Multiple sequence alignment - TraesCS7D01G447500

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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 TraesCS7D01G447500 chr7D 100.000 3841 0 0 1 3841 568009572 568013412 0.000000e+00 7094.0
1 TraesCS7D01G447500 chr7D 96.907 97 3 0 1471 1567 568011135 568011039 3.070000e-36 163.0
2 TraesCS7D01G447500 chr7D 95.146 103 1 3 1467 1566 538028542 538028643 3.970000e-35 159.0
3 TraesCS7D01G447500 chr7B 93.190 2320 106 23 1559 3841 622623886 622626190 0.000000e+00 3362.0
4 TraesCS7D01G447500 chr7B 85.962 1040 116 16 1 1017 622621970 622623002 0.000000e+00 1085.0
5 TraesCS7D01G447500 chr7B 94.333 547 31 0 930 1476 622623343 622623889 0.000000e+00 839.0
6 TraesCS7D01G447500 chr7A 93.556 1800 93 13 2051 3841 655370028 655371813 0.000000e+00 2660.0
7 TraesCS7D01G447500 chr7A 87.609 1493 131 22 1 1476 655367853 655369308 0.000000e+00 1683.0
8 TraesCS7D01G447500 chr7A 89.356 404 28 5 1568 1965 655369324 655369718 9.590000e-136 494.0
9 TraesCS7D01G447500 chr4D 96.970 99 3 0 1471 1569 507164694 507164792 2.370000e-37 167.0
10 TraesCS7D01G447500 chr4D 97.872 94 2 0 1471 1564 507164787 507164694 3.070000e-36 163.0
11 TraesCS7D01G447500 chr3A 98.925 93 1 0 1475 1567 553159606 553159514 2.370000e-37 167.0
12 TraesCS7D01G447500 chr3A 94.175 103 4 2 1463 1565 638201945 638201845 5.140000e-34 156.0
13 TraesCS7D01G447500 chr6B 92.308 117 5 4 1448 1561 504587228 504587113 3.070000e-36 163.0
14 TraesCS7D01G447500 chr5B 93.458 107 5 2 1454 1560 681344988 681345092 1.430000e-34 158.0
15 TraesCS7D01G447500 chr5B 90.517 116 9 2 1445 1560 470992253 470992366 6.650000e-33 152.0
16 TraesCS7D01G447500 chr5D 85.000 120 14 2 2179 2298 485390147 485390032 6.740000e-23 119.0
17 TraesCS7D01G447500 chr2B 73.783 267 44 19 3474 3736 77916901 77917145 8.840000e-12 82.4


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 TraesCS7D01G447500 chr7D 568009572 568013412 3840 False 7094.000000 7094 100.000000 1 3841 1 chr7D.!!$F2 3840
1 TraesCS7D01G447500 chr7B 622621970 622626190 4220 False 1762.000000 3362 91.161667 1 3841 3 chr7B.!!$F1 3840
2 TraesCS7D01G447500 chr7A 655367853 655371813 3960 False 1612.333333 2660 90.173667 1 3841 3 chr7A.!!$F1 3840

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
843 865 0.175989 GAGCGGAGGGATTTCGAACT 59.824 55.000 0.00 0.00 0.00 3.01 F
849 871 0.837940 AGGGATTTCGAACTAGCCCC 59.162 55.000 17.57 13.47 36.19 5.80 F
2009 2511 1.002087 TGTGTGTGTGTGTGTGTACCA 59.998 47.619 0.00 0.00 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 3328 0.323360 GGGATACAACAGGGCAAGCA 60.323 55.0 0.00 0.0 39.74 3.91 R
2747 3451 0.695347 CACTCCTGGAGCCCTCTTTT 59.305 55.0 23.43 0.0 32.04 2.27 R
3750 4470 0.251922 ACCACCTTCTACCGCCACTA 60.252 55.0 0.00 0.0 0.00 2.74 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
49 50 1.389555 ACCGTCGATGTGCATCTAGA 58.610 50.000 3.52 0.00 35.72 2.43
69 70 4.567971 AGAAAGAGATGTCACAAGAGCTG 58.432 43.478 0.00 0.00 0.00 4.24
103 104 4.421479 CCTCCAACGCTCGTCGCT 62.421 66.667 0.00 0.00 43.23 4.93
108 109 2.501222 AACGCTCGTCGCTGTACG 60.501 61.111 0.00 0.00 44.19 3.67
123 124 3.724374 CTGTACGAAAGAACACTCCCAA 58.276 45.455 0.00 0.00 0.00 4.12
131 132 3.593442 AGAACACTCCCAACCATTTGA 57.407 42.857 0.00 0.00 34.24 2.69
139 140 4.040339 ACTCCCAACCATTTGAATCCAAAC 59.960 41.667 0.00 0.00 44.16 2.93
149 150 2.161855 TGAATCCAAACAAGAGCGCAT 58.838 42.857 11.47 0.00 0.00 4.73
180 181 3.604129 TTCGCATGAAGAGGCCGCA 62.604 57.895 9.88 0.69 0.00 5.69
208 209 0.854218 AGAAGAGGATCGGGAGGCTA 59.146 55.000 0.00 0.00 42.67 3.93
214 215 1.335132 GGATCGGGAGGCTACCACAA 61.335 60.000 17.87 0.00 0.00 3.33
225 226 2.230660 GCTACCACAAGCAAGGAAACT 58.769 47.619 0.00 0.00 42.30 2.66
259 261 1.570967 CGGTATCGCATGGTGCATG 59.429 57.895 2.63 0.00 45.36 4.06
343 346 2.328099 CCTCCGCCAAAGAGCACAC 61.328 63.158 0.00 0.00 0.00 3.82
351 354 3.304659 CGCCAAAGAGCACACTTTATTGT 60.305 43.478 0.00 0.00 37.91 2.71
359 362 2.050691 CACACTTTATTGTTGGTGCGC 58.949 47.619 0.00 0.00 33.53 6.09
371 374 2.825836 GTGCGCCTCCTCCAATGG 60.826 66.667 4.18 0.00 0.00 3.16
376 379 2.124570 CCTCCTCCAATGGCCACG 60.125 66.667 8.16 1.14 0.00 4.94
380 383 2.751436 CTCCAATGGCCACGGGTG 60.751 66.667 20.42 15.62 0.00 4.61
411 414 2.144078 ACCACCATGGGTCGTCACA 61.144 57.895 18.09 0.00 43.37 3.58
423 426 0.667487 TCGTCACACTGCTGCTTAGC 60.667 55.000 0.00 0.00 0.00 3.09
428 431 0.534412 ACACTGCTGCTTAGCGATCT 59.466 50.000 0.00 0.00 37.69 2.75
434 437 1.266175 GCTGCTTAGCGATCTACCGTA 59.734 52.381 0.00 0.00 0.00 4.02
449 452 0.759436 CCGTAGCAGGGGGTAGATGT 60.759 60.000 0.00 0.00 0.00 3.06
495 498 2.025321 AGGAAGAGAGTGAGGAGAGGAC 60.025 54.545 0.00 0.00 0.00 3.85
501 504 0.613292 AGTGAGGAGAGGACGCATGT 60.613 55.000 0.00 0.00 0.00 3.21
536 539 1.848652 CCGTCTTGGAACCCTAGAGA 58.151 55.000 0.00 0.00 42.00 3.10
545 548 2.292323 GGAACCCTAGAGAAGAGGACCA 60.292 54.545 0.00 0.00 35.99 4.02
559 562 0.615850 GGACCAAGAGAGACAAGGGG 59.384 60.000 0.00 0.00 0.00 4.79
584 587 2.420129 GGTGGAGCGATTCTTGGTGTAT 60.420 50.000 0.00 0.00 0.00 2.29
590 593 3.130516 AGCGATTCTTGGTGTATCGAGAA 59.869 43.478 7.79 0.00 44.94 2.87
628 634 6.890268 GGTAGGGTTCAGTTGGATAAAAGATT 59.110 38.462 0.00 0.00 0.00 2.40
692 699 7.447238 AGACAAAAATAAACCGATGAGGAGAAA 59.553 33.333 0.00 0.00 45.00 2.52
704 726 5.468746 CGATGAGGAGAAACTAGGAGTAGAG 59.531 48.000 0.00 0.00 0.00 2.43
710 732 8.339720 AGGAGAAACTAGGAGTAGAGATTAGA 57.660 38.462 0.00 0.00 0.00 2.10
714 736 7.450323 AGAAACTAGGAGTAGAGATTAGATGCC 59.550 40.741 0.00 0.00 0.00 4.40
732 754 0.893270 CCTGTTCGGCAATCCACCAA 60.893 55.000 0.00 0.00 0.00 3.67
735 757 0.958822 GTTCGGCAATCCACCAACTT 59.041 50.000 0.00 0.00 0.00 2.66
790 812 6.206634 TGTTTCTCTGCTCCGTTATTTTCAAT 59.793 34.615 0.00 0.00 0.00 2.57
835 857 1.613630 AGTTGTGGAGCGGAGGGAT 60.614 57.895 0.00 0.00 0.00 3.85
837 859 0.322546 GTTGTGGAGCGGAGGGATTT 60.323 55.000 0.00 0.00 0.00 2.17
843 865 0.175989 GAGCGGAGGGATTTCGAACT 59.824 55.000 0.00 0.00 0.00 3.01
849 871 0.837940 AGGGATTTCGAACTAGCCCC 59.162 55.000 17.57 13.47 36.19 5.80
883 907 1.269726 GGAGTAGAGATCAGCTGCAGC 60.270 57.143 31.53 31.53 42.49 5.25
897 921 2.093447 GCTGCAGCTAAGAGGTTCCTTA 60.093 50.000 31.33 0.00 38.21 2.69
903 927 6.126768 TGCAGCTAAGAGGTTCCTTATGTAAT 60.127 38.462 0.00 0.00 0.00 1.89
904 928 6.203723 GCAGCTAAGAGGTTCCTTATGTAATG 59.796 42.308 0.00 0.00 0.00 1.90
907 931 8.989131 AGCTAAGAGGTTCCTTATGTAATGTAA 58.011 33.333 0.00 0.00 0.00 2.41
908 932 9.262358 GCTAAGAGGTTCCTTATGTAATGTAAG 57.738 37.037 0.00 0.00 0.00 2.34
911 935 9.668497 AAGAGGTTCCTTATGTAATGTAAGTTC 57.332 33.333 0.00 0.00 0.00 3.01
952 976 6.834168 AATAGGTTCCTTGTGTAAATGTGG 57.166 37.500 0.00 0.00 0.00 4.17
992 1444 3.123804 CTCCATCGTATCCCTTCGTTTG 58.876 50.000 0.00 0.00 0.00 2.93
1058 1513 4.811364 GCCTGGCCTGCCTTCTCC 62.811 72.222 7.66 0.00 36.94 3.71
1059 1514 3.013932 CCTGGCCTGCCTTCTCCT 61.014 66.667 9.97 0.00 36.94 3.69
1060 1515 2.588989 CTGGCCTGCCTTCTCCTC 59.411 66.667 9.97 0.00 36.94 3.71
1139 1594 4.275508 CCCAGCCGCCATGCCTAT 62.276 66.667 0.00 0.00 0.00 2.57
1160 1615 3.077556 CCCTCACCGTCCCCTGAG 61.078 72.222 0.00 0.00 34.73 3.35
1161 1616 2.283966 CCTCACCGTCCCCTGAGT 60.284 66.667 0.00 0.00 33.32 3.41
1168 1623 2.883828 CGTCCCCTGAGTTGGTGCT 61.884 63.158 0.00 0.00 0.00 4.40
1430 1885 8.741841 TGAATTAATTGTGCTGAATGAATCTCA 58.258 29.630 5.17 0.00 0.00 3.27
1480 1935 9.816787 TTTGGGGATTATTTGTTATATACTCCC 57.183 33.333 8.87 8.87 42.49 4.30
1481 1936 8.766492 TGGGGATTATTTGTTATATACTCCCT 57.234 34.615 14.30 0.00 42.67 4.20
1482 1937 8.832735 TGGGGATTATTTGTTATATACTCCCTC 58.167 37.037 14.30 8.12 42.67 4.30
1483 1938 9.059023 GGGGATTATTTGTTATATACTCCCTCT 57.941 37.037 14.30 0.00 42.67 3.69
1484 1939 9.892130 GGGATTATTTGTTATATACTCCCTCTG 57.108 37.037 9.73 0.00 41.14 3.35
1489 1944 7.743116 TTTGTTATATACTCCCTCTGTTCCA 57.257 36.000 0.00 0.00 0.00 3.53
1490 1945 7.743116 TTGTTATATACTCCCTCTGTTCCAA 57.257 36.000 0.00 0.00 0.00 3.53
1491 1946 7.743116 TGTTATATACTCCCTCTGTTCCAAA 57.257 36.000 0.00 0.00 0.00 3.28
1492 1947 8.331931 TGTTATATACTCCCTCTGTTCCAAAT 57.668 34.615 0.00 0.00 0.00 2.32
1493 1948 8.778059 TGTTATATACTCCCTCTGTTCCAAATT 58.222 33.333 0.00 0.00 0.00 1.82
1496 1951 6.893020 ATACTCCCTCTGTTCCAAATTACT 57.107 37.500 0.00 0.00 0.00 2.24
1497 1952 5.167303 ACTCCCTCTGTTCCAAATTACTC 57.833 43.478 0.00 0.00 0.00 2.59
1498 1953 4.184629 CTCCCTCTGTTCCAAATTACTCG 58.815 47.826 0.00 0.00 0.00 4.18
1499 1954 3.581332 TCCCTCTGTTCCAAATTACTCGT 59.419 43.478 0.00 0.00 0.00 4.18
1500 1955 3.933332 CCCTCTGTTCCAAATTACTCGTC 59.067 47.826 0.00 0.00 0.00 4.20
1501 1956 3.612860 CCTCTGTTCCAAATTACTCGTCG 59.387 47.826 0.00 0.00 0.00 5.12
1502 1957 4.235360 CTCTGTTCCAAATTACTCGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
1503 1958 3.985279 TCTGTTCCAAATTACTCGTCGTG 59.015 43.478 0.00 0.00 0.00 4.35
1504 1959 3.061322 TGTTCCAAATTACTCGTCGTGG 58.939 45.455 0.00 0.00 0.00 4.94
1505 1960 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1506 1961 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1507 1962 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1508 1963 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1509 1964 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1510 1965 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1511 1966 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1512 1967 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1513 1968 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1514 1969 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1515 1970 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1516 1971 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1517 1972 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1518 1973 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
1519 1974 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
1520 1975 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
1521 1976 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
1522 1977 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
1535 1990 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
1536 1991 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
1537 1992 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
1538 1993 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1539 1994 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1540 1995 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1541 1996 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1542 1997 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1543 1998 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
1544 1999 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
1545 2000 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1546 2001 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1547 2002 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1548 2003 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1549 2004 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1550 2005 2.091588 CCACGACGAGTAATTTGGAACG 59.908 50.000 0.00 0.00 0.00 3.95
1551 2006 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
1552 2007 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
1553 2008 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
1554 2009 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1555 2010 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1556 2011 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
1557 2012 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
1558 2013 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1559 2014 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1560 2015 4.720273 AGTAATTTGGAACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
1561 2016 5.901276 AGTAATTTGGAACGGAGGGAGTATA 59.099 40.000 0.00 0.00 0.00 1.47
1880 2351 3.397482 CGCATATGCTCCTAGCTTCTTT 58.603 45.455 24.56 0.00 42.97 2.52
1887 2358 5.108187 TGCTCCTAGCTTCTTTTCATGAT 57.892 39.130 0.00 0.00 42.97 2.45
1890 2361 6.051717 GCTCCTAGCTTCTTTTCATGATACA 58.948 40.000 0.00 0.00 38.45 2.29
1946 2417 6.990939 GGTATCACCACTTAATTAGTTCCCTC 59.009 42.308 0.00 0.00 38.42 4.30
1947 2418 6.893020 ATCACCACTTAATTAGTTCCCTCT 57.107 37.500 0.00 0.00 33.85 3.69
1948 2419 6.049955 TCACCACTTAATTAGTTCCCTCTG 57.950 41.667 0.00 0.00 33.85 3.35
1949 2420 5.546499 TCACCACTTAATTAGTTCCCTCTGT 59.454 40.000 0.00 0.00 33.85 3.41
1950 2421 5.875359 CACCACTTAATTAGTTCCCTCTGTC 59.125 44.000 0.00 0.00 33.85 3.51
2007 2509 2.070028 TGTGTGTGTGTGTGTGTGTAC 58.930 47.619 0.00 0.00 0.00 2.90
2009 2511 1.002087 TGTGTGTGTGTGTGTGTACCA 59.998 47.619 0.00 0.00 0.00 3.25
2012 2540 2.496470 TGTGTGTGTGTGTGTACCAGTA 59.504 45.455 0.00 0.00 0.00 2.74
2036 2708 6.250711 ACCATGATATGTATCCACATGCATT 58.749 36.000 0.00 0.00 45.17 3.56
2049 2749 3.191791 CACATGCATTCACACCTCATGAA 59.808 43.478 0.00 0.00 40.25 2.57
2318 3018 7.719193 TCATTCCACTGAATTTTACTTCTGTCA 59.281 33.333 0.00 0.00 39.20 3.58
2519 3222 2.624636 GTATGTACCCCACGTTCTTGG 58.375 52.381 0.00 0.00 36.26 3.61
2690 3394 6.479006 TCTCAAGTCAGATTGATGATTGGTT 58.521 36.000 0.00 0.00 38.47 3.67
2747 3451 1.299648 CTTCCTGGCGATGAACCCA 59.700 57.895 0.00 0.00 0.00 4.51
2765 3469 0.695347 CAAAAGAGGGCTCCAGGAGT 59.305 55.000 18.37 0.00 31.39 3.85
2863 3567 4.013050 AGAAGAGCCTTATTTTGGTGAGC 58.987 43.478 0.00 0.00 0.00 4.26
2948 3652 7.882791 TGGCTTTAGATCAACAGAAGTGAATTA 59.117 33.333 0.00 0.00 0.00 1.40
3075 3779 2.170187 GAGCTGGGATTCAGAGACATGT 59.830 50.000 0.00 0.00 46.18 3.21
3244 3951 5.939883 TGCACATTACATTCAGCTAGAAACT 59.060 36.000 0.00 0.00 40.22 2.66
3317 4024 5.927689 TCTTAATTTTGCCTGTTTGCATCAG 59.072 36.000 11.07 11.07 41.70 2.90
3408 4116 1.124780 TCCCTGACGAGTTTGTCCAA 58.875 50.000 0.00 0.00 38.11 3.53
3508 4216 1.606889 GTCCTCGACCCTGTCCAGT 60.607 63.158 0.00 0.00 0.00 4.00
3509 4217 1.155390 TCCTCGACCCTGTCCAGTT 59.845 57.895 0.00 0.00 0.00 3.16
3510 4218 0.898789 TCCTCGACCCTGTCCAGTTC 60.899 60.000 0.00 0.00 0.00 3.01
3604 4315 2.354401 CCGCCTGAGCTCCTTCTCA 61.354 63.158 12.15 0.00 40.50 3.27
3621 4332 4.765813 TCTCAATGATGATGAAGCCAGA 57.234 40.909 0.00 0.00 34.37 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.926244 TCTCTTTCTAGATGCACATCGAC 58.074 43.478 5.04 0.00 42.48 4.20
49 50 4.563168 CCTCAGCTCTTGTGACATCTCTTT 60.563 45.833 0.00 0.00 0.00 2.52
103 104 3.460103 GTTGGGAGTGTTCTTTCGTACA 58.540 45.455 0.00 0.00 0.00 2.90
108 109 4.340950 TCAAATGGTTGGGAGTGTTCTTTC 59.659 41.667 0.00 0.00 35.29 2.62
123 124 4.559300 CGCTCTTGTTTGGATTCAAATGGT 60.559 41.667 1.62 0.00 43.73 3.55
131 132 2.414559 CGAATGCGCTCTTGTTTGGATT 60.415 45.455 9.73 0.00 0.00 3.01
139 140 1.341802 GACGACGAATGCGCTCTTG 59.658 57.895 9.73 1.56 42.48 3.02
149 150 2.159352 TCATGCGAAATAGGACGACGAA 60.159 45.455 0.00 0.00 0.00 3.85
180 181 1.732732 CGATCCTCTTCTCAACGCGTT 60.733 52.381 20.79 20.79 0.00 4.84
208 209 1.402787 CCAGTTTCCTTGCTTGTGGT 58.597 50.000 0.00 0.00 0.00 4.16
214 215 1.460699 GGTCCCCAGTTTCCTTGCT 59.539 57.895 0.00 0.00 0.00 3.91
251 253 1.277273 CAGTCTCCTCTTCATGCACCA 59.723 52.381 0.00 0.00 0.00 4.17
259 261 0.539518 GCCTTCCCAGTCTCCTCTTC 59.460 60.000 0.00 0.00 0.00 2.87
343 346 1.135402 GGAGGCGCACCAACAATAAAG 60.135 52.381 10.83 0.00 39.06 1.85
351 354 2.905996 ATTGGAGGAGGCGCACCAA 61.906 57.895 21.48 19.91 44.63 3.67
359 362 2.124570 CGTGGCCATTGGAGGAGG 60.125 66.667 9.72 0.00 0.00 4.30
371 374 1.933115 ATCGATTTTGCACCCGTGGC 61.933 55.000 0.00 0.00 0.00 5.01
376 379 0.377203 GGTCGATCGATTTTGCACCC 59.623 55.000 22.50 11.16 0.00 4.61
380 383 1.083489 TGGTGGTCGATCGATTTTGC 58.917 50.000 22.50 7.64 0.00 3.68
423 426 1.524863 CCCCCTGCTACGGTAGATCG 61.525 65.000 19.02 5.72 0.00 3.69
428 431 0.855598 ATCTACCCCCTGCTACGGTA 59.144 55.000 0.00 0.00 0.00 4.02
434 437 2.614259 CATCTACATCTACCCCCTGCT 58.386 52.381 0.00 0.00 0.00 4.24
536 539 2.903135 CCTTGTCTCTCTTGGTCCTCTT 59.097 50.000 0.00 0.00 0.00 2.85
545 548 0.695347 CCAAGCCCCTTGTCTCTCTT 59.305 55.000 4.48 0.00 39.58 2.85
559 562 0.449388 CAAGAATCGCTCCACCAAGC 59.551 55.000 0.00 0.00 38.97 4.01
590 593 6.117975 TGAACCCTACCTCTCGTTATTTTT 57.882 37.500 0.00 0.00 0.00 1.94
595 601 3.446442 ACTGAACCCTACCTCTCGTTA 57.554 47.619 0.00 0.00 0.00 3.18
606 612 6.552008 TCAATCTTTTATCCAACTGAACCCT 58.448 36.000 0.00 0.00 0.00 4.34
608 614 8.055279 TCATCAATCTTTTATCCAACTGAACC 57.945 34.615 0.00 0.00 0.00 3.62
643 650 3.124686 TTTTTGCCTCACCCACGC 58.875 55.556 0.00 0.00 0.00 5.34
665 672 6.371548 TCTCCTCATCGGTTTATTTTTGTCTG 59.628 38.462 0.00 0.00 0.00 3.51
692 699 6.183361 ACAGGCATCTAATCTCTACTCCTAGT 60.183 42.308 0.00 0.00 0.00 2.57
714 736 0.240945 GTTGGTGGATTGCCGAACAG 59.759 55.000 0.00 0.00 36.79 3.16
732 754 5.583495 CAGATCCTCGTATTTTCTCGAAGT 58.417 41.667 0.00 0.00 35.69 3.01
735 757 3.548214 CGCAGATCCTCGTATTTTCTCGA 60.548 47.826 0.00 0.00 34.88 4.04
764 786 5.529430 TGAAAATAACGGAGCAGAGAAACAA 59.471 36.000 0.00 0.00 0.00 2.83
773 795 4.484236 CTGCAATTGAAAATAACGGAGCA 58.516 39.130 10.34 0.00 0.00 4.26
820 842 1.602237 GAAATCCCTCCGCTCCACA 59.398 57.895 0.00 0.00 0.00 4.17
835 857 1.747355 CTACTCGGGGCTAGTTCGAAA 59.253 52.381 0.00 0.00 32.35 3.46
837 859 0.543277 TCTACTCGGGGCTAGTTCGA 59.457 55.000 0.00 0.00 0.00 3.71
843 865 3.396946 TCCTAAATCTCTACTCGGGGCTA 59.603 47.826 0.00 0.00 0.00 3.93
849 871 8.092068 TGATCTCTACTCCTAAATCTCTACTCG 58.908 40.741 0.00 0.00 0.00 4.18
931 955 4.076394 GCCACATTTACACAAGGAACCTA 58.924 43.478 0.00 0.00 0.00 3.08
941 965 2.566952 GCCTCATGCCACATTTACAC 57.433 50.000 0.00 0.00 0.00 2.90
992 1444 2.233271 CATACTGGGCCATTGGATGTC 58.767 52.381 6.72 0.00 0.00 3.06
1058 1513 0.618458 TCCCGTCCCCAAATTCAGAG 59.382 55.000 0.00 0.00 0.00 3.35
1059 1514 0.618458 CTCCCGTCCCCAAATTCAGA 59.382 55.000 0.00 0.00 0.00 3.27
1060 1515 0.394352 CCTCCCGTCCCCAAATTCAG 60.394 60.000 0.00 0.00 0.00 3.02
1139 1594 2.284847 GGGGACGGTGAGGGGTAA 60.285 66.667 0.00 0.00 0.00 2.85
1270 1725 1.311371 AGAGGAGGGGAGGGGAGAT 60.311 63.158 0.00 0.00 0.00 2.75
1271 1726 2.015726 GAGAGGAGGGGAGGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1325 1780 9.672673 AAATACAAATACACAGAAGCACTAGAT 57.327 29.630 0.00 0.00 0.00 1.98
1327 1782 8.177663 CCAAATACAAATACACAGAAGCACTAG 58.822 37.037 0.00 0.00 0.00 2.57
1430 1885 9.974980 AAACAAACAAATAAACAATACGGAGAT 57.025 25.926 0.00 0.00 0.00 2.75
1476 1931 4.184629 CGAGTAATTTGGAACAGAGGGAG 58.815 47.826 0.00 0.00 42.39 4.30
1477 1932 3.581332 ACGAGTAATTTGGAACAGAGGGA 59.419 43.478 0.00 0.00 42.39 4.20
1478 1933 3.933332 GACGAGTAATTTGGAACAGAGGG 59.067 47.826 0.00 0.00 42.39 4.30
1479 1934 3.612860 CGACGAGTAATTTGGAACAGAGG 59.387 47.826 0.00 0.00 42.39 3.69
1480 1935 4.090066 CACGACGAGTAATTTGGAACAGAG 59.910 45.833 0.00 0.00 42.39 3.35
1481 1936 3.985279 CACGACGAGTAATTTGGAACAGA 59.015 43.478 0.00 0.00 42.39 3.41
1482 1937 3.122948 CCACGACGAGTAATTTGGAACAG 59.877 47.826 0.00 0.00 42.39 3.16
1483 1938 3.061322 CCACGACGAGTAATTTGGAACA 58.939 45.455 0.00 0.00 0.00 3.18
1484 1939 3.062042 ACCACGACGAGTAATTTGGAAC 58.938 45.455 0.00 0.00 0.00 3.62
1485 1940 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
1486 1941 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
1487 1942 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
1488 1943 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
1489 1944 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
1490 1945 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
1491 1946 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
1492 1947 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1493 1948 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1494 1949 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1495 1950 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1496 1951 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
1497 1952 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
1498 1953 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
1511 1966 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
1512 1967 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
1513 1968 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
1514 1969 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
1515 1970 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
1516 1971 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
1517 1972 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1518 1973 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1519 1974 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1520 1975 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
1521 1976 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
1522 1977 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
1523 1978 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
1524 1979 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
1525 1980 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
1526 1981 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
1527 1982 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
1528 1983 3.062042 GTTCCAAATTACTCGTCGTGGT 58.938 45.455 0.00 0.00 0.00 4.16
1529 1984 2.091588 CGTTCCAAATTACTCGTCGTGG 59.908 50.000 0.00 0.00 0.00 4.94
1530 1985 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
1531 1986 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
1532 1987 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
1533 1988 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1534 1989 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
1535 1990 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
1536 1991 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
1537 1992 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
1538 1993 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
1539 1994 7.038799 GGTATATACTCCCTCCGTTCCAAATTA 60.039 40.741 12.54 0.00 0.00 1.40
1540 1995 5.906772 ATATACTCCCTCCGTTCCAAATT 57.093 39.130 0.00 0.00 0.00 1.82
1541 1996 5.247792 GGTATATACTCCCTCCGTTCCAAAT 59.752 44.000 12.54 0.00 0.00 2.32
1542 1997 4.590222 GGTATATACTCCCTCCGTTCCAAA 59.410 45.833 12.54 0.00 0.00 3.28
1543 1998 4.154942 GGTATATACTCCCTCCGTTCCAA 58.845 47.826 12.54 0.00 0.00 3.53
1544 1999 3.140707 TGGTATATACTCCCTCCGTTCCA 59.859 47.826 12.54 0.00 0.00 3.53
1545 2000 3.762823 CTGGTATATACTCCCTCCGTTCC 59.237 52.174 12.54 0.00 0.00 3.62
1546 2001 3.193056 GCTGGTATATACTCCCTCCGTTC 59.807 52.174 12.54 0.00 0.00 3.95
1547 2002 3.163467 GCTGGTATATACTCCCTCCGTT 58.837 50.000 12.54 0.00 0.00 4.44
1548 2003 2.805194 GCTGGTATATACTCCCTCCGT 58.195 52.381 12.54 0.00 0.00 4.69
1549 2004 1.743958 CGCTGGTATATACTCCCTCCG 59.256 57.143 12.54 4.29 0.00 4.63
1550 2005 1.477295 GCGCTGGTATATACTCCCTCC 59.523 57.143 12.54 0.00 0.00 4.30
1551 2006 1.132643 CGCGCTGGTATATACTCCCTC 59.867 57.143 12.54 0.00 0.00 4.30
1552 2007 1.174783 CGCGCTGGTATATACTCCCT 58.825 55.000 12.54 0.00 0.00 4.20
1553 2008 1.132643 CTCGCGCTGGTATATACTCCC 59.867 57.143 12.54 0.00 0.00 4.30
1554 2009 1.811359 ACTCGCGCTGGTATATACTCC 59.189 52.381 12.54 0.00 0.00 3.85
1555 2010 4.649977 CTTACTCGCGCTGGTATATACTC 58.350 47.826 12.54 3.99 0.00 2.59
1556 2011 3.119919 GCTTACTCGCGCTGGTATATACT 60.120 47.826 12.54 0.00 0.00 2.12
1557 2012 3.169733 GCTTACTCGCGCTGGTATATAC 58.830 50.000 5.56 4.14 0.00 1.47
1558 2013 2.163010 GGCTTACTCGCGCTGGTATATA 59.837 50.000 5.56 0.00 0.00 0.86
1559 2014 1.067776 GGCTTACTCGCGCTGGTATAT 60.068 52.381 5.56 0.00 0.00 0.86
1560 2015 0.313043 GGCTTACTCGCGCTGGTATA 59.687 55.000 5.56 0.00 0.00 1.47
1561 2016 1.067582 GGCTTACTCGCGCTGGTAT 59.932 57.895 5.56 0.00 0.00 2.73
1745 2213 2.031191 GGAAGTCGAGACAACGCAAAAA 59.969 45.455 5.99 0.00 0.00 1.94
1746 2214 1.595794 GGAAGTCGAGACAACGCAAAA 59.404 47.619 5.99 0.00 0.00 2.44
1755 2223 4.516365 TTTCTTACCTGGAAGTCGAGAC 57.484 45.455 0.00 0.00 0.00 3.36
1761 2229 5.801380 TCGCTTAATTTCTTACCTGGAAGT 58.199 37.500 0.00 0.00 0.00 3.01
1829 2300 1.931172 GTGTGCTGTACGTGTTGAGTT 59.069 47.619 0.00 0.00 0.00 3.01
1887 2358 3.389656 TGAACAAGACCACTCCATGTGTA 59.610 43.478 0.00 0.00 44.81 2.90
1890 2361 3.795688 ATGAACAAGACCACTCCATGT 57.204 42.857 0.00 0.00 0.00 3.21
1947 2418 4.072131 GTCAGAAAATTACAGCTGGGACA 58.928 43.478 19.93 0.00 0.00 4.02
1948 2419 4.154918 CAGTCAGAAAATTACAGCTGGGAC 59.845 45.833 19.93 10.35 0.00 4.46
1949 2420 4.202461 ACAGTCAGAAAATTACAGCTGGGA 60.202 41.667 19.93 6.18 0.00 4.37
1950 2421 4.074970 ACAGTCAGAAAATTACAGCTGGG 58.925 43.478 19.93 0.00 0.00 4.45
2049 2749 6.408869 CATCCTTGGAAAAATAAGCACCAAT 58.591 36.000 0.00 0.00 39.39 3.16
2318 3018 3.074412 CCACACTCCAGCGTATTTTTCT 58.926 45.455 0.00 0.00 0.00 2.52
2328 3028 1.455383 CCAACCAACCACACTCCAGC 61.455 60.000 0.00 0.00 0.00 4.85
2519 3222 1.731160 GAGTTGTCAGCTGAGTCATGC 59.269 52.381 18.89 4.57 0.00 4.06
2625 3328 0.323360 GGGATACAACAGGGCAAGCA 60.323 55.000 0.00 0.00 39.74 3.91
2690 3394 1.750018 CATCGCCTGCCACCATCAA 60.750 57.895 0.00 0.00 0.00 2.57
2747 3451 0.695347 CACTCCTGGAGCCCTCTTTT 59.305 55.000 23.43 0.00 32.04 2.27
2765 3469 1.902508 GGACTGTCTCCTTCATCCACA 59.097 52.381 7.85 0.00 35.89 4.17
2863 3567 9.005777 GTATACCTATTCAGACTTCAGAGTAGG 57.994 40.741 14.84 14.84 43.05 3.18
3021 3725 6.838382 TCAGATCACTAGCCACTATACAGTA 58.162 40.000 0.00 0.00 32.21 2.74
3075 3779 1.198178 GCGAAAATTAAGGCACACCGA 59.802 47.619 0.00 0.00 42.76 4.69
3317 4024 2.689471 TGCTGCATCCCATGTGAATTAC 59.311 45.455 0.00 0.00 0.00 1.89
3408 4116 1.063867 ACCTCGACCTGCACCTATACT 60.064 52.381 0.00 0.00 0.00 2.12
3438 4146 2.357517 CCACCACCTGTGTCGAGC 60.358 66.667 0.00 0.00 43.85 5.03
3439 4147 1.300931 CACCACCACCTGTGTCGAG 60.301 63.158 0.00 0.00 43.85 4.04
3508 4216 6.547141 ACAACATGAAACTGGATCAAGAAGAA 59.453 34.615 3.42 0.00 0.00 2.52
3509 4217 6.064060 ACAACATGAAACTGGATCAAGAAGA 58.936 36.000 3.42 0.00 0.00 2.87
3510 4218 6.206243 AGACAACATGAAACTGGATCAAGAAG 59.794 38.462 3.42 0.00 0.00 2.85
3590 4301 4.403585 TCATCATTGAGAAGGAGCTCAG 57.596 45.455 17.19 0.00 44.93 3.35
3604 4315 3.201290 GTCGTCTGGCTTCATCATCATT 58.799 45.455 0.00 0.00 0.00 2.57
3736 4456 4.463879 ACTAGCTGCTGCCTGCCG 62.464 66.667 13.43 5.84 42.00 5.69
3750 4470 0.251922 ACCACCTTCTACCGCCACTA 60.252 55.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.