Multiple sequence alignment - TraesCS7A01G313600

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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 TraesCS7A01G313600 chr7A 100.000 5827 0 0 1 5827 446320888 446326714 0.000000e+00 10761.0
1 TraesCS7A01G313600 chr7A 85.495 717 45 27 5041 5741 120466519 120467192 0.000000e+00 693.0
2 TraesCS7A01G313600 chr7A 95.062 81 3 1 4795 4875 735870007 735870086 6.130000e-25 126.0
3 TraesCS7A01G313600 chr7B 93.630 4474 168 44 563 4949 393313882 393318325 0.000000e+00 6575.0
4 TraesCS7A01G313600 chr7B 90.090 888 40 11 4942 5827 393318450 393319291 0.000000e+00 1109.0
5 TraesCS7A01G313600 chr7B 85.515 718 43 26 5043 5739 75034968 75035645 0.000000e+00 693.0
6 TraesCS7A01G313600 chr7B 85.335 716 46 29 5043 5739 75027462 75028137 0.000000e+00 686.0
7 TraesCS7A01G313600 chr7B 91.057 492 34 7 1 489 393313068 393313552 0.000000e+00 656.0
8 TraesCS7A01G313600 chr7D 94.490 3902 148 25 1 3849 393574505 393578392 0.000000e+00 5952.0
9 TraesCS7A01G313600 chr7D 92.555 1867 82 22 3970 5827 393578401 393580219 0.000000e+00 2625.0
10 TraesCS7A01G313600 chr7D 84.379 717 53 27 5041 5739 116436612 116437287 0.000000e+00 649.0
11 TraesCS7A01G313600 chr5A 85.660 265 38 0 4087 4351 707034119 707033855 4.450000e-71 279.0
12 TraesCS7A01G313600 chr5A 93.506 77 4 1 4799 4875 150805071 150805146 4.770000e-21 113.0
13 TraesCS7A01G313600 chr3A 95.062 81 3 1 4795 4875 559499489 559499410 6.130000e-25 126.0
14 TraesCS7A01G313600 chr4A 94.805 77 3 1 4799 4875 619953122 619953197 1.030000e-22 119.0
15 TraesCS7A01G313600 chr5B 92.593 81 5 1 4795 4875 609836124 609836045 1.330000e-21 115.0
16 TraesCS7A01G313600 chr5D 95.238 42 2 0 4643 4684 555451833 555451792 3.770000e-07 67.6
17 TraesCS7A01G313600 chr2D 97.436 39 1 0 4643 4681 197867256 197867294 3.770000e-07 67.6
18 TraesCS7A01G313600 chr2B 82.716 81 6 4 4788 4867 248958441 248958368 1.360000e-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 TraesCS7A01G313600 chr7A 446320888 446326714 5826 False 10761.0 10761 100.000000 1 5827 1 chr7A.!!$F2 5826
1 TraesCS7A01G313600 chr7A 120466519 120467192 673 False 693.0 693 85.495000 5041 5741 1 chr7A.!!$F1 700
2 TraesCS7A01G313600 chr7B 393313068 393319291 6223 False 2780.0 6575 91.592333 1 5827 3 chr7B.!!$F3 5826
3 TraesCS7A01G313600 chr7B 75034968 75035645 677 False 693.0 693 85.515000 5043 5739 1 chr7B.!!$F2 696
4 TraesCS7A01G313600 chr7B 75027462 75028137 675 False 686.0 686 85.335000 5043 5739 1 chr7B.!!$F1 696
5 TraesCS7A01G313600 chr7D 393574505 393580219 5714 False 4288.5 5952 93.522500 1 5827 2 chr7D.!!$F2 5826
6 TraesCS7A01G313600 chr7D 116436612 116437287 675 False 649.0 649 84.379000 5041 5739 1 chr7D.!!$F1 698

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
403 407 0.026803 CGCGCAGAATACTTTGAGCC 59.973 55.000 8.75 0.0 36.89 4.70 F
648 911 0.104120 CGATGCTTGGACGGATGGTA 59.896 55.000 0.00 0.0 0.00 3.25 F
798 1062 0.607489 GCACAACTGCCAGATCCAGT 60.607 55.000 0.00 0.0 44.92 4.00 F
800 1064 1.059098 ACAACTGCCAGATCCAGTGA 58.941 50.000 0.00 0.0 42.37 3.41 F
2400 2727 1.283347 TGCCTCTCAAGGAAGAGCAT 58.717 50.000 0.00 0.0 46.67 3.79 F
3169 3498 2.313317 CCATGCCTGCCTTATGAACAT 58.687 47.619 0.00 0.0 0.00 2.71 F
3544 3891 0.106708 TATGGTGAAGCGCCCTGATC 59.893 55.000 2.29 0.0 32.22 2.92 F
4577 4963 0.389817 TGTCGGTTGCGAGATCAAGG 60.390 55.000 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2727 2.187707 GCGCGGACTAGAAACGATTTA 58.812 47.619 8.83 0.0 0.00 1.40 R
2448 2775 5.295045 CAGTTGCTGATGATACATGCTAACA 59.705 40.000 0.00 0.0 32.44 2.41 R
2964 3293 4.937201 TCAGCAGCTTAAATCGATCCTA 57.063 40.909 0.00 0.0 0.00 2.94 R
3068 3397 2.284699 AACCTCGACCTCCCCAGG 60.285 66.667 0.00 0.0 46.87 4.45 R
3530 3877 0.034186 AATTGGATCAGGGCGCTTCA 60.034 50.000 7.64 0.0 0.00 3.02 R
4645 5031 0.399833 TGGACCTGTTGCAGCACATA 59.600 50.000 0.00 0.0 0.00 2.29 R
4671 5057 0.620030 TATTCCTTGAGCTGCAGGCA 59.380 50.000 17.12 0.0 44.79 4.75 R
5609 6159 2.032808 GTGCTGGAGAACACGAAAGAAC 60.033 50.000 0.00 0.0 0.00 3.01 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
52 53 9.639601 ATTTAAGTAAGAAACAATTTGCTAGCC 57.360 29.630 13.29 0.00 0.00 3.93
297 298 5.542635 AGAAAGATGACACTACAACCACCTA 59.457 40.000 0.00 0.00 0.00 3.08
315 316 5.940470 CCACCTACTAGCCATCCAATTATTC 59.060 44.000 0.00 0.00 0.00 1.75
320 321 7.939039 CCTACTAGCCATCCAATTATTCTCAAA 59.061 37.037 0.00 0.00 0.00 2.69
321 322 9.342308 CTACTAGCCATCCAATTATTCTCAAAA 57.658 33.333 0.00 0.00 0.00 2.44
323 324 8.055181 ACTAGCCATCCAATTATTCTCAAAAGA 58.945 33.333 0.00 0.00 0.00 2.52
403 407 0.026803 CGCGCAGAATACTTTGAGCC 59.973 55.000 8.75 0.00 36.89 4.70
412 416 6.644592 GCAGAATACTTTGAGCCATCTACTAG 59.355 42.308 0.00 0.00 0.00 2.57
414 418 6.841755 AGAATACTTTGAGCCATCTACTAGGT 59.158 38.462 0.00 0.00 0.00 3.08
491 495 2.769663 TGACATTCCCTTATGCGTAGGT 59.230 45.455 0.00 0.00 0.00 3.08
512 516 3.263681 GTGGCTAGGGTAAAGTTCTCCTT 59.736 47.826 0.00 0.00 33.79 3.36
516 520 4.141892 GCTAGGGTAAAGTTCTCCTTCCTC 60.142 50.000 0.00 0.00 29.98 3.71
600 862 1.602237 GTGGCGGGGAAGAGAATCA 59.398 57.895 0.00 0.00 37.82 2.57
601 863 0.181350 GTGGCGGGGAAGAGAATCAT 59.819 55.000 0.00 0.00 37.82 2.45
616 878 0.767375 ATCATGGTGCCTCGGCTTAT 59.233 50.000 9.65 0.00 42.51 1.73
632 894 2.237392 GCTTATTCCTCATAGGGGCGAT 59.763 50.000 0.00 0.00 35.59 4.58
633 895 3.866651 CTTATTCCTCATAGGGGCGATG 58.133 50.000 0.00 0.00 35.59 3.84
648 911 0.104120 CGATGCTTGGACGGATGGTA 59.896 55.000 0.00 0.00 0.00 3.25
651 914 1.264749 TGCTTGGACGGATGGTAGCT 61.265 55.000 0.00 0.00 0.00 3.32
700 963 4.026228 CGATCCTTCTCGAATTCATGTGTG 60.026 45.833 6.22 0.00 41.12 3.82
709 972 3.334691 GAATTCATGTGTGAGGACGGAA 58.665 45.455 0.00 0.00 35.39 4.30
764 1027 1.682451 TTCGGCGATGAGGTTAGGGG 61.682 60.000 11.76 0.00 0.00 4.79
796 1060 0.890542 GTGCACAACTGCCAGATCCA 60.891 55.000 13.17 0.00 43.51 3.41
798 1062 0.607489 GCACAACTGCCAGATCCAGT 60.607 55.000 0.00 0.00 44.92 4.00
799 1063 1.162698 CACAACTGCCAGATCCAGTG 58.837 55.000 0.00 0.00 42.37 3.66
800 1064 1.059098 ACAACTGCCAGATCCAGTGA 58.941 50.000 0.00 0.00 42.37 3.41
801 1065 1.421268 ACAACTGCCAGATCCAGTGAA 59.579 47.619 0.00 0.00 42.37 3.18
802 1066 2.040813 ACAACTGCCAGATCCAGTGAAT 59.959 45.455 0.00 0.00 42.37 2.57
803 1067 3.087031 CAACTGCCAGATCCAGTGAATT 58.913 45.455 0.00 0.00 42.37 2.17
804 1068 3.446442 ACTGCCAGATCCAGTGAATTT 57.554 42.857 0.00 0.00 41.68 1.82
805 1069 3.771216 ACTGCCAGATCCAGTGAATTTT 58.229 40.909 0.00 0.00 41.68 1.82
806 1070 4.154942 ACTGCCAGATCCAGTGAATTTTT 58.845 39.130 0.00 0.00 41.68 1.94
807 1071 5.324409 ACTGCCAGATCCAGTGAATTTTTA 58.676 37.500 0.00 0.00 41.68 1.52
808 1072 5.954150 ACTGCCAGATCCAGTGAATTTTTAT 59.046 36.000 0.00 0.00 41.68 1.40
809 1073 7.118723 ACTGCCAGATCCAGTGAATTTTTATA 58.881 34.615 0.00 0.00 41.68 0.98
810 1074 7.615365 ACTGCCAGATCCAGTGAATTTTTATAA 59.385 33.333 0.00 0.00 41.68 0.98
811 1075 8.537728 TGCCAGATCCAGTGAATTTTTATAAT 57.462 30.769 0.00 0.00 0.00 1.28
812 1076 9.639563 TGCCAGATCCAGTGAATTTTTATAATA 57.360 29.630 0.00 0.00 0.00 0.98
939 1240 4.196193 CAGAATATTTACCAGCCACCGAA 58.804 43.478 0.00 0.00 0.00 4.30
946 1247 2.357517 CAGCCACCGAACGAAGCT 60.358 61.111 0.00 0.00 0.00 3.74
990 1292 5.813157 TCCAAAATGAAGGAAACGGTTTTTC 59.187 36.000 7.65 8.99 0.00 2.29
1058 1366 3.773154 GCCCTCCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
1059 1367 2.612251 CCCTCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
1060 1368 2.612251 CCTCCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
1061 1369 2.018086 CCTCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1062 1370 1.541672 CTCCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1063 1371 2.015726 TCCCTCCTCCTCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
1356 1683 3.007290 GGTAGGGTTCGGTTGTACTCTTT 59.993 47.826 0.00 0.00 28.20 2.52
1398 1725 5.631992 GTGGATTTCCTTCTTTCGATGTTC 58.368 41.667 0.00 0.00 36.82 3.18
1744 2071 2.203070 CCCCGCCTGTGTATGAGC 60.203 66.667 0.00 0.00 0.00 4.26
1986 2313 3.820825 AAACTTGTTCCGGGGCCCC 62.821 63.158 33.22 33.22 0.00 5.80
2148 2475 5.163163 TGCTAAGATGGCCAAGAGATATGTT 60.163 40.000 10.96 0.00 0.00 2.71
2318 2645 8.718102 TTCTACAGGTTTATATTTGAGACAGC 57.282 34.615 0.00 0.00 0.00 4.40
2385 2712 3.775261 ATCAATGGTTTTGCTTTGCCT 57.225 38.095 0.00 0.00 0.00 4.75
2400 2727 1.283347 TGCCTCTCAAGGAAGAGCAT 58.717 50.000 0.00 0.00 46.67 3.79
2448 2775 3.370104 TCCACTCCACAAACCAAAATGT 58.630 40.909 0.00 0.00 0.00 2.71
2809 3136 3.497297 TTGCGATAGTCTTTGCTCGTA 57.503 42.857 0.00 0.00 39.35 3.43
3098 3427 4.225267 AGGTCGAGGTTGAATAATGGTTCT 59.775 41.667 0.00 0.00 0.00 3.01
3169 3498 2.313317 CCATGCCTGCCTTATGAACAT 58.687 47.619 0.00 0.00 0.00 2.71
3187 3516 4.759516 ACATCGGTACCAAAAATGTGTC 57.240 40.909 13.54 0.00 0.00 3.67
3214 3543 4.452455 CCTATGTTATTGGGAAGCTTAGCG 59.548 45.833 0.00 0.00 0.00 4.26
3246 3577 2.401583 TACCCTGCTATGCAACTGTG 57.598 50.000 0.00 0.00 38.41 3.66
3520 3867 7.335627 CAGTCAAAACTGTATGGTCCCTTATA 58.664 38.462 0.00 0.00 46.52 0.98
3521 3868 7.993183 CAGTCAAAACTGTATGGTCCCTTATAT 59.007 37.037 0.00 0.00 46.52 0.86
3535 3882 8.934697 TGGTCCCTTATATATATATGGTGAAGC 58.065 37.037 23.44 19.05 33.76 3.86
3536 3883 8.088981 GGTCCCTTATATATATATGGTGAAGCG 58.911 40.741 23.44 13.04 33.76 4.68
3537 3884 7.599245 GTCCCTTATATATATATGGTGAAGCGC 59.401 40.741 23.44 0.00 33.76 5.92
3538 3885 6.874134 CCCTTATATATATATGGTGAAGCGCC 59.126 42.308 23.44 0.00 33.76 6.53
3539 3886 6.874134 CCTTATATATATATGGTGAAGCGCCC 59.126 42.308 19.74 0.00 32.22 6.13
3540 3887 7.256332 CCTTATATATATATGGTGAAGCGCCCT 60.256 40.741 19.74 0.00 32.22 5.19
3541 3888 2.479566 ATATATGGTGAAGCGCCCTG 57.520 50.000 2.29 0.00 32.22 4.45
3544 3891 0.106708 TATGGTGAAGCGCCCTGATC 59.893 55.000 2.29 0.00 32.22 2.92
3545 3892 2.514824 GGTGAAGCGCCCTGATCC 60.515 66.667 2.29 0.00 0.00 3.36
3546 3893 2.268920 GTGAAGCGCCCTGATCCA 59.731 61.111 2.29 0.00 0.00 3.41
3547 3894 1.377202 GTGAAGCGCCCTGATCCAA 60.377 57.895 2.29 0.00 0.00 3.53
3548 3895 0.749454 GTGAAGCGCCCTGATCCAAT 60.749 55.000 2.29 0.00 0.00 3.16
3600 3950 2.743553 CCCTGATCCAATTTTCCTGCT 58.256 47.619 0.00 0.00 0.00 4.24
3675 4025 2.012673 GTTAGCATTCTGAGCACCTGG 58.987 52.381 0.00 0.00 0.00 4.45
3747 4099 3.146066 TGATTTTCCTCTGTTCCCAACG 58.854 45.455 0.00 0.00 0.00 4.10
3783 4143 6.646267 TGAATTACCATACCTACTGTTCACC 58.354 40.000 0.00 0.00 0.00 4.02
3793 4153 4.058817 CCTACTGTTCACCTTCTGTTGAC 58.941 47.826 0.00 0.00 0.00 3.18
3849 4209 2.744741 TGTTTAGTGTGTGTGTGTGTGG 59.255 45.455 0.00 0.00 0.00 4.17
3880 4266 2.367894 TGCATTTTCAGGTGGCATTCAA 59.632 40.909 0.00 0.00 0.00 2.69
3887 4273 6.662865 TTTCAGGTGGCATTCAAGAATAAA 57.337 33.333 0.00 0.00 0.00 1.40
3889 4275 6.271488 TCAGGTGGCATTCAAGAATAAAAG 57.729 37.500 0.00 0.00 0.00 2.27
3895 4281 6.583806 GTGGCATTCAAGAATAAAAGTCTGTG 59.416 38.462 0.00 0.00 0.00 3.66
3990 4376 4.127566 TGTCCCCGTGCTACTTATTTAC 57.872 45.455 0.00 0.00 0.00 2.01
4081 4467 6.540914 GGAACAACGATCATATTGAGGGTTTA 59.459 38.462 8.02 0.00 0.00 2.01
4126 4512 2.158755 ACTGCCCATAATCCTTCCTTCG 60.159 50.000 0.00 0.00 0.00 3.79
4269 4655 4.180057 GACGATGAAGCTCAAGAAGATGT 58.820 43.478 0.00 0.00 0.00 3.06
4271 4657 4.179298 CGATGAAGCTCAAGAAGATGTGA 58.821 43.478 0.00 0.00 0.00 3.58
4467 4853 1.672030 CATGGACGACTGCTTGCCA 60.672 57.895 0.00 0.00 0.00 4.92
4508 4894 4.759782 ACATCTTACAGGCTGACATGTAC 58.240 43.478 23.66 0.00 31.83 2.90
4513 4899 5.420739 TCTTACAGGCTGACATGTACATACA 59.579 40.000 23.66 10.82 40.98 2.29
4542 4928 1.666189 GATGGACCGTGAAGCTTTAGC 59.334 52.381 0.00 0.00 42.49 3.09
4575 4961 0.601057 TCTGTCGGTTGCGAGATCAA 59.399 50.000 0.00 0.00 0.00 2.57
4577 4963 0.389817 TGTCGGTTGCGAGATCAAGG 60.390 55.000 0.00 0.00 0.00 3.61
4584 4970 3.265791 GTTGCGAGATCAAGGATTCAGT 58.734 45.455 0.00 0.00 0.00 3.41
4592 4978 6.314648 CGAGATCAAGGATTCAGTTTTCATCA 59.685 38.462 0.00 0.00 0.00 3.07
4601 4987 2.571653 TCAGTTTTCATCATCGAGGGGT 59.428 45.455 0.00 0.00 0.00 4.95
4609 4995 3.772572 TCATCATCGAGGGGTGAAGTAAA 59.227 43.478 0.00 0.00 0.00 2.01
4624 5010 5.710567 GTGAAGTAAAGGAGGCAAATTACCT 59.289 40.000 0.00 0.00 41.41 3.08
4645 5031 4.348168 CCTGTCCTGGCTTATATAAGGTGT 59.652 45.833 21.30 0.00 33.95 4.16
4665 5051 0.892358 ATGTGCTGCAACAGGTCCAG 60.892 55.000 2.77 0.00 32.52 3.86
4666 5052 1.526917 GTGCTGCAACAGGTCCAGT 60.527 57.895 2.77 0.00 31.21 4.00
4667 5053 1.526686 TGCTGCAACAGGTCCAGTG 60.527 57.895 0.00 0.00 31.21 3.66
4668 5054 1.526917 GCTGCAACAGGTCCAGTGT 60.527 57.895 0.00 0.00 31.21 3.55
4669 5055 1.789078 GCTGCAACAGGTCCAGTGTG 61.789 60.000 0.00 0.00 31.21 3.82
4670 5056 1.789078 CTGCAACAGGTCCAGTGTGC 61.789 60.000 11.85 11.85 0.00 4.57
4671 5057 1.526917 GCAACAGGTCCAGTGTGCT 60.527 57.895 11.62 0.00 0.00 4.40
4748 5135 3.980646 TTTGCTGAACTGTAATGCGTT 57.019 38.095 0.00 0.00 0.00 4.84
4815 5202 4.739716 GGTGTACATTTGTTTGCTTCAGTG 59.260 41.667 0.00 0.00 0.00 3.66
4818 5205 4.942761 ACATTTGTTTGCTTCAGTGGAT 57.057 36.364 0.00 0.00 0.00 3.41
4844 5231 1.614903 CACAAATCTGGAAGCAGGCAA 59.385 47.619 0.00 0.00 0.00 4.52
4860 5247 5.596772 AGCAGGCAAAGGTTTTCTTTACTTA 59.403 36.000 0.00 0.00 43.32 2.24
4875 5262 9.528018 TTTCTTTACTTACCAAAAATCAGCTTG 57.472 29.630 0.00 0.00 0.00 4.01
4886 5273 7.015195 ACCAAAAATCAGCTTGTAGTAAATGGT 59.985 33.333 0.00 0.00 0.00 3.55
4927 5314 7.421087 TCCTTGGATGAAATGCATTGAAATA 57.579 32.000 13.82 0.00 46.71 1.40
4928 5315 8.025270 TCCTTGGATGAAATGCATTGAAATAT 57.975 30.769 13.82 3.47 46.71 1.28
4929 5316 9.145442 TCCTTGGATGAAATGCATTGAAATATA 57.855 29.630 13.82 0.00 46.71 0.86
4930 5317 9.938280 CCTTGGATGAAATGCATTGAAATATAT 57.062 29.630 13.82 0.00 46.71 0.86
5021 5540 8.586570 TGTCGCAGTTTGATAAAAATGAAAAT 57.413 26.923 7.18 0.00 30.08 1.82
5157 5677 0.827368 GGAAACCAAACCTTGTGCCA 59.173 50.000 0.00 0.00 0.00 4.92
5158 5678 1.416030 GGAAACCAAACCTTGTGCCAT 59.584 47.619 0.00 0.00 0.00 4.40
5159 5679 2.158827 GGAAACCAAACCTTGTGCCATT 60.159 45.455 0.00 0.00 0.00 3.16
5160 5680 2.618442 AACCAAACCTTGTGCCATTG 57.382 45.000 0.00 0.00 0.00 2.82
5161 5681 1.494960 ACCAAACCTTGTGCCATTGT 58.505 45.000 0.00 0.00 0.00 2.71
5395 5924 3.765511 TCATCTGCCAAAATTCTCCAAGG 59.234 43.478 0.00 0.00 0.00 3.61
5469 6012 3.403038 ACTCGTGAAGAAACATGGAAGG 58.597 45.455 0.00 0.00 0.00 3.46
5546 6096 1.969085 TGCTTTGGCCTGAGCATTG 59.031 52.632 23.92 0.28 43.46 2.82
5617 6167 0.457853 TGCTCCGATCCGTTCTTTCG 60.458 55.000 0.00 0.00 0.00 3.46
5618 6168 0.458025 GCTCCGATCCGTTCTTTCGT 60.458 55.000 0.00 0.00 0.00 3.85
5798 6349 8.997323 GCTGAATTATGAGTGCTTACTTGATAT 58.003 33.333 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 8.017587 CATGTATATGCAGCGTTGTAATAAGA 57.982 34.615 0.00 0.00 0.00 2.10
202 203 7.617723 ACTTCATGACTATAGTCTCCACTCTTT 59.382 37.037 28.53 6.91 44.99 2.52
203 204 7.122715 ACTTCATGACTATAGTCTCCACTCTT 58.877 38.462 28.53 8.11 44.99 2.85
297 298 8.055181 TCTTTTGAGAATAATTGGATGGCTAGT 58.945 33.333 0.00 0.00 0.00 2.57
376 380 5.350365 TCAAAGTATTCTGCGCGAGTTTATT 59.650 36.000 12.10 0.00 0.00 1.40
388 392 7.151308 CCTAGTAGATGGCTCAAAGTATTCTG 58.849 42.308 0.00 0.00 0.00 3.02
389 393 6.841755 ACCTAGTAGATGGCTCAAAGTATTCT 59.158 38.462 0.00 0.00 0.00 2.40
403 407 3.819902 GTCTAACCCGGACCTAGTAGATG 59.180 52.174 0.73 0.00 0.00 2.90
414 418 1.646912 TGTCATTGGTCTAACCCGGA 58.353 50.000 0.73 0.00 37.50 5.14
491 495 3.200958 AGGAGAACTTTACCCTAGCCA 57.799 47.619 0.00 0.00 0.00 4.75
512 516 2.822643 ATCGGTGGAGCTTGGGAGGA 62.823 60.000 0.00 0.00 0.00 3.71
516 520 1.153289 CTGATCGGTGGAGCTTGGG 60.153 63.158 0.00 0.00 0.00 4.12
600 862 0.179018 GGAATAAGCCGAGGCACCAT 60.179 55.000 17.18 3.26 44.88 3.55
601 863 1.223487 GGAATAAGCCGAGGCACCA 59.777 57.895 17.18 0.80 44.88 4.17
616 878 0.764369 AGCATCGCCCCTATGAGGAA 60.764 55.000 0.00 0.00 37.67 3.36
632 894 1.220749 GCTACCATCCGTCCAAGCA 59.779 57.895 0.00 0.00 0.00 3.91
633 895 0.530870 GAGCTACCATCCGTCCAAGC 60.531 60.000 0.00 0.00 0.00 4.01
648 911 4.142271 CGACCTACTTGAAGATGAAGAGCT 60.142 45.833 0.00 0.00 0.00 4.09
651 914 3.447586 CCCGACCTACTTGAAGATGAAGA 59.552 47.826 0.00 0.00 0.00 2.87
696 959 1.068474 CGTCAATTCCGTCCTCACAC 58.932 55.000 0.00 0.00 0.00 3.82
700 963 0.531200 ACTCCGTCAATTCCGTCCTC 59.469 55.000 0.00 0.00 0.00 3.71
709 972 3.079578 TCTACGTCAGAACTCCGTCAAT 58.920 45.455 0.00 0.00 36.12 2.57
808 1072 9.923143 TTTTCTCAGAAAGATTCACGTCTATTA 57.077 29.630 0.00 0.00 32.82 0.98
809 1073 8.833231 TTTTCTCAGAAAGATTCACGTCTATT 57.167 30.769 0.00 0.00 32.82 1.73
810 1074 8.833231 TTTTTCTCAGAAAGATTCACGTCTAT 57.167 30.769 0.00 0.00 32.82 1.98
856 1137 6.678568 TCCATCTGCCCTTAAAATGAAAAA 57.321 33.333 0.00 0.00 0.00 1.94
857 1138 6.678568 TTCCATCTGCCCTTAAAATGAAAA 57.321 33.333 0.00 0.00 0.00 2.29
861 1142 5.870978 CAGTTTTCCATCTGCCCTTAAAATG 59.129 40.000 0.00 0.00 0.00 2.32
862 1143 5.543790 ACAGTTTTCCATCTGCCCTTAAAAT 59.456 36.000 0.00 0.00 35.37 1.82
939 1240 1.223187 CAACACGGGTAAAGCTTCGT 58.777 50.000 0.00 1.58 36.19 3.85
946 1247 2.885894 GACCAAATCCAACACGGGTAAA 59.114 45.455 0.00 0.00 34.36 2.01
990 1292 8.970859 ATTGGAACAGAACATTATTAGAGGAG 57.029 34.615 0.00 0.00 42.39 3.69
1058 1366 1.457380 TAGGGGGAACAGTGGGAGGA 61.457 60.000 0.00 0.00 0.00 3.71
1059 1367 0.983378 CTAGGGGGAACAGTGGGAGG 60.983 65.000 0.00 0.00 0.00 4.30
1060 1368 0.042731 TCTAGGGGGAACAGTGGGAG 59.957 60.000 0.00 0.00 0.00 4.30
1061 1369 0.494551 TTCTAGGGGGAACAGTGGGA 59.505 55.000 0.00 0.00 0.00 4.37
1062 1370 0.912486 CTTCTAGGGGGAACAGTGGG 59.088 60.000 0.00 0.00 0.00 4.61
1063 1371 0.253327 GCTTCTAGGGGGAACAGTGG 59.747 60.000 0.00 0.00 0.00 4.00
1338 1665 4.824289 TGATAAAGAGTACAACCGAACCC 58.176 43.478 0.00 0.00 0.00 4.11
1356 1683 2.434688 GCATCGCGCGAGAATGATA 58.565 52.632 36.99 12.77 0.00 2.15
1986 2313 4.293671 TCCTTTGGGGCGGGGTTG 62.294 66.667 0.00 0.00 34.39 3.77
2148 2475 3.623203 GCCTGAGAATGAAACCCTGATCA 60.623 47.826 0.00 0.00 0.00 2.92
2318 2645 4.617959 CTCTGCAATCCCATAATGCTTTG 58.382 43.478 0.00 0.00 40.66 2.77
2385 2712 5.344743 ACGATTTATGCTCTTCCTTGAGA 57.655 39.130 0.00 0.00 36.23 3.27
2400 2727 2.187707 GCGCGGACTAGAAACGATTTA 58.812 47.619 8.83 0.00 0.00 1.40
2448 2775 5.295045 CAGTTGCTGATGATACATGCTAACA 59.705 40.000 0.00 0.00 32.44 2.41
2964 3293 4.937201 TCAGCAGCTTAAATCGATCCTA 57.063 40.909 0.00 0.00 0.00 2.94
3068 3397 2.284699 AACCTCGACCTCCCCAGG 60.285 66.667 0.00 0.00 46.87 4.45
3098 3427 7.048629 TCTTGCAATATTTTTCTCACCAACA 57.951 32.000 0.00 0.00 0.00 3.33
3154 3483 2.332063 ACCGATGTTCATAAGGCAGG 57.668 50.000 6.67 0.00 0.00 4.85
3169 3498 4.696402 GGTATGACACATTTTTGGTACCGA 59.304 41.667 7.57 1.50 0.00 4.69
3187 3516 7.119846 GCTAAGCTTCCCAATAACATAGGTATG 59.880 40.741 0.00 0.00 39.55 2.39
3214 3543 7.958429 TGCATAGCAGGGTATATAACCAAGTTC 60.958 40.741 19.19 3.13 41.45 3.01
3386 3718 6.631962 ACTAAGCACATCTAGGTTCTGTTAC 58.368 40.000 0.00 0.00 0.00 2.50
3458 3805 6.868864 TGAAGTAGCAAACAGAGATAACTGAC 59.131 38.462 0.00 0.00 40.63 3.51
3520 3867 3.774766 TCAGGGCGCTTCACCATATATAT 59.225 43.478 7.64 0.00 0.00 0.86
3521 3868 3.169908 TCAGGGCGCTTCACCATATATA 58.830 45.455 7.64 0.00 0.00 0.86
3524 3871 0.767375 ATCAGGGCGCTTCACCATAT 59.233 50.000 7.64 0.00 0.00 1.78
3525 3872 0.106708 GATCAGGGCGCTTCACCATA 59.893 55.000 7.64 0.00 0.00 2.74
3526 3873 1.153086 GATCAGGGCGCTTCACCAT 60.153 57.895 7.64 0.00 0.00 3.55
3527 3874 2.268920 GATCAGGGCGCTTCACCA 59.731 61.111 7.64 0.00 0.00 4.17
3528 3875 2.514824 GGATCAGGGCGCTTCACC 60.515 66.667 7.64 0.00 0.00 4.02
3529 3876 0.749454 ATTGGATCAGGGCGCTTCAC 60.749 55.000 7.64 0.00 0.00 3.18
3530 3877 0.034186 AATTGGATCAGGGCGCTTCA 60.034 50.000 7.64 0.00 0.00 3.02
3531 3878 1.106285 AAATTGGATCAGGGCGCTTC 58.894 50.000 7.64 0.00 0.00 3.86
3532 3879 1.205417 CAAAATTGGATCAGGGCGCTT 59.795 47.619 7.64 0.00 0.00 4.68
3533 3880 0.819582 CAAAATTGGATCAGGGCGCT 59.180 50.000 7.64 0.00 0.00 5.92
3534 3881 0.532115 ACAAAATTGGATCAGGGCGC 59.468 50.000 0.00 0.00 0.00 6.53
3535 3882 4.362279 CATAACAAAATTGGATCAGGGCG 58.638 43.478 0.00 0.00 0.00 6.13
3536 3883 4.443315 CCCATAACAAAATTGGATCAGGGC 60.443 45.833 0.00 0.00 31.94 5.19
3537 3884 4.716287 ACCCATAACAAAATTGGATCAGGG 59.284 41.667 0.00 0.00 37.43 4.45
3538 3885 5.663456 CACCCATAACAAAATTGGATCAGG 58.337 41.667 0.00 0.00 31.94 3.86
3539 3886 5.111293 GCACCCATAACAAAATTGGATCAG 58.889 41.667 0.00 0.00 31.94 2.90
3540 3887 4.381398 CGCACCCATAACAAAATTGGATCA 60.381 41.667 0.00 0.00 31.94 2.92
3541 3888 4.111916 CGCACCCATAACAAAATTGGATC 58.888 43.478 0.00 0.00 31.94 3.36
3544 3891 3.249917 GTCGCACCCATAACAAAATTGG 58.750 45.455 0.00 0.00 0.00 3.16
3545 3892 3.906998 TGTCGCACCCATAACAAAATTG 58.093 40.909 0.00 0.00 0.00 2.32
3546 3893 3.613910 GCTGTCGCACCCATAACAAAATT 60.614 43.478 0.00 0.00 35.78 1.82
3547 3894 2.094752 GCTGTCGCACCCATAACAAAAT 60.095 45.455 0.00 0.00 35.78 1.82
3548 3895 1.268352 GCTGTCGCACCCATAACAAAA 59.732 47.619 0.00 0.00 35.78 2.44
3600 3950 6.811253 ATGTACTTAACGGCAATTCTCAAA 57.189 33.333 0.00 0.00 0.00 2.69
3699 4049 8.924691 GCTTGTTTATGAATGCAGAATTAACAA 58.075 29.630 16.11 16.11 28.68 2.83
3700 4050 8.306038 AGCTTGTTTATGAATGCAGAATTAACA 58.694 29.630 0.00 0.00 0.00 2.41
3710 4060 6.815142 AGGAAAATCAGCTTGTTTATGAATGC 59.185 34.615 0.00 0.00 0.00 3.56
3747 4099 7.448469 AGGTATGGTAATTCAAGGATGTATTGC 59.552 37.037 0.00 0.00 31.34 3.56
3783 4143 1.532868 CCTTTCAGGCGTCAACAGAAG 59.467 52.381 0.00 0.00 0.00 2.85
3793 4153 3.320673 AAGAAGTCTACCTTTCAGGCG 57.679 47.619 0.00 0.00 39.63 5.52
3849 4209 5.104374 CACCTGAAAATGCATACAATGACC 58.896 41.667 0.00 0.00 0.00 4.02
3889 4275 9.595823 TCATTAGGTAAAATACTAAGCACAGAC 57.404 33.333 0.00 0.00 33.16 3.51
3990 4376 6.815641 GGAGTAGATGCATCATTACCACATAG 59.184 42.308 27.81 0.00 0.00 2.23
4081 4467 4.831107 ACACCTTGCTGTTTTGTTTGATT 58.169 34.783 0.00 0.00 0.00 2.57
4126 4512 9.113876 CAATGACCTTTTGTATTTCGTTCTAAC 57.886 33.333 0.00 0.00 0.00 2.34
4269 4655 2.476018 GCATCACGTTTTGATCGCATCA 60.476 45.455 0.00 0.00 43.68 3.07
4271 4657 1.202177 GGCATCACGTTTTGATCGCAT 60.202 47.619 0.00 0.00 43.68 4.73
4508 4894 4.039245 ACGGTCCATCATCTAGGTTGTATG 59.961 45.833 0.00 0.00 0.00 2.39
4513 4899 2.747177 TCACGGTCCATCATCTAGGTT 58.253 47.619 0.00 0.00 0.00 3.50
4542 4928 0.510359 GACAGAACACAAGAGCAGCG 59.490 55.000 0.00 0.00 0.00 5.18
4575 4961 5.121811 CCTCGATGATGAAAACTGAATCCT 58.878 41.667 0.00 0.00 0.00 3.24
4577 4963 4.274459 CCCCTCGATGATGAAAACTGAATC 59.726 45.833 0.00 0.00 0.00 2.52
4584 4970 3.009033 ACTTCACCCCTCGATGATGAAAA 59.991 43.478 6.63 0.00 0.00 2.29
4592 4978 2.766828 CTCCTTTACTTCACCCCTCGAT 59.233 50.000 0.00 0.00 0.00 3.59
4601 4987 5.710099 CAGGTAATTTGCCTCCTTTACTTCA 59.290 40.000 2.68 0.00 33.31 3.02
4609 4995 2.025887 CAGGACAGGTAATTTGCCTCCT 60.026 50.000 2.68 5.86 32.75 3.69
4624 5010 6.557253 ACATACACCTTATATAAGCCAGGACA 59.443 38.462 15.86 0.00 32.02 4.02
4645 5031 0.399833 TGGACCTGTTGCAGCACATA 59.600 50.000 0.00 0.00 0.00 2.29
4670 5056 0.680280 ATTCCTTGAGCTGCAGGCAG 60.680 55.000 17.12 16.68 46.15 4.85
4671 5057 0.620030 TATTCCTTGAGCTGCAGGCA 59.380 50.000 17.12 0.00 44.79 4.75
4711 5097 1.181098 AAAATCAGCACCGGCAAGCT 61.181 50.000 10.52 10.52 44.61 3.74
4788 5175 4.305989 AGCAAACAAATGTACACCAGTG 57.694 40.909 0.00 0.00 0.00 3.66
4815 5202 5.822519 TGCTTCCAGATTTGTGTATACATCC 59.177 40.000 9.18 0.00 36.53 3.51
4818 5205 5.185454 CCTGCTTCCAGATTTGTGTATACA 58.815 41.667 0.08 0.08 41.77 2.29
4860 5247 7.015195 ACCATTTACTACAAGCTGATTTTTGGT 59.985 33.333 0.00 0.00 0.00 3.67
4875 5262 9.884465 GATCTCATAATGCAAACCATTTACTAC 57.116 33.333 0.00 0.00 41.29 2.73
4886 5273 6.367161 TCCAAGGATGATCTCATAATGCAAA 58.633 36.000 0.00 0.00 36.57 3.68
4981 5500 8.535592 CAAACTGCGACAAATTTTTACAACATA 58.464 29.630 0.00 0.00 0.00 2.29
4982 5501 7.276658 TCAAACTGCGACAAATTTTTACAACAT 59.723 29.630 0.00 0.00 0.00 2.71
4999 5518 8.486383 TGTCATTTTCATTTTTATCAAACTGCG 58.514 29.630 0.00 0.00 0.00 5.18
5069 5589 3.130516 TCAGTTGAGCTATAGGTGAACCG 59.869 47.826 24.59 17.61 39.78 4.44
5100 5620 5.183530 TCAACTGTCCATGATGAAATCCT 57.816 39.130 0.00 0.00 44.73 3.24
5101 5621 5.649395 TCTTCAACTGTCCATGATGAAATCC 59.351 40.000 0.00 0.00 44.73 3.01
5158 5678 9.120538 GGAACCAAATCTTCAGCTATAATACAA 57.879 33.333 0.00 0.00 0.00 2.41
5159 5679 8.271458 TGGAACCAAATCTTCAGCTATAATACA 58.729 33.333 0.00 0.00 0.00 2.29
5160 5680 8.677148 TGGAACCAAATCTTCAGCTATAATAC 57.323 34.615 0.00 0.00 0.00 1.89
5161 5681 9.507329 GATGGAACCAAATCTTCAGCTATAATA 57.493 33.333 0.00 0.00 0.00 0.98
5415 5944 5.911752 TCCAACATCTTATCTTCAGAGCTC 58.088 41.667 5.27 5.27 0.00 4.09
5603 6153 2.325761 AGAACACGAAAGAACGGATCG 58.674 47.619 0.00 0.00 42.05 3.69
5609 6159 2.032808 GTGCTGGAGAACACGAAAGAAC 60.033 50.000 0.00 0.00 0.00 3.01
5617 6167 3.555428 GCTCGTGCTGGAGAACAC 58.445 61.111 1.41 0.00 36.08 3.32
5752 6303 7.692460 TCAGCATACTTGATTCATGAAGTTT 57.308 32.000 14.54 0.00 35.81 2.66
5753 6304 7.692460 TTCAGCATACTTGATTCATGAAGTT 57.308 32.000 14.54 0.00 35.81 2.66
5798 6349 9.990360 TCAACATCTGTCTGTGTTTTAGTAATA 57.010 29.630 0.00 0.00 36.48 0.98
5799 6350 8.902540 TCAACATCTGTCTGTGTTTTAGTAAT 57.097 30.769 0.00 0.00 36.48 1.89
5800 6351 7.985184 ACTCAACATCTGTCTGTGTTTTAGTAA 59.015 33.333 0.00 0.00 36.48 2.24


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

AutoCloner maintained by Alex Coulton.