Multiple sequence alignment - TraesCS2A01G120900

Loading Multiple Alignment...

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 TraesCS2A01G120900 chr2A 100.000 4808 0 0 1 4808 70875771 70870964 0.000000e+00 8879.0
1 TraesCS2A01G120900 chr2A 90.435 115 7 2 1458 1568 717470677 717470563 1.080000e-31 148.0
2 TraesCS2A01G120900 chr2B 87.990 3164 219 71 1 3090 108236472 108233396 0.000000e+00 3589.0
3 TraesCS2A01G120900 chr2B 94.419 1738 85 9 3078 4808 108233373 108231641 0.000000e+00 2662.0
4 TraesCS2A01G120900 chr2B 90.265 113 7 2 1460 1568 200970692 200970580 1.390000e-30 145.0
5 TraesCS2A01G120900 chr2D 88.947 2696 164 56 459 3080 71764371 71761736 0.000000e+00 3205.0
6 TraesCS2A01G120900 chr2D 95.174 1637 70 5 3176 4808 71761510 71759879 0.000000e+00 2577.0
7 TraesCS2A01G120900 chr2D 84.175 297 32 7 72 356 71765647 71765354 1.700000e-69 274.0
8 TraesCS2A01G120900 chr5B 86.458 576 55 13 1015 1568 13216553 13217127 1.140000e-170 610.0
9 TraesCS2A01G120900 chr5B 85.417 576 61 15 1015 1568 638033498 638032924 1.160000e-160 577.0
10 TraesCS2A01G120900 chr5B 85.294 136 6 5 4659 4794 319885796 319885917 1.400000e-25 128.0
11 TraesCS2A01G120900 chr3B 86.111 576 57 15 1015 1568 26976162 26976736 2.480000e-167 599.0
12 TraesCS2A01G120900 chr3B 82.927 574 64 15 1040 1581 483420008 483420579 2.010000e-133 486.0
13 TraesCS2A01G120900 chr1B 85.938 576 57 14 1015 1568 663566258 663565685 1.150000e-165 593.0
14 TraesCS2A01G120900 chr1A 90.000 120 8 2 1453 1568 69816005 69815886 8.330000e-33 152.0
15 TraesCS2A01G120900 chr1A 85.821 134 5 5 4662 4795 102168647 102168528 3.910000e-26 130.0
16 TraesCS2A01G120900 chr1A 100.000 33 0 0 4776 4808 102168552 102168520 1.440000e-05 62.1
17 TraesCS2A01G120900 chr3A 90.435 115 7 2 1458 1568 35609619 35609505 1.080000e-31 148.0


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 TraesCS2A01G120900 chr2A 70870964 70875771 4807 True 8879.000000 8879 100.0000 1 4808 1 chr2A.!!$R1 4807
1 TraesCS2A01G120900 chr2B 108231641 108236472 4831 True 3125.500000 3589 91.2045 1 4808 2 chr2B.!!$R2 4807
2 TraesCS2A01G120900 chr2D 71759879 71765647 5768 True 2018.666667 3205 89.4320 72 4808 3 chr2D.!!$R1 4736
3 TraesCS2A01G120900 chr5B 13216553 13217127 574 False 610.000000 610 86.4580 1015 1568 1 chr5B.!!$F1 553
4 TraesCS2A01G120900 chr5B 638032924 638033498 574 True 577.000000 577 85.4170 1015 1568 1 chr5B.!!$R1 553
5 TraesCS2A01G120900 chr3B 26976162 26976736 574 False 599.000000 599 86.1110 1015 1568 1 chr3B.!!$F1 553
6 TraesCS2A01G120900 chr3B 483420008 483420579 571 False 486.000000 486 82.9270 1040 1581 1 chr3B.!!$F2 541
7 TraesCS2A01G120900 chr1B 663565685 663566258 573 True 593.000000 593 85.9380 1015 1568 1 chr1B.!!$R1 553

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
953 1961 0.171231 GTTTCTTGGCAGGATTCGGC 59.829 55.0 0.0 0.0 0.00 5.54 F
1379 2405 0.266152 GAATCCCTCTCTCCCCCTCA 59.734 60.0 0.0 0.0 0.00 3.86 F
1839 2901 0.329261 TTGGCTGGGTCAATCAGGAG 59.671 55.0 0.0 0.0 33.16 3.69 F
1841 2903 0.329596 GGCTGGGTCAATCAGGAGTT 59.670 55.0 0.0 0.0 33.16 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2227 3300 1.003696 AGCAAGTAGGAACTTCCCAGC 59.996 52.381 4.01 2.45 44.28 4.85 R
2419 3492 1.592064 TTCTGTGCTTCAACATGCGA 58.408 45.000 0.00 0.00 0.00 5.10 R
3639 4854 1.481772 GGAGCACTCTCATCTGAAGCT 59.518 52.381 0.00 0.00 41.13 3.74 R
3891 5106 4.589908 ACCAACTTCCAGATGTACCATTC 58.410 43.478 0.00 0.00 0.00 2.67 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
17 18 2.280797 GACAGCACCTCCAACGCA 60.281 61.111 0.00 0.00 0.00 5.24
27 28 2.711542 CCTCCAACGCAAAGAGGTAAT 58.288 47.619 0.00 0.00 41.96 1.89
49 50 9.615295 GTAATAAAAATCAACAATACACACGGT 57.385 29.630 0.00 0.00 0.00 4.83
57 58 5.236911 TCAACAATACACACGGTCCTAAAAC 59.763 40.000 0.00 0.00 0.00 2.43
67 68 3.245990 ACGGTCCTAAAACGAAAGAAACG 59.754 43.478 0.00 0.00 0.00 3.60
79 80 3.998341 CGAAAGAAACGTAATCCTCCCAA 59.002 43.478 0.00 0.00 0.00 4.12
90 91 1.216977 CCTCCCAACGCGTGATGTA 59.783 57.895 14.98 0.00 0.00 2.29
121 144 1.265635 GGTGGAGACGATGAGAGATCG 59.734 57.143 0.00 0.00 46.02 3.69
186 209 2.352323 GCCCACCAGAAATTAAACACCG 60.352 50.000 0.00 0.00 0.00 4.94
218 245 3.679980 ACACATGCACGTCTCATAAAGTC 59.320 43.478 0.00 0.00 0.00 3.01
280 307 8.341173 GTGATGACTTTGTCAATATCAAGATCC 58.659 37.037 4.46 0.00 45.96 3.36
300 327 3.574396 TCCGTTGACTCAGTCTCTCAAAT 59.426 43.478 6.33 0.00 33.15 2.32
301 328 4.765339 TCCGTTGACTCAGTCTCTCAAATA 59.235 41.667 6.33 0.00 33.15 1.40
313 340 4.926238 GTCTCTCAAATATGCTCATACGGG 59.074 45.833 0.00 0.00 0.00 5.28
314 341 4.021104 TCTCTCAAATATGCTCATACGGGG 60.021 45.833 0.00 0.00 0.00 5.73
328 355 4.016706 GGGGTAGGCTGCACGTGT 62.017 66.667 18.38 0.00 0.00 4.49
379 415 1.065782 GGTTTGCCTCCCTCTTCTCTC 60.066 57.143 0.00 0.00 0.00 3.20
408 1383 7.951530 TTTTTCAGCAAAGGAAAATGATCTC 57.048 32.000 0.00 0.00 42.08 2.75
416 1391 7.067251 AGCAAAGGAAAATGATCTCATCTCTTC 59.933 37.037 0.00 0.00 35.10 2.87
418 1393 8.904834 CAAAGGAAAATGATCTCATCTCTTCAT 58.095 33.333 0.00 0.00 35.10 2.57
428 1403 7.708322 TGATCTCATCTCTTCATAAAGAAACGG 59.292 37.037 0.00 0.00 40.95 4.44
433 1408 9.231297 TCATCTCTTCATAAAGAAACGGAAATT 57.769 29.630 0.00 0.00 40.95 1.82
437 1412 8.172352 TCTTCATAAAGAAACGGAAATTTCCA 57.828 30.769 31.49 13.82 41.75 3.53
438 1413 8.634444 TCTTCATAAAGAAACGGAAATTTCCAA 58.366 29.630 31.49 15.40 41.75 3.53
439 1414 8.582433 TTCATAAAGAAACGGAAATTTCCAAC 57.418 30.769 31.49 19.92 39.24 3.77
440 1415 8.198109 TTCATAAAGAAACGGAAATTTCCAACA 58.802 29.630 31.49 11.47 39.24 3.33
479 1454 8.768501 AAAAAGAAAAGGAAGATGTCTTACCT 57.231 30.769 1.36 5.03 37.52 3.08
480 1455 9.862149 AAAAAGAAAAGGAAGATGTCTTACCTA 57.138 29.630 11.54 0.00 37.52 3.08
561 1544 8.567285 AAATGGTCTTATCTTACAGAACCTTG 57.433 34.615 0.00 0.00 0.00 3.61
563 1546 4.876679 GGTCTTATCTTACAGAACCTTGGC 59.123 45.833 0.00 0.00 0.00 4.52
591 1591 6.299141 ACTATATTTGACCAGGTAAGCCATG 58.701 40.000 0.00 0.00 37.19 3.66
592 1592 2.214376 TTTGACCAGGTAAGCCATGG 57.786 50.000 7.63 7.63 38.33 3.66
595 1595 0.623723 GACCAGGTAAGCCATGGGAA 59.376 55.000 15.13 0.00 37.37 3.97
600 1600 2.755103 CAGGTAAGCCATGGGAAGAAAC 59.245 50.000 15.13 0.00 37.19 2.78
645 1645 3.604582 CAGAATCTCCCAGTTTGTCCTC 58.395 50.000 0.00 0.00 0.00 3.71
651 1651 1.416401 TCCCAGTTTGTCCTCACAGAC 59.584 52.381 0.00 0.00 37.81 3.51
672 1678 7.032580 CAGACATGCTGGAGTAGTATATTAGC 58.967 42.308 8.70 0.00 41.07 3.09
686 1692 7.645058 AGTATATTAGCACCAGCACAATTTT 57.355 32.000 0.00 0.00 45.49 1.82
687 1693 7.483307 AGTATATTAGCACCAGCACAATTTTG 58.517 34.615 0.00 0.00 45.49 2.44
688 1694 3.383620 TTAGCACCAGCACAATTTTGG 57.616 42.857 0.00 0.00 45.49 3.28
717 1723 2.026822 TGGGCACACCACAAATTTGTTT 60.027 40.909 21.10 8.62 46.80 2.83
757 1763 1.222936 CCTCACTGCTCCACATCCC 59.777 63.158 0.00 0.00 0.00 3.85
765 1771 1.609783 CTCCACATCCCTTGTCCCC 59.390 63.158 0.00 0.00 36.00 4.81
800 1806 2.023414 TATCACCAAGCCGCTACCCG 62.023 60.000 0.00 0.00 0.00 5.28
842 1849 0.179056 CCCACATCCGTCCATACCAC 60.179 60.000 0.00 0.00 0.00 4.16
844 1851 1.651987 CACATCCGTCCATACCACAC 58.348 55.000 0.00 0.00 0.00 3.82
899 1906 1.678970 ATCCCAGCGGCACCTTTTC 60.679 57.895 1.45 0.00 0.00 2.29
908 1915 4.404654 CACCTTTTCTGCGCCGGC 62.405 66.667 19.07 19.07 40.52 6.13
922 1930 1.819905 CCGGCCTTGGTTGTTTTGT 59.180 52.632 0.00 0.00 0.00 2.83
928 1936 2.935849 GCCTTGGTTGTTTTGTTTGGAG 59.064 45.455 0.00 0.00 0.00 3.86
953 1961 0.171231 GTTTCTTGGCAGGATTCGGC 59.829 55.000 0.00 0.00 0.00 5.54
961 1969 3.242291 AGGATTCGGCGGGGGATC 61.242 66.667 7.21 6.02 0.00 3.36
1031 2039 1.070445 GCATGGTCCGGGAGATGAG 59.930 63.158 16.66 0.78 0.00 2.90
1373 2399 2.158971 GCAACTCTGAATCCCTCTCTCC 60.159 54.545 0.00 0.00 0.00 3.71
1375 2401 1.062505 ACTCTGAATCCCTCTCTCCCC 60.063 57.143 0.00 0.00 0.00 4.81
1379 2405 0.266152 GAATCCCTCTCTCCCCCTCA 59.734 60.000 0.00 0.00 0.00 3.86
1380 2406 0.955752 AATCCCTCTCTCCCCCTCAT 59.044 55.000 0.00 0.00 0.00 2.90
1381 2407 0.491371 ATCCCTCTCTCCCCCTCATC 59.509 60.000 0.00 0.00 0.00 2.92
1382 2408 1.532794 CCCTCTCTCCCCCTCATCG 60.533 68.421 0.00 0.00 0.00 3.84
1383 2409 2.206536 CCTCTCTCCCCCTCATCGC 61.207 68.421 0.00 0.00 0.00 4.58
1385 2411 2.444706 CTCTCCCCCTCATCGCCA 60.445 66.667 0.00 0.00 0.00 5.69
1387 2413 1.825281 CTCTCCCCCTCATCGCCATC 61.825 65.000 0.00 0.00 0.00 3.51
1435 2478 1.312815 GGCAGCCTGGTGTTCATATC 58.687 55.000 3.29 0.00 0.00 1.63
1443 2486 4.333926 GCCTGGTGTTCATATCAAGTTCTC 59.666 45.833 0.00 0.00 0.00 2.87
1468 2511 7.228706 TCAGATTAGTCACCAAAGTTTTTCTCC 59.771 37.037 0.00 0.00 0.00 3.71
1497 2543 8.572185 TGATGAGATTGTCTATTGTCTAGTAGC 58.428 37.037 0.00 0.00 0.00 3.58
1516 2562 7.313951 AGTAGCAATTCAAGAGCAATTAGTC 57.686 36.000 0.00 0.00 0.00 2.59
1548 2594 7.653647 ACGTCTATTTTTGGCAAACTTCAATA 58.346 30.769 13.10 12.41 0.00 1.90
1565 2611 4.980590 TCAATAATGGCGATTGTGTTCAC 58.019 39.130 3.95 0.00 36.02 3.18
1674 2721 2.286418 CGTCAAAGAAAGGTCTGTGTGC 60.286 50.000 0.00 0.00 39.78 4.57
1677 2724 3.761218 TCAAAGAAAGGTCTGTGTGCAAA 59.239 39.130 0.00 0.00 39.78 3.68
1686 2733 3.002759 GGTCTGTGTGCAAAAGAGTTCTC 59.997 47.826 0.00 0.00 0.00 2.87
1688 2735 3.873361 TCTGTGTGCAAAAGAGTTCTCAG 59.127 43.478 0.00 0.00 0.00 3.35
1690 2737 1.949525 TGTGCAAAAGAGTTCTCAGGC 59.050 47.619 0.00 1.47 0.00 4.85
1720 2770 5.641209 AGCATCTACTCTGTCATGTTTGTTC 59.359 40.000 0.00 0.00 0.00 3.18
1783 2845 5.789710 AATACGTCCGTATTTGGAACAAG 57.210 39.130 16.92 0.00 45.70 3.16
1824 2886 6.687604 AGTAAATAATGACTGGTTGTTTGGC 58.312 36.000 0.00 0.00 0.00 4.52
1826 2888 4.789012 ATAATGACTGGTTGTTTGGCTG 57.211 40.909 0.00 0.00 0.00 4.85
1827 2889 1.331214 ATGACTGGTTGTTTGGCTGG 58.669 50.000 0.00 0.00 0.00 4.85
1830 2892 0.755327 ACTGGTTGTTTGGCTGGGTC 60.755 55.000 0.00 0.00 0.00 4.46
1831 2893 0.754957 CTGGTTGTTTGGCTGGGTCA 60.755 55.000 0.00 0.00 0.00 4.02
1833 2895 1.047801 GGTTGTTTGGCTGGGTCAAT 58.952 50.000 0.00 0.00 0.00 2.57
1834 2896 1.000843 GGTTGTTTGGCTGGGTCAATC 59.999 52.381 0.00 0.00 0.00 2.67
1835 2897 1.686052 GTTGTTTGGCTGGGTCAATCA 59.314 47.619 0.00 0.00 0.00 2.57
1836 2898 1.619654 TGTTTGGCTGGGTCAATCAG 58.380 50.000 0.00 0.00 35.49 2.90
1837 2899 0.890683 GTTTGGCTGGGTCAATCAGG 59.109 55.000 0.00 0.00 33.16 3.86
1838 2900 0.776810 TTTGGCTGGGTCAATCAGGA 59.223 50.000 0.00 0.00 33.16 3.86
1839 2901 0.329261 TTGGCTGGGTCAATCAGGAG 59.671 55.000 0.00 0.00 33.16 3.69
1840 2902 0.842030 TGGCTGGGTCAATCAGGAGT 60.842 55.000 0.00 0.00 33.16 3.85
1841 2903 0.329596 GGCTGGGTCAATCAGGAGTT 59.670 55.000 0.00 0.00 33.16 3.01
1842 2904 1.457346 GCTGGGTCAATCAGGAGTTG 58.543 55.000 0.00 0.00 33.16 3.16
1843 2905 1.952367 GCTGGGTCAATCAGGAGTTGG 60.952 57.143 0.00 0.00 33.16 3.77
1844 2906 1.352352 CTGGGTCAATCAGGAGTTGGT 59.648 52.381 0.00 0.00 0.00 3.67
1845 2907 1.780309 TGGGTCAATCAGGAGTTGGTT 59.220 47.619 0.00 0.00 0.00 3.67
1846 2908 2.176798 TGGGTCAATCAGGAGTTGGTTT 59.823 45.455 0.00 0.00 0.00 3.27
1847 2909 3.396276 TGGGTCAATCAGGAGTTGGTTTA 59.604 43.478 0.00 0.00 0.00 2.01
1848 2910 4.010349 GGGTCAATCAGGAGTTGGTTTAG 58.990 47.826 0.00 0.00 0.00 1.85
1859 2921 8.092687 TCAGGAGTTGGTTTAGTAGTATGAAAC 58.907 37.037 2.68 2.68 33.27 2.78
1860 2922 8.095169 CAGGAGTTGGTTTAGTAGTATGAAACT 58.905 37.037 8.80 0.00 42.62 2.66
1863 2925 8.530269 AGTTGGTTTAGTAGTATGAAACTTCG 57.470 34.615 8.80 0.00 39.80 3.79
1943 3014 6.071108 AGCTATGTTGTCAGATGTAGTTGACT 60.071 38.462 6.24 0.00 43.15 3.41
1944 3015 6.035435 GCTATGTTGTCAGATGTAGTTGACTG 59.965 42.308 6.24 0.00 43.15 3.51
1947 3018 5.163457 TGTTGTCAGATGTAGTTGACTGTCA 60.163 40.000 6.36 6.36 43.15 3.58
1962 3033 6.618287 TGACTGTCATTTTTAGAACAGTGG 57.382 37.500 6.36 0.00 38.37 4.00
2001 3072 2.618442 AAACCATGTGGCTTTGTTGG 57.382 45.000 0.00 0.00 39.32 3.77
2026 3097 7.381408 GGTAGATTTGTTTGCTTTGAACTTACC 59.619 37.037 0.00 0.00 0.00 2.85
2031 3102 8.468720 TTTGTTTGCTTTGAACTTACCTTTAC 57.531 30.769 0.00 0.00 0.00 2.01
2131 3202 4.553330 TTTCCTCTACATTGGACTGACC 57.447 45.455 0.00 0.00 39.54 4.02
2135 3206 3.133003 CCTCTACATTGGACTGACCGATT 59.867 47.826 0.00 0.00 40.58 3.34
2179 3252 7.013274 GGCATATGCAGTCTGGATTTTACTTAA 59.987 37.037 28.07 0.00 44.36 1.85
2180 3253 7.857885 GCATATGCAGTCTGGATTTTACTTAAC 59.142 37.037 22.84 0.00 41.59 2.01
2193 3266 9.968743 GGATTTTACTTAACTAGTTCATGAACG 57.031 33.333 28.18 19.28 45.50 3.95
2205 3278 7.913821 ACTAGTTCATGAACGGTTTTTCTTTTC 59.086 33.333 28.18 4.16 45.50 2.29
2419 3492 8.437360 TTCAGCGACATACATAAGATCAAAAT 57.563 30.769 0.00 0.00 0.00 1.82
2420 3493 8.076714 TCAGCGACATACATAAGATCAAAATC 57.923 34.615 0.00 0.00 0.00 2.17
2434 3507 3.307674 TCAAAATCGCATGTTGAAGCAC 58.692 40.909 0.00 0.00 0.00 4.40
2449 3522 6.995686 TGTTGAAGCACAGAAACCTATTTAGA 59.004 34.615 0.00 0.00 0.00 2.10
2452 3525 8.458573 TGAAGCACAGAAACCTATTTAGAAAA 57.541 30.769 0.00 0.00 0.00 2.29
2617 3690 4.853468 TGTTTTGGGATCTAGGTATGCA 57.147 40.909 0.00 0.00 0.00 3.96
2679 3752 8.334016 TGTGCGCACATATTTTTGTATATTTC 57.666 30.769 37.86 6.73 36.21 2.17
2693 3766 9.573166 TTTTGTATATTTCCTGGAGACCATATG 57.427 33.333 0.00 0.00 30.82 1.78
2798 3871 7.603024 AGTGCTGATAACAACCTTACTCTTTAC 59.397 37.037 0.00 0.00 0.00 2.01
3097 4205 6.396829 AGCAAAATTATCATGTAGGAAGCC 57.603 37.500 0.00 0.00 0.00 4.35
3098 4206 5.009010 AGCAAAATTATCATGTAGGAAGCCG 59.991 40.000 0.00 0.00 0.00 5.52
3152 4260 9.394767 AGTGTAATTATGTCACATATGAAGCAA 57.605 29.630 10.38 0.00 36.31 3.91
3163 4271 8.169268 GTCACATATGAAGCAACACTAACTAAC 58.831 37.037 10.38 0.00 36.31 2.34
3166 4274 9.938280 ACATATGAAGCAACACTAACTAACTTA 57.062 29.630 10.38 0.00 0.00 2.24
3217 4426 7.985184 CAGGTATGAAGCACCACTAACTATTTA 59.015 37.037 0.00 0.00 38.62 1.40
3222 4433 9.686683 ATGAAGCACCACTAACTATTTATTTCT 57.313 29.630 0.00 0.00 0.00 2.52
3281 4492 4.750098 AGAAACGAAACCACATGACACTAG 59.250 41.667 0.00 0.00 0.00 2.57
3288 4499 6.128282 CGAAACCACATGACACTAGCTAATTT 60.128 38.462 0.00 0.00 0.00 1.82
3290 4501 6.500684 ACCACATGACACTAGCTAATTTTG 57.499 37.500 0.00 0.00 0.00 2.44
3299 4510 8.935844 TGACACTAGCTAATTTTGTCATGTAAG 58.064 33.333 17.10 0.00 41.20 2.34
3337 4548 6.198029 CGTCATGTAAGAAGCATCACTAAGAG 59.802 42.308 0.00 0.00 0.00 2.85
3340 4555 6.842437 TGTAAGAAGCATCACTAAGAGACT 57.158 37.500 0.00 0.00 0.00 3.24
3341 4556 7.939784 TGTAAGAAGCATCACTAAGAGACTA 57.060 36.000 0.00 0.00 0.00 2.59
3342 4557 8.349568 TGTAAGAAGCATCACTAAGAGACTAA 57.650 34.615 0.00 0.00 0.00 2.24
3343 4558 8.972127 TGTAAGAAGCATCACTAAGAGACTAAT 58.028 33.333 0.00 0.00 0.00 1.73
3351 4566 9.534565 GCATCACTAAGAGACTAATTATGTTGA 57.465 33.333 0.00 0.00 0.00 3.18
3429 4644 4.858850 TCCCTGTATCAGCAATTGAACAT 58.141 39.130 10.34 0.00 39.77 2.71
3447 4662 2.149383 TGGAGGCACAGCTCCAACT 61.149 57.895 6.94 0.00 45.68 3.16
3624 4839 1.195448 GTGACGGTTGCATCAGTGAAG 59.805 52.381 5.24 0.00 0.00 3.02
3639 4854 4.100963 TCAGTGAAGAACTTTCAGCTGGTA 59.899 41.667 15.13 0.00 36.83 3.25
3919 5134 2.439507 ACATCTGGAAGTTGGTCACACT 59.560 45.455 0.00 0.00 37.97 3.55
3930 5145 1.476891 TGGTCACACTCTTATCCGAGC 59.523 52.381 0.00 0.00 34.35 5.03
3959 5174 1.889829 ACTTCTGGAGACCTTCAGACG 59.110 52.381 7.50 8.60 39.43 4.18
4004 5219 2.480037 GCATTTTTGCTGGGTGTTAAGC 59.520 45.455 0.00 0.00 39.96 3.09
4105 5320 4.062293 CAGGTGTCGAACAACCAATAGAA 58.938 43.478 13.86 0.00 36.16 2.10
4197 5412 5.907207 TGTTGTAGAGCTTGATATCCTGTC 58.093 41.667 0.00 0.00 0.00 3.51
4272 5487 9.748708 TGTTCCTGATAAAGTCAATTTTCTTTG 57.251 29.630 12.25 0.00 36.14 2.77
4302 5517 7.556275 CAGTTGTATGTGTATTGGAAATACCCT 59.444 37.037 7.48 0.00 38.00 4.34
4442 5660 8.815565 TGTAATGTTTTATGGCTATCTGGAAA 57.184 30.769 0.00 0.00 0.00 3.13
4481 5699 6.420903 GCAAGGTTAGAGAATTTTGTCAAACC 59.579 38.462 0.00 0.00 0.00 3.27
4490 5708 0.958091 TTTGTCAAACCGGGATGCAG 59.042 50.000 6.32 0.00 0.00 4.41
4547 5765 6.218019 ACAATTTTGAATGATATGGATGCCG 58.782 36.000 0.00 0.00 0.00 5.69
4569 5787 4.156008 CGGGAAAACTGGGAACTGAATTAG 59.844 45.833 0.00 0.00 0.00 1.73
4637 5858 5.755813 GCATTTGCAGTGACCTATATCTTG 58.244 41.667 5.46 0.00 41.59 3.02
4646 5867 9.413048 GCAGTGACCTATATCTTGTTAGTTATC 57.587 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.800554 CCTCTTTGCGTTGGAGGT 57.199 55.556 0.00 0.00 41.04 3.85
27 28 6.487331 AGGACCGTGTGTATTGTTGATTTTTA 59.513 34.615 0.00 0.00 0.00 1.52
45 46 3.245990 CGTTTCTTTCGTTTTAGGACCGT 59.754 43.478 0.00 0.00 0.00 4.83
46 47 3.245990 ACGTTTCTTTCGTTTTAGGACCG 59.754 43.478 0.00 0.00 38.38 4.79
49 50 6.930722 AGGATTACGTTTCTTTCGTTTTAGGA 59.069 34.615 0.00 0.00 41.72 2.94
57 58 3.592059 TGGGAGGATTACGTTTCTTTCG 58.408 45.455 0.00 0.00 0.00 3.46
67 68 0.108520 TCACGCGTTGGGAGGATTAC 60.109 55.000 10.22 0.00 0.00 1.89
79 80 1.206132 TCCTTTCCATACATCACGCGT 59.794 47.619 5.58 5.58 0.00 6.01
90 91 1.210478 CGTCTCCACCATCCTTTCCAT 59.790 52.381 0.00 0.00 0.00 3.41
121 144 2.941480 ACCATCCAGCATCCAGATTTC 58.059 47.619 0.00 0.00 0.00 2.17
218 245 9.021863 GTCACCTCGTACTAAAAGAATATCTTG 57.978 37.037 0.00 0.00 36.71 3.02
234 261 1.069703 CAAACGTCTCGTCACCTCGTA 60.070 52.381 0.00 0.00 39.99 3.43
236 263 0.317603 ACAAACGTCTCGTCACCTCG 60.318 55.000 0.00 0.00 39.99 4.63
280 307 5.005203 GCATATTTGAGAGACTGAGTCAACG 59.995 44.000 15.86 0.00 34.60 4.10
300 327 1.203137 AGCCTACCCCGTATGAGCATA 60.203 52.381 0.00 0.00 0.00 3.14
301 328 0.471971 AGCCTACCCCGTATGAGCAT 60.472 55.000 0.00 0.00 0.00 3.79
313 340 2.030562 ACACACGTGCAGCCTACC 59.969 61.111 17.22 0.00 0.00 3.18
314 341 3.244105 CACACACGTGCAGCCTAC 58.756 61.111 17.22 0.00 36.06 3.18
340 367 3.932822 ACCACGCACATATACACTTTCA 58.067 40.909 0.00 0.00 0.00 2.69
342 369 4.614993 GCAAACCACGCACATATACACTTT 60.615 41.667 0.00 0.00 0.00 2.66
346 373 1.740585 GGCAAACCACGCACATATACA 59.259 47.619 0.00 0.00 35.26 2.29
403 1378 7.923344 TCCGTTTCTTTATGAAGAGATGAGATC 59.077 37.037 10.53 0.00 42.55 2.75
408 1383 9.846248 AAATTTCCGTTTCTTTATGAAGAGATG 57.154 29.630 0.00 1.95 42.55 2.90
553 1536 7.048512 GTCAAATATAGTACTGCCAAGGTTCT 58.951 38.462 5.39 0.00 0.00 3.01
561 1544 5.291905 ACCTGGTCAAATATAGTACTGCC 57.708 43.478 5.39 0.00 0.00 4.85
563 1546 6.929606 GGCTTACCTGGTCAAATATAGTACTG 59.070 42.308 0.63 0.00 0.00 2.74
591 1591 4.280929 AGTTGTTTATGGCAGTTTCTTCCC 59.719 41.667 0.00 0.00 0.00 3.97
592 1592 5.453567 AGTTGTTTATGGCAGTTTCTTCC 57.546 39.130 0.00 0.00 0.00 3.46
595 1595 6.239036 GGAGAAAGTTGTTTATGGCAGTTTCT 60.239 38.462 0.00 0.00 35.51 2.52
600 1600 5.123979 GGTAGGAGAAAGTTGTTTATGGCAG 59.876 44.000 0.00 0.00 0.00 4.85
645 1645 4.662468 ATACTACTCCAGCATGTCTGTG 57.338 45.455 13.67 9.61 41.25 3.66
651 1651 6.102663 GGTGCTAATATACTACTCCAGCATG 58.897 44.000 0.00 0.00 39.49 4.06
665 1665 5.187576 ACCAAAATTGTGCTGGTGCTAATAT 59.812 36.000 0.00 0.00 41.95 1.28
694 1700 0.758123 AAATTTGTGGTGTGCCCAGG 59.242 50.000 0.00 0.00 46.45 4.45
717 1723 4.565652 GGGAAGGAACAAGAATGCTCTACA 60.566 45.833 0.00 0.00 0.00 2.74
757 1763 2.359967 GGAGGGAGACGGGGACAAG 61.360 68.421 0.00 0.00 0.00 3.16
765 1771 0.039074 GATATGCGTGGAGGGAGACG 60.039 60.000 0.00 0.00 38.63 4.18
800 1806 3.050275 GACGGTGGTGCTGCCTTC 61.050 66.667 0.00 0.00 38.35 3.46
815 1822 2.240162 GACGGATGTGGGTGGGAGAC 62.240 65.000 0.00 0.00 0.00 3.36
870 1877 1.154205 CGCTGGGATGTCAACGGATC 61.154 60.000 0.00 0.00 0.00 3.36
908 1915 2.935849 GCTCCAAACAAAACAACCAAGG 59.064 45.455 0.00 0.00 0.00 3.61
915 1923 1.064946 CGCGGCTCCAAACAAAACA 59.935 52.632 0.00 0.00 0.00 2.83
917 1925 1.668101 AACCGCGGCTCCAAACAAAA 61.668 50.000 28.58 0.00 0.00 2.44
918 1926 1.668101 AAACCGCGGCTCCAAACAAA 61.668 50.000 28.58 0.00 0.00 2.83
922 1930 1.527380 AAGAAACCGCGGCTCCAAA 60.527 52.632 28.58 0.00 0.00 3.28
928 1936 4.404654 CTGCCAAGAAACCGCGGC 62.405 66.667 28.58 9.52 45.11 6.53
1308 2334 1.225704 GATGGGGAAGGTGAGCCTG 59.774 63.158 0.00 0.00 46.33 4.85
1350 2376 0.539051 AGAGGGATTCAGAGTTGCGG 59.461 55.000 0.00 0.00 0.00 5.69
1351 2377 1.480137 AGAGAGGGATTCAGAGTTGCG 59.520 52.381 0.00 0.00 0.00 4.85
1373 2399 2.851102 AGGGATGGCGATGAGGGG 60.851 66.667 0.00 0.00 0.00 4.79
1375 2401 2.281345 GCAGGGATGGCGATGAGG 60.281 66.667 0.00 0.00 0.00 3.86
1379 2405 1.153086 GAACAGCAGGGATGGCGAT 60.153 57.895 0.00 0.00 36.08 4.58
1380 2406 1.913951 ATGAACAGCAGGGATGGCGA 61.914 55.000 0.00 0.00 36.08 5.54
1381 2407 1.033746 AATGAACAGCAGGGATGGCG 61.034 55.000 0.00 0.00 36.08 5.69
1382 2408 0.743097 GAATGAACAGCAGGGATGGC 59.257 55.000 0.00 0.00 0.00 4.40
1383 2409 2.022195 CTGAATGAACAGCAGGGATGG 58.978 52.381 0.00 0.00 0.00 3.51
1435 2478 6.708054 ACTTTGGTGACTAATCTGAGAACTTG 59.292 38.462 0.00 0.00 0.00 3.16
1443 2486 7.363431 GGAGAAAAACTTTGGTGACTAATCTG 58.637 38.462 0.00 0.00 0.00 2.90
1468 2511 7.918033 ACTAGACAATAGACAATCTCATCAACG 59.082 37.037 0.00 0.00 0.00 4.10
1497 2543 7.008440 TCATCGACTAATTGCTCTTGAATTG 57.992 36.000 0.00 0.00 0.00 2.32
1516 2562 4.717991 TGCCAAAAATAGACGTTTCATCG 58.282 39.130 0.00 0.00 0.00 3.84
1548 2594 4.320608 AAAAGTGAACACAATCGCCATT 57.679 36.364 7.68 0.00 0.00 3.16
1653 2700 2.286418 GCACACAGACCTTTCTTTGACG 60.286 50.000 0.00 0.00 33.78 4.35
1674 2721 2.157738 CCCAGCCTGAGAACTCTTTTG 58.842 52.381 0.00 0.00 0.00 2.44
1677 2724 2.183679 CTACCCAGCCTGAGAACTCTT 58.816 52.381 0.00 0.00 0.00 2.85
1690 2737 3.291584 TGACAGAGTAGATGCTACCCAG 58.708 50.000 0.00 0.00 0.00 4.45
1735 2785 4.527038 TCGGTCTCAACTACTTTCAGGATT 59.473 41.667 0.00 0.00 0.00 3.01
1738 2789 3.506455 TCTCGGTCTCAACTACTTTCAGG 59.494 47.826 0.00 0.00 0.00 3.86
1739 2790 4.768130 TCTCGGTCTCAACTACTTTCAG 57.232 45.455 0.00 0.00 0.00 3.02
1740 2791 5.524971 TTTCTCGGTCTCAACTACTTTCA 57.475 39.130 0.00 0.00 0.00 2.69
1741 2792 6.250951 CGTATTTCTCGGTCTCAACTACTTTC 59.749 42.308 0.00 0.00 0.00 2.62
1742 2793 6.091437 CGTATTTCTCGGTCTCAACTACTTT 58.909 40.000 0.00 0.00 0.00 2.66
1743 2794 5.182760 ACGTATTTCTCGGTCTCAACTACTT 59.817 40.000 0.00 0.00 0.00 2.24
1775 2837 4.269183 TCTGACTTTTCAAGCTTGTTCCA 58.731 39.130 25.19 14.09 0.00 3.53
1776 2838 4.900635 TCTGACTTTTCAAGCTTGTTCC 57.099 40.909 25.19 10.70 0.00 3.62
1824 2886 1.352352 ACCAACTCCTGATTGACCCAG 59.648 52.381 0.00 0.00 0.00 4.45
1826 2888 2.586648 AACCAACTCCTGATTGACCC 57.413 50.000 0.00 0.00 0.00 4.46
1827 2889 4.652822 ACTAAACCAACTCCTGATTGACC 58.347 43.478 0.00 0.00 0.00 4.02
1830 2892 8.258007 TCATACTACTAAACCAACTCCTGATTG 58.742 37.037 0.00 0.00 0.00 2.67
1831 2893 8.375493 TCATACTACTAAACCAACTCCTGATT 57.625 34.615 0.00 0.00 0.00 2.57
1833 2895 7.786046 TTCATACTACTAAACCAACTCCTGA 57.214 36.000 0.00 0.00 0.00 3.86
1834 2896 8.095169 AGTTTCATACTACTAAACCAACTCCTG 58.905 37.037 0.00 0.00 34.56 3.86
1835 2897 8.203681 AGTTTCATACTACTAAACCAACTCCT 57.796 34.615 0.00 0.00 34.56 3.69
1836 2898 8.843885 AAGTTTCATACTACTAAACCAACTCC 57.156 34.615 0.00 0.00 35.54 3.85
1837 2899 8.645487 CGAAGTTTCATACTACTAAACCAACTC 58.355 37.037 0.00 0.00 35.54 3.01
1838 2900 8.362639 TCGAAGTTTCATACTACTAAACCAACT 58.637 33.333 0.00 0.00 35.54 3.16
1839 2901 8.524870 TCGAAGTTTCATACTACTAAACCAAC 57.475 34.615 0.00 0.00 35.54 3.77
1840 2902 9.715121 ATTCGAAGTTTCATACTACTAAACCAA 57.285 29.630 3.35 0.00 35.54 3.67
1841 2903 9.146984 CATTCGAAGTTTCATACTACTAAACCA 57.853 33.333 3.35 0.00 35.54 3.67
1842 2904 9.148104 ACATTCGAAGTTTCATACTACTAAACC 57.852 33.333 3.35 0.00 35.54 3.27
1844 2906 9.917129 TGACATTCGAAGTTTCATACTACTAAA 57.083 29.630 3.35 0.00 35.54 1.85
1845 2907 9.917129 TTGACATTCGAAGTTTCATACTACTAA 57.083 29.630 3.35 0.00 35.54 2.24
1846 2908 9.350357 GTTGACATTCGAAGTTTCATACTACTA 57.650 33.333 3.35 0.00 35.54 1.82
1847 2909 8.088981 AGTTGACATTCGAAGTTTCATACTACT 58.911 33.333 3.35 3.84 35.54 2.57
1848 2910 8.162880 CAGTTGACATTCGAAGTTTCATACTAC 58.837 37.037 3.35 1.72 35.54 2.73
1943 3014 6.119536 AGACACCACTGTTCTAAAAATGACA 58.880 36.000 0.00 0.00 0.00 3.58
1944 3015 6.619801 AGACACCACTGTTCTAAAAATGAC 57.380 37.500 0.00 0.00 0.00 3.06
1947 3018 9.349713 TGAATTAGACACCACTGTTCTAAAAAT 57.650 29.630 4.35 0.00 30.51 1.82
2001 3072 8.135529 AGGTAAGTTCAAAGCAAACAAATCTAC 58.864 33.333 0.00 0.00 0.00 2.59
2026 3097 5.364157 AGGCTACATGTTAGAGAGGGTAAAG 59.636 44.000 2.30 0.00 0.00 1.85
2031 3102 2.366916 CCAGGCTACATGTTAGAGAGGG 59.633 54.545 2.30 0.00 0.00 4.30
2095 3166 7.063593 TGTAGAGGAAATATGTCTGAGTAGCT 58.936 38.462 0.00 0.00 0.00 3.32
2131 3202 4.274069 CCAATGAGAAACGCATACAATCG 58.726 43.478 0.00 0.00 0.00 3.34
2135 3206 1.742831 GCCCAATGAGAAACGCATACA 59.257 47.619 0.00 0.00 0.00 2.29
2179 3252 6.937436 AAGAAAAACCGTTCATGAACTAGT 57.063 33.333 30.45 24.78 39.08 2.57
2180 3253 7.378728 GGAAAAGAAAAACCGTTCATGAACTAG 59.621 37.037 30.45 24.23 39.08 2.57
2182 3255 6.040247 GGAAAAGAAAAACCGTTCATGAACT 58.960 36.000 30.45 14.91 39.08 3.01
2193 3266 4.201812 GCTGCACAAAGGAAAAGAAAAACC 60.202 41.667 0.00 0.00 0.00 3.27
2227 3300 1.003696 AGCAAGTAGGAACTTCCCAGC 59.996 52.381 4.01 2.45 44.28 4.85
2386 3459 4.794278 TGTATGTCGCTGAAGGAACTAA 57.206 40.909 0.00 0.00 38.49 2.24
2419 3492 1.592064 TTCTGTGCTTCAACATGCGA 58.408 45.000 0.00 0.00 0.00 5.10
2420 3493 2.046313 GTTTCTGTGCTTCAACATGCG 58.954 47.619 0.00 0.00 0.00 4.73
2449 3522 8.712228 ATCTGTCCAGTAAAGAGGAAATTTTT 57.288 30.769 0.00 0.00 35.29 1.94
2452 3525 6.070767 TCGATCTGTCCAGTAAAGAGGAAATT 60.071 38.462 0.00 0.00 35.29 1.82
2464 3537 5.047021 TCTCAAGAAATTCGATCTGTCCAGT 60.047 40.000 0.00 0.00 0.00 4.00
2468 3541 5.573282 TCGTTCTCAAGAAATTCGATCTGTC 59.427 40.000 0.00 0.00 35.58 3.51
2617 3690 3.201266 TGGAAGGGTTACCGCATAAGATT 59.799 43.478 0.00 0.00 43.47 2.40
2679 3752 2.965671 AATGGCATATGGTCTCCAGG 57.034 50.000 0.00 0.00 36.75 4.45
2693 3766 5.199024 TGGATGTGTATGCAAATAATGGC 57.801 39.130 0.00 0.00 31.17 4.40
2710 3783 7.871973 TCAACATTTTTGGTCAGTAAATGGATG 59.128 33.333 17.05 15.40 41.34 3.51
2895 3969 7.985476 AGTGCACTTAAATAACATCGCTATTT 58.015 30.769 15.25 0.00 34.25 1.40
2900 3974 9.878599 AATTATAGTGCACTTAAATAACATCGC 57.121 29.630 27.06 0.00 0.00 4.58
3189 4398 4.471386 AGTTAGTGGTGCTTCATACCTGAT 59.529 41.667 0.00 0.00 39.01 2.90
3193 4402 8.904099 ATAAATAGTTAGTGGTGCTTCATACC 57.096 34.615 0.00 0.00 38.71 2.73
3217 4426 1.642762 AGGCCCCTGTTGATCAGAAAT 59.357 47.619 0.00 0.00 46.27 2.17
3222 4433 2.989639 CGAGGCCCCTGTTGATCA 59.010 61.111 0.00 0.00 0.00 2.92
3288 4499 9.263538 ACGAAATTTACACTACTTACATGACAA 57.736 29.630 0.00 0.00 0.00 3.18
3290 4501 8.918658 TGACGAAATTTACACTACTTACATGAC 58.081 33.333 0.00 0.00 0.00 3.06
3294 4505 8.821147 ACATGACGAAATTTACACTACTTACA 57.179 30.769 0.00 0.00 0.00 2.41
3299 4510 9.953825 CTTCTTACATGACGAAATTTACACTAC 57.046 33.333 0.00 0.00 0.00 2.73
3313 4524 7.221838 GTCTCTTAGTGATGCTTCTTACATGAC 59.778 40.741 0.00 0.00 32.56 3.06
3447 4662 2.910688 AGAAAGGAAACGCAGTCTGA 57.089 45.000 3.32 0.00 45.00 3.27
3639 4854 1.481772 GGAGCACTCTCATCTGAAGCT 59.518 52.381 0.00 0.00 41.13 3.74
3891 5106 4.589908 ACCAACTTCCAGATGTACCATTC 58.410 43.478 0.00 0.00 0.00 2.67
3919 5134 1.389555 TCGAAGCAGCTCGGATAAGA 58.610 50.000 12.44 0.00 39.35 2.10
3930 5145 2.333014 GTCTCCAGAAGTTCGAAGCAG 58.667 52.381 0.00 0.00 0.00 4.24
3959 5174 4.697352 TGGATTGAAGCTAACTCTTCTTGC 59.303 41.667 5.30 0.00 42.15 4.01
4004 5219 1.134401 ACAATCTGCAGGTCGGGTATG 60.134 52.381 15.13 2.90 0.00 2.39
4008 5223 1.003355 ACACAATCTGCAGGTCGGG 60.003 57.895 15.13 0.00 0.00 5.14
4105 5320 1.065126 GCCAGCAACTCCCTTCTACAT 60.065 52.381 0.00 0.00 0.00 2.29
4141 5356 1.413382 CGGCTTCTCATATCGAGCAC 58.587 55.000 0.00 0.00 41.98 4.40
4159 5374 0.247736 CAACAACCTCTCCTCCTCCG 59.752 60.000 0.00 0.00 0.00 4.63
4169 5384 5.755861 GGATATCAAGCTCTACAACAACCTC 59.244 44.000 4.83 0.00 0.00 3.85
4264 5479 5.359576 ACACATACAACTGGAGCAAAGAAAA 59.640 36.000 0.00 0.00 0.00 2.29
4272 5487 4.513442 TCCAATACACATACAACTGGAGC 58.487 43.478 0.00 0.00 0.00 4.70
4342 5557 9.035338 CACGAAACACAAAAATAACTTGTTTTG 57.965 29.630 10.00 10.00 45.82 2.44
4451 5669 7.500892 TGACAAAATTCTCTAACCTTGCTGTTA 59.499 33.333 0.00 0.00 0.00 2.41
4472 5690 0.179004 ACTGCATCCCGGTTTGACAA 60.179 50.000 0.00 0.00 0.00 3.18
4481 5699 1.375396 TGAACCGAACTGCATCCCG 60.375 57.895 0.00 0.00 0.00 5.14
4547 5765 4.082190 GCTAATTCAGTTCCCAGTTTTCCC 60.082 45.833 0.00 0.00 0.00 3.97
4569 5787 0.451783 GGAATTGTCATGGGTCGTGC 59.548 55.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.