Multiple sequence alignment - TraesCS5A01G261000

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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 TraesCS5A01G261000 chr5A 100.000 4784 0 0 1 4784 474833726 474828943 0.000000e+00 8835.0
1 TraesCS5A01G261000 chr5D 94.887 1545 67 8 3250 4784 371798980 371797438 0.000000e+00 2405.0
2 TraesCS5A01G261000 chr5D 91.171 1144 66 11 2116 3236 371800237 371799106 0.000000e+00 1520.0
3 TraesCS5A01G261000 chr5D 90.357 840 47 16 864 1693 371801541 371800726 0.000000e+00 1072.0
4 TraesCS5A01G261000 chr5D 93.870 522 25 6 307 825 550181277 550181794 0.000000e+00 780.0
5 TraesCS5A01G261000 chr5D 88.013 317 21 4 1712 2018 371800667 371800358 4.550000e-95 359.0
6 TraesCS5A01G261000 chr5B 93.523 1544 74 13 3250 4784 441648459 441646933 0.000000e+00 2274.0
7 TraesCS5A01G261000 chr5B 90.468 1112 67 10 2146 3233 441649683 441648587 0.000000e+00 1430.0
8 TraesCS5A01G261000 chr5B 92.711 878 36 16 830 1699 441651129 441650272 0.000000e+00 1242.0
9 TraesCS5A01G261000 chr5B 93.958 480 28 1 347 825 97489818 97490297 0.000000e+00 725.0
10 TraesCS5A01G261000 chr5B 92.982 57 4 0 4728 4784 441646905 441646849 3.070000e-12 84.2
11 TraesCS5A01G261000 chr5B 91.228 57 5 0 4728 4784 441646947 441646891 1.430000e-10 78.7
12 TraesCS5A01G261000 chr4A 97.098 827 20 4 3 827 5059831 5060655 0.000000e+00 1391.0
13 TraesCS5A01G261000 chr4A 88.254 315 32 4 1010 1324 743703350 743703041 5.850000e-99 372.0
14 TraesCS5A01G261000 chr1A 96.359 824 28 2 3 825 494428562 494429384 0.000000e+00 1354.0
15 TraesCS5A01G261000 chr1A 96.131 827 24 6 3 827 551551816 551550996 0.000000e+00 1343.0
16 TraesCS5A01G261000 chr1A 100.000 29 0 0 1712 1740 12108810 12108838 2.000000e-03 54.7
17 TraesCS5A01G261000 chr3A 96.269 804 27 2 3 804 13072861 13073663 0.000000e+00 1315.0
18 TraesCS5A01G261000 chr3A 95.393 521 23 1 307 826 567653407 567652887 0.000000e+00 828.0
19 TraesCS5A01G261000 chr3A 94.476 525 24 4 307 828 675158991 675158469 0.000000e+00 804.0
20 TraesCS5A01G261000 chr3A 95.425 306 11 3 3 307 675159384 675159081 7.200000e-133 484.0
21 TraesCS5A01G261000 chr3A 95.098 306 12 3 3 307 567653799 567653496 3.350000e-131 479.0
22 TraesCS5A01G261000 chr6A 95.706 489 18 2 307 793 448375202 448374715 0.000000e+00 784.0
23 TraesCS5A01G261000 chr6A 96.050 481 15 3 3 482 604414333 604414810 0.000000e+00 780.0
24 TraesCS5A01G261000 chr6A 95.425 306 11 3 3 307 448375594 448375291 7.200000e-133 484.0
25 TraesCS5A01G261000 chr3D 90.164 366 28 5 1157 1521 501159756 501159398 2.020000e-128 470.0
26 TraesCS5A01G261000 chr7B 89.807 363 30 4 1157 1518 646037728 646037372 4.360000e-125 459.0
27 TraesCS5A01G261000 chr4B 93.791 306 15 4 3 307 35226901 35227203 1.570000e-124 457.0
28 TraesCS5A01G261000 chr6B 88.981 363 33 4 1157 1518 124632628 124632272 4.390000e-120 442.0
29 TraesCS5A01G261000 chr6B 88.686 274 27 2 1238 1510 644070546 644070816 9.920000e-87 331.0
30 TraesCS5A01G261000 chr1B 85.862 290 34 5 1016 1305 634863011 634862729 7.780000e-78 302.0
31 TraesCS5A01G261000 chr1B 85.317 252 30 4 1016 1267 634931565 634931321 2.210000e-63 254.0
32 TraesCS5A01G261000 chr3B 78.339 277 42 7 1006 1282 449163846 449163588 3.830000e-36 163.0
33 TraesCS5A01G261000 chr2A 94.286 35 0 1 1712 1746 18658921 18658889 9.000000e-03 52.8


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 TraesCS5A01G261000 chr5A 474828943 474833726 4783 True 8835.00 8835 100.0000 1 4784 1 chr5A.!!$R1 4783
1 TraesCS5A01G261000 chr5D 371797438 371801541 4103 True 1339.00 2405 91.1070 864 4784 4 chr5D.!!$R1 3920
2 TraesCS5A01G261000 chr5D 550181277 550181794 517 False 780.00 780 93.8700 307 825 1 chr5D.!!$F1 518
3 TraesCS5A01G261000 chr5B 441646849 441651129 4280 True 1021.78 2274 92.1824 830 4784 5 chr5B.!!$R1 3954
4 TraesCS5A01G261000 chr4A 5059831 5060655 824 False 1391.00 1391 97.0980 3 827 1 chr4A.!!$F1 824
5 TraesCS5A01G261000 chr1A 494428562 494429384 822 False 1354.00 1354 96.3590 3 825 1 chr1A.!!$F2 822
6 TraesCS5A01G261000 chr1A 551550996 551551816 820 True 1343.00 1343 96.1310 3 827 1 chr1A.!!$R1 824
7 TraesCS5A01G261000 chr3A 13072861 13073663 802 False 1315.00 1315 96.2690 3 804 1 chr3A.!!$F1 801
8 TraesCS5A01G261000 chr3A 567652887 567653799 912 True 653.50 828 95.2455 3 826 2 chr3A.!!$R1 823
9 TraesCS5A01G261000 chr3A 675158469 675159384 915 True 644.00 804 94.9505 3 828 2 chr3A.!!$R2 825
10 TraesCS5A01G261000 chr6A 448374715 448375594 879 True 634.00 784 95.5655 3 793 2 chr6A.!!$R1 790

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
946 1045 0.107459 GCACAGCAAAACCCCCAAAA 60.107 50.0 0.00 0.0 0.00 2.44 F
1447 1547 0.247736 ACTGGTCTCATCGCTGTTCC 59.752 55.0 0.00 0.0 0.00 3.62 F
1872 2073 0.323451 GGAGCCTTGGGGGTAAGTTG 60.323 60.0 0.00 0.0 44.22 3.16 F
1877 2078 0.611896 CTTGGGGGTAAGTTGGCCTG 60.612 60.0 3.32 0.0 0.00 4.85 F
3201 3744 0.246360 GGGCTTTGTAACATGGCACC 59.754 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2564 0.108992 TAGCAGCAACGGTAAGTCGG 60.109 55.0 0.00 0.0 0.00 4.79 R
2977 3520 0.042188 CAGCGGAGACAAACACGTTG 60.042 55.0 0.00 0.0 43.43 4.10 R
3187 3730 0.312416 GCAACGGTGCCATGTTACAA 59.688 50.0 16.48 0.0 45.68 2.41 R
3434 4090 1.286248 GGGGTGTCAGTATGGGAACT 58.714 55.0 0.00 0.0 36.16 3.01 R
4379 5058 0.179215 GCGAAGAAGACATTGGTGCG 60.179 55.0 0.00 0.0 0.00 5.34 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
221 223 6.947464 TGGACCAATTTTACCAACTTTTTGA 58.053 32.000 0.00 0.00 34.24 2.69
362 456 6.758886 CAGGTGTATAGAGGTTGAATCACTTC 59.241 42.308 0.00 0.00 0.00 3.01
490 585 3.181485 GGTGATGTTTTTCGTGGTTTCCA 60.181 43.478 0.00 0.00 0.00 3.53
588 684 1.620822 GGCAGGTGGATGTTTCTTGT 58.379 50.000 0.00 0.00 0.00 3.16
773 872 1.072505 GGAGGGACGCAGGTTTTCA 59.927 57.895 0.00 0.00 0.00 2.69
827 926 0.527565 GGTGGTTAGTCGCGTCCTTA 59.472 55.000 5.77 0.00 0.00 2.69
828 927 1.622232 GTGGTTAGTCGCGTCCTTAC 58.378 55.000 5.77 7.53 0.00 2.34
922 1021 0.307146 CGTCTCGTTATCCTCGACCC 59.693 60.000 0.00 0.00 33.71 4.46
924 1023 0.178767 TCTCGTTATCCTCGACCCGA 59.821 55.000 0.00 0.00 33.71 5.14
946 1045 0.107459 GCACAGCAAAACCCCCAAAA 60.107 50.000 0.00 0.00 0.00 2.44
1015 1115 1.602323 GAAATGGCGACCACCACCA 60.602 57.895 0.50 0.00 44.17 4.17
1016 1116 1.862602 GAAATGGCGACCACCACCAC 61.863 60.000 0.50 0.00 44.17 4.16
1017 1117 3.860930 AATGGCGACCACCACCACC 62.861 63.158 0.50 0.00 44.17 4.61
1066 1166 4.760047 CCCACCGCCGACTCCTTG 62.760 72.222 0.00 0.00 0.00 3.61
1418 1518 0.299895 CACATCGTGAGCATTCGAGC 59.700 55.000 3.90 0.00 39.38 5.03
1447 1547 0.247736 ACTGGTCTCATCGCTGTTCC 59.752 55.000 0.00 0.00 0.00 3.62
1467 1568 2.288763 CCGCTTGGTTAATTGGTTTGCT 60.289 45.455 0.00 0.00 0.00 3.91
1468 1569 3.389221 CGCTTGGTTAATTGGTTTGCTT 58.611 40.909 0.00 0.00 0.00 3.91
1469 1570 3.184178 CGCTTGGTTAATTGGTTTGCTTG 59.816 43.478 0.00 0.00 0.00 4.01
1470 1571 4.126437 GCTTGGTTAATTGGTTTGCTTGT 58.874 39.130 0.00 0.00 0.00 3.16
1491 1593 4.098044 TGTTATGCGTCTCTAGCTAAGCTT 59.902 41.667 3.48 3.48 40.44 3.74
1521 1623 0.897621 TTGCGAGATGGAGCTCTCAA 59.102 50.000 14.64 0.00 41.49 3.02
1526 1628 3.242673 GCGAGATGGAGCTCTCAATTTTG 60.243 47.826 14.64 5.96 41.49 2.44
1576 1678 8.146412 AGAAATAGACCGTGTTTTAGTACTTGT 58.854 33.333 0.00 0.00 0.00 3.16
1587 1689 2.474410 AGTACTTGTACCTTGCCTGC 57.526 50.000 7.24 0.00 0.00 4.85
1654 1762 9.881529 ATGTTTCATGATTTGTTTTGCATTTAC 57.118 25.926 0.00 0.00 0.00 2.01
1687 1796 9.136952 CCTTTTCTCTGAAATCTTTGCTTAATG 57.863 33.333 0.00 0.00 0.00 1.90
1755 1947 9.877178 GGGAGTATATTAGTATTTGAGTCCATG 57.123 37.037 0.00 0.00 0.00 3.66
1776 1968 8.872134 TCCATGGTAATCGATAATGGTAACTTA 58.128 33.333 12.58 5.99 39.10 2.24
1777 1969 9.667107 CCATGGTAATCGATAATGGTAACTTAT 57.333 33.333 2.57 0.00 34.35 1.73
1846 2047 7.397221 TGTTGTGAGGGATAATATCATCATCC 58.603 38.462 9.59 0.00 38.00 3.51
1854 2055 9.168553 AGGGATAATATCATCATCCTCAATAGG 57.831 37.037 2.41 0.00 45.21 2.57
1872 2073 0.323451 GGAGCCTTGGGGGTAAGTTG 60.323 60.000 0.00 0.00 44.22 3.16
1877 2078 0.611896 CTTGGGGGTAAGTTGGCCTG 60.612 60.000 3.32 0.00 0.00 4.85
1898 2099 6.633856 CCTGAATTAGGCTGCTTAAAATGTT 58.366 36.000 8.33 0.00 40.38 2.71
1899 2100 7.099120 CCTGAATTAGGCTGCTTAAAATGTTT 58.901 34.615 8.33 0.00 40.38 2.83
1900 2101 7.603784 CCTGAATTAGGCTGCTTAAAATGTTTT 59.396 33.333 8.33 0.00 40.38 2.43
1902 2103 9.988815 TGAATTAGGCTGCTTAAAATGTTTTAA 57.011 25.926 8.33 9.56 39.53 1.52
1937 2405 4.142730 GCTCTATCAGTTGCACTTTTGAGG 60.143 45.833 0.00 0.00 0.00 3.86
1990 2458 6.534475 TTATTTCTCTGCTGGAATGCAAAT 57.466 33.333 0.00 0.00 42.83 2.32
2043 2563 2.092753 AGTGTTCCCATATGCTCCAGTG 60.093 50.000 0.00 0.00 0.00 3.66
2044 2564 1.312815 GTTCCCATATGCTCCAGTGC 58.687 55.000 0.00 0.00 0.00 4.40
2054 2575 1.153823 CTCCAGTGCCGACTTACCG 60.154 63.158 0.00 0.00 0.00 4.02
2056 2577 1.005394 CCAGTGCCGACTTACCGTT 60.005 57.895 0.00 0.00 0.00 4.44
2077 2598 3.595173 TGCTGCTACAACGTGATAACAT 58.405 40.909 0.00 0.00 0.00 2.71
2078 2599 4.000325 TGCTGCTACAACGTGATAACATT 59.000 39.130 0.00 0.00 0.00 2.71
2111 2632 8.299262 TCTCTTTCTCAAGAAAATTAGTGACG 57.701 34.615 6.64 0.00 42.72 4.35
2112 2633 8.141909 TCTCTTTCTCAAGAAAATTAGTGACGA 58.858 33.333 6.64 0.00 42.72 4.20
2113 2634 8.657074 TCTTTCTCAAGAAAATTAGTGACGAA 57.343 30.769 6.64 0.00 42.72 3.85
2114 2635 8.548721 TCTTTCTCAAGAAAATTAGTGACGAAC 58.451 33.333 6.64 0.00 42.72 3.95
2150 2671 6.620877 ACATTTACATCCACTTCCACTAGA 57.379 37.500 0.00 0.00 0.00 2.43
2157 2678 5.544176 ACATCCACTTCCACTAGAGAAAGAA 59.456 40.000 0.00 0.00 0.00 2.52
2158 2679 6.043243 ACATCCACTTCCACTAGAGAAAGAAA 59.957 38.462 0.00 0.00 0.00 2.52
2190 2711 6.547510 AGATCAGTTATTATGGGAAAACTGGC 59.452 38.462 12.59 6.87 45.62 4.85
2203 2725 0.752658 AACTGGCAACTTTTCAGGGC 59.247 50.000 0.00 0.00 33.19 5.19
2230 2752 3.670625 TCCAATGTATATAGCAACCCGC 58.329 45.455 0.00 0.00 42.91 6.13
2324 2846 6.294231 GCTTCAGATCCATCGTAGAATGAGTA 60.294 42.308 0.00 0.00 43.58 2.59
2347 2869 6.336842 AGAATTGACCTGGAAGTTGAATTG 57.663 37.500 0.00 0.00 0.00 2.32
2386 2908 4.881850 GGTATGGAGATCATTTCACCGTTT 59.118 41.667 0.00 0.00 37.88 3.60
2426 2948 6.995686 TCCTTGTTTACTTCTTAATGTGCAGA 59.004 34.615 0.00 0.00 0.00 4.26
2531 3053 4.931914 AGGTACTGCTCCTTAACTCAGTA 58.068 43.478 0.00 0.00 40.01 2.74
2533 3055 4.705991 GGTACTGCTCCTTAACTCAGTAGT 59.294 45.833 0.00 0.00 41.13 2.73
2534 3056 6.976877 AGGTACTGCTCCTTAACTCAGTAGTT 60.977 42.308 0.00 0.00 43.45 2.24
2561 3083 4.822026 AGAGTTACTCACCATGCAGTTAC 58.178 43.478 15.23 0.00 32.06 2.50
2571 3093 5.643348 TCACCATGCAGTTACTGAACATAAG 59.357 40.000 17.40 8.19 38.10 1.73
2608 3130 6.621613 GTCCCATCTTTTTCCTTGTGAATAC 58.378 40.000 0.00 0.00 31.67 1.89
2646 3168 8.958506 ACGTCATATACTCTGTTAGAAGAAAGT 58.041 33.333 0.00 0.00 0.00 2.66
2717 3239 1.554160 CAATCAGGCTCTGAGGTGAGT 59.446 52.381 6.83 0.00 44.08 3.41
2726 3248 3.378427 GCTCTGAGGTGAGTTTTTGTTGT 59.622 43.478 6.83 0.00 36.51 3.32
2811 3333 3.270877 CATACTGTACCCAGAAGTTGCC 58.729 50.000 0.00 0.00 41.50 4.52
2865 3387 3.585990 CCACGGAATGCGGATGCC 61.586 66.667 3.21 3.21 41.78 4.40
2866 3388 2.514592 CACGGAATGCGGATGCCT 60.515 61.111 12.75 0.00 41.78 4.75
2889 3411 6.094186 CCTTGAGAGCAAAGGTTCTTATAACC 59.906 42.308 0.00 0.00 40.58 2.85
2924 3467 9.371136 GTTCAGAATTTTCTTTTCCTGAAAACT 57.629 29.630 0.00 0.00 43.34 2.66
2931 3474 5.262588 TCTTTTCCTGAAAACTCCTTTGC 57.737 39.130 1.04 0.00 35.57 3.68
2933 3476 5.186797 TCTTTTCCTGAAAACTCCTTTGCAA 59.813 36.000 0.00 0.00 35.57 4.08
2945 3488 4.646492 ACTCCTTTGCAATGTCAAGTTCTT 59.354 37.500 0.00 0.00 0.00 2.52
2950 3493 3.565307 TGCAATGTCAAGTTCTTTCCCT 58.435 40.909 0.00 0.00 0.00 4.20
2967 3510 1.367471 CTTCACTCCACAGACGGCA 59.633 57.895 0.00 0.00 0.00 5.69
2973 3516 0.868406 CTCCACAGACGGCAAAAGTC 59.132 55.000 0.00 0.00 38.81 3.01
2974 3517 0.878523 TCCACAGACGGCAAAAGTCG 60.879 55.000 0.00 0.00 42.97 4.18
2975 3518 1.569493 CACAGACGGCAAAAGTCGG 59.431 57.895 0.00 0.00 42.97 4.79
2976 3519 2.251642 ACAGACGGCAAAAGTCGGC 61.252 57.895 0.00 0.00 42.97 5.54
2977 3520 2.668550 AGACGGCAAAAGTCGGCC 60.669 61.111 0.00 0.00 46.80 6.13
2982 3525 2.719354 GCAAAAGTCGGCCAACGT 59.281 55.556 2.24 0.00 44.69 3.99
2990 3533 1.153329 TCGGCCAACGTGTTTGTCT 60.153 52.632 2.24 0.00 44.69 3.41
2994 3537 1.278637 CCAACGTGTTTGTCTCCGC 59.721 57.895 0.00 0.00 32.71 5.54
3053 3596 6.633856 AGAAAATGTGGAATGCTATGAAACC 58.366 36.000 0.00 0.00 0.00 3.27
3055 3598 3.342377 TGTGGAATGCTATGAAACCGA 57.658 42.857 0.00 0.00 0.00 4.69
3056 3599 3.680490 TGTGGAATGCTATGAAACCGAA 58.320 40.909 0.00 0.00 0.00 4.30
3057 3600 4.269183 TGTGGAATGCTATGAAACCGAAT 58.731 39.130 0.00 0.00 0.00 3.34
3066 3609 7.490962 TGCTATGAAACCGAATACATTTAGG 57.509 36.000 0.00 0.00 0.00 2.69
3076 3619 9.807921 AACCGAATACATTTAGGGATTTGATAT 57.192 29.630 0.00 0.00 0.00 1.63
3097 3640 1.557371 TGTTACGGAGCATGGGATTGA 59.443 47.619 0.00 0.00 0.00 2.57
3110 3653 5.644644 CATGGGATTGAGTTAAGAAGCAAC 58.355 41.667 0.00 0.00 0.00 4.17
3163 3706 5.068198 GGATGGTGTTCTTTGCATCACATAT 59.932 40.000 0.00 0.00 33.17 1.78
3165 3708 5.008980 TGGTGTTCTTTGCATCACATATCA 58.991 37.500 0.00 0.00 33.17 2.15
3166 3709 5.653330 TGGTGTTCTTTGCATCACATATCAT 59.347 36.000 0.00 0.00 33.17 2.45
3167 3710 6.183360 TGGTGTTCTTTGCATCACATATCATC 60.183 38.462 0.00 0.00 33.17 2.92
3187 3730 4.640771 TCAGATGTTAGAAACTGGGCTT 57.359 40.909 0.00 0.00 0.00 4.35
3196 3739 4.853924 AGAAACTGGGCTTTGTAACATG 57.146 40.909 0.00 0.00 0.00 3.21
3201 3744 0.246360 GGGCTTTGTAACATGGCACC 59.754 55.000 0.00 0.00 0.00 5.01
3240 3783 9.337396 TGAGTACAAGTATCACATTTGTTTTCT 57.663 29.630 0.00 0.00 38.06 2.52
3279 3934 5.262588 TCTGCTAGTTTATTCATCAGCGA 57.737 39.130 0.00 0.00 0.00 4.93
3281 3936 6.283694 TCTGCTAGTTTATTCATCAGCGAAT 58.716 36.000 0.00 0.00 39.03 3.34
3284 3939 8.244494 TGCTAGTTTATTCATCAGCGAATATC 57.756 34.615 0.00 0.00 37.62 1.63
3294 3949 1.605710 CAGCGAATATCCCAAAGGCTG 59.394 52.381 0.00 0.00 40.16 4.85
3328 3984 4.700700 TCCAGTTCTGCACATCTATCATG 58.299 43.478 0.00 0.00 0.00 3.07
3337 3993 2.288729 CACATCTATCATGTGGTTGCCG 59.711 50.000 6.80 0.00 44.04 5.69
3346 4002 1.686355 TGTGGTTGCCGACATCTTTT 58.314 45.000 0.00 0.00 0.00 2.27
3347 4003 1.336440 TGTGGTTGCCGACATCTTTTG 59.664 47.619 0.00 0.00 0.00 2.44
3434 4090 5.453762 CCACATGCATCTGTCTGAGGTAATA 60.454 44.000 0.00 0.00 0.00 0.98
3462 4118 0.341961 ACTGACACCCCCTAGCCATA 59.658 55.000 0.00 0.00 0.00 2.74
3476 4137 1.635487 AGCCATAGAGCTTTGGGACAA 59.365 47.619 11.81 0.00 41.41 3.18
3500 4161 9.286170 CAATTCTGATGATGAGGAGATATTTGT 57.714 33.333 0.00 0.00 0.00 2.83
3596 4258 9.905713 TTTAGAAATGAGGCAATTATACTCACT 57.094 29.630 7.74 4.85 43.29 3.41
3650 4312 9.865321 GTATGTAACCAGTGAACTATCAAACTA 57.135 33.333 0.00 0.00 37.30 2.24
3651 4313 8.773404 ATGTAACCAGTGAACTATCAAACTAC 57.227 34.615 0.00 0.00 37.30 2.73
3660 4324 9.561069 AGTGAACTATCAAACTACTGTGAAAAT 57.439 29.630 0.00 0.00 37.30 1.82
3870 4534 2.687935 ACTGCCACTTTGTTGACGAATT 59.312 40.909 0.00 0.00 0.00 2.17
4019 4683 8.870116 ACTTGCATATGTAGGATATTCTGTACA 58.130 33.333 9.88 0.00 0.00 2.90
4149 4813 6.576185 ACTGCATGAAATTTATTAGGCCTTG 58.424 36.000 12.58 0.00 0.00 3.61
4170 4834 5.957842 TGAAGTGGCAAATATCTTTTCGT 57.042 34.783 0.00 0.00 0.00 3.85
4173 4837 6.150976 TGAAGTGGCAAATATCTTTTCGTGAT 59.849 34.615 0.00 0.00 0.00 3.06
4177 4841 8.131100 AGTGGCAAATATCTTTTCGTGATTATG 58.869 33.333 0.00 0.00 0.00 1.90
4244 4921 8.492673 TTGCTTCAGTACCATTTAAGTATCTG 57.507 34.615 0.00 0.00 0.00 2.90
4245 4922 7.047891 TGCTTCAGTACCATTTAAGTATCTGG 58.952 38.462 0.00 0.00 34.84 3.86
4246 4923 6.017852 GCTTCAGTACCATTTAAGTATCTGGC 60.018 42.308 0.00 0.00 31.72 4.85
4264 4941 4.081142 TCTGGCGTGAAGAAATATCCTGAA 60.081 41.667 0.00 0.00 0.00 3.02
4358 5037 4.037927 AGCAGGCCTTTTAGTATCTGGTA 58.962 43.478 0.00 0.00 32.27 3.25
4361 5040 6.329197 AGCAGGCCTTTTAGTATCTGGTAATA 59.671 38.462 0.00 0.00 32.27 0.98
4368 5047 9.561069 CCTTTTAGTATCTGGTAATAGCACAAT 57.439 33.333 0.00 0.00 0.00 2.71
4379 5058 5.755861 GGTAATAGCACAATGAGGTCTCTTC 59.244 44.000 0.00 0.00 0.00 2.87
4389 5068 0.687354 AGGTCTCTTCGCACCAATGT 59.313 50.000 0.00 0.00 34.80 2.71
4581 5260 2.136026 GGATATTGGGGGAGTTGTCCT 58.864 52.381 0.00 0.00 43.36 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.379813 CCAGAATGTGTGCATTGAGTAACC 60.380 45.833 0.00 0.00 44.61 2.85
1 2 4.216257 ACCAGAATGTGTGCATTGAGTAAC 59.784 41.667 0.00 0.00 44.61 2.50
336 430 5.721960 AGTGATTCAACCTCTATACACCTGT 59.278 40.000 0.00 0.00 0.00 4.00
542 638 3.010226 TTCTCTCCTCCCTCCCCGG 62.010 68.421 0.00 0.00 0.00 5.73
550 646 1.036707 CCCGATCAGTTCTCTCCTCC 58.963 60.000 0.00 0.00 0.00 4.30
588 684 6.697641 AAACCTAGTTTCTTACCTCCATCA 57.302 37.500 0.00 0.00 28.86 3.07
704 803 2.046864 CGACCCAGCCTTCTCTCGA 61.047 63.158 0.00 0.00 0.00 4.04
837 936 9.374838 TCGTCTAATTTGTCCTAAATACCTTTC 57.625 33.333 0.00 0.00 0.00 2.62
922 1021 1.576421 GGGTTTTGCTGTGCTCTCG 59.424 57.895 0.00 0.00 0.00 4.04
924 1023 1.531602 GGGGGTTTTGCTGTGCTCT 60.532 57.895 0.00 0.00 0.00 4.09
1015 1115 1.305381 CGAGGGAGAAGAGGGTGGT 60.305 63.158 0.00 0.00 0.00 4.16
1016 1116 2.726351 GCGAGGGAGAAGAGGGTGG 61.726 68.421 0.00 0.00 0.00 4.61
1017 1117 2.726351 GGCGAGGGAGAAGAGGGTG 61.726 68.421 0.00 0.00 0.00 4.61
1018 1118 2.364448 GGCGAGGGAGAAGAGGGT 60.364 66.667 0.00 0.00 0.00 4.34
1418 1518 3.604582 GATGAGACCAGTCAGAAAAGGG 58.395 50.000 0.00 0.00 0.00 3.95
1447 1547 3.025287 AGCAAACCAATTAACCAAGCG 57.975 42.857 0.00 0.00 0.00 4.68
1467 1568 4.098044 AGCTTAGCTAGAGACGCATAACAA 59.902 41.667 4.30 0.00 36.99 2.83
1468 1569 3.632604 AGCTTAGCTAGAGACGCATAACA 59.367 43.478 4.30 0.00 36.99 2.41
1469 1570 4.231718 AGCTTAGCTAGAGACGCATAAC 57.768 45.455 4.30 0.00 36.99 1.89
1470 1571 4.920640 AAGCTTAGCTAGAGACGCATAA 57.079 40.909 7.32 0.00 38.25 1.90
1549 1651 9.630098 CAAGTACTAAAACACGGTCTATTTCTA 57.370 33.333 0.00 0.00 0.00 2.10
1552 1654 9.196552 GTACAAGTACTAAAACACGGTCTATTT 57.803 33.333 0.00 0.00 33.45 1.40
1560 1662 5.333568 GGCAAGGTACAAGTACTAAAACACG 60.334 44.000 9.94 0.00 36.36 4.49
1567 1669 2.901192 TGCAGGCAAGGTACAAGTACTA 59.099 45.455 9.94 0.00 36.36 1.82
1576 1678 2.315176 ACATGTTTTGCAGGCAAGGTA 58.685 42.857 6.81 0.00 37.24 3.08
1587 1689 4.361420 TGCATCACACAGAACATGTTTTG 58.639 39.130 23.52 23.52 41.41 2.44
1641 1749 8.779354 AAAAGGTTAACTGTAAATGCAAAACA 57.221 26.923 5.42 0.00 0.00 2.83
1654 1762 9.455847 CAAAGATTTCAGAGAAAAGGTTAACTG 57.544 33.333 5.42 0.00 0.00 3.16
1724 1833 9.884814 ACTCAAATACTAATATACTCCCTCTGT 57.115 33.333 0.00 0.00 0.00 3.41
1726 1835 9.536510 GGACTCAAATACTAATATACTCCCTCT 57.463 37.037 0.00 0.00 0.00 3.69
1727 1836 9.310449 TGGACTCAAATACTAATATACTCCCTC 57.690 37.037 0.00 0.00 0.00 4.30
1728 1837 9.845214 ATGGACTCAAATACTAATATACTCCCT 57.155 33.333 0.00 0.00 0.00 4.20
1729 1838 9.877178 CATGGACTCAAATACTAATATACTCCC 57.123 37.037 0.00 0.00 0.00 4.30
1730 1839 9.877178 CCATGGACTCAAATACTAATATACTCC 57.123 37.037 5.56 0.00 0.00 3.85
1846 2047 0.475906 CCCCCAAGGCTCCTATTGAG 59.524 60.000 0.00 0.00 44.47 3.02
1854 2055 0.323451 CCAACTTACCCCCAAGGCTC 60.323 60.000 0.00 0.00 40.58 4.70
1855 2056 1.774300 CCAACTTACCCCCAAGGCT 59.226 57.895 0.00 0.00 40.58 4.58
1856 2057 1.982395 GCCAACTTACCCCCAAGGC 60.982 63.158 0.00 0.00 40.58 4.35
1857 2058 1.304962 GGCCAACTTACCCCCAAGG 60.305 63.158 0.00 0.00 43.78 3.61
1858 2059 0.611896 CAGGCCAACTTACCCCCAAG 60.612 60.000 5.01 0.00 0.00 3.61
1898 2099 9.905713 ACTGATAGAGCAAGGTGATTATTTAAA 57.094 29.630 0.00 0.00 0.00 1.52
1899 2100 9.905713 AACTGATAGAGCAAGGTGATTATTTAA 57.094 29.630 0.00 0.00 0.00 1.52
1900 2101 9.330063 CAACTGATAGAGCAAGGTGATTATTTA 57.670 33.333 0.00 0.00 0.00 1.40
1902 2103 6.261826 GCAACTGATAGAGCAAGGTGATTATT 59.738 38.462 0.00 0.00 0.00 1.40
1966 2434 5.981088 TTGCATTCCAGCAGAGAAATAAA 57.019 34.783 0.00 0.00 46.54 1.40
2043 2563 3.023591 GCAGCAACGGTAAGTCGGC 62.024 63.158 0.00 0.00 34.48 5.54
2044 2564 0.108992 TAGCAGCAACGGTAAGTCGG 60.109 55.000 0.00 0.00 0.00 4.79
2054 2575 3.185594 TGTTATCACGTTGTAGCAGCAAC 59.814 43.478 11.77 11.77 43.68 4.17
2056 2577 3.033368 TGTTATCACGTTGTAGCAGCA 57.967 42.857 0.00 0.00 0.00 4.41
2085 2606 8.930760 CGTCACTAATTTTCTTGAGAAAGAGAT 58.069 33.333 6.32 0.00 43.90 2.75
2086 2607 8.141909 TCGTCACTAATTTTCTTGAGAAAGAGA 58.858 33.333 6.32 0.00 43.90 3.10
2087 2608 8.299262 TCGTCACTAATTTTCTTGAGAAAGAG 57.701 34.615 6.32 7.92 43.90 2.85
2088 2609 8.548721 GTTCGTCACTAATTTTCTTGAGAAAGA 58.451 33.333 6.32 0.00 43.90 2.52
2089 2610 8.552034 AGTTCGTCACTAATTTTCTTGAGAAAG 58.448 33.333 6.32 0.00 38.44 2.62
2090 2611 8.433421 AGTTCGTCACTAATTTTCTTGAGAAA 57.567 30.769 2.16 2.16 36.74 2.52
2091 2612 7.926555 AGAGTTCGTCACTAATTTTCTTGAGAA 59.073 33.333 0.00 0.00 35.01 2.87
2092 2613 7.434492 AGAGTTCGTCACTAATTTTCTTGAGA 58.566 34.615 0.00 0.00 35.01 3.27
2093 2614 7.644986 AGAGTTCGTCACTAATTTTCTTGAG 57.355 36.000 0.00 0.00 35.01 3.02
2094 2615 9.706691 ATAAGAGTTCGTCACTAATTTTCTTGA 57.293 29.630 0.00 0.00 35.01 3.02
2103 2624 9.917129 TGTTGAAATATAAGAGTTCGTCACTAA 57.083 29.630 0.00 0.00 35.01 2.24
2105 2626 9.436957 AATGTTGAAATATAAGAGTTCGTCACT 57.563 29.630 0.00 0.00 39.07 3.41
2126 2647 7.016153 TCTAGTGGAAGTGGATGTAAATGTT 57.984 36.000 0.00 0.00 0.00 2.71
2170 2691 6.016555 AGTTGCCAGTTTTCCCATAATAACT 58.983 36.000 0.00 0.00 0.00 2.24
2180 2701 3.457234 CCTGAAAAGTTGCCAGTTTTCC 58.543 45.455 21.70 9.50 45.98 3.13
2182 2703 2.419990 GCCCTGAAAAGTTGCCAGTTTT 60.420 45.455 3.13 3.13 38.11 2.43
2183 2704 1.138859 GCCCTGAAAAGTTGCCAGTTT 59.861 47.619 0.00 0.00 0.00 2.66
2186 2707 1.286880 CGCCCTGAAAAGTTGCCAG 59.713 57.895 0.00 0.00 0.00 4.85
2188 2709 2.142357 GACCGCCCTGAAAAGTTGCC 62.142 60.000 0.00 0.00 0.00 4.52
2190 2711 1.266989 GAAGACCGCCCTGAAAAGTTG 59.733 52.381 0.00 0.00 0.00 3.16
2203 2725 5.408604 GGTTGCTATATACATTGGAAGACCG 59.591 44.000 0.00 0.00 39.42 4.79
2230 2752 1.401905 GGCTTCAAATTGTAGAGGCCG 59.598 52.381 11.43 0.00 45.23 6.13
2324 2846 5.244626 CCAATTCAACTTCCAGGTCAATTCT 59.755 40.000 0.00 0.00 0.00 2.40
2347 2869 2.561478 TACCCAAGTCAAGAGCAACC 57.439 50.000 0.00 0.00 0.00 3.77
2419 2941 5.593909 TCTCCTGAAAAAGAAATTCTGCACA 59.406 36.000 0.00 0.00 0.00 4.57
2531 3053 7.620880 TGCATGGTGAGTAACTCTATTAAACT 58.379 34.615 0.00 0.00 0.00 2.66
2533 3055 7.620880 ACTGCATGGTGAGTAACTCTATTAAA 58.379 34.615 0.00 0.00 0.00 1.52
2534 3056 7.182817 ACTGCATGGTGAGTAACTCTATTAA 57.817 36.000 0.00 0.00 0.00 1.40
2561 3083 8.276325 GGACGATAAGCATTAACTTATGTTCAG 58.724 37.037 1.71 0.00 41.76 3.02
2571 3093 6.619801 AAAGATGGGACGATAAGCATTAAC 57.380 37.500 0.00 0.00 32.17 2.01
2583 3105 3.146066 TCACAAGGAAAAAGATGGGACG 58.854 45.455 0.00 0.00 0.00 4.79
2608 3130 3.685139 ATATGACGTAGCCCTTCATGG 57.315 47.619 0.00 0.00 32.24 3.66
2657 3179 4.218312 GACTTCCCTTCAAATGGGCATAT 58.782 43.478 0.00 0.00 44.23 1.78
2717 3239 9.734620 CATTTCTGATTGAGAGTACAACAAAAA 57.265 29.630 0.00 0.00 32.50 1.94
2811 3333 5.902681 TCAGATGTTGTATCTCCGGTAAAG 58.097 41.667 0.00 0.00 0.00 1.85
2865 3387 6.183360 CGGTTATAAGAACCTTTGCTCTCAAG 60.183 42.308 4.53 0.00 38.15 3.02
2866 3388 5.642063 CGGTTATAAGAACCTTTGCTCTCAA 59.358 40.000 4.53 0.00 38.15 3.02
2889 3411 9.118236 GAAAAGAAAATTCTGAACAATACCTCG 57.882 33.333 0.00 0.00 37.65 4.63
2924 3467 5.451798 GGAAAGAACTTGACATTGCAAAGGA 60.452 40.000 1.71 0.00 0.00 3.36
2931 3474 5.300286 AGTGAAGGGAAAGAACTTGACATTG 59.700 40.000 0.00 0.00 33.99 2.82
2933 3476 5.053978 AGTGAAGGGAAAGAACTTGACAT 57.946 39.130 0.00 0.00 33.99 3.06
2945 3488 0.679505 CGTCTGTGGAGTGAAGGGAA 59.320 55.000 0.00 0.00 0.00 3.97
2950 3493 0.179234 TTTGCCGTCTGTGGAGTGAA 59.821 50.000 0.00 0.00 0.00 3.18
2967 3510 0.812549 AAACACGTTGGCCGACTTTT 59.187 45.000 21.11 13.63 40.70 2.27
2975 3518 1.278637 CGGAGACAAACACGTTGGC 59.721 57.895 0.00 0.00 46.81 4.52
2976 3519 1.157870 AGCGGAGACAAACACGTTGG 61.158 55.000 0.00 0.00 41.97 3.77
2977 3520 0.042188 CAGCGGAGACAAACACGTTG 60.042 55.000 0.00 0.00 43.43 4.10
2978 3521 0.461339 ACAGCGGAGACAAACACGTT 60.461 50.000 0.00 0.00 0.00 3.99
2979 3522 0.386476 TACAGCGGAGACAAACACGT 59.614 50.000 0.00 0.00 0.00 4.49
2980 3523 0.782384 GTACAGCGGAGACAAACACG 59.218 55.000 0.00 0.00 0.00 4.49
2981 3524 2.150397 AGTACAGCGGAGACAAACAC 57.850 50.000 0.00 0.00 0.00 3.32
2982 3525 2.902705 AAGTACAGCGGAGACAAACA 57.097 45.000 0.00 0.00 0.00 2.83
2990 3533 6.720112 ACCTAATAATGTAAGTACAGCGGA 57.280 37.500 0.00 0.00 39.92 5.54
3023 3566 8.587608 TCATAGCATTCCACATTTTCTTTTCTT 58.412 29.630 0.00 0.00 0.00 2.52
3066 3609 6.373779 CATGCTCCGTAACAATATCAAATCC 58.626 40.000 0.00 0.00 0.00 3.01
3076 3619 2.026729 TCAATCCCATGCTCCGTAACAA 60.027 45.455 0.00 0.00 0.00 2.83
3078 3621 2.213499 CTCAATCCCATGCTCCGTAAC 58.787 52.381 0.00 0.00 0.00 2.50
3080 3623 1.496060 ACTCAATCCCATGCTCCGTA 58.504 50.000 0.00 0.00 0.00 4.02
3097 3640 6.014156 ACTGTCCATCTAGTTGCTTCTTAACT 60.014 38.462 0.00 0.00 41.06 2.24
3163 3706 4.225942 AGCCCAGTTTCTAACATCTGATGA 59.774 41.667 23.59 1.82 0.00 2.92
3165 3708 4.851639 AGCCCAGTTTCTAACATCTGAT 57.148 40.909 0.00 0.00 0.00 2.90
3166 3709 4.640771 AAGCCCAGTTTCTAACATCTGA 57.359 40.909 0.00 0.00 0.00 3.27
3167 3710 4.520492 ACAAAGCCCAGTTTCTAACATCTG 59.480 41.667 0.00 0.00 0.00 2.90
3180 3723 1.067635 GTGCCATGTTACAAAGCCCAG 60.068 52.381 7.36 0.00 0.00 4.45
3187 3730 0.312416 GCAACGGTGCCATGTTACAA 59.688 50.000 16.48 0.00 45.68 2.41
3268 3923 4.763793 CCTTTGGGATATTCGCTGATGAAT 59.236 41.667 2.01 2.01 37.28 2.57
3277 3932 2.874701 CAGACAGCCTTTGGGATATTCG 59.125 50.000 0.00 0.00 33.58 3.34
3279 3934 4.018050 AGTTCAGACAGCCTTTGGGATATT 60.018 41.667 0.00 0.00 33.58 1.28
3281 3936 2.912956 AGTTCAGACAGCCTTTGGGATA 59.087 45.455 0.00 0.00 33.58 2.59
3284 3939 1.882623 GAAGTTCAGACAGCCTTTGGG 59.117 52.381 0.00 0.00 0.00 4.12
3328 3984 1.606668 TCAAAAGATGTCGGCAACCAC 59.393 47.619 0.00 0.00 0.00 4.16
3337 3993 5.334337 GCCTGCCAAAATTTCAAAAGATGTC 60.334 40.000 0.00 0.00 0.00 3.06
3346 4002 1.767681 AGGTTGCCTGCCAAAATTTCA 59.232 42.857 0.00 0.00 34.68 2.69
3347 4003 2.549064 AGGTTGCCTGCCAAAATTTC 57.451 45.000 0.00 0.00 34.68 2.17
3434 4090 1.286248 GGGGTGTCAGTATGGGAACT 58.714 55.000 0.00 0.00 36.16 3.01
3462 4118 3.795688 TCAGAATTGTCCCAAAGCTCT 57.204 42.857 0.00 0.00 0.00 4.09
3508 4169 9.435570 AGGGTTTATGTTAGTGACTGATAGTAT 57.564 33.333 0.00 0.00 0.00 2.12
3631 4293 6.041637 TCACAGTAGTTTGATAGTTCACTGGT 59.958 38.462 0.00 0.00 29.62 4.00
3650 4312 6.540189 GGTCAGATATGTAGCATTTTCACAGT 59.460 38.462 0.00 0.00 0.00 3.55
3651 4313 6.539826 TGGTCAGATATGTAGCATTTTCACAG 59.460 38.462 0.00 0.00 0.00 3.66
3660 4324 7.791029 TGATAGTTTTGGTCAGATATGTAGCA 58.209 34.615 0.00 0.00 0.00 3.49
4091 4755 1.398692 TGTGTTTCTTGCCCTTCACC 58.601 50.000 0.00 0.00 0.00 4.02
4149 4813 5.938322 TCACGAAAAGATATTTGCCACTTC 58.062 37.500 0.00 0.00 0.00 3.01
4173 4837 9.812347 AGGAATATGATATTTGCCACTTCATAA 57.188 29.630 0.00 0.00 34.12 1.90
4177 4841 6.071728 CCCAGGAATATGATATTTGCCACTTC 60.072 42.308 0.00 0.00 0.00 3.01
4217 4894 9.113838 AGATACTTAAATGGTACTGAAGCAATG 57.886 33.333 0.00 0.00 39.48 2.82
4244 4921 3.938963 TGTTCAGGATATTTCTTCACGCC 59.061 43.478 0.00 0.00 0.00 5.68
4245 4922 5.545658 TTGTTCAGGATATTTCTTCACGC 57.454 39.130 0.00 0.00 0.00 5.34
4246 4923 7.307493 TCATTGTTCAGGATATTTCTTCACG 57.693 36.000 0.00 0.00 0.00 4.35
4278 4955 2.034179 GGAAGAAAAGGGGTTCACAACG 59.966 50.000 0.00 0.00 0.00 4.10
4358 5037 4.437239 CGAAGAGACCTCATTGTGCTATT 58.563 43.478 0.00 0.00 0.00 1.73
4361 5040 1.674221 GCGAAGAGACCTCATTGTGCT 60.674 52.381 0.00 0.00 0.00 4.40
4368 5047 0.976641 ATTGGTGCGAAGAGACCTCA 59.023 50.000 0.00 0.00 32.98 3.86
4379 5058 0.179215 GCGAAGAAGACATTGGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
4389 5068 5.066634 CCACAGAGAGTATAAGCGAAGAAGA 59.933 44.000 0.00 0.00 0.00 2.87
4581 5260 4.792068 CTTAACCTGGATTGCCCTTATGA 58.208 43.478 0.00 0.00 35.38 2.15


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

AutoCloner maintained by Alex Coulton.