Multiple sequence alignment - TraesCS3B01G242000

Loading Multiple Alignment...

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 TraesCS3B01G242000 chr3B 100.000 3447 0 0 1 3447 381844469 381841023 0.000000e+00 6366.0
1 TraesCS3B01G242000 chr3B 93.875 702 31 6 1 692 763525857 763525158 0.000000e+00 1048.0
2 TraesCS3B01G242000 chr3B 94.481 308 7 3 393 691 381849225 381848919 1.870000e-127 466.0
3 TraesCS3B01G242000 chr3B 90.096 313 17 8 391 691 763530596 763530286 8.970000e-106 394.0
4 TraesCS3B01G242000 chr3D 97.591 2325 28 7 763 3085 289185686 289183388 0.000000e+00 3958.0
5 TraesCS3B01G242000 chr3D 98.165 327 5 1 3119 3444 289183387 289183061 1.390000e-158 569.0
6 TraesCS3B01G242000 chr3D 80.804 224 31 8 3231 3444 148592509 148592288 7.650000e-37 165.0
7 TraesCS3B01G242000 chr3A 95.185 2222 58 17 813 3008 380068489 380066291 0.000000e+00 3465.0
8 TraesCS3B01G242000 chr3A 92.804 403 17 2 3043 3444 380066298 380065907 1.070000e-159 573.0
9 TraesCS3B01G242000 chr3A 85.965 171 16 7 3233 3399 460160931 460161097 3.540000e-40 176.0
10 TraesCS3B01G242000 chr7D 91.750 703 41 10 1 692 603745344 603744648 0.000000e+00 961.0
11 TraesCS3B01G242000 chr1A 89.474 703 56 12 1 691 494375695 494376391 0.000000e+00 872.0
12 TraesCS3B01G242000 chr1A 87.686 471 48 9 3 470 97813419 97812956 1.090000e-149 540.0
13 TraesCS3B01G242000 chr1A 84.740 308 33 9 394 691 494354008 494354311 2.600000e-76 296.0
14 TraesCS3B01G242000 chr2A 89.078 705 58 12 1 691 419659117 419659816 0.000000e+00 857.0
15 TraesCS3B01G242000 chr2A 84.922 703 76 18 9 691 34339537 34338845 0.000000e+00 684.0
16 TraesCS3B01G242000 chr2A 84.593 701 82 17 9 691 34352925 34352233 0.000000e+00 673.0
17 TraesCS3B01G242000 chr2A 84.451 701 82 17 9 691 34366614 34365923 0.000000e+00 665.0
18 TraesCS3B01G242000 chr2A 80.449 312 38 16 394 691 34383865 34383563 2.080000e-52 217.0
19 TraesCS3B01G242000 chr5B 85.331 709 77 20 3 691 95014282 95014983 0.000000e+00 708.0
20 TraesCS3B01G242000 chr5B 83.200 125 13 6 574 691 94983529 94983652 1.310000e-19 108.0
21 TraesCS3B01G242000 chr6D 83.851 161 20 5 3277 3433 352300669 352300827 7.710000e-32 148.0
22 TraesCS3B01G242000 chrUn 79.812 213 30 11 3231 3433 313152302 313152511 3.590000e-30 143.0
23 TraesCS3B01G242000 chr4D 83.230 161 21 5 3277 3433 164468394 164468236 3.590000e-30 143.0
24 TraesCS3B01G242000 chr4A 79.452 219 30 13 3234 3444 308709185 308709396 1.290000e-29 141.0
25 TraesCS3B01G242000 chr4A 79.039 229 29 16 3231 3447 308716572 308716793 4.640000e-29 139.0
26 TraesCS3B01G242000 chr4A 82.143 112 18 2 3048 3158 649540330 649540220 1.020000e-15 95.3
27 TraesCS3B01G242000 chr4A 74.595 185 46 1 3046 3230 549130999 549131182 2.850000e-11 80.5
28 TraesCS3B01G242000 chr7B 82.022 89 16 0 3049 3137 219044097 219044185 3.690000e-10 76.8
29 TraesCS3B01G242000 chr7B 73.786 206 48 3 3028 3233 350783787 350783588 3.690000e-10 76.8
30 TraesCS3B01G242000 chr6B 91.228 57 4 1 3046 3102 493785274 493785329 3.690000e-10 76.8


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 TraesCS3B01G242000 chr3B 381841023 381844469 3446 True 6366.0 6366 100.0000 1 3447 1 chr3B.!!$R1 3446
1 TraesCS3B01G242000 chr3B 763525158 763525857 699 True 1048.0 1048 93.8750 1 692 1 chr3B.!!$R3 691
2 TraesCS3B01G242000 chr3D 289183061 289185686 2625 True 2263.5 3958 97.8780 763 3444 2 chr3D.!!$R2 2681
3 TraesCS3B01G242000 chr3A 380065907 380068489 2582 True 2019.0 3465 93.9945 813 3444 2 chr3A.!!$R1 2631
4 TraesCS3B01G242000 chr7D 603744648 603745344 696 True 961.0 961 91.7500 1 692 1 chr7D.!!$R1 691
5 TraesCS3B01G242000 chr1A 494375695 494376391 696 False 872.0 872 89.4740 1 691 1 chr1A.!!$F2 690
6 TraesCS3B01G242000 chr2A 419659117 419659816 699 False 857.0 857 89.0780 1 691 1 chr2A.!!$F1 690
7 TraesCS3B01G242000 chr2A 34338845 34339537 692 True 684.0 684 84.9220 9 691 1 chr2A.!!$R1 682
8 TraesCS3B01G242000 chr2A 34352233 34352925 692 True 673.0 673 84.5930 9 691 1 chr2A.!!$R2 682
9 TraesCS3B01G242000 chr2A 34365923 34366614 691 True 665.0 665 84.4510 9 691 1 chr2A.!!$R3 682
10 TraesCS3B01G242000 chr5B 95014282 95014983 701 False 708.0 708 85.3310 3 691 1 chr5B.!!$F2 688

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
461 472 0.108567 GTGAGGAAGGAGAACGAGGC 60.109 60.0 0.00 0.0 0.0 4.70 F
744 768 0.229247 CAAAAACGCCGACGACGTAA 59.771 50.0 10.19 0.0 44.3 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1778 2.026641 CCAGGGTACATTTCCATGCAG 58.973 52.381 0.0 0.0 35.72 4.41 R
2487 2536 3.614616 CAGAGAAAATACTGGCACTCGAC 59.385 47.826 0.0 0.0 0.00 4.20 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
77 78 2.184322 GGTGCTTGATCTCGGCGA 59.816 61.111 10.14 10.14 0.00 5.54
97 98 0.830444 AGACCTGGTCGTTGTAGGCA 60.830 55.000 20.49 0.00 37.67 4.75
283 284 4.460683 CGATCGAACCCCGGGCAA 62.461 66.667 17.73 0.00 39.14 4.52
418 424 3.788145 CCCGGCGGTGGATTGGTA 61.788 66.667 26.32 0.00 0.00 3.25
420 426 2.895372 CGGCGGTGGATTGGTAGC 60.895 66.667 0.00 0.00 0.00 3.58
421 427 2.516225 GGCGGTGGATTGGTAGCC 60.516 66.667 0.00 0.00 37.61 3.93
422 428 2.270850 GCGGTGGATTGGTAGCCA 59.729 61.111 0.00 0.00 37.54 4.75
423 429 1.819632 GCGGTGGATTGGTAGCCAG 60.820 63.158 0.00 0.00 41.34 4.85
443 454 2.694992 GGAAAGGGGATCGGGGGT 60.695 66.667 0.00 0.00 0.00 4.95
461 472 0.108567 GTGAGGAAGGAGAACGAGGC 60.109 60.000 0.00 0.00 0.00 4.70
504 516 2.427453 GAGGAGTCGACAGCAAGGAATA 59.573 50.000 19.50 0.00 0.00 1.75
518 530 8.370182 ACAGCAAGGAATAGTTCAATTGATTTT 58.630 29.630 9.40 0.97 32.68 1.82
628 644 2.741092 GTCTGCTGACCCGGTCAA 59.259 61.111 20.81 6.74 42.26 3.18
629 645 1.296715 GTCTGCTGACCCGGTCAAT 59.703 57.895 20.81 0.00 42.26 2.57
632 648 3.134127 GCTGACCCGGTCAATGCC 61.134 66.667 20.81 6.58 42.26 4.40
692 716 1.812922 GATCAGCAGGCGTGACAGG 60.813 63.158 11.29 0.00 0.00 4.00
693 717 3.320879 ATCAGCAGGCGTGACAGGG 62.321 63.158 11.29 0.00 0.00 4.45
694 718 4.320456 CAGCAGGCGTGACAGGGT 62.320 66.667 11.29 0.00 0.00 4.34
695 719 3.560251 AGCAGGCGTGACAGGGTT 61.560 61.111 11.29 0.00 0.00 4.11
696 720 3.357079 GCAGGCGTGACAGGGTTG 61.357 66.667 11.29 0.00 0.00 3.77
697 721 2.425592 CAGGCGTGACAGGGTTGA 59.574 61.111 0.00 0.00 0.00 3.18
698 722 1.227823 CAGGCGTGACAGGGTTGAA 60.228 57.895 0.00 0.00 0.00 2.69
699 723 0.606401 CAGGCGTGACAGGGTTGAAT 60.606 55.000 0.00 0.00 0.00 2.57
700 724 0.981183 AGGCGTGACAGGGTTGAATA 59.019 50.000 0.00 0.00 0.00 1.75
701 725 1.559682 AGGCGTGACAGGGTTGAATAT 59.440 47.619 0.00 0.00 0.00 1.28
702 726 2.026262 AGGCGTGACAGGGTTGAATATT 60.026 45.455 0.00 0.00 0.00 1.28
703 727 2.752903 GGCGTGACAGGGTTGAATATTT 59.247 45.455 0.00 0.00 0.00 1.40
704 728 3.942748 GGCGTGACAGGGTTGAATATTTA 59.057 43.478 0.00 0.00 0.00 1.40
705 729 4.035208 GGCGTGACAGGGTTGAATATTTAG 59.965 45.833 0.00 0.00 0.00 1.85
706 730 4.873827 GCGTGACAGGGTTGAATATTTAGA 59.126 41.667 0.00 0.00 0.00 2.10
707 731 5.353123 GCGTGACAGGGTTGAATATTTAGAA 59.647 40.000 0.00 0.00 0.00 2.10
708 732 6.674760 GCGTGACAGGGTTGAATATTTAGAAC 60.675 42.308 0.00 0.00 0.00 3.01
709 733 6.183360 CGTGACAGGGTTGAATATTTAGAACC 60.183 42.308 13.05 13.05 37.69 3.62
710 734 6.884836 GTGACAGGGTTGAATATTTAGAACCT 59.115 38.462 17.71 9.78 38.36 3.50
711 735 7.065923 GTGACAGGGTTGAATATTTAGAACCTC 59.934 40.741 17.71 11.71 38.36 3.85
712 736 7.027874 ACAGGGTTGAATATTTAGAACCTCA 57.972 36.000 17.71 0.00 38.36 3.86
713 737 7.112779 ACAGGGTTGAATATTTAGAACCTCAG 58.887 38.462 17.71 12.73 38.36 3.35
714 738 6.543831 CAGGGTTGAATATTTAGAACCTCAGG 59.456 42.308 17.71 0.00 38.36 3.86
715 739 5.828328 GGGTTGAATATTTAGAACCTCAGGG 59.172 44.000 17.71 0.00 38.36 4.45
716 740 5.299531 GGTTGAATATTTAGAACCTCAGGGC 59.700 44.000 13.74 0.00 35.86 5.19
717 741 5.048846 TGAATATTTAGAACCTCAGGGCC 57.951 43.478 0.00 0.00 35.63 5.80
718 742 4.726825 TGAATATTTAGAACCTCAGGGCCT 59.273 41.667 0.00 0.00 35.63 5.19
719 743 5.193728 TGAATATTTAGAACCTCAGGGCCTT 59.806 40.000 1.32 0.00 35.63 4.35
720 744 5.734031 ATATTTAGAACCTCAGGGCCTTT 57.266 39.130 1.32 0.00 35.63 3.11
721 745 3.895704 TTTAGAACCTCAGGGCCTTTT 57.104 42.857 1.32 0.00 35.63 2.27
722 746 3.434940 TTAGAACCTCAGGGCCTTTTC 57.565 47.619 1.32 4.51 35.63 2.29
723 747 1.450360 AGAACCTCAGGGCCTTTTCT 58.550 50.000 1.32 6.99 35.63 2.52
724 748 1.074566 AGAACCTCAGGGCCTTTTCTG 59.925 52.381 1.32 0.66 35.63 3.02
725 749 0.540597 AACCTCAGGGCCTTTTCTGC 60.541 55.000 1.32 0.00 35.63 4.26
726 750 1.075482 CCTCAGGGCCTTTTCTGCA 59.925 57.895 1.32 0.00 0.00 4.41
727 751 0.540365 CCTCAGGGCCTTTTCTGCAA 60.540 55.000 1.32 0.00 0.00 4.08
728 752 1.331214 CTCAGGGCCTTTTCTGCAAA 58.669 50.000 1.32 0.00 0.00 3.68
729 753 1.688197 CTCAGGGCCTTTTCTGCAAAA 59.312 47.619 1.32 0.00 0.00 2.44
730 754 2.102925 CTCAGGGCCTTTTCTGCAAAAA 59.897 45.455 1.32 0.00 30.90 1.94
731 755 2.158971 TCAGGGCCTTTTCTGCAAAAAC 60.159 45.455 1.32 0.00 30.90 2.43
732 756 1.202521 AGGGCCTTTTCTGCAAAAACG 60.203 47.619 0.00 0.00 30.90 3.60
733 757 0.581529 GGCCTTTTCTGCAAAAACGC 59.418 50.000 0.00 13.89 30.90 4.84
734 758 0.581529 GCCTTTTCTGCAAAAACGCC 59.418 50.000 12.46 0.00 30.90 5.68
735 759 0.852136 CCTTTTCTGCAAAAACGCCG 59.148 50.000 0.00 0.00 30.90 6.46
736 760 1.535015 CCTTTTCTGCAAAAACGCCGA 60.535 47.619 0.00 0.00 30.90 5.54
737 761 1.516864 CTTTTCTGCAAAAACGCCGAC 59.483 47.619 0.00 0.00 30.90 4.79
739 763 1.429927 TTCTGCAAAAACGCCGACGA 61.430 50.000 0.00 0.00 43.93 4.20
740 764 1.721133 CTGCAAAAACGCCGACGAC 60.721 57.895 0.00 0.00 43.93 4.34
741 765 2.789723 GCAAAAACGCCGACGACG 60.790 61.111 0.85 0.85 43.93 5.12
743 767 1.845324 CAAAAACGCCGACGACGTA 59.155 52.632 10.19 0.00 44.30 3.57
744 768 0.229247 CAAAAACGCCGACGACGTAA 59.771 50.000 10.19 0.00 44.30 3.18
745 769 0.926846 AAAAACGCCGACGACGTAAA 59.073 45.000 10.19 0.00 44.30 2.01
746 770 0.503961 AAAACGCCGACGACGTAAAG 59.496 50.000 10.19 0.00 44.30 1.85
747 771 0.317770 AAACGCCGACGACGTAAAGA 60.318 50.000 10.19 0.00 44.30 2.52
748 772 0.998727 AACGCCGACGACGTAAAGAC 60.999 55.000 10.19 0.00 44.30 3.01
749 773 2.148365 CGCCGACGACGTAAAGACC 61.148 63.158 0.00 0.00 43.93 3.85
750 774 1.081242 GCCGACGACGTAAAGACCA 60.081 57.895 0.00 0.00 37.88 4.02
751 775 0.664166 GCCGACGACGTAAAGACCAA 60.664 55.000 0.00 0.00 37.88 3.67
752 776 1.769733 CCGACGACGTAAAGACCAAA 58.230 50.000 0.00 0.00 37.88 3.28
753 777 2.126467 CCGACGACGTAAAGACCAAAA 58.874 47.619 0.00 0.00 37.88 2.44
754 778 2.154389 CCGACGACGTAAAGACCAAAAG 59.846 50.000 0.00 0.00 37.88 2.27
755 779 2.409371 CGACGACGTAAAGACCAAAAGC 60.409 50.000 0.00 0.00 34.56 3.51
756 780 2.540931 GACGACGTAAAGACCAAAAGCA 59.459 45.455 0.00 0.00 0.00 3.91
757 781 2.937799 ACGACGTAAAGACCAAAAGCAA 59.062 40.909 0.00 0.00 0.00 3.91
758 782 3.242511 ACGACGTAAAGACCAAAAGCAAC 60.243 43.478 0.00 0.00 0.00 4.17
759 783 3.242478 CGACGTAAAGACCAAAAGCAACA 60.242 43.478 0.00 0.00 0.00 3.33
760 784 4.664188 GACGTAAAGACCAAAAGCAACAA 58.336 39.130 0.00 0.00 0.00 2.83
761 785 5.061920 ACGTAAAGACCAAAAGCAACAAA 57.938 34.783 0.00 0.00 0.00 2.83
766 790 4.385358 AGACCAAAAGCAACAAACGATT 57.615 36.364 0.00 0.00 0.00 3.34
801 825 7.241628 GGAAAAATATAATCTCCACCCCATCT 58.758 38.462 0.00 0.00 0.00 2.90
802 826 7.730332 GGAAAAATATAATCTCCACCCCATCTT 59.270 37.037 0.00 0.00 0.00 2.40
858 883 3.193479 ACGAGATTTGATTTGAAAGGGCC 59.807 43.478 0.00 0.00 0.00 5.80
897 922 0.675522 CGCCCACCCGTAGAACAAAT 60.676 55.000 0.00 0.00 0.00 2.32
959 987 1.045911 ATCCTTCTCCTCGGTGGCTC 61.046 60.000 0.00 0.00 35.26 4.70
1242 1270 1.024579 ATTTCGATTGGCTCCGCGTT 61.025 50.000 4.92 0.00 0.00 4.84
1294 1322 2.297895 TGAGGGCATACGTTGGGCT 61.298 57.895 11.47 0.18 0.00 5.19
1448 1476 6.921307 GTCGTAATTCAATGTTTGTTCCCTTT 59.079 34.615 0.00 0.00 0.00 3.11
2487 2536 1.210931 CATGCACAACCAGGAAGCG 59.789 57.895 0.00 0.00 0.00 4.68
2782 2833 7.658261 TGAGAGGGTTAAGTTATGATGTATCG 58.342 38.462 0.00 0.00 0.00 2.92
2783 2834 6.994221 AGAGGGTTAAGTTATGATGTATCGG 58.006 40.000 0.00 0.00 0.00 4.18
2784 2835 5.548406 AGGGTTAAGTTATGATGTATCGGC 58.452 41.667 0.00 0.00 0.00 5.54
2785 2836 5.071250 AGGGTTAAGTTATGATGTATCGGCA 59.929 40.000 0.00 0.00 0.00 5.69
2786 2837 5.938125 GGGTTAAGTTATGATGTATCGGCAT 59.062 40.000 0.00 0.00 0.00 4.40
2787 2838 6.430000 GGGTTAAGTTATGATGTATCGGCATT 59.570 38.462 0.00 0.00 0.00 3.56
2788 2839 7.360946 GGGTTAAGTTATGATGTATCGGCATTC 60.361 40.741 0.00 0.00 0.00 2.67
2955 3006 5.306394 GCCTTACTCCTGGGTTGTATTATC 58.694 45.833 0.00 0.00 0.00 1.75
3020 3071 0.179094 TCTTGTTTCCGTCACGCACT 60.179 50.000 0.00 0.00 0.00 4.40
3090 3141 0.842635 ATCCTCCCCTGCACAGAATC 59.157 55.000 0.00 0.00 0.00 2.52
3139 3190 2.169769 TGGTTTTCGACTTGTCCTGTCT 59.830 45.455 0.00 0.00 32.70 3.41
3184 3235 1.796459 GCGAATGTTGTGTCGTAAGGT 59.204 47.619 0.00 0.00 39.46 3.50
3437 3488 0.383949 GCAAGCGTTTTGGTCCAGAA 59.616 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.320697 GCCTACAACGACCAGGTCTT 59.679 55.000 17.95 5.25 0.00 3.01
417 423 0.346932 ATCCCCTTTCCCTCTGGCTA 59.653 55.000 0.00 0.00 0.00 3.93
418 424 0.990818 GATCCCCTTTCCCTCTGGCT 60.991 60.000 0.00 0.00 0.00 4.75
420 426 1.700042 CCGATCCCCTTTCCCTCTGG 61.700 65.000 0.00 0.00 0.00 3.86
421 427 1.700042 CCCGATCCCCTTTCCCTCTG 61.700 65.000 0.00 0.00 0.00 3.35
422 428 1.384643 CCCGATCCCCTTTCCCTCT 60.385 63.158 0.00 0.00 0.00 3.69
423 429 2.452937 CCCCGATCCCCTTTCCCTC 61.453 68.421 0.00 0.00 0.00 4.30
443 454 0.251832 AGCCTCGTTCTCCTTCCTCA 60.252 55.000 0.00 0.00 0.00 3.86
461 472 0.457851 CTCACGCTTCCCTCACCTAG 59.542 60.000 0.00 0.00 0.00 3.02
569 581 1.054406 AGTAGGTGTGTGTGTGGGCT 61.054 55.000 0.00 0.00 0.00 5.19
572 586 1.048601 AGGAGTAGGTGTGTGTGTGG 58.951 55.000 0.00 0.00 0.00 4.17
614 630 2.359850 GCATTGACCGGGTCAGCA 60.360 61.111 27.25 17.56 43.69 4.41
628 644 1.005037 TTCAGAGTCGCAACGGCAT 60.005 52.632 0.00 0.00 41.24 4.40
629 645 1.954146 GTTCAGAGTCGCAACGGCA 60.954 57.895 0.00 0.00 41.24 5.69
632 648 1.891060 GCAGGTTCAGAGTCGCAACG 61.891 60.000 2.32 0.00 0.00 4.10
636 658 1.005630 AGTGCAGGTTCAGAGTCGC 60.006 57.895 0.00 0.00 0.00 5.19
637 659 0.600557 AGAGTGCAGGTTCAGAGTCG 59.399 55.000 0.00 0.00 0.00 4.18
692 716 5.299531 GCCCTGAGGTTCTAAATATTCAACC 59.700 44.000 12.82 12.82 38.94 3.77
693 717 5.299531 GGCCCTGAGGTTCTAAATATTCAAC 59.700 44.000 0.00 0.00 34.57 3.18
694 718 5.193728 AGGCCCTGAGGTTCTAAATATTCAA 59.806 40.000 0.00 0.00 34.57 2.69
695 719 4.726825 AGGCCCTGAGGTTCTAAATATTCA 59.273 41.667 0.00 0.00 34.57 2.57
696 720 5.311844 AGGCCCTGAGGTTCTAAATATTC 57.688 43.478 0.00 0.00 34.57 1.75
697 721 5.734031 AAGGCCCTGAGGTTCTAAATATT 57.266 39.130 0.00 0.00 34.57 1.28
698 722 5.734031 AAAGGCCCTGAGGTTCTAAATAT 57.266 39.130 0.00 0.00 34.57 1.28
699 723 5.253096 AGAAAAGGCCCTGAGGTTCTAAATA 59.747 40.000 0.00 0.00 34.57 1.40
700 724 4.044698 AGAAAAGGCCCTGAGGTTCTAAAT 59.955 41.667 0.00 0.00 34.57 1.40
701 725 3.397955 AGAAAAGGCCCTGAGGTTCTAAA 59.602 43.478 0.00 0.00 34.57 1.85
702 726 2.986728 AGAAAAGGCCCTGAGGTTCTAA 59.013 45.455 0.00 0.00 34.57 2.10
703 727 2.305927 CAGAAAAGGCCCTGAGGTTCTA 59.694 50.000 0.00 0.00 34.57 2.10
704 728 1.074566 CAGAAAAGGCCCTGAGGTTCT 59.925 52.381 0.00 0.00 34.57 3.01
705 729 1.539157 CAGAAAAGGCCCTGAGGTTC 58.461 55.000 0.00 0.00 34.57 3.62
706 730 0.540597 GCAGAAAAGGCCCTGAGGTT 60.541 55.000 10.58 0.00 34.57 3.50
707 731 1.075659 GCAGAAAAGGCCCTGAGGT 59.924 57.895 10.58 0.00 34.57 3.85
708 732 0.540365 TTGCAGAAAAGGCCCTGAGG 60.540 55.000 10.58 0.00 32.37 3.86
709 733 1.331214 TTTGCAGAAAAGGCCCTGAG 58.669 50.000 10.58 0.00 32.37 3.35
710 734 1.786937 TTTTGCAGAAAAGGCCCTGA 58.213 45.000 10.58 0.00 32.37 3.86
711 735 2.212652 GTTTTTGCAGAAAAGGCCCTG 58.787 47.619 3.66 0.00 32.62 4.45
712 736 1.202521 CGTTTTTGCAGAAAAGGCCCT 60.203 47.619 3.66 0.00 32.62 5.19
713 737 1.217001 CGTTTTTGCAGAAAAGGCCC 58.783 50.000 3.66 0.00 32.62 5.80
714 738 0.581529 GCGTTTTTGCAGAAAAGGCC 59.418 50.000 24.87 0.00 42.07 5.19
715 739 0.581529 GGCGTTTTTGCAGAAAAGGC 59.418 50.000 26.02 26.02 45.11 4.35
716 740 0.852136 CGGCGTTTTTGCAGAAAAGG 59.148 50.000 15.46 15.72 32.62 3.11
717 741 1.516864 GTCGGCGTTTTTGCAGAAAAG 59.483 47.619 6.85 10.61 40.67 2.27
718 742 1.551145 GTCGGCGTTTTTGCAGAAAA 58.449 45.000 6.85 3.63 40.67 2.29
719 743 0.590230 CGTCGGCGTTTTTGCAGAAA 60.590 50.000 6.85 0.00 40.67 2.52
720 744 1.010574 CGTCGGCGTTTTTGCAGAA 60.011 52.632 6.85 0.00 40.67 3.02
721 745 1.883544 TCGTCGGCGTTTTTGCAGA 60.884 52.632 10.18 0.00 39.49 4.26
722 746 1.721133 GTCGTCGGCGTTTTTGCAG 60.721 57.895 10.18 0.00 39.49 4.41
723 747 2.325166 GTCGTCGGCGTTTTTGCA 59.675 55.556 10.18 0.00 39.49 4.08
724 748 2.144808 TACGTCGTCGGCGTTTTTGC 62.145 55.000 31.09 0.00 42.85 3.68
725 749 0.229247 TTACGTCGTCGGCGTTTTTG 59.771 50.000 31.09 0.00 42.85 2.44
726 750 0.926846 TTTACGTCGTCGGCGTTTTT 59.073 45.000 31.09 7.85 42.85 1.94
727 751 0.503961 CTTTACGTCGTCGGCGTTTT 59.496 50.000 31.09 8.26 42.85 2.43
728 752 0.317770 TCTTTACGTCGTCGGCGTTT 60.318 50.000 31.09 9.09 42.85 3.60
729 753 0.998727 GTCTTTACGTCGTCGGCGTT 60.999 55.000 31.09 14.40 42.85 4.84
730 754 1.441016 GTCTTTACGTCGTCGGCGT 60.441 57.895 28.96 28.96 45.11 5.68
731 755 2.148365 GGTCTTTACGTCGTCGGCG 61.148 63.158 19.06 19.06 41.85 6.46
732 756 0.664166 TTGGTCTTTACGTCGTCGGC 60.664 55.000 0.00 0.00 41.85 5.54
733 757 1.769733 TTTGGTCTTTACGTCGTCGG 58.230 50.000 0.00 0.00 41.85 4.79
734 758 2.409371 GCTTTTGGTCTTTACGTCGTCG 60.409 50.000 0.00 0.00 43.34 5.12
735 759 2.540931 TGCTTTTGGTCTTTACGTCGTC 59.459 45.455 0.00 0.00 0.00 4.20
736 760 2.553086 TGCTTTTGGTCTTTACGTCGT 58.447 42.857 2.21 2.21 0.00 4.34
737 761 3.242478 TGTTGCTTTTGGTCTTTACGTCG 60.242 43.478 0.00 0.00 0.00 5.12
738 762 4.281525 TGTTGCTTTTGGTCTTTACGTC 57.718 40.909 0.00 0.00 0.00 4.34
739 763 4.705337 TTGTTGCTTTTGGTCTTTACGT 57.295 36.364 0.00 0.00 0.00 3.57
740 764 4.028026 CGTTTGTTGCTTTTGGTCTTTACG 60.028 41.667 0.00 0.00 0.00 3.18
741 765 5.096849 TCGTTTGTTGCTTTTGGTCTTTAC 58.903 37.500 0.00 0.00 0.00 2.01
742 766 5.312120 TCGTTTGTTGCTTTTGGTCTTTA 57.688 34.783 0.00 0.00 0.00 1.85
743 767 4.181309 TCGTTTGTTGCTTTTGGTCTTT 57.819 36.364 0.00 0.00 0.00 2.52
744 768 3.859411 TCGTTTGTTGCTTTTGGTCTT 57.141 38.095 0.00 0.00 0.00 3.01
745 769 4.385358 AATCGTTTGTTGCTTTTGGTCT 57.615 36.364 0.00 0.00 0.00 3.85
746 770 5.463499 AAAATCGTTTGTTGCTTTTGGTC 57.537 34.783 0.00 0.00 0.00 4.02
747 771 5.871465 AAAAATCGTTTGTTGCTTTTGGT 57.129 30.435 0.00 0.00 0.00 3.67
781 805 7.297108 TGGTAAAGATGGGGTGGAGATTATATT 59.703 37.037 0.00 0.00 0.00 1.28
789 813 3.089284 GTTTGGTAAAGATGGGGTGGAG 58.911 50.000 0.00 0.00 0.00 3.86
801 825 5.237236 TGGTTTGGTTTTGGTTTGGTAAA 57.763 34.783 0.00 0.00 0.00 2.01
802 826 4.903045 TGGTTTGGTTTTGGTTTGGTAA 57.097 36.364 0.00 0.00 0.00 2.85
959 987 3.081409 ATCCCCTCACGAACCGGG 61.081 66.667 6.32 0.00 37.73 5.73
1242 1270 8.421784 CCAGACCAATCTATAGCTGTAAACTAA 58.578 37.037 0.00 0.00 32.25 2.24
1294 1322 2.036604 TGTCGCTGTATCCACTGTCAAA 59.963 45.455 0.00 0.00 0.00 2.69
1448 1476 2.710377 AGACTGCAACACAAGTCACAA 58.290 42.857 5.68 0.00 32.23 3.33
1489 1537 5.923684 GGGCGAACAAAATTTCATACTTTGA 59.076 36.000 0.00 0.00 34.76 2.69
1729 1778 2.026641 CCAGGGTACATTTCCATGCAG 58.973 52.381 0.00 0.00 35.72 4.41
1956 2005 6.547880 AGACATACACCTATACACTGAGAAGG 59.452 42.308 0.00 0.00 0.00 3.46
2487 2536 3.614616 CAGAGAAAATACTGGCACTCGAC 59.385 47.826 0.00 0.00 0.00 4.20
2782 2833 0.814457 TGTTACCATTGCCGAATGCC 59.186 50.000 0.00 0.00 38.14 4.40
2783 2834 2.645730 TTGTTACCATTGCCGAATGC 57.354 45.000 0.00 0.00 38.14 3.56
2784 2835 6.479095 AATTTTTGTTACCATTGCCGAATG 57.521 33.333 0.00 0.00 39.04 2.67
2785 2836 8.037758 TGATAATTTTTGTTACCATTGCCGAAT 58.962 29.630 0.00 0.00 0.00 3.34
2786 2837 7.378966 TGATAATTTTTGTTACCATTGCCGAA 58.621 30.769 0.00 0.00 0.00 4.30
2787 2838 6.925211 TGATAATTTTTGTTACCATTGCCGA 58.075 32.000 0.00 0.00 0.00 5.54
2788 2839 7.769272 ATGATAATTTTTGTTACCATTGCCG 57.231 32.000 0.00 0.00 0.00 5.69
2929 2980 2.298661 AACCCAGGAGTAAGGCCGG 61.299 63.158 0.00 0.00 0.00 6.13
3020 3071 0.907704 ACGACCCTGGCACCTTCATA 60.908 55.000 0.00 0.00 0.00 2.15
3090 3141 2.088674 CTCGCCTCCCTAATGACCCG 62.089 65.000 0.00 0.00 0.00 5.28
3184 3235 0.318869 CAACGCAGAAGCAATTGCCA 60.319 50.000 26.45 0.00 43.38 4.92


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

AutoCloner maintained by Alex Coulton.