Multiple sequence alignment - TraesCS1D01G080200

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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 TraesCS1D01G080200 chr1D 100.000 3508 0 0 1 3508 62792605 62796112 0.000000e+00 6479.0
1 TraesCS1D01G080200 chr1B 96.038 1464 55 3 1572 3034 100052680 100054141 0.000000e+00 2379.0
2 TraesCS1D01G080200 chr1B 93.727 1100 56 8 243 1334 100044445 100045539 0.000000e+00 1637.0
3 TraesCS1D01G080200 chr1B 91.213 239 14 5 3271 3508 100055788 100056020 5.650000e-83 318.0
4 TraesCS1D01G080200 chr1B 94.318 176 10 0 1398 1573 519817796 519817971 1.600000e-68 270.0
5 TraesCS1D01G080200 chr1B 96.503 143 5 0 3036 3178 100055336 100055478 1.630000e-58 237.0
6 TraesCS1D01G080200 chr1B 95.349 129 5 1 102 229 100044359 100044231 1.650000e-48 204.0
7 TraesCS1D01G080200 chr1B 98.750 80 1 0 3207 3286 100055757 100055836 3.650000e-30 143.0
8 TraesCS1D01G080200 chr1B 92.000 75 6 0 1 75 100044432 100044358 4.790000e-19 106.0
9 TraesCS1D01G080200 chr1A 91.646 1592 116 14 1572 3156 60911109 60912690 0.000000e+00 2187.0
10 TraesCS1D01G080200 chr1A 87.278 731 52 24 693 1410 60910239 60910941 0.000000e+00 797.0
11 TraesCS1D01G080200 chr1A 90.862 580 26 12 1 554 60875187 60875765 0.000000e+00 752.0
12 TraesCS1D01G080200 chr1A 88.809 277 18 2 345 610 60878176 60878450 9.390000e-86 327.0
13 TraesCS1D01G080200 chr1A 86.667 255 22 6 693 937 60875907 60876159 4.460000e-69 272.0
14 TraesCS1D01G080200 chr1A 84.444 90 13 1 2669 2757 438651336 438651425 1.730000e-13 87.9
15 TraesCS1D01G080200 chr5A 86.582 1021 106 24 1653 2651 614364073 614365084 0.000000e+00 1098.0
16 TraesCS1D01G080200 chr5A 82.006 678 65 26 711 1359 614363306 614363955 1.120000e-144 523.0
17 TraesCS1D01G080200 chr5A 79.811 530 49 25 1 498 614362681 614363184 2.020000e-87 333.0
18 TraesCS1D01G080200 chr5D 84.940 1089 137 21 1572 2651 491792372 491793442 0.000000e+00 1077.0
19 TraesCS1D01G080200 chr5D 83.936 747 70 24 693 1410 491791648 491792373 0.000000e+00 669.0
20 TraesCS1D01G080200 chr5D 90.598 234 11 7 7 229 491791070 491791303 2.050000e-77 300.0
21 TraesCS1D01G080200 chr5D 93.855 179 10 1 1396 1573 560061525 560061347 5.770000e-68 268.0
22 TraesCS1D01G080200 chr5B 84.172 1093 132 30 1572 2650 606849852 606850917 0.000000e+00 1022.0
23 TraesCS1D01G080200 chr5B 83.692 650 58 23 693 1315 606849094 606849722 1.410000e-158 569.0
24 TraesCS1D01G080200 chr5B 88.462 234 21 4 1 229 606846870 606847102 9.590000e-71 278.0
25 TraesCS1D01G080200 chrUn 95.473 486 21 1 1572 2057 287999271 287999755 0.000000e+00 774.0
26 TraesCS1D01G080200 chr6D 94.915 177 6 3 1402 1577 389700712 389700538 1.240000e-69 274.0
27 TraesCS1D01G080200 chr6D 93.750 176 10 1 1399 1573 406391534 406391359 2.690000e-66 263.0
28 TraesCS1D01G080200 chr4D 93.889 180 9 2 1403 1581 359125478 359125656 1.600000e-68 270.0
29 TraesCS1D01G080200 chr4D 95.266 169 8 0 1406 1574 11572375 11572543 5.770000e-68 268.0
30 TraesCS1D01G080200 chr7D 94.767 172 8 1 1406 1577 39001282 39001452 2.080000e-67 267.0
31 TraesCS1D01G080200 chr2D 94.220 173 10 0 1401 1573 426427793 426427965 7.470000e-67 265.0
32 TraesCS1D01G080200 chr2A 93.785 177 9 2 1398 1573 746757165 746756990 7.470000e-67 265.0
33 TraesCS1D01G080200 chr4A 84.615 91 12 2 2669 2757 32686551 32686461 4.820000e-14 89.8
34 TraesCS1D01G080200 chr4A 84.706 85 12 1 2669 2752 687284688 687284604 2.240000e-12 84.2
35 TraesCS1D01G080200 chr6A 83.158 95 12 4 2652 2744 115267120 115267212 2.240000e-12 84.2
36 TraesCS1D01G080200 chr7B 83.333 90 13 2 2669 2757 623563521 623563433 8.070000e-12 82.4
37 TraesCS1D01G080200 chr3D 83.333 90 13 2 2669 2756 345466570 345466659 8.070000e-12 82.4
38 TraesCS1D01G080200 chr3B 83.333 90 14 1 2669 2757 508259211 508259122 8.070000e-12 82.4


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 TraesCS1D01G080200 chr1D 62792605 62796112 3507 False 6479.000000 6479 100.000000 1 3508 1 chr1D.!!$F1 3507
1 TraesCS1D01G080200 chr1B 100044445 100045539 1094 False 1637.000000 1637 93.727000 243 1334 1 chr1B.!!$F1 1091
2 TraesCS1D01G080200 chr1B 100052680 100056020 3340 False 769.250000 2379 95.626000 1572 3508 4 chr1B.!!$F3 1936
3 TraesCS1D01G080200 chr1A 60910239 60912690 2451 False 1492.000000 2187 89.462000 693 3156 2 chr1A.!!$F3 2463
4 TraesCS1D01G080200 chr1A 60875187 60878450 3263 False 450.333333 752 88.779333 1 937 3 chr1A.!!$F2 936
5 TraesCS1D01G080200 chr5A 614362681 614365084 2403 False 651.333333 1098 82.799667 1 2651 3 chr5A.!!$F1 2650
6 TraesCS1D01G080200 chr5D 491791070 491793442 2372 False 682.000000 1077 86.491333 7 2651 3 chr5D.!!$F1 2644
7 TraesCS1D01G080200 chr5B 606846870 606850917 4047 False 623.000000 1022 85.442000 1 2650 3 chr5B.!!$F1 2649

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
415 1781 0.622665 ATGCCAAACAGAGGGAGAGG 59.377 55.000 0.00 0.0 0.00 3.69 F
554 1959 1.340017 TGCCAACCTAGCTAGCCTTTG 60.340 52.381 15.74 15.8 0.00 2.77 F
1892 3703 1.000396 GGACATCCTGGCCTTTGCT 60.000 57.895 3.32 0.0 44.12 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 2984 0.375454 TTTCAAACTGTGGCGTGACG 59.625 50.0 0.00 0.0 0.00 4.35 R
2174 4029 0.605589 GCGGGCACACCTTCTTTAGT 60.606 55.0 0.00 0.0 36.97 2.24 R
2950 4914 0.755327 AAACTGTGTGCACTTCCCCC 60.755 55.0 19.41 0.0 0.00 5.40 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
97 134 1.362768 TTAGTGCGCTTCATGCTCAG 58.637 50.000 9.73 0.00 37.04 3.35
229 269 2.224066 GGTTGAATCGAGTCGATCCCAT 60.224 50.000 27.18 12.65 46.30 4.00
232 272 3.487372 TGAATCGAGTCGATCCCATACT 58.513 45.455 27.18 10.77 46.30 2.12
233 273 3.253432 TGAATCGAGTCGATCCCATACTG 59.747 47.826 27.18 0.00 46.30 2.74
234 274 1.605753 TCGAGTCGATCCCATACTGG 58.394 55.000 12.09 0.00 37.25 4.00
237 277 2.225963 CGAGTCGATCCCATACTGGTAC 59.774 54.545 6.73 0.00 35.17 3.34
239 279 3.827302 GAGTCGATCCCATACTGGTACAT 59.173 47.826 0.00 0.00 38.20 2.29
240 280 4.223953 AGTCGATCCCATACTGGTACATT 58.776 43.478 0.00 0.00 38.20 2.71
241 281 4.039245 AGTCGATCCCATACTGGTACATTG 59.961 45.833 0.00 0.00 38.20 2.82
267 325 4.587262 ACCACCCTTTAATTCAAGTTGACC 59.413 41.667 4.68 0.00 0.00 4.02
297 359 6.039616 GTCAAACAAACACTGCCTTGATTAA 58.960 36.000 0.00 0.00 34.44 1.40
305 367 2.505819 ACTGCCTTGATTAACGGGAGAT 59.494 45.455 11.82 0.00 38.40 2.75
415 1781 0.622665 ATGCCAAACAGAGGGAGAGG 59.377 55.000 0.00 0.00 0.00 3.69
448 1814 1.665679 AGAAGCCGCATTGTGTTATCG 59.334 47.619 0.00 0.00 0.00 2.92
465 1831 3.712907 GCTAACTGCCGGTGGGGA 61.713 66.667 1.90 0.00 38.47 4.81
554 1959 1.340017 TGCCAACCTAGCTAGCCTTTG 60.340 52.381 15.74 15.80 0.00 2.77
940 2652 3.350219 ACCACAGTATTGTCACCATCC 57.650 47.619 0.00 0.00 34.62 3.51
943 2655 3.273434 CACAGTATTGTCACCATCCAGG 58.727 50.000 0.00 0.00 38.44 4.45
1077 2806 3.362399 CTCTGTGTCGATGGCCGCT 62.362 63.158 0.00 0.00 38.37 5.52
1078 2807 3.190849 CTGTGTCGATGGCCGCTG 61.191 66.667 0.00 0.00 38.37 5.18
1079 2808 4.758251 TGTGTCGATGGCCGCTGG 62.758 66.667 0.00 0.00 38.37 4.85
1242 2971 3.167485 TGTCAGGGTACGTACCTCAATT 58.833 45.455 36.70 18.68 45.72 2.32
1243 2972 3.194116 TGTCAGGGTACGTACCTCAATTC 59.806 47.826 36.70 22.54 45.72 2.17
1249 2984 4.152938 GGGTACGTACCTCAATTCAAACAC 59.847 45.833 36.70 16.66 45.72 3.32
1251 2986 3.460103 ACGTACCTCAATTCAAACACGT 58.540 40.909 0.00 0.00 36.63 4.49
1257 2992 1.003331 TCAATTCAAACACGTCACGCC 60.003 47.619 0.00 0.00 0.00 5.68
1368 3156 4.755411 TCCATTCTTGAATACGTGAGACC 58.245 43.478 0.00 0.00 0.00 3.85
1373 3161 4.998788 TCTTGAATACGTGAGACCATCTG 58.001 43.478 0.00 0.00 0.00 2.90
1420 3212 6.864151 ATTTTAACTACTACTCCCTCCGTT 57.136 37.500 0.00 0.00 0.00 4.44
1423 3215 1.921748 ACTACTACTCCCTCCGTTCCT 59.078 52.381 0.00 0.00 0.00 3.36
1429 3221 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1430 3222 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
1432 3224 7.786464 ACTACTCCCTCCGTTCCTAAATATTTA 59.214 37.037 7.66 7.66 0.00 1.40
1433 3225 7.628501 ACTCCCTCCGTTCCTAAATATTTAT 57.371 36.000 8.34 0.00 0.00 1.40
1437 3229 9.703677 TCCCTCCGTTCCTAAATATTTATTTTT 57.296 29.630 8.34 0.00 37.16 1.94
1474 3266 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
1475 3267 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
1476 3268 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
1477 3269 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
1479 3271 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
1481 3273 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
1482 3274 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
1484 3276 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
1512 3304 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
1513 3305 7.983307 AGAGTGTAGATTCATTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
1515 3307 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
1516 3308 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
1517 3309 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
1518 3310 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
1519 3311 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
1520 3312 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
1521 3313 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
1522 3314 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
1525 3317 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1526 3318 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
1527 3319 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
1529 3321 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
1531 3323 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
1532 3324 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
1534 3326 5.005779 GCTCCGTATGTAGTCATTTGTTGAG 59.994 44.000 0.00 0.00 34.17 3.02
1536 3328 6.873997 TCCGTATGTAGTCATTTGTTGAGAT 58.126 36.000 0.00 0.00 34.17 2.75
1537 3329 6.978659 TCCGTATGTAGTCATTTGTTGAGATC 59.021 38.462 0.00 0.00 34.17 2.75
1538 3330 6.980978 CCGTATGTAGTCATTTGTTGAGATCT 59.019 38.462 0.00 0.00 34.17 2.75
1539 3331 7.168302 CCGTATGTAGTCATTTGTTGAGATCTC 59.832 40.741 16.21 16.21 34.17 2.75
1540 3332 7.918033 CGTATGTAGTCATTTGTTGAGATCTCT 59.082 37.037 22.95 0.00 34.17 3.10
1544 3336 9.996554 TGTAGTCATTTGTTGAGATCTCTAAAA 57.003 29.630 22.95 18.62 34.17 1.52
1547 3339 9.784531 AGTCATTTGTTGAGATCTCTAAAAAGA 57.215 29.630 22.95 17.47 34.17 2.52
1548 3340 9.818796 GTCATTTGTTGAGATCTCTAAAAAGAC 57.181 33.333 22.95 22.75 34.17 3.01
1549 3341 9.559732 TCATTTGTTGAGATCTCTAAAAAGACA 57.440 29.630 22.95 12.53 0.00 3.41
1610 3411 7.112779 AGAATAGAACAGGTTAGGTGGAAATG 58.887 38.462 0.00 0.00 0.00 2.32
1874 3685 3.414700 GGCGTTGTCTCCTGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
1892 3703 1.000396 GGACATCCTGGCCTTTGCT 60.000 57.895 3.32 0.00 44.12 3.91
1908 3719 2.357517 CTGCACGTGACTCCACCC 60.358 66.667 22.23 0.00 40.12 4.61
1946 3757 1.077501 CTTCCACATGCCATCCGGT 60.078 57.895 0.00 0.00 33.28 5.28
2762 4628 3.880490 GGACTATCAAACAACCACACACA 59.120 43.478 0.00 0.00 0.00 3.72
2901 4865 3.790089 ATAACAACCCTATGCCCTAGC 57.210 47.619 0.00 0.00 40.48 3.42
3026 4990 5.740406 CATACTTGCAGCAAAAACCTTTTG 58.260 37.500 9.65 7.37 0.00 2.44
3122 6279 6.313744 ACTTTTATCAATATTACCTGCGGC 57.686 37.500 0.00 0.00 0.00 6.53
3170 6327 5.794894 ACTAGGATGAGTTTCGTCAAATGT 58.205 37.500 0.00 0.00 34.15 2.71
3174 6331 5.122869 AGGATGAGTTTCGTCAAATGTCATG 59.877 40.000 1.21 0.00 34.15 3.07
3178 6335 6.887368 TGAGTTTCGTCAAATGTCATGTAAG 58.113 36.000 0.00 0.00 0.00 2.34
3180 6337 7.095649 TGAGTTTCGTCAAATGTCATGTAAGAG 60.096 37.037 0.00 0.00 0.00 2.85
3181 6338 6.929049 AGTTTCGTCAAATGTCATGTAAGAGA 59.071 34.615 0.00 0.00 0.00 3.10
3182 6339 6.951256 TTCGTCAAATGTCATGTAAGAGAG 57.049 37.500 0.00 0.00 0.00 3.20
3183 6340 4.864806 TCGTCAAATGTCATGTAAGAGAGC 59.135 41.667 0.00 0.00 0.00 4.09
3184 6341 4.033358 CGTCAAATGTCATGTAAGAGAGCC 59.967 45.833 0.00 0.00 0.00 4.70
3185 6342 4.333926 GTCAAATGTCATGTAAGAGAGCCC 59.666 45.833 0.00 0.00 0.00 5.19
3186 6343 3.567478 AATGTCATGTAAGAGAGCCCC 57.433 47.619 0.00 0.00 0.00 5.80
3187 6344 1.204146 TGTCATGTAAGAGAGCCCCC 58.796 55.000 0.00 0.00 0.00 5.40
3188 6345 1.273838 TGTCATGTAAGAGAGCCCCCT 60.274 52.381 0.00 0.00 0.00 4.79
3189 6346 1.414550 GTCATGTAAGAGAGCCCCCTC 59.585 57.143 0.00 0.00 38.42 4.30
3190 6347 0.761802 CATGTAAGAGAGCCCCCTCC 59.238 60.000 0.00 0.00 38.96 4.30
3191 6348 0.400670 ATGTAAGAGAGCCCCCTCCC 60.401 60.000 0.00 0.00 38.96 4.30
3192 6349 1.766864 GTAAGAGAGCCCCCTCCCC 60.767 68.421 0.00 0.00 38.96 4.81
3193 6350 3.036045 TAAGAGAGCCCCCTCCCCC 62.036 68.421 0.00 0.00 38.96 5.40
3300 6707 6.559042 CACAACTGTGCTAGAAACAAAAAG 57.441 37.500 0.00 0.00 39.39 2.27
3301 6708 5.516339 CACAACTGTGCTAGAAACAAAAAGG 59.484 40.000 0.00 0.00 39.39 3.11
3302 6709 5.185056 ACAACTGTGCTAGAAACAAAAAGGT 59.815 36.000 0.00 0.00 0.00 3.50
3303 6710 5.914898 ACTGTGCTAGAAACAAAAAGGTT 57.085 34.783 0.00 0.00 0.00 3.50
3304 6711 7.094118 ACAACTGTGCTAGAAACAAAAAGGTTA 60.094 33.333 0.00 0.00 0.00 2.85
3305 6712 7.399245 ACTGTGCTAGAAACAAAAAGGTTAA 57.601 32.000 0.00 0.00 0.00 2.01
3306 6713 7.832769 ACTGTGCTAGAAACAAAAAGGTTAAA 58.167 30.769 0.00 0.00 0.00 1.52
3307 6714 8.308207 ACTGTGCTAGAAACAAAAAGGTTAAAA 58.692 29.630 0.00 0.00 0.00 1.52
3308 6715 9.145865 CTGTGCTAGAAACAAAAAGGTTAAAAA 57.854 29.630 0.00 0.00 0.00 1.94
3309 6716 9.145865 TGTGCTAGAAACAAAAAGGTTAAAAAG 57.854 29.630 0.00 0.00 0.00 2.27
3310 6717 8.114290 GTGCTAGAAACAAAAAGGTTAAAAAGC 58.886 33.333 0.00 0.00 0.00 3.51
3311 6718 7.819900 TGCTAGAAACAAAAAGGTTAAAAAGCA 59.180 29.630 0.00 0.00 33.70 3.91
3312 6719 8.114290 GCTAGAAACAAAAAGGTTAAAAAGCAC 58.886 33.333 0.00 0.00 0.00 4.40
3313 6720 7.971183 AGAAACAAAAAGGTTAAAAAGCACA 57.029 28.000 0.00 0.00 0.00 4.57
3314 6721 8.384607 AGAAACAAAAAGGTTAAAAAGCACAA 57.615 26.923 0.00 0.00 0.00 3.33
3315 6722 8.286800 AGAAACAAAAAGGTTAAAAAGCACAAC 58.713 29.630 0.00 0.00 0.00 3.32
3316 6723 7.737972 AACAAAAAGGTTAAAAAGCACAACT 57.262 28.000 0.00 0.00 0.00 3.16
3317 6724 7.127917 ACAAAAAGGTTAAAAAGCACAACTG 57.872 32.000 0.00 0.00 0.00 3.16
3318 6725 6.708502 ACAAAAAGGTTAAAAAGCACAACTGT 59.291 30.769 0.00 0.00 0.00 3.55
3440 7782 6.827586 TGTTGAAACCTATTAACATGGGAC 57.172 37.500 0.00 0.00 34.53 4.46
3441 7783 6.548321 TGTTGAAACCTATTAACATGGGACT 58.452 36.000 0.00 0.00 34.53 3.85
3488 7831 8.477419 AGAAATTCAAGGGTGAAAACAGATTA 57.523 30.769 0.00 0.00 46.66 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 151 3.513912 ACGTTCCTATGTGAGATGAACCA 59.486 43.478 0.00 0.00 33.48 3.67
116 153 4.265556 CGAACGTTCCTATGTGAGATGAAC 59.734 45.833 22.07 0.00 33.66 3.18
188 228 0.107800 TCAACCCCAACGTTCGTTGA 60.108 50.000 30.69 22.04 45.80 3.18
229 269 4.169666 AGGGTGGTTACAATGTACCAGTA 58.830 43.478 12.66 0.00 44.66 2.74
232 272 4.456662 AAAGGGTGGTTACAATGTACCA 57.543 40.909 9.55 9.55 41.97 3.25
233 273 7.177041 TGAATTAAAGGGTGGTTACAATGTACC 59.823 37.037 0.00 0.00 34.93 3.34
234 274 8.113173 TGAATTAAAGGGTGGTTACAATGTAC 57.887 34.615 0.00 0.00 0.00 2.90
237 277 7.666623 ACTTGAATTAAAGGGTGGTTACAATG 58.333 34.615 7.49 0.00 0.00 2.82
239 279 7.342284 TCAACTTGAATTAAAGGGTGGTTACAA 59.658 33.333 7.49 0.00 0.00 2.41
240 280 6.834451 TCAACTTGAATTAAAGGGTGGTTACA 59.166 34.615 7.49 0.00 0.00 2.41
241 281 7.143340 GTCAACTTGAATTAAAGGGTGGTTAC 58.857 38.462 7.49 0.00 0.00 2.50
278 336 3.004315 CCGTTAATCAAGGCAGTGTTTGT 59.996 43.478 8.66 0.00 0.00 2.83
297 359 1.139058 GCTGTGGACATTATCTCCCGT 59.861 52.381 0.00 0.00 0.00 5.28
448 1814 3.043999 ATCCCCACCGGCAGTTAGC 62.044 63.158 0.00 0.00 44.65 3.09
465 1831 8.292448 CAGCTTAGTTGATGACTTTGTTTACAT 58.708 33.333 0.00 0.00 39.86 2.29
943 2655 2.147150 GAAAGACACTTGCAGGGAGTC 58.853 52.381 13.45 13.45 0.00 3.36
1242 2971 1.425267 CTGTGGCGTGACGTGTTTGA 61.425 55.000 6.91 0.00 0.00 2.69
1243 2972 1.011242 CTGTGGCGTGACGTGTTTG 60.011 57.895 6.91 0.00 0.00 2.93
1249 2984 0.375454 TTTCAAACTGTGGCGTGACG 59.625 50.000 0.00 0.00 0.00 4.35
1251 2986 1.131504 GTGTTTCAAACTGTGGCGTGA 59.868 47.619 1.10 0.00 0.00 4.35
1257 2992 4.654091 ATCCCAAGTGTTTCAAACTGTG 57.346 40.909 1.10 0.00 0.00 3.66
1330 3095 8.972127 TCAAGAATGGATATAGGAGTAGTATGC 58.028 37.037 0.00 0.00 0.00 3.14
1368 3156 3.793797 TCAATGCATGCTTTCCAGATG 57.206 42.857 20.33 6.79 0.00 2.90
1373 3161 4.563061 AGAAACTTCAATGCATGCTTTCC 58.437 39.130 20.33 4.00 0.00 3.13
1437 3229 9.137459 TGTGGTAGTCCATTTGAAATTTCTAAA 57.863 29.630 18.64 15.99 46.20 1.85
1438 3230 8.698973 TGTGGTAGTCCATTTGAAATTTCTAA 57.301 30.769 18.64 17.10 46.20 2.10
1448 3240 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
1450 3242 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
1451 3243 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
1455 3247 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
1487 3279 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
1488 3280 7.066766 GGAGCAAAATGAATGAATCTACACTCT 59.933 37.037 0.00 0.00 0.00 3.24
1489 3281 7.192232 GGAGCAAAATGAATGAATCTACACTC 58.808 38.462 0.00 0.00 0.00 3.51
1490 3282 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
1491 3283 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
1492 3284 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
1493 3285 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
1494 3286 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
1495 3287 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
1497 3289 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
1498 3290 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
1499 3291 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
1500 3292 6.037062 TGACTACATACGGAGCAAAATGAATG 59.963 38.462 0.00 0.00 0.00 2.67
1502 3294 5.483811 TGACTACATACGGAGCAAAATGAA 58.516 37.500 0.00 0.00 0.00 2.57
1503 3295 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
1504 3296 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
1505 3297 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
1506 3298 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
1507 3299 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
1508 3300 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
1509 3301 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
1510 3302 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
1511 3303 6.330278 TCTCAACAAATGACTACATACGGAG 58.670 40.000 0.00 0.00 35.50 4.63
1512 3304 6.275494 TCTCAACAAATGACTACATACGGA 57.725 37.500 0.00 0.00 35.50 4.69
1513 3305 6.980978 AGATCTCAACAAATGACTACATACGG 59.019 38.462 0.00 0.00 35.50 4.02
1518 3310 9.996554 TTTTAGAGATCTCAACAAATGACTACA 57.003 29.630 24.39 2.96 33.47 2.74
1521 3313 9.784531 TCTTTTTAGAGATCTCAACAAATGACT 57.215 29.630 24.39 2.42 33.47 3.41
1522 3314 9.818796 GTCTTTTTAGAGATCTCAACAAATGAC 57.181 33.333 24.39 24.76 33.47 3.06
1541 3333 9.908152 CCTCCGTTTCTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
1544 3336 7.399634 TCCCTCCGTTTCTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
1546 3338 6.822170 ACTCCCTCCGTTTCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
1547 3339 6.718294 ACTCCCTCCGTTTCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
1548 3340 8.610035 GTTACTCCCTCCGTTTCTAAATATTTG 58.390 37.037 11.05 1.65 0.00 2.32
1549 3341 8.323567 TGTTACTCCCTCCGTTTCTAAATATTT 58.676 33.333 5.89 5.89 0.00 1.40
1550 3342 7.854337 TGTTACTCCCTCCGTTTCTAAATATT 58.146 34.615 0.00 0.00 0.00 1.28
1551 3343 7.427989 TGTTACTCCCTCCGTTTCTAAATAT 57.572 36.000 0.00 0.00 0.00 1.28
1552 3344 6.855763 TGTTACTCCCTCCGTTTCTAAATA 57.144 37.500 0.00 0.00 0.00 1.40
1553 3345 5.750352 TGTTACTCCCTCCGTTTCTAAAT 57.250 39.130 0.00 0.00 0.00 1.40
1554 3346 5.750352 ATGTTACTCCCTCCGTTTCTAAA 57.250 39.130 0.00 0.00 0.00 1.85
1555 3347 5.246656 TGAATGTTACTCCCTCCGTTTCTAA 59.753 40.000 0.00 0.00 0.00 2.10
1557 3349 3.581332 TGAATGTTACTCCCTCCGTTTCT 59.419 43.478 0.00 0.00 0.00 2.52
1558 3350 3.934068 TGAATGTTACTCCCTCCGTTTC 58.066 45.455 0.00 0.00 0.00 2.78
1559 3351 4.041198 TCTTGAATGTTACTCCCTCCGTTT 59.959 41.667 0.00 0.00 0.00 3.60
1560 3352 3.581332 TCTTGAATGTTACTCCCTCCGTT 59.419 43.478 0.00 0.00 0.00 4.44
1591 3392 3.763057 ACCATTTCCACCTAACCTGTTC 58.237 45.455 0.00 0.00 0.00 3.18
1610 3411 9.750125 AAAAATCAAGAAAAGTCTGATTGTACC 57.250 29.630 0.00 0.00 34.56 3.34
1874 3685 1.000396 AGCAAAGGCCAGGATGTCC 60.000 57.895 5.01 0.00 42.56 4.02
1892 3703 4.293648 CGGGTGGAGTCACGTGCA 62.294 66.667 11.67 0.00 44.50 4.57
2174 4029 0.605589 GCGGGCACACCTTCTTTAGT 60.606 55.000 0.00 0.00 36.97 2.24
2762 4628 1.753078 TACAGGAGCGGCGACAGAT 60.753 57.895 12.98 0.00 0.00 2.90
2901 4865 3.555956 GTGCATTGATACGTTACCCTCTG 59.444 47.826 0.00 0.00 0.00 3.35
2950 4914 0.755327 AAACTGTGTGCACTTCCCCC 60.755 55.000 19.41 0.00 0.00 5.40
3040 5004 7.617041 AAACTGAATGAGCTAAGGTACAATC 57.383 36.000 0.00 0.00 0.00 2.67
3122 6279 5.474532 TCTGTCAAGTTTTCAATGAGATGGG 59.525 40.000 0.00 0.00 0.00 4.00
3170 6327 1.692762 GGAGGGGGCTCTCTTACATGA 60.693 57.143 0.00 0.00 34.39 3.07
3174 6331 1.766864 GGGGAGGGGGCTCTCTTAC 60.767 68.421 0.00 0.00 34.39 2.34
3191 6348 3.310860 GATACATAGGCGGCCGGGG 62.311 68.421 29.38 9.27 0.00 5.73
3192 6349 1.899437 ATGATACATAGGCGGCCGGG 61.899 60.000 29.38 9.65 0.00 5.73
3193 6350 0.821517 TATGATACATAGGCGGCCGG 59.178 55.000 29.38 12.50 0.00 6.13
3194 6351 1.802880 GCTATGATACATAGGCGGCCG 60.803 57.143 24.05 24.05 0.00 6.13
3195 6352 1.482593 AGCTATGATACATAGGCGGCC 59.517 52.381 12.11 12.11 0.00 6.13
3196 6353 2.969628 AGCTATGATACATAGGCGGC 57.030 50.000 16.89 0.00 0.00 6.53
3197 6354 5.584253 AACTAGCTATGATACATAGGCGG 57.416 43.478 16.89 11.09 0.00 6.13
3198 6355 6.967767 GTGTAACTAGCTATGATACATAGGCG 59.032 42.308 16.89 0.00 0.00 5.52
3262 6669 7.127917 CACAGTTGTGCTTTTTAACCTTTTT 57.872 32.000 0.00 0.00 39.39 1.94
3286 6693 8.114290 GTGCTTTTTAACCTTTTTGTTTCTAGC 58.886 33.333 0.00 0.00 0.00 3.42
3287 6694 9.145865 TGTGCTTTTTAACCTTTTTGTTTCTAG 57.854 29.630 0.00 0.00 0.00 2.43
3288 6695 9.490379 TTGTGCTTTTTAACCTTTTTGTTTCTA 57.510 25.926 0.00 0.00 0.00 2.10
3289 6696 7.971183 TGTGCTTTTTAACCTTTTTGTTTCT 57.029 28.000 0.00 0.00 0.00 2.52
3290 6697 8.286800 AGTTGTGCTTTTTAACCTTTTTGTTTC 58.713 29.630 0.00 0.00 0.00 2.78
3291 6698 8.073167 CAGTTGTGCTTTTTAACCTTTTTGTTT 58.927 29.630 0.00 0.00 0.00 2.83
3292 6699 7.227711 ACAGTTGTGCTTTTTAACCTTTTTGTT 59.772 29.630 0.00 0.00 0.00 2.83
3293 6700 6.708502 ACAGTTGTGCTTTTTAACCTTTTTGT 59.291 30.769 0.00 0.00 0.00 2.83
3294 6701 7.127917 ACAGTTGTGCTTTTTAACCTTTTTG 57.872 32.000 0.00 0.00 0.00 2.44
3295 6702 7.659799 AGAACAGTTGTGCTTTTTAACCTTTTT 59.340 29.630 0.00 0.00 26.38 1.94
3296 6703 7.158697 AGAACAGTTGTGCTTTTTAACCTTTT 58.841 30.769 0.00 0.00 26.38 2.27
3297 6704 6.697395 AGAACAGTTGTGCTTTTTAACCTTT 58.303 32.000 0.00 0.00 26.38 3.11
3298 6705 6.280855 AGAACAGTTGTGCTTTTTAACCTT 57.719 33.333 0.00 0.00 26.38 3.50
3299 6706 5.914898 AGAACAGTTGTGCTTTTTAACCT 57.085 34.783 0.00 0.00 26.38 3.50
3300 6707 6.096695 TGAAGAACAGTTGTGCTTTTTAACC 58.903 36.000 6.93 0.00 43.73 2.85
3301 6708 6.253512 CCTGAAGAACAGTTGTGCTTTTTAAC 59.746 38.462 6.93 0.00 43.73 2.01
3302 6709 6.329496 CCTGAAGAACAGTTGTGCTTTTTAA 58.671 36.000 6.93 0.00 43.73 1.52
3303 6710 5.163561 CCCTGAAGAACAGTTGTGCTTTTTA 60.164 40.000 6.93 0.00 43.73 1.52
3304 6711 4.381932 CCCTGAAGAACAGTTGTGCTTTTT 60.382 41.667 6.93 0.00 43.73 1.94
3305 6712 3.131046 CCCTGAAGAACAGTTGTGCTTTT 59.869 43.478 6.93 0.00 43.73 2.27
3306 6713 2.689983 CCCTGAAGAACAGTTGTGCTTT 59.310 45.455 6.93 0.00 43.73 3.51
3307 6714 2.301346 CCCTGAAGAACAGTTGTGCTT 58.699 47.619 5.17 5.17 46.27 3.91
3308 6715 1.212935 ACCCTGAAGAACAGTTGTGCT 59.787 47.619 0.00 0.00 44.40 4.40
3309 6716 1.680338 ACCCTGAAGAACAGTTGTGC 58.320 50.000 0.00 0.00 44.40 4.57
3310 6717 4.440112 GGAAAACCCTGAAGAACAGTTGTG 60.440 45.833 0.00 0.00 44.40 3.33
3311 6718 3.699538 GGAAAACCCTGAAGAACAGTTGT 59.300 43.478 0.00 0.00 44.40 3.32
3312 6719 3.068165 GGGAAAACCCTGAAGAACAGTTG 59.932 47.826 0.00 0.00 44.40 3.16
3313 6720 3.296854 GGGAAAACCCTGAAGAACAGTT 58.703 45.455 0.00 0.00 44.40 3.16
3314 6721 2.748465 CGGGAAAACCCTGAAGAACAGT 60.748 50.000 0.00 0.00 44.44 3.55
3315 6722 1.880027 CGGGAAAACCCTGAAGAACAG 59.120 52.381 0.00 0.00 44.44 3.16
3316 6723 1.477923 CCGGGAAAACCCTGAAGAACA 60.478 52.381 0.00 0.00 44.44 3.18
3317 6724 1.244816 CCGGGAAAACCCTGAAGAAC 58.755 55.000 0.00 0.00 44.44 3.01
3318 6725 0.848053 ACCGGGAAAACCCTGAAGAA 59.152 50.000 6.32 0.00 44.44 2.52
3325 6732 0.831966 ACCAAAAACCGGGAAAACCC 59.168 50.000 6.32 0.00 34.99 4.11
3333 6740 1.880027 CTGGAGAAGACCAAAAACCGG 59.120 52.381 0.00 0.00 39.59 5.28
3440 7782 8.357796 TCTTGCAATGAGATATTCGAAACTAG 57.642 34.615 0.00 0.00 0.00 2.57
3441 7783 8.716646 TTCTTGCAATGAGATATTCGAAACTA 57.283 30.769 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.