Multiple sequence alignment - TraesCS1B01G434400

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 TraesCS1B01G434400 chr1B 100.000 5325 0 0 1 5325 658915841 658910517 0.000000e+00 9834
1 TraesCS1B01G434400 chr1B 88.932 515 50 5 972 1482 637286309 637285798 3.500000e-176 628
2 TraesCS1B01G434400 chr1B 87.525 505 49 5 213 706 619528830 619529331 5.980000e-159 571
3 TraesCS1B01G434400 chr1B 89.421 397 38 4 217 611 619430140 619430534 1.030000e-136 497
4 TraesCS1B01G434400 chr1B 85.185 432 64 0 231 662 619535200 619535631 1.360000e-120 444
5 TraesCS1B01G434400 chr1B 90.071 282 26 2 1489 1769 637285761 637285481 1.090000e-96 364
6 TraesCS1B01G434400 chr1D 92.905 3890 153 35 1492 5325 473861905 473858083 0.000000e+00 5541
7 TraesCS1B01G434400 chr1D 90.015 1362 72 24 1 1317 473863420 473862078 0.000000e+00 1703
8 TraesCS1B01G434400 chr1D 91.617 501 40 2 213 713 451140231 451140729 0.000000e+00 691
9 TraesCS1B01G434400 chr1D 92.908 141 10 0 217 357 451243741 451243881 6.990000e-49 206
10 TraesCS1B01G434400 chr1A 94.683 1279 58 5 1489 2762 568107757 568106484 0.000000e+00 1977
11 TraesCS1B01G434400 chr1A 88.642 1303 79 34 213 1482 568109064 568107798 0.000000e+00 1522
12 TraesCS1B01G434400 chr1A 91.417 501 41 2 213 713 545896228 545896726 0.000000e+00 686
13 TraesCS1B01G434400 chr1A 88.060 134 13 3 2 134 568109229 568109098 7.140000e-34 156
14 TraesCS1B01G434400 chr1A 92.784 97 7 0 2992 3088 351606862 351606766 2.000000e-29 141
15 TraesCS1B01G434400 chrUn 91.462 1265 84 15 3360 4616 1490509 1491757 0.000000e+00 1716
16 TraesCS1B01G434400 chrUn 96.562 640 20 2 4687 5325 1491862 1492500 0.000000e+00 1059
17 TraesCS1B01G434400 chrUn 94.647 411 14 2 2757 3159 477580889 477580479 9.730000e-177 630
18 TraesCS1B01G434400 chr4B 88.544 515 52 5 972 1482 11349855 11349344 7.580000e-173 617
19 TraesCS1B01G434400 chr4B 90.780 282 24 2 1489 1769 11349307 11349027 5.030000e-100 375
20 TraesCS1B01G434400 chr7A 83.832 334 49 4 333 662 625381626 625381958 4.000000e-81 313
21 TraesCS1B01G434400 chr7A 91.000 100 9 0 2987 3086 22891162 22891261 9.300000e-28 135
22 TraesCS1B01G434400 chr7D 83.533 334 50 4 333 662 543393827 543394159 1.860000e-79 307
23 TraesCS1B01G434400 chr7B 93.000 100 7 0 2989 3088 508189378 508189477 4.300000e-31 147
24 TraesCS1B01G434400 chr7B 93.750 96 6 0 2993 3088 194667993 194668088 1.550000e-30 145
25 TraesCS1B01G434400 chr7B 88.596 114 13 0 2975 3088 562993183 562993070 7.190000e-29 139
26 TraesCS1B01G434400 chr4D 91.000 100 9 0 2989 3088 490940037 490940136 9.300000e-28 135
27 TraesCS1B01G434400 chr2D 91.000 100 9 0 2989 3088 260369988 260370087 9.300000e-28 135


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 TraesCS1B01G434400 chr1B 658910517 658915841 5324 True 9834.000000 9834 100.000000 1 5325 1 chr1B.!!$R1 5324
1 TraesCS1B01G434400 chr1B 619528830 619529331 501 False 571.000000 571 87.525000 213 706 1 chr1B.!!$F2 493
2 TraesCS1B01G434400 chr1B 637285481 637286309 828 True 496.000000 628 89.501500 972 1769 2 chr1B.!!$R2 797
3 TraesCS1B01G434400 chr1D 473858083 473863420 5337 True 3622.000000 5541 91.460000 1 5325 2 chr1D.!!$R1 5324
4 TraesCS1B01G434400 chr1A 568106484 568109229 2745 True 1218.333333 1977 90.461667 2 2762 3 chr1A.!!$R2 2760
5 TraesCS1B01G434400 chrUn 1490509 1492500 1991 False 1387.500000 1716 94.012000 3360 5325 2 chrUn.!!$F1 1965
6 TraesCS1B01G434400 chr4B 11349027 11349855 828 True 496.000000 617 89.662000 972 1769 2 chr4B.!!$R1 797

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
874 901 0.254747 CCCGTTAATGGGCCTCTTCA 59.745 55.000 19.97 0.0 43.70 3.02 F
1890 1996 0.036164 ACTTTATGACACGCCAGGCA 59.964 50.000 13.30 0.0 0.00 4.75 F
1995 2101 0.729116 CGTCGCTGATGCTTCCAAAT 59.271 50.000 0.00 0.0 36.97 2.32 F
2009 2115 1.342819 TCCAAATTGCCCGAAAAGGTG 59.657 47.619 0.00 0.0 38.74 4.00 F
3268 3403 0.038166 TAGCCTGGAGCCTTTGTTGG 59.962 55.000 0.00 0.0 45.47 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 2739 1.400846 CATCAGCAATCAGGCAGACAC 59.599 52.381 0.0 0.0 31.88 3.67 R
2990 3117 2.285707 TGGGACAGAGGGAGTAGTAGT 58.714 52.381 0.0 0.0 0.00 2.73 R
3082 3209 3.327757 TCTGCACAACTGATTTACCCTCT 59.672 43.478 0.0 0.0 0.00 3.69 R
3783 3919 5.589855 CCTGAAATATCCAATACTGCACACA 59.410 40.000 0.0 0.0 0.00 3.72 R
4624 4805 0.187117 TCATGGAGCCAAACAACCCA 59.813 50.000 0.0 0.0 0.00 4.51 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
60 61 7.443272 CAGAACATGATAGCATTGTAATCCTGA 59.557 37.037 0.00 0.00 30.68 3.86
88 89 5.118990 TGAAGACCTGTTGACAAGAAGAAG 58.881 41.667 0.00 0.00 0.00 2.85
96 97 7.721399 ACCTGTTGACAAGAAGAAGAAATACAT 59.279 33.333 0.00 0.00 0.00 2.29
114 115 9.599322 GAAATACATCTGATTTTAATAGGTGCG 57.401 33.333 0.00 0.00 0.00 5.34
132 133 0.817634 CGCTTCACACAGGGGAACAA 60.818 55.000 0.00 0.00 0.00 2.83
138 139 2.092158 TCACACAGGGGAACAACATCAA 60.092 45.455 0.00 0.00 0.00 2.57
149 150 6.458210 GGGAACAACATCAAGAATCATTTGT 58.542 36.000 0.00 0.00 0.00 2.83
154 155 8.394971 ACAACATCAAGAATCATTTGTAGTCA 57.605 30.769 0.00 0.00 0.00 3.41
169 172 9.590451 CATTTGTAGTCAATGGCTATTTTTCAT 57.410 29.630 0.00 0.00 33.32 2.57
682 689 1.746991 CTGCTTCCCCTTCGCCTTC 60.747 63.158 0.00 0.00 0.00 3.46
750 759 0.855855 TGGAGGAGGAGGAGGAGGAA 60.856 60.000 0.00 0.00 0.00 3.36
761 770 0.766288 GAGGAGGAAGGAGGGGATGG 60.766 65.000 0.00 0.00 0.00 3.51
762 771 1.238896 AGGAGGAAGGAGGGGATGGA 61.239 60.000 0.00 0.00 0.00 3.41
786 795 1.608283 CCTAGCTAGGGTTTATGCCGC 60.608 57.143 29.47 0.00 39.86 6.53
794 803 1.135939 GTTTATGCCGCGTGGGTTC 59.864 57.895 18.41 0.00 38.44 3.62
795 804 1.003112 TTTATGCCGCGTGGGTTCT 60.003 52.632 18.41 0.00 38.44 3.01
873 900 3.095922 CCCGTTAATGGGCCTCTTC 57.904 57.895 19.97 0.00 43.70 2.87
874 901 0.254747 CCCGTTAATGGGCCTCTTCA 59.745 55.000 19.97 0.00 43.70 3.02
884 911 2.993853 CCTCTTCAGGTCTGGGCC 59.006 66.667 0.00 0.00 34.60 5.80
934 972 3.791993 TTAAATCGTTTTGGGTCGTCG 57.208 42.857 1.69 0.00 0.00 5.12
938 976 0.318107 TCGTTTTGGGTCGTCGTCTC 60.318 55.000 0.00 0.00 0.00 3.36
957 995 5.148502 GTCTCCTTCCACTCTTATCCCATA 58.851 45.833 0.00 0.00 0.00 2.74
959 997 3.904339 TCCTTCCACTCTTATCCCATAGC 59.096 47.826 0.00 0.00 0.00 2.97
961 999 3.344535 TCCACTCTTATCCCATAGCCA 57.655 47.619 0.00 0.00 0.00 4.75
962 1000 2.972713 TCCACTCTTATCCCATAGCCAC 59.027 50.000 0.00 0.00 0.00 5.01
963 1001 2.975489 CCACTCTTATCCCATAGCCACT 59.025 50.000 0.00 0.00 0.00 4.00
969 1007 4.968719 TCTTATCCCATAGCCACTTTCTCA 59.031 41.667 0.00 0.00 0.00 3.27
970 1008 3.853355 ATCCCATAGCCACTTTCTCAG 57.147 47.619 0.00 0.00 0.00 3.35
1001 1055 0.110104 GCAATGGAGCTAGGCCTCAT 59.890 55.000 9.68 2.53 33.47 2.90
1158 1215 0.108186 TGAGCTATGCGGTGGTTGAG 60.108 55.000 0.00 0.00 0.00 3.02
1375 1442 2.207501 ATTCAGCACTCCCTGGCCAG 62.208 60.000 26.87 26.87 33.64 4.85
1391 1458 5.036117 TGGCCAGGTAGATTATTTCAGTC 57.964 43.478 0.00 0.00 0.00 3.51
1410 1477 5.409520 TCAGTCTTTAGTGTTCATGATGCAC 59.590 40.000 17.95 17.95 0.00 4.57
1449 1517 7.309438 GGAGCATTCTTGGTTCAGTAAAATTCT 60.309 37.037 0.00 0.00 32.62 2.40
1482 1550 8.033626 TGTCATTGTGCAGCATAAATAAATGAA 58.966 29.630 8.83 0.00 35.30 2.57
1521 1623 4.655963 TGGGAGAATTCAGAGGAAACAAG 58.344 43.478 8.44 0.00 36.43 3.16
1532 1634 6.826668 TCAGAGGAAACAAGTTATCTGACAA 58.173 36.000 15.57 2.33 38.52 3.18
1574 1676 2.733227 GCCATGTTGTAATGCTGTGAGC 60.733 50.000 0.00 0.00 42.82 4.26
1657 1759 3.181500 GCACCCTGATAAACCAAATCGTC 60.181 47.826 0.00 0.00 0.00 4.20
1776 1878 1.276421 TCTCCAAAGCACCTGTAGAGC 59.724 52.381 0.00 0.00 0.00 4.09
1790 1892 3.999001 CTGTAGAGCTCAGTTCAAATGCA 59.001 43.478 17.77 1.15 0.00 3.96
1805 1907 8.028938 AGTTCAAATGCAGTATAAACCAATGTC 58.971 33.333 0.00 0.00 0.00 3.06
1890 1996 0.036164 ACTTTATGACACGCCAGGCA 59.964 50.000 13.30 0.00 0.00 4.75
1895 2001 0.816825 ATGACACGCCAGGCATCATC 60.817 55.000 13.30 3.61 0.00 2.92
1995 2101 0.729116 CGTCGCTGATGCTTCCAAAT 59.271 50.000 0.00 0.00 36.97 2.32
2009 2115 1.342819 TCCAAATTGCCCGAAAAGGTG 59.657 47.619 0.00 0.00 38.74 4.00
2014 2120 1.452145 TTGCCCGAAAAGGTGACTGC 61.452 55.000 0.00 0.00 42.68 4.40
2029 2135 4.226761 GTGACTGCCGACAAAAATAAAGG 58.773 43.478 0.00 0.00 0.00 3.11
2032 2138 4.142038 ACTGCCGACAAAAATAAAGGACT 58.858 39.130 0.00 0.00 0.00 3.85
2193 2299 3.058224 CCGGAGAAATCGCAAAGAAACTT 60.058 43.478 0.00 0.00 0.00 2.66
2210 2316 8.753497 AAGAAACTTGAGGTAAGAAACTGAAT 57.247 30.769 0.00 0.00 39.76 2.57
2397 2503 2.900106 GCTTCCACTGGGTCCTGCT 61.900 63.158 0.00 0.00 34.93 4.24
2436 2542 6.688637 TCATCACTATGGAAGATGCAAAAG 57.311 37.500 0.00 0.00 39.12 2.27
2438 2544 6.317140 TCATCACTATGGAAGATGCAAAAGTC 59.683 38.462 0.00 0.00 39.12 3.01
2450 2556 2.874701 TGCAAAAGTCTCTGAAGCAGTC 59.125 45.455 0.00 0.00 32.61 3.51
2451 2557 2.225255 GCAAAAGTCTCTGAAGCAGTCC 59.775 50.000 0.00 0.00 32.61 3.85
2452 2558 3.737850 CAAAAGTCTCTGAAGCAGTCCT 58.262 45.455 0.00 0.00 32.61 3.85
2453 2559 4.133078 CAAAAGTCTCTGAAGCAGTCCTT 58.867 43.478 0.00 0.00 36.19 3.36
2462 2568 3.861840 TGAAGCAGTCCTTGTACTATGC 58.138 45.455 0.00 0.00 32.78 3.14
2492 2598 7.989826 ACAGCCATTTTCTTTATCATGTAGAC 58.010 34.615 0.00 0.00 0.00 2.59
2496 2602 9.120538 GCCATTTTCTTTATCATGTAGACCTAA 57.879 33.333 0.00 0.00 0.00 2.69
2609 2716 8.488651 CCTTTTGGTAGTACGAAATAATCAGT 57.511 34.615 10.76 0.00 34.07 3.41
2610 2717 8.943002 CCTTTTGGTAGTACGAAATAATCAGTT 58.057 33.333 10.76 0.00 34.07 3.16
2632 2739 3.882888 TGTTCTGCCACTTTGGTTAAGAG 59.117 43.478 0.00 0.00 40.46 2.85
2834 2960 6.150140 ACTGTTCTATGAGTTCAATTGCTTCC 59.850 38.462 0.00 0.00 0.00 3.46
2916 3043 5.470098 ACCATCATTGTAACACAGTTCTGAC 59.530 40.000 6.83 0.00 0.00 3.51
2971 3098 5.066505 GTGAACTCGGAGGCATGATAATTTT 59.933 40.000 10.23 0.00 0.00 1.82
2974 3101 7.502226 TGAACTCGGAGGCATGATAATTTTAAT 59.498 33.333 10.23 0.00 0.00 1.40
3004 3131 7.122948 CACATTTGACTAACTACTACTCCCTCT 59.877 40.741 0.00 0.00 0.00 3.69
3011 3138 2.242708 ACTACTACTCCCTCTGTCCCAG 59.757 54.545 0.00 0.00 0.00 4.45
3043 3170 7.326547 GTGTCTCAACTTTGTACTAACTCTAGC 59.673 40.741 0.00 0.00 0.00 3.42
3058 3185 5.130292 ACTCTAGCGCAAAGTTGTACTAA 57.870 39.130 11.47 0.00 0.00 2.24
3081 3208 5.892348 AGGTTGAGACACTTATTTTGGGAT 58.108 37.500 0.00 0.00 0.00 3.85
3082 3209 7.027874 AGGTTGAGACACTTATTTTGGGATA 57.972 36.000 0.00 0.00 0.00 2.59
3208 3343 7.309744 CCCACAGCTTTAAACTTTATTCCATCA 60.310 37.037 0.00 0.00 0.00 3.07
3253 3388 8.954350 AGTCATTATGATGCTAAAATCATAGCC 58.046 33.333 0.00 0.00 45.61 3.93
3254 3389 8.954350 GTCATTATGATGCTAAAATCATAGCCT 58.046 33.333 0.00 0.00 45.61 4.58
3255 3390 8.953313 TCATTATGATGCTAAAATCATAGCCTG 58.047 33.333 6.90 6.91 45.61 4.85
3256 3391 7.692460 TTATGATGCTAAAATCATAGCCTGG 57.308 36.000 6.90 0.00 45.61 4.45
3257 3392 5.308976 TGATGCTAAAATCATAGCCTGGA 57.691 39.130 0.00 0.00 46.19 3.86
3258 3393 5.311265 TGATGCTAAAATCATAGCCTGGAG 58.689 41.667 0.00 0.00 46.19 3.86
3259 3394 3.480470 TGCTAAAATCATAGCCTGGAGC 58.520 45.455 0.00 0.00 46.19 4.70
3260 3395 2.816672 GCTAAAATCATAGCCTGGAGCC 59.183 50.000 0.00 0.00 45.47 4.70
3261 3396 3.497584 GCTAAAATCATAGCCTGGAGCCT 60.498 47.826 0.00 0.00 45.47 4.58
3262 3397 3.677156 AAAATCATAGCCTGGAGCCTT 57.323 42.857 0.00 0.00 45.47 4.35
3263 3398 3.677156 AAATCATAGCCTGGAGCCTTT 57.323 42.857 0.00 0.00 45.47 3.11
3264 3399 2.653234 ATCATAGCCTGGAGCCTTTG 57.347 50.000 0.00 0.00 45.47 2.77
3265 3400 1.289160 TCATAGCCTGGAGCCTTTGT 58.711 50.000 0.00 0.00 45.47 2.83
3266 3401 1.635487 TCATAGCCTGGAGCCTTTGTT 59.365 47.619 0.00 0.00 45.47 2.83
3267 3402 1.747355 CATAGCCTGGAGCCTTTGTTG 59.253 52.381 0.00 0.00 45.47 3.33
3268 3403 0.038166 TAGCCTGGAGCCTTTGTTGG 59.962 55.000 0.00 0.00 45.47 3.77
3320 3455 7.410485 GCATATCTGTTAAAGGTAGTTTCAGC 58.590 38.462 0.00 0.00 0.00 4.26
3327 3462 3.963428 AAGGTAGTTTCAGCTCGACAT 57.037 42.857 0.00 0.00 0.00 3.06
3357 3492 7.656137 TCTGTTAAAGGTAGTCTCATGTTTGTC 59.344 37.037 0.00 0.00 0.00 3.18
3388 3523 4.966168 TGGTCTATTACTGCATTCCAGGTA 59.034 41.667 0.00 0.00 46.14 3.08
3649 3784 7.379529 CCTGTTTGTGTGATGTAATTTCTGTTC 59.620 37.037 0.00 0.00 0.00 3.18
3769 3904 7.499200 TTATACTTGGGAAGGTAAAGCAGTA 57.501 36.000 0.00 0.00 0.00 2.74
3775 3910 4.581409 TGGGAAGGTAAAGCAGTACAAAAC 59.419 41.667 0.00 0.00 0.00 2.43
3778 3913 6.239204 GGGAAGGTAAAGCAGTACAAAACAAT 60.239 38.462 0.00 0.00 0.00 2.71
3797 3933 7.887996 AACAATTATTTGTGTGCAGTATTGG 57.112 32.000 3.86 0.00 45.30 3.16
3812 3948 8.725148 GTGCAGTATTGGATATTTCAGGATTAG 58.275 37.037 0.00 0.00 0.00 1.73
4012 4148 4.028993 TGGGGAATGAAACAGTTCCTAC 57.971 45.455 4.36 0.00 42.76 3.18
4019 4155 7.309012 GGGAATGAAACAGTTCCTACCTTAAAC 60.309 40.741 4.36 0.00 42.76 2.01
4036 4172 8.880878 ACCTTAAACATTTTAACGAGCAAAAT 57.119 26.923 0.00 0.00 36.31 1.82
4045 4181 3.853831 AACGAGCAAAATGATCATGCA 57.146 38.095 19.19 0.00 42.45 3.96
4049 4185 4.201851 ACGAGCAAAATGATCATGCACTAC 60.202 41.667 19.19 8.57 42.45 2.73
4050 4186 4.277258 GAGCAAAATGATCATGCACTACG 58.723 43.478 19.19 2.79 42.45 3.51
4053 4189 4.496895 GCAAAATGATCATGCACTACGTTC 59.503 41.667 9.46 0.00 39.81 3.95
4060 4196 3.937814 TCATGCACTACGTTCCTCAAAT 58.062 40.909 0.00 0.00 0.00 2.32
4112 4248 1.022735 CAGCATCCAGGCTTGACATC 58.977 55.000 0.00 0.00 42.71 3.06
4189 4326 1.918253 GCATGATCACCCCCTCTGT 59.082 57.895 0.00 0.00 0.00 3.41
4193 4337 3.435601 GCATGATCACCCCCTCTGTTATT 60.436 47.826 0.00 0.00 0.00 1.40
4197 4341 3.713826 TCACCCCCTCTGTTATTGTTC 57.286 47.619 0.00 0.00 0.00 3.18
4209 4353 7.148507 CCTCTGTTATTGTTCTAGAGCAGTTTG 60.149 40.741 9.79 1.20 34.88 2.93
4230 4374 8.181573 AGTTTGTAATCACCGCATACTATTTTG 58.818 33.333 0.00 0.00 0.00 2.44
4330 4475 6.091441 GGGAGATTCAAGCGCTATAAATACAG 59.909 42.308 12.05 0.00 0.00 2.74
4338 4483 2.404029 CGCTATAAATACAGGCGTGACG 59.596 50.000 14.38 0.00 40.78 4.35
4341 4486 3.513680 ATAAATACAGGCGTGACGTCA 57.486 42.857 15.76 15.76 32.13 4.35
4352 4497 2.385315 CGTGACGTCATCGCTTATCAT 58.615 47.619 23.12 0.00 41.18 2.45
4372 4518 4.660303 TCATGCATGGGAGTAGGAAATAGT 59.340 41.667 25.97 0.00 0.00 2.12
4374 4520 3.069586 TGCATGGGAGTAGGAAATAGTCG 59.930 47.826 0.00 0.00 35.01 4.18
4375 4521 3.069729 GCATGGGAGTAGGAAATAGTCGT 59.930 47.826 0.00 0.00 35.01 4.34
4477 4628 9.498176 GTTATTAGTCAGGAACTCTTACCAAAA 57.502 33.333 0.00 0.00 39.55 2.44
4488 4639 9.626045 GGAACTCTTACCAAAATTTGATGTAAG 57.374 33.333 19.61 19.61 37.05 2.34
4520 4671 3.679389 ACCATGAAATCGTTGCTTCTCT 58.321 40.909 0.00 0.00 0.00 3.10
4528 4679 2.124903 TCGTTGCTTCTCTGTCGAAAC 58.875 47.619 0.00 0.00 0.00 2.78
4529 4680 2.128035 CGTTGCTTCTCTGTCGAAACT 58.872 47.619 0.00 0.00 0.00 2.66
4565 4717 1.863267 CTGTAGATAGCCTGCAGTGC 58.137 55.000 13.81 15.45 46.44 4.40
4616 4768 4.640201 TCTGCTGAAGTTGCTTTACACTTT 59.360 37.500 0.00 0.00 0.00 2.66
4622 4803 4.307443 AGTTGCTTTACACTTTGCCTTC 57.693 40.909 0.00 0.00 0.00 3.46
4624 4805 4.402474 AGTTGCTTTACACTTTGCCTTCTT 59.598 37.500 0.00 0.00 0.00 2.52
5025 5215 6.012745 ACCAAAAGAGAATGCCAAGACTAAT 58.987 36.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 2.398588 TGTCAACAGGTCTTCAGGTCT 58.601 47.619 0.00 0.00 0.00 3.85
88 89 9.599322 CGCACCTATTAAAATCAGATGTATTTC 57.401 33.333 0.00 0.00 0.00 2.17
96 97 5.064707 GTGAAGCGCACCTATTAAAATCAGA 59.935 40.000 11.47 0.00 41.78 3.27
114 115 0.668535 GTTGTTCCCCTGTGTGAAGC 59.331 55.000 0.00 0.00 0.00 3.86
132 133 8.464404 CCATTGACTACAAATGATTCTTGATGT 58.536 33.333 0.00 0.00 39.54 3.06
138 139 8.757982 AATAGCCATTGACTACAAATGATTCT 57.242 30.769 0.00 0.00 39.54 2.40
149 150 7.771361 TCCGTTATGAAAAATAGCCATTGACTA 59.229 33.333 0.00 0.00 0.00 2.59
154 155 8.006298 TGAATCCGTTATGAAAAATAGCCATT 57.994 30.769 0.00 0.00 0.00 3.16
169 172 2.188469 GGCCCGCTGAATCCGTTA 59.812 61.111 0.00 0.00 0.00 3.18
203 207 2.034179 TCATCACCAAGGTATCTACGCG 59.966 50.000 3.53 3.53 0.00 6.01
208 212 2.158900 CGCCTTCATCACCAAGGTATCT 60.159 50.000 0.00 0.00 42.35 1.98
597 604 2.167861 CGAGCGGCCTTCAAGCTAC 61.168 63.158 0.00 0.00 41.84 3.58
750 759 1.007238 TAGGCTCTCCATCCCCTCCT 61.007 60.000 0.00 0.00 33.74 3.69
761 770 3.306433 GCATAAACCCTAGCTAGGCTCTC 60.306 52.174 31.33 13.36 42.26 3.20
762 771 2.635427 GCATAAACCCTAGCTAGGCTCT 59.365 50.000 31.33 19.47 42.26 4.09
857 884 1.065418 ACCTGAAGAGGCCCATTAACG 60.065 52.381 0.00 0.00 44.33 3.18
861 888 0.622665 CAGACCTGAAGAGGCCCATT 59.377 55.000 0.00 0.00 44.33 3.16
874 901 2.693864 CATCCCAGGCCCAGACCT 60.694 66.667 0.00 0.00 42.30 3.85
906 933 4.020039 ACCCAAAACGATTTAATTTCCCCC 60.020 41.667 0.00 0.00 0.00 5.40
934 972 3.375699 TGGGATAAGAGTGGAAGGAGAC 58.624 50.000 0.00 0.00 0.00 3.36
938 976 3.008485 GGCTATGGGATAAGAGTGGAAGG 59.992 52.174 0.00 0.00 0.00 3.46
957 995 0.321475 GAGCAGCTGAGAAAGTGGCT 60.321 55.000 20.43 2.94 39.25 4.75
959 997 1.275856 AGAGAGCAGCTGAGAAAGTGG 59.724 52.381 20.43 0.00 0.00 4.00
961 999 1.338011 GCAGAGAGCAGCTGAGAAAGT 60.338 52.381 20.43 0.00 44.79 2.66
962 1000 1.361793 GCAGAGAGCAGCTGAGAAAG 58.638 55.000 20.43 2.90 44.79 2.62
963 1001 0.389556 CGCAGAGAGCAGCTGAGAAA 60.390 55.000 20.43 0.00 46.13 2.52
969 1007 2.107292 CATTGCGCAGAGAGCAGCT 61.107 57.895 11.31 0.00 46.01 4.24
970 1008 2.403987 CATTGCGCAGAGAGCAGC 59.596 61.111 11.31 0.00 46.01 5.25
1100 1157 2.446802 CCCCAGCCCTCCTACTCC 60.447 72.222 0.00 0.00 0.00 3.85
1158 1215 0.762461 CCTCCTCCACCTCCTCATCC 60.762 65.000 0.00 0.00 0.00 3.51
1391 1458 5.375417 TTGGTGCATCATGAACACTAAAG 57.625 39.130 23.68 1.43 32.73 1.85
1410 1477 0.899720 ATGCTCCTGGTTGCATTTGG 59.100 50.000 18.74 0.00 46.29 3.28
1418 1485 2.158475 TGAACCAAGAATGCTCCTGGTT 60.158 45.455 9.28 9.28 41.67 3.67
1424 1491 7.540055 CAGAATTTTACTGAACCAAGAATGCTC 59.460 37.037 0.00 0.00 37.54 4.26
1449 1517 2.364647 TGCTGCACAATGACAAATTCCA 59.635 40.909 0.00 0.00 0.00 3.53
1542 1644 6.578172 GCATTACAACATGGCAATTGTTTTTC 59.422 34.615 21.14 8.93 39.67 2.29
1545 1647 5.179742 CAGCATTACAACATGGCAATTGTTT 59.820 36.000 21.14 10.15 39.67 2.83
1574 1676 1.447217 TGGAGACACACAGCACAGG 59.553 57.895 0.00 0.00 33.40 4.00
1657 1759 0.917259 CGATCGAAAGCTTCTGACCG 59.083 55.000 10.26 0.00 0.00 4.79
1776 1878 7.144722 TGGTTTATACTGCATTTGAACTGAG 57.855 36.000 0.00 0.00 0.00 3.35
1790 1892 6.352222 CCTCTGTGGAGACATTGGTTTATACT 60.352 42.308 0.00 0.00 46.14 2.12
1805 1907 6.547930 ATCATCATGATATCCTCTGTGGAG 57.452 41.667 8.15 0.00 37.75 3.86
1825 1931 4.124970 CTCGGATCAGCATTCAGAAATCA 58.875 43.478 0.00 0.00 0.00 2.57
1890 1996 5.623824 GCTTGTGCATTTCCTTCTTGATGAT 60.624 40.000 0.00 0.00 39.41 2.45
1895 2001 3.655276 AGCTTGTGCATTTCCTTCTTG 57.345 42.857 0.00 0.00 42.74 3.02
1995 2101 1.452145 GCAGTCACCTTTTCGGGCAA 61.452 55.000 0.00 0.00 36.97 4.52
2009 2115 4.215613 AGTCCTTTATTTTTGTCGGCAGTC 59.784 41.667 0.00 0.00 0.00 3.51
2014 2120 5.935789 TCACCTAGTCCTTTATTTTTGTCGG 59.064 40.000 0.00 0.00 0.00 4.79
2029 2135 5.652994 AGACTCAAGACATTCACCTAGTC 57.347 43.478 0.00 0.00 33.86 2.59
2032 2138 5.580998 AGGTAGACTCAAGACATTCACCTA 58.419 41.667 0.00 0.00 32.22 3.08
2412 2518 6.832384 ACTTTTGCATCTTCCATAGTGATGAT 59.168 34.615 6.41 0.00 39.72 2.45
2413 2519 6.182627 ACTTTTGCATCTTCCATAGTGATGA 58.817 36.000 6.41 0.00 39.72 2.92
2414 2520 6.318144 AGACTTTTGCATCTTCCATAGTGATG 59.682 38.462 0.00 0.00 40.16 3.07
2419 2525 6.111382 TCAGAGACTTTTGCATCTTCCATAG 58.889 40.000 0.00 0.00 0.00 2.23
2436 2542 2.829741 ACAAGGACTGCTTCAGAGAC 57.170 50.000 0.29 0.00 35.18 3.36
2438 2544 3.951775 AGTACAAGGACTGCTTCAGAG 57.048 47.619 0.29 0.00 35.18 3.35
2450 2556 2.874701 GCTGTCCATGCATAGTACAAGG 59.125 50.000 0.00 0.00 0.00 3.61
2451 2557 2.874701 GGCTGTCCATGCATAGTACAAG 59.125 50.000 0.00 0.63 0.00 3.16
2452 2558 2.238395 TGGCTGTCCATGCATAGTACAA 59.762 45.455 0.00 0.00 37.47 2.41
2453 2559 1.836802 TGGCTGTCCATGCATAGTACA 59.163 47.619 0.00 3.29 37.47 2.90
2492 2598 7.592938 TGCACATTTCTACTTGATTTGTTAGG 58.407 34.615 0.00 0.00 0.00 2.69
2496 2602 6.366877 GCATTGCACATTTCTACTTGATTTGT 59.633 34.615 3.15 0.00 0.00 2.83
2557 2663 6.065976 TGATTCTTGAGATTAAGGCCAAGA 57.934 37.500 5.01 0.00 42.00 3.02
2609 2716 4.274147 TCTTAACCAAAGTGGCAGAACAA 58.726 39.130 0.00 0.00 42.67 2.83
2610 2717 3.882888 CTCTTAACCAAAGTGGCAGAACA 59.117 43.478 0.00 0.00 42.67 3.18
2632 2739 1.400846 CATCAGCAATCAGGCAGACAC 59.599 52.381 0.00 0.00 31.88 3.67
2834 2960 4.236935 GTGGTATTGGTTTGCAACTGATG 58.763 43.478 0.00 0.00 0.00 3.07
2916 3043 5.164954 GCTTATATAAAGCTGTCTCGGGAG 58.835 45.833 2.55 0.00 40.01 4.30
2971 3098 9.582431 GTAGTAGTTAGTCAAATGTGCTGATTA 57.418 33.333 0.00 0.00 0.00 1.75
2974 3101 7.228314 AGTAGTAGTTAGTCAAATGTGCTGA 57.772 36.000 0.00 0.00 0.00 4.26
2990 3117 2.285707 TGGGACAGAGGGAGTAGTAGT 58.714 52.381 0.00 0.00 0.00 2.73
3004 3131 4.593206 AGTTGAGACACTTATTCTGGGACA 59.407 41.667 0.00 0.00 0.00 4.02
3043 3170 4.748102 TCTCAACCTTAGTACAACTTTGCG 59.252 41.667 0.00 0.00 0.00 4.85
3058 3185 5.319043 TCCCAAAATAAGTGTCTCAACCT 57.681 39.130 0.00 0.00 0.00 3.50
3081 3208 4.530553 TCTGCACAACTGATTTACCCTCTA 59.469 41.667 0.00 0.00 0.00 2.43
3082 3209 3.327757 TCTGCACAACTGATTTACCCTCT 59.672 43.478 0.00 0.00 0.00 3.69
3259 3394 9.353999 GTAAAAACAATATCTAGCCAACAAAGG 57.646 33.333 0.00 0.00 0.00 3.11
3260 3395 9.906660 TGTAAAAACAATATCTAGCCAACAAAG 57.093 29.630 0.00 0.00 0.00 2.77
3261 3396 9.906660 CTGTAAAAACAATATCTAGCCAACAAA 57.093 29.630 0.00 0.00 0.00 2.83
3262 3397 9.073475 ACTGTAAAAACAATATCTAGCCAACAA 57.927 29.630 0.00 0.00 0.00 2.83
3263 3398 8.630054 ACTGTAAAAACAATATCTAGCCAACA 57.370 30.769 0.00 0.00 0.00 3.33
3264 3399 9.908152 AAACTGTAAAAACAATATCTAGCCAAC 57.092 29.630 0.00 0.00 0.00 3.77
3320 3455 9.828852 GACTACCTTTAACAGATATATGTCGAG 57.171 37.037 2.95 2.64 31.50 4.04
3388 3523 6.260936 CCCTGTAGCTAAACATCGAAATGAAT 59.739 38.462 0.00 0.00 36.67 2.57
3510 3645 9.014297 TGAAGAAAAATCTTTTCCCTCACTATC 57.986 33.333 7.98 0.00 0.00 2.08
3649 3784 8.779303 TGTAACTTGTAACATTAACCTGTCATG 58.221 33.333 0.00 0.00 0.00 3.07
3775 3910 9.970395 ATATCCAATACTGCACACAAATAATTG 57.030 29.630 0.00 0.00 42.46 2.32
3783 3919 5.589855 CCTGAAATATCCAATACTGCACACA 59.410 40.000 0.00 0.00 0.00 3.72
3823 3959 8.299570 CCTTCAATGTCTTGTTATGCTTAACTT 58.700 33.333 19.69 5.62 38.81 2.66
3841 3977 6.146021 GGTAGTTTGTGCAAAATCCTTCAATG 59.854 38.462 0.77 0.00 31.33 2.82
3955 4091 9.768215 TCTTATTTATGACCCAATTCCTTTTCT 57.232 29.630 0.00 0.00 0.00 2.52
4036 4172 2.495669 TGAGGAACGTAGTGCATGATCA 59.504 45.455 0.00 0.00 45.00 2.92
4049 4185 1.402968 CCATCCTGCATTTGAGGAACG 59.597 52.381 0.00 0.00 43.01 3.95
4050 4186 1.753073 CCCATCCTGCATTTGAGGAAC 59.247 52.381 0.00 0.00 43.01 3.62
4053 4189 2.148446 TTCCCATCCTGCATTTGAGG 57.852 50.000 0.00 0.00 0.00 3.86
4060 4196 4.165950 TCTTTATAGCTTTCCCATCCTGCA 59.834 41.667 0.00 0.00 0.00 4.41
4100 4236 3.064545 GGAAATCTTCGATGTCAAGCCTG 59.935 47.826 0.00 0.00 0.00 4.85
4189 4326 9.719355 TGATTACAAACTGCTCTAGAACAATAA 57.281 29.630 0.00 0.00 0.00 1.40
4193 4337 5.932303 GGTGATTACAAACTGCTCTAGAACA 59.068 40.000 0.00 0.00 0.00 3.18
4197 4341 3.307242 GCGGTGATTACAAACTGCTCTAG 59.693 47.826 0.00 0.00 43.84 2.43
4209 4353 7.241663 TCACAAAATAGTATGCGGTGATTAC 57.758 36.000 6.83 0.00 0.00 1.89
4230 4374 4.118410 CACCTTCACATCTATCTGCTCAC 58.882 47.826 0.00 0.00 0.00 3.51
4333 4478 2.097202 GCATGATAAGCGATGACGTCAC 60.097 50.000 22.71 13.72 41.98 3.67
4338 4483 2.161012 CCCATGCATGATAAGCGATGAC 59.839 50.000 28.31 0.00 33.85 3.06
4341 4486 2.039480 ACTCCCATGCATGATAAGCGAT 59.961 45.455 28.31 3.91 33.85 4.58
4352 4497 3.069586 CGACTATTTCCTACTCCCATGCA 59.930 47.826 0.00 0.00 0.00 3.96
4372 4518 8.040716 AGAAGAAAAGAAAAGAAGAAACACGA 57.959 30.769 0.00 0.00 0.00 4.35
4374 4520 9.066939 GTGAGAAGAAAAGAAAAGAAGAAACAC 57.933 33.333 0.00 0.00 0.00 3.32
4375 4521 8.244113 GGTGAGAAGAAAAGAAAAGAAGAAACA 58.756 33.333 0.00 0.00 0.00 2.83
4520 4671 4.237724 CAGAGCTGAATACAGTTTCGACA 58.762 43.478 0.00 0.00 45.04 4.35
4528 4679 2.499289 ACAGGGACAGAGCTGAATACAG 59.501 50.000 4.21 0.00 45.91 2.74
4529 4680 2.540383 ACAGGGACAGAGCTGAATACA 58.460 47.619 4.21 0.00 0.00 2.29
4565 4717 3.132289 AGAGGATTGAATTGGCATTGCAG 59.868 43.478 11.39 0.00 0.00 4.41
4574 4726 5.048224 AGCAGACAAACAGAGGATTGAATTG 60.048 40.000 0.00 0.00 31.80 2.32
4616 4768 1.118838 CCAAACAACCCAAGAAGGCA 58.881 50.000 0.00 0.00 35.39 4.75
4622 4803 1.001181 CATGGAGCCAAACAACCCAAG 59.999 52.381 0.00 0.00 0.00 3.61
4624 4805 0.187117 TCATGGAGCCAAACAACCCA 59.813 50.000 0.00 0.00 0.00 4.51
4788 4977 6.831976 AGTTCAGACCTTCAAGTTAAGATGT 58.168 36.000 0.00 0.00 0.00 3.06
4795 4984 4.822350 GGCTTTAGTTCAGACCTTCAAGTT 59.178 41.667 0.00 0.00 0.00 2.66
4797 4986 4.214332 GTGGCTTTAGTTCAGACCTTCAAG 59.786 45.833 0.00 0.00 0.00 3.02
4994 5184 6.084326 TGGCATTCTCTTTTGGTTAGTTTC 57.916 37.500 0.00 0.00 0.00 2.78
5025 5215 5.047802 GCTTCAGTCAAATTTTGATCAGGGA 60.048 40.000 14.54 6.20 42.47 4.20
5102 5292 1.805254 GACACGACCGGCTAGCTTA 59.195 57.895 15.72 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.