Multiple sequence alignment - TraesCS3D01G434700

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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 TraesCS3D01G434700 chr3D 100.000 6015 0 0 1 6015 547297217 547303231 0.000000e+00 11108
1 TraesCS3D01G434700 chr3D 80.855 2737 356 87 1138 3784 552003086 552000428 0.000000e+00 1997
2 TraesCS3D01G434700 chr3D 82.798 529 78 7 3787 4314 552000383 551999867 1.530000e-125 460
3 TraesCS3D01G434700 chr3D 83.550 462 56 11 4571 5030 551999444 551999001 1.210000e-111 414
4 TraesCS3D01G434700 chr3B 93.181 4429 166 52 1 4343 724736589 724740967 0.000000e+00 6381
5 TraesCS3D01G434700 chr3B 93.900 1295 59 13 4448 5727 724741074 724742363 0.000000e+00 1936
6 TraesCS3D01G434700 chr3B 80.421 2758 348 106 1138 3784 732619327 732616651 0.000000e+00 1925
7 TraesCS3D01G434700 chr3B 84.139 517 69 7 3787 4302 732616606 732616102 7.010000e-134 488
8 TraesCS3D01G434700 chr3B 83.617 470 56 12 4563 5030 732615718 732615268 7.210000e-114 422
9 TraesCS3D01G434700 chr3B 90.228 307 11 6 5722 6015 724742395 724742695 3.400000e-102 383
10 TraesCS3D01G434700 chr3B 79.868 303 50 8 4760 5058 175096909 175096614 1.700000e-50 211
11 TraesCS3D01G434700 chr3A 96.081 3419 103 15 941 4343 684040773 684044176 0.000000e+00 5542
12 TraesCS3D01G434700 chr3A 93.405 1592 70 21 4448 6015 684044282 684045862 0.000000e+00 2326
13 TraesCS3D01G434700 chr3A 80.886 2731 363 81 1138 3784 688693498 688690843 0.000000e+00 2004
14 TraesCS3D01G434700 chr3A 85.474 833 35 23 1 777 684039434 684040236 0.000000e+00 789
15 TraesCS3D01G434700 chr3A 89.588 413 23 12 951 1357 433768343 433767945 1.930000e-139 507
16 TraesCS3D01G434700 chr3A 82.785 517 76 7 3787 4302 688690798 688690294 3.310000e-122 449
17 TraesCS3D01G434700 chr3A 87.073 410 23 13 951 1357 49518226 49518608 2.570000e-118 436
18 TraesCS3D01G434700 chr3A 82.737 475 60 13 4559 5030 688689930 688689475 2.610000e-108 403
19 TraesCS3D01G434700 chr7D 92.349 562 39 4 4647 5205 12707764 12707204 0.000000e+00 797
20 TraesCS3D01G434700 chr7D 92.439 410 15 10 951 1357 85519670 85520066 6.760000e-159 571
21 TraesCS3D01G434700 chr6D 91.463 410 19 10 951 1357 32521951 32521555 3.170000e-152 549
22 TraesCS3D01G434700 chr6D 90.488 410 17 9 951 1357 65145476 65145866 6.910000e-144 521
23 TraesCS3D01G434700 chr2B 89.756 410 27 9 951 1357 765132716 765132319 1.500000e-140 510
24 TraesCS3D01G434700 chr1A 89.024 410 29 10 951 1357 287042325 287041929 1.510000e-135 494
25 TraesCS3D01G434700 chr1A 83.396 265 38 3 4541 4805 22935698 22935956 2.170000e-59 241
26 TraesCS3D01G434700 chr1A 80.357 280 44 8 4760 5035 244562253 244561981 1.020000e-47 202
27 TraesCS3D01G434700 chr2A 82.264 265 41 3 4541 4805 536571028 536570770 2.180000e-54 224
28 TraesCS3D01G434700 chr4B 79.868 303 50 8 4760 5058 489161469 489161764 1.700000e-50 211
29 TraesCS3D01G434700 chr4B 78.276 290 38 18 2115 2394 17357155 17357429 4.820000e-36 163
30 TraesCS3D01G434700 chr7B 79.538 303 51 8 4760 5058 665368557 665368262 7.900000e-49 206
31 TraesCS3D01G434700 chr5D 85.088 114 5 5 1375 1488 562973351 562973250 8.240000e-19 106


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 TraesCS3D01G434700 chr3D 547297217 547303231 6014 False 11108.000000 11108 100.000000 1 6015 1 chr3D.!!$F1 6014
1 TraesCS3D01G434700 chr3D 551999001 552003086 4085 True 957.000000 1997 82.401000 1138 5030 3 chr3D.!!$R1 3892
2 TraesCS3D01G434700 chr3B 724736589 724742695 6106 False 2900.000000 6381 92.436333 1 6015 3 chr3B.!!$F1 6014
3 TraesCS3D01G434700 chr3B 732615268 732619327 4059 True 945.000000 1925 82.725667 1138 5030 3 chr3B.!!$R2 3892
4 TraesCS3D01G434700 chr3A 684039434 684045862 6428 False 2885.666667 5542 91.653333 1 6015 3 chr3A.!!$F2 6014
5 TraesCS3D01G434700 chr3A 688689475 688693498 4023 True 952.000000 2004 82.136000 1138 5030 3 chr3A.!!$R2 3892
6 TraesCS3D01G434700 chr7D 12707204 12707764 560 True 797.000000 797 92.349000 4647 5205 1 chr7D.!!$R1 558

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
277 297 0.030504 TACGAAACCGAAGCACGTCA 59.969 50.000 0.00 0.0 40.78 4.35 F
1093 1532 0.105039 CCGTAATCCTCCACTGCCTC 59.895 60.000 0.00 0.0 0.00 4.70 F
1745 2235 0.178068 TCCGCCTGAGGTGCTAATTC 59.822 55.000 6.51 0.0 0.00 2.17 F
2142 2653 0.249676 CTGCTCTGATCTGTGGCAGT 59.750 55.000 25.54 0.0 43.44 4.40 F
2163 2674 1.391577 TTTGCATCGCCATGTATGCT 58.608 45.000 19.53 0.0 46.87 3.79 F
3507 4075 1.569072 ACCTTGAGGACCAACAACCTT 59.431 47.619 3.59 0.0 36.57 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1561 0.179032 TGCTCGGAAGAAAACCAGCA 60.179 50.000 0.00 0.00 41.32 4.41 R
2499 3028 0.246086 CACCACTCTCTCCTCTGCAC 59.754 60.000 0.00 0.00 0.00 4.57 R
2714 3257 0.740737 GAATGAGCCAATGGGAACGG 59.259 55.000 0.00 0.00 35.59 4.44 R
3458 4026 0.961019 TTGACCTTGCAAGACCATGC 59.039 50.000 28.05 10.02 46.58 4.06 R
3918 4558 1.076014 GGGTTGTTCAACCGGGGAT 59.924 57.895 22.91 0.00 43.75 3.85 R
5368 6274 0.043485 AAGGGTTGGGTTGGGTTGTT 59.957 50.000 0.00 0.00 0.00 2.83 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
80 81 2.651137 CCCGCGTACACACACGAAC 61.651 63.158 4.92 0.00 44.69 3.95
81 82 2.458205 CGCGTACACACACGAACG 59.542 61.111 0.00 0.00 44.69 3.95
127 128 1.249407 ACGCCCGCAAAAATAAGGAA 58.751 45.000 0.00 0.00 0.00 3.36
241 261 0.107703 TAGCATGAAACTGGCGGGAG 60.108 55.000 0.00 0.00 0.00 4.30
254 274 1.675116 GGCGGGAGTTTACTCACTTCC 60.675 57.143 10.20 7.38 44.07 3.46
276 296 0.706729 CTACGAAACCGAAGCACGTC 59.293 55.000 0.00 0.00 40.78 4.34
277 297 0.030504 TACGAAACCGAAGCACGTCA 59.969 50.000 0.00 0.00 40.78 4.35
278 298 0.599204 ACGAAACCGAAGCACGTCAT 60.599 50.000 0.00 0.00 40.78 3.06
281 301 2.571206 GAAACCGAAGCACGTCATTTC 58.429 47.619 0.00 6.09 40.78 2.17
282 302 1.588674 AACCGAAGCACGTCATTTCA 58.411 45.000 0.00 0.00 40.78 2.69
283 303 1.808411 ACCGAAGCACGTCATTTCAT 58.192 45.000 0.00 0.00 40.78 2.57
284 304 2.151202 ACCGAAGCACGTCATTTCATT 58.849 42.857 0.00 0.00 40.78 2.57
285 305 2.552315 ACCGAAGCACGTCATTTCATTT 59.448 40.909 0.00 0.00 40.78 2.32
286 306 3.749088 ACCGAAGCACGTCATTTCATTTA 59.251 39.130 0.00 0.00 40.78 1.40
288 308 5.106317 ACCGAAGCACGTCATTTCATTTATT 60.106 36.000 0.00 0.00 40.78 1.40
340 369 0.633921 TTGAGAGAGAGGAGGGGAGG 59.366 60.000 0.00 0.00 0.00 4.30
341 370 1.292941 TGAGAGAGAGGAGGGGAGGG 61.293 65.000 0.00 0.00 0.00 4.30
342 371 2.018086 AGAGAGAGGAGGGGAGGGG 61.018 68.421 0.00 0.00 0.00 4.79
343 372 2.015726 GAGAGAGGAGGGGAGGGGA 61.016 68.421 0.00 0.00 0.00 4.81
344 373 2.018086 AGAGAGGAGGGGAGGGGAG 61.018 68.421 0.00 0.00 0.00 4.30
432 467 2.019897 GCGGGAAATGAATGGGGCTG 62.020 60.000 0.00 0.00 0.00 4.85
825 891 0.914902 GCCTACCCCATATCCCCTCC 60.915 65.000 0.00 0.00 0.00 4.30
826 892 0.253207 CCTACCCCATATCCCCTCCC 60.253 65.000 0.00 0.00 0.00 4.30
827 893 0.800239 CTACCCCATATCCCCTCCCT 59.200 60.000 0.00 0.00 0.00 4.20
828 894 0.797579 TACCCCATATCCCCTCCCTC 59.202 60.000 0.00 0.00 0.00 4.30
829 895 1.229984 CCCCATATCCCCTCCCTCC 60.230 68.421 0.00 0.00 0.00 4.30
830 896 1.229984 CCCATATCCCCTCCCTCCC 60.230 68.421 0.00 0.00 0.00 4.30
831 897 1.229984 CCATATCCCCTCCCTCCCC 60.230 68.421 0.00 0.00 0.00 4.81
832 898 1.766075 CCATATCCCCTCCCTCCCCT 61.766 65.000 0.00 0.00 0.00 4.79
833 899 0.252927 CATATCCCCTCCCTCCCCTC 60.253 65.000 0.00 0.00 0.00 4.30
834 900 1.465189 ATATCCCCTCCCTCCCCTCC 61.465 65.000 0.00 0.00 0.00 4.30
868 934 3.006859 CACAAAACATTTCCTTCCCCTCC 59.993 47.826 0.00 0.00 0.00 4.30
930 1009 1.386485 CCTCCATCTCCCACCCCAT 60.386 63.158 0.00 0.00 0.00 4.00
933 1012 2.464403 CCATCTCCCACCCCATCCC 61.464 68.421 0.00 0.00 0.00 3.85
934 1013 1.386485 CATCTCCCACCCCATCCCT 60.386 63.158 0.00 0.00 0.00 4.20
935 1014 1.073397 ATCTCCCACCCCATCCCTC 60.073 63.158 0.00 0.00 0.00 4.30
936 1015 2.972589 ATCTCCCACCCCATCCCTCG 62.973 65.000 0.00 0.00 0.00 4.63
1088 1527 1.003051 AGGGCCGTAATCCTCCACT 59.997 57.895 0.00 0.00 0.00 4.00
1089 1528 1.146263 GGGCCGTAATCCTCCACTG 59.854 63.158 0.00 0.00 0.00 3.66
1090 1529 1.523938 GGCCGTAATCCTCCACTGC 60.524 63.158 0.00 0.00 0.00 4.40
1091 1530 1.523938 GCCGTAATCCTCCACTGCC 60.524 63.158 0.00 0.00 0.00 4.85
1092 1531 1.972660 GCCGTAATCCTCCACTGCCT 61.973 60.000 0.00 0.00 0.00 4.75
1093 1532 0.105039 CCGTAATCCTCCACTGCCTC 59.895 60.000 0.00 0.00 0.00 4.70
1094 1533 0.105039 CGTAATCCTCCACTGCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
1095 1534 1.501582 GTAATCCTCCACTGCCTCCT 58.498 55.000 0.00 0.00 0.00 3.69
1096 1535 1.414550 GTAATCCTCCACTGCCTCCTC 59.585 57.143 0.00 0.00 0.00 3.71
1106 1545 2.232298 CTGCCTCCTCCTCGTTGGTC 62.232 65.000 0.00 0.00 37.07 4.02
1107 1546 2.885861 CCTCCTCCTCGTTGGTCG 59.114 66.667 0.00 0.00 41.41 4.79
1122 1561 1.372128 GTCGCTGACGTTTACCGGT 60.372 57.895 13.98 13.98 42.24 5.28
1130 1569 0.464193 ACGTTTACCGGTGCTGGTTT 60.464 50.000 19.93 0.00 43.56 3.27
1131 1570 0.664224 CGTTTACCGGTGCTGGTTTT 59.336 50.000 19.93 0.00 43.56 2.43
1132 1571 1.334329 CGTTTACCGGTGCTGGTTTTC 60.334 52.381 19.93 0.00 43.56 2.29
1348 1818 2.574212 GGTTCGCGCGCTGAATTG 60.574 61.111 30.19 16.36 0.00 2.32
1349 1819 2.173382 GTTCGCGCGCTGAATTGT 59.827 55.556 30.19 0.00 0.00 2.71
1497 1972 4.817909 CCCGCTTACCCCCTCCCT 62.818 72.222 0.00 0.00 0.00 4.20
1552 2027 2.414161 CGCCTTCGGAAAATTGTCTTCC 60.414 50.000 0.00 0.00 39.25 3.46
1601 2076 0.807496 GGTCAGCTGATTTGTCTGGC 59.193 55.000 21.47 2.96 0.00 4.85
1697 2177 0.527113 TCTACCGTGAATTTCGCCGA 59.473 50.000 4.44 0.00 0.00 5.54
1745 2235 0.178068 TCCGCCTGAGGTGCTAATTC 59.822 55.000 6.51 0.00 0.00 2.17
2123 2634 3.724374 GGTAAGTTTTTGTTCCTTGCCC 58.276 45.455 0.00 0.00 35.63 5.36
2142 2653 0.249676 CTGCTCTGATCTGTGGCAGT 59.750 55.000 25.54 0.00 43.44 4.40
2147 2658 3.611057 GCTCTGATCTGTGGCAGTTTTTG 60.611 47.826 12.40 0.00 33.90 2.44
2163 2674 1.391577 TTTGCATCGCCATGTATGCT 58.608 45.000 19.53 0.00 46.87 3.79
2450 2963 2.291741 CAGGTCTGTTGCTGTTTCCTTC 59.708 50.000 0.00 0.00 0.00 3.46
2499 3028 2.076100 TGCTAAATGTGTTCTGCTCCG 58.924 47.619 0.00 0.00 0.00 4.63
2685 3221 7.280356 ACAAACCTAGGTATATGAACATGTCC 58.720 38.462 16.67 0.00 0.00 4.02
3458 4026 9.033481 TCAAGCACAACAAAGAAATCAAAATAG 57.967 29.630 0.00 0.00 0.00 1.73
3483 4051 2.574006 TCTTGCAAGGTCAAGAGCAT 57.426 45.000 25.73 0.00 45.21 3.79
3507 4075 1.569072 ACCTTGAGGACCAACAACCTT 59.431 47.619 3.59 0.00 36.57 3.50
3512 4080 2.105821 TGAGGACCAACAACCTTACTGG 59.894 50.000 0.00 0.00 42.93 4.00
3918 4558 1.073125 TGGTTAAGGCAGCAGCAGTTA 59.927 47.619 2.65 0.00 44.61 2.24
4047 4687 1.408453 ATACTACCAGCGCCCCTTCC 61.408 60.000 2.29 0.00 0.00 3.46
4067 4707 2.288395 CCAACCATTTGAGCTCCACAAC 60.288 50.000 12.15 0.00 34.24 3.32
4302 4943 5.710513 TGTGCTTTCTTTATGTTCATGCT 57.289 34.783 0.00 0.00 0.00 3.79
4344 4986 8.177119 ACTTGCTATTTACAACCTGATTGAAA 57.823 30.769 0.00 0.00 41.23 2.69
4345 4987 8.637986 ACTTGCTATTTACAACCTGATTGAAAA 58.362 29.630 0.00 0.00 41.23 2.29
4346 4988 9.643693 CTTGCTATTTACAACCTGATTGAAAAT 57.356 29.630 0.00 0.00 41.23 1.82
4354 4996 6.633856 ACAACCTGATTGAAAATTATCTGCC 58.366 36.000 0.00 0.00 41.23 4.85
4355 4997 6.438425 ACAACCTGATTGAAAATTATCTGCCT 59.562 34.615 0.00 0.00 41.23 4.75
4356 4998 6.461110 ACCTGATTGAAAATTATCTGCCTG 57.539 37.500 0.00 0.00 0.00 4.85
4357 4999 5.163478 ACCTGATTGAAAATTATCTGCCTGC 60.163 40.000 0.00 0.00 0.00 4.85
4358 5000 5.068723 CCTGATTGAAAATTATCTGCCTGCT 59.931 40.000 0.00 0.00 0.00 4.24
4359 5001 6.406624 CCTGATTGAAAATTATCTGCCTGCTT 60.407 38.462 0.00 0.00 0.00 3.91
4361 5003 5.981088 TTGAAAATTATCTGCCTGCTTGA 57.019 34.783 0.00 0.00 0.00 3.02
4364 5006 7.643569 TGAAAATTATCTGCCTGCTTGATTA 57.356 32.000 4.22 0.00 0.00 1.75
4365 5007 8.065473 TGAAAATTATCTGCCTGCTTGATTAA 57.935 30.769 4.22 0.00 0.00 1.40
4366 5008 8.530311 TGAAAATTATCTGCCTGCTTGATTAAA 58.470 29.630 4.22 0.00 0.00 1.52
4400 5042 6.377996 AGCACCTTTATCATAAATCTGTTGCA 59.622 34.615 9.48 0.00 0.00 4.08
4402 5044 8.352201 GCACCTTTATCATAAATCTGTTGCATA 58.648 33.333 0.00 0.00 0.00 3.14
4505 5400 5.710513 TGCACAATCTTGTCTGCTTAATT 57.289 34.783 6.95 0.00 39.91 1.40
4507 5402 4.325472 GCACAATCTTGTCTGCTTAATTGC 59.675 41.667 0.00 0.00 39.91 3.56
4508 5403 5.463286 CACAATCTTGTCTGCTTAATTGCA 58.537 37.500 0.00 0.00 39.91 4.08
4514 5409 7.628769 TCTTGTCTGCTTAATTGCATATTCA 57.371 32.000 0.00 0.00 42.48 2.57
4553 5448 6.823182 TGGTCTGACCACTAATTTGTATGATG 59.177 38.462 25.12 0.00 44.79 3.07
4565 5460 4.787135 TTGTATGATGCTCCCCATGTTA 57.213 40.909 0.00 0.00 33.29 2.41
4568 5463 5.704354 TGTATGATGCTCCCCATGTTATTT 58.296 37.500 0.00 0.00 33.29 1.40
4580 5475 7.185565 TCCCCATGTTATTTCAGGTTCATAAA 58.814 34.615 0.00 0.00 0.00 1.40
4586 5481 7.375053 TGTTATTTCAGGTTCATAAACAAGGC 58.625 34.615 0.00 0.00 37.10 4.35
4679 5574 6.097356 CAGGATGTTTGAATTTGATGGTGAG 58.903 40.000 0.00 0.00 0.00 3.51
5069 5967 5.348986 TCTATTGGTTAAGCTGATGTCGTC 58.651 41.667 6.19 0.00 0.00 4.20
5096 5994 5.645497 AGTGCATCAAATTCTACTTGACCTC 59.355 40.000 0.00 0.00 35.70 3.85
5153 6051 7.436080 GCATGGTCACAGGATATTATTGTTTTG 59.564 37.037 0.00 0.00 0.00 2.44
5211 6112 1.104577 TTTGGGTCGTTGTTGGCCTC 61.105 55.000 3.32 0.00 0.00 4.70
5216 6117 2.590575 CGTTGTTGGCCTCGGTGT 60.591 61.111 3.32 0.00 0.00 4.16
5227 6130 1.069765 CTCGGTGTCTGCAGGTTGT 59.930 57.895 15.13 0.00 0.00 3.32
5328 6234 3.065925 GCCAATGAAGTAACTCCTGATGC 59.934 47.826 0.00 0.00 0.00 3.91
5368 6274 1.180456 CCCCTTGTGATGCAGCAACA 61.180 55.000 6.05 4.52 0.00 3.33
5388 6294 0.043485 ACAACCCAACCCAACCCTTT 59.957 50.000 0.00 0.00 0.00 3.11
5442 6351 2.230992 GAGAGAGAGAGACTTTGCTGCA 59.769 50.000 0.00 0.00 0.00 4.41
5547 6463 3.795826 GCTTGAATGCATGCTTGATCCTC 60.796 47.826 20.33 7.22 40.80 3.71
5564 6484 0.620121 CTCAGCCCTCCCTCTTTCCT 60.620 60.000 0.00 0.00 0.00 3.36
5568 6488 1.694525 CCCTCCCTCTTTCCTCCCC 60.695 68.421 0.00 0.00 0.00 4.81
5664 6594 2.509336 CCCGCAGTAGCTGTTCCG 60.509 66.667 0.00 0.00 39.10 4.30
5802 6772 0.960861 TCGCTGTCTGTGTCGATCCT 60.961 55.000 0.00 0.00 0.00 3.24
5890 6866 0.182299 TGTGGGCGGCATGATTGATA 59.818 50.000 12.47 0.00 0.00 2.15
5892 6868 1.888512 GTGGGCGGCATGATTGATATT 59.111 47.619 12.47 0.00 0.00 1.28
5894 6870 2.964464 TGGGCGGCATGATTGATATTTT 59.036 40.909 12.47 0.00 0.00 1.82
5896 6872 4.771577 TGGGCGGCATGATTGATATTTTAT 59.228 37.500 12.47 0.00 0.00 1.40
5897 6873 5.105797 TGGGCGGCATGATTGATATTTTATC 60.106 40.000 12.47 0.00 0.00 1.75
5898 6874 5.105797 GGGCGGCATGATTGATATTTTATCA 60.106 40.000 12.47 0.00 33.25 2.15
5900 6876 6.349611 GGCGGCATGATTGATATTTTATCAGT 60.350 38.462 3.07 0.00 32.32 3.41
5901 6877 6.744537 GCGGCATGATTGATATTTTATCAGTC 59.255 38.462 11.13 11.13 35.95 3.51
5902 6878 7.573656 GCGGCATGATTGATATTTTATCAGTCA 60.574 37.037 18.84 18.84 44.78 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 2.136196 TTGCGGGCGTTGATTTGTCC 62.136 55.000 0.00 0.00 0.00 4.02
241 261 5.382618 TTCGTAGAGGGAAGTGAGTAAAC 57.617 43.478 0.00 0.00 38.43 2.01
254 274 1.347320 GTGCTTCGGTTTCGTAGAGG 58.653 55.000 0.00 0.00 38.43 3.69
305 325 6.547141 TCTCTCTCAAAAATGACCATTGTTGT 59.453 34.615 19.45 0.00 43.29 3.32
306 326 6.973843 TCTCTCTCAAAAATGACCATTGTTG 58.026 36.000 15.93 15.93 43.85 3.33
307 327 6.208204 CCTCTCTCTCAAAAATGACCATTGTT 59.792 38.462 0.00 0.00 0.00 2.83
311 331 5.339035 CCTCCTCTCTCTCAAAAATGACCAT 60.339 44.000 0.00 0.00 0.00 3.55
312 332 4.019860 CCTCCTCTCTCTCAAAAATGACCA 60.020 45.833 0.00 0.00 0.00 4.02
314 334 4.512484 CCCTCCTCTCTCTCAAAAATGAC 58.488 47.826 0.00 0.00 0.00 3.06
318 338 3.177228 CTCCCCTCCTCTCTCTCAAAAA 58.823 50.000 0.00 0.00 0.00 1.94
432 467 1.162698 GGGACAGCTTTTTACGACCC 58.837 55.000 0.00 0.00 0.00 4.46
652 693 3.254024 AAGCCGAGCCGATGTTGGT 62.254 57.895 0.00 0.00 0.00 3.67
656 697 2.125512 GTCAAGCCGAGCCGATGT 60.126 61.111 0.00 0.00 0.00 3.06
720 786 0.469917 AGCGGAGGAGAGAGAGAGAG 59.530 60.000 0.00 0.00 0.00 3.20
839 905 1.623311 GGAAATGTTTTGTGGGGAGGG 59.377 52.381 0.00 0.00 0.00 4.30
868 934 0.179097 GAGCGGCAGTAGAAAGAGGG 60.179 60.000 1.45 0.00 0.00 4.30
1088 1527 2.203788 ACCAACGAGGAGGAGGCA 60.204 61.111 5.70 0.00 41.22 4.75
1089 1528 2.579738 GACCAACGAGGAGGAGGC 59.420 66.667 5.70 0.00 41.22 4.70
1090 1529 2.885861 CGACCAACGAGGAGGAGG 59.114 66.667 5.70 0.00 45.77 4.30
1091 1530 2.182030 GCGACCAACGAGGAGGAG 59.818 66.667 5.70 0.00 45.77 3.69
1092 1531 2.282958 AGCGACCAACGAGGAGGA 60.283 61.111 5.70 0.00 45.77 3.71
1093 1532 2.125912 CAGCGACCAACGAGGAGG 60.126 66.667 5.70 0.00 45.77 4.30
1094 1533 1.444553 GTCAGCGACCAACGAGGAG 60.445 63.158 5.70 1.24 45.77 3.69
1095 1534 2.649034 GTCAGCGACCAACGAGGA 59.351 61.111 5.70 0.00 45.77 3.71
1096 1535 2.805353 CGTCAGCGACCAACGAGG 60.805 66.667 0.00 0.00 45.77 4.63
1106 1545 3.007070 GCACCGGTAAACGTCAGCG 62.007 63.158 6.87 13.04 42.24 5.18
1107 1546 1.666872 AGCACCGGTAAACGTCAGC 60.667 57.895 6.87 3.46 42.24 4.26
1122 1561 0.179032 TGCTCGGAAGAAAACCAGCA 60.179 50.000 0.00 0.00 41.32 4.41
1130 1569 1.338136 GGATCCCCTGCTCGGAAGAA 61.338 60.000 0.00 0.00 41.32 2.52
1131 1570 1.762460 GGATCCCCTGCTCGGAAGA 60.762 63.158 0.00 0.00 39.12 2.87
1132 1571 2.825264 GGATCCCCTGCTCGGAAG 59.175 66.667 0.00 0.00 31.75 3.46
1274 1735 1.071857 GGGGGTAGAATTAAGCGAGGG 59.928 57.143 0.00 0.00 0.00 4.30
1370 1841 1.032114 GGCCTCCACCTGGAAATTCG 61.032 60.000 0.00 0.00 44.91 3.34
1372 1843 0.332972 GAGGCCTCCACCTGGAAATT 59.667 55.000 23.19 0.00 44.91 1.82
1373 1844 2.002625 GAGGCCTCCACCTGGAAAT 58.997 57.895 23.19 0.00 44.91 2.17
1497 1972 2.359478 GGGAAGCGGGCGAGAAAA 60.359 61.111 0.00 0.00 0.00 2.29
1552 2027 1.021202 TCCCAGCAAACGAACAAGTG 58.979 50.000 0.00 0.00 0.00 3.16
1601 2076 2.181525 CCGCCTGCCAAAAATCCG 59.818 61.111 0.00 0.00 0.00 4.18
1697 2177 3.230976 GAAAATCCCCCAAGTGTGAACT 58.769 45.455 0.00 0.00 0.00 3.01
1745 2235 2.050918 GAATTACAGGGAGAGGAGGGG 58.949 57.143 0.00 0.00 0.00 4.79
2123 2634 3.067074 CTGCCACAGATCAGAGCAG 57.933 57.895 16.04 16.04 44.31 4.24
2142 2653 2.538437 GCATACATGGCGATGCAAAAA 58.462 42.857 19.03 0.00 46.29 1.94
2163 2674 3.573967 TCAGCTTCAGATCACACACACTA 59.426 43.478 0.00 0.00 0.00 2.74
2450 2963 6.404734 GGTTAAGAATTGTTATGCTGGTGAGG 60.405 42.308 0.00 0.00 0.00 3.86
2499 3028 0.246086 CACCACTCTCTCCTCTGCAC 59.754 60.000 0.00 0.00 0.00 4.57
2714 3257 0.740737 GAATGAGCCAATGGGAACGG 59.259 55.000 0.00 0.00 35.59 4.44
3118 3679 4.038271 TCAGAAGCAAACCTCCATGAAT 57.962 40.909 0.00 0.00 0.00 2.57
3458 4026 0.961019 TTGACCTTGCAAGACCATGC 59.039 50.000 28.05 10.02 46.58 4.06
3483 4051 3.244770 GGTTGTTGGTCCTCAAGGTCATA 60.245 47.826 0.00 0.00 35.80 2.15
3507 4075 3.632643 TCAGATTCATTGCTGCCAGTA 57.367 42.857 0.00 0.00 32.27 2.74
3512 4080 3.564644 AGTAGCATCAGATTCATTGCTGC 59.435 43.478 14.54 13.44 44.65 5.25
3918 4558 1.076014 GGGTTGTTCAACCGGGGAT 59.924 57.895 22.91 0.00 43.75 3.85
4047 4687 2.605338 CGTTGTGGAGCTCAAATGGTTG 60.605 50.000 17.19 0.00 35.95 3.77
4067 4707 2.719979 GCTCATGGATTGCAGCCG 59.280 61.111 0.00 0.00 0.00 5.52
4207 4847 2.287668 CGTCTTTCGAACTGTGAGGAGT 60.288 50.000 0.00 0.00 42.86 3.85
4341 4983 8.931385 TTTAATCAAGCAGGCAGATAATTTTC 57.069 30.769 0.00 0.00 0.00 2.29
4342 4984 9.723601 TTTTTAATCAAGCAGGCAGATAATTTT 57.276 25.926 0.00 0.00 0.00 1.82
4344 4986 7.493645 GCTTTTTAATCAAGCAGGCAGATAATT 59.506 33.333 12.80 0.00 45.19 1.40
4345 4987 6.982724 GCTTTTTAATCAAGCAGGCAGATAAT 59.017 34.615 12.80 0.00 45.19 1.28
4346 4988 6.332630 GCTTTTTAATCAAGCAGGCAGATAA 58.667 36.000 12.80 0.00 45.19 1.75
4348 4990 4.752146 GCTTTTTAATCAAGCAGGCAGAT 58.248 39.130 12.80 0.00 45.19 2.90
4349 4991 4.178545 GCTTTTTAATCAAGCAGGCAGA 57.821 40.909 12.80 0.00 45.19 4.26
4356 4998 4.386954 GTGCTCAAGGCTTTTTAATCAAGC 59.613 41.667 0.00 10.22 45.13 4.01
4357 4999 4.925646 GGTGCTCAAGGCTTTTTAATCAAG 59.074 41.667 0.00 0.00 42.39 3.02
4358 5000 4.588528 AGGTGCTCAAGGCTTTTTAATCAA 59.411 37.500 0.00 0.00 42.39 2.57
4359 5001 4.151883 AGGTGCTCAAGGCTTTTTAATCA 58.848 39.130 0.00 0.00 42.39 2.57
4361 5003 5.551305 AAAGGTGCTCAAGGCTTTTTAAT 57.449 34.783 0.00 0.00 42.39 1.40
4364 5006 4.588528 TGATAAAGGTGCTCAAGGCTTTTT 59.411 37.500 0.00 0.00 42.39 1.94
4365 5007 4.151883 TGATAAAGGTGCTCAAGGCTTTT 58.848 39.130 0.00 0.00 42.39 2.27
4366 5008 3.766545 TGATAAAGGTGCTCAAGGCTTT 58.233 40.909 0.00 0.00 42.39 3.51
4481 5360 3.360249 AAGCAGACAAGATTGTGCAAC 57.640 42.857 2.31 0.00 42.43 4.17
4505 5400 8.093307 ACCAAACAAATAACACATGAATATGCA 58.907 29.630 0.00 0.00 37.85 3.96
4507 5402 9.859427 AGACCAAACAAATAACACATGAATATG 57.141 29.630 0.00 0.00 40.24 1.78
4508 5403 9.859427 CAGACCAAACAAATAACACATGAATAT 57.141 29.630 0.00 0.00 0.00 1.28
4514 5409 6.084326 GGTCAGACCAAACAAATAACACAT 57.916 37.500 15.43 0.00 38.42 3.21
4543 5438 3.668141 ACATGGGGAGCATCATACAAA 57.332 42.857 0.00 0.00 36.25 2.83
4546 5441 5.769662 TGAAATAACATGGGGAGCATCATAC 59.230 40.000 0.00 0.00 36.25 2.39
4553 5448 3.018423 ACCTGAAATAACATGGGGAGC 57.982 47.619 0.00 0.00 0.00 4.70
4565 5460 4.522789 ACGCCTTGTTTATGAACCTGAAAT 59.477 37.500 0.00 0.00 34.80 2.17
4568 5463 3.134574 ACGCCTTGTTTATGAACCTGA 57.865 42.857 0.00 0.00 34.80 3.86
4580 5475 0.464735 TACCAAGTGCAACGCCTTGT 60.465 50.000 12.28 5.16 45.86 3.16
4586 5481 2.413112 CACTGATCTACCAAGTGCAACG 59.587 50.000 0.00 0.00 45.86 4.10
4679 5574 5.632347 CCAATCTTTGTTTGAAGACATCAGC 59.368 40.000 0.00 0.00 39.77 4.26
5069 5967 4.701651 TCAAGTAGAATTTGATGCACTGGG 59.298 41.667 0.00 0.00 30.03 4.45
5096 5994 0.107654 GGAATCCACCGAGGGAGTTG 60.108 60.000 0.00 0.00 41.08 3.16
5153 6051 5.220548 GGTGATGCGAATCATATCATAGCAC 60.221 44.000 9.89 0.00 35.05 4.40
5211 6112 1.095228 AACACAACCTGCAGACACCG 61.095 55.000 17.39 0.00 0.00 4.94
5216 6117 1.604604 GGCTTAACACAACCTGCAGA 58.395 50.000 17.39 0.00 0.00 4.26
5328 6234 2.052104 GGGGGCGATCACCAAAAGG 61.052 63.158 1.44 0.00 0.00 3.11
5368 6274 0.043485 AAGGGTTGGGTTGGGTTGTT 59.957 50.000 0.00 0.00 0.00 2.83
5388 6294 8.272173 ACCTAGCAAGTAAATAGCTAAATCCAA 58.728 33.333 0.00 0.00 40.05 3.53
5442 6351 0.650512 CGGATAAACAATCGCGCAGT 59.349 50.000 8.75 0.00 35.21 4.40
5547 6463 1.631071 GGAGGAAAGAGGGAGGGCTG 61.631 65.000 0.00 0.00 0.00 4.85
5564 6484 0.178858 TTACATCAGGGTGGTGGGGA 60.179 55.000 0.00 0.00 31.38 4.81
5568 6488 8.924511 AGATAAATATTTACATCAGGGTGGTG 57.075 34.615 10.07 0.00 33.91 4.17
5664 6594 3.412237 TGCCAGTGTTTTACTACTCCC 57.588 47.619 0.00 0.00 37.60 4.30
5802 6772 4.854924 CGCCCATCATGCGTCCCA 62.855 66.667 0.00 0.00 46.59 4.37
5890 6866 9.547753 GGTGTGTATACATCTGACTGATAAAAT 57.452 33.333 9.18 0.00 39.39 1.82
5892 6868 7.979537 GTGGTGTGTATACATCTGACTGATAAA 59.020 37.037 9.18 0.00 38.76 1.40
5894 6870 6.238648 CGTGGTGTGTATACATCTGACTGATA 60.239 42.308 9.18 0.00 38.76 2.15
5896 6872 4.142469 CGTGGTGTGTATACATCTGACTGA 60.142 45.833 9.18 0.00 38.76 3.41
5897 6873 4.105486 CGTGGTGTGTATACATCTGACTG 58.895 47.826 9.18 0.00 38.76 3.51
5898 6874 3.130516 CCGTGGTGTGTATACATCTGACT 59.869 47.826 9.18 0.00 38.76 3.41
5900 6876 3.358118 TCCGTGGTGTGTATACATCTGA 58.642 45.455 9.18 0.00 38.76 3.27
5901 6877 3.706698 CTCCGTGGTGTGTATACATCTG 58.293 50.000 9.18 0.00 38.76 2.90
5902 6878 2.100916 GCTCCGTGGTGTGTATACATCT 59.899 50.000 9.18 0.00 38.76 2.90
5907 6884 1.203758 CACTGCTCCGTGGTGTGTATA 59.796 52.381 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.