Multiple sequence alignment - TraesCS2B01G210200

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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 TraesCS2B01G210200 chr2B 100.000 2495 0 0 1 2495 193211907 193209413 0.000000e+00 4608.0
1 TraesCS2B01G210200 chr2B 88.091 529 35 8 1 503 568037665 568037139 9.870000e-169 603.0
2 TraesCS2B01G210200 chr2B 87.239 431 39 10 30 449 798212278 798212703 6.240000e-131 477.0
3 TraesCS2B01G210200 chr2B 83.824 68 8 3 1914 1979 707603469 707603535 7.450000e-06 62.1
4 TraesCS2B01G210200 chr2A 91.532 1299 75 18 862 2129 143276925 143275631 0.000000e+00 1757.0
5 TraesCS2B01G210200 chr2A 95.935 369 15 0 2127 2495 143275585 143275217 1.280000e-167 599.0
6 TraesCS2B01G210200 chr2D 91.933 1252 59 18 862 2100 135485963 135484741 0.000000e+00 1714.0
7 TraesCS2B01G210200 chr2D 95.238 252 11 1 2206 2457 135484745 135484495 5.000000e-107 398.0
8 TraesCS2B01G210200 chr2D 97.872 47 1 0 2449 2495 135484167 135484121 5.720000e-12 82.4
9 TraesCS2B01G210200 chr4A 90.664 482 34 5 30 503 711211083 711210605 4.530000e-177 630.0
10 TraesCS2B01G210200 chr4A 86.590 522 46 10 1 503 600728497 600727981 2.800000e-154 555.0
11 TraesCS2B01G210200 chrUn 89.189 518 33 5 1 497 41407598 41408113 2.110000e-175 625.0
12 TraesCS2B01G210200 chr3D 88.178 516 40 8 1 497 486687730 486688243 1.650000e-166 595.0
13 TraesCS2B01G210200 chr3D 86.142 534 40 11 1 503 35285467 35284937 1.690000e-151 545.0
14 TraesCS2B01G210200 chr3D 89.655 58 2 3 1915 1970 219571968 219572023 1.240000e-08 71.3
15 TraesCS2B01G210200 chr3A 89.149 470 38 7 3 462 584480415 584480881 7.740000e-160 573.0
16 TraesCS2B01G210200 chr3A 89.058 329 30 2 539 862 17589488 17589161 1.070000e-108 403.0
17 TraesCS2B01G210200 chr3A 91.071 56 4 1 1914 1968 536635253 536635308 9.570000e-10 75.0
18 TraesCS2B01G210200 chr4D 87.427 517 39 7 1 497 344952679 344953189 2.780000e-159 571.0
19 TraesCS2B01G210200 chr4D 86.148 527 39 11 1 497 472535 473057 2.820000e-149 538.0
20 TraesCS2B01G210200 chr6D 87.146 529 32 10 1 497 419451983 419452507 3.600000e-158 568.0
21 TraesCS2B01G210200 chr7B 86.905 504 51 9 1 497 655110609 655111104 3.630000e-153 551.0
22 TraesCS2B01G210200 chr7B 87.708 480 34 11 34 503 481887410 481886946 1.020000e-148 536.0
23 TraesCS2B01G210200 chr7B 88.955 335 30 3 534 862 614283203 614283536 8.310000e-110 407.0
24 TraesCS2B01G210200 chr7D 90.954 409 31 4 1 405 607959486 607959080 1.690000e-151 545.0
25 TraesCS2B01G210200 chr7D 95.238 42 2 0 462 503 607958803 607958762 1.600000e-07 67.6
26 TraesCS2B01G210200 chr5A 88.940 434 37 5 1 423 552554823 552554390 2.200000e-145 525.0
27 TraesCS2B01G210200 chr6B 88.605 430 32 12 30 449 88779830 88779408 7.960000e-140 507.0
28 TraesCS2B01G210200 chr6B 87.330 442 40 9 30 461 49951576 49952011 2.230000e-135 492.0
29 TraesCS2B01G210200 chr6B 90.578 329 26 1 534 862 471171502 471171825 4.930000e-117 431.0
30 TraesCS2B01G210200 chr6B 88.393 336 32 4 534 863 456948033 456948367 5.000000e-107 398.0
31 TraesCS2B01G210200 chr6B 90.000 60 3 3 1916 1973 471675171 471675229 9.570000e-10 75.0
32 TraesCS2B01G210200 chr1B 86.499 437 48 8 30 461 145572541 145572111 1.040000e-128 470.0
33 TraesCS2B01G210200 chr1B 89.222 334 31 1 534 862 526343621 526343288 1.790000e-111 412.0
34 TraesCS2B01G210200 chr1B 87.097 62 5 3 1914 1974 156852508 156852567 1.600000e-07 67.6
35 TraesCS2B01G210200 chr3B 89.645 338 25 4 534 865 181672872 181672539 2.970000e-114 422.0
36 TraesCS2B01G210200 chr3B 87.500 352 37 5 530 875 144219090 144218740 1.390000e-107 399.0
37 TraesCS2B01G210200 chr5D 89.697 330 26 6 539 862 505741697 505742024 4.960000e-112 414.0
38 TraesCS2B01G210200 chr5D 94.643 56 1 2 1916 1970 256458100 256458046 4.420000e-13 86.1
39 TraesCS2B01G210200 chr4B 88.286 350 33 4 534 876 625960593 625960245 1.790000e-111 412.0
40 TraesCS2B01G210200 chr1D 91.525 59 2 3 1917 1974 95867032 95866976 7.400000e-11 78.7
41 TraesCS2B01G210200 chr6A 90.000 60 3 3 1916 1973 409430671 409430729 9.570000e-10 75.0


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 TraesCS2B01G210200 chr2B 193209413 193211907 2494 True 4608.000000 4608 100.000000 1 2495 1 chr2B.!!$R1 2494
1 TraesCS2B01G210200 chr2B 568037139 568037665 526 True 603.000000 603 88.091000 1 503 1 chr2B.!!$R2 502
2 TraesCS2B01G210200 chr2A 143275217 143276925 1708 True 1178.000000 1757 93.733500 862 2495 2 chr2A.!!$R1 1633
3 TraesCS2B01G210200 chr2D 135484121 135485963 1842 True 731.466667 1714 95.014333 862 2495 3 chr2D.!!$R1 1633
4 TraesCS2B01G210200 chr4A 600727981 600728497 516 True 555.000000 555 86.590000 1 503 1 chr4A.!!$R1 502
5 TraesCS2B01G210200 chrUn 41407598 41408113 515 False 625.000000 625 89.189000 1 497 1 chrUn.!!$F1 496
6 TraesCS2B01G210200 chr3D 486687730 486688243 513 False 595.000000 595 88.178000 1 497 1 chr3D.!!$F2 496
7 TraesCS2B01G210200 chr3D 35284937 35285467 530 True 545.000000 545 86.142000 1 503 1 chr3D.!!$R1 502
8 TraesCS2B01G210200 chr4D 344952679 344953189 510 False 571.000000 571 87.427000 1 497 1 chr4D.!!$F2 496
9 TraesCS2B01G210200 chr4D 472535 473057 522 False 538.000000 538 86.148000 1 497 1 chr4D.!!$F1 496
10 TraesCS2B01G210200 chr6D 419451983 419452507 524 False 568.000000 568 87.146000 1 497 1 chr6D.!!$F1 496
11 TraesCS2B01G210200 chr7D 607958762 607959486 724 True 306.300000 545 93.096000 1 503 2 chr7D.!!$R1 502

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
727 1042 0.03254 AGCCCGACGAGTTTTTACGT 59.967 50.0 0.0 0.0 45.32 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2002 1.09805 GACAATGATGCACCCCTGAC 58.902 55.0 0.0 0.0 0.0 3.51 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
229 260 5.292101 TCACGTTTTGTTTTTGCTATTTGGG 59.708 36.000 0.00 0.00 0.00 4.12
248 279 5.890424 TGGGAAATCGTAAAGGATGTTTC 57.110 39.130 0.00 0.00 0.00 2.78
291 328 2.180432 AGTTCTTGTAGGTTTCCGCC 57.820 50.000 0.00 0.00 0.00 6.13
354 398 0.179070 TGCAAGTCGGCAGTGTTGTA 60.179 50.000 0.00 0.00 39.25 2.41
372 417 2.705658 TGTATTCGATTCCCAGCCATCT 59.294 45.455 0.00 0.00 0.00 2.90
422 726 2.472695 TGTATTTCCAGCGCACTCTT 57.527 45.000 11.47 0.00 0.00 2.85
504 819 3.953775 CCTGTTGGACCCCACGCT 61.954 66.667 0.00 0.00 30.78 5.07
505 820 2.669569 CTGTTGGACCCCACGCTG 60.670 66.667 0.00 0.00 30.78 5.18
506 821 4.263572 TGTTGGACCCCACGCTGG 62.264 66.667 0.00 0.00 37.25 4.85
507 822 4.265056 GTTGGACCCCACGCTGGT 62.265 66.667 3.82 0.00 39.32 4.00
518 833 2.805353 CGCTGGTCGTCTTCACGG 60.805 66.667 0.00 0.00 46.70 4.94
519 834 2.649034 GCTGGTCGTCTTCACGGA 59.351 61.111 0.00 0.00 46.70 4.69
520 835 1.733399 GCTGGTCGTCTTCACGGAC 60.733 63.158 0.00 0.00 46.70 4.79
544 859 2.741433 ACGTGAGTAGTTCTGGCCA 58.259 52.632 4.71 4.71 46.88 5.36
545 860 1.267121 ACGTGAGTAGTTCTGGCCAT 58.733 50.000 5.51 0.00 46.88 4.40
546 861 1.066858 ACGTGAGTAGTTCTGGCCATG 60.067 52.381 5.51 0.00 46.88 3.66
547 862 1.204704 CGTGAGTAGTTCTGGCCATGA 59.795 52.381 5.51 2.85 0.00 3.07
548 863 2.353704 CGTGAGTAGTTCTGGCCATGAA 60.354 50.000 5.51 9.83 0.00 2.57
549 864 3.674997 GTGAGTAGTTCTGGCCATGAAA 58.325 45.455 5.51 0.00 0.00 2.69
550 865 4.072131 GTGAGTAGTTCTGGCCATGAAAA 58.928 43.478 5.51 1.81 0.00 2.29
551 866 4.154918 GTGAGTAGTTCTGGCCATGAAAAG 59.845 45.833 5.51 0.00 0.00 2.27
552 867 3.084786 AGTAGTTCTGGCCATGAAAAGC 58.915 45.455 5.51 5.95 0.00 3.51
557 872 2.580815 GGCCATGAAAAGCCCAGC 59.419 61.111 0.00 0.00 43.76 4.85
558 873 2.580815 GCCATGAAAAGCCCAGCC 59.419 61.111 0.00 0.00 0.00 4.85
559 874 3.022710 GCCATGAAAAGCCCAGCCC 62.023 63.158 0.00 0.00 0.00 5.19
560 875 2.713967 CCATGAAAAGCCCAGCCCG 61.714 63.158 0.00 0.00 0.00 6.13
561 876 2.362889 ATGAAAAGCCCAGCCCGG 60.363 61.111 0.00 0.00 0.00 5.73
586 901 2.962569 GGCCCGAAAAAGCCTGAC 59.037 61.111 0.00 0.00 46.14 3.51
587 902 2.636412 GGCCCGAAAAAGCCTGACC 61.636 63.158 0.00 0.00 46.14 4.02
588 903 2.636412 GCCCGAAAAAGCCTGACCC 61.636 63.158 0.00 0.00 0.00 4.46
589 904 2.332654 CCCGAAAAAGCCTGACCCG 61.333 63.158 0.00 0.00 0.00 5.28
590 905 2.332654 CCGAAAAAGCCTGACCCGG 61.333 63.158 0.00 0.00 0.00 5.73
632 947 3.295800 CGGGCTCGGGTCTAGTTT 58.704 61.111 0.00 0.00 0.00 2.66
633 948 1.595357 CGGGCTCGGGTCTAGTTTT 59.405 57.895 0.00 0.00 0.00 2.43
634 949 0.036671 CGGGCTCGGGTCTAGTTTTT 60.037 55.000 0.00 0.00 0.00 1.94
635 950 1.450025 GGGCTCGGGTCTAGTTTTTG 58.550 55.000 0.00 0.00 0.00 2.44
636 951 1.002773 GGGCTCGGGTCTAGTTTTTGA 59.997 52.381 0.00 0.00 0.00 2.69
637 952 2.347731 GGCTCGGGTCTAGTTTTTGAG 58.652 52.381 0.00 0.00 0.00 3.02
638 953 1.732809 GCTCGGGTCTAGTTTTTGAGC 59.267 52.381 9.64 9.64 40.31 4.26
639 954 2.347731 CTCGGGTCTAGTTTTTGAGCC 58.652 52.381 0.00 0.00 44.65 4.70
642 957 3.418684 GGGTCTAGTTTTTGAGCCAGA 57.581 47.619 6.37 0.00 46.59 3.86
643 958 3.751518 GGGTCTAGTTTTTGAGCCAGAA 58.248 45.455 6.37 0.00 46.59 3.02
644 959 3.753797 GGGTCTAGTTTTTGAGCCAGAAG 59.246 47.826 6.37 0.00 46.59 2.85
645 960 3.753797 GGTCTAGTTTTTGAGCCAGAAGG 59.246 47.826 0.00 0.00 38.23 3.46
655 970 4.479993 CCAGAAGGCCGGGCTGAG 62.480 72.222 33.52 22.74 0.00 3.35
673 988 3.228017 CCCGGGCCCGTTGTTTTT 61.228 61.111 40.52 0.00 37.81 1.94
674 989 2.028337 CCGGGCCCGTTGTTTTTG 59.972 61.111 40.52 20.46 37.81 2.44
675 990 2.660224 CGGGCCCGTTGTTTTTGC 60.660 61.111 36.64 0.00 34.35 3.68
676 991 2.501610 GGGCCCGTTGTTTTTGCA 59.498 55.556 5.69 0.00 0.00 4.08
677 992 1.070615 GGGCCCGTTGTTTTTGCAT 59.929 52.632 5.69 0.00 0.00 3.96
678 993 0.533978 GGGCCCGTTGTTTTTGCATT 60.534 50.000 5.69 0.00 0.00 3.56
679 994 1.304254 GGCCCGTTGTTTTTGCATTT 58.696 45.000 0.00 0.00 0.00 2.32
680 995 1.673400 GGCCCGTTGTTTTTGCATTTT 59.327 42.857 0.00 0.00 0.00 1.82
681 996 2.098280 GGCCCGTTGTTTTTGCATTTTT 59.902 40.909 0.00 0.00 0.00 1.94
682 997 3.358775 GCCCGTTGTTTTTGCATTTTTC 58.641 40.909 0.00 0.00 0.00 2.29
683 998 3.064682 GCCCGTTGTTTTTGCATTTTTCT 59.935 39.130 0.00 0.00 0.00 2.52
684 999 4.586334 CCCGTTGTTTTTGCATTTTTCTG 58.414 39.130 0.00 0.00 0.00 3.02
685 1000 4.331168 CCCGTTGTTTTTGCATTTTTCTGA 59.669 37.500 0.00 0.00 0.00 3.27
686 1001 5.163814 CCCGTTGTTTTTGCATTTTTCTGAA 60.164 36.000 0.00 0.00 0.00 3.02
687 1002 5.958949 CCGTTGTTTTTGCATTTTTCTGAAG 59.041 36.000 0.00 0.00 0.00 3.02
688 1003 5.958949 CGTTGTTTTTGCATTTTTCTGAAGG 59.041 36.000 0.00 0.00 0.00 3.46
689 1004 6.402011 CGTTGTTTTTGCATTTTTCTGAAGGT 60.402 34.615 0.00 0.00 0.00 3.50
690 1005 6.660887 TGTTTTTGCATTTTTCTGAAGGTC 57.339 33.333 0.00 0.00 0.00 3.85
691 1006 5.290643 TGTTTTTGCATTTTTCTGAAGGTCG 59.709 36.000 0.00 0.00 0.00 4.79
692 1007 3.641437 TTGCATTTTTCTGAAGGTCGG 57.359 42.857 0.00 0.00 0.00 4.79
693 1008 1.885887 TGCATTTTTCTGAAGGTCGGG 59.114 47.619 0.00 0.00 0.00 5.14
694 1009 1.402852 GCATTTTTCTGAAGGTCGGGC 60.403 52.381 0.00 0.00 0.00 6.13
695 1010 1.202348 CATTTTTCTGAAGGTCGGGCC 59.798 52.381 0.00 0.00 37.58 5.80
696 1011 0.887387 TTTTTCTGAAGGTCGGGCCG 60.887 55.000 22.51 22.51 43.70 6.13
697 1012 2.741486 TTTTCTGAAGGTCGGGCCGG 62.741 60.000 27.98 8.04 43.70 6.13
720 1035 4.065281 CCCGAAGCCCGACGAGTT 62.065 66.667 0.00 0.00 41.76 3.01
721 1036 2.048503 CCGAAGCCCGACGAGTTT 60.049 61.111 0.00 0.00 41.76 2.66
722 1037 1.666872 CCGAAGCCCGACGAGTTTT 60.667 57.895 0.00 0.00 41.76 2.43
723 1038 1.226030 CCGAAGCCCGACGAGTTTTT 61.226 55.000 0.00 0.00 41.76 1.94
724 1039 1.421382 CGAAGCCCGACGAGTTTTTA 58.579 50.000 0.00 0.00 41.76 1.52
725 1040 1.125566 CGAAGCCCGACGAGTTTTTAC 59.874 52.381 0.00 0.00 41.76 2.01
726 1041 1.125566 GAAGCCCGACGAGTTTTTACG 59.874 52.381 0.00 0.00 0.00 3.18
727 1042 0.032540 AGCCCGACGAGTTTTTACGT 59.967 50.000 0.00 0.00 45.32 3.57
728 1043 0.162294 GCCCGACGAGTTTTTACGTG 59.838 55.000 0.00 0.00 42.74 4.49
729 1044 1.490621 CCCGACGAGTTTTTACGTGT 58.509 50.000 0.00 0.00 42.74 4.49
730 1045 1.860326 CCCGACGAGTTTTTACGTGTT 59.140 47.619 0.00 0.00 42.74 3.32
731 1046 2.097250 CCCGACGAGTTTTTACGTGTTC 60.097 50.000 0.00 0.00 42.74 3.18
732 1047 2.407609 CCGACGAGTTTTTACGTGTTCG 60.408 50.000 0.00 1.06 42.74 3.95
733 1048 2.407609 CGACGAGTTTTTACGTGTTCGG 60.408 50.000 0.00 0.00 42.74 4.30
734 1049 1.860326 ACGAGTTTTTACGTGTTCGGG 59.140 47.619 0.00 0.00 41.17 5.14
735 1050 1.397567 CGAGTTTTTACGTGTTCGGGC 60.398 52.381 0.00 0.00 41.85 6.13
736 1051 0.946528 AGTTTTTACGTGTTCGGGCC 59.053 50.000 0.00 0.00 41.85 5.80
737 1052 0.384601 GTTTTTACGTGTTCGGGCCG 60.385 55.000 22.51 22.51 41.85 6.13
738 1053 1.505477 TTTTTACGTGTTCGGGCCGG 61.505 55.000 27.98 12.18 41.85 6.13
739 1054 3.880162 TTTACGTGTTCGGGCCGGG 62.880 63.158 27.98 12.73 41.85 5.73
756 1071 4.203618 GCTCGGGCCTAGAAACAC 57.796 61.111 9.63 0.00 0.00 3.32
757 1072 1.295423 GCTCGGGCCTAGAAACACA 59.705 57.895 9.63 0.00 0.00 3.72
758 1073 0.741221 GCTCGGGCCTAGAAACACAG 60.741 60.000 9.63 0.00 0.00 3.66
759 1074 0.108138 CTCGGGCCTAGAAACACAGG 60.108 60.000 0.84 0.00 34.85 4.00
766 1081 2.636830 CCTAGAAACACAGGCCTGATG 58.363 52.381 39.19 30.70 0.00 3.07
767 1082 2.636830 CTAGAAACACAGGCCTGATGG 58.363 52.381 39.19 27.00 0.00 3.51
799 1114 2.526624 GCCTGGGCCTGGGTTTTT 60.527 61.111 28.34 0.00 34.56 1.94
814 1129 2.037871 TTTTTGAGTCGGGCTTGGC 58.962 52.632 0.00 0.00 0.00 4.52
815 1130 0.467290 TTTTTGAGTCGGGCTTGGCT 60.467 50.000 0.00 0.00 0.00 4.75
816 1131 0.398696 TTTTGAGTCGGGCTTGGCTA 59.601 50.000 0.00 0.00 0.00 3.93
817 1132 0.036388 TTTGAGTCGGGCTTGGCTAG 60.036 55.000 0.00 0.00 0.00 3.42
818 1133 1.899437 TTGAGTCGGGCTTGGCTAGG 61.899 60.000 0.00 0.00 0.00 3.02
858 1173 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
859 1174 2.598787 CCCGAGGTTTGGCCAGGTA 61.599 63.158 5.11 0.00 40.61 3.08
860 1175 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
875 1190 1.749634 AGGTATACACGTGAGCAGTCC 59.250 52.381 25.01 15.36 0.00 3.85
911 1228 0.382873 GAACCAAACGACCCAACCAC 59.617 55.000 0.00 0.00 0.00 4.16
912 1229 1.378124 AACCAAACGACCCAACCACG 61.378 55.000 0.00 0.00 0.00 4.94
952 1279 2.681778 CTCCTCCCACTCCACGCT 60.682 66.667 0.00 0.00 0.00 5.07
964 1291 2.092646 ACTCCACGCTACAGATCTCTCT 60.093 50.000 0.00 0.00 0.00 3.10
965 1292 2.548057 CTCCACGCTACAGATCTCTCTC 59.452 54.545 0.00 0.00 0.00 3.20
997 1330 3.650950 GCCCCCTTGCTCTCCACA 61.651 66.667 0.00 0.00 0.00 4.17
1087 1420 4.162690 CTGCTACCCCTCCGGCAC 62.163 72.222 0.00 0.00 33.26 5.01
1320 1653 4.039092 GCTGCCTCCCCTGCTTCA 62.039 66.667 0.00 0.00 0.00 3.02
1321 1654 3.004951 CTGCCTCCCCTGCTTCAT 58.995 61.111 0.00 0.00 0.00 2.57
1350 1683 2.835431 ATCGAGGTCCTCCAGGCG 60.835 66.667 13.54 1.81 35.89 5.52
1425 1761 3.917760 GCCGCCGCTCCAGATACT 61.918 66.667 0.00 0.00 0.00 2.12
1448 1784 2.048127 GGAACCGAGCGCTGAAGT 60.048 61.111 18.48 6.12 0.00 3.01
1457 1793 2.811317 CGCTGAAGTGTCGGAGGC 60.811 66.667 0.00 0.00 30.94 4.70
1522 1858 2.370445 CCCGAGCCTTGATCCACCT 61.370 63.158 0.00 0.00 0.00 4.00
1523 1859 1.153289 CCGAGCCTTGATCCACCTG 60.153 63.158 0.00 0.00 0.00 4.00
1560 1896 2.692557 TGGCATTTCGTTGGGGATTATG 59.307 45.455 0.00 0.00 0.00 1.90
1569 1905 7.556733 TTCGTTGGGGATTATGTATTGTTAC 57.443 36.000 0.00 0.00 0.00 2.50
1628 1964 6.705381 GGGAATTGATGTTTGTTTCATGAACA 59.295 34.615 7.89 3.39 46.19 3.18
1666 2002 7.989826 ACAAACTTTAAGCTATTATCAGCCTG 58.010 34.615 0.00 0.00 42.84 4.85
1709 2045 3.770263 AAGGTGTGCATGAATGATTCG 57.230 42.857 0.00 0.00 0.00 3.34
1856 2193 5.355596 CAGTGTTTGCTTTGGTCCATTTTA 58.644 37.500 0.00 0.00 0.00 1.52
1889 2226 5.408604 CACTTGGATTGCGTTAGTTCTTAGT 59.591 40.000 0.00 0.00 0.00 2.24
1926 2264 8.790718 TCTGTTGAATAGTACGTTTTAGAGACT 58.209 33.333 0.00 0.00 0.00 3.24
1927 2265 8.961294 TGTTGAATAGTACGTTTTAGAGACTC 57.039 34.615 0.00 0.00 0.00 3.36
1928 2266 8.790718 TGTTGAATAGTACGTTTTAGAGACTCT 58.209 33.333 10.47 10.47 0.00 3.24
1929 2267 9.063739 GTTGAATAGTACGTTTTAGAGACTCTG 57.936 37.037 15.55 0.13 0.00 3.35
1930 2268 8.332996 TGAATAGTACGTTTTAGAGACTCTGT 57.667 34.615 15.55 6.44 0.00 3.41
2008 2347 9.941664 GAGCTGATTAAGTAAATACTACGTACA 57.058 33.333 0.00 0.00 34.99 2.90
2046 2385 6.127479 TGGGTTGAAAATAGGCACATATTGTC 60.127 38.462 0.00 0.00 32.22 3.18
2068 2413 4.640201 TCTTCTAAAAGGCCACATGCATAC 59.360 41.667 5.01 0.00 43.89 2.39
2069 2414 4.235079 TCTAAAAGGCCACATGCATACT 57.765 40.909 5.01 0.00 43.89 2.12
2177 2571 2.182827 TGACTGAATGGAGCTGCTAGT 58.817 47.619 6.82 0.29 0.00 2.57
2178 2572 2.568956 TGACTGAATGGAGCTGCTAGTT 59.431 45.455 6.82 0.00 0.00 2.24
2184 2578 1.238439 TGGAGCTGCTAGTTTTGCAC 58.762 50.000 6.82 0.00 36.37 4.57
2189 2583 1.068434 GCTGCTAGTTTTGCACCCAAA 59.932 47.619 0.00 0.00 39.08 3.28
2231 2625 7.419711 AACATGTACTACTAGTAGTTGGCAT 57.580 36.000 34.30 28.94 43.35 4.40
2363 2757 9.556030 GAAGTGCAGTTTACCAAATACTAAATC 57.444 33.333 8.48 0.00 0.00 2.17
2404 2798 6.672266 TCTACCTATGCTTTATGCTAGCTT 57.328 37.500 17.23 12.56 43.37 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.455847 TTTTTCAAATTTGGAAACACAAACAAG 57.544 25.926 21.75 0.00 42.51 3.16
229 260 8.073768 TGTTTGAGAAACATCCTTTACGATTTC 58.926 33.333 0.00 0.00 45.79 2.17
291 328 0.315251 TGGACGAGCTCAGTTGACTG 59.685 55.000 15.40 4.77 45.08 3.51
354 398 1.270518 CGAGATGGCTGGGAATCGAAT 60.271 52.381 0.00 0.00 32.13 3.34
393 697 4.495844 GCGCTGGAAATACAAGGTGATAAC 60.496 45.833 0.00 0.00 0.00 1.89
422 726 0.179020 CGATTGGGCCAGCCTATTGA 60.179 55.000 6.23 0.00 36.10 2.57
521 836 2.662700 CCAGAACTACTCACGTGTCAC 58.337 52.381 16.51 0.00 0.00 3.67
522 837 1.000607 GCCAGAACTACTCACGTGTCA 60.001 52.381 16.51 0.00 0.00 3.58
523 838 1.669211 GGCCAGAACTACTCACGTGTC 60.669 57.143 16.51 4.35 0.00 3.67
524 839 0.317479 GGCCAGAACTACTCACGTGT 59.683 55.000 16.51 0.00 0.00 4.49
525 840 0.317160 TGGCCAGAACTACTCACGTG 59.683 55.000 9.94 9.94 0.00 4.49
526 841 1.066858 CATGGCCAGAACTACTCACGT 60.067 52.381 13.05 0.00 0.00 4.49
527 842 1.204704 TCATGGCCAGAACTACTCACG 59.795 52.381 13.05 0.00 0.00 4.35
528 843 3.334583 TTCATGGCCAGAACTACTCAC 57.665 47.619 13.05 0.00 0.00 3.51
529 844 4.326826 CTTTTCATGGCCAGAACTACTCA 58.673 43.478 13.05 0.00 0.00 3.41
530 845 3.127721 GCTTTTCATGGCCAGAACTACTC 59.872 47.826 13.05 0.00 0.00 2.59
531 846 3.084786 GCTTTTCATGGCCAGAACTACT 58.915 45.455 13.05 0.00 0.00 2.57
532 847 2.164422 GGCTTTTCATGGCCAGAACTAC 59.836 50.000 13.05 6.64 46.84 2.73
533 848 2.446435 GGCTTTTCATGGCCAGAACTA 58.554 47.619 13.05 5.39 46.84 2.24
534 849 1.260544 GGCTTTTCATGGCCAGAACT 58.739 50.000 13.05 0.00 46.84 3.01
535 850 3.820595 GGCTTTTCATGGCCAGAAC 57.179 52.632 13.05 3.86 46.84 3.01
541 856 2.580815 GGCTGGGCTTTTCATGGC 59.419 61.111 0.00 0.00 0.00 4.40
542 857 2.713967 CGGGCTGGGCTTTTCATGG 61.714 63.158 0.00 0.00 0.00 3.66
543 858 2.713967 CCGGGCTGGGCTTTTCATG 61.714 63.158 3.77 0.00 0.00 3.07
544 859 2.362889 CCGGGCTGGGCTTTTCAT 60.363 61.111 3.77 0.00 0.00 2.57
570 885 2.636412 GGGTCAGGCTTTTTCGGGC 61.636 63.158 0.00 0.00 0.00 6.13
571 886 2.332654 CGGGTCAGGCTTTTTCGGG 61.333 63.158 0.00 0.00 0.00 5.14
572 887 2.332654 CCGGGTCAGGCTTTTTCGG 61.333 63.158 0.00 2.50 0.00 4.30
573 888 3.263941 CCGGGTCAGGCTTTTTCG 58.736 61.111 0.00 0.00 0.00 3.46
615 930 0.036671 AAAAACTAGACCCGAGCCCG 60.037 55.000 0.00 0.00 0.00 6.13
616 931 1.002773 TCAAAAACTAGACCCGAGCCC 59.997 52.381 0.00 0.00 0.00 5.19
617 932 2.347731 CTCAAAAACTAGACCCGAGCC 58.652 52.381 0.00 0.00 0.00 4.70
618 933 1.732809 GCTCAAAAACTAGACCCGAGC 59.267 52.381 0.00 3.56 37.81 5.03
619 934 2.289444 TGGCTCAAAAACTAGACCCGAG 60.289 50.000 0.00 0.00 0.00 4.63
620 935 1.695242 TGGCTCAAAAACTAGACCCGA 59.305 47.619 0.00 0.00 0.00 5.14
621 936 2.076863 CTGGCTCAAAAACTAGACCCG 58.923 52.381 0.00 0.00 0.00 5.28
622 937 3.418684 TCTGGCTCAAAAACTAGACCC 57.581 47.619 0.00 0.00 0.00 4.46
623 938 3.753797 CCTTCTGGCTCAAAAACTAGACC 59.246 47.826 0.00 0.00 0.00 3.85
638 953 4.479993 CTCAGCCCGGCCTTCTGG 62.480 72.222 5.55 0.00 38.52 3.86
656 971 3.228017 AAAAACAACGGGCCCGGG 61.228 61.111 44.99 36.81 44.69 5.73
657 972 2.028337 CAAAAACAACGGGCCCGG 59.972 61.111 44.99 31.45 44.69 5.73
658 973 2.660224 GCAAAAACAACGGGCCCG 60.660 61.111 42.17 42.17 46.03 6.13
659 974 0.533978 AATGCAAAAACAACGGGCCC 60.534 50.000 13.57 13.57 0.00 5.80
660 975 1.304254 AAATGCAAAAACAACGGGCC 58.696 45.000 0.00 0.00 0.00 5.80
661 976 3.064682 AGAAAAATGCAAAAACAACGGGC 59.935 39.130 0.00 0.00 0.00 6.13
662 977 4.331168 TCAGAAAAATGCAAAAACAACGGG 59.669 37.500 0.00 0.00 0.00 5.28
663 978 5.462034 TCAGAAAAATGCAAAAACAACGG 57.538 34.783 0.00 0.00 0.00 4.44
664 979 5.958949 CCTTCAGAAAAATGCAAAAACAACG 59.041 36.000 0.00 0.00 0.00 4.10
665 980 6.841119 ACCTTCAGAAAAATGCAAAAACAAC 58.159 32.000 0.00 0.00 0.00 3.32
666 981 6.183360 CGACCTTCAGAAAAATGCAAAAACAA 60.183 34.615 0.00 0.00 0.00 2.83
667 982 5.290643 CGACCTTCAGAAAAATGCAAAAACA 59.709 36.000 0.00 0.00 0.00 2.83
668 983 5.276820 CCGACCTTCAGAAAAATGCAAAAAC 60.277 40.000 0.00 0.00 0.00 2.43
669 984 4.808364 CCGACCTTCAGAAAAATGCAAAAA 59.192 37.500 0.00 0.00 0.00 1.94
670 985 4.367450 CCGACCTTCAGAAAAATGCAAAA 58.633 39.130 0.00 0.00 0.00 2.44
671 986 3.243704 CCCGACCTTCAGAAAAATGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
672 987 2.295909 CCCGACCTTCAGAAAAATGCAA 59.704 45.455 0.00 0.00 0.00 4.08
673 988 1.885887 CCCGACCTTCAGAAAAATGCA 59.114 47.619 0.00 0.00 0.00 3.96
674 989 1.402852 GCCCGACCTTCAGAAAAATGC 60.403 52.381 0.00 0.00 0.00 3.56
675 990 1.202348 GGCCCGACCTTCAGAAAAATG 59.798 52.381 0.00 0.00 34.51 2.32
676 991 1.545841 GGCCCGACCTTCAGAAAAAT 58.454 50.000 0.00 0.00 34.51 1.82
677 992 0.887387 CGGCCCGACCTTCAGAAAAA 60.887 55.000 0.00 0.00 35.61 1.94
678 993 1.302192 CGGCCCGACCTTCAGAAAA 60.302 57.895 0.00 0.00 35.61 2.29
679 994 2.345991 CGGCCCGACCTTCAGAAA 59.654 61.111 0.00 0.00 35.61 2.52
680 995 3.702048 CCGGCCCGACCTTCAGAA 61.702 66.667 3.71 0.00 35.61 3.02
703 1018 3.584868 AAACTCGTCGGGCTTCGGG 62.585 63.158 0.00 0.00 39.77 5.14
704 1019 1.226030 AAAAACTCGTCGGGCTTCGG 61.226 55.000 0.00 0.00 39.77 4.30
705 1020 1.125566 GTAAAAACTCGTCGGGCTTCG 59.874 52.381 0.00 0.00 40.90 3.79
706 1021 1.125566 CGTAAAAACTCGTCGGGCTTC 59.874 52.381 0.00 0.00 0.00 3.86
707 1022 1.142474 CGTAAAAACTCGTCGGGCTT 58.858 50.000 0.00 0.00 0.00 4.35
708 1023 0.032540 ACGTAAAAACTCGTCGGGCT 59.967 50.000 0.00 0.00 35.30 5.19
709 1024 0.162294 CACGTAAAAACTCGTCGGGC 59.838 55.000 0.00 0.00 38.23 6.13
710 1025 1.490621 ACACGTAAAAACTCGTCGGG 58.509 50.000 0.00 0.00 38.23 5.14
711 1026 2.407609 CGAACACGTAAAAACTCGTCGG 60.408 50.000 0.00 0.00 38.23 4.79
712 1027 2.407609 CCGAACACGTAAAAACTCGTCG 60.408 50.000 0.00 0.00 38.23 5.12
713 1028 2.097250 CCCGAACACGTAAAAACTCGTC 60.097 50.000 0.00 0.00 38.23 4.20
714 1029 1.860326 CCCGAACACGTAAAAACTCGT 59.140 47.619 0.00 0.00 40.99 4.18
715 1030 1.397567 GCCCGAACACGTAAAAACTCG 60.398 52.381 0.00 0.00 0.00 4.18
716 1031 1.069703 GGCCCGAACACGTAAAAACTC 60.070 52.381 0.00 0.00 0.00 3.01
717 1032 0.946528 GGCCCGAACACGTAAAAACT 59.053 50.000 0.00 0.00 0.00 2.66
718 1033 0.384601 CGGCCCGAACACGTAAAAAC 60.385 55.000 0.00 0.00 0.00 2.43
719 1034 1.505477 CCGGCCCGAACACGTAAAAA 61.505 55.000 3.71 0.00 0.00 1.94
720 1035 1.960250 CCGGCCCGAACACGTAAAA 60.960 57.895 3.71 0.00 0.00 1.52
721 1036 2.357275 CCGGCCCGAACACGTAAA 60.357 61.111 3.71 0.00 0.00 2.01
722 1037 4.376176 CCCGGCCCGAACACGTAA 62.376 66.667 3.71 0.00 0.00 3.18
739 1054 0.741221 CTGTGTTTCTAGGCCCGAGC 60.741 60.000 0.00 0.00 38.76 5.03
740 1055 0.108138 CCTGTGTTTCTAGGCCCGAG 60.108 60.000 0.00 0.00 0.00 4.63
741 1056 1.980052 CCTGTGTTTCTAGGCCCGA 59.020 57.895 0.00 0.00 0.00 5.14
742 1057 4.617875 CCTGTGTTTCTAGGCCCG 57.382 61.111 0.00 0.00 0.00 6.13
746 1061 2.636830 CATCAGGCCTGTGTTTCTAGG 58.363 52.381 31.58 9.16 37.14 3.02
747 1062 2.636830 CCATCAGGCCTGTGTTTCTAG 58.363 52.381 31.58 13.13 0.00 2.43
748 1063 2.787473 CCATCAGGCCTGTGTTTCTA 57.213 50.000 31.58 11.74 0.00 2.10
749 1064 3.658398 CCATCAGGCCTGTGTTTCT 57.342 52.632 31.58 8.54 0.00 2.52
782 1097 2.526624 AAAAACCCAGGCCCAGGC 60.527 61.111 8.60 0.00 41.06 4.85
796 1111 0.467290 AGCCAAGCCCGACTCAAAAA 60.467 50.000 0.00 0.00 0.00 1.94
797 1112 0.398696 TAGCCAAGCCCGACTCAAAA 59.601 50.000 0.00 0.00 0.00 2.44
798 1113 0.036388 CTAGCCAAGCCCGACTCAAA 60.036 55.000 0.00 0.00 0.00 2.69
799 1114 1.596934 CTAGCCAAGCCCGACTCAA 59.403 57.895 0.00 0.00 0.00 3.02
800 1115 2.359169 CCTAGCCAAGCCCGACTCA 61.359 63.158 0.00 0.00 0.00 3.41
801 1116 2.501610 CCTAGCCAAGCCCGACTC 59.498 66.667 0.00 0.00 0.00 3.36
802 1117 3.787001 GCCTAGCCAAGCCCGACT 61.787 66.667 0.00 0.00 0.00 4.18
841 1156 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
842 1157 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
843 1158 1.208535 TGTATACCTGGCCAAACCTCG 59.791 52.381 7.01 0.00 40.22 4.63
844 1159 2.640184 GTGTATACCTGGCCAAACCTC 58.360 52.381 7.01 0.00 40.22 3.85
845 1160 1.065709 CGTGTATACCTGGCCAAACCT 60.066 52.381 7.01 0.00 40.22 3.50
846 1161 1.339342 ACGTGTATACCTGGCCAAACC 60.339 52.381 7.01 0.00 39.84 3.27
847 1162 1.735571 CACGTGTATACCTGGCCAAAC 59.264 52.381 7.01 0.69 0.00 2.93
848 1163 1.624312 TCACGTGTATACCTGGCCAAA 59.376 47.619 16.51 0.00 0.00 3.28
849 1164 1.206132 CTCACGTGTATACCTGGCCAA 59.794 52.381 16.51 0.00 0.00 4.52
850 1165 0.821517 CTCACGTGTATACCTGGCCA 59.178 55.000 16.51 4.71 0.00 5.36
851 1166 0.529992 GCTCACGTGTATACCTGGCC 60.530 60.000 16.51 0.00 0.00 5.36
852 1167 0.174845 TGCTCACGTGTATACCTGGC 59.825 55.000 16.51 8.57 0.00 4.85
853 1168 1.476891 ACTGCTCACGTGTATACCTGG 59.523 52.381 16.51 0.00 0.00 4.45
854 1169 2.479730 GGACTGCTCACGTGTATACCTG 60.480 54.545 16.51 7.12 0.00 4.00
855 1170 1.749634 GGACTGCTCACGTGTATACCT 59.250 52.381 16.51 0.00 0.00 3.08
856 1171 1.202382 GGGACTGCTCACGTGTATACC 60.202 57.143 16.51 12.06 0.00 2.73
857 1172 1.202382 GGGGACTGCTCACGTGTATAC 60.202 57.143 16.51 4.28 0.00 1.47
858 1173 1.108776 GGGGACTGCTCACGTGTATA 58.891 55.000 16.51 1.89 0.00 1.47
859 1174 1.614241 GGGGGACTGCTCACGTGTAT 61.614 60.000 16.51 0.00 0.00 2.29
860 1175 2.280552 GGGGGACTGCTCACGTGTA 61.281 63.158 16.51 1.31 0.00 2.90
911 1228 1.966451 GGTGGGTTGGAGACTTGCG 60.966 63.158 0.00 0.00 0.00 4.85
912 1229 0.606673 GAGGTGGGTTGGAGACTTGC 60.607 60.000 0.00 0.00 0.00 4.01
952 1279 2.370519 CGGAGAGGGAGAGAGATCTGTA 59.629 54.545 0.00 0.00 0.00 2.74
979 1306 4.785453 GTGGAGAGCAAGGGGGCG 62.785 72.222 0.00 0.00 39.27 6.13
980 1307 3.650950 TGTGGAGAGCAAGGGGGC 61.651 66.667 0.00 0.00 0.00 5.80
1030 1363 4.838152 CGCGGGGTGGATGTCCTG 62.838 72.222 0.00 0.00 36.82 3.86
1086 1419 0.540830 ACGAGGACTTCTCTGCTGGT 60.541 55.000 0.00 0.00 40.30 4.00
1087 1420 0.172352 GACGAGGACTTCTCTGCTGG 59.828 60.000 0.00 0.00 40.30 4.85
1089 1422 1.309499 CCGACGAGGACTTCTCTGCT 61.309 60.000 0.00 0.00 45.00 4.24
1117 1450 0.737367 CAGATGCTGAGCGACGGAAA 60.737 55.000 0.00 0.00 32.44 3.13
1119 1452 2.491621 CAGATGCTGAGCGACGGA 59.508 61.111 0.00 0.00 32.44 4.69
1305 1638 1.000521 CAATGAAGCAGGGGAGGCA 60.001 57.895 0.00 0.00 0.00 4.75
1314 1647 1.198094 TCCCGTCCTCCAATGAAGCA 61.198 55.000 0.00 0.00 0.00 3.91
1317 1650 0.464036 CGATCCCGTCCTCCAATGAA 59.536 55.000 0.00 0.00 0.00 2.57
1320 1653 1.115930 CCTCGATCCCGTCCTCCAAT 61.116 60.000 0.00 0.00 37.05 3.16
1321 1654 1.756950 CCTCGATCCCGTCCTCCAA 60.757 63.158 0.00 0.00 37.05 3.53
1350 1683 0.537653 GGCTGACCTCCTTGGAGTAC 59.462 60.000 14.77 9.01 39.71 2.73
1422 1758 3.136123 CTCGGTTCCGCGGGAGTA 61.136 66.667 27.83 1.61 31.21 2.59
1448 1784 3.744719 CCGACGAAGCCTCCGACA 61.745 66.667 0.00 0.00 0.00 4.35
1457 1793 1.444553 GGAGCAGTCACCGACGAAG 60.445 63.158 0.00 0.00 37.67 3.79
1522 1858 1.545582 GCCAAAATAGCAGCACTTCCA 59.454 47.619 0.00 0.00 0.00 3.53
1523 1859 1.545582 TGCCAAAATAGCAGCACTTCC 59.454 47.619 0.00 0.00 34.69 3.46
1525 1861 3.967332 AATGCCAAAATAGCAGCACTT 57.033 38.095 0.00 0.00 44.90 3.16
1628 1964 6.072119 GCTTAAAGTTTGTAGCAAGGTACCAT 60.072 38.462 15.94 0.00 33.88 3.55
1666 2002 1.098050 GACAATGATGCACCCCTGAC 58.902 55.000 0.00 0.00 0.00 3.51
1709 2045 1.827969 AGCCAGTACAGATGACCTGAC 59.172 52.381 0.00 0.00 45.78 3.51
1856 2193 2.164219 CGCAATCCAAGTGCATAAGGTT 59.836 45.455 0.00 0.00 42.33 3.50
1889 2226 9.146984 CGTACTATTCAACAGAATGAAACCTAA 57.853 33.333 1.21 0.00 42.22 2.69
1926 2264 5.769484 AGACGTTTTAGAGACTTGACAGA 57.231 39.130 0.00 0.00 0.00 3.41
1927 2265 9.790389 ATATAAGACGTTTTAGAGACTTGACAG 57.210 33.333 4.75 0.00 0.00 3.51
2046 2385 4.641989 AGTATGCATGTGGCCTTTTAGAAG 59.358 41.667 10.16 0.00 43.89 2.85
2177 2571 3.744660 AGTTGTTGTTTTGGGTGCAAAA 58.255 36.364 0.00 0.00 0.00 2.44
2178 2572 3.409026 AGTTGTTGTTTTGGGTGCAAA 57.591 38.095 0.00 0.00 0.00 3.68
2184 2578 8.407064 TGTTACTATGTTAGTTGTTGTTTTGGG 58.593 33.333 0.00 0.00 40.14 4.12
2231 2625 4.513442 CAATCGGGTAGTCTTCATTGGAA 58.487 43.478 0.00 0.00 0.00 3.53
2363 2757 4.150804 GGTAGAAGAAACTGAAGCTTCACG 59.849 45.833 25.16 21.18 40.26 4.35


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

AutoCloner maintained by Alex Coulton.