Multiple sequence alignment - TraesCS3A01G531400

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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 TraesCS3A01G531400 chr3A 100.000 2582 0 0 1 2582 744285759 744288340 0.000000e+00 4769.0
1 TraesCS3A01G531400 chr3A 90.528 1193 50 22 702 1865 744266183 744267341 0.000000e+00 1519.0
2 TraesCS3A01G531400 chr3A 92.552 725 41 6 1859 2582 744267916 744268628 0.000000e+00 1027.0
3 TraesCS3A01G531400 chr3A 87.773 687 77 6 22 703 7825189 7824505 0.000000e+00 797.0
4 TraesCS3A01G531400 chr3A 91.199 534 26 7 702 1221 744261931 744262457 0.000000e+00 706.0
5 TraesCS3A01G531400 chr3A 82.734 695 48 47 957 1620 743988024 743988677 1.040000e-153 553.0
6 TraesCS3A01G531400 chr3A 80.000 575 69 21 166 703 708019720 708019155 1.450000e-102 383.0
7 TraesCS3A01G531400 chr3D 90.087 1271 64 32 702 1936 610189975 610191219 0.000000e+00 1592.0
8 TraesCS3A01G531400 chr3D 86.214 943 62 37 702 1612 610186546 610187452 0.000000e+00 959.0
9 TraesCS3A01G531400 chr3D 80.058 687 72 47 964 1611 610138890 610139550 1.410000e-122 449.0
10 TraesCS3A01G531400 chr3D 83.816 414 64 3 2172 2582 56362525 56362112 8.660000e-105 390.0
11 TraesCS3A01G531400 chr3D 83.894 416 60 6 2172 2582 611594095 611593682 8.660000e-105 390.0
12 TraesCS3A01G531400 chr3B 91.318 933 48 13 697 1615 822094298 822095211 0.000000e+00 1243.0
13 TraesCS3A01G531400 chr3B 88.976 1016 58 26 702 1690 822038827 822039815 0.000000e+00 1206.0
14 TraesCS3A01G531400 chr3B 88.681 1016 61 24 702 1690 822066917 822067905 0.000000e+00 1190.0
15 TraesCS3A01G531400 chr3B 90.909 539 27 8 702 1225 822008114 822008645 0.000000e+00 704.0
16 TraesCS3A01G531400 chr3B 90.538 539 29 6 702 1225 822023409 822023940 0.000000e+00 693.0
17 TraesCS3A01G531400 chr3B 79.371 858 76 61 802 1611 821836295 821837099 6.370000e-141 510.0
18 TraesCS3A01G531400 chr3B 84.300 414 62 3 2172 2582 27513651 27514064 4.000000e-108 401.0
19 TraesCS3A01G531400 chr3B 84.058 414 63 3 2172 2582 92330377 92329964 1.860000e-106 396.0
20 TraesCS3A01G531400 chr3B 78.622 566 81 18 166 702 779798309 779798863 3.180000e-89 339.0
21 TraesCS3A01G531400 chr3B 92.308 130 4 2 1643 1770 822095211 822095336 2.040000e-41 180.0
22 TraesCS3A01G531400 chr3B 81.319 91 15 2 2014 2103 737754176 737754265 3.560000e-09 73.1
23 TraesCS3A01G531400 chrUn 90.758 541 28 8 702 1227 459077174 459077707 0.000000e+00 702.0
24 TraesCS3A01G531400 chrUn 91.243 354 15 6 1339 1690 478839170 478838831 3.890000e-128 468.0
25 TraesCS3A01G531400 chr4A 80.803 573 66 22 166 703 127171241 127171804 2.390000e-110 409.0
26 TraesCS3A01G531400 chr2D 84.578 415 60 3 2172 2582 645666300 645665886 2.390000e-110 409.0
27 TraesCS3A01G531400 chr2D 100.000 28 0 0 665 692 88285004 88285031 5.000000e-03 52.8
28 TraesCS3A01G531400 chr7A 80.492 569 69 22 166 702 672449525 672448967 5.180000e-107 398.0
29 TraesCS3A01G531400 chr7A 83.855 415 63 4 2172 2582 144167163 144166749 2.410000e-105 392.0
30 TraesCS3A01G531400 chr7A 75.000 688 113 27 38 702 25254082 25253431 1.970000e-66 263.0
31 TraesCS3A01G531400 chr1B 84.058 414 63 3 2172 2582 453522032 453522445 1.860000e-106 396.0
32 TraesCS3A01G531400 chr1B 79.255 376 46 18 166 515 670359634 670359265 1.540000e-57 233.0
33 TraesCS3A01G531400 chr1B 80.588 170 22 7 1932 2100 621616940 621616781 1.250000e-23 121.0
34 TraesCS3A01G531400 chr6A 83.816 414 64 3 2172 2582 457075054 457075467 8.660000e-105 390.0
35 TraesCS3A01G531400 chr6A 76.720 683 99 29 38 702 174370947 174371587 2.480000e-85 326.0
36 TraesCS3A01G531400 chr5A 79.371 572 74 22 166 702 648912803 648913365 1.890000e-96 363.0
37 TraesCS3A01G531400 chr5A 79.024 553 70 22 166 706 300789550 300789032 1.140000e-88 337.0
38 TraesCS3A01G531400 chr7B 79.371 572 73 25 166 704 540951971 540951412 6.790000e-96 361.0
39 TraesCS3A01G531400 chr1A 78.957 575 77 22 166 705 540378980 540378415 4.090000e-93 351.0
40 TraesCS3A01G531400 chr2B 78.032 569 81 23 168 703 551253450 551254007 4.150000e-83 318.0
41 TraesCS3A01G531400 chr4D 76.409 674 100 37 19 670 185794731 185795367 2.500000e-80 309.0
42 TraesCS3A01G531400 chr4D 80.838 167 21 7 1936 2101 435962567 435962411 1.250000e-23 121.0
43 TraesCS3A01G531400 chr2A 76.287 641 97 26 38 656 167961054 167960447 9.040000e-75 291.0
44 TraesCS3A01G531400 chr4B 79.545 176 23 8 1932 2104 17461821 17461656 2.100000e-21 113.0
45 TraesCS3A01G531400 chr6B 100.000 31 0 0 1737 1767 545216201 545216171 9.980000e-05 58.4


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 TraesCS3A01G531400 chr3A 744285759 744288340 2581 False 4769.0 4769 100.000000 1 2582 1 chr3A.!!$F2 2581
1 TraesCS3A01G531400 chr3A 744261931 744268628 6697 False 1084.0 1519 91.426333 702 2582 3 chr3A.!!$F3 1880
2 TraesCS3A01G531400 chr3A 7824505 7825189 684 True 797.0 797 87.773000 22 703 1 chr3A.!!$R1 681
3 TraesCS3A01G531400 chr3A 743988024 743988677 653 False 553.0 553 82.734000 957 1620 1 chr3A.!!$F1 663
4 TraesCS3A01G531400 chr3A 708019155 708019720 565 True 383.0 383 80.000000 166 703 1 chr3A.!!$R2 537
5 TraesCS3A01G531400 chr3D 610186546 610191219 4673 False 1275.5 1592 88.150500 702 1936 2 chr3D.!!$F2 1234
6 TraesCS3A01G531400 chr3D 610138890 610139550 660 False 449.0 449 80.058000 964 1611 1 chr3D.!!$F1 647
7 TraesCS3A01G531400 chr3B 822038827 822039815 988 False 1206.0 1206 88.976000 702 1690 1 chr3B.!!$F7 988
8 TraesCS3A01G531400 chr3B 822066917 822067905 988 False 1190.0 1190 88.681000 702 1690 1 chr3B.!!$F8 988
9 TraesCS3A01G531400 chr3B 822094298 822095336 1038 False 711.5 1243 91.813000 697 1770 2 chr3B.!!$F9 1073
10 TraesCS3A01G531400 chr3B 822008114 822008645 531 False 704.0 704 90.909000 702 1225 1 chr3B.!!$F5 523
11 TraesCS3A01G531400 chr3B 822023409 822023940 531 False 693.0 693 90.538000 702 1225 1 chr3B.!!$F6 523
12 TraesCS3A01G531400 chr3B 821836295 821837099 804 False 510.0 510 79.371000 802 1611 1 chr3B.!!$F4 809
13 TraesCS3A01G531400 chr3B 779798309 779798863 554 False 339.0 339 78.622000 166 702 1 chr3B.!!$F3 536
14 TraesCS3A01G531400 chrUn 459077174 459077707 533 False 702.0 702 90.758000 702 1227 1 chrUn.!!$F1 525
15 TraesCS3A01G531400 chr4A 127171241 127171804 563 False 409.0 409 80.803000 166 703 1 chr4A.!!$F1 537
16 TraesCS3A01G531400 chr7A 672448967 672449525 558 True 398.0 398 80.492000 166 702 1 chr7A.!!$R3 536
17 TraesCS3A01G531400 chr7A 25253431 25254082 651 True 263.0 263 75.000000 38 702 1 chr7A.!!$R1 664
18 TraesCS3A01G531400 chr6A 174370947 174371587 640 False 326.0 326 76.720000 38 702 1 chr6A.!!$F1 664
19 TraesCS3A01G531400 chr5A 648912803 648913365 562 False 363.0 363 79.371000 166 702 1 chr5A.!!$F1 536
20 TraesCS3A01G531400 chr5A 300789032 300789550 518 True 337.0 337 79.024000 166 706 1 chr5A.!!$R1 540
21 TraesCS3A01G531400 chr7B 540951412 540951971 559 True 361.0 361 79.371000 166 704 1 chr7B.!!$R1 538
22 TraesCS3A01G531400 chr1A 540378415 540378980 565 True 351.0 351 78.957000 166 705 1 chr1A.!!$R1 539
23 TraesCS3A01G531400 chr2B 551253450 551254007 557 False 318.0 318 78.032000 168 703 1 chr2B.!!$F1 535
24 TraesCS3A01G531400 chr4D 185794731 185795367 636 False 309.0 309 76.409000 19 670 1 chr4D.!!$F1 651
25 TraesCS3A01G531400 chr2A 167960447 167961054 607 True 291.0 291 76.287000 38 656 1 chr2A.!!$R1 618

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
33 34 0.026285 CGCCATCGACCGAAACAATC 59.974 55.0 0.0 0.0 38.1 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 10506 0.034337 GGCCAAACCAGACGTGAGTA 59.966 55.0 0.0 0.0 41.8 2.59 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
33 34 0.026285 CGCCATCGACCGAAACAATC 59.974 55.000 0.00 0.00 38.10 2.67
39 45 2.598589 TCGACCGAAACAATCCGTAAG 58.401 47.619 0.00 0.00 0.00 2.34
42 48 3.060363 CGACCGAAACAATCCGTAAGAAG 59.940 47.826 0.00 0.00 43.02 2.85
104 112 5.414454 ACAAATACATGACACATGGTGGTAC 59.586 40.000 14.70 0.00 37.94 3.34
114 122 2.224426 ACATGGTGGTACGAACACACAT 60.224 45.455 0.00 0.00 40.54 3.21
127 135 3.401033 ACACACATCACGATGGAAGAA 57.599 42.857 11.54 0.00 42.91 2.52
137 145 3.063997 CACGATGGAAGAATACCAGCAAC 59.936 47.826 0.00 0.00 42.98 4.17
244 256 7.434013 ACGTTAAAATTTAGGTTTGAACTGCAG 59.566 33.333 13.48 13.48 32.52 4.41
256 271 7.066766 AGGTTTGAACTGCAGATATGAGATTTC 59.933 37.037 23.35 10.70 0.00 2.17
328 350 4.904253 TTTTGGGGTGTCTTTTTACTCG 57.096 40.909 0.00 0.00 0.00 4.18
332 356 5.080969 TGGGGTGTCTTTTTACTCGATAG 57.919 43.478 0.00 0.00 0.00 2.08
333 357 4.081309 TGGGGTGTCTTTTTACTCGATAGG 60.081 45.833 0.00 0.00 0.00 2.57
484 533 0.865769 CTCTACCGTTGCAACACACC 59.134 55.000 28.01 1.98 0.00 4.16
492 541 0.948623 TTGCAACACACCGGATCGAG 60.949 55.000 9.46 0.00 0.00 4.04
501 550 1.067142 CACCGGATCGAGAGTTTCCAA 60.067 52.381 9.46 0.00 35.26 3.53
507 556 4.143094 CGGATCGAGAGTTTCCAAGAAAAC 60.143 45.833 3.08 0.00 39.03 2.43
515 568 6.799512 AGAGTTTCCAAGAAAACATTGTCAG 58.200 36.000 2.73 0.00 40.77 3.51
522 575 6.016860 TCCAAGAAAACATTGTCAGTCAGATG 60.017 38.462 0.00 0.00 0.00 2.90
523 576 5.368256 AGAAAACATTGTCAGTCAGATGC 57.632 39.130 0.00 0.00 0.00 3.91
543 596 7.660617 CAGATGCATTTACTCCAGATCATAACT 59.339 37.037 0.00 0.00 0.00 2.24
613 666 4.747540 TTTCTCATCATCAACCGTTGTG 57.252 40.909 11.01 8.82 0.00 3.33
622 675 1.937223 TCAACCGTTGTGACATGACAC 59.063 47.619 19.48 19.48 40.68 3.67
675 737 3.071167 AGGAACTGGTATATTTCTCCCGC 59.929 47.826 0.00 0.00 37.18 6.13
693 755 3.951655 CTGCAACGCACGGGCATTC 62.952 63.158 11.77 0.00 41.24 2.67
778 845 2.293170 GGCTCTAGTTCCTTTCATGGC 58.707 52.381 0.00 0.00 0.00 4.40
798 865 5.819991 TGGCTCCTTTGATGTAAGAAAGAT 58.180 37.500 0.00 0.00 31.89 2.40
804 871 7.624549 TCCTTTGATGTAAGAAAGATGCTAGT 58.375 34.615 0.00 0.00 31.89 2.57
805 872 8.758829 TCCTTTGATGTAAGAAAGATGCTAGTA 58.241 33.333 0.00 0.00 31.89 1.82
806 873 9.039870 CCTTTGATGTAAGAAAGATGCTAGTAG 57.960 37.037 0.00 0.00 31.89 2.57
807 874 9.593134 CTTTGATGTAAGAAAGATGCTAGTAGT 57.407 33.333 0.00 0.00 31.89 2.73
808 875 8.932945 TTGATGTAAGAAAGATGCTAGTAGTG 57.067 34.615 0.00 0.00 0.00 2.74
809 876 8.293699 TGATGTAAGAAAGATGCTAGTAGTGA 57.706 34.615 0.00 0.00 0.00 3.41
810 877 8.191446 TGATGTAAGAAAGATGCTAGTAGTGAC 58.809 37.037 0.00 0.00 0.00 3.67
854 921 2.203714 GAGGAGGCGGCCCTATCT 60.204 66.667 17.02 8.06 43.12 1.98
855 922 1.076906 GAGGAGGCGGCCCTATCTA 59.923 63.158 17.02 0.00 43.12 1.98
867 934 5.205056 CGGCCCTATCTATATTCCTCTTCT 58.795 45.833 0.00 0.00 0.00 2.85
877 955 1.933021 TTCCTCTTCTCCAAGCGGTA 58.067 50.000 0.00 0.00 36.10 4.02
936 1033 6.648192 TCTCATTTCCTTCTTCATCTTCTCC 58.352 40.000 0.00 0.00 0.00 3.71
948 1048 3.013417 TCATCTTCTCCTCCTCCTCCTTT 59.987 47.826 0.00 0.00 0.00 3.11
976 1076 3.574396 TGCTCACTCGCCTATAAATAGCT 59.426 43.478 0.00 0.00 0.00 3.32
1004 1105 2.440409 CCTGCCATTGTTACTCAAGCT 58.560 47.619 0.00 0.00 39.55 3.74
1241 5637 1.001293 TCCTCATACATCATGCGCCTC 59.999 52.381 4.18 0.00 34.35 4.70
1242 5638 1.066136 CTCATACATCATGCGCCTCG 58.934 55.000 4.18 0.00 34.35 4.63
1288 5697 4.963318 TCTTGCTATGGGACTAAGGATG 57.037 45.455 0.00 0.00 0.00 3.51
1409 5825 1.134189 TGCTGCAGCTGCTAGATCATT 60.134 47.619 36.61 0.00 42.66 2.57
1410 5826 1.264557 GCTGCAGCTGCTAGATCATTG 59.735 52.381 36.61 16.54 42.66 2.82
1411 5827 2.835027 CTGCAGCTGCTAGATCATTGA 58.165 47.619 36.61 13.65 42.66 2.57
1412 5828 3.403968 CTGCAGCTGCTAGATCATTGAT 58.596 45.455 36.61 0.00 42.66 2.57
1413 5829 3.400255 TGCAGCTGCTAGATCATTGATC 58.600 45.455 36.61 17.26 42.66 2.92
1414 5830 3.181458 TGCAGCTGCTAGATCATTGATCA 60.181 43.478 36.61 10.85 40.48 2.92
1415 5831 4.004314 GCAGCTGCTAGATCATTGATCAT 58.996 43.478 31.33 14.04 38.54 2.45
1435 5865 4.260355 ATCATGCATGCACCGCGC 62.260 61.111 25.37 0.00 42.89 6.86
1475 5907 4.648307 TGATCGATCCATCCATCCATCTAG 59.352 45.833 22.31 0.00 0.00 2.43
1552 5986 1.741032 GAGCAGAGCAGGTGCACTC 60.741 63.158 17.98 6.24 43.82 3.51
1735 9647 3.001330 CGCTTGGAATCGGTGTATCTTTC 59.999 47.826 0.00 0.00 0.00 2.62
1736 9648 4.192317 GCTTGGAATCGGTGTATCTTTCT 58.808 43.478 0.00 0.00 0.00 2.52
1737 9649 4.636206 GCTTGGAATCGGTGTATCTTTCTT 59.364 41.667 0.00 0.00 0.00 2.52
1738 9650 5.123979 GCTTGGAATCGGTGTATCTTTCTTT 59.876 40.000 0.00 0.00 0.00 2.52
1842 9758 2.673368 GGTATTGCTCTGTGAAACGAGG 59.327 50.000 0.00 0.00 42.39 4.63
1843 9759 1.813513 ATTGCTCTGTGAAACGAGGG 58.186 50.000 0.00 0.00 42.39 4.30
1855 9771 0.903454 AACGAGGGTCGAATCAGGGT 60.903 55.000 2.82 0.00 43.74 4.34
1961 10458 4.098501 AGTCGTGCTATCAATCATGAGACA 59.901 41.667 0.09 0.00 39.39 3.41
2008 10505 2.285083 TCTTTGTCAAAGGGTGTCACG 58.715 47.619 22.23 0.00 39.01 4.35
2009 10506 2.014128 CTTTGTCAAAGGGTGTCACGT 58.986 47.619 16.31 0.00 34.85 4.49
2010 10507 2.983907 TTGTCAAAGGGTGTCACGTA 57.016 45.000 0.00 0.00 0.00 3.57
2011 10508 2.228138 TGTCAAAGGGTGTCACGTAC 57.772 50.000 0.00 0.00 0.00 3.67
2012 10509 1.758280 TGTCAAAGGGTGTCACGTACT 59.242 47.619 0.00 0.00 0.00 2.73
2013 10510 2.223876 TGTCAAAGGGTGTCACGTACTC 60.224 50.000 0.00 0.00 0.00 2.59
2014 10511 2.033372 TCAAAGGGTGTCACGTACTCA 58.967 47.619 0.00 0.00 0.00 3.41
2015 10512 2.132762 CAAAGGGTGTCACGTACTCAC 58.867 52.381 0.00 7.95 0.00 3.51
2053 10550 3.071602 CCCCATGATCCGATATGTATCCC 59.928 52.174 0.00 0.00 0.00 3.85
2059 10556 5.333581 TGATCCGATATGTATCCCACTCTT 58.666 41.667 0.00 0.00 0.00 2.85
2166 10663 9.985730 TTTTTAATCTATTCATCAATCATGGCC 57.014 29.630 0.00 0.00 32.64 5.36
2177 10674 5.398603 TCAATCATGGCCGTACAAAAATT 57.601 34.783 0.00 0.00 0.00 1.82
2179 10676 7.106439 TCAATCATGGCCGTACAAAAATTAT 57.894 32.000 0.00 0.00 0.00 1.28
2202 10699 1.846439 CCAGGTCCATGAACCACCTAT 59.154 52.381 3.09 0.00 42.12 2.57
2229 10726 1.595993 TACACTCACTGGAGCGAGCC 61.596 60.000 0.00 0.00 45.42 4.70
2230 10727 3.753434 ACTCACTGGAGCGAGCCG 61.753 66.667 0.00 0.00 45.42 5.52
2272 10769 2.506065 CTCCCTTACCGGAGTCAGG 58.494 63.158 9.46 7.88 43.94 3.86
2296 10793 6.313164 GGCAAACCTTATTGTAGTAGACAGTC 59.687 42.308 0.00 0.00 39.88 3.51
2299 10796 5.259632 ACCTTATTGTAGTAGACAGTCGGT 58.740 41.667 0.00 0.00 39.88 4.69
2304 10801 5.869753 TTGTAGTAGACAGTCGGTAAGTC 57.130 43.478 0.00 0.00 39.88 3.01
2318 10815 3.181499 CGGTAAGTCATCGTGCTAAGACT 60.181 47.826 0.00 0.00 42.72 3.24
2321 10818 5.296283 GGTAAGTCATCGTGCTAAGACTCTA 59.704 44.000 0.00 0.00 40.22 2.43
2324 10821 6.268825 AGTCATCGTGCTAAGACTCTAAAA 57.731 37.500 0.00 0.00 36.69 1.52
2330 10827 5.185249 TCGTGCTAAGACTCTAAAAGACCAT 59.815 40.000 0.00 0.00 0.00 3.55
2337 10834 4.705507 AGACTCTAAAAGACCATCGCACTA 59.294 41.667 0.00 0.00 0.00 2.74
2338 10835 5.000012 ACTCTAAAAGACCATCGCACTAG 58.000 43.478 0.00 0.00 0.00 2.57
2339 10836 4.463186 ACTCTAAAAGACCATCGCACTAGT 59.537 41.667 0.00 0.00 0.00 2.57
2340 10837 4.744570 TCTAAAAGACCATCGCACTAGTG 58.255 43.478 18.93 18.93 0.00 2.74
2353 10850 1.927174 CACTAGTGTAGCAACCATCGC 59.073 52.381 15.06 0.00 0.00 4.58
2387 10884 8.329203 AGAGTTGTAGATTGGAAAGATCAAAC 57.671 34.615 0.00 0.00 0.00 2.93
2402 10899 8.472007 AAAGATCAAACCTATAACCACACAAA 57.528 30.769 0.00 0.00 0.00 2.83
2410 10907 4.992319 CCTATAACCACACAAACGAAGACA 59.008 41.667 0.00 0.00 0.00 3.41
2459 10956 0.969149 AGTCCAGCACGACAGAATCA 59.031 50.000 6.04 0.00 35.07 2.57
2473 10970 1.764723 AGAATCATGTGAGATCCGGCA 59.235 47.619 0.00 0.00 0.00 5.69
2501 10998 0.618680 CCTCCACATGTCCTCCTCCA 60.619 60.000 0.00 0.00 0.00 3.86
2566 11063 1.424638 ATTCCTACCCAGGGACATCG 58.575 55.000 14.54 0.00 42.87 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.544267 CGATGGCGAGAAAGTTTATCCC 59.456 50.000 4.70 7.52 40.82 3.85
1 2 3.454375 TCGATGGCGAGAAAGTTTATCC 58.546 45.455 4.70 0.00 42.51 2.59
13 14 0.390603 ATTGTTTCGGTCGATGGCGA 60.391 50.000 0.00 0.00 45.71 5.54
14 15 0.026285 GATTGTTTCGGTCGATGGCG 59.974 55.000 0.00 0.00 39.35 5.69
15 16 0.377203 GGATTGTTTCGGTCGATGGC 59.623 55.000 0.00 0.00 0.00 4.40
16 17 0.650512 CGGATTGTTTCGGTCGATGG 59.349 55.000 0.00 0.00 0.00 3.51
17 18 1.355971 ACGGATTGTTTCGGTCGATG 58.644 50.000 0.00 0.00 32.90 3.84
20 21 2.598589 TCTTACGGATTGTTTCGGTCG 58.401 47.619 0.00 0.00 38.66 4.79
33 34 7.095229 TGTGTGATCATTTTCTTCTTCTTACGG 60.095 37.037 0.00 0.00 0.00 4.02
96 104 1.413077 TGATGTGTGTTCGTACCACCA 59.587 47.619 9.90 4.47 31.71 4.17
104 112 1.708822 TCCATCGTGATGTGTGTTCG 58.291 50.000 8.89 0.00 37.11 3.95
114 122 2.499693 TGCTGGTATTCTTCCATCGTGA 59.500 45.455 0.00 0.00 34.26 4.35
127 135 4.321974 GGCTTGCTTTTAAGTTGCTGGTAT 60.322 41.667 0.00 0.00 0.00 2.73
137 145 7.542025 AGATTTGATGTAGGCTTGCTTTTAAG 58.458 34.615 0.00 0.00 0.00 1.85
201 213 9.902196 ATTTTAACGTAATTGGAGTTTAGGTTG 57.098 29.630 10.21 0.00 37.86 3.77
219 231 7.646130 TCTGCAGTTCAAACCTAAATTTTAACG 59.354 33.333 14.67 0.00 33.06 3.18
314 329 7.039882 TGGATTCCTATCGAGTAAAAAGACAC 58.960 38.462 3.95 0.00 0.00 3.67
316 331 8.664211 ATTGGATTCCTATCGAGTAAAAAGAC 57.336 34.615 3.95 0.00 0.00 3.01
318 333 9.109393 TGAATTGGATTCCTATCGAGTAAAAAG 57.891 33.333 3.95 0.00 38.50 2.27
328 350 6.889301 TGAGCATTGAATTGGATTCCTATC 57.111 37.500 3.95 0.63 38.50 2.08
332 356 6.819649 TGATTTTGAGCATTGAATTGGATTCC 59.180 34.615 0.00 0.00 38.50 3.01
333 357 7.837202 TGATTTTGAGCATTGAATTGGATTC 57.163 32.000 0.00 0.00 39.70 2.52
484 533 2.941453 TCTTGGAAACTCTCGATCCG 57.059 50.000 0.00 0.00 35.96 4.18
492 541 6.564328 ACTGACAATGTTTTCTTGGAAACTC 58.436 36.000 6.15 0.00 39.62 3.01
501 550 4.823442 TGCATCTGACTGACAATGTTTTCT 59.177 37.500 0.00 0.00 0.00 2.52
507 556 6.432607 AGTAAATGCATCTGACTGACAATG 57.567 37.500 0.00 0.00 0.00 2.82
515 568 5.363101 TGATCTGGAGTAAATGCATCTGAC 58.637 41.667 0.00 0.00 0.00 3.51
522 575 7.443575 ACATGAGTTATGATCTGGAGTAAATGC 59.556 37.037 0.00 0.00 39.21 3.56
523 576 8.899427 ACATGAGTTATGATCTGGAGTAAATG 57.101 34.615 0.00 0.00 39.21 2.32
543 596 2.415491 CGACGTGAAGCTTAGGACATGA 60.415 50.000 11.01 0.00 0.00 3.07
595 648 3.066380 TGTCACAACGGTTGATGATGAG 58.934 45.455 26.39 7.68 0.00 2.90
613 666 2.329379 GTCGAGGAACTGTGTCATGTC 58.671 52.381 0.00 0.00 41.55 3.06
622 675 2.111999 TTGGCCAGGTCGAGGAACTG 62.112 60.000 5.11 3.70 45.96 3.16
665 726 2.690778 GCGTTGCAGCGGGAGAAAT 61.691 57.895 24.49 0.00 0.00 2.17
675 737 3.951655 GAATGCCCGTGCGTTGCAG 62.952 63.158 0.86 0.00 46.55 4.41
693 755 3.680937 TCCCGTTTCAAAATACTAGCACG 59.319 43.478 0.00 0.00 0.00 5.34
778 845 6.998968 AGCATCTTTCTTACATCAAAGGAG 57.001 37.500 0.00 0.00 31.55 3.69
804 871 6.253758 TGATTCCCTTTGTCTCTAGTCACTA 58.746 40.000 0.00 0.00 0.00 2.74
805 872 5.087323 TGATTCCCTTTGTCTCTAGTCACT 58.913 41.667 0.00 0.00 0.00 3.41
806 873 5.407407 TGATTCCCTTTGTCTCTAGTCAC 57.593 43.478 0.00 0.00 0.00 3.67
807 874 6.433847 TTTGATTCCCTTTGTCTCTAGTCA 57.566 37.500 0.00 0.00 0.00 3.41
808 875 7.929941 AATTTGATTCCCTTTGTCTCTAGTC 57.070 36.000 0.00 0.00 0.00 2.59
809 876 9.401058 CATAATTTGATTCCCTTTGTCTCTAGT 57.599 33.333 0.00 0.00 0.00 2.57
810 877 8.844244 CCATAATTTGATTCCCTTTGTCTCTAG 58.156 37.037 0.00 0.00 0.00 2.43
877 955 1.604378 CAAAGGATGGACGGGAGCT 59.396 57.895 0.00 0.00 0.00 4.09
905 1002 5.426504 TGAAGAAGGAAATGAGAGATGCTC 58.573 41.667 0.00 0.00 44.21 4.26
936 1033 2.504996 AGCATCAAGAAAGGAGGAGGAG 59.495 50.000 0.00 0.00 0.00 3.69
1004 1105 3.631686 TCTTTTGTGCTTCTTGCTTGCTA 59.368 39.130 0.00 0.00 43.37 3.49
1022 1123 3.070015 CCTTGATTGGTGTTGGCTTCTTT 59.930 43.478 0.00 0.00 0.00 2.52
1288 5697 1.150081 CTCCTGCACCCATCCATCC 59.850 63.158 0.00 0.00 0.00 3.51
1410 5826 2.159558 GGTGCATGCATGATCGATGATC 60.160 50.000 30.64 9.40 39.31 2.92
1411 5827 1.810755 GGTGCATGCATGATCGATGAT 59.189 47.619 30.64 0.00 33.31 2.45
1412 5828 1.232119 GGTGCATGCATGATCGATGA 58.768 50.000 30.64 0.00 33.31 2.92
1413 5829 0.110373 CGGTGCATGCATGATCGATG 60.110 55.000 30.64 9.96 34.84 3.84
1414 5830 1.848932 GCGGTGCATGCATGATCGAT 61.849 55.000 30.64 0.00 0.00 3.59
1415 5831 2.536673 GCGGTGCATGCATGATCGA 61.537 57.895 30.64 7.43 0.00 3.59
1475 5907 3.788333 TCAGGTAGCGTTACATGGTAC 57.212 47.619 21.19 0.00 40.88 3.34
1552 5986 0.738389 GGTCGGTTTACATGCATGGG 59.262 55.000 29.41 7.08 0.00 4.00
1842 9758 1.202382 CCTTACGACCCTGATTCGACC 60.202 57.143 0.00 0.00 39.83 4.79
1843 9759 1.202382 CCCTTACGACCCTGATTCGAC 60.202 57.143 0.00 0.00 39.83 4.20
1855 9771 3.005684 ACACGTATCAAACACCCTTACGA 59.994 43.478 7.67 0.00 39.05 3.43
1961 10458 5.186198 AGCGAGAATTTGGCTAAACTATGT 58.814 37.500 0.00 0.00 34.75 2.29
2008 10505 2.205144 GGCCAAACCAGACGTGAGTAC 61.205 57.143 0.00 0.00 41.80 2.73
2009 10506 0.034337 GGCCAAACCAGACGTGAGTA 59.966 55.000 0.00 0.00 41.80 2.59
2010 10507 1.227853 GGCCAAACCAGACGTGAGT 60.228 57.895 0.00 0.00 43.91 3.41
2011 10508 1.227823 TGGCCAAACCAGACGTGAG 60.228 57.895 0.61 0.00 46.36 3.51
2012 10509 2.911928 TGGCCAAACCAGACGTGA 59.088 55.556 0.61 0.00 46.36 4.35
2059 10556 8.768955 CCAAATTTTATTCATCGAAAACCACAA 58.231 29.630 0.00 0.00 0.00 3.33
2144 10641 6.475504 ACGGCCATGATTGATGAATAGATTA 58.524 36.000 2.24 0.00 33.31 1.75
2149 10646 4.967036 TGTACGGCCATGATTGATGAATA 58.033 39.130 2.24 0.00 33.31 1.75
2150 10647 3.819368 TGTACGGCCATGATTGATGAAT 58.181 40.909 2.24 0.00 33.31 2.57
2166 10663 7.380431 TGGACCTGGTTATAATTTTTGTACG 57.620 36.000 0.00 0.00 0.00 3.67
2177 10674 3.201266 GGTGGTTCATGGACCTGGTTATA 59.799 47.826 24.02 0.00 40.47 0.98
2179 10676 1.353022 GGTGGTTCATGGACCTGGTTA 59.647 52.381 24.02 0.00 40.47 2.85
2202 10699 1.154197 CCAGTGAGTGTAGTCGTCGA 58.846 55.000 0.00 0.00 0.00 4.20
2239 10736 2.428925 GGAGGGGCGATAACGGTGA 61.429 63.158 0.00 0.00 40.15 4.02
2241 10738 3.159347 GGGAGGGGCGATAACGGT 61.159 66.667 0.00 0.00 40.15 4.83
2244 10741 0.395686 GGTAAGGGAGGGGCGATAAC 59.604 60.000 0.00 0.00 0.00 1.89
2270 10767 6.013639 ACTGTCTACTACAATAAGGTTTGCCT 60.014 38.462 0.00 0.00 42.03 4.75
2272 10769 6.034683 CGACTGTCTACTACAATAAGGTTTGC 59.965 42.308 6.21 0.00 37.74 3.68
2296 10793 3.106672 GTCTTAGCACGATGACTTACCG 58.893 50.000 0.00 0.00 0.00 4.02
2299 10796 6.997239 TTAGAGTCTTAGCACGATGACTTA 57.003 37.500 0.00 0.00 39.53 2.24
2304 10801 5.517054 GGTCTTTTAGAGTCTTAGCACGATG 59.483 44.000 0.00 0.00 0.00 3.84
2318 10815 4.219944 ACACTAGTGCGATGGTCTTTTAGA 59.780 41.667 22.90 0.00 0.00 2.10
2321 10818 3.402628 ACACTAGTGCGATGGTCTTTT 57.597 42.857 22.90 0.00 0.00 2.27
2324 10821 1.405821 GCTACACTAGTGCGATGGTCT 59.594 52.381 22.90 3.20 0.00 3.85
2330 10827 0.963225 TGGTTGCTACACTAGTGCGA 59.037 50.000 22.90 10.18 0.00 5.10
2337 10834 1.447838 CGGCGATGGTTGCTACACT 60.448 57.895 0.00 0.00 0.00 3.55
2338 10835 0.810031 ATCGGCGATGGTTGCTACAC 60.810 55.000 23.36 0.00 0.00 2.90
2339 10836 0.809636 CATCGGCGATGGTTGCTACA 60.810 55.000 35.72 0.00 36.51 2.74
2340 10837 0.529773 TCATCGGCGATGGTTGCTAC 60.530 55.000 39.82 0.00 40.15 3.58
2353 10850 5.874810 TCCAATCTACAACTCTTTTCATCGG 59.125 40.000 0.00 0.00 0.00 4.18
2387 10884 4.992319 TGTCTTCGTTTGTGTGGTTATAGG 59.008 41.667 0.00 0.00 0.00 2.57
2402 10899 5.068460 TGGATCCATTTTTGTTTGTCTTCGT 59.932 36.000 11.44 0.00 0.00 3.85
2459 10956 1.383109 TCCCTGCCGGATCTCACAT 60.383 57.895 5.05 0.00 34.86 3.21
2473 10970 2.607750 ATGTGGAGGTGCGTCCCT 60.608 61.111 8.25 0.00 35.49 4.20
2479 10976 1.078143 GGAGGACATGTGGAGGTGC 60.078 63.158 1.15 0.00 0.00 5.01
2501 10998 1.091537 CCGGTGGTGCGAATAACATT 58.908 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.