Multiple sequence alignment - TraesCS6B01G420700

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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 TraesCS6B01G420700 chr6B 100.000 2069 0 0 1 2069 691943917 691945985 0.000000e+00 3821
1 TraesCS6B01G420700 chr6B 91.945 1167 77 12 800 1954 692095005 692093844 0.000000e+00 1618
2 TraesCS6B01G420700 chr6B 81.767 1064 149 29 834 1876 692574296 692575335 0.000000e+00 848
3 TraesCS6B01G420700 chr6B 81.166 1115 155 31 852 1936 692044860 692043771 0.000000e+00 845
4 TraesCS6B01G420700 chr6B 81.093 1116 148 37 852 1933 691976044 691977130 0.000000e+00 833
5 TraesCS6B01G420700 chr6B 80.901 1110 153 41 847 1926 692570577 692571657 0.000000e+00 821
6 TraesCS6B01G420700 chr6B 100.000 391 0 0 2359 2749 691946275 691946665 0.000000e+00 723
7 TraesCS6B01G420700 chr6B 92.602 392 15 5 5 396 692096271 692095894 4.000000e-153 551
8 TraesCS6B01G420700 chr6B 87.500 296 30 3 2360 2655 692073959 692073671 4.390000e-88 335
9 TraesCS6B01G420700 chr6B 84.416 231 11 8 414 619 692095231 692095001 1.290000e-48 204
10 TraesCS6B01G420700 chr6B 96.721 61 2 0 1976 2036 692091216 692091156 4.840000e-18 102
11 TraesCS6B01G420700 chr6D 91.088 1167 87 10 800 1954 454996725 454995564 0.000000e+00 1563
12 TraesCS6B01G420700 chr6D 81.393 1134 150 43 834 1930 455421734 455422843 0.000000e+00 869
13 TraesCS6B01G420700 chr6D 90.955 398 22 4 5 402 454997990 454997607 8.720000e-145 523
14 TraesCS6B01G420700 chr6D 84.753 223 8 10 423 619 454996943 454996721 1.670000e-47 200
15 TraesCS6B01G420700 chr6A 88.326 1165 110 18 800 1954 601264858 601263710 0.000000e+00 1375
16 TraesCS6B01G420700 chr6A 81.745 1123 164 25 852 1954 601257154 601256053 0.000000e+00 900
17 TraesCS6B01G420700 chr6A 82.369 1089 132 38 834 1894 602131331 602132387 0.000000e+00 893
18 TraesCS6B01G420700 chr6A 81.642 1084 145 38 892 1936 602075516 602076584 0.000000e+00 850
19 TraesCS6B01G420700 chr6A 84.438 649 45 18 5 619 601265480 601264854 3.050000e-164 588
20 TraesCS6B01G420700 chr6A 90.026 391 38 1 2360 2749 601262048 601261658 3.160000e-139 505
21 TraesCS6B01G420700 chr6A 92.090 177 13 1 619 794 279296147 279295971 5.880000e-62 248
22 TraesCS6B01G420700 chrUn 90.840 655 53 7 1297 1946 79450177 79449525 0.000000e+00 870
23 TraesCS6B01G420700 chrUn 87.248 298 31 3 2360 2657 79447948 79447658 1.580000e-87 333
24 TraesCS6B01G420700 chr7D 94.286 175 10 0 619 793 587750567 587750393 4.510000e-68 268
25 TraesCS6B01G420700 chr7D 92.571 175 13 0 619 793 43431555 43431381 4.540000e-63 252
26 TraesCS6B01G420700 chr4D 93.714 175 11 0 619 793 465072471 465072297 2.100000e-66 263
27 TraesCS6B01G420700 chr7B 92.350 183 13 1 619 800 600565362 600565180 2.720000e-65 259
28 TraesCS6B01G420700 chr4A 92.614 176 13 0 619 794 395307948 395308123 1.260000e-63 254
29 TraesCS6B01G420700 chr4A 92.000 175 14 0 619 793 394858613 394858439 2.110000e-61 246
30 TraesCS6B01G420700 chr7A 92.000 175 14 0 620 794 723551168 723551342 2.110000e-61 246
31 TraesCS6B01G420700 chr2D 92.000 175 14 0 619 793 95142053 95142227 2.110000e-61 246


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 TraesCS6B01G420700 chr6B 691943917 691946665 2748 False 2272.000000 3821 100.000000 1 2749 2 chr6B.!!$F2 2748
1 TraesCS6B01G420700 chr6B 692043771 692044860 1089 True 845.000000 845 81.166000 852 1936 1 chr6B.!!$R1 1084
2 TraesCS6B01G420700 chr6B 692570577 692575335 4758 False 834.500000 848 81.334000 834 1926 2 chr6B.!!$F3 1092
3 TraesCS6B01G420700 chr6B 691976044 691977130 1086 False 833.000000 833 81.093000 852 1933 1 chr6B.!!$F1 1081
4 TraesCS6B01G420700 chr6B 692091156 692096271 5115 True 618.750000 1618 91.421000 5 2036 4 chr6B.!!$R3 2031
5 TraesCS6B01G420700 chr6D 455421734 455422843 1109 False 869.000000 869 81.393000 834 1930 1 chr6D.!!$F1 1096
6 TraesCS6B01G420700 chr6D 454995564 454997990 2426 True 762.000000 1563 88.932000 5 1954 3 chr6D.!!$R1 1949
7 TraesCS6B01G420700 chr6A 601256053 601257154 1101 True 900.000000 900 81.745000 852 1954 1 chr6A.!!$R2 1102
8 TraesCS6B01G420700 chr6A 602131331 602132387 1056 False 893.000000 893 82.369000 834 1894 1 chr6A.!!$F2 1060
9 TraesCS6B01G420700 chr6A 602075516 602076584 1068 False 850.000000 850 81.642000 892 1936 1 chr6A.!!$F1 1044
10 TraesCS6B01G420700 chr6A 601261658 601265480 3822 True 822.666667 1375 87.596667 5 2749 3 chr6A.!!$R3 2744
11 TraesCS6B01G420700 chrUn 79447658 79450177 2519 True 601.500000 870 89.044000 1297 2657 2 chrUn.!!$R1 1360

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
654 1394 0.0421 GCTACAGAAAATAGCGCGGC 60.042 55.0 8.83 0.0 36.02 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 7929 0.737715 GGTCGCACAGAGGTAGCAAG 60.738 60.0 0.0 0.0 0.0 4.01 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
27 28 1.415672 TTCGGACAAGGCAAGGGAGT 61.416 55.000 0.00 0.00 0.00 3.85
48 49 4.501285 TCCTCCCTCGTCCGCGAT 62.501 66.667 8.23 0.00 46.80 4.58
136 137 0.810648 TGCATCGGATTGGCTTGAAC 59.189 50.000 2.53 0.00 0.00 3.18
181 182 4.055360 TCGTCCGCTGTATTTGAATATGG 58.945 43.478 0.00 0.00 0.00 2.74
182 183 3.363970 CGTCCGCTGTATTTGAATATGGC 60.364 47.826 0.00 0.00 0.00 4.40
183 184 3.815401 GTCCGCTGTATTTGAATATGGCT 59.185 43.478 0.00 0.00 0.00 4.75
184 185 4.994852 GTCCGCTGTATTTGAATATGGCTA 59.005 41.667 0.00 0.00 0.00 3.93
258 260 4.814147 GACAGAAGTCTCATGTGATGTGA 58.186 43.478 6.50 0.00 41.64 3.58
273 275 0.813821 TGTGACTCCTCTCTGATGCG 59.186 55.000 0.00 0.00 0.00 4.73
371 373 2.430694 ACCTCTTTTGTTTTGTCAGCCC 59.569 45.455 0.00 0.00 0.00 5.19
579 1315 3.423848 GCAGCCTGCATAAACAACC 57.576 52.632 12.82 0.00 44.26 3.77
619 1359 3.375922 GCTCCAAATTAACGGAATCGGAA 59.624 43.478 0.00 0.00 41.39 4.30
621 1361 5.493133 TCCAAATTAACGGAATCGGAATG 57.507 39.130 0.00 0.00 41.39 2.67
622 1362 5.186942 TCCAAATTAACGGAATCGGAATGA 58.813 37.500 0.00 0.00 41.39 2.57
624 1364 6.151312 TCCAAATTAACGGAATCGGAATGAAA 59.849 34.615 0.00 0.00 41.39 2.69
645 1385 4.413495 AAAAATAGCGCGCTACAGAAAA 57.587 36.364 40.42 21.55 0.00 2.29
646 1386 4.616181 AAAATAGCGCGCTACAGAAAAT 57.384 36.364 40.42 22.89 0.00 1.82
647 1387 5.728351 AAAATAGCGCGCTACAGAAAATA 57.272 34.783 40.42 19.94 0.00 1.40
649 1389 0.931005 AGCGCGCTACAGAAAATAGC 59.069 50.000 35.79 0.00 41.43 2.97
654 1394 0.042100 GCTACAGAAAATAGCGCGGC 60.042 55.000 8.83 0.00 36.02 6.53
655 1395 0.582005 CTACAGAAAATAGCGCGGCC 59.418 55.000 8.83 0.00 0.00 6.13
656 1396 0.812412 TACAGAAAATAGCGCGGCCC 60.812 55.000 8.83 0.00 0.00 5.80
657 1397 2.516225 AGAAAATAGCGCGGCCCC 60.516 61.111 8.83 0.00 0.00 5.80
659 1399 1.227734 GAAAATAGCGCGGCCCCTA 60.228 57.895 8.83 0.03 0.00 3.53
660 1400 0.816421 GAAAATAGCGCGGCCCCTAA 60.816 55.000 8.83 0.00 0.00 2.69
661 1401 0.394625 AAAATAGCGCGGCCCCTAAA 60.395 50.000 8.83 0.00 0.00 1.85
663 1403 0.394625 AATAGCGCGGCCCCTAAAAA 60.395 50.000 8.83 0.00 0.00 1.94
664 1404 0.179001 ATAGCGCGGCCCCTAAAAAT 60.179 50.000 8.83 0.00 0.00 1.82
666 1406 0.179001 AGCGCGGCCCCTAAAAATAT 60.179 50.000 8.83 0.00 0.00 1.28
668 1408 1.198408 GCGCGGCCCCTAAAAATATAC 59.802 52.381 8.83 0.00 0.00 1.47
669 1409 2.774687 CGCGGCCCCTAAAAATATACT 58.225 47.619 0.00 0.00 0.00 2.12
671 1411 4.510571 CGCGGCCCCTAAAAATATACTAT 58.489 43.478 0.00 0.00 0.00 2.12
672 1412 4.939439 CGCGGCCCCTAAAAATATACTATT 59.061 41.667 0.00 0.00 0.00 1.73
674 1414 6.257193 CGCGGCCCCTAAAAATATACTATTAG 59.743 42.308 0.00 0.00 0.00 1.73
675 1415 7.108194 GCGGCCCCTAAAAATATACTATTAGT 58.892 38.462 0.00 1.30 0.00 2.24
690 1430 8.830201 ATACTATTAGTATACTATAGCGCGCT 57.170 34.615 38.01 38.01 39.49 5.92
691 1431 9.920133 ATACTATTAGTATACTATAGCGCGCTA 57.080 33.333 39.72 39.72 39.49 4.26
692 1432 8.071122 ACTATTAGTATACTATAGCGCGCTAC 57.929 38.462 40.42 28.53 0.00 3.58
693 1433 6.915544 ATTAGTATACTATAGCGCGCTACA 57.084 37.500 40.42 30.43 0.00 2.74
694 1434 6.726258 TTAGTATACTATAGCGCGCTACAA 57.274 37.500 40.42 29.20 0.00 2.41
695 1435 4.967437 AGTATACTATAGCGCGCTACAAC 58.033 43.478 40.42 27.98 0.00 3.32
696 1436 2.305252 TACTATAGCGCGCTACAACG 57.695 50.000 40.42 28.26 0.00 4.10
697 1437 0.379669 ACTATAGCGCGCTACAACGT 59.620 50.000 40.42 28.86 34.88 3.99
698 1438 0.770590 CTATAGCGCGCTACAACGTG 59.229 55.000 40.42 22.16 45.99 4.49
702 1442 3.688136 CGCGCTACAACGTGCTAT 58.312 55.556 5.56 0.00 38.23 2.97
703 1443 1.995991 CGCGCTACAACGTGCTATT 59.004 52.632 5.56 0.00 38.23 1.73
704 1444 1.193644 CGCGCTACAACGTGCTATTA 58.806 50.000 5.56 0.00 38.23 0.98
705 1445 1.187271 CGCGCTACAACGTGCTATTAG 59.813 52.381 5.56 0.00 38.23 1.73
706 1446 1.071436 GCGCTACAACGTGCTATTAGC 60.071 52.381 8.80 8.80 42.82 3.09
707 1447 2.905260 GCTACAACGTGCTATTAGCG 57.095 50.000 10.94 0.54 46.26 4.26
708 1448 2.456989 GCTACAACGTGCTATTAGCGA 58.543 47.619 10.94 0.00 46.26 4.93
709 1449 2.468040 GCTACAACGTGCTATTAGCGAG 59.532 50.000 10.94 9.41 46.26 5.03
710 1450 2.933495 ACAACGTGCTATTAGCGAGA 57.067 45.000 10.94 0.00 46.26 4.04
712 1452 2.094906 ACAACGTGCTATTAGCGAGACA 60.095 45.455 10.94 0.00 46.26 3.41
713 1453 3.116300 CAACGTGCTATTAGCGAGACAT 58.884 45.455 10.94 0.00 46.26 3.06
714 1454 3.438297 ACGTGCTATTAGCGAGACATT 57.562 42.857 10.94 0.00 46.26 2.71
715 1455 4.563337 ACGTGCTATTAGCGAGACATTA 57.437 40.909 10.94 0.00 46.26 1.90
716 1456 4.537965 ACGTGCTATTAGCGAGACATTAG 58.462 43.478 10.94 0.00 46.26 1.73
718 1458 4.613448 CGTGCTATTAGCGAGACATTAGAC 59.387 45.833 10.94 0.00 46.26 2.59
720 1460 6.153067 GTGCTATTAGCGAGACATTAGACAT 58.847 40.000 10.94 0.00 46.26 3.06
723 1463 8.357402 TGCTATTAGCGAGACATTAGACATAAA 58.643 33.333 10.94 0.00 46.26 1.40
724 1464 9.360093 GCTATTAGCGAGACATTAGACATAAAT 57.640 33.333 0.00 0.00 0.00 1.40
738 1478 9.807386 ATTAGACATAAATTAATTTAGCGACGC 57.193 29.630 21.75 13.03 35.88 5.19
739 1479 7.241663 AGACATAAATTAATTTAGCGACGCA 57.758 32.000 23.70 5.17 35.88 5.24
741 1481 8.342634 AGACATAAATTAATTTAGCGACGCAAT 58.657 29.630 23.70 11.12 35.88 3.56
742 1482 8.850454 ACATAAATTAATTTAGCGACGCAATT 57.150 26.923 23.70 20.54 35.88 2.32
743 1483 8.953990 ACATAAATTAATTTAGCGACGCAATTC 58.046 29.630 23.70 0.00 35.88 2.17
744 1484 9.169468 CATAAATTAATTTAGCGACGCAATTCT 57.831 29.630 23.70 2.80 35.88 2.40
745 1485 9.730420 ATAAATTAATTTAGCGACGCAATTCTT 57.270 25.926 23.70 14.66 35.88 2.52
746 1486 8.460831 AAATTAATTTAGCGACGCAATTCTTT 57.539 26.923 23.70 17.29 0.00 2.52
749 1489 4.994220 TTTAGCGACGCAATTCTTTACA 57.006 36.364 23.70 0.00 0.00 2.41
750 1490 2.875080 AGCGACGCAATTCTTTACAC 57.125 45.000 23.70 0.00 0.00 2.90
751 1491 1.126113 AGCGACGCAATTCTTTACACG 59.874 47.619 23.70 0.00 0.00 4.49
752 1492 1.510007 CGACGCAATTCTTTACACGC 58.490 50.000 0.00 0.00 0.00 5.34
753 1493 1.126113 CGACGCAATTCTTTACACGCT 59.874 47.619 0.00 0.00 0.00 5.07
755 1495 3.000078 CGACGCAATTCTTTACACGCTAT 60.000 43.478 0.00 0.00 0.00 2.97
756 1496 4.205588 CGACGCAATTCTTTACACGCTATA 59.794 41.667 0.00 0.00 0.00 1.31
758 1498 4.025979 ACGCAATTCTTTACACGCTATAGC 60.026 41.667 15.09 15.09 37.78 2.97
771 1511 2.186076 GCTATAGCGTGCTATTAGCGG 58.814 52.381 18.62 6.68 46.26 5.52
772 1512 2.186076 CTATAGCGTGCTATTAGCGGC 58.814 52.381 18.62 18.55 46.26 6.53
773 1513 0.732880 ATAGCGTGCTATTAGCGGCG 60.733 55.000 20.72 20.72 46.26 6.46
775 1515 2.658593 CGTGCTATTAGCGGCGCT 60.659 61.111 37.84 37.84 46.26 5.92
776 1516 1.371267 CGTGCTATTAGCGGCGCTA 60.371 57.895 35.39 35.39 46.26 4.26
777 1517 0.732880 CGTGCTATTAGCGGCGCTAT 60.733 55.000 38.35 28.53 46.26 2.97
780 1520 1.201343 GCTATTAGCGGCGCTATAGC 58.799 55.000 37.08 37.08 41.01 2.97
832 1572 2.754254 GTTGCCCATCCGAACCCC 60.754 66.667 0.00 0.00 0.00 4.95
837 1577 4.891727 CCATCCGAACCCCTCGCG 62.892 72.222 0.00 0.00 46.71 5.87
890 3792 5.853936 TGCTATCCATAGTTCCATACACAC 58.146 41.667 0.00 0.00 32.96 3.82
895 3797 6.499106 TCCATAGTTCCATACACACATCAT 57.501 37.500 0.00 0.00 0.00 2.45
949 3853 4.641645 CCACACCCAGGAAGCGCA 62.642 66.667 11.47 0.00 0.00 6.09
983 3909 3.285484 CACCAAGCTGATAGGAAGCAAT 58.715 45.455 0.00 0.00 43.37 3.56
993 3919 1.481871 AGGAAGCAATCATTGGCCAG 58.518 50.000 5.11 0.00 0.00 4.85
1009 3935 1.735973 CAGTCGATCATGGCGAGGA 59.264 57.895 11.02 0.00 38.59 3.71
1053 3979 3.184683 GCAGTCTTCCTCGCGCTG 61.185 66.667 5.56 1.67 0.00 5.18
1131 4057 3.584406 ACCTGAAATCCTGTGAGTCATCA 59.416 43.478 0.00 0.00 0.00 3.07
1147 4074 7.785033 TGAGTCATCACTTCTGCTCAATTATA 58.215 34.615 0.00 0.00 30.63 0.98
1163 4090 9.065871 GCTCAATTATACACACATCTTTGTTTC 57.934 33.333 0.00 0.00 32.34 2.78
1206 4178 1.267806 CTTGCTGACATGGCGTTTTCT 59.732 47.619 0.00 0.00 0.00 2.52
1208 4180 1.001487 TGCTGACATGGCGTTTTCTTG 60.001 47.619 0.00 0.00 0.00 3.02
1304 4283 2.192861 CAAGAAGCCCGGCAACACA 61.193 57.895 13.15 0.00 0.00 3.72
1353 4332 0.040425 GGCGAACGTGCAGTCATTTT 60.040 50.000 0.00 0.00 36.28 1.82
1457 4436 4.439057 GTGCCACCGAGATTATCTTTGTA 58.561 43.478 0.00 0.00 0.00 2.41
1463 4442 5.681982 CACCGAGATTATCTTTGTACTCGAC 59.318 44.000 14.35 0.00 46.21 4.20
1826 4822 9.229784 GTGTGTTCATTGCTGAATAAATGATAG 57.770 33.333 0.00 0.00 43.08 2.08
1836 4840 6.347240 GCTGAATAAATGATAGTCAAGCGAGG 60.347 42.308 0.00 0.00 0.00 4.63
1928 4945 8.479313 TTCTCATTCACATAGTGTATGTTCAC 57.521 34.615 13.81 0.00 46.69 3.18
1954 4971 5.733620 AGTAACGTGTCCTCCATTTCTTA 57.266 39.130 0.00 0.00 0.00 2.10
1960 4977 4.390264 GTGTCCTCCATTTCTTATAGGGC 58.610 47.826 0.00 0.00 32.43 5.19
1961 4978 3.394606 TGTCCTCCATTTCTTATAGGGCC 59.605 47.826 0.00 0.00 30.67 5.80
1962 4979 2.637872 TCCTCCATTTCTTATAGGGCCG 59.362 50.000 0.00 0.00 0.00 6.13
1964 4981 3.557264 CCTCCATTTCTTATAGGGCCGAC 60.557 52.174 0.00 0.00 0.00 4.79
1965 4982 2.370849 TCCATTTCTTATAGGGCCGACC 59.629 50.000 0.00 0.00 40.67 4.79
1969 4986 1.700955 TCTTATAGGGCCGACCAGAC 58.299 55.000 0.00 0.00 43.89 3.51
1971 4988 0.761702 TTATAGGGCCGACCAGACCC 60.762 60.000 0.00 0.00 43.89 4.46
1974 4991 2.446036 GGGCCGACCAGACCCTAT 60.446 66.667 0.00 0.00 40.75 2.57
1978 7863 0.680061 GCCGACCAGACCCTATAAGG 59.320 60.000 0.00 0.00 34.30 2.69
2044 7929 4.815308 CCACTCATCTTTCATCCATGTCTC 59.185 45.833 0.00 0.00 0.00 3.36
2391 8314 0.732571 GGTATGTGCATTGTCGGTGG 59.267 55.000 0.00 0.00 0.00 4.61
2394 8317 2.418368 ATGTGCATTGTCGGTGGTAT 57.582 45.000 0.00 0.00 0.00 2.73
2401 8324 5.405571 GTGCATTGTCGGTGGTATAGATAAG 59.594 44.000 0.00 0.00 0.00 1.73
2460 8383 1.968493 AGTCGCTTGAGTTTCTACCCA 59.032 47.619 0.00 0.00 0.00 4.51
2490 8413 1.874129 TTACCTGGTCCGTCATCCAT 58.126 50.000 0.63 0.00 33.01 3.41
2492 8415 0.991920 ACCTGGTCCGTCATCCATTT 59.008 50.000 0.00 0.00 33.01 2.32
2514 8437 6.462552 TTGTCAAGTTGATCAATTCCACAA 57.537 33.333 12.12 15.33 0.00 3.33
2529 8452 6.847956 ATTCCACAACACAATTTTGACATG 57.152 33.333 0.00 0.00 0.00 3.21
2544 8467 7.913674 TTTTGACATGTGCTATGTATGTACA 57.086 32.000 1.15 0.00 40.98 2.90
2554 8477 7.094118 TGTGCTATGTATGTACACACTAGAACA 60.094 37.037 15.16 15.16 39.30 3.18
2603 8526 3.381590 TGATGAGGTGTCTCCGTCATAAG 59.618 47.826 0.00 0.00 41.99 1.73
2609 8532 3.318275 GGTGTCTCCGTCATAAGATGCTA 59.682 47.826 0.00 0.00 0.00 3.49
2617 8540 4.153117 CCGTCATAAGATGCTATTGGAAGC 59.847 45.833 0.00 0.00 43.08 3.86
2668 8591 5.152923 TCTACTATGTACGAAAGCTGTCG 57.847 43.478 24.67 24.67 46.54 4.35
2704 8628 4.298332 CAAGCAGCGAAAGTTAAAACCAT 58.702 39.130 0.00 0.00 0.00 3.55
2711 8635 6.142320 CAGCGAAAGTTAAAACCATTCTTCAC 59.858 38.462 0.00 0.00 0.00 3.18
2712 8636 5.974751 GCGAAAGTTAAAACCATTCTTCACA 59.025 36.000 0.00 0.00 0.00 3.58
2714 8638 6.142320 CGAAAGTTAAAACCATTCTTCACAGC 59.858 38.462 7.15 0.00 0.00 4.40
2719 8643 7.277760 AGTTAAAACCATTCTTCACAGCAAAAC 59.722 33.333 0.00 0.00 0.00 2.43
2727 8651 4.922206 TCTTCACAGCAAAACCAGGATAT 58.078 39.130 0.00 0.00 0.00 1.63
2736 8660 7.013655 ACAGCAAAACCAGGATATGTATGATTC 59.986 37.037 0.00 0.00 0.00 2.52
2741 8665 9.818270 AAAACCAGGATATGTATGATTCATGAT 57.182 29.630 9.46 4.21 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.843240 CTTGTCCGAAGCGCGCTC 61.843 66.667 36.57 25.09 39.11 5.03
27 28 2.045242 CGGACGAGGGAGGAGACA 60.045 66.667 0.00 0.00 0.00 3.41
46 47 1.750351 TATTACGTGCGTGCTCGATC 58.250 50.000 21.23 2.83 39.71 3.69
47 48 1.850441 GTTATTACGTGCGTGCTCGAT 59.150 47.619 21.23 9.01 39.71 3.59
48 49 1.261989 GTTATTACGTGCGTGCTCGA 58.738 50.000 21.23 2.06 39.71 4.04
83 84 1.798079 GCCGTCTCTATCACCGACAAC 60.798 57.143 0.00 0.00 0.00 3.32
226 228 0.533032 GACTTCTGTCTCTTCCGGGG 59.467 60.000 0.00 0.00 39.94 5.73
254 256 0.813821 CGCATCAGAGAGGAGTCACA 59.186 55.000 0.00 0.00 0.00 3.58
255 257 1.065401 CTCGCATCAGAGAGGAGTCAC 59.935 57.143 0.00 0.00 40.57 3.67
256 258 1.340502 ACTCGCATCAGAGAGGAGTCA 60.341 52.381 0.62 0.00 44.82 3.41
257 259 1.065401 CACTCGCATCAGAGAGGAGTC 59.935 57.143 0.62 0.00 44.82 3.36
258 260 1.102154 CACTCGCATCAGAGAGGAGT 58.898 55.000 0.62 0.00 44.82 3.85
273 275 6.256757 GTCTCAGCCAGTAATCAATTACACTC 59.743 42.308 13.76 3.90 43.83 3.51
562 1296 4.261741 GGATATGGTTGTTTATGCAGGCTG 60.262 45.833 10.94 10.94 0.00 4.85
579 1315 3.512724 GGAGCCAATCAAATGGGGATATG 59.487 47.826 0.00 0.00 41.01 1.78
624 1364 4.413495 TTTTCTGTAGCGCGCTATTTTT 57.587 36.364 39.99 18.75 0.00 1.94
627 1367 3.184581 GCTATTTTCTGTAGCGCGCTATT 59.815 43.478 39.99 20.35 35.68 1.73
629 1369 2.124903 GCTATTTTCTGTAGCGCGCTA 58.875 47.619 35.48 35.48 35.68 4.26
630 1370 0.931005 GCTATTTTCTGTAGCGCGCT 59.069 50.000 38.01 38.01 35.68 5.92
631 1371 3.422646 GCTATTTTCTGTAGCGCGC 57.577 52.632 26.66 26.66 35.68 6.86
635 1375 0.042100 GCCGCGCTATTTTCTGTAGC 60.042 55.000 5.56 0.00 40.83 3.58
636 1376 0.582005 GGCCGCGCTATTTTCTGTAG 59.418 55.000 5.56 0.00 0.00 2.74
637 1377 0.812412 GGGCCGCGCTATTTTCTGTA 60.812 55.000 5.56 0.00 0.00 2.74
638 1378 2.112815 GGGCCGCGCTATTTTCTGT 61.113 57.895 5.56 0.00 0.00 3.41
641 1381 0.816421 TTAGGGGCCGCGCTATTTTC 60.816 55.000 15.00 0.00 0.00 2.29
643 1383 0.394625 TTTTAGGGGCCGCGCTATTT 60.395 50.000 15.00 0.00 0.00 1.40
645 1385 0.179001 ATTTTTAGGGGCCGCGCTAT 60.179 50.000 15.00 0.00 0.00 2.97
646 1386 0.469070 TATTTTTAGGGGCCGCGCTA 59.531 50.000 15.00 0.00 0.00 4.26
647 1387 0.179001 ATATTTTTAGGGGCCGCGCT 60.179 50.000 15.00 0.00 0.00 5.92
649 1389 2.774687 AGTATATTTTTAGGGGCCGCG 58.225 47.619 15.00 0.00 0.00 6.46
664 1404 9.920133 AGCGCGCTATAGTATACTAATAGTATA 57.080 33.333 35.79 14.33 41.36 1.47
666 1406 9.186323 GTAGCGCGCTATAGTATACTAATAGTA 57.814 37.037 39.99 13.74 34.82 1.82
668 1408 8.070007 TGTAGCGCGCTATAGTATACTAATAG 57.930 38.462 39.99 16.68 31.39 1.73
669 1409 8.331022 GTTGTAGCGCGCTATAGTATACTAATA 58.669 37.037 39.99 17.81 31.39 0.98
671 1411 6.537566 GTTGTAGCGCGCTATAGTATACTAA 58.462 40.000 39.99 21.45 31.39 2.24
672 1412 5.220284 CGTTGTAGCGCGCTATAGTATACTA 60.220 44.000 39.99 23.37 0.00 1.82
674 1414 3.777680 CGTTGTAGCGCGCTATAGTATAC 59.222 47.826 39.99 29.12 0.00 1.47
675 1415 3.433274 ACGTTGTAGCGCGCTATAGTATA 59.567 43.478 39.99 21.73 34.88 1.47
677 1417 1.599071 ACGTTGTAGCGCGCTATAGTA 59.401 47.619 39.99 22.81 34.88 1.82
678 1418 0.379669 ACGTTGTAGCGCGCTATAGT 59.620 50.000 39.99 30.85 34.88 2.12
679 1419 0.770590 CACGTTGTAGCGCGCTATAG 59.229 55.000 39.99 30.27 34.88 1.31
680 1420 1.204228 GCACGTTGTAGCGCGCTATA 61.204 55.000 39.99 35.13 37.02 1.31
684 1424 2.020836 AATAGCACGTTGTAGCGCGC 62.021 55.000 26.66 26.66 39.82 6.86
685 1425 1.187271 CTAATAGCACGTTGTAGCGCG 59.813 52.381 0.00 0.00 35.48 6.86
686 1426 1.071436 GCTAATAGCACGTTGTAGCGC 60.071 52.381 7.49 0.00 41.89 5.92
687 1427 2.905260 GCTAATAGCACGTTGTAGCG 57.095 50.000 7.49 0.00 41.89 4.26
688 1428 2.456989 TCGCTAATAGCACGTTGTAGC 58.543 47.619 13.15 0.00 42.58 3.58
689 1429 3.724751 GTCTCGCTAATAGCACGTTGTAG 59.275 47.826 13.15 0.00 42.58 2.74
690 1430 3.127376 TGTCTCGCTAATAGCACGTTGTA 59.873 43.478 13.15 0.00 42.58 2.41
691 1431 2.094906 TGTCTCGCTAATAGCACGTTGT 60.095 45.455 13.15 0.00 42.58 3.32
692 1432 2.526077 TGTCTCGCTAATAGCACGTTG 58.474 47.619 13.15 0.00 42.58 4.10
693 1433 2.933495 TGTCTCGCTAATAGCACGTT 57.067 45.000 13.15 0.00 42.58 3.99
694 1434 3.438297 AATGTCTCGCTAATAGCACGT 57.562 42.857 13.15 1.79 42.58 4.49
695 1435 4.613448 GTCTAATGTCTCGCTAATAGCACG 59.387 45.833 13.15 2.42 42.58 5.34
696 1436 5.520632 TGTCTAATGTCTCGCTAATAGCAC 58.479 41.667 13.15 3.79 42.58 4.40
697 1437 5.767816 TGTCTAATGTCTCGCTAATAGCA 57.232 39.130 13.15 0.00 42.58 3.49
698 1438 8.744008 TTTATGTCTAATGTCTCGCTAATAGC 57.256 34.615 1.41 1.41 38.02 2.97
712 1452 9.807386 GCGTCGCTAAATTAATTTATGTCTAAT 57.193 29.630 18.58 0.00 32.36 1.73
713 1453 8.819015 TGCGTCGCTAAATTAATTTATGTCTAA 58.181 29.630 19.50 0.05 32.36 2.10
714 1454 8.355272 TGCGTCGCTAAATTAATTTATGTCTA 57.645 30.769 19.50 0.70 32.36 2.59
715 1455 7.241663 TGCGTCGCTAAATTAATTTATGTCT 57.758 32.000 19.50 0.00 32.36 3.41
716 1456 7.886191 TTGCGTCGCTAAATTAATTTATGTC 57.114 32.000 19.50 11.90 32.36 3.06
718 1458 9.169468 AGAATTGCGTCGCTAAATTAATTTATG 57.831 29.630 19.50 14.56 32.36 1.90
720 1460 9.562583 AAAGAATTGCGTCGCTAAATTAATTTA 57.437 25.926 19.50 17.54 0.00 1.40
723 1463 8.178964 TGTAAAGAATTGCGTCGCTAAATTAAT 58.821 29.630 19.50 5.58 0.00 1.40
724 1464 7.479291 GTGTAAAGAATTGCGTCGCTAAATTAA 59.521 33.333 19.50 3.13 0.00 1.40
725 1465 6.957077 GTGTAAAGAATTGCGTCGCTAAATTA 59.043 34.615 19.50 7.57 0.00 1.40
726 1466 5.793457 GTGTAAAGAATTGCGTCGCTAAATT 59.207 36.000 19.50 16.10 0.00 1.82
727 1467 5.321516 GTGTAAAGAATTGCGTCGCTAAAT 58.678 37.500 19.50 7.88 0.00 1.40
728 1468 4.664640 CGTGTAAAGAATTGCGTCGCTAAA 60.665 41.667 19.50 5.54 0.00 1.85
729 1469 3.181538 CGTGTAAAGAATTGCGTCGCTAA 60.182 43.478 19.50 11.31 0.00 3.09
730 1470 2.343246 CGTGTAAAGAATTGCGTCGCTA 59.657 45.455 19.50 11.82 0.00 4.26
731 1471 1.126113 CGTGTAAAGAATTGCGTCGCT 59.874 47.619 19.50 0.00 0.00 4.93
732 1472 1.510007 CGTGTAAAGAATTGCGTCGC 58.490 50.000 11.10 11.10 0.00 5.19
733 1473 1.126113 AGCGTGTAAAGAATTGCGTCG 59.874 47.619 0.00 0.00 0.00 5.12
734 1474 2.875080 AGCGTGTAAAGAATTGCGTC 57.125 45.000 0.00 0.00 0.00 5.19
736 1476 4.446234 GCTATAGCGTGTAAAGAATTGCG 58.554 43.478 9.40 0.00 0.00 4.85
751 1491 2.186076 CCGCTAATAGCACGCTATAGC 58.814 52.381 15.09 15.09 42.58 2.97
752 1492 2.186076 GCCGCTAATAGCACGCTATAG 58.814 52.381 13.15 10.32 42.58 1.31
753 1493 1.466866 CGCCGCTAATAGCACGCTATA 60.467 52.381 13.15 1.16 42.58 1.31
755 1495 1.371267 CGCCGCTAATAGCACGCTA 60.371 57.895 13.15 0.39 42.58 4.26
756 1496 2.658593 CGCCGCTAATAGCACGCT 60.659 61.111 13.15 0.00 42.58 5.07
758 1498 0.732880 ATAGCGCCGCTAATAGCACG 60.733 55.000 23.98 17.04 44.62 5.34
760 1500 1.469251 GCTATAGCGCCGCTAATAGCA 60.469 52.381 32.01 14.85 44.62 3.49
761 1501 1.201343 GCTATAGCGCCGCTAATAGC 58.799 55.000 27.92 27.92 44.62 2.97
788 1528 4.210955 GCAAAGCATCCGAACATTGAAAAA 59.789 37.500 0.00 0.00 0.00 1.94
789 1529 3.740321 GCAAAGCATCCGAACATTGAAAA 59.260 39.130 0.00 0.00 0.00 2.29
790 1530 3.005684 AGCAAAGCATCCGAACATTGAAA 59.994 39.130 0.00 0.00 0.00 2.69
791 1531 2.557924 AGCAAAGCATCCGAACATTGAA 59.442 40.909 0.00 0.00 0.00 2.69
792 1532 2.161855 AGCAAAGCATCCGAACATTGA 58.838 42.857 0.00 0.00 0.00 2.57
793 1533 2.642139 AGCAAAGCATCCGAACATTG 57.358 45.000 0.00 0.00 0.00 2.82
794 1534 2.414559 CGAAGCAAAGCATCCGAACATT 60.415 45.455 0.00 0.00 0.00 2.71
795 1535 1.131126 CGAAGCAAAGCATCCGAACAT 59.869 47.619 0.00 0.00 0.00 2.71
798 1538 1.069296 CAACGAAGCAAAGCATCCGAA 60.069 47.619 0.00 0.00 0.00 4.30
837 1577 2.035783 GGTCAAACAGGGGAGGCC 59.964 66.667 0.00 0.00 0.00 5.19
890 3792 5.012046 TGTGGTACTTATAGGCAGGATGATG 59.988 44.000 0.00 0.00 39.69 3.07
895 3797 3.901844 GGATGTGGTACTTATAGGCAGGA 59.098 47.826 0.00 0.00 0.00 3.86
949 3853 1.471676 GCTTGGTGCTATAGCTGTCGT 60.472 52.381 24.61 0.00 42.66 4.34
976 3902 1.202222 CGACTGGCCAATGATTGCTTC 60.202 52.381 7.01 0.00 0.00 3.86
983 3909 1.475571 CCATGATCGACTGGCCAATGA 60.476 52.381 7.01 5.15 0.00 2.57
993 3919 1.269778 TGAATCCTCGCCATGATCGAC 60.270 52.381 0.00 0.00 32.08 4.20
1009 3935 1.945394 CGCTATGGCAGAAAGCTGAAT 59.055 47.619 14.77 0.00 45.17 2.57
1034 3960 4.778415 GCGCGAGGAAGACTGCGA 62.778 66.667 12.10 0.00 44.12 5.10
1038 3964 4.443266 GCCAGCGCGAGGAAGACT 62.443 66.667 23.47 0.00 0.00 3.24
1131 4057 7.334090 AGATGTGTGTATAATTGAGCAGAAGT 58.666 34.615 0.00 0.00 0.00 3.01
1134 4060 7.607607 ACAAAGATGTGTGTATAATTGAGCAGA 59.392 33.333 0.00 0.00 38.69 4.26
1147 4074 6.515272 AAGTTGAGAAACAAAGATGTGTGT 57.485 33.333 0.00 0.00 40.46 3.72
1206 4178 0.947960 TTGATCGCTGCCGTTTTCAA 59.052 45.000 0.00 0.00 35.54 2.69
1208 4180 0.794605 GCTTGATCGCTGCCGTTTTC 60.795 55.000 0.00 0.00 35.54 2.29
1253 4232 1.872679 GAAGTCGTCCGCCGTGATC 60.873 63.158 0.00 0.00 37.94 2.92
1353 4332 3.552384 AAGCGTGTTCACCCCGGA 61.552 61.111 0.73 0.00 0.00 5.14
1379 4358 1.227556 GTAGTCGATGCGGGCCATT 60.228 57.895 4.39 0.00 33.29 3.16
1463 4442 3.141488 CCCACCTCGAGGACTCCG 61.141 72.222 37.69 18.33 38.94 4.63
1743 4722 1.296715 GGAGGCACCCACACTACTG 59.703 63.158 0.00 0.00 0.00 2.74
1826 4822 1.080705 ACGCTACACCTCGCTTGAC 60.081 57.895 0.00 0.00 0.00 3.18
1836 4840 2.032030 ACAAATCAACTGCACGCTACAC 60.032 45.455 0.00 0.00 0.00 2.90
1928 4945 6.164176 AGAAATGGAGGACACGTTACTAAAG 58.836 40.000 0.00 0.00 0.00 1.85
1954 4971 2.446036 GGGTCTGGTCGGCCCTAT 60.446 66.667 2.12 0.00 39.31 2.57
1960 4977 1.687123 CACCTTATAGGGTCTGGTCGG 59.313 57.143 2.99 0.00 40.58 4.79
1961 4978 2.100916 CACACCTTATAGGGTCTGGTCG 59.899 54.545 2.99 0.00 40.58 4.79
1962 4979 3.105283 ACACACCTTATAGGGTCTGGTC 58.895 50.000 12.81 0.00 40.58 4.02
1964 4981 3.104512 TCACACACCTTATAGGGTCTGG 58.895 50.000 12.81 4.83 40.58 3.86
1965 4982 4.162320 ACATCACACACCTTATAGGGTCTG 59.838 45.833 2.99 5.64 40.58 3.51
1969 4986 4.876107 GTGAACATCACACACCTTATAGGG 59.124 45.833 5.65 0.00 46.22 3.53
2044 7929 0.737715 GGTCGCACAGAGGTAGCAAG 60.738 60.000 0.00 0.00 0.00 4.01
2358 8243 4.202315 TGCACATACCCTGCTCGTTATTAT 60.202 41.667 0.00 0.00 35.53 1.28
2419 8342 6.163135 ACTTCTGCTAGACAACTACAAAGT 57.837 37.500 0.00 0.00 37.65 2.66
2460 8383 2.633481 GGACCAGGTAAACTCACTGAGT 59.367 50.000 5.82 5.82 45.64 3.41
2490 8413 6.462552 TGTGGAATTGATCAACTTGACAAA 57.537 33.333 11.07 0.00 32.69 2.83
2492 8415 5.359292 TGTTGTGGAATTGATCAACTTGACA 59.641 36.000 11.07 8.95 40.20 3.58
2514 8437 6.088016 ACATAGCACATGTCAAAATTGTGT 57.912 33.333 0.00 0.00 42.11 3.72
2529 8452 7.255569 TGTTCTAGTGTGTACATACATAGCAC 58.744 38.462 22.72 18.85 38.63 4.40
2584 8507 3.081710 TCTTATGACGGAGACACCTCA 57.918 47.619 0.00 0.00 41.20 3.86
2603 8526 3.778954 ACCTAGGCTTCCAATAGCATC 57.221 47.619 9.30 0.00 43.02 3.91
2609 8532 1.075374 TGTGCAACCTAGGCTTCCAAT 59.925 47.619 9.30 0.00 34.36 3.16
2617 8540 3.350219 AGTGGTATTGTGCAACCTAGG 57.650 47.619 7.41 7.41 36.67 3.02
2668 8591 1.062206 GCTTGCGAAGATGAGCTGC 59.938 57.895 0.00 0.00 32.54 5.25
2690 8613 6.978080 TGCTGTGAAGAATGGTTTTAACTTTC 59.022 34.615 0.00 0.00 0.00 2.62
2696 8619 6.045955 GGTTTTGCTGTGAAGAATGGTTTTA 58.954 36.000 0.00 0.00 0.00 1.52
2704 8628 3.011566 TCCTGGTTTTGCTGTGAAGAA 57.988 42.857 0.00 0.00 0.00 2.52
2711 8635 6.889301 ATCATACATATCCTGGTTTTGCTG 57.111 37.500 0.00 0.00 0.00 4.41
2712 8636 7.062322 TGAATCATACATATCCTGGTTTTGCT 58.938 34.615 0.00 0.00 0.00 3.91
2714 8638 9.070179 TCATGAATCATACATATCCTGGTTTTG 57.930 33.333 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.