Multiple sequence alignment - TraesCS6D01G329900

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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 TraesCS6D01G329900 chr6D 100.000 3117 0 0 1 3117 433591880 433594996 0.000000e+00 5757.0
1 TraesCS6D01G329900 chr6D 88.064 1441 153 15 898 2327 432914457 432913025 0.000000e+00 1690.0
2 TraesCS6D01G329900 chr6D 87.875 1435 162 8 898 2327 433259127 433257700 0.000000e+00 1676.0
3 TraesCS6D01G329900 chr6D 86.923 1430 167 14 899 2315 433155343 433153921 0.000000e+00 1587.0
4 TraesCS6D01G329900 chr6D 94.399 607 33 1 1 607 78769768 78770373 0.000000e+00 931.0
5 TraesCS6D01G329900 chr6D 94.399 607 33 1 1 607 426930196 426929591 0.000000e+00 931.0
6 TraesCS6D01G329900 chr6D 94.399 607 33 1 1 607 465424993 465424388 0.000000e+00 931.0
7 TraesCS6D01G329900 chr6A 94.297 2332 119 10 696 3025 579794872 579797191 0.000000e+00 3557.0
8 TraesCS6D01G329900 chr6A 87.719 1425 160 12 898 2315 579124929 579123513 0.000000e+00 1648.0
9 TraesCS6D01G329900 chr6B 92.525 1766 114 8 1271 3025 655104569 655106327 0.000000e+00 2514.0
10 TraesCS6D01G329900 chr6B 87.491 1423 165 8 898 2315 653715649 653714235 0.000000e+00 1629.0
11 TraesCS6D01G329900 chr6B 87.063 1430 166 16 898 2315 653856552 653855130 0.000000e+00 1598.0
12 TraesCS6D01G329900 chr6B 88.419 1278 135 8 898 2170 653194820 653193551 0.000000e+00 1528.0
13 TraesCS6D01G329900 chr1D 94.737 608 30 2 1 607 467660815 467661421 0.000000e+00 944.0
14 TraesCS6D01G329900 chr1D 94.563 607 31 2 1 607 391097354 391096750 0.000000e+00 937.0
15 TraesCS6D01G329900 chr1D 93.976 83 4 1 3036 3117 120801010 120800928 1.170000e-24 124.0
16 TraesCS6D01G329900 chr7A 94.728 607 31 1 1 607 8944699 8945304 0.000000e+00 942.0
17 TraesCS6D01G329900 chr3A 94.023 619 34 3 1 619 336615297 336614682 0.000000e+00 935.0
18 TraesCS6D01G329900 chr3A 97.959 49 0 1 3043 3090 115079326 115079374 1.990000e-12 84.2
19 TraesCS6D01G329900 chr2D 94.554 606 32 1 2 607 579764495 579765099 0.000000e+00 935.0
20 TraesCS6D01G329900 chrUn 94.408 608 32 2 1 608 90496365 90496970 0.000000e+00 933.0
21 TraesCS6D01G329900 chr2A 98.276 58 0 1 3034 3090 331966839 331966896 1.980000e-17 100.0
22 TraesCS6D01G329900 chr4B 93.750 64 2 2 3029 3091 405954956 405955018 9.200000e-16 95.3
23 TraesCS6D01G329900 chr5B 92.188 64 3 2 3034 3097 209281266 209281327 4.280000e-14 89.8
24 TraesCS6D01G329900 chr7B 94.444 54 1 2 3035 3086 61155792 61155739 7.160000e-12 82.4


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 TraesCS6D01G329900 chr6D 433591880 433594996 3116 False 5757 5757 100.000 1 3117 1 chr6D.!!$F2 3116
1 TraesCS6D01G329900 chr6D 432913025 432914457 1432 True 1690 1690 88.064 898 2327 1 chr6D.!!$R2 1429
2 TraesCS6D01G329900 chr6D 433257700 433259127 1427 True 1676 1676 87.875 898 2327 1 chr6D.!!$R4 1429
3 TraesCS6D01G329900 chr6D 433153921 433155343 1422 True 1587 1587 86.923 899 2315 1 chr6D.!!$R3 1416
4 TraesCS6D01G329900 chr6D 78769768 78770373 605 False 931 931 94.399 1 607 1 chr6D.!!$F1 606
5 TraesCS6D01G329900 chr6D 426929591 426930196 605 True 931 931 94.399 1 607 1 chr6D.!!$R1 606
6 TraesCS6D01G329900 chr6D 465424388 465424993 605 True 931 931 94.399 1 607 1 chr6D.!!$R5 606
7 TraesCS6D01G329900 chr6A 579794872 579797191 2319 False 3557 3557 94.297 696 3025 1 chr6A.!!$F1 2329
8 TraesCS6D01G329900 chr6A 579123513 579124929 1416 True 1648 1648 87.719 898 2315 1 chr6A.!!$R1 1417
9 TraesCS6D01G329900 chr6B 655104569 655106327 1758 False 2514 2514 92.525 1271 3025 1 chr6B.!!$F1 1754
10 TraesCS6D01G329900 chr6B 653714235 653715649 1414 True 1629 1629 87.491 898 2315 1 chr6B.!!$R2 1417
11 TraesCS6D01G329900 chr6B 653855130 653856552 1422 True 1598 1598 87.063 898 2315 1 chr6B.!!$R3 1417
12 TraesCS6D01G329900 chr6B 653193551 653194820 1269 True 1528 1528 88.419 898 2170 1 chr6B.!!$R1 1272
13 TraesCS6D01G329900 chr1D 467660815 467661421 606 False 944 944 94.737 1 607 1 chr1D.!!$F1 606
14 TraesCS6D01G329900 chr1D 391096750 391097354 604 True 937 937 94.563 1 607 1 chr1D.!!$R2 606
15 TraesCS6D01G329900 chr7A 8944699 8945304 605 False 942 942 94.728 1 607 1 chr7A.!!$F1 606
16 TraesCS6D01G329900 chr3A 336614682 336615297 615 True 935 935 94.023 1 619 1 chr3A.!!$R1 618
17 TraesCS6D01G329900 chr2D 579764495 579765099 604 False 935 935 94.554 2 607 1 chr2D.!!$F1 605
18 TraesCS6D01G329900 chrUn 90496365 90496970 605 False 933 933 94.408 1 608 1 chrUn.!!$F1 607

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
855 857 0.250295 ATTATGCCATCCGTCCACCG 60.25 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2799 2833 0.03254 GGCCAAGTTTGTGAAGCCTG 59.967 55.0 0.0 0.0 37.42 4.85 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
79 80 2.365617 GGTACACACATGATCGAGGGAT 59.634 50.000 0.00 0.00 34.96 3.85
106 107 1.803289 GGATTCTTTGGTGGAGCGC 59.197 57.895 0.00 0.00 0.00 5.92
136 137 2.220615 TACACACTGATGGCGACGGG 62.221 60.000 0.00 0.00 0.00 5.28
173 175 0.603569 AGTGCAGATTCGGAGTTCGT 59.396 50.000 0.00 0.00 40.32 3.85
192 194 0.544357 TTGTGGGAGGATGGACTCGT 60.544 55.000 0.00 0.00 38.39 4.18
219 221 4.717629 CGAAGCTGTCGGGCGTCA 62.718 66.667 9.54 0.00 46.45 4.35
344 346 3.241530 TGGTTGAGGACTGCGCCT 61.242 61.111 4.18 0.00 42.17 5.52
451 453 4.161102 GGTATTAGGCCCAGACTATCTGT 58.839 47.826 0.00 0.00 42.80 3.41
464 466 2.437281 ACTATCTGTGCCCCTTCATCAG 59.563 50.000 0.00 0.00 0.00 2.90
533 535 7.393234 AGTCTTGCTGTTGTATGGCTTTATAAA 59.607 33.333 0.00 0.00 0.00 1.40
646 648 6.647334 TGAAAATCAACTGCATGGTAAAGA 57.353 33.333 0.00 0.00 0.00 2.52
647 649 7.230849 TGAAAATCAACTGCATGGTAAAGAT 57.769 32.000 0.00 0.00 0.00 2.40
648 650 7.092079 TGAAAATCAACTGCATGGTAAAGATG 58.908 34.615 0.00 0.00 0.00 2.90
649 651 5.587388 AATCAACTGCATGGTAAAGATGG 57.413 39.130 0.00 0.00 0.00 3.51
650 652 2.754552 TCAACTGCATGGTAAAGATGGC 59.245 45.455 0.00 0.00 0.00 4.40
651 653 2.492881 CAACTGCATGGTAAAGATGGCA 59.507 45.455 0.00 0.00 0.00 4.92
652 654 2.372264 ACTGCATGGTAAAGATGGCAG 58.628 47.619 9.64 9.64 34.17 4.85
653 655 1.066605 CTGCATGGTAAAGATGGCAGC 59.933 52.381 0.00 0.00 0.00 5.25
654 656 0.386838 GCATGGTAAAGATGGCAGCC 59.613 55.000 3.66 3.66 0.00 4.85
655 657 1.766494 CATGGTAAAGATGGCAGCCA 58.234 50.000 18.99 18.99 38.19 4.75
656 658 2.101783 CATGGTAAAGATGGCAGCCAA 58.898 47.619 20.84 0.00 36.95 4.52
657 659 1.544724 TGGTAAAGATGGCAGCCAAC 58.455 50.000 20.84 17.08 36.95 3.77
658 660 1.075374 TGGTAAAGATGGCAGCCAACT 59.925 47.619 20.84 19.49 38.29 3.16
659 661 2.307392 TGGTAAAGATGGCAGCCAACTA 59.693 45.455 23.73 9.81 35.58 2.24
660 662 3.245087 TGGTAAAGATGGCAGCCAACTAA 60.245 43.478 23.73 12.80 35.58 2.24
661 663 3.954258 GGTAAAGATGGCAGCCAACTAAT 59.046 43.478 23.73 17.49 35.58 1.73
662 664 5.130350 GGTAAAGATGGCAGCCAACTAATA 58.870 41.667 23.73 16.56 35.58 0.98
663 665 5.592688 GGTAAAGATGGCAGCCAACTAATAA 59.407 40.000 23.73 7.71 35.58 1.40
664 666 5.582689 AAAGATGGCAGCCAACTAATAAC 57.417 39.130 23.73 6.01 35.58 1.89
665 667 4.235079 AGATGGCAGCCAACTAATAACA 57.765 40.909 22.32 0.00 34.86 2.41
666 668 4.796606 AGATGGCAGCCAACTAATAACAT 58.203 39.130 22.32 0.00 34.86 2.71
667 669 5.940617 AGATGGCAGCCAACTAATAACATA 58.059 37.500 22.32 0.00 34.86 2.29
668 670 6.364701 AGATGGCAGCCAACTAATAACATAA 58.635 36.000 22.32 0.00 34.86 1.90
669 671 5.828299 TGGCAGCCAACTAATAACATAAC 57.172 39.130 13.33 0.00 0.00 1.89
670 672 5.257262 TGGCAGCCAACTAATAACATAACA 58.743 37.500 13.33 0.00 0.00 2.41
671 673 5.890985 TGGCAGCCAACTAATAACATAACAT 59.109 36.000 13.33 0.00 0.00 2.71
672 674 6.039270 TGGCAGCCAACTAATAACATAACATC 59.961 38.462 13.33 0.00 0.00 3.06
673 675 6.039270 GGCAGCCAACTAATAACATAACATCA 59.961 38.462 6.55 0.00 0.00 3.07
674 676 6.912591 GCAGCCAACTAATAACATAACATCAC 59.087 38.462 0.00 0.00 0.00 3.06
675 677 7.417612 CAGCCAACTAATAACATAACATCACC 58.582 38.462 0.00 0.00 0.00 4.02
676 678 7.066887 CAGCCAACTAATAACATAACATCACCA 59.933 37.037 0.00 0.00 0.00 4.17
677 679 7.779798 AGCCAACTAATAACATAACATCACCAT 59.220 33.333 0.00 0.00 0.00 3.55
678 680 7.862372 GCCAACTAATAACATAACATCACCATG 59.138 37.037 0.00 0.00 35.92 3.66
679 681 7.862372 CCAACTAATAACATAACATCACCATGC 59.138 37.037 0.00 0.00 32.57 4.06
680 682 8.404765 CAACTAATAACATAACATCACCATGCA 58.595 33.333 0.00 0.00 32.57 3.96
681 683 8.518430 ACTAATAACATAACATCACCATGCAA 57.482 30.769 0.00 0.00 32.57 4.08
682 684 9.135189 ACTAATAACATAACATCACCATGCAAT 57.865 29.630 0.00 0.00 32.57 3.56
683 685 9.616634 CTAATAACATAACATCACCATGCAATC 57.383 33.333 0.00 0.00 32.57 2.67
684 686 5.918426 AACATAACATCACCATGCAATCA 57.082 34.783 0.00 0.00 32.57 2.57
685 687 5.252969 ACATAACATCACCATGCAATCAC 57.747 39.130 0.00 0.00 32.57 3.06
686 688 4.705991 ACATAACATCACCATGCAATCACA 59.294 37.500 0.00 0.00 32.57 3.58
687 689 5.361571 ACATAACATCACCATGCAATCACAT 59.638 36.000 0.00 0.00 32.57 3.21
688 690 4.811969 AACATCACCATGCAATCACATT 57.188 36.364 0.00 0.00 32.57 2.71
689 691 4.380841 ACATCACCATGCAATCACATTC 57.619 40.909 0.00 0.00 32.57 2.67
690 692 3.764972 ACATCACCATGCAATCACATTCA 59.235 39.130 0.00 0.00 32.57 2.57
691 693 3.853831 TCACCATGCAATCACATTCAC 57.146 42.857 0.00 0.00 0.00 3.18
692 694 2.492881 TCACCATGCAATCACATTCACC 59.507 45.455 0.00 0.00 0.00 4.02
693 695 2.494471 CACCATGCAATCACATTCACCT 59.506 45.455 0.00 0.00 0.00 4.00
694 696 3.695556 CACCATGCAATCACATTCACCTA 59.304 43.478 0.00 0.00 0.00 3.08
695 697 4.158209 CACCATGCAATCACATTCACCTAA 59.842 41.667 0.00 0.00 0.00 2.69
696 698 4.400251 ACCATGCAATCACATTCACCTAAG 59.600 41.667 0.00 0.00 0.00 2.18
697 699 4.400251 CCATGCAATCACATTCACCTAAGT 59.600 41.667 0.00 0.00 0.00 2.24
698 700 5.449588 CCATGCAATCACATTCACCTAAGTC 60.450 44.000 0.00 0.00 0.00 3.01
699 701 4.009675 TGCAATCACATTCACCTAAGTCC 58.990 43.478 0.00 0.00 0.00 3.85
700 702 4.009675 GCAATCACATTCACCTAAGTCCA 58.990 43.478 0.00 0.00 0.00 4.02
739 741 2.027569 CGTTGTGATCACGAATACACGG 59.972 50.000 17.55 0.00 36.25 4.94
744 746 5.412640 TGTGATCACGAATACACGGTTTAT 58.587 37.500 20.54 0.00 36.25 1.40
778 780 3.884774 ACCCAAAGCCTCGGCACA 61.885 61.111 11.02 0.00 44.88 4.57
815 817 6.337356 TCTCATATGCAGATGAAAACGTACA 58.663 36.000 23.27 0.00 35.44 2.90
855 857 0.250295 ATTATGCCATCCGTCCACCG 60.250 55.000 0.00 0.00 0.00 4.94
886 888 4.801330 TCACCGTATCATGTCCATATCC 57.199 45.455 0.00 0.00 0.00 2.59
973 981 0.861837 GCACACACTGCACACTAGTC 59.138 55.000 0.00 0.00 46.29 2.59
1100 1113 0.807667 AGCGATGACTTGTCGATGGC 60.808 55.000 0.00 9.93 41.40 4.40
1128 1141 0.396435 ACGAGAGTTGGATGGTGCAA 59.604 50.000 0.00 0.00 46.40 4.08
1155 1168 2.210116 CGTGTGTATAAGGATGCCACC 58.790 52.381 0.00 0.00 0.00 4.61
1255 1268 3.788333 ATTTGGGCATCAATCAGTTCG 57.212 42.857 0.00 0.00 34.98 3.95
1340 1353 1.835531 GAGGGTTCCTACCGGATTCAA 59.164 52.381 9.46 0.00 46.04 2.69
1353 1366 5.745227 ACCGGATTCAAGTATGAGAATGTT 58.255 37.500 9.46 0.00 36.78 2.71
1561 1577 0.455633 CATTTTCTGCTGTCGCTGCC 60.456 55.000 0.00 0.00 36.97 4.85
2065 2081 5.097234 AGAATGGAGAAGGATATTCCCGAT 58.903 41.667 0.00 0.00 37.19 4.18
2129 2145 3.801050 CACTGCATAGGAAGAACATCTCG 59.199 47.826 0.00 0.00 0.00 4.04
2171 2187 8.721019 ATGCACACAAAGATTAAATAATTGGG 57.279 30.769 0.00 0.00 0.00 4.12
2261 2286 6.844279 GCACGGTACTTTATATTTCATGAACG 59.156 38.462 7.89 6.40 0.00 3.95
2332 2358 5.500234 TGTTATCCTTGGGAGATTTCACAG 58.500 41.667 0.00 0.00 38.17 3.66
2358 2384 8.381387 GTTGTAGAGTTGTAGCAGTTTATAAGC 58.619 37.037 0.00 0.00 0.00 3.09
2411 2444 6.537566 CATGTACAATGCACTCTTTGAGTAC 58.462 40.000 0.00 0.00 41.37 2.73
2414 2447 5.931441 ACAATGCACTCTTTGAGTACTTC 57.069 39.130 4.82 0.00 41.37 3.01
2508 2541 4.927267 TGAAGCCTGAAGGAGGAAATTA 57.073 40.909 0.00 0.00 46.33 1.40
2521 2554 7.830099 AGGAGGAAATTAATGGATGTGAATC 57.170 36.000 0.00 0.00 0.00 2.52
2558 2591 6.266080 TGAACATAACTAGGAAGGGACCTTA 58.734 40.000 3.09 0.00 41.00 2.69
2570 2603 2.707554 GGGACCTTATCTCCCCAATCT 58.292 52.381 0.00 0.00 41.70 2.40
2571 2604 3.056832 GGGACCTTATCTCCCCAATCTT 58.943 50.000 0.00 0.00 41.70 2.40
2572 2605 3.181439 GGGACCTTATCTCCCCAATCTTG 60.181 52.174 0.00 0.00 41.70 3.02
2573 2606 3.459969 GGACCTTATCTCCCCAATCTTGT 59.540 47.826 0.00 0.00 0.00 3.16
2575 2608 4.860022 ACCTTATCTCCCCAATCTTGTTG 58.140 43.478 0.00 0.00 0.00 3.33
2576 2609 3.633986 CCTTATCTCCCCAATCTTGTTGC 59.366 47.826 0.00 0.00 0.00 4.17
2577 2610 2.149973 ATCTCCCCAATCTTGTTGCC 57.850 50.000 0.00 0.00 0.00 4.52
2578 2611 0.776810 TCTCCCCAATCTTGTTGCCA 59.223 50.000 0.00 0.00 0.00 4.92
2591 2625 3.500448 TGTTGCCATACTCCTTCAACA 57.500 42.857 0.00 0.00 42.95 3.33
2614 2648 1.479709 AACATCGACCTCTCTCCCAG 58.520 55.000 0.00 0.00 0.00 4.45
2617 2651 1.943730 ATCGACCTCTCTCCCAGCCT 61.944 60.000 0.00 0.00 0.00 4.58
2676 2710 1.327690 TAGACCGCATGGGGAGTGTC 61.328 60.000 33.50 20.32 41.60 3.67
2696 2730 3.997021 GTCGTGAAATGAGGACACAAGAT 59.003 43.478 0.00 0.00 34.69 2.40
2701 2735 2.885135 ATGAGGACACAAGATGCCAA 57.115 45.000 0.00 0.00 0.00 4.52
2705 2739 0.734889 GGACACAAGATGCCAATCCG 59.265 55.000 0.00 0.00 32.77 4.18
2710 2744 1.833630 ACAAGATGCCAATCCGAGAGA 59.166 47.619 0.00 0.00 32.77 3.10
2766 2800 3.748668 GCCATAGGCTAATGACACACCAT 60.749 47.826 0.00 0.00 46.69 3.55
2778 2812 3.685435 CACCATGGTGGGCACTTC 58.315 61.111 33.56 0.00 43.37 3.01
2786 2820 3.948719 TGGGCACTTCGGGGTCAC 61.949 66.667 0.00 0.00 0.00 3.67
2794 2828 0.537371 CTTCGGGGTCACCAAAGCTT 60.537 55.000 0.00 0.00 40.22 3.74
2799 2833 1.611977 GGGGTCACCAAAGCTTGTAAC 59.388 52.381 0.00 0.00 39.85 2.50
2915 2949 7.063074 GTCTTGCATCTGATCTTTTGGATTTTG 59.937 37.037 0.00 0.00 34.33 2.44
2934 2968 1.355381 TGGATTTGCCCTCACATGACT 59.645 47.619 0.00 0.00 34.97 3.41
2972 3007 8.740906 TCTATTCAGTTTTTGTGGTTGTGTAAA 58.259 29.630 0.00 0.00 0.00 2.01
3025 3061 7.884877 AGTTGGAATCTTTCATCAACACTATGA 59.115 33.333 0.00 0.00 39.84 2.15
3026 3062 8.680903 GTTGGAATCTTTCATCAACACTATGAT 58.319 33.333 0.00 0.00 40.64 2.45
3027 3063 8.812513 TGGAATCTTTCATCAACACTATGATT 57.187 30.769 0.00 0.00 37.96 2.57
3028 3064 9.246670 TGGAATCTTTCATCAACACTATGATTT 57.753 29.630 0.00 0.00 37.96 2.17
3063 3099 9.506018 TTTTGACTATAAACAGTAGGGTAAACC 57.494 33.333 0.00 0.00 40.67 3.27
3073 3109 4.934316 GGTAAACCCCCACTGCAA 57.066 55.556 0.00 0.00 0.00 4.08
3074 3110 2.347630 GGTAAACCCCCACTGCAAC 58.652 57.895 0.00 0.00 0.00 4.17
3075 3111 0.178973 GGTAAACCCCCACTGCAACT 60.179 55.000 0.00 0.00 0.00 3.16
3076 3112 1.699730 GTAAACCCCCACTGCAACTT 58.300 50.000 0.00 0.00 0.00 2.66
3077 3113 2.036387 GTAAACCCCCACTGCAACTTT 58.964 47.619 0.00 0.00 0.00 2.66
3078 3114 1.578897 AAACCCCCACTGCAACTTTT 58.421 45.000 0.00 0.00 0.00 2.27
3079 3115 2.463047 AACCCCCACTGCAACTTTTA 57.537 45.000 0.00 0.00 0.00 1.52
3080 3116 2.694616 ACCCCCACTGCAACTTTTAT 57.305 45.000 0.00 0.00 0.00 1.40
3081 3117 2.970987 ACCCCCACTGCAACTTTTATT 58.029 42.857 0.00 0.00 0.00 1.40
3082 3118 4.120946 ACCCCCACTGCAACTTTTATTA 57.879 40.909 0.00 0.00 0.00 0.98
3083 3119 4.484912 ACCCCCACTGCAACTTTTATTAA 58.515 39.130 0.00 0.00 0.00 1.40
3084 3120 5.090845 ACCCCCACTGCAACTTTTATTAAT 58.909 37.500 0.00 0.00 0.00 1.40
3085 3121 6.257586 ACCCCCACTGCAACTTTTATTAATA 58.742 36.000 0.00 0.00 0.00 0.98
3086 3122 6.726764 ACCCCCACTGCAACTTTTATTAATAA 59.273 34.615 3.71 3.71 0.00 1.40
3087 3123 7.235812 ACCCCCACTGCAACTTTTATTAATAAA 59.764 33.333 15.19 15.19 0.00 1.40
3088 3124 8.097662 CCCCCACTGCAACTTTTATTAATAAAA 58.902 33.333 24.81 24.81 39.24 1.52
3089 3125 9.495572 CCCCACTGCAACTTTTATTAATAAAAA 57.504 29.630 25.80 14.67 40.51 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 3.599730 TCAGTGTGTAGGATGAAGCAG 57.400 47.619 0.00 0.00 0.00 4.24
173 175 0.544357 ACGAGTCCATCCTCCCACAA 60.544 55.000 0.00 0.00 0.00 3.33
192 194 2.159819 GACAGCTTCGTCCTCCTGCA 62.160 60.000 0.00 0.00 0.00 4.41
205 207 4.457496 CCATGACGCCCGACAGCT 62.457 66.667 0.00 0.00 0.00 4.24
219 221 4.094646 TGCCATCGACGCCACCAT 62.095 61.111 4.01 0.00 0.00 3.55
337 339 2.185350 CCTACCAGTCAGGCGCAG 59.815 66.667 10.83 0.00 43.14 5.18
451 453 1.002069 ATCCAACTGATGAAGGGGCA 58.998 50.000 0.00 0.00 30.54 5.36
464 466 2.165845 ACTGTCGCTACACCTATCCAAC 59.834 50.000 0.00 0.00 0.00 3.77
622 624 7.048629 TCTTTACCATGCAGTTGATTTTCAA 57.951 32.000 0.00 0.00 33.32 2.69
623 625 6.647334 TCTTTACCATGCAGTTGATTTTCA 57.353 33.333 0.00 0.00 0.00 2.69
624 626 6.532657 CCATCTTTACCATGCAGTTGATTTTC 59.467 38.462 0.00 0.00 0.00 2.29
625 627 6.400568 CCATCTTTACCATGCAGTTGATTTT 58.599 36.000 0.00 0.00 0.00 1.82
626 628 5.625197 GCCATCTTTACCATGCAGTTGATTT 60.625 40.000 0.00 0.00 0.00 2.17
627 629 4.142093 GCCATCTTTACCATGCAGTTGATT 60.142 41.667 0.00 0.00 0.00 2.57
628 630 3.382546 GCCATCTTTACCATGCAGTTGAT 59.617 43.478 0.00 0.00 0.00 2.57
629 631 2.754552 GCCATCTTTACCATGCAGTTGA 59.245 45.455 0.00 0.00 0.00 3.18
630 632 2.492881 TGCCATCTTTACCATGCAGTTG 59.507 45.455 0.00 0.00 0.00 3.16
631 633 2.756760 CTGCCATCTTTACCATGCAGTT 59.243 45.455 0.00 0.00 0.00 3.16
632 634 2.372264 CTGCCATCTTTACCATGCAGT 58.628 47.619 0.00 0.00 0.00 4.40
633 635 1.066605 GCTGCCATCTTTACCATGCAG 59.933 52.381 5.01 5.01 32.78 4.41
634 636 1.105457 GCTGCCATCTTTACCATGCA 58.895 50.000 0.00 0.00 0.00 3.96
635 637 0.386838 GGCTGCCATCTTTACCATGC 59.613 55.000 15.17 0.00 0.00 4.06
636 638 1.766494 TGGCTGCCATCTTTACCATG 58.234 50.000 19.30 0.00 0.00 3.66
637 639 2.102578 GTTGGCTGCCATCTTTACCAT 58.897 47.619 24.03 0.00 31.53 3.55
638 640 1.075374 AGTTGGCTGCCATCTTTACCA 59.925 47.619 24.03 1.01 30.21 3.25
639 641 1.839424 AGTTGGCTGCCATCTTTACC 58.161 50.000 24.03 4.80 30.21 2.85
640 642 6.094881 TGTTATTAGTTGGCTGCCATCTTTAC 59.905 38.462 30.92 21.70 35.47 2.01
641 643 6.184068 TGTTATTAGTTGGCTGCCATCTTTA 58.816 36.000 30.92 21.37 35.47 1.85
642 644 5.016173 TGTTATTAGTTGGCTGCCATCTTT 58.984 37.500 30.92 22.13 35.47 2.52
643 645 4.599041 TGTTATTAGTTGGCTGCCATCTT 58.401 39.130 30.92 19.49 35.47 2.40
644 646 4.235079 TGTTATTAGTTGGCTGCCATCT 57.765 40.909 29.29 29.29 37.36 2.90
645 647 6.039270 TGTTATGTTATTAGTTGGCTGCCATC 59.961 38.462 24.03 21.57 31.53 3.51
646 648 5.890985 TGTTATGTTATTAGTTGGCTGCCAT 59.109 36.000 24.03 11.42 31.53 4.40
647 649 5.257262 TGTTATGTTATTAGTTGGCTGCCA 58.743 37.500 19.30 19.30 0.00 4.92
648 650 5.828299 TGTTATGTTATTAGTTGGCTGCC 57.172 39.130 12.87 12.87 0.00 4.85
649 651 6.912591 GTGATGTTATGTTATTAGTTGGCTGC 59.087 38.462 0.00 0.00 0.00 5.25
650 652 7.066887 TGGTGATGTTATGTTATTAGTTGGCTG 59.933 37.037 0.00 0.00 0.00 4.85
651 653 7.116075 TGGTGATGTTATGTTATTAGTTGGCT 58.884 34.615 0.00 0.00 0.00 4.75
652 654 7.328277 TGGTGATGTTATGTTATTAGTTGGC 57.672 36.000 0.00 0.00 0.00 4.52
653 655 7.862372 GCATGGTGATGTTATGTTATTAGTTGG 59.138 37.037 0.00 0.00 31.50 3.77
654 656 8.404765 TGCATGGTGATGTTATGTTATTAGTTG 58.595 33.333 0.00 0.00 31.50 3.16
655 657 8.518430 TGCATGGTGATGTTATGTTATTAGTT 57.482 30.769 0.00 0.00 31.50 2.24
656 658 8.518430 TTGCATGGTGATGTTATGTTATTAGT 57.482 30.769 0.00 0.00 31.50 2.24
657 659 9.616634 GATTGCATGGTGATGTTATGTTATTAG 57.383 33.333 0.00 0.00 31.50 1.73
658 660 9.129532 TGATTGCATGGTGATGTTATGTTATTA 57.870 29.630 0.00 0.00 31.50 0.98
659 661 7.922278 GTGATTGCATGGTGATGTTATGTTATT 59.078 33.333 0.00 0.00 31.50 1.40
660 662 7.068470 TGTGATTGCATGGTGATGTTATGTTAT 59.932 33.333 0.00 0.00 31.50 1.89
661 663 6.376581 TGTGATTGCATGGTGATGTTATGTTA 59.623 34.615 0.00 0.00 31.50 2.41
662 664 5.185442 TGTGATTGCATGGTGATGTTATGTT 59.815 36.000 0.00 0.00 31.50 2.71
663 665 4.705991 TGTGATTGCATGGTGATGTTATGT 59.294 37.500 0.00 0.00 31.50 2.29
664 666 5.251601 TGTGATTGCATGGTGATGTTATG 57.748 39.130 0.00 0.00 31.50 1.90
665 667 6.097129 TGAATGTGATTGCATGGTGATGTTAT 59.903 34.615 0.00 0.00 31.50 1.89
666 668 5.418209 TGAATGTGATTGCATGGTGATGTTA 59.582 36.000 0.00 0.00 31.50 2.41
667 669 4.221041 TGAATGTGATTGCATGGTGATGTT 59.779 37.500 0.00 0.00 31.50 2.71
668 670 3.764972 TGAATGTGATTGCATGGTGATGT 59.235 39.130 0.00 0.00 31.50 3.06
669 671 4.109766 GTGAATGTGATTGCATGGTGATG 58.890 43.478 0.00 0.00 0.00 3.07
670 672 3.131577 GGTGAATGTGATTGCATGGTGAT 59.868 43.478 0.00 0.00 0.00 3.06
671 673 2.492881 GGTGAATGTGATTGCATGGTGA 59.507 45.455 0.00 0.00 0.00 4.02
672 674 2.494471 AGGTGAATGTGATTGCATGGTG 59.506 45.455 0.00 0.00 0.00 4.17
673 675 2.811410 AGGTGAATGTGATTGCATGGT 58.189 42.857 0.00 0.00 0.00 3.55
674 676 4.400251 ACTTAGGTGAATGTGATTGCATGG 59.600 41.667 0.00 0.00 0.00 3.66
675 677 5.449588 GGACTTAGGTGAATGTGATTGCATG 60.450 44.000 0.00 0.00 0.00 4.06
676 678 4.641989 GGACTTAGGTGAATGTGATTGCAT 59.358 41.667 0.00 0.00 0.00 3.96
677 679 4.009675 GGACTTAGGTGAATGTGATTGCA 58.990 43.478 0.00 0.00 0.00 4.08
678 680 4.009675 TGGACTTAGGTGAATGTGATTGC 58.990 43.478 0.00 0.00 0.00 3.56
679 681 6.764308 AATGGACTTAGGTGAATGTGATTG 57.236 37.500 0.00 0.00 0.00 2.67
680 682 6.947733 TCAAATGGACTTAGGTGAATGTGATT 59.052 34.615 0.00 0.00 0.00 2.57
681 683 6.484288 TCAAATGGACTTAGGTGAATGTGAT 58.516 36.000 0.00 0.00 0.00 3.06
682 684 5.875224 TCAAATGGACTTAGGTGAATGTGA 58.125 37.500 0.00 0.00 0.00 3.58
683 685 6.207417 ACTTCAAATGGACTTAGGTGAATGTG 59.793 38.462 0.00 0.00 0.00 3.21
684 686 6.306987 ACTTCAAATGGACTTAGGTGAATGT 58.693 36.000 0.00 0.00 0.00 2.71
685 687 6.824305 ACTTCAAATGGACTTAGGTGAATG 57.176 37.500 0.00 0.00 0.00 2.67
686 688 8.328758 TGATACTTCAAATGGACTTAGGTGAAT 58.671 33.333 0.00 0.00 0.00 2.57
687 689 7.685481 TGATACTTCAAATGGACTTAGGTGAA 58.315 34.615 0.00 0.00 0.00 3.18
688 690 7.252612 TGATACTTCAAATGGACTTAGGTGA 57.747 36.000 0.00 0.00 0.00 4.02
689 691 7.921786 TTGATACTTCAAATGGACTTAGGTG 57.078 36.000 0.00 0.00 38.90 4.00
758 760 2.597510 GCCGAGGCTTTGGGTGTT 60.598 61.111 6.90 0.00 38.26 3.32
778 780 4.263462 TGCATATGAGAGTGACCCTTGTTT 60.263 41.667 6.97 0.00 0.00 2.83
973 981 2.404265 TTGATGAACTGCTTGCAACG 57.596 45.000 0.00 0.00 0.00 4.10
1058 1071 3.826754 CGCGAGCTGCTAGGACCA 61.827 66.667 11.72 0.00 43.27 4.02
1100 1113 2.357517 AACTCTCGTGCCTTGCCG 60.358 61.111 0.00 0.00 0.00 5.69
1128 1141 4.799586 GCATCCTTATACACACGGCTGTAT 60.800 45.833 0.00 10.90 39.98 2.29
1155 1168 2.456119 AAATCGCTGCGCCTTCTCG 61.456 57.895 18.65 0.83 0.00 4.04
1179 1192 2.649531 ACCCGACATTGTCCTTGAAA 57.350 45.000 11.12 0.00 0.00 2.69
1255 1268 2.432628 CTCGTTGGTGAGGTCGGC 60.433 66.667 0.00 0.00 32.18 5.54
1340 1353 8.454106 GTGCATCAAAACTAACATTCTCATACT 58.546 33.333 0.00 0.00 0.00 2.12
1353 1366 1.810151 GCCGGAAGTGCATCAAAACTA 59.190 47.619 5.05 0.00 0.00 2.24
1561 1577 1.009829 GCTTAATGACGCCCTCTGTG 58.990 55.000 0.00 0.00 0.00 3.66
1975 1991 6.773200 TCAACAACCAATACTTTGTACCATCA 59.227 34.615 0.00 0.00 34.82 3.07
2065 2081 0.253044 GGCCACACATGCCTCTCTTA 59.747 55.000 0.00 0.00 45.70 2.10
2129 2145 4.898829 TGCATACAAAGATATGTGGCAC 57.101 40.909 11.55 11.55 38.87 5.01
2233 2249 8.445275 TCATGAAATATAAAGTACCGTGCAAT 57.555 30.769 0.00 0.00 0.00 3.56
2332 2358 8.381387 GCTTATAAACTGCTACAACTCTACAAC 58.619 37.037 0.00 0.00 0.00 3.32
2358 2384 3.179010 CACAAGAGACAGTGCAATTCG 57.821 47.619 0.00 0.00 0.00 3.34
2367 2393 1.467734 GCATGAAGGCACAAGAGACAG 59.532 52.381 0.00 0.00 0.00 3.51
2368 2394 1.202794 TGCATGAAGGCACAAGAGACA 60.203 47.619 0.00 0.00 39.25 3.41
2369 2395 1.527034 TGCATGAAGGCACAAGAGAC 58.473 50.000 0.00 0.00 39.25 3.36
2425 2458 6.303054 TGTTTATCTGGTTCCAAGATTGTCA 58.697 36.000 8.31 4.80 0.00 3.58
2529 2562 7.283329 GTCCCTTCCTAGTTATGTTCATCAAT 58.717 38.462 0.00 0.00 0.00 2.57
2558 2591 2.149973 GGCAACAAGATTGGGGAGAT 57.850 50.000 0.00 0.00 0.00 2.75
2572 2605 3.412386 AGTGTTGAAGGAGTATGGCAAC 58.588 45.455 0.00 0.00 39.29 4.17
2573 2606 3.788227 AGTGTTGAAGGAGTATGGCAA 57.212 42.857 0.00 0.00 0.00 4.52
2575 2608 5.001232 TGTTAAGTGTTGAAGGAGTATGGC 58.999 41.667 0.00 0.00 0.00 4.40
2576 2609 6.036083 CGATGTTAAGTGTTGAAGGAGTATGG 59.964 42.308 0.00 0.00 0.00 2.74
2577 2610 6.811665 TCGATGTTAAGTGTTGAAGGAGTATG 59.188 38.462 0.00 0.00 0.00 2.39
2578 2611 6.812160 GTCGATGTTAAGTGTTGAAGGAGTAT 59.188 38.462 0.00 0.00 0.00 2.12
2591 2625 3.025262 GGGAGAGAGGTCGATGTTAAGT 58.975 50.000 0.00 0.00 0.00 2.24
2614 2648 3.512516 GGCGGCTGACATTGAGGC 61.513 66.667 0.00 0.00 0.00 4.70
2617 2651 0.035152 ATCAAGGCGGCTGACATTGA 60.035 50.000 14.21 12.92 34.64 2.57
2651 2685 0.748005 CCCCATGCGGTCTAAAGTGG 60.748 60.000 0.00 0.00 0.00 4.00
2676 2710 3.425359 GCATCTTGTGTCCTCATTTCACG 60.425 47.826 0.00 0.00 35.20 4.35
2696 2730 1.221840 GCCTTCTCTCGGATTGGCA 59.778 57.895 0.00 0.00 40.85 4.92
2701 2735 1.047002 CATGGAGCCTTCTCTCGGAT 58.953 55.000 0.00 0.00 39.31 4.18
2705 2739 0.545646 AAGCCATGGAGCCTTCTCTC 59.454 55.000 18.40 0.00 39.31 3.20
2710 2744 1.687368 GGAATGAAGCCATGGAGCCTT 60.687 52.381 18.40 9.59 32.36 4.35
2778 2812 0.250553 TACAAGCTTTGGTGACCCCG 60.251 55.000 0.00 0.00 35.15 5.73
2786 2820 2.622942 TGAAGCCTGTTACAAGCTTTGG 59.377 45.455 20.29 2.38 46.44 3.28
2794 2828 3.380004 CCAAGTTTGTGAAGCCTGTTACA 59.620 43.478 0.00 0.00 0.00 2.41
2799 2833 0.032540 GGCCAAGTTTGTGAAGCCTG 59.967 55.000 0.00 0.00 37.42 4.85
2915 2949 1.747355 CAGTCATGTGAGGGCAAATCC 59.253 52.381 0.00 0.00 0.00 3.01
2955 2989 5.140747 AGCACTTTACACAACCACAAAAA 57.859 34.783 0.00 0.00 0.00 1.94
2972 3007 1.555967 ACCACACCAACAAAAGCACT 58.444 45.000 0.00 0.00 0.00 4.40
3037 3073 9.506018 GGTTTACCCTACTGTTTATAGTCAAAA 57.494 33.333 0.00 0.00 32.19 2.44
3056 3092 0.178973 AGTTGCAGTGGGGGTTTACC 60.179 55.000 0.00 0.00 39.11 2.85
3057 3093 1.699730 AAGTTGCAGTGGGGGTTTAC 58.300 50.000 0.00 0.00 0.00 2.01
3058 3094 2.463047 AAAGTTGCAGTGGGGGTTTA 57.537 45.000 0.00 0.00 0.00 2.01
3059 3095 1.578897 AAAAGTTGCAGTGGGGGTTT 58.421 45.000 0.00 0.00 0.00 3.27
3060 3096 2.463047 TAAAAGTTGCAGTGGGGGTT 57.537 45.000 0.00 0.00 0.00 4.11
3061 3097 2.694616 ATAAAAGTTGCAGTGGGGGT 57.305 45.000 0.00 0.00 0.00 4.95
3062 3098 5.675684 ATTAATAAAAGTTGCAGTGGGGG 57.324 39.130 0.00 0.00 0.00 5.40
3063 3099 9.495572 TTTTTATTAATAAAAGTTGCAGTGGGG 57.504 29.630 24.93 0.00 41.58 4.96
3080 3116 8.755028 GGTTCCCTGGCTCTTTATTTTTATTAA 58.245 33.333 0.00 0.00 0.00 1.40
3081 3117 7.896496 TGGTTCCCTGGCTCTTTATTTTTATTA 59.104 33.333 0.00 0.00 0.00 0.98
3082 3118 6.728632 TGGTTCCCTGGCTCTTTATTTTTATT 59.271 34.615 0.00 0.00 0.00 1.40
3083 3119 6.260663 TGGTTCCCTGGCTCTTTATTTTTAT 58.739 36.000 0.00 0.00 0.00 1.40
3084 3120 5.646215 TGGTTCCCTGGCTCTTTATTTTTA 58.354 37.500 0.00 0.00 0.00 1.52
3085 3121 4.488770 TGGTTCCCTGGCTCTTTATTTTT 58.511 39.130 0.00 0.00 0.00 1.94
3086 3122 4.126520 TGGTTCCCTGGCTCTTTATTTT 57.873 40.909 0.00 0.00 0.00 1.82
3087 3123 3.825908 TGGTTCCCTGGCTCTTTATTT 57.174 42.857 0.00 0.00 0.00 1.40
3088 3124 3.825908 TTGGTTCCCTGGCTCTTTATT 57.174 42.857 0.00 0.00 0.00 1.40
3089 3125 3.076032 ACTTTGGTTCCCTGGCTCTTTAT 59.924 43.478 0.00 0.00 0.00 1.40
3090 3126 2.445525 ACTTTGGTTCCCTGGCTCTTTA 59.554 45.455 0.00 0.00 0.00 1.85
3091 3127 1.217942 ACTTTGGTTCCCTGGCTCTTT 59.782 47.619 0.00 0.00 0.00 2.52
3092 3128 0.853530 ACTTTGGTTCCCTGGCTCTT 59.146 50.000 0.00 0.00 0.00 2.85
3093 3129 0.402121 GACTTTGGTTCCCTGGCTCT 59.598 55.000 0.00 0.00 0.00 4.09
3094 3130 0.402121 AGACTTTGGTTCCCTGGCTC 59.598 55.000 0.00 0.00 0.00 4.70
3095 3131 0.111253 CAGACTTTGGTTCCCTGGCT 59.889 55.000 0.00 0.00 0.00 4.75
3096 3132 1.527433 GCAGACTTTGGTTCCCTGGC 61.527 60.000 0.00 0.00 0.00 4.85
3097 3133 0.178992 TGCAGACTTTGGTTCCCTGG 60.179 55.000 0.00 0.00 0.00 4.45
3098 3134 3.419793 TGCAGACTTTGGTTCCCTG 57.580 52.632 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.