Multiple sequence alignment - TraesCS2A01G291900

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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 TraesCS2A01G291900 chr2A 100.000 3398 0 0 1 3398 502827254 502823857 0.000000e+00 6276.0
1 TraesCS2A01G291900 chr2A 87.736 1166 119 15 1200 2356 502933923 502935073 0.000000e+00 1339.0
2 TraesCS2A01G291900 chr2A 97.778 90 2 0 2654 2743 125202192 125202281 4.540000e-34 156.0
3 TraesCS2A01G291900 chr2D 94.826 2648 101 19 1 2642 372016990 372014373 0.000000e+00 4098.0
4 TraesCS2A01G291900 chr2D 88.250 1166 113 15 1200 2356 372224105 372225255 0.000000e+00 1373.0
5 TraesCS2A01G291900 chr2D 86.107 691 60 19 2737 3393 372014366 372013678 0.000000e+00 712.0
6 TraesCS2A01G291900 chr2B 93.590 2574 123 14 87 2642 441481421 441478872 0.000000e+00 3801.0
7 TraesCS2A01G291900 chr2B 88.593 1166 109 15 1200 2356 441792712 441793862 0.000000e+00 1395.0
8 TraesCS2A01G291900 chr2B 86.830 448 41 16 2737 3168 441478867 441478422 5.100000e-133 484.0
9 TraesCS2A01G291900 chr2B 92.754 138 7 3 3257 3393 441477919 441477784 2.670000e-46 196.0
10 TraesCS2A01G291900 chr2B 96.739 92 3 0 2654 2745 779865686 779865595 1.630000e-33 154.0
11 TraesCS2A01G291900 chr2B 85.714 105 11 4 3287 3390 495028228 495028127 1.290000e-19 108.0
12 TraesCS2A01G291900 chr5A 84.199 943 128 12 1416 2348 569793580 569794511 0.000000e+00 896.0
13 TraesCS2A01G291900 chr5A 76.852 216 36 13 3120 3322 467062331 467062545 3.580000e-20 110.0
14 TraesCS2A01G291900 chr5A 83.478 115 15 4 3287 3398 385658241 385658354 1.670000e-18 104.0
15 TraesCS2A01G291900 chr5A 80.392 102 12 6 3291 3390 646225780 646225685 1.690000e-08 71.3
16 TraesCS2A01G291900 chr5B 84.278 935 127 11 1416 2340 550488913 550489837 0.000000e+00 894.0
17 TraesCS2A01G291900 chr5B 75.217 230 46 8 3120 3344 275708689 275708466 7.760000e-17 99.0
18 TraesCS2A01G291900 chr5B 82.979 94 14 2 3120 3212 589380982 589380890 2.170000e-12 84.2
19 TraesCS2A01G291900 chr5D 84.171 935 128 11 1416 2340 450577903 450578827 0.000000e+00 889.0
20 TraesCS2A01G291900 chr5D 79.743 311 56 5 1614 1921 447508361 447508667 5.710000e-53 219.0
21 TraesCS2A01G291900 chr5D 93.137 102 6 1 2646 2747 575138 575038 7.600000e-32 148.0
22 TraesCS2A01G291900 chr5D 83.696 92 10 3 3304 3391 429352451 429352361 7.820000e-12 82.4
23 TraesCS2A01G291900 chr1D 97.778 90 2 0 2653 2742 16084853 16084942 4.540000e-34 156.0
24 TraesCS2A01G291900 chr1D 97.778 90 2 0 2653 2742 16086808 16086897 4.540000e-34 156.0
25 TraesCS2A01G291900 chr7B 96.774 93 2 1 2649 2741 40180647 40180738 1.630000e-33 154.0
26 TraesCS2A01G291900 chr4A 90.598 117 8 3 2648 2762 603488788 603488903 5.870000e-33 152.0
27 TraesCS2A01G291900 chr6A 97.701 87 2 0 2654 2740 12435654 12435740 2.110000e-32 150.0
28 TraesCS2A01G291900 chr6A 78.378 111 20 4 3280 3389 135643398 135643505 6.080000e-08 69.4
29 TraesCS2A01G291900 chr1A 92.308 104 6 2 2653 2755 107663280 107663178 2.730000e-31 147.0
30 TraesCS2A01G291900 chr7D 83.000 100 15 2 3291 3390 66819727 66819824 4.670000e-14 89.8
31 TraesCS2A01G291900 chr4B 79.839 124 20 5 3270 3393 561648722 561648840 6.040000e-13 86.1
32 TraesCS2A01G291900 chr7A 75.130 193 32 13 3146 3332 661588327 661588145 3.640000e-10 76.8
33 TraesCS2A01G291900 chr6B 90.196 51 3 2 2519 2567 3325315 3325365 7.870000e-07 65.8


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 TraesCS2A01G291900 chr2A 502823857 502827254 3397 True 6276.000000 6276 100.0000 1 3398 1 chr2A.!!$R1 3397
1 TraesCS2A01G291900 chr2A 502933923 502935073 1150 False 1339.000000 1339 87.7360 1200 2356 1 chr2A.!!$F2 1156
2 TraesCS2A01G291900 chr2D 372013678 372016990 3312 True 2405.000000 4098 90.4665 1 3393 2 chr2D.!!$R1 3392
3 TraesCS2A01G291900 chr2D 372224105 372225255 1150 False 1373.000000 1373 88.2500 1200 2356 1 chr2D.!!$F1 1156
4 TraesCS2A01G291900 chr2B 441477784 441481421 3637 True 1493.666667 3801 91.0580 87 3393 3 chr2B.!!$R3 3306
5 TraesCS2A01G291900 chr2B 441792712 441793862 1150 False 1395.000000 1395 88.5930 1200 2356 1 chr2B.!!$F1 1156
6 TraesCS2A01G291900 chr5A 569793580 569794511 931 False 896.000000 896 84.1990 1416 2348 1 chr5A.!!$F3 932
7 TraesCS2A01G291900 chr5B 550488913 550489837 924 False 894.000000 894 84.2780 1416 2340 1 chr5B.!!$F1 924
8 TraesCS2A01G291900 chr5D 450577903 450578827 924 False 889.000000 889 84.1710 1416 2340 1 chr5D.!!$F2 924

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
723 725 0.310854 CAGAAACGCCAAACTGGTCC 59.689 55.000 0.0 0.0 40.46 4.46 F
815 817 1.072489 TGCACAAACGTGGGGATCTTA 59.928 47.619 0.0 0.0 34.79 2.10 F
1136 1156 1.084289 GATTGGTGTGGTCGGTTAGC 58.916 55.000 0.0 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2391 0.661552 TAAGCCGACGAGGAATCGAG 59.338 55.0 4.44 0.0 45.00 4.04 R
2366 2392 1.315690 ATAAGCCGACGAGGAATCGA 58.684 50.0 4.44 0.0 45.00 3.59 R
2827 2854 0.318762 AGTTTGTCTCCTGACCGCTC 59.681 55.0 0.00 0.0 42.28 5.03 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
54 55 3.447586 CCAACCCACTCTCTAAATCTCGA 59.552 47.826 0.00 0.00 0.00 4.04
108 109 7.118724 CACAACACAATTTGATACAAAGCAAC 58.881 34.615 2.79 0.00 28.88 4.17
165 166 3.020984 ACCTCAATCTCTCTCGACCTTC 58.979 50.000 0.00 0.00 0.00 3.46
166 167 3.020274 CCTCAATCTCTCTCGACCTTCA 58.980 50.000 0.00 0.00 0.00 3.02
236 237 0.642156 TATCTTCCTCCTCCCTGGCA 59.358 55.000 0.00 0.00 35.26 4.92
250 251 2.625087 CCCTGGCATTTCCCATCTCTTT 60.625 50.000 0.00 0.00 33.64 2.52
253 254 3.958798 CTGGCATTTCCCATCTCTTTGAT 59.041 43.478 0.00 0.00 33.64 2.57
282 283 2.307980 TCTTCCTCAACCTCCTCGACTA 59.692 50.000 0.00 0.00 0.00 2.59
289 290 1.293062 ACCTCCTCGACTACCACCTA 58.707 55.000 0.00 0.00 0.00 3.08
346 347 1.490490 TGCAGTCTCACACCTCCTTTT 59.510 47.619 0.00 0.00 0.00 2.27
360 361 0.322456 CCTTTTCAGGTCGGGCATGA 60.322 55.000 0.00 0.00 35.96 3.07
366 367 1.043816 CAGGTCGGGCATGACTCTAT 58.956 55.000 0.00 0.00 38.91 1.98
375 376 2.481854 GCATGACTCTATGTGGCAGAG 58.518 52.381 0.00 0.00 44.28 3.35
402 403 2.361357 CCGAGGAGGACACGGTCT 60.361 66.667 0.00 0.00 45.00 3.85
422 423 3.259374 TCTCTGGACCTGCTCTAACAAAG 59.741 47.826 0.00 0.00 0.00 2.77
430 431 5.437060 ACCTGCTCTAACAAAGTTCTTCAA 58.563 37.500 0.00 0.00 0.00 2.69
431 432 5.297029 ACCTGCTCTAACAAAGTTCTTCAAC 59.703 40.000 0.00 0.00 0.00 3.18
449 450 4.118410 TCAACTTTTCATTTTGCGTGCAT 58.882 34.783 0.00 0.00 0.00 3.96
611 613 6.660094 ACTCGGCCCATAACAAAAAGTATTAA 59.340 34.615 0.00 0.00 0.00 1.40
688 690 4.093850 ACAAACACACAACGTCTCCTAAAC 59.906 41.667 0.00 0.00 0.00 2.01
694 696 6.208204 ACACACAACGTCTCCTAAACTATACT 59.792 38.462 0.00 0.00 0.00 2.12
722 724 1.021968 ACAGAAACGCCAAACTGGTC 58.978 50.000 0.00 0.00 40.46 4.02
723 725 0.310854 CAGAAACGCCAAACTGGTCC 59.689 55.000 0.00 0.00 40.46 4.46
746 748 1.768870 AGCTCAGTGTGGTTTACAGGT 59.231 47.619 0.00 0.00 40.69 4.00
747 749 2.969950 AGCTCAGTGTGGTTTACAGGTA 59.030 45.455 0.00 0.00 40.69 3.08
760 762 9.702494 GTGGTTTACAGGTATATATACAAGTCC 57.298 37.037 21.56 15.85 34.98 3.85
815 817 1.072489 TGCACAAACGTGGGGATCTTA 59.928 47.619 0.00 0.00 34.79 2.10
816 818 2.156098 GCACAAACGTGGGGATCTTAA 58.844 47.619 0.00 0.00 34.79 1.85
817 819 2.095415 GCACAAACGTGGGGATCTTAAC 60.095 50.000 0.00 0.00 34.79 2.01
818 820 3.408634 CACAAACGTGGGGATCTTAACT 58.591 45.455 0.00 0.00 0.00 2.24
819 821 3.818773 CACAAACGTGGGGATCTTAACTT 59.181 43.478 0.00 0.00 0.00 2.66
820 822 3.818773 ACAAACGTGGGGATCTTAACTTG 59.181 43.478 0.00 0.00 0.00 3.16
821 823 3.782656 AACGTGGGGATCTTAACTTGT 57.217 42.857 0.00 0.00 0.00 3.16
822 824 3.782656 ACGTGGGGATCTTAACTTGTT 57.217 42.857 0.00 0.00 0.00 2.83
823 825 3.671716 ACGTGGGGATCTTAACTTGTTC 58.328 45.455 0.00 0.00 0.00 3.18
824 826 3.326880 ACGTGGGGATCTTAACTTGTTCT 59.673 43.478 0.00 0.00 0.00 3.01
825 827 4.202430 ACGTGGGGATCTTAACTTGTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
826 828 4.392138 CGTGGGGATCTTAACTTGTTCTTC 59.608 45.833 0.00 0.00 0.00 2.87
829 831 4.630505 GGGGATCTTAACTTGTTCTTCGAC 59.369 45.833 0.00 0.00 0.00 4.20
853 855 1.502690 ACGTGGGGTATGCCTGAATA 58.497 50.000 0.00 0.00 34.45 1.75
976 986 2.580601 AAAGGACCGGAGACCCACG 61.581 63.158 9.46 0.00 0.00 4.94
983 993 2.671963 GGAGACCCACGCCAAACC 60.672 66.667 0.00 0.00 38.35 3.27
1088 1108 9.674824 TTTCAGTTTTCTCGTTAGTTACTCTAG 57.325 33.333 0.00 0.00 0.00 2.43
1108 1128 2.092538 AGCAGCAATAGCAACAGAGGAT 60.093 45.455 0.00 0.00 45.49 3.24
1109 1129 2.290093 GCAGCAATAGCAACAGAGGATC 59.710 50.000 0.00 0.00 45.49 3.36
1117 1137 2.008329 GCAACAGAGGATCAAGAGCTG 58.992 52.381 0.00 0.00 37.82 4.24
1136 1156 1.084289 GATTGGTGTGGTCGGTTAGC 58.916 55.000 0.00 0.00 0.00 3.09
1162 1182 3.300009 GCTGTCGTGAATTTTGTCAAGG 58.700 45.455 0.00 0.00 0.00 3.61
1203 1223 2.794028 GCTACAGGGGCGTACTCCC 61.794 68.421 12.89 12.89 45.80 4.30
1733 1753 4.008933 GCACCACTGCCTCCTCGT 62.009 66.667 0.00 0.00 37.45 4.18
2405 2431 7.415653 GGCTTATTCGTCTTCTTGATTGGATTT 60.416 37.037 0.00 0.00 0.00 2.17
2474 2501 6.996106 TCTTTTTCTTGTTACAGTACGTGTG 58.004 36.000 0.00 0.00 40.69 3.82
2593 2620 6.792473 ACAGGGAGAATTATATCCATACACCA 59.208 38.462 6.26 0.00 38.77 4.17
2645 2672 3.202151 TCCATTGGGACTGTCCTAAATCC 59.798 47.826 26.29 10.17 40.48 3.01
2648 2675 5.104109 CCATTGGGACTGTCCTAAATCCTAA 60.104 44.000 26.29 5.42 40.48 2.69
2649 2676 6.410853 CCATTGGGACTGTCCTAAATCCTAAT 60.411 42.308 26.29 8.21 40.48 1.73
2650 2677 5.630415 TGGGACTGTCCTAAATCCTAATG 57.370 43.478 25.01 0.00 36.57 1.90
2651 2678 4.141482 TGGGACTGTCCTAAATCCTAATGC 60.141 45.833 25.01 5.49 36.57 3.56
2652 2679 4.103311 GGGACTGTCCTAAATCCTAATGCT 59.897 45.833 25.01 0.00 36.57 3.79
2653 2680 5.398012 GGGACTGTCCTAAATCCTAATGCTT 60.398 44.000 25.01 0.00 36.57 3.91
2654 2681 6.183361 GGGACTGTCCTAAATCCTAATGCTTA 60.183 42.308 25.01 0.00 36.57 3.09
2655 2682 6.706716 GGACTGTCCTAAATCCTAATGCTTAC 59.293 42.308 19.53 0.00 32.53 2.34
2656 2683 7.419172 GGACTGTCCTAAATCCTAATGCTTACT 60.419 40.741 19.53 0.00 32.53 2.24
2657 2684 7.501844 ACTGTCCTAAATCCTAATGCTTACTC 58.498 38.462 0.00 0.00 0.00 2.59
2658 2685 6.827727 TGTCCTAAATCCTAATGCTTACTCC 58.172 40.000 0.00 0.00 0.00 3.85
2659 2686 6.183361 TGTCCTAAATCCTAATGCTTACTCCC 60.183 42.308 0.00 0.00 0.00 4.30
2660 2687 6.043358 GTCCTAAATCCTAATGCTTACTCCCT 59.957 42.308 0.00 0.00 0.00 4.20
2661 2688 6.270231 TCCTAAATCCTAATGCTTACTCCCTC 59.730 42.308 0.00 0.00 0.00 4.30
2662 2689 4.984146 AATCCTAATGCTTACTCCCTCC 57.016 45.455 0.00 0.00 0.00 4.30
2663 2690 2.317040 TCCTAATGCTTACTCCCTCCG 58.683 52.381 0.00 0.00 0.00 4.63
2664 2691 2.040178 CCTAATGCTTACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
2665 2692 3.117398 TCCTAATGCTTACTCCCTCCGTA 60.117 47.826 0.00 0.00 0.00 4.02
2666 2693 3.640029 CCTAATGCTTACTCCCTCCGTAA 59.360 47.826 0.00 0.00 0.00 3.18
2667 2694 4.100498 CCTAATGCTTACTCCCTCCGTAAA 59.900 45.833 0.00 0.00 0.00 2.01
2668 2695 3.538634 ATGCTTACTCCCTCCGTAAAC 57.461 47.619 0.00 0.00 0.00 2.01
2669 2696 2.532843 TGCTTACTCCCTCCGTAAACT 58.467 47.619 0.00 0.00 0.00 2.66
2670 2697 3.700538 TGCTTACTCCCTCCGTAAACTA 58.299 45.455 0.00 0.00 0.00 2.24
2671 2698 4.088634 TGCTTACTCCCTCCGTAAACTAA 58.911 43.478 0.00 0.00 0.00 2.24
2672 2699 4.713321 TGCTTACTCCCTCCGTAAACTAAT 59.287 41.667 0.00 0.00 0.00 1.73
2673 2700 5.893255 TGCTTACTCCCTCCGTAAACTAATA 59.107 40.000 0.00 0.00 0.00 0.98
2674 2701 6.552350 TGCTTACTCCCTCCGTAAACTAATAT 59.448 38.462 0.00 0.00 0.00 1.28
2675 2702 7.725397 TGCTTACTCCCTCCGTAAACTAATATA 59.275 37.037 0.00 0.00 0.00 0.86
2676 2703 8.579863 GCTTACTCCCTCCGTAAACTAATATAA 58.420 37.037 0.00 0.00 0.00 0.98
2678 2705 9.866655 TTACTCCCTCCGTAAACTAATATAAGA 57.133 33.333 0.00 0.00 0.00 2.10
2679 2706 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2680 2707 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2681 2708 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2682 2709 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2683 2710 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2684 2711 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2685 2712 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2686 2713 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2687 2714 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2734 2761 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2827 2854 5.645929 AGCACTAGTATGGATCTCATCTACG 59.354 44.000 0.00 0.00 37.30 3.51
2828 2855 5.644206 GCACTAGTATGGATCTCATCTACGA 59.356 44.000 0.00 0.00 37.30 3.43
2867 2894 5.806286 ACTTATACGCATTTTGATTCACGG 58.194 37.500 0.00 0.00 0.00 4.94
2870 2897 1.261989 CGCATTTTGATTCACGGCAG 58.738 50.000 0.00 0.00 0.00 4.85
2957 2984 5.250543 TCAACCTCCAAAACCATCTGATCTA 59.749 40.000 0.00 0.00 0.00 1.98
3020 3047 9.554395 AAAAAGGTGAAAAACTGAAGAAGAAAA 57.446 25.926 0.00 0.00 0.00 2.29
3023 3050 6.806739 AGGTGAAAAACTGAAGAAGAAAAACG 59.193 34.615 0.00 0.00 0.00 3.60
3060 3099 1.248486 GAAAAACAGGAGGTCCAGCC 58.752 55.000 0.00 0.00 38.89 4.85
3086 3129 2.096367 GGAGGCGACTTTCTCGTTTTTC 60.096 50.000 0.00 0.00 44.92 2.29
3104 3147 6.034577 CGTTTTTCTTCTTCAGTTTTTCACCC 59.965 38.462 0.00 0.00 0.00 4.61
3224 3271 9.932699 TTTTGAAAAGTGTTATTCATGCATTTG 57.067 25.926 0.00 0.00 35.63 2.32
3226 3273 8.523523 TGAAAAGTGTTATTCATGCATTTGAG 57.476 30.769 0.00 0.00 30.94 3.02
3393 3853 9.466497 AATGTGTATGAAAAAGTAGACATCCAT 57.534 29.630 0.00 0.00 34.78 3.41
3395 3855 9.599866 TGTGTATGAAAAAGTAGACATCCATAG 57.400 33.333 0.00 0.00 0.00 2.23
3396 3856 9.817809 GTGTATGAAAAAGTAGACATCCATAGA 57.182 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 0.253160 TGCCAGAACTAGTGGGGGAT 60.253 55.000 10.29 0.00 35.39 3.85
141 142 2.755655 GGTCGAGAGAGATTGAGGTGAA 59.244 50.000 0.00 0.00 43.49 3.18
165 166 6.538742 GTCCGAGAGAGGAATAGAGAGATATG 59.461 46.154 0.00 0.00 42.77 1.78
166 167 6.443849 AGTCCGAGAGAGGAATAGAGAGATAT 59.556 42.308 0.00 0.00 42.77 1.63
255 256 1.909302 GGAGGTTGAGGAAGATGGTGA 59.091 52.381 0.00 0.00 0.00 4.02
282 283 3.209091 CACCCGAGAGATAGGTGGT 57.791 57.895 0.34 0.00 46.01 4.16
289 290 1.690219 GATGGTGGCACCCGAGAGAT 61.690 60.000 32.61 18.69 37.50 2.75
346 347 0.033503 TAGAGTCATGCCCGACCTGA 60.034 55.000 0.00 0.00 36.52 3.86
366 367 4.735132 GCCGCGTACTCTGCCACA 62.735 66.667 4.92 0.00 0.00 4.17
375 376 4.253257 CTCCTCGGAGCCGCGTAC 62.253 72.222 4.92 0.00 39.59 3.67
402 403 2.972713 ACTTTGTTAGAGCAGGTCCAGA 59.027 45.455 0.00 0.00 0.00 3.86
422 423 6.177822 CACGCAAAATGAAAAGTTGAAGAAC 58.822 36.000 0.00 0.00 0.00 3.01
430 431 4.681025 CACTATGCACGCAAAATGAAAAGT 59.319 37.500 0.00 0.00 0.00 2.66
431 432 4.681025 ACACTATGCACGCAAAATGAAAAG 59.319 37.500 0.00 0.00 0.00 2.27
449 450 1.696884 TGGCACCAATCTCACACACTA 59.303 47.619 0.00 0.00 0.00 2.74
611 613 2.760634 TTGTAGCACATGGTCGATGT 57.239 45.000 0.00 0.00 46.98 3.06
688 690 4.201685 CGTTTCTGTGCCGGAAAAGTATAG 60.202 45.833 5.05 0.00 39.92 1.31
694 696 1.357334 GCGTTTCTGTGCCGGAAAA 59.643 52.632 5.05 0.00 39.92 2.29
722 724 1.798813 GTAAACCACACTGAGCTTCGG 59.201 52.381 0.00 0.00 0.00 4.30
723 725 2.476619 CTGTAAACCACACTGAGCTTCG 59.523 50.000 0.00 0.00 32.33 3.79
760 762 6.814644 TCCGGTGTAGAATTATGTAGTGTTTG 59.185 38.462 0.00 0.00 0.00 2.93
815 817 4.849383 CACGTTTTTGTCGAAGAACAAGTT 59.151 37.500 0.00 0.00 39.69 2.66
816 818 4.399978 CACGTTTTTGTCGAAGAACAAGT 58.600 39.130 0.00 0.00 39.69 3.16
817 819 3.783943 CCACGTTTTTGTCGAAGAACAAG 59.216 43.478 0.00 0.00 39.69 3.16
818 820 3.426426 CCCACGTTTTTGTCGAAGAACAA 60.426 43.478 0.00 0.00 39.69 2.83
819 821 2.096174 CCCACGTTTTTGTCGAAGAACA 59.904 45.455 0.00 0.00 39.69 3.18
820 822 2.540157 CCCCACGTTTTTGTCGAAGAAC 60.540 50.000 0.00 0.00 39.69 3.01
821 823 1.671845 CCCCACGTTTTTGTCGAAGAA 59.328 47.619 0.00 0.00 39.69 2.52
822 824 1.301423 CCCCACGTTTTTGTCGAAGA 58.699 50.000 0.00 0.00 0.00 2.87
823 825 1.018910 ACCCCACGTTTTTGTCGAAG 58.981 50.000 0.00 0.00 0.00 3.79
824 826 2.322355 TACCCCACGTTTTTGTCGAA 57.678 45.000 0.00 0.00 0.00 3.71
825 827 2.144730 CATACCCCACGTTTTTGTCGA 58.855 47.619 0.00 0.00 0.00 4.20
826 828 1.400500 GCATACCCCACGTTTTTGTCG 60.400 52.381 0.00 0.00 0.00 4.35
829 831 1.067915 CAGGCATACCCCACGTTTTTG 60.068 52.381 0.00 0.00 36.11 2.44
853 855 6.893005 TCCGGGAAATAGGACAAAACATTATT 59.107 34.615 0.00 0.00 0.00 1.40
983 993 3.019564 GGCATATTATAGGCAGCCCTTG 58.980 50.000 8.22 0.00 42.87 3.61
1041 1054 2.583593 GTAGCTGGAGCGGCTTCG 60.584 66.667 2.97 0.00 44.48 3.79
1088 1108 1.742761 TCCTCTGTTGCTATTGCTGC 58.257 50.000 0.00 0.00 40.48 5.25
1108 1128 1.421268 ACCACACCAATCAGCTCTTGA 59.579 47.619 7.05 0.00 40.85 3.02
1109 1129 1.808945 GACCACACCAATCAGCTCTTG 59.191 52.381 0.00 0.00 0.00 3.02
1117 1137 1.084289 GCTAACCGACCACACCAATC 58.916 55.000 0.00 0.00 0.00 2.67
1136 1156 2.030007 ACAAAATTCACGACAGCCATGG 60.030 45.455 7.63 7.63 0.00 3.66
1162 1182 4.487412 GCTCTGCCCAATGTGCGC 62.487 66.667 0.00 0.00 0.00 6.09
1317 1337 1.148273 GTGGCTGTTGGTGGAGTGA 59.852 57.895 0.00 0.00 0.00 3.41
1365 1385 2.434884 ATCAAGTCCAGCACCGCG 60.435 61.111 0.00 0.00 0.00 6.46
1387 1407 1.735386 CTGCCATCAACAGTCTCCAG 58.265 55.000 0.00 0.00 0.00 3.86
1390 1410 1.975363 GCGCTGCCATCAACAGTCTC 61.975 60.000 0.00 0.00 37.47 3.36
2043 2063 2.479566 ACACGATGCTGGTCTTGAAT 57.520 45.000 0.00 0.00 0.00 2.57
2088 2108 0.761187 AGAGCACCTTGAAGAGCACA 59.239 50.000 11.13 0.00 0.00 4.57
2365 2391 0.661552 TAAGCCGACGAGGAATCGAG 59.338 55.000 4.44 0.00 45.00 4.04
2366 2392 1.315690 ATAAGCCGACGAGGAATCGA 58.684 50.000 4.44 0.00 45.00 3.59
2424 2450 7.434492 AGAACACGATTAATTACTCGATGGAT 58.566 34.615 26.15 15.17 38.24 3.41
2462 2489 3.083293 TGGCACTATCACACGTACTGTA 58.917 45.455 0.00 0.00 0.00 2.74
2593 2620 8.743085 ATGTCATCTTGTACTAGCATTTCATT 57.257 30.769 0.00 0.00 0.00 2.57
2642 2669 2.900546 CGGAGGGAGTAAGCATTAGGAT 59.099 50.000 0.00 0.00 0.00 3.24
2643 2670 2.317040 CGGAGGGAGTAAGCATTAGGA 58.683 52.381 0.00 0.00 0.00 2.94
2645 2672 4.931661 TTACGGAGGGAGTAAGCATTAG 57.068 45.455 0.00 0.00 31.30 1.73
2648 2675 3.105283 AGTTTACGGAGGGAGTAAGCAT 58.895 45.455 5.92 0.00 37.62 3.79
2649 2676 2.532843 AGTTTACGGAGGGAGTAAGCA 58.467 47.619 5.92 0.00 37.62 3.91
2650 2677 4.725790 TTAGTTTACGGAGGGAGTAAGC 57.274 45.455 0.00 0.00 35.75 3.09
2652 2679 9.866655 TCTTATATTAGTTTACGGAGGGAGTAA 57.133 33.333 0.00 0.00 32.84 2.24
2653 2680 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2654 2681 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2655 2682 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2656 2683 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2657 2684 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2658 2685 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2659 2686 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2660 2687 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2661 2688 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2708 2735 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2710 2737 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2717 2744 9.933723 GTTTTGTACTCCCTCTGTAAACTAATA 57.066 33.333 0.00 0.00 0.00 0.98
2718 2745 8.657712 AGTTTTGTACTCCCTCTGTAAACTAAT 58.342 33.333 0.00 0.00 28.23 1.73
2719 2746 8.026396 AGTTTTGTACTCCCTCTGTAAACTAA 57.974 34.615 0.00 0.00 28.23 2.24
2720 2747 7.607615 AGTTTTGTACTCCCTCTGTAAACTA 57.392 36.000 0.00 0.00 28.23 2.24
2721 2748 6.496144 AGTTTTGTACTCCCTCTGTAAACT 57.504 37.500 0.00 0.00 28.23 2.66
2722 2749 8.554528 GTTTAGTTTTGTACTCCCTCTGTAAAC 58.445 37.037 0.00 0.00 38.33 2.01
2723 2750 8.266473 TGTTTAGTTTTGTACTCCCTCTGTAAA 58.734 33.333 0.00 0.00 38.33 2.01
2724 2751 7.794041 TGTTTAGTTTTGTACTCCCTCTGTAA 58.206 34.615 0.00 0.00 38.33 2.41
2725 2752 7.364149 TGTTTAGTTTTGTACTCCCTCTGTA 57.636 36.000 0.00 0.00 38.33 2.74
2726 2753 6.243216 TGTTTAGTTTTGTACTCCCTCTGT 57.757 37.500 0.00 0.00 38.33 3.41
2727 2754 7.745620 ATTGTTTAGTTTTGTACTCCCTCTG 57.254 36.000 0.00 0.00 38.33 3.35
2728 2755 9.856162 TTTATTGTTTAGTTTTGTACTCCCTCT 57.144 29.630 0.00 0.00 38.33 3.69
2729 2756 9.888878 GTTTATTGTTTAGTTTTGTACTCCCTC 57.111 33.333 0.00 0.00 38.33 4.30
2730 2757 9.636789 AGTTTATTGTTTAGTTTTGTACTCCCT 57.363 29.630 0.00 0.00 38.33 4.20
2731 2758 9.673454 CAGTTTATTGTTTAGTTTTGTACTCCC 57.327 33.333 0.00 0.00 38.33 4.30
2827 2854 0.318762 AGTTTGTCTCCTGACCGCTC 59.681 55.000 0.00 0.00 42.28 5.03
2828 2855 0.759346 AAGTTTGTCTCCTGACCGCT 59.241 50.000 0.00 0.00 42.28 5.52
2867 2894 7.518731 TTTGTCACACAAAAATTACTTCTGC 57.481 32.000 0.00 0.00 44.23 4.26
2922 2949 1.343465 TGGAGGTTGACCGAGAAACTC 59.657 52.381 0.00 0.00 42.08 3.01
2957 2984 2.550830 AAACACGCAGATCTCCAAGT 57.449 45.000 0.00 0.00 0.00 3.16
2994 3021 9.554395 TTTTCTTCTTCAGTTTTTCACCTTTTT 57.446 25.926 0.00 0.00 0.00 1.94
2995 3022 9.554395 TTTTTCTTCTTCAGTTTTTCACCTTTT 57.446 25.926 0.00 0.00 0.00 2.27
2996 3023 8.988934 GTTTTTCTTCTTCAGTTTTTCACCTTT 58.011 29.630 0.00 0.00 0.00 3.11
2997 3024 7.328493 CGTTTTTCTTCTTCAGTTTTTCACCTT 59.672 33.333 0.00 0.00 0.00 3.50
2998 3025 6.806739 CGTTTTTCTTCTTCAGTTTTTCACCT 59.193 34.615 0.00 0.00 0.00 4.00
2999 3026 6.804783 TCGTTTTTCTTCTTCAGTTTTTCACC 59.195 34.615 0.00 0.00 0.00 4.02
3000 3027 7.537649 AGTCGTTTTTCTTCTTCAGTTTTTCAC 59.462 33.333 0.00 0.00 0.00 3.18
3002 3029 8.449085 AAGTCGTTTTTCTTCTTCAGTTTTTC 57.551 30.769 0.00 0.00 0.00 2.29
3003 3030 8.812147 AAAGTCGTTTTTCTTCTTCAGTTTTT 57.188 26.923 0.00 0.00 0.00 1.94
3005 3032 8.812147 AAAAAGTCGTTTTTCTTCTTCAGTTT 57.188 26.923 1.95 0.00 41.15 2.66
3017 3044 5.803461 CCCTCGAAAAGAAAAAGTCGTTTTT 59.197 36.000 0.00 0.00 46.44 1.94
3018 3045 5.124297 TCCCTCGAAAAGAAAAAGTCGTTTT 59.876 36.000 0.00 0.00 42.28 2.43
3020 3047 4.193865 TCCCTCGAAAAGAAAAAGTCGTT 58.806 39.130 0.00 0.00 35.09 3.85
3023 3050 6.809689 TGTTTTTCCCTCGAAAAGAAAAAGTC 59.190 34.615 20.94 14.55 46.07 3.01
3036 3075 1.610886 GGACCTCCTGTTTTTCCCTCG 60.611 57.143 0.00 0.00 0.00 4.63
3060 3099 2.245438 GAGAAAGTCGCCTCCCCCAG 62.245 65.000 0.00 0.00 0.00 4.45
3063 3102 2.184579 CGAGAAAGTCGCCTCCCC 59.815 66.667 0.00 0.00 43.03 4.81
3071 3110 7.006187 ACTGAAGAAGAAAAACGAGAAAGTC 57.994 36.000 0.00 0.00 0.00 3.01
3203 3250 9.715121 ATTCTCAAATGCATGAATAACACTTTT 57.285 25.926 0.00 0.00 0.00 2.27
3352 3812 8.702163 TCATACACATTGTACATGTTCTGTAG 57.298 34.615 2.30 0.00 40.99 2.74


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

AutoCloner maintained by Alex Coulton.