Multiple sequence alignment - TraesCS3D01G195300

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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 TraesCS3D01G195300 chr3D 100.000 3384 0 0 1 3384 189005607 189002224 0.000000e+00 6250.0
1 TraesCS3D01G195300 chr3D 94.094 982 54 4 4 982 189027933 189026953 0.000000e+00 1489.0
2 TraesCS3D01G195300 chr3D 93.712 986 57 5 1 982 600839134 600840118 0.000000e+00 1472.0
3 TraesCS3D01G195300 chr3D 92.936 991 61 7 1 982 313209864 313208874 0.000000e+00 1434.0
4 TraesCS3D01G195300 chr3D 92.929 990 60 8 1 982 85881853 85880866 0.000000e+00 1432.0
5 TraesCS3D01G195300 chr3D 92.727 990 59 11 1 982 378939721 378938737 0.000000e+00 1417.0
6 TraesCS3D01G195300 chr3D 92.619 989 61 10 1 982 159610094 159611077 0.000000e+00 1411.0
7 TraesCS3D01G195300 chr5A 93.248 1333 85 4 1655 2985 599254833 599256162 0.000000e+00 1958.0
8 TraesCS3D01G195300 chr5A 90.698 1333 118 6 1655 2985 653279834 653281162 0.000000e+00 1770.0
9 TraesCS3D01G195300 chr5A 88.996 518 45 6 1657 2169 666947936 666947426 6.160000e-177 630.0
10 TraesCS3D01G195300 chr7D 91.467 1336 79 20 1657 2982 574232607 574233917 0.000000e+00 1803.0
11 TraesCS3D01G195300 chr7D 92.988 984 63 6 3 982 73736952 73735971 0.000000e+00 1430.0
12 TraesCS3D01G195300 chr7D 92.821 989 60 9 1 982 438080577 438079593 0.000000e+00 1423.0
13 TraesCS3D01G195300 chr7D 94.845 97 5 0 1530 1626 4643982 4644078 5.850000e-33 152.0
14 TraesCS3D01G195300 chr7D 91.509 106 5 4 1521 1626 529689705 529689604 3.520000e-30 143.0
15 TraesCS3D01G195300 chr5D 91.343 1340 82 17 1657 2987 435542890 435541576 0.000000e+00 1801.0
16 TraesCS3D01G195300 chr5D 98.913 92 1 0 1539 1630 30547739 30547830 7.510000e-37 165.0
17 TraesCS3D01G195300 chr5D 93.204 103 5 2 1538 1640 109535537 109535637 2.100000e-32 150.0
18 TraesCS3D01G195300 chr5D 87.143 70 5 4 1034 1102 373809740 373809674 3.620000e-10 76.8
19 TraesCS3D01G195300 chr6D 91.093 1336 85 21 1658 2984 392885270 392886580 0.000000e+00 1777.0
20 TraesCS3D01G195300 chr6D 89.219 1011 60 27 1655 2659 72195353 72194386 0.000000e+00 1218.0
21 TraesCS3D01G195300 chr4D 90.380 1341 95 14 1655 2986 414509588 414508273 0.000000e+00 1731.0
22 TraesCS3D01G195300 chr4D 89.189 111 11 1 1515 1625 371926923 371926814 1.640000e-28 137.0
23 TraesCS3D01G195300 chr2D 90.075 1340 97 12 1657 2987 468362035 468360723 0.000000e+00 1705.0
24 TraesCS3D01G195300 chr2D 93.408 986 54 10 1 982 60746806 60747784 0.000000e+00 1450.0
25 TraesCS3D01G195300 chr2D 92.047 1031 68 4 1729 2757 57319303 57320321 0.000000e+00 1437.0
26 TraesCS3D01G195300 chr2D 94.572 829 41 1 2161 2985 152092132 152092960 0.000000e+00 1279.0
27 TraesCS3D01G195300 chr2D 93.056 864 53 2 2126 2985 607668338 607667478 0.000000e+00 1256.0
28 TraesCS3D01G195300 chr2D 90.789 456 30 6 1655 2105 607669404 607668956 1.740000e-167 599.0
29 TraesCS3D01G195300 chr2D 95.833 96 3 1 1530 1625 53145717 53145811 1.630000e-33 154.0
30 TraesCS3D01G195300 chr7B 88.024 835 73 12 1655 2484 467712689 467713501 0.000000e+00 963.0
31 TraesCS3D01G195300 chr3A 95.204 563 25 2 980 1542 248551429 248551989 0.000000e+00 889.0
32 TraesCS3D01G195300 chr3A 93.284 402 27 0 2983 3384 248552019 248552420 8.080000e-166 593.0
33 TraesCS3D01G195300 chr3A 100.000 37 0 0 1622 1658 248551986 248552022 6.060000e-08 69.4
34 TraesCS3D01G195300 chr3B 90.819 403 34 2 2983 3384 272953319 272952919 1.380000e-148 536.0
35 TraesCS3D01G195300 chr3B 89.474 190 17 3 1353 1542 272953535 272953349 1.570000e-58 237.0
36 TraesCS3D01G195300 chr2A 92.857 98 7 0 1537 1634 7558658 7558755 3.520000e-30 143.0
37 TraesCS3D01G195300 chr6B 90.654 107 8 2 1520 1625 416897304 416897409 1.270000e-29 141.0
38 TraesCS3D01G195300 chr4B 87.603 121 13 2 1536 1655 23660873 23660754 4.550000e-29 139.0
39 TraesCS3D01G195300 chr6A 91.071 56 2 3 1038 1092 5915930 5915983 4.680000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G195300 chr3D 189002224 189005607 3383 True 6250.000000 6250 100.000000 1 3384 1 chr3D.!!$R2 3383
1 TraesCS3D01G195300 chr3D 189026953 189027933 980 True 1489.000000 1489 94.094000 4 982 1 chr3D.!!$R3 978
2 TraesCS3D01G195300 chr3D 600839134 600840118 984 False 1472.000000 1472 93.712000 1 982 1 chr3D.!!$F2 981
3 TraesCS3D01G195300 chr3D 313208874 313209864 990 True 1434.000000 1434 92.936000 1 982 1 chr3D.!!$R4 981
4 TraesCS3D01G195300 chr3D 85880866 85881853 987 True 1432.000000 1432 92.929000 1 982 1 chr3D.!!$R1 981
5 TraesCS3D01G195300 chr3D 378938737 378939721 984 True 1417.000000 1417 92.727000 1 982 1 chr3D.!!$R5 981
6 TraesCS3D01G195300 chr3D 159610094 159611077 983 False 1411.000000 1411 92.619000 1 982 1 chr3D.!!$F1 981
7 TraesCS3D01G195300 chr5A 599254833 599256162 1329 False 1958.000000 1958 93.248000 1655 2985 1 chr5A.!!$F1 1330
8 TraesCS3D01G195300 chr5A 653279834 653281162 1328 False 1770.000000 1770 90.698000 1655 2985 1 chr5A.!!$F2 1330
9 TraesCS3D01G195300 chr5A 666947426 666947936 510 True 630.000000 630 88.996000 1657 2169 1 chr5A.!!$R1 512
10 TraesCS3D01G195300 chr7D 574232607 574233917 1310 False 1803.000000 1803 91.467000 1657 2982 1 chr7D.!!$F2 1325
11 TraesCS3D01G195300 chr7D 73735971 73736952 981 True 1430.000000 1430 92.988000 3 982 1 chr7D.!!$R1 979
12 TraesCS3D01G195300 chr7D 438079593 438080577 984 True 1423.000000 1423 92.821000 1 982 1 chr7D.!!$R2 981
13 TraesCS3D01G195300 chr5D 435541576 435542890 1314 True 1801.000000 1801 91.343000 1657 2987 1 chr5D.!!$R2 1330
14 TraesCS3D01G195300 chr6D 392885270 392886580 1310 False 1777.000000 1777 91.093000 1658 2984 1 chr6D.!!$F1 1326
15 TraesCS3D01G195300 chr6D 72194386 72195353 967 True 1218.000000 1218 89.219000 1655 2659 1 chr6D.!!$R1 1004
16 TraesCS3D01G195300 chr4D 414508273 414509588 1315 True 1731.000000 1731 90.380000 1655 2986 1 chr4D.!!$R2 1331
17 TraesCS3D01G195300 chr2D 468360723 468362035 1312 True 1705.000000 1705 90.075000 1657 2987 1 chr2D.!!$R1 1330
18 TraesCS3D01G195300 chr2D 60746806 60747784 978 False 1450.000000 1450 93.408000 1 982 1 chr2D.!!$F3 981
19 TraesCS3D01G195300 chr2D 57319303 57320321 1018 False 1437.000000 1437 92.047000 1729 2757 1 chr2D.!!$F2 1028
20 TraesCS3D01G195300 chr2D 152092132 152092960 828 False 1279.000000 1279 94.572000 2161 2985 1 chr2D.!!$F4 824
21 TraesCS3D01G195300 chr2D 607667478 607669404 1926 True 927.500000 1256 91.922500 1655 2985 2 chr2D.!!$R2 1330
22 TraesCS3D01G195300 chr7B 467712689 467713501 812 False 963.000000 963 88.024000 1655 2484 1 chr7B.!!$F1 829
23 TraesCS3D01G195300 chr3A 248551429 248552420 991 False 517.133333 889 96.162667 980 3384 3 chr3A.!!$F1 2404
24 TraesCS3D01G195300 chr3B 272952919 272953535 616 True 386.500000 536 90.146500 1353 3384 2 chr3B.!!$R1 2031

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
819 838 0.522626 TGCGTTCGGTACTTGATCGA 59.477 50.0 17.37 5.47 39.51 3.59 F
1830 1854 0.099968 CGAGCGAACGATAGGGAACA 59.900 55.0 0.00 0.00 43.77 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2825 0.179067 TTCTCCGGCACAACGTTCTT 60.179 50.0 0.0 0.0 0.0 2.52 R
2902 3550 0.906775 GGGTCCGTTCCATTCCTGTA 59.093 55.0 0.0 0.0 0.0 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
82 83 4.338012 TGTCTACATAGTTCTCGAACCCA 58.662 43.478 6.20 0.00 42.06 4.51
97 98 4.155733 CCATAGGGTCCGCACGCA 62.156 66.667 0.00 0.00 37.94 5.24
134 135 9.483916 TGACGATCGGTATTATGAATTTATGTT 57.516 29.630 20.98 0.00 0.00 2.71
288 290 1.906574 TCGGGCATTTTCTGGAGTACT 59.093 47.619 0.00 0.00 0.00 2.73
371 376 1.229209 GAGGTGACCAGGTGGAGGA 60.229 63.158 3.63 0.00 38.94 3.71
606 624 5.351465 CACACAAGTTGACAGTTGTCTTAGT 59.649 40.000 10.54 2.56 43.59 2.24
742 761 2.123683 CTCCCTCGGCCTCAGCTA 60.124 66.667 0.00 0.00 39.73 3.32
761 780 4.076394 GCTAGATCAAGAGTACGAGGGAT 58.924 47.826 0.00 0.00 0.00 3.85
763 782 2.625790 AGATCAAGAGTACGAGGGATGC 59.374 50.000 0.00 0.00 0.00 3.91
764 783 0.738975 TCAAGAGTACGAGGGATGCG 59.261 55.000 0.00 0.00 0.00 4.73
819 838 0.522626 TGCGTTCGGTACTTGATCGA 59.477 50.000 17.37 5.47 39.51 3.59
853 872 3.192844 AGACGTTCGACTACATCAACCAT 59.807 43.478 0.00 0.00 0.00 3.55
909 929 3.311110 TGGACACACTCTCCCGCC 61.311 66.667 0.00 0.00 0.00 6.13
915 935 1.918293 ACACTCTCCCGCCCATTGA 60.918 57.895 0.00 0.00 0.00 2.57
995 1017 2.752354 TCCCAACAAAATAGCACCATCG 59.248 45.455 0.00 0.00 0.00 3.84
1038 1060 8.331931 ACCAATACCTCTTTATAGACCATGAA 57.668 34.615 0.00 0.00 0.00 2.57
1039 1061 8.949421 ACCAATACCTCTTTATAGACCATGAAT 58.051 33.333 0.00 0.00 0.00 2.57
1057 1079 8.717717 ACCATGAATCTTTGTATCCTCTTGATA 58.282 33.333 0.00 0.00 34.76 2.15
1104 1126 5.873164 GCACCCTTTATCGAGAAAGAAGTTA 59.127 40.000 29.16 0.00 38.48 2.24
1142 1164 4.352009 TCCAATGTTTGCAATAGATGGGT 58.648 39.130 16.92 0.00 0.00 4.51
1151 1173 4.917385 TGCAATAGATGGGTGTGTAGTTT 58.083 39.130 0.00 0.00 0.00 2.66
1222 1244 4.142687 GGGTGGTTATTGATGTTTCTGTCG 60.143 45.833 0.00 0.00 0.00 4.35
1235 1257 4.765339 TGTTTCTGTCGTTGATCTAGGAGA 59.235 41.667 0.00 0.00 0.00 3.71
1245 1267 3.636679 TGATCTAGGAGAGTCTTGGTGG 58.363 50.000 0.00 0.00 0.00 4.61
1257 1279 2.295909 GTCTTGGTGGTTTTGCTGCATA 59.704 45.455 1.84 0.00 0.00 3.14
1259 1281 0.595588 TGGTGGTTTTGCTGCATACG 59.404 50.000 1.84 0.00 0.00 3.06
1304 1326 3.127721 GCAAAGGCACTATTCAAGACCTC 59.872 47.826 0.00 0.00 38.49 3.85
1306 1328 4.640771 AAGGCACTATTCAAGACCTCAA 57.359 40.909 0.00 0.00 38.49 3.02
1442 1464 6.314917 TCCTCCTTTTTCTTTTCCTATGCTT 58.685 36.000 0.00 0.00 0.00 3.91
1443 1465 6.209391 TCCTCCTTTTTCTTTTCCTATGCTTG 59.791 38.462 0.00 0.00 0.00 4.01
1503 1525 3.852286 TGCCAAAGAAATGCTAATGCTG 58.148 40.909 0.00 0.00 40.48 4.41
1513 1535 6.430925 AGAAATGCTAATGCTGACAGTTGTAA 59.569 34.615 3.99 0.00 40.48 2.41
1547 1569 9.994017 ATACTCTCTTTTAGTTTAGTACTCCCT 57.006 33.333 0.00 0.00 38.33 4.20
1548 1570 8.352137 ACTCTCTTTTAGTTTAGTACTCCCTC 57.648 38.462 0.00 0.00 38.33 4.30
1549 1571 7.396907 ACTCTCTTTTAGTTTAGTACTCCCTCC 59.603 40.741 0.00 0.00 38.33 4.30
1550 1572 6.376581 TCTCTTTTAGTTTAGTACTCCCTCCG 59.623 42.308 0.00 0.00 38.33 4.63
1551 1573 6.012745 TCTTTTAGTTTAGTACTCCCTCCGT 58.987 40.000 0.00 0.00 38.33 4.69
1552 1574 5.904362 TTTAGTTTAGTACTCCCTCCGTC 57.096 43.478 0.00 0.00 38.33 4.79
1553 1575 2.732763 AGTTTAGTACTCCCTCCGTCC 58.267 52.381 0.00 0.00 28.23 4.79
1554 1576 1.753649 GTTTAGTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
1555 1577 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1556 1578 1.229131 TAGTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
1557 1579 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
1558 1580 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
1559 1581 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
1560 1582 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
1561 1583 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1562 1584 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1563 1585 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1564 1586 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1565 1587 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1566 1588 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1567 1589 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
1568 1590 4.141914 CCTCCGTCCCATAATATAAGAGCC 60.142 50.000 0.00 0.00 0.00 4.70
1569 1591 3.773119 TCCGTCCCATAATATAAGAGCCC 59.227 47.826 0.00 0.00 0.00 5.19
1570 1592 3.775316 CCGTCCCATAATATAAGAGCCCT 59.225 47.826 0.00 0.00 0.00 5.19
1571 1593 4.225267 CCGTCCCATAATATAAGAGCCCTT 59.775 45.833 0.00 0.00 36.43 3.95
1572 1594 5.280521 CCGTCCCATAATATAAGAGCCCTTT 60.281 44.000 0.00 0.00 33.94 3.11
1573 1595 6.238648 CGTCCCATAATATAAGAGCCCTTTT 58.761 40.000 0.00 0.00 33.94 2.27
1574 1596 6.715264 CGTCCCATAATATAAGAGCCCTTTTT 59.285 38.462 0.00 0.00 33.94 1.94
1575 1597 7.881232 CGTCCCATAATATAAGAGCCCTTTTTA 59.119 37.037 0.00 0.00 33.94 1.52
1576 1598 9.011095 GTCCCATAATATAAGAGCCCTTTTTAC 57.989 37.037 0.00 0.00 33.94 2.01
1577 1599 8.729047 TCCCATAATATAAGAGCCCTTTTTACA 58.271 33.333 0.00 0.00 33.94 2.41
1578 1600 8.793592 CCCATAATATAAGAGCCCTTTTTACAC 58.206 37.037 0.00 0.00 33.94 2.90
1579 1601 9.574516 CCATAATATAAGAGCCCTTTTTACACT 57.425 33.333 0.00 0.00 33.94 3.55
1583 1605 8.959705 ATATAAGAGCCCTTTTTACACTACAC 57.040 34.615 0.00 0.00 33.94 2.90
1584 1606 4.976540 AGAGCCCTTTTTACACTACACT 57.023 40.909 0.00 0.00 0.00 3.55
1585 1607 6.429521 AAGAGCCCTTTTTACACTACACTA 57.570 37.500 0.00 0.00 0.00 2.74
1586 1608 6.038997 AGAGCCCTTTTTACACTACACTAG 57.961 41.667 0.00 0.00 0.00 2.57
1587 1609 5.543020 AGAGCCCTTTTTACACTACACTAGT 59.457 40.000 0.00 0.00 40.28 2.57
1600 1622 4.743644 ACTACACTAGTGTCAAAAACGCTC 59.256 41.667 31.11 0.00 45.69 5.03
1601 1623 3.793559 ACACTAGTGTCAAAAACGCTCT 58.206 40.909 22.95 0.00 45.69 4.09
1602 1624 4.189231 ACACTAGTGTCAAAAACGCTCTT 58.811 39.130 22.95 0.00 45.69 2.85
1603 1625 5.353938 ACACTAGTGTCAAAAACGCTCTTA 58.646 37.500 22.95 0.00 45.69 2.10
1604 1626 5.989777 ACACTAGTGTCAAAAACGCTCTTAT 59.010 36.000 22.95 0.00 45.69 1.73
1605 1627 7.149973 ACACTAGTGTCAAAAACGCTCTTATA 58.850 34.615 22.95 0.00 45.69 0.98
1606 1628 7.817962 ACACTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 22.95 0.00 45.69 0.86
1607 1629 8.656849 CACTAGTGTCAAAAACGCTCTTATATT 58.343 33.333 15.06 0.00 45.69 1.28
1608 1630 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
1611 1633 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
1612 1634 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
1613 1635 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
1614 1636 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
1615 1637 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
1616 1638 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
1617 1639 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
1618 1640 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
1619 1641 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
1620 1642 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1724 1747 4.473520 CCCGCAGCCCATTCTCGT 62.474 66.667 0.00 0.00 0.00 4.18
1747 1770 1.962807 TCGGTTAGTCGAAGGAACCAA 59.037 47.619 19.05 3.75 42.36 3.67
1789 1813 5.538118 ACGGAATATTCGCTCATTATGTGA 58.462 37.500 9.32 0.00 35.05 3.58
1817 1841 1.538204 GCATACCTCCAAATCGAGCGA 60.538 52.381 0.00 0.00 0.00 4.93
1830 1854 0.099968 CGAGCGAACGATAGGGAACA 59.900 55.000 0.00 0.00 43.77 3.18
1832 1856 2.798499 CGAGCGAACGATAGGGAACAAT 60.798 50.000 0.00 0.00 43.77 2.71
1858 1884 3.877357 CTCTCGCACGCGCCTCTA 61.877 66.667 5.73 0.00 39.59 2.43
1876 1902 0.250640 TACCCTATCCTCTCGCGACC 60.251 60.000 3.71 0.00 0.00 4.79
1877 1903 2.618219 CCCTATCCTCTCGCGACCG 61.618 68.421 3.71 0.00 0.00 4.79
1982 2014 1.619975 TCCCCTCCGTCTCTCCTCT 60.620 63.158 0.00 0.00 0.00 3.69
2083 2116 4.100084 CGGTGAGAGGCCATGGCA 62.100 66.667 36.56 14.68 44.11 4.92
2203 2833 1.217882 CCAACTCGCTGAAGAACGTT 58.782 50.000 0.00 0.00 0.00 3.99
2322 2968 1.750399 CCGTGCTTCCATTCCTGGG 60.750 63.158 0.00 0.00 43.34 4.45
2350 2996 4.119363 GGCTCTGGCATGGGCTGA 62.119 66.667 8.37 0.00 40.87 4.26
2408 3054 8.548880 AATTAAGTGGGTGATTAGACTAGCTA 57.451 34.615 0.00 0.00 0.00 3.32
2448 3094 9.410556 GCTTCTAGAAGAAATAAGCTCTCATAG 57.589 37.037 32.16 4.04 40.79 2.23
2644 3291 9.601217 GGTTGTATGACTGAGTATGATAACTTT 57.399 33.333 0.00 0.00 0.00 2.66
2654 3301 9.264719 CTGAGTATGATAACTTTGCATGTATGA 57.735 33.333 0.00 0.00 0.00 2.15
2892 3540 3.207778 CAACCCGTTCCACTTTTCTGTA 58.792 45.455 0.00 0.00 0.00 2.74
2902 3550 7.308348 CGTTCCACTTTTCTGTATGTACCAAAT 60.308 37.037 0.00 0.00 0.00 2.32
2968 3616 0.949105 CCGTTCCACTTGGTTCCTCG 60.949 60.000 0.00 0.00 36.34 4.63
3013 3661 5.653769 CCTCAAAAGAGGGCAATTAAGATGA 59.346 40.000 3.58 0.00 38.66 2.92
3020 3668 4.032310 AGGGCAATTAAGATGATTTGGCA 58.968 39.130 11.44 0.00 0.00 4.92
3028 3676 7.828508 ATTAAGATGATTTGGCAGCTGATTA 57.171 32.000 20.43 0.00 34.28 1.75
3041 3689 8.297470 TGGCAGCTGATTATTTTCTCTTATTT 57.703 30.769 20.43 0.00 0.00 1.40
3064 3712 5.389520 TCCCTGTGAATGGTTGAAATACAA 58.610 37.500 0.00 0.00 36.02 2.41
3071 3719 2.852449 TGGTTGAAATACAAGGCGTCA 58.148 42.857 0.00 0.00 39.30 4.35
3130 3778 3.564225 GCCATTATACAGTGCACCCTTAC 59.436 47.826 14.63 0.00 0.00 2.34
3186 3834 5.193679 GGGCAATACATTTGGAGTACTTCT 58.806 41.667 2.07 0.00 0.00 2.85
3187 3835 5.066505 GGGCAATACATTTGGAGTACTTCTG 59.933 44.000 2.07 0.00 0.00 3.02
3202 3850 7.148787 GGAGTACTTCTGTAACAAGATGTTTCG 60.149 40.741 0.00 0.00 41.45 3.46
3270 3918 1.606480 CCTCTCGACTTTGCAGCTTCA 60.606 52.381 0.00 0.00 0.00 3.02
3286 3934 5.106396 GCAGCTTCATGTTGTAAGACTTCAT 60.106 40.000 0.00 0.00 0.00 2.57
3344 3992 1.972588 AGGGAACTCCTGTAGGCAAT 58.027 50.000 0.00 0.00 46.07 3.56
3350 3998 4.838986 GGAACTCCTGTAGGCAATATCCTA 59.161 45.833 0.00 0.00 37.66 2.94
3358 4007 1.068121 GGCAATATCCTAGGCAGGGT 58.932 55.000 2.96 0.00 42.87 4.34
3366 4015 3.414759 TCCTAGGCAGGGTTTCTGATA 57.585 47.619 2.96 0.00 46.18 2.15
3377 4026 5.065731 CAGGGTTTCTGATAAATGCTCAGTC 59.934 44.000 0.42 0.00 46.18 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 0.249741 GTTATGCGTGCGGACCCTAT 60.250 55.000 0.00 0.00 0.00 2.57
134 135 5.406175 CGAACTACCTTCGGTACATCAAAAA 59.594 40.000 0.00 0.00 46.85 1.94
575 593 3.809832 ACTGTCAACTTGTGTGTCTATGC 59.190 43.478 0.00 0.00 0.00 3.14
673 691 2.442212 TGATGAAGTTACCGACGCAA 57.558 45.000 0.00 0.00 0.00 4.85
742 761 2.625790 GCATCCCTCGTACTCTTGATCT 59.374 50.000 0.00 0.00 0.00 2.75
761 780 3.973516 ACGTTCAGCTCGGTCGCA 61.974 61.111 0.00 0.00 0.00 5.10
763 782 2.050351 ACACGTTCAGCTCGGTCG 60.050 61.111 0.00 0.00 0.00 4.79
764 783 2.658707 GCACACGTTCAGCTCGGTC 61.659 63.158 0.00 0.00 0.00 4.79
819 838 1.393539 CGAACGTCTTTGCGATCCAAT 59.606 47.619 0.00 0.00 32.49 3.16
829 848 3.985925 GGTTGATGTAGTCGAACGTCTTT 59.014 43.478 10.09 0.00 36.53 2.52
995 1017 9.668497 GGTATTGGTCTTGTTTATATATCTCCC 57.332 37.037 0.00 0.00 0.00 4.30
1075 1097 6.469410 TCTTTCTCGATAAAGGGTGCTTTTA 58.531 36.000 19.56 0.00 37.13 1.52
1080 1102 4.254492 ACTTCTTTCTCGATAAAGGGTGC 58.746 43.478 19.56 0.00 37.13 5.01
1104 1126 6.655078 ACATTGGAAACACAGAGCTAAAAT 57.345 33.333 0.00 0.00 42.67 1.82
1222 1244 4.142049 CCACCAAGACTCTCCTAGATCAAC 60.142 50.000 0.00 0.00 0.00 3.18
1235 1257 0.746659 GCAGCAAAACCACCAAGACT 59.253 50.000 0.00 0.00 0.00 3.24
1257 1279 8.407064 GCATAATAGGAGAGTATAATACTGCGT 58.593 37.037 0.00 0.00 39.59 5.24
1415 1437 8.285163 AGCATAGGAAAAGAAAAAGGAGGATAT 58.715 33.333 0.00 0.00 0.00 1.63
1503 1525 9.640963 AGAGAGTATTACACATTTACAACTGTC 57.359 33.333 0.00 0.00 0.00 3.51
1538 1560 1.229131 TATGGGACGGAGGGAGTACT 58.771 55.000 0.00 0.00 0.00 2.73
1539 1561 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
1540 1562 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
1541 1563 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
1542 1564 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
1543 1565 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
1544 1566 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
1545 1567 4.141914 GGCTCTTATATTATGGGACGGAGG 60.142 50.000 0.00 0.00 0.00 4.30
1546 1568 4.141914 GGGCTCTTATATTATGGGACGGAG 60.142 50.000 0.00 0.00 0.00 4.63
1547 1569 3.773119 GGGCTCTTATATTATGGGACGGA 59.227 47.826 0.00 0.00 0.00 4.69
1548 1570 3.775316 AGGGCTCTTATATTATGGGACGG 59.225 47.826 0.00 0.00 0.00 4.79
1549 1571 5.422214 AAGGGCTCTTATATTATGGGACG 57.578 43.478 0.00 0.00 0.00 4.79
1550 1572 9.011095 GTAAAAAGGGCTCTTATATTATGGGAC 57.989 37.037 0.00 0.00 32.01 4.46
1551 1573 8.729047 TGTAAAAAGGGCTCTTATATTATGGGA 58.271 33.333 0.00 0.00 32.01 4.37
1552 1574 8.793592 GTGTAAAAAGGGCTCTTATATTATGGG 58.206 37.037 0.00 0.00 32.01 4.00
1553 1575 9.574516 AGTGTAAAAAGGGCTCTTATATTATGG 57.425 33.333 0.00 0.00 32.01 2.74
1557 1579 9.392259 GTGTAGTGTAAAAAGGGCTCTTATATT 57.608 33.333 0.00 0.00 32.01 1.28
1558 1580 8.769359 AGTGTAGTGTAAAAAGGGCTCTTATAT 58.231 33.333 0.00 0.00 32.01 0.86
1559 1581 8.142485 AGTGTAGTGTAAAAAGGGCTCTTATA 57.858 34.615 0.00 0.00 32.01 0.98
1560 1582 7.017319 AGTGTAGTGTAAAAAGGGCTCTTAT 57.983 36.000 0.00 0.00 32.01 1.73
1561 1583 6.429521 AGTGTAGTGTAAAAAGGGCTCTTA 57.570 37.500 0.00 0.00 32.01 2.10
1562 1584 5.306114 AGTGTAGTGTAAAAAGGGCTCTT 57.694 39.130 0.00 0.00 34.07 2.85
1563 1585 4.976540 AGTGTAGTGTAAAAAGGGCTCT 57.023 40.909 0.00 0.00 0.00 4.09
1564 1586 5.791666 ACTAGTGTAGTGTAAAAAGGGCTC 58.208 41.667 0.00 0.00 37.69 4.70
1565 1587 5.820404 ACTAGTGTAGTGTAAAAAGGGCT 57.180 39.130 0.00 0.00 37.69 5.19
1577 1599 4.690122 AGCGTTTTTGACACTAGTGTAGT 58.310 39.130 27.98 6.32 45.05 2.73
1578 1600 4.982916 AGAGCGTTTTTGACACTAGTGTAG 59.017 41.667 27.98 13.76 45.05 2.74
1579 1601 4.940463 AGAGCGTTTTTGACACTAGTGTA 58.060 39.130 27.98 11.50 45.05 2.90
1581 1603 4.795970 AAGAGCGTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
1582 1604 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
1585 1607 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
1586 1608 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
1587 1609 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
1588 1610 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
1589 1611 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
1590 1612 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
1591 1613 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
1592 1614 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
1593 1615 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
1594 1616 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
1595 1617 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
1596 1618 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
1597 1619 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
1598 1620 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
1599 1621 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
1600 1622 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
1601 1623 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
1602 1624 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
1603 1625 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
1604 1626 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
1605 1627 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1606 1628 4.687262 ATATACTCCCTCCGTCCCATAA 57.313 45.455 0.00 0.00 0.00 1.90
1607 1629 5.434044 TGATATATACTCCCTCCGTCCCATA 59.566 44.000 0.00 0.00 0.00 2.74
1608 1630 4.232122 TGATATATACTCCCTCCGTCCCAT 59.768 45.833 0.00 0.00 0.00 4.00
1609 1631 3.594685 TGATATATACTCCCTCCGTCCCA 59.405 47.826 0.00 0.00 0.00 4.37
1610 1632 4.246712 TGATATATACTCCCTCCGTCCC 57.753 50.000 0.00 0.00 0.00 4.46
1611 1633 6.154706 ACAATTGATATATACTCCCTCCGTCC 59.845 42.308 13.59 0.00 0.00 4.79
1612 1634 7.171630 ACAATTGATATATACTCCCTCCGTC 57.828 40.000 13.59 0.00 0.00 4.79
1613 1635 7.342284 CCTACAATTGATATATACTCCCTCCGT 59.658 40.741 13.59 0.00 0.00 4.69
1614 1636 7.560262 TCCTACAATTGATATATACTCCCTCCG 59.440 40.741 13.59 0.00 0.00 4.63
1615 1637 8.840200 TCCTACAATTGATATATACTCCCTCC 57.160 38.462 13.59 0.00 0.00 4.30
1616 1638 8.417884 GCTCCTACAATTGATATATACTCCCTC 58.582 40.741 13.59 0.00 0.00 4.30
1617 1639 7.345914 GGCTCCTACAATTGATATATACTCCCT 59.654 40.741 13.59 0.00 0.00 4.20
1618 1640 7.345914 AGGCTCCTACAATTGATATATACTCCC 59.654 40.741 13.59 0.23 0.00 4.30
1619 1641 8.312669 AGGCTCCTACAATTGATATATACTCC 57.687 38.462 13.59 2.33 0.00 3.85
1620 1642 9.196139 AGAGGCTCCTACAATTGATATATACTC 57.804 37.037 13.59 11.41 0.00 2.59
1710 1733 1.796796 GAACACGAGAATGGGCTGC 59.203 57.895 0.00 0.00 0.00 5.25
1724 1747 2.288395 GGTTCCTTCGACTAACCGAACA 60.288 50.000 6.92 0.00 42.74 3.18
1830 1854 0.827368 GTGCGAGAGGAAGAGGGATT 59.173 55.000 0.00 0.00 0.00 3.01
1832 1856 2.046864 CGTGCGAGAGGAAGAGGGA 61.047 63.158 0.00 0.00 31.65 4.20
1858 1884 1.528776 GGTCGCGAGAGGATAGGGT 60.529 63.158 10.24 0.00 43.49 4.34
1982 2014 2.509111 CTGCTACGCGCCATCACA 60.509 61.111 5.73 0.00 38.05 3.58
2021 2054 2.673200 GCTGCCTGATCTCCACCCA 61.673 63.158 0.00 0.00 0.00 4.51
2083 2116 4.175337 CCGTCGGCATGTCCCCAT 62.175 66.667 0.00 0.00 0.00 4.00
2195 2825 0.179067 TTCTCCGGCACAACGTTCTT 60.179 50.000 0.00 0.00 0.00 2.52
2233 2863 4.060038 CCGTTGTACCTCCGGCGT 62.060 66.667 6.01 0.00 34.62 5.68
2350 2996 3.970640 CCACCTAGCTTTAGAGGGAGAAT 59.029 47.826 5.27 0.00 37.14 2.40
2448 3094 2.176889 TGTACTCCCAGCTCTTACCAC 58.823 52.381 0.00 0.00 0.00 4.16
2644 3291 4.516323 AGTGCACTACATTCATACATGCA 58.484 39.130 20.16 0.00 39.16 3.96
2784 3432 8.789825 ATTTTGGCAGCATTTCATTTGTATTA 57.210 26.923 0.00 0.00 0.00 0.98
2892 3540 5.588648 CGTTCCATTCCTGTATTTGGTACAT 59.411 40.000 0.00 0.00 42.21 2.29
2902 3550 0.906775 GGGTCCGTTCCATTCCTGTA 59.093 55.000 0.00 0.00 0.00 2.74
2968 3616 4.018688 AGGGAACTTAGGGTGTATTTGGTC 60.019 45.833 0.00 0.00 37.44 4.02
2975 3623 4.909088 TCTTTTGAGGGAACTTAGGGTGTA 59.091 41.667 0.00 0.00 44.43 2.90
3013 3661 6.786967 AGAGAAAATAATCAGCTGCCAAAT 57.213 33.333 9.47 0.00 0.00 2.32
3020 3668 9.129532 CAGGGAAATAAGAGAAAATAATCAGCT 57.870 33.333 0.00 0.00 0.00 4.24
3028 3676 7.675619 ACCATTCACAGGGAAATAAGAGAAAAT 59.324 33.333 0.00 0.00 39.39 1.82
3041 3689 4.991776 TGTATTTCAACCATTCACAGGGA 58.008 39.130 0.00 0.00 0.00 4.20
3064 3712 7.549839 TGTGTAACTAATAAGTTATGACGCCT 58.450 34.615 0.00 0.00 46.98 5.52
3186 3834 7.254522 GGAAAGTGTACGAAACATCTTGTTACA 60.255 37.037 0.00 0.00 40.14 2.41
3187 3835 7.042254 AGGAAAGTGTACGAAACATCTTGTTAC 60.042 37.037 0.00 0.00 40.14 2.50
3350 3998 3.026694 GCATTTATCAGAAACCCTGCCT 58.973 45.455 0.00 0.00 42.62 4.75
3358 4007 5.045651 TCCTGGACTGAGCATTTATCAGAAA 60.046 40.000 9.78 0.00 45.80 2.52


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

AutoCloner maintained by Alex Coulton.