Multiple sequence alignment - TraesCS6D01G086800

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 TraesCS6D01G086800 chr6D 100.000 5975 0 0 1 5975 52335557 52341531 0.000000e+00 11034.0
1 TraesCS6D01G086800 chr6D 94.737 38 2 0 5413 5450 52340862 52340825 6.470000e-05 60.2
2 TraesCS6D01G086800 chr6D 94.737 38 2 0 5269 5306 52341006 52340969 6.470000e-05 60.2
3 TraesCS6D01G086800 chr6B 95.322 4211 144 23 1275 5465 119125894 119130071 0.000000e+00 6636.0
4 TraesCS6D01G086800 chr6B 92.260 323 12 5 948 1270 119125497 119125806 4.250000e-121 446.0
5 TraesCS6D01G086800 chr6B 92.965 199 11 1 5502 5697 119130066 119130264 2.730000e-73 287.0
6 TraesCS6D01G086800 chr6B 94.521 73 3 1 534 605 119125358 119125430 1.760000e-20 111.0
7 TraesCS6D01G086800 chr6A 96.498 3741 100 19 2252 5975 63117324 63121050 0.000000e+00 6154.0
8 TraesCS6D01G086800 chr6A 92.937 807 42 10 774 1578 63116512 63117305 0.000000e+00 1160.0
9 TraesCS6D01G086800 chr6A 88.148 540 35 18 1 526 63115470 63115994 3.060000e-172 616.0
10 TraesCS6D01G086800 chr6A 95.714 70 3 0 660 729 63116440 63116509 4.890000e-21 113.0
11 TraesCS6D01G086800 chr6A 100.000 51 0 0 570 620 63116389 63116439 1.770000e-15 95.3
12 TraesCS6D01G086800 chr6A 94.872 39 2 0 5412 5450 63120380 63120342 1.800000e-05 62.1
13 TraesCS6D01G086800 chr6A 92.105 38 3 0 5269 5306 63120523 63120486 3.000000e-03 54.7
14 TraesCS6D01G086800 chr1D 86.136 1320 131 33 3904 5206 245980877 245982161 0.000000e+00 1376.0
15 TraesCS6D01G086800 chr1D 84.134 1166 107 32 964 2113 245973632 245974735 0.000000e+00 1057.0
16 TraesCS6D01G086800 chr1D 88.140 860 56 16 2523 3341 245979356 245980210 0.000000e+00 981.0
17 TraesCS6D01G086800 chr1D 92.527 281 21 0 3340 3620 245980181 245980461 2.590000e-108 403.0
18 TraesCS6D01G086800 chr1D 93.038 158 7 3 2152 2308 245974723 245974877 1.680000e-55 228.0
19 TraesCS6D01G086800 chr1A 86.136 1320 131 30 3905 5206 306642596 306643881 0.000000e+00 1376.0
20 TraesCS6D01G086800 chr1A 86.569 1020 102 18 964 1975 306639429 306640421 0.000000e+00 1092.0
21 TraesCS6D01G086800 chr1A 89.480 846 57 12 2523 3341 306641089 306641929 0.000000e+00 1040.0
22 TraesCS6D01G086800 chr1A 92.553 282 20 1 3340 3620 306641900 306642181 2.590000e-108 403.0
23 TraesCS6D01G086800 chr1B 86.283 1181 112 32 3873 5037 332157799 332156653 0.000000e+00 1238.0
24 TraesCS6D01G086800 chr1B 87.890 1057 83 24 2328 3344 332159474 332158423 0.000000e+00 1201.0
25 TraesCS6D01G086800 chr1B 85.592 1173 121 21 962 2113 332161103 332159958 0.000000e+00 1186.0
26 TraesCS6D01G086800 chr1B 93.238 281 19 0 3340 3620 332158456 332158176 1.200000e-111 414.0
27 TraesCS6D01G086800 chr4A 100.000 29 0 0 2113 2141 570975750 570975722 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G086800 chr6D 52335557 52341531 5974 False 11034.00 11034 100.000000 1 5975 1 chr6D.!!$F1 5974
1 TraesCS6D01G086800 chr6B 119125358 119130264 4906 False 1870.00 6636 93.767000 534 5697 4 chr6B.!!$F1 5163
2 TraesCS6D01G086800 chr6A 63115470 63121050 5580 False 1627.66 6154 94.659400 1 5975 5 chr6A.!!$F1 5974
3 TraesCS6D01G086800 chr1D 245979356 245982161 2805 False 920.00 1376 88.934333 2523 5206 3 chr1D.!!$F2 2683
4 TraesCS6D01G086800 chr1D 245973632 245974877 1245 False 642.50 1057 88.586000 964 2308 2 chr1D.!!$F1 1344
5 TraesCS6D01G086800 chr1A 306639429 306643881 4452 False 977.75 1376 88.684500 964 5206 4 chr1A.!!$F1 4242
6 TraesCS6D01G086800 chr1B 332156653 332161103 4450 True 1009.75 1238 88.250750 962 5037 4 chr1B.!!$R1 4075

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
757 1148 0.315886 TTTGTAGCGACTGAGCGGAA 59.684 50.000 0.0 0.0 43.00 4.30 F
758 1149 0.388134 TTGTAGCGACTGAGCGGAAC 60.388 55.000 0.0 0.0 43.00 3.62 F
1721 2217 0.649475 CAAGAATGCGAGCGAGAAGG 59.351 55.000 0.0 0.0 0.00 3.46 F
1722 2218 1.086634 AAGAATGCGAGCGAGAAGGC 61.087 55.000 0.0 0.0 0.00 4.35 F
2783 3677 2.131776 TTGCCGTTCCCCGATTTTAT 57.868 45.000 0.0 0.0 39.56 1.40 F
3901 4950 1.876156 GACATCATCATTCGGCCTTCC 59.124 52.381 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 2287 0.037697 TCGGTTCGGGAGTTGATGTG 60.038 55.000 0.00 0.0 0.00 3.21 R
2120 2635 1.271379 GGAGCTTTCAGCACTGGGTAA 60.271 52.381 0.00 0.0 45.56 2.85 R
3165 4063 2.617274 GCGCGCTTGACTTCCCTTT 61.617 57.895 26.67 0.0 0.00 3.11 R
3468 4367 2.975489 TCATCTCTAGAGGCCAATTCCC 59.025 50.000 19.67 0.0 0.00 3.97 R
4519 5577 0.321671 CGACCTTCCTGGAGCAAGAA 59.678 55.000 0.00 0.0 39.71 2.52 R
5451 6529 0.734253 CAGTTCGAGGAGTCTTGCCG 60.734 60.000 0.00 0.0 0.00 5.69 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
78 79 0.904649 GGGCCAGCAAAATTTAGCCT 59.095 50.000 4.39 0.00 40.32 4.58
86 87 0.451783 AAAATTTAGCCTGCGAGCGG 59.548 50.000 0.00 0.00 38.01 5.52
89 90 0.676782 ATTTAGCCTGCGAGCGGTTT 60.677 50.000 3.03 0.00 38.01 3.27
90 91 1.296056 TTTAGCCTGCGAGCGGTTTC 61.296 55.000 3.03 0.00 38.01 2.78
116 117 4.156664 TGTCTCTTCGGTTTTCTAGTCG 57.843 45.455 0.00 0.00 0.00 4.18
117 118 2.916089 GTCTCTTCGGTTTTCTAGTCGC 59.084 50.000 0.00 0.00 0.00 5.19
126 127 3.058432 GGTTTTCTAGTCGCTTTTCACCC 60.058 47.826 0.00 0.00 0.00 4.61
127 128 3.478857 TTTCTAGTCGCTTTTCACCCA 57.521 42.857 0.00 0.00 0.00 4.51
128 129 2.743636 TCTAGTCGCTTTTCACCCAG 57.256 50.000 0.00 0.00 0.00 4.45
139 141 2.131776 TTCACCCAGAAAACGGTTGT 57.868 45.000 0.00 0.00 32.05 3.32
141 143 1.746220 TCACCCAGAAAACGGTTGTTG 59.254 47.619 0.00 0.00 38.62 3.33
142 144 1.474879 CACCCAGAAAACGGTTGTTGT 59.525 47.619 0.00 0.00 38.62 3.32
160 162 8.613482 GGTTGTTGTTTTTAGGAGCTAGATATC 58.387 37.037 0.00 0.00 0.00 1.63
543 923 0.472471 AAGAAACGTTCCCAGGAGCA 59.528 50.000 0.00 0.00 0.00 4.26
548 928 4.021925 GTTCCCAGGAGCACCGCT 62.022 66.667 0.00 0.00 43.88 5.52
565 946 1.641577 GCTCGTACCTGTAGGCAAAG 58.358 55.000 0.00 0.00 39.32 2.77
626 1017 5.221009 GGGACGTGTAAAAACATACCAACAA 60.221 40.000 0.00 0.00 0.00 2.83
628 1019 7.308469 GGGACGTGTAAAAACATACCAACAATA 60.308 37.037 0.00 0.00 0.00 1.90
630 1021 9.615295 GACGTGTAAAAACATACCAACAATATT 57.385 29.630 0.00 0.00 0.00 1.28
639 1030 9.541884 AAACATACCAACAATATTTTAGAGGGT 57.458 29.630 0.00 0.00 0.00 4.34
644 1035 8.747538 ACCAACAATATTTTAGAGGGTATGAC 57.252 34.615 0.00 0.00 0.00 3.06
645 1036 8.557450 ACCAACAATATTTTAGAGGGTATGACT 58.443 33.333 0.00 0.00 0.00 3.41
646 1037 9.408648 CCAACAATATTTTAGAGGGTATGACTT 57.591 33.333 0.00 0.00 0.00 3.01
653 1044 5.934402 TTAGAGGGTATGACTTTCAGTCC 57.066 43.478 1.46 0.00 44.44 3.85
654 1045 2.761208 AGAGGGTATGACTTTCAGTCCG 59.239 50.000 1.46 0.00 44.44 4.79
655 1046 1.831736 AGGGTATGACTTTCAGTCCGG 59.168 52.381 0.00 0.00 44.44 5.14
656 1047 1.134491 GGGTATGACTTTCAGTCCGGG 60.134 57.143 0.00 0.00 44.44 5.73
657 1048 1.134491 GGTATGACTTTCAGTCCGGGG 60.134 57.143 0.00 0.00 44.44 5.73
658 1049 0.539986 TATGACTTTCAGTCCGGGGC 59.460 55.000 0.00 0.00 44.44 5.80
729 1120 5.231779 CGAACTAAACGTCGATCTCTCTCTA 59.768 44.000 0.00 0.00 0.00 2.43
731 1122 6.774354 ACTAAACGTCGATCTCTCTCTATC 57.226 41.667 0.00 0.00 0.00 2.08
732 1123 6.518493 ACTAAACGTCGATCTCTCTCTATCT 58.482 40.000 0.00 0.00 0.00 1.98
733 1124 5.666969 AAACGTCGATCTCTCTCTATCTG 57.333 43.478 0.00 0.00 0.00 2.90
735 1126 3.322541 ACGTCGATCTCTCTCTATCTGGA 59.677 47.826 0.00 0.00 0.00 3.86
736 1127 3.678072 CGTCGATCTCTCTCTATCTGGAC 59.322 52.174 0.00 0.00 0.00 4.02
737 1128 3.678072 GTCGATCTCTCTCTATCTGGACG 59.322 52.174 0.00 0.00 0.00 4.79
738 1129 3.322541 TCGATCTCTCTCTATCTGGACGT 59.677 47.826 0.00 0.00 0.00 4.34
739 1130 4.062293 CGATCTCTCTCTATCTGGACGTT 58.938 47.826 0.00 0.00 0.00 3.99
740 1131 4.513692 CGATCTCTCTCTATCTGGACGTTT 59.486 45.833 0.00 0.00 0.00 3.60
741 1132 5.559991 CGATCTCTCTCTATCTGGACGTTTG 60.560 48.000 0.00 0.00 0.00 2.93
742 1133 4.590918 TCTCTCTCTATCTGGACGTTTGT 58.409 43.478 0.00 0.00 0.00 2.83
743 1134 5.742063 TCTCTCTCTATCTGGACGTTTGTA 58.258 41.667 0.00 0.00 0.00 2.41
744 1135 5.818336 TCTCTCTCTATCTGGACGTTTGTAG 59.182 44.000 0.00 0.00 0.00 2.74
745 1136 4.335874 TCTCTCTATCTGGACGTTTGTAGC 59.664 45.833 0.00 0.00 0.00 3.58
746 1137 3.064958 TCTCTATCTGGACGTTTGTAGCG 59.935 47.826 0.00 0.00 0.00 4.26
747 1138 3.011818 TCTATCTGGACGTTTGTAGCGA 58.988 45.455 0.00 0.00 0.00 4.93
748 1139 1.992170 ATCTGGACGTTTGTAGCGAC 58.008 50.000 0.00 0.00 0.00 5.19
749 1140 0.956633 TCTGGACGTTTGTAGCGACT 59.043 50.000 0.00 0.00 0.00 4.18
750 1141 1.060713 CTGGACGTTTGTAGCGACTG 58.939 55.000 0.00 0.00 0.00 3.51
751 1142 0.669619 TGGACGTTTGTAGCGACTGA 59.330 50.000 0.00 0.00 0.00 3.41
752 1143 1.335597 TGGACGTTTGTAGCGACTGAG 60.336 52.381 0.00 0.00 0.00 3.35
753 1144 0.708918 GACGTTTGTAGCGACTGAGC 59.291 55.000 0.00 0.00 37.41 4.26
754 1145 1.002250 ACGTTTGTAGCGACTGAGCG 61.002 55.000 0.00 3.89 43.00 5.03
755 1146 1.674611 CGTTTGTAGCGACTGAGCGG 61.675 60.000 0.00 0.00 43.00 5.52
756 1147 0.388134 GTTTGTAGCGACTGAGCGGA 60.388 55.000 0.00 0.00 43.00 5.54
757 1148 0.315886 TTTGTAGCGACTGAGCGGAA 59.684 50.000 0.00 0.00 43.00 4.30
758 1149 0.388134 TTGTAGCGACTGAGCGGAAC 60.388 55.000 0.00 0.00 43.00 3.62
1097 1494 2.591753 GCATCAGCAGGCTGGGTA 59.408 61.111 20.19 2.59 43.75 3.69
1263 1664 5.307196 ACTCCTGCTTTCTTTGGTTCTACTA 59.693 40.000 0.00 0.00 0.00 1.82
1264 1665 5.548406 TCCTGCTTTCTTTGGTTCTACTAC 58.452 41.667 0.00 0.00 0.00 2.73
1265 1666 5.307196 TCCTGCTTTCTTTGGTTCTACTACT 59.693 40.000 0.00 0.00 0.00 2.57
1269 1670 8.135382 TGCTTTCTTTGGTTCTACTACTCTAT 57.865 34.615 0.00 0.00 0.00 1.98
1312 1796 4.551702 TGTGATTTGGCTAGCAGAGTTA 57.448 40.909 18.24 0.00 0.00 2.24
1319 1803 6.377327 TTTGGCTAGCAGAGTTATTTATGC 57.623 37.500 18.24 0.00 38.97 3.14
1329 1813 9.442047 AGCAGAGTTATTTATGCATACTTATCC 57.558 33.333 5.74 0.00 41.14 2.59
1381 1865 3.497332 TGTCTGCTCGCCTAGGTAATAT 58.503 45.455 11.31 0.00 0.00 1.28
1441 1925 1.202698 ACTGACAGGTTGAGGAACTGC 60.203 52.381 7.51 0.00 41.55 4.40
1534 2020 2.380102 GCATACGCTCTGCTTGATTG 57.620 50.000 0.00 0.00 36.68 2.67
1553 2039 7.928908 TGATTGCTTGTACATTTTCTTTGTC 57.071 32.000 0.00 0.00 0.00 3.18
1554 2040 7.715657 TGATTGCTTGTACATTTTCTTTGTCT 58.284 30.769 0.00 0.00 0.00 3.41
1558 2044 7.715657 TGCTTGTACATTTTCTTTGTCTGAAT 58.284 30.769 0.00 0.00 0.00 2.57
1619 2105 8.610248 TTTTGTGAATATCTGTCCTTCGTTAA 57.390 30.769 0.00 0.00 0.00 2.01
1624 2120 9.704098 GTGAATATCTGTCCTTCGTTAATTTTC 57.296 33.333 0.00 0.00 0.00 2.29
1713 2209 1.917273 CCAAATGCCAAGAATGCGAG 58.083 50.000 0.00 0.00 0.00 5.03
1721 2217 0.649475 CAAGAATGCGAGCGAGAAGG 59.351 55.000 0.00 0.00 0.00 3.46
1722 2218 1.086634 AAGAATGCGAGCGAGAAGGC 61.087 55.000 0.00 0.00 0.00 4.35
1781 2277 6.878389 GCCAAGTATGAATTCCCAAAATCAAA 59.122 34.615 2.27 0.00 28.45 2.69
1782 2278 7.390162 GCCAAGTATGAATTCCCAAAATCAAAA 59.610 33.333 2.27 0.00 28.45 2.44
1789 2287 7.216494 TGAATTCCCAAAATCAAAAGAGTTCC 58.784 34.615 2.27 0.00 0.00 3.62
1799 2297 6.566197 ATCAAAAGAGTTCCACATCAACTC 57.434 37.500 4.69 4.69 46.99 3.01
1893 2391 7.905604 TCATCGTTGTTTCACTCATTATCTT 57.094 32.000 0.00 0.00 0.00 2.40
1894 2392 7.963981 TCATCGTTGTTTCACTCATTATCTTC 58.036 34.615 0.00 0.00 0.00 2.87
1895 2393 6.721571 TCGTTGTTTCACTCATTATCTTCC 57.278 37.500 0.00 0.00 0.00 3.46
1896 2394 6.227522 TCGTTGTTTCACTCATTATCTTCCA 58.772 36.000 0.00 0.00 0.00 3.53
1897 2395 6.708502 TCGTTGTTTCACTCATTATCTTCCAA 59.291 34.615 0.00 0.00 0.00 3.53
1898 2396 7.227711 TCGTTGTTTCACTCATTATCTTCCAAA 59.772 33.333 0.00 0.00 0.00 3.28
1899 2397 7.860373 CGTTGTTTCACTCATTATCTTCCAAAA 59.140 33.333 0.00 0.00 0.00 2.44
1900 2398 8.968242 GTTGTTTCACTCATTATCTTCCAAAAC 58.032 33.333 0.00 0.00 0.00 2.43
1901 2399 8.231692 TGTTTCACTCATTATCTTCCAAAACA 57.768 30.769 0.00 0.00 32.34 2.83
1902 2400 8.859090 TGTTTCACTCATTATCTTCCAAAACAT 58.141 29.630 0.00 0.00 30.48 2.71
1903 2401 9.346725 GTTTCACTCATTATCTTCCAAAACATC 57.653 33.333 0.00 0.00 0.00 3.06
1904 2402 8.868522 TTCACTCATTATCTTCCAAAACATCT 57.131 30.769 0.00 0.00 0.00 2.90
1945 2460 6.202226 GCTTAAGCCATTTCATGTAGCTAAC 58.798 40.000 17.00 0.00 32.39 2.34
2120 2635 6.860790 TTTAGTTTGACCAAGAAAAGGGTT 57.139 33.333 0.00 0.00 37.57 4.11
2230 2746 6.522054 TCGTTGAATTCCTAATGGTATCTCC 58.478 40.000 2.27 0.00 34.23 3.71
2281 2797 8.655651 TTGGTCTAATTGTTGGTCAAATTTTC 57.344 30.769 0.00 0.00 39.62 2.29
2420 3264 6.237861 GCGAAGTTAGTAGCTCAATTTACCAG 60.238 42.308 0.00 0.00 0.00 4.00
2448 3299 7.147302 ACTGGATTTATGACCTTTATACAGGCT 60.147 37.037 4.76 0.00 37.47 4.58
2454 3305 9.914834 TTTATGACCTTTATACAGGCTGTTAAT 57.085 29.630 27.24 16.49 37.47 1.40
2729 3623 2.645838 ATGCATATCCACCACCAGAC 57.354 50.000 0.00 0.00 0.00 3.51
2783 3677 2.131776 TTGCCGTTCCCCGATTTTAT 57.868 45.000 0.00 0.00 39.56 1.40
3084 3982 2.560981 TCTTCTGATGTTCGTGCCACTA 59.439 45.455 0.00 0.00 0.00 2.74
3468 4367 4.083271 TGCTGATCGGAGTATTATCGACAG 60.083 45.833 5.48 0.00 36.34 3.51
3756 4743 8.803235 ACTTTATTTGGTCCTTTTTATCTGGAC 58.197 33.333 0.00 0.00 46.83 4.02
3892 4941 9.794719 ACAATGATCAGAATAGACATCATCATT 57.205 29.630 0.09 0.00 39.13 2.57
3901 4950 1.876156 GACATCATCATTCGGCCTTCC 59.124 52.381 0.00 0.00 0.00 3.46
4176 5228 7.967854 TGAGTACTGTGTTTCTTGAAATGTTTG 59.032 33.333 0.00 0.00 0.00 2.93
4181 5233 9.950680 ACTGTGTTTCTTGAAATGTTTGTATAG 57.049 29.630 0.00 0.00 0.00 1.31
4222 5275 3.820467 TGCGTTCTCATTTCCTCACATTT 59.180 39.130 0.00 0.00 0.00 2.32
4519 5577 7.083875 TCGTTCTGTTTCTGAAATTTTCTGT 57.916 32.000 6.06 0.00 0.00 3.41
4572 5630 2.293399 AGCTTTTGTGACGTTTCCATCC 59.707 45.455 0.00 0.00 0.00 3.51
4780 5843 2.124277 AGGGAAAACATCTAACGCCC 57.876 50.000 0.00 0.00 0.00 6.13
4785 5848 3.304861 GGAAAACATCTAACGCCCGTTTT 60.305 43.478 11.54 0.00 41.20 2.43
4872 5939 3.010138 AGCAGGGGTGCTAAAGAATAACA 59.990 43.478 0.00 0.00 44.28 2.41
5207 6285 5.801380 ACAAATTCTGTACCATTCTACGGT 58.199 37.500 0.00 0.00 36.10 4.83
5451 6529 2.437651 CCCTCTCCTCCAAATCTTCCTC 59.562 54.545 0.00 0.00 0.00 3.71
5465 6543 1.595993 TTCCTCGGCAAGACTCCTCG 61.596 60.000 0.00 0.00 0.00 4.63
5619 6700 1.006571 GGTTTCGACTGCGTCTCCA 60.007 57.895 7.03 0.00 38.98 3.86
5683 6764 1.324736 GCCACGCGAATCTAACTCTTG 59.675 52.381 15.93 0.00 0.00 3.02
5778 6859 4.817936 ATGCAATTTGGCGGCGGC 62.818 61.111 27.76 27.76 36.28 6.53
5842 6923 2.205074 CTTTACGGATCTGCGCTCATT 58.795 47.619 9.73 0.00 0.00 2.57
5851 6932 4.084118 GGATCTGCGCTCATTGATACTTTC 60.084 45.833 9.73 0.00 0.00 2.62
5855 6936 2.033662 GCGCTCATTGATACTTTCGGTC 60.034 50.000 0.00 0.00 0.00 4.79
5897 6978 1.561076 TGATATTGGCTCTGTGCAGGT 59.439 47.619 3.96 0.00 45.15 4.00
5967 7048 2.611473 CGAGATGTGGGTGGATGATAGC 60.611 54.545 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 0.451783 CCGCTCGCAGGCTAAATTTT 59.548 50.000 0.00 0.00 0.00 1.82
68 69 0.676782 ACCGCTCGCAGGCTAAATTT 60.677 50.000 0.00 0.00 0.00 1.82
78 79 0.736053 ACAAAAAGAAACCGCTCGCA 59.264 45.000 0.00 0.00 0.00 5.10
86 87 7.027760 AGAAAACCGAAGAGACAAAAAGAAAC 58.972 34.615 0.00 0.00 0.00 2.78
89 90 7.046033 ACTAGAAAACCGAAGAGACAAAAAGA 58.954 34.615 0.00 0.00 0.00 2.52
90 91 7.247929 ACTAGAAAACCGAAGAGACAAAAAG 57.752 36.000 0.00 0.00 0.00 2.27
126 127 6.094061 TCCTAAAAACAACAACCGTTTTCTG 58.906 36.000 1.86 0.00 43.82 3.02
127 128 6.270156 TCCTAAAAACAACAACCGTTTTCT 57.730 33.333 1.86 0.00 43.82 2.52
128 129 5.005012 GCTCCTAAAAACAACAACCGTTTTC 59.995 40.000 1.86 0.00 43.82 2.29
134 136 6.819397 ATCTAGCTCCTAAAAACAACAACC 57.181 37.500 0.00 0.00 0.00 3.77
510 523 8.408601 GGGAACGTTTCTTATAGTATACAGTGA 58.591 37.037 6.53 0.00 0.00 3.41
526 539 1.235281 GGTGCTCCTGGGAACGTTTC 61.235 60.000 0.46 0.00 0.00 2.78
528 541 2.430367 GGTGCTCCTGGGAACGTT 59.570 61.111 0.00 0.00 0.00 3.99
529 542 4.003788 CGGTGCTCCTGGGAACGT 62.004 66.667 2.85 0.00 41.55 3.99
531 544 4.021925 AGCGGTGCTCCTGGGAAC 62.022 66.667 2.85 0.00 30.62 3.62
543 923 2.413142 GCCTACAGGTACGAGCGGT 61.413 63.158 0.00 0.00 37.57 5.68
548 928 1.200716 CGTCTTTGCCTACAGGTACGA 59.799 52.381 0.00 0.00 37.57 3.43
565 946 2.499827 CCTAGGGCCCAGCTACGTC 61.500 68.421 27.56 0.00 0.00 4.34
644 1035 4.697756 TGCGCCCCGGACTGAAAG 62.698 66.667 0.73 0.00 42.29 2.62
645 1036 4.697756 CTGCGCCCCGGACTGAAA 62.698 66.667 0.73 0.00 0.00 2.69
657 1048 2.870372 CAAACTACTGGGCTGCGC 59.130 61.111 10.06 10.06 0.00 6.09
658 1049 2.690778 GGCAAACTACTGGGCTGCG 61.691 63.158 0.00 0.00 33.76 5.18
697 1088 0.601841 ACGTTTAGTTCGTGGGCTGG 60.602 55.000 0.00 0.00 40.07 4.85
706 1097 5.473796 AGAGAGAGATCGACGTTTAGTTC 57.526 43.478 0.00 0.00 0.00 3.01
729 1120 1.544691 AGTCGCTACAAACGTCCAGAT 59.455 47.619 0.00 0.00 0.00 2.90
731 1122 1.060713 CAGTCGCTACAAACGTCCAG 58.939 55.000 0.00 0.00 0.00 3.86
732 1123 0.669619 TCAGTCGCTACAAACGTCCA 59.330 50.000 0.00 0.00 0.00 4.02
733 1124 1.337821 CTCAGTCGCTACAAACGTCC 58.662 55.000 0.00 0.00 0.00 4.79
735 1126 1.002250 CGCTCAGTCGCTACAAACGT 61.002 55.000 0.00 0.00 0.00 3.99
736 1127 1.674611 CCGCTCAGTCGCTACAAACG 61.675 60.000 0.00 0.00 0.00 3.60
737 1128 0.388134 TCCGCTCAGTCGCTACAAAC 60.388 55.000 0.00 0.00 0.00 2.93
738 1129 0.315886 TTCCGCTCAGTCGCTACAAA 59.684 50.000 0.00 0.00 0.00 2.83
739 1130 0.388134 GTTCCGCTCAGTCGCTACAA 60.388 55.000 0.00 0.00 0.00 2.41
740 1131 1.211969 GTTCCGCTCAGTCGCTACA 59.788 57.895 0.00 0.00 0.00 2.74
741 1132 1.868251 CGTTCCGCTCAGTCGCTAC 60.868 63.158 0.00 0.00 0.00 3.58
742 1133 2.036571 TCGTTCCGCTCAGTCGCTA 61.037 57.895 0.00 0.00 0.00 4.26
743 1134 3.362797 TCGTTCCGCTCAGTCGCT 61.363 61.111 0.00 0.00 0.00 4.93
744 1135 3.173240 GTCGTTCCGCTCAGTCGC 61.173 66.667 0.00 0.00 0.00 5.19
745 1136 2.504244 GGTCGTTCCGCTCAGTCG 60.504 66.667 0.00 0.00 0.00 4.18
746 1137 2.126031 GGGTCGTTCCGCTCAGTC 60.126 66.667 0.00 0.00 37.00 3.51
747 1138 3.692406 GGGGTCGTTCCGCTCAGT 61.692 66.667 8.57 0.00 44.48 3.41
753 1144 3.009612 TTTTTGAGGGGTCGTTCCG 57.990 52.632 0.00 0.00 37.00 4.30
787 1178 2.504244 GGTGTCTCGTTCCGCTCG 60.504 66.667 0.00 0.00 0.00 5.03
792 1183 2.047179 GGGCAGGTGTCTCGTTCC 60.047 66.667 0.00 0.00 0.00 3.62
796 1187 3.374402 AGTCGGGCAGGTGTCTCG 61.374 66.667 0.00 0.00 0.00 4.04
881 1272 4.954118 TGAGTGGGAGGGTGCGGT 62.954 66.667 0.00 0.00 0.00 5.68
1070 1467 3.260483 GCTGATGCAGAGGCGACG 61.260 66.667 0.00 0.00 45.35 5.12
1071 1468 2.125391 TGCTGATGCAGAGGCGAC 60.125 61.111 0.00 0.00 45.31 5.19
1180 1577 3.039202 GAAAGGATGTGGCGCCGTG 62.039 63.158 23.90 0.00 0.00 4.94
1319 1803 9.846248 CAAAGAACTTCTTTTGGGATAAGTATG 57.154 33.333 13.19 0.00 43.62 2.39
1422 1906 1.517242 GCAGTTCCTCAACCTGTCAG 58.483 55.000 0.00 0.00 32.22 3.51
1441 1925 1.807742 TCCCTAAAATCCACAAACGCG 59.192 47.619 3.53 3.53 0.00 6.01
1534 2020 8.579682 AATTCAGACAAAGAAAATGTACAAGC 57.420 30.769 0.00 0.00 0.00 4.01
1740 2236 3.512516 GCACTTGAGGCATCCCGC 61.513 66.667 0.00 0.00 41.28 6.13
1781 2277 2.289694 CGGGAGTTGATGTGGAACTCTT 60.290 50.000 11.35 0.00 45.82 2.85
1782 2278 1.276421 CGGGAGTTGATGTGGAACTCT 59.724 52.381 11.35 0.00 45.82 3.24
1789 2287 0.037697 TCGGTTCGGGAGTTGATGTG 60.038 55.000 0.00 0.00 0.00 3.21
1893 2391 6.379703 TCACAAGAAAAGGAAGATGTTTTGGA 59.620 34.615 0.00 0.00 0.00 3.53
1894 2392 6.572519 TCACAAGAAAAGGAAGATGTTTTGG 58.427 36.000 0.00 0.00 0.00 3.28
1895 2393 7.113965 CGATCACAAGAAAAGGAAGATGTTTTG 59.886 37.037 0.00 0.00 0.00 2.44
1896 2394 7.141363 CGATCACAAGAAAAGGAAGATGTTTT 58.859 34.615 0.00 0.00 0.00 2.43
1897 2395 6.672147 CGATCACAAGAAAAGGAAGATGTTT 58.328 36.000 0.00 0.00 0.00 2.83
1898 2396 5.335191 GCGATCACAAGAAAAGGAAGATGTT 60.335 40.000 0.00 0.00 0.00 2.71
1899 2397 4.154918 GCGATCACAAGAAAAGGAAGATGT 59.845 41.667 0.00 0.00 0.00 3.06
1900 2398 4.394300 AGCGATCACAAGAAAAGGAAGATG 59.606 41.667 0.00 0.00 0.00 2.90
1901 2399 4.583871 AGCGATCACAAGAAAAGGAAGAT 58.416 39.130 0.00 0.00 0.00 2.40
1902 2400 4.008074 AGCGATCACAAGAAAAGGAAGA 57.992 40.909 0.00 0.00 0.00 2.87
1903 2401 4.756084 AAGCGATCACAAGAAAAGGAAG 57.244 40.909 0.00 0.00 0.00 3.46
1904 2402 5.334879 GCTTAAGCGATCACAAGAAAAGGAA 60.335 40.000 12.53 0.00 0.00 3.36
2120 2635 1.271379 GGAGCTTTCAGCACTGGGTAA 60.271 52.381 0.00 0.00 45.56 2.85
2223 2739 5.992217 GGGTTATGTGACATGAAGGAGATAC 59.008 44.000 8.61 0.00 0.00 2.24
2230 2746 5.902613 AATGTGGGTTATGTGACATGAAG 57.097 39.130 8.61 0.00 0.00 3.02
2281 2797 2.038820 AGGTGCCCACAAATTCCAAATG 59.961 45.455 0.40 0.00 0.00 2.32
2420 3264 9.490379 CCTGTATAAAGGTCATAAATCCAGTAC 57.510 37.037 0.03 0.00 32.17 2.73
2448 3299 6.349777 GGCCATAAACACTTGCACTATTAACA 60.350 38.462 0.00 0.00 0.00 2.41
2454 3305 3.147553 TGGCCATAAACACTTGCACTA 57.852 42.857 0.00 0.00 0.00 2.74
2504 3355 5.904362 AGTGGTTTGCTAGATTGATTTCC 57.096 39.130 0.00 0.00 0.00 3.13
2729 3623 9.566530 TTGACAATATTGTTCAATATGTTTCCG 57.433 29.630 21.63 6.41 42.43 4.30
2783 3677 9.920946 AGGCTGAAATTCTAATAAACCTGATTA 57.079 29.630 0.00 0.00 0.00 1.75
3084 3982 7.826690 ACAAACTGAAAGATACAAACACAAGT 58.173 30.769 0.00 0.00 37.43 3.16
3165 4063 2.617274 GCGCGCTTGACTTCCCTTT 61.617 57.895 26.67 0.00 0.00 3.11
3468 4367 2.975489 TCATCTCTAGAGGCCAATTCCC 59.025 50.000 19.67 0.00 0.00 3.97
3753 4740 5.163814 GCCAATTATTAGCATCTCATCGTCC 60.164 44.000 0.00 0.00 0.00 4.79
3756 4743 5.640783 TCTGCCAATTATTAGCATCTCATCG 59.359 40.000 0.00 0.00 35.64 3.84
3833 4820 6.730977 ACATAATAGACCCCACTACATAGCAT 59.269 38.462 0.00 0.00 0.00 3.79
3910 4959 4.391523 GCATTTGCCCATTGTTTTTCGTAT 59.608 37.500 0.00 0.00 34.31 3.06
3911 4960 3.743396 GCATTTGCCCATTGTTTTTCGTA 59.257 39.130 0.00 0.00 34.31 3.43
4017 5067 1.228337 AGACAAGCATGTGCCAGCA 60.228 52.632 0.00 0.00 40.74 4.41
4094 5146 7.884877 AGAAGTCATCATGAACAACATCCTTTA 59.115 33.333 0.00 0.00 37.07 1.85
4222 5275 6.772716 AGATCCTGTTAAGAGCAGTTTGAAAA 59.227 34.615 0.00 0.00 32.41 2.29
4519 5577 0.321671 CGACCTTCCTGGAGCAAGAA 59.678 55.000 0.00 0.00 39.71 2.52
4827 5890 6.259829 GCTTCTCAAGGACTGAATAAGGAATC 59.740 42.308 0.00 0.00 32.17 2.52
5024 6097 2.969821 TACCCACAATCTTGGTTGCT 57.030 45.000 0.00 0.00 34.44 3.91
5077 6153 5.107607 CGATAAGTGCCGTTATATTCCACAC 60.108 44.000 0.00 0.00 0.00 3.82
5451 6529 0.734253 CAGTTCGAGGAGTCTTGCCG 60.734 60.000 0.00 0.00 0.00 5.69
5465 6543 1.275657 CGCGTGTGTTGGACAGTTC 59.724 57.895 0.00 0.00 34.28 3.01
5641 6722 3.940480 TGGGAGAGTGGGGAGGCA 61.940 66.667 0.00 0.00 0.00 4.75
5650 6731 2.932234 CGTGGCGAAGTGGGAGAGT 61.932 63.158 0.00 0.00 0.00 3.24
5652 6733 4.373116 GCGTGGCGAAGTGGGAGA 62.373 66.667 0.00 0.00 0.00 3.71
5673 6754 6.798427 AGTATCCAAGATGCAAGAGTTAGA 57.202 37.500 0.00 0.00 0.00 2.10
5683 6764 4.058817 CCGGAAGTTAGTATCCAAGATGC 58.941 47.826 0.00 0.00 35.34 3.91
5778 6859 1.446099 CACGACGATGTGGGTCCAG 60.446 63.158 0.00 0.00 36.20 3.86
5809 6890 1.604693 CCGTAAAGCCAGACTCACGTT 60.605 52.381 0.00 0.00 0.00 3.99
5842 6923 3.587797 AGAAAGCGACCGAAAGTATCA 57.412 42.857 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.