Multiple sequence alignment - TraesCS3A01G481000

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 TraesCS3A01G481000 chr3A 100.000 4033 0 0 1 4033 712145153 712141121 0.000000e+00 7448
1 TraesCS3A01G481000 chr3D 90.085 3288 178 56 375 3558 576758573 576755330 0.000000e+00 4130
2 TraesCS3A01G481000 chr3D 84.553 861 66 29 3222 4033 576755176 576754334 0.000000e+00 791
3 TraesCS3A01G481000 chr3D 92.508 307 18 2 1 302 576758980 576758674 6.190000e-118 435
4 TraesCS3A01G481000 chr3B 90.881 2226 84 26 1909 4033 766980057 766982264 0.000000e+00 2876
5 TraesCS3A01G481000 chr3B 90.168 1546 87 24 384 1910 766978524 766980023 0.000000e+00 1953
6 TraesCS3A01G481000 chr3B 89.562 297 19 7 22 307 766978121 766978416 2.290000e-97 366
7 TraesCS3A01G481000 chr4B 88.889 108 7 3 3300 3407 609766938 609767040 1.180000e-25 128
8 TraesCS3A01G481000 chr4B 93.902 82 5 0 3300 3381 172833990 172834071 1.520000e-24 124
9 TraesCS3A01G481000 chr5B 93.902 82 5 0 3300 3381 76147882 76147963 1.520000e-24 124
10 TraesCS3A01G481000 chr5B 89.362 94 8 1 3300 3393 655980133 655980224 2.550000e-22 117
11 TraesCS3A01G481000 chr1A 93.902 82 5 0 3300 3381 4012438 4012519 1.520000e-24 124
12 TraesCS3A01G481000 chr1A 93.902 82 5 0 3300 3381 411508331 411508250 1.520000e-24 124
13 TraesCS3A01G481000 chr7D 89.362 94 8 2 3300 3393 86730303 86730394 2.550000e-22 117


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 TraesCS3A01G481000 chr3A 712141121 712145153 4032 True 7448.000000 7448 100.000000 1 4033 1 chr3A.!!$R1 4032
1 TraesCS3A01G481000 chr3D 576754334 576758980 4646 True 1785.333333 4130 89.048667 1 4033 3 chr3D.!!$R1 4032
2 TraesCS3A01G481000 chr3B 766978121 766982264 4143 False 1731.666667 2876 90.203667 22 4033 3 chr3B.!!$F1 4011

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
40 41 0.036952 ACTGTCTGGCGATGGTGAAG 60.037 55.0 0.0 0.0 0.0 3.02 F
553 639 0.179078 TGCAAGCAAAAGCAACAGGG 60.179 50.0 0.0 0.0 37.9 4.45 F
2388 2578 0.602905 CAACCCTCTTCCACACCGAC 60.603 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2139 1.088340 TCGCGAAGTCCGAGTAGAGG 61.088 60.0 6.2 0.0 41.76 3.69 R
2519 2709 0.179070 GATCTTGCCGAAGACCTCCC 60.179 60.0 0.0 0.0 41.12 4.30 R
3225 3458 0.379669 GAACGCATGATTGCCTCCAG 59.620 55.0 0.0 0.0 46.57 3.86 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
40 41 0.036952 ACTGTCTGGCGATGGTGAAG 60.037 55.000 0.00 0.00 0.00 3.02
219 230 1.309499 TTTACAAATCCGGCCGGCAG 61.309 55.000 39.89 27.75 34.68 4.85
254 265 4.463879 CTCTGCCGGAGCCTGGTG 62.464 72.222 5.05 0.00 38.69 4.17
284 296 1.614051 GGAACACACCTGCATGATCCA 60.614 52.381 8.91 0.00 0.00 3.41
288 300 0.921166 ACACCTGCATGATCCATGGA 59.079 50.000 18.88 18.88 41.64 3.41
304 316 9.901172 TGATCCATGGAGAATATATGATCTTTG 57.099 33.333 21.33 2.45 0.00 2.77
306 318 7.114754 TCCATGGAGAATATATGATCTTTGCC 58.885 38.462 11.44 0.00 0.00 4.52
307 319 6.037940 CCATGGAGAATATATGATCTTTGCCG 59.962 42.308 5.56 0.00 0.00 5.69
308 320 4.937620 TGGAGAATATATGATCTTTGCCGC 59.062 41.667 0.00 0.00 0.00 6.53
310 322 3.935203 AGAATATATGATCTTTGCCGCGG 59.065 43.478 24.05 24.05 0.00 6.46
311 323 1.438651 TATATGATCTTTGCCGCGGC 58.561 50.000 42.35 42.35 42.35 6.53
312 324 0.250467 ATATGATCTTTGCCGCGGCT 60.250 50.000 45.79 29.55 42.51 5.52
313 325 1.159713 TATGATCTTTGCCGCGGCTG 61.160 55.000 45.79 34.19 42.51 4.85
314 326 3.880846 GATCTTTGCCGCGGCTGG 61.881 66.667 45.79 33.69 42.51 4.85
343 371 1.661821 GGAATCGATCCGGTGCTCG 60.662 63.158 14.70 14.70 38.79 5.03
344 372 1.359117 GAATCGATCCGGTGCTCGA 59.641 57.895 22.02 22.02 46.71 4.04
345 373 3.765051 ATCGATCCGGTGCTCGAT 58.235 55.556 23.78 23.78 46.39 3.59
346 374 3.031495 TCGATCCGGTGCTCGATC 58.969 61.111 18.01 5.65 38.86 3.69
348 376 2.049985 GATCCGGTGCTCGATCGG 60.050 66.667 16.41 7.26 44.59 4.18
352 380 4.193334 CGGTGCTCGATCGGCTGA 62.193 66.667 22.99 0.00 42.43 4.26
357 385 3.069980 GCTCGATCGGCTGACAGGT 62.070 63.158 16.41 0.00 0.00 4.00
366 394 1.751351 CGGCTGACAGGTTCTCTGATA 59.249 52.381 4.26 0.00 46.18 2.15
368 396 2.763448 GGCTGACAGGTTCTCTGATACT 59.237 50.000 4.26 0.00 46.18 2.12
369 397 3.181480 GGCTGACAGGTTCTCTGATACTC 60.181 52.174 4.26 0.00 46.18 2.59
370 398 3.445450 GCTGACAGGTTCTCTGATACTCA 59.555 47.826 4.26 0.00 46.18 3.41
371 399 4.439974 GCTGACAGGTTCTCTGATACTCAG 60.440 50.000 4.26 0.00 46.18 3.35
390 452 4.527944 TCAGATATTGGAGTCGTGTCTCT 58.472 43.478 0.00 0.00 35.11 3.10
430 506 4.007644 CCGGCAGAGGCAGACACA 62.008 66.667 0.00 0.00 43.71 3.72
431 507 2.267006 CGGCAGAGGCAGACACAT 59.733 61.111 0.00 0.00 43.71 3.21
432 508 2.104859 CGGCAGAGGCAGACACATG 61.105 63.158 0.00 0.00 43.71 3.21
433 509 1.748122 GGCAGAGGCAGACACATGG 60.748 63.158 0.00 0.00 43.71 3.66
434 510 2.404995 GCAGAGGCAGACACATGGC 61.405 63.158 0.00 0.00 45.63 4.40
439 515 3.064324 GCAGACACATGGCACCCC 61.064 66.667 0.00 0.00 0.00 4.95
477 563 3.515286 GATGGACGAGACGGCGGA 61.515 66.667 13.24 0.00 34.63 5.54
494 580 1.450025 GGAGACCGGGCTGTAAAAAG 58.550 55.000 19.29 0.00 0.00 2.27
514 600 0.239879 AAACATTTGCGCCACTACGG 59.760 50.000 4.18 0.00 38.11 4.02
538 624 0.684535 TCTCCGTCCAGAATGTGCAA 59.315 50.000 0.00 0.00 0.00 4.08
548 634 2.867368 CAGAATGTGCAAGCAAAAGCAA 59.133 40.909 0.00 0.00 43.20 3.91
553 639 0.179078 TGCAAGCAAAAGCAACAGGG 60.179 50.000 0.00 0.00 37.90 4.45
588 674 3.095332 GGTCTTCCTACGGGTTCTACTT 58.905 50.000 0.00 0.00 0.00 2.24
593 679 3.535561 TCCTACGGGTTCTACTTCTACG 58.464 50.000 0.00 0.00 0.00 3.51
594 680 3.197766 TCCTACGGGTTCTACTTCTACGA 59.802 47.826 0.00 0.00 0.00 3.43
753 845 1.447643 CTCCATCCATCCCCACGAC 59.552 63.158 0.00 0.00 0.00 4.34
754 846 2.108976 CCATCCATCCCCACGACG 59.891 66.667 0.00 0.00 0.00 5.12
755 847 2.588877 CATCCATCCCCACGACGC 60.589 66.667 0.00 0.00 0.00 5.19
756 848 3.861797 ATCCATCCCCACGACGCC 61.862 66.667 0.00 0.00 0.00 5.68
772 864 1.925972 GCCCTTCACTCTCCCCCTT 60.926 63.158 0.00 0.00 0.00 3.95
773 865 1.994463 CCCTTCACTCTCCCCCTTG 59.006 63.158 0.00 0.00 0.00 3.61
805 912 1.002868 CTCCTGTTGCACCCTCCAG 60.003 63.158 0.00 0.00 0.00 3.86
826 937 0.946221 AAGCCAAGAACTCACTCGCG 60.946 55.000 0.00 0.00 0.00 5.87
840 951 2.051076 CGCGCGCCGGTAACTATA 60.051 61.111 27.72 0.00 0.00 1.31
841 952 2.078914 CGCGCGCCGGTAACTATAG 61.079 63.158 27.72 2.11 0.00 1.31
842 953 1.731969 GCGCGCCGGTAACTATAGG 60.732 63.158 23.24 0.00 0.00 2.57
843 954 1.731969 CGCGCCGGTAACTATAGGC 60.732 63.158 1.90 0.00 45.67 3.93
870 981 2.430694 GGTTGTTCTCCCTTGCAAGTTT 59.569 45.455 24.35 0.00 0.00 2.66
872 983 2.306847 TGTTCTCCCTTGCAAGTTTCC 58.693 47.619 24.35 8.16 0.00 3.13
929 1040 3.164977 TGCGTGGACACTTGGGGA 61.165 61.111 0.56 0.00 0.00 4.81
931 1042 2.347490 CGTGGACACTTGGGGAGG 59.653 66.667 0.56 0.00 0.00 4.30
934 1045 2.936032 GGACACTTGGGGAGGGCT 60.936 66.667 0.00 0.00 29.07 5.19
941 1052 1.345526 ACTTGGGGAGGGCTAGCTAAT 60.346 52.381 15.72 0.11 0.00 1.73
1141 1268 1.374758 CACCTCAGCTTCCACGACC 60.375 63.158 0.00 0.00 0.00 4.79
1147 1274 4.329545 GCTTCCACGACCTGGCCA 62.330 66.667 4.71 4.71 40.39 5.36
1363 1490 3.924013 ATGGAGTCACTCGGGGGCA 62.924 63.158 0.00 0.00 0.00 5.36
1383 1510 3.520862 GCCATGATGCGGGTGGTG 61.521 66.667 0.00 0.00 35.44 4.17
1384 1511 3.520862 CCATGATGCGGGTGGTGC 61.521 66.667 0.00 0.00 0.00 5.01
1386 1513 2.438975 ATGATGCGGGTGGTGCAG 60.439 61.111 0.00 0.00 46.98 4.41
1387 1514 2.970379 ATGATGCGGGTGGTGCAGA 61.970 57.895 0.00 0.00 46.98 4.26
1512 1642 2.496470 GACCGACTACCTCCATTTGACT 59.504 50.000 0.00 0.00 0.00 3.41
1647 1778 5.348451 GCCACACAAATTAATTAAGCACCAG 59.652 40.000 0.01 0.00 0.00 4.00
1665 1796 4.758674 CACCAGGCATCATCATTAACTAGG 59.241 45.833 0.00 0.00 0.00 3.02
1666 1797 4.660303 ACCAGGCATCATCATTAACTAGGA 59.340 41.667 0.00 0.00 0.00 2.94
1667 1798 5.221803 ACCAGGCATCATCATTAACTAGGAG 60.222 44.000 0.00 0.00 0.00 3.69
1686 1817 8.322091 ACTAGGAGTAGTCAGCAACAAATTAAT 58.678 33.333 0.00 0.00 34.00 1.40
1694 1825 8.396272 AGTCAGCAACAAATTAATCAGTAACT 57.604 30.769 0.00 0.00 0.00 2.24
1711 1842 6.546403 TCAGTAACTACATCTGTACCTGATCC 59.454 42.308 0.00 0.00 0.00 3.36
1722 1853 0.761187 ACCTGATCCATCGTCCCATG 59.239 55.000 0.00 0.00 0.00 3.66
1750 1881 1.422531 ATGCAGGGAGAGGAGATGTC 58.577 55.000 0.00 0.00 0.00 3.06
1887 2020 4.206404 GGTACGTGAATACATGATCACACG 59.794 45.833 24.32 24.32 44.84 4.49
1923 2091 6.924612 TCATTTGTCACATTTCATTCAGTTGG 59.075 34.615 0.00 0.00 0.00 3.77
1944 2117 4.895889 TGGACTGATCTCTTGGATACGATT 59.104 41.667 0.00 0.00 42.51 3.34
1945 2118 5.221322 TGGACTGATCTCTTGGATACGATTG 60.221 44.000 0.00 0.00 42.51 2.67
1966 2139 2.732619 GGTGAGGTGGATCCGGGTC 61.733 68.421 6.02 6.02 41.99 4.46
2011 2184 3.844090 GAGGACCAGGAGGCGCTC 61.844 72.222 7.64 2.45 39.06 5.03
2238 2411 4.531854 TGATTAATCATTTTCTCGCCCCA 58.468 39.130 14.23 0.00 0.00 4.96
2240 2413 4.916983 TTAATCATTTTCTCGCCCCATG 57.083 40.909 0.00 0.00 0.00 3.66
2266 2444 1.068333 ACAAATGCAGATGTTGACGCC 60.068 47.619 8.65 0.00 0.00 5.68
2295 2473 1.190643 CCCAGGTTGTGTGTGGTTTT 58.809 50.000 0.00 0.00 0.00 2.43
2296 2474 1.136110 CCCAGGTTGTGTGTGGTTTTC 59.864 52.381 0.00 0.00 0.00 2.29
2297 2475 1.821753 CCAGGTTGTGTGTGGTTTTCA 59.178 47.619 0.00 0.00 0.00 2.69
2302 2480 5.748152 CAGGTTGTGTGTGGTTTTCAATTAG 59.252 40.000 0.00 0.00 0.00 1.73
2310 2488 8.784043 GTGTGTGGTTTTCAATTAGTCTAATCT 58.216 33.333 5.56 0.00 0.00 2.40
2388 2578 0.602905 CAACCCTCTTCCACACCGAC 60.603 60.000 0.00 0.00 0.00 4.79
2535 2725 2.125512 CGGGAGGTCTTCGGCAAG 60.126 66.667 0.00 0.00 0.00 4.01
2565 2755 0.040942 ACAGCAACAATGGCCCCATA 59.959 50.000 0.00 0.00 35.31 2.74
2613 2803 3.755378 AGTAAGCAAAGCAGTTCCATCAG 59.245 43.478 0.00 0.00 0.00 2.90
2614 2804 2.574006 AGCAAAGCAGTTCCATCAGA 57.426 45.000 0.00 0.00 0.00 3.27
2616 2806 3.225104 AGCAAAGCAGTTCCATCAGAAA 58.775 40.909 0.00 0.00 35.85 2.52
2618 2808 3.858503 GCAAAGCAGTTCCATCAGAAACC 60.859 47.826 0.00 0.00 35.85 3.27
2619 2809 3.515602 AAGCAGTTCCATCAGAAACCT 57.484 42.857 0.00 0.00 35.85 3.50
2622 2812 5.184892 AGCAGTTCCATCAGAAACCTAAT 57.815 39.130 0.00 0.00 35.85 1.73
2623 2813 5.574188 AGCAGTTCCATCAGAAACCTAATT 58.426 37.500 0.00 0.00 35.85 1.40
2624 2814 6.012745 AGCAGTTCCATCAGAAACCTAATTT 58.987 36.000 0.00 0.00 35.85 1.82
2671 2866 4.484236 TGTACGTAGGTTTGATGGTAACG 58.516 43.478 0.00 0.00 42.51 3.18
2703 2898 2.837532 AAATTGACACATTGTGGGGC 57.162 45.000 20.33 10.01 37.94 5.80
2741 2936 0.528924 CGTCAGTGGTGATACCGGAA 59.471 55.000 9.46 0.00 42.58 4.30
2897 3092 2.499685 CTAGCGCCCTACACCACC 59.500 66.667 2.29 0.00 0.00 4.61
3011 3206 4.949856 GGACAGAGAATATTTCCAAAGGCA 59.050 41.667 0.00 0.00 0.00 4.75
3014 3209 6.189859 ACAGAGAATATTTCCAAAGGCATCA 58.810 36.000 0.00 0.00 0.00 3.07
3057 3252 1.377987 GCACCCGCCATGTAAAGGA 60.378 57.895 0.00 0.00 0.00 3.36
3150 3347 0.467290 AAAAGGCGGCCTGAAGAACA 60.467 50.000 24.63 0.00 32.13 3.18
3151 3348 1.172812 AAAGGCGGCCTGAAGAACAC 61.173 55.000 24.63 0.00 32.13 3.32
3190 3397 0.838987 TGGTGGGAGGTACCTCAACC 60.839 60.000 36.83 36.83 44.65 3.77
3225 3458 2.027653 AGAGCAGCCTGACCTTTAACTC 60.028 50.000 0.00 0.00 0.00 3.01
3407 3644 3.579151 ACTTCAGGGTAGAACCTTCAGTC 59.421 47.826 0.00 0.00 39.34 3.51
3410 3647 3.076182 TCAGGGTAGAACCTTCAGTCTCT 59.924 47.826 0.00 0.00 39.34 3.10
3411 3648 3.835395 CAGGGTAGAACCTTCAGTCTCTT 59.165 47.826 0.00 0.00 39.34 2.85
3415 4157 6.557633 AGGGTAGAACCTTCAGTCTCTTAAAA 59.442 38.462 0.00 0.00 37.69 1.52
3452 4195 4.335315 TCAGAACTACCTGCACAAGTTTTG 59.665 41.667 12.13 12.13 36.93 2.44
3470 4213 5.239525 AGTTTTGTTAAGCAGGCTCTGTTAG 59.760 40.000 0.00 0.00 33.43 2.34
3477 4220 4.464069 AGCAGGCTCTGTTAGTCTTTAG 57.536 45.455 4.45 0.00 38.42 1.85
3513 4256 3.284617 TGCTCTGAACTATGCATGCAAT 58.715 40.909 26.68 15.44 0.00 3.56
3530 4273 7.083858 GCATGCAATAGTAAAGTTTCTTGTCA 58.916 34.615 14.21 0.00 0.00 3.58
3587 4330 6.496218 AGCTTTTGGAAGGAAATTCTCTTGAT 59.504 34.615 2.31 0.00 38.07 2.57
3611 4354 3.314913 TGTGCATCCAACACTAACAGTTG 59.685 43.478 0.00 0.00 44.47 3.16
3621 4364 6.579666 AACACTAACAGTTGATAGTCCGTA 57.420 37.500 0.00 0.00 32.32 4.02
3688 4431 0.897621 CCAAAGGAATGGGCAGGAAC 59.102 55.000 0.00 0.00 36.79 3.62
3744 4487 2.014010 AGAAATGCCCCAAAAGCTGA 57.986 45.000 0.00 0.00 0.00 4.26
3845 4588 5.938125 TCATAGGTAACAAAGGAGAAACAGC 59.062 40.000 0.00 0.00 41.41 4.40
3862 4605 2.310538 CAGCCCAAGACAAAAGTTCCT 58.689 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 259 4.039092 CCTCCCAGTGGCACCAGG 62.039 72.222 15.27 16.45 0.00 4.45
251 262 2.034221 GTTCCTCCCAGTGGCACC 59.966 66.667 15.27 0.00 0.00 5.01
253 264 2.075566 TGTGTTCCTCCCAGTGGCA 61.076 57.895 2.61 0.00 0.00 4.92
254 265 1.600916 GTGTGTTCCTCCCAGTGGC 60.601 63.158 2.61 0.00 0.00 5.01
255 266 1.073199 GGTGTGTTCCTCCCAGTGG 59.927 63.158 0.63 0.63 0.00 4.00
256 267 0.250467 CAGGTGTGTTCCTCCCAGTG 60.250 60.000 0.00 0.00 35.37 3.66
257 268 2.056906 GCAGGTGTGTTCCTCCCAGT 62.057 60.000 0.00 0.00 35.37 4.00
258 269 1.302832 GCAGGTGTGTTCCTCCCAG 60.303 63.158 0.00 0.00 35.37 4.45
259 270 1.426251 ATGCAGGTGTGTTCCTCCCA 61.426 55.000 0.00 0.00 35.37 4.37
260 271 0.962356 CATGCAGGTGTGTTCCTCCC 60.962 60.000 0.00 0.00 35.37 4.30
284 296 5.587844 GCGGCAAAGATCATATATTCTCCAT 59.412 40.000 0.00 0.00 0.00 3.41
288 300 3.935203 CCGCGGCAAAGATCATATATTCT 59.065 43.478 14.67 0.00 0.00 2.40
325 337 4.345337 GAGCACCGGATCGATTCC 57.655 61.111 9.46 1.43 41.59 3.01
343 371 0.820871 AGAGAACCTGTCAGCCGATC 59.179 55.000 0.00 0.00 0.00 3.69
344 372 0.534412 CAGAGAACCTGTCAGCCGAT 59.466 55.000 0.00 0.00 38.10 4.18
345 373 0.539669 TCAGAGAACCTGTCAGCCGA 60.540 55.000 0.00 0.00 43.38 5.54
346 374 0.534412 ATCAGAGAACCTGTCAGCCG 59.466 55.000 0.00 0.00 43.38 5.52
348 376 3.445450 TGAGTATCAGAGAACCTGTCAGC 59.555 47.826 0.00 0.00 42.56 4.26
363 391 6.205853 AGACACGACTCCAATATCTGAGTATC 59.794 42.308 6.99 4.38 41.74 2.24
366 394 4.274147 AGACACGACTCCAATATCTGAGT 58.726 43.478 6.77 6.77 44.25 3.41
368 396 4.527944 AGAGACACGACTCCAATATCTGA 58.472 43.478 0.00 0.00 37.60 3.27
369 397 4.909696 AGAGACACGACTCCAATATCTG 57.090 45.455 0.00 0.00 37.60 2.90
370 398 4.339814 GGAAGAGACACGACTCCAATATCT 59.660 45.833 0.00 0.00 37.60 1.98
371 399 4.098044 TGGAAGAGACACGACTCCAATATC 59.902 45.833 0.00 0.00 37.60 1.63
372 400 4.023980 TGGAAGAGACACGACTCCAATAT 58.976 43.478 0.00 0.00 37.60 1.28
373 401 3.192844 GTGGAAGAGACACGACTCCAATA 59.807 47.826 0.00 0.00 37.60 1.90
375 403 1.340248 GTGGAAGAGACACGACTCCAA 59.660 52.381 0.00 0.00 37.60 3.53
377 405 1.068194 CAGTGGAAGAGACACGACTCC 60.068 57.143 0.00 0.00 43.41 3.85
378 406 1.068194 CCAGTGGAAGAGACACGACTC 60.068 57.143 1.68 0.00 43.41 3.36
379 407 0.962489 CCAGTGGAAGAGACACGACT 59.038 55.000 1.68 0.00 43.41 4.18
380 408 0.038159 CCCAGTGGAAGAGACACGAC 60.038 60.000 11.95 0.00 43.41 4.34
381 409 1.185618 CCCCAGTGGAAGAGACACGA 61.186 60.000 11.95 0.00 43.41 4.35
382 410 1.293498 CCCCAGTGGAAGAGACACG 59.707 63.158 11.95 0.00 43.41 4.49
390 452 2.547642 CGTTAAACGTACCCCAGTGGAA 60.548 50.000 11.95 0.00 36.74 3.53
433 509 4.892965 TATGCATGGGCGGGGTGC 62.893 66.667 10.16 0.00 45.35 5.01
434 510 2.906897 GTATGCATGGGCGGGGTG 60.907 66.667 10.16 0.00 45.35 4.61
435 511 2.766925 ATGTATGCATGGGCGGGGT 61.767 57.895 10.16 0.00 45.35 4.95
462 538 4.710167 TCTCCGCCGTCTCGTCCA 62.710 66.667 0.00 0.00 0.00 4.02
477 563 2.882761 GTTTCTTTTTACAGCCCGGTCT 59.117 45.455 0.00 0.00 0.00 3.85
494 580 1.602191 CGTAGTGGCGCAAATGTTTC 58.398 50.000 10.83 0.00 0.00 2.78
514 600 1.293924 CATTCTGGACGGAGACATGC 58.706 55.000 0.00 0.00 0.00 4.06
548 634 0.535102 CGACTGCTTGGTTTCCCTGT 60.535 55.000 0.00 0.00 0.00 4.00
553 639 1.531578 GAAGACCGACTGCTTGGTTTC 59.468 52.381 0.00 0.00 38.99 2.78
588 674 2.646175 GCCACTGCTGGGTCGTAGA 61.646 63.158 0.00 0.00 38.13 2.59
609 695 4.160635 GGCGCGGTCAACCAATCG 62.161 66.667 8.83 1.10 35.14 3.34
699 791 1.437573 GGGCAGATTTAAAGGGCGC 59.562 57.895 0.00 0.00 0.00 6.53
700 792 0.395724 AGGGGCAGATTTAAAGGGCG 60.396 55.000 0.00 0.00 0.00 6.13
701 793 1.403814 GAGGGGCAGATTTAAAGGGC 58.596 55.000 0.00 0.00 0.00 5.19
702 794 1.411644 GGGAGGGGCAGATTTAAAGGG 60.412 57.143 0.00 0.00 0.00 3.95
753 845 3.787001 GGGGGAGAGTGAAGGGCG 61.787 72.222 0.00 0.00 0.00 6.13
754 846 1.925972 AAGGGGGAGAGTGAAGGGC 60.926 63.158 0.00 0.00 0.00 5.19
755 847 0.842467 ACAAGGGGGAGAGTGAAGGG 60.842 60.000 0.00 0.00 0.00 3.95
756 848 0.615850 GACAAGGGGGAGAGTGAAGG 59.384 60.000 0.00 0.00 0.00 3.46
772 864 3.134792 GAGCGGCGGAGAGAGACA 61.135 66.667 9.78 0.00 0.00 3.41
773 865 3.894947 GGAGCGGCGGAGAGAGAC 61.895 72.222 9.78 0.00 0.00 3.36
805 912 0.514691 CGAGTGAGTTCTTGGCTTGC 59.485 55.000 0.00 0.00 0.00 4.01
826 937 0.666577 CTGCCTATAGTTACCGGCGC 60.667 60.000 0.00 0.00 45.36 6.53
836 947 4.192317 GAGAACAACCAACCTGCCTATAG 58.808 47.826 0.00 0.00 0.00 1.31
840 951 0.178990 GGAGAACAACCAACCTGCCT 60.179 55.000 0.00 0.00 0.00 4.75
841 952 1.179174 GGGAGAACAACCAACCTGCC 61.179 60.000 0.00 0.00 0.00 4.85
842 953 0.178990 AGGGAGAACAACCAACCTGC 60.179 55.000 0.00 0.00 0.00 4.85
843 954 1.956477 CAAGGGAGAACAACCAACCTG 59.044 52.381 0.00 0.00 0.00 4.00
929 1040 0.400093 AACCCCGATTAGCTAGCCCT 60.400 55.000 12.13 0.00 0.00 5.19
931 1042 0.250338 CCAACCCCGATTAGCTAGCC 60.250 60.000 12.13 0.00 0.00 3.93
934 1045 1.834301 GGCCAACCCCGATTAGCTA 59.166 57.895 0.00 0.00 0.00 3.32
1113 1240 4.803426 CTGAGGTGGCCGTCGAGC 62.803 72.222 0.00 0.00 0.00 5.03
1400 1530 2.203070 CGACATAGGCAGGCACCC 60.203 66.667 0.00 0.00 0.00 4.61
1401 1531 1.521681 GTCGACATAGGCAGGCACC 60.522 63.158 11.55 0.00 0.00 5.01
1403 1533 2.494445 CGTCGACATAGGCAGGCA 59.506 61.111 17.16 0.00 0.00 4.75
1512 1642 4.980805 GACAAGGTGCCGCCGACA 62.981 66.667 0.00 0.00 43.70 4.35
1647 1778 6.998802 ACTACTCCTAGTTAATGATGATGCC 58.001 40.000 0.00 0.00 27.62 4.40
1665 1796 8.034058 ACTGATTAATTTGTTGCTGACTACTC 57.966 34.615 0.00 0.00 0.00 2.59
1666 1797 7.986085 ACTGATTAATTTGTTGCTGACTACT 57.014 32.000 0.00 0.00 0.00 2.57
1667 1798 9.543018 GTTACTGATTAATTTGTTGCTGACTAC 57.457 33.333 0.00 0.00 0.00 2.73
1686 1817 6.546403 GGATCAGGTACAGATGTAGTTACTGA 59.454 42.308 13.97 13.97 33.75 3.41
1694 1825 4.470602 ACGATGGATCAGGTACAGATGTA 58.529 43.478 4.94 0.00 33.75 2.29
1698 1829 2.307768 GGACGATGGATCAGGTACAGA 58.692 52.381 0.00 0.00 0.00 3.41
1700 1831 1.342574 TGGGACGATGGATCAGGTACA 60.343 52.381 0.00 0.00 0.00 2.90
1711 1842 1.819928 TTGGTGTTCATGGGACGATG 58.180 50.000 0.00 0.00 0.00 3.84
1722 1853 1.815003 CTCTCCCTGCATTTGGTGTTC 59.185 52.381 0.00 0.00 0.00 3.18
1819 1950 1.126488 TCCTGGCTCTGGTGATGATC 58.874 55.000 0.00 0.00 0.00 2.92
1923 2091 4.683781 GCAATCGTATCCAAGAGATCAGTC 59.316 45.833 0.00 0.00 36.33 3.51
1944 2117 2.659063 CGGATCCACCTCACCTGCA 61.659 63.158 13.41 0.00 36.31 4.41
1945 2118 2.187946 CGGATCCACCTCACCTGC 59.812 66.667 13.41 0.00 36.31 4.85
1966 2139 1.088340 TCGCGAAGTCCGAGTAGAGG 61.088 60.000 6.20 0.00 41.76 3.69
2011 2184 2.725008 GTCTCCTCCGCCGAGATG 59.275 66.667 3.41 0.00 38.58 2.90
2044 2217 1.405526 CGGTTGATGATCACGAACCCT 60.406 52.381 23.13 0.00 35.40 4.34
2238 2411 7.475015 GTCAACATCTGCATTTGTATGTACAT 58.525 34.615 13.93 13.93 35.89 2.29
2240 2413 5.959527 CGTCAACATCTGCATTTGTATGTAC 59.040 40.000 2.44 0.00 32.44 2.90
2266 2444 4.994756 AACCTGGGCGGGCCAAAG 62.995 66.667 24.45 19.75 37.98 2.77
2302 2480 7.417612 TGCAAAGACAAAGACAAAGATTAGAC 58.582 34.615 0.00 0.00 0.00 2.59
2310 2488 3.381272 CCTCCTGCAAAGACAAAGACAAA 59.619 43.478 0.00 0.00 0.00 2.83
2388 2578 0.179205 GGAACTCGAGGTACGTGACG 60.179 60.000 18.41 2.24 43.13 4.35
2518 2708 1.961180 ATCTTGCCGAAGACCTCCCG 61.961 60.000 0.00 0.00 41.12 5.14
2519 2709 0.179070 GATCTTGCCGAAGACCTCCC 60.179 60.000 0.00 0.00 41.12 4.30
2535 2725 4.380233 CCATTGTTGCTGTCTTTCAGGATC 60.380 45.833 0.00 0.00 43.63 3.36
2565 2755 4.399483 TCTGTTTACTGGGTAGAGGAGT 57.601 45.455 0.00 0.00 0.00 3.85
2634 2829 1.202582 CGTACAACCAGAGGACAGAGG 59.797 57.143 0.00 0.00 0.00 3.69
2671 2866 6.325919 TGTGTCAATTTAACCACTTGATCC 57.674 37.500 0.00 0.00 32.05 3.36
2703 2898 2.669569 CCTGTTGTCCCACCTGCG 60.670 66.667 0.00 0.00 0.00 5.18
2897 3092 2.633509 GGCTTTCCACTGCTGCTGG 61.634 63.158 11.29 6.54 0.00 4.85
3011 3206 1.064906 CAAGAGGACATGGGCAGTGAT 60.065 52.381 0.00 0.00 0.00 3.06
3014 3209 0.326264 GTCAAGAGGACATGGGCAGT 59.674 55.000 0.00 0.00 46.19 4.40
3042 3237 1.472480 CAAAGTCCTTTACATGGCGGG 59.528 52.381 0.00 0.00 0.00 6.13
3057 3252 7.938140 ATGTACACCATATGCTTTACAAAGT 57.062 32.000 0.00 0.00 33.47 2.66
3150 3347 2.427453 ACTACTAGTTGCTATGCTGCGT 59.573 45.455 0.00 0.00 35.36 5.24
3151 3348 2.791560 CACTACTAGTTGCTATGCTGCG 59.208 50.000 0.00 0.00 35.36 5.18
3190 3397 2.992543 GCTGCTCTACTCTGAAGTGTTG 59.007 50.000 0.00 0.00 36.92 3.33
3225 3458 0.379669 GAACGCATGATTGCCTCCAG 59.620 55.000 0.00 0.00 46.57 3.86
3407 3644 7.869937 TCTGAGATGAGACAAGTGTTTTAAGAG 59.130 37.037 0.00 0.00 0.00 2.85
3410 3647 7.987458 AGTTCTGAGATGAGACAAGTGTTTTAA 59.013 33.333 0.00 0.00 0.00 1.52
3411 3648 7.500992 AGTTCTGAGATGAGACAAGTGTTTTA 58.499 34.615 0.00 0.00 0.00 1.52
3415 4157 5.047660 GGTAGTTCTGAGATGAGACAAGTGT 60.048 44.000 0.00 0.00 0.00 3.55
3452 4195 4.195225 AGACTAACAGAGCCTGCTTAAC 57.805 45.455 0.00 0.00 34.37 2.01
3470 4213 9.890352 GAGCATATCATTTTGATTCCTAAAGAC 57.110 33.333 0.00 0.00 38.26 3.01
3477 4220 7.938715 AGTTCAGAGCATATCATTTTGATTCC 58.061 34.615 0.00 0.00 38.26 3.01
3530 4273 6.320494 TGTAACAAGCGTGGTTGATTAAAT 57.680 33.333 17.73 0.00 0.00 1.40
3540 4283 5.351233 TTCACTATTTGTAACAAGCGTGG 57.649 39.130 4.26 0.00 0.00 4.94
3587 4330 4.905429 ACTGTTAGTGTTGGATGCACATA 58.095 39.130 0.00 0.00 39.17 2.29
3611 4354 6.266330 ACCACTATTTTACCCTACGGACTATC 59.734 42.308 0.00 0.00 0.00 2.08
3621 4364 6.715264 CAGAAGTTGAACCACTATTTTACCCT 59.285 38.462 0.00 0.00 0.00 4.34
3688 4431 6.626302 TCCTCACCAAAACTTTACACTTTTG 58.374 36.000 0.00 0.00 37.19 2.44
3744 4487 3.659334 CATCCGTTGCTGTGTGCT 58.341 55.556 0.00 0.00 43.37 4.40
3845 4588 8.348285 TCATAAATAGGAACTTTTGTCTTGGG 57.652 34.615 0.00 0.00 41.75 4.12
3887 4630 6.183361 TGCAAGTAGCCATCAATATGTAGAGT 60.183 38.462 0.00 0.00 44.83 3.24
3888 4631 6.226052 TGCAAGTAGCCATCAATATGTAGAG 58.774 40.000 0.00 0.00 44.83 2.43
3889 4632 6.173427 TGCAAGTAGCCATCAATATGTAGA 57.827 37.500 0.00 0.00 44.83 2.59
3937 4682 4.699925 AGTTGCCAGTACCAAGACTTTA 57.300 40.909 0.00 0.00 0.00 1.85
3938 4683 3.577805 AGTTGCCAGTACCAAGACTTT 57.422 42.857 0.00 0.00 0.00 2.66
3969 4740 3.435671 ACTGACACCGCAGCTTTTAATAC 59.564 43.478 0.00 0.00 39.51 1.89


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

AutoCloner maintained by Alex Coulton.