Multiple sequence alignment - TraesCS3B01G324600

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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 TraesCS3B01G324600 chr3B 100.000 3263 0 0 1 3263 525621601 525618339 0.000000e+00 6026
1 TraesCS3B01G324600 chr3B 97.400 577 15 0 2687 3263 545382030 545382606 0.000000e+00 983
2 TraesCS3B01G324600 chr3A 91.777 2274 134 27 1 2261 518908248 518906015 0.000000e+00 3114
3 TraesCS3B01G324600 chr3A 83.439 314 32 13 2299 2607 518906013 518905715 1.150000e-69 274
4 TraesCS3B01G324600 chr3A 78.491 265 47 6 7 265 745634003 745633743 7.240000e-37 165
5 TraesCS3B01G324600 chr3D 92.947 2155 78 17 353 2466 399677834 399675713 0.000000e+00 3070
6 TraesCS3B01G324600 chr2D 93.966 580 22 3 2687 3263 32777866 32777297 0.000000e+00 865
7 TraesCS3B01G324600 chr1A 91.537 579 45 3 2687 3263 175178984 175179560 0.000000e+00 795
8 TraesCS3B01G324600 chr7D 89.916 595 40 9 2687 3263 217967841 217967249 0.000000e+00 749
9 TraesCS3B01G324600 chr7D 89.280 597 44 9 2685 3263 620261914 620262508 0.000000e+00 730
10 TraesCS3B01G324600 chr7D 77.912 249 51 4 7 253 376356685 376356931 5.640000e-33 152
11 TraesCS3B01G324600 chr6B 88.353 601 44 11 2685 3263 661555917 661555321 0.000000e+00 699
12 TraesCS3B01G324600 chr6B 87.940 597 52 11 2686 3263 36219259 36218664 0.000000e+00 686
13 TraesCS3B01G324600 chr5D 88.127 598 51 9 2685 3263 114472967 114473563 0.000000e+00 693
14 TraesCS3B01G324600 chr2B 88.036 560 47 8 2686 3227 36491690 36492247 0.000000e+00 645
15 TraesCS3B01G324600 chr1B 86.393 610 51 16 2681 3263 602231759 602232363 3.550000e-179 638
16 TraesCS3B01G324600 chr4D 82.353 221 36 3 1 220 58274070 58274288 4.300000e-44 189
17 TraesCS3B01G324600 chrUn 79.545 220 39 6 1 220 99390234 99390021 5.640000e-33 152
18 TraesCS3B01G324600 chr4A 78.298 235 48 3 33 266 602098562 602098330 7.290000e-32 148
19 TraesCS3B01G324600 chr4A 77.333 225 46 5 33 254 490531049 490530827 9.500000e-26 128
20 TraesCS3B01G324600 chr1D 76.448 259 59 2 1 258 364640850 364640593 4.390000e-29 139
21 TraesCS3B01G324600 chr6A 77.253 233 47 5 33 261 116704135 116704365 7.350000e-27 132


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 TraesCS3B01G324600 chr3B 525618339 525621601 3262 True 6026 6026 100.000 1 3263 1 chr3B.!!$R1 3262
1 TraesCS3B01G324600 chr3B 545382030 545382606 576 False 983 983 97.400 2687 3263 1 chr3B.!!$F1 576
2 TraesCS3B01G324600 chr3A 518905715 518908248 2533 True 1694 3114 87.608 1 2607 2 chr3A.!!$R2 2606
3 TraesCS3B01G324600 chr3D 399675713 399677834 2121 True 3070 3070 92.947 353 2466 1 chr3D.!!$R1 2113
4 TraesCS3B01G324600 chr2D 32777297 32777866 569 True 865 865 93.966 2687 3263 1 chr2D.!!$R1 576
5 TraesCS3B01G324600 chr1A 175178984 175179560 576 False 795 795 91.537 2687 3263 1 chr1A.!!$F1 576
6 TraesCS3B01G324600 chr7D 217967249 217967841 592 True 749 749 89.916 2687 3263 1 chr7D.!!$R1 576
7 TraesCS3B01G324600 chr7D 620261914 620262508 594 False 730 730 89.280 2685 3263 1 chr7D.!!$F2 578
8 TraesCS3B01G324600 chr6B 661555321 661555917 596 True 699 699 88.353 2685 3263 1 chr6B.!!$R2 578
9 TraesCS3B01G324600 chr6B 36218664 36219259 595 True 686 686 87.940 2686 3263 1 chr6B.!!$R1 577
10 TraesCS3B01G324600 chr5D 114472967 114473563 596 False 693 693 88.127 2685 3263 1 chr5D.!!$F1 578
11 TraesCS3B01G324600 chr2B 36491690 36492247 557 False 645 645 88.036 2686 3227 1 chr2B.!!$F1 541
12 TraesCS3B01G324600 chr1B 602231759 602232363 604 False 638 638 86.393 2681 3263 1 chr1B.!!$F1 582

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
58 60 0.034059 CGCTAGTCCTTAGGGGCATG 59.966 60.0 0.00 0.0 40.27 4.06 F
64 66 0.183492 TCCTTAGGGGCATGTGCATC 59.817 55.0 7.36 0.0 44.36 3.91 F
379 385 0.454957 CGCTCAAAATTCACTGCCCG 60.455 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1568 0.323269 TGGCATTGGAAATGGCGAGA 60.323 50.0 18.14 2.42 46.12 4.04 R
1540 1572 0.614812 AGGTTGGCATTGGAAATGGC 59.385 50.0 16.99 16.99 43.83 4.40 R
2356 2403 0.959553 AGTGCTACACTACACAGCGT 59.040 50.0 0.00 0.00 43.46 5.07 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
29 31 1.335810 AGTTCAACAGCGACGACTACA 59.664 47.619 0.00 0.00 0.00 2.74
31 33 2.717580 TCAACAGCGACGACTACAAT 57.282 45.000 0.00 0.00 0.00 2.71
34 36 1.992170 ACAGCGACGACTACAATTCC 58.008 50.000 0.00 0.00 0.00 3.01
53 55 3.139565 GGGCGCTAGTCCTTAGGG 58.860 66.667 7.64 0.00 43.31 3.53
57 59 1.759459 GCGCTAGTCCTTAGGGGCAT 61.759 60.000 0.00 0.00 41.37 4.40
58 60 0.034059 CGCTAGTCCTTAGGGGCATG 59.966 60.000 0.00 0.00 40.27 4.06
64 66 0.183492 TCCTTAGGGGCATGTGCATC 59.817 55.000 7.36 0.00 44.36 3.91
65 67 1.168407 CCTTAGGGGCATGTGCATCG 61.168 60.000 7.36 0.00 44.36 3.84
66 68 1.789078 CTTAGGGGCATGTGCATCGC 61.789 60.000 7.36 0.00 44.36 4.58
79 81 1.874019 CATCGCGACTTCCCGACTG 60.874 63.158 12.93 0.00 36.18 3.51
80 82 2.341101 ATCGCGACTTCCCGACTGT 61.341 57.895 12.93 0.00 36.18 3.55
81 83 2.267681 ATCGCGACTTCCCGACTGTC 62.268 60.000 12.93 0.00 36.18 3.51
82 84 2.649034 GCGACTTCCCGACTGTCA 59.351 61.111 8.73 0.00 0.00 3.58
83 85 1.215647 GCGACTTCCCGACTGTCAT 59.784 57.895 8.73 0.00 0.00 3.06
84 86 0.802607 GCGACTTCCCGACTGTCATC 60.803 60.000 8.73 0.00 0.00 2.92
85 87 0.523546 CGACTTCCCGACTGTCATCG 60.524 60.000 8.73 3.42 41.89 3.84
86 88 0.809385 GACTTCCCGACTGTCATCGA 59.191 55.000 8.73 0.00 45.13 3.59
87 89 1.405821 GACTTCCCGACTGTCATCGAT 59.594 52.381 8.73 0.00 45.13 3.59
88 90 2.617308 GACTTCCCGACTGTCATCGATA 59.383 50.000 8.73 0.00 45.13 2.92
105 107 1.984288 ATAAGGTCAAGCCGGCTCCC 61.984 60.000 32.93 28.00 43.70 4.30
126 128 1.476845 TAGGGAAGCGGCAACAGTGA 61.477 55.000 1.45 0.00 0.00 3.41
135 137 4.059459 CAACAGTGACGCGTCGGC 62.059 66.667 31.88 26.05 34.27 5.54
136 138 4.578898 AACAGTGACGCGTCGGCA 62.579 61.111 31.88 14.89 45.13 5.69
147 149 2.307309 CGTCGGCAGCTCGTTTTGA 61.307 57.895 0.00 0.00 0.00 2.69
149 151 1.069090 TCGGCAGCTCGTTTTGACT 59.931 52.632 0.00 0.00 0.00 3.41
174 176 1.613836 AGTAGTCGTTCGGTGGTCTT 58.386 50.000 0.00 0.00 0.00 3.01
185 187 1.473434 CGGTGGTCTTGGAATCTAGGC 60.473 57.143 0.00 0.00 0.00 3.93
218 220 8.621532 TTCTTATGTTTGAGATGCTTTGTACT 57.378 30.769 0.00 0.00 0.00 2.73
220 222 9.719355 TCTTATGTTTGAGATGCTTTGTACTTA 57.281 29.630 0.00 0.00 0.00 2.24
223 225 7.144722 TGTTTGAGATGCTTTGTACTTATGG 57.855 36.000 0.00 0.00 0.00 2.74
224 226 5.818136 TTGAGATGCTTTGTACTTATGGC 57.182 39.130 0.00 0.00 0.00 4.40
225 227 3.871006 TGAGATGCTTTGTACTTATGGCG 59.129 43.478 0.00 0.00 0.00 5.69
226 228 4.119862 GAGATGCTTTGTACTTATGGCGA 58.880 43.478 0.00 0.00 0.00 5.54
227 229 4.513442 AGATGCTTTGTACTTATGGCGAA 58.487 39.130 0.00 0.00 0.00 4.70
228 230 4.332819 AGATGCTTTGTACTTATGGCGAAC 59.667 41.667 0.00 0.00 0.00 3.95
229 231 2.413796 TGCTTTGTACTTATGGCGAACG 59.586 45.455 0.00 0.00 0.00 3.95
230 232 2.786700 GCTTTGTACTTATGGCGAACGC 60.787 50.000 10.81 10.81 41.06 4.84
231 233 2.373540 TTGTACTTATGGCGAACGCT 57.626 45.000 18.14 2.84 41.60 5.07
232 234 2.373540 TGTACTTATGGCGAACGCTT 57.626 45.000 18.14 9.28 41.60 4.68
233 235 3.507103 TGTACTTATGGCGAACGCTTA 57.493 42.857 18.14 8.81 41.60 3.09
234 236 4.049546 TGTACTTATGGCGAACGCTTAT 57.950 40.909 18.14 14.57 41.60 1.73
235 237 5.185668 TGTACTTATGGCGAACGCTTATA 57.814 39.130 18.14 13.71 41.60 0.98
236 238 5.590145 TGTACTTATGGCGAACGCTTATAA 58.410 37.500 18.14 18.68 41.60 0.98
237 239 6.218019 TGTACTTATGGCGAACGCTTATAAT 58.782 36.000 18.14 13.61 41.60 1.28
238 240 7.369607 TGTACTTATGGCGAACGCTTATAATA 58.630 34.615 18.14 12.93 41.60 0.98
244 246 5.779922 TGGCGAACGCTTATAATAGATCTT 58.220 37.500 18.14 0.00 41.60 2.40
327 331 7.158099 AGTTAGGGAACAAATTTGTAGCATC 57.842 36.000 23.53 16.48 41.31 3.91
330 334 6.610075 AGGGAACAAATTTGTAGCATCATT 57.390 33.333 23.53 5.93 41.31 2.57
332 336 5.516339 GGGAACAAATTTGTAGCATCATTCG 59.484 40.000 23.53 0.00 41.31 3.34
379 385 0.454957 CGCTCAAAATTCACTGCCCG 60.455 55.000 0.00 0.00 0.00 6.13
410 416 1.604755 ACAAAATTCACCGCGCTACAA 59.395 42.857 5.56 0.00 0.00 2.41
739 759 3.125573 CGAGGACGAGGACGAGCA 61.126 66.667 0.00 0.00 42.66 4.26
743 763 2.167861 GGACGAGGACGAGCATTGC 61.168 63.158 0.00 0.00 42.66 3.56
744 764 1.446099 GACGAGGACGAGCATTGCA 60.446 57.895 11.91 0.00 42.66 4.08
746 766 1.737735 CGAGGACGAGCATTGCACA 60.738 57.895 11.91 0.00 42.66 4.57
827 847 4.778143 GCCCGCGTCCATCCAAGT 62.778 66.667 4.92 0.00 0.00 3.16
838 858 1.476833 CCATCCAAGTATCCAACGGGG 60.477 57.143 0.00 0.00 38.37 5.73
1260 1292 1.069765 CAACTGCTCCGACACCACT 59.930 57.895 0.00 0.00 0.00 4.00
1269 1301 1.442184 CGACACCACTTCCGTCTCG 60.442 63.158 0.00 0.00 0.00 4.04
1530 1562 1.200760 TCTCCCACATGGACCACCTG 61.201 60.000 0.00 0.00 38.61 4.00
1536 1568 1.374947 CATGGACCACCTGAACCGT 59.625 57.895 0.00 0.00 37.04 4.83
1540 1572 1.080705 GACCACCTGAACCGTCTCG 60.081 63.158 0.00 0.00 0.00 4.04
1666 1698 2.440147 CCATCACCCACCTTGGCA 59.560 61.111 0.00 0.00 35.79 4.92
1689 1721 0.399949 TCACCCACCTGAACCTCAGT 60.400 55.000 3.15 0.00 42.80 3.41
2009 2041 0.033504 CTGTGCTACAACAGGTCGGT 59.966 55.000 0.00 0.00 43.22 4.69
2025 2057 4.500116 GTGCTCTCCGCCGAGGTC 62.500 72.222 2.12 0.00 41.99 3.85
2104 2136 2.578178 CGCAGTCGGAGAAGAGCG 60.578 66.667 0.00 0.00 44.00 5.03
2267 2299 2.014857 CAAGGTGTGCAGATGAGATGG 58.985 52.381 0.00 0.00 0.00 3.51
2313 2360 2.937799 GTGTTGACGAGGTTGGTTTACA 59.062 45.455 0.00 0.00 0.00 2.41
2344 2391 2.218953 TGTTGAATAGTCGGATCCGC 57.781 50.000 29.62 22.76 39.59 5.54
2356 2403 1.400142 CGGATCCGCAATTTGCTGTTA 59.600 47.619 23.37 2.59 42.25 2.41
2357 2404 2.791158 CGGATCCGCAATTTGCTGTTAC 60.791 50.000 23.37 7.74 42.25 2.50
2365 2412 3.608241 GCAATTTGCTGTTACGCTGTGTA 60.608 43.478 14.11 0.00 40.96 2.90
2374 2421 2.624316 TACGCTGTGTAGTGTAGCAC 57.376 50.000 0.00 0.00 45.39 4.40
2384 2431 2.260844 AGTGTAGCACTGCATGTTGT 57.739 45.000 3.30 0.00 43.63 3.32
2448 2495 5.585500 TGACGAAAAATACAACGAAGAGG 57.415 39.130 0.00 0.00 0.00 3.69
2452 2499 2.467566 AAATACAACGAAGAGGCCGT 57.532 45.000 0.00 0.00 42.61 5.68
2466 2513 0.525761 GGCCGTATTTGCAAAGCAGA 59.474 50.000 18.19 0.00 40.61 4.26
2467 2514 1.067915 GGCCGTATTTGCAAAGCAGAA 60.068 47.619 18.19 0.00 40.61 3.02
2468 2515 2.609244 GGCCGTATTTGCAAAGCAGAAA 60.609 45.455 18.19 0.00 40.61 2.52
2482 2529 6.510638 GCAAAGCAGAAAATTCCTCTTGTTTG 60.511 38.462 12.15 12.15 0.00 2.93
2491 2539 3.011566 TCCTCTTGTTTGGTTTGCTGA 57.988 42.857 0.00 0.00 0.00 4.26
2512 2560 7.027161 GCTGACCAATGTCGTTGTTATTATTT 58.973 34.615 4.13 0.00 44.86 1.40
2550 2598 2.739132 GGGTCTTGTCCCGTCGTT 59.261 61.111 0.00 0.00 37.93 3.85
2555 2603 0.669318 TCTTGTCCCGTCGTTGCATC 60.669 55.000 0.00 0.00 0.00 3.91
2568 2616 4.561606 GTCGTTGCATCGTTCTACTGTATT 59.438 41.667 16.21 0.00 0.00 1.89
2575 2635 3.754955 TCGTTCTACTGTATTCACTGCG 58.245 45.455 0.00 0.00 0.00 5.18
2586 2646 4.390603 TGTATTCACTGCGGTATCACAAAC 59.609 41.667 0.00 0.00 0.00 2.93
2616 2676 4.895961 AGTAAAACAGTTACTCCCTCTGC 58.104 43.478 0.00 0.00 29.89 4.26
2617 2677 2.457366 AAACAGTTACTCCCTCTGCG 57.543 50.000 0.00 0.00 33.12 5.18
2618 2678 0.037232 AACAGTTACTCCCTCTGCGC 60.037 55.000 0.00 0.00 33.12 6.09
2619 2679 0.900647 ACAGTTACTCCCTCTGCGCT 60.901 55.000 9.73 0.00 33.12 5.92
2620 2680 0.247736 CAGTTACTCCCTCTGCGCTT 59.752 55.000 9.73 0.00 0.00 4.68
2621 2681 0.247736 AGTTACTCCCTCTGCGCTTG 59.752 55.000 9.73 1.08 0.00 4.01
2622 2682 0.246635 GTTACTCCCTCTGCGCTTGA 59.753 55.000 9.73 6.21 0.00 3.02
2623 2683 0.973632 TTACTCCCTCTGCGCTTGAA 59.026 50.000 9.73 0.00 0.00 2.69
2624 2684 0.973632 TACTCCCTCTGCGCTTGAAA 59.026 50.000 9.73 0.00 0.00 2.69
2625 2685 0.321122 ACTCCCTCTGCGCTTGAAAG 60.321 55.000 9.73 0.00 0.00 2.62
2626 2686 0.036952 CTCCCTCTGCGCTTGAAAGA 60.037 55.000 9.73 0.79 0.00 2.52
2627 2687 0.036952 TCCCTCTGCGCTTGAAAGAG 60.037 55.000 9.73 11.93 37.73 2.85
2628 2688 0.321122 CCCTCTGCGCTTGAAAGAGT 60.321 55.000 17.44 0.00 36.51 3.24
2629 2689 1.066858 CCCTCTGCGCTTGAAAGAGTA 60.067 52.381 17.44 0.00 36.51 2.59
2630 2690 2.419297 CCCTCTGCGCTTGAAAGAGTAT 60.419 50.000 17.44 0.00 36.51 2.12
2631 2691 3.181475 CCCTCTGCGCTTGAAAGAGTATA 60.181 47.826 17.44 0.00 36.51 1.47
2632 2692 3.799420 CCTCTGCGCTTGAAAGAGTATAC 59.201 47.826 17.44 0.00 36.51 1.47
2633 2693 4.440802 CCTCTGCGCTTGAAAGAGTATACT 60.441 45.833 17.44 4.68 36.51 2.12
2634 2694 5.073311 TCTGCGCTTGAAAGAGTATACTT 57.927 39.130 9.73 0.00 0.00 2.24
2635 2695 5.103000 TCTGCGCTTGAAAGAGTATACTTC 58.897 41.667 9.73 1.40 0.00 3.01
2636 2696 4.181578 TGCGCTTGAAAGAGTATACTTCC 58.818 43.478 9.73 0.00 0.00 3.46
2637 2697 4.181578 GCGCTTGAAAGAGTATACTTCCA 58.818 43.478 6.88 0.61 0.00 3.53
2638 2698 4.630069 GCGCTTGAAAGAGTATACTTCCAA 59.370 41.667 6.88 8.08 0.00 3.53
2639 2699 5.446073 GCGCTTGAAAGAGTATACTTCCAAC 60.446 44.000 6.88 0.00 0.00 3.77
2640 2700 5.869888 CGCTTGAAAGAGTATACTTCCAACT 59.130 40.000 6.88 0.00 0.00 3.16
2641 2701 6.369065 CGCTTGAAAGAGTATACTTCCAACTT 59.631 38.462 6.88 2.49 0.00 2.66
2642 2702 7.095187 CGCTTGAAAGAGTATACTTCCAACTTT 60.095 37.037 6.88 10.98 0.00 2.66
2643 2703 9.216117 GCTTGAAAGAGTATACTTCCAACTTTA 57.784 33.333 6.88 0.00 0.00 1.85
2732 2792 0.511221 CTTGGCGTAAACGGTCACTG 59.489 55.000 4.49 0.00 40.23 3.66
2765 2825 2.535012 TGTGGCGTACATTGAAGTGA 57.465 45.000 0.00 0.00 33.42 3.41
2996 3070 1.257750 TGGGTCCCATCTGTCAGACG 61.258 60.000 6.47 0.00 0.00 4.18
3181 3273 8.436200 GCTGCACATAGTACATATAGCTTTAAC 58.564 37.037 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.859080 GTCGTCGCTGTTGAACTCTTT 59.141 47.619 0.00 0.00 0.00 2.52
7 8 0.669077 AGTCGTCGCTGTTGAACTCT 59.331 50.000 0.00 0.00 0.00 3.24
17 18 1.135083 CCTGGAATTGTAGTCGTCGCT 60.135 52.381 0.00 0.00 0.00 4.93
29 31 0.983378 AGGACTAGCGCCCTGGAATT 60.983 55.000 2.29 0.00 0.00 2.17
31 33 0.324923 TAAGGACTAGCGCCCTGGAA 60.325 55.000 2.29 0.00 32.12 3.53
34 36 1.742768 CCTAAGGACTAGCGCCCTG 59.257 63.158 2.29 0.00 32.12 4.45
53 55 2.637715 GAAGTCGCGATGCACATGCC 62.638 60.000 14.06 0.00 41.18 4.40
57 59 2.434185 GGGAAGTCGCGATGCACA 60.434 61.111 14.06 0.00 0.00 4.57
65 67 0.802607 GATGACAGTCGGGAAGTCGC 60.803 60.000 0.00 0.00 35.09 5.19
66 68 0.523546 CGATGACAGTCGGGAAGTCG 60.524 60.000 0.00 0.00 37.94 4.18
79 81 2.128035 CGGCTTGACCTTATCGATGAC 58.872 52.381 8.54 0.00 35.61 3.06
80 82 1.068588 CCGGCTTGACCTTATCGATGA 59.931 52.381 8.54 0.00 35.61 2.92
81 83 1.502231 CCGGCTTGACCTTATCGATG 58.498 55.000 8.54 0.00 35.61 3.84
82 84 0.249911 GCCGGCTTGACCTTATCGAT 60.250 55.000 22.15 2.16 35.61 3.59
83 85 1.143183 GCCGGCTTGACCTTATCGA 59.857 57.895 22.15 0.00 35.61 3.59
84 86 0.876342 GAGCCGGCTTGACCTTATCG 60.876 60.000 33.34 0.00 35.61 2.92
85 87 0.533085 GGAGCCGGCTTGACCTTATC 60.533 60.000 33.34 14.52 35.61 1.75
86 88 1.527370 GGAGCCGGCTTGACCTTAT 59.473 57.895 33.34 4.05 35.61 1.73
87 89 2.666098 GGGAGCCGGCTTGACCTTA 61.666 63.158 33.34 0.00 35.61 2.69
88 90 4.035102 GGGAGCCGGCTTGACCTT 62.035 66.667 33.34 5.97 35.61 3.50
105 107 0.392998 ACTGTTGCCGCTTCCCTATG 60.393 55.000 0.00 0.00 0.00 2.23
115 117 4.059459 GACGCGTCACTGTTGCCG 62.059 66.667 33.09 0.00 0.00 5.69
119 121 4.578898 TGCCGACGCGTCACTGTT 62.579 61.111 35.71 0.44 38.08 3.16
128 130 3.712881 AAAACGAGCTGCCGACGC 61.713 61.111 15.53 0.00 0.00 5.19
135 137 0.940126 ACTGCAGTCAAAACGAGCTG 59.060 50.000 15.25 0.00 36.79 4.24
136 138 2.224066 ACTACTGCAGTCAAAACGAGCT 60.224 45.455 25.56 1.54 33.96 4.09
144 146 3.364664 CGAACGACTACTACTGCAGTCAA 60.365 47.826 25.56 5.78 41.04 3.18
147 149 1.467734 CCGAACGACTACTACTGCAGT 59.532 52.381 25.12 25.12 41.62 4.40
149 151 1.198408 CACCGAACGACTACTACTGCA 59.802 52.381 0.00 0.00 0.00 4.41
163 165 2.500098 CCTAGATTCCAAGACCACCGAA 59.500 50.000 0.00 0.00 0.00 4.30
174 176 8.836413 CATAAGAAAAATTACGCCTAGATTCCA 58.164 33.333 0.00 0.00 0.00 3.53
185 187 9.559958 AGCATCTCAAACATAAGAAAAATTACG 57.440 29.630 0.00 0.00 0.00 3.18
218 220 7.544622 AGATCTATTATAAGCGTTCGCCATAA 58.455 34.615 13.54 15.99 0.00 1.90
220 222 5.967088 AGATCTATTATAAGCGTTCGCCAT 58.033 37.500 13.54 9.79 0.00 4.40
222 224 7.167801 GGATAAGATCTATTATAAGCGTTCGCC 59.832 40.741 13.54 0.00 0.00 5.54
223 225 7.916450 AGGATAAGATCTATTATAAGCGTTCGC 59.084 37.037 9.24 9.24 0.00 4.70
224 226 9.790389 AAGGATAAGATCTATTATAAGCGTTCG 57.210 33.333 0.00 0.00 0.00 3.95
299 303 7.923878 TGCTACAAATTTGTTCCCTAACTTTTC 59.076 33.333 27.66 4.64 42.35 2.29
303 307 6.719370 TGATGCTACAAATTTGTTCCCTAACT 59.281 34.615 27.66 3.41 42.35 2.24
304 308 6.919721 TGATGCTACAAATTTGTTCCCTAAC 58.080 36.000 27.66 13.96 42.35 2.34
327 331 1.439353 CCGGGGCATCTTCACGAATG 61.439 60.000 0.00 0.00 0.00 2.67
330 334 3.781307 CCCGGGGCATCTTCACGA 61.781 66.667 14.71 0.00 0.00 4.35
349 353 0.032130 TTTTGAGCGAGTCAGCGACT 59.968 50.000 10.33 10.33 46.42 4.18
379 385 6.398517 CGCGGTGAATTTTGTTTATCTTCAAC 60.399 38.462 0.00 0.00 31.71 3.18
410 416 4.170468 ACTGGGTCAGAGTTTGATGTTT 57.830 40.909 1.59 0.00 38.29 2.83
539 545 1.341802 CTCTAACTTTCGCGCGCTG 59.658 57.895 30.48 22.06 0.00 5.18
544 550 1.710339 GCCTGCTCTAACTTTCGCG 59.290 57.895 0.00 0.00 0.00 5.87
601 611 4.081862 ACATCTTGTCAAATGCTTCCATGG 60.082 41.667 4.97 4.97 0.00 3.66
719 739 2.800581 CTCGTCCTCGTCCTCGTCG 61.801 68.421 0.00 0.00 38.33 5.12
739 759 1.200716 CTTTCGGCATCAGTGTGCAAT 59.799 47.619 16.15 0.00 46.81 3.56
743 763 1.133253 CGCTTTCGGCATCAGTGTG 59.867 57.895 0.00 0.00 41.91 3.82
744 764 1.005037 TCGCTTTCGGCATCAGTGT 60.005 52.632 0.00 0.00 41.91 3.55
746 766 1.741770 GGTCGCTTTCGGCATCAGT 60.742 57.895 0.00 0.00 43.15 3.41
1235 1267 1.533033 TCGGAGCAGTTGGTGAGGA 60.533 57.895 0.00 0.00 0.00 3.71
1530 1562 0.672401 TGGAAATGGCGAGACGGTTC 60.672 55.000 0.00 0.00 0.00 3.62
1536 1568 0.323269 TGGCATTGGAAATGGCGAGA 60.323 50.000 18.14 2.42 46.12 4.04
1540 1572 0.614812 AGGTTGGCATTGGAAATGGC 59.385 50.000 16.99 16.99 43.83 4.40
1641 1673 2.203862 TGGGTGATGGTGTCGGGA 60.204 61.111 0.00 0.00 0.00 5.14
1666 1698 1.136329 AGGTTCAGGTGGGTGATGCT 61.136 55.000 0.00 0.00 0.00 3.79
1689 1721 1.314730 GCCCTTTGAGAACGTTGGAA 58.685 50.000 5.00 0.00 0.00 3.53
2172 2204 4.124351 CCGAGAACCACCGCGCTA 62.124 66.667 5.56 0.00 0.00 4.26
2267 2299 3.179048 AGAAGCAACAAAAAGTTCACGC 58.821 40.909 0.00 0.00 38.74 5.34
2315 2362 4.033019 CGACTATTCAACATGCAGCAATG 58.967 43.478 0.00 0.94 0.00 2.82
2316 2363 3.065786 CCGACTATTCAACATGCAGCAAT 59.934 43.478 0.00 0.00 0.00 3.56
2317 2364 2.419673 CCGACTATTCAACATGCAGCAA 59.580 45.455 0.00 0.00 0.00 3.91
2318 2365 2.009051 CCGACTATTCAACATGCAGCA 58.991 47.619 0.00 0.00 0.00 4.41
2319 2366 2.279741 TCCGACTATTCAACATGCAGC 58.720 47.619 0.00 0.00 0.00 5.25
2344 2391 2.998772 ACACAGCGTAACAGCAAATTG 58.001 42.857 0.00 0.00 40.15 2.32
2356 2403 0.959553 AGTGCTACACTACACAGCGT 59.040 50.000 0.00 0.00 43.46 5.07
2357 2404 1.340658 CAGTGCTACACTACACAGCG 58.659 55.000 0.00 0.00 43.43 5.18
2365 2412 2.260844 ACAACATGCAGTGCTACACT 57.739 45.000 17.60 0.00 46.51 3.55
2374 2421 4.323417 TGGTTTAGGAGTACAACATGCAG 58.677 43.478 0.00 0.00 0.00 4.41
2384 2431 7.618019 ATTGATCTATGCTGGTTTAGGAGTA 57.382 36.000 0.00 0.00 0.00 2.59
2414 2461 8.121167 TGTATTTTTCGTCAAATGTTTCAACC 57.879 30.769 5.23 0.00 0.00 3.77
2422 2469 7.059488 CCTCTTCGTTGTATTTTTCGTCAAATG 59.941 37.037 5.23 0.00 0.00 2.32
2424 2471 6.423862 CCTCTTCGTTGTATTTTTCGTCAAA 58.576 36.000 0.00 0.00 0.00 2.69
2425 2472 5.559417 GCCTCTTCGTTGTATTTTTCGTCAA 60.559 40.000 0.00 0.00 0.00 3.18
2448 2495 2.346099 TTCTGCTTTGCAAATACGGC 57.654 45.000 13.23 12.95 38.41 5.68
2452 2499 6.996509 AGAGGAATTTTCTGCTTTGCAAATA 58.003 32.000 13.23 4.25 38.41 1.40
2466 2513 5.585844 CAGCAAACCAAACAAGAGGAATTTT 59.414 36.000 0.00 0.00 0.00 1.82
2467 2514 5.104982 TCAGCAAACCAAACAAGAGGAATTT 60.105 36.000 0.00 0.00 0.00 1.82
2468 2515 4.405358 TCAGCAAACCAAACAAGAGGAATT 59.595 37.500 0.00 0.00 0.00 2.17
2482 2529 0.951558 ACGACATTGGTCAGCAAACC 59.048 50.000 0.00 0.72 44.54 3.27
2491 2539 9.005777 ACACTAAATAATAACAACGACATTGGT 57.994 29.630 0.00 0.00 43.20 3.67
2525 2573 1.110518 GGGACAAGACCCCGCAAAAA 61.111 55.000 0.00 0.00 43.81 1.94
2526 2574 1.529713 GGGACAAGACCCCGCAAAA 60.530 57.895 0.00 0.00 43.81 2.44
2527 2575 2.114411 GGGACAAGACCCCGCAAA 59.886 61.111 0.00 0.00 43.81 3.68
2532 2580 2.875804 AACGACGGGACAAGACCCC 61.876 63.158 0.00 0.00 46.62 4.95
2533 2581 1.666872 CAACGACGGGACAAGACCC 60.667 63.158 0.00 0.00 45.92 4.46
2534 2582 2.315386 GCAACGACGGGACAAGACC 61.315 63.158 0.00 0.00 0.00 3.85
2535 2583 0.949105 ATGCAACGACGGGACAAGAC 60.949 55.000 0.00 0.00 0.00 3.01
2536 2584 0.669318 GATGCAACGACGGGACAAGA 60.669 55.000 0.00 0.00 0.00 3.02
2537 2585 1.787847 GATGCAACGACGGGACAAG 59.212 57.895 0.00 0.00 0.00 3.16
2542 2590 0.457166 TAGAACGATGCAACGACGGG 60.457 55.000 23.89 0.00 37.03 5.28
2547 2595 4.561213 TGAATACAGTAGAACGATGCAACG 59.439 41.667 15.38 15.38 39.31 4.10
2550 2598 5.102313 CAGTGAATACAGTAGAACGATGCA 58.898 41.667 0.00 0.00 0.00 3.96
2555 2603 2.852413 CCGCAGTGAATACAGTAGAACG 59.148 50.000 0.00 0.00 0.00 3.95
2568 2616 2.036604 TGAGTTTGTGATACCGCAGTGA 59.963 45.455 0.00 0.00 33.88 3.41
2586 2646 6.869388 GGGAGTAACTGTTTTACTCTTCTGAG 59.131 42.308 18.09 0.00 46.13 3.35
2600 2660 0.900647 AGCGCAGAGGGAGTAACTGT 60.901 55.000 11.47 0.00 34.60 3.55
2607 2667 0.036952 TCTTTCAAGCGCAGAGGGAG 60.037 55.000 11.47 6.87 0.00 4.30
2608 2668 0.036952 CTCTTTCAAGCGCAGAGGGA 60.037 55.000 11.47 8.19 31.91 4.20
2609 2669 0.321122 ACTCTTTCAAGCGCAGAGGG 60.321 55.000 21.50 9.52 38.76 4.30
2610 2670 2.370281 TACTCTTTCAAGCGCAGAGG 57.630 50.000 21.50 10.97 38.76 3.69
2611 2671 4.677584 AGTATACTCTTTCAAGCGCAGAG 58.322 43.478 17.44 17.44 40.08 3.35
2612 2672 4.720649 AGTATACTCTTTCAAGCGCAGA 57.279 40.909 11.47 3.85 0.00 4.26
2613 2673 4.268884 GGAAGTATACTCTTTCAAGCGCAG 59.731 45.833 11.47 0.72 0.00 5.18
2614 2674 4.181578 GGAAGTATACTCTTTCAAGCGCA 58.818 43.478 11.47 0.00 0.00 6.09
2615 2675 4.181578 TGGAAGTATACTCTTTCAAGCGC 58.818 43.478 5.70 0.00 30.93 5.92
2616 2676 5.869888 AGTTGGAAGTATACTCTTTCAAGCG 59.130 40.000 5.70 0.00 41.68 4.68
2617 2677 7.674471 AAGTTGGAAGTATACTCTTTCAAGC 57.326 36.000 5.70 0.00 41.68 4.01
2662 2722 9.261180 CTCTTGTATGAATACGGTCAAACATAT 57.739 33.333 0.00 0.00 36.06 1.78
2663 2723 8.255206 ACTCTTGTATGAATACGGTCAAACATA 58.745 33.333 0.00 0.00 36.06 2.29
2664 2724 7.103641 ACTCTTGTATGAATACGGTCAAACAT 58.896 34.615 0.00 0.00 36.06 2.71
2665 2725 6.460781 ACTCTTGTATGAATACGGTCAAACA 58.539 36.000 0.00 0.00 36.06 2.83
2666 2726 6.588756 TGACTCTTGTATGAATACGGTCAAAC 59.411 38.462 11.92 0.00 36.06 2.93
2667 2727 6.693466 TGACTCTTGTATGAATACGGTCAAA 58.307 36.000 11.92 0.00 36.06 2.69
2668 2728 6.275494 TGACTCTTGTATGAATACGGTCAA 57.725 37.500 11.92 0.00 36.06 3.18
2669 2729 5.907866 TGACTCTTGTATGAATACGGTCA 57.092 39.130 11.01 11.01 36.06 4.02
2670 2730 7.772332 AATTGACTCTTGTATGAATACGGTC 57.228 36.000 0.00 0.00 36.06 4.79
2671 2731 8.255206 TGTAATTGACTCTTGTATGAATACGGT 58.745 33.333 0.00 0.00 36.06 4.83
2672 2732 8.540492 GTGTAATTGACTCTTGTATGAATACGG 58.460 37.037 0.00 0.00 36.06 4.02
2673 2733 9.302345 AGTGTAATTGACTCTTGTATGAATACG 57.698 33.333 0.00 0.00 36.06 3.06
2675 2735 9.599866 CCAGTGTAATTGACTCTTGTATGAATA 57.400 33.333 0.00 0.00 29.24 1.75
2676 2736 8.103305 ACCAGTGTAATTGACTCTTGTATGAAT 58.897 33.333 0.00 0.00 28.63 2.57
2677 2737 7.387673 CACCAGTGTAATTGACTCTTGTATGAA 59.612 37.037 0.00 0.00 29.18 2.57
2678 2738 6.873605 CACCAGTGTAATTGACTCTTGTATGA 59.126 38.462 0.00 0.00 29.18 2.15
2679 2739 6.092670 CCACCAGTGTAATTGACTCTTGTATG 59.907 42.308 0.00 0.00 29.18 2.39
2680 2740 6.173339 CCACCAGTGTAATTGACTCTTGTAT 58.827 40.000 0.00 0.00 29.18 2.29
2681 2741 5.071250 ACCACCAGTGTAATTGACTCTTGTA 59.929 40.000 0.00 0.00 29.18 2.41
2682 2742 4.141482 ACCACCAGTGTAATTGACTCTTGT 60.141 41.667 0.00 0.00 29.99 3.16
2683 2743 4.214119 CACCACCAGTGTAATTGACTCTTG 59.786 45.833 0.00 0.00 41.93 3.02
2732 2792 0.875059 GCCACAACTTCTAGCACCAC 59.125 55.000 0.00 0.00 0.00 4.16
2765 2825 4.210955 CACGTTAATGCCAAGTTTTTGCAT 59.789 37.500 0.00 0.00 34.64 3.96
2848 2908 2.270257 GGTGCAATGGCTGACAGCA 61.270 57.895 27.87 14.84 44.75 4.41
2974 3042 0.987294 CTGACAGATGGGACCCACTT 59.013 55.000 17.78 0.00 35.80 3.16
2996 3070 9.631452 CTCCCTTTTGATTTAATTTTCACTCTC 57.369 33.333 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.