Multiple sequence alignment - TraesCS7B01G484700

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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 TraesCS7B01G484700 chr7B 100.000 3728 0 0 1 3728 741626018 741622291 0.000000e+00 6885
1 TraesCS7B01G484700 chr7B 87.605 1428 157 12 1591 3014 741541915 741543326 0.000000e+00 1639
2 TraesCS7B01G484700 chr7B 84.535 1151 154 13 1449 2593 651134870 651136002 0.000000e+00 1118
3 TraesCS7B01G484700 chr7B 90.909 462 25 11 1044 1489 741541449 741541909 4.120000e-169 604
4 TraesCS7B01G484700 chr7B 80.435 598 87 19 3147 3728 741484408 741484991 2.660000e-116 429
5 TraesCS7B01G484700 chr7A 94.273 1554 80 6 1046 2595 731571401 731569853 0.000000e+00 2368
6 TraesCS7B01G484700 chr7A 84.270 2028 233 40 1015 3017 731095998 731097964 0.000000e+00 1899
7 TraesCS7B01G484700 chr7A 87.846 1555 166 12 1046 2593 675021934 675023472 0.000000e+00 1803
8 TraesCS7B01G484700 chr7A 83.521 1869 205 42 1015 2860 731186470 731188258 0.000000e+00 1650
9 TraesCS7B01G484700 chr7A 83.596 1841 200 43 1044 2860 731157534 731159296 0.000000e+00 1633
10 TraesCS7B01G484700 chr7A 85.201 1615 174 37 1027 2593 731000674 731002271 0.000000e+00 1598
11 TraesCS7B01G484700 chr7A 86.769 1436 140 23 1591 3017 731506620 731505226 0.000000e+00 1554
12 TraesCS7B01G484700 chr7A 85.971 1447 153 22 1576 3017 731220350 731221751 0.000000e+00 1502
13 TraesCS7B01G484700 chr7A 88.317 719 50 19 1 695 731124819 731125527 0.000000e+00 832
14 TraesCS7B01G484700 chr7A 87.795 721 51 22 1 695 731185219 731185928 0.000000e+00 809
15 TraesCS7B01G484700 chr7A 88.958 480 42 10 1027 1499 730881186 730881661 1.930000e-162 582
16 TraesCS7B01G484700 chr7A 89.744 468 30 9 242 695 731156502 731156965 1.930000e-162 582
17 TraesCS7B01G484700 chr7A 88.683 486 36 12 2538 3017 731012437 731012909 3.230000e-160 575
18 TraesCS7B01G484700 chr7A 83.687 613 52 22 1 597 731094817 731095397 5.480000e-148 534
19 TraesCS7B01G484700 chr7A 82.718 596 72 16 3147 3727 731002754 731003333 5.560000e-138 501
20 TraesCS7B01G484700 chr7A 82.246 552 68 16 2479 3017 731013297 731013831 2.040000e-122 449
21 TraesCS7B01G484700 chr7A 80.607 593 74 25 2591 3150 675023665 675024249 1.600000e-113 420
22 TraesCS7B01G484700 chr7A 77.957 558 68 27 3156 3672 675027118 675027661 7.830000e-77 298
23 TraesCS7B01G484700 chr7A 80.926 367 45 12 3145 3502 731568938 731568588 2.210000e-67 267
24 TraesCS7B01G484700 chr7A 81.875 320 34 9 2708 3021 730883156 730883457 8.000000e-62 248
25 TraesCS7B01G484700 chr7A 86.893 206 18 2 813 1009 731186121 731186326 4.850000e-54 222
26 TraesCS7B01G484700 chr7A 80.380 316 39 10 3227 3537 675024380 675024677 6.270000e-53 219
27 TraesCS7B01G484700 chr7A 86.341 205 20 3 813 1009 731125720 731125924 2.250000e-52 217
28 TraesCS7B01G484700 chr7A 86.667 120 13 3 692 809 731095475 731095593 3.020000e-26 130
29 TraesCS7B01G484700 chr7D 93.573 1556 82 10 1046 2595 634650679 634652222 0.000000e+00 2303
30 TraesCS7B01G484700 chr7D 86.839 1588 186 13 1013 2593 583548541 583550112 0.000000e+00 1753
31 TraesCS7B01G484700 chr7D 86.728 1522 162 21 1029 2539 634659517 634661009 0.000000e+00 1655
32 TraesCS7B01G484700 chr7D 89.041 438 40 4 2584 3017 634661016 634661449 1.520000e-148 536
33 TraesCS7B01G484700 chr7D 87.765 425 45 6 2594 3015 634759501 634759081 1.200000e-134 490
34 TraesCS7B01G484700 chr7D 84.633 436 44 10 2594 3017 634652482 634652906 2.680000e-111 412
35 TraesCS7B01G484700 chr7D 78.053 565 71 29 3147 3672 583550998 583551548 1.300000e-79 307
36 TraesCS7B01G484700 chr7D 81.728 301 44 5 3147 3436 634653149 634653449 1.340000e-59 241
37 TraesCS7B01G484700 chr4B 85.054 1773 192 36 864 2598 625072607 625074344 0.000000e+00 1738
38 TraesCS7B01G484700 chr4B 88.527 828 54 23 18 809 625071589 625072411 0.000000e+00 965
39 TraesCS7B01G484700 chr4B 88.108 555 45 8 2479 3016 625074358 625074908 1.130000e-179 640
40 TraesCS7B01G484700 chr4B 92.079 202 16 0 813 1014 625072461 625072662 6.090000e-73 285
41 TraesCS7B01G484700 chr5B 78.161 261 39 9 3147 3403 696682836 696683082 2.320000e-32 150


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 TraesCS7B01G484700 chr7B 741622291 741626018 3727 True 6885.000000 6885 100.000000 1 3728 1 chr7B.!!$R1 3727
1 TraesCS7B01G484700 chr7B 741541449 741543326 1877 False 1121.500000 1639 89.257000 1044 3014 2 chr7B.!!$F3 1970
2 TraesCS7B01G484700 chr7B 651134870 651136002 1132 False 1118.000000 1118 84.535000 1449 2593 1 chr7B.!!$F1 1144
3 TraesCS7B01G484700 chr7B 741484408 741484991 583 False 429.000000 429 80.435000 3147 3728 1 chr7B.!!$F2 581
4 TraesCS7B01G484700 chr7A 731505226 731506620 1394 True 1554.000000 1554 86.769000 1591 3017 1 chr7A.!!$R1 1426
5 TraesCS7B01G484700 chr7A 731220350 731221751 1401 False 1502.000000 1502 85.971000 1576 3017 1 chr7A.!!$F1 1441
6 TraesCS7B01G484700 chr7A 731568588 731571401 2813 True 1317.500000 2368 87.599500 1046 3502 2 chr7A.!!$R2 2456
7 TraesCS7B01G484700 chr7A 731156502 731159296 2794 False 1107.500000 1633 86.670000 242 2860 2 chr7A.!!$F8 2618
8 TraesCS7B01G484700 chr7A 731000674 731003333 2659 False 1049.500000 1598 83.959500 1027 3727 2 chr7A.!!$F4 2700
9 TraesCS7B01G484700 chr7A 731185219 731188258 3039 False 893.666667 1650 86.069667 1 2860 3 chr7A.!!$F9 2859
10 TraesCS7B01G484700 chr7A 731094817 731097964 3147 False 854.333333 1899 84.874667 1 3017 3 chr7A.!!$F6 3016
11 TraesCS7B01G484700 chr7A 675021934 675027661 5727 False 685.000000 1803 81.697500 1046 3672 4 chr7A.!!$F2 2626
12 TraesCS7B01G484700 chr7A 731124819 731125924 1105 False 524.500000 832 87.329000 1 1009 2 chr7A.!!$F7 1008
13 TraesCS7B01G484700 chr7A 731012437 731013831 1394 False 512.000000 575 85.464500 2479 3017 2 chr7A.!!$F5 538
14 TraesCS7B01G484700 chr7A 730881186 730883457 2271 False 415.000000 582 85.416500 1027 3021 2 chr7A.!!$F3 1994
15 TraesCS7B01G484700 chr7D 634659517 634661449 1932 False 1095.500000 1655 87.884500 1029 3017 2 chr7D.!!$F3 1988
16 TraesCS7B01G484700 chr7D 583548541 583551548 3007 False 1030.000000 1753 82.446000 1013 3672 2 chr7D.!!$F1 2659
17 TraesCS7B01G484700 chr7D 634650679 634653449 2770 False 985.333333 2303 86.644667 1046 3436 3 chr7D.!!$F2 2390
18 TraesCS7B01G484700 chr4B 625071589 625074908 3319 False 907.000000 1738 88.442000 18 3016 4 chr4B.!!$F1 2998

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
759 821 0.250467 GCACCAAGTCTGCTTCTCCA 60.250 55.000 0.0 0.0 31.49 3.86 F
1277 1567 1.667154 CTCCTCGGCTTCATGGACGA 61.667 60.000 0.0 0.0 45.06 4.20 F
1826 2269 1.000955 GCTCGTCCTCTTTGTCTTCCA 59.999 52.381 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2139 1.369625 CGAAGGTAATCTTGCGGCTT 58.630 50.0 0.00 0.0 35.50 4.35 R
2115 2579 1.463674 GGCAAAGGATCCGTGTTGAT 58.536 50.0 22.59 0.0 0.00 2.57 R
3436 8354 0.179000 CCCTACTGCCCTGCTTACAG 59.821 60.0 0.00 0.0 44.05 2.74 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
95 97 8.237949 TCACGAACATTTTTAGAAACTGTGAAA 58.762 29.630 0.00 0.00 0.00 2.69
133 135 4.148174 GCAAACCATTTTACTGAAACTCGC 59.852 41.667 0.00 0.00 0.00 5.03
553 580 3.910490 GCCCAAACTTGTGCGCCA 61.910 61.111 4.18 0.00 0.00 5.69
557 585 3.605664 AAACTTGTGCGCCAGGGC 61.606 61.111 4.18 0.00 37.85 5.19
598 627 2.933287 AATCCCTGACCCGCACCA 60.933 61.111 0.00 0.00 0.00 4.17
759 821 0.250467 GCACCAAGTCTGCTTCTCCA 60.250 55.000 0.00 0.00 31.49 3.86
766 828 2.826488 AGTCTGCTTCTCCATGTACCT 58.174 47.619 0.00 0.00 0.00 3.08
805 870 3.243704 CCTGCCGACAAAAAGATTCCAAA 60.244 43.478 0.00 0.00 0.00 3.28
809 874 5.047188 GCCGACAAAAAGATTCCAAAAAGA 58.953 37.500 0.00 0.00 0.00 2.52
810 875 5.696270 GCCGACAAAAAGATTCCAAAAAGAT 59.304 36.000 0.00 0.00 0.00 2.40
811 876 6.202762 GCCGACAAAAAGATTCCAAAAAGATT 59.797 34.615 0.00 0.00 0.00 2.40
884 995 5.512434 TCGTTTTCTAAACGTTTTTGAAGGC 59.488 36.000 20.19 16.23 43.47 4.35
910 1021 5.720371 AACGACAATTTTCCAATCCATGA 57.280 34.783 0.00 0.00 0.00 3.07
912 1023 6.095432 ACGACAATTTTCCAATCCATGAAA 57.905 33.333 0.00 0.00 0.00 2.69
913 1024 6.700352 ACGACAATTTTCCAATCCATGAAAT 58.300 32.000 0.00 0.00 0.00 2.17
1004 1142 4.914177 AGCCACAATTTTCCAATCCATT 57.086 36.364 0.00 0.00 0.00 3.16
1020 1158 8.250332 TCCAATCCATTAAATTTAACTCACTGC 58.750 33.333 12.74 0.00 0.00 4.40
1021 1159 7.492344 CCAATCCATTAAATTTAACTCACTGCC 59.508 37.037 12.74 0.00 0.00 4.85
1038 1315 1.749334 GCCTCACTCCCACTATCCCG 61.749 65.000 0.00 0.00 0.00 5.14
1041 1318 2.108168 CTCACTCCCACTATCCCGAAA 58.892 52.381 0.00 0.00 0.00 3.46
1042 1319 2.700897 CTCACTCCCACTATCCCGAAAT 59.299 50.000 0.00 0.00 0.00 2.17
1277 1567 1.667154 CTCCTCGGCTTCATGGACGA 61.667 60.000 0.00 0.00 45.06 4.20
1290 1580 2.107141 GACGAGGCCGGATTCCAG 59.893 66.667 5.05 0.00 40.78 3.86
1826 2269 1.000955 GCTCGTCCTCTTTGTCTTCCA 59.999 52.381 0.00 0.00 0.00 3.53
1848 2291 3.081061 GTCCACAACTATGCAATGGTCA 58.919 45.455 0.00 0.00 36.85 4.02
1855 2298 3.966979 ACTATGCAATGGTCAATGGTCA 58.033 40.909 0.00 0.00 28.92 4.02
2158 2628 5.048083 CCTCTATCATACCTCTCTGCAGAAC 60.048 48.000 18.85 0.00 0.00 3.01
2260 2730 2.838202 AGCCGAGGGATTCTTGTTCTTA 59.162 45.455 0.00 0.00 0.00 2.10
2603 3466 8.624776 AGCTAATTGATGGTTTTAAGCTGATAC 58.375 33.333 0.00 0.00 0.00 2.24
2621 3577 8.417884 AGCTGATACCTGAGTACTCTTTATTTC 58.582 37.037 23.01 13.00 0.00 2.17
2767 3771 7.355778 CGCCTTTCCTCTTAAGCTATATTTTG 58.644 38.462 0.00 0.00 0.00 2.44
2833 7500 7.420800 ACTTCAGTTGCTTCAAAATTCTACTG 58.579 34.615 0.00 0.00 34.97 2.74
2843 7513 6.509418 TCAAAATTCTACTGCCATGGTTAC 57.491 37.500 14.67 0.00 0.00 2.50
2856 7526 7.120726 ACTGCCATGGTTACATAGAAAGTTAAC 59.879 37.037 14.67 0.00 34.99 2.01
2880 7577 7.630082 ACTATTGTTCTATTGGGCTTGACTAA 58.370 34.615 0.00 0.00 0.00 2.24
2881 7578 8.107095 ACTATTGTTCTATTGGGCTTGACTAAA 58.893 33.333 0.00 0.00 0.00 1.85
2905 7630 3.901844 TGTCAAACTAGCTAGGACAGGTT 59.098 43.478 24.35 6.83 36.15 3.50
2921 7646 4.023291 ACAGGTTGTCAACTCATGGTTTT 58.977 39.130 15.17 0.00 35.74 2.43
2934 7668 2.350899 TGGTTTTGATTCTGCATGCG 57.649 45.000 14.09 8.20 0.00 4.73
2949 7684 2.094752 GCATGCGTGTTTAACTCCCATT 60.095 45.455 0.00 0.00 0.00 3.16
3017 7769 6.929049 AGTTTGGAAAGCTAGTTTTTATTGCC 59.071 34.615 6.00 3.30 34.81 4.52
3027 7813 7.122650 AGCTAGTTTTTATTGCCTGCATCTTTA 59.877 33.333 0.00 0.00 0.00 1.85
3032 7818 9.364989 GTTTTTATTGCCTGCATCTTTATGTAA 57.635 29.630 0.00 0.00 35.38 2.41
3038 7828 7.439157 TGCCTGCATCTTTATGTAATACATC 57.561 36.000 9.43 0.00 39.88 3.06
3059 7849 7.033791 ACATCGTTAGTCATACTTACCAGTTG 58.966 38.462 0.00 0.00 34.06 3.16
3069 7860 8.361139 GTCATACTTACCAGTTGCTACATATCT 58.639 37.037 0.13 0.00 34.06 1.98
3078 7869 9.632638 ACCAGTTGCTACATATCTTTCATTTAT 57.367 29.630 0.13 0.00 0.00 1.40
3111 7903 6.203338 ACAATGTTCAAAATCAGAATGTTGCC 59.797 34.615 0.00 0.00 37.40 4.52
3125 7917 6.653320 CAGAATGTTGCCTAACCAGTAAGTTA 59.347 38.462 0.00 0.00 35.92 2.24
3152 8026 2.092429 TGAAGGCCTTGAGTCTTGTGTT 60.092 45.455 26.25 0.00 0.00 3.32
3162 8065 5.342806 TGAGTCTTGTGTTTATTGCTTCG 57.657 39.130 0.00 0.00 0.00 3.79
3183 8086 5.541845 TCGAAGCTGCAATACAATATAGCT 58.458 37.500 1.02 0.00 42.76 3.32
3188 8091 5.388944 GCTGCAATACAATATAGCTGCTTC 58.611 41.667 7.79 0.00 43.74 3.86
3192 8095 6.543465 TGCAATACAATATAGCTGCTTCTGTT 59.457 34.615 7.79 0.00 0.00 3.16
3194 8097 7.041508 GCAATACAATATAGCTGCTTCTGTTCT 60.042 37.037 7.79 0.00 0.00 3.01
3195 8098 7.959689 ATACAATATAGCTGCTTCTGTTCTG 57.040 36.000 7.79 0.00 0.00 3.02
3198 8101 7.331026 ACAATATAGCTGCTTCTGTTCTGTTA 58.669 34.615 7.79 0.00 0.00 2.41
3210 8113 8.504005 GCTTCTGTTCTGTTATTGTTAAGCTAA 58.496 33.333 0.00 0.00 34.32 3.09
3225 8131 6.971184 TGTTAAGCTAAATCGTACTCTGCTAC 59.029 38.462 0.00 0.00 0.00 3.58
3251 8157 3.873952 GCACATGCCTAGTTCCTAAGAAG 59.126 47.826 0.00 0.00 30.92 2.85
3329 8239 8.824159 ACTAAATACATGTATGCAGATCTGAC 57.176 34.615 27.04 15.68 0.00 3.51
3352 8269 2.471862 GCTAGCTTGATCTTGCTTGC 57.528 50.000 21.87 21.87 46.40 4.01
3398 8316 4.454678 GGATGTTCAAGATGGTGCTGATA 58.545 43.478 0.00 0.00 0.00 2.15
3409 8327 7.643569 AGATGGTGCTGATATAGTCTGATAG 57.356 40.000 0.00 0.00 0.00 2.08
3410 8328 7.181361 AGATGGTGCTGATATAGTCTGATAGT 58.819 38.462 0.00 0.00 0.00 2.12
3437 8355 9.440773 TCCGTATTAAGTATCGTATGTATGTCT 57.559 33.333 0.00 0.00 0.00 3.41
3438 8356 9.486857 CCGTATTAAGTATCGTATGTATGTCTG 57.513 37.037 0.00 0.00 0.00 3.51
3443 8361 9.888878 TTAAGTATCGTATGTATGTCTGTAAGC 57.111 33.333 0.00 0.00 0.00 3.09
3444 8362 7.506328 AGTATCGTATGTATGTCTGTAAGCA 57.494 36.000 0.00 0.00 0.00 3.91
3445 8363 7.585867 AGTATCGTATGTATGTCTGTAAGCAG 58.414 38.462 0.00 0.00 43.87 4.24
3446 8364 5.183014 TCGTATGTATGTCTGTAAGCAGG 57.817 43.478 0.00 0.00 42.78 4.85
3447 8365 4.037565 TCGTATGTATGTCTGTAAGCAGGG 59.962 45.833 0.00 0.00 42.78 4.45
3448 8366 2.691409 TGTATGTCTGTAAGCAGGGC 57.309 50.000 0.00 0.00 42.78 5.19
3451 8369 0.987294 ATGTCTGTAAGCAGGGCAGT 59.013 50.000 0.00 0.00 42.78 4.40
3456 8374 1.153147 GTAAGCAGGGCAGTAGGGC 60.153 63.158 0.00 0.00 42.44 5.19
3467 8385 1.908793 AGTAGGGCACGCTGTCAGT 60.909 57.895 0.93 0.00 0.00 3.41
3472 8390 1.291877 GGGCACGCTGTCAGTAAGTG 61.292 60.000 15.92 15.92 36.05 3.16
3485 8403 6.068010 TGTCAGTAAGTGGAATTTGACCAAT 58.932 36.000 0.00 0.00 39.22 3.16
3487 8405 7.888021 TGTCAGTAAGTGGAATTTGACCAATAT 59.112 33.333 0.00 0.00 39.22 1.28
3503 8421 7.383687 TGACCAATATTGACGTCTAAGACTTT 58.616 34.615 17.23 0.00 0.00 2.66
3518 8436 7.855904 GTCTAAGACTTTGGTTTATGTTGTGTG 59.144 37.037 0.00 0.00 0.00 3.82
3527 8445 6.442952 TGGTTTATGTTGTGTGCTAATGTTC 58.557 36.000 0.00 0.00 0.00 3.18
3530 8448 1.943340 TGTTGTGTGCTAATGTTCGCA 59.057 42.857 0.00 0.00 0.00 5.10
3538 8456 2.159393 TGCTAATGTTCGCATTGGAAGC 60.159 45.455 7.67 7.09 45.37 3.86
3574 8506 0.394216 CCCCGCTTCAATCCATGTCA 60.394 55.000 0.00 0.00 0.00 3.58
3577 8509 2.223641 CCCGCTTCAATCCATGTCATTG 60.224 50.000 7.89 7.89 33.22 2.82
3583 8515 5.533903 GCTTCAATCCATGTCATTGGTCTAT 59.466 40.000 12.44 0.00 38.01 1.98
3584 8516 6.293845 GCTTCAATCCATGTCATTGGTCTATC 60.294 42.308 12.44 0.00 38.01 2.08
3585 8517 6.251255 TCAATCCATGTCATTGGTCTATCA 57.749 37.500 12.44 0.00 38.01 2.15
3587 8519 5.901413 ATCCATGTCATTGGTCTATCAGT 57.099 39.130 0.00 0.00 38.01 3.41
3588 8520 7.071071 TCAATCCATGTCATTGGTCTATCAGTA 59.929 37.037 12.44 0.00 38.01 2.74
3591 8523 5.987953 CCATGTCATTGGTCTATCAGTACTG 59.012 44.000 17.17 17.17 31.74 2.74
3592 8524 6.183360 CCATGTCATTGGTCTATCAGTACTGA 60.183 42.308 27.07 27.07 36.67 3.41
3593 8525 6.456795 TGTCATTGGTCTATCAGTACTGAG 57.543 41.667 28.29 17.09 43.61 3.35
3594 8526 6.187682 TGTCATTGGTCTATCAGTACTGAGA 58.812 40.000 28.29 23.58 43.61 3.27
3596 8528 7.998964 TGTCATTGGTCTATCAGTACTGAGATA 59.001 37.037 28.29 15.65 43.61 1.98
3598 8530 8.851145 TCATTGGTCTATCAGTACTGAGATAAC 58.149 37.037 28.29 22.46 43.61 1.89
3624 8580 5.104776 AGCTTTTATCTGCATGAGTGGAGTA 60.105 40.000 0.00 0.00 43.56 2.59
3686 8642 0.955428 GTTCATCTCCAACGCCTGCA 60.955 55.000 0.00 0.00 0.00 4.41
3694 8650 2.487762 CTCCAACGCCTGCAAAATTCTA 59.512 45.455 0.00 0.00 0.00 2.10
3696 8652 2.228822 CCAACGCCTGCAAAATTCTAGT 59.771 45.455 0.00 0.00 0.00 2.57
3703 8659 5.106712 CGCCTGCAAAATTCTAGTTGAGTTA 60.107 40.000 0.00 0.00 0.00 2.24
3705 8661 6.612306 CCTGCAAAATTCTAGTTGAGTTACC 58.388 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 7.490962 TCGTGAATTTGTAGAAAGTGTTCAT 57.509 32.000 3.93 0.00 36.09 2.57
95 97 5.033589 TGGTTTGCCAATTCACAAAGATT 57.966 34.783 3.25 0.00 42.83 2.40
432 447 6.884280 AATTCAGGATTAAATAGCTTCCCG 57.116 37.500 0.00 0.00 0.00 5.14
514 533 2.198426 CCATTTGCGGGCCCCTAT 59.802 61.111 18.66 0.94 0.00 2.57
553 580 3.394836 GCACTCTCCCTTCGCCCT 61.395 66.667 0.00 0.00 0.00 5.19
557 585 3.916392 AACGCGCACTCTCCCTTCG 62.916 63.158 5.73 0.00 0.00 3.79
668 701 1.569479 GGAACTCTTGCTGCGACCAC 61.569 60.000 0.00 0.00 0.00 4.16
679 712 3.647771 GGGGGCACGGGAACTCTT 61.648 66.667 0.00 0.00 0.00 2.85
726 787 1.826921 GGTGCCATCATGCTCAGGG 60.827 63.158 0.00 0.00 0.00 4.45
759 821 1.688187 GGACGGGTCCCAGGTACAT 60.688 63.158 9.12 0.00 43.94 2.29
884 995 7.812191 TCATGGATTGGAAAATTGTCGTTTTAG 59.188 33.333 0.00 0.00 31.80 1.85
910 1021 4.265073 AGCTCTACGAAGCCATTCAATTT 58.735 39.130 0.00 0.00 43.56 1.82
912 1023 3.118629 TGAGCTCTACGAAGCCATTCAAT 60.119 43.478 16.19 0.00 43.56 2.57
913 1024 2.233676 TGAGCTCTACGAAGCCATTCAA 59.766 45.455 16.19 0.00 43.56 2.69
1004 1142 5.938125 GGAGTGAGGCAGTGAGTTAAATTTA 59.062 40.000 0.00 0.00 0.00 1.40
1014 1152 0.114364 TAGTGGGAGTGAGGCAGTGA 59.886 55.000 0.00 0.00 0.00 3.41
1015 1153 1.137872 GATAGTGGGAGTGAGGCAGTG 59.862 57.143 0.00 0.00 0.00 3.66
1018 1156 0.691078 GGGATAGTGGGAGTGAGGCA 60.691 60.000 0.00 0.00 0.00 4.75
1019 1157 1.749334 CGGGATAGTGGGAGTGAGGC 61.749 65.000 0.00 0.00 0.00 4.70
1020 1158 0.106167 TCGGGATAGTGGGAGTGAGG 60.106 60.000 0.00 0.00 0.00 3.86
1021 1159 1.776662 TTCGGGATAGTGGGAGTGAG 58.223 55.000 0.00 0.00 0.00 3.51
1038 1315 2.973406 AGGGGATCGAGGGTTAGATTTC 59.027 50.000 0.00 0.00 0.00 2.17
1041 1318 2.180308 AGAAGGGGATCGAGGGTTAGAT 59.820 50.000 0.00 0.00 0.00 1.98
1042 1319 1.574339 AGAAGGGGATCGAGGGTTAGA 59.426 52.381 0.00 0.00 0.00 2.10
1347 1637 2.679199 GACGAAGGAGAAATCGGCC 58.321 57.895 0.00 0.00 41.20 6.13
1380 1670 1.202428 GGCATGAAGTAGGAGGACGAC 60.202 57.143 0.00 0.00 0.00 4.34
1617 2060 3.644399 GACGGCGAGGTGGAACTCC 62.644 68.421 16.62 0.00 43.30 3.85
1696 2139 1.369625 CGAAGGTAATCTTGCGGCTT 58.630 50.000 0.00 0.00 35.50 4.35
1826 2269 3.244875 TGACCATTGCATAGTTGTGGACT 60.245 43.478 0.00 0.00 42.55 3.85
1855 2298 2.200955 GAAGGGGAAATGGGAGACTCT 58.799 52.381 1.74 0.00 0.00 3.24
2115 2579 1.463674 GGCAAAGGATCCGTGTTGAT 58.536 50.000 22.59 0.00 0.00 2.57
2158 2628 1.747355 AGCTTCCATTCCTGCGAATTG 59.253 47.619 0.00 0.00 36.54 2.32
2260 2730 2.803030 TACCTTCTAGAGTGCCTCGT 57.197 50.000 0.00 0.00 35.36 4.18
2603 3466 6.301169 ACAGGGAAATAAAGAGTACTCAGG 57.699 41.667 24.44 2.90 0.00 3.86
2621 3577 2.951642 TGCTCTTGAAAACAGAACAGGG 59.048 45.455 0.00 0.00 0.00 4.45
2767 3771 6.683974 TTCCTATCTGCAAAATTACAGAGC 57.316 37.500 10.42 0.00 45.55 4.09
2833 7500 7.625828 AGTTAACTTTCTATGTAACCATGGC 57.374 36.000 13.04 0.00 32.29 4.40
2856 7526 8.506168 TTTAGTCAAGCCCAATAGAACAATAG 57.494 34.615 0.00 0.00 0.00 1.73
2880 7577 5.013183 ACCTGTCCTAGCTAGTTTGACAATT 59.987 40.000 23.22 14.59 35.70 2.32
2881 7578 4.532521 ACCTGTCCTAGCTAGTTTGACAAT 59.467 41.667 23.22 15.61 35.70 2.71
2905 7630 5.507817 GCAGAATCAAAACCATGAGTTGACA 60.508 40.000 0.00 0.00 39.19 3.58
2911 7636 3.863424 GCATGCAGAATCAAAACCATGAG 59.137 43.478 14.21 0.00 33.71 2.90
2921 7646 3.501828 AGTTAAACACGCATGCAGAATCA 59.498 39.130 19.57 0.00 0.00 2.57
2934 7668 8.519526 TCAATCACATAAATGGGAGTTAAACAC 58.480 33.333 0.87 0.00 44.55 3.32
3032 7818 8.461249 ACTGGTAAGTATGACTAACGATGTAT 57.539 34.615 0.00 0.00 33.79 2.29
3038 7828 5.408356 AGCAACTGGTAAGTATGACTAACG 58.592 41.667 0.00 0.00 34.77 3.18
3069 7860 9.521503 TGAACATTGTCGTTGAAATAAATGAAA 57.478 25.926 0.00 0.00 0.00 2.69
3078 7869 7.254137 TCTGATTTTGAACATTGTCGTTGAAA 58.746 30.769 0.00 0.00 31.44 2.69
3086 7877 6.203338 GGCAACATTCTGATTTTGAACATTGT 59.797 34.615 0.00 0.00 30.57 2.71
3100 7892 5.003804 ACTTACTGGTTAGGCAACATTCTG 58.996 41.667 0.00 0.00 36.29 3.02
3111 7903 8.021396 GCCTTCAAACATTAACTTACTGGTTAG 58.979 37.037 0.00 0.00 33.90 2.34
3125 7917 3.837355 AGACTCAAGGCCTTCAAACATT 58.163 40.909 17.29 0.00 0.00 2.71
3162 8065 5.180868 AGCAGCTATATTGTATTGCAGCTTC 59.819 40.000 14.03 1.50 42.25 3.86
3174 8077 6.674694 AACAGAACAGAAGCAGCTATATTG 57.325 37.500 0.00 0.00 0.00 1.90
3176 8079 7.989741 ACAATAACAGAACAGAAGCAGCTATAT 59.010 33.333 0.00 0.00 0.00 0.86
3180 8083 4.392940 ACAATAACAGAACAGAAGCAGCT 58.607 39.130 0.00 0.00 0.00 4.24
3183 8086 6.486657 AGCTTAACAATAACAGAACAGAAGCA 59.513 34.615 0.00 0.00 38.38 3.91
3188 8091 9.478019 CGATTTAGCTTAACAATAACAGAACAG 57.522 33.333 0.00 0.00 0.00 3.16
3192 8095 9.865321 AGTACGATTTAGCTTAACAATAACAGA 57.135 29.630 0.00 0.00 0.00 3.41
3194 8097 9.865321 AGAGTACGATTTAGCTTAACAATAACA 57.135 29.630 0.00 0.00 0.00 2.41
3198 8101 7.042335 AGCAGAGTACGATTTAGCTTAACAAT 58.958 34.615 0.00 0.00 0.00 2.71
3225 8131 3.550437 AGGAACTAGGCATGTGCTAAG 57.450 47.619 4.84 5.44 38.03 2.18
3239 8145 3.718956 CCCATCCCATCTTCTTAGGAACT 59.281 47.826 0.00 0.00 46.37 3.01
3240 8146 3.716872 TCCCATCCCATCTTCTTAGGAAC 59.283 47.826 0.00 0.00 30.71 3.62
3283 8189 6.073327 AGTTAGAAACTTTAAGCAACTGCC 57.927 37.500 0.00 0.00 39.04 4.85
3329 8239 2.641305 AGCAAGATCAAGCTAGCAAGG 58.359 47.619 18.83 5.70 39.78 3.61
3352 8269 4.500545 GCCATCCTACTCCAGATATATGCG 60.501 50.000 0.00 0.00 0.00 4.73
3358 8276 1.427753 TCCGCCATCCTACTCCAGATA 59.572 52.381 0.00 0.00 0.00 1.98
3409 8327 9.831737 ACATACATACGATACTTAATACGGAAC 57.168 33.333 0.00 0.00 0.00 3.62
3436 8354 0.179000 CCCTACTGCCCTGCTTACAG 59.821 60.000 0.00 0.00 44.05 2.74
3437 8355 1.910580 GCCCTACTGCCCTGCTTACA 61.911 60.000 0.00 0.00 0.00 2.41
3438 8356 1.153147 GCCCTACTGCCCTGCTTAC 60.153 63.158 0.00 0.00 0.00 2.34
3439 8357 1.615124 TGCCCTACTGCCCTGCTTA 60.615 57.895 0.00 0.00 0.00 3.09
3440 8358 2.935481 TGCCCTACTGCCCTGCTT 60.935 61.111 0.00 0.00 0.00 3.91
3441 8359 3.721706 GTGCCCTACTGCCCTGCT 61.722 66.667 0.00 0.00 0.00 4.24
3446 8364 4.394712 ACAGCGTGCCCTACTGCC 62.395 66.667 0.00 0.00 34.72 4.85
3447 8365 2.815647 GACAGCGTGCCCTACTGC 60.816 66.667 0.00 0.00 34.72 4.40
3448 8366 1.446792 CTGACAGCGTGCCCTACTG 60.447 63.158 0.00 0.00 37.45 2.74
3451 8369 0.530744 CTTACTGACAGCGTGCCCTA 59.469 55.000 1.25 0.00 0.00 3.53
3456 8374 2.148916 TTCCACTTACTGACAGCGTG 57.851 50.000 1.25 7.66 0.00 5.34
3467 8385 7.392113 ACGTCAATATTGGTCAAATTCCACTTA 59.608 33.333 15.36 0.00 34.45 2.24
3472 8390 6.436843 AGACGTCAATATTGGTCAAATTCC 57.563 37.500 19.50 0.79 31.93 3.01
3485 8403 9.146984 CATAAACCAAAGTCTTAGACGTCAATA 57.853 33.333 19.50 0.00 37.67 1.90
3487 8405 6.987992 ACATAAACCAAAGTCTTAGACGTCAA 59.012 34.615 19.50 9.11 37.67 3.18
3503 8421 6.398234 AACATTAGCACACAACATAAACCA 57.602 33.333 0.00 0.00 0.00 3.67
3518 8436 2.454055 GCTTCCAATGCGAACATTAGC 58.546 47.619 0.00 0.00 44.83 3.09
3527 8445 3.204827 CCGAGGGCTTCCAATGCG 61.205 66.667 0.00 0.00 0.00 4.73
3559 8491 3.698040 AGACCAATGACATGGATTGAAGC 59.302 43.478 17.13 8.69 43.54 3.86
3560 8492 6.769341 TGATAGACCAATGACATGGATTGAAG 59.231 38.462 17.13 7.48 43.54 3.02
3577 8509 7.881232 AGCTAGTTATCTCAGTACTGATAGACC 59.119 40.741 25.35 9.03 39.13 3.85
3587 8519 8.914011 TGCAGATAAAAGCTAGTTATCTCAGTA 58.086 33.333 21.48 12.95 43.35 2.74
3588 8520 7.786030 TGCAGATAAAAGCTAGTTATCTCAGT 58.214 34.615 21.48 6.66 43.35 3.41
3591 8523 8.824159 TCATGCAGATAAAAGCTAGTTATCTC 57.176 34.615 21.48 17.56 43.35 2.75
3592 8524 8.428063 ACTCATGCAGATAAAAGCTAGTTATCT 58.572 33.333 19.73 19.73 45.14 1.98
3593 8525 8.494347 CACTCATGCAGATAAAAGCTAGTTATC 58.506 37.037 16.88 16.88 37.96 1.75
3594 8526 7.443575 CCACTCATGCAGATAAAAGCTAGTTAT 59.556 37.037 0.00 2.92 0.00 1.89
3596 8528 5.587844 CCACTCATGCAGATAAAAGCTAGTT 59.412 40.000 0.00 0.00 0.00 2.24
3598 8530 5.363101 TCCACTCATGCAGATAAAAGCTAG 58.637 41.667 0.00 0.00 0.00 3.42
3676 8632 3.559238 ACTAGAATTTTGCAGGCGTTG 57.441 42.857 0.00 0.00 0.00 4.10
3694 8650 7.227156 AGAAACTCAATCATGGTAACTCAACT 58.773 34.615 0.00 0.00 37.61 3.16
3696 8652 7.522073 GCAAGAAACTCAATCATGGTAACTCAA 60.522 37.037 0.00 0.00 37.61 3.02
3703 8659 2.095059 GCGCAAGAAACTCAATCATGGT 60.095 45.455 0.30 0.00 43.02 3.55
3705 8661 2.912967 GTGCGCAAGAAACTCAATCATG 59.087 45.455 14.00 0.00 43.02 3.07


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

AutoCloner maintained by Alex Coulton.