Multiple sequence alignment - TraesCS4B01G207900

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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 TraesCS4B01G207900 chr4B 100.000 4229 0 0 1 4229 444843637 444839409 0.000000e+00 7810.0
1 TraesCS4B01G207900 chr4B 85.315 429 46 9 2302 2725 269173089 269172673 1.090000e-115 427.0
2 TraesCS4B01G207900 chr4A 90.033 3291 171 69 1 3210 104701763 104704977 0.000000e+00 4115.0
3 TraesCS4B01G207900 chr4A 95.011 461 15 3 3771 4229 104705585 104706039 0.000000e+00 717.0
4 TraesCS4B01G207900 chr4A 87.479 583 31 15 3195 3770 104704994 104705541 5.970000e-178 634.0
5 TraesCS4B01G207900 chr4A 85.535 318 41 4 2293 2605 273736252 273735935 1.130000e-85 327.0
6 TraesCS4B01G207900 chr4D 92.276 1722 76 22 1604 3297 360100038 360098346 0.000000e+00 2390.0
7 TraesCS4B01G207900 chr4D 92.683 1599 69 25 2 1585 360101591 360100026 0.000000e+00 2261.0
8 TraesCS4B01G207900 chr4D 91.847 1018 34 18 3231 4229 360098347 360097360 0.000000e+00 1375.0
9 TraesCS4B01G207900 chr4D 84.932 438 47 11 2293 2725 252174760 252175183 3.910000e-115 425.0
10 TraesCS4B01G207900 chr4D 90.254 236 23 0 2293 2528 340387976 340388211 4.110000e-80 309.0
11 TraesCS4B01G207900 chr7B 92.962 341 20 4 1420 1758 689339423 689339761 1.060000e-135 494.0
12 TraesCS4B01G207900 chr7B 93.598 328 19 1 2031 2356 689354844 689355171 4.910000e-134 488.0
13 TraesCS4B01G207900 chr5D 91.102 236 21 0 2293 2528 47323524 47323289 1.900000e-83 320.0
14 TraesCS4B01G207900 chr1A 83.776 339 38 10 2392 2725 577589438 577589764 5.310000e-79 305.0
15 TraesCS4B01G207900 chr6A 82.353 340 42 11 2392 2725 29758437 29758764 3.220000e-71 279.0
16 TraesCS4B01G207900 chr3A 86.090 266 20 6 2293 2543 679360309 679360572 1.940000e-68 270.0
17 TraesCS4B01G207900 chr2B 100.000 52 0 0 2760 2811 153587573 153587624 3.480000e-16 97.1
18 TraesCS4B01G207900 chr2A 98.077 52 1 0 2760 2811 101379346 101379397 1.620000e-14 91.6
19 TraesCS4B01G207900 chr2D 96.154 52 2 0 2760 2811 102281133 102281184 7.530000e-13 86.1


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 TraesCS4B01G207900 chr4B 444839409 444843637 4228 True 7810.000000 7810 100.000000 1 4229 1 chr4B.!!$R2 4228
1 TraesCS4B01G207900 chr4A 104701763 104706039 4276 False 1822.000000 4115 90.841000 1 4229 3 chr4A.!!$F1 4228
2 TraesCS4B01G207900 chr4D 360097360 360101591 4231 True 2008.666667 2390 92.268667 2 4229 3 chr4D.!!$R1 4227

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
754 785 0.029577 ATTTCCCCTCTCCCCTCCTC 60.030 60.0 0.0 0.0 0.00 3.71 F
957 1000 0.303796 GAGGCTATTAACAACCGCGC 59.696 55.0 0.0 0.0 0.00 6.86 F
1126 1169 0.742635 CGCTCTTGAAGGAAGGCTCC 60.743 60.0 0.0 0.0 42.81 4.70 F
2028 2130 0.032815 GCCCATCTTCTCCTACGAGC 59.967 60.0 0.0 0.0 35.94 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 1864 0.108233 GAGAAGCAGCAGGAGAGGTG 60.108 60.0 0.0 0.0 39.87 4.00 R
2026 2128 0.593128 GCACAAAGAATCCACACGCT 59.407 50.0 0.0 0.0 0.00 5.07 R
2191 2299 0.743097 GGAGTTTCATCAGCATGGGC 59.257 55.0 0.0 0.0 41.61 5.36 R
3319 3538 0.394080 AGGATTTGGCTCAGCTCAGC 60.394 55.0 0.0 0.0 38.84 4.26 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
55 56 2.667481 ACAAATTTGCATCGCGGAATTG 59.333 40.909 18.12 0.18 31.10 2.32
143 147 3.759086 GAGAAGTTGGGGAGAACAAATCC 59.241 47.826 0.00 0.00 35.99 3.01
144 148 2.200373 AGTTGGGGAGAACAAATCCG 57.800 50.000 0.00 0.00 37.75 4.18
206 215 1.686566 CGCGTACACAGCCACATGAG 61.687 60.000 0.00 0.00 0.00 2.90
293 306 3.846360 CCAATCTCGGTATTATCCCGTC 58.154 50.000 0.00 0.00 45.63 4.79
316 329 4.498513 CGGATATTCCAACAGTGCTACGTA 60.499 45.833 0.00 0.00 35.91 3.57
344 357 0.686224 CCACCAACCAAACCATGCAT 59.314 50.000 0.00 0.00 0.00 3.96
351 364 2.440409 ACCAAACCATGCATGAGTCTC 58.560 47.619 28.31 0.00 0.00 3.36
359 372 2.130272 TGCATGAGTCTCGTACCTCT 57.870 50.000 0.00 0.00 0.00 3.69
402 417 5.530543 TCCATTTTTCACCATTTTTGCCTTC 59.469 36.000 0.00 0.00 0.00 3.46
407 422 7.459795 TTTTCACCATTTTTGCCTTCTTTTT 57.540 28.000 0.00 0.00 0.00 1.94
411 426 5.469760 CACCATTTTTGCCTTCTTTTTAGGG 59.530 40.000 0.00 0.00 33.19 3.53
413 428 6.044287 ACCATTTTTGCCTTCTTTTTAGGGAT 59.956 34.615 0.00 0.00 32.80 3.85
415 430 7.094677 CCATTTTTGCCTTCTTTTTAGGGATTG 60.095 37.037 0.00 0.00 32.80 2.67
426 441 3.520290 TTAGGGATTGTGTGACTAGCG 57.480 47.619 0.00 0.00 0.00 4.26
438 453 3.427528 TGTGACTAGCGTTTCATCGTTTC 59.572 43.478 0.00 0.00 0.00 2.78
453 468 3.637432 TCGTTTCGAAGCCGTAGTTTTA 58.363 40.909 15.84 0.00 37.05 1.52
496 511 4.498241 GTTCTTTCTTTGGATCATTGGGC 58.502 43.478 0.00 0.00 0.00 5.36
583 598 3.730761 GGCACGAGCAAGCACCTG 61.731 66.667 7.26 0.00 44.61 4.00
584 599 4.395583 GCACGAGCAAGCACCTGC 62.396 66.667 0.00 0.00 42.97 4.85
585 600 2.974148 CACGAGCAAGCACCTGCA 60.974 61.111 8.00 0.00 45.18 4.41
586 601 2.203195 ACGAGCAAGCACCTGCAA 60.203 55.556 8.00 0.00 45.18 4.08
745 771 1.064166 CATGACAGCCATTTCCCCTCT 60.064 52.381 0.00 0.00 31.94 3.69
754 785 0.029577 ATTTCCCCTCTCCCCTCCTC 60.030 60.000 0.00 0.00 0.00 3.71
769 800 5.496168 TCCCCTCCTCCAAGAAATAAGAAAT 59.504 40.000 0.00 0.00 0.00 2.17
847 882 0.626574 GGAGGGGGTAATTCAGGGGT 60.627 60.000 0.00 0.00 0.00 4.95
864 899 4.158394 CAGGGGTGACGAAATGATGAAAAT 59.842 41.667 0.00 0.00 0.00 1.82
865 900 4.158394 AGGGGTGACGAAATGATGAAAATG 59.842 41.667 0.00 0.00 0.00 2.32
866 901 4.157656 GGGGTGACGAAATGATGAAAATGA 59.842 41.667 0.00 0.00 0.00 2.57
871 906 8.003784 GGTGACGAAATGATGAAAATGAAAAAC 58.996 33.333 0.00 0.00 0.00 2.43
872 907 7.731302 GTGACGAAATGATGAAAATGAAAAACG 59.269 33.333 0.00 0.00 0.00 3.60
873 908 6.580476 ACGAAATGATGAAAATGAAAAACGC 58.420 32.000 0.00 0.00 0.00 4.84
956 999 0.935196 GGAGGCTATTAACAACCGCG 59.065 55.000 0.00 0.00 0.00 6.46
957 1000 0.303796 GAGGCTATTAACAACCGCGC 59.696 55.000 0.00 0.00 0.00 6.86
958 1001 1.011574 GGCTATTAACAACCGCGCG 60.012 57.895 25.67 25.67 0.00 6.86
959 1002 1.650238 GCTATTAACAACCGCGCGC 60.650 57.895 27.36 23.91 0.00 6.86
960 1003 1.366030 CTATTAACAACCGCGCGCG 60.366 57.895 43.73 43.73 39.44 6.86
961 1004 3.423077 TATTAACAACCGCGCGCGC 62.423 57.895 45.06 42.65 38.24 6.86
1077 1120 1.528309 CCCGCTCTCCCTCTCTCTC 60.528 68.421 0.00 0.00 0.00 3.20
1083 1126 2.412591 CTCTCCCTCTCTCTCTCTCCT 58.587 57.143 0.00 0.00 0.00 3.69
1084 1127 2.370189 CTCTCCCTCTCTCTCTCTCCTC 59.630 59.091 0.00 0.00 0.00 3.71
1085 1128 1.421646 CTCCCTCTCTCTCTCTCCTCC 59.578 61.905 0.00 0.00 0.00 4.30
1126 1169 0.742635 CGCTCTTGAAGGAAGGCTCC 60.743 60.000 0.00 0.00 42.81 4.70
1149 1192 1.521616 CTCTGCCTTCTGCTCTCCC 59.478 63.158 0.00 0.00 42.00 4.30
1424 1475 1.091771 ATCGAACGGCCTGCTGATTG 61.092 55.000 4.70 0.00 0.00 2.67
1429 1480 1.237285 ACGGCCTGCTGATTGTTGAC 61.237 55.000 4.70 0.00 0.00 3.18
1498 1555 1.601171 CTGCCTCAAGGTCCAGGAG 59.399 63.158 0.00 0.82 37.57 3.69
1572 1629 4.757149 GCCACTCGCCATTTATTCTCTTAT 59.243 41.667 0.00 0.00 0.00 1.73
1573 1630 5.239525 GCCACTCGCCATTTATTCTCTTATT 59.760 40.000 0.00 0.00 0.00 1.40
1574 1631 6.238759 GCCACTCGCCATTTATTCTCTTATTT 60.239 38.462 0.00 0.00 0.00 1.40
1575 1632 7.041372 GCCACTCGCCATTTATTCTCTTATTTA 60.041 37.037 0.00 0.00 0.00 1.40
1576 1633 9.003658 CCACTCGCCATTTATTCTCTTATTTAT 57.996 33.333 0.00 0.00 0.00 1.40
1593 1650 9.801873 TCTTATTTATTTATGTCTGCCTTTTGC 57.198 29.630 0.00 0.00 41.77 3.68
1594 1651 9.807649 CTTATTTATTTATGTCTGCCTTTTGCT 57.192 29.630 0.00 0.00 42.00 3.91
1595 1652 9.801873 TTATTTATTTATGTCTGCCTTTTGCTC 57.198 29.630 0.00 0.00 42.00 4.26
1596 1653 7.466746 TTTATTTATGTCTGCCTTTTGCTCT 57.533 32.000 0.00 0.00 42.00 4.09
1597 1654 8.574251 TTTATTTATGTCTGCCTTTTGCTCTA 57.426 30.769 0.00 0.00 42.00 2.43
1598 1655 8.574251 TTATTTATGTCTGCCTTTTGCTCTAA 57.426 30.769 0.00 0.00 42.00 2.10
1599 1656 7.651027 ATTTATGTCTGCCTTTTGCTCTAAT 57.349 32.000 0.00 0.00 42.00 1.73
1600 1657 7.466746 TTTATGTCTGCCTTTTGCTCTAATT 57.533 32.000 0.00 0.00 42.00 1.40
1601 1658 5.990120 ATGTCTGCCTTTTGCTCTAATTT 57.010 34.783 0.00 0.00 42.00 1.82
1602 1659 5.789643 TGTCTGCCTTTTGCTCTAATTTT 57.210 34.783 0.00 0.00 42.00 1.82
1810 1904 3.441922 TCATCTCCTCTCGTTTCTCAGTG 59.558 47.826 0.00 0.00 0.00 3.66
1812 1906 2.554462 TCTCCTCTCGTTTCTCAGTGTG 59.446 50.000 0.00 0.00 0.00 3.82
1813 1907 1.000163 TCCTCTCGTTTCTCAGTGTGC 60.000 52.381 0.00 0.00 0.00 4.57
1818 1912 2.058798 TCGTTTCTCAGTGTGCGAATC 58.941 47.619 0.00 0.00 0.00 2.52
1885 1979 5.378230 TGATTGAGAAGCTGGGTATTGAT 57.622 39.130 0.00 0.00 0.00 2.57
2026 2128 1.063942 TGAGCCCATCTTCTCCTACGA 60.064 52.381 0.00 0.00 0.00 3.43
2028 2130 0.032815 GCCCATCTTCTCCTACGAGC 59.967 60.000 0.00 0.00 35.94 5.03
2045 2153 0.593128 AGCGTGTGGATTCTTTGTGC 59.407 50.000 0.00 0.00 0.00 4.57
2077 2185 7.051000 GCTCTAACATCTTCCTGTATTTCCTT 58.949 38.462 0.00 0.00 0.00 3.36
2087 2195 3.944015 CCTGTATTTCCTTCTTGCCTCTG 59.056 47.826 0.00 0.00 0.00 3.35
2131 2239 1.338674 CCCTACGACAACATCAAGCCA 60.339 52.381 0.00 0.00 0.00 4.75
2143 2251 1.672356 CAAGCCAGACCCCGTTCTG 60.672 63.158 0.00 0.00 42.46 3.02
2170 2278 3.311871 AGATTCTCAAGAACATGCGCATC 59.688 43.478 22.51 11.11 36.80 3.91
2183 2291 1.951130 CGCATCCGCAAGCTCGTAT 60.951 57.895 0.00 0.00 38.40 3.06
2191 2299 0.811616 GCAAGCTCGTATGTCCCCTG 60.812 60.000 0.00 0.00 0.00 4.45
2199 2307 1.697394 TATGTCCCCTGCCCATGCT 60.697 57.895 0.00 0.00 38.71 3.79
2209 2317 1.404391 CTGCCCATGCTGATGAAACTC 59.596 52.381 0.00 0.00 38.61 3.01
2486 2594 0.676466 TCCTATGCAAGCCCAACGTG 60.676 55.000 0.00 0.00 0.00 4.49
2545 2653 1.553704 CCCTTACAAGGCGGTAAGTCT 59.446 52.381 22.04 0.00 45.57 3.24
2555 2663 2.223377 GGCGGTAAGTCTTGACAGTTTG 59.777 50.000 3.49 0.00 0.00 2.93
2575 2683 6.710744 AGTTTGAGTTACCAGAACATTCGAAT 59.289 34.615 4.39 4.39 0.00 3.34
2576 2684 7.876068 AGTTTGAGTTACCAGAACATTCGAATA 59.124 33.333 10.97 0.00 0.00 1.75
2577 2685 7.591006 TTGAGTTACCAGAACATTCGAATAC 57.409 36.000 10.97 5.76 0.00 1.89
2610 2718 4.494526 GCAGCATTTCAGTTTTGTGTTTGG 60.495 41.667 0.00 0.00 0.00 3.28
2621 2729 0.461516 TGTGTTTGGCCGTACGTCAA 60.462 50.000 15.21 14.80 0.00 3.18
2626 2734 2.738314 GTTTGGCCGTACGTCAACTAAT 59.262 45.455 15.21 0.00 0.00 1.73
2627 2735 3.865011 TTGGCCGTACGTCAACTAATA 57.135 42.857 15.21 0.00 0.00 0.98
2629 2737 3.510719 TGGCCGTACGTCAACTAATAAC 58.489 45.455 15.21 0.00 0.00 1.89
2630 2738 2.531508 GGCCGTACGTCAACTAATAACG 59.468 50.000 15.21 0.00 41.93 3.18
2631 2739 3.425404 GCCGTACGTCAACTAATAACGA 58.575 45.455 15.21 0.00 39.59 3.85
2632 2740 3.851403 GCCGTACGTCAACTAATAACGAA 59.149 43.478 15.21 0.00 39.59 3.85
2633 2741 4.323336 GCCGTACGTCAACTAATAACGAAA 59.677 41.667 15.21 0.00 39.59 3.46
2634 2742 5.004726 GCCGTACGTCAACTAATAACGAAAT 59.995 40.000 15.21 0.00 39.59 2.17
2635 2743 6.454186 GCCGTACGTCAACTAATAACGAAATT 60.454 38.462 15.21 0.00 39.59 1.82
2692 2804 2.644418 GTGCGCAACATTCAGGCA 59.356 55.556 14.00 0.00 0.00 4.75
2704 2816 0.895100 TTCAGGCAGGCAAGCGAATT 60.895 50.000 0.00 0.00 34.64 2.17
2993 3105 2.182537 CTTCAGCATTTGCCGGGC 59.817 61.111 13.32 13.32 43.38 6.13
3088 3206 3.181483 CGGGCCGGTCCTAATATATGTAC 60.181 52.174 25.54 0.00 34.39 2.90
3093 3218 6.097270 GGCCGGTCCTAATATATGTACATGTA 59.903 42.308 18.81 16.18 0.00 2.29
3125 3250 9.979270 CAGATCTTTGCTTGTAAATTACTACTG 57.021 33.333 4.67 0.00 0.00 2.74
3131 3256 6.942976 TGCTTGTAAATTACTACTGCTAGGT 58.057 36.000 4.67 0.00 0.00 3.08
3134 3259 7.484993 TTGTAAATTACTACTGCTAGGTGGA 57.515 36.000 4.67 0.00 0.00 4.02
3136 3261 8.086143 TGTAAATTACTACTGCTAGGTGGAAT 57.914 34.615 4.67 0.00 0.00 3.01
3249 3468 6.183360 GCATGTCTCCTCTGAATAACTGAAAC 60.183 42.308 0.00 0.00 0.00 2.78
3250 3469 6.419484 TGTCTCCTCTGAATAACTGAAACA 57.581 37.500 0.00 0.00 0.00 2.83
3252 3471 6.183360 TGTCTCCTCTGAATAACTGAAACACA 60.183 38.462 0.00 0.00 0.00 3.72
3253 3472 6.146347 GTCTCCTCTGAATAACTGAAACACAC 59.854 42.308 0.00 0.00 0.00 3.82
3258 3477 7.201732 CCTCTGAATAACTGAAACACACAAACT 60.202 37.037 0.00 0.00 0.00 2.66
3259 3478 7.471721 TCTGAATAACTGAAACACACAAACTG 58.528 34.615 0.00 0.00 0.00 3.16
3260 3479 7.335673 TCTGAATAACTGAAACACACAAACTGA 59.664 33.333 0.00 0.00 0.00 3.41
3261 3480 7.247728 TGAATAACTGAAACACACAAACTGAC 58.752 34.615 0.00 0.00 0.00 3.51
3262 3481 6.751514 ATAACTGAAACACACAAACTGACA 57.248 33.333 0.00 0.00 0.00 3.58
3263 3482 4.419522 ACTGAAACACACAAACTGACAC 57.580 40.909 0.00 0.00 0.00 3.67
3264 3483 3.818210 ACTGAAACACACAAACTGACACA 59.182 39.130 0.00 0.00 0.00 3.72
3265 3484 4.153958 TGAAACACACAAACTGACACAC 57.846 40.909 0.00 0.00 0.00 3.82
3266 3485 3.818210 TGAAACACACAAACTGACACACT 59.182 39.130 0.00 0.00 0.00 3.55
3268 3487 3.052455 ACACACAAACTGACACACTGA 57.948 42.857 0.00 0.00 0.00 3.41
3285 3504 4.063689 CACTGATGTCTCTCACTTTGCTT 58.936 43.478 0.00 0.00 0.00 3.91
3307 3526 7.066645 TGCTTTCATTTCTCCTGTATCTTGATG 59.933 37.037 0.00 0.00 0.00 3.07
3308 3527 6.932356 TTCATTTCTCCTGTATCTTGATGC 57.068 37.500 0.00 0.00 0.00 3.91
3309 3528 5.371526 TCATTTCTCCTGTATCTTGATGCC 58.628 41.667 0.00 0.00 0.00 4.40
3310 3529 3.845781 TTCTCCTGTATCTTGATGCCC 57.154 47.619 0.00 0.00 0.00 5.36
3311 3530 2.050144 TCTCCTGTATCTTGATGCCCC 58.950 52.381 0.00 0.00 0.00 5.80
3312 3531 0.758734 TCCTGTATCTTGATGCCCCG 59.241 55.000 0.00 0.00 0.00 5.73
3313 3532 0.250467 CCTGTATCTTGATGCCCCGG 60.250 60.000 0.00 0.00 0.00 5.73
3314 3533 0.250467 CTGTATCTTGATGCCCCGGG 60.250 60.000 15.80 15.80 0.00 5.73
3315 3534 0.692756 TGTATCTTGATGCCCCGGGA 60.693 55.000 26.32 1.94 0.00 5.14
3316 3535 0.035458 GTATCTTGATGCCCCGGGAG 59.965 60.000 26.32 13.96 0.00 4.30
3317 3536 1.768684 TATCTTGATGCCCCGGGAGC 61.769 60.000 26.32 24.18 0.00 4.70
3318 3537 3.801997 CTTGATGCCCCGGGAGCT 61.802 66.667 26.32 13.27 0.00 4.09
3319 3538 4.113815 TTGATGCCCCGGGAGCTG 62.114 66.667 26.32 5.97 0.00 4.24
3705 3930 0.746659 ACCAAACTTGCAAGCCAGAC 59.253 50.000 26.27 0.00 0.00 3.51
3706 3931 0.032540 CCAAACTTGCAAGCCAGACC 59.967 55.000 26.27 0.00 0.00 3.85
3721 3949 0.985490 AGACCATGAGGGAGAAGGGC 60.985 60.000 0.00 0.00 41.15 5.19
3952 4227 2.356382 CGAGACCTCCAGTGTCATCTAC 59.644 54.545 0.00 0.00 38.70 2.59
3953 4228 3.626930 GAGACCTCCAGTGTCATCTACT 58.373 50.000 0.00 0.00 38.63 2.57
3954 4229 3.626930 AGACCTCCAGTGTCATCTACTC 58.373 50.000 0.00 0.00 35.15 2.59
3955 4230 2.691011 GACCTCCAGTGTCATCTACTCC 59.309 54.545 0.00 0.00 32.91 3.85
3956 4231 2.313342 ACCTCCAGTGTCATCTACTCCT 59.687 50.000 0.00 0.00 0.00 3.69
3957 4232 3.528078 ACCTCCAGTGTCATCTACTCCTA 59.472 47.826 0.00 0.00 0.00 2.94
3964 4239 6.096036 CAGTGTCATCTACTCCTAGTTGTTG 58.904 44.000 0.00 0.00 0.00 3.33
4045 4321 3.067180 ACAAAGCCACAGAAATGTCACAG 59.933 43.478 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.095161 CGATATCTACCTCGCCCACTTC 60.095 54.545 0.34 0.00 0.00 3.01
143 147 2.235016 TCTTCCCCCATTTGAACAACG 58.765 47.619 0.00 0.00 0.00 4.10
144 148 3.006859 CCTTCTTCCCCCATTTGAACAAC 59.993 47.826 0.00 0.00 0.00 3.32
293 306 2.794910 CGTAGCACTGTTGGAATATCCG 59.205 50.000 0.00 0.00 40.17 4.18
316 329 5.209659 TGGTTTGGTTGGTGGTAAATACTT 58.790 37.500 0.00 0.00 0.00 2.24
344 357 1.174783 GGCAAGAGGTACGAGACTCA 58.825 55.000 2.82 0.00 36.20 3.41
351 364 1.066143 AGACCAATGGCAAGAGGTACG 60.066 52.381 0.00 0.00 33.77 3.67
359 372 5.186256 TGGAGTAATTAGACCAATGGCAA 57.814 39.130 0.00 0.00 0.00 4.52
402 417 5.163854 CGCTAGTCACACAATCCCTAAAAAG 60.164 44.000 0.00 0.00 0.00 2.27
407 422 2.453521 ACGCTAGTCACACAATCCCTA 58.546 47.619 0.00 0.00 0.00 3.53
411 426 4.490959 CGATGAAACGCTAGTCACACAATC 60.491 45.833 0.00 0.00 0.00 2.67
413 428 2.729360 CGATGAAACGCTAGTCACACAA 59.271 45.455 0.00 0.00 0.00 3.33
415 430 2.325761 ACGATGAAACGCTAGTCACAC 58.674 47.619 0.00 0.00 36.70 3.82
426 441 1.193874 ACGGCTTCGAAACGATGAAAC 59.806 47.619 23.40 0.00 35.23 2.78
438 453 1.856597 CCGGATAAAACTACGGCTTCG 59.143 52.381 0.00 0.00 39.85 3.79
453 468 4.456806 GCAAATAGCGGTCCGGAT 57.543 55.556 14.38 0.00 0.00 4.18
496 511 3.349006 GCACCGTGACAGCTGTGG 61.349 66.667 27.27 21.69 0.00 4.17
567 582 4.395583 GCAGGTGCTTGCTCGTGC 62.396 66.667 20.67 20.67 40.89 5.34
577 592 2.187599 GACCGTGACATTGCAGGTGC 62.188 60.000 0.00 0.00 42.50 5.01
578 593 0.603707 AGACCGTGACATTGCAGGTG 60.604 55.000 0.00 0.00 35.00 4.00
579 594 0.320771 GAGACCGTGACATTGCAGGT 60.321 55.000 0.00 0.00 38.00 4.00
580 595 1.021390 GGAGACCGTGACATTGCAGG 61.021 60.000 0.00 0.00 0.00 4.85
581 596 0.036952 AGGAGACCGTGACATTGCAG 60.037 55.000 0.00 0.00 0.00 4.41
582 597 0.037326 GAGGAGACCGTGACATTGCA 60.037 55.000 0.00 0.00 0.00 4.08
583 598 0.741221 GGAGGAGACCGTGACATTGC 60.741 60.000 0.00 0.00 0.00 3.56
584 599 0.458543 CGGAGGAGACCGTGACATTG 60.459 60.000 0.00 0.00 46.70 2.82
585 600 1.890894 CGGAGGAGACCGTGACATT 59.109 57.895 0.00 0.00 46.70 2.71
586 601 3.604629 CGGAGGAGACCGTGACAT 58.395 61.111 0.00 0.00 46.70 3.06
603 619 4.888038 AAGAGTTGTTCAACGGGTTAAC 57.112 40.909 9.54 0.00 0.00 2.01
671 687 1.006832 GCTTCGCACGATAACCATGT 58.993 50.000 0.00 0.00 0.00 3.21
745 771 4.088634 TCTTATTTCTTGGAGGAGGGGA 57.911 45.455 0.00 0.00 0.00 4.81
754 785 7.092716 CAGGGTGTTCATTTCTTATTTCTTGG 58.907 38.462 0.00 0.00 0.00 3.61
769 800 0.399949 AGGACAGGACAGGGTGTTCA 60.400 55.000 0.00 0.00 0.00 3.18
810 843 3.103911 GTCCGTTGTCGCTCGTGG 61.104 66.667 0.00 0.00 35.54 4.94
847 882 7.566688 GCGTTTTTCATTTTCATCATTTCGTCA 60.567 33.333 0.00 0.00 0.00 4.35
958 1001 1.418342 TTAATTGGTCGAGCGAGCGC 61.418 55.000 15.93 6.78 44.68 5.92
959 1002 0.297820 GTTAATTGGTCGAGCGAGCG 59.702 55.000 15.93 0.00 44.68 5.03
960 1003 1.641577 AGTTAATTGGTCGAGCGAGC 58.358 50.000 14.43 14.43 42.37 5.03
961 1004 3.791887 CACTAGTTAATTGGTCGAGCGAG 59.208 47.826 10.80 0.00 0.00 5.03
962 1005 3.766151 CACTAGTTAATTGGTCGAGCGA 58.234 45.455 7.07 7.07 0.00 4.93
963 1006 2.281762 GCACTAGTTAATTGGTCGAGCG 59.718 50.000 10.46 0.00 0.00 5.03
969 1012 4.526970 CCCATCAGCACTAGTTAATTGGT 58.473 43.478 0.00 0.00 0.00 3.67
1077 1120 1.953017 CGAGGCGTATGGAGGAGAG 59.047 63.158 0.00 0.00 0.00 3.20
1083 1126 1.756950 AAGAGGCGAGGCGTATGGA 60.757 57.895 0.00 0.00 0.00 3.41
1084 1127 1.592669 CAAGAGGCGAGGCGTATGG 60.593 63.158 0.00 0.00 0.00 2.74
1085 1128 0.596083 CTCAAGAGGCGAGGCGTATG 60.596 60.000 0.00 0.00 0.00 2.39
1126 1169 4.613929 GCAGAAGGCAGAGGTCTG 57.386 61.111 2.37 2.37 46.40 3.51
1205 1251 6.039941 CAGAGAACAGGACCATACCTACTAAG 59.960 46.154 0.00 0.00 38.32 2.18
1279 1325 2.314647 TTACTGACAAGCACGCGGC 61.315 57.895 12.47 11.61 45.30 6.53
1424 1475 2.576615 AGAACTGCAGAAAGGGTCAAC 58.423 47.619 23.35 0.00 0.00 3.18
1429 1480 2.294512 GGTGAAAGAACTGCAGAAAGGG 59.705 50.000 23.35 0.00 0.00 3.95
1498 1555 1.556451 AGGAGGCAATCAAATTTGGGC 59.444 47.619 17.90 17.26 0.00 5.36
1602 1659 9.333724 GGAGGAAACACGGAGATATAAATAAAA 57.666 33.333 0.00 0.00 0.00 1.52
1617 1707 4.814771 AGAGTTGTAAAAGGAGGAAACACG 59.185 41.667 0.00 0.00 0.00 4.49
1770 1864 0.108233 GAGAAGCAGCAGGAGAGGTG 60.108 60.000 0.00 0.00 39.87 4.00
1810 1904 4.554973 GCATTCAGTTTAACAGATTCGCAC 59.445 41.667 0.00 0.00 0.00 5.34
1812 1906 4.722194 TGCATTCAGTTTAACAGATTCGC 58.278 39.130 0.00 0.00 0.00 4.70
1813 1907 6.317088 ACATGCATTCAGTTTAACAGATTCG 58.683 36.000 0.00 0.00 0.00 3.34
1852 1946 7.157347 CCAGCTTCTCAATCATGTAAGCTATA 58.843 38.462 15.47 0.00 45.96 1.31
1853 1947 5.996513 CCAGCTTCTCAATCATGTAAGCTAT 59.003 40.000 15.47 0.71 45.96 2.97
1854 1948 5.363101 CCAGCTTCTCAATCATGTAAGCTA 58.637 41.667 15.47 0.00 45.96 3.32
1865 1959 5.131642 TCTCATCAATACCCAGCTTCTCAAT 59.868 40.000 0.00 0.00 0.00 2.57
1885 1979 3.685139 AGGTTTTCGATCTTGCTCTCA 57.315 42.857 0.00 0.00 0.00 3.27
2026 2128 0.593128 GCACAAAGAATCCACACGCT 59.407 50.000 0.00 0.00 0.00 5.07
2028 2130 3.067106 AGTAGCACAAAGAATCCACACG 58.933 45.455 0.00 0.00 0.00 4.49
2045 2153 5.359576 ACAGGAAGATGTTAGAGCAGAGTAG 59.640 44.000 0.00 0.00 0.00 2.57
2077 2185 1.141657 ACAAAGCTGTCAGAGGCAAGA 59.858 47.619 3.32 0.00 0.00 3.02
2131 2239 0.832135 TCTGCTTCAGAACGGGGTCT 60.832 55.000 0.00 0.00 37.57 3.85
2143 2251 4.660105 GCATGTTCTTGAGAATCTGCTTC 58.340 43.478 16.64 0.00 39.30 3.86
2170 2278 1.883084 GGGACATACGAGCTTGCGG 60.883 63.158 0.00 0.00 35.12 5.69
2183 2291 4.051167 CAGCATGGGCAGGGGACA 62.051 66.667 0.00 0.00 44.61 4.02
2191 2299 0.743097 GGAGTTTCATCAGCATGGGC 59.257 55.000 0.00 0.00 41.61 5.36
2209 2317 0.947244 GCCATTTGCTCCGAGTATGG 59.053 55.000 16.09 16.09 38.98 2.74
2545 2653 5.492895 TGTTCTGGTAACTCAAACTGTCAA 58.507 37.500 0.00 0.00 37.61 3.18
2547 2655 6.564125 CGAATGTTCTGGTAACTCAAACTGTC 60.564 42.308 0.00 0.00 37.61 3.51
2555 2663 9.530633 AATAGTATTCGAATGTTCTGGTAACTC 57.469 33.333 20.87 0.00 37.61 3.01
2575 2683 7.921786 ACTGAAATGCTGCAAGTAAATAGTA 57.078 32.000 6.36 0.00 35.30 1.82
2576 2684 6.824305 ACTGAAATGCTGCAAGTAAATAGT 57.176 33.333 6.36 2.63 35.30 2.12
2577 2685 8.430063 CAAAACTGAAATGCTGCAAGTAAATAG 58.570 33.333 6.36 2.00 35.30 1.73
2610 2718 3.425404 TCGTTATTAGTTGACGTACGGC 58.575 45.455 21.06 18.72 37.95 5.68
2626 2734 9.971744 GGTAATTAAGCGAGTTTAATTTCGTTA 57.028 29.630 18.05 3.07 41.23 3.18
2627 2735 8.885302 GGTAATTAAGCGAGTTTAATTTCGTT 57.115 30.769 18.05 2.82 41.23 3.85
2646 2758 4.201685 CGTCGAAGAAAATCTGCGGTAATT 60.202 41.667 7.84 0.00 45.45 1.40
2647 2759 3.306166 CGTCGAAGAAAATCTGCGGTAAT 59.694 43.478 7.84 0.00 45.45 1.89
2692 2804 2.036256 AGGCCAATTCGCTTGCCT 59.964 55.556 5.01 0.00 36.88 4.75
2986 3098 1.377987 GGATACTGTTTGCCCGGCA 60.378 57.895 8.43 8.43 36.47 5.69
2993 3105 4.115516 CTCCTCGTGATGGATACTGTTTG 58.884 47.826 0.00 0.00 32.56 2.93
3088 3206 6.202379 ACAAGCAAAGATCTGATCGATACATG 59.798 38.462 11.73 10.70 30.84 3.21
3093 3218 7.798596 ATTTACAAGCAAAGATCTGATCGAT 57.201 32.000 11.73 0.00 34.25 3.59
3147 3274 3.817084 GCTTACAAGTAACCCCGTTCTTT 59.183 43.478 0.00 0.00 0.00 2.52
3150 3277 1.728425 CGCTTACAAGTAACCCCGTTC 59.272 52.381 0.00 0.00 0.00 3.95
3249 3468 3.374988 ACATCAGTGTGTCAGTTTGTGTG 59.625 43.478 0.00 0.00 37.14 3.82
3250 3469 3.609853 ACATCAGTGTGTCAGTTTGTGT 58.390 40.909 0.00 0.00 37.14 3.72
3259 3478 3.932545 AGTGAGAGACATCAGTGTGTC 57.067 47.619 14.37 14.37 46.09 3.67
3260 3479 4.375272 CAAAGTGAGAGACATCAGTGTGT 58.625 43.478 0.00 0.00 39.09 3.72
3261 3480 3.186001 GCAAAGTGAGAGACATCAGTGTG 59.814 47.826 0.00 0.00 39.80 3.82
3262 3481 3.070734 AGCAAAGTGAGAGACATCAGTGT 59.929 43.478 0.00 0.00 42.49 3.55
3263 3482 3.661944 AGCAAAGTGAGAGACATCAGTG 58.338 45.455 0.00 0.00 33.12 3.66
3264 3483 4.348863 AAGCAAAGTGAGAGACATCAGT 57.651 40.909 0.00 0.00 34.25 3.41
3265 3484 4.753610 TGAAAGCAAAGTGAGAGACATCAG 59.246 41.667 0.00 0.00 0.00 2.90
3266 3485 4.707105 TGAAAGCAAAGTGAGAGACATCA 58.293 39.130 0.00 0.00 0.00 3.07
3268 3487 6.489361 AGAAATGAAAGCAAAGTGAGAGACAT 59.511 34.615 0.00 0.00 0.00 3.06
3285 3504 5.824624 GGCATCAAGATACAGGAGAAATGAA 59.175 40.000 0.00 0.00 0.00 2.57
3317 3536 0.733729 GATTTGGCTCAGCTCAGCAG 59.266 55.000 13.07 0.00 41.65 4.24
3318 3537 0.679002 GGATTTGGCTCAGCTCAGCA 60.679 55.000 13.07 0.00 41.65 4.41
3319 3538 0.394080 AGGATTTGGCTCAGCTCAGC 60.394 55.000 0.00 0.00 38.84 4.26
3320 3539 1.743958 CAAGGATTTGGCTCAGCTCAG 59.256 52.381 0.00 0.00 0.00 3.35
3321 3540 1.615116 CCAAGGATTTGGCTCAGCTCA 60.615 52.381 0.00 0.00 46.84 4.26
3322 3541 1.101331 CCAAGGATTTGGCTCAGCTC 58.899 55.000 0.00 0.00 46.84 4.09
3323 3542 3.277962 CCAAGGATTTGGCTCAGCT 57.722 52.632 0.00 0.00 46.84 4.24
3348 3567 3.957919 TCCACGCGGAATATCCCA 58.042 55.556 12.47 0.00 38.83 4.37
3488 3711 1.348036 CACGGTCCCTTCCTCTTCTTT 59.652 52.381 0.00 0.00 0.00 2.52
3491 3714 1.079057 GCACGGTCCCTTCCTCTTC 60.079 63.158 0.00 0.00 0.00 2.87
3494 3717 3.692406 ACGCACGGTCCCTTCCTC 61.692 66.667 0.00 0.00 0.00 3.71
3617 3842 3.297830 ACACCGTAACCCGTACTTAAC 57.702 47.619 0.00 0.00 33.66 2.01
3625 3850 3.189285 CAGGTAATTACACCGTAACCCG 58.811 50.000 17.16 0.00 43.84 5.28
3657 3882 5.584253 ACATAAGACGATGCTGACTTACT 57.416 39.130 0.00 0.00 30.96 2.24
3658 3883 6.918569 ACATACATAAGACGATGCTGACTTAC 59.081 38.462 0.00 0.00 30.96 2.34
3659 3884 6.918022 CACATACATAAGACGATGCTGACTTA 59.082 38.462 0.00 0.00 32.31 2.24
3660 3885 5.750547 CACATACATAAGACGATGCTGACTT 59.249 40.000 0.00 0.00 0.00 3.01
3705 3930 2.037620 CTCGCCCTTCTCCCTCATGG 62.038 65.000 0.00 0.00 0.00 3.66
3706 3931 1.333636 ACTCGCCCTTCTCCCTCATG 61.334 60.000 0.00 0.00 0.00 3.07
3721 3949 6.074835 CCATCATGTAATTTCAGTCGTACTCG 60.075 42.308 0.00 0.00 38.55 4.18
3952 4227 5.932883 GGTCCTAAACTTCAACAACTAGGAG 59.067 44.000 0.00 0.00 36.47 3.69
3953 4228 5.510179 CGGTCCTAAACTTCAACAACTAGGA 60.510 44.000 0.00 0.00 34.03 2.94
3954 4229 4.689345 CGGTCCTAAACTTCAACAACTAGG 59.311 45.833 0.00 0.00 0.00 3.02
3955 4230 4.689345 CCGGTCCTAAACTTCAACAACTAG 59.311 45.833 0.00 0.00 0.00 2.57
3956 4231 4.503643 CCCGGTCCTAAACTTCAACAACTA 60.504 45.833 0.00 0.00 0.00 2.24
3957 4232 3.473625 CCGGTCCTAAACTTCAACAACT 58.526 45.455 0.00 0.00 0.00 3.16
3964 4239 0.903236 AGCTCCCGGTCCTAAACTTC 59.097 55.000 0.00 0.00 0.00 3.01
4045 4321 2.491621 GGAAAGCGGCCTTGATGC 59.508 61.111 0.00 0.00 0.00 3.91
4145 4422 3.611517 CGTTGTTCTCAAGCTTGTTCAG 58.388 45.455 25.19 15.78 33.97 3.02


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

AutoCloner maintained by Alex Coulton.