Multiple sequence alignment - TraesCS2B01G562400

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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 TraesCS2B01G562400 chr2B 100.000 3425 0 0 1 3425 754781577 754785001 0.000000e+00 6325.0
1 TraesCS2B01G562400 chr2B 90.909 121 11 0 2654 2774 296067688 296067568 2.730000e-36 163.0
2 TraesCS2B01G562400 chr2A 93.939 1716 87 11 958 2661 749058349 749060059 0.000000e+00 2577.0
3 TraesCS2B01G562400 chr2A 93.265 683 40 4 2749 3425 749060116 749060798 0.000000e+00 1002.0
4 TraesCS2B01G562400 chr2A 88.123 783 68 15 1 772 749056710 749057478 0.000000e+00 907.0
5 TraesCS2B01G562400 chr2A 87.895 190 23 0 212 401 161800483 161800294 1.240000e-54 224.0
6 TraesCS2B01G562400 chr2A 93.333 45 3 0 810 854 697063984 697064028 2.210000e-07 67.6
7 TraesCS2B01G562400 chr2D 93.168 1771 91 17 904 2665 618202193 618203942 0.000000e+00 2573.0
8 TraesCS2B01G562400 chr2D 81.900 1453 224 25 1218 2647 605778320 605776884 0.000000e+00 1190.0
9 TraesCS2B01G562400 chr2D 90.465 818 53 5 1 811 618201312 618202111 0.000000e+00 1055.0
10 TraesCS2B01G562400 chr2D 78.808 1628 289 40 1054 2647 22311853 22310248 0.000000e+00 1044.0
11 TraesCS2B01G562400 chr2D 78.760 1629 289 42 1054 2647 22333953 22332347 0.000000e+00 1038.0
12 TraesCS2B01G562400 chr2D 81.998 1211 191 22 1358 2560 22248560 22247369 0.000000e+00 1003.0
13 TraesCS2B01G562400 chr2D 91.949 708 26 3 2749 3425 618203980 618204687 0.000000e+00 963.0
14 TraesCS2B01G562400 chr2D 79.966 1188 211 19 1060 2231 22361132 22359956 0.000000e+00 850.0
15 TraesCS2B01G562400 chr6D 89.028 1759 171 16 904 2651 26003614 26001867 0.000000e+00 2159.0
16 TraesCS2B01G562400 chr6D 86.975 238 17 5 2890 3119 25997068 25996837 4.390000e-64 255.0
17 TraesCS2B01G562400 chr6D 93.130 131 9 0 3156 3286 25996843 25996713 3.490000e-45 193.0
18 TraesCS2B01G562400 chrUn 78.856 1504 264 35 1060 2542 16881715 16880245 0.000000e+00 966.0
19 TraesCS2B01G562400 chrUn 93.750 112 7 0 2651 2762 1978789 1978678 5.880000e-38 169.0
20 TraesCS2B01G562400 chr1D 86.881 404 39 4 1 401 22953420 22953812 1.130000e-119 440.0
21 TraesCS2B01G562400 chr1D 86.453 406 32 17 1 399 114066277 114066666 1.140000e-114 424.0
22 TraesCS2B01G562400 chr1D 80.741 405 71 5 1 401 400124474 400124073 3.320000e-80 309.0
23 TraesCS2B01G562400 chr6A 86.250 400 40 4 2 397 497472482 497472870 1.470000e-113 420.0
24 TraesCS2B01G562400 chr7D 85.396 404 53 4 1 400 106309471 106309872 6.840000e-112 414.0
25 TraesCS2B01G562400 chr7D 95.556 45 2 0 809 853 518684952 518684908 4.740000e-09 73.1
26 TraesCS2B01G562400 chr7B 85.432 405 52 2 1 402 451948556 451948956 6.840000e-112 414.0
27 TraesCS2B01G562400 chr7B 92.982 114 8 0 2651 2764 715085591 715085478 2.110000e-37 167.0
28 TraesCS2B01G562400 chr7B 97.778 45 1 0 810 854 406854593 406854637 1.020000e-10 78.7
29 TraesCS2B01G562400 chr5A 84.466 412 47 8 1 408 582975670 582976068 1.150000e-104 390.0
30 TraesCS2B01G562400 chr5A 92.982 114 8 0 2650 2763 636310118 636310005 2.110000e-37 167.0
31 TraesCS2B01G562400 chr3D 88.542 192 22 0 212 403 464321197 464321006 2.060000e-57 233.0
32 TraesCS2B01G562400 chr3D 96.875 32 1 0 854 885 535773685 535773716 2.000000e-03 54.7
33 TraesCS2B01G562400 chr3A 94.737 114 6 0 2647 2760 405503659 405503772 9.770000e-41 178.0
34 TraesCS2B01G562400 chr6B 94.643 112 6 0 2650 2761 136452566 136452677 1.260000e-39 174.0
35 TraesCS2B01G562400 chr1A 95.327 107 5 0 2654 2760 112821984 112821878 1.630000e-38 171.0
36 TraesCS2B01G562400 chr7A 92.982 114 8 0 2654 2767 736421827 736421714 2.110000e-37 167.0
37 TraesCS2B01G562400 chr7A 95.556 45 2 0 810 854 126137287 126137243 4.740000e-09 73.1
38 TraesCS2B01G562400 chr3B 92.308 117 9 0 2644 2760 10631043 10630927 2.110000e-37 167.0
39 TraesCS2B01G562400 chr3B 96.774 31 1 0 858 888 712326803 712326833 6.000000e-03 52.8
40 TraesCS2B01G562400 chr4B 100.000 29 0 0 858 886 399194370 399194398 2.000000e-03 54.7
41 TraesCS2B01G562400 chr4B 100.000 29 0 0 861 889 413093017 413092989 2.000000e-03 54.7


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 TraesCS2B01G562400 chr2B 754781577 754785001 3424 False 6325.000000 6325 100.000000 1 3425 1 chr2B.!!$F1 3424
1 TraesCS2B01G562400 chr2A 749056710 749060798 4088 False 1495.333333 2577 91.775667 1 3425 3 chr2A.!!$F2 3424
2 TraesCS2B01G562400 chr2D 618201312 618204687 3375 False 1530.333333 2573 91.860667 1 3425 3 chr2D.!!$F1 3424
3 TraesCS2B01G562400 chr2D 605776884 605778320 1436 True 1190.000000 1190 81.900000 1218 2647 1 chr2D.!!$R5 1429
4 TraesCS2B01G562400 chr2D 22310248 22311853 1605 True 1044.000000 1044 78.808000 1054 2647 1 chr2D.!!$R2 1593
5 TraesCS2B01G562400 chr2D 22332347 22333953 1606 True 1038.000000 1038 78.760000 1054 2647 1 chr2D.!!$R3 1593
6 TraesCS2B01G562400 chr2D 22247369 22248560 1191 True 1003.000000 1003 81.998000 1358 2560 1 chr2D.!!$R1 1202
7 TraesCS2B01G562400 chr2D 22359956 22361132 1176 True 850.000000 850 79.966000 1060 2231 1 chr2D.!!$R4 1171
8 TraesCS2B01G562400 chr6D 26001867 26003614 1747 True 2159.000000 2159 89.028000 904 2651 1 chr6D.!!$R1 1747
9 TraesCS2B01G562400 chrUn 16880245 16881715 1470 True 966.000000 966 78.856000 1060 2542 1 chrUn.!!$R2 1482

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
573 579 0.248565 GGGAGTTACGGGAGTGGAAC 59.751 60.0 0.00 0.0 46.8 3.62 F
1058 1772 0.870307 GTGTATGCGCCAGTACCTCG 60.870 60.0 4.18 0.0 0.0 4.63 F
1842 2586 0.969149 AAGCACTGGTCATCGTCTCA 59.031 50.0 0.00 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2829 0.394488 CAGGTACGCTCTCCTCCAGA 60.394 60.000 0.00 0.0 30.91 3.86 R
2347 3094 1.199327 GATGCATCGGCCATCATTCTG 59.801 52.381 11.68 0.0 40.13 3.02 R
2745 3520 1.271656 ACCTTGTACTTCCTCCGTTCG 59.728 52.381 0.00 0.0 0.00 3.95 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
71 75 1.185315 ACACAACAACCAAGCTTGCT 58.815 45.000 21.43 4.40 0.00 3.91
84 88 0.393537 GCTTGCTGCTATCCACTGGT 60.394 55.000 0.00 0.00 38.95 4.00
148 152 4.346418 TGTGGGACTAAAATTTGGTTGCAT 59.654 37.500 0.00 0.00 0.00 3.96
170 174 2.364970 CGATGAGAGATGGAGGAGCTTT 59.635 50.000 0.00 0.00 0.00 3.51
205 209 4.435436 CCGCTACGACCTGCAGCA 62.435 66.667 8.66 0.00 34.94 4.41
207 211 2.573869 GCTACGACCTGCAGCAGA 59.426 61.111 24.90 1.92 35.35 4.26
250 254 3.742640 GCCTCCATATCCGCCTCATATTC 60.743 52.174 0.00 0.00 0.00 1.75
257 261 0.673985 CCGCCTCATATTCGGACTGA 59.326 55.000 0.00 0.00 45.53 3.41
292 296 2.048222 CAGCTCGGGCGTTTGAGA 60.048 61.111 0.00 0.00 44.37 3.27
426 431 2.693591 TCCGGCTGTAGACTATCTTTGG 59.306 50.000 0.00 0.00 0.00 3.28
445 450 0.655733 GGTGTTCAAGTGTCGGTGTG 59.344 55.000 0.00 0.00 0.00 3.82
458 463 5.464389 AGTGTCGGTGTGATTGTAGTTTTAC 59.536 40.000 0.00 0.00 0.00 2.01
495 500 0.393077 AGTGACCAGAACAAGACCGG 59.607 55.000 0.00 0.00 0.00 5.28
513 518 2.987149 CCGGCACACTATATTTAGCTCG 59.013 50.000 0.00 0.00 0.00 5.03
547 552 3.413327 TGAACCAAATACTTAGGCGCAA 58.587 40.909 10.83 0.00 0.00 4.85
573 579 0.248565 GGGAGTTACGGGAGTGGAAC 59.751 60.000 0.00 0.00 46.80 3.62
613 619 2.027561 TCAAAATACCACTCCCTCCGTG 60.028 50.000 0.00 0.00 0.00 4.94
634 642 9.096160 TCCGTGAACTAATATAAATGCGTTTAA 57.904 29.630 14.81 5.66 33.76 1.52
712 720 6.540189 AGAGGGAGTATCAAATTGTTCATTCG 59.460 38.462 0.00 0.00 36.25 3.34
717 725 6.855836 AGTATCAAATTGTTCATTCGTGCAT 58.144 32.000 0.00 0.00 0.00 3.96
761 773 1.475682 AGGTCGGATAGAACGTTGACC 59.524 52.381 20.07 20.07 42.70 4.02
785 1458 7.988599 ACCGCACACTTAGTATATATTTTGGAA 59.011 33.333 0.00 0.00 0.00 3.53
811 1484 1.641577 CAGGCTCGCTTACCACTTAC 58.358 55.000 0.00 0.00 0.00 2.34
812 1485 1.204941 CAGGCTCGCTTACCACTTACT 59.795 52.381 0.00 0.00 0.00 2.24
813 1486 1.477295 AGGCTCGCTTACCACTTACTC 59.523 52.381 0.00 0.00 0.00 2.59
814 1487 1.471153 GGCTCGCTTACCACTTACTCC 60.471 57.143 0.00 0.00 0.00 3.85
815 1488 1.471153 GCTCGCTTACCACTTACTCCC 60.471 57.143 0.00 0.00 0.00 4.30
816 1489 2.100989 CTCGCTTACCACTTACTCCCT 58.899 52.381 0.00 0.00 0.00 4.20
818 1491 2.494870 TCGCTTACCACTTACTCCCTTC 59.505 50.000 0.00 0.00 0.00 3.46
819 1492 2.734492 CGCTTACCACTTACTCCCTTCG 60.734 54.545 0.00 0.00 0.00 3.79
820 1493 2.233186 GCTTACCACTTACTCCCTTCGT 59.767 50.000 0.00 0.00 0.00 3.85
822 1495 4.492611 CTTACCACTTACTCCCTTCGTTC 58.507 47.826 0.00 0.00 0.00 3.95
823 1496 1.271656 ACCACTTACTCCCTTCGTTCG 59.728 52.381 0.00 0.00 0.00 3.95
824 1497 1.403780 CCACTTACTCCCTTCGTTCGG 60.404 57.143 0.00 0.00 0.00 4.30
825 1498 1.542915 CACTTACTCCCTTCGTTCGGA 59.457 52.381 0.00 0.00 0.00 4.55
826 1499 2.029649 CACTTACTCCCTTCGTTCGGAA 60.030 50.000 0.00 0.00 0.00 4.30
827 1500 2.830321 ACTTACTCCCTTCGTTCGGAAT 59.170 45.455 0.00 0.00 33.26 3.01
828 1501 3.260128 ACTTACTCCCTTCGTTCGGAATT 59.740 43.478 0.00 0.00 33.26 2.17
830 1503 3.242549 ACTCCCTTCGTTCGGAATTAC 57.757 47.619 0.00 0.00 33.26 1.89
835 1508 5.594926 TCCCTTCGTTCGGAATTACTTATC 58.405 41.667 0.00 0.00 33.26 1.75
836 1509 4.443394 CCCTTCGTTCGGAATTACTTATCG 59.557 45.833 0.00 0.00 33.26 2.92
837 1510 5.039333 CCTTCGTTCGGAATTACTTATCGT 58.961 41.667 0.00 0.00 33.26 3.73
839 1512 6.141369 CCTTCGTTCGGAATTACTTATCGTAC 59.859 42.308 0.00 0.00 33.26 3.67
840 1513 6.117911 TCGTTCGGAATTACTTATCGTACA 57.882 37.500 0.00 0.00 0.00 2.90
843 1516 7.701924 TCGTTCGGAATTACTTATCGTACAAAT 59.298 33.333 0.00 0.00 0.00 2.32
845 1518 7.703298 TCGGAATTACTTATCGTACAAATGG 57.297 36.000 0.00 0.00 0.00 3.16
847 1520 8.145767 TCGGAATTACTTATCGTACAAATGGAT 58.854 33.333 0.00 0.00 0.00 3.41
848 1521 8.221100 CGGAATTACTTATCGTACAAATGGATG 58.779 37.037 0.00 0.00 0.00 3.51
855 1528 7.808381 ACTTATCGTACAAATGGATGTATCTCG 59.192 37.037 0.00 0.00 38.03 4.04
856 1529 4.295870 TCGTACAAATGGATGTATCTCGC 58.704 43.478 0.00 0.00 38.03 5.03
857 1530 3.119628 CGTACAAATGGATGTATCTCGCG 59.880 47.826 0.00 0.00 38.03 5.87
861 1534 5.538118 ACAAATGGATGTATCTCGCGATAA 58.462 37.500 10.36 0.42 34.08 1.75
862 1535 5.635280 ACAAATGGATGTATCTCGCGATAAG 59.365 40.000 10.36 0.00 34.08 1.73
863 1536 5.392767 AATGGATGTATCTCGCGATAAGT 57.607 39.130 10.36 0.00 34.08 2.24
864 1537 6.510879 AATGGATGTATCTCGCGATAAGTA 57.489 37.500 10.36 0.00 34.08 2.24
865 1538 5.952526 TGGATGTATCTCGCGATAAGTAA 57.047 39.130 10.36 0.00 34.08 2.24
867 1540 6.920817 TGGATGTATCTCGCGATAAGTAATT 58.079 36.000 10.36 0.00 34.08 1.40
868 1541 7.375834 TGGATGTATCTCGCGATAAGTAATTT 58.624 34.615 10.36 0.00 34.08 1.82
869 1542 7.541091 TGGATGTATCTCGCGATAAGTAATTTC 59.459 37.037 10.36 0.00 34.08 2.17
871 1544 6.661669 TGTATCTCGCGATAAGTAATTTCGA 58.338 36.000 10.36 0.00 34.08 3.71
874 1547 4.435554 TCTCGCGATAAGTAATTTCGAACG 59.564 41.667 10.36 0.00 34.92 3.95
877 1550 4.373717 CGCGATAAGTAATTTCGAACGGAG 60.374 45.833 0.00 0.00 34.92 4.63
878 1551 4.085210 GCGATAAGTAATTTCGAACGGAGG 60.085 45.833 0.00 0.00 34.92 4.30
879 1552 4.443394 CGATAAGTAATTTCGAACGGAGGG 59.557 45.833 0.00 0.00 34.92 4.30
880 1553 3.967332 AAGTAATTTCGAACGGAGGGA 57.033 42.857 0.00 0.00 0.00 4.20
881 1554 3.521947 AGTAATTTCGAACGGAGGGAG 57.478 47.619 0.00 0.00 0.00 4.30
882 1555 2.830321 AGTAATTTCGAACGGAGGGAGT 59.170 45.455 0.00 0.00 0.00 3.85
883 1556 4.019174 AGTAATTTCGAACGGAGGGAGTA 58.981 43.478 0.00 0.00 0.00 2.59
884 1557 3.521947 AATTTCGAACGGAGGGAGTAG 57.478 47.619 0.00 0.00 0.00 2.57
885 1558 2.205022 TTTCGAACGGAGGGAGTAGA 57.795 50.000 0.00 0.00 0.00 2.59
886 1559 2.431954 TTCGAACGGAGGGAGTAGAT 57.568 50.000 0.00 0.00 0.00 1.98
888 1561 3.565764 TCGAACGGAGGGAGTAGATTA 57.434 47.619 0.00 0.00 0.00 1.75
889 1562 3.209410 TCGAACGGAGGGAGTAGATTAC 58.791 50.000 0.00 0.00 0.00 1.89
890 1563 3.118112 TCGAACGGAGGGAGTAGATTACT 60.118 47.826 0.00 0.00 42.86 2.24
892 1565 5.002516 CGAACGGAGGGAGTAGATTACTAT 58.997 45.833 0.00 0.00 39.59 2.12
893 1566 5.472820 CGAACGGAGGGAGTAGATTACTATT 59.527 44.000 0.00 0.00 39.59 1.73
894 1567 6.652481 CGAACGGAGGGAGTAGATTACTATTA 59.348 42.308 0.00 0.00 39.59 0.98
895 1568 7.360776 CGAACGGAGGGAGTAGATTACTATTAC 60.361 44.444 0.00 0.00 39.59 1.89
896 1569 6.845908 ACGGAGGGAGTAGATTACTATTACA 58.154 40.000 0.00 0.00 39.59 2.41
897 1570 7.468496 ACGGAGGGAGTAGATTACTATTACAT 58.532 38.462 0.00 0.00 39.59 2.29
898 1571 7.949006 ACGGAGGGAGTAGATTACTATTACATT 59.051 37.037 0.00 0.00 39.59 2.71
899 1572 9.458727 CGGAGGGAGTAGATTACTATTACATTA 57.541 37.037 0.00 0.00 39.59 1.90
1008 1722 3.181463 TGTGCAGATCGATCATGAATCCA 60.181 43.478 26.47 10.74 0.00 3.41
1050 1764 3.716195 AGGCCAGTGTATGCGCCA 61.716 61.111 5.01 0.00 43.75 5.69
1058 1772 0.870307 GTGTATGCGCCAGTACCTCG 60.870 60.000 4.18 0.00 0.00 4.63
1062 1776 1.320344 ATGCGCCAGTACCTCGAAGA 61.320 55.000 4.18 0.00 0.00 2.87
1102 1816 1.670083 GGAAACGGAGTGAACGGGG 60.670 63.158 0.00 0.00 45.00 5.73
1167 1881 4.357947 GACGTGAGGTCGGCAGCA 62.358 66.667 0.00 0.00 38.86 4.41
1191 1911 2.579241 CTACTCGTCCGACTGCACCG 62.579 65.000 0.00 0.00 0.00 4.94
1206 1926 3.508016 TGCACCGCAGAATGAGAATCAC 61.508 50.000 0.00 0.00 40.64 3.06
1231 1951 2.125673 AGCGCGCGATACACCTTT 60.126 55.556 37.18 0.00 0.00 3.11
1254 1974 3.070159 TCAAGCTTCTATATTCCTGCGCT 59.930 43.478 9.73 0.00 0.00 5.92
1303 2023 1.280998 TGGTAAACAAGGGGCTAGAGC 59.719 52.381 0.00 0.00 41.14 4.09
1731 2475 2.985456 CTCCTCGCCTTGGAAGCT 59.015 61.111 0.00 0.00 32.61 3.74
1737 2481 2.396955 CGCCTTGGAAGCTGAGCAG 61.397 63.158 7.39 0.00 0.00 4.24
1747 2491 4.296265 CTGAGCAGCTGCACATCA 57.704 55.556 38.24 29.91 45.16 3.07
1769 2513 1.764571 TTCCAGTTCCACCCGGTGAG 61.765 60.000 19.81 9.24 35.23 3.51
1779 2523 1.762957 CACCCGGTGAGACTCCATATT 59.237 52.381 12.68 0.00 35.23 1.28
1842 2586 0.969149 AAGCACTGGTCATCGTCTCA 59.031 50.000 0.00 0.00 0.00 3.27
1890 2634 1.222115 ACGAGTTTGCAGAAGCGGTC 61.222 55.000 0.00 0.00 46.23 4.79
1965 2709 4.430765 GACGCGCTCCTCCGGAAA 62.431 66.667 5.73 0.00 0.00 3.13
2015 2759 4.154347 GACGGAGCAGGAGGCCAG 62.154 72.222 5.01 0.00 46.50 4.85
2085 2829 4.070552 GGGGCTCTGTTCGACGCT 62.071 66.667 0.00 0.00 0.00 5.07
2158 2905 3.368571 GGTGCTTGCTCCTGCCAC 61.369 66.667 6.47 0.00 38.71 5.01
2274 3021 2.270205 CCTGCGACAATGAGCCCT 59.730 61.111 0.00 0.00 0.00 5.19
2347 3094 1.574702 GGCGTACAGGGTTTGCAGTC 61.575 60.000 0.00 0.00 0.00 3.51
2406 3153 0.815734 TTCCGATGTTCTCCGTCTCC 59.184 55.000 0.00 0.00 0.00 3.71
2418 3165 4.314440 GTCTCCACCTGGCGCACA 62.314 66.667 10.83 3.75 34.44 4.57
2444 3195 3.270877 GACAAGGATCACCACACATACC 58.729 50.000 0.00 0.00 38.94 2.73
2447 3198 1.480954 AGGATCACCACACATACCGTC 59.519 52.381 0.00 0.00 38.94 4.79
2478 3229 7.710044 GTGATCTTCTTGCAGATCTTCTCAATA 59.290 37.037 13.11 0.00 46.64 1.90
2536 3291 6.096987 TGTGTTTTGGTTATTTGCCTGAACTA 59.903 34.615 0.00 0.00 0.00 2.24
2595 3367 1.742831 GTTGTTTCACACCAGCAGACA 59.257 47.619 0.00 0.00 0.00 3.41
2665 3440 9.159364 GACATTTTAATTAGTACTTCCTCCGTT 57.841 33.333 0.00 0.00 0.00 4.44
2666 3441 9.159364 ACATTTTAATTAGTACTTCCTCCGTTC 57.841 33.333 0.00 0.00 0.00 3.95
2667 3442 7.816945 TTTTAATTAGTACTTCCTCCGTTCG 57.183 36.000 0.00 0.00 0.00 3.95
2668 3443 4.382345 AATTAGTACTTCCTCCGTTCGG 57.618 45.455 0.00 4.74 0.00 4.30
2671 3446 2.454538 AGTACTTCCTCCGTTCGGAAT 58.545 47.619 14.79 2.09 39.64 3.01
2674 3449 3.242549 ACTTCCTCCGTTCGGAATTAC 57.757 47.619 14.79 0.00 39.64 1.89
2675 3450 2.830321 ACTTCCTCCGTTCGGAATTACT 59.170 45.455 14.79 0.00 39.64 2.24
2679 3454 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2680 3455 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2683 3458 2.597305 CGTTCGGAATTACTTGTCGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2687 3462 5.080969 TCGGAATTACTTGTCGGAGAAAT 57.919 39.130 0.00 0.00 39.69 2.17
2688 3463 4.868171 TCGGAATTACTTGTCGGAGAAATG 59.132 41.667 0.00 0.00 39.69 2.32
2689 3464 4.034048 CGGAATTACTTGTCGGAGAAATGG 59.966 45.833 0.00 0.00 39.69 3.16
2699 3474 7.495934 ACTTGTCGGAGAAATGGATGTATTTAG 59.504 37.037 0.00 0.00 39.69 1.85
2700 3475 7.119709 TGTCGGAGAAATGGATGTATTTAGA 57.880 36.000 0.00 0.00 39.69 2.10
2701 3476 7.735917 TGTCGGAGAAATGGATGTATTTAGAT 58.264 34.615 0.00 0.00 39.69 1.98
2702 3477 7.657354 TGTCGGAGAAATGGATGTATTTAGATG 59.343 37.037 0.00 0.00 39.69 2.90
2704 3479 8.866093 TCGGAGAAATGGATGTATTTAGATGTA 58.134 33.333 0.00 0.00 30.78 2.29
2735 3510 9.522804 AGTTCTAGATACATTCATTTTCGAGAC 57.477 33.333 0.00 0.00 0.00 3.36
2736 3511 9.302345 GTTCTAGATACATTCATTTTCGAGACA 57.698 33.333 0.00 0.00 0.00 3.41
2737 3512 9.869757 TTCTAGATACATTCATTTTCGAGACAA 57.130 29.630 0.00 0.00 0.00 3.18
2738 3513 9.869757 TCTAGATACATTCATTTTCGAGACAAA 57.130 29.630 0.00 0.00 0.00 2.83
2745 3520 9.573133 ACATTCATTTTCGAGACAAATAATTCC 57.427 29.630 0.00 0.00 0.00 3.01
2746 3521 8.736742 CATTCATTTTCGAGACAAATAATTCCG 58.263 33.333 0.00 0.00 0.00 4.30
2747 3522 7.603963 TCATTTTCGAGACAAATAATTCCGA 57.396 32.000 0.00 0.00 0.00 4.55
2792 3567 5.799213 AGTATGATATGCTACCCTTGCTTC 58.201 41.667 0.00 0.00 0.00 3.86
2795 3570 4.645535 TGATATGCTACCCTTGCTTCATC 58.354 43.478 0.00 0.00 0.00 2.92
2829 3604 0.586319 CGCCATGTGAAGACAACGTT 59.414 50.000 0.00 0.00 35.11 3.99
2892 3667 1.915141 CTGAGATGTTGGGGTGCTTT 58.085 50.000 0.00 0.00 0.00 3.51
2972 3752 3.075148 GGGAGCACTACTTTGTTCCTTC 58.925 50.000 6.04 0.00 44.27 3.46
3072 3853 3.626996 CTCCATGCCGGCAAGGTCA 62.627 63.158 40.85 26.78 43.70 4.02
3165 3946 4.344679 GCATAATTCAATTCCCATCACCCA 59.655 41.667 0.00 0.00 0.00 4.51
3196 3977 3.056393 ACATCGGATTGTTCTAACGTGGA 60.056 43.478 0.00 0.00 0.00 4.02
3247 4031 4.521146 GAGTTGATGGACTCAATGGTGAT 58.479 43.478 0.44 0.00 45.36 3.06
3321 4105 1.336755 GAACAACAATGGCGGTGTCTT 59.663 47.619 0.00 0.00 0.00 3.01
3333 4117 1.516423 GTGTCTTAGCTCCGGGGAC 59.484 63.158 4.80 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 75 1.866015 AGCTACACCAGTGGATAGCA 58.134 50.000 32.90 11.41 40.59 3.49
74 78 6.522054 GCTTAAATAGCTACACCAGTGGATA 58.478 40.000 18.40 6.95 46.77 2.59
148 152 1.144708 AGCTCCTCCATCTCTCATCGA 59.855 52.381 0.00 0.00 0.00 3.59
170 174 3.555324 TCCCACCTGCAGCGACAA 61.555 61.111 8.66 0.00 0.00 3.18
231 235 3.801114 CGAATATGAGGCGGATATGGA 57.199 47.619 0.00 0.00 0.00 3.41
250 254 1.491670 CACGCCTCATATTCAGTCCG 58.508 55.000 0.00 0.00 0.00 4.79
325 330 2.444624 CGGTCAATGCTCGGTCACG 61.445 63.158 0.00 0.00 42.74 4.35
329 334 4.778143 GCCCGGTCAATGCTCGGT 62.778 66.667 0.00 0.00 41.98 4.69
426 431 0.655733 CACACCGACACTTGAACACC 59.344 55.000 0.00 0.00 0.00 4.16
445 450 7.568199 AGGCCACATATGTAAAACTACAATC 57.432 36.000 8.32 0.00 33.21 2.67
458 463 6.545666 TGGTCACTTTAAATAGGCCACATATG 59.454 38.462 5.01 0.00 0.00 1.78
495 500 8.851416 CAATAGTACGAGCTAAATATAGTGTGC 58.149 37.037 0.00 0.00 0.00 4.57
513 518 8.438676 AGTATTTGGTTCATGAGCAATAGTAC 57.561 34.615 11.93 12.55 44.51 2.73
526 531 3.060736 TGCGCCTAAGTATTTGGTTCA 57.939 42.857 4.18 0.00 43.18 3.18
547 552 2.788215 ACTCCCGTAACTCCCCTATAGT 59.212 50.000 0.00 0.00 0.00 2.12
667 675 8.877195 TCCCTCTCTAAACTAATGTAAACAACT 58.123 33.333 0.00 0.00 0.00 3.16
668 676 9.152595 CTCCCTCTCTAAACTAATGTAAACAAC 57.847 37.037 0.00 0.00 0.00 3.32
669 677 8.877195 ACTCCCTCTCTAAACTAATGTAAACAA 58.123 33.333 0.00 0.00 0.00 2.83
761 773 9.811655 CATTCCAAAATATATACTAAGTGTGCG 57.188 33.333 0.00 0.00 0.00 5.34
785 1458 0.460987 GTAAGCGAGCCTGCTGACAT 60.461 55.000 9.82 0.00 46.60 3.06
789 1462 2.103042 GTGGTAAGCGAGCCTGCTG 61.103 63.158 0.00 0.00 46.60 4.41
811 1484 3.521947 AGTAATTCCGAACGAAGGGAG 57.478 47.619 0.00 0.00 32.78 4.30
812 1485 3.967332 AAGTAATTCCGAACGAAGGGA 57.033 42.857 0.00 0.00 32.78 4.20
813 1486 4.443394 CGATAAGTAATTCCGAACGAAGGG 59.557 45.833 0.00 0.00 32.78 3.95
814 1487 5.039333 ACGATAAGTAATTCCGAACGAAGG 58.961 41.667 4.96 0.00 32.78 3.46
815 1488 6.688385 TGTACGATAAGTAATTCCGAACGAAG 59.312 38.462 4.96 0.00 37.02 3.79
816 1489 6.550843 TGTACGATAAGTAATTCCGAACGAA 58.449 36.000 4.96 0.00 37.02 3.85
818 1491 6.795053 TTGTACGATAAGTAATTCCGAACG 57.205 37.500 4.96 0.00 37.02 3.95
819 1492 8.060090 CCATTTGTACGATAAGTAATTCCGAAC 58.940 37.037 4.96 0.00 37.02 3.95
820 1493 7.980662 TCCATTTGTACGATAAGTAATTCCGAA 59.019 33.333 4.96 0.00 37.02 4.30
822 1495 7.703298 TCCATTTGTACGATAAGTAATTCCG 57.297 36.000 0.00 0.00 37.02 4.30
823 1496 9.052759 ACATCCATTTGTACGATAAGTAATTCC 57.947 33.333 0.00 0.00 37.02 3.01
830 1503 7.201359 GCGAGATACATCCATTTGTACGATAAG 60.201 40.741 0.00 0.00 35.04 1.73
835 1508 3.119628 CGCGAGATACATCCATTTGTACG 59.880 47.826 0.00 0.00 35.04 3.67
836 1509 4.295870 TCGCGAGATACATCCATTTGTAC 58.704 43.478 3.71 0.00 35.04 2.90
837 1510 4.577834 TCGCGAGATACATCCATTTGTA 57.422 40.909 3.71 0.00 36.57 2.41
853 1526 3.483196 CCGTTCGAAATTACTTATCGCGA 59.517 43.478 13.09 13.09 36.56 5.87
854 1527 3.483196 TCCGTTCGAAATTACTTATCGCG 59.517 43.478 0.00 0.00 36.56 5.87
855 1528 4.085210 CCTCCGTTCGAAATTACTTATCGC 60.085 45.833 0.00 0.00 36.56 4.58
856 1529 4.443394 CCCTCCGTTCGAAATTACTTATCG 59.557 45.833 0.00 0.00 37.90 2.92
857 1530 5.594926 TCCCTCCGTTCGAAATTACTTATC 58.405 41.667 0.00 0.00 0.00 1.75
861 1534 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
862 1535 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
863 1536 4.272489 TCTACTCCCTCCGTTCGAAATTA 58.728 43.478 0.00 0.00 0.00 1.40
864 1537 3.094572 TCTACTCCCTCCGTTCGAAATT 58.905 45.455 0.00 0.00 0.00 1.82
865 1538 2.731572 TCTACTCCCTCCGTTCGAAAT 58.268 47.619 0.00 0.00 0.00 2.17
867 1540 2.431954 ATCTACTCCCTCCGTTCGAA 57.568 50.000 0.00 0.00 0.00 3.71
868 1541 2.431954 AATCTACTCCCTCCGTTCGA 57.568 50.000 0.00 0.00 0.00 3.71
869 1542 3.212685 AGTAATCTACTCCCTCCGTTCG 58.787 50.000 0.00 0.00 32.47 3.95
871 1544 7.293073 TGTAATAGTAATCTACTCCCTCCGTT 58.707 38.462 0.00 0.00 40.14 4.44
885 1558 9.944376 ACGAGATGCCAATAATGTAATAGTAAT 57.056 29.630 0.00 0.00 0.00 1.89
888 1561 7.541091 CGTACGAGATGCCAATAATGTAATAGT 59.459 37.037 10.44 0.00 0.00 2.12
889 1562 7.541091 ACGTACGAGATGCCAATAATGTAATAG 59.459 37.037 24.41 0.00 0.00 1.73
890 1563 7.327518 CACGTACGAGATGCCAATAATGTAATA 59.672 37.037 24.41 0.00 0.00 0.98
892 1565 5.460748 CACGTACGAGATGCCAATAATGTAA 59.539 40.000 24.41 0.00 0.00 2.41
893 1566 4.979815 CACGTACGAGATGCCAATAATGTA 59.020 41.667 24.41 0.00 0.00 2.29
894 1567 3.802139 CACGTACGAGATGCCAATAATGT 59.198 43.478 24.41 0.00 0.00 2.71
895 1568 4.048504 TCACGTACGAGATGCCAATAATG 58.951 43.478 24.41 4.75 0.00 1.90
896 1569 4.316205 TCACGTACGAGATGCCAATAAT 57.684 40.909 24.41 0.00 0.00 1.28
897 1570 3.786516 TCACGTACGAGATGCCAATAA 57.213 42.857 24.41 0.00 0.00 1.40
898 1571 3.067601 ACATCACGTACGAGATGCCAATA 59.932 43.478 38.38 11.26 43.63 1.90
899 1572 2.159099 ACATCACGTACGAGATGCCAAT 60.159 45.455 38.38 24.82 43.63 3.16
900 1573 1.203758 ACATCACGTACGAGATGCCAA 59.796 47.619 38.38 12.55 43.63 4.52
901 1574 0.815095 ACATCACGTACGAGATGCCA 59.185 50.000 38.38 13.19 43.63 4.92
902 1575 1.202256 TGACATCACGTACGAGATGCC 60.202 52.381 38.38 32.65 43.63 4.40
940 1613 8.783999 TTAGTAATCAAAATGCGAAAAACGAA 57.216 26.923 0.00 0.00 45.77 3.85
1008 1722 2.761208 CGGTTCCTGACCTCTATTGTCT 59.239 50.000 0.00 0.00 46.92 3.41
1050 1764 5.105029 ACAACGCTGTTCTTCGAGGTACT 62.105 47.826 5.92 0.00 33.55 2.73
1058 1772 0.232303 CACCGACAACGCTGTTCTTC 59.768 55.000 0.00 0.00 35.30 2.87
1062 1776 0.534203 AATCCACCGACAACGCTGTT 60.534 50.000 0.00 0.00 35.30 3.16
1102 1816 2.694043 GATGTTTGAGCGTACGAATGC 58.306 47.619 21.65 0.00 37.95 3.56
1167 1881 3.507009 GTCGGACGAGTAGGCGCT 61.507 66.667 7.64 0.00 33.86 5.92
1191 1911 2.530177 TCGTCGTGATTCTCATTCTGC 58.470 47.619 0.00 0.00 0.00 4.26
1192 1912 3.111838 CCTCGTCGTGATTCTCATTCTG 58.888 50.000 0.00 0.00 0.00 3.02
1193 1913 3.017442 TCCTCGTCGTGATTCTCATTCT 58.983 45.455 0.00 0.00 0.00 2.40
1194 1914 3.367607 CTCCTCGTCGTGATTCTCATTC 58.632 50.000 0.00 0.00 0.00 2.67
1195 1915 2.480416 GCTCCTCGTCGTGATTCTCATT 60.480 50.000 0.00 0.00 0.00 2.57
1197 1917 0.452184 GCTCCTCGTCGTGATTCTCA 59.548 55.000 0.00 0.00 0.00 3.27
1198 1918 0.590230 CGCTCCTCGTCGTGATTCTC 60.590 60.000 0.00 0.00 0.00 2.87
1231 1951 3.809832 GCGCAGGAATATAGAAGCTTGAA 59.190 43.478 2.10 0.00 0.00 2.69
1254 1974 3.283684 CCTTTGTCCAACGCGGCA 61.284 61.111 12.47 0.00 33.14 5.69
1303 2023 1.520174 CGTTGCGAGACTGCATATCAG 59.480 52.381 0.00 1.93 45.78 2.90
1384 2110 3.599584 CTGCCATGGCTGGACAAG 58.400 61.111 35.53 20.49 46.37 3.16
1467 2210 1.230635 GGCACATCACAGCGAAGTGT 61.231 55.000 7.42 0.00 43.68 3.55
1505 2248 1.519455 GCATAGTTCGCTGCGGTCT 60.519 57.895 23.03 20.68 0.00 3.85
1731 2475 4.296265 CTGATGTGCAGCTGCTCA 57.704 55.556 37.03 37.03 46.58 4.26
1747 2491 2.750350 CGGGTGGAACTGGAAGCT 59.250 61.111 0.00 0.00 37.60 3.74
1769 2513 5.545588 TGAGCAGCTGATTAATATGGAGTC 58.454 41.667 20.43 0.00 0.00 3.36
1870 2614 0.814010 ACCGCTTCTGCAAACTCGTT 60.814 50.000 0.00 0.00 39.64 3.85
2085 2829 0.394488 CAGGTACGCTCTCCTCCAGA 60.394 60.000 0.00 0.00 30.91 3.86
2158 2905 4.262617 CAGGCAATGATATCCCTGATCTG 58.737 47.826 16.64 12.20 46.04 2.90
2347 3094 1.199327 GATGCATCGGCCATCATTCTG 59.801 52.381 11.68 0.00 40.13 3.02
2406 3153 3.653009 CACACTGTGCGCCAGGTG 61.653 66.667 23.76 22.16 46.06 4.00
2444 3195 1.728971 GCAAGAAGATCACAGGTGACG 59.271 52.381 3.92 0.00 43.11 4.35
2447 3198 3.049708 TCTGCAAGAAGATCACAGGTG 57.950 47.619 0.00 0.00 42.31 4.00
2478 3229 8.124823 CGATCTACTATGAAATTGTTGCAATGT 58.875 33.333 0.59 0.00 33.47 2.71
2557 3317 6.554334 AACAACACTTTGCAGTACGATAAT 57.446 33.333 0.00 0.00 36.00 1.28
2618 3390 7.581213 TGTCTTGAATGTTCCAACAATAACT 57.419 32.000 0.00 0.00 43.03 2.24
2619 3391 8.816640 AATGTCTTGAATGTTCCAACAATAAC 57.183 30.769 0.00 0.00 43.03 1.89
2665 3440 4.524316 TTTCTCCGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2666 3441 4.034048 CCATTTCTCCGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
2667 3442 5.183228 TCCATTTCTCCGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
2668 3443 6.316390 ACATCCATTTCTCCGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
2671 3446 5.160607 ACATCCATTTCTCCGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
2674 3449 6.683974 AAATACATCCATTTCTCCGACAAG 57.316 37.500 0.00 0.00 0.00 3.16
2675 3450 7.561251 TCTAAATACATCCATTTCTCCGACAA 58.439 34.615 0.00 0.00 30.84 3.18
2679 3454 7.969536 ACATCTAAATACATCCATTTCTCCG 57.030 36.000 0.00 0.00 30.84 4.63
2710 3485 9.302345 TGTCTCGAAAATGAATGTATCTAGAAC 57.698 33.333 0.00 0.00 0.00 3.01
2712 3487 9.869757 TTTGTCTCGAAAATGAATGTATCTAGA 57.130 29.630 0.00 0.00 0.00 2.43
2719 3494 9.573133 GGAATTATTTGTCTCGAAAATGAATGT 57.427 29.630 4.22 0.00 0.00 2.71
2720 3495 8.736742 CGGAATTATTTGTCTCGAAAATGAATG 58.263 33.333 4.22 0.00 0.00 2.67
2721 3496 8.673711 TCGGAATTATTTGTCTCGAAAATGAAT 58.326 29.630 4.22 0.00 0.00 2.57
2722 3497 8.035165 TCGGAATTATTTGTCTCGAAAATGAA 57.965 30.769 4.22 0.00 0.00 2.57
2723 3498 7.603963 TCGGAATTATTTGTCTCGAAAATGA 57.396 32.000 4.22 0.00 0.00 2.57
2724 3499 7.045612 CGTTCGGAATTATTTGTCTCGAAAATG 60.046 37.037 4.22 0.00 37.00 2.32
2725 3500 6.959311 CGTTCGGAATTATTTGTCTCGAAAAT 59.041 34.615 0.00 0.00 37.00 1.82
2726 3501 6.301108 CGTTCGGAATTATTTGTCTCGAAAA 58.699 36.000 0.00 0.00 37.00 2.29
2727 3502 5.163933 CCGTTCGGAATTATTTGTCTCGAAA 60.164 40.000 5.19 0.00 37.00 3.46
2728 3503 4.327898 CCGTTCGGAATTATTTGTCTCGAA 59.672 41.667 5.19 0.00 33.66 3.71
2729 3504 3.861113 CCGTTCGGAATTATTTGTCTCGA 59.139 43.478 5.19 0.00 0.00 4.04
2730 3505 3.861113 TCCGTTCGGAATTATTTGTCTCG 59.139 43.478 11.66 0.00 0.00 4.04
2731 3506 4.270325 CCTCCGTTCGGAATTATTTGTCTC 59.730 45.833 14.79 0.00 33.41 3.36
2732 3507 4.081309 TCCTCCGTTCGGAATTATTTGTCT 60.081 41.667 14.79 0.00 33.41 3.41
2733 3508 4.186159 TCCTCCGTTCGGAATTATTTGTC 58.814 43.478 14.79 0.00 33.41 3.18
2734 3509 4.210724 TCCTCCGTTCGGAATTATTTGT 57.789 40.909 14.79 0.00 33.41 2.83
2735 3510 4.634443 ACTTCCTCCGTTCGGAATTATTTG 59.366 41.667 14.79 1.97 39.64 2.32
2736 3511 4.840271 ACTTCCTCCGTTCGGAATTATTT 58.160 39.130 14.79 0.00 39.64 1.40
2737 3512 4.482952 ACTTCCTCCGTTCGGAATTATT 57.517 40.909 14.79 0.00 39.64 1.40
2738 3513 4.403432 TGTACTTCCTCCGTTCGGAATTAT 59.597 41.667 14.79 3.34 39.64 1.28
2739 3514 3.763360 TGTACTTCCTCCGTTCGGAATTA 59.237 43.478 14.79 1.22 39.64 1.40
2740 3515 2.564062 TGTACTTCCTCCGTTCGGAATT 59.436 45.455 14.79 0.00 39.64 2.17
2741 3516 2.173519 TGTACTTCCTCCGTTCGGAAT 58.826 47.619 14.79 2.09 39.64 3.01
2742 3517 1.619654 TGTACTTCCTCCGTTCGGAA 58.380 50.000 14.79 0.00 38.18 4.30
2743 3518 1.542915 CTTGTACTTCCTCCGTTCGGA 59.457 52.381 13.34 13.34 0.00 4.55
2744 3519 1.403780 CCTTGTACTTCCTCCGTTCGG 60.404 57.143 4.74 4.74 0.00 4.30
2745 3520 1.271656 ACCTTGTACTTCCTCCGTTCG 59.728 52.381 0.00 0.00 0.00 3.95
2746 3521 3.509184 ACTACCTTGTACTTCCTCCGTTC 59.491 47.826 0.00 0.00 0.00 3.95
2747 3522 3.504375 ACTACCTTGTACTTCCTCCGTT 58.496 45.455 0.00 0.00 0.00 4.44
2829 3604 2.741759 TCGCAAGCAGTGTGATAAGA 57.258 45.000 0.00 0.00 41.89 2.10
2892 3667 3.303135 AGGTCACGAGAGCGCCAA 61.303 61.111 2.29 0.00 46.62 4.52
2900 3675 2.561419 TCCCTTAAAGACAGGTCACGAG 59.439 50.000 1.84 0.00 0.00 4.18
2902 3677 3.056107 TGATCCCTTAAAGACAGGTCACG 60.056 47.826 1.84 0.00 0.00 4.35
3072 3853 2.248248 TGATCGTTCACCAAGTCCTCT 58.752 47.619 0.00 0.00 0.00 3.69
3149 3930 3.471430 ACATTGGGTGATGGGAATTGA 57.529 42.857 0.00 0.00 0.00 2.57
3165 3946 4.883585 AGAACAATCCGATGTATGCACATT 59.116 37.500 0.00 0.00 45.58 2.71
3196 3977 4.428209 CATCTCAGTCATGCTTTACTCGT 58.572 43.478 0.00 0.00 0.00 4.18
3321 4105 1.741327 GCGTATTGTCCCCGGAGCTA 61.741 60.000 0.73 0.00 0.00 3.32
3333 4117 4.029418 CACAAGCGATTTTTGAGCGTATTG 59.971 41.667 0.00 0.00 39.85 1.90


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

AutoCloner maintained by Alex Coulton.