Multiple sequence alignment - TraesCS2A01G559500

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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 TraesCS2A01G559500 chr2A 100.000 4360 0 0 1 4360 762316484 762312125 0.000000e+00 8052
1 TraesCS2A01G559500 chr2A 79.752 484 45 31 2 478 753815784 753815347 7.090000e-78 302
2 TraesCS2A01G559500 chr2A 93.878 49 3 0 467 515 753815335 753815287 1.680000e-09 75
3 TraesCS2A01G559500 chr2D 87.291 2628 177 55 6 2524 637633435 637636014 0.000000e+00 2857
4 TraesCS2A01G559500 chr2D 90.000 1810 137 17 2579 4360 637636005 637637798 0.000000e+00 2300
5 TraesCS2A01G559500 chr2D 83.650 263 21 11 2754 3015 597847655 597847896 1.220000e-55 228
6 TraesCS2A01G559500 chr2D 83.270 263 22 11 2754 3015 641893064 641893305 5.680000e-54 222
7 TraesCS2A01G559500 chr2B 87.387 2212 139 54 6 2173 795047721 795049836 0.000000e+00 2410
8 TraesCS2A01G559500 chr2B 92.240 915 58 9 2308 3218 795049836 795050741 0.000000e+00 1284
9 TraesCS2A01G559500 chr2B 87.905 802 54 10 3217 3996 795050835 795051615 0.000000e+00 904
10 TraesCS2A01G559500 chr2B 93.293 328 22 0 4033 4360 795051613 795051940 6.560000e-133 484
11 TraesCS2A01G559500 chr2B 86.563 387 40 5 1218 1604 523781963 523781589 2.430000e-112 416
12 TraesCS2A01G559500 chr2B 91.060 302 22 3 1747 2048 523781555 523781259 1.890000e-108 403
13 TraesCS2A01G559500 chr1A 87.020 547 52 10 1065 1604 168548098 168548632 2.240000e-167 599
14 TraesCS2A01G559500 chr1A 91.262 309 21 3 1745 2047 168548664 168548972 2.430000e-112 416
15 TraesCS2A01G559500 chr5D 79.777 717 83 31 1 676 19106697 19106002 8.540000e-127 464
16 TraesCS2A01G559500 chr5B 79.483 580 66 26 113 663 24678799 24678244 3.200000e-96 363
17 TraesCS2A01G559500 chr7D 90.871 241 22 0 3713 3953 592269337 592269577 1.510000e-84 324
18 TraesCS2A01G559500 chr4A 75.915 328 77 2 4033 4360 736806229 736805904 2.700000e-37 167


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 TraesCS2A01G559500 chr2A 762312125 762316484 4359 True 8052.0 8052 100.00000 1 4360 1 chr2A.!!$R1 4359
1 TraesCS2A01G559500 chr2D 637633435 637637798 4363 False 2578.5 2857 88.64550 6 4360 2 chr2D.!!$F3 4354
2 TraesCS2A01G559500 chr2B 795047721 795051940 4219 False 1270.5 2410 90.20625 6 4360 4 chr2B.!!$F1 4354
3 TraesCS2A01G559500 chr2B 523781259 523781963 704 True 409.5 416 88.81150 1218 2048 2 chr2B.!!$R1 830
4 TraesCS2A01G559500 chr1A 168548098 168548972 874 False 507.5 599 89.14100 1065 2047 2 chr1A.!!$F1 982
5 TraesCS2A01G559500 chr5D 19106002 19106697 695 True 464.0 464 79.77700 1 676 1 chr5D.!!$R1 675
6 TraesCS2A01G559500 chr5B 24678244 24678799 555 True 363.0 363 79.48300 113 663 1 chr5B.!!$R1 550

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
850 915 0.250234 TCTCACGGGCCTCATTTGAG 59.750 55.0 0.84 7.9 41.71 3.02 F
1128 1199 0.034089 CCAACCCAACCCAGGATCTC 60.034 60.0 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2260 0.179037 TGCAGCAAGCTAGGCCATAG 60.179 55.0 5.01 5.13 45.94 2.23 R
3773 4072 0.884704 TCAGTTCTCCTTGCCGTTGC 60.885 55.0 0.00 0.00 38.26 4.17 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
34 35 0.250793 TTTACATGTCGACCGGGCAT 59.749 50.000 8.76 2.38 0.00 4.40
122 123 1.002366 GTTCGCGTCATCAATCTGCT 58.998 50.000 5.77 0.00 0.00 4.24
129 130 4.033684 GCGTCATCAATCTGCTCAAATTC 58.966 43.478 0.00 0.00 0.00 2.17
196 203 8.565896 TTAGTTATGACAAAGCTGAATGTGAT 57.434 30.769 4.93 5.08 0.00 3.06
198 205 6.432162 AGTTATGACAAAGCTGAATGTGATGT 59.568 34.615 4.93 0.00 0.00 3.06
203 210 6.073058 TGACAAAGCTGAATGTGATGTAACTC 60.073 38.462 4.93 0.00 0.00 3.01
348 368 1.152652 TCCTCCTCATCCTCCTCGC 60.153 63.158 0.00 0.00 0.00 5.03
389 409 1.020333 CCTCGTCGTCGAACTCCTCT 61.020 60.000 6.19 0.00 45.61 3.69
773 831 6.183360 CCATCTTTCACTTTCACTATCCGTTC 60.183 42.308 0.00 0.00 0.00 3.95
829 888 4.047822 GAGTGGAGACAGATATTTGCTCG 58.952 47.826 9.79 0.00 44.46 5.03
846 911 2.586792 GCTCTCACGGGCCTCATT 59.413 61.111 0.84 0.00 0.00 2.57
848 913 1.372087 GCTCTCACGGGCCTCATTTG 61.372 60.000 0.84 0.00 0.00 2.32
850 915 0.250234 TCTCACGGGCCTCATTTGAG 59.750 55.000 0.84 7.90 41.71 3.02
852 917 2.044946 ACGGGCCTCATTTGAGCC 60.045 61.111 0.84 7.16 40.75 4.70
853 918 2.830370 CGGGCCTCATTTGAGCCC 60.830 66.667 20.96 20.96 46.14 5.19
854 919 2.830370 GGGCCTCATTTGAGCCCG 60.830 66.667 18.19 2.40 43.41 6.13
976 1046 0.444651 CAGACCAGAGAGTCGTCGTC 59.555 60.000 0.00 0.00 41.83 4.20
977 1047 1.015085 AGACCAGAGAGTCGTCGTCG 61.015 60.000 0.00 0.00 41.83 5.12
978 1048 2.098680 CCAGAGAGTCGTCGTCGC 59.901 66.667 0.00 0.00 36.96 5.19
1063 1133 1.069090 GTCACGCACTCCAACCTCA 59.931 57.895 0.00 0.00 0.00 3.86
1102 1173 2.496817 GGGTCTCGCAGCAGGTAG 59.503 66.667 0.00 0.00 0.00 3.18
1122 1193 2.917227 GCCACCAACCCAACCCAG 60.917 66.667 0.00 0.00 0.00 4.45
1123 1194 2.203625 CCACCAACCCAACCCAGG 60.204 66.667 0.00 0.00 0.00 4.45
1124 1195 2.773527 CCACCAACCCAACCCAGGA 61.774 63.158 0.00 0.00 0.00 3.86
1125 1196 1.464722 CACCAACCCAACCCAGGAT 59.535 57.895 0.00 0.00 0.00 3.24
1126 1197 0.611896 CACCAACCCAACCCAGGATC 60.612 60.000 0.00 0.00 0.00 3.36
1127 1198 0.776080 ACCAACCCAACCCAGGATCT 60.776 55.000 0.00 0.00 0.00 2.75
1128 1199 0.034089 CCAACCCAACCCAGGATCTC 60.034 60.000 0.00 0.00 0.00 2.75
1129 1200 0.698238 CAACCCAACCCAGGATCTCA 59.302 55.000 0.00 0.00 0.00 3.27
1389 1496 5.723672 TCTCCTCTTGTTAACTACTGGTG 57.276 43.478 7.22 5.78 0.00 4.17
1430 1537 2.224018 GGACTGATGATGGTCTGCTCTC 60.224 54.545 0.00 0.00 33.46 3.20
1524 1631 2.791849 GCTCGTCGAGAAGTACACCATC 60.792 54.545 26.11 0.00 0.00 3.51
1601 1711 9.527157 TTCCAGTTTATAAGATGAATTTGGACA 57.473 29.630 0.00 0.00 30.11 4.02
1611 1732 7.865706 AGATGAATTTGGACACCTTGTATAC 57.134 36.000 0.00 0.00 0.00 1.47
1612 1733 6.828785 AGATGAATTTGGACACCTTGTATACC 59.171 38.462 0.00 0.00 0.00 2.73
1616 1737 5.836024 TTTGGACACCTTGTATACCTCTT 57.164 39.130 0.00 0.00 0.00 2.85
1617 1738 4.819105 TGGACACCTTGTATACCTCTTG 57.181 45.455 0.00 0.00 0.00 3.02
1618 1739 4.164981 TGGACACCTTGTATACCTCTTGT 58.835 43.478 0.00 0.00 0.00 3.16
1619 1740 5.335261 TGGACACCTTGTATACCTCTTGTA 58.665 41.667 0.00 0.00 0.00 2.41
1620 1741 5.421056 TGGACACCTTGTATACCTCTTGTAG 59.579 44.000 0.00 0.00 31.61 2.74
1621 1742 5.655532 GGACACCTTGTATACCTCTTGTAGA 59.344 44.000 0.00 0.00 31.61 2.59
1622 1743 6.154021 GGACACCTTGTATACCTCTTGTAGAA 59.846 42.308 0.00 0.00 31.61 2.10
1623 1744 7.147707 GGACACCTTGTATACCTCTTGTAGAAT 60.148 40.741 0.00 0.00 31.61 2.40
1624 1745 8.147244 ACACCTTGTATACCTCTTGTAGAATT 57.853 34.615 0.00 0.00 31.61 2.17
1625 1746 8.258708 ACACCTTGTATACCTCTTGTAGAATTC 58.741 37.037 0.00 0.00 31.61 2.17
1626 1747 8.478877 CACCTTGTATACCTCTTGTAGAATTCT 58.521 37.037 13.56 13.56 31.61 2.40
1627 1748 8.697292 ACCTTGTATACCTCTTGTAGAATTCTC 58.303 37.037 12.24 4.68 31.61 2.87
1641 1762 8.988064 TGTAGAATTCTCAGTCTGAAACATAC 57.012 34.615 12.24 0.00 0.00 2.39
1659 1780 9.989869 GAAACATACTTCAGCTTATTCCTTAAC 57.010 33.333 0.00 0.00 0.00 2.01
1688 1809 3.636300 AGCTTGCATACCTCTAGACTCTG 59.364 47.826 0.00 0.00 0.00 3.35
1708 1830 7.228590 ACTCTGGTAGAGGAGTCTGAATATAC 58.771 42.308 10.31 0.00 46.45 1.47
1731 1853 6.324819 ACTTCAGTTTATCATTTGCAATCGG 58.675 36.000 0.00 0.00 0.00 4.18
1887 2009 2.091885 TCCTTTCAAGGCTTCAACAGGT 60.092 45.455 0.00 0.00 46.06 4.00
1965 2101 2.105649 TGTGCCAACATCAAGGTCAGTA 59.894 45.455 0.00 0.00 0.00 2.74
1989 2125 7.872163 ACATTTGCTTTACACATGTATGTTG 57.128 32.000 0.00 0.00 45.62 3.33
2008 2150 5.112686 TGTTGGATTAAGTTTTTGCACACC 58.887 37.500 0.00 0.00 0.00 4.16
2009 2151 3.971150 TGGATTAAGTTTTTGCACACCG 58.029 40.909 0.00 0.00 0.00 4.94
2026 2168 5.334879 GCACACCGTATGGAATGGAATATTC 60.335 44.000 8.33 6.93 37.73 1.75
2030 2172 4.943705 CCGTATGGAATGGAATATTCCCAG 59.056 45.833 27.97 9.67 45.27 4.45
2056 2198 0.991146 TGCTGATGTTAAGAGCCCCA 59.009 50.000 0.00 0.00 31.31 4.96
2058 2200 1.673168 CTGATGTTAAGAGCCCCAGC 58.327 55.000 0.00 0.00 40.32 4.85
2061 2203 0.034089 ATGTTAAGAGCCCCAGCCAC 60.034 55.000 0.00 0.00 41.25 5.01
2070 2212 2.833913 CCCCAGCCACCTCAGTTGT 61.834 63.158 0.00 0.00 0.00 3.32
2071 2213 1.151450 CCCAGCCACCTCAGTTGTT 59.849 57.895 0.00 0.00 0.00 2.83
2082 2224 3.821033 ACCTCAGTTGTTTACCTTGCATC 59.179 43.478 0.00 0.00 0.00 3.91
2087 2229 4.759693 CAGTTGTTTACCTTGCATCCACTA 59.240 41.667 0.00 0.00 0.00 2.74
2089 2231 5.415701 AGTTGTTTACCTTGCATCCACTATG 59.584 40.000 0.00 0.00 38.74 2.23
2114 2257 5.413309 TTTTCCAAGGCAGAGTTTTGAAA 57.587 34.783 0.00 0.00 0.00 2.69
2117 2260 5.200368 TCCAAGGCAGAGTTTTGAAATTC 57.800 39.130 0.00 0.00 0.00 2.17
2121 2264 6.810182 CCAAGGCAGAGTTTTGAAATTCTATG 59.190 38.462 1.83 2.51 33.83 2.23
2123 2266 5.105063 GGCAGAGTTTTGAAATTCTATGGC 58.895 41.667 12.72 12.72 37.48 4.40
2139 2285 0.475475 TGGCCTAGCTTGCTGCATAT 59.525 50.000 1.84 0.00 45.94 1.78
2145 2291 4.456911 GCCTAGCTTGCTGCATATTAATGA 59.543 41.667 1.84 0.00 45.94 2.57
2164 2310 1.678101 GATTTAGCACCCCATCACTGC 59.322 52.381 0.00 0.00 0.00 4.40
2166 2312 0.253044 TTAGCACCCCATCACTGCTC 59.747 55.000 0.00 0.00 40.47 4.26
2173 2319 0.461548 CCCATCACTGCTCGAGCTAA 59.538 55.000 35.27 17.61 42.66 3.09
2174 2320 1.069823 CCCATCACTGCTCGAGCTAAT 59.930 52.381 35.27 20.46 42.66 1.73
2175 2321 2.484417 CCCATCACTGCTCGAGCTAATT 60.484 50.000 35.27 15.73 42.66 1.40
2176 2322 2.799412 CCATCACTGCTCGAGCTAATTC 59.201 50.000 35.27 8.73 42.66 2.17
2212 2358 2.880890 GTCTGGTATAGCAGCCCAATTG 59.119 50.000 24.11 0.00 0.00 2.32
2214 2360 1.568597 TGGTATAGCAGCCCAATTGGT 59.431 47.619 22.91 6.75 36.04 3.67
2216 2362 3.181445 TGGTATAGCAGCCCAATTGGTAG 60.181 47.826 22.91 12.84 36.04 3.18
2260 2406 8.198109 ACAAGCTGAATTAGTATGTACGAATCT 58.802 33.333 0.00 0.00 31.69 2.40
2272 2418 0.615331 ACGAATCTGTGGCCACATCT 59.385 50.000 37.66 24.56 41.01 2.90
2278 2424 1.278985 TCTGTGGCCACATCTACTTGG 59.721 52.381 37.66 23.12 41.01 3.61
2363 2509 8.425577 ACAGTCATACAGTGCATTATTCTAAC 57.574 34.615 0.00 0.00 0.00 2.34
2456 2625 9.765795 ATTGCAGTGTATATTTCCTTCTAGTAC 57.234 33.333 0.00 0.00 0.00 2.73
2504 2673 4.475016 AGTAAAGCACACTAGGAATCCCAT 59.525 41.667 0.00 0.00 33.88 4.00
2507 2676 2.846206 AGCACACTAGGAATCCCATTCA 59.154 45.455 0.00 0.00 41.03 2.57
2520 2692 5.603170 ATCCCATTCACAAAATGACCATC 57.397 39.130 0.00 0.00 36.92 3.51
2529 2701 6.222389 TCACAAAATGACCATCCAATTCAAC 58.778 36.000 0.00 0.00 29.99 3.18
2594 2767 5.255397 ACAAAAGACCATCCAACCATCTA 57.745 39.130 0.00 0.00 0.00 1.98
2635 2808 5.585390 GAGGAATACAGAATTGTGCCAATG 58.415 41.667 1.83 0.00 38.23 2.82
2636 2809 5.018809 AGGAATACAGAATTGTGCCAATGT 58.981 37.500 1.83 1.09 38.23 2.71
2637 2810 6.186957 AGGAATACAGAATTGTGCCAATGTA 58.813 36.000 1.83 2.94 38.23 2.29
2638 2811 6.835488 AGGAATACAGAATTGTGCCAATGTAT 59.165 34.615 1.83 4.73 38.23 2.29
2647 2820 5.766150 TTGTGCCAATGTATATAACTGGC 57.234 39.130 18.00 18.00 45.41 4.85
2715 2888 4.396357 AAATATTGGTCCTTGGTGTGGA 57.604 40.909 0.00 0.00 0.00 4.02
2719 2896 3.644966 TTGGTCCTTGGTGTGGATATC 57.355 47.619 0.00 0.00 35.87 1.63
2738 2915 9.425248 TGGATATCCTTTGCTATTGAAAAGAAT 57.575 29.630 22.35 0.00 40.47 2.40
2749 2926 5.567138 ATTGAAAAGAATAGGCTGGAACG 57.433 39.130 0.00 0.00 0.00 3.95
2751 2928 4.000988 TGAAAAGAATAGGCTGGAACGTC 58.999 43.478 0.00 0.00 0.00 4.34
2756 2933 1.956629 ATAGGCTGGAACGTCGGGTG 61.957 60.000 0.00 0.00 0.00 4.61
2775 2952 3.815401 GGTGCAAGCTTTCTTCTTCTGTA 59.185 43.478 0.00 0.00 0.00 2.74
2778 2955 3.499918 GCAAGCTTTCTTCTTCTGTAGCA 59.500 43.478 0.00 0.00 0.00 3.49
2785 2962 7.176340 AGCTTTCTTCTTCTGTAGCATGAAATT 59.824 33.333 0.00 0.00 0.00 1.82
2798 2975 8.584157 TGTAGCATGAAATTGAAATTACACCTT 58.416 29.630 0.00 0.00 0.00 3.50
2799 2976 9.076596 GTAGCATGAAATTGAAATTACACCTTC 57.923 33.333 0.00 0.00 0.00 3.46
2867 3044 2.354203 GGTGGGAGACAGATGTGAAGTC 60.354 54.545 0.00 0.00 0.00 3.01
3074 3251 3.581024 AGTAACGACATACGCTTGGAA 57.419 42.857 0.00 0.00 46.94 3.53
3081 3258 3.662186 CGACATACGCTTGGAAAAACAAC 59.338 43.478 0.00 0.00 34.51 3.32
3087 3264 4.359706 ACGCTTGGAAAAACAACTCATTC 58.640 39.130 0.00 0.00 0.00 2.67
3190 3367 2.303311 GGCCAGAGAAAGTGAAGGTAGT 59.697 50.000 0.00 0.00 0.00 2.73
3196 3373 6.591834 CCAGAGAAAGTGAAGGTAGTTACATG 59.408 42.308 0.00 0.00 0.00 3.21
3210 3387 6.496218 GGTAGTTACATGCCTACCTTACCTAT 59.504 42.308 21.17 0.00 46.40 2.57
3247 3522 7.716799 AATTGGTTCTTATAACATTCAGCCA 57.283 32.000 0.00 0.00 0.00 4.75
3252 3527 7.229306 TGGTTCTTATAACATTCAGCCATCATC 59.771 37.037 0.00 0.00 0.00 2.92
3298 3573 4.518970 TGGAAGTGTTATTGAGCAGTTTCC 59.481 41.667 0.00 0.00 33.60 3.13
3311 3586 1.756538 CAGTTTCCTTTGCAGGTTGGT 59.243 47.619 0.00 0.00 41.69 3.67
3335 3610 0.981277 TTCCGGAGAGGGACCCATTC 60.981 60.000 14.60 9.52 41.52 2.67
3411 3686 3.627395 TGGTGTCTCTTCAACTTGTGT 57.373 42.857 0.00 0.00 0.00 3.72
3429 3704 9.598517 AACTTGTGTCAAATTCATTTGTTATGT 57.401 25.926 11.21 3.60 45.49 2.29
3437 3713 8.511321 TCAAATTCATTTGTTATGTAGTCGCTT 58.489 29.630 11.21 0.00 45.49 4.68
3462 3738 6.951062 TCTGTACCTAGTGAGATGATTGAG 57.049 41.667 0.00 0.00 0.00 3.02
3509 3803 3.201045 AGCAAAGGAAGGGGATCTAGAAC 59.799 47.826 0.00 0.00 0.00 3.01
3543 3837 4.079253 TGGAGATTAGTTTGGGTTCAAGC 58.921 43.478 0.00 0.00 33.98 4.01
3596 3891 4.281688 CCAAGAACCAATGACCAAGATTGT 59.718 41.667 0.00 0.00 0.00 2.71
3600 3895 2.158325 ACCAATGACCAAGATTGTGGGT 60.158 45.455 4.71 0.00 43.56 4.51
3624 3920 9.569122 GGTGTAATGGGTATATAAACTTGATGT 57.431 33.333 0.00 0.00 0.00 3.06
3656 3955 3.833650 TGTATCCAGTACCCGAAAACTCA 59.166 43.478 0.00 0.00 32.03 3.41
3702 4001 4.072131 TGGAATCAAAGCAGTAACCTGAC 58.928 43.478 0.00 0.00 41.50 3.51
3746 4045 7.665559 TCAACTTTAGCTATCTGAACCAATGTT 59.334 33.333 0.00 0.00 37.42 2.71
3773 4072 9.245962 GCAATTCAGGAAATTCTAAAGATGATG 57.754 33.333 0.00 0.00 35.32 3.07
3819 4118 1.410365 GCTAGGAGTAGGAGCCACTCA 60.410 57.143 15.82 2.43 43.50 3.41
3828 4127 1.834263 AGGAGCCACTCAATACAGTCC 59.166 52.381 0.00 0.00 31.08 3.85
3829 4128 1.555075 GGAGCCACTCAATACAGTCCA 59.445 52.381 0.00 0.00 31.08 4.02
3848 4147 2.940410 CCAGATGCCATGAAAAATTGCC 59.060 45.455 0.00 0.00 0.00 4.52
3910 4209 7.133891 ACTTGTGCTTCTAATACAATGACAC 57.866 36.000 0.00 0.00 34.22 3.67
3913 4212 7.075674 TGTGCTTCTAATACAATGACACATG 57.924 36.000 0.00 0.00 31.11 3.21
3914 4213 6.878389 TGTGCTTCTAATACAATGACACATGA 59.122 34.615 0.00 0.00 31.11 3.07
3915 4214 7.148423 TGTGCTTCTAATACAATGACACATGAC 60.148 37.037 0.00 0.00 31.11 3.06
3916 4215 6.878389 TGCTTCTAATACAATGACACATGACA 59.122 34.615 0.00 0.00 0.00 3.58
3917 4216 7.390162 TGCTTCTAATACAATGACACATGACAA 59.610 33.333 0.00 0.00 0.00 3.18
3918 4217 8.400947 GCTTCTAATACAATGACACATGACAAT 58.599 33.333 0.00 0.00 0.00 2.71
3919 4218 9.712359 CTTCTAATACAATGACACATGACAATG 57.288 33.333 0.00 2.99 39.89 2.82
3961 4260 3.254166 CAGAAAACAGGAATGGTCACCAG 59.746 47.826 1.19 0.00 36.75 4.00
3996 4295 1.518325 CTTGTAACCACATCGCCACA 58.482 50.000 0.00 0.00 33.76 4.17
4021 4320 3.738282 GTGACAACAACAGAGCTGTAGAG 59.262 47.826 3.21 0.46 44.13 2.43
4059 4358 0.812811 TGCTCATCCAGATCAAGCGC 60.813 55.000 0.00 0.00 35.74 5.92
4090 4389 5.977489 AATCCATGAACATGCATATGAGG 57.023 39.130 6.97 0.00 37.73 3.86
4132 4431 3.944015 GCATTCAGCTCCTTGACTACATT 59.056 43.478 0.00 0.00 41.15 2.71
4147 4446 7.294676 TGACTACATTGTTCATCTTCATTCG 57.705 36.000 0.00 0.00 0.00 3.34
4189 4488 5.064452 CACAGCAAGCTAGACCAATCTTAAG 59.936 44.000 0.00 0.00 36.29 1.85
4280 4579 5.245751 CACTTCCAGCAGAGTATCAGGATAT 59.754 44.000 0.00 0.00 37.82 1.63
4351 4650 1.002087 AGTTGGCCGTCTTCCAGTAAG 59.998 52.381 0.00 0.00 34.66 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.746115 GTCGACATGTAAACAACCACACTA 59.254 41.667 11.55 0.00 0.00 2.74
14 15 0.671163 TGCCCGGTCGACATGTAAAC 60.671 55.000 18.91 0.00 0.00 2.01
15 16 0.250793 ATGCCCGGTCGACATGTAAA 59.749 50.000 18.91 0.00 0.00 2.01
34 35 2.417379 GGATCACGAGTGCTTGCTTCTA 60.417 50.000 0.00 0.00 0.00 2.10
122 123 4.333649 CCTAAGCTCATCTTGCGAATTTGA 59.666 41.667 0.00 0.00 36.25 2.69
129 130 4.142945 GCATTATCCTAAGCTCATCTTGCG 60.143 45.833 0.00 0.00 36.25 4.85
175 180 6.822667 ACATCACATTCAGCTTTGTCATAA 57.177 33.333 0.00 0.00 0.00 1.90
203 210 2.997869 CGCATCGTCACCATCGTG 59.002 61.111 0.00 0.00 41.72 4.35
348 368 1.379642 GGGTACAGGGACTACGACGG 61.380 65.000 0.00 0.00 36.02 4.79
773 831 2.005960 CTTCTACCTCCAGACCCGCG 62.006 65.000 0.00 0.00 0.00 6.46
781 839 1.914108 TCTCCTCGTCTTCTACCTCCA 59.086 52.381 0.00 0.00 0.00 3.86
829 888 1.078143 AAATGAGGCCCGTGAGAGC 60.078 57.895 0.00 0.00 0.00 4.09
991 1061 1.215647 GCTTCGACATGTCTCCGGT 59.784 57.895 22.95 0.00 0.00 5.28
992 1062 0.803768 CAGCTTCGACATGTCTCCGG 60.804 60.000 22.95 8.12 0.00 5.14
993 1063 1.416813 GCAGCTTCGACATGTCTCCG 61.417 60.000 22.95 11.44 0.00 4.63
994 1064 0.390340 TGCAGCTTCGACATGTCTCC 60.390 55.000 22.95 8.69 0.00 3.71
995 1065 0.997932 CTGCAGCTTCGACATGTCTC 59.002 55.000 22.95 9.67 0.00 3.36
1063 1133 3.069318 GTCGGAGGCGAAGGAGGT 61.069 66.667 0.00 0.00 0.00 3.85
1086 1157 2.496817 CCTACCTGCTGCGAGACC 59.503 66.667 0.00 0.00 0.00 3.85
1122 1193 2.045524 TCCAAGCTGGAGATGAGATCC 58.954 52.381 0.00 0.00 42.67 3.36
1351 1455 4.447342 GATGCAGGTGGGGTGGGG 62.447 72.222 0.00 0.00 0.00 4.96
1389 1496 2.481952 CCAACAGCAGCAGTAGAAAGAC 59.518 50.000 0.00 0.00 0.00 3.01
1430 1537 1.369091 GATGTGCAGCCGGTACCTTG 61.369 60.000 10.90 6.93 0.00 3.61
1524 1631 2.780643 TCGTACGCTTCGTCCGAG 59.219 61.111 11.24 0.00 42.50 4.63
1601 1711 8.611051 AGAATTCTACAAGAGGTATACAAGGT 57.389 34.615 6.06 0.00 0.00 3.50
1609 1730 7.175797 TCAGACTGAGAATTCTACAAGAGGTA 58.824 38.462 8.25 0.00 0.00 3.08
1611 1732 6.522625 TCAGACTGAGAATTCTACAAGAGG 57.477 41.667 8.25 0.22 0.00 3.69
1612 1733 7.869937 TGTTTCAGACTGAGAATTCTACAAGAG 59.130 37.037 8.25 2.58 0.00 2.85
1616 1737 8.807118 AGTATGTTTCAGACTGAGAATTCTACA 58.193 33.333 8.25 6.17 34.47 2.74
1617 1738 9.646427 AAGTATGTTTCAGACTGAGAATTCTAC 57.354 33.333 8.25 3.09 36.00 2.59
1618 1739 9.862371 GAAGTATGTTTCAGACTGAGAATTCTA 57.138 33.333 8.25 0.00 36.00 2.10
1619 1740 8.370940 TGAAGTATGTTTCAGACTGAGAATTCT 58.629 33.333 7.95 7.95 36.00 2.40
1620 1741 8.539770 TGAAGTATGTTTCAGACTGAGAATTC 57.460 34.615 5.10 0.00 36.00 2.17
1664 1785 4.714308 AGAGTCTAGAGGTATGCAAGCTTT 59.286 41.667 0.00 0.00 35.60 3.51
1665 1786 4.099266 CAGAGTCTAGAGGTATGCAAGCTT 59.901 45.833 0.00 0.00 35.60 3.74
1666 1787 3.636300 CAGAGTCTAGAGGTATGCAAGCT 59.364 47.826 0.00 0.00 39.11 3.74
1667 1788 3.243704 CCAGAGTCTAGAGGTATGCAAGC 60.244 52.174 0.00 0.00 0.00 4.01
1668 1789 3.957497 ACCAGAGTCTAGAGGTATGCAAG 59.043 47.826 0.00 0.00 31.32 4.01
1688 1809 7.722285 ACTGAAGTATATTCAGACTCCTCTACC 59.278 40.741 21.08 0.00 46.57 3.18
1708 1830 5.230726 GCCGATTGCAAATGATAAACTGAAG 59.769 40.000 1.71 0.00 40.77 3.02
1731 1853 6.920758 AGTTTAGATGTTATGATCGAGTGAGC 59.079 38.462 0.00 0.00 0.00 4.26
1887 2009 6.098409 AGAGGACAAGAAACAGAGTAAACAGA 59.902 38.462 0.00 0.00 0.00 3.41
1989 2125 3.972403 ACGGTGTGCAAAAACTTAATCC 58.028 40.909 0.00 0.00 0.00 3.01
2030 2172 4.213059 GGCTCTTAACATCAGCAGATTAGC 59.787 45.833 0.00 0.00 34.62 3.09
2049 2191 4.106925 CTGAGGTGGCTGGGGCTC 62.107 72.222 0.00 0.00 38.73 4.70
2056 2198 1.774856 AGGTAAACAACTGAGGTGGCT 59.225 47.619 1.20 0.00 0.00 4.75
2058 2200 2.293399 GCAAGGTAAACAACTGAGGTGG 59.707 50.000 1.20 0.00 0.00 4.61
2061 2203 3.191371 GGATGCAAGGTAAACAACTGAGG 59.809 47.826 0.00 0.00 0.00 3.86
2070 2212 6.909550 AAAACATAGTGGATGCAAGGTAAA 57.090 33.333 0.00 0.00 39.39 2.01
2071 2213 6.909550 AAAAACATAGTGGATGCAAGGTAA 57.090 33.333 0.00 0.00 39.39 2.85
2104 2246 6.319911 AGCTAGGCCATAGAATTTCAAAACTC 59.680 38.462 5.01 0.00 32.76 3.01
2111 2253 4.023365 CAGCAAGCTAGGCCATAGAATTTC 60.023 45.833 5.01 0.00 32.76 2.17
2114 2257 2.813354 GCAGCAAGCTAGGCCATAGAAT 60.813 50.000 5.01 0.00 41.15 2.40
2117 2260 0.179037 TGCAGCAAGCTAGGCCATAG 60.179 55.000 5.01 5.13 45.94 2.23
2121 2264 1.613836 AATATGCAGCAAGCTAGGCC 58.386 50.000 0.00 0.00 45.94 5.19
2123 2266 6.754702 ATCATTAATATGCAGCAAGCTAGG 57.245 37.500 0.00 0.00 45.94 3.02
2139 2285 5.593909 CAGTGATGGGGTGCTAAATCATTAA 59.406 40.000 0.00 0.00 32.07 1.40
2145 2291 1.285962 AGCAGTGATGGGGTGCTAAAT 59.714 47.619 0.00 0.00 45.72 1.40
2166 2312 9.941664 ACATCAAATATGAAAAGAATTAGCTCG 57.058 29.630 0.00 0.00 39.49 5.03
2191 2337 2.880890 CAATTGGGCTGCTATACCAGAC 59.119 50.000 0.00 0.00 40.23 3.51
2197 2343 5.368523 AGTTACTACCAATTGGGCTGCTATA 59.631 40.000 27.89 8.78 42.05 1.31
2237 2383 7.649705 CACAGATTCGTACATACTAATTCAGCT 59.350 37.037 0.00 0.00 0.00 4.24
2240 2386 6.700081 GCCACAGATTCGTACATACTAATTCA 59.300 38.462 0.00 0.00 0.00 2.57
2254 2400 2.159043 AGTAGATGTGGCCACAGATTCG 60.159 50.000 39.29 0.00 45.48 3.34
2260 2406 3.955145 CCAAGTAGATGTGGCCACA 57.045 52.632 39.23 39.23 46.44 4.17
2272 2418 0.767998 TCATGTGGGTGTGCCAAGTA 59.232 50.000 0.00 0.00 36.17 2.24
2278 2424 1.001378 GTCAAGTTCATGTGGGTGTGC 60.001 52.381 0.00 0.00 0.00 4.57
2281 2427 3.381272 AGTTTGTCAAGTTCATGTGGGTG 59.619 43.478 0.00 0.00 0.00 4.61
2328 2474 3.695060 ACTGTATGACTGTAGACGGAAGG 59.305 47.826 0.00 0.00 0.00 3.46
2363 2509 6.703607 AGATGAAGACGCATATTCCTACAAAG 59.296 38.462 0.00 0.00 0.00 2.77
2456 2625 2.039084 ACTGCTAGTCAAACCAGGAAGG 59.961 50.000 0.00 0.00 45.67 3.46
2504 2673 6.416631 TGAATTGGATGGTCATTTTGTGAA 57.583 33.333 0.00 0.00 38.90 3.18
2507 2676 5.010516 TCGTTGAATTGGATGGTCATTTTGT 59.989 36.000 0.00 0.00 0.00 2.83
2520 2692 4.236935 CCACCTGAATTTCGTTGAATTGG 58.763 43.478 0.00 0.00 29.75 3.16
2529 2701 2.488153 GAGTTTCCCCACCTGAATTTCG 59.512 50.000 0.00 0.00 0.00 3.46
2556 2729 1.393603 TTGTTTGGAACATCACCGCA 58.606 45.000 0.00 0.00 41.79 5.69
2594 2767 3.767673 TCCTCGCCAACTTAGTCAACTAT 59.232 43.478 0.00 0.00 0.00 2.12
2635 2808 9.216117 CCTGTTTATAAGTGGCCAGTTATATAC 57.784 37.037 36.96 36.96 38.35 1.47
2636 2809 8.380099 CCCTGTTTATAAGTGGCCAGTTATATA 58.620 37.037 36.84 31.77 38.35 0.86
2637 2810 7.147195 ACCCTGTTTATAAGTGGCCAGTTATAT 60.147 37.037 36.84 25.81 38.35 0.86
2638 2811 6.159046 ACCCTGTTTATAAGTGGCCAGTTATA 59.841 38.462 34.67 34.67 37.86 0.98
2647 2820 5.104900 AGCAGAGTACCCTGTTTATAAGTGG 60.105 44.000 6.24 0.00 36.57 4.00
2719 2896 6.976925 CAGCCTATTCTTTTCAATAGCAAAGG 59.023 38.462 0.00 0.00 35.70 3.11
2738 2915 2.283388 ACCCGACGTTCCAGCCTA 60.283 61.111 0.00 0.00 0.00 3.93
2741 2918 4.980805 TGCACCCGACGTTCCAGC 62.981 66.667 0.00 0.00 0.00 4.85
2749 2926 0.238553 GAAGAAAGCTTGCACCCGAC 59.761 55.000 7.33 0.00 33.61 4.79
2751 2928 0.954452 AAGAAGAAAGCTTGCACCCG 59.046 50.000 7.33 0.00 33.61 5.28
2756 2933 3.499918 TGCTACAGAAGAAGAAAGCTTGC 59.500 43.478 0.00 0.00 33.61 4.01
2775 2952 7.899973 AGAAGGTGTAATTTCAATTTCATGCT 58.100 30.769 10.40 0.00 30.25 3.79
2827 3004 8.040002 TCCCACCTATGACATAAATGTTCATA 57.960 34.615 0.00 6.20 41.95 2.15
2867 3044 2.435586 CTCTTGGCACCTGGCTCG 60.436 66.667 0.00 0.00 44.01 5.03
3067 3244 5.351458 ACAGAATGAGTTGTTTTTCCAAGC 58.649 37.500 0.00 0.00 39.69 4.01
3074 3251 7.816945 CAAGTCAAACAGAATGAGTTGTTTT 57.183 32.000 13.36 0.00 46.16 2.43
3081 3258 4.339247 ACCCAACAAGTCAAACAGAATGAG 59.661 41.667 0.00 0.00 39.69 2.90
3087 3264 1.750778 AGCACCCAACAAGTCAAACAG 59.249 47.619 0.00 0.00 0.00 3.16
3160 3337 6.121776 TCACTTTCTCTGGCCTAACAATTA 57.878 37.500 3.32 0.00 0.00 1.40
3161 3338 4.985538 TCACTTTCTCTGGCCTAACAATT 58.014 39.130 3.32 0.00 0.00 2.32
3190 3367 9.833179 ATACTAATAGGTAAGGTAGGCATGTAA 57.167 33.333 0.00 0.00 0.00 2.41
3223 3498 7.716799 TGGCTGAATGTTATAAGAACCAATT 57.283 32.000 0.00 0.00 0.00 2.32
3228 3503 7.229306 TGGATGATGGCTGAATGTTATAAGAAC 59.771 37.037 0.00 0.00 0.00 3.01
3247 3522 6.040842 CCTGAATTTTTAACCGGATGGATGAT 59.959 38.462 9.46 0.00 39.21 2.45
3252 3527 4.705023 ACTCCTGAATTTTTAACCGGATGG 59.295 41.667 9.46 0.00 42.84 3.51
3298 3573 2.223805 GGAAAGTCACCAACCTGCAAAG 60.224 50.000 0.00 0.00 0.00 2.77
3311 3586 0.903454 GGTCCCTCTCCGGAAAGTCA 60.903 60.000 5.23 0.00 32.34 3.41
3335 3610 7.648908 GCCTATATCTCATCTTCTTCATCATCG 59.351 40.741 0.00 0.00 0.00 3.84
3429 3704 5.922053 TCACTAGGTACAGATAAGCGACTA 58.078 41.667 0.00 0.00 0.00 2.59
3437 3713 7.175816 GCTCAATCATCTCACTAGGTACAGATA 59.824 40.741 0.00 0.00 0.00 1.98
3462 3738 1.600957 CACTAGCCAGTACATGCATGC 59.399 52.381 26.53 11.82 32.21 4.06
3543 3837 4.631813 AGCTTTTTAGTAATCCAGCGACTG 59.368 41.667 0.00 0.00 32.31 3.51
3555 3849 6.630203 TCTTGGGGTATGAGCTTTTTAGTA 57.370 37.500 0.00 0.00 0.00 1.82
3596 3891 8.103660 TCAAGTTTATATACCCATTACACCCA 57.896 34.615 0.00 0.00 0.00 4.51
3656 3955 5.049828 GTGGCTAATGAAAAACAGTGCTTT 58.950 37.500 0.00 0.00 0.00 3.51
3706 4005 8.115490 AGCTAAAGTTGAAGATAATGCTTGTT 57.885 30.769 0.00 0.00 0.00 2.83
3721 4020 7.383102 ACATTGGTTCAGATAGCTAAAGTTG 57.617 36.000 0.00 0.00 0.00 3.16
3746 4045 8.352137 TCATCTTTAGAATTTCCTGAATTGCA 57.648 30.769 0.00 0.00 38.06 4.08
3773 4072 0.884704 TCAGTTCTCCTTGCCGTTGC 60.885 55.000 0.00 0.00 38.26 4.17
3819 4118 4.508551 TTCATGGCATCTGGACTGTATT 57.491 40.909 0.00 0.00 0.00 1.89
3828 4127 2.605818 CGGCAATTTTTCATGGCATCTG 59.394 45.455 0.00 0.00 41.79 2.90
3829 4128 2.896168 CGGCAATTTTTCATGGCATCT 58.104 42.857 0.00 0.00 41.79 2.90
3848 4147 4.628333 TCCTCGTAGAAAATAAGTTTGGCG 59.372 41.667 0.00 0.00 34.09 5.69
3890 4189 7.148423 TGTCATGTGTCATTGTATTAGAAGCAC 60.148 37.037 0.00 0.00 0.00 4.40
3919 4218 6.683974 TCTGTTTTAGGAATATGCAAGAGC 57.316 37.500 0.00 0.00 42.57 4.09
3933 4232 6.918022 GTGACCATTCCTGTTTTCTGTTTTAG 59.082 38.462 0.00 0.00 0.00 1.85
3961 4260 2.991250 ACAAGCATGTCCCAGTATGTC 58.009 47.619 0.00 0.00 33.41 3.06
3996 4295 0.839946 AGCTCTGTTGTTGTCACCCT 59.160 50.000 0.00 0.00 0.00 4.34
4002 4301 4.281941 TCATCTCTACAGCTCTGTTGTTGT 59.718 41.667 7.92 0.00 41.83 3.32
4021 4320 4.125912 GCAATGAAGTGCTACGATCATC 57.874 45.455 0.00 0.00 41.51 2.92
4059 4358 4.348656 CATGTTCATGGATTTCGAGCAAG 58.651 43.478 5.02 0.00 0.00 4.01
4132 4431 2.083774 GGCACCGAATGAAGATGAACA 58.916 47.619 0.00 0.00 0.00 3.18
4147 4446 1.076705 GAGGATTCCCCAAGGCACC 60.077 63.158 0.00 0.00 37.41 5.01
4256 4555 2.762887 TCCTGATACTCTGCTGGAAGTG 59.237 50.000 0.00 0.00 35.30 3.16
4280 4579 4.284829 TGTCAACTATGTCAAGATGGCA 57.715 40.909 0.00 0.00 35.91 4.92


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

AutoCloner maintained by Alex Coulton.