Multiple sequence alignment - TraesCS6D01G248300

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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 TraesCS6D01G248300 chr6D 100.000 6554 0 0 1 6554 351415251 351408698 0.000000e+00 12104.0
1 TraesCS6D01G248300 chr6D 91.255 263 13 5 2798 3050 434447163 434447425 3.760000e-92 350.0
2 TraesCS6D01G248300 chr6A 93.266 3386 139 43 3080 6391 491916694 491920064 0.000000e+00 4907.0
3 TraesCS6D01G248300 chr6A 93.180 2654 95 39 168 2792 491914058 491916654 0.000000e+00 3819.0
4 TraesCS6D01G248300 chr6A 89.091 165 16 2 6390 6553 491920376 491920539 3.100000e-48 204.0
5 TraesCS6D01G248300 chr6A 93.506 77 5 0 1 77 491913899 491913975 1.490000e-21 115.0
6 TraesCS6D01G248300 chr6B 94.457 3121 112 22 3446 6534 527931291 527934382 0.000000e+00 4748.0
7 TraesCS6D01G248300 chr6B 97.190 2135 35 13 668 2793 527928640 527930758 0.000000e+00 3587.0
8 TraesCS6D01G248300 chr6B 94.220 519 20 5 106 616 527927815 527928331 0.000000e+00 784.0
9 TraesCS6D01G248300 chr6B 96.774 403 7 3 3049 3450 527930756 527931153 0.000000e+00 667.0
10 TraesCS6D01G248300 chr7D 94.071 253 12 2 2798 3050 587298181 587298430 1.330000e-101 381.0
11 TraesCS6D01G248300 chr7D 95.098 204 10 0 2798 3001 495428735 495428532 8.200000e-84 322.0
12 TraesCS6D01G248300 chr7D 88.750 160 7 6 2910 3058 495428358 495428199 1.120000e-42 185.0
13 TraesCS6D01G248300 chr7D 100.000 37 0 0 1984 2020 577205978 577205942 1.180000e-07 69.4
14 TraesCS6D01G248300 chr5D 90.530 264 15 5 2798 3051 119267581 119267844 2.260000e-89 340.0
15 TraesCS6D01G248300 chr5D 80.977 389 37 16 3237 3606 370748199 370747829 2.330000e-69 274.0
16 TraesCS6D01G248300 chr5D 82.132 319 18 14 5039 5335 370746695 370746394 3.050000e-58 237.0
17 TraesCS6D01G248300 chr5D 86.893 206 14 6 5625 5821 370736338 370736137 1.110000e-52 219.0
18 TraesCS6D01G248300 chr5D 84.466 206 16 7 5625 5821 370746297 370746099 8.680000e-44 189.0
19 TraesCS6D01G248300 chr5D 86.316 95 5 5 4821 4907 370747411 370747317 5.410000e-16 97.1
20 TraesCS6D01G248300 chr2D 90.037 271 16 6 2797 3056 87775219 87774949 2.260000e-89 340.0
21 TraesCS6D01G248300 chr2D 96.078 204 8 0 2798 3001 15514322 15514119 3.790000e-87 333.0
22 TraesCS6D01G248300 chr5A 89.734 263 17 5 2798 3050 463746468 463746730 1.760000e-85 327.0
23 TraesCS6D01G248300 chr5A 85.019 267 30 4 2798 3054 316230793 316231059 5.040000e-66 263.0
24 TraesCS6D01G248300 chr5A 80.851 329 25 20 5938 6242 473323379 473323065 2.380000e-54 224.0
25 TraesCS6D01G248300 chr5A 84.274 248 19 9 3375 3606 473331657 473331414 2.380000e-54 224.0
26 TraesCS6D01G248300 chr7B 88.561 271 21 4 2798 3058 63124578 63124848 2.950000e-83 320.0
27 TraesCS6D01G248300 chr7B 78.639 529 56 32 5524 6018 147727355 147727860 1.380000e-76 298.0
28 TraesCS6D01G248300 chr7B 88.571 245 8 9 4217 4445 147724334 147724574 5.000000e-71 279.0
29 TraesCS6D01G248300 chr7B 84.293 191 9 6 6208 6394 147728840 147729013 4.070000e-37 167.0
30 TraesCS6D01G248300 chr7B 80.000 215 20 11 3975 4176 147723853 147724057 3.190000e-28 137.0
31 TraesCS6D01G248300 chr7B 100.000 34 0 0 6030 6063 147727857 147727890 5.490000e-06 63.9
32 TraesCS6D01G248300 chr4B 88.764 267 19 6 2795 3050 156530872 156531138 3.810000e-82 316.0
33 TraesCS6D01G248300 chr4B 85.818 275 27 6 2798 3061 137740680 137740407 1.390000e-71 281.0
34 TraesCS6D01G248300 chr7A 86.429 280 25 3 2787 3054 198920720 198920998 1.790000e-75 294.0
35 TraesCS6D01G248300 chr5B 83.235 340 24 16 6183 6511 440022253 440021936 1.390000e-71 281.0
36 TraesCS6D01G248300 chr5B 79.439 321 20 24 5039 5335 440025112 440024814 1.120000e-42 185.0
37 TraesCS6D01G248300 chr5B 80.784 255 16 12 5938 6173 440022630 440022390 1.130000e-37 169.0
38 TraesCS6D01G248300 chr5B 85.088 114 5 5 3975 4080 440026599 440026490 8.990000e-19 106.0
39 TraesCS6D01G248300 chr5B 91.781 73 5 1 3520 3592 440026882 440026811 4.180000e-17 100.0
40 TraesCS6D01G248300 chr5B 85.263 95 6 5 4821 4907 440026421 440026327 2.520000e-14 91.6
41 TraesCS6D01G248300 chr5B 100.000 31 0 0 5913 5943 440022688 440022658 2.550000e-04 58.4
42 TraesCS6D01G248300 chr2A 86.235 247 22 5 2823 3059 152007390 152007634 2.340000e-64 257.0
43 TraesCS6D01G248300 chr2A 86.000 50 7 0 195 244 444792771 444792722 3.000000e-03 54.7
44 TraesCS6D01G248300 chr1A 84.644 267 31 3 2798 3054 259841160 259841426 2.340000e-64 257.0
45 TraesCS6D01G248300 chr4A 84.270 267 32 2 2798 3054 512287440 512287706 1.090000e-62 252.0


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 TraesCS6D01G248300 chr6D 351408698 351415251 6553 True 12104.00 12104 100.00000 1 6554 1 chr6D.!!$R1 6553
1 TraesCS6D01G248300 chr6A 491913899 491920539 6640 False 2261.25 4907 92.26075 1 6553 4 chr6A.!!$F1 6552
2 TraesCS6D01G248300 chr6B 527927815 527934382 6567 False 2446.50 4748 95.66025 106 6534 4 chr6B.!!$F1 6428
3 TraesCS6D01G248300 chr7D 495428199 495428735 536 True 253.50 322 91.92400 2798 3058 2 chr7D.!!$R2 260

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
575 605 0.114954 ATCTGCCACCAAACACCCAT 59.885 50.000 0.0 0.0 0.00 4.00 F
1365 1658 0.318360 TGTACAACACCTCGCAGTCG 60.318 55.000 0.0 0.0 0.00 4.18 F
1402 1695 1.149174 CAGCTCCACCACCACAACT 59.851 57.895 0.0 0.0 0.00 3.16 F
2334 2643 1.471684 CCTCTAGCTTTACCACGACGT 59.528 52.381 0.0 0.0 0.00 4.34 F
3461 4229 1.202143 GGTAACAACGCCATTGCTAGC 60.202 52.381 8.1 8.1 42.62 3.42 F
4673 5468 2.111384 GCCATGTAGGAGAGGAGTGAA 58.889 52.381 0.0 0.0 41.22 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1695 0.988063 TAGCAATGCTGGTGGTGGTA 59.012 50.000 19.25 0.00 40.10 3.25 R
3088 3689 1.405872 ATACCCGCTGATACGAACCA 58.594 50.000 0.00 0.00 34.06 3.67 R
3089 3690 2.223876 TGAATACCCGCTGATACGAACC 60.224 50.000 0.00 0.00 34.06 3.62 R
3917 4698 2.066262 TGTTGCTTTAGCGCTCTACAC 58.934 47.619 16.34 5.24 45.83 2.90 R
4901 5696 1.279840 GAACAAAGCGCGCAACTCT 59.720 52.632 35.10 14.66 0.00 3.24 R
5656 6459 1.447643 GTGCATATGGAGCGGGAGT 59.552 57.895 4.56 0.00 33.85 3.85 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
82 83 5.588240 GAACACATCGGACATACACATAGA 58.412 41.667 0.00 0.00 0.00 1.98
83 84 5.188327 ACACATCGGACATACACATAGAG 57.812 43.478 0.00 0.00 0.00 2.43
84 85 3.983988 CACATCGGACATACACATAGAGC 59.016 47.826 0.00 0.00 0.00 4.09
85 86 3.237628 CATCGGACATACACATAGAGCG 58.762 50.000 0.00 0.00 0.00 5.03
87 88 2.032924 TCGGACATACACATAGAGCGTG 59.967 50.000 0.00 0.00 40.32 5.34
89 90 3.633235 GGACATACACATAGAGCGTGAG 58.367 50.000 0.00 0.00 37.80 3.51
101 102 3.742353 CGTGAGCGACAACTCTCG 58.258 61.111 2.21 2.21 44.21 4.04
102 103 1.797933 CGTGAGCGACAACTCTCGG 60.798 63.158 7.83 0.00 45.26 4.63
104 105 0.171455 GTGAGCGACAACTCTCGGAT 59.829 55.000 0.00 0.00 37.58 4.18
126 148 0.735287 GTAAACGAGCGTGAGGGACC 60.735 60.000 0.00 0.00 0.00 4.46
307 333 1.002792 GTTCAGGCGTCACTTGGAAAC 60.003 52.381 0.00 0.00 0.00 2.78
342 368 5.717119 AACCCAGCCAGTAAATCTTCTAT 57.283 39.130 0.00 0.00 0.00 1.98
346 372 6.378280 ACCCAGCCAGTAAATCTTCTATTTTG 59.622 38.462 0.00 0.00 0.00 2.44
426 456 4.104102 TCCATAAGAACACCAACCTGAACT 59.896 41.667 0.00 0.00 0.00 3.01
575 605 0.114954 ATCTGCCACCAAACACCCAT 59.885 50.000 0.00 0.00 0.00 4.00
577 607 1.145945 TCTGCCACCAAACACCCATAA 59.854 47.619 0.00 0.00 0.00 1.90
578 608 1.545582 CTGCCACCAAACACCCATAAG 59.454 52.381 0.00 0.00 0.00 1.73
593 623 3.210227 CCATAAGAGAGAGAGACTGCGA 58.790 50.000 0.00 0.00 0.00 5.10
620 650 8.059461 GGAATAAAAAGGGGAGGAGATAAAGAA 58.941 37.037 0.00 0.00 0.00 2.52
623 653 4.369809 AAGGGGAGGAGATAAAGAAGGA 57.630 45.455 0.00 0.00 0.00 3.36
908 1197 1.069596 GCCCAACCAGCAACCTTTG 59.930 57.895 0.00 0.00 0.00 2.77
932 1221 3.563808 CCAACTCTGTCGATCTCTCTAGG 59.436 52.174 0.00 0.00 0.00 3.02
1167 1460 2.359967 GGGAGCTACCTTCGCACCT 61.360 63.158 8.12 0.00 38.09 4.00
1196 1489 2.923035 CAGGACACACCCCTCGGT 60.923 66.667 0.00 0.00 46.31 4.69
1287 1580 0.395586 AGTTCTTGCAGCACACCCAA 60.396 50.000 0.00 0.00 0.00 4.12
1365 1658 0.318360 TGTACAACACCTCGCAGTCG 60.318 55.000 0.00 0.00 0.00 4.18
1402 1695 1.149174 CAGCTCCACCACCACAACT 59.851 57.895 0.00 0.00 0.00 3.16
1682 1975 3.182572 CGTTAGCAGCCGTTAGATGATTC 59.817 47.826 0.00 0.00 0.00 2.52
2096 2396 4.883585 CCTTGATGTATGCATAACACACCT 59.116 41.667 8.28 0.00 35.07 4.00
2097 2397 6.054941 CCTTGATGTATGCATAACACACCTA 58.945 40.000 8.28 0.00 35.07 3.08
2098 2398 6.542005 CCTTGATGTATGCATAACACACCTAA 59.458 38.462 8.28 1.52 35.07 2.69
2171 2480 4.085357 TCTTGCTGCCGGAACAATATAT 57.915 40.909 5.05 0.00 0.00 0.86
2172 2481 5.222079 TCTTGCTGCCGGAACAATATATA 57.778 39.130 5.05 0.00 0.00 0.86
2173 2482 5.237815 TCTTGCTGCCGGAACAATATATAG 58.762 41.667 5.05 0.00 0.00 1.31
2269 2578 7.074502 CAGTTCACTTTCTGAGCAGTAAATTC 58.925 38.462 0.00 0.00 32.58 2.17
2334 2643 1.471684 CCTCTAGCTTTACCACGACGT 59.528 52.381 0.00 0.00 0.00 4.34
2792 3118 5.825679 ACTTCTACTACACTGCTCATCCTAG 59.174 44.000 0.00 0.00 0.00 3.02
2793 3119 5.375283 TCTACTACACTGCTCATCCTAGT 57.625 43.478 0.00 0.00 0.00 2.57
2794 3120 5.756918 TCTACTACACTGCTCATCCTAGTT 58.243 41.667 0.00 0.00 0.00 2.24
2795 3121 6.896883 TCTACTACACTGCTCATCCTAGTTA 58.103 40.000 0.00 0.00 0.00 2.24
2796 3122 5.838531 ACTACACTGCTCATCCTAGTTAC 57.161 43.478 0.00 0.00 0.00 2.50
2806 3132 5.690632 GCTCATCCTAGTTACTACTCCCTCA 60.691 48.000 0.00 0.00 35.78 3.86
2807 3133 5.692928 TCATCCTAGTTACTACTCCCTCAC 58.307 45.833 0.00 0.00 35.78 3.51
2812 3138 2.308275 AGTTACTACTCCCTCACTCCGT 59.692 50.000 0.00 0.00 0.00 4.69
2824 3150 4.099573 CCCTCACTCCGTGAATAAGTGTAT 59.900 45.833 0.00 0.00 42.26 2.29
3040 3641 5.069501 AGAAGTACACTTATTCACGGACC 57.930 43.478 0.00 0.00 36.11 4.46
3088 3689 2.867109 ACTTGCTGTGTATGCTTCCT 57.133 45.000 0.00 0.00 0.00 3.36
3089 3690 2.430465 ACTTGCTGTGTATGCTTCCTG 58.570 47.619 0.00 0.00 0.00 3.86
3090 3691 1.741706 CTTGCTGTGTATGCTTCCTGG 59.258 52.381 0.00 0.00 0.00 4.45
3119 3730 2.609459 CAGCGGGTATTCATCAGTTGAC 59.391 50.000 0.00 0.00 32.84 3.18
3174 3785 2.337532 CACAAACCAGCTGCTGCC 59.662 61.111 23.86 0.00 40.80 4.85
3196 3807 4.082517 CCTCATCCTACGGTATGATCAGTG 60.083 50.000 0.09 0.00 31.95 3.66
3197 3808 4.470602 TCATCCTACGGTATGATCAGTGT 58.529 43.478 0.09 0.00 0.00 3.55
3198 3809 5.627135 TCATCCTACGGTATGATCAGTGTA 58.373 41.667 0.09 0.66 0.00 2.90
3199 3810 6.246163 TCATCCTACGGTATGATCAGTGTAT 58.754 40.000 0.09 0.00 0.00 2.29
3461 4229 1.202143 GGTAACAACGCCATTGCTAGC 60.202 52.381 8.10 8.10 42.62 3.42
3532 4304 5.404968 GCTGCTATATCACATGAGAGAACAC 59.595 44.000 0.00 0.00 0.00 3.32
3533 4305 6.469782 TGCTATATCACATGAGAGAACACA 57.530 37.500 0.00 0.00 0.00 3.72
3543 4315 3.028130 TGAGAGAACACACACAGTACCA 58.972 45.455 0.00 0.00 0.00 3.25
3662 4443 6.012337 TCCCTTGCTACAATTATGGATTGA 57.988 37.500 9.74 0.00 46.59 2.57
3690 4471 8.562892 CCATGTCAAACTAAATATTCCTAGCTG 58.437 37.037 0.00 0.00 0.00 4.24
3828 4609 5.648960 GGGGTACAGCTAGCTATAAGTCTAG 59.351 48.000 18.86 4.01 36.31 2.43
3917 4698 4.022068 TCAAAAGCTGCTGGTAATTTCCTG 60.022 41.667 1.35 3.29 0.00 3.86
4065 4849 8.886719 AGAATCAACTGTCACATTACATACATG 58.113 33.333 0.00 0.00 0.00 3.21
4122 4906 4.287067 AGTTGATCTGAAGAGGGTGCTTTA 59.713 41.667 0.00 0.00 0.00 1.85
4126 4910 2.979678 TCTGAAGAGGGTGCTTTAAGGT 59.020 45.455 0.00 0.00 0.00 3.50
4393 5177 8.943002 ACTTTCCACGACTACAATTAATTAAGG 58.057 33.333 0.00 1.53 0.00 2.69
4455 5243 5.308014 AGTTACATCAGAAGCAACATGACA 58.692 37.500 0.00 0.00 0.00 3.58
4456 5244 5.942236 AGTTACATCAGAAGCAACATGACAT 59.058 36.000 0.00 0.00 0.00 3.06
4673 5468 2.111384 GCCATGTAGGAGAGGAGTGAA 58.889 52.381 0.00 0.00 41.22 3.18
4675 5470 3.494048 GCCATGTAGGAGAGGAGTGAATG 60.494 52.174 0.00 0.00 41.22 2.67
4837 5632 6.510879 AGCTAATTACACAGCTTTTTACCC 57.489 37.500 0.00 0.00 45.80 3.69
4861 5656 3.815401 CCATTAACCCCTCTGATAAAGCG 59.185 47.826 0.00 0.00 0.00 4.68
4901 5696 7.497579 TGACAGCATCTTAACAGTGAAAAGTTA 59.502 33.333 0.00 0.00 0.00 2.24
4923 5718 3.192954 TTGCGCGCTTTGTTCCCTG 62.193 57.895 33.29 0.00 0.00 4.45
5052 5847 6.769822 CAGCCCATGATATACAGAAAAGAAGT 59.230 38.462 0.00 0.00 0.00 3.01
5412 6211 7.928307 TTAATCTGATGTTCCTTCTCCTTTG 57.072 36.000 0.00 0.00 0.00 2.77
5415 6214 3.149196 TGATGTTCCTTCTCCTTTGCAC 58.851 45.455 0.00 0.00 0.00 4.57
5445 6244 2.568090 CAATCGCAGTGCCCCAAC 59.432 61.111 10.11 0.00 0.00 3.77
5526 6325 2.254350 GGCGCCAAGAAACCGAAC 59.746 61.111 24.80 0.00 0.00 3.95
5621 6420 4.688511 GCTAGCTAGCTATATGTGACGT 57.311 45.455 33.71 0.00 45.62 4.34
5622 6421 5.049398 GCTAGCTAGCTATATGTGACGTT 57.951 43.478 33.71 0.00 45.62 3.99
5656 6459 4.391405 AATCAGATGCATACTCGTGTGA 57.609 40.909 0.00 0.00 31.19 3.58
5664 6467 0.680280 ATACTCGTGTGACTCCCGCT 60.680 55.000 0.00 0.00 0.00 5.52
5702 6505 2.042435 AAGCGGAGGAGGAGGAGG 60.042 66.667 0.00 0.00 0.00 4.30
5967 6776 3.071580 TGCACAACACACACGATCA 57.928 47.368 0.00 0.00 0.00 2.92
5990 6799 5.468540 AGCTTGAAGAGTGTGTGTATGTA 57.531 39.130 0.00 0.00 0.00 2.29
6063 6883 6.446318 TCATCTTTTTGTTATGCCACAAGAC 58.554 36.000 0.00 0.00 37.93 3.01
6107 6927 9.302345 GCTTATCTTACATATATGCGTGTGTAT 57.698 33.333 12.79 1.18 0.00 2.29
6147 6967 6.243148 TGCAAGCATGTATTATGATGGATCT 58.757 36.000 0.00 0.00 0.00 2.75
6148 6968 6.150474 TGCAAGCATGTATTATGATGGATCTG 59.850 38.462 0.00 0.00 0.00 2.90
6162 6982 1.654317 GATCTGCCAGTCTTGCTCTG 58.346 55.000 0.00 0.00 0.00 3.35
6164 6984 0.034476 TCTGCCAGTCTTGCTCTGTG 59.966 55.000 0.00 0.00 0.00 3.66
6174 6994 2.828520 TCTTGCTCTGTGCTAGCTACTT 59.171 45.455 17.23 0.00 42.73 2.24
6254 7074 2.417787 GGTGCAAATCTGGCTGGATTTC 60.418 50.000 13.21 10.17 42.02 2.17
6307 7127 5.835280 AGGTGATCAATCAACAAAAGGAGTT 59.165 36.000 10.49 0.00 46.79 3.01
6337 7157 9.416794 GGAGTAGTATGTTTGATCATATGTCTG 57.583 37.037 1.90 0.00 33.68 3.51
6347 7167 5.499313 TGATCATATGTCTGCCAAGTTGAA 58.501 37.500 3.87 0.00 0.00 2.69
6361 7181 6.030228 GCCAAGTTGAATGCACTATACTTTC 58.970 40.000 3.87 0.00 0.00 2.62
6369 7189 2.093181 TGCACTATACTTTCACCGCCAT 60.093 45.455 0.00 0.00 0.00 4.40
6372 7192 4.755123 GCACTATACTTTCACCGCCATATT 59.245 41.667 0.00 0.00 0.00 1.28
6406 7539 5.045797 GTCAATAATATAGTCCCTCCACCCC 60.046 48.000 0.00 0.00 0.00 4.95
6408 7541 0.116541 ATATAGTCCCTCCACCCCCG 59.883 60.000 0.00 0.00 0.00 5.73
6417 7550 0.401738 CTCCACCCCCGATGCATAAT 59.598 55.000 0.00 0.00 0.00 1.28
6474 7607 6.046593 CCAACAATTACTCTATTGCGGTCTA 58.953 40.000 0.00 0.00 38.74 2.59
6478 7611 8.197988 ACAATTACTCTATTGCGGTCTAAAAG 57.802 34.615 0.00 0.00 38.74 2.27
6485 7618 3.994204 TTGCGGTCTAAAAGGGAAAAC 57.006 42.857 0.00 0.00 0.00 2.43
6500 7633 3.500680 GGGAAAACAATCGCAGTTACTCA 59.499 43.478 0.00 0.00 32.88 3.41
6535 7668 7.642071 AGTTTATGTGTCACAAAAATGATGC 57.358 32.000 10.28 0.69 0.00 3.91
6543 7676 6.148150 GTGTCACAAAAATGATGCCATTGAAT 59.852 34.615 0.00 0.00 41.84 2.57
6544 7677 6.369340 TGTCACAAAAATGATGCCATTGAATC 59.631 34.615 0.00 0.00 41.84 2.52
6545 7678 5.577554 TCACAAAAATGATGCCATTGAATCG 59.422 36.000 0.00 0.00 41.84 3.34
6546 7679 5.349270 CACAAAAATGATGCCATTGAATCGT 59.651 36.000 0.00 0.00 41.84 3.73
6547 7680 6.530887 CACAAAAATGATGCCATTGAATCGTA 59.469 34.615 0.00 0.00 41.84 3.43
6548 7681 7.223193 CACAAAAATGATGCCATTGAATCGTAT 59.777 33.333 0.00 0.00 41.84 3.06
6549 7682 8.412456 ACAAAAATGATGCCATTGAATCGTATA 58.588 29.630 0.00 0.00 41.84 1.47
6550 7683 8.693504 CAAAAATGATGCCATTGAATCGTATAC 58.306 33.333 0.00 0.00 41.84 1.47
6551 7684 7.509141 AAATGATGCCATTGAATCGTATACA 57.491 32.000 3.32 0.00 41.84 2.29
6552 7685 7.692460 AATGATGCCATTGAATCGTATACAT 57.308 32.000 3.32 0.00 41.18 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.960329 TGTGTGTGTTTAAGTTGTCGTTC 58.040 39.130 0.00 0.00 0.00 3.95
29 30 4.092816 GGTTGTGTGTGTTTAAGTTGTCG 58.907 43.478 0.00 0.00 0.00 4.35
68 69 3.633235 CTCACGCTCTATGTGTATGTCC 58.367 50.000 0.00 0.00 37.67 4.02
77 78 0.917259 GTTGTCGCTCACGCTCTATG 59.083 55.000 0.00 0.00 39.84 2.23
79 80 0.168348 GAGTTGTCGCTCACGCTCTA 59.832 55.000 0.00 0.00 39.84 2.43
80 81 1.081108 GAGTTGTCGCTCACGCTCT 60.081 57.895 0.00 0.00 39.84 4.09
82 83 1.081108 GAGAGTTGTCGCTCACGCT 60.081 57.895 0.00 0.00 39.65 5.07
83 84 2.429351 CGAGAGTTGTCGCTCACGC 61.429 63.158 0.00 0.00 41.09 5.34
84 85 1.797933 CCGAGAGTTGTCGCTCACG 60.798 63.158 6.07 6.07 44.85 4.35
85 86 0.171455 ATCCGAGAGTTGTCGCTCAC 59.829 55.000 0.00 0.00 39.81 3.51
87 88 2.097791 ACTTATCCGAGAGTTGTCGCTC 59.902 50.000 0.00 0.00 38.69 5.03
89 90 2.563471 ACTTATCCGAGAGTTGTCGC 57.437 50.000 0.00 0.00 38.69 5.19
90 91 4.494764 CGTTTACTTATCCGAGAGTTGTCG 59.505 45.833 0.00 0.00 39.77 4.35
91 92 5.634896 TCGTTTACTTATCCGAGAGTTGTC 58.365 41.667 0.00 0.00 0.00 3.18
100 101 2.782192 CTCACGCTCGTTTACTTATCCG 59.218 50.000 0.00 0.00 0.00 4.18
101 102 3.114065 CCTCACGCTCGTTTACTTATCC 58.886 50.000 0.00 0.00 0.00 2.59
102 103 3.114065 CCCTCACGCTCGTTTACTTATC 58.886 50.000 0.00 0.00 0.00 1.75
104 105 2.095059 GTCCCTCACGCTCGTTTACTTA 60.095 50.000 0.00 0.00 0.00 2.24
158 184 3.365820 GGATCAAACTTGCTGCAAAATCG 59.634 43.478 16.74 7.15 0.00 3.34
220 246 8.731275 TTTCGGATTTGCTAAATCTCATCTAA 57.269 30.769 16.14 5.56 45.17 2.10
307 333 6.463360 ACTGGCTGGGTTTTACATTTAATTG 58.537 36.000 0.00 0.00 0.00 2.32
342 368 4.317488 GTTCGTCATGTAGGGGTACAAAA 58.683 43.478 0.00 0.00 33.21 2.44
346 372 1.202336 CGGTTCGTCATGTAGGGGTAC 60.202 57.143 0.00 0.00 0.00 3.34
575 605 2.502130 TCCTCGCAGTCTCTCTCTCTTA 59.498 50.000 0.00 0.00 0.00 2.10
577 607 0.908910 TCCTCGCAGTCTCTCTCTCT 59.091 55.000 0.00 0.00 0.00 3.10
578 608 1.745232 TTCCTCGCAGTCTCTCTCTC 58.255 55.000 0.00 0.00 0.00 3.20
593 623 7.409101 TCTTTATCTCCTCCCCTTTTTATTCCT 59.591 37.037 0.00 0.00 0.00 3.36
631 661 0.856641 TTTCACTTTCGTTCCTCGCG 59.143 50.000 0.00 0.00 39.67 5.87
633 663 1.798813 CCCTTTCACTTTCGTTCCTCG 59.201 52.381 0.00 0.00 41.41 4.63
908 1197 0.820871 AGAGATCGACAGAGTTGGCC 59.179 55.000 0.00 0.00 0.00 5.36
932 1221 1.291877 CGCTGTGGACTTGTGGCTAC 61.292 60.000 0.00 0.00 0.00 3.58
1130 1423 3.190849 CTGATGCTGCCGTGGTCG 61.191 66.667 0.00 0.00 0.00 4.79
1131 1424 3.503363 GCTGATGCTGCCGTGGTC 61.503 66.667 0.00 0.00 36.03 4.02
1138 1431 4.853050 AGCTCCCGCTGATGCTGC 62.853 66.667 0.00 0.00 46.86 5.25
1151 1444 4.816990 GAGGTGCGAAGGTAGCTC 57.183 61.111 0.00 0.00 44.11 4.09
1155 1448 2.345760 GGACGGAGGTGCGAAGGTA 61.346 63.158 0.00 0.00 0.00 3.08
1167 1460 3.458163 GTCCTGGCGATGGACGGA 61.458 66.667 8.07 0.00 43.55 4.69
1365 1658 2.741055 GCTCTGGAGGAAGGGGAGC 61.741 68.421 0.00 0.00 41.65 4.70
1402 1695 0.988063 TAGCAATGCTGGTGGTGGTA 59.012 50.000 19.25 0.00 40.10 3.25
1682 1975 7.413548 GCCTACTTTGCTAGCTAGAAGAAAAAG 60.414 40.741 25.15 21.90 0.00 2.27
2008 2306 3.190118 GCTAGCACAAGTGATCAAAGCTT 59.810 43.478 10.63 0.00 32.49 3.74
2096 2396 8.946085 ACGTAGAATTCTCTTGCAAATCAATTA 58.054 29.630 12.24 0.00 33.57 1.40
2097 2397 7.752239 CACGTAGAATTCTCTTGCAAATCAATT 59.248 33.333 12.24 4.81 33.57 2.32
2098 2398 7.246311 CACGTAGAATTCTCTTGCAAATCAAT 58.754 34.615 12.24 0.00 33.57 2.57
2130 2430 5.803020 AGAAATGATGAGTTAAAGGTCGC 57.197 39.130 0.00 0.00 0.00 5.19
2269 2578 1.677637 GAGGTACGAGCAAGAGGGGG 61.678 65.000 0.00 0.00 0.00 5.40
2334 2643 1.862138 TCCTCCCCTCTCCTCACCA 60.862 63.158 0.00 0.00 0.00 4.17
2792 3118 2.720915 ACGGAGTGAGGGAGTAGTAAC 58.279 52.381 0.00 0.00 42.51 2.50
2807 3133 7.203910 AGCTAGAAATACACTTATTCACGGAG 58.796 38.462 0.00 0.00 0.00 4.63
2824 3150 9.174166 ACTTTGACTTAAGACAAAAGCTAGAAA 57.826 29.630 25.68 8.11 38.68 2.52
3001 3592 9.078753 GTGTACTTCTAGCTTTTGTCTTAGATC 57.921 37.037 0.00 0.00 0.00 2.75
3002 3593 8.808092 AGTGTACTTCTAGCTTTTGTCTTAGAT 58.192 33.333 0.00 0.00 0.00 1.98
3003 3594 8.179509 AGTGTACTTCTAGCTTTTGTCTTAGA 57.820 34.615 0.00 0.00 0.00 2.10
3004 3595 8.819643 AAGTGTACTTCTAGCTTTTGTCTTAG 57.180 34.615 0.00 0.00 0.00 2.18
3007 3598 9.425577 GAATAAGTGTACTTCTAGCTTTTGTCT 57.574 33.333 0.00 0.00 37.40 3.41
3008 3599 9.204570 TGAATAAGTGTACTTCTAGCTTTTGTC 57.795 33.333 0.00 0.00 37.40 3.18
3040 3641 6.145338 TGACTAAATAAAGCTACTCCCTCG 57.855 41.667 0.00 0.00 0.00 4.63
3088 3689 1.405872 ATACCCGCTGATACGAACCA 58.594 50.000 0.00 0.00 34.06 3.67
3089 3690 2.223876 TGAATACCCGCTGATACGAACC 60.224 50.000 0.00 0.00 34.06 3.62
3090 3691 3.088194 TGAATACCCGCTGATACGAAC 57.912 47.619 0.00 0.00 34.06 3.95
3196 3807 5.005394 CGCCAGTGACACTTGTACAATATAC 59.995 44.000 9.13 4.88 0.00 1.47
3197 3808 5.106442 CGCCAGTGACACTTGTACAATATA 58.894 41.667 9.13 0.00 0.00 0.86
3198 3809 3.932710 CGCCAGTGACACTTGTACAATAT 59.067 43.478 9.13 0.00 0.00 1.28
3199 3810 3.243941 ACGCCAGTGACACTTGTACAATA 60.244 43.478 9.13 0.00 0.00 1.90
3461 4229 5.153950 AGGAGTACCAACAAAGAAGCTAG 57.846 43.478 0.00 0.00 38.94 3.42
3532 4304 4.894784 AGTGTAGGATTTGGTACTGTGTG 58.105 43.478 0.00 0.00 0.00 3.82
3533 4305 6.675413 TTAGTGTAGGATTTGGTACTGTGT 57.325 37.500 0.00 0.00 0.00 3.72
3662 4443 9.289782 GCTAGGAATATTTAGTTTGACATGGAT 57.710 33.333 0.00 0.00 0.00 3.41
3680 4461 3.654876 TAGCCCACCAGCTAGGAAT 57.345 52.632 8.91 0.00 42.70 3.01
3690 4471 6.067217 ACTGATATCCATTAATAGCCCACC 57.933 41.667 0.00 0.00 0.00 4.61
3828 4609 6.545504 TTCTGTCTCACAAGAATGTTTAGC 57.454 37.500 0.00 0.00 37.82 3.09
3917 4698 2.066262 TGTTGCTTTAGCGCTCTACAC 58.934 47.619 16.34 5.24 45.83 2.90
4100 4884 2.777832 AGCACCCTCTTCAGATCAAC 57.222 50.000 0.00 0.00 0.00 3.18
4126 4910 2.561419 ACTAGCTAGACTGCGGTTTGAA 59.439 45.455 27.45 0.00 38.13 2.69
4346 5130 6.633500 AGTGTATATGTGTGTGCACTTTTT 57.367 33.333 19.41 1.89 45.44 1.94
4393 5177 5.723672 TGGTAGTGCTACTATATTGCCTC 57.276 43.478 8.96 0.00 32.65 4.70
4536 5324 4.388485 TGGATGCTTGTATGCGATTGTAT 58.612 39.130 0.00 0.00 35.36 2.29
4601 5389 3.241530 TTGGCCGTGCAGAGTCCT 61.242 61.111 0.00 0.00 0.00 3.85
4837 5632 4.729868 CTTTATCAGAGGGGTTAATGGGG 58.270 47.826 0.00 0.00 0.00 4.96
4901 5696 1.279840 GAACAAAGCGCGCAACTCT 59.720 52.632 35.10 14.66 0.00 3.24
5206 6003 3.751479 TGGAGGTGGTAATGATGATCG 57.249 47.619 0.00 0.00 0.00 3.69
5526 6325 1.834263 CTTCCTAGGGTGAAGTCCAGG 59.166 57.143 9.46 0.00 35.56 4.45
5620 6419 9.656040 ATGCATCTGATTAATCTCTAGATCAAC 57.344 33.333 16.24 8.50 32.75 3.18
5656 6459 1.447643 GTGCATATGGAGCGGGAGT 59.552 57.895 4.56 0.00 33.85 3.85
5664 6467 2.718663 CGTACGTTACGTGCATATGGA 58.281 47.619 23.65 0.00 46.41 3.41
5967 6776 4.708177 ACATACACACACTCTTCAAGCTT 58.292 39.130 0.00 0.00 0.00 3.74
6063 6883 2.983229 AGCATCTCAGCTTTACACCTG 58.017 47.619 0.00 0.00 43.70 4.00
6087 6907 8.363029 CGTACAATACACACGCATATATGTAAG 58.637 37.037 14.14 8.59 31.65 2.34
6107 6927 3.266636 CTTGCATGGTCCATACGTACAA 58.733 45.455 3.38 4.05 0.00 2.41
6147 6967 1.598962 GCACAGAGCAAGACTGGCA 60.599 57.895 4.24 0.00 44.79 4.92
6148 6968 3.261933 GCACAGAGCAAGACTGGC 58.738 61.111 0.00 0.00 44.79 4.85
6162 6982 5.123344 GCTAGGAGATAGAAGTAGCTAGCAC 59.877 48.000 18.83 12.89 37.69 4.40
6164 6984 5.497474 AGCTAGGAGATAGAAGTAGCTAGC 58.503 45.833 6.62 6.62 43.62 3.42
6254 7074 2.621338 TCGCTTTAGCTCATGAACTGG 58.379 47.619 8.93 0.92 39.32 4.00
6337 7157 5.567138 AAGTATAGTGCATTCAACTTGGC 57.433 39.130 7.91 0.00 0.00 4.52
6347 7167 2.093181 TGGCGGTGAAAGTATAGTGCAT 60.093 45.455 0.00 0.00 0.00 3.96
6372 7192 8.762645 GGGACTATATTATTGACTGATCCATCA 58.237 37.037 0.00 0.00 35.16 3.07
6417 7550 7.545265 GCTTGTCTTAACCAATCAAAATATGCA 59.455 33.333 0.00 0.00 0.00 3.96
6427 7560 5.388111 GTTAACGGCTTGTCTTAACCAATC 58.612 41.667 0.00 0.00 0.00 2.67
6474 7607 4.400529 AACTGCGATTGTTTTCCCTTTT 57.599 36.364 0.00 0.00 0.00 2.27
6478 7611 3.500680 TGAGTAACTGCGATTGTTTTCCC 59.499 43.478 0.00 0.00 0.00 3.97
6485 7618 7.243487 ACACAATAATTGAGTAACTGCGATTG 58.757 34.615 0.00 0.00 32.65 2.67


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

AutoCloner maintained by Alex Coulton.