Multiple sequence alignment - TraesCS2D01G228000

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 TraesCS2D01G228000 chr2D 100.000 5591 0 0 1 5591 196706656 196712246 0.000000e+00 10325
1 TraesCS2D01G228000 chr2B 97.052 2544 58 8 743 3274 254129868 254132406 0.000000e+00 4266
2 TraesCS2D01G228000 chr2B 95.731 1429 31 9 3329 4740 254132410 254133825 0.000000e+00 2274
3 TraesCS2D01G228000 chr2B 82.340 453 33 18 322 748 254124757 254125188 3.210000e-92 350
4 TraesCS2D01G228000 chr2B 89.216 204 22 0 1 204 254124035 254124238 7.190000e-64 255
5 TraesCS2D01G228000 chr2B 92.553 94 4 1 3280 3370 354879125 354879218 1.260000e-26 132
6 TraesCS2D01G228000 chr2B 90.526 95 4 2 4911 5005 254140138 254140227 2.740000e-23 121
7 TraesCS2D01G228000 chr2A 97.145 2487 36 13 886 3360 212898559 212901022 0.000000e+00 4167
8 TraesCS2D01G228000 chr2A 96.761 1482 27 9 3324 4801 212901022 212902486 0.000000e+00 2451
9 TraesCS2D01G228000 chr2A 87.013 924 85 19 1 892 212897323 212898243 0.000000e+00 1009
10 TraesCS2D01G228000 chr2A 79.815 649 90 20 1 615 382230617 382229976 8.600000e-118 435
11 TraesCS2D01G228000 chr2A 93.617 94 3 1 3280 3370 361381703 361381610 2.720000e-28 137
12 TraesCS2D01G228000 chr2A 90.476 105 3 5 4813 4912 196210219 196210117 1.260000e-26 132
13 TraesCS2D01G228000 chr2A 95.181 83 4 0 4923 5005 212902485 212902567 1.260000e-26 132
14 TraesCS2D01G228000 chr5A 90.203 592 24 15 5027 5591 113601293 113600709 0.000000e+00 741
15 TraesCS2D01G228000 chr5A 81.766 351 41 15 150 480 44971858 44972205 7.140000e-69 272
16 TraesCS2D01G228000 chr7A 86.851 616 40 18 5005 5591 583543527 583542924 0.000000e+00 651
17 TraesCS2D01G228000 chr7A 89.254 335 10 12 5280 5591 714911939 714912270 4.060000e-106 396
18 TraesCS2D01G228000 chr7A 81.149 435 55 20 58 470 72858840 72859269 1.940000e-84 324
19 TraesCS2D01G228000 chr7A 80.920 435 56 20 58 470 72821250 72821679 9.040000e-83 318
20 TraesCS2D01G228000 chr6A 89.011 455 28 8 5152 5591 10139321 10139768 1.370000e-150 544
21 TraesCS2D01G228000 chr4B 82.198 646 78 19 3 615 541127063 541127704 6.420000e-144 521
22 TraesCS2D01G228000 chr4B 78.187 353 50 21 151 481 184925958 184926305 3.420000e-47 200
23 TraesCS2D01G228000 chr4B 87.379 103 9 2 4824 4922 351875010 351875112 1.270000e-21 115
24 TraesCS2D01G228000 chr4D 81.579 646 84 17 1 614 437926234 437926876 8.360000e-138 501
25 TraesCS2D01G228000 chr4D 78.560 653 98 21 1 615 472705040 472705688 5.250000e-105 392
26 TraesCS2D01G228000 chr4D 92.553 94 3 2 3278 3368 64347447 64347355 1.260000e-26 132
27 TraesCS2D01G228000 chr5D 81.579 570 73 17 72 615 448344187 448343624 5.140000e-120 442
28 TraesCS2D01G228000 chr5D 79.943 349 43 20 153 477 112905368 112905023 1.210000e-56 231
29 TraesCS2D01G228000 chr5D 79.037 353 45 21 153 481 109547717 109547370 1.220000e-51 215
30 TraesCS2D01G228000 chr5D 95.402 87 2 1 3278 3362 482013902 482013988 2.720000e-28 137
31 TraesCS2D01G228000 chr6B 78.199 633 92 29 3 598 594436482 594437105 4.120000e-96 363
32 TraesCS2D01G228000 chr6B 80.672 238 44 2 67 304 484111469 484111704 3.440000e-42 183
33 TraesCS2D01G228000 chr7D 78.741 588 85 27 63 615 67095168 67094586 1.920000e-94 357
34 TraesCS2D01G228000 chr7D 82.432 148 21 3 66 213 334759276 334759418 2.110000e-24 124
35 TraesCS2D01G228000 chr7D 87.255 102 8 3 4828 4925 622185061 622185161 1.650000e-20 111
36 TraesCS2D01G228000 chr1D 79.535 430 60 18 72 481 367635340 367634919 1.190000e-71 281
37 TraesCS2D01G228000 chr1D 76.274 569 93 25 67 603 494432641 494433199 1.190000e-66 265
38 TraesCS2D01G228000 chr1D 78.450 413 54 13 234 613 231471825 231471415 2.600000e-58 237
39 TraesCS2D01G228000 chr1D 84.615 143 18 4 149 288 45510848 45510989 7.550000e-29 139
40 TraesCS2D01G228000 chr1D 93.617 94 2 2 3275 3364 206040976 206041069 2.720000e-28 137
41 TraesCS2D01G228000 chr1B 75.571 569 100 21 67 603 687660067 687660628 1.560000e-60 244
42 TraesCS2D01G228000 chr1B 90.217 92 6 1 4828 4916 142723454 142723545 3.540000e-22 117
43 TraesCS2D01G228000 chr1A 76.291 523 80 30 116 603 593249864 593250377 7.240000e-59 239
44 TraesCS2D01G228000 chr7B 81.553 309 36 13 186 477 627909017 627909321 9.360000e-58 235
45 TraesCS2D01G228000 chr7B 93.684 95 3 2 3278 3369 348195808 348195902 7.550000e-29 139
46 TraesCS2D01G228000 chr7B 93.478 92 2 2 3280 3368 639796199 639796289 3.510000e-27 134
47 TraesCS2D01G228000 chr7B 90.909 99 5 3 3278 3372 348170313 348170215 4.550000e-26 130
48 TraesCS2D01G228000 chr5B 81.609 261 30 11 238 481 270207312 270207571 3.420000e-47 200
49 TraesCS2D01G228000 chr3D 81.818 209 35 3 68 275 470492923 470492717 7.450000e-39 172
50 TraesCS2D01G228000 chr6D 79.399 233 32 11 265 481 399562198 399561966 3.490000e-32 150
51 TraesCS2D01G228000 chr6D 87.255 102 10 2 4814 4912 305158089 305158190 4.580000e-21 113
52 TraesCS2D01G228000 chr3B 88.350 103 8 2 4828 4926 8855108 8855210 2.740000e-23 121
53 TraesCS2D01G228000 chr3B 90.217 92 6 3 4823 4912 452724744 452724654 3.540000e-22 117
54 TraesCS2D01G228000 chr3B 85.321 109 10 4 4827 4931 678709875 678709769 2.130000e-19 108
55 TraesCS2D01G228000 chr3A 88.889 99 6 3 4820 4913 38015392 38015490 3.540000e-22 117


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 TraesCS2D01G228000 chr2D 196706656 196712246 5590 False 10325.00 10325 100.0000 1 5591 1 chr2D.!!$F1 5590
1 TraesCS2D01G228000 chr2B 254129868 254133825 3957 False 3270.00 4266 96.3915 743 4740 2 chr2B.!!$F4 3997
2 TraesCS2D01G228000 chr2B 254124035 254125188 1153 False 302.50 350 85.7780 1 748 2 chr2B.!!$F3 747
3 TraesCS2D01G228000 chr2A 212897323 212902567 5244 False 1939.75 4167 94.0250 1 5005 4 chr2A.!!$F1 5004
4 TraesCS2D01G228000 chr2A 382229976 382230617 641 True 435.00 435 79.8150 1 615 1 chr2A.!!$R3 614
5 TraesCS2D01G228000 chr5A 113600709 113601293 584 True 741.00 741 90.2030 5027 5591 1 chr5A.!!$R1 564
6 TraesCS2D01G228000 chr7A 583542924 583543527 603 True 651.00 651 86.8510 5005 5591 1 chr7A.!!$R1 586
7 TraesCS2D01G228000 chr4B 541127063 541127704 641 False 521.00 521 82.1980 3 615 1 chr4B.!!$F3 612
8 TraesCS2D01G228000 chr4D 437926234 437926876 642 False 501.00 501 81.5790 1 614 1 chr4D.!!$F1 613
9 TraesCS2D01G228000 chr4D 472705040 472705688 648 False 392.00 392 78.5600 1 615 1 chr4D.!!$F2 614
10 TraesCS2D01G228000 chr5D 448343624 448344187 563 True 442.00 442 81.5790 72 615 1 chr5D.!!$R3 543
11 TraesCS2D01G228000 chr6B 594436482 594437105 623 False 363.00 363 78.1990 3 598 1 chr6B.!!$F2 595
12 TraesCS2D01G228000 chr7D 67094586 67095168 582 True 357.00 357 78.7410 63 615 1 chr7D.!!$R1 552
13 TraesCS2D01G228000 chr1D 494432641 494433199 558 False 265.00 265 76.2740 67 603 1 chr1D.!!$F3 536
14 TraesCS2D01G228000 chr1B 687660067 687660628 561 False 244.00 244 75.5710 67 603 1 chr1B.!!$F2 536
15 TraesCS2D01G228000 chr1A 593249864 593250377 513 False 239.00 239 76.2910 116 603 1 chr1A.!!$F1 487

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
844 1373 0.743345 GCCACGAAATACGCCTTCCT 60.743 55.0 0.00 0.00 46.94 3.36 F
1783 2639 0.108709 TCGTTAAGCGCACGGGTATT 60.109 50.0 17.23 0.04 41.07 1.89 F
3129 3992 0.106708 TGTTCGAAAGGTCAGCAGCT 59.893 50.0 0.00 0.00 0.00 4.24 F
3878 4783 0.620030 TGCCTGGCACTGATACACAT 59.380 50.0 19.30 0.00 31.71 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 3335 0.238289 CACGCACACACATTCCTTCC 59.762 55.000 0.0 0.0 0.0 3.46 R
3234 4097 0.468648 AACCGCCTAATGTCTAGCCC 59.531 55.000 0.0 0.0 0.0 5.19 R
4438 5355 1.806542 CATGTTCTGGTTTCTGTCGGG 59.193 52.381 0.0 0.0 0.0 5.14 R
5436 6425 0.690077 GGGGTAGGTACAGACAGGGG 60.690 65.000 0.0 0.0 0.0 4.79 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
138 143 8.257830 TCTGTCTAGAACTACTATATGATGCG 57.742 38.462 0.00 0.00 0.00 4.73
214 224 3.257469 TCTGCATAGAGCCTTGAACTG 57.743 47.619 0.00 0.00 44.83 3.16
263 274 5.256474 ACAAGATTCCAAGTGAACTATGGG 58.744 41.667 10.04 2.17 35.31 4.00
353 808 3.256631 GGAGTGACTTACGTAGGGTTTCA 59.743 47.826 9.70 1.26 0.00 2.69
416 887 8.641499 TTATCAAGATTTGCTTTTGTTTTCGT 57.359 26.923 0.00 0.00 33.60 3.85
421 892 6.533185 AGATTTGCTTTTGTTTTCGTTTGTG 58.467 32.000 0.00 0.00 0.00 3.33
491 990 4.711846 TGGCTAGAGTCTGCTTTCTGAATA 59.288 41.667 1.86 0.00 0.00 1.75
502 1001 6.707608 TCTGCTTTCTGAATAATGCGATGTAT 59.292 34.615 0.00 0.00 33.47 2.29
572 1087 5.484173 TGATTCATTTAGACGTTGGCATC 57.516 39.130 0.00 0.00 0.00 3.91
585 1100 1.960417 TGGCATCGAAACACACAGAA 58.040 45.000 0.00 0.00 0.00 3.02
598 1113 1.086696 CACAGAAACCGTATGCCTGG 58.913 55.000 0.00 0.00 0.00 4.45
617 1133 1.461888 GGAAAAATGAGTCGTGACGCG 60.462 52.381 3.53 3.53 43.01 6.01
689 1205 1.677820 CCGAAGGCATTCCCGTAAAGT 60.678 52.381 5.38 0.00 46.14 2.66
715 1234 4.875561 AACTATATTTCCGCCTCTCTCC 57.124 45.455 0.00 0.00 0.00 3.71
774 1296 2.301870 AGCAAAACACATCCCGTCTCTA 59.698 45.455 0.00 0.00 0.00 2.43
776 1298 3.864921 GCAAAACACATCCCGTCTCTACT 60.865 47.826 0.00 0.00 0.00 2.57
795 1317 2.682893 GCTATGTGAGCCACGAAGG 58.317 57.895 0.00 0.00 46.41 3.46
844 1373 0.743345 GCCACGAAATACGCCTTCCT 60.743 55.000 0.00 0.00 46.94 3.36
861 1391 6.422701 CGCCTTCCTGATTGATTTACGTATTA 59.577 38.462 0.00 0.00 0.00 0.98
892 1744 6.463472 GGGGATAACGCTATATATGGGGTTAC 60.463 46.154 28.91 23.12 44.74 2.50
896 1748 8.782339 ATAACGCTATATATGGGGTTACAAAC 57.218 34.615 28.91 0.00 44.74 2.93
953 1806 1.630148 CACGCCTTCTAGAACCTTCG 58.370 55.000 0.00 5.39 0.00 3.79
1041 1896 1.740718 GCTCTAGCTAAGCAAAGCCGT 60.741 52.381 17.62 0.00 43.86 5.68
1783 2639 0.108709 TCGTTAAGCGCACGGGTATT 60.109 50.000 17.23 0.04 41.07 1.89
2354 3210 0.392998 ACTTTATGTGCCCTCCAGCG 60.393 55.000 0.00 0.00 34.65 5.18
2405 3261 1.067354 CCTTCTGTGGAAATTGGCAGC 60.067 52.381 0.00 0.00 0.00 5.25
2413 3269 1.139163 GAAATTGGCAGCGGTGTTTG 58.861 50.000 17.07 0.00 0.00 2.93
2487 3343 8.960591 CACTTGTCATAGTAAAATGGAAGGAAT 58.039 33.333 0.00 0.00 0.00 3.01
2488 3344 8.960591 ACTTGTCATAGTAAAATGGAAGGAATG 58.039 33.333 0.00 0.00 0.00 2.67
2643 3499 8.370940 TGATTACAGGGCATATTTTTGAAACAA 58.629 29.630 0.00 0.00 0.00 2.83
3129 3992 0.106708 TGTTCGAAAGGTCAGCAGCT 59.893 50.000 0.00 0.00 0.00 4.24
3234 4097 5.240891 TCAGGTGAGCTTTTAGAATGAGTG 58.759 41.667 0.00 0.00 0.00 3.51
3245 4108 5.957771 TTAGAATGAGTGGGCTAGACATT 57.042 39.130 0.00 0.00 34.55 2.71
3306 4169 8.358895 ACTCCCTACGTAAAGAAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
3307 4170 7.365741 TCCCTACGTAAAGAAATATAAGAGCG 58.634 38.462 0.00 0.00 0.00 5.03
3308 4171 7.013655 TCCCTACGTAAAGAAATATAAGAGCGT 59.986 37.037 0.00 0.00 0.00 5.07
3309 4172 7.650903 CCCTACGTAAAGAAATATAAGAGCGTT 59.349 37.037 0.00 0.00 0.00 4.84
3310 4173 9.028185 CCTACGTAAAGAAATATAAGAGCGTTT 57.972 33.333 0.00 0.00 0.00 3.60
3361 4263 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
3753 4658 6.432783 TGAAATAAATCCACAGGTCAATCGTT 59.567 34.615 0.00 0.00 0.00 3.85
3877 4782 2.065483 TGCCTGGCACTGATACACA 58.935 52.632 19.30 0.00 31.71 3.72
3878 4783 0.620030 TGCCTGGCACTGATACACAT 59.380 50.000 19.30 0.00 31.71 3.21
3879 4784 1.836802 TGCCTGGCACTGATACACATA 59.163 47.619 19.30 0.00 31.71 2.29
3880 4785 2.439135 TGCCTGGCACTGATACACATAT 59.561 45.455 19.30 0.00 31.71 1.78
3881 4786 2.810274 GCCTGGCACTGATACACATATG 59.190 50.000 15.17 0.00 0.00 1.78
3919 4836 5.647658 TCGACGAGTATGTCCCTTTAACTTA 59.352 40.000 0.00 0.00 35.40 2.24
3920 4837 5.741040 CGACGAGTATGTCCCTTTAACTTAC 59.259 44.000 0.00 0.00 35.40 2.34
4438 5355 1.445238 GACGACAGTGGCTCAGAGC 60.445 63.158 14.69 14.69 41.46 4.09
4528 5445 2.514592 GCGATGCAGCTAAGGGCA 60.515 61.111 0.00 0.00 45.23 5.36
4605 5522 2.670509 CGACTAAACTTCCGGGTCTGAC 60.671 54.545 0.00 0.00 0.00 3.51
4773 5706 3.856206 AGACTTCCCTATTTGGCCCTTTA 59.144 43.478 0.00 0.00 0.00 1.85
4801 5736 1.602440 TGCTTCCCTATTTGGCCCTA 58.398 50.000 0.00 0.00 0.00 3.53
4802 5737 2.143602 TGCTTCCCTATTTGGCCCTAT 58.856 47.619 0.00 0.00 0.00 2.57
4803 5738 2.108250 TGCTTCCCTATTTGGCCCTATC 59.892 50.000 0.00 0.00 0.00 2.08
4804 5739 2.876079 GCTTCCCTATTTGGCCCTATCG 60.876 54.545 0.00 0.00 0.00 2.92
4805 5740 0.690762 TCCCTATTTGGCCCTATCGC 59.309 55.000 0.00 0.00 0.00 4.58
4812 5747 2.119832 GGCCCTATCGCCCTCCTA 59.880 66.667 0.00 0.00 43.66 2.94
4813 5748 1.306226 GGCCCTATCGCCCTCCTAT 60.306 63.158 0.00 0.00 43.66 2.57
4814 5749 1.331399 GGCCCTATCGCCCTCCTATC 61.331 65.000 0.00 0.00 43.66 2.08
4815 5750 0.614979 GCCCTATCGCCCTCCTATCA 60.615 60.000 0.00 0.00 0.00 2.15
4816 5751 1.967274 GCCCTATCGCCCTCCTATCAT 60.967 57.143 0.00 0.00 0.00 2.45
4817 5752 2.690026 GCCCTATCGCCCTCCTATCATA 60.690 54.545 0.00 0.00 0.00 2.15
4818 5753 2.959707 CCCTATCGCCCTCCTATCATAC 59.040 54.545 0.00 0.00 0.00 2.39
4819 5754 3.627492 CCCTATCGCCCTCCTATCATACA 60.627 52.174 0.00 0.00 0.00 2.29
4820 5755 4.219115 CCTATCGCCCTCCTATCATACAT 58.781 47.826 0.00 0.00 0.00 2.29
4821 5756 4.279671 CCTATCGCCCTCCTATCATACATC 59.720 50.000 0.00 0.00 0.00 3.06
4822 5757 3.169512 TCGCCCTCCTATCATACATCA 57.830 47.619 0.00 0.00 0.00 3.07
4823 5758 3.713003 TCGCCCTCCTATCATACATCAT 58.287 45.455 0.00 0.00 0.00 2.45
4824 5759 4.867086 TCGCCCTCCTATCATACATCATA 58.133 43.478 0.00 0.00 0.00 2.15
4825 5760 5.269189 TCGCCCTCCTATCATACATCATAA 58.731 41.667 0.00 0.00 0.00 1.90
4826 5761 5.127194 TCGCCCTCCTATCATACATCATAAC 59.873 44.000 0.00 0.00 0.00 1.89
4827 5762 5.105351 CGCCCTCCTATCATACATCATAACA 60.105 44.000 0.00 0.00 0.00 2.41
4828 5763 6.407412 CGCCCTCCTATCATACATCATAACAT 60.407 42.308 0.00 0.00 0.00 2.71
4829 5764 6.989169 GCCCTCCTATCATACATCATAACATC 59.011 42.308 0.00 0.00 0.00 3.06
4830 5765 7.147585 GCCCTCCTATCATACATCATAACATCT 60.148 40.741 0.00 0.00 0.00 2.90
4831 5766 9.426534 CCCTCCTATCATACATCATAACATCTA 57.573 37.037 0.00 0.00 0.00 1.98
4837 5772 8.907829 ATCATACATCATAACATCTACTCCCT 57.092 34.615 0.00 0.00 0.00 4.20
4838 5773 8.354711 TCATACATCATAACATCTACTCCCTC 57.645 38.462 0.00 0.00 0.00 4.30
4839 5774 8.173412 TCATACATCATAACATCTACTCCCTCT 58.827 37.037 0.00 0.00 0.00 3.69
4840 5775 6.662865 ACATCATAACATCTACTCCCTCTG 57.337 41.667 0.00 0.00 0.00 3.35
4841 5776 6.139671 ACATCATAACATCTACTCCCTCTGT 58.860 40.000 0.00 0.00 0.00 3.41
4842 5777 6.266558 ACATCATAACATCTACTCCCTCTGTC 59.733 42.308 0.00 0.00 0.00 3.51
4843 5778 6.019656 TCATAACATCTACTCCCTCTGTCT 57.980 41.667 0.00 0.00 0.00 3.41
4844 5779 6.436027 TCATAACATCTACTCCCTCTGTCTT 58.564 40.000 0.00 0.00 0.00 3.01
4845 5780 7.583625 TCATAACATCTACTCCCTCTGTCTTA 58.416 38.462 0.00 0.00 0.00 2.10
4846 5781 8.228206 TCATAACATCTACTCCCTCTGTCTTAT 58.772 37.037 0.00 0.00 0.00 1.73
4847 5782 9.521841 CATAACATCTACTCCCTCTGTCTTATA 57.478 37.037 0.00 0.00 0.00 0.98
4856 5791 8.937207 ACTCCCTCTGTCTTATATAATAACGT 57.063 34.615 0.00 0.00 0.00 3.99
4857 5792 9.364653 ACTCCCTCTGTCTTATATAATAACGTT 57.635 33.333 5.88 5.88 0.00 3.99
4903 5838 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
4904 5839 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
4905 5840 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
4906 5841 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
4907 5842 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
4908 5843 6.294899 CGTTCTTATATTATGGGACGGAGGAA 60.295 42.308 0.00 0.00 0.00 3.36
4909 5844 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
4910 5845 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
4911 5846 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
4912 5847 7.951806 TCTTATATTATGGGACGGAGGAAGTAA 59.048 37.037 0.00 0.00 0.00 2.24
4913 5848 8.495160 TTATATTATGGGACGGAGGAAGTAAA 57.505 34.615 0.00 0.00 0.00 2.01
4914 5849 5.703730 ATTATGGGACGGAGGAAGTAAAA 57.296 39.130 0.00 0.00 0.00 1.52
4915 5850 5.703730 TTATGGGACGGAGGAAGTAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
4916 5851 4.586306 ATGGGACGGAGGAAGTAAAATT 57.414 40.909 0.00 0.00 0.00 1.82
4917 5852 4.376225 TGGGACGGAGGAAGTAAAATTT 57.624 40.909 0.00 0.00 0.00 1.82
4918 5853 5.502089 TGGGACGGAGGAAGTAAAATTTA 57.498 39.130 0.00 0.00 0.00 1.40
4919 5854 5.247862 TGGGACGGAGGAAGTAAAATTTAC 58.752 41.667 7.75 7.75 0.00 2.01
4920 5855 5.013391 TGGGACGGAGGAAGTAAAATTTACT 59.987 40.000 12.24 12.24 0.00 2.24
4921 5856 6.213195 TGGGACGGAGGAAGTAAAATTTACTA 59.787 38.462 17.58 0.00 0.00 1.82
4922 5857 6.536582 GGGACGGAGGAAGTAAAATTTACTAC 59.463 42.308 17.58 13.62 0.00 2.73
4923 5858 7.326454 GGACGGAGGAAGTAAAATTTACTACT 58.674 38.462 17.58 17.42 0.00 2.57
4924 5859 7.490725 GGACGGAGGAAGTAAAATTTACTACTC 59.509 40.741 25.84 25.84 34.09 2.59
4925 5860 7.899973 ACGGAGGAAGTAAAATTTACTACTCA 58.100 34.615 29.98 0.00 35.34 3.41
4959 5894 7.550196 CCATATTAATTGATGCTAATTTGGCCC 59.450 37.037 0.00 0.00 33.06 5.80
4978 5913 5.542251 TGGCCCTTTAAAATATATGCTTCCC 59.458 40.000 0.00 0.00 0.00 3.97
5009 5944 5.469084 GTCCTAGCCCTTTATAAAATGGACG 59.531 44.000 14.65 4.77 32.78 4.79
5012 5947 3.883489 AGCCCTTTATAAAATGGACGCTC 59.117 43.478 14.65 0.93 32.78 5.03
5018 5953 6.018180 CCTTTATAAAATGGACGCTCCTACAC 60.018 42.308 0.00 0.00 37.46 2.90
5072 6007 1.450025 CGGCAGTTAAGGAAAGTCCC 58.550 55.000 0.00 0.00 37.19 4.46
5217 6192 3.941188 CACCCGTCCCACAGCAGT 61.941 66.667 0.00 0.00 0.00 4.40
5457 6446 0.338814 CCTGTCTGTACCTACCCCCT 59.661 60.000 0.00 0.00 0.00 4.79
5458 6447 1.486211 CTGTCTGTACCTACCCCCTG 58.514 60.000 0.00 0.00 0.00 4.45
5459 6448 1.006758 CTGTCTGTACCTACCCCCTGA 59.993 57.143 0.00 0.00 0.00 3.86
5460 6449 1.649633 TGTCTGTACCTACCCCCTGAT 59.350 52.381 0.00 0.00 0.00 2.90
5461 6450 2.317973 GTCTGTACCTACCCCCTGATC 58.682 57.143 0.00 0.00 0.00 2.92
5462 6451 2.091222 GTCTGTACCTACCCCCTGATCT 60.091 54.545 0.00 0.00 0.00 2.75
5463 6452 3.139770 GTCTGTACCTACCCCCTGATCTA 59.860 52.174 0.00 0.00 0.00 1.98
5470 6459 4.602732 ACCTACCCCCTGATCTACTACTAG 59.397 50.000 0.00 0.00 0.00 2.57
5560 6549 0.613777 CCCTTCACACCTGTAGACCC 59.386 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 27 3.694043 AGCTTTTCTTCAGAGACCCTC 57.306 47.619 0.00 0.00 0.00 4.30
36 38 1.681264 CGGTTGTCCCAAGCTTTTCTT 59.319 47.619 0.00 0.00 34.78 2.52
138 143 9.750783 TGGTCTACTCTAATAGTTGGATATACC 57.249 37.037 0.00 0.00 39.80 2.73
184 190 6.934048 AGGCTCTATGCAGAAAAATAGTTC 57.066 37.500 0.00 0.00 45.15 3.01
214 224 2.023223 CGTGCATTTTGGCTGGTGC 61.023 57.895 0.00 0.00 38.05 5.01
263 274 7.225523 CAATACTTTGAATGTATTGGCAAGC 57.774 36.000 24.77 1.69 46.40 4.01
353 808 1.153289 GCATGTCGAGTGGAGGCAT 60.153 57.895 0.00 0.00 33.73 4.40
416 887 8.602328 CAATAAGCAAACAAAGTTCATCACAAA 58.398 29.630 0.00 0.00 0.00 2.83
421 892 9.677567 TCTTACAATAAGCAAACAAAGTTCATC 57.322 29.630 0.00 0.00 0.00 2.92
491 990 3.874543 TGCGTCCTTTAATACATCGCATT 59.125 39.130 5.29 0.00 45.25 3.56
557 1071 3.059461 GTGTTTCGATGCCAACGTCTAAA 60.059 43.478 0.00 0.00 0.00 1.85
572 1087 3.794536 CATACGGTTTCTGTGTGTTTCG 58.205 45.455 0.00 0.00 0.00 3.46
585 1100 3.426615 TCATTTTTCCAGGCATACGGTT 58.573 40.909 0.00 0.00 0.00 4.44
617 1133 4.034510 CCATGTCCTTCGTTAAGCTTCATC 59.965 45.833 0.00 0.00 0.00 2.92
618 1134 3.941483 CCATGTCCTTCGTTAAGCTTCAT 59.059 43.478 0.00 0.00 0.00 2.57
652 1168 1.202710 TCGGGCTAGCTTTGTTCACAA 60.203 47.619 15.72 0.00 0.00 3.33
715 1234 5.167845 CGGGGATGTGTTTTTATTTTGAGG 58.832 41.667 0.00 0.00 0.00 3.86
795 1317 2.033194 GGTACGTGCTGTTCCTGGC 61.033 63.158 3.01 0.00 35.28 4.85
844 1373 7.283580 CCCCCAAAGTAATACGTAAATCAATCA 59.716 37.037 0.00 0.00 0.00 2.57
861 1391 6.352737 CCATATATAGCGTTATCCCCCAAAGT 60.353 42.308 0.00 0.00 0.00 2.66
892 1744 3.051606 CACGACTGGTGTTCTTGTTTG 57.948 47.619 0.00 0.00 41.89 2.93
953 1806 2.607038 GGGTTTTGCGGAAAGTGATGTC 60.607 50.000 1.41 0.00 0.00 3.06
1024 1879 0.375106 GCACGGCTTTGCTTAGCTAG 59.625 55.000 5.60 4.21 40.99 3.42
1157 2012 1.645034 CACTACATCTCGTGCCCTTG 58.355 55.000 0.00 0.00 0.00 3.61
1512 2368 4.393062 AGTCAAGATGTAAGAAATGCGTGG 59.607 41.667 0.00 0.00 0.00 4.94
1783 2639 3.988379 ATGCGTTCTTTTTCTTGCTCA 57.012 38.095 0.00 0.00 0.00 4.26
2354 3210 5.427036 TTTTGTTCCTTAACGACATGACC 57.573 39.130 0.00 0.00 38.53 4.02
2405 3261 7.346208 AGAAAAGAAAAGAAAACAAACACCG 57.654 32.000 0.00 0.00 0.00 4.94
2413 3269 8.033038 ACAGTACCCAAGAAAAGAAAAGAAAAC 58.967 33.333 0.00 0.00 0.00 2.43
2472 3328 4.923281 GCACACACATTCCTTCCATTTTAC 59.077 41.667 0.00 0.00 0.00 2.01
2479 3335 0.238289 CACGCACACACATTCCTTCC 59.762 55.000 0.00 0.00 0.00 3.46
2487 3343 1.470494 ACACATTTTCACGCACACACA 59.530 42.857 0.00 0.00 0.00 3.72
2488 3344 1.845568 CACACATTTTCACGCACACAC 59.154 47.619 0.00 0.00 0.00 3.82
2695 3551 5.375417 TCATACACAAATTTGACCTGCAG 57.625 39.130 24.64 6.78 0.00 4.41
3234 4097 0.468648 AACCGCCTAATGTCTAGCCC 59.531 55.000 0.00 0.00 0.00 5.19
3245 4108 1.961394 CAGCTATGGTAGAACCGCCTA 59.039 52.381 0.00 0.00 42.58 3.93
3287 4150 9.793252 TCTAAACGCTCTTATATTTCTTTACGT 57.207 29.630 0.00 0.00 0.00 3.57
3303 4166 7.155858 GATCAAAGTAGTGATCTAAACGCTC 57.844 40.000 7.73 0.00 46.97 5.03
3753 4658 4.287845 AGGTCCATCATCTGCAAGCATATA 59.712 41.667 0.00 0.00 0.00 0.86
3899 4816 8.543862 AAAAGTAAGTTAAAGGGACATACTCG 57.456 34.615 0.00 0.00 32.26 4.18
3927 4844 2.804986 TACAAGGAGCATGCCATGAA 57.195 45.000 15.66 0.00 31.38 2.57
4227 5144 3.928727 ATGTGAGTTTCAAGCCACATG 57.071 42.857 0.00 0.00 45.29 3.21
4438 5355 1.806542 CATGTTCTGGTTTCTGTCGGG 59.193 52.381 0.00 0.00 0.00 5.14
4528 5445 3.764466 CTGCGCGAGAAGGTCCCT 61.764 66.667 12.10 0.00 31.05 4.20
4605 5522 3.115556 CACCAACACCCAACACCG 58.884 61.111 0.00 0.00 0.00 4.94
4659 5592 4.322574 GGAGAGTTCACTAACCTACAACCC 60.323 50.000 0.00 0.00 36.15 4.11
4698 5631 6.095440 GGAAACCATACAGTAGCACATCAATT 59.905 38.462 0.00 0.00 0.00 2.32
4699 5632 5.590259 GGAAACCATACAGTAGCACATCAAT 59.410 40.000 0.00 0.00 0.00 2.57
4801 5736 3.713003 TGATGTATGATAGGAGGGCGAT 58.287 45.455 0.00 0.00 0.00 4.58
4802 5737 3.169512 TGATGTATGATAGGAGGGCGA 57.830 47.619 0.00 0.00 0.00 5.54
4803 5738 5.105351 TGTTATGATGTATGATAGGAGGGCG 60.105 44.000 0.00 0.00 0.00 6.13
4804 5739 6.299805 TGTTATGATGTATGATAGGAGGGC 57.700 41.667 0.00 0.00 0.00 5.19
4805 5740 8.316497 AGATGTTATGATGTATGATAGGAGGG 57.684 38.462 0.00 0.00 0.00 4.30
4811 5746 9.997172 AGGGAGTAGATGTTATGATGTATGATA 57.003 33.333 0.00 0.00 0.00 2.15
4812 5747 8.907829 AGGGAGTAGATGTTATGATGTATGAT 57.092 34.615 0.00 0.00 0.00 2.45
4813 5748 8.173412 AGAGGGAGTAGATGTTATGATGTATGA 58.827 37.037 0.00 0.00 0.00 2.15
4814 5749 8.249638 CAGAGGGAGTAGATGTTATGATGTATG 58.750 40.741 0.00 0.00 0.00 2.39
4815 5750 7.952930 ACAGAGGGAGTAGATGTTATGATGTAT 59.047 37.037 0.00 0.00 0.00 2.29
4816 5751 7.298374 ACAGAGGGAGTAGATGTTATGATGTA 58.702 38.462 0.00 0.00 0.00 2.29
4817 5752 6.139671 ACAGAGGGAGTAGATGTTATGATGT 58.860 40.000 0.00 0.00 0.00 3.06
4818 5753 6.493115 AGACAGAGGGAGTAGATGTTATGATG 59.507 42.308 0.00 0.00 0.00 3.07
4819 5754 6.619464 AGACAGAGGGAGTAGATGTTATGAT 58.381 40.000 0.00 0.00 0.00 2.45
4820 5755 6.019656 AGACAGAGGGAGTAGATGTTATGA 57.980 41.667 0.00 0.00 0.00 2.15
4821 5756 6.723298 AAGACAGAGGGAGTAGATGTTATG 57.277 41.667 0.00 0.00 0.00 1.90
4831 5766 8.937207 ACGTTATTATATAAGACAGAGGGAGT 57.063 34.615 1.02 0.00 0.00 3.85
4878 5813 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
4879 5814 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
4880 5815 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
4881 5816 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
4882 5817 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
4883 5818 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
4884 5819 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
4885 5820 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
4886 5821 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
4887 5822 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
4888 5823 8.495160 TTTACTTCCTCCGTCCCATAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
4889 5824 8.495160 TTTTACTTCCTCCGTCCCATAATATA 57.505 34.615 0.00 0.00 0.00 0.86
4890 5825 7.383156 TTTTACTTCCTCCGTCCCATAATAT 57.617 36.000 0.00 0.00 0.00 1.28
4891 5826 6.811634 TTTTACTTCCTCCGTCCCATAATA 57.188 37.500 0.00 0.00 0.00 0.98
4892 5827 5.703730 TTTTACTTCCTCCGTCCCATAAT 57.296 39.130 0.00 0.00 0.00 1.28
4893 5828 5.703730 ATTTTACTTCCTCCGTCCCATAA 57.296 39.130 0.00 0.00 0.00 1.90
4894 5829 5.703730 AATTTTACTTCCTCCGTCCCATA 57.296 39.130 0.00 0.00 0.00 2.74
4895 5830 4.586306 AATTTTACTTCCTCCGTCCCAT 57.414 40.909 0.00 0.00 0.00 4.00
4896 5831 4.376225 AAATTTTACTTCCTCCGTCCCA 57.624 40.909 0.00 0.00 0.00 4.37
4897 5832 5.494724 AGTAAATTTTACTTCCTCCGTCCC 58.505 41.667 14.66 0.00 0.00 4.46
4898 5833 7.326454 AGTAGTAAATTTTACTTCCTCCGTCC 58.674 38.462 23.06 5.03 0.00 4.79
4899 5834 8.031277 TGAGTAGTAAATTTTACTTCCTCCGTC 58.969 37.037 26.18 16.97 30.58 4.79
4900 5835 7.816513 GTGAGTAGTAAATTTTACTTCCTCCGT 59.183 37.037 26.18 11.82 30.58 4.69
4901 5836 8.033626 AGTGAGTAGTAAATTTTACTTCCTCCG 58.966 37.037 26.18 0.00 30.58 4.63
4902 5837 9.722184 AAGTGAGTAGTAAATTTTACTTCCTCC 57.278 33.333 26.18 21.26 30.58 4.30
4954 5889 5.542251 GGGAAGCATATATTTTAAAGGGCCA 59.458 40.000 6.18 0.00 0.00 5.36
4978 5913 8.990163 TTTTATAAAGGGCTAGGACCAAATAG 57.010 34.615 0.00 0.00 29.21 1.73
5048 5983 3.615509 TTCCTTAACTGCCGGCCGG 62.616 63.158 40.26 40.26 38.57 6.13
5436 6425 0.690077 GGGGTAGGTACAGACAGGGG 60.690 65.000 0.00 0.00 0.00 4.79
5457 6446 8.932945 CAATTTCTGCAACTAGTAGTAGATCA 57.067 34.615 11.68 5.15 0.00 2.92
5489 6478 4.700213 CCAGGTTCTGAAACAATTCGGTAT 59.300 41.667 8.34 0.00 41.77 2.73
5560 6549 4.558095 GCAGCCATTTTATGTAGCATCCAG 60.558 45.833 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.