Multiple sequence alignment - TraesCS3B01G159800

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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 TraesCS3B01G159800 chr3B 100.000 2698 0 0 1 2698 154607244 154604547 0.000000e+00 4983.0
1 TraesCS3B01G159800 chr3D 92.283 2138 112 23 608 2697 104016296 104014164 0.000000e+00 2985.0
2 TraesCS3B01G159800 chr3D 85.177 452 51 10 1 443 104016832 104016388 1.470000e-122 449.0
3 TraesCS3B01G159800 chr3A 89.734 1841 125 37 687 2480 552306346 552308169 0.000000e+00 2294.0
4 TraesCS3B01G159800 chr3A 78.571 154 25 4 321 467 203957342 203957494 7.950000e-16 95.3
5 TraesCS3B01G159800 chr7D 84.249 273 37 6 2118 2387 468290792 468290523 7.410000e-66 261.0
6 TraesCS3B01G159800 chr7D 80.827 266 43 8 2120 2381 607724156 607724417 4.550000e-48 202.0
7 TraesCS3B01G159800 chr7D 81.944 144 19 6 333 471 616511364 616511223 6.100000e-22 115.0
8 TraesCS3B01G159800 chr5B 84.483 232 34 2 2118 2348 646483534 646483764 7.510000e-56 228.0
9 TraesCS3B01G159800 chr6B 84.016 244 27 8 2118 2351 65726064 65725823 9.720000e-55 224.0
10 TraesCS3B01G159800 chr1D 84.052 232 36 1 2118 2348 433402342 433402111 3.500000e-54 222.0
11 TraesCS3B01G159800 chr1D 84.286 140 17 5 322 458 345484753 345484616 6.060000e-27 132.0
12 TraesCS3B01G159800 chr1D 84.746 118 17 1 322 438 142153374 142153491 1.700000e-22 117.0
13 TraesCS3B01G159800 chr7A 82.258 248 41 3 2118 2362 269085298 269085545 7.570000e-51 211.0
14 TraesCS3B01G159800 chr7A 76.433 157 29 7 316 468 286118999 286119151 8.010000e-11 78.7
15 TraesCS3B01G159800 chr4D 80.292 274 49 5 2116 2385 502418020 502417748 4.550000e-48 202.0
16 TraesCS3B01G159800 chr1A 85.906 149 17 4 322 467 577888496 577888643 3.600000e-34 156.0
17 TraesCS3B01G159800 chr2D 86.316 95 12 1 348 441 461798227 461798133 4.750000e-18 102.0


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 TraesCS3B01G159800 chr3B 154604547 154607244 2697 True 4983 4983 100.000 1 2698 1 chr3B.!!$R1 2697
1 TraesCS3B01G159800 chr3D 104014164 104016832 2668 True 1717 2985 88.730 1 2697 2 chr3D.!!$R1 2696
2 TraesCS3B01G159800 chr3A 552306346 552308169 1823 False 2294 2294 89.734 687 2480 1 chr3A.!!$F2 1793

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
503 512 0.039437 GTGCCGTTTCAGTCTCTCGA 60.039 55.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2484 2563 0.543277 GATCCACAGAGACCCATGCA 59.457 55.0 0.0 0.0 0.0 3.96 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
69 72 3.625897 CACTGGCCACCTGACCGA 61.626 66.667 0.00 0.00 0.00 4.69
93 96 1.271597 ACAGAGGTGAGGCAAATCCAC 60.272 52.381 0.00 0.00 37.29 4.02
106 109 1.673808 AATCCACGGGCTAGTCGACC 61.674 60.000 13.01 0.00 37.50 4.79
107 110 2.569218 ATCCACGGGCTAGTCGACCT 62.569 60.000 13.01 2.17 39.40 3.85
108 111 2.490217 CACGGGCTAGTCGACCTG 59.510 66.667 13.01 4.33 39.40 4.00
110 113 2.439701 CGGGCTAGTCGACCTGGA 60.440 66.667 13.01 0.00 39.40 3.86
111 114 2.482333 CGGGCTAGTCGACCTGGAG 61.482 68.421 13.01 5.99 39.40 3.86
112 115 2.128507 GGGCTAGTCGACCTGGAGG 61.129 68.421 13.01 0.00 38.04 4.30
113 116 2.787567 GGCTAGTCGACCTGGAGGC 61.788 68.421 13.01 12.92 39.32 4.70
114 117 1.755008 GCTAGTCGACCTGGAGGCT 60.755 63.158 13.01 3.32 39.32 4.58
115 118 1.324005 GCTAGTCGACCTGGAGGCTT 61.324 60.000 13.01 0.00 39.32 4.35
160 168 1.804601 GTAGGGGGAAAAGTCACACG 58.195 55.000 0.00 0.00 34.82 4.49
162 170 0.841289 AGGGGGAAAAGTCACACGAA 59.159 50.000 0.00 0.00 34.82 3.85
165 173 1.871676 GGGGAAAAGTCACACGAAGTC 59.128 52.381 0.00 0.00 41.61 3.01
199 207 3.310774 CCTTCTCGACCTTACATTGCATG 59.689 47.826 0.00 0.00 0.00 4.06
208 216 6.348132 CGACCTTACATTGCATGAAACACTTA 60.348 38.462 0.00 0.00 0.00 2.24
220 228 9.612066 TGCATGAAACACTTACTATATGATTCA 57.388 29.630 0.00 0.00 0.00 2.57
234 242 8.296000 ACTATATGATTCAGTGATTCAGTCTCG 58.704 37.037 19.39 10.99 0.00 4.04
235 243 4.790765 TGATTCAGTGATTCAGTCTCGT 57.209 40.909 12.58 0.00 0.00 4.18
236 244 4.488879 TGATTCAGTGATTCAGTCTCGTG 58.511 43.478 12.58 0.00 0.00 4.35
237 245 4.021981 TGATTCAGTGATTCAGTCTCGTGT 60.022 41.667 12.58 0.00 0.00 4.49
253 261 6.642950 AGTCTCGTGTCATAAGTTTCTCTTTG 59.357 38.462 0.00 0.00 37.56 2.77
276 284 6.614160 TGACAAATAAGATGATGCACTGTTG 58.386 36.000 0.00 0.00 0.00 3.33
287 295 1.547820 TGCACTGTTGTGAAAAAGGCA 59.452 42.857 0.00 0.00 46.55 4.75
290 298 4.039004 TGCACTGTTGTGAAAAAGGCATAT 59.961 37.500 0.00 0.00 46.55 1.78
297 305 9.294030 CTGTTGTGAAAAAGGCATATAATCTTC 57.706 33.333 0.00 0.00 0.00 2.87
331 340 4.370364 ACAAGTTGTGTGAACCAACATC 57.630 40.909 7.96 0.00 43.61 3.06
334 343 3.884895 AGTTGTGTGAACCAACATCTGA 58.115 40.909 13.59 0.00 43.61 3.27
335 344 4.464008 AGTTGTGTGAACCAACATCTGAT 58.536 39.130 13.59 0.00 43.61 2.90
337 346 5.360714 AGTTGTGTGAACCAACATCTGATTT 59.639 36.000 13.59 0.00 43.61 2.17
346 355 6.764308 ACCAACATCTGATTTGATGGTTAG 57.236 37.500 7.22 0.15 44.91 2.34
347 356 5.653769 ACCAACATCTGATTTGATGGTTAGG 59.346 40.000 7.22 4.06 44.91 2.69
349 358 6.039047 CCAACATCTGATTTGATGGTTAGGAG 59.961 42.308 8.96 0.00 41.11 3.69
350 359 5.688807 ACATCTGATTTGATGGTTAGGAGG 58.311 41.667 8.96 0.00 45.78 4.30
352 361 5.359194 TCTGATTTGATGGTTAGGAGGAC 57.641 43.478 0.00 0.00 0.00 3.85
361 370 3.798515 TGGTTAGGAGGACAGTGGTATT 58.201 45.455 0.00 0.00 0.00 1.89
362 371 3.773119 TGGTTAGGAGGACAGTGGTATTC 59.227 47.826 0.00 0.00 0.00 1.75
366 375 4.883021 AGGAGGACAGTGGTATTCTCTA 57.117 45.455 0.00 0.00 0.00 2.43
367 376 5.411103 AGGAGGACAGTGGTATTCTCTAT 57.589 43.478 0.00 0.00 0.00 1.98
368 377 5.782925 AGGAGGACAGTGGTATTCTCTATT 58.217 41.667 0.00 0.00 0.00 1.73
376 385 6.097554 ACAGTGGTATTCTCTATTCACCAGAG 59.902 42.308 0.00 0.00 39.85 3.35
379 388 7.181125 AGTGGTATTCTCTATTCACCAGAGTTT 59.819 37.037 0.00 0.00 39.85 2.66
385 394 7.171630 TCTCTATTCACCAGAGTTTAAGTCC 57.828 40.000 0.00 0.00 40.41 3.85
400 409 2.867109 AGTCCCAGACTTGACATTGG 57.133 50.000 5.04 0.00 40.28 3.16
403 412 1.774254 TCCCAGACTTGACATTGGTGT 59.226 47.619 0.00 0.00 42.49 4.16
405 414 2.554032 CCCAGACTTGACATTGGTGTTC 59.446 50.000 0.00 0.00 39.09 3.18
407 416 1.873591 AGACTTGACATTGGTGTTCGC 59.126 47.619 0.00 0.00 39.09 4.70
413 422 4.052159 TGACATTGGTGTTCGCATTTTT 57.948 36.364 0.00 0.00 39.09 1.94
414 423 4.047822 TGACATTGGTGTTCGCATTTTTC 58.952 39.130 0.00 0.00 39.09 2.29
415 424 4.202101 TGACATTGGTGTTCGCATTTTTCT 60.202 37.500 0.00 0.00 39.09 2.52
424 433 7.655328 TGGTGTTCGCATTTTTCTGATTTATTT 59.345 29.630 0.00 0.00 0.00 1.40
425 434 7.951565 GGTGTTCGCATTTTTCTGATTTATTTG 59.048 33.333 0.00 0.00 0.00 2.32
434 443 6.530019 TTTCTGATTTATTTGAGGCCTTCC 57.470 37.500 6.77 0.00 0.00 3.46
448 457 2.349297 CCTTCCGGCGATATACACTC 57.651 55.000 9.30 0.00 0.00 3.51
453 462 1.335964 CCGGCGATATACACTCAGTGG 60.336 57.143 9.30 0.00 37.94 4.00
454 463 1.335964 CGGCGATATACACTCAGTGGG 60.336 57.143 10.28 0.00 37.94 4.61
455 464 1.961394 GGCGATATACACTCAGTGGGA 59.039 52.381 10.28 0.00 37.94 4.37
466 475 3.258971 CTCAGTGGGAGGAGATGTTTC 57.741 52.381 0.00 0.00 40.13 2.78
467 476 1.909302 TCAGTGGGAGGAGATGTTTCC 59.091 52.381 0.00 0.00 37.52 3.13
468 477 1.630369 CAGTGGGAGGAGATGTTTCCA 59.370 52.381 0.00 0.00 39.84 3.53
469 478 2.240667 CAGTGGGAGGAGATGTTTCCAT 59.759 50.000 0.00 0.00 39.84 3.41
493 502 5.741388 ATCTTAAGATGATGTGCCGTTTC 57.259 39.130 17.26 0.00 32.68 2.78
494 503 4.574892 TCTTAAGATGATGTGCCGTTTCA 58.425 39.130 0.00 0.00 0.00 2.69
496 505 2.479566 AGATGATGTGCCGTTTCAGT 57.520 45.000 0.00 0.00 0.00 3.41
497 506 2.350522 AGATGATGTGCCGTTTCAGTC 58.649 47.619 0.00 0.00 0.00 3.51
499 508 1.795768 TGATGTGCCGTTTCAGTCTC 58.204 50.000 0.00 0.00 0.00 3.36
500 509 1.344438 TGATGTGCCGTTTCAGTCTCT 59.656 47.619 0.00 0.00 0.00 3.10
501 510 1.996191 GATGTGCCGTTTCAGTCTCTC 59.004 52.381 0.00 0.00 0.00 3.20
502 511 0.318699 TGTGCCGTTTCAGTCTCTCG 60.319 55.000 0.00 0.00 0.00 4.04
503 512 0.039437 GTGCCGTTTCAGTCTCTCGA 60.039 55.000 0.00 0.00 0.00 4.04
504 513 0.671796 TGCCGTTTCAGTCTCTCGAA 59.328 50.000 0.00 0.00 0.00 3.71
505 514 1.067974 TGCCGTTTCAGTCTCTCGAAA 59.932 47.619 0.00 0.00 0.00 3.46
506 515 2.132762 GCCGTTTCAGTCTCTCGAAAA 58.867 47.619 0.00 0.00 33.17 2.29
507 516 2.737252 GCCGTTTCAGTCTCTCGAAAAT 59.263 45.455 0.00 0.00 33.17 1.82
508 517 3.423645 GCCGTTTCAGTCTCTCGAAAATG 60.424 47.826 0.00 0.00 33.17 2.32
509 518 3.423645 CCGTTTCAGTCTCTCGAAAATGC 60.424 47.826 0.00 0.00 33.17 3.56
510 519 3.430218 CGTTTCAGTCTCTCGAAAATGCT 59.570 43.478 0.00 0.00 33.17 3.79
511 520 4.084328 CGTTTCAGTCTCTCGAAAATGCTT 60.084 41.667 0.00 0.00 33.17 3.91
512 521 5.118664 CGTTTCAGTCTCTCGAAAATGCTTA 59.881 40.000 0.00 0.00 33.17 3.09
513 522 6.183360 CGTTTCAGTCTCTCGAAAATGCTTAT 60.183 38.462 0.00 0.00 33.17 1.73
514 523 7.009265 CGTTTCAGTCTCTCGAAAATGCTTATA 59.991 37.037 0.00 0.00 33.17 0.98
515 524 7.993821 TTCAGTCTCTCGAAAATGCTTATAG 57.006 36.000 0.00 0.00 0.00 1.31
516 525 6.507900 TCAGTCTCTCGAAAATGCTTATAGG 58.492 40.000 0.00 0.00 0.00 2.57
517 526 5.694006 CAGTCTCTCGAAAATGCTTATAGGG 59.306 44.000 0.00 0.00 0.00 3.53
518 527 5.364157 AGTCTCTCGAAAATGCTTATAGGGT 59.636 40.000 0.00 0.00 0.00 4.34
519 528 5.463724 GTCTCTCGAAAATGCTTATAGGGTG 59.536 44.000 0.00 0.00 0.00 4.61
520 529 5.128827 TCTCTCGAAAATGCTTATAGGGTGT 59.871 40.000 0.00 0.00 0.00 4.16
521 530 5.116180 TCTCGAAAATGCTTATAGGGTGTG 58.884 41.667 0.00 0.00 0.00 3.82
522 531 3.625764 TCGAAAATGCTTATAGGGTGTGC 59.374 43.478 0.00 0.00 0.00 4.57
523 532 3.546020 CGAAAATGCTTATAGGGTGTGCG 60.546 47.826 0.00 0.00 0.00 5.34
524 533 2.710096 AATGCTTATAGGGTGTGCGT 57.290 45.000 0.00 0.00 0.00 5.24
525 534 1.953559 ATGCTTATAGGGTGTGCGTG 58.046 50.000 0.00 0.00 0.00 5.34
526 535 0.107897 TGCTTATAGGGTGTGCGTGG 60.108 55.000 0.00 0.00 0.00 4.94
527 536 0.814010 GCTTATAGGGTGTGCGTGGG 60.814 60.000 0.00 0.00 0.00 4.61
528 537 0.539986 CTTATAGGGTGTGCGTGGGT 59.460 55.000 0.00 0.00 0.00 4.51
529 538 0.250793 TTATAGGGTGTGCGTGGGTG 59.749 55.000 0.00 0.00 0.00 4.61
530 539 2.246761 TATAGGGTGTGCGTGGGTGC 62.247 60.000 0.00 0.00 0.00 5.01
534 543 3.660111 GTGTGCGTGGGTGCCTTC 61.660 66.667 0.00 0.00 0.00 3.46
535 544 4.182433 TGTGCGTGGGTGCCTTCA 62.182 61.111 0.00 0.00 0.00 3.02
536 545 2.672996 GTGCGTGGGTGCCTTCAT 60.673 61.111 0.00 0.00 0.00 2.57
537 546 1.376683 GTGCGTGGGTGCCTTCATA 60.377 57.895 0.00 0.00 0.00 2.15
538 547 1.078497 TGCGTGGGTGCCTTCATAG 60.078 57.895 0.00 0.00 0.00 2.23
539 548 1.819632 GCGTGGGTGCCTTCATAGG 60.820 63.158 0.00 0.00 45.02 2.57
540 549 1.153168 CGTGGGTGCCTTCATAGGG 60.153 63.158 0.00 0.00 42.25 3.53
541 550 1.227383 GTGGGTGCCTTCATAGGGG 59.773 63.158 0.00 0.00 42.25 4.79
550 559 1.971357 CCTTCATAGGGGCGAGTGTAT 59.029 52.381 0.00 0.00 37.94 2.29
555 564 1.399714 TAGGGGCGAGTGTATGTGAG 58.600 55.000 0.00 0.00 0.00 3.51
556 565 0.614979 AGGGGCGAGTGTATGTGAGT 60.615 55.000 0.00 0.00 0.00 3.41
557 566 0.249398 GGGGCGAGTGTATGTGAGTT 59.751 55.000 0.00 0.00 0.00 3.01
562 571 4.243270 GGCGAGTGTATGTGAGTTACTTT 58.757 43.478 0.00 0.00 0.00 2.66
567 576 7.448228 CGAGTGTATGTGAGTTACTTTGATTG 58.552 38.462 0.00 0.00 0.00 2.67
571 580 8.440833 GTGTATGTGAGTTACTTTGATTGTACC 58.559 37.037 0.00 0.00 0.00 3.34
576 585 7.500892 TGTGAGTTACTTTGATTGTACCATGTT 59.499 33.333 0.00 0.00 0.00 2.71
588 597 8.138712 TGATTGTACCATGTTAAAGAAAACACC 58.861 33.333 0.00 0.00 41.89 4.16
589 598 7.406031 TTGTACCATGTTAAAGAAAACACCA 57.594 32.000 0.00 0.00 41.89 4.17
590 599 6.797454 TGTACCATGTTAAAGAAAACACCAC 58.203 36.000 0.00 0.00 41.89 4.16
591 600 5.923733 ACCATGTTAAAGAAAACACCACA 57.076 34.783 0.00 0.00 41.89 4.17
592 601 6.287589 ACCATGTTAAAGAAAACACCACAA 57.712 33.333 0.00 0.00 41.89 3.33
593 602 6.337356 ACCATGTTAAAGAAAACACCACAAG 58.663 36.000 0.00 0.00 41.89 3.16
594 603 6.071051 ACCATGTTAAAGAAAACACCACAAGT 60.071 34.615 0.00 0.00 41.89 3.16
595 604 6.816140 CCATGTTAAAGAAAACACCACAAGTT 59.184 34.615 0.00 0.00 41.89 2.66
596 605 7.333174 CCATGTTAAAGAAAACACCACAAGTTT 59.667 33.333 0.00 0.00 41.89 2.66
598 607 8.664211 TGTTAAAGAAAACACCACAAGTTTTT 57.336 26.923 5.63 0.00 46.01 1.94
678 687 7.093112 CCACCACCTATTAAATTTGAATTCCCA 60.093 37.037 2.27 0.00 0.00 4.37
709 718 9.791801 AAAACCTATTTAATTTGAACATGGCTT 57.208 25.926 0.00 0.00 0.00 4.35
905 914 2.771943 ACTACCAATCATCACCGGTCAT 59.228 45.455 2.59 0.00 32.81 3.06
916 925 1.678627 CACCGGTCATTCTCTCGATCT 59.321 52.381 2.59 0.00 0.00 2.75
993 1030 1.267121 GGGACTACTTGAGGTGCAGA 58.733 55.000 0.00 0.00 0.00 4.26
995 1032 2.038557 GGGACTACTTGAGGTGCAGAAA 59.961 50.000 0.00 0.00 0.00 2.52
1027 1064 4.492570 CGACTATCCAAAGCAAATCGACAC 60.493 45.833 0.00 0.00 0.00 3.67
1095 1132 5.048083 TGCACATCAAATTCTCTACCCAAAC 60.048 40.000 0.00 0.00 0.00 2.93
1096 1133 5.048083 GCACATCAAATTCTCTACCCAAACA 60.048 40.000 0.00 0.00 0.00 2.83
1107 1145 8.506168 TTCTCTACCCAAACAAAGCATATTAG 57.494 34.615 0.00 0.00 0.00 1.73
1116 1154 8.647226 CCAAACAAAGCATATTAGTTAAGCAAC 58.353 33.333 0.00 0.00 34.67 4.17
1132 1189 7.863375 AGTTAAGCAACTATATGTCGACTCATC 59.137 37.037 17.92 0.00 43.33 2.92
1133 1190 6.398234 AAGCAACTATATGTCGACTCATCT 57.602 37.500 17.92 0.00 0.00 2.90
1134 1191 6.007936 AGCAACTATATGTCGACTCATCTC 57.992 41.667 17.92 0.00 0.00 2.75
1135 1192 5.767665 AGCAACTATATGTCGACTCATCTCT 59.232 40.000 17.92 0.54 0.00 3.10
1136 1193 6.072728 AGCAACTATATGTCGACTCATCTCTC 60.073 42.308 17.92 0.00 0.00 3.20
1137 1194 6.293680 GCAACTATATGTCGACTCATCTCTCA 60.294 42.308 17.92 0.00 0.00 3.27
1138 1195 7.574779 GCAACTATATGTCGACTCATCTCTCAT 60.575 40.741 17.92 0.76 0.00 2.90
1139 1196 8.940952 CAACTATATGTCGACTCATCTCTCATA 58.059 37.037 17.92 3.16 0.00 2.15
1140 1197 8.716646 ACTATATGTCGACTCATCTCTCATAG 57.283 38.462 17.92 8.66 0.00 2.23
1221 1281 1.941209 GCAACATGGAGAAGCTCGTCA 60.941 52.381 0.00 0.00 0.00 4.35
1225 1285 1.107114 ATGGAGAAGCTCGTCATCGT 58.893 50.000 0.00 0.00 38.33 3.73
1235 1295 0.526211 TCGTCATCGTAAGCAGCAGT 59.474 50.000 0.00 0.00 38.33 4.40
1460 1520 4.742201 CTGGTGTCCCACGAGGCG 62.742 72.222 0.00 0.00 36.73 5.52
1562 1622 1.154073 CGACCGGAGAAAGACGACC 60.154 63.158 9.46 0.00 0.00 4.79
1930 1999 9.793252 GTTTCATAGACTTTCATGCATACAAAT 57.207 29.630 0.00 0.00 0.00 2.32
2096 2166 8.447924 AATGGACATTCATAAACTGATCTCTG 57.552 34.615 0.00 0.00 32.72 3.35
2142 2219 1.626825 CCTCCGGTCCTTTTTACTCCA 59.373 52.381 0.00 0.00 0.00 3.86
2351 2430 7.766219 TGACTTTAGACAAATCTTATACGCC 57.234 36.000 0.00 0.00 36.29 5.68
2352 2431 7.324935 TGACTTTAGACAAATCTTATACGCCA 58.675 34.615 0.00 0.00 36.29 5.69
2427 2506 6.374053 CCATCACATACAACACATCTTTGGTA 59.626 38.462 0.00 0.00 0.00 3.25
2458 2537 1.093496 CCCCCGAGATACAAAACCGC 61.093 60.000 0.00 0.00 0.00 5.68
2481 2560 7.123830 CGCCTTAAATTGTTAATAGAGAACCG 58.876 38.462 0.00 0.00 0.00 4.44
2484 2563 8.621286 CCTTAAATTGTTAATAGAGAACCGCAT 58.379 33.333 0.00 0.00 0.00 4.73
2485 2564 9.438291 CTTAAATTGTTAATAGAGAACCGCATG 57.562 33.333 0.00 0.00 0.00 4.06
2496 2575 2.191375 CCGCATGCATGGGTCTCT 59.809 61.111 33.67 0.00 38.88 3.10
2510 2589 3.012518 GGGTCTCTGTGGATCAATTGTG 58.987 50.000 5.13 0.00 0.00 3.33
2550 2629 6.793492 TTGTGGTGCTTTTTATTTATTGGC 57.207 33.333 0.00 0.00 0.00 4.52
2569 2648 4.211125 TGGCAGACTTTTTATGTGAACCA 58.789 39.130 0.00 0.00 0.00 3.67
2591 2670 9.875708 AACCATCTAAGATAGATAACTCTCAGT 57.124 33.333 0.00 0.00 43.41 3.41
2607 2686 3.503363 TCTCAGTGGCAAGCTACAAATTG 59.497 43.478 11.14 0.78 0.00 2.32
2677 2758 3.555956 GTGATACCAACACATCTTAGGCG 59.444 47.826 0.00 0.00 38.05 5.52
2680 2761 1.623811 ACCAACACATCTTAGGCGAGT 59.376 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 3.532155 GACCTCGATGCCTCGGCT 61.532 66.667 11.57 0.00 45.10 5.52
69 72 1.131638 TTTGCCTCACCTCTGTCTGT 58.868 50.000 0.00 0.00 0.00 3.41
93 96 2.439701 TCCAGGTCGACTAGCCCG 60.440 66.667 16.46 0.00 0.00 6.13
112 115 1.308783 GCACCTAGGGCACTTGAAGC 61.309 60.000 14.81 0.00 0.00 3.86
113 116 0.678048 GGCACCTAGGGCACTTGAAG 60.678 60.000 14.81 0.00 0.00 3.02
114 117 1.378762 GGCACCTAGGGCACTTGAA 59.621 57.895 14.81 0.00 0.00 2.69
115 118 1.845664 TGGCACCTAGGGCACTTGA 60.846 57.895 14.81 0.00 38.55 3.02
137 145 0.688487 TGACTTTTCCCCCTACGTGG 59.312 55.000 0.00 0.00 0.00 4.94
160 168 2.797177 AGGATGCAAAGGGAGACTTC 57.203 50.000 0.00 0.00 38.85 3.01
162 170 2.238395 GAGAAGGATGCAAAGGGAGACT 59.762 50.000 0.00 0.00 0.00 3.24
165 173 1.208052 TCGAGAAGGATGCAAAGGGAG 59.792 52.381 0.00 0.00 0.00 4.30
208 216 8.296000 CGAGACTGAATCACTGAATCATATAGT 58.704 37.037 0.00 0.00 0.00 2.12
218 226 2.884639 TGACACGAGACTGAATCACTGA 59.115 45.455 0.00 0.00 0.00 3.41
219 227 3.288809 TGACACGAGACTGAATCACTG 57.711 47.619 0.00 0.00 0.00 3.66
220 228 5.184096 ACTTATGACACGAGACTGAATCACT 59.816 40.000 0.00 0.00 0.00 3.41
221 229 5.403246 ACTTATGACACGAGACTGAATCAC 58.597 41.667 0.00 0.00 0.00 3.06
222 230 5.644977 ACTTATGACACGAGACTGAATCA 57.355 39.130 0.00 0.00 0.00 2.57
223 231 6.809196 AGAAACTTATGACACGAGACTGAATC 59.191 38.462 0.00 0.00 0.00 2.52
226 234 5.473846 AGAGAAACTTATGACACGAGACTGA 59.526 40.000 0.00 0.00 0.00 3.41
227 235 5.704888 AGAGAAACTTATGACACGAGACTG 58.295 41.667 0.00 0.00 0.00 3.51
228 236 5.968528 AGAGAAACTTATGACACGAGACT 57.031 39.130 0.00 0.00 0.00 3.24
229 237 6.641314 TCAAAGAGAAACTTATGACACGAGAC 59.359 38.462 0.00 0.00 37.93 3.36
230 238 6.641314 GTCAAAGAGAAACTTATGACACGAGA 59.359 38.462 1.15 0.00 41.07 4.04
231 239 6.420903 TGTCAAAGAGAAACTTATGACACGAG 59.579 38.462 15.77 0.00 43.13 4.18
232 240 6.277605 TGTCAAAGAGAAACTTATGACACGA 58.722 36.000 15.77 3.66 43.13 4.35
233 241 6.525121 TGTCAAAGAGAAACTTATGACACG 57.475 37.500 15.77 0.00 43.13 4.49
253 261 6.525628 CACAACAGTGCATCATCTTATTTGTC 59.474 38.462 0.00 0.00 0.00 3.18
267 275 1.547820 TGCCTTTTTCACAACAGTGCA 59.452 42.857 0.00 0.00 33.28 4.57
276 284 8.470002 ACCAAGAAGATTATATGCCTTTTTCAC 58.530 33.333 0.00 0.00 0.00 3.18
318 326 5.047872 CCATCAAATCAGATGTTGGTTCACA 60.048 40.000 0.00 0.00 43.00 3.58
319 327 5.047802 ACCATCAAATCAGATGTTGGTTCAC 60.048 40.000 3.96 0.00 44.52 3.18
320 328 5.078949 ACCATCAAATCAGATGTTGGTTCA 58.921 37.500 3.96 0.00 44.52 3.18
328 337 5.762218 GTCCTCCTAACCATCAAATCAGATG 59.238 44.000 0.00 0.00 43.90 2.90
329 338 5.429762 TGTCCTCCTAACCATCAAATCAGAT 59.570 40.000 0.00 0.00 0.00 2.90
331 340 5.102953 TGTCCTCCTAACCATCAAATCAG 57.897 43.478 0.00 0.00 0.00 2.90
334 343 4.324563 CCACTGTCCTCCTAACCATCAAAT 60.325 45.833 0.00 0.00 0.00 2.32
335 344 3.009033 CCACTGTCCTCCTAACCATCAAA 59.991 47.826 0.00 0.00 0.00 2.69
337 346 2.187958 CCACTGTCCTCCTAACCATCA 58.812 52.381 0.00 0.00 0.00 3.07
346 355 5.598830 TGAATAGAGAATACCACTGTCCTCC 59.401 44.000 0.00 0.00 0.00 4.30
347 356 6.461788 GGTGAATAGAGAATACCACTGTCCTC 60.462 46.154 0.00 0.00 0.00 3.71
349 358 5.128827 TGGTGAATAGAGAATACCACTGTCC 59.871 44.000 0.00 0.00 36.56 4.02
350 359 6.096987 TCTGGTGAATAGAGAATACCACTGTC 59.903 42.308 0.00 0.00 36.56 3.51
352 361 6.097554 ACTCTGGTGAATAGAGAATACCACTG 59.902 42.308 8.84 0.00 43.41 3.66
361 370 6.154706 GGGACTTAAACTCTGGTGAATAGAGA 59.845 42.308 8.84 0.00 43.41 3.10
362 371 6.070767 TGGGACTTAAACTCTGGTGAATAGAG 60.071 42.308 0.00 0.00 45.59 2.43
366 375 4.597507 TCTGGGACTTAAACTCTGGTGAAT 59.402 41.667 0.00 0.00 0.00 2.57
367 376 3.971305 TCTGGGACTTAAACTCTGGTGAA 59.029 43.478 0.00 0.00 0.00 3.18
368 377 3.323979 GTCTGGGACTTAAACTCTGGTGA 59.676 47.826 0.00 0.00 0.00 4.02
379 388 8.330617 AACACCAATGTCAAGTCTGGGACTTA 62.331 42.308 11.80 0.00 43.76 2.24
385 394 2.224079 CGAACACCAATGTCAAGTCTGG 59.776 50.000 0.00 0.00 38.45 3.86
400 409 8.698854 TCAAATAAATCAGAAAAATGCGAACAC 58.301 29.630 0.00 0.00 0.00 3.32
403 412 7.063308 GCCTCAAATAAATCAGAAAAATGCGAA 59.937 33.333 0.00 0.00 0.00 4.70
405 414 6.237915 GGCCTCAAATAAATCAGAAAAATGCG 60.238 38.462 0.00 0.00 0.00 4.73
407 416 8.782339 AAGGCCTCAAATAAATCAGAAAAATG 57.218 30.769 5.23 0.00 0.00 2.32
413 422 4.199310 CGGAAGGCCTCAAATAAATCAGA 58.801 43.478 5.23 0.00 0.00 3.27
414 423 4.558538 CGGAAGGCCTCAAATAAATCAG 57.441 45.455 5.23 0.00 0.00 2.90
434 443 1.335964 CCCACTGAGTGTATATCGCCG 60.336 57.143 12.15 0.00 0.00 6.46
438 447 4.730966 TCTCCTCCCACTGAGTGTATATC 58.269 47.826 12.15 0.00 39.65 1.63
443 452 1.203237 ACATCTCCTCCCACTGAGTGT 60.203 52.381 12.15 0.00 39.65 3.55
445 454 2.334006 AACATCTCCTCCCACTGAGT 57.666 50.000 0.00 0.00 39.65 3.41
446 455 2.093235 GGAAACATCTCCTCCCACTGAG 60.093 54.545 0.00 0.00 41.07 3.35
448 457 1.630369 TGGAAACATCTCCTCCCACTG 59.370 52.381 0.00 0.00 36.35 3.66
471 480 5.185454 TGAAACGGCACATCATCTTAAGAT 58.815 37.500 12.37 12.37 34.56 2.40
472 481 4.574892 TGAAACGGCACATCATCTTAAGA 58.425 39.130 7.82 7.82 0.00 2.10
475 484 3.932710 GACTGAAACGGCACATCATCTTA 59.067 43.478 0.00 0.00 0.00 2.10
476 485 2.744202 GACTGAAACGGCACATCATCTT 59.256 45.455 0.00 0.00 0.00 2.40
477 486 2.027745 AGACTGAAACGGCACATCATCT 60.028 45.455 0.00 0.00 0.00 2.90
478 487 2.349886 GAGACTGAAACGGCACATCATC 59.650 50.000 0.00 0.00 0.00 2.92
479 488 2.027745 AGAGACTGAAACGGCACATCAT 60.028 45.455 0.00 0.00 0.00 2.45
480 489 1.344438 AGAGACTGAAACGGCACATCA 59.656 47.619 0.00 0.00 0.00 3.07
481 490 1.996191 GAGAGACTGAAACGGCACATC 59.004 52.381 0.00 0.00 0.00 3.06
482 491 1.670087 CGAGAGACTGAAACGGCACAT 60.670 52.381 0.00 0.00 0.00 3.21
483 492 0.318699 CGAGAGACTGAAACGGCACA 60.319 55.000 0.00 0.00 0.00 4.57
485 494 0.671796 TTCGAGAGACTGAAACGGCA 59.328 50.000 0.00 0.00 41.84 5.69
486 495 1.779569 TTTCGAGAGACTGAAACGGC 58.220 50.000 0.00 0.00 41.84 5.68
487 496 3.423645 GCATTTTCGAGAGACTGAAACGG 60.424 47.826 0.00 0.00 41.84 4.44
488 497 3.430218 AGCATTTTCGAGAGACTGAAACG 59.570 43.478 0.00 0.00 41.84 3.60
491 500 6.980978 CCTATAAGCATTTTCGAGAGACTGAA 59.019 38.462 0.00 0.00 41.84 3.02
493 502 5.694006 CCCTATAAGCATTTTCGAGAGACTG 59.306 44.000 0.00 0.00 41.84 3.51
494 503 5.364157 ACCCTATAAGCATTTTCGAGAGACT 59.636 40.000 0.00 0.00 41.84 3.24
496 505 5.128827 ACACCCTATAAGCATTTTCGAGAGA 59.871 40.000 0.00 0.00 39.20 3.10
497 506 5.235186 CACACCCTATAAGCATTTTCGAGAG 59.765 44.000 0.00 0.00 0.00 3.20
499 508 4.260784 GCACACCCTATAAGCATTTTCGAG 60.261 45.833 0.00 0.00 0.00 4.04
500 509 3.625764 GCACACCCTATAAGCATTTTCGA 59.374 43.478 0.00 0.00 0.00 3.71
501 510 3.546020 CGCACACCCTATAAGCATTTTCG 60.546 47.826 0.00 0.00 0.00 3.46
502 511 3.377172 ACGCACACCCTATAAGCATTTTC 59.623 43.478 0.00 0.00 0.00 2.29
503 512 3.128589 CACGCACACCCTATAAGCATTTT 59.871 43.478 0.00 0.00 0.00 1.82
504 513 2.682856 CACGCACACCCTATAAGCATTT 59.317 45.455 0.00 0.00 0.00 2.32
505 514 2.288666 CACGCACACCCTATAAGCATT 58.711 47.619 0.00 0.00 0.00 3.56
506 515 1.475034 CCACGCACACCCTATAAGCAT 60.475 52.381 0.00 0.00 0.00 3.79
507 516 0.107897 CCACGCACACCCTATAAGCA 60.108 55.000 0.00 0.00 0.00 3.91
508 517 0.814010 CCCACGCACACCCTATAAGC 60.814 60.000 0.00 0.00 0.00 3.09
509 518 0.539986 ACCCACGCACACCCTATAAG 59.460 55.000 0.00 0.00 0.00 1.73
510 519 0.250793 CACCCACGCACACCCTATAA 59.749 55.000 0.00 0.00 0.00 0.98
511 520 1.901820 CACCCACGCACACCCTATA 59.098 57.895 0.00 0.00 0.00 1.31
512 521 2.668632 CACCCACGCACACCCTAT 59.331 61.111 0.00 0.00 0.00 2.57
513 522 4.323477 GCACCCACGCACACCCTA 62.323 66.667 0.00 0.00 0.00 3.53
517 526 3.660111 GAAGGCACCCACGCACAC 61.660 66.667 0.00 0.00 0.00 3.82
518 527 2.118233 TATGAAGGCACCCACGCACA 62.118 55.000 0.00 0.00 0.00 4.57
519 528 1.369091 CTATGAAGGCACCCACGCAC 61.369 60.000 0.00 0.00 0.00 5.34
520 529 1.078497 CTATGAAGGCACCCACGCA 60.078 57.895 0.00 0.00 0.00 5.24
521 530 1.819632 CCTATGAAGGCACCCACGC 60.820 63.158 0.00 0.00 35.64 5.34
522 531 1.153168 CCCTATGAAGGCACCCACG 60.153 63.158 0.00 0.00 42.14 4.94
523 532 1.227383 CCCCTATGAAGGCACCCAC 59.773 63.158 0.00 0.00 42.14 4.61
524 533 3.754043 CCCCTATGAAGGCACCCA 58.246 61.111 0.00 0.00 42.14 4.51
529 538 1.227674 CACTCGCCCCTATGAAGGC 60.228 63.158 0.00 0.00 46.17 4.35
530 539 1.410004 TACACTCGCCCCTATGAAGG 58.590 55.000 0.00 0.00 43.25 3.46
531 540 2.365617 ACATACACTCGCCCCTATGAAG 59.634 50.000 0.00 0.00 0.00 3.02
532 541 2.102420 CACATACACTCGCCCCTATGAA 59.898 50.000 0.00 0.00 0.00 2.57
533 542 1.686587 CACATACACTCGCCCCTATGA 59.313 52.381 0.00 0.00 0.00 2.15
534 543 1.686587 TCACATACACTCGCCCCTATG 59.313 52.381 0.00 0.00 0.00 2.23
535 544 1.964223 CTCACATACACTCGCCCCTAT 59.036 52.381 0.00 0.00 0.00 2.57
536 545 1.341679 ACTCACATACACTCGCCCCTA 60.342 52.381 0.00 0.00 0.00 3.53
537 546 0.614979 ACTCACATACACTCGCCCCT 60.615 55.000 0.00 0.00 0.00 4.79
538 547 0.249398 AACTCACATACACTCGCCCC 59.751 55.000 0.00 0.00 0.00 5.80
539 548 2.165845 AGTAACTCACATACACTCGCCC 59.834 50.000 0.00 0.00 0.00 6.13
540 549 3.505464 AGTAACTCACATACACTCGCC 57.495 47.619 0.00 0.00 0.00 5.54
541 550 4.921515 TCAAAGTAACTCACATACACTCGC 59.078 41.667 0.00 0.00 0.00 5.03
542 551 7.116376 ACAATCAAAGTAACTCACATACACTCG 59.884 37.037 0.00 0.00 0.00 4.18
543 552 8.311650 ACAATCAAAGTAACTCACATACACTC 57.688 34.615 0.00 0.00 0.00 3.51
544 553 9.204570 GTACAATCAAAGTAACTCACATACACT 57.795 33.333 0.00 0.00 0.00 3.55
545 554 8.440833 GGTACAATCAAAGTAACTCACATACAC 58.559 37.037 0.00 0.00 0.00 2.90
567 576 6.797454 TGTGGTGTTTTCTTTAACATGGTAC 58.203 36.000 0.00 0.00 39.93 3.34
571 580 7.826260 AACTTGTGGTGTTTTCTTTAACATG 57.174 32.000 0.00 0.00 39.93 3.21
642 651 1.255667 TAGGTGGTGGCCTCGAACTC 61.256 60.000 10.91 1.23 39.94 3.01
705 714 3.034635 TGAGTTGAGGATAGGAGAAGCC 58.965 50.000 0.00 0.00 0.00 4.35
709 718 8.609617 TCTTAAATTGAGTTGAGGATAGGAGA 57.390 34.615 0.00 0.00 0.00 3.71
905 914 7.397892 CCTATTTATAGGCAGATCGAGAGAA 57.602 40.000 2.96 0.00 43.12 2.87
916 925 9.453572 GATGATCACATTTCCTATTTATAGGCA 57.546 33.333 10.39 0.00 41.92 4.75
934 943 1.153597 TGATGCCGCGTGATGATCAC 61.154 55.000 15.36 15.36 43.65 3.06
993 1030 1.206132 TGGATAGTCGCCATGTCGTTT 59.794 47.619 0.00 0.00 0.00 3.60
995 1032 0.821517 TTGGATAGTCGCCATGTCGT 59.178 50.000 0.00 0.00 34.90 4.34
1027 1064 2.503331 TGCAGTAACAGATTGTGGTGG 58.497 47.619 0.00 0.00 0.00 4.61
1107 1145 7.863375 AGATGAGTCGACATATAGTTGCTTAAC 59.137 37.037 19.50 0.00 0.00 2.01
1116 1154 8.716646 ACTATGAGAGATGAGTCGACATATAG 57.283 38.462 19.50 9.16 0.00 1.31
1132 1189 6.861144 TGAAACACAGATGAGACTATGAGAG 58.139 40.000 0.00 0.00 0.00 3.20
1133 1190 6.840780 TGAAACACAGATGAGACTATGAGA 57.159 37.500 0.00 0.00 0.00 3.27
1221 1281 2.215907 CTGCTACTGCTGCTTACGAT 57.784 50.000 0.00 0.00 40.48 3.73
1304 1364 4.776322 CATTCCTCGGCCACGGCA 62.776 66.667 10.83 0.00 44.11 5.69
1460 1520 1.671379 GTTGAAGTCCCGGCACTCC 60.671 63.158 0.00 0.00 0.00 3.85
1719 1779 1.042559 CATTAAACCCGGCTGGCCAT 61.043 55.000 5.51 0.00 37.83 4.40
1763 1825 4.156922 CACGATACTCCTAGATGGATGTCC 59.843 50.000 0.00 0.00 45.16 4.02
2074 2144 5.762218 CCCAGAGATCAGTTTATGAATGTCC 59.238 44.000 0.00 0.00 42.53 4.02
2082 2152 5.339530 CCTTGTTCCCCAGAGATCAGTTTAT 60.340 44.000 0.00 0.00 0.00 1.40
2087 2157 1.407989 GCCTTGTTCCCCAGAGATCAG 60.408 57.143 0.00 0.00 0.00 2.90
2088 2158 0.620556 GCCTTGTTCCCCAGAGATCA 59.379 55.000 0.00 0.00 0.00 2.92
2096 2166 4.551702 AATGTTTATTGCCTTGTTCCCC 57.448 40.909 0.00 0.00 0.00 4.81
2348 2427 5.646360 TCCCTTCTCTACTTTTTATTTGGCG 59.354 40.000 0.00 0.00 0.00 5.69
2427 2506 1.196012 CTCGGGGGCTCTTTAGAAGT 58.804 55.000 0.00 0.00 0.00 3.01
2458 2537 7.981142 TGCGGTTCTCTATTAACAATTTAAGG 58.019 34.615 0.00 0.00 30.58 2.69
2481 2560 1.381928 CCACAGAGACCCATGCATGC 61.382 60.000 21.69 11.82 0.00 4.06
2484 2563 0.543277 GATCCACAGAGACCCATGCA 59.457 55.000 0.00 0.00 0.00 3.96
2485 2564 0.543277 TGATCCACAGAGACCCATGC 59.457 55.000 0.00 0.00 0.00 4.06
2496 2575 7.282332 TCACATTAAACACAATTGATCCACA 57.718 32.000 13.59 0.00 0.00 4.17
2510 2589 8.987890 AGCACCACAAATATTTTCACATTAAAC 58.012 29.630 0.00 0.00 0.00 2.01
2550 2629 9.219603 TCTTAGATGGTTCACATAAAAAGTCTG 57.780 33.333 0.00 0.00 40.72 3.51
2563 2642 9.868160 TGAGAGTTATCTATCTTAGATGGTTCA 57.132 33.333 4.78 2.78 44.81 3.18
2569 2648 7.947332 TGCCACTGAGAGTTATCTATCTTAGAT 59.053 37.037 0.00 0.00 46.67 1.98
2580 2659 3.515502 TGTAGCTTGCCACTGAGAGTTAT 59.484 43.478 0.00 0.00 0.00 1.89
2645 2724 1.684983 GTTGGTATCACTAGCGGCCTA 59.315 52.381 0.00 0.00 0.00 3.93
2646 2725 0.464452 GTTGGTATCACTAGCGGCCT 59.536 55.000 0.00 0.00 0.00 5.19
2648 2727 1.287425 GTGTTGGTATCACTAGCGGC 58.713 55.000 0.00 0.00 33.59 6.53


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

AutoCloner maintained by Alex Coulton.