Multiple sequence alignment - TraesCS7B01G308700

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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 TraesCS7B01G308700 chr7B 100.000 5506 0 0 961 6466 552561701 552567206 0.000000e+00 10168
1 TraesCS7B01G308700 chr7B 100.000 563 0 0 1 563 552560741 552561303 0.000000e+00 1040
2 TraesCS7B01G308700 chr7B 87.963 108 13 0 16 123 552665755 552665648 1.890000e-25 128
3 TraesCS7B01G308700 chr7D 96.475 2014 68 2 4074 6084 519265615 519267628 0.000000e+00 3323
4 TraesCS7B01G308700 chr7D 92.764 2294 118 28 961 3224 519262260 519264535 0.000000e+00 3273
5 TraesCS7B01G308700 chr7D 98.822 849 10 0 3241 4089 519264629 519265477 0.000000e+00 1513
6 TraesCS7B01G308700 chr7D 92.769 567 30 5 1 562 519261699 519262259 0.000000e+00 809
7 TraesCS7B01G308700 chr7D 92.035 565 38 4 5909 6466 519267627 519268191 0.000000e+00 787
8 TraesCS7B01G308700 chr7D 77.734 512 82 17 2129 2615 519262673 519263177 1.060000e-72 285
9 TraesCS7B01G308700 chr7D 82.006 339 56 5 1525 1861 519263587 519263922 3.820000e-72 283
10 TraesCS7B01G308700 chr7D 86.620 142 17 2 5294 5434 519266700 519266840 8.680000e-34 156
11 TraesCS7B01G308700 chr7D 87.963 108 13 0 16 123 519271337 519271230 1.890000e-25 128
12 TraesCS7B01G308700 chr7A 91.750 2303 131 33 969 3242 595070144 595072416 0.000000e+00 3145
13 TraesCS7B01G308700 chr7A 96.154 1924 55 5 4074 5993 595073505 595075413 0.000000e+00 3125
14 TraesCS7B01G308700 chr7A 98.115 849 13 1 3241 4089 595072531 595073376 0.000000e+00 1476
15 TraesCS7B01G308700 chr7A 92.199 564 23 9 1 551 595069573 595070128 0.000000e+00 778
16 TraesCS7B01G308700 chr7A 93.237 414 24 3 6056 6466 595076290 595076702 1.990000e-169 606
17 TraesCS7B01G308700 chr7A 81.361 338 49 9 2285 2615 595070705 595071035 4.970000e-66 263
18 TraesCS7B01G308700 chr7A 80.119 337 60 7 1522 1855 595071442 595071774 1.800000e-60 244
19 TraesCS7B01G308700 chr7A 88.028 142 15 2 5294 5434 595074589 595074729 4.010000e-37 167
20 TraesCS7B01G308700 chr7A 88.889 108 12 0 16 123 595198945 595198838 4.070000e-27 134


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 TraesCS7B01G308700 chr7B 552560741 552567206 6465 False 5604.000 10168 100.000000 1 6466 2 chr7B.!!$F1 6465
1 TraesCS7B01G308700 chr7D 519261699 519268191 6492 False 1303.625 3323 89.903125 1 6466 8 chr7D.!!$F1 6465
2 TraesCS7B01G308700 chr7A 595069573 595076702 7129 False 1225.500 3145 90.120375 1 6466 8 chr7A.!!$F1 6465

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
382 386 0.744414 GCCATTCTTGCGGCTGTCTA 60.744 55.000 0.00 0.0 45.29 2.59 F
1596 1632 0.402121 GTCCCCCACAAGCTTTCTCT 59.598 55.000 0.00 0.0 0.00 3.10 F
1721 1761 0.593128 GCTTCACACTCGCCACAATT 59.407 50.000 0.00 0.0 0.00 2.32 F
1886 1928 1.005557 GCAGCGTGAATCATCGACTTC 60.006 52.381 8.85 0.0 0.00 3.01 F
1980 2022 1.670406 GAGTGACTGTGCAGCCCTG 60.670 63.158 0.00 0.0 0.00 4.45 F
2083 2125 2.221055 GCTTGTTCGTCACAATTCTCGT 59.779 45.455 3.85 0.0 44.72 4.18 F
2105 2147 2.222213 CACACTTTTTATCCACGCGACA 59.778 45.455 15.93 0.0 0.00 4.35 F
4042 4288 2.041755 ACCTGATCCAACCTTTTCCCTC 59.958 50.000 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 1897 0.249826 TCACGCTGCTGTGAACATCA 60.250 50.000 19.55 2.46 45.40 3.07 R
2688 2731 1.478288 GGAAGCAGCTGATATTGGCCT 60.478 52.381 20.43 0.00 0.00 5.19 R
3510 3756 4.024133 CGTTTCATGTCACCTTGTTGATCA 60.024 41.667 0.00 0.00 0.00 2.92 R
4030 4276 1.073098 ATGGACCGAGGGAAAAGGTT 58.927 50.000 0.00 0.00 38.57 3.50 R
4037 4283 0.616395 TGCAGTTATGGACCGAGGGA 60.616 55.000 0.00 0.00 0.00 4.20 R
4042 4288 3.685139 ATCCTATGCAGTTATGGACCG 57.315 47.619 0.00 0.00 0.00 4.79 R
4211 4610 6.076981 AGAAAGATGTGTAAGCCTTTTGTG 57.923 37.500 0.00 0.00 0.00 3.33 R
5513 5914 0.675633 ATGCAACCACAGAAACAGCC 59.324 50.000 0.00 0.00 0.00 4.85 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
104 105 1.228154 GAAGTTGCCGAACCCCACT 60.228 57.895 0.00 0.00 31.81 4.00
287 291 4.509737 GCCGCCGTAGACCTGTCC 62.510 72.222 0.00 0.00 0.00 4.02
288 292 4.189188 CCGCCGTAGACCTGTCCG 62.189 72.222 0.00 0.00 0.00 4.79
300 304 4.467084 TGTCCGCGGATTGGAGGC 62.467 66.667 33.58 17.12 35.82 4.70
306 310 3.207669 CGGATTGGAGGCTGCTGC 61.208 66.667 7.74 7.10 38.76 5.25
382 386 0.744414 GCCATTCTTGCGGCTGTCTA 60.744 55.000 0.00 0.00 45.29 2.59
562 576 2.193248 GGGAATTGCTCCGAGGGG 59.807 66.667 0.00 0.00 46.51 4.79
1288 1302 4.226168 CCAAGAAGGACAAGGAGAAGGTAT 59.774 45.833 0.00 0.00 41.22 2.73
1295 1309 4.382793 GGACAAGGAGAAGGTATACACACC 60.383 50.000 5.01 4.14 39.02 4.16
1296 1310 4.164981 ACAAGGAGAAGGTATACACACCA 58.835 43.478 5.01 0.00 41.40 4.17
1299 1313 4.164981 AGGAGAAGGTATACACACCAACA 58.835 43.478 5.01 0.00 41.40 3.33
1300 1314 4.783227 AGGAGAAGGTATACACACCAACAT 59.217 41.667 5.01 0.00 41.40 2.71
1332 1346 0.531200 ACGCCGTCCTCCTCTTTTAG 59.469 55.000 0.00 0.00 0.00 1.85
1333 1347 0.815734 CGCCGTCCTCCTCTTTTAGA 59.184 55.000 0.00 0.00 0.00 2.10
1334 1348 1.469423 CGCCGTCCTCCTCTTTTAGAC 60.469 57.143 0.00 0.00 0.00 2.59
1341 1355 6.324042 CGTCCTCCTCTTTTAGACTTTAGAC 58.676 44.000 0.00 0.00 0.00 2.59
1342 1356 6.151480 CGTCCTCCTCTTTTAGACTTTAGACT 59.849 42.308 0.00 0.00 0.00 3.24
1343 1357 7.309316 CGTCCTCCTCTTTTAGACTTTAGACTT 60.309 40.741 0.00 0.00 0.00 3.01
1344 1358 8.369424 GTCCTCCTCTTTTAGACTTTAGACTTT 58.631 37.037 0.00 0.00 0.00 2.66
1345 1359 8.935741 TCCTCCTCTTTTAGACTTTAGACTTTT 58.064 33.333 0.00 0.00 0.00 2.27
1369 1384 2.627515 TTATCAGCTCATGGGCACTC 57.372 50.000 22.09 0.00 34.17 3.51
1381 1396 2.536066 TGGGCACTCTAGCTTGAACTA 58.464 47.619 0.00 0.00 34.17 2.24
1443 1462 1.538047 TTTGGTCATCTGGCTTCAGC 58.462 50.000 0.00 0.00 38.36 4.26
1450 1469 3.380637 GTCATCTGGCTTCAGCATTTCAT 59.619 43.478 0.30 0.00 44.36 2.57
1451 1470 3.630769 TCATCTGGCTTCAGCATTTCATC 59.369 43.478 0.30 0.00 44.36 2.92
1455 1474 1.202382 GGCTTCAGCATTTCATCTGGC 60.202 52.381 0.30 0.00 44.36 4.85
1457 1476 2.165845 GCTTCAGCATTTCATCTGGCTT 59.834 45.455 0.00 0.00 41.59 4.35
1458 1477 3.734293 GCTTCAGCATTTCATCTGGCTTC 60.734 47.826 0.00 0.00 41.59 3.86
1488 1522 7.548196 TTTGTCGGATAAATAGCCTAAACTG 57.452 36.000 0.00 0.00 0.00 3.16
1562 1598 3.181482 TGTTCATGTGCATTTTGTTCCGT 60.181 39.130 0.00 0.00 0.00 4.69
1563 1599 3.281341 TCATGTGCATTTTGTTCCGTC 57.719 42.857 0.00 0.00 0.00 4.79
1577 1613 3.459027 CGTCAACACGGTGGATCG 58.541 61.111 13.48 7.80 42.73 3.69
1583 1619 4.157120 CACGGTGGATCGTCCCCC 62.157 72.222 0.00 0.00 41.86 5.40
1594 1630 1.073199 CGTCCCCCACAAGCTTTCT 59.927 57.895 0.00 0.00 0.00 2.52
1596 1632 0.402121 GTCCCCCACAAGCTTTCTCT 59.598 55.000 0.00 0.00 0.00 3.10
1617 1653 9.912634 TTCTCTAAGACATTGCTTTATTTTTGG 57.087 29.630 0.00 0.00 0.00 3.28
1619 1655 5.844301 AAGACATTGCTTTATTTTTGGCG 57.156 34.783 0.00 0.00 0.00 5.69
1627 1663 4.220821 TGCTTTATTTTTGGCGTTATCCCA 59.779 37.500 0.00 0.00 0.00 4.37
1628 1664 4.803613 GCTTTATTTTTGGCGTTATCCCAG 59.196 41.667 0.00 0.00 33.13 4.45
1633 1669 0.693622 TTGGCGTTATCCCAGTTCCA 59.306 50.000 0.00 0.00 33.13 3.53
1710 1750 7.915397 ACATTAATTTTGATATCCGCTTCACAC 59.085 33.333 0.00 0.00 0.00 3.82
1714 1754 1.132588 GATATCCGCTTCACACTCGC 58.867 55.000 0.00 0.00 0.00 5.03
1721 1761 0.593128 GCTTCACACTCGCCACAATT 59.407 50.000 0.00 0.00 0.00 2.32
1732 1772 4.522789 ACTCGCCACAATTATGAACCTTTT 59.477 37.500 0.00 0.00 0.00 2.27
1733 1773 4.804108 TCGCCACAATTATGAACCTTTTG 58.196 39.130 0.00 0.00 0.00 2.44
1735 1775 5.473846 TCGCCACAATTATGAACCTTTTGTA 59.526 36.000 0.00 0.00 0.00 2.41
1740 1780 9.703892 CCACAATTATGAACCTTTTGTAATTGA 57.296 29.630 17.86 0.00 41.66 2.57
1750 1790 5.016831 CCTTTTGTAATTGACTAGCCCCTT 58.983 41.667 0.00 0.00 0.00 3.95
1764 1804 2.242452 AGCCCCTTCCTTAACTTCATCC 59.758 50.000 0.00 0.00 0.00 3.51
1792 1832 1.933247 CTGCGGAGTCTCCTCATTTC 58.067 55.000 17.00 0.29 39.64 2.17
1793 1833 1.480137 CTGCGGAGTCTCCTCATTTCT 59.520 52.381 17.00 0.00 39.64 2.52
1794 1834 2.690497 CTGCGGAGTCTCCTCATTTCTA 59.310 50.000 17.00 0.00 39.64 2.10
1795 1835 3.300388 TGCGGAGTCTCCTCATTTCTAT 58.700 45.455 17.00 0.00 39.64 1.98
1797 1837 4.893524 TGCGGAGTCTCCTCATTTCTATTA 59.106 41.667 17.00 0.00 39.64 0.98
1808 1850 9.956640 CTCCTCATTTCTATTATTTGATAGCCT 57.043 33.333 0.00 0.00 31.15 4.58
1832 1874 3.347590 TCCTCCGAGAGCTCCCCA 61.348 66.667 10.93 0.00 0.00 4.96
1844 1886 2.363359 GAGCTCCCCAATTTTATGGCTG 59.637 50.000 0.87 0.00 39.26 4.85
1855 1897 8.641541 CCCAATTTTATGGCTGAACATATTAGT 58.358 33.333 0.00 0.00 39.26 2.24
1886 1928 1.005557 GCAGCGTGAATCATCGACTTC 60.006 52.381 8.85 0.00 0.00 3.01
1888 1930 3.695816 CAGCGTGAATCATCGACTTCTA 58.304 45.455 8.85 0.00 0.00 2.10
1889 1931 3.728221 CAGCGTGAATCATCGACTTCTAG 59.272 47.826 8.85 0.00 0.00 2.43
1890 1932 3.046390 GCGTGAATCATCGACTTCTAGG 58.954 50.000 8.85 0.00 0.00 3.02
1893 1935 3.799420 GTGAATCATCGACTTCTAGGTGC 59.201 47.826 0.00 0.00 0.00 5.01
1910 1952 4.513777 CCATCCATGGGCCAGATG 57.486 61.111 22.57 22.57 44.31 2.90
1911 1953 4.513777 CATCCATGGGCCAGATGG 57.486 61.111 22.04 21.98 41.70 3.51
1938 1980 2.159043 TCATCTGCGTCCTTCAGATTCC 60.159 50.000 3.02 0.00 45.99 3.01
1980 2022 1.670406 GAGTGACTGTGCAGCCCTG 60.670 63.158 0.00 0.00 0.00 4.45
1991 2033 3.655211 AGCCCTGCCCTTGTCCTG 61.655 66.667 0.00 0.00 0.00 3.86
2002 2044 3.496160 GCCCTTGTCCTGTCTAAAGTTGA 60.496 47.826 0.00 0.00 0.00 3.18
2008 2050 5.741011 TGTCCTGTCTAAAGTTGAGTTGTT 58.259 37.500 0.00 0.00 0.00 2.83
2062 2104 7.549488 AGGTTAAACAAGAAATGAGGAGATACG 59.451 37.037 0.00 0.00 0.00 3.06
2083 2125 2.221055 GCTTGTTCGTCACAATTCTCGT 59.779 45.455 3.85 0.00 44.72 4.18
2088 2130 2.390938 TCGTCACAATTCTCGTCACAC 58.609 47.619 0.00 0.00 0.00 3.82
2091 2133 3.245284 CGTCACAATTCTCGTCACACTTT 59.755 43.478 0.00 0.00 0.00 2.66
2105 2147 2.222213 CACACTTTTTATCCACGCGACA 59.778 45.455 15.93 0.00 0.00 4.35
2149 2191 5.171339 AGCTTGAACTATTGTGATCACCT 57.829 39.130 22.85 12.66 0.00 4.00
2169 2211 4.265353 ACCTTAGGGTAGAGGGAATGAACT 60.265 45.833 2.32 0.00 45.32 3.01
2201 2243 4.920640 TTTGGTCATTTCGTTTTAGGCA 57.079 36.364 0.00 0.00 0.00 4.75
2220 2262 3.258123 GGCATTCCTGTGGTTAATTGTGT 59.742 43.478 0.00 0.00 0.00 3.72
2358 2401 2.621338 CACAAGCTTTCTCTATGGCGA 58.379 47.619 0.00 0.00 0.00 5.54
2438 2481 2.876581 AGGAACGAGGATTTTTGCCTT 58.123 42.857 0.00 0.00 35.44 4.35
2477 2520 7.865706 ATCCGCTTCACATTAACTAAAAGAT 57.134 32.000 0.00 0.00 0.00 2.40
2514 2557 5.629079 AGCCAGTCCTTTTCTTAATTTCG 57.371 39.130 0.00 0.00 0.00 3.46
2526 2569 5.401531 TCTTAATTTCGTCTGCAGTAGGT 57.598 39.130 14.67 0.00 0.00 3.08
2688 2731 3.772572 TCGAATTCTTCTCACCACCCATA 59.227 43.478 3.52 0.00 0.00 2.74
2833 2882 9.892130 ACTATAGGTTAAACAAGATGAGGAAAG 57.108 33.333 4.43 0.00 0.00 2.62
2983 3036 8.633075 AATAAACAGCCAATATTTCAACATCG 57.367 30.769 0.00 0.00 0.00 3.84
3318 3564 6.535508 GGAACTTACTTATGTTACTGCTCTGG 59.464 42.308 0.00 0.00 0.00 3.86
3931 4177 6.813649 TGATTCGAGTGAGGTTAGATTTTCTG 59.186 38.462 0.00 0.00 0.00 3.02
4037 4283 7.476540 GGTTTTATACCTGATCCAACCTTTT 57.523 36.000 0.00 0.00 44.10 2.27
4042 4288 2.041755 ACCTGATCCAACCTTTTCCCTC 59.958 50.000 0.00 0.00 0.00 4.30
4151 4550 5.514500 AGCCTAGGTTTGTTATCCTTTGA 57.486 39.130 11.31 0.00 35.51 2.69
4211 4610 6.346359 GCACATATACGTCCTTCGAATAAACC 60.346 42.308 0.00 0.00 42.86 3.27
4669 5068 5.363101 ACATCGTAGCAGTCATCATTCATT 58.637 37.500 0.00 0.00 0.00 2.57
4765 5164 4.793201 TCCTCGTATTCTGATTCTGAGGA 58.207 43.478 14.03 14.03 46.03 3.71
4975 5374 6.717084 GGATATACAATAAGCAAGAGGCCTTT 59.283 38.462 6.77 0.00 46.50 3.11
5016 5415 3.006537 GCAACCCTACAGTGACTCAAGTA 59.993 47.826 0.00 0.00 0.00 2.24
5017 5416 4.502604 GCAACCCTACAGTGACTCAAGTAA 60.503 45.833 0.00 0.00 0.00 2.24
5027 5426 6.266558 ACAGTGACTCAAGTAATTCTGAGAGT 59.733 38.462 15.41 10.01 41.66 3.24
5075 5474 2.440409 GACAAGCAATCCCACAGTGAT 58.560 47.619 0.62 0.00 0.00 3.06
5114 5513 0.179034 AGCGGCATTCAAGGAGATCC 60.179 55.000 1.45 0.00 0.00 3.36
5140 5539 5.509501 GGGAAAAGAGACATCACAAAATGCA 60.510 40.000 0.00 0.00 0.00 3.96
5166 5565 0.824109 TCCCGTGAGCAATAGGTCTG 59.176 55.000 0.00 0.00 42.66 3.51
5285 5684 4.207891 TCCAAGTGCTTCTGAGTATTCC 57.792 45.455 0.00 0.00 0.00 3.01
5291 5690 3.804873 GTGCTTCTGAGTATTCCGATTCC 59.195 47.826 0.00 0.00 0.00 3.01
5360 5759 5.952526 TGAGTACACGTGAAAGTGATAGA 57.047 39.130 25.01 0.00 44.43 1.98
5401 5800 0.460811 AAATCGCGCTGCTCTGATCA 60.461 50.000 5.56 0.00 0.00 2.92
5462 5861 0.797249 ATCGCCGTCGTCGAAGAAAG 60.797 55.000 9.88 0.35 39.69 2.62
5490 5889 0.238817 GGCGGTTAACAACATTCGCA 59.761 50.000 20.76 0.00 39.99 5.10
5513 5914 5.211174 TCTCCACAGAAGATATCAGCATG 57.789 43.478 5.32 0.97 37.54 4.06
5548 5949 9.088987 TGTGGTTGCATTAGATAGATATGTAGA 57.911 33.333 0.00 0.00 0.00 2.59
5589 5990 1.132977 TGAAGGTCACTAGGGTCCACA 60.133 52.381 11.05 7.44 0.00 4.17
5609 6010 5.452496 CCACAGTGAGTATTCCATCAGGTAG 60.452 48.000 0.62 0.00 35.89 3.18
5794 6195 1.749258 GGCCTGTGGGGAACGAATC 60.749 63.158 0.00 0.00 37.23 2.52
5832 6234 7.847531 CTGTTCTTCAGACATGCCTTGCATAT 61.848 42.308 0.57 0.00 45.90 1.78
5842 6244 1.337703 GCCTTGCATATTGGAATCGCA 59.662 47.619 0.00 0.00 0.00 5.10
5844 6246 3.571571 CCTTGCATATTGGAATCGCATG 58.428 45.455 0.00 0.00 31.67 4.06
5869 6271 2.292267 CTTCCTGAAATGCTATGCGGT 58.708 47.619 0.00 0.00 0.00 5.68
5880 6283 2.028476 TGCTATGCGGTCACTTGTAAGT 60.028 45.455 0.00 0.00 40.60 2.24
5963 6366 6.147821 TCTGTTAGCTTCTGTATGAAACAAGC 59.852 38.462 0.00 0.00 40.72 4.01
5987 6390 1.906574 AGGGTTTAAGAGATGTCGCCA 59.093 47.619 0.00 0.00 0.00 5.69
5991 6394 4.201920 GGGTTTAAGAGATGTCGCCATTTC 60.202 45.833 0.00 0.00 33.47 2.17
5997 6400 5.028549 AGAGATGTCGCCATTTCTGTAAT 57.971 39.130 0.00 0.00 40.12 1.89
5998 6401 4.813161 AGAGATGTCGCCATTTCTGTAATG 59.187 41.667 0.00 0.52 40.12 1.90
6044 6911 7.051623 TGTTTAACTTCTTTGGTCTGCTTCTA 58.948 34.615 0.00 0.00 0.00 2.10
6049 6916 6.352516 ACTTCTTTGGTCTGCTTCTATATGG 58.647 40.000 0.00 0.00 0.00 2.74
6089 7482 9.809096 TTACAGTGATTGCAAAATTAACTTTGA 57.191 25.926 13.28 0.00 38.35 2.69
6182 7576 0.513820 ACGAATTTTGTACGGTGCCG 59.486 50.000 9.29 9.29 46.03 5.69
6197 7591 2.282462 CCGGCTTGAAGGGTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
6200 7594 1.134220 CCGGCTTGAAGGGTGCTTATA 60.134 52.381 0.00 0.00 0.00 0.98
6264 7658 9.139174 CGTACAAAAATTGGAATGAAAGCTATT 57.861 29.630 0.00 0.00 34.12 1.73
6302 7696 1.140816 GTGAGAGAGCGAAACACCAC 58.859 55.000 0.00 0.00 0.00 4.16
6372 7766 2.993899 CAGCGAACCGAACACTATCTTT 59.006 45.455 0.00 0.00 0.00 2.52
6378 7772 5.176958 CGAACCGAACACTATCTTTGACTTT 59.823 40.000 0.00 0.00 0.00 2.66
6418 7818 9.319143 ACTAGTGACTGTATATGAGCAAATTTC 57.681 33.333 0.00 0.00 0.00 2.17
6420 7820 8.565896 AGTGACTGTATATGAGCAAATTTCAA 57.434 30.769 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 1.300931 GCGCCTGAAGATCGCCATA 60.301 57.895 0.00 0.00 42.71 2.74
287 291 4.845580 AGCAGCCTCCAATCCGCG 62.846 66.667 0.00 0.00 0.00 6.46
288 292 3.207669 CAGCAGCCTCCAATCCGC 61.208 66.667 0.00 0.00 0.00 5.54
328 332 2.214216 CGACTCCACCAACCCCTGA 61.214 63.158 0.00 0.00 0.00 3.86
330 334 3.637273 GCGACTCCACCAACCCCT 61.637 66.667 0.00 0.00 0.00 4.79
371 375 3.461773 GCTCCCTAGACAGCCGCA 61.462 66.667 0.00 0.00 0.00 5.69
375 379 4.577246 CGCCGCTCCCTAGACAGC 62.577 72.222 0.00 0.00 0.00 4.40
488 502 4.383602 CTTTTGCCGCCCGTGTCG 62.384 66.667 0.00 0.00 0.00 4.35
489 503 2.458006 CTTCTTTTGCCGCCCGTGTC 62.458 60.000 0.00 0.00 0.00 3.67
490 504 2.517402 TTCTTTTGCCGCCCGTGT 60.517 55.556 0.00 0.00 0.00 4.49
491 505 2.255252 CTTCTTTTGCCGCCCGTG 59.745 61.111 0.00 0.00 0.00 4.94
539 553 2.513897 GGAGCAATTCCCCCGTCG 60.514 66.667 0.00 0.00 40.37 5.12
543 557 2.193248 CCTCGGAGCAATTCCCCC 59.807 66.667 0.00 0.00 43.63 5.40
1288 1302 9.752961 GTATGTATGTATGTATGTTGGTGTGTA 57.247 33.333 0.00 0.00 0.00 2.90
1295 1309 5.631929 ACGGCGTATGTATGTATGTATGTTG 59.368 40.000 12.58 0.00 0.00 3.33
1296 1310 5.775686 ACGGCGTATGTATGTATGTATGTT 58.224 37.500 12.58 0.00 0.00 2.71
1299 1313 4.703575 AGGACGGCGTATGTATGTATGTAT 59.296 41.667 14.74 0.00 0.00 2.29
1300 1314 4.074259 AGGACGGCGTATGTATGTATGTA 58.926 43.478 14.74 0.00 0.00 2.29
1341 1355 8.025445 GTGCCCATGAGCTGATAATAATAAAAG 58.975 37.037 0.00 0.00 0.00 2.27
1342 1356 7.725397 AGTGCCCATGAGCTGATAATAATAAAA 59.275 33.333 0.00 0.00 0.00 1.52
1343 1357 7.233632 AGTGCCCATGAGCTGATAATAATAAA 58.766 34.615 0.00 0.00 0.00 1.40
1344 1358 6.782986 AGTGCCCATGAGCTGATAATAATAA 58.217 36.000 0.00 0.00 0.00 1.40
1345 1359 6.214208 AGAGTGCCCATGAGCTGATAATAATA 59.786 38.462 0.00 0.00 0.00 0.98
1346 1360 5.013913 AGAGTGCCCATGAGCTGATAATAAT 59.986 40.000 0.00 0.00 0.00 1.28
1369 1384 4.210120 GGCGATCACAATAGTTCAAGCTAG 59.790 45.833 0.00 0.00 0.00 3.42
1381 1396 1.202806 CCACCCTATGGCGATCACAAT 60.203 52.381 0.00 0.00 43.24 2.71
1413 1432 5.807011 GCCAGATGACCAAAACAATGTAATC 59.193 40.000 0.00 0.00 0.00 1.75
1443 1462 7.318141 ACAAAATACTGAAGCCAGATGAAATG 58.682 34.615 0.00 0.00 43.02 2.32
1450 1469 3.007506 TCCGACAAAATACTGAAGCCAGA 59.992 43.478 0.00 0.00 43.02 3.86
1451 1470 3.334691 TCCGACAAAATACTGAAGCCAG 58.665 45.455 0.00 0.00 45.76 4.85
1455 1474 8.283291 GGCTATTTATCCGACAAAATACTGAAG 58.717 37.037 0.00 0.00 0.00 3.02
1457 1476 7.506114 AGGCTATTTATCCGACAAAATACTGA 58.494 34.615 0.00 0.00 0.00 3.41
1458 1477 7.730364 AGGCTATTTATCCGACAAAATACTG 57.270 36.000 0.00 0.00 0.00 2.74
1488 1522 3.889538 ACTTTTTGGACCAGTAAAGCTCC 59.110 43.478 21.88 0.00 32.27 4.70
1544 1580 3.010624 TGACGGAACAAAATGCACATG 57.989 42.857 0.00 0.00 0.00 3.21
1545 1581 3.181482 TGTTGACGGAACAAAATGCACAT 60.181 39.130 0.00 0.00 41.80 3.21
1546 1582 2.164422 TGTTGACGGAACAAAATGCACA 59.836 40.909 0.00 0.00 41.80 4.57
1547 1583 2.533942 GTGTTGACGGAACAAAATGCAC 59.466 45.455 4.05 1.08 46.30 4.57
1548 1584 2.792890 CGTGTTGACGGAACAAAATGCA 60.793 45.455 4.05 0.00 46.30 3.96
1562 1598 1.290955 GGACGATCCACCGTGTTGA 59.709 57.895 0.00 0.00 43.49 3.18
1563 1599 1.740296 GGGACGATCCACCGTGTTG 60.740 63.158 0.00 0.00 43.49 3.33
1573 1609 0.322546 AAAGCTTGTGGGGGACGATC 60.323 55.000 0.00 0.00 0.00 3.69
1577 1613 0.402121 AGAGAAAGCTTGTGGGGGAC 59.598 55.000 0.00 0.00 0.00 4.46
1583 1619 5.180868 AGCAATGTCTTAGAGAAAGCTTGTG 59.819 40.000 0.00 0.00 34.97 3.33
1594 1630 6.806249 CGCCAAAAATAAAGCAATGTCTTAGA 59.194 34.615 0.00 0.00 0.00 2.10
1596 1632 6.451393 ACGCCAAAAATAAAGCAATGTCTTA 58.549 32.000 0.00 0.00 0.00 2.10
1617 1653 2.639065 TCATTGGAACTGGGATAACGC 58.361 47.619 0.00 0.00 0.00 4.84
1627 1663 7.645102 TGAAACTTCAGCCATTCATTGGAACT 61.645 38.462 0.00 0.00 39.07 3.01
1628 1664 5.509501 TGAAACTTCAGCCATTCATTGGAAC 60.510 40.000 0.00 0.00 39.07 3.62
1710 1750 4.701956 AAAGGTTCATAATTGTGGCGAG 57.298 40.909 2.06 0.00 0.00 5.03
1714 1754 9.703892 TCAATTACAAAAGGTTCATAATTGTGG 57.296 29.630 12.34 0.00 41.12 4.17
1721 1761 7.338449 GGGCTAGTCAATTACAAAAGGTTCATA 59.662 37.037 0.00 0.00 0.00 2.15
1732 1772 3.460825 AGGAAGGGGCTAGTCAATTACA 58.539 45.455 0.00 0.00 0.00 2.41
1733 1773 4.505324 AAGGAAGGGGCTAGTCAATTAC 57.495 45.455 0.00 0.00 0.00 1.89
1735 1775 4.540502 AGTTAAGGAAGGGGCTAGTCAATT 59.459 41.667 0.00 0.00 0.00 2.32
1740 1780 3.527937 TGAAGTTAAGGAAGGGGCTAGT 58.472 45.455 0.00 0.00 0.00 2.57
1742 1782 3.458487 GGATGAAGTTAAGGAAGGGGCTA 59.542 47.826 0.00 0.00 0.00 3.93
1750 1790 3.132289 CCTACTGCGGATGAAGTTAAGGA 59.868 47.826 0.00 0.00 32.88 3.36
1794 1834 8.325046 GGAGGAGTATCAAGGCTATCAAATAAT 58.675 37.037 0.00 0.00 36.25 1.28
1795 1835 7.525526 CGGAGGAGTATCAAGGCTATCAAATAA 60.526 40.741 0.00 0.00 36.25 1.40
1797 1837 5.279708 CGGAGGAGTATCAAGGCTATCAAAT 60.280 44.000 0.00 0.00 36.25 2.32
1808 1850 2.577700 GAGCTCTCGGAGGAGTATCAA 58.422 52.381 6.43 0.00 41.26 2.57
1813 1855 2.277404 GGGAGCTCTCGGAGGAGT 59.723 66.667 14.64 0.00 41.26 3.85
1855 1897 0.249826 TCACGCTGCTGTGAACATCA 60.250 50.000 19.55 2.46 45.40 3.07
1864 1906 0.299895 GTCGATGATTCACGCTGCTG 59.700 55.000 0.00 0.00 0.00 4.41
1866 1908 1.002366 AAGTCGATGATTCACGCTGC 58.998 50.000 0.00 0.00 0.00 5.25
1893 1935 1.228769 CCATCTGGCCCATGGATGG 60.229 63.158 21.64 21.49 46.63 3.51
1907 1949 2.417933 GGACGCAGATGATATTGCCATC 59.582 50.000 0.00 0.00 40.40 3.51
1908 1950 2.039480 AGGACGCAGATGATATTGCCAT 59.961 45.455 0.00 0.00 37.00 4.40
1909 1951 1.417517 AGGACGCAGATGATATTGCCA 59.582 47.619 0.00 0.00 37.00 4.92
1910 1952 2.175878 AGGACGCAGATGATATTGCC 57.824 50.000 0.00 0.00 37.00 4.52
1911 1953 3.133691 TGAAGGACGCAGATGATATTGC 58.866 45.455 0.00 0.00 36.97 3.56
1920 1962 1.561643 AGGAATCTGAAGGACGCAGA 58.438 50.000 0.00 0.00 45.52 4.26
1923 1965 2.416893 GTGAAAGGAATCTGAAGGACGC 59.583 50.000 0.00 0.00 0.00 5.19
1924 1966 3.003480 GGTGAAAGGAATCTGAAGGACG 58.997 50.000 0.00 0.00 0.00 4.79
1938 1980 5.222631 GTTTACTCTTTGGCATGGTGAAAG 58.777 41.667 0.00 0.00 0.00 2.62
1980 2022 2.814336 CAACTTTAGACAGGACAAGGGC 59.186 50.000 0.00 0.00 0.00 5.19
1982 2024 4.962155 ACTCAACTTTAGACAGGACAAGG 58.038 43.478 0.00 0.00 0.00 3.61
2083 2125 2.477375 GTCGCGTGGATAAAAAGTGTGA 59.523 45.455 5.77 0.00 0.00 3.58
2088 2130 2.440501 GCATGTCGCGTGGATAAAAAG 58.559 47.619 5.77 0.00 0.00 2.27
2105 2147 0.324614 TCCATGACCAGTTGACGCAT 59.675 50.000 0.00 0.00 0.00 4.73
2149 2191 4.695606 ACAGTTCATTCCCTCTACCCTAA 58.304 43.478 0.00 0.00 0.00 2.69
2169 2211 6.565234 ACGAAATGACCAAAACAATGTAACA 58.435 32.000 0.00 0.00 0.00 2.41
2201 2243 4.215399 CACGACACAATTAACCACAGGAAT 59.785 41.667 0.00 0.00 0.00 3.01
2220 2262 4.506288 CGATAACAAATACCAGCATCACGA 59.494 41.667 0.00 0.00 0.00 4.35
2438 2481 9.114952 TGTGAAGCGGATATCAAAATTAATGTA 57.885 29.630 4.83 0.00 0.00 2.29
2477 2520 5.007682 GGACTGGCTAATTACAAAGGTTCA 58.992 41.667 0.00 0.00 0.00 3.18
2514 2557 1.889829 ACTCTGTGACCTACTGCAGAC 59.110 52.381 23.35 7.43 34.68 3.51
2688 2731 1.478288 GGAAGCAGCTGATATTGGCCT 60.478 52.381 20.43 0.00 0.00 5.19
2833 2882 6.369005 CAGAGAATCATGACAAACAAGTGTC 58.631 40.000 0.00 0.00 42.76 3.67
2848 2897 5.952347 TCCTTAGTCTAAGTGCAGAGAATCA 59.048 40.000 16.69 0.00 33.46 2.57
2983 3036 4.440525 CCATGGGTGATAACAGTTGAATGC 60.441 45.833 2.85 0.00 0.00 3.56
3318 3564 6.210287 AGAATAACAGCACACCTACTAGAC 57.790 41.667 0.00 0.00 0.00 2.59
3501 3747 7.819644 TGTCACCTTGTTGATCATATTCAAAG 58.180 34.615 0.00 0.00 37.36 2.77
3510 3756 4.024133 CGTTTCATGTCACCTTGTTGATCA 60.024 41.667 0.00 0.00 0.00 2.92
4030 4276 1.073098 ATGGACCGAGGGAAAAGGTT 58.927 50.000 0.00 0.00 38.57 3.50
4037 4283 0.616395 TGCAGTTATGGACCGAGGGA 60.616 55.000 0.00 0.00 0.00 4.20
4042 4288 3.685139 ATCCTATGCAGTTATGGACCG 57.315 47.619 0.00 0.00 0.00 4.79
4211 4610 6.076981 AGAAAGATGTGTAAGCCTTTTGTG 57.923 37.500 0.00 0.00 0.00 3.33
4651 5050 6.279123 TCTGAGAATGAATGATGACTGCTAC 58.721 40.000 0.00 0.00 0.00 3.58
4691 5090 2.281761 CCTGACGCCCTGTTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
4765 5164 2.881734 CTTTTCCTTTCCCAGCTTCCT 58.118 47.619 0.00 0.00 0.00 3.36
4975 5374 1.076995 TTCTCCCTCGATCGCCTCA 60.077 57.895 11.09 0.00 0.00 3.86
5016 5415 2.936114 GCTGCTGCTCACTCTCAGAATT 60.936 50.000 8.53 0.00 36.03 2.17
5017 5416 1.405797 GCTGCTGCTCACTCTCAGAAT 60.406 52.381 8.53 0.00 36.03 2.40
5027 5426 1.073548 TGTTGGATGCTGCTGCTCA 59.926 52.632 17.00 9.48 40.48 4.26
5114 5513 5.772825 TTTTGTGATGTCTCTTTTCCCTG 57.227 39.130 0.00 0.00 0.00 4.45
5140 5539 3.947834 CCTATTGCTCACGGGAAAATCTT 59.052 43.478 0.00 0.00 0.00 2.40
5166 5565 1.594862 CTTCTCATCCGATTTCCGTGC 59.405 52.381 0.00 0.00 36.31 5.34
5291 5690 2.076622 ATCTCCGTGAAGGCCGATCG 62.077 60.000 8.51 8.51 40.77 3.69
5360 5759 2.107552 TCCCTTCGGTTTCCTTGAATGT 59.892 45.455 0.00 0.00 0.00 2.71
5462 5861 2.443887 TGTTAACCGCCACTACTCAC 57.556 50.000 2.48 0.00 0.00 3.51
5490 5889 5.280062 CCATGCTGATATCTTCTGTGGAGAT 60.280 44.000 3.98 0.00 0.00 2.75
5513 5914 0.675633 ATGCAACCACAGAAACAGCC 59.324 50.000 0.00 0.00 0.00 4.85
5548 5949 5.200483 TCAGAACTCTGTGGGAACAAAATT 58.800 37.500 6.61 0.00 46.06 1.82
5561 5962 3.194542 CCCTAGTGACCTTCAGAACTCTG 59.805 52.174 0.00 0.00 45.08 3.35
5589 5990 6.841229 TGAATCTACCTGATGGAATACTCACT 59.159 38.462 0.00 0.00 35.21 3.41
5609 6010 4.021280 TGATCCAGAGATAGCAGCTGAATC 60.021 45.833 20.43 18.52 30.90 2.52
5794 6195 3.253188 TGAAGAACAGGAATTTCGCAAGG 59.747 43.478 0.00 0.00 38.47 3.61
5842 6244 2.522185 AGCATTTCAGGAAGCACACAT 58.478 42.857 0.00 0.00 0.00 3.21
5844 6246 3.733077 GCATAGCATTTCAGGAAGCACAC 60.733 47.826 0.00 0.00 0.00 3.82
5901 6304 6.073058 TGTTGCATAGAGAAGATTTGTGTCAC 60.073 38.462 0.00 0.00 0.00 3.67
5963 6366 4.120589 GCGACATCTCTTAAACCCTAAGG 58.879 47.826 0.00 0.00 40.04 2.69
5987 6390 3.411415 GCAAGAGCGCATTACAGAAAT 57.589 42.857 11.47 0.00 0.00 2.17
6044 6911 6.109156 TGTAATGAGCGTGGTTATCCATAT 57.891 37.500 0.00 0.00 46.20 1.78
6049 6916 4.430007 TCACTGTAATGAGCGTGGTTATC 58.570 43.478 0.00 0.00 0.00 1.75
6089 7482 2.239907 GCAGGTCTGAAAATACTCCCCT 59.760 50.000 1.65 0.00 0.00 4.79
6182 7576 2.294512 GCATATAAGCACCCTTCAAGCC 59.705 50.000 0.00 0.00 32.47 4.35
6200 7594 7.205737 TCAACTATATCGCATCATTTTGCAT 57.794 32.000 0.00 0.00 42.91 3.96
6217 7611 5.601662 ACGACGGATCAAATCATCAACTAT 58.398 37.500 0.00 0.00 0.00 2.12
6222 7616 4.379339 TGTACGACGGATCAAATCATCA 57.621 40.909 0.00 0.00 0.00 3.07
6264 7658 0.380733 CGAGCAGTGCTATACGGACA 59.619 55.000 19.77 0.00 39.88 4.02
6302 7696 2.374184 TCTTCAACAACCCAACACCAG 58.626 47.619 0.00 0.00 0.00 4.00
6355 7749 6.541111 AAAGTCAAAGATAGTGTTCGGTTC 57.459 37.500 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.