Multiple sequence alignment - TraesCS2A01G573200

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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 TraesCS2A01G573200 chr2A 100.000 3269 0 0 1 3269 768980815 768984083 0.000000e+00 6037
1 TraesCS2A01G573200 chr2A 90.937 1291 71 12 1233 2512 768728834 768730089 0.000000e+00 1694
2 TraesCS2A01G573200 chr2A 82.777 569 76 11 1952 2510 209384901 209384345 3.790000e-134 488
3 TraesCS2A01G573200 chr2A 86.183 427 34 18 626 1029 768728411 768728835 3.870000e-119 438
4 TraesCS2A01G573200 chr2A 87.162 148 18 1 2546 2693 768730267 768730413 2.020000e-37 167
5 TraesCS2A01G573200 chr2D 92.290 2555 105 43 626 3147 643852636 643855131 0.000000e+00 3542
6 TraesCS2A01G573200 chr2D 88.636 572 43 19 6 564 315089756 315090318 0.000000e+00 676
7 TraesCS2A01G573200 chr2D 87.165 522 43 17 4 517 191001792 191001287 3.660000e-159 571
8 TraesCS2A01G573200 chr2D 82.892 567 71 14 1952 2506 194752326 194751774 1.360000e-133 486
9 TraesCS2A01G573200 chr2D 94.697 132 6 1 3139 3269 643865428 643865559 1.540000e-48 204
10 TraesCS2A01G573200 chr2D 91.964 112 8 1 2169 2280 643780404 643780514 4.370000e-34 156
11 TraesCS2A01G573200 chr2B 92.786 1206 80 6 1843 3046 793230347 793229147 0.000000e+00 1738
12 TraesCS2A01G573200 chr2B 92.000 475 27 3 1380 1854 793256635 793256172 0.000000e+00 656
13 TraesCS2A01G573200 chr2B 87.370 578 51 12 4 572 582311640 582311076 0.000000e+00 643
14 TraesCS2A01G573200 chr2B 89.157 498 37 14 83 564 798375916 798376412 3.610000e-169 604
15 TraesCS2A01G573200 chr2B 85.532 470 58 4 1952 2412 250728996 250728528 1.760000e-132 483
16 TraesCS2A01G573200 chr2B 90.393 229 20 2 3042 3269 793184434 793184207 1.910000e-77 300
17 TraesCS2A01G573200 chr2B 91.925 161 13 0 1063 1223 793259065 793258905 3.280000e-55 226
18 TraesCS2A01G573200 chr1A 88.547 585 40 13 4 564 486401860 486401279 0.000000e+00 684
19 TraesCS2A01G573200 chr1A 88.225 586 47 16 1 564 284747041 284747626 0.000000e+00 680
20 TraesCS2A01G573200 chr1A 87.140 591 45 9 5 564 372064505 372065095 2.750000e-180 641
21 TraesCS2A01G573200 chr5D 90.726 496 30 8 1 485 456753447 456753937 0.000000e+00 647
22 TraesCS2A01G573200 chr5B 86.678 593 50 14 3 573 55187962 55188547 5.950000e-177 630
23 TraesCS2A01G573200 chr5B 82.630 403 38 19 177 564 55188020 55187635 8.750000e-86 327
24 TraesCS2A01G573200 chr7A 85.940 569 57 13 1 564 126961074 126961624 1.310000e-163 586
25 TraesCS2A01G573200 chr3D 89.109 202 17 4 368 564 13170760 13170961 2.520000e-61 246
26 TraesCS2A01G573200 chr4A 85.345 232 26 6 1497 1728 590268539 590268316 1.960000e-57 233


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 TraesCS2A01G573200 chr2A 768980815 768984083 3268 False 6037.000000 6037 100.0000 1 3269 1 chr2A.!!$F1 3268
1 TraesCS2A01G573200 chr2A 768728411 768730413 2002 False 766.333333 1694 88.0940 626 2693 3 chr2A.!!$F2 2067
2 TraesCS2A01G573200 chr2A 209384345 209384901 556 True 488.000000 488 82.7770 1952 2510 1 chr2A.!!$R1 558
3 TraesCS2A01G573200 chr2D 643852636 643855131 2495 False 3542.000000 3542 92.2900 626 3147 1 chr2D.!!$F3 2521
4 TraesCS2A01G573200 chr2D 315089756 315090318 562 False 676.000000 676 88.6360 6 564 1 chr2D.!!$F1 558
5 TraesCS2A01G573200 chr2D 191001287 191001792 505 True 571.000000 571 87.1650 4 517 1 chr2D.!!$R1 513
6 TraesCS2A01G573200 chr2D 194751774 194752326 552 True 486.000000 486 82.8920 1952 2506 1 chr2D.!!$R2 554
7 TraesCS2A01G573200 chr2B 793229147 793230347 1200 True 1738.000000 1738 92.7860 1843 3046 1 chr2B.!!$R4 1203
8 TraesCS2A01G573200 chr2B 582311076 582311640 564 True 643.000000 643 87.3700 4 572 1 chr2B.!!$R2 568
9 TraesCS2A01G573200 chr2B 793256172 793259065 2893 True 441.000000 656 91.9625 1063 1854 2 chr2B.!!$R5 791
10 TraesCS2A01G573200 chr1A 486401279 486401860 581 True 684.000000 684 88.5470 4 564 1 chr1A.!!$R1 560
11 TraesCS2A01G573200 chr1A 284747041 284747626 585 False 680.000000 680 88.2250 1 564 1 chr1A.!!$F1 563
12 TraesCS2A01G573200 chr1A 372064505 372065095 590 False 641.000000 641 87.1400 5 564 1 chr1A.!!$F2 559
13 TraesCS2A01G573200 chr5B 55187962 55188547 585 False 630.000000 630 86.6780 3 573 1 chr5B.!!$F1 570
14 TraesCS2A01G573200 chr7A 126961074 126961624 550 False 586.000000 586 85.9400 1 564 1 chr7A.!!$F1 563

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
586 656 0.109319 AATAAAAGCCAGGCGCAACG 60.109 50.0 10.83 0.0 41.38 4.10 F
1013 1106 0.379669 GCAGGAATGGACAAGCATCG 59.620 55.0 0.00 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2167 4439 1.400846 GTGCGAGATGGAGAACGTAGA 59.599 52.381 0.00 0.00 0.0 2.59 R
2870 5297 0.108424 GCACACTGGCTCGAGAAGAT 60.108 55.000 18.75 4.17 0.0 2.40 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
231 238 5.467735 GCATCTTTGATGCCAAAAAGTTTCT 59.532 36.000 18.54 0.00 41.28 2.52
232 239 6.017687 GCATCTTTGATGCCAAAAAGTTTCTT 60.018 34.615 18.54 0.00 41.28 2.52
233 240 7.467675 GCATCTTTGATGCCAAAAAGTTTCTTT 60.468 33.333 18.54 0.00 41.28 2.52
234 241 7.920160 TCTTTGATGCCAAAAAGTTTCTTTT 57.080 28.000 2.21 2.21 41.28 2.27
235 242 8.334263 TCTTTGATGCCAAAAAGTTTCTTTTT 57.666 26.923 12.51 12.51 41.28 1.94
285 320 9.290988 ACTGTTCACCAACATACATATTTACAA 57.709 29.630 0.00 0.00 41.82 2.41
286 321 9.554724 CTGTTCACCAACATACATATTTACAAC 57.445 33.333 0.00 0.00 41.82 3.32
329 364 3.595173 TCGAATGTCGAAACACCATGAT 58.405 40.909 0.00 0.00 46.90 2.45
366 402 1.670087 CGCACCAGAGTGTCTTCGATT 60.670 52.381 0.00 0.00 46.35 3.34
374 410 6.102663 CCAGAGTGTCTTCGATTCTGTAAAT 58.897 40.000 0.00 0.00 34.81 1.40
377 413 8.165428 CAGAGTGTCTTCGATTCTGTAAATTTC 58.835 37.037 0.00 0.00 32.60 2.17
378 414 7.872993 AGAGTGTCTTCGATTCTGTAAATTTCA 59.127 33.333 0.00 0.00 0.00 2.69
379 415 8.023050 AGTGTCTTCGATTCTGTAAATTTCAG 57.977 34.615 0.00 2.77 0.00 3.02
380 416 7.872993 AGTGTCTTCGATTCTGTAAATTTCAGA 59.127 33.333 13.14 13.14 39.71 3.27
528 598 5.011738 AGTTGAGGGACGATTTCTAAACTCA 59.988 40.000 0.00 0.00 32.47 3.41
531 601 3.508793 AGGGACGATTTCTAAACTCACGA 59.491 43.478 0.00 0.00 0.00 4.35
564 634 7.592533 TCGAAGACGAAAAATATACTTATCCCG 59.407 37.037 0.00 0.00 45.74 5.14
577 647 9.802039 ATATACTTATCCCGAAAATAAAAGCCA 57.198 29.630 0.00 0.00 0.00 4.75
578 648 6.451064 ACTTATCCCGAAAATAAAAGCCAG 57.549 37.500 0.00 0.00 0.00 4.85
579 649 5.359860 ACTTATCCCGAAAATAAAAGCCAGG 59.640 40.000 0.00 0.00 0.00 4.45
580 650 1.822371 TCCCGAAAATAAAAGCCAGGC 59.178 47.619 1.84 1.84 0.00 4.85
581 651 1.469079 CCCGAAAATAAAAGCCAGGCG 60.469 52.381 5.55 0.00 0.00 5.52
582 652 1.268265 CGAAAATAAAAGCCAGGCGC 58.732 50.000 5.55 0.00 37.98 6.53
583 653 1.402194 CGAAAATAAAAGCCAGGCGCA 60.402 47.619 10.83 0.00 41.38 6.09
584 654 2.682836 GAAAATAAAAGCCAGGCGCAA 58.317 42.857 10.83 0.00 41.38 4.85
585 655 2.078849 AAATAAAAGCCAGGCGCAAC 57.921 45.000 10.83 0.00 41.38 4.17
586 656 0.109319 AATAAAAGCCAGGCGCAACG 60.109 50.000 10.83 0.00 41.38 4.10
605 675 1.326548 CGCAAGTTATTCCAGTACCGC 59.673 52.381 0.00 0.00 0.00 5.68
606 676 1.326548 GCAAGTTATTCCAGTACCGCG 59.673 52.381 0.00 0.00 0.00 6.46
607 677 2.883574 CAAGTTATTCCAGTACCGCGA 58.116 47.619 8.23 0.00 0.00 5.87
608 678 2.573941 AGTTATTCCAGTACCGCGAC 57.426 50.000 8.23 0.00 0.00 5.19
609 679 1.194495 GTTATTCCAGTACCGCGACG 58.806 55.000 8.23 0.00 0.00 5.12
610 680 0.526096 TTATTCCAGTACCGCGACGC 60.526 55.000 8.23 10.49 0.00 5.19
611 681 2.340453 TATTCCAGTACCGCGACGCC 62.340 60.000 15.34 0.00 0.00 5.68
658 728 3.470888 CTCGACCCCGCCTGGAAT 61.471 66.667 0.00 0.00 37.49 3.01
668 738 2.278857 CCTGGAATCGCCGTCTCG 60.279 66.667 0.00 0.00 40.66 4.04
728 806 0.976641 AATTGTGCTCTCCTCGGTCA 59.023 50.000 0.00 0.00 0.00 4.02
791 869 7.442364 TCGAGGATTGAGGAAATTCATAATCAC 59.558 37.037 13.79 8.78 0.00 3.06
828 906 1.275856 GGCATGGAGGCAACAAAATGA 59.724 47.619 0.00 0.00 43.51 2.57
829 907 2.340337 GCATGGAGGCAACAAAATGAC 58.660 47.619 0.00 0.00 41.41 3.06
850 928 4.526970 ACGGCAGTATTTTGATCCAATCT 58.473 39.130 0.00 0.00 0.00 2.40
877 955 8.749499 CACATCTCAAAATTGTTCTTTGTCTTC 58.251 33.333 0.00 0.00 35.65 2.87
878 956 8.689972 ACATCTCAAAATTGTTCTTTGTCTTCT 58.310 29.630 0.00 0.00 35.65 2.85
880 958 6.974622 TCTCAAAATTGTTCTTTGTCTTCTGC 59.025 34.615 0.00 0.00 35.65 4.26
887 965 4.462483 TGTTCTTTGTCTTCTGCCAGTTTT 59.538 37.500 0.00 0.00 0.00 2.43
888 966 4.900635 TCTTTGTCTTCTGCCAGTTTTC 57.099 40.909 0.00 0.00 0.00 2.29
890 968 5.680619 TCTTTGTCTTCTGCCAGTTTTCTA 58.319 37.500 0.00 0.00 0.00 2.10
891 969 6.299141 TCTTTGTCTTCTGCCAGTTTTCTAT 58.701 36.000 0.00 0.00 0.00 1.98
893 971 5.947228 TGTCTTCTGCCAGTTTTCTATTG 57.053 39.130 0.00 0.00 0.00 1.90
894 972 4.216257 TGTCTTCTGCCAGTTTTCTATTGC 59.784 41.667 0.00 0.00 0.00 3.56
909 988 3.895041 TCTATTGCCGTATCCATCTCACA 59.105 43.478 0.00 0.00 0.00 3.58
914 993 2.666026 CCGTATCCATCTCACATCACG 58.334 52.381 0.00 0.00 0.00 4.35
937 1016 1.729586 AATCGCCTTAGCCCTATCCA 58.270 50.000 0.00 0.00 34.57 3.41
938 1017 1.729586 ATCGCCTTAGCCCTATCCAA 58.270 50.000 0.00 0.00 34.57 3.53
939 1018 1.729586 TCGCCTTAGCCCTATCCAAT 58.270 50.000 0.00 0.00 34.57 3.16
940 1019 1.623811 TCGCCTTAGCCCTATCCAATC 59.376 52.381 0.00 0.00 34.57 2.67
941 1020 1.625818 CGCCTTAGCCCTATCCAATCT 59.374 52.381 0.00 0.00 34.57 2.40
942 1021 2.354203 CGCCTTAGCCCTATCCAATCTC 60.354 54.545 0.00 0.00 34.57 2.75
943 1022 2.639839 GCCTTAGCCCTATCCAATCTCA 59.360 50.000 0.00 0.00 0.00 3.27
944 1023 3.558109 GCCTTAGCCCTATCCAATCTCAC 60.558 52.174 0.00 0.00 0.00 3.51
945 1024 3.648067 CCTTAGCCCTATCCAATCTCACA 59.352 47.826 0.00 0.00 0.00 3.58
947 1026 5.486526 CTTAGCCCTATCCAATCTCACATC 58.513 45.833 0.00 0.00 0.00 3.06
950 1029 3.326006 GCCCTATCCAATCTCACATCTCA 59.674 47.826 0.00 0.00 0.00 3.27
951 1030 4.202398 GCCCTATCCAATCTCACATCTCAA 60.202 45.833 0.00 0.00 0.00 3.02
952 1031 5.688500 GCCCTATCCAATCTCACATCTCAAA 60.689 44.000 0.00 0.00 0.00 2.69
953 1032 6.540995 CCCTATCCAATCTCACATCTCAAAT 58.459 40.000 0.00 0.00 0.00 2.32
954 1033 7.002879 CCCTATCCAATCTCACATCTCAAATT 58.997 38.462 0.00 0.00 0.00 1.82
955 1034 7.040617 CCCTATCCAATCTCACATCTCAAATTG 60.041 40.741 0.00 0.00 0.00 2.32
956 1035 5.571784 TCCAATCTCACATCTCAAATTGC 57.428 39.130 0.00 0.00 0.00 3.56
957 1036 5.258841 TCCAATCTCACATCTCAAATTGCT 58.741 37.500 0.00 0.00 0.00 3.91
958 1037 6.417258 TCCAATCTCACATCTCAAATTGCTA 58.583 36.000 0.00 0.00 0.00 3.49
1009 1102 1.538047 TTCTGCAGGAATGGACAAGC 58.462 50.000 15.13 0.00 0.00 4.01
1013 1106 0.379669 GCAGGAATGGACAAGCATCG 59.620 55.000 0.00 0.00 0.00 3.84
1038 1131 2.281761 ACTCGCTTTGCACCCCTG 60.282 61.111 0.00 0.00 0.00 4.45
1055 1148 1.148310 CTGAACGACGCTCCATTTGT 58.852 50.000 0.00 0.00 0.00 2.83
1061 1154 0.721718 GACGCTCCATTTGTTCTCCG 59.278 55.000 0.00 0.00 0.00 4.63
1069 1162 3.325425 TCCATTTGTTCTCCGTGGTAAGA 59.675 43.478 0.00 0.00 0.00 2.10
1094 1189 9.984190 GAATTTCCTATCTTATTCGTACTTCCT 57.016 33.333 0.00 0.00 0.00 3.36
1110 1206 5.153950 ACTTCCTGAATCTGAACCAGTAC 57.846 43.478 8.26 0.00 32.61 2.73
1115 1211 4.627467 CCTGAATCTGAACCAGTACTTTCG 59.373 45.833 0.00 0.00 32.61 3.46
1132 1228 9.383519 AGTACTTTCGACATATCAAACAATCAT 57.616 29.630 0.00 0.00 0.00 2.45
1195 1291 2.509569 TCCACCTTTTAAGCGCATTCA 58.490 42.857 11.47 0.00 0.00 2.57
1200 1296 6.042143 CCACCTTTTAAGCGCATTCATATTT 58.958 36.000 11.47 0.00 0.00 1.40
1223 3468 4.783055 TGCAGGTTGTGTAAAGGACTAAA 58.217 39.130 0.00 0.00 0.00 1.85
1224 3469 4.577283 TGCAGGTTGTGTAAAGGACTAAAC 59.423 41.667 0.00 0.00 0.00 2.01
1226 3471 5.066764 GCAGGTTGTGTAAAGGACTAAACAA 59.933 40.000 0.00 0.00 0.00 2.83
1240 3485 4.327680 ACTAAACAATGAGGTTCAGGCTC 58.672 43.478 0.00 0.00 0.00 4.70
1253 3498 4.142881 GGTTCAGGCTCGAAAGAATGTTAC 60.143 45.833 1.78 0.00 41.32 2.50
1254 3499 4.537135 TCAGGCTCGAAAGAATGTTACT 57.463 40.909 0.00 0.00 41.32 2.24
1255 3500 4.495422 TCAGGCTCGAAAGAATGTTACTC 58.505 43.478 0.00 0.00 41.32 2.59
1256 3501 4.021456 TCAGGCTCGAAAGAATGTTACTCA 60.021 41.667 0.00 0.00 41.32 3.41
1257 3502 4.872691 CAGGCTCGAAAGAATGTTACTCAT 59.127 41.667 0.00 0.00 41.32 2.90
1258 3503 6.042777 CAGGCTCGAAAGAATGTTACTCATA 58.957 40.000 0.00 0.00 41.32 2.15
1434 3684 7.262772 TGGTATTATACTAGTATCGGCATTGC 58.737 38.462 18.68 0.00 0.00 3.56
1832 4104 7.441760 AGCATCTGAATCACATGAGAATACTTC 59.558 37.037 0.00 0.00 0.00 3.01
1894 4166 5.453903 CCTGTTGCCTGATAATAGCTACACT 60.454 44.000 0.00 0.00 37.34 3.55
2167 4439 1.141657 TGAAGAAGCCACAGTTGAGCT 59.858 47.619 0.00 0.00 38.88 4.09
2366 4649 0.392998 AACATCTTACCAGGCCTGCG 60.393 55.000 28.39 21.83 0.00 5.18
2496 4779 1.901591 TCCTCTGCTTTGGCTTGAAG 58.098 50.000 0.00 0.00 39.59 3.02
2525 4808 2.153645 TGCTCATTCGACAGCAACATT 58.846 42.857 9.84 0.00 42.74 2.71
2662 5089 9.468532 TGTAGAACAAATCAGATGAGATAATCG 57.531 33.333 0.00 0.00 0.00 3.34
2781 5208 4.202202 CGCTCAATCATCCTCTACCTTTCT 60.202 45.833 0.00 0.00 0.00 2.52
2805 5232 3.169378 TGCCTGGGAGCAATGTCA 58.831 55.556 0.00 0.00 40.56 3.58
2861 5288 4.143543 TGGCATCAGATTCAAAACTCACA 58.856 39.130 0.00 0.00 0.00 3.58
2869 5296 6.038603 TCAGATTCAAAACTCACAAAGTCAGG 59.961 38.462 0.00 0.00 37.17 3.86
2870 5297 6.038603 CAGATTCAAAACTCACAAAGTCAGGA 59.961 38.462 0.00 0.00 37.17 3.86
2888 5315 1.919918 GATCTTCTCGAGCCAGTGTG 58.080 55.000 7.81 0.00 0.00 3.82
2937 5364 4.540359 TCCAGCCAAAATTTGATCTTGG 57.460 40.909 7.37 8.86 42.17 3.61
2939 5366 5.083122 TCCAGCCAAAATTTGATCTTGGTA 58.917 37.500 7.37 0.00 41.46 3.25
3076 5504 6.430000 TCTCCAATTGATGATGCAGATGTATG 59.570 38.462 7.12 0.00 0.00 2.39
3084 5512 8.319143 TGATGATGCAGATGTATGAATTACAG 57.681 34.615 0.00 0.00 43.87 2.74
3200 5628 8.402798 ACATCACCAAGTAATGAAAATACACA 57.597 30.769 0.00 0.00 0.00 3.72
3201 5629 9.023962 ACATCACCAAGTAATGAAAATACACAT 57.976 29.630 0.00 0.00 0.00 3.21
3202 5630 9.507280 CATCACCAAGTAATGAAAATACACATC 57.493 33.333 0.00 0.00 0.00 3.06
3203 5631 8.628630 TCACCAAGTAATGAAAATACACATCA 57.371 30.769 0.00 0.00 0.00 3.07
3204 5632 8.511321 TCACCAAGTAATGAAAATACACATCAC 58.489 33.333 0.00 0.00 0.00 3.06
3205 5633 8.514594 CACCAAGTAATGAAAATACACATCACT 58.485 33.333 0.00 0.00 0.00 3.41
3206 5634 9.077885 ACCAAGTAATGAAAATACACATCACTT 57.922 29.630 0.00 0.00 0.00 3.16
3207 5635 9.345517 CCAAGTAATGAAAATACACATCACTTG 57.654 33.333 13.14 13.14 30.56 3.16
3208 5636 8.853345 CAAGTAATGAAAATACACATCACTTGC 58.147 33.333 9.28 0.00 0.00 4.01
3209 5637 7.538575 AGTAATGAAAATACACATCACTTGCC 58.461 34.615 0.00 0.00 0.00 4.52
3210 5638 4.418013 TGAAAATACACATCACTTGCCG 57.582 40.909 0.00 0.00 0.00 5.69
3211 5639 2.919666 AAATACACATCACTTGCCGC 57.080 45.000 0.00 0.00 0.00 6.53
3212 5640 1.819928 AATACACATCACTTGCCGCA 58.180 45.000 0.00 0.00 0.00 5.69
3213 5641 1.086696 ATACACATCACTTGCCGCAC 58.913 50.000 0.00 0.00 0.00 5.34
3214 5642 1.288419 TACACATCACTTGCCGCACG 61.288 55.000 0.00 0.00 0.00 5.34
3215 5643 2.280797 ACATCACTTGCCGCACGT 60.281 55.556 0.00 0.00 0.00 4.49
3216 5644 2.174107 CATCACTTGCCGCACGTG 59.826 61.111 20.90 20.90 35.40 4.49
3217 5645 2.030412 ATCACTTGCCGCACGTGA 59.970 55.556 28.56 28.56 44.37 4.35
3218 5646 1.375908 ATCACTTGCCGCACGTGAT 60.376 52.632 29.98 29.98 44.23 3.06
3219 5647 1.638388 ATCACTTGCCGCACGTGATG 61.638 55.000 32.97 10.68 46.48 3.07
3220 5648 2.280797 ACTTGCCGCACGTGATGT 60.281 55.556 22.23 3.61 0.00 3.06
3221 5649 1.005512 ACTTGCCGCACGTGATGTA 60.006 52.632 22.23 5.51 0.00 2.29
3222 5650 0.601576 ACTTGCCGCACGTGATGTAA 60.602 50.000 22.23 13.36 0.00 2.41
3223 5651 0.515127 CTTGCCGCACGTGATGTAAA 59.485 50.000 22.23 5.38 0.00 2.01
3224 5652 0.945099 TTGCCGCACGTGATGTAAAA 59.055 45.000 22.23 2.15 0.00 1.52
3225 5653 0.236187 TGCCGCACGTGATGTAAAAC 59.764 50.000 22.23 0.00 0.00 2.43
3226 5654 0.787908 GCCGCACGTGATGTAAAACG 60.788 55.000 22.23 10.38 45.15 3.60
3227 5655 0.179235 CCGCACGTGATGTAAAACGG 60.179 55.000 22.23 15.92 43.96 4.44
3228 5656 0.787908 CGCACGTGATGTAAAACGGC 60.788 55.000 22.23 0.00 43.96 5.68
3229 5657 0.453782 GCACGTGATGTAAAACGGCC 60.454 55.000 22.23 0.00 43.96 6.13
3230 5658 0.179235 CACGTGATGTAAAACGGCCG 60.179 55.000 26.86 26.86 43.96 6.13
3231 5659 1.293267 ACGTGATGTAAAACGGCCGG 61.293 55.000 31.76 11.88 43.96 6.13
3232 5660 1.135939 GTGATGTAAAACGGCCGGC 59.864 57.895 31.76 21.18 0.00 6.13
3233 5661 1.302591 TGATGTAAAACGGCCGGCA 60.303 52.632 31.76 19.18 0.00 5.69
3234 5662 1.302383 TGATGTAAAACGGCCGGCAG 61.302 55.000 31.76 28.22 0.00 4.85
3235 5663 2.592623 GATGTAAAACGGCCGGCAGC 62.593 60.000 31.76 17.85 42.60 5.25
3255 5683 2.127758 CGCGAACGCCAAACTGTC 60.128 61.111 13.40 0.00 37.98 3.51
3256 5684 2.127758 GCGAACGCCAAACTGTCG 60.128 61.111 8.03 0.00 34.56 4.35
3257 5685 2.877974 GCGAACGCCAAACTGTCGT 61.878 57.895 8.03 0.00 38.15 4.34
3260 5688 1.639534 AACGCCAAACTGTCGTTCG 59.360 52.632 0.00 0.00 41.86 3.95
3261 5689 1.768112 AACGCCAAACTGTCGTTCGG 61.768 55.000 0.00 0.00 41.86 4.30
3262 5690 1.952133 CGCCAAACTGTCGTTCGGA 60.952 57.895 0.00 0.00 28.11 4.55
3263 5691 1.492319 CGCCAAACTGTCGTTCGGAA 61.492 55.000 0.00 0.00 28.11 4.30
3264 5692 0.658897 GCCAAACTGTCGTTCGGAAA 59.341 50.000 0.00 0.00 28.11 3.13
3265 5693 1.265905 GCCAAACTGTCGTTCGGAAAT 59.734 47.619 0.00 0.00 28.11 2.17
3266 5694 2.287368 GCCAAACTGTCGTTCGGAAATT 60.287 45.455 0.00 0.00 28.11 1.82
3267 5695 3.794138 GCCAAACTGTCGTTCGGAAATTT 60.794 43.478 0.00 0.00 28.11 1.82
3268 5696 3.972502 CCAAACTGTCGTTCGGAAATTTC 59.027 43.478 9.83 9.83 28.11 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 126 7.043059 CCAAGAAACAAAATAGCGCACTTTTTA 60.043 33.333 11.47 0.00 0.00 1.52
285 320 3.758300 CAGCTCGTGACAAACAAAAAGT 58.242 40.909 0.00 0.00 0.00 2.66
286 321 2.531508 GCAGCTCGTGACAAACAAAAAG 59.468 45.455 0.00 0.00 0.00 2.27
329 364 0.525761 GCGCAAGACCCTGCAAAATA 59.474 50.000 0.30 0.00 42.77 1.40
406 458 7.698836 TTTAGTACTCGGTGAACAGTAAAAC 57.301 36.000 0.00 0.00 0.00 2.43
451 518 8.438676 CTATCAAAACCGGATAGTTTTCATCT 57.561 34.615 9.46 0.00 45.73 2.90
542 612 9.603921 TTTTCGGGATAAGTATATTTTTCGTCT 57.396 29.630 0.00 0.00 0.00 4.18
564 634 2.362169 TGCGCCTGGCTTTTATTTTC 57.638 45.000 17.92 0.00 44.05 2.29
569 639 2.950673 CGTTGCGCCTGGCTTTTA 59.049 55.556 17.92 0.00 44.05 1.52
580 650 1.196808 ACTGGAATAACTTGCGTTGCG 59.803 47.619 0.00 0.00 34.59 4.85
581 651 2.989422 ACTGGAATAACTTGCGTTGC 57.011 45.000 0.00 0.00 34.59 4.17
582 652 3.181524 CGGTACTGGAATAACTTGCGTTG 60.182 47.826 0.00 0.00 34.59 4.10
583 653 2.997986 CGGTACTGGAATAACTTGCGTT 59.002 45.455 0.00 0.00 37.15 4.84
584 654 2.613691 CGGTACTGGAATAACTTGCGT 58.386 47.619 0.00 0.00 0.00 5.24
585 655 1.326548 GCGGTACTGGAATAACTTGCG 59.673 52.381 3.34 0.00 0.00 4.85
586 656 1.326548 CGCGGTACTGGAATAACTTGC 59.673 52.381 3.34 0.00 0.00 4.01
587 657 2.601763 GTCGCGGTACTGGAATAACTTG 59.398 50.000 6.13 0.00 0.00 3.16
588 658 2.733227 CGTCGCGGTACTGGAATAACTT 60.733 50.000 6.13 0.00 0.00 2.66
589 659 1.202222 CGTCGCGGTACTGGAATAACT 60.202 52.381 6.13 0.00 0.00 2.24
590 660 1.194495 CGTCGCGGTACTGGAATAAC 58.806 55.000 6.13 0.00 0.00 1.89
591 661 0.526096 GCGTCGCGGTACTGGAATAA 60.526 55.000 6.13 0.00 0.00 1.40
592 662 1.064621 GCGTCGCGGTACTGGAATA 59.935 57.895 6.13 0.00 0.00 1.75
593 663 2.202703 GCGTCGCGGTACTGGAAT 60.203 61.111 6.13 0.00 0.00 3.01
594 664 4.424566 GGCGTCGCGGTACTGGAA 62.425 66.667 11.75 0.00 0.00 3.53
619 689 2.825836 GATTCCAGGCGGCTGTGG 60.826 66.667 33.68 22.74 34.87 4.17
620 690 3.197790 CGATTCCAGGCGGCTGTG 61.198 66.667 33.68 25.11 0.00 3.66
621 691 4.473520 CCGATTCCAGGCGGCTGT 62.474 66.667 33.68 18.63 41.17 4.40
641 711 3.447025 GATTCCAGGCGGGGTCGAG 62.447 68.421 3.19 0.00 39.00 4.04
651 721 2.278857 CGAGACGGCGATTCCAGG 60.279 66.667 16.62 0.00 34.01 4.45
683 753 4.917906 AAGGAAGTAACCTTGATCTGCT 57.082 40.909 0.00 0.00 46.85 4.24
728 806 1.167851 CAGCAAACATCACACGGGAT 58.832 50.000 0.00 0.00 0.00 3.85
736 814 1.898094 ACGCAGGCAGCAAACATCA 60.898 52.632 1.96 0.00 46.13 3.07
791 869 4.212847 CCATGCCTATTTTCGAGTCATCAG 59.787 45.833 0.00 0.00 0.00 2.90
825 903 3.884895 TGGATCAAAATACTGCCGTCAT 58.115 40.909 0.00 0.00 0.00 3.06
826 904 3.342377 TGGATCAAAATACTGCCGTCA 57.658 42.857 0.00 0.00 0.00 4.35
828 906 4.526970 AGATTGGATCAAAATACTGCCGT 58.473 39.130 0.00 0.00 0.00 5.68
829 907 4.576053 TGAGATTGGATCAAAATACTGCCG 59.424 41.667 0.00 0.00 0.00 5.69
850 928 7.999679 AGACAAAGAACAATTTTGAGATGTGA 58.000 30.769 4.87 0.00 38.55 3.58
877 955 1.812571 ACGGCAATAGAAAACTGGCAG 59.187 47.619 14.16 14.16 35.48 4.85
878 956 1.904287 ACGGCAATAGAAAACTGGCA 58.096 45.000 0.00 0.00 35.48 4.92
880 958 4.196193 TGGATACGGCAATAGAAAACTGG 58.804 43.478 0.00 0.00 42.51 4.00
887 965 3.895041 TGTGAGATGGATACGGCAATAGA 59.105 43.478 0.00 0.00 42.51 1.98
888 966 4.257267 TGTGAGATGGATACGGCAATAG 57.743 45.455 0.00 0.00 42.51 1.73
890 968 3.071457 TGATGTGAGATGGATACGGCAAT 59.929 43.478 0.00 0.00 42.51 3.56
891 969 2.433970 TGATGTGAGATGGATACGGCAA 59.566 45.455 0.00 0.00 42.51 4.52
893 971 2.408050 GTGATGTGAGATGGATACGGC 58.592 52.381 0.00 0.00 42.51 5.68
894 972 2.293399 TCGTGATGTGAGATGGATACGG 59.707 50.000 0.00 0.00 42.51 4.02
909 988 1.933853 GCTAAGGCGATTTGTCGTGAT 59.066 47.619 0.00 0.00 35.26 3.06
914 993 2.614829 TAGGGCTAAGGCGATTTGTC 57.385 50.000 0.00 0.00 39.81 3.18
925 1004 5.158141 AGATGTGAGATTGGATAGGGCTAA 58.842 41.667 0.00 0.00 0.00 3.09
937 1016 8.746530 ACATTTAGCAATTTGAGATGTGAGATT 58.253 29.630 0.00 0.00 0.00 2.40
938 1017 8.289939 ACATTTAGCAATTTGAGATGTGAGAT 57.710 30.769 0.00 0.00 0.00 2.75
939 1018 7.692460 ACATTTAGCAATTTGAGATGTGAGA 57.308 32.000 0.00 0.00 0.00 3.27
940 1019 9.844790 TTTACATTTAGCAATTTGAGATGTGAG 57.155 29.630 0.00 0.00 0.00 3.51
978 1071 6.127253 CCATTCCTGCAGAAATAAGAACCAAT 60.127 38.462 17.39 0.00 38.21 3.16
988 1081 2.494870 GCTTGTCCATTCCTGCAGAAAT 59.505 45.455 17.39 2.89 38.21 2.17
993 1086 1.466856 GATGCTTGTCCATTCCTGCA 58.533 50.000 0.00 0.00 34.88 4.41
1009 1102 1.904852 AAGCGAGTGTTGCTGCGATG 61.905 55.000 0.00 0.00 43.14 3.84
1013 1106 2.012948 GCAAAGCGAGTGTTGCTGC 61.013 57.895 1.26 0.00 45.34 5.25
1031 1124 2.432628 GAGCGTCGTTCAGGGGTG 60.433 66.667 4.01 0.00 0.00 4.61
1038 1131 1.798813 AGAACAAATGGAGCGTCGTTC 59.201 47.619 0.00 0.00 34.38 3.95
1055 1148 4.903045 AGGAAATTCTTACCACGGAGAA 57.097 40.909 0.00 0.00 36.43 2.87
1061 1154 9.543783 ACGAATAAGATAGGAAATTCTTACCAC 57.456 33.333 0.00 0.00 37.29 4.16
1069 1162 9.765795 CAGGAAGTACGAATAAGATAGGAAATT 57.234 33.333 0.00 0.00 0.00 1.82
1094 1189 5.221362 TGTCGAAAGTACTGGTTCAGATTCA 60.221 40.000 0.00 0.00 35.18 2.57
1110 1206 6.415867 GGCATGATTGTTTGATATGTCGAAAG 59.584 38.462 0.00 0.00 29.63 2.62
1115 1211 5.893687 TGTGGCATGATTGTTTGATATGTC 58.106 37.500 0.00 0.00 0.00 3.06
1132 1228 4.639755 CACCTATACAATTCACATGTGGCA 59.360 41.667 25.16 13.05 32.27 4.92
1195 1291 6.493458 AGTCCTTTACACAACCTGCAAAATAT 59.507 34.615 0.00 0.00 0.00 1.28
1200 1296 3.290948 AGTCCTTTACACAACCTGCAA 57.709 42.857 0.00 0.00 0.00 4.08
1223 3468 0.976641 TCGAGCCTGAACCTCATTGT 59.023 50.000 0.00 0.00 0.00 2.71
1224 3469 2.099141 TTCGAGCCTGAACCTCATTG 57.901 50.000 0.00 0.00 0.00 2.82
1226 3471 1.902508 TCTTTCGAGCCTGAACCTCAT 59.097 47.619 0.00 0.00 0.00 2.90
1258 3503 9.448587 ACACCAAATAAACCTACCTATCTATCT 57.551 33.333 0.00 0.00 0.00 1.98
1269 3514 8.434392 ACTCTCTTAACACACCAAATAAACCTA 58.566 33.333 0.00 0.00 0.00 3.08
1434 3684 5.278364 GCAGAATAGCAAGATTGATGGAAGG 60.278 44.000 0.00 0.00 0.00 3.46
1679 3929 6.798427 AGCTACAGATGAAAGGATCACTTA 57.202 37.500 0.00 0.00 41.93 2.24
2167 4439 1.400846 GTGCGAGATGGAGAACGTAGA 59.599 52.381 0.00 0.00 0.00 2.59
2496 4779 1.464997 GTCGAATGAGCAAGGACAACC 59.535 52.381 0.00 0.00 0.00 3.77
2781 5208 2.066700 TTGCTCCCAGGCATGACACA 62.067 55.000 0.00 0.00 42.09 3.72
2805 5232 2.025155 CCAGTGACCTACAGATACGCT 58.975 52.381 0.00 0.00 0.00 5.07
2861 5288 2.167487 GGCTCGAGAAGATCCTGACTTT 59.833 50.000 18.75 0.00 32.53 2.66
2869 5296 1.919918 CACACTGGCTCGAGAAGATC 58.080 55.000 18.75 0.00 0.00 2.75
2870 5297 0.108424 GCACACTGGCTCGAGAAGAT 60.108 55.000 18.75 4.17 0.00 2.40
2896 5323 0.757188 AGAGGAGTAGACATGGCCCG 60.757 60.000 0.00 0.00 0.00 6.13
3174 5602 9.508642 TGTGTATTTTCATTACTTGGTGATGTA 57.491 29.630 3.15 0.00 32.49 2.29
3175 5603 8.402798 TGTGTATTTTCATTACTTGGTGATGT 57.597 30.769 3.15 0.00 32.49 3.06
3176 5604 9.507280 GATGTGTATTTTCATTACTTGGTGATG 57.493 33.333 0.00 0.00 31.99 3.07
3177 5605 9.241919 TGATGTGTATTTTCATTACTTGGTGAT 57.758 29.630 0.00 0.00 0.00 3.06
3178 5606 8.511321 GTGATGTGTATTTTCATTACTTGGTGA 58.489 33.333 0.00 0.00 31.11 4.02
3179 5607 8.514594 AGTGATGTGTATTTTCATTACTTGGTG 58.485 33.333 0.00 0.00 37.53 4.17
3180 5608 8.635765 AGTGATGTGTATTTTCATTACTTGGT 57.364 30.769 0.00 0.00 37.53 3.67
3183 5611 8.028938 GGCAAGTGATGTGTATTTTCATTACTT 58.971 33.333 8.68 8.68 45.15 2.24
3184 5612 7.538575 GGCAAGTGATGTGTATTTTCATTACT 58.461 34.615 0.00 0.00 40.73 2.24
3185 5613 6.468956 CGGCAAGTGATGTGTATTTTCATTAC 59.531 38.462 0.00 0.00 32.98 1.89
3186 5614 6.550843 CGGCAAGTGATGTGTATTTTCATTA 58.449 36.000 0.00 0.00 0.00 1.90
3187 5615 5.401550 CGGCAAGTGATGTGTATTTTCATT 58.598 37.500 0.00 0.00 0.00 2.57
3188 5616 4.675146 GCGGCAAGTGATGTGTATTTTCAT 60.675 41.667 0.00 0.00 0.00 2.57
3189 5617 3.365868 GCGGCAAGTGATGTGTATTTTCA 60.366 43.478 0.00 0.00 0.00 2.69
3190 5618 3.171277 GCGGCAAGTGATGTGTATTTTC 58.829 45.455 0.00 0.00 0.00 2.29
3191 5619 2.556189 TGCGGCAAGTGATGTGTATTTT 59.444 40.909 0.00 0.00 0.00 1.82
3192 5620 2.095263 GTGCGGCAAGTGATGTGTATTT 60.095 45.455 3.23 0.00 0.00 1.40
3193 5621 1.468520 GTGCGGCAAGTGATGTGTATT 59.531 47.619 3.23 0.00 0.00 1.89
3194 5622 1.086696 GTGCGGCAAGTGATGTGTAT 58.913 50.000 3.23 0.00 0.00 2.29
3195 5623 1.288419 CGTGCGGCAAGTGATGTGTA 61.288 55.000 3.23 0.00 0.00 2.90
3196 5624 2.606961 CGTGCGGCAAGTGATGTGT 61.607 57.895 3.23 0.00 0.00 3.72
3197 5625 2.174107 CGTGCGGCAAGTGATGTG 59.826 61.111 3.23 0.00 0.00 3.21
3198 5626 2.280797 ACGTGCGGCAAGTGATGT 60.281 55.556 20.42 0.00 0.00 3.06
3199 5627 2.174107 CACGTGCGGCAAGTGATG 59.826 61.111 35.12 15.30 44.22 3.07
3200 5628 2.030412 TCACGTGCGGCAAGTGAT 59.970 55.556 36.22 9.37 44.85 3.06
3202 5630 1.288419 TACATCACGTGCGGCAAGTG 61.288 55.000 33.49 33.49 43.20 3.16
3203 5631 0.601576 TTACATCACGTGCGGCAAGT 60.602 50.000 15.79 15.79 0.00 3.16
3204 5632 0.515127 TTTACATCACGTGCGGCAAG 59.485 50.000 11.67 14.35 0.00 4.01
3205 5633 0.945099 TTTTACATCACGTGCGGCAA 59.055 45.000 11.67 0.00 0.00 4.52
3206 5634 0.236187 GTTTTACATCACGTGCGGCA 59.764 50.000 11.67 0.00 0.00 5.69
3207 5635 0.787908 CGTTTTACATCACGTGCGGC 60.788 55.000 11.67 0.00 0.00 6.53
3208 5636 0.179235 CCGTTTTACATCACGTGCGG 60.179 55.000 11.67 11.59 34.47 5.69
3209 5637 0.787908 GCCGTTTTACATCACGTGCG 60.788 55.000 11.67 6.99 34.47 5.34
3210 5638 0.453782 GGCCGTTTTACATCACGTGC 60.454 55.000 11.67 0.00 34.47 5.34
3211 5639 0.179235 CGGCCGTTTTACATCACGTG 60.179 55.000 19.50 9.94 34.47 4.49
3212 5640 1.293267 CCGGCCGTTTTACATCACGT 61.293 55.000 26.12 0.00 34.47 4.49
3213 5641 1.422269 CCGGCCGTTTTACATCACG 59.578 57.895 26.12 0.00 36.12 4.35
3214 5642 1.135939 GCCGGCCGTTTTACATCAC 59.864 57.895 26.12 0.00 0.00 3.06
3215 5643 1.302383 CTGCCGGCCGTTTTACATCA 61.302 55.000 26.77 7.32 0.00 3.07
3216 5644 1.427819 CTGCCGGCCGTTTTACATC 59.572 57.895 26.77 2.86 0.00 3.06
3217 5645 2.696759 GCTGCCGGCCGTTTTACAT 61.697 57.895 26.77 0.00 34.27 2.29
3218 5646 3.358707 GCTGCCGGCCGTTTTACA 61.359 61.111 26.77 12.71 34.27 2.41
3238 5666 2.127758 GACAGTTTGGCGTTCGCG 60.128 61.111 10.94 0.00 44.73 5.87
3239 5667 2.127758 CGACAGTTTGGCGTTCGC 60.128 61.111 8.75 8.75 45.41 4.70


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

AutoCloner maintained by Alex Coulton.