Multiple sequence alignment - TraesCS7B01G456300

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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 TraesCS7B01G456300 chr7B 100.000 3801 0 0 1 3801 716597642 716593842 0.000000e+00 7020.0
1 TraesCS7B01G456300 chr7B 100.000 3388 0 0 5651 9038 716591992 716588605 0.000000e+00 6257.0
2 TraesCS7B01G456300 chr7B 99.784 3234 6 1 5806 9038 716578338 716575105 0.000000e+00 5932.0
3 TraesCS7B01G456300 chr7B 86.910 2246 223 39 1609 3801 716540938 716538711 0.000000e+00 2453.0
4 TraesCS7B01G456300 chr7B 87.500 1080 130 5 7840 8917 716537247 716536171 0.000000e+00 1242.0
5 TraesCS7B01G456300 chr7B 81.943 803 97 27 604 1391 716541803 716541034 3.560000e-178 636.0
6 TraesCS7B01G456300 chr7B 82.883 555 64 14 1 533 691170311 691169766 3.820000e-128 470.0
7 TraesCS7B01G456300 chr7B 80.261 537 72 22 1 511 37923970 37923442 3.080000e-99 374.0
8 TraesCS7B01G456300 chr7B 93.401 197 13 0 7270 7466 265570185 265570381 8.880000e-75 292.0
9 TraesCS7B01G456300 chr7B 90.355 197 19 0 7270 7466 220064725 220064921 9.000000e-65 259.0
10 TraesCS7B01G456300 chr7B 89.899 198 20 0 7269 7466 446486070 446486267 1.160000e-63 255.0
11 TraesCS7B01G456300 chr7B 74.449 544 106 19 2257 2772 716540004 716539466 4.280000e-48 204.0
12 TraesCS7B01G456300 chr7B 81.651 109 18 2 7063 7170 716377695 716377588 1.250000e-13 89.8
13 TraesCS7B01G456300 chr7B 94.340 53 3 0 527 579 691169741 691169689 2.090000e-11 82.4
14 TraesCS7B01G456300 chr7B 81.000 100 19 0 7071 7170 716488352 716488253 7.520000e-11 80.5
15 TraesCS7B01G456300 chrUn 99.814 3233 6 0 5806 9038 224988561 224991793 0.000000e+00 5938.0
16 TraesCS7B01G456300 chrUn 99.722 3234 8 1 5806 9038 318480296 318483529 0.000000e+00 5921.0
17 TraesCS7B01G456300 chrUn 99.892 1848 2 0 5651 7498 342319939 342318092 0.000000e+00 3402.0
18 TraesCS7B01G456300 chrUn 99.704 1692 3 1 589 2280 378989422 378987733 0.000000e+00 3096.0
19 TraesCS7B01G456300 chrUn 100.000 517 0 0 8522 9038 231072708 231072192 0.000000e+00 955.0
20 TraesCS7B01G456300 chrUn 100.000 487 0 0 3315 3801 404361645 404361159 0.000000e+00 900.0
21 TraesCS7B01G456300 chrUn 99.360 469 1 1 1741 2209 475479244 475479710 0.000000e+00 848.0
22 TraesCS7B01G456300 chr7A 89.932 1907 163 7 1920 3801 715136767 715134865 0.000000e+00 2431.0
23 TraesCS7B01G456300 chr7A 90.992 1099 95 2 2704 3801 715130147 715129052 0.000000e+00 1478.0
24 TraesCS7B01G456300 chr7A 84.624 891 115 13 8160 9038 714864948 714864068 0.000000e+00 867.0
25 TraesCS7B01G456300 chr7A 83.230 805 103 18 609 1391 715138056 715137262 0.000000e+00 710.0
26 TraesCS7B01G456300 chr7A 80.403 546 89 14 8307 8847 715090029 715089497 5.080000e-107 399.0
27 TraesCS7B01G456300 chr7A 90.987 233 19 1 6955 7187 715091621 715091391 6.810000e-81 313.0
28 TraesCS7B01G456300 chr7A 90.000 210 19 2 7889 8098 714865166 714864959 4.160000e-68 270.0
29 TraesCS7B01G456300 chr7A 92.357 157 7 5 6281 6432 715114640 715114484 1.530000e-52 219.0
30 TraesCS7B01G456300 chr7A 94.382 89 4 1 7468 7555 715091111 715091023 1.580000e-27 135.0
31 TraesCS7B01G456300 chr7A 77.727 220 39 7 6967 7183 711590382 711590594 9.530000e-25 126.0
32 TraesCS7B01G456300 chr7A 82.517 143 22 3 371 510 718419931 718419789 1.230000e-23 122.0
33 TraesCS7B01G456300 chr7A 90.217 92 8 1 7464 7554 714872012 714871921 1.590000e-22 119.0
34 TraesCS7B01G456300 chr7D 89.178 1959 178 9 1872 3800 619992236 619994190 0.000000e+00 2412.0
35 TraesCS7B01G456300 chr7D 79.815 1080 167 34 7840 8902 620099533 620100578 0.000000e+00 739.0
36 TraesCS7B01G456300 chr7D 83.396 801 103 16 609 1388 619991234 619992025 0.000000e+00 715.0
37 TraesCS7B01G456300 chr7D 82.468 616 82 13 793 1391 619897282 619896676 4.840000e-142 516.0
38 TraesCS7B01G456300 chr7D 88.679 212 21 3 7840 8049 620124291 620124501 1.160000e-63 255.0
39 TraesCS7B01G456300 chr7D 92.135 89 6 1 7468 7555 620099409 620099497 3.430000e-24 124.0
40 TraesCS7B01G456300 chr5A 78.632 585 113 9 3220 3801 552161622 552162197 2.380000e-100 377.0
41 TraesCS7B01G456300 chr5A 76.023 171 37 3 2757 2925 552160858 552161026 1.620000e-12 86.1
42 TraesCS7B01G456300 chr4B 88.043 276 31 2 7546 7820 42938146 42938420 8.750000e-85 326.0
43 TraesCS7B01G456300 chr1D 90.574 244 23 0 7566 7809 438211197 438210954 3.150000e-84 324.0
44 TraesCS7B01G456300 chr1D 83.113 302 42 8 233 533 357551864 357552157 5.380000e-67 267.0
45 TraesCS7B01G456300 chr3D 88.302 265 30 1 7562 7825 169450449 169450185 5.270000e-82 316.0
46 TraesCS7B01G456300 chr3D 94.340 53 3 0 527 579 585416240 585416188 2.090000e-11 82.4
47 TraesCS7B01G456300 chr2B 87.778 270 29 4 7553 7820 682945388 682945655 6.810000e-81 313.0
48 TraesCS7B01G456300 chr2B 86.525 282 36 2 7541 7821 801215302 801215582 8.810000e-80 309.0
49 TraesCS7B01G456300 chr2B 90.566 53 5 0 527 579 683565926 683565874 4.530000e-08 71.3
50 TraesCS7B01G456300 chr2D 87.085 271 32 3 7552 7821 120561225 120561493 4.100000e-78 303.0
51 TraesCS7B01G456300 chr6B 93.434 198 12 1 7269 7466 373467103 373466907 8.880000e-75 292.0
52 TraesCS7B01G456300 chr3B 92.386 197 15 0 7270 7466 298641848 298642044 1.920000e-71 281.0
53 TraesCS7B01G456300 chr3B 92.453 53 4 0 527 579 168034439 168034387 9.730000e-10 76.8
54 TraesCS7B01G456300 chr5D 76.163 172 37 2 2757 2926 436950341 436950510 4.500000e-13 87.9
55 TraesCS7B01G456300 chr4A 94.340 53 3 0 527 579 669176907 669176959 2.090000e-11 82.4
56 TraesCS7B01G456300 chr5B 88.679 53 6 0 527 579 517219590 517219642 2.110000e-06 65.8
57 TraesCS7B01G456300 chr3A 87.719 57 5 2 526 580 582676883 582676939 2.110000e-06 65.8


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 TraesCS7B01G456300 chr7B 716588605 716597642 9037 True 6638.500000 7020 100.000000 1 9038 2 chr7B.!!$R7 9037
1 TraesCS7B01G456300 chr7B 716575105 716578338 3233 True 5932.000000 5932 99.784000 5806 9038 1 chr7B.!!$R4 3232
2 TraesCS7B01G456300 chr7B 716536171 716541803 5632 True 1133.750000 2453 82.700500 604 8917 4 chr7B.!!$R6 8313
3 TraesCS7B01G456300 chr7B 37923442 37923970 528 True 374.000000 374 80.261000 1 511 1 chr7B.!!$R1 510
4 TraesCS7B01G456300 chr7B 691169689 691170311 622 True 276.200000 470 88.611500 1 579 2 chr7B.!!$R5 578
5 TraesCS7B01G456300 chrUn 224988561 224991793 3232 False 5938.000000 5938 99.814000 5806 9038 1 chrUn.!!$F1 3232
6 TraesCS7B01G456300 chrUn 318480296 318483529 3233 False 5921.000000 5921 99.722000 5806 9038 1 chrUn.!!$F2 3232
7 TraesCS7B01G456300 chrUn 342318092 342319939 1847 True 3402.000000 3402 99.892000 5651 7498 1 chrUn.!!$R2 1847
8 TraesCS7B01G456300 chrUn 378987733 378989422 1689 True 3096.000000 3096 99.704000 589 2280 1 chrUn.!!$R3 1691
9 TraesCS7B01G456300 chrUn 231072192 231072708 516 True 955.000000 955 100.000000 8522 9038 1 chrUn.!!$R1 516
10 TraesCS7B01G456300 chr7A 715134865 715138056 3191 True 1570.500000 2431 86.581000 609 3801 2 chr7A.!!$R7 3192
11 TraesCS7B01G456300 chr7A 715129052 715130147 1095 True 1478.000000 1478 90.992000 2704 3801 1 chr7A.!!$R3 1097
12 TraesCS7B01G456300 chr7A 714864068 714865166 1098 True 568.500000 867 87.312000 7889 9038 2 chr7A.!!$R5 1149
13 TraesCS7B01G456300 chr7A 715089497 715091621 2124 True 282.333333 399 88.590667 6955 8847 3 chr7A.!!$R6 1892
14 TraesCS7B01G456300 chr7D 619991234 619994190 2956 False 1563.500000 2412 86.287000 609 3800 2 chr7D.!!$F2 3191
15 TraesCS7B01G456300 chr7D 619896676 619897282 606 True 516.000000 516 82.468000 793 1391 1 chr7D.!!$R1 598
16 TraesCS7B01G456300 chr7D 620099409 620100578 1169 False 431.500000 739 85.975000 7468 8902 2 chr7D.!!$F3 1434
17 TraesCS7B01G456300 chr5A 552160858 552162197 1339 False 231.550000 377 77.327500 2757 3801 2 chr5A.!!$F1 1044

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
125 128 0.109551 CAGACACATCGAGAGCACGT 60.110 55.000 0.0 0.0 34.70 4.49 F
561 585 0.248949 GTACTAGCCCGTGCAGTAGC 60.249 60.000 0.0 0.0 41.13 3.58 F
579 603 0.319297 GCACGGGTTGACGACTAGTT 60.319 55.000 0.0 0.0 37.61 2.24 F
582 606 1.000938 ACGGGTTGACGACTAGTTCAC 60.001 52.381 0.0 0.0 37.61 3.18 F
583 607 1.268899 CGGGTTGACGACTAGTTCACT 59.731 52.381 0.0 0.0 35.47 3.41 F
584 608 2.288030 CGGGTTGACGACTAGTTCACTT 60.288 50.000 0.0 0.0 35.47 3.16 F
585 609 3.058016 CGGGTTGACGACTAGTTCACTTA 60.058 47.826 0.0 0.0 35.47 2.24 F
2362 2591 3.649981 AGATCCTTGCAGCATATACACCT 59.350 43.478 0.0 0.0 0.00 4.00 F
3264 3921 0.036732 ACCACCATGTTCACGCTCAT 59.963 50.000 0.0 0.0 0.00 2.90 F
3663 4320 0.464452 CGCTTAGGGGGAGGTACAAG 59.536 60.000 0.0 0.0 0.00 3.16 F
3708 4365 2.307768 GGGTCATCATCTGAGGTCGTA 58.692 52.381 0.0 0.0 33.51 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 2529 9.145865 TGAAACTTTCTTAAAATTGTTGTCACC 57.854 29.630 3.22 0.0 0.00 4.02 R
2426 2655 4.324267 CCGTATGACCCTGAAACTTCTTT 58.676 43.478 0.00 0.0 0.00 2.52 R
2504 2733 6.545298 GCAGATTCTTCCTTTGGAGTATCATT 59.455 38.462 0.00 0.0 36.25 2.57 R
2728 2987 6.850752 TCAACACCATAAGACACTGAGATA 57.149 37.500 0.00 0.0 0.00 1.98 R
2773 3032 9.716531 TCTTTTGATCCATATGTCACAGATATC 57.283 33.333 1.24 0.0 0.00 1.63 R
2804 3063 3.583086 CCTGAGGGTTCCTTCAGAGTTTA 59.417 47.826 25.62 0.0 33.66 2.01 R
2881 3140 0.248215 GATTTTCATGGCCGTCTGCG 60.248 55.000 0.00 0.0 42.61 5.18 R
3708 4365 1.136329 AGGTCAGGTCATGGCAGGTT 61.136 55.000 0.00 0.0 34.12 3.50 R
5804 6461 9.162764 TGTTCTGTTCTTCCTGTTTATTATAGC 57.837 33.333 0.00 0.0 0.00 2.97 R
7903 9620 5.938125 TCTTCTTCGGGTTAATTTCCTCAAG 59.062 40.000 0.00 0.0 0.00 3.02 R
8398 10614 4.101114 CCATATACTATACCTGTGGCCCA 58.899 47.826 0.00 0.0 0.00 5.36 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
38 39 7.833786 ACATGTTGAAATAATGAGCACTTGAT 58.166 30.769 0.00 0.00 0.00 2.57
49 50 2.730990 CACTTGATTGGTGGGTGCA 58.269 52.632 0.00 0.00 0.00 4.57
50 51 1.039068 CACTTGATTGGTGGGTGCAA 58.961 50.000 0.00 0.00 0.00 4.08
51 52 1.619827 CACTTGATTGGTGGGTGCAAT 59.380 47.619 0.00 0.00 0.00 3.56
56 57 1.895131 GATTGGTGGGTGCAATGAAGT 59.105 47.619 0.00 0.00 0.00 3.01
125 128 0.109551 CAGACACATCGAGAGCACGT 60.110 55.000 0.00 0.00 34.70 4.49
130 133 1.103803 ACATCGAGAGCACGTATGGT 58.896 50.000 0.00 0.00 39.96 3.55
150 173 6.446781 TGGTGTAACTAAATACCGAGAGAG 57.553 41.667 0.00 0.00 35.98 3.20
158 181 6.069331 ACTAAATACCGAGAGAGAATGGCTA 58.931 40.000 0.00 0.00 0.00 3.93
161 184 5.652994 ATACCGAGAGAGAATGGCTATTC 57.347 43.478 14.51 14.51 42.44 1.75
163 186 2.323959 CGAGAGAGAATGGCTATTCGC 58.676 52.381 16.90 16.90 45.84 4.70
240 263 7.096551 GGTAACCGACAAATAGTAAGTGGTAA 58.903 38.462 0.00 0.00 0.00 2.85
268 291 8.654230 AGCGAAATCATGGATGATATATGTAC 57.346 34.615 2.53 0.00 46.22 2.90
270 293 9.049523 GCGAAATCATGGATGATATATGTACAT 57.950 33.333 13.93 13.93 46.22 2.29
376 400 5.752955 ACATATTTTGTTGTGGCACAAAGAC 59.247 36.000 32.60 22.21 45.21 3.01
378 402 1.846007 TTGTTGTGGCACAAAGACCT 58.154 45.000 32.60 0.00 44.16 3.85
379 403 2.719531 TGTTGTGGCACAAAGACCTA 57.280 45.000 32.60 8.30 44.16 3.08
380 404 3.222173 TGTTGTGGCACAAAGACCTAT 57.778 42.857 32.60 0.00 44.16 2.57
381 405 4.359434 TGTTGTGGCACAAAGACCTATA 57.641 40.909 32.60 6.70 44.16 1.31
382 406 4.069304 TGTTGTGGCACAAAGACCTATAC 58.931 43.478 32.60 18.70 44.16 1.47
383 407 4.069304 GTTGTGGCACAAAGACCTATACA 58.931 43.478 32.60 5.34 44.16 2.29
384 408 3.937814 TGTGGCACAAAGACCTATACAG 58.062 45.455 19.74 0.00 44.16 2.74
385 409 3.580895 TGTGGCACAAAGACCTATACAGA 59.419 43.478 19.74 0.00 44.16 3.41
386 410 4.041075 TGTGGCACAAAGACCTATACAGAA 59.959 41.667 19.74 0.00 44.16 3.02
387 411 5.001232 GTGGCACAAAGACCTATACAGAAA 58.999 41.667 13.86 0.00 44.16 2.52
388 412 5.472137 GTGGCACAAAGACCTATACAGAAAA 59.528 40.000 13.86 0.00 44.16 2.29
389 413 6.151144 GTGGCACAAAGACCTATACAGAAAAT 59.849 38.462 13.86 0.00 44.16 1.82
390 414 6.719370 TGGCACAAAGACCTATACAGAAAATT 59.281 34.615 0.00 0.00 31.92 1.82
391 415 7.094377 TGGCACAAAGACCTATACAGAAAATTC 60.094 37.037 0.00 0.00 31.92 2.17
392 416 7.094377 GGCACAAAGACCTATACAGAAAATTCA 60.094 37.037 0.00 0.00 0.00 2.57
393 417 8.296713 GCACAAAGACCTATACAGAAAATTCAA 58.703 33.333 0.00 0.00 0.00 2.69
429 453 6.834168 ATCCACAATGTTTTAAGTGTAGGG 57.166 37.500 0.00 0.00 0.00 3.53
430 454 5.697067 TCCACAATGTTTTAAGTGTAGGGT 58.303 37.500 0.00 0.00 0.00 4.34
431 455 5.533154 TCCACAATGTTTTAAGTGTAGGGTG 59.467 40.000 0.00 0.00 0.00 4.61
432 456 5.300792 CCACAATGTTTTAAGTGTAGGGTGT 59.699 40.000 0.00 0.00 0.00 4.16
433 457 6.487331 CCACAATGTTTTAAGTGTAGGGTGTA 59.513 38.462 0.00 0.00 0.00 2.90
434 458 7.175990 CCACAATGTTTTAAGTGTAGGGTGTAT 59.824 37.037 0.00 0.00 0.00 2.29
435 459 8.020819 CACAATGTTTTAAGTGTAGGGTGTATG 58.979 37.037 0.00 0.00 0.00 2.39
436 460 7.175990 ACAATGTTTTAAGTGTAGGGTGTATGG 59.824 37.037 0.00 0.00 0.00 2.74
437 461 6.436738 TGTTTTAAGTGTAGGGTGTATGGA 57.563 37.500 0.00 0.00 0.00 3.41
438 462 6.839454 TGTTTTAAGTGTAGGGTGTATGGAA 58.161 36.000 0.00 0.00 0.00 3.53
439 463 7.288560 TGTTTTAAGTGTAGGGTGTATGGAAA 58.711 34.615 0.00 0.00 0.00 3.13
440 464 7.945664 TGTTTTAAGTGTAGGGTGTATGGAAAT 59.054 33.333 0.00 0.00 0.00 2.17
441 465 9.452287 GTTTTAAGTGTAGGGTGTATGGAAATA 57.548 33.333 0.00 0.00 0.00 1.40
553 577 7.933215 AATTTTTGAATAAGTACTAGCCCGT 57.067 32.000 0.00 0.00 0.00 5.28
554 578 6.730960 TTTTTGAATAAGTACTAGCCCGTG 57.269 37.500 0.00 0.00 0.00 4.94
555 579 3.447918 TGAATAAGTACTAGCCCGTGC 57.552 47.619 0.00 0.00 37.95 5.34
556 580 2.761767 TGAATAAGTACTAGCCCGTGCA 59.238 45.455 0.00 0.00 41.13 4.57
557 581 3.181479 TGAATAAGTACTAGCCCGTGCAG 60.181 47.826 0.00 0.00 41.13 4.41
558 582 1.843368 TAAGTACTAGCCCGTGCAGT 58.157 50.000 0.00 0.00 41.13 4.40
559 583 1.843368 AAGTACTAGCCCGTGCAGTA 58.157 50.000 0.00 0.00 41.13 2.74
560 584 1.390565 AGTACTAGCCCGTGCAGTAG 58.609 55.000 0.00 0.00 41.13 2.57
561 585 0.248949 GTACTAGCCCGTGCAGTAGC 60.249 60.000 0.00 0.00 41.13 3.58
571 595 3.562635 GCAGTAGCACGGGTTGAC 58.437 61.111 0.00 0.00 41.58 3.18
572 596 2.380410 GCAGTAGCACGGGTTGACG 61.380 63.158 0.00 0.00 41.58 4.35
573 597 1.287815 CAGTAGCACGGGTTGACGA 59.712 57.895 0.00 0.00 37.61 4.20
574 598 1.007336 CAGTAGCACGGGTTGACGAC 61.007 60.000 0.00 0.00 37.61 4.34
575 599 1.177256 AGTAGCACGGGTTGACGACT 61.177 55.000 0.00 0.00 37.61 4.18
576 600 0.523072 GTAGCACGGGTTGACGACTA 59.477 55.000 0.00 0.00 37.61 2.59
577 601 0.806868 TAGCACGGGTTGACGACTAG 59.193 55.000 0.00 0.00 37.61 2.57
578 602 1.177256 AGCACGGGTTGACGACTAGT 61.177 55.000 0.00 0.00 37.61 2.57
579 603 0.319297 GCACGGGTTGACGACTAGTT 60.319 55.000 0.00 0.00 37.61 2.24
580 604 1.694639 CACGGGTTGACGACTAGTTC 58.305 55.000 0.00 0.00 37.61 3.01
581 605 1.001048 CACGGGTTGACGACTAGTTCA 60.001 52.381 0.00 0.00 37.61 3.18
582 606 1.000938 ACGGGTTGACGACTAGTTCAC 60.001 52.381 0.00 0.00 37.61 3.18
583 607 1.268899 CGGGTTGACGACTAGTTCACT 59.731 52.381 0.00 0.00 35.47 3.41
584 608 2.288030 CGGGTTGACGACTAGTTCACTT 60.288 50.000 0.00 0.00 35.47 3.16
585 609 3.058016 CGGGTTGACGACTAGTTCACTTA 60.058 47.826 0.00 0.00 35.47 2.24
586 610 4.557296 CGGGTTGACGACTAGTTCACTTAA 60.557 45.833 0.00 0.00 35.47 1.85
587 611 4.683320 GGGTTGACGACTAGTTCACTTAAC 59.317 45.833 0.00 0.00 38.46 2.01
2300 2529 4.743057 TCAGTGTCATATGGGTCAGAAG 57.257 45.455 2.13 0.00 0.00 2.85
2327 2556 9.952341 GTGACAACAATTTTAAGAAAGTTTCAC 57.048 29.630 17.65 0.00 0.00 3.18
2362 2591 3.649981 AGATCCTTGCAGCATATACACCT 59.350 43.478 0.00 0.00 0.00 4.00
2398 2627 7.939784 AAACCTTAAGGAAATATCTGTGTCC 57.060 36.000 28.52 0.00 38.94 4.02
2412 2641 5.102953 TCTGTGTCCTATGGATCAAAAGG 57.897 43.478 0.00 0.00 32.73 3.11
2446 2675 5.048713 CCACAAAGAAGTTTCAGGGTCATAC 60.049 44.000 0.00 0.00 0.00 2.39
2462 2691 4.179298 GTCATACGGGTTAGAAGGTGAAC 58.821 47.826 0.00 0.00 0.00 3.18
2504 2733 6.941857 TCACTGTCTTATGGTATAAACAGCA 58.058 36.000 15.60 0.00 38.09 4.41
2527 2756 6.545298 GCAATGATACTCCAAAGGAAGAATCT 59.455 38.462 0.00 0.00 0.00 2.40
2531 2760 4.313020 ACTCCAAAGGAAGAATCTGCAT 57.687 40.909 0.00 0.00 0.00 3.96
2551 2780 9.412460 TCTGCATATGAAGAAAATGTAAAGGAT 57.588 29.630 11.28 0.00 0.00 3.24
2629 2858 5.789643 ATTTAAAGAAGAACCTTGCAGCA 57.210 34.783 0.00 0.00 0.00 4.41
2715 2974 8.122481 AGGAATATCTGGGTTAAAAGGTGAAAT 58.878 33.333 0.00 0.00 0.00 2.17
2773 3032 5.884232 TGATGACCATGAAAATCTGAAGGAG 59.116 40.000 0.00 0.00 0.00 3.69
2804 3063 8.756486 TGTGACATATGGATCAAAAGATCAAT 57.244 30.769 7.80 4.50 33.44 2.57
2880 3139 9.548208 GTTAAAAGAAATCTCAGTGTCTTATGC 57.452 33.333 0.00 0.00 30.24 3.14
2881 3140 6.749923 AAAGAAATCTCAGTGTCTTATGCC 57.250 37.500 0.00 0.00 30.24 4.40
2965 3224 0.942962 GCAAGGAAGCATCAGGATCG 59.057 55.000 0.00 0.00 0.00 3.69
3020 3279 5.670792 AATCTCGGTGTCTTATGGTGTAA 57.329 39.130 0.00 0.00 0.00 2.41
3022 3281 5.670792 TCTCGGTGTCTTATGGTGTAAAT 57.329 39.130 0.00 0.00 0.00 1.40
3028 3287 4.013728 TGTCTTATGGTGTAAATGGCCAC 58.986 43.478 8.16 0.00 34.84 5.01
3037 3296 3.063997 GTGTAAATGGCCACGAGATTCTG 59.936 47.826 8.16 0.00 0.00 3.02
3053 3605 0.473694 TCTGAAGGGAGGCTCCACAA 60.474 55.000 33.27 15.34 38.64 3.33
3058 3610 1.302832 GGGAGGCTCCACAACACAG 60.303 63.158 33.27 0.00 38.64 3.66
3070 3692 4.036262 TCCACAACACAGGAAGAAAATTCG 59.964 41.667 0.00 0.00 0.00 3.34
3079 3701 4.457257 CAGGAAGAAAATTCGAAGGAAGCT 59.543 41.667 3.35 0.00 35.19 3.74
3119 3741 6.367422 GTCAGTCGAAGAGAAAGATGAACAAT 59.633 38.462 0.00 0.00 36.95 2.71
3156 3794 5.535030 ACCAAGGTGAAGTTCATTTTCTACC 59.465 40.000 9.18 3.61 0.00 3.18
3249 3906 3.403558 GGAGAGGGGAGCCACCAC 61.404 72.222 0.00 0.00 43.70 4.16
3250 3907 3.403558 GAGAGGGGAGCCACCACC 61.404 72.222 0.00 0.00 44.65 4.61
3251 3908 4.270153 AGAGGGGAGCCACCACCA 62.270 66.667 0.00 0.00 44.65 4.17
3264 3921 0.036732 ACCACCATGTTCACGCTCAT 59.963 50.000 0.00 0.00 0.00 2.90
3331 3988 2.538141 TTGAGGCCAGGGTCCTTGG 61.538 63.158 15.83 15.83 33.24 3.61
3336 3993 2.829384 GCCAGGGTCCTTGGTCACA 61.829 63.158 20.59 0.00 0.00 3.58
3351 4008 3.632080 ACACCGACAATCCCGCCA 61.632 61.111 0.00 0.00 0.00 5.69
3366 4023 2.440147 CCAACCACCTCCATGCCA 59.560 61.111 0.00 0.00 0.00 4.92
3369 4026 2.541907 AACCACCTCCATGCCAGCT 61.542 57.895 0.00 0.00 0.00 4.24
3423 4080 1.979155 CTCCACCGAGCACCTCTCA 60.979 63.158 0.00 0.00 41.98 3.27
3564 4221 2.705821 CGAGTCCCTCGCTGAGCTT 61.706 63.158 1.78 0.00 46.75 3.74
3629 4286 0.475475 GTGGATCTGCCCATGGATGA 59.525 55.000 15.22 8.54 38.66 2.92
3636 4293 2.772191 CCCATGGATGACCCGGGA 60.772 66.667 32.02 5.69 45.49 5.14
3638 4295 1.612513 CCATGGATGACCCGGGAAA 59.387 57.895 32.02 15.76 37.93 3.13
3663 4320 0.464452 CGCTTAGGGGGAGGTACAAG 59.536 60.000 0.00 0.00 0.00 3.16
3708 4365 2.307768 GGGTCATCATCTGAGGTCGTA 58.692 52.381 0.00 0.00 33.51 3.43
8205 9927 1.920835 GCCCCTCTCCTTGTGTCCT 60.921 63.158 0.00 0.00 0.00 3.85
8398 10614 5.016831 GGTTGTAATGAAGAAATCCCCACT 58.983 41.667 0.00 0.00 0.00 4.00
8520 10744 3.737032 TGTTGATGTTGGTCACGACTA 57.263 42.857 0.00 0.00 31.91 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.956199 CCCACCAATCAAGTGCTCATTAT 59.044 43.478 0.00 0.00 33.75 1.28
25 26 2.173519 CCCACCAATCAAGTGCTCATT 58.826 47.619 0.00 0.00 33.75 2.57
38 39 1.039068 CACTTCATTGCACCCACCAA 58.961 50.000 0.00 0.00 0.00 3.67
49 50 7.147479 ACACATAGCCCTATCTAACACTTCATT 60.147 37.037 0.00 0.00 0.00 2.57
50 51 6.327626 ACACATAGCCCTATCTAACACTTCAT 59.672 38.462 0.00 0.00 0.00 2.57
51 52 5.661312 ACACATAGCCCTATCTAACACTTCA 59.339 40.000 0.00 0.00 0.00 3.02
56 57 4.714802 ACACACACATAGCCCTATCTAACA 59.285 41.667 0.00 0.00 0.00 2.41
108 111 2.112522 CATACGTGCTCTCGATGTGTC 58.887 52.381 0.00 0.00 34.70 3.67
109 112 1.202302 CCATACGTGCTCTCGATGTGT 60.202 52.381 0.00 0.00 34.70 3.72
125 128 7.994911 TCTCTCTCGGTATTTAGTTACACCATA 59.005 37.037 0.00 0.00 0.00 2.74
130 133 7.683704 GCCATTCTCTCTCGGTATTTAGTTACA 60.684 40.741 0.00 0.00 0.00 2.41
131 134 6.641723 GCCATTCTCTCTCGGTATTTAGTTAC 59.358 42.308 0.00 0.00 0.00 2.50
139 162 4.156922 CGAATAGCCATTCTCTCTCGGTAT 59.843 45.833 3.37 0.00 38.77 2.73
143 166 2.323959 GCGAATAGCCATTCTCTCTCG 58.676 52.381 3.37 0.00 38.77 4.04
158 181 7.903995 ATTTTTCAAAATATGTGTGGCGAAT 57.096 28.000 0.00 0.00 36.88 3.34
205 228 1.081094 GTCGGTTACCCATGTTTCCG 58.919 55.000 0.00 0.00 39.31 4.30
223 246 6.694447 TCGCTCTTTACCACTTACTATTTGT 58.306 36.000 0.00 0.00 0.00 2.83
225 248 8.788325 ATTTCGCTCTTTACCACTTACTATTT 57.212 30.769 0.00 0.00 0.00 1.40
240 263 8.045507 ACATATATCATCCATGATTTCGCTCTT 58.954 33.333 7.36 0.00 44.70 2.85
362 386 4.041075 TCTGTATAGGTCTTTGTGCCACAA 59.959 41.667 6.08 6.08 36.11 3.33
403 427 8.966868 CCCTACACTTAAAACATTGTGGATAAT 58.033 33.333 0.00 0.00 35.02 1.28
404 428 7.945664 ACCCTACACTTAAAACATTGTGGATAA 59.054 33.333 0.00 0.00 35.02 1.75
405 429 7.392113 CACCCTACACTTAAAACATTGTGGATA 59.608 37.037 0.00 0.00 35.02 2.59
406 430 6.208599 CACCCTACACTTAAAACATTGTGGAT 59.791 38.462 0.00 0.00 35.02 3.41
407 431 5.533154 CACCCTACACTTAAAACATTGTGGA 59.467 40.000 0.00 0.00 35.02 4.02
408 432 5.300792 ACACCCTACACTTAAAACATTGTGG 59.699 40.000 0.00 0.00 35.02 4.17
409 433 6.385649 ACACCCTACACTTAAAACATTGTG 57.614 37.500 0.00 0.00 36.59 3.33
410 434 7.175990 CCATACACCCTACACTTAAAACATTGT 59.824 37.037 0.00 0.00 0.00 2.71
411 435 7.392113 TCCATACACCCTACACTTAAAACATTG 59.608 37.037 0.00 0.00 0.00 2.82
412 436 7.463431 TCCATACACCCTACACTTAAAACATT 58.537 34.615 0.00 0.00 0.00 2.71
413 437 7.023171 TCCATACACCCTACACTTAAAACAT 57.977 36.000 0.00 0.00 0.00 2.71
414 438 6.436738 TCCATACACCCTACACTTAAAACA 57.563 37.500 0.00 0.00 0.00 2.83
415 439 7.748691 TTTCCATACACCCTACACTTAAAAC 57.251 36.000 0.00 0.00 0.00 2.43
527 551 9.623000 ACGGGCTAGTACTTATTCAAAAATTAT 57.377 29.630 0.00 0.00 0.00 1.28
528 552 8.885722 CACGGGCTAGTACTTATTCAAAAATTA 58.114 33.333 0.00 0.00 0.00 1.40
529 553 7.627726 GCACGGGCTAGTACTTATTCAAAAATT 60.628 37.037 0.00 0.00 36.96 1.82
530 554 6.183360 GCACGGGCTAGTACTTATTCAAAAAT 60.183 38.462 0.00 0.00 36.96 1.82
531 555 5.122711 GCACGGGCTAGTACTTATTCAAAAA 59.877 40.000 0.00 0.00 36.96 1.94
532 556 4.632688 GCACGGGCTAGTACTTATTCAAAA 59.367 41.667 0.00 0.00 36.96 2.44
533 557 4.186159 GCACGGGCTAGTACTTATTCAAA 58.814 43.478 0.00 0.00 36.96 2.69
534 558 3.196039 TGCACGGGCTAGTACTTATTCAA 59.804 43.478 12.74 0.00 41.91 2.69
535 559 2.761767 TGCACGGGCTAGTACTTATTCA 59.238 45.455 12.74 0.00 41.91 2.57
536 560 3.181478 ACTGCACGGGCTAGTACTTATTC 60.181 47.826 12.74 0.00 41.91 1.75
537 561 2.764572 ACTGCACGGGCTAGTACTTATT 59.235 45.455 12.74 0.00 41.91 1.40
538 562 2.385803 ACTGCACGGGCTAGTACTTAT 58.614 47.619 12.74 0.00 41.91 1.73
539 563 1.843368 ACTGCACGGGCTAGTACTTA 58.157 50.000 12.74 0.00 41.91 2.24
540 564 1.749634 CTACTGCACGGGCTAGTACTT 59.250 52.381 12.74 0.00 41.91 2.24
541 565 1.390565 CTACTGCACGGGCTAGTACT 58.609 55.000 12.74 0.00 41.91 2.73
542 566 0.248949 GCTACTGCACGGGCTAGTAC 60.249 60.000 12.74 8.29 41.91 2.73
543 567 0.681887 TGCTACTGCACGGGCTAGTA 60.682 55.000 12.74 15.68 45.31 1.82
544 568 1.982395 TGCTACTGCACGGGCTAGT 60.982 57.895 12.74 15.36 45.31 2.57
545 569 2.892640 TGCTACTGCACGGGCTAG 59.107 61.111 12.74 9.54 45.31 3.42
554 578 2.380410 CGTCAACCCGTGCTACTGC 61.380 63.158 0.00 0.00 40.20 4.40
555 579 1.007336 GTCGTCAACCCGTGCTACTG 61.007 60.000 0.00 0.00 0.00 2.74
556 580 1.177256 AGTCGTCAACCCGTGCTACT 61.177 55.000 0.00 0.00 0.00 2.57
557 581 0.523072 TAGTCGTCAACCCGTGCTAC 59.477 55.000 0.00 0.00 0.00 3.58
558 582 0.806868 CTAGTCGTCAACCCGTGCTA 59.193 55.000 0.00 0.00 0.00 3.49
559 583 1.177256 ACTAGTCGTCAACCCGTGCT 61.177 55.000 0.00 0.00 0.00 4.40
560 584 0.319297 AACTAGTCGTCAACCCGTGC 60.319 55.000 0.00 0.00 0.00 5.34
561 585 1.001048 TGAACTAGTCGTCAACCCGTG 60.001 52.381 0.00 0.00 0.00 4.94
562 586 1.000938 GTGAACTAGTCGTCAACCCGT 60.001 52.381 0.00 0.00 0.00 5.28
563 587 1.268899 AGTGAACTAGTCGTCAACCCG 59.731 52.381 0.00 0.00 0.00 5.28
564 588 3.382048 AAGTGAACTAGTCGTCAACCC 57.618 47.619 0.00 0.00 0.00 4.11
565 589 4.683320 GGTTAAGTGAACTAGTCGTCAACC 59.317 45.833 0.00 2.35 38.21 3.77
566 590 5.284079 TGGTTAAGTGAACTAGTCGTCAAC 58.716 41.667 0.00 0.00 38.21 3.18
567 591 5.518848 TGGTTAAGTGAACTAGTCGTCAA 57.481 39.130 0.00 0.00 38.21 3.18
568 592 5.717078 ATGGTTAAGTGAACTAGTCGTCA 57.283 39.130 0.00 0.00 38.21 4.35
569 593 6.850555 ACTATGGTTAAGTGAACTAGTCGTC 58.149 40.000 0.00 0.00 38.21 4.20
570 594 6.830873 ACTATGGTTAAGTGAACTAGTCGT 57.169 37.500 0.00 0.00 38.21 4.34
571 595 7.983307 AGTACTATGGTTAAGTGAACTAGTCG 58.017 38.462 0.00 0.00 38.21 4.18
572 596 8.404765 GGAGTACTATGGTTAAGTGAACTAGTC 58.595 40.741 0.00 0.00 38.21 2.59
573 597 7.341512 GGGAGTACTATGGTTAAGTGAACTAGT 59.658 40.741 0.00 0.00 38.21 2.57
574 598 7.560626 AGGGAGTACTATGGTTAAGTGAACTAG 59.439 40.741 0.00 0.00 38.21 2.57
575 599 7.416731 AGGGAGTACTATGGTTAAGTGAACTA 58.583 38.462 0.00 0.00 38.21 2.24
576 600 6.262207 AGGGAGTACTATGGTTAAGTGAACT 58.738 40.000 0.00 0.00 38.21 3.01
577 601 6.380560 AGAGGGAGTACTATGGTTAAGTGAAC 59.619 42.308 0.00 0.00 37.31 3.18
578 602 6.380274 CAGAGGGAGTACTATGGTTAAGTGAA 59.620 42.308 0.00 0.00 0.00 3.18
579 603 5.892119 CAGAGGGAGTACTATGGTTAAGTGA 59.108 44.000 0.00 0.00 0.00 3.41
580 604 5.657302 ACAGAGGGAGTACTATGGTTAAGTG 59.343 44.000 0.00 0.00 34.13 3.16
581 605 5.840081 ACAGAGGGAGTACTATGGTTAAGT 58.160 41.667 0.00 0.00 34.13 2.24
582 606 6.459848 CGAACAGAGGGAGTACTATGGTTAAG 60.460 46.154 0.00 0.00 34.13 1.85
583 607 5.359009 CGAACAGAGGGAGTACTATGGTTAA 59.641 44.000 0.00 0.00 34.13 2.01
584 608 4.885907 CGAACAGAGGGAGTACTATGGTTA 59.114 45.833 0.00 0.00 34.13 2.85
585 609 3.700038 CGAACAGAGGGAGTACTATGGTT 59.300 47.826 0.00 0.00 34.13 3.67
586 610 3.053842 TCGAACAGAGGGAGTACTATGGT 60.054 47.826 0.00 0.00 34.13 3.55
587 611 3.552875 TCGAACAGAGGGAGTACTATGG 58.447 50.000 0.00 0.00 34.13 2.74
2300 2529 9.145865 TGAAACTTTCTTAAAATTGTTGTCACC 57.854 29.630 3.22 0.00 0.00 4.02
2327 2556 6.750963 GCTGCAAGGATCTTCTTCAAATTTAG 59.249 38.462 0.00 0.00 0.00 1.85
2392 2621 4.567537 CCACCTTTTGATCCATAGGACACA 60.568 45.833 9.83 0.00 32.98 3.72
2398 2627 4.578105 GCTTCTCCACCTTTTGATCCATAG 59.422 45.833 0.00 0.00 0.00 2.23
2426 2655 4.324267 CCGTATGACCCTGAAACTTCTTT 58.676 43.478 0.00 0.00 0.00 2.52
2446 2675 6.753107 AAATTATGTTCACCTTCTAACCCG 57.247 37.500 0.00 0.00 0.00 5.28
2482 2711 8.046708 TCATTGCTGTTTATACCATAAGACAGT 58.953 33.333 15.03 0.00 37.43 3.55
2504 2733 6.545298 GCAGATTCTTCCTTTGGAGTATCATT 59.455 38.462 0.00 0.00 36.25 2.57
2551 2780 7.233553 CCTTCTAACCCATATGACACTGAGATA 59.766 40.741 3.65 0.00 0.00 1.98
2629 2858 9.730705 CCATATGACACAGATATTTCCTTGTAT 57.269 33.333 3.65 0.00 0.00 2.29
2728 2987 6.850752 TCAACACCATAAGACACTGAGATA 57.149 37.500 0.00 0.00 0.00 1.98
2773 3032 9.716531 TCTTTTGATCCATATGTCACAGATATC 57.283 33.333 1.24 0.00 0.00 1.63
2804 3063 3.583086 CCTGAGGGTTCCTTCAGAGTTTA 59.417 47.826 25.62 0.00 33.66 2.01
2881 3140 0.248215 GATTTTCATGGCCGTCTGCG 60.248 55.000 0.00 0.00 42.61 5.18
2965 3224 5.326900 TCCCTTTCACCTTTTAACCCATAC 58.673 41.667 0.00 0.00 0.00 2.39
3020 3279 2.636830 CTTCAGAATCTCGTGGCCATT 58.363 47.619 9.72 0.00 0.00 3.16
3022 3281 0.250234 CCTTCAGAATCTCGTGGCCA 59.750 55.000 0.00 0.00 0.00 5.36
3028 3287 1.068434 GAGCCTCCCTTCAGAATCTCG 59.932 57.143 0.00 0.00 0.00 4.04
3037 3296 0.606673 GTGTTGTGGAGCCTCCCTTC 60.607 60.000 8.62 0.00 35.03 3.46
3053 3605 4.714632 TCCTTCGAATTTTCTTCCTGTGT 58.285 39.130 0.00 0.00 0.00 3.72
3058 3610 5.644206 AGTAGCTTCCTTCGAATTTTCTTCC 59.356 40.000 0.00 0.00 0.00 3.46
3070 3692 6.014156 ACCCATATGACATAGTAGCTTCCTTC 60.014 42.308 3.65 0.00 0.00 3.46
3079 3701 5.627135 TCGACTGACCCATATGACATAGTA 58.373 41.667 3.65 0.00 0.00 1.82
3119 3741 1.780309 ACCTTGGTTCAGAATGTGGGA 59.220 47.619 0.00 0.00 37.40 4.37
3264 3921 5.221641 TGCCTCTTTCTTGTTCTTGTAGCTA 60.222 40.000 0.00 0.00 0.00 3.32
3336 3993 2.359478 GTTGGCGGGATTGTCGGT 60.359 61.111 0.00 0.00 0.00 4.69
3342 3999 2.355115 GAGGTGGTTGGCGGGATT 59.645 61.111 0.00 0.00 0.00 3.01
3351 4008 2.036256 GCTGGCATGGAGGTGGTT 59.964 61.111 0.00 0.00 0.00 3.67
3366 4023 2.680352 TCGCGGGGAAGAAGAGCT 60.680 61.111 6.13 0.00 0.00 4.09
3369 4026 1.515954 GATGTCGCGGGGAAGAAGA 59.484 57.895 6.13 0.00 0.00 2.87
3390 4047 1.839994 GTGGAGAATGGGATGGAGTCA 59.160 52.381 0.00 0.00 0.00 3.41
3484 4141 2.581354 GTGCTCGCAGGTCTCCAT 59.419 61.111 0.00 0.00 0.00 3.41
3586 4243 3.788766 GAACGCGCGGACATTGCT 61.789 61.111 35.22 7.19 0.00 3.91
3663 4320 4.980805 TTCCGTGCAGCCGTCACC 62.981 66.667 0.00 0.00 0.00 4.02
3708 4365 1.136329 AGGTCAGGTCATGGCAGGTT 61.136 55.000 0.00 0.00 34.12 3.50
5804 6461 9.162764 TGTTCTGTTCTTCCTGTTTATTATAGC 57.837 33.333 0.00 0.00 0.00 2.97
7903 9620 5.938125 TCTTCTTCGGGTTAATTTCCTCAAG 59.062 40.000 0.00 0.00 0.00 3.02
8398 10614 4.101114 CCATATACTATACCTGTGGCCCA 58.899 47.826 0.00 0.00 0.00 5.36
8520 10744 1.129058 AAGGAGAACAACGTGACCCT 58.871 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.