Multiple sequence alignment - TraesCS5B01G096500

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 TraesCS5B01G096500 chr5B 100.000 3135 0 0 1 3135 127769937 127773071 0.000000e+00 5790.0
1 TraesCS5B01G096500 chr5B 97.599 958 16 4 2183 3135 689171656 689170701 0.000000e+00 1635.0
2 TraesCS5B01G096500 chr5B 100.000 30 0 0 1886 1915 127771792 127771821 4.370000e-04 56.5
3 TraesCS5B01G096500 chr5B 100.000 30 0 0 1856 1885 127771822 127771851 4.370000e-04 56.5
4 TraesCS5B01G096500 chrUn 98.837 946 7 2 2194 3135 194117160 194116215 0.000000e+00 1683.0
5 TraesCS5B01G096500 chr6B 98.319 952 12 2 2188 3135 716403997 716404948 0.000000e+00 1666.0
6 TraesCS5B01G096500 chr6B 98.216 953 14 3 2185 3135 37761972 37761021 0.000000e+00 1663.0
7 TraesCS5B01G096500 chr3B 98.316 950 11 4 2191 3135 766104295 766105244 0.000000e+00 1661.0
8 TraesCS5B01G096500 chr3B 98.103 949 14 2 2191 3135 741973406 741974354 0.000000e+00 1650.0
9 TraesCS5B01G096500 chr1B 98.113 954 10 5 2186 3135 560184931 560185880 0.000000e+00 1655.0
10 TraesCS5B01G096500 chr4B 97.910 957 16 2 2183 3135 575730040 575730996 0.000000e+00 1653.0
11 TraesCS5B01G096500 chr2B 98.103 949 14 2 2191 3135 497040148 497041096 0.000000e+00 1650.0
12 TraesCS5B01G096500 chr5D 91.659 1103 34 12 1021 2105 116026517 116027579 0.000000e+00 1474.0
13 TraesCS5B01G096500 chr5D 94.937 79 4 0 2110 2188 116027655 116027733 1.180000e-24 124.0
14 TraesCS5B01G096500 chr5A 89.602 981 58 24 941 1890 123389387 123390354 0.000000e+00 1206.0
15 TraesCS5B01G096500 chr5A 85.350 942 76 25 1 924 123308554 123309451 0.000000e+00 918.0
16 TraesCS5B01G096500 chr5A 90.667 225 15 4 1886 2105 123390320 123390543 8.500000e-76 294.0
17 TraesCS5B01G096500 chr5A 96.203 79 3 0 2110 2188 123390619 123390697 2.540000e-26 130.0
18 TraesCS5B01G096500 chr7A 84.706 85 11 2 75 157 636881565 636881481 2.000000e-12 84.2
19 TraesCS5B01G096500 chr7D 87.879 66 8 0 353 418 178282404 178282469 9.320000e-11 78.7
20 TraesCS5B01G096500 chr1A 75.484 155 23 9 1 154 474222332 474222472 9.390000e-06 62.1


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 TraesCS5B01G096500 chr5B 127769937 127773071 3134 False 1967.666667 5790 100.000000 1 3135 3 chr5B.!!$F1 3134
1 TraesCS5B01G096500 chr5B 689170701 689171656 955 True 1635.000000 1635 97.599000 2183 3135 1 chr5B.!!$R1 952
2 TraesCS5B01G096500 chrUn 194116215 194117160 945 True 1683.000000 1683 98.837000 2194 3135 1 chrUn.!!$R1 941
3 TraesCS5B01G096500 chr6B 716403997 716404948 951 False 1666.000000 1666 98.319000 2188 3135 1 chr6B.!!$F1 947
4 TraesCS5B01G096500 chr6B 37761021 37761972 951 True 1663.000000 1663 98.216000 2185 3135 1 chr6B.!!$R1 950
5 TraesCS5B01G096500 chr3B 766104295 766105244 949 False 1661.000000 1661 98.316000 2191 3135 1 chr3B.!!$F2 944
6 TraesCS5B01G096500 chr3B 741973406 741974354 948 False 1650.000000 1650 98.103000 2191 3135 1 chr3B.!!$F1 944
7 TraesCS5B01G096500 chr1B 560184931 560185880 949 False 1655.000000 1655 98.113000 2186 3135 1 chr1B.!!$F1 949
8 TraesCS5B01G096500 chr4B 575730040 575730996 956 False 1653.000000 1653 97.910000 2183 3135 1 chr4B.!!$F1 952
9 TraesCS5B01G096500 chr2B 497040148 497041096 948 False 1650.000000 1650 98.103000 2191 3135 1 chr2B.!!$F1 944
10 TraesCS5B01G096500 chr5D 116026517 116027733 1216 False 799.000000 1474 93.298000 1021 2188 2 chr5D.!!$F1 1167
11 TraesCS5B01G096500 chr5A 123308554 123309451 897 False 918.000000 918 85.350000 1 924 1 chr5A.!!$F1 923
12 TraesCS5B01G096500 chr5A 123389387 123390697 1310 False 543.333333 1206 92.157333 941 2188 3 chr5A.!!$F2 1247

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
204 205 0.039527 AACGGAAGCAAATTCGTGCC 60.040 50.0 0.00 0.00 46.14 5.01 F
308 310 0.039527 CTGGGAAAACCGAAAAGCCG 60.040 55.0 0.00 0.00 44.64 5.52 F
896 913 0.615850 AAAAGAGCTCCCCTCGGAAG 59.384 55.0 10.93 0.00 45.54 3.46 F
1134 1157 1.216941 GCACGCTGCAATTTGCTGTT 61.217 50.0 23.67 12.35 45.31 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1950 0.250234 GCTGGTCAGTATGCTGGTCA 59.750 55.000 11.15 8.55 42.78 4.02 R
1904 1951 0.539051 AGCTGGTCAGTATGCTGGTC 59.461 55.000 11.15 4.88 42.78 4.02 R
1919 1966 0.970937 TCTGAGACCCCCGTAAGCTG 60.971 60.000 0.00 0.00 0.00 4.24 R
2336 2456 2.011947 GCCCCTAGATTAAAACGCGTT 58.988 47.619 20.79 20.79 0.00 4.84 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
49 50 8.342634 TGACTCTCACGGAATTAAAAGAAAAAG 58.657 33.333 0.00 0.00 0.00 2.27
54 55 8.637281 TCACGGAATTAAAAGAAAAAGGAAAC 57.363 30.769 0.00 0.00 0.00 2.78
55 56 8.251721 TCACGGAATTAAAAGAAAAAGGAAACA 58.748 29.630 0.00 0.00 0.00 2.83
56 57 9.040939 CACGGAATTAAAAGAAAAAGGAAACAT 57.959 29.630 0.00 0.00 0.00 2.71
57 58 9.040939 ACGGAATTAAAAGAAAAAGGAAACATG 57.959 29.630 0.00 0.00 0.00 3.21
58 59 8.009409 CGGAATTAAAAGAAAAAGGAAACATGC 58.991 33.333 0.00 0.00 0.00 4.06
67 68 8.607441 AGAAAAAGGAAACATGCTATTTTTCC 57.393 30.769 20.01 17.52 45.95 3.13
133 134 4.024809 GTGTCTCCACAGAAGTAAAGTTGC 60.025 45.833 0.00 0.00 41.44 4.17
140 141 2.413453 CAGAAGTAAAGTTGCGCCTCTC 59.587 50.000 4.18 0.00 0.00 3.20
152 153 3.659382 GCCTCTCGCGAAAGAAAAC 57.341 52.632 11.91 0.00 0.00 2.43
158 159 4.613031 CCTCTCGCGAAAGAAAACAAAATC 59.387 41.667 11.91 0.00 0.00 2.17
159 160 5.163302 TCTCGCGAAAGAAAACAAAATCA 57.837 34.783 11.33 0.00 0.00 2.57
160 161 5.757886 TCTCGCGAAAGAAAACAAAATCAT 58.242 33.333 11.33 0.00 0.00 2.45
161 162 5.624900 TCTCGCGAAAGAAAACAAAATCATG 59.375 36.000 11.33 0.00 0.00 3.07
185 186 0.401738 CCCCTTTTCTGAGAGGCACA 59.598 55.000 4.20 0.00 0.00 4.57
189 190 1.532868 CTTTTCTGAGAGGCACAACGG 59.467 52.381 0.00 0.00 0.00 4.44
198 199 1.000274 GAGGCACAACGGAAGCAAATT 60.000 47.619 0.00 0.00 0.00 1.82
199 200 1.000274 AGGCACAACGGAAGCAAATTC 60.000 47.619 0.00 0.00 37.17 2.17
200 201 1.052287 GCACAACGGAAGCAAATTCG 58.948 50.000 0.00 0.00 38.95 3.34
201 202 1.599419 GCACAACGGAAGCAAATTCGT 60.599 47.619 0.00 0.00 38.95 3.85
202 203 2.043411 CACAACGGAAGCAAATTCGTG 58.957 47.619 0.00 0.00 38.95 4.35
203 204 1.052287 CAACGGAAGCAAATTCGTGC 58.948 50.000 0.00 0.00 45.28 5.34
204 205 0.039527 AACGGAAGCAAATTCGTGCC 60.040 50.000 0.00 0.00 46.14 5.01
205 206 0.889186 ACGGAAGCAAATTCGTGCCT 60.889 50.000 0.00 0.00 46.14 4.75
206 207 0.179189 CGGAAGCAAATTCGTGCCTC 60.179 55.000 0.00 0.00 46.14 4.70
207 208 0.171231 GGAAGCAAATTCGTGCCTCC 59.829 55.000 4.40 4.40 45.43 4.30
208 209 0.881118 GAAGCAAATTCGTGCCTCCA 59.119 50.000 0.00 0.00 46.14 3.86
209 210 1.474077 GAAGCAAATTCGTGCCTCCAT 59.526 47.619 0.00 0.00 46.14 3.41
210 211 2.418368 AGCAAATTCGTGCCTCCATA 57.582 45.000 0.00 0.00 46.14 2.74
211 212 2.722094 AGCAAATTCGTGCCTCCATAA 58.278 42.857 0.00 0.00 46.14 1.90
212 213 2.684881 AGCAAATTCGTGCCTCCATAAG 59.315 45.455 0.00 0.00 46.14 1.73
213 214 2.682856 GCAAATTCGTGCCTCCATAAGA 59.317 45.455 0.00 0.00 38.66 2.10
214 215 3.128589 GCAAATTCGTGCCTCCATAAGAA 59.871 43.478 0.00 0.00 38.66 2.52
215 216 4.731773 GCAAATTCGTGCCTCCATAAGAAG 60.732 45.833 0.00 0.00 38.66 2.85
216 217 3.914426 ATTCGTGCCTCCATAAGAAGT 57.086 42.857 0.00 0.00 0.00 3.01
217 218 5.353394 AATTCGTGCCTCCATAAGAAGTA 57.647 39.130 0.00 0.00 0.00 2.24
218 219 4.811969 TTCGTGCCTCCATAAGAAGTAA 57.188 40.909 0.00 0.00 0.00 2.24
219 220 5.353394 TTCGTGCCTCCATAAGAAGTAAT 57.647 39.130 0.00 0.00 0.00 1.89
220 221 5.353394 TCGTGCCTCCATAAGAAGTAATT 57.647 39.130 0.00 0.00 0.00 1.40
232 233 7.094205 CCATAAGAAGTAATTTGTGCCTCTTGT 60.094 37.037 0.00 0.00 0.00 3.16
308 310 0.039527 CTGGGAAAACCGAAAAGCCG 60.040 55.000 0.00 0.00 44.64 5.52
338 340 5.353123 AGACACATAAAATCCAATAACGCGT 59.647 36.000 5.58 5.58 0.00 6.01
340 342 7.225931 AGACACATAAAATCCAATAACGCGTAT 59.774 33.333 14.46 5.59 0.00 3.06
369 371 3.844090 GGAGGGAGTGCCGAGAGC 61.844 72.222 0.00 0.00 44.14 4.09
382 384 1.374631 GAGAGCGTGACATGTGGCA 60.375 57.895 1.15 0.00 0.00 4.92
398 400 4.363990 CAGCGGGTGAGAGTGCGT 62.364 66.667 0.00 0.00 0.00 5.24
414 416 3.482783 GTCAAGTGGCGCGCTCTC 61.483 66.667 32.29 20.47 0.00 3.20
426 428 1.846541 GCGCTCTCAGCTTACCTAAG 58.153 55.000 0.00 0.00 39.60 2.18
461 463 1.549170 GGCCCTTGAAGAAGTACTCGA 59.451 52.381 0.00 0.00 0.00 4.04
475 477 5.189659 AGTACTCGATGATTAGTTGCTCC 57.810 43.478 0.00 0.00 0.00 4.70
476 478 3.460857 ACTCGATGATTAGTTGCTCCC 57.539 47.619 0.00 0.00 0.00 4.30
500 502 4.870636 AGAGAGATAGGAGCATGATAGGG 58.129 47.826 0.00 0.00 0.00 3.53
507 509 3.387962 AGGAGCATGATAGGGAGTGAAA 58.612 45.455 0.00 0.00 0.00 2.69
508 510 3.135530 AGGAGCATGATAGGGAGTGAAAC 59.864 47.826 0.00 0.00 0.00 2.78
509 511 3.471680 GAGCATGATAGGGAGTGAAACC 58.528 50.000 0.00 0.00 37.80 3.27
522 524 5.497474 GGAGTGAAACCCTATTTGAAGCTA 58.503 41.667 0.00 0.00 37.80 3.32
542 544 1.669604 TTTGCGTCAAACTACTGGCA 58.330 45.000 1.63 0.00 0.00 4.92
759 762 1.822581 GCAACCAAACGATAATCCGC 58.177 50.000 0.00 0.00 0.00 5.54
770 773 3.190535 ACGATAATCCGCAAACAAAAGCT 59.809 39.130 0.00 0.00 0.00 3.74
788 791 7.015584 ACAAAAGCTTTGAGGAAACTAATGGAT 59.984 33.333 13.54 0.00 44.43 3.41
869 872 3.072622 GGGCCTTCCGATTTTATAGTCCT 59.927 47.826 0.84 0.00 0.00 3.85
871 874 3.988517 GCCTTCCGATTTTATAGTCCTCG 59.011 47.826 0.00 0.00 0.00 4.63
873 876 4.500887 CCTTCCGATTTTATAGTCCTCGCA 60.501 45.833 0.00 0.00 0.00 5.10
874 877 4.659111 TCCGATTTTATAGTCCTCGCAA 57.341 40.909 0.00 0.00 0.00 4.85
876 879 3.493503 CCGATTTTATAGTCCTCGCAACC 59.506 47.826 0.00 0.00 0.00 3.77
891 908 1.539157 CAACCAAAAGAGCTCCCCTC 58.461 55.000 10.93 0.00 41.07 4.30
896 913 0.615850 AAAAGAGCTCCCCTCGGAAG 59.384 55.000 10.93 0.00 45.54 3.46
925 942 8.711457 AGCAAAAATCATCAATAAGAAAAACCG 58.289 29.630 0.00 0.00 0.00 4.44
926 943 8.707839 GCAAAAATCATCAATAAGAAAAACCGA 58.292 29.630 0.00 0.00 0.00 4.69
930 947 8.841444 AATCATCAATAAGAAAAACCGAATCG 57.159 30.769 0.00 0.00 0.00 3.34
931 948 7.603963 TCATCAATAAGAAAAACCGAATCGA 57.396 32.000 3.36 0.00 0.00 3.59
932 949 7.461107 TCATCAATAAGAAAAACCGAATCGAC 58.539 34.615 3.36 0.00 0.00 4.20
933 950 6.173191 TCAATAAGAAAAACCGAATCGACC 57.827 37.500 3.36 0.00 0.00 4.79
934 951 5.122711 TCAATAAGAAAAACCGAATCGACCC 59.877 40.000 3.36 0.00 0.00 4.46
935 952 2.853235 AGAAAAACCGAATCGACCCT 57.147 45.000 3.36 0.00 0.00 4.34
936 953 2.696506 AGAAAAACCGAATCGACCCTC 58.303 47.619 3.36 0.00 0.00 4.30
937 954 2.038033 AGAAAAACCGAATCGACCCTCA 59.962 45.455 3.36 0.00 0.00 3.86
938 955 2.554370 AAAACCGAATCGACCCTCAA 57.446 45.000 3.36 0.00 0.00 3.02
939 956 2.094762 AAACCGAATCGACCCTCAAG 57.905 50.000 3.36 0.00 0.00 3.02
952 969 5.650703 TCGACCCTCAAGAAAAAGAAAAACT 59.349 36.000 0.00 0.00 0.00 2.66
955 972 7.239763 ACCCTCAAGAAAAAGAAAAACTGAA 57.760 32.000 0.00 0.00 0.00 3.02
957 974 7.981789 ACCCTCAAGAAAAAGAAAAACTGAATC 59.018 33.333 0.00 0.00 0.00 2.52
962 979 9.675553 CAAGAAAAAGAAAAACTGAATCGAAAC 57.324 29.630 0.00 0.00 0.00 2.78
972 989 3.059597 ACTGAATCGAAACAAGCACTTCG 60.060 43.478 0.00 0.00 44.48 3.79
989 1006 2.344203 CGTCTTCTCCTCCCGTGCT 61.344 63.158 0.00 0.00 0.00 4.40
1042 1065 4.003788 AGTGTCCCGCCGAGGTTG 62.004 66.667 0.00 0.00 38.74 3.77
1089 1112 2.266055 CTCAAGGACCACGGCCTC 59.734 66.667 0.00 0.00 33.76 4.70
1134 1157 1.216941 GCACGCTGCAATTTGCTGTT 61.217 50.000 23.67 12.35 45.31 3.16
1138 1161 2.063266 CGCTGCAATTTGCTGTTGATT 58.937 42.857 23.67 0.00 45.31 2.57
1147 1170 7.013529 GCAATTTGCTGTTGATTTCTTCATTC 58.986 34.615 14.11 0.00 40.96 2.67
1167 1190 1.776034 GATTCGCGATTCACCCCAGC 61.776 60.000 22.41 0.00 0.00 4.85
1212 1239 4.247380 CTGGAGATGGAGGCGGGC 62.247 72.222 0.00 0.00 0.00 6.13
1365 1401 1.611851 CAGCCTCTCCCACCACTCT 60.612 63.158 0.00 0.00 0.00 3.24
1431 1467 1.519719 CTCTTTCCTCAGGCCCTCG 59.480 63.158 0.00 0.00 0.00 4.63
1576 1623 2.029728 CAGTCAGACGAATGGCGATTTC 59.970 50.000 0.00 0.00 44.57 2.17
1636 1683 4.675671 CGGCTTAGATCGATAATGAGGTCC 60.676 50.000 0.00 0.00 0.00 4.46
1662 1709 2.472695 TTGTAAACGCAGAGCATCCT 57.527 45.000 0.00 0.00 33.66 3.24
1827 1874 7.543756 TGGTTTTAACTGCTTAATTATGAGCC 58.456 34.615 6.68 0.00 37.37 4.70
1890 1937 2.113860 ACTGACCAGCATACGCAATT 57.886 45.000 0.00 0.00 42.27 2.32
1891 1938 2.436417 ACTGACCAGCATACGCAATTT 58.564 42.857 0.00 0.00 42.27 1.82
1892 1939 2.162208 ACTGACCAGCATACGCAATTTG 59.838 45.455 0.00 0.00 42.27 2.32
1893 1940 2.419673 CTGACCAGCATACGCAATTTGA 59.580 45.455 0.00 0.00 42.27 2.69
1894 1941 2.161410 TGACCAGCATACGCAATTTGAC 59.839 45.455 0.00 0.00 42.27 3.18
1895 1942 1.472480 ACCAGCATACGCAATTTGACC 59.528 47.619 0.00 0.00 42.27 4.02
1896 1943 1.472082 CCAGCATACGCAATTTGACCA 59.528 47.619 0.00 0.00 42.27 4.02
1897 1944 2.518949 CAGCATACGCAATTTGACCAC 58.481 47.619 0.00 0.00 42.27 4.16
1898 1945 2.095314 CAGCATACGCAATTTGACCACA 60.095 45.455 0.00 0.00 42.27 4.17
1899 1946 2.754552 AGCATACGCAATTTGACCACAT 59.245 40.909 0.00 0.00 42.27 3.21
1900 1947 3.193267 AGCATACGCAATTTGACCACATT 59.807 39.130 0.00 0.00 42.27 2.71
1901 1948 4.397730 AGCATACGCAATTTGACCACATTA 59.602 37.500 0.00 0.00 42.27 1.90
1902 1949 4.499040 GCATACGCAATTTGACCACATTAC 59.501 41.667 0.00 0.00 38.36 1.89
1903 1950 5.676079 GCATACGCAATTTGACCACATTACT 60.676 40.000 0.00 0.00 38.36 2.24
1904 1951 4.159377 ACGCAATTTGACCACATTACTG 57.841 40.909 0.00 0.00 0.00 2.74
1905 1952 3.818210 ACGCAATTTGACCACATTACTGA 59.182 39.130 0.00 0.00 0.00 3.41
1906 1953 4.158384 CGCAATTTGACCACATTACTGAC 58.842 43.478 0.00 0.00 0.00 3.51
1907 1954 4.485163 GCAATTTGACCACATTACTGACC 58.515 43.478 0.00 0.00 0.00 4.02
1908 1955 4.022416 GCAATTTGACCACATTACTGACCA 60.022 41.667 0.00 0.00 0.00 4.02
1909 1956 5.702865 CAATTTGACCACATTACTGACCAG 58.297 41.667 0.00 0.00 0.00 4.00
1910 1957 2.472695 TGACCACATTACTGACCAGC 57.527 50.000 0.00 0.00 0.00 4.85
1911 1958 1.696884 TGACCACATTACTGACCAGCA 59.303 47.619 0.00 0.00 0.00 4.41
1912 1959 2.305635 TGACCACATTACTGACCAGCAT 59.694 45.455 0.00 0.00 0.00 3.79
1913 1960 3.517500 TGACCACATTACTGACCAGCATA 59.482 43.478 0.00 0.00 0.00 3.14
1914 1961 3.871594 GACCACATTACTGACCAGCATAC 59.128 47.826 0.00 0.00 0.00 2.39
1915 1962 3.519510 ACCACATTACTGACCAGCATACT 59.480 43.478 0.00 0.00 0.00 2.12
1916 1963 3.873361 CCACATTACTGACCAGCATACTG 59.127 47.826 0.00 0.00 44.05 2.74
1936 1983 1.987855 CCAGCTTACGGGGGTCTCA 60.988 63.158 0.00 0.00 0.00 3.27
1974 2021 2.240667 AGAGTCAACCATAAGCCAGCAT 59.759 45.455 0.00 0.00 0.00 3.79
2041 2088 5.532779 AGGATTTCTGTCTTTGTGTCCTTTC 59.467 40.000 0.00 0.00 31.05 2.62
2132 2251 2.283143 TTTGGTGCCAGACTGCCACT 62.283 55.000 15.52 0.00 0.00 4.00
2336 2456 0.963962 GTACTCGTGACAAGGTGGGA 59.036 55.000 0.00 0.00 0.00 4.37
3017 3144 4.200283 GCCGCTCTCCTCGTCTGG 62.200 72.222 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.238232 GCACAGTCATGCCTCTCAA 57.762 52.632 0.00 0.00 39.86 3.02
117 118 1.873591 AGGCGCAACTTTACTTCTGTG 59.126 47.619 10.83 0.00 0.00 3.66
118 119 2.143925 GAGGCGCAACTTTACTTCTGT 58.856 47.619 10.83 0.00 0.00 3.41
140 141 5.559694 ACATGATTTTGTTTTCTTTCGCG 57.440 34.783 0.00 0.00 0.00 5.87
152 153 6.991531 TCAGAAAAGGGGAAAACATGATTTTG 59.008 34.615 0.00 0.00 0.00 2.44
158 159 4.219288 CCTCTCAGAAAAGGGGAAAACATG 59.781 45.833 0.00 0.00 39.51 3.21
159 160 4.411013 CCTCTCAGAAAAGGGGAAAACAT 58.589 43.478 0.00 0.00 39.51 2.71
160 161 3.832527 CCTCTCAGAAAAGGGGAAAACA 58.167 45.455 0.00 0.00 39.51 2.83
161 162 2.558795 GCCTCTCAGAAAAGGGGAAAAC 59.441 50.000 0.00 0.00 39.51 2.43
185 186 0.039527 GGCACGAATTTGCTTCCGTT 60.040 50.000 2.32 0.00 42.56 4.44
189 190 0.881118 TGGAGGCACGAATTTGCTTC 59.119 50.000 5.84 5.84 45.47 3.86
198 199 5.353394 AATTACTTCTTATGGAGGCACGA 57.647 39.130 0.00 0.00 0.00 4.35
199 200 5.354234 ACAAATTACTTCTTATGGAGGCACG 59.646 40.000 0.00 0.00 0.00 5.34
200 201 6.555315 CACAAATTACTTCTTATGGAGGCAC 58.445 40.000 0.00 0.00 0.00 5.01
201 202 5.125417 GCACAAATTACTTCTTATGGAGGCA 59.875 40.000 0.00 0.00 0.00 4.75
202 203 5.450550 GGCACAAATTACTTCTTATGGAGGC 60.451 44.000 0.00 0.00 0.00 4.70
203 204 5.888161 AGGCACAAATTACTTCTTATGGAGG 59.112 40.000 0.00 0.00 0.00 4.30
204 205 6.825721 AGAGGCACAAATTACTTCTTATGGAG 59.174 38.462 0.00 0.00 0.00 3.86
205 206 6.721318 AGAGGCACAAATTACTTCTTATGGA 58.279 36.000 0.00 0.00 0.00 3.41
206 207 7.094205 ACAAGAGGCACAAATTACTTCTTATGG 60.094 37.037 0.00 0.00 0.00 2.74
207 208 7.820648 ACAAGAGGCACAAATTACTTCTTATG 58.179 34.615 0.00 0.00 0.00 1.90
208 209 9.167311 CTACAAGAGGCACAAATTACTTCTTAT 57.833 33.333 0.00 0.00 0.00 1.73
209 210 8.372459 TCTACAAGAGGCACAAATTACTTCTTA 58.628 33.333 0.00 0.00 0.00 2.10
210 211 7.224297 TCTACAAGAGGCACAAATTACTTCTT 58.776 34.615 0.00 0.00 0.00 2.52
211 212 6.769512 TCTACAAGAGGCACAAATTACTTCT 58.230 36.000 0.00 0.00 0.00 2.85
212 213 7.435068 TTCTACAAGAGGCACAAATTACTTC 57.565 36.000 0.00 0.00 0.00 3.01
213 214 7.817418 TTTCTACAAGAGGCACAAATTACTT 57.183 32.000 0.00 0.00 0.00 2.24
214 215 7.817418 TTTTCTACAAGAGGCACAAATTACT 57.183 32.000 0.00 0.00 0.00 2.24
244 245 5.871465 AAATGCACGGAAAAACACTTTTT 57.129 30.435 0.00 0.00 44.93 1.94
245 246 5.871465 AAAATGCACGGAAAAACACTTTT 57.129 30.435 0.00 0.00 37.46 2.27
246 247 5.871465 AAAAATGCACGGAAAAACACTTT 57.129 30.435 0.00 0.00 0.00 2.66
271 272 2.037121 CCAGGTTTGCCTTAGGTTTTGG 59.963 50.000 0.00 0.00 44.18 3.28
272 273 2.037121 CCCAGGTTTGCCTTAGGTTTTG 59.963 50.000 0.00 0.00 44.18 2.44
290 291 0.465824 TCGGCTTTTCGGTTTTCCCA 60.466 50.000 0.00 0.00 36.42 4.37
350 352 1.984570 CTCTCGGCACTCCCTCCAA 60.985 63.158 0.00 0.00 0.00 3.53
351 353 2.363018 CTCTCGGCACTCCCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
352 354 3.844090 GCTCTCGGCACTCCCTCC 61.844 72.222 0.00 0.00 41.35 4.30
363 365 2.447887 GCCACATGTCACGCTCTCG 61.448 63.158 0.00 0.00 42.43 4.04
369 371 3.792047 CCGCTGCCACATGTCACG 61.792 66.667 0.00 0.00 0.00 4.35
382 384 4.057428 GACGCACTCTCACCCGCT 62.057 66.667 0.00 0.00 0.00 5.52
398 400 3.921767 CTGAGAGCGCGCCACTTGA 62.922 63.158 30.33 16.06 0.00 3.02
409 411 2.761208 TCACCTTAGGTAAGCTGAGAGC 59.239 50.000 2.52 0.00 36.16 4.09
414 416 2.693267 GGGTCACCTTAGGTAAGCTG 57.307 55.000 2.52 0.00 32.11 4.24
443 445 4.720649 TCATCGAGTACTTCTTCAAGGG 57.279 45.455 0.00 0.00 33.37 3.95
446 448 7.275779 GCAACTAATCATCGAGTACTTCTTCAA 59.724 37.037 0.00 0.00 0.00 2.69
461 463 3.300388 TCTCTCGGGAGCAACTAATCAT 58.700 45.455 7.67 0.00 39.31 2.45
475 477 2.789213 TCATGCTCCTATCTCTCTCGG 58.211 52.381 0.00 0.00 0.00 4.63
476 478 4.576053 CCTATCATGCTCCTATCTCTCTCG 59.424 50.000 0.00 0.00 0.00 4.04
500 502 7.631717 AATAGCTTCAAATAGGGTTTCACTC 57.368 36.000 0.00 0.00 0.00 3.51
507 509 4.270008 ACGCAAATAGCTTCAAATAGGGT 58.730 39.130 0.00 0.00 42.61 4.34
508 510 4.335315 TGACGCAAATAGCTTCAAATAGGG 59.665 41.667 0.00 0.00 46.97 3.53
509 511 5.484173 TGACGCAAATAGCTTCAAATAGG 57.516 39.130 0.00 0.00 46.97 2.57
519 521 3.727970 GCCAGTAGTTTGACGCAAATAGC 60.728 47.826 7.98 0.00 35.74 2.97
522 524 2.226330 TGCCAGTAGTTTGACGCAAAT 58.774 42.857 7.98 2.20 35.74 2.32
528 530 6.695292 CAATTGAATTGCCAGTAGTTTGAC 57.305 37.500 4.82 0.00 32.92 3.18
759 762 7.826260 TTAGTTTCCTCAAAGCTTTTGTTTG 57.174 32.000 9.53 0.00 36.42 2.93
770 773 8.477419 ACTGAAAATCCATTAGTTTCCTCAAA 57.523 30.769 0.00 0.00 40.61 2.69
808 811 6.183360 GGCCCAGCAATTGACTTATAAAATCT 60.183 38.462 10.34 0.00 0.00 2.40
811 814 5.022787 AGGCCCAGCAATTGACTTATAAAA 58.977 37.500 10.34 0.00 0.00 1.52
820 823 1.678635 CGGAAGGCCCAGCAATTGA 60.679 57.895 10.34 0.00 34.14 2.57
869 872 0.889186 GGGAGCTCTTTTGGTTGCGA 60.889 55.000 14.64 0.00 0.00 5.10
871 874 0.540597 AGGGGAGCTCTTTTGGTTGC 60.541 55.000 14.64 0.00 0.00 4.17
873 876 0.036875 CGAGGGGAGCTCTTTTGGTT 59.963 55.000 14.64 0.00 0.00 3.67
874 877 1.679898 CGAGGGGAGCTCTTTTGGT 59.320 57.895 14.64 0.00 0.00 3.67
876 879 0.324943 TTCCGAGGGGAGCTCTTTTG 59.675 55.000 14.64 3.54 44.98 2.44
891 908 4.439305 TGATGATTTTTGCTTCCTTCCG 57.561 40.909 0.00 0.00 0.00 4.30
924 941 3.994392 TCTTTTTCTTGAGGGTCGATTCG 59.006 43.478 0.00 0.00 0.00 3.34
925 942 5.941948 TTCTTTTTCTTGAGGGTCGATTC 57.058 39.130 0.00 0.00 0.00 2.52
926 943 6.709018 TTTTCTTTTTCTTGAGGGTCGATT 57.291 33.333 0.00 0.00 0.00 3.34
927 944 6.321435 AGTTTTTCTTTTTCTTGAGGGTCGAT 59.679 34.615 0.00 0.00 0.00 3.59
928 945 5.650703 AGTTTTTCTTTTTCTTGAGGGTCGA 59.349 36.000 0.00 0.00 0.00 4.20
929 946 5.743872 CAGTTTTTCTTTTTCTTGAGGGTCG 59.256 40.000 0.00 0.00 0.00 4.79
930 947 6.863275 TCAGTTTTTCTTTTTCTTGAGGGTC 58.137 36.000 0.00 0.00 0.00 4.46
931 948 6.850752 TCAGTTTTTCTTTTTCTTGAGGGT 57.149 33.333 0.00 0.00 0.00 4.34
932 949 7.168135 CGATTCAGTTTTTCTTTTTCTTGAGGG 59.832 37.037 0.00 0.00 0.00 4.30
933 950 7.915397 TCGATTCAGTTTTTCTTTTTCTTGAGG 59.085 33.333 0.00 0.00 0.00 3.86
934 951 8.841444 TCGATTCAGTTTTTCTTTTTCTTGAG 57.159 30.769 0.00 0.00 0.00 3.02
935 952 9.632807 TTTCGATTCAGTTTTTCTTTTTCTTGA 57.367 25.926 0.00 0.00 0.00 3.02
936 953 9.675553 GTTTCGATTCAGTTTTTCTTTTTCTTG 57.324 29.630 0.00 0.00 0.00 3.02
937 954 9.418045 TGTTTCGATTCAGTTTTTCTTTTTCTT 57.582 25.926 0.00 0.00 0.00 2.52
938 955 8.980143 TGTTTCGATTCAGTTTTTCTTTTTCT 57.020 26.923 0.00 0.00 0.00 2.52
939 956 9.675553 CTTGTTTCGATTCAGTTTTTCTTTTTC 57.324 29.630 0.00 0.00 0.00 2.29
952 969 2.869801 ACGAAGTGCTTGTTTCGATTCA 59.130 40.909 12.81 0.00 46.67 2.57
972 989 0.390472 CAAGCACGGGAGGAGAAGAC 60.390 60.000 0.00 0.00 0.00 3.01
989 1006 2.350895 CACCCATCCCGTCTGCAA 59.649 61.111 0.00 0.00 0.00 4.08
1134 1157 3.862845 TCGCGAATCGAATGAAGAAATCA 59.137 39.130 6.20 0.00 45.36 2.57
1147 1170 1.490693 CTGGGGTGAATCGCGAATCG 61.491 60.000 15.24 0.00 40.15 3.34
1162 1185 1.361668 CGATCGGAACAAGTGCTGGG 61.362 60.000 7.38 0.00 0.00 4.45
1167 1190 0.721718 GGAAGCGATCGGAACAAGTG 59.278 55.000 18.30 0.00 0.00 3.16
1212 1239 2.815647 GCCGCCTCGAAGAACAGG 60.816 66.667 0.00 0.00 34.09 4.00
1299 1326 4.404098 CCGTCCCCGTCCCAAAGG 62.404 72.222 0.00 0.00 0.00 3.11
1576 1623 1.591059 CGAGCTGGGATTGAGCGAG 60.591 63.158 0.00 0.00 41.61 5.03
1581 1628 2.688666 AGGGCGAGCTGGGATTGA 60.689 61.111 0.00 0.00 0.00 2.57
1662 1709 5.453339 CGAGCTTTATATCCTCCCAGTTCAA 60.453 44.000 0.00 0.00 0.00 2.69
1827 1874 8.574196 AAGAAATGAAAACGATGTTACTTTGG 57.426 30.769 0.00 0.00 0.00 3.28
1890 1937 2.105649 TGCTGGTCAGTAATGTGGTCAA 59.894 45.455 0.00 0.00 0.00 3.18
1891 1938 1.696884 TGCTGGTCAGTAATGTGGTCA 59.303 47.619 0.00 0.00 0.00 4.02
1892 1939 2.472695 TGCTGGTCAGTAATGTGGTC 57.527 50.000 0.00 0.00 0.00 4.02
1893 1940 3.519510 AGTATGCTGGTCAGTAATGTGGT 59.480 43.478 0.00 0.00 0.00 4.16
1894 1941 3.873361 CAGTATGCTGGTCAGTAATGTGG 59.127 47.826 2.35 0.00 39.01 4.17
1895 1942 4.568359 GTCAGTATGCTGGTCAGTAATGTG 59.432 45.833 11.15 0.00 42.78 3.21
1896 1943 4.383118 GGTCAGTATGCTGGTCAGTAATGT 60.383 45.833 11.15 0.00 42.78 2.71
1897 1944 4.122776 GGTCAGTATGCTGGTCAGTAATG 58.877 47.826 11.15 0.00 42.78 1.90
1898 1945 3.774766 TGGTCAGTATGCTGGTCAGTAAT 59.225 43.478 11.15 0.00 42.78 1.89
1899 1946 3.169908 TGGTCAGTATGCTGGTCAGTAA 58.830 45.455 11.15 0.00 42.78 2.24
1900 1947 2.760650 CTGGTCAGTATGCTGGTCAGTA 59.239 50.000 11.15 0.00 42.78 2.74
1901 1948 1.552337 CTGGTCAGTATGCTGGTCAGT 59.448 52.381 11.15 0.00 42.78 3.41
1902 1949 1.741732 GCTGGTCAGTATGCTGGTCAG 60.742 57.143 20.79 20.79 42.78 3.51
1903 1950 0.250234 GCTGGTCAGTATGCTGGTCA 59.750 55.000 11.15 8.55 42.78 4.02
1904 1951 0.539051 AGCTGGTCAGTATGCTGGTC 59.461 55.000 11.15 4.88 42.78 4.02
1905 1952 0.987294 AAGCTGGTCAGTATGCTGGT 59.013 50.000 11.15 0.00 42.78 4.00
1906 1953 2.555199 GTAAGCTGGTCAGTATGCTGG 58.445 52.381 11.15 0.00 42.78 4.85
1907 1954 2.196749 CGTAAGCTGGTCAGTATGCTG 58.803 52.381 4.14 4.14 43.87 4.41
1908 1955 1.137086 CCGTAAGCTGGTCAGTATGCT 59.863 52.381 0.00 0.00 37.37 3.79
1909 1956 1.571919 CCGTAAGCTGGTCAGTATGC 58.428 55.000 0.00 0.00 34.76 3.14
1910 1957 1.202533 CCCCGTAAGCTGGTCAGTATG 60.203 57.143 0.00 0.00 37.54 2.39
1911 1958 1.120530 CCCCGTAAGCTGGTCAGTAT 58.879 55.000 0.00 0.00 0.00 2.12
1912 1959 0.974010 CCCCCGTAAGCTGGTCAGTA 60.974 60.000 0.00 0.00 0.00 2.74
1913 1960 2.291043 CCCCCGTAAGCTGGTCAGT 61.291 63.158 0.00 0.00 0.00 3.41
1914 1961 2.291043 ACCCCCGTAAGCTGGTCAG 61.291 63.158 0.00 0.00 35.12 3.51
1915 1962 2.203877 ACCCCCGTAAGCTGGTCA 60.204 61.111 0.00 0.00 35.12 4.02
1916 1963 2.582978 GACCCCCGTAAGCTGGTC 59.417 66.667 3.15 3.15 45.13 4.02
1917 1964 1.988406 GAGACCCCCGTAAGCTGGT 60.988 63.158 0.00 0.00 41.61 4.00
1918 1965 1.961180 CTGAGACCCCCGTAAGCTGG 61.961 65.000 0.00 0.00 0.00 4.85
1919 1966 0.970937 TCTGAGACCCCCGTAAGCTG 60.971 60.000 0.00 0.00 0.00 4.24
1936 1983 2.781174 ACTCTCTTCCTCCGGTATCTCT 59.219 50.000 0.00 0.00 0.00 3.10
1974 2021 4.242475 AGAACAAAATACGCGAGATCACA 58.758 39.130 15.93 0.00 0.00 3.58
2041 2088 9.455847 TTGATGATATCGCATATTCTCGATAAG 57.544 33.333 12.58 0.00 46.46 1.73
2105 2153 4.035675 GCAGTCTGGCACCAAACTAATATC 59.964 45.833 1.14 0.00 0.00 1.63
2106 2154 3.947834 GCAGTCTGGCACCAAACTAATAT 59.052 43.478 1.14 0.00 0.00 1.28
2132 2251 5.790593 ACTAGTTTCAGCCACGAAGAATTA 58.209 37.500 0.00 0.00 0.00 1.40
2336 2456 2.011947 GCCCCTAGATTAAAACGCGTT 58.988 47.619 20.79 20.79 0.00 4.84
3017 3144 3.974757 ATAGCTACCGCCGCCGTC 61.975 66.667 0.00 0.00 36.60 4.79


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

AutoCloner maintained by Alex Coulton.