Multiple sequence alignment - TraesCS5D01G192100

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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 TraesCS5D01G192100 chr5D 100.000 5020 0 0 1 5020 294943619 294948638 0.000000e+00 9271.0
1 TraesCS5D01G192100 chr5A 96.549 3651 79 21 780 4420 388572611 388576224 0.000000e+00 6000.0
2 TraesCS5D01G192100 chr5A 89.103 780 59 13 3 781 388571753 388572507 0.000000e+00 946.0
3 TraesCS5D01G192100 chr5A 93.469 245 16 0 4773 5017 388576810 388577054 1.030000e-96 364.0
4 TraesCS5D01G192100 chr5A 84.103 390 39 10 4413 4780 388576304 388576692 6.180000e-94 355.0
5 TraesCS5D01G192100 chr5B 93.702 2064 77 25 2501 4544 336767769 336769799 0.000000e+00 3042.0
6 TraesCS5D01G192100 chr5B 96.315 1547 41 6 936 2476 336766234 336767770 0.000000e+00 2527.0
7 TraesCS5D01G192100 chr5B 92.988 599 27 5 3 600 336765309 336765893 0.000000e+00 859.0
8 TraesCS5D01G192100 chr5B 91.829 257 18 3 607 862 336765981 336766235 6.180000e-94 355.0
9 TraesCS5D01G192100 chr5B 91.489 235 13 2 4731 4965 336769946 336770173 2.920000e-82 316.0
10 TraesCS5D01G192100 chr5B 100.000 29 0 0 4981 5009 332411517 332411489 3.000000e-03 54.7
11 TraesCS5D01G192100 chr6D 84.835 666 67 16 1523 2183 468108872 468109508 1.520000e-179 640.0
12 TraesCS5D01G192100 chr6D 86.538 156 12 1 2092 2247 468109688 468109834 4.020000e-36 163.0
13 TraesCS5D01G192100 chr6D 88.462 52 5 1 4964 5014 423754367 423754316 1.510000e-05 62.1
14 TraesCS5D01G192100 chr3D 84.639 664 73 11 1523 2183 55112514 55111877 7.090000e-178 634.0
15 TraesCS5D01G192100 chr4A 84.211 665 73 14 1523 2183 714208113 714207477 7.140000e-173 617.0
16 TraesCS5D01G192100 chr4A 94.737 38 0 2 4980 5016 634746739 634746703 1.950000e-04 58.4
17 TraesCS5D01G192100 chr3A 84.187 664 76 12 1523 2183 741236192 741236829 7.140000e-173 617.0
18 TraesCS5D01G192100 chr3A 83.974 156 13 3 2092 2247 741237023 741237166 6.780000e-29 139.0
19 TraesCS5D01G192100 chr3A 94.737 38 1 1 4980 5016 27881284 27881247 1.950000e-04 58.4
20 TraesCS5D01G192100 chr1A 83.208 667 80 13 1523 2183 519472096 519471456 2.600000e-162 582.0
21 TraesCS5D01G192100 chr1A 83.333 156 14 3 2092 2247 519471247 519471104 3.150000e-27 134.0
22 TraesCS5D01G192100 chr2B 87.719 57 4 3 4961 5016 363772892 363772838 4.200000e-06 63.9
23 TraesCS5D01G192100 chr3B 94.737 38 1 1 4980 5016 627742817 627742854 1.950000e-04 58.4
24 TraesCS5D01G192100 chr1D 87.037 54 3 3 4966 5016 459867409 459867461 1.950000e-04 58.4
25 TraesCS5D01G192100 chr2A 100.000 28 0 0 4989 5016 42933625 42933598 9.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G192100 chr5D 294943619 294948638 5019 False 9271.00 9271 100.0000 1 5020 1 chr5D.!!$F1 5019
1 TraesCS5D01G192100 chr5A 388571753 388577054 5301 False 1916.25 6000 90.8060 3 5017 4 chr5A.!!$F1 5014
2 TraesCS5D01G192100 chr5B 336765309 336770173 4864 False 1419.80 3042 93.2646 3 4965 5 chr5B.!!$F1 4962
3 TraesCS5D01G192100 chr6D 468108872 468109834 962 False 401.50 640 85.6865 1523 2247 2 chr6D.!!$F1 724
4 TraesCS5D01G192100 chr3D 55111877 55112514 637 True 634.00 634 84.6390 1523 2183 1 chr3D.!!$R1 660
5 TraesCS5D01G192100 chr4A 714207477 714208113 636 True 617.00 617 84.2110 1523 2183 1 chr4A.!!$R2 660
6 TraesCS5D01G192100 chr3A 741236192 741237166 974 False 378.00 617 84.0805 1523 2247 2 chr3A.!!$F1 724
7 TraesCS5D01G192100 chr1A 519471104 519472096 992 True 358.00 582 83.2705 1523 2247 2 chr1A.!!$R1 724

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
22 23 0.457851 CCACCAGAAACCAACGCAAA 59.542 50.0 0.00 0.0 0.00 3.68 F
930 1133 0.468585 ACACACGTACTGTCTCCCCA 60.469 55.0 0.00 0.0 0.00 4.96 F
1569 1776 0.607489 CAGTGTGCCTGCTTTAGCCT 60.607 55.0 0.00 0.0 41.18 4.58 F
1620 1827 2.498291 TTCCTCTGCAGACTGAGCGC 62.498 60.0 13.74 0.0 39.77 5.92 F
3026 3554 0.178068 CCACCTCCCGTAACCTCATG 59.822 60.0 0.00 0.0 0.00 3.07 F
3581 4111 0.534873 AGGAAGCCGAGAAGAAGCTC 59.465 55.0 0.00 0.0 35.30 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1855 0.034476 TGCCTGTTCTCAGCACTCAG 59.966 55.000 0.00 0.0 40.09 3.35 R
2051 2261 0.752658 TCACCTGATCCTGTATGGCG 59.247 55.000 0.00 0.0 35.26 5.69 R
2597 3118 1.446966 GAGCCTGTGACCGAGCTTC 60.447 63.158 0.00 0.0 35.23 3.86 R
3218 3748 1.449726 CTGCTGGCTGCTGTGTTTCA 61.450 55.000 17.45 0.0 43.37 2.69 R
3828 4358 0.249398 ACTACATTCCTGGACCGTGC 59.751 55.000 0.00 0.0 0.00 5.34 R
4748 5398 0.454600 CAGGCCATGCATCTGAACAC 59.545 55.000 5.01 0.0 0.00 3.32 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
22 23 0.457851 CCACCAGAAACCAACGCAAA 59.542 50.000 0.00 0.00 0.00 3.68
23 24 1.535860 CCACCAGAAACCAACGCAAAG 60.536 52.381 0.00 0.00 0.00 2.77
153 154 4.510340 CCTGACCAGTTGTTTAGTGTACAC 59.490 45.833 18.56 18.56 0.00 2.90
154 155 4.444536 TGACCAGTTGTTTAGTGTACACC 58.555 43.478 22.28 7.67 0.00 4.16
195 196 2.631062 ACGTGACCCTTGAGTTATGACA 59.369 45.455 0.00 0.00 0.00 3.58
196 197 3.260884 ACGTGACCCTTGAGTTATGACAT 59.739 43.478 0.00 0.00 0.00 3.06
243 246 4.099266 TGCCTTGTAAAACTGCAACTCAAT 59.901 37.500 0.00 0.00 0.00 2.57
299 302 5.741388 ATTTCCGACTATCACAGAAATGC 57.259 39.130 0.00 0.00 36.18 3.56
308 311 6.392354 ACTATCACAGAAATGCCAAAACATG 58.608 36.000 0.00 0.00 0.00 3.21
338 341 6.512342 ACTATAACCACTGTGTCTACTGTC 57.488 41.667 7.08 0.00 36.93 3.51
348 351 5.651139 ACTGTGTCTACTGTCCGTATAATGT 59.349 40.000 0.00 0.00 34.34 2.71
361 364 4.262079 CCGTATAATGTCCCCTCTCACTTC 60.262 50.000 0.00 0.00 0.00 3.01
369 372 3.057174 GTCCCCTCTCACTTCGCATATAG 60.057 52.174 0.00 0.00 0.00 1.31
464 468 6.407475 TTTTCTTTCTTGCAGAAAAAGCAC 57.593 33.333 8.00 0.00 43.89 4.40
465 469 4.045636 TCTTTCTTGCAGAAAAAGCACC 57.954 40.909 10.97 0.00 42.95 5.01
481 485 1.130561 GCACCGAGTAGATTTGGTTGC 59.869 52.381 0.00 0.00 32.27 4.17
490 494 1.613437 AGATTTGGTTGCGGTCTTTGG 59.387 47.619 0.00 0.00 0.00 3.28
494 498 1.104577 TGGTTGCGGTCTTTGGTTCC 61.105 55.000 0.00 0.00 0.00 3.62
502 506 2.748465 CGGTCTTTGGTTCCTGTTCCTT 60.748 50.000 0.00 0.00 0.00 3.36
512 516 4.394729 GTTCCTGTTCCTTTGATGTGGTA 58.605 43.478 0.00 0.00 0.00 3.25
537 551 1.002087 GTGGCCCCTATGATTAGGTCG 59.998 57.143 0.00 0.00 43.19 4.79
606 703 8.116669 AGCCTAGGTTCAGTTATATGCTAGATA 58.883 37.037 11.31 0.00 0.00 1.98
607 704 8.919145 GCCTAGGTTCAGTTATATGCTAGATAT 58.081 37.037 11.31 0.00 0.00 1.63
634 731 2.484264 GGATTCTTCGGTTGTCTGGTTG 59.516 50.000 0.00 0.00 0.00 3.77
643 740 2.154462 GTTGTCTGGTTGATGGTGAGG 58.846 52.381 0.00 0.00 0.00 3.86
683 780 4.202161 ACGAGGGCTCTGTCTATTATGTTG 60.202 45.833 0.00 0.00 0.00 3.33
712 809 5.347124 TCCTTTTCTTGGGTATAGTCTCCA 58.653 41.667 0.00 0.00 0.00 3.86
742 839 2.168521 GGTGGTGCATCTGCTACTTCTA 59.831 50.000 0.00 0.00 42.66 2.10
751 848 6.155827 GCATCTGCTACTTCTACATCTTAGG 58.844 44.000 0.00 0.00 38.21 2.69
771 868 9.333724 TCTTAGGTTTTGAGTTAGTAACTTTGG 57.666 33.333 16.56 0.64 43.03 3.28
806 1008 5.568620 AGTAATGTTCTCCCATACATCCC 57.431 43.478 0.00 0.00 34.04 3.85
807 1009 4.975147 AGTAATGTTCTCCCATACATCCCA 59.025 41.667 0.00 0.00 34.04 4.37
867 1070 6.193761 CGTTAAACAGCTTTTCCTTAAACGA 58.806 36.000 14.36 0.00 0.00 3.85
878 1081 7.958025 GCTTTTCCTTAAACGATTCTGTAGAAG 59.042 37.037 0.51 0.00 37.48 2.85
909 1112 5.750067 CAGTTGCTTTTGTTACTGCTCAATT 59.250 36.000 0.00 0.00 32.53 2.32
924 1127 3.120991 GCTCAATTCACACACGTACTGTC 60.121 47.826 0.00 0.00 0.00 3.51
927 1130 2.787601 TTCACACACGTACTGTCTCC 57.212 50.000 0.00 0.00 0.00 3.71
930 1133 0.468585 ACACACGTACTGTCTCCCCA 60.469 55.000 0.00 0.00 0.00 4.96
978 1181 5.259832 AGATAGCCGAGTAAAACTGTACC 57.740 43.478 0.00 0.00 0.00 3.34
1365 1568 1.131638 ATAAGATCCAAGCTCGGGCA 58.868 50.000 11.40 0.00 41.70 5.36
1526 1730 5.359756 CACTATTGCTTGCCTCTATGTGTA 58.640 41.667 0.00 0.00 0.00 2.90
1569 1776 0.607489 CAGTGTGCCTGCTTTAGCCT 60.607 55.000 0.00 0.00 41.18 4.58
1620 1827 2.498291 TTCCTCTGCAGACTGAGCGC 62.498 60.000 13.74 0.00 39.77 5.92
1834 2041 4.640771 TCAGCCCTTTGATAACTCAACT 57.359 40.909 0.00 0.00 41.05 3.16
1848 2055 3.672808 ACTCAACTGCTTCTCATTCAGG 58.327 45.455 0.00 0.00 32.42 3.86
2051 2261 5.106908 GCAAGATACAGTGGTTGAAAGAGAC 60.107 44.000 0.00 0.00 0.00 3.36
2119 2330 9.260002 CTTTGTCTTTTATTGTGCATTTACCTT 57.740 29.630 0.00 0.00 0.00 3.50
2383 2900 3.448686 CCGTAAGTCAGCATACCTTCAG 58.551 50.000 0.00 0.00 0.00 3.02
2589 3110 6.120905 AGATATATGATCAGCCATTGCCTTC 58.879 40.000 0.09 0.00 38.69 3.46
2597 3118 3.056393 TCAGCCATTGCCTTCTCAAATTG 60.056 43.478 0.00 0.00 38.69 2.32
2742 3268 9.553064 GTCACTTAATGAAATATCTGAGATGGT 57.447 33.333 4.96 0.00 39.72 3.55
2821 3347 5.445010 GGTTATTTACCGCACTGTCTTAACG 60.445 44.000 0.00 0.00 37.12 3.18
2839 3365 9.974528 GTCTTAACGAATTCTTTTGATTTTTCG 57.025 29.630 2.17 0.00 39.43 3.46
3026 3554 0.178068 CCACCTCCCGTAACCTCATG 59.822 60.000 0.00 0.00 0.00 3.07
3218 3748 7.095183 TCCTGATGAGAAGCCCATATTTATT 57.905 36.000 0.00 0.00 0.00 1.40
3275 3805 0.954452 CTATCCCATCAAAAGCGCCC 59.046 55.000 2.29 0.00 0.00 6.13
3581 4111 0.534873 AGGAAGCCGAGAAGAAGCTC 59.465 55.000 0.00 0.00 35.30 4.09
3617 4147 4.348863 AGCATCTCTCTCTCTCTCTCTC 57.651 50.000 0.00 0.00 0.00 3.20
3618 4148 3.972638 AGCATCTCTCTCTCTCTCTCTCT 59.027 47.826 0.00 0.00 0.00 3.10
3619 4149 4.040217 AGCATCTCTCTCTCTCTCTCTCTC 59.960 50.000 0.00 0.00 0.00 3.20
3620 4150 4.040217 GCATCTCTCTCTCTCTCTCTCTCT 59.960 50.000 0.00 0.00 0.00 3.10
3621 4151 5.782047 CATCTCTCTCTCTCTCTCTCTCTC 58.218 50.000 0.00 0.00 0.00 3.20
3622 4152 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
3623 4153 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3624 4154 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3625 4155 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3626 4156 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3627 4157 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3628 4158 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3629 4159 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3630 4160 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3640 4170 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3642 4172 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
3716 4246 2.875094 AGAAAACTGAGGCAGCTGAT 57.125 45.000 20.43 4.39 34.37 2.90
3793 4323 3.791245 CAGAGGATGAGTTTACTCCAGC 58.209 50.000 7.39 0.00 42.20 4.85
3800 4330 3.995199 TGAGTTTACTCCAGCTTCTGTG 58.005 45.455 7.39 0.00 42.20 3.66
3801 4331 3.641436 TGAGTTTACTCCAGCTTCTGTGA 59.359 43.478 7.39 0.00 42.20 3.58
3802 4332 4.284490 TGAGTTTACTCCAGCTTCTGTGAT 59.716 41.667 7.39 0.00 42.20 3.06
3823 4353 5.470098 TGATAGTGAACAAAGAACAGAAGCC 59.530 40.000 0.00 0.00 0.00 4.35
3828 4358 1.597663 ACAAAGAACAGAAGCCGAACG 59.402 47.619 0.00 0.00 0.00 3.95
3908 4438 2.168728 GAGGAAGAAAGCCCAGTCGTAT 59.831 50.000 0.00 0.00 0.00 3.06
4041 4571 1.617263 GGAAGGAAAAGAAGGAGGCCC 60.617 57.143 0.00 0.00 0.00 5.80
4156 4687 6.114187 TGAAAAGACTGGAGAAGCTATTCA 57.886 37.500 0.00 0.00 37.94 2.57
4195 4726 3.268330 GGGTGGAGTCGGATAAAAAGTC 58.732 50.000 0.00 0.00 0.00 3.01
4197 4728 3.582780 GTGGAGTCGGATAAAAAGTCGT 58.417 45.455 0.00 0.00 0.00 4.34
4344 4877 5.645497 TGCTGTTTGTGTATGTGTATGCATA 59.355 36.000 1.16 1.16 31.49 3.14
4388 4922 1.608590 CATCGTCCTTGCTTTGGTTGT 59.391 47.619 0.00 0.00 0.00 3.32
4458 5078 5.458041 ACAACTCCATGAATTTCACAAGG 57.542 39.130 0.15 4.81 0.00 3.61
4459 5079 4.281688 ACAACTCCATGAATTTCACAAGGG 59.718 41.667 0.15 2.04 0.00 3.95
4460 5080 3.434309 ACTCCATGAATTTCACAAGGGG 58.566 45.455 0.15 6.93 0.00 4.79
4490 5119 8.897752 GGATTATATTTTCAGCATATCAGACCC 58.102 37.037 0.00 0.00 0.00 4.46
4495 5124 7.618019 ATTTTCAGCATATCAGACCCTAGTA 57.382 36.000 0.00 0.00 0.00 1.82
4496 5125 6.406692 TTTCAGCATATCAGACCCTAGTAC 57.593 41.667 0.00 0.00 0.00 2.73
4544 5180 5.105756 GGATGAATCTTTTTGGTTGGACGAT 60.106 40.000 0.00 0.00 0.00 3.73
4545 5181 6.094881 GGATGAATCTTTTTGGTTGGACGATA 59.905 38.462 0.00 0.00 0.00 2.92
4546 5182 6.885952 TGAATCTTTTTGGTTGGACGATAA 57.114 33.333 0.00 0.00 0.00 1.75
4547 5183 7.461182 TGAATCTTTTTGGTTGGACGATAAT 57.539 32.000 0.00 0.00 0.00 1.28
4548 5184 8.568676 TGAATCTTTTTGGTTGGACGATAATA 57.431 30.769 0.00 0.00 0.00 0.98
4549 5185 9.015367 TGAATCTTTTTGGTTGGACGATAATAA 57.985 29.630 0.00 0.00 0.00 1.40
4550 5186 9.849166 GAATCTTTTTGGTTGGACGATAATAAA 57.151 29.630 0.00 0.00 0.00 1.40
4551 5187 9.634163 AATCTTTTTGGTTGGACGATAATAAAC 57.366 29.630 0.00 0.00 0.00 2.01
4552 5188 7.595604 TCTTTTTGGTTGGACGATAATAAACC 58.404 34.615 0.00 0.00 40.59 3.27
4556 5192 4.263816 TGGTTGGACGATAATAAACCCCAA 60.264 41.667 0.00 0.00 39.65 4.12
4558 5194 6.063404 GGTTGGACGATAATAAACCCCAATA 58.937 40.000 0.00 0.00 35.31 1.90
4559 5195 6.546772 GGTTGGACGATAATAAACCCCAATAA 59.453 38.462 0.00 0.00 35.31 1.40
4561 5197 7.753309 TGGACGATAATAAACCCCAATAATG 57.247 36.000 0.00 0.00 0.00 1.90
4563 5199 7.229707 TGGACGATAATAAACCCCAATAATGTG 59.770 37.037 0.00 0.00 0.00 3.21
4565 5201 6.775629 ACGATAATAAACCCCAATAATGTGCT 59.224 34.615 0.00 0.00 0.00 4.40
4568 5204 6.469782 AATAAACCCCAATAATGTGCTGAG 57.530 37.500 0.00 0.00 0.00 3.35
4570 5206 1.640670 ACCCCAATAATGTGCTGAGGT 59.359 47.619 0.00 0.00 0.00 3.85
4595 5236 2.267961 GGACGCGGGATTCCTTGT 59.732 61.111 12.47 0.00 0.00 3.16
4598 5239 2.046314 CGCGGGATTCCTTGTGGT 60.046 61.111 0.00 0.00 34.23 4.16
4687 5337 5.070847 ACAACTTTTTCATTGCAAGGGATCT 59.929 36.000 11.73 0.00 0.00 2.75
4697 5347 0.176680 CAAGGGATCTGTCGGTCCTG 59.823 60.000 0.00 0.00 34.84 3.86
4738 5388 6.302269 ACCATTTGGATCTCTATGATTGGTC 58.698 40.000 3.01 0.00 36.90 4.02
4748 5398 9.883142 GATCTCTATGATTGGTCCTTTATTAGG 57.117 37.037 0.00 0.00 39.43 2.69
4860 5635 6.676990 ATCATCTTGTACTGCCAGATATGA 57.323 37.500 0.00 0.00 0.00 2.15
4862 5637 4.307443 TCTTGTACTGCCAGATATGACG 57.693 45.455 0.00 0.00 0.00 4.35
4865 5640 3.020984 TGTACTGCCAGATATGACGACA 58.979 45.455 0.00 0.00 0.00 4.35
4961 5736 4.873827 TGCAGTTCGATTGGTCCTTATTAC 59.126 41.667 0.00 0.00 0.00 1.89
4999 5774 8.425577 TTTGAGAAACCTTCGATCTATTCATC 57.574 34.615 0.00 0.00 34.02 2.92
5002 5777 7.923344 TGAGAAACCTTCGATCTATTCATCTTC 59.077 37.037 0.00 0.00 34.02 2.87
5019 5794 8.654230 TTCATCTTCAATTATGACAGTAGAGC 57.346 34.615 0.00 0.00 34.61 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.104577 GCGTTGGTTTCTGGTGGGAA 61.105 55.000 0.00 0.00 0.00 3.97
22 23 9.908152 GAAAACATAGTTAATTTGGTACTTGCT 57.092 29.630 0.00 0.00 0.00 3.91
23 24 9.685828 TGAAAACATAGTTAATTTGGTACTTGC 57.314 29.630 0.00 0.00 0.00 4.01
153 154 0.889186 GTGTAGCCAAGGTGGTGTGG 60.889 60.000 0.00 0.00 40.46 4.17
154 155 0.179032 TGTGTAGCCAAGGTGGTGTG 60.179 55.000 0.00 0.00 40.46 3.82
195 196 2.109774 CACATGGGTTTGGGTGCATAT 58.890 47.619 0.00 0.00 0.00 1.78
196 197 1.554836 CACATGGGTTTGGGTGCATA 58.445 50.000 0.00 0.00 0.00 3.14
243 246 4.346709 TGTCTAACACAATCTTGGTCTGGA 59.653 41.667 0.00 0.00 29.30 3.86
299 302 8.760569 GTGGTTATAGTTGTTTTCATGTTTTGG 58.239 33.333 0.00 0.00 0.00 3.28
308 311 7.492352 AGACACAGTGGTTATAGTTGTTTTC 57.508 36.000 5.31 0.00 0.00 2.29
338 341 3.231818 AGTGAGAGGGGACATTATACGG 58.768 50.000 0.00 0.00 0.00 4.02
348 351 2.088104 ATATGCGAAGTGAGAGGGGA 57.912 50.000 0.00 0.00 0.00 4.81
361 364 7.040617 TGGAAGAGGAACTTACTACTATATGCG 60.041 40.741 0.00 0.00 41.55 4.73
464 468 1.006832 CCGCAACCAAATCTACTCGG 58.993 55.000 0.00 0.00 0.00 4.63
465 469 1.659098 GACCGCAACCAAATCTACTCG 59.341 52.381 0.00 0.00 0.00 4.18
481 485 1.202770 AGGAACAGGAACCAAAGACCG 60.203 52.381 0.00 0.00 0.00 4.79
490 494 3.222603 ACCACATCAAAGGAACAGGAAC 58.777 45.455 0.00 0.00 0.00 3.62
494 498 4.214119 CACAGTACCACATCAAAGGAACAG 59.786 45.833 0.00 0.00 0.00 3.16
502 506 1.544537 GGCCACACAGTACCACATCAA 60.545 52.381 0.00 0.00 0.00 2.57
512 516 1.298953 AATCATAGGGGCCACACAGT 58.701 50.000 8.31 0.00 0.00 3.55
537 551 5.449107 AGGCATGCAGATTATGAAATCAC 57.551 39.130 21.36 0.00 43.44 3.06
606 703 4.827284 AGACAACCGAAGAATCCAAAACAT 59.173 37.500 0.00 0.00 0.00 2.71
607 704 4.036262 CAGACAACCGAAGAATCCAAAACA 59.964 41.667 0.00 0.00 0.00 2.83
608 705 4.537015 CAGACAACCGAAGAATCCAAAAC 58.463 43.478 0.00 0.00 0.00 2.43
609 706 3.568007 CCAGACAACCGAAGAATCCAAAA 59.432 43.478 0.00 0.00 0.00 2.44
618 715 1.806542 CCATCAACCAGACAACCGAAG 59.193 52.381 0.00 0.00 0.00 3.79
621 718 0.874390 CACCATCAACCAGACAACCG 59.126 55.000 0.00 0.00 0.00 4.44
634 731 3.128242 CAGAGCATTTTCACCTCACCATC 59.872 47.826 0.00 0.00 0.00 3.51
643 740 3.123621 CCTCGTGTACAGAGCATTTTCAC 59.876 47.826 13.69 0.00 34.56 3.18
683 780 7.447545 AGACTATACCCAAGAAAAGGAACAAAC 59.552 37.037 0.00 0.00 0.00 2.93
773 870 9.646522 ATGGGAGAACATTACTTGCTATAATTT 57.353 29.630 0.00 0.00 0.00 1.82
867 1070 4.357918 ACTGGCACAACTTCTACAGAAT 57.642 40.909 0.00 0.00 38.70 2.40
909 1112 0.956633 GGGAGACAGTACGTGTGTGA 59.043 55.000 9.86 0.00 40.56 3.58
927 1130 5.591877 CCTTCTCATCCTCAAAACTTATGGG 59.408 44.000 0.00 0.00 0.00 4.00
930 1133 6.642733 TCCCTTCTCATCCTCAAAACTTAT 57.357 37.500 0.00 0.00 0.00 1.73
978 1181 6.982141 CCATGGTTATGATCCAACAGAAAATG 59.018 38.462 2.57 0.00 38.52 2.32
1251 1454 9.000486 ACAAAGTAGAAGGTATAAGTTTGCTTC 58.000 33.333 0.00 0.00 36.22 3.86
1526 1730 2.224450 CCCCTGGTTTACTTCAACGAGT 60.224 50.000 0.00 0.00 32.19 4.18
1642 1849 2.433838 CTCAGCACTCAGTGGCCG 60.434 66.667 7.00 0.00 33.64 6.13
1648 1855 0.034476 TGCCTGTTCTCAGCACTCAG 59.966 55.000 0.00 0.00 40.09 3.35
2051 2261 0.752658 TCACCTGATCCTGTATGGCG 59.247 55.000 0.00 0.00 35.26 5.69
2383 2900 2.843401 ATGATGAGCATGAGAGAGGC 57.157 50.000 0.00 0.00 35.42 4.70
2589 3110 2.807967 TGTGACCGAGCTTCAATTTGAG 59.192 45.455 0.00 0.00 0.00 3.02
2597 3118 1.446966 GAGCCTGTGACCGAGCTTC 60.447 63.158 0.00 0.00 35.23 3.86
2629 3151 3.811497 TGATGCAGAGAATTCGGCTTATG 59.189 43.478 16.82 2.89 43.75 1.90
2693 3219 9.407380 TGACTAACATAATCCAATGCTACATTT 57.593 29.630 0.00 0.00 0.00 2.32
3064 3592 5.246307 ACTTCTCAACCTACCAAAGCATAC 58.754 41.667 0.00 0.00 0.00 2.39
3218 3748 1.449726 CTGCTGGCTGCTGTGTTTCA 61.450 55.000 17.45 0.00 43.37 2.69
3275 3805 3.800506 CAGCTTCCTTTGCTTGTTTCAAG 59.199 43.478 5.28 5.28 38.92 3.02
3581 4111 5.911752 AGAGATGCTAATGTGTCTACCTTG 58.088 41.667 0.00 0.00 0.00 3.61
3617 4147 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3618 4148 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3619 4149 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
3620 4150 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
3621 4151 5.070180 ACATGAGAGAGAGAGAGAGAGAGAG 59.930 48.000 0.00 0.00 0.00 3.20
3622 4152 4.964897 ACATGAGAGAGAGAGAGAGAGAGA 59.035 45.833 0.00 0.00 0.00 3.10
3623 4153 5.287674 ACATGAGAGAGAGAGAGAGAGAG 57.712 47.826 0.00 0.00 0.00 3.20
3624 4154 5.899547 ACTACATGAGAGAGAGAGAGAGAGA 59.100 44.000 0.00 0.00 0.00 3.10
3625 4155 5.987953 CACTACATGAGAGAGAGAGAGAGAG 59.012 48.000 0.00 0.00 0.00 3.20
3626 4156 5.425217 ACACTACATGAGAGAGAGAGAGAGA 59.575 44.000 0.00 0.00 0.00 3.10
3627 4157 5.674525 ACACTACATGAGAGAGAGAGAGAG 58.325 45.833 0.00 0.00 0.00 3.20
3628 4158 5.692115 ACACTACATGAGAGAGAGAGAGA 57.308 43.478 0.00 0.00 0.00 3.10
3629 4159 6.821160 TGTTACACTACATGAGAGAGAGAGAG 59.179 42.308 0.00 0.00 0.00 3.20
3630 4160 6.712276 TGTTACACTACATGAGAGAGAGAGA 58.288 40.000 0.00 0.00 0.00 3.10
3640 4170 5.859495 TGTCACCATTGTTACACTACATGA 58.141 37.500 0.00 0.00 0.00 3.07
3642 4172 6.770785 AGTTTGTCACCATTGTTACACTACAT 59.229 34.615 0.00 0.00 28.63 2.29
3716 4246 0.892358 AGTCAGTTGGCTCGTCGGTA 60.892 55.000 0.00 0.00 0.00 4.02
3793 4323 7.439356 TCTGTTCTTTGTTCACTATCACAGAAG 59.561 37.037 0.00 0.00 36.16 2.85
3800 4330 5.389935 CGGCTTCTGTTCTTTGTTCACTATC 60.390 44.000 0.00 0.00 0.00 2.08
3801 4331 4.452455 CGGCTTCTGTTCTTTGTTCACTAT 59.548 41.667 0.00 0.00 0.00 2.12
3802 4332 3.807622 CGGCTTCTGTTCTTTGTTCACTA 59.192 43.478 0.00 0.00 0.00 2.74
3823 4353 3.851845 TTCCTGGACCGTGCGTTCG 62.852 63.158 0.00 0.00 0.00 3.95
3828 4358 0.249398 ACTACATTCCTGGACCGTGC 59.751 55.000 0.00 0.00 0.00 5.34
3834 4364 3.260884 GTCTTGGTGACTACATTCCTGGA 59.739 47.826 0.00 0.00 42.21 3.86
4156 4687 4.141959 CCACCCAACAAACAGAACAGAAAT 60.142 41.667 0.00 0.00 0.00 2.17
4195 4726 4.861210 TGTGCCAACCAAAATTAACTACG 58.139 39.130 0.00 0.00 0.00 3.51
4197 4728 6.472686 AACTGTGCCAACCAAAATTAACTA 57.527 33.333 0.00 0.00 0.00 2.24
4344 4877 1.066573 CAACTGAGACGCCTCCATTCT 60.067 52.381 0.00 0.00 38.66 2.40
4388 4922 2.353605 GCCAAAGCGAAATCATGGGAAA 60.354 45.455 0.00 0.00 0.00 3.13
4458 5078 5.726980 TGCTGAAAATATAATCCATGCCC 57.273 39.130 0.00 0.00 0.00 5.36
4459 5079 8.689061 TGATATGCTGAAAATATAATCCATGCC 58.311 33.333 0.00 0.00 0.00 4.40
4460 5080 9.731819 CTGATATGCTGAAAATATAATCCATGC 57.268 33.333 0.00 0.00 0.00 4.06
4490 5119 1.386533 TCCTTTCGCCCTCGTACTAG 58.613 55.000 0.00 0.00 36.96 2.57
4493 5122 0.458669 TCATCCTTTCGCCCTCGTAC 59.541 55.000 0.00 0.00 36.96 3.67
4495 5124 0.541863 ATTCATCCTTTCGCCCTCGT 59.458 50.000 0.00 0.00 36.96 4.18
4496 5125 1.599542 GAATTCATCCTTTCGCCCTCG 59.400 52.381 0.00 0.00 0.00 4.63
4505 5141 3.931907 TCATCCGGTGAATTCATCCTT 57.068 42.857 12.12 0.00 32.78 3.36
4544 5180 6.549364 CCTCAGCACATTATTGGGGTTTATTA 59.451 38.462 0.00 0.00 33.85 0.98
4545 5181 5.363580 CCTCAGCACATTATTGGGGTTTATT 59.636 40.000 0.00 0.00 33.85 1.40
4546 5182 4.895297 CCTCAGCACATTATTGGGGTTTAT 59.105 41.667 0.00 0.00 33.85 1.40
4547 5183 4.264172 ACCTCAGCACATTATTGGGGTTTA 60.264 41.667 0.00 0.00 43.03 2.01
4548 5184 3.099141 CCTCAGCACATTATTGGGGTTT 58.901 45.455 0.00 0.00 33.85 3.27
4549 5185 2.042979 ACCTCAGCACATTATTGGGGTT 59.957 45.455 0.00 0.00 43.03 4.11
4550 5186 1.640670 ACCTCAGCACATTATTGGGGT 59.359 47.619 0.00 0.00 40.83 4.95
4551 5187 2.442236 ACCTCAGCACATTATTGGGG 57.558 50.000 0.00 0.00 38.47 4.96
4552 5188 2.689983 GGAACCTCAGCACATTATTGGG 59.310 50.000 0.00 0.00 0.00 4.12
4581 5222 0.810031 CTACCACAAGGAATCCCGCG 60.810 60.000 0.00 0.00 38.69 6.46
4633 5274 6.042093 TCACAAGAACCTGAACTCAATCTACT 59.958 38.462 0.00 0.00 0.00 2.57
4687 5337 6.066032 TCTATGTGTATTATCAGGACCGACA 58.934 40.000 0.00 0.00 0.00 4.35
4748 5398 0.454600 CAGGCCATGCATCTGAACAC 59.545 55.000 5.01 0.00 0.00 3.32
4860 5635 5.116180 TCTGAAAGACTGATTGTTTGTCGT 58.884 37.500 0.00 0.00 38.67 4.34
4862 5637 5.008019 TGCTCTGAAAGACTGATTGTTTGTC 59.992 40.000 0.00 0.00 38.67 3.18
4865 5640 5.371526 TCTGCTCTGAAAGACTGATTGTTT 58.628 37.500 0.00 0.00 38.67 2.83


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

AutoCloner maintained by Alex Coulton.