Multiple sequence alignment - TraesCS2D01G457700

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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 TraesCS2D01G457700 chr2D 100.000 5746 0 0 1 5746 565096855 565102600 0.000000e+00 10611.0
1 TraesCS2D01G457700 chr2D 90.560 1822 143 17 1141 2943 565149375 565147564 0.000000e+00 2385.0
2 TraesCS2D01G457700 chr2D 82.481 1935 255 51 1241 3131 577628263 577630157 0.000000e+00 1618.0
3 TraesCS2D01G457700 chr2D 94.217 415 19 5 86 499 630019966 630020376 3.780000e-176 628.0
4 TraesCS2D01G457700 chr2D 85.932 526 55 14 4224 4741 565062943 565062429 1.410000e-150 544.0
5 TraesCS2D01G457700 chr2D 84.480 567 67 13 3194 3754 565147305 565146754 1.820000e-149 540.0
6 TraesCS2D01G457700 chr2D 86.051 509 48 16 4224 4722 565146227 565145732 5.100000e-145 525.0
7 TraesCS2D01G457700 chr2D 87.004 454 36 14 3756 4206 565146715 565146282 1.860000e-134 490.0
8 TraesCS2D01G457700 chr2D 85.714 455 40 14 3756 4206 565063431 565062998 1.890000e-124 457.0
9 TraesCS2D01G457700 chr2D 78.653 698 96 32 4228 4911 577630666 577631324 1.150000e-111 414.0
10 TraesCS2D01G457700 chr2D 83.990 406 28 13 492 871 630020669 630021063 7.080000e-94 355.0
11 TraesCS2D01G457700 chr2D 94.444 216 10 2 656 871 60076754 60076541 1.190000e-86 331.0
12 TraesCS2D01G457700 chr2D 85.425 247 29 5 3509 3754 565063710 565063470 3.440000e-62 250.0
13 TraesCS2D01G457700 chr2D 86.047 86 10 2 3193 3277 577630195 577630279 2.200000e-14 91.6
14 TraesCS2D01G457700 chr2B 96.737 2176 64 4 1134 3308 676764452 676766621 0.000000e+00 3618.0
15 TraesCS2D01G457700 chr2B 90.440 1820 147 15 1142 2943 677017516 677015706 0.000000e+00 2372.0
16 TraesCS2D01G457700 chr2B 95.536 1165 34 7 3771 4924 676767264 676768421 0.000000e+00 1847.0
17 TraesCS2D01G457700 chr2B 81.072 2182 282 78 1169 3280 694777965 694775845 0.000000e+00 1620.0
18 TraesCS2D01G457700 chr2B 80.056 1770 234 67 1572 3280 694699840 694698129 0.000000e+00 1203.0
19 TraesCS2D01G457700 chr2B 85.814 719 69 15 4050 4753 677014465 677013765 0.000000e+00 732.0
20 TraesCS2D01G457700 chr2B 96.000 450 15 2 3306 3754 676766702 676767149 0.000000e+00 728.0
21 TraesCS2D01G457700 chr2B 84.220 545 64 14 3194 3731 677015448 677014919 1.430000e-140 510.0
22 TraesCS2D01G457700 chr2B 92.898 352 14 2 5101 5452 676861147 676861487 8.600000e-138 501.0
23 TraesCS2D01G457700 chr2B 83.731 461 47 14 2558 2991 694605120 694604661 1.490000e-110 411.0
24 TraesCS2D01G457700 chr2B 78.763 598 78 27 4289 4872 694774263 694773701 7.080000e-94 355.0
25 TraesCS2D01G457700 chr2B 77.926 598 83 28 4289 4872 694745551 694744989 1.540000e-85 327.0
26 TraesCS2D01G457700 chr2B 88.104 269 16 3 5476 5743 676861550 676861803 7.230000e-79 305.0
27 TraesCS2D01G457700 chr2B 85.784 204 24 3 3756 3959 677014850 677014652 1.620000e-50 211.0
28 TraesCS2D01G457700 chr2B 84.177 158 15 7 4750 4905 694695610 694695461 1.670000e-30 145.0
29 TraesCS2D01G457700 chr2B 81.068 206 9 11 4921 5107 676768623 676768817 2.790000e-28 137.0
30 TraesCS2D01G457700 chr2B 96.000 75 3 0 872 946 676763616 676763690 7.820000e-24 122.0
31 TraesCS2D01G457700 chr2B 94.937 79 1 1 985 1060 676763687 676763765 2.810000e-23 121.0
32 TraesCS2D01G457700 chr2B 100.000 30 0 0 1 30 676758694 676758723 8.040000e-04 56.5
33 TraesCS2D01G457700 chr2A 95.365 2136 74 11 973 3086 705538902 705541034 0.000000e+00 3373.0
34 TraesCS2D01G457700 chr2A 90.565 1823 142 18 1141 2942 705590360 705588547 0.000000e+00 2386.0
35 TraesCS2D01G457700 chr2A 97.534 1095 23 3 3756 4850 705541826 705542916 0.000000e+00 1869.0
36 TraesCS2D01G457700 chr2A 81.949 1939 263 52 1241 3131 715777175 715775276 0.000000e+00 1561.0
37 TraesCS2D01G457700 chr2A 96.243 559 17 3 3197 3754 705541228 705541783 0.000000e+00 913.0
38 TraesCS2D01G457700 chr2A 83.598 567 70 14 3194 3754 705588285 705587736 1.430000e-140 510.0
39 TraesCS2D01G457700 chr2A 84.774 486 46 11 4267 4739 705587185 705586715 4.060000e-126 462.0
40 TraesCS2D01G457700 chr2A 85.903 454 40 9 3756 4206 705587697 705587265 4.060000e-126 462.0
41 TraesCS2D01G457700 chr2A 94.631 149 7 1 5479 5626 705583549 705583401 4.480000e-56 230.0
42 TraesCS2D01G457700 chr2A 95.588 136 6 0 5237 5372 705583711 705583576 9.690000e-53 219.0
43 TraesCS2D01G457700 chr2A 82.174 230 30 8 4970 5197 705584059 705583839 2.730000e-43 187.0
44 TraesCS2D01G457700 chr2A 95.238 105 2 1 872 976 705538730 705538831 4.610000e-36 163.0
45 TraesCS2D01G457700 chr2A 94.382 89 4 1 3111 3199 705541026 705541113 1.000000e-27 135.0
46 TraesCS2D01G457700 chr2A 88.043 92 6 1 5623 5714 705583116 705583030 2.830000e-18 104.0
47 TraesCS2D01G457700 chr2A 95.082 61 3 0 4864 4924 705542910 705542970 4.740000e-16 97.1
48 TraesCS2D01G457700 chr2A 86.047 86 10 2 3193 3277 715775241 715775157 2.200000e-14 91.6
49 TraesCS2D01G457700 chr5B 83.447 2060 243 46 1135 3153 432707596 432709598 0.000000e+00 1825.0
50 TraesCS2D01G457700 chr5B 77.984 863 107 40 3396 4206 432709969 432710800 1.130000e-126 464.0
51 TraesCS2D01G457700 chr5B 81.180 627 66 26 4206 4817 432710826 432711415 1.890000e-124 457.0
52 TraesCS2D01G457700 chr5A 83.943 1202 165 15 1134 2321 467755272 467754085 0.000000e+00 1125.0
53 TraesCS2D01G457700 chr5A 84.198 405 44 13 4206 4597 467741077 467740680 5.440000e-100 375.0
54 TraesCS2D01G457700 chr5A 81.513 476 44 17 2313 2771 467745298 467744850 9.160000e-93 351.0
55 TraesCS2D01G457700 chr5A 93.548 217 13 1 656 871 472082306 472082522 7.180000e-84 322.0
56 TraesCS2D01G457700 chr7D 94.749 419 17 5 86 499 575423146 575422728 0.000000e+00 647.0
57 TraesCS2D01G457700 chr7D 94.550 422 16 6 84 499 406326261 406326681 0.000000e+00 645.0
58 TraesCS2D01G457700 chr7D 87.023 393 33 11 492 871 126659102 126658715 1.480000e-115 427.0
59 TraesCS2D01G457700 chr7D 85.000 400 36 12 492 871 1411134 1411529 9.030000e-103 385.0
60 TraesCS2D01G457700 chr3D 94.299 421 17 6 86 499 608802693 608802273 6.280000e-179 638.0
61 TraesCS2D01G457700 chr3D 93.062 418 24 5 86 500 156199251 156198836 1.770000e-169 606.0
62 TraesCS2D01G457700 chr3D 94.667 150 7 1 492 641 11367385 11367533 1.250000e-56 231.0
63 TraesCS2D01G457700 chr3D 92.763 152 9 2 492 641 392030758 392030607 9.690000e-53 219.0
64 TraesCS2D01G457700 chr5D 93.587 421 19 6 86 499 539979624 539980043 6.320000e-174 621.0
65 TraesCS2D01G457700 chr5D 85.570 395 35 10 496 876 450616165 450615779 1.500000e-105 394.0
66 TraesCS2D01G457700 chr5D 94.470 217 11 1 656 871 427224267 427224483 3.320000e-87 333.0
67 TraesCS2D01G457700 chr5D 82.878 403 34 11 492 871 558062405 558062795 4.290000e-86 329.0
68 TraesCS2D01G457700 chr6D 93.494 415 21 6 84 495 14600985 14600574 3.810000e-171 612.0
69 TraesCS2D01G457700 chr6D 93.317 419 21 7 86 499 141689724 141689308 3.810000e-171 612.0
70 TraesCS2D01G457700 chr6D 93.151 219 11 2 656 872 54537359 54537143 9.290000e-83 318.0
71 TraesCS2D01G457700 chr6D 93.421 152 7 3 492 641 54537547 54537397 7.490000e-54 222.0
72 TraesCS2D01G457700 chr6D 89.172 157 9 6 492 641 63129182 63129337 7.600000e-44 189.0
73 TraesCS2D01G457700 chr1D 93.269 416 24 3 86 499 450030655 450030242 1.370000e-170 610.0
74 TraesCS2D01G457700 chrUn 85.536 401 32 10 492 871 48356230 48356625 4.170000e-106 396.0
75 TraesCS2D01G457700 chrUn 98.000 50 1 0 20 69 108309313 108309264 2.850000e-13 87.9
76 TraesCS2D01G457700 chr4D 85.039 381 29 12 514 871 49799459 49799084 4.230000e-96 363.0
77 TraesCS2D01G457700 chr4D 83.831 402 30 9 492 869 61596047 61596437 3.290000e-92 350.0
78 TraesCS2D01G457700 chr6A 83.171 410 39 14 492 879 455993464 455993063 1.180000e-91 348.0
79 TraesCS2D01G457700 chr4A 89.404 151 15 1 492 641 487546954 487547104 7.600000e-44 189.0
80 TraesCS2D01G457700 chr7B 76.216 370 51 22 2505 2852 228353080 228352726 1.660000e-35 161.0


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 TraesCS2D01G457700 chr2D 565096855 565102600 5745 False 10611.000000 10611 100.000000 1 5746 1 chr2D.!!$F1 5745
1 TraesCS2D01G457700 chr2D 565145732 565149375 3643 True 985.000000 2385 87.023750 1141 4722 4 chr2D.!!$R3 3581
2 TraesCS2D01G457700 chr2D 577628263 577631324 3061 False 707.866667 1618 82.393667 1241 4911 3 chr2D.!!$F2 3670
3 TraesCS2D01G457700 chr2D 630019966 630021063 1097 False 491.500000 628 89.103500 86 871 2 chr2D.!!$F3 785
4 TraesCS2D01G457700 chr2D 565062429 565063710 1281 True 417.000000 544 85.690333 3509 4741 3 chr2D.!!$R2 1232
5 TraesCS2D01G457700 chr2B 676763616 676768817 5201 False 1095.500000 3618 93.379667 872 5107 6 chr2B.!!$F2 4235
6 TraesCS2D01G457700 chr2B 694773701 694777965 4264 True 987.500000 1620 79.917500 1169 4872 2 chr2B.!!$R5 3703
7 TraesCS2D01G457700 chr2B 677013765 677017516 3751 True 956.250000 2372 86.564500 1142 4753 4 chr2B.!!$R3 3611
8 TraesCS2D01G457700 chr2B 694695461 694699840 4379 True 674.000000 1203 82.116500 1572 4905 2 chr2B.!!$R4 3333
9 TraesCS2D01G457700 chr2B 676861147 676861803 656 False 403.000000 501 90.501000 5101 5743 2 chr2B.!!$F3 642
10 TraesCS2D01G457700 chr2B 694744989 694745551 562 True 327.000000 327 77.926000 4289 4872 1 chr2B.!!$R2 583
11 TraesCS2D01G457700 chr2A 705538730 705542970 4240 False 1091.683333 3373 95.640667 872 4924 6 chr2A.!!$F1 4052
12 TraesCS2D01G457700 chr2A 715775157 715777175 2018 True 826.300000 1561 83.998000 1241 3277 2 chr2A.!!$R2 2036
13 TraesCS2D01G457700 chr2A 705583030 705590360 7330 True 570.000000 2386 88.159500 1141 5714 8 chr2A.!!$R1 4573
14 TraesCS2D01G457700 chr5B 432707596 432711415 3819 False 915.333333 1825 80.870333 1135 4817 3 chr5B.!!$F1 3682
15 TraesCS2D01G457700 chr5A 467754085 467755272 1187 True 1125.000000 1125 83.943000 1134 2321 1 chr5A.!!$R1 1187
16 TraesCS2D01G457700 chr5A 467740680 467745298 4618 True 363.000000 375 82.855500 2313 4597 2 chr5A.!!$R2 2284

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
695 1021 0.031043 GGGGGAAAACCAAAACGTCG 59.969 55.000 0.00 0.00 42.91 5.12 F
1304 2347 0.171231 CATGTCCAGAAGCGACTCGA 59.829 55.000 1.63 0.00 0.00 4.04 F
1441 2484 0.951558 CGAAACCCAGGGTGTTCTTG 59.048 55.000 13.66 3.43 35.34 3.02 F
2431 3517 1.065401 CTCCACTCGACTCTGCTGATC 59.935 57.143 0.00 0.00 0.00 2.92 F
2610 3714 1.202417 GCGCTTGCCTCATACAGAGTA 60.202 52.381 0.00 0.00 43.12 2.59 F
3328 8671 3.865745 ACATTCTAAAGCTCGGATGTTCG 59.134 43.478 0.00 0.00 0.00 3.95 F
4594 12094 1.024271 CGGCATTAGATTGTGTGGGG 58.976 55.000 0.00 0.00 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2935 1.450312 GACGGAGGATGGCAACTGG 60.450 63.158 0.00 0.0 37.61 4.00 R
3235 6588 0.824759 GGTAGCGTGAGAGGGAACAT 59.175 55.000 0.00 0.0 0.00 2.71 R
3245 6598 2.207229 ACTGCCAGTGGTAGCGTGA 61.207 57.895 25.54 0.0 39.03 4.35 R
3569 8919 1.607225 ACCAAGATGGGGCCAGAATA 58.393 50.000 4.39 0.0 43.37 1.75 R
4544 12044 3.106827 TCCTGATGATAGTGCAGTTGGA 58.893 45.455 0.00 0.0 0.00 3.53 R
4637 12137 0.171231 TCATCTTCCTCGTCACTGCG 59.829 55.000 0.00 0.0 0.00 5.18 R
5427 15518 1.178534 CGAAATTGTGGTGGCCTGGT 61.179 55.000 3.32 0.0 0.00 4.00 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
20 21 3.763097 TCAACATAAATCTTGGCGCTG 57.237 42.857 7.64 0.00 0.00 5.18
21 22 2.159393 TCAACATAAATCTTGGCGCTGC 60.159 45.455 7.64 0.00 0.00 5.25
63 64 2.747855 CCGTTGGGGCTGCTCTTC 60.748 66.667 0.00 0.00 0.00 2.87
64 65 2.348998 CGTTGGGGCTGCTCTTCT 59.651 61.111 0.00 0.00 0.00 2.85
65 66 1.302832 CGTTGGGGCTGCTCTTCTT 60.303 57.895 0.00 0.00 0.00 2.52
66 67 1.301677 CGTTGGGGCTGCTCTTCTTC 61.302 60.000 0.00 0.00 0.00 2.87
67 68 0.250901 GTTGGGGCTGCTCTTCTTCA 60.251 55.000 0.00 0.00 0.00 3.02
68 69 0.250901 TTGGGGCTGCTCTTCTTCAC 60.251 55.000 0.00 0.00 0.00 3.18
69 70 1.376466 GGGGCTGCTCTTCTTCACA 59.624 57.895 0.00 0.00 0.00 3.58
70 71 0.676151 GGGGCTGCTCTTCTTCACAG 60.676 60.000 0.00 0.00 0.00 3.66
71 72 0.322975 GGGCTGCTCTTCTTCACAGA 59.677 55.000 0.00 0.00 31.67 3.41
72 73 1.065564 GGGCTGCTCTTCTTCACAGAT 60.066 52.381 0.00 0.00 31.67 2.90
73 74 2.008329 GGCTGCTCTTCTTCACAGATG 58.992 52.381 0.00 0.00 31.67 2.90
74 75 2.008329 GCTGCTCTTCTTCACAGATGG 58.992 52.381 0.00 0.00 31.67 3.51
75 76 2.354503 GCTGCTCTTCTTCACAGATGGA 60.355 50.000 0.00 0.00 31.67 3.41
76 77 3.260740 CTGCTCTTCTTCACAGATGGAC 58.739 50.000 0.00 0.00 31.67 4.02
77 78 2.027745 TGCTCTTCTTCACAGATGGACC 60.028 50.000 0.00 0.00 0.00 4.46
78 79 2.027745 GCTCTTCTTCACAGATGGACCA 60.028 50.000 0.00 0.00 0.00 4.02
79 80 3.557898 GCTCTTCTTCACAGATGGACCAA 60.558 47.826 0.00 0.00 0.00 3.67
80 81 4.645535 CTCTTCTTCACAGATGGACCAAA 58.354 43.478 0.00 0.00 0.00 3.28
81 82 4.645535 TCTTCTTCACAGATGGACCAAAG 58.354 43.478 0.00 0.00 0.00 2.77
82 83 2.783135 TCTTCACAGATGGACCAAAGC 58.217 47.619 0.00 0.00 0.00 3.51
83 84 1.466167 CTTCACAGATGGACCAAAGCG 59.534 52.381 0.00 0.00 0.00 4.68
84 85 0.396435 TCACAGATGGACCAAAGCGT 59.604 50.000 0.00 0.00 0.00 5.07
128 129 1.939934 TCGTTGCAAAGAACACTCCAG 59.060 47.619 12.88 0.00 0.00 3.86
182 183 2.639286 GCCACTTGTCGCAACCTG 59.361 61.111 0.00 0.00 0.00 4.00
183 184 1.891919 GCCACTTGTCGCAACCTGA 60.892 57.895 0.00 0.00 0.00 3.86
267 268 4.048504 CCAAATCTCAAACCGTTTTCACC 58.951 43.478 0.00 0.00 0.00 4.02
271 272 4.300189 TCTCAAACCGTTTTCACCATTG 57.700 40.909 0.00 0.00 0.00 2.82
282 283 0.461870 TCACCATTGGATTCCTCGCG 60.462 55.000 10.37 0.00 0.00 5.87
306 307 5.980715 GTCGAGATCTTCAAAACTAGATCCC 59.019 44.000 0.00 0.00 38.24 3.85
386 387 1.419381 AAAAACCAAACCGGGAGCAT 58.581 45.000 6.32 0.00 40.22 3.79
417 418 3.121030 CTGAAAGAGGCACGCCCG 61.121 66.667 3.95 0.00 39.21 6.13
441 442 0.938713 TTTCGCGAAATCACAACCGT 59.061 45.000 29.22 0.00 0.00 4.83
442 443 0.233590 TTCGCGAAATCACAACCGTG 59.766 50.000 21.14 0.00 45.08 4.94
483 704 3.156723 GTGACTCTCGCGAAAGAAAAC 57.843 47.619 17.91 7.27 0.00 2.43
488 709 5.169836 ACTCTCGCGAAAGAAAACAAAAT 57.830 34.783 17.91 0.00 0.00 1.82
489 710 6.018588 TGACTCTCGCGAAAGAAAACAAAATA 60.019 34.615 17.91 0.00 0.00 1.40
490 711 6.363473 ACTCTCGCGAAAGAAAACAAAATAG 58.637 36.000 17.91 0.00 0.00 1.73
497 798 7.054998 GCGAAAGAAAACAAAATAGAAAACCG 58.945 34.615 0.00 0.00 0.00 4.44
508 809 7.228706 ACAAAATAGAAAACCGTGACTCTCAAT 59.771 33.333 0.00 0.00 0.00 2.57
516 817 7.562454 AAACCGTGACTCTCAATAAAGAAAA 57.438 32.000 0.00 0.00 0.00 2.29
591 894 4.701663 CACAACCGTGCCTCTCAT 57.298 55.556 0.00 0.00 36.06 2.90
645 949 5.427036 AAAAGAAGAAAACGCGTTATGGA 57.573 34.783 26.87 0.00 0.00 3.41
646 950 5.427036 AAAGAAGAAAACGCGTTATGGAA 57.573 34.783 26.87 0.00 0.00 3.53
647 951 4.663636 AGAAGAAAACGCGTTATGGAAG 57.336 40.909 26.87 0.00 0.00 3.46
648 952 2.894307 AGAAAACGCGTTATGGAAGC 57.106 45.000 26.87 9.39 0.00 3.86
649 953 1.467342 AGAAAACGCGTTATGGAAGCC 59.533 47.619 26.87 8.13 0.00 4.35
650 954 0.167251 AAAACGCGTTATGGAAGCCG 59.833 50.000 26.87 0.00 0.00 5.52
652 956 0.671163 AACGCGTTATGGAAGCCGAA 60.671 50.000 25.38 0.00 0.00 4.30
653 957 0.671163 ACGCGTTATGGAAGCCGAAA 60.671 50.000 5.58 0.00 0.00 3.46
654 958 0.247537 CGCGTTATGGAAGCCGAAAC 60.248 55.000 0.00 0.00 0.00 2.78
695 1021 0.031043 GGGGGAAAACCAAAACGTCG 59.969 55.000 0.00 0.00 42.91 5.12
733 1059 5.453281 AAACCGTTTAAAAAGCCGAAAAC 57.547 34.783 0.00 0.00 0.00 2.43
734 1060 4.107363 ACCGTTTAAAAAGCCGAAAACA 57.893 36.364 0.00 0.00 32.61 2.83
745 1071 1.536149 CCGAAAACACGTGCGAAAAA 58.464 45.000 17.22 0.00 0.00 1.94
776 1102 1.339151 ACAAAATCTGGAGGGAGCGTC 60.339 52.381 0.00 0.00 0.00 5.19
781 1107 2.363018 TGGAGGGAGCGTCCAGAG 60.363 66.667 0.00 0.00 42.45 3.35
803 1129 3.027170 GACACGTGGCGAATGGCTG 62.027 63.158 21.57 0.00 42.94 4.85
841 1167 2.290122 CTGATCGTTGCGAGGCTCCT 62.290 60.000 9.32 0.00 39.91 3.69
846 1172 1.293498 GTTGCGAGGCTCCTGAAGA 59.707 57.895 9.32 0.00 0.00 2.87
853 1179 1.376553 GGCTCCTGAAGAAGCGCTT 60.377 57.895 25.35 25.35 40.25 4.68
926 1252 0.751643 GGCCCATTTACTGCATCGGT 60.752 55.000 0.00 0.00 0.00 4.69
927 1253 0.381801 GCCCATTTACTGCATCGGTG 59.618 55.000 0.00 0.00 0.00 4.94
1066 1472 1.158904 ATGGAGGAGGAGGTATCGGA 58.841 55.000 0.00 0.00 0.00 4.55
1067 1473 0.185416 TGGAGGAGGAGGTATCGGAC 59.815 60.000 0.00 0.00 0.00 4.79
1071 2077 1.854280 AGGAGGAGGTATCGGACTCTT 59.146 52.381 0.00 0.00 34.22 2.85
1304 2347 0.171231 CATGTCCAGAAGCGACTCGA 59.829 55.000 1.63 0.00 0.00 4.04
1376 2419 4.148825 CCTTCTCGACCCGGCCAG 62.149 72.222 2.24 0.00 0.00 4.85
1441 2484 0.951558 CGAAACCCAGGGTGTTCTTG 59.048 55.000 13.66 3.43 35.34 3.02
1445 2488 1.672356 CCCAGGGTGTTCTTGAGCG 60.672 63.158 0.00 0.00 0.00 5.03
2431 3517 1.065401 CTCCACTCGACTCTGCTGATC 59.935 57.143 0.00 0.00 0.00 2.92
2610 3714 1.202417 GCGCTTGCCTCATACAGAGTA 60.202 52.381 0.00 0.00 43.12 2.59
2802 5919 6.290605 ACCCGTTTACATATACCAACATACC 58.709 40.000 0.00 0.00 0.00 2.73
2972 6109 9.772973 TTTCTTCATACAGCAAGTAGACTAAAA 57.227 29.630 0.00 0.00 35.85 1.52
3036 6194 7.569599 AGGGTCTCTTTTTGAAGTCCTAATA 57.430 36.000 0.00 0.00 0.00 0.98
3235 6588 9.004717 TCAAATTTGAAACCAGTACATCGATAA 57.995 29.630 18.45 0.00 33.55 1.75
3245 6598 5.011125 CCAGTACATCGATAATGTTCCCTCT 59.989 44.000 0.00 0.00 46.73 3.69
3248 6601 4.950050 ACATCGATAATGTTCCCTCTCAC 58.050 43.478 0.00 0.00 46.73 3.51
3328 8671 3.865745 ACATTCTAAAGCTCGGATGTTCG 59.134 43.478 0.00 0.00 0.00 3.95
3429 8776 8.043710 AGGTCTCTTCCTTGTAATAATGAACTG 58.956 37.037 0.00 0.00 33.52 3.16
3458 8805 6.849085 TCTGAAGAAGTCATCTAAGAGCTT 57.151 37.500 0.00 0.00 37.42 3.74
3503 8852 9.793252 AGTTTAACTTTTGCTTAGATGCATATG 57.207 29.630 3.54 0.00 42.96 1.78
4363 10038 5.649395 TCTTTGATGGGTTCTAATCTTGCTG 59.351 40.000 0.00 0.00 0.00 4.41
4594 12094 1.024271 CGGCATTAGATTGTGTGGGG 58.976 55.000 0.00 0.00 0.00 4.96
4637 12137 5.010719 TGGATCTATACCGACTTTGATGACC 59.989 44.000 0.00 0.00 0.00 4.02
4714 12243 3.370061 GGTTTGGCTAGCGTTACTAACAG 59.630 47.826 9.00 0.00 0.00 3.16
4894 13371 2.016318 GGATCATTCGCATGTGTTGGA 58.984 47.619 6.09 2.82 0.00 3.53
4895 13372 2.032550 GGATCATTCGCATGTGTTGGAG 59.967 50.000 6.09 0.00 0.00 3.86
4960 13642 1.966451 CACGGCCTCAGGTGGTTTC 60.966 63.158 0.00 0.00 0.00 2.78
4964 13646 0.329596 GGCCTCAGGTGGTTTCTGAT 59.670 55.000 0.00 0.00 40.07 2.90
5001 14991 8.472007 TCAAAAACAGAAGTGGTATTGGTATT 57.528 30.769 0.00 0.00 0.00 1.89
5002 14992 8.356657 TCAAAAACAGAAGTGGTATTGGTATTG 58.643 33.333 0.00 0.00 0.00 1.90
5003 14993 8.356657 CAAAAACAGAAGTGGTATTGGTATTGA 58.643 33.333 0.00 0.00 0.00 2.57
5004 14994 7.448748 AAACAGAAGTGGTATTGGTATTGAC 57.551 36.000 0.00 0.00 0.00 3.18
5071 15069 4.415783 GGAAGGCACCGACCAATT 57.584 55.556 0.00 0.00 0.00 2.32
5072 15070 1.883021 GGAAGGCACCGACCAATTG 59.117 57.895 0.00 0.00 0.00 2.32
5080 15078 0.988832 ACCGACCAATTGGCTTCCTA 59.011 50.000 24.79 0.00 39.32 2.94
5220 15223 2.095853 GTGGAGTTATGATGTTGTGCCG 59.904 50.000 0.00 0.00 0.00 5.69
5427 15518 4.776322 CAGCCGCCAATCGTCCCA 62.776 66.667 0.00 0.00 36.19 4.37
5452 15543 1.466950 GCCACCACAATTTCGATTCGA 59.533 47.619 4.29 4.29 0.00 3.71
5453 15544 2.097466 GCCACCACAATTTCGATTCGAT 59.903 45.455 9.96 0.00 35.23 3.59
5454 15545 3.311322 GCCACCACAATTTCGATTCGATA 59.689 43.478 9.96 5.58 35.23 2.92
5455 15546 4.024048 GCCACCACAATTTCGATTCGATAT 60.024 41.667 9.96 7.88 35.23 1.63
5457 15548 5.365942 CACCACAATTTCGATTCGATATCG 58.634 41.667 19.14 19.14 42.38 2.92
5489 15621 4.319377 GCTTTTCAGCTCGATTTTTCTTCG 59.681 41.667 0.00 0.00 43.51 3.79
5651 16072 7.779326 AGGGAGTAAAGGAGAACTAGTACATAC 59.221 40.741 0.00 0.00 0.00 2.39
5652 16073 7.779326 GGGAGTAAAGGAGAACTAGTACATACT 59.221 40.741 0.00 0.00 40.24 2.12
5653 16074 8.839343 GGAGTAAAGGAGAACTAGTACATACTC 58.161 40.741 0.00 7.82 37.73 2.59
5654 16075 8.750515 AGTAAAGGAGAACTAGTACATACTCC 57.249 38.462 17.43 17.43 42.64 3.85
5655 16076 8.334734 AGTAAAGGAGAACTAGTACATACTCCA 58.665 37.037 22.55 9.53 44.11 3.86
5659 16080 5.887035 GGAGAACTAGTACATACTCCAGTGT 59.113 44.000 18.94 0.00 42.11 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.159393 GCAGCGCCAAGATTTATGTTGA 60.159 45.455 2.29 0.00 33.31 3.18
1 2 2.187707 GCAGCGCCAAGATTTATGTTG 58.812 47.619 2.29 0.00 0.00 3.33
2 3 2.566952 GCAGCGCCAAGATTTATGTT 57.433 45.000 2.29 0.00 0.00 2.71
46 47 2.747855 GAAGAGCAGCCCCAACGG 60.748 66.667 0.00 0.00 0.00 4.44
47 48 1.301677 GAAGAAGAGCAGCCCCAACG 61.302 60.000 0.00 0.00 0.00 4.10
48 49 0.250901 TGAAGAAGAGCAGCCCCAAC 60.251 55.000 0.00 0.00 0.00 3.77
49 50 0.250901 GTGAAGAAGAGCAGCCCCAA 60.251 55.000 0.00 0.00 0.00 4.12
50 51 1.376466 GTGAAGAAGAGCAGCCCCA 59.624 57.895 0.00 0.00 0.00 4.96
51 52 0.676151 CTGTGAAGAAGAGCAGCCCC 60.676 60.000 0.00 0.00 0.00 5.80
52 53 0.322975 TCTGTGAAGAAGAGCAGCCC 59.677 55.000 0.00 0.00 0.00 5.19
53 54 2.008329 CATCTGTGAAGAAGAGCAGCC 58.992 52.381 0.00 0.00 0.00 4.85
54 55 2.008329 CCATCTGTGAAGAAGAGCAGC 58.992 52.381 0.00 0.00 0.00 5.25
55 56 3.260740 GTCCATCTGTGAAGAAGAGCAG 58.739 50.000 0.00 0.00 0.00 4.24
56 57 2.027745 GGTCCATCTGTGAAGAAGAGCA 60.028 50.000 0.00 0.00 0.00 4.26
57 58 2.027745 TGGTCCATCTGTGAAGAAGAGC 60.028 50.000 0.00 0.00 0.00 4.09
58 59 3.969287 TGGTCCATCTGTGAAGAAGAG 57.031 47.619 0.00 0.00 0.00 2.85
59 60 4.645535 CTTTGGTCCATCTGTGAAGAAGA 58.354 43.478 0.00 0.00 0.00 2.87
60 61 3.190118 GCTTTGGTCCATCTGTGAAGAAG 59.810 47.826 3.36 0.00 0.00 2.85
61 62 3.149196 GCTTTGGTCCATCTGTGAAGAA 58.851 45.455 3.36 0.00 0.00 2.52
62 63 2.783135 GCTTTGGTCCATCTGTGAAGA 58.217 47.619 3.36 0.00 0.00 2.87
63 64 1.466167 CGCTTTGGTCCATCTGTGAAG 59.534 52.381 0.00 0.00 0.00 3.02
64 65 1.202758 ACGCTTTGGTCCATCTGTGAA 60.203 47.619 0.00 0.00 0.00 3.18
65 66 0.396435 ACGCTTTGGTCCATCTGTGA 59.604 50.000 0.00 0.00 0.00 3.58
66 67 0.798776 GACGCTTTGGTCCATCTGTG 59.201 55.000 0.00 0.00 0.00 3.66
67 68 0.670546 CGACGCTTTGGTCCATCTGT 60.671 55.000 0.00 0.00 33.30 3.41
68 69 0.389817 TCGACGCTTTGGTCCATCTG 60.390 55.000 0.00 0.00 33.30 2.90
69 70 0.320374 TTCGACGCTTTGGTCCATCT 59.680 50.000 0.00 0.00 33.30 2.90
70 71 1.153353 TTTCGACGCTTTGGTCCATC 58.847 50.000 0.00 0.00 33.30 3.51
71 72 1.737793 GATTTCGACGCTTTGGTCCAT 59.262 47.619 0.00 0.00 33.30 3.41
72 73 1.153353 GATTTCGACGCTTTGGTCCA 58.847 50.000 0.00 0.00 33.30 4.02
73 74 1.136057 GTGATTTCGACGCTTTGGTCC 60.136 52.381 0.00 0.00 33.30 4.46
74 75 1.798813 AGTGATTTCGACGCTTTGGTC 59.201 47.619 0.00 0.00 0.00 4.02
75 76 1.878953 AGTGATTTCGACGCTTTGGT 58.121 45.000 0.00 0.00 0.00 3.67
76 77 4.600012 ATTAGTGATTTCGACGCTTTGG 57.400 40.909 0.00 0.00 0.00 3.28
77 78 6.682863 CCTTAATTAGTGATTTCGACGCTTTG 59.317 38.462 0.00 0.00 0.00 2.77
78 79 6.592607 TCCTTAATTAGTGATTTCGACGCTTT 59.407 34.615 0.00 0.00 0.00 3.51
79 80 6.103997 TCCTTAATTAGTGATTTCGACGCTT 58.896 36.000 0.00 0.00 0.00 4.68
80 81 5.657474 TCCTTAATTAGTGATTTCGACGCT 58.343 37.500 0.00 0.00 0.00 5.07
81 82 5.519206 ACTCCTTAATTAGTGATTTCGACGC 59.481 40.000 0.00 0.00 0.00 5.19
82 83 7.914346 AGTACTCCTTAATTAGTGATTTCGACG 59.086 37.037 0.00 0.00 0.00 5.12
83 84 9.235537 GAGTACTCCTTAATTAGTGATTTCGAC 57.764 37.037 12.13 0.00 0.00 4.20
84 85 8.127327 CGAGTACTCCTTAATTAGTGATTTCGA 58.873 37.037 17.23 0.00 0.00 3.71
128 129 0.951040 CTTGTCGTGACCTGGGAAGC 60.951 60.000 0.00 0.00 0.00 3.86
164 165 2.594592 AGGTTGCGACAAGTGGCC 60.595 61.111 6.39 0.00 33.12 5.36
267 268 0.527600 TCGACGCGAGGAATCCAATG 60.528 55.000 15.93 0.00 0.00 2.82
282 283 5.980715 GGGATCTAGTTTTGAAGATCTCGAC 59.019 44.000 11.05 0.00 37.77 4.20
306 307 6.241207 AGTTCGTCAAAACCTATCAACATG 57.759 37.500 0.00 0.00 0.00 3.21
397 398 0.889186 GGGCGTGCCTCTTTCAGAAA 60.889 55.000 11.25 0.00 36.10 2.52
417 418 0.237235 TGTGATTTCGCGAAAGGCAC 59.763 50.000 37.21 37.21 43.84 5.01
450 671 0.591659 GAGTCACGGTTTTGCTTCCC 59.408 55.000 0.00 0.00 0.00 3.97
483 704 6.539649 TGAGAGTCACGGTTTTCTATTTTG 57.460 37.500 0.00 0.00 0.00 2.44
488 709 7.663827 TCTTTATTGAGAGTCACGGTTTTCTA 58.336 34.615 0.00 0.00 0.00 2.10
489 710 6.522054 TCTTTATTGAGAGTCACGGTTTTCT 58.478 36.000 0.00 0.00 0.00 2.52
490 711 6.780706 TCTTTATTGAGAGTCACGGTTTTC 57.219 37.500 0.00 0.00 0.00 2.29
591 894 4.437659 CGAAAAGTCACGGTTTTTCTTCCA 60.438 41.667 12.24 0.00 39.79 3.53
627 930 3.161306 GCTTCCATAACGCGTTTTCTTC 58.839 45.455 31.50 9.88 0.00 2.87
641 945 0.320073 TTCGACGTTTCGGCTTCCAT 60.320 50.000 0.00 0.00 45.90 3.41
643 947 0.582960 TTTTCGACGTTTCGGCTTCC 59.417 50.000 0.00 0.00 45.90 3.46
644 948 1.259770 ACTTTTCGACGTTTCGGCTTC 59.740 47.619 0.00 0.00 45.90 3.86
645 949 1.292992 ACTTTTCGACGTTTCGGCTT 58.707 45.000 0.00 0.00 45.90 4.35
646 950 1.292992 AACTTTTCGACGTTTCGGCT 58.707 45.000 0.00 0.00 45.90 5.52
647 951 2.928295 TAACTTTTCGACGTTTCGGC 57.072 45.000 0.00 0.00 45.90 5.54
648 952 3.429543 TCCATAACTTTTCGACGTTTCGG 59.570 43.478 0.00 0.00 45.90 4.30
650 954 6.069563 GTCTTCCATAACTTTTCGACGTTTC 58.930 40.000 0.00 0.00 0.00 2.78
652 956 4.450080 GGTCTTCCATAACTTTTCGACGTT 59.550 41.667 0.00 0.00 0.00 3.99
653 957 3.992427 GGTCTTCCATAACTTTTCGACGT 59.008 43.478 0.00 0.00 0.00 4.34
654 958 3.060363 CGGTCTTCCATAACTTTTCGACG 59.940 47.826 0.00 0.00 0.00 5.12
667 993 1.457165 GTTTTCCCCCGGTCTTCCA 59.543 57.895 0.00 0.00 0.00 3.53
713 1039 3.858812 GTGTTTTCGGCTTTTTAAACGGT 59.141 39.130 0.00 0.00 34.16 4.83
714 1040 3.061732 CGTGTTTTCGGCTTTTTAAACGG 60.062 43.478 0.00 0.00 34.16 4.44
715 1041 3.543099 ACGTGTTTTCGGCTTTTTAAACG 59.457 39.130 0.00 0.00 34.16 3.60
752 1078 3.005791 CGCTCCCTCCAGATTTTGTTTTT 59.994 43.478 0.00 0.00 0.00 1.94
757 1083 1.373570 GACGCTCCCTCCAGATTTTG 58.626 55.000 0.00 0.00 0.00 2.44
841 1167 4.628074 ACTAGTTAACAAGCGCTTCTTCA 58.372 39.130 22.21 3.42 31.27 3.02
846 1172 3.139077 AGCAACTAGTTAACAAGCGCTT 58.861 40.909 18.98 18.98 0.00 4.68
853 1179 2.340731 TGGGGGAGCAACTAGTTAACA 58.659 47.619 8.04 0.00 0.00 2.41
926 1252 2.571757 CCGAGCTCGCTTACACCA 59.428 61.111 30.49 0.00 38.18 4.17
927 1253 2.202756 CCCGAGCTCGCTTACACC 60.203 66.667 30.49 0.00 38.18 4.16
950 1276 1.426041 ATAATCGTTGCGGCGGACAC 61.426 55.000 9.78 6.34 0.00 3.67
1066 1472 7.265673 GCCTCCTTTTTGTTTTTCTTAAGAGT 58.734 34.615 5.12 0.00 0.00 3.24
1067 1473 6.417930 CGCCTCCTTTTTGTTTTTCTTAAGAG 59.582 38.462 5.12 0.00 0.00 2.85
1071 2077 5.838531 TCGCCTCCTTTTTGTTTTTCTTA 57.161 34.783 0.00 0.00 0.00 2.10
1304 2347 1.184322 TTTGAATGCCGTGGCCATGT 61.184 50.000 23.39 4.73 41.09 3.21
1376 2419 3.347216 AGGGTGTTGTAGATGATGTTGC 58.653 45.455 0.00 0.00 0.00 4.17
1869 2935 1.450312 GACGGAGGATGGCAACTGG 60.450 63.158 0.00 0.00 37.61 4.00
2431 3517 5.707298 ACATCTTTCTGGTAATGTGGTCAAG 59.293 40.000 0.00 0.00 31.41 3.02
2610 3714 6.949352 ACACACAAATCTCAAGATGAACTT 57.051 33.333 0.00 0.00 39.70 2.66
2802 5919 4.858692 CGACTTGCCAGAAAATTAACATGG 59.141 41.667 0.00 0.00 0.00 3.66
2926 6046 7.948278 AGAAATATAAGATACCTTGTCGTGC 57.052 36.000 0.00 0.00 33.94 5.34
2972 6109 7.615365 ACAGATGTCCAAATGTTACCATGTTAT 59.385 33.333 0.00 0.00 0.00 1.89
3036 6194 2.808919 TCTTGGCACTAGCAGTAGAGT 58.191 47.619 0.00 0.00 44.61 3.24
3231 6584 3.460857 AGCGTGAGAGGGAACATTATC 57.539 47.619 0.00 0.00 0.00 1.75
3235 6588 0.824759 GGTAGCGTGAGAGGGAACAT 59.175 55.000 0.00 0.00 0.00 2.71
3245 6598 2.207229 ACTGCCAGTGGTAGCGTGA 61.207 57.895 25.54 0.00 39.03 4.35
3328 8671 6.521133 CGAGCAAAAGTAATCATCAGTTTGTC 59.479 38.462 0.00 0.00 0.00 3.18
3410 8757 5.492895 TCGGCAGTTCATTATTACAAGGAA 58.507 37.500 0.00 0.00 0.00 3.36
3429 8776 3.791245 AGATGACTTCTTCAGATTCGGC 58.209 45.455 0.00 0.00 37.77 5.54
3458 8805 9.223099 GTTAAACTTGGTTCAGCCTACTTATTA 57.777 33.333 0.00 0.00 38.35 0.98
3503 8852 6.148480 ACCAGATAAATCGAATTCATAGCAGC 59.852 38.462 6.22 0.00 0.00 5.25
3569 8919 1.607225 ACCAAGATGGGGCCAGAATA 58.393 50.000 4.39 0.00 43.37 1.75
3754 9119 5.359576 ACCTGAACTGATAAGCAACACAAAA 59.640 36.000 0.00 0.00 0.00 2.44
4363 10038 4.094887 TCTTCTGAAGCACACAAACAAGAC 59.905 41.667 12.54 0.00 0.00 3.01
4544 12044 3.106827 TCCTGATGATAGTGCAGTTGGA 58.893 45.455 0.00 0.00 0.00 3.53
4594 12094 3.118261 TCCAGTCATCTACTCCCAAATGC 60.118 47.826 0.00 0.00 35.76 3.56
4637 12137 0.171231 TCATCTTCCTCGTCACTGCG 59.829 55.000 0.00 0.00 0.00 5.18
4894 13371 1.625315 TGCTGTGCAGTCAGAATACCT 59.375 47.619 8.43 0.00 37.61 3.08
4895 13372 2.099141 TGCTGTGCAGTCAGAATACC 57.901 50.000 8.43 0.00 37.61 2.73
5001 14991 3.536570 TCAAACGTCAACATCCAAGTCA 58.463 40.909 0.00 0.00 0.00 3.41
5002 14992 4.378459 GGATCAAACGTCAACATCCAAGTC 60.378 45.833 9.70 0.00 34.27 3.01
5003 14993 3.502211 GGATCAAACGTCAACATCCAAGT 59.498 43.478 9.70 0.00 34.27 3.16
5004 14994 3.501828 TGGATCAAACGTCAACATCCAAG 59.498 43.478 13.34 0.00 40.07 3.61
5062 15060 1.743394 GTTAGGAAGCCAATTGGTCGG 59.257 52.381 25.19 0.29 37.57 4.79
5063 15061 1.743394 GGTTAGGAAGCCAATTGGTCG 59.257 52.381 25.19 0.88 37.57 4.79
5072 15070 0.179127 GTCGTACGGGTTAGGAAGCC 60.179 60.000 16.52 0.00 45.51 4.35
5080 15078 1.537202 GGCTATATCGTCGTACGGGTT 59.463 52.381 16.52 5.81 42.81 4.11
5220 15223 1.409427 AGCTACCTATCTTGGTCACGC 59.591 52.381 0.00 0.00 41.22 5.34
5427 15518 1.178534 CGAAATTGTGGTGGCCTGGT 61.179 55.000 3.32 0.00 0.00 4.00
5452 15543 4.626042 CTGAAAAGCAGCTAGGTCGATAT 58.374 43.478 0.00 0.00 37.90 1.63
5453 15544 4.046938 CTGAAAAGCAGCTAGGTCGATA 57.953 45.455 0.00 0.00 37.90 2.92
5454 15545 2.898705 CTGAAAAGCAGCTAGGTCGAT 58.101 47.619 0.00 0.00 37.90 3.59
5455 15546 2.370281 CTGAAAAGCAGCTAGGTCGA 57.630 50.000 0.00 0.00 37.90 4.20
5526 15658 9.186323 TGTCGGATTTTAATTTAAACACACATG 57.814 29.630 1.06 0.00 0.00 3.21
5602 15734 8.162085 CCCTAGTTAAAATAGATTTACTCCCCC 58.838 40.741 0.00 0.00 33.26 5.40
5655 16076 4.836125 CTGGAATTTTACACAGCACACT 57.164 40.909 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.