Multiple sequence alignment - TraesCS4B01G331600

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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 TraesCS4B01G331600 chr4B 100.000 2504 0 0 1 2504 621965793 621968296 0.000000e+00 4625
1 TraesCS4B01G331600 chr4B 82.477 331 30 11 1 309 622772944 622772620 5.310000e-67 265
2 TraesCS4B01G331600 chr1B 94.177 1597 77 7 908 2504 394907091 394908671 0.000000e+00 2420
3 TraesCS4B01G331600 chr1B 88.792 1606 168 10 908 2504 678555060 678556662 0.000000e+00 1958
4 TraesCS4B01G331600 chr3B 92.929 1598 99 3 908 2504 810139565 810141149 0.000000e+00 2313
5 TraesCS4B01G331600 chr2B 90.506 1601 143 5 911 2504 534244842 534243244 0.000000e+00 2106
6 TraesCS4B01G331600 chr2B 94.845 194 10 0 430 623 105849950 105849757 1.130000e-78 303
7 TraesCS4B01G331600 chr2B 87.500 128 12 4 498 623 466199751 466199876 7.220000e-31 145
8 TraesCS4B01G331600 chr1A 86.162 1597 210 10 912 2503 341019077 341020667 0.000000e+00 1714
9 TraesCS4B01G331600 chr2D 87.723 953 113 3 910 1861 71256012 71255063 0.000000e+00 1109
10 TraesCS4B01G331600 chr2D 82.055 652 93 11 1857 2504 71245946 71245315 3.670000e-148 534
11 TraesCS4B01G331600 chr2D 82.787 366 54 8 2143 2504 155158921 155158561 4.020000e-83 318
12 TraesCS4B01G331600 chr2D 94.388 196 11 0 430 625 589703088 589702893 4.050000e-78 302
13 TraesCS4B01G331600 chr3A 83.762 622 83 8 1882 2501 63453528 63454133 7.770000e-160 573
14 TraesCS4B01G331600 chr3A 90.148 203 19 1 432 633 670674003 670674205 1.910000e-66 263
15 TraesCS4B01G331600 chr3A 85.507 207 26 4 430 635 581836877 581837080 1.950000e-51 213
16 TraesCS4B01G331600 chr3A 83.582 201 27 5 430 628 314626882 314626686 1.530000e-42 183
17 TraesCS4B01G331600 chr3A 88.060 134 15 1 505 637 618001653 618001520 9.270000e-35 158
18 TraesCS4B01G331600 chr4D 90.762 433 24 6 1 430 486983437 486983856 4.680000e-157 564
19 TraesCS4B01G331600 chr4D 92.949 156 9 2 761 916 486984668 486984821 2.510000e-55 226
20 TraesCS4B01G331600 chr4D 96.491 114 4 0 633 746 486984510 486984623 3.290000e-44 189
21 TraesCS4B01G331600 chr5A 84.045 445 35 14 1 430 667725492 667725915 1.800000e-106 396
22 TraesCS4B01G331600 chr5A 94.416 197 10 1 430 625 569789465 569789269 4.050000e-78 302
23 TraesCS4B01G331600 chr5A 94.697 132 6 1 726 857 667727036 667727166 1.170000e-48 204
24 TraesCS4B01G331600 chr6D 95.361 194 9 0 430 623 11913399 11913206 2.420000e-80 309
25 TraesCS4B01G331600 chrUn 94.898 196 10 0 430 625 29916110 29915915 8.700000e-80 307
26 TraesCS4B01G331600 chrUn 91.781 73 6 0 78 150 224685393 224685465 4.410000e-18 102
27 TraesCS4B01G331600 chr7D 94.898 196 10 0 430 625 41258404 41258209 8.700000e-80 307
28 TraesCS4B01G331600 chr7D 94.388 196 11 0 430 625 141345437 141345632 4.050000e-78 302
29 TraesCS4B01G331600 chr7D 86.029 136 12 6 80 210 254373868 254373735 3.360000e-29 139
30 TraesCS4B01G331600 chr1D 94.388 196 11 0 430 625 489327373 489327178 4.050000e-78 302
31 TraesCS4B01G331600 chr1D 94.388 196 11 0 430 625 489435097 489434902 4.050000e-78 302
32 TraesCS4B01G331600 chr2A 91.346 208 15 3 430 635 471010325 471010119 5.270000e-72 281
33 TraesCS4B01G331600 chr2A 90.640 203 19 0 430 632 699416782 699416580 1.140000e-68 270
34 TraesCS4B01G331600 chr2A 84.862 218 30 3 2283 2499 61840471 61840256 1.510000e-52 217
35 TraesCS4B01G331600 chr2A 87.719 171 21 0 456 626 289614770 289614600 1.520000e-47 200
36 TraesCS4B01G331600 chr7A 88.083 193 20 3 436 626 685382901 685382710 2.510000e-55 226
37 TraesCS4B01G331600 chr7A 86.765 136 11 6 80 210 272942999 272942866 7.220000e-31 145
38 TraesCS4B01G331600 chr7B 85.294 136 13 6 80 210 231698406 231698273 1.560000e-27 134
39 TraesCS4B01G331600 chr4A 91.781 73 6 0 78 150 629106216 629106288 4.410000e-18 102


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 TraesCS4B01G331600 chr4B 621965793 621968296 2503 False 4625.000000 4625 100.000000 1 2504 1 chr4B.!!$F1 2503
1 TraesCS4B01G331600 chr1B 394907091 394908671 1580 False 2420.000000 2420 94.177000 908 2504 1 chr1B.!!$F1 1596
2 TraesCS4B01G331600 chr1B 678555060 678556662 1602 False 1958.000000 1958 88.792000 908 2504 1 chr1B.!!$F2 1596
3 TraesCS4B01G331600 chr3B 810139565 810141149 1584 False 2313.000000 2313 92.929000 908 2504 1 chr3B.!!$F1 1596
4 TraesCS4B01G331600 chr2B 534243244 534244842 1598 True 2106.000000 2106 90.506000 911 2504 1 chr2B.!!$R2 1593
5 TraesCS4B01G331600 chr1A 341019077 341020667 1590 False 1714.000000 1714 86.162000 912 2503 1 chr1A.!!$F1 1591
6 TraesCS4B01G331600 chr2D 71255063 71256012 949 True 1109.000000 1109 87.723000 910 1861 1 chr2D.!!$R2 951
7 TraesCS4B01G331600 chr2D 71245315 71245946 631 True 534.000000 534 82.055000 1857 2504 1 chr2D.!!$R1 647
8 TraesCS4B01G331600 chr3A 63453528 63454133 605 False 573.000000 573 83.762000 1882 2501 1 chr3A.!!$F1 619
9 TraesCS4B01G331600 chr4D 486983437 486984821 1384 False 326.333333 564 93.400667 1 916 3 chr4D.!!$F1 915
10 TraesCS4B01G331600 chr5A 667725492 667727166 1674 False 300.000000 396 89.371000 1 857 2 chr5A.!!$F1 856

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
467 484 0.037232 CAGTGGGAGGAGACGTTTCC 60.037 60.0 17.16 17.16 37.52 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 2764 0.631212 CCCCTACCAAAGCCTTCCAT 59.369 55.0 0.0 0.0 0.0 3.41 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
42 43 1.905894 TCATCATCCAACAGAACCGGA 59.094 47.619 9.46 0.00 0.00 5.14
62 63 0.543277 TGGCTCAATCGATCCTTGCT 59.457 50.000 0.00 0.00 0.00 3.91
63 64 1.224965 GGCTCAATCGATCCTTGCTC 58.775 55.000 0.00 0.00 0.00 4.26
66 69 2.031437 GCTCAATCGATCCTTGCTCAAC 59.969 50.000 0.00 0.00 0.00 3.18
170 173 4.021925 GGCTTGACCCGCACCTCT 62.022 66.667 0.00 0.00 0.00 3.69
227 230 3.102107 CTCGGAGCCAGAGACGACG 62.102 68.421 0.00 0.00 37.93 5.12
317 333 6.384224 CATGGGCATATAGTTTGTGCTTATG 58.616 40.000 2.63 4.37 38.83 1.90
394 411 0.882474 AGCGACTTCTAAGAGCACGT 59.118 50.000 13.91 0.00 36.34 4.49
430 447 2.879103 AAGGATTGACCACGGAACAT 57.121 45.000 0.00 0.00 42.04 2.71
432 449 3.154827 AGGATTGACCACGGAACATTT 57.845 42.857 0.00 0.00 42.04 2.32
434 451 2.163613 GGATTGACCACGGAACATTTCC 59.836 50.000 0.00 0.00 41.53 3.13
442 459 1.064134 GGAACATTTCCGGCGATGC 59.936 57.895 9.30 0.00 40.59 3.91
443 460 1.297598 GAACATTTCCGGCGATGCG 60.298 57.895 9.30 0.00 0.00 4.73
454 471 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
455 472 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
456 473 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
457 474 1.442526 GATGCGCATTCAGTGGGAGG 61.443 60.000 26.12 0.00 43.02 4.30
459 476 1.817099 GCGCATTCAGTGGGAGGAG 60.817 63.158 0.30 0.00 43.02 3.69
462 479 0.460987 GCATTCAGTGGGAGGAGACG 60.461 60.000 0.00 0.00 0.00 4.18
466 483 0.966920 TCAGTGGGAGGAGACGTTTC 59.033 55.000 0.00 0.00 0.00 2.78
467 484 0.037232 CAGTGGGAGGAGACGTTTCC 60.037 60.000 17.16 17.16 37.52 3.13
487 1180 2.099831 CGACGACGAGGTGCCTAC 59.900 66.667 0.00 0.00 42.66 3.18
489 1182 3.392595 GACGACGAGGTGCCTACGG 62.393 68.421 0.00 1.18 0.00 4.02
490 1183 3.437795 CGACGAGGTGCCTACGGT 61.438 66.667 12.22 3.01 0.00 4.83
491 1184 2.181021 GACGAGGTGCCTACGGTG 59.819 66.667 12.22 0.00 0.00 4.94
497 1190 1.445582 GGTGCCTACGGTGACTTCG 60.446 63.158 0.00 0.00 0.00 3.79
498 1191 1.288127 GTGCCTACGGTGACTTCGT 59.712 57.895 0.00 0.00 43.64 3.85
502 1195 2.231964 TGCCTACGGTGACTTCGTAAAT 59.768 45.455 0.00 0.00 41.62 1.40
504 1197 3.681417 GCCTACGGTGACTTCGTAAATTT 59.319 43.478 0.00 0.00 41.62 1.82
507 1200 5.406175 CCTACGGTGACTTCGTAAATTTCAA 59.594 40.000 0.00 0.00 41.62 2.69
513 1206 7.413000 CGGTGACTTCGTAAATTTCAAGATGAT 60.413 37.037 0.00 0.00 0.00 2.45
514 1207 8.879759 GGTGACTTCGTAAATTTCAAGATGATA 58.120 33.333 0.00 0.00 0.00 2.15
519 1212 9.573102 CTTCGTAAATTTCAAGATGATATGACG 57.427 33.333 0.00 0.00 33.53 4.35
520 1213 8.072238 TCGTAAATTTCAAGATGATATGACGG 57.928 34.615 0.00 0.00 33.32 4.79
521 1214 6.792250 CGTAAATTTCAAGATGATATGACGGC 59.208 38.462 0.00 0.00 31.19 5.68
522 1215 6.949352 AAATTTCAAGATGATATGACGGCT 57.051 33.333 0.00 0.00 0.00 5.52
523 1216 6.551385 AATTTCAAGATGATATGACGGCTC 57.449 37.500 0.00 0.00 0.00 4.70
524 1217 4.670896 TTCAAGATGATATGACGGCTCA 57.329 40.909 0.00 0.00 0.00 4.26
525 1218 4.248691 TCAAGATGATATGACGGCTCAG 57.751 45.455 0.00 0.00 0.00 3.35
526 1219 3.638627 TCAAGATGATATGACGGCTCAGT 59.361 43.478 0.00 0.00 0.00 3.41
527 1220 3.932545 AGATGATATGACGGCTCAGTC 57.067 47.619 0.00 1.58 41.30 3.51
528 1221 3.495331 AGATGATATGACGGCTCAGTCT 58.505 45.455 0.00 0.00 41.47 3.24
529 1222 3.894427 AGATGATATGACGGCTCAGTCTT 59.106 43.478 0.00 5.52 41.47 3.01
530 1223 4.343526 AGATGATATGACGGCTCAGTCTTT 59.656 41.667 0.00 1.16 41.47 2.52
531 1224 4.046938 TGATATGACGGCTCAGTCTTTC 57.953 45.455 0.00 4.58 41.47 2.62
532 1225 3.447229 TGATATGACGGCTCAGTCTTTCA 59.553 43.478 0.00 6.41 41.47 2.69
533 1226 2.376808 ATGACGGCTCAGTCTTTCAG 57.623 50.000 0.00 0.00 41.47 3.02
535 1228 1.270826 TGACGGCTCAGTCTTTCAGAG 59.729 52.381 0.00 0.00 41.47 3.35
536 1229 0.605589 ACGGCTCAGTCTTTCAGAGG 59.394 55.000 0.00 0.00 31.57 3.69
537 1230 0.605589 CGGCTCAGTCTTTCAGAGGT 59.394 55.000 0.00 0.00 31.57 3.85
538 1231 1.671261 CGGCTCAGTCTTTCAGAGGTG 60.671 57.143 0.00 0.00 31.57 4.00
539 1232 1.437625 GCTCAGTCTTTCAGAGGTGC 58.562 55.000 0.00 0.00 31.57 5.01
540 1233 1.001860 GCTCAGTCTTTCAGAGGTGCT 59.998 52.381 0.00 0.00 31.57 4.40
541 1234 2.930455 GCTCAGTCTTTCAGAGGTGCTC 60.930 54.545 0.00 0.00 31.57 4.26
543 1236 2.902486 TCAGTCTTTCAGAGGTGCTCAT 59.098 45.455 0.00 0.00 32.06 2.90
545 1238 4.159321 TCAGTCTTTCAGAGGTGCTCATAG 59.841 45.833 0.00 0.00 32.06 2.23
546 1239 3.450457 AGTCTTTCAGAGGTGCTCATAGG 59.550 47.826 0.00 0.00 32.06 2.57
548 1241 1.500474 TTCAGAGGTGCTCATAGGGG 58.500 55.000 0.00 0.00 32.06 4.79
549 1242 0.339859 TCAGAGGTGCTCATAGGGGT 59.660 55.000 0.00 0.00 32.06 4.95
551 1244 1.967066 CAGAGGTGCTCATAGGGGTAG 59.033 57.143 0.00 0.00 32.06 3.18
552 1245 1.133009 AGAGGTGCTCATAGGGGTAGG 60.133 57.143 0.00 0.00 32.06 3.18
553 1246 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
554 1247 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
555 1248 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
556 1249 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
557 1250 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
558 1251 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
559 1252 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
560 1253 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
561 1254 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
564 1257 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
565 1258 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
566 1259 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
569 1262 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
570 1263 2.099446 GTGTGCGTGTGTGCGTTT 59.901 55.556 0.00 0.00 37.81 3.60
572 1265 0.041663 GTGTGCGTGTGTGCGTTTAT 60.042 50.000 0.00 0.00 37.81 1.40
575 1268 2.096664 TGTGCGTGTGTGCGTTTATAAG 60.097 45.455 0.00 0.00 37.81 1.73
576 1269 1.461512 TGCGTGTGTGCGTTTATAAGG 59.538 47.619 0.00 0.00 37.81 2.69
578 1271 2.350498 GCGTGTGTGCGTTTATAAGGAT 59.650 45.455 0.00 0.00 0.00 3.24
579 1272 3.784199 GCGTGTGTGCGTTTATAAGGATG 60.784 47.826 0.00 0.00 0.00 3.51
581 1274 4.491924 CGTGTGTGCGTTTATAAGGATGAC 60.492 45.833 0.00 0.00 0.00 3.06
582 1275 4.630069 GTGTGTGCGTTTATAAGGATGACT 59.370 41.667 0.00 0.00 0.00 3.41
586 1279 6.479001 GTGTGCGTTTATAAGGATGACTGTAT 59.521 38.462 0.00 0.00 0.00 2.29
587 1280 6.478673 TGTGCGTTTATAAGGATGACTGTATG 59.521 38.462 0.00 0.00 0.00 2.39
588 1281 5.465390 TGCGTTTATAAGGATGACTGTATGC 59.535 40.000 0.00 0.00 0.00 3.14
590 1283 5.690409 CGTTTATAAGGATGACTGTATGCGT 59.310 40.000 0.00 0.00 0.00 5.24
591 1284 6.345803 CGTTTATAAGGATGACTGTATGCGTG 60.346 42.308 0.00 0.00 0.00 5.34
592 1285 4.672587 ATAAGGATGACTGTATGCGTGT 57.327 40.909 0.00 0.00 0.00 4.49
593 1286 2.299993 AGGATGACTGTATGCGTGTG 57.700 50.000 0.00 0.00 0.00 3.82
596 1289 3.384789 AGGATGACTGTATGCGTGTGTAT 59.615 43.478 0.00 0.00 0.00 2.29
598 1291 5.243954 AGGATGACTGTATGCGTGTGTATAT 59.756 40.000 0.00 0.00 0.00 0.86
601 1294 5.519722 TGACTGTATGCGTGTGTATATGAG 58.480 41.667 0.00 0.00 0.00 2.90
602 1295 4.299155 ACTGTATGCGTGTGTATATGAGC 58.701 43.478 0.00 0.00 0.00 4.26
603 1296 3.305110 TGTATGCGTGTGTATATGAGCG 58.695 45.455 0.00 0.00 0.00 5.03
604 1297 1.139989 ATGCGTGTGTATATGAGCGC 58.860 50.000 0.00 0.00 44.29 5.92
606 1299 1.209128 GCGTGTGTATATGAGCGCTT 58.791 50.000 13.26 0.00 41.37 4.68
607 1300 1.071239 GCGTGTGTATATGAGCGCTTG 60.071 52.381 13.26 0.00 41.37 4.01
608 1301 1.071239 CGTGTGTATATGAGCGCTTGC 60.071 52.381 13.26 0.00 39.58 4.01
609 1302 1.071239 GTGTGTATATGAGCGCTTGCG 60.071 52.381 13.26 10.90 45.69 4.85
611 1304 1.190323 GTGTATATGAGCGCTTGCGTC 59.810 52.381 13.26 12.36 45.69 5.19
612 1305 1.067060 TGTATATGAGCGCTTGCGTCT 59.933 47.619 13.26 13.17 45.69 4.18
613 1306 1.453524 GTATATGAGCGCTTGCGTCTG 59.546 52.381 13.26 0.00 45.69 3.51
614 1307 0.179100 ATATGAGCGCTTGCGTCTGT 60.179 50.000 13.26 7.66 45.69 3.41
616 1309 1.078759 ATGAGCGCTTGCGTCTGTAC 61.079 55.000 13.26 0.00 45.69 2.90
617 1310 1.444553 GAGCGCTTGCGTCTGTACT 60.445 57.895 13.26 3.73 45.69 2.73
619 1312 2.022129 GCGCTTGCGTCTGTACTGT 61.022 57.895 16.38 0.00 0.00 3.55
620 1313 1.775344 CGCTTGCGTCTGTACTGTG 59.225 57.895 6.86 0.00 0.00 3.66
621 1314 0.939577 CGCTTGCGTCTGTACTGTGT 60.940 55.000 6.86 0.00 0.00 3.72
622 1315 1.217882 GCTTGCGTCTGTACTGTGTT 58.782 50.000 0.00 0.00 0.00 3.32
623 1316 1.192534 GCTTGCGTCTGTACTGTGTTC 59.807 52.381 0.00 0.00 0.00 3.18
624 1317 2.469826 CTTGCGTCTGTACTGTGTTCA 58.530 47.619 0.00 0.00 0.00 3.18
625 1318 2.812358 TGCGTCTGTACTGTGTTCAT 57.188 45.000 0.00 0.00 0.00 2.57
626 1319 3.106242 TGCGTCTGTACTGTGTTCATT 57.894 42.857 0.00 0.00 0.00 2.57
627 1320 3.462982 TGCGTCTGTACTGTGTTCATTT 58.537 40.909 0.00 0.00 0.00 2.32
628 1321 3.874543 TGCGTCTGTACTGTGTTCATTTT 59.125 39.130 0.00 0.00 0.00 1.82
629 1322 4.334203 TGCGTCTGTACTGTGTTCATTTTT 59.666 37.500 0.00 0.00 0.00 1.94
872 1809 2.304761 ACCAGGCTCTAATTTCCGTGAA 59.695 45.455 0.00 0.00 0.00 3.18
895 1832 4.829064 TTGAAGACAATAGCACAACCAC 57.171 40.909 0.00 0.00 0.00 4.16
903 1840 5.275494 ACAATAGCACAACCACGTTAAAAC 58.725 37.500 0.00 0.00 0.00 2.43
969 1907 0.250770 GTGGTGTTGTTCTCCCCTCC 60.251 60.000 0.00 0.00 0.00 4.30
1053 1991 1.066430 CCAAGGAAGGAACCGATCGAA 60.066 52.381 18.66 0.00 34.73 3.71
1105 2043 3.508402 AGAAGAAGAGGAGAACTTCGTCC 59.492 47.826 15.57 2.90 46.11 4.79
1195 2133 0.623723 GGGGTTTAGTCCATCTGCCA 59.376 55.000 0.00 0.00 0.00 4.92
1212 2150 1.728971 GCCATGTACTCGCATATGAGC 59.271 52.381 6.97 0.00 39.68 4.26
1237 2175 1.676678 CTGGAATCCGGCGAAGGAGA 61.677 60.000 9.30 0.00 44.55 3.71
1270 2208 5.409826 CGCAGGATTGAAGATAACCTATTCC 59.590 44.000 0.00 0.00 0.00 3.01
1378 2316 5.048991 GCGGAATATGATGGGTTTACGAATT 60.049 40.000 0.00 0.00 0.00 2.17
1451 2389 9.120538 GAAGTTGCCTGATAATTACCTAATTCA 57.879 33.333 0.00 0.00 37.16 2.57
1501 2439 7.202176 GGAAGATGGGGAAGATCTTAGAGATTT 60.202 40.741 8.25 0.00 39.72 2.17
1516 2454 5.643421 AGAGATTTAGACTACCCTACCGA 57.357 43.478 0.00 0.00 0.00 4.69
1517 2455 6.203526 AGAGATTTAGACTACCCTACCGAT 57.796 41.667 0.00 0.00 0.00 4.18
1530 2468 4.095590 CCGATGGGTTTTGCAGGT 57.904 55.556 0.00 0.00 0.00 4.00
1664 2603 3.556213 CCGATTTTCTGTGGGTAGTGTGA 60.556 47.826 0.00 0.00 0.00 3.58
1825 2764 2.783135 GAGGTGATGCTGGAAGAAACA 58.217 47.619 0.00 0.00 34.07 2.83
1826 2765 3.350833 GAGGTGATGCTGGAAGAAACAT 58.649 45.455 0.00 0.00 34.07 2.71
2014 2965 3.936453 TGTAAATGTAGGAACGACCATGC 59.064 43.478 0.00 0.00 42.04 4.06
2066 3017 2.637947 CTCGACATCTGACTCTCTGGA 58.362 52.381 0.00 0.00 0.00 3.86
2225 3176 4.065321 ACACACCTCAGAAAAGTCTCAG 57.935 45.455 0.00 0.00 28.78 3.35
2261 3212 2.282391 TGTGGATGGTGGTGCAGC 60.282 61.111 9.47 9.47 0.00 5.25
2263 3214 1.299648 GTGGATGGTGGTGCAGCTA 59.700 57.895 18.08 4.01 32.61 3.32
2275 3226 4.081406 TGGTGCAGCTAACAATTCTGATT 58.919 39.130 18.08 0.00 0.00 2.57
2432 3383 2.571653 TCTCCCCGATGTGATGTTCTTT 59.428 45.455 0.00 0.00 0.00 2.52
2436 3387 3.000041 CCCGATGTGATGTTCTTTTCGA 59.000 45.455 0.00 0.00 0.00 3.71
2458 3409 4.634012 AGACTCACCTCGATAGCTATCT 57.366 45.455 27.00 9.42 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.500512 GGTACGCAAGCAACGGTTGA 61.501 55.000 24.20 0.00 42.72 3.18
63 64 1.082366 GGTACGCAAGCAACGGTTG 60.082 57.895 16.35 16.35 42.93 3.77
66 69 0.110373 GAAAGGTACGCAAGCAACGG 60.110 55.000 0.00 0.00 45.62 4.44
153 156 4.021925 AGAGGTGCGGGTCAAGCC 62.022 66.667 0.00 0.00 0.00 4.35
154 157 2.743928 CAGAGGTGCGGGTCAAGC 60.744 66.667 0.00 0.00 0.00 4.01
155 158 2.046892 CCAGAGGTGCGGGTCAAG 60.047 66.667 0.00 0.00 0.00 3.02
317 333 4.757149 ACGCAAATATATCTTCCCTTGCTC 59.243 41.667 13.09 0.00 37.58 4.26
377 393 1.199327 TCCACGTGCTCTTAGAAGTCG 59.801 52.381 10.91 0.00 0.00 4.18
410 427 1.890876 TGTTCCGTGGTCAATCCTTG 58.109 50.000 0.00 0.00 37.07 3.61
439 456 1.452651 CCTCCCACTGAATGCGCAT 60.453 57.895 19.28 19.28 0.00 4.73
440 457 2.046023 CCTCCCACTGAATGCGCA 60.046 61.111 14.96 14.96 0.00 6.09
442 459 0.460987 GTCTCCTCCCACTGAATGCG 60.461 60.000 0.00 0.00 0.00 4.73
443 460 0.460987 CGTCTCCTCCCACTGAATGC 60.461 60.000 0.00 0.00 0.00 3.56
444 461 0.898320 ACGTCTCCTCCCACTGAATG 59.102 55.000 0.00 0.00 0.00 2.67
445 462 1.645710 AACGTCTCCTCCCACTGAAT 58.354 50.000 0.00 0.00 0.00 2.57
446 463 1.343465 GAAACGTCTCCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
448 465 0.037232 GGAAACGTCTCCTCCCACTG 60.037 60.000 0.00 0.00 32.21 3.66
469 486 2.046988 TAGGCACCTCGTCGTCGA 60.047 61.111 4.42 4.42 44.12 4.20
470 487 2.099831 GTAGGCACCTCGTCGTCG 59.900 66.667 0.00 0.00 38.55 5.12
471 488 2.099831 CGTAGGCACCTCGTCGTC 59.900 66.667 0.00 0.00 0.00 4.20
472 489 3.437795 CCGTAGGCACCTCGTCGT 61.438 66.667 0.00 0.00 46.14 4.34
487 1180 5.585500 TCTTGAAATTTACGAAGTCACCG 57.415 39.130 0.00 0.00 43.93 4.94
497 1190 7.865707 AGCCGTCATATCATCTTGAAATTTAC 58.134 34.615 0.00 0.00 0.00 2.01
498 1191 7.714813 TGAGCCGTCATATCATCTTGAAATTTA 59.285 33.333 0.00 0.00 0.00 1.40
502 1195 5.022282 TGAGCCGTCATATCATCTTGAAA 57.978 39.130 0.00 0.00 0.00 2.69
504 1197 3.638627 ACTGAGCCGTCATATCATCTTGA 59.361 43.478 0.00 0.00 30.18 3.02
507 1200 3.495331 AGACTGAGCCGTCATATCATCT 58.505 45.455 1.91 0.00 36.38 2.90
513 1206 3.089284 TCTGAAAGACTGAGCCGTCATA 58.911 45.455 1.91 0.00 38.67 2.15
514 1207 1.895798 TCTGAAAGACTGAGCCGTCAT 59.104 47.619 1.91 0.00 38.67 3.06
515 1208 1.270826 CTCTGAAAGACTGAGCCGTCA 59.729 52.381 1.91 0.00 38.67 4.35
516 1209 1.403514 CCTCTGAAAGACTGAGCCGTC 60.404 57.143 0.00 0.00 38.67 4.79
517 1210 0.605589 CCTCTGAAAGACTGAGCCGT 59.394 55.000 0.00 0.00 38.67 5.68
518 1211 0.605589 ACCTCTGAAAGACTGAGCCG 59.394 55.000 0.00 0.00 38.67 5.52
519 1212 1.943507 GCACCTCTGAAAGACTGAGCC 60.944 57.143 0.00 0.00 38.67 4.70
520 1213 1.001860 AGCACCTCTGAAAGACTGAGC 59.998 52.381 0.00 0.00 38.67 4.26
521 1214 2.298446 TGAGCACCTCTGAAAGACTGAG 59.702 50.000 0.00 0.00 38.67 3.35
522 1215 2.319844 TGAGCACCTCTGAAAGACTGA 58.680 47.619 0.00 0.00 38.67 3.41
523 1216 2.827800 TGAGCACCTCTGAAAGACTG 57.172 50.000 0.00 0.00 38.67 3.51
524 1217 3.450457 CCTATGAGCACCTCTGAAAGACT 59.550 47.826 0.00 0.00 38.67 3.24
525 1218 3.431486 CCCTATGAGCACCTCTGAAAGAC 60.431 52.174 0.00 0.00 38.67 3.01
526 1219 2.768527 CCCTATGAGCACCTCTGAAAGA 59.231 50.000 0.00 0.00 43.69 2.52
527 1220 2.158842 CCCCTATGAGCACCTCTGAAAG 60.159 54.545 0.00 0.00 0.00 2.62
528 1221 1.839994 CCCCTATGAGCACCTCTGAAA 59.160 52.381 0.00 0.00 0.00 2.69
529 1222 1.273838 ACCCCTATGAGCACCTCTGAA 60.274 52.381 0.00 0.00 0.00 3.02
530 1223 0.339859 ACCCCTATGAGCACCTCTGA 59.660 55.000 0.00 0.00 0.00 3.27
531 1224 1.967066 CTACCCCTATGAGCACCTCTG 59.033 57.143 0.00 0.00 0.00 3.35
532 1225 1.133009 CCTACCCCTATGAGCACCTCT 60.133 57.143 0.00 0.00 0.00 3.69
533 1226 1.343069 CCTACCCCTATGAGCACCTC 58.657 60.000 0.00 0.00 0.00 3.85
535 1228 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
536 1229 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
537 1230 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
538 1231 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
539 1232 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
540 1233 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
541 1234 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
543 1236 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
545 1238 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
546 1239 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
548 1241 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
549 1242 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
552 1245 2.037913 TAAACGCACACACGCACACC 62.038 55.000 0.00 0.00 36.19 4.16
553 1246 0.041663 ATAAACGCACACACGCACAC 60.042 50.000 0.00 0.00 36.19 3.82
554 1247 1.499049 TATAAACGCACACACGCACA 58.501 45.000 0.00 0.00 36.19 4.57
555 1248 2.492001 CTTATAAACGCACACACGCAC 58.508 47.619 0.00 0.00 36.19 5.34
556 1249 1.461512 CCTTATAAACGCACACACGCA 59.538 47.619 0.00 0.00 36.19 5.24
557 1250 1.727880 TCCTTATAAACGCACACACGC 59.272 47.619 0.00 0.00 36.19 5.34
558 1251 3.615056 TCATCCTTATAAACGCACACACG 59.385 43.478 0.00 0.00 39.50 4.49
559 1252 4.630069 AGTCATCCTTATAAACGCACACAC 59.370 41.667 0.00 0.00 0.00 3.82
560 1253 4.629634 CAGTCATCCTTATAAACGCACACA 59.370 41.667 0.00 0.00 0.00 3.72
561 1254 4.630069 ACAGTCATCCTTATAAACGCACAC 59.370 41.667 0.00 0.00 0.00 3.82
564 1257 5.465390 GCATACAGTCATCCTTATAAACGCA 59.535 40.000 0.00 0.00 0.00 5.24
565 1258 5.388475 CGCATACAGTCATCCTTATAAACGC 60.388 44.000 0.00 0.00 0.00 4.84
566 1259 5.690409 ACGCATACAGTCATCCTTATAAACG 59.310 40.000 0.00 0.00 0.00 3.60
567 1260 6.479001 ACACGCATACAGTCATCCTTATAAAC 59.521 38.462 0.00 0.00 0.00 2.01
568 1261 6.478673 CACACGCATACAGTCATCCTTATAAA 59.521 38.462 0.00 0.00 0.00 1.40
569 1262 5.983118 CACACGCATACAGTCATCCTTATAA 59.017 40.000 0.00 0.00 0.00 0.98
570 1263 5.068591 ACACACGCATACAGTCATCCTTATA 59.931 40.000 0.00 0.00 0.00 0.98
572 1265 3.194755 ACACACGCATACAGTCATCCTTA 59.805 43.478 0.00 0.00 0.00 2.69
575 1268 2.010145 ACACACGCATACAGTCATCC 57.990 50.000 0.00 0.00 0.00 3.51
576 1269 6.149633 TCATATACACACGCATACAGTCATC 58.850 40.000 0.00 0.00 0.00 2.92
578 1271 5.508200 TCATATACACACGCATACAGTCA 57.492 39.130 0.00 0.00 0.00 3.41
579 1272 4.383052 GCTCATATACACACGCATACAGTC 59.617 45.833 0.00 0.00 0.00 3.51
581 1274 3.361940 CGCTCATATACACACGCATACAG 59.638 47.826 0.00 0.00 0.00 2.74
582 1275 3.305110 CGCTCATATACACACGCATACA 58.695 45.455 0.00 0.00 0.00 2.29
586 1279 2.588731 GCGCTCATATACACACGCA 58.411 52.632 0.00 0.00 45.25 5.24
587 1280 1.071239 CAAGCGCTCATATACACACGC 60.071 52.381 12.06 0.00 46.20 5.34
588 1281 1.071239 GCAAGCGCTCATATACACACG 60.071 52.381 12.06 0.00 34.30 4.49
590 1283 1.208259 CGCAAGCGCTCATATACACA 58.792 50.000 12.06 0.00 35.30 3.72
591 1284 1.190323 GACGCAAGCGCTCATATACAC 59.810 52.381 12.06 0.00 44.19 2.90
592 1285 1.067060 AGACGCAAGCGCTCATATACA 59.933 47.619 12.06 0.00 44.19 2.29
593 1286 1.453524 CAGACGCAAGCGCTCATATAC 59.546 52.381 12.06 1.00 44.19 1.47
596 1289 0.454196 TACAGACGCAAGCGCTCATA 59.546 50.000 12.06 5.16 44.19 2.15
598 1291 1.733041 GTACAGACGCAAGCGCTCA 60.733 57.895 12.06 0.83 44.19 4.26
601 1294 2.022129 ACAGTACAGACGCAAGCGC 61.022 57.895 15.09 0.00 44.19 5.92
602 1295 0.939577 ACACAGTACAGACGCAAGCG 60.940 55.000 13.50 13.50 46.03 4.68
603 1296 1.192534 GAACACAGTACAGACGCAAGC 59.807 52.381 0.00 0.00 45.62 4.01
606 1299 2.812358 ATGAACACAGTACAGACGCA 57.188 45.000 0.00 0.00 0.00 5.24
607 1300 4.468095 AAAATGAACACAGTACAGACGC 57.532 40.909 0.00 0.00 0.00 5.19
631 1324 6.012337 TGCATATACTCAGGGGATTGAAAA 57.988 37.500 0.00 0.00 0.00 2.29
632 1325 5.645056 TGCATATACTCAGGGGATTGAAA 57.355 39.130 0.00 0.00 0.00 2.69
634 1327 5.848286 ATTGCATATACTCAGGGGATTGA 57.152 39.130 0.00 0.00 0.00 2.57
643 1522 8.224025 TGGGGAATTCTTAATTGCATATACTCA 58.776 33.333 5.23 0.00 40.53 3.41
817 1754 1.043116 CCTCGTCCAGCCACTATCCA 61.043 60.000 0.00 0.00 0.00 3.41
832 1769 1.324736 GTTGCGCTATTGTCTTCCTCG 59.675 52.381 9.73 0.00 0.00 4.63
872 1809 5.562696 CGTGGTTGTGCTATTGTCTTCAAAT 60.563 40.000 0.00 0.00 37.11 2.32
943 1880 2.028385 GGAGAACAACACCACCGTATCT 60.028 50.000 0.00 0.00 0.00 1.98
969 1907 0.252197 CCGAGAAACCCTAACCCTGG 59.748 60.000 0.00 0.00 0.00 4.45
1053 1991 1.684386 CCAGGCGCTTCAGGAGATCT 61.684 60.000 7.64 0.00 0.00 2.75
1105 2043 0.691078 TCCTGGAATTCCTCCTCCCG 60.691 60.000 24.73 5.11 45.64 5.14
1195 2133 2.095008 CGGAGCTCATATGCGAGTACAT 60.095 50.000 17.19 0.00 38.13 2.29
1212 2150 4.918201 GCCGGATTCCAGGCGGAG 62.918 72.222 18.42 0.00 44.10 4.63
1378 2316 7.618502 TTTTGTTAAGCACTACAGAAGTTGA 57.381 32.000 0.00 0.00 35.76 3.18
1451 2389 2.696707 CACATCCCCTTAATTGCTGCAT 59.303 45.455 1.84 0.00 0.00 3.96
1501 2439 2.965671 CCCATCGGTAGGGTAGTCTA 57.034 55.000 0.00 0.00 41.61 2.59
1516 2454 3.136260 ACAAATTCACCTGCAAAACCCAT 59.864 39.130 0.00 0.00 0.00 4.00
1517 2455 2.503356 ACAAATTCACCTGCAAAACCCA 59.497 40.909 0.00 0.00 0.00 4.51
1530 2468 4.058124 CCACTCTGACTCGAACAAATTCA 58.942 43.478 0.00 0.00 34.14 2.57
1664 2603 3.122480 TGGTACCAATGTCCCATCAGAT 58.878 45.455 13.60 0.00 0.00 2.90
1825 2764 0.631212 CCCCTACCAAAGCCTTCCAT 59.369 55.000 0.00 0.00 0.00 3.41
1826 2765 2.083715 CCCCTACCAAAGCCTTCCA 58.916 57.895 0.00 0.00 0.00 3.53
1972 2923 2.443958 TGATCAGTCTCGGTCCTCAT 57.556 50.000 0.00 0.00 0.00 2.90
2014 2965 5.636965 CCAGCAGATTCATAGAATTAGACCG 59.363 44.000 0.00 0.00 0.00 4.79
2066 3017 2.038952 GAGCTTGGCCCCAATTTTTCTT 59.961 45.455 0.00 0.00 35.20 2.52
2127 3078 3.952811 GTCACCACTGACGCCTTC 58.047 61.111 0.00 0.00 37.67 3.46
2225 3176 4.991687 CCACAGTTCTCAGTTTCTTCCTAC 59.008 45.833 0.00 0.00 0.00 3.18
2275 3226 7.042992 CGCCGATATTTCATGAGTTTTAGTACA 60.043 37.037 0.00 0.00 0.00 2.90
2436 3387 4.759693 CAGATAGCTATCGAGGTGAGTCTT 59.240 45.833 24.53 3.36 37.76 3.01
2458 3409 1.927487 TCTACGTAAACCCTCAGCCA 58.073 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.