Multiple sequence alignment - TraesCS3D01G412900

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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 TraesCS3D01G412900 chr3D 100.000 4772 0 0 1 4772 525539715 525534944 0.000000e+00 8813.0
1 TraesCS3D01G412900 chr3D 86.383 918 93 15 2912 3806 525640429 525639521 0.000000e+00 974.0
2 TraesCS3D01G412900 chr3D 83.790 839 89 29 1529 2356 525641650 525640848 0.000000e+00 752.0
3 TraesCS3D01G412900 chr3D 88.129 497 51 5 1745 2234 525634702 525634207 6.880000e-163 584.0
4 TraesCS3D01G412900 chr3D 84.483 406 43 10 3284 3679 525632650 525632255 2.690000e-102 383.0
5 TraesCS3D01G412900 chr3D 85.976 328 17 16 1210 1515 525635021 525634701 1.660000e-84 324.0
6 TraesCS3D01G412900 chr3D 80.000 425 76 4 140 563 580120573 580120989 6.000000e-79 305.0
7 TraesCS3D01G412900 chr3D 78.108 539 67 22 854 1375 525642658 525642154 1.300000e-75 294.0
8 TraesCS3D01G412900 chr3D 82.692 312 42 2 2906 3211 525632962 525632657 2.830000e-67 267.0
9 TraesCS3D01G412900 chr3D 78.772 391 75 7 136 525 450261261 450261644 6.130000e-64 255.0
10 TraesCS3D01G412900 chr3D 80.473 338 58 6 134 470 173396760 173396430 7.930000e-63 252.0
11 TraesCS3D01G412900 chr3D 81.544 298 49 4 183 480 364403053 364402762 1.720000e-59 241.0
12 TraesCS3D01G412900 chr3D 87.417 151 11 4 3730 3872 525632138 525631988 2.950000e-37 167.0
13 TraesCS3D01G412900 chr3D 84.211 133 18 1 991 1120 525635149 525635017 5.010000e-25 126.0
14 TraesCS3D01G412900 chr3D 83.088 136 21 1 1 134 529501476 529501611 6.490000e-24 122.0
15 TraesCS3D01G412900 chr3D 90.566 53 5 0 572 624 285108927 285108875 2.380000e-08 71.3
16 TraesCS3D01G412900 chr3D 89.796 49 4 1 593 641 523448251 523448204 1.430000e-05 62.1
17 TraesCS3D01G412900 chr3B 91.984 4179 236 52 1 4112 693471344 693467198 0.000000e+00 5770.0
18 TraesCS3D01G412900 chr3B 85.714 903 98 13 2906 3786 693645982 693645089 0.000000e+00 924.0
19 TraesCS3D01G412900 chr3B 83.814 902 95 31 1416 2292 693736964 693736089 0.000000e+00 809.0
20 TraesCS3D01G412900 chr3B 83.886 844 97 24 1398 2228 693647313 693646496 0.000000e+00 769.0
21 TraesCS3D01G412900 chr3B 90.034 592 49 4 4190 4772 533719998 533720588 0.000000e+00 758.0
22 TraesCS3D01G412900 chr3B 86.213 573 57 7 1783 2355 693601671 693601121 6.830000e-168 601.0
23 TraesCS3D01G412900 chr3B 79.937 638 93 22 3284 3901 693598656 693598034 2.040000e-118 436.0
24 TraesCS3D01G412900 chr3B 76.545 874 99 42 854 1663 693737835 693737004 9.690000e-102 381.0
25 TraesCS3D01G412900 chr3B 85.196 331 41 3 2906 3229 693728929 693728600 2.750000e-87 333.0
26 TraesCS3D01G412900 chr3B 83.121 314 39 4 2906 3211 693598970 693598663 1.690000e-69 274.0
27 TraesCS3D01G412900 chr3B 85.897 234 20 9 1210 1437 693602278 693602052 2.220000e-58 237.0
28 TraesCS3D01G412900 chr3B 80.435 322 42 10 1067 1375 693649630 693649317 4.810000e-55 226.0
29 TraesCS3D01G412900 chr3B 84.906 212 23 6 3669 3872 693726287 693726077 6.260000e-49 206.0
30 TraesCS3D01G412900 chr3B 88.591 149 15 2 3753 3900 693645042 693644895 3.790000e-41 180.0
31 TraesCS3D01G412900 chr3B 81.955 133 21 1 991 1120 693602406 693602274 5.050000e-20 110.0
32 TraesCS3D01G412900 chr3A 93.812 3103 112 22 1124 4190 659624552 659621494 0.000000e+00 4593.0
33 TraesCS3D01G412900 chr3A 82.383 965 111 37 1416 2356 659858087 659857158 0.000000e+00 785.0
34 TraesCS3D01G412900 chr3A 85.588 680 83 10 3287 3953 659822291 659821614 0.000000e+00 699.0
35 TraesCS3D01G412900 chr3A 84.603 617 67 14 1745 2356 659803243 659802650 5.320000e-164 588.0
36 TraesCS3D01G412900 chr3A 86.744 347 34 5 3284 3620 659801158 659800814 4.510000e-100 375.0
37 TraesCS3D01G412900 chr3A 93.162 234 15 1 895 1128 659630805 659630573 4.570000e-90 342.0
38 TraesCS3D01G412900 chr3A 83.841 328 24 15 1210 1515 659803562 659803242 7.820000e-73 285.0
39 TraesCS3D01G412900 chr3A 75.772 615 106 24 134 723 1646920 1646324 2.190000e-68 270.0
40 TraesCS3D01G412900 chr3A 81.818 319 39 8 2906 3211 659801477 659801165 2.850000e-62 250.0
41 TraesCS3D01G412900 chr3A 80.460 348 44 8 2906 3229 659822654 659822307 1.330000e-60 244.0
42 TraesCS3D01G412900 chr3A 86.408 206 19 6 3730 3926 659800647 659800442 2.890000e-52 217.0
43 TraesCS3D01G412900 chr3A 85.385 130 19 0 991 1120 659803687 659803558 8.330000e-28 135.0
44 TraesCS3D01G412900 chr2A 91.047 592 48 4 4186 4772 78669139 78669730 0.000000e+00 795.0
45 TraesCS3D01G412900 chr2A 87.892 223 21 5 2648 2864 42472436 42472658 1.700000e-64 257.0
46 TraesCS3D01G412900 chr2A 75.723 519 92 19 134 641 657060365 657059870 3.710000e-56 230.0
47 TraesCS3D01G412900 chr2D 90.772 596 45 6 4186 4772 205270078 205270672 0.000000e+00 787.0
48 TraesCS3D01G412900 chr2D 89.922 258 21 5 2637 2891 37610176 37610431 1.280000e-85 327.0
49 TraesCS3D01G412900 chr2D 78.834 326 62 5 132 457 622388609 622388291 3.740000e-51 213.0
50 TraesCS3D01G412900 chr2D 75.967 362 61 15 295 641 356729407 356729057 3.820000e-36 163.0
51 TraesCS3D01G412900 chr2D 84.167 120 15 3 1 117 607307102 607306984 3.900000e-21 113.0
52 TraesCS3D01G412900 chr2D 86.486 74 9 1 568 641 481303678 481303606 3.960000e-11 80.5
53 TraesCS3D01G412900 chr2D 87.324 71 5 1 4040 4110 280649430 280649364 1.420000e-10 78.7
54 TraesCS3D01G412900 chr1D 90.971 587 47 4 4189 4772 202765816 202765233 0.000000e+00 785.0
55 TraesCS3D01G412900 chr1D 90.101 596 50 4 4186 4772 440430298 440430893 0.000000e+00 765.0
56 TraesCS3D01G412900 chr1D 90.051 593 50 5 4189 4772 257257480 257256888 0.000000e+00 760.0
57 TraesCS3D01G412900 chr1D 78.032 437 72 14 209 640 458283919 458283502 2.200000e-63 254.0
58 TraesCS3D01G412900 chr1D 75.547 548 91 27 125 651 453184745 453185270 3.710000e-56 230.0
59 TraesCS3D01G412900 chr1D 85.938 128 14 3 1 125 365549495 365549621 3.000000e-27 134.0
60 TraesCS3D01G412900 chr1D 83.942 137 18 3 1 134 470652091 470652226 1.390000e-25 128.0
61 TraesCS3D01G412900 chr1D 86.957 69 9 0 573 641 493731883 493731815 1.420000e-10 78.7
62 TraesCS3D01G412900 chr2B 90.355 591 49 6 4189 4772 600917098 600916509 0.000000e+00 769.0
63 TraesCS3D01G412900 chr2B 78.738 602 102 13 132 720 14314247 14313659 3.490000e-101 379.0
64 TraesCS3D01G412900 chr2B 77.068 532 83 16 140 651 410998392 410998904 2.190000e-68 270.0
65 TraesCS3D01G412900 chr2B 82.031 128 21 1 3 128 773826026 773826153 1.820000e-19 108.0
66 TraesCS3D01G412900 chr2B 79.412 136 11 7 1 134 159102260 159102380 3.960000e-11 80.5
67 TraesCS3D01G412900 chr2B 85.915 71 6 1 4040 4110 326681361 326681427 6.620000e-09 73.1
68 TraesCS3D01G412900 chr4A 90.219 593 51 5 4186 4772 118900849 118901440 0.000000e+00 767.0
69 TraesCS3D01G412900 chr6D 89.966 588 54 4 4189 4772 172025707 172025121 0.000000e+00 754.0
70 TraesCS3D01G412900 chr6D 77.077 349 64 10 134 480 341150058 341149724 2.270000e-43 187.0
71 TraesCS3D01G412900 chr6D 86.061 165 23 0 316 480 447094492 447094328 1.360000e-40 178.0
72 TraesCS3D01G412900 chr6D 90.566 53 4 1 4039 4090 445421221 445421169 8.570000e-08 69.4
73 TraesCS3D01G412900 chr7D 76.772 663 94 33 1 641 31407757 31407133 2.770000e-82 316.0
74 TraesCS3D01G412900 chr7D 85.271 129 15 3 1 126 547482819 547482692 3.880000e-26 130.0
75 TraesCS3D01G412900 chr7D 78.736 174 21 9 571 731 100874922 100874752 8.450000e-18 102.0
76 TraesCS3D01G412900 chr7D 87.143 70 9 0 572 641 138512237 138512306 3.960000e-11 80.5
77 TraesCS3D01G412900 chr7D 88.333 60 5 2 567 625 578622409 578622351 2.380000e-08 71.3
78 TraesCS3D01G412900 chr7D 84.058 69 11 0 573 641 470272142 470272210 3.080000e-07 67.6
79 TraesCS3D01G412900 chr5D 77.234 470 73 15 188 641 483724212 483724663 1.330000e-60 244.0
80 TraesCS3D01G412900 chr5D 94.000 50 2 1 4042 4090 188826619 188826570 1.840000e-09 75.0
81 TraesCS3D01G412900 chr1A 86.266 233 20 4 2639 2869 131291847 131291625 4.770000e-60 243.0
82 TraesCS3D01G412900 chr7B 85.000 220 32 1 288 506 708730672 708730891 6.220000e-54 222.0
83 TraesCS3D01G412900 chr7B 93.220 59 2 2 583 641 643029833 643029777 8.510000e-13 86.1
84 TraesCS3D01G412900 chr7B 93.103 58 4 0 572 629 741881172 741881229 8.510000e-13 86.1
85 TraesCS3D01G412900 chr7B 79.845 129 15 9 502 629 741934285 741934403 3.060000e-12 84.2
86 TraesCS3D01G412900 chr7B 82.353 68 12 0 572 639 494245322 494245389 5.160000e-05 60.2
87 TraesCS3D01G412900 chr4D 78.529 340 55 15 140 473 446648743 446648416 1.740000e-49 207.0
88 TraesCS3D01G412900 chr4D 78.491 265 41 10 209 473 418361876 418361628 4.940000e-35 159.0
89 TraesCS3D01G412900 chr4D 78.210 257 40 9 209 464 418385794 418385553 2.970000e-32 150.0
90 TraesCS3D01G412900 chr4D 77.652 264 42 11 210 473 418362133 418361887 1.380000e-30 145.0
91 TraesCS3D01G412900 chr4D 82.317 164 26 3 310 473 418359755 418359595 6.440000e-29 139.0
92 TraesCS3D01G412900 chr4D 82.609 138 18 4 226 363 494254736 494254605 3.020000e-22 117.0
93 TraesCS3D01G412900 chr4D 96.364 55 1 1 4034 4087 6207648 6207702 6.580000e-14 89.8
94 TraesCS3D01G412900 chr4D 93.878 49 3 0 4034 4082 440036062 440036014 1.840000e-09 75.0
95 TraesCS3D01G412900 chr4D 77.083 144 23 8 500 641 464791477 464791342 1.840000e-09 75.0
96 TraesCS3D01G412900 chr5A 85.950 121 13 3 19 136 28649913 28650032 5.010000e-25 126.0
97 TraesCS3D01G412900 chrUn 90.323 62 5 1 4051 4112 137678223 137678163 3.960000e-11 80.5
98 TraesCS3D01G412900 chr6A 83.750 80 12 1 572 651 540842800 540842722 1.840000e-09 75.0
99 TraesCS3D01G412900 chr6A 82.857 70 12 0 572 641 617255025 617254956 3.990000e-06 63.9


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 TraesCS3D01G412900 chr3D 525534944 525539715 4771 True 8813.000000 8813 100.000000 1 4772 1 chr3D.!!$R5 4771
1 TraesCS3D01G412900 chr3D 525639521 525642658 3137 True 673.333333 974 82.760333 854 3806 3 chr3D.!!$R7 2952
2 TraesCS3D01G412900 chr3D 525631988 525635149 3161 True 308.500000 584 85.484667 991 3872 6 chr3D.!!$R6 2881
3 TraesCS3D01G412900 chr3B 693467198 693471344 4146 True 5770.000000 5770 91.984000 1 4112 1 chr3B.!!$R1 4111
4 TraesCS3D01G412900 chr3B 533719998 533720588 590 False 758.000000 758 90.034000 4190 4772 1 chr3B.!!$F1 582
5 TraesCS3D01G412900 chr3B 693736089 693737835 1746 True 595.000000 809 80.179500 854 2292 2 chr3B.!!$R5 1438
6 TraesCS3D01G412900 chr3B 693644895 693649630 4735 True 524.750000 924 84.656500 1067 3900 4 chr3B.!!$R3 2833
7 TraesCS3D01G412900 chr3B 693598034 693602406 4372 True 331.600000 601 83.424600 991 3901 5 chr3B.!!$R2 2910
8 TraesCS3D01G412900 chr3B 693726077 693728929 2852 True 269.500000 333 85.051000 2906 3872 2 chr3B.!!$R4 966
9 TraesCS3D01G412900 chr3A 659621494 659624552 3058 True 4593.000000 4593 93.812000 1124 4190 1 chr3A.!!$R2 3066
10 TraesCS3D01G412900 chr3A 659857158 659858087 929 True 785.000000 785 82.383000 1416 2356 1 chr3A.!!$R4 940
11 TraesCS3D01G412900 chr3A 659821614 659822654 1040 True 471.500000 699 83.024000 2906 3953 2 chr3A.!!$R6 1047
12 TraesCS3D01G412900 chr3A 659800442 659803687 3245 True 308.333333 588 84.799833 991 3926 6 chr3A.!!$R5 2935
13 TraesCS3D01G412900 chr3A 1646324 1646920 596 True 270.000000 270 75.772000 134 723 1 chr3A.!!$R1 589
14 TraesCS3D01G412900 chr2A 78669139 78669730 591 False 795.000000 795 91.047000 4186 4772 1 chr2A.!!$F2 586
15 TraesCS3D01G412900 chr2D 205270078 205270672 594 False 787.000000 787 90.772000 4186 4772 1 chr2D.!!$F2 586
16 TraesCS3D01G412900 chr1D 202765233 202765816 583 True 785.000000 785 90.971000 4189 4772 1 chr1D.!!$R1 583
17 TraesCS3D01G412900 chr1D 440430298 440430893 595 False 765.000000 765 90.101000 4186 4772 1 chr1D.!!$F2 586
18 TraesCS3D01G412900 chr1D 257256888 257257480 592 True 760.000000 760 90.051000 4189 4772 1 chr1D.!!$R2 583
19 TraesCS3D01G412900 chr1D 453184745 453185270 525 False 230.000000 230 75.547000 125 651 1 chr1D.!!$F3 526
20 TraesCS3D01G412900 chr2B 600916509 600917098 589 True 769.000000 769 90.355000 4189 4772 1 chr2B.!!$R2 583
21 TraesCS3D01G412900 chr2B 14313659 14314247 588 True 379.000000 379 78.738000 132 720 1 chr2B.!!$R1 588
22 TraesCS3D01G412900 chr2B 410998392 410998904 512 False 270.000000 270 77.068000 140 651 1 chr2B.!!$F3 511
23 TraesCS3D01G412900 chr4A 118900849 118901440 591 False 767.000000 767 90.219000 4186 4772 1 chr4A.!!$F1 586
24 TraesCS3D01G412900 chr6D 172025121 172025707 586 True 754.000000 754 89.966000 4189 4772 1 chr6D.!!$R1 583
25 TraesCS3D01G412900 chr7D 31407133 31407757 624 True 316.000000 316 76.772000 1 641 1 chr7D.!!$R1 640

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
476 504 0.037590 AGGACAGAGCGAGAGAGTGT 59.962 55.000 0.0 0.0 0.00 3.55 F
480 516 0.179166 CAGAGCGAGAGAGTGTGAGC 60.179 60.000 0.0 0.0 0.00 4.26 F
481 517 0.322456 AGAGCGAGAGAGTGTGAGCT 60.322 55.000 0.0 0.0 37.69 4.09 F
1592 3759 0.480690 TCTTGCCCCCTAAACAAGCA 59.519 50.000 0.0 0.0 40.45 3.91 F
1611 3779 1.800586 CAGAGCTTTGCTTCGCTACAA 59.199 47.619 0.0 0.0 39.88 2.41 F
2902 7536 1.066573 ACCCTGAGCATCTTGAAGTCG 60.067 52.381 0.0 0.0 34.92 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 3641 1.133790 AGCTTTGCAATCGATGAAGCC 59.866 47.619 22.02 11.5 38.84 4.35 R
2007 4323 2.672996 AACCATGAGCGGCACACC 60.673 61.111 1.29 0.0 0.00 4.16 R
2419 4810 2.746362 CAGCTGTCCTTTGAACCTCATC 59.254 50.000 5.25 0.0 0.00 2.92 R
2500 6302 0.037590 TTGGCCATAAGCGACCTGTT 59.962 50.000 6.09 0.0 45.17 3.16 R
3267 7939 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.0 0.00 4.30 R
4356 11153 0.603569 CTCTAGACAGTGCCCAACGT 59.396 55.000 0.00 0.0 0.00 3.99 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
27 28 4.139234 GACCGGCGGTAGACCCAC 62.139 72.222 34.29 14.24 35.25 4.61
29 30 3.467226 CCGGCGGTAGACCCACAT 61.467 66.667 19.97 0.00 0.00 3.21
61 64 4.415150 TCGTACGGGTCCGCCTCT 62.415 66.667 16.52 0.00 44.19 3.69
114 120 3.311110 GTCCCTCTCCCGTGCACA 61.311 66.667 18.64 0.00 0.00 4.57
177 197 0.749454 GCCCATGTTGAGGAGCGAAT 60.749 55.000 0.00 0.00 0.00 3.34
178 198 1.475034 GCCCATGTTGAGGAGCGAATA 60.475 52.381 0.00 0.00 0.00 1.75
201 224 2.115291 GGAAAGGAGATGGCACGGC 61.115 63.158 0.00 0.00 0.00 5.68
305 329 2.356313 CTGGAGCTGCGACAACGT 60.356 61.111 0.00 0.00 41.98 3.99
324 348 1.198094 TTCCAGATCCGGAGTTGCCA 61.198 55.000 11.34 0.00 36.12 4.92
405 429 0.731417 GCTCGGAGCTGTAGTCGTTA 59.269 55.000 22.32 0.00 38.45 3.18
406 430 1.334243 GCTCGGAGCTGTAGTCGTTAT 59.666 52.381 22.32 0.00 38.45 1.89
435 459 5.595885 CTGGACATCGTAGTTGATGAGATT 58.404 41.667 10.45 0.00 46.98 2.40
474 502 0.618458 AGAGGACAGAGCGAGAGAGT 59.382 55.000 0.00 0.00 0.00 3.24
476 504 0.037590 AGGACAGAGCGAGAGAGTGT 59.962 55.000 0.00 0.00 0.00 3.55
480 516 0.179166 CAGAGCGAGAGAGTGTGAGC 60.179 60.000 0.00 0.00 0.00 4.26
481 517 0.322456 AGAGCGAGAGAGTGTGAGCT 60.322 55.000 0.00 0.00 37.69 4.09
492 545 1.837051 TGTGAGCTGGGTTCGGAGT 60.837 57.895 0.00 0.00 0.00 3.85
533 588 3.534357 TTTTGTGGGACATATGTGGGT 57.466 42.857 14.43 0.00 44.52 4.51
594 666 2.978010 GCCGCCCCATATTCACCG 60.978 66.667 0.00 0.00 0.00 4.94
651 723 1.202054 CGGACGTTTGTTCACGGTTTT 60.202 47.619 0.00 0.00 44.82 2.43
693 775 4.988716 AGTGACCGGACGGCCTGA 62.989 66.667 9.46 0.00 39.32 3.86
694 776 3.771160 GTGACCGGACGGCCTGAT 61.771 66.667 9.46 0.00 39.32 2.90
702 784 2.125512 ACGGCCTGATCAAGCGTC 60.126 61.111 10.13 0.00 0.00 5.19
720 802 0.900421 TCTGAGACGGGTACGAGAGA 59.100 55.000 0.00 0.00 44.60 3.10
735 826 2.428890 CGAGAGACCTGGCTCTAATTGT 59.571 50.000 16.98 0.00 44.92 2.71
747 838 9.396022 CCTGGCTCTAATTGTCTATTTTCTTTA 57.604 33.333 0.00 0.00 0.00 1.85
768 860 9.325198 TCTTTACGATTTAATATCACTGTGCAT 57.675 29.630 2.12 0.80 0.00 3.96
771 863 9.715123 TTACGATTTAATATCACTGTGCATTTG 57.285 29.630 2.12 0.00 0.00 2.32
772 864 7.984391 ACGATTTAATATCACTGTGCATTTGA 58.016 30.769 2.12 0.00 0.00 2.69
773 865 8.124823 ACGATTTAATATCACTGTGCATTTGAG 58.875 33.333 2.12 0.00 0.00 3.02
774 866 7.588854 CGATTTAATATCACTGTGCATTTGAGG 59.411 37.037 2.12 0.00 0.00 3.86
798 914 4.614535 GCAGCAGATCGACACATTTTCTTT 60.615 41.667 0.00 0.00 0.00 2.52
799 915 5.084722 CAGCAGATCGACACATTTTCTTTC 58.915 41.667 0.00 0.00 0.00 2.62
800 916 4.999950 AGCAGATCGACACATTTTCTTTCT 59.000 37.500 0.00 0.00 0.00 2.52
801 917 5.471456 AGCAGATCGACACATTTTCTTTCTT 59.529 36.000 0.00 0.00 0.00 2.52
802 918 6.650807 AGCAGATCGACACATTTTCTTTCTTA 59.349 34.615 0.00 0.00 0.00 2.10
803 919 7.335422 AGCAGATCGACACATTTTCTTTCTTAT 59.665 33.333 0.00 0.00 0.00 1.73
804 920 7.427606 GCAGATCGACACATTTTCTTTCTTATG 59.572 37.037 0.00 0.00 0.00 1.90
872 988 1.226746 CTTCTCGTTCCAAACCGCTT 58.773 50.000 0.00 0.00 0.00 4.68
937 1055 3.232279 CAAGGGTTTGGGGTTTGGA 57.768 52.632 0.00 0.00 0.00 3.53
986 1104 4.500545 CCCGATCTGATTGACCTAGAGTTG 60.501 50.000 6.46 0.00 0.00 3.16
1086 1230 3.706373 GGCAACAGGGAGGAGCGA 61.706 66.667 0.00 0.00 0.00 4.93
1107 1251 3.127533 GCGTTCCTGCCAATCGCT 61.128 61.111 0.00 0.00 42.88 4.93
1452 3601 7.290014 GGTAAATCATAATTTGGGGGATTCAGT 59.710 37.037 0.00 0.00 35.84 3.41
1480 3634 7.068702 TGATAAGGGTGGATTGATTTGCTAAT 58.931 34.615 0.00 0.00 0.00 1.73
1483 3637 7.732222 AAGGGTGGATTGATTTGCTAATTTA 57.268 32.000 0.00 0.00 0.00 1.40
1484 3638 7.732222 AGGGTGGATTGATTTGCTAATTTAA 57.268 32.000 0.00 0.00 0.00 1.52
1486 3640 8.771286 AGGGTGGATTGATTTGCTAATTTAATT 58.229 29.630 0.00 0.00 0.00 1.40
1487 3641 8.829612 GGGTGGATTGATTTGCTAATTTAATTG 58.170 33.333 0.00 0.00 0.00 2.32
1489 3643 8.337532 GTGGATTGATTTGCTAATTTAATTGGC 58.662 33.333 17.21 17.21 45.65 4.52
1592 3759 0.480690 TCTTGCCCCCTAAACAAGCA 59.519 50.000 0.00 0.00 40.45 3.91
1611 3779 1.800586 CAGAGCTTTGCTTCGCTACAA 59.199 47.619 0.00 0.00 39.88 2.41
1622 3790 3.522553 CTTCGCTACAACCTCCCTAAAG 58.477 50.000 0.00 0.00 0.00 1.85
1626 3794 4.040706 TCGCTACAACCTCCCTAAAGAAAA 59.959 41.667 0.00 0.00 0.00 2.29
1627 3795 4.153655 CGCTACAACCTCCCTAAAGAAAAC 59.846 45.833 0.00 0.00 0.00 2.43
1640 3808 7.988599 TCCCTAAAGAAAACTTTTAAAAAGGGC 59.011 33.333 18.00 2.86 37.24 5.19
1647 3815 5.666969 AACTTTTAAAAAGGGCATTTCGC 57.333 34.783 0.00 0.00 41.28 4.70
1792 4099 8.656849 CGTTGTCTATCTTGTATTAAAGCTGTT 58.343 33.333 0.00 0.00 0.00 3.16
2007 4323 2.124983 CTGATGGGTGCCGGACTG 60.125 66.667 5.05 0.00 0.00 3.51
2277 4593 4.391216 CAGCATTTGGTCTCTTACTCTGTG 59.609 45.833 0.00 0.00 0.00 3.66
2341 4661 4.600012 CTGTTTCCAGTATTTAGCACCG 57.400 45.455 0.00 0.00 33.80 4.94
2546 7113 2.171840 TGCCTTGAGGTACTGACTCTC 58.828 52.381 0.00 0.00 41.55 3.20
2709 7340 8.163408 TGTTATATTAATCAAGGATCAGGGGTG 58.837 37.037 0.00 0.00 0.00 4.61
2728 7359 5.867174 GGGGTGCAAAGTTACATTGTATTTC 59.133 40.000 2.34 0.00 0.00 2.17
2882 7514 1.553248 CCCAAGGTCGACTATGAACCA 59.447 52.381 16.46 0.00 0.00 3.67
2902 7536 1.066573 ACCCTGAGCATCTTGAAGTCG 60.067 52.381 0.00 0.00 34.92 4.18
3263 7935 1.820056 TGGAACAGCGGCAAAACGA 60.820 52.632 1.45 0.00 35.47 3.85
3276 7951 2.329379 CAAAACGACGAGGAGGAAGAG 58.671 52.381 0.00 0.00 0.00 2.85
3277 7952 0.889306 AAACGACGAGGAGGAAGAGG 59.111 55.000 0.00 0.00 0.00 3.69
3278 7953 0.037877 AACGACGAGGAGGAAGAGGA 59.962 55.000 0.00 0.00 0.00 3.71
3577 8261 2.575735 TGCCCAGAACTTGATACCATCA 59.424 45.455 0.00 0.00 37.55 3.07
3786 10554 1.524621 GTGACAGGTGCAGCTGTGT 60.525 57.895 45.90 29.49 33.50 3.72
3922 10691 2.943690 TGCCTTTAGTGTGCGTTTTACA 59.056 40.909 0.00 0.00 0.00 2.41
3923 10692 3.002862 TGCCTTTAGTGTGCGTTTTACAG 59.997 43.478 0.00 0.00 0.00 2.74
4023 10796 6.183360 CCTTTACCTGAGCTTATTACTTGTGC 60.183 42.308 0.00 0.00 0.00 4.57
4053 10826 6.301486 AGTTTTAACAAATACTCCCTCCGTT 58.699 36.000 0.00 0.00 0.00 4.44
4159 10956 9.483062 GAAGAAGACATTGACAATCTTTTATCG 57.517 33.333 0.00 0.00 32.83 2.92
4164 10961 8.873830 AGACATTGACAATCTTTTATCGTACAG 58.126 33.333 0.00 0.00 0.00 2.74
4198 10995 3.057526 GGCGCAACTTATCAAAAGAACCT 60.058 43.478 10.83 0.00 0.00 3.50
4233 11030 9.642343 AGTTTAGGTTTAACATCTTCCTTTTCT 57.358 29.630 0.00 0.00 0.00 2.52
4234 11031 9.678941 GTTTAGGTTTAACATCTTCCTTTTCTG 57.321 33.333 0.00 0.00 0.00 3.02
4389 11186 6.983307 CACTGTCTAGAGTTTTGCTAGCATAT 59.017 38.462 20.13 3.03 36.22 1.78
4436 11233 5.615925 ACTCTTTGTCCTAGAACAACACT 57.384 39.130 0.00 0.00 38.80 3.55
4512 11309 3.189287 GTGGTTGAACAATAGGTGCAGAG 59.811 47.826 0.00 0.00 36.08 3.35
4516 11329 5.221244 GGTTGAACAATAGGTGCAGAGTTTT 60.221 40.000 0.00 0.00 36.08 2.43
4543 11356 6.619801 AGTGTTTTAAAGGCTTCTACACAG 57.380 37.500 23.61 0.00 37.46 3.66
4680 11494 7.613551 ACGGATACCTTTGATATCTTTAGGT 57.386 36.000 20.33 20.33 41.80 3.08
4728 11542 8.792633 TCAACTTTAGTTTTATCCACCTCAATG 58.207 33.333 0.00 0.00 35.83 2.82
4752 11566 6.070309 TGCCTTGTTCATAAATTTTATGCCCT 60.070 34.615 19.83 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 102 3.311110 GTGCACGGGAGAGGGACA 61.311 66.667 0.00 0.00 0.00 4.02
177 197 0.753262 GCCATCTCCTTTCCTCGCTA 59.247 55.000 0.00 0.00 0.00 4.26
178 198 1.267574 TGCCATCTCCTTTCCTCGCT 61.268 55.000 0.00 0.00 0.00 4.93
182 202 1.604378 CCGTGCCATCTCCTTTCCT 59.396 57.895 0.00 0.00 0.00 3.36
249 273 4.083862 GGAGCTGGACACCCCGTC 62.084 72.222 0.00 0.00 44.57 4.79
254 278 4.101448 ATGCCGGAGCTGGACACC 62.101 66.667 5.05 0.00 40.80 4.16
256 280 3.785859 GGATGCCGGAGCTGGACA 61.786 66.667 5.05 0.00 40.80 4.02
270 294 4.547905 CGTCGGTGTAGCGCGGAT 62.548 66.667 8.83 0.00 0.00 4.18
305 329 1.198094 TGGCAACTCCGGATCTGGAA 61.198 55.000 23.67 5.51 37.64 3.53
395 419 1.674441 CCAGCTCCGATAACGACTACA 59.326 52.381 0.00 0.00 42.66 2.74
405 429 0.955178 CTACGATGTCCAGCTCCGAT 59.045 55.000 0.00 0.00 0.00 4.18
406 430 0.393944 ACTACGATGTCCAGCTCCGA 60.394 55.000 0.00 0.00 0.00 4.55
435 459 0.105964 CCTCTCCCTCTCCGATTCCA 60.106 60.000 0.00 0.00 0.00 3.53
474 502 1.837051 ACTCCGAACCCAGCTCACA 60.837 57.895 0.00 0.00 0.00 3.58
476 504 1.533033 TCACTCCGAACCCAGCTCA 60.533 57.895 0.00 0.00 0.00 4.26
480 516 2.266055 GCCTCACTCCGAACCCAG 59.734 66.667 0.00 0.00 0.00 4.45
481 517 3.691342 CGCCTCACTCCGAACCCA 61.691 66.667 0.00 0.00 0.00 4.51
492 545 2.264480 CACAATCCGGACGCCTCA 59.736 61.111 6.12 0.00 0.00 3.86
594 666 5.440610 CCCTCATATCCAGCCCAAATATAC 58.559 45.833 0.00 0.00 0.00 1.47
629 701 1.884004 CCGTGAACAAACGTCCGGT 60.884 57.895 0.00 0.00 42.01 5.28
671 753 2.338015 GCCGTCCGGTCACTGTCTA 61.338 63.158 7.66 0.00 37.65 2.59
672 754 3.681835 GCCGTCCGGTCACTGTCT 61.682 66.667 7.66 0.00 37.65 3.41
702 784 1.008329 GTCTCTCGTACCCGTCTCAG 58.992 60.000 0.00 0.00 35.01 3.35
720 802 6.963322 AGAAAATAGACAATTAGAGCCAGGT 58.037 36.000 0.00 0.00 0.00 4.00
747 838 7.984391 TCAAATGCACAGTGATATTAAATCGT 58.016 30.769 4.15 0.00 0.00 3.73
751 843 6.405731 GCCCTCAAATGCACAGTGATATTAAA 60.406 38.462 4.15 0.00 0.00 1.52
768 860 0.391661 GTCGATCTGCTGCCCTCAAA 60.392 55.000 0.00 0.00 0.00 2.69
771 863 1.520342 GTGTCGATCTGCTGCCCTC 60.520 63.158 0.00 0.00 0.00 4.30
772 864 1.620739 ATGTGTCGATCTGCTGCCCT 61.621 55.000 0.00 0.00 0.00 5.19
773 865 0.745845 AATGTGTCGATCTGCTGCCC 60.746 55.000 0.00 0.00 0.00 5.36
774 866 1.089920 AAATGTGTCGATCTGCTGCC 58.910 50.000 0.00 0.00 0.00 4.85
798 914 2.076622 GAGAGCGGAGGCGCATAAGA 62.077 60.000 10.83 0.00 46.35 2.10
799 915 1.663074 GAGAGCGGAGGCGCATAAG 60.663 63.158 10.83 0.00 46.35 1.73
800 916 1.676678 AAGAGAGCGGAGGCGCATAA 61.677 55.000 10.83 0.00 46.35 1.90
801 917 2.127869 AAGAGAGCGGAGGCGCATA 61.128 57.895 10.83 0.00 46.35 3.14
802 918 3.465403 AAGAGAGCGGAGGCGCAT 61.465 61.111 10.83 0.00 46.35 4.73
803 919 4.441695 CAAGAGAGCGGAGGCGCA 62.442 66.667 10.83 0.00 46.35 6.09
872 988 1.382557 TGGGAGCCGAGAGCCAATA 60.383 57.895 0.00 0.00 45.47 1.90
937 1055 4.143333 CGTCTCACCCCGCCGAAT 62.143 66.667 0.00 0.00 0.00 3.34
1101 1245 2.176273 GCGCCTGATGTCAGCGATT 61.176 57.895 21.93 0.00 42.05 3.34
1107 1251 0.178533 TCATGATGCGCCTGATGTCA 59.821 50.000 11.40 4.04 0.00 3.58
1440 3589 3.395607 CCTTATCATCACTGAATCCCCCA 59.604 47.826 0.00 0.00 34.37 4.96
1452 3601 5.302568 GCAAATCAATCCACCCTTATCATCA 59.697 40.000 0.00 0.00 0.00 3.07
1480 3634 5.321959 TGCAATCGATGAAGCCAATTAAA 57.678 34.783 13.19 0.00 0.00 1.52
1483 3637 3.872511 TTGCAATCGATGAAGCCAATT 57.127 38.095 13.19 0.00 0.00 2.32
1484 3638 3.777478 CTTTGCAATCGATGAAGCCAAT 58.223 40.909 0.00 0.00 0.00 3.16
1486 3640 1.135315 GCTTTGCAATCGATGAAGCCA 60.135 47.619 18.04 6.25 34.43 4.75
1487 3641 1.133790 AGCTTTGCAATCGATGAAGCC 59.866 47.619 22.02 11.50 38.84 4.35
1489 3643 8.619146 TTATTTAAGCTTTGCAATCGATGAAG 57.381 30.769 3.20 2.87 0.00 3.02
1622 3790 6.631238 GCGAAATGCCCTTTTTAAAAGTTTTC 59.369 34.615 15.19 15.00 37.76 2.29
1626 3794 4.509970 GTGCGAAATGCCCTTTTTAAAAGT 59.490 37.500 15.19 0.00 45.60 2.66
1627 3795 4.749598 AGTGCGAAATGCCCTTTTTAAAAG 59.250 37.500 10.23 10.23 45.60 2.27
1647 3815 6.258727 ACAACAATCAGATAATTAGCGGAGTG 59.741 38.462 23.17 23.17 37.75 3.51
1652 3820 6.628856 CGGAAACAACAATCAGATAATTAGCG 59.371 38.462 0.00 0.00 0.00 4.26
1792 4099 4.022935 AGAGCTTGAAATTTGCACGATGAA 60.023 37.500 0.00 0.00 0.00 2.57
2007 4323 2.672996 AACCATGAGCGGCACACC 60.673 61.111 1.29 0.00 0.00 4.16
2277 4593 6.183360 TTGATAGGTTTCAAAGTGTGACACAC 60.183 38.462 27.76 27.76 38.47 3.82
2289 4605 6.595326 CAGCACTACAGATTGATAGGTTTCAA 59.405 38.462 0.00 0.00 39.77 2.69
2326 4646 2.981859 AGGTCGGTGCTAAATACTGG 57.018 50.000 0.00 0.00 0.00 4.00
2419 4810 2.746362 CAGCTGTCCTTTGAACCTCATC 59.254 50.000 5.25 0.00 0.00 2.92
2492 6294 5.175859 CCATAAGCGACCTGTTCTAAAAGA 58.824 41.667 0.00 0.00 0.00 2.52
2493 6295 4.201822 GCCATAAGCGACCTGTTCTAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
2494 6296 3.687698 GCCATAAGCGACCTGTTCTAAAA 59.312 43.478 0.00 0.00 0.00 1.52
2500 6302 0.037590 TTGGCCATAAGCGACCTGTT 59.962 50.000 6.09 0.00 45.17 3.16
2546 7113 7.071414 TGACGATGTACCGTAAATATCTAACG 58.929 38.462 0.00 0.00 43.49 3.18
2642 7273 5.559770 TCTCCTGCAATCATTCACAGTTAA 58.440 37.500 0.00 0.00 0.00 2.01
2709 7340 8.190784 AGCTATGGAAATACAATGTAACTTTGC 58.809 33.333 0.00 0.87 0.00 3.68
2728 7359 6.582677 AGTAGCTTGTAGTGATAGCTATGG 57.417 41.667 11.94 0.00 45.96 2.74
2882 7514 1.066573 CGACTTCAAGATGCTCAGGGT 60.067 52.381 0.00 0.00 0.00 4.34
3263 7935 0.257616 CTCCTCCTCTTCCTCCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
3267 7939 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
3270 7942 0.105709 CCTCCTCCTCCTCCTCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
3276 7951 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
3277 7952 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
3278 7953 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
3406 8081 1.153229 GGATGGCGTACACCCCTTC 60.153 63.158 0.00 0.28 0.00 3.46
3577 8261 1.344763 CACTTCACCTTCGTCCTCCTT 59.655 52.381 0.00 0.00 0.00 3.36
3786 10554 5.934043 CAGTGATTTGGACTACTGAACATGA 59.066 40.000 0.00 0.00 42.28 3.07
3922 10691 3.316868 CCGTCCAACCATTTACACAAACT 59.683 43.478 0.00 0.00 0.00 2.66
3923 10692 3.551250 CCCGTCCAACCATTTACACAAAC 60.551 47.826 0.00 0.00 0.00 2.93
3958 10731 5.299531 TGAGAATAGAGCTGCGTAGTATGTT 59.700 40.000 1.53 0.00 0.00 2.71
3959 10732 4.822350 TGAGAATAGAGCTGCGTAGTATGT 59.178 41.667 1.53 0.00 0.00 2.29
3961 10734 4.083749 CGTGAGAATAGAGCTGCGTAGTAT 60.084 45.833 1.53 0.00 0.00 2.12
4023 10796 8.622948 AGGGAGTATTTGTTAAAACTTCAGAG 57.377 34.615 0.00 0.00 0.00 3.35
4053 10826 7.913297 GCTTGCAAAAACGTCTTATATTATGGA 59.087 33.333 0.00 0.00 0.00 3.41
4133 10930 9.483062 CGATAAAAGATTGTCAATGTCTTCTTC 57.517 33.333 1.88 0.75 31.37 2.87
4139 10936 8.869897 TCTGTACGATAAAAGATTGTCAATGTC 58.130 33.333 1.88 0.00 0.00 3.06
4164 10961 2.076863 AGTTGCGCCATTTGTACTCTC 58.923 47.619 4.18 0.00 0.00 3.20
4210 11007 8.990163 ACAGAAAAGGAAGATGTTAAACCTAA 57.010 30.769 0.00 0.00 0.00 2.69
4356 11153 0.603569 CTCTAGACAGTGCCCAACGT 59.396 55.000 0.00 0.00 0.00 3.99
4436 11233 7.821846 TGTGTGATGCTAGTGATTATGTTGTTA 59.178 33.333 0.00 0.00 0.00 2.41
4516 11329 8.958506 TGTGTAGAAGCCTTTAAAACACTTAAA 58.041 29.630 14.73 0.00 37.30 1.52
4527 11340 5.738619 TGATGACTGTGTAGAAGCCTTTA 57.261 39.130 0.00 0.00 0.00 1.85
4543 11356 8.872845 GGATGTTCCATTTGTTTTTATGATGAC 58.127 33.333 0.00 0.00 36.28 3.06
4626 11440 3.958147 TCGGTCATGCTGGTTTCTATAGA 59.042 43.478 0.00 0.00 0.00 1.98
4659 11473 9.442047 CCATGACCTAAAGATATCAAAGGTATC 57.558 37.037 18.41 10.98 40.63 2.24
4680 11494 4.538746 TGCAATTGAGAAAATGCCATGA 57.461 36.364 10.34 0.00 38.00 3.07
4728 11542 6.348498 AGGGCATAAAATTTATGAACAAGGC 58.652 36.000 24.99 11.70 0.00 4.35


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

AutoCloner maintained by Alex Coulton.