Multiple sequence alignment - TraesCS1D01G052800

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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 TraesCS1D01G052800 chr1D 100.000 1589 0 0 1 1589 33662839 33664427 0.000000e+00 2935.0
1 TraesCS1D01G052800 chr1D 100.000 560 0 0 1792 2351 33664630 33665189 0.000000e+00 1035.0
2 TraesCS1D01G052800 chr1D 85.227 528 58 13 882 1398 33712189 33712707 2.070000e-145 525.0
3 TraesCS1D01G052800 chr1D 87.772 368 33 9 1891 2249 33699556 33699920 1.000000e-113 420.0
4 TraesCS1D01G052800 chr1D 77.159 521 53 39 179 683 33642453 33642923 2.330000e-60 243.0
5 TraesCS1D01G052800 chr1D 87.952 166 18 2 1792 1956 33699395 33699559 6.630000e-46 195.0
6 TraesCS1D01G052800 chr1D 81.659 229 16 11 351 573 33705291 33705499 1.450000e-37 167.0
7 TraesCS1D01G052800 chr1D 97.674 43 1 0 979 1021 33643006 33643048 9.010000e-10 75.0
8 TraesCS1D01G052800 chr1B 88.872 656 26 14 11 643 51298889 51299520 0.000000e+00 763.0
9 TraesCS1D01G052800 chr1B 89.726 584 39 14 882 1450 51299805 51300382 0.000000e+00 726.0
10 TraesCS1D01G052800 chr1B 83.243 555 59 24 882 1418 51538893 51539431 1.630000e-131 479.0
11 TraesCS1D01G052800 chr1B 84.444 495 54 18 882 1367 51589994 51590474 1.270000e-127 466.0
12 TraesCS1D01G052800 chr1B 82.098 553 69 22 882 1418 51546297 51546835 1.660000e-121 446.0
13 TraesCS1D01G052800 chr1B 77.000 700 85 42 942 1587 51323245 51323922 4.840000e-87 331.0
14 TraesCS1D01G052800 chr1B 84.703 353 24 14 1792 2143 51300588 51300911 2.250000e-85 326.0
15 TraesCS1D01G052800 chr1B 90.419 167 13 3 1792 1957 51502598 51502762 1.410000e-52 217.0
16 TraesCS1D01G052800 chr1B 86.517 178 15 5 405 580 51143528 51143698 1.110000e-43 187.0
17 TraesCS1D01G052800 chr1B 91.228 114 5 4 761 874 51299626 51299734 1.460000e-32 150.0
18 TraesCS1D01G052800 chr1B 81.579 190 13 8 376 562 51321000 51321170 1.130000e-28 137.0
19 TraesCS1D01G052800 chr1A 86.833 562 38 15 882 1409 32291321 32291880 1.560000e-166 595.0
20 TraesCS1D01G052800 chr1A 88.210 458 23 11 301 745 32290710 32291149 3.460000e-143 518.0
21 TraesCS1D01G052800 chr1A 84.091 484 60 12 941 1417 32451349 32451822 3.560000e-123 451.0
22 TraesCS1D01G052800 chr1A 83.202 506 54 19 939 1432 32302157 32302643 3.590000e-118 435.0
23 TraesCS1D01G052800 chr1A 79.063 726 78 47 903 1587 32376323 32377015 4.640000e-117 431.0
24 TraesCS1D01G052800 chr1A 85.517 435 37 13 976 1403 32454444 32454859 4.640000e-117 431.0
25 TraesCS1D01G052800 chr1A 94.872 195 9 1 295 488 32263923 32264117 1.060000e-78 303.0
26 TraesCS1D01G052800 chr1A 89.506 162 15 1 1 162 32283522 32283681 1.100000e-48 204.0
27 TraesCS1D01G052800 chr1A 90.741 108 4 5 515 622 32451001 32451102 3.150000e-29 139.0
28 TraesCS1D01G052800 chr1A 90.625 96 9 0 760 855 32291136 32291231 6.820000e-26 128.0
29 TraesCS1D01G052800 chr1A 98.148 54 1 0 1792 1845 32302886 32302939 6.920000e-16 95.3
30 TraesCS1D01G052800 chr1A 86.047 86 9 2 409 493 32296798 32296881 3.220000e-14 89.8
31 TraesCS1D01G052800 chr1A 74.483 145 27 9 1448 1587 32291964 32292103 1.000000e-03 54.7


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 TraesCS1D01G052800 chr1D 33662839 33665189 2350 False 1985.000000 2935 100.00000 1 2351 2 chr1D.!!$F4 2350
1 TraesCS1D01G052800 chr1D 33712189 33712707 518 False 525.000000 525 85.22700 882 1398 1 chr1D.!!$F2 516
2 TraesCS1D01G052800 chr1D 33699395 33699920 525 False 307.500000 420 87.86200 1792 2249 2 chr1D.!!$F5 457
3 TraesCS1D01G052800 chr1B 51298889 51300911 2022 False 491.250000 763 88.63225 11 2143 4 chr1B.!!$F6 2132
4 TraesCS1D01G052800 chr1B 51538893 51539431 538 False 479.000000 479 83.24300 882 1418 1 chr1B.!!$F3 536
5 TraesCS1D01G052800 chr1B 51546297 51546835 538 False 446.000000 446 82.09800 882 1418 1 chr1B.!!$F4 536
6 TraesCS1D01G052800 chr1B 51321000 51323922 2922 False 234.000000 331 79.28950 376 1587 2 chr1B.!!$F7 1211
7 TraesCS1D01G052800 chr1A 32376323 32377015 692 False 431.000000 431 79.06300 903 1587 1 chr1A.!!$F4 684
8 TraesCS1D01G052800 chr1A 32451001 32454859 3858 False 340.333333 451 86.78300 515 1417 3 chr1A.!!$F7 902
9 TraesCS1D01G052800 chr1A 32290710 32292103 1393 False 323.925000 595 85.03775 301 1587 4 chr1A.!!$F5 1286
10 TraesCS1D01G052800 chr1A 32302157 32302939 782 False 265.150000 435 90.67500 939 1845 2 chr1A.!!$F6 906

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
722 2385 0.107654 AGCCCGTGAAATGCCTACTC 60.108 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 4456 0.814457 AGACTCTAGAGGCTTGTGCG 59.186 55.0 23.23 0.0 46.84 5.34 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
115 116 6.651225 GCACTTCTCTGTAAACCTTGTCTATT 59.349 38.462 0.00 0.00 0.00 1.73
141 142 3.993920 TGTTACTTCTTACCCAACGGAC 58.006 45.455 0.00 0.00 0.00 4.79
166 167 8.844244 ACTACTATTCAAGAAATGATTGCCATC 58.156 33.333 0.00 0.00 38.03 3.51
174 178 8.036575 TCAAGAAATGATTGCCATCCTAAAAAG 58.963 33.333 0.00 0.00 33.53 2.27
177 181 8.596293 AGAAATGATTGCCATCCTAAAAAGAAA 58.404 29.630 0.00 0.00 33.53 2.52
179 183 7.722949 ATGATTGCCATCCTAAAAAGAAAGA 57.277 32.000 0.00 0.00 0.00 2.52
240 244 5.010516 TGGTAACCAGAAATTTGTGACATGG 59.989 40.000 16.43 2.25 0.00 3.66
258 262 1.809547 TGGTACATGCATGTTCGTTGG 59.190 47.619 35.45 6.24 41.97 3.77
279 283 6.371809 TGGTTTCATGTAGCCGAATATTTC 57.628 37.500 0.93 0.00 0.00 2.17
284 288 5.541845 TCATGTAGCCGAATATTTCAGAGG 58.458 41.667 0.00 0.00 0.00 3.69
287 291 5.741011 TGTAGCCGAATATTTCAGAGGTTT 58.259 37.500 0.00 0.00 0.00 3.27
493 521 2.993471 GCCCGTGAAATGGCCACTG 61.993 63.158 8.16 0.00 43.51 3.66
494 522 2.342650 CCCGTGAAATGGCCACTGG 61.343 63.158 8.16 3.43 43.51 4.00
509 537 1.305633 CTGGCCACTCCCTCAGAGA 60.306 63.158 0.00 0.00 46.50 3.10
642 681 3.297620 GTGGGTGGGCAGCAACTG 61.298 66.667 0.00 0.00 30.38 3.16
643 682 3.497115 TGGGTGGGCAGCAACTGA 61.497 61.111 0.00 0.00 32.44 3.41
644 683 2.203480 GGGTGGGCAGCAACTGAA 60.203 61.111 0.00 0.00 32.44 3.02
695 955 0.306533 CACGCACACTTAACACCCAC 59.693 55.000 0.00 0.00 0.00 4.61
722 2385 0.107654 AGCCCGTGAAATGCCTACTC 60.108 55.000 0.00 0.00 0.00 2.59
723 2386 0.107654 GCCCGTGAAATGCCTACTCT 60.108 55.000 0.00 0.00 0.00 3.24
727 2390 2.271800 CGTGAAATGCCTACTCTCCAC 58.728 52.381 0.00 0.00 0.00 4.02
729 2392 3.526534 GTGAAATGCCTACTCTCCACTC 58.473 50.000 0.00 0.00 0.00 3.51
730 2393 2.501723 TGAAATGCCTACTCTCCACTCC 59.498 50.000 0.00 0.00 0.00 3.85
731 2394 2.254152 AATGCCTACTCTCCACTCCA 57.746 50.000 0.00 0.00 0.00 3.86
732 2395 1.490574 ATGCCTACTCTCCACTCCAC 58.509 55.000 0.00 0.00 0.00 4.02
733 2396 0.409876 TGCCTACTCTCCACTCCACT 59.590 55.000 0.00 0.00 0.00 4.00
734 2397 0.820871 GCCTACTCTCCACTCCACTG 59.179 60.000 0.00 0.00 0.00 3.66
735 2398 0.820871 CCTACTCTCCACTCCACTGC 59.179 60.000 0.00 0.00 0.00 4.40
736 2399 1.618345 CCTACTCTCCACTCCACTGCT 60.618 57.143 0.00 0.00 0.00 4.24
737 2400 2.175202 CTACTCTCCACTCCACTGCTT 58.825 52.381 0.00 0.00 0.00 3.91
738 2401 1.428869 ACTCTCCACTCCACTGCTTT 58.571 50.000 0.00 0.00 0.00 3.51
739 2402 1.771255 ACTCTCCACTCCACTGCTTTT 59.229 47.619 0.00 0.00 0.00 2.27
740 2403 2.149578 CTCTCCACTCCACTGCTTTTG 58.850 52.381 0.00 0.00 0.00 2.44
741 2404 1.202806 TCTCCACTCCACTGCTTTTGG 60.203 52.381 0.00 0.00 35.18 3.28
742 2405 0.843309 TCCACTCCACTGCTTTTGGA 59.157 50.000 2.15 2.15 41.06 3.53
743 2406 1.214175 TCCACTCCACTGCTTTTGGAA 59.786 47.619 3.55 0.00 42.76 3.53
744 2407 2.158475 TCCACTCCACTGCTTTTGGAAT 60.158 45.455 3.55 0.00 42.76 3.01
745 2408 3.073798 TCCACTCCACTGCTTTTGGAATA 59.926 43.478 3.55 0.00 42.76 1.75
746 2409 3.441572 CCACTCCACTGCTTTTGGAATAG 59.558 47.826 3.55 0.00 42.76 1.73
747 2410 4.326826 CACTCCACTGCTTTTGGAATAGA 58.673 43.478 3.55 0.00 42.76 1.98
748 2411 4.946157 CACTCCACTGCTTTTGGAATAGAT 59.054 41.667 3.55 0.00 42.76 1.98
749 2412 5.416952 CACTCCACTGCTTTTGGAATAGATT 59.583 40.000 3.55 0.00 42.76 2.40
750 2413 5.649831 ACTCCACTGCTTTTGGAATAGATTC 59.350 40.000 3.55 0.00 42.76 2.52
751 2414 5.819991 TCCACTGCTTTTGGAATAGATTCT 58.180 37.500 2.44 0.00 40.35 2.40
752 2415 6.957631 TCCACTGCTTTTGGAATAGATTCTA 58.042 36.000 0.00 0.00 40.35 2.10
753 2416 7.402054 TCCACTGCTTTTGGAATAGATTCTAA 58.598 34.615 0.00 0.00 40.35 2.10
754 2417 7.888021 TCCACTGCTTTTGGAATAGATTCTAAA 59.112 33.333 9.07 9.07 42.79 1.85
809 2498 1.603842 CTGTATGGCTGGGTGCAGA 59.396 57.895 0.00 0.00 45.15 4.26
822 2511 1.676635 TGCAGAATGGCTGGCTGTC 60.677 57.895 2.00 0.00 45.03 3.51
823 2512 1.676635 GCAGAATGGCTGGCTGTCA 60.677 57.895 0.00 0.00 45.03 3.58
826 2515 1.203441 AGAATGGCTGGCTGTCAGGA 61.203 55.000 11.76 0.00 43.54 3.86
870 2602 2.029290 CACTACGTCTGTTAAGCCCACT 60.029 50.000 0.00 0.00 0.00 4.00
874 2606 3.858247 ACGTCTGTTAAGCCCACTAATC 58.142 45.455 0.00 0.00 0.00 1.75
875 2607 3.514309 ACGTCTGTTAAGCCCACTAATCT 59.486 43.478 0.00 0.00 0.00 2.40
876 2608 4.113354 CGTCTGTTAAGCCCACTAATCTC 58.887 47.826 0.00 0.00 0.00 2.75
880 2612 4.832248 TGTTAAGCCCACTAATCTCACAG 58.168 43.478 0.00 0.00 0.00 3.66
916 2717 1.012841 CTCCTCCATTCGCTTTGCTC 58.987 55.000 0.00 0.00 0.00 4.26
959 2809 1.686052 GTAGCAGCAGCAGAGGATAGT 59.314 52.381 3.17 0.00 45.49 2.12
960 2810 2.079170 AGCAGCAGCAGAGGATAGTA 57.921 50.000 3.17 0.00 45.49 1.82
961 2811 1.962807 AGCAGCAGCAGAGGATAGTAG 59.037 52.381 3.17 0.00 45.49 2.57
1410 3321 1.815613 CGTCCGATGCTAGATCATCCT 59.184 52.381 0.00 0.00 39.64 3.24
1411 3322 3.010420 CGTCCGATGCTAGATCATCCTA 58.990 50.000 0.00 0.00 39.64 2.94
1494 3574 4.885907 TCAATCGGAGTCTCGGTAGTTTAT 59.114 41.667 7.24 0.00 0.00 1.40
1495 3575 6.057533 TCAATCGGAGTCTCGGTAGTTTATA 58.942 40.000 7.24 0.00 0.00 0.98
1498 3578 4.214971 TCGGAGTCTCGGTAGTTTATATGC 59.785 45.833 7.24 0.00 0.00 3.14
1503 3583 5.775701 AGTCTCGGTAGTTTATATGCCTGAT 59.224 40.000 0.00 0.00 0.00 2.90
1504 3584 6.267928 AGTCTCGGTAGTTTATATGCCTGATT 59.732 38.462 0.00 0.00 0.00 2.57
1505 3585 6.929606 GTCTCGGTAGTTTATATGCCTGATTT 59.070 38.462 0.00 0.00 0.00 2.17
1506 3586 6.929049 TCTCGGTAGTTTATATGCCTGATTTG 59.071 38.462 0.00 0.00 0.00 2.32
1507 3587 6.588204 TCGGTAGTTTATATGCCTGATTTGT 58.412 36.000 0.00 0.00 0.00 2.83
1508 3588 6.481976 TCGGTAGTTTATATGCCTGATTTGTG 59.518 38.462 0.00 0.00 0.00 3.33
1509 3589 6.260050 CGGTAGTTTATATGCCTGATTTGTGT 59.740 38.462 0.00 0.00 0.00 3.72
1510 3590 7.417612 GGTAGTTTATATGCCTGATTTGTGTG 58.582 38.462 0.00 0.00 0.00 3.82
1511 3591 7.067008 GGTAGTTTATATGCCTGATTTGTGTGT 59.933 37.037 0.00 0.00 0.00 3.72
1512 3592 7.088589 AGTTTATATGCCTGATTTGTGTGTC 57.911 36.000 0.00 0.00 0.00 3.67
1513 3593 6.095440 AGTTTATATGCCTGATTTGTGTGTCC 59.905 38.462 0.00 0.00 0.00 4.02
1514 3594 1.167851 ATGCCTGATTTGTGTGTCCG 58.832 50.000 0.00 0.00 0.00 4.79
1515 3595 0.179032 TGCCTGATTTGTGTGTCCGT 60.179 50.000 0.00 0.00 0.00 4.69
1516 3596 0.238289 GCCTGATTTGTGTGTCCGTG 59.762 55.000 0.00 0.00 0.00 4.94
1517 3597 1.593196 CCTGATTTGTGTGTCCGTGT 58.407 50.000 0.00 0.00 0.00 4.49
1518 3598 1.264020 CCTGATTTGTGTGTCCGTGTG 59.736 52.381 0.00 0.00 0.00 3.82
1519 3599 1.939934 CTGATTTGTGTGTCCGTGTGT 59.060 47.619 0.00 0.00 0.00 3.72
1526 3606 1.947642 GTGTCCGTGTGTCCGTGTC 60.948 63.158 0.00 0.00 0.00 3.67
1553 3662 3.318839 CCTGATTTGTGTGTGGTGATGTT 59.681 43.478 0.00 0.00 0.00 2.71
1558 3667 5.749596 TTTGTGTGTGGTGATGTTCTAAG 57.250 39.130 0.00 0.00 0.00 2.18
1898 4014 6.864685 AGCTGTGTGAACATTTCATTTGTATG 59.135 34.615 0.00 0.00 42.47 2.39
1941 4170 8.267894 ACTATAAGTTGAGCATTACCTTGTCAT 58.732 33.333 0.00 0.00 0.00 3.06
1958 4188 6.923508 CCTTGTCATAAAGAACCAAGTTTTCC 59.076 38.462 0.00 0.00 31.68 3.13
2002 4239 7.888546 ACAAAGTAGAGCATTAACATAAACCCT 59.111 33.333 0.00 0.00 0.00 4.34
2003 4240 9.391006 CAAAGTAGAGCATTAACATAAACCCTA 57.609 33.333 0.00 0.00 0.00 3.53
2012 4249 7.544217 GCATTAACATAAACCCTACAACAAAGG 59.456 37.037 0.00 0.00 0.00 3.11
2015 4252 7.663043 AACATAAACCCTACAACAAAGGAAA 57.337 32.000 0.00 0.00 36.08 3.13
2110 4350 7.109501 GCATTGGGATTTTAATAAACCTGGTT 58.890 34.615 6.18 6.18 0.00 3.67
2119 4359 8.890124 TTTTAATAAACCTGGTTTACAAAGCC 57.110 30.769 29.00 0.00 40.16 4.35
2164 4405 9.702726 AAATAATATTGAACACGAACATCGAAG 57.297 29.630 6.78 0.00 43.74 3.79
2181 4426 5.801350 TCGAAGGAAAAACATGCATAGAG 57.199 39.130 0.00 0.00 0.00 2.43
2182 4427 5.245531 TCGAAGGAAAAACATGCATAGAGT 58.754 37.500 0.00 0.00 0.00 3.24
2211 4456 0.610785 TTGGAAGAACAATCCGGCCC 60.611 55.000 0.00 0.00 39.98 5.80
2214 4459 3.561120 AAGAACAATCCGGCCCGCA 62.561 57.895 0.00 0.00 0.00 5.69
2235 4482 3.131400 CACAAGCCTCTAGAGTCTAACCC 59.869 52.174 18.42 0.00 0.00 4.11
2238 4485 5.103430 ACAAGCCTCTAGAGTCTAACCCTAT 60.103 44.000 18.42 0.00 0.00 2.57
2239 4486 4.993028 AGCCTCTAGAGTCTAACCCTATG 58.007 47.826 18.42 0.00 0.00 2.23
2259 4510 6.934645 CCTATGGAGATATTTTGGTAAAGCGA 59.065 38.462 0.00 0.00 0.00 4.93
2261 4512 7.823745 ATGGAGATATTTTGGTAAAGCGATT 57.176 32.000 0.00 0.00 0.00 3.34
2273 4524 5.364446 TGGTAAAGCGATTTGGATACTCCTA 59.636 40.000 9.29 0.00 37.46 2.94
2275 4526 5.353394 AAAGCGATTTGGATACTCCTACA 57.647 39.130 0.00 0.00 37.46 2.74
2286 4537 8.849543 TTGGATACTCCTACAAGTAATAAGGT 57.150 34.615 0.00 0.00 37.46 3.50
2291 4542 7.312415 ACTCCTACAAGTAATAAGGTTGTGT 57.688 36.000 0.00 0.00 35.95 3.72
2293 4544 6.704310 TCCTACAAGTAATAAGGTTGTGTCC 58.296 40.000 0.00 0.00 35.95 4.02
2294 4545 6.270463 TCCTACAAGTAATAAGGTTGTGTCCA 59.730 38.462 0.00 0.00 35.95 4.02
2295 4546 6.594159 CCTACAAGTAATAAGGTTGTGTCCAG 59.406 42.308 0.00 0.00 35.95 3.86
2296 4547 5.937111 ACAAGTAATAAGGTTGTGTCCAGT 58.063 37.500 0.00 0.00 33.16 4.00
2297 4548 5.995897 ACAAGTAATAAGGTTGTGTCCAGTC 59.004 40.000 0.00 0.00 33.16 3.51
2298 4549 4.817517 AGTAATAAGGTTGTGTCCAGTCG 58.182 43.478 0.00 0.00 0.00 4.18
2300 4551 2.806608 TAAGGTTGTGTCCAGTCGTC 57.193 50.000 0.00 0.00 0.00 4.20
2301 4552 0.249322 AAGGTTGTGTCCAGTCGTCG 60.249 55.000 0.00 0.00 0.00 5.12
2302 4553 1.066918 GGTTGTGTCCAGTCGTCGT 59.933 57.895 0.00 0.00 0.00 4.34
2303 4554 0.529119 GGTTGTGTCCAGTCGTCGTT 60.529 55.000 0.00 0.00 0.00 3.85
2304 4555 1.269206 GGTTGTGTCCAGTCGTCGTTA 60.269 52.381 0.00 0.00 0.00 3.18
2307 4558 1.610038 TGTGTCCAGTCGTCGTTATGT 59.390 47.619 0.00 0.00 0.00 2.29
2311 4562 1.200716 TCCAGTCGTCGTTATGTGGTC 59.799 52.381 0.00 0.00 0.00 4.02
2312 4563 1.625616 CAGTCGTCGTTATGTGGTCC 58.374 55.000 0.00 0.00 0.00 4.46
2313 4564 1.068125 CAGTCGTCGTTATGTGGTCCA 60.068 52.381 0.00 0.00 0.00 4.02
2314 4565 1.822990 AGTCGTCGTTATGTGGTCCAT 59.177 47.619 0.00 0.00 37.58 3.41
2317 4568 1.663695 GTCGTTATGTGGTCCATGGG 58.336 55.000 13.02 0.00 34.86 4.00
2319 4570 1.208535 TCGTTATGTGGTCCATGGGTC 59.791 52.381 13.02 5.59 34.86 4.46
2320 4571 1.209504 CGTTATGTGGTCCATGGGTCT 59.790 52.381 13.02 0.00 34.86 3.85
2321 4572 2.643551 GTTATGTGGTCCATGGGTCTG 58.356 52.381 13.02 0.00 34.86 3.51
2322 4573 2.238646 GTTATGTGGTCCATGGGTCTGA 59.761 50.000 13.02 0.00 34.86 3.27
2323 4574 1.600058 ATGTGGTCCATGGGTCTGAT 58.400 50.000 13.02 0.00 30.69 2.90
2325 4576 1.004628 TGTGGTCCATGGGTCTGATTG 59.995 52.381 13.02 0.00 0.00 2.67
2326 4577 1.004745 GTGGTCCATGGGTCTGATTGT 59.995 52.381 13.02 0.00 0.00 2.71
2328 4579 2.916269 TGGTCCATGGGTCTGATTGTAA 59.084 45.455 13.02 0.00 0.00 2.41
2329 4580 3.527253 TGGTCCATGGGTCTGATTGTAAT 59.473 43.478 13.02 0.00 0.00 1.89
2330 4581 4.017591 TGGTCCATGGGTCTGATTGTAATT 60.018 41.667 13.02 0.00 0.00 1.40
2331 4582 4.339247 GGTCCATGGGTCTGATTGTAATTG 59.661 45.833 13.02 0.00 0.00 2.32
2333 4584 5.418840 GTCCATGGGTCTGATTGTAATTGTT 59.581 40.000 13.02 0.00 0.00 2.83
2334 4585 6.601613 GTCCATGGGTCTGATTGTAATTGTTA 59.398 38.462 13.02 0.00 0.00 2.41
2335 4586 7.285401 GTCCATGGGTCTGATTGTAATTGTTAT 59.715 37.037 13.02 0.00 0.00 1.89
2336 4587 7.838696 TCCATGGGTCTGATTGTAATTGTTATT 59.161 33.333 13.02 0.00 0.00 1.40
2337 4588 9.130661 CCATGGGTCTGATTGTAATTGTTATTA 57.869 33.333 2.85 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.913137 ATAGGAAGATCTTAGGCGATGAG 57.087 43.478 8.25 0.00 0.00 2.90
1 2 6.013379 AGAATAGGAAGATCTTAGGCGATGA 58.987 40.000 8.25 0.00 0.00 2.92
2 3 6.279513 AGAATAGGAAGATCTTAGGCGATG 57.720 41.667 8.25 0.00 0.00 3.84
3 4 6.723977 AGAAGAATAGGAAGATCTTAGGCGAT 59.276 38.462 8.25 0.00 33.73 4.58
4 5 6.071984 AGAAGAATAGGAAGATCTTAGGCGA 58.928 40.000 8.25 0.00 33.73 5.54
5 6 6.339587 AGAAGAATAGGAAGATCTTAGGCG 57.660 41.667 8.25 0.00 33.73 5.52
6 7 7.659799 GGAAAGAAGAATAGGAAGATCTTAGGC 59.340 40.741 8.25 0.00 33.73 3.93
7 8 8.709308 TGGAAAGAAGAATAGGAAGATCTTAGG 58.291 37.037 8.25 0.00 33.73 2.69
9 10 9.892130 GTTGGAAAGAAGAATAGGAAGATCTTA 57.108 33.333 8.25 0.00 33.73 2.10
68 69 6.257630 GTGCTAGAGGATGAAGAATCAAAGAC 59.742 42.308 0.00 0.00 39.49 3.01
115 116 5.528320 CCGTTGGGTAAGAAGTAACAAAGAA 59.472 40.000 0.00 0.00 0.00 2.52
141 142 8.295288 GGATGGCAATCATTTCTTGAATAGTAG 58.705 37.037 2.85 0.00 38.03 2.57
191 195 8.819974 CATTTAAACTCACAGCTTCATGTTTTT 58.180 29.630 9.08 4.25 0.00 1.94
240 244 3.552604 AACCAACGAACATGCATGTAC 57.447 42.857 31.55 9.74 40.80 2.90
258 262 7.246674 TCTGAAATATTCGGCTACATGAAAC 57.753 36.000 0.00 0.00 35.98 2.78
493 521 2.363172 GGTCTCTGAGGGAGTGGCC 61.363 68.421 4.59 0.00 42.40 5.36
494 522 2.363172 GGGTCTCTGAGGGAGTGGC 61.363 68.421 4.59 0.00 42.40 5.01
495 523 1.687493 GGGGTCTCTGAGGGAGTGG 60.687 68.421 4.59 0.00 42.40 4.00
496 524 0.326048 ATGGGGTCTCTGAGGGAGTG 60.326 60.000 4.59 0.00 42.40 3.51
497 525 0.031616 GATGGGGTCTCTGAGGGAGT 60.032 60.000 4.59 0.00 42.40 3.85
498 526 0.762461 GGATGGGGTCTCTGAGGGAG 60.762 65.000 4.59 0.00 43.12 4.30
499 527 1.314867 GGATGGGGTCTCTGAGGGA 59.685 63.158 4.59 0.00 0.00 4.20
509 537 1.131303 TCGAAACTGGTGGATGGGGT 61.131 55.000 0.00 0.00 0.00 4.95
616 655 3.902112 CCCACCCACCCAGTTGCT 61.902 66.667 0.00 0.00 0.00 3.91
681 817 5.313280 TGGATTTAGTGGGTGTTAAGTGT 57.687 39.130 0.00 0.00 0.00 3.55
695 955 2.223572 GCATTTCACGGGCTGGATTTAG 60.224 50.000 0.00 0.00 0.00 1.85
722 2385 1.202806 TCCAAAAGCAGTGGAGTGGAG 60.203 52.381 0.00 0.00 40.33 3.86
723 2386 0.843309 TCCAAAAGCAGTGGAGTGGA 59.157 50.000 0.00 0.00 40.33 4.02
727 2390 5.884792 AGAATCTATTCCAAAAGCAGTGGAG 59.115 40.000 3.60 0.00 45.79 3.86
729 2392 7.630242 TTAGAATCTATTCCAAAAGCAGTGG 57.370 36.000 0.00 0.00 37.51 4.00
730 2393 9.912634 TTTTTAGAATCTATTCCAAAAGCAGTG 57.087 29.630 8.38 0.00 38.15 3.66
755 2418 9.981114 ATTCATTCGATTCCAAAAGTAGTTTTT 57.019 25.926 5.51 0.00 39.55 1.94
756 2419 9.981114 AATTCATTCGATTCCAAAAGTAGTTTT 57.019 25.926 2.28 2.28 36.22 2.43
757 2420 9.981114 AAATTCATTCGATTCCAAAAGTAGTTT 57.019 25.926 0.00 0.00 0.00 2.66
809 2498 0.395311 CATCCTGACAGCCAGCCATT 60.395 55.000 0.00 0.00 41.57 3.16
822 2511 7.993101 TCTTCTCAATTTAATTGCTCATCCTG 58.007 34.615 12.39 0.00 40.05 3.86
823 2512 8.465201 GTTCTTCTCAATTTAATTGCTCATCCT 58.535 33.333 12.39 0.00 40.05 3.24
826 2515 8.800332 AGTGTTCTTCTCAATTTAATTGCTCAT 58.200 29.630 12.39 0.00 40.05 2.90
870 2602 2.354103 GCACCAGTGAGCTGTGAGATTA 60.354 50.000 5.38 0.00 41.02 1.75
874 2606 1.670406 GGCACCAGTGAGCTGTGAG 60.670 63.158 5.38 0.00 41.02 3.51
875 2607 2.427320 GGCACCAGTGAGCTGTGA 59.573 61.111 5.38 0.00 41.02 3.58
916 2717 1.402984 GGGACTGTCTGTTGTCTAGCG 60.403 57.143 7.85 0.00 34.01 4.26
959 2809 0.251354 AGACGTACTGGACCGAGCTA 59.749 55.000 0.00 0.00 0.00 3.32
960 2810 1.002379 AGACGTACTGGACCGAGCT 60.002 57.895 0.00 0.00 0.00 4.09
961 2811 1.428620 GAGACGTACTGGACCGAGC 59.571 63.158 0.00 0.00 0.00 5.03
1026 2888 3.007920 AGCAGCAGGAGGGTGGAG 61.008 66.667 0.00 0.00 45.14 3.86
1030 2892 3.386237 GACGAGCAGCAGGAGGGT 61.386 66.667 0.00 0.00 0.00 4.34
1269 3173 2.665185 AAGTTCTCGGTGCGGCAC 60.665 61.111 24.43 24.43 0.00 5.01
1494 3574 2.290008 ACGGACACACAAATCAGGCATA 60.290 45.455 0.00 0.00 0.00 3.14
1495 3575 1.167851 CGGACACACAAATCAGGCAT 58.832 50.000 0.00 0.00 0.00 4.40
1498 3578 1.264020 CACACGGACACACAAATCAGG 59.736 52.381 0.00 0.00 0.00 3.86
1503 3583 1.084935 CGGACACACGGACACACAAA 61.085 55.000 0.00 0.00 0.00 2.83
1504 3584 1.519676 CGGACACACGGACACACAA 60.520 57.895 0.00 0.00 0.00 3.33
1505 3585 2.105328 CGGACACACGGACACACA 59.895 61.111 0.00 0.00 0.00 3.72
1506 3586 2.105528 ACGGACACACGGACACAC 59.894 61.111 0.00 0.00 38.39 3.82
1507 3587 2.105328 CACGGACACACGGACACA 59.895 61.111 0.00 0.00 38.39 3.72
1508 3588 1.947642 GACACGGACACACGGACAC 60.948 63.158 0.00 0.00 38.39 3.67
1509 3589 2.122797 AGACACGGACACACGGACA 61.123 57.895 0.00 0.00 38.39 4.02
1510 3590 1.660575 CAGACACGGACACACGGAC 60.661 63.158 0.00 0.00 38.39 4.79
1511 3591 2.122797 ACAGACACGGACACACGGA 61.123 57.895 0.00 0.00 38.39 4.69
1512 3592 1.949133 CACAGACACGGACACACGG 60.949 63.158 0.00 0.00 38.39 4.94
1513 3593 2.585869 GCACAGACACGGACACACG 61.586 63.158 0.00 0.00 40.31 4.49
1514 3594 2.244651 GGCACAGACACGGACACAC 61.245 63.158 0.00 0.00 0.00 3.82
1515 3595 2.108157 GGCACAGACACGGACACA 59.892 61.111 0.00 0.00 0.00 3.72
1516 3596 1.956170 CAGGCACAGACACGGACAC 60.956 63.158 0.00 0.00 0.00 3.67
1517 3597 1.471829 ATCAGGCACAGACACGGACA 61.472 55.000 0.00 0.00 0.00 4.02
1518 3598 0.320771 AATCAGGCACAGACACGGAC 60.321 55.000 0.00 0.00 0.00 4.79
1519 3599 0.396435 AAATCAGGCACAGACACGGA 59.604 50.000 0.00 0.00 0.00 4.69
1526 3606 1.001048 CCACACACAAATCAGGCACAG 60.001 52.381 0.00 0.00 0.00 3.66
1553 3662 4.927425 GCTGAAACAACGACCATACTTAGA 59.073 41.667 0.00 0.00 0.00 2.10
1558 3667 3.426159 CCATGCTGAAACAACGACCATAC 60.426 47.826 0.00 0.00 0.00 2.39
1858 3974 2.284150 CACAGCTTCGAAAAACGTCTCA 59.716 45.455 0.00 0.00 43.13 3.27
1898 4014 8.430801 ACTTATAGTTCTTCATCAGTTCATGC 57.569 34.615 0.00 0.00 0.00 4.06
1941 4170 5.808030 CGCAAAAGGAAAACTTGGTTCTTTA 59.192 36.000 0.00 0.00 39.96 1.85
1958 4188 6.704819 ACTTTGTTATTTTCTTGCGCAAAAG 58.295 32.000 25.01 20.59 0.00 2.27
2015 4252 7.549134 TCGTACTCATGTTAATGCTCTCATTTT 59.451 33.333 0.00 0.00 42.51 1.82
2068 4305 5.064962 CCCAATGCACATAAAAATTTCGCAT 59.935 36.000 0.00 0.00 40.14 4.73
2099 4336 8.430573 AAATAGGCTTTGTAAACCAGGTTTAT 57.569 30.769 24.78 11.60 39.64 1.40
2164 4405 6.699575 ATGGTACTCTATGCATGTTTTTCC 57.300 37.500 10.16 6.17 0.00 3.13
2181 4426 6.350194 GGATTGTTCTTCCAAGGAAATGGTAC 60.350 42.308 2.78 0.00 41.46 3.34
2182 4427 5.714806 GGATTGTTCTTCCAAGGAAATGGTA 59.285 40.000 2.78 0.00 41.46 3.25
2211 4456 0.814457 AGACTCTAGAGGCTTGTGCG 59.186 55.000 23.23 0.00 46.84 5.34
2214 4459 3.011934 AGGGTTAGACTCTAGAGGCTTGT 59.988 47.826 32.78 12.29 46.84 3.16
2235 4482 7.962964 TCGCTTTACCAAAATATCTCCATAG 57.037 36.000 0.00 0.00 0.00 2.23
2238 4485 7.416213 CCAAATCGCTTTACCAAAATATCTCCA 60.416 37.037 0.00 0.00 0.00 3.86
2239 4486 6.918022 CCAAATCGCTTTACCAAAATATCTCC 59.082 38.462 0.00 0.00 0.00 3.71
2273 4524 5.937111 ACTGGACACAACCTTATTACTTGT 58.063 37.500 0.00 0.00 0.00 3.16
2275 4526 5.221581 ACGACTGGACACAACCTTATTACTT 60.222 40.000 0.00 0.00 0.00 2.24
2286 4537 2.034939 ACATAACGACGACTGGACACAA 59.965 45.455 0.00 0.00 0.00 3.33
2291 4542 1.200716 GACCACATAACGACGACTGGA 59.799 52.381 0.00 0.00 0.00 3.86
2293 4544 1.068125 TGGACCACATAACGACGACTG 60.068 52.381 0.00 0.00 0.00 3.51
2294 4545 1.250328 TGGACCACATAACGACGACT 58.750 50.000 0.00 0.00 0.00 4.18
2295 4546 1.924524 CATGGACCACATAACGACGAC 59.075 52.381 0.00 0.00 37.84 4.34
2296 4547 1.134936 CCATGGACCACATAACGACGA 60.135 52.381 5.56 0.00 37.84 4.20
2297 4548 1.286501 CCATGGACCACATAACGACG 58.713 55.000 5.56 0.00 37.84 5.12
2298 4549 1.065709 ACCCATGGACCACATAACGAC 60.066 52.381 15.22 0.00 37.84 4.34
2300 4551 1.209504 AGACCCATGGACCACATAACG 59.790 52.381 15.22 0.00 37.84 3.18
2301 4552 2.238646 TCAGACCCATGGACCACATAAC 59.761 50.000 15.22 0.00 37.84 1.89
2302 4553 2.556766 TCAGACCCATGGACCACATAA 58.443 47.619 15.22 0.00 37.84 1.90
2303 4554 2.262266 TCAGACCCATGGACCACATA 57.738 50.000 15.22 0.00 37.84 2.29
2304 4555 1.600058 ATCAGACCCATGGACCACAT 58.400 50.000 15.22 0.00 41.57 3.21
2307 4558 1.371467 ACAATCAGACCCATGGACCA 58.629 50.000 15.22 0.00 0.00 4.02
2311 4562 5.920193 AACAATTACAATCAGACCCATGG 57.080 39.130 4.14 4.14 0.00 3.66
2312 4563 9.950680 GTAATAACAATTACAATCAGACCCATG 57.049 33.333 3.91 0.00 37.08 3.66
2313 4564 9.693739 TGTAATAACAATTACAATCAGACCCAT 57.306 29.630 8.18 0.00 42.16 4.00
2314 4565 9.693739 ATGTAATAACAATTACAATCAGACCCA 57.306 29.630 13.28 0.00 46.27 4.51


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

AutoCloner maintained by Alex Coulton.