Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008876.1 Hibiscus syriacus cultivar Beakdansim tig00112114_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: 1683876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:153472 original size:2 final size:2
Alignment explanation
Indices: 153467--153493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
153457 TCTCTCTCTC
153467 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 T
153494 TGCTTGGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:153729 original size:142 final size:135
Alignment explanation
Indices: 153511--153774 Score: 395
Period size: 142 Copynumber: 1.9 Consensus size: 135
153501 GAAACAAGCA
* * * * *
153511 ATTAATTTTGAACCTAAACTTTTGAGTTACTTTTTTATCTTATTTTATACTTACATTTATTTATA
1 ATTAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTTATA
153576 ATGTAATAAATATGCAATATATATATATATATATATTTAACCTAAATTCCAATATAATCATTTTT
66 ATGTAATAAATATGCAATATATA-A-ATAT-T-TA---AA-CTAAATTCCAATATAATCATTTTT
153641 TGTTTTAATCAAT
123 TGTTTTAATCAAT
*
153654 ATTAATTTTCAACCTAAACTTTTGAGTTTC-TTTTAATCTTATTTAAAACTTAAATTTATTTATA
1 ATTAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTTATA
153718 ATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTT
66 ATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTT
153775 AATCAATTGA
Statistics
Matches: 115, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
134 24 0.21
135 2 0.02
138 2 0.02
139 1 0.01
140 4 0.03
141 1 0.01
142 53 0.46
143 28 0.24
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (135 bp):
ATTAATTTTCAACCTAAACTTTTGAGTTACTTTTTAATCTTATTTAAAACTTAAATTTATTTATA
ATGTAATAAATATGCAATATATAAATATTTAAACTAAATTCCAATATAATCATTTTTTGTTTTAA
TCAAT
Found at i:166927 original size:31 final size:30
Alignment explanation
Indices: 166892--166969 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
166882 AAGTAATCGC
166892 ATCTTAATTAAATAAAAACAAACGTGATAAT
1 ATCTTAATTAAATAAAAACAAACGTGAT-AT
* ** *
166923 ATCTTGATTAAATAAAAATGAATGTGATAT
1 ATCTTAATTAAATAAAAACAAACGTGATAT
166953 ATCTTAA-TAAATAAAAA
1 ATCTTAATTAAATAAAAA
166970 TGAAAATGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 10 0.24
30 8 0.19
31 24 0.57
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (30 bp):
ATCTTAATTAAATAAAAACAAACGTGATAT
Found at i:166979 original size:29 final size:29
Alignment explanation
Indices: 166892--166980 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
166882 AAGTAATCGC
*
166892 ATCTTAATTAAATAAAAA-CAAACGTGATAAT
1 ATCTTAA-TAAATAAAAATGAAA-GTGAT-AT
* *
166923 ATCTTGATTAAATAAAAATGAATGTGATAT
1 ATCTT-AATAAATAAAAATGAAAGTGATAT
*
166953 ATCTTAATAAATAAAAATGAAAATGATA
1 ATCTTAATAAATAAAAATGAAAGTGATA
166981 AAATGTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
29 20 0.40
30 7 0.14
31 20 0.40
32 3 0.06
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (29 bp):
ATCTTAATAAATAAAAATGAAAGTGATAT
Found at i:168428 original size:170 final size:171
Alignment explanation
Indices: 168146--168452 Score: 510
Period size: 170 Copynumber: 1.8 Consensus size: 171
168136 TGCAAAATCT
168146 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
1 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
*
168211 AAGCTATCAACTAAAGACCATTATAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTC-C
66 AAGCTATCAACTAAAGACCACTATAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCTC
168275 CAATCCACACTGTTTCTTTTTCGTGATCAAGTCTTTTATAG
131 CAATCCACACTGTTTCTTTTTCGTGATCAAGTCTTTTATAG
* * * *
168316 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTATGAATAACCATAATAGTCTTATATCTG
1 AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
* * **
168381 ACGCTATC-ACTGAAGACCACTATAAATACCCTTAGTCAAGACTGATAAGGGGCTAGAACCTTCT
66 AAGCTATCAACTAAAGACCACTAT-AATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCT
168445 CCAATCCA
130 CCAATCCA
168453 TACTCCATTC
Statistics
Matches: 126, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
169 13 0.10
170 105 0.83
171 8 0.06
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (171 bp):
AAAATCTTACTACTAGATCTATCTAGCATGCTGACCTACGAATAACCATAACAGTCTCATATATG
AAGCTATCAACTAAAGACCACTATAATACCCCAAGTCAAGACTGATAAGGGGCTAGAACCTTCTC
CAATCCACACTGTTTCTTTTTCGTGATCAAGTCTTTTATAG
Found at i:169930 original size:18 final size:18
Alignment explanation
Indices: 169907--169942 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
169897 ATGTCATTGC
169907 TTACATCAATTTAGTTTT
1 TTACATCAATTTAGTTTT
169925 TTACATCAATTTAGTTTT
1 TTACATCAATTTAGTTTT
169943 GATGTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (18 bp):
TTACATCAATTTAGTTTT
Found at i:174587 original size:29 final size:29
Alignment explanation
Indices: 174553--174611 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
174543 CCTAAATTAA
*
174553 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
174582 TTTGATGTAATTGCTTACATCAATTTAGT
1 TTTGATGTAATTGCTTACATCAATTTAGT
174611 T
1 T
174612 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTAATTGCTTACATCAATTTAGT
Found at i:174622 original size:29 final size:29
Alignment explanation
Indices: 174562--174619 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
174552 ATTTGATGTC
* *
174562 ATTGCTTACATCAATTTAGTTTTGATGTA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
*
174591 ATTGCTTACATCAATTTAG-TTAGGTGAA
1 ATTGCTTACATCAATTTAGTTTAGATGAA
174619 A
1 A
174620 ATTAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (29 bp):
ATTGCTTACATCAATTTAGTTTAGATGAA
Found at i:175137 original size:56 final size:57
Alignment explanation
Indices: 175051--175167 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 57
175041 ACAACATTCA
*
175051 ACATCGATTATGTTAGTCAAAAGTTTAGATTGAA-TTTTTTTCT-TGTTTCAAGAGTC
1 ACATCGATTATGTTAATCAAAAGTTTAGATTGAATTTTTTTTCTCT-TTTCAAGAGTC
175107 ACATCGATTTATGTTAATC-AAAGTTTAGATTGAATTTTTTTTCTCTTTTCAAGAGTC
1 ACATCGA-TTATGTTAATCAAAAGTTTAGATTGAATTTTTTTTCTCTTTTCAAGAGTC
175164 ACAT
1 ACAT
175168 TGTATGCAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
56 22 0.39
57 34 0.60
58 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (57 bp):
ACATCGATTATGTTAATCAAAAGTTTAGATTGAATTTTTTTTCTCTTTTCAAGAGTC
Found at i:204348 original size:20 final size:19
Alignment explanation
Indices: 204309--204349 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
204299 GTATAACTTT
**
204309 TAAATTATAAAAAATGTTA
1 TAAATTATAAAAAAAATTA
204328 TAAATTTATAAAAAAAATTA
1 TAAA-TTATAAAAAAAATTA
204348 TA
1 TA
204350 TTATTTTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATTATAAAAAAAATTA
Found at i:222428 original size:87 final size:86
Alignment explanation
Indices: 222264--222432 Score: 232
Period size: 87 Copynumber: 2.0 Consensus size: 86
222254 TAAAACATTA
* * *
222264 TTCTTCTTCATTGGTCCTCTTAACATCCCGATGAATGATCCTTGAGCTTCTATTGAATGAAGATA
1 TTCTTCTTCATTGGTCCTCTTAACATCCCGATGAATGATCCTTAAACTGCTATTGAATGAAGATA
*
222329 ATCTAAACCCATGAGTTTCTTC
66 ACCTAAACCCATG-GTTTCTTC
* * * *
222351 TTCTTCTTCTTTGGTGCTCTTAACTTCCCGATGAATGATTCCTTAAACTGCTATTGAATGAAGGT
1 TTCTTCTTCATTGGTCCTCTTAACATCCCGATGAATGA-TCCTTAAACTGCTATTGAATGAAGAT
*
222416 AACCTAGA-CCATGGTTT
65 AACCTAAACCCATGGTTT
222433 GCAGCTCCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
86 4 0.06
87 40 0.56
88 28 0.39
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (86 bp):
TTCTTCTTCATTGGTCCTCTTAACATCCCGATGAATGATCCTTAAACTGCTATTGAATGAAGATA
ACCTAAACCCATGGTTTCTTC
Found at i:227206 original size:24 final size:24
Alignment explanation
Indices: 227159--227206 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
227149 CATATAGTTC
*
227159 AAAAGAAATTCAGGGTTCCTTGAA
1 AAAAGAAATTCAGGGTTCCGTGAA
*
227183 AAAAGCAATTCAGGGATT-CGTGAA
1 AAAAGAAATTCAGGG-TTCCGTGAA
227207 GCAGGAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAAGAAATTCAGGGTTCCGTGAA
Found at i:234515 original size:16 final size:17
Alignment explanation
Indices: 234477--234515 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
234467 TTTGACTCAA
* *
234477 TATTAGTAAAAATTTAT
1 TATTAATAAAAATATAT
234494 TATTAATAAAAATATAT
1 TATTAATAAAAATATAT
234511 T-TTAA
1 TATTAA
234516 ATCGTTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTAATAAAAATATAT
Found at i:241186 original size:33 final size:33
Alignment explanation
Indices: 241139--241206 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
241129 TTAATGATTT
*
241139 AATAGTTGAGTGGTATAATTGAATTTAAAACTA
1 AATAGTTGAATGGTATAATTGAATTTAAAACTA
*
241172 AATAGTTGAATGGTATAATTGAATTTAAAATTA
1 AATAGTTGAATGGTATAATTGAATTTAAAACTA
241205 AA
1 AA
241207 GTCCAGTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.37
Consensus pattern (33 bp):
AATAGTTGAATGGTATAATTGAATTTAAAACTA
Found at i:246543 original size:22 final size:22
Alignment explanation
Indices: 246500--246546 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
246490 CAGACACCTC
* *
246500 TAAATATATTTATAATGTTTAA
1 TAAATATATATATAATGATTAA
246522 TAAATATATATATATAT-ATTAA
1 TAAATATATATATA-ATGATTAA
246544 TAA
1 TAA
246547 TTTATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAAATATATATATAATGATTAA
Found at i:247493 original size:177 final size:177
Alignment explanation
Indices: 247141--247499 Score: 668
Period size: 177 Copynumber: 2.0 Consensus size: 177
247131 CATAAGTCGC
*
247141 CAAGAAGTTCCTTCTGATCATATCCTTATTGGCAATTCGGATAAGGTGGATTTTGCTTGTCTTAA
1 CAAGGAGTTCCTTCTGATCATATCCTTATTGGCAATTCGGATAAGGTGGATTTTGCTTGTCTTAA
247206 TCTTGTAATTAGCTGTTTTGTAGTGTTCAGTAATATAATTCTCTTGTCCTTATTGCCTGAAACAG
66 TCTTGTAATTAGCTGTTTTGTAGTGTTCAGTAATATAATTCTCTTGTCCTTATTGCCTGAAACAG
247271 ACTCCAACTTCGTTTAATATATATCCGTCCACCACCAAGTCAATCTA
131 ACTCCAACTTCGTTTAATATATATCCGTCCACCACCAAGTCAATCTA
247318 CAAGGAGTTCCTTCTGATCATATCCTTATTGGCAATTCGGATAAGGTGGATTTTGCTTGTCTTAA
1 CAAGGAGTTCCTTCTGATCATATCCTTATTGGCAATTCGGATAAGGTGGATTTTGCTTGTCTTAA
247383 TCTTGTAATTAGCTGTTTTGTAGTGTTCAGT-A-ATAATTCTCTTGTCCTTATTGCCTGAAACAG
66 TCTTGTAATTAGCTGTTTTGTAGTGTTCAGTAATATAATTCTCTTGTCCTTATTGCCTGAAACAG
*
247446 ACTCCAACTTCGTTTAATATATATCCGTCCCCCAACCAAGTTCAATCTA
131 ACTCCAACTTCGTTTAATATATATCCGTCCACC-ACCAAG-TCAATCTA
247495 CAAGG
1 CAAGG
247500 TTGCAGTTAG
Statistics
Matches: 178, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
175 63 0.35
176 7 0.04
177 108 0.61
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (177 bp):
CAAGGAGTTCCTTCTGATCATATCCTTATTGGCAATTCGGATAAGGTGGATTTTGCTTGTCTTAA
TCTTGTAATTAGCTGTTTTGTAGTGTTCAGTAATATAATTCTCTTGTCCTTATTGCCTGAAACAG
ACTCCAACTTCGTTTAATATATATCCGTCCACCACCAAGTCAATCTA
Found at i:252222 original size:200 final size:204
Alignment explanation
Indices: 251894--252304 Score: 751
Period size: 200 Copynumber: 2.0 Consensus size: 204
251884 AATATAGTTA
251894 ATGGTAACAAACCAAAAATTTGGATGAATGTTTTGACATATTTAATTTAGTCCCTGATTTTCTAT
1 ATGGTAACAAACCAAAAATTTGGATGAATGTTTTGACATATTTAATTTAGTCCCTGATTTTCTAT
251959 TCCTTCAAACCCTTTTTTTAACTCAAATTTTCACAAAATTGAATCACATGCTCCTAAACCATCAT
66 TCCTTCAAACCC-TTTTTTAACTCAAATTTTCACAAAATTGAATCACATGCTCCTAAACCATCAT
252024 AGAATATATATGTACTTTCAATTTCAATTTTATAATTAA-TTTTTTATTTTTTTTAATTTAGTCC
130 AGAATATATATGTACTTTCAATTTCAATTTTATAATTAATTTTTTTATTTTTTTTAATTTAGTCC
252088 CTCAATTTTTC
195 CTCAA-TTTTC
252099 ATGGTAACAAACC-AAAATTTGGATGAATGTTTTGACATATTTAA-TTAGTCCCTGATTTTCTAT
1 ATGGTAACAAACCAAAAATTTGGATGAATGTTTTGACATATTTAATTTAGTCCCTGATTTTCTAT
252162 TCCTTCAAACCC-TTTTTAACTCAAA-TTTCACAAAATTGAATCACATGCTCCTAAACCATCATA
66 TCCTTCAAACCCTTTTTTAACTCAAATTTTCACAAAATTGAATCACATGCTCCTAAACCATCATA
*
252225 GAATATATATGTACTTTCAATTTCAATTTTATAATTAATTTTTTTTTTTTTTTTTAATTTAGTCC
131 GAATATATATGTACTTTCAATTTCAATTTTATAATTAA-TTTTTTTATTTTTTTTAATTTAGTCC
252290 CTCAATTTTC
195 CTCAATTTTC
252300 ATGGT
1 ATGGT
252305 TTCTGTATTT
Statistics
Matches: 203, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
200 76 0.37
201 23 0.11
202 29 0.14
203 31 0.15
204 31 0.15
205 13 0.06
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (204 bp):
ATGGTAACAAACCAAAAATTTGGATGAATGTTTTGACATATTTAATTTAGTCCCTGATTTTCTAT
TCCTTCAAACCCTTTTTTAACTCAAATTTTCACAAAATTGAATCACATGCTCCTAAACCATCATA
GAATATATATGTACTTTCAATTTCAATTTTATAATTAATTTTTTTATTTTTTTTAATTTAGTCCC
TCAATTTTC
Found at i:254515 original size:15 final size:14
Alignment explanation
Indices: 254468--254514 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
254458 TTTAAAATTT
*
254468 ATTTTAAAGAAAATC
1 ATTTTAAA-AAACTC
* *
254483 ACTTT-AAAAACTT
1 ATTTTAAAAAACTC
254496 ATTTTAAAAAACTC
1 ATTTTAAAAAACTC
254510 ATTTT
1 ATTTT
254515 TTTTGAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 8 0.31
14 14 0.54
15 4 0.15
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (14 bp):
ATTTTAAAAAACTC
Found at i:273795 original size:29 final size:29
Alignment explanation
Indices: 273645--273824 Score: 107
Period size: 29 Copynumber: 6.2 Consensus size: 29
273635 CCGTTGACCG
*
273645 TTGACAAGA-TGATATTTTAGTAATTATT
1 TTGAAAAGAGTGATATTTTAGTAATTATT
* * * * *
273673 TGGGAAATG-GTGCTATTCTGGTAATTATT
1 T-TGAAAAGAGTGATATTTTAGTAATTATT
* * * * *
273702 TTGAAAAGATTGCTATTTTTGTATTTTTT
1 TTGAAAAGAGTGATATTTTAGTAATTATT
* * * * *
273731 TTAAAAAAAGTGACAATTTAGTAA-AATT
1 TTGAAAAGAGTGATATTTTAGTAATTATT
**
273759 TAAAAAAAGAGTGATATTTTAGTAATTATT
1 T-TGAAAAGAGTGATATTTTAGTAATTATT
* * *
273789 TTGAAAATGA-TGTTATTTTGGTAATTAAT
1 TTGAAAA-GAGTGATATTTTAGTAATTATT
*
273818 TTCAAAA
1 TTGAAAA
273825 TGGTGCTATT
Statistics
Matches: 112, Mismatches: 34, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
28 9 0.08
29 97 0.87
30 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (29 bp):
TTGAAAAGAGTGATATTTTAGTAATTATT
Found at i:273834 original size:29 final size:29
Alignment explanation
Indices: 273773--273834 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
273763 AAAAGAGTGA
* * *
273773 TATTTTAGTAATTATTTTGAAAATGATGT
1 TATTTTAGTAATTAATTTCAAAATGATGC
* *
273802 TATTTTGGTAATTAATTTCAAAATGGTGC
1 TATTTTAGTAATTAATTTCAAAATGATGC
273831 TATT
1 TATT
273835 AATGTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (29 bp):
TATTTTAGTAATTAATTTCAAAATGATGC
Found at i:274836 original size:42 final size:41
Alignment explanation
Indices: 274772--274934 Score: 220
Period size: 42 Copynumber: 3.9 Consensus size: 41
274762 GTATTACCAG
* *
274772 GTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCTCAT
1 GTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTC-CAA
* *
274814 GTCCCTTTGTTGTGTGCAAAGGTAAGCCTTACAGTTTACCAG
1 GTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTT-CCAA
* *
274856 GTCCCTTTGCTGTGTGCAATGGTAAGCCTTACAGTTCCCCAA
1 GTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTT-TCCAA
*
274898 GTCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTT
1 GTCCCTTTGCTGTGTGCAAAGG-TAAGCCTTACAGTTT
274935 TCCTGGGCTC
Statistics
Matches: 108, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
41 3 0.03
42 104 0.96
43 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (41 bp):
GTCCCTTTGCTGTGTGCAAAGGTAAGCCTTACAGTTTCCAA
Found at i:274906 original size:84 final size:84
Alignment explanation
Indices: 274765--274934 Score: 263
Period size: 84 Copynumber: 2.0 Consensus size: 84
274755 GAAGGAAGTA
* * * *
274765 TTACCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCTCATGTCCCTTTGTTGTGTG
1 TTACCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTCCCCAAGTCCCTTTGCTGTGTG
*
274830 CAAAGG-TAAGCCTTACAGT
66 C-AAGGATAAACCTTACAGT
274849 TTACCAGGTCCCTTTGCTGTGTGC-AATGGTAAGCCTTACAGTTCCCCAAGTCCCTTTGCTGTGT
1 TTACCAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTCCCCAAGTCCCTTTGCTGTGT
274913 GCAAGGATAAACCTTACAGT
65 GCAAGGATAAACCTTACAGT
274933 TT
1 TT
274935 TCCTGGGCTC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
83 6 0.08
84 73 0.92
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (84 bp):
TTACCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTCCCCAAGTCCCTTTGCTGTGTG
CAAGGATAAACCTTACAGT
Found at i:285492 original size:31 final size:31
Alignment explanation
Indices: 285454--285517 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
285444 GTGTGAGACA
285454 TGGTGTCATAAAGGTTTTTAAAAGTCTGGTC
1 TGGTGTCATAAAGGTTTTTAAAAGTCTGGTC
285485 TGGTGTCATAAAGGTTTTTAAAAGTCTGGTC
1 TGGTGTCATAAAGGTTTTTAAAAGTCTGGTC
285516 TG
1 TG
285518 CCATTGAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (31 bp):
TGGTGTCATAAAGGTTTTTAAAAGTCTGGTC
Found at i:292986 original size:25 final size:27
Alignment explanation
Indices: 292935--292997 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
292925 TAGATTTTCA
*
292935 TATAAAAAATGGTATAAGAATACAATTT
1 TATAAAAAAT-ATATAAGAATACAATTT
292963 TATAAAAAATATA-AAGAATA-AATTT
1 TATAAAAAATATATAAGAATACAATTT
*
292988 TA-AAATAATA
1 TATAAAAAATA
292998 CAAGTACCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 7 0.21
25 7 0.21
26 7 0.21
27 2 0.06
28 10 0.30
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (27 bp):
TATAAAAAATATATAAGAATACAATTT
Found at i:293309 original size:21 final size:21
Alignment explanation
Indices: 293267--293314 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
293257 TTTTTATTTT
* *
293267 TAAAAAAATTAACTGTTTTTA
1 TAAAAAAATTAAATGTTATTA
293288 TAAAAAAATTAAAT-TTAATTA
1 TAAAAAAATTAAATGTT-ATTA
293309 TAAAAA
1 TAAAAA
293315 TAGATCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAAAAATTAAATGTTATTA
Found at i:304779 original size:24 final size:24
Alignment explanation
Indices: 304752--304803 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
304742 CGTTCATTTA
*
304752 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* ***
304776 CGTTTATGTTTGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
304800 CGTT
1 CGTT
304804 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:304804 original size:24 final size:24
Alignment explanation
Indices: 304763--304809 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
304753 GTTCGTGAAC
304763 GTTCGGTTATGTTCGTTTATGTTT
1 GTTCGGTTATGTTCGTTTATGTTT
304787 GTTCGGTTATGTTCGTTTATGTT
1 GTTCGGTTATGTTCGTTTATGTT
304810 CATTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.26, T:0.57
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTTATGTTT
Found at i:304820 original size:24 final size:24
Alignment explanation
Indices: 304768--304823 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
304758 TGAACGTTCG
** *
304768 GTTATGTTCGTTTATGTTTGTTCG
1 GTTATGTTCGTTTATGTTCATTCA
304792 GTTATGTTCGTTTATGTTCATTCA
1 GTTATGTTCGTTTATGTTCATTCA
*
304816 TTTATGTT
1 GTTATGTT
304824 TAACTCAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.09, G:0.20, T:0.59
Consensus pattern (24 bp):
GTTATGTTCGTTTATGTTCATTCA
Found at i:306883 original size:8 final size:8
Alignment explanation
Indices: 306858--306898 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
306848 CAGTAAGCCA
306858 TTCATCTCT
1 TTCATCT-T
306867 TTC-TCTT
1 TTCATCTT
306874 TTCATCTT
1 TTCATCTT
306882 TTCATCTT
1 TTCATCTT
306890 TTCATCTT
1 TTCATCTT
306898 T
1 T
306899 GTTGATCGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 4 0.13
8 24 0.77
9 3 0.10
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (8 bp):
TTCATCTT
Found at i:310619 original size:24 final size:24
Alignment explanation
Indices: 310592--310649 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
310582 CACTTCACAC
310592 GGCGATCAGATCAGTCTTCTAACT
1 GGCGATCAGATCAGTCTTCTAACT
*
310616 GGCGATCAGATCAGTCTTCTCACT
1 GGCGATCAGATCAGTCTTCTAACT
310640 GGCGAT-AGAT
1 GGCGATCAGAT
310650 TGTTACCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (24 bp):
GGCGATCAGATCAGTCTTCTAACT
Found at i:318817 original size:2 final size:2
Alignment explanation
Indices: 318810--318837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
318800 AAATATTTGA
318810 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
318838 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:336959 original size:15 final size:15
Alignment explanation
Indices: 336939--336976 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
336929 CCCTGCACAA
*
336939 AAATAAATGAGAAAT
1 AAATAAATGAAAAAT
*
336954 AAATAAATTAAAAAT
1 AAATAAATGAAAAAT
336969 AAATAAAT
1 AAATAAAT
336977 AATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAATGAAAAAT
Found at i:336980 original size:26 final size:26
Alignment explanation
Indices: 336937--336989 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
336927 GACCCTGCAC
*
336937 AAAAATAAATGAGAAATAAATAA-ATT
1 AAAAATAAATGAAAAAT-AATAATATT
336963 AAAAATAAAT-AAATAATAATAATATT
1 AAAAATAAATGAAA-AATAATAATATT
336989 A
1 A
336990 TATATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAATAAATGAAAAATAATAATATT
Found at i:337176 original size:35 final size:35
Alignment explanation
Indices: 337001--337188 Score: 118
Period size: 36 Copynumber: 5.3 Consensus size: 35
336991 ATATATAAAC
* ** *
337001 GTTTTCAAAAAC-ATATAATATAAATTTTTTAAAAT
1 GTTTTCAAAAACTATATATTAT-AATTTTCAAAAAA
* * **
337036 GTTTTAAAAAAACTATATATTATATATATTCAAAATG
1 GTTTT-CAAAAACTATATATTATA-ATTTTCAAAAAA
* * * *
337073 GTTTTTAAAAATTATATA-TATAAATGTTTTC-ATAAC
1 GTTTTCAAAAACTATATATTAT-AA--TTTTCAAAAAA
**
337109 GTTTTC-AAAGGTATAT-TATATATATTTT-AAAAAA
1 GTTTTCAAAAACTATATAT-TATA-ATTTTCAAAAAA
337143 GTTTTCAAAAACTATATATTATAATTTTCAAAAAA
1 GTTTTCAAAAACTATATATTATAATTTTCAAAAAA
*
337178 TATTTTCAAAA
1 -GTTTTCAAAA
337189 TTGTTTTTAA
Statistics
Matches: 118, Mismatches: 21, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
34 18 0.15
35 36 0.31
36 40 0.34
37 24 0.20
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (35 bp):
GTTTTCAAAAACTATATATTATAATTTTCAAAAAA
Found at i:337244 original size:35 final size:35
Alignment explanation
Indices: 337203--337372 Score: 101
Period size: 36 Copynumber: 4.7 Consensus size: 35
337193 TTTTAAAAAT
* * *
337203 TATATATTATATAAATGTTTTCATAACGTTTTCAAAG
1 TATATA-T-TATAAATATTTTAAAAACGTTTTCAAAG
* *
337240 TATATATTATATATATTTTAAAAACGTTTTCAAAAAC
1 TATATATTATAAATATTTTAAAAACGTTTTC--AAAG
* * ** * *
337277 TATATATTATATA-ATTTTCAAAATATTTTAAAAAC
1 TATATATTATAAATATTTTAAAAACGTTTT-CAAAG
* * * *
337312 TATATAATATACATATTTTCAAAAAATGTTTT-AAAC
1 TATATATTATAAATATTTT--AAAAACGTTTTCAAAG
** *
337348 TATATATTATATGTATTTTCAAAAC
1 TATATATTATAAATATTTTAAAAAC
337373 AATTTGCAAA
Statistics
Matches: 109, Mismatches: 18, Indels: 15
0.77 0.13 0.11
Matches are distributed among these distances:
34 4 0.04
35 35 0.32
36 39 0.36
37 22 0.20
38 9 0.08
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTATAAATATTTTAAAAACGTTTTCAAAG
Found at i:337245 original size:37 final size:38
Alignment explanation
Indices: 337175--337359 Score: 131
Period size: 37 Copynumber: 5.0 Consensus size: 38
337165 AATTTTCAAA
** * *
337175 AAATATTTTCAAAATTGTTTTTAAAAATTATATATTATAT
1 AAATATTTT-AAAAACG-TTTTCAAAACTATATATTATAT
* * * *
337215 AAATGTTTTCATAACGTTTTC-AAAGTATATATTATAT
1 AAATATTTTAAAAACGTTTTCAAAACTATATATTATAT
337252 --ATATTTTAAAAACGTTTTCAAAAACTATATATTATAT
1 AAATATTTTAAAAACGTTTTC-AAAACTATATATTATAT
* *
337289 -AAT-TTTCAAAATA--TTTTAAAAACTATATA--ATAT
1 AAATATTTTAAAA-ACGTTTTCAAAACTATATATTATAT
* *
337322 ACATATTTTCAAAAAATGTTTT--AAACTATATATTATAT
1 AAATATTTT--AAAAACGTTTTCAAAACTATATATTATAT
337360 GTATTTTCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
33 4 0.03
34 2 0.02
35 30 0.25
36 15 0.13
37 41 0.35
38 15 0.13
39 3 0.03
40 8 0.07
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (38 bp):
AAATATTTTAAAAACGTTTTCAAAACTATATATTATAT
Found at i:337277 original size:122 final size:120
Alignment explanation
Indices: 337059--337299 Score: 396
Period size: 122 Copynumber: 2.0 Consensus size: 120
337049 TATATATTAT
*
337059 ATATATTCAAAATGGTTTTTAAAAATTATATATATAAATGTTTTCATAACGTTTTCAAAGGTATA
1 ATATATTCAAAATGGTTTTTAAAAATTATATATATAAATGTTTTCATAACGTTTTCAAAGATATA
337124 TTATATATATTTTAAAAAAGTTTTCAAAAACTATATA-T-TATAATTTTCAAAAA
66 TTATATATATTTTAAAAAAGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
* *
337177 ATATTTTCAAAATTGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAGTA
1 ATATATTCAAAATGGTTTTTAAAAA-T-TATA-TATATAAATGTTTTCATAACGTTTTCAAAG-A
*
337242 TATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
62 TATATTATATATATTTTAAAAAAGTTTTCAAAAACTATATATTATATAATTTTCAAAA
337300 TATTTTAAAA
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
118 23 0.20
119 1 0.01
120 4 0.04
121 30 0.27
122 40 0.35
123 1 0.01
124 14 0.12
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (120 bp):
ATATATTCAAAATGGTTTTTAAAAATTATATATATAAATGTTTTCATAACGTTTTCAAAGATATA
TTATATATATTTTAAAAAAGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:337348 original size:36 final size:36
Alignment explanation
Indices: 337230--337397 Score: 157
Period size: 36 Copynumber: 4.6 Consensus size: 36
337220 TTTTCATAAC
* *
337230 GTTTTCAAAGTATATATTATATATATTTT--AAAAAC
1 GTTTT-AAACTATATATTATATATATTTTCAAAAAAT
*
337265 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAATAT
1 GTTTT---AAACTATATATTATATATATTTTCAAAAAAT
* * *
337303 -TTTAAAAACTATATAATATACATATTTTCAAAAAAT
1 GTTT-TAAACTATATATTATATATATTTTCAAAAAAT
*
337339 GTTTTAAACTATATATTATATGTATTTTCAAAACAAT
1 GTTTTAAACTATATATTATATATATTTTCAAAA-AAT
** *
337376 -TTGCAAACTATATAATATATAT
1 GTTTTAAACTATATATTATATAT
337398 GTGTATATAT
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
35 20 0.18
36 60 0.55
37 25 0.23
38 4 0.04
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (36 bp):
GTTTTAAACTATATATTATATATATTTTCAAAAAAT
Found at i:337425 original size:7 final size:8
Alignment explanation
Indices: 337410--337434 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
337400 GTATATATGT
337410 ATAAAAAA
1 ATAAAAAA
337418 ATAAAAAA
1 ATAAAAAA
337426 ATAAAAAA
1 ATAAAAAA
337434 A
1 A
337435 ATATGGACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:344166 original size:28 final size:28
Alignment explanation
Indices: 344134--344191 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
344124 GTTTGTAAAA
344134 GAAATAGGTGAATTGAAGTTATGACTGT
1 GAAATAGGTGAATTGAAGTTATGACTGT
344162 GAAATAGGTGAATTGAAGTTATGACTGT
1 GAAATAGGTGAATTGAAGTTATGACTGT
344190 GA
1 GA
344192 GATACCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.31
Consensus pattern (28 bp):
GAAATAGGTGAATTGAAGTTATGACTGT
Found at i:353970 original size:105 final size:105
Alignment explanation
Indices: 353788--353995 Score: 389
Period size: 105 Copynumber: 2.0 Consensus size: 105
353778 TCTTTAACCC
*
353788 ATCTTTGCTGAATCCATCAATAAACTTTTTGAAAACTCATTGGTACTAATATGTAAACTTAGGAT
1 ATCTTCGCTGAATCCATCAATAAACTTTTTGAAAACTCATTGGTACTAATATGTAAACTTAGGAT
353853 TTCTTTTTGGGTTTAGTTTAGGGGCTTATTGGTTTTGAAT
66 TTCTTTTTGGGTTTAGTTTAGGGGCTTATTGGTTTTGAAT
*
353893 ATCTTCGCTGAATCCATCAATAAACTTTTTGAAAACTCATTGGTACTGATATGTAAACTTAGGAT
1 ATCTTCGCTGAATCCATCAATAAACTTTTTGAAAACTCATTGGTACTAATATGTAAACTTAGGAT
*
353958 TTCTTTTTGGGTTTGGTTTAGGGGCTTATTGGTTTTGA
66 TTCTTTTTGGGTTTAGTTTAGGGGCTTATTGGTTTTGA
353996 TGTAATTTTT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43
Consensus pattern (105 bp):
ATCTTCGCTGAATCCATCAATAAACTTTTTGAAAACTCATTGGTACTAATATGTAAACTTAGGAT
TTCTTTTTGGGTTTAGTTTAGGGGCTTATTGGTTTTGAAT
Found at i:354265 original size:2 final size:2
Alignment explanation
Indices: 354258--354297 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
354248 TATTACCCAA
354258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354298 TCAATATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359356 original size:29 final size:30
Alignment explanation
Indices: 359321--359380 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
359311 ATTACCATAA
*
359321 AACTTTAAATT-GATTCAATTGTAGCATTG
1 AACTTTAAATTGGATTCAATTATAGCATTG
** *
359350 AACTTTAGTTTGGCTTCAATTATAGCATTG
1 AACTTTAAATTGGATTCAATTATAGCATTG
359380 A
1 A
359381 GTTGGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (30 bp):
AACTTTAAATTGGATTCAATTATAGCATTG
Found at i:362491 original size:23 final size:23
Alignment explanation
Indices: 362461--362580 Score: 84
Period size: 23 Copynumber: 5.2 Consensus size: 23
362451 AAAAACCTTG
* *
362461 TTTACCAGAGTCGGAGAACTCTA
1 TTTACCAGAGTCGGAAAAATCTA
* *
362484 TTTACCAGACTCGGAAAAATCTG
1 TTTACCAGAGTCGGAAAAATCTA
*
362507 TTTACCAGAG-CTGAAAAA-CTGCA
1 TTTACCAGAGTCGGAAAAATCT--A
* **
362530 TTTACCAGACG-CGGAAAACTCCG
1 TTTACCAGA-GTCGGAAAAATCTA
* **
362553 TTTACCAGAGCCAAAAAAACTCTA
1 TTTACCAGAGTCGGAAAAA-TCTA
362577 TTTA
1 TTTA
362581 AGATATAAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
21 2 0.03
22 8 0.11
23 51 0.68
24 13 0.17
25 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (23 bp):
TTTACCAGAGTCGGAAAAATCTA
Found at i:362570 original size:46 final size:46
Alignment explanation
Indices: 362483--362570 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
362473 GGAGAACTCT
* * **
362483 ATTTACCAGACTCGGAAAAATCTGTTTACCAGAGCTGAAAAACTGC
1 ATTTACCAGACGCGGAAAAATCCGTTTACCAGAGCCAAAAAACTGC
*
362529 ATTTACCAGACGCGGAAAACTCCGTTTACCAGAGCCAAAAAA
1 ATTTACCAGACGCGGAAAAATCCGTTTACCAGAGCCAAAAAA
362571 ACTCTATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (46 bp):
ATTTACCAGACGCGGAAAAATCCGTTTACCAGAGCCAAAAAACTGC
Found at i:364040 original size:27 final size:28
Alignment explanation
Indices: 363976--364040 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
363966 TTATTTTAAG
* *
363976 TTTA-TTTATTTATTGTTTTTTTTACTA
1 TTTATTTTAATTATTGTCTTTTTTACTA
364003 TTT-TTTT-ATTATTGTACTTTTTTA-T-
1 TTTATTTTAATTATTGT-CTTTTTTACTA
364028 TTTATTTTAATTA
1 TTTATTTTAATTA
364041 AGTTTGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
25 3 0.09
26 12 0.38
27 17 0.53
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (28 bp):
TTTATTTTAATTATTGTCTTTTTTACTA
Found at i:364697 original size:33 final size:33
Alignment explanation
Indices: 364660--364724 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
364650 TAAGCCCTCA
* * *
364660 AGCTTCCTCTGTTCGTATATATATCGATGATAG
1 AGCTTCCTCTCTTCATACATATATCGATGATAG
*
364693 AGCTTCCTCTCTTTATACATATATCGATGATA
1 AGCTTCCTCTCTTCATACATATATCGATGATA
364725 TGGTTTCGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (33 bp):
AGCTTCCTCTCTTCATACATATATCGATGATAG
Found at i:364902 original size:22 final size:22
Alignment explanation
Indices: 364875--364920 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
364865 TTGATGGATG
364875 TATGTA-GTATGTATAT-TATATA
1 TATGTATGTA-GTATATATA-ATA
364897 TATGTATGTAGTATATATAATA
1 TATGTATGTAGTATATATAATA
364919 TA
1 TA
364921 CTAGTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (22 bp):
TATGTATGTAGTATATATAATA
Found at i:368217 original size:18 final size:18
Alignment explanation
Indices: 368194--368228 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
368184 TTCCAGGTAT
*
368194 TCCTCCAGCACAAGATAC
1 TCCTCCAACACAAGATAC
368212 TCCTCCAACACAAGATA
1 TCCTCCAACACAAGATA
368229 TGGAACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.37, G:0.09, T:0.17
Consensus pattern (18 bp):
TCCTCCAACACAAGATAC
Found at i:368288 original size:23 final size:23
Alignment explanation
Indices: 368242--368288 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
368232 AACAAATTTC
**
368242 CCTAAAATTCAACACCTATTTAT
1 CCTAAAATTCAACACCTAAATAT
* *
368265 CCTAAAATTCAGCAGCTAAATAT
1 CCTAAAATTCAACACCTAAATAT
368288 C
1 C
368289 TAAGAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (23 bp):
CCTAAAATTCAACACCTAAATAT
Found at i:368979 original size:23 final size:24
Alignment explanation
Indices: 368921--369048 Score: 97
Period size: 23 Copynumber: 5.5 Consensus size: 24
368911 TTTTATATAT
368921 TAAATAGAGTTTTCCGGC-TCTGG
1 TAAATAGAGTTTTCCGGCTTCTGG
** *
368944 TAAACGGAATTTT-CGGCTTCTGG
1 TAAATAGAGTTTTCCGGCTTCTGG
* *
368967 TAAATACAGTTTTCCAGCTT-TGG
1 TAAATAGAGTTTTCCGGCTTCTGG
* * *
368990 TAAACAAATTTTTCCGAG--TCTGG
1 TAAATAGAGTTTTCCG-GCTTCTGG
* *
369013 TAAATAGTGTTCTCCGGC-TCTGG
1 TAAATAGAGTTTTCCGGCTTCTGG
* *
369036 TAAAGAGGGTTTT
1 TAAATAGAGTTTT
369049 TGATTTTGAT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
22 6 0.08
23 68 0.85
24 6 0.08
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (24 bp):
TAAATAGAGTTTTCCGGCTTCTGG
Found at i:369003 original size:46 final size:46
Alignment explanation
Indices: 368921--369039 Score: 123
Period size: 46 Copynumber: 2.6 Consensus size: 46
368911 TTTTATATAT
* * * * **
368921 TAAATAGAGTTTTCCGGCTCTGGTAAACGGAATTTTCGGCTTCTGG
1 TAAATACAGTTTTCCAGCTCTGGTAAACGAAATTTTCCGAGTCTGG
*
368967 TAAATACAGTTTTCCAGCTTTGGTAAAC-AAATTTTTCCGAGTCTGG
1 TAAATACAGTTTTCCAGCTCTGGTAAACGAAA-TTTTCCGAGTCTGG
** * *
369013 TAAATAGTGTTCTCCGGCTCTGGTAAA
1 TAAATACAGTTTTCCAGCTCTGGTAAA
369040 GAGGGTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 2 0.03
46 58 0.97
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
TAAATACAGTTTTCCAGCTCTGGTAAACGAAATTTTCCGAGTCTGG
Found at i:372953 original size:15 final size:15
Alignment explanation
Indices: 372935--372963 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
372925 AAAAGTGTGA
372935 ACAATAAAATAAAAT
1 ACAATAAAATAAAAT
372950 ACAATAAAATAAAA
1 ACAATAAAATAAAA
372964 ATGAAAAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
ACAATAAAATAAAAT
Found at i:372964 original size:21 final size:21
Alignment explanation
Indices: 372940--372979 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
372930 TGTGAACAAT
372940 AAAAT-AAAATACAATAAAATA
1 AAAATGAAAA-ACAATAAAATA
*
372961 AAAATGAAAAACGATAAAA
1 AAAATGAAAAACAATAAAA
372980 AATACCCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAATGAAAAACAATAAAATA
Found at i:373205 original size:9 final size:9
Alignment explanation
Indices: 373191--373221 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
373181 ATAATAAAAC
373191 AAAAATAAA
1 AAAAATAAA
373200 AAAAATAAAA
1 AAAAAT-AAA
373210 AAAAATAAA
1 AAAAATAAA
373219 AAA
1 AAA
373222 TTTCATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:373210 original size:10 final size:10
Alignment explanation
Indices: 373183--373221 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
373173 TTATGCACAT
373183 AATAAAACAAA
1 AATAAAA-AAA
373194 AAT-AAAAAA
1 AATAAAAAAA
373203 AATAAAAAAA
1 AATAAAAAAA
373213 AATAAAAAA
1 AATAAAAAA
373222 TTTCATACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 6 0.22
10 18 0.67
11 3 0.11
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:373215 original size:19 final size:20
Alignment explanation
Indices: 373183--373221 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
373173 TTATGCACAT
373183 AATAAAACAAAAATAAAAAA
1 AATAAAACAAAAATAAAAAA
373203 AATAAAA-AAAAATAAAAAA
1 AATAAAACAAAAATAAAAAA
373222 TTTCATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (20 bp):
AATAAAACAAAAATAAAAAA
Found at i:375028 original size:25 final size:24
Alignment explanation
Indices: 374995--375060 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
374985 GTAATGGATA
374995 AATAATAATTAATAATAACTA-TAAT
1 AATAATAA-TAATAATAA-TAGTAAT
*
375020 AATAATAATAACTAATAATAGTATT
1 AATAATAATAA-TAATAATAGTAAT
*
375045 AATAATTA-AATAATAA
1 AATAATAATAATAATAA
375061 AAAAAGACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 24 0.65
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAATAATAATAATAATAGTAAT
Found at i:375047 original size:28 final size:30
Alignment explanation
Indices: 374993--375060 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
374983 ATGTAATGGA
*
374993 TAAATAATAATTAATAATAACTATAATAA-
1 TAAATAATAACTAATAATAACTATAATAAT
*
375022 T-AATAATAACTAATAAT-AGTATTAATAAT
1 TAAATAATAACTAATAATAACTA-TAATAAT
375051 TAAATAATAA
1 TAAATAATAA
375061 AAAAAGACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 3 0.09
28 21 0.62
29 2 0.06
30 8 0.24
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (30 bp):
TAAATAATAACTAATAATAACTATAATAAT
Found at i:375080 original size:3 final size:3
Alignment explanation
Indices: 374995--375060 Score: 64
Period size: 3 Copynumber: 21.7 Consensus size: 3
374985 GTAATGGATA
*
374995 AAT AAT AATT AAT AAT AACT -AT AAT AAT AAT AAT AACT AAT AAT AGT
1 AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT AAT
* *
375042 ATT AAT AAT TA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
375061 AAAAAGACCC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.04
3 44 0.83
4 7 0.13
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:382893 original size:18 final size:18
Alignment explanation
Indices: 382872--382906 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
382862 TCAACGGGAA
382872 GGGTCAACAGGTCGGGTC
1 GGGTCAACAGGTCGGGTC
*
382890 GGGTCAACGGGTCGGGT
1 GGGTCAACAGGTCGGGT
382907 TATGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
GGGTCAACAGGTCGGGTC
Found at i:387908 original size:21 final size:22
Alignment explanation
Indices: 387867--387909 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
387857 TTTTTAATAA
* *
387867 CTCTGCCTTTATGGTACATTTC
1 CTCTGCATTTATGGCACATTTC
387889 CTCTGCATTTAT-GCACATTTC
1 CTCTGCATTTATGGCACATTTC
387910 GATCGTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (22 bp):
CTCTGCATTTATGGCACATTTC
Found at i:394647 original size:60 final size:60
Alignment explanation
Indices: 394529--394647 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
394519 AACATATAAC
* * * * * *
394529 TCAAAAGATCATTTTGTAACTTTTAATAGTTAAGGGATTTAACAAAACATTATTCTATAG
1 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATAG
* *
394589 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAATGACTCAACAAAATAATATCCTATA
1 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATA
394648 ATGGAGGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (60 bp):
TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATAG
Found at i:396715 original size:207 final size:204
Alignment explanation
Indices: 396354--396770 Score: 782
Period size: 207 Copynumber: 2.0 Consensus size: 204
396344 TAAATATATT
396354 AACTCAAATTAGAAAAGCTCAAGTTTTGAATAGACGATGCCCAAGCATAATTTGAGTTTTCTGAA
1 AACTCAAATTAGAAAAGCTCAAGTTTTGAATAGACGATGCCCAAGCATAATTTGAGTTTTCTGAA
396419 ATAGCTTGTGAGGAAAGATATCTCATTTACGATCTAATGTTGTCCTTTACACAATCAATTACTAG
66 ATAGCTTGTGAGGAAAGATATCTCATTTACGATCTAATGTTGTCCTTTACACAATCAATTACTAG
396484 AGTTTCATATTTGAATTGGATTTTTCATTACTAAAAATAATAAAACCTTATCTTGAAAATACTCG
131 AGTTTCATATTTGAATTGGATTTTTCATTACT-AAAA-AATAAAACCTTATCTTGAAAATACTCG
396549 ATTGTGTTAAG
194 ATTGTGTTAAG
396560 AACTCAAATTAGAAAAGCTCAAGTTTTGAATAGACGATGCCCAAGCATAATTTGAGTTTTTCTGA
1 AACTCAAATTAGAAAAGCTCAAGTTTTGAATAGACGATGCCCAAGCATAATTTGAG-TTTTCTGA
396625 AATAGCTTGTGAGGAAAGATATCTCATTTACGATCTAATGTTGTCCTTTACACAATCAATTACTA
65 AATAGCTTGTGAGGAAAGATATCTCATTTACGATCTAATGTTGTCCTTTACACAATCAATTACTA
396690 GAG-TTCATATTTGAATTGAGATTTTTCATTACTAAAAAATAAAACCTTATCTTGAAAATACTCG
130 GAGTTTCATATTTGAATTG-GATTTTTCATTACTAAAAAATAAAACCTTATCTTGAAAATACTCG
396754 ATTGTGTTAAG
194 ATTGTGTTAAG
396765 ATACTC
1 A-ACTC
396771 GTAGTTTCAG
Statistics
Matches: 208, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
205 39 0.19
206 79 0.38
207 90 0.43
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (204 bp):
AACTCAAATTAGAAAAGCTCAAGTTTTGAATAGACGATGCCCAAGCATAATTTGAGTTTTCTGAA
ATAGCTTGTGAGGAAAGATATCTCATTTACGATCTAATGTTGTCCTTTACACAATCAATTACTAG
AGTTTCATATTTGAATTGGATTTTTCATTACTAAAAAATAAAACCTTATCTTGAAAATACTCGAT
TGTGTTAAG
Found at i:400916 original size:41 final size:41
Alignment explanation
Indices: 400859--400941 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
400849 AAAGCAATAC
*
400859 TAGATGGAACAACAATTATGATTGATTAAAAGTCGCTCTAT
1 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
400900 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
1 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
400941 T
1 T
400942 GTAATTCGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (41 bp):
TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
Found at i:402537 original size:17 final size:17
Alignment explanation
Indices: 402517--402549 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
402507 TTACAGACCC
402517 TTTCTCCTTAAATCATT
1 TTTCTCCTTAAATCATT
*
402534 TTTCTCTTTAAATCAT
1 TTTCTCCTTAAATCAT
402550 GTCTCATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTCTCCTTAAATCATT
Found at i:402971 original size:21 final size:21
Alignment explanation
Indices: 402947--402989 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
402937 TCTTACAACA
402947 CTGCACATAATAATACATCTC
1 CTGCACATAATAATACATCTC
402968 CTGCACATAATAATACATCTC
1 CTGCACATAATAATACATCTC
402989 C
1 C
402990 CACGACATCT
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:0.37, C:0.30, G:0.05, T:0.28
Consensus pattern (21 bp):
CTGCACATAATAATACATCTC
Found at i:429754 original size:33 final size:33
Alignment explanation
Indices: 429678--429762 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
429668 ACCAATTTAG
* * *
429678 AATAATTATTAAATTTTTATCGAACTATTTAAA
1 AATAATCATTAAATTTTTATCAAAATATTTAAA
* * *
429711 AATGACCATTACATTTTTATCAAAATA-TTATAA
1 AATAATCATTAAATTTTTATCAAAATATTTA-AA
*
429744 AATAATCATTAAACTTTTA
1 AATAATCATTAAATTTTTA
429763 CACTTATTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
32 3 0.07
33 38 0.93
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.42
Consensus pattern (33 bp):
AATAATCATTAAATTTTTATCAAAATATTTAAA
Found at i:432841 original size:21 final size:19
Alignment explanation
Indices: 432803--432842 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
432793 TAAGTCTTTA
432803 TTATGTTCATGTAGCTTAT
1 TTATGTTCATGTAGCTTAT
*
432822 TTATGATTTATGTATGCTTAT
1 TTATG-TTCATGTA-GCTTAT
432843 GTCGTATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (19 bp):
TTATGTTCATGTAGCTTAT
Found at i:433046 original size:10 final size:10
Alignment explanation
Indices: 432969--433046 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
432959 GTGTTTGTGT
432969 TGTTCGTTTA
1 TGTTCGTTTA
*
432979 TGTTCATTTATTA
1 TGTTC--GT-TTA
432992 TGTTCGTTTA
1 TGTTCGTTTA
*
433002 TGTTCATTCGTTTG
1 TG----TTCGTTTA
*
433016 TATTCGTTTA
1 TGTTCGTTTA
*
433026 CGTTCGTTTA
1 TGTTCGTTTA
433036 TGTTCGTTTA
1 TGTTCGTTTA
433046 T
1 T
433047 CACTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
10 35 0.66
11 1 0.02
12 1 0.02
13 8 0.15
14 8 0.15
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.59
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:437835 original size:20 final size:21
Alignment explanation
Indices: 437810--437851 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
437800 TTATAAATTT
437810 AAAATAATAAAATTA-ATAAA
1 AAAATAATAAAATTATATAAA
* *
437830 AAAATATTTAAATTATATAAA
1 AAAATAATAAAATTATATAAA
437851 A
1 A
437852 TTTTTGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATAAAATTATATAAA
Found at i:441842 original size:2 final size:2
Alignment explanation
Indices: 441835--441864 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
441825 CGGTAAGGGA
441835 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
441865 CCTTTGCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:452055 original size:24 final size:24
Alignment explanation
Indices: 451997--452043 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
451987 AGTCAGTATT
*
451997 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
452021 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
452044 TCGGATTTTG
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:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:454668 original size:33 final size:33
Alignment explanation
Indices: 454589--454680 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
454579 GGAAATAACT
454589 ATCGCAATGCGAAATGAAAATCGCAA--AGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
454620 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
454653 ATCGCAAAGCAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
454681 CGAATTTAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 25 0.46
33 29 0.54
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:454702 original size:19 final size:19
Alignment explanation
Indices: 454680--454754 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
454670 AAATCGCAAC
454680 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCGTT
*
454699 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
454718 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
* *
454732 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
454751 GCGA
1 GCGA
454755 TAGTCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 3 0.07
19 28 0.64
20 1 0.02
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:454755 original size:19 final size:19
Alignment explanation
Indices: 454690--454755 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
454680 GCGAATTTAG
454690 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
454709 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
454725 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
454742 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
454756 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:454881 original size:14 final size:14
Alignment explanation
Indices: 454862--454898 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
454852 CATCAATTAA
454862 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
454876 ACAAATCATCTTTT
1 ACAAATCAACTTTT
454890 ACAAATCAA
1 ACAAATCAA
454899 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:456314 original size:21 final size:21
Alignment explanation
Indices: 456245--456314 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
456235 CAAGTGAATC
**
456245 GGACTCTTGAATAGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
456265 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
456287 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
456308 GGACTCT
1 GGACTCT
456315 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 14, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 3 0.09
21 29 0.85
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:456809 original size:19 final size:19
Alignment explanation
Indices: 456787--456870 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
456777 AAAAATAACT
*
456787 ATCGCAACGCTAAATGAAA
1 ATCGCAACGCGAAATGAAA
456806 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
456825 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
**
456839 ATCGCAACGCGAAACCAAAA
1 ATCGCAACGCGAAA-TGAAA
456859 ATCGCAACGCGA
1 ATCGCAACGCGA
456871 TTATAGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
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 25 0.45
20 15 0.27
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:456845 original size:33 final size:34
Alignment explanation
Indices: 456803--456867 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
456793 ACGCTAAATG
**
456803 AAAATCGCAACGCGAAA-TGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
456836 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAAATCGCAACG
456868 CGATTATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.08
Consensus pattern (34 bp):
AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
Found at i:456889 original size:19 final size:19
Alignment explanation
Indices: 456876--457009 Score: 179
Period size: 19 Copynumber: 7.3 Consensus size: 19
456866 CGCGATTATA
456876 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTC
456894 G--T--CGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
456909 ATTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
456928 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
456947 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
456966 GTTTCGCGTTACGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
456985 ATTCTCTCGTTGCGATTTTC
1 GTT-TCGCGTTGCGATTTTC
*
457005 ATTTC
1 GTTTC
457010 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
14 12 0.12
16 1 0.01
17 1 0.01
18 1 0.01
19 72 0.69
20 17 0.16
ACGTcount: A:0.08, C:0.21, G:0.22, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:457208 original size:94 final size:93
Alignment explanation
Indices: 457098--457473 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
457088 ATGGATTGCA
* * *
457098 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCATAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
** * *
457163 TAGCAGAATTGATAGCAAACGAACAATT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
457191 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
457256 TTAGCATAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
457285 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
457350 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
457379 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
457440 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
457469 TTACT
1 TTACT
457474 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 42 0.16
93 22 0.08
94 203 0.76
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:459187 original size:20 final size:19
Alignment explanation
Indices: 459161--459267 Score: 116
Period size: 20 Copynumber: 5.8 Consensus size: 19
459151 CTTTTGGTTA
459161 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
*
459180 AGAATGAAAATCGCAACGCAA
1 A-AATGAAAATCGCAACG-AG
**
459201 AAATGACTATCGCAACGAG
1 AAATGAAAATCGCAACGAG
*
459220 --A-G--AATCGCAACGCG
1 AAATGAAAATCGCAACGAG
*
459234 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGAG
459253 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
459268 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 2 0.03
19 29 0.39
20 30 0.40
21 2 0.03
ACGTcount: A:0.49, C:0.20, G:0.21, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGAG
Found at i:459246 original size:19 final size:19
Alignment explanation
Indices: 459161--459272 Score: 117
Period size: 19 Copynumber: 6.1 Consensus size: 19
459151 CTTTTGGTTA
*
459161 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
459180 AGAATGAAAATCGCAACGCAA
1 A-AATGAAAATCGCAACGC-G
**
459201 AAATGACTATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
459218 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
459234 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
*
459253 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
459272 A
1 A
459273 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
18 2 0.03
19 34 0.44
20 28 0.36
21 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:459316 original size:33 final size:33
Alignment explanation
Indices: 459268--459360 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
459258 AAAATCGCAA
**
459268 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
459301 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* **
459334 TGCAATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
459361 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.77
34 12 0.23
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:459957 original size:21 final size:20
Alignment explanation
Indices: 459893--459967 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
459883 GCTATGTAAA
** *
459893 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATTTTCATAT
* *
459913 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCATAT
459933 TCGCATTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCAT-AT
459954 TCGCATTGCGATTT
1 TCGCATTGCGATTT
459968 ACTTAATCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATAT
Found at i:459963 original size:41 final size:40
Alignment explanation
Indices: 459891--459983 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
459881 GCGCTATGTA
*
459891 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
* ** *
459931 ATTCGCATTGCGATTTTCATAATTCGCATTGCGATTTACTT
1 AATCGCATTGCGATAGTCA-AATTCGCATTGCGATTTACGT
*
459972 AATCGCGTTGCG
1 AATCGCATTGCG
459984 GTTTACGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 16 0.36
41 29 0.64
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
Found at i:459982 original size:20 final size:20
Alignment explanation
Indices: 459891--459989 Score: 92
Period size: 20 Copynumber: 4.9 Consensus size: 20
459881 GCGCTATGTA
* *
459891 AATCGCATTGCGATAGT-CAG
1 AATCGCATTGCGAT-TTACAT
* *
459911 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACAT
* *
459931 ATTCGCATTGCGATTTTCAT
1 AATCGCATTGCGATTTACAT
*
459951 AATTCGCATTGCGATTTACTT
1 AA-TCGCATTGCGATTTACAT
* *
459972 AATCGCGTTGCGGTTTAC
1 AATCGCATTGCGATTTAC
459990 GTATTCGCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 47 0.71
21 18 0.27
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:459997 original size:20 final size:20
Alignment explanation
Indices: 459911--459998 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
459901 CGATAGTCAG
459911 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
459931 ATTCGCATTGCGATTTTCAT
1 ATTCGCATTGCGATTTACGT
*
459951 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
459972 AATCGCGTTGCGGTTTACGT
1 ATTCGCATTGCGATTTACGT
459992 ATTCGCA
1 ATTCGCA
459999 ACGCGAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 39 0.68
21 18 0.32
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:460037 original size:61 final size:61
Alignment explanation
Indices: 459890--460041 Score: 162
Period size: 61 Copynumber: 2.5 Consensus size: 61
459880 GGCGCTATGT
* * ** * *
459890 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCAT
1 AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
* * ** * **
459951 AATTCGCATTGCGAT-TTACTTAATCGCGTTGCGGTTTACGTATTCGCAACGCGAATTTGGG
1 AAATCGCATTGCGATAGT-CAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
*
460012 AAATCGCAATGCGATAGTCAGAATCGCGTT
1 AAATCGCATTGCGATAGTCAGAATCGCGTT
460042 ACGAATCTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
60 1 0.01
61 69 0.97
62 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (61 bp):
AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
Found at i:474612 original size:21 final size:21
Alignment explanation
Indices: 474579--474660 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
474569 GTTTCTAGAT
*
474579 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
474600 TCGTAATGCGAACTTGGGCTA
1 TCGCAATGCGAACTTCGACTA
*
474621 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
474642 TCGCAATGCGAACTTCGAC
1 TCGCAATGCGAACTTCGAC
474661 ACGTCCGCGC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:474763 original size:21 final size:21
Alignment explanation
Indices: 474737--474892 Score: 135
Period size: 21 Copynumber: 7.4 Consensus size: 21
474727 ATTTTGGACT
*
474737 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
474758 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
474779 ATCGCAACGAACTTAGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
474800 ATCGCAATGCGAACTTTGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
474821 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
474842 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
474863 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
474884 ATCGCAACG
1 ATCGCAACG
474893 CGAACTTAGA
Statistics
Matches: 108, Mismatches: 15, Indels: 24
0.73 0.10 0.16
Matches are distributed among these distances:
19 27 0.25
21 55 0.51
23 26 0.24
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:474798 original size:42 final size:42
Alignment explanation
Indices: 474733--474911 Score: 295
Period size: 42 Copynumber: 4.3 Consensus size: 42
474723 TGCAATTTTG
*
474733 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
474775 GACTATCGCAACGAACTTAGAATAAATCGCAATGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
474817 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
474859 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
474901 GACTATCGCAA
1 GACTATCGCAA
474912 TGCGAATATG
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:474908 original size:21 final size:20
Alignment explanation
Indices: 474758--474917 Score: 110
Period size: 21 Copynumber: 7.6 Consensus size: 20
474748 TTTGGAATAA
*
474758 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTAGACT
*
474779 ATCGCAA-CGAACTTAGAAT
1 ATCGCAAGCGAACTTAGACT
*
474798 AAATCGCAATGCGAACTTTGACT
1 --ATCGCAA-GCGAACTTAGACT
* * *
474821 ATCGCAA-CGAATTTGGAAT
1 ATCGCAAGCGAACTTAGACT
* *
474840 AAATCGCAACGCAAACTTCGACT
1 --ATCGCAA-GCGAACTTAGACT
* *
474863 ATCGCAA-CGAACTTGGAAT
1 ATCGCAAGCGAACTTAGACT
474882 AAATCGCAACGCGAACTTAGACT
1 --ATCGCAA-GCGAACTTAGACT
474905 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
474918 TATGTAAATC
Statistics
Matches: 110, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
19 28 0.25
21 54 0.49
23 28 0.25
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTAGACT
Found at i:476802 original size:7 final size:7
Alignment explanation
Indices: 476790--476821 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
476780 TATTGATAAA
476790 TTATATT
1 TTATATT
476797 TTATATT
1 TTATATT
476804 TTATATT
1 TTATATT
476811 TTATATT
1 TTATATT
476818 TTAT
1 TTAT
476822 GTTTACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATATT
Found at i:479228 original size:2 final size:2
Alignment explanation
Indices: 479223--479264 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
479213 TATATTTTTA
479223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
479265 TAATAGTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:481076 original size:2 final size:2
Alignment explanation
Indices: 481071--481096 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
481061 ACACGCGTAC
481071 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
481097 TAGCTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:486633 original size:16 final size:16
Alignment explanation
Indices: 486612--486645 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
486602 TTATTGGGAA
*
486612 TGAAGTTGATCTCACG
1 TGAAGTTGATCCCACG
486628 TGAAGTTGATCCCACG
1 TGAAGTTGATCCCACG
486644 TG
1 TG
486646 TGCTGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (16 bp):
TGAAGTTGATCCCACG
Found at i:495385 original size:43 final size:43
Alignment explanation
Indices: 495288--495388 Score: 157
Period size: 43 Copynumber: 2.3 Consensus size: 43
495278 GATGTGACAA
* * * * *
495288 GACTTAGAGAAACAGGCATAGAATTGCAGAGGATACGAAAGAG
1 GACTTAGAGAAGCAGACATACAATTGCAGAGGACACAAAAGAG
495331 GACTTAGAGAAGCAGACATACAATTGCAGAGGACACAAAAGAG
1 GACTTAGAGAAGCAGACATACAATTGCAGAGGACACAAAAGAG
495374 GACTTAGAGAAGCAG
1 GACTTAGAGAAGCAG
495389 TCAGGAACTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.45, C:0.14, G:0.29, T:0.13
Consensus pattern (43 bp):
GACTTAGAGAAGCAGACATACAATTGCAGAGGACACAAAAGAG
Found at i:498675 original size:6 final size:6
Alignment explanation
Indices: 498664--498693 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
498654 AGATGTATAC
498664 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
498694 GTGGTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Found at i:499257 original size:30 final size:30
Alignment explanation
Indices: 499221--499286 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
499211 GAGTGTATAT
499221 ATATATTGTTAATAAGTTAGAAAATTCTAA
1 ATATATTGTTAATAAGTTAGAAAATTCTAA
499251 ATATATTGTTAATAAGTTAGAAAATTCTAA
1 ATATATTGTTAATAAGTTAGAAAATTCTAA
499281 ATATAT
1 ATATAT
499287 AATACCATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (30 bp):
ATATATTGTTAATAAGTTAGAAAATTCTAA
Found at i:499529 original size:21 final size:21
Alignment explanation
Indices: 499497--499539 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
499487 TGAATTCTTA
*
499497 AAATTTGTATTATA-TTTATT
1 AAATTTGTATTAAATTTTATT
*
499517 AAATTTTTAATTAAATTTTATT
1 AAATTTGT-ATTAAATTTTATT
499539 A
1 A
499540 TGACTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AAATTTGTATTAAATTTTATT
Found at i:501393 original size:42 final size:42
Alignment explanation
Indices: 501330--501448 Score: 211
Period size: 42 Copynumber: 2.8 Consensus size: 42
501320 TTCTCCGAAA
* *
501330 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGGTT
*
501372 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGGTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGGTT
501414 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
501449 CGTAATTCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGGTT
Found at i:501756 original size:27 final size:26
Alignment explanation
Indices: 501651--501758 Score: 71
Period size: 30 Copynumber: 4.0 Consensus size: 26
501641 TATTTATTAA
* *
501651 TATTTATAATAATATAATATTATATTTT
1 TATTT-TAATAATAT-ATAATAAATTTT
* * *
501679 TAGTTTAAT-A-ATATAATCAA-TTA
1 TATTTTAATAATATATAATAAATTTT
*
501702 TATTATAATAATATA-AGATATTATATTTTT
1 TATTTTAATAATATATA-ATA--A-A-TTTT
501732 TATTTTAATAATATATAATAAATTTT
1 TATTTTAATAATATATAATAAATTTT
501758 T
1 T
501759 TATATATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
23 9 0.15
24 7 0.11
25 7 0.11
26 6 0.10
27 6 0.10
28 6 0.10
30 19 0.31
31 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTTTAATAATATATAATAAATTTT
Found at i:501769 original size:30 final size:29
Alignment explanation
Indices: 501700--501804 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 29
501690 TATAATCAAT
501700 TATATTATAATAATATA-AGATATTATATTTTT-
1 TATATT-TAATAATATATA-ATA--AT-TTTTTA
501732 TAT-TTTAATAATATATAATAAATTTTTTA
1 TATATTTAATAATATATAAT-AATTTTTTA
** *
501761 TATATTTAATAATGGATAAT-ATTATTTA
1 TATATTTAATAATATATAATAATTTTTTA
501789 TATATTTAAATAATAT
1 TATATTT-AATAATAT
501805 TTTAGTAAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
28 19 0.30
29 11 0.17
30 26 0.41
31 4 0.06
32 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TATATTTAATAATATATAATAATTTTTTA
Found at i:501797 original size:28 final size:27
Alignment explanation
Indices: 501724--501803 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
501714 ATAAGATATT
*
501724 ATATTTTT-TAT-TTTAATAATATATA
1 ATATTTTTATATATTTAATAATAGATA
*
501749 ATAAATTTTTTATATATTTAATAATGGATA
1 AT--A-TTTTTATATATTTAATAATAGATA
501779 ATATTATTTATATATTTAAATAATA
1 ATATT-TTTATATATTT-AATAATA
501804 TTTTAGTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 2 0.04
27 3 0.07
28 17 0.38
29 9 0.20
30 14 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATTTTTATATATTTAATAATAGATA
Found at i:502168 original size:20 final size:20
Alignment explanation
Indices: 502131--502169 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
502121 TTTCCAGATG
**
502131 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
502151 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
502170 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:502179 original size:15 final size:15
Alignment explanation
Indices: 502143--502200 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
502133 TTCCAGAAAT
502143 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
502158 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
502172 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
502187 GTAATTCATTTTCC
1 GTAATTCATTTTCC
502201 GGAAAACCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:502388 original size:13 final size:14
Alignment explanation
Indices: 502370--502403 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
502360 CTTTTCAAGG
502370 TATTGTATT-TATT
1 TATTGTATTATATT
502383 TATTGT-TTATATT
1 TATTGTATTATATT
502396 TATTGTAT
1 TATTGTAT
502404 GTGCCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 16 0.84
14 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (14 bp):
TATTGTATTATATT
Found at i:504201 original size:28 final size:29
Alignment explanation
Indices: 504161--504216 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
504151 AATCTCTATA
504161 AGTTTAAATGTTT-GATAAAT-TATTTTTG
1 AGTTTAAATGTTTAG-TAAATCTATTTTTG
*
504189 AGTTTAGATGTTTAGTAAATCTATTTTT
1 AGTTTAAATGTTTAGTAAATCTATTTTT
504217 AAAAGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (29 bp):
AGTTTAAATGTTTAGTAAATCTATTTTTG
Found at i:509305 original size:17 final size:16
Alignment explanation
Indices: 509267--509305 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
509257 TAATTAGCAA
509267 TTTTTT-AAAATTATT
1 TTTTTTAAAAATTATT
509282 TTTTTTAAAAATTATT
1 TTTTTTAAAAATTATT
509298 TTTATTTA
1 TTT-TTTA
509306 TTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.27
16 12 0.55
17 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTAAAAATTATT
Found at i:511284 original size:102 final size:100
Alignment explanation
Indices: 511141--511340 Score: 350
Period size: 102 Copynumber: 2.0 Consensus size: 100
511131 GATTTAGGGA
511141 TTGGTCATTGCTATTCCGTTGTCTCTCCCTGTGTCTGAACCAGTGTGTTTCTTCACTAAATCCTT
1 TTGGTCATTGCTATTCCGTTGTCTCTCCCTGTGTCTGAACCAGTGTGTTTCTTCACTAAATCCTT
511206 GTCCTACACC-TTGATTAAACAACGGAAATAGGCG
66 GTCCTACACCTTTGATTAAACAACGGAAATAGGCG
511240 TTGGTCATTGCATATTCCGTTATTGTCTCT-CCTGTGTCTGAACCAGTGTGTTTCTTCACTAAAT
1 TTGGTCATTGC-TATTCCG---TTGTCTCTCCCTGTGTCTGAACCAGTGTGTTTCTTCACTAAAT
511304 CCTTGTCCTACACCTTTGATTAAACAACGGAAATAGG
62 CCTTGTCCTACACCTTTGATTAAACAACGGAAATAGG
511341 AAAGAAAATA
Statistics
Matches: 96, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
99 11 0.11
100 7 0.07
102 48 0.50
103 30 0.31
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.36
Consensus pattern (100 bp):
TTGGTCATTGCTATTCCGTTGTCTCTCCCTGTGTCTGAACCAGTGTGTTTCTTCACTAAATCCTT
GTCCTACACCTTTGATTAAACAACGGAAATAGGCG
Found at i:518533 original size:17 final size:16
Alignment explanation
Indices: 518512--518549 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
518502 GAAGTAACAA
518512 TAAAAATAAAAGTAT-C
1 TAAAAATAAAA-TATAC
*
518528 TAAAAATTAAATATAC
1 TAAAAATAAAATATAC
518544 TAAAAA
1 TAAAAA
518550 ATTACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAATAAAATATAC
Found at i:518931 original size:31 final size:31
Alignment explanation
Indices: 518896--519014 Score: 148
Period size: 31 Copynumber: 3.8 Consensus size: 31
518886 GTAACTTTCA
* * *
518896 ATAGTCAGATGACTCAATAAAACAACGCCCT
1 ATAGTCAGATGACTCAACAAAGCAACACCCT
* ** *
518927 ATAGTTAGGGGACTCAACAAAGCAACACCTT
1 ATAGTCAGATGACTCAACAAAGCAACACCCT
518958 ATAGTCAGATGACTCAACAAAGCAACACCCT
1 ATAGTCAGATGACTCAACAAAGCAACACCCT
* * *
518989 ATAATAAGATGACTCCACAAAGCAAC
1 ATAGTCAGATGACTCAACAAAGCAAC
519015 GCCTTATAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 74 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (31 bp):
ATAGTCAGATGACTCAACAAAGCAACACCCT
Found at i:518967 original size:62 final size:62
Alignment explanation
Indices: 518896--519022 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 62
518886 GTAACTTTCA
* * * * *
518896 ATAGTCAGATGACTCAATAAAACAACGCCCTATAGTTAGGGGACTCAACAAAGCAACACCTT
1 ATAGTCAGATGACTCAACAAAACAACACCCTATAATAAGAGGACTCAACAAAGCAACACCTT
* * * *
518958 ATAGTCAGATGACTCAACAAAGCAACACCCTATAATAAGATGACTCCACAAAGCAACGCCTT
1 ATAGTCAGATGACTCAACAAAACAACACCCTATAATAAGAGGACTCAACAAAGCAACACCTT
519020 ATA
1 ATA
519023 ATCGTAATCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (62 bp):
ATAGTCAGATGACTCAACAAAACAACACCCTATAATAAGAGGACTCAACAAAGCAACACCTT
Found at i:519023 original size:31 final size:31
Alignment explanation
Indices: 518937--519024 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
518927 ATAGTTAGGG
* *
518937 GACTCAACAAAGCAACACCTTATAGTCAGAT
1 GACTCAACAAAGCAACACCTTATAATAAGAT
*
518968 GACTCAACAAAGCAACACCCTATAATAAGAT
1 GACTCAACAAAGCAACACCTTATAATAAGAT
* *
518999 GACTCCACAAAGCAACGCCTTATAAT
1 GACTCAACAAAGCAACACCTTATAAT
519025 CGTAATCGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.43, C:0.27, G:0.11, T:0.18
Consensus pattern (31 bp):
GACTCAACAAAGCAACACCTTATAATAAGAT
Found at i:519316 original size:20 final size:20
Alignment explanation
Indices: 519287--519329 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
519277 AATTTAAAGC
* *
519287 TTTTACTTTTTTTAAAATAA
1 TTTTACTTTTCTGAAAATAA
*
519307 TTTTATTTTTCTGAAAATAA
1 TTTTACTTTTCTGAAAATAA
519327 TTT
1 TTT
519330 GTTAACTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTACTTTTCTGAAAATAA
Found at i:523282 original size:23 final size:22
Alignment explanation
Indices: 523256--523314 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
523246 ATGTCATAAC
*
523256 AAACATGTCACAAGAGCATAG-AA
1 AAACATGTCACAA-A-AATAGAAA
* *
523279 AAACATATCATAAAAATAGAAAA
1 AAACATGTCACAAAAATAG-AAA
523302 AAACATGTCACAA
1 AAACATGTCACAA
523315 TAAAGATTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
21 4 0.14
22 1 0.03
23 24 0.83
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.15
Consensus pattern (22 bp):
AAACATGTCACAAAAATAGAAA
Found at i:525811 original size:148 final size:148
Alignment explanation
Indices: 525620--525909 Score: 481
Period size: 148 Copynumber: 2.0 Consensus size: 148
525610 AAACTATTTA
* * *
525620 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
1 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
525685 AATTCAATTCAATTTGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTAAACT
*
525750 TTTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
** *
525768 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACTTAAACTCGAA
1 AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
525833 AATTCAATTCAATTCGACTTTATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTAAACT
525898 ATTTTATAAACT
131 ATTTTATAAACT
525910 AAATTGAGTA
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
148 131 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTAAAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCGAGTAAACT
ATTTTATAAACTGAACTG
Found at i:526123 original size:35 final size:35
Alignment explanation
Indices: 526084--526163 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
526074 GGGGTTGGGC
526084 ATGTAATTGAAGTATTTTGGAATTTAAGGTTTAGA
1 ATGTAATTGAAGTATTTTGGAATTTAAGGTTTAGA
** *
526119 ATGTAATTGAAGTATTTTGGAATTTGGGGTTTATA
1 ATGTAATTGAAGTATTTTGGAATTTAAGGTTTAGA
*
526154 ATATAATTGA
1 ATGTAATTGA
526164 TGAATGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.44
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGGAATTTAAGGTTTAGA
Done.