Multiple sequence alignment - TraesCS4B01G111100

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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 TraesCS4B01G111100 chr4B 100.000 3545 0 0 1 3545 124740518 124744062 0.000000e+00 6547.0
1 TraesCS4B01G111100 chr4B 84.045 445 62 8 1882 2323 473569981 473569543 1.520000e-113 420.0
2 TraesCS4B01G111100 chr4B 91.379 116 10 0 1394 1509 473571692 473571577 3.660000e-35 159.0
3 TraesCS4B01G111100 chr4B 82.390 159 17 6 3217 3375 26483604 26483457 1.030000e-25 128.0
4 TraesCS4B01G111100 chr4B 90.909 88 6 2 1709 1795 473570990 473570904 2.240000e-22 117.0
5 TraesCS4B01G111100 chr4D 94.980 2928 82 23 31 2929 88120835 88123726 0.000000e+00 4532.0
6 TraesCS4B01G111100 chr4D 96.491 285 5 5 2933 3216 88123794 88124074 1.930000e-127 466.0
7 TraesCS4B01G111100 chr4D 83.596 445 64 8 1882 2323 386436134 386435696 3.290000e-110 409.0
8 TraesCS4B01G111100 chr4D 95.349 172 1 2 3375 3545 88124067 88124232 2.100000e-67 267.0
9 TraesCS4B01G111100 chr4D 91.379 116 10 0 1394 1509 386437956 386437841 3.660000e-35 159.0
10 TraesCS4B01G111100 chr4D 90.909 88 6 2 1709 1795 386437284 386437198 2.240000e-22 117.0
11 TraesCS4B01G111100 chr4A 92.243 2965 104 44 31 2931 500899835 500902737 0.000000e+00 4085.0
12 TraesCS4B01G111100 chr4A 84.045 445 62 8 1882 2323 67892522 67892084 1.520000e-113 420.0
13 TraesCS4B01G111100 chr4A 91.034 290 17 5 2934 3216 500902854 500903141 2.000000e-102 383.0
14 TraesCS4B01G111100 chr4A 98.246 171 3 0 3375 3545 500903134 500903304 2.070000e-77 300.0
15 TraesCS4B01G111100 chr4A 91.379 116 10 0 1394 1509 67894297 67894182 3.660000e-35 159.0
16 TraesCS4B01G111100 chr4A 84.277 159 23 2 1208 1365 197971118 197971275 1.700000e-33 154.0
17 TraesCS4B01G111100 chr4A 86.179 123 17 0 3217 3339 712359582 712359460 2.220000e-27 134.0
18 TraesCS4B01G111100 chr1D 87.562 402 50 0 1394 1795 62600891 62600490 1.930000e-127 466.0
19 TraesCS4B01G111100 chr1D 83.445 447 61 10 1882 2323 374471503 374471065 1.530000e-108 403.0
20 TraesCS4B01G111100 chr1D 91.444 187 16 0 1507 1693 374473269 374473083 1.260000e-64 257.0
21 TraesCS4B01G111100 chr1D 87.342 158 20 0 1208 1365 374474030 374473873 7.820000e-42 182.0
22 TraesCS4B01G111100 chr1D 85.294 68 9 1 2865 2932 3256097 3256031 6.350000e-08 69.4
23 TraesCS4B01G111100 chr1B 86.816 402 53 0 1394 1795 99755109 99754708 1.940000e-122 449.0
24 TraesCS4B01G111100 chr1B 84.152 448 58 9 1882 2324 99753564 99753125 4.230000e-114 422.0
25 TraesCS4B01G111100 chr1B 83.221 447 62 10 1882 2323 499469116 499468678 7.130000e-107 398.0
26 TraesCS4B01G111100 chr1B 86.207 290 38 2 1507 1795 499470716 499470428 2.660000e-81 313.0
27 TraesCS4B01G111100 chr1B 87.975 158 19 0 1208 1365 499471527 499471370 1.680000e-43 187.0
28 TraesCS4B01G111100 chr1B 83.740 123 18 2 1388 1509 499470951 499470830 8.040000e-22 115.0
29 TraesCS4B01G111100 chr1A 86.420 405 55 0 1391 1795 60735591 60735995 9.030000e-121 444.0
30 TraesCS4B01G111100 chr1A 84.152 448 58 9 1882 2324 60737113 60737552 4.230000e-114 422.0
31 TraesCS4B01G111100 chr1A 83.296 449 58 11 1882 2323 474226181 474225743 7.130000e-107 398.0
32 TraesCS4B01G111100 chr1A 87.975 158 19 0 1208 1365 474228844 474228687 1.680000e-43 187.0
33 TraesCS4B01G111100 chr1A 82.967 182 29 2 2352 2532 60738591 60738771 2.830000e-36 163.0
34 TraesCS4B01G111100 chr3D 82.870 432 67 7 1882 2311 476553623 476554049 7.180000e-102 381.0
35 TraesCS4B01G111100 chr3D 87.197 289 37 0 1507 1795 476551514 476551802 2.640000e-86 329.0
36 TraesCS4B01G111100 chr3D 87.013 154 18 2 1208 1360 476550594 476550746 4.700000e-39 172.0
37 TraesCS4B01G111100 chr3B 82.262 451 71 9 1876 2323 635220430 635220874 7.180000e-102 381.0
38 TraesCS4B01G111100 chr3B 87.013 154 18 2 1208 1360 635217462 635217614 4.700000e-39 172.0
39 TraesCS4B01G111100 chr3A 87.805 287 35 0 1507 1793 620220605 620220319 1.580000e-88 337.0
40 TraesCS4B01G111100 chr3A 87.013 154 18 2 1208 1360 620221447 620221295 4.700000e-39 172.0
41 TraesCS4B01G111100 chr5D 87.730 163 15 4 3214 3373 478806126 478806286 6.040000e-43 185.0
42 TraesCS4B01G111100 chr6B 87.342 158 14 2 3217 3374 380549915 380549764 3.640000e-40 176.0
43 TraesCS4B01G111100 chr5A 84.868 152 19 3 3222 3371 546782182 546782331 2.200000e-32 150.0
44 TraesCS4B01G111100 chr2B 80.247 162 26 5 3217 3375 213803468 213803310 2.240000e-22 117.0
45 TraesCS4B01G111100 chr2B 77.907 172 32 5 3213 3381 245112829 245112661 6.260000e-18 102.0
46 TraesCS4B01G111100 chr7B 80.000 145 27 2 3205 3348 433312516 433312659 4.840000e-19 106.0
47 TraesCS4B01G111100 chr5B 79.141 163 24 9 3217 3374 534204817 534204974 1.740000e-18 104.0


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 TraesCS4B01G111100 chr4B 124740518 124744062 3544 False 6547.000000 6547 100.000000 1 3545 1 chr4B.!!$F1 3544
1 TraesCS4B01G111100 chr4B 473569543 473571692 2149 True 232.000000 420 88.777667 1394 2323 3 chr4B.!!$R2 929
2 TraesCS4B01G111100 chr4D 88120835 88124232 3397 False 1755.000000 4532 95.606667 31 3545 3 chr4D.!!$F1 3514
3 TraesCS4B01G111100 chr4D 386435696 386437956 2260 True 228.333333 409 88.628000 1394 2323 3 chr4D.!!$R1 929
4 TraesCS4B01G111100 chr4A 500899835 500903304 3469 False 1589.333333 4085 93.841000 31 3545 3 chr4A.!!$F2 3514
5 TraesCS4B01G111100 chr4A 67892084 67894297 2213 True 289.500000 420 87.712000 1394 2323 2 chr4A.!!$R2 929
6 TraesCS4B01G111100 chr1D 374471065 374474030 2965 True 280.666667 403 87.410333 1208 2323 3 chr1D.!!$R3 1115
7 TraesCS4B01G111100 chr1B 99753125 99755109 1984 True 435.500000 449 85.484000 1394 2324 2 chr1B.!!$R1 930
8 TraesCS4B01G111100 chr1B 499468678 499471527 2849 True 253.250000 398 85.285750 1208 2323 4 chr1B.!!$R2 1115
9 TraesCS4B01G111100 chr1A 60735591 60738771 3180 False 343.000000 444 84.513000 1391 2532 3 chr1A.!!$F1 1141
10 TraesCS4B01G111100 chr1A 474225743 474228844 3101 True 292.500000 398 85.635500 1208 2323 2 chr1A.!!$R1 1115
11 TraesCS4B01G111100 chr3D 476550594 476554049 3455 False 294.000000 381 85.693333 1208 2311 3 chr3D.!!$F1 1103
12 TraesCS4B01G111100 chr3B 635217462 635220874 3412 False 276.500000 381 84.637500 1208 2323 2 chr3B.!!$F1 1115
13 TraesCS4B01G111100 chr3A 620220319 620221447 1128 True 254.500000 337 87.409000 1208 1793 2 chr3A.!!$R1 585

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
29 30 0.466124 AGTGCTCCTAATCCGCTTCC 59.534 55.000 0.00 0.0 0.00 3.46 F
755 779 1.000607 ACAGCCGCTGTATATGTACCG 60.001 52.381 24.62 0.0 43.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1254 2.029964 GCCACCTGGTTCGACGAA 59.970 61.111 6.1 6.1 37.57 3.85 R
2728 8335 0.871057 CACACACACACACACACACA 59.129 50.000 0.0 0.0 0.00 3.72 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
24 25 2.009774 CACCAAAGTGCTCCTAATCCG 58.990 52.381 0.00 0.00 37.14 4.18
25 26 1.017387 CCAAAGTGCTCCTAATCCGC 58.983 55.000 0.00 0.00 0.00 5.54
26 27 1.407437 CCAAAGTGCTCCTAATCCGCT 60.407 52.381 0.00 0.00 0.00 5.52
27 28 2.359900 CAAAGTGCTCCTAATCCGCTT 58.640 47.619 0.00 0.00 0.00 4.68
28 29 2.317530 AAGTGCTCCTAATCCGCTTC 57.682 50.000 0.00 0.00 0.00 3.86
29 30 0.466124 AGTGCTCCTAATCCGCTTCC 59.534 55.000 0.00 0.00 0.00 3.46
90 91 7.418597 CCAGTTTGTAGTACTATGAATGCCCTA 60.419 40.741 5.75 0.00 0.00 3.53
100 101 9.425577 GTACTATGAATGCCCTATTCTAAGTTC 57.574 37.037 0.00 0.00 44.49 3.01
101 102 7.454225 ACTATGAATGCCCTATTCTAAGTTCC 58.546 38.462 0.00 0.00 44.49 3.62
132 133 9.778741 AGGTTTATTCATTTCTTTTTCTTTCCC 57.221 29.630 0.00 0.00 0.00 3.97
202 203 3.885297 GCTCCACATTATTATGCCACACT 59.115 43.478 0.00 0.00 35.03 3.55
219 220 4.518970 CCACACTTGTGCCAACTAATTAGT 59.481 41.667 12.50 12.50 44.34 2.24
264 267 3.526931 TCTTGTCGATCTTAGGGCTTG 57.473 47.619 0.00 0.00 0.00 4.01
284 287 5.371526 CTTGCATATGAAGGTGTAGTGGAT 58.628 41.667 6.97 0.00 0.00 3.41
326 329 4.279922 TCGACACTGACACAAGGAAATCTA 59.720 41.667 0.00 0.00 0.00 1.98
413 417 5.009610 CGGGTTAATTGCCAAGCTATTACAT 59.990 40.000 3.50 0.00 36.39 2.29
429 433 7.041780 AGCTATTACATCATTCACCTTAAAGCG 60.042 37.037 0.00 0.00 0.00 4.68
434 442 5.351465 ACATCATTCACCTTAAAGCGTAGTG 59.649 40.000 0.00 0.00 0.00 2.74
452 460 4.755266 AGTGCCCCTAACTACACATTAG 57.245 45.455 0.00 0.00 35.47 1.73
453 461 4.101856 AGTGCCCCTAACTACACATTAGT 58.898 43.478 0.00 0.00 35.47 2.24
454 462 4.534897 AGTGCCCCTAACTACACATTAGTT 59.465 41.667 2.46 2.46 40.48 2.24
455 463 5.722923 AGTGCCCCTAACTACACATTAGTTA 59.277 40.000 4.32 4.32 38.55 2.24
499 511 4.260985 AGTGGACATCATATTTGTGCGAA 58.739 39.130 0.00 0.00 38.16 4.70
512 528 2.535331 TGTGCGAAGAAAACCTTTTGC 58.465 42.857 0.00 0.00 37.19 3.68
626 642 5.426504 CACTAAGCTCCAATCACATCTTCT 58.573 41.667 0.00 0.00 0.00 2.85
637 653 6.153340 CCAATCACATCTTCTTGGTTACCAAT 59.847 38.462 17.85 0.00 43.07 3.16
716 735 5.330455 TCATATACATTCGCCCATCTCTC 57.670 43.478 0.00 0.00 0.00 3.20
717 736 5.019470 TCATATACATTCGCCCATCTCTCT 58.981 41.667 0.00 0.00 0.00 3.10
748 772 3.362581 GCTGAACAGCCGCTGTATA 57.637 52.632 25.96 16.25 44.62 1.47
755 779 1.000607 ACAGCCGCTGTATATGTACCG 60.001 52.381 24.62 0.00 43.46 4.02
782 806 3.905968 ACGGAAAAGGAAAAAGGGAGAA 58.094 40.909 0.00 0.00 0.00 2.87
787 811 5.833667 GGAAAAGGAAAAAGGGAGAAGAGAA 59.166 40.000 0.00 0.00 0.00 2.87
788 812 6.239064 GGAAAAGGAAAAAGGGAGAAGAGAAC 60.239 42.308 0.00 0.00 0.00 3.01
789 813 4.009370 AGGAAAAAGGGAGAAGAGAACG 57.991 45.455 0.00 0.00 0.00 3.95
790 814 3.646637 AGGAAAAAGGGAGAAGAGAACGA 59.353 43.478 0.00 0.00 0.00 3.85
791 815 4.287326 AGGAAAAAGGGAGAAGAGAACGAT 59.713 41.667 0.00 0.00 0.00 3.73
792 816 4.632251 GGAAAAAGGGAGAAGAGAACGATC 59.368 45.833 0.00 0.00 0.00 3.69
794 818 3.878160 AAGGGAGAAGAGAACGATCAC 57.122 47.619 0.00 0.00 0.00 3.06
799 834 4.170256 GGAGAAGAGAACGATCACAAGTC 58.830 47.826 0.00 0.00 0.00 3.01
1197 1254 2.661866 GACGCGTGGTTCAGCTGT 60.662 61.111 20.70 0.00 0.00 4.40
1200 1257 2.551270 GCGTGGTTCAGCTGTTCG 59.449 61.111 14.67 12.76 0.00 3.95
1203 1260 1.853319 GTGGTTCAGCTGTTCGTCG 59.147 57.895 14.67 0.00 0.00 5.12
1989 6571 3.533105 TCCGCGTCCGCCATGTAT 61.533 61.111 4.92 0.00 37.98 2.29
2232 6814 1.002134 CATCTGGTTCCTGGCCGTT 60.002 57.895 0.00 0.00 0.00 4.44
2707 8314 5.518487 TCGGAGCTTGTTTTTGAATTTTGAC 59.482 36.000 0.00 0.00 0.00 3.18
2719 8326 3.127203 TGAATTTTGACCGTGTCGTGTTT 59.873 39.130 0.59 0.00 34.95 2.83
2725 8332 2.170770 GACCGTGTCGTGTTTTGTTTG 58.829 47.619 0.00 0.00 0.00 2.93
2726 8333 1.536331 ACCGTGTCGTGTTTTGTTTGT 59.464 42.857 0.00 0.00 0.00 2.83
2728 8335 2.981140 CCGTGTCGTGTTTTGTTTGTTT 59.019 40.909 0.00 0.00 0.00 2.83
2729 8336 3.181548 CCGTGTCGTGTTTTGTTTGTTTG 60.182 43.478 0.00 0.00 0.00 2.93
2730 8337 3.422546 CGTGTCGTGTTTTGTTTGTTTGT 59.577 39.130 0.00 0.00 0.00 2.83
2731 8338 4.659431 CGTGTCGTGTTTTGTTTGTTTGTG 60.659 41.667 0.00 0.00 0.00 3.33
2774 8384 8.409371 TGTGTGTGTGTCATGTTTGTAATTATT 58.591 29.630 0.00 0.00 0.00 1.40
2775 8385 9.885934 GTGTGTGTGTCATGTTTGTAATTATTA 57.114 29.630 0.00 0.00 0.00 0.98
2985 8716 4.675976 TTGTAGAGTTCAGAAACCCGAA 57.324 40.909 0.00 0.00 35.92 4.30
2986 8717 4.252971 TGTAGAGTTCAGAAACCCGAAG 57.747 45.455 0.00 0.00 35.92 3.79
3018 8749 4.828939 TCAGAGATTGTTTGGCTCAATTGT 59.171 37.500 5.13 0.00 35.94 2.71
3077 8809 1.750206 GGTTGTGATGTGGCATGCATA 59.250 47.619 21.36 4.71 0.00 3.14
3100 8832 3.401033 TGTGCTGCTACACTACAACAT 57.599 42.857 0.00 0.00 41.30 2.71
3184 8916 3.481453 GACCCTCCCTGCTAATCAATTC 58.519 50.000 0.00 0.00 0.00 2.17
3215 8947 2.959030 CGGATCTTCACATACTCCTGGA 59.041 50.000 0.00 0.00 0.00 3.86
3216 8948 3.243569 CGGATCTTCACATACTCCTGGAC 60.244 52.174 0.00 0.00 0.00 4.02
3217 8949 3.706594 GGATCTTCACATACTCCTGGACA 59.293 47.826 0.00 0.00 0.00 4.02
3218 8950 4.202202 GGATCTTCACATACTCCTGGACAG 60.202 50.000 0.00 0.00 0.00 3.51
3219 8951 2.497675 TCTTCACATACTCCTGGACAGC 59.502 50.000 0.00 0.00 0.00 4.40
3220 8952 0.817654 TCACATACTCCTGGACAGCG 59.182 55.000 0.00 0.00 0.00 5.18
3221 8953 0.179100 CACATACTCCTGGACAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
3222 8954 1.227380 CATACTCCTGGACAGCGGC 60.227 63.158 0.00 0.00 0.00 6.53
3223 8955 2.786495 ATACTCCTGGACAGCGGCG 61.786 63.158 0.51 0.51 0.00 6.46
3228 8960 4.803426 CTGGACAGCGGCGGAGAC 62.803 72.222 9.78 0.00 0.00 3.36
3230 8962 4.803426 GGACAGCGGCGGAGACAG 62.803 72.222 9.78 0.00 27.25 3.51
3231 8963 4.803426 GACAGCGGCGGAGACAGG 62.803 72.222 9.78 0.00 27.25 4.00
3277 9009 4.625800 GCGTGAAGCTGATTCCCT 57.374 55.556 2.88 0.00 44.04 4.20
3278 9010 2.859992 GCGTGAAGCTGATTCCCTT 58.140 52.632 2.88 0.00 44.04 3.95
3279 9011 1.168714 GCGTGAAGCTGATTCCCTTT 58.831 50.000 2.88 0.00 44.04 3.11
3280 9012 1.135575 GCGTGAAGCTGATTCCCTTTG 60.136 52.381 2.88 0.00 44.04 2.77
3281 9013 2.154462 CGTGAAGCTGATTCCCTTTGT 58.846 47.619 2.88 0.00 37.08 2.83
3282 9014 3.334691 CGTGAAGCTGATTCCCTTTGTA 58.665 45.455 2.88 0.00 37.08 2.41
3283 9015 3.941483 CGTGAAGCTGATTCCCTTTGTAT 59.059 43.478 2.88 0.00 37.08 2.29
3284 9016 5.116180 CGTGAAGCTGATTCCCTTTGTATA 58.884 41.667 2.88 0.00 37.08 1.47
3285 9017 5.006746 CGTGAAGCTGATTCCCTTTGTATAC 59.993 44.000 2.88 0.00 37.08 1.47
3286 9018 6.116126 GTGAAGCTGATTCCCTTTGTATACT 58.884 40.000 4.17 0.00 37.08 2.12
3287 9019 6.037610 GTGAAGCTGATTCCCTTTGTATACTG 59.962 42.308 4.17 0.00 37.08 2.74
3288 9020 5.700402 AGCTGATTCCCTTTGTATACTGT 57.300 39.130 4.17 0.00 0.00 3.55
3289 9021 6.808321 AGCTGATTCCCTTTGTATACTGTA 57.192 37.500 4.17 0.00 0.00 2.74
3290 9022 6.821388 AGCTGATTCCCTTTGTATACTGTAG 58.179 40.000 4.17 0.00 0.00 2.74
3291 9023 5.992217 GCTGATTCCCTTTGTATACTGTAGG 59.008 44.000 4.17 7.77 0.00 3.18
3292 9024 6.494666 TGATTCCCTTTGTATACTGTAGGG 57.505 41.667 21.84 21.84 45.71 3.53
3322 9054 8.206325 GTGTAACTATACAGCTACAGTACTCA 57.794 38.462 0.00 0.00 42.54 3.41
3323 9055 8.671921 GTGTAACTATACAGCTACAGTACTCAA 58.328 37.037 0.00 0.00 42.54 3.02
3324 9056 9.234827 TGTAACTATACAGCTACAGTACTCAAA 57.765 33.333 0.00 0.00 37.11 2.69
3325 9057 9.719279 GTAACTATACAGCTACAGTACTCAAAG 57.281 37.037 0.00 0.00 32.02 2.77
3326 9058 7.941431 ACTATACAGCTACAGTACTCAAAGT 57.059 36.000 0.00 0.00 0.00 2.66
3327 9059 7.987649 ACTATACAGCTACAGTACTCAAAGTC 58.012 38.462 0.00 0.00 0.00 3.01
3328 9060 7.830201 ACTATACAGCTACAGTACTCAAAGTCT 59.170 37.037 0.00 0.00 0.00 3.24
3329 9061 5.127693 ACAGCTACAGTACTCAAAGTCTG 57.872 43.478 0.00 5.69 33.00 3.51
3330 9062 3.923461 CAGCTACAGTACTCAAAGTCTGC 59.077 47.826 0.00 0.00 31.23 4.26
3331 9063 3.056465 AGCTACAGTACTCAAAGTCTGCC 60.056 47.826 0.00 0.00 31.23 4.85
3332 9064 3.056465 GCTACAGTACTCAAAGTCTGCCT 60.056 47.826 0.00 0.00 31.23 4.75
3333 9065 3.393089 ACAGTACTCAAAGTCTGCCTG 57.607 47.619 0.00 0.00 31.23 4.85
3334 9066 2.037772 ACAGTACTCAAAGTCTGCCTGG 59.962 50.000 0.00 0.00 31.23 4.45
3335 9067 1.625818 AGTACTCAAAGTCTGCCTGGG 59.374 52.381 0.00 0.00 0.00 4.45
3336 9068 0.984230 TACTCAAAGTCTGCCTGGGG 59.016 55.000 0.00 0.00 0.00 4.96
3426 9164 5.735157 TCCTACCATCTACTAGGACTAGGA 58.265 45.833 10.81 1.27 34.71 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.009774 CGGATTAGGAGCACTTTGGTG 58.990 52.381 0.00 0.00 45.53 4.17
5 6 1.679032 GCGGATTAGGAGCACTTTGGT 60.679 52.381 0.00 0.00 0.00 3.67
6 7 1.017387 GCGGATTAGGAGCACTTTGG 58.983 55.000 0.00 0.00 0.00 3.28
7 8 2.029838 AGCGGATTAGGAGCACTTTG 57.970 50.000 0.00 0.00 0.00 2.77
8 9 2.633488 GAAGCGGATTAGGAGCACTTT 58.367 47.619 0.00 0.00 0.00 2.66
9 10 1.134371 GGAAGCGGATTAGGAGCACTT 60.134 52.381 0.00 0.00 0.00 3.16
10 11 0.466124 GGAAGCGGATTAGGAGCACT 59.534 55.000 0.00 0.00 0.00 4.40
11 12 0.466124 AGGAAGCGGATTAGGAGCAC 59.534 55.000 0.00 0.00 0.00 4.40
12 13 1.687123 GTAGGAAGCGGATTAGGAGCA 59.313 52.381 0.00 0.00 0.00 4.26
13 14 1.001068 GGTAGGAAGCGGATTAGGAGC 59.999 57.143 0.00 0.00 0.00 4.70
14 15 2.317040 TGGTAGGAAGCGGATTAGGAG 58.683 52.381 0.00 0.00 0.00 3.69
15 16 2.464796 TGGTAGGAAGCGGATTAGGA 57.535 50.000 0.00 0.00 0.00 2.94
16 17 4.087182 TCTATGGTAGGAAGCGGATTAGG 58.913 47.826 0.00 0.00 0.00 2.69
17 18 5.163499 GGATCTATGGTAGGAAGCGGATTAG 60.163 48.000 0.00 0.00 0.00 1.73
18 19 4.710375 GGATCTATGGTAGGAAGCGGATTA 59.290 45.833 0.00 0.00 0.00 1.75
19 20 3.515901 GGATCTATGGTAGGAAGCGGATT 59.484 47.826 0.00 0.00 0.00 3.01
20 21 3.100671 GGATCTATGGTAGGAAGCGGAT 58.899 50.000 0.00 0.00 0.00 4.18
21 22 2.526432 GGATCTATGGTAGGAAGCGGA 58.474 52.381 0.00 0.00 0.00 5.54
22 23 1.550976 GGGATCTATGGTAGGAAGCGG 59.449 57.143 0.00 0.00 0.00 5.52
23 24 1.550976 GGGGATCTATGGTAGGAAGCG 59.449 57.143 0.00 0.00 0.00 4.68
24 25 2.909217 AGGGGATCTATGGTAGGAAGC 58.091 52.381 0.00 0.00 0.00 3.86
25 26 5.659079 GTGATAGGGGATCTATGGTAGGAAG 59.341 48.000 0.00 0.00 38.71 3.46
26 27 5.318889 AGTGATAGGGGATCTATGGTAGGAA 59.681 44.000 0.00 0.00 38.71 3.36
27 28 4.864406 AGTGATAGGGGATCTATGGTAGGA 59.136 45.833 0.00 0.00 38.71 2.94
28 29 5.213868 AGTGATAGGGGATCTATGGTAGG 57.786 47.826 0.00 0.00 38.71 3.18
29 30 9.357161 GTTATAGTGATAGGGGATCTATGGTAG 57.643 40.741 0.00 0.00 38.71 3.18
132 133 7.728847 TCATCATTAACACGAATGGAATAGG 57.271 36.000 0.00 0.00 37.41 2.57
138 139 5.684184 CAGCAATCATCATTAACACGAATGG 59.316 40.000 0.00 0.00 37.41 3.16
264 267 6.699575 AAAATCCACTACACCTTCATATGC 57.300 37.500 0.00 0.00 0.00 3.14
304 307 3.393800 AGATTTCCTTGTGTCAGTGTCG 58.606 45.455 0.00 0.00 0.00 4.35
413 417 3.682858 GCACTACGCTTTAAGGTGAATGA 59.317 43.478 5.01 0.00 37.77 2.57
429 433 4.482952 AATGTGTAGTTAGGGGCACTAC 57.517 45.455 0.00 0.53 44.78 2.73
434 442 5.045872 CGTAACTAATGTGTAGTTAGGGGC 58.954 45.833 14.05 1.92 39.73 5.80
436 444 7.542025 AGTTCGTAACTAATGTGTAGTTAGGG 58.458 38.462 18.57 10.04 41.97 3.53
499 511 5.914898 AGTGTACAAGCAAAAGGTTTTCT 57.085 34.783 0.00 0.00 0.00 2.52
512 528 4.505922 GCTAGCTGCTGATTAGTGTACAAG 59.494 45.833 13.43 0.00 38.95 3.16
637 653 1.608025 GGTCCGACTGTGATCTTTGCA 60.608 52.381 0.00 0.00 0.00 4.08
716 735 4.737765 GCTGTTCAGCGAATAGTAAGAGAG 59.262 45.833 9.04 0.00 34.13 3.20
717 736 4.440250 GGCTGTTCAGCGAATAGTAAGAGA 60.440 45.833 16.84 0.00 34.13 3.10
755 779 4.500887 CCCTTTTTCCTTTTCCGTTCCTTC 60.501 45.833 0.00 0.00 0.00 3.46
782 806 2.353208 GGCAGACTTGTGATCGTTCTCT 60.353 50.000 0.00 0.00 0.00 3.10
787 811 0.671781 GCTGGCAGACTTGTGATCGT 60.672 55.000 20.86 0.00 0.00 3.73
788 812 0.390866 AGCTGGCAGACTTGTGATCG 60.391 55.000 20.86 0.00 0.00 3.69
789 813 1.085091 CAGCTGGCAGACTTGTGATC 58.915 55.000 20.86 0.00 0.00 2.92
790 814 0.322277 CCAGCTGGCAGACTTGTGAT 60.322 55.000 22.33 0.00 0.00 3.06
791 815 1.071987 CCAGCTGGCAGACTTGTGA 59.928 57.895 22.33 0.00 0.00 3.58
792 816 1.228063 ACCAGCTGGCAGACTTGTG 60.228 57.895 33.06 5.14 39.32 3.33
794 818 2.623915 GCACCAGCTGGCAGACTTG 61.624 63.158 33.06 22.12 39.32 3.16
799 834 3.449227 CCATGCACCAGCTGGCAG 61.449 66.667 33.06 25.23 44.24 4.85
1125 1182 2.366167 AGCTTGCTCCTCCCCGAT 60.366 61.111 0.00 0.00 0.00 4.18
1197 1254 2.029964 GCCACCTGGTTCGACGAA 59.970 61.111 6.10 6.10 37.57 3.85
1200 1257 4.980805 TGCGCCACCTGGTTCGAC 62.981 66.667 18.81 11.80 37.57 4.20
1203 1260 4.643387 ACCTGCGCCACCTGGTTC 62.643 66.667 4.18 0.00 33.84 3.62
2232 6814 1.677552 GCCGAAGAAGGGGAAGACA 59.322 57.895 0.00 0.00 0.00 3.41
2397 7990 1.812093 GCAGTTGGCGGCGTACATA 60.812 57.895 9.37 0.00 0.00 2.29
2707 8314 2.250348 ACAAACAAAACACGACACGG 57.750 45.000 0.00 0.00 0.00 4.94
2719 8326 3.798878 CACACACACACACAAACAAACAA 59.201 39.130 0.00 0.00 0.00 2.83
2725 8332 2.287308 ACACACACACACACACACAAAC 60.287 45.455 0.00 0.00 0.00 2.93
2726 8333 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
2728 8335 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2729 8336 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2730 8337 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2731 8338 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2780 8390 6.262601 GTTCTCATGAACTCCGTTTCAAAAA 58.737 36.000 0.00 0.00 46.56 1.94
2781 8391 5.816919 GTTCTCATGAACTCCGTTTCAAAA 58.183 37.500 0.00 0.00 46.56 2.44
2782 8392 5.418310 GTTCTCATGAACTCCGTTTCAAA 57.582 39.130 0.00 0.00 46.56 2.69
2855 8465 3.143728 GGAAGCCCGTACAAAGAAAAGA 58.856 45.455 0.00 0.00 0.00 2.52
2856 8466 3.554259 GGAAGCCCGTACAAAGAAAAG 57.446 47.619 0.00 0.00 0.00 2.27
2880 8490 8.602424 TGAACTTTATAGATGGGAGAAGAACAA 58.398 33.333 0.00 0.00 0.00 2.83
2977 8708 2.171448 CTGATCATCCTCCTTCGGGTTT 59.829 50.000 0.00 0.00 36.28 3.27
2985 8716 5.397672 CCAAACAATCTCTGATCATCCTCCT 60.398 44.000 0.00 0.00 0.00 3.69
2986 8717 4.820716 CCAAACAATCTCTGATCATCCTCC 59.179 45.833 0.00 0.00 0.00 4.30
3031 8763 9.289303 CTCGCAACAATTAAGCTAAATAAACAT 57.711 29.630 0.00 0.00 0.00 2.71
3077 8809 3.067106 GTTGTAGTGTAGCAGCACATGT 58.933 45.455 12.15 0.00 41.52 3.21
3254 8986 2.826777 AATCAGCTTCACGCCCCAGG 62.827 60.000 0.00 0.00 40.39 4.45
3255 8987 1.372087 GAATCAGCTTCACGCCCCAG 61.372 60.000 0.00 0.00 40.39 4.45
3256 8988 1.377202 GAATCAGCTTCACGCCCCA 60.377 57.895 0.00 0.00 40.39 4.96
3257 8989 2.115291 GGAATCAGCTTCACGCCCC 61.115 63.158 0.00 0.00 40.39 5.80
3258 8990 2.115291 GGGAATCAGCTTCACGCCC 61.115 63.158 0.00 0.00 40.39 6.13
3259 8991 0.678048 AAGGGAATCAGCTTCACGCC 60.678 55.000 0.00 0.00 42.49 5.68
3260 8992 1.135575 CAAAGGGAATCAGCTTCACGC 60.136 52.381 0.00 0.00 42.49 5.34
3261 8993 2.154462 ACAAAGGGAATCAGCTTCACG 58.846 47.619 0.00 0.00 42.49 4.35
3262 8994 6.037610 CAGTATACAAAGGGAATCAGCTTCAC 59.962 42.308 5.50 0.00 37.56 3.18
3263 8995 6.115446 CAGTATACAAAGGGAATCAGCTTCA 58.885 40.000 5.50 0.00 35.41 3.02
3264 8996 6.116126 ACAGTATACAAAGGGAATCAGCTTC 58.884 40.000 5.50 0.00 0.00 3.86
3265 8997 6.067217 ACAGTATACAAAGGGAATCAGCTT 57.933 37.500 5.50 0.00 0.00 3.74
3266 8998 5.700402 ACAGTATACAAAGGGAATCAGCT 57.300 39.130 5.50 0.00 0.00 4.24
3267 8999 5.992217 CCTACAGTATACAAAGGGAATCAGC 59.008 44.000 5.50 0.00 0.00 4.26
3286 9018 6.127535 GCTGTATAGTTACACTGTTCCCTACA 60.128 42.308 0.00 0.00 34.62 2.74
3287 9019 6.096564 AGCTGTATAGTTACACTGTTCCCTAC 59.903 42.308 0.00 0.00 34.62 3.18
3288 9020 6.192773 AGCTGTATAGTTACACTGTTCCCTA 58.807 40.000 0.00 0.00 34.62 3.53
3289 9021 5.024118 AGCTGTATAGTTACACTGTTCCCT 58.976 41.667 0.00 0.00 34.62 4.20
3290 9022 5.340439 AGCTGTATAGTTACACTGTTCCC 57.660 43.478 0.00 0.00 34.62 3.97
3291 9023 6.860080 TGTAGCTGTATAGTTACACTGTTCC 58.140 40.000 11.30 0.00 43.07 3.62
3292 9024 7.536855 ACTGTAGCTGTATAGTTACACTGTTC 58.463 38.462 11.30 0.00 43.07 3.18
3293 9025 7.463961 ACTGTAGCTGTATAGTTACACTGTT 57.536 36.000 11.30 0.00 43.07 3.16
3294 9026 7.828223 AGTACTGTAGCTGTATAGTTACACTGT 59.172 37.037 11.30 11.19 43.07 3.55
3295 9027 8.211116 AGTACTGTAGCTGTATAGTTACACTG 57.789 38.462 11.30 6.64 43.07 3.66
3296 9028 8.045507 TGAGTACTGTAGCTGTATAGTTACACT 58.954 37.037 11.30 8.04 43.07 3.55
3297 9029 8.206325 TGAGTACTGTAGCTGTATAGTTACAC 57.794 38.462 11.30 3.96 43.07 2.90
3298 9030 8.797350 TTGAGTACTGTAGCTGTATAGTTACA 57.203 34.615 13.97 13.97 44.88 2.41
3299 9031 9.719279 CTTTGAGTACTGTAGCTGTATAGTTAC 57.281 37.037 0.00 6.56 40.02 2.50
3300 9032 9.458727 ACTTTGAGTACTGTAGCTGTATAGTTA 57.541 33.333 0.00 0.00 33.08 2.24
3301 9033 8.350852 ACTTTGAGTACTGTAGCTGTATAGTT 57.649 34.615 0.00 0.00 33.08 2.24
3302 9034 7.830201 AGACTTTGAGTACTGTAGCTGTATAGT 59.170 37.037 0.00 0.00 35.06 2.12
3303 9035 8.126074 CAGACTTTGAGTACTGTAGCTGTATAG 58.874 40.741 0.00 0.00 0.00 1.31
3304 9036 7.415318 GCAGACTTTGAGTACTGTAGCTGTATA 60.415 40.741 0.00 0.00 30.96 1.47
3305 9037 6.626181 GCAGACTTTGAGTACTGTAGCTGTAT 60.626 42.308 0.00 0.00 30.96 2.29
3306 9038 5.335740 GCAGACTTTGAGTACTGTAGCTGTA 60.336 44.000 0.00 0.00 30.96 2.74
3307 9039 4.559704 GCAGACTTTGAGTACTGTAGCTGT 60.560 45.833 0.00 0.00 30.96 4.40
3308 9040 3.923461 GCAGACTTTGAGTACTGTAGCTG 59.077 47.826 0.00 7.58 30.96 4.24
3309 9041 3.056465 GGCAGACTTTGAGTACTGTAGCT 60.056 47.826 0.00 0.00 30.96 3.32
3310 9042 3.056465 AGGCAGACTTTGAGTACTGTAGC 60.056 47.826 0.00 0.00 30.96 3.58
3311 9043 4.489810 CAGGCAGACTTTGAGTACTGTAG 58.510 47.826 0.00 0.00 30.96 2.74
3312 9044 3.258372 CCAGGCAGACTTTGAGTACTGTA 59.742 47.826 0.00 0.00 30.96 2.74
3313 9045 2.037772 CCAGGCAGACTTTGAGTACTGT 59.962 50.000 0.00 0.00 30.96 3.55
3314 9046 2.613977 CCCAGGCAGACTTTGAGTACTG 60.614 54.545 0.00 0.00 31.25 2.74
3315 9047 1.625818 CCCAGGCAGACTTTGAGTACT 59.374 52.381 0.00 0.00 0.00 2.73
3316 9048 1.339151 CCCCAGGCAGACTTTGAGTAC 60.339 57.143 0.00 0.00 0.00 2.73
3317 9049 0.984230 CCCCAGGCAGACTTTGAGTA 59.016 55.000 0.00 0.00 0.00 2.59
3318 9050 1.763770 CCCCAGGCAGACTTTGAGT 59.236 57.895 0.00 0.00 0.00 3.41
3319 9051 4.730487 CCCCAGGCAGACTTTGAG 57.270 61.111 0.00 0.00 0.00 3.02
3367 9099 0.471617 ATGTATCCAGGAGCAGTGGC 59.528 55.000 0.00 0.00 41.61 5.01
3368 9100 3.643320 TCTAATGTATCCAGGAGCAGTGG 59.357 47.826 6.93 4.68 36.28 4.00
3369 9101 4.343526 AGTCTAATGTATCCAGGAGCAGTG 59.656 45.833 6.93 0.00 0.00 3.66
3370 9102 4.551671 AGTCTAATGTATCCAGGAGCAGT 58.448 43.478 0.00 0.00 0.00 4.40
3371 9103 6.656632 TTAGTCTAATGTATCCAGGAGCAG 57.343 41.667 0.00 0.00 0.00 4.24
3372 9104 7.618019 AATTAGTCTAATGTATCCAGGAGCA 57.382 36.000 5.86 0.00 0.00 4.26
3373 9105 9.026121 TCTAATTAGTCTAATGTATCCAGGAGC 57.974 37.037 12.19 0.00 0.00 4.70
3375 9107 9.535170 CCTCTAATTAGTCTAATGTATCCAGGA 57.465 37.037 12.19 0.00 0.00 3.86
3376 9108 8.754080 CCCTCTAATTAGTCTAATGTATCCAGG 58.246 40.741 12.19 6.69 0.00 4.45
3377 9109 9.315363 ACCCTCTAATTAGTCTAATGTATCCAG 57.685 37.037 12.19 0.00 0.00 3.86
3378 9110 9.310449 GACCCTCTAATTAGTCTAATGTATCCA 57.690 37.037 12.19 0.00 0.00 3.41
3379 9111 8.751242 GGACCCTCTAATTAGTCTAATGTATCC 58.249 40.741 12.19 3.99 0.00 2.59
3380 9112 9.536510 AGGACCCTCTAATTAGTCTAATGTATC 57.463 37.037 12.19 0.00 0.00 2.24
3421 9159 3.260380 GGATGGATCATCACCACTCCTAG 59.740 52.174 9.68 0.00 42.13 3.02
3422 9160 3.242867 GGATGGATCATCACCACTCCTA 58.757 50.000 9.68 0.00 42.13 2.94
3423 9161 2.053244 GGATGGATCATCACCACTCCT 58.947 52.381 9.68 0.00 42.13 3.69
3424 9162 1.072965 GGGATGGATCATCACCACTCC 59.927 57.143 9.68 0.00 42.13 3.85
3425 9163 2.557920 GGGATGGATCATCACCACTC 57.442 55.000 9.68 0.00 42.13 3.51


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

AutoCloner maintained by Alex Coulton.