Multiple sequence alignment - TraesCS3D01G121600

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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 TraesCS3D01G121600 chr3D 100.000 3314 0 0 1 3314 79422371 79419058 0.000000e+00 6120
1 TraesCS3D01G121600 chr3D 91.629 1338 97 6 1001 2323 79504251 79505588 0.000000e+00 1836
2 TraesCS3D01G121600 chr3D 89.986 1388 118 10 996 2371 79428062 79429440 0.000000e+00 1773
3 TraesCS3D01G121600 chr3A 91.003 3090 173 51 265 3314 93043607 93040583 0.000000e+00 4069
4 TraesCS3D01G121600 chr3A 91.239 1324 107 5 1001 2318 93263757 93265077 0.000000e+00 1794
5 TraesCS3D01G121600 chr3A 91.219 1321 110 4 1001 2318 93337359 93338676 0.000000e+00 1792
6 TraesCS3D01G121600 chr3A 93.208 265 18 0 2052 2316 93265663 93265927 1.120000e-104 390
7 TraesCS3D01G121600 chr3B 90.544 2940 166 50 1 2906 125525323 125522462 0.000000e+00 3786
8 TraesCS3D01G121600 chr3B 91.855 1326 102 3 996 2318 125551787 125553109 0.000000e+00 1845
9 TraesCS3D01G121600 chr3B 91.843 1324 96 7 1001 2318 125778975 125780292 0.000000e+00 1836
10 TraesCS3D01G121600 chr3B 96.825 63 2 0 2945 3007 125522133 125522071 4.520000e-19 106
11 TraesCS3D01G121600 chr1A 82.063 853 128 17 1445 2292 129004474 129003642 0.000000e+00 704
12 TraesCS3D01G121600 chr1A 74.371 437 81 22 1025 1449 129004984 129004567 1.230000e-34 158
13 TraesCS3D01G121600 chr1D 90.492 305 27 1 3009 3311 183080107 183079803 5.150000e-108 401
14 TraesCS3D01G121600 chr1B 89.968 309 31 0 3006 3314 643276190 643276498 1.850000e-107 399
15 TraesCS3D01G121600 chr4B 90.541 296 28 0 3016 3311 447108579 447108284 3.100000e-105 392
16 TraesCS3D01G121600 chr4B 88.571 315 35 1 3001 3314 488151026 488151340 6.710000e-102 381
17 TraesCS3D01G121600 chr2B 89.869 306 27 4 3009 3313 707268419 707268721 1.120000e-104 390
18 TraesCS3D01G121600 chr2A 89.389 311 31 1 3006 3314 34143053 34142743 1.120000e-104 390
19 TraesCS3D01G121600 chr5D 89.967 299 30 0 3016 3314 536935314 536935016 1.440000e-103 387
20 TraesCS3D01G121600 chr2D 89.068 311 32 1 3006 3314 340480909 340481219 5.190000e-103 385


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 TraesCS3D01G121600 chr3D 79419058 79422371 3313 True 6120 6120 100.0000 1 3314 1 chr3D.!!$R1 3313
1 TraesCS3D01G121600 chr3D 79504251 79505588 1337 False 1836 1836 91.6290 1001 2323 1 chr3D.!!$F2 1322
2 TraesCS3D01G121600 chr3D 79428062 79429440 1378 False 1773 1773 89.9860 996 2371 1 chr3D.!!$F1 1375
3 TraesCS3D01G121600 chr3A 93040583 93043607 3024 True 4069 4069 91.0030 265 3314 1 chr3A.!!$R1 3049
4 TraesCS3D01G121600 chr3A 93337359 93338676 1317 False 1792 1792 91.2190 1001 2318 1 chr3A.!!$F1 1317
5 TraesCS3D01G121600 chr3A 93263757 93265927 2170 False 1092 1794 92.2235 1001 2318 2 chr3A.!!$F2 1317
6 TraesCS3D01G121600 chr3B 125522071 125525323 3252 True 1946 3786 93.6845 1 3007 2 chr3B.!!$R1 3006
7 TraesCS3D01G121600 chr3B 125551787 125553109 1322 False 1845 1845 91.8550 996 2318 1 chr3B.!!$F1 1322
8 TraesCS3D01G121600 chr3B 125778975 125780292 1317 False 1836 1836 91.8430 1001 2318 1 chr3B.!!$F2 1317
9 TraesCS3D01G121600 chr1A 129003642 129004984 1342 True 431 704 78.2170 1025 2292 2 chr1A.!!$R1 1267


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
349 353 0.034089 GCTGCTCCCACCACCTTTAT 60.034 55.0 0.0 0.0 0.00 1.40 F
677 724 0.178935 CCTTTGGCTTTCTCCCCCAA 60.179 55.0 0.0 0.0 36.88 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1285 1.076485 GGCGAGGGGGTAGTACTGA 60.076 63.158 5.39 0.0 0.0 3.41 R
2613 2927 0.665670 CGTGGATCTCAGCTATGCGG 60.666 60.000 0.00 0.0 0.0 5.69 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
35 36 1.958715 CACCGTGGAATGCGTCACA 60.959 57.895 0.00 0.00 33.83 3.58
38 39 0.389296 CCGTGGAATGCGTCACAGTA 60.389 55.000 0.00 0.00 33.83 2.74
43 44 3.991773 GTGGAATGCGTCACAGTAAACTA 59.008 43.478 0.00 0.00 34.32 2.24
104 105 1.199327 CGCATACCGATGGATAGACGT 59.801 52.381 0.00 0.00 40.02 4.34
111 112 2.481568 CCGATGGATAGACGTACGCTAA 59.518 50.000 16.72 0.17 0.00 3.09
121 122 5.385396 AGACGTACGCTAATTAAATGTGC 57.615 39.130 16.72 0.00 0.00 4.57
124 125 5.350633 ACGTACGCTAATTAAATGTGCCTA 58.649 37.500 16.72 0.00 0.00 3.93
131 132 6.472163 CGCTAATTAAATGTGCCTAAAACTGG 59.528 38.462 0.00 0.00 0.00 4.00
132 133 6.756542 GCTAATTAAATGTGCCTAAAACTGGG 59.243 38.462 0.00 0.00 0.00 4.45
141 142 3.007614 TGCCTAAAACTGGGTAGACAGAC 59.992 47.826 0.00 0.00 40.97 3.51
160 161 1.284657 CTGATAGTTCAGGCACGCAG 58.715 55.000 0.00 0.00 44.78 5.18
163 164 0.324943 ATAGTTCAGGCACGCAGGTT 59.675 50.000 0.00 0.00 0.00 3.50
165 166 0.324943 AGTTCAGGCACGCAGGTTAT 59.675 50.000 0.00 0.00 0.00 1.89
166 167 0.727398 GTTCAGGCACGCAGGTTATC 59.273 55.000 0.00 0.00 0.00 1.75
167 168 0.613260 TTCAGGCACGCAGGTTATCT 59.387 50.000 0.00 0.00 0.00 1.98
168 169 0.108186 TCAGGCACGCAGGTTATCTG 60.108 55.000 0.00 0.00 46.03 2.90
169 170 0.391661 CAGGCACGCAGGTTATCTGT 60.392 55.000 0.00 0.00 45.08 3.41
172 173 1.438651 GCACGCAGGTTATCTGTTCA 58.561 50.000 0.00 0.00 45.08 3.18
177 178 2.353704 CGCAGGTTATCTGTTCAGTCCA 60.354 50.000 0.00 0.00 45.08 4.02
191 192 5.534278 TGTTCAGTCCAAAGATGTGCAAATA 59.466 36.000 0.00 0.00 0.00 1.40
195 196 6.371548 TCAGTCCAAAGATGTGCAAATACTAC 59.628 38.462 0.00 0.00 0.00 2.73
201 202 8.458052 CCAAAGATGTGCAAATACTACAACATA 58.542 33.333 0.00 0.00 0.00 2.29
210 214 7.663905 TGCAAATACTACAACATATACATCCCC 59.336 37.037 0.00 0.00 0.00 4.81
213 217 5.228945 ACTACAACATATACATCCCCAGC 57.771 43.478 0.00 0.00 0.00 4.85
222 226 6.908593 ACATATACATCCCCAGCTAATATGGA 59.091 38.462 0.00 0.00 40.51 3.41
223 227 5.965033 ATACATCCCCAGCTAATATGGAG 57.035 43.478 0.00 0.00 40.51 3.86
224 228 3.602608 ACATCCCCAGCTAATATGGAGT 58.397 45.455 0.00 0.00 40.51 3.85
225 229 3.983410 ACATCCCCAGCTAATATGGAGTT 59.017 43.478 0.00 0.00 40.51 3.01
226 230 4.202503 ACATCCCCAGCTAATATGGAGTTG 60.203 45.833 0.00 0.00 40.51 3.16
227 231 3.664320 TCCCCAGCTAATATGGAGTTGA 58.336 45.455 0.00 0.00 40.51 3.18
228 232 4.044308 TCCCCAGCTAATATGGAGTTGAA 58.956 43.478 0.00 0.00 40.51 2.69
229 233 4.103153 TCCCCAGCTAATATGGAGTTGAAG 59.897 45.833 0.00 0.00 40.51 3.02
230 234 3.817647 CCCAGCTAATATGGAGTTGAAGC 59.182 47.826 0.00 0.00 40.51 3.86
231 235 3.496130 CCAGCTAATATGGAGTTGAAGCG 59.504 47.826 0.00 0.00 40.51 4.68
232 236 3.496130 CAGCTAATATGGAGTTGAAGCGG 59.504 47.826 0.00 0.00 33.80 5.52
233 237 2.808543 GCTAATATGGAGTTGAAGCGGG 59.191 50.000 0.00 0.00 0.00 6.13
234 238 1.680338 AATATGGAGTTGAAGCGGGC 58.320 50.000 0.00 0.00 0.00 6.13
235 239 0.532862 ATATGGAGTTGAAGCGGGCG 60.533 55.000 0.00 0.00 0.00 6.13
236 240 1.609635 TATGGAGTTGAAGCGGGCGA 61.610 55.000 0.00 0.00 0.00 5.54
270 274 3.127533 GTGGCACGGTGGCTGATC 61.128 66.667 30.89 16.77 44.10 2.92
280 284 1.079197 TGGCTGATCGATGCGTGTT 60.079 52.632 0.54 0.00 0.00 3.32
281 285 0.174617 TGGCTGATCGATGCGTGTTA 59.825 50.000 0.54 0.00 0.00 2.41
282 286 0.855349 GGCTGATCGATGCGTGTTAG 59.145 55.000 0.54 0.00 0.00 2.34
283 287 0.230769 GCTGATCGATGCGTGTTAGC 59.769 55.000 0.54 0.00 37.71 3.09
349 353 0.034089 GCTGCTCCCACCACCTTTAT 60.034 55.000 0.00 0.00 0.00 1.40
351 355 2.356741 GCTGCTCCCACCACCTTTATTA 60.357 50.000 0.00 0.00 0.00 0.98
352 356 3.545703 CTGCTCCCACCACCTTTATTAG 58.454 50.000 0.00 0.00 0.00 1.73
353 357 2.916934 TGCTCCCACCACCTTTATTAGT 59.083 45.455 0.00 0.00 0.00 2.24
354 358 3.332485 TGCTCCCACCACCTTTATTAGTT 59.668 43.478 0.00 0.00 0.00 2.24
355 359 3.945921 GCTCCCACCACCTTTATTAGTTC 59.054 47.826 0.00 0.00 0.00 3.01
364 368 3.776417 ACCTTTATTAGTTCCTACCGGCA 59.224 43.478 0.00 0.00 0.00 5.69
381 385 1.167851 GCATTTGCTGACACTAGCCA 58.832 50.000 0.00 0.00 43.02 4.75
406 437 7.750229 TGCCTGAATTAATGGACAGATTATC 57.250 36.000 14.82 0.00 32.90 1.75
408 439 7.779326 TGCCTGAATTAATGGACAGATTATCAA 59.221 33.333 14.82 0.00 32.90 2.57
423 454 8.959548 ACAGATTATCAAGATGTGCAAATACAA 58.040 29.630 0.00 0.00 33.69 2.41
437 468 5.092105 GCAAATACAACATTCATGCGTACA 58.908 37.500 0.00 0.00 0.00 2.90
438 469 5.003402 GCAAATACAACATTCATGCGTACAC 59.997 40.000 0.00 0.00 0.00 2.90
442 473 3.366724 ACAACATTCATGCGTACACGTAG 59.633 43.478 3.44 0.00 42.22 3.51
451 482 1.517276 GCGTACACGTAGCTGCTAATG 59.483 52.381 11.57 14.65 42.22 1.90
452 483 2.793933 CGTACACGTAGCTGCTAATGT 58.206 47.619 23.45 23.45 34.11 2.71
453 484 3.789791 GCGTACACGTAGCTGCTAATGTA 60.790 47.826 21.94 21.94 42.22 2.29
454 485 3.966844 CGTACACGTAGCTGCTAATGTAG 59.033 47.826 24.47 17.75 34.11 2.74
457 488 4.918037 ACACGTAGCTGCTAATGTAGTAC 58.082 43.478 20.41 5.65 0.00 2.73
459 490 5.206299 CACGTAGCTGCTAATGTAGTACTC 58.794 45.833 11.57 0.00 0.00 2.59
461 492 4.515944 CGTAGCTGCTAATGTAGTACTCCT 59.484 45.833 11.57 0.00 0.00 3.69
462 493 5.699915 CGTAGCTGCTAATGTAGTACTCCTA 59.300 44.000 11.57 0.00 0.00 2.94
495 531 5.221342 ACAGAGATACATTACCAGCTAGCAC 60.221 44.000 18.83 0.00 0.00 4.40
496 532 5.010516 CAGAGATACATTACCAGCTAGCACT 59.989 44.000 18.83 0.42 0.00 4.40
498 534 2.990066 ACATTACCAGCTAGCACTCC 57.010 50.000 18.83 0.00 0.00 3.85
500 536 2.093447 ACATTACCAGCTAGCACTCCAC 60.093 50.000 18.83 0.00 0.00 4.02
503 539 1.127567 ACCAGCTAGCACTCCACCAA 61.128 55.000 18.83 0.00 0.00 3.67
505 541 1.376543 CAGCTAGCACTCCACCAATG 58.623 55.000 18.83 0.00 0.00 2.82
506 542 1.065926 CAGCTAGCACTCCACCAATGA 60.066 52.381 18.83 0.00 0.00 2.57
507 543 1.842562 AGCTAGCACTCCACCAATGAT 59.157 47.619 18.83 0.00 0.00 2.45
508 544 1.945394 GCTAGCACTCCACCAATGATG 59.055 52.381 10.63 0.00 0.00 3.07
509 545 1.945394 CTAGCACTCCACCAATGATGC 59.055 52.381 0.00 0.00 32.29 3.91
510 546 0.330604 AGCACTCCACCAATGATGCT 59.669 50.000 0.00 0.00 35.64 3.79
512 548 1.100510 CACTCCACCAATGATGCTGG 58.899 55.000 0.00 0.00 40.05 4.85
513 549 0.682209 ACTCCACCAATGATGCTGGC 60.682 55.000 0.00 0.00 37.48 4.85
557 597 3.760151 CCGTGCCATGATAATTGATGGAT 59.240 43.478 14.17 0.00 41.63 3.41
566 606 5.687780 TGATAATTGATGGATGACTGCTGT 58.312 37.500 0.00 0.00 0.00 4.40
596 636 2.422939 AGCCTGCCTATCCTATGGAA 57.577 50.000 0.00 0.00 34.34 3.53
664 705 1.039856 CCACCACCTTTGTCCTTTGG 58.960 55.000 0.00 0.00 0.00 3.28
677 724 0.178935 CCTTTGGCTTTCTCCCCCAA 60.179 55.000 0.00 0.00 36.88 4.12
682 729 1.155155 GCTTTCTCCCCCAACCCAA 59.845 57.895 0.00 0.00 0.00 4.12
711 759 2.636893 AGCCTCGCAGAAATATCATCCT 59.363 45.455 0.00 0.00 34.09 3.24
714 762 3.007290 CCTCGCAGAAATATCATCCTGGA 59.993 47.826 0.00 0.00 34.09 3.86
717 765 4.040829 TCGCAGAAATATCATCCTGGACAT 59.959 41.667 0.00 0.00 0.00 3.06
718 766 4.758674 CGCAGAAATATCATCCTGGACATT 59.241 41.667 0.00 0.00 0.00 2.71
719 767 5.106791 CGCAGAAATATCATCCTGGACATTC 60.107 44.000 0.00 0.00 0.00 2.67
720 768 6.002704 GCAGAAATATCATCCTGGACATTCT 58.997 40.000 0.00 0.46 0.00 2.40
721 769 6.489361 GCAGAAATATCATCCTGGACATTCTT 59.511 38.462 0.00 0.00 0.00 2.52
722 770 7.308469 GCAGAAATATCATCCTGGACATTCTTC 60.308 40.741 0.00 0.00 0.00 2.87
723 771 7.718314 CAGAAATATCATCCTGGACATTCTTCA 59.282 37.037 0.00 0.00 0.00 3.02
724 772 7.937942 AGAAATATCATCCTGGACATTCTTCAG 59.062 37.037 0.00 0.00 0.00 3.02
725 773 7.384524 AATATCATCCTGGACATTCTTCAGA 57.615 36.000 0.00 0.00 0.00 3.27
726 774 5.705397 ATCATCCTGGACATTCTTCAGAA 57.295 39.130 0.00 0.00 38.56 3.02
727 775 5.095145 TCATCCTGGACATTCTTCAGAAG 57.905 43.478 3.45 3.45 37.48 2.85
728 776 4.779489 TCATCCTGGACATTCTTCAGAAGA 59.221 41.667 8.95 8.95 37.48 2.87
758 806 2.717639 AAAATCTCATCCCGGACAGG 57.282 50.000 0.73 0.00 40.63 4.00
761 809 0.833287 ATCTCATCCCGGACAGGTTG 59.167 55.000 0.73 0.00 38.74 3.77
770 818 0.888736 CGGACAGGTTGTGGCATTCA 60.889 55.000 0.00 0.00 34.74 2.57
800 848 0.179073 CACCCATCCTCGTCACCATC 60.179 60.000 0.00 0.00 0.00 3.51
813 863 0.374758 CACCATCAGACATTTCGCCG 59.625 55.000 0.00 0.00 0.00 6.46
814 864 0.249120 ACCATCAGACATTTCGCCGA 59.751 50.000 0.00 0.00 0.00 5.54
900 951 2.033448 CAGCCAGGCAACCGGTTA 59.967 61.111 21.79 0.00 37.17 2.85
1230 1297 1.201424 CCCTGGTTCAGTACTACCCC 58.799 60.000 11.54 4.94 33.34 4.95
2482 2658 5.412286 TGTGTAGTTTAACCGGAAATAAGCC 59.588 40.000 9.46 0.00 0.00 4.35
2496 2672 1.397390 TAAGCCCCTCGATTCGGGTC 61.397 60.000 5.04 0.00 41.85 4.46
2613 2927 7.802720 AGAGAAATTTTGTTTTGTTTGTGTTGC 59.197 29.630 0.00 0.00 0.00 4.17
2647 2961 4.579384 ACGGTGGTGGTGGCTTGG 62.579 66.667 0.00 0.00 0.00 3.61
2719 3038 2.267642 CGGCCGATTCAGTCCCAA 59.732 61.111 24.07 0.00 0.00 4.12
2725 3044 1.089920 CGATTCAGTCCCAAGCAAGG 58.910 55.000 0.00 0.00 0.00 3.61
2740 3059 1.898094 AAGGCAGTGATGCAACGCA 60.898 52.632 10.34 0.00 44.86 5.24
2742 3061 2.126734 GCAGTGATGCAACGCACC 60.127 61.111 10.34 0.00 43.04 5.01
2748 3067 0.039346 TGATGCAACGCACCACAATG 60.039 50.000 0.00 0.00 43.04 2.82
2752 3071 0.939106 GCAACGCACCACAATGTTCC 60.939 55.000 0.00 0.00 0.00 3.62
2757 3076 1.164411 GCACCACAATGTTCCGATCA 58.836 50.000 0.00 0.00 0.00 2.92
2759 3078 2.164219 GCACCACAATGTTCCGATCATT 59.836 45.455 0.00 0.00 36.16 2.57
2908 3547 6.705381 GGACATTGATAGGAATCTGACTTGAG 59.295 42.308 0.00 0.00 32.93 3.02
2909 3548 7.192852 ACATTGATAGGAATCTGACTTGAGT 57.807 36.000 0.00 0.00 32.93 3.41
2910 3549 7.046652 ACATTGATAGGAATCTGACTTGAGTG 58.953 38.462 0.00 0.00 32.93 3.51
2912 3551 2.777832 AGGAATCTGACTTGAGTGCC 57.222 50.000 0.00 0.00 0.00 5.01
2913 3552 1.066573 AGGAATCTGACTTGAGTGCCG 60.067 52.381 0.00 0.00 0.00 5.69
2915 3554 2.612972 GGAATCTGACTTGAGTGCCGAA 60.613 50.000 0.00 0.00 0.00 4.30
2930 3569 1.860078 CGAAGGAACTGTCGGTTGC 59.140 57.895 7.93 7.93 44.89 4.17
2931 3570 0.878523 CGAAGGAACTGTCGGTTGCA 60.879 55.000 17.26 0.00 46.57 4.08
2932 3571 1.523758 GAAGGAACTGTCGGTTGCAT 58.476 50.000 17.26 6.17 46.57 3.96
2933 3572 1.464997 GAAGGAACTGTCGGTTGCATC 59.535 52.381 17.26 11.47 46.57 3.91
2934 3573 0.396435 AGGAACTGTCGGTTGCATCA 59.604 50.000 17.26 0.00 46.57 3.07
2935 3574 1.202758 AGGAACTGTCGGTTGCATCAA 60.203 47.619 17.26 0.00 46.57 2.57
2936 3575 1.606668 GGAACTGTCGGTTGCATCAAA 59.393 47.619 10.91 0.00 44.14 2.69
2937 3576 2.034053 GGAACTGTCGGTTGCATCAAAA 59.966 45.455 10.91 0.00 44.14 2.44
2938 3577 3.490078 GGAACTGTCGGTTGCATCAAAAA 60.490 43.478 10.91 0.00 44.14 1.94
2939 3578 3.354089 ACTGTCGGTTGCATCAAAAAG 57.646 42.857 0.00 0.00 0.00 2.27
2940 3579 2.948979 ACTGTCGGTTGCATCAAAAAGA 59.051 40.909 0.00 0.00 0.00 2.52
2941 3580 3.380004 ACTGTCGGTTGCATCAAAAAGAA 59.620 39.130 0.00 0.00 0.00 2.52
2942 3581 4.142271 ACTGTCGGTTGCATCAAAAAGAAA 60.142 37.500 0.00 0.00 0.00 2.52
2943 3582 4.748892 TGTCGGTTGCATCAAAAAGAAAA 58.251 34.783 0.00 0.00 0.00 2.29
3008 3669 7.472334 ACAAATGATGAGCCTAAACAAAGAT 57.528 32.000 0.00 0.00 0.00 2.40
3013 3674 6.121590 TGATGAGCCTAAACAAAGATATGCA 58.878 36.000 0.00 0.00 0.00 3.96
3050 3711 8.253810 AGATGTGAAATCTCTACGAATGAAGAA 58.746 33.333 0.00 0.00 0.00 2.52
3052 3713 6.590292 TGTGAAATCTCTACGAATGAAGAACC 59.410 38.462 0.00 0.00 0.00 3.62
3055 3716 2.159282 TCTCTACGAATGAAGAACCGGC 60.159 50.000 0.00 0.00 0.00 6.13
3069 3730 4.950050 AGAACCGGCATTAACTCTATCAG 58.050 43.478 0.00 0.00 0.00 2.90
3119 3780 8.689251 TGTACTCTATTTTTGATGAACTCGAG 57.311 34.615 11.84 11.84 0.00 4.04
3123 3784 7.065216 TCTATTTTTGATGAACTCGAGCTTG 57.935 36.000 13.61 0.00 0.00 4.01
3128 3789 3.515630 TGATGAACTCGAGCTTGTCATC 58.484 45.455 26.40 26.40 34.73 2.92
3153 3814 9.601217 TCAAGATTACCATAAGCTCTAAAACTC 57.399 33.333 0.00 0.00 0.00 3.01
3159 3820 7.203255 ACCATAAGCTCTAAAACTCACAAAC 57.797 36.000 0.00 0.00 0.00 2.93
3170 3831 9.179909 TCTAAAACTCACAAACAGAAATACCAA 57.820 29.630 0.00 0.00 0.00 3.67
3172 3833 8.474006 AAAACTCACAAACAGAAATACCAAAC 57.526 30.769 0.00 0.00 0.00 2.93
3191 3852 6.324770 ACCAAACAAGAACCAAGAAAGATGAT 59.675 34.615 0.00 0.00 0.00 2.45
3217 3878 2.098770 GGATGCAATGGTTTGAGCTCTC 59.901 50.000 16.19 5.49 34.60 3.20
3247 3908 2.834574 ACGATCAAGCTACTCACTCG 57.165 50.000 0.00 0.00 0.00 4.18
3279 3940 4.917998 CCCTGATAGTACGACAATCAATCG 59.082 45.833 0.00 0.00 45.17 3.34
3294 3955 0.533951 AATCGTACAACCCGGTCTCC 59.466 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.000717 CATTCCACGGTGAAAACCCAC 60.001 52.381 10.28 0.00 36.37 4.61
35 36 2.088950 AATGCCACGCGTAGTTTACT 57.911 45.000 13.44 0.00 0.00 2.24
38 39 0.386731 GCAAATGCCACGCGTAGTTT 60.387 50.000 13.44 7.95 34.31 2.66
59 60 1.566018 GCCAAGACGGTTTCTCCACG 61.566 60.000 0.00 0.00 36.97 4.94
90 91 0.873054 AGCGTACGTCTATCCATCGG 59.127 55.000 17.90 0.00 0.00 4.18
104 105 8.178964 CAGTTTTAGGCACATTTAATTAGCGTA 58.821 33.333 0.00 0.00 0.00 4.42
111 112 7.122204 GTCTACCCAGTTTTAGGCACATTTAAT 59.878 37.037 0.00 0.00 0.00 1.40
121 122 4.527038 TCAGTCTGTCTACCCAGTTTTAGG 59.473 45.833 0.00 0.00 34.02 2.69
124 125 5.780793 ACTATCAGTCTGTCTACCCAGTTTT 59.219 40.000 0.00 0.00 34.02 2.43
160 161 5.940470 ACATCTTTGGACTGAACAGATAACC 59.060 40.000 8.87 6.90 0.00 2.85
163 164 4.937620 GCACATCTTTGGACTGAACAGATA 59.062 41.667 8.87 0.00 0.00 1.98
165 166 3.141398 GCACATCTTTGGACTGAACAGA 58.859 45.455 8.87 0.00 0.00 3.41
166 167 2.880268 TGCACATCTTTGGACTGAACAG 59.120 45.455 0.00 0.00 0.00 3.16
167 168 2.929641 TGCACATCTTTGGACTGAACA 58.070 42.857 0.00 0.00 0.00 3.18
168 169 3.988379 TTGCACATCTTTGGACTGAAC 57.012 42.857 0.00 0.00 0.00 3.18
169 170 5.769662 AGTATTTGCACATCTTTGGACTGAA 59.230 36.000 0.00 0.00 0.00 3.02
172 173 6.237901 TGTAGTATTTGCACATCTTTGGACT 58.762 36.000 0.00 0.00 0.00 3.85
191 192 4.907875 AGCTGGGGATGTATATGTTGTAGT 59.092 41.667 0.00 0.00 0.00 2.73
195 196 7.500227 CCATATTAGCTGGGGATGTATATGTTG 59.500 40.741 0.00 0.00 0.00 3.33
201 202 5.353986 ACTCCATATTAGCTGGGGATGTAT 58.646 41.667 0.00 0.00 36.24 2.29
210 214 3.496130 CCGCTTCAACTCCATATTAGCTG 59.504 47.826 0.00 0.00 0.00 4.24
213 217 2.808543 GCCCGCTTCAACTCCATATTAG 59.191 50.000 0.00 0.00 0.00 1.73
222 226 4.008933 AGCTCGCCCGCTTCAACT 62.009 61.111 0.00 0.00 36.74 3.16
223 227 3.793144 CAGCTCGCCCGCTTCAAC 61.793 66.667 0.00 0.00 38.41 3.18
224 228 3.315142 ATCAGCTCGCCCGCTTCAA 62.315 57.895 0.00 0.00 38.41 2.69
225 229 3.774528 ATCAGCTCGCCCGCTTCA 61.775 61.111 0.00 0.00 38.41 3.02
226 230 3.267860 CATCAGCTCGCCCGCTTC 61.268 66.667 0.00 0.00 38.41 3.86
227 231 3.612247 AACATCAGCTCGCCCGCTT 62.612 57.895 0.00 0.00 38.41 4.68
228 232 4.087892 AACATCAGCTCGCCCGCT 62.088 61.111 0.00 0.00 41.90 5.52
229 233 3.869272 CAACATCAGCTCGCCCGC 61.869 66.667 0.00 0.00 0.00 6.13
230 234 3.869272 GCAACATCAGCTCGCCCG 61.869 66.667 0.00 0.00 0.00 6.13
231 235 2.747460 TGCAACATCAGCTCGCCC 60.747 61.111 0.00 0.00 0.00 6.13
232 236 2.789917 CTGCAACATCAGCTCGCC 59.210 61.111 0.00 0.00 0.00 5.54
349 353 2.026636 AGCAAATGCCGGTAGGAACTAA 60.027 45.455 1.90 0.00 42.48 2.24
351 355 0.328258 AGCAAATGCCGGTAGGAACT 59.672 50.000 1.90 0.00 43.38 3.01
352 356 0.451783 CAGCAAATGCCGGTAGGAAC 59.548 55.000 1.90 0.00 43.38 3.62
353 357 0.326595 TCAGCAAATGCCGGTAGGAA 59.673 50.000 1.90 0.00 43.38 3.36
354 358 0.392461 GTCAGCAAATGCCGGTAGGA 60.392 55.000 1.90 0.00 43.38 2.94
355 359 0.676466 TGTCAGCAAATGCCGGTAGG 60.676 55.000 1.90 0.00 43.38 3.18
364 368 1.747355 GCATGGCTAGTGTCAGCAAAT 59.253 47.619 0.00 0.00 43.67 2.32
381 385 7.946219 TGATAATCTGTCCATTAATTCAGGCAT 59.054 33.333 10.29 0.00 0.00 4.40
406 437 7.671827 CATGAATGTTGTATTTGCACATCTTG 58.328 34.615 0.00 0.00 0.00 3.02
408 439 5.808540 GCATGAATGTTGTATTTGCACATCT 59.191 36.000 0.00 0.00 0.00 2.90
423 454 1.924524 GCTACGTGTACGCATGAATGT 59.075 47.619 7.29 0.00 44.43 2.71
427 458 0.800683 GCAGCTACGTGTACGCATGA 60.801 55.000 7.29 0.00 44.43 3.07
437 468 4.275443 GGAGTACTACATTAGCAGCTACGT 59.725 45.833 0.00 5.29 0.00 3.57
438 469 4.515944 AGGAGTACTACATTAGCAGCTACG 59.484 45.833 8.10 0.00 0.00 3.51
500 536 2.842256 GCCTCGCCAGCATCATTGG 61.842 63.158 0.00 0.00 38.78 3.16
503 539 3.804153 CTCGCCTCGCCAGCATCAT 62.804 63.158 0.00 0.00 0.00 2.45
509 545 4.218578 ATCAGCTCGCCTCGCCAG 62.219 66.667 0.00 0.00 0.00 4.85
510 546 4.519437 CATCAGCTCGCCTCGCCA 62.519 66.667 0.00 0.00 0.00 5.69
557 597 4.284860 AGCACGCGACAGCAGTCA 62.285 61.111 15.93 0.00 45.23 3.41
596 636 1.302033 CTTGCAGCCTCGTGTTCCT 60.302 57.895 0.00 0.00 0.00 3.36
664 705 1.155155 TTGGGTTGGGGGAGAAAGC 59.845 57.895 0.00 0.00 0.00 3.51
699 747 7.935755 TCTGAAGAATGTCCAGGATGATATTTC 59.064 37.037 0.00 0.00 39.69 2.17
711 759 7.880160 TTTCTTTTCTTCTGAAGAATGTCCA 57.120 32.000 27.93 13.85 46.15 4.02
741 789 1.210478 CAACCTGTCCGGGATGAGATT 59.790 52.381 0.00 0.00 36.97 2.40
743 791 0.544357 ACAACCTGTCCGGGATGAGA 60.544 55.000 0.00 0.00 36.97 3.27
758 806 1.069227 GGACGAGTTGAATGCCACAAC 60.069 52.381 0.00 0.00 45.15 3.32
761 809 0.669318 TCGGACGAGTTGAATGCCAC 60.669 55.000 0.00 0.00 0.00 5.01
770 818 1.590147 GATGGGTGTCGGACGAGTT 59.410 57.895 3.34 0.00 0.00 3.01
800 848 2.379634 TGCGTCGGCGAAATGTCTG 61.380 57.895 16.53 0.00 44.10 3.51
897 948 2.343544 AGCGCGTCGTATTCAACTTAAC 59.656 45.455 8.43 0.00 0.00 2.01
900 951 1.389106 GAAGCGCGTCGTATTCAACTT 59.611 47.619 7.77 0.00 0.00 2.66
934 986 2.484417 CGAGAGGGAGAATTGGTGGATG 60.484 54.545 0.00 0.00 0.00 3.51
936 988 1.195115 CGAGAGGGAGAATTGGTGGA 58.805 55.000 0.00 0.00 0.00 4.02
1218 1285 1.076485 GGCGAGGGGGTAGTACTGA 60.076 63.158 5.39 0.00 0.00 3.41
1829 2002 2.962569 CGAAGCAGAGGTGGACGA 59.037 61.111 0.00 0.00 0.00 4.20
2097 2270 2.047844 CAGTCCGACACCAGCAGG 60.048 66.667 0.40 0.00 42.21 4.85
2496 2672 1.366111 AATCCAATCGCGACCCAACG 61.366 55.000 12.93 0.00 0.00 4.10
2609 2923 0.864455 GATCTCAGCTATGCGGCAAC 59.136 55.000 6.82 0.00 34.17 4.17
2613 2927 0.665670 CGTGGATCTCAGCTATGCGG 60.666 60.000 0.00 0.00 0.00 5.69
2725 3044 2.906939 TGGTGCGTTGCATCACTGC 61.907 57.895 0.00 6.39 45.28 4.40
2740 3059 3.016736 GGAATGATCGGAACATTGTGGT 58.983 45.455 16.85 0.00 37.96 4.16
2742 3061 2.032054 CGGGAATGATCGGAACATTGTG 59.968 50.000 16.85 4.34 37.96 3.33
2748 3067 3.060602 GAGATTCGGGAATGATCGGAAC 58.939 50.000 0.00 0.00 0.00 3.62
2752 3071 2.320367 GACGAGATTCGGGAATGATCG 58.680 52.381 17.35 17.35 45.59 3.69
2757 3076 1.001597 GCTACGACGAGATTCGGGAAT 60.002 52.381 0.00 0.00 45.59 3.01
2759 3078 0.745486 TGCTACGACGAGATTCGGGA 60.745 55.000 0.00 0.00 45.59 5.14
2874 3199 5.808366 TCCTATCAATGTCCACTATCCAC 57.192 43.478 0.00 0.00 0.00 4.02
2908 3547 3.550656 CGACAGTTCCTTCGGCAC 58.449 61.111 0.00 0.00 0.00 5.01
2912 3551 0.878523 TGCAACCGACAGTTCCTTCG 60.879 55.000 0.00 0.00 36.18 3.79
2913 3552 1.464997 GATGCAACCGACAGTTCCTTC 59.535 52.381 0.00 0.00 36.18 3.46
2915 3554 0.396435 TGATGCAACCGACAGTTCCT 59.604 50.000 0.00 0.00 36.18 3.36
2917 3556 3.347958 TTTTGATGCAACCGACAGTTC 57.652 42.857 0.00 0.00 36.18 3.01
2918 3557 3.380004 TCTTTTTGATGCAACCGACAGTT 59.620 39.130 0.00 0.00 40.16 3.16
2919 3558 2.948979 TCTTTTTGATGCAACCGACAGT 59.051 40.909 0.00 0.00 0.00 3.55
2920 3559 3.624326 TCTTTTTGATGCAACCGACAG 57.376 42.857 0.00 0.00 0.00 3.51
2921 3560 4.377839 TTTCTTTTTGATGCAACCGACA 57.622 36.364 0.00 0.00 0.00 4.35
2922 3561 5.710613 TTTTTCTTTTTGATGCAACCGAC 57.289 34.783 0.00 0.00 0.00 4.79
2941 3580 5.414765 GGGATCAAGATAACCGACAGTTTTT 59.585 40.000 0.00 0.00 40.05 1.94
2942 3581 4.941873 GGGATCAAGATAACCGACAGTTTT 59.058 41.667 0.00 0.00 40.05 2.43
2943 3582 4.225267 AGGGATCAAGATAACCGACAGTTT 59.775 41.667 0.00 0.00 40.05 2.66
2956 3595 4.285003 TCTTGGTTAACGAAGGGATCAAGA 59.715 41.667 24.60 18.30 37.57 3.02
3034 3695 2.159282 GCCGGTTCTTCATTCGTAGAGA 60.159 50.000 1.90 0.00 38.43 3.10
3037 3698 2.004583 TGCCGGTTCTTCATTCGTAG 57.995 50.000 1.90 0.00 0.00 3.51
3050 3711 2.434336 TGCTGATAGAGTTAATGCCGGT 59.566 45.455 1.90 0.00 0.00 5.28
3052 3713 5.484173 TTTTGCTGATAGAGTTAATGCCG 57.516 39.130 0.00 0.00 0.00 5.69
3069 3730 9.858247 CATATGCATCTTTTATGATGTTTTTGC 57.142 29.630 0.19 0.00 44.02 3.68
3101 3762 6.426633 TGACAAGCTCGAGTTCATCAAAAATA 59.573 34.615 15.13 0.00 0.00 1.40
3107 3768 3.056607 TGATGACAAGCTCGAGTTCATCA 60.057 43.478 28.28 28.28 39.74 3.07
3123 3784 9.547753 TTTAGAGCTTATGGTAATCTTGATGAC 57.452 33.333 0.00 0.00 0.00 3.06
3128 3789 9.383519 TGAGTTTTAGAGCTTATGGTAATCTTG 57.616 33.333 0.00 0.00 0.00 3.02
3134 3795 7.934665 TGTTTGTGAGTTTTAGAGCTTATGGTA 59.065 33.333 0.00 0.00 0.00 3.25
3136 3797 7.173218 TCTGTTTGTGAGTTTTAGAGCTTATGG 59.827 37.037 0.00 0.00 0.00 2.74
3153 3814 7.010091 GGTTCTTGTTTGGTATTTCTGTTTGTG 59.990 37.037 0.00 0.00 0.00 3.33
3159 3820 7.038154 TCTTGGTTCTTGTTTGGTATTTCTG 57.962 36.000 0.00 0.00 0.00 3.02
3170 3831 5.302568 TGCATCATCTTTCTTGGTTCTTGTT 59.697 36.000 0.00 0.00 0.00 2.83
3172 3833 5.381174 TGCATCATCTTTCTTGGTTCTTG 57.619 39.130 0.00 0.00 0.00 3.02
3217 3878 3.874706 AGCTTGATCGTATCGTTCGTAG 58.125 45.455 0.00 0.00 0.00 3.51
3294 3955 2.403252 GGTCTCATGGTGGTAGTTGG 57.597 55.000 0.00 0.00 0.00 3.77



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

AutoCloner maintained by Alex Coulton.