Multiple sequence alignment - TraesCS5D01G140600

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 TraesCS5D01G140600 chr5D 100.000 4721 0 0 1 4721 224312300 224317020 0.000000e+00 8719.0
1 TraesCS5D01G140600 chr5D 75.899 278 57 9 2264 2536 224313531 224313803 2.960000e-27 134.0
2 TraesCS5D01G140600 chr5D 75.899 278 57 9 1232 1504 224314563 224314835 2.960000e-27 134.0
3 TraesCS5D01G140600 chr5D 74.328 335 68 12 3240 3559 224313415 224313746 4.960000e-25 126.0
4 TraesCS5D01G140600 chr5D 74.328 335 68 12 1116 1447 224315539 224315858 4.960000e-25 126.0
5 TraesCS5D01G140600 chr5B 97.431 3153 65 7 634 3778 247064751 247061607 0.000000e+00 5360.0
6 TraesCS5D01G140600 chr5B 95.441 329 12 2 1 329 247065376 247065051 5.410000e-144 521.0
7 TraesCS5D01G140600 chr5B 93.023 258 9 3 331 588 247064995 247064747 7.460000e-98 368.0
8 TraesCS5D01G140600 chr5B 76.172 256 55 6 2264 2516 247064156 247063904 3.830000e-26 130.0
9 TraesCS5D01G140600 chr5B 74.030 335 69 11 3240 3559 247064272 247063941 2.310000e-23 121.0
10 TraesCS5D01G140600 chr5A 96.414 3151 96 7 634 3778 299059136 299062275 0.000000e+00 5177.0
11 TraesCS5D01G140600 chr5A 94.924 788 26 5 3938 4721 340429984 340430761 0.000000e+00 1221.0
12 TraesCS5D01G140600 chr5A 94.797 788 26 6 3938 4721 631284049 631284825 0.000000e+00 1214.0
13 TraesCS5D01G140600 chr5A 93.576 467 22 5 4251 4715 702509210 702508750 0.000000e+00 689.0
14 TraesCS5D01G140600 chr5A 92.259 478 30 4 4245 4721 627028059 627028530 0.000000e+00 671.0
15 TraesCS5D01G140600 chr5A 74.917 303 68 7 1232 1530 299060761 299061059 1.070000e-26 132.0
16 TraesCS5D01G140600 chr5A 74.328 335 68 13 3240 3559 299059613 299059944 4.960000e-25 126.0
17 TraesCS5D01G140600 chr5A 75.781 256 56 6 2264 2516 299059729 299059981 1.780000e-24 124.0
18 TraesCS5D01G140600 chr5A 75.325 231 42 9 3333 3556 299060751 299060973 3.890000e-16 97.1
19 TraesCS5D01G140600 chr5A 88.312 77 4 2 506 582 299058779 299058850 2.340000e-13 87.9
20 TraesCS5D01G140600 chr5A 93.750 48 3 0 3383 3430 560717140 560717093 6.550000e-09 73.1
21 TraesCS5D01G140600 chr7B 95.305 788 29 4 3938 4721 31463672 31462889 0.000000e+00 1243.0
22 TraesCS5D01G140600 chr7B 76.852 216 30 11 2267 2478 145528207 145528008 2.320000e-18 104.0
23 TraesCS5D01G140600 chr7B 83.562 73 9 3 4108 4178 603595110 603595181 1.100000e-06 65.8
24 TraesCS5D01G140600 chr7D 94.790 787 34 3 3938 4721 55079398 55078616 0.000000e+00 1219.0
25 TraesCS5D01G140600 chr7D 94.146 205 11 1 4512 4715 54599792 54599996 1.280000e-80 311.0
26 TraesCS5D01G140600 chr7D 88.542 96 6 2 3802 3897 55079599 55079509 1.390000e-20 111.0
27 TraesCS5D01G140600 chr2D 94.355 744 35 4 2475 3218 61752082 61752818 0.000000e+00 1134.0
28 TraesCS5D01G140600 chr2D 93.249 474 28 1 4248 4721 446606879 446606410 0.000000e+00 695.0
29 TraesCS5D01G140600 chr2D 92.664 259 16 1 1952 2210 61750965 61751220 2.080000e-98 370.0
30 TraesCS5D01G140600 chr2D 96.585 205 6 1 1620 1824 61750748 61750951 5.850000e-89 339.0
31 TraesCS5D01G140600 chr2D 79.333 150 11 10 1069 1217 61752788 61752918 2.340000e-13 87.9
32 TraesCS5D01G140600 chr2D 94.118 51 2 1 576 626 55160175 55160126 5.070000e-10 76.8
33 TraesCS5D01G140600 chr3D 92.688 465 30 1 4251 4715 147611753 147611293 0.000000e+00 667.0
34 TraesCS5D01G140600 chr3D 96.078 51 2 0 576 626 22654809 22654859 3.030000e-12 84.2
35 TraesCS5D01G140600 chr3D 95.918 49 2 0 578 626 26692037 26691989 3.920000e-11 80.5
36 TraesCS5D01G140600 chr3D 91.071 56 5 0 582 637 298466304 298466359 5.070000e-10 76.8
37 TraesCS5D01G140600 chr7A 92.050 478 30 5 4245 4721 19859870 19860340 0.000000e+00 665.0
38 TraesCS5D01G140600 chr7A 96.000 50 2 0 577 626 501147247 501147198 1.090000e-11 82.4
39 TraesCS5D01G140600 chr1B 91.841 478 32 4 4245 4721 488041787 488042258 0.000000e+00 660.0
40 TraesCS5D01G140600 chr1B 91.632 478 33 4 4245 4721 394888888 394889359 0.000000e+00 654.0
41 TraesCS5D01G140600 chr1B 91.981 212 15 2 4512 4721 488040929 488041140 3.570000e-76 296.0
42 TraesCS5D01G140600 chr2B 95.479 376 17 0 2649 3024 759183113 759183488 6.760000e-168 601.0
43 TraesCS5D01G140600 chr2B 92.947 397 28 0 2257 2653 759180596 759180992 3.170000e-161 579.0
44 TraesCS5D01G140600 chr2B 92.236 322 23 2 3446 3766 759189578 759189898 5.570000e-124 455.0
45 TraesCS5D01G140600 chr2B 86.199 413 18 11 3023 3406 759189182 759189584 1.220000e-110 411.0
46 TraesCS5D01G140600 chr2B 97.959 49 1 0 578 626 744873083 744873131 8.420000e-13 86.1
47 TraesCS5D01G140600 chr2A 94.318 352 16 3 1317 1667 62092874 62093222 1.930000e-148 536.0
48 TraesCS5D01G140600 chr2A 83.925 479 34 20 2827 3292 62094341 62094789 7.310000e-113 418.0
49 TraesCS5D01G140600 chr2A 94.167 120 7 0 1092 1211 62094713 62094832 2.900000e-42 183.0
50 TraesCS5D01G140600 chr2A 93.750 80 4 1 1657 1735 62094194 62094273 8.300000e-23 119.0
51 TraesCS5D01G140600 chr2A 94.444 36 2 0 2764 2799 62094305 62094340 6.600000e-04 56.5
52 TraesCS5D01G140600 chr3A 91.870 246 16 3 3938 4180 740441855 740442099 1.630000e-89 340.0
53 TraesCS5D01G140600 chr3A 91.827 208 16 1 4515 4721 32712937 32712730 5.980000e-74 289.0
54 TraesCS5D01G140600 chr3A 91.667 96 7 1 3802 3897 740441652 740441746 1.070000e-26 132.0
55 TraesCS5D01G140600 chr6D 84.444 90 14 0 2266 2355 445852399 445852488 6.510000e-14 89.8
56 TraesCS5D01G140600 chr6D 83.673 98 7 6 2262 2355 445908651 445908743 3.030000e-12 84.2
57 TraesCS5D01G140600 chr6D 80.734 109 13 4 2264 2368 445799913 445799809 1.410000e-10 78.7
58 TraesCS5D01G140600 chr6D 95.455 44 2 0 1280 1323 445799865 445799822 2.360000e-08 71.3
59 TraesCS5D01G140600 chr6A 74.348 230 48 10 1118 1346 592495107 592494888 2.340000e-13 87.9
60 TraesCS5D01G140600 chr6A 83.673 98 7 6 2262 2355 592478441 592478349 3.030000e-12 84.2
61 TraesCS5D01G140600 chr6A 94.231 52 3 0 586 637 31043856 31043805 3.920000e-11 80.5
62 TraesCS5D01G140600 chr6A 82.222 90 16 0 1234 1323 592478438 592478349 1.410000e-10 78.7
63 TraesCS5D01G140600 chr4A 97.917 48 1 0 579 626 547197691 547197738 3.030000e-12 84.2
64 TraesCS5D01G140600 chr4A 86.275 51 4 3 466 514 620490086 620490037 9.000000e-03 52.8
65 TraesCS5D01G140600 chr4D 96.000 50 2 0 577 626 35618783 35618734 1.090000e-11 82.4
66 TraesCS5D01G140600 chr6B 81.111 90 17 0 1234 1323 672507832 672507743 6.550000e-09 73.1
67 TraesCS5D01G140600 chr1D 89.583 48 1 4 466 510 285046753 285046799 1.830000e-04 58.4


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 TraesCS5D01G140600 chr5D 224312300 224317020 4720 False 1847.800000 8719 80.090800 1 4721 5 chr5D.!!$F1 4720
1 TraesCS5D01G140600 chr5B 247061607 247065376 3769 True 1300.000000 5360 87.219400 1 3778 5 chr5B.!!$R1 3777
2 TraesCS5D01G140600 chr5A 340429984 340430761 777 False 1221.000000 1221 94.924000 3938 4721 1 chr5A.!!$F1 783
3 TraesCS5D01G140600 chr5A 631284049 631284825 776 False 1214.000000 1214 94.797000 3938 4721 1 chr5A.!!$F3 783
4 TraesCS5D01G140600 chr5A 299058779 299062275 3496 False 957.333333 5177 80.846167 506 3778 6 chr5A.!!$F4 3272
5 TraesCS5D01G140600 chr7B 31462889 31463672 783 True 1243.000000 1243 95.305000 3938 4721 1 chr7B.!!$R1 783
6 TraesCS5D01G140600 chr7D 55078616 55079599 983 True 665.000000 1219 91.666000 3802 4721 2 chr7D.!!$R1 919
7 TraesCS5D01G140600 chr2D 61750748 61752918 2170 False 482.725000 1134 90.734250 1069 3218 4 chr2D.!!$F1 2149
8 TraesCS5D01G140600 chr1B 488040929 488042258 1329 False 478.000000 660 91.911000 4245 4721 2 chr1B.!!$F2 476
9 TraesCS5D01G140600 chr2B 759180596 759183488 2892 False 590.000000 601 94.213000 2257 3024 2 chr2B.!!$F2 767
10 TraesCS5D01G140600 chr2B 759189182 759189898 716 False 433.000000 455 89.217500 3023 3766 2 chr2B.!!$F3 743
11 TraesCS5D01G140600 chr2A 62092874 62094832 1958 False 262.500000 536 92.120800 1092 3292 5 chr2A.!!$F1 2200

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
988 1330 0.594110 GATCTTCTAGACGCCGGGAG 59.406 60.000 2.18 0.0 0.00 4.30 F
989 1331 1.457009 ATCTTCTAGACGCCGGGAGC 61.457 60.000 2.18 0.0 38.52 4.70 F
2211 4228 2.429930 CAAGCCGGACTGAACCCA 59.570 61.111 5.05 0.0 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 3514 0.535335 TCAGTCCGGCTTGGTATGTC 59.465 55.000 0.0 0.0 39.52 3.06 R
2505 4604 2.049063 ACAGGAACGACGAGCAGC 60.049 61.111 0.0 0.0 0.00 5.25 R
3795 8071 0.318441 GCCAGCCAGACGCATCTATA 59.682 55.000 0.0 0.0 41.38 1.31 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
26 27 3.557577 TTGCATGTGTGAGTGTAATGC 57.442 42.857 0.00 0.00 43.08 3.56
27 28 2.781923 TGCATGTGTGAGTGTAATGCT 58.218 42.857 7.38 0.00 43.17 3.79
69 70 8.720562 CAATTAAATCCCTTTGTTGATTCAACC 58.279 33.333 23.22 8.96 42.96 3.77
164 165 9.943465 GAATCAGAAAACGAGAAAATAATTTGC 57.057 29.630 0.00 0.00 0.00 3.68
209 210 5.441718 AGTTCCTACATCATGTGACCAAT 57.558 39.130 0.00 0.00 0.00 3.16
213 214 6.065976 TCCTACATCATGTGACCAATCTTT 57.934 37.500 0.00 0.00 0.00 2.52
223 224 3.741344 GTGACCAATCTTTATAGCGCGAT 59.259 43.478 12.10 5.99 0.00 4.58
231 232 2.823924 TTATAGCGCGATTGCCCTTA 57.176 45.000 12.10 0.00 38.08 2.69
275 276 4.010349 GGCTAGCAACTTCTGTAACCAAT 58.990 43.478 18.24 0.00 0.00 3.16
282 283 5.334879 GCAACTTCTGTAACCAATGACGAAT 60.335 40.000 0.00 0.00 0.00 3.34
425 480 1.969923 ACCATGCTTGCAAAAGGCTTA 59.030 42.857 0.00 0.00 45.15 3.09
427 482 2.231964 CCATGCTTGCAAAAGGCTTAGA 59.768 45.455 0.00 0.00 45.15 2.10
428 483 3.118884 CCATGCTTGCAAAAGGCTTAGAT 60.119 43.478 0.00 0.00 45.15 1.98
430 485 2.892852 TGCTTGCAAAAGGCTTAGATGT 59.107 40.909 0.00 0.00 45.15 3.06
595 934 9.982651 TTATCGAATTAGAAAATACTCCCTCTG 57.017 33.333 0.00 0.00 0.00 3.35
596 935 7.419711 TCGAATTAGAAAATACTCCCTCTGT 57.580 36.000 0.00 0.00 0.00 3.41
597 936 8.529424 TCGAATTAGAAAATACTCCCTCTGTA 57.471 34.615 0.00 0.00 0.00 2.74
598 937 8.974238 TCGAATTAGAAAATACTCCCTCTGTAA 58.026 33.333 0.00 0.00 0.00 2.41
599 938 9.595823 CGAATTAGAAAATACTCCCTCTGTAAA 57.404 33.333 0.00 0.00 0.00 2.01
612 951 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
613 952 8.882415 TCCCTCTGTAAACTAATATAAAAGCG 57.118 34.615 0.00 0.00 0.00 4.68
614 953 8.480501 TCCCTCTGTAAACTAATATAAAAGCGT 58.519 33.333 0.00 0.00 0.00 5.07
615 954 9.106070 CCCTCTGTAAACTAATATAAAAGCGTT 57.894 33.333 0.00 0.00 0.00 4.84
630 969 6.952935 AAAAGCGTTTAGATCACTAGTGAG 57.047 37.500 28.29 15.13 43.61 3.51
631 970 4.640789 AGCGTTTAGATCACTAGTGAGG 57.359 45.455 28.29 12.41 43.61 3.86
632 971 3.381908 AGCGTTTAGATCACTAGTGAGGG 59.618 47.826 28.29 13.72 43.61 4.30
633 972 3.380637 GCGTTTAGATCACTAGTGAGGGA 59.619 47.826 28.29 14.16 43.61 4.20
638 977 4.864483 AGATCACTAGTGAGGGAGTACA 57.136 45.455 28.29 4.72 38.94 2.90
652 991 0.815734 AGTACATGTAAGCGCGGACT 59.184 50.000 8.83 3.24 0.00 3.85
679 1020 2.388310 TCCGTGTATTTTCGATGCCA 57.612 45.000 0.00 0.00 0.00 4.92
696 1037 2.665185 ACCGAAAGCCACGAGTGC 60.665 61.111 0.00 0.00 0.00 4.40
721 1062 1.638467 GCGGTCAATAGCTTCGCAG 59.362 57.895 0.00 0.00 44.87 5.18
850 1192 1.428448 CAAGAACATTCCTCGCGACA 58.572 50.000 3.71 0.00 0.00 4.35
888 1230 4.775253 TCAAATCTCAATAAAACCACCCCC 59.225 41.667 0.00 0.00 0.00 5.40
971 1313 3.518998 CCGTCCACGAGCTCCGAT 61.519 66.667 8.47 0.00 43.02 4.18
986 1328 1.283181 CGATCTTCTAGACGCCGGG 59.717 63.158 2.18 0.00 0.00 5.73
987 1329 1.164662 CGATCTTCTAGACGCCGGGA 61.165 60.000 2.18 0.00 0.00 5.14
988 1330 0.594110 GATCTTCTAGACGCCGGGAG 59.406 60.000 2.18 0.00 0.00 4.30
989 1331 1.457009 ATCTTCTAGACGCCGGGAGC 61.457 60.000 2.18 0.00 38.52 4.70
990 1332 3.140225 CTTCTAGACGCCGGGAGCC 62.140 68.421 2.18 0.00 38.78 4.70
1219 1561 4.986587 CCGACAACGACGCCGACA 62.987 66.667 0.00 0.00 42.66 4.35
2211 4228 2.429930 CAAGCCGGACTGAACCCA 59.570 61.111 5.05 0.00 0.00 4.51
2505 4604 1.135603 TCCAAATCCGTGTACGTCTCG 60.136 52.381 0.00 0.00 37.74 4.04
3411 7686 1.079503 CCTTCTTCTACTGCAACGCC 58.920 55.000 0.00 0.00 0.00 5.68
3525 7801 0.038166 TGATCCTGGACCTGTTTGGC 59.962 55.000 0.00 0.00 40.22 4.52
3537 7813 2.676121 TTTGGCCTCATGGGTGCG 60.676 61.111 3.32 0.00 37.43 5.34
3573 7849 2.361357 AGGAGGGTGAGGACGTCG 60.361 66.667 9.92 0.00 0.00 5.12
3580 7856 2.034532 TGAGGACGTCGGCCTACA 59.965 61.111 22.60 16.94 35.44 2.74
3721 7997 3.942130 TCTCCGTGCATGATATGTAGG 57.058 47.619 7.72 0.00 0.00 3.18
3739 8015 7.617041 ATGTAGGAGAACTTTGTAGAATTGC 57.383 36.000 0.00 0.00 0.00 3.56
3778 8054 1.519408 CCACGGACCTTGTTTGTAGG 58.481 55.000 0.00 0.00 38.79 3.18
3779 8055 0.872388 CACGGACCTTGTTTGTAGGC 59.128 55.000 0.00 0.00 36.17 3.93
3780 8056 0.763035 ACGGACCTTGTTTGTAGGCT 59.237 50.000 0.00 0.00 36.17 4.58
3781 8057 1.142262 ACGGACCTTGTTTGTAGGCTT 59.858 47.619 0.00 0.00 36.17 4.35
3782 8058 1.535462 CGGACCTTGTTTGTAGGCTTG 59.465 52.381 0.00 0.00 36.17 4.01
3783 8059 2.583143 GGACCTTGTTTGTAGGCTTGT 58.417 47.619 0.00 0.00 36.17 3.16
3784 8060 3.746940 GGACCTTGTTTGTAGGCTTGTA 58.253 45.455 0.00 0.00 36.17 2.41
3785 8061 3.751698 GGACCTTGTTTGTAGGCTTGTAG 59.248 47.826 0.00 0.00 36.17 2.74
3786 8062 3.146847 ACCTTGTTTGTAGGCTTGTAGC 58.853 45.455 0.00 0.00 41.46 3.58
3787 8063 3.146066 CCTTGTTTGTAGGCTTGTAGCA 58.854 45.455 0.00 0.00 44.75 3.49
3788 8064 3.758554 CCTTGTTTGTAGGCTTGTAGCAT 59.241 43.478 0.00 0.00 44.75 3.79
3789 8065 4.941263 CCTTGTTTGTAGGCTTGTAGCATA 59.059 41.667 0.00 0.00 44.75 3.14
3790 8066 5.414454 CCTTGTTTGTAGGCTTGTAGCATAA 59.586 40.000 0.00 0.00 44.75 1.90
3791 8067 6.403636 CCTTGTTTGTAGGCTTGTAGCATAAG 60.404 42.308 0.00 0.00 44.75 1.73
3792 8068 5.556915 TGTTTGTAGGCTTGTAGCATAAGT 58.443 37.500 0.00 0.00 44.75 2.24
3793 8069 5.411361 TGTTTGTAGGCTTGTAGCATAAGTG 59.589 40.000 0.00 0.00 44.75 3.16
3794 8070 4.819105 TGTAGGCTTGTAGCATAAGTGT 57.181 40.909 0.00 0.00 44.75 3.55
3795 8071 5.160607 TGTAGGCTTGTAGCATAAGTGTT 57.839 39.130 0.00 0.00 44.75 3.32
3796 8072 6.288941 TGTAGGCTTGTAGCATAAGTGTTA 57.711 37.500 0.00 0.00 44.75 2.41
3797 8073 6.884832 TGTAGGCTTGTAGCATAAGTGTTAT 58.115 36.000 0.00 0.00 44.75 1.89
3798 8074 8.014070 TGTAGGCTTGTAGCATAAGTGTTATA 57.986 34.615 0.00 0.00 44.75 0.98
3799 8075 8.141909 TGTAGGCTTGTAGCATAAGTGTTATAG 58.858 37.037 0.00 0.00 44.75 1.31
3800 8076 7.361457 AGGCTTGTAGCATAAGTGTTATAGA 57.639 36.000 0.67 0.00 44.75 1.98
3867 8143 3.255888 GCCGGTCAGAAAAGGAAAATTCT 59.744 43.478 1.90 0.00 36.35 2.40
3874 8150 5.304357 TCAGAAAAGGAAAATTCTTGTCCCC 59.696 40.000 0.00 0.00 33.73 4.81
3876 8152 3.628832 AAGGAAAATTCTTGTCCCCCA 57.371 42.857 0.00 0.00 31.25 4.96
3880 8156 4.096681 GGAAAATTCTTGTCCCCCATTCT 58.903 43.478 0.00 0.00 0.00 2.40
3881 8157 4.532126 GGAAAATTCTTGTCCCCCATTCTT 59.468 41.667 0.00 0.00 0.00 2.52
3897 8173 3.611766 TTCTTAGAAAGGAAGGCCTCG 57.388 47.619 5.23 0.00 46.28 4.63
3902 8188 5.189145 TCTTAGAAAGGAAGGCCTCGTAAAT 59.811 40.000 5.23 0.00 46.28 1.40
3907 8193 1.406477 GGAAGGCCTCGTAAATTCCGT 60.406 52.381 5.23 0.00 30.90 4.69
3915 8201 1.067706 TCGTAAATTCCGTTGGCTCGA 60.068 47.619 4.47 0.00 0.00 4.04
3919 8205 2.240493 AATTCCGTTGGCTCGATAGG 57.760 50.000 4.47 0.00 0.00 2.57
3954 8300 4.514585 TTTGTGGTGGGGTGCGCT 62.515 61.111 9.73 0.00 0.00 5.92
4058 8405 2.191802 CTTTTTGCATGCGTGTGTTGA 58.808 42.857 14.09 0.00 0.00 3.18
4285 8635 6.189133 ACCCTGTAGTAAAACCAACTTTTGA 58.811 36.000 0.00 0.00 33.84 2.69
4354 8824 2.492088 GCCCAAACTAGAAACATGGACC 59.508 50.000 0.00 0.00 32.82 4.46
4384 8854 4.826733 TCCTGTTTGTGCAACTAATCACAT 59.173 37.500 0.00 0.00 42.07 3.21
4462 8932 9.224267 CTAGAAAATATGGATTGGATGTACTGG 57.776 37.037 0.00 0.00 0.00 4.00
4533 9004 6.287525 TCCAAAAGAAACCTTTTTATGCCAG 58.712 36.000 0.00 0.00 40.71 4.85
4599 9070 6.408092 GGATCCAAAACCAACTTTTCCTTCTT 60.408 38.462 6.95 0.00 28.85 2.52
4648 9121 7.934120 ACTAGAAAAGAGATGTGCAAACTAACT 59.066 33.333 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.901250 ACAGGTTGAATCAACAAAGGGATT 59.099 37.500 25.14 0.48 45.11 3.01
107 108 8.611757 GCTTTGGTTGTCTTCAAAATTAAACAT 58.388 29.630 0.00 0.00 35.20 2.71
164 165 4.193826 AGATTCGTCATATCCCATTCCG 57.806 45.455 0.00 0.00 0.00 4.30
223 224 8.693625 GTTCTTAGAGTAACTCTATAAGGGCAA 58.306 37.037 10.86 0.00 43.85 4.52
231 232 5.532032 GCCGGAGTTCTTAGAGTAACTCTAT 59.468 44.000 5.05 0.00 46.98 1.98
275 276 7.378966 GGGTATCTCTATCAAATCATTCGTCA 58.621 38.462 0.00 0.00 0.00 4.35
282 283 3.824443 TCGCGGGTATCTCTATCAAATCA 59.176 43.478 6.13 0.00 0.00 2.57
390 445 2.552155 GCATGGTTACAGGTTGAGGTGA 60.552 50.000 0.00 0.00 0.00 4.02
401 456 2.547642 GCCTTTTGCAAGCATGGTTACA 60.548 45.455 10.31 8.26 40.77 2.41
570 625 9.144298 ACAGAGGGAGTATTTTCTAATTCGATA 57.856 33.333 0.00 0.00 0.00 2.92
586 925 9.833917 GCTTTTATATTAGTTTACAGAGGGAGT 57.166 33.333 0.00 0.00 0.00 3.85
587 926 8.979574 CGCTTTTATATTAGTTTACAGAGGGAG 58.020 37.037 0.00 0.00 0.00 4.30
588 927 8.480501 ACGCTTTTATATTAGTTTACAGAGGGA 58.519 33.333 0.00 0.00 0.00 4.20
589 928 8.658499 ACGCTTTTATATTAGTTTACAGAGGG 57.342 34.615 0.00 0.00 0.00 4.30
604 943 9.731819 CTCACTAGTGATCTAAACGCTTTTATA 57.268 33.333 25.35 0.00 39.13 0.98
605 944 7.707035 CCTCACTAGTGATCTAAACGCTTTTAT 59.293 37.037 25.35 0.00 39.13 1.40
606 945 7.033791 CCTCACTAGTGATCTAAACGCTTTTA 58.966 38.462 25.35 0.00 39.13 1.52
607 946 5.869888 CCTCACTAGTGATCTAAACGCTTTT 59.130 40.000 25.35 0.00 39.13 2.27
608 947 5.411781 CCTCACTAGTGATCTAAACGCTTT 58.588 41.667 25.35 0.00 39.13 3.51
609 948 4.142138 CCCTCACTAGTGATCTAAACGCTT 60.142 45.833 25.35 0.00 39.13 4.68
610 949 3.381908 CCCTCACTAGTGATCTAAACGCT 59.618 47.826 25.35 0.00 39.13 5.07
611 950 3.380637 TCCCTCACTAGTGATCTAAACGC 59.619 47.826 25.35 0.00 39.13 4.84
612 951 4.641094 ACTCCCTCACTAGTGATCTAAACG 59.359 45.833 25.35 11.93 39.13 3.60
613 952 6.602406 TGTACTCCCTCACTAGTGATCTAAAC 59.398 42.308 25.35 18.04 39.13 2.01
614 953 6.728411 TGTACTCCCTCACTAGTGATCTAAA 58.272 40.000 25.35 7.78 39.13 1.85
615 954 6.323210 TGTACTCCCTCACTAGTGATCTAA 57.677 41.667 25.35 10.82 39.13 2.10
616 955 5.970501 TGTACTCCCTCACTAGTGATCTA 57.029 43.478 25.35 12.46 39.13 1.98
617 956 4.864483 TGTACTCCCTCACTAGTGATCT 57.136 45.455 25.35 9.09 39.13 2.75
618 957 4.890581 ACATGTACTCCCTCACTAGTGATC 59.109 45.833 25.35 10.58 39.13 2.92
619 958 4.873010 ACATGTACTCCCTCACTAGTGAT 58.127 43.478 25.35 13.06 39.13 3.06
620 959 4.317530 ACATGTACTCCCTCACTAGTGA 57.682 45.455 23.80 23.80 38.06 3.41
621 960 5.450688 GCTTACATGTACTCCCTCACTAGTG 60.451 48.000 17.17 17.17 0.00 2.74
622 961 4.645588 GCTTACATGTACTCCCTCACTAGT 59.354 45.833 4.68 0.00 0.00 2.57
623 962 4.261238 CGCTTACATGTACTCCCTCACTAG 60.261 50.000 4.68 0.00 0.00 2.57
624 963 3.630769 CGCTTACATGTACTCCCTCACTA 59.369 47.826 4.68 0.00 0.00 2.74
625 964 2.427453 CGCTTACATGTACTCCCTCACT 59.573 50.000 4.68 0.00 0.00 3.41
626 965 2.810650 CGCTTACATGTACTCCCTCAC 58.189 52.381 4.68 0.00 0.00 3.51
627 966 1.136305 GCGCTTACATGTACTCCCTCA 59.864 52.381 4.68 0.00 0.00 3.86
628 967 1.854227 GCGCTTACATGTACTCCCTC 58.146 55.000 4.68 0.00 0.00 4.30
629 968 0.102481 CGCGCTTACATGTACTCCCT 59.898 55.000 4.68 0.00 0.00 4.20
630 969 0.874607 CCGCGCTTACATGTACTCCC 60.875 60.000 4.68 0.00 0.00 4.30
631 970 0.101759 TCCGCGCTTACATGTACTCC 59.898 55.000 4.68 0.00 0.00 3.85
632 971 1.197910 GTCCGCGCTTACATGTACTC 58.802 55.000 4.68 0.00 0.00 2.59
633 972 0.815734 AGTCCGCGCTTACATGTACT 59.184 50.000 4.68 0.00 0.00 2.73
638 977 0.673644 AGCAAAGTCCGCGCTTACAT 60.674 50.000 5.56 0.00 29.87 2.29
652 991 5.171147 TCGAAAATACACGGAAAAGCAAA 57.829 34.783 0.00 0.00 0.00 3.68
679 1020 2.665185 GCACTCGTGGCTTTCGGT 60.665 61.111 0.00 0.00 0.00 4.69
788 1130 3.876914 GGAGATGTCATGCCAATTTCGTA 59.123 43.478 0.00 0.00 0.00 3.43
789 1131 2.684881 GGAGATGTCATGCCAATTTCGT 59.315 45.455 0.00 0.00 0.00 3.85
825 1167 1.672881 CGAGGAATGTTCTTGGATGGC 59.327 52.381 0.00 0.00 0.00 4.40
850 1192 0.320374 TTTGAGAGCGATGGTCCGTT 59.680 50.000 0.00 0.00 0.00 4.44
945 1287 2.176055 CGTGGACGGACAGAGACG 59.824 66.667 0.00 0.00 35.37 4.18
971 1313 2.119655 GCTCCCGGCGTCTAGAAGA 61.120 63.158 10.08 0.00 0.00 2.87
1983 3307 2.665185 ACGGGCTCGCACAAGAAC 60.665 61.111 5.51 0.00 40.63 3.01
2187 3514 0.535335 TCAGTCCGGCTTGGTATGTC 59.465 55.000 0.00 0.00 39.52 3.06
2505 4604 2.049063 ACAGGAACGACGAGCAGC 60.049 61.111 0.00 0.00 0.00 5.25
2625 4724 3.333219 TCCTTGAGCCAGCTGGGG 61.333 66.667 33.46 24.49 37.04 4.96
3411 7686 2.100631 GGACGCCATGAAGGACGTG 61.101 63.158 0.00 0.00 45.59 4.49
3525 7801 2.890474 GCGTACGCACCCATGAGG 60.890 66.667 33.90 0.00 41.49 3.86
3580 7856 4.148825 GACGACCAGCGCCAGGAT 62.149 66.667 21.92 7.29 46.04 3.24
3721 7997 4.762251 ACCCTGCAATTCTACAAAGTTCTC 59.238 41.667 0.00 0.00 0.00 2.87
3752 8028 4.974438 AAGGTCCGTGGGGCCAGA 62.974 66.667 4.39 0.00 33.45 3.86
3762 8038 1.535462 CAAGCCTACAAACAAGGTCCG 59.465 52.381 0.00 0.00 36.43 4.79
3778 8054 7.513968 GCATCTATAACACTTATGCTACAAGC 58.486 38.462 0.00 0.00 42.82 4.01
3779 8055 7.382488 ACGCATCTATAACACTTATGCTACAAG 59.618 37.037 0.00 0.00 40.56 3.16
3780 8056 7.207383 ACGCATCTATAACACTTATGCTACAA 58.793 34.615 0.00 0.00 40.56 2.41
3781 8057 6.745116 ACGCATCTATAACACTTATGCTACA 58.255 36.000 0.00 0.00 40.56 2.74
3782 8058 7.061210 CAGACGCATCTATAACACTTATGCTAC 59.939 40.741 0.00 0.00 40.56 3.58
3783 8059 7.084486 CAGACGCATCTATAACACTTATGCTA 58.916 38.462 0.00 0.00 40.56 3.49
3784 8060 5.923114 CAGACGCATCTATAACACTTATGCT 59.077 40.000 0.00 0.00 40.56 3.79
3785 8061 5.119279 CCAGACGCATCTATAACACTTATGC 59.881 44.000 0.00 0.00 39.59 3.14
3786 8062 5.119279 GCCAGACGCATCTATAACACTTATG 59.881 44.000 0.00 0.00 37.47 1.90
3787 8063 5.011125 AGCCAGACGCATCTATAACACTTAT 59.989 40.000 0.00 0.00 41.38 1.73
3788 8064 4.341235 AGCCAGACGCATCTATAACACTTA 59.659 41.667 0.00 0.00 41.38 2.24
3789 8065 3.133003 AGCCAGACGCATCTATAACACTT 59.867 43.478 0.00 0.00 41.38 3.16
3790 8066 2.695666 AGCCAGACGCATCTATAACACT 59.304 45.455 0.00 0.00 41.38 3.55
3791 8067 2.797156 CAGCCAGACGCATCTATAACAC 59.203 50.000 0.00 0.00 41.38 3.32
3792 8068 2.224042 CCAGCCAGACGCATCTATAACA 60.224 50.000 0.00 0.00 41.38 2.41
3793 8069 2.408050 CCAGCCAGACGCATCTATAAC 58.592 52.381 0.00 0.00 41.38 1.89
3794 8070 1.270305 GCCAGCCAGACGCATCTATAA 60.270 52.381 0.00 0.00 41.38 0.98
3795 8071 0.318441 GCCAGCCAGACGCATCTATA 59.682 55.000 0.00 0.00 41.38 1.31
3796 8072 1.070445 GCCAGCCAGACGCATCTAT 59.930 57.895 0.00 0.00 41.38 1.98
3797 8073 2.501128 GCCAGCCAGACGCATCTA 59.499 61.111 0.00 0.00 41.38 1.98
3798 8074 4.827087 CGCCAGCCAGACGCATCT 62.827 66.667 0.00 0.00 41.38 2.90
3839 8115 4.735132 TTTCTGACCGGCCGCTCG 62.735 66.667 22.85 12.52 0.00 5.03
3840 8116 2.358247 TTTTCTGACCGGCCGCTC 60.358 61.111 22.85 17.84 0.00 5.03
3850 8126 5.304357 GGGGACAAGAATTTTCCTTTTCTGA 59.696 40.000 0.00 0.00 32.65 3.27
3867 8143 3.920197 TCCTTTCTAAGAATGGGGGACAA 59.080 43.478 0.00 0.00 0.00 3.18
3874 8150 4.203226 GAGGCCTTCCTTTCTAAGAATGG 58.797 47.826 6.77 0.00 44.46 3.16
3876 8152 3.519913 ACGAGGCCTTCCTTTCTAAGAAT 59.480 43.478 6.77 0.00 44.46 2.40
3880 8156 4.895668 TTTACGAGGCCTTCCTTTCTAA 57.104 40.909 6.77 0.00 44.46 2.10
3881 8157 5.425630 GAATTTACGAGGCCTTCCTTTCTA 58.574 41.667 6.77 0.00 44.46 2.10
3897 8173 3.493503 CCTATCGAGCCAACGGAATTTAC 59.506 47.826 0.00 0.00 0.00 2.01
3902 8188 1.143183 GCCTATCGAGCCAACGGAA 59.857 57.895 0.00 0.00 0.00 4.30
3915 8201 1.009675 AGGGTCTAGTGGTTGGCCTAT 59.990 52.381 3.32 0.00 35.27 2.57
3919 8205 0.400594 AACAGGGTCTAGTGGTTGGC 59.599 55.000 0.00 0.00 0.00 4.52
3920 8206 2.158667 ACAAACAGGGTCTAGTGGTTGG 60.159 50.000 12.07 2.20 44.25 3.77
3922 8208 2.158667 CCACAAACAGGGTCTAGTGGTT 60.159 50.000 0.00 0.00 41.11 3.67
3923 8209 1.420138 CCACAAACAGGGTCTAGTGGT 59.580 52.381 0.00 0.00 41.11 4.16
3924 8210 2.185004 CCACAAACAGGGTCTAGTGG 57.815 55.000 0.00 0.00 40.32 4.00
3954 8300 3.007831 GGCATGAAAAATCAGGGACCAAA 59.992 43.478 0.00 0.00 0.00 3.28
4058 8405 1.878775 GCTGCAGCGAAGGTCAAAT 59.121 52.632 25.23 0.00 33.74 2.32
4285 8635 3.753272 GTGTCTATTTGCACACATCCAGT 59.247 43.478 0.00 0.00 42.20 4.00
4310 8660 5.163395 GCTATCTGCAAAACTACTCCCTAGT 60.163 44.000 0.00 0.00 42.31 2.57
4311 8661 5.293560 GCTATCTGCAAAACTACTCCCTAG 58.706 45.833 0.00 0.00 42.31 3.02
4312 8662 4.101119 GGCTATCTGCAAAACTACTCCCTA 59.899 45.833 0.00 0.00 45.15 3.53
4313 8663 3.118223 GGCTATCTGCAAAACTACTCCCT 60.118 47.826 0.00 0.00 45.15 4.20
4354 8824 0.950836 TGCACAAACAGGAACATCCG 59.049 50.000 0.00 0.00 42.75 4.18
4384 8854 6.238593 GCATAAAAAGTTGGCATTGTTGGAAA 60.239 34.615 0.00 0.00 0.00 3.13
4450 8920 2.105649 TCTGCACAACCAGTACATCCAA 59.894 45.455 0.00 0.00 34.47 3.53
4533 9004 6.884280 AATATAGGCTTCTATTTGCACACC 57.116 37.500 0.00 0.00 35.49 4.16
4599 9070 0.108424 GGCTGTTTGGTTGCACACAA 60.108 50.000 0.00 0.00 0.00 3.33
4648 9121 3.386932 AAGCTGGCTTTTGGATCCATA 57.613 42.857 17.06 8.27 31.29 2.74


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

AutoCloner maintained by Alex Coulton.