 final size:19
Alignment explanation
Indices: 2274880--2274946 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2274870 TTCGAGAATG
2274880 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
2274900 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
2274919 AAAATCGCAACGTGAAACC
1 AAAATCGCAACGCGAAATA
2274938 AAAATCGCA
1 AAAATCGCA
2274947 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 29 0.73
20 11 0.28
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:2275004 original size:14 final size:14
Alignment explanation
Indices: 2274985--2275038 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
2274975 TCATTTCGCT
2274985 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2274999 TTGCGATAGTCATTTCGCG
1 TTGCGAT--TC---TCTCG
2275018 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
2275032 TTGCGAT
1 TTGCGAT
2275039 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 18 0.55
16 2 0.06
17 2 0.06
19 11 0.33
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2275012 original size:33 final size:33
Alignment explanation
Indices: 2274964--2275062 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2274954 TTTCATTTCG
** *
2274964 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2274997 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
2275030 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
2275063 ATTATCTCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 47 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:2275064 original size:20 final size:19
Alignment explanation
Indices: 2274942--2275087 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
2274932 GAAACCAAAA
* *
2274942 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
2274961 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
2274980 TCGCTTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2274996 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
2275013 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
2275029 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
2275046 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
2275066 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
2275086 TC
1 TC
2275088 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 21 0.21
16 2 0.02
17 2 0.02
19 45 0.45
20 30 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:2277296 original size:42 final size:42
Alignment explanation
Indices: 2277174--2277378 Score: 180
Period size: 42 Copynumber: 4.9 Consensus size: 42
2277164 CCCGACTCGC
* * * *
2277174 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * * * *
2277216 CTATCATTCCTCGAGAGTCCCCT-CCACCATTCAAGAGGCAA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
** * * *
2277257 CTGTCATCCCTCAAGAGTCCACTCTTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
* * * *
2277299 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
** * *
2277341 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
2277379 CCCGATTCAC
Statistics
Matches: 124, Mismatches: 37, Indels: 4
0.75 0.22 0.02
Matches are distributed among these distances:
41 31 0.25
42 89 0.72
43 4 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
Found at i:2277313 original size:83 final size:84
Alignment explanation
Indices: 2277174--2277348 Score: 316
Period size: 83 Copynumber: 2.1 Consensus size: 84
2277164 CCCGACTCGC
2277174 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2277239 -CCACCATTCAAGAGGCAA
66 CCCACCATTCAAGAGGCAA
*
2277257 CTGTCATCCCTCAAGAGTCCACTCTTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
* *
2277322 CCCACCGTTCAAGAGGCCA
66 CCCACCATTCAAGAGGCAA
2277341 CTGTCATC
1 CTGTCATC
2277349 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 64 0.73
84 24 0.27
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCATTCAAGAGGCAA
Found at i:2277336 original size:21 final size:21
Alignment explanation
Indices: 2277312--2277378 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2277302 TCATTCCTCG
2277312 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2277333 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2277354 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2277375 AGAG
1 AGAG
2277379 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2278768 original size:14 final size:14
Alignment explanation
Indices: 2278733--2278768 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2278723 GATTGTTTAA
2278733 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
2278747 GTGA-TTGTAAAAG
1 TTGATTTGTAAAAG
2278760 TTGATTTGT
1 TTGATTTGT
2278769 TTAATTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:2278914 original size:14 final size:14
Alignment explanation
Indices: 2278895--2278951 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2278885 GCGAAATGAA
2278895 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2278909 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2278928 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2278942 AATCGCAACG
1 AATCGCAACG
2278952 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2278927 original size:33 final size:33
Alignment explanation
Indices: 2278885--2278966 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
2278875 CTATCGAAAT
2278885 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
2278918 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
* *
2278951 GCGAAATTAAATTCGC
1 GCGAAATGAAAATCGC
2278967 GTTGCGATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGAGAGAATCGCAAC
Found at i:2278933 original size:19 final size:19
Alignment explanation
Indices: 2278885--2278937 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
2278875 CTATCGAAAT
2278885 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
*
2278903 -CG--A-GAGAATCGCAAC
1 GCGAAATGAAAATCGCAAC
2278918 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
2278937 G
1 G
2278938 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:2278984 original size:19 final size:19
Alignment explanation
Indices: 2278962--2279112 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
2278952 CGAAATTAAA
2278962 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2278981 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2278996 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
2279014 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
2279028 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2279047 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2279062 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
2279080 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
2279099 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2279113 AGACATTAAA
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2279008 original size:33 final size:32
Alignment explanation
Indices: 2278966--2279092 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
2278956 ATTAAATTCG
2278966 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
2278999 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2279032 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2279065 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2279093 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2279044 original size:66 final size:66
Alignment explanation
Indices: 2278959--2279091 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2278949 ACGCGAAATT
*
2278959 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2279024 G
66 G
*
2279025 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2279090 G
66 G
2279091 A
1 A
2279092 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2281397 original size:12 final size:12
Alignment explanation
Indices: 2281380--2281404 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2281370 TCTTCGGGGA
2281380 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2281392 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2281404 C
1 C
2281405 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2281613 original size:24 final size:24
Alignment explanation
Indices: 2281579--2281632 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2281569 CTGAAACATC
*
2281579 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
2281603 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2281627 ATCAAA
1 ATCAAA
2281633 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2282444 original size:20 final size:21
Alignment explanation
Indices: 2282419--2282468 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2282409 TTCCTAATTT
*
2282419 GCAATGCGAA-TAAGTAAATC
1 GCAATGCGAATTAAGAAAATC
**
2282439 GCAATGCGAATTTGGAAAATC
1 GCAATGCGAATTAAGAAAATC
2282460 GCAATGCGA
1 GCAATGCGA
2282469 TACTGACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
GCAATGCGAATTAAGAAAATC
Found at i:2282542 original size:20 final size:20
Alignment explanation
Indices: 2282453--2282544 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
2282443 TGCGAATTTG
* *
2282453 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
2282473 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
2282493 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
2282514 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
2282534 GAAAATCGCAA
1 GAAAATCGCAA
2282545 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:2282763 original size:14 final size:14
Alignment explanation
Indices: 2282744--2282773 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2282734 TCATTTGACT
*
2282744 ATCGCAACGGGAAA
1 ATCGCAACGCGAAA
2282758 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2282772 AT
1 AT
2282774 GGCTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:2282833 original size:20 final size:20
Alignment explanation
Indices: 2282758--2282825 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
2282748 CAACGGGAAA
2282758 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** **
2282778 ATCGCAATTCG-AAATGAAT
1 ATCGCAACGCGAAAATGGCT
2282797 AATCGCAACGCGAAAATGGCT
1 -ATCGCAACGCGAAAATGGCT
2282818 ATCGCAAC
1 ATCGCAAC
2282826 TAGAAAATCG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 6 0.16
20 26 0.68
21 6 0.16
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:2282893 original size:19 final size:19
Alignment explanation
Indices: 2282852--2282919 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2282842 GAAATGAAAA
2282852 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2282868 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2282885 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2282904 TCACATTGCGATTTTC
1 TCGCATTGCGATTTTC
2282920 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2283075 original size:14 final size:14
Alignment explanation
Indices: 2283056--2283089 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2283046 CATCAATTAA
2283056 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2283070 ACAAATCATCTTTT
1 ACAAATCAACATTT
2283084 ACAAAT
1 ACAAAT
2283090 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2285018 original size:19 final size:19
Alignment explanation
Indices: 2284953--2285086 Score: 92
Period size: 20 Copynumber: 7.5 Consensus size: 19
2284943 CACGAAACTT
*
2284953 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCG-AAATG
**
2284973 ACTATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATG
*** *
2284993 GCTATCGTAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2285012 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
2285026 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
2285045 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
2285059 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
2285078 -AAATCGCAA
1 AAAATCGCAA
2285087 CGACAAAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 4 0.04
17 4 0.04
18 11 0.12
19 22 0.24
20 26 0.29
21 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:2285031 original size:14 final size:14
Alignment explanation
Indices: 2285012--2285102 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
2285002 ATGCGAAATG
2285012 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2285026 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2285045 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2285059 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2285075 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2285091 AAAATCGCAACG
1 AAAATCGCAACG
2285103 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2285087 original size:32 final size:33
Alignment explanation
Indices: 2284996--2285107 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
2284986 GGAAATGGCT
*
2284996 ATCGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2285029 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2285062 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2285094 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2285108 CACAAATCGC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 29 0.38
33 48 0.62
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2285115 original size:65 final size:66
Alignment explanation
Indices: 2284996--2285118 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
2284986 GGAAATGGCT
* * *
2284996 ATCGTAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
2285061 A
66 A
2285062 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
2285119 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.70
66 15 0.28
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:2285155 original size:14 final size:14
Alignment explanation
Indices: 2285136--2285193 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2285126 TTTCATTTCG
2285136 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2285150 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2285166 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2285182 CGTTGCGATTTT
1 CGTTGCGATTTT
2285194 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2285200 original size:33 final size:33
Alignment explanation
Indices: 2285119--2285209 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
2285109 ACAAATCGCA
*
2285119 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2285152 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2285184 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2285210 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2285246 original size:20 final size:20
Alignment explanation
Indices: 2285194--2285237 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2285184 TTGCGATTTT
*
2285194 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
2285213 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
2285233 CATTT
1 CATTT
2285238 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:2285750 original size:18 final size:18
Alignment explanation
Indices: 2285727--2285774 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2285717 CGGGTCGATC
*
2285727 AGATGATGGCTCTGGGTG
1 AGATGATGGCTCTGGGCG
* *
2285745 AGATGATAGCTTTGGGCG
1 AGATGATGGCTCTGGGCG
*
2285763 AGGTGATGGCTC
1 AGATGATGGCTC
2285775 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.12, G:0.42, T:0.27
Consensus pattern (18 bp):
AGATGATGGCTCTGGGCG
Found at i:2287142 original size:20 final size:20
Alignment explanation
Indices: 2287094--2287152 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2287084 AATAGTTTCT
** *
2287094 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
2287114 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
2287134 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
2287153 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:2287441 original size:22 final size:22
Alignment explanation
Indices: 2287414--2287457 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2287404 GATGGAGATA
2287414 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2287436 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2287458 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2287671 original size:20 final size:20
Alignment explanation
Indices: 2287646--2287697 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2287636 ATTATGTATT
2287646 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
2287666 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
2287686 ATCTCGTTGCGA
1 ATCGCGTTGCGA
2287698 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:2287731 original size:20 final size:20
Alignment explanation
Indices: 2287706--2287759 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2287696 GATTTTGTAT
2287706 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
2287726 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
2287746 TATCGCATTGCGAT
1 TATCGCATTGCGAT
2287760 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:2287731 original size:61 final size:61
Alignment explanation
Indices: 2287625--2287762 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
2287615 CGCTTTGAAA
* * * * *
2287625 ATCGTATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2287686 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2287747 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2287763 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2287778 original size:61 final size:61
Alignment explanation
Indices: 2287645--2287780 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 61
2287635 GATTATGTAT
* * * * * ** *
2287645 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
* * *
2287706 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAA
2287768 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
2287781 TTACTTATTC
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
61 60 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:2287879 original size:20 final size:20
Alignment explanation
Indices: 2287856--2287901 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2287846 CAACGCGAAT
*
2287856 TTGCGATAATGGAGATCGCG
1 TTGCGATAATAGAGATCGCG
* *
2287876 TTGCGA-ATTAGCGATCGCG
1 TTGCGATAATAGAGATCGCG
2287895 TTGCGAT
1 TTGCGAT
2287902 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCG
Found at i:2291815 original size:21 final size:21
Alignment explanation
Indices: 2291777--2291824 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2291767 ATCGCTACGG
*
2291777 TGCTGATATGATAATTCACGAA
1 TGCTGATATGACAATTCAC-AA
*
2291799 -GCTGATATGACAGTTCACAA
1 TGCTGATATGACAATTCACAA
2291819 TGCTGA
1 TGCTGA
2291825 CGTGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCTGATATGACAATTCACAA
Found at i:2292707 original size:21 final size:20
Alignment explanation
Indices: 2292657--2292696 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2292647 ACTATAGACA
* *
2292657 ATCACATTAACATCGTGAAT
1 ATCACATCAGCATCGTGAAT
2292677 ATCACATCAGCATCGTGAAT
1 ATCACATCAGCATCGTGAAT
2292697 TGTCACTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (20 bp):
ATCACATCAGCATCGTGAAT
Found at i:2293495 original size:29 final size:29
Alignment explanation
Indices: 2293463--2293561 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
2293453 TTTAAATTGG
*
2293463 TCCTTAAACTATTGAATATTCCAAATTCA
1 TCCTTAAACTATTGAATATTCTAAATTCA
* *
2293492 TCCTCATACTA-TGAATCTCATTCTAAATT-A
1 TCCTTAAACTATTGAA--T-ATTCTAAATTCA
* * *
2293522 GTCCTTAAACTTTTGAACATTCTAATTTCA
1 -TCCTTAAACTATTGAATATTCTAAATTCA
* *
2293552 CCCCTAAACT
1 TCCTTAAACT
2293562 GTGACTCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 4 0.07
29 26 0.48
30 3 0.06
31 17 0.31
32 4 0.07
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
TCCTTAAACTATTGAATATTCTAAATTCA
Found at i:2303015 original size:17 final size:20
Alignment explanation
Indices: 2302977--2303013 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
2302967 TTTTAAAATA
2302977 ATTAAAATAATTTATTTTTT
1 ATTAAAATAATTTATTTTTT
2302997 ATTAAAAT-A-TTATTTTT
1 ATTAAAATAATTTATTTTT
2303014 ATAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTAAAATAATTTATTTTTT
Found at i:2303201 original size:24 final size:26
Alignment explanation
Indices: 2303174--2303230 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
2303164 TTAGATTATT
2303174 ATATTAAT-ATTA-AAT-ATTTAAATA
1 ATATTAATCATTATAATAATTT-AATA
*
2303198 ATATTATTCATTATTAATAATTTAATA
1 ATATTAATCATTA-TAATAATTTAATA
2303225 ATATTA
1 ATATTA
2303231 TTTCAGTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 7 0.25
25 4 0.14
27 13 0.46
28 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTAATCATTATAATAATTTAATA
Found at i:2303306 original size:53 final size:52
Alignment explanation
Indices: 2303208--2303308 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 52
2303198 ATATTATTCA
** * *
2303208 TTATTAATAATTTAATAATATTATTTCAGTGAAATTAATAAATAATATAAATT
1 TTATTAATAATTTAATAATATTATTAAAATAAAATTAAT-AATAATATAAATT
*
2303261 TTATTAATAATTTATTATATATTATTAAAATAAAATATAAT-ATAATAT
1 TTATTAATAATTTAATA-ATATTATTAAAATAAAAT-TAATAATAATAT
2303309 CTTATATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
53 23 0.56
54 14 0.34
55 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (52 bp):
TTATTAATAATTTAATAATATTATTAAAATAAAATTAATAATAATATAAATT
Found at i:2303322 original size:23 final size:23
Alignment explanation
Indices: 2303296--2303349 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2303286 TAAAATAAAA
*
2303296 TATAATATAATAT-CTTATATTAT
1 TATAATATAAT-TGATTATATTAT
*
2303319 TATAATATAATTGATTATTTTAT
1 TATAATATAATTGATTATATTAT
2303342 TATAATAT
1 TATAATAT
2303350 TAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TATAATATAATTGATTATATTAT
Found at i:2303367 original size:22 final size:23
Alignment explanation
Indices: 2303339--2303385 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2303329 TTGATTATTT
2303339 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
2303361 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
2303384 TA
1 TA
2303386 AATCTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:2306017 original size:23 final size:24
Alignment explanation
Indices: 2305977--2306030 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
2305967 CAATGATTAA
2305977 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
2306001 ATGTAAATT-ATATAGTTTAATTT
1 ATGTAAATTAATATAGTTTAATTT
*
2306024 ATATAAA
1 ATGTAAA
2306031 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAGTTTAATTT
Found at i:2306299 original size:23 final size:23
Alignment explanation
Indices: 2306273--2306336 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2306263 TTTAATTGAT
* *
2306273 AATTTAAATAACATTTGATTTAA
1 AATTTGAATAACATTTGATCTAA
*
2306296 AATTTGAATAATATTTGATCTAA
1 AATTTGAATAACATTTGATCTAA
2306319 AATTTGAATAACATTTGA
1 AATTTGAATAACATTTGA
2306337 GTTATTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (23 bp):
AATTTGAATAACATTTGATCTAA
Found at i:2306313 original size:11 final size:11
Alignment explanation
Indices: 2306273--2306336 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
2306263 TTTAATTGAT
*
2306273 AATTTAAATAA
1 AATTTGAATAA
* *
2306284 CATTTGATTTAA
1 AATTTGA-ATAA
2306296 AATTTGAATAA
1 AATTTGAATAA
* *
2306307 TATTTGATCTAA
1 AATTTGA-ATAA
2306319 AATTTGAATAA
1 AATTTGAATAA
*
2306330 CATTTGA
1 AATTTGA
2306337 GTTATTCAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 23 0.56
12 18 0.44
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (11 bp):
AATTTGAATAA
Found at i:2307182 original size:29 final size:29
Alignment explanation
Indices: 2307090--2307239 Score: 88
Period size: 29 Copynumber: 5.1 Consensus size: 29
2307080 AACTATATAC
* * * *
2307090 TATATTAATATAAATTATAGTTAAGATAAT
1 TATATTAATATAAACTATAGTTTATA-AAG
* * * *
2307120 TAACATTAATATAAACTATA-TACTCTATAG
1 T-ATATTAATATAAACTATAGT-TTATAAAG
*
2307150 TATATTAATATAAACTATAGTTTATAAAT
1 TATATTAATATAAACTATAGTTTATAAAG
* ** ** *
2307179 TATA-TATTATAAGTTATAAATTATATAG
1 TATATTAATATAAACTATAGTTTATAAAG
* * * *
2307207 TACACTAATATAAACTATTGTTTATAAAC
1 TATATTAATATAAACTATAGTTTATAAAG
2307236 TATA
1 TATA
2307240 GGTTACATAT
Statistics
Matches: 86, Mismatches: 30, Indels: 9
0.69 0.24 0.07
Matches are distributed among these distances:
28 20 0.23
29 44 0.51
30 5 0.06
31 17 0.20
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (29 bp):
TATATTAATATAAACTATAGTTTATAAAG
Found at i:2307189 original size:21 final size:21
Alignment explanation
Indices: 2307129--2307205 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
2307119 TTAACATTAA
* *
2307129 TATAAACTATATACTCTATAGTA
1 TATAAATTATATA-T-TATAGTT
* * *
2307152 TATTAA-TATAAACTATAGTT
1 TATAAATTATATATTATAGTT
2307172 TATAAATTATATATTATAAG-T
1 TATAAATTATATATTAT-AGTT
2307193 TATAAATTATATA
1 TATAAATTATATA
2307206 GTACACTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 11 0.24
21 22 0.49
22 7 0.16
23 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (21 bp):
TATAAATTATATATTATAGTT
Found at i:2307267 original size:20 final size:20
Alignment explanation
Indices: 2307244--2307320 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
2307234 ACTATAGGTT
2307244 ACATATATATAGTTTATATA
1 ACATATATATAGTTTATATA
* * *
2307264 ACATATAAATAGATTGTAT-
1 ACATATATATAGTTTATATA
* *
2307283 ATATACATATAGTTTATATA
1 ACATATATATAGTTTATATA
*
2307303 TAC-TATACATAGTTTATA
1 -ACATATATATAGTTTATA
2307321 CATATATATA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 14 0.32
20 29 0.66
21 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (20 bp):
ACATATATATAGTTTATATA
Found at i:2307326 original size:39 final size:38
Alignment explanation
Indices: 2307243--2307330 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
2307233 AACTATAGGT
*
2307243 TACATAT-ATATAGTTTATATAACATATAAATAGATTG
1 TACATATAATATAGTTTATATAACATATAAATAGATTA
* * *
2307280 TATATATACATATAGTTTATATATAC-TATACATAGTTTA
1 TACATATA-ATATAGTTTATATA-ACATATAAATAGATTA
2307319 TACATAT-ATATA
1 TACATATAATATA
2307331 CTATAAGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
37 11 0.26
39 30 0.70
40 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (38 bp):
TACATATAATATAGTTTATATAACATATAAATAGATTA
Found at i:2307350 original size:35 final size:36
Alignment explanation
Indices: 2307311--2307384 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
2307301 TATACTATAC
*
2307311 ATAGTTT-ATACATATATATACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
**
2307346 ATAGTTTACATGTATACATATACTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
2307383 AT
1 AT
2307385 TAACTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 7 0.21
37 27 0.79
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:2307594 original size:19 final size:19
Alignment explanation
Indices: 2307587--2307658 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
2307577 TTTATATATA
*
2307587 TATATATATATATATAGGT
1 TATATATATATATATAGTT
* *
2307606 TATATATATGTATACAGTT
1 TATATATATATATATAGTT
*
2307625 TATATATACTATACATAGTT
1 TATATATA-TATATATAGTT
* *
2307645 TATACATAAATATA
1 TATATATATATATA
2307659 ATATAAGTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
19 28 0.65
20 15 0.35
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (19 bp):
TATATATATATATATAGTT
Found at i:2307941 original size:18 final size:17
Alignment explanation
Indices: 2307915--2307955 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2307905 ATACATAATT
*
2307915 TATATATATAGCTTATAA
1 TATAAATATAGCTTAT-A
*
2307933 TATAAATATAGTTTATA
1 TATAAATATAGCTTATA
2307950 TATAAA
1 TATAAA
2307956 GTTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (17 bp):
TATAAATATAGCTTATA
Found at i:2307991 original size:19 final size:19
Alignment explanation
Indices: 2307938--2307991 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
2307928 TATAATATAA
2307938 ATATAGTTTATATATAAAGTT
1 ATATA-TTTA-ATATAAAGTT
2307959 ATATTATATTAATATAAA-TT
1 ATA-TAT-TTAATATAAAGTT
2307979 ATATACTTTAATA
1 ATATA-TTTAATA
2307992 CTTTATATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.27
20 6 0.20
21 11 0.37
22 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
ATATATTTAATATAAAGTT
Found at i:2308007 original size:9 final size:9
Alignment explanation
Indices: 2307977--2308009 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2307967 TTAATATAAA
2307977 TTATATACT
1 TTATATACT
2307986 TTA-ATACT
1 TTATATACT
*
2307994 TTATATAGT
1 TTATATACT
2308003 TTATATA
1 TTATATA
2308010 TTGTTTACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (9 bp):
TTATATACT
Found at i:2308123 original size:13 final size:13
Alignment explanation
Indices: 2308107--2308163 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
2308097 TACTTAATAT
2308107 ACTATATATATAA
1 ACTATATATATAA
*
2308120 ACTATATACATAA
1 ACTATATATATAA
2308133 ATCTTATATATTATATA
1 A-C-TATATA-TATA-A
**
2308150 TTTATATATATAA
1 ACTATATATATAA
2308163 A
1 A
2308164 TTACATAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
13 14 0.40
14 5 0.14
15 12 0.34
16 3 0.09
17 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ACTATATATATAA
Found at i:2309311 original size:16 final size:16
Alignment explanation
Indices: 2309290--2309321 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2309280 ATGTAATATG
2309290 TCCTACTGAAAAATAA
1 TCCTACTGAAAAATAA
2309306 TCCTACTGAAAAATAA
1 TCCTACTGAAAAATAA
2309322 GAATGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
TCCTACTGAAAAATAA
Found at i:2317218 original size:60 final size:59
Alignment explanation
Indices: 2317163--2317274 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
2317153 CTATGACTCA
2317163 CATTCTAAATTAGTTC-TTAAACTTTTAAACATTTTAATTTTATCCCTAAATTATGATATT
1 CATTCTAAATTAG-TCATTAAACTTTTAAACATTTTAATTTTATCCCTAAATTATGATA-T
* * * *
2317223 CTTTCTAAATTAGTCATCAAACTTTTAAACGTTTCAATTTTATCTCC-AAATT
1 CATTCTAAATTAGTCATTAAACTTTTAAACATTTTAATTTTATC-CCTAAATT
2317275 TATCCAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 42 0.91
61 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (59 bp):
CATTCTAAATTAGTCATTAAACTTTTAAACATTTTAATTTTATCCCTAAATTATGATAT
Found at i:2327214 original size:131 final size:133
Alignment explanation
Indices: 2326962--2327227 Score: 394
Period size: 131 Copynumber: 2.0 Consensus size: 133
2326952 TCTTTTATCT
*
2326962 AACACTCGACTTTCTCCGTTAGTAAGAACCTATCAAACGACTTCAGTAATAAAAGAGAATGTTGT
1 AACACTCAACTTTCTCCGTTAGTAAGAACCTATCAAACGACTTCAGTAATAAAAGAGAATGTTGT
* * * * * *
2327027 TCTCCTTGAAGATTTCGAGTTTGAAAGGTTGTGTCTGAATGACATGTTTGCGTTATTGATAACTG
66 TCTCCTTAAAGATTTCGAGTTTGAAAGGCTATGTCTGAATGACATGTTTGCATTATTAATAACTA
2327092 AGA
131 AGA
* *
2327095 AACACTCAAC-TTCTCCGTTAGTAAGAACCTATCAAACGACTTCAGTAGT-AAAGAGAGTGTTGT
1 AACACTCAACTTTCTCCGTTAGTAAGAACCTATCAAACGACTTCAGTAATAAAAGAGAATGTTGT
* * *
2327158 TCTCCTTAAAGATTTCGAGTTTGAACGGCTATGTCT-ACATGGCATGTTTGTATTATTAATAACT
66 TCTCCTTAAAGATTTCGAGTTTGAAAGGCTATGTCTGA-ATGACATGTTTGCATTATTAATAACT
2327222 AAGA
130 AAGA
2327226 AA
1 AA
2327228 TATTTTAAAC
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
130 1 0.01
131 72 0.60
132 38 0.32
133 9 0.08
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (133 bp):
AACACTCAACTTTCTCCGTTAGTAAGAACCTATCAAACGACTTCAGTAATAAAAGAGAATGTTGT
TCTCCTTAAAGATTTCGAGTTTGAAAGGCTATGTCTGAATGACATGTTTGCATTATTAATAACTA
AGA
Found at i:2328590 original size:22 final size:23
Alignment explanation
Indices: 2328560--2328615 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2328550 AATATTCAAT
2328560 AAATTAAATATAAAAATACTA-A
1 AAATTAAATATAAAAATACTACA
* * *
2328582 AAATAAAAT-TTAAATTACTACA
1 AAATTAAATATAAAAATACTACA
2328604 AAATTAAATATA
1 AAATTAAATATA
2328616 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.33
22 17 0.63
23 1 0.04
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AAATTAAATATAAAAATACTACA
Found at i:2328646 original size:21 final size:21
Alignment explanation
Indices: 2328613--2328660 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2328603 AAAATTAAAT
* *
2328613 ATATAATTTAAAATTAAAAAA
1 ATATTATTAAAAATTAAAAAA
2328634 ATATTATTAAAAATTAAAAAA
1 ATATTATTAAAAATTAAAAAA
*
2328655 AAATTA
1 ATATTA
2328661 AGGATTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATTATTAAAAATTAAAAAA
Found at i:2337391 original size:60 final size:58
Alignment explanation
Indices: 2337283--2337510 Score: 221
Period size: 60 Copynumber: 3.8 Consensus size: 58
2337273 GTGTATATGT
* * * * * *
2337283 ATAGTTT-GGGATGAAATTGGAATCTTCAAAAAGTTAGGGGA-TCAATTTAGAATGAAGGTC
1 ATAGTTTAGGGATGAAATTGAAATATT-TAGAAGTTTGAGGACT-AATTTAGAATGAA--TC
* * *
2337343 ATATTTTAGGGATGAATTTGAAATGTTTAGAAGTTTGAGGACTAATTTAGAATGGTAATC
1 ATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTAATTTAGAAT-G-AATC
* *
2337403 ATAGTTTAGGGATGAAATT-AAATATTTAGAAGTTTGAAGACTAATTTAGAATGATAATT
1 ATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTAATTTAGAATG--AATC
* * *
2337462 ATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTT-AGGGACCAATTTA
1 ATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGA-GGACTAATTTA
2337511 AGTTGTATTT
Statistics
Matches: 144, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.01
59 55 0.38
60 68 0.47
61 18 0.12
62 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (58 bp):
ATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAGGACTAATTTAGAATGAATC
Found at i:2337455 original size:59 final size:60
Alignment explanation
Indices: 2337326--2337497 Score: 240
Period size: 59 Copynumber: 2.9 Consensus size: 60
2337316 TTAGGGGATC
* * * * *
2337326 AATTTAGAATGA-AGGTCATATTTTAGGGATGAATTTGAAATGTTTAGAAGTTTGAGGACT
1 AATTTAGAATGATA-ATCATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAAGACT
*
2337386 AATTTAGAATGGTAATCATAGTTTAGGGATGAAATT-AAATATTTAGAAGTTTGAAGACT
1 AATTTAGAATGATAATCATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAAGACT
* * *
2337445 AATTTAGAATGATAATTATAGTTTAGGGATGAAATTGAAACATTTAAAAGTTT
1 AATTTAGAATGATAATCATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTT
2337498 AGGGACCAAT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
59 55 0.55
60 44 0.44
61 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (60 bp):
AATTTAGAATGATAATCATAGTTTAGGGATGAAATTGAAATATTTAGAAGTTTGAAGACT
Found at i:2341778 original size:2 final size:2
Alignment explanation
Indices: 2341771--2341806 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2341761 AGGACTCATA
2341771 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
2341807 GCACACGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2343701 original size:21 final size:20
Alignment explanation
Indices: 2343619--2343772 Score: 73
Period size: 21 Copynumber: 7.7 Consensus size: 20
2343609 AATGACCAAC
**
2343619 AAATCGCAACGCGA-AAT-A
1 AAATCGCAACGCGATTTTCA
**
2343637 AAATCGCAACGCGA-TCCCA
1 AAATCGCAACGCGATTTTCA
* ** *
2343656 GAATCGCAAATC-AGTTTCCA
1 AAATCGCAACGCGA-TTTTCA
*
2343676 AAATCGCAACGCGATTCTTGA
1 AAATCGCAACGCGATT-TTCA
* * * *
2343697 AAATCGCGATGCGATAGTACA
1 AAATCGCAACGCGAT-TTTCA
* **
2343718 AATTCGCATTGCGATTTTCA
1 AAATCGCAACGCGATTTTCA
* * *
2343738 ATAATCGCAACGCGAATATGA
1 A-AATCGCAACGCGATTTTCA
2343759 AAATCGCAACGCGA
1 AAATCGCAACGCGA
2343773 ACACATAAAT
Statistics
Matches: 101, Mismatches: 28, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
18 15 0.15
19 10 0.10
20 32 0.32
21 44 0.44
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGATTTTCA
Found at i:2343765 original size:20 final size:20
Alignment explanation
Indices: 2343740--2343933 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2343730 GATTTTCAAT
* *
2343740 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2343760 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2343780 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2343800 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2343820 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2343840 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2343860 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2343880 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2343901 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2343921 AATCGCAACGCGA
1 AATCGCAACGCGA
2343934 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2343785 original size:40 final size:39
Alignment explanation
Indices: 2343740--2343933 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
2343730 GATTTTCAAT
* ** *
2343740 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
2343780 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
2343820 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
2343860 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
2343901 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
2343934 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:2343823 original size:60 final size:60
Alignment explanation
Indices: 2343740--2343932 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2343730 GATTTTCAAT
* ** * *
2343740 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2343800 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2343860 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2343921 AATCGCAACGCG
1 AATCGCAACGCG
2343933 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2344343 original size:33 final size:33
Alignment explanation
Indices: 2344304--2344371 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
2344294 TTCACTTAGA
*
2344304 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2344337 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2344370 TT
1 TT
2344372 CAAGTTAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.10, C:0.22, G:0.19, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2344498 original size:22 final size:20
Alignment explanation
Indices: 2344444--2344499 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2344434 ATTGCAGAAG
*
2344444 AGTCGCAACGAGATAAATGA
1 AGTCGCAACGAGAGAAATGA
*
2344464 AATCGCAACGAGAG-AATGA
1 AGTCGCAACGAGAGAAATGA
*
2344483 CTGTCGCAACGAGAGAA
1 -AGTCGCAACGAGAGAA
2344500 TCGCACGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 5 0.17
20 24 0.80
21 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAAATGA
Found at i:2344527 original size:33 final size:34
Alignment explanation
Indices: 2344488--2344554 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
2344478 AATGACTGTC
**
2344488 GCAACGAGAGAATCGC-ACGCGAAATGAAAATCG
1 GCAACGAGAGAATCGCAACGCGAAACCAAAATCG
2344521 GCAACGAGAGAATCGCAACGCGAAACCAAAATCG
1 GCAACGAGAGAATCGCAACGCGAAACCAAAATCG
2344555 CATTGCGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.52
34 15 0.48
ACGTcount: A:0.43, C:0.24, G:0.25, T:0.07
Consensus pattern (34 bp):
GCAACGAGAGAATCGCAACGCGAAACCAAAATCG
Found at i:2344574 original size:19 final size:19
Alignment explanation
Indices: 2344552--2344649 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2344542 GAAACCAAAA
*
2344552 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2344571 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2344585 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2344604 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2344618 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2344637 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2344650 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2344593 original size:14 final size:14
Alignment explanation
Indices: 2344574--2344663 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2344564 TTTCATTTCG
2344574 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2344588 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2344607 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2344621 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2344638 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2344654 CGTTGCGATT
1 CGTTGCGATT
2344664 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2344599 original size:33 final size:33
Alignment explanation
Indices: 2344557--2344671 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2344547 CAAAATCGCA
2344557 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2344590 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2344623 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2344656 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2344672 AACAAAAGAC
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2346589 original size:92 final size:93
Alignment explanation
Indices: 2346342--2346720 Score: 719
Period size: 92 Copynumber: 4.1 Consensus size: 93
2346332 TAGATTGCTT
*
2346342 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2346407 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2346435 AGTAAATTTGTTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-T
1 AGTAAATTTG-TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
2346499 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2346528 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2346592 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2346620 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2346685 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2346712 AGTAAATTT
1 AGTAAATTT
2346721 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
92 170 0.60
93 61 0.22
94 52 0.18
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2346804 original size:19 final size:19
Alignment explanation
Indices: 2346764--2346892 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2346754 TAGTTTACTT
* *
2346764 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2346784 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2346803 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2346822 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2346836 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2346855 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2346869 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2346888 TCGCA
1 TCGCA
2346893 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2346843 original size:33 final size:32
Alignment explanation
Indices: 2346800--2346892 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2346790 CGCGAAACCA
**
2346800 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2346832 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2346865 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2346893 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2346890 original size:52 final size:52
Alignment explanation
Indices: 2346764--2346892 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2346754 TAGTTTACTT
**
2346764 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2346816 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2346869 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2346893 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2346915 original size:19 final size:19
Alignment explanation
Indices: 2346888--2347005 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
2346878 GAAACCAAAA
*
2346888 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2346907 TCACGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2346923 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2346940 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2346956 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2346973 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
2346992 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
2347006 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
14 15 0.19
16 11 0.14
17 11 0.14
19 44 0.54
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2346929 original size:14 final size:14
Alignment explanation
Indices: 2346910--2346966 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2346900 TTTCATTTCA
2346910 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2346924 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2346941 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2346957 CGTTGCGATT
1 CGTTGCGATT
2346967 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2346935 original size:33 final size:33
Alignment explanation
Indices: 2346893--2346985 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
2346883 CAAAATCGCA
* *
2346893 TTGCGATTTTCATTTCACGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2346926 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2346959 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2346986 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2347011 original size:19 final size:19
Alignment explanation
Indices: 2346957--2347021 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
2346947 GCGATTCTGT
*
2346957 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGA-TTTAAGTTTCG
**
2346976 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTAAGTTTCG
2346995 CGTTGCGATTTAAGTTTCG
1 CGTTGCGATTTAAGTTTCG
*
2347014 TGTTGCGA
1 CGTTGCGA
2347022 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 3 0.08
19 37 0.93
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTAAGTTTCG
Found at i:2348920 original size:14 final size:14
Alignment explanation
Indices: 2348901--2348936 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2348891 ATTGTTTAAT
2348901 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2348915 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2348929 TGATTTGT
1 TGATTTGT
2348937 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2349111 original size:20 final size:19
Alignment explanation
Indices: 2349043--2349125 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
2349033 AAAAATGACT
2349043 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2349062 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2349076 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2349095 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2349115 ATCGCAATGCG
1 ATCGCAATGCG
2349126 TTATAATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2349176 original size:19 final size:19
Alignment explanation
Indices: 2349152--2349424 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
2349142 CGATATCTCG
2349152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349171 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349189 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2349203 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349222 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2349241 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349260 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349279 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2349298 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2349312 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2349331 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2349350 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2349364 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2349384 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2349398 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2349417 TTGCGATT
1 TTGCGATT
2349425 GTATTTCCGT
Statistics
Matches: 225, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 21 0.09
19 118 0.52
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2349245 original size:38 final size:38
Alignment explanation
Indices: 2349152--2349424 Score: 345
Period size: 33 Copynumber: 7.7 Consensus size: 38
2349142 CGATATCTCG
2349152 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2349189 TTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
2349222 TTGCGATTTTCATTTCGCATTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2349260 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
2349298 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
*
2349331 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2349364 TTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCA
* *
2349398 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2349425 GTATTTCCGT
Statistics
Matches: 214, Mismatches: 7, Indels: 34
0.84 0.03 0.13
Matches are distributed among these distances:
32 6 0.03
33 69 0.32
34 30 0.14
35 18 0.08
36 18 0.08
37 6 0.03
38 67 0.31
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
Found at i:2349338 original size:52 final size:52
Alignment explanation
Indices: 2349131--2349396 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
2349121 ATGCGTTATA
*
2349131 ATTTCGCATTGCGA-TATCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2349181 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2349233 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2349290 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2349342 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2349395 AT
1 AT
2349397 GTTGGGATTT
Statistics
Matches: 205, Mismatches: 3, Indels: 13
0.93 0.01 0.06
Matches are distributed among these distances:
50 14 0.07
51 30 0.15
52 85 0.41
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2351910 original size:24 final size:24
Alignment explanation
Indices: 2351876--2351922 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2351866 CTGAAACATC
2351876 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2351900 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2351923 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2352620 original size:20 final size:20
Alignment explanation
Indices: 2352592--2352978 Score: 448
Period size: 20 Copynumber: 19.4 Consensus size: 20
2352582 AAATTTCAGT
* * * *
2352592 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2352612 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2352632 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2352652 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2352672 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2352692 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2352712 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2352732 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2352752 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2352772 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2352792 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
2352812 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
2352833 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2352853 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2352873 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2352893 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2352913 GTTGCGATTTACGGATA-GC
1 GTTGCGATTTACGGATACGC
* *
2352932 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* *
2352952 GTTGCGATTTTC--ATTCGC
1 GTTGCGATTTACGGATACGC
2352970 GTTGCGATT
1 GTTGCGATT
2352979 ATTGAAATCG
Statistics
Matches: 321, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
18 14 0.04
19 21 0.07
20 266 0.83
21 18 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2361003 original size:12 final size:12
Alignment explanation
Indices: 2360986--2361030 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2360976 AAAAATTCAA
2360986 GAGCTCGATTTT
1 GAGCTCGATTTT
* *
2360998 GAGCTCGA-CTC
1 GAGCTCGATTTT
2361009 GAGCTCGATTTT
1 GAGCTCGATTTT
2361021 GAGCTCGATT
1 GAGCTCGATT
2361031 CAAGTTCGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (12 bp):
GAGCTCGATTTT
Found at i:2361039 original size:23 final size:23
Alignment explanation
Indices: 2360987--2361039 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
2360977 AAAATTCAAG
*
2360987 AGCTCGATTTTGAGCTCGACTCG
1 AGCTCGATTTTGAGCTCGACTCA
*
2361010 AGCTCGATTTTGAGCTCGATTCA
1 AGCTCGATTTTGAGCTCGACTCA
*
2361033 AGTTCGA
1 AGCTCGA
2361040 ACTCAAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
AGCTCGATTTTGAGCTCGACTCA
Done.