Multiple sequence alignment - TraesCS7D01G482400

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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 TraesCS7D01G482400 chr7D 100.000 2517 0 0 2750 5266 592818044 592820560 0.000000e+00 4649.0
1 TraesCS7D01G482400 chr7D 100.000 2325 0 0 1 2325 592815295 592817619 0.000000e+00 4294.0
2 TraesCS7D01G482400 chr7D 88.491 1034 71 25 3152 4162 592678584 592679592 0.000000e+00 1206.0
3 TraesCS7D01G482400 chr7D 89.177 693 45 8 1041 1703 592677372 592678064 0.000000e+00 837.0
4 TraesCS7D01G482400 chr7D 87.045 687 62 7 1044 1703 592632303 592632989 0.000000e+00 750.0
5 TraesCS7D01G482400 chr7D 80.590 1051 117 51 3147 4140 592633250 592634270 0.000000e+00 730.0
6 TraesCS7D01G482400 chr7D 85.897 702 39 11 1046 1702 592860212 592859526 0.000000e+00 693.0
7 TraesCS7D01G482400 chr7D 87.324 426 38 10 535 946 592860840 592860417 1.720000e-129 473.0
8 TraesCS7D01G482400 chr7D 78.247 639 87 29 3469 4056 592858667 592858030 3.880000e-96 363.0
9 TraesCS7D01G482400 chr7D 82.060 301 32 7 580 859 592675547 592675846 2.450000e-58 237.0
10 TraesCS7D01G482400 chr7D 90.816 98 7 2 919 1016 592677214 592677309 4.280000e-26 130.0
11 TraesCS7D01G482400 chr7B 92.917 1186 55 8 3147 4323 668929667 668928502 0.000000e+00 1698.0
12 TraesCS7D01G482400 chr7B 91.760 983 44 9 1044 1998 668930640 668929667 0.000000e+00 1332.0
13 TraesCS7D01G482400 chr7B 87.441 1051 111 19 2 1048 668931723 668930690 0.000000e+00 1190.0
14 TraesCS7D01G482400 chr7B 87.072 1052 86 31 3452 4471 669140080 669139047 0.000000e+00 1144.0
15 TraesCS7D01G482400 chr7B 92.755 773 50 4 4493 5261 668928137 668927367 0.000000e+00 1112.0
16 TraesCS7D01G482400 chr7B 86.518 853 68 13 1044 1849 669141452 669140600 0.000000e+00 894.0
17 TraesCS7D01G482400 chr7B 88.319 702 43 4 1041 1703 668907225 668907926 0.000000e+00 806.0
18 TraesCS7D01G482400 chr7B 85.283 530 56 15 535 1048 668906649 668907172 1.300000e-145 527.0
19 TraesCS7D01G482400 chr7B 78.150 627 90 23 3476 4056 668913976 668914601 6.490000e-94 355.0
20 TraesCS7D01G482400 chr7B 96.571 175 6 0 4324 4498 668928404 668928230 1.860000e-74 291.0
21 TraesCS7D01G482400 chr7B 82.156 269 30 11 608 859 669175049 669174782 1.150000e-51 215.0
22 TraesCS7D01G482400 chr7B 94.531 128 6 1 3255 3381 669140406 669140279 4.160000e-46 196.0
23 TraesCS7D01G482400 chr7B 87.719 57 3 3 3279 3331 668908531 668908587 4.400000e-06 63.9
24 TraesCS7D01G482400 chr7A 87.243 1168 87 23 3146 4252 685213704 685214870 0.000000e+00 1275.0
25 TraesCS7D01G482400 chr7A 93.333 675 33 6 1041 1703 685212661 685213335 0.000000e+00 987.0
26 TraesCS7D01G482400 chr7A 91.803 671 34 3 1053 1702 685090140 685090810 0.000000e+00 915.0
27 TraesCS7D01G482400 chr7A 88.970 689 43 4 1048 1703 685230681 685229993 0.000000e+00 821.0
28 TraesCS7D01G482400 chr7A 85.653 697 68 8 1044 1709 684292533 684293228 0.000000e+00 704.0
29 TraesCS7D01G482400 chr7A 94.710 397 20 1 2750 3146 162406724 162407119 2.690000e-172 616.0
30 TraesCS7D01G482400 chr7A 79.182 831 98 29 3468 4262 684296585 684297376 1.690000e-139 507.0
31 TraesCS7D01G482400 chr7A 91.620 358 24 4 551 903 685212158 685212514 1.700000e-134 490.0
32 TraesCS7D01G482400 chr7A 92.378 328 21 3 1999 2325 162406391 162406715 1.030000e-126 464.0
33 TraesCS7D01G482400 chr7A 86.916 428 32 13 3179 3604 685094940 685095345 4.810000e-125 459.0
34 TraesCS7D01G482400 chr7A 83.493 521 46 9 3645 4126 685095344 685095863 2.890000e-122 449.0
35 TraesCS7D01G482400 chr7A 78.213 638 83 28 3469 4052 685228845 685228210 1.800000e-94 357.0
36 TraesCS7D01G482400 chr7A 90.182 275 21 3 1727 1996 685213430 685213703 2.330000e-93 353.0
37 TraesCS7D01G482400 chr7A 82.667 375 32 17 588 934 685231284 685230915 8.570000e-78 302.0
38 TraesCS7D01G482400 chr7A 92.500 120 3 4 931 1048 685212499 685212614 3.260000e-37 167.0
39 TraesCS7D01G482400 chr7A 83.439 157 24 2 4293 4449 685215863 685216017 1.530000e-30 145.0
40 TraesCS7D01G482400 chr7A 78.947 171 17 11 3220 3382 684296427 684296586 1.210000e-16 99.0
41 TraesCS7D01G482400 chr7A 78.632 117 7 8 3233 3331 685229163 685229047 1.580000e-05 62.1
42 TraesCS7D01G482400 chr2D 98.741 397 4 1 2750 3146 561051454 561051059 0.000000e+00 704.0
43 TraesCS7D01G482400 chr2D 96.725 397 13 0 2750 3146 537418674 537419070 0.000000e+00 662.0
44 TraesCS7D01G482400 chr2D 97.561 328 6 2 1999 2325 561051789 561051463 1.280000e-155 560.0
45 TraesCS7D01G482400 chr2D 95.732 328 12 2 1999 2325 537418339 537418665 1.300000e-145 527.0
46 TraesCS7D01G482400 chr5A 97.481 397 10 0 2750 3146 382106836 382107232 0.000000e+00 678.0
47 TraesCS7D01G482400 chr5A 96.962 395 10 2 2753 3146 444900002 444899609 0.000000e+00 662.0
48 TraesCS7D01G482400 chr5A 92.988 328 11 5 1999 2325 382106511 382106827 7.990000e-128 468.0
49 TraesCS7D01G482400 chr5A 92.683 328 12 6 1999 2325 444900330 444900014 3.720000e-126 462.0
50 TraesCS7D01G482400 chr5B 96.977 397 11 1 2750 3146 274350268 274350663 0.000000e+00 665.0
51 TraesCS7D01G482400 chr5B 95.466 397 9 2 2750 3146 274461982 274462369 4.480000e-175 625.0
52 TraesCS7D01G482400 chr5B 92.027 301 14 7 1990 2286 274461672 274461966 1.060000e-111 414.0
53 TraesCS7D01G482400 chr5B 91.667 300 16 6 1990 2286 274349959 274350252 1.770000e-109 407.0
54 TraesCS7D01G482400 chr1B 95.511 401 17 1 2750 3149 662721412 662721012 1.600000e-179 640.0
55 TraesCS7D01G482400 chr1B 94.207 328 16 2 1999 2325 662721746 662721421 1.020000e-136 497.0
56 TraesCS7D01G482400 chr2A 78.116 329 44 13 3754 4056 737478780 737478454 3.240000e-42 183.0
57 TraesCS7D01G482400 chr2B 77.448 337 40 17 3754 4056 227683434 227683100 9.070000e-38 169.0
58 TraesCS7D01G482400 chr2B 95.556 45 2 0 4 48 795060863 795060907 7.320000e-09 73.1
59 TraesCS7D01G482400 chr3D 87.603 121 9 5 3023 3141 270624883 270624999 9.200000e-28 135.0
60 TraesCS7D01G482400 chr3D 95.890 73 3 0 2898 2970 529794640 529794568 9.260000e-23 119.0
61 TraesCS7D01G482400 chr3D 94.444 54 3 0 4608 4661 302957190 302957243 3.380000e-12 84.2
62 TraesCS7D01G482400 chr3A 91.837 49 4 0 4616 4664 431708074 431708026 9.460000e-08 69.4
63 TraesCS7D01G482400 chr4A 86.667 60 8 0 4692 4751 440834022 440834081 3.400000e-07 67.6


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 TraesCS7D01G482400 chr7D 592815295 592820560 5265 False 4471.500000 4649 100.000000 1 5266 2 chr7D.!!$F3 5265
1 TraesCS7D01G482400 chr7D 592632303 592634270 1967 False 740.000000 750 83.817500 1044 4140 2 chr7D.!!$F1 3096
2 TraesCS7D01G482400 chr7D 592675547 592679592 4045 False 602.500000 1206 87.636000 580 4162 4 chr7D.!!$F2 3582
3 TraesCS7D01G482400 chr7D 592858030 592860840 2810 True 509.666667 693 83.822667 535 4056 3 chr7D.!!$R1 3521
4 TraesCS7D01G482400 chr7B 668927367 668931723 4356 True 1124.600000 1698 92.288800 2 5261 5 chr7B.!!$R2 5259
5 TraesCS7D01G482400 chr7B 669139047 669141452 2405 True 744.666667 1144 89.373667 1044 4471 3 chr7B.!!$R3 3427
6 TraesCS7D01G482400 chr7B 668906649 668908587 1938 False 465.633333 806 87.107000 535 3331 3 chr7B.!!$F2 2796
7 TraesCS7D01G482400 chr7B 668913976 668914601 625 False 355.000000 355 78.150000 3476 4056 1 chr7B.!!$F1 580
8 TraesCS7D01G482400 chr7A 685090140 685090810 670 False 915.000000 915 91.803000 1053 1702 1 chr7A.!!$F1 649
9 TraesCS7D01G482400 chr7A 685212158 685216017 3859 False 569.500000 1275 89.719500 551 4449 6 chr7A.!!$F5 3898
10 TraesCS7D01G482400 chr7A 162406391 162407119 728 False 540.000000 616 93.544000 1999 3146 2 chr7A.!!$F2 1147
11 TraesCS7D01G482400 chr7A 685094940 685095863 923 False 454.000000 459 85.204500 3179 4126 2 chr7A.!!$F4 947
12 TraesCS7D01G482400 chr7A 684292533 684297376 4843 False 436.666667 704 81.260667 1044 4262 3 chr7A.!!$F3 3218
13 TraesCS7D01G482400 chr7A 685228210 685231284 3074 True 385.525000 821 82.120500 588 4052 4 chr7A.!!$R1 3464
14 TraesCS7D01G482400 chr2D 561051059 561051789 730 True 632.000000 704 98.151000 1999 3146 2 chr2D.!!$R1 1147
15 TraesCS7D01G482400 chr2D 537418339 537419070 731 False 594.500000 662 96.228500 1999 3146 2 chr2D.!!$F1 1147
16 TraesCS7D01G482400 chr5A 382106511 382107232 721 False 573.000000 678 95.234500 1999 3146 2 chr5A.!!$F1 1147
17 TraesCS7D01G482400 chr5A 444899609 444900330 721 True 562.000000 662 94.822500 1999 3146 2 chr5A.!!$R1 1147
18 TraesCS7D01G482400 chr5B 274349959 274350663 704 False 536.000000 665 94.322000 1990 3146 2 chr5B.!!$F1 1156
19 TraesCS7D01G482400 chr5B 274461672 274462369 697 False 519.500000 625 93.746500 1990 3146 2 chr5B.!!$F2 1156
20 TraesCS7D01G482400 chr1B 662721012 662721746 734 True 568.500000 640 94.859000 1999 3149 2 chr1B.!!$R1 1150

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
319 320 0.101579 GAGTAGGCTTCTCAGTCGCC 59.898 60.0 15.36 0.00 44.09 5.54 F
429 430 0.106918 TTTTGGGTGAGTTCGGTGCT 60.107 50.0 0.00 0.00 0.00 4.40 F
431 432 0.759959 TTGGGTGAGTTCGGTGCTTA 59.240 50.0 0.00 0.00 0.00 3.09 F
438 439 0.896226 AGTTCGGTGCTTAGGAGTCC 59.104 55.0 0.00 0.00 0.00 3.85 F
2928 4970 0.107703 TTCACTGATTGCGCCTAGGG 60.108 55.0 11.72 1.58 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 4232 0.535335 GTGCGGAAGGATGAGGTACA 59.465 55.000 0.00 0.0 0.00 2.90 R
2876 4918 1.671054 GTGAAGCCTAGCCGCAACA 60.671 57.895 0.00 0.0 0.00 3.33 R
2928 4970 3.743396 ACTTCACATCGCTCTTGAAGAAC 59.257 43.478 15.59 0.0 46.16 3.01 R
3146 5190 7.133891 TGGATCTCTTTTTCTTTTCGTGATC 57.866 36.000 0.00 0.0 0.00 2.92 R
5229 11669 0.250513 AATCTCCCTTGTCCGAGTGC 59.749 55.000 0.00 0.0 0.00 4.40 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
17 18 4.730487 CAAGAGGGGTGGCTTCTG 57.270 61.111 0.00 0.00 0.00 3.02
27 28 1.229304 TGGCTTCTGCTCCTCCTCA 60.229 57.895 0.00 0.00 39.59 3.86
28 29 0.619832 TGGCTTCTGCTCCTCCTCAT 60.620 55.000 0.00 0.00 39.59 2.90
31 32 2.315176 GCTTCTGCTCCTCCTCATCTA 58.685 52.381 0.00 0.00 36.03 1.98
54 55 1.519455 GATCGGCTCCACCTTGACG 60.519 63.158 0.00 0.00 35.61 4.35
56 57 2.227089 ATCGGCTCCACCTTGACGTC 62.227 60.000 9.11 9.11 35.61 4.34
59 60 1.367840 GCTCCACCTTGACGTCAGT 59.632 57.895 19.11 11.52 0.00 3.41
97 98 3.160748 GCCCAGAGCTCCTCCTCC 61.161 72.222 10.93 0.00 38.99 4.30
129 130 2.762459 TCGGATCCGGAACCAGGG 60.762 66.667 32.79 13.79 40.25 4.45
130 131 4.547367 CGGATCCGGAACCAGGGC 62.547 72.222 28.26 3.35 35.56 5.19
132 133 4.191015 GATCCGGAACCAGGGCCC 62.191 72.222 16.46 16.46 0.00 5.80
173 174 2.268920 GCTTCCTGCCCATCACGA 59.731 61.111 0.00 0.00 35.15 4.35
185 186 0.528924 CATCACGACAACCGGTCCTA 59.471 55.000 8.04 0.00 43.95 2.94
188 189 0.170561 CACGACAACCGGTCCTAGAG 59.829 60.000 8.04 0.00 43.95 2.43
212 213 1.972198 CTGGTGTGCGAAGGAGGTA 59.028 57.895 0.00 0.00 0.00 3.08
217 218 1.139095 GTGCGAAGGAGGTAGGACG 59.861 63.158 0.00 0.00 0.00 4.79
218 219 1.001764 TGCGAAGGAGGTAGGACGA 60.002 57.895 0.00 0.00 0.00 4.20
241 242 2.319438 AGAGGAGGAGGATAGGGTTTGT 59.681 50.000 0.00 0.00 0.00 2.83
245 246 3.523972 GGAGGAGGATAGGGTTTGTTTCT 59.476 47.826 0.00 0.00 0.00 2.52
249 250 2.039879 AGGATAGGGTTTGTTTCTGCGT 59.960 45.455 0.00 0.00 0.00 5.24
250 251 2.418976 GGATAGGGTTTGTTTCTGCGTC 59.581 50.000 0.00 0.00 0.00 5.19
265 266 0.373716 GCGTCCGTCTGGCTTTAATG 59.626 55.000 0.00 0.00 34.14 1.90
266 267 2.004583 CGTCCGTCTGGCTTTAATGA 57.995 50.000 0.00 0.00 34.14 2.57
267 268 2.343101 CGTCCGTCTGGCTTTAATGAA 58.657 47.619 0.00 0.00 34.14 2.57
268 269 2.348666 CGTCCGTCTGGCTTTAATGAAG 59.651 50.000 0.00 0.00 38.45 3.02
275 276 2.760650 CTGGCTTTAATGAAGGGGGAAC 59.239 50.000 0.00 0.00 35.82 3.62
283 284 1.346479 TGAAGGGGGAACGGTTGTCA 61.346 55.000 0.00 0.00 0.00 3.58
292 293 2.293399 GGAACGGTTGTCAAAGCTTCAT 59.707 45.455 0.00 0.00 0.00 2.57
295 296 4.385358 ACGGTTGTCAAAGCTTCATTTT 57.615 36.364 0.00 0.00 0.00 1.82
296 297 4.111916 ACGGTTGTCAAAGCTTCATTTTG 58.888 39.130 0.00 0.00 36.98 2.44
319 320 0.101579 GAGTAGGCTTCTCAGTCGCC 59.898 60.000 15.36 0.00 44.09 5.54
323 324 2.738521 GCTTCTCAGTCGCCGCAA 60.739 61.111 0.00 0.00 0.00 4.85
324 325 3.016474 GCTTCTCAGTCGCCGCAAC 62.016 63.158 0.00 0.00 0.00 4.17
327 328 2.486636 TTCTCAGTCGCCGCAACGAT 62.487 55.000 1.05 0.00 45.06 3.73
333 334 1.739929 TCGCCGCAACGATGTGAAT 60.740 52.632 7.91 0.00 39.48 2.57
334 335 1.580893 CGCCGCAACGATGTGAATG 60.581 57.895 7.91 0.00 39.48 2.67
335 336 1.501741 GCCGCAACGATGTGAATGT 59.498 52.632 7.91 0.00 39.48 2.71
344 345 2.607635 ACGATGTGAATGTCGTATTGGC 59.392 45.455 0.00 0.00 37.03 4.52
352 353 1.227556 GTCGTATTGGCGGATGGCT 60.228 57.895 0.00 0.00 42.94 4.75
354 355 0.753867 TCGTATTGGCGGATGGCTTA 59.246 50.000 0.00 0.00 42.94 3.09
392 393 1.784525 ACGAAGTTTTCCAGAGCGAG 58.215 50.000 0.00 0.00 37.78 5.03
423 424 1.145119 AGAGGGGTTTTGGGTGAGTTC 59.855 52.381 0.00 0.00 0.00 3.01
429 430 0.106918 TTTTGGGTGAGTTCGGTGCT 60.107 50.000 0.00 0.00 0.00 4.40
431 432 0.759959 TTGGGTGAGTTCGGTGCTTA 59.240 50.000 0.00 0.00 0.00 3.09
438 439 0.896226 AGTTCGGTGCTTAGGAGTCC 59.104 55.000 0.00 0.00 0.00 3.85
456 457 2.876879 CGTTGCGGCAGACGTTCAA 61.877 57.895 21.25 0.00 46.52 2.69
462 463 1.157870 CGGCAGACGTTCAAACTGGT 61.158 55.000 3.69 0.00 37.93 4.00
463 464 1.021968 GGCAGACGTTCAAACTGGTT 58.978 50.000 3.69 0.00 33.00 3.67
464 465 1.268539 GGCAGACGTTCAAACTGGTTG 60.269 52.381 0.00 0.00 38.71 3.77
485 486 2.879646 GGGACAATGTTTGTAACCGTCA 59.120 45.455 0.00 0.00 45.52 4.35
549 550 4.979335 TGAGGTTGATTTGGTGATACACA 58.021 39.130 0.00 0.00 35.86 3.72
558 559 6.493115 TGATTTGGTGATACACATTGGAGTTT 59.507 34.615 0.00 0.00 35.86 2.66
565 566 5.724370 TGATACACATTGGAGTTTCCCTAGA 59.276 40.000 0.00 0.00 35.03 2.43
626 629 2.090658 CGTGAGTACATGCTCGAAACAC 59.909 50.000 0.00 0.00 38.28 3.32
781 818 1.160137 CGAAACAGCAAGGAGAAGGG 58.840 55.000 0.00 0.00 0.00 3.95
896 2219 2.643551 CACTCTCCTCCACTCTCTCTC 58.356 57.143 0.00 0.00 0.00 3.20
899 2222 2.774234 CTCTCCTCCACTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
942 2265 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
943 2266 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1027 2424 3.963374 ACTGATTCATACAGCCAGCTAGA 59.037 43.478 0.00 0.00 38.74 2.43
1364 2873 2.595463 CCCATGGCTATGCACGGG 60.595 66.667 6.09 0.00 32.79 5.28
1576 3103 2.667418 CCAGGTGGAGGACTGCAG 59.333 66.667 13.48 13.48 37.39 4.41
1777 3692 2.229302 CTCCGTATAGCTTGGCTAGGTC 59.771 54.545 3.47 0.00 44.66 3.85
1778 3693 2.158505 TCCGTATAGCTTGGCTAGGTCT 60.159 50.000 3.47 0.00 44.66 3.85
1942 3922 3.994392 ACAAAACACTAGTCCATGTAGCG 59.006 43.478 0.00 0.00 0.00 4.26
1943 3923 4.242475 CAAAACACTAGTCCATGTAGCGA 58.758 43.478 0.00 0.00 0.00 4.93
2191 4232 2.887151 AAATACCCTCTGCTGCACTT 57.113 45.000 0.00 0.00 0.00 3.16
2928 4970 0.107703 TTCACTGATTGCGCCTAGGG 60.108 55.000 11.72 1.58 0.00 3.53
3146 5190 0.541863 AGAGTATCCAAACAGGGCCG 59.458 55.000 0.00 0.00 38.24 6.13
3195 5250 0.955428 CAGCGTTCTTTGGGCTAGCA 60.955 55.000 18.24 0.00 34.75 3.49
3721 8856 4.996758 TGCGATTGATCATCATTTATCGGT 59.003 37.500 20.77 0.00 36.37 4.69
4119 9382 6.182627 TGTAGATGTTGGATCTTGAGCATTT 58.817 36.000 0.00 0.00 0.00 2.32
4195 9460 3.839293 CGGAAGTGTTTTGTTTTCACCA 58.161 40.909 0.00 0.00 33.21 4.17
4202 9467 6.930731 AGTGTTTTGTTTTCACCAGTTACAT 58.069 32.000 0.00 0.00 33.21 2.29
4215 9488 0.172803 GTTACATGGCGAGGTCGAGT 59.827 55.000 2.94 0.00 43.02 4.18
4216 9489 0.172578 TTACATGGCGAGGTCGAGTG 59.827 55.000 2.94 0.96 43.02 3.51
4217 9490 2.279502 TACATGGCGAGGTCGAGTGC 62.280 60.000 2.94 0.00 43.02 4.40
4218 9491 3.381983 ATGGCGAGGTCGAGTGCA 61.382 61.111 2.94 0.00 43.02 4.57
4236 9516 1.740043 GCATGCTTTGGTGTATTGGGC 60.740 52.381 11.37 0.00 0.00 5.36
4277 10517 6.598064 GCATTGTACTAATTGTCACCCTTAGT 59.402 38.462 0.00 4.91 38.75 2.24
4284 10524 5.836024 AATTGTCACCCTTAGTACCTCAA 57.164 39.130 0.00 0.00 0.00 3.02
4288 10528 5.556915 TGTCACCCTTAGTACCTCAATTTG 58.443 41.667 0.00 0.00 0.00 2.32
4508 10944 4.579869 ACAATACTCTCAAACCGCTGAAT 58.420 39.130 0.00 0.00 0.00 2.57
4521 10957 0.810648 GCTGAATCAAATGGCACGGA 59.189 50.000 0.00 0.00 0.00 4.69
4538 10978 9.823647 ATGGCACGGAATTAGATTATTAGATAG 57.176 33.333 0.00 0.00 0.00 2.08
4561 11001 6.567050 AGGTAAGCTCGAAACATATACGAAA 58.433 36.000 0.00 0.00 35.70 3.46
4637 11077 9.872757 ACGCCTCAAACGTATATATTATTTTTG 57.127 29.630 0.00 0.00 43.02 2.44
4836 11276 0.895100 GGAAGAGCCATTGTGCCACA 60.895 55.000 0.00 0.00 36.34 4.17
4844 11284 2.406130 CCATTGTGCCACAAACATCAC 58.594 47.619 15.17 0.00 41.96 3.06
4846 11286 2.575694 TTGTGCCACAAACATCACAC 57.424 45.000 8.02 0.00 34.76 3.82
4929 11369 1.831736 CACCTAGACCTCCGTTCCATT 59.168 52.381 0.00 0.00 0.00 3.16
4942 11382 1.205893 GTTCCATTGCCTCTCGAGTCT 59.794 52.381 13.13 0.00 0.00 3.24
4943 11383 1.107114 TCCATTGCCTCTCGAGTCTC 58.893 55.000 13.13 3.12 0.00 3.36
4946 11386 0.736053 ATTGCCTCTCGAGTCTCGAC 59.264 55.000 20.85 11.71 44.82 4.20
4961 11401 1.198867 CTCGACGCCTCTGGATCTATG 59.801 57.143 0.00 0.00 0.00 2.23
4969 11409 4.615513 GCCTCTGGATCTATGTATACCCT 58.384 47.826 0.00 0.00 0.00 4.34
4984 11424 1.439543 ACCCTAGAATGCCTCCCATC 58.560 55.000 0.00 0.00 31.43 3.51
4991 11431 3.359950 AGAATGCCTCCCATCTTTCAAC 58.640 45.455 0.00 0.00 31.43 3.18
4999 11439 5.272402 CCTCCCATCTTTCAACCCTAATTT 58.728 41.667 0.00 0.00 0.00 1.82
5001 11441 6.127338 CCTCCCATCTTTCAACCCTAATTTTC 60.127 42.308 0.00 0.00 0.00 2.29
5005 11445 5.081315 TCTTTCAACCCTAATTTTCCCCA 57.919 39.130 0.00 0.00 0.00 4.96
5011 11451 5.247337 TCAACCCTAATTTTCCCCATTGTTC 59.753 40.000 0.00 0.00 0.00 3.18
5022 11462 2.635714 CCCATTGTTCGGGTTACCTAC 58.364 52.381 0.00 0.00 39.05 3.18
5025 11465 4.102054 CCCATTGTTCGGGTTACCTACTAT 59.898 45.833 0.00 0.00 39.05 2.12
5139 11579 5.743872 TGATCTTCACGACATTATTCACTCG 59.256 40.000 0.00 0.00 0.00 4.18
5140 11580 4.421058 TCTTCACGACATTATTCACTCGG 58.579 43.478 0.00 0.00 0.00 4.63
5143 11583 4.359706 TCACGACATTATTCACTCGGATG 58.640 43.478 0.00 0.00 0.00 3.51
5159 11599 2.009774 GGATGTCAACCATTCACTCGG 58.990 52.381 0.00 0.00 32.56 4.63
5176 11616 7.966246 TCACTCGGAAGTTATCTATCTACTC 57.034 40.000 0.00 0.00 31.71 2.59
5177 11617 6.645827 TCACTCGGAAGTTATCTATCTACTCG 59.354 42.308 0.00 0.00 31.71 4.18
5185 11625 5.124776 AGTTATCTATCTACTCGGATGCTGC 59.875 44.000 0.00 0.00 0.00 5.25
5187 11627 1.889170 CTATCTACTCGGATGCTGCCA 59.111 52.381 0.00 0.00 0.00 4.92
5201 11641 1.268743 GCTGCCAATTCATTCGGCTAC 60.269 52.381 5.45 0.00 46.39 3.58
5221 11661 2.439507 ACCATACCATCCACTTGGCTAG 59.560 50.000 0.00 0.00 40.68 3.42
5225 11665 1.524621 CATCCACTTGGCTAGCCCG 60.525 63.158 30.81 22.81 35.87 6.13
5247 11687 0.616111 AGCACTCGGACAAGGGAGAT 60.616 55.000 0.00 0.00 34.40 2.75
5248 11688 0.250513 GCACTCGGACAAGGGAGATT 59.749 55.000 0.00 0.00 34.40 2.40
5261 11701 2.106166 AGGGAGATTAAGAGCCAGCATG 59.894 50.000 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.204059 AGCAGAAGCCACCCCTCT 60.204 61.111 0.00 0.00 43.56 3.69
4 5 3.334054 GGAGCAGAAGCCACCCCT 61.334 66.667 0.00 0.00 43.56 4.79
5 6 3.334054 AGGAGCAGAAGCCACCCC 61.334 66.667 0.00 0.00 43.56 4.95
6 7 2.270527 GAGGAGCAGAAGCCACCC 59.729 66.667 0.00 0.00 43.56 4.61
9 10 0.619832 ATGAGGAGGAGCAGAAGCCA 60.620 55.000 0.00 0.00 43.56 4.75
47 48 1.067846 TGATTCCGACTGACGTCAAGG 60.068 52.381 20.49 21.13 40.23 3.61
54 55 1.757118 TCCTCCATGATTCCGACTGAC 59.243 52.381 0.00 0.00 0.00 3.51
56 57 1.069823 CCTCCTCCATGATTCCGACTG 59.930 57.143 0.00 0.00 0.00 3.51
59 60 1.748329 CGCCTCCTCCATGATTCCGA 61.748 60.000 0.00 0.00 0.00 4.55
64 65 3.564218 GCCCGCCTCCTCCATGAT 61.564 66.667 0.00 0.00 0.00 2.45
83 84 2.445654 GGGGGAGGAGGAGCTCTG 60.446 72.222 14.64 0.00 0.00 3.35
112 113 2.762459 CCCTGGTTCCGGATCCGA 60.762 66.667 35.42 18.23 42.83 4.55
143 144 2.202756 GAAGCCGTACGCCTCCAG 60.203 66.667 10.49 0.00 38.78 3.86
161 162 2.390599 CGGTTGTCGTGATGGGCAG 61.391 63.158 0.00 0.00 0.00 4.85
173 174 0.178941 ACACCTCTAGGACCGGTTGT 60.179 55.000 9.42 2.93 38.94 3.32
185 186 2.111878 GCACACCAGCACACCTCT 59.888 61.111 0.00 0.00 0.00 3.69
188 189 2.896801 CTTCGCACACCAGCACACC 61.897 63.158 0.00 0.00 0.00 4.16
212 213 0.622154 TCCTCCTCCTCTCTCGTCCT 60.622 60.000 0.00 0.00 0.00 3.85
217 218 2.070573 ACCCTATCCTCCTCCTCTCTC 58.929 57.143 0.00 0.00 0.00 3.20
218 219 2.238819 ACCCTATCCTCCTCCTCTCT 57.761 55.000 0.00 0.00 0.00 3.10
241 242 2.357034 GCCAGACGGACGCAGAAA 60.357 61.111 0.00 0.00 0.00 2.52
245 246 0.036765 ATTAAAGCCAGACGGACGCA 60.037 50.000 0.00 0.00 0.00 5.24
249 250 2.355716 CCCTTCATTAAAGCCAGACGGA 60.356 50.000 0.00 0.00 33.29 4.69
250 251 2.017049 CCCTTCATTAAAGCCAGACGG 58.983 52.381 0.00 0.00 33.29 4.79
265 266 0.179012 TTGACAACCGTTCCCCCTTC 60.179 55.000 0.00 0.00 0.00 3.46
266 267 0.259356 TTTGACAACCGTTCCCCCTT 59.741 50.000 0.00 0.00 0.00 3.95
267 268 0.179001 CTTTGACAACCGTTCCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
268 269 1.802337 GCTTTGACAACCGTTCCCCC 61.802 60.000 0.00 0.00 0.00 5.40
275 276 4.358851 TCAAAATGAAGCTTTGACAACCG 58.641 39.130 0.00 0.00 37.76 4.44
283 284 4.455877 CCTACTCCGTCAAAATGAAGCTTT 59.544 41.667 0.00 0.00 0.00 3.51
292 293 2.631062 TGAGAAGCCTACTCCGTCAAAA 59.369 45.455 0.00 0.00 33.95 2.44
295 296 1.271982 ACTGAGAAGCCTACTCCGTCA 60.272 52.381 0.00 0.00 33.95 4.35
296 297 1.402613 GACTGAGAAGCCTACTCCGTC 59.597 57.143 0.00 0.00 39.75 4.79
313 314 3.112075 CACATCGTTGCGGCGACT 61.112 61.111 12.98 0.00 43.99 4.18
319 320 3.188026 CGACATTCACATCGTTGCG 57.812 52.632 0.00 0.00 33.63 4.85
324 325 2.347568 CGCCAATACGACATTCACATCG 60.348 50.000 0.00 0.00 43.97 3.84
327 328 1.066787 TCCGCCAATACGACATTCACA 60.067 47.619 0.00 0.00 34.06 3.58
333 334 1.522806 GCCATCCGCCAATACGACA 60.523 57.895 0.00 0.00 34.06 4.35
334 335 0.814010 AAGCCATCCGCCAATACGAC 60.814 55.000 0.00 0.00 38.78 4.34
335 336 0.753867 TAAGCCATCCGCCAATACGA 59.246 50.000 0.00 0.00 38.78 3.43
352 353 5.414144 TCGTCACATTCATTTTGGCTGATAA 59.586 36.000 0.00 0.00 0.00 1.75
354 355 3.758023 TCGTCACATTCATTTTGGCTGAT 59.242 39.130 0.00 0.00 0.00 2.90
362 363 6.039270 TCTGGAAAACTTCGTCACATTCATTT 59.961 34.615 0.00 0.00 0.00 2.32
401 402 0.321653 CTCACCCAAAACCCCTCTCG 60.322 60.000 0.00 0.00 0.00 4.04
408 409 0.666374 CACCGAACTCACCCAAAACC 59.334 55.000 0.00 0.00 0.00 3.27
415 416 0.606604 TCCTAAGCACCGAACTCACC 59.393 55.000 0.00 0.00 0.00 4.02
423 424 0.736325 CAACGGACTCCTAAGCACCG 60.736 60.000 0.00 0.00 45.26 4.94
438 439 2.368131 TTTGAACGTCTGCCGCAACG 62.368 55.000 19.63 19.63 44.22 4.10
456 457 3.103742 ACAAACATTGTCCCAACCAGTT 58.896 40.909 0.00 0.00 40.56 3.16
462 463 3.288964 ACGGTTACAAACATTGTCCCAA 58.711 40.909 0.00 0.00 44.12 4.12
463 464 2.879646 GACGGTTACAAACATTGTCCCA 59.120 45.455 0.00 0.00 44.12 4.37
464 465 2.879646 TGACGGTTACAAACATTGTCCC 59.120 45.455 0.00 1.13 44.12 4.46
479 480 3.877508 GCTTTTAGCCATCTAATGACGGT 59.122 43.478 0.00 0.00 34.96 4.83
485 486 6.116126 ACTCGAAAGCTTTTAGCCATCTAAT 58.884 36.000 14.05 0.00 43.77 1.73
572 573 1.136147 CCCGAAGTGTCCGACGTAG 59.864 63.158 0.00 0.00 0.00 3.51
626 629 9.089601 TGTGCTTGCAAAATCTAAATATGATTG 57.910 29.630 0.00 0.00 34.74 2.67
781 818 4.467084 TGGACGAAGATGGCCGGC 62.467 66.667 21.18 21.18 0.00 6.13
896 2219 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
899 2222 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1027 2424 0.401738 TGGTTGGCTAAGCTTGCTCT 59.598 50.000 9.86 0.00 35.38 4.09
1032 2430 1.421646 AGTGAGTGGTTGGCTAAGCTT 59.578 47.619 13.36 3.48 35.38 3.74
1169 2663 3.785859 ATCATCGCGCCCTGGTGT 61.786 61.111 0.00 0.00 0.00 4.16
1485 3012 4.760047 ACGGGACCGCATGAGCAC 62.760 66.667 11.21 0.00 44.19 4.40
1769 3684 1.153269 GCCAAGCTGAGACCTAGCC 60.153 63.158 0.00 0.00 42.07 3.93
1942 3922 3.742882 GCCATGGAAAAGCTCTTGTTTTC 59.257 43.478 18.40 0.00 41.33 2.29
1943 3923 3.494924 GGCCATGGAAAAGCTCTTGTTTT 60.495 43.478 18.40 0.00 0.00 2.43
2173 4214 1.352352 ACAAGTGCAGCAGAGGGTATT 59.648 47.619 0.00 0.00 0.00 1.89
2183 4224 1.065854 AGGATGAGGTACAAGTGCAGC 60.066 52.381 0.00 0.00 0.00 5.25
2191 4232 0.535335 GTGCGGAAGGATGAGGTACA 59.465 55.000 0.00 0.00 0.00 2.90
2876 4918 1.671054 GTGAAGCCTAGCCGCAACA 60.671 57.895 0.00 0.00 0.00 3.33
2928 4970 3.743396 ACTTCACATCGCTCTTGAAGAAC 59.257 43.478 15.59 0.00 46.16 3.01
3146 5190 7.133891 TGGATCTCTTTTTCTTTTCGTGATC 57.866 36.000 0.00 0.00 0.00 2.92
3195 5250 1.973760 CAGTCTGGAGTCTGCAGCT 59.026 57.895 16.11 13.14 35.65 4.24
3742 8881 4.635765 GTGCTCAAAGCTGACCAATGTATA 59.364 41.667 0.11 0.00 42.97 1.47
3745 8884 1.610522 GTGCTCAAAGCTGACCAATGT 59.389 47.619 0.11 0.00 42.97 2.71
3751 8890 0.939577 TCGTCGTGCTCAAAGCTGAC 60.940 55.000 12.07 12.07 42.97 3.51
3883 9034 3.519973 CTGCTGCTGGTGGTCGTCA 62.520 63.158 0.00 0.00 0.00 4.35
4195 9460 0.456221 CTCGACCTCGCCATGTAACT 59.544 55.000 0.00 0.00 39.60 2.24
4202 9467 3.381983 ATGCACTCGACCTCGCCA 61.382 61.111 0.00 0.00 39.60 5.69
4215 9488 1.549620 CCCAATACACCAAAGCATGCA 59.450 47.619 21.98 0.00 0.00 3.96
4216 9489 1.740043 GCCCAATACACCAAAGCATGC 60.740 52.381 10.51 10.51 0.00 4.06
4217 9490 1.134729 GGCCCAATACACCAAAGCATG 60.135 52.381 0.00 0.00 0.00 4.06
4218 9491 1.194218 GGCCCAATACACCAAAGCAT 58.806 50.000 0.00 0.00 0.00 3.79
4236 9516 4.370917 ACAATGCTTTGTTGCTGTTTAGG 58.629 39.130 11.92 0.00 43.57 2.69
4267 10472 5.836024 ACAAATTGAGGTACTAAGGGTGA 57.164 39.130 0.00 0.00 41.55 4.02
4277 10517 6.833041 TCAAAGTCCACTACAAATTGAGGTA 58.167 36.000 0.00 0.00 0.00 3.08
4279 10519 5.997746 TCTCAAAGTCCACTACAAATTGAGG 59.002 40.000 14.10 0.00 41.29 3.86
4284 10524 9.574516 AAAACTATCTCAAAGTCCACTACAAAT 57.425 29.630 0.00 0.00 0.00 2.32
4288 10528 7.278203 GGCTAAAACTATCTCAAAGTCCACTAC 59.722 40.741 0.00 0.00 0.00 2.73
4371 10708 1.967319 TTCTGGAGGTTCTTGCACAC 58.033 50.000 0.00 0.00 0.00 3.82
4498 10934 1.067635 GTGCCATTTGATTCAGCGGTT 60.068 47.619 0.00 0.00 0.00 4.44
4501 10937 0.523968 CCGTGCCATTTGATTCAGCG 60.524 55.000 0.00 0.00 0.00 5.18
4508 10944 7.581213 AATAATCTAATTCCGTGCCATTTGA 57.419 32.000 0.00 0.00 0.00 2.69
4538 10978 6.254157 TGTTTCGTATATGTTTCGAGCTTACC 59.746 38.462 0.00 0.00 35.13 2.85
4594 11034 0.654160 CGTATCAGCCATGCACACAG 59.346 55.000 0.00 0.00 0.00 3.66
4705 11145 4.096382 GTGGGCACTGGATTAATGTGTTAG 59.904 45.833 0.00 0.00 34.52 2.34
4823 11263 1.270199 TGATGTTTGTGGCACAATGGC 60.270 47.619 31.51 23.31 44.16 4.40
4836 11276 0.251165 CCCCCTTCCGTGTGATGTTT 60.251 55.000 0.00 0.00 0.00 2.83
4889 11329 2.044053 CATGCACCGATGGGGGTT 60.044 61.111 0.00 0.00 39.73 4.11
4919 11359 1.218047 CGAGAGGCAATGGAACGGA 59.782 57.895 0.00 0.00 0.00 4.69
4942 11382 1.239347 CATAGATCCAGAGGCGTCGA 58.761 55.000 0.00 0.00 0.00 4.20
4943 11383 0.955178 ACATAGATCCAGAGGCGTCG 59.045 55.000 0.00 0.00 0.00 5.12
4946 11386 3.381908 GGGTATACATAGATCCAGAGGCG 59.618 52.174 5.01 0.00 0.00 5.52
4961 11401 3.517612 TGGGAGGCATTCTAGGGTATAC 58.482 50.000 0.00 0.00 0.00 1.47
4969 11409 4.526970 GTTGAAAGATGGGAGGCATTCTA 58.473 43.478 0.00 0.00 0.00 2.10
4984 11424 6.172630 CAATGGGGAAAATTAGGGTTGAAAG 58.827 40.000 0.00 0.00 0.00 2.62
4991 11431 3.132111 CCGAACAATGGGGAAAATTAGGG 59.868 47.826 0.00 0.00 0.00 3.53
5005 11445 4.102054 CCCATAGTAGGTAACCCGAACAAT 59.898 45.833 0.00 0.00 35.12 2.71
5022 11462 5.595885 CATGTCTTGTGACTCTACCCATAG 58.404 45.833 0.00 0.00 43.29 2.23
5025 11465 2.028112 GCATGTCTTGTGACTCTACCCA 60.028 50.000 0.00 0.00 43.29 4.51
5139 11579 2.009774 CCGAGTGAATGGTTGACATCC 58.990 52.381 0.00 0.00 39.40 3.51
5140 11580 2.972625 TCCGAGTGAATGGTTGACATC 58.027 47.619 0.00 0.00 39.40 3.06
5143 11583 2.767505 ACTTCCGAGTGAATGGTTGAC 58.232 47.619 0.00 0.00 33.99 3.18
5159 11599 7.247728 CAGCATCCGAGTAGATAGATAACTTC 58.752 42.308 0.00 0.00 0.00 3.01
5176 11616 1.598676 CGAATGAATTGGCAGCATCCG 60.599 52.381 0.00 0.00 0.00 4.18
5177 11617 1.269413 CCGAATGAATTGGCAGCATCC 60.269 52.381 0.00 0.00 0.00 3.51
5185 11625 3.502211 GGTATGGTAGCCGAATGAATTGG 59.498 47.826 0.00 0.00 0.00 3.16
5187 11627 4.431416 TGGTATGGTAGCCGAATGAATT 57.569 40.909 0.00 0.00 0.00 2.17
5201 11641 2.811873 GCTAGCCAAGTGGATGGTATGG 60.812 54.545 2.29 0.00 42.75 2.74
5225 11665 2.743928 CCTTGTCCGAGTGCTGGC 60.744 66.667 0.00 0.00 0.00 4.85
5229 11669 0.250513 AATCTCCCTTGTCCGAGTGC 59.749 55.000 0.00 0.00 0.00 4.40
5237 11677 2.092699 GCTGGCTCTTAATCTCCCTTGT 60.093 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.