Multiple sequence alignment - TraesCS2A01G410700

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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 TraesCS2A01G410700 chr2A 100.000 2494 0 0 1 2494 668241767 668244260 0.000000e+00 4606.0
1 TraesCS2A01G410700 chr2A 72.826 460 80 25 2044 2494 579704016 579703593 5.640000e-22 115.0
2 TraesCS2A01G410700 chr2B 90.570 1983 117 30 541 2494 616934161 616936102 0.000000e+00 2562.0
3 TraesCS2A01G410700 chr2B 89.078 293 21 8 1 291 616933606 616933889 1.100000e-93 353.0
4 TraesCS2A01G410700 chr2B 75.610 287 65 5 981 1265 290519726 290520009 1.200000e-28 137.0
5 TraesCS2A01G410700 chr2D 93.620 1489 55 18 544 2012 523028053 523029521 0.000000e+00 2187.0
6 TraesCS2A01G410700 chr2D 90.787 521 34 7 1 507 523027544 523028064 0.000000e+00 684.0
7 TraesCS2A01G410700 chr2D 87.550 498 51 8 1998 2494 523123742 523124229 1.290000e-157 566.0
8 TraesCS2A01G410700 chr2D 76.753 271 63 0 981 1251 220670835 220671105 4.300000e-33 152.0
9 TraesCS2A01G410700 chr6B 83.333 276 44 2 977 1251 502484423 502484149 1.140000e-63 254.0
10 TraesCS2A01G410700 chr6B 86.792 159 21 0 1340 1498 502483350 502483192 7.090000e-41 178.0
11 TraesCS2A01G410700 chr6D 82.971 276 45 2 977 1251 320228156 320228430 5.330000e-62 248.0
12 TraesCS2A01G410700 chr6D 85.806 155 22 0 1341 1495 320229175 320229329 5.520000e-37 165.0
13 TraesCS2A01G410700 chr6A 82.182 275 49 0 977 1251 457685918 457686192 1.150000e-58 237.0
14 TraesCS2A01G410700 chr6A 87.097 155 20 0 1341 1495 457686958 457687112 2.550000e-40 176.0
15 TraesCS2A01G410700 chr3A 78.698 338 66 6 2157 2492 568247724 568247391 1.160000e-53 220.0
16 TraesCS2A01G410700 chr4B 81.564 179 29 4 1075 1251 475811240 475811416 7.190000e-31 145.0
17 TraesCS2A01G410700 chr4A 81.319 182 30 4 1072 1251 68689364 68689543 7.190000e-31 145.0
18 TraesCS2A01G410700 chr4D 81.006 179 30 4 1075 1251 387441775 387441951 3.340000e-29 139.0
19 TraesCS2A01G410700 chr5B 83.065 124 18 3 1362 1483 659984480 659984602 2.620000e-20 110.0
20 TraesCS2A01G410700 chr7B 76.159 151 28 8 2147 2291 465788254 465788106 3.440000e-09 73.1


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 TraesCS2A01G410700 chr2A 668241767 668244260 2493 False 4606.0 4606 100.0000 1 2494 1 chr2A.!!$F1 2493
1 TraesCS2A01G410700 chr2B 616933606 616936102 2496 False 1457.5 2562 89.8240 1 2494 2 chr2B.!!$F2 2493
2 TraesCS2A01G410700 chr2D 523027544 523029521 1977 False 1435.5 2187 92.2035 1 2012 2 chr2D.!!$F3 2011
3 TraesCS2A01G410700 chr6B 502483192 502484423 1231 True 216.0 254 85.0625 977 1498 2 chr6B.!!$R1 521
4 TraesCS2A01G410700 chr6D 320228156 320229329 1173 False 206.5 248 84.3885 977 1495 2 chr6D.!!$F1 518
5 TraesCS2A01G410700 chr6A 457685918 457687112 1194 False 206.5 237 84.6395 977 1495 2 chr6A.!!$F1 518

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
549 645 0.034186 TTTGCGAATCAGGCAGGGAT 60.034 50.0 0.0 0.0 42.12 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 3356 0.247185 CGGGCATTTCACCAAGCATT 59.753 50.0 0.0 0.0 0.0 3.56 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
120 124 5.517770 CAGCTCAAAGTCAAAAGGAAAACAG 59.482 40.000 0.00 0.00 0.00 3.16
121 125 5.418840 AGCTCAAAGTCAAAAGGAAAACAGA 59.581 36.000 0.00 0.00 0.00 3.41
172 176 1.660104 CAATGCCGCCATTTTTGTAGC 59.340 47.619 0.00 0.00 39.60 3.58
176 180 1.064952 GCCGCCATTTTTGTAGCGTAT 59.935 47.619 2.40 0.00 46.85 3.06
187 191 3.349488 TGTAGCGTATGTCGAGAATGG 57.651 47.619 0.00 0.00 42.86 3.16
226 230 1.827344 CTTTTTGGAGGAATCCCAGCC 59.173 52.381 0.00 0.00 34.77 4.85
227 231 1.084018 TTTTGGAGGAATCCCAGCCT 58.916 50.000 0.00 0.00 37.18 4.58
271 275 3.759527 TGTATCTGTCTACACTGCGAC 57.240 47.619 0.00 0.00 0.00 5.19
278 282 0.240145 TCTACACTGCGACGTTGGAG 59.760 55.000 21.60 21.60 0.00 3.86
280 284 0.669619 TACACTGCGACGTTGGAGAA 59.330 50.000 28.85 12.05 0.00 2.87
284 288 0.179215 CTGCGACGTTGGAGAAATGC 60.179 55.000 18.89 0.00 0.00 3.56
315 400 8.915057 AATTTGAAATATCTGATCGTCCATCT 57.085 30.769 0.00 0.00 31.92 2.90
326 411 4.649218 TGATCGTCCATCTGTCCTCATTAA 59.351 41.667 0.00 0.00 31.92 1.40
328 413 3.126831 CGTCCATCTGTCCTCATTAAGC 58.873 50.000 0.00 0.00 0.00 3.09
329 414 3.471680 GTCCATCTGTCCTCATTAAGCC 58.528 50.000 0.00 0.00 0.00 4.35
330 415 2.103094 TCCATCTGTCCTCATTAAGCCG 59.897 50.000 0.00 0.00 0.00 5.52
494 590 3.046087 CTGCTGTGCTGTCGTGGG 61.046 66.667 0.00 0.00 0.00 4.61
510 606 2.685999 GGCAGGGATGGAGCCTTT 59.314 61.111 0.00 0.00 44.92 3.11
511 607 1.000866 GGCAGGGATGGAGCCTTTT 59.999 57.895 0.00 0.00 44.92 2.27
512 608 0.615827 GGCAGGGATGGAGCCTTTTT 60.616 55.000 0.00 0.00 44.92 1.94
547 643 0.602562 TTTTTGCGAATCAGGCAGGG 59.397 50.000 0.00 0.00 42.12 4.45
548 644 0.251121 TTTTGCGAATCAGGCAGGGA 60.251 50.000 0.00 0.00 42.12 4.20
549 645 0.034186 TTTGCGAATCAGGCAGGGAT 60.034 50.000 0.00 0.00 42.12 3.85
550 646 0.749091 TTGCGAATCAGGCAGGGATG 60.749 55.000 0.00 0.00 42.12 3.51
551 647 1.895707 GCGAATCAGGCAGGGATGG 60.896 63.158 0.00 0.00 0.00 3.51
552 648 1.832219 CGAATCAGGCAGGGATGGA 59.168 57.895 0.00 0.00 0.00 3.41
553 649 0.250209 CGAATCAGGCAGGGATGGAG 60.250 60.000 0.00 0.00 0.00 3.86
554 650 0.536915 GAATCAGGCAGGGATGGAGC 60.537 60.000 0.00 0.00 0.00 4.70
566 662 1.282157 GGATGGAGCTTGGTTACAGGT 59.718 52.381 0.00 0.00 0.00 4.00
575 683 0.601558 TGGTTACAGGTCAGAGCGAC 59.398 55.000 0.00 0.00 44.57 5.19
593 701 2.677228 GGATGGGTGGTGTGGAGG 59.323 66.667 0.00 0.00 0.00 4.30
594 702 2.044946 GATGGGTGGTGTGGAGGC 60.045 66.667 0.00 0.00 0.00 4.70
595 703 2.858476 ATGGGTGGTGTGGAGGCA 60.858 61.111 0.00 0.00 0.00 4.75
596 704 2.826777 GATGGGTGGTGTGGAGGCAG 62.827 65.000 0.00 0.00 0.00 4.85
769 884 2.245438 CTCCTCCGGGCCTTGAGAAC 62.245 65.000 19.66 0.00 0.00 3.01
833 948 2.731976 CGTCCGTGGAAAGAAGAGAAAG 59.268 50.000 0.00 0.00 0.00 2.62
901 1019 2.202703 GGGTCGATGACGGTTCGG 60.203 66.667 2.74 0.00 40.21 4.30
912 1030 0.108945 ACGGTTCGGTTCGATCCTTC 60.109 55.000 10.71 1.41 41.78 3.46
927 1045 2.875296 TCCTTCTGGTTGGTTGATTGG 58.125 47.619 0.00 0.00 34.23 3.16
940 1058 5.579047 TGGTTGATTGGTTGATAATGAGGT 58.421 37.500 0.00 0.00 0.00 3.85
947 1065 4.517285 TGGTTGATAATGAGGTTGCTCTC 58.483 43.478 0.00 0.00 0.00 3.20
1287 1571 0.741927 TGCATGCATGGTCTCTCACG 60.742 55.000 27.34 0.00 0.00 4.35
1520 2433 0.249197 TCTCATCGCATCGCTCCTTG 60.249 55.000 0.00 0.00 0.00 3.61
1579 2492 4.519437 GTACCTGCGCCCCCGTAC 62.519 72.222 4.18 6.31 36.67 3.67
1708 2621 1.541588 GGCATGCCCGATCTTATTTCC 59.458 52.381 27.24 0.00 0.00 3.13
1768 2681 0.708918 GCTCGTTGTGTAAGCGACTC 59.291 55.000 0.00 0.00 0.00 3.36
1832 2745 1.550327 TTGTGGTGTGTTTTGCTCCA 58.450 45.000 0.00 0.00 0.00 3.86
1855 2768 1.134367 TCTCCTTATGTGCTCGTTCCG 59.866 52.381 0.00 0.00 0.00 4.30
1897 2810 4.724036 GCACTATCCAAAAGTTTAGACGCG 60.724 45.833 3.53 3.53 0.00 6.01
1919 2832 5.377358 CGTTTGTCTTCTGCTAGTGATTTG 58.623 41.667 0.00 0.00 0.00 2.32
1921 2834 6.292865 CGTTTGTCTTCTGCTAGTGATTTGAA 60.293 38.462 0.00 0.00 0.00 2.69
1922 2835 7.417612 GTTTGTCTTCTGCTAGTGATTTGAAA 58.582 34.615 0.00 0.00 0.00 2.69
1923 2836 7.566760 TTGTCTTCTGCTAGTGATTTGAAAA 57.433 32.000 0.00 0.00 0.00 2.29
1924 2837 7.566760 TGTCTTCTGCTAGTGATTTGAAAAA 57.433 32.000 0.00 0.00 0.00 1.94
1925 2838 7.642669 TGTCTTCTGCTAGTGATTTGAAAAAG 58.357 34.615 0.00 0.00 0.00 2.27
1995 2911 8.644374 TTTAACTTACAATGTAAGGGCATCTT 57.356 30.769 29.73 18.81 39.40 2.40
2001 2917 5.079643 ACAATGTAAGGGCATCTTCAAAGT 58.920 37.500 0.00 0.00 36.93 2.66
2041 2957 4.281435 TGCAAACATCCAGATGACATTGTT 59.719 37.500 14.42 0.00 41.20 2.83
2042 2958 5.221481 TGCAAACATCCAGATGACATTGTTT 60.221 36.000 14.42 8.66 41.20 2.83
2043 2959 5.697633 GCAAACATCCAGATGACATTGTTTT 59.302 36.000 14.42 0.29 41.20 2.43
2044 2960 6.347079 GCAAACATCCAGATGACATTGTTTTG 60.347 38.462 14.42 12.19 41.20 2.44
2045 2961 6.409524 AACATCCAGATGACATTGTTTTGT 57.590 33.333 14.42 0.00 41.20 2.83
2046 2962 6.409524 ACATCCAGATGACATTGTTTTGTT 57.590 33.333 14.42 0.00 41.20 2.83
2075 2991 1.231958 TTTGTCATCCAACGCCGTCC 61.232 55.000 0.00 0.00 31.20 4.79
2121 3037 2.360844 TGTCTGTTTTCTCGCAAACCA 58.639 42.857 0.00 0.00 36.03 3.67
2130 3046 2.229792 TCTCGCAAACCAGAAGCAAAT 58.770 42.857 0.00 0.00 0.00 2.32
2132 3048 2.727798 CTCGCAAACCAGAAGCAAATTG 59.272 45.455 0.00 0.00 0.00 2.32
2133 3049 1.794116 CGCAAACCAGAAGCAAATTGG 59.206 47.619 0.00 0.00 37.98 3.16
2159 3075 2.117423 GGGTGGGGAGTTTGTGGG 59.883 66.667 0.00 0.00 0.00 4.61
2164 3080 1.633945 GTGGGGAGTTTGTGGGAGTAT 59.366 52.381 0.00 0.00 0.00 2.12
2167 3083 1.913419 GGGAGTTTGTGGGAGTATGGA 59.087 52.381 0.00 0.00 0.00 3.41
2169 3085 2.304761 GGAGTTTGTGGGAGTATGGACA 59.695 50.000 0.00 0.00 0.00 4.02
2176 3092 2.279517 GAGTATGGACAGCCGCCG 60.280 66.667 0.00 0.00 36.79 6.46
2195 3111 1.823041 CGTAGGACTCCGACTCCCC 60.823 68.421 6.75 0.00 0.00 4.81
2215 3131 2.203922 GCCCACCCAAAACCCCAT 60.204 61.111 0.00 0.00 0.00 4.00
2223 3139 0.614697 CCAAAACCCCATCAGGACCC 60.615 60.000 0.00 0.00 38.24 4.46
2230 3146 1.528824 CCATCAGGACCCGCATCTT 59.471 57.895 0.00 0.00 36.89 2.40
2240 3156 0.181114 CCCGCATCTTCATCCCTTCA 59.819 55.000 0.00 0.00 0.00 3.02
2242 3158 2.038952 CCCGCATCTTCATCCCTTCATA 59.961 50.000 0.00 0.00 0.00 2.15
2266 3182 0.772124 TATGCATCCCCTTCCCTCCC 60.772 60.000 0.19 0.00 0.00 4.30
2267 3183 2.696125 GCATCCCCTTCCCTCCCA 60.696 66.667 0.00 0.00 0.00 4.37
2291 3207 2.663196 GTTGCCGCTCTACCACCT 59.337 61.111 0.00 0.00 0.00 4.00
2297 3213 3.075005 GCTCTACCACCTCGGCCA 61.075 66.667 2.24 0.00 39.03 5.36
2314 3230 4.035102 ACTCGCCAAGGCCTTCCC 62.035 66.667 17.29 8.50 37.98 3.97
2321 3237 3.009714 AAGGCCTTCCCGGACCTC 61.010 66.667 13.78 0.00 44.54 3.85
2341 3257 3.461773 CGACCTCGGCCACTCCAT 61.462 66.667 2.24 0.00 35.37 3.41
2352 3268 3.390521 ACTCCATCCGCTCGCCAA 61.391 61.111 0.00 0.00 0.00 4.52
2360 3276 2.330041 CGCTCGCCAAACCGTTTT 59.670 55.556 0.00 0.00 0.00 2.43
2365 3281 1.196127 CTCGCCAAACCGTTTTCCTAC 59.804 52.381 0.00 0.00 0.00 3.18
2368 3284 0.945813 CCAAACCGTTTTCCTACGCA 59.054 50.000 0.00 0.00 40.10 5.24
2390 3306 2.567049 GTCCACACCTCTCGTCCG 59.433 66.667 0.00 0.00 0.00 4.79
2391 3307 1.970114 GTCCACACCTCTCGTCCGA 60.970 63.158 0.00 0.00 0.00 4.55
2395 3311 3.054503 CACCTCTCGTCCGACCGT 61.055 66.667 0.00 0.00 0.00 4.83
2397 3313 3.862402 CCTCTCGTCCGACCGTCG 61.862 72.222 14.15 14.15 40.07 5.12
2398 3314 3.117171 CTCTCGTCCGACCGTCGT 61.117 66.667 19.13 0.00 38.40 4.34
2440 3356 4.612412 GGTCACCACGCCCGACAA 62.612 66.667 0.00 0.00 0.00 3.18
2466 3382 1.102978 GGTGAAATGCCCGTGCTAAT 58.897 50.000 0.00 0.00 38.71 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.403583 TCATCAATGAAATCATCTTCAAGATCA 57.596 29.630 0.00 0.00 38.75 2.92
120 124 8.817100 CCAAAGAATTTTACAACTTTTGGAGTC 58.183 33.333 7.17 0.00 35.03 3.36
121 125 8.318412 ACCAAAGAATTTTACAACTTTTGGAGT 58.682 29.630 17.15 0.00 35.03 3.85
172 176 4.230314 AGATGACCATTCTCGACATACG 57.770 45.455 0.00 0.00 44.09 3.06
176 180 3.099905 AGGAAGATGACCATTCTCGACA 58.900 45.455 0.00 0.00 0.00 4.35
187 191 6.581171 AAAAGAATTGTCCAGGAAGATGAC 57.419 37.500 0.00 0.00 0.00 3.06
271 275 7.424803 TCAAATTATATGGCATTTCTCCAACG 58.575 34.615 4.78 0.00 37.13 4.10
300 385 2.890311 GAGGACAGATGGACGATCAGAT 59.110 50.000 0.00 0.00 32.86 2.90
315 400 0.981183 ACCACGGCTTAATGAGGACA 59.019 50.000 0.00 0.00 0.00 4.02
326 411 2.552315 CAAATTCTGTGTAACCACGGCT 59.448 45.455 0.00 0.00 45.84 5.52
354 439 2.741878 CGCTCGTAGAACCCCATGAATT 60.742 50.000 0.00 0.00 34.09 2.17
356 441 0.174845 CGCTCGTAGAACCCCATGAA 59.825 55.000 0.00 0.00 34.09 2.57
494 590 2.982026 AAAAAGGCTCCATCCCTGC 58.018 52.632 0.00 0.00 31.73 4.85
528 624 0.602562 CCCTGCCTGATTCGCAAAAA 59.397 50.000 0.00 0.00 35.40 1.94
529 625 0.251121 TCCCTGCCTGATTCGCAAAA 60.251 50.000 0.00 0.00 35.40 2.44
530 626 0.034186 ATCCCTGCCTGATTCGCAAA 60.034 50.000 0.00 0.00 35.40 3.68
531 627 0.749091 CATCCCTGCCTGATTCGCAA 60.749 55.000 0.00 0.00 35.40 4.85
532 628 1.153107 CATCCCTGCCTGATTCGCA 60.153 57.895 0.00 0.00 34.41 5.10
533 629 1.895707 CCATCCCTGCCTGATTCGC 60.896 63.158 0.00 0.00 0.00 4.70
534 630 0.250209 CTCCATCCCTGCCTGATTCG 60.250 60.000 0.00 0.00 0.00 3.34
535 631 0.536915 GCTCCATCCCTGCCTGATTC 60.537 60.000 0.00 0.00 0.00 2.52
536 632 0.992431 AGCTCCATCCCTGCCTGATT 60.992 55.000 0.00 0.00 0.00 2.57
537 633 0.992431 AAGCTCCATCCCTGCCTGAT 60.992 55.000 0.00 0.00 0.00 2.90
538 634 1.617536 AAGCTCCATCCCTGCCTGA 60.618 57.895 0.00 0.00 0.00 3.86
539 635 1.453379 CAAGCTCCATCCCTGCCTG 60.453 63.158 0.00 0.00 0.00 4.85
540 636 2.687610 CCAAGCTCCATCCCTGCCT 61.688 63.158 0.00 0.00 0.00 4.75
541 637 2.123982 CCAAGCTCCATCCCTGCC 60.124 66.667 0.00 0.00 0.00 4.85
542 638 0.255890 TAACCAAGCTCCATCCCTGC 59.744 55.000 0.00 0.00 0.00 4.85
543 639 1.281867 TGTAACCAAGCTCCATCCCTG 59.718 52.381 0.00 0.00 0.00 4.45
544 640 1.561542 CTGTAACCAAGCTCCATCCCT 59.438 52.381 0.00 0.00 0.00 4.20
545 641 1.408822 CCTGTAACCAAGCTCCATCCC 60.409 57.143 0.00 0.00 0.00 3.85
546 642 1.282157 ACCTGTAACCAAGCTCCATCC 59.718 52.381 0.00 0.00 0.00 3.51
547 643 2.027192 TGACCTGTAACCAAGCTCCATC 60.027 50.000 0.00 0.00 0.00 3.51
548 644 1.985159 TGACCTGTAACCAAGCTCCAT 59.015 47.619 0.00 0.00 0.00 3.41
549 645 1.347707 CTGACCTGTAACCAAGCTCCA 59.652 52.381 0.00 0.00 0.00 3.86
550 646 1.623811 TCTGACCTGTAACCAAGCTCC 59.376 52.381 0.00 0.00 0.00 4.70
551 647 2.933056 GCTCTGACCTGTAACCAAGCTC 60.933 54.545 0.00 0.00 0.00 4.09
552 648 1.002544 GCTCTGACCTGTAACCAAGCT 59.997 52.381 0.00 0.00 0.00 3.74
553 649 1.443802 GCTCTGACCTGTAACCAAGC 58.556 55.000 0.00 0.00 0.00 4.01
554 650 1.272490 TCGCTCTGACCTGTAACCAAG 59.728 52.381 0.00 0.00 0.00 3.61
566 662 2.362503 ACCCATCCGTCGCTCTGA 60.363 61.111 0.00 0.00 0.00 3.27
575 683 2.268920 CTCCACACCACCCATCCG 59.731 66.667 0.00 0.00 0.00 4.18
722 837 0.688487 CCGGGCGAAATATAGGGGAA 59.312 55.000 0.00 0.00 0.00 3.97
833 948 2.903855 CCATGGCTGACGATGGGC 60.904 66.667 0.00 0.00 36.26 5.36
881 996 0.668096 CGAACCGTCATCGACCCAAA 60.668 55.000 0.00 0.00 42.76 3.28
886 1001 1.400990 CGAACCGAACCGTCATCGAC 61.401 60.000 0.00 0.00 42.76 4.20
891 1006 1.213537 GGATCGAACCGAACCGTCA 59.786 57.895 0.00 0.00 38.86 4.35
901 1019 2.474410 ACCAACCAGAAGGATCGAAC 57.526 50.000 0.00 0.00 38.69 3.95
912 1030 5.720371 TTATCAACCAATCAACCAACCAG 57.280 39.130 0.00 0.00 0.00 4.00
927 1045 4.184629 ACGAGAGCAACCTCATTATCAAC 58.815 43.478 0.00 0.00 40.68 3.18
940 1058 2.486203 ACAACAACAACAACGAGAGCAA 59.514 40.909 0.00 0.00 0.00 3.91
947 1065 3.731216 TCACACAAACAACAACAACAACG 59.269 39.130 0.00 0.00 0.00 4.10
1090 1208 4.935495 CACCACCACCTGCTGCGT 62.935 66.667 0.00 0.00 0.00 5.24
1298 1582 1.923204 GCACAGATCGTTCACTAGCTG 59.077 52.381 0.00 0.00 0.00 4.24
1708 2621 1.604593 CACCTCAGCAACAAGGGGG 60.605 63.158 0.00 0.00 36.95 5.40
1832 2745 1.853963 ACGAGCACATAAGGAGACCT 58.146 50.000 0.00 0.00 33.87 3.85
1874 2787 4.648970 GCGTCTAAACTTTTGGATAGTGC 58.351 43.478 0.00 0.00 30.29 4.40
1897 2810 6.545504 TCAAATCACTAGCAGAAGACAAAC 57.454 37.500 0.00 0.00 0.00 2.93
1972 2888 7.398829 TGAAGATGCCCTTACATTGTAAGTTA 58.601 34.615 26.81 16.65 34.68 2.24
1974 2890 5.815581 TGAAGATGCCCTTACATTGTAAGT 58.184 37.500 26.81 14.01 34.68 2.24
1975 2891 6.757897 TTGAAGATGCCCTTACATTGTAAG 57.242 37.500 23.82 23.82 34.68 2.34
1976 2892 6.719370 ACTTTGAAGATGCCCTTACATTGTAA 59.281 34.615 8.86 8.86 34.68 2.41
1977 2893 6.245408 ACTTTGAAGATGCCCTTACATTGTA 58.755 36.000 0.00 0.00 34.68 2.41
1980 2896 6.721318 TCTACTTTGAAGATGCCCTTACATT 58.279 36.000 0.00 0.00 34.68 2.71
1995 2911 6.049149 CAGGCGATTTAAGGATCTACTTTGA 58.951 40.000 0.00 0.00 32.02 2.69
2001 2917 4.415881 TTGCAGGCGATTTAAGGATCTA 57.584 40.909 0.00 0.00 0.00 1.98
2041 2957 2.685388 TGACAAACTGCATCCGAACAAA 59.315 40.909 0.00 0.00 0.00 2.83
2042 2958 2.293170 TGACAAACTGCATCCGAACAA 58.707 42.857 0.00 0.00 0.00 2.83
2043 2959 1.960417 TGACAAACTGCATCCGAACA 58.040 45.000 0.00 0.00 0.00 3.18
2044 2960 3.122937 GATGACAAACTGCATCCGAAC 57.877 47.619 0.00 0.00 35.91 3.95
2138 3054 1.782608 ACAAACTCCCCACCCCCAT 60.783 57.895 0.00 0.00 0.00 4.00
2141 3057 2.117423 CCACAAACTCCCCACCCC 59.883 66.667 0.00 0.00 0.00 4.95
2150 3066 2.290323 GCTGTCCATACTCCCACAAACT 60.290 50.000 0.00 0.00 0.00 2.66
2159 3075 2.279517 CGGCGGCTGTCCATACTC 60.280 66.667 7.61 0.00 0.00 2.59
2176 3092 2.479750 GGGAGTCGGAGTCCTACGC 61.480 68.421 26.66 8.36 37.84 4.42
2195 3111 2.922503 GGGTTTTGGGTGGGCCAG 60.923 66.667 6.40 0.00 36.17 4.85
2204 3120 0.614697 GGGTCCTGATGGGGTTTTGG 60.615 60.000 0.00 0.00 35.33 3.28
2215 3131 0.465705 GATGAAGATGCGGGTCCTGA 59.534 55.000 0.31 0.00 0.00 3.86
2223 3139 5.704515 AGAAATATGAAGGGATGAAGATGCG 59.295 40.000 0.00 0.00 0.00 4.73
2226 3142 8.388589 TGCATAGAAATATGAAGGGATGAAGAT 58.611 33.333 0.00 0.00 0.00 2.40
2230 3146 7.114754 GGATGCATAGAAATATGAAGGGATGA 58.885 38.462 0.00 0.00 0.00 2.92
2240 3156 4.860278 AGGGAAGGGGATGCATAGAAATAT 59.140 41.667 0.00 0.00 0.00 1.28
2242 3158 3.066704 AGGGAAGGGGATGCATAGAAAT 58.933 45.455 0.00 0.00 0.00 2.17
2297 3213 4.035102 GGGAAGGCCTTGGCGAGT 62.035 66.667 26.25 0.00 0.00 4.18
2303 3219 3.330720 AGGTCCGGGAAGGCCTTG 61.331 66.667 26.25 8.70 41.65 3.61
2324 3240 3.432051 GATGGAGTGGCCGAGGTCG 62.432 68.421 0.00 0.00 40.66 4.79
2335 3251 2.954684 TTTGGCGAGCGGATGGAGT 61.955 57.895 0.00 0.00 0.00 3.85
2338 3254 3.508840 GGTTTGGCGAGCGGATGG 61.509 66.667 0.00 0.00 0.00 3.51
2341 3257 4.612412 AACGGTTTGGCGAGCGGA 62.612 61.111 14.97 0.00 44.18 5.54
2352 3268 1.232621 GGCTGCGTAGGAAAACGGTT 61.233 55.000 1.76 0.00 43.06 4.44
2390 3306 0.389426 ATGGTACTTGCACGACGGTC 60.389 55.000 0.00 0.00 0.00 4.79
2391 3307 0.389426 GATGGTACTTGCACGACGGT 60.389 55.000 0.00 0.00 0.00 4.83
2395 3311 1.447140 GCGGATGGTACTTGCACGA 60.447 57.895 0.00 0.00 0.00 4.35
2397 3313 2.112815 GGGCGGATGGTACTTGCAC 61.113 63.158 0.00 0.00 0.00 4.57
2398 3314 2.270850 GGGCGGATGGTACTTGCA 59.729 61.111 0.00 0.00 0.00 4.08
2440 3356 0.247185 CGGGCATTTCACCAAGCATT 59.753 50.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.