Multiple sequence alignment - TraesCS2A01G034800

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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 TraesCS2A01G034800 chr2A 100.000 3921 0 0 1 3921 15230091 15226171 0.000000e+00 7241.0
1 TraesCS2A01G034800 chr2A 88.519 540 60 2 2266 2804 13011222 13011760 0.000000e+00 652.0
2 TraesCS2A01G034800 chr2D 91.567 2597 161 31 628 3197 13193588 13191023 0.000000e+00 3530.0
3 TraesCS2A01G034800 chr2D 96.154 1040 29 9 2887 3921 13190537 13189504 0.000000e+00 1688.0
4 TraesCS2A01G034800 chr2D 88.972 535 59 0 2264 2798 12554767 12555301 0.000000e+00 662.0
5 TraesCS2A01G034800 chr2D 95.890 292 10 2 1 290 13199946 13199655 4.590000e-129 472.0
6 TraesCS2A01G034800 chr2D 83.726 424 66 2 1097 1517 12554277 12554700 7.890000e-107 398.0
7 TraesCS2A01G034800 chr2D 85.350 314 31 4 304 607 13195625 13195317 1.060000e-80 311.0
8 TraesCS2A01G034800 chr2D 86.102 295 18 15 3203 3482 13190851 13190565 2.960000e-76 296.0
9 TraesCS2A01G034800 chr2D 90.341 176 12 2 2638 2808 13424141 13424316 3.940000e-55 226.0
10 TraesCS2A01G034800 chr2D 89.571 163 16 1 1055 1216 13195752 13195590 5.140000e-49 206.0
11 TraesCS2A01G034800 chr2B 91.065 1399 81 16 1799 3197 23716602 23715248 0.000000e+00 1851.0
12 TraesCS2A01G034800 chr2B 92.336 809 24 14 976 1773 23717380 23716599 0.000000e+00 1116.0
13 TraesCS2A01G034800 chr2B 88.440 545 61 2 2264 2807 18951584 18951041 0.000000e+00 656.0
14 TraesCS2A01G034800 chr2B 91.139 237 21 0 1 237 23736250 23736014 4.890000e-84 322.0
15 TraesCS2A01G034800 chr2B 86.972 284 24 4 3203 3474 23715077 23714795 1.370000e-79 307.0
16 TraesCS2A01G034800 chr2B 82.692 260 42 3 3654 3910 632563000 632562741 1.100000e-55 228.0
17 TraesCS2A01G034800 chr7A 86.111 504 68 2 2282 2785 308637299 308636798 3.450000e-150 542.0
18 TraesCS2A01G034800 chr7A 85.227 88 13 0 679 766 518806087 518806000 1.500000e-14 91.6
19 TraesCS2A01G034800 chr5A 83.784 259 40 2 3654 3910 195578499 195578241 1.090000e-60 244.0
20 TraesCS2A01G034800 chr5A 82.692 260 38 7 3654 3908 702569087 702569344 1.420000e-54 224.0
21 TraesCS2A01G034800 chr6D 83.270 263 42 2 3654 3914 447511180 447511442 1.410000e-59 241.0
22 TraesCS2A01G034800 chr4D 82.528 269 44 3 3654 3920 455311271 455311004 2.360000e-57 233.0
23 TraesCS2A01G034800 chr4D 82.946 258 39 5 3654 3908 348057596 348057851 1.100000e-55 228.0
24 TraesCS2A01G034800 chr4D 86.897 145 15 3 3014 3156 84600352 84600210 4.060000e-35 159.0
25 TraesCS2A01G034800 chr3D 83.268 257 38 5 3654 3907 330942019 330942273 8.470000e-57 231.0
26 TraesCS2A01G034800 chr3A 83.398 259 34 8 3654 3907 111818664 111818918 8.470000e-57 231.0
27 TraesCS2A01G034800 chr7D 85.135 222 24 5 2978 3197 423324045 423324259 6.600000e-53 219.0
28 TraesCS2A01G034800 chr7D 82.840 169 28 1 2283 2451 13320789 13320622 2.440000e-32 150.0
29 TraesCS2A01G034800 chr4B 84.656 189 22 5 2993 3180 119849104 119848922 8.650000e-42 182.0
30 TraesCS2A01G034800 chr7B 80.258 233 33 9 2975 3202 692878170 692877946 3.130000e-36 163.0
31 TraesCS2A01G034800 chr4A 75.785 223 34 14 2980 3191 138261640 138261427 1.160000e-15 95.3
32 TraesCS2A01G034800 chr1B 75.785 223 34 14 2980 3191 625055588 625055375 1.160000e-15 95.3


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 TraesCS2A01G034800 chr2A 15226171 15230091 3920 True 7241.000000 7241 100.000000 1 3921 1 chr2A.!!$R1 3920
1 TraesCS2A01G034800 chr2A 13011222 13011760 538 False 652.000000 652 88.519000 2266 2804 1 chr2A.!!$F1 538
2 TraesCS2A01G034800 chr2D 13189504 13199946 10442 True 1083.833333 3530 90.772333 1 3921 6 chr2D.!!$R1 3920
3 TraesCS2A01G034800 chr2D 12554277 12555301 1024 False 530.000000 662 86.349000 1097 2798 2 chr2D.!!$F2 1701
4 TraesCS2A01G034800 chr2B 23714795 23717380 2585 True 1091.333333 1851 90.124333 976 3474 3 chr2B.!!$R4 2498
5 TraesCS2A01G034800 chr2B 18951041 18951584 543 True 656.000000 656 88.440000 2264 2807 1 chr2B.!!$R1 543
6 TraesCS2A01G034800 chr7A 308636798 308637299 501 True 542.000000 542 86.111000 2282 2785 1 chr7A.!!$R1 503

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
693 6431 0.038801 GCTTGCCCTTGCTGAAGAAC 60.039 55.0 0.0 0.0 38.71 3.01 F
1774 7547 0.039035 ACAGTCTCCTTCCTCTCGCT 59.961 55.0 0.0 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 7761 0.179092 GCTATAACAAGCCCGACGGT 60.179 55.0 13.94 0.0 36.45 4.83 R
3578 10146 0.597637 ACAAACACAGACGAGGCGAG 60.598 55.0 0.00 0.0 0.00 5.03 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
79 80 3.745803 GACCTCGACCGCCTCGTT 61.746 66.667 1.28 0.00 43.45 3.85
166 167 2.668457 AGCACAAAGAATGTCGATCGTC 59.332 45.455 15.94 10.48 41.46 4.20
171 172 3.850122 AAGAATGTCGATCGTCACTGA 57.150 42.857 17.03 0.00 0.00 3.41
193 194 1.728971 CGCGAGCTCTTCACAAAGAAT 59.271 47.619 12.85 0.00 40.95 2.40
205 208 7.370383 TCTTCACAAAGAATAAAACTGGCATC 58.630 34.615 0.00 0.00 38.58 3.91
261 264 0.538057 TTGTCCCTCCAAAGCAGCAG 60.538 55.000 0.00 0.00 0.00 4.24
280 283 1.137086 AGGTACGATGAGACCATGCAC 59.863 52.381 0.00 0.00 38.27 4.57
290 293 6.403527 CGATGAGACCATGCACAAATCTAAAA 60.404 38.462 0.00 0.00 32.09 1.52
292 295 5.064441 AGACCATGCACAAATCTAAAAGC 57.936 39.130 0.00 0.00 0.00 3.51
293 296 4.523943 AGACCATGCACAAATCTAAAAGCA 59.476 37.500 0.00 0.00 36.34 3.91
295 298 3.615496 CCATGCACAAATCTAAAAGCAGC 59.385 43.478 0.00 0.00 35.26 5.25
296 299 4.239304 CATGCACAAATCTAAAAGCAGCA 58.761 39.130 0.00 0.00 35.26 4.41
298 301 3.248266 GCACAAATCTAAAAGCAGCAGG 58.752 45.455 0.00 0.00 0.00 4.85
300 303 4.479619 CACAAATCTAAAAGCAGCAGGTC 58.520 43.478 0.00 0.00 0.00 3.85
301 304 3.507622 ACAAATCTAAAAGCAGCAGGTCC 59.492 43.478 0.00 0.00 0.00 4.46
302 305 2.426842 ATCTAAAAGCAGCAGGTCCC 57.573 50.000 0.00 0.00 0.00 4.46
328 4347 2.254651 GTCTTGGTCGTCGACGCT 59.745 61.111 32.19 0.00 39.60 5.07
332 4351 0.732880 CTTGGTCGTCGACGCTGATT 60.733 55.000 32.19 0.00 39.60 2.57
339 4358 0.862283 GTCGACGCTGATTCCTCGAC 60.862 60.000 0.00 5.39 45.73 4.20
343 4362 0.681564 ACGCTGATTCCTCGACCTCT 60.682 55.000 2.36 0.00 0.00 3.69
351 4370 2.470362 CCTCGACCTCTAGCGCGAA 61.470 63.158 12.10 0.00 31.89 4.70
358 4377 1.226717 CTCTAGCGCGAACCAGACC 60.227 63.158 12.10 0.00 0.00 3.85
363 4382 4.796231 CGCGAACCAGACCTCCCG 62.796 72.222 0.00 0.00 0.00 5.14
368 4387 2.465055 GAACCAGACCTCCCGGTTGG 62.465 65.000 0.00 4.32 45.73 3.77
369 4388 4.410400 CCAGACCTCCCGGTTGGC 62.410 72.222 9.58 3.75 45.73 4.52
370 4389 4.410400 CAGACCTCCCGGTTGGCC 62.410 72.222 9.58 0.00 45.73 5.36
425 4444 1.728502 GCTCCGACGTCAGTAACTCAC 60.729 57.143 17.16 0.00 0.00 3.51
433 4452 1.466167 GTCAGTAACTCACGGCGTCTA 59.534 52.381 10.85 0.00 0.00 2.59
486 4515 1.063469 GACATTGAAATACGGTGCGGG 59.937 52.381 0.00 0.00 0.00 6.13
491 4520 1.078708 AAATACGGTGCGGGTCCAG 60.079 57.895 0.00 0.00 0.00 3.86
517 4546 0.105760 ACAATGGGGCAGGTTGACAA 60.106 50.000 2.66 0.00 0.00 3.18
520 4549 0.540365 ATGGGGCAGGTTGACAACTG 60.540 55.000 17.52 13.91 37.76 3.16
548 4577 2.440796 CGGCTACCGGTACTCCCA 60.441 66.667 11.16 0.00 44.15 4.37
579 4608 1.815408 GCCTGTTGCATCGGGATGTAT 60.815 52.381 24.21 0.00 40.80 2.29
641 6378 1.213094 CGGTTGTGACAGTGACGACC 61.213 60.000 17.61 17.61 42.49 4.79
643 6380 0.878961 GTTGTGACAGTGACGACCCC 60.879 60.000 0.00 0.00 0.00 4.95
644 6381 2.049433 GTGACAGTGACGACCCCG 60.049 66.667 0.00 0.00 42.50 5.73
647 6384 4.608774 ACAGTGACGACCCCGGGA 62.609 66.667 26.32 0.00 40.78 5.14
648 6385 4.065281 CAGTGACGACCCCGGGAC 62.065 72.222 26.32 15.08 40.78 4.46
673 6411 2.677979 GCGCCGGGTCAGAACTTTC 61.678 63.158 2.18 0.00 0.00 2.62
693 6431 0.038801 GCTTGCCCTTGCTGAAGAAC 60.039 55.000 0.00 0.00 38.71 3.01
705 6443 2.044946 AAGAACCCCATGGCGAGC 60.045 61.111 6.09 0.00 33.59 5.03
716 6454 1.032114 ATGGCGAGCTAGGTTTTGCC 61.032 55.000 20.49 20.49 43.04 4.52
759 6497 0.545787 TGGTTAGATGTGGACGGGGT 60.546 55.000 0.00 0.00 0.00 4.95
773 6511 1.532238 GGGGTAGGGAAGTGGATGC 59.468 63.158 0.00 0.00 0.00 3.91
778 6516 0.616395 TAGGGAAGTGGATGCGGTCA 60.616 55.000 0.00 0.00 0.00 4.02
839 6577 2.593436 CCGAGGTGGTTTTGCCGT 60.593 61.111 0.00 0.00 41.21 5.68
840 6578 2.613506 CCGAGGTGGTTTTGCCGTC 61.614 63.158 0.00 0.00 41.21 4.79
841 6579 1.597027 CGAGGTGGTTTTGCCGTCT 60.597 57.895 0.00 0.00 41.21 4.18
843 6581 1.674817 CGAGGTGGTTTTGCCGTCTAT 60.675 52.381 0.00 0.00 41.21 1.98
844 6582 2.433436 GAGGTGGTTTTGCCGTCTATT 58.567 47.619 0.00 0.00 41.21 1.73
846 6584 2.817844 AGGTGGTTTTGCCGTCTATTTC 59.182 45.455 0.00 0.00 41.21 2.17
847 6585 2.554893 GGTGGTTTTGCCGTCTATTTCA 59.445 45.455 0.00 0.00 41.21 2.69
848 6586 3.192633 GGTGGTTTTGCCGTCTATTTCAT 59.807 43.478 0.00 0.00 41.21 2.57
849 6587 4.165779 GTGGTTTTGCCGTCTATTTCATG 58.834 43.478 0.00 0.00 41.21 3.07
850 6588 3.823873 TGGTTTTGCCGTCTATTTCATGT 59.176 39.130 0.00 0.00 41.21 3.21
851 6589 4.279671 TGGTTTTGCCGTCTATTTCATGTT 59.720 37.500 0.00 0.00 41.21 2.71
853 6591 5.457140 GTTTTGCCGTCTATTTCATGTTCA 58.543 37.500 0.00 0.00 0.00 3.18
855 6593 4.880886 TGCCGTCTATTTCATGTTCATG 57.119 40.909 6.46 6.46 0.00 3.07
856 6594 4.260985 TGCCGTCTATTTCATGTTCATGT 58.739 39.130 11.73 0.00 0.00 3.21
857 6595 4.094739 TGCCGTCTATTTCATGTTCATGTG 59.905 41.667 11.73 0.00 0.00 3.21
858 6596 4.332543 GCCGTCTATTTCATGTTCATGTGA 59.667 41.667 11.73 3.77 0.00 3.58
866 6619 7.915293 ATTTCATGTTCATGTGAATGCAAAT 57.085 28.000 11.73 6.61 36.33 2.32
870 6623 7.036829 TCATGTTCATGTGAATGCAAATAAGG 58.963 34.615 11.73 0.00 36.33 2.69
895 6648 6.245710 GTGTAAATTTGCGTCTGAAATACGTC 59.754 38.462 0.00 0.00 42.26 4.34
896 6649 5.607119 AAATTTGCGTCTGAAATACGTCT 57.393 34.783 0.00 0.00 42.26 4.18
897 6650 6.715344 AAATTTGCGTCTGAAATACGTCTA 57.285 33.333 0.00 0.00 42.26 2.59
899 6652 4.690184 TTGCGTCTGAAATACGTCTAGA 57.310 40.909 0.00 0.00 42.26 2.43
900 6653 4.012319 TGCGTCTGAAATACGTCTAGAC 57.988 45.455 13.18 13.18 42.26 2.59
916 6669 4.979197 GTCTAGACGGACATTGATGACATC 59.021 45.833 7.22 8.59 36.35 3.06
917 6670 2.814269 AGACGGACATTGATGACATCG 58.186 47.619 10.79 0.26 0.00 3.84
919 6672 0.230515 CGGACATTGATGACATCGCG 59.769 55.000 10.79 0.00 0.00 5.87
920 6673 1.570813 GGACATTGATGACATCGCGA 58.429 50.000 13.09 13.09 0.00 5.87
935 6690 2.184836 CGATTGGTCCGCGGGTTA 59.815 61.111 27.83 8.82 0.00 2.85
937 6692 1.523032 GATTGGTCCGCGGGTTAGG 60.523 63.158 27.83 0.00 0.00 2.69
972 6727 4.487948 CGTATCGGTTGGAGTTGTTCTTA 58.512 43.478 0.00 0.00 0.00 2.10
995 6750 4.082125 GGAATAGCCATATTTGGTCCAGG 58.918 47.826 4.00 0.00 45.57 4.45
1042 6798 0.959372 CTGTCCTCCAAAGCAGCAGG 60.959 60.000 0.00 0.00 0.00 4.85
1043 6799 1.073897 GTCCTCCAAAGCAGCAGGT 59.926 57.895 0.00 0.00 0.00 4.00
1044 6800 0.324943 GTCCTCCAAAGCAGCAGGTA 59.675 55.000 0.00 0.00 0.00 3.08
1045 6801 0.324943 TCCTCCAAAGCAGCAGGTAC 59.675 55.000 0.00 0.00 0.00 3.34
1047 6803 1.677217 CCTCCAAAGCAGCAGGTACTC 60.677 57.143 0.00 0.00 34.60 2.59
1048 6804 0.324943 TCCAAAGCAGCAGGTACTCC 59.675 55.000 0.00 0.00 34.60 3.85
1049 6805 1.021390 CCAAAGCAGCAGGTACTCCG 61.021 60.000 0.00 0.00 34.60 4.63
1092 6853 2.044352 TCCACGGAGCGATGGAGA 60.044 61.111 0.00 0.00 40.17 3.71
1530 7294 4.585162 CCACCAAGGTAGATACTCCAGTAG 59.415 50.000 0.00 0.00 33.52 2.57
1531 7295 5.202004 CACCAAGGTAGATACTCCAGTAGT 58.798 45.833 0.00 0.00 42.62 2.73
1636 7409 0.967380 ACTACCTACCGAACCCACCG 60.967 60.000 0.00 0.00 0.00 4.94
1654 7427 1.068083 GCCGATTGAGGAGATGCGA 59.932 57.895 0.00 0.00 0.00 5.10
1687 7460 2.409870 CCAAGCCGATGCCTCCAAC 61.410 63.158 0.00 0.00 38.69 3.77
1688 7461 1.377725 CAAGCCGATGCCTCCAACT 60.378 57.895 0.00 0.00 38.69 3.16
1689 7462 1.078143 AAGCCGATGCCTCCAACTC 60.078 57.895 0.00 0.00 38.69 3.01
1690 7463 2.514824 GCCGATGCCTCCAACTCC 60.515 66.667 0.00 0.00 0.00 3.85
1691 7464 2.989639 CCGATGCCTCCAACTCCA 59.010 61.111 0.00 0.00 0.00 3.86
1692 7465 1.299648 CCGATGCCTCCAACTCCAA 59.700 57.895 0.00 0.00 0.00 3.53
1731 7504 0.471211 GACCCCATCATCCCGGAGTA 60.471 60.000 0.73 0.00 0.00 2.59
1774 7547 0.039035 ACAGTCTCCTTCCTCTCGCT 59.961 55.000 0.00 0.00 0.00 4.93
1915 7688 2.638329 CGTTGACCACGTCGATCTC 58.362 57.895 0.00 0.00 44.49 2.75
2002 7775 1.005394 CTACACCGTCGGGCTTGTT 60.005 57.895 17.28 0.00 36.48 2.83
2101 7874 3.371166 CCCTCGCCTCCAAGGTTAATTTA 60.371 47.826 0.00 0.00 37.80 1.40
2102 7875 3.877508 CCTCGCCTCCAAGGTTAATTTAG 59.122 47.826 0.00 0.00 37.80 1.85
2103 7876 4.514401 CTCGCCTCCAAGGTTAATTTAGT 58.486 43.478 0.00 0.00 37.80 2.24
2106 7879 3.064958 GCCTCCAAGGTTAATTTAGTCGC 59.935 47.826 0.00 0.00 37.80 5.19
2149 7922 7.104290 GGTAGCTAGAATTAGTTGTTCTTGGT 58.896 38.462 0.00 7.07 40.41 3.67
2150 7923 7.278203 GGTAGCTAGAATTAGTTGTTCTTGGTC 59.722 40.741 0.00 0.64 38.99 4.02
2151 7924 6.769512 AGCTAGAATTAGTTGTTCTTGGTCA 58.230 36.000 0.00 0.00 35.38 4.02
2152 7925 7.398024 AGCTAGAATTAGTTGTTCTTGGTCAT 58.602 34.615 0.00 0.00 35.38 3.06
2153 7926 7.550906 AGCTAGAATTAGTTGTTCTTGGTCATC 59.449 37.037 0.00 0.00 35.38 2.92
2154 7927 7.201652 GCTAGAATTAGTTGTTCTTGGTCATCC 60.202 40.741 0.00 0.00 37.18 3.51
2155 7928 5.643777 AGAATTAGTTGTTCTTGGTCATCCG 59.356 40.000 0.00 0.00 32.17 4.18
2156 7929 4.610605 TTAGTTGTTCTTGGTCATCCGA 57.389 40.909 0.00 0.00 36.30 4.55
2157 7930 3.485463 AGTTGTTCTTGGTCATCCGAA 57.515 42.857 0.00 0.00 36.30 4.30
2176 7949 4.041723 CGAACATCCCCGCAAAATTTATC 58.958 43.478 0.00 0.00 0.00 1.75
2190 7963 7.590689 CGCAAAATTTATCCAATTGCAACTTTT 59.409 29.630 0.00 4.42 44.94 2.27
2191 7964 8.692615 GCAAAATTTATCCAATTGCAACTTTTG 58.307 29.630 21.25 21.25 44.29 2.44
2198 7971 3.248125 CCAATTGCAACTTTTGAACGCAT 59.752 39.130 11.88 0.00 31.67 4.73
2212 7985 5.850557 TGAACGCATCCAAATTATTCCAT 57.149 34.783 0.00 0.00 0.00 3.41
2225 7998 1.953559 ATTCCATAGAACGCGCACAT 58.046 45.000 5.73 0.00 33.97 3.21
2252 8025 6.155910 AGGAGAATTTTGATCAGCAGAGTCTA 59.844 38.462 0.00 0.00 0.00 2.59
2394 8167 3.691342 CCCAAGCCGTCGTCTCCA 61.691 66.667 0.00 0.00 0.00 3.86
2398 8171 0.456221 CAAGCCGTCGTCTCCATACT 59.544 55.000 0.00 0.00 0.00 2.12
2757 8530 0.602905 CCAACCTCGACGCCTTCTTT 60.603 55.000 0.00 0.00 0.00 2.52
2770 8543 1.553706 CTTCTTTGCAGGGAAGCCAT 58.446 50.000 14.67 0.00 33.68 4.40
2819 8592 0.320771 GACACCATCTGTCTGCGGTT 60.321 55.000 0.00 0.00 45.38 4.44
2826 8599 0.109272 TCTGTCTGCGGTTCGATGTC 60.109 55.000 0.00 0.00 0.00 3.06
2827 8600 1.078759 CTGTCTGCGGTTCGATGTCC 61.079 60.000 0.00 0.00 0.00 4.02
2847 8620 7.707624 TGTCCTCTGAATAAATTTGCAGAAT 57.292 32.000 16.07 0.00 36.99 2.40
2850 8623 7.430502 GTCCTCTGAATAAATTTGCAGAATTCG 59.569 37.037 16.07 8.44 36.99 3.34
2851 8624 6.694411 CCTCTGAATAAATTTGCAGAATTCGG 59.306 38.462 16.07 13.67 36.99 4.30
2853 8626 7.250569 TCTGAATAAATTTGCAGAATTCGGTC 58.749 34.615 14.70 0.97 35.42 4.79
2876 8649 9.245962 GGTCATGTATATGTAGTTCAGTGTAAC 57.754 37.037 0.00 0.00 35.73 2.50
2885 8658 3.577919 AGTTCAGTGTAACCCAGTCTCT 58.422 45.455 0.00 0.00 37.80 3.10
2902 8675 8.260818 CCCAGTCTCTTGAGTGAATAAAATCTA 58.739 37.037 2.77 0.00 44.27 1.98
3041 9606 3.363341 AACCACGCGAAAATGATGTTT 57.637 38.095 15.93 0.00 0.00 2.83
3143 9709 8.877808 TCAAACACATTACTAGATATGAGCTG 57.122 34.615 13.31 8.25 0.00 4.24
3253 9821 2.752903 AGGGTCCGTTAAATTGATGCAC 59.247 45.455 0.00 0.00 0.00 4.57
3269 9837 1.271543 TGCACTGTGCCTCAAATAGCT 60.272 47.619 28.17 0.00 44.23 3.32
3304 9872 7.039363 TGTGTCTTTAATTTATTGTTCCTGGGG 60.039 37.037 0.00 0.00 0.00 4.96
3529 10097 9.476202 AAAGAAAAATATTTTCCTGTGTAGCAC 57.524 29.630 13.68 0.00 34.56 4.40
3586 10154 2.584418 CATGGTGCTCTCGCCTCG 60.584 66.667 0.00 0.00 43.26 4.63
3608 10176 3.438781 GTCTGTGTTTGTGTGGTTTCAGA 59.561 43.478 0.00 0.00 0.00 3.27
3609 10177 4.096382 GTCTGTGTTTGTGTGGTTTCAGAT 59.904 41.667 0.00 0.00 34.15 2.90
3610 10178 4.704540 TCTGTGTTTGTGTGGTTTCAGATT 59.295 37.500 0.00 0.00 0.00 2.40
3652 10220 1.283029 TGCAGAGAGCCCTTATTTGCT 59.717 47.619 0.00 0.00 44.83 3.91
3654 10222 2.295885 CAGAGAGCCCTTATTTGCTGG 58.704 52.381 0.00 0.00 38.11 4.85
3753 10321 4.520111 AGCAAATCTAGCACATTGACACAA 59.480 37.500 0.00 0.00 0.00 3.33
3764 10332 6.376299 AGCACATTGACACAACATCAATCTAT 59.624 34.615 0.00 0.00 43.39 1.98
3912 10482 4.866682 TTGTCATTTTTGTTTTTCGGGC 57.133 36.364 0.00 0.00 0.00 6.13
3917 10487 2.217429 TTTTGTTTTTCGGGCTCTGC 57.783 45.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 1.800586 TCGACATTCTTTGTGCTCAGC 59.199 47.619 0.00 0.00 39.18 4.26
166 167 1.803519 GAAGAGCTCGCGGTCAGTG 60.804 63.158 6.13 0.00 40.07 3.66
171 172 0.946221 CTTTGTGAAGAGCTCGCGGT 60.946 55.000 6.13 0.00 37.37 5.68
193 194 4.873827 GTGGACTAATCGATGCCAGTTTTA 59.126 41.667 0.00 0.00 0.00 1.52
205 208 1.734163 GGTTGGTGGTGGACTAATCG 58.266 55.000 0.00 0.00 0.00 3.34
261 264 1.134818 TGTGCATGGTCTCATCGTACC 60.135 52.381 0.00 0.00 36.24 3.34
280 283 3.119352 GGGACCTGCTGCTTTTAGATTTG 60.119 47.826 0.00 0.00 0.00 2.32
302 305 1.443872 CGACCAAGACGAACCGGAG 60.444 63.158 9.46 0.76 0.00 4.63
328 4347 1.309950 CGCTAGAGGTCGAGGAATCA 58.690 55.000 0.00 0.00 0.00 2.57
332 4351 2.864378 TTCGCGCTAGAGGTCGAGGA 62.864 60.000 5.56 0.00 32.31 3.71
339 4358 1.226717 GTCTGGTTCGCGCTAGAGG 60.227 63.158 5.56 0.00 0.00 3.69
343 4362 2.707849 GGAGGTCTGGTTCGCGCTA 61.708 63.158 5.56 0.00 0.00 4.26
402 4421 1.071567 GTTACTGACGTCGGAGCAGC 61.072 60.000 30.55 12.83 33.03 5.25
411 4430 1.081641 CGCCGTGAGTTACTGACGT 60.082 57.895 21.20 0.00 39.27 4.34
461 4490 0.303493 CCGTATTTCAATGTCGGCGG 59.697 55.000 7.21 0.00 33.33 6.13
470 4499 0.674269 GGACCCGCACCGTATTTCAA 60.674 55.000 0.00 0.00 0.00 2.69
471 4500 1.078988 GGACCCGCACCGTATTTCA 60.079 57.895 0.00 0.00 0.00 2.69
486 4515 0.819582 CCCATTGTTGGCATCTGGAC 59.180 55.000 5.63 0.00 42.15 4.02
505 4534 2.359900 CTATCCAGTTGTCAACCTGCC 58.640 52.381 12.17 0.00 0.00 4.85
530 4559 3.909285 GGGAGTACCGGTAGCCGC 61.909 72.222 16.41 13.90 46.86 6.53
538 4567 2.264794 GTGGCACTGGGAGTACCG 59.735 66.667 11.13 0.00 44.64 4.02
539 4568 2.669240 GGTGGCACTGGGAGTACC 59.331 66.667 18.45 0.00 40.81 3.34
560 4589 2.260844 ATACATCCCGATGCAACAGG 57.739 50.000 4.58 0.00 42.39 4.00
564 4593 1.939381 GCGCTATACATCCCGATGCAA 60.939 52.381 0.00 0.00 42.39 4.08
569 4598 2.257371 GCGCGCTATACATCCCGA 59.743 61.111 26.67 0.00 0.00 5.14
611 6348 2.030562 ACAACCGAGTCCTTGGCG 59.969 61.111 0.16 0.00 37.67 5.69
615 6352 1.120530 ACTGTCACAACCGAGTCCTT 58.879 50.000 0.00 0.00 0.00 3.36
620 6357 0.030235 TCGTCACTGTCACAACCGAG 59.970 55.000 0.00 0.00 0.00 4.63
622 6359 1.213094 GGTCGTCACTGTCACAACCG 61.213 60.000 0.00 0.00 0.00 4.44
623 6360 0.878961 GGGTCGTCACTGTCACAACC 60.879 60.000 0.00 0.00 0.00 3.77
626 6363 2.852180 CGGGGTCGTCACTGTCACA 61.852 63.158 0.00 0.00 0.00 3.58
647 6384 4.295119 GACCCGGCGCCATATCGT 62.295 66.667 28.98 13.89 0.00 3.73
648 6385 4.293648 TGACCCGGCGCCATATCG 62.294 66.667 28.98 11.99 0.00 2.92
649 6386 2.357517 CTGACCCGGCGCCATATC 60.358 66.667 28.98 19.75 0.00 1.63
650 6387 2.439960 TTCTGACCCGGCGCCATAT 61.440 57.895 28.98 10.60 0.00 1.78
651 6388 3.078196 TTCTGACCCGGCGCCATA 61.078 61.111 28.98 6.07 0.00 2.74
658 6396 0.602905 AAGCGAAAGTTCTGACCCGG 60.603 55.000 0.00 0.00 0.00 5.73
661 6399 0.238553 GGCAAGCGAAAGTTCTGACC 59.761 55.000 0.00 0.00 0.00 4.02
673 6411 1.518056 TTCTTCAGCAAGGGCAAGCG 61.518 55.000 0.00 0.00 44.61 4.68
693 6431 2.270874 AAACCTAGCTCGCCATGGGG 62.271 60.000 22.46 22.46 37.18 4.96
759 6497 0.616395 TGACCGCATCCACTTCCCTA 60.616 55.000 0.00 0.00 0.00 3.53
831 6569 5.697473 TGAACATGAAATAGACGGCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
832 6570 5.182950 ACATGAACATGAAATAGACGGCAAA 59.817 36.000 19.56 0.00 41.20 3.68
833 6571 4.699735 ACATGAACATGAAATAGACGGCAA 59.300 37.500 19.56 0.00 41.20 4.52
834 6572 4.094739 CACATGAACATGAAATAGACGGCA 59.905 41.667 19.56 0.00 41.20 5.69
835 6573 4.332543 TCACATGAACATGAAATAGACGGC 59.667 41.667 19.56 0.00 41.20 5.68
836 6574 6.421377 TTCACATGAACATGAAATAGACGG 57.579 37.500 19.56 0.92 41.20 4.79
837 6575 6.412943 GCATTCACATGAACATGAAATAGACG 59.587 38.462 19.56 8.89 41.20 4.18
839 6577 7.393841 TGCATTCACATGAACATGAAATAGA 57.606 32.000 19.56 7.75 41.20 1.98
840 6578 8.468720 TTTGCATTCACATGAACATGAAATAG 57.531 30.769 19.56 13.04 41.20 1.73
843 6581 8.828688 TTATTTGCATTCACATGAACATGAAA 57.171 26.923 19.56 13.38 41.20 2.69
844 6582 7.546316 CCTTATTTGCATTCACATGAACATGAA 59.454 33.333 19.56 7.41 41.20 2.57
846 6584 6.814644 ACCTTATTTGCATTCACATGAACATG 59.185 34.615 12.43 12.43 44.15 3.21
847 6585 6.814644 CACCTTATTTGCATTCACATGAACAT 59.185 34.615 0.00 0.00 36.80 2.71
848 6586 6.157904 CACCTTATTTGCATTCACATGAACA 58.842 36.000 0.00 0.00 36.80 3.18
849 6587 6.158598 ACACCTTATTTGCATTCACATGAAC 58.841 36.000 0.00 0.00 36.80 3.18
850 6588 6.343716 ACACCTTATTTGCATTCACATGAA 57.656 33.333 0.00 0.00 38.56 2.57
851 6589 5.981088 ACACCTTATTTGCATTCACATGA 57.019 34.783 0.00 0.00 31.07 3.07
853 6591 9.723601 AAATTTACACCTTATTTGCATTCACAT 57.276 25.926 0.00 0.00 0.00 3.21
866 6619 6.621316 TTTCAGACGCAAATTTACACCTTA 57.379 33.333 0.00 0.00 0.00 2.69
870 6623 6.075280 ACGTATTTCAGACGCAAATTTACAC 58.925 36.000 0.00 0.00 44.14 2.90
895 6648 3.977579 CGATGTCATCAATGTCCGTCTAG 59.022 47.826 13.22 0.00 0.00 2.43
896 6649 3.795488 GCGATGTCATCAATGTCCGTCTA 60.795 47.826 13.22 0.00 0.00 2.59
897 6650 2.814269 CGATGTCATCAATGTCCGTCT 58.186 47.619 13.22 0.00 0.00 4.18
899 6652 1.290203 GCGATGTCATCAATGTCCGT 58.710 50.000 13.22 0.00 0.00 4.69
900 6653 0.230515 CGCGATGTCATCAATGTCCG 59.769 55.000 13.22 0.00 0.00 4.79
902 6655 3.538780 CAATCGCGATGTCATCAATGTC 58.461 45.455 24.47 0.00 0.00 3.06
903 6656 2.288729 CCAATCGCGATGTCATCAATGT 59.711 45.455 24.47 0.00 0.00 2.71
904 6657 2.288729 ACCAATCGCGATGTCATCAATG 59.711 45.455 24.47 14.00 0.00 2.82
905 6658 2.545526 GACCAATCGCGATGTCATCAAT 59.454 45.455 26.02 7.19 0.00 2.57
906 6659 1.933181 GACCAATCGCGATGTCATCAA 59.067 47.619 26.02 0.00 0.00 2.57
907 6660 1.570813 GACCAATCGCGATGTCATCA 58.429 50.000 26.02 0.00 0.00 3.07
908 6661 0.861837 GGACCAATCGCGATGTCATC 59.138 55.000 29.53 21.26 0.00 2.92
910 6663 1.518352 CGGACCAATCGCGATGTCA 60.518 57.895 29.53 4.51 0.00 3.58
912 6665 2.890474 GCGGACCAATCGCGATGT 60.890 61.111 24.47 17.34 43.71 3.06
919 6672 1.523032 CCTAACCCGCGGACCAATC 60.523 63.158 30.73 0.00 0.00 2.67
920 6673 2.587889 CCTAACCCGCGGACCAAT 59.412 61.111 30.73 10.07 0.00 3.16
995 6750 1.021390 CCACCAGCAGACATCGGTTC 61.021 60.000 0.00 0.00 0.00 3.62
1042 6798 1.521580 AGCTATCGCCTACGGAGTAC 58.478 55.000 0.00 0.00 39.29 2.73
1043 6799 2.267174 AAGCTATCGCCTACGGAGTA 57.733 50.000 0.00 0.00 42.66 2.59
1044 6800 1.878734 GTAAGCTATCGCCTACGGAGT 59.121 52.381 0.00 0.00 40.62 3.85
1045 6801 1.199558 GGTAAGCTATCGCCTACGGAG 59.800 57.143 0.00 0.00 40.63 4.63
1047 6803 0.956633 TGGTAAGCTATCGCCTACGG 59.043 55.000 0.00 0.00 40.63 4.02
1048 6804 3.243336 GAATGGTAAGCTATCGCCTACG 58.757 50.000 0.00 0.00 34.57 3.51
1049 6805 3.586892 GGAATGGTAAGCTATCGCCTAC 58.413 50.000 0.00 0.00 36.60 3.18
1061 6821 1.200519 CGTGGAGGAGGGAATGGTAA 58.799 55.000 0.00 0.00 0.00 2.85
1136 6897 3.965539 CTCAGGGAACAGCGGCTGG 62.966 68.421 31.38 14.22 35.51 4.85
1519 7283 9.835389 CTAGACAACTAACTACTACTGGAGTAT 57.165 37.037 0.00 0.00 39.98 2.12
1526 7290 9.012161 CCAAGAACTAGACAACTAACTACTACT 57.988 37.037 0.00 0.00 0.00 2.57
1527 7291 7.754475 GCCAAGAACTAGACAACTAACTACTAC 59.246 40.741 0.00 0.00 0.00 2.73
1530 7294 5.868258 GGCCAAGAACTAGACAACTAACTAC 59.132 44.000 0.00 0.00 0.00 2.73
1531 7295 5.541101 TGGCCAAGAACTAGACAACTAACTA 59.459 40.000 0.61 0.00 0.00 2.24
1590 7356 0.321996 GCGAAGGGGAAGAACAGAGT 59.678 55.000 0.00 0.00 0.00 3.24
1636 7409 1.068083 TCGCATCTCCTCAATCGGC 59.932 57.895 0.00 0.00 0.00 5.54
1687 7460 1.739562 GAGCACGACAGGCTTGGAG 60.740 63.158 0.00 0.00 42.78 3.86
1688 7461 2.343758 GAGCACGACAGGCTTGGA 59.656 61.111 0.00 0.00 42.78 3.53
1689 7462 2.743928 GGAGCACGACAGGCTTGG 60.744 66.667 0.00 0.00 42.78 3.61
1690 7463 2.031516 CAGGAGCACGACAGGCTTG 61.032 63.158 0.00 0.00 42.78 4.01
1691 7464 2.345244 CAGGAGCACGACAGGCTT 59.655 61.111 0.00 0.00 42.78 4.35
1692 7465 3.699894 CCAGGAGCACGACAGGCT 61.700 66.667 0.00 0.00 46.07 4.58
1774 7547 0.943835 CTGTGTCCGCGTCAACATCA 60.944 55.000 4.92 6.92 0.00 3.07
1803 7576 4.451150 CTGTAAGGAGCGCCCGCA 62.451 66.667 15.50 6.73 44.88 5.69
1988 7761 0.179092 GCTATAACAAGCCCGACGGT 60.179 55.000 13.94 0.00 36.45 4.83
2101 7874 1.410850 ATTGATGGGGATCCGCGACT 61.411 55.000 22.58 10.74 35.24 4.18
2102 7875 0.951040 GATTGATGGGGATCCGCGAC 60.951 60.000 22.58 18.29 35.24 5.19
2103 7876 1.371183 GATTGATGGGGATCCGCGA 59.629 57.895 22.58 12.85 35.24 5.87
2106 7879 2.029288 CGCGATTGATGGGGATCCG 61.029 63.158 0.00 0.00 35.24 4.18
2149 7922 1.904990 TTGCGGGGATGTTCGGATGA 61.905 55.000 0.00 0.00 0.00 2.92
2150 7923 1.029408 TTTGCGGGGATGTTCGGATG 61.029 55.000 0.00 0.00 0.00 3.51
2151 7924 0.322997 TTTTGCGGGGATGTTCGGAT 60.323 50.000 0.00 0.00 0.00 4.18
2152 7925 0.322997 ATTTTGCGGGGATGTTCGGA 60.323 50.000 0.00 0.00 0.00 4.55
2153 7926 0.530288 AATTTTGCGGGGATGTTCGG 59.470 50.000 0.00 0.00 0.00 4.30
2154 7927 2.362169 AAATTTTGCGGGGATGTTCG 57.638 45.000 0.00 0.00 0.00 3.95
2155 7928 4.142049 TGGATAAATTTTGCGGGGATGTTC 60.142 41.667 0.00 0.00 0.00 3.18
2156 7929 3.772025 TGGATAAATTTTGCGGGGATGTT 59.228 39.130 0.00 0.00 0.00 2.71
2157 7930 3.370104 TGGATAAATTTTGCGGGGATGT 58.630 40.909 0.00 0.00 0.00 3.06
2176 7949 2.606725 TGCGTTCAAAAGTTGCAATTGG 59.393 40.909 0.59 0.00 31.69 3.16
2190 7963 5.850557 ATGGAATAATTTGGATGCGTTCA 57.149 34.783 0.00 0.00 0.00 3.18
2191 7964 7.202016 TCTATGGAATAATTTGGATGCGTTC 57.798 36.000 0.00 0.00 0.00 3.95
2198 7971 4.024387 GCGCGTTCTATGGAATAATTTGGA 60.024 41.667 8.43 0.00 33.71 3.53
2212 7985 0.179137 CTCCTCATGTGCGCGTTCTA 60.179 55.000 8.43 0.00 0.00 2.10
2225 7998 5.169992 TCTGCTGATCAAAATTCTCCTCA 57.830 39.130 0.00 0.00 0.00 3.86
2252 8025 1.611977 CCTGCCATCGATTGCATCATT 59.388 47.619 22.82 0.00 36.79 2.57
2389 8162 1.386533 GGGACGAACGAGTATGGAGA 58.613 55.000 0.14 0.00 0.00 3.71
2394 8167 1.660560 CGGTGGGGACGAACGAGTAT 61.661 60.000 0.14 0.00 0.00 2.12
2398 8171 3.980989 CACGGTGGGGACGAACGA 61.981 66.667 0.00 0.00 34.93 3.85
2770 8543 4.020617 CTCCACGGGGCTGAGCAA 62.021 66.667 6.82 0.00 0.00 3.91
2819 8592 5.879777 TGCAAATTTATTCAGAGGACATCGA 59.120 36.000 0.00 0.00 0.00 3.59
2826 8599 6.694411 CCGAATTCTGCAAATTTATTCAGAGG 59.306 38.462 3.52 9.57 36.97 3.69
2827 8600 7.253422 ACCGAATTCTGCAAATTTATTCAGAG 58.747 34.615 3.52 7.46 36.97 3.35
2847 8620 7.147966 ACACTGAACTACATATACATGACCGAA 60.148 37.037 0.00 0.00 35.96 4.30
2850 8623 9.245962 GTTACACTGAACTACATATACATGACC 57.754 37.037 0.00 0.00 35.96 4.02
2851 8624 9.245962 GGTTACACTGAACTACATATACATGAC 57.754 37.037 0.00 0.00 35.96 3.06
2853 8626 8.201464 TGGGTTACACTGAACTACATATACATG 58.799 37.037 0.00 0.00 38.21 3.21
2876 8649 7.108847 AGATTTTATTCACTCAAGAGACTGGG 58.891 38.462 3.73 0.00 0.00 4.45
2902 8675 4.769688 TGAATTACTGACCGATTGCTCAT 58.230 39.130 0.00 0.00 0.00 2.90
3027 9592 5.117592 CAGGACTTTGAAACATCATTTTCGC 59.882 40.000 0.00 0.00 38.17 4.70
3069 9634 4.954202 ACATCACTCTCTTAACATCCCGTA 59.046 41.667 0.00 0.00 0.00 4.02
3151 9717 9.328845 ACTATTCAATGCTGATTTTGTTTTTGT 57.671 25.926 0.00 0.00 0.00 2.83
3152 9718 9.588774 CACTATTCAATGCTGATTTTGTTTTTG 57.411 29.630 0.00 0.00 0.00 2.44
3170 9736 6.368791 GTGACATTACTGTTCAGCACTATTCA 59.631 38.462 0.00 0.00 35.14 2.57
3253 9821 7.062605 CACAAATAAAAGCTATTTGAGGCACAG 59.937 37.037 21.67 0.00 43.76 3.66
3304 9872 5.403897 TTCTCAATCGACACACAAGAAAC 57.596 39.130 0.00 0.00 0.00 2.78
3480 10048 6.764877 TCGAACACAATGAGAGTCTTTTAC 57.235 37.500 0.00 0.00 0.00 2.01
3578 10146 0.597637 ACAAACACAGACGAGGCGAG 60.598 55.000 0.00 0.00 0.00 5.03
3586 10154 3.438781 TCTGAAACCACACAAACACAGAC 59.561 43.478 0.00 0.00 0.00 3.51
3627 10195 1.885049 TAAGGGCTCTCTGCAATCCT 58.115 50.000 0.00 0.00 45.15 3.24
3681 10249 1.888512 TCCGGTACACCTGTAACACTC 59.111 52.381 0.00 0.00 38.08 3.51
3682 10250 1.999648 TCCGGTACACCTGTAACACT 58.000 50.000 0.00 0.00 38.08 3.55
3753 10321 8.836268 AATTTTGCAACAACATAGATTGATGT 57.164 26.923 0.00 0.00 42.56 3.06
3890 10460 4.938226 AGCCCGAAAAACAAAAATGACAAA 59.062 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.