Multiple sequence alignment - TraesCS2B01G380800

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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 TraesCS2B01G380800 chr2B 100.000 3583 0 0 1 3583 544989382 544992964 0.000000e+00 6617.0
1 TraesCS2B01G380800 chr2B 86.667 180 10 7 3411 3583 544992994 544992822 1.700000e-43 187.0
2 TraesCS2B01G380800 chr2A 94.320 2641 83 15 873 3491 607483762 607486357 0.000000e+00 3984.0
3 TraesCS2B01G380800 chr2A 95.000 1400 48 9 873 2259 610117251 610118641 0.000000e+00 2178.0
4 TraesCS2B01G380800 chr2A 97.347 1244 31 1 2250 3493 610118818 610120059 0.000000e+00 2113.0
5 TraesCS2B01G380800 chr2A 82.759 87 9 6 3450 3535 444786918 444786837 4.960000e-09 73.1
6 TraesCS2B01G380800 chr2D 95.988 2019 48 7 1480 3496 462204773 462206760 0.000000e+00 3249.0
7 TraesCS2B01G380800 chr2D 91.360 544 24 13 873 1394 462204220 462204762 0.000000e+00 723.0
8 TraesCS2B01G380800 chr2D 96.078 51 1 1 3485 3535 534925553 534925504 8.240000e-12 82.4
9 TraesCS2B01G380800 chr2D 91.379 58 4 1 3478 3535 556926418 556926474 1.070000e-10 78.7
10 TraesCS2B01G380800 chr7A 98.370 859 9 3 1 856 460545313 460546169 0.000000e+00 1504.0
11 TraesCS2B01G380800 chr3A 98.368 858 10 2 1 856 171240884 171241739 0.000000e+00 1504.0
12 TraesCS2B01G380800 chr4A 98.364 856 12 1 2 857 436873162 436874015 0.000000e+00 1502.0
13 TraesCS2B01G380800 chr4A 86.957 69 7 2 3468 3535 636257557 636257624 3.840000e-10 76.8
14 TraesCS2B01G380800 chr3B 98.037 866 13 2 1 864 545642356 545641493 0.000000e+00 1502.0
15 TraesCS2B01G380800 chr3B 98.021 859 15 1 1 859 816597604 816596748 0.000000e+00 1491.0
16 TraesCS2B01G380800 chr3B 90.323 62 4 2 3475 3535 113917164 113917104 2.970000e-11 80.5
17 TraesCS2B01G380800 chr3B 91.667 60 2 3 3488 3546 777994696 777994753 2.970000e-11 80.5
18 TraesCS2B01G380800 chr7B 98.364 856 10 2 1 856 456485359 456486210 0.000000e+00 1500.0
19 TraesCS2B01G380800 chr7B 84.810 79 8 4 3489 3566 611975408 611975333 3.840000e-10 76.8
20 TraesCS2B01G380800 chr1A 98.252 858 11 2 1 856 119733657 119732802 0.000000e+00 1498.0
21 TraesCS2B01G380800 chr6B 98.252 858 10 3 1 856 40128080 40128934 0.000000e+00 1496.0
22 TraesCS2B01G380800 chr6A 98.140 860 10 2 1 856 12429360 12430217 0.000000e+00 1495.0
23 TraesCS2B01G380800 chrUn 92.982 57 3 1 3479 3535 3346388 3346443 8.240000e-12 82.4
24 TraesCS2B01G380800 chrUn 97.674 43 1 0 3488 3530 10254801 10254759 1.380000e-09 75.0
25 TraesCS2B01G380800 chrUn 97.674 43 1 0 3488 3530 86974735 86974693 1.380000e-09 75.0
26 TraesCS2B01G380800 chrUn 97.674 43 1 0 3488 3530 253929080 253929122 1.380000e-09 75.0
27 TraesCS2B01G380800 chrUn 97.619 42 1 0 3488 3529 101630799 101630840 4.960000e-09 73.1
28 TraesCS2B01G380800 chrUn 92.157 51 4 0 3480 3530 156526292 156526242 4.960000e-09 73.1
29 TraesCS2B01G380800 chrUn 95.455 44 2 0 3489 3532 36436975 36436932 1.780000e-08 71.3
30 TraesCS2B01G380800 chrUn 95.556 45 1 1 3489 3533 41223908 41223865 1.780000e-08 71.3
31 TraesCS2B01G380800 chrUn 97.561 41 1 0 3488 3528 46240432 46240392 1.780000e-08 71.3
32 TraesCS2B01G380800 chrUn 92.157 51 3 1 3481 3530 90492607 90492657 1.780000e-08 71.3
33 TraesCS2B01G380800 chrUn 93.617 47 3 0 3482 3528 299168585 299168539 1.780000e-08 71.3
34 TraesCS2B01G380800 chrUn 93.750 48 2 1 3488 3535 362464953 362464999 1.780000e-08 71.3
35 TraesCS2B01G380800 chr5D 93.103 58 1 3 3488 3544 242016829 242016774 8.240000e-12 82.4
36 TraesCS2B01G380800 chr5D 96.000 50 2 0 3481 3530 482013896 482013945 8.240000e-12 82.4
37 TraesCS2B01G380800 chr5A 93.103 58 1 3 3488 3544 312242181 312242126 8.240000e-12 82.4
38 TraesCS2B01G380800 chr5A 90.323 62 3 3 3486 3546 32836424 32836483 1.070000e-10 78.7
39 TraesCS2B01G380800 chr5A 89.062 64 3 4 3489 3551 622398169 622398229 3.840000e-10 76.8
40 TraesCS2B01G380800 chr1D 94.444 54 1 2 3482 3535 263868014 263867963 8.240000e-12 82.4
41 TraesCS2B01G380800 chr1D 94.231 52 2 1 3484 3535 206041071 206041021 1.070000e-10 78.7
42 TraesCS2B01G380800 chr1D 95.833 48 2 0 3482 3529 209139270 209139317 1.070000e-10 78.7
43 TraesCS2B01G380800 chr1D 91.071 56 4 1 3475 3530 239333496 239333442 1.380000e-09 75.0
44 TraesCS2B01G380800 chr1D 88.889 63 4 3 3485 3546 245217190 245217250 1.380000e-09 75.0
45 TraesCS2B01G380800 chr1D 86.765 68 5 3 3468 3535 469154019 469153956 4.960000e-09 73.1
46 TraesCS2B01G380800 chr6D 96.000 50 1 1 3486 3535 199210415 199210367 2.970000e-11 80.5
47 TraesCS2B01G380800 chr6D 97.778 45 1 0 3487 3531 25878829 25878785 1.070000e-10 78.7
48 TraesCS2B01G380800 chr6D 97.727 44 1 0 3487 3530 386924868 386924911 3.840000e-10 76.8
49 TraesCS2B01G380800 chr6D 94.000 50 2 1 3486 3535 20553666 20553714 1.380000e-09 75.0
50 TraesCS2B01G380800 chr6D 92.308 52 4 0 3479 3530 299191253 299191304 1.380000e-09 75.0
51 TraesCS2B01G380800 chr6D 93.878 49 3 0 3481 3529 448788052 448788100 1.380000e-09 75.0
52 TraesCS2B01G380800 chr6D 93.617 47 3 0 3482 3528 14174047 14174001 1.780000e-08 71.3
53 TraesCS2B01G380800 chr6D 90.741 54 4 1 3476 3529 469492327 469492379 1.780000e-08 71.3
54 TraesCS2B01G380800 chr6D 90.741 54 4 1 3476 3529 469511135 469511187 1.780000e-08 71.3
55 TraesCS2B01G380800 chr4B 96.000 50 1 1 3486 3535 192792744 192792792 2.970000e-11 80.5
56 TraesCS2B01G380800 chr4B 96.000 50 1 1 3486 3535 640009162 640009114 2.970000e-11 80.5
57 TraesCS2B01G380800 chr4B 96.000 50 1 1 3486 3535 643804295 643804247 2.970000e-11 80.5
58 TraesCS2B01G380800 chr3D 94.231 52 3 0 3484 3535 278515035 278514984 2.970000e-11 80.5
59 TraesCS2B01G380800 chr3D 92.727 55 3 1 3481 3535 133521013 133521066 1.070000e-10 78.7
60 TraesCS2B01G380800 chr3D 91.379 58 2 3 3487 3543 47799618 47799563 3.840000e-10 76.8
61 TraesCS2B01G380800 chr3D 90.000 60 4 2 3475 3533 68079333 68079391 3.840000e-10 76.8
62 TraesCS2B01G380800 chr4D 95.918 49 1 1 3487 3535 252173790 252173743 1.070000e-10 78.7
63 TraesCS2B01G380800 chr4D 97.778 45 1 0 3486 3530 423945311 423945355 1.070000e-10 78.7
64 TraesCS2B01G380800 chr4D 92.453 53 4 0 3478 3530 334963108 334963160 3.840000e-10 76.8
65 TraesCS2B01G380800 chr4D 92.453 53 2 2 3479 3530 498762403 498762454 1.380000e-09 75.0
66 TraesCS2B01G380800 chr4D 87.302 63 6 2 3483 3544 82867097 82867036 1.780000e-08 71.3
67 TraesCS2B01G380800 chr7D 85.526 76 8 3 3471 3545 627408995 627409068 3.840000e-10 76.8
68 TraesCS2B01G380800 chr7D 86.765 68 5 3 3468 3535 540570406 540570469 4.960000e-09 73.1


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 TraesCS2B01G380800 chr2B 544989382 544992964 3582 False 6617.0 6617 100.0000 1 3583 1 chr2B.!!$F1 3582
1 TraesCS2B01G380800 chr2A 607483762 607486357 2595 False 3984.0 3984 94.3200 873 3491 1 chr2A.!!$F1 2618
2 TraesCS2B01G380800 chr2A 610117251 610120059 2808 False 2145.5 2178 96.1735 873 3493 2 chr2A.!!$F2 2620
3 TraesCS2B01G380800 chr2D 462204220 462206760 2540 False 1986.0 3249 93.6740 873 3496 2 chr2D.!!$F2 2623
4 TraesCS2B01G380800 chr7A 460545313 460546169 856 False 1504.0 1504 98.3700 1 856 1 chr7A.!!$F1 855
5 TraesCS2B01G380800 chr3A 171240884 171241739 855 False 1504.0 1504 98.3680 1 856 1 chr3A.!!$F1 855
6 TraesCS2B01G380800 chr4A 436873162 436874015 853 False 1502.0 1502 98.3640 2 857 1 chr4A.!!$F1 855
7 TraesCS2B01G380800 chr3B 545641493 545642356 863 True 1502.0 1502 98.0370 1 864 1 chr3B.!!$R2 863
8 TraesCS2B01G380800 chr3B 816596748 816597604 856 True 1491.0 1491 98.0210 1 859 1 chr3B.!!$R3 858
9 TraesCS2B01G380800 chr7B 456485359 456486210 851 False 1500.0 1500 98.3640 1 856 1 chr7B.!!$F1 855
10 TraesCS2B01G380800 chr1A 119732802 119733657 855 True 1498.0 1498 98.2520 1 856 1 chr1A.!!$R1 855
11 TraesCS2B01G380800 chr6B 40128080 40128934 854 False 1496.0 1496 98.2520 1 856 1 chr6B.!!$F1 855
12 TraesCS2B01G380800 chr6A 12429360 12430217 857 False 1495.0 1495 98.1400 1 856 1 chr6A.!!$F1 855

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
933 943 0.324285 CCTGCCTCTGAAGCTCAACT 59.676 55.0 0.0 0.0 0.00 3.16 F
1350 1382 0.036010 ACGAAGGTGCTGCTTGCTAT 60.036 50.0 0.0 0.0 43.37 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1951 0.109781 CGGCATTTTGGTTCCAGTCG 60.110 55.0 0.0 0.0 0.00 4.18 R
3137 3365 0.611896 GGCTGTGGCAACTACCCAAT 60.612 55.0 0.0 0.0 40.87 3.16 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
216 218 3.152341 GCTGCCTGCATAGTTAATGGAT 58.848 45.455 0.00 0.00 42.31 3.41
217 219 3.571401 GCTGCCTGCATAGTTAATGGATT 59.429 43.478 0.00 0.00 42.31 3.01
352 354 3.496130 CCTGGCGCATAGAAATAAGAGTG 59.504 47.826 10.83 0.00 0.00 3.51
655 657 5.419542 AGCGTGTATGTGTGAAATAGATGT 58.580 37.500 0.00 0.00 0.00 3.06
809 819 6.852853 GTCGCCAATGTCATAATATTGAACTG 59.147 38.462 0.00 0.00 36.41 3.16
864 874 5.049543 CGGACGTTCTTCTAGTTAGGATAGG 60.050 48.000 0.00 0.00 0.00 2.57
865 875 5.827267 GGACGTTCTTCTAGTTAGGATAGGT 59.173 44.000 0.00 0.00 0.00 3.08
866 876 6.320926 GGACGTTCTTCTAGTTAGGATAGGTT 59.679 42.308 0.00 0.00 0.00 3.50
867 877 7.500559 GGACGTTCTTCTAGTTAGGATAGGTTA 59.499 40.741 0.00 0.00 0.00 2.85
868 878 8.219546 ACGTTCTTCTAGTTAGGATAGGTTAC 57.780 38.462 0.00 0.00 0.00 2.50
869 879 8.052141 ACGTTCTTCTAGTTAGGATAGGTTACT 58.948 37.037 0.00 0.00 0.00 2.24
870 880 9.553064 CGTTCTTCTAGTTAGGATAGGTTACTA 57.447 37.037 0.00 0.00 0.00 1.82
933 943 0.324285 CCTGCCTCTGAAGCTCAACT 59.676 55.000 0.00 0.00 0.00 3.16
943 953 4.287067 TCTGAAGCTCAACTATTTGGGAGT 59.713 41.667 0.00 0.00 34.78 3.85
944 954 4.985538 TGAAGCTCAACTATTTGGGAGTT 58.014 39.130 0.00 0.00 34.78 3.01
999 1025 2.363147 GAGAGCGAGGGTCTGGGT 60.363 66.667 1.58 0.00 40.67 4.51
1173 1205 3.041627 GCTCTTCTCCGTCGACGCT 62.042 63.158 31.73 0.00 38.18 5.07
1350 1382 0.036010 ACGAAGGTGCTGCTTGCTAT 60.036 50.000 0.00 0.00 43.37 2.97
1365 1397 7.630242 TGCTTGCTATTGCTTTTACTATCTT 57.370 32.000 0.00 0.00 40.48 2.40
1368 1403 7.800847 GCTTGCTATTGCTTTTACTATCTTAGC 59.199 37.037 0.00 0.00 40.48 3.09
1474 1509 1.940613 GGCAGGCTACGTTTCATTAGG 59.059 52.381 0.00 0.00 0.00 2.69
1518 1553 3.804036 TGCCGATGTTCATACTAAAGGG 58.196 45.455 0.00 0.00 0.00 3.95
1553 1588 6.015033 CTGGATTCAGAACAAGCTGTTTGTG 61.015 44.000 10.67 0.00 44.53 3.33
1567 1602 1.065551 GTTTGTGGGCTGCGATATTCC 59.934 52.381 0.00 0.00 0.00 3.01
1592 1628 6.585416 GGGAAGATTGCCATTATTTGTTGAT 58.415 36.000 0.00 0.00 38.72 2.57
1754 1792 3.617263 CGGGAACTGATGTAGCTGTAAAC 59.383 47.826 0.00 0.00 36.31 2.01
1910 1951 6.426980 TCTTCATCAATGTGCTTGTATGTC 57.573 37.500 0.00 0.00 36.20 3.06
2125 2166 4.018409 GGATTTGCGGGAAAGCCT 57.982 55.556 20.11 0.00 45.30 4.58
2259 2300 4.286808 TCAGAGTTTGGGACATGAGATCAA 59.713 41.667 0.00 0.00 39.30 2.57
2462 2689 0.330604 ATGGTGCAGATTGGCAGACT 59.669 50.000 0.00 0.00 45.96 3.24
2606 2834 3.382546 ACATCATTATGCCCAGTTGAAGC 59.617 43.478 0.00 0.00 36.50 3.86
2786 3014 5.405935 AAGCTTCCACAAAACTTTGAAGT 57.594 34.783 9.12 0.00 40.55 3.01
2851 3079 1.339055 TGGTGACTGGTGCATAGAAGC 60.339 52.381 7.80 6.01 0.00 3.86
2907 3135 2.371510 AGAGCCTCTGACTGAGCTTTTT 59.628 45.455 0.00 0.00 41.35 1.94
3062 3290 7.280205 GCACTGTTGCTTATATTAACCTACTGT 59.720 37.037 0.00 0.00 46.17 3.55
3137 3365 8.700051 TGTTTTTCTTGGATGAAATTTGAGGTA 58.300 29.630 0.00 0.00 36.07 3.08
3293 3523 8.531982 AGTTACTAGTGACTCATGAAGCAATAA 58.468 33.333 14.22 0.00 0.00 1.40
3494 3724 7.156876 TGGATCAATTTTGACATGTACTTCC 57.843 36.000 0.00 0.00 40.49 3.46
3495 3725 6.947733 TGGATCAATTTTGACATGTACTTCCT 59.052 34.615 0.00 0.00 40.49 3.36
3496 3726 7.121168 TGGATCAATTTTGACATGTACTTCCTC 59.879 37.037 0.00 0.00 40.49 3.71
3497 3727 6.817765 TCAATTTTGACATGTACTTCCTCC 57.182 37.500 0.00 0.00 31.01 4.30
3498 3728 5.411361 TCAATTTTGACATGTACTTCCTCCG 59.589 40.000 0.00 0.00 31.01 4.63
3499 3729 4.345859 TTTTGACATGTACTTCCTCCGT 57.654 40.909 0.00 0.00 0.00 4.69
3500 3730 5.471556 TTTTGACATGTACTTCCTCCGTA 57.528 39.130 0.00 0.00 0.00 4.02
3501 3731 5.471556 TTTGACATGTACTTCCTCCGTAA 57.528 39.130 0.00 0.00 0.00 3.18
3502 3732 5.471556 TTGACATGTACTTCCTCCGTAAA 57.528 39.130 0.00 0.00 0.00 2.01
3503 3733 5.068234 TGACATGTACTTCCTCCGTAAAG 57.932 43.478 0.00 0.00 0.00 1.85
3504 3734 4.768448 TGACATGTACTTCCTCCGTAAAGA 59.232 41.667 0.00 0.00 0.00 2.52
3505 3735 5.244402 TGACATGTACTTCCTCCGTAAAGAA 59.756 40.000 0.00 0.00 0.00 2.52
3506 3736 6.105397 ACATGTACTTCCTCCGTAAAGAAA 57.895 37.500 0.00 0.00 0.00 2.52
3507 3737 6.708285 ACATGTACTTCCTCCGTAAAGAAAT 58.292 36.000 0.00 0.00 0.00 2.17
3508 3738 7.844009 ACATGTACTTCCTCCGTAAAGAAATA 58.156 34.615 0.00 0.00 0.00 1.40
3509 3739 8.483758 ACATGTACTTCCTCCGTAAAGAAATAT 58.516 33.333 0.00 0.00 0.00 1.28
3510 3740 9.976511 CATGTACTTCCTCCGTAAAGAAATATA 57.023 33.333 0.00 0.00 0.00 0.86
3515 3745 7.927092 ACTTCCTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 0.00 4.09
3516 3746 6.444633 TCCTCCGTAAAGAAATATAAGAGCG 58.555 40.000 0.00 0.00 0.00 5.03
3517 3747 6.040166 TCCTCCGTAAAGAAATATAAGAGCGT 59.960 38.462 0.00 0.00 0.00 5.07
3518 3748 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
3519 3749 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
3520 3750 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3521 3751 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3522 3752 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
3532 3762 9.900710 ATATAAGAGCGTTTAGATCACTACAAG 57.099 33.333 0.00 0.00 37.82 3.16
3533 3763 5.646577 AGAGCGTTTAGATCACTACAAGT 57.353 39.130 0.00 0.00 37.82 3.16
3534 3764 6.754702 AGAGCGTTTAGATCACTACAAGTA 57.245 37.500 0.00 0.00 37.82 2.24
3535 3765 6.553524 AGAGCGTTTAGATCACTACAAGTAC 58.446 40.000 0.00 0.00 37.82 2.73
3536 3766 6.150641 AGAGCGTTTAGATCACTACAAGTACA 59.849 38.462 0.00 0.00 37.82 2.90
3537 3767 6.864342 AGCGTTTAGATCACTACAAGTACAT 58.136 36.000 0.00 0.00 0.00 2.29
3538 3768 6.752351 AGCGTTTAGATCACTACAAGTACATG 59.248 38.462 0.00 0.00 0.00 3.21
3539 3769 6.530534 GCGTTTAGATCACTACAAGTACATGT 59.469 38.462 8.98 8.98 37.32 3.21
3540 3770 7.253684 GCGTTTAGATCACTACAAGTACATGTC 60.254 40.741 7.07 0.00 34.75 3.06
3541 3771 7.753580 CGTTTAGATCACTACAAGTACATGTCA 59.246 37.037 7.07 0.00 34.75 3.58
3542 3772 9.419297 GTTTAGATCACTACAAGTACATGTCAA 57.581 33.333 7.07 0.00 34.75 3.18
3543 3773 9.990360 TTTAGATCACTACAAGTACATGTCAAA 57.010 29.630 7.07 0.00 34.75 2.69
3544 3774 9.990360 TTAGATCACTACAAGTACATGTCAAAA 57.010 29.630 7.07 0.00 34.75 2.44
3546 3776 9.507329 AGATCACTACAAGTACATGTCAAAATT 57.493 29.630 7.07 0.00 34.75 1.82
3547 3777 9.546909 GATCACTACAAGTACATGTCAAAATTG 57.453 33.333 7.07 3.46 34.75 2.32
3548 3778 8.669946 TCACTACAAGTACATGTCAAAATTGA 57.330 30.769 7.07 0.00 34.75 2.57
3549 3779 9.283768 TCACTACAAGTACATGTCAAAATTGAT 57.716 29.630 7.07 2.47 39.73 2.57
3550 3780 9.546909 CACTACAAGTACATGTCAAAATTGATC 57.453 33.333 7.07 0.00 39.73 2.92
3551 3781 8.730680 ACTACAAGTACATGTCAAAATTGATCC 58.269 33.333 7.07 0.00 39.73 3.36
3552 3782 7.523293 ACAAGTACATGTCAAAATTGATCCA 57.477 32.000 12.76 0.00 39.73 3.41
3553 3783 8.125978 ACAAGTACATGTCAAAATTGATCCAT 57.874 30.769 12.76 0.00 39.73 3.41
3554 3784 8.030692 ACAAGTACATGTCAAAATTGATCCATG 58.969 33.333 18.04 18.04 42.59 3.66
3555 3785 7.707624 AGTACATGTCAAAATTGATCCATGT 57.292 32.000 23.95 23.95 46.99 3.21
3556 3786 7.765307 AGTACATGTCAAAATTGATCCATGTC 58.235 34.615 24.09 18.32 44.61 3.06
3557 3787 6.845758 ACATGTCAAAATTGATCCATGTCT 57.154 33.333 18.94 5.76 44.61 3.41
3558 3788 7.235935 ACATGTCAAAATTGATCCATGTCTT 57.764 32.000 18.94 5.26 44.61 3.01
3559 3789 7.318141 ACATGTCAAAATTGATCCATGTCTTC 58.682 34.615 18.94 0.00 44.61 2.87
3560 3790 6.897706 TGTCAAAATTGATCCATGTCTTCA 57.102 33.333 0.00 0.00 39.73 3.02
3561 3791 7.470935 TGTCAAAATTGATCCATGTCTTCAT 57.529 32.000 0.00 0.00 39.73 2.57
3562 3792 7.898918 TGTCAAAATTGATCCATGTCTTCATT 58.101 30.769 0.00 0.00 39.73 2.57
3563 3793 9.022884 TGTCAAAATTGATCCATGTCTTCATTA 57.977 29.630 0.00 0.00 39.73 1.90
3571 3801 7.999679 TGATCCATGTCTTCATTATTTTCACC 58.000 34.615 0.00 0.00 31.15 4.02
3572 3802 7.614974 TGATCCATGTCTTCATTATTTTCACCA 59.385 33.333 0.00 0.00 31.15 4.17
3573 3803 7.773489 TCCATGTCTTCATTATTTTCACCAA 57.227 32.000 0.00 0.00 31.15 3.67
3574 3804 8.365060 TCCATGTCTTCATTATTTTCACCAAT 57.635 30.769 0.00 0.00 31.15 3.16
3575 3805 9.473007 TCCATGTCTTCATTATTTTCACCAATA 57.527 29.630 0.00 0.00 31.15 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 114 1.739466 GGAACGAAGCATGAATGAGCA 59.261 47.619 0.00 0.00 0.00 4.26
352 354 6.657541 TCAATTGAATACCTAACCTGGACAAC 59.342 38.462 5.45 0.00 0.00 3.32
809 819 2.821378 ACGGGGCCACATTAACTTTAAC 59.179 45.455 5.46 0.00 0.00 2.01
843 853 8.052141 AGTAACCTATCCTAACTAGAAGAACGT 58.948 37.037 0.00 0.00 0.00 3.99
866 876 9.610705 CAGTCAAACCTAGTCATACTACTAGTA 57.389 37.037 1.89 1.89 45.00 1.82
867 877 7.556996 CCAGTCAAACCTAGTCATACTACTAGT 59.443 40.741 0.00 0.00 45.00 2.57
868 878 7.556996 ACCAGTCAAACCTAGTCATACTACTAG 59.443 40.741 4.41 4.41 45.71 2.57
869 879 7.338703 CACCAGTCAAACCTAGTCATACTACTA 59.661 40.741 0.00 0.00 0.00 1.82
870 880 6.153000 CACCAGTCAAACCTAGTCATACTACT 59.847 42.308 0.00 0.00 0.00 2.57
871 881 6.152323 TCACCAGTCAAACCTAGTCATACTAC 59.848 42.308 0.00 0.00 0.00 2.73
1173 1205 3.749064 GACTCGTCCTCAGCGCCA 61.749 66.667 2.29 0.00 0.00 5.69
1197 1229 3.695606 GTGTGGAGCAGCCGGAGA 61.696 66.667 5.05 0.00 40.66 3.71
1405 1440 3.709141 AGTTAACACATGGCCCTGTTTTT 59.291 39.130 16.30 12.38 32.77 1.94
1474 1509 2.749621 CCAAAACCTGGTCATGCTAGTC 59.250 50.000 0.00 0.00 40.78 2.59
1501 1536 9.895138 TTAAACTACCCCTTTAGTATGAACATC 57.105 33.333 0.00 0.00 31.73 3.06
1553 1588 2.358737 CCCGGAATATCGCAGCCC 60.359 66.667 0.73 0.00 0.00 5.19
1567 1602 4.654091 ACAAATAATGGCAATCTTCCCG 57.346 40.909 0.00 0.00 0.00 5.14
1592 1628 5.429681 TCAGCAGCAATTTACCCTAGTTA 57.570 39.130 0.00 0.00 0.00 2.24
1910 1951 0.109781 CGGCATTTTGGTTCCAGTCG 60.110 55.000 0.00 0.00 0.00 4.18
2259 2300 4.271696 TCTCGTTCACAGGTTTCATCAT 57.728 40.909 0.00 0.00 0.00 2.45
2462 2689 3.259064 GTTATGTTCCGCTGCTTCACTA 58.741 45.455 0.00 0.00 0.00 2.74
2606 2834 3.006110 GGTTGGTCCATGCCATATTGATG 59.994 47.826 7.83 0.00 38.48 3.07
2786 3014 8.334263 TGTGCTCAAATAACATGAACAGATAA 57.666 30.769 0.00 0.00 0.00 1.75
2851 3079 5.521372 TGTCTAGATTGTTGCTGAATCATCG 59.479 40.000 0.00 0.00 33.03 3.84
2907 3135 9.109393 GACAGAATTATTAGTTTATGACCAGCA 57.891 33.333 0.00 0.00 0.00 4.41
2956 3184 8.389603 CAAAAAGAAAAATAAGAAAGCACTGCA 58.610 29.630 3.30 0.00 0.00 4.41
3062 3290 2.495155 AGCATGTTGACCATACTGCA 57.505 45.000 0.00 0.00 30.71 4.41
3137 3365 0.611896 GGCTGTGGCAACTACCCAAT 60.612 55.000 0.00 0.00 40.87 3.16
3293 3523 3.589988 CTCTACTGAAGCGTGGTTTGAT 58.410 45.455 0.00 0.00 0.00 2.57
3448 3678 8.365060 TCCATGTCTTCATTATTTTCACCAAT 57.635 30.769 0.00 0.00 31.15 3.16
3449 3679 7.773489 TCCATGTCTTCATTATTTTCACCAA 57.227 32.000 0.00 0.00 31.15 3.67
3450 3680 7.614974 TGATCCATGTCTTCATTATTTTCACCA 59.385 33.333 0.00 0.00 31.15 4.17
3472 3702 7.475840 GGAGGAAGTACATGTCAAAATTGATC 58.524 38.462 0.00 0.00 39.73 2.92
3494 3724 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3495 3725 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
3496 3726 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
3506 3736 9.900710 CTTGTAGTGATCTAAACGCTCTTATAT 57.099 33.333 0.00 0.00 0.00 0.86
3507 3737 8.900781 ACTTGTAGTGATCTAAACGCTCTTATA 58.099 33.333 0.00 0.00 0.00 0.98
3508 3738 7.773149 ACTTGTAGTGATCTAAACGCTCTTAT 58.227 34.615 0.00 0.00 0.00 1.73
3509 3739 7.154435 ACTTGTAGTGATCTAAACGCTCTTA 57.846 36.000 0.00 0.00 0.00 2.10
3510 3740 6.026947 ACTTGTAGTGATCTAAACGCTCTT 57.973 37.500 0.00 0.00 0.00 2.85
3511 3741 5.646577 ACTTGTAGTGATCTAAACGCTCT 57.353 39.130 0.00 0.00 0.00 4.09
3512 3742 6.320171 TGTACTTGTAGTGATCTAAACGCTC 58.680 40.000 0.00 0.00 0.00 5.03
3513 3743 6.263516 TGTACTTGTAGTGATCTAAACGCT 57.736 37.500 0.00 0.00 0.00 5.07
3514 3744 6.530534 ACATGTACTTGTAGTGATCTAAACGC 59.469 38.462 12.39 0.00 0.00 4.84
3515 3745 7.753580 TGACATGTACTTGTAGTGATCTAAACG 59.246 37.037 13.86 0.00 0.00 3.60
3516 3746 8.981724 TGACATGTACTTGTAGTGATCTAAAC 57.018 34.615 13.86 0.00 0.00 2.01
3517 3747 9.990360 TTTGACATGTACTTGTAGTGATCTAAA 57.010 29.630 13.86 4.52 0.00 1.85
3518 3748 9.990360 TTTTGACATGTACTTGTAGTGATCTAA 57.010 29.630 13.86 2.58 0.00 2.10
3520 3750 9.507329 AATTTTGACATGTACTTGTAGTGATCT 57.493 29.630 13.86 0.00 0.00 2.75
3521 3751 9.546909 CAATTTTGACATGTACTTGTAGTGATC 57.453 33.333 13.86 2.40 0.00 2.92
3522 3752 9.283768 TCAATTTTGACATGTACTTGTAGTGAT 57.716 29.630 13.86 4.89 31.01 3.06
3523 3753 8.669946 TCAATTTTGACATGTACTTGTAGTGA 57.330 30.769 13.86 10.42 31.01 3.41
3524 3754 9.546909 GATCAATTTTGACATGTACTTGTAGTG 57.453 33.333 13.86 8.49 40.49 2.74
3525 3755 8.730680 GGATCAATTTTGACATGTACTTGTAGT 58.269 33.333 13.86 0.00 40.49 2.73
3526 3756 8.729756 TGGATCAATTTTGACATGTACTTGTAG 58.270 33.333 13.86 0.75 40.49 2.74
3527 3757 8.628630 TGGATCAATTTTGACATGTACTTGTA 57.371 30.769 13.86 0.00 40.49 2.41
3528 3758 7.523293 TGGATCAATTTTGACATGTACTTGT 57.477 32.000 13.78 13.78 40.49 3.16
3529 3759 8.030692 ACATGGATCAATTTTGACATGTACTTG 58.969 33.333 19.70 7.18 45.31 3.16
3530 3760 8.125978 ACATGGATCAATTTTGACATGTACTT 57.874 30.769 19.70 4.47 45.31 2.24
3531 3761 7.613022 AGACATGGATCAATTTTGACATGTACT 59.387 33.333 20.52 17.16 46.22 2.73
3532 3762 7.765307 AGACATGGATCAATTTTGACATGTAC 58.235 34.615 20.52 15.98 46.22 2.90
3533 3763 7.943079 AGACATGGATCAATTTTGACATGTA 57.057 32.000 20.52 0.00 46.22 2.29
3535 3765 7.317390 TGAAGACATGGATCAATTTTGACATG 58.683 34.615 16.35 16.35 42.59 3.21
3536 3766 7.470935 TGAAGACATGGATCAATTTTGACAT 57.529 32.000 0.00 0.00 40.49 3.06
3537 3767 6.897706 TGAAGACATGGATCAATTTTGACA 57.102 33.333 0.00 0.00 40.49 3.58
3545 3775 8.469200 GGTGAAAATAATGAAGACATGGATCAA 58.531 33.333 0.00 0.00 36.79 2.57
3546 3776 7.614974 TGGTGAAAATAATGAAGACATGGATCA 59.385 33.333 0.00 0.00 36.79 2.92
3547 3777 7.999679 TGGTGAAAATAATGAAGACATGGATC 58.000 34.615 0.00 0.00 36.79 3.36
3548 3778 7.959658 TGGTGAAAATAATGAAGACATGGAT 57.040 32.000 0.00 0.00 36.79 3.41
3549 3779 7.773489 TTGGTGAAAATAATGAAGACATGGA 57.227 32.000 0.00 0.00 36.79 3.41


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

AutoCloner maintained by Alex Coulton.