Multiple sequence alignment - TraesCS1B01G017700

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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 TraesCS1B01G017700 chr1B 100.000 1489 0 0 844 2332 8658466 8659954 0.000000e+00 2750.0
1 TraesCS1B01G017700 chr1B 100.000 501 0 0 1 501 8657623 8658123 0.000000e+00 926.0
2 TraesCS1B01G017700 chr1B 86.000 200 18 7 1140 1331 51590260 51590457 3.040000e-49 206.0
3 TraesCS1B01G017700 chr1A 82.195 1449 165 51 923 2330 7642645 7644041 0.000000e+00 1160.0
4 TraesCS1B01G017700 chr1A 81.788 593 66 31 859 1429 7962355 7962927 2.110000e-125 459.0
5 TraesCS1B01G017700 chr1A 79.618 471 25 29 52 501 7642081 7642501 2.950000e-69 272.0
6 TraesCS1B01G017700 chr1A 85.279 197 16 11 1144 1331 32451564 32451756 8.510000e-45 191.0
7 TraesCS1B01G017700 chr1A 93.651 63 4 0 325 387 7962120 7962182 6.860000e-16 95.3
8 TraesCS1B01G017700 chr7B 85.496 393 30 10 942 1322 452468120 452468497 3.640000e-103 385.0
9 TraesCS1B01G017700 chr1D 84.304 395 31 24 956 1337 6548480 6548104 7.920000e-95 357.0
10 TraesCS1B01G017700 chr1D 81.663 409 38 21 950 1334 6399957 6399562 2.910000e-79 305.0
11 TraesCS1B01G017700 chr1D 87.179 195 16 6 1144 1331 33712464 33712656 1.820000e-51 213.0
12 TraesCS1B01G017700 chr1D 85.204 196 18 8 1144 1331 33663996 33664188 8.510000e-45 191.0


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 TraesCS1B01G017700 chr1B 8657623 8659954 2331 False 1838.00 2750 100.0000 1 2332 2 chr1B.!!$F2 2331
1 TraesCS1B01G017700 chr1A 7642081 7644041 1960 False 716.00 1160 80.9065 52 2330 2 chr1A.!!$F2 2278
2 TraesCS1B01G017700 chr1A 7962120 7962927 807 False 277.15 459 87.7195 325 1429 2 chr1A.!!$F3 1104

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
221 226 0.17576 TATCTGCTTGTCGTCCTGCC 59.824 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1425 0.031994 GCAGTCTAGCTAGCCAGAGC 59.968 60.0 13.48 10.54 43.19 4.09 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
21 22 4.992381 AGCGTTTAGATCACTGAAACAC 57.008 40.909 0.00 0.00 33.57 3.32
22 23 4.632153 AGCGTTTAGATCACTGAAACACT 58.368 39.130 0.00 0.00 33.57 3.55
23 24 4.686554 AGCGTTTAGATCACTGAAACACTC 59.313 41.667 0.00 0.00 33.57 3.51
24 25 4.447724 GCGTTTAGATCACTGAAACACTCA 59.552 41.667 0.00 0.00 33.57 3.41
25 26 5.120830 GCGTTTAGATCACTGAAACACTCAT 59.879 40.000 0.00 0.00 33.57 2.90
26 27 6.310467 GCGTTTAGATCACTGAAACACTCATA 59.690 38.462 0.00 0.00 33.57 2.15
27 28 7.010552 GCGTTTAGATCACTGAAACACTCATAT 59.989 37.037 0.00 0.00 33.57 1.78
28 29 8.873830 CGTTTAGATCACTGAAACACTCATATT 58.126 33.333 0.00 0.00 33.57 1.28
33 34 9.512588 AGATCACTGAAACACTCATATTTTTCT 57.487 29.630 0.00 0.00 32.14 2.52
85 86 8.612619 GCGAATATTACATATAGATGGTTTGGG 58.387 37.037 1.85 0.00 37.39 4.12
88 89 5.654901 TTACATATAGATGGTTTGGGGCA 57.345 39.130 1.85 0.00 37.39 5.36
109 110 4.036498 GCAGATCATATGGATTGCCTATGC 59.964 45.833 2.13 0.00 36.00 3.14
120 121 1.240641 TGCCTATGCACAACCGTTGG 61.241 55.000 15.60 5.90 44.23 3.77
121 122 1.241315 GCCTATGCACAACCGTTGGT 61.241 55.000 15.60 0.00 35.61 3.67
131 132 2.290008 ACAACCGTTGGTGCAGATCATA 60.290 45.455 15.60 0.00 35.34 2.15
147 152 6.735968 GCAGATCATACACTACTGATTCGGAA 60.736 42.308 0.00 0.00 32.36 4.30
178 183 2.753043 CCCATGGCCACAGCTGAC 60.753 66.667 23.35 9.20 39.73 3.51
188 193 4.641645 CAGCTGACGGGGTGGCAA 62.642 66.667 8.42 0.00 0.00 4.52
189 194 4.643387 AGCTGACGGGGTGGCAAC 62.643 66.667 0.00 0.00 0.00 4.17
191 196 3.953775 CTGACGGGGTGGCAACCT 61.954 66.667 23.12 1.09 46.70 3.50
192 197 3.491598 CTGACGGGGTGGCAACCTT 62.492 63.158 23.12 8.95 46.70 3.50
193 198 2.119484 CTGACGGGGTGGCAACCTTA 62.119 60.000 23.12 4.51 46.70 2.69
194 199 1.301954 GACGGGGTGGCAACCTTAT 59.698 57.895 23.12 7.03 46.70 1.73
195 200 0.746923 GACGGGGTGGCAACCTTATC 60.747 60.000 23.12 12.73 46.70 1.75
196 201 1.453197 CGGGGTGGCAACCTTATCC 60.453 63.158 23.12 2.69 46.70 2.59
197 202 1.694856 GGGGTGGCAACCTTATCCA 59.305 57.895 23.12 0.00 46.70 3.41
198 203 0.395724 GGGGTGGCAACCTTATCCAG 60.396 60.000 23.12 0.00 46.70 3.86
216 221 2.480416 CCAGGTCTATCTGCTTGTCGTC 60.480 54.545 0.00 0.00 33.64 4.20
217 222 1.751924 AGGTCTATCTGCTTGTCGTCC 59.248 52.381 0.00 0.00 0.00 4.79
218 223 1.751924 GGTCTATCTGCTTGTCGTCCT 59.248 52.381 0.00 0.00 0.00 3.85
219 224 2.480416 GGTCTATCTGCTTGTCGTCCTG 60.480 54.545 0.00 0.00 0.00 3.86
220 225 1.135139 TCTATCTGCTTGTCGTCCTGC 59.865 52.381 0.00 0.00 0.00 4.85
221 226 0.175760 TATCTGCTTGTCGTCCTGCC 59.824 55.000 0.00 0.00 0.00 4.85
223 228 3.573772 CTGCTTGTCGTCCTGCCGA 62.574 63.158 0.00 0.00 33.79 5.54
226 231 1.874019 CTTGTCGTCCTGCCGATCG 60.874 63.158 8.51 8.51 39.34 3.69
227 232 2.266376 CTTGTCGTCCTGCCGATCGA 62.266 60.000 18.66 0.00 39.34 3.59
228 233 1.663379 TTGTCGTCCTGCCGATCGAT 61.663 55.000 18.66 0.00 39.34 3.59
229 234 1.370657 GTCGTCCTGCCGATCGATC 60.371 63.158 18.66 15.68 39.34 3.69
231 236 2.340443 GTCCTGCCGATCGATCCC 59.660 66.667 18.66 11.25 0.00 3.85
232 237 2.917751 TCCTGCCGATCGATCCCC 60.918 66.667 18.66 10.90 0.00 4.81
233 238 2.919856 CCTGCCGATCGATCCCCT 60.920 66.667 18.66 0.00 0.00 4.79
234 239 2.653702 CTGCCGATCGATCCCCTC 59.346 66.667 18.66 6.83 0.00 4.30
235 240 2.123468 TGCCGATCGATCCCCTCA 60.123 61.111 18.66 9.21 0.00 3.86
236 241 2.152297 CTGCCGATCGATCCCCTCAG 62.152 65.000 18.66 15.60 0.00 3.35
237 242 2.653702 CCGATCGATCCCCTCAGC 59.346 66.667 18.66 0.00 0.00 4.26
238 243 2.203082 CCGATCGATCCCCTCAGCA 61.203 63.158 18.66 0.00 0.00 4.41
283 295 0.388649 CGCAAGAAGTGACTAGGCGT 60.389 55.000 10.51 0.00 38.25 5.68
290 302 5.148651 AGAAGTGACTAGGCGTGTAAAAT 57.851 39.130 0.00 0.00 0.00 1.82
291 303 4.929808 AGAAGTGACTAGGCGTGTAAAATG 59.070 41.667 0.00 0.00 0.00 2.32
296 308 4.628333 TGACTAGGCGTGTAAAATGTAAGC 59.372 41.667 0.00 0.00 0.00 3.09
341 363 2.877582 CGCAGGCAAAAGCATCGC 60.878 61.111 0.00 0.00 0.00 4.58
378 400 0.538516 ACGAGCTCCACTCACTCAGT 60.539 55.000 8.47 0.00 46.63 3.41
393 415 4.802051 AGTCGTAGCCCGGCCGTA 62.802 66.667 26.12 7.20 43.96 4.02
394 416 4.261781 GTCGTAGCCCGGCCGTAG 62.262 72.222 26.12 16.51 34.29 3.51
426 448 1.150827 CTTGAGCAAGCACATGTCGA 58.849 50.000 0.00 0.00 0.00 4.20
449 471 5.360591 ACATCGAGTGAATTATTGGAGACC 58.639 41.667 0.00 0.00 0.00 3.85
450 472 4.402056 TCGAGTGAATTATTGGAGACCC 57.598 45.455 0.00 0.00 0.00 4.46
452 474 3.134804 CGAGTGAATTATTGGAGACCCCT 59.865 47.826 0.00 0.00 35.38 4.79
455 483 2.852449 TGAATTATTGGAGACCCCTGCT 59.148 45.455 0.00 0.00 35.38 4.24
890 938 1.741706 CACCTTGGCATTGCTAGACAG 59.258 52.381 8.82 0.00 0.00 3.51
899 947 2.231716 TTGCTAGACAGGACAGCCTA 57.768 50.000 0.00 0.00 44.80 3.93
900 948 2.461300 TGCTAGACAGGACAGCCTAT 57.539 50.000 0.00 0.00 44.80 2.57
901 949 3.595190 TGCTAGACAGGACAGCCTATA 57.405 47.619 0.00 0.00 44.80 1.31
902 950 4.119556 TGCTAGACAGGACAGCCTATAT 57.880 45.455 0.00 0.00 44.80 0.86
904 952 4.281941 TGCTAGACAGGACAGCCTATATTG 59.718 45.833 0.00 0.00 44.80 1.90
905 953 4.524714 GCTAGACAGGACAGCCTATATTGA 59.475 45.833 0.00 0.00 44.80 2.57
906 954 4.946478 AGACAGGACAGCCTATATTGAC 57.054 45.455 0.00 0.00 44.80 3.18
907 955 3.319405 AGACAGGACAGCCTATATTGACG 59.681 47.826 0.00 0.00 44.80 4.35
908 956 3.031736 ACAGGACAGCCTATATTGACGT 58.968 45.455 0.00 0.00 44.80 4.34
909 957 4.212716 ACAGGACAGCCTATATTGACGTA 58.787 43.478 0.00 0.00 44.80 3.57
910 958 4.278669 ACAGGACAGCCTATATTGACGTAG 59.721 45.833 0.00 0.00 44.80 3.51
911 959 4.519350 CAGGACAGCCTATATTGACGTAGA 59.481 45.833 0.00 0.00 44.80 2.59
912 960 4.519730 AGGACAGCCTATATTGACGTAGAC 59.480 45.833 0.00 0.00 44.74 2.59
913 961 4.465016 GACAGCCTATATTGACGTAGACG 58.535 47.826 0.00 0.00 46.33 4.18
914 962 3.235195 CAGCCTATATTGACGTAGACGC 58.765 50.000 1.14 0.00 44.43 5.19
920 968 0.458543 ATTGACGTAGACGCAGCAGG 60.459 55.000 1.14 0.00 44.43 4.85
943 991 1.665916 GCAGCAGCGAACTCTGTCA 60.666 57.895 0.00 0.00 36.49 3.58
968 1022 0.461548 CTAGCATCTCCGGTGAAGCA 59.538 55.000 28.95 16.92 33.66 3.91
1041 1101 2.124693 CCTCCTCGTCCTGCTCCTC 61.125 68.421 0.00 0.00 0.00 3.71
1077 1137 4.508128 CCCGTCCGTCCGTCCATG 62.508 72.222 0.00 0.00 0.00 3.66
1079 1139 3.445687 CGTCCGTCCGTCCATGGA 61.446 66.667 11.44 11.44 35.04 3.41
1082 1142 0.314302 GTCCGTCCGTCCATGGATAG 59.686 60.000 19.62 15.02 40.91 2.08
1084 1144 1.143481 TCCGTCCGTCCATGGATAGTA 59.857 52.381 19.62 0.00 40.91 1.82
1085 1145 1.540267 CCGTCCGTCCATGGATAGTAG 59.460 57.143 19.62 9.88 40.91 2.57
1086 1146 2.228059 CGTCCGTCCATGGATAGTAGT 58.772 52.381 19.62 0.00 40.91 2.73
1098 1169 7.123397 TCCATGGATAGTAGTAATGAGCATCTC 59.877 40.741 11.44 0.00 34.92 2.75
1100 1171 9.183368 CATGGATAGTAGTAATGAGCATCTCTA 57.817 37.037 0.00 0.00 34.92 2.43
1105 1176 7.504924 AGTAGTAATGAGCATCTCTACTCAC 57.495 40.000 15.33 6.84 45.19 3.51
1108 1179 1.393603 TGAGCATCTCTACTCACCGG 58.606 55.000 0.00 0.00 37.99 5.28
1113 1184 4.208686 CTCTACTCACCGGCCGGC 62.209 72.222 43.58 21.18 39.32 6.13
1119 1190 4.382320 TCACCGGCCGGCACTTAC 62.382 66.667 43.58 9.46 39.32 2.34
1123 1194 1.145377 CCGGCCGGCACTTACTTAT 59.855 57.895 34.96 0.00 0.00 1.73
1125 1196 0.655733 CGGCCGGCACTTACTTATTG 59.344 55.000 30.85 0.00 0.00 1.90
1126 1197 1.741055 CGGCCGGCACTTACTTATTGA 60.741 52.381 30.85 0.00 0.00 2.57
1128 1199 2.629051 GCCGGCACTTACTTATTGAGT 58.371 47.619 24.80 0.00 42.55 3.41
1130 1201 4.186159 GCCGGCACTTACTTATTGAGTTA 58.814 43.478 24.80 0.00 39.86 2.24
1131 1202 4.814771 GCCGGCACTTACTTATTGAGTTAT 59.185 41.667 24.80 0.00 39.86 1.89
1132 1203 5.296035 GCCGGCACTTACTTATTGAGTTATT 59.704 40.000 24.80 0.00 39.86 1.40
1133 1204 6.715464 CCGGCACTTACTTATTGAGTTATTG 58.285 40.000 0.00 0.00 39.86 1.90
1134 1205 6.238374 CCGGCACTTACTTATTGAGTTATTGG 60.238 42.308 0.00 0.00 39.86 3.16
1135 1206 6.537301 CGGCACTTACTTATTGAGTTATTGGA 59.463 38.462 0.00 0.00 39.86 3.53
1358 1434 3.827898 GTCCGCGCTACTGGCTCT 61.828 66.667 5.56 0.00 39.13 4.09
1362 1438 4.154347 GCGCTACTGGCTCTGGCT 62.154 66.667 0.00 0.00 39.13 4.75
1363 1439 2.786495 GCGCTACTGGCTCTGGCTA 61.786 63.158 0.00 0.00 39.13 3.93
1372 1448 0.673437 GGCTCTGGCTAGCTAGACTG 59.327 60.000 25.33 25.25 42.37 3.51
1373 1449 0.031994 GCTCTGGCTAGCTAGACTGC 59.968 60.000 25.33 23.00 39.50 4.40
1374 1450 1.691196 CTCTGGCTAGCTAGACTGCT 58.309 55.000 25.33 5.04 46.11 4.24
1375 1451 2.857483 CTCTGGCTAGCTAGACTGCTA 58.143 52.381 25.33 10.91 43.74 3.49
1421 1504 4.822026 AGATCTGTTCGTCCCTACTTTTG 58.178 43.478 0.00 0.00 0.00 2.44
1426 1509 3.878699 TGTTCGTCCCTACTTTTGTTTCC 59.121 43.478 0.00 0.00 0.00 3.13
1427 1510 2.758009 TCGTCCCTACTTTTGTTTCCG 58.242 47.619 0.00 0.00 0.00 4.30
1431 1517 4.603985 GTCCCTACTTTTGTTTCCGTTTG 58.396 43.478 0.00 0.00 0.00 2.93
1445 1531 1.263217 CCGTTTGCTTTACGTTGCTCT 59.737 47.619 0.00 0.00 37.30 4.09
1447 1533 2.713976 CGTTTGCTTTACGTTGCTCTTG 59.286 45.455 0.00 0.00 34.47 3.02
1479 1565 9.819267 GACTGAAAATAAAGTAGCTACCTACAT 57.181 33.333 20.31 6.20 45.15 2.29
1484 1570 8.785184 AAATAAAGTAGCTACCTACATCCTCT 57.215 34.615 20.31 0.00 45.15 3.69
1498 1584 0.322816 TCCTCTGCATTGGCTGTTCC 60.323 55.000 0.00 0.00 41.91 3.62
1499 1585 0.609957 CCTCTGCATTGGCTGTTCCA 60.610 55.000 0.00 0.00 44.85 3.53
1511 1601 1.335324 GCTGTTCCACTGCATGTTGTC 60.335 52.381 0.00 0.00 41.83 3.18
1520 1610 4.036734 CCACTGCATGTTGTCTAAGTGTTT 59.963 41.667 0.00 0.00 34.57 2.83
1521 1611 5.207768 CACTGCATGTTGTCTAAGTGTTTC 58.792 41.667 0.00 0.00 32.33 2.78
1562 1652 6.342111 TGTTGATGTAATAACGATGCCACTA 58.658 36.000 0.00 0.00 0.00 2.74
1581 1671 6.324819 CCACTAACAATTTGGCTTCTATGTG 58.675 40.000 0.78 0.00 0.00 3.21
1590 1680 3.814625 TGGCTTCTATGTGTTGTGTTGA 58.185 40.909 0.00 0.00 0.00 3.18
1596 1686 6.197096 GCTTCTATGTGTTGTGTTGAAACTTG 59.803 38.462 0.00 0.00 0.00 3.16
1603 1693 5.866633 GTGTTGTGTTGAAACTTGGAATCAA 59.133 36.000 0.00 0.00 0.00 2.57
1604 1694 6.534793 GTGTTGTGTTGAAACTTGGAATCAAT 59.465 34.615 0.00 0.00 35.70 2.57
1605 1695 6.756074 TGTTGTGTTGAAACTTGGAATCAATC 59.244 34.615 0.00 0.00 35.70 2.67
1608 1698 4.582656 TGTTGAAACTTGGAATCAATCGGT 59.417 37.500 0.00 0.00 35.70 4.69
1609 1699 5.068460 TGTTGAAACTTGGAATCAATCGGTT 59.932 36.000 0.00 0.00 35.70 4.44
1610 1700 6.263392 TGTTGAAACTTGGAATCAATCGGTTA 59.737 34.615 0.00 0.00 35.70 2.85
1613 1703 8.568676 TGAAACTTGGAATCAATCGGTTATTA 57.431 30.769 0.00 0.00 31.75 0.98
1638 1728 3.069872 TGGCTTGTCTGTTAAACGGAGTA 59.930 43.478 0.00 0.00 45.00 2.59
1643 1733 6.457257 GCTTGTCTGTTAAACGGAGTAAACAA 60.457 38.462 0.00 0.00 45.00 2.83
1646 1736 7.411274 TGTCTGTTAAACGGAGTAAACAATTG 58.589 34.615 3.24 3.24 45.00 2.32
1684 1778 5.862924 TTTTATGAGAGAAACGGAGCAAG 57.137 39.130 0.00 0.00 0.00 4.01
1685 1779 1.731720 ATGAGAGAAACGGAGCAAGC 58.268 50.000 0.00 0.00 0.00 4.01
1687 1781 1.002430 TGAGAGAAACGGAGCAAGCAT 59.998 47.619 0.00 0.00 0.00 3.79
1688 1782 2.079925 GAGAGAAACGGAGCAAGCATT 58.920 47.619 0.00 0.00 0.00 3.56
1699 1794 3.119388 GGAGCAAGCATTTTCATGTAGCA 60.119 43.478 0.00 0.00 32.28 3.49
1704 1799 5.050227 GCAAGCATTTTCATGTAGCAAAACA 60.050 36.000 0.00 0.00 32.28 2.83
1707 1802 6.947258 AGCATTTTCATGTAGCAAAACAAAC 58.053 32.000 0.00 0.00 32.02 2.93
1716 1811 4.464597 TGTAGCAAAACAAACTTCCCAAGT 59.535 37.500 0.00 0.00 45.46 3.16
1728 1823 5.499004 ACTTCCCAAGTTTCACAGCTATA 57.501 39.130 0.00 0.00 39.04 1.31
1735 1830 7.769044 TCCCAAGTTTCACAGCTATATTAACTC 59.231 37.037 0.00 0.00 0.00 3.01
1894 1989 8.394121 TGCAAATACCTGTTTGAATTGTTTTTC 58.606 29.630 3.74 0.00 40.64 2.29
1945 2040 4.724303 ACACGACGAACACATTTTTCAAA 58.276 34.783 0.00 0.00 0.00 2.69
1947 2042 5.229052 ACACGACGAACACATTTTTCAAATG 59.771 36.000 0.00 7.52 0.00 2.32
1953 2048 6.036953 ACGAACACATTTTTCAAATGCATGTT 59.963 30.769 13.74 13.74 32.83 2.71
1954 2049 6.570789 CGAACACATTTTTCAAATGCATGTTC 59.429 34.615 21.70 21.70 38.68 3.18
1986 2102 8.760980 TTCTAATGGTACCAAATATTTCCTGG 57.239 34.615 20.76 0.17 36.24 4.45
1990 2106 6.844097 TGGTACCAAATATTTCCTGGAAAC 57.156 37.500 23.29 8.58 34.23 2.78
1998 2114 9.717942 CCAAATATTTCCTGGAAACATTGTTTA 57.282 29.630 22.52 11.45 41.51 2.01
2001 2117 9.927668 AATATTTCCTGGAAACATTGTTTACAG 57.072 29.630 33.64 33.64 41.51 2.74
2002 2118 6.783708 TTTCCTGGAAACATTGTTTACAGT 57.216 33.333 35.63 11.12 38.40 3.55
2173 2295 5.890334 TGAACATTCTTTGAACACCTGAAC 58.110 37.500 0.00 0.00 0.00 3.18
2175 2297 6.096705 TGAACATTCTTTGAACACCTGAACAT 59.903 34.615 0.00 0.00 0.00 2.71
2176 2298 6.469782 ACATTCTTTGAACACCTGAACATT 57.530 33.333 0.00 0.00 0.00 2.71
2177 2299 6.877236 ACATTCTTTGAACACCTGAACATTT 58.123 32.000 0.00 0.00 0.00 2.32
2178 2300 7.330262 ACATTCTTTGAACACCTGAACATTTT 58.670 30.769 0.00 0.00 0.00 1.82
2179 2301 7.823799 ACATTCTTTGAACACCTGAACATTTTT 59.176 29.630 0.00 0.00 0.00 1.94
2180 2302 9.311916 CATTCTTTGAACACCTGAACATTTTTA 57.688 29.630 0.00 0.00 0.00 1.52
2181 2303 9.883142 ATTCTTTGAACACCTGAACATTTTTAA 57.117 25.926 0.00 0.00 0.00 1.52
2183 2305 9.883142 TCTTTGAACACCTGAACATTTTTAAAT 57.117 25.926 0.00 0.00 0.00 1.40
2248 2370 3.575256 AGTTCACCATTGATGTTGCACAT 59.425 39.130 2.02 2.02 42.43 3.21
2250 2372 2.892215 TCACCATTGATGTTGCACATGT 59.108 40.909 6.52 0.00 39.27 3.21
2256 2378 2.429478 TGATGTTGCACATGTCCAGAG 58.571 47.619 0.00 0.00 39.27 3.35
2260 2382 4.817318 TGTTGCACATGTCCAGAGTATA 57.183 40.909 0.00 0.00 0.00 1.47
2261 2383 4.758688 TGTTGCACATGTCCAGAGTATAG 58.241 43.478 0.00 0.00 0.00 1.31
2266 2388 7.544804 TGCACATGTCCAGAGTATAGATAAT 57.455 36.000 0.00 0.00 0.00 1.28
2308 2430 1.581934 GCAGATGCACCGCTAATACA 58.418 50.000 0.00 0.00 41.59 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.632153 AGTGTTTCAGTGATCTAAACGCT 58.368 39.130 13.31 13.31 44.70 5.07
1 2 4.447724 TGAGTGTTTCAGTGATCTAAACGC 59.552 41.667 9.85 9.85 41.58 4.84
2 3 6.712241 ATGAGTGTTTCAGTGATCTAAACG 57.288 37.500 0.00 0.00 39.68 3.60
7 8 9.512588 AGAAAAATATGAGTGTTTCAGTGATCT 57.487 29.630 0.00 0.00 39.68 2.75
67 68 4.910913 TCTGCCCCAAACCATCTATATGTA 59.089 41.667 0.00 0.00 0.00 2.29
70 71 4.603171 TGATCTGCCCCAAACCATCTATAT 59.397 41.667 0.00 0.00 0.00 0.86
73 74 2.204463 TGATCTGCCCCAAACCATCTA 58.796 47.619 0.00 0.00 0.00 1.98
74 75 1.002069 TGATCTGCCCCAAACCATCT 58.998 50.000 0.00 0.00 0.00 2.90
85 86 3.083122 AGGCAATCCATATGATCTGCC 57.917 47.619 23.68 23.68 46.68 4.85
109 110 0.238289 GATCTGCACCAACGGTTGTG 59.762 55.000 18.73 16.48 31.02 3.33
115 116 2.621338 AGTGTATGATCTGCACCAACG 58.379 47.619 9.92 0.00 41.00 4.10
120 121 5.400782 CGAATCAGTAGTGTATGATCTGCAC 59.599 44.000 0.00 0.65 40.45 4.57
121 122 5.507985 CCGAATCAGTAGTGTATGATCTGCA 60.508 44.000 0.00 0.00 35.11 4.41
124 125 6.513556 CGTTCCGAATCAGTAGTGTATGATCT 60.514 42.308 0.00 0.00 35.11 2.75
131 132 2.818432 ACTCGTTCCGAATCAGTAGTGT 59.182 45.455 0.00 0.00 34.74 3.55
178 183 1.453197 GGATAAGGTTGCCACCCCG 60.453 63.158 2.72 0.00 45.63 5.73
190 195 5.537188 GACAAGCAGATAGACCTGGATAAG 58.463 45.833 0.00 0.00 34.82 1.73
191 196 4.038042 CGACAAGCAGATAGACCTGGATAA 59.962 45.833 0.00 0.00 34.82 1.75
192 197 3.570125 CGACAAGCAGATAGACCTGGATA 59.430 47.826 0.00 0.00 34.82 2.59
193 198 2.363680 CGACAAGCAGATAGACCTGGAT 59.636 50.000 0.00 0.00 34.82 3.41
194 199 1.751351 CGACAAGCAGATAGACCTGGA 59.249 52.381 0.00 0.00 34.82 3.86
195 200 1.478510 ACGACAAGCAGATAGACCTGG 59.521 52.381 0.00 0.00 34.82 4.45
196 201 2.480416 GGACGACAAGCAGATAGACCTG 60.480 54.545 0.00 0.00 37.23 4.00
197 202 1.751924 GGACGACAAGCAGATAGACCT 59.248 52.381 0.00 0.00 0.00 3.85
198 203 1.751924 AGGACGACAAGCAGATAGACC 59.248 52.381 0.00 0.00 0.00 3.85
199 204 2.803451 CAGGACGACAAGCAGATAGAC 58.197 52.381 0.00 0.00 0.00 2.59
200 205 1.135139 GCAGGACGACAAGCAGATAGA 59.865 52.381 0.00 0.00 0.00 1.98
216 221 2.919856 AGGGGATCGATCGGCAGG 60.920 66.667 18.81 0.00 0.00 4.85
217 222 2.152297 CTGAGGGGATCGATCGGCAG 62.152 65.000 18.81 17.05 0.00 4.85
218 223 2.123468 TGAGGGGATCGATCGGCA 60.123 61.111 18.81 10.90 0.00 5.69
219 224 2.653702 CTGAGGGGATCGATCGGC 59.346 66.667 18.81 7.81 0.00 5.54
220 225 2.152297 CTGCTGAGGGGATCGATCGG 62.152 65.000 18.81 3.37 0.00 4.18
221 226 1.288439 CTGCTGAGGGGATCGATCG 59.712 63.158 18.81 9.36 0.00 3.69
223 228 3.882825 CCTGCTGAGGGGATCGAT 58.117 61.111 0.00 0.00 35.40 3.59
237 242 2.268280 CAGAGCCAGCAGACCCTG 59.732 66.667 0.00 0.00 34.12 4.45
238 243 3.007920 CCAGAGCCAGCAGACCCT 61.008 66.667 0.00 0.00 0.00 4.34
253 258 0.107993 CTTCTTGCGATGAGAGCCCA 60.108 55.000 0.00 0.00 0.00 5.36
283 295 5.907207 TGCCAACTTTGCTTACATTTTACA 58.093 33.333 0.00 0.00 0.00 2.41
290 302 3.490761 GCTTTCTGCCAACTTTGCTTACA 60.491 43.478 0.00 0.00 35.15 2.41
291 303 3.052745 GCTTTCTGCCAACTTTGCTTAC 58.947 45.455 0.00 0.00 35.15 2.34
296 308 3.719924 TCATTGCTTTCTGCCAACTTTG 58.280 40.909 0.00 0.00 42.00 2.77
341 363 1.078918 TCGGCAGAGCAGTGAATGG 60.079 57.895 0.00 0.00 0.00 3.16
399 421 3.437795 CTTGCTCAAGCCGGCCAG 61.438 66.667 26.15 18.08 41.18 4.85
407 429 1.136141 GTCGACATGTGCTTGCTCAAG 60.136 52.381 11.55 5.31 41.24 3.02
408 430 0.867746 GTCGACATGTGCTTGCTCAA 59.132 50.000 11.55 0.00 0.00 3.02
426 448 5.360591 GGTCTCCAATAATTCACTCGATGT 58.639 41.667 0.00 0.00 0.00 3.06
449 471 2.829003 CATGGCAGCAGAGCAGGG 60.829 66.667 0.00 0.00 35.83 4.45
450 472 2.829003 CCATGGCAGCAGAGCAGG 60.829 66.667 0.00 0.00 35.83 4.85
474 502 4.202609 GGGTGGGAGATATCAATTCCATGT 60.203 45.833 5.32 0.00 32.50 3.21
475 503 4.202599 TGGGTGGGAGATATCAATTCCATG 60.203 45.833 5.32 0.00 32.50 3.66
476 504 3.989558 TGGGTGGGAGATATCAATTCCAT 59.010 43.478 5.32 0.00 32.50 3.41
477 505 3.138283 GTGGGTGGGAGATATCAATTCCA 59.862 47.826 5.32 4.11 32.50 3.53
846 888 3.951680 TGTAGATACAAGACGATGCAGGA 59.048 43.478 0.00 0.00 32.40 3.86
852 894 4.279145 AGGTGGTGTAGATACAAGACGAT 58.721 43.478 0.00 0.00 38.04 3.73
890 938 4.613167 CGTCTACGTCAATATAGGCTGTCC 60.613 50.000 0.00 0.00 34.11 4.02
898 946 3.304458 CCTGCTGCGTCTACGTCAATATA 60.304 47.826 4.24 0.00 42.22 0.86
899 947 2.543861 CCTGCTGCGTCTACGTCAATAT 60.544 50.000 4.24 0.00 42.22 1.28
900 948 1.202256 CCTGCTGCGTCTACGTCAATA 60.202 52.381 4.24 0.00 42.22 1.90
901 949 0.458543 CCTGCTGCGTCTACGTCAAT 60.459 55.000 4.24 0.00 42.22 2.57
902 950 1.080772 CCTGCTGCGTCTACGTCAA 60.081 57.895 4.24 0.00 42.22 3.18
904 952 1.226435 CTCCTGCTGCGTCTACGTC 60.226 63.158 4.24 0.00 42.22 4.34
905 953 2.878429 CTCCTGCTGCGTCTACGT 59.122 61.111 4.24 0.00 42.22 3.57
906 954 2.580867 GCTCCTGCTGCGTCTACG 60.581 66.667 0.00 0.00 38.14 3.51
907 955 1.518133 CTGCTCCTGCTGCGTCTAC 60.518 63.158 0.00 0.00 40.48 2.59
908 956 2.888111 CTGCTCCTGCTGCGTCTA 59.112 61.111 0.00 0.00 40.48 2.59
914 962 3.128188 CTGCTGCTGCTCCTGCTG 61.128 66.667 17.00 1.17 40.48 4.41
920 968 2.738695 GAGTTCGCTGCTGCTGCTC 61.739 63.158 25.43 14.45 40.48 4.26
935 983 4.599041 AGATGCTAGAGAACTGACAGAGT 58.401 43.478 10.08 0.00 35.94 3.24
943 991 2.028130 CACCGGAGATGCTAGAGAACT 58.972 52.381 9.46 0.00 0.00 3.01
968 1022 0.743701 CGCCATCTCTCTGCTTGCTT 60.744 55.000 0.00 0.00 0.00 3.91
1028 1088 2.438614 CGAGGAGGAGCAGGACGA 60.439 66.667 0.00 0.00 0.00 4.20
1029 1089 2.752238 ACGAGGAGGAGCAGGACG 60.752 66.667 0.00 0.00 0.00 4.79
1030 1090 2.766400 CGACGAGGAGGAGCAGGAC 61.766 68.421 0.00 0.00 0.00 3.85
1064 1124 0.106369 ACTATCCATGGACGGACGGA 60.106 55.000 18.99 0.00 38.07 4.69
1073 1133 7.123997 AGAGATGCTCATTACTACTATCCATGG 59.876 40.741 4.97 4.97 32.06 3.66
1074 1134 8.065473 AGAGATGCTCATTACTACTATCCATG 57.935 38.462 0.00 0.00 32.06 3.66
1075 1135 9.184523 GTAGAGATGCTCATTACTACTATCCAT 57.815 37.037 14.18 0.00 32.50 3.41
1077 1137 8.801882 AGTAGAGATGCTCATTACTACTATCC 57.198 38.462 18.60 3.25 37.79 2.59
1079 1139 9.226606 GTGAGTAGAGATGCTCATTACTACTAT 57.773 37.037 19.35 8.21 42.72 2.12
1082 1142 6.566942 CGGTGAGTAGAGATGCTCATTACTAC 60.567 46.154 13.87 13.87 42.72 2.73
1084 1144 4.277174 CGGTGAGTAGAGATGCTCATTACT 59.723 45.833 0.00 0.00 42.72 2.24
1085 1145 4.541779 CGGTGAGTAGAGATGCTCATTAC 58.458 47.826 0.00 0.00 42.72 1.89
1086 1146 3.570125 CCGGTGAGTAGAGATGCTCATTA 59.430 47.826 0.00 0.00 42.72 1.90
1098 1169 4.814294 GTGCCGGCCGGTGAGTAG 62.814 72.222 42.53 18.40 37.65 2.57
1105 1176 0.463116 AATAAGTAAGTGCCGGCCGG 60.463 55.000 40.26 40.26 38.57 6.13
1108 1179 2.629051 ACTCAATAAGTAAGTGCCGGC 58.371 47.619 22.73 22.73 36.07 6.13
1113 1184 9.436957 ACAGTCCAATAACTCAATAAGTAAGTG 57.563 33.333 0.00 0.00 37.17 3.16
1119 1190 7.530010 CAACCACAGTCCAATAACTCAATAAG 58.470 38.462 0.00 0.00 0.00 1.73
1123 1194 3.568007 GCAACCACAGTCCAATAACTCAA 59.432 43.478 0.00 0.00 0.00 3.02
1125 1196 3.146066 TGCAACCACAGTCCAATAACTC 58.854 45.455 0.00 0.00 0.00 3.01
1126 1197 3.222173 TGCAACCACAGTCCAATAACT 57.778 42.857 0.00 0.00 0.00 2.24
1128 1199 3.305950 GCAATGCAACCACAGTCCAATAA 60.306 43.478 0.00 0.00 0.00 1.40
1130 1201 1.001181 GCAATGCAACCACAGTCCAAT 59.999 47.619 0.00 0.00 0.00 3.16
1131 1202 0.388659 GCAATGCAACCACAGTCCAA 59.611 50.000 0.00 0.00 0.00 3.53
1132 1203 0.754587 TGCAATGCAACCACAGTCCA 60.755 50.000 5.01 0.00 34.76 4.02
1133 1204 0.038892 CTGCAATGCAACCACAGTCC 60.039 55.000 9.92 0.00 38.41 3.85
1134 1205 0.953727 TCTGCAATGCAACCACAGTC 59.046 50.000 9.92 0.00 38.41 3.51
1135 1206 0.956633 CTCTGCAATGCAACCACAGT 59.043 50.000 9.92 0.00 38.41 3.55
1349 1420 1.495148 TCTAGCTAGCCAGAGCCAGTA 59.505 52.381 16.35 0.00 43.97 2.74
1352 1423 0.260230 AGTCTAGCTAGCCAGAGCCA 59.740 55.000 13.48 0.00 43.97 4.75
1353 1424 0.673437 CAGTCTAGCTAGCCAGAGCC 59.327 60.000 13.48 2.97 43.97 4.70
1354 1425 0.031994 GCAGTCTAGCTAGCCAGAGC 59.968 60.000 13.48 10.54 43.19 4.09
1384 1463 1.202580 AGATCTAACTGACGGCATGGC 60.203 52.381 9.69 9.69 0.00 4.40
1421 1504 2.214690 GCAACGTAAAGCAAACGGAAAC 59.785 45.455 9.75 0.00 44.48 2.78
1426 1509 2.663279 AGAGCAACGTAAAGCAAACG 57.337 45.000 9.73 4.26 45.64 3.60
1427 1510 3.042887 CCAAGAGCAACGTAAAGCAAAC 58.957 45.455 9.73 2.23 0.00 2.93
1431 1517 0.521735 CCCCAAGAGCAACGTAAAGC 59.478 55.000 0.00 0.00 0.00 3.51
1445 1531 6.377146 GCTACTTTATTTTCAGTCATCCCCAA 59.623 38.462 0.00 0.00 0.00 4.12
1447 1533 6.122964 AGCTACTTTATTTTCAGTCATCCCC 58.877 40.000 0.00 0.00 0.00 4.81
1476 1562 3.186345 CAGCCAATGCAGAGGATGT 57.814 52.632 15.21 0.00 41.13 3.06
1479 1565 0.322816 GGAACAGCCAATGCAGAGGA 60.323 55.000 11.16 0.00 41.13 3.71
1498 1584 4.818534 AACACTTAGACAACATGCAGTG 57.181 40.909 0.00 0.00 38.09 3.66
1499 1585 5.008019 CAGAAACACTTAGACAACATGCAGT 59.992 40.000 0.00 0.00 0.00 4.40
1511 1601 6.912591 CACAAACTAAAGCCAGAAACACTTAG 59.087 38.462 0.00 0.00 0.00 2.18
1520 1610 2.930950 ACAGCACAAACTAAAGCCAGA 58.069 42.857 0.00 0.00 0.00 3.86
1521 1611 3.066621 TCAACAGCACAAACTAAAGCCAG 59.933 43.478 0.00 0.00 0.00 4.85
1562 1652 5.984926 CACAACACATAGAAGCCAAATTGTT 59.015 36.000 0.00 0.00 0.00 2.83
1581 1671 6.074888 CGATTGATTCCAAGTTTCAACACAAC 60.075 38.462 0.00 0.00 35.48 3.32
1590 1680 8.575649 ACTAATAACCGATTGATTCCAAGTTT 57.424 30.769 0.00 0.00 35.48 2.66
1596 1686 5.531287 AGCCAACTAATAACCGATTGATTCC 59.469 40.000 0.00 0.00 0.00 3.01
1603 1693 4.876107 CAGACAAGCCAACTAATAACCGAT 59.124 41.667 0.00 0.00 0.00 4.18
1604 1694 4.250464 CAGACAAGCCAACTAATAACCGA 58.750 43.478 0.00 0.00 0.00 4.69
1605 1695 4.000988 ACAGACAAGCCAACTAATAACCG 58.999 43.478 0.00 0.00 0.00 4.44
1608 1698 7.308109 CCGTTTAACAGACAAGCCAACTAATAA 60.308 37.037 0.00 0.00 0.00 1.40
1609 1699 6.148150 CCGTTTAACAGACAAGCCAACTAATA 59.852 38.462 0.00 0.00 0.00 0.98
1610 1700 5.048991 CCGTTTAACAGACAAGCCAACTAAT 60.049 40.000 0.00 0.00 0.00 1.73
1613 1703 2.616842 CCGTTTAACAGACAAGCCAACT 59.383 45.455 0.00 0.00 0.00 3.16
1664 1758 3.262420 GCTTGCTCCGTTTCTCTCATAA 58.738 45.455 0.00 0.00 0.00 1.90
1666 1760 1.002430 TGCTTGCTCCGTTTCTCTCAT 59.998 47.619 0.00 0.00 0.00 2.90
1667 1761 0.392706 TGCTTGCTCCGTTTCTCTCA 59.607 50.000 0.00 0.00 0.00 3.27
1677 1771 3.119388 TGCTACATGAAAATGCTTGCTCC 60.119 43.478 0.00 0.00 0.00 4.70
1684 1778 6.947258 AGTTTGTTTTGCTACATGAAAATGC 58.053 32.000 0.00 0.00 0.00 3.56
1685 1779 8.063630 GGAAGTTTGTTTTGCTACATGAAAATG 58.936 33.333 0.00 0.00 0.00 2.32
1687 1781 6.536941 GGGAAGTTTGTTTTGCTACATGAAAA 59.463 34.615 0.00 0.00 0.00 2.29
1688 1782 6.045955 GGGAAGTTTGTTTTGCTACATGAAA 58.954 36.000 0.00 0.00 0.00 2.69
1707 1802 8.398665 GTTAATATAGCTGTGAAACTTGGGAAG 58.601 37.037 0.00 0.00 38.04 3.46
1716 1811 6.471198 CACGTCGAGTTAATATAGCTGTGAAA 59.529 38.462 0.00 0.00 0.00 2.69
1720 1815 4.201980 TGCACGTCGAGTTAATATAGCTGT 60.202 41.667 0.00 0.00 0.00 4.40
1723 1818 4.915667 TCATGCACGTCGAGTTAATATAGC 59.084 41.667 0.00 0.00 0.00 2.97
1728 1823 3.309682 CCATTCATGCACGTCGAGTTAAT 59.690 43.478 0.00 0.00 0.00 1.40
1735 1830 1.086067 AGAGCCATTCATGCACGTCG 61.086 55.000 0.00 0.00 0.00 5.12
1869 1964 8.394121 TGAAAAACAATTCAAACAGGTATTTGC 58.606 29.630 0.00 0.00 39.08 3.68
1915 2010 8.838452 AAAATGTGTTCGTCGTGTATTAAAAA 57.162 26.923 0.00 0.00 0.00 1.94
1916 2011 8.838452 AAAAATGTGTTCGTCGTGTATTAAAA 57.162 26.923 0.00 0.00 0.00 1.52
1917 2012 8.121086 TGAAAAATGTGTTCGTCGTGTATTAAA 58.879 29.630 0.00 0.00 0.00 1.52
1918 2013 7.628235 TGAAAAATGTGTTCGTCGTGTATTAA 58.372 30.769 0.00 0.00 0.00 1.40
1919 2014 7.175073 TGAAAAATGTGTTCGTCGTGTATTA 57.825 32.000 0.00 0.00 0.00 0.98
1920 2015 6.050454 TGAAAAATGTGTTCGTCGTGTATT 57.950 33.333 0.00 0.00 0.00 1.89
1921 2016 5.660629 TGAAAAATGTGTTCGTCGTGTAT 57.339 34.783 0.00 0.00 0.00 2.29
1922 2017 5.466432 TTGAAAAATGTGTTCGTCGTGTA 57.534 34.783 0.00 0.00 0.00 2.90
1923 2018 4.343811 TTGAAAAATGTGTTCGTCGTGT 57.656 36.364 0.00 0.00 0.00 4.49
1924 2019 5.646021 CATTTGAAAAATGTGTTCGTCGTG 58.354 37.500 4.84 0.00 0.00 4.35
1925 2020 4.206200 GCATTTGAAAAATGTGTTCGTCGT 59.794 37.500 12.82 0.00 0.00 4.34
1928 2023 5.523188 ACATGCATTTGAAAAATGTGTTCGT 59.477 32.000 12.82 3.38 30.53 3.85
1929 2024 5.976586 ACATGCATTTGAAAAATGTGTTCG 58.023 33.333 12.82 2.91 30.53 3.95
1982 2098 5.514274 ACACTGTAAACAATGTTTCCAGG 57.486 39.130 27.10 20.03 31.70 4.45
1985 2101 9.953697 TGTTTATACACTGTAAACAATGTTTCC 57.046 29.630 15.22 4.43 44.52 3.13
2145 2267 6.979817 CAGGTGTTCAAAGAATGTTCATGAAA 59.020 34.615 10.35 1.23 37.18 2.69
2146 2268 6.320926 TCAGGTGTTCAAAGAATGTTCATGAA 59.679 34.615 3.38 3.38 34.83 2.57
2248 2370 9.868160 TCAGAAGAATTATCTATACTCTGGACA 57.132 33.333 5.78 0.00 37.40 4.02
2250 2372 9.868160 TGTCAGAAGAATTATCTATACTCTGGA 57.132 33.333 5.78 0.00 37.40 3.86
2266 2388 6.035843 GCAACATTTCTTTGTGTCAGAAGAA 58.964 36.000 7.06 7.06 39.42 2.52
2273 2395 4.149396 GCATCTGCAACATTTCTTTGTGTC 59.851 41.667 0.00 0.00 41.59 3.67
2275 2397 4.640805 GCATCTGCAACATTTCTTTGTG 57.359 40.909 0.00 0.00 41.59 3.33


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

AutoCloner maintained by Alex Coulton.