Multiple sequence alignment - TraesCS1B01G116300

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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 TraesCS1B01G116300 chr1B 100.000 3512 0 0 1 3512 136913931 136917442 0.000000e+00 6486.0
1 TraesCS1B01G116300 chr1D 89.159 1725 123 19 8 1708 83824285 83825969 0.000000e+00 2091.0
2 TraesCS1B01G116300 chr1D 88.960 1250 113 14 1606 2849 83858606 83859836 0.000000e+00 1520.0
3 TraesCS1B01G116300 chr1D 92.197 974 70 6 1702 2670 83826340 83827312 0.000000e+00 1373.0
4 TraesCS1B01G116300 chr1D 93.885 278 15 2 1333 1610 83828381 83828656 5.420000e-113 418.0
5 TraesCS1B01G116300 chr6D 96.636 654 21 1 2860 3512 201580429 201579776 0.000000e+00 1085.0
6 TraesCS1B01G116300 chr4B 96.330 654 23 1 2860 3512 4207506 4208159 0.000000e+00 1074.0
7 TraesCS1B01G116300 chr1A 89.236 864 78 5 952 1806 100373138 100373995 0.000000e+00 1066.0
8 TraesCS1B01G116300 chr1A 90.987 699 61 2 1964 2662 100392651 100393347 0.000000e+00 941.0
9 TraesCS1B01G116300 chr1A 90.843 688 46 8 168 848 100363807 100364484 0.000000e+00 905.0
10 TraesCS1B01G116300 chr1A 93.468 444 27 2 8 450 100363369 100363811 0.000000e+00 658.0
11 TraesCS1B01G116300 chr1A 82.243 107 12 3 2670 2775 239828588 239828488 6.250000e-13 86.1
12 TraesCS1B01G116300 chr6B 95.872 654 26 1 2860 3512 601116602 601115949 0.000000e+00 1057.0
13 TraesCS1B01G116300 chr6B 95.107 654 30 2 2860 3512 230627994 230628646 0.000000e+00 1029.0
14 TraesCS1B01G116300 chr6B 91.262 103 9 0 2365 2467 296399349 296399247 1.310000e-29 141.0
15 TraesCS1B01G116300 chr5B 95.406 653 28 2 2860 3511 649411731 649412382 0.000000e+00 1038.0
16 TraesCS1B01G116300 chr5B 81.481 108 10 5 2671 2775 463943812 463943712 2.910000e-11 80.5
17 TraesCS1B01G116300 chr6A 95.107 654 31 1 2860 3512 21702601 21701948 0.000000e+00 1029.0
18 TraesCS1B01G116300 chr6A 94.801 654 32 2 2860 3512 9066206 9066858 0.000000e+00 1018.0
19 TraesCS1B01G116300 chr6A 84.314 153 15 6 2365 2517 250209896 250210039 1.310000e-29 141.0
20 TraesCS1B01G116300 chr3A 94.954 654 32 1 2860 3512 684766716 684767369 0.000000e+00 1024.0
21 TraesCS1B01G116300 chr5A 94.801 654 33 1 2860 3512 384442986 384443639 0.000000e+00 1018.0
22 TraesCS1B01G116300 chr5A 89.552 134 14 0 1505 1638 399459951 399459818 1.680000e-38 171.0
23 TraesCS1B01G116300 chr5A 84.153 183 18 5 950 1127 399461555 399461379 2.170000e-37 167.0
24 TraesCS1B01G116300 chr5A 86.420 81 7 2 865 942 399461663 399461584 6.250000e-13 86.1
25 TraesCS1B01G116300 chr2A 89.545 220 21 2 2365 2582 24439753 24439534 9.600000e-71 278.0
26 TraesCS1B01G116300 chr2A 87.742 155 17 2 2217 2370 24440550 24440397 2.790000e-41 180.0
27 TraesCS1B01G116300 chr2D 89.498 219 22 1 2365 2582 22848847 22848629 3.450000e-70 276.0
28 TraesCS1B01G116300 chr2D 87.742 155 17 2 2217 2370 22849643 22849490 2.790000e-41 180.0
29 TraesCS1B01G116300 chr2B 89.401 217 21 2 2365 2579 37736776 37736992 4.470000e-69 272.0
30 TraesCS1B01G116300 chr2B 89.352 216 22 1 2365 2579 37570376 37570591 1.610000e-68 270.0
31 TraesCS1B01G116300 chr2B 89.032 155 15 2 2217 2370 38390958 38391111 1.290000e-44 191.0
32 TraesCS1B01G116300 chr2B 88.387 155 16 2 2217 2370 37735951 37736104 5.990000e-43 185.0
33 TraesCS1B01G116300 chr2B 87.742 155 17 2 2217 2370 37569544 37569697 2.790000e-41 180.0
34 TraesCS1B01G116300 chr2B 87.742 155 17 2 2217 2370 38456537 38456690 2.790000e-41 180.0
35 TraesCS1B01G116300 chr2B 85.542 166 13 7 984 1145 38385251 38385409 2.810000e-36 163.0


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 TraesCS1B01G116300 chr1B 136913931 136917442 3511 False 6486.0 6486 100.0000 1 3512 1 chr1B.!!$F1 3511
1 TraesCS1B01G116300 chr1D 83858606 83859836 1230 False 1520.0 1520 88.9600 1606 2849 1 chr1D.!!$F1 1243
2 TraesCS1B01G116300 chr1D 83824285 83828656 4371 False 1294.0 2091 91.7470 8 2670 3 chr1D.!!$F2 2662
3 TraesCS1B01G116300 chr6D 201579776 201580429 653 True 1085.0 1085 96.6360 2860 3512 1 chr6D.!!$R1 652
4 TraesCS1B01G116300 chr4B 4207506 4208159 653 False 1074.0 1074 96.3300 2860 3512 1 chr4B.!!$F1 652
5 TraesCS1B01G116300 chr1A 100373138 100373995 857 False 1066.0 1066 89.2360 952 1806 1 chr1A.!!$F1 854
6 TraesCS1B01G116300 chr1A 100392651 100393347 696 False 941.0 941 90.9870 1964 2662 1 chr1A.!!$F2 698
7 TraesCS1B01G116300 chr1A 100363369 100364484 1115 False 781.5 905 92.1555 8 848 2 chr1A.!!$F3 840
8 TraesCS1B01G116300 chr6B 601115949 601116602 653 True 1057.0 1057 95.8720 2860 3512 1 chr6B.!!$R2 652
9 TraesCS1B01G116300 chr6B 230627994 230628646 652 False 1029.0 1029 95.1070 2860 3512 1 chr6B.!!$F1 652
10 TraesCS1B01G116300 chr5B 649411731 649412382 651 False 1038.0 1038 95.4060 2860 3511 1 chr5B.!!$F1 651
11 TraesCS1B01G116300 chr6A 21701948 21702601 653 True 1029.0 1029 95.1070 2860 3512 1 chr6A.!!$R1 652
12 TraesCS1B01G116300 chr6A 9066206 9066858 652 False 1018.0 1018 94.8010 2860 3512 1 chr6A.!!$F1 652
13 TraesCS1B01G116300 chr3A 684766716 684767369 653 False 1024.0 1024 94.9540 2860 3512 1 chr3A.!!$F1 652
14 TraesCS1B01G116300 chr5A 384442986 384443639 653 False 1018.0 1018 94.8010 2860 3512 1 chr5A.!!$F1 652
15 TraesCS1B01G116300 chr2A 24439534 24440550 1016 True 229.0 278 88.6435 2217 2582 2 chr2A.!!$R1 365
16 TraesCS1B01G116300 chr2D 22848629 22849643 1014 True 228.0 276 88.6200 2217 2582 2 chr2D.!!$R1 365
17 TraesCS1B01G116300 chr2B 37735951 37736992 1041 False 228.5 272 88.8940 2217 2579 2 chr2B.!!$F5 362
18 TraesCS1B01G116300 chr2B 37569544 37570591 1047 False 225.0 270 88.5470 2217 2579 2 chr2B.!!$F4 362

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
867 1159 0.030603 GGACCCTCCTCCTCAATCCT 60.031 60.0 0.0 0.0 32.53 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2741 4130 0.100682 GTATTGCTCGAGCCTCGTGA 59.899 55.0 33.23 12.04 41.35 4.35 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
47 48 4.717629 CCTCGTCGTCGGCAAGCA 62.718 66.667 1.55 0.00 37.69 3.91
99 100 2.352032 CGCTCCCGTCCTCCTCTTT 61.352 63.158 0.00 0.00 0.00 2.52
129 130 2.544685 CTGCTCTGTTTCGGTATCCAG 58.455 52.381 0.00 0.00 0.00 3.86
195 196 2.616510 CGAGGAATTCTTGCTCCAGGTT 60.617 50.000 5.23 0.00 44.27 3.50
214 494 0.916086 TGTCGTATTCTTGGGGGCAT 59.084 50.000 0.00 0.00 0.00 4.40
310 590 4.452733 GCGAAGGGGACGGACAGG 62.453 72.222 0.00 0.00 0.00 4.00
509 792 4.270153 TGCCAGAGTGGGGGAGGT 62.270 66.667 0.00 0.00 38.19 3.85
519 802 2.369001 GGGGAGGTAGTCCTGGCT 59.631 66.667 0.00 0.00 46.06 4.75
561 844 1.517257 CGTCGAGGACCATGCTCAC 60.517 63.158 0.00 0.00 34.19 3.51
590 873 1.587043 CTGAAGTCGGACTCGGAGCA 61.587 60.000 11.71 4.61 36.95 4.26
802 1094 3.880846 CCAGGCGCTTGCGGATTC 61.881 66.667 15.01 0.00 40.46 2.52
848 1140 2.047040 CCATGATTGATCTCGTCGACG 58.953 52.381 31.30 31.30 41.45 5.12
849 1141 2.047040 CATGATTGATCTCGTCGACGG 58.953 52.381 35.05 25.32 40.29 4.79
850 1142 1.375551 TGATTGATCTCGTCGACGGA 58.624 50.000 35.05 29.10 40.29 4.69
853 1145 1.651240 TTGATCTCGTCGACGGACCC 61.651 60.000 35.05 23.53 40.17 4.46
854 1146 1.818785 GATCTCGTCGACGGACCCT 60.819 63.158 35.05 17.14 40.17 4.34
855 1147 1.774046 GATCTCGTCGACGGACCCTC 61.774 65.000 35.05 20.70 40.17 4.30
856 1148 3.507009 CTCGTCGACGGACCCTCC 61.507 72.222 35.05 0.00 40.17 4.30
857 1149 3.972971 CTCGTCGACGGACCCTCCT 62.973 68.421 35.05 0.00 40.17 3.69
858 1150 3.507009 CGTCGACGGACCCTCCTC 61.507 72.222 29.70 0.00 40.17 3.71
859 1151 3.139469 GTCGACGGACCCTCCTCC 61.139 72.222 0.00 0.00 37.19 4.30
860 1152 3.336568 TCGACGGACCCTCCTCCT 61.337 66.667 0.00 0.00 33.30 3.69
861 1153 2.829458 CGACGGACCCTCCTCCTC 60.829 72.222 0.00 0.00 33.30 3.71
862 1154 2.359404 GACGGACCCTCCTCCTCA 59.641 66.667 0.00 0.00 33.30 3.86
863 1155 1.305046 GACGGACCCTCCTCCTCAA 60.305 63.158 0.00 0.00 33.30 3.02
864 1156 0.688087 GACGGACCCTCCTCCTCAAT 60.688 60.000 0.00 0.00 33.30 2.57
865 1157 0.688087 ACGGACCCTCCTCCTCAATC 60.688 60.000 0.00 0.00 33.30 2.67
866 1158 1.403687 CGGACCCTCCTCCTCAATCC 61.404 65.000 0.00 0.00 33.30 3.01
867 1159 0.030603 GGACCCTCCTCCTCAATCCT 60.031 60.000 0.00 0.00 32.53 3.24
868 1160 1.419381 GACCCTCCTCCTCAATCCTC 58.581 60.000 0.00 0.00 0.00 3.71
869 1161 0.719015 ACCCTCCTCCTCAATCCTCA 59.281 55.000 0.00 0.00 0.00 3.86
870 1162 1.296523 ACCCTCCTCCTCAATCCTCAT 59.703 52.381 0.00 0.00 0.00 2.90
871 1163 1.977129 CCCTCCTCCTCAATCCTCATC 59.023 57.143 0.00 0.00 0.00 2.92
942 1237 2.756340 GAAAATTGCACACGCGCG 59.244 55.556 30.96 30.96 42.97 6.86
943 1238 2.008697 GAAAATTGCACACGCGCGT 61.009 52.632 32.73 32.73 42.97 6.01
957 1255 1.951130 CGCGTGGATTCCATCTCGG 60.951 63.158 9.01 0.00 35.28 4.63
974 1272 4.595538 GTCGCCGACACACCACCA 62.596 66.667 13.23 0.00 32.09 4.17
975 1273 4.595538 TCGCCGACACACCACCAC 62.596 66.667 0.00 0.00 0.00 4.16
976 1274 4.602259 CGCCGACACACCACCACT 62.602 66.667 0.00 0.00 0.00 4.00
977 1275 2.203153 GCCGACACACCACCACTT 60.203 61.111 0.00 0.00 0.00 3.16
978 1276 2.542907 GCCGACACACCACCACTTG 61.543 63.158 0.00 0.00 0.00 3.16
989 1288 3.953775 CCACTTGGACGTGGCCCT 61.954 66.667 0.00 0.00 46.98 5.19
1012 1317 0.108424 GTGCAAGATGAGCGAGTCCT 60.108 55.000 0.00 0.00 33.85 3.85
1020 1325 0.251832 TGAGCGAGTCCTTCTCCCTT 60.252 55.000 0.00 0.00 39.84 3.95
1314 1619 1.803334 TGTCACCTGGCAACGTTATC 58.197 50.000 0.00 0.00 42.51 1.75
1319 1624 1.559682 ACCTGGCAACGTTATCTGGAT 59.440 47.619 23.10 11.20 42.51 3.41
1320 1625 1.942657 CCTGGCAACGTTATCTGGATG 59.057 52.381 15.91 0.00 42.51 3.51
1323 1628 1.408266 GGCAACGTTATCTGGATGGGT 60.408 52.381 0.00 0.00 0.00 4.51
1324 1629 1.670811 GCAACGTTATCTGGATGGGTG 59.329 52.381 0.00 0.00 0.00 4.61
1330 1638 4.700213 ACGTTATCTGGATGGGTGAAAAAG 59.300 41.667 0.00 0.00 0.00 2.27
1332 1640 5.590259 CGTTATCTGGATGGGTGAAAAAGAT 59.410 40.000 0.00 0.00 0.00 2.40
1341 1649 6.352137 GGATGGGTGAAAAAGATTTGCCTTAT 60.352 38.462 0.00 0.00 0.00 1.73
1367 1675 4.553330 AGGACATGTACAAGGTCGATTT 57.447 40.909 11.55 7.23 32.39 2.17
1368 1676 4.253685 AGGACATGTACAAGGTCGATTTG 58.746 43.478 11.55 10.10 32.39 2.32
1405 1713 2.357034 TTGCGCAGGTTCTCCGAC 60.357 61.111 11.31 0.00 39.05 4.79
1408 1716 2.504244 CGCAGGTTCTCCGACGTC 60.504 66.667 5.18 5.18 39.05 4.34
1410 1718 1.444553 GCAGGTTCTCCGACGTCAG 60.445 63.158 17.16 3.99 39.05 3.51
1416 1724 0.039437 TTCTCCGACGTCAGTTCAGC 60.039 55.000 17.16 0.00 0.00 4.26
1446 1754 0.908198 ATGGAGAGCCGCTTCTCTTT 59.092 50.000 15.19 5.27 43.05 2.52
1491 1799 1.221021 CGGGAACTACTCAAGGCCC 59.779 63.158 0.00 0.00 39.41 5.80
1500 1808 1.903404 CTCAAGGCCCGCCAGTTTT 60.903 57.895 8.74 0.00 38.92 2.43
1503 1811 2.200337 AAGGCCCGCCAGTTTTGAC 61.200 57.895 8.74 0.00 38.92 3.18
1509 1817 0.391927 CCGCCAGTTTTGACGGGATA 60.392 55.000 0.00 0.00 45.37 2.59
1545 1853 2.565841 GATTTAAGCACGCTCCATCCT 58.434 47.619 0.00 0.00 0.00 3.24
1566 1874 1.795768 TCTTGACTGAATGCCGTGTC 58.204 50.000 0.00 0.00 0.00 3.67
1568 1876 2.079158 CTTGACTGAATGCCGTGTCAT 58.921 47.619 0.00 0.00 38.89 3.06
1644 1952 2.303890 AGCACACATCAAGGTCATGAGA 59.696 45.455 0.00 0.00 31.76 3.27
1671 1979 0.112995 AGCCAGGCATGAAGGAACAA 59.887 50.000 15.80 0.00 0.00 2.83
1672 1980 0.968405 GCCAGGCATGAAGGAACAAA 59.032 50.000 6.55 0.00 0.00 2.83
1679 1987 2.802247 GCATGAAGGAACAAAAGTTGGC 59.198 45.455 0.00 0.00 34.12 4.52
1682 1990 2.755655 TGAAGGAACAAAAGTTGGCGAA 59.244 40.909 0.00 0.00 34.12 4.70
1689 1997 3.964909 ACAAAAGTTGGCGAACATCTTC 58.035 40.909 14.35 0.00 37.98 2.87
1690 1998 3.632145 ACAAAAGTTGGCGAACATCTTCT 59.368 39.130 14.35 0.00 37.98 2.85
1704 2389 2.203470 TCTTCTGTTGCCATGCATCA 57.797 45.000 0.00 0.00 38.76 3.07
1708 2393 2.172679 TCTGTTGCCATGCATCAATGT 58.827 42.857 0.00 0.00 37.72 2.71
1725 2410 4.752879 TACGAAGGCTGCCGGCAC 62.753 66.667 29.03 21.99 44.01 5.01
1836 2521 0.108207 CTCTGATGGACATGGGAGCC 59.892 60.000 0.00 0.00 0.00 4.70
1851 2536 3.118884 TGGGAGCCGAATACAACTTCTAC 60.119 47.826 0.00 0.00 0.00 2.59
1869 2554 0.742281 ACGGCTCTGACATCACATGC 60.742 55.000 0.00 0.00 0.00 4.06
1881 2566 3.711190 ACATCACATGCTCATACCCTACA 59.289 43.478 0.00 0.00 0.00 2.74
1884 2569 4.513442 TCACATGCTCATACCCTACAAAC 58.487 43.478 0.00 0.00 0.00 2.93
1901 2586 6.636850 CCTACAAACGGAAAATTCACAAGAAG 59.363 38.462 0.00 0.00 37.14 2.85
1974 2659 0.179045 ATATGCGGCCTGGAGTGAAC 60.179 55.000 0.00 0.00 0.00 3.18
2055 2740 6.363065 AGATATCATCCATGGTGATATTGGC 58.637 40.000 30.08 23.15 44.90 4.52
2067 2752 3.434641 GTGATATTGGCGACATGATGGAG 59.565 47.826 0.00 0.00 42.32 3.86
2103 2788 2.559440 GTCTTCATGCCTCATGGTCTC 58.441 52.381 6.92 0.00 41.66 3.36
2169 2854 0.031010 AGGGTTTAGAGAGGCCGGAT 60.031 55.000 5.05 0.00 0.00 4.18
2226 2911 7.121315 AGAGAACTTAAACAAGGCATGGTTATC 59.879 37.037 0.52 0.00 40.79 1.75
2274 2959 3.360340 GCTTTGCTGAGGCGTGCT 61.360 61.111 0.00 0.00 42.25 4.40
2346 3031 1.392589 ACAGAAGCTTTGGTGGTGTG 58.607 50.000 0.00 0.00 0.00 3.82
2486 3858 1.603802 CTGTTCCAGTGCGACAACAAT 59.396 47.619 0.00 0.00 0.00 2.71
2526 3898 1.529826 GCCTAAGCACTTCAATTCGCG 60.530 52.381 0.00 0.00 39.53 5.87
2539 3911 0.107703 ATTCGCGATGCCCTTGAGAA 60.108 50.000 10.88 0.00 32.40 2.87
2540 3912 0.321210 TTCGCGATGCCCTTGAGAAA 60.321 50.000 10.88 0.00 0.00 2.52
2590 3970 8.588290 ATGAAACATAGGGTACTATTTTTGCA 57.412 30.769 4.23 0.00 38.83 4.08
2640 4020 3.567478 AGAACCTCTCACAAGCTGTTT 57.433 42.857 0.00 0.00 0.00 2.83
2641 4021 4.689612 AGAACCTCTCACAAGCTGTTTA 57.310 40.909 0.00 0.00 0.00 2.01
2643 4023 6.360370 AGAACCTCTCACAAGCTGTTTATA 57.640 37.500 0.00 0.00 0.00 0.98
2649 4029 6.431234 CCTCTCACAAGCTGTTTATAGGTTTT 59.569 38.462 0.00 0.00 36.34 2.43
2651 4035 6.995686 TCTCACAAGCTGTTTATAGGTTTTGA 59.004 34.615 6.95 6.95 40.49 2.69
2652 4036 7.202016 TCACAAGCTGTTTATAGGTTTTGAG 57.798 36.000 4.02 0.00 38.92 3.02
2702 4086 9.424319 CTAAGATTTGTTCTAGCTTGTCTTGTA 57.576 33.333 0.00 0.00 33.05 2.41
2705 4089 8.585881 AGATTTGTTCTAGCTTGTCTTGTACTA 58.414 33.333 0.00 0.00 30.96 1.82
2755 4144 2.064723 TATGCTCACGAGGCTCGAGC 62.065 60.000 40.35 35.51 43.74 5.03
2763 4152 1.203928 CGAGGCTCGAGCAATACAAG 58.796 55.000 36.27 16.83 43.74 3.16
2782 4171 6.899393 ACAAGAAACAATTCCAAGCTATCA 57.101 33.333 0.00 0.00 36.12 2.15
2798 4189 7.980662 CCAAGCTATCATATACATCCTCTTCTG 59.019 40.741 0.00 0.00 0.00 3.02
2813 4204 5.479724 TCCTCTTCTGGCTCTATCATGTATG 59.520 44.000 0.00 0.00 0.00 2.39
2814 4205 5.245751 CCTCTTCTGGCTCTATCATGTATGT 59.754 44.000 0.00 0.00 0.00 2.29
2815 4206 6.094193 TCTTCTGGCTCTATCATGTATGTG 57.906 41.667 0.00 0.00 0.00 3.21
2834 4225 5.818136 TGTGTCCTCTTCAAAGTTTTCAG 57.182 39.130 0.00 0.00 0.00 3.02
2835 4226 4.640201 TGTGTCCTCTTCAAAGTTTTCAGG 59.360 41.667 0.00 0.00 0.00 3.86
2838 4229 6.017852 GTGTCCTCTTCAAAGTTTTCAGGTAG 60.018 42.308 0.00 0.00 0.00 3.18
2854 4245 7.496529 TTCAGGTAGAAAAGTTGTTCATCTG 57.503 36.000 0.00 0.00 32.05 2.90
2855 4246 5.470098 TCAGGTAGAAAAGTTGTTCATCTGC 59.530 40.000 0.00 0.00 0.00 4.26
2856 4247 4.762251 AGGTAGAAAAGTTGTTCATCTGCC 59.238 41.667 0.00 0.00 41.50 4.85
2857 4248 4.518970 GGTAGAAAAGTTGTTCATCTGCCA 59.481 41.667 3.75 0.00 41.05 4.92
2858 4249 5.183904 GGTAGAAAAGTTGTTCATCTGCCAT 59.816 40.000 3.75 0.00 41.05 4.40
2903 4294 2.401766 GGCGTCTCACCATTGCAGG 61.402 63.158 0.00 0.00 0.00 4.85
2941 4332 1.469308 AGCGTCTAGAGAAACGACTGG 59.531 52.381 5.93 0.00 41.29 4.00
2996 4387 6.654582 GGAGGACGGTTGGTTTTAATTAACTA 59.345 38.462 0.00 0.00 0.00 2.24
3006 4397 8.570068 TGGTTTTAATTAACTATGTCCTCACC 57.430 34.615 0.00 0.00 0.00 4.02
3055 4446 2.418669 TCCAACTCTCAAAAGGGGTCT 58.581 47.619 0.00 0.00 0.00 3.85
3108 4499 2.111999 TTTGGCAGGGAGACGGTGAG 62.112 60.000 0.00 0.00 0.00 3.51
3111 4502 1.617947 GGCAGGGAGACGGTGAGAAT 61.618 60.000 0.00 0.00 0.00 2.40
3184 4575 2.450476 GTGGCCTTGGAATTCATGACT 58.550 47.619 3.32 0.00 0.00 3.41
3499 5817 8.141909 TGCTCGCAATAAGAGTAATACTATTGT 58.858 33.333 10.24 1.05 37.99 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.051237 GGTTGAAGGTGAATTTTCTGCAC 58.949 43.478 0.00 0.00 0.00 4.57
10 11 3.960102 AGGTTGAAGGTGAATTTTCTGCA 59.040 39.130 0.00 0.00 0.00 4.41
11 12 4.550422 GAGGTTGAAGGTGAATTTTCTGC 58.450 43.478 0.00 0.00 0.00 4.26
12 13 4.275936 ACGAGGTTGAAGGTGAATTTTCTG 59.724 41.667 0.00 0.00 0.00 3.02
28 29 2.049433 CTTGCCGACGACGAGGTT 60.049 61.111 9.28 0.00 42.66 3.50
99 100 0.969149 AACAGAGCAGGACATCGTCA 59.031 50.000 0.00 0.00 33.68 4.35
107 108 1.480954 GGATACCGAAACAGAGCAGGA 59.519 52.381 0.00 0.00 0.00 3.86
195 196 0.916086 ATGCCCCCAAGAATACGACA 59.084 50.000 0.00 0.00 0.00 4.35
328 608 4.514577 CCGCCGCTGATCGTCCTT 62.515 66.667 0.00 0.00 36.19 3.36
397 677 3.770040 CGCGGATGGGACCTGACA 61.770 66.667 0.00 0.00 0.00 3.58
495 778 0.688087 GGACTACCTCCCCCACTCTG 60.688 65.000 0.00 0.00 31.83 3.35
509 792 2.592993 GCACCCACAGCCAGGACTA 61.593 63.158 0.00 0.00 0.00 2.59
561 844 1.227089 CGACTTCAGCCTCATCCCG 60.227 63.158 0.00 0.00 0.00 5.14
797 1089 1.005630 CGGGCTCGGAGATGAATCC 60.006 63.158 9.69 0.00 33.89 3.01
802 1094 1.090052 GGAAAACGGGCTCGGAGATG 61.090 60.000 12.42 0.00 41.39 2.90
812 1104 1.199097 CATGGTCGAAAGGAAAACGGG 59.801 52.381 0.00 0.00 0.00 5.28
848 1140 0.030603 AGGATTGAGGAGGAGGGTCC 60.031 60.000 0.00 0.00 36.58 4.46
849 1141 1.343478 TGAGGATTGAGGAGGAGGGTC 60.343 57.143 0.00 0.00 0.00 4.46
850 1142 0.719015 TGAGGATTGAGGAGGAGGGT 59.281 55.000 0.00 0.00 0.00 4.34
853 1145 9.659135 AATATATAGATGAGGATTGAGGAGGAG 57.341 37.037 0.00 0.00 0.00 3.69
854 1146 9.653516 GAATATATAGATGAGGATTGAGGAGGA 57.346 37.037 0.00 0.00 0.00 3.71
855 1147 8.575589 CGAATATATAGATGAGGATTGAGGAGG 58.424 40.741 0.00 0.00 0.00 4.30
856 1148 8.575589 CCGAATATATAGATGAGGATTGAGGAG 58.424 40.741 0.00 0.00 0.00 3.69
857 1149 7.507277 CCCGAATATATAGATGAGGATTGAGGA 59.493 40.741 3.66 0.00 0.00 3.71
858 1150 7.665690 CCCGAATATATAGATGAGGATTGAGG 58.334 42.308 3.66 0.00 0.00 3.86
859 1151 7.151308 GCCCGAATATATAGATGAGGATTGAG 58.849 42.308 3.66 0.00 0.00 3.02
860 1152 6.042093 GGCCCGAATATATAGATGAGGATTGA 59.958 42.308 0.00 0.00 0.00 2.57
861 1153 6.226787 GGCCCGAATATATAGATGAGGATTG 58.773 44.000 0.00 0.00 0.00 2.67
862 1154 5.011125 CGGCCCGAATATATAGATGAGGATT 59.989 44.000 0.00 0.00 0.00 3.01
863 1155 4.524714 CGGCCCGAATATATAGATGAGGAT 59.475 45.833 0.00 0.00 0.00 3.24
864 1156 3.889538 CGGCCCGAATATATAGATGAGGA 59.110 47.826 0.00 0.00 0.00 3.71
865 1157 3.005897 CCGGCCCGAATATATAGATGAGG 59.994 52.174 3.71 0.00 0.00 3.86
866 1158 3.005897 CCCGGCCCGAATATATAGATGAG 59.994 52.174 3.71 0.00 0.00 2.90
867 1159 2.963101 CCCGGCCCGAATATATAGATGA 59.037 50.000 3.71 0.00 0.00 2.92
868 1160 2.548067 GCCCGGCCCGAATATATAGATG 60.548 54.545 3.71 0.00 0.00 2.90
869 1161 1.692519 GCCCGGCCCGAATATATAGAT 59.307 52.381 3.71 0.00 0.00 1.98
870 1162 1.117150 GCCCGGCCCGAATATATAGA 58.883 55.000 3.71 0.00 0.00 1.98
871 1163 0.249322 CGCCCGGCCCGAATATATAG 60.249 60.000 3.71 0.00 0.00 1.31
896 1188 1.456705 TGGGTTGGGTGGAACAAGC 60.457 57.895 0.00 0.00 44.16 4.01
898 1190 1.075896 GGTGGGTTGGGTGGAACAA 60.076 57.895 0.00 0.00 44.16 2.83
900 1192 2.203582 GGGTGGGTTGGGTGGAAC 60.204 66.667 0.00 0.00 0.00 3.62
945 1240 4.345337 GGCGACCGAGATGGAATC 57.655 61.111 0.00 0.00 46.04 2.52
957 1255 4.595538 TGGTGGTGTGTCGGCGAC 62.596 66.667 31.68 31.68 0.00 5.19
973 1271 2.669569 CAGGGCCACGTCCAAGTG 60.670 66.667 6.18 0.00 41.53 3.16
974 1272 3.953775 CCAGGGCCACGTCCAAGT 61.954 66.667 6.18 0.00 0.00 3.16
989 1288 3.120385 CGCTCATCTTGCACGCCA 61.120 61.111 0.00 0.00 0.00 5.69
1012 1317 2.592993 CGGGTGGAGCAAGGGAGAA 61.593 63.158 0.00 0.00 0.00 2.87
1034 1339 2.359850 GCACCTCCGCAATGGACA 60.360 61.111 0.00 0.00 43.74 4.02
1126 1431 4.844420 CTGGAGAAGGACGATGCC 57.156 61.111 0.00 0.00 0.00 4.40
1251 1556 1.079405 TCCGGAAGCAATGTCGACC 60.079 57.895 14.12 0.00 0.00 4.79
1304 1609 1.670811 CACCCATCCAGATAACGTTGC 59.329 52.381 11.99 2.73 0.00 4.17
1306 1611 3.992943 TTCACCCATCCAGATAACGTT 57.007 42.857 5.88 5.88 0.00 3.99
1310 1615 7.579339 GCAAATCTTTTTCACCCATCCAGATAA 60.579 37.037 0.00 0.00 0.00 1.75
1314 1619 4.248058 GCAAATCTTTTTCACCCATCCAG 58.752 43.478 0.00 0.00 0.00 3.86
1319 1624 6.432403 AATAAGGCAAATCTTTTTCACCCA 57.568 33.333 0.00 0.00 0.00 4.51
1320 1625 6.934083 TGAAATAAGGCAAATCTTTTTCACCC 59.066 34.615 0.00 0.00 33.85 4.61
1323 1628 8.428063 TCCTTGAAATAAGGCAAATCTTTTTCA 58.572 29.630 0.83 0.00 37.34 2.69
1324 1629 8.712363 GTCCTTGAAATAAGGCAAATCTTTTTC 58.288 33.333 0.83 0.00 37.34 2.29
1330 1638 6.633856 ACATGTCCTTGAAATAAGGCAAATC 58.366 36.000 0.00 0.00 37.34 2.17
1332 1640 6.491745 TGTACATGTCCTTGAAATAAGGCAAA 59.508 34.615 0.00 0.00 37.34 3.68
1341 1649 4.062293 CGACCTTGTACATGTCCTTGAAA 58.938 43.478 0.00 0.00 0.00 2.69
1367 1675 2.826128 AGCTCGTCAACATAGAAGACCA 59.174 45.455 0.00 0.00 0.00 4.02
1368 1676 3.512033 AGCTCGTCAACATAGAAGACC 57.488 47.619 0.00 0.00 0.00 3.85
1405 1713 1.690283 CCATGCTCGCTGAACTGACG 61.690 60.000 0.00 0.00 0.00 4.35
1408 1716 2.758089 GGCCATGCTCGCTGAACTG 61.758 63.158 0.00 0.00 0.00 3.16
1410 1718 2.117156 ATGGCCATGCTCGCTGAAC 61.117 57.895 20.04 0.00 0.00 3.18
1416 1724 1.597302 CTCTCCATGGCCATGCTCG 60.597 63.158 36.08 25.22 37.49 5.03
1446 1754 2.298163 GGTGTTCCTTCCGTACAAGAGA 59.702 50.000 0.00 0.00 0.00 3.10
1491 1799 1.006832 CTATCCCGTCAAAACTGGCG 58.993 55.000 0.00 0.00 36.57 5.69
1500 1808 2.163010 GTCGAACTTGTCTATCCCGTCA 59.837 50.000 0.00 0.00 0.00 4.35
1503 1811 2.527100 GTGTCGAACTTGTCTATCCCG 58.473 52.381 0.00 0.00 0.00 5.14
1545 1853 3.056179 TGACACGGCATTCAGTCAAGATA 60.056 43.478 0.00 0.00 37.99 1.98
1566 1874 5.279384 GCAAGCTCCATGTCAGATTTTATG 58.721 41.667 0.00 0.00 0.00 1.90
1568 1876 3.696051 GGCAAGCTCCATGTCAGATTTTA 59.304 43.478 0.00 0.00 0.00 1.52
1632 1940 2.967599 TGATCCGTCTCATGACCTTG 57.032 50.000 0.00 0.00 39.94 3.61
1633 1941 2.419297 GCTTGATCCGTCTCATGACCTT 60.419 50.000 0.00 0.00 39.94 3.50
1644 1952 1.452651 CATGCCTGGCTTGATCCGT 60.453 57.895 25.63 0.00 36.06 4.69
1671 1979 3.214328 ACAGAAGATGTTCGCCAACTTT 58.786 40.909 0.00 0.00 39.96 2.66
1672 1980 2.851195 ACAGAAGATGTTCGCCAACTT 58.149 42.857 0.00 0.00 39.96 2.66
1704 2389 1.449601 CCGGCAGCCTTCGTACATT 60.450 57.895 10.54 0.00 0.00 2.71
1708 2393 4.752879 GTGCCGGCAGCCTTCGTA 62.753 66.667 33.73 0.00 42.71 3.43
1725 2410 1.196127 CATATGCATGTGTAGGCGCAG 59.804 52.381 14.79 0.00 38.63 5.18
1836 2521 3.791887 CAGAGCCGTAGAAGTTGTATTCG 59.208 47.826 0.00 0.00 34.27 3.34
1851 2536 0.461516 AGCATGTGATGTCAGAGCCG 60.462 55.000 0.00 0.00 0.00 5.52
1869 2554 6.373216 TGAATTTTCCGTTTGTAGGGTATGAG 59.627 38.462 0.00 0.00 0.00 2.90
1881 2566 4.142049 TGGCTTCTTGTGAATTTTCCGTTT 60.142 37.500 0.00 0.00 0.00 3.60
1884 2569 3.568538 CTGGCTTCTTGTGAATTTTCCG 58.431 45.455 0.00 0.00 0.00 4.30
1901 2586 1.068333 CATTGTACACAACTGCCTGGC 60.068 52.381 12.87 12.87 38.86 4.85
1974 2659 0.376152 GCTTGTGCATGTCGATCCAG 59.624 55.000 0.00 0.00 39.41 3.86
2007 2692 5.120399 TCTTCCTTCAGAGACTCGAGTATC 58.880 45.833 28.47 28.47 36.58 2.24
2022 2707 6.654161 CACCATGGATGATATCTTCTTCCTTC 59.346 42.308 21.47 2.21 45.03 3.46
2055 2740 3.193263 CAACCTTCTCTCCATCATGTCG 58.807 50.000 0.00 0.00 0.00 4.35
2067 2752 1.671379 GACGGCACCCAACCTTCTC 60.671 63.158 0.00 0.00 0.00 2.87
2103 2788 1.508088 GATTCCAAGCAAGTGCCCG 59.492 57.895 0.00 0.00 43.38 6.13
2169 2854 2.136791 GGATCTCAATCCCGGCTCA 58.863 57.895 0.00 0.00 45.11 4.26
2346 3031 2.806288 ACACATTACTTTCGATGCGC 57.194 45.000 0.00 0.00 0.00 6.09
2486 3858 2.357154 GCTTTGGGAAGGCCATTCTCTA 60.357 50.000 5.01 0.00 39.36 2.43
2623 4003 4.532521 ACCTATAAACAGCTTGTGAGAGGT 59.467 41.667 9.81 9.81 35.29 3.85
2679 4063 7.445945 AGTACAAGACAAGCTAGAACAAATCT 58.554 34.615 0.00 0.00 42.48 2.40
2682 4066 8.951787 TTTAGTACAAGACAAGCTAGAACAAA 57.048 30.769 0.00 0.00 0.00 2.83
2724 4113 8.572185 AGCCTCGTGAGCATATATAACATATAG 58.428 37.037 0.00 0.00 0.00 1.31
2730 4119 4.099120 CGAGCCTCGTGAGCATATATAAC 58.901 47.826 5.82 0.00 34.72 1.89
2731 4120 4.007659 TCGAGCCTCGTGAGCATATATAA 58.992 43.478 14.64 0.00 41.35 0.98
2732 4121 3.606687 TCGAGCCTCGTGAGCATATATA 58.393 45.455 14.64 0.00 41.35 0.86
2733 4122 2.421775 CTCGAGCCTCGTGAGCATATAT 59.578 50.000 14.64 0.00 41.35 0.86
2734 4123 1.807142 CTCGAGCCTCGTGAGCATATA 59.193 52.381 14.64 0.00 41.35 0.86
2735 4124 0.595588 CTCGAGCCTCGTGAGCATAT 59.404 55.000 14.64 0.00 41.35 1.78
2736 4125 2.025719 CTCGAGCCTCGTGAGCATA 58.974 57.895 14.64 0.00 41.35 3.14
2737 4126 2.804167 CTCGAGCCTCGTGAGCAT 59.196 61.111 14.64 0.00 41.35 3.79
2740 4129 0.382158 TATTGCTCGAGCCTCGTGAG 59.618 55.000 33.23 9.24 41.35 3.51
2741 4130 0.100682 GTATTGCTCGAGCCTCGTGA 59.899 55.000 33.23 12.04 41.35 4.35
2742 4131 0.179137 TGTATTGCTCGAGCCTCGTG 60.179 55.000 33.23 13.01 41.35 4.35
2743 4132 0.530744 TTGTATTGCTCGAGCCTCGT 59.469 50.000 33.23 18.48 41.35 4.18
2744 4133 1.202302 TCTTGTATTGCTCGAGCCTCG 60.202 52.381 33.23 8.05 42.10 4.63
2745 4134 2.586258 TCTTGTATTGCTCGAGCCTC 57.414 50.000 33.23 20.05 41.18 4.70
2746 4135 3.003480 GTTTCTTGTATTGCTCGAGCCT 58.997 45.455 33.23 22.62 41.18 4.58
2747 4136 2.742053 TGTTTCTTGTATTGCTCGAGCC 59.258 45.455 33.23 18.73 41.18 4.70
2748 4137 4.404507 TTGTTTCTTGTATTGCTCGAGC 57.595 40.909 30.42 30.42 42.50 5.03
2755 4144 9.294030 GATAGCTTGGAATTGTTTCTTGTATTG 57.706 33.333 0.00 0.00 32.16 1.90
2782 4171 7.417554 TGATAGAGCCAGAAGAGGATGTATAT 58.582 38.462 0.00 0.00 34.15 0.86
2789 4180 3.921104 ACATGATAGAGCCAGAAGAGGA 58.079 45.455 0.00 0.00 0.00 3.71
2798 4189 4.526262 AGAGGACACATACATGATAGAGCC 59.474 45.833 0.00 0.00 0.00 4.70
2813 4204 4.640647 ACCTGAAAACTTTGAAGAGGACAC 59.359 41.667 0.00 0.00 0.00 3.67
2814 4205 4.855340 ACCTGAAAACTTTGAAGAGGACA 58.145 39.130 0.00 0.00 0.00 4.02
2815 4206 6.289064 TCTACCTGAAAACTTTGAAGAGGAC 58.711 40.000 0.00 0.00 0.00 3.85
2834 4225 4.518970 TGGCAGATGAACAACTTTTCTACC 59.481 41.667 0.00 0.00 0.00 3.18
2835 4226 5.689383 TGGCAGATGAACAACTTTTCTAC 57.311 39.130 0.00 0.00 0.00 2.59
2838 4229 8.844244 AGATATATGGCAGATGAACAACTTTTC 58.156 33.333 4.57 0.00 0.00 2.29
2849 4240 6.126681 TGGTATTCCCAGATATATGGCAGATG 60.127 42.308 11.09 0.00 38.72 2.90
2850 4241 5.972502 TGGTATTCCCAGATATATGGCAGAT 59.027 40.000 11.09 0.00 38.72 2.90
2851 4242 5.349690 TGGTATTCCCAGATATATGGCAGA 58.650 41.667 11.09 1.07 38.72 4.26
2852 4243 5.698741 TGGTATTCCCAGATATATGGCAG 57.301 43.478 11.09 0.00 38.72 4.85
2903 4294 1.457346 CTCCTCAACATGCTTCCACC 58.543 55.000 0.00 0.00 0.00 4.61
2941 4332 0.752658 AACTTGCCTTTCCAACTGCC 59.247 50.000 0.00 0.00 0.00 4.85
3025 4416 7.201947 CCCTTTTGAGAGTTGGAAGAAAGAAAT 60.202 37.037 0.00 0.00 0.00 2.17
3043 4434 3.963476 TCTTTGGAAGACCCCTTTTGA 57.037 42.857 0.00 0.00 34.81 2.69
3124 4515 2.274645 CCACGCTCCATTTGGCCAA 61.275 57.895 16.05 16.05 34.44 4.52
3184 4575 2.026262 GGGCCTCATTCTTGACCTGTAA 60.026 50.000 0.84 0.00 0.00 2.41
3445 5763 5.564550 CATATAAGGCTGGGTATTGCTCTT 58.435 41.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.