Multiple sequence alignment - TraesCS6B01G441300

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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 TraesCS6B01G441300 chr6B 100.000 2866 0 0 518 3383 705630170 705627305 0.000000e+00 5293.0
1 TraesCS6B01G441300 chr6B 95.508 2293 78 10 518 2794 705797146 705794863 0.000000e+00 3640.0
2 TraesCS6B01G441300 chr6B 93.987 2295 84 11 518 2794 706133239 706130981 0.000000e+00 3424.0
3 TraesCS6B01G441300 chr6B 89.690 1387 123 10 1248 2626 706158792 706157418 0.000000e+00 1751.0
4 TraesCS6B01G441300 chr6B 85.697 1692 171 27 1129 2794 705581235 705579589 0.000000e+00 1718.0
5 TraesCS6B01G441300 chr6B 85.948 1530 179 23 1282 2789 705896911 705895396 0.000000e+00 1602.0
6 TraesCS6B01G441300 chr6B 85.478 1267 153 11 1129 2388 705927517 705926275 0.000000e+00 1291.0
7 TraesCS6B01G441300 chr6B 84.343 1188 162 18 1619 2794 705641805 705640630 0.000000e+00 1142.0
8 TraesCS6B01G441300 chr6B 100.000 313 0 0 1 313 705630687 705630375 2.260000e-161 579.0
9 TraesCS6B01G441300 chr6B 93.333 300 19 1 15 313 705797482 705797183 3.100000e-120 442.0
10 TraesCS6B01G441300 chr6B 81.508 557 37 18 2793 3307 706130941 706130409 6.800000e-107 398.0
11 TraesCS6B01G441300 chr6B 89.000 300 32 1 15 313 706133576 706133277 1.480000e-98 370.0
12 TraesCS6B01G441300 chr6B 86.479 355 19 12 2791 3119 705794823 705794472 2.480000e-96 363.0
13 TraesCS6B01G441300 chr6B 79.278 526 48 16 2791 3273 705895351 705894844 9.120000e-81 311.0
14 TraesCS6B01G441300 chr6B 84.950 299 29 2 3024 3307 705579336 705579039 4.270000e-74 289.0
15 TraesCS6B01G441300 chr6B 81.572 407 23 19 2791 3169 706157176 706156794 4.270000e-74 289.0
16 TraesCS6B01G441300 chr6B 82.731 249 37 6 811 1053 705927803 705927555 2.040000e-52 217.0
17 TraesCS6B01G441300 chr6B 88.824 170 15 2 2791 2958 705640591 705640424 4.420000e-49 206.0
18 TraesCS6B01G441300 chr6B 88.489 139 8 2 2791 2929 705579549 705579419 9.710000e-36 161.0
19 TraesCS6B01G441300 chr6B 90.991 111 8 2 2791 2899 705900748 705900638 7.560000e-32 148.0
20 TraesCS6B01G441300 chr6B 92.982 57 4 0 2970 3026 705579417 705579361 2.160000e-12 84.2
21 TraesCS6B01G441300 chr6A 88.423 1503 144 9 1248 2728 609636527 609635033 0.000000e+00 1784.0
22 TraesCS6B01G441300 chr6A 83.117 1540 202 31 1248 2771 609738922 609737425 0.000000e+00 1351.0
23 TraesCS6B01G441300 chr6A 78.562 1474 249 48 1289 2742 609821329 609819903 0.000000e+00 909.0
24 TraesCS6B01G441300 chr6A 78.766 1361 230 37 1289 2629 609815073 609813752 0.000000e+00 857.0
25 TraesCS6B01G441300 chr6A 84.151 265 30 7 787 1049 609719053 609718799 2.610000e-61 246.0
26 TraesCS6B01G441300 chr6A 89.908 109 7 3 2823 2930 609629377 609629272 1.640000e-28 137.0
27 TraesCS6B01G441300 chr6A 100.000 30 0 0 278 307 599868046 599868075 4.720000e-04 56.5
28 TraesCS6B01G441300 chr6D 84.045 1147 139 16 1276 2403 463051768 463050647 0.000000e+00 1064.0
29 TraesCS6B01G441300 chr6D 78.893 1464 243 45 1298 2743 463079839 463078424 0.000000e+00 931.0
30 TraesCS6B01G441300 chr6D 85.172 290 24 6 3055 3329 462871341 462871056 2.570000e-71 279.0
31 TraesCS6B01G441300 chr7A 90.291 103 10 0 519 621 1472410 1472512 5.890000e-28 135.0
32 TraesCS6B01G441300 chr3B 87.500 104 13 0 518 621 805714002 805713899 1.650000e-23 121.0
33 TraesCS6B01G441300 chr5B 85.577 104 15 0 518 621 24683888 24683991 3.570000e-20 110.0
34 TraesCS6B01G441300 chr5B 95.652 46 2 0 1087 1132 230250809 230250764 1.300000e-09 75.0
35 TraesCS6B01G441300 chr2A 90.667 75 4 3 876 949 112488290 112488362 2.780000e-16 97.1
36 TraesCS6B01G441300 chr5A 90.909 66 6 0 518 583 43395188 43395253 4.650000e-14 89.8
37 TraesCS6B01G441300 chr5A 95.122 41 2 0 1087 1127 282597861 282597821 7.840000e-07 65.8
38 TraesCS6B01G441300 chr7D 90.000 60 2 4 1087 1144 62191424 62191481 1.300000e-09 75.0
39 TraesCS6B01G441300 chr7D 100.000 29 0 0 279 307 34067441 34067469 2.000000e-03 54.7
40 TraesCS6B01G441300 chr5D 95.652 46 2 0 1087 1132 214921961 214921916 1.300000e-09 75.0
41 TraesCS6B01G441300 chr4A 93.617 47 3 0 570 616 632619319 632619365 1.680000e-08 71.3
42 TraesCS6B01G441300 chr2B 95.455 44 1 1 1089 1132 620274857 620274899 6.060000e-08 69.4
43 TraesCS6B01G441300 chr7B 93.182 44 2 1 1089 1132 123667010 123667052 2.820000e-06 63.9
44 TraesCS6B01G441300 chr7B 97.222 36 1 0 1087 1122 466955372 466955407 1.010000e-05 62.1
45 TraesCS6B01G441300 chr3D 96.875 32 0 1 277 307 1914246 1914215 6.000000e-03 52.8
46 TraesCS6B01G441300 chr1D 100.000 28 0 0 280 307 418966567 418966594 6.000000e-03 52.8
47 TraesCS6B01G441300 chr1D 100.000 28 0 0 280 307 418996979 418997006 6.000000e-03 52.8
48 TraesCS6B01G441300 chr1B 100.000 28 0 0 280 307 550640072 550640099 6.000000e-03 52.8
49 TraesCS6B01G441300 chr1B 94.286 35 1 1 274 307 559098475 559098509 6.000000e-03 52.8


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 TraesCS6B01G441300 chr6B 705627305 705630687 3382 True 2936.000000 5293 100.000000 1 3383 2 chr6B.!!$R2 3382
1 TraesCS6B01G441300 chr6B 705794472 705797482 3010 True 1481.666667 3640 91.773333 15 3119 3 chr6B.!!$R4 3104
2 TraesCS6B01G441300 chr6B 706130409 706133576 3167 True 1397.333333 3424 88.165000 15 3307 3 chr6B.!!$R7 3292
3 TraesCS6B01G441300 chr6B 706156794 706158792 1998 True 1020.000000 1751 85.631000 1248 3169 2 chr6B.!!$R8 1921
4 TraesCS6B01G441300 chr6B 705926275 705927803 1528 True 754.000000 1291 84.104500 811 2388 2 chr6B.!!$R6 1577
5 TraesCS6B01G441300 chr6B 705894844 705900748 5904 True 687.000000 1602 85.405667 1282 3273 3 chr6B.!!$R5 1991
6 TraesCS6B01G441300 chr6B 705640424 705641805 1381 True 674.000000 1142 86.583500 1619 2958 2 chr6B.!!$R3 1339
7 TraesCS6B01G441300 chr6B 705579039 705581235 2196 True 563.050000 1718 88.029500 1129 3307 4 chr6B.!!$R1 2178
8 TraesCS6B01G441300 chr6A 609635033 609636527 1494 True 1784.000000 1784 88.423000 1248 2728 1 chr6A.!!$R2 1480
9 TraesCS6B01G441300 chr6A 609737425 609738922 1497 True 1351.000000 1351 83.117000 1248 2771 1 chr6A.!!$R4 1523
10 TraesCS6B01G441300 chr6A 609819903 609821329 1426 True 909.000000 909 78.562000 1289 2742 1 chr6A.!!$R6 1453
11 TraesCS6B01G441300 chr6A 609813752 609815073 1321 True 857.000000 857 78.766000 1289 2629 1 chr6A.!!$R5 1340
12 TraesCS6B01G441300 chr6D 463050647 463051768 1121 True 1064.000000 1064 84.045000 1276 2403 1 chr6D.!!$R2 1127
13 TraesCS6B01G441300 chr6D 463078424 463079839 1415 True 931.000000 931 78.893000 1298 2743 1 chr6D.!!$R3 1445

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
102 104 0.451383 TACGTGTATTCGACGGTGGG 59.549 55.0 0.0 0.0 41.21 4.61 F
1872 4442 0.394352 CCGGAGAAATCCCACCAAGG 60.394 60.0 0.0 0.0 37.03 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 4570 1.137594 AGGGTTTCCGGGATTCCACA 61.138 55.0 16.26 0.0 38.33 4.17 R
3359 6098 0.892063 TCGTCATTGACCCGTCATCA 59.108 50.0 11.12 0.0 39.64 3.07 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
22 23 1.810755 CCTTTTTCGGTAGAAGGCACC 59.189 52.381 0.00 0.00 37.70 5.01
51 52 2.963548 TACTGTGTCGTTGTCCAACA 57.036 45.000 10.49 0.00 41.20 3.33
78 79 7.608761 TGGAACACATATAAGTTTACTTGACCC 59.391 37.037 5.41 0.00 37.40 4.46
80 81 6.704310 ACACATATAAGTTTACTTGACCCGT 58.296 36.000 5.41 0.00 37.40 5.28
94 96 1.913403 GACCCGTTGTACGTGTATTCG 59.087 52.381 0.00 0.00 40.58 3.34
99 101 2.584791 GTTGTACGTGTATTCGACGGT 58.415 47.619 0.00 0.00 41.21 4.83
101 103 1.135717 TGTACGTGTATTCGACGGTGG 60.136 52.381 0.00 0.00 41.21 4.61
102 104 0.451383 TACGTGTATTCGACGGTGGG 59.549 55.000 0.00 0.00 41.21 4.61
174 176 5.956068 AAAAACAAAAGCTTTGCCTTTGA 57.044 30.435 13.54 0.00 40.98 2.69
213 215 4.219033 AGAAGAAAAATTGTACAAGCGCG 58.781 39.130 14.65 0.00 0.00 6.86
309 311 4.901197 TTAACATGCTCCCTCTTACACA 57.099 40.909 0.00 0.00 0.00 3.72
785 787 5.334421 AGTGATCCTACTATAGGCCGAAAT 58.666 41.667 4.43 0.00 45.82 2.17
999 1013 2.359850 CCGGCTGGCAGCTAAACA 60.360 61.111 35.73 0.00 41.99 2.83
1034 1048 3.573558 GCCGTTTCTTGCGATCCA 58.426 55.556 0.00 0.00 0.00 3.41
1101 1115 3.666345 AGTACAGTACTCCCTCCGATT 57.334 47.619 7.48 0.00 32.47 3.34
1135 1149 3.697045 TCGTGGTTTCAGTTCCAAACATT 59.303 39.130 0.00 0.00 35.74 2.71
1265 1280 3.944055 ACTCTTAACACGTGCAGATCT 57.056 42.857 17.22 0.00 0.00 2.75
1473 4036 1.283321 GCCTTGAGATCTTGGGACCTT 59.717 52.381 11.96 0.00 0.00 3.50
1872 4442 0.394352 CCGGAGAAATCCCACCAAGG 60.394 60.000 0.00 0.00 37.03 3.61
1936 4507 4.497291 AATAAGCTCACCGGAACCATTA 57.503 40.909 9.46 1.77 0.00 1.90
1999 4570 5.699143 ACCTTGCTGAAAATAGGCTATCAT 58.301 37.500 7.63 0.00 0.00 2.45
2409 4986 8.918202 ACAGTCTTTGTTGGAAATATAAGTGA 57.082 30.769 0.00 0.00 36.31 3.41
2496 5080 4.354087 TGCTCCCATGTCCTACTATCTCTA 59.646 45.833 0.00 0.00 0.00 2.43
2549 5142 7.877003 ACTTACCTGATGATGTAGAGTATTCG 58.123 38.462 0.00 0.00 0.00 3.34
2661 5300 1.494721 GGCCATCTGTAATTCTGGGGA 59.505 52.381 0.00 0.00 0.00 4.81
2687 5330 3.436615 GGACCTTCCCAACCTTCTCTTTT 60.437 47.826 0.00 0.00 0.00 2.27
2853 5545 7.932335 ACTGTTCTAATACTGGAGTTATCGAG 58.068 38.462 0.00 0.00 37.31 4.04
2862 5554 5.172205 ACTGGAGTTATCGAGAAAAAGCTC 58.828 41.667 0.00 0.00 35.04 4.09
2870 5562 7.544566 AGTTATCGAGAAAAAGCTCATAACGAA 59.455 33.333 0.00 0.00 39.89 3.85
2911 5603 4.649674 AGAAAAGTACAGACAGTGTGGAGA 59.350 41.667 0.00 0.00 40.69 3.71
2912 5604 4.323553 AAAGTACAGACAGTGTGGAGAC 57.676 45.455 0.00 0.00 40.69 3.36
2925 5617 3.997021 GTGTGGAGACAGTGTTAGGATTG 59.003 47.826 0.00 0.00 44.46 2.67
2930 5622 5.071788 TGGAGACAGTGTTAGGATTGACTTT 59.928 40.000 0.00 0.00 35.01 2.66
2945 5637 7.775093 AGGATTGACTTTACTTGCATATGCTTA 59.225 33.333 27.13 14.73 42.66 3.09
2997 5689 0.394352 CCATAACAGGCGCCTTTCCT 60.394 55.000 30.60 13.97 0.00 3.36
3026 5718 2.224079 CCTTGTCTTGGTCACATTGTCG 59.776 50.000 0.00 0.00 0.00 4.35
3037 5758 4.748102 GGTCACATTGTCGTTAGTCTCAAA 59.252 41.667 0.00 0.00 0.00 2.69
3119 5841 8.246908 TGAAATGCTTGCATATTTTTCTTCTG 57.753 30.769 8.61 0.00 0.00 3.02
3120 5842 6.657836 AATGCTTGCATATTTTTCTTCTGC 57.342 33.333 8.61 0.00 0.00 4.26
3189 5913 3.012518 AGTAAGCACATTGGTCATCAGC 58.987 45.455 0.00 0.00 0.00 4.26
3225 5964 2.030805 AGGCTGAGTTTGCGTTTCATTC 60.031 45.455 0.00 0.00 0.00 2.67
3259 5998 3.060615 CCTTGCTGCTGGCTGGAC 61.061 66.667 0.00 0.00 42.39 4.02
3269 6008 2.169561 TGCTGGCTGGACATAATAACGA 59.830 45.455 0.00 0.00 0.00 3.85
3275 6014 5.003804 GGCTGGACATAATAACGAATGGAT 58.996 41.667 0.00 0.00 0.00 3.41
3276 6015 5.473504 GGCTGGACATAATAACGAATGGATT 59.526 40.000 0.00 0.00 0.00 3.01
3307 6046 3.985008 ACACAATCAGTAAGCACGTACA 58.015 40.909 0.00 0.00 0.00 2.90
3308 6047 4.566004 ACACAATCAGTAAGCACGTACAT 58.434 39.130 0.00 0.00 0.00 2.29
3309 6048 5.716094 ACACAATCAGTAAGCACGTACATA 58.284 37.500 0.00 0.00 0.00 2.29
3310 6049 6.160684 ACACAATCAGTAAGCACGTACATAA 58.839 36.000 0.00 0.00 0.00 1.90
3311 6050 6.647481 ACACAATCAGTAAGCACGTACATAAA 59.353 34.615 0.00 0.00 0.00 1.40
3312 6051 7.148639 ACACAATCAGTAAGCACGTACATAAAG 60.149 37.037 0.00 0.00 0.00 1.85
3313 6052 6.872020 ACAATCAGTAAGCACGTACATAAAGT 59.128 34.615 0.00 0.00 0.00 2.66
3314 6053 7.386848 ACAATCAGTAAGCACGTACATAAAGTT 59.613 33.333 0.00 0.00 0.00 2.66
3315 6054 6.939551 TCAGTAAGCACGTACATAAAGTTC 57.060 37.500 0.00 0.00 0.00 3.01
3316 6055 6.448852 TCAGTAAGCACGTACATAAAGTTCA 58.551 36.000 0.00 0.00 0.00 3.18
3317 6056 6.924612 TCAGTAAGCACGTACATAAAGTTCAA 59.075 34.615 0.00 0.00 0.00 2.69
3318 6057 7.007697 CAGTAAGCACGTACATAAAGTTCAAC 58.992 38.462 0.00 0.00 0.00 3.18
3319 6058 5.352643 AAGCACGTACATAAAGTTCAACC 57.647 39.130 0.00 0.00 0.00 3.77
3320 6059 4.382291 AGCACGTACATAAAGTTCAACCA 58.618 39.130 0.00 0.00 0.00 3.67
3321 6060 4.817464 AGCACGTACATAAAGTTCAACCAA 59.183 37.500 0.00 0.00 0.00 3.67
3322 6061 5.049680 AGCACGTACATAAAGTTCAACCAAG 60.050 40.000 0.00 0.00 0.00 3.61
3323 6062 5.049954 GCACGTACATAAAGTTCAACCAAGA 60.050 40.000 0.00 0.00 0.00 3.02
3324 6063 6.512091 GCACGTACATAAAGTTCAACCAAGAA 60.512 38.462 0.00 0.00 0.00 2.52
3325 6064 7.581476 CACGTACATAAAGTTCAACCAAGAAT 58.419 34.615 0.00 0.00 0.00 2.40
3326 6065 7.744715 CACGTACATAAAGTTCAACCAAGAATC 59.255 37.037 0.00 0.00 0.00 2.52
3327 6066 7.094933 ACGTACATAAAGTTCAACCAAGAATCC 60.095 37.037 0.00 0.00 0.00 3.01
3328 6067 6.254281 ACATAAAGTTCAACCAAGAATCCG 57.746 37.500 0.00 0.00 0.00 4.18
3329 6068 5.768164 ACATAAAGTTCAACCAAGAATCCGT 59.232 36.000 0.00 0.00 0.00 4.69
3330 6069 6.264518 ACATAAAGTTCAACCAAGAATCCGTT 59.735 34.615 0.00 0.00 0.00 4.44
3331 6070 4.568152 AAGTTCAACCAAGAATCCGTTG 57.432 40.909 0.00 0.00 38.56 4.10
3332 6071 3.551846 AGTTCAACCAAGAATCCGTTGT 58.448 40.909 0.00 0.00 38.39 3.32
3333 6072 3.951680 AGTTCAACCAAGAATCCGTTGTT 59.048 39.130 0.00 0.00 38.39 2.83
3334 6073 4.401202 AGTTCAACCAAGAATCCGTTGTTT 59.599 37.500 0.00 0.00 38.39 2.83
3335 6074 5.591067 AGTTCAACCAAGAATCCGTTGTTTA 59.409 36.000 0.00 0.00 38.39 2.01
3336 6075 5.682943 TCAACCAAGAATCCGTTGTTTAG 57.317 39.130 0.00 0.00 38.39 1.85
3337 6076 4.023536 TCAACCAAGAATCCGTTGTTTAGC 60.024 41.667 0.00 0.00 38.39 3.09
3338 6077 3.751518 ACCAAGAATCCGTTGTTTAGCT 58.248 40.909 0.00 0.00 0.00 3.32
3339 6078 4.142038 ACCAAGAATCCGTTGTTTAGCTT 58.858 39.130 0.00 0.00 0.00 3.74
3340 6079 5.310451 ACCAAGAATCCGTTGTTTAGCTTA 58.690 37.500 0.00 0.00 0.00 3.09
3341 6080 5.411669 ACCAAGAATCCGTTGTTTAGCTTAG 59.588 40.000 0.00 0.00 0.00 2.18
3342 6081 5.411669 CCAAGAATCCGTTGTTTAGCTTAGT 59.588 40.000 0.00 0.00 0.00 2.24
3343 6082 6.307155 CAAGAATCCGTTGTTTAGCTTAGTG 58.693 40.000 0.00 0.00 0.00 2.74
3344 6083 5.548406 AGAATCCGTTGTTTAGCTTAGTGT 58.452 37.500 0.00 0.00 0.00 3.55
3345 6084 5.995897 AGAATCCGTTGTTTAGCTTAGTGTT 59.004 36.000 0.00 0.00 0.00 3.32
3346 6085 5.607119 ATCCGTTGTTTAGCTTAGTGTTG 57.393 39.130 0.00 0.00 0.00 3.33
3347 6086 4.444536 TCCGTTGTTTAGCTTAGTGTTGT 58.555 39.130 0.00 0.00 0.00 3.32
3348 6087 4.877251 TCCGTTGTTTAGCTTAGTGTTGTT 59.123 37.500 0.00 0.00 0.00 2.83
3349 6088 6.047870 TCCGTTGTTTAGCTTAGTGTTGTTA 58.952 36.000 0.00 0.00 0.00 2.41
3350 6089 6.707161 TCCGTTGTTTAGCTTAGTGTTGTTAT 59.293 34.615 0.00 0.00 0.00 1.89
3351 6090 7.013529 CCGTTGTTTAGCTTAGTGTTGTTATC 58.986 38.462 0.00 0.00 0.00 1.75
3352 6091 7.095355 CCGTTGTTTAGCTTAGTGTTGTTATCT 60.095 37.037 0.00 0.00 0.00 1.98
3353 6092 8.280497 CGTTGTTTAGCTTAGTGTTGTTATCTT 58.720 33.333 0.00 0.00 0.00 2.40
3361 6100 9.944376 AGCTTAGTGTTGTTATCTTAAAGATGA 57.056 29.630 0.00 0.00 35.37 2.92
3366 6105 8.873830 AGTGTTGTTATCTTAAAGATGATGACG 58.126 33.333 0.00 0.00 35.37 4.35
3367 6106 8.116753 GTGTTGTTATCTTAAAGATGATGACGG 58.883 37.037 0.00 0.00 35.37 4.79
3368 6107 7.279981 TGTTGTTATCTTAAAGATGATGACGGG 59.720 37.037 0.00 0.00 35.37 5.28
3369 6108 6.884832 TGTTATCTTAAAGATGATGACGGGT 58.115 36.000 0.00 0.00 35.37 5.28
3370 6109 6.984474 TGTTATCTTAAAGATGATGACGGGTC 59.016 38.462 0.00 0.00 35.37 4.46
3371 6110 5.614324 ATCTTAAAGATGATGACGGGTCA 57.386 39.130 3.69 3.69 37.51 4.02
3372 6111 5.414789 TCTTAAAGATGATGACGGGTCAA 57.585 39.130 5.50 0.00 43.58 3.18
3373 6112 5.989477 TCTTAAAGATGATGACGGGTCAAT 58.011 37.500 5.50 0.00 43.58 2.57
3374 6113 5.817296 TCTTAAAGATGATGACGGGTCAATG 59.183 40.000 5.50 0.00 43.58 2.82
3375 6114 3.912496 AAGATGATGACGGGTCAATGA 57.088 42.857 5.50 0.00 43.58 2.57
3376 6115 3.185246 AGATGATGACGGGTCAATGAC 57.815 47.619 4.51 4.51 43.58 3.06
3377 6116 1.860950 GATGATGACGGGTCAATGACG 59.139 52.381 7.35 0.00 43.58 4.35
3378 6117 0.892063 TGATGACGGGTCAATGACGA 59.108 50.000 7.35 0.00 43.58 4.20
3379 6118 1.480545 TGATGACGGGTCAATGACGAT 59.519 47.619 7.35 0.00 43.58 3.73
3380 6119 2.691011 TGATGACGGGTCAATGACGATA 59.309 45.455 7.35 0.00 43.58 2.92
3381 6120 3.320826 TGATGACGGGTCAATGACGATAT 59.679 43.478 7.35 0.00 43.58 1.63
3382 6121 4.521256 TGATGACGGGTCAATGACGATATA 59.479 41.667 7.35 0.00 43.58 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.422402 TGCCTTCTACCGAAAAAGGGT 59.578 47.619 2.82 0.00 39.98 4.34
1 2 1.810755 GTGCCTTCTACCGAAAAAGGG 59.189 52.381 2.82 0.00 39.98 3.95
2 3 1.810755 GGTGCCTTCTACCGAAAAAGG 59.189 52.381 0.00 0.00 42.07 3.11
10 11 0.179045 ATGATGCGGTGCCTTCTACC 60.179 55.000 0.00 0.00 34.81 3.18
11 12 1.221414 GATGATGCGGTGCCTTCTAC 58.779 55.000 0.00 0.00 0.00 2.59
12 13 0.829990 TGATGATGCGGTGCCTTCTA 59.170 50.000 0.00 0.00 0.00 2.10
13 14 0.182061 ATGATGATGCGGTGCCTTCT 59.818 50.000 0.00 0.00 0.00 2.85
22 23 2.463876 ACGACACAGTATGATGATGCG 58.536 47.619 0.00 0.00 39.69 4.73
51 52 9.174166 GGTCAAGTAAACTTATATGTGTTCCAT 57.826 33.333 0.00 0.00 34.58 3.41
63 64 4.981674 CGTACAACGGGTCAAGTAAACTTA 59.018 41.667 0.00 0.00 38.08 2.24
80 81 2.583739 CACCGTCGAATACACGTACAA 58.416 47.619 0.00 0.00 35.39 2.41
94 96 3.869065 TCATTGACTATTTCCCACCGTC 58.131 45.455 0.00 0.00 0.00 4.79
99 101 7.402054 ACACATTACTCATTGACTATTTCCCA 58.598 34.615 0.00 0.00 0.00 4.37
101 103 8.540492 CGTACACATTACTCATTGACTATTTCC 58.460 37.037 0.00 0.00 0.00 3.13
102 104 8.056571 GCGTACACATTACTCATTGACTATTTC 58.943 37.037 0.00 0.00 0.00 2.17
169 171 9.364989 CTTCTTCTTCTACCAGTCTATTCAAAG 57.635 37.037 0.00 0.00 0.00 2.77
173 175 9.930693 TTTTCTTCTTCTTCTACCAGTCTATTC 57.069 33.333 0.00 0.00 0.00 1.75
213 215 0.392461 TCCTGGCGTTGCACTATTCC 60.392 55.000 0.00 0.00 0.00 3.01
785 787 1.472552 CGTCAACCTTGTCAGTGACCA 60.473 52.381 20.43 8.88 0.00 4.02
832 834 1.071385 CGCCCTTATCTGAATCCTGCT 59.929 52.381 0.00 0.00 0.00 4.24
987 1001 2.170166 CCTTCCATTGTTTAGCTGCCA 58.830 47.619 0.00 0.00 0.00 4.92
994 1008 3.258123 GGCTTGCTTCCTTCCATTGTTTA 59.742 43.478 0.00 0.00 0.00 2.01
999 1013 1.598701 GCGGCTTGCTTCCTTCCATT 61.599 55.000 0.00 0.00 41.73 3.16
1054 1068 6.093771 CACTAGTAACGAGGACAACAGAGTAT 59.906 42.308 0.00 0.00 0.00 2.12
1101 1115 5.587043 ACTGAAACCACGACACTTATTTTGA 59.413 36.000 0.00 0.00 0.00 2.69
1151 1165 1.268999 GCAGCAATGACAAAACCGACA 60.269 47.619 0.00 0.00 0.00 4.35
1265 1280 2.945440 GCACATGTAAGATTGCCTCCCA 60.945 50.000 0.00 0.00 0.00 4.37
1999 4570 1.137594 AGGGTTTCCGGGATTCCACA 61.138 55.000 16.26 0.00 38.33 4.17
2425 5002 2.237893 CCACCGGTTACCTCCAATACTT 59.762 50.000 2.97 0.00 0.00 2.24
2520 5108 9.815306 ATACTCTACATCATCAGGTAAGTACAT 57.185 33.333 0.00 0.00 0.00 2.29
2521 5109 9.642343 AATACTCTACATCATCAGGTAAGTACA 57.358 33.333 0.00 0.00 0.00 2.90
2523 5111 9.000486 CGAATACTCTACATCATCAGGTAAGTA 58.000 37.037 0.00 0.00 0.00 2.24
2524 5112 7.502895 ACGAATACTCTACATCATCAGGTAAGT 59.497 37.037 0.00 0.00 0.00 2.24
2525 5113 7.877003 ACGAATACTCTACATCATCAGGTAAG 58.123 38.462 0.00 0.00 0.00 2.34
2526 5114 7.818997 ACGAATACTCTACATCATCAGGTAA 57.181 36.000 0.00 0.00 0.00 2.85
2549 5142 6.756542 GGTGGCATGAAACCAAATATTAGAAC 59.243 38.462 11.32 0.00 39.39 3.01
2645 5284 4.054369 TCCCAATCCCCAGAATTACAGAT 58.946 43.478 0.00 0.00 0.00 2.90
2647 5286 3.555966 GTCCCAATCCCCAGAATTACAG 58.444 50.000 0.00 0.00 0.00 2.74
2687 5330 5.050159 CGATCTCACCGAATCATTTATTGCA 60.050 40.000 0.00 0.00 0.00 4.08
2853 5545 6.378582 TGTCCAATTCGTTATGAGCTTTTTC 58.621 36.000 0.00 0.00 0.00 2.29
2862 5554 5.088739 GCTTTGACTGTCCAATTCGTTATG 58.911 41.667 5.17 0.00 0.00 1.90
2870 5562 3.777106 TCTCTGCTTTGACTGTCCAAT 57.223 42.857 5.17 0.00 0.00 3.16
2911 5603 6.204882 GCAAGTAAAGTCAATCCTAACACTGT 59.795 38.462 0.00 0.00 0.00 3.55
2912 5604 6.204688 TGCAAGTAAAGTCAATCCTAACACTG 59.795 38.462 0.00 0.00 0.00 3.66
2925 5617 6.542370 TCCCTTAAGCATATGCAAGTAAAGTC 59.458 38.462 28.62 0.00 45.16 3.01
2930 5622 5.130350 GGTTCCCTTAAGCATATGCAAGTA 58.870 41.667 28.62 14.77 45.16 2.24
2980 5672 2.116238 TCTAGGAAAGGCGCCTGTTAT 58.884 47.619 33.60 19.53 36.96 1.89
3026 5718 6.877322 TGTAAGCAGGGTAATTTGAGACTAAC 59.123 38.462 0.00 0.00 0.00 2.34
3037 5758 8.090788 TCTCTCTATTTTGTAAGCAGGGTAAT 57.909 34.615 0.00 0.00 0.00 1.89
3096 5817 6.877322 AGCAGAAGAAAAATATGCAAGCATTT 59.123 30.769 13.32 2.28 39.34 2.32
3189 5913 2.754552 TCAGCCTCCAAAATCCGAATTG 59.245 45.455 0.00 0.00 0.00 2.32
3225 5964 3.181516 GCAAGGAGAAAACTGCTATCACG 60.182 47.826 0.00 0.00 0.00 4.35
3269 6008 8.352137 TGATTGTGTTCTATGTTCAATCCATT 57.648 30.769 11.75 0.00 41.73 3.16
3275 6014 7.443879 TGCTTACTGATTGTGTTCTATGTTCAA 59.556 33.333 0.00 0.00 0.00 2.69
3276 6015 6.934083 TGCTTACTGATTGTGTTCTATGTTCA 59.066 34.615 0.00 0.00 0.00 3.18
3307 6046 6.264518 ACAACGGATTCTTGGTTGAACTTTAT 59.735 34.615 16.79 0.00 42.70 1.40
3308 6047 5.591067 ACAACGGATTCTTGGTTGAACTTTA 59.409 36.000 16.79 0.00 42.70 1.85
3309 6048 4.401202 ACAACGGATTCTTGGTTGAACTTT 59.599 37.500 16.79 0.00 42.70 2.66
3310 6049 3.951680 ACAACGGATTCTTGGTTGAACTT 59.048 39.130 16.79 0.02 42.70 2.66
3311 6050 3.551846 ACAACGGATTCTTGGTTGAACT 58.448 40.909 16.79 0.27 42.70 3.01
3312 6051 3.982576 ACAACGGATTCTTGGTTGAAC 57.017 42.857 16.79 0.00 42.70 3.18
3313 6052 4.993029 AAACAACGGATTCTTGGTTGAA 57.007 36.364 16.79 0.00 42.70 2.69
3314 6053 4.023536 GCTAAACAACGGATTCTTGGTTGA 60.024 41.667 16.79 0.00 42.70 3.18
3315 6054 4.023193 AGCTAAACAACGGATTCTTGGTTG 60.023 41.667 11.51 11.51 44.90 3.77
3316 6055 4.142038 AGCTAAACAACGGATTCTTGGTT 58.858 39.130 0.00 0.00 33.13 3.67
3317 6056 3.751518 AGCTAAACAACGGATTCTTGGT 58.248 40.909 0.00 0.00 0.00 3.67
3318 6057 4.766404 AAGCTAAACAACGGATTCTTGG 57.234 40.909 0.00 0.00 0.00 3.61
3319 6058 6.073222 ACACTAAGCTAAACAACGGATTCTTG 60.073 38.462 0.00 0.00 0.00 3.02
3320 6059 5.995897 ACACTAAGCTAAACAACGGATTCTT 59.004 36.000 0.00 0.00 0.00 2.52
3321 6060 5.548406 ACACTAAGCTAAACAACGGATTCT 58.452 37.500 0.00 0.00 0.00 2.40
3322 6061 5.857822 ACACTAAGCTAAACAACGGATTC 57.142 39.130 0.00 0.00 0.00 2.52
3323 6062 5.529800 ACAACACTAAGCTAAACAACGGATT 59.470 36.000 0.00 0.00 0.00 3.01
3324 6063 5.061179 ACAACACTAAGCTAAACAACGGAT 58.939 37.500 0.00 0.00 0.00 4.18
3325 6064 4.444536 ACAACACTAAGCTAAACAACGGA 58.555 39.130 0.00 0.00 0.00 4.69
3326 6065 4.806342 ACAACACTAAGCTAAACAACGG 57.194 40.909 0.00 0.00 0.00 4.44
3327 6066 7.793902 AGATAACAACACTAAGCTAAACAACG 58.206 34.615 0.00 0.00 0.00 4.10
3335 6074 9.944376 TCATCTTTAAGATAACAACACTAAGCT 57.056 29.630 7.18 0.00 32.12 3.74
3340 6079 8.873830 CGTCATCATCTTTAAGATAACAACACT 58.126 33.333 7.18 0.00 32.12 3.55
3341 6080 8.116753 CCGTCATCATCTTTAAGATAACAACAC 58.883 37.037 7.18 0.25 32.12 3.32
3342 6081 7.279981 CCCGTCATCATCTTTAAGATAACAACA 59.720 37.037 7.18 0.00 32.12 3.33
3343 6082 7.280205 ACCCGTCATCATCTTTAAGATAACAAC 59.720 37.037 7.18 3.95 32.12 3.32
3344 6083 7.335627 ACCCGTCATCATCTTTAAGATAACAA 58.664 34.615 7.18 0.00 32.12 2.83
3345 6084 6.884832 ACCCGTCATCATCTTTAAGATAACA 58.115 36.000 7.18 0.00 32.12 2.41
3346 6085 6.984474 TGACCCGTCATCATCTTTAAGATAAC 59.016 38.462 7.18 3.64 31.60 1.89
3347 6086 7.119709 TGACCCGTCATCATCTTTAAGATAA 57.880 36.000 7.18 0.00 31.60 1.75
3348 6087 6.724893 TGACCCGTCATCATCTTTAAGATA 57.275 37.500 7.18 0.00 31.60 1.98
3349 6088 5.614324 TGACCCGTCATCATCTTTAAGAT 57.386 39.130 0.99 0.99 32.81 2.40
3350 6089 5.414789 TTGACCCGTCATCATCTTTAAGA 57.585 39.130 0.00 0.00 39.64 2.10
3351 6090 5.817296 TCATTGACCCGTCATCATCTTTAAG 59.183 40.000 0.00 0.00 39.64 1.85
3352 6091 5.584649 GTCATTGACCCGTCATCATCTTTAA 59.415 40.000 5.44 0.00 39.64 1.52
3353 6092 5.116180 GTCATTGACCCGTCATCATCTTTA 58.884 41.667 5.44 0.00 39.64 1.85
3354 6093 3.941483 GTCATTGACCCGTCATCATCTTT 59.059 43.478 5.44 0.00 39.64 2.52
3355 6094 3.535561 GTCATTGACCCGTCATCATCTT 58.464 45.455 5.44 0.00 39.64 2.40
3356 6095 2.481969 CGTCATTGACCCGTCATCATCT 60.482 50.000 11.12 0.00 39.64 2.90
3357 6096 1.860950 CGTCATTGACCCGTCATCATC 59.139 52.381 11.12 0.00 39.64 2.92
3358 6097 1.480545 TCGTCATTGACCCGTCATCAT 59.519 47.619 11.12 0.00 39.64 2.45
3359 6098 0.892063 TCGTCATTGACCCGTCATCA 59.108 50.000 11.12 0.00 39.64 3.07
3360 6099 2.225068 ATCGTCATTGACCCGTCATC 57.775 50.000 11.12 0.00 39.64 2.92


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

AutoCloner maintained by Alex Coulton.