Multiple sequence alignment - TraesCS7D01G313400

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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 TraesCS7D01G313400 chr7D 100.000 4552 0 0 1 4552 397202019 397197468 0.000000e+00 8407
1 TraesCS7D01G313400 chr7D 83.865 502 60 11 259 748 602073920 602074412 4.150000e-125 459
2 TraesCS7D01G313400 chr7D 83.367 493 57 18 259 744 386763063 386762589 2.520000e-117 433
3 TraesCS7D01G313400 chr7B 94.454 1785 50 14 2096 3840 400929865 400928090 0.000000e+00 2702
4 TraesCS7D01G313400 chr7B 91.519 1521 74 28 615 2095 400937038 400935533 0.000000e+00 2043
5 TraesCS7D01G313400 chr7B 97.598 458 10 1 4096 4552 400927705 400927248 0.000000e+00 784
6 TraesCS7D01G313400 chr7A 94.468 1410 44 10 2328 3707 452751445 452752850 0.000000e+00 2141
7 TraesCS7D01G313400 chr7A 86.497 1844 139 55 17 1793 452748742 452750542 0.000000e+00 1925
8 TraesCS7D01G313400 chr7A 93.161 541 31 6 1794 2331 452750604 452751141 0.000000e+00 789
9 TraesCS7D01G313400 chr7A 92.600 500 17 5 4058 4552 452754506 452754990 0.000000e+00 701
10 TraesCS7D01G313400 chr7A 88.068 352 24 10 3700 4039 452753997 452754342 7.090000e-108 401
11 TraesCS7D01G313400 chr4B 86.032 494 54 5 272 754 400701956 400701467 2.430000e-142 516
12 TraesCS7D01G313400 chr4B 81.947 493 70 11 259 740 601746070 601746554 2.550000e-107 399
13 TraesCS7D01G313400 chr4B 79.870 154 23 6 597 748 41755374 41755521 6.230000e-19 106
14 TraesCS7D01G313400 chr3A 83.034 501 69 5 259 748 16154049 16154544 1.500000e-119 440
15 TraesCS7D01G313400 chr3A 81.898 453 66 9 259 697 721343052 721342602 7.190000e-98 368
16 TraesCS7D01G313400 chr3A 80.279 502 73 13 259 748 496047164 496047651 5.600000e-94 355
17 TraesCS7D01G313400 chr1B 82.329 498 72 9 259 745 669074460 669074952 7.040000e-113 418
18 TraesCS7D01G313400 chr3D 81.836 501 75 11 259 748 374036006 374036501 1.520000e-109 407
19 TraesCS7D01G313400 chr4D 79.699 532 83 19 233 748 362801455 362800933 1.200000e-95 361
20 TraesCS7D01G313400 chr2D 77.823 496 80 11 263 747 102861349 102861825 3.470000e-71 279
21 TraesCS7D01G313400 chr1D 81.200 250 38 3 508 748 403764146 403764395 4.650000e-45 193
22 TraesCS7D01G313400 chr5D 74.046 393 81 13 369 748 32241366 32241750 1.710000e-29 141
23 TraesCS7D01G313400 chr5D 73.537 393 84 12 369 748 32164714 32165099 1.030000e-26 132
24 TraesCS7D01G313400 chr3B 82.313 147 24 2 603 748 487798348 487798493 4.780000e-25 126


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 TraesCS7D01G313400 chr7D 397197468 397202019 4551 True 8407.0 8407 100.0000 1 4552 1 chr7D.!!$R2 4551
1 TraesCS7D01G313400 chr7B 400935533 400937038 1505 True 2043.0 2043 91.5190 615 2095 1 chr7B.!!$R1 1480
2 TraesCS7D01G313400 chr7B 400927248 400929865 2617 True 1743.0 2702 96.0260 2096 4552 2 chr7B.!!$R2 2456
3 TraesCS7D01G313400 chr7A 452748742 452754990 6248 False 1191.4 2141 90.9588 17 4552 5 chr7A.!!$F1 4535
4 TraesCS7D01G313400 chr4D 362800933 362801455 522 True 361.0 361 79.6990 233 748 1 chr4D.!!$R1 515

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
86 87 0.105401 CTCTTCTACCCCCTCCCCTC 60.105 65.0 0.0 0.0 0.0 4.30 F
1403 1469 0.104934 ACGGGGAGGAGGAGCATTAT 60.105 55.0 0.0 0.0 0.0 1.28 F
1690 1756 0.671472 AAACACTAGTAACGCCCCGC 60.671 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 1995 0.107508 TGCTAGCCTTGCTGATGGTC 60.108 55.000 13.29 0.0 40.10 4.02 R
3115 3567 1.211949 TGGTAGGCTTCAGGTTATGCC 59.788 52.381 0.00 0.0 45.21 4.40 R
3604 4082 1.332997 GCAGAGGAAATCCAATCGCAG 59.667 52.381 1.67 0.0 38.89 5.18 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
26 27 7.993821 TTTTCTAAACAAAATCGCACAATGA 57.006 28.000 0.00 0.00 0.00 2.57
78 79 5.012251 ACTTTCTCTTCAACTCTTCTACCCC 59.988 44.000 0.00 0.00 0.00 4.95
79 80 3.442076 TCTCTTCAACTCTTCTACCCCC 58.558 50.000 0.00 0.00 0.00 5.40
80 81 3.077695 TCTCTTCAACTCTTCTACCCCCT 59.922 47.826 0.00 0.00 0.00 4.79
85 86 0.860901 ACTCTTCTACCCCCTCCCCT 60.861 60.000 0.00 0.00 0.00 4.79
86 87 0.105401 CTCTTCTACCCCCTCCCCTC 60.105 65.000 0.00 0.00 0.00 4.30
88 89 2.623297 CTTCTACCCCCTCCCCTCCC 62.623 70.000 0.00 0.00 0.00 4.30
89 90 3.373846 CTACCCCCTCCCCTCCCA 61.374 72.222 0.00 0.00 0.00 4.37
90 91 2.882676 TACCCCCTCCCCTCCCAA 60.883 66.667 0.00 0.00 0.00 4.12
91 92 2.501943 CTACCCCCTCCCCTCCCAAA 62.502 65.000 0.00 0.00 0.00 3.28
92 93 2.076570 TACCCCCTCCCCTCCCAAAA 62.077 60.000 0.00 0.00 0.00 2.44
93 94 2.626467 CCCCCTCCCCTCCCAAAAG 61.626 68.421 0.00 0.00 0.00 2.27
94 95 2.360585 CCCTCCCCTCCCAAAAGC 59.639 66.667 0.00 0.00 0.00 3.51
96 97 1.304464 CCTCCCCTCCCAAAAGCAC 60.304 63.158 0.00 0.00 0.00 4.40
97 98 1.675641 CTCCCCTCCCAAAAGCACG 60.676 63.158 0.00 0.00 0.00 5.34
98 99 2.124507 CTCCCCTCCCAAAAGCACGA 62.125 60.000 0.00 0.00 0.00 4.35
99 100 1.228429 CCCCTCCCAAAAGCACGAA 60.228 57.895 0.00 0.00 0.00 3.85
100 101 1.524008 CCCCTCCCAAAAGCACGAAC 61.524 60.000 0.00 0.00 0.00 3.95
101 102 0.821711 CCCTCCCAAAAGCACGAACA 60.822 55.000 0.00 0.00 0.00 3.18
102 103 1.247567 CCTCCCAAAAGCACGAACAT 58.752 50.000 0.00 0.00 0.00 2.71
104 105 2.817258 CCTCCCAAAAGCACGAACATAA 59.183 45.455 0.00 0.00 0.00 1.90
105 106 3.119849 CCTCCCAAAAGCACGAACATAAG 60.120 47.826 0.00 0.00 0.00 1.73
106 107 3.482436 TCCCAAAAGCACGAACATAAGT 58.518 40.909 0.00 0.00 0.00 2.24
183 185 9.534565 ACTAAAAGAAAGAGAAAAAGGATTTGC 57.465 29.630 0.00 0.00 39.02 3.68
204 206 6.348621 TGCAATTCAGCAAGAAAAGAAAAC 57.651 33.333 0.00 0.00 42.46 2.43
205 207 6.108015 TGCAATTCAGCAAGAAAAGAAAACT 58.892 32.000 0.00 0.00 42.46 2.66
213 215 4.792704 GCAAGAAAAGAAAACTCGGATGCA 60.793 41.667 0.00 0.00 0.00 3.96
214 216 4.489679 AGAAAAGAAAACTCGGATGCAC 57.510 40.909 0.00 0.00 0.00 4.57
228 230 4.474226 GGATGCACCGACTTTATTCATC 57.526 45.455 0.00 0.00 0.00 2.92
276 280 6.475504 TCCAGATATCAAAGTTCAGCAGAAA 58.524 36.000 5.32 0.00 35.08 2.52
303 307 6.857964 ACAAAGCATCTCGAACACAATAAAAG 59.142 34.615 0.00 0.00 0.00 2.27
327 332 6.833933 AGTTACATTAAGATTTCATGACCCCC 59.166 38.462 0.00 0.00 0.00 5.40
335 340 2.765689 TTCATGACCCCCAAACAACT 57.234 45.000 0.00 0.00 0.00 3.16
365 370 0.528466 TCAGAATGAGCCGTCGATGC 60.528 55.000 0.00 0.00 42.56 3.91
407 412 3.435186 GAGCCGGCTTGACCTTGC 61.435 66.667 33.34 11.55 35.61 4.01
418 423 0.895100 TGACCTTGCCAATGACAGCC 60.895 55.000 0.00 0.00 0.00 4.85
489 495 2.978010 CGCCGTTGAACCCTTGCT 60.978 61.111 0.00 0.00 0.00 3.91
491 497 1.007387 GCCGTTGAACCCTTGCTTG 60.007 57.895 0.00 0.00 0.00 4.01
492 498 1.007387 CCGTTGAACCCTTGCTTGC 60.007 57.895 0.00 0.00 0.00 4.01
493 499 1.732917 CGTTGAACCCTTGCTTGCA 59.267 52.632 0.00 0.00 0.00 4.08
494 500 0.318107 CGTTGAACCCTTGCTTGCAG 60.318 55.000 0.00 0.00 0.00 4.41
542 551 2.135933 GTCACAAGACGAGAAACCCTG 58.864 52.381 0.00 0.00 34.60 4.45
553 562 2.113243 GAAACCCTGACCTCACCGCT 62.113 60.000 0.00 0.00 0.00 5.52
566 575 2.747855 CCGCTCCAAAGAGGTGGC 60.748 66.667 0.00 0.00 40.79 5.01
568 577 2.328099 CGCTCCAAAGAGGTGGCAC 61.328 63.158 9.70 9.70 40.79 5.01
581 590 4.195308 GGCACAAATCTACGCCGA 57.805 55.556 0.00 0.00 34.26 5.54
586 595 1.324736 CACAAATCTACGCCGAAGCTC 59.675 52.381 0.00 0.00 36.60 4.09
599 617 1.310904 GAAGCTCCGTCGACTAGGAT 58.689 55.000 14.70 0.00 35.75 3.24
611 629 3.142951 CGACTAGGATGAACTCGAGGAT 58.857 50.000 18.41 4.87 0.00 3.24
613 631 3.226777 ACTAGGATGAACTCGAGGATGG 58.773 50.000 18.41 0.00 0.00 3.51
651 669 2.770164 ACTCAAAGAAGTAGCGCCAT 57.230 45.000 2.29 0.00 0.00 4.40
656 674 3.118629 TCAAAGAAGTAGCGCCATCATCT 60.119 43.478 2.29 0.00 0.00 2.90
667 685 1.145598 CATCATCTGGCCGAGCACT 59.854 57.895 0.00 0.00 0.00 4.40
671 698 3.040206 ATCTGGCCGAGCACTGCAT 62.040 57.895 3.30 0.00 0.00 3.96
710 738 6.505044 AAACCTAACCTAAATTGCTAACCG 57.495 37.500 0.00 0.00 0.00 4.44
745 773 2.017559 GATTCTCCTCCCCGTCACCG 62.018 65.000 0.00 0.00 0.00 4.94
772 821 7.148255 GCAACTGGTGACAAATTACATCAGATA 60.148 37.037 19.90 0.00 44.88 1.98
775 824 7.984050 ACTGGTGACAAATTACATCAGATAGAG 59.016 37.037 19.90 2.51 44.88 2.43
776 825 8.078060 TGGTGACAAATTACATCAGATAGAGA 57.922 34.615 0.00 0.00 37.44 3.10
777 826 8.708378 TGGTGACAAATTACATCAGATAGAGAT 58.292 33.333 0.00 0.00 37.44 2.75
778 827 9.202273 GGTGACAAATTACATCAGATAGAGATC 57.798 37.037 0.00 0.00 0.00 2.75
801 857 5.939883 TCAATCAAACTACAGATGGACCAAG 59.060 40.000 0.00 0.00 0.00 3.61
813 870 6.376581 ACAGATGGACCAAGAAAATCTGATTC 59.623 38.462 21.84 1.86 44.53 2.52
814 871 5.890419 AGATGGACCAAGAAAATCTGATTCC 59.110 40.000 0.00 0.00 0.00 3.01
945 1005 3.838271 GGCCGCTCATCTCGTCCA 61.838 66.667 0.00 0.00 0.00 4.02
948 1008 1.953138 CCGCTCATCTCGTCCATGC 60.953 63.158 0.00 0.00 0.00 4.06
949 1009 2.298629 CGCTCATCTCGTCCATGCG 61.299 63.158 0.00 0.00 36.19 4.73
967 1028 2.748268 GAGAAAGCTCGGCACTCAG 58.252 57.895 0.00 0.00 0.00 3.35
983 1044 0.247736 TCAGCGCCTCTTTCCTTCTC 59.752 55.000 2.29 0.00 0.00 2.87
1033 1099 2.836360 TCCCTATCCGACCGCCAC 60.836 66.667 0.00 0.00 0.00 5.01
1034 1100 3.925090 CCCTATCCGACCGCCACC 61.925 72.222 0.00 0.00 0.00 4.61
1035 1101 4.280494 CCTATCCGACCGCCACCG 62.280 72.222 0.00 0.00 0.00 4.94
1036 1102 4.944372 CTATCCGACCGCCACCGC 62.944 72.222 0.00 0.00 0.00 5.68
1216 1282 4.011517 TTTCGGCCCGGTGAGGAC 62.012 66.667 1.90 0.00 45.00 3.85
1299 1365 3.496331 GATACAGAGGAGGAAGAGGAGG 58.504 54.545 0.00 0.00 0.00 4.30
1403 1469 0.104934 ACGGGGAGGAGGAGCATTAT 60.105 55.000 0.00 0.00 0.00 1.28
1487 1553 2.904866 TTCGTGTGCAACCTGCCC 60.905 61.111 0.00 0.00 44.23 5.36
1624 1690 8.949177 TCGGATTCATACTGTTATTATACGCTA 58.051 33.333 0.00 0.00 0.00 4.26
1625 1691 9.731819 CGGATTCATACTGTTATTATACGCTAT 57.268 33.333 0.00 0.00 0.00 2.97
1681 1747 1.278127 GGGCCAGCTGAAACACTAGTA 59.722 52.381 17.39 0.00 0.00 1.82
1689 1755 1.337074 TGAAACACTAGTAACGCCCCG 60.337 52.381 0.00 0.00 0.00 5.73
1690 1756 0.671472 AAACACTAGTAACGCCCCGC 60.671 55.000 0.00 0.00 0.00 6.13
1741 1813 2.711895 ACTAGGAGATAGGCATGGCT 57.288 50.000 26.37 26.37 35.63 4.75
1860 1995 4.081420 ACATAGAGTTAACTCACCTGCCTG 60.081 45.833 31.80 19.98 45.21 4.85
2109 2244 6.064717 GTGGGGTTTATATCAGATGCTTCTT 58.935 40.000 0.00 0.00 0.00 2.52
2227 2371 6.723298 ATGATGTCCTAGTTTAGGTCTCAG 57.277 41.667 2.30 0.00 46.32 3.35
2230 2374 7.179966 TGATGTCCTAGTTTAGGTCTCAGTAA 58.820 38.462 2.30 0.00 46.32 2.24
2336 2787 8.592105 TTTTGTTGCTTCCAATTAAGATTCTG 57.408 30.769 0.00 0.00 32.75 3.02
2432 2883 3.055094 AGTCGAGGATGTGGCTTTGTTAT 60.055 43.478 0.00 0.00 0.00 1.89
2498 2949 6.348498 TCGATGGATTTGTGAGTCATACAAT 58.652 36.000 0.00 0.00 37.81 2.71
2504 2955 5.627499 TTTGTGAGTCATACAATTGGCTC 57.373 39.130 10.83 9.26 46.31 4.70
2656 3107 4.069304 TGTTTGTAAAACTAGCGGCTCAT 58.931 39.130 5.39 0.00 0.00 2.90
2940 3391 9.976511 CAATACGGTATAATTCTTCAACCTCTA 57.023 33.333 0.22 0.00 0.00 2.43
2986 3437 6.320164 CGGGTTTGATATTAGAATGGAAACCA 59.680 38.462 17.52 0.00 41.67 3.67
3115 3567 7.326063 GGATTACATTTGTTCCAGAAAGTTTCG 59.674 37.037 9.91 5.41 34.02 3.46
3130 3582 1.132453 GTTTCGGCATAACCTGAAGCC 59.868 52.381 0.00 0.00 43.61 4.35
3376 3832 1.903183 ACCCTTGAGAGTTAGACCTGC 59.097 52.381 0.00 0.00 0.00 4.85
3560 4023 2.198336 TGGGTTGACCATATACCGGTT 58.802 47.619 15.04 3.05 46.80 4.44
3561 4024 3.382278 TGGGTTGACCATATACCGGTTA 58.618 45.455 15.04 5.61 46.80 2.85
3588 4066 4.371624 AATCTTGTGTGGGATCTTGACA 57.628 40.909 0.00 0.00 0.00 3.58
3599 4077 6.599244 TGTGGGATCTTGACAATTCATTCTAC 59.401 38.462 0.00 0.00 0.00 2.59
3602 4080 6.484977 GGGATCTTGACAATTCATTCTACTCC 59.515 42.308 0.00 0.00 0.00 3.85
3603 4081 7.278875 GGATCTTGACAATTCATTCTACTCCT 58.721 38.462 0.00 0.00 0.00 3.69
3604 4082 7.440856 GGATCTTGACAATTCATTCTACTCCTC 59.559 40.741 0.00 0.00 0.00 3.71
3605 4083 7.487822 TCTTGACAATTCATTCTACTCCTCT 57.512 36.000 0.00 0.00 0.00 3.69
3629 4112 3.683847 CGATTGGATTTCCTCTGCCTCTT 60.684 47.826 0.00 0.00 36.82 2.85
3630 4113 3.356529 TTGGATTTCCTCTGCCTCTTC 57.643 47.619 0.00 0.00 36.82 2.87
3631 4114 2.555664 TGGATTTCCTCTGCCTCTTCT 58.444 47.619 0.00 0.00 36.82 2.85
3683 4169 3.617263 GTCTTCCACGATTGTATCACACC 59.383 47.826 0.00 0.00 0.00 4.16
3706 5346 0.827507 GGATGTTGCCAAGGGTGTGT 60.828 55.000 0.00 0.00 0.00 3.72
3724 5364 3.758023 TGTGTATTTGCTTGATGTGGAGG 59.242 43.478 0.00 0.00 0.00 4.30
3821 5461 0.706433 ATGAGGATGTTGCCAAGGGT 59.294 50.000 0.00 0.00 0.00 4.34
3822 5462 0.251297 TGAGGATGTTGCCAAGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
3823 5463 0.251341 GAGGATGTTGCCAAGGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
3845 5485 2.775384 TGTACAGGTTTGAGGGACACTT 59.225 45.455 0.00 0.00 0.00 3.16
3846 5486 3.201266 TGTACAGGTTTGAGGGACACTTT 59.799 43.478 0.00 0.00 0.00 2.66
3876 5516 6.847956 TCATGCCAAAATTTGAGAACTTTG 57.152 33.333 7.37 0.00 0.00 2.77
3903 5543 4.346418 ACATTGTTTGAAATAGGTGGCCAA 59.654 37.500 7.24 0.00 0.00 4.52
3962 5602 8.429299 GTTTTCTTTATCTCTTCAGTCGACTTC 58.571 37.037 17.26 0.00 0.00 3.01
3971 5611 1.886542 TCAGTCGACTTCTGCAGCTTA 59.113 47.619 17.26 0.00 33.48 3.09
3973 5613 2.410053 CAGTCGACTTCTGCAGCTTAAC 59.590 50.000 17.26 2.37 0.00 2.01
3984 5631 1.541588 GCAGCTTAACAGGAACAAGGG 59.458 52.381 0.00 0.00 0.00 3.95
3991 5638 2.197324 AGGAACAAGGGCGCCAAA 59.803 55.556 30.85 0.00 0.00 3.28
3997 5644 3.243401 GGAACAAGGGCGCCAAATTATAG 60.243 47.826 30.85 10.83 0.00 1.31
3998 5645 3.012934 ACAAGGGCGCCAAATTATAGT 57.987 42.857 30.85 11.50 0.00 2.12
3999 5646 4.159244 ACAAGGGCGCCAAATTATAGTA 57.841 40.909 30.85 0.00 0.00 1.82
4006 5657 6.097696 AGGGCGCCAAATTATAGTAATTTGTT 59.902 34.615 30.85 8.06 42.84 2.83
4033 5684 7.990541 TGTAACATAATACGAACGCATTAGT 57.009 32.000 6.16 0.00 0.00 2.24
4075 5925 2.954318 CCTCTGCACCATTCATAAAGGG 59.046 50.000 0.00 0.00 42.15 3.95
4086 5936 8.480501 CACCATTCATAAAGGGATGAAAAATCT 58.519 33.333 3.16 0.00 46.22 2.40
4094 5944 9.725019 ATAAAGGGATGAAAAATCTCAAAAACC 57.275 29.630 0.00 0.00 0.00 3.27
4103 5954 9.541143 TGAAAAATCTCAAAAACCTATGAAACC 57.459 29.630 0.00 0.00 0.00 3.27
4127 5978 7.950684 ACCTTCATACTACAGGAATCTAGCATA 59.049 37.037 0.00 0.00 0.00 3.14
4206 6061 7.759886 TGTGGTCAACATTTAAATTCGAAAACA 59.240 29.630 0.00 1.83 32.36 2.83
4236 6091 2.698855 TGAATGCTGAACTAGAGGCC 57.301 50.000 0.00 0.00 0.00 5.19
4300 6155 4.372656 AGCAAAGTATACGATCTTCAGCC 58.627 43.478 0.00 0.00 0.00 4.85
4320 6175 3.871594 GCCGAAGAGCAACATGTACTATT 59.128 43.478 0.00 3.39 0.00 1.73
4321 6176 4.260375 GCCGAAGAGCAACATGTACTATTG 60.260 45.833 12.02 2.22 0.00 1.90
4367 6222 3.821033 ACTGTAACTGACAAAATCTGGGC 59.179 43.478 0.00 0.00 37.70 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.039870 TCATTGTGCGATTTTGTTTAGAAAAAT 57.960 25.926 0.00 0.00 39.36 1.82
1 2 8.412608 TCATTGTGCGATTTTGTTTAGAAAAA 57.587 26.923 0.00 0.00 0.00 1.94
2 3 7.918033 TCTCATTGTGCGATTTTGTTTAGAAAA 59.082 29.630 0.00 0.00 0.00 2.29
3 4 7.421599 TCTCATTGTGCGATTTTGTTTAGAAA 58.578 30.769 0.00 0.00 0.00 2.52
4 5 6.964908 TCTCATTGTGCGATTTTGTTTAGAA 58.035 32.000 0.00 0.00 0.00 2.10
5 6 6.204688 ACTCTCATTGTGCGATTTTGTTTAGA 59.795 34.615 0.00 0.00 0.00 2.10
6 7 6.303970 CACTCTCATTGTGCGATTTTGTTTAG 59.696 38.462 0.00 0.00 0.00 1.85
7 8 6.142139 CACTCTCATTGTGCGATTTTGTTTA 58.858 36.000 0.00 0.00 0.00 2.01
8 9 4.977963 CACTCTCATTGTGCGATTTTGTTT 59.022 37.500 0.00 0.00 0.00 2.83
9 10 4.539870 CACTCTCATTGTGCGATTTTGTT 58.460 39.130 0.00 0.00 0.00 2.83
10 11 4.151258 CACTCTCATTGTGCGATTTTGT 57.849 40.909 0.00 0.00 0.00 2.83
55 56 5.483811 GGGGTAGAAGAGTTGAAGAGAAAG 58.516 45.833 0.00 0.00 0.00 2.62
78 79 1.304464 GTGCTTTTGGGAGGGGAGG 60.304 63.158 0.00 0.00 0.00 4.30
79 80 1.675641 CGTGCTTTTGGGAGGGGAG 60.676 63.158 0.00 0.00 0.00 4.30
80 81 1.710996 TTCGTGCTTTTGGGAGGGGA 61.711 55.000 0.00 0.00 0.00 4.81
85 86 3.482436 ACTTATGTTCGTGCTTTTGGGA 58.518 40.909 0.00 0.00 0.00 4.37
86 87 3.915437 ACTTATGTTCGTGCTTTTGGG 57.085 42.857 0.00 0.00 0.00 4.12
88 89 8.227791 AGTTATGTACTTATGTTCGTGCTTTTG 58.772 33.333 0.00 0.00 31.29 2.44
89 90 8.319143 AGTTATGTACTTATGTTCGTGCTTTT 57.681 30.769 0.00 0.00 31.29 2.27
90 91 7.900782 AGTTATGTACTTATGTTCGTGCTTT 57.099 32.000 0.00 0.00 31.29 3.51
91 92 7.900782 AAGTTATGTACTTATGTTCGTGCTT 57.099 32.000 0.00 0.00 45.22 3.91
92 93 8.866956 GTTAAGTTATGTACTTATGTTCGTGCT 58.133 33.333 0.00 0.00 46.07 4.40
93 94 8.649841 TGTTAAGTTATGTACTTATGTTCGTGC 58.350 33.333 0.00 0.00 46.07 5.34
104 105 8.799367 GGGACCAATTTTGTTAAGTTATGTACT 58.201 33.333 0.00 0.00 39.32 2.73
105 106 8.799367 AGGGACCAATTTTGTTAAGTTATGTAC 58.201 33.333 0.00 0.00 0.00 2.90
106 107 8.798402 CAGGGACCAATTTTGTTAAGTTATGTA 58.202 33.333 0.00 0.00 0.00 2.29
168 170 5.697633 TGCTGAATTGCAAATCCTTTTTCTC 59.302 36.000 11.91 3.24 40.29 2.87
183 185 6.074676 CCGAGTTTTCTTTTCTTGCTGAATTG 60.075 38.462 0.00 0.00 34.24 2.32
194 196 3.565516 GGTGCATCCGAGTTTTCTTTTC 58.434 45.455 0.00 0.00 0.00 2.29
246 248 7.613022 TGCTGAACTTTGATATCTGGATCTTTT 59.387 33.333 3.98 0.00 0.00 2.27
249 251 6.099413 TCTGCTGAACTTTGATATCTGGATCT 59.901 38.462 3.98 0.00 0.00 2.75
251 253 6.244552 TCTGCTGAACTTTGATATCTGGAT 57.755 37.500 3.98 0.00 0.00 3.41
252 254 5.682234 TCTGCTGAACTTTGATATCTGGA 57.318 39.130 3.98 0.00 0.00 3.86
253 255 6.748333 TTTCTGCTGAACTTTGATATCTGG 57.252 37.500 5.41 0.00 31.02 3.86
254 256 8.886719 TGTATTTCTGCTGAACTTTGATATCTG 58.113 33.333 5.41 0.00 31.02 2.90
255 257 9.453572 TTGTATTTCTGCTGAACTTTGATATCT 57.546 29.630 5.41 0.00 31.02 1.98
276 280 7.609760 TTATTGTGTTCGAGATGCTTTGTAT 57.390 32.000 0.00 0.00 0.00 2.29
303 307 6.605594 TGGGGGTCATGAAATCTTAATGTAAC 59.394 38.462 0.00 0.00 0.00 2.50
311 315 3.855668 TGTTTGGGGGTCATGAAATCTT 58.144 40.909 0.00 0.00 0.00 2.40
320 324 3.071892 CAGTAGTAGTTGTTTGGGGGTCA 59.928 47.826 0.00 0.00 0.00 4.02
327 332 3.386486 TGACGGCAGTAGTAGTTGTTTG 58.614 45.455 0.00 0.00 0.00 2.93
335 340 2.099263 GCTCATTCTGACGGCAGTAGTA 59.901 50.000 19.93 2.75 42.84 1.82
370 375 3.766691 GTAGGGGAGCGGCGACAA 61.767 66.667 12.98 0.00 0.00 3.18
407 412 1.004044 AGACTTCCTGGCTGTCATTGG 59.996 52.381 16.90 0.00 33.56 3.16
418 423 0.597637 ACGTGCACGAAGACTTCCTG 60.598 55.000 42.94 12.22 43.02 3.86
476 482 1.000938 CTCTGCAAGCAAGGGTTCAAC 60.001 52.381 0.00 0.00 0.00 3.18
489 495 2.301009 TCAGTGCTTCAGATCTCTGCAA 59.699 45.455 13.30 0.00 43.46 4.08
491 497 2.270047 GTCAGTGCTTCAGATCTCTGC 58.730 52.381 2.21 0.00 43.46 4.26
492 498 3.252400 GTGTCAGTGCTTCAGATCTCTG 58.748 50.000 0.00 0.56 45.08 3.35
493 499 2.233431 GGTGTCAGTGCTTCAGATCTCT 59.767 50.000 0.00 0.00 0.00 3.10
494 500 2.028658 TGGTGTCAGTGCTTCAGATCTC 60.029 50.000 0.00 0.00 0.00 2.75
542 551 0.390472 CTCTTTGGAGCGGTGAGGTC 60.390 60.000 0.00 0.00 46.08 3.85
553 562 2.158475 AGATTTGTGCCACCTCTTTGGA 60.158 45.455 0.00 0.00 39.24 3.53
566 575 3.877801 GCTTCGGCGTAGATTTGTG 57.122 52.632 18.00 0.00 0.00 3.33
581 590 1.025812 CATCCTAGTCGACGGAGCTT 58.974 55.000 15.96 0.00 31.82 3.74
586 595 1.003759 CGAGTTCATCCTAGTCGACGG 60.004 57.143 10.46 6.53 40.07 4.79
599 617 1.541379 TTCGACCATCCTCGAGTTCA 58.459 50.000 12.31 0.00 43.34 3.18
611 629 1.368579 GTCTTCCGGGTTTCGACCA 59.631 57.895 0.00 0.00 42.43 4.02
613 631 1.262417 GTTTGTCTTCCGGGTTTCGAC 59.738 52.381 0.00 2.12 42.43 4.20
619 637 2.171870 TCTTTGAGTTTGTCTTCCGGGT 59.828 45.455 0.00 0.00 0.00 5.28
651 669 2.580815 CAGTGCTCGGCCAGATGA 59.419 61.111 2.24 0.00 0.00 2.92
656 674 3.709633 AGATGCAGTGCTCGGCCA 61.710 61.111 17.60 0.00 34.03 5.36
658 676 3.873883 GCAGATGCAGTGCTCGGC 61.874 66.667 17.60 17.92 41.59 5.54
664 682 2.284263 TAGTCTTCGCAGATGCAGTG 57.716 50.000 5.55 0.00 42.21 3.66
689 716 4.225717 TCCGGTTAGCAATTTAGGTTAGGT 59.774 41.667 0.00 0.00 0.00 3.08
745 773 4.022416 TGATGTAATTTGTCACCAGTTGCC 60.022 41.667 0.00 0.00 0.00 4.52
748 776 8.321353 TCTATCTGATGTAATTTGTCACCAGTT 58.679 33.333 0.00 0.00 0.00 3.16
749 777 7.851228 TCTATCTGATGTAATTTGTCACCAGT 58.149 34.615 0.00 0.00 0.00 4.00
772 821 7.271511 GTCCATCTGTAGTTTGATTGATCTCT 58.728 38.462 0.00 0.00 0.00 3.10
775 824 6.115446 TGGTCCATCTGTAGTTTGATTGATC 58.885 40.000 0.00 0.00 0.00 2.92
776 825 6.065976 TGGTCCATCTGTAGTTTGATTGAT 57.934 37.500 0.00 0.00 0.00 2.57
777 826 5.497464 TGGTCCATCTGTAGTTTGATTGA 57.503 39.130 0.00 0.00 0.00 2.57
778 827 5.939883 TCTTGGTCCATCTGTAGTTTGATTG 59.060 40.000 0.00 0.00 0.00 2.67
801 857 9.054922 TCAAATTTTGGTTGGAATCAGATTTTC 57.945 29.630 9.18 0.00 0.00 2.29
813 870 7.983307 TGTCAAAGAATTCAAATTTTGGTTGG 58.017 30.769 8.44 0.00 0.00 3.77
814 871 9.654417 GATGTCAAAGAATTCAAATTTTGGTTG 57.346 29.630 8.44 5.26 0.00 3.77
949 1009 1.357991 GCTGAGTGCCGAGCTTTCTC 61.358 60.000 0.00 0.00 35.15 2.87
967 1028 1.450491 GGGAGAAGGAAAGAGGCGC 60.450 63.158 0.00 0.00 0.00 6.53
991 1052 3.482783 GAACAGCCGAGCACGAGC 61.483 66.667 4.70 7.00 42.66 5.03
992 1053 1.803519 GAGAACAGCCGAGCACGAG 60.804 63.158 4.70 0.00 42.66 4.18
993 1054 2.258591 GAGAACAGCCGAGCACGA 59.741 61.111 4.70 0.00 42.66 4.35
997 1058 2.185608 GAGGGAGAACAGCCGAGC 59.814 66.667 0.00 0.00 0.00 5.03
1006 1067 0.483328 CGGATAGGGAGGAGGGAGAA 59.517 60.000 0.00 0.00 0.00 2.87
1584 1650 4.383861 CCGACAGCAGAGCAGGCA 62.384 66.667 0.00 0.00 0.00 4.75
1624 1690 5.924356 TCATGGATGATAAACACCGTGTAT 58.076 37.500 4.17 0.00 37.63 2.29
1625 1691 5.346181 TCATGGATGATAAACACCGTGTA 57.654 39.130 4.17 0.00 37.63 2.90
1689 1755 3.875510 AAGCCACTTGGAGCCAGGC 62.876 63.158 1.84 1.84 45.54 4.85
1690 1756 1.975407 CAAGCCACTTGGAGCCAGG 60.975 63.158 0.00 0.00 37.77 4.45
1741 1813 2.970379 ATGGTCCATGGCTGCACGA 61.970 57.895 6.96 0.00 0.00 4.35
1860 1995 0.107508 TGCTAGCCTTGCTGATGGTC 60.108 55.000 13.29 0.00 40.10 4.02
1951 2086 0.940126 ACTGCTGTTTTCTCTGCACG 59.060 50.000 0.00 0.00 37.36 5.34
2109 2244 3.130633 CACCACGAGAGACATGAAAACA 58.869 45.455 0.00 0.00 0.00 2.83
2227 2371 8.624776 AGGCAGCAATTAGAATGTAGATTTTAC 58.375 33.333 0.00 0.00 0.00 2.01
2230 2374 7.651027 AAGGCAGCAATTAGAATGTAGATTT 57.349 32.000 0.00 0.00 0.00 2.17
2336 2787 9.252962 CAAATATTAACATCAAAATGAGCCTCC 57.747 33.333 0.00 0.00 36.67 4.30
2432 2883 3.912899 TCTGCAAGAGAACGCATCA 57.087 47.368 0.00 0.00 38.67 3.07
2498 2949 4.640771 ACTACAGAGAAAATGGAGCCAA 57.359 40.909 0.00 0.00 31.22 4.52
2504 2955 7.969536 TGAGAAGAAACTACAGAGAAAATGG 57.030 36.000 0.00 0.00 0.00 3.16
2656 3107 4.142227 GGATTTCTCCTACTAGCAACGACA 60.142 45.833 0.00 0.00 38.65 4.35
2936 3387 7.169982 CGAGGGAATAAGTAGCAAAACATAGAG 59.830 40.741 0.00 0.00 0.00 2.43
2940 3391 4.881850 CCGAGGGAATAAGTAGCAAAACAT 59.118 41.667 0.00 0.00 0.00 2.71
3030 3481 2.158986 CCGAGATGCAGATTCTGAAGGT 60.159 50.000 17.87 0.00 32.44 3.50
3103 3555 3.081804 AGGTTATGCCGAAACTTTCTGG 58.918 45.455 0.12 4.48 43.70 3.86
3115 3567 1.211949 TGGTAGGCTTCAGGTTATGCC 59.788 52.381 0.00 0.00 45.21 4.40
3130 3582 7.416213 GCTTAGATATCATGGAGCTACTGGTAG 60.416 44.444 5.32 3.62 36.29 3.18
3376 3832 7.379529 CCAGACAAAAATAAACACAGTAGCTTG 59.620 37.037 0.00 0.00 0.00 4.01
3560 4023 6.566079 AGATCCCACACAAGATTTCAGATA 57.434 37.500 0.00 0.00 0.00 1.98
3561 4024 5.447778 AGATCCCACACAAGATTTCAGAT 57.552 39.130 0.00 0.00 0.00 2.90
3588 4066 5.543507 ATCGCAGAGGAGTAGAATGAATT 57.456 39.130 0.00 0.00 43.63 2.17
3599 4077 2.158842 AGGAAATCCAATCGCAGAGGAG 60.159 50.000 1.67 0.00 38.35 3.69
3602 4080 2.871022 CAGAGGAAATCCAATCGCAGAG 59.129 50.000 1.67 0.00 38.35 3.35
3603 4081 2.910199 CAGAGGAAATCCAATCGCAGA 58.090 47.619 1.67 0.00 39.18 4.26
3604 4082 1.332997 GCAGAGGAAATCCAATCGCAG 59.667 52.381 1.67 0.00 38.89 5.18
3605 4083 1.382522 GCAGAGGAAATCCAATCGCA 58.617 50.000 1.67 0.00 38.89 5.10
3629 4112 3.141398 GTGACACTGGCATCAAAGAAGA 58.859 45.455 0.00 0.00 0.00 2.87
3630 4113 2.880268 TGTGACACTGGCATCAAAGAAG 59.120 45.455 7.20 0.00 0.00 2.85
3631 4114 2.618241 GTGTGACACTGGCATCAAAGAA 59.382 45.455 8.76 0.00 0.00 2.52
3706 5346 2.025037 AGGCCTCCACATCAAGCAAATA 60.025 45.455 0.00 0.00 0.00 1.40
3724 5364 5.249420 AGAAGACTTTATTGACCTCAAGGC 58.751 41.667 0.00 0.00 39.47 4.35
3774 5414 3.243873 ACATGATCACTATGGCAGTACGG 60.244 47.826 0.00 0.00 34.98 4.02
3776 5416 4.697514 ACACATGATCACTATGGCAGTAC 58.302 43.478 0.00 0.00 34.98 2.73
3821 5461 2.506231 TGTCCCTCAAACCTGTACAACA 59.494 45.455 0.00 0.00 0.00 3.33
3822 5462 2.876550 GTGTCCCTCAAACCTGTACAAC 59.123 50.000 0.00 0.00 0.00 3.32
3823 5463 2.775384 AGTGTCCCTCAAACCTGTACAA 59.225 45.455 0.00 0.00 0.00 2.41
3845 5485 8.954950 TCTCAAATTTTGGCATGAAAAACTAA 57.045 26.923 9.18 0.00 29.78 2.24
3846 5486 8.825745 GTTCTCAAATTTTGGCATGAAAAACTA 58.174 29.630 9.18 0.00 29.78 2.24
3876 5516 4.690280 CCACCTATTTCAAACAATGTTGCC 59.310 41.667 0.00 0.00 0.00 4.52
3879 5519 4.346418 TGGCCACCTATTTCAAACAATGTT 59.654 37.500 0.00 0.00 0.00 2.71
3891 5531 3.906846 TCAAAACCAATTGGCCACCTATT 59.093 39.130 24.79 6.41 39.32 1.73
3946 5586 2.227626 CTGCAGAAGTCGACTGAAGAGA 59.772 50.000 20.85 1.06 42.01 3.10
3962 5602 2.227388 CCTTGTTCCTGTTAAGCTGCAG 59.773 50.000 10.11 10.11 0.00 4.41
3971 5611 2.597510 GGCGCCCTTGTTCCTGTT 60.598 61.111 18.11 0.00 0.00 3.16
3973 5613 1.535204 ATTTGGCGCCCTTGTTCCTG 61.535 55.000 26.77 0.00 0.00 3.86
3984 5631 7.979115 TGAACAAATTACTATAATTTGGCGC 57.021 32.000 26.16 18.56 46.44 6.53
4006 5657 7.471657 AATGCGTTCGTATTATGTTACATGA 57.528 32.000 8.26 0.00 0.00 3.07
4033 5684 3.193267 GGTTTGCTGAGATGTTGCCATTA 59.807 43.478 0.00 0.00 0.00 1.90
4054 5886 2.954318 CCCTTTATGAATGGTGCAGAGG 59.046 50.000 0.00 0.00 0.00 3.69
4101 5952 6.136857 TGCTAGATTCCTGTAGTATGAAGGT 58.863 40.000 0.00 0.00 32.59 3.50
4103 5954 9.800433 CATATGCTAGATTCCTGTAGTATGAAG 57.200 37.037 0.00 0.00 28.72 3.02
4118 5969 8.439971 TGATTTGGTAAGGTTCATATGCTAGAT 58.560 33.333 0.00 0.00 0.00 1.98
4127 5978 8.314021 GGAGAATTTTGATTTGGTAAGGTTCAT 58.686 33.333 0.00 0.00 0.00 2.57
4194 6049 9.796120 TTCAAATACTTGAGTGTTTTCGAATTT 57.204 25.926 0.00 0.00 42.48 1.82
4206 6061 8.097038 TCTAGTTCAGCATTCAAATACTTGAGT 58.903 33.333 0.00 0.00 42.48 3.41
4236 6091 6.028987 GCGGTTTAGAAGTACTCTGAACTAG 58.971 44.000 19.50 16.42 45.56 2.57
4300 6155 5.109210 TCCAATAGTACATGTTGCTCTTCG 58.891 41.667 2.30 0.00 0.00 3.79
4367 6222 8.705134 TGTCTGTTAAACGACTGTTATAATGTG 58.295 33.333 0.00 0.00 37.31 3.21


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

AutoCloner maintained by Alex Coulton.