Multiple sequence alignment - TraesCS5A01G070000

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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 TraesCS5A01G070000 chr5A 100.000 2330 0 0 1 2330 78367981 78370310 0.000000e+00 4303.0
1 TraesCS5A01G070000 chr5A 89.377 1412 129 15 742 2141 78426303 78427705 0.000000e+00 1757.0
2 TraesCS5A01G070000 chr5A 84.240 882 99 15 742 1614 78474209 78475059 0.000000e+00 822.0
3 TraesCS5A01G070000 chr5A 94.005 417 21 3 208 624 78425872 78426284 1.520000e-176 628.0
4 TraesCS5A01G070000 chr5A 78.741 715 115 26 742 1430 78480344 78481047 5.910000e-121 444.0
5 TraesCS5A01G070000 chr5A 92.195 205 11 2 8 208 78424744 78424947 3.790000e-73 285.0
6 TraesCS5A01G070000 chr5A 86.792 265 19 8 361 624 78473941 78474190 4.900000e-72 281.0
7 TraesCS5A01G070000 chr5A 91.391 151 8 3 178 328 78473797 78473942 3.930000e-48 202.0
8 TraesCS5A01G070000 chr5B 91.892 888 61 7 759 1646 90988080 90988956 0.000000e+00 1230.0
9 TraesCS5A01G070000 chr5B 85.634 891 101 13 742 1614 91108604 91109485 0.000000e+00 911.0
10 TraesCS5A01G070000 chr5B 89.087 449 39 9 1696 2139 90989847 90990290 1.220000e-152 549.0
11 TraesCS5A01G070000 chr5B 94.688 320 16 1 305 624 90987751 90988069 1.610000e-136 496.0
12 TraesCS5A01G070000 chr5B 94.081 321 11 3 1 321 90987413 90987725 4.500000e-132 481.0
13 TraesCS5A01G070000 chr5B 84.459 444 43 13 178 620 91108163 91108581 4.630000e-112 414.0
14 TraesCS5A01G070000 chr5B 100.000 37 0 0 1648 1684 90989263 90989299 4.150000e-08 69.4
15 TraesCS5A01G070000 chr5B 94.444 36 2 0 4 39 91002556 91002591 3.230000e-04 56.5
16 TraesCS5A01G070000 chr5D 82.791 860 106 22 764 1614 84178047 84178873 0.000000e+00 730.0
17 TraesCS5A01G070000 chr5D 85.441 261 23 6 361 620 84011506 84011752 8.260000e-65 257.0
18 TraesCS5A01G070000 chr5D 89.404 151 11 3 178 328 84011362 84011507 3.950000e-43 185.0
19 TraesCS5A01G070000 chr5D 76.955 243 44 11 273 507 84185056 84185294 6.760000e-26 128.0
20 TraesCS5A01G070000 chr2A 78.359 841 133 28 760 1559 691119699 691120531 1.240000e-137 499.0
21 TraesCS5A01G070000 chr2A 80.980 510 83 9 929 1428 691159528 691160033 2.170000e-105 392.0
22 TraesCS5A01G070000 chr2A 89.286 84 8 1 178 260 691137721 691137804 1.140000e-18 104.0
23 TraesCS5A01G070000 chr2B 80.828 652 101 16 796 1428 654699584 654698938 7.480000e-135 490.0
24 TraesCS5A01G070000 chr2B 79.654 693 122 12 754 1428 654528206 654527515 4.500000e-132 481.0
25 TraesCS5A01G070000 chr2B 86.813 91 7 4 181 269 654727559 654727472 1.910000e-16 97.1
26 TraesCS5A01G070000 chr7D 95.833 120 5 0 625 744 102302091 102302210 6.570000e-46 195.0
27 TraesCS5A01G070000 chr7D 90.580 138 11 2 625 761 584458329 584458465 5.110000e-42 182.0
28 TraesCS5A01G070000 chr7A 92.424 132 9 1 621 752 565857578 565857708 1.100000e-43 187.0
29 TraesCS5A01G070000 chr7A 93.496 123 8 0 629 751 132902495 132902373 1.420000e-42 183.0
30 TraesCS5A01G070000 chr6B 95.000 120 4 2 625 743 83661499 83661617 1.100000e-43 187.0
31 TraesCS5A01G070000 chr6B 93.496 123 8 0 621 743 644370773 644370895 1.420000e-42 183.0
32 TraesCS5A01G070000 chr3B 95.000 120 4 2 625 743 211632845 211632727 1.100000e-43 187.0
33 TraesCS5A01G070000 chr1B 95.000 120 4 2 625 743 197566471 197566353 1.100000e-43 187.0
34 TraesCS5A01G070000 chr4D 94.167 120 7 0 625 744 291740470 291740589 1.420000e-42 183.0
35 TraesCS5A01G070000 chr1D 84.536 194 21 7 2139 2327 486709245 486709434 1.420000e-42 183.0
36 TraesCS5A01G070000 chr2D 86.667 90 9 2 181 269 547945302 547945215 1.910000e-16 97.1
37 TraesCS5A01G070000 chrUn 87.805 82 9 1 181 261 248123412 248123331 6.850000e-16 95.3


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 TraesCS5A01G070000 chr5A 78367981 78370310 2329 False 4303.00 4303 100.000000 1 2330 1 chr5A.!!$F1 2329
1 TraesCS5A01G070000 chr5A 78424744 78427705 2961 False 890.00 1757 91.859000 8 2141 3 chr5A.!!$F3 2133
2 TraesCS5A01G070000 chr5A 78480344 78481047 703 False 444.00 444 78.741000 742 1430 1 chr5A.!!$F2 688
3 TraesCS5A01G070000 chr5A 78473797 78475059 1262 False 435.00 822 87.474333 178 1614 3 chr5A.!!$F4 1436
4 TraesCS5A01G070000 chr5B 91108163 91109485 1322 False 662.50 911 85.046500 178 1614 2 chr5B.!!$F3 1436
5 TraesCS5A01G070000 chr5B 90987413 90990290 2877 False 565.08 1230 93.949600 1 2139 5 chr5B.!!$F2 2138
6 TraesCS5A01G070000 chr5D 84178047 84178873 826 False 730.00 730 82.791000 764 1614 1 chr5D.!!$F1 850
7 TraesCS5A01G070000 chr2A 691119699 691120531 832 False 499.00 499 78.359000 760 1559 1 chr2A.!!$F1 799
8 TraesCS5A01G070000 chr2A 691159528 691160033 505 False 392.00 392 80.980000 929 1428 1 chr2A.!!$F3 499
9 TraesCS5A01G070000 chr2B 654698938 654699584 646 True 490.00 490 80.828000 796 1428 1 chr2B.!!$R2 632
10 TraesCS5A01G070000 chr2B 654527515 654528206 691 True 481.00 481 79.654000 754 1428 1 chr2B.!!$R1 674

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
633 1608 0.395862 TTGAAACCAGCCGTCCCAAA 60.396 50.0 0.0 0.0 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 4156 0.529992 GTTCCGGCCAAGGTAGATCG 60.53 60.0 2.24 0.0 0.0 3.69 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
89 90 5.128663 TCTCAAACTATAGTAGGTGCATGCA 59.871 40.000 18.46 18.46 0.00 3.96
403 1375 0.894141 TGGCAGCAAAACACACAACT 59.106 45.000 0.00 0.00 0.00 3.16
404 1376 1.280066 GGCAGCAAAACACACAACTG 58.720 50.000 0.00 0.00 0.00 3.16
423 1395 2.422127 CTGTGAGTTTTCGGTGGTTGTT 59.578 45.455 0.00 0.00 0.00 2.83
545 1520 9.730705 AATTGAAGAGTCACTTTCTATCATTGA 57.269 29.630 0.00 0.00 39.13 2.57
571 1546 1.164411 TTGGTCTTTGCGGCATACTG 58.836 50.000 2.28 0.00 0.00 2.74
608 1583 5.170021 GTTGCATTATGGAGATGTTTGCAA 58.830 37.500 0.00 0.00 43.84 4.08
624 1599 3.641437 TGCAACTATGTTGAAACCAGC 57.359 42.857 13.75 0.00 0.00 4.85
625 1600 2.295909 TGCAACTATGTTGAAACCAGCC 59.704 45.455 13.75 0.00 0.00 4.85
627 1602 2.552315 CAACTATGTTGAAACCAGCCGT 59.448 45.455 4.60 0.00 0.00 5.68
628 1603 2.423577 ACTATGTTGAAACCAGCCGTC 58.576 47.619 0.00 0.00 0.00 4.79
629 1604 1.737793 CTATGTTGAAACCAGCCGTCC 59.262 52.381 0.00 0.00 0.00 4.79
630 1605 0.893727 ATGTTGAAACCAGCCGTCCC 60.894 55.000 0.00 0.00 0.00 4.46
631 1606 1.527380 GTTGAAACCAGCCGTCCCA 60.527 57.895 0.00 0.00 0.00 4.37
632 1607 1.104577 GTTGAAACCAGCCGTCCCAA 61.105 55.000 0.00 0.00 0.00 4.12
633 1608 0.395862 TTGAAACCAGCCGTCCCAAA 60.396 50.000 0.00 0.00 0.00 3.28
634 1609 0.395862 TGAAACCAGCCGTCCCAAAA 60.396 50.000 0.00 0.00 0.00 2.44
636 1611 1.343142 GAAACCAGCCGTCCCAAAATT 59.657 47.619 0.00 0.00 0.00 1.82
637 1612 0.966179 AACCAGCCGTCCCAAAATTC 59.034 50.000 0.00 0.00 0.00 2.17
639 1614 1.256812 CCAGCCGTCCCAAAATTCTT 58.743 50.000 0.00 0.00 0.00 2.52
640 1615 1.067635 CCAGCCGTCCCAAAATTCTTG 60.068 52.381 0.00 0.00 0.00 3.02
641 1616 1.613437 CAGCCGTCCCAAAATTCTTGT 59.387 47.619 0.00 0.00 0.00 3.16
642 1617 1.886542 AGCCGTCCCAAAATTCTTGTC 59.113 47.619 0.00 0.00 0.00 3.18
643 1618 1.886542 GCCGTCCCAAAATTCTTGTCT 59.113 47.619 0.00 0.00 0.00 3.41
645 1620 3.504520 GCCGTCCCAAAATTCTTGTCTTA 59.495 43.478 0.00 0.00 0.00 2.10
646 1621 4.022676 GCCGTCCCAAAATTCTTGTCTTAA 60.023 41.667 0.00 0.00 0.00 1.85
647 1622 5.336451 GCCGTCCCAAAATTCTTGTCTTAAT 60.336 40.000 0.00 0.00 0.00 1.40
648 1623 6.687604 CCGTCCCAAAATTCTTGTCTTAATT 58.312 36.000 0.00 0.00 0.00 1.40
649 1624 7.151976 CCGTCCCAAAATTCTTGTCTTAATTT 58.848 34.615 0.00 0.00 36.98 1.82
650 1625 7.655732 CCGTCCCAAAATTCTTGTCTTAATTTT 59.344 33.333 0.00 0.00 42.88 1.82
651 1626 9.040939 CGTCCCAAAATTCTTGTCTTAATTTTT 57.959 29.630 0.00 0.00 41.17 1.94
730 1705 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
731 1706 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
732 1707 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
733 1708 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
869 1858 2.350676 CGTGTCTAATTGCTTGCTTGCA 60.351 45.455 0.27 0.27 41.65 4.08
889 1880 7.813148 GCTTGCAGCAGAATATATTTCATGAAT 59.187 33.333 9.40 2.50 41.89 2.57
982 1979 6.963322 AGCTAAGACCAAAATCTCCAATAGT 58.037 36.000 0.00 0.00 0.00 2.12
1002 2006 9.438291 CAATAGTAATCCGCTAGAAAACAAATG 57.562 33.333 0.00 0.00 0.00 2.32
1064 2068 1.152984 TGCTTGTCCTGGTGGTGTG 60.153 57.895 0.00 0.00 34.23 3.82
1078 2082 2.550487 GTGTGCCTCACCGCAATAA 58.450 52.632 0.00 0.00 41.30 1.40
1191 2195 4.077188 GAGTGTTGTGCCGCGCTC 62.077 66.667 5.56 0.00 35.51 5.03
1365 2382 7.275779 GCACTATCCATAAATGTATAGGTGTCG 59.724 40.741 7.28 0.00 32.78 4.35
1373 2390 1.065199 TGTATAGGTGTCGGTCGGTCT 60.065 52.381 0.00 0.00 0.00 3.85
1458 2503 3.175152 GTTGTTGTGTGATTTGAACGCA 58.825 40.909 0.00 0.00 36.31 5.24
1464 2510 3.228749 GTGTGATTTGAACGCATGTCTG 58.771 45.455 0.00 0.00 0.00 3.51
1484 2530 8.722480 TGTCTGTCTCATTAATCTATTGTTGG 57.278 34.615 0.00 0.00 0.00 3.77
1579 2634 9.816354 ATTTTAAGTTGTGAGTTTGTTATTGCT 57.184 25.926 0.00 0.00 0.00 3.91
1581 2636 6.449635 AAGTTGTGAGTTTGTTATTGCTCA 57.550 33.333 0.00 0.00 35.85 4.26
1607 2662 6.833342 AAATTGTGTCTTTTCAATGAGCAC 57.167 33.333 0.00 0.00 34.98 4.40
1617 2672 6.260050 TCTTTTCAATGAGCACGTAAAAGTCT 59.740 34.615 12.93 0.00 36.08 3.24
1619 2674 6.462073 TTCAATGAGCACGTAAAAGTCTAC 57.538 37.500 0.00 0.00 0.00 2.59
1622 2677 4.530710 TGAGCACGTAAAAGTCTACCAT 57.469 40.909 0.00 0.00 0.00 3.55
1624 2679 5.647589 TGAGCACGTAAAAGTCTACCATAG 58.352 41.667 0.00 0.00 0.00 2.23
1732 3629 7.057894 GGATTATTGGTAGGTATCCACAACAA 58.942 38.462 0.00 0.00 35.82 2.83
1733 3630 7.012989 GGATTATTGGTAGGTATCCACAACAAC 59.987 40.741 0.00 0.00 35.82 3.32
1734 3631 4.708576 TTGGTAGGTATCCACAACAACA 57.291 40.909 0.00 0.00 34.45 3.33
1735 3632 4.919774 TGGTAGGTATCCACAACAACAT 57.080 40.909 0.00 0.00 0.00 2.71
1736 3633 6.375830 TTGGTAGGTATCCACAACAACATA 57.624 37.500 0.00 0.00 34.45 2.29
1737 3634 6.569127 TGGTAGGTATCCACAACAACATAT 57.431 37.500 0.00 0.00 0.00 1.78
1739 3636 5.763204 GGTAGGTATCCACAACAACATATGG 59.237 44.000 7.80 0.00 0.00 2.74
1753 3650 2.304092 CATATGGCCAACTGCACTGAT 58.696 47.619 10.96 0.00 43.89 2.90
1766 3663 3.659786 TGCACTGATATATACGGTTGGC 58.340 45.455 0.00 0.00 0.00 4.52
1777 3674 0.669318 ACGGTTGGCTGTACATGACG 60.669 55.000 0.00 0.00 31.28 4.35
1852 3753 9.640974 TTTTCAAGTTCGAAATTTTACTAGTCG 57.359 29.630 8.33 0.00 34.94 4.18
1853 3754 7.342318 TCAAGTTCGAAATTTTACTAGTCGG 57.658 36.000 8.33 0.00 32.68 4.79
1854 3755 5.774878 AGTTCGAAATTTTACTAGTCGGC 57.225 39.130 0.00 0.00 32.68 5.54
1862 3763 4.612264 TTTTACTAGTCGGCCTCTTGTT 57.388 40.909 14.28 3.43 0.00 2.83
1878 3779 7.015877 GCCTCTTGTTGATTTTAGTTCGTAAG 58.984 38.462 0.00 0.00 0.00 2.34
1896 3797 1.080638 AGTTTGGTCCCCTTGCCATA 58.919 50.000 0.00 0.00 34.37 2.74
1906 3807 2.618709 CCCCTTGCCATAGAATTCGTTC 59.381 50.000 0.00 0.00 0.00 3.95
1947 3848 8.915036 ACCTAATACATGTTTTGTGGTTTTGTA 58.085 29.630 2.30 0.00 39.48 2.41
1979 3884 1.141858 TGACCTGCACACCACATGTTA 59.858 47.619 0.00 0.00 40.64 2.41
1981 3886 1.142870 ACCTGCACACCACATGTTACT 59.857 47.619 0.00 0.00 40.64 2.24
2035 3940 2.503331 CAGCAAGTGGGTTCATGTGTA 58.497 47.619 0.00 0.00 0.00 2.90
2055 3960 5.118203 GTGTAACAGTGTTAATGGTCTCGTC 59.882 44.000 17.16 2.16 36.32 4.20
2095 4000 2.927553 ATGCGACAAAGATGGCTTTC 57.072 45.000 0.00 0.00 42.27 2.62
2103 4008 5.691305 CGACAAAGATGGCTTTCAATCAAAA 59.309 36.000 0.00 0.00 42.27 2.44
2135 4040 4.082463 GGCGTGAAATTTTTGGGAGTCATA 60.082 41.667 0.00 0.00 0.00 2.15
2141 4046 7.976175 GTGAAATTTTTGGGAGTCATATTCCTC 59.024 37.037 0.00 0.00 35.01 3.71
2142 4047 7.124147 TGAAATTTTTGGGAGTCATATTCCTCC 59.876 37.037 8.40 8.40 45.44 4.30
2143 4048 5.796502 TTTTTGGGAGTCATATTCCTCCT 57.203 39.130 14.31 0.00 45.46 3.69
2144 4049 5.373812 TTTTGGGAGTCATATTCCTCCTC 57.626 43.478 14.31 7.66 45.46 3.71
2145 4050 2.977808 TGGGAGTCATATTCCTCCTCC 58.022 52.381 14.31 0.00 45.46 4.30
2147 4052 2.261729 GGAGTCATATTCCTCCTCCCC 58.738 57.143 9.34 0.00 43.29 4.81
2148 4053 2.261729 GAGTCATATTCCTCCTCCCCC 58.738 57.143 0.00 0.00 0.00 5.40
2149 4054 1.876473 AGTCATATTCCTCCTCCCCCT 59.124 52.381 0.00 0.00 0.00 4.79
2150 4055 2.158081 AGTCATATTCCTCCTCCCCCTC 60.158 54.545 0.00 0.00 0.00 4.30
2151 4056 1.152271 TCATATTCCTCCTCCCCCTCC 59.848 57.143 0.00 0.00 0.00 4.30
2152 4057 1.153132 CATATTCCTCCTCCCCCTCCT 59.847 57.143 0.00 0.00 0.00 3.69
2153 4058 0.868186 TATTCCTCCTCCCCCTCCTC 59.132 60.000 0.00 0.00 0.00 3.71
2154 4059 0.938926 ATTCCTCCTCCCCCTCCTCT 60.939 60.000 0.00 0.00 0.00 3.69
2155 4060 1.595058 TTCCTCCTCCCCCTCCTCTC 61.595 65.000 0.00 0.00 0.00 3.20
2156 4061 2.612251 CTCCTCCCCCTCCTCTCC 59.388 72.222 0.00 0.00 0.00 3.71
2157 4062 3.036959 TCCTCCCCCTCCTCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
2158 4063 4.179599 CCTCCCCCTCCTCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
2159 4064 3.039526 CTCCCCCTCCTCTCCCCT 61.040 72.222 0.00 0.00 0.00 4.79
2160 4065 3.036959 TCCCCCTCCTCTCCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
2161 4066 4.548513 CCCCCTCCTCTCCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
2231 4136 3.011517 GGGGGCTCTCTCCTTGCA 61.012 66.667 0.00 0.00 0.00 4.08
2232 4137 2.606587 GGGGGCTCTCTCCTTGCAA 61.607 63.158 0.00 0.00 0.00 4.08
2233 4138 1.077858 GGGGCTCTCTCCTTGCAAG 60.078 63.158 19.93 19.93 0.00 4.01
2235 4140 1.748500 GGCTCTCTCCTTGCAAGGC 60.749 63.158 36.24 24.01 46.06 4.35
2236 4141 1.002868 GCTCTCTCCTTGCAAGGCA 60.003 57.895 36.24 24.58 46.06 4.75
2237 4142 1.025647 GCTCTCTCCTTGCAAGGCAG 61.026 60.000 36.24 30.96 46.06 4.85
2238 4143 0.392729 CTCTCTCCTTGCAAGGCAGG 60.393 60.000 36.24 26.86 46.06 4.85
2239 4144 0.837691 TCTCTCCTTGCAAGGCAGGA 60.838 55.000 36.24 28.91 46.06 3.86
2240 4145 0.255318 CTCTCCTTGCAAGGCAGGAT 59.745 55.000 36.24 0.00 46.06 3.24
2241 4146 0.700564 TCTCCTTGCAAGGCAGGATT 59.299 50.000 36.24 0.00 46.06 3.01
2242 4147 0.815734 CTCCTTGCAAGGCAGGATTG 59.184 55.000 36.24 17.14 46.06 2.67
2260 4165 2.838225 CCGTGGGGCGATCTACCT 60.838 66.667 2.08 0.00 44.77 3.08
2261 4166 2.432300 CCGTGGGGCGATCTACCTT 61.432 63.158 2.08 0.00 44.77 3.50
2262 4167 1.227263 CGTGGGGCGATCTACCTTG 60.227 63.158 2.08 0.00 44.77 3.61
2263 4168 1.146263 GTGGGGCGATCTACCTTGG 59.854 63.158 2.08 0.00 0.00 3.61
2264 4169 2.111251 GGGGCGATCTACCTTGGC 59.889 66.667 2.08 0.00 0.00 4.52
2265 4170 2.111251 GGGCGATCTACCTTGGCC 59.889 66.667 0.00 0.00 43.01 5.36
2266 4171 2.280186 GGCGATCTACCTTGGCCG 60.280 66.667 0.00 0.00 33.58 6.13
2267 4172 2.280186 GCGATCTACCTTGGCCGG 60.280 66.667 0.00 0.00 0.00 6.13
2268 4173 2.792947 GCGATCTACCTTGGCCGGA 61.793 63.158 5.05 0.00 0.00 5.14
2269 4174 1.820581 CGATCTACCTTGGCCGGAA 59.179 57.895 5.05 0.00 0.00 4.30
2270 4175 0.529992 CGATCTACCTTGGCCGGAAC 60.530 60.000 5.05 0.00 0.00 3.62
2309 4214 4.758251 CGACGATGGGCTGCCACA 62.758 66.667 22.05 16.09 0.00 4.17
2310 4215 2.821366 GACGATGGGCTGCCACAG 60.821 66.667 22.05 10.80 34.12 3.66
2311 4216 3.612247 GACGATGGGCTGCCACAGT 62.612 63.158 22.05 14.02 33.43 3.55
2312 4217 3.129502 CGATGGGCTGCCACAGTG 61.130 66.667 22.05 8.66 33.43 3.66
2313 4218 2.753043 GATGGGCTGCCACAGTGG 60.753 66.667 22.05 16.16 41.55 4.00
2323 4228 4.662961 CACAGTGGCGAGCGTGGA 62.663 66.667 0.00 0.00 0.00 4.02
2324 4229 4.363990 ACAGTGGCGAGCGTGGAG 62.364 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 2.172679 TCACATTTGATGCATGCACCT 58.827 42.857 25.37 8.32 0.00 4.00
89 90 3.056322 GCTTGGAGCCTTTCACATTTGAT 60.056 43.478 0.00 0.00 34.48 2.57
261 1191 8.652290 AGAGGGTCATGTTTTCTATCTATAACC 58.348 37.037 0.00 0.00 0.00 2.85
403 1375 2.116827 ACAACCACCGAAAACTCACA 57.883 45.000 0.00 0.00 0.00 3.58
404 1376 3.497297 AAACAACCACCGAAAACTCAC 57.503 42.857 0.00 0.00 0.00 3.51
545 1520 1.156736 CCGCAAAGACCAATTCGTCT 58.843 50.000 0.00 0.00 45.12 4.18
571 1546 0.950555 TGCAACATCACGACTCAGGC 60.951 55.000 0.00 0.00 0.00 4.85
580 1555 5.762825 ACATCTCCATAATGCAACATCAC 57.237 39.130 0.00 0.00 0.00 3.06
608 1583 2.423577 GACGGCTGGTTTCAACATAGT 58.576 47.619 0.00 0.00 0.00 2.12
624 1599 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
625 1600 8.587952 AAAATTAAGACAAGAATTTTGGGACG 57.412 30.769 4.90 0.00 41.43 4.79
704 1679 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
705 1680 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
706 1681 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
707 1682 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
708 1683 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
709 1684 8.477419 TTGTCCCAAAATTCTTGTCTTAGATT 57.523 30.769 0.00 0.00 0.00 2.40
710 1685 8.477419 TTTGTCCCAAAATTCTTGTCTTAGAT 57.523 30.769 0.00 0.00 0.00 1.98
711 1686 7.014230 CCTTTGTCCCAAAATTCTTGTCTTAGA 59.986 37.037 0.00 0.00 0.00 2.10
712 1687 7.147976 CCTTTGTCCCAAAATTCTTGTCTTAG 58.852 38.462 0.00 0.00 0.00 2.18
713 1688 6.041523 CCCTTTGTCCCAAAATTCTTGTCTTA 59.958 38.462 0.00 0.00 0.00 2.10
714 1689 5.163311 CCCTTTGTCCCAAAATTCTTGTCTT 60.163 40.000 0.00 0.00 0.00 3.01
715 1690 4.344968 CCCTTTGTCCCAAAATTCTTGTCT 59.655 41.667 0.00 0.00 0.00 3.41
716 1691 4.343814 TCCCTTTGTCCCAAAATTCTTGTC 59.656 41.667 0.00 0.00 0.00 3.18
717 1692 4.294347 TCCCTTTGTCCCAAAATTCTTGT 58.706 39.130 0.00 0.00 0.00 3.16
718 1693 4.344968 ACTCCCTTTGTCCCAAAATTCTTG 59.655 41.667 0.00 0.00 0.00 3.02
719 1694 4.556697 ACTCCCTTTGTCCCAAAATTCTT 58.443 39.130 0.00 0.00 0.00 2.52
720 1695 4.199002 ACTCCCTTTGTCCCAAAATTCT 57.801 40.909 0.00 0.00 0.00 2.40
721 1696 5.952347 AGATACTCCCTTTGTCCCAAAATTC 59.048 40.000 0.00 0.00 0.00 2.17
722 1697 5.903923 AGATACTCCCTTTGTCCCAAAATT 58.096 37.500 0.00 0.00 0.00 1.82
723 1698 5.536497 AGATACTCCCTTTGTCCCAAAAT 57.464 39.130 0.00 0.00 0.00 1.82
724 1699 5.333566 AAGATACTCCCTTTGTCCCAAAA 57.666 39.130 0.00 0.00 0.00 2.44
725 1700 5.333566 AAAGATACTCCCTTTGTCCCAAA 57.666 39.130 0.00 0.00 33.07 3.28
726 1701 5.333566 AAAAGATACTCCCTTTGTCCCAA 57.666 39.130 0.00 0.00 34.42 4.12
727 1702 5.333566 AAAAAGATACTCCCTTTGTCCCA 57.666 39.130 0.00 0.00 34.42 4.37
982 1979 4.702612 TGGCATTTGTTTTCTAGCGGATTA 59.297 37.500 0.00 0.00 0.00 1.75
1064 2068 0.679960 ACCCTTTATTGCGGTGAGGC 60.680 55.000 0.00 0.00 0.00 4.70
1078 2082 1.076024 ACAGATGCCATGAACACCCTT 59.924 47.619 0.00 0.00 0.00 3.95
1144 2148 3.498661 GGACTCTCTGTTGGGTTTTCCAT 60.499 47.826 0.00 0.00 46.52 3.41
1191 2195 2.359975 GACAGGTTGGCCTTCCCG 60.360 66.667 3.32 1.06 44.18 5.14
1354 2367 1.332997 CAGACCGACCGACACCTATAC 59.667 57.143 0.00 0.00 0.00 1.47
1356 2369 0.323178 ACAGACCGACCGACACCTAT 60.323 55.000 0.00 0.00 0.00 2.57
1365 2382 2.885266 TGCATATCTAGACAGACCGACC 59.115 50.000 0.00 0.00 32.25 4.79
1458 2503 9.334947 CCAACAATAGATTAATGAGACAGACAT 57.665 33.333 0.00 0.00 0.00 3.06
1464 2510 8.594881 ATCGTCCAACAATAGATTAATGAGAC 57.405 34.615 0.00 0.00 0.00 3.36
1509 2560 2.582052 CACTTTTGCCCTCCTTACACA 58.418 47.619 0.00 0.00 0.00 3.72
1604 2659 6.716898 AAACTATGGTAGACTTTTACGTGC 57.283 37.500 0.00 0.00 0.00 5.34
1707 3603 6.597562 TGTTGTGGATACCTACCAATAATCC 58.402 40.000 0.00 0.00 39.22 3.01
1732 3629 1.004628 TCAGTGCAGTTGGCCATATGT 59.995 47.619 6.09 0.00 43.89 2.29
1733 3630 1.753930 TCAGTGCAGTTGGCCATATG 58.246 50.000 6.09 10.09 43.89 1.78
1734 3631 2.742428 ATCAGTGCAGTTGGCCATAT 57.258 45.000 6.09 0.00 43.89 1.78
1735 3632 3.862877 ATATCAGTGCAGTTGGCCATA 57.137 42.857 6.09 0.00 43.89 2.74
1736 3633 2.742428 ATATCAGTGCAGTTGGCCAT 57.258 45.000 6.09 0.00 43.89 4.40
1737 3634 3.862877 ATATATCAGTGCAGTTGGCCA 57.137 42.857 0.00 0.00 43.89 5.36
1739 3636 3.679980 CCGTATATATCAGTGCAGTTGGC 59.320 47.826 0.00 0.00 45.13 4.52
1753 3650 5.563280 CGTCATGTACAGCCAACCGTATATA 60.563 44.000 0.33 0.00 0.00 0.86
1777 3674 6.092122 TCGTTTTGATCAATGTAGTGACCATC 59.908 38.462 9.40 0.00 0.00 3.51
1848 3746 2.568623 AAATCAACAAGAGGCCGACT 57.431 45.000 0.00 0.00 0.00 4.18
1852 3753 4.215613 ACGAACTAAAATCAACAAGAGGCC 59.784 41.667 0.00 0.00 0.00 5.19
1853 3754 5.358298 ACGAACTAAAATCAACAAGAGGC 57.642 39.130 0.00 0.00 0.00 4.70
1854 3755 8.084590 ACTTACGAACTAAAATCAACAAGAGG 57.915 34.615 0.00 0.00 0.00 3.69
1862 3763 6.205270 GGGACCAAACTTACGAACTAAAATCA 59.795 38.462 0.00 0.00 0.00 2.57
1906 3807 6.220930 TGTATTAGGTTGCGAAATAGGCTAG 58.779 40.000 0.00 0.00 0.00 3.42
1952 3853 1.421268 TGGTGTGCAGGTCAGAGATTT 59.579 47.619 0.00 0.00 0.00 2.17
1953 3854 1.059098 TGGTGTGCAGGTCAGAGATT 58.941 50.000 0.00 0.00 0.00 2.40
1995 3900 1.818674 GGCGAGGGTGACAAAAATGAT 59.181 47.619 0.00 0.00 0.00 2.45
1997 3902 0.958091 TGGCGAGGGTGACAAAAATG 59.042 50.000 0.00 0.00 0.00 2.32
2027 3932 6.530120 AGACCATTAACACTGTTACACATGA 58.470 36.000 0.00 0.00 0.00 3.07
2035 3940 4.602340 AGACGAGACCATTAACACTGTT 57.398 40.909 0.00 0.00 0.00 3.16
2103 4008 6.459435 CCCAAAAATTTCACGCCAAGATTTTT 60.459 34.615 0.00 0.00 39.27 1.94
2118 4023 7.423844 GGAGGAATATGACTCCCAAAAATTT 57.576 36.000 12.76 0.00 46.01 1.82
2135 4040 0.938926 AGAGGAGGGGGAGGAGGAAT 60.939 60.000 0.00 0.00 0.00 3.01
2141 4046 4.179599 GGGGAGAGGAGGGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
2142 4047 3.039526 AGGGGAGAGGAGGGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
2143 4048 3.036959 GAGGGGAGAGGAGGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
2144 4049 4.548513 CGAGGGGAGAGGAGGGGG 62.549 77.778 0.00 0.00 0.00 5.40
2214 4119 2.549169 CTTGCAAGGAGAGAGCCCCC 62.549 65.000 19.14 0.00 0.00 5.40
2215 4120 1.077858 CTTGCAAGGAGAGAGCCCC 60.078 63.158 19.14 0.00 0.00 5.80
2216 4121 4.633769 CTTGCAAGGAGAGAGCCC 57.366 61.111 19.14 0.00 0.00 5.19
2225 4130 1.217244 GCAATCCTGCCTTGCAAGG 59.783 57.895 36.58 36.58 46.44 3.61
2226 4131 4.904466 GCAATCCTGCCTTGCAAG 57.096 55.556 19.93 19.93 46.44 4.01
2243 4148 2.432300 AAGGTAGATCGCCCCACGG 61.432 63.158 5.86 0.00 43.89 4.94
2244 4149 1.227263 CAAGGTAGATCGCCCCACG 60.227 63.158 5.86 0.00 45.62 4.94
2245 4150 1.146263 CCAAGGTAGATCGCCCCAC 59.854 63.158 5.86 0.00 0.00 4.61
2246 4151 2.742116 GCCAAGGTAGATCGCCCCA 61.742 63.158 5.86 0.00 0.00 4.96
2247 4152 2.111251 GCCAAGGTAGATCGCCCC 59.889 66.667 5.86 0.00 0.00 5.80
2248 4153 2.111251 GGCCAAGGTAGATCGCCC 59.889 66.667 0.00 1.14 33.30 6.13
2249 4154 2.280186 CGGCCAAGGTAGATCGCC 60.280 66.667 2.24 1.69 36.21 5.54
2250 4155 2.280186 CCGGCCAAGGTAGATCGC 60.280 66.667 2.24 0.00 0.00 4.58
2251 4156 0.529992 GTTCCGGCCAAGGTAGATCG 60.530 60.000 2.24 0.00 0.00 3.69
2252 4157 0.529992 CGTTCCGGCCAAGGTAGATC 60.530 60.000 2.24 0.00 0.00 2.75
2253 4158 1.262640 ACGTTCCGGCCAAGGTAGAT 61.263 55.000 2.24 0.00 0.00 1.98
2254 4159 1.909781 ACGTTCCGGCCAAGGTAGA 60.910 57.895 2.24 0.00 0.00 2.59
2255 4160 1.740296 CACGTTCCGGCCAAGGTAG 60.740 63.158 2.24 0.00 0.00 3.18
2256 4161 2.344500 CACGTTCCGGCCAAGGTA 59.656 61.111 2.24 0.00 0.00 3.08
2257 4162 4.636435 CCACGTTCCGGCCAAGGT 62.636 66.667 2.24 0.00 0.00 3.50
2292 4197 4.758251 TGTGGCAGCCCATCGTCG 62.758 66.667 9.64 0.00 44.51 5.12
2293 4198 2.821366 CTGTGGCAGCCCATCGTC 60.821 66.667 9.64 0.00 44.51 4.20
2294 4199 3.640407 ACTGTGGCAGCCCATCGT 61.640 61.111 9.64 0.00 44.51 3.73
2295 4200 3.129502 CACTGTGGCAGCCCATCG 61.130 66.667 9.64 0.00 44.51 3.84
2296 4201 2.753043 CCACTGTGGCAGCCCATC 60.753 66.667 14.87 0.00 44.51 3.51
2306 4211 4.662961 TCCACGCTCGCCACTGTG 62.663 66.667 0.00 0.00 0.00 3.66
2307 4212 4.363990 CTCCACGCTCGCCACTGT 62.364 66.667 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.