Multiple sequence alignment - TraesCS7D01G340200

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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 TraesCS7D01G340200 chr7D 100.000 3811 0 0 1 3811 435422771 435418961 0.000000e+00 7038.0
1 TraesCS7D01G340200 chr7A 93.381 3641 170 39 1 3589 485499291 485495670 0.000000e+00 5323.0
2 TraesCS7D01G340200 chr7A 81.720 93 11 5 3612 3702 717565849 717565761 5.280000e-09 73.1
3 TraesCS7D01G340200 chr7A 80.952 84 8 5 3631 3711 603337266 603337188 4.110000e-05 60.2
4 TraesCS7D01G340200 chr7B 93.414 3644 123 64 1 3601 451936655 451933086 0.000000e+00 5291.0
5 TraesCS7D01G340200 chr4D 94.318 88 5 0 3717 3804 16423549 16423462 6.640000e-28 135.0
6 TraesCS7D01G340200 chr5B 94.253 87 5 0 3725 3811 540345281 540345367 2.390000e-27 134.0
7 TraesCS7D01G340200 chr5B 92.857 42 3 0 3659 3700 282559194 282559153 1.140000e-05 62.1
8 TraesCS7D01G340200 chr4B 91.398 93 8 0 3719 3811 605885770 605885862 1.110000e-25 128.0
9 TraesCS7D01G340200 chrUn 79.808 104 17 2 3609 3711 31488462 31488362 5.280000e-09 73.1
10 TraesCS7D01G340200 chr6B 84.932 73 7 1 3632 3704 566638539 566638607 1.900000e-08 71.3
11 TraesCS7D01G340200 chr6D 87.500 64 3 2 3649 3711 289352755 289352814 6.830000e-08 69.4
12 TraesCS7D01G340200 chr5A 80.000 90 16 2 3614 3703 582590901 582590988 8.840000e-07 65.8
13 TraesCS7D01G340200 chr2A 79.381 97 16 3 3612 3708 74563647 74563555 8.840000e-07 65.8
14 TraesCS7D01G340200 chr2A 100.000 28 0 0 3586 3613 712821029 712821056 7.000000e-03 52.8
15 TraesCS7D01G340200 chr2A 100.000 28 0 0 3586 3613 712832283 712832310 7.000000e-03 52.8
16 TraesCS7D01G340200 chr4A 83.333 66 6 3 3647 3711 420508949 420509010 5.320000e-04 56.5


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 TraesCS7D01G340200 chr7D 435418961 435422771 3810 True 7038 7038 100.000 1 3811 1 chr7D.!!$R1 3810
1 TraesCS7D01G340200 chr7A 485495670 485499291 3621 True 5323 5323 93.381 1 3589 1 chr7A.!!$R1 3588
2 TraesCS7D01G340200 chr7B 451933086 451936655 3569 True 5291 5291 93.414 1 3601 1 chr7B.!!$R1 3600

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
582 616 0.036952 ACTCATCGCTCCAGTTGGTG 60.037 55.0 0.0 0.0 36.34 4.17 F
2181 2219 0.250338 GTTGCGAGGATATGGGTCCC 60.250 60.0 0.0 0.0 39.17 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2357 0.177604 CCTTCTCTGGCAGGCAGTAG 59.822 60.0 22.68 17.61 0.0 2.57 R
3076 3129 0.179048 TGGAGAACACACACAGGCAG 60.179 55.0 0.00 0.00 0.0 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
43 57 0.259938 ATTCTCCATTGCCCACCTCC 59.740 55.000 0.00 0.00 0.00 4.30
200 224 1.382695 GTTCCCCCTCTGATCCGGA 60.383 63.158 6.61 6.61 0.00 5.14
316 343 0.721718 CCTGCTTGTTTCGATCGGTC 59.278 55.000 16.41 6.71 0.00 4.79
323 350 2.285024 TTTCGATCGGTCCGGGGTT 61.285 57.895 16.41 0.00 0.00 4.11
324 351 2.510064 TTTCGATCGGTCCGGGGTTG 62.510 60.000 16.41 2.47 0.00 3.77
354 381 1.552348 GCGCGATGATGTAGCAGGTC 61.552 60.000 12.10 0.00 0.00 3.85
443 471 4.790861 GGGTCGTCGGTCCTTCGC 62.791 72.222 0.00 0.00 0.00 4.70
518 547 4.406648 TTTCTCAGGTATGATGATGCGT 57.593 40.909 0.00 0.00 34.12 5.24
526 555 5.119743 CAGGTATGATGATGCGTGTTCATAG 59.880 44.000 7.37 0.00 34.03 2.23
527 556 4.991056 GGTATGATGATGCGTGTTCATAGT 59.009 41.667 7.37 0.00 34.03 2.12
533 562 7.084486 TGATGATGCGTGTTCATAGTACTATC 58.916 38.462 12.62 3.00 34.03 2.08
534 563 6.635030 TGATGCGTGTTCATAGTACTATCT 57.365 37.500 12.62 0.00 0.00 1.98
580 614 0.247460 TGACTCATCGCTCCAGTTGG 59.753 55.000 0.00 0.00 0.00 3.77
581 615 0.247736 GACTCATCGCTCCAGTTGGT 59.752 55.000 0.00 0.00 36.34 3.67
582 616 0.036952 ACTCATCGCTCCAGTTGGTG 60.037 55.000 0.00 0.00 36.34 4.17
676 711 5.930837 TGCCCCTAAAATTAAATCTGGTG 57.069 39.130 0.00 0.00 0.00 4.17
686 721 0.606401 AAATCTGGTGTGTGCCCTCG 60.606 55.000 0.00 0.00 0.00 4.63
687 722 3.612247 ATCTGGTGTGTGCCCTCGC 62.612 63.158 0.00 0.00 0.00 5.03
691 726 3.490759 GTGTGTGCCCTCGCGATG 61.491 66.667 10.36 6.89 38.08 3.84
699 734 1.079819 CCCTCGCGATGTTCTGTGT 60.080 57.895 10.36 0.00 0.00 3.72
715 750 6.642950 TGTTCTGTGTTTTTGACGATTTTTGT 59.357 30.769 0.00 0.00 0.00 2.83
717 752 7.271936 TCTGTGTTTTTGACGATTTTTGTTC 57.728 32.000 0.00 0.00 0.00 3.18
721 756 7.169982 TGTGTTTTTGACGATTTTTGTTCAAGT 59.830 29.630 0.00 0.00 0.00 3.16
730 765 1.757682 TTTGTTCAAGTTCTGCCGGT 58.242 45.000 1.90 0.00 0.00 5.28
738 773 1.069090 GTTCTGCCGGTCACTGACA 59.931 57.895 11.34 0.00 33.68 3.58
777 812 1.013596 TGCAGATTTAATGGGCGACG 58.986 50.000 0.00 0.00 0.00 5.12
1134 1169 5.692928 CAGGATTCCATTCTCATCTTCCTT 58.307 41.667 5.29 0.00 30.05 3.36
1191 1226 1.153086 GGGCACTGATTCCATCGCT 60.153 57.895 0.00 0.00 0.00 4.93
1197 1232 0.933097 CTGATTCCATCGCTTCGGTG 59.067 55.000 0.00 0.00 37.76 4.94
1368 1403 2.159014 CCTCCGGGTGATTAACATCGAA 60.159 50.000 0.00 0.00 32.79 3.71
1409 1444 1.694150 TCAGTTTCAGGTGGACCAGAG 59.306 52.381 0.00 0.00 38.89 3.35
1659 1694 4.753186 ACCCTCAGAAGAAAGAGAACCTA 58.247 43.478 0.00 0.00 33.74 3.08
1731 1769 3.941483 CTGCTCCTATCGAACCAATTGTT 59.059 43.478 4.43 0.00 40.81 2.83
1971 2009 1.492176 GATGGGGAAGGCATGAAGAGA 59.508 52.381 0.00 0.00 0.00 3.10
1977 2015 2.275318 GAAGGCATGAAGAGAGGAACG 58.725 52.381 0.00 0.00 0.00 3.95
2029 2067 2.668457 GCGGCTTATATTCTCGACCATG 59.332 50.000 0.00 0.00 0.00 3.66
2181 2219 0.250338 GTTGCGAGGATATGGGTCCC 60.250 60.000 0.00 0.00 39.17 4.46
2319 2357 3.321111 AGCTGATTCCAATTGATCATGGC 59.679 43.478 7.12 9.58 36.62 4.40
2368 2406 5.376854 TTCTCTCTTGCATTACTTTTGGC 57.623 39.130 0.00 0.00 0.00 4.52
2379 2418 1.216178 CTTTTGGCCCCTTGCATCG 59.784 57.895 0.00 0.00 43.89 3.84
2390 2429 4.622933 GCCCCTTGCATCGTATCATACATA 60.623 45.833 0.00 0.00 40.77 2.29
2395 2434 4.998788 TGCATCGTATCATACATAGCTCC 58.001 43.478 0.00 0.00 0.00 4.70
2413 2452 3.672511 GCTCCTGAGTCATGCAAATGTTG 60.673 47.826 0.00 0.00 0.00 3.33
2418 2457 5.575606 CCTGAGTCATGCAAATGTTGATTTC 59.424 40.000 0.00 0.00 28.65 2.17
2430 2469 4.902443 TGTTGATTTCGTTGCCTTGTTA 57.098 36.364 0.00 0.00 0.00 2.41
2431 2470 5.446143 TGTTGATTTCGTTGCCTTGTTAT 57.554 34.783 0.00 0.00 0.00 1.89
2450 2489 6.563422 TGTTATTATGCAGTTTGAGGATTGC 58.437 36.000 0.00 0.00 37.09 3.56
2525 2564 7.414222 AACCATTGCATACATTGAATCTCTT 57.586 32.000 0.00 0.00 30.32 2.85
2693 2732 4.647424 CAGGGAGACTGTGAATAGAGAC 57.353 50.000 0.00 0.00 42.42 3.36
2777 2816 1.292541 GTTCCTGGAGACGGTGTCC 59.707 63.158 16.90 16.90 32.18 4.02
2886 2925 6.142817 GGTTTGCTGTAAGTATGTTTCACAG 58.857 40.000 0.00 0.00 39.65 3.66
3034 3074 6.404513 GCGTTAGACCTTATCACTGAACTAGT 60.405 42.308 0.00 0.00 41.36 2.57
3036 3076 7.485277 CGTTAGACCTTATCACTGAACTAGTTG 59.515 40.741 14.14 1.75 37.60 3.16
3038 3078 7.164230 AGACCTTATCACTGAACTAGTTGAG 57.836 40.000 19.09 19.09 37.60 3.02
3039 3079 5.725362 ACCTTATCACTGAACTAGTTGAGC 58.275 41.667 20.38 4.06 37.60 4.26
3040 3080 5.482175 ACCTTATCACTGAACTAGTTGAGCT 59.518 40.000 20.38 9.25 37.60 4.09
3041 3081 6.014156 ACCTTATCACTGAACTAGTTGAGCTT 60.014 38.462 20.38 9.08 37.60 3.74
3044 3084 5.537300 TCACTGAACTAGTTGAGCTTCTT 57.463 39.130 20.38 0.00 37.60 2.52
3045 3085 6.650427 TCACTGAACTAGTTGAGCTTCTTA 57.350 37.500 20.38 0.00 37.60 2.10
3047 3087 5.635700 CACTGAACTAGTTGAGCTTCTTACC 59.364 44.000 20.38 0.00 37.60 2.85
3048 3088 4.806330 TGAACTAGTTGAGCTTCTTACCG 58.194 43.478 14.14 0.00 0.00 4.02
3049 3089 3.870633 ACTAGTTGAGCTTCTTACCGG 57.129 47.619 0.00 0.00 0.00 5.28
3051 3091 2.457366 AGTTGAGCTTCTTACCGGTG 57.543 50.000 19.93 0.15 0.00 4.94
3052 3092 0.796927 GTTGAGCTTCTTACCGGTGC 59.203 55.000 19.93 12.08 0.00 5.01
3056 3096 0.685097 AGCTTCTTACCGGTGCTTCA 59.315 50.000 19.93 0.00 0.00 3.02
3058 3098 1.398390 GCTTCTTACCGGTGCTTCATG 59.602 52.381 19.93 0.00 0.00 3.07
3076 3129 0.878416 TGCATAGCAAACGGTTGTCC 59.122 50.000 15.84 0.00 34.76 4.02
3081 3134 2.193536 GCAAACGGTTGTCCTGCCT 61.194 57.895 15.84 0.00 37.06 4.75
3091 3144 0.463654 TGTCCTGCCTGTGTGTGTTC 60.464 55.000 0.00 0.00 0.00 3.18
3099 3152 2.420642 CCTGTGTGTGTTCTCCATCTG 58.579 52.381 0.00 0.00 0.00 2.90
3147 3200 5.041940 CGGAAGTGCTACTAGTATTGTTCC 58.958 45.833 16.43 16.43 0.00 3.62
3152 3205 5.066246 AGTGCTACTAGTATTGTTCCGAGTC 59.934 44.000 2.33 0.00 0.00 3.36
3154 3207 6.259608 GTGCTACTAGTATTGTTCCGAGTCTA 59.740 42.308 2.33 0.00 0.00 2.59
3166 3220 2.881513 TCCGAGTCTATAGCAGCTTCTG 59.118 50.000 0.00 0.00 34.12 3.02
3183 3239 1.957177 TCTGCATCTGGGTCGTCTATC 59.043 52.381 0.00 0.00 0.00 2.08
3208 3264 1.739196 GTGTTCTACCGGCGGTTCC 60.739 63.158 38.73 21.49 37.09 3.62
3214 3270 3.359515 TACCGGCGGTTCCATCGTG 62.360 63.158 38.73 3.54 37.09 4.35
3218 3274 2.162754 GGCGGTTCCATCGTGTACG 61.163 63.158 0.00 0.00 36.23 3.67
3220 3276 1.213537 CGGTTCCATCGTGTACGGT 59.786 57.895 4.44 0.00 40.29 4.83
3221 3277 0.799534 CGGTTCCATCGTGTACGGTC 60.800 60.000 4.44 0.00 40.29 4.79
3249 3309 7.149307 TCTCCGGTTGTTTCATTTTTATTTCC 58.851 34.615 0.00 0.00 0.00 3.13
3253 3317 5.388994 GGTTGTTTCATTTTTATTTCCGCGG 60.389 40.000 22.12 22.12 0.00 6.46
3260 3324 4.522722 TTTTTATTTCCGCGGGTTGATT 57.477 36.364 27.83 7.23 0.00 2.57
3275 3339 1.226603 GATTCTCACGACCGACCGG 60.227 63.158 6.94 6.94 42.03 5.28
3353 3417 2.803956 GTGCAGCGGTTTACTTTGACTA 59.196 45.455 0.00 0.00 0.00 2.59
3356 3420 3.497262 GCAGCGGTTTACTTTGACTAACT 59.503 43.478 0.00 0.00 0.00 2.24
3357 3421 4.610680 GCAGCGGTTTACTTTGACTAACTG 60.611 45.833 0.00 0.00 0.00 3.16
3368 3432 3.586100 TGACTAACTGCGCACTGAATA 57.414 42.857 5.66 0.00 0.00 1.75
3373 3439 6.072728 TGACTAACTGCGCACTGAATAAAAAT 60.073 34.615 5.66 0.00 0.00 1.82
3405 3471 0.733729 ATCGTGCGTGACTAGACTCC 59.266 55.000 0.00 0.00 0.00 3.85
3437 3503 8.712363 TCGCTTAAATATCTGCATATCAACTTC 58.288 33.333 0.00 0.00 0.00 3.01
3514 3583 7.351166 TCTCATTTTTATCTTTATCCCCGGTT 58.649 34.615 0.00 0.00 0.00 4.44
3563 3632 1.917273 CAATCTTTGCTGGAATGCCG 58.083 50.000 0.00 0.00 36.79 5.69
3572 3641 1.599542 GCTGGAATGCCGAGTTATCAC 59.400 52.381 0.00 0.00 36.79 3.06
3601 3670 4.914177 TGGTTTATACTCCCTCCGTTTT 57.086 40.909 0.00 0.00 0.00 2.43
3602 3671 5.245584 TGGTTTATACTCCCTCCGTTTTT 57.754 39.130 0.00 0.00 0.00 1.94
3603 3672 6.371595 TGGTTTATACTCCCTCCGTTTTTA 57.628 37.500 0.00 0.00 0.00 1.52
3604 3673 6.777782 TGGTTTATACTCCCTCCGTTTTTAA 58.222 36.000 0.00 0.00 0.00 1.52
3605 3674 7.230027 TGGTTTATACTCCCTCCGTTTTTAAA 58.770 34.615 0.00 0.00 0.00 1.52
3606 3675 7.889600 TGGTTTATACTCCCTCCGTTTTTAAAT 59.110 33.333 0.00 0.00 0.00 1.40
3607 3676 9.394767 GGTTTATACTCCCTCCGTTTTTAAATA 57.605 33.333 0.00 0.00 0.00 1.40
3642 3711 7.745620 AGCCCTTCTAAATATTTCAATACGG 57.254 36.000 3.39 0.47 0.00 4.02
3643 3712 7.514721 AGCCCTTCTAAATATTTCAATACGGA 58.485 34.615 3.39 0.00 0.00 4.69
3644 3713 7.996644 AGCCCTTCTAAATATTTCAATACGGAA 59.003 33.333 3.39 0.00 0.00 4.30
3645 3714 8.793592 GCCCTTCTAAATATTTCAATACGGAAT 58.206 33.333 3.39 0.00 0.00 3.01
3658 3727 8.989653 TTCAATACGGAATATATACGAATGCA 57.010 30.769 14.42 0.00 0.00 3.96
3659 3728 9.594478 TTCAATACGGAATATATACGAATGCAT 57.406 29.630 14.42 0.00 0.00 3.96
3660 3729 9.030301 TCAATACGGAATATATACGAATGCATG 57.970 33.333 14.42 0.00 0.00 4.06
3661 3730 8.817100 CAATACGGAATATATACGAATGCATGT 58.183 33.333 14.42 0.00 0.00 3.21
3665 3734 9.459640 ACGGAATATATACGAATGCATGTATAC 57.540 33.333 15.45 0.00 36.62 1.47
3666 3735 9.458374 CGGAATATATACGAATGCATGTATACA 57.542 33.333 15.45 8.27 36.62 2.29
3743 3812 8.579850 AATAGGTTTGCTATTTCACATCAAGA 57.420 30.769 0.00 0.00 0.00 3.02
3744 3813 8.757982 ATAGGTTTGCTATTTCACATCAAGAT 57.242 30.769 0.00 0.00 0.00 2.40
3745 3814 6.860080 AGGTTTGCTATTTCACATCAAGATG 58.140 36.000 8.45 8.45 44.15 2.90
3770 3839 8.683615 TGTGAAATACTTATCTCACATCTACGT 58.316 33.333 1.91 0.00 42.36 3.57
3771 3840 9.171701 GTGAAATACTTATCTCACATCTACGTC 57.828 37.037 0.00 0.00 38.43 4.34
3772 3841 8.350722 TGAAATACTTATCTCACATCTACGTCC 58.649 37.037 0.00 0.00 0.00 4.79
3773 3842 7.818997 AATACTTATCTCACATCTACGTCCA 57.181 36.000 0.00 0.00 0.00 4.02
3774 3843 5.759506 ACTTATCTCACATCTACGTCCAG 57.240 43.478 0.00 0.00 0.00 3.86
3775 3844 5.437946 ACTTATCTCACATCTACGTCCAGA 58.562 41.667 0.00 0.00 0.00 3.86
3776 3845 5.886474 ACTTATCTCACATCTACGTCCAGAA 59.114 40.000 0.00 0.00 0.00 3.02
3777 3846 4.640789 ATCTCACATCTACGTCCAGAAC 57.359 45.455 0.00 0.00 0.00 3.01
3778 3847 2.753452 TCTCACATCTACGTCCAGAACC 59.247 50.000 0.00 0.00 0.00 3.62
3779 3848 1.471287 TCACATCTACGTCCAGAACCG 59.529 52.381 0.00 0.00 0.00 4.44
3780 3849 1.201647 CACATCTACGTCCAGAACCGT 59.798 52.381 0.00 0.00 40.87 4.83
3781 3850 1.891150 ACATCTACGTCCAGAACCGTT 59.109 47.619 0.00 0.00 38.43 4.44
3782 3851 2.259618 CATCTACGTCCAGAACCGTTG 58.740 52.381 0.00 0.00 38.43 4.10
3783 3852 1.608055 TCTACGTCCAGAACCGTTGA 58.392 50.000 0.00 0.00 38.43 3.18
3784 3853 2.165167 TCTACGTCCAGAACCGTTGAT 58.835 47.619 0.00 0.00 38.43 2.57
3785 3854 3.346315 TCTACGTCCAGAACCGTTGATA 58.654 45.455 0.00 0.00 38.43 2.15
3786 3855 3.949754 TCTACGTCCAGAACCGTTGATAT 59.050 43.478 0.00 0.00 38.43 1.63
3787 3856 3.604875 ACGTCCAGAACCGTTGATATT 57.395 42.857 0.00 0.00 32.50 1.28
3788 3857 3.259064 ACGTCCAGAACCGTTGATATTG 58.741 45.455 0.00 0.00 32.50 1.90
3789 3858 3.259064 CGTCCAGAACCGTTGATATTGT 58.741 45.455 0.00 0.00 0.00 2.71
3790 3859 3.682858 CGTCCAGAACCGTTGATATTGTT 59.317 43.478 0.00 0.00 0.00 2.83
3791 3860 4.153475 CGTCCAGAACCGTTGATATTGTTT 59.847 41.667 0.00 0.00 0.00 2.83
3792 3861 5.390613 GTCCAGAACCGTTGATATTGTTTG 58.609 41.667 0.00 0.00 0.00 2.93
3793 3862 5.048991 GTCCAGAACCGTTGATATTGTTTGT 60.049 40.000 0.00 0.00 0.00 2.83
3794 3863 5.180492 TCCAGAACCGTTGATATTGTTTGTC 59.820 40.000 0.00 0.00 0.00 3.18
3795 3864 5.181245 CCAGAACCGTTGATATTGTTTGTCT 59.819 40.000 0.00 0.00 0.00 3.41
3796 3865 6.293955 CCAGAACCGTTGATATTGTTTGTCTT 60.294 38.462 0.00 0.00 0.00 3.01
3797 3866 7.138736 CAGAACCGTTGATATTGTTTGTCTTT 58.861 34.615 0.00 0.00 0.00 2.52
3798 3867 8.286800 CAGAACCGTTGATATTGTTTGTCTTTA 58.713 33.333 0.00 0.00 0.00 1.85
3799 3868 8.842280 AGAACCGTTGATATTGTTTGTCTTTAA 58.158 29.630 0.00 0.00 0.00 1.52
3800 3869 9.620660 GAACCGTTGATATTGTTTGTCTTTAAT 57.379 29.630 0.00 0.00 0.00 1.40
3801 3870 9.974980 AACCGTTGATATTGTTTGTCTTTAATT 57.025 25.926 0.00 0.00 0.00 1.40
3802 3871 9.974980 ACCGTTGATATTGTTTGTCTTTAATTT 57.025 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 57 0.995675 AGGAACAGGGATGGATGGGG 60.996 60.000 0.00 0.00 0.00 4.96
138 159 2.665000 CTCCTTCCTTGCTCCGCA 59.335 61.111 0.00 0.00 36.47 5.69
200 224 2.618045 GGATTGGATTGGAACTCACCGT 60.618 50.000 0.00 0.00 0.00 4.83
324 351 1.009675 CATCGCGCAATGGTTAGCC 60.010 57.895 8.75 0.00 0.00 3.93
334 361 1.592400 CCTGCTACATCATCGCGCA 60.592 57.895 8.75 0.00 0.00 6.09
354 381 4.093952 CAAGCAGCAACGGCCGAG 62.094 66.667 35.90 24.47 42.56 4.63
443 471 1.095600 TCCGATGACGAGAGAACCAG 58.904 55.000 0.00 0.00 42.66 4.00
518 547 6.573434 CAGGCACAAGATAGTACTATGAACA 58.427 40.000 20.13 0.00 0.00 3.18
526 555 0.931005 GCGCAGGCACAAGATAGTAC 59.069 55.000 0.30 0.00 39.62 2.73
527 556 0.527600 CGCGCAGGCACAAGATAGTA 60.528 55.000 8.75 0.00 39.92 1.82
676 711 2.740714 GAACATCGCGAGGGCACAC 61.741 63.158 25.76 7.37 39.92 3.82
686 721 2.713976 CGTCAAAAACACAGAACATCGC 59.286 45.455 0.00 0.00 0.00 4.58
687 722 4.190304 TCGTCAAAAACACAGAACATCG 57.810 40.909 0.00 0.00 0.00 3.84
691 726 7.044589 ACAAAAATCGTCAAAAACACAGAAC 57.955 32.000 0.00 0.00 0.00 3.01
699 734 8.431593 CAGAACTTGAACAAAAATCGTCAAAAA 58.568 29.630 0.00 0.00 0.00 1.94
715 750 0.468226 AGTGACCGGCAGAACTTGAA 59.532 50.000 0.00 0.00 0.00 2.69
717 752 0.249868 TCAGTGACCGGCAGAACTTG 60.250 55.000 0.00 0.00 0.00 3.16
721 756 1.112916 TCTGTCAGTGACCGGCAGAA 61.113 55.000 20.43 0.00 33.84 3.02
730 765 1.649321 AGATTGCCCTCTGTCAGTGA 58.351 50.000 3.43 0.00 0.00 3.41
738 773 3.507622 GCACAAAAGTTAGATTGCCCTCT 59.492 43.478 0.00 0.00 0.00 3.69
777 812 3.774066 GCTACAGGCACATTTTGGATTC 58.226 45.455 0.00 0.00 41.35 2.52
1074 1109 1.290203 AACAGTGTGCTGAACGACTG 58.710 50.000 13.46 13.46 45.28 3.51
1359 1394 1.434555 CACTGGCGGTTTCGATGTTA 58.565 50.000 0.00 0.00 39.00 2.41
1365 1400 2.281208 TTCCCACTGGCGGTTTCG 60.281 61.111 0.00 0.00 39.81 3.46
1368 1403 0.112412 ATTTCTTCCCACTGGCGGTT 59.888 50.000 0.00 0.00 0.00 4.44
1409 1444 0.727398 GAGGTACTTGACATTGCGGC 59.273 55.000 0.00 0.00 41.55 6.53
1731 1769 0.952010 GCTTCGCCTTCCGGTTAACA 60.952 55.000 8.10 0.00 37.59 2.41
1755 1793 7.814642 AGTCAATCATTTTCATCACTTCAGAC 58.185 34.615 0.00 0.00 0.00 3.51
1971 2009 1.885163 CTTCCCCTACACGCGTTCCT 61.885 60.000 10.22 0.00 0.00 3.36
1977 2015 2.436115 GCACCTTCCCCTACACGC 60.436 66.667 0.00 0.00 0.00 5.34
2029 2067 1.061131 CGATTCACGATCACCAACTGC 59.939 52.381 0.00 0.00 45.77 4.40
2181 2219 0.593128 CCTTCACTGGAAAAGCACGG 59.407 55.000 0.00 0.00 31.35 4.94
2319 2357 0.177604 CCTTCTCTGGCAGGCAGTAG 59.822 60.000 22.68 17.61 0.00 2.57
2366 2404 0.250901 ATGATACGATGCAAGGGGCC 60.251 55.000 0.00 0.00 43.89 5.80
2368 2406 3.401033 TGTATGATACGATGCAAGGGG 57.599 47.619 0.00 0.00 0.00 4.79
2379 2418 6.825944 TGACTCAGGAGCTATGTATGATAC 57.174 41.667 0.00 0.00 0.00 2.24
2390 2429 2.290768 ACATTTGCATGACTCAGGAGCT 60.291 45.455 0.00 0.00 34.11 4.09
2395 2434 5.285370 CGAAATCAACATTTGCATGACTCAG 59.715 40.000 0.00 0.00 31.94 3.35
2413 2452 6.033341 TGCATAATAACAAGGCAACGAAATC 58.967 36.000 0.00 0.00 46.39 2.17
2418 2457 4.355543 ACTGCATAATAACAAGGCAACG 57.644 40.909 0.00 0.00 46.39 4.10
2430 2469 4.142093 GGTGCAATCCTCAAACTGCATAAT 60.142 41.667 0.00 0.00 45.77 1.28
2431 2470 3.193267 GGTGCAATCCTCAAACTGCATAA 59.807 43.478 0.00 0.00 45.77 1.90
2450 2489 2.069273 CAGTAAAGCCACTCGAAGGTG 58.931 52.381 5.56 1.94 37.00 4.00
2525 2564 1.248101 TGATGTCCTCTTCCGCGTCA 61.248 55.000 4.92 0.00 0.00 4.35
2693 2732 3.305267 GGATGATGTCCTCGATCACAGAG 60.305 52.174 3.28 0.00 44.16 3.35
2777 2816 0.039074 GGTGGCGGTCTATGATCTCG 60.039 60.000 0.00 0.00 0.00 4.04
3034 3074 0.685097 AGCACCGGTAAGAAGCTCAA 59.315 50.000 6.87 0.00 0.00 3.02
3036 3076 1.337823 TGAAGCACCGGTAAGAAGCTC 60.338 52.381 15.91 10.42 33.83 4.09
3038 3078 1.398390 CATGAAGCACCGGTAAGAAGC 59.602 52.381 6.87 6.19 0.00 3.86
3039 3079 1.398390 GCATGAAGCACCGGTAAGAAG 59.602 52.381 6.87 0.00 44.79 2.85
3040 3080 1.448985 GCATGAAGCACCGGTAAGAA 58.551 50.000 6.87 0.00 44.79 2.52
3041 3081 3.153024 GCATGAAGCACCGGTAAGA 57.847 52.632 6.87 0.00 44.79 2.10
3051 3091 1.133025 ACCGTTTGCTATGCATGAAGC 59.867 47.619 10.16 12.14 45.96 3.86
3052 3092 3.173599 CAACCGTTTGCTATGCATGAAG 58.826 45.455 10.16 0.00 38.76 3.02
3056 3096 1.472480 GGACAACCGTTTGCTATGCAT 59.528 47.619 3.79 3.79 38.76 3.96
3058 3098 1.135689 CAGGACAACCGTTTGCTATGC 60.136 52.381 0.00 0.00 41.83 3.14
3062 3115 2.193536 GGCAGGACAACCGTTTGCT 61.194 57.895 5.80 0.00 41.83 3.91
3063 3116 2.193536 AGGCAGGACAACCGTTTGC 61.194 57.895 0.00 0.00 41.83 3.68
3076 3129 0.179048 TGGAGAACACACACAGGCAG 60.179 55.000 0.00 0.00 0.00 4.85
3081 3134 1.140652 TGCAGATGGAGAACACACACA 59.859 47.619 0.00 0.00 0.00 3.72
3091 3144 2.681848 GGTCTGTCAATTGCAGATGGAG 59.318 50.000 25.16 6.90 43.73 3.86
3099 3152 1.873591 ACTCGTTGGTCTGTCAATTGC 59.126 47.619 0.00 0.00 0.00 3.56
3123 3176 5.393896 GGAACAATACTAGTAGCACTTCCGT 60.394 44.000 8.85 0.00 0.00 4.69
3131 3184 5.754543 AGACTCGGAACAATACTAGTAGC 57.245 43.478 8.85 0.00 0.00 3.58
3132 3185 8.658609 GCTATAGACTCGGAACAATACTAGTAG 58.341 40.741 8.85 0.00 0.00 2.57
3133 3186 8.152898 TGCTATAGACTCGGAACAATACTAGTA 58.847 37.037 4.77 4.77 0.00 1.82
3166 3220 3.126831 CAAAGATAGACGACCCAGATGC 58.873 50.000 0.00 0.00 0.00 3.91
3183 3239 2.159181 CCGGTAGAACACGGCAAAG 58.841 57.895 0.00 0.00 43.96 2.77
3203 3259 0.244450 TGACCGTACACGATGGAACC 59.756 55.000 2.76 0.00 43.02 3.62
3208 3264 2.460918 GGAGATTGACCGTACACGATG 58.539 52.381 2.76 0.00 43.02 3.84
3218 3274 2.500229 TGAAACAACCGGAGATTGACC 58.500 47.619 9.46 0.00 0.00 4.02
3220 3276 5.782893 AAAATGAAACAACCGGAGATTGA 57.217 34.783 9.46 0.00 0.00 2.57
3221 3277 8.532977 AATAAAAATGAAACAACCGGAGATTG 57.467 30.769 9.46 4.81 0.00 2.67
3231 3289 4.686554 CCCGCGGAAATAAAAATGAAACAA 59.313 37.500 30.73 0.00 0.00 2.83
3232 3290 4.238514 CCCGCGGAAATAAAAATGAAACA 58.761 39.130 30.73 0.00 0.00 2.83
3233 3291 4.239304 ACCCGCGGAAATAAAAATGAAAC 58.761 39.130 30.73 0.00 0.00 2.78
3260 3324 2.045634 ATCCGGTCGGTCGTGAGA 60.046 61.111 9.36 0.00 36.47 3.27
3275 3339 5.942236 TCCTCAGCTAATTATGCCATTGATC 59.058 40.000 0.00 0.00 0.00 2.92
3353 3417 6.968904 CAGATATTTTTATTCAGTGCGCAGTT 59.031 34.615 16.79 3.76 0.00 3.16
3356 3420 5.163673 TGCAGATATTTTTATTCAGTGCGCA 60.164 36.000 5.66 5.66 0.00 6.09
3357 3421 5.273170 TGCAGATATTTTTATTCAGTGCGC 58.727 37.500 0.00 0.00 0.00 6.09
3368 3432 5.677091 GCACGATCCAGTTGCAGATATTTTT 60.677 40.000 0.00 0.00 0.00 1.94
3373 3439 1.802508 CGCACGATCCAGTTGCAGATA 60.803 52.381 0.00 0.00 0.00 1.98
3405 3471 4.380531 TGCAGATATTTAAGCGAAGAGGG 58.619 43.478 0.00 0.00 0.00 4.30
3437 3503 6.128902 ACGTTGAGTGCTAACTAGAAAAATCG 60.129 38.462 0.00 0.00 36.52 3.34
3514 3583 2.601314 CGCATACTTTAGTAGCGCACAA 59.399 45.455 11.47 0.00 39.35 3.33
3562 3631 2.415168 ACCAAACATGCGTGATAACTCG 59.585 45.455 14.17 0.00 36.33 4.18
3563 3632 4.419522 AACCAAACATGCGTGATAACTC 57.580 40.909 14.17 0.00 0.00 3.01
3572 3641 3.945285 AGGGAGTATAAACCAAACATGCG 59.055 43.478 0.00 0.00 0.00 4.73
3616 3685 9.280174 CCGTATTGAAATATTTAGAAGGGCTTA 57.720 33.333 0.00 0.00 0.00 3.09
3617 3686 7.996644 TCCGTATTGAAATATTTAGAAGGGCTT 59.003 33.333 0.00 0.00 0.00 4.35
3618 3687 7.514721 TCCGTATTGAAATATTTAGAAGGGCT 58.485 34.615 0.00 0.00 0.00 5.19
3619 3688 7.739498 TCCGTATTGAAATATTTAGAAGGGC 57.261 36.000 0.00 0.00 0.00 5.19
3632 3701 9.425577 TGCATTCGTATATATTCCGTATTGAAA 57.574 29.630 0.00 0.00 0.00 2.69
3633 3702 8.989653 TGCATTCGTATATATTCCGTATTGAA 57.010 30.769 0.00 0.00 0.00 2.69
3634 3703 9.030301 CATGCATTCGTATATATTCCGTATTGA 57.970 33.333 0.00 0.00 0.00 2.57
3635 3704 8.817100 ACATGCATTCGTATATATTCCGTATTG 58.183 33.333 0.00 0.00 0.00 1.90
3636 3705 8.942338 ACATGCATTCGTATATATTCCGTATT 57.058 30.769 0.00 0.00 0.00 1.89
3639 3708 9.459640 GTATACATGCATTCGTATATATTCCGT 57.540 33.333 15.94 2.09 34.13 4.69
3640 3709 9.458374 TGTATACATGCATTCGTATATATTCCG 57.542 33.333 15.94 0.00 34.13 4.30
3717 3786 9.679661 TCTTGATGTGAAATAGCAAACCTATTA 57.320 29.630 0.00 0.00 44.11 0.98
3718 3787 8.579850 TCTTGATGTGAAATAGCAAACCTATT 57.420 30.769 0.00 0.00 46.25 1.73
3719 3788 8.627403 CATCTTGATGTGAAATAGCAAACCTAT 58.373 33.333 2.66 0.00 38.40 2.57
3720 3789 7.611467 ACATCTTGATGTGAAATAGCAAACCTA 59.389 33.333 14.58 0.00 32.79 3.08
3721 3790 6.435277 ACATCTTGATGTGAAATAGCAAACCT 59.565 34.615 14.58 0.00 32.79 3.50
3722 3791 6.624423 ACATCTTGATGTGAAATAGCAAACC 58.376 36.000 14.58 0.00 32.79 3.27
3745 3814 9.171701 GACGTAGATGTGAGATAAGTATTTCAC 57.828 37.037 12.73 12.73 43.91 3.18
3746 3815 8.350722 GGACGTAGATGTGAGATAAGTATTTCA 58.649 37.037 0.00 0.00 0.00 2.69
3747 3816 8.350722 TGGACGTAGATGTGAGATAAGTATTTC 58.649 37.037 0.00 0.00 0.00 2.17
3748 3817 8.234136 TGGACGTAGATGTGAGATAAGTATTT 57.766 34.615 0.00 0.00 0.00 1.40
3749 3818 7.720074 TCTGGACGTAGATGTGAGATAAGTATT 59.280 37.037 0.00 0.00 0.00 1.89
3750 3819 7.225011 TCTGGACGTAGATGTGAGATAAGTAT 58.775 38.462 0.00 0.00 0.00 2.12
3751 3820 6.589135 TCTGGACGTAGATGTGAGATAAGTA 58.411 40.000 0.00 0.00 0.00 2.24
3752 3821 5.437946 TCTGGACGTAGATGTGAGATAAGT 58.562 41.667 0.00 0.00 0.00 2.24
3753 3822 6.202937 GTTCTGGACGTAGATGTGAGATAAG 58.797 44.000 0.00 0.00 0.00 1.73
3754 3823 5.067413 GGTTCTGGACGTAGATGTGAGATAA 59.933 44.000 0.00 0.00 0.00 1.75
3755 3824 4.579340 GGTTCTGGACGTAGATGTGAGATA 59.421 45.833 0.00 0.00 0.00 1.98
3756 3825 3.381908 GGTTCTGGACGTAGATGTGAGAT 59.618 47.826 0.00 0.00 0.00 2.75
3757 3826 2.753452 GGTTCTGGACGTAGATGTGAGA 59.247 50.000 0.00 0.00 0.00 3.27
3758 3827 2.478031 CGGTTCTGGACGTAGATGTGAG 60.478 54.545 0.00 0.00 0.00 3.51
3759 3828 1.471287 CGGTTCTGGACGTAGATGTGA 59.529 52.381 0.00 0.00 0.00 3.58
3760 3829 1.201647 ACGGTTCTGGACGTAGATGTG 59.798 52.381 0.00 0.00 42.15 3.21
3761 3830 1.542492 ACGGTTCTGGACGTAGATGT 58.458 50.000 0.00 0.00 42.15 3.06
3762 3831 2.094906 TCAACGGTTCTGGACGTAGATG 60.095 50.000 0.00 0.00 43.31 2.90
3763 3832 2.165167 TCAACGGTTCTGGACGTAGAT 58.835 47.619 0.00 0.00 43.31 1.98
3764 3833 1.608055 TCAACGGTTCTGGACGTAGA 58.392 50.000 0.00 0.00 43.31 2.59
3765 3834 2.649331 ATCAACGGTTCTGGACGTAG 57.351 50.000 0.00 0.00 43.31 3.51
3766 3835 4.082081 ACAATATCAACGGTTCTGGACGTA 60.082 41.667 0.00 0.00 43.31 3.57
3767 3836 3.259064 CAATATCAACGGTTCTGGACGT 58.741 45.455 0.00 0.00 46.48 4.34
3768 3837 3.259064 ACAATATCAACGGTTCTGGACG 58.741 45.455 0.00 0.00 0.00 4.79
3769 3838 5.048991 ACAAACAATATCAACGGTTCTGGAC 60.049 40.000 0.00 0.00 0.00 4.02
3770 3839 5.067273 ACAAACAATATCAACGGTTCTGGA 58.933 37.500 0.00 0.00 0.00 3.86
3771 3840 5.181245 AGACAAACAATATCAACGGTTCTGG 59.819 40.000 0.00 0.00 0.00 3.86
3772 3841 6.241207 AGACAAACAATATCAACGGTTCTG 57.759 37.500 0.00 0.00 0.00 3.02
3773 3842 6.877611 AAGACAAACAATATCAACGGTTCT 57.122 33.333 0.00 0.00 0.00 3.01
3774 3843 9.620660 ATTAAAGACAAACAATATCAACGGTTC 57.379 29.630 0.00 0.00 0.00 3.62
3775 3844 9.974980 AATTAAAGACAAACAATATCAACGGTT 57.025 25.926 0.00 0.00 0.00 4.44
3776 3845 9.974980 AAATTAAAGACAAACAATATCAACGGT 57.025 25.926 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.