Multiple sequence alignment - TraesCS7B01G064700

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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 TraesCS7B01G064700 chr7B 100.000 3859 0 0 1 3859 70242477 70246335 0.000000e+00 7127
1 TraesCS7B01G064700 chr7B 95.054 3336 146 10 1 3318 70338665 70341999 0.000000e+00 5228
2 TraesCS7B01G064700 chr7B 97.019 2818 72 8 506 3318 69849048 69851858 0.000000e+00 4728
3 TraesCS7B01G064700 chr7B 96.877 2818 76 8 506 3318 69912320 69915130 0.000000e+00 4706
4 TraesCS7B01G064700 chr7B 97.377 2707 63 7 506 3206 70068703 70071407 0.000000e+00 4599
5 TraesCS7B01G064700 chr7B 95.991 2819 99 10 506 3318 69992205 69995015 0.000000e+00 4567
6 TraesCS7B01G064700 chr7B 96.124 387 8 4 3479 3859 69851857 69852242 3.270000e-175 625
7 TraesCS7B01G064700 chr7B 96.094 384 9 6 3479 3859 70341998 70342378 4.230000e-174 621
8 TraesCS7B01G064700 chr7B 95.855 386 10 3 3479 3859 69995014 69995398 1.520000e-173 619
9 TraesCS7B01G064700 chr7B 95.607 387 10 4 3479 3859 69915129 69915514 7.090000e-172 614
10 TraesCS7B01G064700 chr7B 96.839 348 9 2 3513 3859 70071903 70072249 7.190000e-162 580
11 TraesCS7B01G064700 chr7B 91.429 210 17 1 299 507 367756956 367757165 1.750000e-73 287
12 TraesCS7B01G064700 chr6B 95.674 2820 102 9 506 3318 548948104 548950910 0.000000e+00 4514
13 TraesCS7B01G064700 chr6B 95.675 2821 101 10 506 3318 549028616 549031423 0.000000e+00 4514
14 TraesCS7B01G064700 chr6B 95.090 387 11 5 3479 3859 548950909 548951293 1.530000e-168 603
15 TraesCS7B01G064700 chr6B 94.629 391 10 4 3479 3859 549031422 549031811 2.570000e-166 595
16 TraesCS7B01G064700 chr6B 93.567 171 11 0 3314 3484 95349409 95349579 4.950000e-64 255
17 TraesCS7B01G064700 chr7D 93.207 2841 128 29 506 3318 110890088 110892891 0.000000e+00 4117
18 TraesCS7B01G064700 chr7D 96.345 383 11 3 3479 3859 110892890 110893271 9.100000e-176 627
19 TraesCS7B01G064700 chr7D 94.382 178 9 1 122 298 126883566 126883743 4.910000e-69 272
20 TraesCS7B01G064700 chr7D 92.529 174 13 0 3308 3481 618492435 618492608 2.300000e-62 250
21 TraesCS7B01G064700 chr7D 98.450 129 1 1 1 128 185242103 185242231 3.880000e-55 226
22 TraesCS7B01G064700 chr7D 97.674 129 2 1 1 128 561094502 561094374 1.800000e-53 220
23 TraesCS7B01G064700 chrUn 88.205 2518 218 50 854 3318 16612153 16614644 0.000000e+00 2931
24 TraesCS7B01G064700 chrUn 87.912 2548 221 42 816 3318 272511471 272513976 0.000000e+00 2918
25 TraesCS7B01G064700 chrUn 87.808 2559 222 50 816 3318 16657284 16659808 0.000000e+00 2915
26 TraesCS7B01G064700 chrUn 87.687 2542 215 50 816 3305 16444485 16441990 0.000000e+00 2870
27 TraesCS7B01G064700 chrUn 87.943 2032 164 39 1313 3305 344031471 344033460 0.000000e+00 2320
28 TraesCS7B01G064700 chrUn 92.067 1563 107 13 1594 3148 379234392 379232839 0.000000e+00 2183
29 TraesCS7B01G064700 chrUn 87.711 651 62 13 2669 3305 16547539 16548185 0.000000e+00 743
30 TraesCS7B01G064700 chrUn 87.711 651 62 13 2669 3305 203045617 203046263 0.000000e+00 743
31 TraesCS7B01G064700 chrUn 93.567 171 10 1 3314 3483 3054594 3054764 1.780000e-63 254
32 TraesCS7B01G064700 chrUn 92.647 68 5 0 3247 3314 24179809 24179742 8.820000e-17 99
33 TraesCS7B01G064700 chrUn 92.647 68 5 0 3247 3314 434209238 434209305 8.820000e-17 99
34 TraesCS7B01G064700 chr2B 91.115 1767 143 12 1218 2973 27356054 27357817 0.000000e+00 2381
35 TraesCS7B01G064700 chr2B 87.941 340 30 8 851 1187 27287296 27287627 1.300000e-104 390
36 TraesCS7B01G064700 chr2B 93.023 172 12 0 3314 3485 391518993 391519164 6.400000e-63 252
37 TraesCS7B01G064700 chr2D 88.517 1106 98 17 2234 3318 19848198 19847101 0.000000e+00 1312
38 TraesCS7B01G064700 chr2D 97.674 129 2 1 1 128 10828051 10827923 1.800000e-53 220
39 TraesCS7B01G064700 chr2D 92.647 68 5 0 3247 3314 15276894 15276961 8.820000e-17 99
40 TraesCS7B01G064700 chr7A 94.517 383 18 3 3479 3859 116021538 116021919 4.290000e-164 588
41 TraesCS7B01G064700 chr7A 93.923 181 7 2 123 299 85435456 85435276 1.770000e-68 270
42 TraesCS7B01G064700 chr5A 97.268 183 4 1 121 302 436893949 436893767 3.740000e-80 309
43 TraesCS7B01G064700 chr5A 93.452 168 11 0 3313 3480 44602569 44602736 2.300000e-62 250
44 TraesCS7B01G064700 chr3B 91.866 209 17 0 299 507 583847673 583847881 3.770000e-75 292
45 TraesCS7B01G064700 chr3B 91.866 209 16 1 299 507 154705039 154704832 1.360000e-74 291
46 TraesCS7B01G064700 chr3B 95.152 165 8 0 3316 3480 428703873 428704037 1.060000e-65 261
47 TraesCS7B01G064700 chr3B 93.567 171 9 2 3317 3485 664118004 664117834 1.780000e-63 254
48 TraesCS7B01G064700 chr3B 93.023 172 12 0 3317 3488 39913015 39912844 6.400000e-63 252
49 TraesCS7B01G064700 chr3B 91.011 178 13 2 123 298 603859120 603858944 1.790000e-58 237
50 TraesCS7B01G064700 chr1A 96.111 180 6 1 121 299 445501201 445501380 3.770000e-75 292
51 TraesCS7B01G064700 chr1A 91.388 209 18 0 299 507 49302276 49302068 1.750000e-73 287
52 TraesCS7B01G064700 chr4B 91.388 209 18 0 299 507 68661451 68661659 1.750000e-73 287
53 TraesCS7B01G064700 chr1B 91.388 209 18 0 299 507 94561759 94561967 1.750000e-73 287
54 TraesCS7B01G064700 chr1B 91.346 208 18 0 299 506 629797904 629798111 6.310000e-73 285
55 TraesCS7B01G064700 chr1B 97.674 129 2 1 1 128 279187482 279187610 1.800000e-53 220
56 TraesCS7B01G064700 chr1B 97.674 129 2 1 1 128 629797790 629797918 1.800000e-53 220
57 TraesCS7B01G064700 chr1D 91.388 209 17 1 299 507 6551411 6551618 6.310000e-73 285
58 TraesCS7B01G064700 chr1D 97.674 129 2 1 1 128 21655521 21655393 1.800000e-53 220
59 TraesCS7B01G064700 chr4A 92.265 181 13 1 3307 3487 741783857 741783678 4.950000e-64 255
60 TraesCS7B01G064700 chr4A 90.576 191 18 0 117 307 574212296 574212486 1.780000e-63 254
61 TraesCS7B01G064700 chr4A 91.011 178 14 2 120 295 4199723 4199900 4.980000e-59 239
62 TraesCS7B01G064700 chr4D 90.164 183 14 3 119 298 55062377 55062196 6.450000e-58 235
63 TraesCS7B01G064700 chr5B 97.674 129 2 1 1 128 482994266 482994138 1.800000e-53 220
64 TraesCS7B01G064700 chr2A 97.674 129 2 1 1 128 695285618 695285746 1.800000e-53 220


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 TraesCS7B01G064700 chr7B 70242477 70246335 3858 False 7127.0 7127 100.0000 1 3859 1 chr7B.!!$F1 3858
1 TraesCS7B01G064700 chr7B 70338665 70342378 3713 False 2924.5 5228 95.5740 1 3859 2 chr7B.!!$F7 3858
2 TraesCS7B01G064700 chr7B 69849048 69852242 3194 False 2676.5 4728 96.5715 506 3859 2 chr7B.!!$F3 3353
3 TraesCS7B01G064700 chr7B 69912320 69915514 3194 False 2660.0 4706 96.2420 506 3859 2 chr7B.!!$F4 3353
4 TraesCS7B01G064700 chr7B 69992205 69995398 3193 False 2593.0 4567 95.9230 506 3859 2 chr7B.!!$F5 3353
5 TraesCS7B01G064700 chr7B 70068703 70072249 3546 False 2589.5 4599 97.1080 506 3859 2 chr7B.!!$F6 3353
6 TraesCS7B01G064700 chr6B 548948104 548951293 3189 False 2558.5 4514 95.3820 506 3859 2 chr6B.!!$F2 3353
7 TraesCS7B01G064700 chr6B 549028616 549031811 3195 False 2554.5 4514 95.1520 506 3859 2 chr6B.!!$F3 3353
8 TraesCS7B01G064700 chr7D 110890088 110893271 3183 False 2372.0 4117 94.7760 506 3859 2 chr7D.!!$F4 3353
9 TraesCS7B01G064700 chrUn 16612153 16614644 2491 False 2931.0 2931 88.2050 854 3318 1 chrUn.!!$F3 2464
10 TraesCS7B01G064700 chrUn 272511471 272513976 2505 False 2918.0 2918 87.9120 816 3318 1 chrUn.!!$F6 2502
11 TraesCS7B01G064700 chrUn 16657284 16659808 2524 False 2915.0 2915 87.8080 816 3318 1 chrUn.!!$F4 2502
12 TraesCS7B01G064700 chrUn 16441990 16444485 2495 True 2870.0 2870 87.6870 816 3305 1 chrUn.!!$R1 2489
13 TraesCS7B01G064700 chrUn 344031471 344033460 1989 False 2320.0 2320 87.9430 1313 3305 1 chrUn.!!$F7 1992
14 TraesCS7B01G064700 chrUn 379232839 379234392 1553 True 2183.0 2183 92.0670 1594 3148 1 chrUn.!!$R3 1554
15 TraesCS7B01G064700 chrUn 16547539 16548185 646 False 743.0 743 87.7110 2669 3305 1 chrUn.!!$F2 636
16 TraesCS7B01G064700 chrUn 203045617 203046263 646 False 743.0 743 87.7110 2669 3305 1 chrUn.!!$F5 636
17 TraesCS7B01G064700 chr2B 27356054 27357817 1763 False 2381.0 2381 91.1150 1218 2973 1 chr2B.!!$F2 1755
18 TraesCS7B01G064700 chr2D 19847101 19848198 1097 True 1312.0 1312 88.5170 2234 3318 1 chr2D.!!$R2 1084

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
449 451 0.548926 TTCACCCCAGCACCTATCCA 60.549 55.0 0.0 0.0 0.00 3.41 F
672 675 0.911045 TGCCTCTCCTTGATCTGGCA 60.911 55.0 0.0 0.0 46.59 4.92 F
1589 1653 1.056660 CCCTAACCCATGCTATCCGT 58.943 55.0 0.0 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2479 0.031716 TAGCCCATCCAGCAGAGACT 60.032 55.000 0.0 0.0 0.0 3.24 R
2654 2750 1.281656 CGTTTTTGGTGAGGACGGC 59.718 57.895 0.0 0.0 0.0 5.68 R
3372 3702 0.035439 ATTCACTCATTTCGCCCCGT 60.035 50.000 0.0 0.0 0.0 5.28 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
27 28 2.207501 TACCCTTCCTCTCGCCTCGT 62.208 60.000 0.00 0.00 0.00 4.18
67 68 3.906649 GCAGCAGCGTCGTCATCG 61.907 66.667 0.00 0.00 38.55 3.84
81 82 1.263484 GTCATCGTCGCGATCCTTCTA 59.737 52.381 14.06 0.00 45.19 2.10
83 84 1.531578 CATCGTCGCGATCCTTCTAGA 59.468 52.381 14.06 2.63 45.19 2.43
118 119 2.815647 GGCGCTTCGGAGTCTTGG 60.816 66.667 7.64 0.00 0.00 3.61
151 152 0.946221 GCCACGTTGAGAGGAGTGTG 60.946 60.000 0.00 0.00 31.73 3.82
253 255 5.929697 AACACATGTACTTGACATCACAG 57.070 39.130 15.13 0.00 46.33 3.66
328 330 3.407967 GGAAGATCCCGGTGGGCA 61.408 66.667 0.00 0.00 43.94 5.36
349 351 2.740714 GCGATCGCGTGGCTTCTTT 61.741 57.895 26.12 0.00 40.36 2.52
363 365 5.117592 GTGGCTTCTTTGATTTTGTTGATCG 59.882 40.000 0.00 0.00 0.00 3.69
364 366 4.622740 GGCTTCTTTGATTTTGTTGATCGG 59.377 41.667 0.00 0.00 0.00 4.18
367 369 3.571828 TCTTTGATTTTGTTGATCGGCCA 59.428 39.130 2.24 0.00 0.00 5.36
373 375 0.801872 TTGTTGATCGGCCATTGTCG 59.198 50.000 2.24 0.00 42.14 4.35
402 404 6.515272 TGTTTCTTTTGCTCTTTCTCTGTT 57.485 33.333 0.00 0.00 0.00 3.16
414 416 6.625960 GCTCTTTCTCTGTTGTTTCTTTTGGT 60.626 38.462 0.00 0.00 0.00 3.67
431 433 1.001974 TGGTCGTATCTGTGCTGCTTT 59.998 47.619 0.00 0.00 0.00 3.51
433 435 2.337583 GTCGTATCTGTGCTGCTTTCA 58.662 47.619 0.00 0.00 0.00 2.69
449 451 0.548926 TTCACCCCAGCACCTATCCA 60.549 55.000 0.00 0.00 0.00 3.41
489 491 2.883122 TTTGTATACAAAGCGGGGGT 57.117 45.000 23.91 0.00 40.55 4.95
672 675 0.911045 TGCCTCTCCTTGATCTGGCA 60.911 55.000 0.00 0.00 46.59 4.92
681 686 2.141011 TTGATCTGGCACCCCACAGG 62.141 60.000 0.00 0.00 43.78 4.00
760 783 2.671351 CGGGGGATAATTCGATCGAGTG 60.671 54.545 18.54 0.00 0.00 3.51
1031 1063 1.487142 TCCTCAAGTCGTTTGTTCCCA 59.513 47.619 3.16 0.00 38.01 4.37
1465 1522 4.216257 TCATCATCTTCATCATCTACGCGA 59.784 41.667 15.93 0.00 0.00 5.87
1589 1653 1.056660 CCCTAACCCATGCTATCCGT 58.943 55.000 0.00 0.00 0.00 4.69
1592 1656 3.162666 CCTAACCCATGCTATCCGTCTA 58.837 50.000 0.00 0.00 0.00 2.59
1815 1891 1.076533 CGTCGACCCGTGATCTTTGG 61.077 60.000 10.58 0.00 0.00 3.28
1840 1916 8.400186 GGTAACTGCTTTAACTTGTTAGTTCAA 58.600 33.333 0.00 0.00 43.45 2.69
1893 1978 4.090786 TGCTGTTGTAATGATACGTTGTCG 59.909 41.667 0.00 0.00 43.34 4.35
2064 2150 1.677052 GTTCGTGCCAAAACCCTGTTA 59.323 47.619 0.00 0.00 0.00 2.41
2206 2296 4.957954 TCCTTTACAGGGCGAATTACTAGA 59.042 41.667 0.00 0.00 41.25 2.43
2227 2317 8.709308 ACTAGATCAGGCTAATTGTTAATGACT 58.291 33.333 0.00 0.00 0.00 3.41
2331 2422 5.730568 GCTTATTTGCAGGGTAAAGTGATCG 60.731 44.000 0.00 0.00 0.00 3.69
2388 2479 2.103432 TCGCTGGTAAACTTCCTCAACA 59.897 45.455 0.00 0.00 0.00 3.33
2654 2750 1.448540 AAGAATGTCGAGCTGCCCG 60.449 57.895 0.00 0.00 0.00 6.13
2824 2930 7.618502 TTTGTTAGCTAGTAGAGTCTGAGAG 57.381 40.000 1.86 0.00 0.00 3.20
2850 2957 6.825721 TGCCTTTAATTTTGTGAACCATTGTT 59.174 30.769 0.00 0.00 37.42 2.83
3112 3230 0.455815 CCCAAAGGGCGTCTTATTGC 59.544 55.000 0.00 0.00 35.35 3.56
3134 3254 0.675633 ATGCAACTTGAACCTGGTGC 59.324 50.000 0.00 0.00 0.00 5.01
3203 3516 1.021920 GCTCCTGCTCTTTTCCCGTC 61.022 60.000 0.00 0.00 36.03 4.79
3222 3535 3.627577 CGTCAGGCTGCCTTGTTAATTAT 59.372 43.478 20.79 0.00 0.00 1.28
3254 3581 2.476126 TTTTCGCGGGGAAGTATGAA 57.524 45.000 6.13 0.00 35.70 2.57
3258 3585 0.876342 CGCGGGGAAGTATGAAGCTC 60.876 60.000 0.00 0.00 0.00 4.09
3326 3656 7.553881 AATTGTTTGTCATATACTTCCTCCG 57.446 36.000 0.00 0.00 0.00 4.63
3327 3657 5.670792 TGTTTGTCATATACTTCCTCCGT 57.329 39.130 0.00 0.00 0.00 4.69
3328 3658 6.045072 TGTTTGTCATATACTTCCTCCGTT 57.955 37.500 0.00 0.00 0.00 4.44
3329 3659 6.103997 TGTTTGTCATATACTTCCTCCGTTC 58.896 40.000 0.00 0.00 0.00 3.95
3330 3660 6.070995 TGTTTGTCATATACTTCCTCCGTTCT 60.071 38.462 0.00 0.00 0.00 3.01
3331 3661 6.540438 TTGTCATATACTTCCTCCGTTCTT 57.460 37.500 0.00 0.00 0.00 2.52
3332 3662 7.649533 TTGTCATATACTTCCTCCGTTCTTA 57.350 36.000 0.00 0.00 0.00 2.10
3333 3663 7.649533 TGTCATATACTTCCTCCGTTCTTAA 57.350 36.000 0.00 0.00 0.00 1.85
3334 3664 8.070034 TGTCATATACTTCCTCCGTTCTTAAA 57.930 34.615 0.00 0.00 0.00 1.52
3335 3665 8.701895 TGTCATATACTTCCTCCGTTCTTAAAT 58.298 33.333 0.00 0.00 0.00 1.40
3341 3671 9.901172 ATACTTCCTCCGTTCTTAAATATTTGT 57.099 29.630 11.05 0.00 0.00 2.83
3342 3672 8.265165 ACTTCCTCCGTTCTTAAATATTTGTC 57.735 34.615 11.05 0.00 0.00 3.18
3343 3673 8.101419 ACTTCCTCCGTTCTTAAATATTTGTCT 58.899 33.333 11.05 0.00 0.00 3.41
3344 3674 8.857694 TTCCTCCGTTCTTAAATATTTGTCTT 57.142 30.769 11.05 0.00 0.00 3.01
3345 3675 8.857694 TCCTCCGTTCTTAAATATTTGTCTTT 57.142 30.769 11.05 0.00 0.00 2.52
3346 3676 8.943002 TCCTCCGTTCTTAAATATTTGTCTTTC 58.057 33.333 11.05 0.00 0.00 2.62
3347 3677 8.947115 CCTCCGTTCTTAAATATTTGTCTTTCT 58.053 33.333 11.05 0.00 0.00 2.52
3376 3706 9.273016 AGATTTCAATAAGTGATTACATACGGG 57.727 33.333 0.00 0.00 35.70 5.28
3377 3707 7.795482 TTTCAATAAGTGATTACATACGGGG 57.205 36.000 0.00 0.00 35.70 5.73
3378 3708 5.302360 TCAATAAGTGATTACATACGGGGC 58.698 41.667 0.00 0.00 0.00 5.80
3379 3709 2.234300 AAGTGATTACATACGGGGCG 57.766 50.000 0.00 0.00 0.00 6.13
3380 3710 1.405872 AGTGATTACATACGGGGCGA 58.594 50.000 0.00 0.00 0.00 5.54
3381 3711 1.758280 AGTGATTACATACGGGGCGAA 59.242 47.619 0.00 0.00 0.00 4.70
3382 3712 2.168936 AGTGATTACATACGGGGCGAAA 59.831 45.455 0.00 0.00 0.00 3.46
3383 3713 3.135994 GTGATTACATACGGGGCGAAAT 58.864 45.455 0.00 0.00 0.00 2.17
3384 3714 3.059188 GTGATTACATACGGGGCGAAATG 60.059 47.826 0.00 0.00 33.06 2.32
3385 3715 2.983907 TTACATACGGGGCGAAATGA 57.016 45.000 0.00 0.00 31.99 2.57
3386 3716 2.519377 TACATACGGGGCGAAATGAG 57.481 50.000 0.00 0.00 31.99 2.90
3387 3717 0.539986 ACATACGGGGCGAAATGAGT 59.460 50.000 0.00 0.00 31.99 3.41
3388 3718 0.937304 CATACGGGGCGAAATGAGTG 59.063 55.000 0.00 0.00 0.00 3.51
3389 3719 0.828022 ATACGGGGCGAAATGAGTGA 59.172 50.000 0.00 0.00 0.00 3.41
3390 3720 0.609151 TACGGGGCGAAATGAGTGAA 59.391 50.000 0.00 0.00 0.00 3.18
3391 3721 0.035439 ACGGGGCGAAATGAGTGAAT 60.035 50.000 0.00 0.00 0.00 2.57
3392 3722 0.657840 CGGGGCGAAATGAGTGAATC 59.342 55.000 0.00 0.00 0.00 2.52
3393 3723 1.743772 CGGGGCGAAATGAGTGAATCT 60.744 52.381 0.00 0.00 0.00 2.40
3394 3724 2.483013 CGGGGCGAAATGAGTGAATCTA 60.483 50.000 0.00 0.00 0.00 1.98
3395 3725 2.872858 GGGGCGAAATGAGTGAATCTAC 59.127 50.000 0.00 0.00 0.00 2.59
3396 3726 3.531538 GGGCGAAATGAGTGAATCTACA 58.468 45.455 0.00 0.00 0.00 2.74
3397 3727 3.309954 GGGCGAAATGAGTGAATCTACAC 59.690 47.826 0.00 0.00 40.60 2.90
3439 3769 6.258230 ACATCTGTATGTTGTGTCCATTTG 57.742 37.500 0.00 0.00 44.07 2.32
3440 3770 6.003326 ACATCTGTATGTTGTGTCCATTTGA 58.997 36.000 0.00 0.00 44.07 2.69
3441 3771 6.489700 ACATCTGTATGTTGTGTCCATTTGAA 59.510 34.615 0.00 0.00 44.07 2.69
3442 3772 6.951062 TCTGTATGTTGTGTCCATTTGAAA 57.049 33.333 0.00 0.00 0.00 2.69
3443 3773 7.523293 TCTGTATGTTGTGTCCATTTGAAAT 57.477 32.000 0.00 0.00 0.00 2.17
3444 3774 7.369607 TCTGTATGTTGTGTCCATTTGAAATG 58.630 34.615 10.84 10.84 0.00 2.32
3445 3775 5.925397 TGTATGTTGTGTCCATTTGAAATGC 59.075 36.000 12.26 0.87 0.00 3.56
3446 3776 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
3447 3777 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
3448 3778 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
3449 3779 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
3450 3780 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
3451 3781 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
3452 3782 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
3453 3783 6.095377 GTGTCCATTTGAAATGCCTAGAAAG 58.905 40.000 12.26 0.00 0.00 2.62
3454 3784 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
3455 3785 6.071952 TGTCCATTTGAAATGCCTAGAAAGAC 60.072 38.462 12.26 11.27 0.00 3.01
3456 3786 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
3457 3787 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
3458 3788 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
3459 3789 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
3460 3790 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
3465 3795 9.226345 GAAATGCCTAGAAAGACAAATATTTCG 57.774 33.333 0.00 0.00 40.33 3.46
3466 3796 6.677781 TGCCTAGAAAGACAAATATTTCGG 57.322 37.500 0.00 0.00 40.33 4.30
3467 3797 6.411376 TGCCTAGAAAGACAAATATTTCGGA 58.589 36.000 0.00 0.00 40.33 4.55
3468 3798 6.882140 TGCCTAGAAAGACAAATATTTCGGAA 59.118 34.615 0.00 0.00 40.33 4.30
3469 3799 7.148306 TGCCTAGAAAGACAAATATTTCGGAAC 60.148 37.037 0.00 0.00 40.33 3.62
3470 3800 7.148306 GCCTAGAAAGACAAATATTTCGGAACA 60.148 37.037 0.00 0.00 40.33 3.18
3471 3801 8.391106 CCTAGAAAGACAAATATTTCGGAACAG 58.609 37.037 0.00 0.00 40.33 3.16
3472 3802 7.979444 AGAAAGACAAATATTTCGGAACAGA 57.021 32.000 0.00 0.00 40.33 3.41
3473 3803 8.034058 AGAAAGACAAATATTTCGGAACAGAG 57.966 34.615 0.00 0.00 40.33 3.35
3474 3804 6.743575 AAGACAAATATTTCGGAACAGAGG 57.256 37.500 0.00 0.00 0.00 3.69
3475 3805 5.186198 AGACAAATATTTCGGAACAGAGGG 58.814 41.667 0.00 0.00 0.00 4.30
3476 3806 5.045869 AGACAAATATTTCGGAACAGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
3477 3807 5.186198 ACAAATATTTCGGAACAGAGGGAG 58.814 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.262824 GAAGGATCGCGACGATGACG 61.263 60.000 12.93 0.00 47.00 4.35
81 82 1.066143 CGGCACCTATCAACACCTTCT 60.066 52.381 0.00 0.00 0.00 2.85
83 84 0.035439 CCGGCACCTATCAACACCTT 60.035 55.000 0.00 0.00 0.00 3.50
253 255 7.749570 CAGAAGTCTGTGATGTCATTTCAAATC 59.250 37.037 0.00 0.00 39.09 2.17
328 330 4.742201 AAGCCACGCGATCGCTGT 62.742 61.111 34.69 29.19 39.84 4.40
349 351 3.257873 ACAATGGCCGATCAACAAAATCA 59.742 39.130 0.00 0.00 0.00 2.57
367 369 4.024977 GCAAAAGAAACAAATGCCGACAAT 60.025 37.500 0.00 0.00 0.00 2.71
373 375 5.525012 AGAAAGAGCAAAAGAAACAAATGCC 59.475 36.000 0.00 0.00 37.73 4.40
383 385 6.375455 AGAAACAACAGAGAAAGAGCAAAAGA 59.625 34.615 0.00 0.00 0.00 2.52
402 404 4.024387 GCACAGATACGACCAAAAGAAACA 60.024 41.667 0.00 0.00 0.00 2.83
414 416 2.337583 GTGAAAGCAGCACAGATACGA 58.662 47.619 0.00 0.00 36.31 3.43
431 433 0.327480 ATGGATAGGTGCTGGGGTGA 60.327 55.000 0.00 0.00 0.00 4.02
433 435 0.624500 ACATGGATAGGTGCTGGGGT 60.625 55.000 0.00 0.00 0.00 4.95
449 451 1.750193 CAACCAACCGAGCCATACAT 58.250 50.000 0.00 0.00 0.00 2.29
489 491 4.020307 CCTACCTTACCGAACAAGGGTTTA 60.020 45.833 12.42 0.00 45.81 2.01
601 603 3.861840 AGTGCAGCGTATGTACAGATTT 58.138 40.909 0.33 0.00 46.08 2.17
602 604 3.526931 AGTGCAGCGTATGTACAGATT 57.473 42.857 0.33 0.00 46.08 2.40
760 783 2.612221 CCTCTTCCACGTAACAACTCCC 60.612 54.545 0.00 0.00 0.00 4.30
1031 1063 1.792949 GAACACAACTCGATTGCTCGT 59.207 47.619 7.28 1.82 45.25 4.18
1231 1284 0.582005 AAGCAGAAAACGAGCGTCAC 59.418 50.000 0.00 0.00 0.00 3.67
1465 1522 1.487558 ACGTACCCTTGTGTTCTTGGT 59.512 47.619 0.00 0.00 0.00 3.67
1589 1653 0.798159 CACTGCACGCAAAGCATAGA 59.202 50.000 0.00 0.00 41.82 1.98
1592 1656 1.454572 TTCCACTGCACGCAAAGCAT 61.455 50.000 0.00 0.00 41.82 3.79
1655 1724 4.722700 GAGCACACCGGCCACCAT 62.723 66.667 0.00 0.00 0.00 3.55
1776 1845 0.261696 ATCCATAAGTTGGGGTGGGC 59.738 55.000 0.00 0.00 46.45 5.36
1815 1891 9.434559 CTTGAACTAACAAGTTAAAGCAGTTAC 57.565 33.333 3.10 0.00 41.32 2.50
1840 1916 4.094887 CACAACGCAGATTAATTAGCCACT 59.905 41.667 7.29 0.00 0.00 4.00
1872 1957 5.798434 TCTCGACAACGTATCATTACAACAG 59.202 40.000 0.00 0.00 40.69 3.16
2018 2103 4.942761 AAACATGAAAGGTGAGTGCATT 57.057 36.364 0.00 0.00 0.00 3.56
2206 2296 7.255381 GCATCAGTCATTAACAATTAGCCTGAT 60.255 37.037 0.00 0.00 37.56 2.90
2227 2317 5.178623 CACTCGTTAGTTGGTAAAAGCATCA 59.821 40.000 0.00 0.00 31.97 3.07
2331 2422 1.275573 GTACTCCACACTCTTGGTCCC 59.724 57.143 0.00 0.00 37.93 4.46
2388 2479 0.031716 TAGCCCATCCAGCAGAGACT 60.032 55.000 0.00 0.00 0.00 3.24
2654 2750 1.281656 CGTTTTTGGTGAGGACGGC 59.718 57.895 0.00 0.00 0.00 5.68
2691 2787 5.531122 TTATTTCTCTATGGTGACGGAGG 57.469 43.478 0.00 0.00 0.00 4.30
2758 2855 4.162320 TCAGACCTGTTGAAGTATCATCCC 59.838 45.833 0.00 0.00 34.96 3.85
2824 2930 6.259829 ACAATGGTTCACAAAATTAAAGGCAC 59.740 34.615 0.00 0.00 0.00 5.01
2986 3102 4.662278 AGCCACCACACACTGTAATTAAT 58.338 39.130 0.00 0.00 0.00 1.40
3112 3230 2.030540 CACCAGGTTCAAGTTGCATCAG 60.031 50.000 0.00 0.00 0.00 2.90
3134 3254 2.154007 GTCTGTCTCTCGTTTTCGCTTG 59.846 50.000 0.00 0.00 43.73 4.01
3203 3516 4.398988 TGTGATAATTAACAAGGCAGCCTG 59.601 41.667 17.05 11.99 32.13 4.85
3239 3554 0.876342 GAGCTTCATACTTCCCCGCG 60.876 60.000 0.00 0.00 0.00 6.46
3254 3581 2.450867 TCTAGCATGGACTCAGAGCT 57.549 50.000 0.00 0.00 40.04 4.09
3318 3648 8.494016 AGACAAATATTTAAGAACGGAGGAAG 57.506 34.615 0.00 0.00 0.00 3.46
3319 3649 8.857694 AAGACAAATATTTAAGAACGGAGGAA 57.142 30.769 0.00 0.00 0.00 3.36
3320 3650 8.857694 AAAGACAAATATTTAAGAACGGAGGA 57.142 30.769 0.00 0.00 0.00 3.71
3321 3651 8.947115 AGAAAGACAAATATTTAAGAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
3350 3680 9.273016 CCCGTATGTAATCACTTATTGAAATCT 57.727 33.333 0.00 0.00 37.92 2.40
3351 3681 8.504005 CCCCGTATGTAATCACTTATTGAAATC 58.496 37.037 0.00 0.00 37.92 2.17
3352 3682 7.040686 GCCCCGTATGTAATCACTTATTGAAAT 60.041 37.037 0.00 0.00 37.92 2.17
3353 3683 6.261381 GCCCCGTATGTAATCACTTATTGAAA 59.739 38.462 0.00 0.00 37.92 2.69
3354 3684 5.761234 GCCCCGTATGTAATCACTTATTGAA 59.239 40.000 0.00 0.00 37.92 2.69
3355 3685 5.302360 GCCCCGTATGTAATCACTTATTGA 58.698 41.667 0.00 0.00 39.11 2.57
3356 3686 4.151689 CGCCCCGTATGTAATCACTTATTG 59.848 45.833 0.00 0.00 0.00 1.90
3357 3687 4.039488 TCGCCCCGTATGTAATCACTTATT 59.961 41.667 0.00 0.00 0.00 1.40
3358 3688 3.575256 TCGCCCCGTATGTAATCACTTAT 59.425 43.478 0.00 0.00 0.00 1.73
3359 3689 2.957680 TCGCCCCGTATGTAATCACTTA 59.042 45.455 0.00 0.00 0.00 2.24
3360 3690 1.758280 TCGCCCCGTATGTAATCACTT 59.242 47.619 0.00 0.00 0.00 3.16
3361 3691 1.405872 TCGCCCCGTATGTAATCACT 58.594 50.000 0.00 0.00 0.00 3.41
3362 3692 2.228138 TTCGCCCCGTATGTAATCAC 57.772 50.000 0.00 0.00 0.00 3.06
3363 3693 2.983907 TTTCGCCCCGTATGTAATCA 57.016 45.000 0.00 0.00 0.00 2.57
3364 3694 3.395639 TCATTTCGCCCCGTATGTAATC 58.604 45.455 0.00 0.00 0.00 1.75
3365 3695 3.181458 ACTCATTTCGCCCCGTATGTAAT 60.181 43.478 0.00 0.00 0.00 1.89
3366 3696 2.168936 ACTCATTTCGCCCCGTATGTAA 59.831 45.455 0.00 0.00 0.00 2.41
3367 3697 1.758280 ACTCATTTCGCCCCGTATGTA 59.242 47.619 0.00 0.00 0.00 2.29
3368 3698 0.539986 ACTCATTTCGCCCCGTATGT 59.460 50.000 0.00 0.00 0.00 2.29
3369 3699 0.937304 CACTCATTTCGCCCCGTATG 59.063 55.000 0.00 0.00 0.00 2.39
3370 3700 0.828022 TCACTCATTTCGCCCCGTAT 59.172 50.000 0.00 0.00 0.00 3.06
3371 3701 0.609151 TTCACTCATTTCGCCCCGTA 59.391 50.000 0.00 0.00 0.00 4.02
3372 3702 0.035439 ATTCACTCATTTCGCCCCGT 60.035 50.000 0.00 0.00 0.00 5.28
3373 3703 0.657840 GATTCACTCATTTCGCCCCG 59.342 55.000 0.00 0.00 0.00 5.73
3374 3704 2.044123 AGATTCACTCATTTCGCCCC 57.956 50.000 0.00 0.00 0.00 5.80
3375 3705 3.309954 GTGTAGATTCACTCATTTCGCCC 59.690 47.826 0.00 0.00 35.68 6.13
3376 3706 4.184629 AGTGTAGATTCACTCATTTCGCC 58.815 43.478 0.00 0.00 44.07 5.54
3414 3744 7.828717 TCAAATGGACACAACATACAGATGTAT 59.171 33.333 0.00 0.00 45.93 2.29
3415 3745 7.164803 TCAAATGGACACAACATACAGATGTA 58.835 34.615 0.00 0.00 45.93 2.29
3417 3747 6.499234 TCAAATGGACACAACATACAGATG 57.501 37.500 0.00 0.00 39.16 2.90
3418 3748 7.523293 TTTCAAATGGACACAACATACAGAT 57.477 32.000 0.00 0.00 0.00 2.90
3419 3749 6.951062 TTTCAAATGGACACAACATACAGA 57.049 33.333 0.00 0.00 0.00 3.41
3420 3750 6.089820 GCATTTCAAATGGACACAACATACAG 59.910 38.462 12.14 0.00 0.00 2.74
3421 3751 5.925397 GCATTTCAAATGGACACAACATACA 59.075 36.000 12.14 0.00 0.00 2.29
3422 3752 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
3423 3753 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
3424 3754 4.040706 AGGCATTTCAAATGGACACAACAT 59.959 37.500 12.14 0.00 0.00 2.71
3425 3755 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
3426 3756 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
3427 3757 5.076182 TCTAGGCATTTCAAATGGACACAA 58.924 37.500 12.14 0.00 0.00 3.33
3428 3758 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
3429 3759 5.643379 TTCTAGGCATTTCAAATGGACAC 57.357 39.130 12.14 0.00 0.00 3.67
3430 3760 6.009589 TCTTTCTAGGCATTTCAAATGGACA 58.990 36.000 12.14 0.00 0.00 4.02
3431 3761 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
3432 3762 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
3433 3763 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
3434 3764 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
3439 3769 9.226345 CGAAATATTTGTCTTTCTAGGCATTTC 57.774 33.333 5.17 0.00 35.56 2.17
3440 3770 8.190784 CCGAAATATTTGTCTTTCTAGGCATTT 58.809 33.333 5.17 0.00 35.56 2.32
3441 3771 7.556275 TCCGAAATATTTGTCTTTCTAGGCATT 59.444 33.333 5.17 0.00 35.56 3.56
3442 3772 7.054124 TCCGAAATATTTGTCTTTCTAGGCAT 58.946 34.615 5.17 0.00 35.56 4.40
3443 3773 6.411376 TCCGAAATATTTGTCTTTCTAGGCA 58.589 36.000 5.17 0.00 33.22 4.75
3444 3774 6.920569 TCCGAAATATTTGTCTTTCTAGGC 57.079 37.500 5.17 0.00 30.80 3.93
3445 3775 8.263940 TGTTCCGAAATATTTGTCTTTCTAGG 57.736 34.615 5.17 0.00 30.80 3.02
3446 3776 9.151471 TCTGTTCCGAAATATTTGTCTTTCTAG 57.849 33.333 5.17 0.00 30.80 2.43
3447 3777 9.151471 CTCTGTTCCGAAATATTTGTCTTTCTA 57.849 33.333 5.17 0.00 30.80 2.10
3448 3778 7.119846 CCTCTGTTCCGAAATATTTGTCTTTCT 59.880 37.037 5.17 0.00 30.80 2.52
3449 3779 7.244192 CCTCTGTTCCGAAATATTTGTCTTTC 58.756 38.462 5.17 0.00 0.00 2.62
3450 3780 6.151144 CCCTCTGTTCCGAAATATTTGTCTTT 59.849 38.462 5.17 0.00 0.00 2.52
3451 3781 5.648092 CCCTCTGTTCCGAAATATTTGTCTT 59.352 40.000 5.17 0.00 0.00 3.01
3452 3782 5.045869 TCCCTCTGTTCCGAAATATTTGTCT 60.046 40.000 5.17 0.00 0.00 3.41
3453 3783 5.183228 TCCCTCTGTTCCGAAATATTTGTC 58.817 41.667 5.17 0.00 0.00 3.18
3454 3784 5.174037 TCCCTCTGTTCCGAAATATTTGT 57.826 39.130 5.17 0.00 0.00 2.83
3455 3785 5.186198 ACTCCCTCTGTTCCGAAATATTTG 58.814 41.667 5.17 0.00 0.00 2.32
3456 3786 5.437191 ACTCCCTCTGTTCCGAAATATTT 57.563 39.130 0.00 0.00 0.00 1.40
3457 3787 6.749036 ATACTCCCTCTGTTCCGAAATATT 57.251 37.500 0.00 0.00 0.00 1.28
3458 3788 8.437274 AATATACTCCCTCTGTTCCGAAATAT 57.563 34.615 0.00 0.00 0.00 1.28
3459 3789 7.850935 AATATACTCCCTCTGTTCCGAAATA 57.149 36.000 0.00 0.00 0.00 1.40
3460 3790 6.749036 AATATACTCCCTCTGTTCCGAAAT 57.251 37.500 0.00 0.00 0.00 2.17
3461 3791 6.155565 TGAAATATACTCCCTCTGTTCCGAAA 59.844 38.462 0.00 0.00 0.00 3.46
3462 3792 5.659525 TGAAATATACTCCCTCTGTTCCGAA 59.340 40.000 0.00 0.00 0.00 4.30
3463 3793 5.205821 TGAAATATACTCCCTCTGTTCCGA 58.794 41.667 0.00 0.00 0.00 4.55
3464 3794 5.531122 TGAAATATACTCCCTCTGTTCCG 57.469 43.478 0.00 0.00 0.00 4.30
3465 3795 8.652290 ACTAATGAAATATACTCCCTCTGTTCC 58.348 37.037 0.00 0.00 0.00 3.62
3466 3796 9.482627 CACTAATGAAATATACTCCCTCTGTTC 57.517 37.037 0.00 0.00 0.00 3.18
3467 3797 8.993424 ACACTAATGAAATATACTCCCTCTGTT 58.007 33.333 0.00 0.00 0.00 3.16
3468 3798 8.424918 CACACTAATGAAATATACTCCCTCTGT 58.575 37.037 0.00 0.00 0.00 3.41
3469 3799 8.424918 ACACACTAATGAAATATACTCCCTCTG 58.575 37.037 0.00 0.00 0.00 3.35
3470 3800 8.554490 ACACACTAATGAAATATACTCCCTCT 57.446 34.615 0.00 0.00 0.00 3.69
3471 3801 9.614792 AAACACACTAATGAAATATACTCCCTC 57.385 33.333 0.00 0.00 0.00 4.30
3472 3802 9.396022 CAAACACACTAATGAAATATACTCCCT 57.604 33.333 0.00 0.00 0.00 4.20
3473 3803 9.391006 TCAAACACACTAATGAAATATACTCCC 57.609 33.333 0.00 0.00 0.00 4.30
3477 3807 9.370126 GCGATCAAACACACTAATGAAATATAC 57.630 33.333 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.