Multiple sequence alignment - TraesCS2D01G022100

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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 TraesCS2D01G022100 chr2D 100.000 1677 0 0 1 1677 10161002 10159326 0.000000e+00 3097
1 TraesCS2D01G022100 chr2D 100.000 546 0 0 1950 2495 10159053 10158508 0.000000e+00 1009
2 TraesCS2D01G022100 chr4A 95.159 723 33 2 740 1461 501259838 501260559 0.000000e+00 1140
3 TraesCS2D01G022100 chr4A 93.601 547 34 1 1950 2495 501260931 501261477 0.000000e+00 815
4 TraesCS2D01G022100 chr4A 95.455 220 10 0 1458 1677 501260627 501260846 3.950000e-93 351
5 TraesCS2D01G022100 chr4A 87.013 154 18 2 537 688 630901421 630901268 3.300000e-39 172
6 TraesCS2D01G022100 chr5B 92.956 724 47 4 740 1461 27448507 27447786 0.000000e+00 1051
7 TraesCS2D01G022100 chr5B 91.225 547 44 4 1950 2495 27447413 27446870 0.000000e+00 741
8 TraesCS2D01G022100 chr5B 82.645 484 54 15 16 471 120043811 120044292 3.870000e-108 401
9 TraesCS2D01G022100 chr5B 94.521 219 12 0 1458 1676 27447718 27447500 3.070000e-89 339
10 TraesCS2D01G022100 chr5B 75.591 508 69 26 16 475 112553630 112553130 1.510000e-47 200
11 TraesCS2D01G022100 chr5B 95.062 81 4 0 608 688 426622517 426622437 7.240000e-26 128
12 TraesCS2D01G022100 chr5B 90.588 85 8 0 608 692 468875017 468874933 2.030000e-21 113
13 TraesCS2D01G022100 chr1B 81.339 702 89 26 16 692 452765889 452765205 1.310000e-147 532
14 TraesCS2D01G022100 chr3A 82.837 571 77 12 135 688 747184710 747184144 2.230000e-135 492
15 TraesCS2D01G022100 chr2A 82.867 572 72 15 135 687 342644126 342643562 8.020000e-135 490
16 TraesCS2D01G022100 chr2A 83.088 408 46 13 135 524 678999988 678999586 1.420000e-92 350
17 TraesCS2D01G022100 chrUn 84.058 345 34 9 135 464 480425240 480424902 1.860000e-81 313
18 TraesCS2D01G022100 chr7D 84.058 345 34 9 135 464 171751496 171751158 1.860000e-81 313
19 TraesCS2D01G022100 chr5D 84.058 345 34 9 135 464 507875602 507875264 1.860000e-81 313
20 TraesCS2D01G022100 chr1D 88.278 273 9 5 1 250 7706660 7706388 3.120000e-79 305
21 TraesCS2D01G022100 chr1D 90.045 221 12 7 477 689 7701550 7701332 6.800000e-71 278
22 TraesCS2D01G022100 chr1D 85.271 258 16 4 246 481 7705527 7705270 1.920000e-61 246
23 TraesCS2D01G022100 chr5A 97.260 146 4 0 543 688 44599524 44599379 5.330000e-62 248
24 TraesCS2D01G022100 chr6D 88.535 157 13 4 536 688 430313968 430314123 4.240000e-43 185
25 TraesCS2D01G022100 chr3D 87.097 155 17 2 537 688 144759764 144759610 3.300000e-39 172


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 TraesCS2D01G022100 chr2D 10158508 10161002 2494 True 2053.000000 3097 100.000000 1 2495 2 chr2D.!!$R1 2494
1 TraesCS2D01G022100 chr4A 501259838 501261477 1639 False 768.666667 1140 94.738333 740 2495 3 chr4A.!!$F1 1755
2 TraesCS2D01G022100 chr5B 27446870 27448507 1637 True 710.333333 1051 92.900667 740 2495 3 chr5B.!!$R4 1755
3 TraesCS2D01G022100 chr1B 452765205 452765889 684 True 532.000000 532 81.339000 16 692 1 chr1B.!!$R1 676
4 TraesCS2D01G022100 chr3A 747184144 747184710 566 True 492.000000 492 82.837000 135 688 1 chr3A.!!$R1 553
5 TraesCS2D01G022100 chr2A 342643562 342644126 564 True 490.000000 490 82.867000 135 687 1 chr2A.!!$R1 552
6 TraesCS2D01G022100 chr1D 7701332 7706660 5328 True 276.333333 305 87.864667 1 689 3 chr1D.!!$R1 688

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
665 5311 0.035152 TCCCTCGGCAGTAGAACGTA 60.035 55.0 0.0 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 6968 0.483328 CTCCCCCTCTCCCTTCGATA 59.517 60.0 0.0 0.0 0.0 2.92 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
100 101 6.486320 TCACATCAATTACAAGCTCAGTTTGA 59.514 34.615 8.44 8.13 0.00 2.69
131 133 0.390340 CTGTTGCCGCTTCTCTGCTA 60.390 55.000 0.00 0.00 0.00 3.49
152 177 5.922544 GCTATTTGCACAACTGAAACTGAAT 59.077 36.000 0.00 0.00 42.31 2.57
159 184 5.751680 CACAACTGAAACTGAATACACCTG 58.248 41.667 0.00 0.00 0.00 4.00
184 209 0.528249 CGCAAAGCAAGCACCAAACT 60.528 50.000 0.00 0.00 0.00 2.66
220 245 2.467826 GCAGCAGAGCAATCGTCCC 61.468 63.158 0.00 0.00 0.00 4.46
278 1168 4.099170 AACGGTCTCGACGGCTCG 62.099 66.667 0.00 0.77 41.65 5.03
300 1190 4.409218 GCGTCGCACCCTGTACGA 62.409 66.667 13.44 0.00 37.53 3.43
301 1191 2.256158 CGTCGCACCCTGTACGAA 59.744 61.111 0.00 0.00 33.01 3.85
304 1194 0.523072 GTCGCACCCTGTACGAAGTA 59.477 55.000 0.00 0.00 45.11 2.24
399 1311 4.776322 CGCGCCCTGATGGAACCA 62.776 66.667 0.00 0.00 35.39 3.67
405 1317 0.911769 CCCTGATGGAACCACAGCTA 59.088 55.000 13.74 0.00 35.39 3.32
442 1354 0.558712 AGCGAACCCTAGGGAGAGAT 59.441 55.000 35.38 19.17 38.96 2.75
515 5153 0.462581 GATGGCGATGAAGTGAGGCA 60.463 55.000 0.00 0.00 43.15 4.75
521 5159 1.673923 CGATGAAGTGAGGCAAGAGCA 60.674 52.381 0.00 0.00 44.61 4.26
523 5161 1.597742 TGAAGTGAGGCAAGAGCAAC 58.402 50.000 0.00 0.00 44.61 4.17
530 5176 1.745489 GGCAAGAGCAACGGGTAGG 60.745 63.158 0.00 0.00 44.61 3.18
561 5207 0.817634 CCGATGGGCCGCTTATTTCA 60.818 55.000 0.00 0.00 0.00 2.69
592 5238 2.202388 CGAAAGCTGCGCATGGTG 60.202 61.111 12.24 0.00 0.00 4.17
593 5239 2.956987 GAAAGCTGCGCATGGTGT 59.043 55.556 12.24 5.94 0.00 4.16
594 5240 1.634757 CGAAAGCTGCGCATGGTGTA 61.635 55.000 12.24 0.00 0.00 2.90
595 5241 0.097674 GAAAGCTGCGCATGGTGTAG 59.902 55.000 12.24 0.00 0.00 2.74
596 5242 0.606401 AAAGCTGCGCATGGTGTAGT 60.606 50.000 12.24 0.00 0.00 2.73
597 5243 0.606401 AAGCTGCGCATGGTGTAGTT 60.606 50.000 12.24 0.00 0.00 2.24
598 5244 0.606401 AGCTGCGCATGGTGTAGTTT 60.606 50.000 12.24 0.00 0.00 2.66
599 5245 0.179189 GCTGCGCATGGTGTAGTTTC 60.179 55.000 12.24 0.00 0.00 2.78
600 5246 1.442769 CTGCGCATGGTGTAGTTTCT 58.557 50.000 12.24 0.00 0.00 2.52
601 5247 1.129251 CTGCGCATGGTGTAGTTTCTG 59.871 52.381 12.24 0.00 0.00 3.02
602 5248 0.179189 GCGCATGGTGTAGTTTCTGC 60.179 55.000 0.30 0.00 0.00 4.26
603 5249 1.155889 CGCATGGTGTAGTTTCTGCA 58.844 50.000 0.00 0.00 0.00 4.41
604 5250 1.535028 CGCATGGTGTAGTTTCTGCAA 59.465 47.619 0.00 0.00 0.00 4.08
605 5251 2.413239 CGCATGGTGTAGTTTCTGCAAG 60.413 50.000 0.00 0.00 0.00 4.01
606 5252 2.669391 GCATGGTGTAGTTTCTGCAAGC 60.669 50.000 0.00 0.00 0.00 4.01
607 5253 2.340210 TGGTGTAGTTTCTGCAAGCA 57.660 45.000 0.00 0.00 0.00 3.91
608 5254 2.862541 TGGTGTAGTTTCTGCAAGCAT 58.137 42.857 0.00 0.00 0.00 3.79
609 5255 2.813754 TGGTGTAGTTTCTGCAAGCATC 59.186 45.455 0.00 0.00 0.00 3.91
610 5256 2.159653 GGTGTAGTTTCTGCAAGCATCG 60.160 50.000 0.00 0.00 0.00 3.84
611 5257 2.480419 GTGTAGTTTCTGCAAGCATCGT 59.520 45.455 0.00 0.00 0.00 3.73
612 5258 3.058914 GTGTAGTTTCTGCAAGCATCGTT 60.059 43.478 0.00 0.00 0.00 3.85
613 5259 2.693797 AGTTTCTGCAAGCATCGTTG 57.306 45.000 0.00 0.00 0.00 4.10
614 5260 1.267806 AGTTTCTGCAAGCATCGTTGG 59.732 47.619 0.00 0.00 0.00 3.77
615 5261 1.266718 GTTTCTGCAAGCATCGTTGGA 59.733 47.619 0.00 0.00 0.00 3.53
616 5262 1.825090 TTCTGCAAGCATCGTTGGAT 58.175 45.000 0.00 0.00 0.00 3.41
625 5271 0.949397 CATCGTTGGATGCCTGATGG 59.051 55.000 0.00 0.00 43.26 3.51
626 5272 0.839277 ATCGTTGGATGCCTGATGGA 59.161 50.000 0.00 0.00 34.57 3.41
627 5273 0.107703 TCGTTGGATGCCTGATGGAC 60.108 55.000 0.00 0.00 34.57 4.02
628 5274 1.431488 CGTTGGATGCCTGATGGACG 61.431 60.000 0.00 0.00 34.57 4.79
629 5275 1.097547 GTTGGATGCCTGATGGACGG 61.098 60.000 0.00 0.00 34.57 4.79
630 5276 1.561769 TTGGATGCCTGATGGACGGT 61.562 55.000 0.00 0.00 34.57 4.83
631 5277 1.524621 GGATGCCTGATGGACGGTG 60.525 63.158 0.00 0.00 34.57 4.94
632 5278 2.124570 ATGCCTGATGGACGGTGC 60.125 61.111 0.00 0.00 34.57 5.01
633 5279 2.874648 GATGCCTGATGGACGGTGCA 62.875 60.000 4.40 4.40 36.24 4.57
634 5280 2.821366 GCCTGATGGACGGTGCAG 60.821 66.667 8.63 0.00 34.57 4.41
635 5281 2.821366 CCTGATGGACGGTGCAGC 60.821 66.667 11.11 11.11 34.57 5.25
636 5282 3.190849 CTGATGGACGGTGCAGCG 61.191 66.667 34.46 34.46 0.00 5.18
637 5283 4.758251 TGATGGACGGTGCAGCGG 62.758 66.667 37.73 21.90 0.00 5.52
654 5300 2.202892 GGAACGATGTCCCTCGGC 60.203 66.667 0.00 0.00 42.88 5.54
655 5301 2.577059 GAACGATGTCCCTCGGCA 59.423 61.111 0.00 0.00 42.88 5.69
656 5302 1.519455 GAACGATGTCCCTCGGCAG 60.519 63.158 0.00 0.00 42.88 4.85
657 5303 2.227089 GAACGATGTCCCTCGGCAGT 62.227 60.000 0.00 0.00 42.88 4.40
658 5304 0.968901 AACGATGTCCCTCGGCAGTA 60.969 55.000 0.00 0.00 42.88 2.74
659 5305 1.360551 CGATGTCCCTCGGCAGTAG 59.639 63.158 0.00 0.00 35.03 2.57
660 5306 1.101635 CGATGTCCCTCGGCAGTAGA 61.102 60.000 0.00 0.00 35.03 2.59
661 5307 1.112113 GATGTCCCTCGGCAGTAGAA 58.888 55.000 0.00 0.00 0.00 2.10
662 5308 0.824759 ATGTCCCTCGGCAGTAGAAC 59.175 55.000 0.00 0.00 0.00 3.01
663 5309 1.139095 GTCCCTCGGCAGTAGAACG 59.861 63.158 0.00 0.00 0.00 3.95
664 5310 1.303888 TCCCTCGGCAGTAGAACGT 60.304 57.895 0.00 0.00 0.00 3.99
665 5311 0.035152 TCCCTCGGCAGTAGAACGTA 60.035 55.000 0.00 0.00 0.00 3.57
666 5312 0.100146 CCCTCGGCAGTAGAACGTAC 59.900 60.000 0.00 0.00 0.00 3.67
667 5313 0.100146 CCTCGGCAGTAGAACGTACC 59.900 60.000 0.00 0.00 0.00 3.34
668 5314 0.806868 CTCGGCAGTAGAACGTACCA 59.193 55.000 0.00 0.00 0.00 3.25
669 5315 1.200716 CTCGGCAGTAGAACGTACCAA 59.799 52.381 0.00 0.00 0.00 3.67
670 5316 1.200716 TCGGCAGTAGAACGTACCAAG 59.799 52.381 0.00 0.00 0.00 3.61
671 5317 1.068055 CGGCAGTAGAACGTACCAAGT 60.068 52.381 0.00 0.00 0.00 3.16
672 5318 2.603953 GGCAGTAGAACGTACCAAGTC 58.396 52.381 0.00 0.00 0.00 3.01
673 5319 2.029649 GGCAGTAGAACGTACCAAGTCA 60.030 50.000 0.00 0.00 0.00 3.41
674 5320 3.243336 GCAGTAGAACGTACCAAGTCAG 58.757 50.000 0.00 0.00 0.00 3.51
675 5321 3.057736 GCAGTAGAACGTACCAAGTCAGA 60.058 47.826 0.00 0.00 0.00 3.27
676 5322 4.724303 CAGTAGAACGTACCAAGTCAGAG 58.276 47.826 0.00 0.00 0.00 3.35
677 5323 3.757493 AGTAGAACGTACCAAGTCAGAGG 59.243 47.826 0.00 0.00 0.00 3.69
678 5324 2.872732 AGAACGTACCAAGTCAGAGGA 58.127 47.619 0.00 0.00 0.00 3.71
679 5325 3.432378 AGAACGTACCAAGTCAGAGGAT 58.568 45.455 0.00 0.00 0.00 3.24
680 5326 3.193691 AGAACGTACCAAGTCAGAGGATG 59.806 47.826 0.00 0.00 0.00 3.51
681 5327 2.526432 ACGTACCAAGTCAGAGGATGT 58.474 47.619 0.00 0.00 0.00 3.06
682 5328 2.492484 ACGTACCAAGTCAGAGGATGTC 59.508 50.000 0.00 0.00 0.00 3.06
683 5329 2.478031 CGTACCAAGTCAGAGGATGTCG 60.478 54.545 0.00 0.00 0.00 4.35
684 5330 1.633774 ACCAAGTCAGAGGATGTCGT 58.366 50.000 0.00 0.00 0.00 4.34
685 5331 1.971357 ACCAAGTCAGAGGATGTCGTT 59.029 47.619 0.00 0.00 0.00 3.85
686 5332 2.028930 ACCAAGTCAGAGGATGTCGTTC 60.029 50.000 0.00 0.00 0.00 3.95
687 5333 2.611518 CAAGTCAGAGGATGTCGTTCC 58.388 52.381 0.00 0.00 35.90 3.62
692 5338 4.887957 AGGATGTCGTTCCTCCCA 57.112 55.556 0.00 0.00 42.71 4.37
693 5339 3.324246 AGGATGTCGTTCCTCCCAT 57.676 52.632 0.00 0.00 42.71 4.00
694 5340 0.833287 AGGATGTCGTTCCTCCCATG 59.167 55.000 0.00 0.00 42.71 3.66
695 5341 0.179045 GGATGTCGTTCCTCCCATGG 60.179 60.000 4.14 4.14 32.68 3.66
696 5342 0.830648 GATGTCGTTCCTCCCATGGA 59.169 55.000 15.22 0.00 0.00 3.41
704 5350 2.827423 CTCCCATGGAGCATCGCT 59.173 61.111 15.22 0.00 43.29 4.93
705 5351 2.052779 CTCCCATGGAGCATCGCTA 58.947 57.895 15.22 0.00 43.29 4.26
706 5352 0.037512 CTCCCATGGAGCATCGCTAG 60.038 60.000 15.22 0.00 43.29 3.42
707 5353 1.004080 CCCATGGAGCATCGCTAGG 60.004 63.158 15.22 0.00 39.88 3.02
708 5354 1.475169 CCCATGGAGCATCGCTAGGA 61.475 60.000 15.22 0.00 39.88 2.94
709 5355 0.037512 CCATGGAGCATCGCTAGGAG 60.038 60.000 5.56 0.00 39.88 3.69
710 5356 0.037512 CATGGAGCATCGCTAGGAGG 60.038 60.000 0.00 0.00 39.88 4.30
716 5362 1.365633 CATCGCTAGGAGGCTGACC 59.634 63.158 0.00 0.00 0.00 4.02
717 5363 1.075970 ATCGCTAGGAGGCTGACCA 60.076 57.895 0.00 0.00 39.06 4.02
718 5364 0.687757 ATCGCTAGGAGGCTGACCAA 60.688 55.000 0.00 0.00 39.06 3.67
719 5365 1.142748 CGCTAGGAGGCTGACCAAG 59.857 63.158 0.00 0.00 39.06 3.61
720 5366 1.608717 CGCTAGGAGGCTGACCAAGT 61.609 60.000 0.00 0.00 39.06 3.16
721 5367 1.486211 GCTAGGAGGCTGACCAAGTA 58.514 55.000 0.00 0.00 39.06 2.24
722 5368 1.831736 GCTAGGAGGCTGACCAAGTAA 59.168 52.381 0.00 0.00 39.06 2.24
723 5369 2.436173 GCTAGGAGGCTGACCAAGTAAT 59.564 50.000 0.00 0.00 39.06 1.89
724 5370 3.493524 GCTAGGAGGCTGACCAAGTAATC 60.494 52.174 0.00 0.00 39.06 1.75
725 5371 2.839228 AGGAGGCTGACCAAGTAATCT 58.161 47.619 0.00 0.00 39.06 2.40
726 5372 3.995636 AGGAGGCTGACCAAGTAATCTA 58.004 45.455 0.00 0.00 39.06 1.98
727 5373 4.561752 AGGAGGCTGACCAAGTAATCTAT 58.438 43.478 0.00 0.00 39.06 1.98
728 5374 4.346418 AGGAGGCTGACCAAGTAATCTATG 59.654 45.833 0.00 0.00 39.06 2.23
729 5375 4.345257 GGAGGCTGACCAAGTAATCTATGA 59.655 45.833 0.00 0.00 39.06 2.15
730 5376 5.283457 AGGCTGACCAAGTAATCTATGAC 57.717 43.478 0.00 0.00 39.06 3.06
731 5377 4.965532 AGGCTGACCAAGTAATCTATGACT 59.034 41.667 0.00 0.00 39.06 3.41
732 5378 5.069781 AGGCTGACCAAGTAATCTATGACTC 59.930 44.000 0.00 0.00 39.06 3.36
733 5379 5.069781 GGCTGACCAAGTAATCTATGACTCT 59.930 44.000 0.00 0.00 35.26 3.24
734 5380 6.212955 GCTGACCAAGTAATCTATGACTCTC 58.787 44.000 0.00 0.00 0.00 3.20
735 5381 6.716934 TGACCAAGTAATCTATGACTCTCC 57.283 41.667 0.00 0.00 0.00 3.71
736 5382 5.598830 TGACCAAGTAATCTATGACTCTCCC 59.401 44.000 0.00 0.00 0.00 4.30
737 5383 5.782925 ACCAAGTAATCTATGACTCTCCCT 58.217 41.667 0.00 0.00 0.00 4.20
738 5384 6.923670 ACCAAGTAATCTATGACTCTCCCTA 58.076 40.000 0.00 0.00 0.00 3.53
743 5389 5.941146 AATCTATGACTCTCCCTAGTCCT 57.059 43.478 1.82 0.00 44.40 3.85
854 5500 1.697291 GGATCTGTCCCCATCCTTCCT 60.697 57.143 0.00 0.00 38.69 3.36
958 5605 1.627424 GCGCACGGTCGTAATACAC 59.373 57.895 0.30 0.00 0.00 2.90
1018 5665 2.948801 GATGGAGGGAGTAGCGGGGT 62.949 65.000 0.00 0.00 0.00 4.95
1101 5748 2.474410 AGGAGAAGGGTAAAAGTGCG 57.526 50.000 0.00 0.00 0.00 5.34
1194 5851 1.247567 AAGTTTGGTGCCCGATCAAG 58.752 50.000 0.00 0.00 0.00 3.02
1245 5903 3.519579 TCGGTTTGTGTTCACGTTCTTA 58.480 40.909 0.00 0.00 0.00 2.10
1413 6071 1.063006 CTTGGGCATGATGAACGCG 59.937 57.895 3.53 3.53 0.00 6.01
1423 6081 0.726827 GATGAACGCGGAATCAGCAA 59.273 50.000 12.47 0.00 32.43 3.91
1433 6091 3.316308 GCGGAATCAGCAAAGGATATTGT 59.684 43.478 0.00 0.00 32.80 2.71
1467 6267 4.061596 GCCAGTTCATAGAAGCCTATCAC 58.938 47.826 0.00 0.00 33.47 3.06
1508 6308 4.412858 AGGAGGATGATGAGCAGAAGAAAT 59.587 41.667 0.00 0.00 0.00 2.17
1582 6382 6.763610 GGTTCGAGTATGAATTTCTTCCAGAT 59.236 38.462 0.00 0.00 0.00 2.90
2051 6851 2.802415 CGATGGTTCTGGCAGATCAGAG 60.802 54.545 19.50 13.00 43.64 3.35
2069 6869 1.006639 GAGAAGGGAGAGGAGGTCACT 59.993 57.143 0.00 0.00 0.00 3.41
2124 6924 1.574263 GGGAGTCCCTAAGAAGCTGT 58.426 55.000 22.04 0.00 41.34 4.40
2137 6937 2.749441 GCTGTTGCTGGAGGAGGC 60.749 66.667 0.00 0.00 36.03 4.70
2139 6939 2.853542 TGTTGCTGGAGGAGGCCA 60.854 61.111 5.01 0.00 36.30 5.36
2233 7034 1.602327 AAGGAGAAGCGGGGTACGTC 61.602 60.000 0.00 0.00 46.52 4.34
2237 7038 1.447314 GAAGCGGGGTACGTCCAAG 60.447 63.158 0.00 0.00 46.52 3.61
2304 7105 1.002134 ATGACAACCAAGGGCTCCG 60.002 57.895 0.00 0.00 0.00 4.63
2347 7149 3.690460 ACCCTAATGGCAAGAAGTTCAG 58.310 45.455 5.50 0.00 37.83 3.02
2418 7220 0.462759 GATCCTGGGGCAGAAACGAG 60.463 60.000 0.00 0.00 32.44 4.18
2434 7236 3.000684 ACGAGGCATCAGTAGTAGTGA 57.999 47.619 10.11 10.11 31.21 3.41
2453 7255 5.347342 AGTGATGACGAGAATGAAGCTAAG 58.653 41.667 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 1.251251 GGCAACAGCAGGAGAAATGT 58.749 50.000 0.00 0.00 0.00 2.71
131 133 6.697019 GTGTATTCAGTTTCAGTTGTGCAAAT 59.303 34.615 0.00 0.00 0.00 2.32
152 177 1.790755 CTTTGCGCTGTACAGGTGTA 58.209 50.000 23.95 8.51 0.00 2.90
159 184 0.998727 GTGCTTGCTTTGCGCTGTAC 60.999 55.000 9.73 0.00 40.11 2.90
184 209 1.793581 CTTGCCTCGCGTTGCATTA 59.206 52.632 21.89 10.39 37.33 1.90
220 245 2.100216 CCGCCGCCGATTTTTCTG 59.900 61.111 0.00 0.00 36.29 3.02
379 1291 4.161295 TTCCATCAGGGCGCGAGG 62.161 66.667 12.10 0.00 36.21 4.63
399 1311 1.592223 GGCGGTGAAGAGTAGCTGT 59.408 57.895 0.00 0.00 0.00 4.40
442 1354 2.882876 GTCGGCCAGTCGCTCTTA 59.117 61.111 2.24 0.00 37.74 2.10
484 1399 1.428448 TCGCCATCGTTTCACTCAAG 58.572 50.000 0.00 0.00 36.96 3.02
485 1400 1.731709 CATCGCCATCGTTTCACTCAA 59.268 47.619 0.00 0.00 36.96 3.02
515 5153 1.885163 CGACCCTACCCGTTGCTCTT 61.885 60.000 0.00 0.00 0.00 2.85
521 5159 1.980772 CAGTCCGACCCTACCCGTT 60.981 63.158 0.00 0.00 0.00 4.44
523 5161 3.145551 CCAGTCCGACCCTACCCG 61.146 72.222 0.00 0.00 0.00 5.28
561 5207 1.541588 GCTTTCGCTCTGGTGGAAATT 59.458 47.619 0.00 0.00 0.00 1.82
581 5227 1.129251 CAGAAACTACACCATGCGCAG 59.871 52.381 18.32 5.51 0.00 5.18
584 5230 1.155889 TGCAGAAACTACACCATGCG 58.844 50.000 0.00 0.00 36.47 4.73
585 5231 2.669391 GCTTGCAGAAACTACACCATGC 60.669 50.000 0.00 0.00 0.00 4.06
586 5232 2.553602 TGCTTGCAGAAACTACACCATG 59.446 45.455 0.00 0.00 0.00 3.66
587 5233 2.862541 TGCTTGCAGAAACTACACCAT 58.137 42.857 0.00 0.00 0.00 3.55
588 5234 2.340210 TGCTTGCAGAAACTACACCA 57.660 45.000 0.00 0.00 0.00 4.17
589 5235 2.159653 CGATGCTTGCAGAAACTACACC 60.160 50.000 0.87 0.00 0.00 4.16
590 5236 2.480419 ACGATGCTTGCAGAAACTACAC 59.520 45.455 0.87 0.00 0.00 2.90
591 5237 2.766313 ACGATGCTTGCAGAAACTACA 58.234 42.857 0.87 0.00 0.00 2.74
592 5238 3.482786 CAACGATGCTTGCAGAAACTAC 58.517 45.455 0.87 0.00 0.00 2.73
593 5239 2.483877 CCAACGATGCTTGCAGAAACTA 59.516 45.455 0.87 0.00 0.00 2.24
594 5240 1.267806 CCAACGATGCTTGCAGAAACT 59.732 47.619 0.87 0.00 0.00 2.66
595 5241 1.266718 TCCAACGATGCTTGCAGAAAC 59.733 47.619 0.87 0.00 0.00 2.78
596 5242 1.603456 TCCAACGATGCTTGCAGAAA 58.397 45.000 0.87 0.00 0.00 2.52
597 5243 1.469703 CATCCAACGATGCTTGCAGAA 59.530 47.619 0.87 0.00 39.59 3.02
598 5244 1.089112 CATCCAACGATGCTTGCAGA 58.911 50.000 0.87 0.00 39.59 4.26
599 5245 3.616935 CATCCAACGATGCTTGCAG 57.383 52.632 0.87 0.00 39.59 4.41
607 5253 0.839277 TCCATCAGGCATCCAACGAT 59.161 50.000 0.00 0.00 33.74 3.73
608 5254 0.107703 GTCCATCAGGCATCCAACGA 60.108 55.000 0.00 0.00 33.74 3.85
609 5255 1.431488 CGTCCATCAGGCATCCAACG 61.431 60.000 0.00 0.00 33.74 4.10
610 5256 1.097547 CCGTCCATCAGGCATCCAAC 61.098 60.000 0.00 0.00 33.74 3.77
611 5257 1.224315 CCGTCCATCAGGCATCCAA 59.776 57.895 0.00 0.00 33.74 3.53
612 5258 1.995066 ACCGTCCATCAGGCATCCA 60.995 57.895 0.00 0.00 33.74 3.41
613 5259 1.524621 CACCGTCCATCAGGCATCC 60.525 63.158 0.00 0.00 33.74 3.51
614 5260 2.182842 GCACCGTCCATCAGGCATC 61.183 63.158 0.00 0.00 33.74 3.91
615 5261 2.124570 GCACCGTCCATCAGGCAT 60.125 61.111 0.00 0.00 33.74 4.40
616 5262 3.610619 CTGCACCGTCCATCAGGCA 62.611 63.158 0.00 0.00 33.74 4.75
617 5263 2.821366 CTGCACCGTCCATCAGGC 60.821 66.667 0.00 0.00 33.74 4.85
618 5264 2.821366 GCTGCACCGTCCATCAGG 60.821 66.667 0.00 0.00 0.00 3.86
619 5265 3.190849 CGCTGCACCGTCCATCAG 61.191 66.667 0.00 0.00 0.00 2.90
620 5266 4.758251 CCGCTGCACCGTCCATCA 62.758 66.667 0.00 0.00 0.00 3.07
628 5274 3.499737 CATCGTTCCCGCTGCACC 61.500 66.667 0.00 0.00 0.00 5.01
629 5275 2.740714 GACATCGTTCCCGCTGCAC 61.741 63.158 0.00 0.00 33.66 4.57
630 5276 2.434185 GACATCGTTCCCGCTGCA 60.434 61.111 0.00 0.00 33.66 4.41
631 5277 3.195698 GGACATCGTTCCCGCTGC 61.196 66.667 0.00 0.00 33.66 5.25
632 5278 2.511600 GGGACATCGTTCCCGCTG 60.512 66.667 4.14 0.00 46.24 5.18
637 5283 2.202892 GCCGAGGGACATCGTTCC 60.203 66.667 5.64 0.00 41.12 3.62
638 5284 1.519455 CTGCCGAGGGACATCGTTC 60.519 63.158 5.64 0.00 41.12 3.95
639 5285 0.968901 TACTGCCGAGGGACATCGTT 60.969 55.000 5.64 0.00 41.12 3.85
640 5286 1.379443 TACTGCCGAGGGACATCGT 60.379 57.895 5.64 0.00 41.12 3.73
641 5287 1.101635 TCTACTGCCGAGGGACATCG 61.102 60.000 0.00 0.00 42.36 3.84
642 5288 1.112113 TTCTACTGCCGAGGGACATC 58.888 55.000 0.00 0.00 0.00 3.06
643 5289 0.824759 GTTCTACTGCCGAGGGACAT 59.175 55.000 0.00 0.00 0.00 3.06
644 5290 1.592400 CGTTCTACTGCCGAGGGACA 61.592 60.000 0.00 0.00 0.00 4.02
645 5291 1.139095 CGTTCTACTGCCGAGGGAC 59.861 63.158 0.00 0.00 0.00 4.46
646 5292 0.035152 TACGTTCTACTGCCGAGGGA 60.035 55.000 0.00 0.00 0.00 4.20
647 5293 0.100146 GTACGTTCTACTGCCGAGGG 59.900 60.000 0.00 0.00 0.00 4.30
648 5294 0.100146 GGTACGTTCTACTGCCGAGG 59.900 60.000 0.00 0.00 0.00 4.63
649 5295 0.806868 TGGTACGTTCTACTGCCGAG 59.193 55.000 0.00 0.00 0.00 4.63
650 5296 1.200716 CTTGGTACGTTCTACTGCCGA 59.799 52.381 0.00 0.00 0.00 5.54
651 5297 1.068055 ACTTGGTACGTTCTACTGCCG 60.068 52.381 0.00 0.00 0.00 5.69
652 5298 2.029649 TGACTTGGTACGTTCTACTGCC 60.030 50.000 0.00 0.00 0.00 4.85
653 5299 3.057736 TCTGACTTGGTACGTTCTACTGC 60.058 47.826 0.00 0.00 0.00 4.40
654 5300 4.379603 CCTCTGACTTGGTACGTTCTACTG 60.380 50.000 0.00 0.00 0.00 2.74
655 5301 3.757493 CCTCTGACTTGGTACGTTCTACT 59.243 47.826 0.00 0.00 0.00 2.57
656 5302 3.755378 TCCTCTGACTTGGTACGTTCTAC 59.245 47.826 0.00 0.00 0.00 2.59
657 5303 4.025040 TCCTCTGACTTGGTACGTTCTA 57.975 45.455 0.00 0.00 0.00 2.10
658 5304 2.872732 TCCTCTGACTTGGTACGTTCT 58.127 47.619 0.00 0.00 0.00 3.01
659 5305 3.056749 ACATCCTCTGACTTGGTACGTTC 60.057 47.826 0.00 0.00 0.00 3.95
660 5306 2.897969 ACATCCTCTGACTTGGTACGTT 59.102 45.455 0.00 0.00 0.00 3.99
661 5307 2.492484 GACATCCTCTGACTTGGTACGT 59.508 50.000 0.00 0.00 0.00 3.57
662 5308 2.478031 CGACATCCTCTGACTTGGTACG 60.478 54.545 0.00 0.00 0.00 3.67
663 5309 2.492484 ACGACATCCTCTGACTTGGTAC 59.508 50.000 0.00 0.00 0.00 3.34
664 5310 2.803956 ACGACATCCTCTGACTTGGTA 58.196 47.619 0.00 0.00 0.00 3.25
665 5311 1.633774 ACGACATCCTCTGACTTGGT 58.366 50.000 0.00 0.00 0.00 3.67
666 5312 2.611518 GAACGACATCCTCTGACTTGG 58.388 52.381 0.00 0.00 0.00 3.61
667 5313 2.611518 GGAACGACATCCTCTGACTTG 58.388 52.381 0.00 0.00 36.50 3.16
676 5322 4.440604 CTCCATGGGAGGAACGACATCC 62.441 59.091 13.02 8.88 45.43 3.51
677 5323 0.830648 TCCATGGGAGGAACGACATC 59.169 55.000 13.02 0.00 33.93 3.06
678 5324 0.833287 CTCCATGGGAGGAACGACAT 59.167 55.000 13.02 0.00 45.43 3.06
679 5325 2.286826 CTCCATGGGAGGAACGACA 58.713 57.895 13.02 0.00 45.43 4.35
680 5326 1.899437 TGCTCCATGGGAGGAACGAC 61.899 60.000 13.02 0.00 46.83 4.34
681 5327 1.612146 TGCTCCATGGGAGGAACGA 60.612 57.895 13.02 0.00 46.83 3.85
682 5328 2.989639 TGCTCCATGGGAGGAACG 59.010 61.111 13.02 0.00 46.83 3.95
688 5334 1.475169 CCTAGCGATGCTCCATGGGA 61.475 60.000 13.02 0.00 40.44 4.37
689 5335 1.004080 CCTAGCGATGCTCCATGGG 60.004 63.158 13.02 3.69 40.44 4.00
690 5336 0.037512 CTCCTAGCGATGCTCCATGG 60.038 60.000 4.97 4.97 40.44 3.66
691 5337 0.037512 CCTCCTAGCGATGCTCCATG 60.038 60.000 0.00 0.00 40.44 3.66
692 5338 1.825281 GCCTCCTAGCGATGCTCCAT 61.825 60.000 0.00 0.00 40.44 3.41
693 5339 2.502492 GCCTCCTAGCGATGCTCCA 61.502 63.158 0.00 0.00 40.44 3.86
694 5340 2.206536 AGCCTCCTAGCGATGCTCC 61.207 63.158 0.00 0.00 37.92 4.70
695 5341 1.006337 CAGCCTCCTAGCGATGCTC 60.006 63.158 0.00 0.00 40.14 4.26
696 5342 1.456518 TCAGCCTCCTAGCGATGCT 60.457 57.895 0.00 0.00 42.56 3.79
697 5343 1.300542 GTCAGCCTCCTAGCGATGC 60.301 63.158 0.00 0.00 38.01 3.91
698 5344 1.365633 GGTCAGCCTCCTAGCGATG 59.634 63.158 0.00 0.00 38.01 3.84
699 5345 0.687757 TTGGTCAGCCTCCTAGCGAT 60.688 55.000 0.00 0.00 38.01 4.58
700 5346 1.304962 TTGGTCAGCCTCCTAGCGA 60.305 57.895 0.00 0.00 38.01 4.93
701 5347 1.142748 CTTGGTCAGCCTCCTAGCG 59.857 63.158 0.00 0.00 38.01 4.26
702 5348 1.486211 TACTTGGTCAGCCTCCTAGC 58.514 55.000 0.00 0.00 32.62 3.42
703 5349 3.964031 AGATTACTTGGTCAGCCTCCTAG 59.036 47.826 0.00 0.00 34.83 3.02
704 5350 3.995636 AGATTACTTGGTCAGCCTCCTA 58.004 45.455 0.00 0.00 35.27 2.94
705 5351 2.839228 AGATTACTTGGTCAGCCTCCT 58.161 47.619 0.00 0.00 35.27 3.69
706 5352 4.345257 TCATAGATTACTTGGTCAGCCTCC 59.655 45.833 0.00 0.00 35.27 4.30
707 5353 5.069781 AGTCATAGATTACTTGGTCAGCCTC 59.930 44.000 0.00 0.00 35.27 4.70
708 5354 4.965532 AGTCATAGATTACTTGGTCAGCCT 59.034 41.667 0.00 0.00 35.27 4.58
709 5355 5.069781 AGAGTCATAGATTACTTGGTCAGCC 59.930 44.000 0.00 0.00 0.00 4.85
710 5356 6.155475 AGAGTCATAGATTACTTGGTCAGC 57.845 41.667 0.00 0.00 0.00 4.26
711 5357 6.239176 GGGAGAGTCATAGATTACTTGGTCAG 60.239 46.154 0.00 0.00 0.00 3.51
712 5358 5.598830 GGGAGAGTCATAGATTACTTGGTCA 59.401 44.000 0.00 0.00 0.00 4.02
713 5359 5.836358 AGGGAGAGTCATAGATTACTTGGTC 59.164 44.000 0.00 0.00 0.00 4.02
714 5360 5.782925 AGGGAGAGTCATAGATTACTTGGT 58.217 41.667 0.00 0.00 0.00 3.67
715 5361 7.007723 ACTAGGGAGAGTCATAGATTACTTGG 58.992 42.308 0.00 0.00 0.00 3.61
716 5362 7.175990 GGACTAGGGAGAGTCATAGATTACTTG 59.824 44.444 5.96 0.00 46.51 3.16
717 5363 7.074494 AGGACTAGGGAGAGTCATAGATTACTT 59.926 40.741 5.96 0.00 46.51 2.24
718 5364 6.564927 AGGACTAGGGAGAGTCATAGATTACT 59.435 42.308 5.96 0.00 46.51 2.24
719 5365 6.786122 AGGACTAGGGAGAGTCATAGATTAC 58.214 44.000 5.96 0.00 46.51 1.89
720 5366 7.409408 AAGGACTAGGGAGAGTCATAGATTA 57.591 40.000 5.96 0.00 46.51 1.75
721 5367 5.941146 AGGACTAGGGAGAGTCATAGATT 57.059 43.478 5.96 0.00 46.51 2.40
722 5368 5.222254 GGAAGGACTAGGGAGAGTCATAGAT 60.222 48.000 5.96 0.00 46.51 1.98
723 5369 4.105057 GGAAGGACTAGGGAGAGTCATAGA 59.895 50.000 5.96 0.00 46.51 1.98
724 5370 4.403734 GGAAGGACTAGGGAGAGTCATAG 58.596 52.174 5.96 0.00 46.51 2.23
725 5371 3.140519 GGGAAGGACTAGGGAGAGTCATA 59.859 52.174 5.96 0.00 46.51 2.15
726 5372 2.090999 GGGAAGGACTAGGGAGAGTCAT 60.091 54.545 5.96 0.00 46.51 3.06
727 5373 1.288335 GGGAAGGACTAGGGAGAGTCA 59.712 57.143 5.96 0.00 46.51 3.41
728 5374 1.751382 CGGGAAGGACTAGGGAGAGTC 60.751 61.905 0.00 0.00 44.39 3.36
729 5375 0.259356 CGGGAAGGACTAGGGAGAGT 59.741 60.000 0.00 0.00 0.00 3.24
730 5376 0.259356 ACGGGAAGGACTAGGGAGAG 59.741 60.000 0.00 0.00 0.00 3.20
731 5377 0.708802 AACGGGAAGGACTAGGGAGA 59.291 55.000 0.00 0.00 0.00 3.71
732 5378 2.308690 CTAACGGGAAGGACTAGGGAG 58.691 57.143 0.00 0.00 0.00 4.30
733 5379 1.063417 CCTAACGGGAAGGACTAGGGA 60.063 57.143 0.00 0.00 36.08 4.20
734 5380 1.342774 ACCTAACGGGAAGGACTAGGG 60.343 57.143 6.93 0.00 37.57 3.53
735 5381 1.755380 CACCTAACGGGAAGGACTAGG 59.245 57.143 6.93 0.00 37.57 3.02
736 5382 2.426381 GTCACCTAACGGGAAGGACTAG 59.574 54.545 6.93 0.00 37.57 2.57
737 5383 2.450476 GTCACCTAACGGGAAGGACTA 58.550 52.381 6.93 0.00 37.57 2.59
738 5384 1.264295 GTCACCTAACGGGAAGGACT 58.736 55.000 6.93 0.00 37.57 3.85
870 5516 1.134580 AGGAACGATCTACTCCGACGA 60.135 52.381 0.00 0.00 34.22 4.20
871 5517 1.261089 GAGGAACGATCTACTCCGACG 59.739 57.143 0.00 0.00 34.22 5.12
872 5518 2.563702 AGAGGAACGATCTACTCCGAC 58.436 52.381 0.00 0.00 34.22 4.79
873 5519 3.278668 AAGAGGAACGATCTACTCCGA 57.721 47.619 0.00 0.00 34.22 4.55
874 5520 4.352887 GAAAAGAGGAACGATCTACTCCG 58.647 47.826 0.00 0.00 34.22 4.63
875 5521 4.684877 GGAAAAGAGGAACGATCTACTCC 58.315 47.826 0.00 0.00 0.00 3.85
877 5523 3.762823 ACGGAAAAGAGGAACGATCTACT 59.237 43.478 0.00 0.00 0.00 2.57
958 5605 1.057851 TCCGCCTAGGGTTTATGGGG 61.058 60.000 11.72 0.08 41.52 4.96
998 5645 2.210711 CCCGCTACTCCCTCCATCC 61.211 68.421 0.00 0.00 0.00 3.51
1018 5665 1.004745 GAGTTTCAGCCCCCTCATCAA 59.995 52.381 0.00 0.00 0.00 2.57
1194 5851 3.331718 ACCTCCTTACAGTCTATCCCC 57.668 52.381 0.00 0.00 0.00 4.81
1245 5903 1.834263 CTCCTCCTTCCCGATTCTTGT 59.166 52.381 0.00 0.00 0.00 3.16
1413 6071 6.127647 TGTTGACAATATCCTTTGCTGATTCC 60.128 38.462 0.00 0.00 0.00 3.01
1423 6081 5.473504 GGCCGATAATGTTGACAATATCCTT 59.526 40.000 11.60 0.00 36.07 3.36
1433 6091 3.342377 TGAACTGGCCGATAATGTTGA 57.658 42.857 0.00 0.00 0.00 3.18
1508 6308 4.311613 TCTCTCATCCTCCTCTCCTTCTA 58.688 47.826 0.00 0.00 0.00 2.10
1582 6382 3.936453 GCCGACCACATGTATAACAGAAA 59.064 43.478 0.00 0.00 0.00 2.52
1970 6770 2.584391 GCTCCCACTTCCTGTCCGT 61.584 63.158 0.00 0.00 0.00 4.69
1971 6771 2.266055 GCTCCCACTTCCTGTCCG 59.734 66.667 0.00 0.00 0.00 4.79
2051 6851 2.661718 CTAGTGACCTCCTCTCCCTTC 58.338 57.143 0.00 0.00 0.00 3.46
2069 6869 1.282447 TGTTTATTCTTGGCCGGGCTA 59.718 47.619 29.87 21.26 0.00 3.93
2124 6924 4.020617 CGTGGCCTCCTCCAGCAA 62.021 66.667 3.32 0.00 36.67 3.91
2137 6937 2.670148 CCCCTCCTTTCCTCCGTGG 61.670 68.421 0.00 0.00 37.10 4.94
2139 6939 2.285442 CCCCCTCCTTTCCTCCGT 60.285 66.667 0.00 0.00 0.00 4.69
2167 6968 0.483328 CTCCCCCTCTCCCTTCGATA 59.517 60.000 0.00 0.00 0.00 2.92
2171 6972 2.041265 TGCTCCCCCTCTCCCTTC 59.959 66.667 0.00 0.00 0.00 3.46
2233 7034 1.077212 CCCATCTCAGCACCCTTGG 60.077 63.158 0.00 0.00 0.00 3.61
2237 7038 1.222936 CAGACCCATCTCAGCACCC 59.777 63.158 0.00 0.00 30.42 4.61
2304 7105 4.379339 TTTTGTTGCTGTTAGTGTTCCC 57.621 40.909 0.00 0.00 0.00 3.97
2347 7149 2.325101 ATCAGCCCTCTCCCTCCTCC 62.325 65.000 0.00 0.00 0.00 4.30
2418 7220 3.315470 TCGTCATCACTACTACTGATGCC 59.685 47.826 3.90 0.00 43.26 4.40
2434 7236 5.355596 CCTTCTTAGCTTCATTCTCGTCAT 58.644 41.667 0.00 0.00 0.00 3.06
2453 7255 3.020237 GCCCTCACTCCGTCCCTTC 62.020 68.421 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.