Multiple sequence alignment - TraesCS6B01G048300

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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 TraesCS6B01G048300 chr6B 100.000 2533 0 0 1 2533 28257622 28255090 0.000000e+00 4678.0
1 TraesCS6B01G048300 chr6B 92.024 840 47 14 729 1552 28925765 28926600 0.000000e+00 1162.0
2 TraesCS6B01G048300 chr6B 86.200 971 90 26 749 1697 28517566 28516618 0.000000e+00 1011.0
3 TraesCS6B01G048300 chr6B 88.026 760 55 20 810 1549 29060786 29060043 0.000000e+00 867.0
4 TraesCS6B01G048300 chr6B 93.625 549 34 1 1 549 28925127 28925674 0.000000e+00 819.0
5 TraesCS6B01G048300 chr6B 90.323 279 17 7 2251 2527 28213980 28213710 8.620000e-95 357.0
6 TraesCS6B01G048300 chr6B 77.352 287 46 12 1606 1880 38878412 38878691 4.360000e-33 152.0
7 TraesCS6B01G048300 chr6B 96.875 64 2 0 627 690 28925705 28925768 9.580000e-20 108.0
8 TraesCS6B01G048300 chr6D 91.176 1156 67 17 736 1877 16307505 16306371 0.000000e+00 1537.0
9 TraesCS6B01G048300 chr6D 92.272 647 41 8 911 1552 16390173 16389531 0.000000e+00 909.0
10 TraesCS6B01G048300 chr6D 87.617 751 64 14 853 1584 24001426 24002166 0.000000e+00 845.0
11 TraesCS6B01G048300 chr6D 88.092 739 49 29 846 1553 29381439 29380709 0.000000e+00 841.0
12 TraesCS6B01G048300 chr6D 92.123 292 22 1 108 399 16308289 16307999 6.520000e-111 411.0
13 TraesCS6B01G048300 chr6D 94.969 159 6 2 2251 2409 16305909 16305753 5.410000e-62 248.0
14 TraesCS6B01G048300 chr6D 93.506 154 8 1 1909 2062 16306297 16306146 7.050000e-56 228.0
15 TraesCS6B01G048300 chr6D 80.456 307 38 10 1596 1887 24002231 24002530 5.490000e-52 215.0
16 TraesCS6B01G048300 chr6D 94.545 110 4 1 1 110 16308968 16308861 4.330000e-38 169.0
17 TraesCS6B01G048300 chr6D 92.632 95 6 1 2325 2418 16305332 16305238 4.400000e-28 135.0
18 TraesCS6B01G048300 chr6D 85.859 99 3 2 2168 2255 16306038 16305940 7.460000e-16 95.3
19 TraesCS6B01G048300 chr6A 86.762 1322 102 40 749 2038 16594037 16592757 0.000000e+00 1404.0
20 TraesCS6B01G048300 chr6A 85.859 990 103 27 749 1710 16658939 16657959 0.000000e+00 1018.0
21 TraesCS6B01G048300 chr6A 91.727 278 17 4 2251 2526 16592436 16592163 5.110000e-102 381.0
22 TraesCS6B01G048300 chr6A 88.742 151 13 4 2316 2465 16591696 16591549 5.570000e-42 182.0
23 TraesCS6B01G048300 chr6A 84.848 132 10 5 619 750 16659104 16658983 9.510000e-25 124.0
24 TraesCS6B01G048300 chr6A 76.371 237 50 4 316 549 190028 189795 3.420000e-24 122.0
25 TraesCS6B01G048300 chr6A 75.949 237 51 4 316 549 163430 163197 1.590000e-22 117.0
26 TraesCS6B01G048300 chr1B 86.640 988 83 36 810 1759 587472695 587473671 0.000000e+00 1048.0
27 TraesCS6B01G048300 chr5A 77.370 327 54 14 3 313 591445222 591445544 2.590000e-40 176.0
28 TraesCS6B01G048300 chr7A 78.222 225 42 6 312 533 118161725 118161945 1.220000e-28 137.0
29 TraesCS6B01G048300 chr5D 96.774 62 2 0 2082 2143 446902786 446902847 1.240000e-18 104.0
30 TraesCS6B01G048300 chr4A 96.610 59 2 0 2085 2143 506202793 506202735 5.770000e-17 99.0
31 TraesCS6B01G048300 chr1A 89.286 84 2 2 2060 2143 435407819 435407895 5.770000e-17 99.0
32 TraesCS6B01G048300 chr2A 94.915 59 3 0 2085 2143 193694960 193694902 2.680000e-15 93.5
33 TraesCS6B01G048300 chr2D 75.789 190 38 7 364 549 582146611 582146796 3.470000e-14 89.8
34 TraesCS6B01G048300 chr3D 86.905 84 4 3 2060 2143 497762836 497762760 1.250000e-13 87.9


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 TraesCS6B01G048300 chr6B 28255090 28257622 2532 True 4678.000000 4678 100.000000 1 2533 1 chr6B.!!$R2 2532
1 TraesCS6B01G048300 chr6B 28516618 28517566 948 True 1011.000000 1011 86.200000 749 1697 1 chr6B.!!$R3 948
2 TraesCS6B01G048300 chr6B 29060043 29060786 743 True 867.000000 867 88.026000 810 1549 1 chr6B.!!$R4 739
3 TraesCS6B01G048300 chr6B 28925127 28926600 1473 False 696.333333 1162 94.174667 1 1552 3 chr6B.!!$F2 1551
4 TraesCS6B01G048300 chr6D 16389531 16390173 642 True 909.000000 909 92.272000 911 1552 1 chr6D.!!$R1 641
5 TraesCS6B01G048300 chr6D 29380709 29381439 730 True 841.000000 841 88.092000 846 1553 1 chr6D.!!$R2 707
6 TraesCS6B01G048300 chr6D 24001426 24002530 1104 False 530.000000 845 84.036500 853 1887 2 chr6D.!!$F1 1034
7 TraesCS6B01G048300 chr6D 16305238 16308968 3730 True 403.328571 1537 92.115714 1 2418 7 chr6D.!!$R3 2417
8 TraesCS6B01G048300 chr6A 16591549 16594037 2488 True 655.666667 1404 89.077000 749 2526 3 chr6A.!!$R3 1777
9 TraesCS6B01G048300 chr6A 16657959 16659104 1145 True 571.000000 1018 85.353500 619 1710 2 chr6A.!!$R4 1091
10 TraesCS6B01G048300 chr1B 587472695 587473671 976 False 1048.000000 1048 86.640000 810 1759 1 chr1B.!!$F1 949

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
587 1325 0.178978 TGCCCCTGTTGCAATGTACA 60.179 50.0 0.59 0.0 35.4 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 3199 0.034186 CAGCAACAGGGGCAAGGATA 60.034 55.0 0.0 0.0 0.0 2.59 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
55 56 5.395435 GGACCAACTTAGGTTCCTATGTCTC 60.395 48.000 14.77 10.73 43.38 3.36
64 65 5.021458 AGGTTCCTATGTCTCCGACTTTTA 58.979 41.667 0.00 0.00 33.15 1.52
110 684 3.880490 AGGCTAGATGGATATCGACGATC 59.120 47.826 14.80 1.24 38.38 3.69
197 771 1.877637 TCCAAAGTGTGTGGATGACG 58.122 50.000 0.00 0.00 40.33 4.35
233 807 2.830104 TGATCAGATGAGCCATCAACG 58.170 47.619 14.93 5.79 42.72 4.10
282 856 3.708631 CAGAGGTGGTGAGTGGAAGATAT 59.291 47.826 0.00 0.00 0.00 1.63
376 950 4.119442 ACCGTGCGTCTTTACATAGAAT 57.881 40.909 0.00 0.00 0.00 2.40
385 959 6.926272 GCGTCTTTACATAGAATGGAGAAGAT 59.074 38.462 0.00 0.00 32.93 2.40
403 977 4.774660 AGATGAGTCAGGAAGATTGCAT 57.225 40.909 0.00 0.00 0.00 3.96
414 988 5.295292 CAGGAAGATTGCATCGTTCTACAAT 59.705 40.000 0.00 0.00 35.52 2.71
504 1232 2.911819 TAATTTTCGAAAGGCCAGCG 57.088 45.000 10.98 5.41 0.00 5.18
537 1265 2.625790 GGGTGCTGTACTATCCTCTGAG 59.374 54.545 0.00 0.00 0.00 3.35
559 1297 5.039645 AGTTCCCTCCTAATCTCAATCCAA 58.960 41.667 0.00 0.00 0.00 3.53
563 1301 6.367983 TCCCTCCTAATCTCAATCCAAAATG 58.632 40.000 0.00 0.00 0.00 2.32
565 1303 7.128728 TCCCTCCTAATCTCAATCCAAAATGTA 59.871 37.037 0.00 0.00 0.00 2.29
572 1310 6.899393 TCTCAATCCAAAATGTATATGCCC 57.101 37.500 0.00 0.00 0.00 5.36
573 1311 5.774690 TCTCAATCCAAAATGTATATGCCCC 59.225 40.000 0.00 0.00 0.00 5.80
574 1312 5.714863 TCAATCCAAAATGTATATGCCCCT 58.285 37.500 0.00 0.00 0.00 4.79
575 1313 5.539574 TCAATCCAAAATGTATATGCCCCTG 59.460 40.000 0.00 0.00 0.00 4.45
576 1314 4.534647 TCCAAAATGTATATGCCCCTGT 57.465 40.909 0.00 0.00 0.00 4.00
577 1315 4.877773 TCCAAAATGTATATGCCCCTGTT 58.122 39.130 0.00 0.00 0.00 3.16
578 1316 4.648762 TCCAAAATGTATATGCCCCTGTTG 59.351 41.667 0.00 0.00 0.00 3.33
579 1317 4.370917 CAAAATGTATATGCCCCTGTTGC 58.629 43.478 0.00 0.00 0.00 4.17
580 1318 3.311167 AATGTATATGCCCCTGTTGCA 57.689 42.857 0.00 0.00 43.97 4.08
581 1319 2.816777 TGTATATGCCCCTGTTGCAA 57.183 45.000 0.00 0.00 42.92 4.08
582 1320 3.311167 TGTATATGCCCCTGTTGCAAT 57.689 42.857 0.59 0.00 42.92 3.56
583 1321 2.957680 TGTATATGCCCCTGTTGCAATG 59.042 45.455 0.59 0.00 42.92 2.82
584 1322 2.163810 ATATGCCCCTGTTGCAATGT 57.836 45.000 0.59 0.00 42.92 2.71
585 1323 2.816777 TATGCCCCTGTTGCAATGTA 57.183 45.000 0.59 0.00 42.92 2.29
586 1324 1.185315 ATGCCCCTGTTGCAATGTAC 58.815 50.000 0.59 0.00 42.92 2.90
587 1325 0.178978 TGCCCCTGTTGCAATGTACA 60.179 50.000 0.59 0.00 35.40 2.90
588 1326 1.185315 GCCCCTGTTGCAATGTACAT 58.815 50.000 0.59 1.41 0.00 2.29
589 1327 2.291217 TGCCCCTGTTGCAATGTACATA 60.291 45.455 9.21 0.00 35.40 2.29
590 1328 2.958355 GCCCCTGTTGCAATGTACATAT 59.042 45.455 9.21 0.00 0.00 1.78
591 1329 4.141287 GCCCCTGTTGCAATGTACATATA 58.859 43.478 9.21 0.00 0.00 0.86
592 1330 4.582656 GCCCCTGTTGCAATGTACATATAA 59.417 41.667 9.21 2.19 0.00 0.98
593 1331 5.068460 GCCCCTGTTGCAATGTACATATAAA 59.932 40.000 9.21 0.97 0.00 1.40
594 1332 6.239289 GCCCCTGTTGCAATGTACATATAAAT 60.239 38.462 9.21 0.00 0.00 1.40
595 1333 7.040062 GCCCCTGTTGCAATGTACATATAAATA 60.040 37.037 9.21 1.78 0.00 1.40
596 1334 8.514594 CCCCTGTTGCAATGTACATATAAATAG 58.485 37.037 9.21 10.50 0.00 1.73
597 1335 8.023128 CCCTGTTGCAATGTACATATAAATAGC 58.977 37.037 9.21 5.81 0.00 2.97
598 1336 8.023128 CCTGTTGCAATGTACATATAAATAGCC 58.977 37.037 9.21 0.00 0.00 3.93
599 1337 8.457238 TGTTGCAATGTACATATAAATAGCCA 57.543 30.769 9.21 0.00 0.00 4.75
600 1338 9.076781 TGTTGCAATGTACATATAAATAGCCAT 57.923 29.630 9.21 0.00 0.00 4.40
603 1341 9.958180 TGCAATGTACATATAAATAGCCATACT 57.042 29.630 9.21 0.00 0.00 2.12
699 1491 4.833478 ATCGAAGCCCATCTAATAGCAT 57.167 40.909 0.00 0.00 0.00 3.79
700 1492 4.193826 TCGAAGCCCATCTAATAGCATC 57.806 45.455 0.00 0.00 0.00 3.91
701 1493 3.834813 TCGAAGCCCATCTAATAGCATCT 59.165 43.478 0.00 0.00 0.00 2.90
707 1499 6.825610 AGCCCATCTAATAGCATCTAATAGC 58.174 40.000 0.00 0.00 0.00 2.97
708 1500 6.385176 AGCCCATCTAATAGCATCTAATAGCA 59.615 38.462 0.00 0.00 0.00 3.49
709 1501 7.050377 GCCCATCTAATAGCATCTAATAGCAA 58.950 38.462 0.00 0.00 0.00 3.91
710 1502 7.554118 GCCCATCTAATAGCATCTAATAGCAAA 59.446 37.037 0.00 0.00 0.00 3.68
711 1503 8.887717 CCCATCTAATAGCATCTAATAGCAAAC 58.112 37.037 0.00 0.00 0.00 2.93
712 1504 8.598924 CCATCTAATAGCATCTAATAGCAAACG 58.401 37.037 0.00 0.00 0.00 3.60
713 1505 8.598924 CATCTAATAGCATCTAATAGCAAACGG 58.401 37.037 0.00 0.00 0.00 4.44
727 1519 5.200368 AGCAAACGGAAAAGAATTCATGT 57.800 34.783 8.44 0.00 0.00 3.21
964 1925 4.025401 GCCGCCAACACCACTTCG 62.025 66.667 0.00 0.00 0.00 3.79
965 1926 3.353836 CCGCCAACACCACTTCGG 61.354 66.667 0.00 0.00 42.50 4.30
1271 2271 0.400213 TGGTTGAATCGCAGGTCCTT 59.600 50.000 0.00 0.00 0.00 3.36
1445 2445 2.990479 CTCCCCAAGAAGTCCCCG 59.010 66.667 0.00 0.00 0.00 5.73
1499 2502 0.393077 AGAAGACCACCACCAAGTCG 59.607 55.000 0.00 0.00 35.65 4.18
1675 2763 1.478105 GTGATTTCTGTGGGAATGGCC 59.522 52.381 0.00 0.00 33.53 5.36
1749 2843 4.816385 TGAATCTTGTGAGTCTTTGTCACC 59.184 41.667 0.99 0.00 43.19 4.02
1753 2847 1.486310 TGTGAGTCTTTGTCACCTGCT 59.514 47.619 0.99 0.00 43.19 4.24
1795 2889 5.302568 TGGTTTGCATCTGAAAATGAGACTT 59.697 36.000 0.00 0.00 0.00 3.01
1815 2909 1.217882 GTCCGTGTGTTCTTGACCAG 58.782 55.000 0.00 0.00 0.00 4.00
1860 2955 8.997323 ACTTCAGTCAGTCATCTTAATTTCTTG 58.003 33.333 0.00 0.00 0.00 3.02
1880 2976 7.672983 TCTTGTCCTGAATGTTATCTTTCAC 57.327 36.000 0.00 0.00 35.13 3.18
1895 3043 3.254166 TCTTTCACTTTTCATCCAGCTGC 59.746 43.478 8.66 0.00 0.00 5.25
1898 3046 1.201647 CACTTTTCATCCAGCTGCAGG 59.798 52.381 17.12 4.46 0.00 4.85
1899 3047 0.815734 CTTTTCATCCAGCTGCAGGG 59.184 55.000 17.12 9.41 0.00 4.45
1900 3048 0.405198 TTTTCATCCAGCTGCAGGGA 59.595 50.000 17.12 15.00 37.64 4.20
1901 3049 0.627451 TTTCATCCAGCTGCAGGGAT 59.373 50.000 17.12 16.68 44.65 3.85
1902 3050 0.182061 TTCATCCAGCTGCAGGGATC 59.818 55.000 18.56 1.48 41.93 3.36
1903 3051 0.693430 TCATCCAGCTGCAGGGATCT 60.693 55.000 18.56 3.83 41.93 2.75
1904 3052 0.535328 CATCCAGCTGCAGGGATCTG 60.535 60.000 18.56 14.79 41.93 2.90
1999 3160 9.308318 GTGGTAAGCAAAATTCTTCAAAACTTA 57.692 29.630 0.00 0.00 0.00 2.24
2038 3199 2.808543 GCGGACAGTTCAACTTTGATCT 59.191 45.455 0.00 0.00 37.64 2.75
2053 3214 2.492025 TGATCTATCCTTGCCCCTGTT 58.508 47.619 0.00 0.00 0.00 3.16
2072 3341 1.176527 TGCTGGGCTAGATGCAAAAC 58.823 50.000 0.43 0.00 45.15 2.43
2080 3349 4.379918 GGGCTAGATGCAAAACAGACTTTC 60.380 45.833 0.00 0.00 45.15 2.62
2083 3352 4.739046 AGATGCAAAACAGACTTTCGAG 57.261 40.909 0.00 0.00 0.00 4.04
2085 3354 4.576463 AGATGCAAAACAGACTTTCGAGTT 59.424 37.500 0.00 0.00 0.00 3.01
2086 3355 4.695217 TGCAAAACAGACTTTCGAGTTT 57.305 36.364 0.00 0.00 33.32 2.66
2087 3356 4.658071 TGCAAAACAGACTTTCGAGTTTC 58.342 39.130 0.00 0.00 31.69 2.78
2088 3357 3.719352 GCAAAACAGACTTTCGAGTTTCG 59.281 43.478 0.00 0.00 42.10 3.46
2119 3388 7.118723 TCTGATTTATGTTAGCCAAATGAGGT 58.881 34.615 0.00 0.00 0.00 3.85
2124 3393 3.343617 TGTTAGCCAAATGAGGTACTGC 58.656 45.455 0.00 0.00 41.55 4.40
2130 3399 5.264395 AGCCAAATGAGGTACTGCTAATTT 58.736 37.500 0.00 0.00 41.55 1.82
2131 3400 5.716703 AGCCAAATGAGGTACTGCTAATTTT 59.283 36.000 0.00 0.00 41.55 1.82
2132 3401 5.807011 GCCAAATGAGGTACTGCTAATTTTG 59.193 40.000 0.00 0.00 41.55 2.44
2133 3402 6.332630 CCAAATGAGGTACTGCTAATTTTGG 58.667 40.000 0.00 0.00 41.55 3.28
2134 3403 6.152661 CCAAATGAGGTACTGCTAATTTTGGA 59.847 38.462 4.95 0.00 41.55 3.53
2135 3404 7.147846 CCAAATGAGGTACTGCTAATTTTGGAT 60.148 37.037 4.95 0.00 41.55 3.41
2136 3405 7.961326 AATGAGGTACTGCTAATTTTGGATT 57.039 32.000 0.00 0.00 41.55 3.01
2137 3406 7.573968 ATGAGGTACTGCTAATTTTGGATTC 57.426 36.000 0.00 0.00 41.55 2.52
2138 3407 6.480763 TGAGGTACTGCTAATTTTGGATTCA 58.519 36.000 0.00 0.00 41.55 2.57
2139 3408 6.374333 TGAGGTACTGCTAATTTTGGATTCAC 59.626 38.462 0.00 0.00 41.55 3.18
2140 3409 5.652452 AGGTACTGCTAATTTTGGATTCACC 59.348 40.000 0.00 0.00 37.18 4.02
2141 3410 5.163550 GGTACTGCTAATTTTGGATTCACCC 60.164 44.000 0.00 0.00 38.00 4.61
2142 3411 4.415596 ACTGCTAATTTTGGATTCACCCA 58.584 39.130 0.00 0.00 38.00 4.51
2143 3412 5.025453 ACTGCTAATTTTGGATTCACCCAT 58.975 37.500 0.00 0.00 35.87 4.00
2144 3413 5.484998 ACTGCTAATTTTGGATTCACCCATT 59.515 36.000 0.00 0.00 35.87 3.16
2145 3414 6.013466 ACTGCTAATTTTGGATTCACCCATTT 60.013 34.615 0.00 0.00 35.87 2.32
2146 3415 6.405538 TGCTAATTTTGGATTCACCCATTTC 58.594 36.000 0.00 0.00 35.87 2.17
2147 3416 5.519927 GCTAATTTTGGATTCACCCATTTCG 59.480 40.000 0.00 0.00 35.87 3.46
2148 3417 3.311486 TTTTGGATTCACCCATTTCGC 57.689 42.857 0.00 0.00 35.87 4.70
2149 3418 1.916506 TTGGATTCACCCATTTCGCA 58.083 45.000 0.00 0.00 35.87 5.10
2150 3419 1.916506 TGGATTCACCCATTTCGCAA 58.083 45.000 0.00 0.00 38.00 4.85
2151 3420 2.242926 TGGATTCACCCATTTCGCAAA 58.757 42.857 0.00 0.00 38.00 3.68
2152 3421 2.630098 TGGATTCACCCATTTCGCAAAA 59.370 40.909 0.00 0.00 38.00 2.44
2153 3422 3.070159 TGGATTCACCCATTTCGCAAAAA 59.930 39.130 0.00 0.00 38.00 1.94
2154 3423 4.252878 GGATTCACCCATTTCGCAAAAAT 58.747 39.130 0.00 0.00 0.00 1.82
2155 3424 5.047021 TGGATTCACCCATTTCGCAAAAATA 60.047 36.000 0.00 0.00 38.00 1.40
2156 3425 5.872070 GGATTCACCCATTTCGCAAAAATAA 59.128 36.000 0.00 0.00 0.00 1.40
2157 3426 6.370166 GGATTCACCCATTTCGCAAAAATAAA 59.630 34.615 0.00 0.00 0.00 1.40
2158 3427 7.095017 GGATTCACCCATTTCGCAAAAATAAAA 60.095 33.333 0.00 0.00 0.00 1.52
2159 3428 7.553881 TTCACCCATTTCGCAAAAATAAAAA 57.446 28.000 0.00 0.00 0.00 1.94
2160 3429 7.736447 TCACCCATTTCGCAAAAATAAAAAT 57.264 28.000 0.00 0.00 0.00 1.82
2161 3430 8.833231 TCACCCATTTCGCAAAAATAAAAATA 57.167 26.923 0.00 0.00 0.00 1.40
2162 3431 9.273016 TCACCCATTTCGCAAAAATAAAAATAA 57.727 25.926 0.00 0.00 0.00 1.40
2163 3432 9.884465 CACCCATTTCGCAAAAATAAAAATAAA 57.116 25.926 0.00 0.00 0.00 1.40
2198 3467 5.068198 CACCCAAGGATGAAACAGATATTGG 59.932 44.000 0.00 0.00 36.53 3.16
2273 3592 8.381387 GGAAACAATTTCAGTAGATCTACGAAC 58.619 37.037 25.89 17.65 41.43 3.95
2347 3666 3.050275 GGCTTCCAGTCCGTGTGC 61.050 66.667 0.00 0.00 0.00 4.57
2405 4407 0.179000 CCAGCCCCACTATCACACTC 59.821 60.000 0.00 0.00 0.00 3.51
2412 4414 1.846439 CCACTATCACACTCCCCCATT 59.154 52.381 0.00 0.00 0.00 3.16
2413 4415 2.242196 CCACTATCACACTCCCCCATTT 59.758 50.000 0.00 0.00 0.00 2.32
2444 4446 1.467713 GCGTCTCTAGTTTCTCACCGG 60.468 57.143 0.00 0.00 0.00 5.28
2445 4447 1.811359 CGTCTCTAGTTTCTCACCGGT 59.189 52.381 0.00 0.00 0.00 5.28
2450 4452 0.971386 TAGTTTCTCACCGGTGACCC 59.029 55.000 33.23 19.32 35.46 4.46
2458 4460 1.072648 TCACCGGTGACCCCTAAAAAG 59.927 52.381 33.23 2.97 34.14 2.27
2460 4462 1.776063 ACCGGTGACCCCTAAAAAGAA 59.224 47.619 6.12 0.00 0.00 2.52
2462 4464 2.039348 CCGGTGACCCCTAAAAAGAAGA 59.961 50.000 0.00 0.00 0.00 2.87
2464 4466 4.332828 CGGTGACCCCTAAAAAGAAGATT 58.667 43.478 0.00 0.00 0.00 2.40
2465 4467 4.765339 CGGTGACCCCTAAAAAGAAGATTT 59.235 41.667 0.00 0.00 0.00 2.17
2466 4468 5.106277 CGGTGACCCCTAAAAAGAAGATTTC 60.106 44.000 0.00 0.00 0.00 2.17
2467 4469 5.106277 GGTGACCCCTAAAAAGAAGATTTCG 60.106 44.000 0.00 0.00 34.02 3.46
2468 4470 4.457949 TGACCCCTAAAAAGAAGATTTCGC 59.542 41.667 0.00 0.00 34.02 4.70
2469 4471 4.663334 ACCCCTAAAAAGAAGATTTCGCT 58.337 39.130 0.00 0.00 34.02 4.93
2470 4472 4.700692 ACCCCTAAAAAGAAGATTTCGCTC 59.299 41.667 0.00 0.00 34.02 5.03
2471 4473 4.096532 CCCCTAAAAAGAAGATTTCGCTCC 59.903 45.833 0.00 0.00 34.02 4.70
2472 4474 4.201822 CCCTAAAAAGAAGATTTCGCTCCG 60.202 45.833 0.00 0.00 34.02 4.63
2473 4475 4.630069 CCTAAAAAGAAGATTTCGCTCCGA 59.370 41.667 0.00 0.00 34.02 4.55
2474 4476 5.121768 CCTAAAAAGAAGATTTCGCTCCGAA 59.878 40.000 0.00 0.00 44.28 4.30
2482 4484 3.372795 TTCGCTCCGAAAGTGTTGT 57.627 47.368 0.00 0.00 43.00 3.32
2483 4485 1.658994 TTCGCTCCGAAAGTGTTGTT 58.341 45.000 0.00 0.00 43.00 2.83
2484 4486 2.512485 TCGCTCCGAAAGTGTTGTTA 57.488 45.000 0.00 0.00 36.81 2.41
2485 4487 2.823984 TCGCTCCGAAAGTGTTGTTAA 58.176 42.857 0.00 0.00 36.81 2.01
2486 4488 2.798283 TCGCTCCGAAAGTGTTGTTAAG 59.202 45.455 0.00 0.00 36.81 1.85
2487 4489 2.661979 CGCTCCGAAAGTGTTGTTAAGC 60.662 50.000 0.00 0.00 0.00 3.09
2488 4490 2.350484 GCTCCGAAAGTGTTGTTAAGCC 60.350 50.000 0.00 0.00 0.00 4.35
2489 4491 2.223745 TCCGAAAGTGTTGTTAAGCCC 58.776 47.619 0.00 0.00 0.00 5.19
2490 4492 1.069500 CCGAAAGTGTTGTTAAGCCCG 60.069 52.381 0.00 0.00 0.00 6.13
2491 4493 1.868498 CGAAAGTGTTGTTAAGCCCGA 59.132 47.619 0.00 0.00 0.00 5.14
2492 4494 2.096417 CGAAAGTGTTGTTAAGCCCGAG 60.096 50.000 0.00 0.00 0.00 4.63
2493 4495 1.235724 AAGTGTTGTTAAGCCCGAGC 58.764 50.000 0.00 0.00 40.32 5.03
2513 4515 3.443099 CTATGTGAGCTCGGATGAACA 57.557 47.619 9.64 7.01 0.00 3.18
2514 4516 2.306341 ATGTGAGCTCGGATGAACAG 57.694 50.000 9.64 0.00 0.00 3.16
2515 4517 0.969149 TGTGAGCTCGGATGAACAGT 59.031 50.000 9.64 0.00 0.00 3.55
2516 4518 2.167662 TGTGAGCTCGGATGAACAGTA 58.832 47.619 9.64 0.00 0.00 2.74
2517 4519 2.560981 TGTGAGCTCGGATGAACAGTAA 59.439 45.455 9.64 0.00 0.00 2.24
2518 4520 3.006430 TGTGAGCTCGGATGAACAGTAAA 59.994 43.478 9.64 0.00 0.00 2.01
2519 4521 3.994392 GTGAGCTCGGATGAACAGTAAAA 59.006 43.478 9.64 0.00 0.00 1.52
2520 4522 4.631813 GTGAGCTCGGATGAACAGTAAAAT 59.368 41.667 9.64 0.00 0.00 1.82
2521 4523 5.810587 GTGAGCTCGGATGAACAGTAAAATA 59.189 40.000 9.64 0.00 0.00 1.40
2522 4524 6.312918 GTGAGCTCGGATGAACAGTAAAATAA 59.687 38.462 9.64 0.00 0.00 1.40
2523 4525 6.876789 TGAGCTCGGATGAACAGTAAAATAAA 59.123 34.615 9.64 0.00 0.00 1.40
2524 4526 7.389330 TGAGCTCGGATGAACAGTAAAATAAAA 59.611 33.333 9.64 0.00 0.00 1.52
2525 4527 8.106247 AGCTCGGATGAACAGTAAAATAAAAA 57.894 30.769 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 7.908601 GGCAGTAGTATGAAAAATAAAAGTCGG 59.091 37.037 0.00 0.00 0.00 4.79
64 65 7.716998 CCTCTACATGGCAGTAGTATGAAAAAT 59.283 37.037 17.67 0.00 41.68 1.82
136 710 8.522003 TGTGCAATTGTGTATATGTGAAGATTT 58.478 29.630 7.40 0.00 0.00 2.17
179 753 0.874390 CCGTCATCCACACACTTTGG 59.126 55.000 0.00 0.00 35.18 3.28
192 766 0.919289 AATCCCCCTTCCACCGTCAT 60.919 55.000 0.00 0.00 0.00 3.06
197 771 2.292192 TGATCAAAATCCCCCTTCCACC 60.292 50.000 0.00 0.00 0.00 4.61
233 807 3.118371 CCCAATCCAGTCTTACCACCTAC 60.118 52.174 0.00 0.00 0.00 3.18
346 920 0.675837 AGACGCACGGTAGCTGTCTA 60.676 55.000 18.06 0.00 42.27 2.59
350 924 0.989890 GTAAAGACGCACGGTAGCTG 59.010 55.000 0.00 0.00 0.00 4.24
376 950 4.053009 TCTTCCTGACTCATCTTCTCCA 57.947 45.455 0.00 0.00 0.00 3.86
385 959 2.234661 ACGATGCAATCTTCCTGACTCA 59.765 45.455 0.00 0.00 42.58 3.41
414 988 9.083080 CGTGAACAGTAATACATCTACAATGAA 57.917 33.333 0.00 0.00 0.00 2.57
504 1232 1.351350 ACAGCACCCTAACTTCCCTTC 59.649 52.381 0.00 0.00 0.00 3.46
537 1265 5.373812 TTGGATTGAGATTAGGAGGGAAC 57.626 43.478 0.00 0.00 0.00 3.62
559 1297 3.641046 TGCAACAGGGGCATATACATTT 58.359 40.909 0.00 0.00 36.11 2.32
563 1301 2.958355 ACATTGCAACAGGGGCATATAC 59.042 45.455 0.00 0.00 41.58 1.47
565 1303 2.163810 ACATTGCAACAGGGGCATAT 57.836 45.000 0.00 0.00 41.58 1.78
569 1307 1.185315 ATGTACATTGCAACAGGGGC 58.815 50.000 0.00 0.00 0.00 5.80
570 1308 6.707440 TTTATATGTACATTGCAACAGGGG 57.293 37.500 14.77 0.00 0.00 4.79
571 1309 8.023128 GCTATTTATATGTACATTGCAACAGGG 58.977 37.037 14.77 0.00 0.00 4.45
572 1310 8.023128 GGCTATTTATATGTACATTGCAACAGG 58.977 37.037 14.77 0.00 0.00 4.00
573 1311 8.567104 TGGCTATTTATATGTACATTGCAACAG 58.433 33.333 14.77 6.72 0.00 3.16
574 1312 8.457238 TGGCTATTTATATGTACATTGCAACA 57.543 30.769 14.77 0.00 0.00 3.33
577 1315 9.958180 AGTATGGCTATTTATATGTACATTGCA 57.042 29.630 14.77 0.00 0.00 4.08
612 1350 9.297037 GGTATTAAGTGGCTATCAATACCAATT 57.703 33.333 17.81 0.00 45.42 2.32
613 1351 8.863872 GGTATTAAGTGGCTATCAATACCAAT 57.136 34.615 17.81 0.00 45.42 3.16
616 1354 8.863872 ATTGGTATTAAGTGGCTATCAATACC 57.136 34.615 16.73 16.73 45.93 2.73
619 1357 9.014297 GCTAATTGGTATTAAGTGGCTATCAAT 57.986 33.333 0.00 0.00 30.91 2.57
620 1358 7.996066 TGCTAATTGGTATTAAGTGGCTATCAA 59.004 33.333 0.00 0.00 34.02 2.57
621 1359 7.513856 TGCTAATTGGTATTAAGTGGCTATCA 58.486 34.615 0.00 0.00 34.02 2.15
622 1360 7.979444 TGCTAATTGGTATTAAGTGGCTATC 57.021 36.000 0.00 0.00 34.02 2.08
623 1361 8.940397 ATTGCTAATTGGTATTAAGTGGCTAT 57.060 30.769 0.00 0.00 34.02 2.97
624 1362 8.760980 AATTGCTAATTGGTATTAAGTGGCTA 57.239 30.769 0.00 0.00 34.02 3.93
625 1363 7.660030 AATTGCTAATTGGTATTAAGTGGCT 57.340 32.000 0.00 0.00 34.02 4.75
672 1410 2.906691 AGATGGGCTTCGATTCTGAG 57.093 50.000 0.00 0.00 0.00 3.35
699 1491 8.330466 TGAATTCTTTTCCGTTTGCTATTAGA 57.670 30.769 7.05 0.00 0.00 2.10
700 1492 9.013490 CATGAATTCTTTTCCGTTTGCTATTAG 57.987 33.333 7.05 0.00 0.00 1.73
701 1493 8.519526 ACATGAATTCTTTTCCGTTTGCTATTA 58.480 29.630 7.05 0.00 0.00 0.98
707 1499 5.527951 TGGACATGAATTCTTTTCCGTTTG 58.472 37.500 17.21 0.00 0.00 2.93
708 1500 5.782893 TGGACATGAATTCTTTTCCGTTT 57.217 34.783 17.21 0.00 0.00 3.60
709 1501 5.982890 ATGGACATGAATTCTTTTCCGTT 57.017 34.783 17.21 8.27 0.00 4.44
710 1502 5.982890 AATGGACATGAATTCTTTTCCGT 57.017 34.783 17.21 15.19 0.00 4.69
711 1503 6.389091 TGAAATGGACATGAATTCTTTTCCG 58.611 36.000 17.21 0.13 0.00 4.30
712 1504 8.782339 ATTGAAATGGACATGAATTCTTTTCC 57.218 30.769 16.09 16.09 0.00 3.13
727 1519 7.016957 AGAGATCAGCCTATGTATTGAAATGGA 59.983 37.037 0.00 0.00 0.00 3.41
881 1829 3.880846 GAGGGCGCGGCTTTCATG 61.881 66.667 32.30 0.00 0.00 3.07
962 1923 2.125229 CGACGAGGACTCTCCCGA 60.125 66.667 0.00 0.00 37.19 5.14
964 1925 3.519930 GGCGACGAGGACTCTCCC 61.520 72.222 0.00 0.00 37.19 4.30
1499 2502 2.041115 GGCGGTCTTCTTCTTGGGC 61.041 63.158 0.00 0.00 0.00 5.36
1675 2763 5.974108 AGGATTGAAAGGATTGCATCTTTG 58.026 37.500 12.79 0.00 33.85 2.77
1697 2785 6.649973 CAGCCATAGATTCACAGGAGAATTAG 59.350 42.308 0.00 0.00 38.30 1.73
1749 2843 0.315886 TGCTGTGGATGCAAAAGCAG 59.684 50.000 18.29 9.41 38.88 4.24
1753 2847 2.104451 ACCAAATGCTGTGGATGCAAAA 59.896 40.909 7.74 0.00 44.01 2.44
1762 2856 2.734606 CAGATGCAAACCAAATGCTGTG 59.265 45.455 0.00 0.00 44.14 3.66
1764 2858 3.306917 TCAGATGCAAACCAAATGCTG 57.693 42.857 0.00 0.00 44.14 4.41
1795 2889 0.537653 TGGTCAAGAACACACGGACA 59.462 50.000 0.00 0.00 0.00 4.02
1860 2955 8.567948 TGAAAAGTGAAAGATAACATTCAGGAC 58.432 33.333 0.00 0.00 35.02 3.85
1880 2976 0.815734 CCCTGCAGCTGGATGAAAAG 59.184 55.000 19.69 0.00 0.00 2.27
1895 3043 5.191426 ACTGTTGATTCATTCAGATCCCTG 58.809 41.667 19.29 0.00 41.74 4.45
1938 3098 5.475220 TGCCCTCGTCATTTTTATCTTTCAA 59.525 36.000 0.00 0.00 0.00 2.69
1999 3160 1.730121 CGCAAGAATGTTTCGCTGCAT 60.730 47.619 0.00 0.00 40.90 3.96
2038 3199 0.034186 CAGCAACAGGGGCAAGGATA 60.034 55.000 0.00 0.00 0.00 2.59
2053 3214 1.176527 GTTTTGCATCTAGCCCAGCA 58.823 50.000 0.00 0.00 44.83 4.41
2080 3349 0.179161 ATCAGAGCCGTCGAAACTCG 60.179 55.000 0.00 0.00 42.10 4.18
2083 3352 3.617263 ACATAAATCAGAGCCGTCGAAAC 59.383 43.478 0.00 0.00 0.00 2.78
2085 3354 3.520290 ACATAAATCAGAGCCGTCGAA 57.480 42.857 0.00 0.00 0.00 3.71
2086 3355 3.520290 AACATAAATCAGAGCCGTCGA 57.480 42.857 0.00 0.00 0.00 4.20
2087 3356 3.182572 GCTAACATAAATCAGAGCCGTCG 59.817 47.826 0.00 0.00 0.00 5.12
2088 3357 3.495001 GGCTAACATAAATCAGAGCCGTC 59.505 47.826 0.00 0.00 40.07 4.79
2089 3358 3.467803 GGCTAACATAAATCAGAGCCGT 58.532 45.455 0.00 0.00 40.07 5.68
2119 3388 5.575157 TGGGTGAATCCAAAATTAGCAGTA 58.425 37.500 0.00 0.00 38.11 2.74
2124 3393 5.519927 GCGAAATGGGTGAATCCAAAATTAG 59.480 40.000 0.00 0.00 40.62 1.73
2130 3399 1.916506 TGCGAAATGGGTGAATCCAA 58.083 45.000 0.00 0.00 40.62 3.53
2131 3400 1.916506 TTGCGAAATGGGTGAATCCA 58.083 45.000 0.00 0.00 41.60 3.41
2132 3401 3.311486 TTTTGCGAAATGGGTGAATCC 57.689 42.857 0.00 0.00 0.00 3.01
2133 3402 6.959671 TTATTTTTGCGAAATGGGTGAATC 57.040 33.333 0.00 0.00 0.00 2.52
2134 3403 7.736447 TTTTATTTTTGCGAAATGGGTGAAT 57.264 28.000 0.00 0.00 0.00 2.57
2135 3404 7.553881 TTTTTATTTTTGCGAAATGGGTGAA 57.446 28.000 0.00 0.00 0.00 3.18
2136 3405 7.736447 ATTTTTATTTTTGCGAAATGGGTGA 57.264 28.000 0.00 0.00 0.00 4.02
2137 3406 9.884465 TTTATTTTTATTTTTGCGAAATGGGTG 57.116 25.926 0.00 0.00 0.00 4.61
2162 3431 5.547276 TCATCCTTGGGTGAATCCAATTTTT 59.453 36.000 0.00 0.00 44.79 1.94
2163 3432 5.092968 TCATCCTTGGGTGAATCCAATTTT 58.907 37.500 0.00 0.00 44.79 1.82
2164 3433 4.686891 TCATCCTTGGGTGAATCCAATTT 58.313 39.130 0.00 0.00 44.79 1.82
2165 3434 4.335735 TCATCCTTGGGTGAATCCAATT 57.664 40.909 0.00 0.00 44.79 2.32
2166 3435 4.335735 TTCATCCTTGGGTGAATCCAAT 57.664 40.909 10.99 0.00 44.79 3.16
2198 3467 2.759538 ATAGACGAACGCTGCTACTC 57.240 50.000 0.00 0.00 0.00 2.59
2341 3660 1.078497 TAGAGGCCCAATGCACACG 60.078 57.895 0.00 0.00 43.89 4.49
2347 3666 1.099879 GTGCAGCTAGAGGCCCAATG 61.100 60.000 0.00 0.00 43.05 2.82
2384 4386 1.082019 TGTGATAGTGGGGCTGGGA 59.918 57.895 0.00 0.00 0.00 4.37
2422 4424 1.199558 GGTGAGAAACTAGAGACGCGT 59.800 52.381 13.85 13.85 0.00 6.01
2423 4425 1.790838 CGGTGAGAAACTAGAGACGCG 60.791 57.143 3.53 3.53 0.00 6.01
2426 4428 2.818432 TCACCGGTGAGAAACTAGAGAC 59.182 50.000 33.23 0.00 34.14 3.36
2429 4431 1.891150 GGTCACCGGTGAGAAACTAGA 59.109 52.381 37.04 10.36 40.75 2.43
2444 4446 5.619309 GCGAAATCTTCTTTTTAGGGGTCAC 60.619 44.000 0.00 0.00 0.00 3.67
2445 4447 4.457949 GCGAAATCTTCTTTTTAGGGGTCA 59.542 41.667 0.00 0.00 0.00 4.02
2450 4452 4.630069 TCGGAGCGAAATCTTCTTTTTAGG 59.370 41.667 0.00 0.00 31.06 2.69
2464 4466 1.658994 AACAACACTTTCGGAGCGAA 58.341 45.000 0.00 0.00 44.28 4.70
2465 4467 2.512485 TAACAACACTTTCGGAGCGA 57.488 45.000 0.00 0.00 0.00 4.93
2466 4468 2.661979 GCTTAACAACACTTTCGGAGCG 60.662 50.000 0.00 0.00 0.00 5.03
2467 4469 2.350484 GGCTTAACAACACTTTCGGAGC 60.350 50.000 0.00 0.00 0.00 4.70
2468 4470 2.225727 GGGCTTAACAACACTTTCGGAG 59.774 50.000 0.00 0.00 0.00 4.63
2469 4471 2.223745 GGGCTTAACAACACTTTCGGA 58.776 47.619 0.00 0.00 0.00 4.55
2470 4472 1.069500 CGGGCTTAACAACACTTTCGG 60.069 52.381 0.00 0.00 0.00 4.30
2471 4473 1.868498 TCGGGCTTAACAACACTTTCG 59.132 47.619 0.00 0.00 0.00 3.46
2472 4474 2.350484 GCTCGGGCTTAACAACACTTTC 60.350 50.000 0.00 0.00 35.22 2.62
2473 4475 1.607148 GCTCGGGCTTAACAACACTTT 59.393 47.619 0.00 0.00 35.22 2.66
2474 4476 1.235724 GCTCGGGCTTAACAACACTT 58.764 50.000 0.00 0.00 35.22 3.16
2475 4477 2.928416 GCTCGGGCTTAACAACACT 58.072 52.632 0.00 0.00 35.22 3.55
2493 4495 3.181482 ACTGTTCATCCGAGCTCACATAG 60.181 47.826 15.40 1.37 0.00 2.23
2494 4496 2.760650 ACTGTTCATCCGAGCTCACATA 59.239 45.455 15.40 0.00 0.00 2.29
2495 4497 1.552337 ACTGTTCATCCGAGCTCACAT 59.448 47.619 15.40 1.13 0.00 3.21
2496 4498 0.969149 ACTGTTCATCCGAGCTCACA 59.031 50.000 15.40 8.29 0.00 3.58
2497 4499 2.941453 TACTGTTCATCCGAGCTCAC 57.059 50.000 15.40 3.47 0.00 3.51
2498 4500 3.953712 TTTACTGTTCATCCGAGCTCA 57.046 42.857 15.40 0.00 0.00 4.26
2499 4501 6.903883 TTATTTTACTGTTCATCCGAGCTC 57.096 37.500 2.73 2.73 0.00 4.09
2500 4502 7.681939 TTTTATTTTACTGTTCATCCGAGCT 57.318 32.000 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.