Multiple sequence alignment - TraesCS7D01G481900

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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 TraesCS7D01G481900 chr7D 100.000 2384 0 0 1 2384 591920084 591917701 0.000000e+00 4403.0
1 TraesCS7D01G481900 chr7D 86.287 649 79 8 696 1339 591929759 591929116 0.000000e+00 697.0
2 TraesCS7D01G481900 chr7D 88.861 404 31 4 1995 2384 591888152 591887749 3.560000e-133 484.0
3 TraesCS7D01G481900 chr7D 88.119 404 34 4 1995 2384 591908892 591908489 3.590000e-128 468.0
4 TraesCS7D01G481900 chr7D 80.702 114 20 2 1754 1866 335458802 335458690 1.170000e-13 87.9
5 TraesCS7D01G481900 chr7B 89.588 1335 110 10 1 1335 670639863 670641168 0.000000e+00 1668.0
6 TraesCS7D01G481900 chr7B 90.062 1288 100 9 1 1287 670662130 670663390 0.000000e+00 1644.0
7 TraesCS7D01G481900 chr7B 91.353 1168 79 7 1 1168 670512828 670513973 0.000000e+00 1578.0
8 TraesCS7D01G481900 chr7B 91.010 1168 82 8 1 1168 670683917 670685061 0.000000e+00 1554.0
9 TraesCS7D01G481900 chr7B 90.847 1169 81 10 1 1168 670458837 670459980 0.000000e+00 1543.0
10 TraesCS7D01G481900 chr7B 88.642 1171 95 19 192 1339 670724042 670725197 0.000000e+00 1391.0
11 TraesCS7D01G481900 chr7B 92.017 952 70 6 1 950 670751171 670752118 0.000000e+00 1332.0
12 TraesCS7D01G481900 chr7B 90.568 774 52 8 395 1168 670632210 670632962 0.000000e+00 1005.0
13 TraesCS7D01G481900 chr7B 89.889 722 47 8 1 722 670476386 670477081 0.000000e+00 905.0
14 TraesCS7D01G481900 chr7B 89.889 722 47 8 1 722 670494643 670495338 0.000000e+00 905.0
15 TraesCS7D01G481900 chr7B 90.137 659 54 6 686 1338 670812702 670813355 0.000000e+00 846.0
16 TraesCS7D01G481900 chr7B 89.984 619 59 1 717 1335 670477236 670477851 0.000000e+00 797.0
17 TraesCS7D01G481900 chr7B 89.822 619 60 1 717 1335 670495493 670496108 0.000000e+00 791.0
18 TraesCS7D01G481900 chr7B 85.049 408 46 7 1992 2384 670451576 670451983 3.690000e-108 401.0
19 TraesCS7D01G481900 chr7B 85.012 407 47 5 1992 2384 670487076 670487482 3.690000e-108 401.0
20 TraesCS7D01G481900 chr7B 84.767 407 48 5 1992 2384 670505569 670505975 1.720000e-106 396.0
21 TraesCS7D01G481900 chr7B 84.767 407 48 4 1992 2384 670893018 670893424 1.720000e-106 396.0
22 TraesCS7D01G481900 chr7B 84.767 407 48 4 1992 2384 670922471 670922877 1.720000e-106 396.0
23 TraesCS7D01G481900 chr7B 83.784 407 52 4 1992 2384 670882645 670883051 8.050000e-100 374.0
24 TraesCS7D01G481900 chr7B 83.784 407 52 4 1992 2384 671185226 671185632 8.050000e-100 374.0
25 TraesCS7D01G481900 chr7B 90.594 202 19 0 1992 2193 670959471 670959672 3.910000e-68 268.0
26 TraesCS7D01G481900 chr7B 90.594 202 19 0 1992 2193 671210297 671210498 3.910000e-68 268.0
27 TraesCS7D01G481900 chr7B 90.099 202 20 0 1992 2193 671023903 671024104 1.820000e-66 263.0
28 TraesCS7D01G481900 chr7B 90.099 202 20 0 1992 2193 671140296 671140497 1.820000e-66 263.0
29 TraesCS7D01G481900 chr7B 89.604 202 21 0 1992 2193 670915744 670915945 8.460000e-65 257.0
30 TraesCS7D01G481900 chr7B 89.604 202 21 0 1992 2193 671102083 671102284 8.460000e-65 257.0
31 TraesCS7D01G481900 chr7B 90.476 189 18 0 2196 2384 670818437 670818625 1.410000e-62 250.0
32 TraesCS7D01G481900 chr7B 95.122 41 2 0 1722 1762 311478630 311478670 5.500000e-07 65.8
33 TraesCS7D01G481900 chr3B 89.588 1335 110 10 1 1335 19773994 19772689 0.000000e+00 1668.0
34 TraesCS7D01G481900 chr7A 86.866 1340 111 26 1 1339 683145464 683144189 0.000000e+00 1439.0
35 TraesCS7D01G481900 chr7A 88.272 648 66 8 696 1339 683235258 683234617 0.000000e+00 767.0
36 TraesCS7D01G481900 chr7A 87.161 701 55 11 1 701 683194743 683194078 0.000000e+00 763.0
37 TraesCS7D01G481900 chr7A 84.691 405 41 6 1995 2384 683144194 683143796 3.720000e-103 385.0
38 TraesCS7D01G481900 chrUn 90.568 774 52 8 395 1168 372004594 372005346 0.000000e+00 1005.0
39 TraesCS7D01G481900 chrUn 92.157 408 21 6 473 880 147178269 147178665 1.240000e-157 566.0
40 TraesCS7D01G481900 chrUn 86.139 404 42 2 1995 2384 351740298 351739895 7.880000e-115 424.0
41 TraesCS7D01G481900 chrUn 84.108 409 45 6 1996 2384 147127130 147127538 6.220000e-101 377.0
42 TraesCS7D01G481900 chrUn 84.029 407 50 6 1992 2384 147237913 147238318 6.220000e-101 377.0
43 TraesCS7D01G481900 chrUn 84.108 409 45 6 1996 2384 147274467 147274875 6.220000e-101 377.0
44 TraesCS7D01G481900 chrUn 84.108 409 45 6 1996 2384 359975552 359975144 6.220000e-101 377.0
45 TraesCS7D01G481900 chrUn 83.784 407 52 4 1992 2384 147307391 147307797 8.050000e-100 374.0
46 TraesCS7D01G481900 chrUn 83.619 409 47 5 1996 2384 147207936 147208344 1.350000e-97 366.0
47 TraesCS7D01G481900 chrUn 94.180 189 11 0 2196 2384 147195458 147195646 3.000000e-74 289.0
48 TraesCS7D01G481900 chrUn 80.344 407 47 7 1992 2384 147156096 147156483 6.490000e-71 278.0
49 TraesCS7D01G481900 chrUn 90.099 202 20 0 1992 2193 147260411 147260612 1.820000e-66 263.0
50 TraesCS7D01G481900 chrUn 90.099 202 20 0 1992 2193 402104301 402104502 1.820000e-66 263.0
51 TraesCS7D01G481900 chrUn 89.604 202 21 0 1992 2193 147190123 147190324 8.460000e-65 257.0
52 TraesCS7D01G481900 chrUn 88.614 202 22 1 1992 2193 147113252 147113452 6.580000e-61 244.0
53 TraesCS7D01G481900 chr6D 83.279 616 74 12 1342 1949 89058923 89058329 7.500000e-150 540.0
54 TraesCS7D01G481900 chr6D 91.379 58 5 0 1895 1952 89058326 89058269 1.960000e-11 80.5
55 TraesCS7D01G481900 chr6A 88.672 256 28 1 1512 1766 107177785 107177530 6.400000e-81 311.0


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 TraesCS7D01G481900 chr7D 591917701 591920084 2383 True 4403.00 4403 100.0000 1 2384 1 chr7D.!!$R4 2383
1 TraesCS7D01G481900 chr7D 591929116 591929759 643 True 697.00 697 86.2870 696 1339 1 chr7D.!!$R5 643
2 TraesCS7D01G481900 chr7B 670639863 670641168 1305 False 1668.00 1668 89.5880 1 1335 1 chr7B.!!$F8 1334
3 TraesCS7D01G481900 chr7B 670662130 670663390 1260 False 1644.00 1644 90.0620 1 1287 1 chr7B.!!$F9 1286
4 TraesCS7D01G481900 chr7B 670512828 670513973 1145 False 1578.00 1578 91.3530 1 1168 1 chr7B.!!$F6 1167
5 TraesCS7D01G481900 chr7B 670683917 670685061 1144 False 1554.00 1554 91.0100 1 1168 1 chr7B.!!$F10 1167
6 TraesCS7D01G481900 chr7B 670458837 670459980 1143 False 1543.00 1543 90.8470 1 1168 1 chr7B.!!$F3 1167
7 TraesCS7D01G481900 chr7B 670724042 670725197 1155 False 1391.00 1391 88.6420 192 1339 1 chr7B.!!$F11 1147
8 TraesCS7D01G481900 chr7B 670751171 670752118 947 False 1332.00 1332 92.0170 1 950 1 chr7B.!!$F12 949
9 TraesCS7D01G481900 chr7B 670632210 670632962 752 False 1005.00 1005 90.5680 395 1168 1 chr7B.!!$F7 773
10 TraesCS7D01G481900 chr7B 670476386 670477851 1465 False 851.00 905 89.9365 1 1335 2 chr7B.!!$F25 1334
11 TraesCS7D01G481900 chr7B 670494643 670496108 1465 False 848.00 905 89.8555 1 1335 2 chr7B.!!$F26 1334
12 TraesCS7D01G481900 chr7B 670812702 670813355 653 False 846.00 846 90.1370 686 1338 1 chr7B.!!$F13 652
13 TraesCS7D01G481900 chr3B 19772689 19773994 1305 True 1668.00 1668 89.5880 1 1335 1 chr3B.!!$R1 1334
14 TraesCS7D01G481900 chr7A 683143796 683145464 1668 True 912.00 1439 85.7785 1 2384 2 chr7A.!!$R3 2383
15 TraesCS7D01G481900 chr7A 683234617 683235258 641 True 767.00 767 88.2720 696 1339 1 chr7A.!!$R2 643
16 TraesCS7D01G481900 chr7A 683194078 683194743 665 True 763.00 763 87.1610 1 701 1 chr7A.!!$R1 700
17 TraesCS7D01G481900 chrUn 372004594 372005346 752 False 1005.00 1005 90.5680 395 1168 1 chrUn.!!$F12 773
18 TraesCS7D01G481900 chr6D 89058269 89058923 654 True 310.25 540 87.3290 1342 1952 2 chr6D.!!$R1 610

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
584 624 0.108756 GCTTTTCTACCGAGGACGCT 60.109 55.0 0.0 0.0 38.29 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 2030 0.035056 GTAGCACCAACAGGAGCCAT 60.035 55.0 0.28 0.0 39.5 4.4 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
72 73 4.670735 CGACCGGTTTGTTCAAATACCATC 60.671 45.833 9.42 0.00 0.00 3.51
76 77 6.661805 ACCGGTTTGTTCAAATACCATCTAAT 59.338 34.615 0.00 0.00 0.00 1.73
140 141 3.492656 CCTGTATCACTATCGTGGTTGGG 60.493 52.174 0.00 0.00 41.53 4.12
350 351 8.947304 TTTGAATATTCCGTAAACCGTTAAAC 57.053 30.769 12.90 0.00 33.66 2.01
404 413 7.756722 CGTTGGAAAGAAATGCATTAGAAGAAT 59.243 33.333 13.39 0.00 0.00 2.40
572 581 3.089784 CGTATGCGGCGCTTTTCT 58.910 55.556 33.26 14.18 0.00 2.52
584 624 0.108756 GCTTTTCTACCGAGGACGCT 60.109 55.000 0.00 0.00 38.29 5.07
683 723 5.940192 ATCTTTTGTCGTGTTAATCAGCA 57.060 34.783 0.00 0.00 0.00 4.41
705 745 1.061566 GAAAGCGGTGCGTGTATAACC 59.938 52.381 0.00 0.00 0.00 2.85
796 1000 3.511699 ACGTGCACGCCATGATATATAG 58.488 45.455 37.35 8.10 44.43 1.31
797 1001 3.056821 ACGTGCACGCCATGATATATAGT 60.057 43.478 37.35 11.31 44.43 2.12
798 1002 4.157105 ACGTGCACGCCATGATATATAGTA 59.843 41.667 37.35 0.00 44.43 1.82
841 1051 1.195448 CACACTCCGTTCATGTTGAGC 59.805 52.381 0.00 0.00 0.00 4.26
845 1055 1.671054 CCGTTCATGTTGAGCCGGT 60.671 57.895 1.90 0.00 37.69 5.28
951 1164 2.011947 CCATCGTCTTGCACACATCAT 58.988 47.619 0.00 0.00 0.00 2.45
954 1167 0.519792 CGTCTTGCACACATCATGCG 60.520 55.000 0.00 0.00 46.49 4.73
977 1190 0.537143 ACCTCAAAGCGCATTCACCA 60.537 50.000 11.47 0.00 0.00 4.17
978 1191 0.597568 CCTCAAAGCGCATTCACCAA 59.402 50.000 11.47 0.00 0.00 3.67
1029 1242 3.423154 GCGGCGGGTGAGAACAAG 61.423 66.667 9.78 0.00 0.00 3.16
1037 1250 3.735591 CGGGTGAGAACAAGAGGTTAAA 58.264 45.455 0.00 0.00 40.63 1.52
1200 1414 2.861935 CACAAAGGCAAAGCTCAACTTG 59.138 45.455 0.00 0.00 39.09 3.16
1215 1429 4.733725 TTGCCCTACCCTCCGCCT 62.734 66.667 0.00 0.00 0.00 5.52
1313 1533 4.360405 GTTGCCACCGGACCCCAT 62.360 66.667 9.46 0.00 0.00 4.00
1345 1565 3.299190 CGCCGCCCAAGGGAAAAA 61.299 61.111 9.92 0.00 37.50 1.94
1373 1593 4.456806 GACATGGGTCGTATGCCC 57.543 61.111 0.00 7.33 46.26 5.36
1374 1594 1.830145 GACATGGGTCGTATGCCCT 59.170 57.895 13.51 0.00 46.22 5.19
1395 1615 2.885113 TCGTGAGACCCGCATCAG 59.115 61.111 0.00 0.00 33.31 2.90
1396 1616 2.887568 CGTGAGACCCGCATCAGC 60.888 66.667 0.00 0.00 37.42 4.26
1398 1618 1.812922 GTGAGACCCGCATCAGCTG 60.813 63.158 7.63 7.63 39.10 4.24
1399 1619 2.285773 TGAGACCCGCATCAGCTGT 61.286 57.895 14.67 0.00 39.10 4.40
1401 1621 1.364626 GAGACCCGCATCAGCTGTTG 61.365 60.000 18.61 18.61 39.10 3.33
1405 1625 1.236616 CCCGCATCAGCTGTTGACAA 61.237 55.000 25.50 0.67 38.99 3.18
1406 1626 0.110056 CCGCATCAGCTGTTGACAAC 60.110 55.000 25.50 11.54 38.99 3.32
1421 1641 2.290367 TGACAACTGGCAAACGAATCTG 59.710 45.455 0.00 0.00 0.00 2.90
1430 1650 2.922335 GCAAACGAATCTGAAAGCACCC 60.922 50.000 0.00 0.00 0.00 4.61
1435 1655 0.332972 AATCTGAAAGCACCCTCCCC 59.667 55.000 0.00 0.00 0.00 4.81
1447 1669 1.275421 CCCTCCCCTTCTTCCACCTC 61.275 65.000 0.00 0.00 0.00 3.85
1450 1672 0.547712 TCCCCTTCTTCCACCTCTGG 60.548 60.000 0.00 0.00 39.23 3.86
1455 1677 0.321671 TTCTTCCACCTCTGGCTTCG 59.678 55.000 0.00 0.00 37.49 3.79
1462 1684 0.033991 ACCTCTGGCTTCGCTCTCTA 60.034 55.000 0.00 0.00 0.00 2.43
1476 1699 7.392494 TTCGCTCTCTACTCTTTCTTATTCA 57.608 36.000 0.00 0.00 0.00 2.57
1481 1704 5.950549 TCTCTACTCTTTCTTATTCACCGGT 59.049 40.000 0.00 0.00 0.00 5.28
1484 1707 2.678336 CTCTTTCTTATTCACCGGTGGC 59.322 50.000 33.40 0.00 0.00 5.01
1488 1711 0.675522 CTTATTCACCGGTGGCCGTT 60.676 55.000 33.40 16.07 46.80 4.44
1489 1712 0.612229 TTATTCACCGGTGGCCGTTA 59.388 50.000 33.40 11.27 46.80 3.18
1497 1720 0.810031 CGGTGGCCGTTATTCTCCTG 60.810 60.000 0.00 0.00 42.73 3.86
1504 1728 3.383825 GGCCGTTATTCTCCTGACTTCTA 59.616 47.826 0.00 0.00 0.00 2.10
1516 1740 0.528470 GACTTCTACACAGGCTCGCT 59.472 55.000 0.00 0.00 0.00 4.93
1551 1775 2.923655 CGTAGATGACGTGCAGTTTCAT 59.076 45.455 0.00 4.65 46.86 2.57
1559 1783 5.277825 TGACGTGCAGTTTCATTAAAAAGG 58.722 37.500 0.00 0.00 0.00 3.11
1591 1815 3.998672 GTGGCGGTTCCTCGTGGA 61.999 66.667 1.10 1.10 41.36 4.02
1596 1820 2.273179 CGGTTCCTCGTGGACTCCA 61.273 63.158 19.95 0.00 43.06 3.86
1609 1833 1.139058 GGACTCCATATCTTGTGGCGT 59.861 52.381 0.00 0.00 37.38 5.68
1612 1836 0.104120 TCCATATCTTGTGGCGTCGG 59.896 55.000 0.00 0.00 36.66 4.79
1620 1844 3.195698 GTGGCGTCGGGATCTTGC 61.196 66.667 0.00 0.00 0.00 4.01
1637 1861 3.967335 CGGATCCCGCTCGACCTC 61.967 72.222 6.06 0.00 41.17 3.85
1694 1918 2.048023 CGTGCTGATGGTGGCCATT 61.048 57.895 9.72 0.00 45.26 3.16
1717 1941 2.202987 CGAGCATGGCAGGGACTC 60.203 66.667 0.00 0.00 34.60 3.36
1719 1943 1.395045 CGAGCATGGCAGGGACTCTA 61.395 60.000 0.00 0.00 34.60 2.43
1720 1944 0.392336 GAGCATGGCAGGGACTCTAG 59.608 60.000 0.00 0.00 34.60 2.43
1730 1954 1.043673 GGGACTCTAGCATGGACGGT 61.044 60.000 0.00 0.00 0.00 4.83
1774 1999 0.671251 GAGGAGATGTCAGGGCGTAG 59.329 60.000 0.00 0.00 0.00 3.51
1776 2001 0.755698 GGAGATGTCAGGGCGTAGGA 60.756 60.000 0.00 0.00 0.00 2.94
1777 2002 0.386113 GAGATGTCAGGGCGTAGGAC 59.614 60.000 0.00 0.00 0.00 3.85
1790 2015 1.754621 TAGGACTGCAGCGAGGGAG 60.755 63.158 15.27 0.00 0.00 4.30
1797 2022 2.493973 CAGCGAGGGAGTGCTCTC 59.506 66.667 7.26 7.26 40.03 3.20
1805 2030 2.497675 GAGGGAGTGCTCTCATGTGTTA 59.502 50.000 17.04 0.00 41.50 2.41
1806 2031 3.110705 AGGGAGTGCTCTCATGTGTTAT 58.889 45.455 17.04 0.00 42.05 1.89
1808 2033 3.201290 GGAGTGCTCTCATGTGTTATGG 58.799 50.000 17.04 0.00 42.05 2.74
1831 2056 1.238439 CTGTTGGTGCTACTTGGTGG 58.762 55.000 0.00 0.00 0.00 4.61
1832 2057 0.548989 TGTTGGTGCTACTTGGTGGT 59.451 50.000 0.00 0.00 0.00 4.16
1833 2058 1.064314 TGTTGGTGCTACTTGGTGGTT 60.064 47.619 0.00 0.00 0.00 3.67
1846 2071 0.179124 GGTGGTTCTAGCTGCTCGAG 60.179 60.000 4.91 8.45 0.00 4.04
1848 2073 1.323271 TGGTTCTAGCTGCTCGAGGG 61.323 60.000 15.58 0.00 0.00 4.30
1853 2078 3.740495 TAGCTGCTCGAGGGGAGGG 62.740 68.421 15.58 0.00 43.36 4.30
1859 2084 2.286962 TCGAGGGGAGGGGAGAGA 60.287 66.667 0.00 0.00 0.00 3.10
1860 2085 2.197324 CGAGGGGAGGGGAGAGAG 59.803 72.222 0.00 0.00 0.00 3.20
1861 2086 2.387772 CGAGGGGAGGGGAGAGAGA 61.388 68.421 0.00 0.00 0.00 3.10
1862 2087 1.541672 GAGGGGAGGGGAGAGAGAG 59.458 68.421 0.00 0.00 0.00 3.20
1863 2088 0.996762 GAGGGGAGGGGAGAGAGAGA 60.997 65.000 0.00 0.00 0.00 3.10
1864 2089 0.556380 AGGGGAGGGGAGAGAGAGAA 60.556 60.000 0.00 0.00 0.00 2.87
1865 2090 0.340208 GGGGAGGGGAGAGAGAGAAA 59.660 60.000 0.00 0.00 0.00 2.52
1866 2091 1.061735 GGGGAGGGGAGAGAGAGAAAT 60.062 57.143 0.00 0.00 0.00 2.17
1867 2092 2.325484 GGGAGGGGAGAGAGAGAAATC 58.675 57.143 0.00 0.00 0.00 2.17
1868 2093 2.359781 GGGAGGGGAGAGAGAGAAATCA 60.360 54.545 0.00 0.00 0.00 2.57
1869 2094 3.379452 GGAGGGGAGAGAGAGAAATCAA 58.621 50.000 0.00 0.00 0.00 2.57
1870 2095 3.777522 GGAGGGGAGAGAGAGAAATCAAA 59.222 47.826 0.00 0.00 0.00 2.69
1871 2096 4.383661 GGAGGGGAGAGAGAGAAATCAAAC 60.384 50.000 0.00 0.00 0.00 2.93
1872 2097 3.196685 AGGGGAGAGAGAGAAATCAAACG 59.803 47.826 0.00 0.00 0.00 3.60
1873 2098 3.195825 GGGGAGAGAGAGAAATCAAACGA 59.804 47.826 0.00 0.00 0.00 3.85
1874 2099 4.429108 GGGAGAGAGAGAAATCAAACGAG 58.571 47.826 0.00 0.00 0.00 4.18
1875 2100 4.158764 GGGAGAGAGAGAAATCAAACGAGA 59.841 45.833 0.00 0.00 0.00 4.04
1876 2101 5.339990 GGAGAGAGAGAAATCAAACGAGAG 58.660 45.833 0.00 0.00 0.00 3.20
1877 2102 5.124776 GGAGAGAGAGAAATCAAACGAGAGA 59.875 44.000 0.00 0.00 0.00 3.10
1878 2103 6.183360 GGAGAGAGAGAAATCAAACGAGAGAT 60.183 42.308 0.00 0.00 0.00 2.75
1879 2104 7.169158 AGAGAGAGAAATCAAACGAGAGATT 57.831 36.000 0.00 0.00 36.09 2.40
1889 2114 5.760193 CAAACGAGAGATTGAAGTCAGAG 57.240 43.478 0.00 0.00 45.49 3.35
1904 2129 0.329596 CAGAGGTGGAAGAAAGGGGG 59.670 60.000 0.00 0.00 0.00 5.40
1916 2141 2.386391 AAAGGGGGAGGGTGCTTTGG 62.386 60.000 0.00 0.00 0.00 3.28
1945 2227 2.034687 CCAACTGTCAGCAGGGGG 59.965 66.667 0.00 0.00 46.62 5.40
1960 2242 4.131088 GGGAGCGGGTCTCACGAC 62.131 72.222 7.19 0.00 43.70 4.34
1961 2243 4.477975 GGAGCGGGTCTCACGACG 62.478 72.222 7.19 0.00 43.70 5.12
1962 2244 4.477975 GAGCGGGTCTCACGACGG 62.478 72.222 0.00 0.00 41.16 4.79
1966 2248 3.756727 GGGTCTCACGACGGGGAC 61.757 72.222 9.43 9.43 41.16 4.46
1978 2260 4.201951 GGGGACGTACGACTCGTA 57.798 61.111 24.41 7.22 41.54 3.43
2003 2285 3.625314 TTTTTCCCACCCAAGCTGT 57.375 47.368 0.00 0.00 0.00 4.40
2011 2293 2.817844 CCCACCCAAGCTGTTAGTTTAC 59.182 50.000 0.00 0.00 0.00 2.01
2079 2361 0.748005 GCATACCCGTTCCTGCACAT 60.748 55.000 0.00 0.00 34.77 3.21
2080 2362 1.299541 CATACCCGTTCCTGCACATC 58.700 55.000 0.00 0.00 0.00 3.06
2089 2371 2.046023 CTGCACATCCCGCTTCCA 60.046 61.111 0.00 0.00 0.00 3.53
2111 2393 1.799519 CGAGCACGTCTCAGTCTGC 60.800 63.158 13.14 0.00 41.98 4.26
2115 2397 1.735920 CACGTCTCAGTCTGCAGCC 60.736 63.158 9.47 0.00 0.00 4.85
2117 2399 2.965783 GTCTCAGTCTGCAGCCGA 59.034 61.111 9.47 4.08 0.00 5.54
2118 2400 1.515020 GTCTCAGTCTGCAGCCGAT 59.485 57.895 9.47 0.00 0.00 4.18
2143 2425 2.256591 GCACACACCTGCTCCACAG 61.257 63.158 0.00 0.00 46.77 3.66
2149 2431 2.359602 CCTGCTCCACAGCCACAG 60.360 66.667 0.00 0.00 46.26 3.66
2150 2432 3.054503 CTGCTCCACAGCCACAGC 61.055 66.667 0.00 0.00 46.26 4.40
2217 2513 4.304432 CCCTAGGGGCTTCCTCTC 57.696 66.667 21.44 0.00 44.06 3.20
2218 2514 1.314867 CCCTAGGGGCTTCCTCTCA 59.685 63.158 21.44 0.00 44.06 3.27
2243 2540 2.031120 CTGGTGTTCAAGAAGCCCAAA 58.969 47.619 3.01 0.00 0.00 3.28
2250 2547 3.011566 TCAAGAAGCCCAAACTGTTCA 57.988 42.857 0.00 0.00 0.00 3.18
2259 2556 1.196808 CCAAACTGTTCATCGTTCCCG 59.803 52.381 0.00 0.00 0.00 5.14
2285 2582 1.902508 CCTAGTGCTCCAACAGAAGGA 59.097 52.381 0.00 0.00 0.00 3.36
2290 2587 1.202806 TGCTCCAACAGAAGGAACTGG 60.203 52.381 0.00 0.00 40.86 4.00
2322 2619 1.094785 CAAGCCGTGGTATTTCCCTG 58.905 55.000 0.00 0.00 34.77 4.45
2323 2620 0.034477 AAGCCGTGGTATTTCCCTGG 60.034 55.000 0.00 0.00 34.77 4.45
2325 2622 1.029947 GCCGTGGTATTTCCCTGGTG 61.030 60.000 0.00 0.00 33.60 4.17
2331 2628 1.408822 GGTATTTCCCTGGTGCTCCTG 60.409 57.143 6.34 5.52 34.23 3.86
2378 2675 1.040646 GCACCGAGATCCCATAGTCA 58.959 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.626302 TCATTTAAACCGGACCAATTTCATC 58.374 36.000 9.46 0.00 0.00 2.92
72 73 9.948964 TCCATCAAATATCTGGTCACATATTAG 57.051 33.333 0.00 0.00 0.00 1.73
76 77 8.542926 CCTATCCATCAAATATCTGGTCACATA 58.457 37.037 0.00 0.00 0.00 2.29
89 90 4.744237 CCATCCAACCCTATCCATCAAAT 58.256 43.478 0.00 0.00 0.00 2.32
140 141 3.365472 TCCCCTAAAACGGACCTAGTAC 58.635 50.000 0.00 0.00 0.00 2.73
350 351 9.774742 GGTTAAGCATCAATGTTAAGTTAGAAG 57.225 33.333 0.00 0.00 0.00 2.85
404 413 6.198966 GTCTTTTCTTAAACGGACGTTGTCTA 59.801 38.462 11.12 0.00 38.47 2.59
584 624 6.403049 TGCTGATTTTACTACTTTCGATGGA 58.597 36.000 0.00 0.00 0.00 3.41
683 723 2.373540 TATACACGCACCGCTTTCTT 57.626 45.000 0.00 0.00 0.00 2.52
705 745 7.431249 TGGTTGTATTTCTCCTAGCTTATACG 58.569 38.462 0.00 0.00 0.00 3.06
816 1026 2.762745 ACATGAACGGAGTGTGGTTAC 58.237 47.619 0.00 0.00 45.00 2.50
841 1051 1.301716 CTCACTGGAACCACACCGG 60.302 63.158 0.00 0.00 42.50 5.28
845 1055 1.451504 CAGCCTCACTGGAACCACA 59.548 57.895 0.00 0.00 43.19 4.17
951 1164 2.664851 CGCTTTGAGGTGGACGCA 60.665 61.111 0.00 0.00 0.00 5.24
954 1167 0.169009 GAATGCGCTTTGAGGTGGAC 59.831 55.000 13.85 0.00 0.00 4.02
977 1190 1.268899 CCTCTACCACAGTCGAACGTT 59.731 52.381 0.00 0.00 0.00 3.99
978 1191 0.879765 CCTCTACCACAGTCGAACGT 59.120 55.000 0.00 0.00 0.00 3.99
1029 1242 4.918588 TCTTTCTCACCCCATTTAACCTC 58.081 43.478 0.00 0.00 0.00 3.85
1037 1250 1.002857 CCCCTTCTTTCTCACCCCAT 58.997 55.000 0.00 0.00 0.00 4.00
1058 1271 2.551270 CTGCGGCGAACTTGTCAC 59.449 61.111 12.98 0.00 0.00 3.67
1061 1274 1.079127 ATAGCTGCGGCGAACTTGT 60.079 52.632 12.98 0.00 44.37 3.16
1215 1429 3.392947 TCACCTCCATTACCAGTTTGACA 59.607 43.478 0.00 0.00 0.00 3.58
1265 1479 3.785189 AAGAGCGGTGCGTCGTGTT 62.785 57.895 0.00 0.00 0.00 3.32
1266 1480 3.785189 AAAGAGCGGTGCGTCGTGT 62.785 57.895 0.00 0.00 0.00 4.49
1365 1585 0.248661 CTCACGACAGAGGGCATACG 60.249 60.000 0.00 0.00 31.94 3.06
1371 1591 2.701780 CGGGTCTCACGACAGAGGG 61.702 68.421 0.00 0.00 42.05 4.30
1373 1593 1.938657 ATGCGGGTCTCACGACAGAG 61.939 60.000 0.00 0.00 42.05 3.35
1374 1594 1.934220 GATGCGGGTCTCACGACAGA 61.934 60.000 0.00 0.00 42.05 3.41
1394 1614 1.134946 GTTTGCCAGTTGTCAACAGCT 59.865 47.619 23.32 4.66 37.94 4.24
1395 1615 1.559831 GTTTGCCAGTTGTCAACAGC 58.440 50.000 17.78 18.36 34.61 4.40
1396 1616 1.400142 TCGTTTGCCAGTTGTCAACAG 59.600 47.619 17.78 9.68 0.00 3.16
1398 1618 2.553079 TTCGTTTGCCAGTTGTCAAC 57.447 45.000 7.68 7.68 0.00 3.18
1399 1619 2.948979 AGATTCGTTTGCCAGTTGTCAA 59.051 40.909 0.00 0.00 0.00 3.18
1401 1621 2.548057 TCAGATTCGTTTGCCAGTTGTC 59.452 45.455 0.00 0.00 0.00 3.18
1405 1625 2.030805 GCTTTCAGATTCGTTTGCCAGT 60.031 45.455 0.00 0.00 0.00 4.00
1406 1626 2.030893 TGCTTTCAGATTCGTTTGCCAG 60.031 45.455 0.00 0.00 0.00 4.85
1421 1641 0.405973 AAGAAGGGGAGGGTGCTTTC 59.594 55.000 0.00 0.00 0.00 2.62
1430 1650 0.908198 CAGAGGTGGAAGAAGGGGAG 59.092 60.000 0.00 0.00 0.00 4.30
1455 1677 5.974751 CGGTGAATAAGAAAGAGTAGAGAGC 59.025 44.000 0.00 0.00 0.00 4.09
1462 1684 3.868754 GCCACCGGTGAATAAGAAAGAGT 60.869 47.826 36.07 0.00 0.00 3.24
1481 1704 1.568504 AGTCAGGAGAATAACGGCCA 58.431 50.000 2.24 0.00 0.00 5.36
1484 1707 5.105877 TGTGTAGAAGTCAGGAGAATAACGG 60.106 44.000 0.00 0.00 0.00 4.44
1497 1720 0.528470 AGCGAGCCTGTGTAGAAGTC 59.472 55.000 0.00 0.00 0.00 3.01
1516 1740 4.720902 TACGCCCTCGGACCGACA 62.721 66.667 13.88 0.00 40.69 4.35
1544 1768 5.009310 GGTGGACGACCTTTTTAATGAAACT 59.991 40.000 5.33 0.00 42.25 2.66
1546 1770 5.441709 GGTGGACGACCTTTTTAATGAAA 57.558 39.130 5.33 0.00 42.25 2.69
1559 1783 2.657237 CACAGGGAGGTGGACGAC 59.343 66.667 0.00 0.00 35.13 4.34
1572 1796 2.738521 CACGAGGAACCGCCACAG 60.739 66.667 0.00 0.00 40.02 3.66
1596 1820 1.000955 GATCCCGACGCCACAAGATAT 59.999 52.381 0.00 0.00 0.00 1.63
1660 1884 2.653448 CGAGCTGCTCCGTCATCG 60.653 66.667 22.97 7.41 0.00 3.84
1663 1887 4.724602 GCACGAGCTGCTCCGTCA 62.725 66.667 22.97 0.00 43.33 4.35
1694 1918 4.100084 CTGCCATGCTCGGGTCCA 62.100 66.667 0.00 0.00 0.00 4.02
1717 1941 1.369091 GCACCAACCGTCCATGCTAG 61.369 60.000 0.00 0.00 33.44 3.42
1719 1943 2.672996 GCACCAACCGTCCATGCT 60.673 61.111 0.00 0.00 33.44 3.79
1720 1944 2.672996 AGCACCAACCGTCCATGC 60.673 61.111 0.00 0.00 36.52 4.06
1730 1954 4.299796 GCCCCCTTCCAGCACCAA 62.300 66.667 0.00 0.00 0.00 3.67
1774 1999 3.386237 ACTCCCTCGCTGCAGTCC 61.386 66.667 16.64 0.00 0.00 3.85
1776 2001 4.385405 GCACTCCCTCGCTGCAGT 62.385 66.667 16.64 0.00 0.00 4.40
1777 2002 4.079850 AGCACTCCCTCGCTGCAG 62.080 66.667 10.11 10.11 37.02 4.41
1784 2009 0.901124 ACACATGAGAGCACTCCCTC 59.099 55.000 8.77 0.00 41.99 4.30
1790 2015 2.611292 GAGCCATAACACATGAGAGCAC 59.389 50.000 0.00 0.00 0.00 4.40
1797 2022 2.424601 CCAACAGGAGCCATAACACATG 59.575 50.000 0.00 0.00 0.00 3.21
1805 2030 0.035056 GTAGCACCAACAGGAGCCAT 60.035 55.000 0.28 0.00 39.50 4.40
1806 2031 1.127567 AGTAGCACCAACAGGAGCCA 61.128 55.000 0.28 0.00 39.50 4.75
1808 2033 1.160137 CAAGTAGCACCAACAGGAGC 58.840 55.000 0.00 0.00 39.04 4.70
1831 2056 1.038130 TCCCCTCGAGCAGCTAGAAC 61.038 60.000 6.99 0.00 0.00 3.01
1832 2057 0.753479 CTCCCCTCGAGCAGCTAGAA 60.753 60.000 6.99 0.00 0.00 2.10
1833 2058 1.152860 CTCCCCTCGAGCAGCTAGA 60.153 63.158 6.99 5.00 0.00 2.43
1846 2071 0.340208 TTTCTCTCTCTCCCCTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
1848 2073 3.039252 TGATTTCTCTCTCTCCCCTCC 57.961 52.381 0.00 0.00 0.00 4.30
1853 2078 5.124776 TCTCTCGTTTGATTTCTCTCTCTCC 59.875 44.000 0.00 0.00 0.00 3.71
1859 2084 7.158021 ACTTCAATCTCTCGTTTGATTTCTCT 58.842 34.615 0.00 0.00 32.27 3.10
1860 2085 7.116948 TGACTTCAATCTCTCGTTTGATTTCTC 59.883 37.037 0.00 0.00 32.27 2.87
1861 2086 6.931281 TGACTTCAATCTCTCGTTTGATTTCT 59.069 34.615 0.00 0.00 32.27 2.52
1862 2087 7.116948 TCTGACTTCAATCTCTCGTTTGATTTC 59.883 37.037 0.00 0.00 32.27 2.17
1863 2088 6.931281 TCTGACTTCAATCTCTCGTTTGATTT 59.069 34.615 0.00 0.00 32.27 2.17
1864 2089 6.459066 TCTGACTTCAATCTCTCGTTTGATT 58.541 36.000 0.00 0.00 32.27 2.57
1865 2090 6.030548 TCTGACTTCAATCTCTCGTTTGAT 57.969 37.500 0.00 0.00 32.27 2.57
1866 2091 5.453567 TCTGACTTCAATCTCTCGTTTGA 57.546 39.130 0.00 0.00 0.00 2.69
1867 2092 4.624882 CCTCTGACTTCAATCTCTCGTTTG 59.375 45.833 0.00 0.00 0.00 2.93
1868 2093 4.282195 ACCTCTGACTTCAATCTCTCGTTT 59.718 41.667 0.00 0.00 0.00 3.60
1869 2094 3.829601 ACCTCTGACTTCAATCTCTCGTT 59.170 43.478 0.00 0.00 0.00 3.85
1870 2095 3.192422 CACCTCTGACTTCAATCTCTCGT 59.808 47.826 0.00 0.00 0.00 4.18
1871 2096 3.428725 CCACCTCTGACTTCAATCTCTCG 60.429 52.174 0.00 0.00 0.00 4.04
1872 2097 3.766591 TCCACCTCTGACTTCAATCTCTC 59.233 47.826 0.00 0.00 0.00 3.20
1873 2098 3.784178 TCCACCTCTGACTTCAATCTCT 58.216 45.455 0.00 0.00 0.00 3.10
1874 2099 4.221703 TCTTCCACCTCTGACTTCAATCTC 59.778 45.833 0.00 0.00 0.00 2.75
1875 2100 4.163427 TCTTCCACCTCTGACTTCAATCT 58.837 43.478 0.00 0.00 0.00 2.40
1876 2101 4.543590 TCTTCCACCTCTGACTTCAATC 57.456 45.455 0.00 0.00 0.00 2.67
1877 2102 4.982241 TTCTTCCACCTCTGACTTCAAT 57.018 40.909 0.00 0.00 0.00 2.57
1878 2103 4.444876 CCTTTCTTCCACCTCTGACTTCAA 60.445 45.833 0.00 0.00 0.00 2.69
1879 2104 3.071602 CCTTTCTTCCACCTCTGACTTCA 59.928 47.826 0.00 0.00 0.00 3.02
1889 2114 1.691823 CCTCCCCCTTTCTTCCACC 59.308 63.158 0.00 0.00 0.00 4.61
1904 2129 0.322546 ACGAATCCCAAAGCACCCTC 60.323 55.000 0.00 0.00 0.00 4.30
1916 2141 2.034053 TGACAGTTGGCAAAACGAATCC 59.966 45.455 0.00 0.00 0.00 3.01
1952 2234 2.034879 GTACGTCCCCGTCGTGAGA 61.035 63.158 0.00 0.00 46.28 3.27
1953 2235 2.482374 GTACGTCCCCGTCGTGAG 59.518 66.667 0.00 0.00 46.28 3.51
1954 2236 3.422303 CGTACGTCCCCGTCGTGA 61.422 66.667 7.22 0.00 46.28 4.35
1955 2237 3.422303 TCGTACGTCCCCGTCGTG 61.422 66.667 16.05 0.00 46.28 4.35
1956 2238 3.423154 GTCGTACGTCCCCGTCGT 61.423 66.667 16.05 0.00 46.28 4.34
1957 2239 3.088500 GAGTCGTACGTCCCCGTCG 62.089 68.421 16.05 0.00 46.28 5.12
1958 2240 2.787915 GAGTCGTACGTCCCCGTC 59.212 66.667 16.05 0.00 46.28 4.79
1960 2242 1.809619 TACGAGTCGTACGTCCCCG 60.810 63.158 21.10 17.13 43.62 5.73
1961 2243 4.201951 TACGAGTCGTACGTCCCC 57.798 61.111 21.10 3.96 43.62 4.81
1985 2267 1.872773 AACAGCTTGGGTGGGAAAAA 58.127 45.000 1.94 0.00 35.13 1.94
1986 2268 2.091555 ACTAACAGCTTGGGTGGGAAAA 60.092 45.455 1.94 0.00 35.13 2.29
1987 2269 1.497286 ACTAACAGCTTGGGTGGGAAA 59.503 47.619 1.94 0.00 35.13 3.13
1988 2270 1.145571 ACTAACAGCTTGGGTGGGAA 58.854 50.000 1.94 0.00 35.13 3.97
1989 2271 1.145571 AACTAACAGCTTGGGTGGGA 58.854 50.000 1.94 0.00 35.13 4.37
1990 2272 1.995376 AAACTAACAGCTTGGGTGGG 58.005 50.000 1.94 0.00 35.13 4.61
1991 2273 3.751518 AGTAAACTAACAGCTTGGGTGG 58.248 45.455 1.94 0.00 35.13 4.61
1992 2274 5.278315 GGAAAGTAAACTAACAGCTTGGGTG 60.278 44.000 0.00 0.00 37.06 4.61
1993 2275 4.825634 GGAAAGTAAACTAACAGCTTGGGT 59.174 41.667 0.00 0.00 0.00 4.51
1994 2276 4.217767 GGGAAAGTAAACTAACAGCTTGGG 59.782 45.833 0.00 0.00 0.00 4.12
1995 2277 5.070685 AGGGAAAGTAAACTAACAGCTTGG 58.929 41.667 0.00 0.00 0.00 3.61
1996 2278 6.294010 GGAAGGGAAAGTAAACTAACAGCTTG 60.294 42.308 0.00 0.00 0.00 4.01
1997 2279 5.768662 GGAAGGGAAAGTAAACTAACAGCTT 59.231 40.000 0.00 0.00 0.00 3.74
1998 2280 5.314529 GGAAGGGAAAGTAAACTAACAGCT 58.685 41.667 0.00 0.00 0.00 4.24
1999 2281 4.458295 GGGAAGGGAAAGTAAACTAACAGC 59.542 45.833 0.00 0.00 0.00 4.40
2003 2285 5.935668 AAGGGGAAGGGAAAGTAAACTAA 57.064 39.130 0.00 0.00 0.00 2.24
2011 2293 1.895798 GCTTCAAAGGGGAAGGGAAAG 59.104 52.381 5.22 0.00 43.54 2.62
2060 2342 0.748005 ATGTGCAGGAACGGGTATGC 60.748 55.000 0.00 0.00 39.14 3.14
2098 2380 2.653702 GGCTGCAGACTGAGACGT 59.346 61.111 20.43 0.00 0.00 4.34
2122 2404 2.203195 GGAGCAGGTGTGTGCACA 60.203 61.111 17.42 17.42 46.60 4.57
2124 2406 2.203195 GTGGAGCAGGTGTGTGCA 60.203 61.111 0.00 0.00 46.60 4.57
2125 2407 2.203195 TGTGGAGCAGGTGTGTGC 60.203 61.111 0.00 0.00 44.35 4.57
2126 2408 2.256591 GCTGTGGAGCAGGTGTGTG 61.257 63.158 0.00 0.00 45.46 3.82
2127 2409 2.111878 GCTGTGGAGCAGGTGTGT 59.888 61.111 0.00 0.00 45.46 3.72
2179 2461 0.748005 TTCCATAGCTTTCCGCCTGC 60.748 55.000 0.00 0.00 40.39 4.85
2185 2467 2.106684 CCTAGGGGTTCCATAGCTTTCC 59.893 54.545 0.00 0.00 34.83 3.13
2207 2503 1.298014 CAGGTGGTGAGAGGAAGCC 59.702 63.158 0.00 0.00 0.00 4.35
2319 2616 0.036732 TAAACAGCAGGAGCACCAGG 59.963 55.000 2.07 0.00 45.49 4.45
2322 2619 1.308783 GGCTAAACAGCAGGAGCACC 61.309 60.000 0.00 0.00 45.49 5.01
2323 2620 1.639298 CGGCTAAACAGCAGGAGCAC 61.639 60.000 0.00 0.00 45.49 4.40
2325 2622 2.754995 GCGGCTAAACAGCAGGAGC 61.755 63.158 0.00 0.00 39.55 4.70
2342 2639 1.655350 GCATATTTCGCACGGCTGC 60.655 57.895 0.00 0.00 40.38 5.25
2344 2641 4.217035 TGCATATTTCGCACGGCT 57.783 50.000 0.00 0.00 33.55 5.52
2353 2650 3.795688 ATGGGATCTCGGTGCATATTT 57.204 42.857 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.