Multiple sequence alignment - TraesCS3B01G476700

Loading Multiple Alignment...

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 TraesCS3B01G476700 chr3B 100.000 2975 0 0 1 2975 725275180 725278154 0.000000e+00 5494.0
1 TraesCS3B01G476700 chr3B 90.562 1600 72 29 562 2108 725181832 725183405 0.000000e+00 2045.0
2 TraesCS3B01G476700 chr3B 88.774 775 44 15 2238 2975 540465416 540466184 0.000000e+00 909.0
3 TraesCS3B01G476700 chr3B 84.464 457 51 13 2455 2907 378428038 378428478 1.640000e-117 433.0
4 TraesCS3B01G476700 chr3D 92.057 1536 85 15 586 2108 547632629 547634140 0.000000e+00 2126.0
5 TraesCS3B01G476700 chr3D 90.173 1445 81 24 760 2174 547779451 547778038 0.000000e+00 1825.0
6 TraesCS3B01G476700 chr3D 79.615 520 83 14 1 517 272534208 272534707 4.720000e-93 351.0
7 TraesCS3B01G476700 chr3D 80.995 442 63 10 1 437 14736539 14736964 6.150000e-87 331.0
8 TraesCS3B01G476700 chr3D 84.868 152 10 8 585 729 547779599 547779454 1.110000e-29 141.0
9 TraesCS3B01G476700 chr3A 90.526 1615 93 34 562 2143 684639801 684641388 0.000000e+00 2080.0
10 TraesCS3B01G476700 chr3A 89.655 1653 102 31 562 2174 684698405 684696782 0.000000e+00 2041.0
11 TraesCS3B01G476700 chr3A 87.500 920 69 18 1209 2105 13823478 13822582 0.000000e+00 1020.0
12 TraesCS3B01G476700 chr6B 89.290 775 42 13 2238 2975 20868910 20868140 0.000000e+00 933.0
13 TraesCS3B01G476700 chr2B 88.677 786 48 19 2228 2975 577430592 577431374 0.000000e+00 920.0
14 TraesCS3B01G476700 chr4A 82.671 554 85 7 5 555 463892087 463892632 5.770000e-132 481.0
15 TraesCS3B01G476700 chr4D 82.130 554 88 7 4 555 113243869 113243325 5.810000e-127 464.0
16 TraesCS3B01G476700 chr4D 88.312 231 26 1 68 297 65541788 65541558 2.920000e-70 276.0
17 TraesCS3B01G476700 chr2D 79.966 584 62 28 2413 2949 639149788 639150363 2.160000e-101 379.0
18 TraesCS3B01G476700 chr1A 80.271 517 81 13 1 514 377496151 377496649 1.300000e-98 370.0
19 TraesCS3B01G476700 chr4B 82.850 414 62 6 4 416 96194219 96193814 2.180000e-96 363.0
20 TraesCS3B01G476700 chr1D 79.651 516 83 17 1 514 302883243 302883738 4.720000e-93 351.0
21 TraesCS3B01G476700 chr5B 84.818 303 41 5 4 304 256054688 256054389 1.730000e-77 300.0
22 TraesCS3B01G476700 chr5D 89.744 156 14 2 2753 2907 8265953 8265799 6.500000e-47 198.0
23 TraesCS3B01G476700 chr5D 89.103 156 15 2 2753 2907 546029062 546028908 3.030000e-45 193.0
24 TraesCS3B01G476700 chr1B 85.526 76 11 0 384 459 561545824 561545749 2.460000e-11 80.5


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 TraesCS3B01G476700 chr3B 725275180 725278154 2974 False 5494 5494 100.0000 1 2975 1 chr3B.!!$F4 2974
1 TraesCS3B01G476700 chr3B 725181832 725183405 1573 False 2045 2045 90.5620 562 2108 1 chr3B.!!$F3 1546
2 TraesCS3B01G476700 chr3B 540465416 540466184 768 False 909 909 88.7740 2238 2975 1 chr3B.!!$F2 737
3 TraesCS3B01G476700 chr3D 547632629 547634140 1511 False 2126 2126 92.0570 586 2108 1 chr3D.!!$F3 1522
4 TraesCS3B01G476700 chr3D 547778038 547779599 1561 True 983 1825 87.5205 585 2174 2 chr3D.!!$R1 1589
5 TraesCS3B01G476700 chr3A 684639801 684641388 1587 False 2080 2080 90.5260 562 2143 1 chr3A.!!$F1 1581
6 TraesCS3B01G476700 chr3A 684696782 684698405 1623 True 2041 2041 89.6550 562 2174 1 chr3A.!!$R2 1612
7 TraesCS3B01G476700 chr3A 13822582 13823478 896 True 1020 1020 87.5000 1209 2105 1 chr3A.!!$R1 896
8 TraesCS3B01G476700 chr6B 20868140 20868910 770 True 933 933 89.2900 2238 2975 1 chr6B.!!$R1 737
9 TraesCS3B01G476700 chr2B 577430592 577431374 782 False 920 920 88.6770 2228 2975 1 chr2B.!!$F1 747
10 TraesCS3B01G476700 chr4A 463892087 463892632 545 False 481 481 82.6710 5 555 1 chr4A.!!$F1 550
11 TraesCS3B01G476700 chr4D 113243325 113243869 544 True 464 464 82.1300 4 555 1 chr4D.!!$R2 551
12 TraesCS3B01G476700 chr2D 639149788 639150363 575 False 379 379 79.9660 2413 2949 1 chr2D.!!$F1 536

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
267 269 0.107606 ACTGTTGTGGCGTTGGTGTA 60.108 50.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2131 0.389948 CTTCGTCCTGCACCTACACC 60.39 60.0 0.0 0.0 0.0 4.16 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
28 29 2.143122 ACAAGCAGTATGTGGTGTTCG 58.857 47.619 0.00 0.00 39.31 3.95
35 36 0.967662 TATGTGGTGTTCGTCGGGAA 59.032 50.000 0.00 0.00 0.00 3.97
46 47 4.005978 TCGGGAAGGCTCCAGGGA 62.006 66.667 0.00 0.00 44.51 4.20
80 82 3.054878 GGAAGCTTGCAATGAACAAGTG 58.945 45.455 13.73 0.00 45.09 3.16
81 83 2.806608 AGCTTGCAATGAACAAGTGG 57.193 45.000 0.00 0.00 45.09 4.00
91 93 1.202758 TGAACAAGTGGCAGGGTACAG 60.203 52.381 0.00 0.00 0.00 2.74
92 94 0.537371 AACAAGTGGCAGGGTACAGC 60.537 55.000 0.00 0.00 0.00 4.40
93 95 1.073025 CAAGTGGCAGGGTACAGCA 59.927 57.895 0.00 0.00 32.52 4.41
97 99 0.821711 GTGGCAGGGTACAGCAACAA 60.822 55.000 6.79 0.00 35.37 2.83
98 100 0.821711 TGGCAGGGTACAGCAACAAC 60.822 55.000 0.00 0.00 32.52 3.32
100 102 1.028905 GCAGGGTACAGCAACAACAA 58.971 50.000 0.00 0.00 0.00 2.83
101 103 1.407258 GCAGGGTACAGCAACAACAAA 59.593 47.619 0.00 0.00 0.00 2.83
104 106 3.068024 CAGGGTACAGCAACAACAAACAT 59.932 43.478 0.00 0.00 0.00 2.71
106 108 4.890581 AGGGTACAGCAACAACAAACATAA 59.109 37.500 0.00 0.00 0.00 1.90
123 125 8.222637 ACAAACATAAAGGGTTTAAGACTAGGT 58.777 33.333 0.00 0.00 36.38 3.08
128 130 4.070681 AGGGTTTAAGACTAGGTAGGCA 57.929 45.455 0.00 0.00 32.29 4.75
132 134 4.141688 GGTTTAAGACTAGGTAGGCAGCAT 60.142 45.833 0.00 0.00 32.29 3.79
214 216 1.609208 CCACACTTTGGGGTGAAGAG 58.391 55.000 0.00 0.00 42.54 2.85
230 232 4.259356 TGAAGAGCTTCATCCTCATTGTG 58.741 43.478 8.76 0.00 43.90 3.33
238 240 1.089920 ATCCTCATTGTGCAGTTCGC 58.910 50.000 0.00 0.00 42.89 4.70
249 251 3.737172 AGTTCGCCGCCATTGCAC 61.737 61.111 0.00 0.00 37.32 4.57
262 264 0.248990 ATTGCACTGTTGTGGCGTTG 60.249 50.000 0.00 0.00 43.97 4.10
267 269 0.107606 ACTGTTGTGGCGTTGGTGTA 60.108 50.000 0.00 0.00 0.00 2.90
273 275 1.007038 TGGCGTTGGTGTAGTCGTC 60.007 57.895 0.00 0.00 0.00 4.20
279 281 2.248487 GTTGGTGTAGTCGTCGTGATC 58.752 52.381 0.00 0.00 0.00 2.92
296 298 2.139917 GATCGTGTGTAAGGTGCAACA 58.860 47.619 3.64 0.00 39.98 3.33
302 304 3.250040 GTGTGTAAGGTGCAACAGGTAAG 59.750 47.826 3.64 0.00 39.98 2.34
329 331 3.454812 CCACATAGGGTACAAGGTTAGCT 59.545 47.826 0.00 0.00 0.00 3.32
341 343 1.308783 GGTTAGCTCACCTTGCAGCC 61.309 60.000 9.97 0.00 36.17 4.85
348 350 2.203394 ACCTTGCAGCCTGTGTGG 60.203 61.111 0.00 0.00 39.35 4.17
359 361 1.470805 GCCTGTGTGGAACCAAACAAC 60.471 52.381 16.28 9.03 42.83 3.32
360 362 1.202245 CCTGTGTGGAACCAAACAACG 60.202 52.381 16.28 7.22 42.83 4.10
361 363 1.470890 CTGTGTGGAACCAAACAACGT 59.529 47.619 16.28 0.00 42.83 3.99
362 364 1.887198 TGTGTGGAACCAAACAACGTT 59.113 42.857 13.68 0.00 40.80 3.99
363 365 3.079578 TGTGTGGAACCAAACAACGTTA 58.920 40.909 13.68 0.00 40.80 3.18
364 366 3.504906 TGTGTGGAACCAAACAACGTTAA 59.495 39.130 13.68 0.00 40.80 2.01
379 381 3.965209 CGTTAACGTGTAGATGTGTGG 57.035 47.619 19.75 0.00 34.11 4.17
383 385 2.163818 ACGTGTAGATGTGTGGGTTG 57.836 50.000 0.00 0.00 0.00 3.77
388 390 2.969262 TGTAGATGTGTGGGTTGAGACA 59.031 45.455 0.00 0.00 0.00 3.41
394 396 1.680735 GTGTGGGTTGAGACAATGCAA 59.319 47.619 0.00 0.00 0.00 4.08
400 402 1.532868 GTTGAGACAATGCAAGACGCT 59.467 47.619 0.00 0.00 43.06 5.07
417 419 1.266124 GCTAAACACCGTGCGCAAAC 61.266 55.000 14.00 0.00 0.00 2.93
419 421 2.061182 TAAACACCGTGCGCAAACCC 62.061 55.000 14.00 0.00 0.00 4.11
438 440 0.835941 CCTCCTCTAATGCAGGCAGT 59.164 55.000 0.00 0.00 0.00 4.40
439 441 1.202627 CCTCCTCTAATGCAGGCAGTC 60.203 57.143 0.00 0.00 0.00 3.51
440 442 1.761784 CTCCTCTAATGCAGGCAGTCT 59.238 52.381 0.00 0.00 0.00 3.24
441 443 1.759445 TCCTCTAATGCAGGCAGTCTC 59.241 52.381 0.00 0.00 0.00 3.36
442 444 1.537776 CCTCTAATGCAGGCAGTCTCG 60.538 57.143 0.00 0.00 0.00 4.04
446 448 1.094073 AATGCAGGCAGTCTCGATGC 61.094 55.000 0.73 0.73 43.09 3.91
449 451 1.521010 CAGGCAGTCTCGATGCAGG 60.521 63.158 11.32 0.00 45.68 4.85
459 461 1.442520 CGATGCAGGCAACCAAACG 60.443 57.895 0.00 0.00 37.17 3.60
462 464 2.050077 GCAGGCAACCAAACGAGC 60.050 61.111 0.00 0.00 37.17 5.03
467 469 1.065600 GCAACCAAACGAGCTGCAA 59.934 52.632 1.02 0.00 33.19 4.08
473 475 2.621055 ACCAAACGAGCTGCAAATGTTA 59.379 40.909 1.02 0.00 0.00 2.41
474 476 3.067461 ACCAAACGAGCTGCAAATGTTAA 59.933 39.130 1.02 0.00 0.00 2.01
475 477 4.047822 CCAAACGAGCTGCAAATGTTAAA 58.952 39.130 1.02 0.00 0.00 1.52
476 478 4.685628 CCAAACGAGCTGCAAATGTTAAAT 59.314 37.500 1.02 0.00 0.00 1.40
505 507 2.282887 TTTTTCCTCGGCCAGGCC 60.283 61.111 22.33 22.33 46.75 5.19
524 527 4.164988 AGGCCTAATTGAGAAGTGTATGCT 59.835 41.667 1.29 0.00 0.00 3.79
529 532 6.148480 CCTAATTGAGAAGTGTATGCTATGCC 59.852 42.308 0.00 0.00 0.00 4.40
532 535 0.868406 GAAGTGTATGCTATGCCGGC 59.132 55.000 22.73 22.73 0.00 6.13
538 541 2.159310 TGTATGCTATGCCGGCAAAAAC 60.159 45.455 36.33 23.80 43.14 2.43
540 544 0.525761 TGCTATGCCGGCAAAAACTC 59.474 50.000 36.33 18.92 36.71 3.01
542 546 1.732405 GCTATGCCGGCAAAAACTCAC 60.732 52.381 36.33 13.22 0.00 3.51
551 555 3.123050 GGCAAAAACTCACATGACAACC 58.877 45.455 0.00 0.00 0.00 3.77
555 559 5.445806 GCAAAAACTCACATGACAACCAAAC 60.446 40.000 0.00 0.00 0.00 2.93
556 560 5.398603 AAAACTCACATGACAACCAAACA 57.601 34.783 0.00 0.00 0.00 2.83
557 561 5.596836 AAACTCACATGACAACCAAACAT 57.403 34.783 0.00 0.00 0.00 2.71
558 562 6.707440 AAACTCACATGACAACCAAACATA 57.293 33.333 0.00 0.00 0.00 2.29
559 563 5.689383 ACTCACATGACAACCAAACATAC 57.311 39.130 0.00 0.00 0.00 2.39
560 564 4.518970 ACTCACATGACAACCAAACATACC 59.481 41.667 0.00 0.00 0.00 2.73
576 580 5.599999 ACATACCCTTAGAGATGTCACAC 57.400 43.478 0.00 0.00 0.00 3.82
582 586 2.347697 TAGAGATGTCACACGCACAC 57.652 50.000 0.00 0.00 0.00 3.82
608 613 1.679680 CATTGAGGTCACCCATGCATC 59.320 52.381 0.00 0.00 0.00 3.91
610 615 1.206811 TGAGGTCACCCATGCATCCA 61.207 55.000 0.00 0.00 0.00 3.41
732 750 8.298854 CAAACCTTGTCTGATGATCATAACAAA 58.701 33.333 21.64 9.64 34.05 2.83
733 751 7.621428 ACCTTGTCTGATGATCATAACAAAG 57.379 36.000 21.64 19.36 34.05 2.77
734 752 7.397221 ACCTTGTCTGATGATCATAACAAAGA 58.603 34.615 21.71 13.15 34.05 2.52
735 753 7.551974 ACCTTGTCTGATGATCATAACAAAGAG 59.448 37.037 21.71 17.53 34.05 2.85
736 754 7.767659 CCTTGTCTGATGATCATAACAAAGAGA 59.232 37.037 21.64 11.85 34.05 3.10
737 755 8.484641 TTGTCTGATGATCATAACAAAGAGAC 57.515 34.615 20.22 16.05 32.55 3.36
739 757 8.096414 TGTCTGATGATCATAACAAAGAGACAA 58.904 33.333 8.54 1.71 0.00 3.18
742 760 9.932699 CTGATGATCATAACAAAGAGACAAATC 57.067 33.333 8.54 0.00 0.00 2.17
745 764 9.676861 ATGATCATAACAAAGAGACAAATCAGA 57.323 29.630 6.36 0.00 0.00 3.27
748 767 8.853077 TCATAACAAAGAGACAAATCAGACAT 57.147 30.769 0.00 0.00 0.00 3.06
779 798 5.441718 AAGAATCTCCTAACCTTCATGCA 57.558 39.130 0.00 0.00 0.00 3.96
780 799 5.643421 AGAATCTCCTAACCTTCATGCAT 57.357 39.130 0.00 0.00 0.00 3.96
781 800 5.374921 AGAATCTCCTAACCTTCATGCATG 58.625 41.667 21.07 21.07 0.00 4.06
782 801 2.923121 TCTCCTAACCTTCATGCATGC 58.077 47.619 22.25 11.82 0.00 4.06
783 802 2.239402 TCTCCTAACCTTCATGCATGCA 59.761 45.455 25.04 25.04 0.00 3.96
793 812 2.776312 CATGCATGCATGTCTTCCTC 57.224 50.000 40.30 9.65 46.20 3.71
797 816 2.092592 TGCATGCATGTCTTCCTCTCAT 60.093 45.455 26.79 0.00 0.00 2.90
798 817 2.950309 GCATGCATGTCTTCCTCTCATT 59.050 45.455 26.79 0.00 0.00 2.57
805 824 3.141398 TGTCTTCCTCTCATTGCACAAC 58.859 45.455 0.00 0.00 0.00 3.32
823 842 6.127925 TGCACAACATATTCTTTGTCTCATCC 60.128 38.462 0.00 0.00 33.59 3.51
825 844 7.362401 GCACAACATATTCTTTGTCTCATCCTT 60.362 37.037 0.00 0.00 33.59 3.36
832 854 7.684937 ATTCTTTGTCTCATCCTTTCTTCTG 57.315 36.000 0.00 0.00 0.00 3.02
877 913 3.454812 TCTCTTCTTATAAGCACCCCACC 59.545 47.826 7.67 0.00 0.00 4.61
878 914 3.186283 TCTTCTTATAAGCACCCCACCA 58.814 45.455 7.67 0.00 0.00 4.17
879 915 3.785887 TCTTCTTATAAGCACCCCACCAT 59.214 43.478 7.67 0.00 0.00 3.55
913 952 0.980231 CCCCACCTCCTCTTCTCCTG 60.980 65.000 0.00 0.00 0.00 3.86
926 965 3.517100 TCTTCTCCTGCTAGCTCATTGTT 59.483 43.478 17.23 0.00 0.00 2.83
927 966 3.533606 TCTCCTGCTAGCTCATTGTTC 57.466 47.619 17.23 0.00 0.00 3.18
928 967 2.833943 TCTCCTGCTAGCTCATTGTTCA 59.166 45.455 17.23 0.00 0.00 3.18
929 968 3.261643 TCTCCTGCTAGCTCATTGTTCAA 59.738 43.478 17.23 0.00 0.00 2.69
930 969 4.005650 CTCCTGCTAGCTCATTGTTCAAA 58.994 43.478 17.23 0.00 0.00 2.69
931 970 4.397420 TCCTGCTAGCTCATTGTTCAAAA 58.603 39.130 17.23 0.00 0.00 2.44
932 971 4.216257 TCCTGCTAGCTCATTGTTCAAAAC 59.784 41.667 17.23 0.00 0.00 2.43
965 1004 8.256611 TCAAACACATATTTTCTGTCTCTAGC 57.743 34.615 0.00 0.00 0.00 3.42
987 1040 1.613836 CTCATTGCCCATAAGCTCCC 58.386 55.000 0.00 0.00 0.00 4.30
988 1041 0.179020 TCATTGCCCATAAGCTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
989 1042 0.466189 CATTGCCCATAAGCTCCCGT 60.466 55.000 0.00 0.00 0.00 5.28
990 1043 0.466189 ATTGCCCATAAGCTCCCGTG 60.466 55.000 0.00 0.00 0.00 4.94
991 1044 1.558167 TTGCCCATAAGCTCCCGTGA 61.558 55.000 0.00 0.00 0.00 4.35
992 1045 1.227674 GCCCATAAGCTCCCGTGAG 60.228 63.158 0.00 0.00 41.84 3.51
1026 1104 2.752238 CTGTCCTCCTCGCCGTCT 60.752 66.667 0.00 0.00 0.00 4.18
1109 1187 3.077556 GGAGAAGGGCTGCTCGGA 61.078 66.667 0.00 0.00 31.95 4.55
1241 1322 0.905337 AGCTCCCGTGGTAAGAAGCT 60.905 55.000 0.00 0.00 0.00 3.74
1248 1341 1.238439 GTGGTAAGAAGCTGCAGCAA 58.762 50.000 38.24 16.44 45.16 3.91
1355 1454 0.108898 CAGTGCTCCGAGTCCTTCAG 60.109 60.000 0.00 0.00 0.00 3.02
1363 1462 0.323908 CGAGTCCTTCAGGAGGGTCT 60.324 60.000 0.00 0.00 46.49 3.85
1470 1578 0.042361 CCGACTCCGAATACGACGAG 60.042 60.000 0.00 0.00 42.66 4.18
1524 1632 2.776913 CCCGTTCGAGAGCTCTCCC 61.777 68.421 32.86 21.23 39.79 4.30
1532 1640 4.500116 GAGCTCTCCCGTCCACGC 62.500 72.222 6.43 0.00 38.18 5.34
1959 2079 1.520342 GCTGGAGCTCGTCATGGAC 60.520 63.158 7.83 0.00 38.21 4.02
1988 2124 1.891919 GCTAATCGATGGCGCCCAA 60.892 57.895 26.77 6.41 36.95 4.12
1990 2126 0.798776 CTAATCGATGGCGCCCAATC 59.201 55.000 26.77 20.04 36.95 2.67
1991 2127 0.605319 TAATCGATGGCGCCCAATCC 60.605 55.000 26.77 7.27 36.95 3.01
1992 2128 4.908687 TCGATGGCGCCCAATCCG 62.909 66.667 26.77 19.02 36.95 4.18
2169 2324 8.816640 TGAGAAAATTCTTTTGGTCTTTATGC 57.183 30.769 0.00 0.00 37.73 3.14
2174 2329 9.705290 AAAATTCTTTTGGTCTTTATGCGTTAT 57.295 25.926 0.00 0.00 0.00 1.89
2177 2332 9.783256 ATTCTTTTGGTCTTTATGCGTTATAAC 57.217 29.630 5.47 5.47 31.11 1.89
2178 2333 8.556213 TCTTTTGGTCTTTATGCGTTATAACT 57.444 30.769 13.56 0.00 31.11 2.24
2179 2334 9.005777 TCTTTTGGTCTTTATGCGTTATAACTT 57.994 29.630 13.56 1.64 31.11 2.66
2202 2357 8.614346 ACTTATAAGTAGACAGAGTAAGCTTCG 58.386 37.037 16.60 0.00 37.52 3.79
2203 2358 8.503458 TTATAAGTAGACAGAGTAAGCTTCGT 57.497 34.615 0.00 0.00 0.00 3.85
2204 2359 9.605275 TTATAAGTAGACAGAGTAAGCTTCGTA 57.395 33.333 0.00 0.00 0.00 3.43
2205 2360 8.680039 ATAAGTAGACAGAGTAAGCTTCGTAT 57.320 34.615 0.00 0.00 0.00 3.06
2206 2361 7.393841 AAGTAGACAGAGTAAGCTTCGTATT 57.606 36.000 0.00 0.00 0.00 1.89
2207 2362 7.393841 AGTAGACAGAGTAAGCTTCGTATTT 57.606 36.000 0.00 0.00 0.00 1.40
2208 2363 7.828712 AGTAGACAGAGTAAGCTTCGTATTTT 58.171 34.615 0.00 0.00 0.00 1.82
2209 2364 8.305317 AGTAGACAGAGTAAGCTTCGTATTTTT 58.695 33.333 0.00 0.00 0.00 1.94
2232 2387 4.587189 CCAGTACTAGGCGCCGGC 62.587 72.222 23.20 19.07 38.90 6.13
2233 2388 4.925576 CAGTACTAGGCGCCGGCG 62.926 72.222 43.13 43.13 41.24 6.46
2266 2421 1.079543 AGATCACTCCACACGCAGC 60.080 57.895 0.00 0.00 0.00 5.25
2302 2460 3.897505 CCCCTTGTCTTTTTCACATCCTT 59.102 43.478 0.00 0.00 0.00 3.36
2490 2659 0.741915 TCGTTGGTTCCAGCAAAACC 59.258 50.000 6.51 7.70 45.30 3.27
2578 2747 4.701956 AACGGATGTTTATTCCAGCAAG 57.298 40.909 0.00 0.00 33.53 4.01
2591 2760 5.441718 TTCCAGCAAGAATCAGAAGGTAT 57.558 39.130 0.00 0.00 0.00 2.73
2700 2873 2.215196 GTCACTGGGTCGTAGCAAAAA 58.785 47.619 0.00 0.00 0.00 1.94
2829 3014 0.753262 CGGCCTATGGTTGTAGCTCT 59.247 55.000 0.00 0.00 0.00 4.09
2915 3122 2.678934 TAGCCCGTCGTTGCCTCT 60.679 61.111 0.85 0.00 0.00 3.69
2924 3131 2.427506 GTCGTTGCCTCTCCTCAAAAT 58.572 47.619 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.081420 ACCACATACTGCTTGTCCTAGAAG 60.081 45.833 0.00 0.00 0.00 2.85
1 2 3.838317 ACCACATACTGCTTGTCCTAGAA 59.162 43.478 0.00 0.00 0.00 2.10
2 3 3.195610 CACCACATACTGCTTGTCCTAGA 59.804 47.826 0.00 0.00 0.00 2.43
13 14 1.346365 CCGACGAACACCACATACTG 58.654 55.000 0.00 0.00 0.00 2.74
14 15 0.245539 CCCGACGAACACCACATACT 59.754 55.000 0.00 0.00 0.00 2.12
19 20 1.666872 CCTTCCCGACGAACACCAC 60.667 63.158 0.00 0.00 0.00 4.16
20 21 2.738480 CCTTCCCGACGAACACCA 59.262 61.111 0.00 0.00 0.00 4.17
28 29 3.787001 CCCTGGAGCCTTCCCGAC 61.787 72.222 0.00 0.00 43.33 4.79
35 36 1.972588 ACTGTAAATCCCTGGAGCCT 58.027 50.000 0.00 0.00 0.00 4.58
46 47 5.016173 TGCAAGCTTCCCATAACTGTAAAT 58.984 37.500 0.00 0.00 0.00 1.40
80 82 0.821711 TGTTGTTGCTGTACCCTGCC 60.822 55.000 0.00 0.00 34.87 4.85
81 83 1.028905 TTGTTGTTGCTGTACCCTGC 58.971 50.000 0.00 0.00 36.19 4.85
91 93 7.492994 TCTTAAACCCTTTATGTTTGTTGTTGC 59.507 33.333 0.00 0.00 36.63 4.17
92 94 8.813282 GTCTTAAACCCTTTATGTTTGTTGTTG 58.187 33.333 0.00 0.00 36.63 3.33
93 95 8.755028 AGTCTTAAACCCTTTATGTTTGTTGTT 58.245 29.630 0.00 0.00 36.63 2.83
97 99 8.222637 ACCTAGTCTTAAACCCTTTATGTTTGT 58.777 33.333 0.00 0.00 36.63 2.83
98 100 8.631480 ACCTAGTCTTAAACCCTTTATGTTTG 57.369 34.615 0.00 0.00 36.63 2.93
100 102 8.546322 CCTACCTAGTCTTAAACCCTTTATGTT 58.454 37.037 0.00 0.00 0.00 2.71
101 103 7.365384 GCCTACCTAGTCTTAAACCCTTTATGT 60.365 40.741 0.00 0.00 0.00 2.29
104 106 6.024893 TGCCTACCTAGTCTTAAACCCTTTA 58.975 40.000 0.00 0.00 0.00 1.85
106 108 4.432316 TGCCTACCTAGTCTTAAACCCTT 58.568 43.478 0.00 0.00 0.00 3.95
132 134 5.181245 GCACAAACTTGGAGTAAGCATCTTA 59.819 40.000 0.00 0.00 40.16 2.10
165 167 1.069049 GCCAACTTCAACCTTGCATGT 59.931 47.619 0.00 0.00 0.00 3.21
214 216 2.089980 ACTGCACAATGAGGATGAAGC 58.910 47.619 0.00 0.00 0.00 3.86
238 240 1.372004 CACAACAGTGCAATGGCGG 60.372 57.895 19.57 9.56 45.35 6.13
249 251 0.586319 CTACACCAACGCCACAACAG 59.414 55.000 0.00 0.00 0.00 3.16
252 254 0.876777 CGACTACACCAACGCCACAA 60.877 55.000 0.00 0.00 0.00 3.33
262 264 0.445436 ACGATCACGACGACTACACC 59.555 55.000 0.00 0.00 42.66 4.16
267 269 1.150827 TACACACGATCACGACGACT 58.849 50.000 0.00 0.00 42.66 4.18
273 275 0.713883 GCACCTTACACACGATCACG 59.286 55.000 0.00 0.00 45.75 4.35
279 281 0.586319 CCTGTTGCACCTTACACACG 59.414 55.000 0.00 0.00 0.00 4.49
296 298 2.119495 CCCTATGTGGTGAGCTTACCT 58.881 52.381 26.35 10.79 41.43 3.08
302 304 2.420129 CCTTGTACCCTATGTGGTGAGC 60.420 54.545 0.00 0.00 39.53 4.26
329 331 1.526686 CACACAGGCTGCAAGGTGA 60.527 57.895 15.89 0.00 35.33 4.02
337 339 0.385390 GTTTGGTTCCACACAGGCTG 59.615 55.000 14.16 14.16 37.29 4.85
338 340 0.033601 TGTTTGGTTCCACACAGGCT 60.034 50.000 6.71 0.00 37.29 4.58
341 343 1.470890 ACGTTGTTTGGTTCCACACAG 59.529 47.619 10.12 4.10 29.96 3.66
359 361 2.664568 CCCACACATCTACACGTTAACG 59.335 50.000 25.68 25.68 46.33 3.18
360 362 3.656559 ACCCACACATCTACACGTTAAC 58.343 45.455 0.00 0.00 0.00 2.01
361 363 4.059511 CAACCCACACATCTACACGTTAA 58.940 43.478 0.00 0.00 0.00 2.01
362 364 3.321396 TCAACCCACACATCTACACGTTA 59.679 43.478 0.00 0.00 0.00 3.18
363 365 2.103432 TCAACCCACACATCTACACGTT 59.897 45.455 0.00 0.00 0.00 3.99
364 366 1.689813 TCAACCCACACATCTACACGT 59.310 47.619 0.00 0.00 0.00 4.49
371 373 2.095059 GCATTGTCTCAACCCACACATC 60.095 50.000 0.00 0.00 0.00 3.06
379 381 1.400242 GCGTCTTGCATTGTCTCAACC 60.400 52.381 0.00 0.00 45.45 3.77
400 402 1.355916 GGTTTGCGCACGGTGTTTA 59.644 52.632 11.12 0.00 0.00 2.01
417 419 1.348008 TGCCTGCATTAGAGGAGGGG 61.348 60.000 3.70 0.00 46.20 4.79
420 422 1.761784 AGACTGCCTGCATTAGAGGAG 59.238 52.381 0.00 0.00 31.48 3.69
438 440 0.250684 TTTGGTTGCCTGCATCGAGA 60.251 50.000 0.00 0.00 0.00 4.04
439 441 0.109597 GTTTGGTTGCCTGCATCGAG 60.110 55.000 0.00 0.00 0.00 4.04
440 442 1.851021 CGTTTGGTTGCCTGCATCGA 61.851 55.000 0.00 0.00 0.00 3.59
441 443 1.442520 CGTTTGGTTGCCTGCATCG 60.443 57.895 0.00 0.00 0.00 3.84
442 444 0.109597 CTCGTTTGGTTGCCTGCATC 60.110 55.000 0.00 0.00 0.00 3.91
446 448 1.283793 CAGCTCGTTTGGTTGCCTG 59.716 57.895 0.00 0.00 0.00 4.85
449 451 0.527385 TTTGCAGCTCGTTTGGTTGC 60.527 50.000 0.00 0.00 40.44 4.17
482 484 1.215382 GGCCGAGGAAAAACATGCC 59.785 57.895 0.00 0.00 0.00 4.40
484 486 0.527565 CCTGGCCGAGGAAAAACATG 59.472 55.000 14.21 0.00 46.33 3.21
485 487 1.250840 GCCTGGCCGAGGAAAAACAT 61.251 55.000 21.37 0.00 46.33 2.71
505 507 6.128715 CGGCATAGCATACACTTCTCAATTAG 60.129 42.308 0.00 0.00 0.00 1.73
506 508 5.696270 CGGCATAGCATACACTTCTCAATTA 59.304 40.000 0.00 0.00 0.00 1.40
508 510 4.060900 CGGCATAGCATACACTTCTCAAT 58.939 43.478 0.00 0.00 0.00 2.57
509 511 3.457234 CGGCATAGCATACACTTCTCAA 58.543 45.455 0.00 0.00 0.00 3.02
512 515 1.541233 GCCGGCATAGCATACACTTCT 60.541 52.381 24.80 0.00 0.00 2.85
524 527 1.610363 TGTGAGTTTTTGCCGGCATA 58.390 45.000 33.25 24.43 0.00 3.14
529 532 2.772568 TGTCATGTGAGTTTTTGCCG 57.227 45.000 0.00 0.00 0.00 5.69
532 535 5.636965 TGTTTGGTTGTCATGTGAGTTTTTG 59.363 36.000 0.00 0.00 0.00 2.44
538 541 4.082787 GGGTATGTTTGGTTGTCATGTGAG 60.083 45.833 0.00 0.00 0.00 3.51
540 544 3.826157 AGGGTATGTTTGGTTGTCATGTG 59.174 43.478 0.00 0.00 0.00 3.21
542 546 5.943416 TCTAAGGGTATGTTTGGTTGTCATG 59.057 40.000 0.00 0.00 0.00 3.07
551 555 6.313905 GTGTGACATCTCTAAGGGTATGTTTG 59.686 42.308 0.00 0.00 32.87 2.93
555 559 4.611943 CGTGTGACATCTCTAAGGGTATG 58.388 47.826 0.00 0.00 0.00 2.39
556 560 3.068307 GCGTGTGACATCTCTAAGGGTAT 59.932 47.826 0.00 0.00 0.00 2.73
557 561 2.426024 GCGTGTGACATCTCTAAGGGTA 59.574 50.000 0.00 0.00 0.00 3.69
558 562 1.204941 GCGTGTGACATCTCTAAGGGT 59.795 52.381 0.00 0.00 0.00 4.34
559 563 1.204704 TGCGTGTGACATCTCTAAGGG 59.795 52.381 0.00 0.00 0.00 3.95
560 564 2.263077 GTGCGTGTGACATCTCTAAGG 58.737 52.381 0.00 0.00 0.00 2.69
582 586 1.868997 GGTGACCTCAATGTGTGCG 59.131 57.895 0.00 0.00 0.00 5.34
608 613 1.333636 TGTTTGGGCTGGGTGTTTGG 61.334 55.000 0.00 0.00 0.00 3.28
610 615 1.334384 GGTGTTTGGGCTGGGTGTTT 61.334 55.000 0.00 0.00 0.00 2.83
700 717 5.125100 TCATCAGACAAGGTTTGATTTGC 57.875 39.130 0.18 0.00 35.63 3.68
732 750 8.908786 TTTAAGTTGATGTCTGATTTGTCTCT 57.091 30.769 0.00 0.00 0.00 3.10
733 751 9.604626 CTTTTAAGTTGATGTCTGATTTGTCTC 57.395 33.333 0.00 0.00 0.00 3.36
734 752 9.342308 TCTTTTAAGTTGATGTCTGATTTGTCT 57.658 29.630 0.00 0.00 0.00 3.41
735 753 9.950680 TTCTTTTAAGTTGATGTCTGATTTGTC 57.049 29.630 0.00 0.00 0.00 3.18
742 760 8.558973 AGGAGATTCTTTTAAGTTGATGTCTG 57.441 34.615 0.00 0.00 0.00 3.51
745 764 9.232473 GGTTAGGAGATTCTTTTAAGTTGATGT 57.768 33.333 0.00 0.00 0.00 3.06
748 767 9.503399 GAAGGTTAGGAGATTCTTTTAAGTTGA 57.497 33.333 0.00 0.00 0.00 3.18
779 798 2.950309 GCAATGAGAGGAAGACATGCAT 59.050 45.455 0.00 0.00 0.00 3.96
780 799 2.290450 TGCAATGAGAGGAAGACATGCA 60.290 45.455 0.00 0.00 0.00 3.96
781 800 2.097142 GTGCAATGAGAGGAAGACATGC 59.903 50.000 0.00 0.00 0.00 4.06
782 801 3.340928 TGTGCAATGAGAGGAAGACATG 58.659 45.455 0.00 0.00 0.00 3.21
783 802 3.708403 TGTGCAATGAGAGGAAGACAT 57.292 42.857 0.00 0.00 0.00 3.06
793 812 7.310664 AGACAAAGAATATGTTGTGCAATGAG 58.689 34.615 4.83 0.00 38.07 2.90
797 816 6.631971 TGAGACAAAGAATATGTTGTGCAA 57.368 33.333 4.83 0.00 38.07 4.08
798 817 6.127925 GGATGAGACAAAGAATATGTTGTGCA 60.128 38.462 4.83 0.00 38.07 4.57
805 824 9.393512 AGAAGAAAGGATGAGACAAAGAATATG 57.606 33.333 0.00 0.00 0.00 1.78
825 844 7.913297 CCAATTAAACGTGTTTTCTCAGAAGAA 59.087 33.333 2.97 0.00 39.78 2.52
832 854 4.866921 AGGCCAATTAAACGTGTTTTCTC 58.133 39.130 5.01 0.00 34.23 2.87
847 870 5.825151 GTGCTTATAAGAAGAGAAGGCCAAT 59.175 40.000 16.85 0.00 0.00 3.16
877 913 1.133792 GGGGTTGGAGATGGGTGTATG 60.134 57.143 0.00 0.00 0.00 2.39
878 914 1.222567 GGGGTTGGAGATGGGTGTAT 58.777 55.000 0.00 0.00 0.00 2.29
879 915 0.178858 TGGGGTTGGAGATGGGTGTA 60.179 55.000 0.00 0.00 0.00 2.90
913 952 5.362556 TGAGTTTTGAACAATGAGCTAGC 57.637 39.130 6.62 6.62 0.00 3.42
926 965 9.868277 AATATGTGTTTGAACTTTGAGTTTTGA 57.132 25.926 0.00 0.00 38.80 2.69
931 970 9.520204 CAGAAAATATGTGTTTGAACTTTGAGT 57.480 29.630 0.00 0.00 0.00 3.41
932 971 9.520204 ACAGAAAATATGTGTTTGAACTTTGAG 57.480 29.630 0.00 0.00 29.79 3.02
964 1003 0.957362 GCTTATGGGCAATGAGGAGC 59.043 55.000 0.00 0.00 0.00 4.70
965 1004 2.502295 GAGCTTATGGGCAATGAGGAG 58.498 52.381 0.00 0.00 34.17 3.69
994 1047 3.803082 CAGGCACGCCATTCACGG 61.803 66.667 11.35 0.00 38.92 4.94
995 1048 3.027170 GACAGGCACGCCATTCACG 62.027 63.158 11.35 0.00 38.92 4.35
1330 1429 3.385384 CTCGGAGCACTGCAGGGA 61.385 66.667 23.23 4.98 0.00 4.20
1398 1500 4.704833 GCCCTGAGCTTCACGGCA 62.705 66.667 15.80 0.00 44.51 5.69
1470 1578 2.124778 GGGCTCTGCTGCTTCTCC 60.125 66.667 0.00 0.00 0.00 3.71
1532 1640 4.143740 AGGAGAACCTGCTCTGGG 57.856 61.111 0.00 0.00 45.92 4.45
1606 1720 2.256158 CGTGTACGCCGTCTCCAA 59.744 61.111 0.00 0.00 0.00 3.53
1959 2079 1.592669 CGATTAGCAGCCACCGAGG 60.593 63.158 0.00 0.00 41.84 4.63
1988 2124 4.157120 GCACCTACACCGGCGGAT 62.157 66.667 35.78 22.33 0.00 4.18
1992 2128 3.702048 TCCTGCACCTACACCGGC 61.702 66.667 0.00 0.00 0.00 6.13
1993 2129 2.264794 GTCCTGCACCTACACCGG 59.735 66.667 0.00 0.00 0.00 5.28
1995 2131 0.389948 CTTCGTCCTGCACCTACACC 60.390 60.000 0.00 0.00 0.00 4.16
2079 2221 1.066573 CCTCCACTTGGCACTGAGTAG 60.067 57.143 0.00 0.00 34.44 2.57
2176 2331 8.614346 CGAAGCTTACTCTGTCTACTTATAAGT 58.386 37.037 21.35 21.35 42.91 2.24
2177 2332 8.614346 ACGAAGCTTACTCTGTCTACTTATAAG 58.386 37.037 11.05 11.05 0.00 1.73
2178 2333 8.503458 ACGAAGCTTACTCTGTCTACTTATAA 57.497 34.615 0.00 0.00 0.00 0.98
2179 2334 9.775854 ATACGAAGCTTACTCTGTCTACTTATA 57.224 33.333 0.00 0.00 0.00 0.98
2180 2335 8.680039 ATACGAAGCTTACTCTGTCTACTTAT 57.320 34.615 0.00 0.00 0.00 1.73
2181 2336 8.503458 AATACGAAGCTTACTCTGTCTACTTA 57.497 34.615 0.00 0.00 0.00 2.24
2182 2337 7.393841 AATACGAAGCTTACTCTGTCTACTT 57.606 36.000 0.00 0.00 0.00 2.24
2183 2338 7.393841 AAATACGAAGCTTACTCTGTCTACT 57.606 36.000 0.00 0.00 0.00 2.57
2184 2339 8.463456 AAAAATACGAAGCTTACTCTGTCTAC 57.537 34.615 0.00 0.00 0.00 2.59
2214 2369 4.587189 CCGGCGCCTAGTACTGGC 62.587 72.222 26.68 20.22 46.42 4.85
2215 2370 4.587189 GCCGGCGCCTAGTACTGG 62.587 72.222 26.68 17.44 0.00 4.00
2216 2371 4.925576 CGCCGGCGCCTAGTACTG 62.926 72.222 38.48 5.99 0.00 2.74
2235 2390 4.521062 GATCTGAGGGCTGCGCGT 62.521 66.667 8.43 0.00 0.00 6.01
2266 2421 3.759618 GACAAGGGGAGAGAGATATACGG 59.240 52.174 0.00 0.00 0.00 4.02
2302 2460 0.604073 TCGTTTAGGATGTGGACGCA 59.396 50.000 0.00 0.00 34.04 5.24
2332 2490 2.399448 CGGCCGCATAGTTTTGTTTTT 58.601 42.857 14.67 0.00 0.00 1.94
2456 2615 2.350192 CCAACGAACCTTTTTGTTTGCC 59.650 45.455 0.00 0.00 37.24 4.52
2490 2659 5.403897 TTTTCTGCTACAACTGTTCTTCG 57.596 39.130 0.00 0.00 0.00 3.79
2624 2793 6.122850 GCTTTTGCTGGAAACATTTTCTTT 57.877 33.333 0.00 0.00 43.35 2.52
2747 2923 4.796231 GTGGTGCGACGGCGATCT 62.796 66.667 18.90 0.00 44.10 2.75
2889 3096 3.766691 GACGGGCTACAAGCGGGA 61.767 66.667 0.00 0.00 43.62 5.14
2915 3122 1.222567 GGAGCCCCCTATTTTGAGGA 58.777 55.000 0.00 0.00 39.15 3.71
2954 3161 3.730761 GTGCTGCAAGTCGGCCAG 61.731 66.667 2.77 0.00 46.56 4.85


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

AutoCloner maintained by Alex Coulton.