Multiple sequence alignment - TraesCS2B01G082700

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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 TraesCS2B01G082700 chr2B 100.000 5261 0 0 1 5261 46092746 46087486 0.000000e+00 9716.0
1 TraesCS2B01G082700 chr2B 92.496 573 41 1 1483 2053 11991980 11992552 0.000000e+00 819.0
2 TraesCS2B01G082700 chr2B 90.698 559 25 12 3434 3965 11992888 11993446 0.000000e+00 719.0
3 TraesCS2B01G082700 chr2B 89.885 524 28 6 987 1500 11991457 11991965 0.000000e+00 651.0
4 TraesCS2B01G082700 chr2B 91.618 346 24 3 2196 2539 11992546 11992888 1.710000e-129 473.0
5 TraesCS2B01G082700 chr2B 83.030 165 26 2 1193 1356 762500750 762500587 1.180000e-31 148.0
6 TraesCS2B01G082700 chr2B 100.000 76 0 0 4778 4853 46079964 46079889 1.980000e-29 141.0
7 TraesCS2B01G082700 chr2B 91.765 85 6 1 5040 5123 46079574 46079490 3.330000e-22 117.0
8 TraesCS2B01G082700 chr2B 91.860 86 3 2 4778 4863 46079747 46079666 3.330000e-22 117.0
9 TraesCS2B01G082700 chr2B 100.000 59 0 0 4721 4779 46079852 46079794 5.570000e-20 110.0
10 TraesCS2B01G082700 chr2B 86.957 69 3 4 911 975 11991394 11991460 7.310000e-09 73.1
11 TraesCS2B01G082700 chr2A 95.243 4709 174 28 1 4696 30553892 30549221 0.000000e+00 7409.0
12 TraesCS2B01G082700 chr2A 91.090 1156 73 15 911 2053 8147657 8148795 0.000000e+00 1537.0
13 TraesCS2B01G082700 chr2A 95.736 727 30 1 3246 3971 8149878 8150604 0.000000e+00 1170.0
14 TraesCS2B01G082700 chr2A 84.728 478 36 16 2768 3215 8149413 8149883 1.340000e-120 444.0
15 TraesCS2B01G082700 chr2A 90.511 274 19 2 2196 2465 8148789 8149059 6.480000e-94 355.0
16 TraesCS2B01G082700 chr2A 90.566 212 20 0 2560 2771 8149100 8149311 1.120000e-71 281.0
17 TraesCS2B01G082700 chr2A 88.119 202 16 4 5030 5226 30548448 30548250 3.170000e-57 233.0
18 TraesCS2B01G082700 chr2A 82.967 182 29 2 1176 1356 753250417 753250237 4.220000e-36 163.0
19 TraesCS2B01G082700 chr2D 95.156 4707 160 36 1 4696 28734122 28729473 0.000000e+00 7367.0
20 TraesCS2B01G082700 chr2D 89.977 1327 76 20 987 2293 8973673 8972384 0.000000e+00 1661.0
21 TraesCS2B01G082700 chr2D 90.694 720 40 12 1861 2580 8849654 8848962 0.000000e+00 933.0
22 TraesCS2B01G082700 chr2D 93.362 467 27 2 3079 3541 8970639 8970173 0.000000e+00 688.0
23 TraesCS2B01G082700 chr2D 93.793 435 22 2 3539 3971 8960223 8959792 0.000000e+00 649.0
24 TraesCS2B01G082700 chr2D 92.174 460 29 5 2286 2743 8971167 8970713 1.230000e-180 643.0
25 TraesCS2B01G082700 chr2D 89.565 460 27 8 4793 5244 28729253 28728807 9.890000e-157 564.0
26 TraesCS2B01G082700 chr2D 91.771 401 27 1 3571 3971 8839849 8839455 2.140000e-153 553.0
27 TraesCS2B01G082700 chr2D 86.588 425 27 13 2747 3142 8848935 8848512 4.840000e-120 442.0
28 TraesCS2B01G082700 chr2D 74.155 592 91 36 1176 1759 621544343 621543806 6.960000e-44 189.0
29 TraesCS2B01G082700 chr2D 94.681 94 5 0 3482 3575 8848509 8848416 4.250000e-31 147.0
30 TraesCS2B01G082700 chr3D 88.262 1312 80 25 987 2283 564002900 564001648 0.000000e+00 1502.0
31 TraesCS2B01G082700 chr6D 82.960 446 38 17 4809 5244 158489021 158489438 8.320000e-98 368.0
32 TraesCS2B01G082700 chr7B 93.897 213 7 3 4774 4981 747311296 747311507 3.060000e-82 316.0
33 TraesCS2B01G082700 chr7B 95.506 178 7 1 4447 4623 747310916 747311093 3.100000e-72 283.0
34 TraesCS2B01G082700 chr7B 100.000 47 0 0 4733 4779 747311206 747311252 2.610000e-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 TraesCS2B01G082700 chr2B 46087486 46092746 5260 True 9716.000000 9716 100.000000 1 5261 1 chr2B.!!$R1 5260
1 TraesCS2B01G082700 chr2B 11991394 11993446 2052 False 547.020000 819 90.330800 911 3965 5 chr2B.!!$F1 3054
2 TraesCS2B01G082700 chr2A 30548250 30553892 5642 True 3821.000000 7409 91.681000 1 5226 2 chr2A.!!$R2 5225
3 TraesCS2B01G082700 chr2A 8147657 8150604 2947 False 757.400000 1537 90.526200 911 3971 5 chr2A.!!$F1 3060
4 TraesCS2B01G082700 chr2D 28728807 28734122 5315 True 3965.500000 7367 92.360500 1 5244 2 chr2D.!!$R6 5243
5 TraesCS2B01G082700 chr2D 8970173 8973673 3500 True 997.333333 1661 91.837667 987 3541 3 chr2D.!!$R5 2554
6 TraesCS2B01G082700 chr2D 8848416 8849654 1238 True 507.333333 933 90.654333 1861 3575 3 chr2D.!!$R4 1714
7 TraesCS2B01G082700 chr3D 564001648 564002900 1252 True 1502.000000 1502 88.262000 987 2283 1 chr3D.!!$R1 1296
8 TraesCS2B01G082700 chr7B 747310916 747311507 591 False 228.966667 316 96.467667 4447 4981 3 chr7B.!!$F1 534

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
337 343 2.035066 GCACATCCATTGCCCTTGATAC 59.965 50.0 0.00 0.00 33.58 2.24 F
1956 2044 0.801067 CGGCACAGAGTAAGGCGTAC 60.801 60.0 2.11 2.11 44.84 3.67 F
2319 3632 0.529378 CCAATTGCTCCAAGGCTGTC 59.471 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2230 0.389817 TCAGACGGTCATTCTTGCCG 60.390 55.000 11.27 0.0 43.59 5.69 R
2904 4331 2.167487 CTCTGACTCCCTTGAAGCTACC 59.833 54.545 0.00 0.0 0.00 3.18 R
4281 5777 0.033699 AAAGGGCAGATTCAGAGGGC 60.034 55.000 0.00 0.0 0.00 5.19 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
36 37 5.529800 TGGAATCATTACTCATGTGCAGATG 59.470 40.000 17.43 17.43 34.06 2.90
37 38 5.530171 GGAATCATTACTCATGTGCAGATGT 59.470 40.000 21.93 7.85 34.06 3.06
38 39 6.373186 AATCATTACTCATGTGCAGATGTG 57.627 37.500 21.93 21.22 34.06 3.21
130 132 9.942850 TTCATTTCACAGATTAGATGACTGTTA 57.057 29.630 0.00 0.00 41.93 2.41
158 161 5.072055 TCCTGAATTCTTGTTTGCAGATCA 58.928 37.500 7.05 0.00 0.00 2.92
167 170 6.675026 TCTTGTTTGCAGATCAGATTTCTTG 58.325 36.000 0.00 0.00 0.00 3.02
176 179 6.581542 GCAGATCAGATTTCTTGTTTTCACAG 59.418 38.462 0.00 0.00 33.22 3.66
223 226 4.037923 AGTTTGCACACTATGTTTTCAGGG 59.962 41.667 3.03 0.00 0.00 4.45
225 228 3.146066 TGCACACTATGTTTTCAGGGTC 58.854 45.455 0.00 0.00 0.00 4.46
230 233 6.208644 CACACTATGTTTTCAGGGTCAAAAG 58.791 40.000 0.00 0.00 0.00 2.27
231 234 6.039270 CACACTATGTTTTCAGGGTCAAAAGA 59.961 38.462 0.00 0.00 0.00 2.52
232 235 6.039382 ACACTATGTTTTCAGGGTCAAAAGAC 59.961 38.462 0.00 0.00 0.00 3.01
240 246 4.579869 TCAGGGTCAAAAGACTGATAAGC 58.420 43.478 0.00 0.00 35.24 3.09
248 254 6.525976 GTCAAAAGACTGATAAGCAATTGAGC 59.474 38.462 10.34 0.00 0.00 4.26
273 279 4.614475 TGATGTTCTGGACTATCACTCCT 58.386 43.478 0.00 0.00 0.00 3.69
329 335 2.747396 TTTTCTGCACATCCATTGCC 57.253 45.000 0.00 0.00 39.39 4.52
336 342 2.309613 GCACATCCATTGCCCTTGATA 58.690 47.619 0.00 0.00 33.58 2.15
337 343 2.035066 GCACATCCATTGCCCTTGATAC 59.965 50.000 0.00 0.00 33.58 2.24
344 350 5.192927 TCCATTGCCCTTGATACTGTAAAG 58.807 41.667 0.00 0.00 0.00 1.85
352 358 6.602009 GCCCTTGATACTGTAAAGTGGTATTT 59.398 38.462 0.00 0.00 0.00 1.40
353 359 7.771826 GCCCTTGATACTGTAAAGTGGTATTTA 59.228 37.037 0.00 0.00 0.00 1.40
354 360 9.326413 CCCTTGATACTGTAAAGTGGTATTTAG 57.674 37.037 0.00 0.00 0.00 1.85
359 365 9.530633 GATACTGTAAAGTGGTATTTAGACAGG 57.469 37.037 0.00 0.00 34.91 4.00
362 368 4.650972 AAAGTGGTATTTAGACAGGCCA 57.349 40.909 5.01 0.00 0.00 5.36
363 369 4.650972 AAGTGGTATTTAGACAGGCCAA 57.349 40.909 5.01 0.00 0.00 4.52
364 370 4.862641 AGTGGTATTTAGACAGGCCAAT 57.137 40.909 5.01 0.00 0.00 3.16
365 371 4.526970 AGTGGTATTTAGACAGGCCAATG 58.473 43.478 5.01 0.00 0.00 2.82
366 372 3.066760 GTGGTATTTAGACAGGCCAATGC 59.933 47.826 5.01 0.00 0.00 3.56
409 415 7.979444 TGAACTAGTTTATTTCCCTGAAGTG 57.021 36.000 10.02 0.00 0.00 3.16
465 471 5.734720 TCATGGACAGTTATCTTTGACCTC 58.265 41.667 0.00 0.00 31.70 3.85
466 472 5.485353 TCATGGACAGTTATCTTTGACCTCT 59.515 40.000 0.00 0.00 31.70 3.69
486 492 5.467035 TCTGTTTGGAAATAGGCAAAAGG 57.533 39.130 0.00 0.00 0.00 3.11
579 586 7.859377 CGCTTTATGCTGTTTTAATGATGAGAT 59.141 33.333 0.00 0.00 40.11 2.75
597 604 9.768662 TGATGAGATTTCAATTCATTCTCGATA 57.231 29.630 0.00 0.00 36.78 2.92
616 623 6.822442 TCGATAACCTAAATCTGCATTACCA 58.178 36.000 0.00 0.00 0.00 3.25
619 626 8.230486 CGATAACCTAAATCTGCATTACCAATC 58.770 37.037 0.00 0.00 0.00 2.67
688 695 4.651994 GTCTCAAAACATATGGTGCTTCG 58.348 43.478 7.80 0.00 0.00 3.79
731 738 3.981071 TTGGAGTGATACAAGACTGGG 57.019 47.619 0.00 0.00 0.00 4.45
799 807 4.747810 CATGCTTTGTTCCCAGGATAAAC 58.252 43.478 0.00 0.00 0.00 2.01
819 827 9.730420 GATAAACGGTTGTGATAAGCAATTAAT 57.270 29.630 0.00 0.00 0.00 1.40
863 871 5.641209 CACTCCTCTTTTTCTGTGAGGTATG 59.359 44.000 7.94 4.72 45.46 2.39
930 942 8.255206 TGATAGTGTAAACTGGTATTTGTCGAT 58.745 33.333 0.00 0.00 0.00 3.59
1008 1038 3.334691 CTTCGTGGTAAAGATGGCAGAA 58.665 45.455 0.00 0.00 0.00 3.02
1061 1091 8.121833 AGGAGCCTATACAATCAATCTAGAGAT 58.878 37.037 0.00 0.00 36.07 2.75
1155 1185 1.477700 GCCATTGCAATTGCTACTCCA 59.522 47.619 29.37 6.89 42.66 3.86
1381 1420 1.572415 AGAATGGGGATGGCATTGACT 59.428 47.619 0.00 0.00 0.00 3.41
1413 1453 2.253452 CTGCGTGCTGTTTCTGCC 59.747 61.111 0.00 0.00 0.00 4.85
1422 1462 1.151668 CTGTTTCTGCCCAGTCGAAG 58.848 55.000 0.00 0.00 0.00 3.79
1510 1587 3.691609 GGCAGAAAAGTTATCTGGTGGAG 59.308 47.826 5.76 0.00 43.60 3.86
1611 1690 2.674796 AGGCTGCTTACCTAACTTCG 57.325 50.000 0.00 0.00 35.10 3.79
1710 1789 3.196469 TGATGGATGACACAGAGAAGGTC 59.804 47.826 0.00 0.00 0.00 3.85
1875 1958 6.962686 TGCAAGTATTATCATCTGTGCAATC 58.037 36.000 0.00 0.00 37.78 2.67
1956 2044 0.801067 CGGCACAGAGTAAGGCGTAC 60.801 60.000 2.11 2.11 44.84 3.67
2077 2165 1.377856 GCCCCTGAACTGCTTCCTC 60.378 63.158 0.00 0.00 0.00 3.71
2142 2230 5.390991 CCGAGAATCTGGCTTAAACTTGAAC 60.391 44.000 0.00 0.00 0.00 3.18
2144 2232 4.455877 AGAATCTGGCTTAAACTTGAACGG 59.544 41.667 0.00 0.00 0.00 4.44
2208 2296 7.447374 TGTCAACCTTGGTTTGAGTAATATG 57.553 36.000 1.76 0.00 33.63 1.78
2319 3632 0.529378 CCAATTGCTCCAAGGCTGTC 59.471 55.000 0.00 0.00 0.00 3.51
2370 3683 1.078356 GGAGGAAGTTCCGAAGCCC 60.078 63.158 16.31 9.79 42.75 5.19
2616 3935 8.268850 ACAAGAATGTGAATGATGTACCTTAC 57.731 34.615 0.00 0.00 38.69 2.34
2622 3942 5.163550 TGTGAATGATGTACCTTACTCGAGG 60.164 44.000 18.41 1.51 42.75 4.63
2904 4331 4.015084 AGATCAAAACATTGAGGAGGCAG 58.985 43.478 0.00 0.00 34.02 4.85
3340 4808 2.601666 AGCAGCGTGAGAGGGACA 60.602 61.111 0.00 0.00 0.00 4.02
3768 5264 1.686325 GGCGCCCTATCCTGAAGACA 61.686 60.000 18.11 0.00 0.00 3.41
3780 5276 6.939132 ATCCTGAAGACAATCATTGATGAC 57.061 37.500 3.79 0.00 40.03 3.06
3909 5405 0.248825 CTGAGCCCGAGTCTGAATCG 60.249 60.000 19.40 19.40 39.86 3.34
4050 5546 4.446413 AACGCGGACCGGGATCAC 62.446 66.667 34.58 7.41 42.31 3.06
4068 5564 2.653702 GGCGCAGAGTCTGACAGT 59.346 61.111 24.55 0.00 32.44 3.55
4206 5702 2.281484 GGCAACAAGTCTCGCCCA 60.281 61.111 0.00 0.00 38.67 5.36
4248 5744 3.068881 CCACCCTCGAAGAAGCCA 58.931 61.111 0.00 0.00 34.09 4.75
4281 5777 4.117372 GTTCGTCTTGGTCGCGCG 62.117 66.667 26.76 26.76 0.00 6.86
4303 5802 1.208052 CCTCTGAATCTGCCCTTTCGA 59.792 52.381 0.00 0.00 0.00 3.71
4361 5860 2.925306 GCCGTCTTGTTCGCTCTTTAGA 60.925 50.000 0.00 0.00 0.00 2.10
4366 5865 2.342910 TGTTCGCTCTTTAGACCGTC 57.657 50.000 0.00 0.00 0.00 4.79
4401 5900 2.166459 TCTGCAGTAGCTTTGCTCGTAT 59.834 45.455 14.67 0.00 42.02 3.06
4412 5911 9.286946 GTAGCTTTGCTCGTATTATCGTTATAT 57.713 33.333 0.00 0.00 40.44 0.86
4418 5919 9.983804 TTGCTCGTATTATCGTTATATAGTCAG 57.016 33.333 0.00 0.00 0.00 3.51
4624 6126 0.234884 CTGTTTTCCGCGACTGTTCC 59.765 55.000 8.23 0.00 0.00 3.62
4625 6127 0.179067 TGTTTTCCGCGACTGTTCCT 60.179 50.000 8.23 0.00 0.00 3.36
4628 6130 0.319555 TTTCCGCGACTGTTCCTCTG 60.320 55.000 8.23 0.00 0.00 3.35
4632 6134 3.175240 CGACTGTTCCTCTGCGCG 61.175 66.667 0.00 0.00 0.00 6.86
4633 6135 2.811317 GACTGTTCCTCTGCGCGG 60.811 66.667 10.86 10.86 0.00 6.46
4634 6136 4.379243 ACTGTTCCTCTGCGCGGG 62.379 66.667 17.88 11.97 0.00 6.13
4635 6137 4.069232 CTGTTCCTCTGCGCGGGA 62.069 66.667 17.88 14.28 0.00 5.14
4661 6163 3.004315 ACAAACATTTGGCTCCGTTACTG 59.996 43.478 9.09 0.00 42.34 2.74
4668 6175 2.388232 GCTCCGTTACTGGTTGCCG 61.388 63.158 0.00 0.00 0.00 5.69
4696 6203 1.616865 TGTCCCGTGACGAGAATTTCT 59.383 47.619 6.54 0.00 44.86 2.52
4697 6204 2.260481 GTCCCGTGACGAGAATTTCTC 58.740 52.381 15.17 15.17 40.06 2.87
4705 6212 3.139029 GAGAATTTCTCGGTGCGGT 57.861 52.632 10.52 0.00 33.35 5.68
4707 6214 1.134694 GAATTTCTCGGTGCGGTGC 59.865 57.895 0.00 0.00 0.00 5.01
4710 6217 2.449031 ATTTCTCGGTGCGGTGCAGA 62.449 55.000 0.00 0.00 40.08 4.26
4711 6218 3.573772 TTCTCGGTGCGGTGCAGAG 62.574 63.158 0.00 0.00 40.08 3.35
4712 6219 4.363990 CTCGGTGCGGTGCAGAGT 62.364 66.667 0.00 0.00 40.08 3.24
4713 6220 2.986979 TCGGTGCGGTGCAGAGTA 60.987 61.111 0.00 0.00 40.08 2.59
4714 6221 2.507102 CGGTGCGGTGCAGAGTAG 60.507 66.667 0.00 0.00 40.08 2.57
4715 6222 2.970639 GGTGCGGTGCAGAGTAGA 59.029 61.111 0.00 0.00 40.08 2.59
4716 6223 1.446272 GGTGCGGTGCAGAGTAGAC 60.446 63.158 0.00 0.00 40.08 2.59
4717 6224 1.289066 GTGCGGTGCAGAGTAGACA 59.711 57.895 0.00 0.00 40.08 3.41
4718 6225 1.009389 GTGCGGTGCAGAGTAGACAC 61.009 60.000 0.00 0.00 40.08 3.67
4719 6226 1.289066 GCGGTGCAGAGTAGACACA 59.711 57.895 0.00 0.00 36.00 3.72
4720 6227 0.108615 GCGGTGCAGAGTAGACACAT 60.109 55.000 0.00 0.00 36.00 3.21
4721 6228 1.673033 GCGGTGCAGAGTAGACACATT 60.673 52.381 0.00 0.00 36.00 2.71
4722 6229 2.688507 CGGTGCAGAGTAGACACATTT 58.311 47.619 0.00 0.00 36.00 2.32
4723 6230 3.067106 CGGTGCAGAGTAGACACATTTT 58.933 45.455 0.00 0.00 36.00 1.82
4724 6231 3.120546 CGGTGCAGAGTAGACACATTTTG 60.121 47.826 0.00 0.00 36.00 2.44
4725 6232 3.189287 GGTGCAGAGTAGACACATTTTGG 59.811 47.826 0.00 0.00 36.00 3.28
4726 6233 2.813754 TGCAGAGTAGACACATTTTGGC 59.186 45.455 0.00 0.00 0.00 4.52
4728 6235 3.120060 GCAGAGTAGACACATTTTGGCTG 60.120 47.826 0.00 0.00 46.52 4.85
4729 6236 3.438087 CAGAGTAGACACATTTTGGCTGG 59.562 47.826 0.00 0.00 46.52 4.85
4730 6237 3.327757 AGAGTAGACACATTTTGGCTGGA 59.672 43.478 0.00 0.00 46.52 3.86
4731 6238 3.412386 AGTAGACACATTTTGGCTGGAC 58.588 45.455 0.00 0.00 46.52 4.02
4928 6827 1.880675 ACGGCCATAGATAGTCGACAG 59.119 52.381 19.50 0.00 0.00 3.51
4989 7163 1.347707 TGTCGCACCTTCTCATTTCCT 59.652 47.619 0.00 0.00 0.00 3.36
4990 7164 2.224523 TGTCGCACCTTCTCATTTCCTT 60.225 45.455 0.00 0.00 0.00 3.36
4991 7165 2.416893 GTCGCACCTTCTCATTTCCTTC 59.583 50.000 0.00 0.00 0.00 3.46
4992 7166 1.740025 CGCACCTTCTCATTTCCTTCC 59.260 52.381 0.00 0.00 0.00 3.46
5000 7174 0.395586 TCATTTCCTTCCCATGGCCG 60.396 55.000 6.09 0.00 0.00 6.13
5022 7196 3.013219 GCCAGATTTCCTTCACTTCCTC 58.987 50.000 0.00 0.00 0.00 3.71
5028 7202 1.801242 TCCTTCACTTCCTCACACCA 58.199 50.000 0.00 0.00 0.00 4.17
5045 7219 1.202698 ACCAGACAGACAAAGAGGTGC 60.203 52.381 0.00 0.00 0.00 5.01
5071 7245 0.182299 CCCTCCTCCTCATTTCTGCC 59.818 60.000 0.00 0.00 0.00 4.85
5141 7316 1.013596 TTGTCCGTGTTGCAACAGAG 58.986 50.000 31.81 25.89 40.05 3.35
5145 7320 2.033151 GTCCGTGTTGCAACAGAGTTAC 60.033 50.000 31.81 21.54 40.05 2.50
5147 7322 1.591158 CGTGTTGCAACAGAGTTACGT 59.409 47.619 31.81 0.00 40.05 3.57
5199 7374 1.081892 CTGACACGGCATCTTCCAAG 58.918 55.000 0.00 0.00 0.00 3.61
5200 7375 0.955428 TGACACGGCATCTTCCAAGC 60.955 55.000 0.00 0.00 0.00 4.01
5207 7382 1.589716 GCATCTTCCAAGCACGCCTT 61.590 55.000 0.00 0.00 0.00 4.35
5210 7390 0.884704 TCTTCCAAGCACGCCTTCAC 60.885 55.000 0.00 0.00 0.00 3.18
5226 7406 1.795768 TCACAACTTGTCCTCGCATC 58.204 50.000 0.00 0.00 0.00 3.91
5228 7408 0.321653 ACAACTTGTCCTCGCATCCC 60.322 55.000 0.00 0.00 0.00 3.85
5230 7410 1.207089 CAACTTGTCCTCGCATCCCTA 59.793 52.381 0.00 0.00 0.00 3.53
5233 7413 1.414181 CTTGTCCTCGCATCCCTACAT 59.586 52.381 0.00 0.00 0.00 2.29
5235 7415 1.412710 TGTCCTCGCATCCCTACATTC 59.587 52.381 0.00 0.00 0.00 2.67
5236 7416 1.689273 GTCCTCGCATCCCTACATTCT 59.311 52.381 0.00 0.00 0.00 2.40
5237 7417 1.688735 TCCTCGCATCCCTACATTCTG 59.311 52.381 0.00 0.00 0.00 3.02
5238 7418 1.414181 CCTCGCATCCCTACATTCTGT 59.586 52.381 0.00 0.00 0.00 3.41
5239 7419 2.477825 CTCGCATCCCTACATTCTGTG 58.522 52.381 0.00 0.00 0.00 3.66
5240 7420 2.101415 CTCGCATCCCTACATTCTGTGA 59.899 50.000 0.00 0.00 0.00 3.58
5241 7421 2.101415 TCGCATCCCTACATTCTGTGAG 59.899 50.000 0.00 0.00 0.00 3.51
5242 7422 2.216898 GCATCCCTACATTCTGTGAGC 58.783 52.381 0.00 0.00 0.00 4.26
5244 7424 1.951209 TCCCTACATTCTGTGAGCCA 58.049 50.000 0.00 0.00 0.00 4.75
5245 7425 1.833630 TCCCTACATTCTGTGAGCCAG 59.166 52.381 0.00 0.00 42.97 4.85
5246 7426 1.661341 CCTACATTCTGTGAGCCAGC 58.339 55.000 0.00 0.00 41.25 4.85
5247 7427 1.065926 CCTACATTCTGTGAGCCAGCA 60.066 52.381 0.00 0.00 41.25 4.41
5248 7428 2.421107 CCTACATTCTGTGAGCCAGCAT 60.421 50.000 0.00 0.00 41.25 3.79
5249 7429 1.747709 ACATTCTGTGAGCCAGCATC 58.252 50.000 0.00 0.00 41.25 3.91
5250 7430 1.281287 ACATTCTGTGAGCCAGCATCT 59.719 47.619 0.00 0.00 41.25 2.90
5251 7431 1.941294 CATTCTGTGAGCCAGCATCTC 59.059 52.381 0.00 0.00 41.25 2.75
5252 7432 0.251354 TTCTGTGAGCCAGCATCTCC 59.749 55.000 0.00 0.00 41.25 3.71
5253 7433 0.906282 TCTGTGAGCCAGCATCTCCA 60.906 55.000 0.00 0.00 41.25 3.86
5254 7434 0.180642 CTGTGAGCCAGCATCTCCAT 59.819 55.000 0.00 0.00 33.59 3.41
5255 7435 0.622136 TGTGAGCCAGCATCTCCATT 59.378 50.000 0.00 0.00 0.00 3.16
5256 7436 1.307097 GTGAGCCAGCATCTCCATTC 58.693 55.000 0.00 0.00 0.00 2.67
5257 7437 0.182061 TGAGCCAGCATCTCCATTCC 59.818 55.000 0.00 0.00 0.00 3.01
5258 7438 0.473326 GAGCCAGCATCTCCATTCCT 59.527 55.000 0.00 0.00 0.00 3.36
5259 7439 0.924823 AGCCAGCATCTCCATTCCTT 59.075 50.000 0.00 0.00 0.00 3.36
5260 7440 1.030457 GCCAGCATCTCCATTCCTTG 58.970 55.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.025396 CGTCCATGATTTCAGTATCTGCAC 60.025 45.833 0.00 0.00 0.00 4.57
37 38 4.122046 CGTCCATGATTTCAGTATCTGCA 58.878 43.478 0.00 0.00 0.00 4.41
38 39 3.496130 CCGTCCATGATTTCAGTATCTGC 59.504 47.826 0.00 0.00 0.00 4.26
39 40 4.697514 ACCGTCCATGATTTCAGTATCTG 58.302 43.478 0.00 0.00 0.00 2.90
40 41 5.359194 AACCGTCCATGATTTCAGTATCT 57.641 39.130 0.00 0.00 0.00 1.98
41 42 7.155328 AGATAACCGTCCATGATTTCAGTATC 58.845 38.462 0.00 0.00 0.00 2.24
42 43 7.067496 AGATAACCGTCCATGATTTCAGTAT 57.933 36.000 0.00 0.00 0.00 2.12
43 44 6.479972 AGATAACCGTCCATGATTTCAGTA 57.520 37.500 0.00 0.00 0.00 2.74
130 132 8.125978 TCTGCAAACAAGAATTCAGGATAAAT 57.874 30.769 8.44 0.00 0.00 1.40
225 228 6.384224 TGCTCAATTGCTTATCAGTCTTTTG 58.616 36.000 0.00 0.00 0.00 2.44
230 233 6.127810 TCAATGCTCAATTGCTTATCAGTC 57.872 37.500 0.00 0.00 44.63 3.51
231 234 6.096423 ACATCAATGCTCAATTGCTTATCAGT 59.904 34.615 0.00 0.00 44.63 3.41
232 235 6.504398 ACATCAATGCTCAATTGCTTATCAG 58.496 36.000 0.00 0.00 44.63 2.90
240 246 5.100259 GTCCAGAACATCAATGCTCAATTG 58.900 41.667 0.00 0.00 46.10 2.32
248 254 5.757320 GGAGTGATAGTCCAGAACATCAATG 59.243 44.000 0.00 0.00 37.65 2.82
273 279 6.672266 AGACAAATACCTCACAGAAGAAGA 57.328 37.500 0.00 0.00 0.00 2.87
336 342 6.171213 GCCTGTCTAAATACCACTTTACAGT 58.829 40.000 0.00 0.00 0.00 3.55
337 343 5.585047 GGCCTGTCTAAATACCACTTTACAG 59.415 44.000 0.00 0.00 0.00 2.74
344 350 3.066760 GCATTGGCCTGTCTAAATACCAC 59.933 47.826 3.32 0.00 0.00 4.16
359 365 5.818857 ACAAATGAAGATTATTGGCATTGGC 59.181 36.000 2.73 2.73 40.13 4.52
362 368 9.504708 TTCAAACAAATGAAGATTATTGGCATT 57.495 25.926 0.00 0.00 34.50 3.56
363 369 8.938906 GTTCAAACAAATGAAGATTATTGGCAT 58.061 29.630 0.00 0.00 39.84 4.40
364 370 8.149647 AGTTCAAACAAATGAAGATTATTGGCA 58.850 29.630 0.00 0.00 39.84 4.92
365 371 8.538409 AGTTCAAACAAATGAAGATTATTGGC 57.462 30.769 0.00 0.00 39.84 4.52
409 415 3.065786 CCACACATGAGTAATGATGCCAC 59.934 47.826 0.00 0.00 38.72 5.01
465 471 5.213891 ACCTTTTGCCTATTTCCAAACAG 57.786 39.130 0.00 0.00 31.30 3.16
466 472 5.622346 AACCTTTTGCCTATTTCCAAACA 57.378 34.783 0.00 0.00 31.30 2.83
528 534 3.245586 ACATGGTTTATGAAGCCAGGGAA 60.246 43.478 10.73 0.00 39.21 3.97
529 535 2.311542 ACATGGTTTATGAAGCCAGGGA 59.688 45.455 10.73 0.00 39.21 4.20
536 542 4.882671 AAGCGCTACATGGTTTATGAAG 57.117 40.909 12.05 0.00 39.21 3.02
593 600 7.490962 TTGGTAATGCAGATTTAGGTTATCG 57.509 36.000 0.00 0.00 0.00 2.92
597 604 6.891908 ACAGATTGGTAATGCAGATTTAGGTT 59.108 34.615 0.00 0.00 0.00 3.50
616 623 9.691362 ATAATTTCTTGCAACGTTAAACAGATT 57.309 25.926 0.00 0.00 0.00 2.40
688 695 1.089920 CTGCCACACTGGTTAGCATC 58.910 55.000 0.00 0.00 40.46 3.91
799 807 6.377327 AGGATTAATTGCTTATCACAACCG 57.623 37.500 0.00 0.00 0.00 4.44
819 827 1.351017 GACAATCCAGGACACCAAGGA 59.649 52.381 0.00 0.00 35.17 3.36
863 871 9.396022 TCAGAAAATATTTCAAGTCCCAGATAC 57.604 33.333 0.10 0.00 0.00 2.24
930 942 8.907222 TTGATGATAATTAGCTAGTGCAATCA 57.093 30.769 1.93 9.92 42.74 2.57
960 972 2.065899 TAACCAAGCCAAACTGCAGT 57.934 45.000 15.25 15.25 0.00 4.40
1008 1038 3.897505 AGCCTGACTTTGCTTTACCATTT 59.102 39.130 0.00 0.00 32.94 2.32
1061 1091 2.565834 ACCTTAAGCCGCTTACTGAAGA 59.434 45.455 12.50 0.00 34.25 2.87
1284 1317 2.428530 GAGGGTTCCAATGAGATTTGCC 59.571 50.000 0.00 0.00 0.00 4.52
1395 1435 2.253452 GCAGAAACAGCACGCAGG 59.747 61.111 0.00 0.00 0.00 4.85
1413 1453 1.068194 GGAGTGTCAGACTTCGACTGG 60.068 57.143 1.31 0.00 33.83 4.00
1510 1587 4.213270 TGTTACATCTGCAAGTTGTACAGC 59.787 41.667 4.48 0.72 45.80 4.40
1611 1690 5.650543 ACCACAAAGTTTTTCATCACAGAC 58.349 37.500 0.00 0.00 0.00 3.51
1710 1789 3.212685 GGCCTTCAGAGGATCAAGAATG 58.787 50.000 0.00 0.00 46.74 2.67
1723 1802 1.610522 CAACTTCACCTTGGCCTTCAG 59.389 52.381 3.32 0.00 0.00 3.02
1875 1958 1.553706 AGTTACTGTACCTGGACCCG 58.446 55.000 0.00 0.00 0.00 5.28
1956 2044 1.946768 TGGGCTTTCAAAAGTGTCTCG 59.053 47.619 4.54 0.00 38.28 4.04
2043 2131 1.200020 GGGGCATTCTTCTCAAACACG 59.800 52.381 0.00 0.00 0.00 4.49
2077 2165 4.999950 AGTTCCAGCTGACTTTGTTAGATG 59.000 41.667 17.39 1.59 35.76 2.90
2142 2230 0.389817 TCAGACGGTCATTCTTGCCG 60.390 55.000 11.27 0.00 43.59 5.69
2144 2232 5.351465 TCTTTTATCAGACGGTCATTCTTGC 59.649 40.000 11.27 0.00 0.00 4.01
2208 2296 3.054878 CTCATTGTTTGTTTCTGCCTGC 58.945 45.455 0.00 0.00 0.00 4.85
2370 3683 1.648467 GCTCAACCTTAGCCCGCTTG 61.648 60.000 0.00 0.00 33.73 4.01
2399 3714 1.656652 CTTGGATGGTAGTGCTTCCG 58.343 55.000 0.00 0.00 0.00 4.30
2616 3935 2.100197 TGTATCACCAACTCCCTCGAG 58.900 52.381 5.13 5.13 42.32 4.04
2622 3942 6.096987 TCTGATCTACTTGTATCACCAACTCC 59.903 42.308 0.00 0.00 0.00 3.85
2904 4331 2.167487 CTCTGACTCCCTTGAAGCTACC 59.833 54.545 0.00 0.00 0.00 3.18
3228 4696 7.287696 ACTTCAACATAAAACTGGACATCCTTT 59.712 33.333 0.00 0.00 36.82 3.11
3340 4808 5.222007 ACTCCATGTTGATTCTGTTCTTCCT 60.222 40.000 0.00 0.00 0.00 3.36
3426 4895 5.841237 TCTAAGAGGGATATCAAACTCCAGG 59.159 44.000 4.83 2.99 32.90 4.45
3768 5264 5.447778 ACTTCTGAGGGTCATCAATGATT 57.552 39.130 0.00 0.00 39.30 2.57
3780 5276 2.833794 TCGTCAACAAACTTCTGAGGG 58.166 47.619 0.00 0.00 0.00 4.30
3909 5405 2.672760 GCTGTCGGAGTCTTCTTCTTCC 60.673 54.545 0.00 0.00 0.00 3.46
3915 5411 2.569134 GCGCTGTCGGAGTCTTCT 59.431 61.111 0.00 0.00 35.95 2.85
4050 5546 2.505777 CTGTCAGACTCTGCGCCG 60.506 66.667 4.18 0.00 0.00 6.46
4068 5564 1.296715 GCGCCTCCTTTCTTCCTCA 59.703 57.895 0.00 0.00 0.00 3.86
4130 5626 1.078848 CTGCTGCTAGGACCACCAC 60.079 63.158 0.00 0.00 38.94 4.16
4131 5627 2.959484 GCTGCTGCTAGGACCACCA 61.959 63.158 8.53 0.00 35.90 4.17
4132 5628 2.124942 GCTGCTGCTAGGACCACC 60.125 66.667 8.53 0.00 36.03 4.61
4206 5702 0.618968 CCTTGGAGCTACTGGGAGGT 60.619 60.000 0.00 0.00 0.00 3.85
4233 5729 0.765510 ACTTTGGCTTCTTCGAGGGT 59.234 50.000 0.00 0.00 0.00 4.34
4248 5744 3.551846 ACGAACCAATCACCTGAACTTT 58.448 40.909 0.00 0.00 0.00 2.66
4281 5777 0.033699 AAAGGGCAGATTCAGAGGGC 60.034 55.000 0.00 0.00 0.00 5.19
4282 5778 1.745141 CGAAAGGGCAGATTCAGAGGG 60.745 57.143 0.00 0.00 0.00 4.30
4303 5802 2.972713 ACCATACGAATACCATGCCTCT 59.027 45.455 0.00 0.00 0.00 3.69
4366 5865 1.979469 CTGCAGAAACGAGTACGACAG 59.021 52.381 8.42 0.00 42.66 3.51
4401 5900 7.663081 AGGTTCCGACTGACTATATAACGATAA 59.337 37.037 0.00 0.00 0.00 1.75
4412 5911 1.616865 CACCAAGGTTCCGACTGACTA 59.383 52.381 0.00 0.00 0.00 2.59
4418 5919 2.227194 ACAATTCACCAAGGTTCCGAC 58.773 47.619 0.00 0.00 0.00 4.79
4595 6097 0.237498 CGGAAAACAGGCGGAAAGAC 59.763 55.000 0.00 0.00 0.00 3.01
4632 6134 0.608130 GCCAAATGTTTGTCCCTCCC 59.392 55.000 4.92 0.00 36.45 4.30
4633 6135 1.546029 GAGCCAAATGTTTGTCCCTCC 59.454 52.381 4.92 0.00 36.45 4.30
4634 6136 1.546029 GGAGCCAAATGTTTGTCCCTC 59.454 52.381 4.92 6.98 36.45 4.30
4635 6137 1.632589 GGAGCCAAATGTTTGTCCCT 58.367 50.000 4.92 0.00 36.45 4.20
4668 6175 1.566018 CGTCACGGGACAAAGCCTTC 61.566 60.000 19.62 0.00 44.54 3.46
4696 6203 2.986979 TACTCTGCACCGCACCGA 60.987 61.111 0.00 0.00 33.79 4.69
4697 6204 2.507102 CTACTCTGCACCGCACCG 60.507 66.667 0.00 0.00 33.79 4.94
4699 6206 1.009389 GTGTCTACTCTGCACCGCAC 61.009 60.000 0.00 0.00 33.79 5.34
4701 6208 0.108615 ATGTGTCTACTCTGCACCGC 60.109 55.000 0.00 0.00 32.62 5.68
4703 6210 3.189287 CCAAAATGTGTCTACTCTGCACC 59.811 47.826 0.00 0.00 32.62 5.01
4705 6212 2.813754 GCCAAAATGTGTCTACTCTGCA 59.186 45.455 0.00 0.00 0.00 4.41
4707 6214 3.438087 CCAGCCAAAATGTGTCTACTCTG 59.562 47.826 0.00 0.00 0.00 3.35
4710 6217 3.073062 AGTCCAGCCAAAATGTGTCTACT 59.927 43.478 0.00 0.00 0.00 2.57
4711 6218 3.412386 AGTCCAGCCAAAATGTGTCTAC 58.588 45.455 0.00 0.00 0.00 2.59
4712 6219 3.559171 GGAGTCCAGCCAAAATGTGTCTA 60.559 47.826 3.60 0.00 0.00 2.59
4713 6220 2.508526 GAGTCCAGCCAAAATGTGTCT 58.491 47.619 0.00 0.00 0.00 3.41
4714 6221 1.541588 GGAGTCCAGCCAAAATGTGTC 59.458 52.381 3.60 0.00 0.00 3.67
4715 6222 1.133513 TGGAGTCCAGCCAAAATGTGT 60.134 47.619 8.12 0.00 31.13 3.72
4716 6223 1.619654 TGGAGTCCAGCCAAAATGTG 58.380 50.000 8.12 0.00 31.13 3.21
4717 6224 2.225091 TGATGGAGTCCAGCCAAAATGT 60.225 45.455 24.26 0.00 39.46 2.71
4718 6225 2.449464 TGATGGAGTCCAGCCAAAATG 58.551 47.619 24.26 0.00 39.46 2.32
4719 6226 2.905415 TGATGGAGTCCAGCCAAAAT 57.095 45.000 24.26 1.44 39.46 1.82
4720 6227 2.673775 TTGATGGAGTCCAGCCAAAA 57.326 45.000 24.26 9.67 39.46 2.44
4721 6228 2.905415 ATTGATGGAGTCCAGCCAAA 57.095 45.000 24.26 13.38 39.46 3.28
4722 6229 4.464008 GAATATTGATGGAGTCCAGCCAA 58.536 43.478 24.26 23.98 39.46 4.52
4723 6230 3.494924 CGAATATTGATGGAGTCCAGCCA 60.495 47.826 24.26 14.53 39.46 4.75
4724 6231 3.070018 CGAATATTGATGGAGTCCAGCC 58.930 50.000 24.26 15.11 39.46 4.85
4725 6232 3.070018 CCGAATATTGATGGAGTCCAGC 58.930 50.000 20.80 20.80 40.77 4.85
4726 6233 4.039730 AGACCGAATATTGATGGAGTCCAG 59.960 45.833 18.69 2.05 36.75 3.86
4727 6234 3.967326 AGACCGAATATTGATGGAGTCCA 59.033 43.478 15.88 15.88 38.19 4.02
4728 6235 4.039245 TGAGACCGAATATTGATGGAGTCC 59.961 45.833 0.73 0.73 0.00 3.85
4729 6236 5.201713 TGAGACCGAATATTGATGGAGTC 57.798 43.478 0.00 0.00 0.00 3.36
4730 6237 4.502259 GCTGAGACCGAATATTGATGGAGT 60.502 45.833 0.00 0.00 0.00 3.85
4731 6238 3.993081 GCTGAGACCGAATATTGATGGAG 59.007 47.826 0.00 0.00 0.00 3.86
4928 6827 3.431922 TGATACTGTTGTAGTAGCCGC 57.568 47.619 0.00 0.00 45.48 6.53
4991 7165 4.528039 AATCTGGCCGGCCATGGG 62.528 66.667 46.65 34.56 46.15 4.00
4992 7166 2.442643 AAATCTGGCCGGCCATGG 60.443 61.111 46.65 35.31 46.15 3.66
5000 7174 2.095461 GGAAGTGAAGGAAATCTGGCC 58.905 52.381 0.00 0.00 0.00 5.36
5022 7196 2.158900 ACCTCTTTGTCTGTCTGGTGTG 60.159 50.000 0.00 0.00 0.00 3.82
5045 7219 3.086600 GAGGAGGAGGGTGCTGGG 61.087 72.222 0.00 0.00 0.00 4.45
5052 7226 0.182299 GGCAGAAATGAGGAGGAGGG 59.818 60.000 0.00 0.00 0.00 4.30
5071 7245 8.553459 AGAGGACACTAAATGTATTTTCTGTG 57.447 34.615 12.09 12.09 43.56 3.66
5080 7255 7.390823 TGTGCAAATAGAGGACACTAAATGTA 58.609 34.615 0.00 0.00 43.56 2.29
5199 7374 0.317020 GACAAGTTGTGAAGGCGTGC 60.317 55.000 14.57 0.00 0.00 5.34
5200 7375 0.307760 GGACAAGTTGTGAAGGCGTG 59.692 55.000 14.57 0.00 0.00 5.34
5207 7382 1.608025 GGATGCGAGGACAAGTTGTGA 60.608 52.381 14.57 0.00 0.00 3.58
5210 7390 0.036010 AGGGATGCGAGGACAAGTTG 60.036 55.000 0.00 0.00 0.00 3.16
5236 7416 0.622136 AATGGAGATGCTGGCTCACA 59.378 50.000 0.00 0.00 34.07 3.58
5237 7417 1.307097 GAATGGAGATGCTGGCTCAC 58.693 55.000 0.00 0.00 34.07 3.51
5238 7418 0.182061 GGAATGGAGATGCTGGCTCA 59.818 55.000 0.00 0.00 34.07 4.26
5239 7419 0.473326 AGGAATGGAGATGCTGGCTC 59.527 55.000 0.00 0.00 0.00 4.70
5240 7420 0.924823 AAGGAATGGAGATGCTGGCT 59.075 50.000 0.00 0.00 0.00 4.75
5241 7421 1.030457 CAAGGAATGGAGATGCTGGC 58.970 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.