Multiple sequence alignment - TraesCS6A01G001500

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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 TraesCS6A01G001500 chr6A 100.000 3317 0 0 1 3317 785778 789094 0.000000e+00 6126.0
1 TraesCS6A01G001500 chr6A 91.963 1182 70 9 946 2110 22070801 22071974 0.000000e+00 1633.0
2 TraesCS6A01G001500 chr6A 80.623 578 68 29 1 550 157466027 157466588 1.110000e-109 407.0
3 TraesCS6A01G001500 chr6D 92.025 1906 87 31 666 2530 2108608 2106727 0.000000e+00 2617.0
4 TraesCS6A01G001500 chr6D 82.874 689 82 19 1 666 91237378 91236703 1.330000e-163 586.0
5 TraesCS6A01G001500 chr6D 88.626 211 15 6 2747 2956 107544012 107543810 7.110000e-62 248.0
6 TraesCS6A01G001500 chr6D 75.045 557 97 28 129 658 450897986 450898527 1.550000e-53 220.0
7 TraesCS6A01G001500 chr6D 92.174 115 8 1 2635 2749 2106739 2106626 9.520000e-36 161.0
8 TraesCS6A01G001500 chr6B 90.227 1719 112 26 793 2471 4451358 4453060 0.000000e+00 2193.0
9 TraesCS6A01G001500 chr6B 92.665 1118 67 8 994 2110 4459542 4458439 0.000000e+00 1596.0
10 TraesCS6A01G001500 chr6B 87.500 752 61 17 1899 2639 4422211 4421482 0.000000e+00 837.0
11 TraesCS6A01G001500 chr6B 86.885 549 55 9 2747 3293 25578297 25578830 1.700000e-167 599.0
12 TraesCS6A01G001500 chr6B 88.859 377 36 5 1528 1903 4449855 4449484 3.020000e-125 459.0
13 TraesCS6A01G001500 chr6B 73.473 573 102 34 129 667 684679321 684679877 1.580000e-38 171.0
14 TraesCS6A01G001500 chr6B 95.000 40 2 0 2756 2795 334644837 334644876 2.760000e-06 63.9
15 TraesCS6A01G001500 chr6B 81.013 79 9 3 2617 2689 4421422 4421344 1.290000e-04 58.4
16 TraesCS6A01G001500 chr2B 84.862 1090 144 15 1001 2084 792389026 792390100 0.000000e+00 1079.0
17 TraesCS6A01G001500 chr2B 87.209 172 19 2 964 1135 773386491 773386659 3.380000e-45 193.0
18 TraesCS6A01G001500 chr2B 81.304 230 32 6 446 666 170767764 170767991 3.400000e-40 176.0
19 TraesCS6A01G001500 chr2B 91.304 46 3 1 2750 2794 726227685 726227730 9.940000e-06 62.1
20 TraesCS6A01G001500 chr2A 86.823 554 55 11 2747 3293 327151118 327151660 1.320000e-168 603.0
21 TraesCS6A01G001500 chr2A 85.965 57 7 1 592 648 526102381 526102436 3.570000e-05 60.2
22 TraesCS6A01G001500 chr7D 82.891 678 90 13 7 665 186856607 186855937 1.330000e-163 586.0
23 TraesCS6A01G001500 chr7D 82.496 697 81 27 1 665 553590584 553591271 1.030000e-159 573.0
24 TraesCS6A01G001500 chr7D 86.364 352 34 8 1 339 174066897 174067247 4.040000e-99 372.0
25 TraesCS6A01G001500 chr3D 82.714 700 79 23 1 666 418761359 418760668 4.770000e-163 584.0
26 TraesCS6A01G001500 chr3D 82.602 684 62 29 1 650 499580592 499581252 4.840000e-153 551.0
27 TraesCS6A01G001500 chr3D 80.936 577 74 23 1 549 143947065 143947633 1.100000e-114 424.0
28 TraesCS6A01G001500 chr3D 76.833 600 78 35 4 570 470689972 470689401 7.010000e-72 281.0
29 TraesCS6A01G001500 chr3D 74.619 197 30 15 1684 1870 457032531 457032717 5.940000e-08 69.4
30 TraesCS6A01G001500 chrUn 82.403 699 83 17 1 665 239228468 239227776 1.030000e-159 573.0
31 TraesCS6A01G001500 chr7B 86.576 514 46 14 2750 3256 679625608 679625111 2.250000e-151 545.0
32 TraesCS6A01G001500 chr5B 81.766 702 82 21 1 665 6721660 6720968 2.250000e-151 545.0
33 TraesCS6A01G001500 chr5B 83.792 327 33 10 139 453 272385054 272384736 3.240000e-75 292.0
34 TraesCS6A01G001500 chr1A 84.838 554 56 12 2743 3293 86130337 86130865 1.750000e-147 532.0
35 TraesCS6A01G001500 chr5D 83.000 600 59 23 1 565 368075815 368076406 1.370000e-138 503.0
36 TraesCS6A01G001500 chr5D 80.989 647 71 27 1 606 435191287 435191922 1.800000e-127 466.0
37 TraesCS6A01G001500 chr2D 80.801 599 80 17 1 570 432128463 432129055 1.410000e-118 436.0
38 TraesCS6A01G001500 chr4D 80.597 603 77 26 1 570 102600202 102600797 2.360000e-116 429.0
39 TraesCS6A01G001500 chr5A 82.000 450 62 11 1 438 651970852 651971294 6.760000e-97 364.0
40 TraesCS6A01G001500 chr3B 80.363 331 43 10 256 570 207290736 207291060 7.160000e-57 231.0
41 TraesCS6A01G001500 chr3B 74.619 197 30 15 1684 1870 603832342 603832528 5.940000e-08 69.4
42 TraesCS6A01G001500 chr3A 74.619 197 30 15 1684 1870 599899198 599899384 5.940000e-08 69.4
43 TraesCS6A01G001500 chr1B 85.294 68 7 3 2750 2816 323619427 323619362 2.140000e-07 67.6
44 TraesCS6A01G001500 chr1B 91.489 47 3 1 2749 2794 546701686 546701640 2.760000e-06 63.9


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 TraesCS6A01G001500 chr6A 785778 789094 3316 False 6126.0 6126 100.0000 1 3317 1 chr6A.!!$F1 3316
1 TraesCS6A01G001500 chr6A 22070801 22071974 1173 False 1633.0 1633 91.9630 946 2110 1 chr6A.!!$F2 1164
2 TraesCS6A01G001500 chr6A 157466027 157466588 561 False 407.0 407 80.6230 1 550 1 chr6A.!!$F3 549
3 TraesCS6A01G001500 chr6D 2106626 2108608 1982 True 1389.0 2617 92.0995 666 2749 2 chr6D.!!$R3 2083
4 TraesCS6A01G001500 chr6D 91236703 91237378 675 True 586.0 586 82.8740 1 666 1 chr6D.!!$R1 665
5 TraesCS6A01G001500 chr6D 450897986 450898527 541 False 220.0 220 75.0450 129 658 1 chr6D.!!$F1 529
6 TraesCS6A01G001500 chr6B 4451358 4453060 1702 False 2193.0 2193 90.2270 793 2471 1 chr6B.!!$F1 1678
7 TraesCS6A01G001500 chr6B 4458439 4459542 1103 True 1596.0 1596 92.6650 994 2110 1 chr6B.!!$R2 1116
8 TraesCS6A01G001500 chr6B 25578297 25578830 533 False 599.0 599 86.8850 2747 3293 1 chr6B.!!$F2 546
9 TraesCS6A01G001500 chr6B 4421344 4422211 867 True 447.7 837 84.2565 1899 2689 2 chr6B.!!$R3 790
10 TraesCS6A01G001500 chr2B 792389026 792390100 1074 False 1079.0 1079 84.8620 1001 2084 1 chr2B.!!$F4 1083
11 TraesCS6A01G001500 chr2A 327151118 327151660 542 False 603.0 603 86.8230 2747 3293 1 chr2A.!!$F1 546
12 TraesCS6A01G001500 chr7D 186855937 186856607 670 True 586.0 586 82.8910 7 665 1 chr7D.!!$R1 658
13 TraesCS6A01G001500 chr7D 553590584 553591271 687 False 573.0 573 82.4960 1 665 1 chr7D.!!$F2 664
14 TraesCS6A01G001500 chr3D 418760668 418761359 691 True 584.0 584 82.7140 1 666 1 chr3D.!!$R1 665
15 TraesCS6A01G001500 chr3D 499580592 499581252 660 False 551.0 551 82.6020 1 650 1 chr3D.!!$F3 649
16 TraesCS6A01G001500 chr3D 143947065 143947633 568 False 424.0 424 80.9360 1 549 1 chr3D.!!$F1 548
17 TraesCS6A01G001500 chr3D 470689401 470689972 571 True 281.0 281 76.8330 4 570 1 chr3D.!!$R2 566
18 TraesCS6A01G001500 chrUn 239227776 239228468 692 True 573.0 573 82.4030 1 665 1 chrUn.!!$R1 664
19 TraesCS6A01G001500 chr5B 6720968 6721660 692 True 545.0 545 81.7660 1 665 1 chr5B.!!$R1 664
20 TraesCS6A01G001500 chr1A 86130337 86130865 528 False 532.0 532 84.8380 2743 3293 1 chr1A.!!$F1 550
21 TraesCS6A01G001500 chr5D 368075815 368076406 591 False 503.0 503 83.0000 1 565 1 chr5D.!!$F1 564
22 TraesCS6A01G001500 chr5D 435191287 435191922 635 False 466.0 466 80.9890 1 606 1 chr5D.!!$F2 605
23 TraesCS6A01G001500 chr2D 432128463 432129055 592 False 436.0 436 80.8010 1 570 1 chr2D.!!$F1 569
24 TraesCS6A01G001500 chr4D 102600202 102600797 595 False 429.0 429 80.5970 1 570 1 chr4D.!!$F1 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
780 853 0.112412 ATCCCACCCCACACTGTTTC 59.888 55.0 0.0 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 3006 1.009389 GCGCCTATCAGTCGCCATAC 61.009 60.0 0.0 0.0 42.71 2.39 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
52 55 3.474600 CACTAGCTATCAATGCTTGCCT 58.525 45.455 0.00 0.00 41.46 4.75
68 71 1.883275 TGCCTACATGAAAACAACCCG 59.117 47.619 0.00 0.00 0.00 5.28
104 107 7.124298 TCAAATCCATCACAACTAGCTACTACT 59.876 37.037 0.00 0.00 0.00 2.57
106 109 8.713708 AATCCATCACAACTAGCTACTACTAT 57.286 34.615 0.00 0.00 0.00 2.12
112 115 8.307921 TCACAACTAGCTACTACTATATCACG 57.692 38.462 0.00 0.00 0.00 4.35
145 149 2.034305 CGGAAGATCTAACCCTACCACG 59.966 54.545 11.65 0.00 0.00 4.94
173 179 7.868922 CGACAGATCTAGCTAGAACTAGTAGAA 59.131 40.741 27.40 3.83 40.50 2.10
180 186 6.330178 AGCTAGAACTAGTAGAAAGGAGGA 57.670 41.667 3.59 0.00 35.65 3.71
211 218 1.717194 TACAAACGCCATCGGAAGAC 58.283 50.000 0.00 0.00 46.97 3.01
264 284 4.408276 AGAGGAGCAGTAAGTAGTCAACA 58.592 43.478 0.00 0.00 0.00 3.33
334 354 1.890894 CGGAGGGAAAGCTCGAGAA 59.109 57.895 18.75 0.00 0.00 2.87
335 355 0.179124 CGGAGGGAAAGCTCGAGAAG 60.179 60.000 18.75 0.00 0.00 2.85
336 356 0.176910 GGAGGGAAAGCTCGAGAAGG 59.823 60.000 18.75 0.00 0.00 3.46
337 357 0.176910 GAGGGAAAGCTCGAGAAGGG 59.823 60.000 18.75 0.00 0.00 3.95
388 413 2.223595 CGGCGGTCATCTGGCTATATAG 60.224 54.545 5.30 5.30 42.38 1.31
390 415 3.024547 GCGGTCATCTGGCTATATAGGA 58.975 50.000 11.72 1.15 0.00 2.94
446 471 2.868196 GCCGCTTTTCCGAAGACC 59.132 61.111 0.00 0.00 0.00 3.85
447 472 1.671379 GCCGCTTTTCCGAAGACCT 60.671 57.895 0.00 0.00 0.00 3.85
498 559 1.153107 TCCCATGCATTGCTCGAGG 60.153 57.895 15.58 5.80 0.00 4.63
522 583 3.243101 TGACTCGCTGGAAACTATCGATC 60.243 47.826 0.00 0.00 0.00 3.69
531 592 0.462789 AACTATCGATCCGGGCGTTT 59.537 50.000 15.42 8.59 0.00 3.60
535 596 0.748450 ATCGATCCGGGCGTTTCTAA 59.252 50.000 15.42 0.00 0.00 2.10
611 672 4.662961 GGCAACCAAACAGGCCGC 62.663 66.667 0.00 0.00 43.14 6.53
615 676 0.460987 CAACCAAACAGGCCGCAAAA 60.461 50.000 0.00 0.00 43.14 2.44
616 677 0.461163 AACCAAACAGGCCGCAAAAC 60.461 50.000 0.00 0.00 43.14 2.43
669 735 3.323751 GCAACCAAATGCATCCTTCTT 57.676 42.857 0.00 0.00 45.70 2.52
670 736 3.667360 GCAACCAAATGCATCCTTCTTT 58.333 40.909 0.00 0.00 45.70 2.52
702 768 8.533569 ACAAAATTGTCTCTTTTCTTAGGGAA 57.466 30.769 0.00 0.00 36.50 3.97
703 769 8.633561 ACAAAATTGTCTCTTTTCTTAGGGAAG 58.366 33.333 0.00 0.00 36.50 3.46
704 770 6.825944 AATTGTCTCTTTTCTTAGGGAAGC 57.174 37.500 0.00 0.00 35.16 3.86
710 783 7.287696 TGTCTCTTTTCTTAGGGAAGCAAAAAT 59.712 33.333 0.00 0.00 35.16 1.82
719 792 9.705290 TCTTAGGGAAGCAAAAATAACAAATTC 57.295 29.630 0.00 0.00 32.21 2.17
758 831 2.887568 GCCCAGCATCTCGTGTCG 60.888 66.667 0.00 0.00 0.00 4.35
767 840 2.298158 ATCTCGTGTCGGCATCCCAC 62.298 60.000 0.00 0.00 0.00 4.61
780 853 0.112412 ATCCCACCCCACACTGTTTC 59.888 55.000 0.00 0.00 0.00 2.78
781 854 0.991355 TCCCACCCCACACTGTTTCT 60.991 55.000 0.00 0.00 0.00 2.52
782 855 0.823356 CCCACCCCACACTGTTTCTG 60.823 60.000 0.00 0.00 0.00 3.02
783 856 1.455383 CCACCCCACACTGTTTCTGC 61.455 60.000 0.00 0.00 0.00 4.26
784 857 0.466189 CACCCCACACTGTTTCTGCT 60.466 55.000 0.00 0.00 0.00 4.24
785 858 1.136828 ACCCCACACTGTTTCTGCTA 58.863 50.000 0.00 0.00 0.00 3.49
787 860 2.154462 CCCCACACTGTTTCTGCTAAG 58.846 52.381 0.00 0.00 0.00 2.18
788 861 2.154462 CCCACACTGTTTCTGCTAAGG 58.846 52.381 0.00 0.00 0.00 2.69
789 862 2.224523 CCCACACTGTTTCTGCTAAGGA 60.225 50.000 0.00 0.00 0.00 3.36
794 867 5.809562 CACACTGTTTCTGCTAAGGAGATAG 59.190 44.000 0.00 0.00 0.00 2.08
795 868 5.717178 ACACTGTTTCTGCTAAGGAGATAGA 59.283 40.000 0.00 0.00 0.00 1.98
796 869 6.039616 CACTGTTTCTGCTAAGGAGATAGAC 58.960 44.000 0.00 0.00 0.00 2.59
797 870 5.955355 ACTGTTTCTGCTAAGGAGATAGACT 59.045 40.000 0.00 0.00 0.00 3.24
891 1000 2.852449 TGGAAAGATGGAGCTAACCCAT 59.148 45.455 5.14 5.14 46.40 4.00
916 1025 4.462133 CAGCCATGGATTCTTCTCATCTT 58.538 43.478 18.40 0.00 0.00 2.40
917 1026 4.276183 CAGCCATGGATTCTTCTCATCTTG 59.724 45.833 18.40 0.00 0.00 3.02
918 1027 4.079901 AGCCATGGATTCTTCTCATCTTGT 60.080 41.667 18.40 0.00 0.00 3.16
930 1048 9.967346 TTCTTCTCATCTTGTATAAGTATTCCG 57.033 33.333 0.00 0.00 35.38 4.30
965 1088 1.728971 CGATCAGCAAGTGAAGTGACC 59.271 52.381 0.00 0.00 39.19 4.02
966 1089 2.771089 GATCAGCAAGTGAAGTGACCA 58.229 47.619 0.00 0.00 39.19 4.02
967 1090 2.936919 TCAGCAAGTGAAGTGACCAT 57.063 45.000 0.00 0.00 29.64 3.55
968 1091 2.771089 TCAGCAAGTGAAGTGACCATC 58.229 47.619 0.00 0.00 29.64 3.51
970 1093 0.798776 GCAAGTGAAGTGACCATCGG 59.201 55.000 0.00 0.00 0.00 4.18
971 1094 1.608025 GCAAGTGAAGTGACCATCGGA 60.608 52.381 0.00 0.00 0.00 4.55
972 1095 2.341257 CAAGTGAAGTGACCATCGGAG 58.659 52.381 0.00 0.00 0.00 4.63
974 1097 0.895530 GTGAAGTGACCATCGGAGGA 59.104 55.000 0.93 0.00 0.00 3.71
975 1098 1.134965 GTGAAGTGACCATCGGAGGAG 60.135 57.143 0.93 0.00 0.00 3.69
976 1099 0.461961 GAAGTGACCATCGGAGGAGG 59.538 60.000 0.93 0.00 0.00 4.30
987 1118 2.946785 TCGGAGGAGGGAGAAGAATAC 58.053 52.381 0.00 0.00 0.00 1.89
988 1119 2.243994 TCGGAGGAGGGAGAAGAATACA 59.756 50.000 0.00 0.00 0.00 2.29
989 1120 3.031736 CGGAGGAGGGAGAAGAATACAA 58.968 50.000 0.00 0.00 0.00 2.41
990 1121 3.068873 CGGAGGAGGGAGAAGAATACAAG 59.931 52.174 0.00 0.00 0.00 3.16
1416 1571 2.601966 GGATCGGCCGGAGAGGAT 60.602 66.667 27.83 10.35 45.00 3.24
1938 2093 4.680237 CTCGTCAACCGGCAGGCA 62.680 66.667 0.00 0.00 42.76 4.75
2117 2281 3.777522 CAGGAGGAGGAGGTTGTTAAGAT 59.222 47.826 0.00 0.00 0.00 2.40
2155 2319 3.336997 TCAAGAGGAGGAGAAGGAGGTTA 59.663 47.826 0.00 0.00 0.00 2.85
2271 2438 1.830477 GAGCAGAGTGAACAGGAGGAT 59.170 52.381 0.00 0.00 0.00 3.24
2455 2625 5.576384 CGCTTTATTGTGGCATTTGTAATGT 59.424 36.000 0.00 0.00 0.00 2.71
2569 2742 4.202253 TGTCTAATCTTGATCGGTGGATGG 60.202 45.833 0.00 0.00 31.51 3.51
2576 2749 0.834612 GATCGGTGGATGGTTGGGTA 59.165 55.000 0.00 0.00 31.51 3.69
2647 2902 1.068402 TGCTTGTTGATTGACATGCCG 60.068 47.619 11.66 0.00 45.11 5.69
2648 2903 1.068333 GCTTGTTGATTGACATGCCGT 60.068 47.619 0.00 0.00 41.94 5.68
2650 2905 1.164411 TGTTGATTGACATGCCGTCC 58.836 50.000 0.00 0.00 44.71 4.79
2710 2971 1.134068 GGACCCTCTTAAGACATGGCC 60.134 57.143 0.00 0.00 0.00 5.36
2719 2980 1.156736 AAGACATGGCCGTTTCTTCG 58.843 50.000 18.79 0.00 0.00 3.79
2721 2982 2.253414 GACATGGCCGTTTCTTCGCC 62.253 60.000 3.72 0.00 0.00 5.54
2724 2985 3.431725 GGCCGTTTCTTCGCCAGG 61.432 66.667 0.00 0.00 0.00 4.45
2745 3006 8.255394 CCAGGAGGCAATTTTTATGTTAAAAG 57.745 34.615 0.00 0.00 31.14 2.27
2756 3017 8.958175 TTTTTATGTTAAAAGTATGGCGACTG 57.042 30.769 0.00 0.00 0.00 3.51
2771 3032 4.529219 CTGATAGGCGCCGGTGCA 62.529 66.667 38.40 22.04 37.32 4.57
2787 3048 1.375013 GCACCGGCCTAACTTTCGA 60.375 57.895 0.00 0.00 0.00 3.71
2790 3051 1.449070 CCGGCCTAACTTTCGACCC 60.449 63.158 0.00 0.00 0.00 4.46
2835 3096 2.866762 GGATGTCTACAGCCGTTGATTC 59.133 50.000 0.99 0.00 43.02 2.52
2852 3113 0.253207 TTCCTTCTTCCTCCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
2905 3166 3.716006 CACTCGCCCAACGCACAG 61.716 66.667 0.00 0.00 43.23 3.66
2995 3262 4.430765 GTCCCCGTCATCGCACGT 62.431 66.667 0.00 0.00 38.14 4.49
3009 3276 1.890894 CACGTCCTCCCAATCTCGT 59.109 57.895 0.00 0.00 0.00 4.18
3146 3413 3.777925 CCGCCGTCGAGTTTGCAG 61.778 66.667 0.00 0.00 38.10 4.41
3149 3416 2.680913 GCCGTCGAGTTTGCAGCAT 61.681 57.895 0.00 0.00 0.00 3.79
3150 3417 1.358725 GCCGTCGAGTTTGCAGCATA 61.359 55.000 0.00 0.00 0.00 3.14
3195 3464 3.914312 TCGAGCAACTAGAGAAACCAAG 58.086 45.455 0.00 0.00 0.00 3.61
3202 3471 4.022413 ACTAGAGAAACCAAGAAAGCCC 57.978 45.455 0.00 0.00 0.00 5.19
3241 3511 1.540146 GCCGGTTCCAGCAAACAAAAT 60.540 47.619 1.90 0.00 0.00 1.82
3256 3526 0.975887 AAAATTGCCGGTTCCAGCAT 59.024 45.000 1.90 0.00 39.11 3.79
3288 3558 1.012998 TCGTCGTCGATTCGTAGCG 60.013 57.895 5.89 9.50 41.35 4.26
3292 3562 5.764578 TCGTCGTCGATTCGTAGCGAAAA 62.765 47.826 18.31 10.73 44.63 2.29
3300 3570 2.673976 TCGTAGCGAAAACAAAAGCC 57.326 45.000 0.00 0.00 31.06 4.35
3301 3571 1.070443 TCGTAGCGAAAACAAAAGCCG 60.070 47.619 0.00 0.00 31.06 5.52
3302 3572 1.681825 GTAGCGAAAACAAAAGCCGG 58.318 50.000 0.00 0.00 0.00 6.13
3303 3573 1.002142 GTAGCGAAAACAAAAGCCGGT 60.002 47.619 1.90 0.00 35.17 5.28
3304 3574 0.458260 AGCGAAAACAAAAGCCGGTT 59.542 45.000 1.90 0.00 0.00 4.44
3305 3575 0.850217 GCGAAAACAAAAGCCGGTTC 59.150 50.000 1.90 0.00 0.00 3.62
3306 3576 1.535226 GCGAAAACAAAAGCCGGTTCT 60.535 47.619 1.90 0.00 0.00 3.01
3307 3577 2.287129 GCGAAAACAAAAGCCGGTTCTA 60.287 45.455 1.90 0.00 0.00 2.10
3308 3578 3.551551 CGAAAACAAAAGCCGGTTCTAG 58.448 45.455 1.90 0.00 0.00 2.43
3309 3579 3.305964 GAAAACAAAAGCCGGTTCTAGC 58.694 45.455 1.90 0.00 0.00 3.42
3310 3580 2.271944 AACAAAAGCCGGTTCTAGCT 57.728 45.000 1.90 0.00 42.40 3.32
3314 3584 1.218316 AAGCCGGTTCTAGCTTCCG 59.782 57.895 1.90 1.62 46.11 4.30
3315 3585 1.255667 AAGCCGGTTCTAGCTTCCGA 61.256 55.000 17.19 0.00 46.11 4.55
3316 3586 1.518792 GCCGGTTCTAGCTTCCGAC 60.519 63.158 17.19 6.25 46.05 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 55 3.741249 TGCTACGGGTTGTTTTCATGTA 58.259 40.909 0.00 0.00 0.00 2.29
68 71 4.096833 TGTGATGGATTTGAAGCATGCTAC 59.903 41.667 23.00 11.17 0.00 3.58
104 107 4.581409 TCCGATCTGTTTGACCGTGATATA 59.419 41.667 0.00 0.00 27.18 0.86
106 109 2.756207 TCCGATCTGTTTGACCGTGATA 59.244 45.455 0.00 0.00 27.18 2.15
145 149 5.987347 ACTAGTTCTAGCTAGATCTGTCGAC 59.013 44.000 31.54 21.75 40.54 4.20
173 179 5.825593 TGTAAGTTCAATCACTCCTCCTT 57.174 39.130 0.00 0.00 0.00 3.36
180 186 3.880490 TGGCGTTTGTAAGTTCAATCACT 59.120 39.130 0.00 0.00 0.00 3.41
264 284 3.003113 GCAACTACTCCGGCGACCT 62.003 63.158 9.30 0.00 0.00 3.85
388 413 3.564027 CGCCAATTCGGTCGCTCC 61.564 66.667 0.00 0.00 36.97 4.70
420 445 1.130009 GAAAAGCGGCGAGACGAAC 59.870 57.895 12.98 0.00 35.47 3.95
498 559 2.197577 GATAGTTTCCAGCGAGTCAGC 58.802 52.381 0.00 0.00 37.41 4.26
531 592 2.284331 TCAGCCAGGCCCGTTAGA 60.284 61.111 8.22 0.00 0.00 2.10
645 711 1.972795 AGGATGCATTTGGTTGCTTGT 59.027 42.857 0.00 0.00 43.18 3.16
698 764 7.549134 CCCTAGAATTTGTTATTTTTGCTTCCC 59.451 37.037 0.00 0.00 0.00 3.97
699 765 8.094548 ACCCTAGAATTTGTTATTTTTGCTTCC 58.905 33.333 0.00 0.00 0.00 3.46
701 767 8.646900 TCACCCTAGAATTTGTTATTTTTGCTT 58.353 29.630 0.00 0.00 0.00 3.91
702 768 8.189119 TCACCCTAGAATTTGTTATTTTTGCT 57.811 30.769 0.00 0.00 0.00 3.91
703 769 8.825667 TTCACCCTAGAATTTGTTATTTTTGC 57.174 30.769 0.00 0.00 0.00 3.68
710 783 6.289834 TCACGTTTCACCCTAGAATTTGTTA 58.710 36.000 0.00 0.00 0.00 2.41
719 792 1.939838 GCACCTCACGTTTCACCCTAG 60.940 57.143 0.00 0.00 0.00 3.02
758 831 3.661648 AGTGTGGGGTGGGATGCC 61.662 66.667 0.00 0.00 0.00 4.40
767 840 2.154462 CTTAGCAGAAACAGTGTGGGG 58.846 52.381 0.00 0.00 0.00 4.96
805 889 4.155826 TGCTATCGTCCAACTCCATTTTTG 59.844 41.667 0.00 0.00 0.00 2.44
806 890 4.331968 TGCTATCGTCCAACTCCATTTTT 58.668 39.130 0.00 0.00 0.00 1.94
810 894 1.202580 GCTGCTATCGTCCAACTCCAT 60.203 52.381 0.00 0.00 0.00 3.41
859 955 4.520846 CTTTCCATCACGCGCGCC 62.521 66.667 32.58 8.11 0.00 6.53
891 1000 1.492176 GAGAAGAATCCATGGCTGGGA 59.508 52.381 6.96 0.27 43.34 4.37
916 1025 7.356089 AGTTCATGGACGGAATACTTATACA 57.644 36.000 0.00 0.00 0.00 2.29
917 1026 6.867293 GGAGTTCATGGACGGAATACTTATAC 59.133 42.308 0.00 0.00 0.00 1.47
918 1027 6.551975 TGGAGTTCATGGACGGAATACTTATA 59.448 38.462 0.00 0.00 0.00 0.98
930 1048 3.388308 CTGATCGATGGAGTTCATGGAC 58.612 50.000 0.54 0.00 42.07 4.02
965 1088 1.781786 TTCTTCTCCCTCCTCCGATG 58.218 55.000 0.00 0.00 0.00 3.84
966 1089 2.785357 ATTCTTCTCCCTCCTCCGAT 57.215 50.000 0.00 0.00 0.00 4.18
967 1090 2.243994 TGTATTCTTCTCCCTCCTCCGA 59.756 50.000 0.00 0.00 0.00 4.55
968 1091 2.667470 TGTATTCTTCTCCCTCCTCCG 58.333 52.381 0.00 0.00 0.00 4.63
970 1093 5.659079 TCTTCTTGTATTCTTCTCCCTCCTC 59.341 44.000 0.00 0.00 0.00 3.71
971 1094 5.594777 TCTTCTTGTATTCTTCTCCCTCCT 58.405 41.667 0.00 0.00 0.00 3.69
972 1095 5.941555 TCTTCTTGTATTCTTCTCCCTCC 57.058 43.478 0.00 0.00 0.00 4.30
974 1097 7.456269 TCTTCTTCTTCTTGTATTCTTCTCCCT 59.544 37.037 0.00 0.00 0.00 4.20
975 1098 7.616313 TCTTCTTCTTCTTGTATTCTTCTCCC 58.384 38.462 0.00 0.00 0.00 4.30
976 1099 9.097257 CATCTTCTTCTTCTTGTATTCTTCTCC 57.903 37.037 0.00 0.00 0.00 3.71
977 1100 9.097257 CCATCTTCTTCTTCTTGTATTCTTCTC 57.903 37.037 0.00 0.00 0.00 2.87
978 1101 7.552330 GCCATCTTCTTCTTCTTGTATTCTTCT 59.448 37.037 0.00 0.00 0.00 2.85
987 1118 1.061711 CGCGCCATCTTCTTCTTCTTG 59.938 52.381 0.00 0.00 0.00 3.02
988 1119 1.363744 CGCGCCATCTTCTTCTTCTT 58.636 50.000 0.00 0.00 0.00 2.52
989 1120 1.086634 GCGCGCCATCTTCTTCTTCT 61.087 55.000 23.24 0.00 0.00 2.85
990 1121 1.349973 GCGCGCCATCTTCTTCTTC 59.650 57.895 23.24 0.00 0.00 2.87
1311 1466 1.825285 CGATCGGCATGCGGAAGAAG 61.825 60.000 28.71 16.91 0.00 2.85
1416 1571 1.081092 CTCCCACTCCCTCTTCCCA 59.919 63.158 0.00 0.00 0.00 4.37
1645 1800 2.352032 GGTCGTCCTCCACCTCCTG 61.352 68.421 0.00 0.00 0.00 3.86
1646 1801 2.037527 GGTCGTCCTCCACCTCCT 59.962 66.667 0.00 0.00 0.00 3.69
1647 1802 2.037527 AGGTCGTCCTCCACCTCC 59.962 66.667 0.00 0.00 38.83 4.30
1668 1823 5.083533 AGTAGTTGATCTTGAGCTTCAGG 57.916 43.478 0.00 0.00 0.00 3.86
2155 2319 1.520787 CGACCGGCGGCTTCTTAAT 60.521 57.895 28.71 2.71 36.03 1.40
2348 2515 8.774183 ACAATTACCCCATGTGAGTAATACTAA 58.226 33.333 10.79 0.00 36.04 2.24
2538 2711 6.321435 ACCGATCAAGATTAGACACAGATACA 59.679 38.462 0.00 0.00 0.00 2.29
2539 2712 6.638873 CACCGATCAAGATTAGACACAGATAC 59.361 42.308 0.00 0.00 0.00 2.24
2541 2714 5.452496 CCACCGATCAAGATTAGACACAGAT 60.452 44.000 0.00 0.00 0.00 2.90
2543 2716 4.115516 CCACCGATCAAGATTAGACACAG 58.884 47.826 0.00 0.00 0.00 3.66
2545 2718 4.386867 TCCACCGATCAAGATTAGACAC 57.613 45.455 0.00 0.00 0.00 3.67
2546 2719 4.202253 CCATCCACCGATCAAGATTAGACA 60.202 45.833 0.00 0.00 0.00 3.41
2548 2721 3.967326 ACCATCCACCGATCAAGATTAGA 59.033 43.478 0.00 0.00 0.00 2.10
2549 2722 4.342862 ACCATCCACCGATCAAGATTAG 57.657 45.455 0.00 0.00 0.00 1.73
2569 2742 2.488153 GTGCAGAATGGAACTACCCAAC 59.512 50.000 0.00 0.00 39.09 3.77
2576 2749 6.594788 ACATATTTTGTGCAGAATGGAACT 57.405 33.333 0.00 0.00 39.09 3.01
2647 2902 6.650807 TGTGAGTTCTTATTTGTCTGATGGAC 59.349 38.462 0.00 0.00 44.70 4.02
2648 2903 6.768483 TGTGAGTTCTTATTTGTCTGATGGA 58.232 36.000 0.00 0.00 0.00 3.41
2691 2952 1.473434 CGGCCATGTCTTAAGAGGGTC 60.473 57.143 5.12 8.69 0.00 4.46
2710 2971 3.876300 CCTCCTGGCGAAGAAACG 58.124 61.111 0.00 0.00 0.00 3.60
2721 2982 8.831715 ACTTTTAACATAAAAATTGCCTCCTG 57.168 30.769 0.00 0.00 0.00 3.86
2745 3006 1.009389 GCGCCTATCAGTCGCCATAC 61.009 60.000 0.00 0.00 42.71 2.39
2771 3032 1.294459 GGTCGAAAGTTAGGCCGGT 59.706 57.895 1.90 0.00 0.00 5.28
2835 3096 1.694525 GGGGAGGGGAGGAAGAAGG 60.695 68.421 0.00 0.00 0.00 3.46
2852 3113 3.163594 GTGCGAATCAGAATCGTTTTGG 58.836 45.455 9.61 0.00 42.15 3.28
2987 3254 1.144057 GATTGGGAGGACGTGCGAT 59.856 57.895 0.00 0.00 0.00 4.58
2995 3262 1.064906 ACGACTACGAGATTGGGAGGA 60.065 52.381 0.00 0.00 42.66 3.71
3079 3346 2.036346 GCTTTGATTGGTTGCTGGAACT 59.964 45.455 11.83 0.00 34.66 3.01
3167 3434 7.442969 TGGTTTCTCTAGTTGCTCGAATTTTTA 59.557 33.333 0.00 0.00 0.00 1.52
3174 3443 3.572682 TCTTGGTTTCTCTAGTTGCTCGA 59.427 43.478 0.00 0.00 0.00 4.04
3183 3452 2.370849 ACGGGCTTTCTTGGTTTCTCTA 59.629 45.455 0.00 0.00 0.00 2.43
3195 3464 2.217429 TTTTGCTTCAACGGGCTTTC 57.783 45.000 0.00 0.00 0.00 2.62
3223 3493 2.032979 GCAATTTTGTTTGCTGGAACCG 60.033 45.455 2.08 0.00 46.66 4.44
3256 3526 4.990426 TCGACGACGACAATCTATGGTATA 59.010 41.667 5.75 0.00 43.81 1.47
3280 3550 2.600320 CGGCTTTTGTTTTCGCTACGAA 60.600 45.455 0.00 0.00 44.28 3.85
3288 3558 3.004419 AGCTAGAACCGGCTTTTGTTTTC 59.996 43.478 0.00 0.00 34.96 2.29
3292 3562 2.152016 GAAGCTAGAACCGGCTTTTGT 58.848 47.619 0.00 0.00 46.91 2.83
3293 3563 1.468914 GGAAGCTAGAACCGGCTTTTG 59.531 52.381 0.00 0.00 46.91 2.44
3294 3564 1.822506 GGAAGCTAGAACCGGCTTTT 58.177 50.000 0.00 0.00 46.91 2.27
3295 3565 0.391263 CGGAAGCTAGAACCGGCTTT 60.391 55.000 0.00 0.00 46.91 3.51
3297 3567 1.681327 TCGGAAGCTAGAACCGGCT 60.681 57.895 17.73 0.00 45.61 5.52
3298 3568 1.518792 GTCGGAAGCTAGAACCGGC 60.519 63.158 17.73 14.29 45.61 6.13
3299 3569 4.808649 GTCGGAAGCTAGAACCGG 57.191 61.111 17.73 0.00 45.61 5.28


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

AutoCloner maintained by Alex Coulton.