Multiple sequence alignment - TraesCS7D01G213600

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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 TraesCS7D01G213600 chr7D 100.000 4241 0 0 1 4241 172264426 172260186 0.000000e+00 7832
1 TraesCS7D01G213600 chr7D 100.000 3915 0 0 4642 8556 172259785 172255871 0.000000e+00 7230
2 TraesCS7D01G213600 chr7D 93.240 932 54 2 4643 5565 26763066 26763997 0.000000e+00 1363
3 TraesCS7D01G213600 chr7D 91.853 761 49 9 3484 4241 14165225 14164475 0.000000e+00 1050
4 TraesCS7D01G213600 chr7D 83.172 618 49 27 5108 5717 501000501 501001071 1.650000e-141 514
5 TraesCS7D01G213600 chr7B 93.156 3565 127 52 1 3484 138259440 138255912 0.000000e+00 5123
6 TraesCS7D01G213600 chr7B 92.637 2241 113 32 5715 7929 138255914 138253700 0.000000e+00 3177
7 TraesCS7D01G213600 chr7B 90.941 574 39 5 7992 8556 138253689 138253120 0.000000e+00 760
8 TraesCS7D01G213600 chr7A 93.232 2822 140 27 5750 8556 174918520 174915735 0.000000e+00 4106
9 TraesCS7D01G213600 chr7A 93.288 2190 111 18 1306 3468 174920771 174918591 0.000000e+00 3197
10 TraesCS7D01G213600 chr7A 81.570 917 69 42 327 1204 174921785 174920930 0.000000e+00 665
11 TraesCS7D01G213600 chr7A 87.541 305 15 13 15 304 174922147 174921851 1.780000e-86 331
12 TraesCS7D01G213600 chr5D 94.059 1094 50 4 4643 5723 23656285 23657376 0.000000e+00 1646
13 TraesCS7D01G213600 chr5D 93.407 1092 52 8 4643 5717 325473717 325474805 0.000000e+00 1600
14 TraesCS7D01G213600 chr5D 90.741 1080 83 10 4643 5711 381788774 381787701 0.000000e+00 1424
15 TraesCS7D01G213600 chr2D 93.878 1078 58 3 4643 5717 49188245 49189317 0.000000e+00 1618
16 TraesCS7D01G213600 chr2D 93.008 758 41 5 3484 4241 186649934 186649189 0.000000e+00 1096
17 TraesCS7D01G213600 chr2D 91.984 761 49 7 3484 4241 563800968 563800217 0.000000e+00 1057
18 TraesCS7D01G213600 chr6D 94.135 989 49 6 4643 5625 7659691 7660676 0.000000e+00 1496
19 TraesCS7D01G213600 chr6D 91.421 1084 76 9 4643 5718 428424085 428425159 0.000000e+00 1471
20 TraesCS7D01G213600 chr6D 95.812 764 28 2 3478 4241 7658863 7659622 0.000000e+00 1230
21 TraesCS7D01G213600 chr2A 90.385 1092 85 8 4643 5718 103114377 103113290 0.000000e+00 1417
22 TraesCS7D01G213600 chr2A 89.720 1070 95 8 4643 5706 541390258 541391318 0.000000e+00 1352
23 TraesCS7D01G213600 chr5A 89.440 1089 66 8 4643 5715 698171807 698172862 0.000000e+00 1328
24 TraesCS7D01G213600 chr3D 94.401 768 33 7 3480 4241 384654216 384653453 0.000000e+00 1171
25 TraesCS7D01G213600 chr3D 92.539 764 45 7 3482 4241 173705378 173704623 0.000000e+00 1085
26 TraesCS7D01G213600 chr3D 92.157 765 43 8 3480 4241 25158195 25157445 0.000000e+00 1064
27 TraesCS7D01G213600 chr1D 92.005 763 53 6 3482 4241 361101077 361100320 0.000000e+00 1064
28 TraesCS7D01G213600 chr1D 91.711 760 52 6 3482 4241 259540089 259539341 0.000000e+00 1044


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 TraesCS7D01G213600 chr7D 172255871 172264426 8555 True 7531.00 7832 100.000000 1 8556 2 chr7D.!!$R2 8555
1 TraesCS7D01G213600 chr7D 26763066 26763997 931 False 1363.00 1363 93.240000 4643 5565 1 chr7D.!!$F1 922
2 TraesCS7D01G213600 chr7D 14164475 14165225 750 True 1050.00 1050 91.853000 3484 4241 1 chr7D.!!$R1 757
3 TraesCS7D01G213600 chr7D 501000501 501001071 570 False 514.00 514 83.172000 5108 5717 1 chr7D.!!$F2 609
4 TraesCS7D01G213600 chr7B 138253120 138259440 6320 True 3020.00 5123 92.244667 1 8556 3 chr7B.!!$R1 8555
5 TraesCS7D01G213600 chr7A 174915735 174922147 6412 True 2074.75 4106 88.907750 15 8556 4 chr7A.!!$R1 8541
6 TraesCS7D01G213600 chr5D 23656285 23657376 1091 False 1646.00 1646 94.059000 4643 5723 1 chr5D.!!$F1 1080
7 TraesCS7D01G213600 chr5D 325473717 325474805 1088 False 1600.00 1600 93.407000 4643 5717 1 chr5D.!!$F2 1074
8 TraesCS7D01G213600 chr5D 381787701 381788774 1073 True 1424.00 1424 90.741000 4643 5711 1 chr5D.!!$R1 1068
9 TraesCS7D01G213600 chr2D 49188245 49189317 1072 False 1618.00 1618 93.878000 4643 5717 1 chr2D.!!$F1 1074
10 TraesCS7D01G213600 chr2D 186649189 186649934 745 True 1096.00 1096 93.008000 3484 4241 1 chr2D.!!$R1 757
11 TraesCS7D01G213600 chr2D 563800217 563800968 751 True 1057.00 1057 91.984000 3484 4241 1 chr2D.!!$R2 757
12 TraesCS7D01G213600 chr6D 428424085 428425159 1074 False 1471.00 1471 91.421000 4643 5718 1 chr6D.!!$F1 1075
13 TraesCS7D01G213600 chr6D 7658863 7660676 1813 False 1363.00 1496 94.973500 3478 5625 2 chr6D.!!$F2 2147
14 TraesCS7D01G213600 chr2A 103113290 103114377 1087 True 1417.00 1417 90.385000 4643 5718 1 chr2A.!!$R1 1075
15 TraesCS7D01G213600 chr2A 541390258 541391318 1060 False 1352.00 1352 89.720000 4643 5706 1 chr2A.!!$F1 1063
16 TraesCS7D01G213600 chr5A 698171807 698172862 1055 False 1328.00 1328 89.440000 4643 5715 1 chr5A.!!$F1 1072
17 TraesCS7D01G213600 chr3D 384653453 384654216 763 True 1171.00 1171 94.401000 3480 4241 1 chr3D.!!$R3 761
18 TraesCS7D01G213600 chr3D 173704623 173705378 755 True 1085.00 1085 92.539000 3482 4241 1 chr3D.!!$R2 759
19 TraesCS7D01G213600 chr3D 25157445 25158195 750 True 1064.00 1064 92.157000 3480 4241 1 chr3D.!!$R1 761
20 TraesCS7D01G213600 chr1D 361100320 361101077 757 True 1064.00 1064 92.005000 3482 4241 1 chr1D.!!$R2 759
21 TraesCS7D01G213600 chr1D 259539341 259540089 748 True 1044.00 1044 91.711000 3482 4241 1 chr1D.!!$R1 759

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
752 845 0.981277 TTCATTCCGACCTCCCTCCC 60.981 60.000 0.00 0.0 0.00 4.30 F
1349 1523 1.273327 CCCCATTTCCAAGCACTTCAC 59.727 52.381 0.00 0.0 0.00 3.18 F
1672 1869 0.317479 GGTGCCTGACGTGTACTTCT 59.683 55.000 0.00 0.0 0.00 2.85 F
2114 2311 0.657840 GCAAACGGGCAGCATACTAG 59.342 55.000 0.00 0.0 0.00 2.57 F
2991 3195 1.069636 GCAAAAACCAGAGCTGTCTCG 60.070 52.381 0.00 0.0 44.02 4.04 F
3879 4126 1.445582 GCGGCGCGGCTATATAAGT 60.446 57.895 30.06 0.0 0.00 2.24 F
4905 5182 1.380650 GAGGTTCGGCTCCTCCTCT 60.381 63.158 9.27 0.0 43.90 3.69 F
5889 6231 0.655733 CAAGTTCACAACCGCTCGTT 59.344 50.000 0.00 0.0 33.90 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1620 1817 0.673985 CCAACTCCACAGACAGACGA 59.326 55.000 0.00 0.00 0.00 4.20 R
2970 3174 1.949525 GAGACAGCTCTGGTTTTTGCA 59.050 47.619 1.66 0.00 38.16 4.08 R
3429 3635 4.112634 TGTTAGGACAAAATGGGAGCTT 57.887 40.909 0.00 0.00 31.49 3.74 R
3706 3947 4.373116 ATGACGAGGCGCGGTGTT 62.373 61.111 16.41 0.00 46.49 3.32 R
4905 5182 0.898789 AGGAAGAACGCGAGGAGGAA 60.899 55.000 15.93 0.00 0.00 3.36 R
5362 5660 0.471211 TTCTCCTCCTTGACACGGGT 60.471 55.000 0.00 0.00 0.00 5.28 R
6205 6549 0.321034 CAAGTACTGCTGCAGCCTCA 60.321 55.000 34.64 16.55 41.18 3.86 R
7595 7943 0.600782 CACCAAACAATGCACCAGCC 60.601 55.000 0.00 0.00 41.13 4.85 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
68 69 1.228367 GGGGATCATCAATGCCGCT 60.228 57.895 0.00 0.00 46.56 5.52
100 106 2.802057 GCCTTCATGATGAGGCAAATGC 60.802 50.000 26.77 9.27 39.14 3.56
212 218 1.743252 CTCTCGCCTGCACTTTCCC 60.743 63.158 0.00 0.00 0.00 3.97
218 224 2.328099 CCTGCACTTTCCCTCACGC 61.328 63.158 0.00 0.00 0.00 5.34
219 225 1.302033 CTGCACTTTCCCTCACGCT 60.302 57.895 0.00 0.00 0.00 5.07
220 226 1.572085 CTGCACTTTCCCTCACGCTG 61.572 60.000 0.00 0.00 0.00 5.18
221 227 2.970974 GCACTTTCCCTCACGCTGC 61.971 63.158 0.00 0.00 0.00 5.25
222 228 1.597854 CACTTTCCCTCACGCTGCA 60.598 57.895 0.00 0.00 0.00 4.41
223 229 1.598130 ACTTTCCCTCACGCTGCAC 60.598 57.895 0.00 0.00 0.00 4.57
225 231 3.113514 TTTCCCTCACGCTGCACCA 62.114 57.895 0.00 0.00 0.00 4.17
226 232 3.825160 TTCCCTCACGCTGCACCAC 62.825 63.158 0.00 0.00 0.00 4.16
230 236 4.662961 TCACGCTGCACCACCGAG 62.663 66.667 0.00 0.00 0.00 4.63
244 250 3.389329 ACCACCGAGCTCATCTGAAATAT 59.611 43.478 15.40 0.00 0.00 1.28
247 253 3.389329 ACCGAGCTCATCTGAAATATGGT 59.611 43.478 15.40 5.11 0.00 3.55
248 254 3.744942 CCGAGCTCATCTGAAATATGGTG 59.255 47.826 15.40 0.00 0.00 4.17
249 255 3.186001 CGAGCTCATCTGAAATATGGTGC 59.814 47.826 15.40 0.00 0.00 5.01
250 256 4.387598 GAGCTCATCTGAAATATGGTGCT 58.612 43.478 9.40 0.00 37.31 4.40
251 257 4.135306 AGCTCATCTGAAATATGGTGCTG 58.865 43.478 0.00 0.00 35.16 4.41
253 259 5.059161 GCTCATCTGAAATATGGTGCTGTA 58.941 41.667 0.00 0.00 0.00 2.74
254 260 5.528690 GCTCATCTGAAATATGGTGCTGTAA 59.471 40.000 0.00 0.00 0.00 2.41
255 261 6.206243 GCTCATCTGAAATATGGTGCTGTAAT 59.794 38.462 0.00 0.00 0.00 1.89
258 264 7.557358 TCATCTGAAATATGGTGCTGTAATTGT 59.443 33.333 0.00 0.00 0.00 2.71
259 265 7.320443 TCTGAAATATGGTGCTGTAATTGTC 57.680 36.000 0.00 0.00 0.00 3.18
288 304 6.878389 AGAAAACATGCAAAGTTTCCAAGAAA 59.122 30.769 17.56 0.00 38.17 2.52
306 322 3.753272 AGAAATTGTCCTGTTCATCACCG 59.247 43.478 0.00 0.00 0.00 4.94
310 326 2.766313 TGTCCTGTTCATCACCGAAAG 58.234 47.619 0.00 0.00 0.00 2.62
336 399 2.543641 GCTGTTTATCCATTTGCAGGC 58.456 47.619 0.00 0.00 0.00 4.85
431 499 4.664677 GCAGTCGACACGCCAGGT 62.665 66.667 19.50 0.00 0.00 4.00
483 551 2.590575 GTGGTGGTGTGGTGTCCG 60.591 66.667 0.00 0.00 0.00 4.79
493 561 2.904866 GGTGTCCGTTGCAAGCCA 60.905 61.111 0.00 0.00 0.00 4.75
595 665 8.024145 TCCCCACACAAAATTATAAAACAAGT 57.976 30.769 0.00 0.00 0.00 3.16
712 805 3.637273 ACTTGACTGGGTCCCCGC 61.637 66.667 5.13 0.00 39.42 6.13
752 845 0.981277 TTCATTCCGACCTCCCTCCC 60.981 60.000 0.00 0.00 0.00 4.30
790 883 2.705826 GATTCTTCTGCCGCGCTG 59.294 61.111 5.56 0.00 0.00 5.18
839 936 3.692406 GTTCGAGGGCTGGACGGT 61.692 66.667 0.00 0.00 0.00 4.83
926 1026 2.933834 CCACCTTCTCCCGGGGTT 60.934 66.667 23.50 0.00 0.00 4.11
1072 1188 1.909700 TTGATTCAGTTCAGGGTGGC 58.090 50.000 0.00 0.00 0.00 5.01
1107 1223 3.368236 GCACTAGCGTAGGTTTTCAAGAG 59.632 47.826 0.00 0.00 40.68 2.85
1244 1387 1.657751 GAGTGGGGAAATGAAGCCGC 61.658 60.000 0.00 0.00 37.60 6.53
1287 1430 4.987912 ACGGGCAATTCAACTGTTATTTTG 59.012 37.500 0.00 0.00 0.00 2.44
1349 1523 1.273327 CCCCATTTCCAAGCACTTCAC 59.727 52.381 0.00 0.00 0.00 3.18
1357 1531 4.085357 TCCAAGCACTTCACAGTACAAT 57.915 40.909 0.00 0.00 0.00 2.71
1448 1635 4.692228 TGCCACTTTCTTGAAACCATTTC 58.308 39.130 0.00 0.00 40.08 2.17
1613 1810 5.416952 ACTCTCAACCATCATTTTCCATGAC 59.583 40.000 0.00 0.00 0.00 3.06
1620 1817 4.081862 CCATCATTTTCCATGACAACAGCT 60.082 41.667 0.00 0.00 0.00 4.24
1671 1868 0.669625 GGGTGCCTGACGTGTACTTC 60.670 60.000 0.00 0.00 0.00 3.01
1672 1869 0.317479 GGTGCCTGACGTGTACTTCT 59.683 55.000 0.00 0.00 0.00 2.85
1698 1895 3.249189 AGAAGCGGGGGACAAGCA 61.249 61.111 0.00 0.00 37.88 3.91
1857 2054 4.276055 AGGGTGCAGAATTCCCCT 57.724 55.556 12.83 12.83 42.80 4.79
1920 2117 4.800554 CTCGCCAAGGACCTTGTT 57.199 55.556 28.45 0.00 39.58 2.83
2010 2207 7.189693 TGATAATGTGATAAAGAACATCGGC 57.810 36.000 0.00 0.00 35.99 5.54
2056 2253 0.890683 AGCATTTGGTAGCAACAGGC 59.109 50.000 6.90 11.04 45.30 4.85
2066 2263 3.803082 CAACAGGCGTGCCGATGG 61.803 66.667 6.26 0.00 41.95 3.51
2114 2311 0.657840 GCAAACGGGCAGCATACTAG 59.342 55.000 0.00 0.00 0.00 2.57
2151 2348 1.277557 GATGGCTATTCTGAGGGCGAT 59.722 52.381 0.00 0.00 0.00 4.58
2205 2402 3.151958 AAGAGCACTGCACGACGGT 62.152 57.895 3.30 0.00 38.94 4.83
2268 2465 1.733399 GTCTCACGAGTTCGGTGGC 60.733 63.158 6.48 0.00 44.95 5.01
2970 3174 1.464608 CGTGACGTGCAGGAAATCATT 59.535 47.619 14.38 0.00 34.35 2.57
2991 3195 1.069636 GCAAAAACCAGAGCTGTCTCG 60.070 52.381 0.00 0.00 44.02 4.04
3391 3597 7.790823 AAAAATCCAAATTCAGAACTGTTGG 57.209 32.000 12.91 12.91 36.28 3.77
3429 3635 6.991938 ACATTTGCCTTGCAGTAATAAGAAA 58.008 32.000 0.00 0.00 40.61 2.52
3879 4126 1.445582 GCGGCGCGGCTATATAAGT 60.446 57.895 30.06 0.00 0.00 2.24
4023 4294 2.612251 CCTCTCCCTCCCCCTCTC 59.388 72.222 0.00 0.00 0.00 3.20
4203 4474 1.917336 GAGTGCCCATTCCCCCGTTA 61.917 60.000 0.00 0.00 0.00 3.18
4680 4951 4.656117 TTCGAGCGTCGCCAGCAA 62.656 61.111 14.86 0.00 40.21 3.91
4701 4972 2.047655 CGGCTAGCGTCCACCAAA 60.048 61.111 9.00 0.00 0.00 3.28
4782 5053 4.373116 GGCCGCACACTCGAGGAA 62.373 66.667 18.41 0.00 0.00 3.36
4905 5182 1.380650 GAGGTTCGGCTCCTCCTCT 60.381 63.158 9.27 0.00 43.90 3.69
4917 5200 1.751162 CTCCTCTTCCTCCTCGCGT 60.751 63.158 5.77 0.00 0.00 6.01
5062 5345 2.756283 CCTCGTCGGCTCCTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
5066 5349 4.516195 GTCGGCTCCTCCTTCGCC 62.516 72.222 0.00 0.00 40.40 5.54
5071 5354 2.904131 CTCCTCCTTCGCCCTTCC 59.096 66.667 0.00 0.00 0.00 3.46
5441 5739 1.443194 GCGACTACTCGGCGTTCAA 60.443 57.895 6.85 0.00 40.53 2.69
5748 6078 5.812642 TGTTTCAACAATTTAACAATGCGGT 59.187 32.000 0.00 0.00 35.67 5.68
5877 6219 6.318648 ACTCTTTCATTGTACTTGCAAGTTCA 59.681 34.615 35.20 31.61 40.37 3.18
5889 6231 0.655733 CAAGTTCACAACCGCTCGTT 59.344 50.000 0.00 0.00 33.90 3.85
5920 6264 7.172190 ACATCACTAGCTAACATGAATATGCAC 59.828 37.037 0.00 0.00 37.85 4.57
6043 6387 6.471146 GGAGATACTTATCAAGATGGTGCAT 58.529 40.000 0.00 0.00 35.17 3.96
6070 6414 3.208594 CAATGCTAGTATCTGCAAGGCA 58.791 45.455 0.00 0.00 42.74 4.75
6130 6474 1.267121 ACGGCAAGACACTAGTGGAT 58.733 50.000 26.12 11.72 34.19 3.41
6136 6480 1.944177 AGACACTAGTGGATGCAGGT 58.056 50.000 26.12 2.84 34.19 4.00
6205 6549 0.625683 AGCCCATGGGATCCAAGACT 60.626 55.000 36.00 16.14 36.95 3.24
6295 6639 3.133003 AGGAAGGTCATGTTATCACCTCG 59.867 47.826 3.66 0.00 39.80 4.63
6304 6648 5.650703 TCATGTTATCACCTCGAAGTACTCA 59.349 40.000 0.00 0.00 0.00 3.41
6388 6732 2.261052 GTGCTGCTCGCTCTCACT 59.739 61.111 0.00 0.00 40.11 3.41
6421 6765 4.778415 CTCGCCACGGTGGTCTCG 62.778 72.222 26.86 21.23 40.46 4.04
6478 6822 2.233922 CGAGTTCATGGGTTCACCTAGT 59.766 50.000 0.00 0.00 41.11 2.57
6793 7137 0.921256 AGCCATACTTGGAGGGCCTT 60.921 55.000 7.89 0.00 46.92 4.35
6796 7140 1.005924 CCATACTTGGAGGGCCTTGTT 59.994 52.381 7.89 0.00 46.92 2.83
6829 7173 2.158959 GCTAACGACGACGCTGCAT 61.159 57.895 7.30 0.00 43.96 3.96
6964 7308 1.123861 AGAACCTCAGCCAGCAGTCA 61.124 55.000 0.00 0.00 0.00 3.41
7370 7714 3.334054 GCTTCTGGGCCCTGGAGT 61.334 66.667 31.76 0.00 0.00 3.85
7468 7812 1.227823 CTTCCACAAGGGCGACACA 60.228 57.895 0.00 0.00 36.21 3.72
7595 7943 4.452455 GTCTTGGCTTTATACCATCCATCG 59.548 45.833 0.00 0.00 36.96 3.84
7624 7973 6.314784 GTGCATTGTTTGGTGTAACTAGATC 58.685 40.000 0.00 0.00 36.74 2.75
7628 7977 7.521529 CATTGTTTGGTGTAACTAGATCACAG 58.478 38.462 0.00 0.00 36.74 3.66
7630 7979 6.822442 TGTTTGGTGTAACTAGATCACAGAA 58.178 36.000 0.00 0.00 36.74 3.02
7637 7986 9.052759 GGTGTAACTAGATCACAGAAAGAAAAA 57.947 33.333 0.00 0.00 36.74 1.94
7648 7997 9.750125 ATCACAGAAAGAAAAATGAGGTAAAAC 57.250 29.630 0.00 0.00 0.00 2.43
7654 8003 9.256477 GAAAGAAAAATGAGGTAAAACGGAATT 57.744 29.630 0.00 0.00 0.00 2.17
7655 8004 8.587952 AAGAAAAATGAGGTAAAACGGAATTG 57.412 30.769 0.00 0.00 0.00 2.32
7656 8005 7.947282 AGAAAAATGAGGTAAAACGGAATTGA 58.053 30.769 0.00 0.00 0.00 2.57
7657 8006 8.082242 AGAAAAATGAGGTAAAACGGAATTGAG 58.918 33.333 0.00 0.00 0.00 3.02
7658 8007 5.897377 AATGAGGTAAAACGGAATTGAGG 57.103 39.130 0.00 0.00 0.00 3.86
7659 8008 4.360951 TGAGGTAAAACGGAATTGAGGT 57.639 40.909 0.00 0.00 0.00 3.85
7660 8009 5.486735 TGAGGTAAAACGGAATTGAGGTA 57.513 39.130 0.00 0.00 0.00 3.08
7661 8010 5.867330 TGAGGTAAAACGGAATTGAGGTAA 58.133 37.500 0.00 0.00 0.00 2.85
7662 8011 6.297582 TGAGGTAAAACGGAATTGAGGTAAA 58.702 36.000 0.00 0.00 0.00 2.01
7663 8012 6.771749 TGAGGTAAAACGGAATTGAGGTAAAA 59.228 34.615 0.00 0.00 0.00 1.52
7664 8013 6.973843 AGGTAAAACGGAATTGAGGTAAAAC 58.026 36.000 0.00 0.00 0.00 2.43
7665 8014 5.852755 GGTAAAACGGAATTGAGGTAAAACG 59.147 40.000 0.00 0.00 0.00 3.60
7666 8015 4.492791 AAACGGAATTGAGGTAAAACGG 57.507 40.909 0.00 0.00 0.00 4.44
7667 8016 3.405823 ACGGAATTGAGGTAAAACGGA 57.594 42.857 0.00 0.00 0.00 4.69
7668 8017 3.742385 ACGGAATTGAGGTAAAACGGAA 58.258 40.909 0.00 0.00 0.00 4.30
7699 8050 8.562892 GCAGATGCAATGTAACTAAAGTCATAT 58.437 33.333 0.00 0.00 41.59 1.78
7704 8055 8.836413 TGCAATGTAACTAAAGTCATATTAGGC 58.164 33.333 0.00 0.00 35.20 3.93
7724 8076 8.800370 TTAGGCATGATATGTACAGTTTTTCA 57.200 30.769 0.33 0.40 0.00 2.69
7756 8109 9.281371 GTTTGTCTTCTTAGGGTGTAATTAAGT 57.719 33.333 0.00 0.00 0.00 2.24
7812 8167 3.275143 CTTGGTTGGTTTGGGTTTTTCC 58.725 45.455 0.00 0.00 0.00 3.13
7864 8219 7.701539 TGTATCCAGAGCAAAATTGTATGTT 57.298 32.000 0.00 0.00 0.00 2.71
7887 8242 5.765176 TGTTGCAGAACTCATTTGAGATTG 58.235 37.500 14.29 9.58 44.74 2.67
7929 8300 6.769512 TCACTTAAACTGGCTTCAGAACTAT 58.230 36.000 0.00 0.00 40.86 2.12
7973 8344 9.781633 ATTATGTAGTTCTACTCGACTGACTAT 57.218 33.333 10.65 0.00 0.00 2.12
7990 8361 5.397360 TGACTATGCTCATGATCTTCCCTA 58.603 41.667 0.00 0.00 0.00 3.53
8001 8372 5.698741 TGATCTTCCCTAGAGCAAATTCA 57.301 39.130 0.00 0.00 45.77 2.57
8004 8375 5.698741 TCTTCCCTAGAGCAAATTCATCA 57.301 39.130 0.00 0.00 0.00 3.07
8013 8384 6.317789 AGAGCAAATTCATCAAAACGAGAA 57.682 33.333 0.00 0.00 0.00 2.87
8045 8416 7.615582 TTCTTGAATGCTTTCATCGACTATT 57.384 32.000 15.04 0.00 41.38 1.73
8051 8422 7.009568 AATGCTTTCATCGACTATTCAAGTC 57.990 36.000 0.00 0.00 40.69 3.01
8077 8448 4.823790 TGAGGCGATCATGATGAAAATG 57.176 40.909 14.30 0.00 31.12 2.32
8199 8571 6.548993 AGGCCTCATTTATTCTCAAGAAATCC 59.451 38.462 0.00 0.00 37.61 3.01
8317 8693 6.579666 TCGAAGGCTGTTATATTATACCGT 57.420 37.500 0.00 0.00 0.00 4.83
8394 8771 1.332144 GGTACCCAGATACGGCCACA 61.332 60.000 2.24 0.00 0.00 4.17
8485 8865 8.767478 AAATTTTCAGAGAATGTAATGCTTGG 57.233 30.769 0.00 0.00 26.21 3.61
8503 8883 1.066215 TGGAATCTCCATGTGGACGTG 60.066 52.381 0.00 0.00 42.67 4.49
8529 8909 0.827368 GTCGGATCTCCAGCTTCCTT 59.173 55.000 0.10 0.00 35.14 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 106 4.869440 CTGCTCTCCGCTCCGCTG 62.869 72.222 0.00 0.00 40.11 5.18
108 114 2.615869 CTTCCTTCTTTCTGCTCTCCG 58.384 52.381 0.00 0.00 0.00 4.63
218 224 1.812922 GATGAGCTCGGTGGTGCAG 60.813 63.158 9.64 0.00 35.16 4.41
219 225 2.265739 GATGAGCTCGGTGGTGCA 59.734 61.111 9.64 0.00 35.16 4.57
220 226 1.812922 CAGATGAGCTCGGTGGTGC 60.813 63.158 9.64 0.00 0.00 5.01
221 227 0.247460 TTCAGATGAGCTCGGTGGTG 59.753 55.000 9.64 2.27 0.00 4.17
222 228 0.976641 TTTCAGATGAGCTCGGTGGT 59.023 50.000 9.64 0.00 0.00 4.16
223 229 2.322355 ATTTCAGATGAGCTCGGTGG 57.678 50.000 9.64 0.00 0.00 4.61
225 231 3.389329 ACCATATTTCAGATGAGCTCGGT 59.611 43.478 9.64 2.39 0.00 4.69
226 232 3.744942 CACCATATTTCAGATGAGCTCGG 59.255 47.826 9.64 1.71 0.00 4.63
228 234 4.213694 CAGCACCATATTTCAGATGAGCTC 59.786 45.833 6.82 6.82 35.01 4.09
230 236 3.881688 ACAGCACCATATTTCAGATGAGC 59.118 43.478 0.00 0.00 0.00 4.26
231 237 7.741027 ATTACAGCACCATATTTCAGATGAG 57.259 36.000 0.00 0.00 0.00 2.90
244 250 3.826524 TCTTTGGACAATTACAGCACCA 58.173 40.909 0.00 0.00 0.00 4.17
247 253 6.214191 TGTTTTCTTTGGACAATTACAGCA 57.786 33.333 0.00 0.00 0.00 4.41
248 254 6.346838 GCATGTTTTCTTTGGACAATTACAGC 60.347 38.462 0.00 0.00 0.00 4.40
249 255 6.700960 TGCATGTTTTCTTTGGACAATTACAG 59.299 34.615 0.00 0.00 0.00 2.74
250 256 6.577103 TGCATGTTTTCTTTGGACAATTACA 58.423 32.000 0.00 0.00 0.00 2.41
251 257 7.475771 TTGCATGTTTTCTTTGGACAATTAC 57.524 32.000 0.00 0.00 0.00 1.89
253 259 6.598850 ACTTTGCATGTTTTCTTTGGACAATT 59.401 30.769 0.00 0.00 0.00 2.32
254 260 6.114767 ACTTTGCATGTTTTCTTTGGACAAT 58.885 32.000 0.00 0.00 0.00 2.71
255 261 5.486526 ACTTTGCATGTTTTCTTTGGACAA 58.513 33.333 0.00 0.00 0.00 3.18
258 264 5.584251 GGAAACTTTGCATGTTTTCTTTGGA 59.416 36.000 16.10 0.00 37.70 3.53
259 265 5.353678 TGGAAACTTTGCATGTTTTCTTTGG 59.646 36.000 18.75 0.00 37.70 3.28
288 304 3.417069 TTCGGTGATGAACAGGACAAT 57.583 42.857 0.00 0.00 0.00 2.71
310 326 1.014352 AATGGATAAACAGCGGTCGC 58.986 50.000 7.32 7.32 42.33 5.19
318 334 2.533916 TGGCCTGCAAATGGATAAACA 58.466 42.857 3.32 0.00 0.00 2.83
321 337 3.317455 AGATGGCCTGCAAATGGATAA 57.683 42.857 3.32 0.00 0.00 1.75
322 338 3.317455 AAGATGGCCTGCAAATGGATA 57.683 42.857 3.32 0.00 0.00 2.59
323 339 2.170012 AAGATGGCCTGCAAATGGAT 57.830 45.000 3.32 0.00 0.00 3.41
324 340 2.378038 GTAAGATGGCCTGCAAATGGA 58.622 47.619 3.32 0.00 0.00 3.41
325 341 1.410153 GGTAAGATGGCCTGCAAATGG 59.590 52.381 3.32 0.00 0.00 3.16
336 399 3.611766 AGTTTCGGTCAGGTAAGATGG 57.388 47.619 0.00 0.00 0.00 3.51
380 443 1.740332 TTGTCCACGGCGACTTCAGA 61.740 55.000 16.62 0.00 33.70 3.27
447 515 4.531732 ACCACATATGCCACCTTCATTTTT 59.468 37.500 1.58 0.00 0.00 1.94
629 705 3.269347 CGGTAAAGCGGCCCGATG 61.269 66.667 7.68 0.00 44.41 3.84
752 845 9.846248 AGAATCGAGAGGAACAAAAATAAATTG 57.154 29.630 0.00 0.00 0.00 2.32
813 910 2.378084 GCCCTCGAACGAACGAACC 61.378 63.158 0.14 0.00 41.67 3.62
864 961 0.395036 TCTCTCTCCTCCTCCGCTTG 60.395 60.000 0.00 0.00 0.00 4.01
1050 1166 3.221771 CCACCCTGAACTGAATCAAACA 58.778 45.455 0.00 0.00 0.00 2.83
1072 1188 1.702886 CTAGTGCCTGACAGTTGACG 58.297 55.000 0.93 0.00 32.79 4.35
1244 1387 3.499737 GAGCACATGGAACGGCCG 61.500 66.667 26.86 26.86 40.66 6.13
1287 1430 3.073209 ACTCCTTGAAGGGGAAGAAGAAC 59.927 47.826 19.91 0.00 38.47 3.01
1349 1523 8.816640 AACAGCCAAATTAAAGAATTGTACTG 57.183 30.769 0.00 0.00 35.38 2.74
1448 1635 0.732571 CCAATCCCCGATTGTTGACG 59.267 55.000 12.15 0.00 45.41 4.35
1620 1817 0.673985 CCAACTCCACAGACAGACGA 59.326 55.000 0.00 0.00 0.00 4.20
1630 1827 1.547372 AGCAAATGCATCCAACTCCAC 59.453 47.619 8.28 0.00 45.16 4.02
1686 1883 4.323477 TTCCGTGCTTGTCCCCCG 62.323 66.667 0.00 0.00 0.00 5.73
1818 2015 4.740822 ACCTCCAATGTGGCGGGC 62.741 66.667 8.14 0.00 46.54 6.13
1821 2018 2.672651 TGCACCTCCAATGTGGCG 60.673 61.111 0.00 0.00 37.47 5.69
1824 2021 0.679002 CCCTCTGCACCTCCAATGTG 60.679 60.000 0.00 0.00 36.79 3.21
1857 2054 2.276201 GCTATGTGCATCACGTTGGTA 58.724 47.619 0.00 0.00 42.31 3.25
2010 2207 1.270732 GGTATCCTGCTGAGCTCATGG 60.271 57.143 18.63 18.75 0.00 3.66
2061 2258 2.887568 GTGCCGACTGCTCCATCG 60.888 66.667 0.00 0.00 42.00 3.84
2110 2307 2.094494 CACAGGAACGCTGATCACTAGT 60.094 50.000 0.00 0.00 0.00 2.57
2114 2311 1.662629 CATCACAGGAACGCTGATCAC 59.337 52.381 0.00 0.00 28.99 3.06
2151 2348 5.423886 TCATTTGCCACAACTATCGTCATA 58.576 37.500 0.00 0.00 0.00 2.15
2268 2465 2.304180 AGGGAGTGAACTGAATGACTGG 59.696 50.000 0.00 0.00 0.00 4.00
2970 3174 1.949525 GAGACAGCTCTGGTTTTTGCA 59.050 47.619 1.66 0.00 38.16 4.08
2991 3195 5.877564 ACTAGAAAGCAGCTTTATTGTCCTC 59.122 40.000 20.65 5.76 33.49 3.71
3389 3595 5.451242 GGCAAATGTTTTCAGTTACTCACCA 60.451 40.000 0.00 0.00 35.89 4.17
3391 3597 5.831997 AGGCAAATGTTTTCAGTTACTCAC 58.168 37.500 0.00 0.00 35.89 3.51
3429 3635 4.112634 TGTTAGGACAAAATGGGAGCTT 57.887 40.909 0.00 0.00 31.49 3.74
3706 3947 4.373116 ATGACGAGGCGCGGTGTT 62.373 61.111 16.41 0.00 46.49 3.32
4659 4930 1.064296 CTGGCGACGCTCGAAGTAT 59.936 57.895 20.77 0.00 43.74 2.12
4680 4951 4.436998 GTGGACGCTAGCCGCTGT 62.437 66.667 9.66 0.07 41.76 4.40
4905 5182 0.898789 AGGAAGAACGCGAGGAGGAA 60.899 55.000 15.93 0.00 0.00 3.36
4917 5200 1.595993 CGGAGGAGTGCGAGGAAGAA 61.596 60.000 0.00 0.00 40.58 2.52
5062 5345 2.063015 TTTGGCTTGAGGAAGGGCGA 62.063 55.000 0.00 0.00 0.00 5.54
5066 5349 1.160137 CGTCTTTGGCTTGAGGAAGG 58.840 55.000 0.00 0.00 0.00 3.46
5071 5354 1.301677 GGCTCCGTCTTTGGCTTGAG 61.302 60.000 0.00 0.00 0.00 3.02
5362 5660 0.471211 TTCTCCTCCTTGACACGGGT 60.471 55.000 0.00 0.00 0.00 5.28
5367 5665 1.544825 CGGCCTTCTCCTCCTTGACA 61.545 60.000 0.00 0.00 0.00 3.58
5856 6193 6.201226 TGTGAACTTGCAAGTACAATGAAA 57.799 33.333 31.31 3.26 38.57 2.69
5877 6219 0.745128 TGTTTGGAACGAGCGGTTGT 60.745 50.000 0.46 0.46 39.50 3.32
5889 6231 6.048732 TCATGTTAGCTAGTGATGTTTGGA 57.951 37.500 0.00 0.00 0.00 3.53
5920 6264 1.337823 ACATCTTCCGACCCTGTTTCG 60.338 52.381 0.00 0.00 36.20 3.46
6043 6387 2.610479 GCAGATACTAGCATTGCCGCTA 60.610 50.000 4.70 0.00 43.56 4.26
6070 6414 1.078848 GACCAGGACATCAAGCGCT 60.079 57.895 2.64 2.64 0.00 5.92
6124 6468 0.607489 GAACAGCACCTGCATCCACT 60.607 55.000 0.00 0.00 45.16 4.00
6160 6504 4.339530 TCATCGATCTTTCGGATGAAGAGT 59.660 41.667 7.52 0.00 45.53 3.24
6205 6549 0.321034 CAAGTACTGCTGCAGCCTCA 60.321 55.000 34.64 16.55 41.18 3.86
6382 6726 3.889134 CTTGGGCAGCGCAGTGAGA 62.889 63.158 11.47 0.00 0.00 3.27
6421 6765 2.354259 CTGTCTTGCTCCTTCATGACC 58.646 52.381 0.00 0.00 39.18 4.02
6491 6835 2.012948 GCAGCTTTGTCGCAGCAAC 61.013 57.895 0.00 0.00 41.41 4.17
6578 6922 1.346479 ATGCTCCTGATCAGCCTGCT 61.346 55.000 17.76 7.74 35.89 4.24
6793 7137 2.636412 CCGGACGAGAGAGCCAACA 61.636 63.158 0.00 0.00 0.00 3.33
6796 7140 2.831894 TTAGCCGGACGAGAGAGCCA 62.832 60.000 5.05 0.00 0.00 4.75
6886 7230 4.477975 GACGACCGGACGAGCAGG 62.478 72.222 31.92 2.91 37.91 4.85
7370 7714 2.261671 GCCGTTCTCGAGGAAGCA 59.738 61.111 13.56 0.00 39.71 3.91
7595 7943 0.600782 CACCAAACAATGCACCAGCC 60.601 55.000 0.00 0.00 41.13 4.85
7624 7973 7.167468 CCGTTTTACCTCATTTTTCTTTCTGTG 59.833 37.037 0.00 0.00 0.00 3.66
7628 7977 8.812147 ATTCCGTTTTACCTCATTTTTCTTTC 57.188 30.769 0.00 0.00 0.00 2.62
7630 7979 8.417884 TCAATTCCGTTTTACCTCATTTTTCTT 58.582 29.630 0.00 0.00 0.00 2.52
7637 7986 4.918588 ACCTCAATTCCGTTTTACCTCAT 58.081 39.130 0.00 0.00 0.00 2.90
7638 7987 4.360951 ACCTCAATTCCGTTTTACCTCA 57.639 40.909 0.00 0.00 0.00 3.86
7648 7997 4.957759 ATTCCGTTTTACCTCAATTCCG 57.042 40.909 0.00 0.00 0.00 4.30
7654 8003 3.745799 TGCAGAATTCCGTTTTACCTCA 58.254 40.909 0.65 0.00 0.00 3.86
7655 8004 4.000988 TCTGCAGAATTCCGTTTTACCTC 58.999 43.478 15.67 0.00 0.00 3.85
7656 8005 4.015872 TCTGCAGAATTCCGTTTTACCT 57.984 40.909 15.67 0.00 0.00 3.08
7657 8006 4.662145 CATCTGCAGAATTCCGTTTTACC 58.338 43.478 22.50 0.00 0.00 2.85
7658 8007 4.098416 GCATCTGCAGAATTCCGTTTTAC 58.902 43.478 22.50 0.00 41.59 2.01
7659 8008 4.355543 GCATCTGCAGAATTCCGTTTTA 57.644 40.909 22.50 0.00 41.59 1.52
7660 8009 3.221964 GCATCTGCAGAATTCCGTTTT 57.778 42.857 22.50 0.00 41.59 2.43
7661 8010 2.927553 GCATCTGCAGAATTCCGTTT 57.072 45.000 22.50 0.00 41.59 3.60
7699 8050 8.800370 TGAAAAACTGTACATATCATGCCTAA 57.200 30.769 0.00 0.00 0.00 2.69
7701 8052 7.886629 ATGAAAAACTGTACATATCATGCCT 57.113 32.000 0.00 0.00 0.00 4.75
7715 8067 8.693542 AGAAGACAAACAAGAATGAAAAACTG 57.306 30.769 0.00 0.00 0.00 3.16
7724 8076 6.365520 ACACCCTAAGAAGACAAACAAGAAT 58.634 36.000 0.00 0.00 0.00 2.40
7756 8109 8.725405 TGTTAACGAATATCATCAAAGCCTAA 57.275 30.769 0.26 0.00 0.00 2.69
7790 8144 3.275143 GAAAAACCCAAACCAACCAAGG 58.725 45.455 0.00 0.00 0.00 3.61
7812 8167 5.403897 TTTTGCAGTACGTCTTTTCTGAG 57.596 39.130 0.00 0.00 0.00 3.35
7823 8178 7.010697 TGGATACATACAATTTTGCAGTACG 57.989 36.000 0.00 0.00 46.17 3.67
7864 8219 5.532032 TCAATCTCAAATGAGTTCTGCAACA 59.468 36.000 10.06 0.00 42.60 3.33
7950 8321 6.017770 GCATAGTCAGTCGAGTAGAACTACAT 60.018 42.308 13.34 0.54 38.48 2.29
7973 8344 2.632028 GCTCTAGGGAAGATCATGAGCA 59.368 50.000 14.38 0.00 43.18 4.26
7990 8361 5.947228 TCTCGTTTTGATGAATTTGCTCT 57.053 34.783 0.00 0.00 0.00 4.09
8001 8372 4.452455 AGAAACTGCGATTCTCGTTTTGAT 59.548 37.500 0.00 0.00 42.81 2.57
8004 8375 4.272504 TCAAGAAACTGCGATTCTCGTTTT 59.727 37.500 0.00 0.00 42.81 2.43
8013 8384 4.022935 TGAAAGCATTCAAGAAACTGCGAT 60.023 37.500 1.05 0.00 42.47 4.58
8027 8398 6.992063 ACTTGAATAGTCGATGAAAGCATT 57.008 33.333 0.00 0.00 29.77 3.56
8045 8416 1.410517 GATCGCCTCATCTGGACTTGA 59.589 52.381 0.00 0.00 0.00 3.02
8051 8422 2.028385 TCATCATGATCGCCTCATCTGG 60.028 50.000 4.86 0.00 42.91 3.86
8067 8438 3.513680 GCATCTGTGCCATTTTCATCA 57.486 42.857 0.00 0.00 45.76 3.07
8179 8551 9.927668 GGTTTTGGATTTCTTGAGAATAAATGA 57.072 29.630 0.00 0.00 33.54 2.57
8199 8571 7.606456 ACCATATAGAACTGTGTACTGGTTTTG 59.394 37.037 0.00 0.00 30.56 2.44
8317 8693 0.684535 TCCGCAAGATTCACACTCCA 59.315 50.000 0.00 0.00 43.02 3.86
8359 8735 3.031736 GGTACCATCTAGCTCAGACCAA 58.968 50.000 7.15 0.00 35.62 3.67
8394 8771 1.270625 TGAGTTCCGTTTCGCCAGAAT 60.271 47.619 0.00 0.00 36.09 2.40
8402 8779 3.334691 TCATGATGGTGAGTTCCGTTTC 58.665 45.455 0.00 0.00 0.00 2.78
8406 8783 1.600957 GCATCATGATGGTGAGTTCCG 59.399 52.381 31.62 7.75 39.16 4.30
8485 8865 1.009829 GCACGTCCACATGGAGATTC 58.990 55.000 0.00 0.00 46.49 2.52
8529 8909 3.135167 TCAGATGTGCCATCTGCTATTGA 59.865 43.478 27.24 14.73 43.79 2.57


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

AutoCloner maintained by Alex Coulton.