Multiple sequence alignment - TraesCS7A01G154500

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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 TraesCS7A01G154500 chr7A 100.000 3657 0 0 1 3657 107795236 107791580 0.000000e+00 6754
1 TraesCS7A01G154500 chr7B 91.539 2931 139 55 1 2883 61080177 61077308 0.000000e+00 3938
2 TraesCS7A01G154500 chr7B 88.971 136 15 0 2973 3108 61074493 61074358 6.280000e-38 169
3 TraesCS7A01G154500 chr7B 88.119 101 10 2 3136 3236 61074356 61074258 6.420000e-23 119
4 TraesCS7A01G154500 chr7D 92.765 2253 88 26 557 2773 102902742 102900529 0.000000e+00 3188
5 TraesCS7A01G154500 chr7D 79.737 913 68 52 2782 3657 102900217 102899385 1.480000e-153 553
6 TraesCS7A01G154500 chr7D 87.893 413 19 19 114 507 102903150 102902750 1.200000e-124 457
7 TraesCS7A01G154500 chr7D 87.218 133 11 3 1 133 102903428 102903302 2.940000e-31 147
8 TraesCS7A01G154500 chr5D 88.138 1627 148 30 997 2605 497493230 497491631 0.000000e+00 1893
9 TraesCS7A01G154500 chr5B 88.846 1560 135 26 1054 2606 616439691 616438164 0.000000e+00 1881
10 TraesCS7A01G154500 chr5A 87.630 1633 154 34 997 2619 621540391 621538797 0.000000e+00 1853
11 TraesCS7A01G154500 chr2D 73.080 1289 286 49 1230 2480 147968257 147966992 5.690000e-108 401
12 TraesCS7A01G154500 chr2A 72.551 1286 298 43 1230 2480 154413987 154415252 5.770000e-98 368
13 TraesCS7A01G154500 chr2A 75.238 525 110 16 1242 1756 154422555 154422041 7.900000e-57 231
14 TraesCS7A01G154500 chr1B 71.460 1363 317 57 1231 2551 674004543 674003211 2.760000e-76 296
15 TraesCS7A01G154500 chr3B 71.574 1277 297 54 1231 2468 64538341 64539590 1.660000e-73 287
16 TraesCS7A01G154500 chr2B 71.313 1363 303 69 1239 2551 207482283 207483607 1.670000e-68 270


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 TraesCS7A01G154500 chr7A 107791580 107795236 3656 True 6754.000000 6754 100.00000 1 3657 1 chr7A.!!$R1 3656
1 TraesCS7A01G154500 chr7B 61074258 61080177 5919 True 1408.666667 3938 89.54300 1 3236 3 chr7B.!!$R1 3235
2 TraesCS7A01G154500 chr7D 102899385 102903428 4043 True 1086.250000 3188 86.90325 1 3657 4 chr7D.!!$R1 3656
3 TraesCS7A01G154500 chr5D 497491631 497493230 1599 True 1893.000000 1893 88.13800 997 2605 1 chr5D.!!$R1 1608
4 TraesCS7A01G154500 chr5B 616438164 616439691 1527 True 1881.000000 1881 88.84600 1054 2606 1 chr5B.!!$R1 1552
5 TraesCS7A01G154500 chr5A 621538797 621540391 1594 True 1853.000000 1853 87.63000 997 2619 1 chr5A.!!$R1 1622
6 TraesCS7A01G154500 chr2D 147966992 147968257 1265 True 401.000000 401 73.08000 1230 2480 1 chr2D.!!$R1 1250
7 TraesCS7A01G154500 chr2A 154413987 154415252 1265 False 368.000000 368 72.55100 1230 2480 1 chr2A.!!$F1 1250
8 TraesCS7A01G154500 chr2A 154422041 154422555 514 True 231.000000 231 75.23800 1242 1756 1 chr2A.!!$R1 514
9 TraesCS7A01G154500 chr1B 674003211 674004543 1332 True 296.000000 296 71.46000 1231 2551 1 chr1B.!!$R1 1320
10 TraesCS7A01G154500 chr3B 64538341 64539590 1249 False 287.000000 287 71.57400 1231 2468 1 chr3B.!!$F1 1237
11 TraesCS7A01G154500 chr2B 207482283 207483607 1324 False 270.000000 270 71.31300 1239 2551 1 chr2B.!!$F1 1312

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
983 1219 0.336737 GAGGAGGAGGAGGAGACCAA 59.663 60.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2892 3479 1.05504 AGCAAGTGCCTCTTCAGAGT 58.945 50.0 0.0 0.0 43.38 3.24 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
77 80 2.686558 ACAAAACTATGCACGCACTG 57.313 45.000 0.00 0.00 0.00 3.66
94 97 3.118956 GCACTGCTAACTACTGATCCTGT 60.119 47.826 0.00 0.00 0.00 4.00
112 115 3.256558 CTGTCGAGACATGCATCTTCAA 58.743 45.455 6.37 0.00 41.01 2.69
154 339 7.149307 TGTATTACAGAACAGTCGATTTGTCA 58.851 34.615 6.07 0.00 0.00 3.58
180 365 6.124340 TCTCATCTGAATACCACATGCAAAT 58.876 36.000 0.00 0.00 0.00 2.32
181 366 7.281841 TCTCATCTGAATACCACATGCAAATA 58.718 34.615 0.00 0.00 0.00 1.40
250 435 2.743928 CCTTGACCTCGGTGCTGC 60.744 66.667 0.00 0.00 0.00 5.25
308 493 4.379603 CCAAGATATACCTCACGATCGACC 60.380 50.000 24.34 0.00 0.00 4.79
317 502 1.154016 ACGATCGACCGAGCTGTTG 60.154 57.895 24.34 0.00 0.00 3.33
381 574 4.113354 CAAGACGCACTAGTATTTCTCCC 58.887 47.826 0.00 0.00 0.00 4.30
382 575 2.694109 AGACGCACTAGTATTTCTCCCC 59.306 50.000 0.00 0.00 0.00 4.81
394 587 2.514458 TTCTCCCCAAATCTTCCTGC 57.486 50.000 0.00 0.00 0.00 4.85
427 620 4.473444 TGAATTAATTCATGGCCCCTCTC 58.527 43.478 23.86 0.00 41.51 3.20
438 631 1.043673 GCCCCTCTCGGTGATGTAGT 61.044 60.000 0.00 0.00 0.00 2.73
439 632 1.753141 GCCCCTCTCGGTGATGTAGTA 60.753 57.143 0.00 0.00 0.00 1.82
440 633 2.231529 CCCCTCTCGGTGATGTAGTAG 58.768 57.143 0.00 0.00 0.00 2.57
441 634 2.158652 CCCCTCTCGGTGATGTAGTAGA 60.159 54.545 0.00 0.00 0.00 2.59
442 635 3.498841 CCCCTCTCGGTGATGTAGTAGAT 60.499 52.174 0.00 0.00 0.00 1.98
443 636 4.145807 CCCTCTCGGTGATGTAGTAGATT 58.854 47.826 0.00 0.00 0.00 2.40
444 637 4.216687 CCCTCTCGGTGATGTAGTAGATTC 59.783 50.000 0.00 0.00 0.00 2.52
445 638 5.067273 CCTCTCGGTGATGTAGTAGATTCT 58.933 45.833 0.00 0.00 0.00 2.40
446 639 5.180492 CCTCTCGGTGATGTAGTAGATTCTC 59.820 48.000 0.00 0.00 0.00 2.87
447 640 4.750598 TCTCGGTGATGTAGTAGATTCTCG 59.249 45.833 0.00 0.00 0.00 4.04
448 641 4.700700 TCGGTGATGTAGTAGATTCTCGA 58.299 43.478 0.00 0.00 0.00 4.04
463 660 1.804748 TCTCGATCGTATCCATCCACG 59.195 52.381 15.94 0.00 39.48 4.94
480 677 2.580470 CGCTAATGCTCGCTGTCCG 61.580 63.158 0.00 0.00 36.97 4.79
488 690 3.708220 CTCGCTGTCCGGAGAAGCC 62.708 68.421 25.93 13.22 37.59 4.35
513 715 3.119708 GGCGTGATCTTTCTTGCAATCTT 60.120 43.478 0.00 0.00 0.00 2.40
574 776 4.624024 GTGCACAATTTTGACATCTCCATG 59.376 41.667 13.17 0.00 35.92 3.66
582 784 2.187100 TGACATCTCCATGTGGCACTA 58.813 47.619 19.83 5.69 43.79 2.74
663 874 2.104859 CATCACCACTGCAGCCTCG 61.105 63.158 15.27 0.00 0.00 4.63
741 956 3.224806 CGATACGCATCGCTGTGG 58.775 61.111 4.88 0.00 46.80 4.17
765 980 5.218139 CCATCTTGTTCACTCTTTTCTTGC 58.782 41.667 0.00 0.00 0.00 4.01
771 986 5.053811 TGTTCACTCTTTTCTTGCGACATA 58.946 37.500 0.00 0.00 0.00 2.29
911 1144 5.735354 GCCACAAGCTCCTGATTGATTATTG 60.735 44.000 0.98 0.00 41.64 1.90
919 1152 7.225538 AGCTCCTGATTGATTATTGAACTAACG 59.774 37.037 0.00 0.00 0.00 3.18
922 1155 8.474831 TCCTGATTGATTATTGAACTAACGAGA 58.525 33.333 0.00 0.00 0.00 4.04
932 1165 9.926751 TTATTGAACTAACGAGATAGTAGTTCG 57.073 33.333 14.66 4.95 45.57 3.95
983 1219 0.336737 GAGGAGGAGGAGGAGACCAA 59.663 60.000 0.00 0.00 0.00 3.67
992 1228 1.229658 AGGAGACCAAGGTGGGGAG 60.230 63.158 0.00 0.00 43.37 4.30
1016 1252 2.449322 CATGGGGGAGGAGGAGGG 60.449 72.222 0.00 0.00 0.00 4.30
1023 1259 2.693017 GAGGAGGAGGGGCAGAGA 59.307 66.667 0.00 0.00 0.00 3.10
1147 1383 1.512926 GTGAGCACAACGGAACATCT 58.487 50.000 0.00 0.00 0.00 2.90
1156 1395 2.586258 ACGGAACATCTTCTCCATCG 57.414 50.000 0.00 0.00 0.00 3.84
1215 1465 2.811431 CGTGTTAATGGATGTGTGGTGT 59.189 45.455 0.00 0.00 0.00 4.16
1216 1466 3.252215 CGTGTTAATGGATGTGTGGTGTT 59.748 43.478 0.00 0.00 0.00 3.32
1217 1467 4.545610 GTGTTAATGGATGTGTGGTGTTG 58.454 43.478 0.00 0.00 0.00 3.33
1218 1468 4.037446 GTGTTAATGGATGTGTGGTGTTGT 59.963 41.667 0.00 0.00 0.00 3.32
1219 1469 4.037327 TGTTAATGGATGTGTGGTGTTGTG 59.963 41.667 0.00 0.00 0.00 3.33
1220 1470 2.655090 ATGGATGTGTGGTGTTGTGA 57.345 45.000 0.00 0.00 0.00 3.58
1711 1961 2.356553 GTGCTCGCCGTTGGTGTA 60.357 61.111 0.00 0.00 34.40 2.90
2674 2942 1.337167 TGATCGCCGATGGAATGCTAG 60.337 52.381 3.34 0.00 0.00 3.42
2680 2948 3.119459 CGCCGATGGAATGCTAGTAGTAT 60.119 47.826 0.00 0.00 0.00 2.12
2682 2950 5.392703 CGCCGATGGAATGCTAGTAGTATTA 60.393 44.000 12.80 0.34 30.60 0.98
2683 2951 6.574350 GCCGATGGAATGCTAGTAGTATTAT 58.426 40.000 12.80 4.98 30.60 1.28
2684 2952 6.477033 GCCGATGGAATGCTAGTAGTATTATG 59.523 42.308 12.80 3.04 30.60 1.90
2685 2953 7.548097 CCGATGGAATGCTAGTAGTATTATGT 58.452 38.462 12.80 3.09 30.60 2.29
2705 2973 9.609346 ATTATGTTATGTAGTGTTTGACCCTAC 57.391 33.333 0.00 0.00 33.32 3.18
2706 2974 6.422344 TGTTATGTAGTGTTTGACCCTACA 57.578 37.500 6.00 6.00 43.58 2.74
2707 2975 6.828788 TGTTATGTAGTGTTTGACCCTACAA 58.171 36.000 7.34 0.00 42.93 2.41
2708 2976 7.281098 TGTTATGTAGTGTTTGACCCTACAAA 58.719 34.615 7.34 0.00 42.93 2.83
2718 2986 5.506730 TTGACCCTACAAACCATATGACA 57.493 39.130 3.65 0.00 0.00 3.58
2746 3027 3.969287 TGAACTGTTCAGGAGATGGAG 57.031 47.619 18.69 0.00 34.08 3.86
2773 3054 6.038271 AGTGAATTGGCCTCGTATGATTTTAC 59.962 38.462 3.32 0.00 0.00 2.01
2774 3055 6.038271 GTGAATTGGCCTCGTATGATTTTACT 59.962 38.462 3.32 0.00 0.00 2.24
2775 3056 7.225931 GTGAATTGGCCTCGTATGATTTTACTA 59.774 37.037 3.32 0.00 0.00 1.82
2813 3399 4.521256 GCACTTTGGAGGGTTTATACACAA 59.479 41.667 0.00 0.00 0.00 3.33
2863 3450 0.393132 GCTGTCCTAAGTCTTGCCCC 60.393 60.000 0.00 0.00 0.00 5.80
2884 3471 5.246203 CCCCTGACTTATCCAAATCGATCTA 59.754 44.000 0.00 0.00 0.00 1.98
2904 3491 9.944663 CGATCTATAATATAACTCTGAAGAGGC 57.055 37.037 11.87 0.00 46.13 4.70
2910 3497 1.889545 AACTCTGAAGAGGCACTTGC 58.110 50.000 11.87 0.00 46.13 4.01
2917 3504 4.456911 TCTGAAGAGGCACTTGCTTTTATG 59.543 41.667 0.75 0.00 41.55 1.90
2918 3505 4.397420 TGAAGAGGCACTTGCTTTTATGA 58.603 39.130 0.75 0.00 41.55 2.15
2968 3566 8.531982 AGTATACTCAAGTCTCAACTGCAAATA 58.468 33.333 0.00 0.00 35.36 1.40
3019 6333 7.265599 TGATACCTCCTTCTTATTTGACCAA 57.734 36.000 0.00 0.00 0.00 3.67
3044 6358 5.861787 GGTTTTCGGATTGTTGGAATAACAG 59.138 40.000 0.00 0.00 0.00 3.16
3051 6365 5.337491 GGATTGTTGGAATAACAGGCAATGT 60.337 40.000 0.00 0.00 46.97 2.71
3121 6451 7.561021 TCTAACAAAACTAAGCACATGTGAA 57.439 32.000 29.80 12.37 0.00 3.18
3133 6463 7.760131 AAGCACATGTGAATGCATATAAAAC 57.240 32.000 29.80 6.14 44.59 2.43
3134 6464 6.865411 AGCACATGTGAATGCATATAAAACA 58.135 32.000 29.80 0.88 44.59 2.83
3162 6492 9.499479 AGAACTAACATATCTATGGATTTGCTG 57.501 33.333 8.99 3.50 38.00 4.41
3196 6531 8.519799 ACACAATATCCAATAAAAGGACGAAT 57.480 30.769 0.00 0.00 38.13 3.34
3197 6532 8.621286 ACACAATATCCAATAAAAGGACGAATC 58.379 33.333 0.00 0.00 38.13 2.52
3198 6533 7.798516 CACAATATCCAATAAAAGGACGAATCG 59.201 37.037 0.00 0.00 38.13 3.34
3204 6539 6.875195 TCCAATAAAAGGACGAATCGTAAGTT 59.125 34.615 8.77 3.62 41.37 2.66
3207 6542 7.998753 ATAAAAGGACGAATCGTAAGTTAGG 57.001 36.000 8.77 0.00 41.37 2.69
3237 6572 3.594603 CCGGAGGCCTACTAACATATG 57.405 52.381 14.69 0.00 46.14 1.78
3238 6573 3.162666 CCGGAGGCCTACTAACATATGA 58.837 50.000 14.69 0.00 46.14 2.15
3239 6574 3.056749 CCGGAGGCCTACTAACATATGAC 60.057 52.174 14.69 0.00 46.14 3.06
3241 6576 3.576648 GAGGCCTACTAACATATGACGC 58.423 50.000 4.42 0.00 0.00 5.19
3242 6577 2.963101 AGGCCTACTAACATATGACGCA 59.037 45.455 1.29 0.00 0.00 5.24
3243 6578 3.578716 AGGCCTACTAACATATGACGCAT 59.421 43.478 1.29 0.00 0.00 4.73
3244 6579 3.679980 GGCCTACTAACATATGACGCATG 59.320 47.826 10.38 0.00 0.00 4.06
3245 6580 4.556233 GCCTACTAACATATGACGCATGA 58.444 43.478 10.38 0.00 0.00 3.07
3246 6581 4.623167 GCCTACTAACATATGACGCATGAG 59.377 45.833 10.38 0.00 0.00 2.90
3247 6582 5.773575 CCTACTAACATATGACGCATGAGT 58.226 41.667 10.38 0.12 0.00 3.41
3248 6583 5.631096 CCTACTAACATATGACGCATGAGTG 59.369 44.000 6.88 0.00 0.00 3.51
3249 6584 5.262588 ACTAACATATGACGCATGAGTGA 57.737 39.130 6.88 0.00 0.00 3.41
3250 6585 5.284864 ACTAACATATGACGCATGAGTGAG 58.715 41.667 6.88 6.15 0.00 3.51
3251 6586 3.103447 ACATATGACGCATGAGTGAGG 57.897 47.619 6.88 0.00 0.00 3.86
3252 6587 2.695147 ACATATGACGCATGAGTGAGGA 59.305 45.455 6.88 0.00 0.00 3.71
3253 6588 3.323115 ACATATGACGCATGAGTGAGGAT 59.677 43.478 6.88 0.00 0.00 3.24
3254 6589 2.235845 ATGACGCATGAGTGAGGATG 57.764 50.000 6.88 0.00 0.00 3.51
3255 6590 0.176449 TGACGCATGAGTGAGGATGG 59.824 55.000 6.88 0.00 0.00 3.51
3256 6591 0.176680 GACGCATGAGTGAGGATGGT 59.823 55.000 6.88 0.00 0.00 3.55
3257 6592 0.107993 ACGCATGAGTGAGGATGGTG 60.108 55.000 0.00 0.00 0.00 4.17
3258 6593 0.812811 CGCATGAGTGAGGATGGTGG 60.813 60.000 0.00 0.00 0.00 4.61
3259 6594 0.543277 GCATGAGTGAGGATGGTGGA 59.457 55.000 0.00 0.00 0.00 4.02
3260 6595 1.474677 GCATGAGTGAGGATGGTGGAG 60.475 57.143 0.00 0.00 0.00 3.86
3271 6606 0.041238 ATGGTGGAGGAGGAGAACGA 59.959 55.000 0.00 0.00 0.00 3.85
3388 6723 4.742438 TTCAATTAGAACGGTTGCTCAC 57.258 40.909 0.00 0.00 0.00 3.51
3393 6728 0.178068 AGAACGGTTGCTCACACAGT 59.822 50.000 0.00 0.00 0.00 3.55
3394 6729 1.411246 AGAACGGTTGCTCACACAGTA 59.589 47.619 0.00 0.00 0.00 2.74
3395 6730 1.792949 GAACGGTTGCTCACACAGTAG 59.207 52.381 0.00 0.00 0.00 2.57
3396 6731 0.033504 ACGGTTGCTCACACAGTAGG 59.966 55.000 0.00 0.00 0.00 3.18
3397 6732 0.033504 CGGTTGCTCACACAGTAGGT 59.966 55.000 0.00 0.00 0.00 3.08
3398 6733 1.797025 GGTTGCTCACACAGTAGGTC 58.203 55.000 0.00 0.00 0.00 3.85
3399 6734 1.419374 GTTGCTCACACAGTAGGTCG 58.581 55.000 0.00 0.00 0.00 4.79
3400 6735 1.000607 GTTGCTCACACAGTAGGTCGA 60.001 52.381 0.00 0.00 0.00 4.20
3401 6736 0.596577 TGCTCACACAGTAGGTCGAC 59.403 55.000 7.13 7.13 0.00 4.20
3402 6737 0.882474 GCTCACACAGTAGGTCGACT 59.118 55.000 16.46 4.12 0.00 4.18
3403 6738 1.269998 GCTCACACAGTAGGTCGACTT 59.730 52.381 16.46 10.98 0.00 3.01
3404 6739 2.288273 GCTCACACAGTAGGTCGACTTT 60.288 50.000 16.46 6.93 0.00 2.66
3405 6740 3.799232 GCTCACACAGTAGGTCGACTTTT 60.799 47.826 16.46 4.32 0.00 2.27
3406 6741 4.558095 GCTCACACAGTAGGTCGACTTTTA 60.558 45.833 16.46 3.31 0.00 1.52
3407 6742 5.710984 CTCACACAGTAGGTCGACTTTTAT 58.289 41.667 16.46 0.00 0.00 1.40
3408 6743 5.706916 TCACACAGTAGGTCGACTTTTATC 58.293 41.667 16.46 0.00 0.00 1.75
3409 6744 5.242171 TCACACAGTAGGTCGACTTTTATCA 59.758 40.000 16.46 0.00 0.00 2.15
3410 6745 5.345202 CACACAGTAGGTCGACTTTTATCAC 59.655 44.000 16.46 2.28 0.00 3.06
3411 6746 5.010314 ACACAGTAGGTCGACTTTTATCACA 59.990 40.000 16.46 0.00 0.00 3.58
3412 6747 5.345202 CACAGTAGGTCGACTTTTATCACAC 59.655 44.000 16.46 0.73 0.00 3.82
3413 6748 5.243283 ACAGTAGGTCGACTTTTATCACACT 59.757 40.000 16.46 3.29 0.00 3.55
3414 6749 5.800941 CAGTAGGTCGACTTTTATCACACTC 59.199 44.000 16.46 0.00 0.00 3.51
3415 6750 4.866508 AGGTCGACTTTTATCACACTCA 57.133 40.909 16.46 0.00 0.00 3.41
3432 6767 3.262915 CACTCAAGAAGGGGTCTGAGATT 59.737 47.826 5.01 0.00 36.40 2.40
3434 6769 4.352298 ACTCAAGAAGGGGTCTGAGATTTT 59.648 41.667 5.01 0.00 36.40 1.82
3435 6770 4.911390 TCAAGAAGGGGTCTGAGATTTTC 58.089 43.478 0.00 0.00 36.40 2.29
3438 6773 5.590976 AGAAGGGGTCTGAGATTTTCTTT 57.409 39.130 0.00 0.00 34.29 2.52
3439 6774 5.565509 AGAAGGGGTCTGAGATTTTCTTTC 58.434 41.667 0.00 0.00 34.29 2.62
3487 6822 3.018423 TCGAGAGATCCATTGGTCTCA 57.982 47.619 24.64 11.14 42.57 3.27
3499 6834 3.801114 TTGGTCTCACCTACATGATCG 57.199 47.619 0.00 0.00 39.58 3.69
3541 6876 8.522830 CCAATAAGTGTGATATGAGTGGTTTTT 58.477 33.333 0.00 0.00 0.00 1.94
3570 6905 2.131067 ACCCGGTTTTGGCCAGTTG 61.131 57.895 5.11 0.00 0.00 3.16
3571 6906 2.028925 CCGGTTTTGGCCAGTTGC 59.971 61.111 5.11 0.00 40.16 4.17
3572 6907 2.790791 CCGGTTTTGGCCAGTTGCA 61.791 57.895 5.11 0.00 43.89 4.08
3573 6908 1.367102 CGGTTTTGGCCAGTTGCAT 59.633 52.632 5.11 0.00 43.89 3.96
3651 6989 6.478512 TTCAGTAGCATTTTTGGTTTTCCT 57.521 33.333 0.00 0.00 41.38 3.36
3652 6990 5.841810 TCAGTAGCATTTTTGGTTTTCCTG 58.158 37.500 0.00 0.00 41.38 3.86
3653 6991 5.596361 TCAGTAGCATTTTTGGTTTTCCTGA 59.404 36.000 0.00 0.00 41.38 3.86
3656 6994 7.442062 CAGTAGCATTTTTGGTTTTCCTGATTT 59.558 33.333 0.00 0.00 41.38 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 28 1.005450 GGTGTTGGAAGATGGGCCTTA 59.995 52.381 4.53 0.00 0.00 2.69
26 29 0.251787 GGTGTTGGAAGATGGGCCTT 60.252 55.000 4.53 0.00 0.00 4.35
77 80 3.878103 TCTCGACAGGATCAGTAGTTAGC 59.122 47.826 0.00 0.00 0.00 3.09
94 97 3.867493 GTGATTGAAGATGCATGTCTCGA 59.133 43.478 2.46 1.21 0.00 4.04
120 290 5.767665 ACTGTTCTGTAATACATGTTGGCAA 59.232 36.000 2.30 0.00 0.00 4.52
138 308 4.299155 TGAGAGTGACAAATCGACTGTTC 58.701 43.478 3.66 0.00 0.00 3.18
154 339 4.162888 TGCATGTGGTATTCAGATGAGAGT 59.837 41.667 7.21 0.00 46.50 3.24
197 382 5.401674 CACAGTACTCCTACTTGTTTTCGTC 59.598 44.000 0.00 0.00 30.03 4.20
317 502 1.021390 ATACAGCTGCCAACGAGTGC 61.021 55.000 15.27 0.00 0.00 4.40
354 547 0.530744 TACTAGTGCGTCTTGGGCTG 59.469 55.000 5.39 0.00 0.00 4.85
381 574 2.997986 GCATTTGTGCAGGAAGATTTGG 59.002 45.455 0.00 0.00 34.41 3.28
382 575 3.678072 CAGCATTTGTGCAGGAAGATTTG 59.322 43.478 3.03 0.00 37.25 2.32
427 620 5.614923 ATCGAGAATCTACTACATCACCG 57.385 43.478 0.00 0.00 0.00 4.94
438 631 5.354513 GTGGATGGATACGATCGAGAATCTA 59.645 44.000 24.34 17.97 42.51 1.98
439 632 4.156922 GTGGATGGATACGATCGAGAATCT 59.843 45.833 24.34 6.71 42.51 2.40
440 633 4.416620 GTGGATGGATACGATCGAGAATC 58.583 47.826 24.34 19.20 42.51 2.52
441 634 3.119814 CGTGGATGGATACGATCGAGAAT 60.120 47.826 24.34 11.91 42.54 2.40
442 635 2.225727 CGTGGATGGATACGATCGAGAA 59.774 50.000 24.34 7.09 42.54 2.87
443 636 1.804748 CGTGGATGGATACGATCGAGA 59.195 52.381 24.34 9.67 42.54 4.04
444 637 1.729472 GCGTGGATGGATACGATCGAG 60.729 57.143 24.34 0.00 42.54 4.04
445 638 0.240145 GCGTGGATGGATACGATCGA 59.760 55.000 24.34 5.87 42.54 3.59
446 639 0.241213 AGCGTGGATGGATACGATCG 59.759 55.000 14.88 14.88 42.54 3.69
447 640 3.570926 TTAGCGTGGATGGATACGATC 57.429 47.619 0.00 0.00 42.54 3.69
448 641 3.849911 CATTAGCGTGGATGGATACGAT 58.150 45.455 0.00 0.00 42.54 3.73
463 660 2.240500 CCGGACAGCGAGCATTAGC 61.241 63.158 0.00 0.00 42.56 3.09
480 677 1.078143 ATCACGCCTTGGCTTCTCC 60.078 57.895 10.12 0.00 0.00 3.71
488 690 1.536766 TGCAAGAAAGATCACGCCTTG 59.463 47.619 0.00 4.35 37.76 3.61
496 698 8.081025 AGTTCAAGAAAGATTGCAAGAAAGATC 58.919 33.333 4.94 0.00 0.00 2.75
574 776 3.201290 CAGATGGAAGTGATAGTGCCAC 58.799 50.000 0.00 0.00 34.89 5.01
663 874 2.027314 TGGTGCGCATGTGTTTGC 59.973 55.556 15.91 0.00 39.29 3.68
741 956 5.218139 CAAGAAAAGAGTGAACAAGATGGC 58.782 41.667 0.00 0.00 0.00 4.40
765 980 0.100682 ACGCCACTGTAGCTATGTCG 59.899 55.000 0.00 0.00 0.00 4.35
806 1039 2.125106 GGGCAGGTCACACCGATC 60.125 66.667 0.00 0.00 44.90 3.69
875 1108 1.070577 GCTTGTGGCTTATGCGTATCG 60.071 52.381 0.00 0.00 40.82 2.92
911 1144 6.770076 ACACGAACTACTATCTCGTTAGTTC 58.230 40.000 9.66 9.66 42.86 3.01
919 1152 6.743627 CAGAGACAAACACGAACTACTATCTC 59.256 42.308 0.00 0.00 0.00 2.75
922 1155 6.207025 AGTCAGAGACAAACACGAACTACTAT 59.793 38.462 0.00 0.00 34.60 2.12
932 1165 4.047822 CAGTCAGAGTCAGAGACAAACAC 58.952 47.826 11.40 0.00 34.60 3.32
965 1201 0.338120 CTTGGTCTCCTCCTCCTCCT 59.662 60.000 0.00 0.00 0.00 3.69
983 1219 3.603330 ATGGCTTCCCTCCCCACCT 62.603 63.158 0.00 0.00 0.00 4.00
992 1228 3.825623 CCTCCCCCATGGCTTCCC 61.826 72.222 6.09 0.00 0.00 3.97
1016 1252 2.768492 CCGCCATTGCTTCTCTGCC 61.768 63.158 0.00 0.00 34.43 4.85
1057 1293 1.005394 CCGCGTACTTGTTGGTCCT 60.005 57.895 4.92 0.00 0.00 3.85
1147 1383 1.062886 AGAGGATGGACCGATGGAGAA 60.063 52.381 0.00 0.00 44.74 2.87
1156 1395 1.781786 TGCAGAGTAGAGGATGGACC 58.218 55.000 0.00 0.00 39.35 4.46
1215 1465 1.225855 GTCTGCGTCCACAATCACAA 58.774 50.000 0.00 0.00 0.00 3.33
1216 1466 0.105778 TGTCTGCGTCCACAATCACA 59.894 50.000 0.00 0.00 0.00 3.58
1217 1467 0.792640 CTGTCTGCGTCCACAATCAC 59.207 55.000 0.00 0.00 0.00 3.06
1218 1468 0.950555 GCTGTCTGCGTCCACAATCA 60.951 55.000 0.00 0.00 0.00 2.57
1219 1469 1.790387 GCTGTCTGCGTCCACAATC 59.210 57.895 0.00 0.00 0.00 2.67
1220 1470 3.972227 GCTGTCTGCGTCCACAAT 58.028 55.556 0.00 0.00 0.00 2.71
1504 1754 3.838271 ACGGGCGCGATCATGAGT 61.838 61.111 30.98 0.77 0.00 3.41
1621 1871 0.249398 GGAGCTTGGCGAGGAAGTAA 59.751 55.000 3.44 0.00 0.00 2.24
1966 2234 1.736681 GTCAGATGCTGGAAGAAGTGC 59.263 52.381 0.00 0.00 34.07 4.40
2075 2343 4.988598 CTTGGTCACGCCCACGCT 62.989 66.667 0.00 0.00 45.53 5.07
2496 2764 3.367498 GCAGAAGAAGTAGAAGAAGGCGA 60.367 47.826 0.00 0.00 0.00 5.54
2661 2929 8.988064 AACATAATACTACTAGCATTCCATCG 57.012 34.615 0.00 0.00 0.00 3.84
2701 2969 8.724229 CATGTCATATGTCATATGGTTTGTAGG 58.276 37.037 25.76 9.58 42.23 3.18
2705 2973 8.843262 AGTTCATGTCATATGTCATATGGTTTG 58.157 33.333 25.76 20.23 42.23 2.93
2706 2974 8.843262 CAGTTCATGTCATATGTCATATGGTTT 58.157 33.333 25.76 12.37 42.23 3.27
2707 2975 7.994911 ACAGTTCATGTCATATGTCATATGGTT 59.005 33.333 25.76 12.64 42.23 3.67
2708 2976 7.512130 ACAGTTCATGTCATATGTCATATGGT 58.488 34.615 25.76 13.53 42.23 3.55
2709 2977 7.974482 ACAGTTCATGTCATATGTCATATGG 57.026 36.000 25.76 13.96 42.23 2.74
2710 2978 9.048446 TGAACAGTTCATGTCATATGTCATATG 57.952 33.333 22.11 22.11 43.00 1.78
2711 2979 9.269453 CTGAACAGTTCATGTCATATGTCATAT 57.731 33.333 16.53 0.00 43.00 1.78
2712 2980 7.712205 CCTGAACAGTTCATGTCATATGTCATA 59.288 37.037 16.53 0.00 43.00 2.15
2714 2982 5.876460 CCTGAACAGTTCATGTCATATGTCA 59.124 40.000 16.53 5.11 43.00 3.58
2715 2983 6.108687 TCCTGAACAGTTCATGTCATATGTC 58.891 40.000 16.53 0.00 43.00 3.06
2716 2984 6.053632 TCCTGAACAGTTCATGTCATATGT 57.946 37.500 16.53 0.00 43.00 2.29
2717 2985 6.343703 TCTCCTGAACAGTTCATGTCATATG 58.656 40.000 16.53 0.00 43.00 1.78
2718 2986 6.550938 TCTCCTGAACAGTTCATGTCATAT 57.449 37.500 16.53 0.00 43.00 1.78
2746 3027 3.531538 TCATACGAGGCCAATTCACTTC 58.468 45.455 5.01 0.00 0.00 3.01
2773 3054 6.253746 CAAAGTGCAGCACTATAAAAGCTAG 58.746 40.000 28.48 5.53 44.62 3.42
2774 3055 5.123820 CCAAAGTGCAGCACTATAAAAGCTA 59.876 40.000 28.48 0.00 44.62 3.32
2775 3056 4.082571 CCAAAGTGCAGCACTATAAAAGCT 60.083 41.667 28.48 7.40 44.62 3.74
2813 3399 5.480772 ACAGTACTGCTAGGTTACTGTCATT 59.519 40.000 22.90 0.00 45.51 2.57
2884 3471 7.659390 GCAAGTGCCTCTTCAGAGTTATATTAT 59.341 37.037 3.15 0.00 40.48 1.28
2888 3475 4.467795 AGCAAGTGCCTCTTCAGAGTTATA 59.532 41.667 0.00 0.00 43.38 0.98
2889 3476 3.262915 AGCAAGTGCCTCTTCAGAGTTAT 59.737 43.478 0.00 0.00 43.38 1.89
2891 3478 1.419387 AGCAAGTGCCTCTTCAGAGTT 59.581 47.619 0.00 0.00 43.38 3.01
2892 3479 1.055040 AGCAAGTGCCTCTTCAGAGT 58.945 50.000 0.00 0.00 43.38 3.24
2893 3480 2.181954 AAGCAAGTGCCTCTTCAGAG 57.818 50.000 0.00 0.00 43.38 3.35
2894 3481 2.645838 AAAGCAAGTGCCTCTTCAGA 57.354 45.000 0.00 0.00 43.38 3.27
2895 3482 4.456911 TCATAAAAGCAAGTGCCTCTTCAG 59.543 41.667 0.00 0.00 43.38 3.02
2896 3483 4.216257 GTCATAAAAGCAAGTGCCTCTTCA 59.784 41.667 0.00 0.00 43.38 3.02
2899 3486 3.754965 TGTCATAAAAGCAAGTGCCTCT 58.245 40.909 0.00 0.00 43.38 3.69
2900 3487 4.479619 CTTGTCATAAAAGCAAGTGCCTC 58.520 43.478 0.00 0.00 43.38 4.70
2908 3495 7.386848 GGACTTGTAGTACTTGTCATAAAAGCA 59.613 37.037 19.89 0.00 0.00 3.91
2909 3496 7.603024 AGGACTTGTAGTACTTGTCATAAAAGC 59.397 37.037 19.89 7.73 35.35 3.51
2938 3536 8.531982 TGCAGTTGAGACTTGAGTATACTATTT 58.468 33.333 5.09 0.00 32.54 1.40
2951 3549 9.768662 ATTTCATTTTATTTGCAGTTGAGACTT 57.231 25.926 0.00 0.00 32.54 3.01
2952 3550 9.768662 AATTTCATTTTATTTGCAGTTGAGACT 57.231 25.926 0.00 0.00 36.25 3.24
2954 3552 9.985730 AGAATTTCATTTTATTTGCAGTTGAGA 57.014 25.926 0.00 0.00 0.00 3.27
2982 6296 8.606830 AGAAGGAGGTATCATTTAGAACAAAGT 58.393 33.333 0.00 0.00 27.44 2.66
2983 6297 9.454859 AAGAAGGAGGTATCATTTAGAACAAAG 57.545 33.333 0.00 0.00 27.44 2.77
2998 6312 5.550403 ACCTTGGTCAAATAAGAAGGAGGTA 59.450 40.000 0.00 0.00 37.27 3.08
3002 6316 6.016610 CGAAAACCTTGGTCAAATAAGAAGGA 60.017 38.462 0.00 0.00 37.27 3.36
3019 6333 5.536916 TGTTATTCCAACAATCCGAAAACCT 59.463 36.000 0.00 0.00 0.00 3.50
3134 6464 9.717942 GCAAATCCATAGATATGTTAGTTCTCT 57.282 33.333 0.00 0.00 30.42 3.10
3149 6479 6.974622 GTGTTTGTATTCCAGCAAATCCATAG 59.025 38.462 0.00 0.00 37.02 2.23
3152 6482 4.586421 TGTGTTTGTATTCCAGCAAATCCA 59.414 37.500 0.00 0.00 37.02 3.41
3196 6531 0.039618 ACCCCGTCCCTAACTTACGA 59.960 55.000 0.00 0.00 38.89 3.43
3197 6532 0.897621 AACCCCGTCCCTAACTTACG 59.102 55.000 0.00 0.00 36.42 3.18
3198 6533 1.208052 GGAACCCCGTCCCTAACTTAC 59.792 57.143 0.00 0.00 0.00 2.34
3219 6554 3.614390 GCGTCATATGTTAGTAGGCCTCC 60.614 52.174 9.68 0.00 0.00 4.30
3230 6565 3.132824 TCCTCACTCATGCGTCATATGTT 59.867 43.478 1.90 0.00 0.00 2.71
3236 6571 0.176449 CCATCCTCACTCATGCGTCA 59.824 55.000 0.00 0.00 0.00 4.35
3237 6572 0.176680 ACCATCCTCACTCATGCGTC 59.823 55.000 0.00 0.00 0.00 5.19
3238 6573 0.107993 CACCATCCTCACTCATGCGT 60.108 55.000 0.00 0.00 0.00 5.24
3239 6574 0.812811 CCACCATCCTCACTCATGCG 60.813 60.000 0.00 0.00 0.00 4.73
3241 6576 1.140452 CCTCCACCATCCTCACTCATG 59.860 57.143 0.00 0.00 0.00 3.07
3242 6577 1.008815 TCCTCCACCATCCTCACTCAT 59.991 52.381 0.00 0.00 0.00 2.90
3243 6578 0.413434 TCCTCCACCATCCTCACTCA 59.587 55.000 0.00 0.00 0.00 3.41
3244 6579 1.118838 CTCCTCCACCATCCTCACTC 58.881 60.000 0.00 0.00 0.00 3.51
3245 6580 0.326048 CCTCCTCCACCATCCTCACT 60.326 60.000 0.00 0.00 0.00 3.41
3246 6581 0.325671 TCCTCCTCCACCATCCTCAC 60.326 60.000 0.00 0.00 0.00 3.51
3247 6582 0.031716 CTCCTCCTCCACCATCCTCA 60.032 60.000 0.00 0.00 0.00 3.86
3248 6583 0.263172 TCTCCTCCTCCACCATCCTC 59.737 60.000 0.00 0.00 0.00 3.71
3249 6584 0.719015 TTCTCCTCCTCCACCATCCT 59.281 55.000 0.00 0.00 0.00 3.24
3250 6585 0.833949 GTTCTCCTCCTCCACCATCC 59.166 60.000 0.00 0.00 0.00 3.51
3251 6586 0.461961 CGTTCTCCTCCTCCACCATC 59.538 60.000 0.00 0.00 0.00 3.51
3252 6587 0.041238 TCGTTCTCCTCCTCCACCAT 59.959 55.000 0.00 0.00 0.00 3.55
3253 6588 0.612174 CTCGTTCTCCTCCTCCACCA 60.612 60.000 0.00 0.00 0.00 4.17
3254 6589 0.612453 ACTCGTTCTCCTCCTCCACC 60.612 60.000 0.00 0.00 0.00 4.61
3255 6590 0.528470 CACTCGTTCTCCTCCTCCAC 59.472 60.000 0.00 0.00 0.00 4.02
3256 6591 0.112606 ACACTCGTTCTCCTCCTCCA 59.887 55.000 0.00 0.00 0.00 3.86
3257 6592 2.125773 TACACTCGTTCTCCTCCTCC 57.874 55.000 0.00 0.00 0.00 4.30
3258 6593 4.883006 ACTAATACACTCGTTCTCCTCCTC 59.117 45.833 0.00 0.00 0.00 3.71
3259 6594 4.857679 ACTAATACACTCGTTCTCCTCCT 58.142 43.478 0.00 0.00 0.00 3.69
3260 6595 4.639310 TGACTAATACACTCGTTCTCCTCC 59.361 45.833 0.00 0.00 0.00 4.30
3271 6606 7.287466 AGAGCATGAGAAGATGACTAATACACT 59.713 37.037 0.00 0.00 0.00 3.55
3336 6671 6.478016 GTCGACCGCCTTATAAGATAAAAACT 59.522 38.462 14.28 0.00 0.00 2.66
3344 6679 4.460948 AAAAGTCGACCGCCTTATAAGA 57.539 40.909 13.01 0.00 0.00 2.10
3388 6723 5.345202 GTGTGATAAAAGTCGACCTACTGTG 59.655 44.000 13.01 0.00 0.00 3.66
3393 6728 5.970317 TGAGTGTGATAAAAGTCGACCTA 57.030 39.130 13.01 1.80 0.00 3.08
3394 6729 4.866508 TGAGTGTGATAAAAGTCGACCT 57.133 40.909 13.01 0.00 0.00 3.85
3395 6730 5.227908 TCTTGAGTGTGATAAAAGTCGACC 58.772 41.667 13.01 0.00 0.00 4.79
3396 6731 6.128795 CCTTCTTGAGTGTGATAAAAGTCGAC 60.129 42.308 7.70 7.70 0.00 4.20
3397 6732 5.926542 CCTTCTTGAGTGTGATAAAAGTCGA 59.073 40.000 0.00 0.00 0.00 4.20
3398 6733 5.120830 CCCTTCTTGAGTGTGATAAAAGTCG 59.879 44.000 0.00 0.00 0.00 4.18
3399 6734 5.412904 CCCCTTCTTGAGTGTGATAAAAGTC 59.587 44.000 0.00 0.00 0.00 3.01
3400 6735 5.163088 ACCCCTTCTTGAGTGTGATAAAAGT 60.163 40.000 0.00 0.00 0.00 2.66
3401 6736 5.316987 ACCCCTTCTTGAGTGTGATAAAAG 58.683 41.667 0.00 0.00 0.00 2.27
3402 6737 5.073144 AGACCCCTTCTTGAGTGTGATAAAA 59.927 40.000 0.00 0.00 0.00 1.52
3403 6738 4.597507 AGACCCCTTCTTGAGTGTGATAAA 59.402 41.667 0.00 0.00 0.00 1.40
3404 6739 4.020218 CAGACCCCTTCTTGAGTGTGATAA 60.020 45.833 0.00 0.00 28.96 1.75
3405 6740 3.515502 CAGACCCCTTCTTGAGTGTGATA 59.484 47.826 0.00 0.00 28.96 2.15
3406 6741 2.304180 CAGACCCCTTCTTGAGTGTGAT 59.696 50.000 0.00 0.00 28.96 3.06
3407 6742 1.694150 CAGACCCCTTCTTGAGTGTGA 59.306 52.381 0.00 0.00 28.96 3.58
3408 6743 1.694150 TCAGACCCCTTCTTGAGTGTG 59.306 52.381 0.00 0.00 28.96 3.82
3409 6744 1.974236 CTCAGACCCCTTCTTGAGTGT 59.026 52.381 0.00 0.00 28.96 3.55
3410 6745 2.251818 TCTCAGACCCCTTCTTGAGTG 58.748 52.381 0.88 0.00 34.04 3.51
3411 6746 2.704190 TCTCAGACCCCTTCTTGAGT 57.296 50.000 0.88 0.00 34.04 3.41
3412 6747 4.566426 AAATCTCAGACCCCTTCTTGAG 57.434 45.455 0.00 0.00 33.83 3.02
3413 6748 4.599241 AGAAAATCTCAGACCCCTTCTTGA 59.401 41.667 0.00 0.00 28.96 3.02
3414 6749 4.916183 AGAAAATCTCAGACCCCTTCTTG 58.084 43.478 0.00 0.00 28.96 3.02
3415 6750 5.590976 AAGAAAATCTCAGACCCCTTCTT 57.409 39.130 0.00 0.00 28.96 2.52
3432 6767 8.966868 AGATATAAATTTTGCGGGAGAAAGAAA 58.033 29.630 0.00 0.00 0.00 2.52
3434 6769 8.405531 CAAGATATAAATTTTGCGGGAGAAAGA 58.594 33.333 0.00 0.00 0.00 2.52
3435 6770 7.168135 GCAAGATATAAATTTTGCGGGAGAAAG 59.832 37.037 0.00 0.00 41.61 2.62
3438 6773 6.072112 GCAAGATATAAATTTTGCGGGAGA 57.928 37.500 0.00 0.00 41.61 3.71
3487 6822 2.034685 CCACATCGTCGATCATGTAGGT 59.965 50.000 4.34 0.00 31.78 3.08
3499 6834 4.832608 GGGCCGGTCCACATCGTC 62.833 72.222 23.50 0.00 36.21 4.20
3541 6876 2.362717 CAAAACCGGGTGGAAGCTTAAA 59.637 45.455 6.32 0.00 39.21 1.52
3543 6878 1.611519 CAAAACCGGGTGGAAGCTTA 58.388 50.000 6.32 0.00 39.21 3.09
3557 6892 2.137523 CTTCATGCAACTGGCCAAAAC 58.862 47.619 7.01 0.00 43.89 2.43
3571 6906 5.655893 AAAAATTGCGTGAAACCTTCATG 57.344 34.783 4.55 4.55 46.86 3.07
3624 6962 8.620416 GGAAAACCAAAAATGCTACTGAAAATT 58.380 29.630 0.00 0.00 0.00 1.82
3628 6966 6.097554 TCAGGAAAACCAAAAATGCTACTGAA 59.902 34.615 0.00 0.00 0.00 3.02
3632 6970 7.728847 AAATCAGGAAAACCAAAAATGCTAC 57.271 32.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.