Multiple sequence alignment - TraesCS7B01G352400

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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 TraesCS7B01G352400 chr7B 100.000 3959 0 0 1 3959 608899534 608903492 0.000000e+00 7312.0
1 TraesCS7B01G352400 chr7D 94.430 3555 139 25 436 3959 560999921 561003447 0.000000e+00 5413.0
2 TraesCS7B01G352400 chr7D 87.466 1859 210 13 616 2466 560913125 560914968 0.000000e+00 2121.0
3 TraesCS7B01G352400 chr7D 96.774 155 4 1 271 425 560999785 560999938 1.410000e-64 257.0
4 TraesCS7B01G352400 chr7D 80.000 255 36 13 1 249 560981555 560981310 1.460000e-39 174.0
5 TraesCS7B01G352400 chr7D 86.184 152 18 3 271 421 560912597 560912746 1.140000e-35 161.0
6 TraesCS7B01G352400 chr7D 97.674 43 1 0 1 43 560999504 560999546 1.530000e-09 75.0
7 TraesCS7B01G352400 chr7A 89.640 2500 246 11 436 2930 645087548 645090039 0.000000e+00 3169.0
8 TraesCS7B01G352400 chr7A 86.901 626 53 14 3016 3640 645090093 645090690 0.000000e+00 675.0
9 TraesCS7B01G352400 chr6D 82.999 2294 345 30 503 2782 81935623 81933361 0.000000e+00 2034.0
10 TraesCS7B01G352400 chr6D 82.546 2286 351 36 510 2781 82139368 82137117 0.000000e+00 1967.0
11 TraesCS7B01G352400 chr6D 82.101 2313 369 24 814 3105 83020780 83018492 0.000000e+00 1936.0
12 TraesCS7B01G352400 chr6D 77.664 1755 330 38 503 2249 82237869 82236169 0.000000e+00 1013.0
13 TraesCS7B01G352400 chr6D 91.892 74 6 0 3106 3179 83018425 83018352 1.950000e-18 104.0
14 TraesCS7B01G352400 chr6D 91.176 68 6 0 503 570 82221623 82221556 4.210000e-15 93.5
15 TraesCS7B01G352400 chr6A 82.868 2294 347 31 503 2782 98324092 98321831 0.000000e+00 2017.0
16 TraesCS7B01G352400 chr6A 82.508 2281 358 29 510 2781 98813838 98811590 0.000000e+00 1964.0
17 TraesCS7B01G352400 chr6A 73.924 2278 522 45 503 2764 98982587 98980366 0.000000e+00 850.0
18 TraesCS7B01G352400 chr6A 73.442 2278 530 47 503 2764 99016393 99014175 0.000000e+00 785.0
19 TraesCS7B01G352400 chr6B 82.686 2293 344 34 503 2783 156741225 156738974 0.000000e+00 1986.0
20 TraesCS7B01G352400 chr6B 82.185 2279 353 41 518 2781 157027632 157025392 0.000000e+00 1910.0
21 TraesCS7B01G352400 chr2B 80.645 186 26 9 71 249 621539400 621539218 6.900000e-28 135.0


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 TraesCS7B01G352400 chr7B 608899534 608903492 3958 False 7312 7312 100.000000 1 3959 1 chr7B.!!$F1 3958
1 TraesCS7B01G352400 chr7D 560999504 561003447 3943 False 1915 5413 96.292667 1 3959 3 chr7D.!!$F2 3958
2 TraesCS7B01G352400 chr7D 560912597 560914968 2371 False 1141 2121 86.825000 271 2466 2 chr7D.!!$F1 2195
3 TraesCS7B01G352400 chr7A 645087548 645090690 3142 False 1922 3169 88.270500 436 3640 2 chr7A.!!$F1 3204
4 TraesCS7B01G352400 chr6D 81933361 81935623 2262 True 2034 2034 82.999000 503 2782 1 chr6D.!!$R1 2279
5 TraesCS7B01G352400 chr6D 82137117 82139368 2251 True 1967 1967 82.546000 510 2781 1 chr6D.!!$R2 2271
6 TraesCS7B01G352400 chr6D 83018352 83020780 2428 True 1020 1936 86.996500 814 3179 2 chr6D.!!$R5 2365
7 TraesCS7B01G352400 chr6D 82236169 82237869 1700 True 1013 1013 77.664000 503 2249 1 chr6D.!!$R4 1746
8 TraesCS7B01G352400 chr6A 98321831 98324092 2261 True 2017 2017 82.868000 503 2782 1 chr6A.!!$R1 2279
9 TraesCS7B01G352400 chr6A 98811590 98813838 2248 True 1964 1964 82.508000 510 2781 1 chr6A.!!$R2 2271
10 TraesCS7B01G352400 chr6A 98980366 98982587 2221 True 850 850 73.924000 503 2764 1 chr6A.!!$R3 2261
11 TraesCS7B01G352400 chr6A 99014175 99016393 2218 True 785 785 73.442000 503 2764 1 chr6A.!!$R4 2261
12 TraesCS7B01G352400 chr6B 156738974 156741225 2251 True 1986 1986 82.686000 503 2783 1 chr6B.!!$R1 2280
13 TraesCS7B01G352400 chr6B 157025392 157027632 2240 True 1910 1910 82.185000 518 2781 1 chr6B.!!$R2 2263

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
933 1370 0.039180 TCTCTCAAGACGGTGGCCTA 59.961 55.0 3.32 0.00 0.00 3.93 F
937 1374 0.325296 TCAAGACGGTGGCCTATCCT 60.325 55.0 3.32 0.00 35.26 3.24 F
1158 1598 0.809241 CCAGCAGCATCGTCTTCCTC 60.809 60.0 0.00 0.00 0.00 3.71 F
2934 3385 0.321298 TTGGCAAGTCCTACTTCGCC 60.321 55.0 18.36 18.36 36.03 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2493 2944 0.029834 CAACAAGCGCTTTGAGCTGT 59.970 50.000 22.51 12.59 45.31 4.40 R
2813 3264 0.657368 GTCAGCTTGTTTTGCGGACG 60.657 55.000 3.65 0.00 43.17 4.79 R
2950 3401 1.202533 AGCAGCCTAATATCAACGCGT 60.203 47.619 5.58 5.58 0.00 6.01 R
3752 4291 3.057876 GTCATGTTGTCGGCACCAATAAA 60.058 43.478 0.00 0.00 0.00 1.40 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
110 111 8.700722 TTCACATGGTGTAAATATGAATTTGC 57.299 30.769 0.00 0.00 37.97 3.68
111 112 7.264221 TCACATGGTGTAAATATGAATTTGCC 58.736 34.615 0.00 0.00 37.01 4.52
112 113 7.040494 CACATGGTGTAAATATGAATTTGCCA 58.960 34.615 0.00 0.00 37.01 4.92
113 114 7.711772 CACATGGTGTAAATATGAATTTGCCAT 59.288 33.333 0.00 0.00 40.28 4.40
114 115 8.078959 CATGGTGTAAATATGAATTTGCCATG 57.921 34.615 18.30 18.30 43.94 3.66
115 116 6.580788 TGGTGTAAATATGAATTTGCCATGG 58.419 36.000 7.63 7.63 37.01 3.66
116 117 6.155910 TGGTGTAAATATGAATTTGCCATGGT 59.844 34.615 14.67 0.00 37.01 3.55
117 118 6.701400 GGTGTAAATATGAATTTGCCATGGTC 59.299 38.462 14.67 6.41 37.01 4.02
118 119 7.264221 GTGTAAATATGAATTTGCCATGGTCA 58.736 34.615 14.67 9.10 37.01 4.02
119 120 7.927629 GTGTAAATATGAATTTGCCATGGTCAT 59.072 33.333 14.67 15.78 37.01 3.06
120 121 9.140874 TGTAAATATGAATTTGCCATGGTCATA 57.859 29.630 19.02 19.02 37.01 2.15
121 122 9.630098 GTAAATATGAATTTGCCATGGTCATAG 57.370 33.333 20.51 0.00 36.02 2.23
122 123 7.844493 AATATGAATTTGCCATGGTCATAGT 57.156 32.000 20.51 17.18 35.32 2.12
123 124 4.987408 TGAATTTGCCATGGTCATAGTG 57.013 40.909 14.67 0.00 0.00 2.74
124 125 4.343231 TGAATTTGCCATGGTCATAGTGT 58.657 39.130 14.67 0.00 0.00 3.55
125 126 5.504853 TGAATTTGCCATGGTCATAGTGTA 58.495 37.500 14.67 0.00 0.00 2.90
126 127 5.948758 TGAATTTGCCATGGTCATAGTGTAA 59.051 36.000 14.67 2.79 0.00 2.41
127 128 6.435591 TGAATTTGCCATGGTCATAGTGTAAA 59.564 34.615 14.67 2.12 0.00 2.01
128 129 6.849085 ATTTGCCATGGTCATAGTGTAAAA 57.151 33.333 14.67 1.44 0.00 1.52
129 130 6.849085 TTTGCCATGGTCATAGTGTAAAAT 57.151 33.333 14.67 0.00 0.00 1.82
130 131 6.849085 TTGCCATGGTCATAGTGTAAAATT 57.151 33.333 14.67 0.00 0.00 1.82
131 132 6.849085 TGCCATGGTCATAGTGTAAAATTT 57.151 33.333 14.67 0.00 0.00 1.82
132 133 7.238486 TGCCATGGTCATAGTGTAAAATTTT 57.762 32.000 14.67 8.75 0.00 1.82
133 134 7.319646 TGCCATGGTCATAGTGTAAAATTTTC 58.680 34.615 14.67 0.37 0.00 2.29
134 135 6.756542 GCCATGGTCATAGTGTAAAATTTTCC 59.243 38.462 14.67 0.00 0.00 3.13
135 136 7.578571 GCCATGGTCATAGTGTAAAATTTTCCA 60.579 37.037 14.67 5.73 0.00 3.53
136 137 8.477256 CCATGGTCATAGTGTAAAATTTTCCAT 58.523 33.333 6.72 7.80 0.00 3.41
137 138 9.304731 CATGGTCATAGTGTAAAATTTTCCATG 57.695 33.333 19.58 19.58 40.45 3.66
138 139 8.415950 TGGTCATAGTGTAAAATTTTCCATGT 57.584 30.769 6.72 0.00 0.00 3.21
139 140 8.865090 TGGTCATAGTGTAAAATTTTCCATGTT 58.135 29.630 6.72 0.00 0.00 2.71
140 141 9.353999 GGTCATAGTGTAAAATTTTCCATGTTC 57.646 33.333 6.72 0.00 0.00 3.18
141 142 9.906660 GTCATAGTGTAAAATTTTCCATGTTCA 57.093 29.630 6.72 0.00 0.00 3.18
147 148 9.715123 GTGTAAAATTTTCCATGTTCAAAAAGG 57.285 29.630 6.72 0.00 0.00 3.11
148 149 9.672673 TGTAAAATTTTCCATGTTCAAAAAGGA 57.327 25.926 6.72 0.00 0.00 3.36
225 226 8.565896 TGCCATCATACATGAAGTAAATATCC 57.434 34.615 0.00 0.00 40.69 2.59
226 227 8.162746 TGCCATCATACATGAAGTAAATATCCA 58.837 33.333 0.00 0.00 40.69 3.41
227 228 9.182214 GCCATCATACATGAAGTAAATATCCAT 57.818 33.333 0.00 0.00 40.69 3.41
231 232 9.725019 TCATACATGAAGTAAATATCCATGGTC 57.275 33.333 12.58 0.00 38.98 4.02
232 233 9.730705 CATACATGAAGTAAATATCCATGGTCT 57.269 33.333 12.58 3.10 38.98 3.85
247 248 7.487822 TCCATGGTCTAAAAATAAATTGCCA 57.512 32.000 12.58 0.00 0.00 4.92
248 249 8.088463 TCCATGGTCTAAAAATAAATTGCCAT 57.912 30.769 12.58 0.00 34.89 4.40
249 250 8.203485 TCCATGGTCTAAAAATAAATTGCCATC 58.797 33.333 12.58 0.00 32.55 3.51
250 251 7.986320 CCATGGTCTAAAAATAAATTGCCATCA 59.014 33.333 2.57 0.00 32.55 3.07
261 262 8.827177 AATAAATTGCCATCATATTCAGCAAG 57.173 30.769 0.00 0.00 45.67 4.01
266 267 4.820173 TGCCATCATATTCAGCAAGAAGAG 59.180 41.667 0.00 0.00 40.15 2.85
267 268 5.061853 GCCATCATATTCAGCAAGAAGAGA 58.938 41.667 0.00 0.00 40.15 3.10
268 269 5.706369 GCCATCATATTCAGCAAGAAGAGAT 59.294 40.000 0.00 0.00 40.15 2.75
269 270 6.348622 GCCATCATATTCAGCAAGAAGAGATG 60.349 42.308 15.81 15.81 40.15 2.90
273 435 9.842775 ATCATATTCAGCAAGAAGAGATGTTTA 57.157 29.630 0.00 0.00 40.15 2.01
276 438 6.791887 TTCAGCAAGAAGAGATGTTTAGTG 57.208 37.500 0.00 0.00 0.00 2.74
346 508 5.334414 GCAAAGTGATGTCAGGTCAAGTAAG 60.334 44.000 0.00 0.00 0.00 2.34
385 547 4.640771 AATTCAGGCAAGGACTAAGTCA 57.359 40.909 0.00 0.00 33.68 3.41
407 569 6.683715 TCAAACGATGACTACACAATCTACA 58.316 36.000 0.00 0.00 31.50 2.74
408 570 7.149307 TCAAACGATGACTACACAATCTACAA 58.851 34.615 0.00 0.00 31.50 2.41
409 571 7.654116 TCAAACGATGACTACACAATCTACAAA 59.346 33.333 0.00 0.00 31.50 2.83
410 572 8.443160 CAAACGATGACTACACAATCTACAAAT 58.557 33.333 0.00 0.00 0.00 2.32
411 573 7.757097 ACGATGACTACACAATCTACAAATC 57.243 36.000 0.00 0.00 0.00 2.17
412 574 7.320399 ACGATGACTACACAATCTACAAATCA 58.680 34.615 0.00 0.00 0.00 2.57
413 575 7.981789 ACGATGACTACACAATCTACAAATCAT 59.018 33.333 0.00 0.00 0.00 2.45
414 576 8.820933 CGATGACTACACAATCTACAAATCATT 58.179 33.333 0.00 0.00 0.00 2.57
499 663 4.251268 GTTGGGCGACTTGTTAGTAGATT 58.749 43.478 0.00 0.00 33.84 2.40
500 664 5.413499 GTTGGGCGACTTGTTAGTAGATTA 58.587 41.667 0.00 0.00 33.84 1.75
603 1016 5.277825 CAAATTTCTTTGTGGCGACTACAA 58.722 37.500 0.00 2.64 37.54 2.41
661 1080 3.393278 TCCTTATTTACCCCCAATCCTCG 59.607 47.826 0.00 0.00 0.00 4.63
684 1103 3.053544 TCCTCCTTGACGATTAGACCTCT 60.054 47.826 0.00 0.00 0.00 3.69
751 1176 2.762327 CCCATGCTAGCTTCACCAAAAT 59.238 45.455 17.23 0.00 0.00 1.82
859 1296 2.028203 GTCTTCTGCTTGCTCTCTCCTT 60.028 50.000 0.00 0.00 0.00 3.36
918 1355 1.594310 GTTCCTTGCCGAGCTCTCT 59.406 57.895 12.85 0.00 0.00 3.10
933 1370 0.039180 TCTCTCAAGACGGTGGCCTA 59.961 55.000 3.32 0.00 0.00 3.93
937 1374 0.325296 TCAAGACGGTGGCCTATCCT 60.325 55.000 3.32 0.00 35.26 3.24
989 1426 4.344865 GGAAGGGGTCGCCTGCAA 62.345 66.667 15.70 0.00 0.00 4.08
1008 1445 1.649321 AGCAAGACAGGATGGTCAGA 58.351 50.000 0.00 0.00 43.62 3.27
1158 1598 0.809241 CCAGCAGCATCGTCTTCCTC 60.809 60.000 0.00 0.00 0.00 3.71
1225 1671 3.329889 CACCACCTGCCAGGCCTA 61.330 66.667 11.63 0.00 39.63 3.93
1227 1673 1.004230 ACCACCTGCCAGGCCTATA 59.996 57.895 11.63 0.00 39.63 1.31
1416 1865 6.855914 TCGATCTGTGTTTCAACAAATTTAGC 59.144 34.615 0.00 0.00 41.21 3.09
1678 2127 1.620819 GCCTGTTCAAGAGACTGGAGA 59.379 52.381 4.62 0.00 0.00 3.71
1680 2129 3.307339 GCCTGTTCAAGAGACTGGAGAAT 60.307 47.826 4.62 0.00 0.00 2.40
1941 2390 4.803426 CACGGGCAGCTCTCGTCC 62.803 72.222 7.93 0.00 34.73 4.79
2109 2558 4.520179 CACAGGATGAGACAATTGATGGA 58.480 43.478 13.59 0.00 39.69 3.41
2394 2845 4.020128 AGGGTCTTTGATCTGACAGTTACC 60.020 45.833 1.59 0.00 35.11 2.85
2493 2944 1.133915 GTAATTCCCCCGCAGATTGGA 60.134 52.381 0.00 0.00 0.00 3.53
2550 3001 5.499004 TTAATAAGCTATCCGGGCAGATT 57.501 39.130 0.00 6.79 0.00 2.40
2556 3007 1.349026 CTATCCGGGCAGATTCCACAT 59.651 52.381 0.00 0.00 0.00 3.21
2611 3062 3.193691 AGACCTGTCCAGTAACAATCTCG 59.806 47.826 0.00 0.00 0.00 4.04
2813 3264 2.381911 AGCACATCAACCCATCATTCC 58.618 47.619 0.00 0.00 0.00 3.01
2817 3268 1.949525 CATCAACCCATCATTCCGTCC 59.050 52.381 0.00 0.00 0.00 4.79
2860 3311 1.067706 TGGCCTTTGTGATTGCATTCG 60.068 47.619 3.32 0.00 0.00 3.34
2934 3385 0.321298 TTGGCAAGTCCTACTTCGCC 60.321 55.000 18.36 18.36 36.03 5.54
2950 3401 3.342377 TCGCCTCACATATTGGTTCAA 57.658 42.857 0.00 0.00 0.00 2.69
2951 3402 3.006940 TCGCCTCACATATTGGTTCAAC 58.993 45.455 0.00 0.00 0.00 3.18
2957 3408 2.908009 CACATATTGGTTCAACGCGTTG 59.092 45.455 39.16 39.16 41.71 4.10
2969 3420 1.217882 ACGCGTTGATATTAGGCTGC 58.782 50.000 5.58 0.00 0.00 5.25
3001 3452 1.169577 AGCAACACGTCCAACAAACA 58.830 45.000 0.00 0.00 0.00 2.83
3002 3453 1.542030 AGCAACACGTCCAACAAACAA 59.458 42.857 0.00 0.00 0.00 2.83
3009 3460 4.082679 ACACGTCCAACAAACAAAAGCTTA 60.083 37.500 0.00 0.00 0.00 3.09
3196 3730 2.684001 AATGTTGCATTGAGGCATGG 57.316 45.000 0.00 0.00 44.48 3.66
3197 3731 1.855295 ATGTTGCATTGAGGCATGGA 58.145 45.000 0.00 0.00 44.48 3.41
3205 3739 3.131577 GCATTGAGGCATGGAGAATTTCA 59.868 43.478 0.00 0.00 0.00 2.69
3236 3770 1.295357 TAAGCGTGCACGTGGAATGG 61.295 55.000 36.80 10.33 42.22 3.16
3238 3772 2.398554 GCGTGCACGTGGAATGGAT 61.399 57.895 36.80 0.00 42.22 3.41
3253 3787 2.559698 TGGATGTCTTTGCGGAAAGA 57.440 45.000 25.88 25.88 44.40 2.52
3278 3812 6.037610 ACAATCTTTGCTCGTAGAATCATTCC 59.962 38.462 0.00 0.00 34.09 3.01
3291 3825 5.491070 AGAATCATTCCGTGTCATTCTTCA 58.509 37.500 0.00 0.00 31.11 3.02
3298 3832 6.928979 TTCCGTGTCATTCTTCAGTTTAAA 57.071 33.333 0.00 0.00 0.00 1.52
3353 3889 8.143193 ACATCACATTTTCTTTCAAATGCACTA 58.857 29.630 6.14 0.00 44.76 2.74
3362 3898 7.792374 TCTTTCAAATGCACTATCTATGTCC 57.208 36.000 0.00 0.00 0.00 4.02
3381 3917 7.648177 ATGTCCCACTGGGTAATCTATAATT 57.352 36.000 14.25 0.00 44.74 1.40
3467 4003 7.433680 ACCAATAAAGAAGACATGTTGAAACC 58.566 34.615 0.00 0.00 0.00 3.27
3501 4038 5.931532 ACACTCATGTCAGCTTTAAATTCG 58.068 37.500 0.00 0.00 31.55 3.34
3603 4140 5.545658 AACGCATTGTACAACTATTCCAG 57.454 39.130 11.22 0.00 0.00 3.86
3633 4170 7.037873 AGTGTATTTAGTTTATCCAGTGGGTGA 60.038 37.037 9.92 0.00 34.93 4.02
3636 4173 6.381498 TTTAGTTTATCCAGTGGGTGATGA 57.619 37.500 9.92 0.00 34.93 2.92
3640 4177 2.260639 ATCCAGTGGGTGATGAGAGT 57.739 50.000 9.92 0.00 34.93 3.24
3641 4178 1.561643 TCCAGTGGGTGATGAGAGTC 58.438 55.000 9.92 0.00 34.93 3.36
3695 4232 3.308117 CCTTGGAGCTTGTACATGGGTTA 60.308 47.826 10.47 0.00 0.00 2.85
3698 4235 4.269183 TGGAGCTTGTACATGGGTTATTG 58.731 43.478 10.47 0.00 0.00 1.90
3714 4251 7.122048 TGGGTTATTGATTCATCCACATACAA 58.878 34.615 0.00 0.00 0.00 2.41
3752 4291 6.808829 TCATTTTCACAGACAAGCTTGAATT 58.191 32.000 32.50 10.86 0.00 2.17
3835 4382 5.860941 TCTGAATCCATAGTCCACTCTTC 57.139 43.478 0.00 0.00 0.00 2.87
3843 4390 2.131776 AGTCCACTCTTCTCCCTACG 57.868 55.000 0.00 0.00 0.00 3.51
3861 4408 5.337330 CCCTACGTTCCTAAGTCTGAAACAT 60.337 44.000 0.00 0.00 0.00 2.71
3868 4415 7.307989 CGTTCCTAAGTCTGAAACATCAAACAT 60.308 37.037 0.00 0.00 0.00 2.71
3873 4420 6.259550 AGTCTGAAACATCAAACATAAGGC 57.740 37.500 0.00 0.00 0.00 4.35
3877 4424 5.639757 TGAAACATCAAACATAAGGCATCG 58.360 37.500 0.00 0.00 0.00 3.84
3883 4430 8.445275 ACATCAAACATAAGGCATCGTTTATA 57.555 30.769 0.00 0.00 30.71 0.98
3884 4431 9.066892 ACATCAAACATAAGGCATCGTTTATAT 57.933 29.630 0.00 0.00 30.71 0.86
3885 4432 9.897744 CATCAAACATAAGGCATCGTTTATATT 57.102 29.630 0.00 0.00 30.71 1.28
3886 4433 9.897744 ATCAAACATAAGGCATCGTTTATATTG 57.102 29.630 0.00 0.00 30.71 1.90
3887 4434 7.860373 TCAAACATAAGGCATCGTTTATATTGC 59.140 33.333 0.00 0.00 30.71 3.56
3928 4476 9.442047 GGAAATAGGTGAAGATGATACATAAGG 57.558 37.037 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 9.149225 GCAAATTCATATTTACACCATGTGAAA 57.851 29.630 0.49 0.00 35.95 2.69
85 86 7.763528 GGCAAATTCATATTTACACCATGTGAA 59.236 33.333 0.49 0.00 36.53 3.18
86 87 7.093596 TGGCAAATTCATATTTACACCATGTGA 60.094 33.333 0.49 0.00 33.22 3.58
87 88 7.040494 TGGCAAATTCATATTTACACCATGTG 58.960 34.615 0.00 0.00 34.26 3.21
88 89 7.180322 TGGCAAATTCATATTTACACCATGT 57.820 32.000 0.00 0.00 32.75 3.21
90 91 7.147514 ACCATGGCAAATTCATATTTACACCAT 60.148 33.333 13.04 0.00 39.37 3.55
91 92 6.155910 ACCATGGCAAATTCATATTTACACCA 59.844 34.615 13.04 0.00 36.06 4.17
92 93 6.581712 ACCATGGCAAATTCATATTTACACC 58.418 36.000 13.04 0.00 32.75 4.16
93 94 7.264221 TGACCATGGCAAATTCATATTTACAC 58.736 34.615 13.04 0.00 32.75 2.90
94 95 7.415592 TGACCATGGCAAATTCATATTTACA 57.584 32.000 13.04 0.00 32.75 2.41
96 97 9.365906 ACTATGACCATGGCAAATTCATATTTA 57.634 29.630 17.71 3.48 32.75 1.40
97 98 8.145767 CACTATGACCATGGCAAATTCATATTT 58.854 33.333 17.71 8.96 34.29 1.40
98 99 7.288389 ACACTATGACCATGGCAAATTCATATT 59.712 33.333 17.71 12.06 30.68 1.28
101 102 4.957954 ACACTATGACCATGGCAAATTCAT 59.042 37.500 13.04 15.23 0.00 2.57
102 103 4.343231 ACACTATGACCATGGCAAATTCA 58.657 39.130 13.04 8.16 0.00 2.57
103 104 4.989279 ACACTATGACCATGGCAAATTC 57.011 40.909 13.04 1.41 0.00 2.17
104 105 6.849085 TTTACACTATGACCATGGCAAATT 57.151 33.333 13.04 0.00 0.00 1.82
105 106 6.849085 TTTTACACTATGACCATGGCAAAT 57.151 33.333 13.04 5.62 0.00 2.32
106 107 6.849085 ATTTTACACTATGACCATGGCAAA 57.151 33.333 13.04 0.00 0.00 3.68
107 108 6.849085 AATTTTACACTATGACCATGGCAA 57.151 33.333 13.04 0.00 0.00 4.52
108 109 6.849085 AAATTTTACACTATGACCATGGCA 57.151 33.333 13.04 11.62 0.00 4.92
109 110 6.756542 GGAAAATTTTACACTATGACCATGGC 59.243 38.462 13.04 5.35 0.00 4.40
110 111 7.835822 TGGAAAATTTTACACTATGACCATGG 58.164 34.615 11.95 11.19 0.00 3.66
111 112 9.304731 CATGGAAAATTTTACACTATGACCATG 57.695 33.333 18.07 19.02 41.95 3.66
112 113 9.034800 ACATGGAAAATTTTACACTATGACCAT 57.965 29.630 18.07 12.44 32.99 3.55
113 114 8.415950 ACATGGAAAATTTTACACTATGACCA 57.584 30.769 18.07 10.75 32.99 4.02
114 115 9.353999 GAACATGGAAAATTTTACACTATGACC 57.646 33.333 18.07 5.39 32.99 4.02
115 116 9.906660 TGAACATGGAAAATTTTACACTATGAC 57.093 29.630 18.07 12.00 32.99 3.06
121 122 9.715123 CCTTTTTGAACATGGAAAATTTTACAC 57.285 29.630 18.07 6.28 32.99 2.90
122 123 9.672673 TCCTTTTTGAACATGGAAAATTTTACA 57.327 25.926 18.02 18.02 35.06 2.41
199 200 9.013229 GGATATTTACTTCATGTATGATGGCAA 57.987 33.333 11.09 5.16 36.56 4.52
200 201 8.162746 TGGATATTTACTTCATGTATGATGGCA 58.837 33.333 11.09 0.00 36.56 4.92
201 202 8.565896 TGGATATTTACTTCATGTATGATGGC 57.434 34.615 11.09 0.00 36.56 4.40
205 206 9.725019 GACCATGGATATTTACTTCATGTATGA 57.275 33.333 21.47 0.00 34.94 2.15
206 207 9.730705 AGACCATGGATATTTACTTCATGTATG 57.269 33.333 21.47 0.00 34.94 2.39
221 222 9.206690 TGGCAATTTATTTTTAGACCATGGATA 57.793 29.630 21.47 8.10 0.00 2.59
222 223 8.088463 TGGCAATTTATTTTTAGACCATGGAT 57.912 30.769 21.47 9.22 0.00 3.41
223 224 7.487822 TGGCAATTTATTTTTAGACCATGGA 57.512 32.000 21.47 0.00 0.00 3.41
224 225 7.986320 TGATGGCAATTTATTTTTAGACCATGG 59.014 33.333 11.19 11.19 35.58 3.66
225 226 8.945481 TGATGGCAATTTATTTTTAGACCATG 57.055 30.769 0.00 0.00 35.58 3.66
233 234 9.616156 TGCTGAATATGATGGCAATTTATTTTT 57.384 25.926 0.00 0.00 0.00 1.94
234 235 9.616156 TTGCTGAATATGATGGCAATTTATTTT 57.384 25.926 0.00 0.00 37.87 1.82
235 236 9.268268 CTTGCTGAATATGATGGCAATTTATTT 57.732 29.630 0.00 0.00 41.12 1.40
236 237 8.644216 TCTTGCTGAATATGATGGCAATTTATT 58.356 29.630 0.00 0.00 41.12 1.40
237 238 8.185506 TCTTGCTGAATATGATGGCAATTTAT 57.814 30.769 0.00 0.00 41.12 1.40
238 239 7.585579 TCTTGCTGAATATGATGGCAATTTA 57.414 32.000 0.00 0.00 41.12 1.40
239 240 6.474140 TCTTGCTGAATATGATGGCAATTT 57.526 33.333 0.00 0.00 41.12 1.82
240 241 6.322969 TCTTCTTGCTGAATATGATGGCAATT 59.677 34.615 0.00 0.00 41.12 2.32
241 242 5.831525 TCTTCTTGCTGAATATGATGGCAAT 59.168 36.000 0.00 0.00 41.12 3.56
242 243 5.195185 TCTTCTTGCTGAATATGATGGCAA 58.805 37.500 0.00 0.00 39.99 4.52
243 244 4.784177 TCTTCTTGCTGAATATGATGGCA 58.216 39.130 0.00 0.00 33.71 4.92
244 245 5.061853 TCTCTTCTTGCTGAATATGATGGC 58.938 41.667 0.00 0.00 33.71 4.40
245 246 6.711194 ACATCTCTTCTTGCTGAATATGATGG 59.289 38.462 19.58 11.10 38.41 3.51
246 247 7.731882 ACATCTCTTCTTGCTGAATATGATG 57.268 36.000 17.07 17.07 39.08 3.07
247 248 8.749026 AAACATCTCTTCTTGCTGAATATGAT 57.251 30.769 12.34 0.00 33.71 2.45
248 249 9.322773 CTAAACATCTCTTCTTGCTGAATATGA 57.677 33.333 12.34 0.00 33.71 2.15
249 250 9.107177 ACTAAACATCTCTTCTTGCTGAATATG 57.893 33.333 0.00 0.00 33.71 1.78
250 251 9.107177 CACTAAACATCTCTTCTTGCTGAATAT 57.893 33.333 0.00 0.00 33.71 1.28
255 256 6.426328 ACTTCACTAAACATCTCTTCTTGCTG 59.574 38.462 0.00 0.00 0.00 4.41
261 262 7.062839 CACTAGCACTTCACTAAACATCTCTTC 59.937 40.741 0.00 0.00 0.00 2.87
266 267 4.631813 CCCACTAGCACTTCACTAAACATC 59.368 45.833 0.00 0.00 0.00 3.06
267 268 4.286032 TCCCACTAGCACTTCACTAAACAT 59.714 41.667 0.00 0.00 0.00 2.71
268 269 3.644265 TCCCACTAGCACTTCACTAAACA 59.356 43.478 0.00 0.00 0.00 2.83
269 270 4.267349 TCCCACTAGCACTTCACTAAAC 57.733 45.455 0.00 0.00 0.00 2.01
273 435 2.037772 CACTTCCCACTAGCACTTCACT 59.962 50.000 0.00 0.00 0.00 3.41
276 438 1.348036 ACCACTTCCCACTAGCACTTC 59.652 52.381 0.00 0.00 0.00 3.01
346 508 7.677041 GCCTGAATTTTTAAAACATGCCATAGC 60.677 37.037 0.00 3.99 40.48 2.97
385 547 7.956420 TTTGTAGATTGTGTAGTCATCGTTT 57.044 32.000 0.00 0.00 0.00 3.60
603 1016 6.590656 TCCCATTTTGTCTATCCCTTGTAT 57.409 37.500 0.00 0.00 0.00 2.29
661 1080 3.025262 AGGTCTAATCGTCAAGGAGGAC 58.975 50.000 0.00 0.00 34.42 3.85
684 1103 8.316946 CCTCTCACTGGATATAAAGCATCAATA 58.683 37.037 0.00 0.00 0.00 1.90
698 1121 4.040217 GCTTATGATGTCCTCTCACTGGAT 59.960 45.833 0.00 0.00 35.87 3.41
699 1122 3.386078 GCTTATGATGTCCTCTCACTGGA 59.614 47.826 0.00 0.00 0.00 3.86
751 1176 5.586243 GCAGCTGAAGTTTCTTCATGGTATA 59.414 40.000 20.43 0.00 0.00 1.47
918 1355 0.325296 AGGATAGGCCACCGTCTTGA 60.325 55.000 5.01 0.00 40.02 3.02
933 1370 0.250038 CATTCCGCCATGACGAGGAT 60.250 55.000 1.83 0.00 34.06 3.24
937 1374 2.513666 GCCATTCCGCCATGACGA 60.514 61.111 1.83 0.00 34.06 4.20
989 1426 1.277557 GTCTGACCATCCTGTCTTGCT 59.722 52.381 0.00 0.00 36.21 3.91
1008 1445 1.446792 CGAAGGCAGCGAGACATGT 60.447 57.895 0.00 0.00 0.00 3.21
1158 1598 1.009829 GCTGGTTAAGGCTGACATCG 58.990 55.000 0.00 0.00 0.00 3.84
1225 1671 6.947464 AGATGTTTAGTACCTGCAACTGTAT 58.053 36.000 0.00 0.00 0.00 2.29
1227 1673 5.221641 TGAGATGTTTAGTACCTGCAACTGT 60.222 40.000 0.00 0.00 0.00 3.55
1678 2127 5.766150 TTGTTGTCGTTCAAATGGAGATT 57.234 34.783 0.00 0.00 37.81 2.40
1680 2129 6.429692 ACATATTGTTGTCGTTCAAATGGAGA 59.570 34.615 0.00 0.00 37.81 3.71
1693 2142 2.945668 GCTCCCCTGACATATTGTTGTC 59.054 50.000 0.00 0.00 45.05 3.18
1941 2390 7.215789 ACAGATGCTTCAGATTACCTATTCTG 58.784 38.462 2.07 0.00 40.58 3.02
2097 2546 8.036575 TGAAGATTTCCAAATCCATCAATTGTC 58.963 33.333 5.13 0.00 44.55 3.18
2109 2558 5.560724 TCGAGAACCTGAAGATTTCCAAAT 58.439 37.500 0.00 0.00 0.00 2.32
2394 2845 3.068590 GGTATTCAAGTGATGGGCCATTG 59.931 47.826 22.20 15.70 0.00 2.82
2493 2944 0.029834 CAACAAGCGCTTTGAGCTGT 59.970 50.000 22.51 12.59 45.31 4.40
2611 3062 1.379642 GCAACTGGGATAGCACCTGC 61.380 60.000 0.00 0.00 42.49 4.85
2813 3264 0.657368 GTCAGCTTGTTTTGCGGACG 60.657 55.000 3.65 0.00 43.17 4.79
2817 3268 3.291585 CTTGTAGTCAGCTTGTTTTGCG 58.708 45.455 0.00 0.00 35.28 4.85
2860 3311 1.369625 CCTACACCGAAGAATGCACC 58.630 55.000 0.00 0.00 0.00 5.01
2871 3322 1.551430 TCATACAACACCCCTACACCG 59.449 52.381 0.00 0.00 0.00 4.94
2934 3385 2.415168 ACGCGTTGAACCAATATGTGAG 59.585 45.455 5.58 0.00 0.00 3.51
2950 3401 1.202533 AGCAGCCTAATATCAACGCGT 60.203 47.619 5.58 5.58 0.00 6.01
2951 3402 1.502231 AGCAGCCTAATATCAACGCG 58.498 50.000 3.53 3.53 0.00 6.01
2957 3408 5.476091 ACCTTGAGTAGCAGCCTAATATC 57.524 43.478 0.00 0.00 0.00 1.63
2969 3420 4.056050 ACGTGTTGCTAAACCTTGAGTAG 58.944 43.478 0.00 0.00 35.25 2.57
3001 3452 5.491982 CTCACACCTACAGGATAAGCTTTT 58.508 41.667 3.20 0.00 38.94 2.27
3002 3453 4.624125 GCTCACACCTACAGGATAAGCTTT 60.624 45.833 3.20 0.00 38.94 3.51
3009 3460 3.788227 TTTTGCTCACACCTACAGGAT 57.212 42.857 1.29 0.00 38.94 3.24
3091 3559 9.534565 GAGTGCATATTCTAGTTCAAGTCATTA 57.465 33.333 0.00 0.00 0.00 1.90
3092 3560 8.263640 AGAGTGCATATTCTAGTTCAAGTCATT 58.736 33.333 0.00 0.00 0.00 2.57
3196 3730 3.944087 ACTAGTGCACCCTGAAATTCTC 58.056 45.455 14.63 0.00 0.00 2.87
3197 3731 5.491982 CTTACTAGTGCACCCTGAAATTCT 58.508 41.667 14.63 0.00 0.00 2.40
3205 3739 0.246635 CACGCTTACTAGTGCACCCT 59.753 55.000 14.63 0.00 35.23 4.34
3227 3761 1.202065 CGCAAAGACATCCATTCCACG 60.202 52.381 0.00 0.00 0.00 4.94
3253 3787 6.037610 GGAATGATTCTACGAGCAAAGATTGT 59.962 38.462 5.03 0.00 0.00 2.71
3254 3788 6.425504 GGAATGATTCTACGAGCAAAGATTG 58.574 40.000 5.03 0.00 0.00 2.67
3323 3859 9.362539 GCATTTGAAAGAAAATGTGATGTAGAT 57.637 29.630 10.40 0.00 45.37 1.98
3381 3917 7.775093 ACTAAGTGAGCAGCCATAATTCAATTA 59.225 33.333 0.00 0.00 30.12 1.40
3394 3930 1.273606 TGAGGTGACTAAGTGAGCAGC 59.726 52.381 0.00 0.00 44.43 5.25
3395 3931 3.667497 TTGAGGTGACTAAGTGAGCAG 57.333 47.619 0.00 0.00 44.43 4.24
3501 4038 5.046663 TCCCCTTTTCCATTTTATCTTGTGC 60.047 40.000 0.00 0.00 0.00 4.57
3584 4121 7.010552 CACTCTACTGGAATAGTTGTACAATGC 59.989 40.741 12.26 1.37 40.89 3.56
3603 4140 9.530633 CCACTGGATAAACTAAATACACTCTAC 57.469 37.037 0.00 0.00 0.00 2.59
3633 4170 6.096705 CCTTGTACATTCTCTCAGACTCTCAT 59.903 42.308 0.00 0.00 0.00 2.90
3636 4173 5.329399 ACCTTGTACATTCTCTCAGACTCT 58.671 41.667 0.00 0.00 0.00 3.24
3640 4177 4.284490 AGCAACCTTGTACATTCTCTCAGA 59.716 41.667 0.00 0.00 0.00 3.27
3641 4178 4.573900 AGCAACCTTGTACATTCTCTCAG 58.426 43.478 0.00 0.00 0.00 3.35
3695 4232 4.036734 GCGGTTGTATGTGGATGAATCAAT 59.963 41.667 0.00 0.00 0.00 2.57
3698 4235 3.206150 AGCGGTTGTATGTGGATGAATC 58.794 45.455 0.00 0.00 0.00 2.52
3714 4251 1.859302 AAATGAGGAGAGAGAGCGGT 58.141 50.000 0.00 0.00 0.00 5.68
3752 4291 3.057876 GTCATGTTGTCGGCACCAATAAA 60.058 43.478 0.00 0.00 0.00 1.40
3835 4382 3.618351 TCAGACTTAGGAACGTAGGGAG 58.382 50.000 0.00 0.00 0.00 4.30
3843 4390 7.259290 TGTTTGATGTTTCAGACTTAGGAAC 57.741 36.000 0.00 0.00 37.74 3.62
3861 4408 7.860373 GCAATATAAACGATGCCTTATGTTTGA 59.140 33.333 0.00 0.00 36.14 2.69
3933 4481 7.580007 ACCAGAAGTTTAAGGTTCCTTAAGAA 58.420 34.615 19.16 7.58 38.98 2.52


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

AutoCloner maintained by Alex Coulton.