Multiple sequence alignment - TraesCS4B01G239100

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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 TraesCS4B01G239100 chr4B 100.000 6811 0 0 1 6811 496279212 496286022 0.000000e+00 12578.0
1 TraesCS4B01G239100 chr4D 92.292 3542 178 46 705 4213 401203347 401206826 0.000000e+00 4940.0
2 TraesCS4B01G239100 chr4D 95.776 2107 59 16 3871 5962 417679235 417681326 0.000000e+00 3371.0
3 TraesCS4B01G239100 chr4D 94.576 1862 63 12 4209 6053 401206910 401208750 0.000000e+00 2844.0
4 TraesCS4B01G239100 chr4D 91.458 1358 62 24 541 1871 417670906 417672236 0.000000e+00 1816.0
5 TraesCS4B01G239100 chr4D 93.493 1168 50 12 2742 3891 417678042 417679201 0.000000e+00 1712.0
6 TraesCS4B01G239100 chr4D 96.567 903 24 5 1856 2754 417674153 417675052 0.000000e+00 1489.0
7 TraesCS4B01G239100 chr4D 85.072 556 53 19 172 708 401202397 401202941 2.160000e-149 540.0
8 TraesCS4B01G239100 chr4D 100.000 29 0 0 5902 5930 401208714 401208742 3.000000e-03 54.7
9 TraesCS4B01G239100 chr4A 93.628 1899 55 20 2918 4798 58913230 58915080 0.000000e+00 2776.0
10 TraesCS4B01G239100 chr4A 94.630 1378 43 16 1553 2921 58911795 58913150 0.000000e+00 2106.0
11 TraesCS4B01G239100 chr4A 95.013 1143 37 6 4797 5938 58915184 58916307 0.000000e+00 1777.0
12 TraesCS4B01G239100 chr4A 86.704 1602 91 49 1 1555 58910006 58911532 0.000000e+00 1666.0
13 TraesCS4B01G239100 chr4A 84.848 66 9 1 6 71 595222269 595222205 1.590000e-06 65.8
14 TraesCS4B01G239100 chr5A 88.020 601 36 11 6234 6811 647446194 647445607 0.000000e+00 678.0
15 TraesCS4B01G239100 chr5A 96.460 226 8 0 6224 6449 633284255 633284030 2.320000e-99 374.0
16 TraesCS4B01G239100 chr5A 93.388 242 16 0 6221 6462 647370891 647370650 6.490000e-95 359.0
17 TraesCS4B01G239100 chr5A 93.137 102 7 0 6710 6811 633283688 633283587 4.260000e-32 150.0
18 TraesCS4B01G239100 chr5A 88.710 62 5 2 6055 6116 647481798 647481739 2.630000e-09 75.0
19 TraesCS4B01G239100 chr5A 94.595 37 2 0 6077 6113 633284389 633284353 2.650000e-04 58.4
20 TraesCS4B01G239100 chr5D 83.356 727 60 29 6127 6811 520164302 520163595 3.490000e-172 616.0
21 TraesCS4B01G239100 chr5D 94.215 242 14 0 6221 6462 520133983 520133742 3.000000e-98 370.0
22 TraesCS4B01G239100 chr5D 86.709 158 15 4 6654 6811 520194911 520194760 3.270000e-38 171.0
23 TraesCS4B01G239100 chr5D 94.118 102 6 0 6710 6811 520133335 520133234 9.150000e-34 156.0
24 TraesCS4B01G239100 chr5D 96.970 33 1 0 6051 6083 520164328 520164296 1.000000e-03 56.5
25 TraesCS4B01G239100 chr3D 83.943 629 41 29 6225 6811 157377655 157377045 1.290000e-151 547.0
26 TraesCS4B01G239100 chr3D 93.137 102 7 0 6710 6811 157371687 157371586 4.260000e-32 150.0
27 TraesCS4B01G239100 chr3D 84.270 89 2 4 6078 6166 157378003 157377927 7.320000e-10 76.8
28 TraesCS4B01G239100 chr3B 83.699 638 36 30 6225 6811 228672365 228671745 2.160000e-149 540.0
29 TraesCS4B01G239100 chr3A 94.314 299 14 2 6170 6465 170983800 170984098 8.050000e-124 455.0
30 TraesCS4B01G239100 chr3A 93.878 245 12 1 6218 6462 170992887 170993128 3.880000e-97 366.0
31 TraesCS4B01G239100 chr3A 90.845 142 7 1 6670 6811 170989443 170989578 1.170000e-42 185.0
32 TraesCS4B01G239100 chr5B 81.731 104 14 5 250 350 482501034 482500933 1.570000e-11 82.4
33 TraesCS4B01G239100 chr1A 87.879 66 8 0 7 72 9960028 9960093 2.040000e-10 78.7
34 TraesCS4B01G239100 chr7B 88.710 62 6 1 6 67 33066771 33066711 2.630000e-09 75.0
35 TraesCS4B01G239100 chr7A 85.484 62 9 0 6 67 85200787 85200726 1.590000e-06 65.8
36 TraesCS4B01G239100 chr2B 92.683 41 3 0 6 46 644545462 644545502 7.380000e-05 60.2


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 TraesCS4B01G239100 chr4B 496279212 496286022 6810 False 12578.000 12578 100.00000 1 6811 1 chr4B.!!$F1 6810
1 TraesCS4B01G239100 chr4D 417670906 417681326 10420 False 2097.000 3371 94.32350 541 5962 4 chr4D.!!$F2 5421
2 TraesCS4B01G239100 chr4D 401202397 401208750 6353 False 2094.675 4940 92.98500 172 6053 4 chr4D.!!$F1 5881
3 TraesCS4B01G239100 chr4A 58910006 58916307 6301 False 2081.250 2776 92.49375 1 5938 4 chr4A.!!$F1 5937
4 TraesCS4B01G239100 chr5A 647445607 647446194 587 True 678.000 678 88.02000 6234 6811 1 chr5A.!!$R2 577
5 TraesCS4B01G239100 chr5D 520163595 520164328 733 True 336.250 616 90.16300 6051 6811 2 chr5D.!!$R3 760
6 TraesCS4B01G239100 chr5D 520133234 520133983 749 True 263.000 370 94.16650 6221 6811 2 chr5D.!!$R2 590
7 TraesCS4B01G239100 chr3D 157377045 157378003 958 True 311.900 547 84.10650 6078 6811 2 chr3D.!!$R2 733
8 TraesCS4B01G239100 chr3B 228671745 228672365 620 True 540.000 540 83.69900 6225 6811 1 chr3B.!!$R1 586
9 TraesCS4B01G239100 chr3A 170989443 170993128 3685 False 275.500 366 92.36150 6218 6811 2 chr3A.!!$F2 593

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
997 1452 0.391927 CGCCCGATTGTTAGGTTGGA 60.392 55.0 0.00 0.0 0.00 3.53 F
1093 1549 0.246635 CCAGACCGTACCAACCTCTG 59.753 60.0 0.00 0.0 31.15 3.35 F
1523 2001 0.677288 TCCCAGTACGTGACACTTGG 59.323 55.0 0.00 0.0 31.57 3.61 F
2435 5129 1.093159 CTGCAGTCCTTTCATCCAGC 58.907 55.0 5.25 0.0 0.00 4.85 F
3417 9217 0.912487 ATACCGTTTCTGAGGGGCCA 60.912 55.0 4.39 0.0 37.62 5.36 F
5187 11261 0.311790 GTGACCACACAACAGCATGG 59.688 55.0 0.00 0.0 45.32 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 4693 1.656587 TCAGGGCAACAGTCATAGGT 58.343 50.000 0.0 0.0 39.74 3.08 R
2396 5090 1.933853 GCGCTACAACAGAGGTAATGG 59.066 52.381 0.0 0.0 0.00 3.16 R
2800 8501 2.997485 GTGGAAATCACTGCTTCACC 57.003 50.000 0.0 0.0 42.86 4.02 R
3696 9498 0.178068 AGCAAGACTGGACACAACGT 59.822 50.000 0.0 0.0 0.00 3.99 R
5294 11368 0.472925 ACCCCATTTCAAACCACCCC 60.473 55.000 0.0 0.0 0.00 4.95 R
6483 12801 0.107993 CGAGATCAAGGGCAGAGCAA 60.108 55.000 0.0 0.0 0.00 3.91 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
54 55 2.672651 TCGCAGCAACATGTGGGG 60.673 61.111 0.00 0.00 0.00 4.96
81 89 6.075315 TCATCTAGTTCCTATCGGGATCAAA 58.925 40.000 0.00 0.00 44.66 2.69
161 169 7.877097 AGGAATCATATGACATAGAAAGTGAGC 59.123 37.037 7.78 0.00 0.00 4.26
173 181 3.199508 AGAAAGTGAGCTGACATGCCTAT 59.800 43.478 5.98 0.00 0.00 2.57
199 207 7.478322 AGTGAAAGAATGTCATTGATGCATAC 58.522 34.615 1.88 0.00 32.95 2.39
235 243 8.902540 TTTTTCATTGAGTCTAAGCTAAGACA 57.097 30.769 6.76 0.00 46.89 3.41
242 250 7.956328 TGAGTCTAAGCTAAGACATCCTTTA 57.044 36.000 6.76 0.00 46.89 1.85
350 360 5.942977 TCCTATTCCTATGTACTCCCTCA 57.057 43.478 0.00 0.00 0.00 3.86
351 361 5.642165 TCCTATTCCTATGTACTCCCTCAC 58.358 45.833 0.00 0.00 0.00 3.51
374 384 8.029642 CACTTTCATAATAAGTGTCGAGGTTT 57.970 34.615 7.40 0.00 44.63 3.27
383 397 2.963782 AGTGTCGAGGTTTAGTTCCACT 59.036 45.455 0.00 0.00 0.00 4.00
530 549 8.159447 TGCTAATAGGAAATAAGATGCATGTCT 58.841 33.333 2.46 0.00 0.00 3.41
536 555 8.388484 AGGAAATAAGATGCATGTCTTATCAC 57.612 34.615 18.46 15.23 45.83 3.06
558 599 3.634397 TCTATGAACAAAGGAGGCCTG 57.366 47.619 12.00 0.00 32.13 4.85
560 601 3.782523 TCTATGAACAAAGGAGGCCTGAT 59.217 43.478 12.00 0.00 32.13 2.90
561 602 2.496899 TGAACAAAGGAGGCCTGATC 57.503 50.000 12.00 0.17 32.13 2.92
562 603 1.004745 TGAACAAAGGAGGCCTGATCC 59.995 52.381 12.00 5.45 32.13 3.36
564 605 0.551131 ACAAAGGAGGCCTGATCCCT 60.551 55.000 12.00 7.66 37.57 4.20
565 606 1.274416 ACAAAGGAGGCCTGATCCCTA 60.274 52.381 12.00 0.00 37.57 3.53
997 1452 0.391927 CGCCCGATTGTTAGGTTGGA 60.392 55.000 0.00 0.00 0.00 3.53
1093 1549 0.246635 CCAGACCGTACCAACCTCTG 59.753 60.000 0.00 0.00 31.15 3.35
1113 1573 1.400530 CCCCCTCCCGCTACAACTAG 61.401 65.000 0.00 0.00 0.00 2.57
1125 1585 4.395542 CGCTACAACTAGTTCCACTACTCT 59.604 45.833 4.77 0.00 0.00 3.24
1128 1588 5.000570 ACAACTAGTTCCACTACTCTCCT 57.999 43.478 4.77 0.00 0.00 3.69
1144 1604 3.210227 TCTCCTCTAATCAGCTCACTCG 58.790 50.000 0.00 0.00 0.00 4.18
1197 1666 2.346541 CCGGCAGCAGACAGAGAGA 61.347 63.158 0.00 0.00 0.00 3.10
1212 1681 4.219507 ACAGAGAGATCAGCGAAGAAGAAA 59.780 41.667 0.00 0.00 0.00 2.52
1331 1800 6.119536 TGCTAATGTCCTAGTGGTTAATTGG 58.880 40.000 0.00 0.00 34.23 3.16
1490 1968 8.347771 CAACATTATTCTCGAACAATCATGGAT 58.652 33.333 12.34 2.96 0.00 3.41
1523 2001 0.677288 TCCCAGTACGTGACACTTGG 59.323 55.000 0.00 0.00 31.57 3.61
1631 2374 5.243060 TCTCAAGAACAAGGTCGAAGATGTA 59.757 40.000 0.00 0.00 40.67 2.29
1726 2469 1.626825 TGCTGGGTAAGTCAACCTACC 59.373 52.381 0.08 0.08 39.65 3.18
1753 2496 2.128035 CGTTCAACAGACCAGTCACTC 58.872 52.381 0.00 0.00 0.00 3.51
2015 4693 4.202451 TGCTAATGTATGGGCAGCTATGAA 60.202 41.667 0.00 0.00 33.38 2.57
2169 4847 5.568620 ACTCAATCACCTTACACTCCTTT 57.431 39.130 0.00 0.00 0.00 3.11
2175 4853 9.483489 TCAATCACCTTACACTCCTTTATAGTA 57.517 33.333 0.00 0.00 0.00 1.82
2176 4854 9.751542 CAATCACCTTACACTCCTTTATAGTAG 57.248 37.037 0.00 0.00 0.00 2.57
2177 4855 9.490083 AATCACCTTACACTCCTTTATAGTAGT 57.510 33.333 0.00 0.00 0.00 2.73
2217 4897 3.194116 CCCCTTCACAATGAAAGATGTGG 59.806 47.826 6.11 0.00 45.41 4.17
2270 4964 3.281727 ACACTCAGGTGACATGTGTTT 57.718 42.857 1.15 0.00 45.61 2.83
2296 4990 4.667573 TGGTTGCAGGGACAAATATAACA 58.332 39.130 0.00 0.00 0.00 2.41
2396 5090 1.794714 TCCCCTCAGCCATCTAGTTC 58.205 55.000 0.00 0.00 0.00 3.01
2435 5129 1.093159 CTGCAGTCCTTTCATCCAGC 58.907 55.000 5.25 0.00 0.00 4.85
2674 5371 1.803334 TATGGGTTCTTGTCACACGC 58.197 50.000 0.00 0.00 0.00 5.34
2720 5417 6.256975 ACGAACTTCCTTTAAAAATTTGGCAC 59.743 34.615 0.00 0.00 0.00 5.01
2736 5433 1.464997 GGCACGAGAACCACTGAATTC 59.535 52.381 0.00 0.00 0.00 2.17
2800 8501 5.041191 AGGCTTAATGAGACCCTATTGTG 57.959 43.478 0.00 0.00 31.76 3.33
2931 8721 7.719633 CACAATGGTTACTACTTATTAGGCCAT 59.280 37.037 5.01 0.00 39.02 4.40
2956 8746 6.041409 TGCCATCCTTTTGTGAAATTAGTTGA 59.959 34.615 0.00 0.00 0.00 3.18
2996 8786 2.700897 CCAGGCCTGTACTAGTAATGCT 59.299 50.000 30.63 0.00 0.00 3.79
3078 8874 5.160641 CGCAACCACTAATAGTTTGCAATT 58.839 37.500 22.17 0.00 40.26 2.32
3138 8938 8.908903 ACTTATATCTGATCGGTAGATGATTCC 58.091 37.037 0.42 0.00 37.19 3.01
3139 8939 6.723298 ATATCTGATCGGTAGATGATTCCC 57.277 41.667 0.42 0.00 37.19 3.97
3140 8940 3.165875 TCTGATCGGTAGATGATTCCCC 58.834 50.000 0.42 0.00 37.19 4.81
3141 8941 2.234908 CTGATCGGTAGATGATTCCCCC 59.765 54.545 0.00 0.00 37.19 5.40
3240 9040 5.332743 GAAATATCCAGGGCCAATCCAATA 58.667 41.667 6.18 0.00 36.21 1.90
3334 9134 1.457303 CGGTGAGCACTCTTTTTCTCG 59.543 52.381 0.16 0.00 0.00 4.04
3337 9137 3.553096 GGTGAGCACTCTTTTTCTCGAGA 60.553 47.826 12.08 12.08 0.00 4.04
3343 9143 3.610242 CACTCTTTTTCTCGAGATGTCGG 59.390 47.826 17.44 7.95 46.80 4.79
3417 9217 0.912487 ATACCGTTTCTGAGGGGCCA 60.912 55.000 4.39 0.00 37.62 5.36
3485 9285 6.756074 TGCTGGAATTGTTGAGTTTAAACTTG 59.244 34.615 21.40 3.28 39.88 3.16
3695 9497 2.540515 ACGATGACTGGCATTAGAACG 58.459 47.619 0.00 0.00 37.34 3.95
3696 9498 2.165641 ACGATGACTGGCATTAGAACGA 59.834 45.455 8.31 0.00 37.34 3.85
3700 9502 2.288579 TGACTGGCATTAGAACGACGTT 60.289 45.455 14.11 14.11 0.00 3.99
3836 9638 4.026356 AGTGGATTCTGGAAAGGACTTG 57.974 45.455 0.00 0.00 0.00 3.16
4201 10068 5.844004 TGTGACTGTCTTCCTAGAAACTTC 58.156 41.667 9.51 0.00 30.65 3.01
4233 10190 6.515272 ACTATTTATCCAAGTGCAGGTTTG 57.485 37.500 0.00 0.00 0.00 2.93
4318 10275 3.397482 GGCGATGCAGTTATCTCAGATT 58.603 45.455 0.00 0.00 0.00 2.40
4376 10333 7.815641 TGATTGTATTTCAACATACACACTGG 58.184 34.615 0.00 0.00 38.99 4.00
4423 10382 2.270986 GCACAAAGGGCCAGGACAG 61.271 63.158 6.18 0.00 0.00 3.51
4619 10579 7.720957 TCCACATCCCAGATCTATATTTGTTTG 59.279 37.037 0.00 0.00 0.00 2.93
4646 10606 6.664515 TGTACTTCAAATCCAAAGCTAAACG 58.335 36.000 0.00 0.00 0.00 3.60
4967 11032 9.513906 TGTGAACTTATCCAAATGAGTCAATTA 57.486 29.630 0.00 0.00 30.94 1.40
5035 11100 7.554835 GGGGTTTCTTTCCATTTTGTTACTTTT 59.445 33.333 0.00 0.00 0.00 2.27
5036 11101 8.952278 GGGTTTCTTTCCATTTTGTTACTTTTT 58.048 29.630 0.00 0.00 0.00 1.94
5060 11125 6.867662 TTTTCTCAGTTCTAGCAAAGGAAG 57.132 37.500 0.00 0.00 0.00 3.46
5103 11168 6.094603 CAGTGCAGTATTGAGAAAAATAGCCT 59.905 38.462 0.00 0.00 0.00 4.58
5108 11173 7.571026 CAGTATTGAGAAAAATAGCCTCATCG 58.429 38.462 0.00 0.00 36.88 3.84
5187 11261 0.311790 GTGACCACACAACAGCATGG 59.688 55.000 0.00 0.00 45.32 3.66
5294 11368 2.616960 TGCAACTACACAGCCTATTCG 58.383 47.619 0.00 0.00 0.00 3.34
5324 11398 6.421501 GGTTTGAAATGGGGTTTACTTTAACG 59.578 38.462 0.00 0.00 0.00 3.18
5563 11638 6.647212 TTTATGTCTTTGTGCATCTACTCG 57.353 37.500 0.00 0.00 0.00 4.18
5593 11668 3.565482 TCTGTTGAAAAGTGGCATGAGAC 59.435 43.478 0.00 0.00 0.00 3.36
5660 11735 0.459585 TTCGCTACGAGGGATTGCAC 60.460 55.000 0.00 0.00 37.03 4.57
5934 12009 9.593134 TCTCTAATTGCTAAAGATGTTCTTCTC 57.407 33.333 0.00 0.00 35.27 2.87
5938 12013 7.608308 ATTGCTAAAGATGTTCTTCTCTGTC 57.392 36.000 0.00 0.00 35.27 3.51
5946 12021 0.603569 TTCTTCTCTGTCGTGCCCTC 59.396 55.000 0.00 0.00 0.00 4.30
5948 12023 0.605589 CTTCTCTGTCGTGCCCTCTT 59.394 55.000 0.00 0.00 0.00 2.85
5972 12047 2.871182 TACTGCCTCGTAGCAAGATG 57.129 50.000 3.86 0.00 43.52 2.90
5981 12056 1.743772 CGTAGCAAGATGTTCAGGGGG 60.744 57.143 0.00 0.00 0.00 5.40
5997 12077 2.732619 GGGGTCCCCTCGTAGCAAG 61.733 68.421 21.13 0.00 41.34 4.01
6021 12101 8.171164 AGAGGGCAGTAAAATATAAATCAAGC 57.829 34.615 0.00 0.00 0.00 4.01
6107 12187 3.197116 AGCTAACAAACGGGCTACAGTAT 59.803 43.478 0.00 0.00 32.94 2.12
6108 12188 3.554731 GCTAACAAACGGGCTACAGTATC 59.445 47.826 0.00 0.00 0.00 2.24
6109 12189 3.688694 AACAAACGGGCTACAGTATCA 57.311 42.857 0.00 0.00 0.00 2.15
6110 12190 3.247006 ACAAACGGGCTACAGTATCAG 57.753 47.619 0.00 0.00 0.00 2.90
6111 12191 2.565834 ACAAACGGGCTACAGTATCAGT 59.434 45.455 0.00 0.00 0.00 3.41
6112 12192 3.765511 ACAAACGGGCTACAGTATCAGTA 59.234 43.478 0.00 0.00 0.00 2.74
6113 12193 4.404715 ACAAACGGGCTACAGTATCAGTAT 59.595 41.667 0.00 0.00 0.00 2.12
6151 12231 1.153745 CACACGAGGCAGTCCTAGC 60.154 63.158 0.00 0.00 44.46 3.42
6152 12232 1.304547 ACACGAGGCAGTCCTAGCT 60.305 57.895 0.00 0.00 44.46 3.32
6153 12233 0.034380 ACACGAGGCAGTCCTAGCTA 60.034 55.000 0.00 0.00 44.46 3.32
6154 12234 1.323412 CACGAGGCAGTCCTAGCTAT 58.677 55.000 0.00 0.00 44.46 2.97
6168 12248 3.057876 CCTAGCTATGAAGGCTACACTCG 60.058 52.174 0.00 0.00 40.74 4.18
6323 12617 3.067106 AGTTGCCGTTGTAGATCACTTG 58.933 45.455 0.00 0.00 0.00 3.16
6452 12749 0.898326 ATGCCCTTTTTCACCCGGAC 60.898 55.000 0.73 0.00 0.00 4.79
6483 12801 4.630644 TGGCATCTTCTTCTTCTTCACT 57.369 40.909 0.00 0.00 0.00 3.41
6504 12822 0.529555 GCTCTGCCCTTGATCTCGTC 60.530 60.000 0.00 0.00 0.00 4.20
6526 12883 2.202756 GGGTCGACGTCTCCATGC 60.203 66.667 21.92 7.11 0.00 4.06
6527 12884 2.202756 GGTCGACGTCTCCATGCC 60.203 66.667 14.70 2.89 0.00 4.40
6528 12885 2.202756 GTCGACGTCTCCATGCCC 60.203 66.667 14.70 0.00 0.00 5.36
6529 12886 2.678580 TCGACGTCTCCATGCCCA 60.679 61.111 14.70 0.00 0.00 5.36
6530 12887 2.058001 TCGACGTCTCCATGCCCAT 61.058 57.895 14.70 0.00 0.00 4.00
6531 12888 0.753848 TCGACGTCTCCATGCCCATA 60.754 55.000 14.70 0.00 0.00 2.74
6581 12995 4.021925 GGCGGTGCACCTCCTCTT 62.022 66.667 33.27 0.00 37.89 2.85
6582 12996 2.743928 GCGGTGCACCTCCTCTTG 60.744 66.667 32.28 16.54 0.00 3.02
6591 13011 0.689623 ACCTCCTCTTGCTCTTGGTG 59.310 55.000 0.00 0.00 0.00 4.17
6699 13251 2.890109 CGCGGCCTTGCTGATGATC 61.890 63.158 0.00 0.00 37.02 2.92
6700 13252 2.550101 GCGGCCTTGCTGATGATCC 61.550 63.158 0.00 0.00 37.02 3.36
6701 13253 1.895707 CGGCCTTGCTGATGATCCC 60.896 63.158 0.00 0.00 37.02 3.85
6702 13254 1.895707 GGCCTTGCTGATGATCCCG 60.896 63.158 0.00 0.00 0.00 5.14
6703 13255 2.550101 GCCTTGCTGATGATCCCGC 61.550 63.158 0.00 0.00 0.00 6.13
6704 13256 1.147824 CCTTGCTGATGATCCCGCT 59.852 57.895 5.61 0.00 0.00 5.52
6774 13326 4.796231 ATCGCACACCGCTCCGAC 62.796 66.667 0.00 0.00 39.08 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.280789 AGGAACTAGATGATACCCCACA 57.719 45.455 0.00 0.00 36.02 4.17
161 169 6.765036 ACATTCTTTCACTATAGGCATGTCAG 59.235 38.462 0.00 0.00 0.00 3.51
173 181 7.634671 ATGCATCAATGACATTCTTTCACTA 57.365 32.000 0.00 0.00 0.00 2.74
350 360 9.367444 CTAAACCTCGACACTTATTATGAAAGT 57.633 33.333 0.00 0.00 37.67 2.66
351 361 9.367444 ACTAAACCTCGACACTTATTATGAAAG 57.633 33.333 0.00 0.00 0.00 2.62
401 415 8.998814 TGAAAGATTGGTTTATATCCTACTCCA 58.001 33.333 0.00 0.00 0.00 3.86
523 542 7.776933 TGTTCATAGAAGTGATAAGACATGC 57.223 36.000 0.00 0.00 0.00 4.06
527 546 9.092876 CTCCTTTGTTCATAGAAGTGATAAGAC 57.907 37.037 0.00 0.00 0.00 3.01
530 549 6.823689 GCCTCCTTTGTTCATAGAAGTGATAA 59.176 38.462 0.00 0.00 0.00 1.75
532 551 5.189180 GCCTCCTTTGTTCATAGAAGTGAT 58.811 41.667 0.00 0.00 0.00 3.06
536 555 3.944015 CAGGCCTCCTTTGTTCATAGAAG 59.056 47.826 0.00 0.00 0.00 2.85
558 599 7.708752 TGTTTTTGTTTGTTTGTGATAGGGATC 59.291 33.333 0.00 0.00 0.00 3.36
560 601 6.936279 TGTTTTTGTTTGTTTGTGATAGGGA 58.064 32.000 0.00 0.00 0.00 4.20
561 602 7.602517 TTGTTTTTGTTTGTTTGTGATAGGG 57.397 32.000 0.00 0.00 0.00 3.53
562 603 8.174422 CCTTTGTTTTTGTTTGTTTGTGATAGG 58.826 33.333 0.00 0.00 0.00 2.57
564 605 7.119846 CCCCTTTGTTTTTGTTTGTTTGTGATA 59.880 33.333 0.00 0.00 0.00 2.15
565 606 6.072230 CCCCTTTGTTTTTGTTTGTTTGTGAT 60.072 34.615 0.00 0.00 0.00 3.06
1093 1549 4.484872 GTTGTAGCGGGAGGGGGC 62.485 72.222 0.00 0.00 0.00 5.80
1113 1573 5.221165 GCTGATTAGAGGAGAGTAGTGGAAC 60.221 48.000 0.00 0.00 0.00 3.62
1125 1585 1.678627 GCGAGTGAGCTGATTAGAGGA 59.321 52.381 0.00 0.00 0.00 3.71
1128 1588 1.678627 GAGGCGAGTGAGCTGATTAGA 59.321 52.381 0.00 0.00 37.29 2.10
1160 1620 0.663568 GGTGTTCACCTGTCGAGACG 60.664 60.000 13.97 0.00 0.00 4.18
1197 1666 2.489722 GGCCTTTTTCTTCTTCGCTGAT 59.510 45.455 0.00 0.00 0.00 2.90
1212 1681 4.596585 CCACCACCACCGGCCTTT 62.597 66.667 0.00 0.00 0.00 3.11
1331 1800 2.360475 GGACCAGCTGCAGTTCCC 60.360 66.667 16.64 6.50 0.00 3.97
1459 1937 5.281693 TGTTCGAGAATAATGTTGCACAG 57.718 39.130 0.00 0.00 0.00 3.66
1490 1968 2.322658 ACTGGGAAAGAACACCGTAGA 58.677 47.619 0.00 0.00 0.00 2.59
1567 2310 8.470002 AGTAATAGATTCCCTGCAAATCAAAAC 58.530 33.333 11.24 5.00 35.92 2.43
1572 2315 8.910351 AAGTAGTAATAGATTCCCTGCAAATC 57.090 34.615 1.98 1.98 34.08 2.17
1726 2469 1.872952 TGGTCTGTTGAACGAATGCAG 59.127 47.619 0.00 0.00 31.14 4.41
1778 2521 2.044908 AGCCCCATCCAGGATTTCTTTT 59.955 45.455 0.00 0.00 41.22 2.27
1779 2522 1.648037 AGCCCCATCCAGGATTTCTTT 59.352 47.619 0.00 0.00 41.22 2.52
2015 4693 1.656587 TCAGGGCAACAGTCATAGGT 58.343 50.000 0.00 0.00 39.74 3.08
2248 4942 3.386768 ACACATGTCACCTGAGTGTAC 57.613 47.619 0.00 0.00 44.83 2.90
2249 4943 4.415881 AAACACATGTCACCTGAGTGTA 57.584 40.909 0.00 0.00 44.83 2.90
2250 4944 3.281727 AAACACATGTCACCTGAGTGT 57.718 42.857 0.00 0.00 44.83 3.55
2251 4945 4.380531 ACTAAACACATGTCACCTGAGTG 58.619 43.478 0.00 0.00 46.00 3.51
2252 4946 4.689612 ACTAAACACATGTCACCTGAGT 57.310 40.909 0.00 0.00 0.00 3.41
2253 4947 4.214119 CCAACTAAACACATGTCACCTGAG 59.786 45.833 0.00 0.00 0.00 3.35
2254 4948 4.133820 CCAACTAAACACATGTCACCTGA 58.866 43.478 0.00 0.00 0.00 3.86
2255 4949 3.882888 ACCAACTAAACACATGTCACCTG 59.117 43.478 0.00 0.00 0.00 4.00
2256 4950 4.164843 ACCAACTAAACACATGTCACCT 57.835 40.909 0.00 0.00 0.00 4.00
2257 4951 4.606961 CAACCAACTAAACACATGTCACC 58.393 43.478 0.00 0.00 0.00 4.02
2258 4952 4.041723 GCAACCAACTAAACACATGTCAC 58.958 43.478 0.00 0.00 0.00 3.67
2259 4953 3.696548 TGCAACCAACTAAACACATGTCA 59.303 39.130 0.00 0.00 0.00 3.58
2260 4954 4.290155 CTGCAACCAACTAAACACATGTC 58.710 43.478 0.00 0.00 0.00 3.06
2261 4955 3.068024 CCTGCAACCAACTAAACACATGT 59.932 43.478 0.00 0.00 0.00 3.21
2270 4964 2.738587 TTTGTCCCTGCAACCAACTA 57.261 45.000 0.00 0.00 0.00 2.24
2296 4990 3.197983 TCATCCCTGGTTGGTTATTCCT 58.802 45.455 0.00 0.00 37.07 3.36
2396 5090 1.933853 GCGCTACAACAGAGGTAATGG 59.066 52.381 0.00 0.00 0.00 3.16
2435 5129 8.162878 AGATGCATAATCCAAACAGATACAAG 57.837 34.615 0.00 0.00 35.72 3.16
2555 5251 3.896648 TCTCATGCAACTCGGTTTTTC 57.103 42.857 0.00 0.00 0.00 2.29
2674 5371 8.846607 GTTCGTTTAATAAAGTTTACCTGCATG 58.153 33.333 0.00 0.00 0.00 4.06
2720 5417 3.057019 TCAACGAATTCAGTGGTTCTCG 58.943 45.455 6.22 0.00 0.00 4.04
2736 5433 5.728351 TCTGGTAACTCTTTTGTTCAACG 57.272 39.130 0.00 0.00 37.61 4.10
2800 8501 2.997485 GTGGAAATCACTGCTTCACC 57.003 50.000 0.00 0.00 42.86 4.02
2931 8721 6.041409 TCAACTAATTTCACAAAAGGATGGCA 59.959 34.615 0.00 0.00 0.00 4.92
2956 8746 3.236632 GGTAACGACCGTATGGACTTT 57.763 47.619 8.33 4.14 39.21 2.66
3021 8811 5.948992 ATTCTTAGAGTGTGCAAAACCTC 57.051 39.130 0.00 0.00 0.00 3.85
3334 9134 6.579292 CGAATAGTAAGAACATCCGACATCTC 59.421 42.308 0.00 0.00 0.00 2.75
3337 9137 5.301045 TCCGAATAGTAAGAACATCCGACAT 59.699 40.000 0.00 0.00 0.00 3.06
3343 9143 9.760077 TTAAGGAATCCGAATAGTAAGAACATC 57.240 33.333 0.00 0.00 0.00 3.06
3485 9285 5.629079 ACAGGCAAGCTTAATGTAACTTC 57.371 39.130 0.00 0.00 0.00 3.01
3671 9473 4.054780 TCTAATGCCAGTCATCGTTACC 57.945 45.455 0.00 0.00 33.40 2.85
3695 9497 0.582005 GCAAGACTGGACACAACGTC 59.418 55.000 0.00 0.00 44.57 4.34
3696 9498 0.178068 AGCAAGACTGGACACAACGT 59.822 50.000 0.00 0.00 0.00 3.99
3700 9502 5.865085 AGTTAATTAGCAAGACTGGACACA 58.135 37.500 1.97 0.00 0.00 3.72
3836 9638 7.838771 AACTAACCATAATTAGTGTCGGAAC 57.161 36.000 0.00 0.00 43.17 3.62
4201 10068 9.764363 TGCACTTGGATAAATAGTACATAGAAG 57.236 33.333 0.00 0.00 0.00 2.85
4286 10243 1.600957 CTGCATCGCCGATGAAGAATT 59.399 47.619 27.58 0.00 45.93 2.17
4318 10275 8.198109 GGAATGTGCTAGAATTGTAGAGAAGTA 58.802 37.037 13.55 0.00 0.00 2.24
4510 10469 8.133024 TGTACCAAAATGGAGCAAGAAATAAT 57.867 30.769 2.85 0.00 40.96 1.28
4646 10606 8.515414 AGAATATTTCCAAAAGCTTGTACTGTC 58.485 33.333 0.00 0.00 0.00 3.51
4688 10648 8.884124 TCAAGGGAAAATACTGAGAATGAAAT 57.116 30.769 0.00 0.00 0.00 2.17
4967 11032 7.575720 GCTTTGCAGTTCAACTTGGTATAATCT 60.576 37.037 0.00 0.00 33.73 2.40
5001 11066 9.130661 CAAAATGGAAAGAAACCCCTTTTTATT 57.869 29.630 0.00 0.00 36.31 1.40
5036 11101 6.828785 ACTTCCTTTGCTAGAACTGAGAAAAA 59.171 34.615 0.00 0.00 0.00 1.94
5037 11102 6.357367 ACTTCCTTTGCTAGAACTGAGAAAA 58.643 36.000 0.00 0.00 0.00 2.29
5057 11122 3.380637 TGCGGGAGATCAAGTAGTACTTC 59.619 47.826 12.75 2.57 36.03 3.01
5060 11125 2.688958 ACTGCGGGAGATCAAGTAGTAC 59.311 50.000 2.65 0.00 0.00 2.73
5103 11168 1.040646 GATGGTGAGCCTACCGATGA 58.959 55.000 2.87 0.00 43.87 2.92
5108 11173 2.892215 GGTACTAGATGGTGAGCCTACC 59.108 54.545 0.00 0.12 41.24 3.18
5208 11282 7.015974 TCACATTCCACAGCAGATCTAGATTAT 59.984 37.037 6.70 0.00 0.00 1.28
5294 11368 0.472925 ACCCCATTTCAAACCACCCC 60.473 55.000 0.00 0.00 0.00 4.95
5324 11398 8.986477 ATTGAACATAACATAACTTCTTTGCC 57.014 30.769 0.00 0.00 0.00 4.52
5563 11638 3.065371 CCACTTTTCAACAGAGGTGACAC 59.935 47.826 0.00 0.00 0.00 3.67
5593 11668 2.936498 CCTGGTAAATACAAGCGGTCAG 59.064 50.000 0.00 0.00 0.00 3.51
5660 11735 5.416326 TGTACCCATTCCTTTGTAAAATCCG 59.584 40.000 0.00 0.00 0.00 4.18
5835 11910 7.727181 AGGAATACTACATGTGGAGACAATAC 58.273 38.462 16.98 0.00 46.06 1.89
5837 11912 6.814954 AGGAATACTACATGTGGAGACAAT 57.185 37.500 16.98 0.00 46.06 2.71
5934 12009 4.330074 CAGTAAAATAAGAGGGCACGACAG 59.670 45.833 0.00 0.00 0.00 3.51
5938 12013 2.354821 GGCAGTAAAATAAGAGGGCACG 59.645 50.000 0.00 0.00 0.00 5.34
5946 12021 5.810587 TCTTGCTACGAGGCAGTAAAATAAG 59.189 40.000 7.07 0.00 43.39 1.73
5948 12023 5.333299 TCTTGCTACGAGGCAGTAAAATA 57.667 39.130 7.07 0.00 43.39 1.40
5982 12057 1.817209 CCTCTTGCTACGAGGGGAC 59.183 63.158 0.00 0.00 43.47 4.46
5997 12077 7.940850 TGCTTGATTTATATTTTACTGCCCTC 58.059 34.615 0.00 0.00 0.00 4.30
6107 12187 7.276658 CACTGTCCTAGAGAGAGTAATACTGA 58.723 42.308 0.00 0.00 46.94 3.41
6108 12188 6.017440 GCACTGTCCTAGAGAGAGTAATACTG 60.017 46.154 0.00 1.25 46.94 2.74
6109 12189 6.059484 GCACTGTCCTAGAGAGAGTAATACT 58.941 44.000 9.63 0.00 46.94 2.12
6110 12190 5.823570 TGCACTGTCCTAGAGAGAGTAATAC 59.176 44.000 9.63 0.00 46.94 1.89
6111 12191 5.823570 GTGCACTGTCCTAGAGAGAGTAATA 59.176 44.000 10.32 0.43 46.94 0.98
6112 12192 4.642885 GTGCACTGTCCTAGAGAGAGTAAT 59.357 45.833 10.32 0.00 46.94 1.89
6113 12193 4.011023 GTGCACTGTCCTAGAGAGAGTAA 58.989 47.826 10.32 1.89 46.94 2.24
6125 12205 3.044305 GCCTCGTGTGCACTGTCC 61.044 66.667 19.41 2.46 0.00 4.02
6151 12231 2.871182 TGCGAGTGTAGCCTTCATAG 57.129 50.000 0.00 0.00 0.00 2.23
6152 12232 3.194755 TCTTTGCGAGTGTAGCCTTCATA 59.805 43.478 0.00 0.00 0.00 2.15
6153 12233 2.028112 TCTTTGCGAGTGTAGCCTTCAT 60.028 45.455 0.00 0.00 0.00 2.57
6154 12234 1.343142 TCTTTGCGAGTGTAGCCTTCA 59.657 47.619 0.00 0.00 0.00 3.02
6168 12248 1.204792 GCTCGCTAGCTACTCTTTGC 58.795 55.000 13.93 0.00 45.85 3.68
6323 12617 1.522580 GCAGATGACGGCTTCCTCC 60.523 63.158 0.00 0.00 34.59 4.30
6452 12749 3.369381 AAGATGCCATCTTCGTCGG 57.631 52.632 14.17 0.00 46.17 4.79
6477 12795 0.879765 CAAGGGCAGAGCAAGTGAAG 59.120 55.000 0.00 0.00 0.00 3.02
6478 12796 0.473755 TCAAGGGCAGAGCAAGTGAA 59.526 50.000 0.00 0.00 0.00 3.18
6479 12797 0.694771 ATCAAGGGCAGAGCAAGTGA 59.305 50.000 0.00 0.00 0.00 3.41
6480 12798 1.093159 GATCAAGGGCAGAGCAAGTG 58.907 55.000 0.00 0.00 0.00 3.16
6483 12801 0.107993 CGAGATCAAGGGCAGAGCAA 60.108 55.000 0.00 0.00 0.00 3.91
6504 12822 1.080705 GGAGACGTCGACCCAACAG 60.081 63.158 19.22 0.00 0.00 3.16
6526 12883 1.147824 CTCCAGCTGCCACTATGGG 59.852 63.158 8.66 0.00 38.19 4.00
6527 12884 0.763652 ATCTCCAGCTGCCACTATGG 59.236 55.000 8.66 0.00 41.55 2.74
6528 12885 1.542767 CCATCTCCAGCTGCCACTATG 60.543 57.143 8.66 6.95 0.00 2.23
6529 12886 0.763652 CCATCTCCAGCTGCCACTAT 59.236 55.000 8.66 0.00 0.00 2.12
6530 12887 0.325577 TCCATCTCCAGCTGCCACTA 60.326 55.000 8.66 0.00 0.00 2.74
6531 12888 1.614525 TCCATCTCCAGCTGCCACT 60.615 57.895 8.66 0.00 0.00 4.00
6582 12996 1.599576 GGGAGAGGTCACCAAGAGC 59.400 63.158 0.00 0.00 45.07 4.09


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

AutoCloner maintained by Alex Coulton.