Multiple sequence alignment - TraesCS3A01G461200

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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 TraesCS3A01G461200 chr3A 100.000 5367 0 0 1 5367 697259144 697264510 0.000000e+00 9912.0
1 TraesCS3A01G461200 chr3B 93.664 4530 221 29 4 4527 747832451 747836920 0.000000e+00 6715.0
2 TraesCS3A01G461200 chr3B 93.642 4530 222 29 4 4527 747848978 747853447 0.000000e+00 6709.0
3 TraesCS3A01G461200 chr3B 93.887 3599 163 24 936 4527 747820896 747824444 0.000000e+00 5374.0
4 TraesCS3A01G461200 chr3B 94.461 2654 120 9 1877 4527 747838343 747840972 0.000000e+00 4061.0
5 TraesCS3A01G461200 chr3B 95.186 1454 63 5 3081 4527 748414696 748416149 0.000000e+00 2290.0
6 TraesCS3A01G461200 chr3B 93.001 843 52 7 4527 5364 748416247 748417087 0.000000e+00 1223.0
7 TraesCS3A01G461200 chr3B 92.299 844 57 7 4527 5364 747841264 747842105 0.000000e+00 1192.0
8 TraesCS3A01G461200 chr3B 92.299 844 57 7 4527 5364 747853739 747854580 0.000000e+00 1192.0
9 TraesCS3A01G461200 chr3B 92.180 844 58 6 4527 5364 747824736 747825577 0.000000e+00 1186.0
10 TraesCS3A01G461200 chr3B 91.825 844 61 6 4527 5364 747837212 747838053 0.000000e+00 1170.0
11 TraesCS3A01G461200 chr3D 93.832 3356 180 15 970 4312 561170550 561173891 0.000000e+00 5025.0
12 TraesCS3A01G461200 chr3D 94.546 2622 121 11 1702 4312 561154907 561157517 0.000000e+00 4030.0
13 TraesCS3A01G461200 chr3D 95.011 2245 95 10 2283 4527 561375378 561377605 0.000000e+00 3509.0
14 TraesCS3A01G461200 chr3D 93.125 2240 128 13 3 2238 561373159 561375376 0.000000e+00 3260.0
15 TraesCS3A01G461200 chr3D 92.099 848 50 7 4527 5364 561377707 561378547 0.000000e+00 1179.0
16 TraesCS3A01G461200 chr3D 89.549 488 36 10 3 489 561170079 561170552 5.950000e-169 604.0
17 TraesCS3A01G461200 chrUn 92.455 2134 123 18 435 2564 354241765 354243864 0.000000e+00 3014.0
18 TraesCS3A01G461200 chrUn 96.756 1387 45 0 3141 4527 331495092 331496478 0.000000e+00 2313.0
19 TraesCS3A01G461200 chrUn 82.766 1880 293 22 2572 4428 108321567 108323438 0.000000e+00 1648.0
20 TraesCS3A01G461200 chrUn 92.877 1067 66 6 4 1070 354040176 354041232 0.000000e+00 1541.0
21 TraesCS3A01G461200 chrUn 92.784 1067 66 7 4 1070 354097490 354096435 0.000000e+00 1533.0
22 TraesCS3A01G461200 chrUn 91.943 844 60 6 4527 5364 331496770 331497611 0.000000e+00 1175.0
23 TraesCS3A01G461200 chrUn 94.030 469 26 2 4527 4993 455312296 455311828 0.000000e+00 710.0
24 TraesCS3A01G461200 chrUn 95.556 45 2 0 5323 5367 452588691 452588647 7.460000e-09 73.1
25 TraesCS3A01G461200 chr6A 82.749 2197 322 43 2208 4371 572136397 572138569 0.000000e+00 1905.0
26 TraesCS3A01G461200 chr6A 80.268 522 90 9 1011 1528 158908018 158908530 1.090000e-101 381.0
27 TraesCS3A01G461200 chr5A 82.721 1904 294 27 2577 4452 705844231 705842335 0.000000e+00 1661.0
28 TraesCS3A01G461200 chr4B 82.686 1906 293 29 2576 4452 665877247 665875350 0.000000e+00 1657.0
29 TraesCS3A01G461200 chr6D 75.594 1053 195 33 3 1011 427481192 427482226 1.050000e-126 464.0
30 TraesCS3A01G461200 chr6D 79.754 568 100 12 1013 1572 120649204 120649764 1.080000e-106 398.0


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 TraesCS3A01G461200 chr3A 697259144 697264510 5366 False 9912.000000 9912 100.000000 1 5367 1 chr3A.!!$F1 5366
1 TraesCS3A01G461200 chr3B 747848978 747854580 5602 False 3950.500000 6709 92.970500 4 5364 2 chr3B.!!$F3 5360
2 TraesCS3A01G461200 chr3B 747832451 747842105 9654 False 3284.500000 6715 93.062250 4 5364 4 chr3B.!!$F2 5360
3 TraesCS3A01G461200 chr3B 747820896 747825577 4681 False 3280.000000 5374 93.033500 936 5364 2 chr3B.!!$F1 4428
4 TraesCS3A01G461200 chr3B 748414696 748417087 2391 False 1756.500000 2290 94.093500 3081 5364 2 chr3B.!!$F4 2283
5 TraesCS3A01G461200 chr3D 561154907 561157517 2610 False 4030.000000 4030 94.546000 1702 4312 1 chr3D.!!$F1 2610
6 TraesCS3A01G461200 chr3D 561170079 561173891 3812 False 2814.500000 5025 91.690500 3 4312 2 chr3D.!!$F2 4309
7 TraesCS3A01G461200 chr3D 561373159 561378547 5388 False 2649.333333 3509 93.411667 3 5364 3 chr3D.!!$F3 5361
8 TraesCS3A01G461200 chrUn 354241765 354243864 2099 False 3014.000000 3014 92.455000 435 2564 1 chrUn.!!$F3 2129
9 TraesCS3A01G461200 chrUn 331495092 331497611 2519 False 1744.000000 2313 94.349500 3141 5364 2 chrUn.!!$F4 2223
10 TraesCS3A01G461200 chrUn 108321567 108323438 1871 False 1648.000000 1648 82.766000 2572 4428 1 chrUn.!!$F1 1856
11 TraesCS3A01G461200 chrUn 354040176 354041232 1056 False 1541.000000 1541 92.877000 4 1070 1 chrUn.!!$F2 1066
12 TraesCS3A01G461200 chrUn 354096435 354097490 1055 True 1533.000000 1533 92.784000 4 1070 1 chrUn.!!$R1 1066
13 TraesCS3A01G461200 chr6A 572136397 572138569 2172 False 1905.000000 1905 82.749000 2208 4371 1 chr6A.!!$F2 2163
14 TraesCS3A01G461200 chr6A 158908018 158908530 512 False 381.000000 381 80.268000 1011 1528 1 chr6A.!!$F1 517
15 TraesCS3A01G461200 chr5A 705842335 705844231 1896 True 1661.000000 1661 82.721000 2577 4452 1 chr5A.!!$R1 1875
16 TraesCS3A01G461200 chr4B 665875350 665877247 1897 True 1657.000000 1657 82.686000 2576 4452 1 chr4B.!!$R1 1876
17 TraesCS3A01G461200 chr6D 427481192 427482226 1034 False 464.000000 464 75.594000 3 1011 1 chr6D.!!$F2 1008
18 TraesCS3A01G461200 chr6D 120649204 120649764 560 False 398.000000 398 79.754000 1013 1572 1 chr6D.!!$F1 559

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
628 657 1.251251 AAGAACTGGCCATGACTTGC 58.749 50.000 5.51 0.00 0.00 4.01 F
687 725 1.409661 GGTTCTAATCGGTGGGCCAAT 60.410 52.381 8.40 0.00 34.09 3.16 F
1203 1246 1.755179 CATACTTTGAGCACCCCCTG 58.245 55.000 0.00 0.00 0.00 4.45 F
2691 2769 1.937924 ATTAGTTGCAGGGCCCCCTC 61.938 60.000 21.43 8.55 46.28 4.30 F
4228 4337 2.102109 TTGGCGGCTTCGACTTGGTA 62.102 55.000 11.43 0.00 43.56 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1877 0.478072 AAATGTGGTGAGCTGGGTCA 59.522 50.000 0.00 0.00 0.00 4.02 R
2278 2339 0.684535 TTCAGGAGGACATTGCGACA 59.315 50.000 0.00 0.00 0.00 4.35 R
3188 3296 0.817654 TCGAAGCACCGATCTGTGAT 59.182 50.000 20.09 11.76 38.55 3.06 R
4285 8446 2.435059 GACTGCTCGCCCTCCAAC 60.435 66.667 0.00 0.00 0.00 3.77 R
5196 9667 1.110518 TCTGTCACCGCCACTACACA 61.111 55.000 0.00 0.00 0.00 3.72 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
160 173 6.120220 AGGAATCCCCGTTACTTGAAATTAG 58.880 40.000 0.00 0.00 40.87 1.73
278 292 4.216472 GGTGGTCTTTCCTTCTAGCTTTTG 59.784 45.833 0.00 0.00 37.07 2.44
279 293 4.216472 GTGGTCTTTCCTTCTAGCTTTTGG 59.784 45.833 0.00 0.00 37.07 3.28
342 357 9.896645 ATTTCATACTAGAGATGTCAATTGTGT 57.103 29.630 5.13 0.00 0.00 3.72
360 375 9.033481 CAATTGTGTTATCTTGTTGTTGTGATT 57.967 29.630 0.00 0.00 0.00 2.57
363 378 6.971756 TGTGTTATCTTGTTGTTGTGATTGTG 59.028 34.615 0.00 0.00 0.00 3.33
365 380 8.126074 GTGTTATCTTGTTGTTGTGATTGTGTA 58.874 33.333 0.00 0.00 0.00 2.90
366 381 8.341903 TGTTATCTTGTTGTTGTGATTGTGTAG 58.658 33.333 0.00 0.00 0.00 2.74
367 382 5.749596 TCTTGTTGTTGTGATTGTGTAGG 57.250 39.130 0.00 0.00 0.00 3.18
368 383 5.432645 TCTTGTTGTTGTGATTGTGTAGGA 58.567 37.500 0.00 0.00 0.00 2.94
369 384 6.061441 TCTTGTTGTTGTGATTGTGTAGGAT 58.939 36.000 0.00 0.00 0.00 3.24
370 385 7.220740 TCTTGTTGTTGTGATTGTGTAGGATA 58.779 34.615 0.00 0.00 0.00 2.59
371 386 7.882791 TCTTGTTGTTGTGATTGTGTAGGATAT 59.117 33.333 0.00 0.00 0.00 1.63
534 563 2.124151 AACCATCATGGGCTCCGC 60.124 61.111 9.04 0.00 43.37 5.54
601 630 8.557029 GCATGAGGTAGTAAATAATTGTGTACC 58.443 37.037 0.00 0.00 0.00 3.34
628 657 1.251251 AAGAACTGGCCATGACTTGC 58.749 50.000 5.51 0.00 0.00 4.01
644 673 8.715998 CCATGACTTGCTATTATTAGTGTCATC 58.284 37.037 17.14 4.26 38.86 2.92
687 725 1.409661 GGTTCTAATCGGTGGGCCAAT 60.410 52.381 8.40 0.00 34.09 3.16
785 823 6.876257 GGCATCAAGGAGATTGGTAATACTAG 59.124 42.308 0.00 0.00 39.54 2.57
793 831 9.047947 AGGAGATTGGTAATACTAGAAAACACT 57.952 33.333 0.00 0.00 0.00 3.55
849 889 3.892284 TGTGTCTAACCAAGGCTTTTGA 58.108 40.909 0.00 0.00 0.00 2.69
934 974 8.667463 GGTATTTTCCTTTGTGCGTTATTACTA 58.333 33.333 0.00 0.00 0.00 1.82
1050 1090 8.591114 ATCTTGATTTTGAGAATTCAGATGGT 57.409 30.769 8.44 0.00 34.15 3.55
1059 1102 4.437239 AGAATTCAGATGGTGATGACGAC 58.563 43.478 8.44 0.00 34.17 4.34
1060 1103 3.893326 ATTCAGATGGTGATGACGACA 57.107 42.857 0.00 0.00 34.17 4.35
1203 1246 1.755179 CATACTTTGAGCACCCCCTG 58.245 55.000 0.00 0.00 0.00 4.45
1250 1295 2.900122 TGCTTCTAGCGTTTCATTGC 57.100 45.000 0.00 0.00 46.26 3.56
1345 1394 7.720074 TCGTGTAAGACTGATCATAGGAAGTAT 59.280 37.037 0.00 0.00 0.00 2.12
1347 1396 7.596995 GTGTAAGACTGATCATAGGAAGTATGC 59.403 40.741 0.00 0.00 38.82 3.14
1368 1417 9.502091 GTATGCTTGAATACCATTAGGACAATA 57.498 33.333 0.00 0.00 38.69 1.90
1377 1426 4.975147 ACCATTAGGACAATATGTCTCCCA 59.025 41.667 10.06 0.00 46.19 4.37
1628 1677 8.967664 ACACATACTACAAGAACTTTAACCAA 57.032 30.769 0.00 0.00 0.00 3.67
1726 1776 8.770438 ACTTAGCTAAAAAGAGTTCATGAGAG 57.230 34.615 7.74 0.00 0.00 3.20
1804 1857 7.450074 TGGACCTAAATAATTCTATCATGCGT 58.550 34.615 0.00 0.00 0.00 5.24
1824 1877 3.064820 CGTTGGAGTAAAGTTTGTGCTGT 59.935 43.478 0.00 0.00 0.00 4.40
1848 1901 2.173519 CCAGCTCACCACATTTCCATT 58.826 47.619 0.00 0.00 0.00 3.16
1894 1947 8.307582 ACTAGCATGTAGGTTAGTAAGAACAT 57.692 34.615 0.00 0.87 33.73 2.71
1950 2003 9.878599 ACATTCTTATTTTGACTTTCAGTTACG 57.121 29.630 0.00 0.00 0.00 3.18
1968 2021 8.178964 TCAGTTACGCAAAATGAACATAATACC 58.821 33.333 0.00 0.00 39.12 2.73
2009 2062 6.683974 ATCGCATTAGTAGCATCAAACTTT 57.316 33.333 0.00 0.00 0.00 2.66
2138 2191 8.356657 CGAAGAGAATATCCTATTGTTCACTCT 58.643 37.037 0.00 0.00 33.38 3.24
2191 2252 7.812690 AAAAACCGGTAGAGAGTGTTTATTT 57.187 32.000 8.00 0.00 0.00 1.40
2219 2280 2.501316 ACACATATACACCTGCTCAGCA 59.499 45.455 0.00 0.00 36.92 4.41
2277 2338 3.052944 CCTGAAATAGGGTGGATGGGAAA 60.053 47.826 0.00 0.00 43.33 3.13
2278 2339 4.387891 CCTGAAATAGGGTGGATGGGAAAT 60.388 45.833 0.00 0.00 43.33 2.17
2279 2340 4.545678 TGAAATAGGGTGGATGGGAAATG 58.454 43.478 0.00 0.00 0.00 2.32
2384 2445 6.064060 TGAAGAGACCAGATGAATGTGTTTT 58.936 36.000 0.00 0.00 0.00 2.43
2466 2527 5.520748 ACCTTCACTTTATTCCAGTCCAT 57.479 39.130 0.00 0.00 0.00 3.41
2478 2539 6.620877 ATTCCAGTCCATCACAACTAGTAA 57.379 37.500 0.00 0.00 0.00 2.24
2480 2541 7.727578 TTCCAGTCCATCACAACTAGTAATA 57.272 36.000 0.00 0.00 0.00 0.98
2552 2627 6.425577 AGTAACTCTCGTAGTGAAGTCATC 57.574 41.667 0.00 0.00 38.88 2.92
2567 2642 8.762645 AGTGAAGTCATCCTCAAATAGTATCAA 58.237 33.333 0.00 0.00 0.00 2.57
2691 2769 1.937924 ATTAGTTGCAGGGCCCCCTC 61.938 60.000 21.43 8.55 46.28 4.30
2718 2796 2.296471 CTCCGTCCCTATATGTGTCACC 59.704 54.545 0.00 0.00 0.00 4.02
2939 3026 6.055231 TGTGGTATGACTCTTTTTGAAACG 57.945 37.500 0.00 0.00 0.00 3.60
3137 3241 9.586150 GCTGTCATTTGTATATGAAAATACTCG 57.414 33.333 0.00 0.00 36.37 4.18
3139 3243 9.103861 TGTCATTTGTATATGAAAATACTCGCA 57.896 29.630 0.00 0.00 36.37 5.10
3155 3263 8.723942 AATACTCGCACTCTTCTAATTTGATT 57.276 30.769 0.00 0.00 0.00 2.57
3160 3268 8.317891 TCGCACTCTTCTAATTTGATTTAACA 57.682 30.769 0.00 0.00 0.00 2.41
3188 3296 6.377996 ACTGCAATATCTGTAAATTTGGCAGA 59.622 34.615 21.42 21.42 42.49 4.26
3442 3550 7.388500 CCACCCTTTTTCTACTACGAAAATGTA 59.612 37.037 0.00 0.00 41.12 2.29
3505 3613 9.300681 AGATTTCTTTATGACATTCAACCTGAA 57.699 29.630 0.00 0.00 41.09 3.02
3563 3671 6.538263 AGGAAAAGAGGCTACATCCATAATC 58.462 40.000 9.80 0.00 0.00 1.75
4007 4115 4.555262 CAATGGTGTTAATGTGTTGTCCC 58.445 43.478 0.00 0.00 0.00 4.46
4069 4177 2.484062 GGGCATCCACATGAAGGCG 61.484 63.158 0.00 0.00 38.06 5.52
4088 4196 3.445857 GCGGTGGTTTCTGTAGAGATAC 58.554 50.000 2.36 2.36 31.31 2.24
4165 4274 4.044426 CGCTCATTGAGATTGATGACGTA 58.956 43.478 17.87 0.00 0.00 3.57
4228 4337 2.102109 TTGGCGGCTTCGACTTGGTA 62.102 55.000 11.43 0.00 43.56 3.25
4285 8446 2.677836 CAACAGATACAACCGTGATGGG 59.322 50.000 0.00 0.00 44.64 4.00
4300 8461 4.785453 GGGTTGGAGGGCGAGCAG 62.785 72.222 0.00 0.00 0.00 4.24
4377 8544 5.974108 GGCGAGGATGTAGCCTAATTATTA 58.026 41.667 0.00 0.00 46.83 0.98
4437 8606 4.433615 ACCGCAACTTATCAGTGTATGAG 58.566 43.478 0.00 0.00 42.53 2.90
4487 8656 5.243730 CCAGAATTTGGTGGTTTGTGTAGAT 59.756 40.000 0.10 0.00 42.41 1.98
4730 9198 3.179443 TCATACGGGAATGCAGAAGAC 57.821 47.619 0.00 0.00 0.00 3.01
4778 9246 5.265989 CTCTCTGTCCCTTTTCTAGGTAGT 58.734 45.833 0.00 0.00 43.07 2.73
4856 9325 4.597004 AGTTCTTAGACCGTACTGATCCA 58.403 43.478 0.00 0.00 0.00 3.41
4865 9334 2.104111 CCGTACTGATCCATTAAGCCCA 59.896 50.000 0.00 0.00 0.00 5.36
4934 9403 6.627087 TCTGTAGATTTTGGATCTTGAGGT 57.373 37.500 0.00 0.00 0.00 3.85
4986 9455 0.392461 CGGAGGGGTGTGGTAATGTG 60.392 60.000 0.00 0.00 0.00 3.21
5024 9493 9.890629 ATCTGAACATAATCTTGCTAACTAACA 57.109 29.630 0.00 0.00 0.00 2.41
5045 9514 4.346129 CAGAGTTGAGTTTCTGTTGTTGC 58.654 43.478 0.00 0.00 36.82 4.17
5068 9537 3.272574 TCATTCTTGGAGACTGCATCC 57.727 47.619 0.00 0.00 37.35 3.51
5095 9564 4.094476 AGGAAGTGGAGGATTTAAGACGA 58.906 43.478 0.00 0.00 0.00 4.20
5171 9640 9.119418 TCTTTCAGTTGTATTTTGAATCACTCA 57.881 29.630 0.00 0.00 31.54 3.41
5207 9678 6.315393 AGGTTAATAAAGATTGTGTAGTGGCG 59.685 38.462 0.00 0.00 0.00 5.69
5232 9703 2.846206 ACAGATACCTTGATTGCCTCCA 59.154 45.455 0.00 0.00 0.00 3.86
5253 9724 3.795688 AAATCACCACAGATCCACAGT 57.204 42.857 0.00 0.00 0.00 3.55
5254 9725 4.908601 AAATCACCACAGATCCACAGTA 57.091 40.909 0.00 0.00 0.00 2.74
5259 9730 5.977635 TCACCACAGATCCACAGTAAATAG 58.022 41.667 0.00 0.00 0.00 1.73
5348 9823 4.657408 TTGGCTCGCCATGGTGCA 62.657 61.111 20.97 10.14 46.64 4.57
5364 9839 1.002624 GCATTGGACCTTCCCGTGA 60.003 57.895 0.00 0.00 35.03 4.35
5365 9840 1.026718 GCATTGGACCTTCCCGTGAG 61.027 60.000 0.00 0.00 35.03 3.51
5366 9841 0.324943 CATTGGACCTTCCCGTGAGT 59.675 55.000 0.00 0.00 35.03 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179062 GCTGATCGGATTGACCAGCT 60.179 55.000 17.42 0.00 44.75 4.24
1 2 2.315246 GCTGATCGGATTGACCAGC 58.685 57.895 5.48 11.98 42.52 4.85
204 217 3.676093 TGTCACAACACGGCCATAATTA 58.324 40.909 2.24 0.00 0.00 1.40
205 218 2.487762 CTGTCACAACACGGCCATAATT 59.512 45.455 2.24 0.00 0.00 1.40
206 219 2.083774 CTGTCACAACACGGCCATAAT 58.916 47.619 2.24 0.00 0.00 1.28
207 220 1.202710 ACTGTCACAACACGGCCATAA 60.203 47.619 2.24 0.00 0.00 1.90
342 357 7.717436 TCCTACACAATCACAACAACAAGATAA 59.283 33.333 0.00 0.00 0.00 1.75
375 392 7.067981 AGCCATTGAGGAGAAGAACAATAATTC 59.932 37.037 0.00 0.00 41.22 2.17
413 442 7.274447 CACACCCCAATGAATAATTAAAGCAT 58.726 34.615 0.00 0.00 0.00 3.79
432 461 3.003480 GTGAGATGAGTTAAGCACACCC 58.997 50.000 0.00 0.00 0.00 4.61
534 563 4.533707 TGGAGCATCTATATTCCTCAAGGG 59.466 45.833 0.00 0.00 32.85 3.95
601 630 5.829924 AGTCATGGCCAGTTCTTATAATTGG 59.170 40.000 13.05 0.00 0.00 3.16
616 645 5.765182 ACACTAATAATAGCAAGTCATGGCC 59.235 40.000 0.00 0.00 31.96 5.36
712 750 4.141088 ACCCATTCTCACATATGCCTTGAT 60.141 41.667 1.58 0.00 0.00 2.57
785 823 7.869429 AGACAAATGGAATGAATCAGTGTTTTC 59.131 33.333 0.00 0.00 0.00 2.29
793 831 8.805175 ACATAACAAGACAAATGGAATGAATCA 58.195 29.630 0.00 0.00 0.00 2.57
802 841 5.177327 GGTGCAAACATAACAAGACAAATGG 59.823 40.000 0.00 0.00 0.00 3.16
849 889 4.088634 TCACTATGCCCTGAAAGCAAAAT 58.911 39.130 0.00 0.00 44.83 1.82
934 974 5.651139 AGCAAGAGCATCATGTGATAAAGTT 59.349 36.000 0.00 0.00 45.49 2.66
1044 1084 1.205655 CCAGTGTCGTCATCACCATCT 59.794 52.381 0.00 0.00 36.58 2.90
1050 1090 2.823154 TGTATCACCAGTGTCGTCATCA 59.177 45.455 0.00 0.00 0.00 3.07
1059 1102 2.092323 TCGGTCTCTGTATCACCAGTG 58.908 52.381 0.00 0.00 34.02 3.66
1060 1103 2.093106 GTCGGTCTCTGTATCACCAGT 58.907 52.381 0.00 0.00 34.02 4.00
1178 1221 2.493278 GGGTGCTCAAAGTATGCATGTT 59.507 45.455 10.16 0.00 39.00 2.71
1203 1246 7.127686 ACAAACAATGCTAAAACAGTACGTAC 58.872 34.615 18.10 18.10 0.00 3.67
1250 1295 8.969121 TCAAACTTCACAATGCAATTATACAG 57.031 30.769 0.00 0.00 32.46 2.74
1329 1378 9.149225 GTATTCAAGCATACTTCCTATGATCAG 57.851 37.037 0.09 0.00 35.06 2.90
1345 1394 7.998383 ACATATTGTCCTAATGGTATTCAAGCA 59.002 33.333 0.00 0.00 40.55 3.91
1368 1417 5.181245 CGTTTGATTACTTTGTGGGAGACAT 59.819 40.000 0.00 0.00 33.40 3.06
1369 1418 4.513692 CGTTTGATTACTTTGTGGGAGACA 59.486 41.667 0.00 0.00 0.00 3.41
1377 1426 8.132995 CCTTTTAGGTTCGTTTGATTACTTTGT 58.867 33.333 0.00 0.00 0.00 2.83
1514 1563 9.988350 CCACAAATCATATGTCTTGTAACTAAC 57.012 33.333 18.44 0.00 31.00 2.34
1627 1676 7.043565 GTGATGCATAATTTGGGATTTCTGTT 58.956 34.615 0.00 0.00 0.00 3.16
1628 1677 6.381994 AGTGATGCATAATTTGGGATTTCTGT 59.618 34.615 0.00 0.00 0.00 3.41
1692 1742 8.779354 ACTCTTTTTAGCTAAGTCCTATTGTG 57.221 34.615 6.24 0.00 0.00 3.33
1721 1771 6.605194 TCTTCAAGCTTAGCTTCTATCTCTCA 59.395 38.462 17.37 0.00 46.77 3.27
1726 1776 4.742659 CGGTCTTCAAGCTTAGCTTCTATC 59.257 45.833 17.37 6.79 46.77 2.08
1804 1857 4.095782 GTCACAGCACAAACTTTACTCCAA 59.904 41.667 0.00 0.00 0.00 3.53
1824 1877 0.478072 AAATGTGGTGAGCTGGGTCA 59.522 50.000 0.00 0.00 0.00 4.02
1836 1889 6.040166 CCTCCTTAGATTCAATGGAAATGTGG 59.960 42.308 0.00 0.00 36.43 4.17
1848 1901 4.289672 AGTTTCCAAGCCTCCTTAGATTCA 59.710 41.667 0.00 0.00 0.00 2.57
1894 1947 8.919145 ACAATGTGGTTTAATTCTTTAAGACCA 58.081 29.630 0.00 0.00 36.82 4.02
1950 2003 7.540745 ACGTTTCTGGTATTATGTTCATTTTGC 59.459 33.333 0.00 0.00 0.00 3.68
1968 2021 8.987599 AATGCGATATGTAATAAACGTTTCTG 57.012 30.769 18.42 0.00 35.94 3.02
2009 2062 4.566837 TCTTGAGGCTATTTATGGAGGGA 58.433 43.478 0.00 0.00 0.00 4.20
2069 2122 9.905713 AACTAATAGGAAATTCAGCTATCACAA 57.094 29.630 0.00 0.00 0.00 3.33
2191 2252 7.390823 TGAGCAGGTGTATATGTGTAAAAGAA 58.609 34.615 0.00 0.00 0.00 2.52
2277 2338 0.904649 TCAGGAGGACATTGCGACAT 59.095 50.000 0.00 0.00 0.00 3.06
2278 2339 0.684535 TTCAGGAGGACATTGCGACA 59.315 50.000 0.00 0.00 0.00 4.35
2279 2340 1.066858 TCTTCAGGAGGACATTGCGAC 60.067 52.381 0.00 0.00 0.00 5.19
2426 2487 7.773690 AGTGAAGGTACATGTCTAACTTTGTTT 59.226 33.333 0.00 0.00 0.00 2.83
2542 2617 8.948631 TTGATACTATTTGAGGATGACTTCAC 57.051 34.615 0.00 0.00 32.02 3.18
2604 2680 9.857957 AGAAATAGAAAACTAACCGAGAACTAG 57.142 33.333 0.00 0.00 0.00 2.57
2691 2769 4.101119 ACACATATAGGGACGGAGAAAAGG 59.899 45.833 0.00 0.00 0.00 3.11
2718 2796 8.771920 TGCTAATAGGGAAATACGATTACATG 57.228 34.615 0.00 0.00 0.00 3.21
2939 3026 3.733443 AAAATGACAGTCAAGGCAACC 57.267 42.857 7.50 0.00 37.17 3.77
3136 3240 8.840867 GTTGTTAAATCAAATTAGAAGAGTGCG 58.159 33.333 0.00 0.00 0.00 5.34
3137 3241 9.677567 TGTTGTTAAATCAAATTAGAAGAGTGC 57.322 29.630 0.00 0.00 0.00 4.40
3160 3268 6.813152 GCCAAATTTACAGATATTGCAGTGTT 59.187 34.615 0.00 0.00 0.00 3.32
3188 3296 0.817654 TCGAAGCACCGATCTGTGAT 59.182 50.000 20.09 11.76 38.55 3.06
3505 3613 6.869913 CACACAAATGCTTAGAATCCACAAAT 59.130 34.615 0.00 0.00 0.00 2.32
3563 3671 5.374921 AGGTGATCTATTCTCAATTGGCAG 58.625 41.667 5.42 0.00 0.00 4.85
4007 4115 3.006967 CCTCCTCCAATACCGGTGAATAG 59.993 52.174 19.93 8.05 0.00 1.73
4069 4177 4.978083 TCGTATCTCTACAGAAACCACC 57.022 45.455 0.00 0.00 30.24 4.61
4088 4196 9.937175 CCTAAAAATCCTCTTATTAGCTTTTCG 57.063 33.333 0.00 0.00 0.00 3.46
4165 4274 9.902684 ACAATTCTATCATCAGTCAGAGATTTT 57.097 29.630 0.00 0.00 0.00 1.82
4285 8446 2.435059 GACTGCTCGCCCTCCAAC 60.435 66.667 0.00 0.00 0.00 3.77
4300 8461 4.884247 AGTAGTGGTAGAACAAAGCAGAC 58.116 43.478 0.00 0.00 0.00 3.51
4437 8606 6.476380 TCTTGAAAACAACATCAACTCAATGC 59.524 34.615 0.00 0.00 32.46 3.56
4487 8656 7.770897 AGAAGCTAAACAAAAGAAGTCTCTTCA 59.229 33.333 11.27 0.00 41.23 3.02
4536 8997 7.391275 TGACTGCAGAAAAAGATATGATGTTGA 59.609 33.333 23.35 0.00 0.00 3.18
4544 9005 6.506500 CAGGTTGACTGCAGAAAAAGATAT 57.493 37.500 23.35 0.00 40.97 1.63
4833 9302 5.748402 TGGATCAGTACGGTCTAAGAACTA 58.252 41.667 0.00 0.00 0.00 2.24
4856 9325 6.904626 ACTCTCACAATTCTATGGGCTTAAT 58.095 36.000 0.00 0.00 0.00 1.40
4934 9403 9.314133 AGATAATATAGTCTGTGCCATGTTCTA 57.686 33.333 0.00 0.00 0.00 2.10
4986 9455 2.337583 TGTTCAGATGCAACGTCTAGC 58.662 47.619 0.00 0.00 0.00 3.42
5024 9493 4.265073 AGCAACAACAGAAACTCAACTCT 58.735 39.130 0.00 0.00 0.00 3.24
5029 9498 6.712095 AGAATGATAGCAACAACAGAAACTCA 59.288 34.615 0.00 0.00 0.00 3.41
5045 9514 4.996122 GGATGCAGTCTCCAAGAATGATAG 59.004 45.833 8.46 0.00 42.41 2.08
5068 9537 5.423610 TCTTAAATCCTCCACTTCCTCTCTG 59.576 44.000 0.00 0.00 0.00 3.35
5186 9657 5.583061 CACCGCCACTACACAATCTTTATTA 59.417 40.000 0.00 0.00 0.00 0.98
5189 9660 3.007074 TCACCGCCACTACACAATCTTTA 59.993 43.478 0.00 0.00 0.00 1.85
5196 9667 1.110518 TCTGTCACCGCCACTACACA 61.111 55.000 0.00 0.00 0.00 3.72
5207 9678 2.945668 GGCAATCAAGGTATCTGTCACC 59.054 50.000 0.00 0.00 36.22 4.02
5232 9703 4.104383 ACTGTGGATCTGTGGTGATTTT 57.896 40.909 0.00 0.00 0.00 1.82
5253 9724 8.946085 CAGTAATGCAGGTTTCAGTTCTATTTA 58.054 33.333 0.00 0.00 0.00 1.40
5254 9725 7.448469 ACAGTAATGCAGGTTTCAGTTCTATTT 59.552 33.333 0.00 0.00 0.00 1.40
5259 9730 5.438761 AACAGTAATGCAGGTTTCAGTTC 57.561 39.130 0.00 0.00 0.00 3.01
5348 9823 2.773458 ACTCACGGGAAGGTCCAAT 58.227 52.632 0.00 0.00 38.64 3.16


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

AutoCloner maintained by Alex Coulton.