Multiple sequence alignment - TraesCS6A01G227000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G227000 chr6A 100.000 2384 0 0 1 2384 427448905 427446522 0.000000e+00 4403.0
1 TraesCS6A01G227000 chr6A 86.379 580 71 6 250 825 497996869 497996294 5.590000e-176 627.0
2 TraesCS6A01G227000 chr6D 89.273 2200 131 39 250 2383 293319152 293321312 0.000000e+00 2658.0
3 TraesCS6A01G227000 chr6D 87.857 140 15 1 6 145 293319010 293319147 1.900000e-36 163.0
4 TraesCS6A01G227000 chr6B 91.765 1530 90 19 878 2383 457877483 457879000 0.000000e+00 2095.0
5 TraesCS6A01G227000 chr2A 86.986 584 66 8 250 829 2742318 2741741 0.000000e+00 649.0
6 TraesCS6A01G227000 chr2A 91.566 83 7 0 167 249 670311993 670311911 5.380000e-22 115.0
7 TraesCS6A01G227000 chr7A 86.770 582 62 11 250 822 142950960 142950385 3.340000e-178 634.0
8 TraesCS6A01G227000 chr2D 86.426 582 70 7 250 828 131775096 131775671 1.560000e-176 628.0
9 TraesCS6A01G227000 chr4B 85.838 579 72 8 250 824 17070794 17070222 7.290000e-170 606.0
10 TraesCS6A01G227000 chr3A 87.151 537 59 7 276 810 711257158 711256630 3.390000e-168 601.0
11 TraesCS6A01G227000 chr3A 92.857 84 5 1 167 249 472910817 472910900 1.160000e-23 121.0
12 TraesCS6A01G227000 chr3A 88.636 88 10 0 167 254 380173956 380173869 9.010000e-20 108.0
13 TraesCS6A01G227000 chr1B 85.492 579 71 11 250 823 22398647 22399217 2.040000e-165 592.0
14 TraesCS6A01G227000 chr1B 85.077 583 69 15 250 826 26425675 26425105 1.590000e-161 579.0
15 TraesCS6A01G227000 chr1B 90.476 84 7 1 166 249 338467854 338467936 2.510000e-20 110.0
16 TraesCS6A01G227000 chr3B 85.103 584 75 8 250 825 821758660 821758081 9.490000e-164 586.0
17 TraesCS6A01G227000 chr2B 95.238 84 4 0 167 250 693065470 693065387 1.490000e-27 134.0
18 TraesCS6A01G227000 chr1A 92.771 83 6 0 167 249 566106857 566106775 1.160000e-23 121.0
19 TraesCS6A01G227000 chr1A 91.765 85 7 0 167 251 76494941 76494857 4.160000e-23 119.0
20 TraesCS6A01G227000 chr7B 93.590 78 3 1 164 241 27998252 27998327 5.380000e-22 115.0
21 TraesCS6A01G227000 chr5A 90.476 84 8 0 167 250 689515221 689515138 6.970000e-21 111.0
22 TraesCS6A01G227000 chr5D 96.364 55 2 0 91 145 324369019 324368965 9.070000e-15 91.6
23 TraesCS6A01G227000 chr5D 92.727 55 4 0 91 145 60534337 60534391 1.960000e-11 80.5
24 TraesCS6A01G227000 chr5B 94.545 55 3 0 91 145 375796456 375796402 4.220000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G227000 chr6A 427446522 427448905 2383 True 4403.0 4403 100.000 1 2384 1 chr6A.!!$R1 2383
1 TraesCS6A01G227000 chr6A 497996294 497996869 575 True 627.0 627 86.379 250 825 1 chr6A.!!$R2 575
2 TraesCS6A01G227000 chr6D 293319010 293321312 2302 False 1410.5 2658 88.565 6 2383 2 chr6D.!!$F1 2377
3 TraesCS6A01G227000 chr6B 457877483 457879000 1517 False 2095.0 2095 91.765 878 2383 1 chr6B.!!$F1 1505
4 TraesCS6A01G227000 chr2A 2741741 2742318 577 True 649.0 649 86.986 250 829 1 chr2A.!!$R1 579
5 TraesCS6A01G227000 chr7A 142950385 142950960 575 True 634.0 634 86.770 250 822 1 chr7A.!!$R1 572
6 TraesCS6A01G227000 chr2D 131775096 131775671 575 False 628.0 628 86.426 250 828 1 chr2D.!!$F1 578
7 TraesCS6A01G227000 chr4B 17070222 17070794 572 True 606.0 606 85.838 250 824 1 chr4B.!!$R1 574
8 TraesCS6A01G227000 chr3A 711256630 711257158 528 True 601.0 601 87.151 276 810 1 chr3A.!!$R2 534
9 TraesCS6A01G227000 chr1B 22398647 22399217 570 False 592.0 592 85.492 250 823 1 chr1B.!!$F1 573
10 TraesCS6A01G227000 chr1B 26425105 26425675 570 True 579.0 579 85.077 250 826 1 chr1B.!!$R1 576
11 TraesCS6A01G227000 chr3B 821758081 821758660 579 True 586.0 586 85.103 250 825 1 chr3B.!!$R1 575

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
218 219 0.042131 AGGTGGGAGTACGGATGGAA 59.958 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1493 1.752498 ACCGCAAGTACCATATCGACA 59.248 47.619 0.0 0.0 0.0 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 8.457261 ACTTTGCAGAATGTAATTTGAGATCTC 58.543 33.333 16.21 16.21 41.29 2.75
59 60 7.926674 TTGCAGAATGTAATTTGAGATCTCA 57.073 32.000 21.67 21.67 35.19 3.27
60 61 7.926674 TGCAGAATGTAATTTGAGATCTCAA 57.073 32.000 30.05 30.05 42.70 3.02
79 80 7.624360 TCTCAACAAAGCTAAAGAAACAAGA 57.376 32.000 0.00 0.00 0.00 3.02
85 86 9.651913 AACAAAGCTAAAGAAACAAGATTCAAA 57.348 25.926 0.00 0.00 0.00 2.69
114 115 3.532155 CTCTTCTCCTCCCGCCGG 61.532 72.222 0.00 0.00 0.00 6.13
145 146 2.753168 CGGTCTGTCCCATCTCCTATGA 60.753 54.545 0.00 0.00 0.00 2.15
146 147 2.896685 GGTCTGTCCCATCTCCTATGAG 59.103 54.545 0.00 0.00 40.17 2.90
147 148 2.896685 GTCTGTCCCATCTCCTATGAGG 59.103 54.545 0.00 0.00 39.23 3.86
149 150 3.051803 TCTGTCCCATCTCCTATGAGGTT 60.052 47.826 0.00 0.00 39.23 3.50
150 151 4.170053 TCTGTCCCATCTCCTATGAGGTTA 59.830 45.833 0.00 0.00 39.23 2.85
151 152 4.483950 TGTCCCATCTCCTATGAGGTTAG 58.516 47.826 0.00 0.00 39.23 2.34
152 153 4.170053 TGTCCCATCTCCTATGAGGTTAGA 59.830 45.833 0.00 0.00 39.23 2.10
153 154 5.148502 GTCCCATCTCCTATGAGGTTAGAA 58.851 45.833 0.00 0.00 39.23 2.10
154 155 5.602978 GTCCCATCTCCTATGAGGTTAGAAA 59.397 44.000 0.00 0.00 39.23 2.52
155 156 5.841237 TCCCATCTCCTATGAGGTTAGAAAG 59.159 44.000 0.00 0.00 39.23 2.62
156 157 5.012561 CCCATCTCCTATGAGGTTAGAAAGG 59.987 48.000 0.00 0.00 39.23 3.11
157 158 5.841237 CCATCTCCTATGAGGTTAGAAAGGA 59.159 44.000 0.00 0.00 39.23 3.36
158 159 6.327626 CCATCTCCTATGAGGTTAGAAAGGAA 59.672 42.308 0.00 0.00 39.23 3.36
159 160 7.147479 CCATCTCCTATGAGGTTAGAAAGGAAA 60.147 40.741 0.00 0.00 39.23 3.13
160 161 7.808279 TCTCCTATGAGGTTAGAAAGGAAAA 57.192 36.000 0.00 0.00 39.23 2.29
161 162 8.214721 TCTCCTATGAGGTTAGAAAGGAAAAA 57.785 34.615 0.00 0.00 39.23 1.94
162 163 8.322091 TCTCCTATGAGGTTAGAAAGGAAAAAG 58.678 37.037 0.00 0.00 39.23 2.27
163 164 7.402862 TCCTATGAGGTTAGAAAGGAAAAAGG 58.597 38.462 0.00 0.00 36.53 3.11
164 165 7.238933 TCCTATGAGGTTAGAAAGGAAAAAGGA 59.761 37.037 0.00 0.00 36.53 3.36
165 166 7.888546 CCTATGAGGTTAGAAAGGAAAAAGGAA 59.111 37.037 0.00 0.00 0.00 3.36
166 167 9.297037 CTATGAGGTTAGAAAGGAAAAAGGAAA 57.703 33.333 0.00 0.00 0.00 3.13
167 168 7.964666 TGAGGTTAGAAAGGAAAAAGGAAAA 57.035 32.000 0.00 0.00 0.00 2.29
168 169 8.368962 TGAGGTTAGAAAGGAAAAAGGAAAAA 57.631 30.769 0.00 0.00 0.00 1.94
169 170 8.474831 TGAGGTTAGAAAGGAAAAAGGAAAAAG 58.525 33.333 0.00 0.00 0.00 2.27
170 171 8.603898 AGGTTAGAAAGGAAAAAGGAAAAAGA 57.396 30.769 0.00 0.00 0.00 2.52
171 172 9.042450 AGGTTAGAAAGGAAAAAGGAAAAAGAA 57.958 29.630 0.00 0.00 0.00 2.52
172 173 9.661563 GGTTAGAAAGGAAAAAGGAAAAAGAAA 57.338 29.630 0.00 0.00 0.00 2.52
208 209 3.209091 CGTAGGATGAGGTGGGAGT 57.791 57.895 0.00 0.00 0.00 3.85
209 210 2.359981 CGTAGGATGAGGTGGGAGTA 57.640 55.000 0.00 0.00 0.00 2.59
210 211 1.955080 CGTAGGATGAGGTGGGAGTAC 59.045 57.143 0.00 0.00 0.00 2.73
211 212 1.955080 GTAGGATGAGGTGGGAGTACG 59.045 57.143 0.00 0.00 0.00 3.67
212 213 0.397254 AGGATGAGGTGGGAGTACGG 60.397 60.000 0.00 0.00 0.00 4.02
213 214 0.396695 GGATGAGGTGGGAGTACGGA 60.397 60.000 0.00 0.00 0.00 4.69
214 215 1.705873 GATGAGGTGGGAGTACGGAT 58.294 55.000 0.00 0.00 0.00 4.18
215 216 1.341531 GATGAGGTGGGAGTACGGATG 59.658 57.143 0.00 0.00 0.00 3.51
216 217 0.686441 TGAGGTGGGAGTACGGATGG 60.686 60.000 0.00 0.00 0.00 3.51
217 218 0.396695 GAGGTGGGAGTACGGATGGA 60.397 60.000 0.00 0.00 0.00 3.41
218 219 0.042131 AGGTGGGAGTACGGATGGAA 59.958 55.000 0.00 0.00 0.00 3.53
219 220 0.464452 GGTGGGAGTACGGATGGAAG 59.536 60.000 0.00 0.00 0.00 3.46
220 221 0.179081 GTGGGAGTACGGATGGAAGC 60.179 60.000 0.00 0.00 0.00 3.86
221 222 0.616395 TGGGAGTACGGATGGAAGCA 60.616 55.000 0.00 0.00 0.00 3.91
222 223 0.759346 GGGAGTACGGATGGAAGCAT 59.241 55.000 0.00 0.00 0.00 3.79
223 224 1.541233 GGGAGTACGGATGGAAGCATG 60.541 57.143 0.00 0.00 0.00 4.06
224 225 1.541233 GGAGTACGGATGGAAGCATGG 60.541 57.143 0.00 0.00 0.00 3.66
225 226 0.469917 AGTACGGATGGAAGCATGGG 59.530 55.000 0.00 0.00 0.00 4.00
226 227 0.535102 GTACGGATGGAAGCATGGGG 60.535 60.000 0.00 0.00 0.00 4.96
227 228 0.692756 TACGGATGGAAGCATGGGGA 60.693 55.000 0.00 0.00 0.00 4.81
228 229 1.228063 CGGATGGAAGCATGGGGAG 60.228 63.158 0.00 0.00 0.00 4.30
229 230 1.152368 GGATGGAAGCATGGGGAGG 59.848 63.158 0.00 0.00 0.00 4.30
230 231 1.152368 GATGGAAGCATGGGGAGGG 59.848 63.158 0.00 0.00 0.00 4.30
231 232 1.309013 ATGGAAGCATGGGGAGGGA 60.309 57.895 0.00 0.00 0.00 4.20
232 233 1.358830 ATGGAAGCATGGGGAGGGAG 61.359 60.000 0.00 0.00 0.00 4.30
233 234 2.194326 GAAGCATGGGGAGGGAGC 59.806 66.667 0.00 0.00 0.00 4.70
234 235 2.614969 AAGCATGGGGAGGGAGCA 60.615 61.111 0.00 0.00 0.00 4.26
235 236 2.621517 GAAGCATGGGGAGGGAGCAG 62.622 65.000 0.00 0.00 0.00 4.24
236 237 4.201122 GCATGGGGAGGGAGCAGG 62.201 72.222 0.00 0.00 0.00 4.85
237 238 4.201122 CATGGGGAGGGAGCAGGC 62.201 72.222 0.00 0.00 0.00 4.85
238 239 4.765970 ATGGGGAGGGAGCAGGCA 62.766 66.667 0.00 0.00 0.00 4.75
240 241 4.120755 GGGGAGGGAGCAGGCAAG 62.121 72.222 0.00 0.00 0.00 4.01
241 242 3.334054 GGGAGGGAGCAGGCAAGT 61.334 66.667 0.00 0.00 0.00 3.16
242 243 2.270527 GGAGGGAGCAGGCAAGTC 59.729 66.667 0.00 0.00 0.00 3.01
243 244 2.125350 GAGGGAGCAGGCAAGTCG 60.125 66.667 0.00 0.00 0.00 4.18
244 245 2.604686 AGGGAGCAGGCAAGTCGA 60.605 61.111 0.00 0.00 0.00 4.20
245 246 2.172483 GAGGGAGCAGGCAAGTCGAA 62.172 60.000 0.00 0.00 0.00 3.71
246 247 1.078143 GGGAGCAGGCAAGTCGAAT 60.078 57.895 0.00 0.00 0.00 3.34
247 248 1.092345 GGGAGCAGGCAAGTCGAATC 61.092 60.000 0.00 0.00 0.00 2.52
248 249 1.092345 GGAGCAGGCAAGTCGAATCC 61.092 60.000 0.00 0.00 0.00 3.01
274 275 1.383109 ATGGAGGTGCGGAGGATCA 60.383 57.895 0.00 0.00 36.25 2.92
352 361 4.612412 GGGGTTGTGTGGCGACGA 62.612 66.667 0.00 0.00 32.16 4.20
401 410 2.605257 CCATGTTCTATCCCCGTCCTA 58.395 52.381 0.00 0.00 0.00 2.94
469 479 1.270305 GGATCTTGCGGGATTCGATCA 60.270 52.381 0.00 0.00 42.43 2.92
480 490 2.468831 GATTCGATCAGTGCTGGTCTC 58.531 52.381 10.31 0.00 38.53 3.36
501 511 5.488919 TCTCTGGTGAATCTATTTGGGTCTT 59.511 40.000 0.00 0.00 0.00 3.01
528 539 5.375417 TCGTTCGTCTTCATTTAGGTGTA 57.625 39.130 0.00 0.00 0.00 2.90
531 542 7.537715 TCGTTCGTCTTCATTTAGGTGTATAA 58.462 34.615 0.00 0.00 0.00 0.98
614 630 2.483188 GCTGGTCCTATGGTCCTTAACG 60.483 54.545 2.01 0.00 32.23 3.18
625 641 0.877071 TCCTTAACGCGACGACTTCT 59.123 50.000 15.93 0.00 0.00 2.85
716 733 2.671351 GCTCGCTTCAGTGCTTGTAGTA 60.671 50.000 0.00 0.00 0.00 1.82
729 746 3.487209 GCTTGTAGTAGTCGCTAGGTGAC 60.487 52.174 3.39 3.39 42.60 3.67
840 858 3.643159 AAAAATGTTCAAGAGGCGTCC 57.357 42.857 2.06 0.00 0.00 4.79
841 859 1.534729 AAATGTTCAAGAGGCGTCCC 58.465 50.000 2.06 0.00 0.00 4.46
842 860 0.673644 AATGTTCAAGAGGCGTCCCG 60.674 55.000 2.06 0.00 35.76 5.14
843 861 2.434359 GTTCAAGAGGCGTCCCGG 60.434 66.667 2.06 0.00 35.76 5.73
844 862 2.602267 TTCAAGAGGCGTCCCGGA 60.602 61.111 0.73 0.00 35.76 5.14
845 863 2.211410 TTCAAGAGGCGTCCCGGAA 61.211 57.895 0.73 2.11 35.76 4.30
871 894 0.811915 ACACCATCGTCTCTTCCGAG 59.188 55.000 0.00 0.00 37.81 4.63
913 940 1.141019 GCAGCGTCTCCGTCCATAA 59.859 57.895 0.00 0.00 36.15 1.90
1068 1108 4.175337 CCACCGACGCCCCATCAT 62.175 66.667 0.00 0.00 0.00 2.45
1119 1159 1.529948 CCCTATCCGCTACGTCCCA 60.530 63.158 0.00 0.00 0.00 4.37
1251 1312 4.208686 GCCGGCTTCCTCGACGAT 62.209 66.667 22.15 0.00 37.71 3.73
1426 1491 1.201429 AATGAGGCTGGGAGGTCGTT 61.201 55.000 0.00 0.00 0.00 3.85
1427 1492 1.617947 ATGAGGCTGGGAGGTCGTTC 61.618 60.000 0.00 0.00 0.00 3.95
1428 1493 1.985116 GAGGCTGGGAGGTCGTTCT 60.985 63.158 0.00 0.00 0.00 3.01
1429 1494 2.232298 GAGGCTGGGAGGTCGTTCTG 62.232 65.000 0.00 0.00 0.00 3.02
1430 1495 2.584391 GGCTGGGAGGTCGTTCTGT 61.584 63.158 0.00 0.00 0.00 3.41
1443 1508 4.201990 GGTCGTTCTGTCGATATGGTACTT 60.202 45.833 0.00 0.00 41.78 2.24
1445 1510 3.486108 CGTTCTGTCGATATGGTACTTGC 59.514 47.826 0.00 0.00 0.00 4.01
1526 1594 4.795268 TCGGTGATCAATCTAAGTATCGC 58.205 43.478 0.00 0.00 0.00 4.58
1628 1697 5.652891 TCTCTGCGAGGTTCTCTTTATAGTT 59.347 40.000 5.87 0.00 0.00 2.24
1633 1702 5.626132 GCGAGGTTCTCTTTATAGTTCGATC 59.374 44.000 0.00 0.00 0.00 3.69
1733 1802 2.578495 CTTCGATTCTTGCTGTTGTGC 58.422 47.619 0.00 0.00 0.00 4.57
1737 1809 2.046313 GATTCTTGCTGTTGTGCGTTG 58.954 47.619 0.00 0.00 35.36 4.10
1738 1810 0.808125 TTCTTGCTGTTGTGCGTTGT 59.192 45.000 0.00 0.00 35.36 3.32
1739 1811 0.808125 TCTTGCTGTTGTGCGTTGTT 59.192 45.000 0.00 0.00 35.36 2.83
1807 1879 7.645002 AGTATACTAGAGATACCTGATTCCCC 58.355 42.308 2.75 0.00 31.27 4.81
1824 1896 7.000472 TGATTCCCCAATCTCTTTGATCATAC 59.000 38.462 0.00 0.00 39.49 2.39
1825 1897 5.974156 TCCCCAATCTCTTTGATCATACA 57.026 39.130 0.00 0.00 37.53 2.29
1848 1928 6.594937 ACAGGTGCAATTTTAGCCATTTTATG 59.405 34.615 0.00 0.00 0.00 1.90
1949 2032 2.752354 TCATCGCAAATAAACACAGGGG 59.248 45.455 0.00 0.00 0.00 4.79
1954 2037 2.497273 GCAAATAAACACAGGGGATGCT 59.503 45.455 0.00 0.00 0.00 3.79
1971 2054 3.492102 TGCTTAGCTGGAACTTCAGTT 57.508 42.857 5.60 0.00 41.64 3.16
1982 2065 8.594550 AGCTGGAACTTCAGTTAACTCTTATTA 58.405 33.333 4.77 0.00 38.56 0.98
2001 2084 9.023962 TCTTATTATGTTCCTTTGCAAGACAAT 57.976 29.630 0.00 0.00 38.31 2.71
2027 2111 9.567776 TTTAGTGATTTGTTAGGAGTTTGATGA 57.432 29.630 0.00 0.00 0.00 2.92
2028 2112 9.739276 TTAGTGATTTGTTAGGAGTTTGATGAT 57.261 29.630 0.00 0.00 0.00 2.45
2037 2121 3.588842 AGGAGTTTGATGATCAACCAGGA 59.411 43.478 7.48 0.00 35.89 3.86
2099 2184 3.896648 ATTTCGTAAGCAATATGCCCG 57.103 42.857 0.00 0.00 46.52 6.13
2108 2193 1.334960 GCAATATGCCCGTGATTTCCG 60.335 52.381 0.00 0.00 37.42 4.30
2180 2267 3.866496 GCAAGTCGCATTCTATTAGCAC 58.134 45.455 0.00 0.00 41.79 4.40
2298 2385 5.185828 AGTTGCTTTTGTTCTCTTCCTTGTT 59.814 36.000 0.00 0.00 0.00 2.83
2299 2386 5.248870 TGCTTTTGTTCTCTTCCTTGTTC 57.751 39.130 0.00 0.00 0.00 3.18
2302 2389 6.601613 TGCTTTTGTTCTCTTCCTTGTTCTAA 59.398 34.615 0.00 0.00 0.00 2.10
2304 2391 7.592903 GCTTTTGTTCTCTTCCTTGTTCTAATG 59.407 37.037 0.00 0.00 0.00 1.90
2305 2392 8.746052 TTTTGTTCTCTTCCTTGTTCTAATGA 57.254 30.769 0.00 0.00 0.00 2.57
2306 2393 8.924511 TTTGTTCTCTTCCTTGTTCTAATGAT 57.075 30.769 0.00 0.00 0.00 2.45
2307 2394 8.924511 TTGTTCTCTTCCTTGTTCTAATGATT 57.075 30.769 0.00 0.00 0.00 2.57
2356 2443 1.580845 ATTTCTGCTCGTGGCTGTGC 61.581 55.000 5.00 0.00 42.39 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.462174 CTCAAATTACATTCTGCAAAGTGTAAA 57.538 29.630 11.55 0.00 39.58 2.01
28 29 8.845227 TCTCAAATTACATTCTGCAAAGTGTAA 58.155 29.630 10.15 10.15 40.20 2.41
29 30 8.389779 TCTCAAATTACATTCTGCAAAGTGTA 57.610 30.769 0.00 0.00 0.00 2.90
58 59 8.633075 TGAATCTTGTTTCTTTAGCTTTGTTG 57.367 30.769 0.00 0.00 0.00 3.33
59 60 9.651913 TTTGAATCTTGTTTCTTTAGCTTTGTT 57.348 25.926 0.00 0.00 0.00 2.83
60 61 9.651913 TTTTGAATCTTGTTTCTTTAGCTTTGT 57.348 25.926 0.00 0.00 0.00 2.83
66 67 8.137437 TCTGCCTTTTGAATCTTGTTTCTTTAG 58.863 33.333 0.00 0.00 0.00 1.85
67 68 8.006298 TCTGCCTTTTGAATCTTGTTTCTTTA 57.994 30.769 0.00 0.00 0.00 1.85
68 69 6.877236 TCTGCCTTTTGAATCTTGTTTCTTT 58.123 32.000 0.00 0.00 0.00 2.52
79 80 5.303845 AGAAGAGCTTTTCTGCCTTTTGAAT 59.696 36.000 18.10 0.00 36.12 2.57
85 86 2.374839 AGGAGAAGAGCTTTTCTGCCTT 59.625 45.455 27.75 13.07 43.95 4.35
145 146 8.603898 TCTTTTTCCTTTTTCCTTTCTAACCT 57.396 30.769 0.00 0.00 0.00 3.50
146 147 9.661563 TTTCTTTTTCCTTTTTCCTTTCTAACC 57.338 29.630 0.00 0.00 0.00 2.85
179 180 3.600388 CTCATCCTACGGCTGTCTTTTT 58.400 45.455 0.00 0.00 0.00 1.94
180 181 2.093447 CCTCATCCTACGGCTGTCTTTT 60.093 50.000 0.00 0.00 0.00 2.27
181 182 1.482593 CCTCATCCTACGGCTGTCTTT 59.517 52.381 0.00 0.00 0.00 2.52
182 183 1.115467 CCTCATCCTACGGCTGTCTT 58.885 55.000 0.00 0.00 0.00 3.01
183 184 0.033011 ACCTCATCCTACGGCTGTCT 60.033 55.000 0.00 0.00 0.00 3.41
184 185 0.103208 CACCTCATCCTACGGCTGTC 59.897 60.000 0.00 0.00 0.00 3.51
185 186 1.330655 CCACCTCATCCTACGGCTGT 61.331 60.000 2.42 2.42 0.00 4.40
186 187 1.443407 CCACCTCATCCTACGGCTG 59.557 63.158 0.00 0.00 0.00 4.85
187 188 1.762460 CCCACCTCATCCTACGGCT 60.762 63.158 0.00 0.00 0.00 5.52
188 189 1.749334 CTCCCACCTCATCCTACGGC 61.749 65.000 0.00 0.00 0.00 5.68
189 190 0.397254 ACTCCCACCTCATCCTACGG 60.397 60.000 0.00 0.00 0.00 4.02
190 191 1.955080 GTACTCCCACCTCATCCTACG 59.045 57.143 0.00 0.00 0.00 3.51
191 192 1.955080 CGTACTCCCACCTCATCCTAC 59.045 57.143 0.00 0.00 0.00 3.18
192 193 1.133575 CCGTACTCCCACCTCATCCTA 60.134 57.143 0.00 0.00 0.00 2.94
193 194 0.397254 CCGTACTCCCACCTCATCCT 60.397 60.000 0.00 0.00 0.00 3.24
194 195 0.396695 TCCGTACTCCCACCTCATCC 60.397 60.000 0.00 0.00 0.00 3.51
195 196 1.341531 CATCCGTACTCCCACCTCATC 59.658 57.143 0.00 0.00 0.00 2.92
196 197 1.414158 CATCCGTACTCCCACCTCAT 58.586 55.000 0.00 0.00 0.00 2.90
197 198 0.686441 CCATCCGTACTCCCACCTCA 60.686 60.000 0.00 0.00 0.00 3.86
198 199 0.396695 TCCATCCGTACTCCCACCTC 60.397 60.000 0.00 0.00 0.00 3.85
199 200 0.042131 TTCCATCCGTACTCCCACCT 59.958 55.000 0.00 0.00 0.00 4.00
200 201 0.464452 CTTCCATCCGTACTCCCACC 59.536 60.000 0.00 0.00 0.00 4.61
201 202 0.179081 GCTTCCATCCGTACTCCCAC 60.179 60.000 0.00 0.00 0.00 4.61
202 203 0.616395 TGCTTCCATCCGTACTCCCA 60.616 55.000 0.00 0.00 0.00 4.37
203 204 0.759346 ATGCTTCCATCCGTACTCCC 59.241 55.000 0.00 0.00 0.00 4.30
204 205 1.541233 CCATGCTTCCATCCGTACTCC 60.541 57.143 0.00 0.00 0.00 3.85
205 206 1.541233 CCCATGCTTCCATCCGTACTC 60.541 57.143 0.00 0.00 0.00 2.59
206 207 0.469917 CCCATGCTTCCATCCGTACT 59.530 55.000 0.00 0.00 0.00 2.73
207 208 0.535102 CCCCATGCTTCCATCCGTAC 60.535 60.000 0.00 0.00 0.00 3.67
208 209 0.692756 TCCCCATGCTTCCATCCGTA 60.693 55.000 0.00 0.00 0.00 4.02
209 210 1.987807 CTCCCCATGCTTCCATCCGT 61.988 60.000 0.00 0.00 0.00 4.69
210 211 1.228063 CTCCCCATGCTTCCATCCG 60.228 63.158 0.00 0.00 0.00 4.18
211 212 1.152368 CCTCCCCATGCTTCCATCC 59.848 63.158 0.00 0.00 0.00 3.51
212 213 1.152368 CCCTCCCCATGCTTCCATC 59.848 63.158 0.00 0.00 0.00 3.51
213 214 1.309013 TCCCTCCCCATGCTTCCAT 60.309 57.895 0.00 0.00 0.00 3.41
214 215 2.002977 CTCCCTCCCCATGCTTCCA 61.003 63.158 0.00 0.00 0.00 3.53
215 216 2.922234 CTCCCTCCCCATGCTTCC 59.078 66.667 0.00 0.00 0.00 3.46
216 217 2.194326 GCTCCCTCCCCATGCTTC 59.806 66.667 0.00 0.00 0.00 3.86
217 218 2.614969 TGCTCCCTCCCCATGCTT 60.615 61.111 0.00 0.00 0.00 3.91
218 219 3.095163 CTGCTCCCTCCCCATGCT 61.095 66.667 0.00 0.00 0.00 3.79
219 220 4.201122 CCTGCTCCCTCCCCATGC 62.201 72.222 0.00 0.00 0.00 4.06
220 221 4.201122 GCCTGCTCCCTCCCCATG 62.201 72.222 0.00 0.00 0.00 3.66
221 222 4.765970 TGCCTGCTCCCTCCCCAT 62.766 66.667 0.00 0.00 0.00 4.00
223 224 4.120755 CTTGCCTGCTCCCTCCCC 62.121 72.222 0.00 0.00 0.00 4.81
224 225 3.334054 ACTTGCCTGCTCCCTCCC 61.334 66.667 0.00 0.00 0.00 4.30
225 226 2.270527 GACTTGCCTGCTCCCTCC 59.729 66.667 0.00 0.00 0.00 4.30
226 227 2.125350 CGACTTGCCTGCTCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
227 228 1.557269 ATTCGACTTGCCTGCTCCCT 61.557 55.000 0.00 0.00 0.00 4.20
228 229 1.078143 ATTCGACTTGCCTGCTCCC 60.078 57.895 0.00 0.00 0.00 4.30
229 230 1.092345 GGATTCGACTTGCCTGCTCC 61.092 60.000 0.00 0.00 0.00 4.70
230 231 1.092345 GGGATTCGACTTGCCTGCTC 61.092 60.000 0.00 0.00 0.00 4.26
231 232 1.078143 GGGATTCGACTTGCCTGCT 60.078 57.895 0.00 0.00 0.00 4.24
232 233 0.178068 TAGGGATTCGACTTGCCTGC 59.822 55.000 15.49 0.00 35.47 4.85
233 234 1.757118 TCTAGGGATTCGACTTGCCTG 59.243 52.381 15.49 7.63 35.47 4.85
234 235 1.757699 GTCTAGGGATTCGACTTGCCT 59.242 52.381 11.65 11.65 38.60 4.75
235 236 1.202545 GGTCTAGGGATTCGACTTGCC 60.203 57.143 0.00 0.00 0.00 4.52
236 237 1.480954 TGGTCTAGGGATTCGACTTGC 59.519 52.381 0.00 0.00 0.00 4.01
237 238 3.493350 CCATGGTCTAGGGATTCGACTTG 60.493 52.174 2.57 0.00 29.57 3.16
238 239 2.700897 CCATGGTCTAGGGATTCGACTT 59.299 50.000 2.57 0.00 29.57 3.01
239 240 2.091278 TCCATGGTCTAGGGATTCGACT 60.091 50.000 12.58 0.00 33.51 4.18
240 241 2.297597 CTCCATGGTCTAGGGATTCGAC 59.702 54.545 12.58 0.00 38.82 4.20
241 242 2.598565 CTCCATGGTCTAGGGATTCGA 58.401 52.381 12.58 0.00 38.82 3.71
242 243 1.620819 CCTCCATGGTCTAGGGATTCG 59.379 57.143 12.58 0.00 38.82 3.34
446 456 0.529773 CGAATCCCGCAAGATCCGAA 60.530 55.000 0.00 0.00 43.02 4.30
469 479 1.277557 GATTCACCAGAGACCAGCACT 59.722 52.381 0.00 0.00 0.00 4.40
480 490 5.256474 ACAAGACCCAAATAGATTCACCAG 58.744 41.667 0.00 0.00 0.00 4.00
501 511 4.921515 CCTAAATGAAGACGAACGAAGACA 59.078 41.667 0.14 0.00 0.00 3.41
614 630 1.733360 AGACAGTAGAGAAGTCGTCGC 59.267 52.381 0.00 0.00 37.36 5.19
625 641 8.248945 GCAAACCTTATTGTAGTAGACAGTAGA 58.751 37.037 0.00 0.00 39.88 2.59
716 733 1.330655 CCATGGGTCACCTAGCGACT 61.331 60.000 2.85 0.00 37.76 4.18
838 856 0.765135 TGGTGTTCTTCCTTCCGGGA 60.765 55.000 0.00 0.00 43.41 5.14
840 858 1.739067 GATGGTGTTCTTCCTTCCGG 58.261 55.000 0.00 0.00 0.00 5.14
841 859 1.337823 ACGATGGTGTTCTTCCTTCCG 60.338 52.381 0.00 0.00 0.00 4.30
842 860 2.028020 AGACGATGGTGTTCTTCCTTCC 60.028 50.000 0.00 0.00 0.00 3.46
843 861 3.056465 AGAGACGATGGTGTTCTTCCTTC 60.056 47.826 0.00 0.00 0.00 3.46
844 862 2.900546 AGAGACGATGGTGTTCTTCCTT 59.099 45.455 0.00 0.00 0.00 3.36
845 863 2.530701 AGAGACGATGGTGTTCTTCCT 58.469 47.619 0.00 0.00 0.00 3.36
871 894 0.582960 TCGTTTCGTTTTCCGCTTCC 59.417 50.000 0.00 0.00 36.19 3.46
875 898 1.183419 CGTTTTCGTTTCGTTTTCCGC 59.817 47.619 0.00 0.00 38.65 5.54
888 911 2.470286 GGAGACGCTGCGTTTTCG 59.530 61.111 29.54 0.00 41.37 3.46
1251 1312 3.975591 AGGTCCCCCTCGTCGTCA 61.976 66.667 0.00 0.00 35.62 4.35
1426 1491 2.034179 CCGCAAGTACCATATCGACAGA 59.966 50.000 0.00 0.00 0.00 3.41
1427 1492 2.223735 ACCGCAAGTACCATATCGACAG 60.224 50.000 0.00 0.00 0.00 3.51
1428 1493 1.752498 ACCGCAAGTACCATATCGACA 59.248 47.619 0.00 0.00 0.00 4.35
1429 1494 2.034305 AGACCGCAAGTACCATATCGAC 59.966 50.000 0.00 0.00 0.00 4.20
1430 1495 2.304092 AGACCGCAAGTACCATATCGA 58.696 47.619 0.00 0.00 0.00 3.59
1443 1508 5.410746 CGATAACCTAACTAGATAGACCGCA 59.589 44.000 8.54 0.00 0.00 5.69
1445 1510 5.936956 ACCGATAACCTAACTAGATAGACCG 59.063 44.000 8.54 4.70 0.00 4.79
1526 1594 3.289834 AAGGGCAACGCAGCAGTG 61.290 61.111 1.99 0.00 35.83 3.66
1628 1697 2.869801 GCAACAATCCATAACCGATCGA 59.130 45.455 18.66 0.00 0.00 3.59
1633 1702 5.499139 AACATAGCAACAATCCATAACCG 57.501 39.130 0.00 0.00 0.00 4.44
1717 1786 2.046313 CAACGCACAACAGCAAGAATC 58.954 47.619 0.00 0.00 0.00 2.52
1733 1802 6.183360 ACACCATCTATGCAAGATAAACAACG 60.183 38.462 9.96 0.00 43.42 4.10
1737 1809 7.761409 TCAAACACCATCTATGCAAGATAAAC 58.239 34.615 9.96 0.00 43.42 2.01
1738 1810 7.936496 TCAAACACCATCTATGCAAGATAAA 57.064 32.000 9.96 0.00 43.42 1.40
1739 1811 8.523915 AATCAAACACCATCTATGCAAGATAA 57.476 30.769 9.96 0.00 43.42 1.75
1785 1857 6.485388 TGGGGAATCAGGTATCTCTAGTAT 57.515 41.667 0.00 0.00 0.00 2.12
1792 1864 4.837218 AGAGATTGGGGAATCAGGTATCT 58.163 43.478 0.00 0.00 0.00 1.98
1798 1870 5.443283 TGATCAAAGAGATTGGGGAATCAG 58.557 41.667 0.00 0.00 39.62 2.90
1800 1872 7.000472 TGTATGATCAAAGAGATTGGGGAATC 59.000 38.462 0.00 0.00 39.62 2.52
1807 1879 5.587443 TGCACCTGTATGATCAAAGAGATTG 59.413 40.000 0.00 0.00 37.00 2.67
1824 1896 6.037391 CCATAAAATGGCTAAAATTGCACCTG 59.963 38.462 0.00 0.00 44.70 4.00
1825 1897 6.114767 CCATAAAATGGCTAAAATTGCACCT 58.885 36.000 0.00 0.00 44.70 4.00
1884 1964 4.158579 ACATCACTGCTCGTCAAAGAGATA 59.841 41.667 0.00 0.00 40.57 1.98
1895 1975 2.536725 AGTGCAACATCACTGCTCG 58.463 52.632 0.00 0.00 44.88 5.03
1949 2032 3.604582 ACTGAAGTTCCAGCTAAGCATC 58.395 45.455 0.00 0.00 37.68 3.91
1954 2037 6.420913 AGAGTTAACTGAAGTTCCAGCTAA 57.579 37.500 14.14 0.00 39.31 3.09
1971 2054 9.733556 TCTTGCAAAGGAACATAATAAGAGTTA 57.266 29.630 0.00 0.00 46.24 2.24
1982 2065 6.925165 CACTAAATTGTCTTGCAAAGGAACAT 59.075 34.615 0.00 0.00 46.24 2.71
1987 2070 7.439056 ACAAATCACTAAATTGTCTTGCAAAGG 59.561 33.333 0.00 0.00 46.24 3.11
2001 2084 9.567776 TCATCAAACTCCTAACAAATCACTAAA 57.432 29.630 0.00 0.00 0.00 1.85
2026 2110 6.319658 TGAAAATTGAGCTATCCTGGTTGATC 59.680 38.462 0.00 0.00 0.00 2.92
2027 2111 6.096001 GTGAAAATTGAGCTATCCTGGTTGAT 59.904 38.462 0.00 0.00 0.00 2.57
2028 2112 5.415701 GTGAAAATTGAGCTATCCTGGTTGA 59.584 40.000 0.00 0.00 0.00 3.18
2037 2121 9.525409 GCATTGATTAAGTGAAAATTGAGCTAT 57.475 29.630 0.00 0.00 0.00 2.97
2099 2184 2.352960 GCATCAACTCCTCGGAAATCAC 59.647 50.000 0.00 0.00 0.00 3.06
2108 2193 5.293560 GTTATCCTAGTGCATCAACTCCTC 58.706 45.833 0.00 0.00 0.00 3.71
2164 2251 3.446310 TTCCGTGCTAATAGAATGCGA 57.554 42.857 0.00 0.00 0.00 5.10
2166 2253 6.494842 TCAATTTTCCGTGCTAATAGAATGC 58.505 36.000 0.00 0.00 0.00 3.56
2180 2267 3.421844 AGAAGAGGGGTTCAATTTTCCG 58.578 45.455 0.00 0.00 0.00 4.30
2269 2356 5.393027 GGAAGAGAACAAAAGCAACTCACAA 60.393 40.000 0.00 0.00 0.00 3.33
2307 2394 9.353431 ACAACAACAAGCATATCCATAATCATA 57.647 29.630 0.00 0.00 0.00 2.15
2356 2443 3.433319 GCATCTGCTCATGCCCAG 58.567 61.111 8.76 6.20 43.03 4.45


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.