Multiple sequence alignment - TraesCS7B01G383500

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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 TraesCS7B01G383500 chr7B 100.000 4031 0 0 1 4031 649210250 649214280 0.000000e+00 7444.0
1 TraesCS7B01G383500 chr7B 94.758 2995 102 9 1071 4031 649013452 649016425 0.000000e+00 4610.0
2 TraesCS7B01G383500 chr7B 92.799 1597 92 10 1685 3274 649097684 649099264 0.000000e+00 2290.0
3 TraesCS7B01G383500 chr7B 93.776 964 56 2 2043 3006 649318793 649319752 0.000000e+00 1445.0
4 TraesCS7B01G383500 chr7B 85.219 1299 148 21 2354 3617 648917753 648919042 0.000000e+00 1295.0
5 TraesCS7B01G383500 chr7B 83.756 1342 156 40 1071 2362 648916557 648917886 0.000000e+00 1214.0
6 TraesCS7B01G383500 chr7B 84.372 1139 131 30 1200 2299 648783030 648784160 0.000000e+00 1074.0
7 TraesCS7B01G383500 chr7B 91.911 717 34 5 3319 4031 649099260 649099956 0.000000e+00 981.0
8 TraesCS7B01G383500 chr7B 86.166 918 79 21 1 888 649012386 649013285 0.000000e+00 948.0
9 TraesCS7B01G383500 chr7B 87.637 639 36 10 3398 4031 649319789 649320389 0.000000e+00 702.0
10 TraesCS7B01G383500 chr7B 84.539 401 45 8 1147 1533 649247417 649247814 8.180000e-102 381.0
11 TraesCS7B01G383500 chr7B 96.154 52 2 0 905 956 649013269 649013320 7.180000e-13 86.1
12 TraesCS7B01G383500 chr7D 92.058 1939 90 27 1071 2975 581384540 581386448 0.000000e+00 2669.0
13 TraesCS7B01G383500 chr7D 93.891 1686 65 10 2354 4031 581453406 581455061 0.000000e+00 2508.0
14 TraesCS7B01G383500 chr7D 93.676 1091 43 7 2946 4031 581389610 581390679 0.000000e+00 1609.0
15 TraesCS7B01G383500 chr7D 86.023 1295 141 16 2354 3617 581290806 581292091 0.000000e+00 1352.0
16 TraesCS7B01G383500 chr7D 94.797 615 31 1 1068 1681 581452232 581452846 0.000000e+00 957.0
17 TraesCS7B01G383500 chr7D 94.003 617 34 1 1749 2362 581452923 581453539 0.000000e+00 931.0
18 TraesCS7B01G383500 chr7D 88.663 688 67 6 1685 2362 581290253 581290939 0.000000e+00 828.0
19 TraesCS7B01G383500 chr7D 89.028 638 53 6 1 627 581383314 581383945 0.000000e+00 774.0
20 TraesCS7B01G383500 chr7D 82.750 829 108 20 2354 3164 581297801 581298612 0.000000e+00 706.0
21 TraesCS7B01G383500 chr7D 87.637 639 38 17 3398 4031 581690342 581690944 0.000000e+00 704.0
22 TraesCS7B01G383500 chr7D 83.968 630 57 25 1071 1675 581289597 581290207 7.560000e-157 564.0
23 TraesCS7B01G383500 chr7D 93.151 365 19 5 3002 3365 581386449 581386808 7.670000e-147 531.0
24 TraesCS7B01G383500 chr7D 88.235 357 32 9 93 443 581451276 581451628 6.230000e-113 418.0
25 TraesCS7B01G383500 chr7D 93.657 268 16 1 3399 3666 581386810 581387076 2.260000e-107 399.0
26 TraesCS7B01G383500 chr7D 91.667 240 19 1 619 858 581384103 581384341 8.350000e-87 331.0
27 TraesCS7B01G383500 chr7D 89.904 208 12 7 3817 4019 581388970 581389173 4.000000e-65 259.0
28 TraesCS7B01G383500 chr7D 93.130 131 9 0 3693 3823 581387074 581387204 4.110000e-45 193.0
29 TraesCS7B01G383500 chr7D 93.617 47 3 0 1685 1731 581452877 581452923 2.010000e-08 71.3
30 TraesCS7B01G383500 chr7A 94.140 1314 57 10 2354 3659 673245031 673246332 0.000000e+00 1982.0
31 TraesCS7B01G383500 chr7A 93.873 963 58 1 2044 3006 673314538 673315499 0.000000e+00 1450.0
32 TraesCS7B01G383500 chr7A 85.758 1299 142 20 2354 3617 673127650 673128940 0.000000e+00 1334.0
33 TraesCS7B01G383500 chr7A 84.678 1351 141 38 1073 2362 673126438 673127783 0.000000e+00 1288.0
34 TraesCS7B01G383500 chr7A 95.745 611 26 0 1071 1681 673243857 673244467 0.000000e+00 985.0
35 TraesCS7B01G383500 chr7A 94.042 621 30 2 1749 2362 673244544 673245164 0.000000e+00 935.0
36 TraesCS7B01G383500 chr7A 86.427 641 47 21 3398 4031 673315536 673316143 0.000000e+00 665.0
37 TraesCS7B01G383500 chr7A 90.055 181 18 0 676 856 673243447 673243627 6.740000e-58 235.0
38 TraesCS7B01G383500 chr7A 91.489 47 4 0 1685 1731 673244498 673244544 9.350000e-07 65.8
39 TraesCS7B01G383500 chr5B 94.059 101 5 1 971 1070 656900479 656900579 6.980000e-33 152.0
40 TraesCS7B01G383500 chr5B 94.681 94 3 2 978 1071 441123819 441123910 1.170000e-30 145.0
41 TraesCS7B01G383500 chr6B 93.269 104 3 3 961 1064 1904167 1904068 2.510000e-32 150.0
42 TraesCS7B01G383500 chr6B 90.991 111 7 3 961 1070 712657206 712657098 3.250000e-31 147.0
43 TraesCS7B01G383500 chr1A 94.845 97 3 2 974 1070 542850912 542851006 2.510000e-32 150.0
44 TraesCS7B01G383500 chr1A 92.727 55 4 0 520 574 481926977 481927031 3.340000e-11 80.5
45 TraesCS7B01G383500 chr3B 91.818 110 4 4 961 1070 52884828 52884932 9.030000e-32 148.0
46 TraesCS7B01G383500 chr3B 92.857 98 5 2 974 1071 31255976 31256071 1.510000e-29 141.0
47 TraesCS7B01G383500 chr2D 90.000 120 5 5 964 1082 573575461 573575574 9.030000e-32 148.0
48 TraesCS7B01G383500 chr4A 93.814 97 4 2 974 1070 714057479 714057573 1.170000e-30 145.0


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 TraesCS7B01G383500 chr7B 649210250 649214280 4030 False 7444.000000 7444 100.000000 1 4031 1 chr7B.!!$F2 4030
1 TraesCS7B01G383500 chr7B 649012386 649016425 4039 False 1881.366667 4610 92.359333 1 4031 3 chr7B.!!$F5 4030
2 TraesCS7B01G383500 chr7B 649097684 649099956 2272 False 1635.500000 2290 92.355000 1685 4031 2 chr7B.!!$F6 2346
3 TraesCS7B01G383500 chr7B 648916557 648919042 2485 False 1254.500000 1295 84.487500 1071 3617 2 chr7B.!!$F4 2546
4 TraesCS7B01G383500 chr7B 648783030 648784160 1130 False 1074.000000 1074 84.372000 1200 2299 1 chr7B.!!$F1 1099
5 TraesCS7B01G383500 chr7B 649318793 649320389 1596 False 1073.500000 1445 90.706500 2043 4031 2 chr7B.!!$F7 1988
6 TraesCS7B01G383500 chr7D 581451276 581455061 3785 False 977.060000 2508 92.908600 93 4031 5 chr7D.!!$F5 3938
7 TraesCS7B01G383500 chr7D 581289597 581292091 2494 False 914.666667 1352 86.218000 1071 3617 3 chr7D.!!$F3 2546
8 TraesCS7B01G383500 chr7D 581383314 581390679 7365 False 845.625000 2669 92.033875 1 4031 8 chr7D.!!$F4 4030
9 TraesCS7B01G383500 chr7D 581297801 581298612 811 False 706.000000 706 82.750000 2354 3164 1 chr7D.!!$F1 810
10 TraesCS7B01G383500 chr7D 581690342 581690944 602 False 704.000000 704 87.637000 3398 4031 1 chr7D.!!$F2 633
11 TraesCS7B01G383500 chr7A 673126438 673128940 2502 False 1311.000000 1334 85.218000 1073 3617 2 chr7A.!!$F1 2544
12 TraesCS7B01G383500 chr7A 673314538 673316143 1605 False 1057.500000 1450 90.150000 2044 4031 2 chr7A.!!$F3 1987
13 TraesCS7B01G383500 chr7A 673243447 673246332 2885 False 840.560000 1982 93.094200 676 3659 5 chr7A.!!$F2 2983

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
997 1543 0.178947 CCAAGGCCACTTAAACCCCA 60.179 55.000 5.01 0.00 34.49 4.96 F
1906 2539 0.179004 TGTTGATGGTTCTGCCGGTT 60.179 50.000 1.90 0.00 41.21 4.44 F
1923 2556 1.065854 GGTTGTCTAGCTGCAGTGGAT 60.066 52.381 16.64 1.84 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2848 0.542702 CCTCCTGGGCCACAACAAAT 60.543 55.0 0.0 0.0 0.0 2.32 R
2938 3751 1.014352 CTAACATGGTAAGTGCCCGC 58.986 55.0 0.0 0.0 0.0 6.13 R
3171 7184 2.015736 AAGCTCCTGAATGTGCGTAG 57.984 50.0 0.0 0.0 0.0 3.51 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
71 72 6.669591 TGGTTCTCTTGATCCTATCTTTCTCA 59.330 38.462 0.00 0.00 34.11 3.27
73 74 6.723298 TCTCTTGATCCTATCTTTCTCACC 57.277 41.667 0.00 0.00 0.00 4.02
355 367 2.542178 TCGTGGAATTGTGACACTTTCG 59.458 45.455 7.20 2.05 33.13 3.46
364 376 4.659111 TGTGACACTTTCGGTTTAGAGA 57.341 40.909 7.20 0.00 0.00 3.10
417 429 8.269424 GTCATCTGAAAACATTATACAGCTACG 58.731 37.037 0.00 0.00 0.00 3.51
418 430 8.194769 TCATCTGAAAACATTATACAGCTACGA 58.805 33.333 0.00 0.00 0.00 3.43
427 439 0.956902 TACAGCTACGACGAGGCACA 60.957 55.000 0.00 0.00 0.00 4.57
448 460 1.474143 GGGCAGAGCAGATCCTGTAAC 60.474 57.143 0.00 0.00 33.43 2.50
449 461 1.208052 GGCAGAGCAGATCCTGTAACA 59.792 52.381 0.00 0.00 33.43 2.41
450 462 2.158842 GGCAGAGCAGATCCTGTAACAT 60.159 50.000 0.00 0.00 33.43 2.71
456 469 6.039829 CAGAGCAGATCCTGTAACATGTACTA 59.960 42.308 0.00 0.00 33.43 1.82
461 474 8.979574 GCAGATCCTGTAACATGTACTATAAAC 58.020 37.037 0.00 0.00 33.43 2.01
487 500 1.734655 TGCTCCTTTTCCTCCTCACT 58.265 50.000 0.00 0.00 0.00 3.41
524 537 0.521867 CGCATGCATGGTCAAACTCG 60.522 55.000 27.34 15.52 0.00 4.18
647 846 0.755698 CTACCAAGCTCCTCCGCCTA 60.756 60.000 0.00 0.00 0.00 3.93
651 850 1.000486 AAGCTCCTCCGCCTACTCA 60.000 57.895 0.00 0.00 0.00 3.41
657 856 1.608717 CCTCCGCCTACTCACTGCTT 61.609 60.000 0.00 0.00 0.00 3.91
664 863 0.945743 CTACTCACTGCTTGCGTGCA 60.946 55.000 3.48 3.48 41.05 4.57
670 869 3.639008 TGCTTGCGTGCAGTGTCG 61.639 61.111 0.00 5.70 38.12 4.35
885 1090 5.590976 GGGGGATCTTTCATTTAGAGGAT 57.409 43.478 0.00 0.00 0.00 3.24
886 1091 5.565509 GGGGGATCTTTCATTTAGAGGATC 58.434 45.833 0.00 0.00 36.98 3.36
945 1454 2.222908 CGGTGCGTTTTGTGCAAATTTT 60.223 40.909 0.00 0.00 45.23 1.82
960 1506 4.741235 GCAAATTTTAAGGTTTGACCGGGT 60.741 41.667 6.32 0.00 44.90 5.28
962 1508 4.594123 ATTTTAAGGTTTGACCGGGTTG 57.406 40.909 6.32 0.00 44.90 3.77
963 1509 3.294038 TTTAAGGTTTGACCGGGTTGA 57.706 42.857 6.32 0.00 44.90 3.18
964 1510 2.259266 TAAGGTTTGACCGGGTTGAC 57.741 50.000 6.32 0.43 44.90 3.18
965 1511 0.816421 AAGGTTTGACCGGGTTGACG 60.816 55.000 6.32 0.00 44.90 4.35
966 1512 1.227615 GGTTTGACCGGGTTGACGA 60.228 57.895 6.32 0.00 35.47 4.20
967 1513 0.604511 GGTTTGACCGGGTTGACGAT 60.605 55.000 6.32 0.00 35.47 3.73
968 1514 1.338011 GGTTTGACCGGGTTGACGATA 60.338 52.381 6.32 0.00 35.47 2.92
969 1515 2.415776 GTTTGACCGGGTTGACGATAA 58.584 47.619 6.32 0.00 35.47 1.75
991 1537 2.034999 CCCGCCAAGGCCACTTAA 59.965 61.111 5.01 0.00 39.21 1.85
992 1538 1.605165 CCCGCCAAGGCCACTTAAA 60.605 57.895 5.01 0.00 39.21 1.52
993 1539 1.584495 CCGCCAAGGCCACTTAAAC 59.416 57.895 5.01 0.00 37.98 2.01
994 1540 1.584495 CGCCAAGGCCACTTAAACC 59.416 57.895 5.01 0.00 37.98 3.27
995 1541 1.873270 CGCCAAGGCCACTTAAACCC 61.873 60.000 5.01 0.00 37.98 4.11
997 1543 0.178947 CCAAGGCCACTTAAACCCCA 60.179 55.000 5.01 0.00 34.49 4.96
998 1544 0.966179 CAAGGCCACTTAAACCCCAC 59.034 55.000 5.01 0.00 34.49 4.61
999 1545 0.558712 AAGGCCACTTAAACCCCACA 59.441 50.000 5.01 0.00 34.49 4.17
1000 1546 0.783850 AGGCCACTTAAACCCCACAT 59.216 50.000 5.01 0.00 0.00 3.21
1002 1548 1.627864 GCCACTTAAACCCCACATGT 58.372 50.000 0.00 0.00 0.00 3.21
1004 1550 2.870175 CCACTTAAACCCCACATGTCA 58.130 47.619 0.00 0.00 0.00 3.58
1005 1551 2.819608 CCACTTAAACCCCACATGTCAG 59.180 50.000 0.00 0.00 0.00 3.51
1006 1552 3.497763 CCACTTAAACCCCACATGTCAGA 60.498 47.826 0.00 0.00 0.00 3.27
1007 1553 3.753272 CACTTAAACCCCACATGTCAGAG 59.247 47.826 0.00 0.00 0.00 3.35
1008 1554 3.650942 ACTTAAACCCCACATGTCAGAGA 59.349 43.478 0.00 0.00 0.00 3.10
1009 1555 2.568623 AAACCCCACATGTCAGAGAC 57.431 50.000 0.00 0.00 0.00 3.36
1010 1556 1.434188 AACCCCACATGTCAGAGACA 58.566 50.000 0.00 1.95 46.90 3.41
1011 1557 0.979665 ACCCCACATGTCAGAGACAG 59.020 55.000 0.00 1.52 46.04 3.51
1012 1558 0.392193 CCCCACATGTCAGAGACAGC 60.392 60.000 0.00 0.00 46.04 4.40
1013 1559 0.738762 CCCACATGTCAGAGACAGCG 60.739 60.000 0.00 2.51 46.04 5.18
1014 1560 0.738762 CCACATGTCAGAGACAGCGG 60.739 60.000 0.00 2.63 46.04 5.52
1015 1561 1.079543 ACATGTCAGAGACAGCGGC 60.080 57.895 6.01 0.00 46.04 6.53
1016 1562 2.163390 CATGTCAGAGACAGCGGCG 61.163 63.158 0.51 0.51 46.04 6.46
1017 1563 3.362399 ATGTCAGAGACAGCGGCGG 62.362 63.158 9.78 0.00 46.04 6.13
1023 1569 4.853142 AGACAGCGGCGGGGGATA 62.853 66.667 9.78 0.00 0.00 2.59
1024 1570 3.626924 GACAGCGGCGGGGGATAT 61.627 66.667 9.78 0.00 0.00 1.63
1025 1571 2.203728 ACAGCGGCGGGGGATATA 60.204 61.111 9.78 0.00 0.00 0.86
1026 1572 1.612442 ACAGCGGCGGGGGATATAT 60.612 57.895 9.78 0.00 0.00 0.86
1028 1574 1.305802 AGCGGCGGGGGATATATGA 60.306 57.895 9.78 0.00 0.00 2.15
1029 1575 0.691078 AGCGGCGGGGGATATATGAT 60.691 55.000 9.78 0.00 0.00 2.45
1030 1576 1.045407 GCGGCGGGGGATATATGATA 58.955 55.000 9.78 0.00 0.00 2.15
1031 1577 1.414919 GCGGCGGGGGATATATGATAA 59.585 52.381 9.78 0.00 0.00 1.75
1032 1578 2.158871 GCGGCGGGGGATATATGATAAA 60.159 50.000 9.78 0.00 0.00 1.40
1033 1579 3.728845 CGGCGGGGGATATATGATAAAG 58.271 50.000 0.00 0.00 0.00 1.85
1035 1581 3.714798 GGCGGGGGATATATGATAAAGGA 59.285 47.826 0.00 0.00 0.00 3.36
1036 1582 4.351111 GGCGGGGGATATATGATAAAGGAT 59.649 45.833 0.00 0.00 0.00 3.24
1039 1585 6.263168 GCGGGGGATATATGATAAAGGATTTG 59.737 42.308 0.00 0.00 39.63 2.32
1041 1587 6.263168 GGGGGATATATGATAAAGGATTTGCG 59.737 42.308 0.00 0.00 39.63 4.85
1043 1589 7.556275 GGGGATATATGATAAAGGATTTGCGAA 59.444 37.037 0.00 0.00 39.63 4.70
1045 1591 8.946085 GGATATATGATAAAGGATTTGCGAACA 58.054 33.333 0.00 0.00 39.63 3.18
1048 1594 5.309323 TGATAAAGGATTTGCGAACAAGG 57.691 39.130 0.00 0.00 39.63 3.61
1049 1595 4.157656 TGATAAAGGATTTGCGAACAAGGG 59.842 41.667 0.00 0.00 39.63 3.95
1050 1596 1.256812 AAGGATTTGCGAACAAGGGG 58.743 50.000 0.00 0.00 37.04 4.79
1051 1597 0.611896 AGGATTTGCGAACAAGGGGG 60.612 55.000 0.00 0.00 37.04 5.40
1132 1710 3.143515 AGCTGCTCGATCTCGCCA 61.144 61.111 0.00 0.00 39.60 5.69
1142 1720 0.605589 GATCTCGCCAATCGGAGGAT 59.394 55.000 0.00 0.00 39.05 3.24
1245 1841 1.228124 CCCCCATCGTTGTGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
1261 1857 1.075050 TGTGTAGGTCCTCCTCTTCGT 59.925 52.381 0.00 0.00 43.94 3.85
1426 2022 2.285743 GGAAGCTCCCCCAGACCT 60.286 66.667 0.00 0.00 0.00 3.85
1452 2048 1.777272 GGCTTCTACCAGGGGAATCAT 59.223 52.381 0.00 0.00 0.00 2.45
1562 2158 1.337823 GGTCATGGACTGCTGTAACGT 60.338 52.381 0.00 0.00 32.47 3.99
1620 2217 0.864797 GCGACGAGTTCCGGTACATC 60.865 60.000 14.14 6.98 43.93 3.06
1683 2280 2.280186 GGCTATTCCGGCCTGTCG 60.280 66.667 0.00 0.00 45.57 4.35
1747 2380 2.350895 TGGAGGACCAACATGGCG 59.649 61.111 0.00 0.00 42.67 5.69
1765 2398 0.879765 CGTCTGTCTTACCGGAGTGT 59.120 55.000 9.46 0.00 0.00 3.55
1794 2427 0.804989 CATCTGAAACCGGGAGTTGC 59.195 55.000 6.32 0.00 39.19 4.17
1819 2452 3.900601 TCATAAGGAGAAGAGATGGAGCC 59.099 47.826 0.00 0.00 0.00 4.70
1823 2456 0.249405 GAGAAGAGATGGAGCCGCAG 60.249 60.000 0.00 0.00 0.00 5.18
1829 2462 0.833287 AGATGGAGCCGCAGTATTGT 59.167 50.000 0.00 0.00 0.00 2.71
1848 2481 1.517276 GTTGTCGCTAATGATCGGTCG 59.483 52.381 0.00 0.00 0.00 4.79
1906 2539 0.179004 TGTTGATGGTTCTGCCGGTT 60.179 50.000 1.90 0.00 41.21 4.44
1923 2556 1.065854 GGTTGTCTAGCTGCAGTGGAT 60.066 52.381 16.64 1.84 0.00 3.41
2082 2730 6.100004 TCTTAAAGACTATGACCGCAAAGAG 58.900 40.000 0.00 0.00 0.00 2.85
2139 2791 1.414181 CTTGGAGGGCGACACATAGAT 59.586 52.381 0.00 0.00 0.00 1.98
2196 2848 7.186570 TCATCCAGAATGTGACTTGATCTTA 57.813 36.000 0.00 0.00 36.68 2.10
2660 3452 4.102649 GTGTGTACTTGTTTTGTCTTGGC 58.897 43.478 0.00 0.00 0.00 4.52
2696 3489 3.262151 TGGACAACGGGAGATTGTGATAA 59.738 43.478 0.00 0.00 40.36 1.75
2710 3503 8.218338 AGATTGTGATAACACTTTGGATGATC 57.782 34.615 4.65 0.00 46.07 2.92
2745 3545 2.889170 TTGGTGCTATGTTTGCCCTA 57.111 45.000 0.00 0.00 0.00 3.53
2827 3634 7.814264 AGGAAATGTCATAATGTTCATCCTC 57.186 36.000 0.00 0.00 0.00 3.71
2869 3676 6.729187 ACACAAAATTGCTTCAGAAGACTAC 58.271 36.000 14.86 0.00 0.00 2.73
2874 3681 6.566197 AATTGCTTCAGAAGACTACAAAGG 57.434 37.500 14.86 0.00 0.00 3.11
2963 6967 4.564821 GGGCACTTACCATGTTAGTCTTGA 60.565 45.833 0.00 0.00 0.00 3.02
3140 7148 1.206132 CTGGTCAACCTATGTACGGCA 59.794 52.381 0.10 0.00 36.82 5.69
3171 7184 2.915738 CAGAGCTGCAATCTTGTTCC 57.084 50.000 1.02 0.00 0.00 3.62
3174 7187 3.373439 CAGAGCTGCAATCTTGTTCCTAC 59.627 47.826 1.02 0.00 0.00 3.18
3412 7442 3.882888 GGAAATAAGATTGCACGGGATCA 59.117 43.478 0.00 0.00 0.00 2.92
3513 7544 3.802866 TGCGCTAATGATATGTGTTCCA 58.197 40.909 9.73 0.00 0.00 3.53
3666 7709 6.866480 ACATTGAAGAAGAAAAGAAGCACAA 58.134 32.000 0.00 0.00 0.00 3.33
3667 7710 6.753744 ACATTGAAGAAGAAAAGAAGCACAAC 59.246 34.615 0.00 0.00 0.00 3.32
3668 7711 5.895636 TGAAGAAGAAAAGAAGCACAACA 57.104 34.783 0.00 0.00 0.00 3.33
3669 7712 5.640732 TGAAGAAGAAAAGAAGCACAACAC 58.359 37.500 0.00 0.00 0.00 3.32
3670 7713 5.182950 TGAAGAAGAAAAGAAGCACAACACA 59.817 36.000 0.00 0.00 0.00 3.72
3671 7714 5.841957 AGAAGAAAAGAAGCACAACACAT 57.158 34.783 0.00 0.00 0.00 3.21
3672 7715 6.942532 AGAAGAAAAGAAGCACAACACATA 57.057 33.333 0.00 0.00 0.00 2.29
3673 7716 7.516198 AGAAGAAAAGAAGCACAACACATAT 57.484 32.000 0.00 0.00 0.00 1.78
3674 7717 8.621532 AGAAGAAAAGAAGCACAACACATATA 57.378 30.769 0.00 0.00 0.00 0.86
3675 7718 8.725148 AGAAGAAAAGAAGCACAACACATATAG 58.275 33.333 0.00 0.00 0.00 1.31
3676 7719 7.986085 AGAAAAGAAGCACAACACATATAGT 57.014 32.000 0.00 0.00 0.00 2.12
3677 7720 8.034058 AGAAAAGAAGCACAACACATATAGTC 57.966 34.615 0.00 0.00 0.00 2.59
3678 7721 6.743575 AAAGAAGCACAACACATATAGTCC 57.256 37.500 0.00 0.00 0.00 3.85
3679 7722 5.420725 AGAAGCACAACACATATAGTCCA 57.579 39.130 0.00 0.00 0.00 4.02
3680 7723 5.994250 AGAAGCACAACACATATAGTCCAT 58.006 37.500 0.00 0.00 0.00 3.41
3681 7724 5.819379 AGAAGCACAACACATATAGTCCATG 59.181 40.000 0.00 0.00 0.00 3.66
3682 7725 4.454678 AGCACAACACATATAGTCCATGG 58.545 43.478 4.97 4.97 0.00 3.66
3683 7726 4.080356 AGCACAACACATATAGTCCATGGT 60.080 41.667 12.58 0.00 0.00 3.55
3684 7727 4.640201 GCACAACACATATAGTCCATGGTT 59.360 41.667 12.58 4.13 0.00 3.67
3685 7728 5.820423 GCACAACACATATAGTCCATGGTTA 59.180 40.000 12.58 6.42 0.00 2.85
3686 7729 6.486657 GCACAACACATATAGTCCATGGTTAT 59.513 38.462 12.58 13.18 0.00 1.89
3747 7790 8.871686 ACAAAACAAACAATTTTAGAGCTAGG 57.128 30.769 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 218 0.762418 AATGGTGTTGTCCACTCCGA 59.238 50.000 0.00 0.00 43.94 4.55
235 236 8.700973 GGAATTTAAACCCTTATGAGGCATTAA 58.299 33.333 0.00 3.37 42.09 1.40
355 367 6.097696 AGGATCTGCTAGAGTTTCTCTAAACC 59.902 42.308 7.70 2.59 45.11 3.27
417 429 3.655810 CTCTGCCCTGTGCCTCGTC 62.656 68.421 0.00 0.00 40.16 4.20
418 430 3.699894 CTCTGCCCTGTGCCTCGT 61.700 66.667 0.00 0.00 40.16 4.18
427 439 0.031716 TACAGGATCTGCTCTGCCCT 60.032 55.000 0.00 0.00 34.37 5.19
469 482 1.905894 AGAGTGAGGAGGAAAAGGAGC 59.094 52.381 0.00 0.00 0.00 4.70
478 491 3.440127 AGGAAGAAGAAGAGTGAGGAGG 58.560 50.000 0.00 0.00 0.00 4.30
487 500 1.002087 GCGTCCCAAGGAAGAAGAAGA 59.998 52.381 0.43 0.00 33.09 2.87
524 537 0.460459 GTTCTGGCCGGCTAGAGTTC 60.460 60.000 36.51 26.93 35.06 3.01
633 832 1.000486 TGAGTAGGCGGAGGAGCTT 60.000 57.895 0.00 0.00 37.29 3.74
647 846 2.203056 TGCACGCAAGCAGTGAGT 60.203 55.556 16.88 0.00 41.49 3.41
680 879 2.590007 GAAGCATCGCCGGAGCAT 60.590 61.111 5.05 0.00 39.83 3.79
706 905 0.033991 AAGCAGAGGAGCTCGGTAGA 60.034 55.000 7.83 0.00 45.89 2.59
863 1068 5.311913 AGATCCTCTAAATGAAAGATCCCCC 59.688 44.000 0.00 0.00 36.19 5.40
864 1069 6.446909 AGATCCTCTAAATGAAAGATCCCC 57.553 41.667 0.00 0.00 36.19 4.81
865 1070 8.759481 AAAAGATCCTCTAAATGAAAGATCCC 57.241 34.615 0.00 0.00 36.19 3.85
889 1094 8.954950 TCTAAATGGCATTTTCTCAACAAAAA 57.045 26.923 28.56 7.07 33.82 1.94
890 1095 7.656948 CCTCTAAATGGCATTTTCTCAACAAAA 59.343 33.333 28.56 7.55 33.82 2.44
891 1096 7.015098 TCCTCTAAATGGCATTTTCTCAACAAA 59.985 33.333 28.56 8.25 33.82 2.83
892 1097 6.493115 TCCTCTAAATGGCATTTTCTCAACAA 59.507 34.615 28.56 8.93 33.82 2.83
893 1098 6.009589 TCCTCTAAATGGCATTTTCTCAACA 58.990 36.000 28.56 9.63 33.82 3.33
894 1099 6.515272 TCCTCTAAATGGCATTTTCTCAAC 57.485 37.500 28.56 0.00 33.82 3.18
895 1100 7.121382 AGATCCTCTAAATGGCATTTTCTCAA 58.879 34.615 28.56 11.02 33.82 3.02
896 1101 6.666678 AGATCCTCTAAATGGCATTTTCTCA 58.333 36.000 28.56 11.38 33.82 3.27
897 1102 8.860780 ATAGATCCTCTAAATGGCATTTTCTC 57.139 34.615 28.56 15.88 31.96 2.87
898 1103 9.294614 GAATAGATCCTCTAAATGGCATTTTCT 57.705 33.333 28.56 23.72 31.96 2.52
899 1104 8.233190 CGAATAGATCCTCTAAATGGCATTTTC 58.767 37.037 28.56 18.70 31.96 2.29
900 1105 7.175641 CCGAATAGATCCTCTAAATGGCATTTT 59.824 37.037 28.56 11.25 31.96 1.82
901 1106 6.656693 CCGAATAGATCCTCTAAATGGCATTT 59.343 38.462 26.86 26.86 31.96 2.32
902 1107 6.176183 CCGAATAGATCCTCTAAATGGCATT 58.824 40.000 6.96 6.96 31.96 3.56
903 1108 5.249393 ACCGAATAGATCCTCTAAATGGCAT 59.751 40.000 0.00 0.00 31.96 4.40
945 1454 1.540797 CGTCAACCCGGTCAAACCTTA 60.541 52.381 0.00 0.00 35.66 2.69
973 1519 3.577334 TTAAGTGGCCTTGGCGGGG 62.577 63.158 3.32 0.00 31.89 5.73
974 1520 1.605165 TTTAAGTGGCCTTGGCGGG 60.605 57.895 3.32 0.00 31.89 6.13
977 1523 1.541310 GGGGTTTAAGTGGCCTTGGC 61.541 60.000 3.32 2.49 31.89 4.52
978 1524 0.178947 TGGGGTTTAAGTGGCCTTGG 60.179 55.000 3.32 0.00 31.89 3.61
979 1525 0.966179 GTGGGGTTTAAGTGGCCTTG 59.034 55.000 3.32 0.00 31.89 3.61
980 1526 0.558712 TGTGGGGTTTAAGTGGCCTT 59.441 50.000 3.32 0.00 34.56 4.35
981 1527 0.783850 ATGTGGGGTTTAAGTGGCCT 59.216 50.000 3.32 0.00 0.00 5.19
982 1528 0.894835 CATGTGGGGTTTAAGTGGCC 59.105 55.000 0.00 0.00 0.00 5.36
983 1529 1.544246 GACATGTGGGGTTTAAGTGGC 59.456 52.381 1.15 0.00 0.00 5.01
985 1531 3.750371 TCTGACATGTGGGGTTTAAGTG 58.250 45.455 1.15 0.00 0.00 3.16
988 1534 3.392947 TGTCTCTGACATGTGGGGTTTAA 59.607 43.478 1.15 0.00 37.67 1.52
989 1535 2.976185 TGTCTCTGACATGTGGGGTTTA 59.024 45.455 1.15 0.00 37.67 2.01
991 1537 1.349026 CTGTCTCTGACATGTGGGGTT 59.651 52.381 1.15 0.00 41.94 4.11
992 1538 0.979665 CTGTCTCTGACATGTGGGGT 59.020 55.000 1.15 0.00 41.94 4.95
993 1539 0.392193 GCTGTCTCTGACATGTGGGG 60.392 60.000 1.15 0.00 41.94 4.96
994 1540 0.738762 CGCTGTCTCTGACATGTGGG 60.739 60.000 1.15 0.00 41.94 4.61
995 1541 0.738762 CCGCTGTCTCTGACATGTGG 60.739 60.000 1.15 7.76 41.94 4.17
997 1543 1.079543 GCCGCTGTCTCTGACATGT 60.080 57.895 0.00 0.00 41.94 3.21
998 1544 2.163390 CGCCGCTGTCTCTGACATG 61.163 63.158 0.65 0.00 41.94 3.21
999 1545 2.182791 CGCCGCTGTCTCTGACAT 59.817 61.111 0.65 0.00 41.94 3.06
1000 1546 4.056125 CCGCCGCTGTCTCTGACA 62.056 66.667 0.37 0.37 40.50 3.58
1006 1552 2.725127 TATATCCCCCGCCGCTGTCT 62.725 60.000 0.00 0.00 0.00 3.41
1007 1553 1.614241 ATATATCCCCCGCCGCTGTC 61.614 60.000 0.00 0.00 0.00 3.51
1008 1554 1.612442 ATATATCCCCCGCCGCTGT 60.612 57.895 0.00 0.00 0.00 4.40
1009 1555 1.153369 CATATATCCCCCGCCGCTG 60.153 63.158 0.00 0.00 0.00 5.18
1010 1556 0.691078 ATCATATATCCCCCGCCGCT 60.691 55.000 0.00 0.00 0.00 5.52
1011 1557 1.045407 TATCATATATCCCCCGCCGC 58.955 55.000 0.00 0.00 0.00 6.53
1012 1558 3.494398 CCTTTATCATATATCCCCCGCCG 60.494 52.174 0.00 0.00 0.00 6.46
1013 1559 3.714798 TCCTTTATCATATATCCCCCGCC 59.285 47.826 0.00 0.00 0.00 6.13
1014 1560 5.568620 ATCCTTTATCATATATCCCCCGC 57.431 43.478 0.00 0.00 0.00 6.13
1015 1561 6.263168 GCAAATCCTTTATCATATATCCCCCG 59.737 42.308 0.00 0.00 0.00 5.73
1016 1562 6.263168 CGCAAATCCTTTATCATATATCCCCC 59.737 42.308 0.00 0.00 0.00 5.40
1017 1563 7.054124 TCGCAAATCCTTTATCATATATCCCC 58.946 38.462 0.00 0.00 0.00 4.81
1019 1565 8.946085 TGTTCGCAAATCCTTTATCATATATCC 58.054 33.333 0.00 0.00 0.00 2.59
1023 1569 7.255590 CCCTTGTTCGCAAATCCTTTATCATAT 60.256 37.037 0.00 0.00 36.56 1.78
1024 1570 6.039270 CCCTTGTTCGCAAATCCTTTATCATA 59.961 38.462 0.00 0.00 36.56 2.15
1025 1571 5.163519 CCCTTGTTCGCAAATCCTTTATCAT 60.164 40.000 0.00 0.00 36.56 2.45
1026 1572 4.157656 CCCTTGTTCGCAAATCCTTTATCA 59.842 41.667 0.00 0.00 36.56 2.15
1028 1574 3.447229 CCCCTTGTTCGCAAATCCTTTAT 59.553 43.478 0.00 0.00 36.56 1.40
1029 1575 2.823154 CCCCTTGTTCGCAAATCCTTTA 59.177 45.455 0.00 0.00 36.56 1.85
1030 1576 1.618343 CCCCTTGTTCGCAAATCCTTT 59.382 47.619 0.00 0.00 36.56 3.11
1031 1577 1.256812 CCCCTTGTTCGCAAATCCTT 58.743 50.000 0.00 0.00 36.56 3.36
1032 1578 0.611896 CCCCCTTGTTCGCAAATCCT 60.612 55.000 0.00 0.00 36.56 3.24
1033 1579 1.890174 CCCCCTTGTTCGCAAATCC 59.110 57.895 0.00 0.00 36.56 3.01
1048 1594 3.682696 GGGATAATTGACGATAACCCCC 58.317 50.000 0.00 0.00 0.00 5.40
1049 1595 3.682696 GGGGATAATTGACGATAACCCC 58.317 50.000 0.00 0.00 46.94 4.95
1050 1596 3.332034 CGGGGATAATTGACGATAACCC 58.668 50.000 0.00 0.00 35.80 4.11
1051 1597 3.332034 CCGGGGATAATTGACGATAACC 58.668 50.000 0.00 0.00 0.00 2.85
1052 1598 2.740447 GCCGGGGATAATTGACGATAAC 59.260 50.000 2.18 0.00 0.00 1.89
1053 1599 2.610976 CGCCGGGGATAATTGACGATAA 60.611 50.000 14.46 0.00 0.00 1.75
1054 1600 1.067425 CGCCGGGGATAATTGACGATA 60.067 52.381 14.46 0.00 0.00 2.92
1055 1601 0.320421 CGCCGGGGATAATTGACGAT 60.320 55.000 14.46 0.00 0.00 3.73
1056 1602 1.068417 CGCCGGGGATAATTGACGA 59.932 57.895 14.46 0.00 0.00 4.20
1058 1604 2.258726 GGCGCCGGGGATAATTGAC 61.259 63.158 24.68 0.85 0.00 3.18
1060 1606 3.353836 CGGCGCCGGGGATAATTG 61.354 66.667 40.50 8.79 35.56 2.32
1132 1710 0.034059 GATGCGTCCATCCTCCGATT 59.966 55.000 0.00 0.00 41.62 3.34
1288 1884 0.250814 AGGTCGTCGGTGAGTCTCTT 60.251 55.000 0.65 0.00 0.00 2.85
1426 2022 1.550130 CCCTGGTAGAAGCCGGTCAA 61.550 60.000 1.90 0.00 33.07 3.18
1562 2158 0.707024 TGAGGAGCAGAGAAGGAGGA 59.293 55.000 0.00 0.00 0.00 3.71
1620 2217 4.101790 GTGGCGGGATTGCACACG 62.102 66.667 0.00 0.00 39.86 4.49
1683 2280 1.749258 GAAATGAGGGGACACGGCC 60.749 63.158 0.00 0.00 0.00 6.13
1747 2380 3.442977 ACATACACTCCGGTAAGACAGAC 59.557 47.826 0.00 0.00 0.00 3.51
1765 2398 5.600898 TCCCGGTTTCAGATGAATAGACATA 59.399 40.000 0.00 0.00 33.54 2.29
1794 2427 5.521906 TCCATCTCTTCTCCTTATGAACG 57.478 43.478 0.00 0.00 0.00 3.95
1819 2452 3.305897 TCATTAGCGACAACAATACTGCG 59.694 43.478 0.00 0.00 0.00 5.18
1823 2456 4.506654 ACCGATCATTAGCGACAACAATAC 59.493 41.667 0.00 0.00 36.35 1.89
1829 2462 1.402613 TCGACCGATCATTAGCGACAA 59.597 47.619 0.00 0.00 36.35 3.18
1906 2539 2.432146 CCTTATCCACTGCAGCTAGACA 59.568 50.000 15.27 0.00 0.00 3.41
2082 2730 3.053455 GACGCTATGCTTCAGTATCCAC 58.947 50.000 0.00 0.00 0.00 4.02
2139 2791 5.419542 CAATCGAAGTCCTCATCAAGGTAA 58.580 41.667 0.00 0.00 46.32 2.85
2196 2848 0.542702 CCTCCTGGGCCACAACAAAT 60.543 55.000 0.00 0.00 0.00 2.32
2495 3278 5.772521 ACCAAATTCAAGCAGACATACAAC 58.227 37.500 0.00 0.00 0.00 3.32
2497 3280 4.458989 GGACCAAATTCAAGCAGACATACA 59.541 41.667 0.00 0.00 0.00 2.29
2660 3452 2.554032 GTTGTCCAGAACCATTGGTCTG 59.446 50.000 19.92 19.92 33.12 3.51
2696 3489 7.114754 AGTGATAATGTGATCATCCAAAGTGT 58.885 34.615 0.00 0.00 38.11 3.55
2710 3503 6.017400 AGCACCAAAAGAAGTGATAATGTG 57.983 37.500 0.00 0.00 36.01 3.21
2827 3634 9.965824 ATTTTGTGTCAAAAGTTATCTAACAGG 57.034 29.630 12.07 0.00 38.62 4.00
2869 3676 5.709164 CCCATAGATAAAGAGGATGCCTTTG 59.291 44.000 9.77 0.00 35.65 2.77
2874 3681 6.547510 ACAAAACCCATAGATAAAGAGGATGC 59.452 38.462 0.00 0.00 0.00 3.91
2938 3751 1.014352 CTAACATGGTAAGTGCCCGC 58.986 55.000 0.00 0.00 0.00 6.13
2963 6967 5.130311 TGGAGTGTATGTGCACCATTATAGT 59.870 40.000 15.69 5.01 40.04 2.12
3171 7184 2.015736 AAGCTCCTGAATGTGCGTAG 57.984 50.000 0.00 0.00 0.00 3.51
3174 7187 2.015736 ACTAAGCTCCTGAATGTGCG 57.984 50.000 0.00 0.00 0.00 5.34
3412 7442 8.416329 ACAGAACAATGTCTGAAATTAGCTTTT 58.584 29.630 15.92 0.00 46.76 2.27
3513 7544 4.156739 GGCTAGCTGACAACTAAAAAGCAT 59.843 41.667 15.72 0.00 36.32 3.79
3666 7709 7.977818 ACATCATAACCATGGACTATATGTGT 58.022 34.615 21.47 19.55 32.61 3.72
3667 7710 9.371136 GTACATCATAACCATGGACTATATGTG 57.629 37.037 21.47 19.07 32.90 3.21
3668 7711 9.100197 TGTACATCATAACCATGGACTATATGT 57.900 33.333 21.47 21.50 36.22 2.29
3672 7715 9.326489 ACTATGTACATCATAACCATGGACTAT 57.674 33.333 21.47 11.79 38.38 2.12
3673 7716 8.721133 ACTATGTACATCATAACCATGGACTA 57.279 34.615 21.47 9.81 38.38 2.59
3674 7717 7.618019 ACTATGTACATCATAACCATGGACT 57.382 36.000 21.47 7.60 38.38 3.85
3675 7718 8.677148 AAACTATGTACATCATAACCATGGAC 57.323 34.615 21.47 2.78 38.38 4.02
3676 7719 8.713971 AGAAACTATGTACATCATAACCATGGA 58.286 33.333 21.47 0.00 38.38 3.41
3677 7720 8.908786 AGAAACTATGTACATCATAACCATGG 57.091 34.615 12.68 11.19 38.38 3.66
3678 7721 9.770097 AGAGAAACTATGTACATCATAACCATG 57.230 33.333 12.68 0.00 38.38 3.66
3679 7722 9.770097 CAGAGAAACTATGTACATCATAACCAT 57.230 33.333 12.68 0.00 38.38 3.55
3680 7723 8.977412 TCAGAGAAACTATGTACATCATAACCA 58.023 33.333 12.68 0.00 38.38 3.67
3681 7724 9.988815 ATCAGAGAAACTATGTACATCATAACC 57.011 33.333 12.68 0.00 38.38 2.85
3684 7727 9.367160 TGGATCAGAGAAACTATGTACATCATA 57.633 33.333 12.68 0.00 37.91 2.15
3685 7728 8.255111 TGGATCAGAGAAACTATGTACATCAT 57.745 34.615 12.68 0.00 40.25 2.45
3686 7729 7.660030 TGGATCAGAGAAACTATGTACATCA 57.340 36.000 12.68 0.00 0.00 3.07
3875 7922 4.498345 GGACCAGACGCAACATAACAAAAA 60.498 41.667 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.