Multiple sequence alignment - TraesCS1B01G315100

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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 TraesCS1B01G315100 chr1B 100.000 2978 0 0 1 2978 539590545 539587568 0.000000e+00 5500.0
1 TraesCS1B01G315100 chr1B 80.103 779 122 15 2232 2978 646482173 646481396 1.560000e-152 549.0
2 TraesCS1B01G315100 chr1D 90.575 2175 135 31 11 2149 402007486 402005346 0.000000e+00 2817.0
3 TraesCS1B01G315100 chr1D 90.537 2177 134 32 11 2149 401922270 401920128 0.000000e+00 2813.0
4 TraesCS1B01G315100 chr1D 90.496 2178 135 33 10 2149 402109051 402106908 0.000000e+00 2809.0
5 TraesCS1B01G315100 chr1D 90.607 2140 126 39 50 2149 402052494 402050390 0.000000e+00 2769.0
6 TraesCS1B01G315100 chr1D 91.596 1535 93 20 621 2149 401775356 401773852 0.000000e+00 2087.0
7 TraesCS1B01G315100 chr1D 81.957 654 102 7 2257 2897 468038956 468039606 9.390000e-150 540.0
8 TraesCS1B01G315100 chr1D 78.378 777 130 20 2233 2978 204281480 204280711 1.250000e-128 470.0
9 TraesCS1B01G315100 chr1D 77.128 787 125 34 2232 2977 393398069 393398841 3.570000e-109 405.0
10 TraesCS1B01G315100 chr1D 75.794 756 172 8 1212 1960 433092961 433093712 3.630000e-99 372.0
11 TraesCS1B01G315100 chr1D 78.763 598 88 22 2410 2977 466379000 466378412 6.070000e-97 364.0
12 TraesCS1B01G315100 chr1D 75.099 759 172 14 1212 1960 433060896 433061647 3.680000e-89 339.0
13 TraesCS1B01G315100 chr1D 88.837 215 19 2 355 569 401775569 401775360 2.940000e-65 259.0
14 TraesCS1B01G315100 chr1D 92.381 105 8 0 1699 1803 402123835 402123731 1.850000e-32 150.0
15 TraesCS1B01G315100 chr1A 94.007 1602 71 15 568 2149 497585915 497584319 0.000000e+00 2403.0
16 TraesCS1B01G315100 chr1A 91.009 1546 84 19 617 2149 497580789 497579286 0.000000e+00 2034.0
17 TraesCS1B01G315100 chr1A 81.297 663 97 14 2258 2897 561126538 561125880 2.050000e-141 512.0
18 TraesCS1B01G315100 chr1A 75.033 757 176 10 1212 1960 531513470 531514221 3.680000e-89 339.0
19 TraesCS1B01G315100 chr1A 92.481 133 7 3 374 506 497580940 497580811 1.410000e-43 187.0
20 TraesCS1B01G315100 chr1A 93.043 115 8 0 460 574 497587959 497587845 5.110000e-38 169.0
21 TraesCS1B01G315100 chr7D 86.780 1180 128 22 954 2125 506882646 506883805 0.000000e+00 1290.0
22 TraesCS1B01G315100 chr7D 77.964 776 133 14 2235 2978 232413745 232414514 4.530000e-123 451.0
23 TraesCS1B01G315100 chr7D 77.407 779 130 28 2233 2978 125911396 125910631 3.550000e-114 422.0
24 TraesCS1B01G315100 chr7D 80.235 597 89 12 2411 2978 563902769 563902173 3.550000e-114 422.0
25 TraesCS1B01G315100 chr7D 84.076 157 24 1 2 157 229231889 229232045 1.850000e-32 150.0
26 TraesCS1B01G315100 chr7B 86.901 1168 131 16 951 2113 535506074 535507224 0.000000e+00 1290.0
27 TraesCS1B01G315100 chr7B 79.233 756 120 25 2254 2978 465598470 465599219 2.670000e-135 492.0
28 TraesCS1B01G315100 chr7B 78.831 770 120 29 2228 2964 104255933 104256692 2.080000e-131 479.0
29 TraesCS1B01G315100 chr7B 77.806 784 126 26 2234 2978 607289455 607288681 9.800000e-120 440.0
30 TraesCS1B01G315100 chr7B 80.311 579 87 11 2425 2978 439862646 439863222 2.140000e-111 412.0
31 TraesCS1B01G315100 chr2A 81.579 646 89 15 2360 2978 46320709 46321351 9.520000e-140 507.0
32 TraesCS1B01G315100 chr2A 78.198 688 108 17 2324 2978 657505910 657505232 4.620000e-108 401.0
33 TraesCS1B01G315100 chr6A 79.491 707 110 19 2302 2978 33261417 33262118 1.250000e-128 470.0
34 TraesCS1B01G315100 chr6A 78.712 761 120 23 2235 2978 384316807 384317542 1.250000e-128 470.0
35 TraesCS1B01G315100 chr6A 80.142 282 43 10 3 279 137389739 137390012 6.510000e-47 198.0
36 TraesCS1B01G315100 chr6A 87.931 58 5 2 565 620 578721681 578721738 1.920000e-07 67.6
37 TraesCS1B01G315100 chr2B 79.462 706 98 23 2309 2978 572098153 572097459 9.730000e-125 457.0
38 TraesCS1B01G315100 chr2B 77.506 778 137 25 2230 2978 800112313 800111545 1.640000e-117 433.0
39 TraesCS1B01G315100 chr5B 80.882 612 81 20 2393 2978 588518161 588518762 1.630000e-122 449.0
40 TraesCS1B01G315100 chr6B 79.751 642 105 15 2232 2855 583052810 583053444 2.720000e-120 442.0
41 TraesCS1B01G315100 chr6B 90.741 54 3 2 565 616 277616247 277616300 1.480000e-08 71.3
42 TraesCS1B01G315100 chr4D 77.853 736 126 27 2270 2978 367948710 367949435 3.550000e-114 422.0
43 TraesCS1B01G315100 chr4D 79.787 376 51 9 2628 2978 70471510 70471885 1.770000e-62 250.0
44 TraesCS1B01G315100 chr4D 94.805 77 3 1 2902 2978 324477425 324477350 5.210000e-23 119.0
45 TraesCS1B01G315100 chr3B 81.051 533 86 7 2315 2833 474005708 474006239 7.680000e-111 411.0
46 TraesCS1B01G315100 chr3B 79.542 611 82 16 2393 2978 672849791 672850383 2.150000e-106 396.0
47 TraesCS1B01G315100 chr3B 91.837 49 3 1 311 359 2268853 2268806 1.920000e-07 67.6
48 TraesCS1B01G315100 chr6D 77.516 636 106 26 2232 2840 389599718 389600343 6.110000e-92 348.0
49 TraesCS1B01G315100 chr6D 90.741 54 3 2 565 616 392273171 392273224 1.480000e-08 71.3
50 TraesCS1B01G315100 chrUn 79.612 515 77 15 2230 2739 337012465 337011974 7.900000e-91 344.0
51 TraesCS1B01G315100 chrUn 85.714 77 5 6 3 77 41020799 41020871 3.180000e-10 76.8
52 TraesCS1B01G315100 chrUn 95.455 44 2 0 3 46 41038913 41038956 1.480000e-08 71.3
53 TraesCS1B01G315100 chr4A 79.417 515 78 16 2230 2739 556156189 556155698 3.680000e-89 339.0
54 TraesCS1B01G315100 chr7A 78.842 449 62 20 2535 2957 392912786 392912345 3.780000e-69 272.0
55 TraesCS1B01G315100 chr7A 84.848 66 5 5 565 626 462978642 462978578 8.910000e-06 62.1
56 TraesCS1B01G315100 chr3D 77.378 389 55 16 2622 2978 448874335 448873948 1.810000e-47 200.0
57 TraesCS1B01G315100 chr5A 79.182 269 43 10 1 263 704859540 704859801 1.100000e-39 174.0


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 TraesCS1B01G315100 chr1B 539587568 539590545 2977 True 5500.00 5500 100.0000 1 2978 1 chr1B.!!$R1 2977
1 TraesCS1B01G315100 chr1B 646481396 646482173 777 True 549.00 549 80.1030 2232 2978 1 chr1B.!!$R2 746
2 TraesCS1B01G315100 chr1D 402005346 402007486 2140 True 2817.00 2817 90.5750 11 2149 1 chr1D.!!$R3 2138
3 TraesCS1B01G315100 chr1D 401920128 401922270 2142 True 2813.00 2813 90.5370 11 2149 1 chr1D.!!$R2 2138
4 TraesCS1B01G315100 chr1D 402106908 402109051 2143 True 2809.00 2809 90.4960 10 2149 1 chr1D.!!$R5 2139
5 TraesCS1B01G315100 chr1D 402050390 402052494 2104 True 2769.00 2769 90.6070 50 2149 1 chr1D.!!$R4 2099
6 TraesCS1B01G315100 chr1D 401773852 401775569 1717 True 1173.00 2087 90.2165 355 2149 2 chr1D.!!$R8 1794
7 TraesCS1B01G315100 chr1D 468038956 468039606 650 False 540.00 540 81.9570 2257 2897 1 chr1D.!!$F4 640
8 TraesCS1B01G315100 chr1D 204280711 204281480 769 True 470.00 470 78.3780 2233 2978 1 chr1D.!!$R1 745
9 TraesCS1B01G315100 chr1D 393398069 393398841 772 False 405.00 405 77.1280 2232 2977 1 chr1D.!!$F1 745
10 TraesCS1B01G315100 chr1D 433092961 433093712 751 False 372.00 372 75.7940 1212 1960 1 chr1D.!!$F3 748
11 TraesCS1B01G315100 chr1D 466378412 466379000 588 True 364.00 364 78.7630 2410 2977 1 chr1D.!!$R7 567
12 TraesCS1B01G315100 chr1D 433060896 433061647 751 False 339.00 339 75.0990 1212 1960 1 chr1D.!!$F2 748
13 TraesCS1B01G315100 chr1A 497579286 497587959 8673 True 1198.25 2403 92.6350 374 2149 4 chr1A.!!$R2 1775
14 TraesCS1B01G315100 chr1A 561125880 561126538 658 True 512.00 512 81.2970 2258 2897 1 chr1A.!!$R1 639
15 TraesCS1B01G315100 chr1A 531513470 531514221 751 False 339.00 339 75.0330 1212 1960 1 chr1A.!!$F1 748
16 TraesCS1B01G315100 chr7D 506882646 506883805 1159 False 1290.00 1290 86.7800 954 2125 1 chr7D.!!$F3 1171
17 TraesCS1B01G315100 chr7D 232413745 232414514 769 False 451.00 451 77.9640 2235 2978 1 chr7D.!!$F2 743
18 TraesCS1B01G315100 chr7D 125910631 125911396 765 True 422.00 422 77.4070 2233 2978 1 chr7D.!!$R1 745
19 TraesCS1B01G315100 chr7D 563902173 563902769 596 True 422.00 422 80.2350 2411 2978 1 chr7D.!!$R2 567
20 TraesCS1B01G315100 chr7B 535506074 535507224 1150 False 1290.00 1290 86.9010 951 2113 1 chr7B.!!$F4 1162
21 TraesCS1B01G315100 chr7B 465598470 465599219 749 False 492.00 492 79.2330 2254 2978 1 chr7B.!!$F3 724
22 TraesCS1B01G315100 chr7B 104255933 104256692 759 False 479.00 479 78.8310 2228 2964 1 chr7B.!!$F1 736
23 TraesCS1B01G315100 chr7B 607288681 607289455 774 True 440.00 440 77.8060 2234 2978 1 chr7B.!!$R1 744
24 TraesCS1B01G315100 chr7B 439862646 439863222 576 False 412.00 412 80.3110 2425 2978 1 chr7B.!!$F2 553
25 TraesCS1B01G315100 chr2A 46320709 46321351 642 False 507.00 507 81.5790 2360 2978 1 chr2A.!!$F1 618
26 TraesCS1B01G315100 chr2A 657505232 657505910 678 True 401.00 401 78.1980 2324 2978 1 chr2A.!!$R1 654
27 TraesCS1B01G315100 chr6A 33261417 33262118 701 False 470.00 470 79.4910 2302 2978 1 chr6A.!!$F1 676
28 TraesCS1B01G315100 chr6A 384316807 384317542 735 False 470.00 470 78.7120 2235 2978 1 chr6A.!!$F3 743
29 TraesCS1B01G315100 chr2B 572097459 572098153 694 True 457.00 457 79.4620 2309 2978 1 chr2B.!!$R1 669
30 TraesCS1B01G315100 chr2B 800111545 800112313 768 True 433.00 433 77.5060 2230 2978 1 chr2B.!!$R2 748
31 TraesCS1B01G315100 chr5B 588518161 588518762 601 False 449.00 449 80.8820 2393 2978 1 chr5B.!!$F1 585
32 TraesCS1B01G315100 chr6B 583052810 583053444 634 False 442.00 442 79.7510 2232 2855 1 chr6B.!!$F2 623
33 TraesCS1B01G315100 chr4D 367948710 367949435 725 False 422.00 422 77.8530 2270 2978 1 chr4D.!!$F2 708
34 TraesCS1B01G315100 chr3B 474005708 474006239 531 False 411.00 411 81.0510 2315 2833 1 chr3B.!!$F1 518
35 TraesCS1B01G315100 chr3B 672849791 672850383 592 False 396.00 396 79.5420 2393 2978 1 chr3B.!!$F2 585
36 TraesCS1B01G315100 chr6D 389599718 389600343 625 False 348.00 348 77.5160 2232 2840 1 chr6D.!!$F1 608

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
287 291 0.041839 GTGCTTGCTCACTGTTCACG 60.042 55.0 0.00 0.0 34.29 4.35 F
338 342 0.171231 GAAGCCGGATTTGCCAAGTC 59.829 55.0 6.32 0.0 35.94 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 3769 0.392461 ACGTGAACAGCACCTTGTGT 60.392 50.0 0.0 0.0 44.85 3.72 R
2282 9322 0.471211 TCGGAGACTTGTCCCCTGTT 60.471 55.0 0.1 0.0 32.26 3.16 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
46 47 3.260205 TGGTGATTTCCTTCTCCCTTCT 58.740 45.455 0.00 0.00 0.00 2.85
48 49 3.521531 GGTGATTTCCTTCTCCCTTCTCT 59.478 47.826 0.00 0.00 0.00 3.10
52 53 5.785423 TGATTTCCTTCTCCCTTCTCTGTTA 59.215 40.000 0.00 0.00 0.00 2.41
61 62 9.508642 CTTCTCCCTTCTCTGTTAAATTAAGTT 57.491 33.333 0.00 0.00 0.00 2.66
111 114 6.488683 TCCGATTGAAACTACATCTTTTGGTT 59.511 34.615 0.00 0.00 0.00 3.67
112 115 6.582295 CCGATTGAAACTACATCTTTTGGTTG 59.418 38.462 0.00 0.00 0.00 3.77
116 119 5.888724 TGAAACTACATCTTTTGGTTGTCCA 59.111 36.000 0.00 0.00 42.66 4.02
133 136 8.208224 TGGTTGTCCAATGATCGTTTATACTAT 58.792 33.333 0.00 0.00 41.25 2.12
163 166 6.220930 TGCTTGTTTCAACTAGATAACTCGT 58.779 36.000 0.00 0.00 34.37 4.18
165 168 6.145696 GCTTGTTTCAACTAGATAACTCGTGT 59.854 38.462 0.00 0.00 34.37 4.49
178 181 4.966850 AACTCGTGTTAGTTCGTTGATG 57.033 40.909 0.05 0.00 34.60 3.07
186 189 6.079763 GTGTTAGTTCGTTGATGTACGTAGA 58.920 40.000 0.00 0.00 42.01 2.59
205 209 6.912051 ACGTAGATTTATTTCGTACGTGCATA 59.088 34.615 16.05 7.35 45.79 3.14
225 229 6.120378 CATATGTTGCATGGATATGAGAGC 57.880 41.667 11.87 0.00 36.36 4.09
233 237 4.330250 CATGGATATGAGAGCCCGAATTT 58.670 43.478 0.00 0.00 36.36 1.82
235 239 3.136443 TGGATATGAGAGCCCGAATTTGT 59.864 43.478 0.00 0.00 29.75 2.83
236 240 3.499918 GGATATGAGAGCCCGAATTTGTG 59.500 47.826 0.00 0.00 0.00 3.33
248 252 2.708962 CGAATTTGTGATACGCGAATGC 59.291 45.455 15.93 0.00 29.62 3.56
263 267 2.223021 CGAATGCGGACACACCTAAATG 60.223 50.000 0.00 0.00 36.31 2.32
275 279 1.106285 CCTAAATGAGGGGTGCTTGC 58.894 55.000 0.00 0.00 42.39 4.01
276 280 1.341383 CCTAAATGAGGGGTGCTTGCT 60.341 52.381 0.00 0.00 42.39 3.91
278 282 0.112995 AAATGAGGGGTGCTTGCTCA 59.887 50.000 0.00 0.00 0.00 4.26
279 283 0.610232 AATGAGGGGTGCTTGCTCAC 60.610 55.000 0.00 0.00 36.28 3.51
282 286 2.113986 GGGGTGCTTGCTCACTGT 59.886 61.111 0.00 0.00 37.16 3.55
284 288 1.518903 GGGGTGCTTGCTCACTGTTC 61.519 60.000 0.00 0.00 37.16 3.18
285 289 0.819259 GGGTGCTTGCTCACTGTTCA 60.819 55.000 4.78 0.00 37.16 3.18
287 291 0.041839 GTGCTTGCTCACTGTTCACG 60.042 55.000 0.00 0.00 34.29 4.35
288 292 0.179086 TGCTTGCTCACTGTTCACGA 60.179 50.000 0.00 0.00 0.00 4.35
292 296 1.286501 TGCTCACTGTTCACGAACAC 58.713 50.000 8.51 0.21 45.42 3.32
294 298 1.835121 CTCACTGTTCACGAACACGA 58.165 50.000 8.51 7.59 45.42 4.35
297 301 0.868602 ACTGTTCACGAACACGACCG 60.869 55.000 8.51 2.09 45.42 4.79
298 302 1.545614 CTGTTCACGAACACGACCGG 61.546 60.000 8.51 0.00 45.42 5.28
320 324 0.531974 GTGCCCACAGACGTTTGAGA 60.532 55.000 13.73 0.00 0.00 3.27
321 325 0.179234 TGCCCACAGACGTTTGAGAA 59.821 50.000 13.73 0.00 0.00 2.87
331 335 1.535462 ACGTTTGAGAAGCCGGATTTG 59.465 47.619 6.32 0.00 0.00 2.32
336 340 0.453390 GAGAAGCCGGATTTGCCAAG 59.547 55.000 6.32 0.00 35.94 3.61
337 341 0.251341 AGAAGCCGGATTTGCCAAGT 60.251 50.000 6.32 0.00 35.94 3.16
338 342 0.171231 GAAGCCGGATTTGCCAAGTC 59.829 55.000 6.32 0.00 35.94 3.01
339 343 1.250840 AAGCCGGATTTGCCAAGTCC 61.251 55.000 5.05 8.84 35.94 3.85
340 344 1.976474 GCCGGATTTGCCAAGTCCA 60.976 57.895 17.84 0.00 35.94 4.02
341 345 1.883021 CCGGATTTGCCAAGTCCAC 59.117 57.895 17.84 0.00 35.94 4.02
342 346 1.595093 CCGGATTTGCCAAGTCCACC 61.595 60.000 17.84 0.00 35.94 4.61
345 349 0.890683 GATTTGCCAAGTCCACCCTG 59.109 55.000 0.00 0.00 0.00 4.45
370 374 1.267121 GCTCTTAGGTCCTCACACCA 58.733 55.000 0.00 0.00 39.16 4.17
389 393 4.612412 GTCACGGGCCGACCAACA 62.612 66.667 35.78 6.02 40.22 3.33
421 425 1.003718 GGGTTGTAGCCTGCGAGTT 60.004 57.895 0.00 0.00 31.81 3.01
454 458 4.469657 ACATAAGTCAAAGGCCAAACAGA 58.530 39.130 5.01 0.00 0.00 3.41
455 459 4.520492 ACATAAGTCAAAGGCCAAACAGAG 59.480 41.667 5.01 0.00 0.00 3.35
458 462 1.338020 GTCAAAGGCCAAACAGAGGTG 59.662 52.381 5.01 0.00 0.00 4.00
492 496 6.449635 TTGTTTACAAAGAGCTCACATTGT 57.550 33.333 25.67 25.67 39.23 2.71
563 567 6.680810 CAACCAACAGATGATACAACACAAT 58.319 36.000 0.00 0.00 0.00 2.71
637 2587 7.663493 GGGAGAAATGAAGAGAGAGAAAAAGAA 59.337 37.037 0.00 0.00 0.00 2.52
645 2595 8.428063 TGAAGAGAGAGAAAAAGAAAGAGATGT 58.572 33.333 0.00 0.00 0.00 3.06
673 2623 8.417780 ACTCTCGATCATTGAAGAAAACATAG 57.582 34.615 0.00 0.00 0.00 2.23
759 2712 8.773645 TGATCAATTATTACTCCACTAATTGCG 58.226 33.333 0.00 0.00 40.31 4.85
849 2830 5.105797 TGTTTATCAAGTGCACCATGGATTC 60.106 40.000 21.47 7.22 0.00 2.52
853 2834 2.198827 AGTGCACCATGGATTCGAAA 57.801 45.000 21.47 0.00 0.00 3.46
864 2845 1.474077 GGATTCGAAACCTTGCATGCT 59.526 47.619 20.33 0.00 0.00 3.79
877 2858 4.023707 CCTTGCATGCTTGTATAAGTAGCC 60.024 45.833 20.33 0.00 36.27 3.93
909 2890 2.224066 CCATACGAACTCCATCACCTCC 60.224 54.545 0.00 0.00 0.00 4.30
911 2892 0.898320 ACGAACTCCATCACCTCCTG 59.102 55.000 0.00 0.00 0.00 3.86
975 2959 6.919721 TGGTACACAAAGGCTAAATTCATTC 58.080 36.000 0.00 0.00 0.00 2.67
997 2981 3.067180 CAGAGCTAGCTTGAGAAGAGAGG 59.933 52.174 20.42 0.00 0.00 3.69
1110 3094 1.299648 CAAGAAGACATGCCCCCGA 59.700 57.895 0.00 0.00 0.00 5.14
1299 3283 3.570212 AACTTCCCCAGCCTGCGT 61.570 61.111 0.00 0.00 0.00 5.24
1387 3371 3.982372 GACATCGTCGCCTTCGCCA 62.982 63.158 0.00 0.00 35.26 5.69
1782 3769 3.762288 AGTACTACAAGAATGTCCTCGCA 59.238 43.478 0.00 0.00 41.05 5.10
1824 8852 4.373116 GCCGCCCTTCTCACGACA 62.373 66.667 0.00 0.00 0.00 4.35
1972 9000 0.249911 GAAGTGCAGGGTCGTCAACT 60.250 55.000 0.00 0.00 0.00 3.16
2078 9113 7.894847 ACTTGTGATTTTCGTTCAATTTTCAC 58.105 30.769 0.00 0.00 34.33 3.18
2139 9177 5.714333 TCTTTGGCTGCTTAATTATTGGTGA 59.286 36.000 0.00 0.00 0.00 4.02
2149 9187 8.190122 TGCTTAATTATTGGTGATGCAGTTAAG 58.810 33.333 0.00 0.00 32.59 1.85
2150 9188 7.168135 GCTTAATTATTGGTGATGCAGTTAAGC 59.832 37.037 9.39 9.39 42.00 3.09
2188 9226 9.594478 TTAGTATCATTTTTCTGAGTATTCGCA 57.406 29.630 0.00 0.00 0.00 5.10
2189 9227 8.492673 AGTATCATTTTTCTGAGTATTCGCAA 57.507 30.769 0.00 0.00 0.00 4.85
2190 9228 8.946085 AGTATCATTTTTCTGAGTATTCGCAAA 58.054 29.630 0.00 0.00 0.00 3.68
2191 9229 9.554724 GTATCATTTTTCTGAGTATTCGCAAAA 57.445 29.630 0.00 0.00 0.00 2.44
2220 9258 9.308000 AGTATTAATTTTGGAGTTGGAATCACA 57.692 29.630 0.00 0.00 0.00 3.58
2223 9261 6.923199 AATTTTGGAGTTGGAATCACATCT 57.077 33.333 0.00 0.00 0.00 2.90
2224 9262 6.923199 ATTTTGGAGTTGGAATCACATCTT 57.077 33.333 0.00 0.00 0.00 2.40
2225 9263 6.729690 TTTTGGAGTTGGAATCACATCTTT 57.270 33.333 0.00 0.00 0.00 2.52
2226 9264 5.710513 TTGGAGTTGGAATCACATCTTTG 57.289 39.130 0.00 0.00 0.00 2.77
2227 9265 4.081406 TGGAGTTGGAATCACATCTTTGG 58.919 43.478 0.00 0.00 0.00 3.28
2228 9266 3.119352 GGAGTTGGAATCACATCTTTGGC 60.119 47.826 0.00 0.00 0.00 4.52
2260 9300 0.040514 CACAACGCTGATCCGCAAAA 60.041 50.000 9.90 0.00 0.00 2.44
2282 9322 3.995219 CTGCAGCATCTGTCCGCGA 62.995 63.158 8.23 0.00 33.43 5.87
2298 9340 0.670854 GCGAACAGGGGACAAGTCTC 60.671 60.000 0.00 0.00 0.00 3.36
2493 9552 4.957759 AAATTCAACGAGATTAACCGGG 57.042 40.909 6.32 0.00 0.00 5.73
2514 9577 5.233263 CGGGTGTTTAACAAGTTTTTCATGG 59.767 40.000 0.00 0.00 0.00 3.66
2516 9579 6.819146 GGGTGTTTAACAAGTTTTTCATGGAA 59.181 34.615 0.00 0.00 0.00 3.53
2524 9587 8.421249 AACAAGTTTTTCATGGAAGGATCATA 57.579 30.769 0.00 0.00 0.00 2.15
2649 9729 5.626543 CACAATGTGTAGAGCAACATTGAAC 59.373 40.000 26.59 0.00 42.42 3.18
2715 9799 0.612229 ATGATATCCTCGGCTGCTGG 59.388 55.000 8.89 4.68 0.00 4.85
2754 9849 2.548920 CCTCCATCGCCATAGAACTTCC 60.549 54.545 0.00 0.00 0.00 3.46
2762 9857 1.206371 CCATAGAACTTCCCGACGGTT 59.794 52.381 13.94 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.558380 ATTTCCTCGCTGCCCCTTCC 62.558 60.000 0.00 0.00 0.00 3.46
8 9 1.379044 CATTTCCTCGCTGCCCCTT 60.379 57.895 0.00 0.00 0.00 3.95
9 10 2.273449 CATTTCCTCGCTGCCCCT 59.727 61.111 0.00 0.00 0.00 4.79
10 11 2.830370 CCATTTCCTCGCTGCCCC 60.830 66.667 0.00 0.00 0.00 5.80
11 12 2.044946 ACCATTTCCTCGCTGCCC 60.045 61.111 0.00 0.00 0.00 5.36
12 13 0.749454 ATCACCATTTCCTCGCTGCC 60.749 55.000 0.00 0.00 0.00 4.85
13 14 1.098050 AATCACCATTTCCTCGCTGC 58.902 50.000 0.00 0.00 0.00 5.25
14 15 3.411415 GAAATCACCATTTCCTCGCTG 57.589 47.619 0.00 0.00 41.51 5.18
37 38 9.862149 AAAACTTAATTTAACAGAGAAGGGAGA 57.138 29.630 0.00 0.00 0.00 3.71
66 67 5.766670 TCGGACAGTATCCTAAACATACGAT 59.233 40.000 0.00 0.00 46.69 3.73
68 69 5.428496 TCGGACAGTATCCTAAACATACG 57.572 43.478 0.00 0.00 46.69 3.06
69 70 7.431249 TCAATCGGACAGTATCCTAAACATAC 58.569 38.462 0.00 0.00 46.69 2.39
80 83 7.113658 AGATGTAGTTTCAATCGGACAGTAT 57.886 36.000 0.00 0.00 0.00 2.12
89 92 7.595130 GGACAACCAAAAGATGTAGTTTCAATC 59.405 37.037 0.00 0.00 30.44 2.67
142 145 9.188588 CTAACACGAGTTATCTAGTTGAAACAA 57.811 33.333 5.90 0.00 39.36 2.83
143 146 8.355169 ACTAACACGAGTTATCTAGTTGAAACA 58.645 33.333 5.90 0.00 39.36 2.83
157 160 4.365723 ACATCAACGAACTAACACGAGTT 58.634 39.130 3.19 3.19 42.42 3.01
158 161 3.973657 ACATCAACGAACTAACACGAGT 58.026 40.909 0.00 0.00 0.00 4.18
159 162 4.028757 CGTACATCAACGAACTAACACGAG 59.971 45.833 0.00 0.00 45.68 4.18
163 166 6.239908 TCTACGTACATCAACGAACTAACA 57.760 37.500 3.10 0.00 45.68 2.41
205 209 3.418995 GGCTCTCATATCCATGCAACAT 58.581 45.455 0.00 0.00 31.73 2.71
223 227 1.014352 GCGTATCACAAATTCGGGCT 58.986 50.000 0.00 0.00 0.00 5.19
225 229 1.282817 TCGCGTATCACAAATTCGGG 58.717 50.000 5.77 0.00 36.19 5.14
248 252 1.406887 CCCCTCATTTAGGTGTGTCCG 60.407 57.143 0.00 0.00 44.90 4.79
250 254 2.711542 CACCCCTCATTTAGGTGTGTC 58.288 52.381 0.18 0.00 45.78 3.67
256 260 1.106285 GCAAGCACCCCTCATTTAGG 58.894 55.000 0.00 0.00 46.09 2.69
263 267 1.673665 CAGTGAGCAAGCACCCCTC 60.674 63.158 0.00 0.00 39.59 4.30
267 271 0.308993 GTGAACAGTGAGCAAGCACC 59.691 55.000 0.00 0.00 39.59 5.01
272 276 2.017138 TGTTCGTGAACAGTGAGCAA 57.983 45.000 11.21 0.00 45.42 3.91
273 277 3.750828 TGTTCGTGAACAGTGAGCA 57.249 47.368 11.21 0.00 45.42 4.26
282 286 1.299316 GTCCGGTCGTGTTCGTGAA 60.299 57.895 0.00 0.00 38.33 3.18
284 288 3.095278 CGTCCGGTCGTGTTCGTG 61.095 66.667 13.16 0.00 38.33 4.35
285 289 3.585990 ACGTCCGGTCGTGTTCGT 61.586 61.111 25.54 11.03 42.56 3.85
297 301 4.295119 ACGTCTGTGGGCACGTCC 62.295 66.667 0.00 0.00 46.04 4.79
302 306 0.179234 TTCTCAAACGTCTGTGGGCA 59.821 50.000 0.00 0.00 0.00 5.36
304 308 0.868406 GCTTCTCAAACGTCTGTGGG 59.132 55.000 0.00 0.00 0.00 4.61
307 311 0.600255 CCGGCTTCTCAAACGTCTGT 60.600 55.000 0.00 0.00 0.00 3.41
309 313 0.608640 ATCCGGCTTCTCAAACGTCT 59.391 50.000 0.00 0.00 0.00 4.18
311 315 1.535462 CAAATCCGGCTTCTCAAACGT 59.465 47.619 0.00 0.00 0.00 3.99
320 324 1.250840 GGACTTGGCAAATCCGGCTT 61.251 55.000 12.45 0.00 37.80 4.35
321 325 1.678970 GGACTTGGCAAATCCGGCT 60.679 57.895 12.45 0.00 37.80 5.52
331 335 0.912486 ATCTACAGGGTGGACTTGGC 59.088 55.000 0.00 0.00 0.00 4.52
345 349 7.180165 GGTGTGAGGACCTAAGAGCATCTAC 62.180 52.000 0.15 0.00 37.50 2.59
370 374 3.632080 TTGGTCGGCCCGTGACAT 61.632 61.111 2.12 0.00 38.10 3.06
389 393 0.678950 CAACCCCGTTGGATTGCTTT 59.321 50.000 0.00 0.00 39.56 3.51
411 415 1.362406 GAGCCAACTAACTCGCAGGC 61.362 60.000 0.00 0.00 42.31 4.85
421 425 6.640518 CCTTTGACTTATGTAGAGCCAACTA 58.359 40.000 0.00 0.00 0.00 2.24
492 496 6.042777 GTGATGAGTGAGTCGAATGGAAATA 58.957 40.000 0.00 0.00 0.00 1.40
586 2526 9.783256 CCTCCGTTCCTAAATATAAACTTTTTG 57.217 33.333 0.00 0.00 0.00 2.44
587 2527 8.963725 CCCTCCGTTCCTAAATATAAACTTTTT 58.036 33.333 0.00 0.00 0.00 1.94
589 2529 7.864770 TCCCTCCGTTCCTAAATATAAACTTT 58.135 34.615 0.00 0.00 0.00 2.66
592 2532 7.059202 TCTCCCTCCGTTCCTAAATATAAAC 57.941 40.000 0.00 0.00 0.00 2.01
593 2533 7.679732 TTCTCCCTCCGTTCCTAAATATAAA 57.320 36.000 0.00 0.00 0.00 1.40
606 2548 2.763448 CTCTCTTCATTTCTCCCTCCGT 59.237 50.000 0.00 0.00 0.00 4.69
637 2587 8.628630 TCAATGATCGAGAGTATACATCTCTT 57.371 34.615 20.50 12.96 41.58 2.85
648 2598 7.493971 CCTATGTTTTCTTCAATGATCGAGAGT 59.506 37.037 0.00 0.00 0.00 3.24
849 2830 2.987413 TACAAGCATGCAAGGTTTCG 57.013 45.000 21.98 0.00 0.00 3.46
853 2834 4.576463 GCTACTTATACAAGCATGCAAGGT 59.424 41.667 21.98 16.42 36.26 3.50
864 2845 3.965347 GAGTGGAGGGGCTACTTATACAA 59.035 47.826 0.00 0.00 38.58 2.41
877 2858 0.689745 TTCGTATGGGGAGTGGAGGG 60.690 60.000 0.00 0.00 0.00 4.30
934 2915 3.845781 ACCAGAGAGTGTGTGATTTGT 57.154 42.857 0.00 0.00 0.00 2.83
975 2959 3.067180 CCTCTCTTCTCAAGCTAGCTCTG 59.933 52.174 19.65 17.53 0.00 3.35
997 2981 4.503314 GGAAGCTGCGGCCATTGC 62.503 66.667 15.55 4.37 39.73 3.56
1110 3094 2.362369 CCTCACGATGGCCTCCACT 61.362 63.158 3.32 0.00 35.80 4.00
1782 3769 0.392461 ACGTGAACAGCACCTTGTGT 60.392 50.000 0.00 0.00 44.85 3.72
1824 8852 3.371063 ATCTGTGTCGTCGCCGGT 61.371 61.111 1.90 0.00 33.95 5.28
1972 9000 6.393171 GTGATGATTCATGGATCGATCAGTA 58.607 40.000 25.93 12.49 33.56 2.74
2078 9113 4.678509 ACAACCAATTACAGTACATGCG 57.321 40.909 0.00 0.00 0.00 4.73
2162 9200 9.594478 TGCGAATACTCAGAAAAATGATACTAA 57.406 29.630 0.00 0.00 0.00 2.24
2163 9201 9.594478 TTGCGAATACTCAGAAAAATGATACTA 57.406 29.630 0.00 0.00 0.00 1.82
2164 9202 8.492673 TTGCGAATACTCAGAAAAATGATACT 57.507 30.769 0.00 0.00 0.00 2.12
2165 9203 9.554724 TTTTGCGAATACTCAGAAAAATGATAC 57.445 29.630 0.00 0.00 0.00 2.24
2194 9232 9.308000 TGTGATTCCAACTCCAAAATTAATACT 57.692 29.630 0.00 0.00 0.00 2.12
2197 9235 9.039165 AGATGTGATTCCAACTCCAAAATTAAT 57.961 29.630 0.00 0.00 0.00 1.40
2198 9236 8.421249 AGATGTGATTCCAACTCCAAAATTAA 57.579 30.769 0.00 0.00 0.00 1.40
2199 9237 8.421249 AAGATGTGATTCCAACTCCAAAATTA 57.579 30.769 0.00 0.00 0.00 1.40
2200 9238 6.923199 AGATGTGATTCCAACTCCAAAATT 57.077 33.333 0.00 0.00 0.00 1.82
2201 9239 6.923199 AAGATGTGATTCCAACTCCAAAAT 57.077 33.333 0.00 0.00 0.00 1.82
2202 9240 6.462768 CCAAAGATGTGATTCCAACTCCAAAA 60.463 38.462 0.00 0.00 0.00 2.44
2203 9241 5.010922 CCAAAGATGTGATTCCAACTCCAAA 59.989 40.000 0.00 0.00 0.00 3.28
2204 9242 4.523943 CCAAAGATGTGATTCCAACTCCAA 59.476 41.667 0.00 0.00 0.00 3.53
2205 9243 4.081406 CCAAAGATGTGATTCCAACTCCA 58.919 43.478 0.00 0.00 0.00 3.86
2206 9244 3.119352 GCCAAAGATGTGATTCCAACTCC 60.119 47.826 0.00 0.00 0.00 3.85
2207 9245 3.760684 AGCCAAAGATGTGATTCCAACTC 59.239 43.478 0.00 0.00 0.00 3.01
2208 9246 3.508793 CAGCCAAAGATGTGATTCCAACT 59.491 43.478 0.00 0.00 0.00 3.16
2209 9247 3.841643 CAGCCAAAGATGTGATTCCAAC 58.158 45.455 0.00 0.00 0.00 3.77
2210 9248 2.231964 GCAGCCAAAGATGTGATTCCAA 59.768 45.455 0.00 0.00 0.00 3.53
2211 9249 1.820519 GCAGCCAAAGATGTGATTCCA 59.179 47.619 0.00 0.00 0.00 3.53
2212 9250 2.097825 AGCAGCCAAAGATGTGATTCC 58.902 47.619 0.00 0.00 0.00 3.01
2213 9251 3.863142 AAGCAGCCAAAGATGTGATTC 57.137 42.857 0.00 0.00 0.00 2.52
2214 9252 3.698040 CCTAAGCAGCCAAAGATGTGATT 59.302 43.478 0.00 0.00 0.00 2.57
2215 9253 3.285484 CCTAAGCAGCCAAAGATGTGAT 58.715 45.455 0.00 0.00 0.00 3.06
2216 9254 2.618816 CCCTAAGCAGCCAAAGATGTGA 60.619 50.000 0.00 0.00 0.00 3.58
2217 9255 1.747355 CCCTAAGCAGCCAAAGATGTG 59.253 52.381 0.00 0.00 0.00 3.21
2218 9256 1.957113 GCCCTAAGCAGCCAAAGATGT 60.957 52.381 0.00 0.00 42.97 3.06
2219 9257 0.743097 GCCCTAAGCAGCCAAAGATG 59.257 55.000 0.00 0.00 42.97 2.90
2220 9258 3.197664 GCCCTAAGCAGCCAAAGAT 57.802 52.632 0.00 0.00 42.97 2.40
2221 9259 4.743018 GCCCTAAGCAGCCAAAGA 57.257 55.556 0.00 0.00 42.97 2.52
2242 9280 0.881118 ATTTTGCGGATCAGCGTTGT 59.119 45.000 13.25 0.00 40.67 3.32
2266 9306 2.815211 TTCGCGGACAGATGCTGC 60.815 61.111 6.13 0.00 34.37 5.25
2282 9322 0.471211 TCGGAGACTTGTCCCCTGTT 60.471 55.000 0.10 0.00 32.26 3.16
2320 9367 1.153369 GCAGGCAGCGTTGGATAGA 60.153 57.895 0.16 0.00 0.00 1.98
2471 9529 5.352016 CACCCGGTTAATCTCGTTGAATTTA 59.648 40.000 0.00 0.00 0.00 1.40
2493 9552 7.762159 TCCTTCCATGAAAAACTTGTTAAACAC 59.238 33.333 0.00 0.00 0.00 3.32
2514 9577 5.661056 TGTATGGGACGATATGATCCTTC 57.339 43.478 0.00 0.00 35.15 3.46
2516 9579 6.322456 CAGTATGTATGGGACGATATGATCCT 59.678 42.308 0.00 0.00 35.15 3.24
2524 9587 3.501349 AGAGCAGTATGTATGGGACGAT 58.499 45.455 0.00 0.00 39.31 3.73
2649 9729 6.909849 TTTGTTGATTGATTCATTCGTTCG 57.090 33.333 4.58 0.00 33.34 3.95
2715 9799 2.658422 CAAGGTGGCCATTGCACC 59.342 61.111 9.72 4.60 40.13 5.01
2915 10052 4.142315 GGATGAGTTGTTGTGCTATGCATT 60.142 41.667 3.54 0.00 41.91 3.56


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

AutoCloner maintained by Alex Coulton.