Multiple sequence alignment - TraesCS2B01G179800

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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 TraesCS2B01G179800 chr2B 100.000 3764 0 0 1 3764 154268479 154272242 0.000000e+00 6951.0
1 TraesCS2B01G179800 chr2B 82.558 86 7 5 582 661 764914687 764914770 6.750000e-08 69.4
2 TraesCS2B01G179800 chr2A 94.227 3118 102 33 686 3764 101992250 101995328 0.000000e+00 4689.0
3 TraesCS2B01G179800 chr2D 96.472 2494 68 6 1018 3503 102879383 102881864 0.000000e+00 4100.0
4 TraesCS2B01G179800 chr2D 84.190 506 78 2 2 506 447326320 447326824 1.210000e-134 490.0
5 TraesCS2B01G179800 chr2D 95.472 265 11 1 3501 3764 102881946 102882210 4.500000e-114 422.0
6 TraesCS2B01G179800 chr2D 85.714 280 17 10 686 944 102878673 102878950 1.330000e-69 274.0
7 TraesCS2B01G179800 chr3B 95.890 511 21 0 1 511 737485953 737486463 0.000000e+00 828.0
8 TraesCS2B01G179800 chr3B 95.695 511 22 0 1 511 737450633 737451143 0.000000e+00 822.0
9 TraesCS2B01G179800 chr3B 95.322 513 23 1 4 516 22644081 22643570 0.000000e+00 813.0
10 TraesCS2B01G179800 chr3B 84.252 508 80 0 2 509 160018929 160018422 2.610000e-136 496.0
11 TraesCS2B01G179800 chr1B 94.767 516 26 1 1 516 139473813 139474327 0.000000e+00 802.0
12 TraesCS2B01G179800 chr7B 89.526 506 52 1 3 508 686914259 686914763 1.140000e-179 640.0
13 TraesCS2B01G179800 chr7B 94.872 39 2 0 582 620 482084878 482084840 1.130000e-05 62.1
14 TraesCS2B01G179800 chr7B 90.698 43 2 2 583 623 591469687 591469645 5.250000e-04 56.5
15 TraesCS2B01G179800 chr7A 92.922 438 30 1 79 516 98779883 98780319 1.470000e-178 636.0
16 TraesCS2B01G179800 chr6B 89.173 508 55 0 1 508 41519769 41520276 5.300000e-178 634.0
17 TraesCS2B01G179800 chr3A 82.558 86 8 5 582 661 36655790 36655706 6.750000e-08 69.4
18 TraesCS2B01G179800 chr7D 92.857 42 3 0 579 620 386595612 386595653 1.130000e-05 62.1
19 TraesCS2B01G179800 chr4D 92.683 41 3 0 580 620 38445543 38445583 4.060000e-05 60.2
20 TraesCS2B01G179800 chrUn 86.792 53 2 5 578 627 37366801 37366851 2.000000e-03 54.7
21 TraesCS2B01G179800 chr5D 87.500 48 5 1 581 627 97413957 97413910 2.000000e-03 54.7
22 TraesCS2B01G179800 chr1A 87.234 47 5 1 582 627 516064702 516064748 7.000000e-03 52.8


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 TraesCS2B01G179800 chr2B 154268479 154272242 3763 False 6951.000000 6951 100.000000 1 3764 1 chr2B.!!$F1 3763
1 TraesCS2B01G179800 chr2A 101992250 101995328 3078 False 4689.000000 4689 94.227000 686 3764 1 chr2A.!!$F1 3078
2 TraesCS2B01G179800 chr2D 102878673 102882210 3537 False 1598.666667 4100 92.552667 686 3764 3 chr2D.!!$F2 3078
3 TraesCS2B01G179800 chr2D 447326320 447326824 504 False 490.000000 490 84.190000 2 506 1 chr2D.!!$F1 504
4 TraesCS2B01G179800 chr3B 737485953 737486463 510 False 828.000000 828 95.890000 1 511 1 chr3B.!!$F2 510
5 TraesCS2B01G179800 chr3B 737450633 737451143 510 False 822.000000 822 95.695000 1 511 1 chr3B.!!$F1 510
6 TraesCS2B01G179800 chr3B 22643570 22644081 511 True 813.000000 813 95.322000 4 516 1 chr3B.!!$R1 512
7 TraesCS2B01G179800 chr3B 160018422 160018929 507 True 496.000000 496 84.252000 2 509 1 chr3B.!!$R2 507
8 TraesCS2B01G179800 chr1B 139473813 139474327 514 False 802.000000 802 94.767000 1 516 1 chr1B.!!$F1 515
9 TraesCS2B01G179800 chr7B 686914259 686914763 504 False 640.000000 640 89.526000 3 508 1 chr7B.!!$F1 505
10 TraesCS2B01G179800 chr6B 41519769 41520276 507 False 634.000000 634 89.173000 1 508 1 chr6B.!!$F1 507

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
531 533 0.034089 GCTGGCCCTTGGTCTGTATT 60.034 55.0 0.0 0.0 0.0 1.89 F
698 700 0.035820 TGTGTTCCCAACCTATCGGC 60.036 55.0 0.0 0.0 0.0 5.54 F
935 974 0.252012 CCACCTCTCCCACTCTCACT 60.252 60.0 0.0 0.0 0.0 3.41 F
936 975 1.181786 CACCTCTCCCACTCTCACTC 58.818 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1939 0.820871 GCTGAGGAAGACGATGGACT 59.179 55.000 0.0 0.0 0.00 3.85 R
1680 2096 1.003839 GCCGACCTTGGTGATGTCA 60.004 57.895 0.0 0.0 0.00 3.58 R
2358 2774 1.255882 GGACCACATGCAAACCATCA 58.744 50.000 0.0 0.0 29.71 3.07 R
2791 3207 3.038280 CACTGGGAGTATATGGACACCA 58.962 50.000 0.0 0.0 38.19 4.17 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
49 50 1.144936 GGTCAGCCGAGAAGATGGG 59.855 63.158 0.00 0.00 0.00 4.00
119 120 3.881220 CACAACCCCAATACTATCCGTT 58.119 45.455 0.00 0.00 0.00 4.44
125 126 4.346127 ACCCCAATACTATCCGTTAGTTCC 59.654 45.833 1.17 0.00 41.49 3.62
126 127 4.591924 CCCCAATACTATCCGTTAGTTCCT 59.408 45.833 1.17 0.00 41.49 3.36
215 217 6.481644 CCTCTTTCAGCCATGTTATTCTAGAC 59.518 42.308 0.00 0.00 0.00 2.59
229 231 7.504238 TGTTATTCTAGACCTTTGAAGCCAAAA 59.496 33.333 0.00 0.00 41.28 2.44
287 289 5.350091 GTCAGTGACTCTTCTAATTTCCTGC 59.650 44.000 16.26 0.00 0.00 4.85
386 388 3.256631 TCTTACTCCACTTACCCAACGTC 59.743 47.826 0.00 0.00 0.00 4.34
511 513 0.451783 CAAAACAGCTCATACCGGCC 59.548 55.000 0.00 0.00 0.00 6.13
512 514 1.024579 AAAACAGCTCATACCGGCCG 61.025 55.000 21.04 21.04 0.00 6.13
513 515 4.530857 ACAGCTCATACCGGCCGC 62.531 66.667 22.85 3.50 0.00 6.53
514 516 4.227134 CAGCTCATACCGGCCGCT 62.227 66.667 22.85 9.53 0.00 5.52
515 517 4.227134 AGCTCATACCGGCCGCTG 62.227 66.667 22.85 16.69 0.00 5.18
528 530 4.335647 CGCTGGCCCTTGGTCTGT 62.336 66.667 0.00 0.00 0.00 3.41
529 531 2.954684 CGCTGGCCCTTGGTCTGTA 61.955 63.158 0.00 0.00 0.00 2.74
530 532 1.609783 GCTGGCCCTTGGTCTGTAT 59.390 57.895 0.00 0.00 0.00 2.29
531 533 0.034089 GCTGGCCCTTGGTCTGTATT 60.034 55.000 0.00 0.00 0.00 1.89
532 534 1.755179 CTGGCCCTTGGTCTGTATTG 58.245 55.000 0.00 0.00 0.00 1.90
533 535 0.331278 TGGCCCTTGGTCTGTATTGG 59.669 55.000 0.00 0.00 0.00 3.16
534 536 1.037579 GGCCCTTGGTCTGTATTGGC 61.038 60.000 0.00 0.00 36.68 4.52
535 537 1.037579 GCCCTTGGTCTGTATTGGCC 61.038 60.000 0.00 0.00 0.00 5.36
536 538 0.625849 CCCTTGGTCTGTATTGGCCT 59.374 55.000 3.32 0.00 0.00 5.19
537 539 1.005924 CCCTTGGTCTGTATTGGCCTT 59.994 52.381 3.32 0.00 0.00 4.35
538 540 2.557452 CCCTTGGTCTGTATTGGCCTTT 60.557 50.000 3.32 0.00 0.00 3.11
539 541 3.308832 CCCTTGGTCTGTATTGGCCTTTA 60.309 47.826 3.32 0.00 0.00 1.85
540 542 4.536765 CCTTGGTCTGTATTGGCCTTTAT 58.463 43.478 3.32 0.00 0.00 1.40
541 543 4.956075 CCTTGGTCTGTATTGGCCTTTATT 59.044 41.667 3.32 0.00 0.00 1.40
542 544 6.126409 CCTTGGTCTGTATTGGCCTTTATTA 58.874 40.000 3.32 0.00 0.00 0.98
543 545 6.039382 CCTTGGTCTGTATTGGCCTTTATTAC 59.961 42.308 3.32 0.00 0.00 1.89
544 546 6.321821 TGGTCTGTATTGGCCTTTATTACT 57.678 37.500 3.32 0.00 0.00 2.24
545 547 6.727394 TGGTCTGTATTGGCCTTTATTACTT 58.273 36.000 3.32 0.00 0.00 2.24
546 548 6.826741 TGGTCTGTATTGGCCTTTATTACTTC 59.173 38.462 3.32 0.00 0.00 3.01
547 549 6.826741 GGTCTGTATTGGCCTTTATTACTTCA 59.173 38.462 3.32 0.00 0.00 3.02
548 550 7.502561 GGTCTGTATTGGCCTTTATTACTTCAT 59.497 37.037 3.32 0.00 0.00 2.57
549 551 8.345565 GTCTGTATTGGCCTTTATTACTTCATG 58.654 37.037 3.32 0.00 0.00 3.07
550 552 7.502226 TCTGTATTGGCCTTTATTACTTCATGG 59.498 37.037 3.32 0.00 0.00 3.66
551 553 7.122715 TGTATTGGCCTTTATTACTTCATGGT 58.877 34.615 3.32 0.00 0.00 3.55
552 554 6.715347 ATTGGCCTTTATTACTTCATGGTC 57.285 37.500 3.32 0.00 0.00 4.02
553 555 5.450818 TGGCCTTTATTACTTCATGGTCT 57.549 39.130 3.32 0.00 0.00 3.85
554 556 5.826643 TGGCCTTTATTACTTCATGGTCTT 58.173 37.500 3.32 0.00 0.00 3.01
555 557 5.885912 TGGCCTTTATTACTTCATGGTCTTC 59.114 40.000 3.32 0.00 0.00 2.87
556 558 5.299531 GGCCTTTATTACTTCATGGTCTTCC 59.700 44.000 0.00 0.00 0.00 3.46
568 570 3.893753 TGGTCTTCCATTTCCAAGGAA 57.106 42.857 0.00 0.00 41.41 3.36
573 575 2.113860 TCCATTTCCAAGGAAGCTCG 57.886 50.000 1.32 0.00 35.38 5.03
574 576 1.098050 CCATTTCCAAGGAAGCTCGG 58.902 55.000 1.32 0.00 35.38 4.63
575 577 1.614317 CCATTTCCAAGGAAGCTCGGT 60.614 52.381 1.32 0.00 35.38 4.69
576 578 1.470098 CATTTCCAAGGAAGCTCGGTG 59.530 52.381 1.32 0.00 35.38 4.94
577 579 0.472471 TTTCCAAGGAAGCTCGGTGT 59.528 50.000 1.32 0.00 35.38 4.16
578 580 0.472471 TTCCAAGGAAGCTCGGTGTT 59.528 50.000 0.00 0.00 0.00 3.32
579 581 0.472471 TCCAAGGAAGCTCGGTGTTT 59.528 50.000 0.00 0.00 0.00 2.83
580 582 1.133915 TCCAAGGAAGCTCGGTGTTTT 60.134 47.619 0.00 0.00 0.00 2.43
581 583 1.681264 CCAAGGAAGCTCGGTGTTTTT 59.319 47.619 0.00 0.00 0.00 1.94
601 603 6.555463 TTTTTACTCCCTCCGTCTCATAAT 57.445 37.500 0.00 0.00 0.00 1.28
602 604 7.664552 TTTTTACTCCCTCCGTCTCATAATA 57.335 36.000 0.00 0.00 0.00 0.98
603 605 7.850935 TTTTACTCCCTCCGTCTCATAATAT 57.149 36.000 0.00 0.00 0.00 1.28
604 606 8.945195 TTTTACTCCCTCCGTCTCATAATATA 57.055 34.615 0.00 0.00 0.00 0.86
605 607 8.945195 TTTACTCCCTCCGTCTCATAATATAA 57.055 34.615 0.00 0.00 0.00 0.98
606 608 8.945195 TTACTCCCTCCGTCTCATAATATAAA 57.055 34.615 0.00 0.00 0.00 1.40
607 609 7.850935 ACTCCCTCCGTCTCATAATATAAAA 57.149 36.000 0.00 0.00 0.00 1.52
608 610 7.897864 ACTCCCTCCGTCTCATAATATAAAAG 58.102 38.462 0.00 0.00 0.00 2.27
609 611 7.509659 ACTCCCTCCGTCTCATAATATAAAAGT 59.490 37.037 0.00 0.00 0.00 2.66
610 612 8.945195 TCCCTCCGTCTCATAATATAAAAGTA 57.055 34.615 0.00 0.00 0.00 2.24
611 613 9.543231 TCCCTCCGTCTCATAATATAAAAGTAT 57.457 33.333 0.00 0.00 0.00 2.12
612 614 9.804758 CCCTCCGTCTCATAATATAAAAGTATC 57.195 37.037 0.00 0.00 0.00 2.24
657 659 9.787435 ATACTTTTATATTATGAAACGCAGGGA 57.213 29.630 0.00 0.00 0.00 4.20
658 660 8.154649 ACTTTTATATTATGAAACGCAGGGAG 57.845 34.615 0.00 0.00 0.00 4.30
659 661 7.773690 ACTTTTATATTATGAAACGCAGGGAGT 59.226 33.333 0.00 0.00 0.00 3.85
660 662 9.268268 CTTTTATATTATGAAACGCAGGGAGTA 57.732 33.333 0.00 0.00 0.00 2.59
661 663 8.597662 TTTATATTATGAAACGCAGGGAGTAC 57.402 34.615 0.00 0.00 0.00 2.73
662 664 3.965379 TTATGAAACGCAGGGAGTACA 57.035 42.857 0.00 0.00 0.00 2.90
663 665 4.481368 TTATGAAACGCAGGGAGTACAT 57.519 40.909 0.00 0.00 0.00 2.29
664 666 2.380084 TGAAACGCAGGGAGTACATC 57.620 50.000 0.00 0.00 0.00 3.06
665 667 1.899814 TGAAACGCAGGGAGTACATCT 59.100 47.619 0.00 0.00 0.00 2.90
666 668 2.301870 TGAAACGCAGGGAGTACATCTT 59.698 45.455 0.00 0.00 0.00 2.40
667 669 3.244422 TGAAACGCAGGGAGTACATCTTT 60.244 43.478 0.00 0.00 0.00 2.52
668 670 3.418684 AACGCAGGGAGTACATCTTTT 57.581 42.857 0.00 0.00 0.00 2.27
669 671 3.418684 ACGCAGGGAGTACATCTTTTT 57.581 42.857 0.00 0.00 0.00 1.94
670 672 4.546829 ACGCAGGGAGTACATCTTTTTA 57.453 40.909 0.00 0.00 0.00 1.52
671 673 4.504858 ACGCAGGGAGTACATCTTTTTAG 58.495 43.478 0.00 0.00 0.00 1.85
672 674 4.222145 ACGCAGGGAGTACATCTTTTTAGA 59.778 41.667 0.00 0.00 0.00 2.10
673 675 5.175859 CGCAGGGAGTACATCTTTTTAGAA 58.824 41.667 0.00 0.00 0.00 2.10
674 676 5.817816 CGCAGGGAGTACATCTTTTTAGAAT 59.182 40.000 0.00 0.00 0.00 2.40
675 677 6.238211 CGCAGGGAGTACATCTTTTTAGAATG 60.238 42.308 0.00 0.00 0.00 2.67
676 678 6.599638 GCAGGGAGTACATCTTTTTAGAATGT 59.400 38.462 0.00 0.00 0.00 2.71
677 679 7.769044 GCAGGGAGTACATCTTTTTAGAATGTA 59.231 37.037 0.00 0.00 0.00 2.29
678 680 9.838339 CAGGGAGTACATCTTTTTAGAATGTAT 57.162 33.333 0.00 0.00 31.50 2.29
687 689 9.573133 CATCTTTTTAGAATGTATTGTGTTCCC 57.427 33.333 0.00 0.00 0.00 3.97
688 690 8.698973 TCTTTTTAGAATGTATTGTGTTCCCA 57.301 30.769 0.00 0.00 0.00 4.37
689 691 9.137459 TCTTTTTAGAATGTATTGTGTTCCCAA 57.863 29.630 0.00 0.00 0.00 4.12
690 692 9.191995 CTTTTTAGAATGTATTGTGTTCCCAAC 57.808 33.333 0.00 0.00 0.00 3.77
691 693 6.827586 TTAGAATGTATTGTGTTCCCAACC 57.172 37.500 0.00 0.00 0.00 3.77
692 694 4.998051 AGAATGTATTGTGTTCCCAACCT 58.002 39.130 0.00 0.00 0.00 3.50
693 695 6.134535 AGAATGTATTGTGTTCCCAACCTA 57.865 37.500 0.00 0.00 0.00 3.08
694 696 6.731467 AGAATGTATTGTGTTCCCAACCTAT 58.269 36.000 0.00 0.00 0.00 2.57
695 697 6.828785 AGAATGTATTGTGTTCCCAACCTATC 59.171 38.462 0.00 0.00 0.00 2.08
696 698 4.509616 TGTATTGTGTTCCCAACCTATCG 58.490 43.478 0.00 0.00 0.00 2.92
697 699 2.483014 TTGTGTTCCCAACCTATCGG 57.517 50.000 0.00 0.00 0.00 4.18
698 700 0.035820 TGTGTTCCCAACCTATCGGC 60.036 55.000 0.00 0.00 0.00 5.54
819 839 3.636043 CCGACACACACCACGCAC 61.636 66.667 0.00 0.00 0.00 5.34
921 960 2.014550 CCCATCCCCATTCCCACCT 61.015 63.158 0.00 0.00 0.00 4.00
931 970 0.419459 ATTCCCACCTCTCCCACTCT 59.581 55.000 0.00 0.00 0.00 3.24
932 971 0.252284 TTCCCACCTCTCCCACTCTC 60.252 60.000 0.00 0.00 0.00 3.20
933 972 1.079256 CCCACCTCTCCCACTCTCA 59.921 63.158 0.00 0.00 0.00 3.27
934 973 1.261238 CCCACCTCTCCCACTCTCAC 61.261 65.000 0.00 0.00 0.00 3.51
935 974 0.252012 CCACCTCTCCCACTCTCACT 60.252 60.000 0.00 0.00 0.00 3.41
936 975 1.181786 CACCTCTCCCACTCTCACTC 58.818 60.000 0.00 0.00 0.00 3.51
944 983 2.055042 CACTCTCACTCCCCCTCCG 61.055 68.421 0.00 0.00 0.00 4.63
965 1004 1.452108 CTCCACCCAAATCTCGCCC 60.452 63.158 0.00 0.00 0.00 6.13
967 1006 2.440247 CACCCAAATCTCGCCCCC 60.440 66.667 0.00 0.00 0.00 5.40
1012 1054 4.227134 CCGCCATGTCCTCCTCCG 62.227 72.222 0.00 0.00 0.00 4.63
1426 1842 4.465512 GCATCAACGCCACCGCTG 62.466 66.667 0.00 0.00 38.22 5.18
1427 1843 4.465512 CATCAACGCCACCGCTGC 62.466 66.667 0.00 0.00 38.22 5.25
1523 1939 1.603455 CCAAGGCCTTCTTCCGCAA 60.603 57.895 17.29 0.00 32.41 4.85
1647 2063 1.750399 GTACAGGGACTACCGCCGA 60.750 63.158 0.00 0.00 46.96 5.54
1748 2164 4.176752 GCCTCGCCCCAAGGGTAG 62.177 72.222 4.11 0.00 46.51 3.18
1761 2177 1.670083 GGGTAGCAAGAAACCGCGT 60.670 57.895 4.92 0.00 36.57 6.01
2295 2711 2.289945 CCAGAGGCCTTGGTATGCTATC 60.290 54.545 20.06 0.00 0.00 2.08
2358 2774 1.707427 GGCAGGATGGATTGGGACTAT 59.293 52.381 0.00 0.00 35.86 2.12
2397 2813 1.683011 CGAGGGTGGAAGGCAATGAAT 60.683 52.381 0.00 0.00 0.00 2.57
2445 2861 1.809619 CACATCACCCGACGCGATT 60.810 57.895 15.93 0.00 0.00 3.34
2502 2918 2.094762 ACCTCTACATCGCAACCAAC 57.905 50.000 0.00 0.00 0.00 3.77
2511 2927 1.169661 TCGCAACCAACGAGCCATTT 61.170 50.000 0.00 0.00 33.96 2.32
2562 2978 2.736144 ACCATGTGCATTTGCTTGAG 57.264 45.000 3.94 0.00 42.66 3.02
2624 3040 2.286477 ACGAGACGACAGCGATCAATAG 60.286 50.000 7.09 0.00 41.64 1.73
2697 3113 4.950050 AGGTATTCTACAGATCAAAGGCG 58.050 43.478 0.00 0.00 0.00 5.52
2808 3225 9.614792 GATAATTATTGGTGTCCATATACTCCC 57.385 37.037 0.00 0.00 33.06 4.30
2810 3227 4.982241 ATTGGTGTCCATATACTCCCAG 57.018 45.455 0.00 0.00 33.06 4.45
2861 3278 5.653769 ACTTCATCCAGGGTTTGTCATATTG 59.346 40.000 0.00 0.00 0.00 1.90
2908 3329 4.334759 GTCATAGCATGCTCAGTTGATTGT 59.665 41.667 26.57 0.00 0.00 2.71
3006 3428 4.631813 CCAAATAGTAACACTCAGTGAGCC 59.368 45.833 20.31 3.45 36.96 4.70
3013 3435 2.409406 ACACTCAGTGAGCCTTTTGCG 61.409 52.381 20.31 1.63 40.18 4.85
3066 3488 3.494048 GCAGTATCTCTGAGTCCCCATTG 60.494 52.174 4.32 0.00 46.27 2.82
3192 3614 5.236695 GTCAAAAGTTAGAACAGAGGTCACC 59.763 44.000 0.00 0.00 0.00 4.02
3224 3646 4.335315 CAGATTACCATGTATGCCGTGTTT 59.665 41.667 0.00 0.00 0.00 2.83
3362 3784 4.486125 TGGAAGCTATGACATAACAGCA 57.514 40.909 10.54 0.00 36.47 4.41
3453 3875 3.169908 GAGAAAAGAGAGGAGACCAGGT 58.830 50.000 0.00 0.00 0.00 4.00
3564 4072 2.778299 TGAGTATTTGTCACAGTGGGC 58.222 47.619 0.00 0.00 0.00 5.36
3708 4216 3.270877 GGCATAAGTCCTTCACAATCGT 58.729 45.455 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 6.519419 GCGTTTGGCAAATGAATATTTTCAAC 59.481 34.615 30.87 7.50 42.54 3.18
119 120 7.094933 GCGAGGAAAAACAAGATAAAGGAACTA 60.095 37.037 0.00 0.00 38.49 2.24
125 126 5.316770 CGAGCGAGGAAAAACAAGATAAAG 58.683 41.667 0.00 0.00 0.00 1.85
126 127 4.378046 GCGAGCGAGGAAAAACAAGATAAA 60.378 41.667 0.00 0.00 0.00 1.40
215 217 4.861102 AGAGATGTTTTGGCTTCAAAGG 57.139 40.909 0.00 0.00 40.89 3.11
229 231 4.961730 AGTTGCTCTATCAGGAAGAGATGT 59.038 41.667 4.34 0.00 42.63 3.06
316 318 3.531538 GCTAAATCACGATCCCAACTGA 58.468 45.455 0.00 0.00 0.00 3.41
511 513 2.257409 ATACAGACCAAGGGCCAGCG 62.257 60.000 6.18 0.00 0.00 5.18
512 514 0.034089 AATACAGACCAAGGGCCAGC 60.034 55.000 6.18 0.00 0.00 4.85
513 515 1.683011 CCAATACAGACCAAGGGCCAG 60.683 57.143 6.18 0.00 0.00 4.85
514 516 0.331278 CCAATACAGACCAAGGGCCA 59.669 55.000 6.18 0.00 0.00 5.36
515 517 1.037579 GCCAATACAGACCAAGGGCC 61.038 60.000 0.00 0.00 33.93 5.80
516 518 1.037579 GGCCAATACAGACCAAGGGC 61.038 60.000 0.00 0.00 39.18 5.19
517 519 0.625849 AGGCCAATACAGACCAAGGG 59.374 55.000 5.01 0.00 0.00 3.95
518 520 2.514458 AAGGCCAATACAGACCAAGG 57.486 50.000 5.01 0.00 0.00 3.61
519 521 6.828785 AGTAATAAAGGCCAATACAGACCAAG 59.171 38.462 5.01 0.00 0.00 3.61
520 522 6.727394 AGTAATAAAGGCCAATACAGACCAA 58.273 36.000 5.01 0.00 0.00 3.67
521 523 6.321821 AGTAATAAAGGCCAATACAGACCA 57.678 37.500 5.01 0.00 0.00 4.02
522 524 6.826741 TGAAGTAATAAAGGCCAATACAGACC 59.173 38.462 5.01 0.00 0.00 3.85
523 525 7.859325 TGAAGTAATAAAGGCCAATACAGAC 57.141 36.000 5.01 0.00 0.00 3.51
524 526 7.502226 CCATGAAGTAATAAAGGCCAATACAGA 59.498 37.037 5.01 0.00 0.00 3.41
525 527 7.285401 ACCATGAAGTAATAAAGGCCAATACAG 59.715 37.037 5.01 0.00 0.00 2.74
526 528 7.122715 ACCATGAAGTAATAAAGGCCAATACA 58.877 34.615 5.01 0.00 0.00 2.29
527 529 7.502561 AGACCATGAAGTAATAAAGGCCAATAC 59.497 37.037 5.01 0.15 0.00 1.89
528 530 7.582719 AGACCATGAAGTAATAAAGGCCAATA 58.417 34.615 5.01 0.00 0.00 1.90
529 531 6.435164 AGACCATGAAGTAATAAAGGCCAAT 58.565 36.000 5.01 0.00 0.00 3.16
530 532 5.826643 AGACCATGAAGTAATAAAGGCCAA 58.173 37.500 5.01 0.00 0.00 4.52
531 533 5.450818 AGACCATGAAGTAATAAAGGCCA 57.549 39.130 5.01 0.00 0.00 5.36
532 534 5.299531 GGAAGACCATGAAGTAATAAAGGCC 59.700 44.000 0.00 0.00 35.97 5.19
533 535 5.885912 TGGAAGACCATGAAGTAATAAAGGC 59.114 40.000 0.00 0.00 41.77 4.35
553 555 2.436417 CGAGCTTCCTTGGAAATGGAA 58.564 47.619 3.54 0.00 39.73 3.53
554 556 1.340017 CCGAGCTTCCTTGGAAATGGA 60.340 52.381 3.54 0.00 44.32 3.41
555 557 1.098050 CCGAGCTTCCTTGGAAATGG 58.902 55.000 3.54 0.16 44.32 3.16
556 558 1.470098 CACCGAGCTTCCTTGGAAATG 59.530 52.381 3.54 0.00 44.32 2.32
557 559 1.073923 ACACCGAGCTTCCTTGGAAAT 59.926 47.619 3.54 0.00 44.32 2.17
558 560 0.472471 ACACCGAGCTTCCTTGGAAA 59.528 50.000 3.54 0.00 44.32 3.13
559 561 0.472471 AACACCGAGCTTCCTTGGAA 59.528 50.000 4.04 1.86 44.32 3.53
560 562 0.472471 AAACACCGAGCTTCCTTGGA 59.528 50.000 4.04 0.00 44.32 3.53
561 563 1.318576 AAAACACCGAGCTTCCTTGG 58.681 50.000 0.00 0.00 46.57 3.61
578 580 6.555463 ATTATGAGACGGAGGGAGTAAAAA 57.445 37.500 0.00 0.00 0.00 1.94
579 581 7.850935 ATATTATGAGACGGAGGGAGTAAAA 57.149 36.000 0.00 0.00 0.00 1.52
580 582 8.945195 TTATATTATGAGACGGAGGGAGTAAA 57.055 34.615 0.00 0.00 0.00 2.01
581 583 8.945195 TTTATATTATGAGACGGAGGGAGTAA 57.055 34.615 0.00 0.00 0.00 2.24
582 584 8.945195 TTTTATATTATGAGACGGAGGGAGTA 57.055 34.615 0.00 0.00 0.00 2.59
583 585 7.509659 ACTTTTATATTATGAGACGGAGGGAGT 59.490 37.037 0.00 0.00 0.00 3.85
584 586 7.897864 ACTTTTATATTATGAGACGGAGGGAG 58.102 38.462 0.00 0.00 0.00 4.30
585 587 7.850935 ACTTTTATATTATGAGACGGAGGGA 57.149 36.000 0.00 0.00 0.00 4.20
586 588 9.804758 GATACTTTTATATTATGAGACGGAGGG 57.195 37.037 0.00 0.00 0.00 4.30
631 633 9.787435 TCCCTGCGTTTCATAATATAAAAGTAT 57.213 29.630 0.00 0.00 0.00 2.12
632 634 9.268268 CTCCCTGCGTTTCATAATATAAAAGTA 57.732 33.333 0.00 0.00 0.00 2.24
633 635 7.773690 ACTCCCTGCGTTTCATAATATAAAAGT 59.226 33.333 0.00 0.00 0.00 2.66
634 636 8.154649 ACTCCCTGCGTTTCATAATATAAAAG 57.845 34.615 0.00 0.00 0.00 2.27
635 637 9.048446 GTACTCCCTGCGTTTCATAATATAAAA 57.952 33.333 0.00 0.00 0.00 1.52
636 638 8.205512 TGTACTCCCTGCGTTTCATAATATAAA 58.794 33.333 0.00 0.00 0.00 1.40
637 639 7.728148 TGTACTCCCTGCGTTTCATAATATAA 58.272 34.615 0.00 0.00 0.00 0.98
638 640 7.292713 TGTACTCCCTGCGTTTCATAATATA 57.707 36.000 0.00 0.00 0.00 0.86
639 641 6.169557 TGTACTCCCTGCGTTTCATAATAT 57.830 37.500 0.00 0.00 0.00 1.28
640 642 5.601583 TGTACTCCCTGCGTTTCATAATA 57.398 39.130 0.00 0.00 0.00 0.98
641 643 4.481368 TGTACTCCCTGCGTTTCATAAT 57.519 40.909 0.00 0.00 0.00 1.28
642 644 3.965379 TGTACTCCCTGCGTTTCATAA 57.035 42.857 0.00 0.00 0.00 1.90
643 645 3.704566 AGATGTACTCCCTGCGTTTCATA 59.295 43.478 0.00 0.00 0.00 2.15
644 646 2.501723 AGATGTACTCCCTGCGTTTCAT 59.498 45.455 0.00 0.00 0.00 2.57
645 647 1.899814 AGATGTACTCCCTGCGTTTCA 59.100 47.619 0.00 0.00 0.00 2.69
646 648 2.674796 AGATGTACTCCCTGCGTTTC 57.325 50.000 0.00 0.00 0.00 2.78
647 649 3.418684 AAAGATGTACTCCCTGCGTTT 57.581 42.857 0.00 0.00 0.00 3.60
648 650 3.418684 AAAAGATGTACTCCCTGCGTT 57.581 42.857 0.00 0.00 0.00 4.84
649 651 3.418684 AAAAAGATGTACTCCCTGCGT 57.581 42.857 0.00 0.00 0.00 5.24
650 652 4.755411 TCTAAAAAGATGTACTCCCTGCG 58.245 43.478 0.00 0.00 0.00 5.18
651 653 6.599638 ACATTCTAAAAAGATGTACTCCCTGC 59.400 38.462 0.00 0.00 0.00 4.85
652 654 9.838339 ATACATTCTAAAAAGATGTACTCCCTG 57.162 33.333 0.00 0.00 31.56 4.45
661 663 9.573133 GGGAACACAATACATTCTAAAAAGATG 57.427 33.333 0.00 0.00 0.00 2.90
662 664 9.308000 TGGGAACACAATACATTCTAAAAAGAT 57.692 29.630 0.00 0.00 33.40 2.40
663 665 8.698973 TGGGAACACAATACATTCTAAAAAGA 57.301 30.769 0.00 0.00 33.40 2.52
664 666 9.191995 GTTGGGAACACAATACATTCTAAAAAG 57.808 33.333 0.00 0.00 42.67 2.27
665 667 8.145122 GGTTGGGAACACAATACATTCTAAAAA 58.855 33.333 0.00 0.00 42.67 1.94
666 668 7.507616 AGGTTGGGAACACAATACATTCTAAAA 59.492 33.333 0.00 0.00 42.67 1.52
667 669 7.007723 AGGTTGGGAACACAATACATTCTAAA 58.992 34.615 0.00 0.00 42.67 1.85
668 670 6.548321 AGGTTGGGAACACAATACATTCTAA 58.452 36.000 0.00 0.00 42.67 2.10
669 671 6.134535 AGGTTGGGAACACAATACATTCTA 57.865 37.500 0.00 0.00 42.67 2.10
670 672 4.998051 AGGTTGGGAACACAATACATTCT 58.002 39.130 0.00 0.00 42.67 2.40
671 673 6.238374 CGATAGGTTGGGAACACAATACATTC 60.238 42.308 0.00 0.00 42.67 2.67
672 674 5.588648 CGATAGGTTGGGAACACAATACATT 59.411 40.000 0.00 0.00 42.67 2.71
673 675 5.123227 CGATAGGTTGGGAACACAATACAT 58.877 41.667 0.00 0.00 42.67 2.29
674 676 4.509616 CGATAGGTTGGGAACACAATACA 58.490 43.478 0.00 0.00 42.67 2.29
691 693 0.465705 TTCCCTGCTCTTGCCGATAG 59.534 55.000 0.00 0.00 38.71 2.08
692 694 0.465705 CTTCCCTGCTCTTGCCGATA 59.534 55.000 0.00 0.00 38.71 2.92
693 695 1.222936 CTTCCCTGCTCTTGCCGAT 59.777 57.895 0.00 0.00 38.71 4.18
694 696 1.913262 TCTTCCCTGCTCTTGCCGA 60.913 57.895 0.00 0.00 38.71 5.54
695 697 1.743252 GTCTTCCCTGCTCTTGCCG 60.743 63.158 0.00 0.00 38.71 5.69
696 698 1.743252 CGTCTTCCCTGCTCTTGCC 60.743 63.158 0.00 0.00 38.71 4.52
697 699 1.016653 GTCGTCTTCCCTGCTCTTGC 61.017 60.000 0.00 0.00 40.20 4.01
698 700 0.605589 AGTCGTCTTCCCTGCTCTTG 59.394 55.000 0.00 0.00 0.00 3.02
819 839 1.160137 CTGTCTTCCTTCCTTTGCGG 58.840 55.000 0.00 0.00 0.00 5.69
921 960 1.388531 GGGGAGTGAGAGTGGGAGA 59.611 63.158 0.00 0.00 0.00 3.71
944 983 2.464459 CGAGATTTGGGTGGAGCGC 61.464 63.158 0.00 0.00 0.00 5.92
1012 1054 2.971452 GTCGTGGTCCTCCTGGTC 59.029 66.667 0.00 0.00 34.23 4.02
1155 1565 1.074752 GCACGAAGAAGGAGAAGCAG 58.925 55.000 0.00 0.00 0.00 4.24
1497 1913 1.172812 AGAAGGCCTTGGCGTTGAAC 61.173 55.000 26.25 4.63 0.00 3.18
1523 1939 0.820871 GCTGAGGAAGACGATGGACT 59.179 55.000 0.00 0.00 0.00 3.85
1680 2096 1.003839 GCCGACCTTGGTGATGTCA 60.004 57.895 0.00 0.00 0.00 3.58
1747 2163 2.594962 CGACACGCGGTTTCTTGCT 61.595 57.895 12.47 0.00 36.03 3.91
1748 2164 2.127758 CGACACGCGGTTTCTTGC 60.128 61.111 12.47 0.00 36.03 4.01
2148 2564 3.623703 GCATTGGGGTCACCTTGTATGTA 60.624 47.826 0.00 0.00 41.11 2.29
2358 2774 1.255882 GGACCACATGCAAACCATCA 58.744 50.000 0.00 0.00 29.71 3.07
2397 2813 6.570692 GTCCAAGTTCGGATACATCTTCTTA 58.429 40.000 0.00 0.00 37.41 2.10
2445 2861 6.382859 TGATAAGCTTGGTCACCTTATCTACA 59.617 38.462 9.86 8.06 43.72 2.74
2502 2918 4.624024 TCGAAGTAGTTGTAAAATGGCTCG 59.376 41.667 0.00 0.00 0.00 5.03
2511 2927 5.190992 TGAGCTTGTCGAAGTAGTTGTAA 57.809 39.130 0.00 0.00 0.00 2.41
2562 2978 4.957296 TCGACCAAAGCTCCTTATAATCC 58.043 43.478 0.00 0.00 0.00 3.01
2673 3089 4.985409 GCCTTTGATCTGTAGAATACCTCG 59.015 45.833 0.00 0.00 42.12 4.63
2791 3207 3.038280 CACTGGGAGTATATGGACACCA 58.962 50.000 0.00 0.00 38.19 4.17
2808 3225 4.124351 CCATTGCGCCAGCCACTG 62.124 66.667 4.18 0.00 44.33 3.66
2810 3227 3.372730 TTCCATTGCGCCAGCCAC 61.373 61.111 4.18 0.00 44.33 5.01
3006 3428 3.654414 AGAAGTAGAGACACCGCAAAAG 58.346 45.455 0.00 0.00 0.00 2.27
3013 3435 5.106078 CCAGACACTAAGAAGTAGAGACACC 60.106 48.000 0.00 0.00 33.48 4.16
3017 3439 6.129414 AGTCCAGACACTAAGAAGTAGAGA 57.871 41.667 0.00 0.00 33.48 3.10
3066 3488 2.881111 AGAGAAACCCCAAGCTAACC 57.119 50.000 0.00 0.00 0.00 2.85
3177 3599 1.555075 GCCATGGTGACCTCTGTTCTA 59.445 52.381 14.67 0.00 0.00 2.10
3224 3646 7.221450 AGGCAAGTAAGTTACTTATGACAACA 58.779 34.615 24.33 0.00 46.66 3.33
3246 3668 1.749634 AGAGCAAGCATCATTCAAGGC 59.250 47.619 0.00 0.00 0.00 4.35
3362 3784 5.468746 TGCAAACGCACTATTCTAGAAGTTT 59.531 36.000 11.53 11.07 33.43 2.66
3708 4216 7.706159 TCAAACTTAACTACTAGTGTGACGAA 58.294 34.615 5.39 0.00 34.50 3.85


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

AutoCloner maintained by Alex Coulton.