Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003744.1 Hibiscus syriacus cultivar Beakdansim tig00008013_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: 2457414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1963479 original size:112 final size:112
Alignment explanation
Indices: 1963117--1963578 Score: 730
Period size: 112 Copynumber: 4.1 Consensus size: 112
1963107 GATACTTATA
* * *
1963117 ATAAAGTATCGACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1963182 TTTGTCATTTGTTTA-TCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACT-TGTTATATTGTTATGGATCAATATATTTTT
* * *
1963229 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1963294 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
* * *
1963340 ATAAAGTATGGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1963405 TTTGTCATTTTTTTACTTGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
* *
1963452 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1963517 TTTATCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
*
1963564 ATAAAGTATCAACAC
1 ATAAAGTATCGACAC
1963579 AAACCGACAA
Statistics
Matches: 322, Mismatches: 26, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
111 101 0.31
112 221 0.69
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
Found at i:1963505 original size:223 final size:224
Alignment explanation
Indices: 1963117--1963578 Score: 730
Period size: 223 Copynumber: 2.1 Consensus size: 224
1963107 GATACTTATA
* *
1963117 ATAAAGTATCGACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1963182 TTTGTCATTTGTTTATCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTGTTTATCTGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTTT
* * *
1963247 CAATATATCCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGATTTTGTCA-TTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGATTTTATCATTTTTTTACCT
*
1963311 GTTATATTGTTATGGATCGATATATTTTT
196 GTTATATTGTTATGGATCAATATATTTTT
* * * *
1963340 ATAAAGTATGGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
1963405 TTTGTCATTTTTTTA-CTTGTTATATTGTTATAGATCAATATATTTTTATAAAGTATCGACACTT
66 TTTGTCATTTGTTTATC-TGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTT
* * * *
1963469 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAATCGGTTTTATCATTTTTTTACT
130 TCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGATTTTATCATTTTTTTACC
1963534 TGTTATATTGTTATGGATCAATATATTTTT
195 TGTTATATTGTTATGGATCAATATATTTTT
*
1963564 ATAAAGTATCAACAC
1 ATAAAGTATCGACAC
1963579 AAACCGACAA
Statistics
Matches: 217, Mismatches: 20, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
222 1 0.00
223 166 0.76
224 50 0.23
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (224 bp):
ATAAAGTATCGACACTATCAACATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTGTTTATCTGTTATATTGTTATAGATCAATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAAACCGATTTTATCATTTTTTTACCT
GTTATATTGTTATGGATCAATATATTTTT
Found at i:1965446 original size:23 final size:22
Alignment explanation
Indices: 1965416--1965501 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 22
1965406 GTCACTTTTC
1965416 AACCATTATTGGTGCCAACTATG
1 AACCATTATT-GTGCCAACTATG
* *
1965439 AACCATTATTGTTGCCAACTTTC
1 AACCATTATTG-TGCCAACTATG
*
1965462 AATGCATTA-T-T--CAACTATG
1 AA-CCATTATTGTGCCAACTATG
1965481 AACCATTATTGATGCCAACTA
1 AACCATTATTG-TGCCAACTA
1965502 GCTTGACAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
18 5 0.10
19 9 0.18
21 2 0.04
22 1 0.02
23 28 0.56
24 5 0.10
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (22 bp):
AACCATTATTGTGCCAACTATG
Found at i:1975824 original size:21 final size:20
Alignment explanation
Indices: 1975784--1975824 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1975774 TTATTTAATG
* *
1975784 AAATATTATAATTTTTTATT
1 AAATATTATAAATGTTTATT
1975804 AAATATTATAAAATGTTTATT
1 AAATATTAT-AAATGTTTATT
1975825 TTATGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AAATATTATAAATGTTTATT
Found at i:1976826 original size:14 final size:14
Alignment explanation
Indices: 1976807--1976853 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1976797 ATAATTATAC
1976807 TATTTAATTTAATT
1 TATTTAATTTAATT
* *
1976821 TATTTAACTTCATT
1 TATTTAATTTAATT
1976835 TATTT-ATTTATATT
1 TATTTAATTTA-ATT
1976849 TATTT
1 TATTT
1976854 CTTTAGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTAATTTAATT
Found at i:1976853 original size:18 final size:18
Alignment explanation
Indices: 1976807--1976864 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
1976797 ATAATTATAC
1976807 TATTTAATTTAATTTATTTA
1 TATTT-ATTT-ATTTATTTA
*
1976827 -ACTTCATTTATTTATTTA
1 TA-TTTATTTATTTATTTA
* *
1976845 TATTTATTTCTTTAGTTA
1 TATTTATTTATTTATTTA
1976863 TA
1 TA
1976865 ATTTTATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 24 0.75
19 6 0.19
20 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTTATTTATTTATTTA
Found at i:1977444 original size:36 final size:38
Alignment explanation
Indices: 1977379--1977454 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
1977369 AAAAAATATA
*
1977379 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
1977417 TATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATACACCAAAGTATTAATAAAATAGAAAAGC
1977453 TA
1 TA
1977455 CCCTCTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:1977902 original size:18 final size:17
Alignment explanation
Indices: 1977879--1977921 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1977869 ATATATACAT
1977879 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1977897 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1977914 ATAA-AATA
1 ATAATAATA
1977922 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1978355 original size:37 final size:36
Alignment explanation
Indices: 1978312--1978413 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
1978302 ATAGTAGAAC
1978312 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
1978349 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1978383 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1978414 TAGAACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1979257 original size:105 final size:105
Alignment explanation
Indices: 1978961--1980138 Score: 1767
Period size: 105 Copynumber: 11.3 Consensus size: 105
1978951 CATTGTTCCA
* * ** *
1978961 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
1979025 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
1979067 ATTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1979127 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1979167 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1979232 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1979272 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
1979337 AGCGGTCCCTTCGTCGTGAAGTTGAATTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1979377 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1979437 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1979477 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* *
1979542 AGCGGTCCCTTCGTCGTGAAGTTGAATTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1979582 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1979642 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1979682 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1979747 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1979787 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1979852 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1979892 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
1979957 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1979999 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * * *
1980064 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1980105 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1980139 CGCGGATGGC
Statistics
Matches: 992, Mismatches: 59, Indels: 39
0.91 0.05 0.04
Matches are distributed among these distances:
100 261 0.26
101 11 0.01
102 9 0.01
103 2 0.00
104 15 0.02
105 479 0.48
106 95 0.10
107 98 0.10
109 22 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1979431 original size:205 final size:206
Alignment explanation
Indices: 1978961--1980138 Score: 1758
Period size: 205 Copynumber: 5.6 Consensus size: 206
1978951 CATTGTTCCA
* * *
1978961 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-C-TGAAA-T-TTTGTTGACAAC
* * * * *
1979026 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGATTCCAATATCCTTCGTTGTGAAG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
1979091 TTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
126 TTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
1979151 AACTTGCGTTGTCTGG
191 AACTTGCATTGTCTGG
* * * * *
1979167 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAACT--GAAATT-TTGTTGACAACC
1979232 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1979297 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
127 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1979362 ATTTGCATTGTCTGG
192 ACTTGCATTGTCTGG
*
1979377 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTGTTGACAACCAGCG
1979441 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
*
1979506 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAATTT
131 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1979571 GCATTGTCTGG
196 GCATTGTCTGG
* *
1979582 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTGTTGACAACCAGCG
1979646 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
1979711 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
1979776 GCATTGTCTGG
196 GCATTGTCTGG
* *
1979787 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ACT--GAAATT-TTGTTGACAACC
* *
1979852 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
1979917 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
127 TGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
*
1979982 GAACTTGCGTTGTCTGG
190 GAACTTGCATTGTCTGG
*
1979999 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AACTGA-AA--T-TTTGTTGACAAC
* * * * * *
1980064 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTG
*
1980129 GAGTTGAAAT
123 AAGTTGAAAT
1980139 CGCGGATGGC
Statistics
Matches: 906, Mismatches: 43, Indels: 36
0.92 0.04 0.04
Matches are distributed among these distances:
204 1 0.00
205 483 0.53
206 48 0.05
207 2 0.00
208 5 0.01
209 9 0.01
210 181 0.20
211 9 0.01
212 91 0.10
213 52 0.06
214 4 0.00
216 21 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTGTTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCATTGTCTGG
Found at i:1979580 original size:310 final size:312
Alignment explanation
Indices: 1978961--1980138 Score: 1831
Period size: 310 Copynumber: 3.8 Consensus size: 312
1978951 CATTGTTCCA
* **
1978961 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAG-A-TTGGAAATTGTTTGTTGACA
* * * * *
1979024 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGATTCCAATATCCTTCGTTGTGA
63 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
**
1979089 AGTTGAAATTGAATCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
128 AGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
1979152 ACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAG
193 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
*
1979217 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
258 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
1979272 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGAAA-TTGTTTGTTGACAAC
* *
1979336 CAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
1979401 TTGAAATTGGCTCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
130 TTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
1979464 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTT
195 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
* *
1979529 GTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCATTGTCTGG
260 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
1979582 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T-GAAA-T-TTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGAAATTGTTTGTTGACAACC
1979642 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
1979707 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-ATT-GAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1979772 ACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
193 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
*
1979837 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
258 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
1979892 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATT-GG-AAATTGTTTGTTGACAA
1979957 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
1980022 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AATTGA-AAG-T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * * * *
1980087 TGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
190 TGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1980139 CGCGGATGGC
Statistics
Matches: 807, Mismatches: 37, Indels: 36
0.92 0.04 0.04
Matches are distributed among these distances:
305 91 0.11
306 1 0.00
307 5 0.01
308 5 0.01
309 3 0.00
310 478 0.59
311 41 0.05
312 3 0.00
314 1 0.00
315 3 0.00
316 3 0.00
317 96 0.12
318 51 0.06
319 4 0.00
321 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (312 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGAAATTGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG
TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:1980914 original size:65 final size:67
Alignment explanation
Indices: 1980729--1981196 Score: 242
Period size: 65 Copynumber: 6.9 Consensus size: 67
1980719 GGAAACGATC
* * * * *
1980729 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAA
1980794 TAAAT
63 TAAAT
** * * *
1980799 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
1980864 AT
66 AT
* * ** *
1980866 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGATAGATGAAATTTGTTTTAAGAGAAACT-
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TA
*
1980928 -GT
65 AAT
** * * * * * * *
1980930 CTCAAGAGAGACAAAACTT-AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAA
1 -TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAG
* * *
1980994 GAAAACATAT
58 GGAAATAAAT
* * * * *
1981004 TCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACT-
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TA
*
1981066 -GT
65 AAT
* * * * * *
1981068 CTCAAGAGAGACAAAATTT-TGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAG
1 -TC-A-A-AG----ATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAG
***
1981132 GGAAATGTTT
58 GGAAATAAAT
* *
1981142 TCAATG--TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATCTTGTTTTAAG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT-TTGTTTTAAG
1981197 AAAAACAATC
Statistics
Matches: 315, Mismatches: 57, Indels: 57
0.73 0.13 0.13
Matches are distributed among these distances:
64 9 0.03
65 124 0.39
66 7 0.02
67 25 0.08
68 35 0.11
69 3 0.01
70 8 0.03
71 2 0.01
72 5 0.02
73 95 0.30
74 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:1980926 original size:36 final size:36
Alignment explanation
Indices: 1980874--1981136 Score: 247
Period size: 36 Copynumber: 7.4 Consensus size: 36
1980864 ATTCAAAGAT
* * **
1980874 TTTGTTTCAAGGGAAACTGTCTCAAGATAGATGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1980910 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1980946 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1980983 TTTGTTTCAA-AGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
1981012 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1981048 TTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
1981084 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
1981121 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
1981137 TGTTTTCAAT
Statistics
Matches: 186, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.09
30 2 0.01
31 1 0.01
34 1 0.01
35 3 0.02
36 96 0.52
37 64 0.34
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1980987 original size:138 final size:137
Alignment explanation
Indices: 1980823--1981202 Score: 483
Period size: 138 Copynumber: 2.8 Consensus size: 137
1980813 TTTCAAGAGT
* * * *
1980823 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* *
1980888 AACTGTCTCAAGATAGATGAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 AACTGTCTCAAGAGAGA-AAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
1980953 CCAAAAGA
130 CCAAAAGA
* * * *
1980961 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
* * * *
1981026 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT
66 AACTGTCTCAAGAGAGA-AAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
* **
1981091 TCAAGGGA
130 CCAAAAGA
* * * * * * *
1981099 AACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAG
1 AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGG
* *
1981163 AAACTGTCTCAAGAGAGACAAATCTTGTTTTAAGAAAAAC
65 AAACTGTCTCAAGAGAGAAAAAT-TTGTTTTAAGAGAAAC
1981203 AATCATGAGT
Statistics
Matches: 207, Mismatches: 33, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
137 7 0.03
138 200 0.97
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (137 bp):
AACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGAAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTC
CAAAAGA
Found at i:1981042 original size:102 final size:102
Alignment explanation
Indices: 1980910--1981094 Score: 291
Period size: 102 Copynumber: 1.8 Consensus size: 102
1980900 ATAGATGAAA
* *
1980910 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAG
*
1980975 AGACGAAA-TTTGTTTCAAAGAAAACATATTCAAATAT
65 AGACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
* * * *
1981012 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
1981077 GACAAAATTTTGTTTCAA
66 GACAAAATTTTGTTTCAA
1981095 GGGAAACTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
101 28 0.37
102 47 0.63
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTTGTTTCAAAGAAAACATATTCAAATAT
Found at i:1982103 original size:22 final size:22
Alignment explanation
Indices: 1982078--1982121 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1982068 CATTTTTGTT
1982078 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
1982100 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
1982122 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1982763 original size:19 final size:20
Alignment explanation
Indices: 1982729--1982767 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1982719 CTTTTTCTTT
*
1982729 TTTCTTTTTGTTCTTTTTTC
1 TTTCTTTTTGTGCTTTTTTC
1982749 TTTCTTTTT-TGCTTTTTTC
1 TTTCTTTTTGTGCTTTTTTC
1982768 CCCTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTGTGCTTTTTTC
Found at i:1982774 original size:27 final size:27
Alignment explanation
Indices: 1982722--1982774 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1982712 TTTGTCCCTT
* **
1982722 TTTCTTTTTTCTTTTTGTTCTTTTTTC
1 TTTCTTTTTTCTTTTTGTCCCCTTTTC
1982749 TTTCTTTTTTGCTTTTT-TCCCCTTTT
1 TTTCTTTTTT-CTTTTTGTCCCCTTTT
1982775 TATTCTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTCTTTTTTCTTTTTGTCCCCTTTTC
Found at i:1983969 original size:8 final size:8
Alignment explanation
Indices: 1983953--1983991 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1983943 AATGTAGATG
1983953 AAAATGCA
1 AAAATGCA
*
1983961 AAAAGGCA
1 AAAATGCA
1983969 AAAATGC-
1 AAAATGCA
1983976 AAAATGCA
1 AAAATGCA
*
1983984 AGAATGCA
1 AAAATGCA
1983992 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1983979 original size:15 final size:15
Alignment explanation
Indices: 1983953--1983991 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1983943 AATGTAGATG
1983953 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1983969 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1983984 AGAATGCA
1 AAAATGCA
1983992 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1986501 original size:27 final size:26
Alignment explanation
Indices: 1986470--1986550 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 26
1986460 GAAATGTGTT
*
1986470 AGATAAACAAGGTAAAGAAAACAAATA
1 AGATAAA-AAGGTAAAGAAAAAAAATA
* * *
1986497 AGATAAAAGGGAAAAATAAAAAAAATA
1 AGATAAAAAGG-TAAAGAAAAAAAATA
* *
1986524 AAATAAATAAGATAAAGAAAAAAAATA
1 AGATAAA-AAGGTAAAGAAAAAAAATA
1986551 GTAAAGTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
26 3 0.07
27 38 0.88
28 2 0.05
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.12
Consensus pattern (26 bp):
AGATAAAAAGGTAAAGAAAAAAAATA
Found at i:1986522 original size:9 final size:9
Alignment explanation
Indices: 1986508--1986550 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1986498 GATAAAAGGG
1986508 AAAAATAAA
1 AAAAATAAA
1986517 AAAAATAAA
1 AAAAATAAA
* *
1986526 ATAAATAAG
1 AAAAATAAA
* *
1986535 ATAAAGAAA
1 AAAAATAAA
1986544 AAAAATA
1 AAAAATA
1986551 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (9 bp):
AAAAATAAA
Found at i:1986663 original size:36 final size:38
Alignment explanation
Indices: 1986598--1986673 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
1986588 GAAAAAAATA
*
1986598 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACACCAAAGTATTAATAAAATAGAA-AAGC
*
1986636 TATATATATACACCAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATACACCAAAGTATTAATAAAATAGAAAAGC
1986672 TA
1 TA
1986674 CCCTCTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATATATACACCAAAGTATTAATAAAATAGAAAAGC
Found at i:1986858 original size:21 final size:19
Alignment explanation
Indices: 1986834--1986873 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1986824 AACGAAAATA
*
1986834 ATAAAATATATATATATATAT
1 ATAAAAT-TATA-AGATATAT
1986855 ATAAAATTATAAGATATAT
1 ATAAAATTATAAGATATAT
1986874 TACGTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
ATAAAATTATAAGATATAT
Found at i:1986928 original size:17 final size:17
Alignment explanation
Indices: 1986908--1986942 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1986898 AATAAAAATA
1986908 ATTAAGAATATATATAT
1 ATTAAGAATATATATAT
* *
1986925 ATTAATAATATGTATAT
1 ATTAAGAATATATATAT
1986942 A
1 A
1986943 AATAAACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
ATTAAGAATATATATAT
Found at i:1987131 original size:18 final size:17
Alignment explanation
Indices: 1987108--1987150 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1987098 ATATATACAT
1987108 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1987126 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1987143 ATAA-AATA
1 ATAATAATA
1987151 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1987585 original size:37 final size:36
Alignment explanation
Indices: 1987542--1987643 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
1987532 ATAGTAGAAC
1987542 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
1987579 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1987613 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1987644 TAGAACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1990046 original size:28 final size:28
Alignment explanation
Indices: 1990014--1990067 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1990004 TAAGATTCAA
1990014 GATTTAG-GATTTAGGGGTTAATATTTAT
1 GATTTAGAG-TTTAGGGGTTAATATTTAT
*
1990042 GATTTAGAGTTTAGGGTTTAATATTT
1 GATTTAGAGTTTAGGGGTTAATATTT
1990068 GGATTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (28 bp):
GATTTAGAGTTTAGGGGTTAATATTTAT
Found at i:1990294 original size:62 final size:63
Alignment explanation
Indices: 1990218--1990341 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 63
1990208 CTTCCATGCG
1990218 TTTTGCATGGATTTCTATTATTATAAAAAATTCTTCCATTATTGCTATACA-GGACCACAACA
1 TTTTGCATGGATTTCTATTATTATAAAAAATTCTTCCATTATTGCTATACAGGGACCACAACA
* *
1990280 TTTTGCATGGATTTCTATTATTATAAAAAATTCTTTCATTATTGCTATACAGGGGCCACAAC
1 TTTTGCATGGATTTCTATTATTATAAAAAATTCTTCCATTATTGCTATACAGGGACCACAAC
1990342 GATGGTATGG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
62 50 0.85
63 9 0.15
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (63 bp):
TTTTGCATGGATTTCTATTATTATAAAAAATTCTTCCATTATTGCTATACAGGGACCACAACA
Found at i:1990479 original size:29 final size:29
Alignment explanation
Indices: 1990439--1990500 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1990429 CTATTTCACG
1990439 AAATAATCTTTCAACTACATTATTAGA-A
1 AAATAATCTTTCAACTACATTATTAGAGA
* * * *
1990467 AAATAATTTTTTCTATTACATTATTTGAGA
1 AAATAA-TCTTTCAACTACATTATTAGAGA
1990497 AAAT
1 AAAT
1990501 TTTCCGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.21
29 17 0.61
30 5 0.18
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATAATCTTTCAACTACATTATTAGAGA
Found at i:1993532 original size:7 final size:7
Alignment explanation
Indices: 1993515--1993556 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
1993505 TCGTAAAATC
1993515 TCTTT-T
1 TCTTTCT
1993521 TCTTTCT
1 TCTTTCT
1993528 TCTTTCT
1 TCTTTCT
1993535 TCTTTCT
1 TCTTTCT
1993542 TCTTTCT
1 TCTTTCT
1993549 TCTTTCT
1 TCTTTCT
1993556 T
1 T
1993557 GCAGAGCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TCTTTCT
Found at i:1995240 original size:31 final size:30
Alignment explanation
Indices: 1995163--1995250 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
1995153 AAAATTTAGA
*
1995163 TACTAAAATTAAACAAAAAGTTAACAATAGGGG
1 TACTAAAATGAAACAAAAAG-T-A-AATAGGGG
* *
1995196 AACTAAAACGAAACAAAAAGTAAAT-GTCGGG
1 TACTAAAATGAAACAAAAAGTAAATAG--GGG
1995227 TACTAAAATGAAACAAAAAGTAAA
1 TACTAAAATGAAACAAAAAGTAAA
1995251 CATTAGGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
29 1 0.02
30 3 0.06
31 26 0.54
32 1 0.02
33 17 0.35
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (30 bp):
TACTAAAATGAAACAAAAAGTAAATAGGGG
Found at i:2008768 original size:14 final size:14
Alignment explanation
Indices: 2008751--2008778 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2008741 ATCATAACAA
2008751 AATTATATAACTAT
1 AATTATATAACTAT
2008765 AATTATATAACTAT
1 AATTATATAACTAT
2008779 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:2009370 original size:17 final size:16
Alignment explanation
Indices: 2009348--2009416 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
2009338 CCGTGTCTCG
*
2009348 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
2009365 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
2009380 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
2009397 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
2009412 ACCCG
1 ACCCG
2009417 ATACCCGGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 21 0.48
16 6 0.14
17 17 0.39
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:2009380 original size:15 final size:15
Alignment explanation
Indices: 2009360--2009416 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
2009350 CCGGATGTTA
2009360 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
2009375 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
2009391 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
2009407 CGGGTACCCG
1 CGGGTACCCG
2009417 ATACCCGGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:2009384 original size:32 final size:32
Alignment explanation
Indices: 2009348--2009416 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
2009338 CCGTGTCTCG
2009348 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
* *
2009380 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGGGT
2009412 ACCCG
1 ACCCG
2009417 ATACCCGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGGGT
Found at i:2011224 original size:21 final size:21
Alignment explanation
Indices: 2011200--2011239 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2011190 GTTATTTTAT
2011200 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2011221 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2011240 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2011285 original size:33 final size:33
Alignment explanation
Indices: 2011234--2011332 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2011224 TTTGTTTCAA
2011234 TTATCGAAC-TTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
2011266 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
* * * *
2011299 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
2011332 T
1 T
2011333 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 9 0.15
33 53 0.85
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTTGAAGTTTTTAAGTATTTGAAT
Found at i:2011297 original size:17 final size:17
Alignment explanation
Indices: 2011243--2011297 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
2011233 ATTATCGAAC
2011243 TTGAAGTTTTTAAGTAT
1 TTGAAGTTTTTAAGTAT
* * *
2011260 TTGAA-TTTAT-CGAACT
1 TTGAAGTTTTTAAGTA-T
2011276 TTGAAGTTTTTAAGTAT
1 TTGAAGTTTTTAAGTAT
2011293 TTGAA
1 TTGAA
2011298 TTTATCAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.07
16 10 0.34
17 15 0.52
18 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (17 bp):
TTGAAGTTTTTAAGTAT
Found at i:2011361 original size:13 final size:13
Alignment explanation
Indices: 2011318--2011372 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2011308 TTGGAAGTAT
2011318 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2011331 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2011345 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2011358 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2011371 TT
1 TT
2011373 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2011594 original size:21 final size:21
Alignment explanation
Indices: 2011568--2011624 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
2011558 TGGAGCGTGG
*
2011568 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
2011589 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
2011610 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
2011625 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:2011794 original size:15 final size:15
Alignment explanation
Indices: 2011769--2011824 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2011759 ATCTGGAATA
*
2011769 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2011784 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
2011799 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
2011816 TTAAAACCG
1 TTAAAACCG
2011825 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2011833 original size:21 final size:18
Alignment explanation
Indices: 2011788--2011821 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2011778 GTTTTTTTAT
2011788 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
2011805 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
2011822 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:2012151 original size:15 final size:15
Alignment explanation
Indices: 2012131--2012171 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
2012121 CCGGATGTTA
2012131 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
2012146 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
2012161 CGGGTACCCGG
1 CGGGTACCCGG
2012172 ATTTTGCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:2014446 original size:26 final size:25
Alignment explanation
Indices: 2014417--2014468 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2014407 TAGTGTATAA
*
2014417 ATAT-TTAAATTCATAATATTTTAT
1 ATATATTAAATTAATAATATTTTAT
*
2014441 ATATATTAACTTAATAATATTTT-T
1 ATATATTAAATTAATAATATTTTAT
2014465 ATAT
1 ATAT
2014469 TAACTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATATTAAATTAATAATATTTTAT
Found at i:2014457 original size:25 final size:23
Alignment explanation
Indices: 2014429--2014515 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 23
2014419 ATTTAAATTC
2014429 ATAATATTTTATATATATTAACTTA
1 ATAATATTTT-T-TATATTAACTTA
2014454 ATAATA-TTTTTATATTAACTTA
1 ATAATATTTTTTATATTAACTTA
*
2014476 TTAAATATATTTTGT-TATTAACTTA
1 AT-AATAT-TTTT-TATATTAACTTA
2014501 ATTTAAT-TTTTTTAT
1 A--TAATATTTTTTAT
2014516 TTTTATTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
22 13 0.25
23 6 0.11
24 8 0.15
25 21 0.40
26 4 0.08
27 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (23 bp):
ATAATATTTTTTATATTAACTTA
Found at i:2014470 original size:22 final size:24
Alignment explanation
Indices: 2014442--2014502 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
2014432 ATATTTTATA
2014442 TATATTAACTTAAT-AATAT-TTT
1 TATATTAACTTAATAAATATATTT
*
2014464 TATATTAACTTATTAAATATATTT
1 TATATTAACTTAATAAATATATTT
*
2014488 TGTTATTAACTTAAT
1 T-ATATTAACTTAAT
2014503 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.39
23 5 0.15
24 4 0.12
25 11 0.33
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTAACTTAATAAATATATTT
Found at i:2019190 original size:21 final size:21
Alignment explanation
Indices: 2019165--2019207 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2019155 TAGAACATTT
2019165 TTTCAACAATCAAGCAACCTA
1 TTTCAACAATCAAGCAACCTA
2019186 TTTCAACAATCAAGCAACCTA
1 TTTCAACAATCAAGCAACCTA
2019207 T
1 T
2019208 CTTATGGTTG
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:0.42, C:0.28, G:0.05, T:0.26
Consensus pattern (21 bp):
TTTCAACAATCAAGCAACCTA
Found at i:2019603 original size:22 final size:23
Alignment explanation
Indices: 2019548--2019593 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2019538 TTAAGTTATT
*
2019548 TATATAGA-AATTTTATTTAAAA
1 TATATAAATAATTTTATTTAAAA
*
2019570 TATATAAATAATTTTATTAAAAA
1 TATATAAATAATTTTATTTAAAA
2019593 T
1 T
2019594 TAAATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATATAAATAATTTTATTTAAAA
Found at i:2024580 original size:16 final size:16
Alignment explanation
Indices: 2024559--2024601 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
2024549 ACGATGGACT
*
2024559 CTTCGATTTCTTCATC
1 CTTCGATCTCTTCATC
2024575 CTTCGATCTCTTCATC
1 CTTCGATCTCTTCATC
2024591 CTTCGATCTCT
1 CTTCGATCTCT
2024602 ATGGTTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.12, C:0.35, G:0.07, T:0.47
Consensus pattern (16 bp):
CTTCGATCTCTTCATC
Found at i:2024587 original size:9 final size:9
Alignment explanation
Indices: 2024557--2024601 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 9
2024547 CAACGATGGA
2024557 CTCTTCGAT
1 CTCTTCGAT
*
2024566 TTCTTC-AT
1 CTCTTCGAT
2024574 C-CTTCGAT
1 CTCTTCGAT
2024582 CTCTTC-AT
1 CTCTTCGAT
2024590 C-CTTCGAT
1 CTCTTCGAT
2024598 CTCT
1 CTCT
2024602 ATGGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
7 8 0.27
8 11 0.37
9 11 0.37
ACGTcount: A:0.11, C:0.36, G:0.07, T:0.47
Consensus pattern (9 bp):
CTCTTCGAT
Found at i:2028538 original size:29 final size:27
Alignment explanation
Indices: 2028506--2028560 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2028496 AAATTATAAA
* *
2028506 AAAAACTCAAATTCTTAAAAATCAACCAT
1 AAAAA-TCAAAATCTGAAAAAT-AACCAT
*
2028535 AAAAATTAAAATCTGAAAAATAACCA
1 AAAAATCAAAATCTGAAAAATAACCA
2028561 CAAATTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.22
28 13 0.57
29 5 0.22
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (27 bp):
AAAAATCAAAATCTGAAAAATAACCAT
Found at i:2039926 original size:30 final size:30
Alignment explanation
Indices: 2039892--2039959 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
2039882 TCACAAGATA
*
2039892 GTGGATTTACTAGTGTGAAGGAAAGTAAAG
1 GTGGAATTACTAGTGTGAAGGAAAGTAAAG
2039922 GTGGAATTACTAGTGTGAAGGAAAGTAAAG
1 GTGGAATTACTAGTGTGAAGGAAAGTAAAG
2039952 GTGGAATT
1 GTGGAATT
2039960 GGAGCAATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (30 bp):
GTGGAATTACTAGTGTGAAGGAAAGTAAAG
Found at i:2046160 original size:3 final size:3
Alignment explanation
Indices: 2046152--2046185 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2046142 ATGAAATGTT
2046152 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2046186 GAGAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2046331 original size:21 final size:20
Alignment explanation
Indices: 2046307--2046379 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
2046297 ACCCAGTTTC
2046307 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
* *
2046328 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
* *
2046348 CGAATTTGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
2046368 -AATTTCGCAACA
1 CAAATTCGCAACA
2046380 GGTTTTAGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
19 9 0.21
20 21 0.49
21 13 0.30
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:2048544 original size:21 final size:21
Alignment explanation
Indices: 2048518--2048588 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
2048508 GTGAATTGGG
* *
2048518 CTCTTGAATGGTGGGATGGAC
1 CTCTTGAATGGTGGGAGGGGC
* * **
2048539 CTCTTGAACGATGACAGGGGC
1 CTCTTGAATGGTGGGAGGGGC
2048560 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAATGGTGGGAGGGGC
2048581 CTCTTGAA
1 CTCTTGAA
2048589 CGATGACAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGC
Found at i:2048584 original size:42 final size:42
Alignment explanation
Indices: 2048518--2048598 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
2048508 GTGAATTGGG
*
2048518 CTCTTGAATGGTGGGATGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
*
2048560 CTCTTGAATGGTGGGAGGGGCCTCTTGAACGATGACAGG
1 CTCTTGAATGGTGGGAGGGACCTCTTGAACGATGACAGG
2048599 TGAATCAGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:2048995 original size:62 final size:63
Alignment explanation
Indices: 2048887--2049005 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 63
2048877 TAGAGCGGCT
* * * * *
2048887 ACCTCATCACGTAAAGTAGATACCTCACCACGTAGTGCATCATTGTCATCGCGTAAAACATCC
1 ACCTCACCACGTAAAATAGATACCTCACCACGCAGTGCACCATTGTCATCACGTAAAACATCC
* * *
2048950 ACCTCACCACGTAAAATCG-TACCTCATCACGCCA-TGCACCATTGTCTTCACGTAAA
1 ACCTCACCACGTAAAATAGATACCTCACCACG-CAGTGCACCATTGTCATCACGTAAA
2049006 GTACCGACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 30 0.64
63 17 0.36
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.24
Consensus pattern (63 bp):
ACCTCACCACGTAAAATAGATACCTCACCACGCAGTGCACCATTGTCATCACGTAAAACATCC
Found at i:2050758 original size:19 final size:20
Alignment explanation
Indices: 2050718--2050760 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2050708 AAACTTGAAT
2050718 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
2050738 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
2050757 TCGC
1 TCGC
2050761 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:2051356 original size:20 final size:20
Alignment explanation
Indices: 2051331--2051373 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
2051321 ACGCGCTTTA
2051331 CGAATTTGACTTATGTGTTG
1 CGAATTTGACTTATGTGTTG
*
2051351 CGAATTTGACTTTTGTGTTG
1 CGAATTTGACTTATGTGTTG
2051371 CGA
1 CGA
2051374 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.44
Consensus pattern (20 bp):
CGAATTTGACTTATGTGTTG
Found at i:2051844 original size:14 final size:14
Alignment explanation
Indices: 2051825--2051864 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2051815 ATTAGTTAGT
2051825 ATTATATATATTTA
1 ATTATATATATTTA
*
2051839 ATTATATTTA-TTA
1 ATTATATATATTTA
2051852 ATT-TATA-ATTTA
1 ATTATATATATTTA
2051864 A
1 A
2051865 AATTATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 1 0.04
12 7 0.30
13 6 0.26
14 9 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTATATATATTTA
Found at i:2053363 original size:37 final size:36
Alignment explanation
Indices: 2053288--2053363 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
2053278 TTTTTATATT
*
2053288 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
2053324 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
2053361 TTT
1 TTT
2053364 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:2053545 original size:20 final size:20
Alignment explanation
Indices: 2053509--2053546 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2053499 ATCCTATTCC
**
2053509 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
2053529 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
2053547 GTGAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:2057219 original size:29 final size:29
Alignment explanation
Indices: 2057155--2057219 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
2057145 GAATTAGAAT
* *
2057155 TTGTTTTATTATCTGTCTAGAATGAATAG
1 TTGTTTTATTATCTGTCTAGAAGGAATAA
* *
2057184 TTATTTTATTGTCTGTCTAGAAGGAATAA
1 TTGTTTTATTATCTGTCTAGAAGGAATAA
2057213 TTGTTTT
1 TTGTTTT
2057220 TTTCACAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (29 bp):
TTGTTTTATTATCTGTCTAGAAGGAATAA
Found at i:2057472 original size:15 final size:15
Alignment explanation
Indices: 2057452--2057481 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2057442 GAGAACCATT
*
2057452 AATTTAATTTATAAA
1 AATTTAAATTATAAA
2057467 AATTTAAATTATAAA
1 AATTTAAATTATAAA
2057482 GAACTCAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTAAATTATAAA
Found at i:2057798 original size:20 final size:21
Alignment explanation
Indices: 2057770--2057813 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2057760 ATTTATTAAA
2057770 ATTAAATAT-TATATAAATTT
1 ATTAAATATATATATAAATTT
* * *
2057790 ATTAGATATATTTATAATTTT
1 ATTAAATATATATATAAATTT
2057811 ATT
1 ATT
2057814 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAAATATATATATAAATTT
Found at i:2058128 original size:15 final size:15
Alignment explanation
Indices: 2058108--2058139 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2058098 ATGTCACATT
2058108 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
2058123 CAGAGCTAATTCATA
1 CAGAGCTAATTCATA
2058138 CA
1 CA
2058140 AAGCCTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (15 bp):
CAGAGCTAATTCATA
Found at i:2060818 original size:38 final size:34
Alignment explanation
Indices: 2060767--2060849 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 34
2060757 TTCAGTTAAT
2060767 TTTGTT-TA-TTACCATTTAATATCAGTTATTGTAA-
1 TTTGTTATATTTACCATTTAAT-TC--TTATTGTAAG
2060801 TTTGGTTATCATTTACCATTTAATTCTTATTGTAAG
1 TTT-GTTAT-ATTTACCATTTAATTCTTATTGTAAG
2060837 TTTGTTATATTTA
1 TTTGTTATATTTA
2060850 AAATTATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
34 8 0.18
35 17 0.39
36 4 0.09
37 3 0.07
38 12 0.27
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (34 bp):
TTTGTTATATTTACCATTTAATTCTTATTGTAAG
Found at i:2067826 original size:52 final size:52
Alignment explanation
Indices: 2067767--2067874 Score: 137
Period size: 52 Copynumber: 2.1 Consensus size: 52
2067757 GATAGATTTT
* * * *
2067767 AATAAAAAATTA-TATTTTATTCGAACTCATCATCTCGACGTGACGAGTTCG
1 AATAAAAAAATATTATTTTATTCGAACTCATCATCTCAACATGACGAGTTCC
* * * *
2067818 AATAAAAAAATATTTTTTTATTGGAATTCGTCATCTCAACATGACGAGTTCC
1 AATAAAAAAATATTATTTTATTCGAACTCATCATCTCAACATGACGAGTTCC
2067870 AATAA
1 AATAA
2067875 CACTGTAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 11 0.23
52 37 0.77
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (52 bp):
AATAAAAAAATATTATTTTATTCGAACTCATCATCTCAACATGACGAGTTCC
Found at i:2083419 original size:29 final size:30
Alignment explanation
Indices: 2083360--2083420 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
2083350 AATTTTATTT
**
2083360 TTTTTAAATATTTTTTATAAAAAATGTTTA
1 TTTTTAAATATTTTTTATAAAAAATAATTA
*
2083390 TTTTTAAA-ATTTTATT-TAATAAATAATTA
1 TTTTTAAATATTTT-TTATAAAAAATAATTA
2083419 TT
1 TT
2083421 GATAGAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTTAAATATTTTTTATAAAAAATAATTA
Found at i:2084164 original size:17 final size:17
Alignment explanation
Indices: 2084139--2084189 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
2084129 CCGGTTTCAG
*
2084139 TTTTAAAAAAATCGGTT
1 TTTTAAAAAAACCGGTT
*
2084156 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
2084171 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
2084188 TT
1 TT
2084190 AATATTCCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:2084386 original size:21 final size:21
Alignment explanation
Indices: 2084362--2084414 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2084352 ACACTTAGGG
2084362 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
2084383 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
2084404 TACCGATTCCC
1 AACCGATTCCC
2084415 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:2084625 original size:13 final size:13
Alignment explanation
Indices: 2084604--2084658 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2084594 AAGTTCGATA
*
2084604 AATTCAAATACTT
1 AATTGAAATACTT
2084617 AATTGAAATACTT
1 AATTGAAATACTT
* *
2084630 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2084644 AATTGAAATACTT
1 AATTGAAATACTT
2084657 AA
1 AA
2084659 ATACTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2084689 original size:33 final size:33
Alignment explanation
Indices: 2084644--2084742 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2084634 AACTCAACAT
* * *
2084644 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
*
2084677 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
2084710 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
2084742 A
1 A
2084743 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 13 0.21
33 48 0.79
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTCGATA
Found at i:2084761 original size:21 final size:21
Alignment explanation
Indices: 2084737--2084776 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2084727 ACTTCAAGTT
2084737 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2084758 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2084777 ATAAATAAAC
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:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2084784 original size:21 final size:21
Alignment explanation
Indices: 2084739--2084784 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2084729 TTCAAGTTCG
*
2084739 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTTTACA
*
2084760 ATAATTGAAATAAAGTTATA-A
1 ATAATTGAAACAAAGTT-TACA
2084781 ATAA
1 ATAA
2084785 ACTACATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.30
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTTACA
Found at i:2093774 original size:156 final size:156
Alignment explanation
Indices: 2093474--2093791 Score: 496
Period size: 156 Copynumber: 2.0 Consensus size: 156
2093464 GTCAAAGAGA
* * *
2093474 ATCCACGCCAACTAAATGAGGAAACAACCAATGGGGATTCTTCTGTAATTCATAAATCCCTGACA
1 ATCCAGGCCAACTAAATGAGGAAACAACCAATGGAGATTCTTCTGTAATTCATAAATCCCTAACA
*
2093539 CTAAGTGTCTCACCTAGAGTGAATCAGAGTAGGAAGAGTGTGAGGACATCTTCAATGTACACTAC
66 CTAAGTGTCTCACCTAGAGTGAATCAGAGTAGGAAGAGTCTGAGGACATCTTCAATGTACACTAC
2093604 TTCACAAAAAGATCTTACGGATGATG
131 TTCACAAAAAGATCTTACGGATGATG
* * * **
2093630 GTCCAGGCCAGCTAACTGAGGAAACAACTGATGGAGATTCTTCTGTAATT-ATTAAATCGCC-AA
1 ATCCAGGCCAACTAAATGAGGAAACAACCAATGGAGATTCTTCTGTAATTCA-TAAATC-CCTAA
* *
2093693 CACTAAGTGTCTCACCTAGGGTGAATCAGAGTAGGAAGAGTCTGAGGACATCTTCAATGTACTCT
64 CACTAAGTGTCTCACCTAGAGTGAATCAGAGTAGGAAGAGTCTGAGGACATCTTCAATGTACACT
*
2093758 GCTTCACAAAAAGATCTTACGGATGATG
129 ACTTCACAAAAAGATCTTACGGATGATG
2093786 ATCCAG
1 ATCCAG
2093792 AGACTACTTG
Statistics
Matches: 147, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
155 1 0.01
156 144 0.98
157 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (156 bp):
ATCCAGGCCAACTAAATGAGGAAACAACCAATGGAGATTCTTCTGTAATTCATAAATCCCTAACA
CTAAGTGTCTCACCTAGAGTGAATCAGAGTAGGAAGAGTCTGAGGACATCTTCAATGTACACTAC
TTCACAAAAAGATCTTACGGATGATG
Found at i:2096188 original size:184 final size:182
Alignment explanation
Indices: 2095855--2096213 Score: 700
Period size: 184 Copynumber: 2.0 Consensus size: 182
2095845 TAAAATTCAG
2095855 CAGTTGTTTATTTTTTCTCAATAACCCGTTTCAAGTTTGCAATAAACAGGCAGATCAGTAGGGCA
1 CAGTTGTTTATTTTTTCTCAATAACCCGTTTCAAGTTTGCAATAAACAGGCAGATCAGTAGGGCA
2095920 TAAGAAAATGCATACTTCACCTTCGTGAAGCACTGCATTTATCAAATTCAATATTAAGATTGTTG
66 TAAGAAAATGCATACTTCACCTTCGTGAAGCACTGCATTTATCAAATTCAATATTAAGATTGTTG
2095985 TTACATATAAAGATGGAAAATTAGGAAACATTATGTCAATTTATTCAATATT
131 TTACATATAAAGATGGAAAATTAGGAAACATTATGTCAATTTATTCAATATT
2096037 CAGTTGTTTATTTTTTTCTCAATAACCCCGTTTCAAGTTTGCAATAAACAGGCAGATCAGTAGGG
1 CAGTTGTTTA-TTTTTTCTCAATAA-CCCGTTTCAAGTTTGCAATAAACAGGCAGATCAGTAGGG
2096102 CATAAGAAAATGCATACTTCACCTTCGTGAAGCACTGCATTTATCAAATTCAATATTAAGATTGT
64 CATAAGAAAATGCATACTTCACCTTCGTGAAGCACTGCATTTATCAAATTCAATATTAAGATTGT
2096167 TGTTACATATAAAGATGGAAAATTAGGAAACATTATGTCAATTTATT
129 TGTTACATATAAAGATGGAAAATTAGGAAACATTATGTCAATTTATT
2096214 GATTTTCAGA
Statistics
Matches: 175, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
182 10 0.06
183 14 0.08
184 151 0.86
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (182 bp):
CAGTTGTTTATTTTTTCTCAATAACCCGTTTCAAGTTTGCAATAAACAGGCAGATCAGTAGGGCA
TAAGAAAATGCATACTTCACCTTCGTGAAGCACTGCATTTATCAAATTCAATATTAAGATTGTTG
TTACATATAAAGATGGAAAATTAGGAAACATTATGTCAATTTATTCAATATT
Found at i:2099928 original size:24 final size:22
Alignment explanation
Indices: 2099900--2099958 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 22
2099890 TATTTATTTT
2099900 TTTAAAAATATATTATTTTAAAT-
1 TTTAAAAATA-ATTA-TTTAAATA
2099923 TATTAATATAA-AATTATTTAAATA
1 T-TTAA-A-AATAATTATTTAAATA
2099947 TTTAAAAATAAT
1 TTTAAAAATAAT
2099959 AATAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
21 2 0.06
22 4 0.13
23 12 0.39
24 9 0.29
25 2 0.06
26 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAAAATAATTATTTAAATA
Found at i:2101606 original size:8 final size:8
Alignment explanation
Indices: 2101593--2101631 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
2101583 AAAATTAGAT
2101593 TAAAAAAA
1 TAAAAAAA
2101601 TAAAAAAAA
1 T-AAAAAAA
2101610 TAAAAAAA
1 TAAAAAAA
2101618 TAATAAATAA
1 TAA-AAA-AA
2101628 TAAA
1 TAAA
2101632 CAAACCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 11 0.39
9 12 0.43
10 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAAAAAA
Found at i:2101615 original size:17 final size:18
Alignment explanation
Indices: 2101593--2101631 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2101583 AAAATTAGAT
2101593 TAAAAAAATAA-AAAAAA
1 TAAAAAAATAATAAAAAA
*
2101610 TAAAAAAATAATAAATAA
1 TAAAAAAATAATAAAAAA
2101628 TAAA
1 TAAA
2101632 CAAACCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (18 bp):
TAAAAAAATAATAAAAAA
Found at i:2101648 original size:31 final size:31
Alignment explanation
Indices: 2101613--2101687 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
2101603 AAAAAAATAA
*
2101613 AAAAATAATAAATAATAAACAAACCTTGTCC
1 AAAAAGAATAAATAATAAACAAACCTTGTCC
2101644 AAAAAGAATAAATAATAAACAAACCTTGTCC
1 AAAAAGAATAAATAATAAACAAACCTTGTCC
2101675 AAAAAGAATAAAT
1 AAAAAGAATAAAT
2101688 GTTTGCGACG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.20
Consensus pattern (31 bp):
AAAAAGAATAAATAATAAACAAACCTTGTCC
Found at i:2104385 original size:17 final size:17
Alignment explanation
Indices: 2104363--2104396 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2104353 ACTGAATATT
*
2104363 AAATTTTAAACGGTGTA
1 AAATTTTAAACAGTGTA
2104380 AAATTTTAAACAGTGTA
1 AAATTTTAAACAGTGTA
2104397 TTGAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (17 bp):
AAATTTTAAACAGTGTA
Found at i:2104527 original size:17 final size:17
Alignment explanation
Indices: 2104505--2104538 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2104495 ACTTAATATT
2104505 AAATTTTAAACGGTGTA
1 AAATTTTAAACGGTGTA
2104522 AAATTTTAAACGGTGTA
1 AAATTTTAAACGGTGTA
2104539 TTGAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
AAATTTTAAACGGTGTA
Found at i:2104584 original size:142 final size:143
Alignment explanation
Indices: 2104357--2104645 Score: 508
Period size: 144 Copynumber: 2.0 Consensus size: 143
2104347 TTCAAAACTG
2104357 AATATTAAATTTTAAACGGTGTAAAATTTTAAACAGTGTATTGAAATAAAATAAAAACTTAAGTT
1 AATATTAAATTTTAAACGGTGTAAAATTTTAAACAGTGTATTGAAATAAAATAAAAACTTAAGTT
*
2104422 TTAGGTATGACTTT-AAAAAAATAAAAGGTTTAAGTATTTAAACGAATAAATAATAATAATTTAG
66 TTAGGTATGACTTTAAAAAAAATAAAAGGTTTAAGTATTTAAACGAATAAAAAATAATAATTTAG
*
2104486 ATATTAAATACTT
131 ATATTAAATACGT
*
2104499 AATATTAAATTTTAAACGGTGTAAAATTTTAAACGGTGTATTGAAATAAAATAAAAACTTAAGTT
1 AATATTAAATTTTAAACGGTGTAAAATTTTAAACAGTGTATTGAAATAAAATAAAAACTTAAG-T
* * *
2104564 TTTAGGTATGATTTTGAAAAAAATAAAAGGTTTAAGTATTTAAATGAATAAAAAATAATAATTTA
65 TTTAGGTATGACTTTAAAAAAAATAAAAGGTTTAAGTATTTAAACGAATAAAAAATAATAATTTA
2104629 GATATTAAATACGT
130 GATATTAAATACGT
2104643 AAT
1 AAT
2104646 TTACCCTAAT
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
142 62 0.44
143 15 0.11
144 63 0.45
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.36
Consensus pattern (143 bp):
AATATTAAATTTTAAACGGTGTAAAATTTTAAACAGTGTATTGAAATAAAATAAAAACTTAAGTT
TTAGGTATGACTTTAAAAAAAATAAAAGGTTTAAGTATTTAAACGAATAAAAAATAATAATTTAG
ATATTAAATACGT
Found at i:2108858 original size:128 final size:128
Alignment explanation
Indices: 2108628--2109234 Score: 968
Period size: 128 Copynumber: 4.7 Consensus size: 128
2108618 ACTATTCACA
* * *
2108628 TGAAGGCGCGTTCTCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCAA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
2108693 TTATGTCATTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTACTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * * *
2108756 TAAAGGCGCATTCCCGGGGGCTCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
2108821 TTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
2108884 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCA-ATGAATATGCTATCATTGCCCT
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGA-GAATATGTTATCATTGCCCT
2108948 ATTATGTCACTCATGTCCCTC-AGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
65 ATTATGTCACTCATGTCCCTCGA-GGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* ** *
2109012 TGAAGGTGCGTTCCTAGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * *
2109077 TTATGTCACTCATATCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTTAGGGGACT
66 TTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
2109140 TGAAGGCACGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
2109205 TTATGTCACTCATATCCCTC-AGGGACACTA
66 TTATGTCACTCATGTCCCTCGA-GGACACTA
2109235 GATGGATTGT
Statistics
Matches: 443, Mismatches: 31, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
127 2 0.00
128 440 0.99
129 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:2109669 original size:34 final size:34
Alignment explanation
Indices: 2109630--2109736 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
2109620 TAAGTTGAAA
* *
2109630 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
2109664 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
2109698 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
2109732 TTTAA
1 TTTAA
2109737 AAACATTTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:2110366 original size:21 final size:21
Alignment explanation
Indices: 2110257--2110372 Score: 137
Period size: 21 Copynumber: 5.5 Consensus size: 21
2110247 TATGATATAA
* *
2110257 AACCCTACGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
2110278 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
2110299 AACCCTGCGGGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
*
2110320 AA-CCTGGCGGGCAAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
2110341 AACCCTGCGGCCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
2110362 AACCCTGCGGG
1 AACCCTGCGGG
2110373 GATGGCATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.08
21 68 0.85
22 6 0.08
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:2110372 original size:42 final size:42
Alignment explanation
Indices: 2110274--2110365 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
2110264 CGGGCTAGGC
* *
2110274 ATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGAA
1 ATGTAACCTGGCGGGCAAGGAATGTAACCCTGCGGCCTCGAA
*
2110316 ATGTAACCTGGCGGGCAAGGAATGTAACCCTGCGGCCTCGGA
1 ATGTAACCTGGCGGGCAAGGAATGTAACCCTGCGGCCTCGAA
2110358 ATGTAACC
1 ATGTAACC
2110366 CTGCGGGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.18
Consensus pattern (42 bp):
ATGTAACCTGGCGGGCAAGGAATGTAACCCTGCGGCCTCGAA
Found at i:2110401 original size:21 final size:21
Alignment explanation
Indices: 2110375--2110422 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
2110365 CCTGCGGGGA
*
2110375 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
2110396 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
*
2110417 GGGCAT
1 TGGCAT
2110423 GTACCCTTAC
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:0.21, C:0.12, G:0.42, T:0.25
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:2112212 original size:30 final size:32
Alignment explanation
Indices: 2112148--2112226 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
2112138 TGTATAATTC
*
2112148 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
2112182 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
2112212 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
2112227 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:2113295 original size:20 final size:20
Alignment explanation
Indices: 2113116--2113306 Score: 108
Period size: 20 Copynumber: 9.6 Consensus size: 20
2113106 AAATGACCAA
2113116 CAAATTCGCAACGCGAA-TT
1 CAAATTCGCAACGCGAATTT
* * *
2113135 CTAATTTCGCAAC-CCAGTTT
1 C-AAATTCGCAACGCGAATTT
*
2113155 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
2113178 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
** *
2113196 CCAAATTCGCATTGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
* * **
2113217 CAAATTCTCAATGCGAAAGT
1 CAAATTCGCAACGCGAATTT
**
2113237 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
2113257 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
2113276 CAAATTCGTAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
2113296 -AATTTCGCAAC
1 CAAATTCGCAAC
2113307 AGGTTTTAGT
Statistics
Matches: 137, Mismatches: 23, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
18 1 0.01
19 28 0.20
20 88 0.64
21 18 0.13
22 1 0.01
23 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:2114074 original size:12 final size:12
Alignment explanation
Indices: 2114053--2114086 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2114043 ACCACATTTC
*
2114053 CAATACCAAACA
1 CAATATCAAACA
2114065 CAATATCAAACA
1 CAATATCAAACA
*
2114077 CAATCTCAAA
1 CAATATCAAA
2114087 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2114239 original size:24 final size:24
Alignment explanation
Indices: 2114212--2114258 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2114202 GTATTCGAAA
2114212 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
2114236 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
2114259 TTTTAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2114448 original size:3 final size:3
Alignment explanation
Indices: 2114440--2114467 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2114430 ATACAACCCT
2114440 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2114468 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2116553 original size:18 final size:18
Alignment explanation
Indices: 2116530--2116565 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2116520 AAGCAAAAGG
*
2116530 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2116548 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2116566 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2116907 original size:20 final size:21
Alignment explanation
Indices: 2116877--2116939 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
2116867 CGCGAAATAA
*
2116877 GCATTGCGAATTTGACTATT-
1 GCATAGCGAATTTGACTATTC
*
2116897 GCGTAGCGAATTTGACT-TTC
1 GCATAGCGAATTTGACTATTC
*
2116917 GCATTGCGAATTTGACTA-TC
1 GCATAGCGAATTTGACTATTC
2116937 GCA
1 GCA
2116940 ACGCTTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.05
20 35 0.95
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (21 bp):
GCATAGCGAATTTGACTATTC
Found at i:2117067 original size:25 final size:25
Alignment explanation
Indices: 2117029--2117078 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2117019 AAATCAATTA
*
2117029 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2117054 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
2117079 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:2117486 original size:18 final size:18
Alignment explanation
Indices: 2117465--2117501 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2117455 GTAATTGGAG
2117465 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2117483 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2117501 T
1 T
2117502 ATAAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2117508 original size:24 final size:24
Alignment explanation
Indices: 2117457--2117509 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2117447 TTTCATATGT
* * *
2117457 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2117481 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
2117505 AATTT
1 AATTT
2117510 CAGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2117813 original size:39 final size:39
Alignment explanation
Indices: 2117770--2117856 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
2117760 TCCGATGCTC
2117770 ATCAAAATCCAAAGCTCATATGGT-GCTAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGGC-AAGCAAAAGGAA
*
2117809 ATCAAAATCCAAATCTCATATGGTGGCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGGCAAGCAAAAGGAA
2117848 ATCAAAATC
1 ATCAAAATC
2117857 TACAACTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 44 0.96
40 2 0.04
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGGCAAGCAAAAGGAA
Found at i:2118139 original size:20 final size:21
Alignment explanation
Indices: 2118114--2118158 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
2118104 GCAACGCTTA
* *
2118114 TTTCGCGTTGCGAATTTG-AC
1 TTTCGCATTGCAAATTTGTAC
2118134 TTTCGCATTGCAAATTTGTAC
1 TTTCGCATTGCAAATTTGTAC
2118155 TTTC
1 TTTC
2118159 AACATGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTCGCATTGCAAATTTGTAC
Found at i:2118340 original size:61 final size:63
Alignment explanation
Indices: 2118209--2118349 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 63
2118199 TTTTAGAAAC
* *
2118209 AACAAATCAACTTTTATAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATTAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATTAAATT
2118274 A
63 A
* * ** *
2118275 AACAAATCAACTTTTACAAATCAATT-AA-TAAAAAAATAAATCTTATTTCCTCA-TAAATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATTAAATT-A
2118336 AACAAATCAACTTT
1 AACAAATCAACTTT
2118350 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
60 6 0.09
61 34 0.51
62 2 0.03
66 25 0.37
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.33
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATTAAATTA
Found at i:2119746 original size:21 final size:21
Alignment explanation
Indices: 2119722--2119817 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
2119712 GGCAAGACCA
*
2119722 CTTGAACGATGACAGTGGCCT
1 CTTGAACGATGACAGGGGCCT
* ** *
2119743 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGACAGGGGCCT
* *
2119764 CTTCG-ATGATGATAGGGGCCT
1 CTT-GAACGATGACAGGGGCCT
* *
2119785 CTTGAACGAT-AGGAGGTGCCT
1 CTTGAACGATGA-CAGGGGCCT
*
2119806 CTTGAATGATGA
1 CTTGAACGATGA
2119818 TAGGTGCATC
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (21 bp):
CTTGAACGATGACAGGGGCCT
Found at i:2119800 original size:42 final size:42
Alignment explanation
Indices: 2119722--2119821 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
2119712 GGCAAGACCA
* * * * * *
2119722 CTTGAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
*
2119764 CTTCG-ATGATGATAGGGGCCTCTTGAACGATAGGAGGTGCCT
1 CTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
2119806 CTTGAATGATGATAGG
1 CTTGAATGATGATAGG
2119822 TGCATCGGGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 47 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (42 bp):
CTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGGGGCCT
Found at i:2119822 original size:21 final size:21
Alignment explanation
Indices: 2119769--2119824 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2119759 GGCTTCTTCG
*
2119769 ATGATGATAGGGGCCTCTTGA
1 ATGATGATAGGTGCCTCTTGA
* *
2119790 ACGAT-AGGAGGTGCCTCTTGA
1 ATGATGA-TAGGTGCCTCTTGA
2119811 ATGATGATAGGTGC
1 ATGATGATAGGTGC
2119825 ATCGGGCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (21 bp):
ATGATGATAGGTGCCTCTTGA
Found at i:2122301 original size:22 final size:22
Alignment explanation
Indices: 2122270--2122328 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
2122260 AGATGGAGAT
*
2122270 AGACGTATTTCGTCGGAAAT-G
1 AGACGGATTTCGTCGGAAATGG
* * *
2122291 AGGACGGATTTTGTCAGAGATGG
1 A-GACGGATTTCGTCGGAAATGG
*
2122314 AGACGGATGTCGTCG
1 AGACGGATTTCGTCG
2122329 TAGAGAGTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 1 0.03
22 26 0.90
23 2 0.07
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25
Consensus pattern (22 bp):
AGACGGATTTCGTCGGAAATGG
Found at i:2122512 original size:21 final size:21
Alignment explanation
Indices: 2122488--2122542 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
2122478 TCGCGTTGCA
*
2122488 AATTTGGAATATCGGAACGCG
1 AATTTGGAAAATCGGAACGCG
* *
2122509 AATTTGGAAAATTGTAACGCG
1 AATTTGGAAAATCGGAACGCG
2122530 AATTTGGAAAATC
1 AATTTGGAAAATC
2122543 ACAATGCGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (21 bp):
AATTTGGAAAATCGGAACGCG
Found at i:2122551 original size:21 final size:21
Alignment explanation
Indices: 2122488--2122551 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
2122478 TCGCGTTGCA
* *
2122488 AATTTGGAATATCGGAACGCG
1 AATTTGGAAAATCGCAACGCG
* *
2122509 AATTTGGAAAATTGTAACGCG
1 AATTTGGAAAATCGCAACGCG
* *
2122530 AATTTGGAAAATCACAATGCG
1 AATTTGGAAAATCGCAACGCG
2122551 A
1 A
2122552 TTTACATATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.25
Consensus pattern (21 bp):
AATTTGGAAAATCGCAACGCG
Found at i:2122608 original size:20 final size:20
Alignment explanation
Indices: 2122559--2122614 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2122549 CGATTTACAT
2122559 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
2122579 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
2122599 ATTCGCGTTGC-AAATT
1 ATTCGCGTTGCGAAATT
2122615 TGTTGGTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.20
20 23 0.77
21 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:2123646 original size:25 final size:25
Alignment explanation
Indices: 2123612--2123662 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2123602 ACTGCCTGAG
2123612 ATAACAAAGTTCTTCGAAAGCCTCC
1 ATAACAAAGTTCTTCGAAAGCCTCC
2123637 ATAACAAAGTTCTTCGAAAGCCTCC
1 ATAACAAAGTTCTTCGAAAGCCTCC
2123662 A
1 A
2123663 AAACGACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (25 bp):
ATAACAAAGTTCTTCGAAAGCCTCC
Found at i:2126257 original size:17 final size:17
Alignment explanation
Indices: 2126230--2126285 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
2126220 AATTTACAAT
2126230 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
2126246 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2126263 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2126280 TAATTA
1 TAATTA
2126286 ATTTGATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
16 5 0.13
17 34 0.87
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:2127942 original size:20 final size:20
Alignment explanation
Indices: 2127917--2127954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2127907 CGAAGTCAAA
2127917 TTCGCAACAAGAATTTACAT
1 TTCGCAACAAGAATTTACAT
* *
2127937 TTCGCAGCACGAATTTAC
1 TTCGCAACAAGAATTTAC
2127955 CAAATTCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (20 bp):
TTCGCAACAAGAATTTACAT
Found at i:2128002 original size:20 final size:20
Alignment explanation
Indices: 2127979--2128054 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
2127969 ATTTTTCAAA
*
2127979 TTCGCAACTCGAATTTTAAT
1 TTCGCAACTCGAATTCTAAT
*
2127999 TTCGCAACTCGAATTCGAAT
1 TTCGCAACTCGAATTCTAAT
*
2128019 TTCGCAACTCGAATTCACCAAT
1 TTCGCAACTCGAATT--CTAAT
2128041 TTCGCAACTC-AATT
1 TTCGCAACTCGAATT
2128055 TTTGAATTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 33 0.65
21 4 0.08
22 14 0.27
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (20 bp):
TTCGCAACTCGAATTCTAAT
Found at i:2128013 original size:82 final size:82
Alignment explanation
Indices: 2127917--2128089 Score: 188
Period size: 82 Copynumber: 2.1 Consensus size: 82
2127907 CGAAGTCAAA
* * * * *
2127917 TTCGCAACAAGAATT-TACATTTCGCAGCACGAATTTACCAAATTCGCAATTC-ATTTTTCAAAT
1 TTCGCAACTAGAATTCGA-ATTTCGCAACACGAATTCACCAAATTCGCAACTCAATTTTT-AAAT
* *
2127980 TCGCAACTCGAATTTTAAT
64 TCGCAACTCGAATATGAAT
* * * *
2127999 TTCGCAACTCGAATTCGAATTTCGCAACTCGAATTCACCAATTTCGCAACTCAATTTTTGAATTC
1 TTCGCAACTAGAATTCGAATTTCGCAACACGAATTCACCAAATTCGCAACTCAATTTTTAAATTC
* * *
2128064 GTAACTTGAATATGGAT
66 GCAACTCGAATATGAAT
2128081 TTCGCAACT
1 TTCGCAACT
2128090 TGAAAATCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
82 68 0.91
83 7 0.09
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.34
Consensus pattern (82 bp):
TTCGCAACTAGAATTCGAATTTCGCAACACGAATTCACCAAATTCGCAACTCAATTTTTAAATTC
GCAACTCGAATATGAAT
Found at i:2128105 original size:82 final size:82
Alignment explanation
Indices: 2127937--2128118 Score: 197
Period size: 82 Copynumber: 2.2 Consensus size: 82
2127927 GAATTTACAT
* * * * * *
2127937 TTCGCAGCACGAATTTACCAAATTCGCAATTCATTTTTCAAATTCGCAACTCGAATTTTAATTTC
1 TTCGCAACTCGAATTCACCAAATTCGCAACTCATTTTTCAAATTCGCAACTCGAATATGAATTTC
* *
2128002 GCAACTCGAATTCGAAT
66 GCAACTCGAAATCGAAA
* * * * *
2128019 TTCGCAACTCGAATTCACCAATTTCGCAACTCAATTTTT-GAATTCGTAACTTGAATATGGATTT
1 TTCGCAACTCGAATTCACCAAATTCGCAACTC-ATTTTTCAAATTCGCAACTCGAATATGAATTT
*
2128083 CGCAACTTGAAAATC-AAA
65 CGCAACTCG-AAATCGAAA
2128101 TTCGCAACTCGAAATTCA
1 TTCGCAACTCG-AATTCA
2128119 TGTTGCGAAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
82 67 0.81
83 16 0.19
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (82 bp):
TTCGCAACTCGAATTCACCAAATTCGCAACTCATTTTTCAAATTCGCAACTCGAATATGAATTTC
GCAACTCGAAATCGAAA
Found at i:2128163 original size:20 final size:22
Alignment explanation
Indices: 2128136--2128190 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
2128126 AATTTAAAAA
2128136 TCGAGTTGCGAAAAA-G-AAAT
1 TCGAGTTGCGAAAAATGCAAAT
*
2128156 TCGTGTTGCGAAAAATGTCAAAT
1 TCGAGTTGCGAAAAATG-CAAAT
2128179 TCGAGTTGCGAA
1 TCGAGTTGCGAA
2128191 TTCGATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 14 0.47
21 1 0.03
23 15 0.50
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGAGTTGCGAAAAATGCAAAT
Found at i:2129040 original size:2 final size:2
Alignment explanation
Indices: 2129033--2129060 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2129023 CATACATTGT
2129033 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
2129061 AATTTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2130188 original size:183 final size:182
Alignment explanation
Indices: 2129866--2130252 Score: 586
Period size: 183 Copynumber: 2.1 Consensus size: 182
2129856 ATTTTCTAAT
* * * *
2129866 TTATATAA-AAATTAAATATTTTTTTAATTCAAAAAAAATTTATAATTAATTTAAATAATATATA
1 TTATATAATATATTTAATA-TTTTTTAATTCAAAAAAAATTTAAAAATAATTTAAATAATATATA
* *
2129930 ATTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
65 ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTA
*
2129995 TTGGATCTTAAATTATTAATTGAATTTTAAAT-AGTTTGGGCTT-AGCCCATATA
130 TTAGATCTTAAATTATTAATTGAATTTTAAATGA-TTTGGG-TTGAGCCCATATA
*
2130048 TTATATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTAAAAATAATTTAAATAATATA
1 -T-TATATAATATATTTAATATTTTTTAATTCAAAAAA-AATTTAAAAATAATTTAAATAATATA
*
2130112 TAATTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGT
63 TAATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGT
**
2130176 TATTAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATA
128 TATTAGATCTTAAATTATTAATTGAATTTTAAATGATTTGGGTTGAGCCCATATA
2130231 TTATATAATATATTTAATATTT
1 TTATATAATATATTTAATATTT
2130253 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
181 21 0.11
182 3 0.02
183 92 0.49
184 64 0.34
185 8 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (182 bp):
TTATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTAAAAATAATTTAAATAATATATAA
TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGAATTTTAAATGATTTGGGTTGAGCCCATATA
Done.