Multiple sequence alignment - TraesCS5A01G196700

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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 TraesCS5A01G196700 chr5A 100.000 4601 0 0 1 4601 400503525 400498925 0.000000e+00 8497.0
1 TraesCS5A01G196700 chr5A 88.412 2632 130 86 2048 4601 400412156 400414690 0.000000e+00 3009.0
2 TraesCS5A01G196700 chr5A 92.472 1448 55 22 654 2060 400410665 400412099 0.000000e+00 2021.0
3 TraesCS5A01G196700 chr5A 86.140 873 70 29 3758 4601 400425615 400426465 0.000000e+00 894.0
4 TraesCS5A01G196700 chr5D 87.434 2077 116 60 2048 4034 298692926 298694947 0.000000e+00 2255.0
5 TraesCS5A01G196700 chr5D 94.080 1419 57 10 654 2060 298691466 298692869 0.000000e+00 2130.0
6 TraesCS5A01G196700 chr5D 91.846 650 49 2 1 646 560428047 560427398 0.000000e+00 904.0
7 TraesCS5A01G196700 chr5D 89.538 650 64 2 1 646 33061747 33062396 0.000000e+00 821.0
8 TraesCS5A01G196700 chr5D 89.247 651 65 2 1 646 37034122 37033472 0.000000e+00 809.0
9 TraesCS5A01G196700 chr5D 87.034 617 33 17 4018 4601 298695584 298696186 0.000000e+00 652.0
10 TraesCS5A01G196700 chr5B 85.818 1234 99 50 2532 3728 339426510 339427704 0.000000e+00 1240.0
11 TraesCS5A01G196700 chr5B 90.113 708 41 12 654 1345 339424278 339424972 0.000000e+00 893.0
12 TraesCS5A01G196700 chr5B 88.679 689 39 15 1382 2060 339424975 339425634 0.000000e+00 804.0
13 TraesCS5A01G196700 chr5B 88.506 522 25 9 3773 4277 339427720 339428223 2.370000e-167 599.0
14 TraesCS5A01G196700 chr5B 89.628 376 30 4 2168 2534 339426012 339426387 1.940000e-128 470.0
15 TraesCS5A01G196700 chr5B 93.082 159 9 2 4443 4601 339429203 339429359 9.960000e-57 231.0
16 TraesCS5A01G196700 chr2B 90.112 890 46 14 3121 3995 98483993 98483131 0.000000e+00 1118.0
17 TraesCS5A01G196700 chr2B 90.123 81 8 0 2258 2338 678198055 678197975 6.300000e-19 106.0
18 TraesCS5A01G196700 chr2B 90.909 77 7 0 2258 2334 677955900 677955976 2.260000e-18 104.0
19 TraesCS5A01G196700 chr2B 87.500 56 3 4 3198 3252 55924447 55924499 1.380000e-05 62.1
20 TraesCS5A01G196700 chr3B 90.034 893 44 19 3120 3995 712414652 712413788 0.000000e+00 1114.0
21 TraesCS5A01G196700 chr7A 89.787 891 48 15 3121 3995 576477109 576477972 0.000000e+00 1101.0
22 TraesCS5A01G196700 chr7A 89.250 893 50 16 3121 3995 528226371 528225507 0.000000e+00 1075.0
23 TraesCS5A01G196700 chr7A 85.612 139 20 0 1854 1992 677871601 677871739 3.710000e-31 147.0
24 TraesCS5A01G196700 chr6A 89.326 890 53 14 3121 3995 549488453 549487591 0.000000e+00 1079.0
25 TraesCS5A01G196700 chr6A 91.411 652 50 4 1 646 93311156 93310505 0.000000e+00 889.0
26 TraesCS5A01G196700 chr6A 91.231 650 53 2 1 646 93345291 93344642 0.000000e+00 881.0
27 TraesCS5A01G196700 chr6B 91.631 705 30 9 3294 3995 242425456 242424778 0.000000e+00 948.0
28 TraesCS5A01G196700 chr6B 91.952 497 17 6 3499 3995 241094571 241095044 0.000000e+00 675.0
29 TraesCS5A01G196700 chr3D 92.308 650 46 2 1 646 607906278 607905629 0.000000e+00 920.0
30 TraesCS5A01G196700 chr3D 91.118 653 51 2 1 646 556022462 556021810 0.000000e+00 878.0
31 TraesCS5A01G196700 chr4D 91.077 650 49 6 1 646 315903210 315903854 0.000000e+00 870.0
32 TraesCS5A01G196700 chr4D 89.831 118 12 0 1867 1984 373933602 373933485 7.970000e-33 152.0
33 TraesCS5A01G196700 chr4D 88.889 117 13 0 1867 1983 373857823 373857707 1.330000e-30 145.0
34 TraesCS5A01G196700 chrUn 90.061 654 60 3 1 649 76026027 76025374 0.000000e+00 843.0
35 TraesCS5A01G196700 chr4B 89.831 118 12 0 1867 1984 460032090 460031973 7.970000e-33 152.0
36 TraesCS5A01G196700 chr4A 89.256 121 13 0 1864 1984 90519138 90519258 7.970000e-33 152.0
37 TraesCS5A01G196700 chr1B 88.333 120 14 0 1864 1983 651558032 651557913 1.330000e-30 145.0
38 TraesCS5A01G196700 chr2D 92.405 79 6 0 2260 2338 565860998 565860920 3.760000e-21 113.0
39 TraesCS5A01G196700 chr2D 92.208 77 6 0 2258 2334 642783384 642783460 4.870000e-20 110.0
40 TraesCS5A01G196700 chr2D 90.000 80 8 0 2258 2337 565758780 565758701 2.260000e-18 104.0
41 TraesCS5A01G196700 chr2A 93.151 73 5 0 2266 2338 706200532 706200460 1.750000e-19 108.0
42 TraesCS5A01G196700 chr1D 97.826 46 1 0 3980 4025 53404361 53404316 3.820000e-11 80.5
43 TraesCS5A01G196700 chr1A 95.918 49 2 0 3980 4028 53414661 53414613 3.820000e-11 80.5


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 TraesCS5A01G196700 chr5A 400498925 400503525 4600 True 8497.000000 8497 100.000000 1 4601 1 chr5A.!!$R1 4600
1 TraesCS5A01G196700 chr5A 400410665 400414690 4025 False 2515.000000 3009 90.442000 654 4601 2 chr5A.!!$F2 3947
2 TraesCS5A01G196700 chr5A 400425615 400426465 850 False 894.000000 894 86.140000 3758 4601 1 chr5A.!!$F1 843
3 TraesCS5A01G196700 chr5D 298691466 298696186 4720 False 1679.000000 2255 89.516000 654 4601 3 chr5D.!!$F2 3947
4 TraesCS5A01G196700 chr5D 560427398 560428047 649 True 904.000000 904 91.846000 1 646 1 chr5D.!!$R2 645
5 TraesCS5A01G196700 chr5D 33061747 33062396 649 False 821.000000 821 89.538000 1 646 1 chr5D.!!$F1 645
6 TraesCS5A01G196700 chr5D 37033472 37034122 650 True 809.000000 809 89.247000 1 646 1 chr5D.!!$R1 645
7 TraesCS5A01G196700 chr5B 339424278 339429359 5081 False 706.166667 1240 89.304333 654 4601 6 chr5B.!!$F1 3947
8 TraesCS5A01G196700 chr2B 98483131 98483993 862 True 1118.000000 1118 90.112000 3121 3995 1 chr2B.!!$R1 874
9 TraesCS5A01G196700 chr3B 712413788 712414652 864 True 1114.000000 1114 90.034000 3120 3995 1 chr3B.!!$R1 875
10 TraesCS5A01G196700 chr7A 576477109 576477972 863 False 1101.000000 1101 89.787000 3121 3995 1 chr7A.!!$F1 874
11 TraesCS5A01G196700 chr7A 528225507 528226371 864 True 1075.000000 1075 89.250000 3121 3995 1 chr7A.!!$R1 874
12 TraesCS5A01G196700 chr6A 549487591 549488453 862 True 1079.000000 1079 89.326000 3121 3995 1 chr6A.!!$R3 874
13 TraesCS5A01G196700 chr6A 93310505 93311156 651 True 889.000000 889 91.411000 1 646 1 chr6A.!!$R1 645
14 TraesCS5A01G196700 chr6A 93344642 93345291 649 True 881.000000 881 91.231000 1 646 1 chr6A.!!$R2 645
15 TraesCS5A01G196700 chr6B 242424778 242425456 678 True 948.000000 948 91.631000 3294 3995 1 chr6B.!!$R1 701
16 TraesCS5A01G196700 chr3D 607905629 607906278 649 True 920.000000 920 92.308000 1 646 1 chr3D.!!$R2 645
17 TraesCS5A01G196700 chr3D 556021810 556022462 652 True 878.000000 878 91.118000 1 646 1 chr3D.!!$R1 645
18 TraesCS5A01G196700 chr4D 315903210 315903854 644 False 870.000000 870 91.077000 1 646 1 chr4D.!!$F1 645
19 TraesCS5A01G196700 chrUn 76025374 76026027 653 True 843.000000 843 90.061000 1 649 1 chrUn.!!$R1 648

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
788 804 0.924090 GCTTAGCGATTCCACACTCG 59.076 55.0 0.0 0.0 37.92 4.18 F
1350 1395 0.036732 ATTCCTCTGCGTTTGCTCCA 59.963 50.0 0.0 0.0 43.34 3.86 F
2056 2120 0.176680 CAGCTCGCCCTCAAGTACAT 59.823 55.0 0.0 0.0 0.00 2.29 F
2355 2700 0.905357 AGGTGAGCCTTAACTGCGAT 59.095 50.0 0.0 0.0 44.18 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2082 0.253327 GAAGGAGGTTGGGCTCGATT 59.747 55.0 0.00 0.00 0.00 3.34 R
2897 3431 0.107066 TACGAGCGGGGTATCACTCA 60.107 55.0 0.00 0.00 0.00 3.41 R
3220 3782 0.251354 AGCCACATAGCACAGGACAG 59.749 55.0 0.00 0.00 34.23 3.51 R
3756 4334 1.526575 TAAAACCCAGCAGCAGCAGC 61.527 55.0 3.17 0.46 45.49 5.25 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
30 31 0.950555 GATCCGTTGCTGCAGTGTGA 60.951 55.000 16.64 5.84 0.00 3.58
60 61 1.929169 CATGATGCACAGTGGTAGTCG 59.071 52.381 1.84 0.00 0.00 4.18
90 91 3.639561 TGATAGCGGTACAGATAGCCAAA 59.360 43.478 4.17 0.00 0.00 3.28
161 162 1.067142 GGCTCGTGGTGTATTGTCTGA 60.067 52.381 0.00 0.00 0.00 3.27
170 171 2.092968 GTGTATTGTCTGAGGCCCATGA 60.093 50.000 0.00 0.00 0.00 3.07
172 173 2.359981 ATTGTCTGAGGCCCATGATG 57.640 50.000 0.00 0.00 0.00 3.07
204 205 2.490328 ACCATTGACAAACACTTGCG 57.510 45.000 0.00 0.00 35.84 4.85
274 278 2.574006 TCTCTTGCCATTTGAGCTGT 57.426 45.000 0.00 0.00 0.00 4.40
361 365 0.940519 TAGTGCGTGCGCGTTTAGTT 60.941 50.000 22.18 4.21 45.51 2.24
383 387 3.545574 TGGCTGTGTCCACGCTCA 61.546 61.111 11.79 7.35 33.59 4.26
429 433 2.655090 TTTGGATCAACACCTGCTCA 57.345 45.000 0.00 0.00 0.00 4.26
510 518 5.124457 AGCTTCGGTCGTATGACTTTACTAA 59.876 40.000 14.61 0.00 44.83 2.24
515 523 7.315142 TCGGTCGTATGACTTTACTAATTGTT 58.685 34.615 14.61 0.00 44.83 2.83
530 538 9.522804 TTACTAATTGTTGGTGTGATTTTTGTC 57.477 29.630 0.00 0.00 0.00 3.18
533 541 3.779759 TGTTGGTGTGATTTTTGTCTGC 58.220 40.909 0.00 0.00 0.00 4.26
542 552 2.826979 TTTTTGTCTGCGTGCGTTTA 57.173 40.000 0.00 0.00 0.00 2.01
548 558 1.193650 GTCTGCGTGCGTTTATGTTGA 59.806 47.619 0.00 0.00 0.00 3.18
556 566 2.939756 TGCGTTTATGTTGACTGTGTGT 59.060 40.909 0.00 0.00 0.00 3.72
563 573 8.705134 CGTTTATGTTGACTGTGTGTATCTTAA 58.295 33.333 0.00 0.00 0.00 1.85
574 584 7.122799 ACTGTGTGTATCTTAACTATGCAGAGA 59.877 37.037 16.75 0.35 0.00 3.10
583 593 7.295340 TCTTAACTATGCAGAGACCAGGTATA 58.705 38.462 16.75 0.00 0.00 1.47
594 604 6.040955 CAGAGACCAGGTATATGCTCTTTGTA 59.959 42.308 5.21 0.00 30.87 2.41
646 656 8.593945 AAGCTAATAAAATCCATCCTTTGTCA 57.406 30.769 0.00 0.00 0.00 3.58
648 658 9.205513 AGCTAATAAAATCCATCCTTTGTCAAT 57.794 29.630 0.00 0.00 0.00 2.57
685 695 3.493767 ACCTTTCCCAGAGAGTGAAAC 57.506 47.619 0.00 0.00 0.00 2.78
788 804 0.924090 GCTTAGCGATTCCACACTCG 59.076 55.000 0.00 0.00 37.92 4.18
1173 1213 2.818274 CGCCTACGACCCTTTGCC 60.818 66.667 0.00 0.00 43.93 4.52
1236 1281 0.179161 CGCTCCTGTTCTAGTGTCGG 60.179 60.000 0.00 0.00 0.00 4.79
1241 1286 1.162698 CTGTTCTAGTGTCGGTCGGA 58.837 55.000 0.00 0.00 0.00 4.55
1267 1312 1.269448 GAATTGGAGGCGCTTGTTTCA 59.731 47.619 7.64 0.00 0.00 2.69
1301 1346 2.292016 TGTTTACACATGCCTGTTTCCG 59.708 45.455 0.00 0.00 31.62 4.30
1325 1370 2.414029 CGAATCCGAGAGATGCTAGCTC 60.414 54.545 17.23 10.86 38.22 4.09
1334 1379 4.367450 AGAGATGCTAGCTCGAAACATTC 58.633 43.478 17.23 3.38 37.46 2.67
1350 1395 0.036732 ATTCCTCTGCGTTTGCTCCA 59.963 50.000 0.00 0.00 43.34 3.86
1352 1397 1.302033 CCTCTGCGTTTGCTCCAGT 60.302 57.895 0.00 0.00 43.34 4.00
1380 1432 3.917760 CCGTCGGGATGCCCTCTC 61.918 72.222 2.34 0.00 42.67 3.20
1409 1461 0.953471 TGTTTGTTCCGATCGGCCTG 60.953 55.000 29.62 5.97 34.68 4.85
1426 1478 1.234821 CTGTGGAGGCGCTTGTTTTA 58.765 50.000 7.64 0.00 0.00 1.52
1450 1502 3.809279 TCTTCGTTTTCGGTTTACCCTTC 59.191 43.478 0.00 0.00 44.25 3.46
1527 1583 3.520290 TTGGTAGATTGCCGAGTAGTG 57.480 47.619 0.00 0.00 0.00 2.74
1602 1658 4.372235 CGATCCGTCGCGTTAAGT 57.628 55.556 5.77 0.00 41.49 2.24
1629 1685 6.045318 TCAAGCTAGCTTCACATCAATAGAC 58.955 40.000 27.08 0.00 33.42 2.59
1630 1686 5.604758 AGCTAGCTTCACATCAATAGACA 57.395 39.130 12.68 0.00 0.00 3.41
1702 1765 6.650120 TGAGTTTCCTAATAAGTGATGGGAC 58.350 40.000 0.00 0.00 0.00 4.46
1708 1771 3.543680 AATAAGTGATGGGACCGTCTG 57.456 47.619 11.56 0.00 33.41 3.51
1786 1849 5.647658 TGGATACCAAATCTAACTGCTGTTG 59.352 40.000 18.22 8.91 37.59 3.33
1831 1895 2.036089 CTCTAATTACTGGTCTCCCGCC 59.964 54.545 0.00 0.00 0.00 6.13
2056 2120 0.176680 CAGCTCGCCCTCAAGTACAT 59.823 55.000 0.00 0.00 0.00 2.29
2147 2474 5.308825 ACTAATTAGCAGTGGCATATGACC 58.691 41.667 12.54 7.63 44.61 4.02
2255 2600 2.840038 AGACATGCCCTAACATCACAGA 59.160 45.455 0.00 0.00 0.00 3.41
2355 2700 0.905357 AGGTGAGCCTTAACTGCGAT 59.095 50.000 0.00 0.00 44.18 4.58
2357 2702 0.924090 GTGAGCCTTAACTGCGATCG 59.076 55.000 11.69 11.69 0.00 3.69
2373 2721 4.385748 TGCGATCGATTATTGTGCTATCAC 59.614 41.667 21.57 0.00 43.40 3.06
2392 2743 2.165030 CACCTTTCATGCTTGGCCTTAG 59.835 50.000 3.32 2.21 0.00 2.18
2394 2745 2.165030 CCTTTCATGCTTGGCCTTAGTG 59.835 50.000 3.32 0.00 0.00 2.74
2395 2746 2.584835 TTCATGCTTGGCCTTAGTGT 57.415 45.000 3.32 0.00 0.00 3.55
2404 2755 4.575236 GCTTGGCCTTAGTGTCCTTTATAC 59.425 45.833 3.32 0.00 0.00 1.47
2455 2806 7.110155 TCGTCATACCTCAGTCAGCATATATA 58.890 38.462 0.00 0.00 0.00 0.86
2530 2888 5.703876 CTTGTTTCAGAGTTATTGGAAGGC 58.296 41.667 0.00 0.00 0.00 4.35
2588 3073 5.348986 ACTATGCTATCGTCGTTCATGTTT 58.651 37.500 0.00 0.00 0.00 2.83
2597 3082 3.304123 CGTCGTTCATGTTTTTGGCCTTA 60.304 43.478 3.32 0.00 0.00 2.69
2598 3083 4.612943 GTCGTTCATGTTTTTGGCCTTAA 58.387 39.130 3.32 0.00 0.00 1.85
2613 3098 9.702253 TTTTGGCCTTAAGTCACCATAAATATA 57.298 29.630 3.32 0.00 30.85 0.86
2626 3145 6.372659 CACCATAAATATAGTCCTGTCCATGC 59.627 42.308 0.00 0.00 0.00 4.06
2640 3159 3.455910 TGTCCATGCTATTTGGCTCTAGT 59.544 43.478 0.00 0.00 34.06 2.57
2641 3160 4.061596 GTCCATGCTATTTGGCTCTAGTC 58.938 47.826 0.00 0.00 34.06 2.59
2642 3161 3.711190 TCCATGCTATTTGGCTCTAGTCA 59.289 43.478 0.00 0.00 34.06 3.41
2643 3162 4.349048 TCCATGCTATTTGGCTCTAGTCAT 59.651 41.667 0.00 0.00 34.06 3.06
2644 3163 5.068636 CCATGCTATTTGGCTCTAGTCATT 58.931 41.667 0.00 0.00 0.00 2.57
2645 3164 5.048921 CCATGCTATTTGGCTCTAGTCATTG 60.049 44.000 0.00 0.00 0.00 2.82
2646 3165 5.357742 TGCTATTTGGCTCTAGTCATTGA 57.642 39.130 0.00 0.00 0.00 2.57
2647 3166 5.118990 TGCTATTTGGCTCTAGTCATTGAC 58.881 41.667 8.82 8.82 0.00 3.18
2731 3262 6.544928 TCAGAGTAAATATGCCAAGTCAGA 57.455 37.500 0.00 0.00 0.00 3.27
2758 3289 7.877612 TCACTAGTGTTTTGCATCAATCTAGAA 59.122 33.333 21.99 0.00 0.00 2.10
2759 3290 8.671921 CACTAGTGTTTTGCATCAATCTAGAAT 58.328 33.333 15.06 0.00 0.00 2.40
2760 3291 9.236006 ACTAGTGTTTTGCATCAATCTAGAATT 57.764 29.630 16.79 0.00 0.00 2.17
2761 3292 9.713740 CTAGTGTTTTGCATCAATCTAGAATTC 57.286 33.333 0.00 0.00 0.00 2.17
2827 3361 6.693315 TGCCTCCTTAAGTTATATTTGTGC 57.307 37.500 0.97 0.00 0.00 4.57
2832 3366 7.552687 CCTCCTTAAGTTATATTTGTGCTGTGA 59.447 37.037 0.97 0.00 0.00 3.58
2841 3375 2.042686 TTGTGCTGTGAACTGCTCTT 57.957 45.000 12.64 0.00 40.79 2.85
2842 3376 1.586422 TGTGCTGTGAACTGCTCTTC 58.414 50.000 12.64 3.36 40.79 2.87
2845 3379 2.551459 GTGCTGTGAACTGCTCTTCATT 59.449 45.455 12.64 0.00 40.79 2.57
2853 3387 4.214971 TGAACTGCTCTTCATTTTCTGCTC 59.785 41.667 0.00 0.00 0.00 4.26
2857 3391 2.748532 GCTCTTCATTTTCTGCTCTGCT 59.251 45.455 0.00 0.00 0.00 4.24
2863 3397 4.329392 TCATTTTCTGCTCTGCTGAATCA 58.671 39.130 11.47 4.19 43.68 2.57
2866 3400 2.220479 TCTGCTCTGCTGAATCATCG 57.780 50.000 0.00 0.00 33.82 3.84
2868 3402 1.859703 CTGCTCTGCTGAATCATCGAC 59.140 52.381 0.00 0.00 0.00 4.20
2883 3417 1.227089 CGACCTCCCGATTCTGCAG 60.227 63.158 7.63 7.63 0.00 4.41
2956 3490 7.843490 TGTACAGTAGATGCCAACTTTAATC 57.157 36.000 0.00 0.00 0.00 1.75
3030 3565 3.380004 TGTTCTTCGTTTTGTCATGCCTT 59.620 39.130 0.00 0.00 0.00 4.35
3032 3567 5.066634 TGTTCTTCGTTTTGTCATGCCTTAA 59.933 36.000 0.00 0.00 0.00 1.85
3033 3568 5.356882 TCTTCGTTTTGTCATGCCTTAAG 57.643 39.130 0.00 0.00 0.00 1.85
3034 3569 4.819630 TCTTCGTTTTGTCATGCCTTAAGT 59.180 37.500 0.97 0.00 0.00 2.24
3035 3570 4.742438 TCGTTTTGTCATGCCTTAAGTC 57.258 40.909 0.97 0.00 0.00 3.01
3036 3571 4.130857 TCGTTTTGTCATGCCTTAAGTCA 58.869 39.130 0.97 0.00 0.00 3.41
3037 3572 4.024387 TCGTTTTGTCATGCCTTAAGTCAC 60.024 41.667 0.97 0.00 0.00 3.67
3091 3627 7.670559 TCATCATCCATATTTATTCATGGTGCA 59.329 33.333 0.00 0.00 42.07 4.57
3092 3628 7.457024 TCATCCATATTTATTCATGGTGCAG 57.543 36.000 0.00 0.00 42.07 4.41
3093 3629 7.005902 TCATCCATATTTATTCATGGTGCAGT 58.994 34.615 0.00 0.00 42.07 4.40
3095 3631 8.795513 CATCCATATTTATTCATGGTGCAGTTA 58.204 33.333 0.00 0.00 42.07 2.24
3098 3650 9.630098 CCATATTTATTCATGGTGCAGTTATTC 57.370 33.333 0.00 0.00 37.51 1.75
3109 3661 6.870769 TGGTGCAGTTATTCTAAGGTAGTAC 58.129 40.000 0.00 0.00 0.00 2.73
3163 3725 9.575868 AGCTAACTATACTACAGTGTGTATCAT 57.424 33.333 16.59 10.04 31.66 2.45
3172 3734 8.349568 ACTACAGTGTGTATCATTCTAGACAA 57.650 34.615 5.88 0.00 31.66 3.18
3173 3735 8.972127 ACTACAGTGTGTATCATTCTAGACAAT 58.028 33.333 5.88 0.00 31.66 2.71
3220 3782 3.290948 TGGCCTTGGTCACCATAATAC 57.709 47.619 3.32 0.00 31.53 1.89
3234 3800 5.698089 CACCATAATACTGTCCTGTGCTATG 59.302 44.000 0.00 0.00 0.00 2.23
3274 3840 6.360370 AGCATCAAACACCTTCTCTAAGTA 57.640 37.500 0.00 0.00 0.00 2.24
3281 3847 9.886132 TCAAACACCTTCTCTAAGTATTTATCC 57.114 33.333 0.00 0.00 0.00 2.59
3309 3875 6.808829 ACACACAGAATTCAATGATGTTTGT 58.191 32.000 8.44 9.11 31.78 2.83
3312 3878 8.270799 CACACAGAATTCAATGATGTTTGTTTC 58.729 33.333 8.44 0.00 0.00 2.78
3313 3879 7.980662 ACACAGAATTCAATGATGTTTGTTTCA 59.019 29.630 8.44 0.00 0.00 2.69
3314 3880 8.819015 CACAGAATTCAATGATGTTTGTTTCAA 58.181 29.630 8.44 0.00 0.00 2.69
3342 3909 0.181114 TGTGCCAAGTCAGCTCACTT 59.819 50.000 0.00 0.00 37.05 3.16
3373 3940 1.203287 TCAATCTGACGCTGACAGAGG 59.797 52.381 6.65 0.00 45.49 3.69
3408 3979 8.646004 ACAGCTCTGTATATGTTATCATGTCTT 58.354 33.333 0.00 0.00 42.90 3.01
3538 4116 8.253810 CACTCCTAGAGATTTGAATCACTTGTA 58.746 37.037 8.58 0.00 37.49 2.41
3566 4144 5.263185 CCAACTTAACTCTGTTTCAACACG 58.737 41.667 0.00 0.00 34.70 4.49
3567 4145 4.531659 ACTTAACTCTGTTTCAACACGC 57.468 40.909 0.00 0.00 34.70 5.34
3728 4306 8.363390 TCTTGATTGATACCATAGTAGCTTCTG 58.637 37.037 2.65 0.00 35.83 3.02
3735 4313 3.710165 ACCATAGTAGCTTCTGGTTACCC 59.290 47.826 2.65 0.00 38.88 3.69
3754 4332 5.152623 ACCCGTAGTACCTTTTAAGTTCC 57.847 43.478 0.00 0.00 0.00 3.62
3755 4333 4.840680 ACCCGTAGTACCTTTTAAGTTCCT 59.159 41.667 0.00 0.00 0.00 3.36
3756 4334 5.173664 CCCGTAGTACCTTTTAAGTTCCTG 58.826 45.833 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.523072 GTGCATCATGTTCGCAAGGT 59.477 50.000 7.78 0.00 37.41 3.50
60 61 1.961394 TGTACCGCTATCACATCCCTC 59.039 52.381 0.00 0.00 0.00 4.30
90 91 4.389992 GCCGTCAATATCATCGAACATGAT 59.610 41.667 0.00 5.41 41.25 2.45
161 162 2.060275 TCTTAGCATCATCATGGGCCT 58.940 47.619 4.53 0.00 0.00 5.19
170 171 8.523915 TTGTCAATGGTAAATCTTAGCATCAT 57.476 30.769 10.57 0.00 34.93 2.45
172 173 8.243426 TGTTTGTCAATGGTAAATCTTAGCATC 58.757 33.333 10.57 1.77 34.93 3.91
204 205 2.247437 GCGATCCCATGCTTCCGAC 61.247 63.158 0.00 0.00 0.00 4.79
298 302 2.747686 GCGGAACCAGAACCTCCA 59.252 61.111 0.00 0.00 0.00 3.86
380 384 1.706301 CAAGCGCACGTGATCTGAG 59.294 57.895 22.23 7.63 0.00 3.35
383 387 2.357396 TGCAAGCGCACGTGATCT 60.357 55.556 22.23 12.05 45.36 2.75
429 433 4.989279 AAAAGCAATGATAATCCACGCT 57.011 36.364 0.00 0.00 31.74 5.07
510 518 4.810491 GCAGACAAAAATCACACCAACAAT 59.190 37.500 0.00 0.00 0.00 2.71
515 523 2.020720 ACGCAGACAAAAATCACACCA 58.979 42.857 0.00 0.00 0.00 4.17
530 538 1.194547 AGTCAACATAAACGCACGCAG 59.805 47.619 0.00 0.00 0.00 5.18
533 541 2.033236 ACACAGTCAACATAAACGCACG 60.033 45.455 0.00 0.00 0.00 5.34
542 552 9.371136 CATAGTTAAGATACACACAGTCAACAT 57.629 33.333 0.00 0.00 0.00 2.71
548 558 7.122799 TCTCTGCATAGTTAAGATACACACAGT 59.877 37.037 0.00 0.00 0.00 3.55
556 566 6.136857 ACCTGGTCTCTGCATAGTTAAGATA 58.863 40.000 0.00 0.00 0.00 1.98
563 573 4.221703 GCATATACCTGGTCTCTGCATAGT 59.778 45.833 14.90 0.00 0.00 2.12
574 584 7.346471 ACAAATACAAAGAGCATATACCTGGT 58.654 34.615 4.05 4.05 0.00 4.00
583 593 9.453572 TCAAGAAGATACAAATACAAAGAGCAT 57.546 29.630 0.00 0.00 0.00 3.79
621 631 8.593945 TGACAAAGGATGGATTTTATTAGCTT 57.406 30.769 0.00 0.00 0.00 3.74
658 668 4.036852 CACTCTCTGGGAAAGGTTGTTTTC 59.963 45.833 0.00 0.00 36.55 2.29
685 695 0.721718 GTGCCGAGAAAGTTCGATGG 59.278 55.000 0.00 0.00 43.03 3.51
788 804 0.603975 GATAGGCCCGAATGGAGTGC 60.604 60.000 0.00 0.00 37.49 4.40
790 806 0.399949 TGGATAGGCCCGAATGGAGT 60.400 55.000 0.00 0.00 37.49 3.85
1162 1202 1.675641 CAGAAGGGGCAAAGGGTCG 60.676 63.158 0.00 0.00 0.00 4.79
1163 1203 1.979155 GCAGAAGGGGCAAAGGGTC 60.979 63.158 0.00 0.00 0.00 4.46
1236 1281 0.179108 CTCCAATTCCGAGGTCCGAC 60.179 60.000 0.00 0.00 41.76 4.79
1267 1312 6.668323 CATGTGTAAACAGAAAACGAGGATT 58.332 36.000 0.00 0.00 0.00 3.01
1301 1346 3.730662 GCTAGCATCTCTCGGATTCGATC 60.731 52.174 10.63 0.00 45.04 3.69
1325 1370 2.574322 CAAACGCAGAGGAATGTTTCG 58.426 47.619 0.00 0.00 32.58 3.46
1334 1379 1.294659 GACTGGAGCAAACGCAGAGG 61.295 60.000 0.00 0.00 0.00 3.69
1378 1430 1.264288 GAACAAACAGACGCAAGGGAG 59.736 52.381 0.00 0.00 46.39 4.30
1380 1432 0.310854 GGAACAAACAGACGCAAGGG 59.689 55.000 0.00 0.00 46.39 3.95
1409 1461 1.197036 GAGTAAAACAAGCGCCTCCAC 59.803 52.381 2.29 0.00 0.00 4.02
1426 1478 3.133691 GGGTAAACCGAAAACGAAGAGT 58.866 45.455 0.00 0.00 36.71 3.24
1450 1502 2.717485 CCTGGATTTGATGCGCGG 59.283 61.111 8.83 0.00 0.00 6.46
1527 1583 1.510480 AACAGCGACAGGAAGCAAGC 61.510 55.000 0.00 0.00 35.48 4.01
1602 1658 5.405935 TTGATGTGAAGCTAGCTTGAGTA 57.594 39.130 33.91 17.70 36.26 2.59
1708 1771 3.486285 GCAGGTTGCTGAAGAAAGC 57.514 52.632 0.00 0.00 40.96 3.51
1786 1849 8.252964 AGAACGACCAACACTAATTTAAGATC 57.747 34.615 0.00 0.00 0.00 2.75
1831 1895 5.220739 GCAGTTAATTACAGCAGTCCATCAG 60.221 44.000 0.00 0.00 38.96 2.90
2018 2082 0.253327 GAAGGAGGTTGGGCTCGATT 59.747 55.000 0.00 0.00 0.00 3.34
2056 2120 1.067364 CACCTTCAAACAGCACATGCA 59.933 47.619 6.64 0.00 45.16 3.96
2255 2600 5.277925 GCATAGCACCTGCAAAACAAAATTT 60.278 36.000 0.00 0.00 45.16 1.82
2355 2700 6.345298 TGAAAGGTGATAGCACAATAATCGA 58.655 36.000 13.97 0.00 46.96 3.59
2357 2702 6.860023 GCATGAAAGGTGATAGCACAATAATC 59.140 38.462 13.97 4.34 46.96 1.75
2373 2721 2.165030 CACTAAGGCCAAGCATGAAAGG 59.835 50.000 5.01 0.00 0.00 3.11
2404 2755 1.816835 AGAACAAGCATGGACAGCATG 59.183 47.619 0.00 0.00 46.00 4.06
2418 2769 4.710324 AGGTATGACGAAACCAAGAACAA 58.290 39.130 0.00 0.00 38.30 2.83
2455 2806 6.163476 ACACAATATGTTCGACACACTATGT 58.837 36.000 3.13 5.80 41.55 2.29
2551 3034 8.407064 ACGATAGCATAGTAAGCTCCATATTAC 58.593 37.037 2.57 0.00 42.32 1.89
2554 3037 6.238511 CGACGATAGCATAGTAAGCTCCATAT 60.239 42.308 2.57 0.00 42.32 1.78
2555 3038 5.064834 CGACGATAGCATAGTAAGCTCCATA 59.935 44.000 2.57 0.00 42.32 2.74
2588 3073 9.349713 CTATATTTATGGTGACTTAAGGCCAAA 57.650 33.333 5.01 4.58 34.39 3.28
2597 3082 7.347222 TGGACAGGACTATATTTATGGTGACTT 59.653 37.037 0.00 0.00 0.00 3.01
2598 3083 6.844388 TGGACAGGACTATATTTATGGTGACT 59.156 38.462 0.00 0.00 0.00 3.41
2613 3098 2.684927 GCCAAATAGCATGGACAGGACT 60.685 50.000 0.00 0.00 40.56 3.85
2626 3145 6.577103 TGAGTCAATGACTAGAGCCAAATAG 58.423 40.000 16.71 0.00 43.53 1.73
2640 3159 6.430616 TGTTTGATGCTACAATGAGTCAATGA 59.569 34.615 15.15 0.00 0.00 2.57
2641 3160 6.525628 GTGTTTGATGCTACAATGAGTCAATG 59.474 38.462 6.65 6.65 0.00 2.82
2642 3161 6.349611 GGTGTTTGATGCTACAATGAGTCAAT 60.350 38.462 0.00 0.00 0.00 2.57
2643 3162 5.048782 GGTGTTTGATGCTACAATGAGTCAA 60.049 40.000 0.00 0.00 0.00 3.18
2644 3163 4.455533 GGTGTTTGATGCTACAATGAGTCA 59.544 41.667 0.00 0.00 0.00 3.41
2645 3164 4.697352 AGGTGTTTGATGCTACAATGAGTC 59.303 41.667 0.00 0.00 0.00 3.36
2646 3165 4.655963 AGGTGTTTGATGCTACAATGAGT 58.344 39.130 0.00 0.00 0.00 3.41
2647 3166 5.048504 ACAAGGTGTTTGATGCTACAATGAG 60.049 40.000 0.00 0.00 39.21 2.90
2676 3195 8.459635 GCATCATGAGATTGCTTATATTGACAT 58.540 33.333 11.67 0.00 30.20 3.06
2678 3197 7.120873 AGGCATCATGAGATTGCTTATATTGAC 59.879 37.037 17.01 1.32 32.47 3.18
2680 3199 7.094334 ACAGGCATCATGAGATTGCTTATATTG 60.094 37.037 17.01 9.86 32.47 1.90
2681 3200 6.946583 ACAGGCATCATGAGATTGCTTATATT 59.053 34.615 17.01 0.00 32.47 1.28
2682 3201 6.482524 ACAGGCATCATGAGATTGCTTATAT 58.517 36.000 17.01 0.00 32.47 0.86
2683 3202 5.872963 ACAGGCATCATGAGATTGCTTATA 58.127 37.500 17.01 0.00 32.47 0.98
2684 3203 4.726583 ACAGGCATCATGAGATTGCTTAT 58.273 39.130 17.01 0.00 32.47 1.73
2731 3262 8.043113 TCTAGATTGATGCAAAACACTAGTGAT 58.957 33.333 29.30 15.34 0.00 3.06
2758 3289 1.974236 AGCGCCCTTAGCATCTAGAAT 59.026 47.619 2.29 0.00 44.04 2.40
2759 3290 1.414158 AGCGCCCTTAGCATCTAGAA 58.586 50.000 2.29 0.00 44.04 2.10
2760 3291 1.414158 AAGCGCCCTTAGCATCTAGA 58.586 50.000 2.29 0.00 44.04 2.43
2761 3292 2.297597 AGTAAGCGCCCTTAGCATCTAG 59.702 50.000 2.29 0.00 44.04 2.43
2775 3306 5.840940 AAACAAAGCTGTAGTAGTAAGCG 57.159 39.130 0.00 0.00 41.88 4.68
2827 3361 5.450171 CAGAAAATGAAGAGCAGTTCACAG 58.550 41.667 3.10 0.00 39.25 3.66
2832 3366 4.215827 CAGAGCAGAAAATGAAGAGCAGTT 59.784 41.667 0.00 0.00 36.14 3.16
2841 3375 4.329392 TGATTCAGCAGAGCAGAAAATGA 58.671 39.130 1.05 0.00 37.58 2.57
2842 3376 4.696899 TGATTCAGCAGAGCAGAAAATG 57.303 40.909 1.05 0.00 37.58 2.32
2845 3379 2.934553 CGATGATTCAGCAGAGCAGAAA 59.065 45.455 2.47 0.00 37.58 2.52
2853 3387 1.539929 GGGAGGTCGATGATTCAGCAG 60.540 57.143 2.47 0.00 0.00 4.24
2857 3391 1.704641 ATCGGGAGGTCGATGATTCA 58.295 50.000 0.00 0.00 46.52 2.57
2866 3400 1.522580 GCTGCAGAATCGGGAGGTC 60.523 63.158 20.43 0.00 0.00 3.85
2868 3402 1.523258 CTGCTGCAGAATCGGGAGG 60.523 63.158 24.88 0.00 32.44 4.30
2897 3431 0.107066 TACGAGCGGGGTATCACTCA 60.107 55.000 0.00 0.00 0.00 3.41
2928 3462 5.995565 AGTTGGCATCTACTGTACAAGTA 57.004 39.130 0.00 1.31 40.56 2.24
2956 3490 6.391227 AAACAAGTGACTCCAACAAATAGG 57.609 37.500 0.00 0.00 0.00 2.57
2968 3503 6.207417 CCATCAGGTCAAATAAACAAGTGACT 59.793 38.462 0.00 0.00 40.20 3.41
3030 3565 4.522789 TGCTCGATGCTATATGGTGACTTA 59.477 41.667 8.07 0.00 43.37 2.24
3032 3567 2.893489 TGCTCGATGCTATATGGTGACT 59.107 45.455 8.07 0.00 43.37 3.41
3033 3568 3.303881 TGCTCGATGCTATATGGTGAC 57.696 47.619 8.07 0.00 43.37 3.67
3034 3569 5.859205 ATATGCTCGATGCTATATGGTGA 57.141 39.130 8.07 0.00 43.37 4.02
3035 3570 6.200475 CAGAATATGCTCGATGCTATATGGTG 59.800 42.308 8.07 7.17 43.37 4.17
3036 3571 6.127225 ACAGAATATGCTCGATGCTATATGGT 60.127 38.462 8.07 6.87 43.37 3.55
3037 3572 6.279123 ACAGAATATGCTCGATGCTATATGG 58.721 40.000 8.07 0.00 43.37 2.74
3078 3614 8.052748 ACCTTAGAATAACTGCACCATGAATAA 58.947 33.333 0.00 0.00 0.00 1.40
3083 3619 6.349300 ACTACCTTAGAATAACTGCACCATG 58.651 40.000 0.00 0.00 0.00 3.66
3087 3623 8.901793 AGTAGTACTACCTTAGAATAACTGCAC 58.098 37.037 25.97 0.91 36.75 4.57
3163 3725 8.360390 ACAATGATAGCGTCATATTGTCTAGAA 58.640 33.333 7.86 0.00 46.80 2.10
3194 3756 0.329596 GGTGACCAAGGCCAAGAGAT 59.670 55.000 5.01 0.00 0.00 2.75
3220 3782 0.251354 AGCCACATAGCACAGGACAG 59.749 55.000 0.00 0.00 34.23 3.51
3234 3800 4.635765 TGATGCTACAATAACTGAAGCCAC 59.364 41.667 0.00 0.00 32.14 5.01
3281 3847 9.467258 AAACATCATTGAATTCTGTGTGTTAAG 57.533 29.630 18.92 7.66 0.00 1.85
3295 3861 9.212641 TGACTTTTTGAAACAAACATCATTGAA 57.787 25.926 0.00 0.00 34.38 2.69
3297 3863 9.991388 ATTGACTTTTTGAAACAAACATCATTG 57.009 25.926 0.00 0.00 36.37 2.82
3298 3864 9.991388 CATTGACTTTTTGAAACAAACATCATT 57.009 25.926 0.00 0.00 0.00 2.57
3309 3875 5.486526 ACTTGGCACATTGACTTTTTGAAA 58.513 33.333 0.00 0.00 39.30 2.69
3312 3878 4.431809 TGACTTGGCACATTGACTTTTTG 58.568 39.130 0.00 0.00 39.30 2.44
3313 3879 4.685924 CTGACTTGGCACATTGACTTTTT 58.314 39.130 0.00 0.00 39.30 1.94
3314 3880 3.491447 GCTGACTTGGCACATTGACTTTT 60.491 43.478 0.00 0.00 39.30 2.27
3342 3909 3.887741 CGTCAGATTGATGCAAAACACA 58.112 40.909 0.00 0.00 0.00 3.72
3401 3972 8.671921 AGCACAAATATAACTGAAGAAGACATG 58.328 33.333 0.00 0.00 0.00 3.21
3408 3979 8.094548 AGTACACAGCACAAATATAACTGAAGA 58.905 33.333 0.00 0.00 32.67 2.87
3538 4116 2.938956 ACAGAGTTAAGTTGGCAGCT 57.061 45.000 0.00 0.00 0.00 4.24
3566 4144 4.945246 TGGTCCTCGTCTGAAAATATAGC 58.055 43.478 0.00 0.00 0.00 2.97
3567 4145 6.806751 TCTTGGTCCTCGTCTGAAAATATAG 58.193 40.000 0.00 0.00 0.00 1.31
3735 4313 5.347907 CAGCAGGAACTTAAAAGGTACTACG 59.652 44.000 0.00 0.00 33.59 3.51
3755 4333 4.591399 AACCCAGCAGCAGCAGCA 62.591 61.111 12.92 0.00 45.49 4.41
3756 4334 1.526575 TAAAACCCAGCAGCAGCAGC 61.527 55.000 3.17 0.46 45.49 5.25


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

AutoCloner maintained by Alex Coulton.