Multiple sequence alignment - TraesCS1B01G269900

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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 TraesCS1B01G269900 chr1B 100.000 3915 0 0 1 3915 474452729 474448815 0.000000e+00 7230
1 TraesCS1B01G269900 chr1D 93.928 2701 146 9 677 3365 352235630 352232936 0.000000e+00 4063
2 TraesCS1B01G269900 chr1D 91.713 362 18 6 6 356 352236296 352235936 3.510000e-135 492
3 TraesCS1B01G269900 chr1D 93.885 278 10 5 412 683 352235939 352235663 2.810000e-111 412
4 TraesCS1B01G269900 chr1D 95.187 187 7 2 3729 3915 352232827 352232643 1.060000e-75 294
5 TraesCS1B01G269900 chr1A 93.879 2663 145 9 672 3320 452761390 452758732 0.000000e+00 3999
6 TraesCS1B01G269900 chr1A 93.182 396 21 5 290 683 452761815 452761424 9.430000e-161 577
7 TraesCS1B01G269900 chr1A 81.987 594 55 17 3357 3915 452757856 452757280 1.280000e-124 457
8 TraesCS1B01G269900 chr1A 91.892 148 3 7 6 148 452762311 452762168 8.580000e-47 198
9 TraesCS1B01G269900 chr5A 91.584 404 25 5 3483 3880 6168114 6168514 2.060000e-152 549
10 TraesCS1B01G269900 chr2A 93.610 313 14 4 3483 3791 38315994 38316304 2.760000e-126 462
11 TraesCS1B01G269900 chr3B 77.083 576 117 14 1067 1636 672744666 672744100 6.310000e-83 318
12 TraesCS1B01G269900 chr3D 77.447 470 100 6 1067 1533 511181109 511180643 3.850000e-70 276


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 TraesCS1B01G269900 chr1B 474448815 474452729 3914 True 7230.00 7230 100.00000 1 3915 1 chr1B.!!$R1 3914
1 TraesCS1B01G269900 chr1D 352232643 352236296 3653 True 1315.25 4063 93.67825 6 3915 4 chr1D.!!$R1 3909
2 TraesCS1B01G269900 chr1A 452757280 452762311 5031 True 1307.75 3999 90.23500 6 3915 4 chr1A.!!$R1 3909
3 TraesCS1B01G269900 chr3B 672744100 672744666 566 True 318.00 318 77.08300 1067 1636 1 chr3B.!!$R1 569

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
190 205 0.027194 CTGTGGCGCGAATGATCTTG 59.973 55.0 12.1 0.0 0.0 3.02 F
1065 1356 0.181587 TGGTCTTCCCTTGTTTCGCA 59.818 50.0 0.0 0.0 0.0 5.10 F
2566 2858 0.034059 ACAGCTTCGGAGTGGTTCTG 59.966 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1485 0.036732 TCTCATCTGGGTGCCAACAC 59.963 55.000 0.00 0.0 46.66 3.32 R
2596 2888 0.607489 CTGGAGCTGTGGAAACCTGG 60.607 60.000 0.00 0.0 0.00 4.45 R
3503 4639 1.383109 TGATCGGAGGGAGCACCAT 60.383 57.895 1.58 0.0 43.89 3.55 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
31 36 3.036959 TCCTCCCTCCTCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
96 102 2.727392 CCGGTTCCCACCTATGCGA 61.727 63.158 0.00 0.00 41.64 5.10
152 166 4.564769 CGCCTCTTCTCTCAGATTTTGTAC 59.435 45.833 0.00 0.00 0.00 2.90
159 173 8.370940 TCTTCTCTCAGATTTTGTACATGTTCT 58.629 33.333 2.30 0.00 0.00 3.01
161 175 8.539770 TCTCTCAGATTTTGTACATGTTCTTC 57.460 34.615 2.30 0.00 0.00 2.87
168 182 6.403866 TTTTGTACATGTTCTTCCATGCTT 57.596 33.333 2.30 0.00 44.88 3.91
190 205 0.027194 CTGTGGCGCGAATGATCTTG 59.973 55.000 12.10 0.00 0.00 3.02
198 213 1.745141 GCGAATGATCTTGGGAGTGCT 60.745 52.381 0.00 0.00 0.00 4.40
282 476 0.968901 AGAGTTGCCATGCCCATGTG 60.969 55.000 7.42 1.07 37.11 3.21
340 565 3.989787 CGGGTTTGTTGCTGGGGC 61.990 66.667 0.00 0.00 39.26 5.80
373 598 1.149627 CAAGGGGTTTGTCCGTCCA 59.850 57.895 0.00 0.00 37.00 4.02
437 663 0.624500 TGGGAGGGAAATCAGGGAGG 60.625 60.000 0.00 0.00 0.00 4.30
507 734 5.467735 CCTTTTGGAGATTTTTCTTTGCTGG 59.532 40.000 0.00 0.00 44.07 4.85
610 839 9.797556 ATATTTAATAAGAAAAACCTCGTTGGC 57.202 29.630 0.00 0.00 40.22 4.52
624 857 4.881850 CCTCGTTGGCTGTTCCTATAAATT 59.118 41.667 0.00 0.00 35.26 1.82
695 978 6.074569 CGGTTGCAAGTTTTTACTGTTATTGG 60.075 38.462 0.00 0.00 0.00 3.16
704 987 4.847990 TTACTGTTATTGGTAGGGGTGG 57.152 45.455 0.00 0.00 0.00 4.61
713 996 4.513406 TTGGTAGGGGTGGTGATTAATC 57.487 45.455 8.60 8.60 0.00 1.75
957 1243 4.800993 CGTACAGGTGAAGCTTGAATCTAG 59.199 45.833 2.10 0.00 0.00 2.43
967 1258 6.992123 TGAAGCTTGAATCTAGAAGTTGTCAA 59.008 34.615 2.10 1.77 0.00 3.18
969 1260 6.763355 AGCTTGAATCTAGAAGTTGTCAAGA 58.237 36.000 23.58 0.00 42.87 3.02
1045 1336 5.488341 TGAGGGTTATTCTTCTACTGTTGC 58.512 41.667 0.00 0.00 0.00 4.17
1065 1356 0.181587 TGGTCTTCCCTTGTTTCGCA 59.818 50.000 0.00 0.00 0.00 5.10
1069 1360 2.416893 GTCTTCCCTTGTTTCGCATCTC 59.583 50.000 0.00 0.00 0.00 2.75
1077 1368 1.800586 TGTTTCGCATCTCAAGCTGAC 59.199 47.619 0.00 0.00 0.00 3.51
1081 1372 0.575859 CGCATCTCAAGCTGACATCG 59.424 55.000 0.00 0.00 0.00 3.84
1112 1403 2.808523 TCTGTTCAGCAGTCAGTGAG 57.191 50.000 0.00 0.00 45.23 3.51
1151 1442 6.290294 ACTCAAATCCTCATGGAATTTTGG 57.710 37.500 9.75 5.43 46.80 3.28
1156 1447 4.125124 TCCTCATGGAATTTTGGGAACA 57.875 40.909 0.00 0.00 39.87 3.18
1167 1458 3.034924 TGGGAACAACACTGATGGC 57.965 52.632 0.00 0.00 37.44 4.40
1194 1485 1.881252 CCGATTTACCGGCGTGGAG 60.881 63.158 6.01 0.00 43.25 3.86
1206 1497 2.194597 GTGGAGTGTTGGCACCCA 59.805 61.111 0.00 0.00 46.35 4.51
1298 1589 5.111989 TCAGAATTGTAGCAGTATGACAGC 58.888 41.667 0.00 0.00 39.69 4.40
1330 1621 6.152661 TCTGTCAAACAACAACTTTTCAGGAT 59.847 34.615 0.00 0.00 0.00 3.24
1394 1685 3.118261 TCATTGGACCTCTCCTACAATGC 60.118 47.826 10.00 0.00 44.76 3.56
1405 1696 2.487762 TCCTACAATGCTTTTTCTGGCG 59.512 45.455 0.00 0.00 0.00 5.69
1486 1777 3.056607 CCAGTTTAGTGGCCAAATTCCAG 60.057 47.826 7.24 0.00 33.63 3.86
1488 1779 2.298729 GTTTAGTGGCCAAATTCCAGCA 59.701 45.455 7.24 0.00 33.63 4.41
1494 1785 1.070601 GGCCAAATTCCAGCACAGTTT 59.929 47.619 0.00 0.00 0.00 2.66
1495 1786 2.407090 GCCAAATTCCAGCACAGTTTC 58.593 47.619 0.00 0.00 0.00 2.78
1497 1788 3.740764 GCCAAATTCCAGCACAGTTTCAA 60.741 43.478 0.00 0.00 0.00 2.69
1505 1796 4.816385 TCCAGCACAGTTTCAACTTCTTAG 59.184 41.667 0.00 0.00 37.08 2.18
1509 1800 4.506654 GCACAGTTTCAACTTCTTAGTCGA 59.493 41.667 0.00 0.00 37.08 4.20
1513 1804 8.428536 CACAGTTTCAACTTCTTAGTCGATTAG 58.571 37.037 0.00 0.00 37.08 1.73
1516 1807 8.521176 AGTTTCAACTTCTTAGTCGATTAGCTA 58.479 33.333 0.00 0.00 35.21 3.32
1527 1818 8.942338 TTAGTCGATTAGCTACATTCAATGTT 57.058 30.769 8.69 0.00 41.63 2.71
1538 1829 3.890756 ACATTCAATGTTGCAGAGAACCA 59.109 39.130 0.00 0.00 41.63 3.67
1559 1850 4.202609 CCAACTATCAGGGCCTATTCCATT 60.203 45.833 5.28 0.00 0.00 3.16
1568 1859 4.835056 AGGGCCTATTCCATTTTCATTAGC 59.165 41.667 2.82 0.00 0.00 3.09
1570 1861 5.509670 GGGCCTATTCCATTTTCATTAGCAC 60.510 44.000 0.84 0.00 0.00 4.40
1575 1866 9.090692 CCTATTCCATTTTCATTAGCACAAAAG 57.909 33.333 0.00 0.00 0.00 2.27
1579 1870 8.140677 TCCATTTTCATTAGCACAAAAGTTTG 57.859 30.769 2.22 2.22 43.62 2.93
1580 1871 7.226325 TCCATTTTCATTAGCACAAAAGTTTGG 59.774 33.333 8.55 0.00 42.34 3.28
1635 1926 2.785269 TGGGGCTCCATTAGATGAATGT 59.215 45.455 0.00 0.00 43.09 2.71
1671 1962 0.109964 GCAAGAACAACGCGGCAATA 60.110 50.000 12.47 0.00 0.00 1.90
1672 1963 1.664588 GCAAGAACAACGCGGCAATAA 60.665 47.619 12.47 0.00 0.00 1.40
1680 1971 1.008538 CGCGGCAATAATTGGAGCC 60.009 57.895 0.00 6.76 43.61 4.70
1797 2088 4.519540 TGAAAATAAGTGGGCAAAGAGC 57.480 40.909 0.00 0.00 44.65 4.09
1835 2126 8.642908 AAAACAATCAAGGTAAACTACTTTGC 57.357 30.769 4.32 0.00 43.13 3.68
1892 2184 7.655732 GGCAATGTCCAAAACAATAACTTACTT 59.344 33.333 0.00 0.00 42.37 2.24
1930 2222 7.047891 TGTCAATTATCCAGGTGTCTATGTTC 58.952 38.462 0.00 0.00 0.00 3.18
2023 2315 3.052869 TCATAGCTACTGGAAGGACAGGA 60.053 47.826 0.00 0.00 42.75 3.86
2099 2391 7.362662 GCTACAAGATTCACAACATTCTGAAA 58.637 34.615 0.00 0.00 30.32 2.69
2184 2476 5.957798 TCTTGGATTTTGCATTGCTAAGAG 58.042 37.500 10.49 3.81 0.00 2.85
2207 2499 4.196971 GGAGAAGTTGTTGGTGTACAAGT 58.803 43.478 0.00 0.00 42.05 3.16
2305 2597 1.745087 AGAATTGGTATTGGTGCAGCG 59.255 47.619 11.91 0.00 0.00 5.18
2317 2609 2.174349 GCAGCGAAAGGTCTTGCG 59.826 61.111 6.73 6.73 44.19 4.85
2467 2759 1.171308 CCCATCTCAGCACCTTTGTG 58.829 55.000 0.00 0.00 45.65 3.33
2473 2765 0.179234 TCAGCACCTTTGTGAACGGA 59.821 50.000 0.00 0.00 45.76 4.69
2476 2768 0.868406 GCACCTTTGTGAACGGAGAG 59.132 55.000 0.00 0.00 45.76 3.20
2566 2858 0.034059 ACAGCTTCGGAGTGGTTCTG 59.966 55.000 0.00 0.00 0.00 3.02
2596 2888 2.363925 ACCGGTGAGAGGCCTACC 60.364 66.667 6.12 9.62 0.00 3.18
2608 2900 1.765074 GCCTACCCAGGTTTCCACA 59.235 57.895 0.00 0.00 44.68 4.17
2666 2958 5.163205 TGGATCACCTACCTATCCAACAATG 60.163 44.000 0.85 0.00 44.75 2.82
2695 2987 3.320826 TCCAAGACTCAATCGACAAGTCA 59.679 43.478 19.82 3.18 41.49 3.41
2743 3035 2.555757 GCTGATGCAGTTCCTGAAAGTT 59.444 45.455 0.00 0.00 39.41 2.66
2767 3059 0.304705 GTTCTTGCACAGTCACCACG 59.695 55.000 0.00 0.00 0.00 4.94
2920 3212 3.622612 TCATTGTCGCCATGTAATCACAG 59.377 43.478 0.00 0.00 38.30 3.66
3057 3349 7.095649 ACGCTGCACACAATGTATATATAGTTG 60.096 37.037 12.82 12.82 0.00 3.16
3132 3424 9.303537 GCGAGGATAATTTTCATACTACCTATC 57.696 37.037 0.00 0.00 0.00 2.08
3203 3495 1.039068 TGCCATATTGGGATTTGCGG 58.961 50.000 0.00 0.00 38.19 5.69
3208 3500 2.799126 TATTGGGATTTGCGGTCTGT 57.201 45.000 0.00 0.00 0.00 3.41
3322 3616 2.737359 GCATGTGTTGCCAAGGATGATG 60.737 50.000 0.00 0.00 46.15 3.07
3353 4466 3.788766 CGTGTAGCGTGCCCTTGC 61.789 66.667 0.00 0.00 35.54 4.01
3408 4541 0.321564 TTTGTCCCTGTGCATCCTCG 60.322 55.000 0.00 0.00 0.00 4.63
3415 4548 1.134580 CCTGTGCATCCTCGATGTCTT 60.135 52.381 0.00 0.00 41.60 3.01
3432 4565 7.872993 TCGATGTCTTGACTAGTTCTTGATTTT 59.127 33.333 0.00 0.00 0.00 1.82
3436 4569 9.261180 TGTCTTGACTAGTTCTTGATTTTACAG 57.739 33.333 0.00 0.00 0.00 2.74
3439 4572 8.603242 TTGACTAGTTCTTGATTTTACAGACC 57.397 34.615 0.00 0.00 0.00 3.85
3446 4579 6.335471 TCTTGATTTTACAGACCGAGTGTA 57.665 37.500 0.00 0.00 0.00 2.90
3503 4639 6.487331 ACACGAATGTTTGAAATGGTACCTTA 59.513 34.615 14.36 0.00 34.46 2.69
3518 4654 1.048724 CCTTATGGTGCTCCCTCCGA 61.049 60.000 1.59 0.00 0.00 4.55
3540 4676 3.857383 ATCAGAAAAGTGGACGTCTGACG 60.857 47.826 26.94 26.94 46.80 4.35
3545 4681 1.080772 GTGGACGTCTGACGATGCA 60.081 57.895 33.99 24.57 46.05 3.96
3551 4687 0.710567 CGTCTGACGATGCACTCAAC 59.289 55.000 24.86 0.00 46.05 3.18
3557 4693 2.948979 TGACGATGCACTCAACCTTTTT 59.051 40.909 0.00 0.00 0.00 1.94
3566 4702 5.407995 TGCACTCAACCTTTTTGAAACTTTG 59.592 36.000 0.00 0.00 0.00 2.77
3569 4705 7.464577 GCACTCAACCTTTTTGAAACTTTGATC 60.465 37.037 0.00 0.00 0.00 2.92
3634 4770 8.793592 GGTTTTACCAGCCATAATTATTCCTAG 58.206 37.037 0.00 0.00 38.42 3.02
3636 4772 9.930158 TTTTACCAGCCATAATTATTCCTAGTT 57.070 29.630 0.00 0.00 0.00 2.24
3677 4833 5.733676 TCTGTAGCATGCTGTGATAGAAAA 58.266 37.500 30.42 2.54 27.45 2.29
3678 4834 5.582269 TCTGTAGCATGCTGTGATAGAAAAC 59.418 40.000 30.42 15.88 27.45 2.43
3679 4835 5.491070 TGTAGCATGCTGTGATAGAAAACT 58.509 37.500 30.42 0.60 27.45 2.66
3680 4836 4.959596 AGCATGCTGTGATAGAAAACTG 57.040 40.909 21.98 0.00 0.00 3.16
3681 4837 4.330250 AGCATGCTGTGATAGAAAACTGT 58.670 39.130 21.98 0.00 0.00 3.55
3682 4838 5.491070 AGCATGCTGTGATAGAAAACTGTA 58.509 37.500 21.98 0.00 0.00 2.74
3683 4839 5.583854 AGCATGCTGTGATAGAAAACTGTAG 59.416 40.000 21.98 0.00 0.00 2.74
3720 4876 8.359642 CAAATTGTAGACAATGAAAAGGAGGAA 58.640 33.333 8.61 0.00 45.06 3.36
3722 4878 7.234355 ATTGTAGACAATGAAAAGGAGGAACT 58.766 34.615 7.09 0.00 44.22 3.01
3725 4881 5.810095 AGACAATGAAAAGGAGGAACTAGG 58.190 41.667 0.00 0.00 41.55 3.02
3741 4897 5.396884 GGAACTAGGTAGCACTTGATCCAAT 60.397 44.000 0.00 0.00 36.01 3.16
3743 4899 4.471386 ACTAGGTAGCACTTGATCCAATGT 59.529 41.667 0.00 0.00 0.00 2.71
3768 4924 1.134640 TGACGTAGGTGTTGTGTGCTT 60.135 47.619 0.00 0.00 0.00 3.91
3828 4996 5.277683 CCTGATGATAAGTTACATGTGCTGC 60.278 44.000 9.11 0.00 0.00 5.25
3852 5020 2.744202 GCGTTGTGGACTGAAATCTGAT 59.256 45.455 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 36 1.548269 GGGAGAAGAGTCTGTGAGTGG 59.452 57.143 0.00 0.00 32.80 4.00
96 102 3.764466 CCTGAAGCTCGCCGTCCT 61.764 66.667 0.00 0.00 0.00 3.85
159 173 1.667151 GCCACAGCAAAGCATGGAA 59.333 52.632 14.26 0.00 38.73 3.53
161 175 2.126228 CGCCACAGCAAAGCATGG 60.126 61.111 7.67 7.67 39.21 3.66
168 182 1.980951 GATCATTCGCGCCACAGCAA 61.981 55.000 0.00 0.00 39.83 3.91
190 205 2.493973 CAGAGCTCGAGCACTCCC 59.506 66.667 36.87 19.95 45.16 4.30
198 213 1.371183 CAACCAACCCAGAGCTCGA 59.629 57.895 8.37 0.00 0.00 4.04
224 239 2.398554 CCAAGAACCCGCATCCACG 61.399 63.158 0.00 0.00 0.00 4.94
275 469 4.776322 TTCCTCGCCGCACATGGG 62.776 66.667 0.00 0.00 0.00 4.00
282 476 3.006706 CGATTTCTTCCTCGCCGC 58.993 61.111 0.00 0.00 0.00 6.53
418 644 0.624500 CCTCCCTGATTTCCCTCCCA 60.625 60.000 0.00 0.00 0.00 4.37
507 734 5.946377 TCCAGAAAGAAGAAAATCTAAGGGC 59.054 40.000 0.00 0.00 0.00 5.19
624 857 6.826668 ACCATCAATCGAGACCACAATTATA 58.173 36.000 0.00 0.00 0.00 0.98
713 996 5.540911 AGAATAAGTGCAATTGGTTTGGTG 58.459 37.500 10.14 0.00 35.75 4.17
718 1001 5.990996 CACCAAAGAATAAGTGCAATTGGTT 59.009 36.000 10.14 4.36 44.83 3.67
749 1035 2.760634 TGATGCGAAGGTTCTGCTAA 57.239 45.000 0.00 0.00 0.00 3.09
754 1040 7.642669 CAAATAACATATGATGCGAAGGTTCT 58.357 34.615 10.38 0.00 0.00 3.01
937 1223 5.012561 ACTTCTAGATTCAAGCTTCACCTGT 59.987 40.000 0.00 0.00 0.00 4.00
938 1224 5.486526 ACTTCTAGATTCAAGCTTCACCTG 58.513 41.667 0.00 0.00 0.00 4.00
957 1243 3.491267 CACCTCTCGTTCTTGACAACTTC 59.509 47.826 0.00 0.00 0.00 3.01
967 1258 1.811359 CCTAACGTCACCTCTCGTTCT 59.189 52.381 6.23 0.00 45.03 3.01
1045 1336 0.875059 GCGAAACAAGGGAAGACCAG 59.125 55.000 0.00 0.00 43.89 4.00
1065 1356 2.871022 GCATTCGATGTCAGCTTGAGAT 59.129 45.455 0.00 0.00 32.62 2.75
1077 1368 5.633927 TGAACAGATTTCAAGCATTCGATG 58.366 37.500 0.00 0.00 0.00 3.84
1081 1372 4.801891 TGCTGAACAGATTTCAAGCATTC 58.198 39.130 5.97 0.00 32.16 2.67
1151 1442 2.778299 TGTAGCCATCAGTGTTGTTCC 58.222 47.619 0.70 0.00 0.00 3.62
1194 1485 0.036732 TCTCATCTGGGTGCCAACAC 59.963 55.000 0.00 0.00 46.66 3.32
1298 1589 1.872952 TGTTGTTTGACAGATCCAGCG 59.127 47.619 0.00 0.00 0.00 5.18
1330 1621 3.312890 GGGAGATCTCTTGAGGGATTGA 58.687 50.000 21.81 0.00 0.00 2.57
1344 1635 3.838903 AGTATGGTATTTCCCGGGAGATC 59.161 47.826 28.82 19.21 34.77 2.75
1394 1685 1.250154 TGGGATGGCGCCAGAAAAAG 61.250 55.000 35.36 0.00 0.00 2.27
1405 1696 9.590451 CATATTTGATATATTTTGTGGGATGGC 57.410 33.333 0.00 0.00 0.00 4.40
1486 1777 4.506654 TCGACTAAGAAGTTGAAACTGTGC 59.493 41.667 0.00 0.00 42.18 4.57
1488 1779 7.116519 GCTAATCGACTAAGAAGTTGAAACTGT 59.883 37.037 0.00 0.00 46.87 3.55
1495 1786 8.635877 AATGTAGCTAATCGACTAAGAAGTTG 57.364 34.615 0.00 0.00 38.34 3.16
1497 1788 7.997482 TGAATGTAGCTAATCGACTAAGAAGT 58.003 34.615 0.00 0.00 39.21 3.01
1505 1796 5.904080 GCAACATTGAATGTAGCTAATCGAC 59.096 40.000 11.70 0.00 44.07 4.20
1509 1800 6.825213 TCTCTGCAACATTGAATGTAGCTAAT 59.175 34.615 11.70 0.00 44.07 1.73
1513 1804 4.952262 TCTCTGCAACATTGAATGTAGC 57.048 40.909 11.70 3.98 44.07 3.58
1527 1818 2.237143 CCCTGATAGTTGGTTCTCTGCA 59.763 50.000 0.00 0.00 0.00 4.41
1538 1829 5.669798 AAATGGAATAGGCCCTGATAGTT 57.330 39.130 0.00 0.00 0.00 2.24
1559 1850 4.813697 GCCCAAACTTTTGTGCTAATGAAA 59.186 37.500 2.33 0.00 38.31 2.69
1568 1859 0.529555 CGGTGGCCCAAACTTTTGTG 60.530 55.000 0.00 0.00 36.45 3.33
1570 1861 0.461961 TTCGGTGGCCCAAACTTTTG 59.538 50.000 0.00 0.00 37.90 2.44
1575 1866 1.507562 CAAAATTCGGTGGCCCAAAC 58.492 50.000 0.00 0.00 0.00 2.93
1579 1870 2.264480 GGCAAAATTCGGTGGCCC 59.736 61.111 0.00 0.00 38.70 5.80
1580 1871 2.126110 CGGCAAAATTCGGTGGCC 60.126 61.111 0.00 0.00 41.20 5.36
1635 1926 0.109153 TGCTCTTTGCTGAAGCCTGA 59.891 50.000 0.00 0.00 43.37 3.86
1680 1971 1.529438 ACAACTACGACGCCAACAATG 59.471 47.619 0.00 0.00 0.00 2.82
1797 2088 7.280652 ACCTTGATTGTTTTTGTTCCTTTGATG 59.719 33.333 0.00 0.00 0.00 3.07
1835 2126 8.731275 ACCCAAAATAAAAGAAAAGGAAACAG 57.269 30.769 0.00 0.00 0.00 3.16
1892 2184 7.730084 TGGATAATTGACAAAACCATGACAAA 58.270 30.769 0.00 0.00 38.19 2.83
1930 2222 6.486253 TTCATCTTTGAAACTGGATTCTCG 57.514 37.500 0.00 0.00 38.90 4.04
2023 2315 1.909302 AGCACTGCCCTGTACATAGTT 59.091 47.619 0.00 0.00 0.00 2.24
2184 2476 3.202829 TGTACACCAACAACTTCTCCC 57.797 47.619 0.00 0.00 0.00 4.30
2207 2499 2.775384 AGAGTGAACCTTTGGGTGTGTA 59.225 45.455 0.00 0.00 46.67 2.90
2305 2597 3.371285 GGTGAAGATACGCAAGACCTTTC 59.629 47.826 0.00 0.00 43.62 2.62
2317 2609 4.142600 GGATTGCAAGTGTGGTGAAGATAC 60.143 45.833 4.94 0.00 0.00 2.24
2467 2759 4.811557 CCAATATCTCCAAACTCTCCGTTC 59.188 45.833 0.00 0.00 33.90 3.95
2473 2765 7.056635 CCACATAACCAATATCTCCAAACTCT 58.943 38.462 0.00 0.00 0.00 3.24
2476 2768 5.359576 TGCCACATAACCAATATCTCCAAAC 59.640 40.000 0.00 0.00 0.00 2.93
2566 2858 1.009829 CACCGGTGATAAGCTCAAGC 58.990 55.000 31.31 0.00 42.49 4.01
2596 2888 0.607489 CTGGAGCTGTGGAAACCTGG 60.607 60.000 0.00 0.00 0.00 4.45
2666 2958 2.611292 CGATTGAGTCTTGGAGAATGGC 59.389 50.000 0.00 0.00 0.00 4.40
2695 2987 5.192522 ACTGTCATTGTCCTTCCCTATCAAT 59.807 40.000 0.00 0.00 0.00 2.57
2743 3035 0.742635 TGACTGTGCAAGAACACGCA 60.743 50.000 0.00 0.00 43.74 5.24
2767 3059 2.579738 GTGGGTCTCTCCTTCGCC 59.420 66.667 0.00 0.00 36.25 5.54
3057 3349 5.351740 GTGGATAAGAGAACCAAGCTACAAC 59.648 44.000 0.00 0.00 35.40 3.32
3132 3424 5.952347 ACTAACAGGTACCCCATTCTTAG 57.048 43.478 8.74 7.19 0.00 2.18
3199 3491 1.522806 GTGTTCACCACAGACCGCA 60.523 57.895 0.00 0.00 43.92 5.69
3203 3495 1.981256 AATGGGTGTTCACCACAGAC 58.019 50.000 21.25 6.33 46.44 3.51
3208 3500 4.663120 AGGCTATATAATGGGTGTTCACCA 59.337 41.667 21.25 9.68 43.22 4.17
3284 3578 5.470098 ACACATGCACTACAAAAAGAGGTAG 59.530 40.000 0.00 0.00 42.07 3.18
3322 3616 3.680789 GCTACACGCATCAACATTAACC 58.319 45.455 0.00 0.00 38.92 2.85
3353 4466 8.560576 AAAGAGAAAACAAATAACATGACACG 57.439 30.769 0.00 0.00 0.00 4.49
3415 4548 6.866770 CGGTCTGTAAAATCAAGAACTAGTCA 59.133 38.462 0.00 0.00 0.00 3.41
3432 4565 5.443283 AGGACAATATACACTCGGTCTGTA 58.557 41.667 0.00 0.00 0.00 2.74
3436 4569 7.924412 TCAATAAAGGACAATATACACTCGGTC 59.076 37.037 0.00 0.00 0.00 4.79
3439 4572 9.529325 TTCTCAATAAAGGACAATATACACTCG 57.471 33.333 0.00 0.00 0.00 4.18
3480 4616 7.362574 CCATAAGGTACCATTTCAAACATTCGT 60.363 37.037 15.94 0.00 0.00 3.85
3503 4639 1.383109 TGATCGGAGGGAGCACCAT 60.383 57.895 1.58 0.00 43.89 3.55
3515 4651 1.993370 GACGTCCACTTTTCTGATCGG 59.007 52.381 3.51 0.00 0.00 4.18
3518 4654 3.654414 GTCAGACGTCCACTTTTCTGAT 58.346 45.455 13.01 0.00 44.72 2.90
3540 4676 5.351458 AGTTTCAAAAAGGTTGAGTGCATC 58.649 37.500 0.00 0.00 0.00 3.91
3545 4681 7.610865 TGATCAAAGTTTCAAAAAGGTTGAGT 58.389 30.769 0.00 0.00 0.00 3.41
3551 4687 9.709495 TTCCATATGATCAAAGTTTCAAAAAGG 57.291 29.630 3.65 0.00 0.00 3.11
3557 4693 8.105097 TCGTTTTCCATATGATCAAAGTTTCA 57.895 30.769 3.65 0.00 0.00 2.69
3566 4702 7.601073 TCAGCATATCGTTTTCCATATGATC 57.399 36.000 3.65 0.00 35.70 2.92
3569 4705 7.809665 TCATTCAGCATATCGTTTTCCATATG 58.190 34.615 0.00 0.00 36.45 1.78
3580 4716 9.836076 ATGTTGATATTTTCATTCAGCATATCG 57.164 29.630 0.51 0.00 38.85 2.92
3652 4788 4.941657 TCTATCACAGCATGCTACAGAAG 58.058 43.478 22.19 15.07 42.53 2.85
3661 4817 6.974932 ACTACAGTTTTCTATCACAGCATG 57.025 37.500 0.00 0.00 46.00 4.06
3706 4862 5.250774 TGCTACCTAGTTCCTCCTTTTCATT 59.749 40.000 0.00 0.00 0.00 2.57
3708 4864 4.020485 GTGCTACCTAGTTCCTCCTTTTCA 60.020 45.833 0.00 0.00 0.00 2.69
3720 4876 4.471386 ACATTGGATCAAGTGCTACCTAGT 59.529 41.667 0.00 0.00 0.00 2.57
3722 4878 6.239600 GGATACATTGGATCAAGTGCTACCTA 60.240 42.308 11.00 0.00 0.00 3.08
3725 4881 5.468072 CAGGATACATTGGATCAAGTGCTAC 59.532 44.000 11.00 0.00 41.41 3.58
3768 4924 8.445275 TTTTGCTCTAGTCTGAAACATGTTTA 57.555 30.769 23.33 5.99 32.11 2.01
3828 4996 2.485426 AGATTTCAGTCCACAACGCATG 59.515 45.455 0.00 0.00 0.00 4.06
3852 5020 8.417106 TGATTGCAGTAAATAACAAAAGGTTGA 58.583 29.630 0.00 0.00 40.73 3.18


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

AutoCloner maintained by Alex Coulton.