Multiple sequence alignment - TraesCS2A01G161000

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 TraesCS2A01G161000 chr2A 100.000 5052 0 0 1 5052 111920942 111925993 0.000000e+00 9330.0
1 TraesCS2A01G161000 chr2A 86.385 1469 134 40 585 2011 112744408 112745852 0.000000e+00 1544.0
2 TraesCS2A01G161000 chr2A 85.658 1520 159 35 539 2011 113312436 113310929 0.000000e+00 1544.0
3 TraesCS2A01G161000 chr2A 87.847 864 68 21 2075 2912 113310843 113309991 0.000000e+00 979.0
4 TraesCS2A01G161000 chr2A 86.758 876 63 30 2075 2906 112745938 112746804 0.000000e+00 926.0
5 TraesCS2A01G161000 chr2A 86.431 538 42 15 3935 4466 113309512 113309000 1.230000e-155 560.0
6 TraesCS2A01G161000 chr2A 89.975 399 26 10 3933 4326 112747467 112747856 2.100000e-138 503.0
7 TraesCS2A01G161000 chr2A 74.897 972 168 48 2707 3659 113195492 113194578 1.720000e-99 374.0
8 TraesCS2A01G161000 chr2A 81.042 480 81 6 302 774 113344548 113344072 1.720000e-99 374.0
9 TraesCS2A01G161000 chr2A 79.854 412 68 13 3263 3664 112746880 112747286 2.300000e-73 287.0
10 TraesCS2A01G161000 chr2A 91.160 181 7 6 3686 3859 112747260 112747438 2.350000e-58 237.0
11 TraesCS2A01G161000 chr2A 78.988 257 47 4 283 534 113343777 113343523 8.700000e-38 169.0
12 TraesCS2A01G161000 chr2A 78.544 261 51 3 282 537 113319644 113319384 3.130000e-37 167.0
13 TraesCS2A01G161000 chr2A 77.519 258 33 17 3677 3926 113196702 113196462 1.140000e-26 132.0
14 TraesCS2A01G161000 chr2A 82.883 111 13 2 4464 4573 113250412 113250307 1.500000e-15 95.3
15 TraesCS2A01G161000 chr2A 83.516 91 12 2 181 271 113318467 113318380 1.170000e-11 82.4
16 TraesCS2A01G161000 chr2A 97.222 36 1 0 4713 4748 112748503 112748538 1.520000e-05 62.1
17 TraesCS2A01G161000 chr2D 93.366 2276 100 27 1 2257 111587673 111589916 0.000000e+00 3319.0
18 TraesCS2A01G161000 chr2D 86.776 2019 174 47 627 2621 112098952 112100901 0.000000e+00 2163.0
19 TraesCS2A01G161000 chr2D 90.048 1035 89 8 2637 3664 111590313 111591340 0.000000e+00 1328.0
20 TraesCS2A01G161000 chr2D 87.725 1002 101 16 705 1694 112181370 112180379 0.000000e+00 1149.0
21 TraesCS2A01G161000 chr2D 82.134 1237 132 59 3256 4444 112101324 112102519 0.000000e+00 977.0
22 TraesCS2A01G161000 chr2D 94.514 638 18 10 3686 4318 111591314 111591939 0.000000e+00 968.0
23 TraesCS2A01G161000 chr2D 80.595 1345 157 58 2636 3926 112179452 112178158 0.000000e+00 942.0
24 TraesCS2A01G161000 chr2D 87.912 728 33 24 1797 2512 112180279 112179595 0.000000e+00 806.0
25 TraesCS2A01G161000 chr2D 96.259 401 14 1 4634 5034 111592462 111592861 0.000000e+00 656.0
26 TraesCS2A01G161000 chr2D 86.296 540 47 15 3933 4466 112178119 112177601 3.420000e-156 562.0
27 TraesCS2A01G161000 chr2D 90.202 347 33 1 2638 2984 112100962 112101307 7.710000e-123 451.0
28 TraesCS2A01G161000 chr2D 92.138 318 19 3 2294 2610 111589910 111590222 1.290000e-120 444.0
29 TraesCS2A01G161000 chr2D 82.809 477 74 7 302 774 112283212 112282740 2.180000e-113 420.0
30 TraesCS2A01G161000 chr2D 91.813 171 7 4 4306 4476 111591956 111592119 1.090000e-56 231.0
31 TraesCS2A01G161000 chr2D 81.070 243 40 5 295 534 112289576 112289337 6.680000e-44 189.0
32 TraesCS2A01G161000 chr2D 97.000 100 3 0 4474 4573 111592201 111592300 8.700000e-38 169.0
33 TraesCS2A01G161000 chr2D 79.720 286 16 15 4753 5013 112103577 112103845 8.700000e-38 169.0
34 TraesCS2A01G161000 chr2D 87.912 91 8 3 181 271 112186200 112186113 2.490000e-18 104.0
35 TraesCS2A01G161000 chr2D 96.667 60 2 0 4573 4632 111592356 111592415 3.220000e-17 100.0
36 TraesCS2A01G161000 chr2D 96.610 59 2 0 4573 4631 112102666 112102724 1.160000e-16 99.0
37 TraesCS2A01G161000 chr2D 86.842 76 4 2 4634 4703 112102772 112102847 4.190000e-11 80.5
38 TraesCS2A01G161000 chr2B 89.325 1349 69 30 487 1828 161721916 161723196 0.000000e+00 1624.0
39 TraesCS2A01G161000 chr2B 89.615 1040 88 16 2636 3664 161723997 161725027 0.000000e+00 1304.0
40 TraesCS2A01G161000 chr2B 88.806 1072 92 20 725 1774 162007423 162008488 0.000000e+00 1290.0
41 TraesCS2A01G161000 chr2B 90.909 968 37 28 3686 4632 161725001 161725938 0.000000e+00 1253.0
42 TraesCS2A01G161000 chr2B 87.127 971 88 27 741 1694 162449043 162448093 0.000000e+00 1066.0
43 TraesCS2A01G161000 chr2B 90.780 705 34 16 1935 2632 161723281 161723961 0.000000e+00 913.0
44 TraesCS2A01G161000 chr2B 81.430 1007 133 37 2636 3622 162447147 162446175 0.000000e+00 774.0
45 TraesCS2A01G161000 chr2B 87.037 540 43 13 3933 4466 162445875 162445357 7.290000e-163 584.0
46 TraesCS2A01G161000 chr2B 92.875 393 21 6 4667 5052 161726032 161726424 9.500000e-157 564.0
47 TraesCS2A01G161000 chr2B 87.403 516 33 15 3935 4444 162010632 162011121 9.500000e-157 564.0
48 TraesCS2A01G161000 chr2B 84.706 595 47 19 2048 2621 162008757 162009328 5.710000e-154 555.0
49 TraesCS2A01G161000 chr2B 92.837 349 24 1 2636 2984 162009399 162009746 5.840000e-139 505.0
50 TraesCS2A01G161000 chr2B 79.296 483 75 9 295 774 162497549 162497089 1.060000e-81 315.0
51 TraesCS2A01G161000 chr2B 86.301 292 20 8 4753 5034 162012126 162012407 2.960000e-77 300.0
52 TraesCS2A01G161000 chr2B 84.452 283 32 9 2341 2621 162447480 162447208 8.340000e-68 268.0
53 TraesCS2A01G161000 chr2B 81.548 336 49 8 3324 3654 162009946 162010273 1.080000e-66 265.0
54 TraesCS2A01G161000 chr2B 88.688 221 18 3 1797 2013 162447987 162447770 3.880000e-66 263.0
55 TraesCS2A01G161000 chr2B 92.818 181 8 3 2117 2297 162447668 162447493 1.800000e-64 257.0
56 TraesCS2A01G161000 chr2B 89.205 176 12 4 3686 3854 162010257 162010432 3.960000e-51 213.0
57 TraesCS2A01G161000 chr2B 81.735 219 35 4 306 521 162495488 162495272 1.450000e-40 178.0
58 TraesCS2A01G161000 chr2B 94.286 105 6 0 1797 1901 162008568 162008672 1.460000e-35 161.0
59 TraesCS2A01G161000 chr2B 78.947 247 40 8 296 537 162499141 162498902 1.880000e-34 158.0
60 TraesCS2A01G161000 chr2B 95.385 65 3 0 4573 4637 162011265 162011329 2.490000e-18 104.0
61 TraesCS2A01G161000 chr2B 77.249 189 32 10 90 274 162497965 162497784 3.220000e-17 100.0
62 TraesCS2A01G161000 chr2B 91.803 61 5 0 181 241 162495822 162495762 9.010000e-13 86.1
63 TraesCS2A01G161000 chr2B 83.696 92 10 3 181 271 162482288 162482201 1.170000e-11 82.4
64 TraesCS2A01G161000 chr2B 86.842 76 4 2 4634 4703 162011361 162011436 4.190000e-11 80.5
65 TraesCS2A01G161000 chr2B 95.349 43 2 0 4634 4676 161725984 161726026 9.080000e-08 69.4


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 TraesCS2A01G161000 chr2A 111920942 111925993 5051 False 9330.000000 9330 100.000000 1 5052 1 chr2A.!!$F1 5051
1 TraesCS2A01G161000 chr2A 113309000 113312436 3436 True 1027.666667 1544 86.645333 539 4466 3 chr2A.!!$R3 3927
2 TraesCS2A01G161000 chr2A 112744408 112748538 4130 False 593.183333 1544 88.559000 585 4748 6 chr2A.!!$F2 4163
3 TraesCS2A01G161000 chr2A 113343523 113344548 1025 True 271.500000 374 80.015000 283 774 2 chr2A.!!$R5 491
4 TraesCS2A01G161000 chr2A 113194578 113196702 2124 True 253.000000 374 76.208000 2707 3926 2 chr2A.!!$R2 1219
5 TraesCS2A01G161000 chr2D 111587673 111592861 5188 False 901.875000 3319 93.975625 1 5034 8 chr2D.!!$F1 5033
6 TraesCS2A01G161000 chr2D 112177601 112181370 3769 True 864.750000 1149 85.632000 705 4466 4 chr2D.!!$R4 3761
7 TraesCS2A01G161000 chr2D 112098952 112103845 4893 False 656.583333 2163 87.047333 627 5013 6 chr2D.!!$F2 4386
8 TraesCS2A01G161000 chr2B 161721916 161726424 4508 False 954.566667 1624 91.475500 487 5052 6 chr2B.!!$F1 4565
9 TraesCS2A01G161000 chr2B 162445357 162449043 3686 True 535.333333 1066 86.925333 741 4466 6 chr2B.!!$R2 3725
10 TraesCS2A01G161000 chr2B 162007423 162012407 4984 False 403.750000 1290 88.731900 725 5034 10 chr2B.!!$F2 4309

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
19 20 0.918983 CTCTAGGCCCATCCCAAACA 59.081 55.0 0.0 0.0 34.51 2.83 F
1781 1833 0.175302 TGTTGTTGCTTTGGTGCCTG 59.825 50.0 0.0 0.0 0.00 4.85 F
2403 2668 0.304705 CGTGACTGAGTGGTTGTTGC 59.695 55.0 0.0 0.0 0.00 4.17 F
3245 3657 0.249953 TTCGCAGCCCGTTGTTTAGA 60.250 50.0 0.0 0.0 38.35 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 2176 0.112412 GAAAGGGTCCCTGCCTTTGA 59.888 55.0 12.53 0.0 34.47 2.69 R
3227 3639 0.249953 TTCTAAACAACGGGCTGCGA 60.250 50.0 0.00 0.0 0.00 5.10 R
3451 4011 0.389025 ATCGATACCGTGCATCAGCA 59.611 50.0 0.00 0.0 40.93 4.41 R
4248 5090 1.177401 CCTTCAAAGCCAAGGCCTAC 58.823 55.0 5.16 0.0 43.17 3.18 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
19 20 0.918983 CTCTAGGCCCATCCCAAACA 59.081 55.000 0.00 0.00 34.51 2.83
26 27 2.093500 GGCCCATCCCAAACATCTTTTC 60.093 50.000 0.00 0.00 0.00 2.29
46 47 8.241367 TCTTTTCATTTTCCTTCTAATAACCGC 58.759 33.333 0.00 0.00 0.00 5.68
92 93 7.566858 TTCAGTAACCGTCGTTTCTAATAAC 57.433 36.000 0.00 0.00 33.17 1.89
130 131 6.364976 CCCGCCTTTTGTTATTTTTGTAGAAG 59.635 38.462 0.00 0.00 0.00 2.85
201 202 7.041780 CCATAGTTTAGCCATCACAACTCATAC 60.042 40.741 0.00 0.00 31.83 2.39
241 242 1.203052 GTACGTAGCACCTAACTGCCA 59.797 52.381 0.00 0.00 37.96 4.92
319 320 2.036733 CCCCGATTTAATCCAGCGTCTA 59.963 50.000 0.00 0.00 0.00 2.59
322 323 3.123621 CCGATTTAATCCAGCGTCTATGC 59.876 47.826 0.00 0.00 0.00 3.14
352 355 2.629017 AAACAATGGGCATCCTTCCT 57.371 45.000 0.00 0.00 0.00 3.36
367 370 6.295292 GCATCCTTCCTGGTTTTCATTAAAGT 60.295 38.462 0.00 0.00 37.07 2.66
396 399 3.572255 TCCAACCCATTTCTGTGTTTAGC 59.428 43.478 0.00 0.00 0.00 3.09
416 419 3.828451 AGCCACCATAATTCATATGCACC 59.172 43.478 0.00 0.00 40.15 5.01
469 472 1.792949 GTTTGAGTCGATGAGTGCGTT 59.207 47.619 0.00 0.00 0.00 4.84
699 706 2.487372 TGACATGAAGCGCAAAATGCTA 59.513 40.909 11.47 0.00 43.14 3.49
880 901 2.674220 CCTTCCTCCACTCCCCAGC 61.674 68.421 0.00 0.00 0.00 4.85
1427 1465 4.023622 CAGATCGTCATGTTCCTCGACTAT 60.024 45.833 0.00 0.00 35.24 2.12
1529 1567 2.125350 GTCTTCTGCCGCCTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
1587 1629 0.813610 TCCCTCGCACTGTTGTGTTG 60.814 55.000 0.00 0.00 45.44 3.33
1740 1792 2.953466 ACATTTATTGCTGCTGCTGG 57.047 45.000 17.00 0.00 40.48 4.85
1774 1826 7.305533 GCAGCATTTATTTTTGTTGTTGCTTTG 60.306 33.333 0.00 0.00 40.15 2.77
1775 1827 7.166142 CAGCATTTATTTTTGTTGTTGCTTTGG 59.834 33.333 0.00 0.00 37.10 3.28
1778 1830 3.820777 TTTTTGTTGTTGCTTTGGTGC 57.179 38.095 0.00 0.00 0.00 5.01
1779 1831 1.731720 TTTGTTGTTGCTTTGGTGCC 58.268 45.000 0.00 0.00 0.00 5.01
1780 1832 0.901124 TTGTTGTTGCTTTGGTGCCT 59.099 45.000 0.00 0.00 0.00 4.75
1781 1833 0.175302 TGTTGTTGCTTTGGTGCCTG 59.825 50.000 0.00 0.00 0.00 4.85
1932 2058 2.028476 ACCTAGACGCTATGCACACAAA 60.028 45.455 0.00 0.00 0.00 2.83
1981 2136 4.855531 AGCGTTTTTATGAGCGTTTTCTT 58.144 34.783 0.00 0.00 34.34 2.52
2016 2179 4.500265 GCCCACAGAAAGGCTCAA 57.500 55.556 0.00 0.00 46.14 3.02
2019 2182 1.251251 CCCACAGAAAGGCTCAAAGG 58.749 55.000 0.00 0.00 0.00 3.11
2020 2183 0.600057 CCACAGAAAGGCTCAAAGGC 59.400 55.000 0.00 0.00 41.73 4.35
2403 2668 0.304705 CGTGACTGAGTGGTTGTTGC 59.695 55.000 0.00 0.00 0.00 4.17
2577 2848 5.462398 CCAATCAACTACTAGTAACATCGGC 59.538 44.000 3.76 0.00 0.00 5.54
2611 2919 2.168521 TGCTATCAAGTCCACTACTGCC 59.831 50.000 0.00 0.00 38.88 4.85
2632 2963 7.093988 ACTGCCACTAGCTACTGATAGAATATG 60.094 40.741 2.27 0.00 44.23 1.78
2633 2964 6.948309 TGCCACTAGCTACTGATAGAATATGA 59.052 38.462 2.27 0.00 44.23 2.15
2634 2965 7.617329 TGCCACTAGCTACTGATAGAATATGAT 59.383 37.037 2.27 0.00 44.23 2.45
2906 3275 3.502979 GTCTCTCGGTGAGTTCTTACACT 59.497 47.826 6.93 0.00 43.13 3.55
2912 3281 3.979495 CGGTGAGTTCTTACACTACACAC 59.021 47.826 0.00 0.00 37.22 3.82
2913 3282 3.979495 GGTGAGTTCTTACACTACACACG 59.021 47.826 0.00 0.00 35.23 4.49
2915 3284 5.458891 GTGAGTTCTTACACTACACACGAT 58.541 41.667 0.00 0.00 34.65 3.73
2927 3296 7.790000 ACACTACACACGATTAATTGTTGTAC 58.210 34.615 17.74 0.00 0.00 2.90
2935 3304 1.823797 TAATTGTTGTACCCGTGGCC 58.176 50.000 0.00 0.00 0.00 5.36
2945 3341 2.325082 CCCGTGGCCGTTTCTTCAG 61.325 63.158 0.00 0.00 0.00 3.02
2984 3380 5.449304 CAGCCCGTAGTTTTGTTTAGAAAG 58.551 41.667 0.00 0.00 0.00 2.62
2993 3389 2.357760 TTTAGAAAGCGCCGCCGT 60.358 55.556 4.98 0.00 36.67 5.68
3021 3417 4.361451 CATAGCCTGCAAAGAAAACGAT 57.639 40.909 0.00 0.00 0.00 3.73
3022 3418 4.737054 CATAGCCTGCAAAGAAAACGATT 58.263 39.130 0.00 0.00 0.00 3.34
3023 3419 5.879237 CATAGCCTGCAAAGAAAACGATTA 58.121 37.500 0.00 0.00 0.00 1.75
3073 3484 7.899178 TTTTTAGAGAAACTGCATATCGTCA 57.101 32.000 0.00 0.00 0.00 4.35
3074 3485 8.492673 TTTTTAGAGAAACTGCATATCGTCAT 57.507 30.769 0.00 0.00 0.00 3.06
3075 3486 8.492673 TTTTAGAGAAACTGCATATCGTCATT 57.507 30.769 0.00 0.00 0.00 2.57
3076 3487 9.594478 TTTTAGAGAAACTGCATATCGTCATTA 57.406 29.630 0.00 0.00 0.00 1.90
3130 3541 4.806330 ACATACACAGAAACTACACGAGG 58.194 43.478 0.00 0.00 0.00 4.63
3142 3553 2.721425 ACACGAGGGACCAAGAAAAA 57.279 45.000 0.00 0.00 0.00 1.94
3174 3585 6.257630 GCCATAGAAACTTTGCAAAAGAAACA 59.742 34.615 13.84 0.00 0.00 2.83
3227 3639 7.423199 GTGGTTTCTTTAAAGGAAATCGACTT 58.577 34.615 10.60 0.00 36.81 3.01
3245 3657 0.249953 TTCGCAGCCCGTTGTTTAGA 60.250 50.000 0.00 0.00 38.35 2.10
3289 3825 8.685427 TGCATAAATATTGTTGCTACTTCATGT 58.315 29.630 18.45 0.00 36.10 3.21
3356 3910 2.645838 TTCTCTTCACAGGCTTTGCT 57.354 45.000 0.00 0.00 0.00 3.91
3422 3976 1.874019 CGAGGATGCGTTCGAGGTG 60.874 63.158 0.00 0.00 39.06 4.00
3451 4011 2.743838 CGGTACACCTGTCCACTTTTGT 60.744 50.000 0.00 0.00 0.00 2.83
3511 4090 1.136611 CGTACTGACGCTCTTTTGCAC 60.137 52.381 0.00 0.00 43.21 4.57
3516 4095 3.181487 ACTGACGCTCTTTTGCACAAAAT 60.181 39.130 8.86 0.00 39.29 1.82
3543 4122 2.652530 GTGCTGCACAACATGGGG 59.347 61.111 26.70 0.00 34.08 4.96
3638 4220 6.264744 GCTGAGGTATACACAATAGTCCACTA 59.735 42.308 5.01 0.00 0.00 2.74
3799 4431 4.766373 GCTAGCTACCTACCTACCTAAAGG 59.234 50.000 7.70 0.00 42.82 3.11
3873 4523 5.629079 TGACATATACTACATGCTCTCGG 57.371 43.478 0.00 0.00 0.00 4.63
3899 4549 3.119955 GCTTCCCGGTAAAGTTGATTGTC 60.120 47.826 13.58 0.00 0.00 3.18
3972 4806 8.710551 TGACATGAATTTTGTTTTCATATGTGC 58.289 29.630 0.00 0.00 40.84 4.57
4202 5044 2.259204 GCATGCATGCGTGTTGGT 59.741 55.556 33.99 4.12 44.67 3.67
4234 5076 2.596346 AGATCCAGATCGAGCAGTGAT 58.404 47.619 2.38 1.04 42.48 3.06
4246 5088 0.817229 GCAGTGATCCTTGCTAGGCC 60.817 60.000 9.60 0.00 41.69 5.19
4247 5089 0.543277 CAGTGATCCTTGCTAGGCCA 59.457 55.000 9.60 7.13 41.69 5.36
4248 5090 0.835941 AGTGATCCTTGCTAGGCCAG 59.164 55.000 9.60 0.97 41.69 4.85
4338 5317 6.706270 CGTTATTAGCTATGACAGAAATGGGT 59.294 38.462 0.00 0.00 0.00 4.51
4379 5358 5.888161 CCTTTTTCTCACCCTGCACTATAAT 59.112 40.000 0.00 0.00 0.00 1.28
4380 5359 7.054124 CCTTTTTCTCACCCTGCACTATAATA 58.946 38.462 0.00 0.00 0.00 0.98
4381 5360 7.227512 CCTTTTTCTCACCCTGCACTATAATAG 59.772 40.741 0.00 0.00 0.00 1.73
4382 5361 6.808321 TTTCTCACCCTGCACTATAATAGT 57.192 37.500 0.00 0.00 40.28 2.12
4383 5362 6.808321 TTCTCACCCTGCACTATAATAGTT 57.192 37.500 0.00 0.00 36.76 2.24
4387 5366 6.346096 TCACCCTGCACTATAATAGTTGTTC 58.654 40.000 0.00 0.00 36.76 3.18
4389 5368 7.343574 TCACCCTGCACTATAATAGTTGTTCTA 59.656 37.037 0.00 0.00 36.76 2.10
4422 5411 7.395190 TGCTTCATTGTTAGCTTGTTATGAT 57.605 32.000 0.00 0.00 38.22 2.45
4423 5412 7.252708 TGCTTCATTGTTAGCTTGTTATGATG 58.747 34.615 0.00 1.26 38.22 3.07
4556 5799 1.772836 ATGCAATCAAGGGAGAAGCC 58.227 50.000 0.00 0.00 0.00 4.35
4696 6061 0.725117 GTGGCGGAGTAAATTCCACG 59.275 55.000 0.00 0.00 37.96 4.94
4842 6922 0.443869 GCAGCATCGAATCACGTGTT 59.556 50.000 16.51 9.22 43.13 3.32
4861 6941 6.094603 ACGTGTTACGACCAAGAATACTCTAT 59.905 38.462 8.48 0.00 46.05 1.98
4862 6942 6.414109 CGTGTTACGACCAAGAATACTCTATG 59.586 42.308 0.00 0.00 46.05 2.23
5016 7131 0.734253 GATTCGATCCCCGCTCGATG 60.734 60.000 0.00 0.00 43.93 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.566724 TGAAAAGATGTTTGGGATGGGC 59.433 45.455 0.00 0.00 0.00 5.36
26 27 4.334481 ACGGCGGTTATTAGAAGGAAAATG 59.666 41.667 13.24 0.00 0.00 2.32
92 93 2.531376 GGCGGGATAAAAGCGACCG 61.531 63.158 0.00 0.00 46.78 4.79
130 131 2.267174 ACAGATATGATGCCCACTGC 57.733 50.000 0.00 0.00 41.77 4.40
144 145 5.405269 GCGGTTTCTTTAATGCAAAACAGAT 59.595 36.000 11.95 0.00 34.15 2.90
352 355 5.410439 GGAGCGTCTACTTTAATGAAAACCA 59.590 40.000 0.00 0.00 0.00 3.67
367 370 1.906574 AGAAATGGGTTGGAGCGTCTA 59.093 47.619 0.00 0.00 0.00 2.59
396 399 3.191162 CCGGTGCATATGAATTATGGTGG 59.809 47.826 6.97 0.00 38.53 4.61
469 472 4.141846 TGTTGTTGCTCCAAAAATAGCCAA 60.142 37.500 0.00 0.00 37.97 4.52
699 706 7.509546 AGAAATGGTATGTCGACATAATTCCT 58.490 34.615 33.71 22.64 40.18 3.36
880 901 0.379669 GAAGCTGATGCCGATGGTTG 59.620 55.000 0.00 0.00 40.80 3.77
1587 1629 5.376537 CGTCAAAGACCCACGTTAATTAAC 58.623 41.667 16.87 16.87 0.00 2.01
1894 2020 3.587933 TTCACGCCCGCAACCAAC 61.588 61.111 0.00 0.00 0.00 3.77
1924 2050 4.358851 TCTTTGCATGTACTTTTGTGTGC 58.641 39.130 0.00 0.00 37.24 4.57
1932 2058 3.138304 TGCGAACTCTTTGCATGTACTT 58.862 40.909 0.00 0.00 44.84 2.24
1981 2136 1.747355 GGCGGAAGTACTAGTAGTGCA 59.253 52.381 19.00 0.00 32.98 4.57
2013 2176 0.112412 GAAAGGGTCCCTGCCTTTGA 59.888 55.000 12.53 0.00 34.47 2.69
2016 2179 3.181282 GGAAAGGGTCCCTGCCTT 58.819 61.111 12.53 1.26 41.10 4.35
2403 2668 1.394917 GTCAGCCTGCGTAGACAAATG 59.605 52.381 0.53 0.00 0.00 2.32
2590 2863 2.168521 GGCAGTAGTGGACTTGATAGCA 59.831 50.000 0.00 0.00 35.64 3.49
2632 2963 3.485877 GCGTCTCATACACCTGCAAAATC 60.486 47.826 0.00 0.00 0.00 2.17
2633 2964 2.420022 GCGTCTCATACACCTGCAAAAT 59.580 45.455 0.00 0.00 0.00 1.82
2634 2965 1.804151 GCGTCTCATACACCTGCAAAA 59.196 47.619 0.00 0.00 0.00 2.44
2906 3275 5.348179 CGGGTACAACAATTAATCGTGTGTA 59.652 40.000 0.00 4.21 0.00 2.90
2912 3281 3.486209 GCCACGGGTACAACAATTAATCG 60.486 47.826 0.00 0.00 0.00 3.34
2913 3282 3.181494 GGCCACGGGTACAACAATTAATC 60.181 47.826 0.00 0.00 0.00 1.75
2915 3284 2.161030 GGCCACGGGTACAACAATTAA 58.839 47.619 0.00 0.00 0.00 1.40
2927 3296 2.281208 TGAAGAAACGGCCACGGG 60.281 61.111 2.24 0.00 46.48 5.28
2935 3304 4.134546 CGTCGATTTTCACTGAAGAAACG 58.865 43.478 0.00 2.07 37.24 3.60
2945 3341 1.225745 CTGCGCCGTCGATTTTCAC 60.226 57.895 4.18 0.00 38.10 3.18
2969 3365 2.857104 GCGGCGCTTTCTAAACAAAACT 60.857 45.455 26.86 0.00 0.00 2.66
3021 3417 4.125703 ACCACCACGTTTACGACAATTAA 58.874 39.130 9.53 0.00 43.02 1.40
3022 3418 3.726607 ACCACCACGTTTACGACAATTA 58.273 40.909 9.53 0.00 43.02 1.40
3023 3419 2.563702 ACCACCACGTTTACGACAATT 58.436 42.857 9.53 0.00 43.02 2.32
3142 3553 5.016173 TGCAAAGTTTCTATGGCTATGGTT 58.984 37.500 0.00 0.00 0.00 3.67
3191 3603 7.401955 TTTAAAGAAACCACCCGAGTTTTTA 57.598 32.000 0.00 0.00 37.55 1.52
3198 3610 3.860968 TCCTTTAAAGAAACCACCCGA 57.139 42.857 16.98 0.00 0.00 5.14
3227 3639 0.249953 TTCTAAACAACGGGCTGCGA 60.250 50.000 0.00 0.00 0.00 5.10
3422 3976 1.804326 CAGGTGTACCGCGCACTAC 60.804 63.158 8.75 6.36 42.08 2.73
3451 4011 0.389025 ATCGATACCGTGCATCAGCA 59.611 50.000 0.00 0.00 40.93 4.41
3511 4090 7.418840 TGTGCAGCACCTATTTTAAATTTTG 57.581 32.000 23.06 0.00 32.73 2.44
3516 4095 5.521906 TGTTGTGCAGCACCTATTTTAAA 57.478 34.783 23.06 4.83 32.73 1.52
3543 4122 1.599240 GAGGATCCCGATGCCTTGC 60.599 63.158 8.55 0.00 30.70 4.01
3873 4523 1.804748 CAACTTTACCGGGAAGCAGTC 59.195 52.381 16.93 0.00 0.00 3.51
3899 4549 8.767478 AACATTTCATTGCTTTATTTCTCCAG 57.233 30.769 0.00 0.00 0.00 3.86
3929 4579 5.538053 TCATGTCAAACTCAAAGCCCATAAA 59.462 36.000 0.00 0.00 0.00 1.40
3972 4806 1.331214 AACATGACCAAGCCAGGTTG 58.669 50.000 0.00 2.60 43.38 3.77
4202 5044 9.157104 GCTCGATCTGGATCTTATATATCGATA 57.843 37.037 7.75 7.75 41.75 2.92
4246 5088 1.815003 CTTCAAAGCCAAGGCCTACTG 59.185 52.381 5.16 0.12 43.17 2.74
4247 5089 1.272147 CCTTCAAAGCCAAGGCCTACT 60.272 52.381 5.16 0.20 43.17 2.57
4248 5090 1.177401 CCTTCAAAGCCAAGGCCTAC 58.823 55.000 5.16 0.00 43.17 3.18
4338 5317 1.729586 AGGAGGGCTACTTTGTCACA 58.270 50.000 0.00 0.00 0.00 3.58
4389 5368 9.793252 CAAGCTAACAATGAAGCAATAAGTAAT 57.207 29.630 13.01 0.00 41.32 1.89
4393 5375 9.793252 ATAACAAGCTAACAATGAAGCAATAAG 57.207 29.630 13.01 3.14 41.32 1.73
4395 5377 8.955388 TCATAACAAGCTAACAATGAAGCAATA 58.045 29.630 13.01 3.46 41.32 1.90
4396 5385 7.829725 TCATAACAAGCTAACAATGAAGCAAT 58.170 30.769 13.01 1.58 41.32 3.56
4406 5395 7.105588 AGATCACACATCATAACAAGCTAACA 58.894 34.615 0.00 0.00 0.00 2.41
4696 6061 1.211818 GGTCGCATGCTCGATCTGTC 61.212 60.000 17.13 0.00 40.84 3.51
4842 6922 8.209584 AGTAGTCATAGAGTATTCTTGGTCGTA 58.790 37.037 0.00 0.00 34.79 3.43
4861 6941 1.618837 GTGTGAGCCAAGGAGTAGTCA 59.381 52.381 0.00 0.00 0.00 3.41
4862 6942 1.618837 TGTGTGAGCCAAGGAGTAGTC 59.381 52.381 0.00 0.00 0.00 2.59
4896 7004 3.134623 CAGCCAGGTAGGTGAATGTGATA 59.865 47.826 0.00 0.00 40.61 2.15
4930 7038 1.610363 TAAACAAAGCGGGTGCATGA 58.390 45.000 0.00 0.00 46.23 3.07
5016 7131 2.476320 GCTTGCAAGCCGGAGATCC 61.476 63.158 36.21 9.51 46.20 3.36


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

AutoCloner maintained by Alex Coulton.