Multiple sequence alignment - TraesCS5A01G147800

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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 TraesCS5A01G147800 chr5A 100.000 2630 0 0 1 2630 325806204 325803575 0.000000e+00 4857
1 TraesCS5A01G147800 chr5B 98.971 875 6 3 1758 2630 703797377 703796504 0.000000e+00 1563
2 TraesCS5A01G147800 chr5B 96.789 872 25 3 1759 2630 612298721 612297853 0.000000e+00 1452
3 TraesCS5A01G147800 chr5B 92.121 660 45 6 730 1387 273886403 273885749 0.000000e+00 924
4 TraesCS5A01G147800 chr5B 82.459 667 78 15 4 646 17588426 17587775 4.950000e-152 547
5 TraesCS5A01G147800 chr5B 94.079 304 16 2 1389 1691 273885687 273885385 6.630000e-126 460
6 TraesCS5A01G147800 chr6B 96.789 872 24 3 1760 2630 23427098 23426230 0.000000e+00 1452
7 TraesCS5A01G147800 chr6B 96.334 873 28 4 1760 2630 23475247 23474377 0.000000e+00 1432
8 TraesCS5A01G147800 chr6B 78.924 446 85 6 6 449 529865618 529866056 7.120000e-76 294
9 TraesCS5A01G147800 chr5D 85.244 881 89 18 1760 2625 552389644 552390498 0.000000e+00 869
10 TraesCS5A01G147800 chr5D 94.920 374 19 0 1386 1759 231613554 231613927 1.050000e-163 586
11 TraesCS5A01G147800 chr5D 87.052 502 21 9 894 1390 231613042 231613504 6.450000e-146 527
12 TraesCS5A01G147800 chr2B 82.034 885 103 21 1759 2630 67885013 67884172 0.000000e+00 702
13 TraesCS5A01G147800 chr2B 78.125 448 96 2 3 449 184870461 184870907 1.540000e-72 283
14 TraesCS5A01G147800 chr7A 84.234 666 74 21 1 643 732056141 732055484 1.030000e-173 619
15 TraesCS5A01G147800 chr7A 80.030 656 80 26 1 642 730767130 730766512 3.110000e-119 438
16 TraesCS5A01G147800 chr7A 91.473 129 11 0 1759 1887 668000971 668001099 7.480000e-41 178
17 TraesCS5A01G147800 chr4D 83.766 616 66 17 1 586 215455688 215456299 1.060000e-153 553
18 TraesCS5A01G147800 chr4B 82.890 602 78 16 3 586 237140875 237141469 3.880000e-143 518
19 TraesCS5A01G147800 chr2A 85.558 457 58 2 1 449 554098913 554099369 3.060000e-129 472
20 TraesCS5A01G147800 chr2A 79.431 457 65 15 142 584 674687232 674687673 1.980000e-76 296
21 TraesCS5A01G147800 chr2A 91.406 128 11 0 1760 1887 461494371 461494244 2.690000e-40 176
22 TraesCS5A01G147800 chr2D 88.270 341 30 4 1 331 432865603 432865263 1.470000e-107 399
23 TraesCS5A01G147800 chr2D 81.465 437 65 3 2 434 557095446 557095022 6.970000e-91 344
24 TraesCS5A01G147800 chr6D 81.308 428 76 2 22 449 350126185 350125762 6.970000e-91 344
25 TraesCS5A01G147800 chrUn 79.431 457 65 15 142 584 400892553 400892112 1.980000e-76 296
26 TraesCS5A01G147800 chrUn 79.212 457 66 15 142 584 400894081 400893640 9.210000e-75 291


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 TraesCS5A01G147800 chr5A 325803575 325806204 2629 True 4857.0 4857 100.0000 1 2630 1 chr5A.!!$R1 2629
1 TraesCS5A01G147800 chr5B 703796504 703797377 873 True 1563.0 1563 98.9710 1758 2630 1 chr5B.!!$R3 872
2 TraesCS5A01G147800 chr5B 612297853 612298721 868 True 1452.0 1452 96.7890 1759 2630 1 chr5B.!!$R2 871
3 TraesCS5A01G147800 chr5B 273885385 273886403 1018 True 692.0 924 93.1000 730 1691 2 chr5B.!!$R4 961
4 TraesCS5A01G147800 chr5B 17587775 17588426 651 True 547.0 547 82.4590 4 646 1 chr5B.!!$R1 642
5 TraesCS5A01G147800 chr6B 23426230 23427098 868 True 1452.0 1452 96.7890 1760 2630 1 chr6B.!!$R1 870
6 TraesCS5A01G147800 chr6B 23474377 23475247 870 True 1432.0 1432 96.3340 1760 2630 1 chr6B.!!$R2 870
7 TraesCS5A01G147800 chr5D 552389644 552390498 854 False 869.0 869 85.2440 1760 2625 1 chr5D.!!$F1 865
8 TraesCS5A01G147800 chr5D 231613042 231613927 885 False 556.5 586 90.9860 894 1759 2 chr5D.!!$F2 865
9 TraesCS5A01G147800 chr2B 67884172 67885013 841 True 702.0 702 82.0340 1759 2630 1 chr2B.!!$R1 871
10 TraesCS5A01G147800 chr7A 732055484 732056141 657 True 619.0 619 84.2340 1 643 1 chr7A.!!$R2 642
11 TraesCS5A01G147800 chr7A 730766512 730767130 618 True 438.0 438 80.0300 1 642 1 chr7A.!!$R1 641
12 TraesCS5A01G147800 chr4D 215455688 215456299 611 False 553.0 553 83.7660 1 586 1 chr4D.!!$F1 585
13 TraesCS5A01G147800 chr4B 237140875 237141469 594 False 518.0 518 82.8900 3 586 1 chr4B.!!$F1 583
14 TraesCS5A01G147800 chrUn 400892112 400894081 1969 True 293.5 296 79.3215 142 584 2 chrUn.!!$R1 442

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
674 2266 0.107456 ATCTAGGGCGCATGTTGGAG 59.893 55.0 10.83 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 3379 0.321298 TCCAGTTAACAAGAGGCGCC 60.321 55.0 21.89 21.89 0.0 6.53 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
102 103 0.600255 CAGAAGTTGTTCTCGGCGGT 60.600 55.000 7.21 0.00 41.40 5.68
153 154 2.488355 CATGGCGTACTCGTCCGT 59.512 61.111 0.00 0.00 41.33 4.69
276 285 3.557595 GTCCGAGAAATTCATCTGCGAAT 59.442 43.478 0.00 0.00 37.20 3.34
289 1826 2.622011 GCGAATGTGGCCGGTTGAA 61.622 57.895 1.90 0.00 0.00 2.69
360 1897 2.435586 TCCCGAGACCGAGACGTC 60.436 66.667 7.70 7.70 38.22 4.34
463 2014 3.851184 CGGGGGAGGAGGGAGGAT 61.851 72.222 0.00 0.00 0.00 3.24
464 2015 2.122189 GGGGGAGGAGGGAGGATG 60.122 72.222 0.00 0.00 0.00 3.51
465 2016 2.122189 GGGGAGGAGGGAGGATGG 60.122 72.222 0.00 0.00 0.00 3.51
466 2017 2.851588 GGGAGGAGGGAGGATGGC 60.852 72.222 0.00 0.00 0.00 4.40
467 2018 3.237741 GGAGGAGGGAGGATGGCG 61.238 72.222 0.00 0.00 0.00 5.69
468 2019 3.934962 GAGGAGGGAGGATGGCGC 61.935 72.222 0.00 0.00 0.00 6.53
577 2147 1.601166 GGGTTTTTATAGCGCCCGAT 58.399 50.000 2.29 0.00 0.00 4.18
609 2201 4.504112 TTTTTCCCACGCCGGATT 57.496 50.000 5.05 0.00 36.56 3.01
610 2202 3.646787 TTTTTCCCACGCCGGATTA 57.353 47.368 5.05 0.00 36.56 1.75
611 2203 2.131776 TTTTTCCCACGCCGGATTAT 57.868 45.000 5.05 0.00 36.56 1.28
625 2217 2.715532 GATTATCCCGCGCCTGCTGA 62.716 60.000 0.00 0.00 39.65 4.26
658 2250 4.508128 CCCGCGCACGTGGTATCT 62.508 66.667 18.88 0.00 43.79 1.98
659 2251 2.410060 CCGCGCACGTGGTATCTA 59.590 61.111 18.88 0.00 40.65 1.98
660 2252 1.657487 CCGCGCACGTGGTATCTAG 60.657 63.158 18.88 0.00 40.65 2.43
661 2253 1.657487 CGCGCACGTGGTATCTAGG 60.657 63.158 18.88 0.00 33.53 3.02
662 2254 1.299926 GCGCACGTGGTATCTAGGG 60.300 63.158 18.88 0.00 0.00 3.53
663 2255 1.299926 CGCACGTGGTATCTAGGGC 60.300 63.158 18.88 0.00 0.00 5.19
664 2256 1.299926 GCACGTGGTATCTAGGGCG 60.300 63.158 18.88 0.00 0.00 6.13
665 2257 1.299926 CACGTGGTATCTAGGGCGC 60.300 63.158 7.95 0.00 0.00 6.53
666 2258 1.755395 ACGTGGTATCTAGGGCGCA 60.755 57.895 10.83 0.00 0.00 6.09
667 2259 1.113517 ACGTGGTATCTAGGGCGCAT 61.114 55.000 10.83 0.00 0.00 4.73
668 2260 0.667487 CGTGGTATCTAGGGCGCATG 60.667 60.000 10.83 0.00 0.00 4.06
669 2261 0.393077 GTGGTATCTAGGGCGCATGT 59.607 55.000 10.83 0.00 0.00 3.21
670 2262 1.128200 TGGTATCTAGGGCGCATGTT 58.872 50.000 10.83 0.00 0.00 2.71
671 2263 1.202639 TGGTATCTAGGGCGCATGTTG 60.203 52.381 10.83 0.00 0.00 3.33
672 2264 1.512926 GTATCTAGGGCGCATGTTGG 58.487 55.000 10.83 0.00 0.00 3.77
673 2265 1.070134 GTATCTAGGGCGCATGTTGGA 59.930 52.381 10.83 0.00 0.00 3.53
674 2266 0.107456 ATCTAGGGCGCATGTTGGAG 59.893 55.000 10.83 0.00 0.00 3.86
675 2267 0.975556 TCTAGGGCGCATGTTGGAGA 60.976 55.000 10.83 0.00 0.00 3.71
676 2268 0.107456 CTAGGGCGCATGTTGGAGAT 59.893 55.000 10.83 0.00 0.00 2.75
677 2269 0.179048 TAGGGCGCATGTTGGAGATG 60.179 55.000 10.83 0.00 0.00 2.90
678 2270 2.410469 GGCGCATGTTGGAGATGC 59.590 61.111 10.83 0.00 42.41 3.91
679 2271 2.117156 GGCGCATGTTGGAGATGCT 61.117 57.895 10.83 0.00 43.45 3.79
680 2272 1.354506 GCGCATGTTGGAGATGCTC 59.645 57.895 0.30 0.00 43.45 4.26
681 2273 1.094073 GCGCATGTTGGAGATGCTCT 61.094 55.000 0.30 0.00 43.45 4.09
682 2274 1.376543 CGCATGTTGGAGATGCTCTT 58.623 50.000 8.18 0.00 43.45 2.85
683 2275 1.063616 CGCATGTTGGAGATGCTCTTG 59.936 52.381 8.18 0.00 43.45 3.02
684 2276 1.202268 GCATGTTGGAGATGCTCTTGC 60.202 52.381 3.13 0.00 42.52 4.01
685 2277 1.404391 CATGTTGGAGATGCTCTTGCC 59.596 52.381 0.00 0.00 38.71 4.52
686 2278 0.401356 TGTTGGAGATGCTCTTGCCA 59.599 50.000 0.00 0.00 38.71 4.92
687 2279 1.202915 TGTTGGAGATGCTCTTGCCAA 60.203 47.619 0.00 0.00 38.71 4.52
688 2280 1.888512 GTTGGAGATGCTCTTGCCAAA 59.111 47.619 0.00 0.00 40.02 3.28
689 2281 1.830279 TGGAGATGCTCTTGCCAAAG 58.170 50.000 0.00 0.00 38.71 2.77
690 2282 1.074405 TGGAGATGCTCTTGCCAAAGT 59.926 47.619 0.00 0.00 38.71 2.66
691 2283 1.471684 GGAGATGCTCTTGCCAAAGTG 59.528 52.381 0.00 0.00 38.71 3.16
692 2284 2.430465 GAGATGCTCTTGCCAAAGTGA 58.570 47.619 0.00 0.00 38.71 3.41
693 2285 2.816087 GAGATGCTCTTGCCAAAGTGAA 59.184 45.455 0.00 0.00 38.71 3.18
694 2286 2.818432 AGATGCTCTTGCCAAAGTGAAG 59.182 45.455 0.00 0.00 38.71 3.02
695 2287 2.057137 TGCTCTTGCCAAAGTGAAGT 57.943 45.000 0.00 0.00 38.71 3.01
696 2288 1.949525 TGCTCTTGCCAAAGTGAAGTC 59.050 47.619 0.00 0.00 38.71 3.01
697 2289 2.225467 GCTCTTGCCAAAGTGAAGTCT 58.775 47.619 0.00 0.00 34.78 3.24
698 2290 2.620585 GCTCTTGCCAAAGTGAAGTCTT 59.379 45.455 0.00 0.00 34.78 3.01
699 2291 3.815401 GCTCTTGCCAAAGTGAAGTCTTA 59.185 43.478 0.00 0.00 34.78 2.10
700 2292 4.083590 GCTCTTGCCAAAGTGAAGTCTTAG 60.084 45.833 0.00 0.00 34.78 2.18
701 2293 3.815401 TCTTGCCAAAGTGAAGTCTTAGC 59.185 43.478 0.00 0.00 34.78 3.09
702 2294 3.207265 TGCCAAAGTGAAGTCTTAGCA 57.793 42.857 0.00 0.00 35.76 3.49
703 2295 2.878406 TGCCAAAGTGAAGTCTTAGCAC 59.122 45.455 0.00 0.00 34.34 4.40
704 2296 2.878406 GCCAAAGTGAAGTCTTAGCACA 59.122 45.455 7.06 0.00 35.08 4.57
705 2297 3.315191 GCCAAAGTGAAGTCTTAGCACAA 59.685 43.478 7.06 0.00 35.08 3.33
706 2298 4.555511 GCCAAAGTGAAGTCTTAGCACAAG 60.556 45.833 7.06 0.00 35.08 3.16
707 2299 4.576463 CCAAAGTGAAGTCTTAGCACAAGT 59.424 41.667 7.06 0.00 35.08 3.16
708 2300 5.066505 CCAAAGTGAAGTCTTAGCACAAGTT 59.933 40.000 7.06 0.00 35.08 2.66
709 2301 6.260050 CCAAAGTGAAGTCTTAGCACAAGTTA 59.740 38.462 7.06 0.00 35.08 2.24
710 2302 7.348201 CAAAGTGAAGTCTTAGCACAAGTTAG 58.652 38.462 7.06 0.00 35.08 2.34
711 2303 5.542779 AGTGAAGTCTTAGCACAAGTTAGG 58.457 41.667 7.06 0.00 35.08 2.69
712 2304 5.070580 AGTGAAGTCTTAGCACAAGTTAGGT 59.929 40.000 7.06 0.00 35.08 3.08
713 2305 6.267014 AGTGAAGTCTTAGCACAAGTTAGGTA 59.733 38.462 7.06 0.00 35.08 3.08
714 2306 6.586844 GTGAAGTCTTAGCACAAGTTAGGTAG 59.413 42.308 0.00 0.00 32.96 3.18
715 2307 6.492429 TGAAGTCTTAGCACAAGTTAGGTAGA 59.508 38.462 0.00 0.00 0.00 2.59
716 2308 6.912951 AGTCTTAGCACAAGTTAGGTAGAA 57.087 37.500 0.00 0.00 0.00 2.10
717 2309 7.299246 AGTCTTAGCACAAGTTAGGTAGAAA 57.701 36.000 0.00 0.00 0.00 2.52
718 2310 7.908453 AGTCTTAGCACAAGTTAGGTAGAAAT 58.092 34.615 0.00 0.00 0.00 2.17
719 2311 8.376270 AGTCTTAGCACAAGTTAGGTAGAAATT 58.624 33.333 0.00 0.00 0.00 1.82
720 2312 9.649167 GTCTTAGCACAAGTTAGGTAGAAATTA 57.351 33.333 0.00 0.00 0.00 1.40
721 2313 9.649167 TCTTAGCACAAGTTAGGTAGAAATTAC 57.351 33.333 0.00 0.00 0.00 1.89
722 2314 9.431887 CTTAGCACAAGTTAGGTAGAAATTACA 57.568 33.333 0.00 0.00 0.00 2.41
723 2315 9.953565 TTAGCACAAGTTAGGTAGAAATTACAT 57.046 29.630 0.00 0.00 0.00 2.29
724 2316 8.268850 AGCACAAGTTAGGTAGAAATTACATG 57.731 34.615 0.00 0.00 0.00 3.21
725 2317 7.336931 AGCACAAGTTAGGTAGAAATTACATGG 59.663 37.037 0.00 0.00 0.00 3.66
726 2318 7.415206 GCACAAGTTAGGTAGAAATTACATGGG 60.415 40.741 0.00 0.00 0.00 4.00
727 2319 7.827236 CACAAGTTAGGTAGAAATTACATGGGA 59.173 37.037 0.00 0.00 0.00 4.37
728 2320 7.827729 ACAAGTTAGGTAGAAATTACATGGGAC 59.172 37.037 0.00 0.00 0.00 4.46
729 2321 7.750947 AGTTAGGTAGAAATTACATGGGACT 57.249 36.000 0.00 0.00 0.00 3.85
730 2322 8.849543 AGTTAGGTAGAAATTACATGGGACTA 57.150 34.615 0.00 0.00 0.00 2.59
731 2323 9.448587 AGTTAGGTAGAAATTACATGGGACTAT 57.551 33.333 0.00 0.00 0.00 2.12
732 2324 9.708092 GTTAGGTAGAAATTACATGGGACTATC 57.292 37.037 0.00 0.00 0.00 2.08
733 2325 7.931015 AGGTAGAAATTACATGGGACTATCA 57.069 36.000 0.00 0.00 0.00 2.15
734 2326 7.736893 AGGTAGAAATTACATGGGACTATCAC 58.263 38.462 0.00 0.00 0.00 3.06
735 2327 7.347222 AGGTAGAAATTACATGGGACTATCACA 59.653 37.037 0.00 0.00 32.34 3.58
736 2328 8.157476 GGTAGAAATTACATGGGACTATCACAT 58.843 37.037 0.00 0.00 42.15 3.21
769 2361 0.603569 ACTGGACTTGACGCTAGTGG 59.396 55.000 8.42 0.00 0.00 4.00
771 2363 1.000955 CTGGACTTGACGCTAGTGGTT 59.999 52.381 8.42 0.00 0.00 3.67
834 2426 8.975439 CGTTTAGTAGACAAATATATTTCCGCT 58.025 33.333 7.76 8.09 0.00 5.52
837 2429 7.062749 AGTAGACAAATATATTTCCGCTGGA 57.937 36.000 7.76 0.00 0.00 3.86
848 2440 2.094659 CCGCTGGACGTGTGATGAC 61.095 63.158 0.00 0.00 41.42 3.06
852 2444 2.683968 GCTGGACGTGTGATGACTTTA 58.316 47.619 0.00 0.00 0.00 1.85
864 2456 7.148590 CGTGTGATGACTTTATCAATCTCAACA 60.149 37.037 0.00 0.00 41.93 3.33
870 2462 7.532571 TGACTTTATCAATCTCAACAGCATTG 58.467 34.615 0.00 0.00 33.02 2.82
947 2541 0.388649 ACGAGCAAGTAGTTCAGGCG 60.389 55.000 0.00 0.00 0.00 5.52
1052 2647 2.011046 GCAGCTCCTGATCAGAACCAC 61.011 57.143 24.62 8.46 32.44 4.16
1057 2652 1.221840 CTGATCAGAACCACCCGGG 59.778 63.158 22.25 22.25 44.81 5.73
1098 2694 3.889538 CCATACATAACCTCAGGTCGAGA 59.110 47.826 0.00 0.00 45.45 4.04
1156 2753 3.253677 CGAAGCTAGTCGATTCCAGGTAT 59.746 47.826 1.44 0.00 43.86 2.73
1157 2754 4.454847 CGAAGCTAGTCGATTCCAGGTATA 59.545 45.833 1.44 0.00 43.86 1.47
1300 2897 2.125952 CAGCCTGCGACACGATCA 60.126 61.111 0.00 0.00 0.00 2.92
1695 3352 1.822371 GGTGGTTTTGTGTTGTGACCT 59.178 47.619 0.00 0.00 0.00 3.85
1698 3355 1.470805 GGTTTTGTGTTGTGACCTGCC 60.471 52.381 0.00 0.00 0.00 4.85
1710 3367 3.309582 CCTGCCGGGTGTATCACT 58.690 61.111 2.18 0.00 34.40 3.41
1719 3376 3.113322 CGGGTGTATCACTGTATCAACG 58.887 50.000 0.06 0.00 34.40 4.10
1722 3379 2.534349 GTGTATCACTGTATCAACGCCG 59.466 50.000 0.00 0.00 0.00 6.46
1737 3394 3.035576 GCCGGCGCCTCTTGTTAAC 62.036 63.158 26.68 0.00 0.00 2.01
1747 3404 4.455877 CGCCTCTTGTTAACTGGAAAAGAT 59.544 41.667 7.22 0.00 0.00 2.40
2172 3837 2.665185 GACCAGCGACGGCAGTTT 60.665 61.111 0.00 0.00 43.41 2.66
2205 3872 0.657368 CGACGAGTTGTTTTGCTGGC 60.657 55.000 0.00 0.00 0.00 4.85
2428 4109 2.161609 CCGACCAATGGCAAGTTACTTC 59.838 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 202 1.609840 GCGGCTAATCATCGACGAGC 61.610 60.000 3.01 0.00 0.00 5.03
247 248 0.442699 GAATTTCTCGGACACGCCAC 59.557 55.000 0.00 0.00 40.69 5.01
550 2115 0.315869 CTATAAAAACCCGCGCGCAG 60.316 55.000 32.61 23.79 0.00 5.18
551 2116 1.716760 CTATAAAAACCCGCGCGCA 59.283 52.632 32.61 9.24 0.00 6.09
597 2189 2.032071 GGGATAATCCGGCGTGGG 59.968 66.667 6.01 0.00 37.43 4.61
605 2197 3.050275 GCAGGCGCGGGATAATCC 61.050 66.667 8.83 0.00 35.23 3.01
606 2198 2.031163 AGCAGGCGCGGGATAATC 59.969 61.111 8.83 0.00 45.49 1.75
607 2199 2.281070 CAGCAGGCGCGGGATAAT 60.281 61.111 8.83 0.00 45.49 1.28
608 2200 2.923426 CTTCAGCAGGCGCGGGATAA 62.923 60.000 8.83 0.00 45.49 1.75
609 2201 3.445518 CTTCAGCAGGCGCGGGATA 62.446 63.158 8.83 0.00 45.49 2.59
610 2202 4.845580 CTTCAGCAGGCGCGGGAT 62.846 66.667 8.83 0.00 45.49 3.85
643 2235 1.657487 CCTAGATACCACGTGCGCG 60.657 63.158 19.78 19.78 44.93 6.86
644 2236 1.299926 CCCTAGATACCACGTGCGC 60.300 63.158 10.91 0.00 0.00 6.09
645 2237 1.299926 GCCCTAGATACCACGTGCG 60.300 63.158 10.91 6.24 0.00 5.34
646 2238 1.299926 CGCCCTAGATACCACGTGC 60.300 63.158 10.91 0.00 0.00 5.34
647 2239 1.299926 GCGCCCTAGATACCACGTG 60.300 63.158 9.08 9.08 0.00 4.49
648 2240 1.113517 ATGCGCCCTAGATACCACGT 61.114 55.000 4.18 0.00 0.00 4.49
649 2241 0.667487 CATGCGCCCTAGATACCACG 60.667 60.000 4.18 0.00 0.00 4.94
650 2242 0.393077 ACATGCGCCCTAGATACCAC 59.607 55.000 4.18 0.00 0.00 4.16
651 2243 1.128200 AACATGCGCCCTAGATACCA 58.872 50.000 4.18 0.00 0.00 3.25
652 2244 1.512926 CAACATGCGCCCTAGATACC 58.487 55.000 4.18 0.00 0.00 2.73
653 2245 1.070134 TCCAACATGCGCCCTAGATAC 59.930 52.381 4.18 0.00 0.00 2.24
654 2246 1.344438 CTCCAACATGCGCCCTAGATA 59.656 52.381 4.18 0.00 0.00 1.98
655 2247 0.107456 CTCCAACATGCGCCCTAGAT 59.893 55.000 4.18 0.00 0.00 1.98
656 2248 0.975556 TCTCCAACATGCGCCCTAGA 60.976 55.000 4.18 0.00 0.00 2.43
657 2249 0.107456 ATCTCCAACATGCGCCCTAG 59.893 55.000 4.18 0.00 0.00 3.02
658 2250 0.179048 CATCTCCAACATGCGCCCTA 60.179 55.000 4.18 0.00 0.00 3.53
659 2251 1.452651 CATCTCCAACATGCGCCCT 60.453 57.895 4.18 0.00 0.00 5.19
660 2252 3.113745 CATCTCCAACATGCGCCC 58.886 61.111 4.18 0.00 0.00 6.13
661 2253 2.410469 GCATCTCCAACATGCGCC 59.590 61.111 4.18 0.00 37.51 6.53
674 2266 2.555757 ACTTCACTTTGGCAAGAGCATC 59.444 45.455 0.00 0.00 44.61 3.91
675 2267 2.555757 GACTTCACTTTGGCAAGAGCAT 59.444 45.455 0.00 0.00 44.61 3.79
676 2268 1.949525 GACTTCACTTTGGCAAGAGCA 59.050 47.619 0.00 0.00 44.61 4.26
677 2269 2.225467 AGACTTCACTTTGGCAAGAGC 58.775 47.619 0.00 0.00 41.10 4.09
678 2270 4.083590 GCTAAGACTTCACTTTGGCAAGAG 60.084 45.833 0.00 4.08 33.72 2.85
679 2271 3.815401 GCTAAGACTTCACTTTGGCAAGA 59.185 43.478 0.00 0.00 33.72 3.02
680 2272 3.565482 TGCTAAGACTTCACTTTGGCAAG 59.435 43.478 0.00 0.00 35.93 4.01
681 2273 3.315191 GTGCTAAGACTTCACTTTGGCAA 59.685 43.478 0.00 0.00 38.22 4.52
682 2274 2.878406 GTGCTAAGACTTCACTTTGGCA 59.122 45.455 0.00 0.00 36.21 4.92
683 2275 2.878406 TGTGCTAAGACTTCACTTTGGC 59.122 45.455 8.12 0.00 0.00 4.52
684 2276 4.576463 ACTTGTGCTAAGACTTCACTTTGG 59.424 41.667 8.05 0.83 0.00 3.28
685 2277 5.741388 ACTTGTGCTAAGACTTCACTTTG 57.259 39.130 8.05 0.00 0.00 2.77
686 2278 6.483640 CCTAACTTGTGCTAAGACTTCACTTT 59.516 38.462 8.05 3.12 0.00 2.66
687 2279 5.992217 CCTAACTTGTGCTAAGACTTCACTT 59.008 40.000 8.05 0.00 0.00 3.16
688 2280 5.070580 ACCTAACTTGTGCTAAGACTTCACT 59.929 40.000 8.05 0.00 0.00 3.41
689 2281 5.298347 ACCTAACTTGTGCTAAGACTTCAC 58.702 41.667 8.05 0.00 0.00 3.18
690 2282 5.546621 ACCTAACTTGTGCTAAGACTTCA 57.453 39.130 8.05 0.00 0.00 3.02
691 2283 6.921914 TCTACCTAACTTGTGCTAAGACTTC 58.078 40.000 8.05 0.00 0.00 3.01
692 2284 6.912951 TCTACCTAACTTGTGCTAAGACTT 57.087 37.500 8.05 0.00 0.00 3.01
693 2285 6.912951 TTCTACCTAACTTGTGCTAAGACT 57.087 37.500 8.05 0.00 0.00 3.24
694 2286 8.549338 AATTTCTACCTAACTTGTGCTAAGAC 57.451 34.615 8.05 0.00 0.00 3.01
695 2287 9.649167 GTAATTTCTACCTAACTTGTGCTAAGA 57.351 33.333 8.05 0.00 0.00 2.10
696 2288 9.431887 TGTAATTTCTACCTAACTTGTGCTAAG 57.568 33.333 0.58 0.58 0.00 2.18
697 2289 9.953565 ATGTAATTTCTACCTAACTTGTGCTAA 57.046 29.630 0.00 0.00 0.00 3.09
698 2290 9.378551 CATGTAATTTCTACCTAACTTGTGCTA 57.621 33.333 0.00 0.00 0.00 3.49
699 2291 7.336931 CCATGTAATTTCTACCTAACTTGTGCT 59.663 37.037 0.00 0.00 0.00 4.40
700 2292 7.415206 CCCATGTAATTTCTACCTAACTTGTGC 60.415 40.741 0.00 0.00 0.00 4.57
701 2293 7.827236 TCCCATGTAATTTCTACCTAACTTGTG 59.173 37.037 0.00 0.00 0.00 3.33
702 2294 7.827729 GTCCCATGTAATTTCTACCTAACTTGT 59.172 37.037 0.00 0.00 0.00 3.16
703 2295 8.047310 AGTCCCATGTAATTTCTACCTAACTTG 58.953 37.037 0.00 0.00 0.00 3.16
704 2296 8.159229 AGTCCCATGTAATTTCTACCTAACTT 57.841 34.615 0.00 0.00 0.00 2.66
705 2297 7.750947 AGTCCCATGTAATTTCTACCTAACT 57.249 36.000 0.00 0.00 0.00 2.24
706 2298 9.708092 GATAGTCCCATGTAATTTCTACCTAAC 57.292 37.037 0.00 0.00 0.00 2.34
707 2299 9.442062 TGATAGTCCCATGTAATTTCTACCTAA 57.558 33.333 0.00 0.00 0.00 2.69
708 2300 8.867097 GTGATAGTCCCATGTAATTTCTACCTA 58.133 37.037 0.00 0.00 0.00 3.08
709 2301 7.347222 TGTGATAGTCCCATGTAATTTCTACCT 59.653 37.037 0.00 0.00 0.00 3.08
710 2302 7.506114 TGTGATAGTCCCATGTAATTTCTACC 58.494 38.462 0.00 0.00 0.00 3.18
711 2303 8.993121 CATGTGATAGTCCCATGTAATTTCTAC 58.007 37.037 0.00 0.00 33.06 2.59
712 2304 8.933653 TCATGTGATAGTCCCATGTAATTTCTA 58.066 33.333 0.00 0.00 37.73 2.10
713 2305 7.805163 TCATGTGATAGTCCCATGTAATTTCT 58.195 34.615 0.00 0.00 37.73 2.52
714 2306 8.509690 CATCATGTGATAGTCCCATGTAATTTC 58.490 37.037 0.00 0.00 37.73 2.17
715 2307 7.449395 CCATCATGTGATAGTCCCATGTAATTT 59.551 37.037 0.00 0.00 37.73 1.82
716 2308 6.944290 CCATCATGTGATAGTCCCATGTAATT 59.056 38.462 0.00 0.00 37.73 1.40
717 2309 6.479006 CCATCATGTGATAGTCCCATGTAAT 58.521 40.000 0.00 0.00 37.73 1.89
718 2310 5.221904 CCCATCATGTGATAGTCCCATGTAA 60.222 44.000 0.00 0.00 37.73 2.41
719 2311 4.286808 CCCATCATGTGATAGTCCCATGTA 59.713 45.833 0.00 0.00 37.73 2.29
720 2312 3.073503 CCCATCATGTGATAGTCCCATGT 59.926 47.826 0.00 0.00 37.73 3.21
721 2313 3.073503 ACCCATCATGTGATAGTCCCATG 59.926 47.826 0.00 0.00 37.82 3.66
722 2314 3.330198 ACCCATCATGTGATAGTCCCAT 58.670 45.455 0.00 0.00 32.63 4.00
723 2315 2.775418 ACCCATCATGTGATAGTCCCA 58.225 47.619 0.00 0.00 32.63 4.37
724 2316 3.136443 TGAACCCATCATGTGATAGTCCC 59.864 47.826 0.00 0.00 31.50 4.46
725 2317 4.422073 TGAACCCATCATGTGATAGTCC 57.578 45.455 0.00 0.00 31.50 3.85
726 2318 5.431765 ACTTGAACCCATCATGTGATAGTC 58.568 41.667 0.00 0.00 42.87 2.59
727 2319 5.441718 ACTTGAACCCATCATGTGATAGT 57.558 39.130 0.00 0.00 42.87 2.12
728 2320 6.481313 CAGTACTTGAACCCATCATGTGATAG 59.519 42.308 0.00 0.00 43.88 2.08
729 2321 6.348498 CAGTACTTGAACCCATCATGTGATA 58.652 40.000 0.00 0.00 43.88 2.15
730 2322 5.188434 CAGTACTTGAACCCATCATGTGAT 58.812 41.667 0.00 0.00 43.88 3.06
731 2323 4.565444 CCAGTACTTGAACCCATCATGTGA 60.565 45.833 0.00 0.00 43.88 3.58
732 2324 3.691118 CCAGTACTTGAACCCATCATGTG 59.309 47.826 0.00 0.00 43.88 3.21
733 2325 3.587061 TCCAGTACTTGAACCCATCATGT 59.413 43.478 0.00 3.07 45.44 3.21
734 2326 3.941483 GTCCAGTACTTGAACCCATCATG 59.059 47.826 0.00 0.00 38.03 3.07
735 2327 3.846588 AGTCCAGTACTTGAACCCATCAT 59.153 43.478 0.00 0.00 38.03 2.45
736 2328 3.248024 AGTCCAGTACTTGAACCCATCA 58.752 45.455 0.00 0.00 33.35 3.07
737 2329 3.983044 AGTCCAGTACTTGAACCCATC 57.017 47.619 0.00 0.00 33.35 3.51
781 2373 8.510243 ACATTGAAAAGGCTGATTTTTCTTTT 57.490 26.923 9.95 0.00 42.31 2.27
782 2374 8.510243 AACATTGAAAAGGCTGATTTTTCTTT 57.490 26.923 9.95 0.00 42.31 2.52
785 2377 6.200854 ACGAACATTGAAAAGGCTGATTTTTC 59.799 34.615 3.06 3.06 42.22 2.29
826 2418 0.036388 ATCACACGTCCAGCGGAAAT 60.036 50.000 0.00 0.00 46.52 2.17
834 2426 4.529109 TGATAAAGTCATCACACGTCCA 57.471 40.909 0.00 0.00 29.93 4.02
837 2429 6.398095 TGAGATTGATAAAGTCATCACACGT 58.602 36.000 0.00 0.00 36.54 4.49
864 2456 8.715191 TTTTCTAAAATGAACACAACAATGCT 57.285 26.923 0.00 0.00 0.00 3.79
892 2484 7.645058 ATTTAACCATCAGGAGGTGTAATTG 57.355 36.000 0.00 0.00 39.86 2.32
900 2492 7.119387 AGGTCTTTTATTTAACCATCAGGAGG 58.881 38.462 0.00 0.00 38.69 4.30
947 2541 1.285950 GTTTTCCCTGCGCAAGTCC 59.714 57.895 13.05 0.00 41.68 3.85
1018 2613 1.153745 GCTGCGATTGGACTCGAGT 60.154 57.895 20.18 20.18 41.12 4.18
1052 2647 4.146058 GGTAATTAACCGCCCGGG 57.854 61.111 19.09 19.09 38.88 5.73
1098 2694 1.246649 TGTGTGCTGCCAATCGATTT 58.753 45.000 8.21 0.00 0.00 2.17
1196 2793 2.475371 GATGGATGGATCGGCCCTGG 62.475 65.000 0.00 0.00 34.97 4.45
1667 3324 2.365582 ACACAAAACCACCAGACAGAC 58.634 47.619 0.00 0.00 0.00 3.51
1695 3352 1.411246 GATACAGTGATACACCCGGCA 59.589 52.381 0.00 0.00 34.49 5.69
1698 3355 3.113322 CGTTGATACAGTGATACACCCG 58.887 50.000 0.00 0.00 34.49 5.28
1719 3376 2.744709 TTAACAAGAGGCGCCGGC 60.745 61.111 23.20 19.07 38.90 6.13
1722 3379 0.321298 TCCAGTTAACAAGAGGCGCC 60.321 55.000 21.89 21.89 0.00 6.53
1737 3394 8.807948 TCCCTAAACTGATTTATCTTTTCCAG 57.192 34.615 0.00 0.00 29.85 3.86
1747 3404 5.531659 TGCAACGTTTCCCTAAACTGATTTA 59.468 36.000 0.00 0.00 42.39 1.40
1901 3561 0.536460 TGGGAAGAAAAGTGGTCGGC 60.536 55.000 0.00 0.00 0.00 5.54
2205 3872 3.249799 TCACCGCAAGAAAACACACTATG 59.750 43.478 0.00 0.00 43.02 2.23
2264 3931 4.037208 CAGTCCAAGCAAAACAACTCATCT 59.963 41.667 0.00 0.00 0.00 2.90
2428 4109 1.982073 GATCGCCGGTTCCAGCAAAG 61.982 60.000 1.90 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.