Multiple sequence alignment - TraesCS7D01G277600

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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 TraesCS7D01G277600 chr7D 100.000 6491 0 0 1 6491 266397995 266391505 0.000000e+00 11987.0
1 TraesCS7D01G277600 chr7D 79.551 401 56 24 272 651 32866536 32866141 4.990000e-66 263.0
2 TraesCS7D01G277600 chr7D 88.776 196 19 3 5692 5885 266391047 266391241 3.030000e-58 237.0
3 TraesCS7D01G277600 chr7D 84.500 200 29 2 5687 5885 112193453 112193651 5.130000e-46 196.0
4 TraesCS7D01G277600 chr7D 84.343 198 30 1 5688 5884 494611964 494612161 6.640000e-45 193.0
5 TraesCS7D01G277600 chr7D 84.103 195 30 1 5691 5885 494613157 494612964 3.090000e-43 187.0
6 TraesCS7D01G277600 chr7D 100.000 31 0 0 5660 5690 269373323 269373353 2.530000e-04 58.4
7 TraesCS7D01G277600 chr7A 93.442 3858 157 28 4 3798 291813884 291810060 0.000000e+00 5635.0
8 TraesCS7D01G277600 chr7A 96.029 2065 50 20 3835 5885 291809400 291807354 0.000000e+00 3330.0
9 TraesCS7D01G277600 chr7A 89.394 594 39 12 5900 6490 291807373 291806801 0.000000e+00 726.0
10 TraesCS7D01G277600 chr7A 84.096 459 55 12 5965 6417 669438277 669437831 1.670000e-115 427.0
11 TraesCS7D01G277600 chr7A 89.394 198 18 3 5690 5885 291806352 291806548 5.030000e-61 246.0
12 TraesCS7D01G277600 chr7A 97.436 39 1 0 3796 3834 291809465 291809427 4.200000e-07 67.6
13 TraesCS7D01G277600 chr7A 100.000 29 0 0 5662 5690 44444165 44444193 3.000000e-03 54.7
14 TraesCS7D01G277600 chr7B 94.681 1880 65 18 3835 5695 246513553 246511690 0.000000e+00 2885.0
15 TraesCS7D01G277600 chr7B 94.749 1695 49 15 825 2503 246519571 246517901 0.000000e+00 2601.0
16 TraesCS7D01G277600 chr7B 95.683 996 38 4 2805 3798 246514622 246513630 0.000000e+00 1596.0
17 TraesCS7D01G277600 chr7B 90.964 332 12 2 2492 2806 246515030 246514700 1.290000e-116 431.0
18 TraesCS7D01G277600 chr7B 87.245 196 22 3 5691 5885 717179148 717179341 3.050000e-53 220.0
19 TraesCS7D01G277600 chr7B 86.735 196 23 3 5691 5885 717253801 717253994 1.420000e-51 215.0
20 TraesCS7D01G277600 chr1A 87.009 585 47 14 5039 5611 585006697 585006130 3.300000e-177 632.0
21 TraesCS7D01G277600 chr1A 96.774 31 1 0 5660 5690 267144783 267144813 1.200000e-02 52.8
22 TraesCS7D01G277600 chr4D 78.125 416 53 24 270 652 490401001 490401411 5.060000e-56 230.0
23 TraesCS7D01G277600 chr4D 100.000 31 0 0 5660 5690 499408109 499408139 2.530000e-04 58.4
24 TraesCS7D01G277600 chr3D 78.019 414 58 17 269 653 45667508 45667917 5.060000e-56 230.0
25 TraesCS7D01G277600 chr3D 76.873 307 42 16 272 560 48384943 48385238 5.240000e-31 147.0
26 TraesCS7D01G277600 chr3B 78.313 415 46 27 268 657 633132346 633132741 1.820000e-55 228.0
27 TraesCS7D01G277600 chr5D 77.887 407 60 16 270 652 422770059 422769659 6.550000e-55 226.0
28 TraesCS7D01G277600 chr5D 79.000 300 33 17 271 552 486243938 486244225 1.860000e-40 178.0
29 TraesCS7D01G277600 chr1D 87.179 195 23 2 5691 5884 319431811 319431618 3.050000e-53 220.0
30 TraesCS7D01G277600 chr1D 92.473 93 7 0 1744 1836 332929725 332929633 4.080000e-27 134.0
31 TraesCS7D01G277600 chr4A 76.923 416 60 18 270 653 717812584 717812995 3.070000e-48 204.0
32 TraesCS7D01G277600 chr4A 75.904 415 63 20 271 652 713975719 713975309 1.860000e-40 178.0
33 TraesCS7D01G277600 chr4A 85.106 94 11 3 1744 1836 37060207 37060116 6.930000e-15 93.5
34 TraesCS7D01G277600 chr5B 80.000 300 38 11 271 552 597291569 597291864 1.100000e-47 202.0
35 TraesCS7D01G277600 chr2D 76.441 399 62 18 270 653 595407026 595407407 3.090000e-43 187.0
36 TraesCS7D01G277600 chr2D 90.323 93 9 0 1744 1836 120105956 120106048 8.840000e-24 122.0
37 TraesCS7D01G277600 chr2D 73.086 405 59 37 268 647 2609920 2610299 1.490000e-16 99.0
38 TraesCS7D01G277600 chr2B 75.819 397 67 18 271 647 689489281 689488894 2.410000e-39 174.0
39 TraesCS7D01G277600 chr2B 83.871 93 14 1 1744 1836 340594026 340594117 3.220000e-13 87.9
40 TraesCS7D01G277600 chr2B 100.000 28 0 0 5663 5690 710747572 710747545 1.200000e-02 52.8
41 TraesCS7D01G277600 chr6D 76.678 283 35 20 5905 6167 445901569 445901298 1.900000e-25 128.0
42 TraesCS7D01G277600 chr6D 85.106 94 14 0 1743 1836 423793035 423792942 5.360000e-16 97.1
43 TraesCS7D01G277600 chr6B 92.683 82 6 0 1744 1825 394650008 394650089 1.140000e-22 119.0
44 TraesCS7D01G277600 chr6B 98.305 59 1 0 1265 1323 679563196 679563254 3.200000e-18 104.0
45 TraesCS7D01G277600 chr6B 97.059 34 0 1 5658 5690 566337938 566337905 1.000000e-03 56.5
46 TraesCS7D01G277600 chr6B 100.000 28 0 0 5661 5688 390628820 390628793 1.200000e-02 52.8
47 TraesCS7D01G277600 chr1B 89.247 93 9 1 1744 1836 674667159 674667068 1.480000e-21 115.0
48 TraesCS7D01G277600 chr5A 100.000 29 0 0 5662 5690 302553414 302553386 3.000000e-03 54.7


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 TraesCS7D01G277600 chr7D 266391505 266397995 6490 True 11987.00 11987 100.00000 1 6491 1 chr7D.!!$R2 6490
1 TraesCS7D01G277600 chr7A 291806801 291813884 7083 True 2439.65 5635 94.07525 4 6490 4 chr7A.!!$R2 6486
2 TraesCS7D01G277600 chr7B 246511690 246519571 7881 True 1878.25 2885 94.01925 825 5695 4 chr7B.!!$R1 4870
3 TraesCS7D01G277600 chr1A 585006130 585006697 567 True 632.00 632 87.00900 5039 5611 1 chr1A.!!$R1 572

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
306 308 0.322816 ACCGAGCTCAAATGCACCAT 60.323 50.000 15.40 0.0 34.99 3.55 F
664 669 1.270252 CCATGTCCCTTTTTGTGGTGC 60.270 52.381 0.00 0.0 0.00 5.01 F
2033 2054 0.967380 CTGGGGCAATTGAGTGGGTC 60.967 60.000 10.34 0.0 0.00 4.46 F
2057 2078 1.884497 CGGCAGGGTGATGTTAAACCA 60.884 52.381 0.00 0.0 38.27 3.67 F
2354 2405 2.076863 GCGTATGTTCTGGCTTCTTGT 58.923 47.619 0.00 0.0 0.00 3.16 F
3784 6840 2.227194 GCCTTCGTTCCTTCCTTTTCA 58.773 47.619 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1463 0.100325 CTGCGCACAAAACAGGTCAA 59.900 50.000 5.66 0.00 0.00 3.18 R
2502 5436 1.067060 GAACTTGCAGGGTTCAACCAC 59.933 52.381 21.67 0.00 41.02 4.16 R
3943 7622 0.237235 GAGATCAGCGACTAGGAGCG 59.763 60.000 0.00 2.41 38.61 5.03 R
4150 7831 2.733956 ACCTTCTTGTTGCCTTTGTCA 58.266 42.857 0.00 0.00 0.00 3.58 R
4246 7927 0.882927 TCCGGTGTTTCTTGAAGGCG 60.883 55.000 0.00 0.00 0.00 5.52 R
5593 9301 2.637382 TGCCTCCAGATGTACAACAAGA 59.363 45.455 0.00 0.00 0.00 3.02 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
19 20 2.446848 CCCGTGGCATCCTCCATCT 61.447 63.158 0.00 0.00 38.57 2.90
21 22 1.227764 CGTGGCATCCTCCATCTGG 60.228 63.158 0.00 0.00 38.57 3.86
30 31 1.521010 CTCCATCTGGCAGCGACAG 60.521 63.158 10.34 5.20 40.64 3.51
50 51 2.456119 GCTGGTGACGAATGCGGAG 61.456 63.158 0.00 0.00 43.17 4.63
81 82 3.145422 GACGCTAGAGGAGGCAGGC 62.145 68.421 0.00 0.00 0.00 4.85
130 132 4.582701 TTTTTAGGACGAAGGTGTACGA 57.417 40.909 0.00 0.00 0.00 3.43
131 133 3.837213 TTTAGGACGAAGGTGTACGAG 57.163 47.619 0.00 0.00 0.00 4.18
167 169 3.118542 GGATTAGTGGCTTAACCGTACG 58.881 50.000 8.69 8.69 43.94 3.67
178 180 1.515081 AACCGTACGTCAAACCATGG 58.485 50.000 15.21 11.19 0.00 3.66
199 201 3.193267 GGTTGATGGCTTGATGCTAAACA 59.807 43.478 0.00 0.00 42.39 2.83
221 223 5.939883 ACATCAAGAGGATTTTGATCGTCAA 59.060 36.000 10.55 0.00 41.91 3.18
229 231 7.829211 AGAGGATTTTGATCGTCAAATCCTTTA 59.171 33.333 29.39 10.88 44.75 1.85
282 284 2.288961 TCCGTGCGAAAGTCCTATTC 57.711 50.000 0.00 0.00 0.00 1.75
287 289 4.499188 CCGTGCGAAAGTCCTATTCTGATA 60.499 45.833 0.00 0.00 0.00 2.15
288 290 4.441415 CGTGCGAAAGTCCTATTCTGATAC 59.559 45.833 0.00 0.00 0.00 2.24
305 307 0.323302 TACCGAGCTCAAATGCACCA 59.677 50.000 15.40 0.00 34.99 4.17
306 308 0.322816 ACCGAGCTCAAATGCACCAT 60.323 50.000 15.40 0.00 34.99 3.55
313 315 3.704566 AGCTCAAATGCACCATGATGAAT 59.295 39.130 0.00 0.00 34.99 2.57
315 317 5.009710 AGCTCAAATGCACCATGATGAATAG 59.990 40.000 0.00 0.00 34.99 1.73
323 325 7.878547 TGCACCATGATGAATAGTAAAATCA 57.121 32.000 0.00 0.00 33.80 2.57
324 326 8.291191 TGCACCATGATGAATAGTAAAATCAA 57.709 30.769 0.00 0.00 33.06 2.57
393 395 6.482641 TGACAAATGTTTTGTATGCTTGCATT 59.517 30.769 13.52 0.00 31.96 3.56
464 468 9.598517 AAATGTTCTCAAAACTAGCATTTTTGA 57.401 25.926 15.19 15.19 46.03 2.69
477 481 6.399204 AGCATTTTTGAAGCATCGATTTTC 57.601 33.333 10.92 10.92 0.00 2.29
510 515 7.599621 GTCACAATTTCCATGAATGTCATTTCA 59.400 33.333 0.00 0.38 34.28 2.69
631 636 1.798735 CAGGGTGCATTTGAGCTCG 59.201 57.895 9.64 0.00 34.99 5.03
656 661 5.625150 GAGCATATACTCCATGTCCCTTTT 58.375 41.667 0.00 0.00 0.00 2.27
664 669 1.270252 CCATGTCCCTTTTTGTGGTGC 60.270 52.381 0.00 0.00 0.00 5.01
669 674 3.769844 TGTCCCTTTTTGTGGTGCTTTTA 59.230 39.130 0.00 0.00 0.00 1.52
673 678 6.589907 GTCCCTTTTTGTGGTGCTTTTATATG 59.410 38.462 0.00 0.00 0.00 1.78
674 679 6.495181 TCCCTTTTTGTGGTGCTTTTATATGA 59.505 34.615 0.00 0.00 0.00 2.15
682 689 9.727859 TTGTGGTGCTTTTATATGAGTAAGTAA 57.272 29.630 0.00 0.00 0.00 2.24
703 710 2.905415 TAAGTACTCCTTCCGTCCCA 57.095 50.000 0.00 0.00 34.46 4.37
715 722 1.958579 TCCGTCCCATAATGTAGTCGG 59.041 52.381 0.00 0.00 38.36 4.79
723 730 4.269363 CCCATAATGTAGTCGGAAAACGTC 59.731 45.833 0.00 0.00 44.69 4.34
734 741 4.327898 GTCGGAAAACGTCAGTGCATTATA 59.672 41.667 0.00 0.00 44.69 0.98
743 750 4.051922 GTCAGTGCATTATAAGACGGAGG 58.948 47.826 0.00 0.00 0.00 4.30
749 756 4.523173 TGCATTATAAGACGGAGGGAGTAG 59.477 45.833 0.00 0.00 0.00 2.57
754 761 7.565190 TTATAAGACGGAGGGAGTAGATAGA 57.435 40.000 0.00 0.00 0.00 1.98
855 876 1.301423 TCAAACTCGGGGTTTTCGTG 58.699 50.000 2.57 0.00 44.77 4.35
967 988 2.362963 GACACCCCCAAATCCCCC 59.637 66.667 0.00 0.00 0.00 5.40
1032 1053 2.932234 CGAGTCCACCGCCAACTCT 61.932 63.158 0.00 0.00 37.79 3.24
1369 1390 3.451178 AGAGTTATATGCACAGGGACGTT 59.549 43.478 0.00 0.00 0.00 3.99
1436 1457 3.347216 AGCGCAGATGGTAATTTCTTGT 58.653 40.909 11.47 0.00 0.00 3.16
1442 1463 5.648092 GCAGATGGTAATTTCTTGTACACCT 59.352 40.000 0.00 0.00 0.00 4.00
1528 1549 2.939103 CCTATCAGTTTCCTTCGGCTTG 59.061 50.000 0.00 0.00 0.00 4.01
1787 1808 3.311596 GTGTCGCAGTTTTGAACTAACCT 59.688 43.478 0.00 0.00 40.46 3.50
1812 1833 7.103641 TCAGTTCAAAACTAGTTCAAGACTGT 58.896 34.615 25.23 4.81 40.46 3.55
1836 1857 3.214328 CACTTATTTTGGATCGGAGGGG 58.786 50.000 0.00 0.00 0.00 4.79
1946 1967 1.405463 TGCTGCACGATCTCTAACGAT 59.595 47.619 0.00 0.00 0.00 3.73
2021 2042 4.278513 CCGTTTGTCCCTGGGGCA 62.279 66.667 17.92 17.92 34.68 5.36
2033 2054 0.967380 CTGGGGCAATTGAGTGGGTC 60.967 60.000 10.34 0.00 0.00 4.46
2057 2078 1.884497 CGGCAGGGTGATGTTAAACCA 60.884 52.381 0.00 0.00 38.27 3.67
2354 2405 2.076863 GCGTATGTTCTGGCTTCTTGT 58.923 47.619 0.00 0.00 0.00 3.16
2356 2407 3.682858 GCGTATGTTCTGGCTTCTTGTAA 59.317 43.478 0.00 0.00 0.00 2.41
2436 2487 4.825546 ATTGCAAACTTGAGTCTGAGTG 57.174 40.909 1.71 0.00 0.00 3.51
2532 5466 4.589908 ACCCTGCAAGTTCTAATTAGGTG 58.410 43.478 12.54 7.19 0.00 4.00
2614 5589 9.084164 CAGTGTAACAGTAGTATATGGTTGAAC 57.916 37.037 0.00 0.00 41.43 3.18
2669 5644 5.625150 AGTAAAGATGCTTGAGTTGAAGGT 58.375 37.500 0.00 0.00 0.00 3.50
2863 5917 7.844493 ATGCATTAACCCATTGACTTATCAT 57.156 32.000 0.00 0.00 33.85 2.45
3000 6054 3.610040 TGTGATCCTTGCGTGATTAGT 57.390 42.857 0.00 0.00 0.00 2.24
3023 6077 8.709386 AGTGTATACTGCTTCTTCATTACTTG 57.291 34.615 4.17 0.00 35.34 3.16
3146 6200 7.589958 TTCTTTCTTTTTACCAGCATACCAA 57.410 32.000 0.00 0.00 0.00 3.67
3203 6257 2.965831 TCCACCCTATCACATCAGTAGC 59.034 50.000 0.00 0.00 0.00 3.58
3261 6317 2.314323 GGCCAAAAATGATGCCGATT 57.686 45.000 0.00 0.00 33.59 3.34
3266 6322 4.629200 GCCAAAAATGATGCCGATTGTTTA 59.371 37.500 0.00 0.00 0.00 2.01
3267 6323 5.121454 GCCAAAAATGATGCCGATTGTTTAA 59.879 36.000 0.00 0.00 0.00 1.52
3507 6563 5.202004 TGAGTCCCTTGAGGTAAGATACTC 58.798 45.833 0.00 0.00 42.34 2.59
3518 6574 3.892588 GGTAAGATACTCCCTCTGTCCAG 59.107 52.174 0.00 0.00 0.00 3.86
3538 6594 2.810274 AGTGCTTGCACATCACAAGTAG 59.190 45.455 24.82 0.00 45.09 2.57
3609 6665 5.447573 GCACAAGATCTTCAGAAAAGTGAC 58.552 41.667 18.78 9.68 0.00 3.67
3723 6779 2.428530 TGCTGTATTCGATGAGAGCTGT 59.571 45.455 14.68 0.00 0.00 4.40
3784 6840 2.227194 GCCTTCGTTCCTTCCTTTTCA 58.773 47.619 0.00 0.00 0.00 2.69
3790 6846 6.016610 CCTTCGTTCCTTCCTTTTCAATTGTA 60.017 38.462 5.13 0.00 0.00 2.41
3841 7520 5.068460 TCCATTTTTGTTGTGTACTCAAGGG 59.932 40.000 10.50 0.60 0.00 3.95
3923 7602 4.415596 TGGTGAGCCATTGACCTTTTATT 58.584 39.130 0.00 0.00 40.46 1.40
4150 7831 5.663106 TCTGAGAATTGCTCTATACCAAGGT 59.337 40.000 0.00 0.00 44.27 3.50
4246 7927 4.081642 TCAGACCCTACTCTGTTATGTTGC 60.082 45.833 0.00 0.00 39.08 4.17
4351 8032 4.041691 ACTTAGTTGCTTGGAAGGCTCTTA 59.958 41.667 0.00 0.00 0.00 2.10
4609 8290 8.281212 ACTCCTTTGGTGAATGACATTAATAC 57.719 34.615 0.00 1.39 0.00 1.89
4742 8423 6.126332 TGAGACTATATCCAGAAGAGTGTCCT 60.126 42.308 0.00 0.00 31.30 3.85
4796 8477 9.952030 TGCCGAAATGGTTATTATGATAATCTA 57.048 29.630 0.13 0.00 41.21 1.98
5154 8852 6.533819 TTACAGTGACAACTTTATTGGTCG 57.466 37.500 0.00 0.00 32.98 4.79
5592 9300 8.966868 TCTGTTCTGGACTTAATTTTCAAGTTT 58.033 29.630 0.00 0.00 36.38 2.66
5593 9301 9.586435 CTGTTCTGGACTTAATTTTCAAGTTTT 57.414 29.630 0.00 0.00 36.38 2.43
5618 9326 2.488153 GTTGTACATCTGGAGGCAAACC 59.512 50.000 0.00 0.00 0.00 3.27
5720 9428 5.043189 AGCATAAAACTACCACTTTTCGC 57.957 39.130 0.00 0.00 0.00 4.70
5782 9490 2.346766 TACCTACCAGAATCGGCGTA 57.653 50.000 6.85 0.00 0.00 4.42
5869 9577 4.202111 GCCCGCATGTAAGATAACCATTTT 60.202 41.667 0.00 0.00 0.00 1.82
5870 9578 5.681179 GCCCGCATGTAAGATAACCATTTTT 60.681 40.000 0.00 0.00 0.00 1.94
5890 9598 6.520792 TTTTTGACCGTTTTGTTTCGAAAA 57.479 29.167 13.10 0.34 31.70 2.29
5891 9599 6.520792 TTTTGACCGTTTTGTTTCGAAAAA 57.479 29.167 13.10 3.93 0.00 1.94
5942 9650 4.714632 ACTGTTAACTTACATGTGTGGCT 58.285 39.130 9.11 0.00 0.00 4.75
5998 9706 1.219213 TCCCTCTTCTCCCCTGATCTC 59.781 57.143 0.00 0.00 0.00 2.75
6002 9710 3.490348 CTCTTCTCCCCTGATCTCTCTC 58.510 54.545 0.00 0.00 0.00 3.20
6003 9711 2.176798 TCTTCTCCCCTGATCTCTCTCC 59.823 54.545 0.00 0.00 0.00 3.71
6081 9789 2.913578 CAGGCAAGCAGGGCAACA 60.914 61.111 4.10 0.00 39.74 3.33
6082 9790 2.118951 AGGCAAGCAGGGCAACAT 59.881 55.556 4.10 0.00 39.74 2.71
6130 9838 2.753043 GAGGTGGGCATGCACTGG 60.753 66.667 22.81 0.00 0.00 4.00
6131 9839 3.259314 AGGTGGGCATGCACTGGA 61.259 61.111 22.81 0.00 0.00 3.86
6132 9840 2.753043 GGTGGGCATGCACTGGAG 60.753 66.667 22.81 0.00 0.00 3.86
6133 9841 3.446570 GTGGGCATGCACTGGAGC 61.447 66.667 22.81 0.00 0.00 4.70
6134 9842 3.654143 TGGGCATGCACTGGAGCT 61.654 61.111 22.81 0.00 34.99 4.09
6135 9843 3.138798 GGGCATGCACTGGAGCTG 61.139 66.667 21.36 0.00 34.99 4.24
6138 9846 2.762234 GCATGCACTGGAGCTGCTC 61.762 63.158 21.17 21.17 36.45 4.26
6208 9916 5.414789 AGAGAGCTTAGAGAAAGGGAAAC 57.585 43.478 0.00 0.00 35.58 2.78
6347 10080 1.043673 AGGTAGTAGCGGCAAGGAGG 61.044 60.000 1.45 0.00 0.00 4.30
6348 10081 1.041447 GGTAGTAGCGGCAAGGAGGA 61.041 60.000 1.45 0.00 0.00 3.71
6349 10082 0.386113 GTAGTAGCGGCAAGGAGGAG 59.614 60.000 1.45 0.00 0.00 3.69
6350 10083 0.755698 TAGTAGCGGCAAGGAGGAGG 60.756 60.000 1.45 0.00 0.00 4.30
6351 10084 2.058595 GTAGCGGCAAGGAGGAGGA 61.059 63.158 1.45 0.00 0.00 3.71
6381 10114 3.478274 GGCAGGGAGGAGGAGCAG 61.478 72.222 0.00 0.00 0.00 4.24
6382 10115 4.173924 GCAGGGAGGAGGAGCAGC 62.174 72.222 0.00 0.00 0.00 5.25
6402 10135 3.150335 CAGCTAGCGGCAGGGAGA 61.150 66.667 9.55 0.00 44.79 3.71
6405 10138 2.818132 CTAGCGGCAGGGAGAAGG 59.182 66.667 1.45 0.00 0.00 3.46
6408 10141 4.847444 GCGGCAGGGAGAAGGAGC 62.847 72.222 0.00 0.00 0.00 4.70
6409 10142 3.393970 CGGCAGGGAGAAGGAGCA 61.394 66.667 0.00 0.00 0.00 4.26
6410 10143 2.588989 GGCAGGGAGAAGGAGCAG 59.411 66.667 0.00 0.00 0.00 4.24
6411 10144 2.124778 GCAGGGAGAAGGAGCAGC 60.125 66.667 0.00 0.00 0.00 5.25
6412 10145 2.964310 GCAGGGAGAAGGAGCAGCA 61.964 63.158 0.00 0.00 0.00 4.41
6413 10146 1.221293 CAGGGAGAAGGAGCAGCAG 59.779 63.158 0.00 0.00 0.00 4.24
6414 10147 2.124778 GGGAGAAGGAGCAGCAGC 60.125 66.667 0.00 0.00 42.56 5.25
6415 10148 2.667418 GGAGAAGGAGCAGCAGCA 59.333 61.111 3.17 0.00 45.49 4.41
6416 10149 1.449956 GGAGAAGGAGCAGCAGCAG 60.450 63.158 3.17 0.00 45.49 4.24
6417 10150 2.046120 AGAAGGAGCAGCAGCAGC 60.046 61.111 3.17 0.46 45.49 5.25
6430 10163 2.736995 GCAGCGGTCGTGCTACAA 60.737 61.111 9.43 0.00 45.23 2.41
6431 10164 2.730672 GCAGCGGTCGTGCTACAAG 61.731 63.158 9.43 0.00 45.23 3.16
6432 10165 2.094659 CAGCGGTCGTGCTACAAGG 61.095 63.158 0.00 0.00 45.23 3.61
6433 10166 2.260434 GCGGTCGTGCTACAAGGA 59.740 61.111 0.00 0.00 0.00 3.36
6434 10167 1.805945 GCGGTCGTGCTACAAGGAG 60.806 63.158 0.00 0.00 0.00 3.69
6435 10168 1.805945 CGGTCGTGCTACAAGGAGC 60.806 63.158 0.00 0.00 43.16 4.70
6436 10169 1.805945 GGTCGTGCTACAAGGAGCG 60.806 63.158 0.00 0.00 45.99 5.03
6437 10170 1.805945 GTCGTGCTACAAGGAGCGG 60.806 63.158 0.00 0.00 45.99 5.52
6438 10171 3.188786 CGTGCTACAAGGAGCGGC 61.189 66.667 0.00 0.00 45.99 6.53
6469 10202 0.531532 CCATAGGCGAGGCAGTTGAG 60.532 60.000 0.00 0.00 0.00 3.02
6473 10206 2.659610 GCGAGGCAGTTGAGGTCT 59.340 61.111 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.366837 ATGGAGGATGCCACGGGA 60.367 61.111 0.00 0.00 41.56 5.14
1 2 2.111878 GATGGAGGATGCCACGGG 59.888 66.667 0.00 0.00 41.56 5.28
2 3 1.227764 CAGATGGAGGATGCCACGG 60.228 63.158 0.00 0.00 41.56 4.94
12 13 1.521010 CTGTCGCTGCCAGATGGAG 60.521 63.158 2.18 0.00 37.39 3.86
14 15 1.521010 CTCTGTCGCTGCCAGATGG 60.521 63.158 8.69 0.00 38.23 3.51
30 31 2.456119 CCGCATTCGTCACCAGCTC 61.456 63.158 0.00 0.00 0.00 4.09
32 33 2.434185 TCCGCATTCGTCACCAGC 60.434 61.111 0.00 0.00 0.00 4.85
35 36 3.195698 GCCTCCGCATTCGTCACC 61.196 66.667 0.00 0.00 34.03 4.02
112 113 3.005554 CTCTCGTACACCTTCGTCCTAA 58.994 50.000 0.00 0.00 0.00 2.69
114 115 1.002888 TCTCTCGTACACCTTCGTCCT 59.997 52.381 0.00 0.00 0.00 3.85
115 116 1.446907 TCTCTCGTACACCTTCGTCC 58.553 55.000 0.00 0.00 0.00 4.79
117 118 3.626670 CCTAATCTCTCGTACACCTTCGT 59.373 47.826 0.00 0.00 0.00 3.85
118 119 3.003482 CCCTAATCTCTCGTACACCTTCG 59.997 52.174 0.00 0.00 0.00 3.79
128 130 2.108168 TCCCACAACCCTAATCTCTCG 58.892 52.381 0.00 0.00 0.00 4.04
130 132 5.131142 CACTAATCCCACAACCCTAATCTCT 59.869 44.000 0.00 0.00 0.00 3.10
131 133 5.368989 CACTAATCCCACAACCCTAATCTC 58.631 45.833 0.00 0.00 0.00 2.75
236 238 7.235606 AGGCAGGCACTTTACATCTTATATCTA 59.764 37.037 0.00 0.00 34.60 1.98
238 240 6.234177 AGGCAGGCACTTTACATCTTATATC 58.766 40.000 0.00 0.00 34.60 1.63
282 284 2.286294 GTGCATTTGAGCTCGGTATCAG 59.714 50.000 9.64 0.00 34.99 2.90
287 289 0.322816 ATGGTGCATTTGAGCTCGGT 60.323 50.000 9.64 0.00 34.99 4.69
288 290 0.099968 CATGGTGCATTTGAGCTCGG 59.900 55.000 9.64 0.00 34.99 4.63
363 365 6.321717 AGCATACAAAACATTTGTCATACCG 58.678 36.000 11.40 0.00 34.11 4.02
485 490 7.668492 TGAAATGACATTCATGGAAATTGTGA 58.332 30.769 0.05 0.00 37.15 3.58
518 523 9.934190 GACAAATGTTTTGTATGCTTGAATTTT 57.066 25.926 5.66 0.00 31.96 1.82
519 524 9.107177 TGACAAATGTTTTGTATGCTTGAATTT 57.893 25.926 5.66 0.00 31.96 1.82
520 525 8.659925 TGACAAATGTTTTGTATGCTTGAATT 57.340 26.923 5.66 0.00 31.96 2.17
521 526 8.659925 TTGACAAATGTTTTGTATGCTTGAAT 57.340 26.923 5.66 0.00 31.96 2.57
598 603 3.756434 GCACCCTGCTAAACAGTGAAATA 59.244 43.478 0.00 0.00 45.68 1.40
603 608 1.538047 ATGCACCCTGCTAAACAGTG 58.462 50.000 0.00 0.00 45.68 3.66
610 615 0.329261 AGCTCAAATGCACCCTGCTA 59.671 50.000 0.00 0.00 45.31 3.49
612 617 1.509923 GAGCTCAAATGCACCCTGC 59.490 57.895 9.40 0.00 45.29 4.85
617 622 2.093216 CTCCCGAGCTCAAATGCAC 58.907 57.895 15.40 0.00 34.99 4.57
642 647 2.297033 CACCACAAAAAGGGACATGGAG 59.703 50.000 0.00 0.00 0.00 3.86
656 661 9.727859 TTACTTACTCATATAAAAGCACCACAA 57.272 29.630 0.00 0.00 0.00 3.33
673 678 8.681806 ACGGAAGGAGTACTTATTTACTTACTC 58.318 37.037 0.00 0.00 40.21 2.59
674 679 8.586879 ACGGAAGGAGTACTTATTTACTTACT 57.413 34.615 0.00 0.00 40.21 2.24
682 689 3.716431 TGGGACGGAAGGAGTACTTATT 58.284 45.455 0.00 0.00 40.21 1.40
694 701 2.363038 CCGACTACATTATGGGACGGAA 59.637 50.000 18.87 0.00 35.87 4.30
703 710 5.575606 CACTGACGTTTTCCGACTACATTAT 59.424 40.000 0.00 0.00 40.70 1.28
715 722 5.952064 CGTCTTATAATGCACTGACGTTTTC 59.048 40.000 12.16 0.00 41.23 2.29
723 730 3.069586 TCCCTCCGTCTTATAATGCACTG 59.930 47.826 0.00 0.00 0.00 3.66
734 741 5.548836 ACTATCTATCTACTCCCTCCGTCTT 59.451 44.000 0.00 0.00 0.00 3.01
821 842 6.239036 CCCGAGTTTGATTTTCCTTTCTTTCT 60.239 38.462 0.00 0.00 0.00 2.52
967 988 2.417515 GCCTTCTCTTCACTAGGGTTCG 60.418 54.545 0.00 0.00 0.00 3.95
1032 1053 2.098298 GTCGCGCTCGTTACGGTA 59.902 61.111 5.56 0.00 36.96 4.02
1393 1414 2.354704 CCCGGTAATGAAGAAGTCAGCA 60.355 50.000 0.00 0.00 40.43 4.41
1436 1457 2.685897 GCACAAAACAGGTCAAGGTGTA 59.314 45.455 0.00 0.00 0.00 2.90
1442 1463 0.100325 CTGCGCACAAAACAGGTCAA 59.900 50.000 5.66 0.00 0.00 3.18
1528 1549 2.029020 GGAATCAGCCAACTTTTCCCAC 60.029 50.000 0.00 0.00 32.73 4.61
1787 1808 7.064609 CACAGTCTTGAACTAGTTTTGAACTGA 59.935 37.037 29.27 14.06 42.84 3.41
1812 1833 4.513442 CCTCCGATCCAAAATAAGTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
1836 1857 3.012518 AGTGAGTGCAATCAATAGTGCC 58.987 45.455 19.78 4.44 45.98 5.01
1946 1967 6.901081 ACATCATATATCTTGACAGACCGA 57.099 37.500 0.00 0.00 0.00 4.69
2021 2042 1.837439 TGCCGATAGACCCACTCAATT 59.163 47.619 0.00 0.00 39.76 2.32
2033 2054 3.469008 TTAACATCACCCTGCCGATAG 57.531 47.619 0.00 0.00 0.00 2.08
2057 2078 2.616842 CCGGTCACTAACAGCAAGTTTT 59.383 45.455 0.00 0.00 41.64 2.43
2354 2405 9.554724 GAAGAAACACGATGCTGAAAATAATTA 57.445 29.630 0.00 0.00 0.00 1.40
2356 2407 7.752239 CAGAAGAAACACGATGCTGAAAATAAT 59.248 33.333 0.00 0.00 0.00 1.28
2436 2487 8.443937 CAAAAGTACTAGAAAGTGGAAGTATGC 58.556 37.037 0.00 0.00 36.36 3.14
2502 5436 1.067060 GAACTTGCAGGGTTCAACCAC 59.933 52.381 21.67 0.00 41.02 4.16
2532 5466 8.919777 ATTTTATCCCTACTTAGCATACCAAC 57.080 34.615 0.00 0.00 0.00 3.77
2771 5746 7.281098 ACTATCGTGAAAGTAGACCTCATAGA 58.719 38.462 0.00 0.00 0.00 1.98
2863 5917 3.770263 GCAGATAGCAATGTCAAGCAA 57.230 42.857 3.81 0.00 44.79 3.91
2942 5996 1.433534 GCAGACACACTAGTCTTGCC 58.566 55.000 0.00 0.00 46.26 4.52
3000 6054 7.492669 GCTCAAGTAATGAAGAAGCAGTATACA 59.507 37.037 5.50 0.00 37.67 2.29
3023 6077 2.945008 TGTGCAATTGTATGCCTAGCTC 59.055 45.455 7.40 0.00 45.83 4.09
3082 6136 6.485313 CAGTCTGTGTTATTGTTTGGGAGTAA 59.515 38.462 0.00 0.00 0.00 2.24
3146 6200 8.900781 CAAATTCAGGTGTCTCTATCATTGAAT 58.099 33.333 0.00 0.00 35.56 2.57
3203 6257 6.663093 AGGTATCTATGAAGTGATCTAGCCAG 59.337 42.308 0.00 0.00 0.00 4.85
3236 6290 3.309410 CGGCATCATTTTTGGCCAATTAC 59.691 43.478 21.26 3.25 46.75 1.89
3241 6297 1.193323 ATCGGCATCATTTTTGGCCA 58.807 45.000 0.00 0.00 46.75 5.36
3378 6434 1.611673 CGTTGCTCACCTGGGAAAGAT 60.612 52.381 0.00 0.00 0.00 2.40
3507 6563 1.673665 GCAAGCACTGGACAGAGGG 60.674 63.158 6.29 0.00 0.00 4.30
3518 6574 2.807967 TCTACTTGTGATGTGCAAGCAC 59.192 45.455 17.76 17.76 45.09 4.40
3538 6594 8.241367 AGTCCAAAATTACAAACCGAACATATC 58.759 33.333 0.00 0.00 0.00 1.63
3723 6779 6.335781 AGGGTGGCATAAATAAGGAAGTTA 57.664 37.500 0.00 0.00 0.00 2.24
3805 7458 8.303156 CACAACAAAAATGGACTGGTAATATCA 58.697 33.333 0.00 0.00 0.00 2.15
3923 7602 6.649141 GGAGCGGAACATGATTATTATGTGTA 59.351 38.462 0.00 0.00 38.67 2.90
3943 7622 0.237235 GAGATCAGCGACTAGGAGCG 59.763 60.000 0.00 2.41 38.61 5.03
4150 7831 2.733956 ACCTTCTTGTTGCCTTTGTCA 58.266 42.857 0.00 0.00 0.00 3.58
4246 7927 0.882927 TCCGGTGTTTCTTGAAGGCG 60.883 55.000 0.00 0.00 0.00 5.52
4316 7997 6.273071 CAAGCAACTAAGTTTAAAACCAGCT 58.727 36.000 0.00 0.00 0.00 4.24
4336 8017 3.615155 AGTTCATAAGAGCCTTCCAAGC 58.385 45.455 0.00 0.00 0.00 4.01
4374 8055 8.942338 AAAAAGGATGTTAAACTTCCAAGAAC 57.058 30.769 9.42 0.00 42.90 3.01
4400 8081 7.105588 TCTACGACTGTACAGTAATAAGGACA 58.894 38.462 27.98 5.88 42.66 4.02
4609 8290 4.199310 ACTGATTTCACATACAATCCGGG 58.801 43.478 0.00 0.00 0.00 5.73
4638 8319 3.965379 TCAGGCAATGCAAAATGACAT 57.035 38.095 7.79 0.00 0.00 3.06
4742 8423 9.179909 TGAGTAGTGAAATTTTCCACAGTTTTA 57.820 29.630 11.37 0.00 35.84 1.52
4808 8489 7.556275 GTCTGGACCATGAATCCTTTAATTACA 59.444 37.037 14.84 0.00 37.13 2.41
5154 8852 3.686241 TGTCATGTCTCAAGCTGCAATAC 59.314 43.478 1.02 0.00 0.00 1.89
5592 9300 3.072330 TGCCTCCAGATGTACAACAAGAA 59.928 43.478 0.00 0.00 0.00 2.52
5593 9301 2.637382 TGCCTCCAGATGTACAACAAGA 59.363 45.455 0.00 0.00 0.00 3.02
5618 9326 7.543172 CAGGAACATATTTTCAAACATGGACAG 59.457 37.037 4.11 0.00 0.00 3.51
5652 9360 8.392479 ACGGAGGGAGTATTAGATAAATAGACT 58.608 37.037 0.00 0.00 30.55 3.24
5657 9365 5.720520 GGGACGGAGGGAGTATTAGATAAAT 59.279 44.000 0.00 0.00 0.00 1.40
5741 9449 5.888412 ATCAGTCACAAACGAATTTTTGC 57.112 34.783 3.08 0.00 39.67 3.68
5750 9458 4.082408 TCTGGTAGGTATCAGTCACAAACG 60.082 45.833 0.00 0.00 35.90 3.60
5757 9465 3.305471 GCCGATTCTGGTAGGTATCAGTC 60.305 52.174 0.00 0.00 35.90 3.51
5782 9490 5.306678 TGATTTGGGTTTTATGAAACAGCCT 59.693 36.000 14.30 0.00 45.52 4.58
5902 9610 4.872664 ACAGTCAAACAAACGGTCAAAAA 58.127 34.783 0.00 0.00 0.00 1.94
5903 9611 4.506886 ACAGTCAAACAAACGGTCAAAA 57.493 36.364 0.00 0.00 0.00 2.44
5910 9618 7.694784 ACATGTAAGTTAACAGTCAAACAAACG 59.305 33.333 8.61 0.00 31.70 3.60
5942 9650 3.258372 GGTAGGAGACAACTGACATGTGA 59.742 47.826 1.15 0.00 0.00 3.58
6058 9766 3.123620 CCTGCTTGCCTGCTCGTC 61.124 66.667 0.00 0.00 0.00 4.20
6095 9803 3.300934 CTCCTACTGCAGCGTGCCA 62.301 63.158 15.27 0.00 44.23 4.92
6208 9916 1.133637 TCTCTCCTCCCCATCTTCTCG 60.134 57.143 0.00 0.00 0.00 4.04
6308 10016 1.264749 ACTGCTCCTTGCCGGTGATA 61.265 55.000 1.90 0.00 42.00 2.15
6411 10144 3.181967 GTAGCACGACCGCTGCTG 61.182 66.667 20.87 0.00 44.85 4.41
6412 10145 3.220999 TTGTAGCACGACCGCTGCT 62.221 57.895 17.99 17.99 46.82 4.24
6413 10146 2.730672 CTTGTAGCACGACCGCTGC 61.731 63.158 8.62 7.89 43.68 5.25
6414 10147 2.094659 CCTTGTAGCACGACCGCTG 61.095 63.158 8.62 0.00 43.68 5.18
6415 10148 2.214181 CTCCTTGTAGCACGACCGCT 62.214 60.000 0.00 0.00 46.26 5.52
6416 10149 1.805945 CTCCTTGTAGCACGACCGC 60.806 63.158 0.00 0.00 0.00 5.68
6417 10150 1.805945 GCTCCTTGTAGCACGACCG 60.806 63.158 0.00 0.00 42.30 4.79
6418 10151 1.805945 CGCTCCTTGTAGCACGACC 60.806 63.158 0.00 0.00 42.91 4.79
6419 10152 1.805945 CCGCTCCTTGTAGCACGAC 60.806 63.158 0.00 0.00 42.91 4.34
6420 10153 2.571757 CCGCTCCTTGTAGCACGA 59.428 61.111 0.00 0.00 42.91 4.35
6421 10154 3.188786 GCCGCTCCTTGTAGCACG 61.189 66.667 0.00 0.00 42.91 5.34
6422 10155 3.188786 CGCCGCTCCTTGTAGCAC 61.189 66.667 0.00 0.00 42.91 4.40
6423 10156 4.451150 CCGCCGCTCCTTGTAGCA 62.451 66.667 0.00 0.00 42.91 3.49
6473 10206 2.520982 CAGGATCCGGCCGGTCTA 60.521 66.667 41.57 25.51 36.47 2.59


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

AutoCloner maintained by Alex Coulton.