Multiple sequence alignment - TraesCS2A01G414200

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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 TraesCS2A01G414200 chr2A 100.000 3006 0 0 1 3006 671282546 671285551 0.000000e+00 5552
1 TraesCS2A01G414200 chr2D 91.630 2927 141 33 1 2901 526345596 526348444 0.000000e+00 3952
2 TraesCS2A01G414200 chr2D 95.062 81 4 0 2926 3006 526348826 526348906 8.750000e-26 128
3 TraesCS2A01G414200 chr2B 93.399 1530 70 14 834 2360 622673325 622674826 0.000000e+00 2237
4 TraesCS2A01G414200 chr2B 94.955 773 24 10 1 767 622657364 622658127 0.000000e+00 1197
5 TraesCS2A01G414200 chr6A 90.909 374 31 2 239 609 464538478 464538851 1.610000e-137 499
6 TraesCS2A01G414200 chr6D 90.374 374 33 2 239 609 325756235 325756608 3.480000e-134 488
7 TraesCS2A01G414200 chr6B 89.655 377 36 2 239 612 497216207 497215831 7.540000e-131 477
8 TraesCS2A01G414200 chr7D 85.870 276 39 0 282 557 433876570 433876845 8.150000e-76 294
9 TraesCS2A01G414200 chr7B 84.828 290 44 0 282 571 451289912 451290201 2.930000e-75 292
10 TraesCS2A01G414200 chr7A 85.612 278 40 0 280 557 484525275 484525552 2.930000e-75 292
11 TraesCS2A01G414200 chr3B 80.435 276 46 6 287 558 826725618 826725889 1.410000e-48 204


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 TraesCS2A01G414200 chr2A 671282546 671285551 3005 False 5552 5552 100.000 1 3006 1 chr2A.!!$F1 3005
1 TraesCS2A01G414200 chr2D 526345596 526348906 3310 False 2040 3952 93.346 1 3006 2 chr2D.!!$F1 3005
2 TraesCS2A01G414200 chr2B 622673325 622674826 1501 False 2237 2237 93.399 834 2360 1 chr2B.!!$F2 1526
3 TraesCS2A01G414200 chr2B 622657364 622658127 763 False 1197 1197 94.955 1 767 1 chr2B.!!$F1 766

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
613 615 0.178941 ACCAGGAGTACCCGTGAAGT 60.179 55.0 0.0 0.0 40.87 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2498 2523 0.098552 TGCGTTTGCTCATATTGCCG 59.901 50.0 0.0 0.0 43.34 5.69 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
62 63 1.975327 CCACGTCACCATCCTCACT 59.025 57.895 0.00 0.00 0.00 3.41
198 199 1.501169 GTGCAACAAATCTTGCCACC 58.499 50.000 0.00 0.00 45.13 4.61
204 205 1.956477 ACAAATCTTGCCACCTCACAC 59.044 47.619 0.00 0.00 0.00 3.82
225 226 1.798813 CGTGAAAAGTACTCACTGGCC 59.201 52.381 10.85 0.00 40.90 5.36
613 615 0.178941 ACCAGGAGTACCCGTGAAGT 60.179 55.000 0.00 0.00 40.87 3.01
618 620 0.669625 GAGTACCCGTGAAGTGCACC 60.670 60.000 14.63 0.00 44.85 5.01
628 630 0.669318 GAAGTGCACCGATCCGAACA 60.669 55.000 14.63 0.00 0.00 3.18
629 631 0.250124 AAGTGCACCGATCCGAACAA 60.250 50.000 14.63 0.00 0.00 2.83
630 632 0.949105 AGTGCACCGATCCGAACAAC 60.949 55.000 14.63 0.00 0.00 3.32
681 690 4.503123 CCCTTGTGTGAATTTCCCTTTTCC 60.503 45.833 0.00 0.00 0.00 3.13
693 711 9.685276 GAATTTCCCTTTTCCATTTTAATCCAT 57.315 29.630 0.00 0.00 0.00 3.41
698 716 7.677745 TCCCTTTTCCATTTTAATCCATCTCAA 59.322 33.333 0.00 0.00 0.00 3.02
699 717 8.320617 CCCTTTTCCATTTTAATCCATCTCAAA 58.679 33.333 0.00 0.00 0.00 2.69
700 718 9.895138 CCTTTTCCATTTTAATCCATCTCAAAT 57.105 29.630 0.00 0.00 0.00 2.32
771 790 2.724174 GCGTTTTCCGAAATCTTTGTGG 59.276 45.455 0.00 0.00 39.56 4.17
788 807 1.678970 GGCAAATTCGTGGAGGCCT 60.679 57.895 3.86 3.86 38.37 5.19
790 809 1.508088 CAAATTCGTGGAGGCCTGC 59.492 57.895 18.95 18.95 0.00 4.85
791 810 1.678970 AAATTCGTGGAGGCCTGCC 60.679 57.895 22.95 17.17 0.00 4.85
792 811 2.424842 AAATTCGTGGAGGCCTGCCA 62.425 55.000 22.95 19.60 38.92 4.92
806 825 4.681978 GCCACGCCTCTGACGGTT 62.682 66.667 0.00 0.00 34.00 4.44
807 826 2.738521 CCACGCCTCTGACGGTTG 60.739 66.667 0.00 0.00 34.00 3.77
808 827 3.414700 CACGCCTCTGACGGTTGC 61.415 66.667 0.00 0.00 34.00 4.17
809 828 3.616721 ACGCCTCTGACGGTTGCT 61.617 61.111 0.00 0.00 34.00 3.91
810 829 2.357517 CGCCTCTGACGGTTGCTT 60.358 61.111 0.00 0.00 0.00 3.91
811 830 2.671177 CGCCTCTGACGGTTGCTTG 61.671 63.158 0.00 0.00 0.00 4.01
812 831 1.598130 GCCTCTGACGGTTGCTTGT 60.598 57.895 0.00 0.00 0.00 3.16
813 832 1.845809 GCCTCTGACGGTTGCTTGTG 61.846 60.000 0.00 0.00 0.00 3.33
814 833 0.249868 CCTCTGACGGTTGCTTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
815 834 1.581934 CTCTGACGGTTGCTTGTGAA 58.418 50.000 0.00 0.00 0.00 3.18
816 835 1.261619 CTCTGACGGTTGCTTGTGAAC 59.738 52.381 0.00 0.00 0.00 3.18
898 917 3.610619 TACGGTCGCGTCCCTCTCA 62.611 63.158 16.75 0.00 0.00 3.27
998 1018 2.896243 GAGACGCTCGAACTTGTAGA 57.104 50.000 0.00 0.00 0.00 2.59
1015 1035 0.673644 AGAAATGGCGTCCAACCTCG 60.674 55.000 2.68 0.00 36.95 4.63
1022 1042 3.499737 GTCCAACCTCGGCATGCG 61.500 66.667 12.44 7.41 0.00 4.73
1137 1157 2.669229 TCCGCCAGTACGTCGACA 60.669 61.111 17.16 0.00 0.00 4.35
1138 1158 1.989966 CTCCGCCAGTACGTCGACAT 61.990 60.000 17.16 1.85 0.00 3.06
1142 1162 1.202110 CGCCAGTACGTCGACATACTT 60.202 52.381 20.83 4.92 28.91 2.24
1188 1208 0.642800 GAGTTCATGCTCTCGTTCGC 59.357 55.000 0.00 0.00 32.99 4.70
1204 1224 1.163420 TCGCACGTGCTCATGGTTTT 61.163 50.000 35.27 0.00 39.32 2.43
1453 1473 2.031012 CAACTGCTCGGCTCCACA 59.969 61.111 0.00 0.00 0.00 4.17
1524 1544 1.001268 ACCATCGATCGATCACTTCCG 60.001 52.381 27.20 14.09 31.62 4.30
1526 1546 0.668535 ATCGATCGATCACTTCCGCA 59.331 50.000 24.60 0.00 0.00 5.69
1528 1548 0.848942 CGATCGATCACTTCCGCAAG 59.151 55.000 24.40 0.96 35.50 4.01
1529 1549 1.799181 CGATCGATCACTTCCGCAAGT 60.799 52.381 24.40 0.00 44.26 3.16
1530 1550 2.540973 CGATCGATCACTTCCGCAAGTA 60.541 50.000 24.40 0.00 41.24 2.24
1531 1551 3.643763 GATCGATCACTTCCGCAAGTAT 58.356 45.455 20.52 0.00 41.24 2.12
1532 1552 2.809446 TCGATCACTTCCGCAAGTATG 58.191 47.619 0.00 0.00 41.24 2.39
1547 1567 5.980698 CAAGTATGCAACTCCTAGTCATG 57.019 43.478 0.00 0.00 37.50 3.07
1549 1569 1.945387 ATGCAACTCCTAGTCATGCG 58.055 50.000 0.00 0.00 35.34 4.73
1565 1585 2.563427 CGTCTCAGAGTGCTCGCA 59.437 61.111 0.00 0.00 34.09 5.10
1583 1605 1.019278 CACCCGTGTGTGCCTATGTC 61.019 60.000 0.00 0.00 37.72 3.06
1587 1609 1.070821 CGTGTGTGCCTATGTCTGTG 58.929 55.000 0.00 0.00 0.00 3.66
1589 1611 1.800586 GTGTGTGCCTATGTCTGTGTG 59.199 52.381 0.00 0.00 0.00 3.82
1738 1760 3.876589 GAAGGGGCTCGCAACGACA 62.877 63.158 0.00 0.00 0.00 4.35
1766 1788 4.308458 CGCTGGTGGTCGGGTTCA 62.308 66.667 0.00 0.00 0.00 3.18
1934 1956 0.036732 GGTGGTGCATCAGAACCTGA 59.963 55.000 0.00 0.00 44.65 3.86
1991 2013 3.134127 GCCATGGGAGCGTGGAAC 61.134 66.667 15.13 0.00 37.72 3.62
1993 2015 2.819595 CATGGGAGCGTGGAACCG 60.820 66.667 0.00 0.00 0.00 4.44
2017 2039 3.214328 GGTTGTGTGATTTGTGACCTCT 58.786 45.455 0.00 0.00 0.00 3.69
2071 2095 6.947733 TGTGTTAATTGTTTCAGGATCAGGAT 59.052 34.615 0.00 0.00 0.00 3.24
2127 2151 3.590720 CGTGCAATAATCGAAGCATGA 57.409 42.857 0.00 0.00 44.53 3.07
2196 2220 6.640499 TGTGTGTTTGTAGCTTTGCAATAATC 59.360 34.615 0.00 0.00 0.00 1.75
2223 2247 9.352784 GAAGCATGCTTGTAAATTATGTTTGTA 57.647 29.630 36.48 0.00 36.26 2.41
2224 2248 8.915871 AGCATGCTTGTAAATTATGTTTGTAG 57.084 30.769 16.30 0.00 0.00 2.74
2266 2290 5.592282 TCTTTGAGTTTGTAGCATGTTCCAA 59.408 36.000 0.00 0.00 0.00 3.53
2267 2291 6.265196 TCTTTGAGTTTGTAGCATGTTCCAAT 59.735 34.615 0.00 0.00 0.00 3.16
2298 2322 3.068590 ACTTTGAGCACATTCCACCAAAG 59.931 43.478 0.00 0.00 43.37 2.77
2401 2426 4.280174 GGATATACTAAGCGAACACCCTCA 59.720 45.833 0.00 0.00 0.00 3.86
2406 2431 2.270352 AAGCGAACACCCTCATTCAA 57.730 45.000 0.00 0.00 0.00 2.69
2417 2442 2.484417 CCCTCATTCAAGTCAGATCCCG 60.484 54.545 0.00 0.00 0.00 5.14
2418 2443 2.432146 CCTCATTCAAGTCAGATCCCGA 59.568 50.000 0.00 0.00 0.00 5.14
2443 2468 5.316987 CACAAATCCTAAAGTGTTCCCTCT 58.683 41.667 0.00 0.00 0.00 3.69
2444 2469 5.182001 CACAAATCCTAAAGTGTTCCCTCTG 59.818 44.000 0.00 0.00 0.00 3.35
2446 2471 4.828072 ATCCTAAAGTGTTCCCTCTGAC 57.172 45.455 0.00 0.00 0.00 3.51
2456 2481 1.229336 CCCTCTGACCACACCCTCT 60.229 63.158 0.00 0.00 0.00 3.69
2467 2492 2.609737 CCACACCCTCTGAACGAACTAC 60.610 54.545 0.00 0.00 0.00 2.73
2477 2502 4.634443 TCTGAACGAACTACGAGATGATGA 59.366 41.667 0.00 0.00 45.77 2.92
2493 2518 6.173339 AGATGATGACAGTAATGGTTCGTTT 58.827 36.000 0.00 0.00 0.00 3.60
2496 2521 5.872617 TGATGACAGTAATGGTTCGTTTAGG 59.127 40.000 0.00 0.00 0.00 2.69
2497 2522 5.471556 TGACAGTAATGGTTCGTTTAGGA 57.528 39.130 0.00 0.00 0.00 2.94
2498 2523 5.232463 TGACAGTAATGGTTCGTTTAGGAC 58.768 41.667 0.00 0.00 0.00 3.85
2515 2540 1.268032 GGACGGCAATATGAGCAAACG 60.268 52.381 0.00 0.00 0.00 3.60
2528 2553 0.740516 GCAAACGCATTTGGGGATGG 60.741 55.000 7.44 0.00 44.64 3.51
2547 2573 5.125417 GGATGGCACTTTTGTTATAAGAGCA 59.875 40.000 0.00 0.00 39.83 4.26
2548 2574 6.183360 GGATGGCACTTTTGTTATAAGAGCAT 60.183 38.462 0.00 0.00 39.83 3.79
2549 2575 5.953183 TGGCACTTTTGTTATAAGAGCATG 58.047 37.500 0.00 0.00 39.83 4.06
2550 2576 5.105797 TGGCACTTTTGTTATAAGAGCATGG 60.106 40.000 0.00 0.00 39.83 3.66
2551 2577 4.800471 GCACTTTTGTTATAAGAGCATGGC 59.200 41.667 0.00 0.00 38.53 4.40
2552 2578 5.622007 GCACTTTTGTTATAAGAGCATGGCA 60.622 40.000 0.00 0.00 38.53 4.92
2562 2588 6.796785 ATAAGAGCATGGCAATTTTTACCT 57.203 33.333 0.00 0.00 0.00 3.08
2568 2594 5.473162 AGCATGGCAATTTTTACCTTTTTCC 59.527 36.000 0.00 0.00 0.00 3.13
2575 2601 9.225436 GGCAATTTTTACCTTTTTCCATTGATA 57.775 29.630 0.00 0.00 0.00 2.15
2618 2644 5.664294 ATCAGCATGGCAATTTTCACTAA 57.336 34.783 0.00 0.00 36.16 2.24
2651 2677 0.748450 CCGGCAATTCTCCATGCAAT 59.252 50.000 0.00 0.00 44.32 3.56
2657 2683 5.566032 CGGCAATTCTCCATGCAATAATCAT 60.566 40.000 0.00 0.00 44.32 2.45
2665 2691 8.158169 TCTCCATGCAATAATCATGACTAAAC 57.842 34.615 0.00 0.00 42.84 2.01
2724 2763 9.676195 TGACAATTGTTTATACAACATGACAAG 57.324 29.630 13.36 0.00 46.38 3.16
2767 2807 2.942376 CCTTATGTAACAGCATGGCGAA 59.058 45.455 0.00 0.00 43.62 4.70
2772 2812 5.772825 ATGTAACAGCATGGCGAATTTAT 57.227 34.783 0.00 0.00 43.62 1.40
2780 2820 4.274459 AGCATGGCGAATTTATCTGTTCTC 59.726 41.667 0.00 0.00 0.00 2.87
2789 2829 6.455513 CGAATTTATCTGTTCTCGCATGACAA 60.456 38.462 0.00 0.00 0.00 3.18
2798 2838 1.329906 CTCGCATGACAATTCTGGAGC 59.670 52.381 0.00 0.00 0.00 4.70
2799 2839 1.089112 CGCATGACAATTCTGGAGCA 58.911 50.000 0.00 0.00 0.00 4.26
2802 2842 3.428452 CGCATGACAATTCTGGAGCATTT 60.428 43.478 0.00 0.00 0.00 2.32
2852 2892 1.068055 GCTCGTTCGTTCCTACTTGGA 60.068 52.381 0.00 0.00 44.51 3.53
2861 2901 2.514160 GTTCCTACTTGGATGGGGGAAT 59.486 50.000 0.00 0.00 45.68 3.01
2874 2914 5.779771 GGATGGGGGAATAATATTTTGCTCA 59.220 40.000 0.00 0.00 0.00 4.26
2877 2917 4.021104 GGGGGAATAATATTTTGCTCAGGC 60.021 45.833 0.00 0.00 39.26 4.85
2904 2944 3.543680 CCTAAGGGAACGTCATCATGT 57.456 47.619 0.00 0.00 33.58 3.21
2905 2945 3.873910 CCTAAGGGAACGTCATCATGTT 58.126 45.455 0.00 0.00 34.18 2.71
2906 2946 5.018539 CCTAAGGGAACGTCATCATGTTA 57.981 43.478 0.00 0.00 31.41 2.41
2907 2947 5.611374 CCTAAGGGAACGTCATCATGTTAT 58.389 41.667 0.00 0.00 31.41 1.89
2908 2948 6.055588 CCTAAGGGAACGTCATCATGTTATT 58.944 40.000 0.00 0.00 31.41 1.40
2909 2949 5.818136 AAGGGAACGTCATCATGTTATTG 57.182 39.130 0.00 0.00 31.41 1.90
2910 2950 4.199310 AGGGAACGTCATCATGTTATTGG 58.801 43.478 0.00 0.00 31.41 3.16
2911 2951 3.315191 GGGAACGTCATCATGTTATTGGG 59.685 47.826 0.00 0.00 31.41 4.12
2912 2952 3.315191 GGAACGTCATCATGTTATTGGGG 59.685 47.826 0.00 0.00 31.41 4.96
2913 2953 2.930950 ACGTCATCATGTTATTGGGGG 58.069 47.619 0.00 0.00 0.00 5.40
2914 2954 2.241176 ACGTCATCATGTTATTGGGGGT 59.759 45.455 0.00 0.00 0.00 4.95
2915 2955 3.456644 ACGTCATCATGTTATTGGGGGTA 59.543 43.478 0.00 0.00 0.00 3.69
2916 2956 4.080243 ACGTCATCATGTTATTGGGGGTAA 60.080 41.667 0.00 0.00 0.00 2.85
2917 2957 4.884744 CGTCATCATGTTATTGGGGGTAAA 59.115 41.667 0.00 0.00 0.00 2.01
2918 2958 5.358442 CGTCATCATGTTATTGGGGGTAAAA 59.642 40.000 0.00 0.00 0.00 1.52
2919 2959 6.127591 CGTCATCATGTTATTGGGGGTAAAAA 60.128 38.462 0.00 0.00 0.00 1.94
2951 3348 6.609237 TTCAGCCTGATCGATCAAATTTAG 57.391 37.500 27.09 14.96 36.18 1.85
2964 3361 3.572255 TCAAATTTAGTGGTTGTCAGGGC 59.428 43.478 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.970937 CGACCCAGTAGAAGAGCCCA 60.971 60.000 0.00 0.00 0.00 5.36
158 159 2.719426 CGTGGTTCGTAGAAGGTTCT 57.281 50.000 0.00 0.00 45.90 3.01
193 194 1.098712 TTTTCACGGTGTGAGGTGGC 61.099 55.000 8.17 0.00 43.69 5.01
194 195 0.944386 CTTTTCACGGTGTGAGGTGG 59.056 55.000 8.17 0.00 43.69 4.61
198 199 3.489785 GTGAGTACTTTTCACGGTGTGAG 59.510 47.826 8.17 7.22 43.69 3.51
225 226 5.083136 CATAGGCTGCACGTACATAAAAG 57.917 43.478 0.50 0.00 0.00 2.27
601 603 2.025418 CGGTGCACTTCACGGGTAC 61.025 63.158 17.98 0.00 46.56 3.34
613 615 1.669760 GGTTGTTCGGATCGGTGCA 60.670 57.895 0.00 0.00 0.00 4.57
618 620 2.194271 GAAGCTAGGTTGTTCGGATCG 58.806 52.381 12.82 0.00 0.00 3.69
628 630 0.250513 CGAGCCAAGGAAGCTAGGTT 59.749 55.000 6.94 6.94 41.75 3.50
629 631 0.905337 ACGAGCCAAGGAAGCTAGGT 60.905 55.000 0.00 0.00 41.75 3.08
630 632 0.250513 AACGAGCCAAGGAAGCTAGG 59.749 55.000 0.00 0.00 41.75 3.02
725 743 5.356190 AGAACCGTTCATGTAAGATCGAGTA 59.644 40.000 13.69 0.00 33.72 2.59
771 790 1.508088 CAGGCCTCCACGAATTTGC 59.492 57.895 0.00 0.00 0.00 3.68
790 809 2.738521 CAACCGTCAGAGGCGTGG 60.739 66.667 0.00 0.00 33.69 4.94
791 810 3.414700 GCAACCGTCAGAGGCGTG 61.415 66.667 0.00 0.00 33.69 5.34
792 811 3.165160 AAGCAACCGTCAGAGGCGT 62.165 57.895 0.00 0.00 33.69 5.68
794 813 1.598130 ACAAGCAACCGTCAGAGGC 60.598 57.895 0.00 0.00 33.69 4.70
795 814 0.249868 TCACAAGCAACCGTCAGAGG 60.250 55.000 0.00 0.00 37.30 3.69
796 815 1.261619 GTTCACAAGCAACCGTCAGAG 59.738 52.381 0.00 0.00 0.00 3.35
797 816 1.134521 AGTTCACAAGCAACCGTCAGA 60.135 47.619 0.00 0.00 0.00 3.27
798 817 1.299541 AGTTCACAAGCAACCGTCAG 58.700 50.000 0.00 0.00 0.00 3.51
799 818 1.400142 CAAGTTCACAAGCAACCGTCA 59.600 47.619 0.00 0.00 0.00 4.35
800 819 1.268539 CCAAGTTCACAAGCAACCGTC 60.269 52.381 0.00 0.00 0.00 4.79
801 820 0.738389 CCAAGTTCACAAGCAACCGT 59.262 50.000 0.00 0.00 0.00 4.83
802 821 1.002468 CTCCAAGTTCACAAGCAACCG 60.002 52.381 0.00 0.00 0.00 4.44
803 822 1.269257 GCTCCAAGTTCACAAGCAACC 60.269 52.381 0.00 0.00 33.21 3.77
804 823 1.597937 CGCTCCAAGTTCACAAGCAAC 60.598 52.381 0.00 0.00 33.21 4.17
805 824 0.662619 CGCTCCAAGTTCACAAGCAA 59.337 50.000 0.00 0.00 33.21 3.91
806 825 1.165907 CCGCTCCAAGTTCACAAGCA 61.166 55.000 0.00 0.00 33.21 3.91
807 826 1.576421 CCGCTCCAAGTTCACAAGC 59.424 57.895 0.00 0.00 0.00 4.01
808 827 1.856265 GCCCGCTCCAAGTTCACAAG 61.856 60.000 0.00 0.00 0.00 3.16
809 828 1.896660 GCCCGCTCCAAGTTCACAA 60.897 57.895 0.00 0.00 0.00 3.33
810 829 2.281484 GCCCGCTCCAAGTTCACA 60.281 61.111 0.00 0.00 0.00 3.58
811 830 3.423154 CGCCCGCTCCAAGTTCAC 61.423 66.667 0.00 0.00 0.00 3.18
996 1016 0.673644 CGAGGTTGGACGCCATTTCT 60.674 55.000 0.00 0.00 31.53 2.52
998 1018 1.674322 CCGAGGTTGGACGCCATTT 60.674 57.895 0.00 0.00 31.53 2.32
1137 1157 1.153901 CGTGGACGCGGTGAAGTAT 60.154 57.895 12.47 0.00 0.00 2.12
1138 1158 2.256158 CGTGGACGCGGTGAAGTA 59.744 61.111 12.47 0.00 0.00 2.24
1164 1184 1.615883 ACGAGAGCATGAACTCACACT 59.384 47.619 15.98 0.00 39.26 3.55
1188 1208 4.378046 GGTTAGTAAAACCATGAGCACGTG 60.378 45.833 12.28 12.28 40.03 4.49
1204 1224 0.388907 AAAGAAGCGCGCGGTTAGTA 60.389 50.000 42.26 0.00 35.84 1.82
1499 1519 4.179926 AGTGATCGATCGATGGTAATGG 57.820 45.455 33.86 0.00 34.60 3.16
1526 1546 4.446371 GCATGACTAGGAGTTGCATACTT 58.554 43.478 0.00 0.00 37.17 2.24
1528 1548 2.797156 CGCATGACTAGGAGTTGCATAC 59.203 50.000 0.00 0.00 32.90 2.39
1529 1549 2.430694 ACGCATGACTAGGAGTTGCATA 59.569 45.455 0.00 0.00 32.90 3.14
1530 1550 1.208052 ACGCATGACTAGGAGTTGCAT 59.792 47.619 0.00 0.00 32.90 3.96
1531 1551 0.608130 ACGCATGACTAGGAGTTGCA 59.392 50.000 0.00 0.00 32.90 4.08
1532 1552 1.134965 AGACGCATGACTAGGAGTTGC 60.135 52.381 0.00 0.00 30.68 4.17
1533 1553 2.164422 TGAGACGCATGACTAGGAGTTG 59.836 50.000 0.00 0.00 0.00 3.16
1534 1554 2.425312 CTGAGACGCATGACTAGGAGTT 59.575 50.000 0.00 0.00 0.00 3.01
1535 1555 2.020720 CTGAGACGCATGACTAGGAGT 58.979 52.381 0.00 0.00 0.00 3.85
1536 1556 2.290367 CTCTGAGACGCATGACTAGGAG 59.710 54.545 0.00 0.64 0.00 3.69
1547 1567 2.878520 GCGAGCACTCTGAGACGC 60.879 66.667 12.44 16.89 39.33 5.19
1549 1569 1.445238 GGTGCGAGCACTCTGAGAC 60.445 63.158 24.79 5.54 45.52 3.36
1565 1585 1.192146 AGACATAGGCACACACGGGT 61.192 55.000 0.00 0.00 0.00 5.28
1576 1596 1.406069 GCCTGGACACACAGACATAGG 60.406 57.143 0.00 0.00 40.97 2.57
1577 1597 1.406069 GGCCTGGACACACAGACATAG 60.406 57.143 0.00 0.00 40.97 2.23
1583 1605 2.666190 CACGGCCTGGACACACAG 60.666 66.667 0.00 0.00 38.21 3.66
1888 1910 4.545706 GCCGCACCGATCATGGGA 62.546 66.667 11.40 0.00 31.94 4.37
1916 1938 3.631453 TCAGGTTCTGATGCACCAC 57.369 52.632 0.00 0.00 35.39 4.16
1991 2013 1.028905 ACAAATCACACAACCACCGG 58.971 50.000 0.00 0.00 0.00 5.28
1993 2015 2.223711 GGTCACAAATCACACAACCACC 60.224 50.000 0.00 0.00 0.00 4.61
1999 2021 3.558931 ACAGAGGTCACAAATCACACA 57.441 42.857 0.00 0.00 0.00 3.72
2017 2039 7.667557 ACACTACTAGAAGTTCAGCAAATACA 58.332 34.615 5.50 0.00 0.00 2.29
2096 2120 3.447752 TTATTGCACGAACATCACACG 57.552 42.857 0.00 0.00 0.00 4.49
2196 2220 7.062138 ACAAACATAATTTACAAGCATGCTTCG 59.938 33.333 29.81 24.55 33.42 3.79
2246 2270 5.069318 TCATTGGAACATGCTACAAACTCA 58.931 37.500 0.00 0.00 39.30 3.41
2266 2290 3.743521 TGTGCTCAAAGTAGTGCTTCAT 58.256 40.909 0.00 0.00 36.17 2.57
2267 2291 3.192541 TGTGCTCAAAGTAGTGCTTCA 57.807 42.857 0.00 0.00 36.17 3.02
2370 2395 9.525409 GTGTTCGCTTAGTATATCCTTAAAAGA 57.475 33.333 0.00 0.00 0.00 2.52
2371 2396 8.762426 GGTGTTCGCTTAGTATATCCTTAAAAG 58.238 37.037 0.00 0.00 0.00 2.27
2401 2426 1.833630 TGCTCGGGATCTGACTTGAAT 59.166 47.619 0.00 0.00 0.00 2.57
2406 2431 0.976641 TTTGTGCTCGGGATCTGACT 59.023 50.000 0.00 0.00 0.00 3.41
2417 2442 4.082733 GGGAACACTTTAGGATTTGTGCTC 60.083 45.833 0.00 0.00 34.14 4.26
2418 2443 3.826729 GGGAACACTTTAGGATTTGTGCT 59.173 43.478 0.00 0.00 34.14 4.40
2443 2468 0.757561 TCGTTCAGAGGGTGTGGTCA 60.758 55.000 0.00 0.00 0.00 4.02
2444 2469 0.391597 TTCGTTCAGAGGGTGTGGTC 59.608 55.000 0.00 0.00 0.00 4.02
2446 2471 0.393077 AGTTCGTTCAGAGGGTGTGG 59.607 55.000 0.00 0.00 0.00 4.17
2456 2481 4.155280 TGTCATCATCTCGTAGTTCGTTCA 59.845 41.667 0.00 0.00 40.80 3.18
2467 2492 4.442403 CGAACCATTACTGTCATCATCTCG 59.558 45.833 0.00 0.00 0.00 4.04
2493 2518 3.202906 GTTTGCTCATATTGCCGTCCTA 58.797 45.455 0.00 0.00 0.00 2.94
2496 2521 1.856014 GCGTTTGCTCATATTGCCGTC 60.856 52.381 0.00 0.00 38.39 4.79
2497 2522 0.098728 GCGTTTGCTCATATTGCCGT 59.901 50.000 0.00 0.00 38.39 5.68
2498 2523 0.098552 TGCGTTTGCTCATATTGCCG 59.901 50.000 0.00 0.00 43.34 5.69
2499 2524 2.497107 ATGCGTTTGCTCATATTGCC 57.503 45.000 0.00 0.00 43.34 4.52
2500 2525 3.000523 CCAAATGCGTTTGCTCATATTGC 59.999 43.478 23.33 0.00 42.66 3.56
2501 2526 3.552699 CCCAAATGCGTTTGCTCATATTG 59.447 43.478 23.33 8.97 42.66 1.90
2505 2530 0.247185 CCCCAAATGCGTTTGCTCAT 59.753 50.000 23.33 0.00 42.66 2.90
2515 2540 0.614812 AAAGTGCCATCCCCAAATGC 59.385 50.000 0.00 0.00 0.00 3.56
2528 2553 4.800471 GCCATGCTCTTATAACAAAAGTGC 59.200 41.667 3.61 3.61 41.52 4.40
2547 2573 7.723172 TCAATGGAAAAAGGTAAAAATTGCCAT 59.277 29.630 0.00 0.00 37.96 4.40
2548 2574 7.056635 TCAATGGAAAAAGGTAAAAATTGCCA 58.943 30.769 0.14 0.00 37.96 4.92
2549 2575 7.503521 TCAATGGAAAAAGGTAAAAATTGCC 57.496 32.000 0.00 0.00 35.41 4.52
2586 2612 3.852286 TGCCATGCTGATTGAATGAAAC 58.148 40.909 0.00 0.00 33.39 2.78
2630 2656 2.417257 GCATGGAGAATTGCCGGCA 61.417 57.895 29.03 29.03 32.66 5.69
2651 2677 7.985184 AGAGTAATTGCCGTTTAGTCATGATTA 59.015 33.333 0.00 0.00 33.36 1.75
2657 2683 3.682858 GCAGAGTAATTGCCGTTTAGTCA 59.317 43.478 0.00 0.00 35.54 3.41
2665 2691 0.804364 TTGCAGCAGAGTAATTGCCG 59.196 50.000 0.00 0.00 42.48 5.69
2735 2774 6.717540 TGCTGTTACATAAGGTTTACCATGTT 59.282 34.615 9.37 0.00 35.22 2.71
2737 2776 6.751514 TGCTGTTACATAAGGTTTACCATG 57.248 37.500 1.13 0.08 38.89 3.66
2767 2807 6.932356 ATTGTCATGCGAGAACAGATAAAT 57.068 33.333 0.00 0.00 0.00 1.40
2772 2812 3.681417 CAGAATTGTCATGCGAGAACAGA 59.319 43.478 0.00 0.00 0.00 3.41
2780 2820 1.089112 TGCTCCAGAATTGTCATGCG 58.911 50.000 0.00 0.00 0.00 4.73
2821 2861 1.136721 ACGAACGAGCGTTTTCAATCG 60.137 47.619 9.80 9.88 42.71 3.34
2832 2872 1.068055 TCCAAGTAGGAACGAACGAGC 60.068 52.381 0.14 0.00 45.65 5.03
2844 2884 8.806146 CAAAATATTATTCCCCCATCCAAGTAG 58.194 37.037 0.00 0.00 0.00 2.57
2852 2892 5.781818 CCTGAGCAAAATATTATTCCCCCAT 59.218 40.000 0.00 0.00 0.00 4.00
2861 2901 4.127171 GAGGTCGCCTGAGCAAAATATTA 58.873 43.478 2.98 0.00 45.10 0.98
2919 2959 5.452078 TCGATCAGGCTGAAAATGTTTTT 57.548 34.783 22.84 0.46 0.00 1.94
2920 2960 5.183713 TGATCGATCAGGCTGAAAATGTTTT 59.816 36.000 23.99 1.31 32.11 2.43
2921 2961 4.701651 TGATCGATCAGGCTGAAAATGTTT 59.298 37.500 23.99 2.18 32.11 2.83
2922 2962 4.264253 TGATCGATCAGGCTGAAAATGTT 58.736 39.130 23.99 3.04 32.11 2.71
2923 2963 3.877559 TGATCGATCAGGCTGAAAATGT 58.122 40.909 23.99 3.91 32.11 2.71
2924 2964 4.888038 TTGATCGATCAGGCTGAAAATG 57.112 40.909 25.95 11.39 38.19 2.32
2935 3332 6.652900 TGACAACCACTAAATTTGATCGATCA 59.347 34.615 23.99 23.99 34.44 2.92
2951 3348 3.577805 ATATTAGGCCCTGACAACCAC 57.422 47.619 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.