Multiple sequence alignment - TraesCS1A01G308300

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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 TraesCS1A01G308300 chr1A 100.000 4025 0 0 1 4025 499624633 499620609 0.000000e+00 7433.0
1 TraesCS1A01G308300 chr1A 88.076 2734 266 35 745 3457 542440251 542437557 0.000000e+00 3188.0
2 TraesCS1A01G308300 chr1D 96.097 3305 99 15 729 4022 403948372 403945087 0.000000e+00 5361.0
3 TraesCS1A01G308300 chr1D 88.196 2728 275 28 745 3457 446708254 446705559 0.000000e+00 3210.0
4 TraesCS1A01G308300 chr1D 97.891 569 11 1 1 568 403948939 403948371 0.000000e+00 983.0
5 TraesCS1A01G308300 chr1D 98.225 169 3 0 565 733 339368659 339368491 3.040000e-76 296.0
6 TraesCS1A01G308300 chr1D 96.571 175 5 1 564 737 452004162 452004336 5.090000e-74 289.0
7 TraesCS1A01G308300 chr1B 94.982 3268 132 20 729 3986 543469025 543465780 0.000000e+00 5097.0
8 TraesCS1A01G308300 chr1B 87.757 2728 280 32 745 3457 611523270 611525958 0.000000e+00 3138.0
9 TraesCS1A01G308300 chr1B 92.632 570 38 4 1 568 543469591 543469024 0.000000e+00 817.0
10 TraesCS1A01G308300 chr1B 95.385 65 2 1 1102 1166 543469515 543469452 7.120000e-18 102.0
11 TraesCS1A01G308300 chr1B 100.000 37 0 0 3986 4022 543464473 543464437 7.220000e-08 69.4
12 TraesCS1A01G308300 chr5D 98.235 170 3 0 564 733 447433600 447433769 8.460000e-77 298.0
13 TraesCS1A01G308300 chr2D 99.390 164 1 0 564 727 18206973 18207136 8.460000e-77 298.0
14 TraesCS1A01G308300 chr2D 98.802 167 2 0 567 733 330215064 330215230 8.460000e-77 298.0
15 TraesCS1A01G308300 chr2D 98.780 164 2 0 564 727 628554735 628554898 3.930000e-75 292.0
16 TraesCS1A01G308300 chr4D 98.795 166 2 0 566 731 281177252 281177087 3.040000e-76 296.0
17 TraesCS1A01G308300 chrUn 97.619 168 4 0 567 734 90921968 90922135 5.090000e-74 289.0
18 TraesCS1A01G308300 chr7D 96.023 176 7 0 563 738 184379817 184379992 1.830000e-73 287.0


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 TraesCS1A01G308300 chr1A 499620609 499624633 4024 True 7433.00 7433 100.00000 1 4025 1 chr1A.!!$R1 4024
1 TraesCS1A01G308300 chr1A 542437557 542440251 2694 True 3188.00 3188 88.07600 745 3457 1 chr1A.!!$R2 2712
2 TraesCS1A01G308300 chr1D 446705559 446708254 2695 True 3210.00 3210 88.19600 745 3457 1 chr1D.!!$R2 2712
3 TraesCS1A01G308300 chr1D 403945087 403948939 3852 True 3172.00 5361 96.99400 1 4022 2 chr1D.!!$R3 4021
4 TraesCS1A01G308300 chr1B 611523270 611525958 2688 False 3138.00 3138 87.75700 745 3457 1 chr1B.!!$F1 2712
5 TraesCS1A01G308300 chr1B 543464437 543469591 5154 True 1521.35 5097 95.74975 1 4022 4 chr1B.!!$R1 4021

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
193 195 0.820871 GTGACTCTAGTCCTGCTGGG 59.179 60.0 10.07 0.0 44.15 4.45 F
1332 1338 0.650512 CACCACGTAATGATGACGGC 59.349 55.0 7.33 0.0 44.58 5.68 F
2619 2628 1.972660 GCGAGTATGCTGGGGAGGTT 61.973 60.0 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1630 0.250640 GCCCTGATATCACTGGCCAG 60.251 60.000 31.6 31.6 34.37 4.85 R
2677 2686 1.273606 CGTCTTCTCACCAGGACACAT 59.726 52.381 0.0 0.0 0.00 3.21 R
3883 3915 0.035056 CAGCCAGGGGTCCAGTTAAG 60.035 60.000 0.0 0.0 0.00 1.85 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
193 195 0.820871 GTGACTCTAGTCCTGCTGGG 59.179 60.000 10.07 0.00 44.15 4.45
240 242 3.865745 CGATGGAAAGAGTATGGTGTCAC 59.134 47.826 0.00 0.00 0.00 3.67
436 439 3.127425 AGTGTTTCTTGGTGTCCTAGC 57.873 47.619 0.00 0.00 0.00 3.42
547 550 6.822676 AGAAGGAAATGCTTCATCTAGTTGAG 59.177 38.462 15.64 1.11 31.23 3.02
566 569 4.338012 TGAGAACTGCAATGATCCAATGT 58.662 39.130 0.00 0.00 0.00 2.71
567 570 5.499313 TGAGAACTGCAATGATCCAATGTA 58.501 37.500 0.00 0.00 0.00 2.29
568 571 5.355071 TGAGAACTGCAATGATCCAATGTAC 59.645 40.000 0.00 0.00 0.00 2.90
569 572 5.503927 AGAACTGCAATGATCCAATGTACT 58.496 37.500 0.00 0.00 0.00 2.73
570 573 5.587844 AGAACTGCAATGATCCAATGTACTC 59.412 40.000 0.00 0.00 0.00 2.59
571 574 4.202441 ACTGCAATGATCCAATGTACTCC 58.798 43.478 0.00 0.00 0.00 3.85
572 575 3.554934 TGCAATGATCCAATGTACTCCC 58.445 45.455 0.00 0.00 0.00 4.30
573 576 3.202818 TGCAATGATCCAATGTACTCCCT 59.797 43.478 0.00 0.00 0.00 4.20
574 577 3.817647 GCAATGATCCAATGTACTCCCTC 59.182 47.826 0.00 0.00 0.00 4.30
575 578 4.392940 CAATGATCCAATGTACTCCCTCC 58.607 47.826 0.00 0.00 0.00 4.30
576 579 2.039418 TGATCCAATGTACTCCCTCCG 58.961 52.381 0.00 0.00 0.00 4.63
577 580 2.040178 GATCCAATGTACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
578 581 1.946984 TCCAATGTACTCCCTCCGTT 58.053 50.000 0.00 0.00 0.00 4.44
579 582 1.829222 TCCAATGTACTCCCTCCGTTC 59.171 52.381 0.00 0.00 0.00 3.95
580 583 1.134491 CCAATGTACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 0.00 3.62
581 584 1.831736 CAATGTACTCCCTCCGTTCCT 59.168 52.381 0.00 0.00 0.00 3.36
582 585 3.028850 CAATGTACTCCCTCCGTTCCTA 58.971 50.000 0.00 0.00 0.00 2.94
583 586 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
584 587 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
585 588 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
586 589 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
587 590 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
588 591 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
589 592 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
590 593 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
591 594 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
592 595 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
593 596 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
594 597 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
595 598 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
596 599 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
597 600 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
598 601 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
599 602 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
600 603 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
613 616 8.990163 TTGTCTTTCTAGAGGTTTTAAATGGT 57.010 30.769 0.00 0.00 0.00 3.55
614 617 8.391075 TGTCTTTCTAGAGGTTTTAAATGGTG 57.609 34.615 0.00 0.00 0.00 4.17
615 618 8.215050 TGTCTTTCTAGAGGTTTTAAATGGTGA 58.785 33.333 0.00 0.00 0.00 4.02
616 619 8.504815 GTCTTTCTAGAGGTTTTAAATGGTGAC 58.495 37.037 0.00 0.00 0.00 3.67
617 620 8.437575 TCTTTCTAGAGGTTTTAAATGGTGACT 58.562 33.333 0.00 0.00 0.00 3.41
618 621 9.720769 CTTTCTAGAGGTTTTAAATGGTGACTA 57.279 33.333 0.00 0.00 0.00 2.59
619 622 9.498176 TTTCTAGAGGTTTTAAATGGTGACTAC 57.502 33.333 0.00 0.00 0.00 2.73
620 623 8.197592 TCTAGAGGTTTTAAATGGTGACTACA 57.802 34.615 0.00 0.00 0.00 2.74
621 624 8.822805 TCTAGAGGTTTTAAATGGTGACTACAT 58.177 33.333 0.00 0.00 0.00 2.29
623 626 8.788325 AGAGGTTTTAAATGGTGACTACATAC 57.212 34.615 0.00 0.00 0.00 2.39
624 627 7.548075 AGAGGTTTTAAATGGTGACTACATACG 59.452 37.037 0.00 0.00 0.00 3.06
625 628 6.596497 AGGTTTTAAATGGTGACTACATACGG 59.404 38.462 0.00 0.00 0.00 4.02
626 629 6.594937 GGTTTTAAATGGTGACTACATACGGA 59.405 38.462 0.00 0.00 0.00 4.69
627 630 7.119553 GGTTTTAAATGGTGACTACATACGGAA 59.880 37.037 0.00 0.00 0.00 4.30
628 631 7.599630 TTTAAATGGTGACTACATACGGAAC 57.400 36.000 0.00 0.00 0.00 3.62
629 632 4.811969 AATGGTGACTACATACGGAACA 57.188 40.909 0.00 0.00 0.00 3.18
630 633 4.811969 ATGGTGACTACATACGGAACAA 57.188 40.909 0.00 0.00 0.00 2.83
631 634 4.603989 TGGTGACTACATACGGAACAAA 57.396 40.909 0.00 0.00 0.00 2.83
632 635 4.958509 TGGTGACTACATACGGAACAAAA 58.041 39.130 0.00 0.00 0.00 2.44
633 636 5.553123 TGGTGACTACATACGGAACAAAAT 58.447 37.500 0.00 0.00 0.00 1.82
634 637 5.410132 TGGTGACTACATACGGAACAAAATG 59.590 40.000 0.00 0.00 0.00 2.32
635 638 5.640357 GGTGACTACATACGGAACAAAATGA 59.360 40.000 0.00 0.00 0.00 2.57
636 639 6.183360 GGTGACTACATACGGAACAAAATGAG 60.183 42.308 0.00 0.00 0.00 2.90
637 640 6.367969 GTGACTACATACGGAACAAAATGAGT 59.632 38.462 0.00 0.00 0.00 3.41
638 641 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
639 642 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
640 643 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
641 644 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
642 645 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
643 646 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
644 647 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
645 648 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
646 649 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
647 650 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
680 683 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
681 684 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
682 685 6.943718 TGTCTATATACATCCGTATGTGGTGA 59.056 38.462 3.56 0.00 45.99 4.02
683 686 7.094506 TGTCTATATACATCCGTATGTGGTGAC 60.095 40.741 3.56 5.93 45.99 3.67
684 687 3.746045 ATACATCCGTATGTGGTGACC 57.254 47.619 3.56 0.00 45.99 4.02
685 688 1.271856 ACATCCGTATGTGGTGACCA 58.728 50.000 0.00 0.00 44.79 4.02
686 689 1.837439 ACATCCGTATGTGGTGACCAT 59.163 47.619 7.94 0.00 44.79 3.55
687 690 2.238646 ACATCCGTATGTGGTGACCATT 59.761 45.455 7.94 0.86 44.79 3.16
688 691 3.278574 CATCCGTATGTGGTGACCATTT 58.721 45.455 7.94 0.45 35.28 2.32
689 692 2.705730 TCCGTATGTGGTGACCATTTG 58.294 47.619 7.94 0.00 35.28 2.32
690 693 2.303311 TCCGTATGTGGTGACCATTTGA 59.697 45.455 7.94 0.00 35.28 2.69
691 694 3.078097 CCGTATGTGGTGACCATTTGAA 58.922 45.455 7.94 0.00 35.28 2.69
692 695 3.504134 CCGTATGTGGTGACCATTTGAAA 59.496 43.478 7.94 0.00 35.28 2.69
693 696 4.157656 CCGTATGTGGTGACCATTTGAAAT 59.842 41.667 7.94 0.00 35.28 2.17
694 697 5.331902 CGTATGTGGTGACCATTTGAAATC 58.668 41.667 7.94 0.00 35.28 2.17
695 698 5.123820 CGTATGTGGTGACCATTTGAAATCT 59.876 40.000 7.94 0.00 35.28 2.40
696 699 5.649782 ATGTGGTGACCATTTGAAATCTC 57.350 39.130 7.94 0.00 35.28 2.75
697 700 4.728772 TGTGGTGACCATTTGAAATCTCT 58.271 39.130 7.94 0.00 35.28 3.10
698 701 5.875224 TGTGGTGACCATTTGAAATCTCTA 58.125 37.500 7.94 0.00 35.28 2.43
699 702 5.939883 TGTGGTGACCATTTGAAATCTCTAG 59.060 40.000 7.94 0.00 35.28 2.43
700 703 6.173339 GTGGTGACCATTTGAAATCTCTAGA 58.827 40.000 7.94 0.00 35.28 2.43
701 704 6.655003 GTGGTGACCATTTGAAATCTCTAGAA 59.345 38.462 7.94 0.00 35.28 2.10
702 705 7.174946 GTGGTGACCATTTGAAATCTCTAGAAA 59.825 37.037 7.94 0.00 35.28 2.52
703 706 7.391554 TGGTGACCATTTGAAATCTCTAGAAAG 59.608 37.037 0.00 0.00 0.00 2.62
704 707 7.607991 GGTGACCATTTGAAATCTCTAGAAAGA 59.392 37.037 0.00 0.00 0.00 2.52
705 708 8.447053 GTGACCATTTGAAATCTCTAGAAAGAC 58.553 37.037 0.00 0.00 0.00 3.01
706 709 8.156820 TGACCATTTGAAATCTCTAGAAAGACA 58.843 33.333 0.00 0.00 0.00 3.41
707 710 8.924511 ACCATTTGAAATCTCTAGAAAGACAA 57.075 30.769 0.00 0.00 0.00 3.18
708 711 9.354673 ACCATTTGAAATCTCTAGAAAGACAAA 57.645 29.630 0.00 4.41 0.00 2.83
721 724 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
722 725 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
723 726 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
724 727 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
725 728 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
726 729 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
727 730 6.069705 ACAAATATTTAGGAACGGAGGGAA 57.930 37.500 0.00 0.00 0.00 3.97
771 777 9.823647 CCATCAATTCTTGTAGTTCACTATAGT 57.176 33.333 0.00 0.00 0.00 2.12
861 867 6.544197 TGTTTTACTTTCATGCTGGTTGTAGA 59.456 34.615 0.00 0.00 0.00 2.59
862 868 6.801539 TTTACTTTCATGCTGGTTGTAGAG 57.198 37.500 0.00 0.00 0.00 2.43
876 882 4.322049 GGTTGTAGAGTCACATGCAGTACT 60.322 45.833 0.00 0.00 0.00 2.73
911 917 2.134789 ACCATGCTTCAGGATTCACC 57.865 50.000 0.00 0.00 39.35 4.02
941 947 6.293955 GCTGCTTACTCCTTTGTGATTTTGTA 60.294 38.462 0.00 0.00 0.00 2.41
1023 1029 3.217626 GGACAGGGCTAGGAATTTCATG 58.782 50.000 0.00 0.00 0.00 3.07
1065 1071 2.241941 TCTGGATGCCAAGCCATTAAGA 59.758 45.455 0.00 0.00 42.18 2.10
1201 1207 1.026718 CCTTCCTGCCGTTGGATCAC 61.027 60.000 0.00 0.00 33.09 3.06
1332 1338 0.650512 CACCACGTAATGATGACGGC 59.349 55.000 7.33 0.00 44.58 5.68
1985 1994 2.511600 GGTCGTGCGGGGATTCAG 60.512 66.667 0.00 0.00 0.00 3.02
2242 2251 3.130633 CCAGTTTGTGTCGTCAATGAGA 58.869 45.455 0.00 0.00 0.00 3.27
2271 2280 2.158325 TGAGAAAGGACCTGGGCATTTT 60.158 45.455 14.14 7.30 0.00 1.82
2619 2628 1.972660 GCGAGTATGCTGGGGAGGTT 61.973 60.000 0.00 0.00 0.00 3.50
2677 2686 8.514594 GTGAAGATGATTACATTTTTCAGACCA 58.485 33.333 0.00 0.00 39.08 4.02
2891 2900 1.021390 GGAGATGACAAGCACCCACG 61.021 60.000 0.00 0.00 0.00 4.94
2964 2973 0.328258 ACTATGGTGTGGTTGGAGCC 59.672 55.000 0.00 0.00 0.00 4.70
3038 3051 5.652452 GGTTACTTTGATTCACATTAGGGCT 59.348 40.000 0.00 0.00 0.00 5.19
3047 3060 7.161404 TGATTCACATTAGGGCTCATGTATAC 58.839 38.462 0.00 0.00 32.16 1.47
3200 3215 6.205076 TCGCTATATTTCTGGAGTGACTAGTC 59.795 42.308 16.32 16.32 0.00 2.59
3215 3230 7.001073 AGTGACTAGTCATGTGATCTAGCATA 58.999 38.462 27.54 0.00 42.18 3.14
3218 3233 8.157476 TGACTAGTCATGTGATCTAGCATAGTA 58.843 37.037 21.74 0.00 35.81 1.82
3219 3234 8.330466 ACTAGTCATGTGATCTAGCATAGTAC 57.670 38.462 14.20 0.00 40.38 2.73
3221 3236 7.213216 AGTCATGTGATCTAGCATAGTACTG 57.787 40.000 5.39 0.00 40.38 2.74
3223 3238 7.939588 AGTCATGTGATCTAGCATAGTACTGTA 59.060 37.037 5.39 0.00 40.38 2.74
3224 3239 8.233868 GTCATGTGATCTAGCATAGTACTGTAG 58.766 40.741 5.39 1.71 40.38 2.74
3225 3240 6.561737 TGTGATCTAGCATAGTACTGTAGC 57.438 41.667 5.39 6.77 40.38 3.58
3226 3241 6.062095 TGTGATCTAGCATAGTACTGTAGCA 58.938 40.000 5.39 0.00 40.38 3.49
3227 3242 6.546034 TGTGATCTAGCATAGTACTGTAGCAA 59.454 38.462 5.39 0.00 40.38 3.91
3305 3321 4.530094 TTGTTCGAACAAACTGCTGTAG 57.470 40.909 34.99 0.00 45.17 2.74
3420 3445 4.864916 AAGCTGCATCTGTGTTTATACG 57.135 40.909 1.02 0.00 0.00 3.06
3516 3546 4.825634 ACCTTTTAGCTTTACTTGTGGGTC 59.174 41.667 0.00 0.00 0.00 4.46
3517 3547 5.070685 CCTTTTAGCTTTACTTGTGGGTCT 58.929 41.667 0.00 0.00 0.00 3.85
3568 3598 7.781693 AGGAACATATACCATCTTTTGAGCATT 59.218 33.333 0.00 0.00 0.00 3.56
3587 3617 3.594603 TTTGCTCTACTCACTACCTGC 57.405 47.619 0.00 0.00 0.00 4.85
3634 3666 4.122776 CTGCTAGCGATTCTACCAATGTT 58.877 43.478 10.77 0.00 0.00 2.71
3656 3688 1.492176 GATTGGCTCCTGGGAAGATGA 59.508 52.381 0.00 0.00 0.00 2.92
3673 3705 7.148623 GGGAAGATGATTAATAATCGGTCGTTC 60.149 40.741 7.09 5.50 40.84 3.95
3679 3711 2.214387 ATAATCGGTCGTTCGGAACC 57.786 50.000 14.83 1.29 0.00 3.62
3760 3792 1.153289 CCTCTGTTCTGCCGGATGG 60.153 63.158 5.05 0.00 38.77 3.51
3761 3793 1.599047 CTCTGTTCTGCCGGATGGT 59.401 57.895 5.05 0.00 37.67 3.55
3762 3794 0.742281 CTCTGTTCTGCCGGATGGTG 60.742 60.000 5.05 0.00 37.67 4.17
3788 3820 0.387202 TTGTGCCCACCATTTGTTCG 59.613 50.000 0.00 0.00 0.00 3.95
3811 3843 0.884704 ACTTGGTGGATGCGTGTGTC 60.885 55.000 0.00 0.00 0.00 3.67
3883 3915 1.201647 TGTGTAGGCTAGCGTCAGTTC 59.798 52.381 14.21 0.00 0.00 3.01
3951 3988 3.920412 GCTGTAAAAACATGTGGCTTAGC 59.080 43.478 0.00 0.00 0.00 3.09
4022 5367 6.544564 TCACCGTCCCAAATTCTATATTTTCC 59.455 38.462 0.00 0.00 0.00 3.13
4023 5368 5.529800 ACCGTCCCAAATTCTATATTTTCCG 59.470 40.000 0.00 0.00 0.00 4.30
4024 5369 5.449304 CGTCCCAAATTCTATATTTTCCGC 58.551 41.667 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.328382 TGAACATAAGTAAGCTGGCGT 57.672 42.857 0.00 0.00 0.00 5.68
193 195 3.403558 GTCACAGAGGGAGGGGGC 61.404 72.222 0.00 0.00 0.00 5.80
436 439 8.843262 TCAGTAGCATTGATAATGGAAGAATTG 58.157 33.333 9.23 0.00 39.31 2.32
484 487 3.687212 CGTAGCATTGAACCATTGGTACA 59.313 43.478 9.20 0.00 43.06 2.90
547 550 5.220931 GGAGTACATTGGATCATTGCAGTTC 60.221 44.000 0.00 0.00 0.00 3.01
566 569 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
567 570 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
568 571 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
569 572 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
570 573 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
571 574 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
572 575 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
573 576 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
574 577 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
587 590 9.416284 ACCATTTAAAACCTCTAGAAAGACAAA 57.584 29.630 0.00 0.00 0.00 2.83
588 591 8.846211 CACCATTTAAAACCTCTAGAAAGACAA 58.154 33.333 0.00 0.00 0.00 3.18
589 592 8.215050 TCACCATTTAAAACCTCTAGAAAGACA 58.785 33.333 0.00 0.00 0.00 3.41
590 593 8.504815 GTCACCATTTAAAACCTCTAGAAAGAC 58.495 37.037 0.00 0.00 0.00 3.01
591 594 8.437575 AGTCACCATTTAAAACCTCTAGAAAGA 58.562 33.333 0.00 0.00 0.00 2.52
592 595 8.622948 AGTCACCATTTAAAACCTCTAGAAAG 57.377 34.615 0.00 0.00 0.00 2.62
593 596 9.498176 GTAGTCACCATTTAAAACCTCTAGAAA 57.502 33.333 0.00 0.00 0.00 2.52
594 597 8.653191 TGTAGTCACCATTTAAAACCTCTAGAA 58.347 33.333 0.00 0.00 0.00 2.10
595 598 8.197592 TGTAGTCACCATTTAAAACCTCTAGA 57.802 34.615 0.00 0.00 0.00 2.43
597 600 9.880157 GTATGTAGTCACCATTTAAAACCTCTA 57.120 33.333 0.00 0.00 0.00 2.43
598 601 7.548075 CGTATGTAGTCACCATTTAAAACCTCT 59.452 37.037 0.00 0.00 0.00 3.69
599 602 7.201582 CCGTATGTAGTCACCATTTAAAACCTC 60.202 40.741 0.00 0.00 0.00 3.85
600 603 6.596497 CCGTATGTAGTCACCATTTAAAACCT 59.404 38.462 0.00 0.00 0.00 3.50
601 604 6.594937 TCCGTATGTAGTCACCATTTAAAACC 59.405 38.462 0.00 0.00 0.00 3.27
602 605 7.599630 TCCGTATGTAGTCACCATTTAAAAC 57.400 36.000 0.00 0.00 0.00 2.43
603 606 7.660617 TGTTCCGTATGTAGTCACCATTTAAAA 59.339 33.333 0.00 0.00 0.00 1.52
604 607 7.160049 TGTTCCGTATGTAGTCACCATTTAAA 58.840 34.615 0.00 0.00 0.00 1.52
605 608 6.699366 TGTTCCGTATGTAGTCACCATTTAA 58.301 36.000 0.00 0.00 0.00 1.52
606 609 6.283544 TGTTCCGTATGTAGTCACCATTTA 57.716 37.500 0.00 0.00 0.00 1.40
607 610 5.155278 TGTTCCGTATGTAGTCACCATTT 57.845 39.130 0.00 0.00 0.00 2.32
608 611 4.811969 TGTTCCGTATGTAGTCACCATT 57.188 40.909 0.00 0.00 0.00 3.16
609 612 4.811969 TTGTTCCGTATGTAGTCACCAT 57.188 40.909 0.00 0.00 0.00 3.55
610 613 4.603989 TTTGTTCCGTATGTAGTCACCA 57.396 40.909 0.00 0.00 0.00 4.17
611 614 5.640357 TCATTTTGTTCCGTATGTAGTCACC 59.360 40.000 0.00 0.00 0.00 4.02
612 615 6.367969 ACTCATTTTGTTCCGTATGTAGTCAC 59.632 38.462 0.00 0.00 0.00 3.67
613 616 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
614 617 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
615 618 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
616 619 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
617 620 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
618 621 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
619 622 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
620 623 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
621 624 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
622 625 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
623 626 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
624 627 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
654 657 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
655 658 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
656 659 7.614192 TCACCACATACGGATGTATATAGACAT 59.386 37.037 14.23 12.70 44.82 3.06
657 660 6.943718 TCACCACATACGGATGTATATAGACA 59.056 38.462 14.23 2.07 44.82 3.41
658 661 7.249147 GTCACCACATACGGATGTATATAGAC 58.751 42.308 14.23 12.97 44.82 2.59
659 662 6.376299 GGTCACCACATACGGATGTATATAGA 59.624 42.308 14.23 4.80 44.82 1.98
660 663 6.152154 TGGTCACCACATACGGATGTATATAG 59.848 42.308 14.23 0.00 44.82 1.31
661 664 6.011481 TGGTCACCACATACGGATGTATATA 58.989 40.000 14.23 0.00 44.82 0.86
662 665 4.836175 TGGTCACCACATACGGATGTATAT 59.164 41.667 14.23 0.00 44.82 0.86
663 666 4.216708 TGGTCACCACATACGGATGTATA 58.783 43.478 14.23 0.00 44.82 1.47
664 667 3.035363 TGGTCACCACATACGGATGTAT 58.965 45.455 14.23 1.38 44.82 2.29
665 668 2.458620 TGGTCACCACATACGGATGTA 58.541 47.619 14.23 0.00 44.82 2.29
667 670 2.620251 ATGGTCACCACATACGGATG 57.380 50.000 5.94 5.94 35.80 3.51
668 671 3.054728 TCAAATGGTCACCACATACGGAT 60.055 43.478 0.00 0.00 35.80 4.18
669 672 2.303311 TCAAATGGTCACCACATACGGA 59.697 45.455 0.00 0.00 35.80 4.69
670 673 2.705730 TCAAATGGTCACCACATACGG 58.294 47.619 0.00 0.00 35.80 4.02
671 674 4.757799 TTTCAAATGGTCACCACATACG 57.242 40.909 0.00 0.00 35.80 3.06
672 675 6.375455 AGAGATTTCAAATGGTCACCACATAC 59.625 38.462 0.00 0.00 35.80 2.39
673 676 6.484288 AGAGATTTCAAATGGTCACCACATA 58.516 36.000 0.00 0.00 35.80 2.29
674 677 5.327732 AGAGATTTCAAATGGTCACCACAT 58.672 37.500 0.00 0.00 35.80 3.21
675 678 4.728772 AGAGATTTCAAATGGTCACCACA 58.271 39.130 0.00 0.00 35.80 4.17
676 679 6.173339 TCTAGAGATTTCAAATGGTCACCAC 58.827 40.000 0.00 0.00 35.80 4.16
677 680 6.373005 TCTAGAGATTTCAAATGGTCACCA 57.627 37.500 0.00 0.00 38.19 4.17
678 681 7.607991 TCTTTCTAGAGATTTCAAATGGTCACC 59.392 37.037 0.00 0.00 0.00 4.02
679 682 8.447053 GTCTTTCTAGAGATTTCAAATGGTCAC 58.553 37.037 0.00 0.00 0.00 3.67
680 683 8.156820 TGTCTTTCTAGAGATTTCAAATGGTCA 58.843 33.333 0.00 0.00 0.00 4.02
681 684 8.553459 TGTCTTTCTAGAGATTTCAAATGGTC 57.447 34.615 0.00 0.00 0.00 4.02
682 685 8.924511 TTGTCTTTCTAGAGATTTCAAATGGT 57.075 30.769 0.00 0.00 0.00 3.55
695 698 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
696 699 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
697 700 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
698 701 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
699 702 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
700 703 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
701 704 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
702 705 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
703 706 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
704 707 5.703730 TCCCTCCGTTCCTAAATATTTGT 57.296 39.130 11.05 0.00 0.00 2.83
705 708 7.937394 ACTATTCCCTCCGTTCCTAAATATTTG 59.063 37.037 11.05 1.40 0.00 2.32
706 709 8.042286 ACTATTCCCTCCGTTCCTAAATATTT 57.958 34.615 5.89 5.89 0.00 1.40
707 710 7.628501 ACTATTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
708 711 7.513091 AGAACTATTCCCTCCGTTCCTAAATAT 59.487 37.037 0.00 0.00 37.15 1.28
709 712 6.842807 AGAACTATTCCCTCCGTTCCTAAATA 59.157 38.462 0.00 0.00 37.15 1.40
710 713 5.666265 AGAACTATTCCCTCCGTTCCTAAAT 59.334 40.000 0.00 0.00 37.15 1.40
711 714 5.028131 AGAACTATTCCCTCCGTTCCTAAA 58.972 41.667 0.00 0.00 37.15 1.85
712 715 4.617593 AGAACTATTCCCTCCGTTCCTAA 58.382 43.478 0.00 0.00 37.15 2.69
713 716 4.213513 GAGAACTATTCCCTCCGTTCCTA 58.786 47.826 0.00 0.00 37.15 2.94
714 717 3.032459 GAGAACTATTCCCTCCGTTCCT 58.968 50.000 0.00 0.00 37.15 3.36
715 718 2.764572 TGAGAACTATTCCCTCCGTTCC 59.235 50.000 0.00 0.00 37.15 3.62
716 719 4.467198 TTGAGAACTATTCCCTCCGTTC 57.533 45.455 0.00 0.00 36.81 3.95
717 720 4.323562 CCTTTGAGAACTATTCCCTCCGTT 60.324 45.833 0.00 0.00 0.00 4.44
718 721 3.197983 CCTTTGAGAACTATTCCCTCCGT 59.802 47.826 0.00 0.00 0.00 4.69
719 722 3.432326 CCCTTTGAGAACTATTCCCTCCG 60.432 52.174 0.00 0.00 0.00 4.63
720 723 3.685835 GCCCTTTGAGAACTATTCCCTCC 60.686 52.174 0.00 0.00 0.00 4.30
721 724 3.054361 TGCCCTTTGAGAACTATTCCCTC 60.054 47.826 0.00 0.00 0.00 4.30
722 725 2.919602 TGCCCTTTGAGAACTATTCCCT 59.080 45.455 0.00 0.00 0.00 4.20
723 726 3.017442 GTGCCCTTTGAGAACTATTCCC 58.983 50.000 0.00 0.00 0.00 3.97
724 727 3.017442 GGTGCCCTTTGAGAACTATTCC 58.983 50.000 0.00 0.00 0.00 3.01
725 728 3.017442 GGGTGCCCTTTGAGAACTATTC 58.983 50.000 0.00 0.00 0.00 1.75
726 729 2.378547 TGGGTGCCCTTTGAGAACTATT 59.621 45.455 8.91 0.00 36.94 1.73
727 730 1.992557 TGGGTGCCCTTTGAGAACTAT 59.007 47.619 8.91 0.00 36.94 2.12
771 777 4.891992 TCCAAACCAAAACAGAAACCAA 57.108 36.364 0.00 0.00 0.00 3.67
941 947 7.881751 GGAAAAACCTTAGTGGACTATACAGTT 59.118 37.037 0.00 0.00 39.71 3.16
985 991 5.336690 CCCTGTCCATGTTAAATCAACCAAG 60.337 44.000 0.00 0.00 36.20 3.61
1065 1071 4.530875 CAGGGAACATTGGAGCTAAAGAT 58.469 43.478 0.00 0.00 0.00 2.40
1192 1198 0.321653 AAGGTGGCGAGTGATCCAAC 60.322 55.000 0.00 0.00 40.32 3.77
1201 1207 0.737715 GTAGCACTGAAGGTGGCGAG 60.738 60.000 0.00 0.00 45.44 5.03
1621 1630 0.250640 GCCCTGATATCACTGGCCAG 60.251 60.000 31.60 31.60 34.37 4.85
2242 2251 3.713764 CCAGGTCCTTTCTCATGGTCTAT 59.286 47.826 0.00 0.00 0.00 1.98
2271 2280 8.930846 GGTATTTGACCTCAGTAGTATAGGTA 57.069 38.462 4.19 0.00 45.89 3.08
2619 2628 9.241919 TCCAAATTAACTTGAAGCTCATCAATA 57.758 29.630 0.00 0.00 38.55 1.90
2677 2686 1.273606 CGTCTTCTCACCAGGACACAT 59.726 52.381 0.00 0.00 0.00 3.21
2731 2740 5.824624 CAGGTGATACATATGTGCTTTCCTT 59.175 40.000 18.81 3.01 0.00 3.36
2964 2973 3.649277 CTTGCTCCGACTGGTCCCG 62.649 68.421 0.00 0.00 36.30 5.14
3019 3031 5.359009 ACATGAGCCCTAATGTGAATCAAAG 59.641 40.000 0.00 0.00 33.47 2.77
3038 3051 5.188751 TGTTGATCCACCACAGTATACATGA 59.811 40.000 5.50 0.00 0.00 3.07
3047 3060 1.471287 CTGCATGTTGATCCACCACAG 59.529 52.381 0.00 0.00 0.00 3.66
3200 3215 7.026562 GCTACAGTACTATGCTAGATCACATG 58.973 42.308 0.00 0.00 0.00 3.21
3215 3230 3.399330 ACGTGCAAATTGCTACAGTACT 58.601 40.909 19.34 0.00 45.31 2.73
3218 3233 3.181491 ACAAACGTGCAAATTGCTACAGT 60.181 39.130 19.34 13.29 45.31 3.55
3219 3234 3.371168 ACAAACGTGCAAATTGCTACAG 58.629 40.909 19.34 12.78 45.31 2.74
3221 3236 5.150683 TGATACAAACGTGCAAATTGCTAC 58.849 37.500 19.34 13.64 45.31 3.58
3223 3238 4.235939 TGATACAAACGTGCAAATTGCT 57.764 36.364 19.34 0.00 45.31 3.91
3224 3239 4.258977 CGATGATACAAACGTGCAAATTGC 60.259 41.667 11.58 11.58 45.29 3.56
3225 3240 5.085390 TCGATGATACAAACGTGCAAATTG 58.915 37.500 0.00 0.00 0.00 2.32
3226 3241 5.289917 TCGATGATACAAACGTGCAAATT 57.710 34.783 0.00 0.00 0.00 1.82
3227 3242 4.937696 TCGATGATACAAACGTGCAAAT 57.062 36.364 0.00 0.00 0.00 2.32
3305 3321 2.014128 ACATATGCGGTGCCAAGTAAC 58.986 47.619 1.58 0.00 0.00 2.50
3354 3373 2.813754 TGTGCAGCATTTCAAGACTACC 59.186 45.455 0.00 0.00 0.00 3.18
3420 3445 3.604582 AGCCTTTCTTCTGCTGTATCAC 58.395 45.455 0.00 0.00 33.23 3.06
3500 3530 6.614087 TGGTATATAGACCCACAAGTAAAGCT 59.386 38.462 13.92 0.00 38.89 3.74
3568 3598 1.825474 GGCAGGTAGTGAGTAGAGCAA 59.175 52.381 0.00 0.00 0.00 3.91
3584 3614 2.281970 TGCAAGGTGAGCAGGCAG 60.282 61.111 0.00 0.00 37.02 4.85
3618 3648 5.990408 CCAATCTAACATTGGTAGAATCGC 58.010 41.667 15.13 0.00 42.63 4.58
3634 3666 2.568546 TCTTCCCAGGAGCCAATCTA 57.431 50.000 0.00 0.00 0.00 1.98
3656 3688 4.746611 GGTTCCGAACGACCGATTATTAAT 59.253 41.667 5.19 0.00 0.00 1.40
3673 3705 0.387622 TTACTGTCTTCGCGGTTCCG 60.388 55.000 6.13 6.90 0.00 4.30
3679 3711 3.341857 AGATAGCTTACTGTCTTCGCG 57.658 47.619 0.00 0.00 41.18 5.87
3788 3820 1.299541 CACGCATCCACCAAGTATCC 58.700 55.000 0.00 0.00 0.00 2.59
3883 3915 0.035056 CAGCCAGGGGTCCAGTTAAG 60.035 60.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.