Multiple sequence alignment - TraesCS3A01G345800

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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 TraesCS3A01G345800 chr3A 100.000 4052 0 0 1 4052 595062575 595058524 0.000000e+00 7483.0
1 TraesCS3A01G345800 chr3B 91.193 3168 158 55 61 3184 594746320 594743230 0.000000e+00 4193.0
2 TraesCS3A01G345800 chr3B 93.286 1415 61 19 1238 2639 680235315 680233922 0.000000e+00 2056.0
3 TraesCS3A01G345800 chr3B 86.994 692 53 20 3371 4049 594739882 594739215 0.000000e+00 745.0
4 TraesCS3A01G345800 chr3B 95.312 64 3 0 3290 3353 594743105 594743042 7.170000e-18 102.0
5 TraesCS3A01G345800 chr3D 92.942 2706 101 32 613 3272 452619953 452617292 0.000000e+00 3856.0
6 TraesCS3A01G345800 chr3D 89.275 690 31 16 3370 4052 452617108 452616455 0.000000e+00 824.0
7 TraesCS3A01G345800 chr3D 85.667 600 49 17 1 582 452621021 452620441 7.500000e-167 597.0
8 TraesCS3A01G345800 chr3D 93.750 64 4 0 3290 3353 452617227 452617164 3.330000e-16 97.1
9 TraesCS3A01G345800 chr5B 93.216 1415 62 19 1238 2639 411026785 411025392 0.000000e+00 2050.0
10 TraesCS3A01G345800 chr1B 93.074 1415 64 19 1238 2639 353273956 353272563 0.000000e+00 2039.0
11 TraesCS3A01G345800 chr1B 82.377 1918 305 24 1074 2976 532693355 532695254 0.000000e+00 1639.0
12 TraesCS3A01G345800 chr7A 93.111 1408 65 17 1238 2634 608482221 608483607 0.000000e+00 2034.0
13 TraesCS3A01G345800 chr1D 82.488 1913 312 18 1074 2976 397285115 397287014 0.000000e+00 1655.0
14 TraesCS3A01G345800 chr1A 82.264 1917 312 24 1074 2976 494799607 494801509 0.000000e+00 1631.0
15 TraesCS3A01G345800 chr2D 82.193 1213 199 12 1115 2320 432871707 432870505 0.000000e+00 1027.0
16 TraesCS3A01G345800 chr7D 97.279 441 10 2 2316 2755 236582801 236582362 0.000000e+00 747.0


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 TraesCS3A01G345800 chr3A 595058524 595062575 4051 True 7483.000 7483 100.000000 1 4052 1 chr3A.!!$R1 4051
1 TraesCS3A01G345800 chr3B 680233922 680235315 1393 True 2056.000 2056 93.286000 1238 2639 1 chr3B.!!$R1 1401
2 TraesCS3A01G345800 chr3B 594739215 594746320 7105 True 1680.000 4193 91.166333 61 4049 3 chr3B.!!$R2 3988
3 TraesCS3A01G345800 chr3D 452616455 452621021 4566 True 1343.525 3856 90.408500 1 4052 4 chr3D.!!$R1 4051
4 TraesCS3A01G345800 chr5B 411025392 411026785 1393 True 2050.000 2050 93.216000 1238 2639 1 chr5B.!!$R1 1401
5 TraesCS3A01G345800 chr1B 353272563 353273956 1393 True 2039.000 2039 93.074000 1238 2639 1 chr1B.!!$R1 1401
6 TraesCS3A01G345800 chr1B 532693355 532695254 1899 False 1639.000 1639 82.377000 1074 2976 1 chr1B.!!$F1 1902
7 TraesCS3A01G345800 chr7A 608482221 608483607 1386 False 2034.000 2034 93.111000 1238 2634 1 chr7A.!!$F1 1396
8 TraesCS3A01G345800 chr1D 397285115 397287014 1899 False 1655.000 1655 82.488000 1074 2976 1 chr1D.!!$F1 1902
9 TraesCS3A01G345800 chr1A 494799607 494801509 1902 False 1631.000 1631 82.264000 1074 2976 1 chr1A.!!$F1 1902
10 TraesCS3A01G345800 chr2D 432870505 432871707 1202 True 1027.000 1027 82.193000 1115 2320 1 chr2D.!!$R1 1205

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
943 1454 0.103572 ATACCATTTCCGTCCGTCCG 59.896 55.0 0.0 0.0 0.0 4.79 F
2175 2720 0.397254 TCTCCGTCTCATTCTCCCCC 60.397 60.0 0.0 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2822 1.076632 CTCGGAGTAGAGCAGGGGT 60.077 63.158 0.00 0.0 0.00 4.95 R
3286 3831 0.036388 GATCAGGCAGACCGGTTTCA 60.036 55.000 9.42 0.0 42.76 2.69 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
36 37 1.092921 TTCAACGTGTGTGGAGGCAC 61.093 55.000 0.00 0.00 39.65 5.01
40 41 3.022287 GTGTGTGGAGGCACGTTG 58.978 61.111 0.00 0.00 41.94 4.10
41 42 2.899838 TGTGTGGAGGCACGTTGC 60.900 61.111 0.00 0.00 44.08 4.17
42 43 4.012895 GTGTGGAGGCACGTTGCG 62.013 66.667 0.00 0.00 46.21 4.85
107 116 8.149647 AGTTGCCATGATCAACAAAGAAAATTA 58.850 29.630 23.37 0.00 44.50 1.40
122 131 8.866956 CAAAGAAAATTATTTCAGCTCATCCAC 58.133 33.333 4.34 0.00 46.03 4.02
127 136 8.443953 AAATTATTTCAGCTCATCCACTCTAC 57.556 34.615 0.00 0.00 0.00 2.59
128 137 6.798427 TTATTTCAGCTCATCCACTCTACT 57.202 37.500 0.00 0.00 0.00 2.57
129 138 4.727507 TTTCAGCTCATCCACTCTACTC 57.272 45.455 0.00 0.00 0.00 2.59
130 139 2.660572 TCAGCTCATCCACTCTACTCC 58.339 52.381 0.00 0.00 0.00 3.85
131 140 2.243478 TCAGCTCATCCACTCTACTCCT 59.757 50.000 0.00 0.00 0.00 3.69
132 141 3.030291 CAGCTCATCCACTCTACTCCTT 58.970 50.000 0.00 0.00 0.00 3.36
133 142 3.068024 CAGCTCATCCACTCTACTCCTTC 59.932 52.174 0.00 0.00 0.00 3.46
134 143 3.052944 AGCTCATCCACTCTACTCCTTCT 60.053 47.826 0.00 0.00 0.00 2.85
135 144 4.167113 AGCTCATCCACTCTACTCCTTCTA 59.833 45.833 0.00 0.00 0.00 2.10
148 157 1.063567 TCCTTCTAGGAGGGAGTCAGC 60.064 57.143 17.66 0.00 40.06 4.26
178 187 1.541670 GGACGTTTGCCTCAAGGTACA 60.542 52.381 0.00 0.00 37.57 2.90
179 188 2.423577 GACGTTTGCCTCAAGGTACAT 58.576 47.619 0.00 0.00 37.57 2.29
180 189 2.151202 ACGTTTGCCTCAAGGTACATG 58.849 47.619 0.00 0.00 37.57 3.21
199 209 0.848305 GCTGCTTTGTGCTTGTTTCG 59.152 50.000 0.00 0.00 43.37 3.46
235 245 3.160269 CCTCAAGGAAGGAAAACTGCAT 58.840 45.455 0.00 0.00 38.87 3.96
247 257 4.441792 GAAAACTGCATTGTGTTTCCCTT 58.558 39.130 2.65 0.00 35.63 3.95
261 271 2.620112 CCCTTGTGAAGCCTGCGTG 61.620 63.158 0.00 0.00 0.00 5.34
270 280 2.731691 AAGCCTGCGTGGTCGAACAT 62.732 55.000 6.36 0.00 39.71 2.71
291 301 6.360618 ACATAATCTTTCCAGAGGCCTAAAG 58.639 40.000 16.59 16.59 30.36 1.85
299 309 3.054361 TCCAGAGGCCTAAAGAAATGGAC 60.054 47.826 4.42 0.00 30.85 4.02
324 335 2.494059 ACAAAGATGTTGCGTGCTAGT 58.506 42.857 0.00 0.00 35.91 2.57
326 337 4.062293 ACAAAGATGTTGCGTGCTAGTAA 58.938 39.130 0.00 0.00 35.91 2.24
338 349 0.179084 GCTAGTAACGGCCATGCTCA 60.179 55.000 2.24 0.00 0.00 4.26
340 351 0.179084 TAGTAACGGCCATGCTCAGC 60.179 55.000 2.24 0.00 0.00 4.26
341 352 2.124736 TAACGGCCATGCTCAGCC 60.125 61.111 2.24 0.90 46.17 4.85
379 397 1.068741 CCCGATCTTCTCCCGGTAAAG 59.931 57.143 0.00 0.67 41.53 1.85
380 398 1.538419 CCGATCTTCTCCCGGTAAAGC 60.538 57.143 0.00 0.00 38.55 3.51
381 399 1.136305 CGATCTTCTCCCGGTAAAGCA 59.864 52.381 0.00 0.00 0.00 3.91
420 438 0.107508 CATTCTCGTGTGCCCCATCT 60.108 55.000 0.00 0.00 0.00 2.90
421 439 0.179000 ATTCTCGTGTGCCCCATCTC 59.821 55.000 0.00 0.00 0.00 2.75
422 440 1.191489 TTCTCGTGTGCCCCATCTCA 61.191 55.000 0.00 0.00 0.00 3.27
423 441 0.977627 TCTCGTGTGCCCCATCTCAT 60.978 55.000 0.00 0.00 0.00 2.90
425 443 1.524621 CGTGTGCCCCATCTCATCC 60.525 63.158 0.00 0.00 0.00 3.51
426 444 1.524621 GTGTGCCCCATCTCATCCG 60.525 63.158 0.00 0.00 0.00 4.18
427 445 1.995066 TGTGCCCCATCTCATCCGT 60.995 57.895 0.00 0.00 0.00 4.69
429 447 2.427753 GCCCCATCTCATCCGTCC 59.572 66.667 0.00 0.00 0.00 4.79
430 448 2.737180 CCCCATCTCATCCGTCCG 59.263 66.667 0.00 0.00 0.00 4.79
431 449 2.134287 CCCCATCTCATCCGTCCGT 61.134 63.158 0.00 0.00 0.00 4.69
432 450 1.068083 CCCATCTCATCCGTCCGTG 59.932 63.158 0.00 0.00 0.00 4.94
512 530 4.635925 GCGACACGATCCGATGAT 57.364 55.556 0.00 0.00 0.00 2.45
513 531 2.425278 GCGACACGATCCGATGATC 58.575 57.895 0.00 0.00 43.36 2.92
558 579 3.239449 ACTCACCACACTCATCCAACTA 58.761 45.455 0.00 0.00 0.00 2.24
561 582 4.096681 TCACCACACTCATCCAACTAGAT 58.903 43.478 0.00 0.00 0.00 1.98
563 584 5.719563 TCACCACACTCATCCAACTAGATTA 59.280 40.000 0.00 0.00 0.00 1.75
572 593 5.491078 TCATCCAACTAGATTAACCCAACCT 59.509 40.000 0.00 0.00 0.00 3.50
575 596 4.524053 CAACTAGATTAACCCAACCTCCC 58.476 47.826 0.00 0.00 0.00 4.30
576 597 3.810623 ACTAGATTAACCCAACCTCCCA 58.189 45.455 0.00 0.00 0.00 4.37
577 598 4.380791 ACTAGATTAACCCAACCTCCCAT 58.619 43.478 0.00 0.00 0.00 4.00
635 1111 1.228510 CCTTCCAGCCATCTTCCCC 59.771 63.158 0.00 0.00 0.00 4.81
646 1122 0.110486 ATCTTCCCCGGCGCAATAAT 59.890 50.000 10.83 0.00 0.00 1.28
648 1124 0.872388 CTTCCCCGGCGCAATAATAC 59.128 55.000 10.83 0.00 0.00 1.89
649 1125 0.180642 TTCCCCGGCGCAATAATACA 59.819 50.000 10.83 0.00 0.00 2.29
650 1126 0.398696 TCCCCGGCGCAATAATACAT 59.601 50.000 10.83 0.00 0.00 2.29
652 1128 2.038689 TCCCCGGCGCAATAATACATAA 59.961 45.455 10.83 0.00 0.00 1.90
654 1130 2.160813 CCCGGCGCAATAATACATAACC 59.839 50.000 10.83 0.00 0.00 2.85
658 1134 5.274718 CGGCGCAATAATACATAACCAAAA 58.725 37.500 10.83 0.00 0.00 2.44
742 1231 5.646467 AAAATAATTCCCGTGATACGACG 57.354 39.130 2.52 0.00 46.05 5.12
751 1240 2.160065 CCGTGATACGACGTTCACAAAC 60.160 50.000 27.15 12.01 46.05 2.93
753 1242 2.156310 GTGATACGACGTTCACAAACCC 59.844 50.000 25.06 8.40 41.48 4.11
759 1248 3.626670 ACGACGTTCACAAACCCATAAAA 59.373 39.130 0.00 0.00 31.27 1.52
760 1249 4.276431 ACGACGTTCACAAACCCATAAAAT 59.724 37.500 0.00 0.00 31.27 1.82
763 1252 7.024768 CGACGTTCACAAACCCATAAAATAAT 58.975 34.615 0.00 0.00 31.27 1.28
764 1253 8.176365 CGACGTTCACAAACCCATAAAATAATA 58.824 33.333 0.00 0.00 31.27 0.98
765 1254 9.281075 GACGTTCACAAACCCATAAAATAATAC 57.719 33.333 0.00 0.00 31.27 1.89
766 1255 7.964011 ACGTTCACAAACCCATAAAATAATACG 59.036 33.333 0.00 0.00 31.27 3.06
767 1256 7.964011 CGTTCACAAACCCATAAAATAATACGT 59.036 33.333 0.00 0.00 31.27 3.57
801 1290 0.744771 GACACAGGGCGGATTCCTTC 60.745 60.000 0.30 0.00 31.06 3.46
802 1291 1.452108 CACAGGGCGGATTCCTTCC 60.452 63.158 0.30 2.31 41.59 3.46
803 1292 1.616628 ACAGGGCGGATTCCTTCCT 60.617 57.895 0.30 4.64 42.99 3.36
804 1293 1.147153 CAGGGCGGATTCCTTCCTC 59.853 63.158 9.83 2.54 42.99 3.71
833 1322 2.976494 AAAGTCCCACCCAACCAGCG 62.976 60.000 0.00 0.00 0.00 5.18
837 1326 4.974721 CCACCCAACCAGCGGCTT 62.975 66.667 0.00 0.00 0.00 4.35
838 1327 2.033448 CACCCAACCAGCGGCTTA 59.967 61.111 0.00 0.00 0.00 3.09
849 1355 3.994392 ACCAGCGGCTTATTATTACATCG 59.006 43.478 0.00 0.00 0.00 3.84
853 1359 3.060363 GCGGCTTATTATTACATCGTCGG 59.940 47.826 0.00 0.00 0.00 4.79
854 1360 4.478699 CGGCTTATTATTACATCGTCGGA 58.521 43.478 0.00 0.00 0.00 4.55
855 1361 4.557690 CGGCTTATTATTACATCGTCGGAG 59.442 45.833 0.00 0.00 0.00 4.63
856 1362 5.467705 GGCTTATTATTACATCGTCGGAGT 58.532 41.667 0.00 0.00 0.00 3.85
857 1363 6.615088 GGCTTATTATTACATCGTCGGAGTA 58.385 40.000 0.00 0.00 0.00 2.59
888 1394 1.187087 AATCTCACTCCACTCCGTCC 58.813 55.000 0.00 0.00 0.00 4.79
889 1395 0.333312 ATCTCACTCCACTCCGTCCT 59.667 55.000 0.00 0.00 0.00 3.85
890 1396 0.609406 TCTCACTCCACTCCGTCCTG 60.609 60.000 0.00 0.00 0.00 3.86
891 1397 0.896019 CTCACTCCACTCCGTCCTGT 60.896 60.000 0.00 0.00 0.00 4.00
940 1451 2.813061 CGTAATACCATTTCCGTCCGT 58.187 47.619 0.00 0.00 0.00 4.69
941 1452 2.791004 CGTAATACCATTTCCGTCCGTC 59.209 50.000 0.00 0.00 0.00 4.79
942 1453 2.320745 AATACCATTTCCGTCCGTCC 57.679 50.000 0.00 0.00 0.00 4.79
943 1454 0.103572 ATACCATTTCCGTCCGTCCG 59.896 55.000 0.00 0.00 0.00 4.79
949 1460 4.668118 TCCGTCCGTCCGCCAAAC 62.668 66.667 0.00 0.00 0.00 2.93
1953 2498 1.594293 CTCCGGCAAGTCAACGTGT 60.594 57.895 0.00 0.00 0.00 4.49
2175 2720 0.397254 TCTCCGTCTCATTCTCCCCC 60.397 60.000 0.00 0.00 0.00 5.40
2277 2822 4.830765 GCCGTGCCGATGCTGGTA 62.831 66.667 0.00 0.00 38.71 3.25
2475 3020 2.358003 GTGCTCAGCTTGGCGTCT 60.358 61.111 0.00 0.00 0.00 4.18
2478 3023 2.675056 GCTCAGCTTGGCGTCTGTG 61.675 63.158 0.00 0.84 0.00 3.66
2535 3080 0.400213 TCGTGGAAAAGCTGGTCCAT 59.600 50.000 18.90 0.00 45.50 3.41
3059 3604 2.909006 TGATGGCCTCCTAGGATGAATC 59.091 50.000 17.48 16.99 37.67 2.52
3085 3630 3.059597 CACGCTCTTCTTGTACAAACCAG 60.060 47.826 10.03 5.95 0.00 4.00
3123 3668 2.096218 GGCTGTGTCACGATTCTTTGAC 60.096 50.000 0.00 7.86 42.18 3.18
3140 3685 3.842732 TGACGCGAGAGAGATAACAAA 57.157 42.857 15.93 0.00 33.96 2.83
3141 3686 4.168922 TGACGCGAGAGAGATAACAAAA 57.831 40.909 15.93 0.00 33.96 2.44
3142 3687 4.744570 TGACGCGAGAGAGATAACAAAAT 58.255 39.130 15.93 0.00 33.96 1.82
3164 3709 3.062763 GTGAGTGAGTGGTGTTGATCAG 58.937 50.000 0.00 0.00 0.00 2.90
3165 3710 2.072298 GAGTGAGTGGTGTTGATCAGC 58.928 52.381 2.05 2.05 43.90 4.26
3177 3722 2.780065 TGATCAGCAAACAACTGTGC 57.220 45.000 0.00 0.00 41.22 4.57
3189 3734 0.108138 AACTGTGCATACGGAGCTCC 60.108 55.000 23.79 23.79 36.65 4.70
3209 3754 3.592814 CCGGCTCGGCTCGATGTA 61.593 66.667 0.56 0.00 41.17 2.29
3210 3755 2.411701 CGGCTCGGCTCGATGTAA 59.588 61.111 0.00 0.00 34.61 2.41
3214 3759 1.527311 GGCTCGGCTCGATGTAAAATC 59.473 52.381 0.00 0.00 34.61 2.17
3217 3762 1.483004 TCGGCTCGATGTAAAATCCCA 59.517 47.619 0.00 0.00 0.00 4.37
3244 3789 6.812656 CCGTTTGTATACCAAAATTTTACCCC 59.187 38.462 2.44 0.00 44.36 4.95
3245 3790 6.527372 CGTTTGTATACCAAAATTTTACCCCG 59.473 38.462 2.44 0.00 44.36 5.73
3246 3791 7.377398 GTTTGTATACCAAAATTTTACCCCGT 58.623 34.615 2.44 0.00 44.36 5.28
3247 3792 7.536159 TTGTATACCAAAATTTTACCCCGTT 57.464 32.000 2.44 0.00 0.00 4.44
3248 3793 7.155655 TGTATACCAAAATTTTACCCCGTTC 57.844 36.000 2.44 0.00 0.00 3.95
3273 3818 9.087424 TCTTCTTCTTGACACGAAATATACATG 57.913 33.333 0.00 0.00 0.00 3.21
3275 3820 9.599866 TTCTTCTTGACACGAAATATACATGAT 57.400 29.630 0.00 0.00 0.00 2.45
3297 3899 4.146745 ACTACAAAAGTGAAACCGGTCT 57.853 40.909 8.04 0.00 36.93 3.85
3302 3904 0.535102 AAGTGAAACCGGTCTGCCTG 60.535 55.000 8.04 0.00 37.80 4.85
3339 3941 4.116961 TGAGCTACCGGTATTCGATTTTG 58.883 43.478 16.25 0.69 42.43 2.44
3362 3997 1.014564 GGAAAGCAACCGTCTCCTCG 61.015 60.000 0.00 0.00 0.00 4.63
3510 7273 1.526917 GATGATTGGGACCAGCGGG 60.527 63.158 0.00 0.00 41.29 6.13
3564 7327 1.401931 CCGTCCAGGTTGTGTACGTAG 60.402 57.143 0.00 0.00 34.51 3.51
3566 7329 2.483877 CGTCCAGGTTGTGTACGTAGTA 59.516 50.000 0.00 0.00 45.11 1.82
3636 7400 2.364324 AGGTTCTACTTCACGTCTGCAA 59.636 45.455 0.00 0.00 0.00 4.08
3646 7410 3.649986 GTCTGCAACGCAACGGCT 61.650 61.111 0.00 0.00 38.41 5.52
3648 7412 4.389576 CTGCAACGCAACGGCTCC 62.390 66.667 0.00 0.00 38.41 4.70
3717 7484 2.656651 CGCCAAGATCTCCGCTCG 60.657 66.667 11.11 1.65 0.00 5.03
3877 7644 2.471743 GTGTTTCCTCGTCGAGAAAGTG 59.528 50.000 23.74 6.47 0.00 3.16
3885 7652 3.082548 TCGTCGAGAAAGTGAAGGATCT 58.917 45.455 0.00 0.00 0.00 2.75
3887 7654 2.926838 GTCGAGAAAGTGAAGGATCTGC 59.073 50.000 0.00 0.00 0.00 4.26
3902 7669 0.104855 TCTGCGCTGTTCTGTTCTGT 59.895 50.000 9.73 0.00 0.00 3.41
3903 7670 0.510359 CTGCGCTGTTCTGTTCTGTC 59.490 55.000 9.73 0.00 0.00 3.51
3904 7671 0.880278 TGCGCTGTTCTGTTCTGTCC 60.880 55.000 9.73 0.00 0.00 4.02
3905 7672 0.601311 GCGCTGTTCTGTTCTGTCCT 60.601 55.000 0.00 0.00 0.00 3.85
3906 7673 1.871080 CGCTGTTCTGTTCTGTCCTT 58.129 50.000 0.00 0.00 0.00 3.36
3907 7674 1.795286 CGCTGTTCTGTTCTGTCCTTC 59.205 52.381 0.00 0.00 0.00 3.46
3908 7675 2.546795 CGCTGTTCTGTTCTGTCCTTCT 60.547 50.000 0.00 0.00 0.00 2.85
3909 7676 2.805099 GCTGTTCTGTTCTGTCCTTCTG 59.195 50.000 0.00 0.00 0.00 3.02
3910 7677 3.397482 CTGTTCTGTTCTGTCCTTCTGG 58.603 50.000 0.00 0.00 0.00 3.86
3911 7678 2.104792 TGTTCTGTTCTGTCCTTCTGGG 59.895 50.000 0.00 0.00 0.00 4.45
3912 7679 2.103153 TCTGTTCTGTCCTTCTGGGT 57.897 50.000 0.00 0.00 36.25 4.51
3913 7680 1.694150 TCTGTTCTGTCCTTCTGGGTG 59.306 52.381 0.00 0.00 36.25 4.61
3914 7681 0.108585 TGTTCTGTCCTTCTGGGTGC 59.891 55.000 0.00 0.00 36.25 5.01
3928 7695 1.313091 GGGTGCCCGAATTTGACCTC 61.313 60.000 0.00 0.00 0.00 3.85
3934 7701 0.804989 CCGAATTTGACCTCTGCACC 59.195 55.000 0.00 0.00 0.00 5.01
3949 7716 3.677648 ACCACTCCGTTCCGACCG 61.678 66.667 0.00 0.00 0.00 4.79
3957 7724 2.047560 GTTCCGACCGAAGTGGGG 60.048 66.667 0.00 0.00 41.95 4.96
3988 7763 3.057946 GCACAGACTGGAAAGATGGTTTC 60.058 47.826 7.51 0.00 0.00 2.78
3989 7764 4.136796 CACAGACTGGAAAGATGGTTTCA 58.863 43.478 7.51 0.00 0.00 2.69
3990 7765 4.023707 CACAGACTGGAAAGATGGTTTCAC 60.024 45.833 7.51 0.00 0.00 3.18
3991 7766 4.136796 CAGACTGGAAAGATGGTTTCACA 58.863 43.478 0.00 0.00 0.00 3.58
3992 7767 4.763793 CAGACTGGAAAGATGGTTTCACAT 59.236 41.667 0.00 0.00 0.00 3.21
3993 7768 5.242393 CAGACTGGAAAGATGGTTTCACATT 59.758 40.000 0.00 0.00 0.00 2.71
3994 7769 5.242393 AGACTGGAAAGATGGTTTCACATTG 59.758 40.000 0.31 0.00 0.00 2.82
3995 7770 4.895297 ACTGGAAAGATGGTTTCACATTGT 59.105 37.500 0.31 0.00 0.00 2.71
3996 7771 5.363580 ACTGGAAAGATGGTTTCACATTGTT 59.636 36.000 0.31 0.00 0.00 2.83
3997 7772 6.127083 ACTGGAAAGATGGTTTCACATTGTTT 60.127 34.615 0.31 0.00 0.00 2.83
4002 7777 4.840115 AGATGGTTTCACATTGTTTGGGAT 59.160 37.500 0.00 0.00 37.67 3.85
4006 7781 5.819901 TGGTTTCACATTGTTTGGGATTTTC 59.180 36.000 0.00 0.00 37.67 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.655733 CCTCCACACACGTTGAACAC 59.344 55.000 0.00 0.00 0.00 3.32
107 116 4.100808 GGAGTAGAGTGGATGAGCTGAAAT 59.899 45.833 0.00 0.00 0.00 2.17
112 121 3.052944 AGAAGGAGTAGAGTGGATGAGCT 60.053 47.826 0.00 0.00 0.00 4.09
113 122 3.295973 AGAAGGAGTAGAGTGGATGAGC 58.704 50.000 0.00 0.00 0.00 4.26
128 137 1.063567 GCTGACTCCCTCCTAGAAGGA 60.064 57.143 0.00 0.00 43.43 3.36
129 138 1.408969 GCTGACTCCCTCCTAGAAGG 58.591 60.000 0.00 0.00 36.46 3.46
130 139 1.342474 TGGCTGACTCCCTCCTAGAAG 60.342 57.143 0.00 0.00 0.00 2.85
131 140 0.710588 TGGCTGACTCCCTCCTAGAA 59.289 55.000 0.00 0.00 0.00 2.10
132 141 0.710588 TTGGCTGACTCCCTCCTAGA 59.289 55.000 0.00 0.00 0.00 2.43
133 142 1.799933 ATTGGCTGACTCCCTCCTAG 58.200 55.000 0.00 0.00 0.00 3.02
134 143 2.270434 AATTGGCTGACTCCCTCCTA 57.730 50.000 0.00 0.00 0.00 2.94
135 144 2.122768 CTAATTGGCTGACTCCCTCCT 58.877 52.381 0.00 0.00 0.00 3.69
199 209 3.265791 CTTGAGGCATACTGTTCCACTC 58.734 50.000 0.00 0.00 0.00 3.51
235 245 1.754226 GGCTTCACAAGGGAAACACAA 59.246 47.619 0.00 0.00 0.00 3.33
247 257 2.280797 GACCACGCAGGCTTCACA 60.281 61.111 0.00 0.00 43.14 3.58
261 271 4.811557 CCTCTGGAAAGATTATGTTCGACC 59.188 45.833 0.00 0.00 0.00 4.79
270 280 6.636454 TTCTTTAGGCCTCTGGAAAGATTA 57.364 37.500 23.04 11.13 37.66 1.75
291 301 6.074142 GCAACATCTTTGTTCTTGTCCATTTC 60.074 38.462 0.00 0.00 44.24 2.17
299 309 2.468777 GCACGCAACATCTTTGTTCTTG 59.531 45.455 0.00 0.00 44.24 3.02
324 335 2.124736 GGCTGAGCATGGCCGTTA 60.125 61.111 6.82 0.00 38.91 3.18
361 372 1.136305 TGCTTTACCGGGAGAAGATCG 59.864 52.381 6.32 0.00 0.00 3.69
416 434 0.179100 AAGCACGGACGGATGAGATG 60.179 55.000 0.00 0.00 0.00 2.90
420 438 3.429043 GTAAAGCACGGACGGATGA 57.571 52.632 0.00 0.00 0.00 2.92
443 461 4.681978 ACCTCTGCGTTGACGGCC 62.682 66.667 5.62 0.00 40.23 6.13
510 528 4.927422 TCGAGGTGTTTTGGTTTTTGATC 58.073 39.130 0.00 0.00 0.00 2.92
512 530 3.428316 GCTCGAGGTGTTTTGGTTTTTGA 60.428 43.478 15.58 0.00 0.00 2.69
513 531 2.857748 GCTCGAGGTGTTTTGGTTTTTG 59.142 45.455 15.58 0.00 0.00 2.44
558 579 2.514160 GGATGGGAGGTTGGGTTAATCT 59.486 50.000 0.00 0.00 30.60 2.40
561 582 1.004436 GGGATGGGAGGTTGGGTTAA 58.996 55.000 0.00 0.00 0.00 2.01
563 584 2.246126 GGGGATGGGAGGTTGGGTT 61.246 63.158 0.00 0.00 0.00 4.11
572 593 2.842462 CGTCGGATGGGGATGGGA 60.842 66.667 0.00 0.00 0.00 4.37
575 596 4.626081 GGCCGTCGGATGGGGATG 62.626 72.222 17.49 0.00 0.00 3.51
615 1091 1.454663 GGAAGATGGCTGGAAGGGC 60.455 63.158 0.00 0.00 0.00 5.19
635 1111 4.475763 TTGGTTATGTATTATTGCGCCG 57.524 40.909 4.18 0.00 0.00 6.46
646 1122 5.133941 TGTTGCTCTGGTTTTGGTTATGTA 58.866 37.500 0.00 0.00 0.00 2.29
648 1124 4.582701 TGTTGCTCTGGTTTTGGTTATG 57.417 40.909 0.00 0.00 0.00 1.90
649 1125 4.832266 TGATGTTGCTCTGGTTTTGGTTAT 59.168 37.500 0.00 0.00 0.00 1.89
650 1126 4.211125 TGATGTTGCTCTGGTTTTGGTTA 58.789 39.130 0.00 0.00 0.00 2.85
652 1128 2.665165 TGATGTTGCTCTGGTTTTGGT 58.335 42.857 0.00 0.00 0.00 3.67
654 1130 4.508461 TGATGATGTTGCTCTGGTTTTG 57.492 40.909 0.00 0.00 0.00 2.44
658 1134 3.276857 GTGATGATGATGTTGCTCTGGT 58.723 45.455 0.00 0.00 0.00 4.00
716 1202 7.357859 CGTCGTATCACGGGAATTATTTTAGTC 60.358 40.741 0.00 0.00 42.81 2.59
729 1218 0.109643 TGTGAACGTCGTATCACGGG 60.110 55.000 23.26 0.00 46.99 5.28
759 1248 5.049474 TCGCGGTGTTGATACTACGTATTAT 60.049 40.000 6.13 5.23 0.00 1.28
760 1249 4.272261 TCGCGGTGTTGATACTACGTATTA 59.728 41.667 6.13 0.00 0.00 0.98
763 1252 2.006169 TCGCGGTGTTGATACTACGTA 58.994 47.619 6.13 0.00 0.00 3.57
764 1253 0.804364 TCGCGGTGTTGATACTACGT 59.196 50.000 6.13 0.00 0.00 3.57
765 1254 1.186030 GTCGCGGTGTTGATACTACG 58.814 55.000 6.13 0.00 0.00 3.51
766 1255 1.916000 GTGTCGCGGTGTTGATACTAC 59.084 52.381 6.13 0.00 0.00 2.73
767 1256 1.540707 TGTGTCGCGGTGTTGATACTA 59.459 47.619 6.13 0.00 0.00 1.82
768 1257 0.315886 TGTGTCGCGGTGTTGATACT 59.684 50.000 6.13 0.00 0.00 2.12
769 1258 0.713883 CTGTGTCGCGGTGTTGATAC 59.286 55.000 6.13 0.00 0.00 2.24
770 1259 0.389296 CCTGTGTCGCGGTGTTGATA 60.389 55.000 6.13 0.00 0.00 2.15
801 1290 0.251634 GGACTTTGAGAGCTGGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
802 1291 0.251634 GGGACTTTGAGAGCTGGGAG 59.748 60.000 0.00 0.00 0.00 4.30
803 1292 0.473694 TGGGACTTTGAGAGCTGGGA 60.474 55.000 0.00 0.00 0.00 4.37
804 1293 0.322008 GTGGGACTTTGAGAGCTGGG 60.322 60.000 0.00 0.00 0.00 4.45
833 1322 5.467705 ACTCCGACGATGTAATAATAAGCC 58.532 41.667 0.00 0.00 0.00 4.35
849 1355 9.362539 TGAGATTTTTGTTATTACTACTCCGAC 57.637 33.333 0.00 0.00 0.00 4.79
857 1363 9.220767 GAGTGGAGTGAGATTTTTGTTATTACT 57.779 33.333 0.00 0.00 0.00 2.24
940 1451 1.838073 GAGGAGGAAGGTTTGGCGGA 61.838 60.000 0.00 0.00 0.00 5.54
941 1452 1.377333 GAGGAGGAAGGTTTGGCGG 60.377 63.158 0.00 0.00 0.00 6.13
942 1453 0.391793 GAGAGGAGGAAGGTTTGGCG 60.392 60.000 0.00 0.00 0.00 5.69
943 1454 0.034960 GGAGAGGAGGAAGGTTTGGC 60.035 60.000 0.00 0.00 0.00 4.52
949 1460 1.383803 CCCTGGGAGAGGAGGAAGG 60.384 68.421 7.01 0.00 46.33 3.46
1599 2131 3.034924 CTCCTCCAGGATCTCCTCG 57.965 63.158 0.00 0.00 46.65 4.63
2058 2603 3.123620 CTCTTGCTGGCCTCGCAC 61.124 66.667 17.99 0.00 37.07 5.34
2196 2741 3.781770 GAGCAGCCGGATCTCGTGG 62.782 68.421 5.05 0.00 37.11 4.94
2277 2822 1.076632 CTCGGAGTAGAGCAGGGGT 60.077 63.158 0.00 0.00 0.00 4.95
2550 3095 2.357034 TTCTTCGTGCTCGTGGGC 60.357 61.111 8.17 0.00 38.33 5.36
2562 3107 3.491652 GCCAGCGCGTCCTTCTTC 61.492 66.667 8.43 0.00 0.00 2.87
3059 3604 4.990543 TTGTACAAGAAGAGCGTGATTG 57.009 40.909 3.59 0.00 0.00 2.67
3085 3630 0.533085 GCCTGCCTAATCGGACCTTC 60.533 60.000 0.00 0.00 33.16 3.46
3091 3636 0.811616 GACACAGCCTGCCTAATCGG 60.812 60.000 0.00 0.00 0.00 4.18
3123 3668 4.562789 TCACATTTTGTTATCTCTCTCGCG 59.437 41.667 0.00 0.00 0.00 5.87
3140 3685 3.558931 TCAACACCACTCACTCACATT 57.441 42.857 0.00 0.00 0.00 2.71
3141 3686 3.071457 TGATCAACACCACTCACTCACAT 59.929 43.478 0.00 0.00 0.00 3.21
3142 3687 2.433970 TGATCAACACCACTCACTCACA 59.566 45.455 0.00 0.00 0.00 3.58
3164 3709 1.265635 TCCGTATGCACAGTTGTTTGC 59.734 47.619 0.00 0.00 39.33 3.68
3165 3710 2.665519 GCTCCGTATGCACAGTTGTTTG 60.666 50.000 0.00 0.00 0.00 2.93
3166 3711 1.535462 GCTCCGTATGCACAGTTGTTT 59.465 47.619 0.00 0.00 0.00 2.83
3167 3712 1.156736 GCTCCGTATGCACAGTTGTT 58.843 50.000 0.00 0.00 0.00 2.83
3197 3742 1.483004 TGGGATTTTACATCGAGCCGA 59.517 47.619 0.00 0.00 41.13 5.54
3200 3745 2.480419 CGGATGGGATTTTACATCGAGC 59.520 50.000 0.00 0.00 43.34 5.03
3201 3746 3.728845 ACGGATGGGATTTTACATCGAG 58.271 45.455 0.00 0.00 43.34 4.04
3202 3747 3.830744 ACGGATGGGATTTTACATCGA 57.169 42.857 0.00 0.00 43.34 3.59
3203 3748 4.095782 ACAAACGGATGGGATTTTACATCG 59.904 41.667 0.00 0.00 43.34 3.84
3204 3749 5.576447 ACAAACGGATGGGATTTTACATC 57.424 39.130 0.00 0.00 42.05 3.06
3205 3750 7.229907 GGTATACAAACGGATGGGATTTTACAT 59.770 37.037 5.01 0.00 0.00 2.29
3206 3751 6.543100 GGTATACAAACGGATGGGATTTTACA 59.457 38.462 5.01 0.00 0.00 2.41
3207 3752 6.543100 TGGTATACAAACGGATGGGATTTTAC 59.457 38.462 5.01 0.00 0.00 2.01
3208 3753 6.660800 TGGTATACAAACGGATGGGATTTTA 58.339 36.000 5.01 0.00 0.00 1.52
3209 3754 5.511363 TGGTATACAAACGGATGGGATTTT 58.489 37.500 5.01 0.00 0.00 1.82
3210 3755 5.118729 TGGTATACAAACGGATGGGATTT 57.881 39.130 5.01 0.00 0.00 2.17
3244 3789 4.772046 TTTCGTGTCAAGAAGAAGAACG 57.228 40.909 1.46 0.00 33.54 3.95
3245 3790 8.922676 TGTATATTTCGTGTCAAGAAGAAGAAC 58.077 33.333 1.46 0.52 0.00 3.01
3246 3791 9.653287 ATGTATATTTCGTGTCAAGAAGAAGAA 57.347 29.630 1.46 0.00 0.00 2.52
3247 3792 9.087424 CATGTATATTTCGTGTCAAGAAGAAGA 57.913 33.333 1.46 0.00 0.00 2.87
3248 3793 9.087424 TCATGTATATTTCGTGTCAAGAAGAAG 57.913 33.333 1.46 0.00 0.00 2.85
3273 3818 5.930569 AGACCGGTTTCACTTTTGTAGTATC 59.069 40.000 9.42 0.00 34.56 2.24
3275 3820 5.051816 CAGACCGGTTTCACTTTTGTAGTA 58.948 41.667 9.42 0.00 34.56 1.82
3277 3822 3.303791 GCAGACCGGTTTCACTTTTGTAG 60.304 47.826 9.42 0.00 0.00 2.74
3278 3823 2.614983 GCAGACCGGTTTCACTTTTGTA 59.385 45.455 9.42 0.00 0.00 2.41
3280 3825 1.269051 GGCAGACCGGTTTCACTTTTG 60.269 52.381 9.42 0.00 0.00 2.44
3281 3826 1.029681 GGCAGACCGGTTTCACTTTT 58.970 50.000 9.42 0.00 0.00 2.27
3282 3827 0.182775 AGGCAGACCGGTTTCACTTT 59.817 50.000 9.42 0.00 42.76 2.66
3283 3828 0.535102 CAGGCAGACCGGTTTCACTT 60.535 55.000 9.42 0.00 42.76 3.16
3284 3829 1.071471 CAGGCAGACCGGTTTCACT 59.929 57.895 9.42 2.33 42.76 3.41
3285 3830 0.321653 ATCAGGCAGACCGGTTTCAC 60.322 55.000 9.42 0.00 42.76 3.18
3286 3831 0.036388 GATCAGGCAGACCGGTTTCA 60.036 55.000 9.42 0.00 42.76 2.69
3287 3832 0.250513 AGATCAGGCAGACCGGTTTC 59.749 55.000 9.42 0.00 42.76 2.78
3297 3899 1.895798 AGACGTCAGAAAGATCAGGCA 59.104 47.619 19.50 0.00 0.00 4.75
3302 3904 3.502191 AGCTCAGACGTCAGAAAGATC 57.498 47.619 19.50 3.38 0.00 2.75
3354 3956 2.510768 AATAATCACGGCGAGGAGAC 57.489 50.000 16.62 0.00 0.00 3.36
3410 7165 4.994217 CCACCCAATGATAACAAAAACCAC 59.006 41.667 0.00 0.00 0.00 4.16
3466 7226 0.106819 AATCACTCTCTGGCCATGGC 60.107 55.000 29.47 29.47 41.06 4.40
3467 7227 1.676746 CAATCACTCTCTGGCCATGG 58.323 55.000 5.51 7.63 0.00 3.66
3468 7228 1.022735 GCAATCACTCTCTGGCCATG 58.977 55.000 5.51 0.02 0.00 3.66
3469 7229 0.463295 CGCAATCACTCTCTGGCCAT 60.463 55.000 5.51 0.00 0.00 4.40
3470 7230 1.078918 CGCAATCACTCTCTGGCCA 60.079 57.895 4.71 4.71 0.00 5.36
3471 7231 0.809241 CTCGCAATCACTCTCTGGCC 60.809 60.000 0.00 0.00 0.00 5.36
3473 7233 1.144565 CGCTCGCAATCACTCTCTGG 61.145 60.000 0.00 0.00 0.00 3.86
3474 7234 0.179153 TCGCTCGCAATCACTCTCTG 60.179 55.000 0.00 0.00 0.00 3.35
3533 7296 1.153489 CTGGACGGACAGCAGATGG 60.153 63.158 0.00 0.00 0.00 3.51
3564 7327 1.443872 CGTGGAGTGGAGCACGTAC 60.444 63.158 0.00 0.00 39.64 3.67
3606 7370 1.406180 GAAGTAGAACCTCCGCCTCTC 59.594 57.143 0.00 0.00 0.00 3.20
3666 7430 1.374758 GATCGATCATCCGCCACCC 60.375 63.158 20.52 0.00 0.00 4.61
3678 7445 0.736636 TACTCGTTGCACCGATCGAT 59.263 50.000 18.66 0.00 36.08 3.59
3877 7644 1.005340 CAGAACAGCGCAGATCCTTC 58.995 55.000 11.47 0.97 0.00 3.46
3885 7652 0.880278 GGACAGAACAGAACAGCGCA 60.880 55.000 11.47 0.00 0.00 6.09
3887 7654 1.795286 GAAGGACAGAACAGAACAGCG 59.205 52.381 0.00 0.00 0.00 5.18
3911 7678 0.804989 CAGAGGTCAAATTCGGGCAC 59.195 55.000 0.00 0.00 0.00 5.01
3912 7679 0.960364 GCAGAGGTCAAATTCGGGCA 60.960 55.000 0.00 0.00 0.00 5.36
3913 7680 0.960364 TGCAGAGGTCAAATTCGGGC 60.960 55.000 0.00 0.00 0.00 6.13
3914 7681 0.804989 GTGCAGAGGTCAAATTCGGG 59.195 55.000 0.00 0.00 0.00 5.14
3949 7716 1.149401 GCCCAGATAGCCCCACTTC 59.851 63.158 0.00 0.00 0.00 3.01
3988 7763 6.047870 TCACTTGAAAATCCCAAACAATGTG 58.952 36.000 0.00 0.00 0.00 3.21
3989 7764 6.232581 TCACTTGAAAATCCCAAACAATGT 57.767 33.333 0.00 0.00 0.00 2.71
3990 7765 6.203338 CCTTCACTTGAAAATCCCAAACAATG 59.797 38.462 0.00 0.00 33.07 2.82
3991 7766 6.099557 TCCTTCACTTGAAAATCCCAAACAAT 59.900 34.615 0.00 0.00 33.07 2.71
3992 7767 5.423610 TCCTTCACTTGAAAATCCCAAACAA 59.576 36.000 0.00 0.00 33.07 2.83
3993 7768 4.959210 TCCTTCACTTGAAAATCCCAAACA 59.041 37.500 0.00 0.00 33.07 2.83
3994 7769 5.509670 CCTCCTTCACTTGAAAATCCCAAAC 60.510 44.000 0.00 0.00 33.07 2.93
3995 7770 4.588528 CCTCCTTCACTTGAAAATCCCAAA 59.411 41.667 0.00 0.00 33.07 3.28
3996 7771 4.141041 TCCTCCTTCACTTGAAAATCCCAA 60.141 41.667 0.00 0.00 33.07 4.12
3997 7772 3.397618 TCCTCCTTCACTTGAAAATCCCA 59.602 43.478 0.00 0.00 33.07 4.37
4002 7777 3.632145 GTGCTTCCTCCTTCACTTGAAAA 59.368 43.478 0.00 0.00 33.07 2.29
4006 7781 1.151668 CGTGCTTCCTCCTTCACTTG 58.848 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.