Multiple sequence alignment - TraesCS5D01G341300

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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 TraesCS5D01G341300 chr5D 100.000 2849 0 0 1 2849 429576380 429579228 0.000000e+00 5262.0
1 TraesCS5D01G341300 chr5D 74.502 502 100 23 1356 1840 520910185 520910675 2.900000e-45 193.0
2 TraesCS5D01G341300 chr5D 87.826 115 14 0 1726 1840 424033837 424033951 4.950000e-28 135.0
3 TraesCS5D01G341300 chr5B 92.089 2212 74 20 641 2788 518809565 518811739 0.000000e+00 3022.0
4 TraesCS5D01G341300 chr5B 81.517 211 34 5 1634 1840 656926286 656926495 4.880000e-38 169.0
5 TraesCS5D01G341300 chr5B 81.818 165 30 0 1676 1840 512213142 512213306 3.830000e-29 139.0
6 TraesCS5D01G341300 chr5A 88.402 2121 134 45 723 2797 545530311 545532365 0.000000e+00 2451.0
7 TraesCS5D01G341300 chr5A 97.436 117 3 0 619 735 545529960 545530076 1.730000e-47 200.0
8 TraesCS5D01G341300 chr5A 81.991 211 33 5 1634 1840 649441941 649442150 1.050000e-39 174.0
9 TraesCS5D01G341300 chr1D 87.322 702 72 9 1141 1838 18893906 18893218 0.000000e+00 787.0
10 TraesCS5D01G341300 chr1D 88.958 480 46 5 5 480 335999449 335999925 1.140000e-163 586.0
11 TraesCS5D01G341300 chr1D 84.055 577 73 12 1 567 437470392 437470959 3.230000e-149 538.0
12 TraesCS5D01G341300 chr1B 86.938 712 77 9 1137 1845 28025030 28024332 0.000000e+00 785.0
13 TraesCS5D01G341300 chr1A 86.517 712 80 9 1137 1845 20889597 20888899 0.000000e+00 769.0
14 TraesCS5D01G341300 chr2D 85.185 567 55 9 1 564 556707939 556707399 3.210000e-154 555.0
15 TraesCS5D01G341300 chr2D 81.326 573 95 9 1 566 629482590 629482023 3.350000e-124 455.0
16 TraesCS5D01G341300 chr2D 81.271 582 84 21 1 567 291844609 291844038 5.600000e-122 448.0
17 TraesCS5D01G341300 chr2D 80.903 576 94 12 1 566 14960777 14960208 9.370000e-120 440.0
18 TraesCS5D01G341300 chr7D 83.189 577 77 17 2 564 539129274 539129844 7.040000e-141 510.0
19 TraesCS5D01G341300 chr7D 82.143 112 14 3 1402 1513 262286127 262286232 1.090000e-14 91.6
20 TraesCS5D01G341300 chr2A 82.384 562 88 9 5 564 167394546 167395098 1.990000e-131 479.0
21 TraesCS5D01G341300 chr3A 81.882 574 82 18 6 564 59951313 59950747 5.560000e-127 464.0
22 TraesCS5D01G341300 chr7B 83.019 106 12 3 1408 1513 241757693 241757594 1.090000e-14 91.6


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 TraesCS5D01G341300 chr5D 429576380 429579228 2848 False 5262.0 5262 100.000 1 2849 1 chr5D.!!$F2 2848
1 TraesCS5D01G341300 chr5B 518809565 518811739 2174 False 3022.0 3022 92.089 641 2788 1 chr5B.!!$F2 2147
2 TraesCS5D01G341300 chr5A 545529960 545532365 2405 False 1325.5 2451 92.919 619 2797 2 chr5A.!!$F2 2178
3 TraesCS5D01G341300 chr1D 18893218 18893906 688 True 787.0 787 87.322 1141 1838 1 chr1D.!!$R1 697
4 TraesCS5D01G341300 chr1D 437470392 437470959 567 False 538.0 538 84.055 1 567 1 chr1D.!!$F2 566
5 TraesCS5D01G341300 chr1B 28024332 28025030 698 True 785.0 785 86.938 1137 1845 1 chr1B.!!$R1 708
6 TraesCS5D01G341300 chr1A 20888899 20889597 698 True 769.0 769 86.517 1137 1845 1 chr1A.!!$R1 708
7 TraesCS5D01G341300 chr2D 556707399 556707939 540 True 555.0 555 85.185 1 564 1 chr2D.!!$R3 563
8 TraesCS5D01G341300 chr2D 629482023 629482590 567 True 455.0 455 81.326 1 566 1 chr2D.!!$R4 565
9 TraesCS5D01G341300 chr2D 291844038 291844609 571 True 448.0 448 81.271 1 567 1 chr2D.!!$R2 566
10 TraesCS5D01G341300 chr2D 14960208 14960777 569 True 440.0 440 80.903 1 566 1 chr2D.!!$R1 565
11 TraesCS5D01G341300 chr7D 539129274 539129844 570 False 510.0 510 83.189 2 564 1 chr7D.!!$F2 562
12 TraesCS5D01G341300 chr2A 167394546 167395098 552 False 479.0 479 82.384 5 564 1 chr2A.!!$F1 559
13 TraesCS5D01G341300 chr3A 59950747 59951313 566 True 464.0 464 81.882 6 564 1 chr3A.!!$R1 558

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
29 30 0.178964 CCCTCAAGTGGGCAAAGGAA 60.179 55.0 0.00 0.0 40.84 3.36 F
587 624 0.313987 TCGCATGTGTCTATAGCCGG 59.686 55.0 6.09 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1823 0.846427 TGGAGAGGGGCAGGTTGAAT 60.846 55.000 0.0 0.0 0.0 2.57 R
2568 2940 2.125512 CGGACACCCTAGCACTGC 60.126 66.667 0.0 0.0 0.0 4.40 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 30 0.178964 CCCTCAAGTGGGCAAAGGAA 60.179 55.000 0.00 0.00 40.84 3.36
32 33 2.556114 CCTCAAGTGGGCAAAGGAAGAT 60.556 50.000 0.00 0.00 0.00 2.40
210 216 4.687215 GCTGCAGCAGGGACGACA 62.687 66.667 33.36 0.00 41.59 4.35
275 287 2.089980 GACTACACCCGCTTCTACAGA 58.910 52.381 0.00 0.00 0.00 3.41
325 349 2.108157 CGGGCGCAATGGCTAGTA 59.892 61.111 10.83 0.00 44.11 1.82
332 362 3.243636 GGCGCAATGGCTAGTAGTAGTAA 60.244 47.826 10.83 0.00 40.72 2.24
396 429 4.116747 TGAAATTTCGCCAAGTTTGTGT 57.883 36.364 13.34 0.00 0.00 3.72
407 440 3.490761 CCAAGTTTGTGTCAAAATCGCCT 60.491 43.478 0.00 0.00 0.00 5.52
463 497 3.388841 GGTGACCTGTGGACCGAT 58.611 61.111 0.00 0.00 0.00 4.18
467 501 1.218316 GACCTGTGGACCGATGACC 59.782 63.158 0.00 0.00 0.00 4.02
496 530 0.822121 GTCGTTCCCAAAGGCCAGTT 60.822 55.000 5.01 0.00 0.00 3.16
542 579 1.230497 TTTTTCAACGCCCTGGGGA 59.770 52.632 16.03 0.00 37.50 4.81
567 604 2.354259 ACAGCTGCAGATGCTCTAAAC 58.646 47.619 30.85 2.01 42.66 2.01
568 605 2.027377 ACAGCTGCAGATGCTCTAAACT 60.027 45.455 30.85 6.76 42.66 2.66
569 606 2.608546 CAGCTGCAGATGCTCTAAACTC 59.391 50.000 20.45 0.00 42.66 3.01
570 607 1.592081 GCTGCAGATGCTCTAAACTCG 59.408 52.381 20.43 0.00 42.66 4.18
571 608 1.592081 CTGCAGATGCTCTAAACTCGC 59.408 52.381 8.42 0.00 42.66 5.03
572 609 1.066929 TGCAGATGCTCTAAACTCGCA 60.067 47.619 6.35 0.00 42.66 5.10
573 610 2.208431 GCAGATGCTCTAAACTCGCAT 58.792 47.619 0.00 0.00 46.15 4.73
574 611 2.033065 GCAGATGCTCTAAACTCGCATG 60.033 50.000 0.22 0.00 43.77 4.06
575 612 3.193263 CAGATGCTCTAAACTCGCATGT 58.807 45.455 0.22 0.00 43.77 3.21
576 613 3.001026 CAGATGCTCTAAACTCGCATGTG 59.999 47.826 0.00 0.00 44.94 3.21
577 614 2.455674 TGCTCTAAACTCGCATGTGT 57.544 45.000 6.09 0.00 0.00 3.72
578 615 2.337583 TGCTCTAAACTCGCATGTGTC 58.662 47.619 6.09 0.00 0.00 3.67
579 616 2.029020 TGCTCTAAACTCGCATGTGTCT 60.029 45.455 6.09 0.00 0.00 3.41
580 617 3.192633 TGCTCTAAACTCGCATGTGTCTA 59.807 43.478 6.09 0.00 0.00 2.59
581 618 4.142160 TGCTCTAAACTCGCATGTGTCTAT 60.142 41.667 6.09 0.00 0.00 1.98
582 619 5.067283 TGCTCTAAACTCGCATGTGTCTATA 59.933 40.000 6.09 0.00 0.00 1.31
583 620 5.627367 GCTCTAAACTCGCATGTGTCTATAG 59.373 44.000 6.09 5.99 0.00 1.31
584 621 5.520632 TCTAAACTCGCATGTGTCTATAGC 58.479 41.667 6.09 0.00 0.00 2.97
585 622 2.802787 ACTCGCATGTGTCTATAGCC 57.197 50.000 6.09 0.00 0.00 3.93
586 623 1.001268 ACTCGCATGTGTCTATAGCCG 60.001 52.381 6.09 0.00 0.00 5.52
587 624 0.313987 TCGCATGTGTCTATAGCCGG 59.686 55.000 6.09 0.00 0.00 6.13
588 625 1.284982 CGCATGTGTCTATAGCCGGC 61.285 60.000 21.89 21.89 0.00 6.13
589 626 1.284982 GCATGTGTCTATAGCCGGCG 61.285 60.000 23.20 6.78 0.00 6.46
590 627 1.006102 ATGTGTCTATAGCCGGCGC 60.006 57.895 23.20 0.00 0.00 6.53
591 628 1.744320 ATGTGTCTATAGCCGGCGCA 61.744 55.000 23.20 14.18 37.52 6.09
592 629 1.661821 GTGTCTATAGCCGGCGCAG 60.662 63.158 23.20 18.99 37.52 5.18
611 648 3.112709 GGAACGCGCCACTCTGTC 61.113 66.667 5.73 0.00 0.00 3.51
612 649 2.049063 GAACGCGCCACTCTGTCT 60.049 61.111 5.73 0.00 0.00 3.41
613 650 1.211969 GAACGCGCCACTCTGTCTA 59.788 57.895 5.73 0.00 0.00 2.59
614 651 0.798771 GAACGCGCCACTCTGTCTAG 60.799 60.000 5.73 0.00 0.00 2.43
615 652 2.580867 CGCGCCACTCTGTCTAGC 60.581 66.667 0.00 0.00 0.00 3.42
616 653 2.573869 GCGCCACTCTGTCTAGCA 59.426 61.111 0.00 0.00 0.00 3.49
617 654 1.518133 GCGCCACTCTGTCTAGCAG 60.518 63.158 0.00 7.59 46.34 4.24
721 758 9.744468 AAATAACACTCGCAAAAGAAGTAAATT 57.256 25.926 0.00 0.00 0.00 1.82
762 1045 7.486802 AAAATGCAATTCAGTTTTTCTCCTG 57.513 32.000 0.00 0.00 39.65 3.86
800 1083 6.183361 CCCTATCACCTATCCCGTCTATCTAT 60.183 46.154 0.00 0.00 0.00 1.98
855 1138 1.078709 GTGCGTGCATGACATGTACT 58.921 50.000 27.17 0.00 44.75 2.73
856 1139 1.061131 GTGCGTGCATGACATGTACTC 59.939 52.381 27.17 22.17 44.75 2.59
857 1140 1.337635 TGCGTGCATGACATGTACTCA 60.338 47.619 27.17 24.10 42.68 3.41
858 1141 1.061131 GCGTGCATGACATGTACTCAC 59.939 52.381 27.17 19.32 42.68 3.51
928 1212 5.685728 ACGAGATAGATGGATGGATCGATA 58.314 41.667 0.00 0.00 33.43 2.92
983 1303 1.376037 CTGTGACCGGCCTTCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
1010 1330 2.615240 CCAACCGACTGATGATGTCCAA 60.615 50.000 0.00 0.00 0.00 3.53
1181 1504 3.334751 CTTCCACAACGCGTGCGA 61.335 61.111 22.32 2.71 44.91 5.10
1449 1772 2.895680 GCTGAGATCACCCTCGCA 59.104 61.111 0.00 0.00 35.99 5.10
1500 1823 3.429141 GTCAGCCTCGTCGACGGA 61.429 66.667 35.05 21.95 40.29 4.69
2066 2423 7.125963 TCCATCAAATTCATTTTGGGATGATCA 59.874 33.333 0.00 0.00 44.07 2.92
2103 2460 7.875971 AGAAATTGTCTGACAACTACATTTCC 58.124 34.615 26.76 16.91 41.40 3.13
2110 2467 6.039382 GTCTGACAACTACATTTCCCAGTTTT 59.961 38.462 2.24 0.00 30.20 2.43
2146 2503 3.558033 TCGTAAATCCATTTTAGCCCCC 58.442 45.455 0.00 0.00 30.46 5.40
2268 2637 1.291877 GCCATATCCCGTCGTGCATC 61.292 60.000 0.00 0.00 0.00 3.91
2269 2638 0.670546 CCATATCCCGTCGTGCATCC 60.671 60.000 0.00 0.00 0.00 3.51
2270 2639 0.670546 CATATCCCGTCGTGCATCCC 60.671 60.000 0.00 0.00 0.00 3.85
2271 2640 2.154798 ATATCCCGTCGTGCATCCCG 62.155 60.000 0.00 0.00 0.00 5.14
2275 2644 4.771356 CGTCGTGCATCCCGTCGT 62.771 66.667 6.67 0.00 33.44 4.34
2276 2645 3.179265 GTCGTGCATCCCGTCGTG 61.179 66.667 0.00 0.00 0.00 4.35
2319 2688 2.031314 CCACAGTAAGCTGCGATGAATG 59.969 50.000 0.00 0.00 46.30 2.67
2419 2791 3.127352 GAGGTAGCAGGAGGACGCG 62.127 68.421 3.53 3.53 0.00 6.01
2423 2795 1.094073 GTAGCAGGAGGACGCGACTA 61.094 60.000 15.93 0.00 31.88 2.59
2482 2854 1.446966 GAGACGAGGAAGCAGGCAC 60.447 63.158 0.00 0.00 0.00 5.01
2651 3023 6.324561 GGAAGATCATCTTTCCATAAAGGC 57.675 41.667 0.16 0.00 42.09 4.35
2664 3036 1.061546 TAAAGGCGAGGGAAGTTGGT 58.938 50.000 0.00 0.00 0.00 3.67
2689 3061 4.625311 GGCAATTACACATGCTTTGGTAAC 59.375 41.667 0.00 0.00 42.20 2.50
2733 3106 0.709992 TGGGGGCTATTTTTGGCTCT 59.290 50.000 0.00 0.00 0.00 4.09
2734 3107 1.341976 TGGGGGCTATTTTTGGCTCTC 60.342 52.381 0.00 0.00 0.00 3.20
2736 3109 1.025041 GGGCTATTTTTGGCTCTCCG 58.975 55.000 0.00 0.00 34.14 4.63
2802 3184 5.984627 TGATGTCATTAGTTTGTGTTGACG 58.015 37.500 0.00 0.00 39.58 4.35
2803 3185 5.525745 TGATGTCATTAGTTTGTGTTGACGT 59.474 36.000 0.00 0.00 39.58 4.34
2804 3186 6.702282 TGATGTCATTAGTTTGTGTTGACGTA 59.298 34.615 0.00 0.00 39.58 3.57
2805 3187 7.386573 TGATGTCATTAGTTTGTGTTGACGTAT 59.613 33.333 0.00 0.00 39.58 3.06
2806 3188 8.766000 ATGTCATTAGTTTGTGTTGACGTATA 57.234 30.769 0.00 0.00 39.58 1.47
2807 3189 8.590719 TGTCATTAGTTTGTGTTGACGTATAA 57.409 30.769 0.00 0.00 39.58 0.98
2808 3190 9.043079 TGTCATTAGTTTGTGTTGACGTATAAA 57.957 29.630 0.00 0.00 39.58 1.40
2811 3193 8.785101 CATTAGTTTGTGTTGACGTATAAATGC 58.215 33.333 0.00 0.00 0.00 3.56
2812 3194 6.307031 AGTTTGTGTTGACGTATAAATGCA 57.693 33.333 0.00 0.00 0.00 3.96
2813 3195 6.908825 AGTTTGTGTTGACGTATAAATGCAT 58.091 32.000 0.00 0.00 0.00 3.96
2814 3196 8.035165 AGTTTGTGTTGACGTATAAATGCATA 57.965 30.769 0.00 0.00 0.00 3.14
2815 3197 8.508062 AGTTTGTGTTGACGTATAAATGCATAA 58.492 29.630 0.00 0.00 0.00 1.90
2816 3198 9.284594 GTTTGTGTTGACGTATAAATGCATAAT 57.715 29.630 0.00 0.00 0.00 1.28
2817 3199 9.497030 TTTGTGTTGACGTATAAATGCATAATC 57.503 29.630 0.00 0.00 0.00 1.75
2818 3200 7.635423 TGTGTTGACGTATAAATGCATAATCC 58.365 34.615 0.00 0.00 0.00 3.01
2819 3201 7.281100 TGTGTTGACGTATAAATGCATAATCCA 59.719 33.333 0.00 0.00 0.00 3.41
2820 3202 7.586300 GTGTTGACGTATAAATGCATAATCCAC 59.414 37.037 0.00 0.00 0.00 4.02
2821 3203 7.281100 TGTTGACGTATAAATGCATAATCCACA 59.719 33.333 0.00 0.00 0.00 4.17
2822 3204 7.977789 TGACGTATAAATGCATAATCCACAT 57.022 32.000 0.00 0.00 0.00 3.21
2823 3205 8.389779 TGACGTATAAATGCATAATCCACATT 57.610 30.769 0.00 0.00 35.59 2.71
2824 3206 8.845227 TGACGTATAAATGCATAATCCACATTT 58.155 29.630 0.00 5.62 44.09 2.32
2825 3207 9.329913 GACGTATAAATGCATAATCCACATTTC 57.670 33.333 0.00 0.00 41.70 2.17
2826 3208 8.296713 ACGTATAAATGCATAATCCACATTTCC 58.703 33.333 0.00 0.00 41.70 3.13
2827 3209 8.514594 CGTATAAATGCATAATCCACATTTCCT 58.485 33.333 0.00 0.00 41.70 3.36
2828 3210 9.846248 GTATAAATGCATAATCCACATTTCCTC 57.154 33.333 0.00 0.00 41.70 3.71
2829 3211 6.795144 AAATGCATAATCCACATTTCCTCA 57.205 33.333 0.00 0.00 39.20 3.86
2830 3212 6.989155 AATGCATAATCCACATTTCCTCAT 57.011 33.333 0.00 0.00 29.94 2.90
2831 3213 6.585695 ATGCATAATCCACATTTCCTCATC 57.414 37.500 0.00 0.00 0.00 2.92
2832 3214 5.447757 TGCATAATCCACATTTCCTCATCA 58.552 37.500 0.00 0.00 0.00 3.07
2833 3215 5.892686 TGCATAATCCACATTTCCTCATCAA 59.107 36.000 0.00 0.00 0.00 2.57
2834 3216 6.183360 TGCATAATCCACATTTCCTCATCAAC 60.183 38.462 0.00 0.00 0.00 3.18
2835 3217 6.040166 GCATAATCCACATTTCCTCATCAACT 59.960 38.462 0.00 0.00 0.00 3.16
2836 3218 7.417116 GCATAATCCACATTTCCTCATCAACTT 60.417 37.037 0.00 0.00 0.00 2.66
2837 3219 6.521151 AATCCACATTTCCTCATCAACTTC 57.479 37.500 0.00 0.00 0.00 3.01
2838 3220 4.984295 TCCACATTTCCTCATCAACTTCA 58.016 39.130 0.00 0.00 0.00 3.02
2839 3221 5.005740 TCCACATTTCCTCATCAACTTCAG 58.994 41.667 0.00 0.00 0.00 3.02
2840 3222 4.380233 CCACATTTCCTCATCAACTTCAGC 60.380 45.833 0.00 0.00 0.00 4.26
2841 3223 4.458295 CACATTTCCTCATCAACTTCAGCT 59.542 41.667 0.00 0.00 0.00 4.24
2842 3224 5.048224 CACATTTCCTCATCAACTTCAGCTT 60.048 40.000 0.00 0.00 0.00 3.74
2843 3225 5.537674 ACATTTCCTCATCAACTTCAGCTTT 59.462 36.000 0.00 0.00 0.00 3.51
2844 3226 6.041296 ACATTTCCTCATCAACTTCAGCTTTT 59.959 34.615 0.00 0.00 0.00 2.27
2845 3227 5.443185 TTCCTCATCAACTTCAGCTTTTG 57.557 39.130 0.00 0.00 0.00 2.44
2846 3228 3.822735 TCCTCATCAACTTCAGCTTTTGG 59.177 43.478 0.00 0.00 0.00 3.28
2847 3229 3.057033 CCTCATCAACTTCAGCTTTTGGG 60.057 47.826 0.00 0.00 0.00 4.12
2848 3230 3.565307 TCATCAACTTCAGCTTTTGGGT 58.435 40.909 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.750350 CCACTTGAGGGCGGACTT 59.250 61.111 0.00 0.00 0.00 3.01
23 24 1.203052 TCGCGGACGTAATCTTCCTTT 59.797 47.619 6.13 0.00 41.18 3.11
29 30 1.064296 CTGCTCGCGGACGTAATCT 59.936 57.895 6.13 0.00 41.18 2.40
32 33 3.367743 ACCTGCTCGCGGACGTAA 61.368 61.111 6.13 0.00 41.18 3.18
275 287 1.202580 GCCATCTACATGCCGAGAAGT 60.203 52.381 0.00 0.00 0.00 3.01
316 330 5.619220 ACTACGCTTACTACTACTAGCCAT 58.381 41.667 0.00 0.00 0.00 4.40
324 348 5.957798 ACATGCAAACTACGCTTACTACTA 58.042 37.500 0.00 0.00 0.00 1.82
325 349 4.817517 ACATGCAAACTACGCTTACTACT 58.182 39.130 0.00 0.00 0.00 2.57
332 362 5.768317 ACATAAAAACATGCAAACTACGCT 58.232 33.333 0.00 0.00 0.00 5.07
396 429 4.782019 ATTGCAAACTAGGCGATTTTGA 57.218 36.364 13.18 0.00 31.29 2.69
463 497 2.646719 CGACTTCGTTCCCGGTCA 59.353 61.111 0.00 0.00 33.95 4.02
481 515 1.627864 GCTAAACTGGCCTTTGGGAA 58.372 50.000 3.32 0.00 33.58 3.97
482 516 0.608035 CGCTAAACTGGCCTTTGGGA 60.608 55.000 3.32 0.00 33.58 4.37
496 530 2.188469 GGGATGAACCGGCGCTAA 59.812 61.111 7.64 0.00 40.11 3.09
542 579 2.037136 GCATCTGCAGCTGTTCGGT 61.037 57.895 18.20 0.00 41.59 4.69
567 604 1.667177 CCGGCTATAGACACATGCGAG 60.667 57.143 6.37 0.00 0.00 5.03
568 605 0.313987 CCGGCTATAGACACATGCGA 59.686 55.000 6.37 0.00 0.00 5.10
569 606 1.284982 GCCGGCTATAGACACATGCG 61.285 60.000 22.15 0.00 0.00 4.73
570 607 1.284982 CGCCGGCTATAGACACATGC 61.285 60.000 26.68 1.51 0.00 4.06
571 608 1.284982 GCGCCGGCTATAGACACATG 61.285 60.000 26.68 4.89 35.83 3.21
572 609 1.006102 GCGCCGGCTATAGACACAT 60.006 57.895 26.68 0.00 35.83 3.21
573 610 2.349969 CTGCGCCGGCTATAGACACA 62.350 60.000 26.68 8.32 40.82 3.72
574 611 1.661821 CTGCGCCGGCTATAGACAC 60.662 63.158 26.68 3.83 40.82 3.67
575 612 2.728180 CTGCGCCGGCTATAGACA 59.272 61.111 26.68 11.51 40.82 3.41
576 613 2.735100 GCTGCGCCGGCTATAGAC 60.735 66.667 26.68 11.52 40.82 2.59
577 614 4.342987 CGCTGCGCCGGCTATAGA 62.343 66.667 26.68 2.01 40.82 1.98
594 631 2.209064 TAGACAGAGTGGCGCGTTCC 62.209 60.000 8.43 0.88 0.00 3.62
595 632 0.798771 CTAGACAGAGTGGCGCGTTC 60.799 60.000 8.43 0.58 0.00 3.95
596 633 1.213013 CTAGACAGAGTGGCGCGTT 59.787 57.895 8.43 0.00 0.00 4.84
597 634 2.878429 CTAGACAGAGTGGCGCGT 59.122 61.111 8.43 0.00 0.00 6.01
598 635 2.580867 GCTAGACAGAGTGGCGCG 60.581 66.667 0.00 0.00 0.00 6.86
599 636 2.573869 TGCTAGACAGAGTGGCGC 59.426 61.111 0.00 0.00 0.00 6.53
605 642 8.522003 ATGTTCATCATATACTGCTAGACAGAG 58.478 37.037 17.52 0.26 41.01 3.35
606 643 8.414629 ATGTTCATCATATACTGCTAGACAGA 57.585 34.615 17.52 5.44 41.01 3.41
609 646 9.526713 CCATATGTTCATCATATACTGCTAGAC 57.473 37.037 1.24 0.00 44.90 2.59
610 647 9.479549 TCCATATGTTCATCATATACTGCTAGA 57.520 33.333 1.24 0.00 44.90 2.43
613 650 7.498239 GCATCCATATGTTCATCATATACTGCT 59.502 37.037 1.24 0.00 44.90 4.24
614 651 7.281549 TGCATCCATATGTTCATCATATACTGC 59.718 37.037 1.24 14.36 44.90 4.40
615 652 8.726870 TGCATCCATATGTTCATCATATACTG 57.273 34.615 1.24 1.70 44.90 2.74
616 653 7.498239 GCTGCATCCATATGTTCATCATATACT 59.502 37.037 1.24 0.00 44.90 2.12
617 654 7.498239 AGCTGCATCCATATGTTCATCATATAC 59.502 37.037 1.02 0.00 44.90 1.47
721 758 8.908786 TTGCATTTTTGGTGTGGAATTTATTA 57.091 26.923 0.00 0.00 0.00 0.98
800 1083 3.196300 ACCACAGGAGTAGGTAGGTAGA 58.804 50.000 0.00 0.00 32.92 2.59
855 1138 1.192146 AGAAGCAAGTAGGGGCGTGA 61.192 55.000 0.00 0.00 34.54 4.35
856 1139 0.321653 AAGAAGCAAGTAGGGGCGTG 60.322 55.000 0.00 0.00 34.54 5.34
857 1140 0.321653 CAAGAAGCAAGTAGGGGCGT 60.322 55.000 0.00 0.00 34.54 5.68
858 1141 0.321653 ACAAGAAGCAAGTAGGGGCG 60.322 55.000 0.00 0.00 34.54 6.13
928 1212 4.043037 GGTAGAACACCTCGATCGATTT 57.957 45.455 19.78 9.50 44.79 2.17
952 1272 1.082690 GTCACAGGAAGCAGCTAAGC 58.917 55.000 0.00 0.00 0.00 3.09
983 1303 0.458543 CATCAGTCGGTTGGAGACGG 60.459 60.000 0.00 0.00 42.97 4.79
1500 1823 0.846427 TGGAGAGGGGCAGGTTGAAT 60.846 55.000 0.00 0.00 0.00 2.57
1528 1851 2.265182 CGCCGTCCCCATTGTTGTT 61.265 57.895 0.00 0.00 0.00 2.83
2146 2503 7.201504 GCCACGATGATCACATTATGAGATTAG 60.202 40.741 6.59 2.62 41.91 1.73
2269 2638 4.428922 CACGCACATGCACGACGG 62.429 66.667 14.19 0.99 42.21 4.79
2319 2688 2.719354 GACAACGCCACCAACACC 59.281 61.111 0.00 0.00 0.00 4.16
2358 2727 2.943680 ATCACTCGGCATCGTCGCTG 62.944 60.000 1.82 1.82 39.79 5.18
2568 2940 2.125512 CGGACACCCTAGCACTGC 60.126 66.667 0.00 0.00 0.00 4.40
2651 3023 2.359975 GCCCACCAACTTCCCTCG 60.360 66.667 0.00 0.00 0.00 4.63
2664 3036 2.028294 CCAAAGCATGTGTAATTGCCCA 60.028 45.455 0.00 0.00 39.72 5.36
2693 3066 6.666113 CCCCAATAACTATTGTTAACCCAGTT 59.334 38.462 16.21 16.21 41.36 3.16
2706 3079 5.306937 GCCAAAAATAGCCCCCAATAACTAT 59.693 40.000 0.00 0.00 0.00 2.12
2712 3085 2.118679 GAGCCAAAAATAGCCCCCAAT 58.881 47.619 0.00 0.00 0.00 3.16
2733 3106 2.935505 GTGTGGCACCATTTACGGA 58.064 52.632 16.26 0.00 0.00 4.69
2790 3172 8.662369 TTATGCATTTATACGTCAACACAAAC 57.338 30.769 3.54 0.00 0.00 2.93
2791 3173 9.497030 GATTATGCATTTATACGTCAACACAAA 57.503 29.630 3.54 0.00 0.00 2.83
2797 3179 7.793927 TGTGGATTATGCATTTATACGTCAA 57.206 32.000 3.54 0.00 0.00 3.18
2798 3180 7.977789 ATGTGGATTATGCATTTATACGTCA 57.022 32.000 3.54 4.51 0.00 4.35
2799 3181 9.329913 GAAATGTGGATTATGCATTTATACGTC 57.670 33.333 3.54 0.00 41.24 4.34
2800 3182 8.296713 GGAAATGTGGATTATGCATTTATACGT 58.703 33.333 3.54 0.00 41.24 3.57
2801 3183 8.514594 AGGAAATGTGGATTATGCATTTATACG 58.485 33.333 3.54 0.00 41.24 3.06
2802 3184 9.846248 GAGGAAATGTGGATTATGCATTTATAC 57.154 33.333 3.54 0.20 41.24 1.47
2803 3185 9.585369 TGAGGAAATGTGGATTATGCATTTATA 57.415 29.630 3.54 0.00 41.24 0.98
2804 3186 8.481492 TGAGGAAATGTGGATTATGCATTTAT 57.519 30.769 3.54 0.00 41.24 1.40
2805 3187 7.894753 TGAGGAAATGTGGATTATGCATTTA 57.105 32.000 3.54 0.00 41.24 1.40
2806 3188 6.795144 TGAGGAAATGTGGATTATGCATTT 57.205 33.333 3.54 0.00 43.06 2.32
2807 3189 6.551975 TGATGAGGAAATGTGGATTATGCATT 59.448 34.615 3.54 0.00 34.69 3.56
2808 3190 6.072649 TGATGAGGAAATGTGGATTATGCAT 58.927 36.000 3.79 3.79 0.00 3.96
2809 3191 5.447757 TGATGAGGAAATGTGGATTATGCA 58.552 37.500 0.00 0.00 0.00 3.96
2810 3192 6.040166 AGTTGATGAGGAAATGTGGATTATGC 59.960 38.462 0.00 0.00 0.00 3.14
2811 3193 7.578310 AGTTGATGAGGAAATGTGGATTATG 57.422 36.000 0.00 0.00 0.00 1.90
2812 3194 7.835682 TGAAGTTGATGAGGAAATGTGGATTAT 59.164 33.333 0.00 0.00 0.00 1.28
2813 3195 7.174413 TGAAGTTGATGAGGAAATGTGGATTA 58.826 34.615 0.00 0.00 0.00 1.75
2814 3196 6.012113 TGAAGTTGATGAGGAAATGTGGATT 58.988 36.000 0.00 0.00 0.00 3.01
2815 3197 5.573219 TGAAGTTGATGAGGAAATGTGGAT 58.427 37.500 0.00 0.00 0.00 3.41
2816 3198 4.984295 TGAAGTTGATGAGGAAATGTGGA 58.016 39.130 0.00 0.00 0.00 4.02
2817 3199 4.380233 GCTGAAGTTGATGAGGAAATGTGG 60.380 45.833 0.00 0.00 0.00 4.17
2818 3200 4.458295 AGCTGAAGTTGATGAGGAAATGTG 59.542 41.667 0.00 0.00 0.00 3.21
2819 3201 4.660168 AGCTGAAGTTGATGAGGAAATGT 58.340 39.130 0.00 0.00 0.00 2.71
2820 3202 5.640189 AAGCTGAAGTTGATGAGGAAATG 57.360 39.130 0.00 0.00 0.00 2.32
2821 3203 6.453092 CAAAAGCTGAAGTTGATGAGGAAAT 58.547 36.000 0.00 0.00 0.00 2.17
2822 3204 5.221303 CCAAAAGCTGAAGTTGATGAGGAAA 60.221 40.000 0.00 0.00 0.00 3.13
2823 3205 4.279169 CCAAAAGCTGAAGTTGATGAGGAA 59.721 41.667 0.00 0.00 0.00 3.36
2824 3206 3.822735 CCAAAAGCTGAAGTTGATGAGGA 59.177 43.478 0.00 0.00 0.00 3.71
2825 3207 3.057033 CCCAAAAGCTGAAGTTGATGAGG 60.057 47.826 0.00 0.00 0.00 3.86
2826 3208 3.571401 ACCCAAAAGCTGAAGTTGATGAG 59.429 43.478 0.00 0.00 0.00 2.90
2827 3209 3.565307 ACCCAAAAGCTGAAGTTGATGA 58.435 40.909 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.