Multiple sequence alignment - TraesCS1B01G097700

Loading Multiple Alignment...

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 TraesCS1B01G097700 chr1B 100.000 4138 0 0 1 4138 104463533 104467670 0.000000e+00 7642.0
1 TraesCS1B01G097700 chr1B 96.053 76 2 1 3639 3714 104467092 104467166 5.620000e-24 122.0
2 TraesCS1B01G097700 chr1B 96.053 76 2 1 3560 3634 104467171 104467246 5.620000e-24 122.0
3 TraesCS1B01G097700 chr1B 92.453 53 1 3 3672 3722 154165151 154165100 5.740000e-09 73.1
4 TraesCS1B01G097700 chr1B 93.182 44 3 0 3543 3586 5875425 5875382 9.600000e-07 65.8
5 TraesCS1B01G097700 chr1B 100.000 28 0 0 3543 3570 278693845 278693818 7.000000e-03 52.8
6 TraesCS1B01G097700 chr1A 92.622 3470 139 46 3 3421 62610503 62613906 0.000000e+00 4881.0
7 TraesCS1B01G097700 chr1A 94.928 414 19 2 3727 4138 62614184 62614597 0.000000e+00 647.0
8 TraesCS1B01G097700 chr1A 92.683 41 3 0 3544 3584 295578233 295578193 4.470000e-05 60.2
9 TraesCS1B01G097700 chr1A 88.636 44 3 2 3542 3584 298569724 298569682 7.000000e-03 52.8
10 TraesCS1B01G097700 chr1D 95.079 2479 81 12 946 3421 63633623 63636063 0.000000e+00 3864.0
11 TraesCS1B01G097700 chr1D 91.638 885 48 12 1 875 63632762 63633630 0.000000e+00 1201.0
12 TraesCS1B01G097700 chr1D 91.784 426 18 6 3726 4138 63636364 63636785 9.970000e-161 577.0
13 TraesCS1B01G097700 chr1D 94.000 50 0 3 3675 3722 239333484 239333436 5.740000e-09 73.1
14 TraesCS1B01G097700 chr1D 100.000 29 0 0 3596 3624 359725887 359725859 2.000000e-03 54.7
15 TraesCS1B01G097700 chr1D 100.000 28 0 0 3543 3570 198756566 198756539 7.000000e-03 52.8
16 TraesCS1B01G097700 chr5B 91.489 94 4 4 2668 2759 70795656 70795565 4.340000e-25 126.0
17 TraesCS1B01G097700 chr5A 92.222 90 4 3 2671 2759 48467057 48467144 1.560000e-24 124.0
18 TraesCS1B01G097700 chr5A 88.298 94 11 0 2666 2759 559809635 559809542 3.380000e-21 113.0
19 TraesCS1B01G097700 chr5A 89.610 77 8 0 2683 2759 48467144 48467068 9.470000e-17 99.0
20 TraesCS1B01G097700 chr5D 88.542 96 9 2 2665 2759 443636604 443636510 9.400000e-22 115.0
21 TraesCS1B01G097700 chr3D 88.172 93 11 0 2667 2759 417504619 417504527 1.220000e-20 111.0
22 TraesCS1B01G097700 chr3D 86.250 80 11 0 2998 3077 144291490 144291569 2.050000e-13 87.9
23 TraesCS1B01G097700 chr3D 83.908 87 14 0 2989 3075 192058869 192058955 2.650000e-12 84.2
24 TraesCS1B01G097700 chr3D 96.774 31 1 0 2762 2792 79508489 79508459 7.000000e-03 52.8
25 TraesCS1B01G097700 chr3B 88.043 92 11 0 2667 2758 543879537 543879446 4.370000e-20 110.0
26 TraesCS1B01G097700 chr3A 82.828 99 17 0 2998 3096 262522792 262522694 5.700000e-14 89.8
27 TraesCS1B01G097700 chr3A 83.146 89 15 0 2989 3077 163923979 163924067 9.530000e-12 82.4
28 TraesCS1B01G097700 chr3A 91.837 49 1 3 3676 3722 37500752 37500799 9.600000e-07 65.8
29 TraesCS1B01G097700 chr2A 94.000 50 0 3 3675 3722 722077289 722077241 5.740000e-09 73.1
30 TraesCS1B01G097700 chr2A 92.857 42 3 0 3543 3584 698684601 698684642 1.240000e-05 62.1
31 TraesCS1B01G097700 chr2A 100.000 29 0 0 1951 1979 262576672 262576700 2.000000e-03 54.7
32 TraesCS1B01G097700 chr2D 93.878 49 0 3 3676 3722 490677512 490677465 2.060000e-08 71.3
33 TraesCS1B01G097700 chr4A 95.349 43 0 2 3674 3714 619146765 619146807 2.670000e-07 67.6
34 TraesCS1B01G097700 chr6A 93.333 45 1 1 3675 3717 74350700 74350744 9.600000e-07 65.8
35 TraesCS1B01G097700 chr4D 91.837 49 1 3 3676 3722 220349162 220349209 9.600000e-07 65.8
36 TraesCS1B01G097700 chr2B 88.889 54 2 4 3591 3640 156612521 156612468 3.450000e-06 63.9
37 TraesCS1B01G097700 chr2B 100.000 29 0 0 1951 1979 265219152 265219180 2.000000e-03 54.7


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 TraesCS1B01G097700 chr1B 104463533 104467670 4137 False 2628.666667 7642 97.368667 1 4138 3 chr1B.!!$F1 4137
1 TraesCS1B01G097700 chr1A 62610503 62614597 4094 False 2764.000000 4881 93.775000 3 4138 2 chr1A.!!$F1 4135
2 TraesCS1B01G097700 chr1D 63632762 63636785 4023 False 1880.666667 3864 92.833667 1 4138 3 chr1D.!!$F1 4137

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
972 997 0.110486 ATGTTCCCAACCGAGTGCTT 59.890 50.000 0.00 0.00 0.0 3.91 F
1528 1554 0.248458 GGCACAGGTTCGTGTTTGTG 60.248 55.000 7.97 7.97 42.8 3.33 F
2747 2820 2.677836 GCTTGATACATCCGTTTGAGCA 59.322 45.455 0.00 0.00 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2907 2980 0.458669 CAGATGGAACCAAGCATGCC 59.541 55.0 15.66 0.0 0.00 4.40 R
3017 3090 0.445829 CGTATTGGACGCACAATGCA 59.554 50.0 16.64 0.0 46.27 3.96 R
3820 4010 1.368641 CAGAATTCGCCGACATCCAA 58.631 50.0 0.00 0.0 0.00 3.53 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
38 39 2.805099 GCAAGAGTGAGTGAAGAACTGG 59.195 50.000 0.00 0.00 40.07 4.00
39 40 3.742640 GCAAGAGTGAGTGAAGAACTGGT 60.743 47.826 0.00 0.00 40.07 4.00
71 79 2.088178 CCAAGATTGTTTGCGCGCC 61.088 57.895 30.77 14.34 0.00 6.53
72 80 1.371512 CAAGATTGTTTGCGCGCCA 60.372 52.632 30.77 16.58 0.00 5.69
73 81 1.081242 AAGATTGTTTGCGCGCCAG 60.081 52.632 30.77 0.00 0.00 4.85
74 82 3.174573 GATTGTTTGCGCGCCAGC 61.175 61.111 30.77 21.07 40.74 4.85
75 83 4.722855 ATTGTTTGCGCGCCAGCC 62.723 61.111 30.77 14.29 41.18 4.85
119 127 9.142515 TCAGTTTAATTGCATGCAAATTTAGAG 57.857 29.630 34.84 22.01 39.55 2.43
129 137 7.775093 TGCATGCAAATTTAGAGGTAGTTATCT 59.225 33.333 20.30 0.00 0.00 1.98
142 150 8.817876 AGAGGTAGTTATCTTTAAGCTCAAAGT 58.182 33.333 9.22 0.19 37.20 2.66
184 192 2.700897 ACTCCCACCCTCTCATTTATCG 59.299 50.000 0.00 0.00 0.00 2.92
231 242 5.041951 TGTTTACTAAAAGGAAGCGCATG 57.958 39.130 11.47 0.00 0.00 4.06
294 305 9.887629 CTGATAGCTGGATGAATAATCTAACAT 57.112 33.333 0.00 0.00 35.43 2.71
395 406 3.268330 TGATGCAGAATGAGCTGTCTTC 58.732 45.455 0.00 0.00 39.69 2.87
581 595 9.471702 ACATGAGATTGTTTTCCTTGATAGAAT 57.528 29.630 0.00 0.00 0.00 2.40
628 645 4.110482 CCTTACTGCATGTACCGTAGAAC 58.890 47.826 4.80 0.00 0.00 3.01
665 682 5.567138 AGCAAGTCATGGTTTACTTATGC 57.433 39.130 0.00 0.00 35.94 3.14
668 685 3.873910 AGTCATGGTTTACTTATGCGCT 58.126 40.909 9.73 0.00 0.00 5.92
708 725 6.714810 TGAGATAGATACAGAGGAGAGAAAGC 59.285 42.308 0.00 0.00 0.00 3.51
733 750 3.883489 GACAAAGGGAAGCAAAGTAGTGT 59.117 43.478 0.00 0.00 0.00 3.55
784 801 5.363939 AGCTGTACATCTTAAGCATTCCTC 58.636 41.667 0.00 0.00 38.14 3.71
836 855 1.455383 CCATTGGGGCCATTACGCTC 61.455 60.000 4.39 0.00 0.00 5.03
841 860 0.977395 GGGGCCATTACGCTCTCTAT 59.023 55.000 4.39 0.00 0.00 1.98
856 881 7.867752 ACGCTCTCTATAGAATGAAGTAGAAC 58.132 38.462 3.57 0.00 0.00 3.01
891 916 3.431486 CCATTTCTCTCCACTAGTCCTGC 60.431 52.174 0.00 0.00 0.00 4.85
893 918 1.032657 TCTCTCCACTAGTCCTGCGC 61.033 60.000 0.00 0.00 0.00 6.09
897 922 2.656646 CACTAGTCCTGCGCCACA 59.343 61.111 4.18 0.00 0.00 4.17
915 940 5.466728 CGCCACATGCTATTAGTATTTGTCT 59.533 40.000 7.02 0.00 38.05 3.41
972 997 0.110486 ATGTTCCCAACCGAGTGCTT 59.890 50.000 0.00 0.00 0.00 3.91
1040 1065 7.309438 GGTTCTGATAAAAAGATGCTTGGTTCT 60.309 37.037 0.00 0.00 0.00 3.01
1167 1192 9.643693 CATCCAGCAAGTAATAACTTTGAATTT 57.356 29.630 0.00 0.00 43.60 1.82
1218 1244 4.414852 CCCATTTCTCGTACTGCATTTTG 58.585 43.478 0.00 0.00 0.00 2.44
1231 1257 2.627221 TGCATTTTGCTTCTGTTGCCTA 59.373 40.909 0.75 0.00 45.31 3.93
1528 1554 0.248458 GGCACAGGTTCGTGTTTGTG 60.248 55.000 7.97 7.97 42.80 3.33
1748 1775 8.902806 TGTACAATTTGAAGTCTTGAACATTCT 58.097 29.630 2.79 0.00 0.00 2.40
1994 2023 6.302615 CAACGTTCTTCTCTTTGATGATGAC 58.697 40.000 0.00 0.00 0.00 3.06
1997 2026 5.443824 CGTTCTTCTCTTTGATGATGACGTG 60.444 44.000 0.00 0.00 32.85 4.49
2234 2263 5.399858 TCTAAGAGCGATGTGTACAGTTTC 58.600 41.667 0.00 0.00 0.00 2.78
2332 2361 6.334102 TGTCACATGGGTAATTTTTGTACC 57.666 37.500 0.00 0.00 40.38 3.34
2566 2595 3.499918 GCATGAGTTAAGCAGTCTGTGTT 59.500 43.478 0.00 0.00 0.00 3.32
2642 2671 2.887152 CTGGAACTTACAAAGCTTGCCT 59.113 45.455 0.00 0.00 0.00 4.75
2673 2702 7.279981 TGTTTTGAATGGATGAGTAATACTCCG 59.720 37.037 16.89 0.00 44.44 4.63
2676 2705 5.833667 TGAATGGATGAGTAATACTCCGTCT 59.166 40.000 16.89 0.53 44.44 4.18
2681 2710 3.959293 TGAGTAATACTCCGTCTGTCCA 58.041 45.455 16.89 0.00 44.44 4.02
2739 2812 7.715265 ACTATTTTAGTGCTTGATACATCCG 57.285 36.000 0.00 0.00 37.69 4.18
2747 2820 2.677836 GCTTGATACATCCGTTTGAGCA 59.322 45.455 0.00 0.00 0.00 4.26
2771 2844 9.162793 GCATCAAGTAATTCATCAAGTAATTCG 57.837 33.333 0.00 0.00 0.00 3.34
2776 2849 7.335627 AGTAATTCATCAAGTAATTCGGGACA 58.664 34.615 0.00 0.00 0.00 4.02
2798 2871 7.151694 ACAGAGGGAGTACTAGCTAAGAATA 57.848 40.000 0.00 0.00 0.00 1.75
2907 2980 6.764308 ACTGTGATTAACATCATTCTTGGG 57.236 37.500 0.00 0.00 41.64 4.12
2986 3059 6.828785 ACTTGTAACACCATTTCTTCTTCTGT 59.171 34.615 0.00 0.00 0.00 3.41
3210 3283 1.112315 ATTGTTGTTCTTGCGGGGCA 61.112 50.000 0.00 0.00 36.47 5.36
3211 3284 1.112315 TTGTTGTTCTTGCGGGGCAT 61.112 50.000 0.00 0.00 38.76 4.40
3409 3484 4.824289 CTTATGCCATTTGCTTCCAAGTT 58.176 39.130 0.00 0.00 42.00 2.66
3421 3496 4.263639 TGCTTCCAAGTTCAGATTCCAGAT 60.264 41.667 0.00 0.00 0.00 2.90
3422 3497 4.704057 GCTTCCAAGTTCAGATTCCAGATT 59.296 41.667 0.00 0.00 0.00 2.40
3423 3498 5.392811 GCTTCCAAGTTCAGATTCCAGATTG 60.393 44.000 0.00 0.00 0.00 2.67
3424 3499 4.592942 TCCAAGTTCAGATTCCAGATTGG 58.407 43.478 0.00 0.00 39.43 3.16
3425 3500 4.043310 TCCAAGTTCAGATTCCAGATTGGT 59.957 41.667 0.00 0.00 39.03 3.67
3426 3501 4.768968 CCAAGTTCAGATTCCAGATTGGTT 59.231 41.667 0.00 0.00 39.03 3.67
3427 3502 5.945784 CCAAGTTCAGATTCCAGATTGGTTA 59.054 40.000 0.00 0.00 39.03 2.85
3428 3503 6.127897 CCAAGTTCAGATTCCAGATTGGTTAC 60.128 42.308 0.00 0.00 39.03 2.50
3429 3504 6.126863 AGTTCAGATTCCAGATTGGTTACA 57.873 37.500 0.00 0.00 39.03 2.41
3430 3505 6.725364 AGTTCAGATTCCAGATTGGTTACAT 58.275 36.000 0.00 0.00 39.03 2.29
3431 3506 7.861629 AGTTCAGATTCCAGATTGGTTACATA 58.138 34.615 0.00 0.00 39.03 2.29
3432 3507 8.497745 AGTTCAGATTCCAGATTGGTTACATAT 58.502 33.333 0.00 0.00 39.03 1.78
3433 3508 8.778358 GTTCAGATTCCAGATTGGTTACATATC 58.222 37.037 0.00 0.00 39.03 1.63
3434 3509 8.033178 TCAGATTCCAGATTGGTTACATATCA 57.967 34.615 0.00 0.00 39.03 2.15
3435 3510 8.663167 TCAGATTCCAGATTGGTTACATATCAT 58.337 33.333 0.00 0.00 39.03 2.45
3436 3511 9.293404 CAGATTCCAGATTGGTTACATATCATT 57.707 33.333 0.00 0.00 39.03 2.57
3437 3512 9.512588 AGATTCCAGATTGGTTACATATCATTC 57.487 33.333 0.00 0.00 39.03 2.67
3438 3513 9.288576 GATTCCAGATTGGTTACATATCATTCA 57.711 33.333 0.00 0.00 39.03 2.57
3439 3514 9.645128 ATTCCAGATTGGTTACATATCATTCAA 57.355 29.630 0.00 0.00 39.03 2.69
3440 3515 9.645128 TTCCAGATTGGTTACATATCATTCAAT 57.355 29.630 0.00 0.00 39.03 2.57
3441 3516 9.288576 TCCAGATTGGTTACATATCATTCAATC 57.711 33.333 0.00 0.00 39.03 2.67
3442 3517 9.070179 CCAGATTGGTTACATATCATTCAATCA 57.930 33.333 13.30 0.00 40.52 2.57
3461 3536 9.874205 TTCAATCAACAAATTTCTCTTTCTGTT 57.126 25.926 0.00 0.00 0.00 3.16
3491 3585 8.413229 TGTTTCTTTGTAAGAATCTTGGAAAGG 58.587 33.333 19.54 8.38 46.15 3.11
3506 3600 5.382664 TGGAAAGGTTTTACTGGACTCTT 57.617 39.130 0.00 0.00 0.00 2.85
3526 3620 5.374071 TCTTAAACAGAAACAGAAGGGGAC 58.626 41.667 0.00 0.00 0.00 4.46
3541 3636 1.065551 GGGGACAAAGTCGCATAATGC 59.934 52.381 14.74 0.00 45.38 3.56
3542 3637 2.017049 GGGACAAAGTCGCATAATGCT 58.983 47.619 9.02 0.00 43.51 3.79
3543 3638 2.423538 GGGACAAAGTCGCATAATGCTT 59.576 45.455 9.02 0.00 43.51 3.91
3544 3639 3.429085 GGACAAAGTCGCATAATGCTTG 58.571 45.455 0.00 0.00 42.25 4.01
3545 3640 3.119849 GGACAAAGTCGCATAATGCTTGT 60.120 43.478 0.00 0.00 42.25 3.16
3547 3642 4.969816 ACAAAGTCGCATAATGCTTGTAC 58.030 39.130 0.00 0.00 42.25 2.90
3548 3643 4.695455 ACAAAGTCGCATAATGCTTGTACT 59.305 37.500 0.00 0.00 42.25 2.73
3551 3646 6.978343 AAGTCGCATAATGCTTGTACTAAA 57.022 33.333 0.00 0.00 42.25 1.85
3552 3647 7.553881 AAGTCGCATAATGCTTGTACTAAAT 57.446 32.000 0.00 0.00 42.25 1.40
3553 3648 7.178712 AGTCGCATAATGCTTGTACTAAATC 57.821 36.000 0.00 0.00 42.25 2.17
3556 3651 6.761242 TCGCATAATGCTTGTACTAAATCAGT 59.239 34.615 0.00 0.00 42.25 3.41
3557 3652 6.847792 CGCATAATGCTTGTACTAAATCAGTG 59.152 38.462 0.00 0.00 42.25 3.66
3558 3653 7.254421 CGCATAATGCTTGTACTAAATCAGTGA 60.254 37.037 0.00 0.00 42.25 3.41
3559 3654 7.852945 GCATAATGCTTGTACTAAATCAGTGAC 59.147 37.037 0.00 0.00 40.96 3.67
3561 3656 6.727824 ATGCTTGTACTAAATCAGTGACAC 57.272 37.500 0.00 0.00 38.24 3.67
3562 3657 5.853936 TGCTTGTACTAAATCAGTGACACT 58.146 37.500 1.07 1.07 38.24 3.55
3563 3658 6.288294 TGCTTGTACTAAATCAGTGACACTT 58.712 36.000 5.04 0.00 38.24 3.16
3566 3661 8.936864 GCTTGTACTAAATCAGTGACACTTATT 58.063 33.333 5.04 7.30 38.24 1.40
3592 3781 6.952773 AGTACTGAGGAAGTAGATGCTAAG 57.047 41.667 0.00 0.00 42.15 2.18
3600 3789 6.066032 AGGAAGTAGATGCTAAGGAGTACTC 58.934 44.000 14.87 14.87 0.00 2.59
3622 3811 8.874744 ACTCCTTCGTAAAGAAATATAAGAGC 57.125 34.615 0.00 0.00 38.57 4.09
3623 3812 8.697292 ACTCCTTCGTAAAGAAATATAAGAGCT 58.303 33.333 0.00 0.00 38.57 4.09
3624 3813 9.535878 CTCCTTCGTAAAGAAATATAAGAGCTT 57.464 33.333 0.00 0.00 38.57 3.74
3640 3829 6.917217 AAGAGCTTAGATCACTAAATGCAC 57.083 37.500 0.00 0.00 38.01 4.57
3641 3830 6.232581 AGAGCTTAGATCACTAAATGCACT 57.767 37.500 0.00 0.00 38.01 4.40
3642 3831 6.648192 AGAGCTTAGATCACTAAATGCACTT 58.352 36.000 0.00 0.00 38.01 3.16
3643 3832 7.786030 AGAGCTTAGATCACTAAATGCACTTA 58.214 34.615 0.00 0.00 38.01 2.24
3644 3833 8.428063 AGAGCTTAGATCACTAAATGCACTTAT 58.572 33.333 0.00 0.00 38.01 1.73
3645 3834 8.970859 AGCTTAGATCACTAAATGCACTTATT 57.029 30.769 0.00 0.00 38.01 1.40
3646 3835 9.401058 AGCTTAGATCACTAAATGCACTTATTT 57.599 29.630 0.00 0.00 38.01 1.40
3671 3860 6.909550 AGTATGGAGGAAGTAGATGCTAAG 57.090 41.667 0.00 0.00 0.00 2.18
3676 3865 5.103643 TGGAGGAAGTAGATGCTAAGGAGTA 60.104 44.000 0.00 0.00 0.00 2.59
3677 3866 5.242171 GGAGGAAGTAGATGCTAAGGAGTAC 59.758 48.000 0.00 0.00 0.00 2.73
3678 3867 6.020881 AGGAAGTAGATGCTAAGGAGTACT 57.979 41.667 0.00 0.00 0.00 2.73
3679 3868 6.066032 AGGAAGTAGATGCTAAGGAGTACTC 58.934 44.000 14.87 14.87 0.00 2.59
3702 3891 9.825109 ACTCCTTCTGTAAAGAAATATAAGAGC 57.175 33.333 0.00 0.00 0.00 4.09
3721 3910 7.393841 AAGAGCTTAGATCACTACGTTTAGT 57.606 36.000 0.00 0.00 39.30 2.24
3722 3911 8.503458 AAGAGCTTAGATCACTACGTTTAGTA 57.497 34.615 0.00 0.00 36.31 1.82
3786 3976 7.560262 AGTTACTACCATACATGAACTAGCAGA 59.440 37.037 0.00 0.00 0.00 4.26
3790 3980 6.239217 ACCATACATGAACTAGCAGATGAA 57.761 37.500 0.00 0.00 0.00 2.57
3796 3986 6.882656 ACATGAACTAGCAGATGAACTACAT 58.117 36.000 0.00 0.00 42.47 2.29
3820 4010 4.198530 GCTACGGTCTAGAGGACTAAACT 58.801 47.826 0.00 0.00 43.97 2.66
3830 4020 3.195825 AGAGGACTAAACTTGGATGTCGG 59.804 47.826 0.00 0.00 0.00 4.79
3919 4110 1.486310 CCAGTACATGGCTGGCTTCTA 59.514 52.381 20.66 0.00 45.72 2.10
3940 4131 2.570442 AAACTACAGAGCGAGCTAGC 57.430 50.000 11.29 11.29 37.41 3.42
4043 4245 1.200839 GGCGACGAACTTGAACGTG 59.799 57.895 0.00 0.00 42.74 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 79 3.880846 GCGCGAGGGAAATGGCTG 61.881 66.667 12.10 0.00 0.00 4.85
72 80 3.918253 TTGCGCGAGGGAAATGGCT 62.918 57.895 12.10 0.00 0.00 4.75
73 81 2.283472 AATTGCGCGAGGGAAATGGC 62.283 55.000 12.10 0.00 0.00 4.40
74 82 0.173255 AAATTGCGCGAGGGAAATGG 59.827 50.000 12.10 0.00 0.00 3.16
75 83 1.135431 TGAAATTGCGCGAGGGAAATG 60.135 47.619 12.10 0.00 0.00 2.32
119 127 9.000486 ACAACTTTGAGCTTAAAGATAACTACC 58.000 33.333 31.10 0.00 39.46 3.18
129 137 4.274147 TGGTCCACAACTTTGAGCTTAAA 58.726 39.130 3.40 3.40 0.00 1.52
142 150 1.423541 ACATTACTGCCTGGTCCACAA 59.576 47.619 0.00 0.00 0.00 3.33
184 192 0.036671 AACCGCCACAAGGTAGCTAC 60.037 55.000 15.88 15.88 41.95 3.58
231 242 4.232221 CACCAGATGAACACTTGCAAATC 58.768 43.478 0.00 0.00 0.00 2.17
581 595 8.033038 GGGAACTACAGAAATCACGCATATATA 58.967 37.037 0.00 0.00 0.00 0.86
657 674 4.278669 TGGAAAAACCAAAGCGCATAAGTA 59.721 37.500 11.47 0.00 46.75 2.24
708 725 4.580580 ACTACTTTGCTTCCCTTTGTCTTG 59.419 41.667 0.00 0.00 0.00 3.02
784 801 9.237846 GAAGTTGAATTTTAGGAAACAAGTGAG 57.762 33.333 0.00 0.00 0.00 3.51
841 860 7.894364 AGGTGACTTAGGTTCTACTTCATTCTA 59.106 37.037 0.00 0.00 37.44 2.10
893 918 8.613060 ATCAGACAAATACTAATAGCATGTGG 57.387 34.615 0.00 0.00 0.00 4.17
924 949 6.238538 CGGAACTGTAACTGTAATTTTGTGGT 60.239 38.462 0.00 0.00 0.00 4.16
933 958 7.171337 GGAACATAAACGGAACTGTAACTGTAA 59.829 37.037 0.00 0.00 0.00 2.41
972 997 5.659463 AGCTCATACAAAAACAAACAAGCA 58.341 33.333 0.00 0.00 0.00 3.91
1040 1065 0.895530 CCGAGAACAAGTCCTGGCTA 59.104 55.000 0.00 0.00 0.00 3.93
1528 1554 4.725790 AATGCAGAATTCCTAAACAGGC 57.274 40.909 0.65 0.00 0.00 4.85
1856 1885 5.453339 CCGTTGTATCCATGATAAGACTGGT 60.453 44.000 0.00 0.00 0.00 4.00
1859 1888 4.654262 ACCCGTTGTATCCATGATAAGACT 59.346 41.667 0.00 0.00 0.00 3.24
2015 2044 3.318839 CAGGAGCTTGGTTTGACAAATCA 59.681 43.478 9.86 9.86 0.00 2.57
2234 2263 1.001406 AGCTCCAGAAGAACAACTCCG 59.999 52.381 0.00 0.00 0.00 4.63
2332 2361 2.653726 TGTGCAGTATTGGCCTATTGG 58.346 47.619 4.63 0.00 0.00 3.16
2333 2362 3.696051 ACTTGTGCAGTATTGGCCTATTG 59.304 43.478 4.63 0.00 31.97 1.90
2334 2363 3.696051 CACTTGTGCAGTATTGGCCTATT 59.304 43.478 4.63 0.00 32.76 1.73
2335 2364 3.054434 TCACTTGTGCAGTATTGGCCTAT 60.054 43.478 3.32 4.11 32.76 2.57
2336 2365 2.304470 TCACTTGTGCAGTATTGGCCTA 59.696 45.455 3.32 0.00 32.76 3.93
2337 2366 1.073763 TCACTTGTGCAGTATTGGCCT 59.926 47.619 3.32 0.00 32.76 5.19
2338 2367 1.533625 TCACTTGTGCAGTATTGGCC 58.466 50.000 0.00 0.00 32.76 5.36
2339 2368 3.012518 AGATCACTTGTGCAGTATTGGC 58.987 45.455 0.00 0.00 32.76 4.52
2673 2702 3.368236 GCGTCAAGTAATTCTGGACAGAC 59.632 47.826 0.67 0.00 44.98 3.51
2676 2705 3.006430 TGAGCGTCAAGTAATTCTGGACA 59.994 43.478 10.92 0.00 44.98 4.02
2681 2710 3.432252 CCGTTTGAGCGTCAAGTAATTCT 59.568 43.478 1.72 0.00 37.70 2.40
2729 2802 4.135747 TGATGCTCAAACGGATGTATCA 57.864 40.909 0.00 0.00 0.00 2.15
2739 2812 8.025445 ACTTGATGAATTACTTGATGCTCAAAC 58.975 33.333 1.25 0.00 35.73 2.93
2747 2820 8.840321 CCCGAATTACTTGATGAATTACTTGAT 58.160 33.333 0.00 0.00 0.00 2.57
2750 2823 7.827236 TGTCCCGAATTACTTGATGAATTACTT 59.173 33.333 0.00 0.00 0.00 2.24
2751 2824 7.335627 TGTCCCGAATTACTTGATGAATTACT 58.664 34.615 0.00 0.00 0.00 2.24
2752 2825 7.494625 TCTGTCCCGAATTACTTGATGAATTAC 59.505 37.037 0.00 0.00 0.00 1.89
2753 2826 7.561251 TCTGTCCCGAATTACTTGATGAATTA 58.439 34.615 0.00 0.00 0.00 1.40
2754 2827 6.414732 TCTGTCCCGAATTACTTGATGAATT 58.585 36.000 0.00 0.00 0.00 2.17
2755 2828 5.989477 TCTGTCCCGAATTACTTGATGAAT 58.011 37.500 0.00 0.00 0.00 2.57
2756 2829 5.414789 TCTGTCCCGAATTACTTGATGAA 57.585 39.130 0.00 0.00 0.00 2.57
2757 2830 4.141937 CCTCTGTCCCGAATTACTTGATGA 60.142 45.833 0.00 0.00 0.00 2.92
2758 2831 4.122776 CCTCTGTCCCGAATTACTTGATG 58.877 47.826 0.00 0.00 0.00 3.07
2759 2832 3.134804 CCCTCTGTCCCGAATTACTTGAT 59.865 47.826 0.00 0.00 0.00 2.57
2760 2833 2.500098 CCCTCTGTCCCGAATTACTTGA 59.500 50.000 0.00 0.00 0.00 3.02
2761 2834 2.500098 TCCCTCTGTCCCGAATTACTTG 59.500 50.000 0.00 0.00 0.00 3.16
2771 2844 1.215924 AGCTAGTACTCCCTCTGTCCC 59.784 57.143 0.00 0.00 0.00 4.46
2776 2849 7.991174 TGATATTCTTAGCTAGTACTCCCTCT 58.009 38.462 0.00 0.00 0.00 3.69
2798 2871 7.769970 ACAACAAACACAATTTCTGGAAATGAT 59.230 29.630 9.00 0.00 40.57 2.45
2841 2914 7.775093 TGAGCATAAAACTGGCTGTAGAAATAT 59.225 33.333 0.00 0.00 38.15 1.28
2849 2922 6.588719 TTTTATGAGCATAAAACTGGCTGT 57.411 33.333 19.17 0.00 38.15 4.40
2854 2927 9.683069 GGGACATATTTTATGAGCATAAAACTG 57.317 33.333 23.22 22.86 38.23 3.16
2855 2928 9.420118 TGGGACATATTTTATGAGCATAAAACT 57.580 29.630 23.22 16.65 38.23 2.66
2856 2929 9.463443 GTGGGACATATTTTATGAGCATAAAAC 57.537 33.333 23.22 13.86 44.52 2.43
2907 2980 0.458669 CAGATGGAACCAAGCATGCC 59.541 55.000 15.66 0.00 0.00 4.40
2986 3059 4.371786 TGCAAACTGTTTCAAACAACACA 58.628 34.783 4.13 0.00 41.61 3.72
3017 3090 0.445829 CGTATTGGACGCACAATGCA 59.554 50.000 16.64 0.00 46.27 3.96
3128 3201 1.079819 GAGTGCAGCTTAGCGTCCA 60.080 57.895 0.00 0.00 37.31 4.02
3141 3214 0.451783 CATACAAAAGGCCGGAGTGC 59.548 55.000 5.05 0.00 0.00 4.40
3210 3283 1.367102 CAAAAACCGCCTGCCACAT 59.633 52.632 0.00 0.00 0.00 3.21
3211 3284 0.752009 TACAAAAACCGCCTGCCACA 60.752 50.000 0.00 0.00 0.00 4.17
3409 3484 8.033178 TGATATGTAACCAATCTGGAATCTGA 57.967 34.615 0.00 0.00 40.96 3.27
3435 3510 9.874205 AACAGAAAGAGAAATTTGTTGATTGAA 57.126 25.926 0.00 0.00 0.00 2.69
3436 3511 9.874205 AAACAGAAAGAGAAATTTGTTGATTGA 57.126 25.926 0.00 0.00 0.00 2.57
3472 3547 9.416284 AGTAAAACCTTTCCAAGATTCTTACAA 57.584 29.630 0.00 0.00 0.00 2.41
3474 3549 8.297426 CCAGTAAAACCTTTCCAAGATTCTTAC 58.703 37.037 0.00 0.00 0.00 2.34
3476 3551 7.014326 GTCCAGTAAAACCTTTCCAAGATTCTT 59.986 37.037 0.00 0.00 0.00 2.52
3477 3552 6.490381 GTCCAGTAAAACCTTTCCAAGATTCT 59.510 38.462 0.00 0.00 0.00 2.40
3478 3553 6.490381 AGTCCAGTAAAACCTTTCCAAGATTC 59.510 38.462 0.00 0.00 0.00 2.52
3479 3554 6.373759 AGTCCAGTAAAACCTTTCCAAGATT 58.626 36.000 0.00 0.00 0.00 2.40
3481 3556 5.132144 AGAGTCCAGTAAAACCTTTCCAAGA 59.868 40.000 0.00 0.00 0.00 3.02
3483 3558 5.382664 AGAGTCCAGTAAAACCTTTCCAA 57.617 39.130 0.00 0.00 0.00 3.53
3485 3560 7.283807 TGTTTAAGAGTCCAGTAAAACCTTTCC 59.716 37.037 0.00 0.00 0.00 3.13
3487 3562 8.050930 TCTGTTTAAGAGTCCAGTAAAACCTTT 58.949 33.333 0.00 0.00 0.00 3.11
3491 3585 8.671028 TGTTTCTGTTTAAGAGTCCAGTAAAAC 58.329 33.333 0.00 0.00 35.91 2.43
3502 3596 5.470437 GTCCCCTTCTGTTTCTGTTTAAGAG 59.530 44.000 0.00 0.00 35.91 2.85
3506 3600 4.781775 TGTCCCCTTCTGTTTCTGTTTA 57.218 40.909 0.00 0.00 0.00 2.01
3551 3646 9.862371 CTCAGTACTAAAATAAGTGTCACTGAT 57.138 33.333 6.18 0.77 39.15 2.90
3552 3647 8.304596 CCTCAGTACTAAAATAAGTGTCACTGA 58.695 37.037 6.18 0.00 37.97 3.41
3553 3648 8.304596 TCCTCAGTACTAAAATAAGTGTCACTG 58.695 37.037 6.18 0.00 33.78 3.66
3556 3651 8.867097 ACTTCCTCAGTACTAAAATAAGTGTCA 58.133 33.333 0.00 0.00 31.97 3.58
3563 3658 9.422681 AGCATCTACTTCCTCAGTACTAAAATA 57.577 33.333 0.00 0.00 36.88 1.40
3566 3661 8.818622 TTAGCATCTACTTCCTCAGTACTAAA 57.181 34.615 0.00 0.00 36.88 1.85
3568 3663 6.999272 CCTTAGCATCTACTTCCTCAGTACTA 59.001 42.308 0.00 0.00 36.88 1.82
3569 3664 5.830991 CCTTAGCATCTACTTCCTCAGTACT 59.169 44.000 0.00 0.00 36.88 2.73
3570 3665 5.828859 TCCTTAGCATCTACTTCCTCAGTAC 59.171 44.000 0.00 0.00 36.88 2.73
3574 3760 4.873010 ACTCCTTAGCATCTACTTCCTCA 58.127 43.478 0.00 0.00 0.00 3.86
3614 3803 9.698309 GTGCATTTAGTGATCTAAGCTCTTATA 57.302 33.333 0.00 0.00 37.44 0.98
3615 3804 8.428063 AGTGCATTTAGTGATCTAAGCTCTTAT 58.572 33.333 0.00 0.00 37.44 1.73
3616 3805 7.786030 AGTGCATTTAGTGATCTAAGCTCTTA 58.214 34.615 0.00 0.00 37.44 2.10
3618 3807 6.232581 AGTGCATTTAGTGATCTAAGCTCT 57.767 37.500 0.00 0.00 37.44 4.09
3619 3808 6.917217 AAGTGCATTTAGTGATCTAAGCTC 57.083 37.500 0.00 0.00 37.44 4.09
3633 3822 9.474313 TTCCTCCATACTAAAATAAGTGCATTT 57.526 29.630 0.00 0.00 0.00 2.32
3634 3823 9.125026 CTTCCTCCATACTAAAATAAGTGCATT 57.875 33.333 0.00 0.00 0.00 3.56
3635 3824 8.275040 ACTTCCTCCATACTAAAATAAGTGCAT 58.725 33.333 0.00 0.00 0.00 3.96
3636 3825 7.630082 ACTTCCTCCATACTAAAATAAGTGCA 58.370 34.615 0.00 0.00 0.00 4.57
3637 3826 9.262358 CTACTTCCTCCATACTAAAATAAGTGC 57.738 37.037 0.00 0.00 0.00 4.40
3641 3830 9.998106 GCATCTACTTCCTCCATACTAAAATAA 57.002 33.333 0.00 0.00 0.00 1.40
3642 3831 9.381038 AGCATCTACTTCCTCCATACTAAAATA 57.619 33.333 0.00 0.00 0.00 1.40
3643 3832 8.268878 AGCATCTACTTCCTCCATACTAAAAT 57.731 34.615 0.00 0.00 0.00 1.82
3644 3833 7.676683 AGCATCTACTTCCTCCATACTAAAA 57.323 36.000 0.00 0.00 0.00 1.52
3645 3834 8.777578 TTAGCATCTACTTCCTCCATACTAAA 57.222 34.615 0.00 0.00 0.00 1.85
3646 3835 7.451877 CCTTAGCATCTACTTCCTCCATACTAA 59.548 40.741 0.00 0.00 0.00 2.24
3647 3836 6.948886 CCTTAGCATCTACTTCCTCCATACTA 59.051 42.308 0.00 0.00 0.00 1.82
3648 3837 5.777732 CCTTAGCATCTACTTCCTCCATACT 59.222 44.000 0.00 0.00 0.00 2.12
3649 3838 5.775701 TCCTTAGCATCTACTTCCTCCATAC 59.224 44.000 0.00 0.00 0.00 2.39
3650 3839 5.965486 TCCTTAGCATCTACTTCCTCCATA 58.035 41.667 0.00 0.00 0.00 2.74
3651 3840 4.820775 TCCTTAGCATCTACTTCCTCCAT 58.179 43.478 0.00 0.00 0.00 3.41
3652 3841 4.219115 CTCCTTAGCATCTACTTCCTCCA 58.781 47.826 0.00 0.00 0.00 3.86
3653 3842 4.219919 ACTCCTTAGCATCTACTTCCTCC 58.780 47.826 0.00 0.00 0.00 4.30
3654 3843 6.066032 AGTACTCCTTAGCATCTACTTCCTC 58.934 44.000 0.00 0.00 0.00 3.71
3655 3844 6.020881 AGTACTCCTTAGCATCTACTTCCT 57.979 41.667 0.00 0.00 0.00 3.36
3656 3845 5.242171 GGAGTACTCCTTAGCATCTACTTCC 59.758 48.000 31.12 2.50 46.16 3.46
3657 3846 6.321848 GGAGTACTCCTTAGCATCTACTTC 57.678 45.833 31.12 2.05 46.16 3.01
3676 3865 9.825109 GCTCTTATATTTCTTTACAGAAGGAGT 57.175 33.333 0.00 0.00 40.28 3.85
3695 3884 9.122779 ACTAAACGTAGTGATCTAAGCTCTTAT 57.877 33.333 0.00 0.00 45.00 1.73
3696 3885 8.503458 ACTAAACGTAGTGATCTAAGCTCTTA 57.497 34.615 0.00 0.00 45.00 2.10
3697 3886 7.393841 ACTAAACGTAGTGATCTAAGCTCTT 57.606 36.000 0.00 0.00 45.00 2.85
3698 3887 7.227116 CCTACTAAACGTAGTGATCTAAGCTCT 59.773 40.741 1.13 0.00 45.00 4.09
3699 3888 7.354257 CCTACTAAACGTAGTGATCTAAGCTC 58.646 42.308 1.13 0.00 45.00 4.09
3700 3889 6.262720 CCCTACTAAACGTAGTGATCTAAGCT 59.737 42.308 1.13 0.00 45.00 3.74
3701 3890 6.261826 TCCCTACTAAACGTAGTGATCTAAGC 59.738 42.308 1.13 0.00 45.00 3.09
3702 3891 7.498570 ACTCCCTACTAAACGTAGTGATCTAAG 59.501 40.741 1.13 0.00 45.00 2.18
3703 3892 7.341805 ACTCCCTACTAAACGTAGTGATCTAA 58.658 38.462 1.13 0.00 45.00 2.10
3704 3893 6.893583 ACTCCCTACTAAACGTAGTGATCTA 58.106 40.000 1.13 0.00 45.00 1.98
3705 3894 5.753716 ACTCCCTACTAAACGTAGTGATCT 58.246 41.667 1.13 0.00 45.00 2.75
3706 3895 6.765512 AGTACTCCCTACTAAACGTAGTGATC 59.234 42.308 1.13 0.00 43.34 2.92
3707 3896 6.657875 AGTACTCCCTACTAAACGTAGTGAT 58.342 40.000 1.13 0.00 43.34 3.06
3708 3897 6.054860 AGTACTCCCTACTAAACGTAGTGA 57.945 41.667 1.13 0.00 43.34 3.41
3709 3898 7.849804 TTAGTACTCCCTACTAAACGTAGTG 57.150 40.000 0.00 0.00 42.59 2.74
3719 3908 9.884814 ATCTTATCATGTTTAGTACTCCCTACT 57.115 33.333 0.00 0.00 39.24 2.57
3786 3976 4.737855 AGACCGTAGCAATGTAGTTCAT 57.262 40.909 0.00 0.00 38.57 2.57
3790 3980 3.884091 CCTCTAGACCGTAGCAATGTAGT 59.116 47.826 0.00 0.00 0.00 2.73
3820 4010 1.368641 CAGAATTCGCCGACATCCAA 58.631 50.000 0.00 0.00 0.00 3.53
3830 4020 2.688507 TGTTCAGAGACCAGAATTCGC 58.311 47.619 0.00 0.00 0.00 4.70
3919 4110 3.056465 AGCTAGCTCGCTCTGTAGTTTTT 60.056 43.478 12.68 0.00 34.57 1.94
3940 4131 6.031751 AGAGAAGTTAAGTTAGGTGAGCAG 57.968 41.667 0.00 0.00 0.00 4.24
3953 4144 5.862323 GCGTCATCTTGTGTAGAGAAGTTAA 59.138 40.000 0.00 0.00 36.02 2.01
4088 4290 2.718073 GGCCATGAAGCAGCCCAAG 61.718 63.158 0.00 0.00 41.00 3.61


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

AutoCloner maintained by Alex Coulton.