Multiple sequence alignment - TraesCS4B01G350900

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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 TraesCS4B01G350900 chr4B 100.000 5568 0 0 1 5568 643480862 643486429 0.000000e+00 10283.0
1 TraesCS4B01G350900 chr4B 91.221 4021 309 25 884 4877 643528061 643532064 0.000000e+00 5430.0
2 TraesCS4B01G350900 chr4B 87.086 3957 455 35 944 4875 643629063 643632988 0.000000e+00 4425.0
3 TraesCS4B01G350900 chr4B 82.857 665 75 19 4875 5520 643532095 643532739 1.350000e-155 560.0
4 TraesCS4B01G350900 chr4B 83.184 559 45 17 1 557 643556563 643557074 3.040000e-127 466.0
5 TraesCS4B01G350900 chr4B 89.960 249 13 9 4632 4876 643538688 643538928 1.510000e-80 311.0
6 TraesCS4B01G350900 chr4B 79.722 360 67 4 3134 3487 643537360 643537719 7.160000e-64 255.0
7 TraesCS4B01G350900 chr4D 95.240 4286 165 20 623 4877 500196798 500201075 0.000000e+00 6748.0
8 TraesCS4B01G350900 chr4D 87.272 3952 454 30 947 4875 500300904 500304829 0.000000e+00 4466.0
9 TraesCS4B01G350900 chr4D 96.442 2052 46 13 623 2648 500151547 500153597 0.000000e+00 3360.0
10 TraesCS4B01G350900 chr4D 96.296 2052 49 13 623 2648 500193132 500195182 0.000000e+00 3343.0
11 TraesCS4B01G350900 chr4D 95.150 701 24 4 4875 5565 500201106 500201806 0.000000e+00 1098.0
12 TraesCS4B01G350900 chr4D 82.290 655 76 20 4875 5514 500155467 500156096 1.060000e-146 531.0
13 TraesCS4B01G350900 chrUn 91.878 4014 296 19 884 4877 60417335 60413332 0.000000e+00 5579.0
14 TraesCS4B01G350900 chrUn 91.613 4018 285 30 884 4875 16761307 16757316 0.000000e+00 5505.0
15 TraesCS4B01G350900 chrUn 93.966 2917 163 9 1965 4877 60473878 60470971 0.000000e+00 4399.0
16 TraesCS4B01G350900 chrUn 87.858 2339 244 9 947 3284 60491694 60489395 0.000000e+00 2710.0
17 TraesCS4B01G350900 chrUn 95.677 694 14 1 4875 5568 60470940 60470263 0.000000e+00 1101.0
18 TraesCS4B01G350900 chrUn 82.411 705 81 19 4875 5568 60413301 60412629 4.840000e-160 575.0
19 TraesCS4B01G350900 chrUn 82.796 558 47 17 2 557 60476746 60476236 2.360000e-123 453.0
20 TraesCS4B01G350900 chrUn 85.302 381 37 8 5091 5469 16757230 16756867 5.270000e-100 375.0
21 TraesCS4B01G350900 chrUn 86.007 293 30 7 4589 4877 60493850 60493565 2.520000e-78 303.0
22 TraesCS4B01G350900 chrUn 86.007 293 30 7 4589 4877 318519301 318519586 2.520000e-78 303.0
23 TraesCS4B01G350900 chrUn 78.977 352 42 17 197 545 60492408 60492086 1.570000e-50 211.0
24 TraesCS4B01G350900 chrUn 78.977 352 42 17 197 545 318520743 318521065 1.570000e-50 211.0
25 TraesCS4B01G350900 chrUn 91.304 46 4 0 4876 4921 16757282 16757237 4.660000e-06 63.9
26 TraesCS4B01G350900 chr5A 89.201 4454 349 69 948 5316 680865453 680869859 0.000000e+00 5439.0
27 TraesCS4B01G350900 chr5A 92.281 3679 254 18 884 4543 680921159 680924826 0.000000e+00 5193.0
28 TraesCS4B01G350900 chr5A 88.322 3725 400 19 944 4655 680981135 680984837 0.000000e+00 4436.0
29 TraesCS4B01G350900 chr5A 84.050 558 40 22 1 557 680864197 680864706 5.010000e-135 492.0
30 TraesCS4B01G350900 chr2B 98.333 60 1 0 4664 4723 44178341 44178400 7.630000e-19 106.0


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 TraesCS4B01G350900 chr4B 643480862 643486429 5567 False 10283.000000 10283 100.000000 1 5568 1 chr4B.!!$F1 5567
1 TraesCS4B01G350900 chr4B 643629063 643632988 3925 False 4425.000000 4425 87.086000 944 4875 1 chr4B.!!$F3 3931
2 TraesCS4B01G350900 chr4B 643528061 643532739 4678 False 2995.000000 5430 87.039000 884 5520 2 chr4B.!!$F4 4636
3 TraesCS4B01G350900 chr4B 643556563 643557074 511 False 466.000000 466 83.184000 1 557 1 chr4B.!!$F2 556
4 TraesCS4B01G350900 chr4B 643537360 643538928 1568 False 283.000000 311 84.841000 3134 4876 2 chr4B.!!$F5 1742
5 TraesCS4B01G350900 chr4D 500300904 500304829 3925 False 4466.000000 4466 87.272000 947 4875 1 chr4D.!!$F1 3928
6 TraesCS4B01G350900 chr4D 500193132 500201806 8674 False 3729.666667 6748 95.562000 623 5565 3 chr4D.!!$F3 4942
7 TraesCS4B01G350900 chr4D 500151547 500156096 4549 False 1945.500000 3360 89.366000 623 5514 2 chr4D.!!$F2 4891
8 TraesCS4B01G350900 chrUn 60412629 60417335 4706 True 3077.000000 5579 87.144500 884 5568 2 chrUn.!!$R2 4684
9 TraesCS4B01G350900 chrUn 60470263 60476746 6483 True 1984.333333 4399 90.813000 2 5568 3 chrUn.!!$R3 5566
10 TraesCS4B01G350900 chrUn 16756867 16761307 4440 True 1981.300000 5505 89.406333 884 5469 3 chrUn.!!$R1 4585
11 TraesCS4B01G350900 chrUn 60489395 60493850 4455 True 1074.666667 2710 84.280667 197 4877 3 chrUn.!!$R4 4680
12 TraesCS4B01G350900 chrUn 318519301 318521065 1764 False 257.000000 303 82.492000 197 4877 2 chrUn.!!$F1 4680
13 TraesCS4B01G350900 chr5A 680921159 680924826 3667 False 5193.000000 5193 92.281000 884 4543 1 chr5A.!!$F1 3659
14 TraesCS4B01G350900 chr5A 680981135 680984837 3702 False 4436.000000 4436 88.322000 944 4655 1 chr5A.!!$F2 3711
15 TraesCS4B01G350900 chr5A 680864197 680869859 5662 False 2965.500000 5439 86.625500 1 5316 2 chr5A.!!$F3 5315

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
346 509 0.029700 TGTGCGAAGACGAAGACGAA 59.970 50.000 0.00 0.00 42.66 3.85 F
839 2220 0.447801 GTGCCATCACACATTCGGTC 59.552 55.000 0.00 0.00 42.66 4.79 F
1605 6698 0.460811 TTCCTGAGCTGCGCATACTG 60.461 55.000 12.24 9.33 0.00 2.74 F
1615 6708 2.230940 CGCATACTGGTTCTCGCCG 61.231 63.158 0.00 0.00 0.00 6.46 F
1740 6833 5.065731 GTCCTTGGCAAATAGTTCATCTCTG 59.934 44.000 0.00 0.00 0.00 3.35 F
3360 9081 3.572584 CACTGCAATCCTTTTCTCTTGC 58.427 45.455 0.00 0.00 43.25 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 6698 0.025898 GCGTATTTTCGGCGAGAACC 59.974 55.0 15.41 8.13 38.83 3.62 R
1773 6866 0.391793 GAGCCTTTGGGAGTTCTCCG 60.392 60.0 12.01 0.51 33.58 4.63 R
3225 8941 5.544176 ACCTCTCATCGGGATAATTGTACAT 59.456 40.0 0.00 0.00 0.00 2.29 R
3360 9081 6.713762 TTCCTCCTATAAATTGTTGCCATG 57.286 37.5 0.00 0.00 0.00 3.66 R
3808 9533 6.303839 TGTTAGTCCTTTGGCTTAAACTCAT 58.696 36.0 0.00 0.00 0.00 2.90 R
5134 11991 0.667993 CTGGAAAAGCTGACGCCAAA 59.332 50.0 0.00 0.00 36.60 3.28 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
24 25 1.364626 GACATGACTTGCTGGGAGCG 61.365 60.000 0.00 0.00 46.26 5.03
30 31 0.816825 ACTTGCTGGGAGCGCATATG 60.817 55.000 11.47 0.00 46.26 1.78
56 57 3.002042 CGCCATTGATTCTCACTTGCTAG 59.998 47.826 0.00 0.00 0.00 3.42
79 81 3.336138 AGGCAAAGGACAGCTTAGTAC 57.664 47.619 0.00 0.00 0.00 2.73
102 104 7.123355 ACTCGATCAGTACTTAGTAGTAGGT 57.877 40.000 0.00 0.00 37.53 3.08
103 105 6.985645 ACTCGATCAGTACTTAGTAGTAGGTG 59.014 42.308 0.00 0.00 37.53 4.00
104 106 5.757320 TCGATCAGTACTTAGTAGTAGGTGC 59.243 44.000 0.00 1.52 37.53 5.01
105 107 5.049543 CGATCAGTACTTAGTAGTAGGTGCC 60.050 48.000 0.00 0.00 37.53 5.01
137 139 0.610174 TCACTGATGACTGCCTCCAC 59.390 55.000 0.00 0.00 0.00 4.02
187 189 4.365514 TGCAGAGGTTAATCTCACCAAA 57.634 40.909 17.90 0.00 36.67 3.28
189 191 4.041567 TGCAGAGGTTAATCTCACCAAAGA 59.958 41.667 17.90 0.00 36.67 2.52
190 192 5.003804 GCAGAGGTTAATCTCACCAAAGAA 58.996 41.667 17.90 0.00 36.67 2.52
191 193 5.649831 GCAGAGGTTAATCTCACCAAAGAAT 59.350 40.000 17.90 0.00 36.67 2.40
192 194 6.823689 GCAGAGGTTAATCTCACCAAAGAATA 59.176 38.462 17.90 0.00 36.67 1.75
193 195 7.201652 GCAGAGGTTAATCTCACCAAAGAATAC 60.202 40.741 17.90 0.00 36.67 1.89
195 197 8.261522 AGAGGTTAATCTCACCAAAGAATACTC 58.738 37.037 17.90 0.00 36.67 2.59
197 199 8.043710 AGGTTAATCTCACCAAAGAATACTCAG 58.956 37.037 0.00 0.00 36.67 3.35
214 358 0.459934 CAGGCACTCAGCTGAGCTAC 60.460 60.000 37.78 27.57 45.79 3.58
216 360 1.153469 GCACTCAGCTGAGCTACCC 60.153 63.158 37.78 20.15 45.79 3.69
257 401 1.334992 CTACCACACGCGTTCGACTG 61.335 60.000 10.22 0.00 39.41 3.51
263 407 1.227031 ACGCGTTCGACTGGTCAAA 60.227 52.632 5.58 0.00 39.41 2.69
264 408 0.806884 ACGCGTTCGACTGGTCAAAA 60.807 50.000 5.58 0.00 39.41 2.44
265 409 0.382636 CGCGTTCGACTGGTCAAAAC 60.383 55.000 0.00 4.30 38.10 2.43
268 412 1.071698 CGTTCGACTGGTCAAAACGAC 60.072 52.381 22.37 0.00 44.29 4.34
272 416 1.849097 GACTGGTCAAAACGACGACT 58.151 50.000 0.00 0.00 46.42 4.18
275 419 3.118542 ACTGGTCAAAACGACGACTAAC 58.881 45.455 0.00 0.00 46.42 2.34
307 467 9.628500 ATGAATAGTTAAAGAGGGAATACCAAC 57.372 33.333 0.00 0.00 43.89 3.77
308 468 8.050930 TGAATAGTTAAAGAGGGAATACCAACC 58.949 37.037 0.00 0.00 43.89 3.77
309 469 5.853572 AGTTAAAGAGGGAATACCAACCA 57.146 39.130 0.00 0.00 43.89 3.67
310 470 5.816682 AGTTAAAGAGGGAATACCAACCAG 58.183 41.667 0.00 0.00 43.89 4.00
311 471 2.808906 AAGAGGGAATACCAACCAGC 57.191 50.000 0.00 0.00 43.89 4.85
312 472 1.972588 AGAGGGAATACCAACCAGCT 58.027 50.000 0.00 0.00 43.89 4.24
326 489 1.522355 CAGCTGGCTCATACCACCG 60.522 63.158 5.57 0.00 35.33 4.94
346 509 0.029700 TGTGCGAAGACGAAGACGAA 59.970 50.000 0.00 0.00 42.66 3.85
347 510 0.703466 GTGCGAAGACGAAGACGAAG 59.297 55.000 0.00 0.00 42.66 3.79
348 511 0.589708 TGCGAAGACGAAGACGAAGA 59.410 50.000 0.00 0.00 42.66 2.87
349 512 0.976253 GCGAAGACGAAGACGAAGAC 59.024 55.000 0.00 0.00 42.66 3.01
350 513 1.240010 CGAAGACGAAGACGAAGACG 58.760 55.000 0.00 0.00 42.66 4.18
351 514 1.136419 CGAAGACGAAGACGAAGACGA 60.136 52.381 0.00 0.00 41.06 4.20
352 515 2.661169 CGAAGACGAAGACGAAGACGAA 60.661 50.000 0.00 0.00 41.06 3.85
353 516 2.598000 AGACGAAGACGAAGACGAAG 57.402 50.000 0.00 0.00 42.66 3.79
354 517 2.141517 AGACGAAGACGAAGACGAAGA 58.858 47.619 0.00 0.00 42.66 2.87
355 518 2.096318 AGACGAAGACGAAGACGAAGAC 60.096 50.000 0.00 0.00 42.66 3.01
356 519 1.240010 CGAAGACGAAGACGAAGACG 58.760 55.000 0.00 0.00 42.66 4.18
357 520 1.604396 GAAGACGAAGACGAAGACGG 58.396 55.000 0.00 0.00 44.46 4.79
358 521 1.196354 GAAGACGAAGACGAAGACGGA 59.804 52.381 0.00 0.00 44.46 4.69
367 530 0.739561 ACGAAGACGGAGACTATGCC 59.260 55.000 0.00 0.00 44.46 4.40
380 543 3.136763 GACTATGCCACATCAGACCATG 58.863 50.000 0.00 0.00 0.00 3.66
437 613 1.851658 AAAAATTGTGTCGCTGGCAC 58.148 45.000 6.38 6.38 37.37 5.01
438 614 0.743688 AAAATTGTGTCGCTGGCACA 59.256 45.000 11.07 11.07 44.05 4.57
454 630 1.668047 GCACAGCAGTTTGGCTCATTC 60.668 52.381 0.00 0.00 43.68 2.67
456 669 1.250328 CAGCAGTTTGGCTCATTCCA 58.750 50.000 0.00 0.00 43.68 3.53
478 691 4.855388 CAGATTTCATTTTCGGAGTTGCTG 59.145 41.667 0.00 0.00 0.00 4.41
492 706 4.054671 GAGTTGCTGGCTAGTAGCTATTG 58.945 47.826 21.20 6.28 41.99 1.90
517 731 9.295825 TGCTTCCATAAGATTTCTTTTAAGTCA 57.704 29.630 0.00 0.13 37.40 3.41
526 740 9.566432 AAGATTTCTTTTAAGTCACACTCATCT 57.434 29.630 0.00 0.00 30.82 2.90
557 1481 3.219176 ACTCCATCTACCGGATTCGTA 57.781 47.619 9.46 0.00 31.27 3.43
559 1483 4.150359 ACTCCATCTACCGGATTCGTATT 58.850 43.478 9.46 0.00 31.27 1.89
560 1484 4.587684 ACTCCATCTACCGGATTCGTATTT 59.412 41.667 9.46 0.00 31.27 1.40
561 1485 5.070047 ACTCCATCTACCGGATTCGTATTTT 59.930 40.000 9.46 0.00 31.27 1.82
562 1486 5.294356 TCCATCTACCGGATTCGTATTTTG 58.706 41.667 9.46 0.00 31.27 2.44
564 1488 5.405571 CCATCTACCGGATTCGTATTTTGAG 59.594 44.000 9.46 0.00 31.27 3.02
565 1489 5.587388 TCTACCGGATTCGTATTTTGAGT 57.413 39.130 9.46 0.00 33.95 3.41
566 1490 5.969423 TCTACCGGATTCGTATTTTGAGTT 58.031 37.500 9.46 0.00 33.95 3.01
579 1881 8.479689 TCGTATTTTGAGTTCTATATTCCCACA 58.520 33.333 0.00 0.00 0.00 4.17
585 1887 7.675161 TGAGTTCTATATTCCCACATGAAGA 57.325 36.000 0.00 0.00 0.00 2.87
611 1919 3.121929 TCTAGTTTGGCTGGAGAGGAT 57.878 47.619 0.00 0.00 30.82 3.24
636 1978 5.049828 CCAACCAAACCATCTTTGAAACTC 58.950 41.667 0.00 0.00 0.00 3.01
677 2024 1.415659 AGCTGCTTCTCGCCTCATTAT 59.584 47.619 0.00 0.00 38.05 1.28
745 2124 3.100671 ACCCTAAGCTAGGTCTTGTCTG 58.899 50.000 0.00 0.00 44.73 3.51
771 2150 7.698130 GTGAGTCCACATTACTGCAAAATATTC 59.302 37.037 0.00 0.00 42.72 1.75
823 2204 1.310216 TGTGCCAGCATCATCAGTGC 61.310 55.000 0.00 0.00 42.81 4.40
839 2220 0.447801 GTGCCATCACACATTCGGTC 59.552 55.000 0.00 0.00 42.66 4.79
841 2222 0.447801 GCCATCACACATTCGGTCAC 59.552 55.000 0.00 0.00 0.00 3.67
1140 2567 1.270785 TGCTTCAAATCACGGCTCTCA 60.271 47.619 0.00 0.00 0.00 3.27
1605 6698 0.460811 TTCCTGAGCTGCGCATACTG 60.461 55.000 12.24 9.33 0.00 2.74
1615 6708 2.230940 CGCATACTGGTTCTCGCCG 61.231 63.158 0.00 0.00 0.00 6.46
1740 6833 5.065731 GTCCTTGGCAAATAGTTCATCTCTG 59.934 44.000 0.00 0.00 0.00 3.35
3225 8941 6.813293 TCACTCCAAGGAAATGATCATCTA 57.187 37.500 9.06 0.00 0.00 1.98
3360 9081 3.572584 CACTGCAATCCTTTTCTCTTGC 58.427 45.455 0.00 0.00 43.25 4.01
4104 9830 9.793259 AGATCTTGTTTCTGTTTGTTCCTTATA 57.207 29.630 0.00 0.00 0.00 0.98
4225 9951 2.619177 TGTCTATAGCTTCGGAGTGCTC 59.381 50.000 10.14 0.00 38.85 4.26
4369 10753 4.264253 TGCTACAAGATAACAGCAATGCT 58.736 39.130 0.00 0.00 40.87 3.79
4370 10754 4.701651 TGCTACAAGATAACAGCAATGCTT 59.298 37.500 4.36 0.00 40.87 3.91
4441 10825 1.098050 GCTCCATGACATCACCCAAC 58.902 55.000 0.00 0.00 0.00 3.77
4660 11147 7.094205 GCTAATACATCCATGTCAAATTAGGGG 60.094 40.741 15.93 0.00 41.97 4.79
4831 11351 6.006449 AGCAATTTTCACTGAACTAGGTGAT 58.994 36.000 0.00 0.00 41.27 3.06
4973 11828 4.384098 CCCATCAACTTATGCAGGACACTA 60.384 45.833 0.00 0.00 0.00 2.74
4974 11829 5.185454 CCATCAACTTATGCAGGACACTAA 58.815 41.667 0.00 0.00 0.00 2.24
5134 11991 5.195940 CCCTTGATGTGTGGATTGTAATCT 58.804 41.667 4.75 0.00 35.73 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.900941 GAGAATCAATGGCGGCACATATGC 62.901 50.000 16.34 6.47 43.38 3.14
30 31 2.481212 TGAGAATCAATGGCGGCAC 58.519 52.632 16.34 0.00 45.97 5.01
56 57 2.284190 CTAAGCTGTCCTTTGCCTAGC 58.716 52.381 0.00 0.00 34.95 3.42
79 81 6.073657 GCACCTACTACTAAGTACTGATCGAG 60.074 46.154 0.00 0.00 37.15 4.04
93 95 1.644864 ACCACCTAGGCACCTACTACT 59.355 52.381 9.30 0.00 43.14 2.57
94 96 2.156102 ACCACCTAGGCACCTACTAC 57.844 55.000 9.30 0.00 43.14 2.73
96 98 1.078989 AGAACCACCTAGGCACCTACT 59.921 52.381 9.30 0.00 43.14 2.57
97 99 1.207329 CAGAACCACCTAGGCACCTAC 59.793 57.143 9.30 0.00 43.14 3.18
99 101 0.473886 ACAGAACCACCTAGGCACCT 60.474 55.000 9.30 0.00 43.14 4.00
100 102 0.036294 GACAGAACCACCTAGGCACC 60.036 60.000 9.30 0.00 43.14 5.01
101 103 0.685097 TGACAGAACCACCTAGGCAC 59.315 55.000 9.30 0.00 43.14 5.01
102 104 0.685097 GTGACAGAACCACCTAGGCA 59.315 55.000 9.30 0.00 43.14 4.75
103 105 0.977395 AGTGACAGAACCACCTAGGC 59.023 55.000 9.30 0.00 43.14 3.93
104 106 2.248248 TCAGTGACAGAACCACCTAGG 58.752 52.381 7.41 7.41 45.67 3.02
105 107 3.511540 TCATCAGTGACAGAACCACCTAG 59.488 47.826 0.00 0.00 35.23 3.02
137 139 4.124351 CCATGCAGGCGGCTTGTG 62.124 66.667 20.46 8.42 44.00 3.33
151 153 4.907875 ACCTCTGCATGTATAAGTACCCAT 59.092 41.667 0.00 0.00 0.00 4.00
187 189 2.168106 CAGCTGAGTGCCTGAGTATTCT 59.832 50.000 8.42 0.00 44.23 2.40
189 191 2.168106 CTCAGCTGAGTGCCTGAGTATT 59.832 50.000 31.71 0.00 44.23 1.89
190 192 1.755959 CTCAGCTGAGTGCCTGAGTAT 59.244 52.381 31.71 0.00 44.23 2.12
191 193 1.180907 CTCAGCTGAGTGCCTGAGTA 58.819 55.000 31.71 0.00 44.23 2.59
192 194 1.973760 CTCAGCTGAGTGCCTGAGT 59.026 57.895 31.71 0.00 44.23 3.41
193 195 1.448189 GCTCAGCTGAGTGCCTGAG 60.448 63.158 37.25 16.74 43.85 3.35
195 197 0.459934 GTAGCTCAGCTGAGTGCCTG 60.460 60.000 37.25 18.13 43.85 4.85
197 199 1.153469 GGTAGCTCAGCTGAGTGCC 60.153 63.158 37.25 30.62 43.85 5.01
214 358 3.455910 TCACTGGGTAAGAATGAGATGGG 59.544 47.826 0.00 0.00 0.00 4.00
216 360 5.738909 AGTTCACTGGGTAAGAATGAGATG 58.261 41.667 0.00 0.00 0.00 2.90
257 401 4.519191 TTTGTTAGTCGTCGTTTTGACC 57.481 40.909 0.00 0.00 45.23 4.02
263 407 9.362539 ACTATTCATTATTTGTTAGTCGTCGTT 57.637 29.630 0.00 0.00 0.00 3.85
264 408 8.922058 ACTATTCATTATTTGTTAGTCGTCGT 57.078 30.769 0.00 0.00 0.00 4.34
288 432 4.398358 GCTGGTTGGTATTCCCTCTTTAAC 59.602 45.833 0.00 0.00 0.00 2.01
301 461 1.209504 GTATGAGCCAGCTGGTTGGTA 59.790 52.381 32.81 18.48 40.49 3.25
304 464 0.035152 TGGTATGAGCCAGCTGGTTG 60.035 55.000 32.81 9.43 37.57 3.77
305 465 0.035056 GTGGTATGAGCCAGCTGGTT 60.035 55.000 32.81 28.59 39.53 3.67
306 466 1.604378 GTGGTATGAGCCAGCTGGT 59.396 57.895 32.81 19.96 39.53 4.00
307 467 4.547859 GTGGTATGAGCCAGCTGG 57.452 61.111 29.34 29.34 39.53 4.85
311 471 0.740868 CACACGGTGGTATGAGCCAG 60.741 60.000 13.48 0.00 39.53 4.85
312 472 1.295101 CACACGGTGGTATGAGCCA 59.705 57.895 13.48 0.00 35.93 4.75
326 489 0.659417 TCGTCTTCGTCTTCGCACAC 60.659 55.000 0.00 0.00 38.33 3.82
346 509 1.671845 GCATAGTCTCCGTCTTCGTCT 59.328 52.381 0.00 0.00 35.01 4.18
347 510 1.268640 GGCATAGTCTCCGTCTTCGTC 60.269 57.143 0.00 0.00 35.01 4.20
348 511 0.739561 GGCATAGTCTCCGTCTTCGT 59.260 55.000 0.00 0.00 35.01 3.85
349 512 0.738975 TGGCATAGTCTCCGTCTTCG 59.261 55.000 0.00 0.00 0.00 3.79
350 513 1.476891 TGTGGCATAGTCTCCGTCTTC 59.523 52.381 0.00 0.00 0.00 2.87
351 514 1.557099 TGTGGCATAGTCTCCGTCTT 58.443 50.000 0.00 0.00 0.00 3.01
352 515 1.683917 GATGTGGCATAGTCTCCGTCT 59.316 52.381 0.00 0.00 0.00 4.18
353 516 1.409064 TGATGTGGCATAGTCTCCGTC 59.591 52.381 0.00 0.00 0.00 4.79
354 517 1.410517 CTGATGTGGCATAGTCTCCGT 59.589 52.381 0.00 0.00 0.00 4.69
355 518 1.683385 TCTGATGTGGCATAGTCTCCG 59.317 52.381 0.00 0.00 0.00 4.63
356 519 2.224161 GGTCTGATGTGGCATAGTCTCC 60.224 54.545 0.00 0.00 0.00 3.71
357 520 2.432146 TGGTCTGATGTGGCATAGTCTC 59.568 50.000 0.00 0.00 0.00 3.36
358 521 2.470990 TGGTCTGATGTGGCATAGTCT 58.529 47.619 0.00 0.00 0.00 3.24
367 530 1.078214 ACGGGCATGGTCTGATGTG 60.078 57.895 0.00 0.00 0.00 3.21
380 543 3.802948 TCTCTCTATTCTTTGACGGGC 57.197 47.619 0.00 0.00 0.00 6.13
437 613 1.201647 CTGGAATGAGCCAAACTGCTG 59.798 52.381 0.00 0.00 42.95 4.41
438 614 1.074405 TCTGGAATGAGCCAAACTGCT 59.926 47.619 0.00 0.00 46.37 4.24
439 615 1.538047 TCTGGAATGAGCCAAACTGC 58.462 50.000 0.00 0.00 37.52 4.40
454 630 4.082571 AGCAACTCCGAAAATGAAATCTGG 60.083 41.667 0.00 0.00 0.00 3.86
456 669 4.082571 CCAGCAACTCCGAAAATGAAATCT 60.083 41.667 0.00 0.00 0.00 2.40
492 706 9.561270 GTGACTTAAAAGAAATCTTATGGAAGC 57.439 33.333 0.00 0.00 34.61 3.86
520 734 5.651387 TGGAGTTACTTGACTCAGATGAG 57.349 43.478 8.30 8.30 46.21 2.90
523 737 6.322712 GGTAGATGGAGTTACTTGACTCAGAT 59.677 42.308 7.27 0.00 46.21 2.90
526 740 4.398358 CGGTAGATGGAGTTACTTGACTCA 59.602 45.833 7.27 0.00 46.21 3.41
532 746 4.037684 CGAATCCGGTAGATGGAGTTACTT 59.962 45.833 0.00 0.00 39.30 2.24
536 750 2.385803 ACGAATCCGGTAGATGGAGTT 58.614 47.619 0.00 0.00 39.30 3.01
557 1481 9.699410 TTCATGTGGGAATATAGAACTCAAAAT 57.301 29.630 0.00 0.00 0.00 1.82
559 1483 8.548025 TCTTCATGTGGGAATATAGAACTCAAA 58.452 33.333 0.00 0.00 0.00 2.69
560 1484 8.089625 TCTTCATGTGGGAATATAGAACTCAA 57.910 34.615 0.00 0.00 0.00 3.02
561 1485 7.675161 TCTTCATGTGGGAATATAGAACTCA 57.325 36.000 0.00 0.00 0.00 3.41
562 1486 7.118971 GCATCTTCATGTGGGAATATAGAACTC 59.881 40.741 0.00 0.00 31.86 3.01
564 1488 6.150140 GGCATCTTCATGTGGGAATATAGAAC 59.850 42.308 0.00 0.00 31.86 3.01
565 1489 6.183361 TGGCATCTTCATGTGGGAATATAGAA 60.183 38.462 0.00 0.00 31.86 2.10
566 1490 5.310331 TGGCATCTTCATGTGGGAATATAGA 59.690 40.000 0.00 0.00 31.86 1.98
611 1919 3.320610 TCAAAGATGGTTTGGTTGGGA 57.679 42.857 0.00 0.00 0.00 4.37
636 1978 1.105457 CCTCACAGGAGAGAGAGCAG 58.895 60.000 0.00 0.00 44.26 4.24
745 2124 4.829064 TTTTGCAGTAATGTGGACTCAC 57.171 40.909 0.00 0.00 43.87 3.51
777 2156 2.029739 TCAGCCAAGTGACGAACGATAA 60.030 45.455 0.14 0.00 0.00 1.75
823 2204 1.733912 CTGTGACCGAATGTGTGATGG 59.266 52.381 0.00 0.00 0.00 3.51
839 2220 3.916172 GCAATATGTTCTGCAACACTGTG 59.084 43.478 6.19 6.19 45.47 3.66
841 2222 4.163458 TGCAATATGTTCTGCAACACTG 57.837 40.909 0.00 0.00 45.47 3.66
1605 6698 0.025898 GCGTATTTTCGGCGAGAACC 59.974 55.000 15.41 8.13 38.83 3.62
1615 6708 2.745281 TGGTGCCAGTAAGCGTATTTTC 59.255 45.455 0.00 0.00 34.65 2.29
1773 6866 0.391793 GAGCCTTTGGGAGTTCTCCG 60.392 60.000 12.01 0.51 33.58 4.63
2193 7831 2.903135 TGGTCCATCAAAATTGTTCCCC 59.097 45.455 0.00 0.00 0.00 4.81
3225 8941 5.544176 ACCTCTCATCGGGATAATTGTACAT 59.456 40.000 0.00 0.00 0.00 2.29
3360 9081 6.713762 TTCCTCCTATAAATTGTTGCCATG 57.286 37.500 0.00 0.00 0.00 3.66
3808 9533 6.303839 TGTTAGTCCTTTGGCTTAAACTCAT 58.696 36.000 0.00 0.00 0.00 2.90
3882 9607 3.704566 AGTCGCAATGTATAACTGGAGGA 59.295 43.478 0.00 0.00 0.00 3.71
4147 9873 7.692291 CCATACTCTGCGTTTACATGTAAAAAG 59.308 37.037 28.05 24.28 36.86 2.27
4225 9951 4.750098 CGCCCTGTTATCAGTTGTAATAGG 59.250 45.833 0.30 0.00 39.06 2.57
4228 9954 4.216411 ACGCCCTGTTATCAGTTGTAAT 57.784 40.909 0.30 0.00 39.82 1.89
4369 10753 3.624410 CGCAATTCTCCATCATGTCAGAA 59.376 43.478 0.00 0.00 0.00 3.02
4370 10754 3.200483 CGCAATTCTCCATCATGTCAGA 58.800 45.455 0.00 0.00 0.00 3.27
4453 10837 5.152623 TCTCAGTAGAAACTTGTCCCATG 57.847 43.478 0.00 0.00 31.97 3.66
4660 11147 6.985188 TTAGCAGAACAATTAGGACACATC 57.015 37.500 0.00 0.00 0.00 3.06
4973 11828 1.473434 GGAAGGGTCATCGAAGCGATT 60.473 52.381 0.00 0.00 44.59 3.34
5134 11991 0.667993 CTGGAAAAGCTGACGCCAAA 59.332 50.000 0.00 0.00 36.60 3.28
5441 13220 4.566759 TCAGCTACTAAAACGTCATGATGC 59.433 41.667 15.01 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.