Multiple sequence alignment - TraesCS7A01G471900

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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 TraesCS7A01G471900 chr7A 100.000 2420 0 0 1 2420 668099779 668097360 0.000000e+00 4470
1 TraesCS7A01G471900 chr7A 90.118 1437 109 16 66 1486 668257532 668256113 0.000000e+00 1836
2 TraesCS7A01G471900 chr7A 85.194 797 101 11 739 1524 668770258 668769468 0.000000e+00 802
3 TraesCS7A01G471900 chr7A 97.159 176 1 3 1516 1690 641434437 641434265 6.540000e-76 294
4 TraesCS7A01G471900 chr7A 84.466 309 34 10 1690 1996 668769475 668769179 2.350000e-75 292
5 TraesCS7A01G471900 chr7A 97.576 165 2 1 1525 1689 685912172 685912334 5.090000e-72 281
6 TraesCS7A01G471900 chr7A 77.262 431 92 3 1028 1455 668250772 668251199 5.170000e-62 248
7 TraesCS7A01G471900 chr7B 92.308 1404 81 12 142 1524 639364467 639363070 0.000000e+00 1969
8 TraesCS7A01G471900 chr7B 90.438 753 41 7 1690 2420 639363077 639362334 0.000000e+00 963
9 TraesCS7A01G471900 chr7B 80.751 1252 211 16 289 1523 639515672 639514434 0.000000e+00 950
10 TraesCS7A01G471900 chr7B 83.713 307 35 8 1690 1992 639514440 639514145 2.370000e-70 276
11 TraesCS7A01G471900 chr7B 86.667 150 18 2 2238 2387 639488079 639488226 5.350000e-37 165
12 TraesCS7A01G471900 chr7D 89.103 1404 119 16 142 1524 576749991 576751381 0.000000e+00 1714
13 TraesCS7A01G471900 chr7D 94.917 1023 51 1 503 1524 576674548 576673526 0.000000e+00 1600
14 TraesCS7A01G471900 chr7D 91.327 588 27 6 1690 2262 576673533 576672955 0.000000e+00 782
15 TraesCS7A01G471900 chr5A 97.590 166 3 1 1525 1690 91122747 91122583 1.420000e-72 283
16 TraesCS7A01G471900 chr3A 97.576 165 2 1 1525 1689 119691779 119691941 5.090000e-72 281
17 TraesCS7A01G471900 chr3A 97.024 168 2 2 1522 1689 174284562 174284726 1.830000e-71 279
18 TraesCS7A01G471900 chr3A 96.407 167 3 1 1523 1689 538841709 538841872 3.070000e-69 272
19 TraesCS7A01G471900 chr1A 97.561 164 2 1 1524 1687 95858866 95859027 1.830000e-71 279
20 TraesCS7A01G471900 chr6A 96.450 169 4 1 1525 1693 465615429 465615263 6.590000e-71 278
21 TraesCS7A01G471900 chr4A 95.455 176 4 3 1520 1695 620192489 620192660 6.590000e-71 278


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 TraesCS7A01G471900 chr7A 668097360 668099779 2419 True 4470 4470 100.000 1 2420 1 chr7A.!!$R2 2419
1 TraesCS7A01G471900 chr7A 668256113 668257532 1419 True 1836 1836 90.118 66 1486 1 chr7A.!!$R3 1420
2 TraesCS7A01G471900 chr7A 668769179 668770258 1079 True 547 802 84.830 739 1996 2 chr7A.!!$R4 1257
3 TraesCS7A01G471900 chr7B 639362334 639364467 2133 True 1466 1969 91.373 142 2420 2 chr7B.!!$R1 2278
4 TraesCS7A01G471900 chr7B 639514145 639515672 1527 True 613 950 82.232 289 1992 2 chr7B.!!$R2 1703
5 TraesCS7A01G471900 chr7D 576749991 576751381 1390 False 1714 1714 89.103 142 1524 1 chr7D.!!$F1 1382
6 TraesCS7A01G471900 chr7D 576672955 576674548 1593 True 1191 1600 93.122 503 2262 2 chr7D.!!$R1 1759

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
685 712 0.179215 GATGTGCTTGCCTTTCGTCG 60.179 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2125 0.110486 TCCAACACAGAAAGCCCCTC 59.89 55.0 0.0 0.0 0.0 4.3 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
27 28 4.827087 CTGCCGCAGCACCGATCT 62.827 66.667 7.61 0.00 46.52 2.75
30 31 2.887568 CCGCAGCACCGATCTGTC 60.888 66.667 0.00 0.00 34.21 3.51
31 32 2.887568 CGCAGCACCGATCTGTCC 60.888 66.667 0.00 0.00 34.21 4.02
32 33 2.887568 GCAGCACCGATCTGTCCG 60.888 66.667 0.00 0.00 34.21 4.79
39 40 2.049985 CGATCTGTCCGGATCCGC 60.050 66.667 29.12 16.47 38.97 5.54
40 41 2.556459 CGATCTGTCCGGATCCGCT 61.556 63.158 29.12 7.88 38.97 5.52
41 42 1.742768 GATCTGTCCGGATCCGCTT 59.257 57.895 29.12 8.42 36.91 4.68
42 43 0.598680 GATCTGTCCGGATCCGCTTG 60.599 60.000 29.12 15.45 36.91 4.01
43 44 2.650813 ATCTGTCCGGATCCGCTTGC 62.651 60.000 29.12 16.87 38.24 4.01
44 45 4.467084 TGTCCGGATCCGCTTGCC 62.467 66.667 29.12 13.29 38.24 4.52
55 56 4.802051 GCTTGCCGGATGCTGGGA 62.802 66.667 5.05 0.00 42.00 4.37
56 57 2.515523 CTTGCCGGATGCTGGGAG 60.516 66.667 5.05 0.00 42.00 4.30
57 58 4.113815 TTGCCGGATGCTGGGAGG 62.114 66.667 5.05 0.00 42.00 4.30
60 61 2.844362 CCGGATGCTGGGAGGCTA 60.844 66.667 0.00 0.00 0.00 3.93
61 62 2.739784 CGGATGCTGGGAGGCTAG 59.260 66.667 0.00 0.00 0.00 3.42
62 63 2.429494 GGATGCTGGGAGGCTAGC 59.571 66.667 6.04 6.04 40.29 3.42
63 64 2.030262 GATGCTGGGAGGCTAGCG 59.970 66.667 9.00 0.00 42.74 4.26
64 65 3.527775 GATGCTGGGAGGCTAGCGG 62.528 68.421 9.00 0.00 42.74 5.52
66 67 3.787001 GCTGGGAGGCTAGCGGTT 61.787 66.667 9.00 0.00 0.00 4.44
67 68 2.187946 CTGGGAGGCTAGCGGTTG 59.812 66.667 9.00 0.00 0.00 3.77
68 69 4.096003 TGGGAGGCTAGCGGTTGC 62.096 66.667 12.66 12.66 43.24 4.17
106 107 4.082523 GCCAGCGCCAGGTACTCA 62.083 66.667 16.78 0.00 34.60 3.41
111 112 2.391389 GCGCCAGGTACTCACAAGC 61.391 63.158 0.00 0.00 34.60 4.01
112 113 1.005037 CGCCAGGTACTCACAAGCA 60.005 57.895 0.00 0.00 34.60 3.91
136 137 2.747855 CGCCCAGAAAGCAGGTCC 60.748 66.667 0.00 0.00 0.00 4.46
137 138 2.361737 GCCCAGAAAGCAGGTCCC 60.362 66.667 0.00 0.00 0.00 4.46
138 139 2.045926 CCCAGAAAGCAGGTCCCG 60.046 66.667 0.00 0.00 0.00 5.14
139 140 2.592993 CCCAGAAAGCAGGTCCCGA 61.593 63.158 0.00 0.00 0.00 5.14
140 141 1.078848 CCAGAAAGCAGGTCCCGAG 60.079 63.158 0.00 0.00 0.00 4.63
141 142 1.743252 CAGAAAGCAGGTCCCGAGC 60.743 63.158 0.00 0.00 0.00 5.03
142 143 2.815647 GAAAGCAGGTCCCGAGCG 60.816 66.667 0.00 0.00 0.00 5.03
143 144 4.394712 AAAGCAGGTCCCGAGCGG 62.395 66.667 1.06 1.06 0.00 5.52
159 160 4.570874 GGGCCCTTCATCTCCGGC 62.571 72.222 17.04 0.00 40.85 6.13
178 179 3.702048 GCACGGTCAGCCCCACTA 61.702 66.667 0.00 0.00 0.00 2.74
185 186 2.109799 CAGCCCCACTATGCCTCG 59.890 66.667 0.00 0.00 0.00 4.63
245 254 2.419297 CCTGTCTCACCTGCACTAATCC 60.419 54.545 0.00 0.00 0.00 3.01
246 255 2.234661 CTGTCTCACCTGCACTAATCCA 59.765 50.000 0.00 0.00 0.00 3.41
263 272 1.355210 CACAACTGTTCCCACGCAC 59.645 57.895 0.00 0.00 0.00 5.34
268 277 1.358759 CTGTTCCCACGCACAAACC 59.641 57.895 0.00 0.00 0.00 3.27
272 281 1.134936 GTTCCCACGCACAAACCTTTT 60.135 47.619 0.00 0.00 0.00 2.27
281 295 4.336993 ACGCACAAACCTTTTATCTGAACA 59.663 37.500 0.00 0.00 0.00 3.18
317 337 3.260884 GTGTTCCCTATCCAGTCTTCACA 59.739 47.826 0.00 0.00 0.00 3.58
337 357 0.318120 ATGGAAACCGCCAGCAAAAG 59.682 50.000 0.00 0.00 42.15 2.27
370 390 3.885521 GCGCTCCATGAAGCTGCC 61.886 66.667 1.32 0.00 40.23 4.85
460 480 0.831307 GGTGGGTATGAGTGGGAGAC 59.169 60.000 0.00 0.00 0.00 3.36
685 712 0.179215 GATGTGCTTGCCTTTCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
858 891 1.765314 GTGCCTGGATCATCACCTAGT 59.235 52.381 0.00 0.00 0.00 2.57
867 900 4.501229 GGATCATCACCTAGTCTGCAGAAG 60.501 50.000 20.19 13.37 0.00 2.85
1024 1059 1.590610 GGAGACGAGCTCTCAGTGCA 61.591 60.000 12.85 0.00 46.81 4.57
1065 1100 2.008045 GCGGTGGTATTCAAGCCGTTA 61.008 52.381 0.00 0.00 43.78 3.18
1092 1127 4.586884 ACTTCATCTACACCGACTCTGTA 58.413 43.478 0.00 0.00 0.00 2.74
1105 1140 4.038361 CGACTCTGTACTGGAATTCGATG 58.962 47.826 0.00 0.00 0.00 3.84
1493 1532 4.276642 TCTGTTTATGGTTGCCATGCATA 58.723 39.130 10.64 0.00 44.84 3.14
1524 1563 5.662674 AGTAAGAACCCTGTGTCTGTATC 57.337 43.478 0.00 0.00 0.00 2.24
1525 1564 5.334421 AGTAAGAACCCTGTGTCTGTATCT 58.666 41.667 0.00 0.00 0.00 1.98
1526 1565 6.491383 AGTAAGAACCCTGTGTCTGTATCTA 58.509 40.000 0.00 0.00 0.00 1.98
1527 1566 7.126733 AGTAAGAACCCTGTGTCTGTATCTAT 58.873 38.462 0.00 0.00 0.00 1.98
1528 1567 5.860941 AGAACCCTGTGTCTGTATCTATG 57.139 43.478 0.00 0.00 0.00 2.23
1529 1568 5.273208 AGAACCCTGTGTCTGTATCTATGT 58.727 41.667 0.00 0.00 0.00 2.29
1530 1569 5.721960 AGAACCCTGTGTCTGTATCTATGTT 59.278 40.000 0.00 0.00 0.00 2.71
1531 1570 6.213600 AGAACCCTGTGTCTGTATCTATGTTT 59.786 38.462 0.00 0.00 0.00 2.83
1532 1571 6.374417 ACCCTGTGTCTGTATCTATGTTTT 57.626 37.500 0.00 0.00 0.00 2.43
1533 1572 6.779860 ACCCTGTGTCTGTATCTATGTTTTT 58.220 36.000 0.00 0.00 0.00 1.94
1534 1573 7.913789 ACCCTGTGTCTGTATCTATGTTTTTA 58.086 34.615 0.00 0.00 0.00 1.52
1535 1574 8.380099 ACCCTGTGTCTGTATCTATGTTTTTAA 58.620 33.333 0.00 0.00 0.00 1.52
1536 1575 9.226606 CCCTGTGTCTGTATCTATGTTTTTAAA 57.773 33.333 0.00 0.00 0.00 1.52
1538 1577 9.760660 CTGTGTCTGTATCTATGTTTTTAAAGC 57.239 33.333 0.00 0.00 0.00 3.51
1539 1578 8.440059 TGTGTCTGTATCTATGTTTTTAAAGCG 58.560 33.333 0.00 0.00 0.00 4.68
1540 1579 8.440833 GTGTCTGTATCTATGTTTTTAAAGCGT 58.559 33.333 0.00 0.00 0.00 5.07
1541 1580 8.653338 TGTCTGTATCTATGTTTTTAAAGCGTC 58.347 33.333 0.00 0.00 0.00 5.19
1542 1581 8.114905 GTCTGTATCTATGTTTTTAAAGCGTCC 58.885 37.037 0.00 0.00 0.00 4.79
1543 1582 7.279313 TCTGTATCTATGTTTTTAAAGCGTCCC 59.721 37.037 0.00 0.00 0.00 4.46
1544 1583 7.107542 TGTATCTATGTTTTTAAAGCGTCCCT 58.892 34.615 0.00 0.00 0.00 4.20
1545 1584 8.259411 TGTATCTATGTTTTTAAAGCGTCCCTA 58.741 33.333 0.00 0.00 0.00 3.53
1546 1585 9.101655 GTATCTATGTTTTTAAAGCGTCCCTAA 57.898 33.333 0.00 0.00 0.00 2.69
1547 1586 7.605410 TCTATGTTTTTAAAGCGTCCCTAAG 57.395 36.000 0.00 0.00 0.00 2.18
1548 1587 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
1549 1588 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
1550 1589 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
1551 1590 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
1552 1591 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
1578 1617 4.144703 GTCGAACCGCTCCCCCTC 62.145 72.222 0.00 0.00 0.00 4.30
1586 1625 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
1596 1635 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
1597 1636 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
1598 1637 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
1599 1638 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
1600 1639 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
1601 1640 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
1602 1641 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
1603 1642 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
1604 1643 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
1605 1644 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
1623 1662 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
1631 1670 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
1632 1671 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
1665 1704 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
1666 1705 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
1667 1706 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
1668 1707 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
1669 1708 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
1688 1727 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
1689 1728 2.223180 GGCGTCGCCTTAAAAACATAGG 60.223 50.000 28.98 0.00 46.69 2.57
1690 1729 2.417586 GCGTCGCCTTAAAAACATAGGT 59.582 45.455 5.75 0.00 0.00 3.08
1691 1730 3.484721 GCGTCGCCTTAAAAACATAGGTC 60.485 47.826 5.75 0.00 0.00 3.85
1692 1731 3.930848 CGTCGCCTTAAAAACATAGGTCT 59.069 43.478 0.00 0.00 0.00 3.85
1693 1732 4.201685 CGTCGCCTTAAAAACATAGGTCTG 60.202 45.833 0.00 0.00 0.00 3.51
1694 1733 4.694037 GTCGCCTTAAAAACATAGGTCTGT 59.306 41.667 0.00 0.00 0.00 3.41
1695 1734 5.870978 GTCGCCTTAAAAACATAGGTCTGTA 59.129 40.000 0.00 0.00 0.00 2.74
1696 1735 6.537660 GTCGCCTTAAAAACATAGGTCTGTAT 59.462 38.462 0.00 0.00 0.00 2.29
1772 1812 3.194116 TGCTTGCATTTCCTCTCCAATTC 59.806 43.478 0.00 0.00 0.00 2.17
1913 1953 6.012858 AGTGTTGTTAAGGGTAGGATGATTCA 60.013 38.462 0.00 0.00 0.00 2.57
1914 1954 6.316390 GTGTTGTTAAGGGTAGGATGATTCAG 59.684 42.308 0.00 0.00 0.00 3.02
1915 1955 6.214615 TGTTGTTAAGGGTAGGATGATTCAGA 59.785 38.462 0.00 0.00 0.00 3.27
1916 1956 6.235231 TGTTAAGGGTAGGATGATTCAGAC 57.765 41.667 0.00 0.00 0.00 3.51
1917 1957 5.964477 TGTTAAGGGTAGGATGATTCAGACT 59.036 40.000 0.00 0.00 0.00 3.24
1918 1958 6.443849 TGTTAAGGGTAGGATGATTCAGACTT 59.556 38.462 0.00 0.00 0.00 3.01
1919 1959 7.037586 TGTTAAGGGTAGGATGATTCAGACTTT 60.038 37.037 0.00 0.00 0.00 2.66
1920 1960 5.622346 AGGGTAGGATGATTCAGACTTTC 57.378 43.478 0.00 0.00 0.00 2.62
1970 2017 0.828762 AGCCTGCAGCCAAACAATCA 60.829 50.000 8.66 0.00 45.47 2.57
2032 2082 2.548057 TCACATCAACTTTCGGAACAGC 59.452 45.455 0.00 0.00 0.00 4.40
2033 2083 2.549754 CACATCAACTTTCGGAACAGCT 59.450 45.455 0.00 0.00 0.00 4.24
2045 2095 2.996621 CGGAACAGCTTCAGGAAACTAG 59.003 50.000 0.00 0.00 40.21 2.57
2062 2112 4.920640 ACTAGGTACCATCTCATTGTCG 57.079 45.455 15.94 0.00 0.00 4.35
2075 2125 4.913345 TCTCATTGTCGTAGTTACAACGTG 59.087 41.667 0.00 0.00 39.51 4.49
2115 2180 1.578206 GCGAAGAGCCAACACCTTCC 61.578 60.000 0.00 0.00 40.81 3.46
2118 2183 0.846693 AAGAGCCAACACCTTCCTGT 59.153 50.000 0.00 0.00 0.00 4.00
2146 2211 1.301716 GGCGACAAGCTGTCCTTCA 60.302 57.895 9.71 0.00 44.20 3.02
2197 2262 4.400251 TGTGGGAGAAAGAATTGATGCATC 59.600 41.667 20.14 20.14 0.00 3.91
2212 2277 1.342975 TGCATCTCTAGGTGCTACCCA 60.343 52.381 15.78 0.00 39.75 4.51
2213 2278 1.342819 GCATCTCTAGGTGCTACCCAG 59.657 57.143 7.98 0.00 39.75 4.45
2225 2290 2.650322 TGCTACCCAGGGTCCAAAATAA 59.350 45.455 17.08 0.00 37.09 1.40
2263 2328 6.917477 TCTCTGTTTATGTTTGTCATGTTTGC 59.083 34.615 0.00 0.00 37.91 3.68
2279 2344 7.786305 CATGTTTGCATGTCTAGTTAACTTG 57.214 36.000 14.49 12.21 45.48 3.16
2280 2345 5.757886 TGTTTGCATGTCTAGTTAACTTGC 58.242 37.500 14.49 16.76 43.98 4.01
2281 2346 4.661993 TTGCATGTCTAGTTAACTTGCG 57.338 40.909 14.49 3.32 45.63 4.85
2282 2347 3.659786 TGCATGTCTAGTTAACTTGCGT 58.340 40.909 14.49 6.87 45.63 5.24
2299 2366 5.067283 ACTTGCGTTTTTGTATCCTGTCTTT 59.933 36.000 0.00 0.00 0.00 2.52
2305 2372 6.801862 CGTTTTTGTATCCTGTCTTTCCAATC 59.198 38.462 0.00 0.00 0.00 2.67
2351 2418 5.982356 TCTCTGTTTCTGCTTACTATGCAT 58.018 37.500 3.79 3.79 39.86 3.96
2379 2446 9.350357 CATCTACAGTAATAACGTGTGTTTACT 57.650 33.333 0.00 0.00 39.54 2.24
2384 2451 7.042523 ACAGTAATAACGTGTGTTTACTTCACC 60.043 37.037 8.93 0.00 39.54 4.02
2417 2484 0.887933 ATTTTACTGCCCTTGGTGCG 59.112 50.000 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.887568 GACAGATCGGTGCTGCGG 60.888 66.667 2.27 0.00 36.86 5.69
14 15 2.887568 GGACAGATCGGTGCTGCG 60.888 66.667 10.15 0.00 36.86 5.18
15 16 2.887568 CGGACAGATCGGTGCTGC 60.888 66.667 14.86 0.00 36.86 5.25
16 17 2.021068 ATCCGGACAGATCGGTGCTG 62.021 60.000 6.12 9.00 46.82 4.41
17 18 1.739338 GATCCGGACAGATCGGTGCT 61.739 60.000 6.12 0.00 46.82 4.40
18 19 1.300233 GATCCGGACAGATCGGTGC 60.300 63.158 6.12 5.17 46.82 5.01
19 20 1.364171 GGATCCGGACAGATCGGTG 59.636 63.158 6.12 0.00 46.82 4.94
20 21 2.194212 CGGATCCGGACAGATCGGT 61.194 63.158 26.95 0.00 46.82 4.69
22 23 2.049985 GCGGATCCGGACAGATCG 60.050 66.667 33.98 7.85 43.07 3.69
23 24 0.598680 CAAGCGGATCCGGACAGATC 60.599 60.000 33.98 16.22 41.69 2.75
24 25 1.443407 CAAGCGGATCCGGACAGAT 59.557 57.895 33.98 1.91 40.19 2.90
25 26 2.892640 CAAGCGGATCCGGACAGA 59.107 61.111 33.98 0.00 40.19 3.41
26 27 2.892425 GCAAGCGGATCCGGACAG 60.892 66.667 33.98 16.01 40.19 3.51
27 28 4.467084 GGCAAGCGGATCCGGACA 62.467 66.667 33.98 0.00 40.19 4.02
31 32 4.609018 ATCCGGCAAGCGGATCCG 62.609 66.667 30.03 30.03 41.93 4.18
32 33 2.974698 CATCCGGCAAGCGGATCC 60.975 66.667 11.84 0.00 43.59 3.36
33 34 3.654020 GCATCCGGCAAGCGGATC 61.654 66.667 11.84 4.96 43.59 3.36
43 44 2.844362 TAGCCTCCCAGCATCCGG 60.844 66.667 0.00 0.00 34.23 5.14
44 45 2.739784 CTAGCCTCCCAGCATCCG 59.260 66.667 0.00 0.00 34.23 4.18
45 46 2.429494 GCTAGCCTCCCAGCATCC 59.571 66.667 2.29 0.00 37.73 3.51
46 47 2.030262 CGCTAGCCTCCCAGCATC 59.970 66.667 9.66 0.00 37.66 3.91
47 48 3.554342 CCGCTAGCCTCCCAGCAT 61.554 66.667 9.66 0.00 37.66 3.79
49 50 3.787001 AACCGCTAGCCTCCCAGC 61.787 66.667 9.66 0.00 0.00 4.85
50 51 2.187946 CAACCGCTAGCCTCCCAG 59.812 66.667 9.66 0.00 0.00 4.45
51 52 4.096003 GCAACCGCTAGCCTCCCA 62.096 66.667 9.66 0.00 34.30 4.37
91 92 1.005037 TTGTGAGTACCTGGCGCTG 60.005 57.895 7.64 0.00 0.00 5.18
92 93 1.293498 CTTGTGAGTACCTGGCGCT 59.707 57.895 7.64 0.00 0.00 5.92
93 94 2.391389 GCTTGTGAGTACCTGGCGC 61.391 63.158 0.00 0.00 0.00 6.53
94 95 0.602638 TTGCTTGTGAGTACCTGGCG 60.603 55.000 0.00 0.00 0.00 5.69
95 96 1.160137 CTTGCTTGTGAGTACCTGGC 58.840 55.000 0.00 0.00 0.00 4.85
96 97 1.813513 CCTTGCTTGTGAGTACCTGG 58.186 55.000 0.00 0.00 0.00 4.45
97 98 1.160137 GCCTTGCTTGTGAGTACCTG 58.840 55.000 0.00 0.00 0.00 4.00
136 137 4.918201 GATGAAGGGCCCGCTCGG 62.918 72.222 18.44 0.48 0.00 4.63
137 138 3.798954 GAGATGAAGGGCCCGCTCG 62.799 68.421 18.44 0.00 0.00 5.03
138 139 2.110006 GAGATGAAGGGCCCGCTC 59.890 66.667 18.44 17.97 0.00 5.03
139 140 3.483869 GGAGATGAAGGGCCCGCT 61.484 66.667 18.44 7.84 0.00 5.52
140 141 4.918201 CGGAGATGAAGGGCCCGC 62.918 72.222 18.44 13.87 33.47 6.13
141 142 4.241555 CCGGAGATGAAGGGCCCG 62.242 72.222 18.44 0.00 39.85 6.13
142 143 4.570874 GCCGGAGATGAAGGGCCC 62.571 72.222 16.46 16.46 39.67 5.80
143 144 3.764160 CTGCCGGAGATGAAGGGCC 62.764 68.421 5.05 0.00 44.96 5.80
144 145 2.203126 CTGCCGGAGATGAAGGGC 60.203 66.667 5.05 0.00 45.76 5.19
145 146 2.203126 GCTGCCGGAGATGAAGGG 60.203 66.667 5.05 0.00 0.00 3.95
245 254 1.355210 GTGCGTGGGAACAGTTGTG 59.645 57.895 0.00 0.00 44.46 3.33
246 255 0.678366 TTGTGCGTGGGAACAGTTGT 60.678 50.000 0.00 0.00 44.46 3.32
263 272 9.533253 AATGTTTCTGTTCAGATAAAAGGTTTG 57.467 29.630 3.28 0.00 0.00 2.93
268 277 7.177392 AGGGGAATGTTTCTGTTCAGATAAAAG 59.823 37.037 3.28 0.00 0.00 2.27
272 281 5.014123 ACAGGGGAATGTTTCTGTTCAGATA 59.986 40.000 3.28 0.00 37.18 1.98
281 295 2.490902 GGGAACACAGGGGAATGTTTCT 60.491 50.000 0.00 0.00 39.13 2.52
317 337 0.755686 TTTTGCTGGCGGTTTCCATT 59.244 45.000 0.00 0.00 35.22 3.16
337 357 2.173382 GCACGACATTGGTGACGC 59.827 61.111 0.00 0.00 45.15 5.19
370 390 1.079127 CAGTAGCCGTCCACCTTGG 60.079 63.158 0.00 0.00 39.43 3.61
460 480 2.822637 ATGGCGGGGTAGATGCAGG 61.823 63.158 0.00 0.00 0.00 4.85
674 701 0.320374 ATCTTCACCGACGAAAGGCA 59.680 50.000 0.00 0.00 41.50 4.75
685 712 2.151202 TGGAAGCGAACAATCTTCACC 58.849 47.619 4.66 0.00 40.20 4.02
867 900 2.039405 CAGGAGCTCAGCAAGGTGC 61.039 63.158 17.19 2.29 45.46 5.01
1065 1100 5.711036 AGAGTCGGTGTAGATGAAGTAAAGT 59.289 40.000 0.00 0.00 0.00 2.66
1092 1127 3.057969 TGCTGAACATCGAATTCCAGT 57.942 42.857 9.57 0.00 0.00 4.00
1105 1140 0.654683 GTGATCGCCTCATGCTGAAC 59.345 55.000 0.00 0.00 35.97 3.18
1120 1155 0.036105 TGCTGAGCCAACATCGTGAT 60.036 50.000 0.23 0.00 0.00 3.06
1435 1470 9.129209 CATGATAAAATCTTGCATCATTAGCAG 57.871 33.333 0.00 0.00 43.75 4.24
1493 1532 4.223032 CACAGGGTTCTTACTAGACCACAT 59.777 45.833 0.00 0.00 0.00 3.21
1524 1563 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
1525 1564 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
1526 1565 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
1527 1566 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
1528 1567 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
1529 1568 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
1530 1569 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
1531 1570 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
1532 1571 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
1533 1572 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
1534 1573 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
1535 1574 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
1561 1600 4.144703 GAGGGGGAGCGGTTCGAC 62.145 72.222 0.00 0.00 0.00 4.20
1569 1608 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
1570 1609 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
1577 1616 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
1578 1617 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
1579 1618 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
1580 1619 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
1581 1620 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
1582 1621 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
1583 1622 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
1584 1623 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
1585 1624 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
1586 1625 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
1587 1626 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
1588 1627 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
1606 1645 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
1614 1653 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
1615 1654 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
1652 1691 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
1653 1692 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
1654 1693 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
1655 1694 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
1656 1695 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
1657 1696 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
1669 1708 2.417586 ACCTATGTTTTTAAGGCGACGC 59.582 45.455 12.43 12.43 33.42 5.19
1670 1709 3.930848 AGACCTATGTTTTTAAGGCGACG 59.069 43.478 0.00 0.00 33.42 5.12
1671 1710 4.694037 ACAGACCTATGTTTTTAAGGCGAC 59.306 41.667 0.00 0.00 33.42 5.19
1672 1711 4.901868 ACAGACCTATGTTTTTAAGGCGA 58.098 39.130 0.00 0.00 33.42 5.54
1673 1712 6.920569 ATACAGACCTATGTTTTTAAGGCG 57.079 37.500 0.00 0.00 34.56 5.52
1674 1713 8.182227 GTGAATACAGACCTATGTTTTTAAGGC 58.818 37.037 0.00 0.00 34.56 4.35
1675 1714 8.674607 GGTGAATACAGACCTATGTTTTTAAGG 58.325 37.037 0.00 0.00 34.56 2.69
1676 1715 9.449719 AGGTGAATACAGACCTATGTTTTTAAG 57.550 33.333 0.00 0.00 41.01 1.85
1677 1716 9.444600 GAGGTGAATACAGACCTATGTTTTTAA 57.555 33.333 0.00 0.00 42.95 1.52
1678 1717 8.598916 TGAGGTGAATACAGACCTATGTTTTTA 58.401 33.333 0.00 0.00 42.95 1.52
1679 1718 7.458397 TGAGGTGAATACAGACCTATGTTTTT 58.542 34.615 0.00 0.00 42.95 1.94
1680 1719 7.016153 TGAGGTGAATACAGACCTATGTTTT 57.984 36.000 0.00 0.00 42.95 2.43
1681 1720 6.620877 TGAGGTGAATACAGACCTATGTTT 57.379 37.500 0.00 0.00 42.95 2.83
1682 1721 6.620877 TTGAGGTGAATACAGACCTATGTT 57.379 37.500 0.00 0.00 42.95 2.71
1683 1722 6.620877 TTTGAGGTGAATACAGACCTATGT 57.379 37.500 0.00 0.00 42.95 2.29
1684 1723 7.770433 TCAATTTGAGGTGAATACAGACCTATG 59.230 37.037 0.00 0.00 42.95 2.23
1685 1724 7.861629 TCAATTTGAGGTGAATACAGACCTAT 58.138 34.615 0.00 0.00 42.95 2.57
1686 1725 7.252612 TCAATTTGAGGTGAATACAGACCTA 57.747 36.000 0.00 0.00 42.95 3.08
1687 1726 6.126863 TCAATTTGAGGTGAATACAGACCT 57.873 37.500 0.00 0.00 45.73 3.85
1688 1727 6.817765 TTCAATTTGAGGTGAATACAGACC 57.182 37.500 0.00 0.00 0.00 3.85
1689 1728 8.968242 GTTTTTCAATTTGAGGTGAATACAGAC 58.032 33.333 0.00 0.00 33.90 3.51
1690 1729 8.912988 AGTTTTTCAATTTGAGGTGAATACAGA 58.087 29.630 0.00 0.00 33.90 3.41
1691 1730 9.533253 AAGTTTTTCAATTTGAGGTGAATACAG 57.467 29.630 0.00 0.00 33.90 2.74
1695 1734 8.992073 GCATAAGTTTTTCAATTTGAGGTGAAT 58.008 29.630 0.00 0.00 33.90 2.57
1696 1735 8.203485 AGCATAAGTTTTTCAATTTGAGGTGAA 58.797 29.630 0.00 0.00 31.99 3.18
1772 1812 8.783093 TGGACCATTTAGCATTAAATTAGATCG 58.217 33.333 0.00 0.00 37.38 3.69
1805 1845 5.480073 ACAAGCACAGAAGAAGAGAGATACT 59.520 40.000 0.00 0.00 0.00 2.12
1913 1953 5.536538 TCATGTCTACACACTCTGAAAGTCT 59.463 40.000 0.00 0.00 35.45 3.24
1914 1954 5.773575 TCATGTCTACACACTCTGAAAGTC 58.226 41.667 0.00 0.00 35.45 3.01
1915 1955 5.791336 TCATGTCTACACACTCTGAAAGT 57.209 39.130 0.00 0.00 39.44 2.66
1916 1956 7.516481 CAAATCATGTCTACACACTCTGAAAG 58.484 38.462 0.00 0.00 34.48 2.62
1917 1957 6.073058 GCAAATCATGTCTACACACTCTGAAA 60.073 38.462 0.00 0.00 34.48 2.69
1918 1958 5.409520 GCAAATCATGTCTACACACTCTGAA 59.590 40.000 0.00 0.00 34.48 3.02
1919 1959 4.931601 GCAAATCATGTCTACACACTCTGA 59.068 41.667 0.00 0.00 34.48 3.27
1920 1960 4.934001 AGCAAATCATGTCTACACACTCTG 59.066 41.667 0.00 0.00 34.48 3.35
1987 2034 9.283768 TGACAATGTGTTCAAAAGATACTACAT 57.716 29.630 0.00 0.00 0.00 2.29
2032 2082 5.422331 TGAGATGGTACCTAGTTTCCTGAAG 59.578 44.000 14.36 0.00 0.00 3.02
2033 2083 5.338632 TGAGATGGTACCTAGTTTCCTGAA 58.661 41.667 14.36 0.00 0.00 3.02
2045 2095 4.650754 ACTACGACAATGAGATGGTACC 57.349 45.455 4.43 4.43 0.00 3.34
2062 2112 1.274447 AGCCCCTCACGTTGTAACTAC 59.726 52.381 0.00 0.00 0.00 2.73
2075 2125 0.110486 TCCAACACAGAAAGCCCCTC 59.890 55.000 0.00 0.00 0.00 4.30
2115 2180 4.047834 TCGCCAAGACAGCAACAG 57.952 55.556 0.00 0.00 0.00 3.16
2146 2211 1.067295 TGAGAAGGTCACCCAGCATT 58.933 50.000 0.00 0.00 0.00 3.56
2172 2237 3.507233 GCATCAATTCTTTCTCCCACACA 59.493 43.478 0.00 0.00 0.00 3.72
2212 2277 4.415596 TGCAACATCTTATTTTGGACCCT 58.584 39.130 0.00 0.00 0.00 4.34
2213 2278 4.799564 TGCAACATCTTATTTTGGACCC 57.200 40.909 0.00 0.00 0.00 4.46
2225 2290 7.334090 ACATAAACAGAGACTATGCAACATCT 58.666 34.615 0.00 0.00 0.00 2.90
2276 2341 4.749245 AGACAGGATACAAAAACGCAAG 57.251 40.909 0.00 0.00 42.67 4.01
2277 2342 5.506649 GGAAAGACAGGATACAAAAACGCAA 60.507 40.000 0.00 0.00 41.41 4.85
2278 2343 4.023536 GGAAAGACAGGATACAAAAACGCA 60.024 41.667 0.00 0.00 41.41 5.24
2279 2344 4.023536 TGGAAAGACAGGATACAAAAACGC 60.024 41.667 0.00 0.00 41.41 4.84
2280 2345 5.682943 TGGAAAGACAGGATACAAAAACG 57.317 39.130 0.00 0.00 41.41 3.60
2281 2346 7.657336 TGATTGGAAAGACAGGATACAAAAAC 58.343 34.615 0.00 0.00 41.41 2.43
2282 2347 7.831691 TGATTGGAAAGACAGGATACAAAAA 57.168 32.000 0.00 0.00 41.41 1.94
2299 2366 4.292186 AGCTGAGCTTTAGTTGATTGGA 57.708 40.909 0.00 0.00 33.89 3.53
2305 2372 3.935828 GGAACCTAGCTGAGCTTTAGTTG 59.064 47.826 14.14 0.00 40.44 3.16
2351 2418 6.519679 ACACACGTTATTACTGTAGATGGA 57.480 37.500 0.00 0.00 0.00 3.41
2368 2435 5.917541 AACATAGGTGAAGTAAACACACG 57.082 39.130 0.00 0.00 39.65 4.49
2379 2446 9.019656 AGTAAAATTGCACATAACATAGGTGAA 57.980 29.630 6.38 0.00 42.63 3.18
2384 2451 6.697019 GGGCAGTAAAATTGCACATAACATAG 59.303 38.462 0.00 0.00 44.32 2.23


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

AutoCloner maintained by Alex Coulton.