Multiple sequence alignment - TraesCS5B01G087000

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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 TraesCS5B01G087000 chr5B 100.000 5657 0 0 1 5657 111204315 111198659 0.000000e+00 10447.0
1 TraesCS5B01G087000 chr5B 93.478 138 7 1 3144 3281 111201100 111200965 2.670000e-48 204.0
2 TraesCS5B01G087000 chr5B 93.478 138 7 1 3216 3351 111201172 111201035 2.670000e-48 204.0
3 TraesCS5B01G087000 chr5A 93.063 5276 243 50 1 5230 98033183 98038381 0.000000e+00 7601.0
4 TraesCS5B01G087000 chr5A 83.452 423 36 16 5259 5657 98039072 98039484 4.170000e-96 363.0
5 TraesCS5B01G087000 chr5A 95.455 132 6 0 3216 3347 98036300 98036431 1.600000e-50 211.0
6 TraesCS5B01G087000 chr5A 95.238 63 3 0 3286 3348 98036300 98036362 3.610000e-17 100.0
7 TraesCS5B01G087000 chr5D 93.223 4309 196 37 1 4271 102035975 102031725 0.000000e+00 6252.0
8 TraesCS5B01G087000 chr5D 97.503 921 19 2 4321 5241 102031165 102030249 0.000000e+00 1570.0
9 TraesCS5B01G087000 chr5D 82.873 362 26 20 5302 5657 102027743 102027412 5.540000e-75 292.0
10 TraesCS5B01G087000 chr5D 89.894 188 18 1 5240 5427 102028044 102027858 2.040000e-59 241.0
11 TraesCS5B01G087000 chr4B 78.672 919 134 41 1775 2654 18424000 18424895 6.400000e-154 555.0
12 TraesCS5B01G087000 chr4B 92.917 240 13 3 3976 4211 237949692 237949931 4.200000e-91 346.0
13 TraesCS5B01G087000 chr4B 91.597 238 12 6 3980 4211 618251815 618251580 7.070000e-84 322.0
14 TraesCS5B01G087000 chr4B 78.274 336 56 11 1109 1437 18423391 18423716 3.460000e-47 200.0
15 TraesCS5B01G087000 chr4B 75.969 387 69 17 1107 1479 38614997 38615373 1.620000e-40 178.0
16 TraesCS5B01G087000 chr4B 90.244 41 4 0 3475 3515 18425374 18425414 3.000000e-03 54.7
17 TraesCS5B01G087000 chr4B 96.875 32 1 0 1067 1098 38614999 38615030 3.000000e-03 54.7
18 TraesCS5B01G087000 chr4D 76.610 1056 171 51 1659 2667 9563004 9564030 3.910000e-141 512.0
19 TraesCS5B01G087000 chr4D 77.454 377 64 14 1107 1473 9562466 9562831 7.430000e-49 206.0
20 TraesCS5B01G087000 chr4D 81.977 172 25 3 3650 3821 9564770 9564935 2.120000e-29 141.0
21 TraesCS5B01G087000 chr4D 81.481 81 11 3 3475 3553 9564590 9564668 4.730000e-06 63.9
22 TraesCS5B01G087000 chr4D 96.875 32 1 0 1067 1098 9562468 9562499 3.000000e-03 54.7
23 TraesCS5B01G087000 chr7A 91.286 241 15 5 3975 4211 689543836 689543598 1.970000e-84 324.0
24 TraesCS5B01G087000 chr2B 90.361 249 17 6 3972 4216 755034740 755034495 2.540000e-83 320.0
25 TraesCS5B01G087000 chr1D 90.871 241 17 4 3975 4211 452489599 452489838 9.150000e-83 318.0
26 TraesCS5B01G087000 chr1B 90.000 240 20 3 3976 4211 334657309 334657548 1.980000e-79 307.0
27 TraesCS5B01G087000 chr6D 88.048 251 23 6 3966 4212 470928158 470928405 1.990000e-74 291.0
28 TraesCS5B01G087000 chr4A 77.403 385 64 15 1107 1478 593765169 593764795 2.070000e-49 207.0
29 TraesCS5B01G087000 chr4A 82.036 167 24 3 3650 3816 593762898 593762738 2.750000e-28 137.0
30 TraesCS5B01G087000 chr4A 80.247 81 9 3 1070 1149 593765164 593765090 3.000000e-03 54.7


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 TraesCS5B01G087000 chr5B 111198659 111204315 5656 True 3618.333333 10447 95.652000 1 5657 3 chr5B.!!$R1 5656
1 TraesCS5B01G087000 chr5A 98033183 98039484 6301 False 2068.750000 7601 91.802000 1 5657 4 chr5A.!!$F1 5656
2 TraesCS5B01G087000 chr5D 102027412 102035975 8563 True 2088.750000 6252 90.873250 1 5657 4 chr5D.!!$R1 5656
3 TraesCS5B01G087000 chr4B 18423391 18425414 2023 False 269.900000 555 82.396667 1109 3515 3 chr4B.!!$F2 2406

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
419 431 0.114954 TCTTTGGCATGCCTCCCTTT 59.885 50.0 35.53 0.0 36.94 3.11 F
1246 1263 0.887933 CGCCAGGTGCATAGGTTTTT 59.112 50.0 0.00 0.0 41.33 1.94 F
1529 1560 0.112218 AACCCATGCCTGCACTGTTA 59.888 50.0 0.00 0.0 0.00 2.41 F
2465 2534 0.038166 ACCACATGAATCGCCAGGTT 59.962 50.0 0.00 0.0 0.00 3.50 F
3726 3854 0.820871 GAAGGGAGTCTCATCGCACT 59.179 55.0 1.47 0.0 34.74 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1509 1540 0.112218 AACAGTGCAGGCATGGGTTA 59.888 50.000 0.00 0.00 0.00 2.85 R
2370 2439 0.179108 GGCTCCCTGTACATGTCGAC 60.179 60.000 9.11 9.11 0.00 4.20 R
2855 2964 1.000060 GTGCATTTTTGCTGCCAGAGA 60.000 47.619 0.00 0.00 38.89 3.10 R
4168 4305 0.850883 AGGCCCCCTCTCATTTTGGA 60.851 55.000 0.00 0.00 0.00 3.53 R
5577 9285 0.179020 CAAAGCTGGGGTCAGTGTGA 60.179 55.000 0.00 0.00 42.78 3.58 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
45 46 0.539051 CCTCTCTGCCCTCATTTCGT 59.461 55.000 0.00 0.00 0.00 3.85
137 147 2.198980 CCTCCCTCCCTCCCTACG 59.801 72.222 0.00 0.00 0.00 3.51
306 316 2.817396 GCTTCTCTCCAGCCACGC 60.817 66.667 0.00 0.00 0.00 5.34
394 404 0.598065 GGTGCTTCTGGCGTCAAAAT 59.402 50.000 0.00 0.00 45.43 1.82
396 406 2.545742 GGTGCTTCTGGCGTCAAAATTT 60.546 45.455 0.00 0.00 45.43 1.82
412 424 3.323751 AATTTCTGTCTTTGGCATGCC 57.676 42.857 30.54 30.54 0.00 4.40
413 425 1.999648 TTTCTGTCTTTGGCATGCCT 58.000 45.000 35.53 0.00 36.94 4.75
419 431 0.114954 TCTTTGGCATGCCTCCCTTT 59.885 50.000 35.53 0.00 36.94 3.11
456 468 2.852449 TGCTTTATGTCAACCCGTGAA 58.148 42.857 0.00 0.00 38.23 3.18
461 473 1.438651 ATGTCAACCCGTGAATCGTG 58.561 50.000 0.00 0.00 38.23 4.35
467 479 1.542492 ACCCGTGAATCGTGTAGTCT 58.458 50.000 0.00 0.00 37.94 3.24
480 497 4.156556 TCGTGTAGTCTAATGGCGTAGTTT 59.843 41.667 0.00 0.00 0.00 2.66
487 504 7.772332 AGTCTAATGGCGTAGTTTTATCTTG 57.228 36.000 0.00 0.00 0.00 3.02
502 519 8.993121 AGTTTTATCTTGAGATATATTGTGCCG 58.007 33.333 1.79 0.00 36.94 5.69
503 520 8.988934 GTTTTATCTTGAGATATATTGTGCCGA 58.011 33.333 1.79 0.00 36.94 5.54
504 521 8.763049 TTTATCTTGAGATATATTGTGCCGAG 57.237 34.615 1.79 0.00 36.94 4.63
541 558 3.731565 GCGTATGCTGACAAATTGCATCA 60.732 43.478 3.68 0.00 44.91 3.07
566 583 7.759489 TCCTATGTTTGTTGAGTAGCATTTT 57.241 32.000 0.00 0.00 0.00 1.82
568 585 7.446931 TCCTATGTTTGTTGAGTAGCATTTTGA 59.553 33.333 0.00 0.00 0.00 2.69
584 601 7.496704 GCATTTTGATGCCGTATATATTGTG 57.503 36.000 0.00 0.00 41.47 3.33
585 602 7.304735 GCATTTTGATGCCGTATATATTGTGA 58.695 34.615 0.00 0.00 41.47 3.58
586 603 7.807433 GCATTTTGATGCCGTATATATTGTGAA 59.193 33.333 0.00 0.00 41.47 3.18
587 604 9.676195 CATTTTGATGCCGTATATATTGTGAAA 57.324 29.630 0.00 0.00 0.00 2.69
619 636 5.335191 GGGATGTTTGTAGCTTTCAGACTTG 60.335 44.000 0.00 0.00 0.00 3.16
620 637 4.552166 TGTTTGTAGCTTTCAGACTTGC 57.448 40.909 0.00 0.00 0.00 4.01
631 648 3.325293 TCAGACTTGCCTGATGAACTC 57.675 47.619 0.00 0.00 38.18 3.01
632 649 2.902486 TCAGACTTGCCTGATGAACTCT 59.098 45.455 0.00 0.00 38.18 3.24
640 657 2.613133 GCCTGATGAACTCTGCAGAATC 59.387 50.000 18.85 17.23 0.00 2.52
642 659 4.515361 CCTGATGAACTCTGCAGAATCTT 58.485 43.478 18.85 15.90 0.00 2.40
647 664 5.679734 TGAACTCTGCAGAATCTTTCAAC 57.320 39.130 18.85 2.95 0.00 3.18
649 666 2.481952 ACTCTGCAGAATCTTTCAACGC 59.518 45.455 18.85 0.00 0.00 4.84
680 697 7.384660 TCAGTGTTGGATTATGCAAATTTTGAC 59.615 33.333 13.26 5.18 26.96 3.18
687 704 6.873076 GGATTATGCAAATTTTGACTGTGGAA 59.127 34.615 13.26 0.00 0.00 3.53
704 721 9.169468 GACTGTGGAATTATTTTATTACATGCG 57.831 33.333 0.00 0.00 31.31 4.73
735 752 2.501723 AGTACATGGTTGTGCTAGAGGG 59.498 50.000 0.00 0.00 45.56 4.30
750 767 2.050077 GGGCTGCTTTCGTTGTGC 60.050 61.111 0.00 0.00 0.00 4.57
758 775 1.860326 GCTTTCGTTGTGCTTGCATTT 59.140 42.857 0.00 0.00 0.00 2.32
764 781 2.676076 GTTGTGCTTGCATTTACCCAG 58.324 47.619 0.00 0.00 0.00 4.45
790 807 9.132521 GTGATATGTTCATTGGACTTTTTCTTG 57.867 33.333 0.00 0.00 36.54 3.02
813 830 2.136863 TGGGTGGTAAGGTTGAGGAAA 58.863 47.619 0.00 0.00 0.00 3.13
872 889 5.806654 AATTTCTGGTGCCAGTAAACATT 57.193 34.783 16.85 4.15 43.96 2.71
929 946 6.072342 TCCGCTAGTTTTTCTTATTTGGTTCC 60.072 38.462 0.00 0.00 0.00 3.62
968 985 7.281100 GTCCTGGACATTTCCTTTACTTATCTG 59.719 40.741 21.70 0.00 43.31 2.90
1209 1226 2.106684 GGGTTCTGGAAGTCTCTTGGTT 59.893 50.000 0.00 0.00 33.76 3.67
1242 1259 1.622607 TAAGCGCCAGGTGCATAGGT 61.623 55.000 27.03 2.45 42.00 3.08
1246 1263 0.887933 CGCCAGGTGCATAGGTTTTT 59.112 50.000 0.00 0.00 41.33 1.94
1259 1276 5.221501 GCATAGGTTTTTACATGGATGCCAT 60.222 40.000 0.00 0.00 46.37 4.40
1267 1284 2.811410 ACATGGATGCCATTTGTCTGT 58.189 42.857 0.00 0.00 42.23 3.41
1388 1407 4.682787 CTTTTGAAAGGTTTGGTCCTGTC 58.317 43.478 0.00 0.00 41.07 3.51
1406 1425 2.027561 TGTCAGGGATGTTTACCTTCCG 60.028 50.000 0.00 0.00 38.09 4.30
1491 1518 5.371115 TGGCTGTTTTGCTATTAACTGTC 57.629 39.130 0.00 0.00 0.00 3.51
1496 1523 6.236017 TGTTTTGCTATTAACTGTCGGAAG 57.764 37.500 0.00 0.00 0.00 3.46
1500 1527 4.242475 TGCTATTAACTGTCGGAAGTGTG 58.758 43.478 0.00 0.00 0.00 3.82
1509 1540 1.404035 GTCGGAAGTGTGCCAAGTTTT 59.596 47.619 0.00 0.00 0.00 2.43
1521 1552 2.612721 GCCAAGTTTTAACCCATGCCTG 60.613 50.000 0.00 0.00 0.00 4.85
1524 1555 1.618343 AGTTTTAACCCATGCCTGCAC 59.382 47.619 0.00 0.00 0.00 4.57
1529 1560 0.112218 AACCCATGCCTGCACTGTTA 59.888 50.000 0.00 0.00 0.00 2.41
1554 1585 8.411318 ACAGCATAAACTTTGAAACTTTTCTG 57.589 30.769 3.48 0.00 38.02 3.02
1555 1586 8.250332 ACAGCATAAACTTTGAAACTTTTCTGA 58.750 29.630 3.48 0.00 38.02 3.27
1557 1588 9.305925 AGCATAAACTTTGAAACTTTTCTGAAG 57.694 29.630 12.73 12.73 38.02 3.02
1558 1589 9.087424 GCATAAACTTTGAAACTTTTCTGAAGT 57.913 29.630 13.58 13.58 41.44 3.01
1647 1678 1.507141 GGTGTTGACCTCTGCAACCG 61.507 60.000 0.00 0.00 43.71 4.44
1654 1685 1.600636 CCTCTGCAACCGCCTTTGA 60.601 57.895 0.00 0.00 37.32 2.69
1732 1769 6.269077 TCACTGGTTTATTCCTGTCACTAGAA 59.731 38.462 0.00 0.00 37.51 2.10
1742 1779 5.907207 TCCTGTCACTAGAATACTTGATGC 58.093 41.667 0.00 0.00 0.00 3.91
1743 1780 5.422012 TCCTGTCACTAGAATACTTGATGCA 59.578 40.000 0.00 0.00 0.00 3.96
1744 1781 6.070824 TCCTGTCACTAGAATACTTGATGCAA 60.071 38.462 0.00 0.00 0.00 4.08
1745 1782 6.765036 CCTGTCACTAGAATACTTGATGCAAT 59.235 38.462 0.00 0.00 0.00 3.56
1796 1842 6.287525 TCTTCATCGTTGCCATGTATGATTA 58.712 36.000 0.00 0.00 0.00 1.75
2038 2084 4.200092 AGAAGATAAAATGGGGCGAAGTC 58.800 43.478 0.00 0.00 0.00 3.01
2123 2172 3.799232 GCTCTTTATGAGAACCGCCGTAT 60.799 47.826 0.00 0.00 45.39 3.06
2134 2196 2.879826 ACCGCCGTATGTAGTTGTTAC 58.120 47.619 0.00 0.00 0.00 2.50
2145 2207 6.628919 ATGTAGTTGTTACACAAGAAACCC 57.371 37.500 0.00 0.00 44.68 4.11
2247 2310 1.571460 CTTCGCCAAGAGTGCACAC 59.429 57.895 21.04 13.64 0.00 3.82
2370 2439 5.957842 TTGCCCTACTTTGTGTAATGAAG 57.042 39.130 0.00 0.00 0.00 3.02
2465 2534 0.038166 ACCACATGAATCGCCAGGTT 59.962 50.000 0.00 0.00 0.00 3.50
2540 2609 2.297597 AGAGGATATGCGCACTAGAACC 59.702 50.000 14.90 10.94 0.00 3.62
2593 2662 5.202046 GAAGATTTGCTTCGTCTTCTCTG 57.798 43.478 7.01 0.00 43.22 3.35
2670 2741 4.997395 CCGTTCCTCTCATTATGGTAATGG 59.003 45.833 9.18 2.37 0.00 3.16
2684 2787 4.088634 TGGTAATGGCTCTCAAATTTGCT 58.911 39.130 13.54 0.00 0.00 3.91
2729 2832 7.177216 TCTGGAATCTTGTACATGCTTTTGAAT 59.823 33.333 0.00 0.00 0.00 2.57
2745 2848 5.756195 TTTGAATGGACAAGTGTTGAGAG 57.244 39.130 0.00 0.00 0.00 3.20
2836 2945 9.830975 ACCAAATACCTATTTTTATCCAAATGC 57.169 29.630 0.00 0.00 33.88 3.56
2855 2964 3.778954 GCCTCACTATGGCTAATTCCT 57.221 47.619 0.00 0.00 46.38 3.36
2860 2969 5.279406 CCTCACTATGGCTAATTCCTCTCTG 60.279 48.000 0.00 0.00 0.00 3.35
2871 2980 2.592102 TCCTCTCTGGCAGCAAAAAT 57.408 45.000 10.34 0.00 35.26 1.82
2872 2981 2.165167 TCCTCTCTGGCAGCAAAAATG 58.835 47.619 10.34 0.00 35.26 2.32
2873 2982 1.403780 CCTCTCTGGCAGCAAAAATGC 60.404 52.381 10.34 0.00 43.09 3.56
2874 2983 1.271379 CTCTCTGGCAGCAAAAATGCA 59.729 47.619 10.34 0.00 45.68 3.96
2875 2984 1.000060 TCTCTGGCAGCAAAAATGCAC 60.000 47.619 10.34 0.00 45.68 4.57
2956 3084 6.567687 TTGTGTGTAACCAATGAACATAGG 57.432 37.500 0.00 0.00 34.36 2.57
3018 3146 3.939066 ACTAGCACAGTTGTGGAATACC 58.061 45.455 13.63 0.00 45.72 2.73
3021 3149 5.514834 ACTAGCACAGTTGTGGAATACCAAT 60.515 40.000 13.63 0.00 45.72 3.16
3126 3254 3.392947 TGAACACCCATCCACTAGTGAAA 59.607 43.478 24.68 12.09 34.33 2.69
3136 3264 7.037438 CCATCCACTAGTGAAATTTTGGATTG 58.963 38.462 24.68 7.78 41.04 2.67
3166 3294 3.930336 TCCTGTGCTGTTAATGTCTGAG 58.070 45.455 0.00 0.00 0.00 3.35
3167 3295 3.578282 TCCTGTGCTGTTAATGTCTGAGA 59.422 43.478 0.00 0.00 0.00 3.27
3277 3405 6.539173 AGACCCATCACATACAACTTGTTTA 58.461 36.000 0.00 0.00 0.00 2.01
3394 3522 7.220108 GTGAAACCTGTAATTGTTGTGAACTTC 59.780 37.037 0.00 0.00 0.00 3.01
3447 3575 4.870123 TTTTGCTTGGCACAGTATCAAT 57.130 36.364 0.00 0.00 42.39 2.57
3594 3722 1.067635 GCTTGGCATCCAACATTCGTT 60.068 47.619 0.00 0.00 38.75 3.85
3605 3733 7.201350 GCATCCAACATTCGTTAAGTTTTGATC 60.201 37.037 0.00 0.00 32.75 2.92
3726 3854 0.820871 GAAGGGAGTCTCATCGCACT 59.179 55.000 1.47 0.00 34.74 4.40
3759 3887 3.567585 TGCGTCATCCAAAAGAACATGAA 59.432 39.130 0.00 0.00 0.00 2.57
3947 4080 6.428771 GCTGTTTATACCTGTAACCTTGTTCA 59.571 38.462 0.00 0.00 0.00 3.18
3981 4114 6.289064 AGTATTAGCTTGCCATTGTACTACC 58.711 40.000 0.00 0.00 0.00 3.18
3984 4117 2.092914 AGCTTGCCATTGTACTACCTCC 60.093 50.000 0.00 0.00 0.00 4.30
3989 4122 2.104967 CCATTGTACTACCTCCGTCCA 58.895 52.381 0.00 0.00 0.00 4.02
4001 4134 3.036091 CCTCCGTCCAGGTTTATTAGGA 58.964 50.000 0.00 0.00 41.99 2.94
4035 4169 3.896888 TGAGCCAAACTTTGACCATTCAT 59.103 39.130 2.87 0.00 0.00 2.57
4036 4170 4.240096 GAGCCAAACTTTGACCATTCATG 58.760 43.478 2.87 0.00 0.00 3.07
4200 4337 0.179009 GGGGCCTAATAAACCCGGAC 60.179 60.000 0.73 0.00 45.27 4.79
4260 4397 6.736110 AATAACAATTATCAGCCTGGCATT 57.264 33.333 22.65 8.43 0.00 3.56
4300 4437 5.756347 TCTCTTTCTAGCGCTGTTGTTTTTA 59.244 36.000 22.90 0.00 0.00 1.52
4304 4441 5.487153 TCTAGCGCTGTTGTTTTTACAAA 57.513 34.783 22.90 0.00 0.00 2.83
4388 5036 6.363357 GTGAAGAAAATCAAGAAACGAATGGG 59.637 38.462 0.00 0.00 0.00 4.00
4401 5049 2.038557 ACGAATGGGTGCAGTTCTTAGT 59.961 45.455 0.00 0.00 0.00 2.24
4428 5079 4.341487 TCCTTCTCGTTAATCCAGACTCA 58.659 43.478 0.00 0.00 0.00 3.41
4430 5081 5.067936 TCCTTCTCGTTAATCCAGACTCATC 59.932 44.000 0.00 0.00 0.00 2.92
4431 5082 4.553756 TCTCGTTAATCCAGACTCATCG 57.446 45.455 0.00 0.00 0.00 3.84
4503 5154 8.759481 TGCATATACTTGTCATAAAATTCCCA 57.241 30.769 0.00 0.00 0.00 4.37
4681 5332 0.981183 TGGTTACATCCTCTGCGGTT 59.019 50.000 0.00 0.00 0.00 4.44
4887 5543 5.757808 CCATGTACTTTGTTTGGGAAAAAGG 59.242 40.000 0.00 0.00 35.64 3.11
5024 5680 4.631773 CACCAGGTGCCATCAGAG 57.368 61.111 6.67 0.00 0.00 3.35
5113 5771 1.374758 CCTATGGATCGCTTCGGGC 60.375 63.158 0.00 0.00 37.64 6.13
5145 5803 3.457234 CTTTTGTGGTTCCCAGCTTTTC 58.543 45.455 0.00 0.00 32.34 2.29
5150 5808 2.430694 GTGGTTCCCAGCTTTTCTTTGT 59.569 45.455 0.00 0.00 32.34 2.83
5152 5810 2.035961 GGTTCCCAGCTTTTCTTTGTCC 59.964 50.000 0.00 0.00 0.00 4.02
5193 5851 1.906105 TTTCGGCTAGGCGGGTGATT 61.906 55.000 34.63 0.00 0.00 2.57
5247 8112 4.105217 TCCATCCATTATGAATGACCTGCT 59.895 41.667 0.00 0.00 41.46 4.24
5368 9058 0.468226 AGCTCAGGTTCGGTTTGACA 59.532 50.000 0.00 0.00 0.00 3.58
5406 9096 5.361857 AGATTTGATTGGTTGGGATAAGCAG 59.638 40.000 0.00 0.00 0.00 4.24
5418 9108 5.188434 TGGGATAAGCAGATTCTTGTGAAG 58.812 41.667 0.00 0.00 35.44 3.02
5438 9128 6.808704 GTGAAGATTTAGGTGATTTTTCTGGC 59.191 38.462 0.00 0.00 0.00 4.85
5448 9138 0.106419 TTTTTCTGGCGGACCCAAGT 60.106 50.000 0.00 0.00 44.81 3.16
5449 9139 0.766131 TTTTCTGGCGGACCCAAGTA 59.234 50.000 0.00 0.00 44.81 2.24
5450 9140 0.035739 TTTCTGGCGGACCCAAGTAC 59.964 55.000 0.00 0.00 44.81 2.73
5451 9141 1.122632 TTCTGGCGGACCCAAGTACA 61.123 55.000 0.00 0.00 44.81 2.90
5452 9142 0.907704 TCTGGCGGACCCAAGTACAT 60.908 55.000 0.00 0.00 44.81 2.29
5453 9143 0.828022 CTGGCGGACCCAAGTACATA 59.172 55.000 0.00 0.00 44.81 2.29
5531 9236 4.948341 TTCCTGTGTGCTAGTTAGTTCA 57.052 40.909 0.00 0.00 0.00 3.18
5534 9239 5.479306 TCCTGTGTGCTAGTTAGTTCATTC 58.521 41.667 0.00 0.00 0.00 2.67
5577 9285 3.988379 TTTCGTCTTACAGTACACGGT 57.012 42.857 10.19 0.00 33.02 4.83
5580 9288 2.224079 TCGTCTTACAGTACACGGTCAC 59.776 50.000 10.19 0.00 33.02 3.67
5615 9323 1.080995 GCTTTTTGCCGCACAACACA 61.081 50.000 0.00 0.00 38.23 3.72
5617 9325 1.728971 CTTTTTGCCGCACAACACAAA 59.271 42.857 0.00 0.00 38.23 2.83
5618 9326 1.354040 TTTTGCCGCACAACACAAAG 58.646 45.000 0.00 0.00 38.23 2.77
5619 9327 0.244994 TTTGCCGCACAACACAAAGT 59.755 45.000 0.00 0.00 38.23 2.66
5620 9328 1.095600 TTGCCGCACAACACAAAGTA 58.904 45.000 0.00 0.00 31.73 2.24
5622 9330 1.001924 TGCCGCACAACACAAAGTATG 60.002 47.619 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.040499 CGAAGGGGAATGGGGGAAAA 59.960 55.000 0.00 0.00 0.00 2.29
306 316 1.654220 CTCAAGGTTTGCACGGTGG 59.346 57.895 10.60 0.00 0.00 4.61
315 325 2.224646 GGTCAGAGGAAGCTCAAGGTTT 60.225 50.000 0.00 0.00 35.69 3.27
318 328 1.066286 CAGGTCAGAGGAAGCTCAAGG 60.066 57.143 0.00 0.00 0.00 3.61
382 392 3.904136 AGACAGAAATTTTGACGCCAG 57.096 42.857 0.00 0.00 0.00 4.85
394 404 1.888512 GAGGCATGCCAAAGACAGAAA 59.111 47.619 37.18 0.00 38.92 2.52
396 406 0.322816 GGAGGCATGCCAAAGACAGA 60.323 55.000 37.18 0.00 38.92 3.41
412 424 5.063204 TGTGTGTCTACAATCAAAAGGGAG 58.937 41.667 0.00 0.00 38.82 4.30
413 425 5.042463 TGTGTGTCTACAATCAAAAGGGA 57.958 39.130 0.00 0.00 38.82 4.20
419 431 7.174772 ACATAAAGCATGTGTGTCTACAATCAA 59.825 33.333 0.00 0.00 46.41 2.57
456 468 3.881688 ACTACGCCATTAGACTACACGAT 59.118 43.478 0.00 0.00 0.00 3.73
461 473 8.753175 CAAGATAAAACTACGCCATTAGACTAC 58.247 37.037 0.00 0.00 0.00 2.73
480 497 7.178451 TCCTCGGCACAATATATCTCAAGATAA 59.822 37.037 3.94 0.00 40.09 1.75
487 504 5.392767 TTCTCCTCGGCACAATATATCTC 57.607 43.478 0.00 0.00 0.00 2.75
493 510 1.837439 ACCATTCTCCTCGGCACAATA 59.163 47.619 0.00 0.00 0.00 1.90
500 517 2.693069 GCATATCACCATTCTCCTCGG 58.307 52.381 0.00 0.00 0.00 4.63
502 519 3.393089 ACGCATATCACCATTCTCCTC 57.607 47.619 0.00 0.00 0.00 3.71
503 520 4.825422 CATACGCATATCACCATTCTCCT 58.175 43.478 0.00 0.00 0.00 3.69
504 521 3.372206 GCATACGCATATCACCATTCTCC 59.628 47.826 0.00 0.00 38.36 3.71
541 558 7.944729 AAATGCTACTCAACAAACATAGGAT 57.055 32.000 0.00 0.00 0.00 3.24
566 583 9.676195 CAAAATTTCACAATATATACGGCATCA 57.324 29.630 0.00 0.00 0.00 3.07
568 585 8.637986 ACCAAAATTTCACAATATATACGGCAT 58.362 29.630 0.00 0.00 0.00 4.40
571 588 7.865385 CCCACCAAAATTTCACAATATATACGG 59.135 37.037 0.00 0.00 0.00 4.02
579 596 5.565455 ACATCCCACCAAAATTTCACAAT 57.435 34.783 0.00 0.00 0.00 2.71
581 598 5.121811 CAAACATCCCACCAAAATTTCACA 58.878 37.500 0.00 0.00 0.00 3.58
582 599 5.122519 ACAAACATCCCACCAAAATTTCAC 58.877 37.500 0.00 0.00 0.00 3.18
583 600 5.365021 ACAAACATCCCACCAAAATTTCA 57.635 34.783 0.00 0.00 0.00 2.69
584 601 5.408299 GCTACAAACATCCCACCAAAATTTC 59.592 40.000 0.00 0.00 0.00 2.17
585 602 5.071653 AGCTACAAACATCCCACCAAAATTT 59.928 36.000 0.00 0.00 0.00 1.82
586 603 4.592778 AGCTACAAACATCCCACCAAAATT 59.407 37.500 0.00 0.00 0.00 1.82
587 604 4.159557 AGCTACAAACATCCCACCAAAAT 58.840 39.130 0.00 0.00 0.00 1.82
588 605 3.571590 AGCTACAAACATCCCACCAAAA 58.428 40.909 0.00 0.00 0.00 2.44
589 606 3.237268 AGCTACAAACATCCCACCAAA 57.763 42.857 0.00 0.00 0.00 3.28
619 636 2.105006 TTCTGCAGAGTTCATCAGGC 57.895 50.000 17.43 0.00 0.00 4.85
620 637 4.139859 AGATTCTGCAGAGTTCATCAGG 57.860 45.455 22.17 0.00 0.00 3.86
631 648 1.464687 CCGCGTTGAAAGATTCTGCAG 60.465 52.381 7.63 7.63 0.00 4.41
632 649 0.516877 CCGCGTTGAAAGATTCTGCA 59.483 50.000 4.92 0.00 0.00 4.41
640 657 1.531149 ACACTGAATCCGCGTTGAAAG 59.469 47.619 4.92 0.00 0.00 2.62
642 659 1.262950 CAACACTGAATCCGCGTTGAA 59.737 47.619 4.92 0.00 39.39 2.69
647 664 1.086696 AATCCAACACTGAATCCGCG 58.913 50.000 0.00 0.00 0.00 6.46
649 666 3.627123 TGCATAATCCAACACTGAATCCG 59.373 43.478 0.00 0.00 0.00 4.18
680 697 9.515020 AACGCATGTAATAAAATAATTCCACAG 57.485 29.630 0.00 0.00 0.00 3.66
687 704 8.967218 GCATGACAACGCATGTAATAAAATAAT 58.033 29.630 0.00 0.00 45.70 1.28
711 728 2.301583 TCTAGCACAACCATGTACTGCA 59.698 45.455 4.14 0.00 37.82 4.41
712 729 2.932614 CTCTAGCACAACCATGTACTGC 59.067 50.000 0.00 0.00 37.82 4.40
715 732 2.906354 CCCTCTAGCACAACCATGTAC 58.094 52.381 0.00 0.00 37.82 2.90
735 752 1.543106 GCAAGCACAACGAAAGCAGC 61.543 55.000 0.00 0.00 0.00 5.25
750 767 6.095300 TGAACATATCACTGGGTAAATGCAAG 59.905 38.462 0.00 0.00 31.50 4.01
764 781 9.132521 CAAGAAAAAGTCCAATGAACATATCAC 57.867 33.333 0.00 0.00 41.93 3.06
790 807 1.544759 CCTCAACCTTACCACCCACAC 60.545 57.143 0.00 0.00 0.00 3.82
813 830 7.961326 ACCTGTAAAATCTGCTATTTTGGAT 57.039 32.000 16.04 0.00 33.73 3.41
885 902 4.994852 GCGGATTTATCAGCAAGTATGGTA 59.005 41.667 9.50 0.00 45.40 3.25
1062 1079 0.337082 TCCTTGGGGGACTACGATGA 59.663 55.000 0.00 0.00 39.58 2.92
1209 1226 1.013596 CGCTTAATGGGATGTTGCGA 58.986 50.000 0.00 0.00 43.81 5.10
1242 1259 6.164876 CAGACAAATGGCATCCATGTAAAAA 58.835 36.000 0.00 0.00 44.40 1.94
1246 1263 3.966979 ACAGACAAATGGCATCCATGTA 58.033 40.909 0.00 0.00 44.40 2.29
1275 1292 9.883142 AAAATGAAGAAATGTTTGTTAGGTGAA 57.117 25.926 0.00 0.00 0.00 3.18
1309 1328 8.690884 TGAGAGAACCATGTTAAACAAATCAAA 58.309 29.630 0.00 0.00 0.00 2.69
1314 1333 7.556275 AGAGTTGAGAGAACCATGTTAAACAAA 59.444 33.333 0.00 0.00 0.00 2.83
1324 1343 1.980765 TGCCAGAGTTGAGAGAACCAT 59.019 47.619 0.00 0.00 0.00 3.55
1388 1407 3.270877 CTTCGGAAGGTAAACATCCCTG 58.729 50.000 9.93 0.00 0.00 4.45
1406 1425 8.843885 AAACTTACCCGCTATAATAATCCTTC 57.156 34.615 0.00 0.00 0.00 3.46
1418 1437 9.942850 ATTTTACTTACTAAAACTTACCCGCTA 57.057 29.630 0.00 0.00 37.19 4.26
1440 1459 5.879777 AGTTTGGCAACTGCTTACAAATTTT 59.120 32.000 0.00 0.00 42.05 1.82
1474 1501 6.077838 CACTTCCGACAGTTAATAGCAAAAC 58.922 40.000 0.00 0.00 0.00 2.43
1491 1518 3.368495 GTTAAAACTTGGCACACTTCCG 58.632 45.455 0.00 0.00 39.29 4.30
1496 1523 3.389221 CATGGGTTAAAACTTGGCACAC 58.611 45.455 0.00 0.00 39.29 3.82
1500 1527 1.623311 AGGCATGGGTTAAAACTTGGC 59.377 47.619 0.00 10.22 33.00 4.52
1509 1540 0.112218 AACAGTGCAGGCATGGGTTA 59.888 50.000 0.00 0.00 0.00 2.85
1521 1552 5.757886 TCAAAGTTTATGCTGTAACAGTGC 58.242 37.500 0.00 0.00 33.43 4.40
1524 1555 8.856490 AAGTTTCAAAGTTTATGCTGTAACAG 57.144 30.769 0.00 0.00 34.12 3.16
1529 1560 8.250332 TCAGAAAAGTTTCAAAGTTTATGCTGT 58.750 29.630 18.14 0.92 39.61 4.40
1564 1595 9.304731 GAAACAAATGTTATGCATATGTGTCAT 57.695 29.630 17.23 10.68 37.25 3.06
1566 1597 8.686397 TGAAACAAATGTTATGCATATGTGTC 57.314 30.769 16.01 16.01 37.25 3.67
1567 1598 9.656040 AATGAAACAAATGTTATGCATATGTGT 57.344 25.926 7.36 3.48 37.25 3.72
1602 1633 2.712057 AAGCTGGAAAATGTTCGCAG 57.288 45.000 8.85 8.85 36.18 5.18
1762 1799 4.092091 GGCAACGATGAAGAGAAAGTACAG 59.908 45.833 0.00 0.00 0.00 2.74
1796 1842 5.786975 ACCCTGGGAATCATTTCAGAAAAAT 59.213 36.000 22.23 0.00 33.23 1.82
2038 2084 9.907576 GAAAAGTCATGATAGTACTTGAAATCG 57.092 33.333 0.00 0.00 33.85 3.34
2134 2196 4.683832 CTCTAGTATCCGGGTTTCTTGTG 58.316 47.826 0.00 0.00 0.00 3.33
2145 2207 1.982660 TGTCCAGGCTCTAGTATCCG 58.017 55.000 0.00 0.00 0.00 4.18
2370 2439 0.179108 GGCTCCCTGTACATGTCGAC 60.179 60.000 9.11 9.11 0.00 4.20
2540 2609 9.799106 AAAAATGGGAATATATACCTGACTCTG 57.201 33.333 7.62 0.00 0.00 3.35
2593 2662 2.880890 ACAGTCATTTCAACTGAGCACC 59.119 45.455 10.04 0.00 45.64 5.01
2729 2832 2.092968 AGCAACTCTCAACACTTGTCCA 60.093 45.455 0.00 0.00 0.00 4.02
2745 2848 1.021968 AAACCAGAACGACCAGCAAC 58.978 50.000 0.00 0.00 0.00 4.17
2836 2945 4.837860 AGAGAGGAATTAGCCATAGTGAGG 59.162 45.833 0.00 0.00 0.00 3.86
2855 2964 1.000060 GTGCATTTTTGCTGCCAGAGA 60.000 47.619 0.00 0.00 38.89 3.10
2860 2969 2.730550 ACTAGTGCATTTTTGCTGCC 57.269 45.000 0.00 0.00 38.89 4.85
2871 2980 3.813166 GCTACAACAGGAAAACTAGTGCA 59.187 43.478 0.00 0.00 0.00 4.57
2872 2981 4.065789 AGCTACAACAGGAAAACTAGTGC 58.934 43.478 0.00 0.00 0.00 4.40
2873 2982 5.297547 TCAGCTACAACAGGAAAACTAGTG 58.702 41.667 0.00 0.00 0.00 2.74
2874 2983 5.546621 TCAGCTACAACAGGAAAACTAGT 57.453 39.130 0.00 0.00 0.00 2.57
2875 2984 8.607459 CAATATCAGCTACAACAGGAAAACTAG 58.393 37.037 0.00 0.00 0.00 2.57
2956 3084 6.716628 TGTGCAAATAGATAAGGAATCCCATC 59.283 38.462 0.00 0.00 34.90 3.51
3006 3134 6.265577 GCACTCAATATTGGTATTCCACAAC 58.734 40.000 15.36 0.00 44.22 3.32
3007 3135 5.359576 GGCACTCAATATTGGTATTCCACAA 59.640 40.000 15.36 0.00 44.22 3.33
3008 3136 4.887071 GGCACTCAATATTGGTATTCCACA 59.113 41.667 15.36 0.00 44.22 4.17
3009 3137 5.133221 AGGCACTCAATATTGGTATTCCAC 58.867 41.667 15.36 0.06 44.22 4.02
3010 3138 5.387113 AGGCACTCAATATTGGTATTCCA 57.613 39.130 15.36 0.00 42.66 3.53
3011 3139 6.016777 CAGAAGGCACTCAATATTGGTATTCC 60.017 42.308 15.36 10.16 38.49 3.01
3012 3140 6.767902 TCAGAAGGCACTCAATATTGGTATTC 59.232 38.462 15.36 14.22 38.49 1.75
3013 3141 6.662755 TCAGAAGGCACTCAATATTGGTATT 58.337 36.000 15.36 7.88 38.49 1.89
3014 3142 6.252599 TCAGAAGGCACTCAATATTGGTAT 57.747 37.500 15.36 0.00 38.49 2.73
3015 3143 5.692115 TCAGAAGGCACTCAATATTGGTA 57.308 39.130 15.36 0.00 38.49 3.25
3016 3144 4.574674 TCAGAAGGCACTCAATATTGGT 57.425 40.909 15.36 9.29 38.49 3.67
3017 3145 5.188434 TCTTCAGAAGGCACTCAATATTGG 58.812 41.667 15.36 8.69 38.49 3.16
3018 3146 6.036953 GTCTCTTCAGAAGGCACTCAATATTG 59.963 42.308 9.29 9.29 38.49 1.90
3021 3149 4.528206 TGTCTCTTCAGAAGGCACTCAATA 59.472 41.667 10.42 0.00 38.49 1.90
3126 3254 1.474077 GAGCAGCGGTCAATCCAAAAT 59.526 47.619 3.45 0.00 35.57 1.82
3136 3264 4.385405 AGCACAGGAGCAGCGGTC 62.385 66.667 0.00 0.08 36.85 4.79
3166 3294 6.145338 TGGGTCTTATACGATCTTCACTTC 57.855 41.667 0.00 0.00 0.00 3.01
3167 3295 6.323996 TGATGGGTCTTATACGATCTTCACTT 59.676 38.462 0.00 0.00 0.00 3.16
3197 3325 7.011482 CACAGGAGCCTATATGTAAACAACTTC 59.989 40.741 0.00 0.00 0.00 3.01
3277 3405 3.336509 ACAGGACAGGAGCCTATATGT 57.663 47.619 0.00 0.00 33.51 2.29
3623 3751 3.063316 GCCCAAACACAACATTGAACAAC 59.937 43.478 0.00 0.00 0.00 3.32
3726 3854 2.499693 TGGATGACGCACAGGAGATTTA 59.500 45.455 0.00 0.00 0.00 1.40
3759 3887 4.954089 AGTAGGATCTCCTTTTGTCCTCT 58.046 43.478 3.64 0.00 46.09 3.69
3859 3991 4.049546 GCAAATGCAATGAAGGCAGATA 57.950 40.909 7.02 0.00 45.68 1.98
3860 3992 2.901249 GCAAATGCAATGAAGGCAGAT 58.099 42.857 7.02 0.00 45.68 2.90
3893 4025 1.602851 GATGCTGGTGCTTGCTCTATG 59.397 52.381 0.00 0.00 40.48 2.23
3947 4080 4.757149 GGCAAGCTAATACTTTCGATGGAT 59.243 41.667 0.00 0.00 0.00 3.41
3981 4114 4.056092 GTCCTAATAAACCTGGACGGAG 57.944 50.000 0.00 0.00 39.39 4.63
3989 4122 6.920695 AAATACTGGGGTCCTAATAAACCT 57.079 37.500 0.00 0.00 35.78 3.50
4001 4134 2.897326 GTTTGGCTCAAAATACTGGGGT 59.103 45.455 2.47 0.00 35.03 4.95
4076 4210 7.725251 AGCTCTTTCAAATACAAATCCAACAA 58.275 30.769 0.00 0.00 0.00 2.83
4157 4294 6.490040 CCCTCTCATTTTGGACTAAAGTTTGA 59.510 38.462 0.00 0.00 0.00 2.69
4168 4305 0.850883 AGGCCCCCTCTCATTTTGGA 60.851 55.000 0.00 0.00 0.00 3.53
4200 4337 7.723324 TCCTCAAATAAGATTTACTACCTCCG 58.277 38.462 0.00 0.00 0.00 4.63
4260 4397 7.865706 AGAAAGAGACAGCTTAAAACTTTCA 57.134 32.000 21.20 0.00 41.93 2.69
4304 4441 6.019156 CGAGCATGTTAACAAAACAAATTGGT 60.019 34.615 13.23 9.06 34.56 3.67
4388 5036 3.077359 AGGAATGCACTAAGAACTGCAC 58.923 45.455 0.00 0.00 45.91 4.57
4401 5049 4.081142 TCTGGATTAACGAGAAGGAATGCA 60.081 41.667 0.00 0.00 30.75 3.96
4428 5079 1.819928 TTGTGGTATGCAGCAACGAT 58.180 45.000 0.00 0.00 33.05 3.73
4430 5081 3.969117 ATATTGTGGTATGCAGCAACG 57.031 42.857 0.00 0.00 33.05 4.10
4431 5082 6.317789 ACATATATTGTGGTATGCAGCAAC 57.682 37.500 0.00 0.00 37.11 4.17
4681 5332 1.117749 AGCTAGATGGAGATGCGGCA 61.118 55.000 4.58 4.58 0.00 5.69
4887 5543 3.876914 TCAGTGTTGGATCAACTCACAAC 59.123 43.478 11.36 0.00 43.85 3.32
4920 5576 4.047125 CCACCCACTGGCCCGATT 62.047 66.667 0.00 0.00 31.36 3.34
5023 5679 5.013183 AGCATCACCACCTAAAGAGTAAACT 59.987 40.000 0.00 0.00 0.00 2.66
5024 5680 5.246307 AGCATCACCACCTAAAGAGTAAAC 58.754 41.667 0.00 0.00 0.00 2.01
5113 5771 1.659335 CACAAAAGGCAGCTGCACG 60.659 57.895 37.63 22.45 44.36 5.34
5150 5808 6.001460 AGATATGTTTTGTTCGTCAAAGGGA 58.999 36.000 8.06 0.00 45.14 4.20
5152 5810 7.059488 CGAAAGATATGTTTTGTTCGTCAAAGG 59.941 37.037 0.00 0.00 45.14 3.11
5193 5851 3.443329 CGGATTGATGGTCACAATTTCCA 59.557 43.478 0.00 0.00 37.96 3.53
5247 8112 5.717078 ACGTAGATGTAGAGTTTTCCACA 57.283 39.130 0.00 0.00 0.00 4.17
5368 9058 6.875195 CCAATCAAATCTTGTGGTTTAGCAAT 59.125 34.615 0.00 0.00 0.00 3.56
5418 9108 4.398044 TCCGCCAGAAAAATCACCTAAATC 59.602 41.667 0.00 0.00 0.00 2.17
5438 9128 9.582431 CTTATATTGTATATGTACTTGGGTCCG 57.418 37.037 1.08 0.00 0.00 4.79
5531 9236 4.060205 GGCATGTCAAAGCAAAACAGAAT 58.940 39.130 0.00 0.00 0.00 2.40
5534 9239 3.102052 AGGCATGTCAAAGCAAAACAG 57.898 42.857 0.00 0.00 0.00 3.16
5563 9271 3.004002 TCAGTGTGACCGTGTACTGTAAG 59.996 47.826 0.00 0.00 40.91 2.34
5577 9285 0.179020 CAAAGCTGGGGTCAGTGTGA 60.179 55.000 0.00 0.00 42.78 3.58
5580 9288 0.825010 AAGCAAAGCTGGGGTCAGTG 60.825 55.000 0.00 0.00 42.78 3.66


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

AutoCloner maintained by Alex Coulton.