Multiple sequence alignment - TraesCS6B01G400900

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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 TraesCS6B01G400900 chr6B 100.000 2631 0 0 1 2631 676731772 676729142 0.000000e+00 4859.0
1 TraesCS6B01G400900 chr6B 91.159 656 41 9 83 734 676499115 676498473 0.000000e+00 874.0
2 TraesCS6B01G400900 chr6B 84.176 771 67 27 1734 2496 676491961 676491238 0.000000e+00 697.0
3 TraesCS6B01G400900 chr6B 84.226 672 68 21 9 663 678540103 678540753 1.030000e-173 619.0
4 TraesCS6B01G400900 chr6B 90.756 476 22 2 1233 1686 676492453 676491978 1.340000e-172 616.0
5 TraesCS6B01G400900 chr6B 87.572 523 38 17 1810 2320 676536785 676536278 4.880000e-162 580.0
6 TraesCS6B01G400900 chr6B 80.888 811 80 37 17 800 676373424 676372662 1.060000e-158 569.0
7 TraesCS6B01G400900 chr6B 79.820 778 72 42 1387 2112 678175129 678175873 3.040000e-134 488.0
8 TraesCS6B01G400900 chr6B 78.539 890 83 52 1382 2215 678357390 678358227 1.090000e-133 486.0
9 TraesCS6B01G400900 chr6B 81.138 615 52 32 1394 1972 677045195 677044609 4.020000e-118 435.0
10 TraesCS6B01G400900 chr6B 80.892 628 55 33 1382 1972 677336549 677335950 4.020000e-118 435.0
11 TraesCS6B01G400900 chr6B 83.120 468 38 19 1390 1833 678092317 678091867 3.180000e-104 388.0
12 TraesCS6B01G400900 chr6B 82.629 426 51 16 829 1234 677088555 677088133 3.220000e-94 355.0
13 TraesCS6B01G400900 chr6B 79.820 555 47 27 1387 1905 678543076 678543601 6.970000e-91 344.0
14 TraesCS6B01G400900 chr6B 91.139 237 19 1 1001 1235 678174645 678174881 1.170000e-83 320.0
15 TraesCS6B01G400900 chr6B 79.834 481 58 19 1767 2219 676865074 676864605 5.470000e-82 315.0
16 TraesCS6B01G400900 chr6B 82.298 322 33 13 934 1234 677045745 677045427 9.340000e-65 257.0
17 TraesCS6B01G400900 chr6B 80.473 338 27 15 922 1234 678356830 678357153 3.410000e-54 222.0
18 TraesCS6B01G400900 chr6B 79.331 329 49 15 916 1235 678542516 678542834 2.050000e-51 213.0
19 TraesCS6B01G400900 chr6B 81.522 276 28 14 1476 1748 676537350 676537095 3.430000e-49 206.0
20 TraesCS6B01G400900 chr6B 80.851 282 23 10 1234 1486 676538088 676537809 2.670000e-45 193.0
21 TraesCS6B01G400900 chr6B 89.172 157 14 1 1390 1543 677087875 677087719 2.670000e-45 193.0
22 TraesCS6B01G400900 chr6B 90.714 140 10 1 1236 1375 676865621 676865485 1.610000e-42 183.0
23 TraesCS6B01G400900 chr6B 88.966 145 7 4 1233 1371 677088098 677087957 1.250000e-38 171.0
24 TraesCS6B01G400900 chr6B 88.732 142 10 4 1234 1372 678174919 678175057 4.500000e-38 169.0
25 TraesCS6B01G400900 chr6B 88.571 140 13 1 1233 1372 678542862 678542998 1.620000e-37 167.0
26 TraesCS6B01G400900 chr6B 82.474 194 26 5 1233 1419 678092534 678092342 2.100000e-36 163.0
27 TraesCS6B01G400900 chr6B 93.269 104 4 2 1 101 676499239 676499136 1.630000e-32 150.0
28 TraesCS6B01G400900 chr6B 81.765 170 17 10 424 581 675627687 675627520 2.130000e-26 130.0
29 TraesCS6B01G400900 chr6B 87.342 79 7 3 822 898 678093054 678092977 1.300000e-13 87.9
30 TraesCS6B01G400900 chr6B 97.917 48 1 0 819 866 678356664 678356711 1.680000e-12 84.2
31 TraesCS6B01G400900 chr6B 87.838 74 3 3 802 869 677337184 677337111 6.040000e-12 82.4
32 TraesCS6B01G400900 chr6B 91.111 45 3 1 2331 2374 676315291 676315247 2.830000e-05 60.2
33 TraesCS6B01G400900 chr6A 82.550 1106 91 38 1234 2270 593929707 593928635 0.000000e+00 880.0
34 TraesCS6B01G400900 chr6A 83.303 557 54 23 1842 2367 594366495 594367043 6.590000e-131 477.0
35 TraesCS6B01G400900 chr6A 77.978 890 92 60 1390 2219 593991969 593991124 1.840000e-126 462.0
36 TraesCS6B01G400900 chr6A 80.375 586 54 27 1235 1785 569678865 569678306 3.180000e-104 388.0
37 TraesCS6B01G400900 chr6A 77.761 652 73 39 1390 2005 594253825 594253210 4.200000e-88 335.0
38 TraesCS6B01G400900 chr6A 78.201 578 46 27 67 597 593931052 593930508 1.980000e-76 296.0
39 TraesCS6B01G400900 chr6A 85.000 300 32 3 936 1235 594254350 594254064 2.560000e-75 292.0
40 TraesCS6B01G400900 chr6A 84.062 320 27 8 927 1235 593992517 593992211 1.190000e-73 287.0
41 TraesCS6B01G400900 chr6A 82.286 350 43 12 1387 1729 594366132 594366469 4.290000e-73 285.0
42 TraesCS6B01G400900 chr6A 81.152 382 28 21 1733 2105 594320067 594320413 1.550000e-67 267.0
43 TraesCS6B01G400900 chr6A 81.625 283 29 11 964 1225 594365591 594365871 2.050000e-51 213.0
44 TraesCS6B01G400900 chr6A 90.698 129 6 3 2254 2379 593928683 593928558 1.620000e-37 167.0
45 TraesCS6B01G400900 chr6A 89.344 122 6 3 799 913 593930273 593930152 2.110000e-31 147.0
46 TraesCS6B01G400900 chr6A 83.916 143 13 4 421 559 593776403 593776539 7.640000e-26 128.0
47 TraesCS6B01G400900 chr6A 83.333 126 5 9 799 908 594364969 594365094 4.630000e-18 102.0
48 TraesCS6B01G400900 chr6A 86.111 72 7 3 829 898 594318905 594318975 1.010000e-09 75.0
49 TraesCS6B01G400900 chr6D 84.945 817 68 26 12 778 447216687 447215876 0.000000e+00 776.0
50 TraesCS6B01G400900 chr6D 78.289 1239 136 56 1233 2392 447761314 447762498 0.000000e+00 675.0
51 TraesCS6B01G400900 chr6D 89.865 444 44 1 322 765 447214692 447214250 1.060000e-158 569.0
52 TraesCS6B01G400900 chr6D 79.117 838 84 44 1406 2178 447738184 447738995 6.540000e-136 494.0
53 TraesCS6B01G400900 chr6D 89.674 368 24 8 2010 2368 447212934 447212572 8.580000e-125 457.0
54 TraesCS6B01G400900 chr6D 82.386 528 43 19 1234 1728 447213562 447213052 5.240000e-112 414.0
55 TraesCS6B01G400900 chr6D 78.932 674 61 40 1590 2219 447278099 447277463 1.480000e-102 383.0
56 TraesCS6B01G400900 chr6D 84.848 330 39 9 896 1219 447737559 447737883 3.270000e-84 322.0
57 TraesCS6B01G400900 chr6D 84.158 303 21 11 1390 1674 447278419 447278126 4.320000e-68 268.0
58 TraesCS6B01G400900 chr6D 91.111 135 12 0 1101 1235 447761146 447761280 1.610000e-42 183.0
59 TraesCS6B01G400900 chr6D 79.668 241 33 9 437 663 447737168 447737406 2.710000e-35 159.0
60 TraesCS6B01G400900 chr6D 86.869 99 5 2 823 913 447214116 447214018 1.290000e-18 104.0
61 TraesCS6B01G400900 chr6D 91.781 73 3 2 828 898 447279152 447279081 5.990000e-17 99.0
62 TraesCS6B01G400900 chr6D 86.170 94 8 2 2484 2572 447212509 447212416 2.160000e-16 97.1
63 TraesCS6B01G400900 chr6D 89.333 75 8 0 471 545 446728795 446728721 7.750000e-16 95.3
64 TraesCS6B01G400900 chr6D 91.379 58 3 1 7 62 447759361 447759418 7.810000e-11 78.7
65 TraesCS6B01G400900 chr7A 79.882 1183 117 50 1234 2364 19012472 19013585 0.000000e+00 754.0
66 TraesCS6B01G400900 chr1B 96.774 62 2 0 2568 2629 630741602 630741541 1.290000e-18 104.0


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 TraesCS6B01G400900 chr6B 676729142 676731772 2630 True 4859.000000 4859 100.000000 1 2631 1 chr6B.!!$R4 2630
1 TraesCS6B01G400900 chr6B 676491238 676492453 1215 True 656.500000 697 87.466000 1233 2496 2 chr6B.!!$R5 1263
2 TraesCS6B01G400900 chr6B 676372662 676373424 762 True 569.000000 569 80.888000 17 800 1 chr6B.!!$R3 783
3 TraesCS6B01G400900 chr6B 676498473 676499239 766 True 512.000000 874 92.214000 1 734 2 chr6B.!!$R6 733
4 TraesCS6B01G400900 chr6B 677044609 677045745 1136 True 346.000000 435 81.718000 934 1972 2 chr6B.!!$R9 1038
5 TraesCS6B01G400900 chr6B 678540103 678543601 3498 False 335.750000 619 82.987000 9 1905 4 chr6B.!!$F3 1896
6 TraesCS6B01G400900 chr6B 676536278 676538088 1810 True 326.333333 580 83.315000 1234 2320 3 chr6B.!!$R7 1086
7 TraesCS6B01G400900 chr6B 678174645 678175873 1228 False 325.666667 488 86.563667 1001 2112 3 chr6B.!!$F1 1111
8 TraesCS6B01G400900 chr6B 678356664 678358227 1563 False 264.066667 486 85.643000 819 2215 3 chr6B.!!$F2 1396
9 TraesCS6B01G400900 chr6B 677335950 677337184 1234 True 258.700000 435 84.365000 802 1972 2 chr6B.!!$R11 1170
10 TraesCS6B01G400900 chr6B 676864605 676865621 1016 True 249.000000 315 85.274000 1236 2219 2 chr6B.!!$R8 983
11 TraesCS6B01G400900 chr6B 677087719 677088555 836 True 239.666667 355 86.922333 829 1543 3 chr6B.!!$R10 714
12 TraesCS6B01G400900 chr6B 678091867 678093054 1187 True 212.966667 388 84.312000 822 1833 3 chr6B.!!$R12 1011
13 TraesCS6B01G400900 chr6A 569678306 569678865 559 True 388.000000 388 80.375000 1235 1785 1 chr6A.!!$R1 550
14 TraesCS6B01G400900 chr6A 593991124 593992517 1393 True 374.500000 462 81.020000 927 2219 2 chr6A.!!$R3 1292
15 TraesCS6B01G400900 chr6A 593928558 593931052 2494 True 372.500000 880 85.198250 67 2379 4 chr6A.!!$R2 2312
16 TraesCS6B01G400900 chr6A 594253210 594254350 1140 True 313.500000 335 81.380500 936 2005 2 chr6A.!!$R4 1069
17 TraesCS6B01G400900 chr6A 594364969 594367043 2074 False 269.250000 477 82.636750 799 2367 4 chr6A.!!$F3 1568
18 TraesCS6B01G400900 chr6D 447212416 447216687 4271 True 402.850000 776 86.651500 12 2572 6 chr6D.!!$R2 2560
19 TraesCS6B01G400900 chr6D 447737168 447738995 1827 False 325.000000 494 81.211000 437 2178 3 chr6D.!!$F1 1741
20 TraesCS6B01G400900 chr6D 447759361 447762498 3137 False 312.233333 675 86.926333 7 2392 3 chr6D.!!$F2 2385
21 TraesCS6B01G400900 chr6D 447277463 447279152 1689 True 250.000000 383 84.957000 828 2219 3 chr6D.!!$R3 1391
22 TraesCS6B01G400900 chr7A 19012472 19013585 1113 False 754.000000 754 79.882000 1234 2364 1 chr7A.!!$F1 1130

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
665 3262 0.509929 GGTTTACCGACAGCAACGTC 59.49 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2591 8685 0.034477 AAGTAATGGAACCGGGGCAG 60.034 55.0 6.32 0.0 0.0 4.85 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
107 982 4.505039 GGATTACTCCAGCCATTAACCGAT 60.505 45.833 0.00 0.00 41.64 4.18
113 988 0.670162 AGCCATTAACCGATGCATGC 59.330 50.000 11.82 11.82 0.00 4.06
378 1300 2.859165 TTCCTTGACATTCCTTCGCT 57.141 45.000 0.00 0.00 0.00 4.93
412 1345 3.958147 ATGGGCGCGAGTGAACAGG 62.958 63.158 12.10 0.00 0.00 4.00
420 1355 2.027625 GAGTGAACAGGTTCGGCGG 61.028 63.158 7.21 0.00 42.28 6.13
422 1357 3.235481 TGAACAGGTTCGGCGGGA 61.235 61.111 7.21 0.00 42.28 5.14
446 1382 0.618458 ATGGACACTGCCATTACGGT 59.382 50.000 0.00 0.00 46.29 4.83
591 1544 1.133513 ACTTGGCCATGGTTCTGAACA 60.134 47.619 21.67 8.66 0.00 3.18
665 3262 0.509929 GGTTTACCGACAGCAACGTC 59.490 55.000 0.00 0.00 0.00 4.34
683 3285 4.308458 CCACGAGCCCACAACCGA 62.308 66.667 0.00 0.00 0.00 4.69
820 4919 5.233050 CGCTCCTTTGACATGACTAATAGTG 59.767 44.000 0.00 1.00 0.00 2.74
871 4971 6.906157 ATTGACCAGAATTTTGACACTGAT 57.094 33.333 0.00 0.00 32.90 2.90
958 5617 1.725164 GACTCCAAGTTCTTAACGCCG 59.275 52.381 0.00 0.00 36.23 6.46
984 5679 2.723334 TACCAAACTGCCCCTCCCCT 62.723 60.000 0.00 0.00 0.00 4.79
985 5680 2.356667 CAAACTGCCCCTCCCCTC 59.643 66.667 0.00 0.00 0.00 4.30
986 5681 3.330720 AAACTGCCCCTCCCCTCG 61.331 66.667 0.00 0.00 0.00 4.63
987 5682 4.658786 AACTGCCCCTCCCCTCGT 62.659 66.667 0.00 0.00 0.00 4.18
992 5687 2.764547 CCCCTCCCCTCGTCCTTC 60.765 72.222 0.00 0.00 0.00 3.46
993 5688 2.764547 CCCTCCCCTCGTCCTTCC 60.765 72.222 0.00 0.00 0.00 3.46
994 5689 3.148279 CCTCCCCTCGTCCTTCCG 61.148 72.222 0.00 0.00 0.00 4.30
995 5690 3.839432 CTCCCCTCGTCCTTCCGC 61.839 72.222 0.00 0.00 0.00 5.54
996 5691 4.377760 TCCCCTCGTCCTTCCGCT 62.378 66.667 0.00 0.00 0.00 5.52
997 5692 3.391382 CCCCTCGTCCTTCCGCTT 61.391 66.667 0.00 0.00 0.00 4.68
998 5693 2.125512 CCCTCGTCCTTCCGCTTG 60.126 66.667 0.00 0.00 0.00 4.01
999 5694 2.125512 CCTCGTCCTTCCGCTTGG 60.126 66.667 0.00 0.00 0.00 3.61
1030 5725 4.528674 CCAACCGGCTCTCATCTG 57.471 61.111 0.00 0.00 0.00 2.90
1073 5791 1.734477 CACCGGAGCTCAACTGACG 60.734 63.158 17.19 8.44 0.00 4.35
1167 5939 1.210722 CCTGTCCTTCTAAGCCCCTTC 59.789 57.143 0.00 0.00 0.00 3.46
1674 7241 3.476419 CGGTGGGGATTAGGCCGT 61.476 66.667 0.00 0.00 37.87 5.68
1716 7288 0.395724 ACCCAATTCGATTCCTGGCC 60.396 55.000 0.00 0.00 0.00 5.36
1719 7291 1.027357 CAATTCGATTCCTGGCCTGG 58.973 55.000 22.36 22.36 0.00 4.45
1720 7292 0.625849 AATTCGATTCCTGGCCTGGT 59.374 50.000 26.40 10.03 0.00 4.00
1721 7293 0.181350 ATTCGATTCCTGGCCTGGTC 59.819 55.000 26.40 17.12 0.00 4.02
1747 7344 3.027412 AGAGTGGCTGTACATAGAGTGG 58.973 50.000 0.00 0.00 0.00 4.00
1798 7406 3.913163 AGTGAGTTCATCTTCCTTCCCTT 59.087 43.478 0.00 0.00 0.00 3.95
1834 7718 0.326595 AGTGAGCTCTCGTCCTCTGA 59.673 55.000 16.19 0.00 0.00 3.27
1859 7747 2.839486 CTGTGTACAGCTCCCTTTGA 57.161 50.000 0.00 0.00 37.15 2.69
1914 7815 4.129380 TGAGTGACAAATTGGAGACACAG 58.871 43.478 13.50 0.00 42.67 3.66
1916 7817 3.117888 AGTGACAAATTGGAGACACAGGT 60.118 43.478 13.50 0.00 42.67 4.00
1917 7818 4.102524 AGTGACAAATTGGAGACACAGGTA 59.897 41.667 13.50 0.00 42.67 3.08
1918 7819 4.213482 GTGACAAATTGGAGACACAGGTAC 59.787 45.833 0.00 0.00 42.67 3.34
1942 7843 0.250209 ATGCATCTGATCTGTCCCGC 60.250 55.000 0.00 0.00 0.00 6.13
1981 7942 3.237746 TCCTTGGATGATTTGTTTGCCA 58.762 40.909 0.00 0.00 0.00 4.92
1982 7943 3.645212 TCCTTGGATGATTTGTTTGCCAA 59.355 39.130 0.00 0.00 34.54 4.52
2056 8023 3.057104 CCCCTGTTTCGGTTTTGGATAAC 60.057 47.826 0.00 0.00 0.00 1.89
2139 8132 0.609131 CGGATCAGGCCACCAACTTT 60.609 55.000 5.01 0.00 0.00 2.66
2147 8140 0.675633 GCCACCAACTTTCAGCACAT 59.324 50.000 0.00 0.00 0.00 3.21
2242 8285 6.092122 TCCTGCTCGTGATATTTTTACTGTTG 59.908 38.462 0.00 0.00 0.00 3.33
2329 8388 3.470888 CGGAGCGGTTGGGATCCT 61.471 66.667 12.58 0.00 40.33 3.24
2430 8517 0.942410 TCGGTTCTGTTTCTTCGCCG 60.942 55.000 0.00 0.00 39.13 6.46
2435 8522 1.956297 TCTGTTTCTTCGCCGGAAAA 58.044 45.000 5.05 0.00 34.97 2.29
2444 8531 2.840066 CGCCGGAAAACAGTTGCCA 61.840 57.895 5.05 0.00 30.51 4.92
2446 8533 1.659794 CCGGAAAACAGTTGCCAGG 59.340 57.895 0.00 4.82 30.51 4.45
2458 8545 0.323360 TTGCCAGGCTCACCAATACC 60.323 55.000 14.15 0.00 39.06 2.73
2468 8555 2.171237 CTCACCAATACCCATCAGCTGA 59.829 50.000 20.79 20.79 0.00 4.26
2496 8585 2.393768 GGCGCCATGTCTGTCAGTG 61.394 63.158 24.80 0.00 0.00 3.66
2507 8597 0.394192 CTGTCAGTGGGCTCTTGTCA 59.606 55.000 0.00 0.00 0.00 3.58
2508 8598 0.836606 TGTCAGTGGGCTCTTGTCAA 59.163 50.000 0.00 0.00 0.00 3.18
2534 8628 1.133869 GTATTGCGTGCGGTGTTCC 59.866 57.895 0.00 0.00 0.00 3.62
2566 8660 1.557651 GAACGAGAAGTATCGGTGCC 58.442 55.000 0.00 0.00 44.10 5.01
2572 8666 3.344515 GAGAAGTATCGGTGCCCTTTTT 58.655 45.455 0.00 0.00 0.00 1.94
2594 8688 6.635030 TTTTTAGAAGAAAAGGACTCCTGC 57.365 37.500 0.00 0.00 32.13 4.85
2595 8689 2.869101 AGAAGAAAAGGACTCCTGCC 57.131 50.000 0.00 0.00 32.13 4.85
2596 8690 1.352687 AGAAGAAAAGGACTCCTGCCC 59.647 52.381 0.00 0.00 32.13 5.36
2597 8691 0.405973 AAGAAAAGGACTCCTGCCCC 59.594 55.000 0.00 0.00 32.13 5.80
2598 8692 1.377333 GAAAAGGACTCCTGCCCCG 60.377 63.158 0.00 0.00 32.13 5.73
2599 8693 2.821679 GAAAAGGACTCCTGCCCCGG 62.822 65.000 0.00 0.00 32.13 5.73
2600 8694 4.658786 AAGGACTCCTGCCCCGGT 62.659 66.667 0.00 0.00 32.13 5.28
2601 8695 4.658786 AGGACTCCTGCCCCGGTT 62.659 66.667 0.00 0.00 29.57 4.44
2602 8696 4.097361 GGACTCCTGCCCCGGTTC 62.097 72.222 0.00 0.00 0.00 3.62
2603 8697 4.097361 GACTCCTGCCCCGGTTCC 62.097 72.222 0.00 0.00 0.00 3.62
2604 8698 4.974438 ACTCCTGCCCCGGTTCCA 62.974 66.667 0.00 0.00 0.00 3.53
2605 8699 3.411517 CTCCTGCCCCGGTTCCAT 61.412 66.667 0.00 0.00 0.00 3.41
2606 8700 2.938798 TCCTGCCCCGGTTCCATT 60.939 61.111 0.00 0.00 0.00 3.16
2607 8701 1.616930 TCCTGCCCCGGTTCCATTA 60.617 57.895 0.00 0.00 0.00 1.90
2608 8702 1.453197 CCTGCCCCGGTTCCATTAC 60.453 63.158 0.00 0.00 0.00 1.89
2609 8703 1.607612 CTGCCCCGGTTCCATTACT 59.392 57.895 0.00 0.00 0.00 2.24
2610 8704 0.034477 CTGCCCCGGTTCCATTACTT 60.034 55.000 0.00 0.00 0.00 2.24
2611 8705 0.322997 TGCCCCGGTTCCATTACTTG 60.323 55.000 0.00 0.00 0.00 3.16
2612 8706 0.034863 GCCCCGGTTCCATTACTTGA 60.035 55.000 0.00 0.00 0.00 3.02
2613 8707 1.614850 GCCCCGGTTCCATTACTTGAA 60.615 52.381 0.00 0.00 0.00 2.69
2614 8708 2.797786 CCCCGGTTCCATTACTTGAAA 58.202 47.619 0.00 0.00 0.00 2.69
2615 8709 3.361786 CCCCGGTTCCATTACTTGAAAT 58.638 45.455 0.00 0.00 0.00 2.17
2616 8710 3.130340 CCCCGGTTCCATTACTTGAAATG 59.870 47.826 0.00 0.00 36.74 2.32
2617 8711 4.013728 CCCGGTTCCATTACTTGAAATGA 58.986 43.478 0.00 0.00 38.84 2.57
2618 8712 4.461081 CCCGGTTCCATTACTTGAAATGAA 59.539 41.667 0.00 0.00 38.84 2.57
2619 8713 5.047660 CCCGGTTCCATTACTTGAAATGAAA 60.048 40.000 0.00 0.00 38.84 2.69
2620 8714 5.861787 CCGGTTCCATTACTTGAAATGAAAC 59.138 40.000 0.00 0.00 38.84 2.78
2621 8715 5.861787 CGGTTCCATTACTTGAAATGAAACC 59.138 40.000 7.44 7.44 45.66 3.27
2623 8717 7.637709 GTTCCATTACTTGAAATGAAACCAC 57.362 36.000 0.00 0.00 38.84 4.16
2624 8718 6.968263 TCCATTACTTGAAATGAAACCACA 57.032 33.333 0.00 0.00 38.84 4.17
2625 8719 6.980593 TCCATTACTTGAAATGAAACCACAG 58.019 36.000 0.00 0.00 38.84 3.66
2626 8720 6.775142 TCCATTACTTGAAATGAAACCACAGA 59.225 34.615 0.00 0.00 38.84 3.41
2627 8721 7.286546 TCCATTACTTGAAATGAAACCACAGAA 59.713 33.333 0.00 0.00 38.84 3.02
2628 8722 8.090214 CCATTACTTGAAATGAAACCACAGAAT 58.910 33.333 0.00 0.00 38.84 2.40
2629 8723 9.480053 CATTACTTGAAATGAAACCACAGAATT 57.520 29.630 0.00 0.00 38.84 2.17
2630 8724 9.696917 ATTACTTGAAATGAAACCACAGAATTC 57.303 29.630 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 968 1.601162 GCATGCATCGGTTAATGGCTG 60.601 52.381 14.21 0.00 0.00 4.85
113 988 4.821589 GACAAGCGGGCCTCGGAG 62.822 72.222 14.29 0.00 39.69 4.63
172 1058 2.563427 GCTCCTGTCTTTTGCGCC 59.437 61.111 4.18 0.00 0.00 6.53
288 1204 0.176680 AGATGCTCCGATCGCTGTTT 59.823 50.000 10.32 0.00 0.00 2.83
360 1277 1.404181 CGAGCGAAGGAATGTCAAGGA 60.404 52.381 0.00 0.00 0.00 3.36
387 1309 2.106683 ACTCGCGCCCATTGTTAGC 61.107 57.895 0.00 0.00 0.00 3.09
389 1311 0.320858 TTCACTCGCGCCCATTGTTA 60.321 50.000 0.00 0.00 0.00 2.41
393 1315 2.031919 TGTTCACTCGCGCCCATT 59.968 55.556 0.00 0.00 0.00 3.16
420 1355 2.512515 GCAGTGTCCATCGGCTCC 60.513 66.667 0.00 0.00 0.00 4.70
422 1357 2.202236 AATGGCAGTGTCCATCGGCT 62.202 55.000 16.32 2.35 45.64 5.52
446 1382 1.001293 GACACAGTGGCATCTCAGTCA 59.999 52.381 0.00 0.00 0.00 3.41
488 1433 0.387750 GCCTCCGCTTTGCTTGAAAG 60.388 55.000 0.00 0.00 43.63 2.62
621 3218 1.157870 CGGCACACTGAAAGAACGGT 61.158 55.000 0.00 0.00 37.43 4.83
653 3250 3.403057 CGTGGGACGTTGCTGTCG 61.403 66.667 0.00 0.00 39.83 4.35
820 4919 4.157656 TGCATTACAAACCAGTATCTTGCC 59.842 41.667 0.00 0.00 30.29 4.52
871 4971 6.398234 TGCCAACTTGCTTTGAAATACTAA 57.602 33.333 0.00 0.00 0.00 2.24
958 5617 3.431415 AGGGGCAGTTTGGTAAATTCTC 58.569 45.455 0.00 0.00 0.00 2.87
984 5679 1.327690 ATAGCCAAGCGGAAGGACGA 61.328 55.000 0.00 0.00 35.47 4.20
985 5680 0.387929 TATAGCCAAGCGGAAGGACG 59.612 55.000 0.00 0.00 0.00 4.79
986 5681 2.614829 TTATAGCCAAGCGGAAGGAC 57.385 50.000 0.00 0.00 0.00 3.85
987 5682 3.740115 GATTTATAGCCAAGCGGAAGGA 58.260 45.455 0.00 0.00 0.00 3.36
988 5683 2.480419 CGATTTATAGCCAAGCGGAAGG 59.520 50.000 0.00 0.00 29.44 3.46
989 5684 3.390135 TCGATTTATAGCCAAGCGGAAG 58.610 45.455 0.00 0.00 33.87 3.46
990 5685 3.390135 CTCGATTTATAGCCAAGCGGAA 58.610 45.455 0.00 0.00 33.87 4.30
991 5686 2.288825 CCTCGATTTATAGCCAAGCGGA 60.289 50.000 0.00 0.00 33.87 5.54
992 5687 2.069273 CCTCGATTTATAGCCAAGCGG 58.931 52.381 0.00 0.00 33.87 5.52
993 5688 1.461127 GCCTCGATTTATAGCCAAGCG 59.539 52.381 0.00 0.00 34.36 4.68
994 5689 1.807142 GGCCTCGATTTATAGCCAAGC 59.193 52.381 0.00 0.00 43.32 4.01
998 5693 2.152016 GGTTGGCCTCGATTTATAGCC 58.848 52.381 3.32 0.00 44.13 3.93
999 5694 1.798813 CGGTTGGCCTCGATTTATAGC 59.201 52.381 3.32 0.00 0.00 2.97
1167 5939 2.360726 GCGGGTTGGTAGTTGGGG 60.361 66.667 0.00 0.00 0.00 4.96
1636 7183 2.486951 TCTTCTATACAGCGAACGGC 57.513 50.000 0.00 0.00 44.05 5.68
1674 7241 4.778958 TCTTAAAACTCCAATCTACCGGGA 59.221 41.667 6.32 0.00 0.00 5.14
1716 7288 3.340814 ACAGCCACTCTAATTGACCAG 57.659 47.619 0.00 0.00 0.00 4.00
1719 7291 6.806751 TCTATGTACAGCCACTCTAATTGAC 58.193 40.000 0.33 0.00 0.00 3.18
1720 7292 6.607600 ACTCTATGTACAGCCACTCTAATTGA 59.392 38.462 0.33 0.00 0.00 2.57
1721 7293 6.699204 CACTCTATGTACAGCCACTCTAATTG 59.301 42.308 0.33 0.00 0.00 2.32
1747 7344 2.416432 CGGGGAGGAGGAAGACGAC 61.416 68.421 0.00 0.00 0.00 4.34
1785 7393 3.213160 AGTGGAGAAGGGAAGGAAGAT 57.787 47.619 0.00 0.00 0.00 2.40
1788 7396 2.418669 ACAAGTGGAGAAGGGAAGGAA 58.581 47.619 0.00 0.00 0.00 3.36
1789 7397 2.118403 ACAAGTGGAGAAGGGAAGGA 57.882 50.000 0.00 0.00 0.00 3.36
1790 7398 2.637872 TGTACAAGTGGAGAAGGGAAGG 59.362 50.000 0.00 0.00 0.00 3.46
1791 7399 4.559862 ATGTACAAGTGGAGAAGGGAAG 57.440 45.455 0.00 0.00 0.00 3.46
1792 7400 5.338632 TCTATGTACAAGTGGAGAAGGGAA 58.661 41.667 0.00 0.00 0.00 3.97
1798 7406 4.399618 GCTCACTCTATGTACAAGTGGAGA 59.600 45.833 20.69 9.41 40.60 3.71
1914 7815 3.188667 CAGATCAGATGCATGCATGTACC 59.811 47.826 36.73 21.84 36.70 3.34
1916 7817 4.062991 GACAGATCAGATGCATGCATGTA 58.937 43.478 36.73 23.60 36.70 2.29
1917 7818 2.879026 GACAGATCAGATGCATGCATGT 59.121 45.455 36.73 30.15 36.70 3.21
1918 7819 2.226674 GGACAGATCAGATGCATGCATG 59.773 50.000 36.73 24.86 36.70 4.06
1942 7843 1.269998 GGATGGATAAGACTCCCGTCG 59.730 57.143 0.00 0.00 44.93 5.12
1981 7942 2.622064 ACGGAGCAGAGAGTTGTTTT 57.378 45.000 0.00 0.00 0.00 2.43
1982 7943 2.622064 AACGGAGCAGAGAGTTGTTT 57.378 45.000 0.00 0.00 0.00 2.83
2056 8023 2.202987 GCCACTGATCGCTGGAGG 60.203 66.667 11.78 0.97 0.00 4.30
2139 8132 1.064463 GGGGGATTTCTCATGTGCTGA 60.064 52.381 0.00 0.00 0.00 4.26
2147 8140 1.327690 CGGAGTCGGGGGATTTCTCA 61.328 60.000 0.00 0.00 0.00 3.27
2242 8285 6.255887 CAGTAAAATACCACGGATCTGAAGAC 59.744 42.308 9.00 0.00 0.00 3.01
2288 8333 2.804527 GTCCCTCGGTCAACAGTAAAAC 59.195 50.000 0.00 0.00 0.00 2.43
2329 8388 1.478654 GCAAGTTGAAGAGTTGGGGGA 60.479 52.381 7.16 0.00 38.80 4.81
2392 8455 2.354259 GATCAAGAAGCTGTCCAGGTG 58.646 52.381 0.00 0.00 39.39 4.00
2393 8456 1.066573 CGATCAAGAAGCTGTCCAGGT 60.067 52.381 0.00 0.00 41.53 4.00
2394 8457 1.649664 CGATCAAGAAGCTGTCCAGG 58.350 55.000 0.00 0.00 0.00 4.45
2395 8458 1.066573 ACCGATCAAGAAGCTGTCCAG 60.067 52.381 0.00 0.00 0.00 3.86
2430 8517 0.315251 GAGCCTGGCAACTGTTTTCC 59.685 55.000 22.65 0.00 37.61 3.13
2435 8522 2.113986 GGTGAGCCTGGCAACTGT 59.886 61.111 22.65 0.00 37.61 3.55
2444 8531 1.492176 CTGATGGGTATTGGTGAGCCT 59.508 52.381 0.00 0.00 35.40 4.58
2446 8533 1.133976 AGCTGATGGGTATTGGTGAGC 60.134 52.381 0.00 0.00 0.00 4.26
2468 8555 2.108514 CATGGCGCCACTCGAACAT 61.109 57.895 35.50 10.89 41.67 2.71
2473 8562 3.190849 CAGACATGGCGCCACTCG 61.191 66.667 35.50 25.28 42.12 4.18
2476 8565 2.358615 TGACAGACATGGCGCCAC 60.359 61.111 35.50 20.38 37.19 5.01
2496 8585 2.887152 ACTTCAATGTTGACAAGAGCCC 59.113 45.455 0.00 0.00 36.83 5.19
2507 8597 2.414029 CCGCACGCAATACTTCAATGTT 60.414 45.455 0.00 0.00 0.00 2.71
2508 8598 1.130373 CCGCACGCAATACTTCAATGT 59.870 47.619 0.00 0.00 0.00 2.71
2542 8636 2.095532 ACCGATACTTCTCGTTCGTCAG 59.904 50.000 0.00 0.00 36.93 3.51
2546 8640 1.189403 GCACCGATACTTCTCGTTCG 58.811 55.000 0.00 0.00 36.93 3.95
2572 8666 5.070685 GGCAGGAGTCCTTTTCTTCTAAAA 58.929 41.667 9.68 0.00 0.00 1.52
2573 8667 4.506802 GGGCAGGAGTCCTTTTCTTCTAAA 60.507 45.833 9.68 0.00 36.28 1.85
2574 8668 3.009143 GGGCAGGAGTCCTTTTCTTCTAA 59.991 47.826 9.68 0.00 36.28 2.10
2575 8669 2.572104 GGGCAGGAGTCCTTTTCTTCTA 59.428 50.000 9.68 0.00 36.28 2.10
2576 8670 1.352687 GGGCAGGAGTCCTTTTCTTCT 59.647 52.381 9.68 0.00 36.28 2.85
2577 8671 1.614583 GGGGCAGGAGTCCTTTTCTTC 60.615 57.143 9.68 0.00 40.27 2.87
2578 8672 0.405973 GGGGCAGGAGTCCTTTTCTT 59.594 55.000 9.68 0.00 40.27 2.52
2579 8673 1.842381 CGGGGCAGGAGTCCTTTTCT 61.842 60.000 9.68 0.00 40.27 2.52
2580 8674 1.377333 CGGGGCAGGAGTCCTTTTC 60.377 63.158 9.68 1.40 40.27 2.29
2581 8675 2.757077 CGGGGCAGGAGTCCTTTT 59.243 61.111 9.68 0.00 40.27 2.27
2582 8676 3.330720 CCGGGGCAGGAGTCCTTT 61.331 66.667 9.68 0.00 40.27 3.11
2583 8677 4.658786 ACCGGGGCAGGAGTCCTT 62.659 66.667 9.68 0.00 40.27 3.36
2584 8678 4.658786 AACCGGGGCAGGAGTCCT 62.659 66.667 5.62 5.62 40.27 3.85
2585 8679 4.097361 GAACCGGGGCAGGAGTCC 62.097 72.222 6.32 0.00 39.43 3.85
2586 8680 4.097361 GGAACCGGGGCAGGAGTC 62.097 72.222 6.32 2.51 34.73 3.36
2587 8681 4.974438 TGGAACCGGGGCAGGAGT 62.974 66.667 6.32 0.00 34.73 3.85
2588 8682 1.632018 TAATGGAACCGGGGCAGGAG 61.632 60.000 6.32 0.00 34.73 3.69
2589 8683 1.616930 TAATGGAACCGGGGCAGGA 60.617 57.895 6.32 0.00 34.73 3.86
2590 8684 1.453197 GTAATGGAACCGGGGCAGG 60.453 63.158 6.32 0.00 37.30 4.85
2591 8685 0.034477 AAGTAATGGAACCGGGGCAG 60.034 55.000 6.32 0.00 0.00 4.85
2592 8686 0.322997 CAAGTAATGGAACCGGGGCA 60.323 55.000 6.32 0.00 0.00 5.36
2593 8687 0.034863 TCAAGTAATGGAACCGGGGC 60.035 55.000 6.32 0.00 0.00 5.80
2594 8688 2.500392 TTCAAGTAATGGAACCGGGG 57.500 50.000 6.32 0.00 0.00 5.73
2595 8689 4.013728 TCATTTCAAGTAATGGAACCGGG 58.986 43.478 6.32 0.00 36.41 5.73
2596 8690 5.637006 TTCATTTCAAGTAATGGAACCGG 57.363 39.130 0.00 0.00 36.41 5.28
2597 8691 6.927933 GTTTCATTTCAAGTAATGGAACCG 57.072 37.500 10.70 0.00 43.55 4.44
2599 8693 7.206687 TGTGGTTTCATTTCAAGTAATGGAAC 58.793 34.615 12.52 12.52 46.41 3.62
2600 8694 7.286546 TCTGTGGTTTCATTTCAAGTAATGGAA 59.713 33.333 0.00 0.00 36.41 3.53
2601 8695 6.775142 TCTGTGGTTTCATTTCAAGTAATGGA 59.225 34.615 0.00 0.00 36.41 3.41
2602 8696 6.980593 TCTGTGGTTTCATTTCAAGTAATGG 58.019 36.000 0.00 0.00 36.41 3.16
2603 8697 9.480053 AATTCTGTGGTTTCATTTCAAGTAATG 57.520 29.630 0.00 0.00 36.95 1.90
2604 8698 9.696917 GAATTCTGTGGTTTCATTTCAAGTAAT 57.303 29.630 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.