Multiple sequence alignment - TraesCS1B01G241100

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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 TraesCS1B01G241100 chr1B 100.000 6543 0 0 1 6543 428727525 428720983 0.000000e+00 12083.0
1 TraesCS1B01G241100 chr1B 88.776 98 8 3 494 590 634153498 634153593 4.150000e-22 117.0
2 TraesCS1B01G241100 chr1B 89.796 49 4 1 4212 4260 4516626 4516673 1.970000e-05 62.1
3 TraesCS1B01G241100 chr1D 92.719 5686 221 59 847 6429 316623107 316617512 0.000000e+00 8028.0
4 TraesCS1B01G241100 chr1D 98.844 173 2 0 602 774 316623607 316623435 6.370000e-80 309.0
5 TraesCS1B01G241100 chr1D 80.702 399 59 10 2599 2989 442682854 442682466 1.780000e-75 294.0
6 TraesCS1B01G241100 chr1D 88.000 175 16 4 6343 6515 102156649 102156478 1.110000e-47 202.0
7 TraesCS1B01G241100 chr1D 88.421 95 7 4 4965 5057 128529105 128529197 1.930000e-20 111.0
8 TraesCS1B01G241100 chr1A 93.125 1789 81 10 3025 4778 397739986 397738205 0.000000e+00 2584.0
9 TraesCS1B01G241100 chr1A 94.934 1658 62 9 4880 6523 397738033 397736384 0.000000e+00 2577.0
10 TraesCS1B01G241100 chr1A 92.639 1277 81 5 1769 3034 397742702 397741428 0.000000e+00 1825.0
11 TraesCS1B01G241100 chr1A 93.511 1048 32 13 673 1692 397743744 397742705 0.000000e+00 1526.0
12 TraesCS1B01G241100 chr1A 80.876 251 29 9 2627 2876 535892373 535892605 5.210000e-41 180.0
13 TraesCS1B01G241100 chr1A 93.000 100 5 1 4777 4874 397738177 397738078 1.900000e-30 145.0
14 TraesCS1B01G241100 chr2B 98.812 589 6 1 1 588 776654619 776655207 0.000000e+00 1048.0
15 TraesCS1B01G241100 chr2B 98.299 588 9 1 1 588 359639639 359639053 0.000000e+00 1029.0
16 TraesCS1B01G241100 chr2B 92.308 91 7 0 4965 5055 528474081 528474171 5.320000e-26 130.0
17 TraesCS1B01G241100 chr2B 95.556 45 1 1 4215 4258 113263465 113263421 3.270000e-08 71.3
18 TraesCS1B01G241100 chr4A 98.157 597 11 0 1 597 559058222 559057626 0.000000e+00 1042.0
19 TraesCS1B01G241100 chr7A 97.815 595 13 0 1 595 494198104 494198698 0.000000e+00 1027.0
20 TraesCS1B01G241100 chr7A 94.483 435 19 4 1 433 678606240 678606671 0.000000e+00 665.0
21 TraesCS1B01G241100 chr7A 93.893 393 19 5 1 390 238254059 238253669 7.310000e-164 588.0
22 TraesCS1B01G241100 chr7A 88.827 179 16 4 6343 6519 189710975 189710799 3.970000e-52 217.0
23 TraesCS1B01G241100 chr7A 86.316 190 20 6 6332 6519 222779296 222779481 1.110000e-47 202.0
24 TraesCS1B01G241100 chr2A 97.635 592 6 2 1 590 554516715 554517300 0.000000e+00 1009.0
25 TraesCS1B01G241100 chr2A 87.500 104 11 2 4967 5070 168984236 168984135 1.150000e-22 119.0
26 TraesCS1B01G241100 chr3B 98.381 556 8 1 1 555 520469414 520469969 0.000000e+00 976.0
27 TraesCS1B01G241100 chr3B 87.500 104 10 3 494 596 744558753 744558854 4.150000e-22 117.0
28 TraesCS1B01G241100 chr3A 93.103 435 21 5 1 433 750212479 750212906 4.310000e-176 628.0
29 TraesCS1B01G241100 chr7D 91.061 179 12 4 6338 6514 197873086 197873262 8.480000e-59 239.0
30 TraesCS1B01G241100 chr5A 90.000 180 13 5 6338 6514 546802843 546802666 1.840000e-55 228.0
31 TraesCS1B01G241100 chr5A 90.000 50 5 0 4212 4261 558163579 558163628 1.520000e-06 65.8
32 TraesCS1B01G241100 chr5B 88.587 184 18 3 6338 6519 586912595 586912777 3.070000e-53 220.0
33 TraesCS1B01G241100 chr5B 86.916 107 10 4 494 598 304281129 304281233 4.150000e-22 117.0
34 TraesCS1B01G241100 chr3D 88.587 184 16 5 6338 6520 64836236 64836057 1.100000e-52 219.0
35 TraesCS1B01G241100 chr2D 88.571 175 16 4 6343 6515 30004793 30004965 6.650000e-50 209.0
36 TraesCS1B01G241100 chr2D 97.727 44 1 0 4215 4258 74129607 74129564 7.040000e-10 76.8
37 TraesCS1B01G241100 chr7B 90.816 98 9 0 4965 5062 36432574 36432671 1.480000e-26 132.0
38 TraesCS1B01G241100 chr7B 92.391 92 7 0 4979 5070 611724059 611723968 1.480000e-26 132.0
39 TraesCS1B01G241100 chr6A 87.778 90 11 0 4965 5054 506643236 506643325 8.970000e-19 106.0
40 TraesCS1B01G241100 chr6A 95.918 49 2 0 4212 4260 25634532 25634580 5.440000e-11 80.5
41 TraesCS1B01G241100 chr4B 84.404 109 14 2 4965 5070 469505202 469505094 3.230000e-18 104.0
42 TraesCS1B01G241100 chr6D 95.122 41 2 0 4220 4260 120648397 120648437 1.520000e-06 65.8
43 TraesCS1B01G241100 chr5D 90.000 50 5 0 4212 4261 441390797 441390846 1.520000e-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 TraesCS1B01G241100 chr1B 428720983 428727525 6542 True 12083.0 12083 100.0000 1 6543 1 chr1B.!!$R1 6542
1 TraesCS1B01G241100 chr1D 316617512 316623607 6095 True 4168.5 8028 95.7815 602 6429 2 chr1D.!!$R3 5827
2 TraesCS1B01G241100 chr1A 397736384 397743744 7360 True 1731.4 2584 93.4418 673 6523 5 chr1A.!!$R1 5850
3 TraesCS1B01G241100 chr2B 776654619 776655207 588 False 1048.0 1048 98.8120 1 588 1 chr2B.!!$F2 587
4 TraesCS1B01G241100 chr2B 359639053 359639639 586 True 1029.0 1029 98.2990 1 588 1 chr2B.!!$R2 587
5 TraesCS1B01G241100 chr4A 559057626 559058222 596 True 1042.0 1042 98.1570 1 597 1 chr4A.!!$R1 596
6 TraesCS1B01G241100 chr7A 494198104 494198698 594 False 1027.0 1027 97.8150 1 595 1 chr7A.!!$F2 594
7 TraesCS1B01G241100 chr2A 554516715 554517300 585 False 1009.0 1009 97.6350 1 590 1 chr2A.!!$F1 589
8 TraesCS1B01G241100 chr3B 520469414 520469969 555 False 976.0 976 98.3810 1 555 1 chr3B.!!$F1 554

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
801 806 0.608640 TCCCACGCTCTTTCTCCTTC 59.391 55.000 0.00 0.0 0.00 3.46 F
802 807 0.610687 CCCACGCTCTTTCTCCTTCT 59.389 55.000 0.00 0.0 0.00 2.85 F
955 1223 1.208293 GACCTAGTGCTTGCTAAGGCT 59.792 52.381 7.86 0.0 39.59 4.58 F
2487 2807 0.813184 AGATTGTGAATGCTTGGGCG 59.187 50.000 0.00 0.0 42.25 6.13 F
2502 2822 0.814457 GGGCGTTGTTCCATAATGCA 59.186 50.000 0.00 0.0 40.83 3.96 F
2503 2823 1.469079 GGGCGTTGTTCCATAATGCAC 60.469 52.381 0.00 0.0 40.83 4.57 F
2673 2994 1.473258 TGCCACTGCTTTTGTGTCTT 58.527 45.000 0.00 0.0 38.71 3.01 F
2675 2996 2.233431 TGCCACTGCTTTTGTGTCTTTT 59.767 40.909 0.00 0.0 38.71 2.27 F
4868 6727 2.879026 GGACAGTTGACCTGAGAAAACC 59.121 50.000 0.00 0.0 44.49 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2167 0.858961 GCAGCAAGCAAGTATTCGCG 60.859 55.000 0.00 0.00 44.79 5.87 R
2487 2807 2.825532 AGGTGGTGCATTATGGAACAAC 59.174 45.455 11.91 11.91 43.97 3.32 R
2608 2928 3.501062 GGTTAGGTAAACTGTTGACCAGC 59.499 47.826 25.42 13.62 45.68 4.85 R
4298 6119 2.371841 AGTGCTCTTGGACCACAATACA 59.628 45.455 0.00 0.00 38.65 2.29 R
4611 6439 9.507280 AGAGCATTTCATTTTATTGTTCATACG 57.493 29.630 0.00 0.00 0.00 3.06 R
4720 6548 4.641989 ACAGGAGGTTCATCAATGTAATGC 59.358 41.667 0.00 0.00 0.00 3.56 R
4868 6727 1.151668 GCACAAGTCCTGCTGTACTG 58.848 55.000 0.00 0.00 0.00 2.74 R
4874 6733 3.689347 TGAATTATGCACAAGTCCTGCT 58.311 40.909 2.31 0.00 35.53 4.24 R
6315 8227 0.038599 TCCACGCCCTGTCTACTACA 59.961 55.000 0.00 0.00 36.42 2.74 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
219 223 2.225727 GGTTTTCCTTAGCAGACAACCG 59.774 50.000 0.00 0.00 36.94 4.44
314 318 2.039787 TGGGGTGGAGGCGTGATA 59.960 61.111 0.00 0.00 0.00 2.15
799 804 1.280457 AATCCCACGCTCTTTCTCCT 58.720 50.000 0.00 0.00 0.00 3.69
801 806 0.608640 TCCCACGCTCTTTCTCCTTC 59.391 55.000 0.00 0.00 0.00 3.46
802 807 0.610687 CCCACGCTCTTTCTCCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
804 809 1.548269 CCACGCTCTTTCTCCTTCTCT 59.452 52.381 0.00 0.00 0.00 3.10
867 1127 4.065281 CCCACGACCGACCAGTCC 62.065 72.222 0.00 0.00 32.91 3.85
883 1143 2.519302 CCACCGCCATCAATCCCC 60.519 66.667 0.00 0.00 0.00 4.81
955 1223 1.208293 GACCTAGTGCTTGCTAAGGCT 59.792 52.381 7.86 0.00 39.59 4.58
1496 1772 8.753175 CGAGGTAGCAATTGTAAACTAGTATTC 58.247 37.037 7.40 0.00 0.00 1.75
1530 1809 2.442087 GGGTAGCCCAATGTGCCC 60.442 66.667 0.00 0.00 44.65 5.36
1554 1833 1.457823 CCTGTTGCCTGCTTGCTTGA 61.458 55.000 0.00 0.00 0.00 3.02
1556 1835 1.814394 CTGTTGCCTGCTTGCTTGATA 59.186 47.619 0.00 0.00 0.00 2.15
1557 1836 1.541147 TGTTGCCTGCTTGCTTGATAC 59.459 47.619 0.00 0.00 0.00 2.24
1560 1839 2.449464 TGCCTGCTTGCTTGATACATT 58.551 42.857 0.00 0.00 0.00 2.71
1574 1857 7.147863 TGCTTGATACATTTGCAATGGTAGAAT 60.148 33.333 0.00 0.00 0.00 2.40
1588 1871 2.609459 GGTAGAATTGGATGCTGTGACG 59.391 50.000 0.00 0.00 0.00 4.35
1607 1890 1.927174 CGGTGACAGCTTGTAGTATGC 59.073 52.381 2.72 0.00 0.00 3.14
1610 1893 2.854777 GTGACAGCTTGTAGTATGCGAG 59.145 50.000 0.00 0.00 35.03 5.03
1611 1894 2.752903 TGACAGCTTGTAGTATGCGAGA 59.247 45.455 0.00 0.00 33.54 4.04
1721 2010 4.903054 AGAATGAGAGCATGTCTTGTTGA 58.097 39.130 0.00 0.00 34.71 3.18
1730 2019 3.265791 CATGTCTTGTTGAGTCCTAGCC 58.734 50.000 0.00 0.00 0.00 3.93
1900 2190 2.353889 CGAATACTTGCTTGCTGCTGAT 59.646 45.455 0.00 0.00 43.37 2.90
1934 2224 2.658285 TGCATGTGGATCATTCCTTCC 58.342 47.619 0.00 0.00 43.07 3.46
1944 2234 2.524306 TCATTCCTTCCGGTGCAAATT 58.476 42.857 0.00 0.00 0.00 1.82
1945 2235 2.896685 TCATTCCTTCCGGTGCAAATTT 59.103 40.909 0.00 0.00 0.00 1.82
1993 2284 3.120234 CGTCACGGGGTTAAAATTGGTAC 60.120 47.826 0.00 0.00 0.00 3.34
2107 2399 8.616076 CATCTTCCAGTAAGCGAAAATAAGATT 58.384 33.333 0.00 0.00 34.97 2.40
2145 2437 4.957296 ACACGTTTTCCTGTATCTCACTT 58.043 39.130 0.00 0.00 0.00 3.16
2154 2446 6.716934 TCCTGTATCTCACTTTATCTCCAC 57.283 41.667 0.00 0.00 0.00 4.02
2175 2467 2.595463 GTTCTGTGCCAGCAGCCA 60.595 61.111 0.00 0.00 42.71 4.75
2177 2469 1.228644 TTCTGTGCCAGCAGCCATT 60.229 52.632 0.00 0.00 42.71 3.16
2240 2532 4.272748 ACGTTGTACAGCTCTTCCTTTTTC 59.727 41.667 8.15 0.00 0.00 2.29
2288 2580 4.732784 TGTGCTTTTCTTTTCTGTGTCAC 58.267 39.130 0.00 0.00 0.00 3.67
2354 2646 7.962373 TCTTCTAATACAAAATGACGCATGTTG 59.038 33.333 16.38 16.38 42.80 3.33
2421 2722 8.274939 CGGAACTAATGTTTAGTGTTCGTTTTA 58.725 33.333 0.94 0.00 38.20 1.52
2487 2807 0.813184 AGATTGTGAATGCTTGGGCG 59.187 50.000 0.00 0.00 42.25 6.13
2502 2822 0.814457 GGGCGTTGTTCCATAATGCA 59.186 50.000 0.00 0.00 40.83 3.96
2503 2823 1.469079 GGGCGTTGTTCCATAATGCAC 60.469 52.381 0.00 0.00 40.83 4.57
2523 2843 5.189736 TGCACCACCTGTCTATATTCTCTTT 59.810 40.000 0.00 0.00 0.00 2.52
2608 2928 9.807649 AGTATTTGTACGTATAAGGTTAACAGG 57.192 33.333 8.10 0.00 0.00 4.00
2611 2931 5.653507 TGTACGTATAAGGTTAACAGGCTG 58.346 41.667 14.16 14.16 0.00 4.85
2673 2994 1.473258 TGCCACTGCTTTTGTGTCTT 58.527 45.000 0.00 0.00 38.71 3.01
2675 2996 2.233431 TGCCACTGCTTTTGTGTCTTTT 59.767 40.909 0.00 0.00 38.71 2.27
3020 3341 5.899120 ACTGTATCGAGTCTCTTGCTTTA 57.101 39.130 0.00 0.00 0.00 1.85
3175 4947 4.848562 TCAGCGAGAGTCTAAAACTTCA 57.151 40.909 0.00 0.00 38.74 3.02
3417 5190 4.439057 TCGTGGTGACCTTTCAATATAGC 58.561 43.478 2.11 0.00 31.90 2.97
3446 5219 8.296713 TGCCATTCTTGAACTGTTAGTTTAATC 58.703 33.333 0.00 0.00 38.80 1.75
3450 5223 7.647907 TCTTGAACTGTTAGTTTAATCGACC 57.352 36.000 0.00 0.00 38.80 4.79
3452 5225 7.597743 TCTTGAACTGTTAGTTTAATCGACCTC 59.402 37.037 0.00 0.00 38.80 3.85
3487 5260 2.906389 ACTGTAGGCAGATTCACTTCCA 59.094 45.455 1.30 0.00 45.28 3.53
3492 5279 6.662755 TGTAGGCAGATTCACTTCCATTTAT 58.337 36.000 0.00 0.00 34.40 1.40
3493 5280 7.801104 TGTAGGCAGATTCACTTCCATTTATA 58.199 34.615 0.00 0.00 34.40 0.98
3494 5281 7.715249 TGTAGGCAGATTCACTTCCATTTATAC 59.285 37.037 0.00 0.00 34.40 1.47
3495 5282 6.662755 AGGCAGATTCACTTCCATTTATACA 58.337 36.000 0.00 0.00 34.40 2.29
3496 5283 7.118723 AGGCAGATTCACTTCCATTTATACAA 58.881 34.615 0.00 0.00 34.40 2.41
3497 5284 7.615365 AGGCAGATTCACTTCCATTTATACAAA 59.385 33.333 0.00 0.00 34.40 2.83
3498 5285 8.250332 GGCAGATTCACTTCCATTTATACAAAA 58.750 33.333 0.00 0.00 32.27 2.44
3499 5286 9.638239 GCAGATTCACTTCCATTTATACAAAAA 57.362 29.630 0.00 0.00 0.00 1.94
3580 5371 9.976511 TGTTGAATATAGTTACTGTAGGCATAC 57.023 33.333 0.53 0.53 0.00 2.39
3597 5388 6.062095 AGGCATACTCACTTTTGTTTGTACT 58.938 36.000 0.00 0.00 0.00 2.73
3638 5429 4.648762 TGTGGTCAGGATTTGTTGAAACAT 59.351 37.500 0.00 0.00 38.95 2.71
3639 5430 5.830457 TGTGGTCAGGATTTGTTGAAACATA 59.170 36.000 0.00 0.00 38.95 2.29
3640 5431 6.149633 GTGGTCAGGATTTGTTGAAACATAC 58.850 40.000 0.00 0.00 38.95 2.39
3641 5432 5.830457 TGGTCAGGATTTGTTGAAACATACA 59.170 36.000 0.00 0.00 38.95 2.29
3642 5433 6.016360 TGGTCAGGATTTGTTGAAACATACAG 60.016 38.462 0.00 0.00 38.95 2.74
3776 5570 7.201705 GCTCTTTCCTGGTTGGTGTATAATAAC 60.202 40.741 0.00 0.00 37.07 1.89
3781 5575 6.050432 CCTGGTTGGTGTATAATAACGCTTA 58.950 40.000 0.00 0.00 0.00 3.09
3881 5675 4.202253 TGCATTGCTAGTGACCTGGTATAG 60.202 45.833 10.49 4.14 0.00 1.31
3894 5688 9.498176 GTGACCTGGTATAGTTTTCTTTTCTTA 57.502 33.333 0.00 0.00 0.00 2.10
4051 5845 9.896645 AAGATCAAGATGTTGTATCTGTAATGT 57.103 29.630 14.09 1.36 33.99 2.71
4103 5897 7.092079 TGATGAATTTGGATTGTTAACTGCAG 58.908 34.615 13.48 13.48 0.00 4.41
4111 5905 3.435105 TTGTTAACTGCAGTGGCTTTG 57.565 42.857 22.49 0.00 41.91 2.77
4128 5922 6.319658 GTGGCTTTGCATATGTATATGGCTAT 59.680 38.462 12.42 0.00 40.31 2.97
4216 6010 9.632638 ATCTATTTTACTACTACCTCCGTACAA 57.367 33.333 0.00 0.00 0.00 2.41
4226 6047 4.081322 ACCTCCGTACAATTTGAACTGT 57.919 40.909 2.79 0.00 0.00 3.55
4611 6439 4.067896 CCAGATGCCTATAATGACCACAC 58.932 47.826 0.00 0.00 0.00 3.82
4720 6548 7.448161 TGGTTTCATTAGTGCATATATTCAGGG 59.552 37.037 0.00 0.00 0.00 4.45
4722 6550 6.125589 TCATTAGTGCATATATTCAGGGCA 57.874 37.500 0.00 0.00 0.00 5.36
4737 6565 3.953612 TCAGGGCATTACATTGATGAACC 59.046 43.478 0.00 0.00 0.00 3.62
4752 6580 3.616956 TGAACCTCCTGTCATTAGCTG 57.383 47.619 0.00 0.00 0.00 4.24
4831 6688 9.856162 TCACCCTAAAGTCTAAAACAGTTTATT 57.144 29.630 0.00 0.00 0.00 1.40
4868 6727 2.879026 GGACAGTTGACCTGAGAAAACC 59.121 50.000 0.00 0.00 44.49 3.27
4874 6733 4.163458 AGTTGACCTGAGAAAACCAGTACA 59.837 41.667 0.00 0.00 0.00 2.90
4875 6734 4.336889 TGACCTGAGAAAACCAGTACAG 57.663 45.455 0.00 0.00 0.00 2.74
4876 6735 3.067833 GACCTGAGAAAACCAGTACAGC 58.932 50.000 0.00 0.00 0.00 4.40
4889 6787 1.349026 AGTACAGCAGGACTTGTGCAT 59.651 47.619 0.00 0.00 43.82 3.96
4921 6819 7.832503 TCGATAACAATGGATATAGCATGTG 57.167 36.000 0.00 0.00 0.00 3.21
4939 6837 6.423604 AGCATGTGTTTTAATGTTTGTAAGGC 59.576 34.615 0.00 0.00 0.00 4.35
4973 6873 3.163467 AGTGTGTTCTGGTACTACCTCC 58.837 50.000 6.79 0.00 39.58 4.30
4991 6891 3.056107 CCTCCGTCTGGAATTAGTTGACA 60.056 47.826 0.00 0.00 45.87 3.58
5013 6913 5.575606 ACACTCAAACGGATGTATCTAAACG 59.424 40.000 0.00 0.00 0.00 3.60
5034 6934 8.718102 AAACGTATTTCAGTGCTAGATACATT 57.282 30.769 0.00 0.00 0.00 2.71
5116 7018 2.521126 TCACAGTCGTCCAGATAACCA 58.479 47.619 0.00 0.00 0.00 3.67
5157 7059 5.636965 CGAAAGAGCACTTCCATATATGAGG 59.363 44.000 14.54 6.21 35.05 3.86
5161 7063 5.424895 AGAGCACTTCCATATATGAGGATCC 59.575 44.000 14.54 2.48 33.10 3.36
5163 7065 5.549228 AGCACTTCCATATATGAGGATCCAA 59.451 40.000 15.82 1.39 33.10 3.53
5178 7081 9.887862 ATGAGGATCCAATATCCATTTAACTTT 57.112 29.630 15.82 0.00 40.61 2.66
5180 7083 7.955918 AGGATCCAATATCCATTTAACTTTGC 58.044 34.615 15.82 0.00 40.61 3.68
5379 7282 6.128200 TGTTGATCCATCAGTCTTTGAAATCG 60.128 38.462 0.00 0.00 39.77 3.34
5381 7284 5.352293 TGATCCATCAGTCTTTGAAATCGTG 59.648 40.000 0.00 0.00 39.77 4.35
5393 7296 4.661993 TGAAATCGTGTGTGTTAGATGC 57.338 40.909 0.00 0.00 0.00 3.91
5635 7538 3.457749 TGTGTTACATGGCATCCATCCTA 59.542 43.478 0.00 0.00 43.15 2.94
5793 7704 3.315191 TGTGAGCCTTTTAAACACTGCTC 59.685 43.478 15.35 15.35 44.11 4.26
5831 7742 2.029623 GTCTATCTACTTGGTCGCCCA 58.970 52.381 0.00 0.00 39.65 5.36
5867 7778 6.256975 TCATGTCGAAGTTAATTTGGATACCG 59.743 38.462 0.00 0.00 0.00 4.02
5919 7830 4.133856 AGCAGAAATCGAAGTTTTGTCG 57.866 40.909 0.00 0.00 39.88 4.35
6046 7958 2.483889 GGGATTAAGGCCTCACTTCGAG 60.484 54.545 5.23 0.00 41.89 4.04
6130 8042 5.539955 AGCAGACAAAATTTACACCCAATCT 59.460 36.000 0.00 0.00 0.00 2.40
6159 8071 1.545841 CCAAGGGGAAACTAGCCAAC 58.454 55.000 0.00 0.00 35.59 3.77
6217 8129 6.935167 TCTGCTCACTTTATACTCAACATCA 58.065 36.000 0.00 0.00 0.00 3.07
6273 8185 7.123098 TCAACATCTTCATGACCAAAGCATAAT 59.877 33.333 0.00 0.00 33.72 1.28
6315 8227 2.899256 AGCATAATTGGCCACAAAGTGT 59.101 40.909 3.88 0.00 40.55 3.55
6326 8238 3.741344 GCCACAAAGTGTGTAGTAGACAG 59.259 47.826 0.00 0.00 46.45 3.51
6328 8240 4.307432 CACAAAGTGTGTAGTAGACAGGG 58.693 47.826 0.00 0.00 43.08 4.45
6331 8243 0.886563 GTGTGTAGTAGACAGGGCGT 59.113 55.000 0.00 0.00 39.29 5.68
6332 8244 0.885879 TGTGTAGTAGACAGGGCGTG 59.114 55.000 5.50 5.50 39.29 5.34
6333 8245 0.172803 GTGTAGTAGACAGGGCGTGG 59.827 60.000 12.33 0.00 39.29 4.94
6334 8246 0.038599 TGTAGTAGACAGGGCGTGGA 59.961 55.000 12.33 0.00 32.86 4.02
6335 8247 0.739561 GTAGTAGACAGGGCGTGGAG 59.260 60.000 12.33 0.00 0.00 3.86
6336 8248 0.330604 TAGTAGACAGGGCGTGGAGT 59.669 55.000 12.33 2.35 0.00 3.85
6367 8279 5.204292 TCTACACCTGAGCTCATATGTCTT 58.796 41.667 27.40 12.73 0.00 3.01
6465 8380 7.493743 AGAAATATTTGTTGTGCATGCAAAA 57.506 28.000 24.58 21.90 36.00 2.44
6518 8433 6.201997 GGCGTGGTAAAGAAAACAAAATTGAT 59.798 34.615 0.00 0.00 0.00 2.57
6534 8449 9.429359 ACAAAATTGATGTTACTTTCAAACACA 57.571 25.926 0.00 0.00 39.51 3.72
6540 8455 8.417780 TGATGTTACTTTCAAACACATTTTGG 57.582 30.769 0.00 0.00 39.51 3.28
6541 8456 7.493971 TGATGTTACTTTCAAACACATTTTGGG 59.506 33.333 0.00 0.00 39.51 4.12
6542 8457 6.109359 TGTTACTTTCAAACACATTTTGGGG 58.891 36.000 0.00 0.00 32.07 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 223 6.967135 AGATCTTCTTTTACCCACGAAAAAC 58.033 36.000 0.00 0.00 0.00 2.43
764 769 1.215655 GATTTGGATCGGACGGCTCG 61.216 60.000 0.00 0.00 0.00 5.03
799 804 0.981277 GGGACGGGAATGGGAGAGAA 60.981 60.000 0.00 0.00 0.00 2.87
801 806 3.231298 GGGACGGGAATGGGAGAG 58.769 66.667 0.00 0.00 0.00 3.20
855 1115 4.736896 GCGGTGGACTGGTCGGTC 62.737 72.222 1.48 1.48 35.66 4.79
867 1127 1.526917 GAGGGGATTGATGGCGGTG 60.527 63.158 0.00 0.00 0.00 4.94
883 1143 1.768077 GGGGAGGTGGAGATGGGAG 60.768 68.421 0.00 0.00 0.00 4.30
1496 1772 5.477637 GGCTACCCCTTATACAGAAGTAGAG 59.522 48.000 0.00 0.00 33.09 2.43
1514 1790 0.687427 AATGGGCACATTGGGCTACC 60.687 55.000 14.84 5.01 45.27 3.18
1530 1809 1.938016 GCAAGCAGGCAACAGGAAATG 60.938 52.381 0.00 0.00 41.41 2.32
1554 1833 7.658525 TCCAATTCTACCATTGCAAATGTAT 57.341 32.000 1.71 0.00 33.42 2.29
1556 1835 5.999205 TCCAATTCTACCATTGCAAATGT 57.001 34.783 1.71 6.33 33.42 2.71
1557 1836 5.235616 GCATCCAATTCTACCATTGCAAATG 59.764 40.000 1.71 2.47 33.42 2.32
1560 1839 4.025360 AGCATCCAATTCTACCATTGCAA 58.975 39.130 0.00 0.00 33.42 4.08
1574 1857 0.602638 GTCACCGTCACAGCATCCAA 60.603 55.000 0.00 0.00 0.00 3.53
1588 1871 1.927174 CGCATACTACAAGCTGTCACC 59.073 52.381 0.00 0.00 0.00 4.02
1607 1890 3.594603 ACCATGAACAACTAGGTCTCG 57.405 47.619 0.00 0.00 34.06 4.04
1610 1893 3.502211 CCACAACCATGAACAACTAGGTC 59.498 47.826 0.00 0.00 0.00 3.85
1611 1894 3.117663 ACCACAACCATGAACAACTAGGT 60.118 43.478 0.00 0.00 0.00 3.08
1721 2010 1.063114 ACCAATCTACCGGCTAGGACT 60.063 52.381 0.00 0.00 45.00 3.85
1730 2019 3.188460 CACAAGGAAACACCAATCTACCG 59.812 47.826 0.00 0.00 42.04 4.02
1877 2167 0.858961 GCAGCAAGCAAGTATTCGCG 60.859 55.000 0.00 0.00 44.79 5.87
1900 2190 2.882137 CACATGCATCATGCCATGAGTA 59.118 45.455 21.66 5.60 44.80 2.59
2107 2399 6.671614 AAACGTGTCACTTTATCTTGAACA 57.328 33.333 0.65 0.00 0.00 3.18
2240 2532 3.258971 TCAAAACAAAACCAAGGCCTG 57.741 42.857 5.69 0.00 0.00 4.85
2395 2696 5.834239 ACGAACACTAAACATTAGTTCCG 57.166 39.130 0.15 6.97 36.84 4.30
2441 2742 9.468532 GCATCCATCTTAAATAGGAAACAAATC 57.531 33.333 0.00 0.00 33.17 2.17
2487 2807 2.825532 AGGTGGTGCATTATGGAACAAC 59.174 45.455 11.91 11.91 43.97 3.32
2552 2872 6.760770 GCTTAGCCATCTATTATCAGTCATCC 59.239 42.308 0.00 0.00 0.00 3.51
2608 2928 3.501062 GGTTAGGTAAACTGTTGACCAGC 59.499 47.826 25.42 13.62 45.68 4.85
2611 2931 5.618236 AGAAGGTTAGGTAAACTGTTGACC 58.382 41.667 17.89 17.89 38.23 4.02
2642 2963 7.546667 ACAAAAGCAGTGGCATAAAATATTCTG 59.453 33.333 0.00 0.00 44.61 3.02
2643 2964 7.546667 CACAAAAGCAGTGGCATAAAATATTCT 59.453 33.333 0.00 0.00 44.61 2.40
2651 2972 3.641437 GACACAAAAGCAGTGGCATAA 57.359 42.857 0.00 0.00 44.47 1.90
3005 3326 7.284351 CAAAAAGTAGTAAAGCAAGAGACTCG 58.716 38.462 0.00 0.00 0.00 4.18
3020 3341 4.952460 TGTCGCTCTAACCAAAAAGTAGT 58.048 39.130 0.00 0.00 0.00 2.73
3175 4947 8.960591 CATATACCTGAAACACCTTTGAAATCT 58.039 33.333 0.00 0.00 0.00 2.40
3417 5190 3.947910 AACAGTTCAAGAATGGCATGG 57.052 42.857 0.00 0.00 0.00 3.66
3450 5223 7.702772 CTGCCTACAGTAACTGTATAAACAGAG 59.297 40.741 12.23 0.00 45.88 3.35
3452 5225 7.757097 CTGCCTACAGTAACTGTATAAACAG 57.243 40.000 0.00 4.04 44.49 3.16
3575 5366 9.724839 TTTAAGTACAAACAAAAGTGAGTATGC 57.275 29.630 0.00 0.00 0.00 3.14
3638 5429 7.663905 ACAAGCAAAATAGAATGGTGTACTGTA 59.336 33.333 0.00 0.00 0.00 2.74
3639 5430 6.490040 ACAAGCAAAATAGAATGGTGTACTGT 59.510 34.615 0.00 0.00 0.00 3.55
3640 5431 6.913170 ACAAGCAAAATAGAATGGTGTACTG 58.087 36.000 0.00 0.00 0.00 2.74
3641 5432 7.014230 ACAACAAGCAAAATAGAATGGTGTACT 59.986 33.333 0.00 0.00 36.98 2.73
3642 5433 7.145323 ACAACAAGCAAAATAGAATGGTGTAC 58.855 34.615 0.00 0.00 36.98 2.90
3776 5570 6.532657 AGATTGAATGGCAAAAGAAATAAGCG 59.467 34.615 0.00 0.00 40.48 4.68
3781 5575 5.553123 TGCAGATTGAATGGCAAAAGAAAT 58.447 33.333 0.00 0.00 40.48 2.17
4048 5842 8.322091 AGGAAAGCTACTACAAGTCAAATACAT 58.678 33.333 0.00 0.00 0.00 2.29
4049 5843 7.602644 CAGGAAAGCTACTACAAGTCAAATACA 59.397 37.037 0.00 0.00 0.00 2.29
4050 5844 7.413109 GCAGGAAAGCTACTACAAGTCAAATAC 60.413 40.741 0.00 0.00 0.00 1.89
4051 5845 6.594159 GCAGGAAAGCTACTACAAGTCAAATA 59.406 38.462 0.00 0.00 0.00 1.40
4052 5846 5.412904 GCAGGAAAGCTACTACAAGTCAAAT 59.587 40.000 0.00 0.00 0.00 2.32
4103 5897 4.460382 AGCCATATACATATGCAAAGCCAC 59.540 41.667 1.58 0.00 38.99 5.01
4285 6106 7.120579 TGGACCACAATACATAATTTCACAGTC 59.879 37.037 0.00 0.00 0.00 3.51
4287 6108 7.389803 TGGACCACAATACATAATTTCACAG 57.610 36.000 0.00 0.00 0.00 3.66
4298 6119 2.371841 AGTGCTCTTGGACCACAATACA 59.628 45.455 0.00 0.00 38.65 2.29
4611 6439 9.507280 AGAGCATTTCATTTTATTGTTCATACG 57.493 29.630 0.00 0.00 0.00 3.06
4720 6548 4.641989 ACAGGAGGTTCATCAATGTAATGC 59.358 41.667 0.00 0.00 0.00 3.56
4722 6550 6.065976 TGACAGGAGGTTCATCAATGTAAT 57.934 37.500 0.00 0.00 0.00 1.89
4752 6580 2.041701 AGGATACATGGGCAAAATGGC 58.958 47.619 0.00 0.00 40.39 4.40
4784 6641 9.196552 GGGTGAGAAAATCAATTAAGAAAACAG 57.803 33.333 0.00 0.00 40.43 3.16
4868 6727 1.151668 GCACAAGTCCTGCTGTACTG 58.848 55.000 0.00 0.00 0.00 2.74
4874 6733 3.689347 TGAATTATGCACAAGTCCTGCT 58.311 40.909 2.31 0.00 35.53 4.24
4875 6734 4.644103 ATGAATTATGCACAAGTCCTGC 57.356 40.909 2.31 0.00 35.03 4.85
4876 6735 5.065090 TCGAATGAATTATGCACAAGTCCTG 59.935 40.000 2.31 0.00 0.00 3.86
4921 6819 5.061684 GGATGCGCCTTACAAACATTAAAAC 59.938 40.000 4.18 0.00 0.00 2.43
4939 6837 3.873361 AGAACACACTCATTATGGATGCG 59.127 43.478 0.00 0.00 35.64 4.73
4973 6873 4.556233 TGAGTGTCAACTAATTCCAGACG 58.444 43.478 0.00 0.00 36.52 4.18
4991 6891 5.717119 ACGTTTAGATACATCCGTTTGAGT 58.283 37.500 0.00 0.00 0.00 3.41
5013 6913 7.932120 ACGAATGTATCTAGCACTGAAATAC 57.068 36.000 0.00 0.00 0.00 1.89
5034 6934 3.430895 GGAATTAGTTGACGCTCAAACGA 59.569 43.478 0.00 0.00 38.22 3.85
5062 6962 2.856222 ACTTCAGAAAAGCACTCCCTG 58.144 47.619 0.00 0.00 0.00 4.45
5097 6997 2.029380 TGTGGTTATCTGGACGACTGTG 60.029 50.000 0.00 0.00 0.00 3.66
5098 6998 2.231478 CTGTGGTTATCTGGACGACTGT 59.769 50.000 0.00 0.00 0.00 3.55
5157 7059 8.632679 TCAGCAAAGTTAAATGGATATTGGATC 58.367 33.333 0.00 0.00 0.00 3.36
5161 7063 9.643693 AGTTTCAGCAAAGTTAAATGGATATTG 57.356 29.630 0.00 0.00 0.00 1.90
5379 7282 4.000325 TGGTGTATGCATCTAACACACAC 59.000 43.478 25.14 20.41 44.18 3.82
5381 7284 4.695455 ACTTGGTGTATGCATCTAACACAC 59.305 41.667 25.14 21.56 44.18 3.82
5555 7458 6.546403 TCAGACTGTCAGTATACTAATCCCAC 59.454 42.308 5.21 0.00 0.00 4.61
5635 7538 2.549754 CACAACGCTCCTCTCAAACATT 59.450 45.455 0.00 0.00 0.00 2.71
5793 7704 4.974103 AGACGATTCAGTTTTCAGAACG 57.026 40.909 0.00 0.00 0.00 3.95
5831 7742 2.916702 TCGACATGATAAGCCTGCAT 57.083 45.000 0.00 0.00 0.00 3.96
5867 7778 5.801947 CACATGTAGGAAAATAAACAGCAGC 59.198 40.000 0.00 0.00 0.00 5.25
5940 7851 2.626785 TGGTCATCTACAAAGGGTCCA 58.373 47.619 0.00 0.00 0.00 4.02
6046 7958 3.628017 AGCACACAAATTTTACACTCGC 58.372 40.909 0.00 0.00 0.00 5.03
6130 8042 2.286121 CCCCTTGGGCCCTGTCTA 60.286 66.667 25.70 0.00 35.35 2.59
6153 8065 0.184451 CTGCTCCCCATATGTTGGCT 59.816 55.000 1.24 0.00 44.97 4.75
6154 8066 1.458639 GCTGCTCCCCATATGTTGGC 61.459 60.000 1.24 1.62 44.97 4.52
6159 8071 1.538512 CAAATCGCTGCTCCCCATATG 59.461 52.381 0.00 0.00 0.00 1.78
6206 8118 8.668353 GCTGATTGTAATTCTTGATGTTGAGTA 58.332 33.333 0.00 0.00 0.00 2.59
6217 8129 7.831193 ACTTCTACCATGCTGATTGTAATTCTT 59.169 33.333 0.00 0.00 0.00 2.52
6273 8185 1.227586 TGCTTGTACGGCGGTTTGA 60.228 52.632 13.24 0.00 0.00 2.69
6315 8227 0.038599 TCCACGCCCTGTCTACTACA 59.961 55.000 0.00 0.00 36.42 2.74
6316 8228 0.739561 CTCCACGCCCTGTCTACTAC 59.260 60.000 0.00 0.00 0.00 2.73
6326 8238 1.228154 AAACTCCAACTCCACGCCC 60.228 57.895 0.00 0.00 0.00 6.13
6328 8240 2.067013 GTAGAAACTCCAACTCCACGC 58.933 52.381 0.00 0.00 0.00 5.34
6331 8243 3.071023 CAGGTGTAGAAACTCCAACTCCA 59.929 47.826 0.07 0.00 40.97 3.86
6332 8244 3.323979 TCAGGTGTAGAAACTCCAACTCC 59.676 47.826 0.07 0.00 40.97 3.85
6333 8245 4.561105 CTCAGGTGTAGAAACTCCAACTC 58.439 47.826 0.07 0.00 40.97 3.01
6334 8246 3.244249 GCTCAGGTGTAGAAACTCCAACT 60.244 47.826 0.07 0.00 40.97 3.16
6335 8247 3.067833 GCTCAGGTGTAGAAACTCCAAC 58.932 50.000 0.07 0.00 40.97 3.77
6336 8248 2.972713 AGCTCAGGTGTAGAAACTCCAA 59.027 45.455 0.07 0.00 40.97 3.53
6412 8327 7.444299 AGTATGCCACACAAAAATTCAGATTT 58.556 30.769 0.00 0.00 37.06 2.17
6413 8328 6.996509 AGTATGCCACACAAAAATTCAGATT 58.003 32.000 0.00 0.00 0.00 2.40
6414 8329 6.594788 AGTATGCCACACAAAAATTCAGAT 57.405 33.333 0.00 0.00 0.00 2.90
6415 8330 6.403866 AAGTATGCCACACAAAAATTCAGA 57.596 33.333 0.00 0.00 0.00 3.27
6416 8331 8.586570 TTAAAGTATGCCACACAAAAATTCAG 57.413 30.769 0.00 0.00 0.00 3.02
6426 8341 9.855021 ACAAATATTTCTTAAAGTATGCCACAC 57.145 29.630 0.00 0.00 0.00 3.82
6518 8433 6.109359 CCCCAAAATGTGTTTGAAAGTAACA 58.891 36.000 0.44 0.00 33.37 2.41


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

AutoCloner maintained by Alex Coulton.