Multiple sequence alignment - TraesCS5A01G412800

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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 TraesCS5A01G412800 chr5A 100.000 4113 0 0 1 4113 601344565 601340453 0.000000e+00 7596.0
1 TraesCS5A01G412800 chr5A 89.495 1485 110 22 2638 4113 601256333 601254886 0.000000e+00 1836.0
2 TraesCS5A01G412800 chr5A 83.197 1589 147 57 2098 3621 601087308 601085775 0.000000e+00 1345.0
3 TraesCS5A01G412800 chr5A 87.172 1029 90 23 2635 3629 600503647 600502627 0.000000e+00 1131.0
4 TraesCS5A01G412800 chr5A 84.605 760 60 17 1888 2626 601257297 601256574 0.000000e+00 702.0
5 TraesCS5A01G412800 chr5A 88.645 502 40 6 2681 3167 601166999 601166500 2.740000e-166 595.0
6 TraesCS5A01G412800 chr5A 88.377 456 26 7 932 1366 601258388 601257939 1.310000e-144 523.0
7 TraesCS5A01G412800 chr5A 83.898 472 59 11 3628 4093 601482890 601482430 6.310000e-118 435.0
8 TraesCS5A01G412800 chr5A 83.054 478 38 23 926 1374 600504919 600504456 1.070000e-105 394.0
9 TraesCS5A01G412800 chr5A 81.690 355 60 5 3716 4067 600502494 600502142 1.450000e-74 291.0
10 TraesCS5A01G412800 chr5A 77.844 501 53 21 2172 2626 600504364 600503876 1.470000e-64 257.0
11 TraesCS5A01G412800 chr5A 92.121 165 13 0 3915 4079 601245328 601245164 2.470000e-57 233.0
12 TraesCS5A01G412800 chr5A 77.230 426 52 18 3392 3777 601155977 601155557 1.500000e-49 207.0
13 TraesCS5A01G412800 chr5A 81.227 277 24 3 1604 1868 601257674 601257414 9.020000e-47 198.0
14 TraesCS5A01G412800 chr5A 85.294 170 10 2 2472 2626 601098760 601098591 1.180000e-35 161.0
15 TraesCS5A01G412800 chr5A 76.316 266 33 9 2210 2454 601168398 601168142 9.340000e-22 115.0
16 TraesCS5A01G412800 chr5A 89.706 68 1 4 3558 3623 601498605 601498542 9.480000e-12 82.4
17 TraesCS5A01G412800 chr5B 93.001 1486 71 13 2648 4113 590806043 590804571 0.000000e+00 2137.0
18 TraesCS5A01G412800 chr5B 85.914 2144 133 68 606 2626 590808326 590806229 0.000000e+00 2130.0
19 TraesCS5A01G412800 chr5B 87.769 1022 84 20 2639 3623 590183548 590182531 0.000000e+00 1157.0
20 TraesCS5A01G412800 chr5B 86.938 467 45 6 2638 3088 590256481 590256015 1.020000e-140 510.0
21 TraesCS5A01G412800 chr5B 84.165 461 43 19 926 1366 590184899 590184449 1.770000e-113 420.0
22 TraesCS5A01G412800 chr5B 82.549 510 31 10 2098 2592 590503167 590502701 2.980000e-106 396.0
23 TraesCS5A01G412800 chr5B 78.947 456 60 16 2889 3323 590613630 590613190 1.130000e-70 278.0
24 TraesCS5A01G412800 chr5B 88.646 229 21 1 1138 1366 590530760 590530537 1.460000e-69 274.0
25 TraesCS5A01G412800 chr5B 88.199 161 16 3 3716 3874 590181891 590181732 5.430000e-44 189.0
26 TraesCS5A01G412800 chr5B 89.286 140 15 0 1149 1288 590456604 590456465 4.230000e-40 176.0
27 TraesCS5A01G412800 chr5B 87.333 150 18 1 3628 3777 590606208 590606060 1.970000e-38 171.0
28 TraesCS5A01G412800 chr5B 91.304 69 6 0 1978 2046 590455521 590455453 1.220000e-15 95.3
29 TraesCS5A01G412800 chr5D 90.891 1493 97 15 2639 4102 481761195 481759713 0.000000e+00 1967.0
30 TraesCS5A01G412800 chr5D 84.805 1257 119 41 2635 3827 481564308 481563060 0.000000e+00 1197.0
31 TraesCS5A01G412800 chr5D 86.079 783 77 20 2638 3403 481643433 481642666 0.000000e+00 813.0
32 TraesCS5A01G412800 chr5D 86.740 724 51 18 1601 2290 481762196 481761484 0.000000e+00 763.0
33 TraesCS5A01G412800 chr5D 83.784 703 67 20 929 1592 481762950 481762256 1.260000e-174 623.0
34 TraesCS5A01G412800 chr5D 84.578 415 57 4 2889 3302 481749908 481749500 4.950000e-109 405.0
35 TraesCS5A01G412800 chr5D 83.476 466 35 20 926 1374 481565729 481565289 2.980000e-106 396.0
36 TraesCS5A01G412800 chr5D 81.055 512 65 25 3136 3623 481738197 481737694 3.000000e-101 379.0
37 TraesCS5A01G412800 chr5D 88.104 269 15 3 2398 2651 481761480 481761214 1.860000e-78 303.0
38 TraesCS5A01G412800 chr5D 84.000 275 37 5 3716 3986 481738830 481738559 1.470000e-64 257.0
39 TraesCS5A01G412800 chr5D 83.908 174 9 2 2472 2626 481643840 481643667 9.210000e-32 148.0
40 TraesCS5A01G412800 chr5D 83.436 163 10 7 3474 3623 481749403 481749245 7.170000e-28 135.0
41 TraesCS5A01G412800 chr5D 79.191 173 24 8 3452 3614 481561173 481561003 4.350000e-20 110.0
42 TraesCS5A01G412800 chr5D 100.000 28 0 0 3628 3655 481749216 481749189 7.000000e-03 52.8
43 TraesCS5A01G412800 chr2B 94.728 607 26 5 4 605 717047380 717046775 0.000000e+00 939.0
44 TraesCS5A01G412800 chr2B 93.624 596 33 5 1 593 5055257 5054664 0.000000e+00 885.0
45 TraesCS5A01G412800 chr4B 94.224 606 31 4 1 605 636073441 636074043 0.000000e+00 922.0
46 TraesCS5A01G412800 chr4B 93.234 606 33 8 1 603 636069073 636069673 0.000000e+00 885.0
47 TraesCS5A01G412800 chr1B 93.750 608 34 4 1 605 624829391 624829997 0.000000e+00 909.0
48 TraesCS5A01G412800 chr7D 93.279 610 34 6 1 605 493546376 493546983 0.000000e+00 893.0
49 TraesCS5A01G412800 chr7D 92.997 614 35 7 1 608 493550803 493551414 0.000000e+00 889.0
50 TraesCS5A01G412800 chr4A 93.223 605 40 1 1 605 732493320 732492717 0.000000e+00 889.0
51 TraesCS5A01G412800 chr6B 93.069 606 37 4 1 605 115442880 115443481 0.000000e+00 881.0


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 TraesCS5A01G412800 chr5A 601340453 601344565 4112 True 7596.000000 7596 100.000000 1 4113 1 chr5A.!!$R5 4112
1 TraesCS5A01G412800 chr5A 601085775 601087308 1533 True 1345.000000 1345 83.197000 2098 3621 1 chr5A.!!$R1 1523
2 TraesCS5A01G412800 chr5A 601254886 601258388 3502 True 814.750000 1836 85.926000 932 4113 4 chr5A.!!$R10 3181
3 TraesCS5A01G412800 chr5A 600502142 600504919 2777 True 518.250000 1131 82.440000 926 4067 4 chr5A.!!$R8 3141
4 TraesCS5A01G412800 chr5A 601166500 601168398 1898 True 355.000000 595 82.480500 2210 3167 2 chr5A.!!$R9 957
5 TraesCS5A01G412800 chr5B 590804571 590808326 3755 True 2133.500000 2137 89.457500 606 4113 2 chr5B.!!$R8 3507
6 TraesCS5A01G412800 chr5B 590181732 590184899 3167 True 588.666667 1157 86.711000 926 3874 3 chr5B.!!$R6 2948
7 TraesCS5A01G412800 chr5D 481759713 481762950 3237 True 914.000000 1967 87.379750 929 4102 4 chr5D.!!$R5 3173
8 TraesCS5A01G412800 chr5D 481561003 481565729 4726 True 567.666667 1197 82.490667 926 3827 3 chr5D.!!$R1 2901
9 TraesCS5A01G412800 chr5D 481642666 481643840 1174 True 480.500000 813 84.993500 2472 3403 2 chr5D.!!$R2 931
10 TraesCS5A01G412800 chr5D 481737694 481738830 1136 True 318.000000 379 82.527500 3136 3986 2 chr5D.!!$R3 850
11 TraesCS5A01G412800 chr2B 717046775 717047380 605 True 939.000000 939 94.728000 4 605 1 chr2B.!!$R2 601
12 TraesCS5A01G412800 chr2B 5054664 5055257 593 True 885.000000 885 93.624000 1 593 1 chr2B.!!$R1 592
13 TraesCS5A01G412800 chr4B 636069073 636074043 4970 False 903.500000 922 93.729000 1 605 2 chr4B.!!$F1 604
14 TraesCS5A01G412800 chr1B 624829391 624829997 606 False 909.000000 909 93.750000 1 605 1 chr1B.!!$F1 604
15 TraesCS5A01G412800 chr7D 493546376 493551414 5038 False 891.000000 893 93.138000 1 608 2 chr7D.!!$F1 607
16 TraesCS5A01G412800 chr4A 732492717 732493320 603 True 889.000000 889 93.223000 1 605 1 chr4A.!!$R1 604
17 TraesCS5A01G412800 chr6B 115442880 115443481 601 False 881.000000 881 93.069000 1 605 1 chr6B.!!$F1 604

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
157 4526 0.173481 CCGAAGCAGAGTCCGAATGA 59.827 55.000 0.0 0.0 0.00 2.57 F
669 9474 0.179020 TCCTAATGCGATTGGCCCAG 60.179 55.000 0.0 0.0 42.61 4.45 F
1419 10372 0.588737 TGCGAGCAATGCGTTTGTAA 59.411 45.000 0.0 0.0 37.65 2.41 F
2951 13711 1.138069 GAAGCTAGGGAGAAGTCAGCC 59.862 57.143 0.0 0.0 32.58 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 10328 0.664166 GCACAGAAATGTTGCACGGG 60.664 55.0 0.0 0.0 0.00 5.28 R
2633 12477 0.817634 TGACCTTGGGTGCTTCGTTG 60.818 55.0 0.0 0.0 35.25 4.10 R
3023 13783 1.039856 GGTGTGGTTTGACATTGCCT 58.960 50.0 0.0 0.0 0.00 4.75 R
3770 14609 1.039856 ACACATGGCACCAAAACTCC 58.960 50.0 0.0 0.0 0.00 3.85 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
72 73 4.635765 CGAAGCACTTGGATTAGGAATCAA 59.364 41.667 1.90 0.00 39.71 2.57
153 4522 3.760035 GCCCGAAGCAGAGTCCGA 61.760 66.667 0.00 0.00 42.97 4.55
157 4526 0.173481 CCGAAGCAGAGTCCGAATGA 59.827 55.000 0.00 0.00 0.00 2.57
160 4529 2.223688 CGAAGCAGAGTCCGAATGAGAT 60.224 50.000 0.00 0.00 0.00 2.75
180 4549 1.371267 CAGCGAACCGACTCGACAA 60.371 57.895 9.87 0.00 41.44 3.18
242 4611 7.336427 TGTTTTAGACTCGGGTTTTGTTTAGAA 59.664 33.333 0.00 0.00 0.00 2.10
539 9343 1.826921 GGTAGCCGGATCGTGAGGA 60.827 63.158 5.05 0.00 0.00 3.71
575 9379 6.408206 CCCAAAATCGTAGTTATCTCCCTCTT 60.408 42.308 0.00 0.00 0.00 2.85
598 9403 0.323451 GAAAGATCGGGCCCCAGTTT 60.323 55.000 18.66 11.05 0.00 2.66
614 9419 3.002656 CCAGTTTACATCATAAGCCAGCG 59.997 47.826 0.00 0.00 0.00 5.18
660 9465 3.306917 TTCGACAAACTCCTAATGCGA 57.693 42.857 0.00 0.00 0.00 5.10
669 9474 0.179020 TCCTAATGCGATTGGCCCAG 60.179 55.000 0.00 0.00 42.61 4.45
689 9494 5.291858 CCCAGTTCTGAAAAAGAAGCAAAAC 59.708 40.000 1.00 0.00 45.69 2.43
716 9521 4.910195 TCATCCTCTTTAAGCAGAAGCAA 58.090 39.130 0.00 0.00 45.49 3.91
719 9524 6.265196 TCATCCTCTTTAAGCAGAAGCAAAAA 59.735 34.615 0.00 0.00 45.49 1.94
732 9555 6.421801 GCAGAAGCAAAAACACAATTCTGTAT 59.578 34.615 12.70 0.00 43.42 2.29
734 9557 6.421801 AGAAGCAAAAACACAATTCTGTATGC 59.578 34.615 9.61 9.61 33.22 3.14
757 9580 1.202132 GCTGTGTGCGTGTTTCTTTCA 60.202 47.619 0.00 0.00 0.00 2.69
758 9581 2.708514 CTGTGTGCGTGTTTCTTTCAG 58.291 47.619 0.00 0.00 0.00 3.02
813 9636 1.985473 AAATGGCTGAAGCTGACACA 58.015 45.000 1.74 0.00 41.70 3.72
814 9637 2.211250 AATGGCTGAAGCTGACACAT 57.789 45.000 1.74 0.00 41.70 3.21
815 9638 3.354948 AATGGCTGAAGCTGACACATA 57.645 42.857 1.74 0.00 41.70 2.29
816 9639 2.099141 TGGCTGAAGCTGACACATAC 57.901 50.000 1.74 0.00 41.70 2.39
817 9640 1.002366 GGCTGAAGCTGACACATACG 58.998 55.000 1.74 0.00 41.70 3.06
818 9641 1.673033 GGCTGAAGCTGACACATACGT 60.673 52.381 1.74 0.00 41.70 3.57
819 9642 2.416836 GGCTGAAGCTGACACATACGTA 60.417 50.000 0.00 0.00 41.70 3.57
820 9643 2.854777 GCTGAAGCTGACACATACGTAG 59.145 50.000 0.08 0.00 38.21 3.51
821 9644 3.673594 GCTGAAGCTGACACATACGTAGT 60.674 47.826 0.08 0.00 41.06 2.73
822 9645 4.486090 CTGAAGCTGACACATACGTAGTT 58.514 43.478 0.08 0.00 37.78 2.24
823 9646 4.878439 TGAAGCTGACACATACGTAGTTT 58.122 39.130 0.08 0.00 37.78 2.66
824 9647 5.294356 TGAAGCTGACACATACGTAGTTTT 58.706 37.500 0.08 0.00 37.78 2.43
825 9648 5.756347 TGAAGCTGACACATACGTAGTTTTT 59.244 36.000 0.08 0.00 37.78 1.94
854 9677 2.500098 AGGCAATGACACATACGTAGGT 59.500 45.455 7.13 7.13 0.00 3.08
861 9684 3.257375 TGACACATACGTAGGTGCTTCTT 59.743 43.478 33.32 18.09 41.29 2.52
878 9701 3.524648 TTGGCCGTGGGACGAACTC 62.525 63.158 0.00 0.00 46.05 3.01
881 9704 2.315386 GCCGTGGGACGAACTCAAC 61.315 63.158 0.00 0.00 46.05 3.18
977 9853 2.207229 CGTCCCCACTCACTCACCA 61.207 63.158 0.00 0.00 0.00 4.17
1000 9876 0.842467 CCCACTCCCCCTCTTCACTT 60.842 60.000 0.00 0.00 0.00 3.16
1004 9880 1.612442 TCCCCCTCTTCACTTCCCG 60.612 63.158 0.00 0.00 0.00 5.14
1006 9882 2.592993 CCCCTCTTCACTTCCCGCA 61.593 63.158 0.00 0.00 0.00 5.69
1083 9981 1.153168 CGGCCGTTCCATCAATCCT 60.153 57.895 19.50 0.00 34.01 3.24
1084 9982 0.748005 CGGCCGTTCCATCAATCCTT 60.748 55.000 19.50 0.00 34.01 3.36
1087 9985 2.091541 GCCGTTCCATCAATCCTTCAA 58.908 47.619 0.00 0.00 0.00 2.69
1136 10040 1.371389 GCTCCTTGTCGTCGTCGTT 60.371 57.895 1.33 0.00 38.33 3.85
1378 10328 1.409381 CCAGATCTTTCCCTGCCTTCC 60.409 57.143 0.00 0.00 0.00 3.46
1387 10337 3.365265 CTGCCTTCCCCGTGCAAC 61.365 66.667 0.00 0.00 34.06 4.17
1388 10338 4.196778 TGCCTTCCCCGTGCAACA 62.197 61.111 0.00 0.00 35.74 3.33
1419 10372 0.588737 TGCGAGCAATGCGTTTGTAA 59.411 45.000 0.00 0.00 37.65 2.41
1480 10433 1.689273 GGTAGGACTGTGGATAGGCTG 59.311 57.143 0.00 0.00 0.00 4.85
1488 10441 4.353777 ACTGTGGATAGGCTGAGAACTTA 58.646 43.478 0.00 0.00 0.00 2.24
1490 10443 4.610333 TGTGGATAGGCTGAGAACTTAGA 58.390 43.478 0.00 0.00 0.00 2.10
1624 10797 3.679502 GCATACTTGAAATTTGGGTGTGC 59.320 43.478 15.15 15.15 37.71 4.57
1680 10853 1.142262 ACGGGTTCAGGTTGTAGCTTT 59.858 47.619 0.00 0.00 0.00 3.51
1681 10854 2.369532 ACGGGTTCAGGTTGTAGCTTTA 59.630 45.455 0.00 0.00 0.00 1.85
1682 10855 3.008704 ACGGGTTCAGGTTGTAGCTTTAT 59.991 43.478 0.00 0.00 0.00 1.40
1683 10856 4.007659 CGGGTTCAGGTTGTAGCTTTATT 58.992 43.478 0.00 0.00 0.00 1.40
1684 10857 4.457949 CGGGTTCAGGTTGTAGCTTTATTT 59.542 41.667 0.00 0.00 0.00 1.40
1685 10858 5.644636 CGGGTTCAGGTTGTAGCTTTATTTA 59.355 40.000 0.00 0.00 0.00 1.40
1786 10987 7.307989 GGTGCTATCACGTATGAGCATTTTAAT 60.308 37.037 17.29 0.00 44.03 1.40
1787 10988 8.708742 GTGCTATCACGTATGAGCATTTTAATA 58.291 33.333 17.29 0.00 38.05 0.98
1788 10989 8.708742 TGCTATCACGTATGAGCATTTTAATAC 58.291 33.333 12.03 0.00 38.57 1.89
1955 11272 8.533569 TTAGATTGTATCCATGACACTGTCTA 57.466 34.615 10.54 0.00 33.15 2.59
1966 11283 3.704566 TGACACTGTCTACCTTGTCAGTT 59.295 43.478 10.54 0.00 42.61 3.16
2003 11320 2.357517 CTGCTGTGGACGGGACAC 60.358 66.667 0.00 0.00 39.26 3.67
2063 11380 9.088512 GATATGTAAATTATGGGATCTGTCGAC 57.911 37.037 9.11 9.11 0.00 4.20
2072 11389 5.414789 TGGGATCTGTCGACTTTCATTTA 57.585 39.130 17.92 0.00 0.00 1.40
2073 11390 5.989477 TGGGATCTGTCGACTTTCATTTAT 58.011 37.500 17.92 0.00 0.00 1.40
2113 11430 6.114187 TGTGATCTGAATGTCCTAACAAGT 57.886 37.500 0.00 0.00 39.30 3.16
2117 11434 7.766278 GTGATCTGAATGTCCTAACAAGTATGT 59.234 37.037 0.00 0.00 43.14 2.29
2120 11437 9.770097 ATCTGAATGTCCTAACAAGTATGTATG 57.230 33.333 0.00 0.00 39.40 2.39
2205 11526 5.391310 GCCATGGCTGATCGATTATAACTTG 60.391 44.000 29.98 0.00 38.26 3.16
2239 11560 1.660019 TTTGGGGGTGAGGCCAAGAA 61.660 55.000 5.01 0.00 39.65 2.52
2455 11860 2.939640 GCGATGCCTTCCTTTGTCCTTA 60.940 50.000 0.00 0.00 0.00 2.69
2456 11861 3.545703 CGATGCCTTCCTTTGTCCTTAT 58.454 45.455 0.00 0.00 0.00 1.73
2462 12058 5.119694 GCCTTCCTTTGTCCTTATAGTCTG 58.880 45.833 0.00 0.00 0.00 3.51
2489 12092 4.966965 TGTCTACTGCTCTAGTTGCTAC 57.033 45.455 10.68 0.00 40.89 3.58
2553 12182 9.987272 CACTTATCCATGATATACTCTGTTTCA 57.013 33.333 0.00 0.00 0.00 2.69
2633 12477 9.982651 TGACTTGGATATTATGCTAAGTAGTTC 57.017 33.333 10.59 3.58 0.00 3.01
2654 13398 2.317609 CGAAGCACCCAAGGTCACG 61.318 63.158 0.00 0.00 31.02 4.35
2672 13417 7.717568 AGGTCACGTATATTCCATAGCATATC 58.282 38.462 0.00 0.00 0.00 1.63
2676 13421 8.749354 TCACGTATATTCCATAGCATATCTTGT 58.251 33.333 0.00 0.00 0.00 3.16
2951 13711 1.138069 GAAGCTAGGGAGAAGTCAGCC 59.862 57.143 0.00 0.00 32.58 4.85
3003 13763 2.868899 CTTTGTGGGAGGAAAGAGCTT 58.131 47.619 0.00 0.00 31.89 3.74
3023 13783 1.501170 TGGGAACTTGGATGGAAACCA 59.499 47.619 0.00 0.00 36.78 3.67
3026 13786 1.546029 GAACTTGGATGGAAACCAGGC 59.454 52.381 0.00 0.00 41.06 4.85
3076 13836 1.956869 ACACTGGAGGATGGTGATGA 58.043 50.000 0.00 0.00 35.28 2.92
3113 13873 9.347240 CCAACCAATAGAGATCTCATTACAAAT 57.653 33.333 24.39 3.88 0.00 2.32
3205 13971 1.831736 ACGAGTTCCCTTGTCCATAGG 59.168 52.381 0.00 0.00 28.47 2.57
3439 14234 8.010733 TCCCCAAATTCTCATGATATTTTGAC 57.989 34.615 21.02 0.00 0.00 3.18
3440 14235 7.840716 TCCCCAAATTCTCATGATATTTTGACT 59.159 33.333 21.02 0.00 0.00 3.41
3441 14236 7.924412 CCCCAAATTCTCATGATATTTTGACTG 59.076 37.037 21.02 12.98 0.00 3.51
3442 14237 8.472413 CCCAAATTCTCATGATATTTTGACTGT 58.528 33.333 21.02 0.00 0.00 3.55
3443 14238 9.865321 CCAAATTCTCATGATATTTTGACTGTT 57.135 29.630 21.02 0.63 0.00 3.16
3455 14250 9.334693 GATATTTTGACTGTTTGACATGAAGAC 57.665 33.333 0.00 0.00 0.00 3.01
3552 14359 2.158755 CCCACAGACTTGTCCAAACTCT 60.159 50.000 0.00 0.00 34.62 3.24
3625 14464 5.162075 GCTCGTGCTTTCTTTCTTCTACTA 58.838 41.667 1.41 0.00 36.03 1.82
3657 14496 8.695456 AGAATTCAAGTTTTCAACCTAACATGT 58.305 29.630 8.44 0.00 0.00 3.21
3699 14538 2.101415 GCCTTTGCCAACTCTTGAAACT 59.899 45.455 0.00 0.00 0.00 2.66
3727 14566 5.582665 GCAGAGTTCACCCTCTTACATAAAG 59.417 44.000 0.00 0.00 39.81 1.85
3752 14591 6.876257 GTCTTCATGTTCTTCTCTACCATGTT 59.124 38.462 0.00 0.00 35.54 2.71
3770 14609 8.158169 ACCATGTTGCATGTCTTATATAAGTG 57.842 34.615 19.58 12.96 34.93 3.16
3796 15202 1.825090 TGGTGCCATGTGTTCATCTC 58.175 50.000 0.00 0.00 31.15 2.75
3905 15972 1.064825 ACCGGAAACAGAAGGTGGAT 58.935 50.000 9.46 0.00 35.36 3.41
4002 16072 2.693074 GTCCAACAAACAGGGTCAACAT 59.307 45.455 0.00 0.00 0.00 2.71
4059 16944 1.477295 GGAACGTGGAGGACCTCTAAG 59.523 57.143 20.97 19.00 37.04 2.18
4069 16954 4.024670 GAGGACCTCTAAGCCTTGAGTTA 58.975 47.826 14.72 0.00 30.70 2.24
4070 16955 4.027437 AGGACCTCTAAGCCTTGAGTTAG 58.973 47.826 0.00 0.00 0.00 2.34
4107 17047 3.143728 GGATGTACAAAAGAACACCGGT 58.856 45.455 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 1.821753 CCAGACTGAGAGTCCACGATT 59.178 52.381 3.32 0.00 46.18 3.34
153 4522 2.427453 AGTCGGTTCGCTGTATCTCATT 59.573 45.455 0.00 0.00 0.00 2.57
157 4526 0.377554 CGAGTCGGTTCGCTGTATCT 59.622 55.000 4.10 0.00 33.39 1.98
160 4529 1.229975 TGTCGAGTCGGTTCGCTGTA 61.230 55.000 13.54 0.00 40.29 2.74
180 4549 6.466885 ACTATTTATTAGAGGCAGACGTGT 57.533 37.500 0.00 0.00 0.00 4.49
539 9343 2.225017 ACGATTTTGGGTGGGACTTGAT 60.225 45.455 0.00 0.00 0.00 2.57
598 9403 2.628178 AGCTACGCTGGCTTATGATGTA 59.372 45.455 0.00 0.00 37.57 2.29
614 9419 1.360820 GCTTTCTCCCGTTGAGCTAC 58.639 55.000 0.00 0.00 41.18 3.58
618 9423 3.876300 CGGCTTTCTCCCGTTGAG 58.124 61.111 0.00 0.00 40.84 3.02
632 9437 1.136057 GGAGTTTGTCGAATTCACGGC 60.136 52.381 6.22 0.00 38.42 5.68
660 9465 3.575805 TCTTTTTCAGAACTGGGCCAAT 58.424 40.909 8.04 0.00 0.00 3.16
669 9474 5.419542 AGGGTTTTGCTTCTTTTTCAGAAC 58.580 37.500 0.00 0.00 36.51 3.01
689 9494 3.708631 TCTGCTTAAAGAGGATGAGAGGG 59.291 47.826 0.00 0.00 0.00 4.30
716 9521 3.980775 GCACGCATACAGAATTGTGTTTT 59.019 39.130 14.05 0.00 38.23 2.43
719 9524 2.160219 CAGCACGCATACAGAATTGTGT 59.840 45.455 13.33 13.33 38.23 3.72
734 9557 1.651132 GAAACACGCACACAGCACG 60.651 57.895 0.00 0.00 46.13 5.34
792 9615 2.694628 TGTGTCAGCTTCAGCCATTTTT 59.305 40.909 0.00 0.00 43.38 1.94
797 9620 1.672737 CGTATGTGTCAGCTTCAGCCA 60.673 52.381 0.00 0.00 43.38 4.75
798 9621 1.002366 CGTATGTGTCAGCTTCAGCC 58.998 55.000 0.00 0.00 43.38 4.85
799 9622 1.714794 ACGTATGTGTCAGCTTCAGC 58.285 50.000 0.00 0.00 42.49 4.26
800 9623 4.098055 ACTACGTATGTGTCAGCTTCAG 57.902 45.455 0.00 0.00 0.00 3.02
801 9624 4.514781 AACTACGTATGTGTCAGCTTCA 57.485 40.909 0.00 0.00 0.00 3.02
802 9625 5.840940 AAAACTACGTATGTGTCAGCTTC 57.159 39.130 0.00 0.00 0.00 3.86
827 9650 4.277174 ACGTATGTGTCATTGCCTCAAAAA 59.723 37.500 0.00 0.00 0.00 1.94
828 9651 3.818210 ACGTATGTGTCATTGCCTCAAAA 59.182 39.130 0.00 0.00 0.00 2.44
829 9652 3.407698 ACGTATGTGTCATTGCCTCAAA 58.592 40.909 0.00 0.00 0.00 2.69
830 9653 3.052455 ACGTATGTGTCATTGCCTCAA 57.948 42.857 0.00 0.00 0.00 3.02
831 9654 2.760634 ACGTATGTGTCATTGCCTCA 57.239 45.000 0.00 0.00 0.00 3.86
832 9655 3.123804 CCTACGTATGTGTCATTGCCTC 58.876 50.000 0.00 0.00 0.00 4.70
833 9656 2.500098 ACCTACGTATGTGTCATTGCCT 59.500 45.455 2.46 0.00 0.00 4.75
834 9657 2.607635 CACCTACGTATGTGTCATTGCC 59.392 50.000 19.31 0.00 0.00 4.52
835 9658 2.030457 GCACCTACGTATGTGTCATTGC 59.970 50.000 25.41 11.48 34.94 3.56
836 9659 3.521560 AGCACCTACGTATGTGTCATTG 58.478 45.455 25.41 6.28 34.94 2.82
837 9660 3.887621 AGCACCTACGTATGTGTCATT 57.112 42.857 25.41 11.26 34.94 2.57
838 9661 3.447586 AGAAGCACCTACGTATGTGTCAT 59.552 43.478 25.41 15.28 34.94 3.06
854 9677 3.565214 TCCCACGGCCAAGAAGCA 61.565 61.111 2.24 0.00 0.00 3.91
861 9684 3.998672 GAGTTCGTCCCACGGCCA 61.999 66.667 2.24 0.00 42.81 5.36
977 9853 0.547954 GAAGAGGGGGAGTGGGAGTT 60.548 60.000 0.00 0.00 0.00 3.01
1072 9970 2.291540 GGGTGGTTGAAGGATTGATGGA 60.292 50.000 0.00 0.00 0.00 3.41
1122 10020 1.545614 CCCACAACGACGACGACAAG 61.546 60.000 15.32 3.15 42.66 3.16
1124 10022 2.026445 CCCACAACGACGACGACA 59.974 61.111 15.32 0.00 42.66 4.35
1378 10328 0.664166 GCACAGAAATGTTGCACGGG 60.664 55.000 0.00 0.00 0.00 5.28
1387 10337 3.670500 CTCGCACAGCACAGAAATG 57.330 52.632 0.00 0.00 0.00 2.32
1488 10441 8.314751 CAGATCCCCTAATTTACATATCGTTCT 58.685 37.037 0.00 0.00 0.00 3.01
1490 10443 7.974504 ACAGATCCCCTAATTTACATATCGTT 58.025 34.615 0.00 0.00 0.00 3.85
1539 10497 5.545063 TTGTAGGACATTCAAGTCACAGA 57.455 39.130 0.00 0.00 40.29 3.41
1624 10797 4.921470 ATAAGTGAAAACATCGTGGTCG 57.079 40.909 0.00 0.00 38.55 4.79
1683 10856 9.429109 TCAGTGACCATACATAATTACTCCTAA 57.571 33.333 0.00 0.00 0.00 2.69
1684 10857 9.429109 TTCAGTGACCATACATAATTACTCCTA 57.571 33.333 0.00 0.00 0.00 2.94
1685 10858 7.914427 TCAGTGACCATACATAATTACTCCT 57.086 36.000 0.00 0.00 0.00 3.69
1947 11264 4.060038 ACAACTGACAAGGTAGACAGTG 57.940 45.455 0.00 0.00 42.17 3.66
1951 11268 7.924947 ACTAGTTAAACAACTGACAAGGTAGAC 59.075 37.037 0.00 0.00 34.37 2.59
1955 11272 9.052759 CAATACTAGTTAAACAACTGACAAGGT 57.947 33.333 0.00 0.00 34.37 3.50
2003 11320 2.584236 AGCCTATCCACAGTACTACCG 58.416 52.381 0.00 0.00 0.00 4.02
2060 11377 2.757868 TGCCCCCAATAAATGAAAGTCG 59.242 45.455 0.00 0.00 0.00 4.18
2063 11380 5.619132 AGAATGCCCCCAATAAATGAAAG 57.381 39.130 0.00 0.00 0.00 2.62
2072 11389 1.645919 ACAGGTTAGAATGCCCCCAAT 59.354 47.619 0.00 0.00 0.00 3.16
2073 11390 1.080638 ACAGGTTAGAATGCCCCCAA 58.919 50.000 0.00 0.00 0.00 4.12
2113 11430 6.808321 ACTGAGGAAGTTAAGCCATACATA 57.192 37.500 0.00 0.00 34.57 2.29
2205 11526 3.181472 CCCCCAAATTTCAAGCATAGCTC 60.181 47.826 0.00 0.00 38.25 4.09
2239 11560 8.831550 GTTCTGACTTCTGAATAACTGAAAACT 58.168 33.333 2.34 0.00 36.46 2.66
2275 11596 5.552870 ACTCCCAGTATAAGGCTACAATG 57.447 43.478 0.00 0.00 0.00 2.82
2276 11597 7.873699 ATTACTCCCAGTATAAGGCTACAAT 57.126 36.000 0.00 0.00 29.64 2.71
2455 11860 6.833416 AGAGCAGTAGACATCTTTCAGACTAT 59.167 38.462 0.00 0.00 0.00 2.12
2456 11861 6.184068 AGAGCAGTAGACATCTTTCAGACTA 58.816 40.000 0.00 0.00 0.00 2.59
2462 12058 5.518487 GCAACTAGAGCAGTAGACATCTTTC 59.482 44.000 0.00 0.00 36.04 2.62
2553 12182 8.813951 ACTGAGCTACTTGGTTAAACTACTAAT 58.186 33.333 0.00 0.00 0.00 1.73
2555 12184 7.771927 ACTGAGCTACTTGGTTAAACTACTA 57.228 36.000 0.00 0.00 0.00 1.82
2633 12477 0.817634 TGACCTTGGGTGCTTCGTTG 60.818 55.000 0.00 0.00 35.25 4.10
2676 13421 9.613428 CCAGTTAATCCAGTCACAAGATAATTA 57.387 33.333 0.00 0.00 0.00 1.40
3003 13763 1.501170 TGGTTTCCATCCAAGTTCCCA 59.499 47.619 0.00 0.00 31.50 4.37
3023 13783 1.039856 GGTGTGGTTTGACATTGCCT 58.960 50.000 0.00 0.00 0.00 4.75
3026 13786 1.313772 TCCGGTGTGGTTTGACATTG 58.686 50.000 0.00 0.00 39.52 2.82
3076 13836 4.535781 TCTATTGGTTGGCATGCTGTATT 58.464 39.130 18.92 0.00 0.00 1.89
3113 13873 1.424302 CTCTATCACCGAGGGAGGGTA 59.576 57.143 0.00 0.00 35.58 3.69
3205 13971 9.083080 GTTGCTGACAAACCCAATATAAATTAC 57.917 33.333 0.00 0.00 37.58 1.89
3256 14032 5.971202 GTGTCATTCTATGGCCATTTTAACG 59.029 40.000 26.37 8.75 32.84 3.18
3439 14234 2.872245 ACACCGTCTTCATGTCAAACAG 59.128 45.455 0.00 0.00 0.00 3.16
3440 14235 2.912771 ACACCGTCTTCATGTCAAACA 58.087 42.857 0.00 0.00 0.00 2.83
3441 14236 4.056050 ACTACACCGTCTTCATGTCAAAC 58.944 43.478 0.00 0.00 0.00 2.93
3442 14237 4.330944 ACTACACCGTCTTCATGTCAAA 57.669 40.909 0.00 0.00 0.00 2.69
3443 14238 5.654603 ATACTACACCGTCTTCATGTCAA 57.345 39.130 0.00 0.00 0.00 3.18
3444 14239 6.954487 ATATACTACACCGTCTTCATGTCA 57.046 37.500 0.00 0.00 0.00 3.58
3445 14240 9.909644 AAATATATACTACACCGTCTTCATGTC 57.090 33.333 0.00 0.00 0.00 3.06
3489 14284 4.530161 AGTCTCTTCAGTAGCCACTTGATT 59.470 41.667 0.00 0.00 30.46 2.57
3552 14359 5.126222 TGCACAGTTCAAATGGAAAAGTACA 59.874 36.000 0.00 0.00 37.23 2.90
3657 14496 8.537728 AAGGCAGATATTTCATTTATTGTGGA 57.462 30.769 0.00 0.00 0.00 4.02
3699 14538 1.140312 AGAGGGTGAACTCTGCCAAA 58.860 50.000 0.00 0.00 45.70 3.28
3727 14566 6.402222 ACATGGTAGAGAAGAACATGAAGAC 58.598 40.000 7.62 0.00 40.92 3.01
3752 14591 8.892723 CAAAACTCCACTTATATAAGACATGCA 58.107 33.333 25.83 2.79 37.08 3.96
3770 14609 1.039856 ACACATGGCACCAAAACTCC 58.960 50.000 0.00 0.00 0.00 3.85
3905 15972 3.023119 ACTTTGTGCACACAGAATCCAA 58.977 40.909 33.66 16.37 42.94 3.53


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

AutoCloner maintained by Alex Coulton.