Multiple sequence alignment - TraesCS3B01G299000

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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 TraesCS3B01G299000 chr3B 100.000 2516 0 0 1 2516 479888137 479885622 0.000000e+00 4647.0
1 TraesCS3B01G299000 chr3B 87.435 1743 202 11 1 1732 718831363 718829627 0.000000e+00 1989.0
2 TraesCS3B01G299000 chr3B 97.872 47 1 0 1996 2042 479886106 479886060 5.770000e-12 82.4
3 TraesCS3B01G299000 chr3B 97.872 47 1 0 2032 2078 479886142 479886096 5.770000e-12 82.4
4 TraesCS3B01G299000 chr3B 100.000 33 0 0 1605 1637 479886912 479886880 7.510000e-06 62.1
5 TraesCS3B01G299000 chr6B 85.507 2063 251 30 5 2023 567118189 567116131 0.000000e+00 2109.0
6 TraesCS3B01G299000 chr6B 85.621 1989 223 38 1 1942 446289943 446287971 0.000000e+00 2030.0
7 TraesCS3B01G299000 chr6B 87.493 1743 207 9 1 1732 147950693 147948951 0.000000e+00 2001.0
8 TraesCS3B01G299000 chr6B 100.000 33 0 0 1605 1637 147949462 147949430 7.510000e-06 62.1
9 TraesCS3B01G299000 chr6B 100.000 33 0 0 1605 1637 446288714 446288682 7.510000e-06 62.1
10 TraesCS3B01G299000 chr3D 85.778 2018 237 30 1 1972 558679297 558681310 0.000000e+00 2091.0
11 TraesCS3B01G299000 chr3D 100.000 33 0 0 1605 1637 558680528 558680560 7.510000e-06 62.1
12 TraesCS3B01G299000 chr4D 89.396 1622 160 9 1 1614 473971227 473969610 0.000000e+00 2032.0
13 TraesCS3B01G299000 chr4D 100.000 30 0 0 1608 1637 473969995 473969966 3.500000e-04 56.5
14 TraesCS3B01G299000 chr5B 87.730 1736 199 10 1 1726 659536134 659537865 0.000000e+00 2013.0
15 TraesCS3B01G299000 chr5B 89.006 1619 165 10 1 1611 649874488 649876101 0.000000e+00 1991.0
16 TraesCS3B01G299000 chr5B 100.000 33 0 0 1605 1637 659537365 659537397 7.510000e-06 62.1
17 TraesCS3B01G299000 chr7B 88.964 1622 166 9 1 1614 36428072 36426456 0.000000e+00 1991.0
18 TraesCS3B01G299000 chr7B 85.294 544 72 8 1522 2060 404760431 404759891 2.830000e-154 555.0
19 TraesCS3B01G299000 chr7B 82.736 307 27 10 2192 2492 404759831 404759545 1.490000e-62 250.0
20 TraesCS3B01G299000 chr7B 77.778 234 42 9 2033 2261 404759892 404760120 4.370000e-28 135.0
21 TraesCS3B01G299000 chr7B 100.000 33 0 0 1605 1637 36426844 36426812 7.510000e-06 62.1
22 TraesCS3B01G299000 chr2B 88.758 1610 171 8 1 1603 664330490 664328884 0.000000e+00 1962.0
23 TraesCS3B01G299000 chr7D 85.352 1420 171 28 514 1904 449978235 449976824 0.000000e+00 1435.0
24 TraesCS3B01G299000 chr6D 83.006 1324 182 18 720 2008 345634645 345635960 0.000000e+00 1158.0
25 TraesCS3B01G299000 chr5D 84.658 541 65 15 1509 2042 391235690 391236219 7.970000e-145 523.0
26 TraesCS3B01G299000 chr5D 88.095 252 28 2 2032 2281 391236173 391236424 5.260000e-77 298.0
27 TraesCS3B01G299000 chr5D 87.591 137 10 4 2381 2513 391236499 391236632 4.330000e-33 152.0
28 TraesCS3B01G299000 chr5D 96.970 33 1 0 1605 1637 387243004 387243036 3.500000e-04 56.5
29 TraesCS3B01G299000 chr5D 96.970 33 1 0 1605 1637 391235455 391235487 3.500000e-04 56.5
30 TraesCS3B01G299000 chr2D 100.000 33 0 0 1605 1637 12314846 12314814 7.510000e-06 62.1
31 TraesCS3B01G299000 chr1D 100.000 33 0 0 1605 1637 491070534 491070502 7.510000e-06 62.1


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 TraesCS3B01G299000 chr3B 479885622 479888137 2515 True 1218.475 4647 98.9360 1 2516 4 chr3B.!!$R2 2515
1 TraesCS3B01G299000 chr3B 718829627 718831363 1736 True 1989.000 1989 87.4350 1 1732 1 chr3B.!!$R1 1731
2 TraesCS3B01G299000 chr6B 567116131 567118189 2058 True 2109.000 2109 85.5070 5 2023 1 chr6B.!!$R1 2018
3 TraesCS3B01G299000 chr6B 446287971 446289943 1972 True 1046.050 2030 92.8105 1 1942 2 chr6B.!!$R3 1941
4 TraesCS3B01G299000 chr6B 147948951 147950693 1742 True 1031.550 2001 93.7465 1 1732 2 chr6B.!!$R2 1731
5 TraesCS3B01G299000 chr3D 558679297 558681310 2013 False 1076.550 2091 92.8890 1 1972 2 chr3D.!!$F1 1971
6 TraesCS3B01G299000 chr4D 473969610 473971227 1617 True 1044.250 2032 94.6980 1 1637 2 chr4D.!!$R1 1636
7 TraesCS3B01G299000 chr5B 649874488 649876101 1613 False 1991.000 1991 89.0060 1 1611 1 chr5B.!!$F1 1610
8 TraesCS3B01G299000 chr5B 659536134 659537865 1731 False 1037.550 2013 93.8650 1 1726 2 chr5B.!!$F2 1725
9 TraesCS3B01G299000 chr7B 36426456 36428072 1616 True 1026.550 1991 94.4820 1 1637 2 chr7B.!!$R1 1636
10 TraesCS3B01G299000 chr7B 404759545 404760431 886 True 402.500 555 84.0150 1522 2492 2 chr7B.!!$R2 970
11 TraesCS3B01G299000 chr2B 664328884 664330490 1606 True 1962.000 1962 88.7580 1 1603 1 chr2B.!!$R1 1602
12 TraesCS3B01G299000 chr7D 449976824 449978235 1411 True 1435.000 1435 85.3520 514 1904 1 chr7D.!!$R1 1390
13 TraesCS3B01G299000 chr6D 345634645 345635960 1315 False 1158.000 1158 83.0060 720 2008 1 chr6D.!!$F1 1288
14 TraesCS3B01G299000 chr5D 391235455 391236632 1177 False 257.375 523 89.3285 1509 2513 4 chr5D.!!$F2 1004

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
174 177 0.035056 GTGGACAAGCTAGGTGGCAT 60.035 55.0 0.0 0.0 34.17 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1546 0.037882 TCTTCACGAGCAGCCTTCTG 60.038 55.0 0.0 0.0 43.16 3.02 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
57 58 5.163519 CGCCAAATGGATAGGTGAGAAAAAT 60.164 40.000 2.98 0.00 37.39 1.82
106 109 1.322442 GGTTTCAAGCAGGCAAGTCT 58.678 50.000 0.00 0.00 0.00 3.24
174 177 0.035056 GTGGACAAGCTAGGTGGCAT 60.035 55.000 0.00 0.00 34.17 4.40
184 187 2.418197 GCTAGGTGGCATAACACGAGAA 60.418 50.000 0.00 0.00 42.23 2.87
199 202 2.225963 ACGAGAAGGTGTGACTTACGAG 59.774 50.000 0.00 0.00 35.70 4.18
200 203 2.483106 CGAGAAGGTGTGACTTACGAGA 59.517 50.000 0.00 0.00 34.59 4.04
246 249 0.107214 AACCAGTGGTGTCAGTGTGG 60.107 55.000 17.56 0.00 41.52 4.17
247 250 0.980754 ACCAGTGGTGTCAGTGTGGA 60.981 55.000 15.86 0.00 41.52 4.02
262 265 4.040755 AGTGTGGAAGGCCTCATAAGTAT 58.959 43.478 5.23 0.00 39.63 2.12
283 286 3.386867 CTGGCCGTGCTCGCATTTC 62.387 63.158 1.89 0.00 35.54 2.17
312 315 0.884514 GCCAAGGAGAGAAACTTGCC 59.115 55.000 0.00 0.00 42.01 4.52
363 367 2.508526 GAGTTCACATTGGAAGCCACT 58.491 47.619 0.00 0.00 30.78 4.00
430 434 0.471617 GTGGCCTGAGTATGATGGCT 59.528 55.000 3.32 0.00 44.36 4.75
494 504 7.885922 GGGAAGAAGAAGAAAGAAGAGGTTTAT 59.114 37.037 0.00 0.00 0.00 1.40
547 557 5.304101 ACCAGAATGAAACAATTTGGTAGCA 59.696 36.000 0.78 0.00 39.69 3.49
553 563 5.771469 TGAAACAATTTGGTAGCAGTCATG 58.229 37.500 0.78 0.00 0.00 3.07
566 576 1.065636 CAGTCATGTCATGGAGCCACT 60.066 52.381 12.90 5.72 0.00 4.00
602 612 3.906660 GACAATGTGACGGTCCAGA 57.093 52.632 5.55 0.00 0.00 3.86
718 728 1.612442 GGAGGTAGGAGTGGTGGCA 60.612 63.158 0.00 0.00 0.00 4.92
728 738 2.447572 TGGTGGCAGTGGAGGACA 60.448 61.111 0.00 0.00 0.00 4.02
741 751 4.290196 AGTGGAGGACAGACTAGTCTTAGT 59.710 45.833 23.01 18.07 42.79 2.24
784 794 1.622607 TATTGGTGGGCGTGGAGGAG 61.623 60.000 0.00 0.00 0.00 3.69
795 805 0.610687 GTGGAGGAGGGACAAGTCTG 59.389 60.000 0.00 0.00 0.00 3.51
825 835 4.115199 GGGGGCGGTCATGCTTCT 62.115 66.667 0.00 0.00 34.52 2.85
827 837 2.268920 GGGCGGTCATGCTTCTGA 59.731 61.111 0.00 0.00 34.52 3.27
832 842 1.470098 GCGGTCATGCTTCTGATGTTT 59.530 47.619 0.00 0.00 0.00 2.83
845 855 3.769844 TCTGATGTTTCTAGGAGGTGGAC 59.230 47.826 0.00 0.00 0.00 4.02
883 894 7.462571 AGGCCTATTGACGTTTTTCTTAATT 57.537 32.000 1.29 0.00 0.00 1.40
886 897 7.238571 GCCTATTGACGTTTTTCTTAATTCGA 58.761 34.615 0.00 0.00 0.00 3.71
1011 1025 3.370840 TTTGTAGGCATGGCTTCATCT 57.629 42.857 28.30 4.19 0.00 2.90
1032 1046 4.804420 TCCATGAGGAGGCCGCCT 62.804 66.667 30.18 30.18 39.61 5.52
1048 1062 0.308993 GCCTTGTGCTGACTGTGAAC 59.691 55.000 0.00 0.00 36.87 3.18
1275 1289 5.671493 CCGGTATGGTCAAAGAGTAATCTT 58.329 41.667 0.00 0.00 0.00 2.40
1308 1325 7.965107 GGTTCAACTTCAAGTCATAATGCTAAG 59.035 37.037 0.00 0.00 0.00 2.18
1370 1388 4.769688 TGCAAGTACTTCACATGGATAGG 58.230 43.478 4.77 0.00 0.00 2.57
1381 1399 6.806668 TCACATGGATAGGTCAAGATGTTA 57.193 37.500 0.00 0.00 0.00 2.41
1410 1428 5.590259 AGATGTTCAAAAGGACCAATATCGG 59.410 40.000 0.00 0.00 0.00 4.18
1415 1433 5.515106 TCAAAAGGACCAATATCGGGATTT 58.485 37.500 0.00 0.00 0.00 2.17
1432 1450 2.943036 TTTTCTTAGGAGGCAACGGT 57.057 45.000 0.00 0.00 46.39 4.83
1459 1477 3.060003 CGAAGAAGCATATCAAAGAGCCG 60.060 47.826 0.00 0.00 0.00 5.52
1466 1484 2.533266 TATCAAAGAGCCGAGGATGC 57.467 50.000 0.00 0.00 0.00 3.91
1468 1486 0.324614 TCAAAGAGCCGAGGATGCAA 59.675 50.000 0.00 0.00 0.00 4.08
1479 1497 2.560861 GATGCAAAGCGCCGTCAA 59.439 55.556 2.29 0.00 41.33 3.18
1513 1531 2.622064 ACGAAAGAAGTGCAAGGAGT 57.378 45.000 0.00 0.00 0.00 3.85
1520 1538 2.180276 GAAGTGCAAGGAGTAGAGGGA 58.820 52.381 0.00 0.00 0.00 4.20
1528 1546 4.065789 CAAGGAGTAGAGGGAACACAAAC 58.934 47.826 0.00 0.00 0.00 2.93
1604 1622 0.179936 CAAGAGGAGGATGAGGCACC 59.820 60.000 0.00 0.00 0.00 5.01
1607 1625 0.467804 GAGGAGGATGAGGCACCTTC 59.532 60.000 0.00 0.00 36.57 3.46
1611 1629 0.329596 AGGATGAGGCACCTTCCAAC 59.670 55.000 9.57 0.00 34.01 3.77
1614 1632 2.238521 GATGAGGCACCTTCCAACAAA 58.761 47.619 0.00 0.00 0.00 2.83
1615 1633 1.398692 TGAGGCACCTTCCAACAAAC 58.601 50.000 0.00 0.00 0.00 2.93
1618 1636 1.299850 GCACCTTCCAACAAACGCC 60.300 57.895 0.00 0.00 0.00 5.68
1619 1637 1.734388 GCACCTTCCAACAAACGCCT 61.734 55.000 0.00 0.00 0.00 5.52
1621 1639 2.159382 CACCTTCCAACAAACGCCTAT 58.841 47.619 0.00 0.00 0.00 2.57
1623 1641 2.224670 ACCTTCCAACAAACGCCTATGA 60.225 45.455 0.00 0.00 0.00 2.15
1625 1643 1.434555 TCCAACAAACGCCTATGACG 58.565 50.000 0.00 0.00 0.00 4.35
1628 1646 2.093152 CCAACAAACGCCTATGACGTAC 59.907 50.000 0.00 0.00 44.30 3.67
1629 1647 2.000429 ACAAACGCCTATGACGTACC 58.000 50.000 0.00 0.00 44.30 3.34
1630 1648 1.273048 ACAAACGCCTATGACGTACCA 59.727 47.619 0.00 0.00 44.30 3.25
1631 1649 1.657094 CAAACGCCTATGACGTACCAC 59.343 52.381 0.00 0.00 44.30 4.16
1632 1650 0.174162 AACGCCTATGACGTACCACC 59.826 55.000 0.00 0.00 44.30 4.61
1633 1651 1.298863 CGCCTATGACGTACCACCG 60.299 63.158 0.00 0.00 0.00 4.94
1634 1652 1.066918 GCCTATGACGTACCACCGG 59.933 63.158 0.00 0.00 0.00 5.28
1636 1654 1.679139 CCTATGACGTACCACCGGTA 58.321 55.000 6.87 0.00 37.09 4.02
1668 1689 2.482485 GCGTTAGTGAAGTTGTACGC 57.518 50.000 0.00 0.00 45.73 4.42
1767 1846 9.783256 ACTTTAGTGTTAAAACAGACAAATGTC 57.217 29.630 5.40 5.40 45.08 3.06
1800 1879 7.848223 TGTGACTGAAATATTGTCAGGTATG 57.152 36.000 21.37 7.11 45.66 2.39
1965 2046 2.880879 CGCATCCGACCAGACACG 60.881 66.667 0.00 0.00 36.29 4.49
2006 2087 3.744003 TACCGAGCCCTACCGCCAT 62.744 63.158 0.00 0.00 0.00 4.40
2027 2108 4.221422 GAGCGGCGGTAGGATGCA 62.221 66.667 13.22 0.00 0.00 3.96
2028 2109 4.530857 AGCGGCGGTAGGATGCAC 62.531 66.667 11.06 0.00 0.00 4.57
2030 2111 4.155733 CGGCGGTAGGATGCACCA 62.156 66.667 0.00 0.00 42.04 4.17
2031 2112 2.513897 GGCGGTAGGATGCACCAC 60.514 66.667 7.86 4.50 42.04 4.16
2032 2113 2.513897 GCGGTAGGATGCACCACC 60.514 66.667 7.86 10.63 42.04 4.61
2033 2114 2.189521 CGGTAGGATGCACCACCC 59.810 66.667 7.86 5.90 42.04 4.61
2034 2115 2.367202 CGGTAGGATGCACCACCCT 61.367 63.158 7.86 6.15 42.04 4.34
2035 2116 1.046472 CGGTAGGATGCACCACCCTA 61.046 60.000 7.86 5.29 42.04 3.53
2037 2118 0.468648 GTAGGATGCACCACCCTACC 59.531 60.000 18.42 7.26 44.02 3.18
2038 2119 1.046472 TAGGATGCACCACCCTACCG 61.046 60.000 7.86 0.00 42.04 4.02
2039 2120 2.513897 GATGCACCACCCTACCGC 60.514 66.667 0.00 0.00 0.00 5.68
2040 2121 4.109675 ATGCACCACCCTACCGCC 62.110 66.667 0.00 0.00 0.00 6.13
2081 2162 3.319198 CCACCCTACCGCCACTGT 61.319 66.667 0.00 0.00 0.00 3.55
2121 2202 3.114616 ACTCGCACGCAGCATCAC 61.115 61.111 0.00 0.00 46.13 3.06
2128 2209 0.239082 CACGCAGCATCACACATGTT 59.761 50.000 0.00 0.00 0.00 2.71
2159 2240 0.824759 GCGTGAGAACCAGGGTCTAT 59.175 55.000 7.13 0.00 0.00 1.98
2160 2241 1.202428 GCGTGAGAACCAGGGTCTATC 60.202 57.143 7.13 2.54 0.00 2.08
2161 2242 1.065701 CGTGAGAACCAGGGTCTATCG 59.934 57.143 7.13 11.53 0.00 2.92
2162 2243 1.112113 TGAGAACCAGGGTCTATCGC 58.888 55.000 7.13 0.00 0.00 4.58
2163 2244 0.389757 GAGAACCAGGGTCTATCGCC 59.610 60.000 7.13 0.00 0.00 5.54
2164 2245 0.325296 AGAACCAGGGTCTATCGCCA 60.325 55.000 4.67 0.00 0.00 5.69
2165 2246 0.179081 GAACCAGGGTCTATCGCCAC 60.179 60.000 0.00 0.00 0.00 5.01
2166 2247 0.617820 AACCAGGGTCTATCGCCACT 60.618 55.000 0.00 0.00 0.00 4.00
2167 2248 1.330655 ACCAGGGTCTATCGCCACTG 61.331 60.000 0.00 0.00 0.00 3.66
2168 2249 1.330655 CCAGGGTCTATCGCCACTGT 61.331 60.000 0.00 0.00 0.00 3.55
2169 2250 0.103208 CAGGGTCTATCGCCACTGTC 59.897 60.000 0.00 0.00 0.00 3.51
2170 2251 0.033011 AGGGTCTATCGCCACTGTCT 60.033 55.000 0.00 0.00 0.00 3.41
2171 2252 0.386113 GGGTCTATCGCCACTGTCTC 59.614 60.000 0.00 0.00 0.00 3.36
2172 2253 0.386113 GGTCTATCGCCACTGTCTCC 59.614 60.000 0.00 0.00 0.00 3.71
2173 2254 0.029567 GTCTATCGCCACTGTCTCCG 59.970 60.000 0.00 0.00 0.00 4.63
2174 2255 1.101635 TCTATCGCCACTGTCTCCGG 61.102 60.000 0.00 0.00 0.00 5.14
2175 2256 2.685387 CTATCGCCACTGTCTCCGGC 62.685 65.000 0.00 0.00 42.64 6.13
2179 2260 3.066190 CCACTGTCTCCGGCGGTA 61.066 66.667 27.32 12.96 0.00 4.02
2180 2261 2.490217 CACTGTCTCCGGCGGTAG 59.510 66.667 27.32 20.80 0.00 3.18
2181 2262 3.450115 ACTGTCTCCGGCGGTAGC 61.450 66.667 27.32 16.58 44.18 3.58
2191 2272 2.357517 GCGGTAGCAGTGCACACT 60.358 61.111 21.04 17.92 44.35 3.55
2192 2273 2.383527 GCGGTAGCAGTGCACACTC 61.384 63.158 21.04 7.26 44.35 3.51
2193 2274 1.290324 CGGTAGCAGTGCACACTCT 59.710 57.895 21.04 14.40 40.20 3.24
2194 2275 0.526211 CGGTAGCAGTGCACACTCTA 59.474 55.000 21.04 13.39 40.20 2.43
2211 2328 0.898789 CTACCACCACAGACTCCGGT 60.899 60.000 0.00 0.00 0.00 5.28
2238 2355 2.301583 GGGCTAAATCCCTGCAAAACAA 59.698 45.455 0.00 0.00 43.13 2.83
2266 2383 4.666512 AGCAACATGTTAGACAGGGAAAT 58.333 39.130 11.53 0.00 33.62 2.17
2267 2384 4.460382 AGCAACATGTTAGACAGGGAAATG 59.540 41.667 11.53 0.00 33.62 2.32
2268 2385 4.458989 GCAACATGTTAGACAGGGAAATGA 59.541 41.667 11.53 0.00 33.62 2.57
2269 2386 5.048083 GCAACATGTTAGACAGGGAAATGAA 60.048 40.000 11.53 0.00 33.62 2.57
2270 2387 6.516527 GCAACATGTTAGACAGGGAAATGAAA 60.517 38.462 11.53 0.00 33.62 2.69
2271 2388 7.432869 CAACATGTTAGACAGGGAAATGAAAA 58.567 34.615 11.53 0.00 33.62 2.29
2272 2389 7.595819 ACATGTTAGACAGGGAAATGAAAAA 57.404 32.000 0.00 0.00 33.62 1.94
2273 2390 7.661040 ACATGTTAGACAGGGAAATGAAAAAG 58.339 34.615 0.00 0.00 33.62 2.27
2274 2391 7.505585 ACATGTTAGACAGGGAAATGAAAAAGA 59.494 33.333 0.00 0.00 33.62 2.52
2294 2411 9.665719 AAAAAGAATGTGTATCTTTTGGTTGTT 57.334 25.926 13.24 0.00 45.79 2.83
2309 2460 4.883083 TGGTTGTTAACTTTGTTGCACAA 58.117 34.783 7.22 0.00 36.11 3.33
2325 2476 7.824672 TGTTGCACAAGGAAAAATGAAAAATT 58.175 26.923 0.00 0.00 0.00 1.82
2369 2520 4.582240 TGGTAGTTCAAATGACATGCAACA 59.418 37.500 0.00 0.00 0.00 3.33
2370 2521 5.243507 TGGTAGTTCAAATGACATGCAACAT 59.756 36.000 0.00 0.00 0.00 2.71
2371 2522 5.801947 GGTAGTTCAAATGACATGCAACATC 59.198 40.000 0.00 0.00 0.00 3.06
2373 2524 3.490800 TCAAATGACATGCAACATCCG 57.509 42.857 0.00 0.00 0.00 4.18
2374 2525 3.080319 TCAAATGACATGCAACATCCGA 58.920 40.909 0.00 0.00 0.00 4.55
2376 2527 4.880696 TCAAATGACATGCAACATCCGATA 59.119 37.500 0.00 0.00 0.00 2.92
2377 2528 5.356470 TCAAATGACATGCAACATCCGATAA 59.644 36.000 0.00 0.00 0.00 1.75
2378 2529 6.039605 TCAAATGACATGCAACATCCGATAAT 59.960 34.615 0.00 0.00 0.00 1.28
2379 2530 7.228308 TCAAATGACATGCAACATCCGATAATA 59.772 33.333 0.00 0.00 0.00 0.98
2393 2544 9.173021 ACATCCGATAATAAGTTCAAATGACAA 57.827 29.630 0.00 0.00 0.00 3.18
2407 2558 6.148948 TCAAATGACAAAAATCATGTCCGAC 58.851 36.000 4.40 0.00 45.19 4.79
2422 2573 2.155155 GTCCGACAGCGTTAGTTCAAAG 59.845 50.000 0.00 0.00 35.23 2.77
2428 2579 2.096909 CAGCGTTAGTTCAAAGGACACG 60.097 50.000 0.00 0.00 0.00 4.49
2437 2588 2.503331 TCAAAGGACACGCATCATGTT 58.497 42.857 0.00 0.00 0.00 2.71
2491 2646 6.751888 GCCATTATAGTTCAAATGACCAACAC 59.248 38.462 0.00 0.00 35.53 3.32
2496 2651 3.059166 GTTCAAATGACCAACACCATGC 58.941 45.455 0.00 0.00 0.00 4.06
2498 2653 0.975887 AAATGACCAACACCATGCCC 59.024 50.000 0.00 0.00 0.00 5.36
2513 2668 0.756903 TGCCCGGTAGAATCCTAAGC 59.243 55.000 0.00 0.00 0.00 3.09
2514 2669 0.756903 GCCCGGTAGAATCCTAAGCA 59.243 55.000 0.00 0.00 0.00 3.91
2515 2670 1.348036 GCCCGGTAGAATCCTAAGCAT 59.652 52.381 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.961360 ATCATCAACCTTGTCGAGATACTA 57.039 37.500 0.00 0.00 0.00 1.82
64 66 3.417069 ACCAATCATCAACCTTGTCGA 57.583 42.857 0.00 0.00 0.00 4.20
106 109 7.760437 TGAATCTAATGATTTGTTGATGCGAA 58.240 30.769 0.00 0.00 42.43 4.70
174 177 4.555313 CGTAAGTCACACCTTCTCGTGTTA 60.555 45.833 0.00 0.00 44.57 2.41
184 187 2.584236 ACACTCTCGTAAGTCACACCT 58.416 47.619 0.00 0.00 39.48 4.00
246 249 4.636249 CCAGTGATACTTATGAGGCCTTC 58.364 47.826 6.77 0.10 0.00 3.46
247 250 3.181450 GCCAGTGATACTTATGAGGCCTT 60.181 47.826 6.77 0.00 34.94 4.35
283 286 4.776322 TCCTTGGCCGCCGTCATG 62.776 66.667 4.58 0.00 0.00 3.07
312 315 0.176680 CGGTCCTCCCATCAGAACAG 59.823 60.000 0.00 0.00 0.00 3.16
337 341 2.189594 TCCAATGTGAACTCCTGCAG 57.810 50.000 6.78 6.78 0.00 4.41
363 367 2.252072 GAGGCGCCCATGTCAACCTA 62.252 60.000 26.15 0.00 0.00 3.08
494 504 4.038883 CAGCTAGATCATCCATGTCACTCA 59.961 45.833 0.00 0.00 0.00 3.41
547 557 1.065636 CAGTGGCTCCATGACATGACT 60.066 52.381 17.24 8.77 35.31 3.41
553 563 0.674895 GTGTCCAGTGGCTCCATGAC 60.675 60.000 3.51 0.00 0.00 3.06
566 576 2.028130 GTCCACAATTGTTGGTGTCCA 58.972 47.619 8.77 0.00 33.19 4.02
602 612 3.758554 GGTGCATCTCCTAACATTGTGTT 59.241 43.478 0.00 0.67 43.88 3.32
698 708 0.910088 GCCACCACTCCTACCTCCTT 60.910 60.000 0.00 0.00 0.00 3.36
718 728 3.818295 AAGACTAGTCTGTCCTCCACT 57.182 47.619 25.83 4.12 40.36 4.00
728 738 4.701171 GTGCACTACCACTAAGACTAGTCT 59.299 45.833 20.00 20.00 36.14 3.24
741 751 3.056458 CCACCTCGTGCACTACCA 58.944 61.111 16.19 0.00 31.34 3.25
784 794 0.036858 GCACCTCTCAGACTTGTCCC 60.037 60.000 0.00 0.00 0.00 4.46
795 805 3.866582 CCCCCATCGGCACCTCTC 61.867 72.222 0.00 0.00 0.00 3.20
813 823 3.005554 AGAAACATCAGAAGCATGACCG 58.994 45.455 0.00 0.00 30.46 4.79
825 835 3.516586 TGTCCACCTCCTAGAAACATCA 58.483 45.455 0.00 0.00 0.00 3.07
827 837 5.014123 TCAATTGTCCACCTCCTAGAAACAT 59.986 40.000 5.13 0.00 0.00 2.71
832 842 5.777449 TCTATCAATTGTCCACCTCCTAGA 58.223 41.667 5.13 0.00 0.00 2.43
845 855 6.429385 GTCAATAGGCCTTCCTCTATCAATTG 59.571 42.308 12.58 10.95 43.06 2.32
958 972 9.912634 AGTGGTTGTTAGTGAAAAATATCAATG 57.087 29.630 0.00 0.00 0.00 2.82
1011 1025 2.669133 CGGCCTCCTCATGGAACCA 61.669 63.158 0.00 0.00 42.66 3.67
1032 1046 2.106477 TGTGTTCACAGTCAGCACAA 57.894 45.000 0.00 0.00 37.16 3.33
1042 1056 3.063316 CACTTGTTCGACATGTGTTCACA 59.937 43.478 1.15 8.09 44.42 3.58
1071 1085 4.834496 TCCTTCATCTTGTCAAATTTGGCT 59.166 37.500 22.47 0.29 33.01 4.75
1080 1094 9.519191 TTCATATCTTTTTCCTTCATCTTGTCA 57.481 29.630 0.00 0.00 0.00 3.58
1129 1143 3.561143 ACACCTTCACCTTGCAAACATA 58.439 40.909 0.00 0.00 0.00 2.29
1315 1333 5.401550 CGGTGACTGCATATGAAAAACATT 58.598 37.500 6.97 0.00 40.07 2.71
1316 1334 4.675146 GCGGTGACTGCATATGAAAAACAT 60.675 41.667 12.26 0.00 42.39 2.71
1370 1388 7.658179 TGAACATCTTCTGTAACATCTTGAC 57.342 36.000 0.00 0.00 36.98 3.18
1381 1399 4.792068 TGGTCCTTTTGAACATCTTCTGT 58.208 39.130 0.00 0.00 35.14 3.41
1410 1428 2.683362 CCGTTGCCTCCTAAGAAAATCC 59.317 50.000 0.00 0.00 0.00 3.01
1415 1433 1.418637 ACAACCGTTGCCTCCTAAGAA 59.581 47.619 11.29 0.00 0.00 2.52
1432 1450 6.402550 GCTCTTTGATATGCTTCTTCGAACAA 60.403 38.462 0.00 0.00 0.00 2.83
1466 1484 0.385974 CTCCTTTTGACGGCGCTTTG 60.386 55.000 6.90 0.00 0.00 2.77
1468 1486 0.534203 TTCTCCTTTTGACGGCGCTT 60.534 50.000 6.90 0.00 0.00 4.68
1479 1497 5.228945 TCTTTCGTTCCATCTTCTCCTTT 57.771 39.130 0.00 0.00 0.00 3.11
1513 1531 3.496160 GCCTTCTGTTTGTGTTCCCTCTA 60.496 47.826 0.00 0.00 0.00 2.43
1520 1538 1.678101 GAGCAGCCTTCTGTTTGTGTT 59.322 47.619 0.00 0.00 42.29 3.32
1528 1546 0.037882 TCTTCACGAGCAGCCTTCTG 60.038 55.000 0.00 0.00 43.16 3.02
1604 1622 2.159707 CGTCATAGGCGTTTGTTGGAAG 60.160 50.000 0.00 0.00 0.00 3.46
1607 1625 1.153353 ACGTCATAGGCGTTTGTTGG 58.847 50.000 0.00 0.00 39.79 3.77
1611 1629 1.657094 GTGGTACGTCATAGGCGTTTG 59.343 52.381 0.86 0.00 42.85 2.93
1614 1632 1.811860 GGTGGTACGTCATAGGCGT 59.188 57.895 1.34 1.34 45.11 5.68
1615 1633 1.298863 CGGTGGTACGTCATAGGCG 60.299 63.158 0.00 0.00 0.00 5.52
1626 1644 0.895100 ACAAGCTCGTACCGGTGGTA 60.895 55.000 19.93 0.22 37.09 3.25
1628 1646 1.736645 CACAAGCTCGTACCGGTGG 60.737 63.158 19.93 9.49 0.00 4.61
1629 1647 1.007336 GTCACAAGCTCGTACCGGTG 61.007 60.000 19.93 0.15 0.00 4.94
1630 1648 1.288127 GTCACAAGCTCGTACCGGT 59.712 57.895 13.98 13.98 0.00 5.28
1631 1649 1.800315 CGTCACAAGCTCGTACCGG 60.800 63.158 0.00 0.00 0.00 5.28
1632 1650 2.434134 GCGTCACAAGCTCGTACCG 61.434 63.158 0.00 0.00 0.00 4.02
1633 1651 2.434134 CGCGTCACAAGCTCGTACC 61.434 63.158 0.00 0.00 0.00 3.34
1634 1652 1.273455 AACGCGTCACAAGCTCGTAC 61.273 55.000 14.44 0.00 32.71 3.67
1636 1654 1.002250 CTAACGCGTCACAAGCTCGT 61.002 55.000 14.44 0.00 34.63 4.18
1637 1655 1.002250 ACTAACGCGTCACAAGCTCG 61.002 55.000 14.44 0.00 0.00 5.03
1640 1660 0.856641 TTCACTAACGCGTCACAAGC 59.143 50.000 14.44 0.00 0.00 4.01
1648 1668 1.201629 GCGTACAACTTCACTAACGCG 60.202 52.381 3.53 3.53 44.88 6.01
1668 1689 5.859114 CGAAATACCATCGAATAGTCTCAGG 59.141 44.000 0.00 0.00 42.76 3.86
1718 1754 8.340618 AGTTCAACATACATAGTTCAAGCATT 57.659 30.769 0.00 0.00 0.00 3.56
1767 1846 7.974675 ACAATATTTCAGTCACAAATAGGTCG 58.025 34.615 0.00 0.00 30.94 4.79
1800 1879 8.079809 ACATAACTAAACAAGCAACATTGGTAC 58.920 33.333 0.00 0.00 38.04 3.34
1866 1947 1.453762 CTCCGGCGGTAGGGTCTAAG 61.454 65.000 27.32 8.56 0.00 2.18
1965 2046 0.530744 TCCCGTGCAGTATCAGACAC 59.469 55.000 0.00 0.00 0.00 3.67
1982 2063 0.822944 GGTAGGGCTCGGTACTCTCC 60.823 65.000 0.00 0.00 0.00 3.71
2006 2087 4.862447 TCCTACCGCCGCTCGCTA 62.862 66.667 0.00 0.00 36.73 4.26
2010 2091 4.221422 TGCATCCTACCGCCGCTC 62.221 66.667 0.00 0.00 0.00 5.03
2011 2092 4.530857 GTGCATCCTACCGCCGCT 62.531 66.667 0.00 0.00 0.00 5.52
2013 2094 4.155733 TGGTGCATCCTACCGCCG 62.156 66.667 0.00 0.00 41.18 6.46
2023 2104 4.109675 GGCGGTAGGGTGGTGCAT 62.110 66.667 0.00 0.00 0.00 3.96
2025 2106 2.660258 CTATGGCGGTAGGGTGGTGC 62.660 65.000 0.00 0.00 0.00 5.01
2026 2107 1.445942 CTATGGCGGTAGGGTGGTG 59.554 63.158 0.00 0.00 0.00 4.17
2027 2108 2.440817 GCTATGGCGGTAGGGTGGT 61.441 63.158 0.00 0.00 0.00 4.16
2028 2109 2.426023 GCTATGGCGGTAGGGTGG 59.574 66.667 0.00 0.00 0.00 4.61
2081 2162 4.613143 GGGTCCTACCGCCATAGA 57.387 61.111 0.00 0.00 39.83 1.98
2104 2185 3.114616 GTGATGCTGCGTGCGAGT 61.115 61.111 0.00 0.00 46.63 4.18
2110 2191 0.953727 AAACATGTGTGATGCTGCGT 59.046 45.000 0.00 0.00 0.00 5.24
2121 2202 1.875963 GCCCGACCAGAAACATGTG 59.124 57.895 0.00 0.00 0.00 3.21
2162 2243 3.064987 CTACCGCCGGAGACAGTGG 62.065 68.421 11.71 0.00 39.63 4.00
2163 2244 2.490217 CTACCGCCGGAGACAGTG 59.510 66.667 11.71 0.00 0.00 3.66
2164 2245 3.450115 GCTACCGCCGGAGACAGT 61.450 66.667 11.71 0.00 0.00 3.55
2165 2246 3.417275 CTGCTACCGCCGGAGACAG 62.417 68.421 11.71 9.96 34.43 3.51
2166 2247 3.449227 CTGCTACCGCCGGAGACA 61.449 66.667 11.71 3.06 34.43 3.41
2167 2248 3.450115 ACTGCTACCGCCGGAGAC 61.450 66.667 11.71 0.00 34.43 3.36
2168 2249 3.449227 CACTGCTACCGCCGGAGA 61.449 66.667 11.71 0.00 34.43 3.71
2173 2254 3.423154 GTGTGCACTGCTACCGCC 61.423 66.667 19.41 0.00 34.43 6.13
2174 2255 2.357517 AGTGTGCACTGCTACCGC 60.358 61.111 19.41 0.00 40.75 5.68
2175 2256 0.526211 TAGAGTGTGCACTGCTACCG 59.474 55.000 19.41 0.00 42.66 4.02
2176 2257 1.404315 GGTAGAGTGTGCACTGCTACC 60.404 57.143 29.69 29.69 44.65 3.18
2177 2258 1.272490 TGGTAGAGTGTGCACTGCTAC 59.728 52.381 23.83 23.83 42.66 3.58
2178 2259 1.272490 GTGGTAGAGTGTGCACTGCTA 59.728 52.381 19.41 13.21 42.66 3.49
2179 2260 0.034059 GTGGTAGAGTGTGCACTGCT 59.966 55.000 19.41 15.77 42.66 4.24
2180 2261 0.951040 GGTGGTAGAGTGTGCACTGC 60.951 60.000 19.41 11.00 42.66 4.40
2181 2262 0.392706 TGGTGGTAGAGTGTGCACTG 59.607 55.000 19.41 0.00 42.66 3.66
2182 2263 0.393077 GTGGTGGTAGAGTGTGCACT 59.607 55.000 19.41 4.31 45.84 4.40
2183 2264 0.105964 TGTGGTGGTAGAGTGTGCAC 59.894 55.000 10.75 10.75 0.00 4.57
2184 2265 0.392706 CTGTGGTGGTAGAGTGTGCA 59.607 55.000 0.00 0.00 0.00 4.57
2185 2266 0.679505 TCTGTGGTGGTAGAGTGTGC 59.320 55.000 0.00 0.00 0.00 4.57
2186 2267 1.964223 AGTCTGTGGTGGTAGAGTGTG 59.036 52.381 0.00 0.00 0.00 3.82
2187 2268 2.240279 GAGTCTGTGGTGGTAGAGTGT 58.760 52.381 0.00 0.00 0.00 3.55
2188 2269 1.546476 GGAGTCTGTGGTGGTAGAGTG 59.454 57.143 0.00 0.00 0.00 3.51
2189 2270 1.887088 CGGAGTCTGTGGTGGTAGAGT 60.887 57.143 0.00 0.00 0.00 3.24
2190 2271 0.811915 CGGAGTCTGTGGTGGTAGAG 59.188 60.000 0.00 0.00 0.00 2.43
2191 2272 0.611062 CCGGAGTCTGTGGTGGTAGA 60.611 60.000 0.00 0.00 0.00 2.59
2192 2273 0.898789 ACCGGAGTCTGTGGTGGTAG 60.899 60.000 9.46 0.00 33.91 3.18
2193 2274 1.154454 ACCGGAGTCTGTGGTGGTA 59.846 57.895 9.46 0.00 33.91 3.25
2194 2275 2.122989 ACCGGAGTCTGTGGTGGT 60.123 61.111 9.46 0.00 33.91 4.16
2238 2355 5.010012 CCCTGTCTAACATGTTGCTTCTTTT 59.990 40.000 21.42 0.00 0.00 2.27
2266 2383 9.311916 CAACCAAAAGATACACATTCTTTTTCA 57.688 29.630 8.30 0.00 46.18 2.69
2267 2384 9.313118 ACAACCAAAAGATACACATTCTTTTTC 57.687 29.630 8.30 0.00 46.18 2.29
2268 2385 9.665719 AACAACCAAAAGATACACATTCTTTTT 57.334 25.926 8.30 0.00 46.18 1.94
2271 2388 9.744468 GTTAACAACCAAAAGATACACATTCTT 57.256 29.630 0.00 0.00 34.95 2.52
2272 2389 9.131791 AGTTAACAACCAAAAGATACACATTCT 57.868 29.630 8.61 0.00 0.00 2.40
2273 2390 9.744468 AAGTTAACAACCAAAAGATACACATTC 57.256 29.630 8.61 0.00 0.00 2.67
2325 2476 5.186409 ACCATTCGTTGCTAGTTCCTACTTA 59.814 40.000 0.00 0.00 35.78 2.24
2328 2479 3.858247 ACCATTCGTTGCTAGTTCCTAC 58.142 45.455 0.00 0.00 0.00 3.18
2332 2483 4.927425 TGAACTACCATTCGTTGCTAGTTC 59.073 41.667 18.81 18.81 45.59 3.01
2342 2493 5.030295 GCATGTCATTTGAACTACCATTCG 58.970 41.667 0.00 0.00 0.00 3.34
2378 2529 9.474920 GGACATGATTTTTGTCATTTGAACTTA 57.525 29.630 0.00 0.00 44.22 2.24
2379 2530 7.169645 CGGACATGATTTTTGTCATTTGAACTT 59.830 33.333 0.00 0.00 44.22 2.66
2393 2544 1.808411 ACGCTGTCGGACATGATTTT 58.192 45.000 11.86 0.00 40.69 1.82
2407 2558 2.096909 CGTGTCCTTTGAACTAACGCTG 60.097 50.000 0.00 0.00 0.00 5.18
2422 2573 1.290203 ATCGAACATGATGCGTGTCC 58.710 50.000 0.00 0.00 31.86 4.02
2428 2579 1.502231 ACCGCTATCGAACATGATGC 58.498 50.000 0.00 0.00 38.10 3.91
2437 2588 3.249320 GTGTGTCATACTACCGCTATCGA 59.751 47.826 0.00 0.00 38.10 3.59
2491 2646 1.348064 TAGGATTCTACCGGGCATGG 58.652 55.000 6.32 0.00 34.73 3.66


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

AutoCloner maintained by Alex Coulton.