Multiple sequence alignment - TraesCS1B01G124000

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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 TraesCS1B01G124000 chr1B 100.000 3295 0 0 1 3295 150548181 150544887 0.000000e+00 6085.0
1 TraesCS1B01G124000 chr1B 94.902 863 21 5 1 840 547981392 547982254 0.000000e+00 1328.0
2 TraesCS1B01G124000 chr1A 91.889 1615 81 15 1157 2754 104242658 104241077 0.000000e+00 2211.0
3 TraesCS1B01G124000 chr1A 95.006 861 23 6 1 841 176448654 176449514 0.000000e+00 1334.0
4 TraesCS1B01G124000 chr1A 88.645 502 36 5 2788 3286 104240044 104239561 2.830000e-165 592.0
5 TraesCS1B01G124000 chr1A 92.086 139 11 0 914 1052 104242802 104242664 2.590000e-46 196.0
6 TraesCS1B01G124000 chr1D 93.010 1030 43 8 1728 2754 101101377 101102380 0.000000e+00 1476.0
7 TraesCS1B01G124000 chr1D 93.543 573 36 1 1157 1729 101100497 101101068 0.000000e+00 852.0
8 TraesCS1B01G124000 chr1D 90.419 334 20 4 2962 3291 101102602 101102927 2.350000e-116 429.0
9 TraesCS1B01G124000 chr1D 96.250 160 6 0 2788 2947 101102471 101102630 2.520000e-66 263.0
10 TraesCS1B01G124000 chr1D 92.086 139 11 0 914 1052 101100353 101100491 2.590000e-46 196.0
11 TraesCS1B01G124000 chr1D 97.059 34 1 0 868 901 101100334 101100367 1.280000e-04 58.4
12 TraesCS1B01G124000 chr4A 95.136 884 20 4 1 861 725886980 725887863 0.000000e+00 1373.0
13 TraesCS1B01G124000 chr4A 95.370 864 17 5 1 841 85201210 85202073 0.000000e+00 1352.0
14 TraesCS1B01G124000 chr3B 95.130 883 19 4 1 860 805825727 805826608 0.000000e+00 1371.0
15 TraesCS1B01G124000 chr5B 94.910 884 21 5 1 861 42146610 42147492 0.000000e+00 1362.0
16 TraesCS1B01G124000 chr5B 95.139 864 19 5 1 841 320481458 320482321 0.000000e+00 1341.0
17 TraesCS1B01G124000 chr5B 91.765 85 5 1 2973 3057 485406153 485406071 2.080000e-22 117.0
18 TraesCS1B01G124000 chr6B 95.255 864 18 5 1 841 18717519 18718382 0.000000e+00 1347.0
19 TraesCS1B01G124000 chr4B 95.139 864 19 5 1 841 612492700 612491837 0.000000e+00 1341.0
20 TraesCS1B01G124000 chr2B 95.017 863 20 5 1 840 232938738 232939600 0.000000e+00 1334.0
21 TraesCS1B01G124000 chr7B 93.326 884 33 4 1 861 684305574 684306454 0.000000e+00 1282.0
22 TraesCS1B01G124000 chr7B 93.520 787 27 4 79 841 683474446 683475232 0.000000e+00 1149.0
23 TraesCS1B01G124000 chr7B 92.437 357 10 3 521 861 614390479 614390834 8.210000e-136 494.0
24 TraesCS1B01G124000 chr7A 93.287 864 21 7 1 841 552575623 552576472 0.000000e+00 1240.0
25 TraesCS1B01G124000 chrUn 90.033 301 13 3 575 859 124973937 124974236 1.120000e-99 374.0
26 TraesCS1B01G124000 chrUn 89.769 303 13 7 575 861 259180986 259181286 4.020000e-99 372.0
27 TraesCS1B01G124000 chr5A 91.765 85 5 1 2973 3057 510032156 510032238 2.080000e-22 117.0
28 TraesCS1B01G124000 chr5D 87.059 85 7 2 2973 3057 403160413 403160493 3.500000e-15 93.5
29 TraesCS1B01G124000 chr5D 85.882 85 8 2 2973 3057 403166141 403166221 1.630000e-13 87.9
30 TraesCS1B01G124000 chr3A 88.158 76 8 1 2982 3057 109315117 109315043 4.530000e-14 89.8


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 TraesCS1B01G124000 chr1B 150544887 150548181 3294 True 6085.000000 6085 100.000000 1 3295 1 chr1B.!!$R1 3294
1 TraesCS1B01G124000 chr1B 547981392 547982254 862 False 1328.000000 1328 94.902000 1 840 1 chr1B.!!$F1 839
2 TraesCS1B01G124000 chr1A 176448654 176449514 860 False 1334.000000 1334 95.006000 1 841 1 chr1A.!!$F1 840
3 TraesCS1B01G124000 chr1A 104239561 104242802 3241 True 999.666667 2211 90.873333 914 3286 3 chr1A.!!$R1 2372
4 TraesCS1B01G124000 chr1D 101100334 101102927 2593 False 545.733333 1476 93.727833 868 3291 6 chr1D.!!$F1 2423
5 TraesCS1B01G124000 chr4A 725886980 725887863 883 False 1373.000000 1373 95.136000 1 861 1 chr4A.!!$F2 860
6 TraesCS1B01G124000 chr4A 85201210 85202073 863 False 1352.000000 1352 95.370000 1 841 1 chr4A.!!$F1 840
7 TraesCS1B01G124000 chr3B 805825727 805826608 881 False 1371.000000 1371 95.130000 1 860 1 chr3B.!!$F1 859
8 TraesCS1B01G124000 chr5B 42146610 42147492 882 False 1362.000000 1362 94.910000 1 861 1 chr5B.!!$F1 860
9 TraesCS1B01G124000 chr5B 320481458 320482321 863 False 1341.000000 1341 95.139000 1 841 1 chr5B.!!$F2 840
10 TraesCS1B01G124000 chr6B 18717519 18718382 863 False 1347.000000 1347 95.255000 1 841 1 chr6B.!!$F1 840
11 TraesCS1B01G124000 chr4B 612491837 612492700 863 True 1341.000000 1341 95.139000 1 841 1 chr4B.!!$R1 840
12 TraesCS1B01G124000 chr2B 232938738 232939600 862 False 1334.000000 1334 95.017000 1 840 1 chr2B.!!$F1 839
13 TraesCS1B01G124000 chr7B 684305574 684306454 880 False 1282.000000 1282 93.326000 1 861 1 chr7B.!!$F3 860
14 TraesCS1B01G124000 chr7B 683474446 683475232 786 False 1149.000000 1149 93.520000 79 841 1 chr7B.!!$F2 762
15 TraesCS1B01G124000 chr7A 552575623 552576472 849 False 1240.000000 1240 93.287000 1 841 1 chr7A.!!$F1 840

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
906 943 0.033405 CCAGTCGAGAGGAACCCCTA 60.033 60.0 0.00 0.0 44.53 3.53 F
1675 1726 0.037605 AGTCGTGAACGGGACAATCC 60.038 55.0 2.59 0.0 40.29 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 2532 0.179076 TGTGATCTATGCTGGCGGTG 60.179 55.000 0.0 0.0 0.0 4.94 R
3268 4636 1.004440 GAGGGTTGAGCTTGCGACT 60.004 57.895 0.0 0.0 0.0 4.18 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
617 629 7.383300 GCTTGCTGAATTTCTTAATCACACTTT 59.617 33.333 0.00 0.00 0.00 2.66
643 656 6.358974 TCTTTCATCATGTGAAGTCAGGTA 57.641 37.500 9.59 0.00 46.85 3.08
721 734 7.391148 TGCAAAAAGTTGTCTCTAGTTCTTT 57.609 32.000 0.00 0.00 37.06 2.52
752 780 3.367025 GCAGCAAATCTTAGCAAGCTTTG 59.633 43.478 15.06 15.06 43.73 2.77
849 886 5.934781 CTCTCTTTGAGGGCCTATATGTTT 58.065 41.667 5.73 0.00 39.08 2.83
853 890 6.122277 TCTTTGAGGGCCTATATGTTTTCAG 58.878 40.000 5.73 0.00 0.00 3.02
892 929 2.510768 GGTATCATCCGACACCAGTC 57.489 55.000 0.00 0.00 38.70 3.51
901 938 3.796667 GACACCAGTCGAGAGGAAC 57.203 57.895 9.90 0.00 34.60 3.62
902 939 0.244178 GACACCAGTCGAGAGGAACC 59.756 60.000 9.90 0.00 34.60 3.62
903 940 1.186267 ACACCAGTCGAGAGGAACCC 61.186 60.000 9.90 0.00 0.00 4.11
904 941 1.609794 ACCAGTCGAGAGGAACCCC 60.610 63.158 9.90 0.00 0.00 4.95
906 943 0.033405 CCAGTCGAGAGGAACCCCTA 60.033 60.000 0.00 0.00 44.53 3.53
907 944 1.618888 CCAGTCGAGAGGAACCCCTAA 60.619 57.143 0.00 0.00 44.53 2.69
908 945 2.176889 CAGTCGAGAGGAACCCCTAAA 58.823 52.381 0.00 0.00 44.53 1.85
909 946 2.565834 CAGTCGAGAGGAACCCCTAAAA 59.434 50.000 0.00 0.00 44.53 1.52
910 947 3.007614 CAGTCGAGAGGAACCCCTAAAAA 59.992 47.826 0.00 0.00 44.53 1.94
1052 1089 0.974383 ACGGAAGTACTGGACAAGGG 59.026 55.000 0.00 0.00 46.88 3.95
1054 1091 1.067071 CGGAAGTACTGGACAAGGGTC 60.067 57.143 0.00 0.00 43.55 4.46
1055 1092 2.258109 GGAAGTACTGGACAAGGGTCT 58.742 52.381 0.00 0.00 43.77 3.85
1056 1093 2.638363 GGAAGTACTGGACAAGGGTCTT 59.362 50.000 0.00 0.00 43.77 3.01
1057 1094 3.306849 GGAAGTACTGGACAAGGGTCTTC 60.307 52.174 0.00 0.00 43.77 2.87
1058 1095 1.893801 AGTACTGGACAAGGGTCTTCG 59.106 52.381 0.00 0.00 43.77 3.79
1059 1096 1.617357 GTACTGGACAAGGGTCTTCGT 59.383 52.381 0.00 0.00 43.77 3.85
1060 1097 0.393077 ACTGGACAAGGGTCTTCGTG 59.607 55.000 0.00 0.00 43.77 4.35
1061 1098 0.951040 CTGGACAAGGGTCTTCGTGC 60.951 60.000 0.00 0.00 43.77 5.34
1062 1099 1.671379 GGACAAGGGTCTTCGTGCC 60.671 63.158 0.00 0.00 43.77 5.01
1063 1100 1.070786 GACAAGGGTCTTCGTGCCA 59.929 57.895 0.00 0.00 40.99 4.92
1064 1101 0.951040 GACAAGGGTCTTCGTGCCAG 60.951 60.000 0.00 0.00 40.99 4.85
1065 1102 1.371183 CAAGGGTCTTCGTGCCAGA 59.629 57.895 0.00 0.00 0.00 3.86
1066 1103 0.671781 CAAGGGTCTTCGTGCCAGAG 60.672 60.000 0.00 0.00 0.00 3.35
1067 1104 2.435059 GGGTCTTCGTGCCAGAGC 60.435 66.667 0.00 0.00 37.94 4.09
1068 1105 2.659610 GGTCTTCGTGCCAGAGCT 59.340 61.111 0.00 0.00 40.80 4.09
1069 1106 1.446966 GGTCTTCGTGCCAGAGCTC 60.447 63.158 5.27 5.27 40.80 4.09
1075 1112 4.154347 GTGCCAGAGCTCGGGAGG 62.154 72.222 33.73 21.80 40.80 4.30
1088 1125 4.527583 GGAGGCCGAGCAGCAGAG 62.528 72.222 0.00 0.00 0.00 3.35
1093 1130 3.767806 CCGAGCAGCAGAGCAGGA 61.768 66.667 0.00 0.00 36.92 3.86
1094 1131 2.508887 CGAGCAGCAGAGCAGGAC 60.509 66.667 0.00 0.00 36.85 3.85
1095 1132 2.508887 GAGCAGCAGAGCAGGACG 60.509 66.667 0.00 0.00 36.85 4.79
1096 1133 4.756458 AGCAGCAGAGCAGGACGC 62.756 66.667 0.00 0.00 42.91 5.19
1098 1135 2.814341 CAGCAGAGCAGGACGCAG 60.814 66.667 0.00 0.00 46.13 5.18
1099 1136 2.993840 AGCAGAGCAGGACGCAGA 60.994 61.111 0.00 0.00 46.13 4.26
1100 1137 2.508887 GCAGAGCAGGACGCAGAG 60.509 66.667 0.00 0.00 46.13 3.35
1101 1138 2.999485 GCAGAGCAGGACGCAGAGA 61.999 63.158 0.00 0.00 46.13 3.10
1102 1139 1.815196 CAGAGCAGGACGCAGAGAT 59.185 57.895 0.00 0.00 46.13 2.75
1103 1140 0.528033 CAGAGCAGGACGCAGAGATG 60.528 60.000 0.00 0.00 46.13 2.90
1104 1141 1.882167 GAGCAGGACGCAGAGATGC 60.882 63.158 0.00 0.00 46.13 3.91
1113 1150 2.202797 CAGAGATGCGGGACACGG 60.203 66.667 0.00 0.00 44.51 4.94
1114 1151 4.148825 AGAGATGCGGGACACGGC 62.149 66.667 0.00 0.00 44.51 5.68
1115 1152 4.148825 GAGATGCGGGACACGGCT 62.149 66.667 0.00 0.00 44.51 5.52
1116 1153 3.665675 GAGATGCGGGACACGGCTT 62.666 63.158 0.00 0.00 44.51 4.35
1117 1154 3.195698 GATGCGGGACACGGCTTC 61.196 66.667 0.00 0.00 44.51 3.86
1118 1155 4.778143 ATGCGGGACACGGCTTCC 62.778 66.667 0.00 0.00 44.51 3.46
1131 1168 4.521062 CTTCCCAGCGCGGAGGAG 62.521 72.222 17.96 0.98 36.56 3.69
1143 1180 3.771160 GAGGAGGCCCGAAGCGAA 61.771 66.667 0.00 0.00 45.17 4.70
1144 1181 3.724914 GAGGAGGCCCGAAGCGAAG 62.725 68.421 0.00 0.00 45.17 3.79
1145 1182 4.840005 GGAGGCCCGAAGCGAAGG 62.840 72.222 0.00 0.00 45.17 3.46
1194 1231 3.267860 GCGGAGAAGCAGGCGATG 61.268 66.667 0.00 0.00 37.05 3.84
1224 1261 7.615403 TGATCCAATGGTACTATGATAAGCTC 58.385 38.462 0.00 0.00 0.00 4.09
1271 1308 6.516739 TCAAGACTCGTCTGATTATGAAGT 57.483 37.500 0.00 0.00 40.36 3.01
1347 1384 2.223433 CCGTGACTGGAACCGTCTATAC 60.223 54.545 13.46 6.26 32.70 1.47
1375 1412 2.028876 TGTTCGGCTCCTTCGATGATA 58.971 47.619 0.00 0.00 36.49 2.15
1384 1421 5.047660 GGCTCCTTCGATGATATCAGTAAGT 60.048 44.000 11.78 0.00 0.00 2.24
1394 1431 1.867363 ATCAGTAAGTCCTTCCGCCT 58.133 50.000 0.00 0.00 0.00 5.52
1444 1481 4.982295 CCATTGATGCACATGCTTATCAAG 59.018 41.667 18.74 12.98 42.62 3.02
1454 1491 4.141620 ACATGCTTATCAAGATCCCTCGTT 60.142 41.667 0.00 0.00 0.00 3.85
1460 1497 7.226720 TGCTTATCAAGATCCCTCGTTTTTATC 59.773 37.037 0.00 0.00 0.00 1.75
1532 1569 2.764128 TCCGCCTGGGAGGATGAC 60.764 66.667 8.01 0.00 40.94 3.06
1538 1575 1.689575 GCCTGGGAGGATGACACTCTA 60.690 57.143 0.00 0.00 37.67 2.43
1541 1578 3.303938 CTGGGAGGATGACACTCTACAT 58.696 50.000 0.00 0.00 35.34 2.29
1587 1624 4.961435 AGAGAGCAGCAAAAATTAGAGC 57.039 40.909 0.00 0.00 0.00 4.09
1675 1726 0.037605 AGTCGTGAACGGGACAATCC 60.038 55.000 2.59 0.00 40.29 3.01
1710 1761 2.232696 GAGGAGGTTTGGACTCTCACTC 59.767 54.545 0.00 0.00 35.34 3.51
1711 1762 1.067495 GGAGGTTTGGACTCTCACTCG 60.067 57.143 0.00 0.00 35.34 4.18
1717 1768 1.079750 GGACTCTCACTCGGGCAAC 60.080 63.158 0.00 0.00 0.00 4.17
1730 1781 6.601613 TCACTCGGGCAACTTTTAATGATTAT 59.398 34.615 0.00 0.00 0.00 1.28
1731 1782 7.122055 TCACTCGGGCAACTTTTAATGATTATT 59.878 33.333 0.00 0.00 0.00 1.40
1732 1783 8.402472 CACTCGGGCAACTTTTAATGATTATTA 58.598 33.333 0.00 0.00 0.00 0.98
1834 2198 4.301072 ACTGTACTACATTGTTGCCCAT 57.699 40.909 0.00 0.00 0.00 4.00
1835 2199 4.009675 ACTGTACTACATTGTTGCCCATG 58.990 43.478 0.00 0.00 0.00 3.66
1836 2200 3.351740 TGTACTACATTGTTGCCCATGG 58.648 45.455 4.14 4.14 0.00 3.66
1837 2201 1.851304 ACTACATTGTTGCCCATGGG 58.149 50.000 27.87 27.87 38.57 4.00
1853 2217 6.656693 TGCCCATGGGTTTAATTAATTGTTTG 59.343 34.615 31.58 0.00 37.65 2.93
1982 2346 6.260936 CCGAGGATGAATATTTAAGCTGTGTT 59.739 38.462 0.00 0.00 0.00 3.32
1997 2361 5.491982 AGCTGTGTTTCTATTCCCTACAAG 58.508 41.667 0.00 0.00 0.00 3.16
1998 2362 5.248477 AGCTGTGTTTCTATTCCCTACAAGA 59.752 40.000 0.00 0.00 0.00 3.02
1999 2363 6.069963 AGCTGTGTTTCTATTCCCTACAAGAT 60.070 38.462 0.00 0.00 0.00 2.40
2018 2382 2.526888 TCTATTCCAGACCCACTCGT 57.473 50.000 0.00 0.00 0.00 4.18
2029 2393 2.317609 CCACTCGTTCACGCTTGGG 61.318 63.158 9.93 0.00 37.35 4.12
2031 2395 0.319211 CACTCGTTCACGCTTGGGTA 60.319 55.000 0.00 0.00 39.60 3.69
2033 2397 1.001633 ACTCGTTCACGCTTGGGTAAT 59.998 47.619 0.00 0.00 39.60 1.89
2069 2433 2.246719 AGCTCACCACACTCAAGTTC 57.753 50.000 0.00 0.00 0.00 3.01
2073 2437 3.470709 CTCACCACACTCAAGTTCACAT 58.529 45.455 0.00 0.00 0.00 3.21
2084 2448 5.069516 ACTCAAGTTCACATTTGGCTTCATT 59.930 36.000 0.00 0.00 0.00 2.57
2088 2452 4.341806 AGTTCACATTTGGCTTCATTGTCA 59.658 37.500 0.00 0.00 0.00 3.58
2168 2532 4.630069 TCTCGAAGTTTATTTACTGCCAGC 59.370 41.667 0.00 0.00 0.00 4.85
2190 2554 1.154197 CGCCAGCATAGATCACATGG 58.846 55.000 0.00 4.37 0.00 3.66
2222 2587 1.877165 GATTTCGGAGGCGACGGAC 60.877 63.158 0.00 0.00 0.00 4.79
2272 2637 2.054140 TTTCACGCCGTGTTGCTTCC 62.054 55.000 17.83 0.00 34.79 3.46
2305 2670 2.049185 TGAGCTGAGAGTCTCCGCC 61.049 63.158 27.06 19.98 40.68 6.13
2333 2698 5.052481 CACAGTGTGAAGATGAGACTTTGA 58.948 41.667 18.83 0.00 35.23 2.69
2516 2882 2.422597 TGTTGCTCACTTATCCCGTTG 58.577 47.619 0.00 0.00 0.00 4.10
2633 2999 5.294552 GTGAATCCTACCATAGTTGACTTGC 59.705 44.000 0.00 0.00 0.00 4.01
2699 3065 3.044305 GAGCGCACACCAGTCACC 61.044 66.667 11.47 0.00 0.00 4.02
2700 3066 4.969196 AGCGCACACCAGTCACCG 62.969 66.667 11.47 0.00 0.00 4.94
2779 3180 3.764237 TTTTACCTCCAGTGGTCACTC 57.236 47.619 9.54 0.00 40.20 3.51
2780 3181 2.391926 TTACCTCCAGTGGTCACTCA 57.608 50.000 9.54 0.00 40.20 3.41
2783 3184 0.979665 CCTCCAGTGGTCACTCACAT 59.020 55.000 9.54 0.00 40.20 3.21
2784 3185 1.349026 CCTCCAGTGGTCACTCACATT 59.651 52.381 9.54 0.00 40.20 2.71
2786 3187 3.007940 CCTCCAGTGGTCACTCACATTTA 59.992 47.826 9.54 0.00 40.20 1.40
2792 3215 4.997395 AGTGGTCACTCACATTTATCACAC 59.003 41.667 0.00 0.00 36.92 3.82
2840 4205 3.432326 GGATACAAGAGTCGGCCTTCAAT 60.432 47.826 0.00 0.00 0.00 2.57
2901 4266 5.355596 TGAAGTGCAAATCCAAAATCGTTT 58.644 33.333 0.00 0.00 0.00 3.60
2935 4300 2.464459 GCAAATCGTCCGGCCTCAG 61.464 63.158 0.00 0.00 0.00 3.35
2948 4313 0.947244 GCCTCAGCCGGATACATTTG 59.053 55.000 5.05 0.00 0.00 2.32
2966 4331 3.518634 TTGAAGTGCAAGTCCCAAAAC 57.481 42.857 0.00 0.00 31.55 2.43
2971 4336 0.394488 TGCAAGTCCCAAAACGTCCA 60.394 50.000 0.00 0.00 0.00 4.02
3130 4495 2.228822 CCTTATCACTTTGCCGTTTGCT 59.771 45.455 0.00 0.00 42.00 3.91
3131 4496 3.492313 CTTATCACTTTGCCGTTTGCTC 58.508 45.455 0.00 0.00 42.00 4.26
3136 4501 1.152860 TTTGCCGTTTGCTCCTCCA 60.153 52.632 0.00 0.00 42.00 3.86
3138 4503 3.423154 GCCGTTTGCTCCTCCACG 61.423 66.667 0.00 0.00 36.87 4.94
3161 4526 1.220206 CCGCCTCTTGCATCTCTGT 59.780 57.895 0.00 0.00 41.33 3.41
3191 4556 3.691118 TGCTTCAACATCCTTGCATAGAC 59.309 43.478 0.00 0.00 0.00 2.59
3217 4582 2.655364 ACGATCTTCGCCGCATCG 60.655 61.111 8.76 8.76 45.12 3.84
3291 4659 0.037447 GCAAGCTCAACCCTCCTCTT 59.963 55.000 0.00 0.00 0.00 2.85
3292 4660 1.948144 GCAAGCTCAACCCTCCTCTTC 60.948 57.143 0.00 0.00 0.00 2.87
3293 4661 1.349026 CAAGCTCAACCCTCCTCTTCA 59.651 52.381 0.00 0.00 0.00 3.02
3294 4662 1.734655 AGCTCAACCCTCCTCTTCAA 58.265 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.489990 AGTTATGATTGAACTCATCAGACTTG 57.510 34.615 0.00 0.00 39.77 3.16
175 180 8.035394 AGCATAGCGTTTGTAGCATATATAACT 58.965 33.333 0.00 0.00 37.01 2.24
287 292 5.841810 CAAAAGACCTGCATTTTGGAACTA 58.158 37.500 13.17 0.00 40.87 2.24
617 629 6.547141 ACCTGACTTCACATGATGAAAGAAAA 59.453 34.615 15.49 4.13 46.80 2.29
643 656 8.331740 CAATGACATTCCCATTCCTAGGTATAT 58.668 37.037 9.08 0.00 32.40 0.86
721 734 7.806409 TGCTAAGATTTGCTGCATAAGATTA 57.194 32.000 1.84 0.00 0.00 1.75
752 780 8.622948 TTCCAAAAGAAAAGGAGATAGAGTTC 57.377 34.615 0.00 0.00 32.11 3.01
862 899 1.137086 GGATGATACCGGATGATCCCG 59.863 57.143 9.46 1.66 41.29 5.14
863 900 1.137086 CGGATGATACCGGATGATCCC 59.863 57.143 9.46 4.89 43.53 3.85
909 946 3.840124 ACTTCCTCTCGACTGGTTTTT 57.160 42.857 0.00 0.00 0.00 1.94
910 947 3.840124 AACTTCCTCTCGACTGGTTTT 57.160 42.857 0.00 0.00 0.00 2.43
911 948 3.840124 AAACTTCCTCTCGACTGGTTT 57.160 42.857 0.00 0.00 0.00 3.27
912 949 3.840124 AAAACTTCCTCTCGACTGGTT 57.160 42.857 0.00 0.00 0.00 3.67
913 950 3.388350 AGAAAAACTTCCTCTCGACTGGT 59.612 43.478 0.00 0.00 0.00 4.00
914 951 3.991121 GAGAAAAACTTCCTCTCGACTGG 59.009 47.826 0.00 0.00 0.00 4.00
1034 1071 0.974383 ACCCTTGTCCAGTACTTCCG 59.026 55.000 0.00 0.00 0.00 4.30
1038 1075 1.893801 CGAAGACCCTTGTCCAGTACT 59.106 52.381 0.00 0.00 42.81 2.73
1052 1089 4.177229 GAGCTCTGGCACGAAGAC 57.823 61.111 6.43 0.00 41.70 3.01
1058 1095 4.154347 CCTCCCGAGCTCTGGCAC 62.154 72.222 18.76 0.00 41.70 5.01
1071 1108 4.527583 CTCTGCTGCTCGGCCTCC 62.528 72.222 0.00 0.00 0.00 4.30
1076 1113 3.767806 TCCTGCTCTGCTGCTCGG 61.768 66.667 0.00 0.00 0.00 4.63
1077 1114 2.508887 GTCCTGCTCTGCTGCTCG 60.509 66.667 0.00 0.00 0.00 5.03
1078 1115 2.508887 CGTCCTGCTCTGCTGCTC 60.509 66.667 0.00 0.00 0.00 4.26
1079 1116 4.756458 GCGTCCTGCTCTGCTGCT 62.756 66.667 0.00 0.00 41.73 4.24
1081 1118 2.814341 CTGCGTCCTGCTCTGCTG 60.814 66.667 0.00 0.00 46.63 4.41
1082 1119 2.993840 TCTGCGTCCTGCTCTGCT 60.994 61.111 0.00 0.00 46.63 4.24
1083 1120 2.295472 ATCTCTGCGTCCTGCTCTGC 62.295 60.000 0.00 0.00 46.63 4.26
1084 1121 0.528033 CATCTCTGCGTCCTGCTCTG 60.528 60.000 0.00 0.00 46.63 3.35
1085 1122 1.815196 CATCTCTGCGTCCTGCTCT 59.185 57.895 0.00 0.00 46.63 4.09
1086 1123 1.882167 GCATCTCTGCGTCCTGCTC 60.882 63.158 0.00 0.00 46.63 4.26
1087 1124 2.186384 GCATCTCTGCGTCCTGCT 59.814 61.111 0.00 0.00 46.63 4.24
1095 1132 2.887568 CGTGTCCCGCATCTCTGC 60.888 66.667 0.00 0.00 45.31 4.26
1096 1133 2.202797 CCGTGTCCCGCATCTCTG 60.203 66.667 0.00 0.00 34.38 3.35
1097 1134 4.148825 GCCGTGTCCCGCATCTCT 62.149 66.667 0.00 0.00 34.38 3.10
1098 1135 3.665675 AAGCCGTGTCCCGCATCTC 62.666 63.158 0.00 0.00 34.38 2.75
1099 1136 3.665675 GAAGCCGTGTCCCGCATCT 62.666 63.158 0.00 0.00 34.38 2.90
1100 1137 3.195698 GAAGCCGTGTCCCGCATC 61.196 66.667 0.00 0.00 34.38 3.91
1101 1138 4.778143 GGAAGCCGTGTCCCGCAT 62.778 66.667 0.00 0.00 34.38 4.73
1114 1151 4.521062 CTCCTCCGCGCTGGGAAG 62.521 72.222 16.35 6.09 38.76 3.46
1126 1163 3.724914 CTTCGCTTCGGGCCTCCTC 62.725 68.421 0.84 0.00 37.74 3.71
1127 1164 3.775654 CTTCGCTTCGGGCCTCCT 61.776 66.667 0.84 0.00 37.74 3.69
1128 1165 4.840005 CCTTCGCTTCGGGCCTCC 62.840 72.222 0.84 0.00 37.74 4.30
1145 1182 4.603946 GGTAGGCATCGTCCGGGC 62.604 72.222 0.00 0.00 0.00 6.13
1146 1183 4.280494 CGGTAGGCATCGTCCGGG 62.280 72.222 0.00 0.00 39.41 5.73
1148 1185 2.473664 GATCCGGTAGGCATCGTCCG 62.474 65.000 0.00 3.25 42.22 4.79
1149 1186 1.289380 GATCCGGTAGGCATCGTCC 59.711 63.158 0.00 0.00 37.47 4.79
1150 1187 1.289380 GGATCCGGTAGGCATCGTC 59.711 63.158 0.00 0.00 37.47 4.20
1151 1188 1.456892 TGGATCCGGTAGGCATCGT 60.457 57.895 7.39 0.00 37.47 3.73
1152 1189 1.290324 CTGGATCCGGTAGGCATCG 59.710 63.158 12.93 0.00 37.47 3.84
1153 1190 0.832135 TCCTGGATCCGGTAGGCATC 60.832 60.000 19.51 0.00 37.47 3.91
1154 1191 0.833834 CTCCTGGATCCGGTAGGCAT 60.834 60.000 19.51 0.00 37.47 4.40
1155 1192 1.457643 CTCCTGGATCCGGTAGGCA 60.458 63.158 19.51 4.61 37.47 4.75
1159 1196 1.048601 GCAATCTCCTGGATCCGGTA 58.951 55.000 19.51 2.25 32.76 4.02
1194 1231 6.611613 TCATAGTACCATTGGATCATCTCC 57.388 41.667 10.37 0.00 45.19 3.71
1224 1261 2.237392 AGAATCCGGTTCCTTCTCCTTG 59.763 50.000 0.00 0.00 37.56 3.61
1375 1412 1.867363 AGGCGGAAGGACTTACTGAT 58.133 50.000 0.00 0.00 0.00 2.90
1384 1421 0.539986 AAGCGAATTAGGCGGAAGGA 59.460 50.000 0.00 0.00 35.00 3.36
1394 1431 4.511617 TTCATTGTTGCCAAGCGAATTA 57.488 36.364 0.00 0.00 33.17 1.40
1410 1447 2.028294 TGCATCAATGGCGGTTTTCATT 60.028 40.909 0.00 0.00 34.31 2.57
1444 1481 2.287103 GCACGGATAAAAACGAGGGATC 59.713 50.000 0.00 0.00 0.00 3.36
1538 1575 8.472413 CCCATGACTTCAATTGAAAAGATATGT 58.528 33.333 20.82 13.33 33.07 2.29
1541 1578 8.648698 TTCCCATGACTTCAATTGAAAAGATA 57.351 30.769 20.82 7.37 33.07 1.98
1553 1590 2.235650 CTGCTCTCTTCCCATGACTTCA 59.764 50.000 0.00 0.00 0.00 3.02
1587 1624 3.055719 AAACACATCCAGCGGCCG 61.056 61.111 24.05 24.05 0.00 6.13
1634 1671 5.163723 ACTGAAGATAATGTTGCGATTGTGG 60.164 40.000 0.00 0.00 0.00 4.17
1675 1726 1.755959 CCTCCTCACTGATGGTCTGAG 59.244 57.143 0.00 0.00 0.00 3.35
1807 2169 5.411361 GGCAACAATGTAGTACAGTTGATGA 59.589 40.000 27.16 0.00 36.78 2.92
1820 2184 2.317371 AACCCATGGGCAACAATGTA 57.683 45.000 31.73 0.00 39.32 2.29
1821 2185 1.433121 AAACCCATGGGCAACAATGT 58.567 45.000 31.73 5.43 39.32 2.71
1822 2186 3.692257 TTAAACCCATGGGCAACAATG 57.308 42.857 31.73 4.61 39.32 2.82
1834 2198 6.591935 TGCACCAAACAATTAATTAAACCCA 58.408 32.000 1.21 0.00 0.00 4.51
1835 2199 6.931840 TCTGCACCAAACAATTAATTAAACCC 59.068 34.615 1.21 0.00 0.00 4.11
1836 2200 7.655732 ACTCTGCACCAAACAATTAATTAAACC 59.344 33.333 1.21 0.00 0.00 3.27
1837 2201 8.587952 ACTCTGCACCAAACAATTAATTAAAC 57.412 30.769 1.21 0.00 0.00 2.01
1853 2217 3.231207 TCTAGATAGGGACTCTGCACC 57.769 52.381 0.00 0.00 41.75 5.01
1982 2346 9.094578 CTGGAATAGATCTTGTAGGGAATAGAA 57.905 37.037 0.00 0.00 0.00 2.10
1997 2361 2.959707 ACGAGTGGGTCTGGAATAGATC 59.040 50.000 0.00 0.00 37.83 2.75
1998 2362 3.033659 ACGAGTGGGTCTGGAATAGAT 57.966 47.619 0.00 0.00 37.83 1.98
1999 2363 2.526888 ACGAGTGGGTCTGGAATAGA 57.473 50.000 0.00 0.00 0.00 1.98
2069 2433 4.624015 AGTTGACAATGAAGCCAAATGTG 58.376 39.130 0.00 0.00 29.96 3.21
2073 2437 3.953612 ACAGAGTTGACAATGAAGCCAAA 59.046 39.130 0.00 0.00 0.00 3.28
2084 2448 1.053835 TGGCCTCCACAGAGTTGACA 61.054 55.000 3.32 0.00 38.58 3.58
2139 2503 7.412020 GGCAGTAAATAAACTTCGAGAACTCTG 60.412 40.741 0.41 0.00 0.00 3.35
2168 2532 0.179076 TGTGATCTATGCTGGCGGTG 60.179 55.000 0.00 0.00 0.00 4.94
2190 2554 1.059264 CGAAATCGAGCAACCGACTTC 59.941 52.381 0.00 7.11 40.18 3.01
2272 2637 2.049156 TCACCAGCAAGCTCGACG 60.049 61.111 0.00 0.00 0.00 5.12
2293 2658 3.894947 GCCTCGGCGGAGACTCTC 61.895 72.222 21.85 0.00 43.27 3.20
2305 2670 1.073964 CATCTTCACACTGTGCCTCG 58.926 55.000 7.90 0.00 32.98 4.63
2333 2698 4.887071 TGGTGTAAAAGCTTTGACATCAGT 59.113 37.500 30.94 9.38 37.65 3.41
2345 2710 1.272490 GGCCTTCCTTGGTGTAAAAGC 59.728 52.381 0.00 0.00 0.00 3.51
2346 2711 2.558359 CTGGCCTTCCTTGGTGTAAAAG 59.442 50.000 3.32 0.00 0.00 2.27
2516 2882 6.018262 TGCAAATTACCACTACGAGCATATTC 60.018 38.462 0.00 0.00 0.00 1.75
2591 2957 3.804036 TCACCAAACAGGACTACACAAG 58.196 45.455 0.00 0.00 41.22 3.16
2633 2999 3.179599 GCATCAAACAGAAAAACGTTCCG 59.820 43.478 0.00 0.00 0.00 4.30
2699 3065 3.009723 ACACAATCCTGCATAAAGACCG 58.990 45.455 0.00 0.00 0.00 4.79
2700 3066 4.009675 TGACACAATCCTGCATAAAGACC 58.990 43.478 0.00 0.00 0.00 3.85
2738 3104 3.916359 TGCCATTTGATTGCCATTGAT 57.084 38.095 0.00 0.00 0.00 2.57
2755 3156 2.092323 GACCACTGGAGGTAAAATGCC 58.908 52.381 0.71 0.00 43.38 4.40
2779 3180 5.801350 AATGAGTCCGTGTGATAAATGTG 57.199 39.130 0.00 0.00 0.00 3.21
2780 3181 6.706270 GGATAATGAGTCCGTGTGATAAATGT 59.294 38.462 0.00 0.00 0.00 2.71
2783 3184 6.228616 TGGATAATGAGTCCGTGTGATAAA 57.771 37.500 0.00 0.00 38.64 1.40
2784 3185 5.862678 TGGATAATGAGTCCGTGTGATAA 57.137 39.130 0.00 0.00 38.64 1.75
2786 3187 4.590647 AGATGGATAATGAGTCCGTGTGAT 59.409 41.667 0.00 0.00 38.64 3.06
2792 3215 3.324117 CTGCAGATGGATAATGAGTCCG 58.676 50.000 8.42 0.00 38.64 4.79
2840 4205 1.365633 GGACGTTTTGGGCATGCAA 59.634 52.632 21.36 2.70 0.00 4.08
2901 4266 5.182950 ACGATTTGCACTTTGAATGTATCCA 59.817 36.000 0.00 0.00 0.00 3.41
2935 4300 1.742831 TGCACTTCAAATGTATCCGGC 59.257 47.619 0.00 0.00 0.00 6.13
2948 4313 1.404035 ACGTTTTGGGACTTGCACTTC 59.596 47.619 0.00 0.00 0.00 3.01
2966 4331 1.179174 TATCCGGATGAGGCTGGACG 61.179 60.000 27.55 0.00 45.67 4.79
2971 4336 2.705658 TCAAATGTATCCGGATGAGGCT 59.294 45.455 27.55 2.14 0.00 4.58
3009 4374 7.919690 TGATTTCCTCGTCAAATTGCTATTAG 58.080 34.615 0.00 0.00 0.00 1.73
3058 4423 8.885722 GGAATATCCGTTGTTTATTACACTTCA 58.114 33.333 0.00 0.00 36.21 3.02
3059 4424 8.340443 GGGAATATCCGTTGTTTATTACACTTC 58.660 37.037 0.00 0.00 37.43 3.01
3062 4427 7.496591 TCTGGGAATATCCGTTGTTTATTACAC 59.503 37.037 0.00 0.00 37.43 2.90
3063 4428 7.496591 GTCTGGGAATATCCGTTGTTTATTACA 59.503 37.037 0.00 0.00 37.43 2.41
3064 4429 7.713942 AGTCTGGGAATATCCGTTGTTTATTAC 59.286 37.037 0.00 0.00 37.43 1.89
3161 4526 2.143122 GGATGTTGAAGCACTTGACGA 58.857 47.619 0.00 0.00 0.00 4.20
3191 4556 1.812214 GCGAAGATCGTGCTAAGCCG 61.812 60.000 1.45 0.00 42.81 5.52
3217 4582 5.215252 TGAAGATGGACGATTTAGATCCC 57.785 43.478 0.00 0.00 0.00 3.85
3259 4627 2.421775 TGAGCTTGCGACTGTTTCAAAA 59.578 40.909 0.00 0.00 0.00 2.44
3262 4630 1.330521 GTTGAGCTTGCGACTGTTTCA 59.669 47.619 0.00 0.00 0.00 2.69
3268 4636 1.004440 GAGGGTTGAGCTTGCGACT 60.004 57.895 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.