Multiple sequence alignment - TraesCS6B01G086000

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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 TraesCS6B01G086000 chr6B 100.000 4546 0 0 1 4546 62405901 62401356 0.000000e+00 8395.0
1 TraesCS6B01G086000 chr6B 78.759 1370 225 43 1019 2365 60107951 60106625 0.000000e+00 857.0
2 TraesCS6B01G086000 chr6B 78.079 1364 234 36 1036 2371 79555806 79554480 0.000000e+00 802.0
3 TraesCS6B01G086000 chr6B 77.875 1365 234 39 1036 2371 79438313 79436988 0.000000e+00 785.0
4 TraesCS6B01G086000 chr6B 74.702 1257 247 51 1036 2267 60593846 60595056 1.140000e-135 494.0
5 TraesCS6B01G086000 chr6B 75.272 1011 171 51 1005 1992 82165930 82166884 4.230000e-110 409.0
6 TraesCS6B01G086000 chr6B 75.937 694 135 20 1700 2367 79847694 79848381 1.220000e-85 327.0
7 TraesCS6B01G086000 chr6B 79.196 423 67 10 1021 1440 45551874 45552278 1.610000e-69 274.0
8 TraesCS6B01G086000 chr6B 77.642 492 80 20 1706 2173 82426825 82426340 5.800000e-69 272.0
9 TraesCS6B01G086000 chr6B 77.305 282 56 7 1903 2177 77392323 77392603 4.710000e-35 159.0
10 TraesCS6B01G086000 chr6B 81.000 100 16 3 2219 2318 79291307 79291403 4.880000e-10 76.8
11 TraesCS6B01G086000 chr6B 84.848 66 8 2 3128 3191 82186967 82187032 1.060000e-06 65.8
12 TraesCS6B01G086000 chr6B 86.538 52 6 1 3137 3187 82161545 82161596 6.350000e-04 56.5
13 TraesCS6B01G086000 chrUn 94.877 4060 115 26 531 4546 101885580 101889590 0.000000e+00 6259.0
14 TraesCS6B01G086000 chrUn 78.550 1324 227 33 1036 2335 112304486 112303196 0.000000e+00 819.0
15 TraesCS6B01G086000 chrUn 77.841 1232 222 27 1052 2267 27743583 27744779 0.000000e+00 715.0
16 TraesCS6B01G086000 chrUn 88.419 544 33 5 1 540 101884989 101885506 2.990000e-176 628.0
17 TraesCS6B01G086000 chrUn 74.793 1206 214 60 1005 2177 26705231 26704083 1.150000e-125 460.0
18 TraesCS6B01G086000 chrUn 75.665 1015 164 50 1003 1992 26970977 26970021 3.250000e-116 429.0
19 TraesCS6B01G086000 chrUn 79.375 640 104 16 1735 2361 112677728 112678352 4.200000e-115 425.0
20 TraesCS6B01G086000 chrUn 79.801 604 96 10 1779 2368 112892052 112892643 2.530000e-112 416.0
21 TraesCS6B01G086000 chrUn 76.983 643 127 13 1694 2318 27883985 27883346 9.360000e-92 348.0
22 TraesCS6B01G086000 chrUn 72.744 1086 219 48 1095 2158 27082708 27083738 1.240000e-75 294.0
23 TraesCS6B01G086000 chrUn 75.256 683 135 18 1700 2355 27448394 27449069 1.240000e-75 294.0
24 TraesCS6B01G086000 chrUn 72.970 1047 183 49 1160 2173 26996632 26995653 1.610000e-69 274.0
25 TraesCS6B01G086000 chrUn 78.589 397 75 10 1052 1442 76751763 76751371 2.100000e-63 254.0
26 TraesCS6B01G086000 chrUn 85.714 63 3 6 3110 3169 27874826 27874885 1.370000e-05 62.1
27 TraesCS6B01G086000 chrUn 94.595 37 2 0 375 411 101885395 101885431 1.770000e-04 58.4
28 TraesCS6B01G086000 chr6A 96.423 3802 95 19 769 4546 34177952 34181736 0.000000e+00 6229.0
29 TraesCS6B01G086000 chr6A 78.862 1107 184 27 1020 2107 33224456 33223381 0.000000e+00 702.0
30 TraesCS6B01G086000 chr6A 77.642 653 121 17 1686 2318 46062365 46063012 1.540000e-99 374.0
31 TraesCS6B01G086000 chr6A 87.742 155 15 4 546 697 105536562 105536715 1.300000e-40 178.0
32 TraesCS6B01G086000 chr6A 96.970 66 2 0 704 769 34175680 34175745 1.340000e-20 111.0
33 TraesCS6B01G086000 chr6A 90.476 42 4 0 3248 3289 33406513 33406554 6.350000e-04 56.5
34 TraesCS6B01G086000 chr2A 82.931 1160 168 25 1033 2184 762930826 762929689 0.000000e+00 1018.0
35 TraesCS6B01G086000 chr2A 82.593 563 60 21 2491 3036 762929435 762928894 3.200000e-126 462.0
36 TraesCS6B01G086000 chr2A 87.662 154 16 3 546 697 654603208 654603360 4.670000e-40 176.0
37 TraesCS6B01G086000 chr2A 82.635 167 12 7 2201 2351 762929620 762929455 1.030000e-26 132.0
38 TraesCS6B01G086000 chr6D 79.368 538 83 22 1005 1527 29094619 29094095 2.010000e-93 353.0
39 TraesCS6B01G086000 chr6D 80.387 413 63 14 1036 1439 29152838 29152435 9.560000e-77 298.0
40 TraesCS6B01G086000 chr6D 79.070 387 72 8 1052 1432 27329055 27328672 1.620000e-64 257.0
41 TraesCS6B01G086000 chr6D 78.356 365 67 10 1070 1431 27126866 27126511 4.580000e-55 226.0
42 TraesCS6B01G086000 chr6D 77.869 366 67 11 1070 1431 27209603 27209248 9.910000e-52 215.0
43 TraesCS6B01G086000 chr6D 77.099 393 64 19 1056 1439 28305120 28304745 2.140000e-48 204.0
44 TraesCS6B01G086000 chr6D 87.692 65 6 2 354 418 462080332 462080270 1.750000e-09 75.0
45 TraesCS6B01G086000 chr7B 87.975 158 13 5 546 698 632179714 632179870 1.000000e-41 182.0
46 TraesCS6B01G086000 chr7B 89.109 101 9 2 2367 2465 245070343 245070443 1.720000e-24 124.0
47 TraesCS6B01G086000 chr7B 89.474 95 9 1 2372 2465 296356906 296356812 7.990000e-23 119.0
48 TraesCS6B01G086000 chr7B 100.000 28 0 0 53 80 610467287 610467260 8.000000e-03 52.8
49 TraesCS6B01G086000 chr5B 86.420 162 17 5 538 696 61558788 61558947 6.050000e-39 172.0
50 TraesCS6B01G086000 chr5B 86.335 161 18 4 538 696 604227694 604227852 6.050000e-39 172.0
51 TraesCS6B01G086000 chr5B 79.845 129 21 5 2140 2267 697029572 697029448 6.260000e-14 89.8
52 TraesCS6B01G086000 chr3D 85.294 170 21 4 538 705 420484230 420484397 6.050000e-39 172.0
53 TraesCS6B01G086000 chr3D 90.722 97 8 1 2370 2465 336537981 336537885 1.330000e-25 128.0
54 TraesCS6B01G086000 chr3D 89.000 100 8 3 2370 2467 336537885 336537983 2.220000e-23 121.0
55 TraesCS6B01G086000 chr3A 85.714 161 19 4 538 696 219342751 219342909 2.810000e-37 167.0
56 TraesCS6B01G086000 chr1B 84.706 170 22 4 538 705 524162459 524162292 2.810000e-37 167.0
57 TraesCS6B01G086000 chr1A 90.722 97 8 1 2370 2465 64714429 64714333 1.330000e-25 128.0
58 TraesCS6B01G086000 chr3B 86.486 111 11 4 2364 2472 609305095 609304987 7.990000e-23 119.0
59 TraesCS6B01G086000 chr3B 100.000 28 0 0 53 80 140986392 140986419 8.000000e-03 52.8
60 TraesCS6B01G086000 chr7A 88.421 95 9 2 2372 2465 375916029 375915936 3.720000e-21 113.0
61 TraesCS6B01G086000 chr2D 89.655 58 6 0 35 92 502931826 502931769 1.750000e-09 75.0
62 TraesCS6B01G086000 chr7D 100.000 28 0 0 53 80 561697086 561697059 8.000000e-03 52.8


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 TraesCS6B01G086000 chr6B 62401356 62405901 4545 True 8395.000000 8395 100.000000 1 4546 1 chr6B.!!$R2 4545
1 TraesCS6B01G086000 chr6B 60106625 60107951 1326 True 857.000000 857 78.759000 1019 2365 1 chr6B.!!$R1 1346
2 TraesCS6B01G086000 chr6B 79554480 79555806 1326 True 802.000000 802 78.079000 1036 2371 1 chr6B.!!$R4 1335
3 TraesCS6B01G086000 chr6B 79436988 79438313 1325 True 785.000000 785 77.875000 1036 2371 1 chr6B.!!$R3 1335
4 TraesCS6B01G086000 chr6B 60593846 60595056 1210 False 494.000000 494 74.702000 1036 2267 1 chr6B.!!$F2 1231
5 TraesCS6B01G086000 chr6B 82165930 82166884 954 False 409.000000 409 75.272000 1005 1992 1 chr6B.!!$F7 987
6 TraesCS6B01G086000 chr6B 79847694 79848381 687 False 327.000000 327 75.937000 1700 2367 1 chr6B.!!$F5 667
7 TraesCS6B01G086000 chrUn 101884989 101889590 4601 False 2315.133333 6259 92.630333 1 4546 3 chrUn.!!$F7 4545
8 TraesCS6B01G086000 chrUn 112303196 112304486 1290 True 819.000000 819 78.550000 1036 2335 1 chrUn.!!$R6 1299
9 TraesCS6B01G086000 chrUn 27743583 27744779 1196 False 715.000000 715 77.841000 1052 2267 1 chrUn.!!$F3 1215
10 TraesCS6B01G086000 chrUn 26704083 26705231 1148 True 460.000000 460 74.793000 1005 2177 1 chrUn.!!$R1 1172
11 TraesCS6B01G086000 chrUn 26970021 26970977 956 True 429.000000 429 75.665000 1003 1992 1 chrUn.!!$R2 989
12 TraesCS6B01G086000 chrUn 112677728 112678352 624 False 425.000000 425 79.375000 1735 2361 1 chrUn.!!$F5 626
13 TraesCS6B01G086000 chrUn 112892052 112892643 591 False 416.000000 416 79.801000 1779 2368 1 chrUn.!!$F6 589
14 TraesCS6B01G086000 chrUn 27883346 27883985 639 True 348.000000 348 76.983000 1694 2318 1 chrUn.!!$R4 624
15 TraesCS6B01G086000 chrUn 27082708 27083738 1030 False 294.000000 294 72.744000 1095 2158 1 chrUn.!!$F1 1063
16 TraesCS6B01G086000 chrUn 27448394 27449069 675 False 294.000000 294 75.256000 1700 2355 1 chrUn.!!$F2 655
17 TraesCS6B01G086000 chrUn 26995653 26996632 979 True 274.000000 274 72.970000 1160 2173 1 chrUn.!!$R3 1013
18 TraesCS6B01G086000 chr6A 34175680 34181736 6056 False 3170.000000 6229 96.696500 704 4546 2 chr6A.!!$F4 3842
19 TraesCS6B01G086000 chr6A 33223381 33224456 1075 True 702.000000 702 78.862000 1020 2107 1 chr6A.!!$R1 1087
20 TraesCS6B01G086000 chr6A 46062365 46063012 647 False 374.000000 374 77.642000 1686 2318 1 chr6A.!!$F2 632
21 TraesCS6B01G086000 chr2A 762928894 762930826 1932 True 537.333333 1018 82.719667 1033 3036 3 chr2A.!!$R1 2003
22 TraesCS6B01G086000 chr6D 29094095 29094619 524 True 353.000000 353 79.368000 1005 1527 1 chr6D.!!$R5 522

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
489 493 0.242017 CTGCTTGCTGTTTGGCCTAC 59.758 55.000 3.32 2.54 0.00 3.18 F
1551 3918 0.528901 TGGTGGACAACGTCGACAAG 60.529 55.000 17.16 6.85 41.79 3.16 F
1554 3921 0.460459 TGGACAACGTCGACAAGCAA 60.460 50.000 17.16 0.00 32.65 3.91 F
2375 4854 3.492011 GCGGTGGTGTTTTATATACTCCG 59.508 47.826 0.00 0.00 37.85 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 3921 0.865639 GCGCTCGTTTGTGTTGCTTT 60.866 50.000 0.00 0.0 0.00 3.51 R
3495 6005 1.133199 ACCATGTCCACCACCAATGTT 60.133 47.619 0.00 0.0 0.00 2.71 R
3514 6024 4.035558 TGTGCTGTGAAAGATCAACTTGAC 59.964 41.667 0.00 0.0 38.98 3.18 R
3912 6426 0.609957 CAAGGCAGCTGGATGGACAA 60.610 55.000 17.12 0.0 0.00 3.18 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
25 26 2.196595 AGGAAAATGGTCAGATCCCGA 58.803 47.619 0.00 0.00 0.00 5.14
31 32 5.582689 AAATGGTCAGATCCCGATTTTTC 57.417 39.130 0.00 0.00 0.00 2.29
33 34 4.301072 TGGTCAGATCCCGATTTTTCTT 57.699 40.909 0.00 0.00 0.00 2.52
44 45 4.220602 CCCGATTTTTCTTGAATCAGGGTT 59.779 41.667 13.62 0.00 39.61 4.11
110 111 2.308570 TCCAGGAGAGGCTGCATTTTAA 59.691 45.455 0.50 0.00 0.00 1.52
116 117 4.488879 GAGAGGCTGCATTTTAAGTTTGG 58.511 43.478 0.50 0.00 0.00 3.28
117 118 4.151883 AGAGGCTGCATTTTAAGTTTGGA 58.848 39.130 0.50 0.00 0.00 3.53
123 124 2.663119 GCATTTTAAGTTTGGAGCAGCG 59.337 45.455 0.00 0.00 0.00 5.18
141 142 4.167483 GCACGGCGATGCAAATTT 57.833 50.000 22.96 0.00 45.39 1.82
142 143 3.320884 GCACGGCGATGCAAATTTA 57.679 47.368 22.96 0.00 45.39 1.40
143 144 0.913876 GCACGGCGATGCAAATTTAC 59.086 50.000 22.96 0.00 45.39 2.01
144 145 1.179332 CACGGCGATGCAAATTTACG 58.821 50.000 16.62 0.00 0.00 3.18
145 146 0.800012 ACGGCGATGCAAATTTACGT 59.200 45.000 16.62 0.00 0.00 3.57
146 147 1.201987 ACGGCGATGCAAATTTACGTC 60.202 47.619 16.62 1.07 0.00 4.34
147 148 1.201976 CGGCGATGCAAATTTACGTCA 60.202 47.619 0.00 0.00 0.00 4.35
148 149 2.173964 GGCGATGCAAATTTACGTCAC 58.826 47.619 10.52 1.58 0.00 3.67
149 150 2.159572 GGCGATGCAAATTTACGTCACT 60.160 45.455 10.52 0.00 0.00 3.41
150 151 3.488489 GCGATGCAAATTTACGTCACTT 58.512 40.909 10.52 0.00 0.00 3.16
151 152 3.297979 GCGATGCAAATTTACGTCACTTG 59.702 43.478 10.52 0.00 0.00 3.16
152 153 3.845775 CGATGCAAATTTACGTCACTTGG 59.154 43.478 10.52 0.00 0.00 3.61
153 154 4.377943 CGATGCAAATTTACGTCACTTGGA 60.378 41.667 10.52 0.00 0.00 3.53
154 155 4.481930 TGCAAATTTACGTCACTTGGAG 57.518 40.909 0.00 0.00 0.00 3.86
155 156 3.252215 TGCAAATTTACGTCACTTGGAGG 59.748 43.478 0.00 0.00 37.42 4.30
156 157 3.500680 GCAAATTTACGTCACTTGGAGGA 59.499 43.478 0.00 0.00 35.40 3.71
157 158 4.378459 GCAAATTTACGTCACTTGGAGGAG 60.378 45.833 0.00 0.00 35.40 3.69
158 159 4.884668 AATTTACGTCACTTGGAGGAGA 57.115 40.909 0.00 0.00 35.40 3.71
159 160 5.422214 AATTTACGTCACTTGGAGGAGAT 57.578 39.130 0.00 0.00 35.40 2.75
160 161 4.884668 TTTACGTCACTTGGAGGAGATT 57.115 40.909 0.00 0.00 35.40 2.40
161 162 4.884668 TTACGTCACTTGGAGGAGATTT 57.115 40.909 0.00 0.00 35.40 2.17
162 163 3.771577 ACGTCACTTGGAGGAGATTTT 57.228 42.857 0.00 0.00 35.40 1.82
194 195 7.179269 TGCCTAAAACTAGGACCACATAATTT 58.821 34.615 2.27 0.00 39.60 1.82
282 286 1.398692 TGCAAACTCTGTTGAACCCC 58.601 50.000 0.00 0.00 0.00 4.95
312 316 2.725221 ATGTTGGAGATGCTCTTCCC 57.275 50.000 0.00 0.00 0.00 3.97
371 375 1.900016 CATGCCTGGCACTGTGTGT 60.900 57.895 25.99 2.60 43.04 3.72
411 415 1.675219 GACCCAACTGCTAACCGGA 59.325 57.895 9.46 0.00 0.00 5.14
432 436 1.073199 GGCCTGTGTGCTACAACCT 59.927 57.895 0.00 0.00 39.20 3.50
436 440 1.308047 CTGTGTGCTACAACCTGCAA 58.692 50.000 0.00 0.00 41.10 4.08
465 469 2.750237 CCCAACTGCTAACCGGGC 60.750 66.667 6.32 0.00 0.00 6.13
469 473 3.268103 AACTGCTAACCGGGCTGGG 62.268 63.158 18.49 5.37 44.64 4.45
489 493 0.242017 CTGCTTGCTGTTTGGCCTAC 59.758 55.000 3.32 2.54 0.00 3.18
491 495 1.875963 CTTGCTGTTTGGCCTACCG 59.124 57.895 3.32 0.00 39.70 4.02
518 522 7.015877 GGAGTTTTTGGGGTCTATTTTTACCTT 59.984 37.037 0.00 0.00 35.97 3.50
520 524 9.436866 AGTTTTTGGGGTCTATTTTTACCTTTA 57.563 29.630 0.00 0.00 35.97 1.85
521 525 9.701098 GTTTTTGGGGTCTATTTTTACCTTTAG 57.299 33.333 0.00 0.00 35.97 1.85
523 527 5.512298 TGGGGTCTATTTTTACCTTTAGGC 58.488 41.667 0.00 0.00 39.32 3.93
524 528 5.254501 TGGGGTCTATTTTTACCTTTAGGCT 59.745 40.000 0.00 0.00 39.32 4.58
525 529 6.447735 TGGGGTCTATTTTTACCTTTAGGCTA 59.552 38.462 0.00 0.00 39.32 3.93
527 531 8.003044 GGGGTCTATTTTTACCTTTAGGCTAAT 58.997 37.037 7.96 0.00 39.32 1.73
528 532 8.847196 GGGTCTATTTTTACCTTTAGGCTAATG 58.153 37.037 7.96 10.32 39.32 1.90
529 533 9.404848 GGTCTATTTTTACCTTTAGGCTAATGT 57.595 33.333 7.96 10.89 39.32 2.71
747 847 5.453339 CCTCTTCTACACTTCACTTCACCAA 60.453 44.000 0.00 0.00 0.00 3.67
880 3187 4.517934 CCGGACGCCCCTCTCCTA 62.518 72.222 0.00 0.00 0.00 2.94
988 3295 1.207089 CTGACCGCTCCTCCATTGTTA 59.793 52.381 0.00 0.00 0.00 2.41
993 3300 1.066143 CGCTCCTCCATTGTTACAGGT 60.066 52.381 0.00 0.00 0.00 4.00
994 3301 2.167693 CGCTCCTCCATTGTTACAGGTA 59.832 50.000 0.00 0.00 0.00 3.08
995 3302 3.532542 GCTCCTCCATTGTTACAGGTAC 58.467 50.000 0.00 0.00 0.00 3.34
996 3303 3.681874 GCTCCTCCATTGTTACAGGTACC 60.682 52.174 2.73 2.73 0.00 3.34
997 3304 3.517901 CTCCTCCATTGTTACAGGTACCA 59.482 47.826 15.94 0.00 0.00 3.25
998 3305 3.517901 TCCTCCATTGTTACAGGTACCAG 59.482 47.826 15.94 9.05 0.00 4.00
999 3306 3.270877 CTCCATTGTTACAGGTACCAGC 58.729 50.000 15.94 0.00 0.00 4.85
1000 3307 2.640332 TCCATTGTTACAGGTACCAGCA 59.360 45.455 15.94 0.00 0.00 4.41
1027 3334 4.827087 AGATGACCAGCCGCAGCG 62.827 66.667 8.18 8.18 46.67 5.18
1375 3715 1.638388 CGTGCTCATCCACAACGCAT 61.638 55.000 0.00 0.00 35.47 4.73
1549 3916 1.227031 GTGGTGGACAACGTCGACA 60.227 57.895 17.16 0.00 41.79 4.35
1550 3917 0.806884 GTGGTGGACAACGTCGACAA 60.807 55.000 17.16 0.00 41.79 3.18
1551 3918 0.528901 TGGTGGACAACGTCGACAAG 60.529 55.000 17.16 6.85 41.79 3.16
1552 3919 1.563173 GTGGACAACGTCGACAAGC 59.437 57.895 17.16 0.00 40.20 4.01
1553 3920 1.142097 TGGACAACGTCGACAAGCA 59.858 52.632 17.16 0.00 32.65 3.91
1554 3921 0.460459 TGGACAACGTCGACAAGCAA 60.460 50.000 17.16 0.00 32.65 3.91
1871 4252 4.035102 GGCAGAGGGTGGTGGTCC 62.035 72.222 0.00 0.00 0.00 4.46
2368 4847 3.741249 TCTTGTGCGGTGGTGTTTTATA 58.259 40.909 0.00 0.00 0.00 0.98
2375 4854 3.492011 GCGGTGGTGTTTTATATACTCCG 59.508 47.826 0.00 0.00 37.85 4.63
2553 5039 4.582656 TGGGTTGAAATTGGTCTACTGTTG 59.417 41.667 0.00 0.00 0.00 3.33
2986 5486 9.687717 GTAATTGGCGAATAATTGTTCATTTTG 57.312 29.630 14.36 0.15 0.00 2.44
3242 5751 5.172205 GGCTCTGGTTAACTTGTCTCTTAG 58.828 45.833 5.42 0.00 0.00 2.18
3284 5793 7.013178 TGAGTGTGCATCTTCTTCATTTTTACA 59.987 33.333 0.00 0.00 0.00 2.41
3418 5928 8.581057 ACAGCTATGAGTTTATCTAAACATCG 57.419 34.615 13.65 0.26 45.97 3.84
3495 6005 5.512753 TTGACTTATGCTTGCAGAAACAA 57.487 34.783 13.59 13.59 0.00 2.83
3514 6024 1.631405 AACATTGGTGGTGGACATGG 58.369 50.000 0.00 0.00 0.00 3.66
3516 6026 1.176527 CATTGGTGGTGGACATGGTC 58.823 55.000 0.00 0.00 0.00 4.02
3517 6027 0.776810 ATTGGTGGTGGACATGGTCA 59.223 50.000 0.00 0.00 33.68 4.02
3750 6264 2.158564 CCACCTGGCCACTCATATCAAT 60.159 50.000 0.00 0.00 0.00 2.57
3912 6426 5.488919 TCACTATTGGATGAGGAACCTTTCT 59.511 40.000 0.00 0.00 0.00 2.52
3943 6457 3.057033 CAGCTGCCTTGCTTTCATTTACT 60.057 43.478 0.00 0.00 41.98 2.24
3998 6512 5.753721 AGTGCAATTTCTTCTCCTCTAGT 57.246 39.130 0.00 0.00 0.00 2.57
4004 6518 6.093357 GCAATTTCTTCTCCTCTAGTTCCTTG 59.907 42.308 0.00 0.00 0.00 3.61
4200 6718 5.536161 ACAATACCTGAACACTTGCTTCATT 59.464 36.000 0.00 0.00 0.00 2.57
4249 6767 6.938507 ACTATGCCATTTGACATTTCACATT 58.061 32.000 0.00 0.00 0.00 2.71
4250 6768 8.065473 ACTATGCCATTTGACATTTCACATTA 57.935 30.769 0.00 0.00 0.00 1.90
4278 6796 6.870971 TTATTTTGGATCGTTATGCTACCC 57.129 37.500 0.00 0.00 0.00 3.69
4505 7023 5.788450 CAGTCTATGTTCTTCACTCTTGGT 58.212 41.667 0.00 0.00 0.00 3.67
4527 7045 9.562408 TTGGTCATGTTAGATGTTTAACACTTA 57.438 29.630 0.00 0.00 43.93 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.973973 TCGGGATCTGACCATTTTCCTAT 59.026 43.478 0.00 0.00 0.00 2.57
16 17 6.441093 TGATTCAAGAAAAATCGGGATCTG 57.559 37.500 0.00 0.00 36.18 2.90
25 26 7.177392 CAGACCTAACCCTGATTCAAGAAAAAT 59.823 37.037 0.00 0.00 32.37 1.82
31 32 3.878778 CCAGACCTAACCCTGATTCAAG 58.121 50.000 0.00 0.00 32.37 3.02
33 34 1.559682 GCCAGACCTAACCCTGATTCA 59.440 52.381 0.00 0.00 32.37 2.57
44 45 2.373836 TGCCAAAGTTTAGCCAGACCTA 59.626 45.455 3.51 0.00 0.00 3.08
110 111 2.980233 GTGCCGCTGCTCCAAACT 60.980 61.111 0.70 0.00 38.71 2.66
123 124 0.179150 TAAATTTGCATCGCCGTGCC 60.179 50.000 0.00 0.00 44.43 5.01
139 140 4.884668 AATCTCCTCCAAGTGACGTAAA 57.115 40.909 0.00 0.00 0.00 2.01
140 141 4.884668 AAATCTCCTCCAAGTGACGTAA 57.115 40.909 0.00 0.00 0.00 3.18
141 142 4.884668 AAAATCTCCTCCAAGTGACGTA 57.115 40.909 0.00 0.00 0.00 3.57
142 143 3.771577 AAAATCTCCTCCAAGTGACGT 57.228 42.857 0.00 0.00 0.00 4.34
160 161 3.576550 CCTAGTTTTAGGCAGCCCAAAAA 59.423 43.478 18.13 16.60 40.10 1.94
161 162 3.161866 CCTAGTTTTAGGCAGCCCAAAA 58.838 45.455 13.23 13.23 40.10 2.44
162 163 2.377193 TCCTAGTTTTAGGCAGCCCAAA 59.623 45.455 8.22 3.86 45.25 3.28
180 181 7.617723 TGCCTTAATGTAAAATTATGTGGTCCT 59.382 33.333 0.00 0.00 0.00 3.85
194 195 4.042311 TCTCCAACACCTGCCTTAATGTAA 59.958 41.667 0.00 0.00 0.00 2.41
269 273 1.028905 TTTTGCGGGGTTCAACAGAG 58.971 50.000 0.00 0.00 0.00 3.35
282 286 4.324402 GCATCTCCAACATTAGTTTTTGCG 59.676 41.667 0.00 0.00 35.28 4.85
312 316 0.875474 CCGTTTGGCCAACTTTGCTG 60.875 55.000 20.35 2.78 32.53 4.41
341 345 2.961062 GCCAGGCATGATTAAGATTGGT 59.039 45.455 6.55 0.00 0.00 3.67
411 415 2.813726 TTGTAGCACACAGGCCGGT 61.814 57.895 1.28 1.28 38.72 5.28
420 424 0.821711 GGGTTGCAGGTTGTAGCACA 60.822 55.000 0.00 0.00 41.05 4.57
421 425 0.821711 TGGGTTGCAGGTTGTAGCAC 60.822 55.000 0.00 0.00 41.05 4.40
432 436 2.283101 GGTCATGCCTGGGTTGCA 60.283 61.111 0.00 0.00 43.97 4.08
436 440 2.162906 AGTTGGGTCATGCCTGGGT 61.163 57.895 0.00 0.00 37.43 4.51
445 449 1.373435 CCGGTTAGCAGTTGGGTCA 59.627 57.895 0.00 0.00 0.00 4.02
469 473 1.526575 TAGGCCAAACAGCAAGCAGC 61.527 55.000 5.01 0.00 46.19 5.25
471 475 1.178534 GGTAGGCCAAACAGCAAGCA 61.179 55.000 5.01 0.00 34.09 3.91
489 493 0.694196 TAGACCCCAAAAACTCCCGG 59.306 55.000 0.00 0.00 0.00 5.73
491 495 5.818678 AAAAATAGACCCCAAAAACTCCC 57.181 39.130 0.00 0.00 0.00 4.30
518 522 8.444010 TCTATATGGCCTAAACATTAGCCTAA 57.556 34.615 3.32 0.00 45.94 2.69
520 524 6.730977 TCTCTATATGGCCTAAACATTAGCCT 59.269 38.462 3.32 0.00 45.94 4.58
521 525 6.947464 TCTCTATATGGCCTAAACATTAGCC 58.053 40.000 3.32 0.00 45.96 3.93
525 529 9.920946 TCTTTTTCTCTATATGGCCTAAACATT 57.079 29.630 3.32 0.00 0.00 2.71
527 531 9.342308 CATCTTTTTCTCTATATGGCCTAAACA 57.658 33.333 3.32 0.00 0.00 2.83
528 532 9.561069 TCATCTTTTTCTCTATATGGCCTAAAC 57.439 33.333 3.32 0.00 0.00 2.01
660 746 4.720902 CAGCACGGCCCACCATGA 62.721 66.667 0.00 0.00 34.57 3.07
892 3199 2.279318 GCGGCGCTAACCCTAGAC 60.279 66.667 26.86 0.00 0.00 2.59
954 3261 0.923358 GGTCAGAGGAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
988 3295 1.274703 CCCTCCATGCTGGTACCTGT 61.275 60.000 18.89 0.00 39.03 4.00
993 3300 2.364973 TCGCCCTCCATGCTGGTA 60.365 61.111 2.68 0.00 39.03 3.25
994 3301 3.790437 CTCGCCCTCCATGCTGGT 61.790 66.667 2.68 0.00 39.03 4.00
995 3302 2.815945 ATCTCGCCCTCCATGCTGG 61.816 63.158 0.00 0.00 39.43 4.85
996 3303 1.597302 CATCTCGCCCTCCATGCTG 60.597 63.158 0.00 0.00 0.00 4.41
997 3304 1.763655 TCATCTCGCCCTCCATGCT 60.764 57.895 0.00 0.00 0.00 3.79
998 3305 1.596477 GTCATCTCGCCCTCCATGC 60.596 63.158 0.00 0.00 0.00 4.06
999 3306 1.070445 GGTCATCTCGCCCTCCATG 59.930 63.158 0.00 0.00 0.00 3.66
1000 3307 1.383109 TGGTCATCTCGCCCTCCAT 60.383 57.895 0.00 0.00 0.00 3.41
1202 3515 2.094170 GCCAAGGAGGGGAGGGTTTT 62.094 60.000 0.00 0.00 38.09 2.43
1375 3715 2.429930 CAGGACCTTGTTCGGCCA 59.570 61.111 2.24 0.00 0.00 5.36
1552 3919 1.252524 CGCTCGTTTGTGTTGCTTTTG 59.747 47.619 0.00 0.00 0.00 2.44
1553 3920 1.544686 CGCTCGTTTGTGTTGCTTTT 58.455 45.000 0.00 0.00 0.00 2.27
1554 3921 0.865639 GCGCTCGTTTGTGTTGCTTT 60.866 50.000 0.00 0.00 0.00 3.51
1871 4252 5.239306 TGATCTTTCTGCAACAGTAAACCAG 59.761 40.000 0.00 0.00 32.61 4.00
2267 4729 6.030228 GCAGTAAAGGAAACAAGTGATATGC 58.970 40.000 0.00 0.00 0.00 3.14
2375 4854 4.929808 AGCGACAATTAATATGGATCGGAC 59.070 41.667 0.00 0.00 0.00 4.79
2986 5486 6.706270 TCACAATGAAGACTCCTAAAAGTGAC 59.294 38.462 0.00 0.00 0.00 3.67
3171 5680 1.428448 TCCGAGCAACAGAAATGACG 58.572 50.000 0.00 0.00 0.00 4.35
3242 5751 3.194542 ACACTCAGACAATCAGCTAGTCC 59.805 47.826 0.00 0.00 32.82 3.85
3418 5928 4.264460 AGACAAGAGGAGACATCAACAC 57.736 45.455 0.00 0.00 0.00 3.32
3495 6005 1.133199 ACCATGTCCACCACCAATGTT 60.133 47.619 0.00 0.00 0.00 2.71
3514 6024 4.035558 TGTGCTGTGAAAGATCAACTTGAC 59.964 41.667 0.00 0.00 38.98 3.18
3516 6026 4.556942 TGTGCTGTGAAAGATCAACTTG 57.443 40.909 0.00 0.00 38.98 3.16
3517 6027 6.712095 TCTTATGTGCTGTGAAAGATCAACTT 59.288 34.615 0.00 0.00 40.98 2.66
3599 6109 7.495901 ACAGTTCAGATACCTCAACATAGATG 58.504 38.462 0.00 0.00 0.00 2.90
3750 6264 2.282674 CAGCCTGCCAGGAAAGCA 60.283 61.111 16.85 0.00 37.67 3.91
3774 6288 1.563410 CAGGGCCTGGAGAAAAGATCT 59.437 52.381 26.34 0.00 42.61 2.75
3912 6426 0.609957 CAAGGCAGCTGGATGGACAA 60.610 55.000 17.12 0.00 0.00 3.18
3943 6457 0.797579 AGGGGAGTACCAAGGAGGAA 59.202 55.000 0.00 0.00 42.91 3.36
4249 6767 8.500753 AGCATAACGATCCAAAATAAACAGTA 57.499 30.769 0.00 0.00 0.00 2.74
4250 6768 7.391148 AGCATAACGATCCAAAATAAACAGT 57.609 32.000 0.00 0.00 0.00 3.55
4278 6796 6.255887 GTCTCCTGACAATAAATAGTTCACCG 59.744 42.308 0.00 0.00 42.48 4.94


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

AutoCloner maintained by Alex Coulton.