Multiple sequence alignment - TraesCS5D01G098500

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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 TraesCS5D01G098500 chr5D 100.000 5594 0 0 1 5594 109946445 109940852 0.000000e+00 10331.0
1 TraesCS5D01G098500 chr5D 95.485 598 12 3 4680 5271 3612427 3611839 0.000000e+00 941.0
2 TraesCS5D01G098500 chr5D 74.003 1204 293 15 2612 3802 110367344 110368540 6.560000e-129 472.0
3 TraesCS5D01G098500 chr5D 72.827 1093 273 18 2527 3604 110348828 110349911 8.920000e-93 351.0
4 TraesCS5D01G098500 chr5B 96.788 2989 66 7 1536 4514 122830380 122833348 0.000000e+00 4961.0
5 TraesCS5D01G098500 chr5B 93.554 1179 66 7 375 1549 122828765 122829937 0.000000e+00 1748.0
6 TraesCS5D01G098500 chr5B 84.279 1374 216 0 2524 3897 34720239 34721612 0.000000e+00 1341.0
7 TraesCS5D01G098500 chr5B 88.056 1080 122 6 758 1832 34718789 34719866 0.000000e+00 1273.0
8 TraesCS5D01G098500 chr5B 80.692 549 106 0 3958 4506 34721646 34722194 1.440000e-115 427.0
9 TraesCS5D01G098500 chr5B 84.615 403 35 15 1 385 34717819 34718212 5.290000e-100 375.0
10 TraesCS5D01G098500 chr5B 88.809 277 25 5 1 277 122828310 122828580 8.980000e-88 335.0
11 TraesCS5D01G098500 chr5B 73.256 946 233 14 2672 3604 122437540 122436602 1.500000e-85 327.0
12 TraesCS5D01G098500 chr5B 93.506 154 6 1 4527 4680 122833334 122833483 5.640000e-55 226.0
13 TraesCS5D01G098500 chr5A 97.885 1513 27 2 3002 4514 117388437 117389944 0.000000e+00 2612.0
14 TraesCS5D01G098500 chr5A 94.258 1463 81 3 375 1836 117379201 117380661 0.000000e+00 2233.0
15 TraesCS5D01G098500 chr5A 94.772 1052 37 6 1919 2956 117387383 117388430 0.000000e+00 1622.0
16 TraesCS5D01G098500 chr5A 73.920 1204 294 15 2612 3802 116586240 116585044 3.050000e-127 466.0
17 TraesCS5D01G098500 chr5A 92.171 281 15 5 1 277 117378688 117378965 1.890000e-104 390.0
18 TraesCS5D01G098500 chr5A 73.130 722 180 10 2930 3642 116776469 116775753 4.330000e-61 246.0
19 TraesCS5D01G098500 chr5A 94.156 154 5 1 4527 4680 117389930 117390079 1.210000e-56 231.0
20 TraesCS5D01G098500 chr5A 98.039 51 1 0 1869 1919 117387349 117387399 7.720000e-14 89.8
21 TraesCS5D01G098500 chr5A 75.342 146 30 5 1094 1233 578023056 578023201 1.300000e-06 65.8
22 TraesCS5D01G098500 chr7D 95.978 920 22 3 4681 5594 144159706 144158796 0.000000e+00 1480.0
23 TraesCS5D01G098500 chr7D 90.782 933 58 13 4680 5594 19207089 19206167 0.000000e+00 1221.0
24 TraesCS5D01G098500 chr3D 95.652 920 23 5 4681 5594 553039006 553039914 0.000000e+00 1461.0
25 TraesCS5D01G098500 chr3D 95.652 920 23 4 4681 5594 553077526 553078434 0.000000e+00 1461.0
26 TraesCS5D01G098500 chr3D 95.119 922 28 4 4681 5594 120626123 120627035 0.000000e+00 1437.0
27 TraesCS5D01G098500 chr3D 90.000 990 90 6 827 1815 582015984 582016965 0.000000e+00 1271.0
28 TraesCS5D01G098500 chr3D 83.117 1386 230 4 2524 3907 582017419 582018802 0.000000e+00 1260.0
29 TraesCS5D01G098500 chr2D 95.326 920 27 6 4682 5594 461080532 461081442 0.000000e+00 1447.0
30 TraesCS5D01G098500 chr2D 94.060 926 38 3 4677 5594 55162139 55161223 0.000000e+00 1389.0
31 TraesCS5D01G098500 chr2D 88.547 585 51 10 5014 5594 182377700 182378272 0.000000e+00 695.0
32 TraesCS5D01G098500 chr3B 83.478 1386 225 4 2524 3907 779546962 779545579 0.000000e+00 1288.0
33 TraesCS5D01G098500 chr3B 90.141 994 82 8 827 1815 779548399 779547417 0.000000e+00 1279.0
34 TraesCS5D01G098500 chr3B 82.192 1387 237 10 2524 3907 725096738 725098117 0.000000e+00 1184.0
35 TraesCS5D01G098500 chr3B 88.190 652 75 2 1159 1809 725095628 725096278 0.000000e+00 776.0
36 TraesCS5D01G098500 chr3B 85.592 583 71 5 5014 5593 39339763 39339191 2.880000e-167 599.0
37 TraesCS5D01G098500 chr3B 85.249 583 73 5 5014 5593 39316643 39316071 6.240000e-164 588.0
38 TraesCS5D01G098500 chr3B 93.056 216 14 1 949 1164 725036658 725036872 1.170000e-81 315.0
39 TraesCS5D01G098500 chrUn 93.981 648 19 7 4675 5311 95200509 95201147 0.000000e+00 963.0
40 TraesCS5D01G098500 chr1B 88.536 724 74 5 4873 5594 640440482 640441198 0.000000e+00 869.0
41 TraesCS5D01G098500 chr3A 87.074 557 58 9 5034 5586 446567406 446567952 7.960000e-173 617.0


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 TraesCS5D01G098500 chr5D 109940852 109946445 5593 True 10331.0 10331 100.00000 1 5594 1 chr5D.!!$R2 5593
1 TraesCS5D01G098500 chr5D 3611839 3612427 588 True 941.0 941 95.48500 4680 5271 1 chr5D.!!$R1 591
2 TraesCS5D01G098500 chr5D 110367344 110368540 1196 False 472.0 472 74.00300 2612 3802 1 chr5D.!!$F2 1190
3 TraesCS5D01G098500 chr5D 110348828 110349911 1083 False 351.0 351 72.82700 2527 3604 1 chr5D.!!$F1 1077
4 TraesCS5D01G098500 chr5B 122828310 122833483 5173 False 1817.5 4961 93.16425 1 4680 4 chr5B.!!$F2 4679
5 TraesCS5D01G098500 chr5B 34717819 34722194 4375 False 854.0 1341 84.41050 1 4506 4 chr5B.!!$F1 4505
6 TraesCS5D01G098500 chr5B 122436602 122437540 938 True 327.0 327 73.25600 2672 3604 1 chr5B.!!$R1 932
7 TraesCS5D01G098500 chr5A 117378688 117380661 1973 False 1311.5 2233 93.21450 1 1836 2 chr5A.!!$F2 1835
8 TraesCS5D01G098500 chr5A 117387349 117390079 2730 False 1138.7 2612 96.21300 1869 4680 4 chr5A.!!$F3 2811
9 TraesCS5D01G098500 chr5A 116585044 116586240 1196 True 466.0 466 73.92000 2612 3802 1 chr5A.!!$R1 1190
10 TraesCS5D01G098500 chr5A 116775753 116776469 716 True 246.0 246 73.13000 2930 3642 1 chr5A.!!$R2 712
11 TraesCS5D01G098500 chr7D 144158796 144159706 910 True 1480.0 1480 95.97800 4681 5594 1 chr7D.!!$R2 913
12 TraesCS5D01G098500 chr7D 19206167 19207089 922 True 1221.0 1221 90.78200 4680 5594 1 chr7D.!!$R1 914
13 TraesCS5D01G098500 chr3D 553039006 553039914 908 False 1461.0 1461 95.65200 4681 5594 1 chr3D.!!$F2 913
14 TraesCS5D01G098500 chr3D 553077526 553078434 908 False 1461.0 1461 95.65200 4681 5594 1 chr3D.!!$F3 913
15 TraesCS5D01G098500 chr3D 120626123 120627035 912 False 1437.0 1437 95.11900 4681 5594 1 chr3D.!!$F1 913
16 TraesCS5D01G098500 chr3D 582015984 582018802 2818 False 1265.5 1271 86.55850 827 3907 2 chr3D.!!$F4 3080
17 TraesCS5D01G098500 chr2D 461080532 461081442 910 False 1447.0 1447 95.32600 4682 5594 1 chr2D.!!$F2 912
18 TraesCS5D01G098500 chr2D 55161223 55162139 916 True 1389.0 1389 94.06000 4677 5594 1 chr2D.!!$R1 917
19 TraesCS5D01G098500 chr2D 182377700 182378272 572 False 695.0 695 88.54700 5014 5594 1 chr2D.!!$F1 580
20 TraesCS5D01G098500 chr3B 779545579 779548399 2820 True 1283.5 1288 86.80950 827 3907 2 chr3B.!!$R3 3080
21 TraesCS5D01G098500 chr3B 725095628 725098117 2489 False 980.0 1184 85.19100 1159 3907 2 chr3B.!!$F2 2748
22 TraesCS5D01G098500 chr3B 39339191 39339763 572 True 599.0 599 85.59200 5014 5593 1 chr3B.!!$R2 579
23 TraesCS5D01G098500 chr3B 39316071 39316643 572 True 588.0 588 85.24900 5014 5593 1 chr3B.!!$R1 579
24 TraesCS5D01G098500 chrUn 95200509 95201147 638 False 963.0 963 93.98100 4675 5311 1 chrUn.!!$F1 636
25 TraesCS5D01G098500 chr1B 640440482 640441198 716 False 869.0 869 88.53600 4873 5594 1 chr1B.!!$F1 721
26 TraesCS5D01G098500 chr3A 446567406 446567952 546 False 617.0 617 87.07400 5034 5586 1 chr3A.!!$F1 552

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
976 1405 3.244044 GCAAAACTGGGCATTTTGGTAGA 60.244 43.478 17.24 0.00 43.96 2.59 F
1521 1950 0.468226 TTGACAAGCCAAGAGACGGT 59.532 50.000 0.00 0.00 0.00 4.83 F
2199 3186 1.067846 ACAATACTGCTTCGACTCGCA 60.068 47.619 3.58 3.58 34.54 5.10 F
2451 3444 1.477553 TCATTTGGCATTCAGGAGGC 58.522 50.000 0.00 0.00 0.00 4.70 F
3381 4380 1.298157 TTTCTCATTGCCGGTCGCTG 61.298 55.000 1.90 0.00 38.78 5.18 F
4439 5444 0.462581 GCATCAGAGGACGCCATCAA 60.463 55.000 0.00 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 3194 0.099436 GTGTGCTTCGGGAATCATGC 59.901 55.000 0.00 0.0 0.00 4.06 R
2747 3746 0.268869 AGGAGGGCACATATCTCCCA 59.731 55.000 5.12 0.0 46.07 4.37 R
3329 4328 0.390340 TGGAACTGCGATGTGCTCTC 60.390 55.000 0.00 0.0 46.63 3.20 R
4268 5273 0.177141 CATGGCCCCAGCTTCAAATG 59.823 55.000 0.00 0.0 39.73 2.32 R
4507 5512 0.664224 TTTTTGAAACCGACCTCCGC 59.336 50.000 0.00 0.0 36.84 5.54 R
5447 6487 4.196778 TCCCCTGTTTGGCGTGCA 62.197 61.111 0.00 0.0 0.00 4.57 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
125 137 9.961265 ATAGTTGACAAATTTCATGATGCATAG 57.039 29.630 0.00 0.00 0.00 2.23
180 192 4.350368 TGACAAGTTCTGCATTCCACTA 57.650 40.909 0.00 0.00 0.00 2.74
239 255 6.028146 TCTGTACTATCTACGCAAACCAAA 57.972 37.500 0.00 0.00 0.00 3.28
311 369 7.175467 TGCAGACATGAACTGATCTTTATTTGT 59.825 33.333 21.63 0.00 37.54 2.83
386 587 5.134202 TGCATATAGATTAGTGTGTCCCG 57.866 43.478 0.00 0.00 0.00 5.14
389 679 5.864474 GCATATAGATTAGTGTGTCCCGAAG 59.136 44.000 0.00 0.00 0.00 3.79
434 727 3.367992 TTGTGCACGATTGATGCTTTT 57.632 38.095 13.13 0.00 43.77 2.27
529 822 8.033038 CAGTTAGTGTAGCAACTCAAAGGTATA 58.967 37.037 0.00 0.00 32.72 1.47
532 825 9.595823 TTAGTGTAGCAACTCAAAGGTATATTC 57.404 33.333 0.00 0.00 0.00 1.75
656 952 7.873505 ACCAAGAGTTCATGTCTACTTCTTTAC 59.126 37.037 0.00 0.00 0.00 2.01
664 960 9.692749 TTCATGTCTACTTCTTTACTACAGTTG 57.307 33.333 0.00 0.00 0.00 3.16
678 977 5.869579 ACTACAGTTGTGTCATTTGGAGAT 58.130 37.500 0.00 0.00 38.19 2.75
684 983 7.448161 ACAGTTGTGTCATTTGGAGATTGATTA 59.552 33.333 0.00 0.00 26.76 1.75
738 1037 4.438336 GCATCCTGAATTGACTGTGACATG 60.438 45.833 0.00 0.00 0.00 3.21
742 1041 4.083643 CCTGAATTGACTGTGACATGTGAC 60.084 45.833 8.67 8.67 0.00 3.67
840 1264 7.698130 GGCAATTGACACTTATGAAGTTATGAC 59.302 37.037 10.34 0.00 40.46 3.06
976 1405 3.244044 GCAAAACTGGGCATTTTGGTAGA 60.244 43.478 17.24 0.00 43.96 2.59
1062 1491 2.997315 CTCACCACCCTGCTCGGA 60.997 66.667 0.00 0.00 33.16 4.55
1185 1614 1.322637 CGTGATCTTGATGTGCAGACG 59.677 52.381 0.00 0.00 0.00 4.18
1189 1618 1.432514 TCTTGATGTGCAGACGAAGC 58.567 50.000 0.00 0.00 0.00 3.86
1256 1685 8.181573 GGATTGCATAGACGACTTTATGAAAAA 58.818 33.333 0.00 0.00 30.62 1.94
1467 1896 1.320344 CCATCGACCCTCGTCTTCCA 61.320 60.000 0.00 0.00 41.35 3.53
1520 1949 1.813513 ATTGACAAGCCAAGAGACGG 58.186 50.000 0.00 0.00 0.00 4.79
1521 1950 0.468226 TTGACAAGCCAAGAGACGGT 59.532 50.000 0.00 0.00 0.00 4.83
1662 2547 2.358737 GGCCAGTTCCAGTGTCGG 60.359 66.667 0.00 0.00 0.00 4.79
1854 2758 6.064060 TGGATCCCATCATACTTTGATCAAC 58.936 40.000 7.89 0.00 43.40 3.18
1903 2807 3.957497 ACTTGTTTGATTTGCTGGGTGTA 59.043 39.130 0.00 0.00 0.00 2.90
1904 2808 4.202111 ACTTGTTTGATTTGCTGGGTGTAC 60.202 41.667 0.00 0.00 0.00 2.90
1905 2809 3.291584 TGTTTGATTTGCTGGGTGTACA 58.708 40.909 0.00 0.00 0.00 2.90
1906 2810 3.894427 TGTTTGATTTGCTGGGTGTACAT 59.106 39.130 0.00 0.00 0.00 2.29
1907 2811 5.073428 TGTTTGATTTGCTGGGTGTACATA 58.927 37.500 0.00 0.00 0.00 2.29
1908 2812 5.714333 TGTTTGATTTGCTGGGTGTACATAT 59.286 36.000 0.00 0.00 0.00 1.78
1909 2813 6.887002 TGTTTGATTTGCTGGGTGTACATATA 59.113 34.615 0.00 0.00 0.00 0.86
1910 2814 7.559533 TGTTTGATTTGCTGGGTGTACATATAT 59.440 33.333 0.00 0.00 0.00 0.86
1911 2815 9.062524 GTTTGATTTGCTGGGTGTACATATATA 57.937 33.333 0.00 0.00 0.00 0.86
1912 2816 9.634021 TTTGATTTGCTGGGTGTACATATATAA 57.366 29.630 0.00 0.00 0.00 0.98
1913 2817 8.615878 TGATTTGCTGGGTGTACATATATAAC 57.384 34.615 0.00 0.00 0.00 1.89
1914 2818 8.214364 TGATTTGCTGGGTGTACATATATAACA 58.786 33.333 0.00 0.00 0.00 2.41
1915 2819 7.795482 TTTGCTGGGTGTACATATATAACAC 57.205 36.000 16.74 16.74 42.17 3.32
1916 2820 6.487299 TGCTGGGTGTACATATATAACACA 57.513 37.500 22.45 10.46 44.18 3.72
1917 2821 7.073457 TGCTGGGTGTACATATATAACACAT 57.927 36.000 22.45 0.00 44.18 3.21
1918 2822 7.513856 TGCTGGGTGTACATATATAACACATT 58.486 34.615 22.45 0.00 44.18 2.71
2031 2947 1.469308 GATATACTGAGGAGGCGACCG 59.531 57.143 0.00 0.00 34.73 4.79
2089 3033 3.537337 TCAGGGGGATTTAGGAACTTCA 58.463 45.455 0.00 0.00 41.75 3.02
2199 3186 1.067846 ACAATACTGCTTCGACTCGCA 60.068 47.619 3.58 3.58 34.54 5.10
2223 3216 1.838112 AAAGCATGATTCCCGAAGCA 58.162 45.000 0.00 0.00 41.24 3.91
2280 3273 7.778853 TCCTTACTTAGTTACTACATCCTCCTG 59.221 40.741 0.00 0.00 0.00 3.86
2302 3295 3.498397 GTGTTTCACTATATCCATGCCCG 59.502 47.826 0.00 0.00 0.00 6.13
2451 3444 1.477553 TCATTTGGCATTCAGGAGGC 58.522 50.000 0.00 0.00 0.00 4.70
2466 3464 1.559831 GAGGCGTGCCATTTTTATGC 58.440 50.000 14.29 0.00 38.92 3.14
3124 4123 6.239856 AGGAGATAGGAGATGGGTATTTCT 57.760 41.667 0.00 0.00 0.00 2.52
3329 4328 6.039941 AGACTATCTCTGAACTGTTATTCCCG 59.960 42.308 0.00 0.00 0.00 5.14
3381 4380 1.298157 TTTCTCATTGCCGGTCGCTG 61.298 55.000 1.90 0.00 38.78 5.18
3438 4443 2.942710 TCGAAGTTTAGAGTTCTGCGG 58.057 47.619 0.00 0.00 33.82 5.69
4020 5025 5.431073 TCTCCTCCAGAAATTTCAGATGGAT 59.569 40.000 21.53 0.00 39.25 3.41
4268 5273 1.200948 GAGCAATGGCAAAGGACTGAC 59.799 52.381 0.00 0.00 44.61 3.51
4425 5430 0.547471 TTCAGGAGGTGGAGGCATCA 60.547 55.000 0.00 0.00 0.00 3.07
4439 5444 0.462581 GCATCAGAGGACGCCATCAA 60.463 55.000 0.00 0.00 0.00 2.57
4454 5459 2.610433 CATCAAGAGCGCAGTTACTCA 58.390 47.619 11.47 0.00 35.28 3.41
4506 5511 6.658816 TCCGAATATGGGGTGATGAAAATATG 59.341 38.462 0.00 0.00 0.00 1.78
4507 5512 6.127647 CCGAATATGGGGTGATGAAAATATGG 60.128 42.308 0.00 0.00 0.00 2.74
4508 5513 6.610075 AATATGGGGTGATGAAAATATGGC 57.390 37.500 0.00 0.00 0.00 4.40
4509 5514 2.305928 TGGGGTGATGAAAATATGGCG 58.694 47.619 0.00 0.00 0.00 5.69
4510 5515 1.613437 GGGGTGATGAAAATATGGCGG 59.387 52.381 0.00 0.00 0.00 6.13
4511 5516 2.582052 GGGTGATGAAAATATGGCGGA 58.418 47.619 0.00 0.00 0.00 5.54
4512 5517 2.554032 GGGTGATGAAAATATGGCGGAG 59.446 50.000 0.00 0.00 0.00 4.63
4513 5518 2.554032 GGTGATGAAAATATGGCGGAGG 59.446 50.000 0.00 0.00 0.00 4.30
4514 5519 3.214328 GTGATGAAAATATGGCGGAGGT 58.786 45.455 0.00 0.00 0.00 3.85
4515 5520 3.251004 GTGATGAAAATATGGCGGAGGTC 59.749 47.826 0.00 0.00 0.00 3.85
4516 5521 1.948104 TGAAAATATGGCGGAGGTCG 58.052 50.000 0.00 0.00 42.76 4.79
4517 5522 1.226746 GAAAATATGGCGGAGGTCGG 58.773 55.000 0.00 0.00 39.69 4.79
4518 5523 0.544697 AAAATATGGCGGAGGTCGGT 59.455 50.000 0.00 0.00 39.69 4.69
4519 5524 0.544697 AAATATGGCGGAGGTCGGTT 59.455 50.000 0.00 0.00 39.69 4.44
4520 5525 0.544697 AATATGGCGGAGGTCGGTTT 59.455 50.000 0.00 0.00 39.69 3.27
4521 5526 0.106149 ATATGGCGGAGGTCGGTTTC 59.894 55.000 0.00 0.00 39.69 2.78
4522 5527 1.259142 TATGGCGGAGGTCGGTTTCA 61.259 55.000 0.00 0.00 39.69 2.69
4523 5528 2.031465 GGCGGAGGTCGGTTTCAA 59.969 61.111 0.00 0.00 39.69 2.69
4524 5529 1.598685 GGCGGAGGTCGGTTTCAAA 60.599 57.895 0.00 0.00 39.69 2.69
4525 5530 1.167781 GGCGGAGGTCGGTTTCAAAA 61.168 55.000 0.00 0.00 39.69 2.44
4526 5531 0.664224 GCGGAGGTCGGTTTCAAAAA 59.336 50.000 0.00 0.00 39.69 1.94
4602 5607 6.256321 GCACACAACTCATCTGACAAATTTTT 59.744 34.615 0.00 0.00 0.00 1.94
4608 5613 9.185192 CAACTCATCTGACAAATTTTTAGGTTC 57.815 33.333 0.00 0.00 0.00 3.62
4615 5620 9.801873 TCTGACAAATTTTTAGGTTCTCTTTTG 57.198 29.630 0.00 0.00 0.00 2.44
4616 5621 8.419076 TGACAAATTTTTAGGTTCTCTTTTGC 57.581 30.769 0.00 0.00 0.00 3.68
4617 5622 7.494298 TGACAAATTTTTAGGTTCTCTTTTGCC 59.506 33.333 0.00 0.00 0.00 4.52
4623 5628 1.783365 AGGTTCTCTTTTGCCTCCCTT 59.217 47.619 0.00 0.00 0.00 3.95
4624 5629 2.986728 AGGTTCTCTTTTGCCTCCCTTA 59.013 45.455 0.00 0.00 0.00 2.69
4625 5630 3.009584 AGGTTCTCTTTTGCCTCCCTTAG 59.990 47.826 0.00 0.00 0.00 2.18
4639 5644 4.381411 CTCCCTTAGTTAGGCTGCATAAC 58.619 47.826 24.87 24.87 43.27 1.89
5007 6021 0.403271 AGCAGATTGAGGTGCCAACT 59.597 50.000 0.00 0.00 40.81 3.16
5325 6362 4.821589 GGAACGGCGCCCTCAGAG 62.822 72.222 23.46 8.22 0.00 3.35
5498 6538 4.451150 ATCGCACGCACCGGTCAT 62.451 61.111 2.59 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 122 8.929746 CGTATCAAGTACTATGCATCATGAAAT 58.070 33.333 0.19 0.00 0.00 2.17
111 123 7.384932 CCGTATCAAGTACTATGCATCATGAAA 59.615 37.037 0.19 0.00 0.00 2.69
125 137 3.493503 GCAAGCATACCCGTATCAAGTAC 59.506 47.826 0.00 0.00 0.00 2.73
180 192 4.782156 AGAGTCATCAGAGGGTTGAAGAAT 59.218 41.667 0.00 0.00 0.00 2.40
218 234 7.549839 ACTATTTGGTTTGCGTAGATAGTACA 58.450 34.615 0.00 0.00 29.73 2.90
281 339 6.862711 AAGATCAGTTCATGTCTGCATATG 57.137 37.500 13.07 0.00 33.30 1.78
293 351 6.093495 CCCGCTAACAAATAAAGATCAGTTCA 59.907 38.462 0.00 0.00 0.00 3.18
311 369 4.099881 CCAGTATTAGTTGTACCCCGCTAA 59.900 45.833 0.00 0.00 0.00 3.09
386 587 0.831307 ATAGTCGGGCTCCCAACTTC 59.169 55.000 3.55 0.00 35.37 3.01
389 679 1.379527 CAAATAGTCGGGCTCCCAAC 58.620 55.000 5.70 0.00 35.37 3.77
400 690 4.092821 TCGTGCACAATACAGCAAATAGTC 59.907 41.667 18.64 0.00 43.20 2.59
434 727 8.871629 TCATGGAAGTTACTTTATGCCTTTTA 57.128 30.769 14.33 0.20 0.00 1.52
608 904 8.153479 TGGTACATAGACACATGAATAAATGC 57.847 34.615 0.00 0.00 0.00 3.56
656 952 6.427853 TCAATCTCCAAATGACACAACTGTAG 59.572 38.462 0.00 0.00 0.00 2.74
684 983 8.767478 CAAACCTGCAATTTCTATCAGAATTT 57.233 30.769 0.00 0.00 33.67 1.82
809 1233 4.148079 TCATAAGTGTCAATTGCCAACCA 58.852 39.130 0.00 0.00 0.00 3.67
976 1405 6.653020 TCTGTTGGATGCTTTATGAGTGTAT 58.347 36.000 0.00 0.00 0.00 2.29
1062 1491 1.257743 TCAGCTTTGCGTACTCCTCT 58.742 50.000 0.00 0.00 0.00 3.69
1093 1522 3.447586 TCTTTCATGAACTCTACCTCCCG 59.552 47.826 7.89 0.00 0.00 5.14
1185 1614 1.272147 ACTTGGTCCCTCCATTGCTTC 60.272 52.381 0.00 0.00 46.60 3.86
1189 1618 3.577389 GGACTTGGTCCCTCCATTG 57.423 57.895 5.48 0.00 46.19 2.82
1256 1685 1.688197 CAATGTCAGTTTGGCCAAGGT 59.312 47.619 19.48 7.08 0.00 3.50
1467 1896 2.364970 GTCTGGCTCAGCATAGAGTGAT 59.635 50.000 0.00 0.00 37.94 3.06
1497 1926 3.674997 GTCTCTTGGCTTGTCAATACCA 58.325 45.455 3.85 3.85 0.00 3.25
1520 1949 4.125703 CTCCATTAGGCACTTGATGAGAC 58.874 47.826 0.00 0.00 41.75 3.36
1521 1950 3.135348 CCTCCATTAGGCACTTGATGAGA 59.865 47.826 0.00 0.00 41.75 3.27
1572 2457 4.594920 CCAGGACCCACAATAGATATCACT 59.405 45.833 5.32 0.00 0.00 3.41
1662 2547 2.535331 TGCGACAAAGAAACAAAAGCC 58.465 42.857 0.00 0.00 0.00 4.35
1854 2758 3.525537 AGCAACTGAATAGATGTGGACG 58.474 45.455 0.00 0.00 0.00 4.79
1974 2890 8.947055 ACAAGCAGAAAAACATGTTTTCTATT 57.053 26.923 31.10 18.82 44.30 1.73
1976 2892 8.898761 TCTACAAGCAGAAAAACATGTTTTCTA 58.101 29.630 31.10 14.94 44.30 2.10
1977 2893 7.771183 TCTACAAGCAGAAAAACATGTTTTCT 58.229 30.769 31.10 25.16 46.29 2.52
1978 2894 7.915397 TCTCTACAAGCAGAAAAACATGTTTTC 59.085 33.333 31.10 23.75 41.45 2.29
1979 2895 7.771183 TCTCTACAAGCAGAAAAACATGTTTT 58.229 30.769 27.01 27.01 43.88 2.43
1983 2899 6.860023 CCTTTCTCTACAAGCAGAAAAACATG 59.140 38.462 0.00 0.00 38.00 3.21
2022 2938 2.540101 CAGAATGAAATACGGTCGCCTC 59.460 50.000 0.00 0.00 39.69 4.70
2089 3033 8.958119 TCTACTGTAGAAACAAGTGAAAATGT 57.042 30.769 14.87 0.00 34.49 2.71
2184 3171 1.295792 TTTTTGCGAGTCGAAGCAGT 58.704 45.000 18.61 0.00 44.72 4.40
2207 3194 0.099436 GTGTGCTTCGGGAATCATGC 59.901 55.000 0.00 0.00 0.00 4.06
2208 3195 0.374758 CGTGTGCTTCGGGAATCATG 59.625 55.000 0.00 0.00 0.00 3.07
2217 3210 1.730176 CACAAAGAACGTGTGCTTCG 58.270 50.000 0.00 0.00 39.93 3.79
2223 3216 5.153918 TTCTGTGCTACACAAAGAACGTGT 61.154 41.667 1.64 1.19 45.88 4.49
2270 3263 6.183361 GGATATAGTGAAACACAGGAGGATGT 60.183 42.308 4.75 0.00 41.43 3.06
2280 3273 3.498397 CGGGCATGGATATAGTGAAACAC 59.502 47.826 0.00 0.00 41.43 3.32
2302 3295 2.434774 ACGGAGTTTCCCAAGGCC 59.565 61.111 0.00 0.00 37.78 5.19
2328 3321 6.434340 ACCCTTTATTTCCTCAATGAACAGAC 59.566 38.462 0.00 0.00 0.00 3.51
2389 3382 8.732746 TTTCCAGAGCAATTAAATAGGAGTAC 57.267 34.615 0.00 0.00 0.00 2.73
2451 3444 4.920340 TGTTAACAGCATAAAAATGGCACG 59.080 37.500 3.59 0.00 0.00 5.34
2747 3746 0.268869 AGGAGGGCACATATCTCCCA 59.731 55.000 5.12 0.00 46.07 4.37
2794 3793 4.853924 GTGAACCACCACATTTCTTCAT 57.146 40.909 0.00 0.00 37.04 2.57
3124 4123 8.319057 ACCATACTTCTATTGATAAGGTCACA 57.681 34.615 0.00 0.00 36.32 3.58
3329 4328 0.390340 TGGAACTGCGATGTGCTCTC 60.390 55.000 0.00 0.00 46.63 3.20
3381 4380 7.217200 TCTGTTCAGCATACCCAAATATACTC 58.783 38.462 0.00 0.00 0.00 2.59
3438 4443 8.429641 TCCTCACCATTTTCTATATCAAGTACC 58.570 37.037 0.00 0.00 0.00 3.34
4020 5025 4.222145 ACTCTGGGAAAGAAATAGTACGCA 59.778 41.667 0.00 0.00 33.37 5.24
4227 5232 1.021390 AGCAGGTGAAGCGGAAATCG 61.021 55.000 0.00 0.00 42.76 3.34
4268 5273 0.177141 CATGGCCCCAGCTTCAAATG 59.823 55.000 0.00 0.00 39.73 2.32
4290 5295 1.622811 ACCTCCAGCTTCTCAAGACTG 59.377 52.381 0.00 0.00 34.54 3.51
4409 5414 0.690411 CTCTGATGCCTCCACCTCCT 60.690 60.000 0.00 0.00 0.00 3.69
4425 5430 1.519719 GCTCTTGATGGCGTCCTCT 59.480 57.895 3.88 0.00 0.00 3.69
4439 5444 0.969894 AAGGTGAGTAACTGCGCTCT 59.030 50.000 9.73 0.00 33.22 4.09
4454 5459 2.448931 TGGGGTGGTTCGGAAGGT 60.449 61.111 0.00 0.00 0.00 3.50
4506 5511 1.167781 TTTTGAAACCGACCTCCGCC 61.168 55.000 0.00 0.00 36.84 6.13
4507 5512 0.664224 TTTTTGAAACCGACCTCCGC 59.336 50.000 0.00 0.00 36.84 5.54
4525 5530 3.596046 TGGTCCTCCTCCACCATATTTTT 59.404 43.478 0.00 0.00 37.78 1.94
4526 5531 3.197983 TGGTCCTCCTCCACCATATTTT 58.802 45.455 0.00 0.00 37.78 1.82
4527 5532 2.858644 TGGTCCTCCTCCACCATATTT 58.141 47.619 0.00 0.00 37.78 1.40
4528 5533 2.587060 TGGTCCTCCTCCACCATATT 57.413 50.000 0.00 0.00 37.78 1.28
4529 5534 2.412591 CTTGGTCCTCCTCCACCATAT 58.587 52.381 0.00 0.00 42.42 1.78
4530 5535 1.625228 CCTTGGTCCTCCTCCACCATA 60.625 57.143 0.00 0.00 42.42 2.74
4531 5536 0.916358 CCTTGGTCCTCCTCCACCAT 60.916 60.000 0.00 0.00 42.42 3.55
4532 5537 1.538876 CCTTGGTCCTCCTCCACCA 60.539 63.158 0.00 0.00 41.13 4.17
4602 5607 2.632537 AGGGAGGCAAAAGAGAACCTA 58.367 47.619 0.00 0.00 30.95 3.08
4608 5613 4.518249 CCTAACTAAGGGAGGCAAAAGAG 58.482 47.826 0.00 0.00 42.32 2.85
4616 5621 1.204146 TGCAGCCTAACTAAGGGAGG 58.796 55.000 0.00 0.00 46.65 4.30
4617 5622 4.101741 AGTTATGCAGCCTAACTAAGGGAG 59.898 45.833 18.54 0.00 46.65 4.30
4623 5628 8.801882 ATTACAAAAGTTATGCAGCCTAACTA 57.198 30.769 19.84 7.10 38.22 2.24
4624 5629 7.703058 ATTACAAAAGTTATGCAGCCTAACT 57.297 32.000 15.32 15.32 40.30 2.24
4625 5630 8.757164 AAATTACAAAAGTTATGCAGCCTAAC 57.243 30.769 11.56 11.56 0.00 2.34
4639 5644 7.784633 TTTGCTCCAAGGAAAATTACAAAAG 57.215 32.000 0.00 0.00 32.52 2.27
4808 5822 4.772100 TCATCATATGGATTGGAGTAGCGA 59.228 41.667 2.13 0.00 32.57 4.93
4924 5938 2.604174 GCGTCAGACCGGTTTGTGG 61.604 63.158 23.20 16.86 0.00 4.17
5007 6021 2.349755 GCGGAGGCACCTACCAAA 59.650 61.111 0.00 0.00 39.62 3.28
5447 6487 4.196778 TCCCCTGTTTGGCGTGCA 62.197 61.111 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.