Multiple sequence alignment - TraesCS1B01G180100

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 TraesCS1B01G180100 chr1B 100.000 4400 0 0 1 4400 326911448 326915847 0.000000e+00 8126.0
1 TraesCS1B01G180100 chr1B 88.788 1106 93 14 1413 2495 327228260 327229357 0.000000e+00 1327.0
2 TraesCS1B01G180100 chr1B 88.225 1138 95 21 2494 3604 327229390 327230515 0.000000e+00 1323.0
3 TraesCS1B01G180100 chr1B 88.988 1008 77 9 395 1396 327227295 327228274 0.000000e+00 1216.0
4 TraesCS1B01G180100 chr1B 84.536 873 90 27 2709 3561 322475506 322476353 0.000000e+00 822.0
5 TraesCS1B01G180100 chr1B 88.855 655 49 5 1841 2495 327343065 327343695 0.000000e+00 784.0
6 TraesCS1B01G180100 chr1B 88.845 511 49 2 1961 2471 350442785 350442283 4.830000e-174 621.0
7 TraesCS1B01G180100 chr1B 84.945 631 45 22 527 1111 327339079 327339705 1.050000e-165 593.0
8 TraesCS1B01G180100 chr1B 83.721 645 83 17 759 1396 322473546 322474175 1.360000e-164 590.0
9 TraesCS1B01G180100 chr1B 88.462 442 44 6 1413 1853 327341193 327341628 1.080000e-145 527.0
10 TraesCS1B01G180100 chr1B 86.151 491 44 17 1 475 327226855 327227337 3.930000e-140 508.0
11 TraesCS1B01G180100 chr1B 84.783 368 51 4 1418 1785 322474166 322474528 8.990000e-97 364.0
12 TraesCS1B01G180100 chr1B 79.859 427 55 14 1 423 350444478 350444079 2.590000e-72 283.0
13 TraesCS1B01G180100 chr1B 84.815 270 25 5 1128 1396 327340953 327341207 1.570000e-64 257.0
14 TraesCS1B01G180100 chr1B 76.895 277 53 10 3608 3879 343994507 343994237 3.550000e-31 147.0
15 TraesCS1B01G180100 chr1D 94.266 2546 89 15 1413 3916 226943748 226946278 0.000000e+00 3840.0
16 TraesCS1B01G180100 chr1D 96.228 1405 42 7 1 1396 226942360 226943762 0.000000e+00 2290.0
17 TraesCS1B01G180100 chr1D 87.687 1941 136 50 1743 3604 227374625 227376541 0.000000e+00 2165.0
18 TraesCS1B01G180100 chr1D 91.135 1004 76 9 395 1390 227373210 227374208 0.000000e+00 1349.0
19 TraesCS1B01G180100 chr1D 86.545 1100 98 16 1419 2495 208416170 208415098 0.000000e+00 1166.0
20 TraesCS1B01G180100 chr1D 85.382 1033 103 27 2600 3604 208413329 208412317 0.000000e+00 1027.0
21 TraesCS1B01G180100 chr1D 88.509 818 70 10 2810 3604 226827568 226828384 0.000000e+00 968.0
22 TraesCS1B01G180100 chr1D 86.674 893 82 24 2700 3573 223164293 223165167 0.000000e+00 955.0
23 TraesCS1B01G180100 chr1D 90.432 648 47 8 1850 2495 226826343 226826977 0.000000e+00 839.0
24 TraesCS1B01G180100 chr1D 88.735 648 42 12 759 1396 226825346 226825972 0.000000e+00 763.0
25 TraesCS1B01G180100 chr1D 90.625 512 40 2 1961 2472 261723862 261724365 0.000000e+00 673.0
26 TraesCS1B01G180100 chr1D 92.391 460 32 2 3916 4372 226946323 226946782 0.000000e+00 652.0
27 TraesCS1B01G180100 chr1D 89.143 525 51 4 1955 2478 227648719 227649238 0.000000e+00 649.0
28 TraesCS1B01G180100 chr1D 86.519 586 55 14 2895 3457 226469232 226469816 1.340000e-174 623.0
29 TraesCS1B01G180100 chr1D 90.411 438 35 5 678 1111 208417413 208416979 1.780000e-158 569.0
30 TraesCS1B01G180100 chr1D 87.551 490 46 10 1 475 227372765 227373254 1.790000e-153 553.0
31 TraesCS1B01G180100 chr1D 88.987 454 38 8 667 1111 227646984 227647434 6.430000e-153 551.0
32 TraesCS1B01G180100 chr1D 85.516 504 60 5 656 1147 261722735 261723237 8.440000e-142 514.0
33 TraesCS1B01G180100 chr1D 87.918 389 42 3 1413 1800 226825958 226826342 1.870000e-123 453.0
34 TraesCS1B01G180100 chr1D 86.701 391 49 1 1413 1800 227648242 227648632 8.740000e-117 431.0
35 TraesCS1B01G180100 chr1D 86.286 350 42 5 1413 1758 227374200 227374547 4.150000e-100 375.0
36 TraesCS1B01G180100 chr1D 86.054 294 36 4 91 382 226824469 226824759 1.190000e-80 311.0
37 TraesCS1B01G180100 chr1D 87.361 269 22 2 1128 1395 227647998 227648255 9.250000e-77 298.0
38 TraesCS1B01G180100 chr1D 80.191 419 57 16 1 408 261722142 261722545 1.550000e-74 291.0
39 TraesCS1B01G180100 chr1D 86.296 270 25 2 1128 1396 208416420 208416162 2.590000e-72 283.0
40 TraesCS1B01G180100 chr1D 90.756 119 9 1 1278 1394 477867556 477867438 1.640000e-34 158.0
41 TraesCS1B01G180100 chr1D 86.093 151 12 6 527 668 208417602 208417452 2.120000e-33 154.0
42 TraesCS1B01G180100 chr1D 87.037 108 7 1 279 379 227646583 227646690 1.000000e-21 115.0
43 TraesCS1B01G180100 chr1D 80.368 163 13 11 59 206 208418390 208418232 6.020000e-19 106.0
44 TraesCS1B01G180100 chr1A 87.196 1109 106 17 1413 2495 294040053 294041151 0.000000e+00 1229.0
45 TraesCS1B01G180100 chr1A 86.288 1145 82 35 2494 3604 294041184 294042287 0.000000e+00 1175.0
46 TraesCS1B01G180100 chr1A 87.968 1014 69 21 395 1396 294039095 294040067 0.000000e+00 1147.0
47 TraesCS1B01G180100 chr1A 84.045 890 93 28 2709 3579 290126432 290127291 0.000000e+00 811.0
48 TraesCS1B01G180100 chr1A 89.194 509 45 4 1971 2478 338594656 338594157 1.040000e-175 627.0
49 TraesCS1B01G180100 chr1A 84.945 631 75 15 758 1384 290124481 290125095 4.830000e-174 621.0
50 TraesCS1B01G180100 chr1A 85.685 496 43 17 1 474 294038649 294039138 8.500000e-137 497.0
51 TraesCS1B01G180100 chr1A 84.022 363 52 5 1423 1785 290125103 290125459 1.170000e-90 344.0
52 TraesCS1B01G180100 chr1A 80.872 413 55 15 1 401 338596475 338596075 1.990000e-78 303.0
53 TraesCS1B01G180100 chr1A 79.851 268 44 8 3616 3880 580438356 580438096 2.090000e-43 187.0
54 TraesCS1B01G180100 chr1A 84.615 104 12 3 438 539 338596070 338595969 2.800000e-17 100.0
55 TraesCS1B01G180100 chr3A 87.636 461 51 4 3916 4372 685360924 685361382 8.380000e-147 531.0
56 TraesCS1B01G180100 chr5B 86.768 461 55 4 3916 4372 446878981 446878523 3.930000e-140 508.0
57 TraesCS1B01G180100 chrUn 86.534 453 53 8 3923 4370 115044127 115044576 3.950000e-135 492.0
58 TraesCS1B01G180100 chrUn 79.545 220 36 8 3664 3880 29316703 29316916 9.860000e-32 148.0
59 TraesCS1B01G180100 chr7B 86.334 461 52 5 3916 4372 69538691 69539144 3.950000e-135 492.0
60 TraesCS1B01G180100 chr7B 75.627 279 58 9 3608 3880 641169402 641169128 3.570000e-26 130.0
61 TraesCS1B01G180100 chr7D 79.730 740 89 31 2711 3446 90410250 90410932 3.080000e-131 479.0
62 TraesCS1B01G180100 chr7D 79.927 274 44 8 3614 3883 572758630 572758896 1.620000e-44 191.0
63 TraesCS1B01G180100 chr7D 75.986 279 54 12 3609 3880 13620137 13620409 9.930000e-27 132.0
64 TraesCS1B01G180100 chr2B 83.807 457 70 3 3919 4371 26242915 26242459 8.740000e-117 431.0
65 TraesCS1B01G180100 chr2B 83.117 462 71 5 3919 4374 26245456 26244996 8.800000e-112 414.0
66 TraesCS1B01G180100 chr4D 77.528 356 67 11 4023 4371 485381364 485381015 7.460000e-48 202.0
67 TraesCS1B01G180100 chr2D 80.216 278 44 6 3610 3879 617544092 617544366 9.650000e-47 198.0
68 TraesCS1B01G180100 chr2D 76.190 189 42 3 3962 4149 616359714 616359528 3.620000e-16 97.1
69 TraesCS1B01G180100 chr4A 89.109 101 10 1 3628 3728 166302837 166302936 1.660000e-24 124.0
70 TraesCS1B01G180100 chr5D 88.000 75 8 1 3627 3701 26712930 26713003 2.180000e-13 87.9


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 TraesCS1B01G180100 chr1B 326911448 326915847 4399 False 8126.000000 8126 100.000000 1 4400 1 chr1B.!!$F1 4399
1 TraesCS1B01G180100 chr1B 327226855 327230515 3660 False 1093.500000 1327 88.038000 1 3604 4 chr1B.!!$F3 3603
2 TraesCS1B01G180100 chr1B 322473546 322476353 2807 False 592.000000 822 84.346667 759 3561 3 chr1B.!!$F2 2802
3 TraesCS1B01G180100 chr1B 327339079 327343695 4616 False 540.250000 784 86.769250 527 2495 4 chr1B.!!$F4 1968
4 TraesCS1B01G180100 chr1B 350442283 350444478 2195 True 452.000000 621 84.352000 1 2471 2 chr1B.!!$R2 2470
5 TraesCS1B01G180100 chr1D 226942360 226946782 4422 False 2260.666667 3840 94.295000 1 4372 3 chr1D.!!$F4 4371
6 TraesCS1B01G180100 chr1D 227372765 227376541 3776 False 1110.500000 2165 88.164750 1 3604 4 chr1D.!!$F5 3603
7 TraesCS1B01G180100 chr1D 223164293 223165167 874 False 955.000000 955 86.674000 2700 3573 1 chr1D.!!$F1 873
8 TraesCS1B01G180100 chr1D 226824469 226828384 3915 False 666.800000 968 88.329600 91 3604 5 chr1D.!!$F3 3513
9 TraesCS1B01G180100 chr1D 226469232 226469816 584 False 623.000000 623 86.519000 2895 3457 1 chr1D.!!$F2 562
10 TraesCS1B01G180100 chr1D 208412317 208418390 6073 True 550.833333 1166 85.849167 59 3604 6 chr1D.!!$R2 3545
11 TraesCS1B01G180100 chr1D 261722142 261724365 2223 False 492.666667 673 85.444000 1 2472 3 chr1D.!!$F7 2471
12 TraesCS1B01G180100 chr1D 227646583 227649238 2655 False 408.800000 649 87.845800 279 2478 5 chr1D.!!$F6 2199
13 TraesCS1B01G180100 chr1A 294038649 294042287 3638 False 1012.000000 1229 86.784250 1 3604 4 chr1A.!!$F2 3603
14 TraesCS1B01G180100 chr1A 290124481 290127291 2810 False 592.000000 811 84.337333 758 3579 3 chr1A.!!$F1 2821
15 TraesCS1B01G180100 chr1A 338594157 338596475 2318 True 343.333333 627 84.893667 1 2478 3 chr1A.!!$R2 2477
16 TraesCS1B01G180100 chr7D 90410250 90410932 682 False 479.000000 479 79.730000 2711 3446 1 chr7D.!!$F2 735
17 TraesCS1B01G180100 chr2B 26242459 26245456 2997 True 422.500000 431 83.462000 3919 4374 2 chr2B.!!$R1 455

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
250 286 2.143925 GTGTGCCTACTGTGGTTCTTC 58.856 52.381 0.0 0.0 0.00 2.87 F
621 1109 2.740981 GTGCTGGTCTTGATGTCTTCTG 59.259 50.000 0.0 0.0 0.00 3.02 F
1408 3516 1.110518 GGAAGTGTCCCCCGCAAAAA 61.111 55.000 0.0 0.0 38.08 1.94 F
2526 6430 0.104671 TTCTTTGTGCAAGGCAAGGC 59.895 50.000 0.0 0.0 41.47 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 3497 1.110518 TTTTTGCGGGGGACACTTCC 61.111 55.0 0.00 0.00 41.95 3.46 R
2046 5867 2.160417 CCAAAGTTGTAGCTAGCTGCAC 59.840 50.0 31.79 24.86 45.94 4.57 R
3253 9165 1.508632 CGTCCACCTGTAAACACCAG 58.491 55.0 0.00 0.00 0.00 4.00 R
3685 9617 0.102663 TGGTTTTTCGCCCGGTTTTC 59.897 50.0 0.00 0.00 0.00 2.29 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
159 189 5.574082 TGCCGTGGTAATTATTTTTCATCG 58.426 37.500 0.00 0.00 0.00 3.84
250 286 2.143925 GTGTGCCTACTGTGGTTCTTC 58.856 52.381 0.00 0.00 0.00 2.87
325 695 5.348724 TGATTTAATCTCACTTGCAGACGAC 59.651 40.000 6.50 0.00 0.00 4.34
401 786 7.817478 TGTATGTCTAGTCAATCGTGATGTTTT 59.183 33.333 0.00 0.00 35.80 2.43
621 1109 2.740981 GTGCTGGTCTTGATGTCTTCTG 59.259 50.000 0.00 0.00 0.00 3.02
737 1346 7.011482 ACCTAGTATGCGTTCAAGATTTTGATC 59.989 37.037 0.00 0.00 42.60 2.92
849 1612 7.571080 TGCACATGAATTTTCTCATAGCATA 57.429 32.000 0.00 0.00 39.31 3.14
1111 1905 4.199432 TGCAAAAGGAAGTCTGCAAAAA 57.801 36.364 0.00 0.00 41.61 1.94
1317 3425 6.017933 GTGCATGAAGTGAAGAAATTAGACG 58.982 40.000 0.00 0.00 0.00 4.18
1384 3492 6.959639 TTCCTATGATTTCATTTACCAGGC 57.040 37.500 0.00 0.00 37.76 4.85
1385 3493 6.012337 TCCTATGATTTCATTTACCAGGCA 57.988 37.500 0.00 0.00 37.76 4.75
1386 3494 5.827797 TCCTATGATTTCATTTACCAGGCAC 59.172 40.000 0.00 0.00 37.76 5.01
1387 3495 5.010012 CCTATGATTTCATTTACCAGGCACC 59.990 44.000 0.00 0.00 37.76 5.01
1388 3496 4.046286 TGATTTCATTTACCAGGCACCT 57.954 40.909 0.00 0.00 0.00 4.00
1389 3497 3.763360 TGATTTCATTTACCAGGCACCTG 59.237 43.478 9.87 9.87 43.26 4.00
1397 3505 4.386413 CAGGCACCTGGAAGTGTC 57.614 61.111 8.93 0.00 42.82 3.67
1398 3506 1.302832 CAGGCACCTGGAAGTGTCC 60.303 63.158 8.93 0.00 43.55 4.02
1399 3507 2.034221 GGCACCTGGAAGTGTCCC 59.966 66.667 0.00 0.00 44.23 4.46
1400 3508 2.034221 GCACCTGGAAGTGTCCCC 59.966 66.667 0.00 0.00 44.23 4.81
1401 3509 2.757077 CACCTGGAAGTGTCCCCC 59.243 66.667 0.00 0.00 44.23 5.40
1402 3510 2.928396 ACCTGGAAGTGTCCCCCG 60.928 66.667 0.00 0.00 44.23 5.73
1403 3511 4.410400 CCTGGAAGTGTCCCCCGC 62.410 72.222 0.00 0.00 44.23 6.13
1404 3512 3.636231 CTGGAAGTGTCCCCCGCA 61.636 66.667 0.00 0.00 44.23 5.69
1405 3513 3.172106 TGGAAGTGTCCCCCGCAA 61.172 61.111 0.00 0.00 44.23 4.85
1406 3514 2.114411 GGAAGTGTCCCCCGCAAA 59.886 61.111 0.00 0.00 38.08 3.68
1407 3515 1.529713 GGAAGTGTCCCCCGCAAAA 60.530 57.895 0.00 0.00 38.08 2.44
1408 3516 1.110518 GGAAGTGTCCCCCGCAAAAA 61.111 55.000 0.00 0.00 38.08 1.94
1523 3631 1.660560 GCCAGGTCACATGGTGCATC 61.661 60.000 10.85 0.00 40.17 3.91
1624 3733 7.566760 TTTTCAAGCACGTCCATCATATTAT 57.433 32.000 0.00 0.00 0.00 1.28
1739 3856 9.487790 AAAATATGGTCAAGTACAATGTTTTGG 57.512 29.630 9.39 0.00 39.82 3.28
1754 3969 2.323939 TTTGGCATTAACAAGTCGCG 57.676 45.000 0.00 0.00 0.00 5.87
1887 5557 8.462811 AGTCTATTATGGTTCAGATAGCATACG 58.537 37.037 0.00 0.00 37.99 3.06
1964 5651 6.043474 TGCTTTCTTAACTAGGGTGAAGGTTA 59.957 38.462 0.00 0.00 35.22 2.85
2024 5838 5.635700 ACAAGTTCTTCGCTGTCTAATCTTC 59.364 40.000 0.00 0.00 0.00 2.87
2025 5839 4.749976 AGTTCTTCGCTGTCTAATCTTCC 58.250 43.478 0.00 0.00 0.00 3.46
2026 5840 4.220821 AGTTCTTCGCTGTCTAATCTTCCA 59.779 41.667 0.00 0.00 0.00 3.53
2027 5841 4.801330 TCTTCGCTGTCTAATCTTCCAA 57.199 40.909 0.00 0.00 0.00 3.53
2028 5842 4.748892 TCTTCGCTGTCTAATCTTCCAAG 58.251 43.478 0.00 0.00 0.00 3.61
2029 5843 4.220821 TCTTCGCTGTCTAATCTTCCAAGT 59.779 41.667 0.00 0.00 0.00 3.16
2030 5844 4.537135 TCGCTGTCTAATCTTCCAAGTT 57.463 40.909 0.00 0.00 0.00 2.66
2046 5867 8.373220 TCTTCCAAGTTCTAACCTTTACCTAAG 58.627 37.037 0.00 0.00 0.00 2.18
2067 5888 2.160417 GTGCAGCTAGCTACAACTTTGG 59.840 50.000 19.26 3.92 45.94 3.28
2338 6159 2.178912 TGGATCACTTTGTCCGTTCC 57.821 50.000 0.00 0.00 37.32 3.62
2495 6365 6.375455 CCGTACCTACTCACTTTAGGAACTTA 59.625 42.308 2.38 0.00 38.84 2.24
2526 6430 0.104671 TTCTTTGTGCAAGGCAAGGC 59.895 50.000 0.00 0.00 41.47 4.35
2580 6484 7.120726 AGCATTATACAACCAAAGAACTGTACC 59.879 37.037 0.00 0.00 0.00 3.34
2855 8705 8.794335 TGTACAATTGTAATGCTACCATGTTA 57.206 30.769 19.63 0.00 31.52 2.41
2892 8746 1.197430 ACTACAGCCAAGCTCAGCCT 61.197 55.000 0.00 0.00 36.40 4.58
3170 9065 2.843113 AGGTTCAGCTCTCCTTAGCAAT 59.157 45.455 0.00 0.00 45.30 3.56
3211 9106 5.368145 TGTGTGATTCAAGAAGCTAGTGTT 58.632 37.500 0.00 0.00 0.00 3.32
3215 9110 4.686091 TGATTCAAGAAGCTAGTGTTCGTG 59.314 41.667 13.14 13.14 35.48 4.35
3217 9112 3.902150 TCAAGAAGCTAGTGTTCGTGAG 58.098 45.455 16.12 4.35 37.46 3.51
3223 9121 3.839293 AGCTAGTGTTCGTGAGTTGATC 58.161 45.455 0.00 0.00 0.00 2.92
3224 9122 3.508012 AGCTAGTGTTCGTGAGTTGATCT 59.492 43.478 0.00 0.00 0.00 2.75
3253 9165 1.040646 TATGGTGATCGCAGGTCTCC 58.959 55.000 8.82 3.83 0.00 3.71
3326 9238 1.117142 AAACTCAAGGACCCGTCGGA 61.117 55.000 14.39 0.00 0.00 4.55
3417 9331 2.736670 AGATGTTTACCTCATGGCCC 57.263 50.000 0.00 0.00 36.63 5.80
3420 9334 0.035820 TGTTTACCTCATGGCCCGAC 60.036 55.000 0.00 0.00 36.63 4.79
3607 9534 9.099454 AGATTATGTCATCGGAAGTACTTTTTC 57.901 33.333 10.02 0.00 0.00 2.29
3632 9559 6.787085 TTTCTTTTCGAAACAAAGGCAAAA 57.213 29.167 10.79 0.41 36.72 2.44
3650 9582 4.380444 GCAAAAGATTTGCCTCGTCCATTA 60.380 41.667 15.12 0.00 39.38 1.90
3657 9589 4.893424 TTGCCTCGTCCATTAATTAAGC 57.107 40.909 3.94 0.05 0.00 3.09
3662 9594 5.065988 GCCTCGTCCATTAATTAAGCAGAAA 59.934 40.000 3.94 0.00 0.00 2.52
3666 9598 7.974675 TCGTCCATTAATTAAGCAGAAAAGAG 58.025 34.615 3.94 0.00 0.00 2.85
3668 9600 8.237267 CGTCCATTAATTAAGCAGAAAAGAGTT 58.763 33.333 3.94 0.00 0.00 3.01
3669 9601 9.346725 GTCCATTAATTAAGCAGAAAAGAGTTG 57.653 33.333 3.94 0.00 0.00 3.16
3670 9602 8.028938 TCCATTAATTAAGCAGAAAAGAGTTGC 58.971 33.333 3.94 0.00 38.09 4.17
3671 9603 7.276438 CCATTAATTAAGCAGAAAAGAGTTGCC 59.724 37.037 3.94 0.00 38.58 4.52
3672 9604 4.790765 ATTAAGCAGAAAAGAGTTGCCC 57.209 40.909 0.00 0.00 38.58 5.36
3685 9617 6.530019 AAGAGTTGCCCAGTTAATTATTGG 57.470 37.500 8.78 8.78 0.00 3.16
3695 9627 5.106442 CAGTTAATTATTGGAAAACCGGGC 58.894 41.667 6.32 0.00 0.00 6.13
3702 9634 0.102663 TGGAAAACCGGGCGAAAAAC 59.897 50.000 6.32 0.00 0.00 2.43
3714 9646 2.482142 GGCGAAAAACCATCACAAACCA 60.482 45.455 0.00 0.00 0.00 3.67
3749 9681 3.418684 GGATACCCAACACACAGTCTT 57.581 47.619 0.00 0.00 0.00 3.01
3754 9686 2.026262 ACCCAACACACAGTCTTCAACT 60.026 45.455 0.00 0.00 39.44 3.16
3775 9707 1.718757 GGGCATCATCAAGACCGCAC 61.719 60.000 0.00 0.00 31.28 5.34
3811 9743 5.718801 TCATCACTTCTCCTCTAGTAGGT 57.281 43.478 0.00 0.00 46.62 3.08
3833 9765 2.420022 CTCATCGCCAACCCTAAAACAG 59.580 50.000 0.00 0.00 0.00 3.16
3835 9767 1.600023 TCGCCAACCCTAAAACAGTG 58.400 50.000 0.00 0.00 0.00 3.66
3856 9788 0.384353 GCAAACGACTCCGACTTTGC 60.384 55.000 9.09 9.09 44.45 3.68
3880 9812 2.118679 AGATGATCATCGACCCAACCA 58.881 47.619 26.09 0.00 42.48 3.67
3883 9815 1.006832 GATCATCGACCCAACCAACG 58.993 55.000 0.00 0.00 0.00 4.10
3884 9816 1.024579 ATCATCGACCCAACCAACGC 61.025 55.000 0.00 0.00 0.00 4.84
3897 9829 0.387929 CCAACGCGGAAGAGGCTATA 59.612 55.000 12.47 0.00 36.56 1.31
3903 9835 1.404851 GCGGAAGAGGCTATATGGAGC 60.405 57.143 0.00 0.00 42.05 4.70
3940 9917 2.944349 GACGGAGAACTACGAAGGAGAT 59.056 50.000 13.52 0.00 39.85 2.75
3998 9975 1.141665 CACCCATCGCTCGTCATCA 59.858 57.895 0.00 0.00 0.00 3.07
4011 9988 2.299013 TCGTCATCATATACCACCTGGC 59.701 50.000 0.00 0.00 39.32 4.85
4037 10014 0.969894 ACGGCAGCTTAGACTTCACT 59.030 50.000 0.00 0.00 0.00 3.41
4084 10061 4.069232 CACGCCGGAGAAGAGCCA 62.069 66.667 13.83 0.00 0.00 4.75
4118 10095 3.054503 CCACGTCTCCGACCTCGT 61.055 66.667 0.00 0.00 37.74 4.18
4145 10122 4.392940 CCCCATTATTGTTGCCACAAAAA 58.607 39.130 7.52 0.00 46.17 1.94
4309 10287 1.360551 CGGCTAGATCCGTGTGAGG 59.639 63.158 0.00 0.00 44.18 3.86
4310 10288 1.384989 CGGCTAGATCCGTGTGAGGT 61.385 60.000 0.00 0.00 44.18 3.85
4359 10340 2.386661 AAGGTCAACGATAGCCACAG 57.613 50.000 0.00 0.00 42.67 3.66
4372 10353 3.129502 CACAGCCACCGCCATCAG 61.130 66.667 0.00 0.00 34.57 2.90
4377 10358 4.511246 CCACCGCCATCAGCCCAT 62.511 66.667 0.00 0.00 38.78 4.00
4378 10359 3.214123 CACCGCCATCAGCCCATG 61.214 66.667 0.00 0.00 38.78 3.66
4379 10360 4.511246 ACCGCCATCAGCCCATGG 62.511 66.667 4.14 4.14 45.70 3.66
4394 10375 2.753701 TGGCGTACCAAGCACCAT 59.246 55.556 0.00 0.00 45.37 3.55
4395 10376 1.673993 TGGCGTACCAAGCACCATG 60.674 57.895 0.00 0.00 45.37 3.66
4396 10377 2.485122 GCGTACCAAGCACCATGC 59.515 61.111 0.00 0.00 45.46 4.06
4397 10378 3.051392 GCGTACCAAGCACCATGCC 62.051 63.158 0.00 0.00 46.52 4.40
4398 10379 2.749865 CGTACCAAGCACCATGCCG 61.750 63.158 0.00 0.00 46.52 5.69
4399 10380 2.045438 TACCAAGCACCATGCCGG 60.045 61.111 0.00 0.00 46.52 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 97 4.284746 AGAACAAGAAGTAGAAGTCCCTGG 59.715 45.833 0.00 0.00 0.00 4.45
159 189 1.194781 TGAGGGGCAGAGTCAACCTC 61.195 60.000 12.72 12.72 46.14 3.85
325 695 2.736826 GCCCCTTCCTCTTCTCCCG 61.737 68.421 0.00 0.00 0.00 5.14
621 1109 2.030451 CCCGTACTACCGCTTCTAATCC 60.030 54.545 0.00 0.00 0.00 3.01
676 1277 2.561478 TCAGGGGTAGAACAAAGCAC 57.439 50.000 0.00 0.00 0.00 4.40
1114 1908 8.902540 CCAGATGGTATTTACAGCTAATACAA 57.097 34.615 16.13 8.30 39.24 2.41
1317 3425 7.573968 AATTCATAATTGAAGTAGGAGTGCC 57.426 36.000 0.00 0.00 44.75 5.01
1381 3489 2.529744 GGGACACTTCCAGGTGCCT 61.530 63.158 0.00 0.00 44.98 4.75
1382 3490 2.034221 GGGACACTTCCAGGTGCC 59.966 66.667 0.00 0.00 44.98 5.01
1383 3491 2.034221 GGGGACACTTCCAGGTGC 59.966 66.667 0.00 0.00 44.98 5.01
1384 3492 2.757077 GGGGGACACTTCCAGGTG 59.243 66.667 0.00 0.00 44.98 4.00
1385 3493 2.928396 CGGGGGACACTTCCAGGT 60.928 66.667 0.00 0.00 44.98 4.00
1386 3494 4.410400 GCGGGGGACACTTCCAGG 62.410 72.222 0.00 0.00 44.98 4.45
1387 3495 2.690653 TTTGCGGGGGACACTTCCAG 62.691 60.000 0.00 0.00 44.98 3.86
1388 3496 2.285889 TTTTGCGGGGGACACTTCCA 62.286 55.000 0.00 0.00 44.98 3.53
1389 3497 1.110518 TTTTTGCGGGGGACACTTCC 61.111 55.000 0.00 0.00 41.95 3.46
1390 3498 2.421220 TTTTTGCGGGGGACACTTC 58.579 52.632 0.00 0.00 0.00 3.01
1391 3499 4.688770 TTTTTGCGGGGGACACTT 57.311 50.000 0.00 0.00 0.00 3.16
1408 3516 2.452600 TCACTTCCAGGTGCCTTTTT 57.547 45.000 0.00 0.00 37.16 1.94
1409 3517 2.430694 GTTTCACTTCCAGGTGCCTTTT 59.569 45.455 0.00 0.00 37.16 2.27
1410 3518 2.031870 GTTTCACTTCCAGGTGCCTTT 58.968 47.619 0.00 0.00 37.16 3.11
1411 3519 1.692411 GTTTCACTTCCAGGTGCCTT 58.308 50.000 0.00 0.00 37.16 4.35
1453 3561 2.923121 AGAGCAACATATGGCGTTGAT 58.077 42.857 7.80 1.19 45.05 2.57
1454 3562 2.401583 AGAGCAACATATGGCGTTGA 57.598 45.000 7.80 0.00 45.30 3.18
1523 3631 5.410132 TGTATATTGACAACTCAAACACCGG 59.590 40.000 0.00 0.00 39.90 5.28
1559 3667 3.181507 CCTTTGCATCCACAGTACATTCG 60.182 47.826 0.00 0.00 0.00 3.34
1624 3733 6.435591 CACAGAGGAGTATGGATTCATAGCTA 59.564 42.308 0.00 0.00 36.62 3.32
1713 3829 9.487790 CCAAAACATTGTACTTGACCATATTTT 57.512 29.630 11.31 0.00 0.00 1.82
1726 3842 7.358023 CGACTTGTTAATGCCAAAACATTGTAC 60.358 37.037 0.16 0.00 40.43 2.90
1739 3856 2.309898 ACAACGCGACTTGTTAATGC 57.690 45.000 15.93 0.00 29.66 3.56
1754 3969 4.445385 CCTTGACAGCAAAGCAAATACAAC 59.555 41.667 0.00 0.00 32.73 3.32
1863 5531 7.093945 TGCGTATGCTATCTGAACCATAATAGA 60.094 37.037 8.69 0.00 43.34 1.98
2024 5838 6.148976 GCACTTAGGTAAAGGTTAGAACTTGG 59.851 42.308 0.00 0.00 39.73 3.61
2025 5839 6.708949 TGCACTTAGGTAAAGGTTAGAACTTG 59.291 38.462 0.00 0.00 39.73 3.16
2026 5840 6.834107 TGCACTTAGGTAAAGGTTAGAACTT 58.166 36.000 0.00 0.00 39.73 2.66
2027 5841 6.429521 TGCACTTAGGTAAAGGTTAGAACT 57.570 37.500 0.00 0.00 39.73 3.01
2028 5842 5.121925 GCTGCACTTAGGTAAAGGTTAGAAC 59.878 44.000 0.00 0.00 39.73 3.01
2029 5843 5.012768 AGCTGCACTTAGGTAAAGGTTAGAA 59.987 40.000 1.02 0.00 39.73 2.10
2030 5844 4.530946 AGCTGCACTTAGGTAAAGGTTAGA 59.469 41.667 1.02 0.00 39.73 2.10
2046 5867 2.160417 CCAAAGTTGTAGCTAGCTGCAC 59.840 50.000 31.79 24.86 45.94 4.57
2067 5888 7.254286 GCTCCTTCGAGAAGATATTCTTGAAAC 60.254 40.741 25.59 15.47 45.68 2.78
2338 6159 2.825532 CCCACCAACTTCAAATGTAGGG 59.174 50.000 0.00 0.00 0.00 3.53
2495 6365 2.233271 CACAAAGAACTGGCCATCACT 58.767 47.619 5.51 2.48 0.00 3.41
2526 6430 8.122472 ACTGTCCAGTTAAAATATTTGAAGGG 57.878 34.615 0.39 5.65 38.83 3.95
2603 6512 5.957771 TCTACTGAAACTGGAATGCCTAT 57.042 39.130 0.00 0.00 34.31 2.57
2855 8705 6.174720 TGTAGTCAAGAGAACTTTGGACAT 57.825 37.500 3.37 0.00 33.97 3.06
3211 9106 9.140286 CATAAAAGTAAGAAGATCAACTCACGA 57.860 33.333 0.00 0.00 0.00 4.35
3215 9110 9.436957 TCACCATAAAAGTAAGAAGATCAACTC 57.563 33.333 0.00 0.00 0.00 3.01
3223 9121 6.238211 CCTGCGATCACCATAAAAGTAAGAAG 60.238 42.308 0.00 0.00 0.00 2.85
3224 9122 5.584649 CCTGCGATCACCATAAAAGTAAGAA 59.415 40.000 0.00 0.00 0.00 2.52
3253 9165 1.508632 CGTCCACCTGTAAACACCAG 58.491 55.000 0.00 0.00 0.00 4.00
3326 9238 3.759618 GCTCGATCCTACTACATAGCCTT 59.240 47.826 0.00 0.00 0.00 4.35
3417 9331 0.962489 AGGGCATTATCTCTCCGTCG 59.038 55.000 0.00 0.00 0.00 5.12
3420 9334 4.499183 GATGTAAGGGCATTATCTCTCCG 58.501 47.826 0.00 0.00 0.00 4.63
3514 9438 4.269603 CGTCTCAAATCCAGCTCATTACTG 59.730 45.833 0.00 0.00 34.82 2.74
3632 9559 6.238759 GCTTAATTAATGGACGAGGCAAATCT 60.239 38.462 0.00 0.00 0.00 2.40
3642 9569 7.752695 ACTCTTTTCTGCTTAATTAATGGACG 58.247 34.615 0.00 0.00 0.00 4.79
3650 9582 4.588528 TGGGCAACTCTTTTCTGCTTAATT 59.411 37.500 0.00 0.00 36.32 1.40
3657 9589 5.712152 ATTAACTGGGCAACTCTTTTCTG 57.288 39.130 0.00 0.00 0.00 3.02
3662 9594 6.252995 TCCAATAATTAACTGGGCAACTCTT 58.747 36.000 14.08 0.00 0.00 2.85
3666 9598 6.370442 GGTTTTCCAATAATTAACTGGGCAAC 59.630 38.462 14.08 14.81 40.31 4.17
3668 9600 5.336849 CGGTTTTCCAATAATTAACTGGGCA 60.337 40.000 14.08 2.90 40.70 5.36
3669 9601 5.106442 CGGTTTTCCAATAATTAACTGGGC 58.894 41.667 14.08 5.68 40.70 5.36
3670 9602 5.656480 CCGGTTTTCCAATAATTAACTGGG 58.344 41.667 14.08 3.79 40.14 4.45
3671 9603 5.656480 CCCGGTTTTCCAATAATTAACTGG 58.344 41.667 0.00 9.67 42.33 4.00
3672 9604 5.106442 GCCCGGTTTTCCAATAATTAACTG 58.894 41.667 0.00 0.00 40.70 3.16
3685 9617 0.102663 TGGTTTTTCGCCCGGTTTTC 59.897 50.000 0.00 0.00 0.00 2.29
3695 9627 3.796178 CAGTGGTTTGTGATGGTTTTTCG 59.204 43.478 0.00 0.00 0.00 3.46
3702 9634 0.518636 CGCTCAGTGGTTTGTGATGG 59.481 55.000 0.00 0.00 0.00 3.51
3728 9660 1.628846 AGACTGTGTGTTGGGTATCCC 59.371 52.381 0.00 0.00 45.71 3.85
3736 9668 3.809832 CCCTAGTTGAAGACTGTGTGTTG 59.190 47.826 0.00 0.00 39.48 3.33
3737 9669 3.744530 GCCCTAGTTGAAGACTGTGTGTT 60.745 47.826 0.00 0.00 39.48 3.32
3744 9676 3.776969 TGATGATGCCCTAGTTGAAGACT 59.223 43.478 0.00 0.00 42.55 3.24
3745 9677 4.142609 TGATGATGCCCTAGTTGAAGAC 57.857 45.455 0.00 0.00 0.00 3.01
3748 9680 4.517285 GTCTTGATGATGCCCTAGTTGAA 58.483 43.478 0.00 0.00 0.00 2.69
3749 9681 3.118261 GGTCTTGATGATGCCCTAGTTGA 60.118 47.826 0.00 0.00 0.00 3.18
3754 9686 0.106708 GCGGTCTTGATGATGCCCTA 59.893 55.000 0.00 0.00 0.00 3.53
3775 9707 4.216366 AGTGATGATGATGACGTCTACG 57.784 45.455 17.92 0.04 46.33 3.51
3811 9743 2.039216 TGTTTTAGGGTTGGCGATGAGA 59.961 45.455 0.00 0.00 0.00 3.27
3833 9765 0.318784 AGTCGGAGTCGTTTGCTCAC 60.319 55.000 0.00 0.00 37.69 3.51
3835 9767 1.192534 CAAAGTCGGAGTCGTTTGCTC 59.807 52.381 0.00 0.00 37.69 4.26
3856 9788 0.668706 GGGTCGATGATCATCTGCGG 60.669 60.000 28.48 15.86 35.72 5.69
3880 9812 1.000955 CCATATAGCCTCTTCCGCGTT 59.999 52.381 4.92 0.00 0.00 4.84
3883 9815 1.404851 GCTCCATATAGCCTCTTCCGC 60.405 57.143 0.00 0.00 36.45 5.54
3884 9816 2.663826 GCTCCATATAGCCTCTTCCG 57.336 55.000 0.00 0.00 36.45 4.30
3897 9829 2.441532 GCCTGCATGTGGCTCCAT 60.442 61.111 19.86 0.00 46.38 3.41
3903 9835 1.748122 GTCAGAGGCCTGCATGTGG 60.748 63.158 12.00 0.00 40.20 4.17
3940 9917 2.671619 GCGCCAACCTTGCCTACA 60.672 61.111 0.00 0.00 0.00 2.74
3998 9975 2.526046 GCGGGGCCAGGTGGTATAT 61.526 63.158 4.39 0.00 37.57 0.86
4037 10014 2.664851 CCTCGGCTGTTTGTCGCA 60.665 61.111 0.00 0.00 44.46 5.10
4084 10061 1.890510 GGCGTCGGTTGAGGTTGTT 60.891 57.895 0.00 0.00 32.59 2.83
4118 10095 2.183679 GGCAACAATAATGGGGGTGAA 58.816 47.619 0.00 0.00 0.00 3.18
4142 10119 1.219522 CGGTGTTCGCTCGAGGTTTT 61.220 55.000 15.58 0.00 0.00 2.43
4145 10122 2.981909 TCGGTGTTCGCTCGAGGT 60.982 61.111 15.58 0.00 39.05 3.85
4309 10287 3.741860 AGCTCTGCTGTTGCACAC 58.258 55.556 11.90 0.00 45.31 3.82
4372 10353 3.518068 GCTTGGTACGCCATGGGC 61.518 66.667 15.13 4.92 45.56 5.36
4373 10354 2.045438 TGCTTGGTACGCCATGGG 60.045 61.111 15.13 6.26 45.56 4.00
4374 10355 2.406616 GGTGCTTGGTACGCCATGG 61.407 63.158 7.63 7.63 45.56 3.66
4375 10356 1.673993 TGGTGCTTGGTACGCCATG 60.674 57.895 0.00 0.00 45.56 3.66
4376 10357 2.753701 TGGTGCTTGGTACGCCAT 59.246 55.556 0.00 0.00 45.56 4.40
4378 10359 3.051392 GCATGGTGCTTGGTACGCC 62.051 63.158 0.00 0.00 40.96 5.68
4379 10360 2.485122 GCATGGTGCTTGGTACGC 59.515 61.111 0.00 0.00 40.96 4.42
4380 10361 2.749865 CGGCATGGTGCTTGGTACG 61.750 63.158 1.64 0.00 44.28 3.67
4381 10362 2.406616 CCGGCATGGTGCTTGGTAC 61.407 63.158 1.64 0.00 44.28 3.34
4382 10363 2.045438 CCGGCATGGTGCTTGGTA 60.045 61.111 1.64 0.00 44.28 3.25


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

AutoCloner maintained by Alex Coulton.