Multiple sequence alignment - TraesCS4A01G342400

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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 TraesCS4A01G342400 chr4A 100.000 8449 0 0 1 8449 622228928 622220480 0.000000e+00 15603.0
1 TraesCS4A01G342400 chr5B 92.553 3008 158 25 6 2995 689952200 689949241 0.000000e+00 4253.0
2 TraesCS4A01G342400 chr5B 94.584 2622 100 22 5246 7849 689946730 689944133 0.000000e+00 4017.0
3 TraesCS4A01G342400 chr5B 98.036 2291 40 4 2966 5252 689949067 689946778 0.000000e+00 3976.0
4 TraesCS4A01G342400 chr5B 86.688 308 23 10 8153 8449 689943507 689943207 8.180000e-85 326.0
5 TraesCS4A01G342400 chr5D 87.534 3281 230 74 5246 8446 546700645 546703826 0.000000e+00 3627.0
6 TraesCS4A01G342400 chr5D 91.288 2663 160 32 2624 5252 546697973 546700597 0.000000e+00 3567.0
7 TraesCS4A01G342400 chr5D 91.709 2569 145 41 30 2551 546694586 546697133 0.000000e+00 3502.0
8 TraesCS4A01G342400 chr5D 86.747 83 11 0 4311 4393 459324797 459324715 9.030000e-15 93.5
9 TraesCS4A01G342400 chr6D 86.747 83 11 0 4311 4393 57248665 57248583 9.030000e-15 93.5
10 TraesCS4A01G342400 chr7D 85.542 83 11 1 4311 4393 553198502 553198421 1.510000e-12 86.1
11 TraesCS4A01G342400 chr7D 88.136 59 2 3 8385 8441 230377334 230377279 1.970000e-06 65.8
12 TraesCS4A01G342400 chr7A 86.765 68 7 2 8374 8441 242945855 242945790 3.270000e-09 75.0
13 TraesCS4A01G342400 chr7B 88.136 59 2 3 8385 8441 201258607 201258552 1.970000e-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 TraesCS4A01G342400 chr4A 622220480 622228928 8448 True 15603.000000 15603 100.00000 1 8449 1 chr4A.!!$R1 8448
1 TraesCS4A01G342400 chr5B 689943207 689952200 8993 True 3143.000000 4253 92.96525 6 8449 4 chr5B.!!$R1 8443
2 TraesCS4A01G342400 chr5D 546694586 546703826 9240 False 3565.333333 3627 90.17700 30 8446 3 chr5D.!!$F1 8416

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
918 932 0.037590 CCCAACGACATCCCTTTCCA 59.962 55.000 0.00 0.00 0.00 3.53 F
1660 1695 0.178903 TCTACCAGGGACAGCTTGGT 60.179 55.000 11.63 11.63 46.44 3.67 F
1736 1771 0.179282 GAGCAGCGTGTTTTCGTACG 60.179 55.000 9.53 9.53 42.79 3.67 F
1869 1904 1.203287 CAAGCTGAGGAGATCACGACA 59.797 52.381 0.00 0.00 33.22 4.35 F
1993 2028 1.271856 TGCTTATCGGTCTTGGTGGA 58.728 50.000 0.00 0.00 0.00 4.02 F
2089 2124 1.607767 GGAAACCATGCAAATGCCGTT 60.608 47.619 2.46 0.34 41.18 4.44 F
2176 2211 2.158449 GCTTGGTCTTGTGACTGATTCG 59.842 50.000 0.00 0.00 42.54 3.34 F
2402 2451 4.446371 AGAGCGCTTCTTATTGCATAAGT 58.554 39.130 13.26 0.00 42.21 2.24 F
4326 5379 4.045104 GTCAGTGCCATCTAACGTCATAG 58.955 47.826 0.00 0.00 0.00 2.23 F
4716 5774 3.137544 TGGGGCTTGTCTTCACTTTCTTA 59.862 43.478 0.00 0.00 0.00 2.10 F
5542 6684 1.131693 ACATTGATGCATGTGCGACAG 59.868 47.619 2.46 0.00 45.83 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2124 0.250553 CCAACTTAGGTCCAACGCCA 60.251 55.000 0.00 0.00 0.00 5.69 R
3511 4541 4.199432 TCAGAATGCTCAAGAGGAGTTC 57.801 45.455 0.00 3.24 45.88 3.01 R
3650 4680 7.042335 ACAGAACAACTAGCTTATGTACATCC 58.958 38.462 12.68 2.34 0.00 3.51 R
3670 4702 7.094377 GGAACAGCATAGTGGAATTAAACAGAA 60.094 37.037 0.00 0.00 0.00 3.02 R
3933 4986 6.413052 CAAGGATATCTTCCCATATCTGTGG 58.587 44.000 2.05 0.00 46.81 4.17 R
4297 5350 1.073025 GATGGCACTGACCACACCA 59.927 57.895 0.00 0.00 44.17 4.17 R
4326 5379 3.939066 AGGTTCAATACAGTAGGCACAC 58.061 45.455 0.00 0.00 0.00 3.82 R
4447 5502 3.073678 GGCCCACATTCAAACAAAATCC 58.926 45.455 0.00 0.00 0.00 3.01 R
5453 6595 2.028112 GTGAGACTCCAAGCACACCATA 60.028 50.000 0.00 0.00 0.00 2.74 R
6607 7753 2.095919 CCGTTTTGCCTGCAGTAGTTAC 60.096 50.000 13.81 4.35 0.00 2.50 R
7574 8740 0.764890 TGCTTTGCTACCTCCACACT 59.235 50.000 0.00 0.00 0.00 3.55 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
21 22 1.347707 ACCAGAGGCAATCTTTCGACA 59.652 47.619 0.00 0.00 35.47 4.35
25 26 3.686241 CAGAGGCAATCTTTCGACATTGA 59.314 43.478 12.87 0.00 35.47 2.57
140 141 7.946219 TGGATAAAGATCAATAAGGCATGTGAT 59.054 33.333 0.00 0.00 33.27 3.06
172 176 6.012658 ACAACAGTCATGCGATGTTTTTAT 57.987 33.333 7.13 0.00 35.04 1.40
234 238 8.117813 TCCTCACAATTGAAACTAAAATACCC 57.882 34.615 13.59 0.00 0.00 3.69
270 274 9.299963 CAATCATATGCAAATTCGAGGTAAAAA 57.700 29.630 0.00 0.00 0.00 1.94
434 438 2.004583 TGGCGAGTGAAGTTATTCCG 57.995 50.000 0.00 0.00 34.28 4.30
436 440 1.405121 GGCGAGTGAAGTTATTCCGGT 60.405 52.381 0.00 0.00 34.28 5.28
442 446 5.636543 CGAGTGAAGTTATTCCGGTTTTACT 59.363 40.000 0.00 0.00 34.28 2.24
443 447 6.400727 CGAGTGAAGTTATTCCGGTTTTACTG 60.401 42.308 0.00 0.00 34.28 2.74
444 448 5.704053 AGTGAAGTTATTCCGGTTTTACTGG 59.296 40.000 0.00 0.00 46.14 4.00
460 471 9.788960 GGTTTTACTGGAATTGTTTCATAGATC 57.211 33.333 0.00 0.00 33.23 2.75
461 472 9.788960 GTTTTACTGGAATTGTTTCATAGATCC 57.211 33.333 0.00 0.00 33.23 3.36
464 475 6.051717 ACTGGAATTGTTTCATAGATCCGAG 58.948 40.000 0.00 0.00 33.23 4.63
484 495 7.779073 TCCGAGTTACAACCCAAAAATTAAAA 58.221 30.769 0.00 0.00 0.00 1.52
486 497 7.707464 CCGAGTTACAACCCAAAAATTAAAACT 59.293 33.333 0.00 0.00 0.00 2.66
487 498 9.733219 CGAGTTACAACCCAAAAATTAAAACTA 57.267 29.630 0.00 0.00 0.00 2.24
629 641 8.872845 CCCAATTTTTGCAAGTTTTATAGCTAG 58.127 33.333 0.00 0.00 0.00 3.42
671 683 9.646522 AAGATGTGCCAGATAATATAAGGTTTT 57.353 29.630 0.00 0.00 0.00 2.43
684 696 5.880054 ATAAGGTTTTCAAGATGGTCACG 57.120 39.130 0.00 0.00 0.00 4.35
689 701 5.411669 AGGTTTTCAAGATGGTCACGTTATC 59.588 40.000 0.00 0.00 0.00 1.75
758 771 6.628919 AAGTTTAAACACACCATAGACACC 57.371 37.500 20.06 0.00 0.00 4.16
760 773 2.922740 AAACACACCATAGACACCGT 57.077 45.000 0.00 0.00 0.00 4.83
783 797 6.348458 CGTGTCCAGCTGATTGAAAATTTAGA 60.348 38.462 17.39 0.00 0.00 2.10
784 798 7.370383 GTGTCCAGCTGATTGAAAATTTAGAA 58.630 34.615 17.39 0.00 0.00 2.10
785 799 7.867403 GTGTCCAGCTGATTGAAAATTTAGAAA 59.133 33.333 17.39 0.00 0.00 2.52
786 800 8.420222 TGTCCAGCTGATTGAAAATTTAGAAAA 58.580 29.630 17.39 0.00 0.00 2.29
787 801 9.260002 GTCCAGCTGATTGAAAATTTAGAAAAA 57.740 29.630 17.39 0.00 0.00 1.94
788 802 9.260002 TCCAGCTGATTGAAAATTTAGAAAAAC 57.740 29.630 17.39 0.00 0.00 2.43
789 803 8.498358 CCAGCTGATTGAAAATTTAGAAAAACC 58.502 33.333 17.39 0.00 0.00 3.27
790 804 9.044150 CAGCTGATTGAAAATTTAGAAAAACCA 57.956 29.630 8.42 0.00 0.00 3.67
915 929 1.880646 CGAACCCAACGACATCCCTTT 60.881 52.381 0.00 0.00 0.00 3.11
917 931 0.037734 ACCCAACGACATCCCTTTCC 59.962 55.000 0.00 0.00 0.00 3.13
918 932 0.037590 CCCAACGACATCCCTTTCCA 59.962 55.000 0.00 0.00 0.00 3.53
919 933 1.340991 CCCAACGACATCCCTTTCCAT 60.341 52.381 0.00 0.00 0.00 3.41
1103 1117 1.230853 TCCCCTCCTCCTCCAGGTA 60.231 63.158 0.00 0.00 43.95 3.08
1504 1532 2.305009 CTTCCATTCCAGGCCATTCTC 58.695 52.381 5.01 0.00 0.00 2.87
1540 1568 1.257743 TCCTCCACAGGAACTTCTCG 58.742 55.000 0.00 0.00 46.84 4.04
1578 1606 3.697045 CACCATTTGCGGGTAAAATCCTA 59.303 43.478 0.00 0.00 36.72 2.94
1593 1621 3.953542 ATCCTAACCCATTTCACCCTC 57.046 47.619 0.00 0.00 0.00 4.30
1603 1633 2.799126 TTTCACCCTCCGCACATTAT 57.201 45.000 0.00 0.00 0.00 1.28
1644 1679 0.864377 CGCCGCTCGTTTCGATTCTA 60.864 55.000 0.00 0.00 34.61 2.10
1660 1695 0.178903 TCTACCAGGGACAGCTTGGT 60.179 55.000 11.63 11.63 46.44 3.67
1736 1771 0.179282 GAGCAGCGTGTTTTCGTACG 60.179 55.000 9.53 9.53 42.79 3.67
1841 1876 8.068380 CGATAGTTATTCTCAAGTACATCGACA 58.932 37.037 0.00 0.00 0.00 4.35
1851 1886 4.801330 AGTACATCGACATTCTGTCCAA 57.199 40.909 0.00 0.00 44.20 3.53
1864 1899 1.829849 CTGTCCAAGCTGAGGAGATCA 59.170 52.381 8.35 3.38 35.42 2.92
1868 1903 1.470632 CCAAGCTGAGGAGATCACGAC 60.471 57.143 0.00 0.00 33.22 4.34
1869 1904 1.203287 CAAGCTGAGGAGATCACGACA 59.797 52.381 0.00 0.00 33.22 4.35
1993 2028 1.271856 TGCTTATCGGTCTTGGTGGA 58.728 50.000 0.00 0.00 0.00 4.02
2026 2061 7.865530 TTATGGGGTTACTGATGATAGCTTA 57.134 36.000 0.00 0.00 0.00 3.09
2089 2124 1.607767 GGAAACCATGCAAATGCCGTT 60.608 47.619 2.46 0.34 41.18 4.44
2176 2211 2.158449 GCTTGGTCTTGTGACTGATTCG 59.842 50.000 0.00 0.00 42.54 3.34
2302 2337 5.600696 TCAAACCTTTGCTGATTTCTTTCC 58.399 37.500 0.00 0.00 38.05 3.13
2402 2451 4.446371 AGAGCGCTTCTTATTGCATAAGT 58.554 39.130 13.26 0.00 42.21 2.24
2409 2459 6.477033 CGCTTCTTATTGCATAAGTACACTCT 59.523 38.462 12.59 0.00 42.21 3.24
2425 2475 7.668492 AGTACACTCTTTTAACTACTTCCTGG 58.332 38.462 0.00 0.00 0.00 4.45
2605 3169 5.590663 GGAGACAGATGGGACCTTTAAAATC 59.409 44.000 0.00 0.00 0.00 2.17
2613 3177 5.701224 TGGGACCTTTAAAATCAAGAGTGT 58.299 37.500 0.00 0.00 0.00 3.55
2767 3590 5.127682 TCCAGACTAACCTATTTCCCGTTAC 59.872 44.000 0.00 0.00 0.00 2.50
2769 3592 4.706962 AGACTAACCTATTTCCCGTTACGT 59.293 41.667 3.52 0.00 0.00 3.57
2971 3997 9.846248 CTGACTTGAAAAAGGTAAGAAATATGG 57.154 33.333 0.00 0.00 0.00 2.74
3332 4361 4.810191 AGGACTAAGAGGTCACATTGTC 57.190 45.455 0.00 0.00 37.91 3.18
3572 4602 6.612247 ATTATTGCATTGTGGAATTGCATG 57.388 33.333 1.94 0.00 39.21 4.06
3650 4680 6.493116 AGCTTATGATCTTCGCTTGATTTTG 58.507 36.000 0.00 0.00 0.00 2.44
3666 4698 8.072567 GCTTGATTTTGGATGTACATAAGCTAG 58.927 37.037 20.67 15.34 35.29 3.42
3670 4702 8.807948 ATTTTGGATGTACATAAGCTAGTTGT 57.192 30.769 8.71 0.00 0.00 3.32
3846 4892 6.840705 ACATCATGCTGGTTATAATTCCCTTT 59.159 34.615 1.02 0.00 0.00 3.11
3861 4907 7.855784 AATTCCCTTTCTGGTTGAGTATTTT 57.144 32.000 0.00 0.00 0.00 1.82
4297 5350 7.575909 CGCTTATCAGTAGCTGTAATAGTCCAT 60.576 40.741 0.00 0.00 36.49 3.41
4326 5379 4.045104 GTCAGTGCCATCTAACGTCATAG 58.955 47.826 0.00 0.00 0.00 2.23
4536 5591 5.708736 TTCCTATGCACCTTCTGGAAATA 57.291 39.130 0.00 0.00 37.04 1.40
4557 5612 8.800370 AAATATTTCCCTCAGAGAAGTTCTTC 57.200 34.615 6.88 4.58 32.41 2.87
4716 5774 3.137544 TGGGGCTTGTCTTCACTTTCTTA 59.862 43.478 0.00 0.00 0.00 2.10
5142 6202 6.430308 CCTCTTCTGGAATATTCATGTGGATG 59.570 42.308 17.07 8.91 0.00 3.51
5279 6393 5.730568 GCTCCTTAAATATGTTGTCTTGCCG 60.731 44.000 0.00 0.00 0.00 5.69
5388 6503 5.144692 TCTTCTGCATGACTCCTATATGC 57.855 43.478 0.00 0.00 45.53 3.14
5542 6684 1.131693 ACATTGATGCATGTGCGACAG 59.868 47.619 2.46 0.00 45.83 3.51
5826 6968 7.909267 TCTTTCTATTAATGCATTGAGACACG 58.091 34.615 22.27 11.20 0.00 4.49
5941 7084 3.809279 GGGCCTTTTGTTTGTCTCAATTG 59.191 43.478 0.84 0.00 0.00 2.32
6283 7428 9.971922 CTTCCTATGAGTTTGATTTCTTGTTTT 57.028 29.630 0.00 0.00 0.00 2.43
6531 7677 7.770897 TGGTTATGTGCTATTTTTGTTTTTGGT 59.229 29.630 0.00 0.00 0.00 3.67
6532 7678 8.616942 GGTTATGTGCTATTTTTGTTTTTGGTT 58.383 29.630 0.00 0.00 0.00 3.67
6536 7682 9.777297 ATGTGCTATTTTTGTTTTTGGTTATCT 57.223 25.926 0.00 0.00 0.00 1.98
6835 7981 3.372795 CATGGCATTGGCAATGGTC 57.627 52.632 34.19 21.64 45.97 4.02
6862 8008 7.113965 GCAGAAGATCGCCAAATAAATTATGTG 59.886 37.037 0.00 0.00 0.00 3.21
6892 8038 3.338249 GCTCTTTGCTGAACAGGTATGA 58.662 45.455 3.99 0.00 38.95 2.15
6895 8041 5.448360 GCTCTTTGCTGAACAGGTATGATTC 60.448 44.000 3.99 0.00 38.95 2.52
6896 8042 5.809001 TCTTTGCTGAACAGGTATGATTCT 58.191 37.500 3.99 0.00 0.00 2.40
6943 8091 5.103290 TCAATGAACGTCAAGCTTTTACC 57.897 39.130 0.00 0.00 0.00 2.85
6944 8092 4.576873 TCAATGAACGTCAAGCTTTTACCA 59.423 37.500 0.00 0.00 0.00 3.25
6947 8095 4.130857 TGAACGTCAAGCTTTTACCATCA 58.869 39.130 0.00 2.02 0.00 3.07
6951 8099 4.943705 ACGTCAAGCTTTTACCATCATCAT 59.056 37.500 0.00 0.00 0.00 2.45
6954 8102 7.931407 ACGTCAAGCTTTTACCATCATCATATA 59.069 33.333 0.00 0.00 0.00 0.86
7019 8174 8.687242 CATATACCTGTCTTTGTAGAGTCTTGA 58.313 37.037 0.00 0.00 0.00 3.02
7091 8248 8.317679 CCTATAGATCATTACCTCCAGAAAAGG 58.682 40.741 0.00 0.00 39.96 3.11
7097 8254 5.951747 TCATTACCTCCAGAAAAGGGAATTG 59.048 40.000 0.00 0.00 43.67 2.32
7141 8298 4.000325 TGCCACTGTACACATACATGTTC 59.000 43.478 2.30 0.00 40.57 3.18
7145 8302 4.870426 CACTGTACACATACATGTTCTCCC 59.130 45.833 2.30 0.00 40.57 4.30
7147 8304 3.841255 TGTACACATACATGTTCTCCCCA 59.159 43.478 2.30 0.00 39.39 4.96
7152 8309 4.080582 CACATACATGTTCTCCCCAGGTTA 60.081 45.833 2.30 0.00 39.39 2.85
7155 8312 4.034285 ACATGTTCTCCCCAGGTTAAAG 57.966 45.455 0.00 0.00 0.00 1.85
7157 8314 4.292306 ACATGTTCTCCCCAGGTTAAAGAT 59.708 41.667 0.00 0.00 0.00 2.40
7160 8317 4.105697 TGTTCTCCCCAGGTTAAAGATGTT 59.894 41.667 0.00 0.00 0.00 2.71
7161 8318 4.301072 TCTCCCCAGGTTAAAGATGTTG 57.699 45.455 0.00 0.00 0.00 3.33
7186 8343 5.163343 ACAGTAAGCACTCTTGTCAGGTTTA 60.163 40.000 0.00 0.00 33.85 2.01
7187 8344 5.406780 CAGTAAGCACTCTTGTCAGGTTTAG 59.593 44.000 0.00 0.00 33.85 1.85
7189 8346 2.706190 AGCACTCTTGTCAGGTTTAGGT 59.294 45.455 0.00 0.00 0.00 3.08
7195 8352 5.780793 ACTCTTGTCAGGTTTAGGTATCAGT 59.219 40.000 0.00 0.00 0.00 3.41
7225 8387 7.281100 GCTAATACCTTGCATTTGTACTCTTCT 59.719 37.037 0.00 0.00 0.00 2.85
7427 8589 3.243737 GGTCACCCAAGGATGTTTTTGTC 60.244 47.826 0.00 0.00 0.00 3.18
7436 8598 4.770795 AGGATGTTTTTGTCGCTATAGCT 58.229 39.130 21.98 0.00 39.32 3.32
7529 8695 2.048503 ACAGTAACAGCGGACGGC 60.049 61.111 0.00 0.00 44.05 5.68
7574 8740 2.426522 CGAAAGATGAACAAGGGCTGA 58.573 47.619 0.00 0.00 0.00 4.26
7601 8767 3.118223 GGAGGTAGCAAAGCAGGAAGTAT 60.118 47.826 0.00 0.00 0.00 2.12
7610 8776 5.308825 CAAAGCAGGAAGTATATACTGGGG 58.691 45.833 16.11 7.72 36.50 4.96
7629 8795 4.590647 TGGGGCAAATCTAGAGTCTAGATG 59.409 45.833 33.48 26.44 34.75 2.90
7692 8858 2.507886 TCCTGTGTGAGAAACTTTGGGA 59.492 45.455 0.00 0.00 0.00 4.37
7704 8870 3.173953 ACTTTGGGAGCATCATTTCCA 57.826 42.857 0.00 0.00 36.25 3.53
7722 8888 0.322546 CACAGTCCCAGGTAAAGGCC 60.323 60.000 0.00 0.00 0.00 5.19
7784 8950 6.662234 GGAGTTTTTAGGGGCTGTAGTTTAAT 59.338 38.462 0.00 0.00 0.00 1.40
7785 8952 7.177921 GGAGTTTTTAGGGGCTGTAGTTTAATT 59.822 37.037 0.00 0.00 0.00 1.40
7836 9003 5.930405 GTTCGTTAAACGGACCAATTGTAT 58.070 37.500 4.43 0.00 44.03 2.29
7837 9004 7.059448 GTTCGTTAAACGGACCAATTGTATA 57.941 36.000 4.43 0.00 44.03 1.47
7895 9071 6.723298 TTGTCACAAATTAACAACTCCCAT 57.277 33.333 0.00 0.00 0.00 4.00
7933 9189 2.141517 CATGAATAGAGGAAGCTGCCG 58.858 52.381 4.63 0.00 0.00 5.69
7954 9222 4.513692 CCGTTACACAATGAAAAGGACAGA 59.486 41.667 0.00 0.00 0.00 3.41
8012 9344 8.526147 AGCAAGAGTTCAGTGCATTATTATTTT 58.474 29.630 9.53 0.00 40.83 1.82
8013 9345 9.143631 GCAAGAGTTCAGTGCATTATTATTTTT 57.856 29.630 0.00 0.00 38.19 1.94
8094 9428 8.423906 TCATAAAAAGTGGGGCAAAATAACTA 57.576 30.769 0.00 0.00 0.00 2.24
8102 9436 4.534103 TGGGGCAAAATAACTAAAAGGCAT 59.466 37.500 0.00 0.00 0.00 4.40
8111 9447 7.418337 AATAACTAAAAGGCATACCCCAAAG 57.582 36.000 0.00 0.00 36.11 2.77
8112 9448 3.708451 ACTAAAAGGCATACCCCAAAGG 58.292 45.455 0.00 0.00 43.78 3.11
8132 9468 9.429359 CCAAAGGACAGATCATCAACTATATAC 57.571 37.037 0.00 0.00 0.00 1.47
8138 9474 8.190326 ACAGATCATCAACTATATACGGGAAA 57.810 34.615 0.00 0.00 0.00 3.13
8142 9478 9.268268 GATCATCAACTATATACGGGAAAAACA 57.732 33.333 0.00 0.00 0.00 2.83
8144 9480 9.451002 TCATCAACTATATACGGGAAAAACAAA 57.549 29.630 0.00 0.00 0.00 2.83
8205 9699 4.033817 TGCCTCATTTTTGCGTTCTTTTTG 59.966 37.500 0.00 0.00 0.00 2.44
8266 9768 1.039856 GACAACCCATGTGTTTGCCT 58.960 50.000 0.00 0.00 44.12 4.75
8297 9801 4.341520 CGATGGTAGAGCTAACCTTAACCT 59.658 45.833 16.54 0.00 37.91 3.50
8309 9813 4.868314 ACCTTAACCTAGCCGATATCAC 57.132 45.455 3.12 0.00 0.00 3.06
8312 9816 2.821991 AACCTAGCCGATATCACTGC 57.178 50.000 3.12 2.28 0.00 4.40
8314 9818 2.251818 ACCTAGCCGATATCACTGCAT 58.748 47.619 3.12 0.00 0.00 3.96
8327 9831 8.127327 CGATATCACTGCATCTCTCAAAATTTT 58.873 33.333 3.12 0.00 0.00 1.82
8436 9942 9.159364 ACGATTAAGGAACTAATGACTTTTACC 57.841 33.333 0.00 0.00 38.49 2.85
8437 9943 8.325997 CGATTAAGGAACTAATGACTTTTACCG 58.674 37.037 0.00 0.00 38.49 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.224523 TGTCGAAAGATTGCCTCTGGTT 60.225 45.455 0.00 0.00 45.19 3.67
1 2 1.347707 TGTCGAAAGATTGCCTCTGGT 59.652 47.619 0.00 0.00 45.19 4.00
2 3 2.099141 TGTCGAAAGATTGCCTCTGG 57.901 50.000 0.00 0.00 45.19 3.86
3 4 3.686241 TCAATGTCGAAAGATTGCCTCTG 59.314 43.478 7.78 0.00 45.19 3.35
4 5 3.942829 TCAATGTCGAAAGATTGCCTCT 58.057 40.909 7.78 0.00 45.19 3.69
67 68 5.665459 TGTAAAATGTGTTTTGGTCCAAGG 58.335 37.500 4.09 0.00 38.01 3.61
99 100 6.842163 TCTTTATCCAAAAATTGCTCGAGAC 58.158 36.000 18.75 8.32 0.00 3.36
140 141 8.888716 ACATCGCATGACTGTTGTTATATTTTA 58.111 29.630 0.00 0.00 0.00 1.52
145 146 6.735678 AAACATCGCATGACTGTTGTTATA 57.264 33.333 0.00 0.00 33.60 0.98
146 147 5.627499 AAACATCGCATGACTGTTGTTAT 57.373 34.783 0.00 0.00 33.60 1.89
147 148 5.431420 AAAACATCGCATGACTGTTGTTA 57.569 34.783 0.00 0.00 33.60 2.41
148 149 3.988379 AAACATCGCATGACTGTTGTT 57.012 38.095 0.00 0.48 33.60 2.83
150 151 6.932901 AATAAAAACATCGCATGACTGTTG 57.067 33.333 0.00 0.00 33.60 3.33
151 152 8.677300 AGATAATAAAAACATCGCATGACTGTT 58.323 29.630 0.00 0.00 34.71 3.16
153 154 9.162793 GAAGATAATAAAAACATCGCATGACTG 57.837 33.333 0.00 0.00 0.00 3.51
172 176 7.981789 AGAAACGACATTGCATAGAGAAGATAA 59.018 33.333 0.00 0.00 0.00 1.75
232 236 9.991906 ATTTGCATATGATTGAGAAAAATAGGG 57.008 29.630 6.97 0.00 0.00 3.53
242 246 6.309712 ACCTCGAATTTGCATATGATTGAG 57.690 37.500 6.97 7.28 0.00 3.02
434 438 9.788960 GATCTATGAAACAATTCCAGTAAAACC 57.211 33.333 0.00 0.00 34.49 3.27
436 440 8.673711 CGGATCTATGAAACAATTCCAGTAAAA 58.326 33.333 0.00 0.00 34.49 1.52
442 446 5.989477 ACTCGGATCTATGAAACAATTCCA 58.011 37.500 0.00 0.00 34.49 3.53
443 447 6.927294 AACTCGGATCTATGAAACAATTCC 57.073 37.500 0.00 0.00 34.49 3.01
444 448 8.420374 TGTAACTCGGATCTATGAAACAATTC 57.580 34.615 0.00 0.00 36.04 2.17
460 471 7.707464 AGTTTTAATTTTTGGGTTGTAACTCGG 59.293 33.333 0.00 0.00 29.87 4.63
461 472 8.637281 AGTTTTAATTTTTGGGTTGTAACTCG 57.363 30.769 0.00 0.00 29.87 4.18
511 523 5.857268 AGCTAAATTTGGCATGTTGTTTCT 58.143 33.333 25.86 0.93 37.10 2.52
590 602 8.825667 TGCAAAAATTGGGTTCTATAGAAAAC 57.174 30.769 16.73 12.60 35.58 2.43
608 620 8.296713 CACTCCTAGCTATAAAACTTGCAAAAA 58.703 33.333 0.00 0.00 0.00 1.94
613 625 5.671493 TCCACTCCTAGCTATAAAACTTGC 58.329 41.667 0.00 0.00 0.00 4.01
629 641 4.874966 CACATCTTTTCATCTCTCCACTCC 59.125 45.833 0.00 0.00 0.00 3.85
665 677 3.208747 ACGTGACCATCTTGAAAACCT 57.791 42.857 0.00 0.00 0.00 3.50
671 683 9.878667 TTTATTTAGATAACGTGACCATCTTGA 57.121 29.630 7.32 0.14 31.60 3.02
733 746 7.041916 CGGTGTCTATGGTGTGTTTAAACTTTA 60.042 37.037 18.72 3.20 0.00 1.85
743 756 1.000506 GACACGGTGTCTATGGTGTGT 59.999 52.381 29.09 0.00 43.73 3.72
758 771 3.837213 ATTTTCAATCAGCTGGACACG 57.163 42.857 15.13 0.00 0.00 4.49
760 773 7.523293 TTCTAAATTTTCAATCAGCTGGACA 57.477 32.000 15.13 0.00 0.00 4.02
818 832 2.045536 GACTTGCAGGCCCAGAGG 60.046 66.667 0.00 0.00 0.00 3.69
942 956 9.768662 GAGGTAAGGGATGTCGTTATTTATTTA 57.231 33.333 0.00 0.00 0.00 1.40
946 960 5.737063 GCGAGGTAAGGGATGTCGTTATTTA 60.737 44.000 0.00 0.00 33.19 1.40
990 1004 0.035458 CCAGGGGCATTCTCGGTATC 59.965 60.000 0.00 0.00 0.00 2.24
1410 1430 3.509137 TTCACCGTGACTCACCGCC 62.509 63.158 0.00 0.00 0.00 6.13
1433 1453 2.764010 AGTCAACAAAAGTCAAACCCCC 59.236 45.455 0.00 0.00 0.00 5.40
1540 1568 4.314440 TGGACCTGGTCGTGCAGC 62.314 66.667 19.98 6.19 32.65 5.25
1578 1606 1.304134 GCGGAGGGTGAAATGGGTT 60.304 57.895 0.00 0.00 0.00 4.11
1644 1679 2.839098 CACCAAGCTGTCCCTGGT 59.161 61.111 0.95 0.95 0.00 4.00
1736 1771 1.190323 CACAAACTCGTCGTTGCTCTC 59.810 52.381 0.00 0.00 35.61 3.20
1820 1855 8.535592 CAGAATGTCGATGTACTTGAGAATAAC 58.464 37.037 0.00 0.00 0.00 1.89
1841 1876 2.544721 TCTCCTCAGCTTGGACAGAAT 58.455 47.619 1.29 0.00 0.00 2.40
1851 1886 0.814457 GTGTCGTGATCTCCTCAGCT 59.186 55.000 0.00 0.00 33.51 4.24
1868 1903 2.266554 GAAGGCGACATCTTCAGAGTG 58.733 52.381 0.00 0.00 40.08 3.51
1869 1904 1.895798 TGAAGGCGACATCTTCAGAGT 59.104 47.619 0.00 0.00 43.70 3.24
1936 1971 3.994931 AGAACCAAGGGTTTAGCGTAT 57.005 42.857 1.65 0.00 46.95 3.06
1993 2028 3.105283 AGTAACCCCATAAAGAGCGAGT 58.895 45.455 0.00 0.00 0.00 4.18
2026 2061 2.289072 CGATAACCAGAGGCAATCCGAT 60.289 50.000 0.00 0.00 37.47 4.18
2089 2124 0.250553 CCAACTTAGGTCCAACGCCA 60.251 55.000 0.00 0.00 0.00 5.69
2093 2128 4.204799 ACTGAAACCAACTTAGGTCCAAC 58.795 43.478 0.00 0.00 42.25 3.77
2098 2133 6.605594 TGATTGAAACTGAAACCAACTTAGGT 59.394 34.615 0.00 0.00 45.91 3.08
2176 2211 8.545229 TCAAAGAATCAAACTTCTCTGAGATC 57.455 34.615 8.42 0.49 34.40 2.75
2302 2337 7.647907 AGAAAAATAACAGAAAATGCTGCAG 57.352 32.000 10.11 10.11 39.51 4.41
2340 2375 6.021074 GCTATTCGCTATTGATATGACACTCG 60.021 42.308 0.00 0.00 35.14 4.18
2366 2401 3.599343 AGCGCTCTAACAATCATGTTCA 58.401 40.909 2.64 0.00 46.78 3.18
2402 2451 7.525029 GCTCCAGGAAGTAGTTAAAAGAGTGTA 60.525 40.741 0.00 0.00 0.00 2.90
2409 2459 6.182507 TGAAGCTCCAGGAAGTAGTTAAAA 57.817 37.500 0.00 0.00 0.00 1.52
2425 2475 2.751166 TGCCTCTACACTTGAAGCTC 57.249 50.000 0.00 0.00 0.00 4.09
2613 3177 9.494271 GTGAGAGGAAATATTACATCTGCATTA 57.506 33.333 0.00 0.00 0.00 1.90
2767 3590 5.753921 GGTTCAGTAAAGATCCCTATTGACG 59.246 44.000 0.00 0.00 0.00 4.35
2769 3592 6.884472 TGGTTCAGTAAAGATCCCTATTGA 57.116 37.500 0.00 0.00 0.00 2.57
2971 3997 8.988064 TCAAAGTATGTCTCTGAATCAGTAAC 57.012 34.615 10.36 9.92 32.61 2.50
3332 4361 4.237724 TGTCAAGATCACTAAGCTCAACG 58.762 43.478 0.00 0.00 0.00 4.10
3511 4541 4.199432 TCAGAATGCTCAAGAGGAGTTC 57.801 45.455 0.00 3.24 45.88 3.01
3572 4602 7.394077 AGACTTTGTACTAGAAAGGTCTCCTAC 59.606 40.741 9.79 0.00 35.15 3.18
3650 4680 7.042335 ACAGAACAACTAGCTTATGTACATCC 58.958 38.462 12.68 2.34 0.00 3.51
3666 4698 7.538678 CAGCATAGTGGAATTAAACAGAACAAC 59.461 37.037 0.00 0.00 0.00 3.32
3670 4702 7.094377 GGAACAGCATAGTGGAATTAAACAGAA 60.094 37.037 0.00 0.00 0.00 3.02
3933 4986 6.413052 CAAGGATATCTTCCCATATCTGTGG 58.587 44.000 2.05 0.00 46.81 4.17
4297 5350 1.073025 GATGGCACTGACCACACCA 59.927 57.895 0.00 0.00 44.17 4.17
4326 5379 3.939066 AGGTTCAATACAGTAGGCACAC 58.061 45.455 0.00 0.00 0.00 3.82
4447 5502 3.073678 GGCCCACATTCAAACAAAATCC 58.926 45.455 0.00 0.00 0.00 3.01
4513 5568 4.591321 TTTCCAGAAGGTGCATAGGAAT 57.409 40.909 0.00 0.00 35.32 3.01
4536 5591 7.401493 TGATAGAAGAACTTCTCTGAGGGAAAT 59.599 37.037 18.46 5.61 46.13 2.17
4619 5676 1.133482 ACTGAACACAAGGGGGAAAGG 60.133 52.381 0.00 0.00 0.00 3.11
5111 6171 5.280499 TGAATATTCCAGAAGAGGGTGAGA 58.720 41.667 12.90 0.00 0.00 3.27
5142 6202 4.644103 ATGCTCCAAATGACTGCATTAC 57.356 40.909 0.00 0.00 43.71 1.89
5222 6282 7.127339 AGACATAAGGAAGGTATAAAGCAGGAA 59.873 37.037 0.00 0.00 0.00 3.36
5279 6393 9.959749 TGTAAGAAACATTGGATTCAAAAGTAC 57.040 29.630 0.00 0.00 36.36 2.73
5388 6503 3.976793 ATGCCAAATTAGAGTGCATCG 57.023 42.857 0.00 0.00 38.17 3.84
5453 6595 2.028112 GTGAGACTCCAAGCACACCATA 60.028 50.000 0.00 0.00 0.00 2.74
5573 6715 7.736447 TTTTGTTCAACCAACACTTGAAAAT 57.264 28.000 0.00 0.00 45.12 1.82
5818 6960 2.820059 ATGCAGAAGTTCGTGTCTCA 57.180 45.000 0.00 0.00 0.00 3.27
6133 7278 4.096984 GCATTTCCTTCTCGATGAACCAAT 59.903 41.667 0.00 0.00 0.00 3.16
6283 7428 7.230747 TCATAGGAAACTCAGTCAAATGGAAA 58.769 34.615 0.00 0.00 43.67 3.13
6593 7739 6.766084 GCAGTAGTTACAAGTGCAAGAATAG 58.234 40.000 0.00 0.00 41.87 1.73
6607 7753 2.095919 CCGTTTTGCCTGCAGTAGTTAC 60.096 50.000 13.81 4.35 0.00 2.50
6835 7981 3.673746 TTTATTTGGCGATCTTCTGCG 57.326 42.857 0.00 0.00 0.00 5.18
6921 8067 4.576873 TGGTAAAAGCTTGACGTTCATTGA 59.423 37.500 0.00 0.00 0.00 2.57
6923 8069 5.240623 TGATGGTAAAAGCTTGACGTTCATT 59.759 36.000 0.00 0.00 0.00 2.57
6924 8070 4.759693 TGATGGTAAAAGCTTGACGTTCAT 59.240 37.500 0.00 1.05 0.00 2.57
6925 8071 4.130857 TGATGGTAAAAGCTTGACGTTCA 58.869 39.130 0.00 5.59 0.00 3.18
6926 8072 4.742438 TGATGGTAAAAGCTTGACGTTC 57.258 40.909 0.00 3.11 0.00 3.95
6927 8073 4.759693 TGATGATGGTAAAAGCTTGACGTT 59.240 37.500 0.00 0.00 0.00 3.99
6928 8074 4.323417 TGATGATGGTAAAAGCTTGACGT 58.677 39.130 0.00 0.00 0.00 4.34
6929 8075 4.944962 TGATGATGGTAAAAGCTTGACG 57.055 40.909 0.00 0.00 0.00 4.35
6930 8076 9.884465 GTTATATGATGATGGTAAAAGCTTGAC 57.116 33.333 0.00 0.87 0.00 3.18
6931 8077 9.625747 TGTTATATGATGATGGTAAAAGCTTGA 57.374 29.630 0.00 0.00 0.00 3.02
7011 8164 6.038714 ACATCAGGTTCAAAACTTCAAGACTC 59.961 38.462 0.00 0.00 0.00 3.36
7060 8217 9.535170 TCTGGAGGTAATGATCTATAGGTAAAG 57.465 37.037 0.00 0.00 0.00 1.85
7091 8248 8.784043 ACTTGTCAAGTATTCTTACACAATTCC 58.216 33.333 16.74 0.00 40.69 3.01
7097 8254 6.856426 GGCAAACTTGTCAAGTATTCTTACAC 59.144 38.462 18.45 3.29 41.91 2.90
7141 8298 4.010349 GTCAACATCTTTAACCTGGGGAG 58.990 47.826 0.00 0.00 0.00 4.30
7145 8302 6.348540 GCTTACTGTCAACATCTTTAACCTGG 60.349 42.308 0.00 0.00 0.00 4.45
7147 8304 6.204882 GTGCTTACTGTCAACATCTTTAACCT 59.795 38.462 0.00 0.00 0.00 3.50
7152 8309 5.615289 AGAGTGCTTACTGTCAACATCTTT 58.385 37.500 0.00 0.00 0.00 2.52
7155 8312 4.752101 ACAAGAGTGCTTACTGTCAACATC 59.248 41.667 0.00 0.00 31.81 3.06
7157 8314 4.119862 GACAAGAGTGCTTACTGTCAACA 58.880 43.478 0.00 0.00 31.81 3.33
7160 8317 3.243873 CCTGACAAGAGTGCTTACTGTCA 60.244 47.826 3.45 3.45 34.31 3.58
7161 8318 3.243907 ACCTGACAAGAGTGCTTACTGTC 60.244 47.826 0.00 0.00 31.81 3.51
7189 8346 6.584185 TGCAAGGTATTAGCGATACTGATA 57.416 37.500 11.42 0.00 40.43 2.15
7195 8352 7.214381 AGTACAAATGCAAGGTATTAGCGATA 58.786 34.615 0.00 0.00 0.00 2.92
7208 8370 3.503363 CCTGCAGAAGAGTACAAATGCAA 59.497 43.478 17.39 0.00 42.52 4.08
7436 8598 9.895138 TGTCTGATGATATTTCATTCTTTCTCA 57.105 29.630 0.00 0.00 42.73 3.27
7574 8740 0.764890 TGCTTTGCTACCTCCACACT 59.235 50.000 0.00 0.00 0.00 3.55
7601 8767 5.716979 AGACTCTAGATTTGCCCCAGTATA 58.283 41.667 0.00 0.00 0.00 1.47
7610 8776 4.987912 GGTGCATCTAGACTCTAGATTTGC 59.012 45.833 23.61 23.61 32.37 3.68
7629 8795 2.029518 GCAAAGGTGGCTTGGTGC 59.970 61.111 0.00 0.00 41.94 5.01
7692 8858 1.355381 TGGGACTGTGGAAATGATGCT 59.645 47.619 0.00 0.00 0.00 3.79
7704 8870 0.770557 TGGCCTTTACCTGGGACTGT 60.771 55.000 3.32 0.00 0.00 3.55
7722 8888 6.512903 GCCACATGAATGTTCATCTCTATGTG 60.513 42.308 13.79 13.79 45.62 3.21
7748 8914 4.325344 CCCTAAAAACTCCAGATCCCACAT 60.325 45.833 0.00 0.00 0.00 3.21
7784 8950 7.233962 TGAAGTCTATACCCAGAGTACAACAAA 59.766 37.037 0.00 0.00 32.46 2.83
7785 8952 6.722590 TGAAGTCTATACCCAGAGTACAACAA 59.277 38.462 0.00 0.00 32.46 2.83
7830 8997 9.733556 TTCTCAAATGTACACTTGGTATACAAT 57.266 29.630 16.37 0.00 38.65 2.71
7865 9033 9.944663 GAGTTGTTAATTTGTGACAATAGAACA 57.055 29.630 12.48 12.48 37.95 3.18
7866 9034 9.394477 GGAGTTGTTAATTTGTGACAATAGAAC 57.606 33.333 0.00 4.52 37.95 3.01
7867 9035 8.573035 GGGAGTTGTTAATTTGTGACAATAGAA 58.427 33.333 0.00 0.00 37.95 2.10
7869 9037 7.881142 TGGGAGTTGTTAATTTGTGACAATAG 58.119 34.615 0.00 0.00 37.95 1.73
7895 9071 1.618487 TGCATGCATGAACAAGGACA 58.382 45.000 30.64 12.71 0.00 4.02
7922 9178 0.107831 TTGTGTAACGGCAGCTTCCT 59.892 50.000 0.00 0.00 42.39 3.36
7933 9189 7.480810 ACTTTCTGTCCTTTTCATTGTGTAAC 58.519 34.615 0.00 0.00 37.35 2.50
7954 9222 8.951243 GGATACAAGCTTATCTTTTCAGACTTT 58.049 33.333 0.00 0.00 31.27 2.66
8058 9391 7.102346 CCCCACTTTTTATGATGCAAAATACA 58.898 34.615 0.00 0.00 0.00 2.29
8059 9392 6.037062 GCCCCACTTTTTATGATGCAAAATAC 59.963 38.462 0.00 0.00 0.00 1.89
8065 9399 2.533916 TGCCCCACTTTTTATGATGCA 58.466 42.857 0.00 0.00 0.00 3.96
8094 9428 2.158234 TGTCCTTTGGGGTATGCCTTTT 60.158 45.455 0.00 0.00 36.25 2.27
8102 9436 3.459828 TGATGATCTGTCCTTTGGGGTA 58.540 45.455 0.00 0.00 36.25 3.69
8111 9447 6.377429 TCCCGTATATAGTTGATGATCTGTCC 59.623 42.308 0.00 0.00 0.00 4.02
8112 9448 7.392494 TCCCGTATATAGTTGATGATCTGTC 57.608 40.000 0.00 0.00 0.00 3.51
8191 9683 4.212214 ACAAGCAAACAAAAAGAACGCAAA 59.788 33.333 0.00 0.00 0.00 3.68
8266 9768 6.604795 AGGTTAGCTCTACCATCGTTAAACTA 59.395 38.462 17.53 0.00 38.16 2.24
8297 9801 3.425659 AGAGATGCAGTGATATCGGCTA 58.574 45.455 12.98 3.28 0.00 3.93
8309 9813 4.817517 AGCCAAAATTTTGAGAGATGCAG 58.182 39.130 28.44 11.85 40.55 4.41
8312 9816 7.596494 TGTTAGAGCCAAAATTTTGAGAGATG 58.404 34.615 28.44 13.75 40.55 2.90
8314 9818 7.765695 ATGTTAGAGCCAAAATTTTGAGAGA 57.234 32.000 28.44 9.70 40.55 3.10
8352 9858 7.904094 CACTAGATGCACTTTCATTAGTCTTC 58.096 38.462 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.