Multiple sequence alignment - TraesCS2D01G561300

Loading Multiple Alignment...

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 TraesCS2D01G561300 chr2D 100.000 3632 0 0 1 3632 633697887 633694256 0.000000e+00 6708.0
1 TraesCS2D01G561300 chr2D 82.319 690 82 13 234 919 608428469 608429122 2.450000e-156 562.0
2 TraesCS2D01G561300 chr2D 73.684 361 72 14 341 683 369374168 369374523 6.370000e-23 119.0
3 TraesCS2D01G561300 chr2D 85.185 108 14 2 3160 3265 280064037 280063930 3.830000e-20 110.0
4 TraesCS2D01G561300 chr2D 88.710 62 7 0 342 403 369374249 369374310 3.890000e-10 76.8
5 TraesCS2D01G561300 chr2A 93.191 2012 93 25 915 2899 779912906 779914900 0.000000e+00 2916.0
6 TraesCS2D01G561300 chr2A 93.978 714 10 5 2919 3632 779929376 779930056 0.000000e+00 1050.0
7 TraesCS2D01G561300 chr2A 88.657 432 33 9 915 1338 779911876 779912299 2.500000e-141 512.0
8 TraesCS2D01G561300 chr6D 93.275 922 35 8 1 919 291475713 291476610 0.000000e+00 1334.0
9 TraesCS2D01G561300 chr6D 73.504 351 55 18 336 683 207082673 207082358 8.300000e-17 99.0
10 TraesCS2D01G561300 chr6D 90.164 61 6 0 342 402 362725163 362725103 3.010000e-11 80.5
11 TraesCS2D01G561300 chr5D 84.344 709 71 20 234 922 159293535 159292847 0.000000e+00 658.0
12 TraesCS2D01G561300 chr3D 82.283 587 76 16 341 920 63768060 63768625 1.960000e-132 483.0
13 TraesCS2D01G561300 chr3D 81.971 416 49 10 303 692 63767904 63768319 2.700000e-86 329.0
14 TraesCS2D01G561300 chr3D 77.266 629 90 26 300 914 378023218 378022629 1.630000e-83 320.0
15 TraesCS2D01G561300 chr4B 83.190 464 44 11 1253 1683 158331024 158330562 9.450000e-106 394.0
16 TraesCS2D01G561300 chr4B 86.310 168 21 2 3367 3533 128564657 128564491 8.010000e-42 182.0
17 TraesCS2D01G561300 chr5A 77.323 635 88 32 300 919 317506955 317506362 1.260000e-84 324.0
18 TraesCS2D01G561300 chr5A 81.201 383 55 3 300 681 312506923 312507289 3.550000e-75 292.0
19 TraesCS2D01G561300 chr7D 78.922 408 59 8 241 630 173716764 173716366 6.020000e-63 252.0
20 TraesCS2D01G561300 chr7D 79.412 204 32 9 338 540 173716430 173716236 6.330000e-28 135.0
21 TraesCS2D01G561300 chr4D 86.905 168 20 2 3367 3533 92223479 92223313 1.720000e-43 187.0
22 TraesCS2D01G561300 chr4D 91.935 62 4 1 338 398 32248613 32248552 6.460000e-13 86.1
23 TraesCS2D01G561300 chr7B 78.571 280 58 2 414 692 714611232 714611510 2.230000e-42 183.0
24 TraesCS2D01G561300 chrUn 82.353 102 16 2 3160 3260 104674129 104674229 1.800000e-13 87.9
25 TraesCS2D01G561300 chrUn 82.353 102 16 2 3160 3260 104795103 104795203 1.800000e-13 87.9
26 TraesCS2D01G561300 chr2B 80.000 90 15 3 2009 2097 709783998 709783911 3.030000e-06 63.9


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 TraesCS2D01G561300 chr2D 633694256 633697887 3631 True 6708 6708 100.000 1 3632 1 chr2D.!!$R2 3631
1 TraesCS2D01G561300 chr2D 608428469 608429122 653 False 562 562 82.319 234 919 1 chr2D.!!$F1 685
2 TraesCS2D01G561300 chr2A 779911876 779914900 3024 False 1714 2916 90.924 915 2899 2 chr2A.!!$F2 1984
3 TraesCS2D01G561300 chr2A 779929376 779930056 680 False 1050 1050 93.978 2919 3632 1 chr2A.!!$F1 713
4 TraesCS2D01G561300 chr6D 291475713 291476610 897 False 1334 1334 93.275 1 919 1 chr6D.!!$F1 918
5 TraesCS2D01G561300 chr5D 159292847 159293535 688 True 658 658 84.344 234 922 1 chr5D.!!$R1 688
6 TraesCS2D01G561300 chr3D 63767904 63768625 721 False 406 483 82.127 303 920 2 chr3D.!!$F1 617
7 TraesCS2D01G561300 chr3D 378022629 378023218 589 True 320 320 77.266 300 914 1 chr3D.!!$R1 614
8 TraesCS2D01G561300 chr5A 317506362 317506955 593 True 324 324 77.323 300 919 1 chr5A.!!$R1 619

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
26 27 0.031043 GCTGCAATGAAGCACACACA 59.969 50.0 8.65 0.0 40.11 3.72 F
1001 1168 0.030603 GGGAAGGAGATGGAGAGGGT 60.031 60.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 2844 0.100503 GCACCAAAGTCAAGTGCGTT 59.899 50.0 0.0 0.0 46.43 4.84 R
2904 4122 0.179092 GGGTGTACCTACATGGCGTC 60.179 60.0 0.0 0.0 38.63 5.19 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
26 27 0.031043 GCTGCAATGAAGCACACACA 59.969 50.000 8.65 0.00 40.11 3.72
175 176 3.612247 GAGCAGCACACGGGATGGT 62.612 63.158 0.00 0.00 0.00 3.55
176 177 3.434319 GCAGCACACGGGATGGTG 61.434 66.667 12.96 12.96 46.09 4.17
185 186 1.451387 CGGGATGGTGTAGTTGGCC 60.451 63.158 0.00 0.00 0.00 5.36
186 187 1.910580 CGGGATGGTGTAGTTGGCCT 61.911 60.000 3.32 0.00 0.00 5.19
187 188 0.331616 GGGATGGTGTAGTTGGCCTT 59.668 55.000 3.32 0.00 0.00 4.35
189 190 0.811281 GATGGTGTAGTTGGCCTTGC 59.189 55.000 3.32 0.00 0.00 4.01
609 746 0.678395 CTCTGGCGGCATCTATGACT 59.322 55.000 13.85 0.00 32.20 3.41
906 1073 1.067582 GCTATCAGCCGGCTTACGT 59.932 57.895 30.60 15.43 42.24 3.57
914 1081 0.529992 GCCGGCTTACGTCTAGCATT 60.530 55.000 22.15 0.00 42.24 3.56
922 1089 0.739813 ACGTCTAGCATTGGCCGAAC 60.740 55.000 0.00 0.00 42.56 3.95
923 1090 1.429148 CGTCTAGCATTGGCCGAACC 61.429 60.000 0.00 0.00 42.56 3.62
924 1091 0.107654 GTCTAGCATTGGCCGAACCT 60.108 55.000 0.00 0.00 42.56 3.50
925 1092 0.618458 TCTAGCATTGGCCGAACCTT 59.382 50.000 0.00 0.00 42.56 3.50
929 1096 0.171231 GCATTGGCCGAACCTTCTTC 59.829 55.000 0.00 0.00 40.22 2.87
933 1100 1.292541 GGCCGAACCTTCTTCGACT 59.707 57.895 4.08 0.00 43.97 4.18
939 1106 4.201695 GCCGAACCTTCTTCGACTTAAATC 60.202 45.833 4.08 0.00 43.97 2.17
959 1126 1.001760 TCTACCAGCCCAGAGGTCC 59.998 63.158 0.00 0.00 39.31 4.46
962 1129 2.822643 TACCAGCCCAGAGGTCCAGG 62.823 65.000 0.00 0.00 39.31 4.45
975 1142 2.738521 CCAGGAACCGTGTCGCAG 60.739 66.667 0.00 0.00 0.00 5.18
985 1152 2.682136 TGTCGCAGGAATCCGGGA 60.682 61.111 0.00 0.00 0.00 5.14
987 1154 1.521681 GTCGCAGGAATCCGGGAAG 60.522 63.158 0.00 0.00 0.00 3.46
998 1165 0.105964 TCCGGGAAGGAGATGGAGAG 60.106 60.000 0.00 0.00 45.98 3.20
1001 1168 0.030603 GGGAAGGAGATGGAGAGGGT 60.031 60.000 0.00 0.00 0.00 4.34
1002 1169 1.626631 GGGAAGGAGATGGAGAGGGTT 60.627 57.143 0.00 0.00 0.00 4.11
1003 1170 2.200955 GGAAGGAGATGGAGAGGGTTT 58.799 52.381 0.00 0.00 0.00 3.27
1004 1171 3.385115 GGAAGGAGATGGAGAGGGTTTA 58.615 50.000 0.00 0.00 0.00 2.01
1005 1172 3.780850 GGAAGGAGATGGAGAGGGTTTAA 59.219 47.826 0.00 0.00 0.00 1.52
1056 1223 0.752009 TAGACGCTCTTCCTCGCCAT 60.752 55.000 0.00 0.00 0.00 4.40
1072 1239 0.870307 CCATCGTTCGATCACGTCCC 60.870 60.000 9.29 0.00 41.16 4.46
1077 1244 3.060020 TTCGATCACGTCCCGGAGC 62.060 63.158 0.73 0.00 40.69 4.70
1099 1267 2.158959 CGACAATCGCTGGACGGAC 61.159 63.158 0.00 0.00 43.89 4.79
1116 1284 4.742201 CGGCTACGCACCAGCACT 62.742 66.667 3.88 0.00 40.95 4.40
1120 1288 1.516386 CTACGCACCAGCACTACCG 60.516 63.158 0.00 0.00 42.27 4.02
1171 2368 2.691674 GAAGATGGGCTCGAGCGGAG 62.692 65.000 29.81 0.00 46.06 4.63
1307 2507 2.359975 CCCGGACAAGGCCAAGAC 60.360 66.667 5.01 0.00 0.00 3.01
1320 2520 2.091112 CAAGACGCTGCTCCTCGTG 61.091 63.158 0.00 0.00 39.22 4.35
1359 2559 3.161450 TCCGGGGACATAGCCAGC 61.161 66.667 0.00 0.00 0.00 4.85
1361 2561 2.589540 CGGGGACATAGCCAGCAA 59.410 61.111 0.00 0.00 0.00 3.91
1371 2571 0.533531 TAGCCAGCAAGCATGGATCG 60.534 55.000 12.62 0.00 40.51 3.69
1386 2586 0.170116 GATCGCCAAATCCACGCAAA 59.830 50.000 0.00 0.00 0.00 3.68
1420 2620 3.326880 GGAGGACCAAGTTTCTTCCTACA 59.673 47.826 0.00 0.00 38.78 2.74
1498 2698 5.412904 GGTGGCTTCCATGATATAAGTAAGC 59.587 44.000 0.00 0.00 35.28 3.09
1516 2716 8.915057 AAGTAAGCAAGAGTTCATATGCATAT 57.085 30.769 13.63 13.63 41.18 1.78
1518 2718 9.429359 AGTAAGCAAGAGTTCATATGCATATAC 57.571 33.333 18.70 14.11 41.18 1.47
1519 2719 9.429359 GTAAGCAAGAGTTCATATGCATATACT 57.571 33.333 18.70 18.35 41.18 2.12
1522 2722 9.429359 AGCAAGAGTTCATATGCATATACTAAC 57.571 33.333 18.70 19.87 41.18 2.34
1527 2739 7.624549 AGTTCATATGCATATACTAACCCCTG 58.375 38.462 18.70 4.74 0.00 4.45
1538 2750 6.910259 ATACTAACCCCTGATTTCCTTCTT 57.090 37.500 0.00 0.00 0.00 2.52
1549 2761 5.116180 TGATTTCCTTCTTGTATACAGGCG 58.884 41.667 10.02 4.07 0.00 5.52
1560 2772 3.259876 TGTATACAGGCGAAGGTTTCACT 59.740 43.478 0.08 0.00 0.00 3.41
1565 2777 1.172812 GGCGAAGGTTTCACTTGGCT 61.173 55.000 11.59 0.00 46.97 4.75
1568 2780 1.001378 CGAAGGTTTCACTTGGCTTGG 60.001 52.381 0.00 0.00 0.00 3.61
1573 2785 3.636764 AGGTTTCACTTGGCTTGGTTTAG 59.363 43.478 0.00 0.00 0.00 1.85
1587 2799 5.163923 GCTTGGTTTAGCAATTCATTCAAGC 60.164 40.000 0.00 0.00 44.53 4.01
1599 2811 9.230932 GCAATTCATTCAAGCTAGATTTCTAAC 57.769 33.333 0.00 0.00 0.00 2.34
1601 2813 7.539712 TTCATTCAAGCTAGATTTCTAACCG 57.460 36.000 0.00 0.00 0.00 4.44
1607 2819 6.932400 TCAAGCTAGATTTCTAACCGTTTCAA 59.068 34.615 0.00 0.00 0.00 2.69
1656 2874 0.752743 TTGACTTTGGTGCTGCAGCT 60.753 50.000 36.61 17.15 42.66 4.24
1677 2895 3.601443 ACACTGAGTCCTATGCACTTC 57.399 47.619 0.00 0.00 0.00 3.01
1680 2898 2.094494 ACTGAGTCCTATGCACTTCACG 60.094 50.000 0.00 0.00 0.00 4.35
1717 2935 3.515330 ACATCCCCGACTACTTTTACG 57.485 47.619 0.00 0.00 0.00 3.18
1888 3106 6.435292 ACCAAGTACTCACTGAAAAGGTAT 57.565 37.500 0.00 0.00 34.36 2.73
1889 3107 7.549147 ACCAAGTACTCACTGAAAAGGTATA 57.451 36.000 0.00 0.00 34.36 1.47
1890 3108 8.147244 ACCAAGTACTCACTGAAAAGGTATAT 57.853 34.615 0.00 0.00 34.36 0.86
1891 3109 9.263446 ACCAAGTACTCACTGAAAAGGTATATA 57.737 33.333 0.00 0.00 34.36 0.86
1898 3116 7.866393 ACTCACTGAAAAGGTATATATACGTGC 59.134 37.037 16.65 10.87 34.11 5.34
1899 3117 7.718525 TCACTGAAAAGGTATATATACGTGCA 58.281 34.615 16.65 13.87 34.11 4.57
1901 3119 7.116376 CACTGAAAAGGTATATATACGTGCAGG 59.884 40.741 26.34 18.91 34.11 4.85
1902 3120 6.460781 TGAAAAGGTATATATACGTGCAGGG 58.539 40.000 16.65 0.00 34.11 4.45
1914 3132 3.531538 ACGTGCAGGGTATAACATCAAG 58.468 45.455 11.67 0.00 0.00 3.02
1917 3135 4.034048 CGTGCAGGGTATAACATCAAGTTC 59.966 45.833 0.00 0.00 41.64 3.01
1920 3138 5.189736 TGCAGGGTATAACATCAAGTTCTCT 59.810 40.000 0.00 0.00 41.64 3.10
1927 3145 9.827411 GGTATAACATCAAGTTCTCTTTGTTTC 57.173 33.333 0.00 0.00 41.64 2.78
1934 3152 8.811378 CATCAAGTTCTCTTTGTTTCTTTTTCC 58.189 33.333 0.00 0.00 0.00 3.13
1948 3166 0.404040 TTTTCCTCCTCCCGCATGTT 59.596 50.000 0.00 0.00 0.00 2.71
2003 3221 8.875803 TGAAGTATTGGTAATGATAACAACGAC 58.124 33.333 0.00 0.00 41.35 4.34
2004 3222 8.780846 AAGTATTGGTAATGATAACAACGACA 57.219 30.769 0.00 0.00 41.35 4.35
2029 3247 2.165167 TGCTTGCAGGATCCTTTTCTG 58.835 47.619 13.00 1.99 0.00 3.02
2048 3266 4.035102 GCTTGACCGGCCCTTCCT 62.035 66.667 0.00 0.00 0.00 3.36
2117 3335 5.866207 AGATAAAATATGGAACCGAGTCCC 58.134 41.667 2.32 0.00 36.80 4.46
2162 3380 1.682854 CCAACCATCACCATATGCACC 59.317 52.381 0.00 0.00 0.00 5.01
2204 3422 2.626840 GTTCCTCTTGTGATGGAGAGC 58.373 52.381 0.00 0.00 38.43 4.09
2325 3543 2.250031 CTCCCTATCATCTGCAGAGCT 58.750 52.381 22.96 11.23 0.00 4.09
2409 3627 8.861086 TCCTGTAGAATCAGATGGTTATCTTAC 58.139 37.037 0.00 0.00 41.71 2.34
2474 3692 4.685169 AAAGTTGTCATCCAAGCATACG 57.315 40.909 0.00 0.00 32.51 3.06
2562 3780 1.338200 GGGTGTGTGTTTTGTTGGCAA 60.338 47.619 0.00 0.00 0.00 4.52
2572 3790 4.142271 TGTTTTGTTGGCAACTCTAAGGTG 60.142 41.667 28.71 0.00 35.59 4.00
2605 3823 2.288457 TGCTTGGTCTCTTCTTGTCGAG 60.288 50.000 0.00 0.00 0.00 4.04
2701 3919 4.914312 TTCAAGCTATTGTTAACCGACG 57.086 40.909 2.48 0.00 37.68 5.12
2747 3965 7.462109 TGTGTTGTTAAGCATTTTGTTGATC 57.538 32.000 0.00 0.00 0.00 2.92
2854 4072 2.038033 TGACACACCTACTTACCTTGGC 59.962 50.000 0.00 0.00 0.00 4.52
2867 4085 0.389166 CCTTGGCGACTCACTCTGTC 60.389 60.000 0.00 0.00 0.00 3.51
2899 4117 0.249398 GGCGCTAGGGAAAGTTCTGA 59.751 55.000 11.61 0.00 0.00 3.27
2900 4118 1.338769 GGCGCTAGGGAAAGTTCTGAA 60.339 52.381 11.61 0.00 0.00 3.02
2901 4119 2.633488 GCGCTAGGGAAAGTTCTGAAT 58.367 47.619 11.61 0.00 0.00 2.57
2902 4120 2.352960 GCGCTAGGGAAAGTTCTGAATG 59.647 50.000 11.61 0.00 0.00 2.67
2903 4121 3.861840 CGCTAGGGAAAGTTCTGAATGA 58.138 45.455 0.00 0.00 0.00 2.57
2904 4122 3.868077 CGCTAGGGAAAGTTCTGAATGAG 59.132 47.826 0.00 0.00 0.00 2.90
2905 4123 4.382040 CGCTAGGGAAAGTTCTGAATGAGA 60.382 45.833 0.00 0.00 0.00 3.27
2906 4124 4.873259 GCTAGGGAAAGTTCTGAATGAGAC 59.127 45.833 0.00 0.00 0.00 3.36
2907 4125 3.931578 AGGGAAAGTTCTGAATGAGACG 58.068 45.455 0.00 0.00 0.00 4.18
2908 4126 2.416893 GGGAAAGTTCTGAATGAGACGC 59.583 50.000 0.00 0.00 0.00 5.19
2909 4127 2.416893 GGAAAGTTCTGAATGAGACGCC 59.583 50.000 0.00 0.00 0.00 5.68
2910 4128 2.839486 AAGTTCTGAATGAGACGCCA 57.161 45.000 0.00 0.00 0.00 5.69
2911 4129 3.340814 AAGTTCTGAATGAGACGCCAT 57.659 42.857 0.00 0.00 0.00 4.40
2912 4130 2.625737 AGTTCTGAATGAGACGCCATG 58.374 47.619 0.00 0.00 0.00 3.66
2913 4131 2.027745 AGTTCTGAATGAGACGCCATGT 60.028 45.455 0.00 0.00 0.00 3.21
2914 4132 3.195610 AGTTCTGAATGAGACGCCATGTA 59.804 43.478 0.00 0.00 0.00 2.29
2915 4133 3.443099 TCTGAATGAGACGCCATGTAG 57.557 47.619 0.00 0.00 0.00 2.74
2916 4134 2.101415 TCTGAATGAGACGCCATGTAGG 59.899 50.000 0.00 0.00 41.84 3.18
2917 4135 1.831106 TGAATGAGACGCCATGTAGGT 59.169 47.619 0.00 0.00 40.61 3.08
3009 4227 3.721035 ACCGGTTAGACTTTGTGTGTAC 58.279 45.455 0.00 0.00 0.00 2.90
3170 4388 5.047021 GTCTCATAGTTCATAGCAGGCCATA 60.047 44.000 5.01 0.00 0.00 2.74
3205 4423 6.935240 TCAAATTTCTCCTAGACTTCTCCA 57.065 37.500 0.00 0.00 0.00 3.86
3357 4575 1.303643 CCCTTGGTTGGCTCACTCC 60.304 63.158 0.00 0.00 0.00 3.85
3423 4641 3.496130 CAGCGTAAATAATCTGCCAGGAG 59.504 47.826 0.00 0.00 0.00 3.69
3504 4722 6.721318 ACAATGGTCCAGTCACACTAATTAT 58.279 36.000 0.00 0.00 0.00 1.28
3505 4723 7.175104 ACAATGGTCCAGTCACACTAATTATT 58.825 34.615 0.00 0.00 0.00 1.40
3506 4724 8.325787 ACAATGGTCCAGTCACACTAATTATTA 58.674 33.333 0.00 0.00 0.00 0.98
3507 4725 8.830580 CAATGGTCCAGTCACACTAATTATTAG 58.169 37.037 10.15 10.15 39.18 1.73
3508 4726 6.346096 TGGTCCAGTCACACTAATTATTAGC 58.654 40.000 11.50 0.00 36.71 3.09
3509 4727 6.070481 TGGTCCAGTCACACTAATTATTAGCA 60.070 38.462 11.50 0.00 36.71 3.49
3510 4728 6.258068 GGTCCAGTCACACTAATTATTAGCAC 59.742 42.308 11.50 4.42 36.71 4.40
3511 4729 6.816640 GTCCAGTCACACTAATTATTAGCACA 59.183 38.462 11.50 0.00 36.71 4.57
3512 4730 7.495934 GTCCAGTCACACTAATTATTAGCACAT 59.504 37.037 11.50 0.00 36.71 3.21
3513 4731 8.700973 TCCAGTCACACTAATTATTAGCACATA 58.299 33.333 11.50 0.00 36.71 2.29
3514 4732 9.494271 CCAGTCACACTAATTATTAGCACATAT 57.506 33.333 11.50 0.00 36.71 1.78
3565 4783 1.288752 CCAACACCATTGAACGGGC 59.711 57.895 0.00 0.00 0.00 6.13
3566 4784 1.459455 CCAACACCATTGAACGGGCA 61.459 55.000 0.00 0.00 0.00 5.36
3567 4785 0.602562 CAACACCATTGAACGGGCAT 59.397 50.000 0.00 0.00 0.00 4.40
3568 4786 0.602562 AACACCATTGAACGGGCATG 59.397 50.000 0.00 0.00 0.00 4.06
3569 4787 1.250154 ACACCATTGAACGGGCATGG 61.250 55.000 0.00 4.20 38.31 3.66
3570 4788 0.964860 CACCATTGAACGGGCATGGA 60.965 55.000 10.99 0.00 36.33 3.41
3571 4789 0.965363 ACCATTGAACGGGCATGGAC 60.965 55.000 10.99 0.00 36.33 4.02
3572 4790 0.964860 CCATTGAACGGGCATGGACA 60.965 55.000 0.00 0.00 34.46 4.02
3573 4791 0.887247 CATTGAACGGGCATGGACAA 59.113 50.000 0.00 0.00 0.00 3.18
3574 4792 0.887933 ATTGAACGGGCATGGACAAC 59.112 50.000 0.00 0.00 0.00 3.32
3575 4793 1.175983 TTGAACGGGCATGGACAACC 61.176 55.000 0.00 0.00 0.00 3.77
3585 4803 3.430473 TGGACAACCATCACCAACC 57.570 52.632 0.00 0.00 41.77 3.77
3622 4840 1.078759 CATCAGCGTGTCGTCTTCCC 61.079 60.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.108615 CGATGAGCTTCAACGACCCT 60.109 55.000 9.18 0.00 43.94 4.34
193 194 1.606668 CCGCTCTTGCTACACCAAAAA 59.393 47.619 0.00 0.00 36.97 1.94
194 195 1.234821 CCGCTCTTGCTACACCAAAA 58.765 50.000 0.00 0.00 36.97 2.44
196 197 1.671054 GCCGCTCTTGCTACACCAA 60.671 57.895 0.00 0.00 36.97 3.67
197 198 2.047274 GCCGCTCTTGCTACACCA 60.047 61.111 0.00 0.00 36.97 4.17
198 199 1.811679 GAGCCGCTCTTGCTACACC 60.812 63.158 13.42 0.00 39.69 4.16
199 200 1.811679 GGAGCCGCTCTTGCTACAC 60.812 63.158 19.68 0.00 39.59 2.90
200 201 2.579201 GGAGCCGCTCTTGCTACA 59.421 61.111 19.68 0.00 39.59 2.74
201 202 2.356818 ATCGGAGCCGCTCTTGCTAC 62.357 60.000 19.68 1.39 39.69 3.58
202 203 1.676678 AATCGGAGCCGCTCTTGCTA 61.677 55.000 19.68 2.29 39.69 3.49
203 204 3.023949 AATCGGAGCCGCTCTTGCT 62.024 57.895 19.68 2.38 43.03 3.91
204 205 2.512515 AATCGGAGCCGCTCTTGC 60.513 61.111 19.68 2.84 39.59 4.01
205 206 2.176273 CCAATCGGAGCCGCTCTTG 61.176 63.158 19.68 15.32 39.59 3.02
206 207 2.187946 CCAATCGGAGCCGCTCTT 59.812 61.111 19.68 4.00 39.59 2.85
207 208 3.854669 CCCAATCGGAGCCGCTCT 61.855 66.667 19.68 0.00 39.59 4.09
208 209 3.682292 AACCCAATCGGAGCCGCTC 62.682 63.158 12.27 12.27 39.59 5.03
209 210 3.717294 AACCCAATCGGAGCCGCT 61.717 61.111 3.59 0.00 39.59 5.52
217 218 0.237235 CGGTCACAACAACCCAATCG 59.763 55.000 0.00 0.00 32.89 3.34
497 539 1.692148 GCGATCGTTGATGCCGTCAA 61.692 55.000 17.81 0.00 44.36 3.18
906 1073 0.618458 AAGGTTCGGCCAATGCTAGA 59.382 50.000 2.24 0.00 40.61 2.43
914 1081 1.005394 GTCGAAGAAGGTTCGGCCA 60.005 57.895 2.24 0.00 40.29 5.36
922 1089 5.742926 GGTAGACGATTTAAGTCGAAGAAGG 59.257 44.000 24.82 0.00 44.06 3.46
923 1090 6.320171 TGGTAGACGATTTAAGTCGAAGAAG 58.680 40.000 24.82 0.00 44.06 2.85
924 1091 6.258230 TGGTAGACGATTTAAGTCGAAGAA 57.742 37.500 24.82 6.42 44.06 2.52
925 1092 5.675575 GCTGGTAGACGATTTAAGTCGAAGA 60.676 44.000 24.82 7.83 44.06 2.87
929 1096 3.114065 GGCTGGTAGACGATTTAAGTCG 58.886 50.000 17.64 17.64 46.56 4.18
933 1100 3.101437 TCTGGGCTGGTAGACGATTTAA 58.899 45.455 0.00 0.00 0.00 1.52
939 1106 1.668101 GACCTCTGGGCTGGTAGACG 61.668 65.000 0.00 0.00 36.59 4.18
959 1126 2.709125 TTCCTGCGACACGGTTCCTG 62.709 60.000 0.00 0.00 0.00 3.86
962 1129 1.359459 GGATTCCTGCGACACGGTTC 61.359 60.000 0.00 0.00 0.00 3.62
975 1142 0.398318 CCATCTCCTTCCCGGATTCC 59.602 60.000 0.73 0.00 42.12 3.01
985 1152 6.190587 CAAATTAAACCCTCTCCATCTCCTT 58.809 40.000 0.00 0.00 0.00 3.36
987 1154 4.889995 CCAAATTAAACCCTCTCCATCTCC 59.110 45.833 0.00 0.00 0.00 3.71
998 1165 2.361119 GGCGGAGATCCAAATTAAACCC 59.639 50.000 0.00 0.00 35.14 4.11
1085 1253 4.814294 GCCGTCCGTCCAGCGATT 62.814 66.667 0.00 0.00 44.77 3.34
1195 2395 2.487428 CTCGTGCAGGAGGAGACG 59.513 66.667 25.34 5.65 38.64 4.18
1290 2490 2.359975 GTCTTGGCCTTGTCCGGG 60.360 66.667 3.32 0.00 0.00 5.73
1291 2491 2.742372 CGTCTTGGCCTTGTCCGG 60.742 66.667 3.32 0.00 0.00 5.14
1359 2559 1.269413 GGATTTGGCGATCCATGCTTG 60.269 52.381 13.13 0.00 44.15 4.01
1361 2561 2.724520 GGATTTGGCGATCCATGCT 58.275 52.632 13.13 0.00 44.15 3.79
1371 2571 1.632422 CAGATTTGCGTGGATTTGGC 58.368 50.000 0.00 0.00 0.00 4.52
1386 2586 0.468400 GGTCCTCCTCGGTAGCAGAT 60.468 60.000 0.00 0.00 0.00 2.90
1392 2592 1.897802 GAAACTTGGTCCTCCTCGGTA 59.102 52.381 0.00 0.00 34.23 4.02
1498 2698 9.155975 GGGTTAGTATATGCATATGAACTCTTG 57.844 37.037 26.21 0.00 0.00 3.02
1516 2716 5.550403 ACAAGAAGGAAATCAGGGGTTAGTA 59.450 40.000 0.00 0.00 0.00 1.82
1518 2718 4.923415 ACAAGAAGGAAATCAGGGGTTAG 58.077 43.478 0.00 0.00 0.00 2.34
1519 2719 6.652205 ATACAAGAAGGAAATCAGGGGTTA 57.348 37.500 0.00 0.00 0.00 2.85
1520 2720 3.903530 ACAAGAAGGAAATCAGGGGTT 57.096 42.857 0.00 0.00 0.00 4.11
1521 2721 5.491078 TGTATACAAGAAGGAAATCAGGGGT 59.509 40.000 2.20 0.00 0.00 4.95
1522 2722 6.001449 TGTATACAAGAAGGAAATCAGGGG 57.999 41.667 2.20 0.00 0.00 4.79
1527 2739 5.357257 TCGCCTGTATACAAGAAGGAAATC 58.643 41.667 11.96 0.00 30.92 2.17
1538 2750 3.259876 AGTGAAACCTTCGCCTGTATACA 59.740 43.478 5.25 5.25 40.99 2.29
1549 2761 2.031870 ACCAAGCCAAGTGAAACCTTC 58.968 47.619 0.00 0.00 37.80 3.46
1560 2772 4.888326 ATGAATTGCTAAACCAAGCCAA 57.112 36.364 0.00 0.00 42.05 4.52
1565 2777 6.100404 AGCTTGAATGAATTGCTAAACCAA 57.900 33.333 0.00 0.00 31.71 3.67
1568 2780 9.578439 AAATCTAGCTTGAATGAATTGCTAAAC 57.422 29.630 0.99 0.00 36.07 2.01
1573 2785 9.230932 GTTAGAAATCTAGCTTGAATGAATTGC 57.769 33.333 0.99 0.00 0.00 3.56
1612 2826 5.581085 GTGCGTTATGGTTAGAGATTCAACT 59.419 40.000 0.00 0.00 0.00 3.16
1614 2828 5.730550 AGTGCGTTATGGTTAGAGATTCAA 58.269 37.500 0.00 0.00 0.00 2.69
1620 2834 4.495422 AGTCAAGTGCGTTATGGTTAGAG 58.505 43.478 0.00 0.00 0.00 2.43
1628 2842 2.031157 GCACCAAAGTCAAGTGCGTTAT 60.031 45.455 0.00 0.00 46.43 1.89
1630 2844 0.100503 GCACCAAAGTCAAGTGCGTT 59.899 50.000 0.00 0.00 46.43 4.84
1649 2863 0.894141 AGGACTCAGTGTAGCTGCAG 59.106 55.000 10.11 10.11 44.66 4.41
1656 2874 4.082190 GTGAAGTGCATAGGACTCAGTGTA 60.082 45.833 0.00 0.00 0.00 2.90
1717 2935 0.610232 ATCTGCAAAGCTGGGGTGAC 60.610 55.000 0.00 0.00 0.00 3.67
1865 3083 4.772886 ACCTTTTCAGTGAGTACTTGGT 57.227 40.909 0.00 0.00 34.07 3.67
1888 3106 7.706100 TGATGTTATACCCTGCACGTATATA 57.294 36.000 8.89 4.16 30.70 0.86
1889 3107 6.599356 TGATGTTATACCCTGCACGTATAT 57.401 37.500 8.89 0.00 30.70 0.86
1890 3108 6.041182 ACTTGATGTTATACCCTGCACGTATA 59.959 38.462 5.24 5.24 0.00 1.47
1891 3109 4.948341 TGATGTTATACCCTGCACGTAT 57.052 40.909 6.85 6.85 0.00 3.06
1892 3110 4.160814 ACTTGATGTTATACCCTGCACGTA 59.839 41.667 0.00 0.00 0.00 3.57
1893 3111 3.055385 ACTTGATGTTATACCCTGCACGT 60.055 43.478 0.00 0.00 0.00 4.49
1894 3112 3.531538 ACTTGATGTTATACCCTGCACG 58.468 45.455 0.00 0.00 0.00 5.34
1895 3113 5.186198 AGAACTTGATGTTATACCCTGCAC 58.814 41.667 0.00 0.00 39.30 4.57
1896 3114 5.189736 AGAGAACTTGATGTTATACCCTGCA 59.810 40.000 0.00 0.00 39.30 4.41
1897 3115 5.675538 AGAGAACTTGATGTTATACCCTGC 58.324 41.667 0.00 0.00 39.30 4.85
1898 3116 7.607991 ACAAAGAGAACTTGATGTTATACCCTG 59.392 37.037 0.00 0.00 39.30 4.45
1899 3117 7.690256 ACAAAGAGAACTTGATGTTATACCCT 58.310 34.615 0.00 0.00 39.30 4.34
1901 3119 9.827411 GAAACAAAGAGAACTTGATGTTATACC 57.173 33.333 0.00 0.00 36.60 2.73
1914 3132 7.101652 AGGAGGAAAAAGAAACAAAGAGAAC 57.898 36.000 0.00 0.00 0.00 3.01
1917 3135 5.010112 GGGAGGAGGAAAAAGAAACAAAGAG 59.990 44.000 0.00 0.00 0.00 2.85
1920 3138 3.634910 CGGGAGGAGGAAAAAGAAACAAA 59.365 43.478 0.00 0.00 0.00 2.83
1927 3145 1.098050 CATGCGGGAGGAGGAAAAAG 58.902 55.000 0.00 0.00 32.11 2.27
1928 3146 0.404040 ACATGCGGGAGGAGGAAAAA 59.596 50.000 0.00 0.00 35.40 1.94
1934 3152 0.321564 TCACAAACATGCGGGAGGAG 60.322 55.000 0.00 0.00 0.00 3.69
1986 3204 6.632834 GCATCATTGTCGTTGTTATCATTACC 59.367 38.462 0.00 0.00 0.00 2.85
1998 3216 1.200716 CCTGCAAGCATCATTGTCGTT 59.799 47.619 0.00 0.00 32.56 3.85
2001 3219 2.034305 GGATCCTGCAAGCATCATTGTC 59.966 50.000 3.84 0.00 32.56 3.18
2003 3221 2.307768 AGGATCCTGCAAGCATCATTG 58.692 47.619 15.29 0.00 0.00 2.82
2004 3222 2.750141 AGGATCCTGCAAGCATCATT 57.250 45.000 15.29 0.00 0.00 2.57
2048 3266 2.030007 GTGCCTTAGCTTGAATTGCACA 60.030 45.455 14.46 0.00 45.08 4.57
2117 3335 9.202273 GGTAGAACAGAAGAATGCTATATCTTG 57.798 37.037 0.00 0.00 36.08 3.02
2204 3422 6.623767 GCTCTACCAATTGTTTGAAGGCTTAG 60.624 42.308 0.00 0.00 34.60 2.18
2325 3543 2.940158 TCGACGGGAGATCCTCAATAA 58.060 47.619 0.00 0.00 35.95 1.40
2409 3627 4.568359 CGGTGACAACATTCCTTGATAGAG 59.432 45.833 0.00 0.00 0.00 2.43
2474 3692 0.308993 GCAATAGCACCAGATTCCGC 59.691 55.000 0.00 0.00 41.58 5.54
2519 3737 1.355381 ACTCATCTGGCAATGTTGGGA 59.645 47.619 8.72 0.00 0.00 4.37
2562 3780 5.308825 CAACAACAATCTCCACCTTAGAGT 58.691 41.667 0.00 0.00 32.93 3.24
2572 3790 2.887152 AGACCAAGCAACAACAATCTCC 59.113 45.455 0.00 0.00 0.00 3.71
2605 3823 6.127196 CCTCCTACAAGATATCCAGCTTATCC 60.127 46.154 0.00 0.00 0.00 2.59
2701 3919 7.331934 ACACAAGATATGATCGGTACATAATGC 59.668 37.037 0.00 0.00 34.58 3.56
2747 3965 4.023707 AGCTGGAAGAAATTTCTCAACACG 60.024 41.667 20.71 13.30 36.28 4.49
2806 4024 3.073678 ACAACGAATAAGATGCAGTGCA 58.926 40.909 22.22 22.22 44.86 4.57
2807 4025 3.747099 ACAACGAATAAGATGCAGTGC 57.253 42.857 8.58 8.58 0.00 4.40
2808 4026 5.248087 CGTAACAACGAATAAGATGCAGTG 58.752 41.667 0.00 0.00 34.64 3.66
2809 4027 4.328983 CCGTAACAACGAATAAGATGCAGT 59.671 41.667 0.00 0.00 34.64 4.40
2820 4038 1.925847 GTGTGTCACCGTAACAACGAA 59.074 47.619 0.00 0.00 34.64 3.85
2832 4050 3.660865 CCAAGGTAAGTAGGTGTGTCAC 58.339 50.000 0.00 0.00 0.00 3.67
2854 4072 3.249091 CATGGAAAGACAGAGTGAGTCG 58.751 50.000 0.00 0.00 40.84 4.18
2886 4104 3.866449 GCGTCTCATTCAGAACTTTCCCT 60.866 47.826 0.00 0.00 30.72 4.20
2899 4117 2.764010 TGTACCTACATGGCGTCTCATT 59.236 45.455 0.00 0.00 40.22 2.57
2900 4118 2.100916 GTGTACCTACATGGCGTCTCAT 59.899 50.000 0.00 0.00 38.63 2.90
2901 4119 1.475280 GTGTACCTACATGGCGTCTCA 59.525 52.381 0.00 0.00 38.63 3.27
2902 4120 1.202382 GGTGTACCTACATGGCGTCTC 60.202 57.143 0.00 0.00 38.63 3.36
2903 4121 0.822164 GGTGTACCTACATGGCGTCT 59.178 55.000 0.00 0.00 38.63 4.18
2904 4122 0.179092 GGGTGTACCTACATGGCGTC 60.179 60.000 0.00 0.00 38.63 5.19
2905 4123 1.619807 GGGGTGTACCTACATGGCGT 61.620 60.000 0.00 0.00 38.63 5.68
2906 4124 1.145377 GGGGTGTACCTACATGGCG 59.855 63.158 0.00 0.00 38.63 5.69
2907 4125 0.916809 AAGGGGTGTACCTACATGGC 59.083 55.000 0.00 0.00 40.87 4.40
2908 4126 3.971305 TGATAAGGGGTGTACCTACATGG 59.029 47.826 0.00 0.00 40.87 3.66
2909 4127 4.202326 GGTGATAAGGGGTGTACCTACATG 60.202 50.000 0.44 0.00 40.87 3.21
2910 4128 3.971971 GGTGATAAGGGGTGTACCTACAT 59.028 47.826 0.44 0.00 40.87 2.29
2911 4129 3.246057 TGGTGATAAGGGGTGTACCTACA 60.246 47.826 0.44 0.00 40.87 2.74
2912 4130 3.377573 TGGTGATAAGGGGTGTACCTAC 58.622 50.000 0.44 0.00 40.87 3.18
2913 4131 3.780516 TGGTGATAAGGGGTGTACCTA 57.219 47.619 0.44 0.00 40.87 3.08
2914 4132 2.653543 TGGTGATAAGGGGTGTACCT 57.346 50.000 0.44 0.00 44.56 3.08
2915 4133 2.224209 CGATGGTGATAAGGGGTGTACC 60.224 54.545 0.00 0.00 39.11 3.34
2916 4134 2.433239 ACGATGGTGATAAGGGGTGTAC 59.567 50.000 0.00 0.00 0.00 2.90
2917 4135 2.696707 GACGATGGTGATAAGGGGTGTA 59.303 50.000 0.00 0.00 0.00 2.90
2978 4196 9.590451 CACAAAGTCTAACCGGTATTAGAATAA 57.410 33.333 15.95 0.00 41.67 1.40
3009 4227 2.026822 ACTCTGGCCTAAATGACCACTG 60.027 50.000 3.32 0.00 0.00 3.66
3030 4248 6.015350 GGCATAGCTAGAACACCTACATTAGA 60.015 42.308 0.00 0.00 0.00 2.10
3170 4388 6.368805 AGGAGAAATTTGAAGACAAAGAGGT 58.631 36.000 0.00 0.00 46.84 3.85
3205 4423 4.937781 CGAAGGACGACGACTGTT 57.062 55.556 0.00 0.00 45.77 3.16
3357 4575 7.802117 TGGTCCTTAAAATATCTCCCTAACTG 58.198 38.462 0.00 0.00 0.00 3.16
3476 4694 4.157246 AGTGTGACTGGACCATTGTACTA 58.843 43.478 0.00 0.00 0.00 1.82
3521 4739 8.100791 GCAGGTTGGATATGATGTAATAACCTA 58.899 37.037 0.00 0.00 43.33 3.08
3522 4740 6.942576 GCAGGTTGGATATGATGTAATAACCT 59.057 38.462 0.00 0.00 45.36 3.50
3568 4786 1.073923 AGAGGTTGGTGATGGTTGTCC 59.926 52.381 0.00 0.00 0.00 4.02
3569 4787 2.568623 AGAGGTTGGTGATGGTTGTC 57.431 50.000 0.00 0.00 0.00 3.18
3570 4788 2.489073 GGAAGAGGTTGGTGATGGTTGT 60.489 50.000 0.00 0.00 0.00 3.32
3571 4789 2.162681 GGAAGAGGTTGGTGATGGTTG 58.837 52.381 0.00 0.00 0.00 3.77
3572 4790 2.040412 GAGGAAGAGGTTGGTGATGGTT 59.960 50.000 0.00 0.00 0.00 3.67
3573 4791 1.630878 GAGGAAGAGGTTGGTGATGGT 59.369 52.381 0.00 0.00 0.00 3.55
3574 4792 1.406069 CGAGGAAGAGGTTGGTGATGG 60.406 57.143 0.00 0.00 0.00 3.51
3575 4793 1.550524 TCGAGGAAGAGGTTGGTGATG 59.449 52.381 0.00 0.00 0.00 3.07
3576 4794 1.827969 CTCGAGGAAGAGGTTGGTGAT 59.172 52.381 3.91 0.00 34.74 3.06
3577 4795 1.203013 TCTCGAGGAAGAGGTTGGTGA 60.203 52.381 13.56 0.00 38.71 4.02
3578 4796 1.257743 TCTCGAGGAAGAGGTTGGTG 58.742 55.000 13.56 0.00 38.71 4.17
3585 4803 1.139947 GGCGGTTCTCGAGGAAGAG 59.860 63.158 13.56 0.00 42.43 2.85


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

AutoCloner maintained by Alex Coulton.