Multiple sequence alignment - TraesCS5A01G321400

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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 TraesCS5A01G321400 chr5A 100.000 4377 0 0 1 4377 534241359 534245735 0.000000e+00 8083.0
1 TraesCS5A01G321400 chr5A 82.622 328 52 5 1589 1914 66518685 66518361 7.160000e-73 285.0
2 TraesCS5A01G321400 chr5B 91.211 3857 196 71 601 4377 506948785 506952578 0.000000e+00 5112.0
3 TraesCS5A01G321400 chr5B 89.524 525 53 2 1 525 506945757 506946279 0.000000e+00 664.0
4 TraesCS5A01G321400 chr5B 83.756 394 57 6 1997 2388 50344870 50344482 2.490000e-97 366.0
5 TraesCS5A01G321400 chr5D 93.566 1803 86 18 1960 3759 420871403 420873178 0.000000e+00 2660.0
6 TraesCS5A01G321400 chr5D 87.165 1418 105 34 585 1962 420869961 420871341 0.000000e+00 1539.0
7 TraesCS5A01G321400 chr5D 87.711 651 31 19 3752 4377 420873229 420873855 0.000000e+00 713.0
8 TraesCS5A01G321400 chr5D 91.238 525 43 3 1 525 420869347 420869868 0.000000e+00 712.0
9 TraesCS5A01G321400 chr5D 80.229 349 55 8 2771 3117 410377233 410376897 2.610000e-62 250.0
10 TraesCS5A01G321400 chr5D 91.549 71 5 1 500 570 420869900 420869969 3.600000e-16 97.1
11 TraesCS5A01G321400 chr4D 94.508 1220 57 6 1971 3188 69350502 69349291 0.000000e+00 1873.0
12 TraesCS5A01G321400 chr6D 94.016 1220 63 5 1971 3188 299212624 299213835 0.000000e+00 1840.0
13 TraesCS5A01G321400 chr6D 85.354 198 22 6 3096 3290 149898271 149898078 9.600000e-47 198.0
14 TraesCS5A01G321400 chr6D 85.714 84 8 1 3461 3544 149897351 149897272 7.800000e-13 86.1
15 TraesCS5A01G321400 chr6A 93.745 1231 64 6 1960 3188 212307925 212309144 0.000000e+00 1834.0
16 TraesCS5A01G321400 chr6A 85.185 81 8 1 3461 3541 195132503 195132579 3.630000e-11 80.5
17 TraesCS5A01G321400 chrUn 93.551 1225 65 6 1966 3188 52774589 52773377 0.000000e+00 1812.0
18 TraesCS5A01G321400 chrUn 93.420 1231 67 6 1960 3188 258404454 258405672 0.000000e+00 1812.0
19 TraesCS5A01G321400 chrUn 94.776 268 14 0 1698 1965 52774921 52774654 6.770000e-113 418.0
20 TraesCS5A01G321400 chrUn 95.094 265 13 0 1698 1962 258404128 258404392 6.770000e-113 418.0
21 TraesCS5A01G321400 chr2D 92.377 1220 61 6 1971 3188 476480287 476479098 0.000000e+00 1709.0
22 TraesCS5A01G321400 chr7A 92.687 547 38 2 3102 3648 169760732 169761276 0.000000e+00 787.0
23 TraesCS5A01G321400 chr3B 92.139 547 38 2 3102 3648 219749706 219749165 0.000000e+00 767.0
24 TraesCS5A01G321400 chr3B 91.773 547 40 3 3102 3648 218228804 218228263 0.000000e+00 756.0
25 TraesCS5A01G321400 chr3B 91.225 547 41 3 3102 3648 58466247 58466786 0.000000e+00 737.0
26 TraesCS5A01G321400 chr3B 80.630 413 65 12 1506 1914 558374463 558374062 5.500000e-79 305.0
27 TraesCS5A01G321400 chr1D 94.340 265 15 0 1698 1962 76794947 76795211 1.470000e-109 407.0
28 TraesCS5A01G321400 chr3A 83.692 325 48 5 1592 1914 157049695 157049374 7.110000e-78 302.0
29 TraesCS5A01G321400 chr3A 79.903 413 68 12 1506 1914 54751678 54751277 5.540000e-74 289.0
30 TraesCS5A01G321400 chr7D 83.209 268 32 9 2297 2563 603698830 603699085 2.630000e-57 233.0


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 TraesCS5A01G321400 chr5A 534241359 534245735 4376 False 8083.00 8083 100.0000 1 4377 1 chr5A.!!$F1 4376
1 TraesCS5A01G321400 chr5B 506945757 506952578 6821 False 2888.00 5112 90.3675 1 4377 2 chr5B.!!$F1 4376
2 TraesCS5A01G321400 chr5D 420869347 420873855 4508 False 1144.22 2660 90.2458 1 4377 5 chr5D.!!$F1 4376
3 TraesCS5A01G321400 chr4D 69349291 69350502 1211 True 1873.00 1873 94.5080 1971 3188 1 chr4D.!!$R1 1217
4 TraesCS5A01G321400 chr6D 299212624 299213835 1211 False 1840.00 1840 94.0160 1971 3188 1 chr6D.!!$F1 1217
5 TraesCS5A01G321400 chr6A 212307925 212309144 1219 False 1834.00 1834 93.7450 1960 3188 1 chr6A.!!$F2 1228
6 TraesCS5A01G321400 chrUn 52773377 52774921 1544 True 1115.00 1812 94.1635 1698 3188 2 chrUn.!!$R1 1490
7 TraesCS5A01G321400 chrUn 258404128 258405672 1544 False 1115.00 1812 94.2570 1698 3188 2 chrUn.!!$F1 1490
8 TraesCS5A01G321400 chr2D 476479098 476480287 1189 True 1709.00 1709 92.3770 1971 3188 1 chr2D.!!$R1 1217
9 TraesCS5A01G321400 chr7A 169760732 169761276 544 False 787.00 787 92.6870 3102 3648 1 chr7A.!!$F1 546
10 TraesCS5A01G321400 chr3B 219749165 219749706 541 True 767.00 767 92.1390 3102 3648 1 chr3B.!!$R2 546
11 TraesCS5A01G321400 chr3B 218228263 218228804 541 True 756.00 756 91.7730 3102 3648 1 chr3B.!!$R1 546
12 TraesCS5A01G321400 chr3B 58466247 58466786 539 False 737.00 737 91.2250 3102 3648 1 chr3B.!!$F1 546

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
578 634 0.110688 CACCACTCGCAACGACATTG 60.111 55.0 0.0 0.0 41.69 2.82 F
1121 3569 0.108567 GCTGTCCTCTTCCGAGTTCC 60.109 60.0 0.0 0.0 35.43 3.62 F
1125 3573 0.324460 TCCTCTTCCGAGTTCCTCCC 60.324 60.0 0.0 0.0 35.43 4.30 F
1126 3574 0.324830 CCTCTTCCGAGTTCCTCCCT 60.325 60.0 0.0 0.0 35.43 4.20 F
1151 3599 0.452784 GCGCTGCCGTTCTTACTTTG 60.453 55.0 0.0 0.0 36.67 2.77 F
1625 4154 0.674895 GGCCGTGCAAGACTGATCTT 60.675 55.0 0.0 0.0 46.63 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 4443 0.110678 ACGAGTCAGACTGGTGGAGA 59.889 55.000 16.80 0.0 35.80 3.71 R
2869 5479 1.137086 GAGACTGAAATAGGAGGCGCA 59.863 52.381 10.83 0.0 0.00 6.09 R
2870 5480 1.410882 AGAGACTGAAATAGGAGGCGC 59.589 52.381 0.00 0.0 0.00 6.53 R
3034 5644 2.944129 TGAAAGAGGTTTCTTGGGTGG 58.056 47.619 0.01 0.0 42.80 4.61 R
3130 5741 2.092968 GCTGGTATCTTGGTCCACATCA 60.093 50.000 0.00 0.0 0.00 3.07 R
3463 6080 1.346395 ACATCGAGTGGGCACTGTAAA 59.654 47.619 0.00 0.0 42.66 2.01 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
33 34 3.483574 GCACAACGGAAGATGTATCAACG 60.484 47.826 0.00 0.00 45.89 4.10
208 209 0.530650 CATAGATCGCCGCTGGTTGT 60.531 55.000 0.00 0.00 0.00 3.32
240 241 2.512896 GATGGCTGTAGCAGGGGG 59.487 66.667 6.18 0.00 44.36 5.40
241 242 2.286425 ATGGCTGTAGCAGGGGGT 60.286 61.111 6.18 0.00 44.36 4.95
242 243 2.330924 GATGGCTGTAGCAGGGGGTC 62.331 65.000 6.18 0.00 44.36 4.46
243 244 3.009115 GGCTGTAGCAGGGGGTCA 61.009 66.667 6.18 0.00 44.36 4.02
275 276 1.067582 CTCCCCTAATGACGACGGC 59.932 63.158 0.00 0.00 0.00 5.68
287 288 1.153647 CGACGGCTGTAGCATGGAA 60.154 57.895 0.00 0.00 44.36 3.53
315 316 0.525761 GTTGCAGCTCCGCCAAAATA 59.474 50.000 0.00 0.00 0.00 1.40
336 337 2.663196 GTTGTAGCAGGGGTCGCT 59.337 61.111 0.00 0.00 43.62 4.93
412 413 1.073199 CTGGTTCCAGTTTCCGCCT 59.927 57.895 10.40 0.00 0.00 5.52
425 426 3.357079 CGCCTTCGGTTGCAGCTT 61.357 61.111 0.00 0.00 0.00 3.74
435 436 0.593128 GTTGCAGCTTCACCAACGAT 59.407 50.000 0.00 0.00 30.89 3.73
436 437 1.804151 GTTGCAGCTTCACCAACGATA 59.196 47.619 0.00 0.00 30.89 2.92
496 497 3.496131 CGGTCGCAACATTCCCCG 61.496 66.667 0.00 0.00 0.00 5.73
498 499 1.451387 GGTCGCAACATTCCCCGAT 60.451 57.895 0.00 0.00 31.96 4.18
518 574 1.672030 TCGGTTCTAGCACGACGGA 60.672 57.895 0.00 0.00 0.00 4.69
528 584 4.578898 ACGACGGACGCAGCACAA 62.579 61.111 0.00 0.00 46.94 3.33
574 630 2.658707 GAGCACCACTCGCAACGAC 61.659 63.158 0.00 0.00 35.18 4.34
575 631 2.964925 GCACCACTCGCAACGACA 60.965 61.111 0.00 0.00 0.00 4.35
576 632 2.317609 GCACCACTCGCAACGACAT 61.318 57.895 0.00 0.00 0.00 3.06
577 633 1.841663 GCACCACTCGCAACGACATT 61.842 55.000 0.00 0.00 0.00 2.71
578 634 0.110688 CACCACTCGCAACGACATTG 60.111 55.000 0.00 0.00 41.69 2.82
579 635 0.531974 ACCACTCGCAACGACATTGT 60.532 50.000 0.00 0.00 40.77 2.71
599 655 3.553095 GACCCCCTCGCAGCAAAGT 62.553 63.158 0.00 0.00 0.00 2.66
626 3060 1.209747 GGCCCCTAGTAGTCAAGGTTG 59.790 57.143 0.00 0.00 0.00 3.77
632 3066 3.576982 CCTAGTAGTCAAGGTTGTGTCCA 59.423 47.826 0.00 0.00 0.00 4.02
636 3070 1.774254 AGTCAAGGTTGTGTCCATCCA 59.226 47.619 0.00 0.00 33.55 3.41
640 3074 2.751259 CAAGGTTGTGTCCATCCAGATG 59.249 50.000 0.40 0.40 38.51 2.90
874 3321 2.363795 AAGCCCAGATCCGACGGA 60.364 61.111 20.85 20.85 35.55 4.69
958 3406 1.490490 ACTGGGAAGCAGTTGTTGAGA 59.510 47.619 0.00 0.00 0.00 3.27
967 3415 2.607635 GCAGTTGTTGAGACTCGAAACA 59.392 45.455 13.85 9.78 32.19 2.83
1112 3560 4.299547 TGCGCACGCTGTCCTCTT 62.300 61.111 16.77 0.00 42.51 2.85
1113 3561 3.482783 GCGCACGCTGTCCTCTTC 61.483 66.667 7.96 0.00 38.26 2.87
1114 3562 2.811317 CGCACGCTGTCCTCTTCC 60.811 66.667 0.00 0.00 0.00 3.46
1115 3563 2.811317 GCACGCTGTCCTCTTCCG 60.811 66.667 0.00 0.00 0.00 4.30
1116 3564 2.962569 CACGCTGTCCTCTTCCGA 59.037 61.111 0.00 0.00 0.00 4.55
1117 3565 1.153939 CACGCTGTCCTCTTCCGAG 60.154 63.158 0.00 0.00 37.01 4.63
1118 3566 1.604023 ACGCTGTCCTCTTCCGAGT 60.604 57.895 0.00 0.00 35.43 4.18
1119 3567 1.179814 ACGCTGTCCTCTTCCGAGTT 61.180 55.000 0.00 0.00 35.43 3.01
1120 3568 0.456995 CGCTGTCCTCTTCCGAGTTC 60.457 60.000 0.00 0.00 35.43 3.01
1121 3569 0.108567 GCTGTCCTCTTCCGAGTTCC 60.109 60.000 0.00 0.00 35.43 3.62
1122 3570 1.551452 CTGTCCTCTTCCGAGTTCCT 58.449 55.000 0.00 0.00 35.43 3.36
1123 3571 1.474879 CTGTCCTCTTCCGAGTTCCTC 59.525 57.143 0.00 0.00 35.43 3.71
1124 3572 0.818938 GTCCTCTTCCGAGTTCCTCC 59.181 60.000 0.00 0.00 35.43 4.30
1125 3573 0.324460 TCCTCTTCCGAGTTCCTCCC 60.324 60.000 0.00 0.00 35.43 4.30
1126 3574 0.324830 CCTCTTCCGAGTTCCTCCCT 60.325 60.000 0.00 0.00 35.43 4.20
1127 3575 1.107945 CTCTTCCGAGTTCCTCCCTC 58.892 60.000 0.00 0.00 32.47 4.30
1128 3576 0.705253 TCTTCCGAGTTCCTCCCTCT 59.295 55.000 0.00 0.00 0.00 3.69
1129 3577 1.077334 TCTTCCGAGTTCCTCCCTCTT 59.923 52.381 0.00 0.00 0.00 2.85
1130 3578 1.205893 CTTCCGAGTTCCTCCCTCTTG 59.794 57.143 0.00 0.00 0.00 3.02
1131 3579 1.219393 CCGAGTTCCTCCCTCTTGC 59.781 63.158 0.00 0.00 0.00 4.01
1132 3580 1.153745 CGAGTTCCTCCCTCTTGCG 60.154 63.158 0.00 0.00 0.00 4.85
1133 3581 1.448717 GAGTTCCTCCCTCTTGCGC 60.449 63.158 0.00 0.00 0.00 6.09
1150 3598 1.866925 GCGCTGCCGTTCTTACTTT 59.133 52.632 0.00 0.00 36.67 2.66
1151 3599 0.452784 GCGCTGCCGTTCTTACTTTG 60.453 55.000 0.00 0.00 36.67 2.77
1159 3607 4.639310 TGCCGTTCTTACTTTGTTGGTAAA 59.361 37.500 0.00 0.00 0.00 2.01
1161 3609 6.183360 TGCCGTTCTTACTTTGTTGGTAAATT 60.183 34.615 0.00 0.00 0.00 1.82
1162 3610 6.361481 GCCGTTCTTACTTTGTTGGTAAATTC 59.639 38.462 0.00 0.00 0.00 2.17
1163 3611 7.645402 CCGTTCTTACTTTGTTGGTAAATTCT 58.355 34.615 0.00 0.00 0.00 2.40
1164 3612 7.589954 CCGTTCTTACTTTGTTGGTAAATTCTG 59.410 37.037 0.00 0.00 0.00 3.02
1166 3614 9.797556 GTTCTTACTTTGTTGGTAAATTCTGTT 57.202 29.630 0.00 0.00 0.00 3.16
1306 3772 3.254166 TCTCATCTGCTGTTTTTCTTGCC 59.746 43.478 0.00 0.00 0.00 4.52
1354 3820 1.773856 TTGGTGGCCAGATTCGGTCA 61.774 55.000 5.11 0.00 38.69 4.02
1361 3827 2.300152 GGCCAGATTCGGTCATCTATGA 59.700 50.000 0.00 0.00 31.86 2.15
1368 3834 5.931146 AGATTCGGTCATCTATGAATGAAGC 59.069 40.000 12.30 12.30 38.13 3.86
1369 3835 4.670896 TCGGTCATCTATGAATGAAGCA 57.329 40.909 0.00 0.00 38.75 3.91
1391 3860 9.638239 AAGCACGATATTTAACAATGTTTCAAT 57.362 25.926 3.17 6.24 0.00 2.57
1421 3890 4.525912 ATCAACTGACCAAATTCTTGCC 57.474 40.909 0.00 0.00 0.00 4.52
1426 3895 6.097554 TCAACTGACCAAATTCTTGCCTTTTA 59.902 34.615 0.00 0.00 0.00 1.52
1462 3934 4.121317 CGGCAAATTCATGGCAAACATAT 58.879 39.130 0.00 0.00 45.50 1.78
1464 3936 5.064962 CGGCAAATTCATGGCAAACATATTT 59.935 36.000 0.00 0.00 45.50 1.40
1545 4070 8.852135 CCTATATATAGCCTAAGTAACTCCAGC 58.148 40.741 13.49 0.00 0.00 4.85
1559 4088 8.549338 AGTAACTCCAGCTTTTATTTGTCTAC 57.451 34.615 0.00 0.00 0.00 2.59
1568 4097 9.394477 CAGCTTTTATTTGTCTACAAGTTTACC 57.606 33.333 0.00 0.00 37.15 2.85
1613 4142 1.067060 GAATTTATCCCTTGGCCGTGC 59.933 52.381 0.00 0.00 0.00 5.34
1624 4153 1.078848 GGCCGTGCAAGACTGATCT 60.079 57.895 0.00 0.00 36.42 2.75
1625 4154 0.674895 GGCCGTGCAAGACTGATCTT 60.675 55.000 0.00 0.00 46.63 2.40
1626 4155 1.160137 GCCGTGCAAGACTGATCTTT 58.840 50.000 0.00 0.00 42.91 2.52
1777 4306 3.521560 GCACAACTGAATACGGAGATCA 58.478 45.455 0.00 0.00 0.00 2.92
1914 4443 7.630082 TGAGGCAGTATGTACCTTTTCTTTAT 58.370 34.615 0.00 0.00 39.31 1.40
1928 4457 6.433847 TTTTCTTTATCTCCACCAGTCTGA 57.566 37.500 0.00 0.00 0.00 3.27
1969 4562 5.163693 TGCTTCATTCTGTTATGCATGAGTG 60.164 40.000 10.16 5.22 0.00 3.51
1984 4577 1.339535 TGAGTGTGCTGTTGTGTGGAA 60.340 47.619 0.00 0.00 0.00 3.53
1991 4584 3.612423 GTGCTGTTGTGTGGAAAAAGTTC 59.388 43.478 0.00 0.00 0.00 3.01
1995 4588 4.915704 TGTTGTGTGGAAAAAGTTCGATC 58.084 39.130 0.00 0.00 34.28 3.69
1996 4589 4.396478 TGTTGTGTGGAAAAAGTTCGATCA 59.604 37.500 0.00 0.00 34.28 2.92
2041 4634 4.162320 TCACTCTTATCGCCCTTTCATTCT 59.838 41.667 0.00 0.00 0.00 2.40
2169 4762 3.559171 GGCTGGAATACCTTCACAGTCAA 60.559 47.826 0.00 0.00 35.81 3.18
2196 4789 5.392380 GCCAGCGATTATTCATAGGGATTTG 60.392 44.000 0.00 0.00 0.00 2.32
2511 5105 3.492102 CCAGAACTCTTCACTGGGAAA 57.508 47.619 0.00 0.00 44.96 3.13
2709 5309 4.202101 TGCAACTGATTTTCGTCCAATGTT 60.202 37.500 0.00 0.00 0.00 2.71
2710 5310 4.744631 GCAACTGATTTTCGTCCAATGTTT 59.255 37.500 0.00 0.00 0.00 2.83
2827 5431 3.808728 ACTTTGTGCAAGTGAGCTCTTA 58.191 40.909 16.19 0.00 44.70 2.10
2868 5478 2.592861 CAAGCCTATCCCAGCGCC 60.593 66.667 2.29 0.00 0.00 6.53
2869 5479 2.770048 AAGCCTATCCCAGCGCCT 60.770 61.111 2.29 0.00 0.00 5.52
2870 5480 3.112205 AAGCCTATCCCAGCGCCTG 62.112 63.158 2.29 1.18 0.00 4.85
3001 5611 6.174049 TGTCACCGACCATGTTAATTTATCA 58.826 36.000 0.00 0.00 0.00 2.15
3034 5644 3.031736 TGATCCCAGTGGTAAGTAGAGC 58.968 50.000 8.74 0.06 0.00 4.09
3057 5668 3.068165 CACCCAAGAAACCTCTTTCAACC 59.932 47.826 0.00 0.00 40.05 3.77
3070 5681 7.114095 ACCTCTTTCAACCAACTTAACACTTA 58.886 34.615 0.00 0.00 0.00 2.24
3089 5700 8.306313 ACACTTAATCCTATACTGACACATCA 57.694 34.615 0.00 0.00 0.00 3.07
3130 5741 0.036306 AGAATGCCGAGTTCCCGTTT 59.964 50.000 0.00 0.00 0.00 3.60
3184 5795 3.399330 TCTGGAAATGGTCGACACTTTC 58.601 45.455 23.47 23.47 0.00 2.62
3378 5993 3.075582 AGATTGGCCGTCCTAGGATAGTA 59.924 47.826 16.27 0.00 36.82 1.82
3382 5997 2.488710 GGCCGTCCTAGGATAGTACTGT 60.489 54.545 16.27 0.00 36.82 3.55
3463 6080 2.270205 CCTCTGGTGCGGCTCATT 59.730 61.111 0.00 0.00 0.00 2.57
3569 6186 9.117183 TCATTGATTGAGATTTATCAGTTGGAG 57.883 33.333 0.00 0.00 32.76 3.86
3704 6322 4.161295 ATTGCGCGCCAGCCTCTA 62.161 61.111 30.77 3.44 41.18 2.43
3718 6336 4.649674 CCAGCCTCTAGTGGTATTCTTGTA 59.350 45.833 12.31 0.00 0.00 2.41
3739 6357 5.989168 TGTAACTCATTTTGTCACGATGTCT 59.011 36.000 0.00 0.00 0.00 3.41
3740 6358 5.597813 AACTCATTTTGTCACGATGTCTC 57.402 39.130 0.00 0.00 0.00 3.36
3847 6527 2.379907 AGACCAAACATTCTCCACCCAT 59.620 45.455 0.00 0.00 0.00 4.00
3848 6528 3.165071 GACCAAACATTCTCCACCCATT 58.835 45.455 0.00 0.00 0.00 3.16
3852 6532 5.604650 ACCAAACATTCTCCACCCATTAAAA 59.395 36.000 0.00 0.00 0.00 1.52
3853 6533 6.100424 ACCAAACATTCTCCACCCATTAAAAA 59.900 34.615 0.00 0.00 0.00 1.94
3855 6535 6.994421 AACATTCTCCACCCATTAAAAACT 57.006 33.333 0.00 0.00 0.00 2.66
3857 6537 8.485578 AACATTCTCCACCCATTAAAAACTAA 57.514 30.769 0.00 0.00 0.00 2.24
3858 6538 8.485578 ACATTCTCCACCCATTAAAAACTAAA 57.514 30.769 0.00 0.00 0.00 1.85
3859 6539 9.100197 ACATTCTCCACCCATTAAAAACTAAAT 57.900 29.630 0.00 0.00 0.00 1.40
3863 6543 9.027202 TCTCCACCCATTAAAAACTAAATAACC 57.973 33.333 0.00 0.00 0.00 2.85
3864 6544 8.722622 TCCACCCATTAAAAACTAAATAACCA 57.277 30.769 0.00 0.00 0.00 3.67
3898 6578 0.250124 ACGGGTCAAAAGTGATCGCA 60.250 50.000 9.33 0.00 35.52 5.10
3905 6585 3.498397 GTCAAAAGTGATCGCAGGAAAGA 59.502 43.478 9.33 0.00 35.80 2.52
3906 6586 4.024048 GTCAAAAGTGATCGCAGGAAAGAA 60.024 41.667 9.33 0.00 35.80 2.52
3908 6588 3.409026 AAGTGATCGCAGGAAAGAAGT 57.591 42.857 9.33 0.00 0.00 3.01
3909 6589 2.693069 AGTGATCGCAGGAAAGAAGTG 58.307 47.619 9.33 0.00 0.00 3.16
3939 6639 7.067008 CCGTTCACAAATATAAGATGTTCCCTT 59.933 37.037 0.00 0.00 0.00 3.95
4038 6756 3.027292 TTTTTCCGACAGGCACGC 58.973 55.556 0.00 0.00 37.47 5.34
4325 7046 1.727335 GCTTAACTGAGTTGGACGAGC 59.273 52.381 8.33 6.00 0.00 5.03
4326 7047 2.866460 GCTTAACTGAGTTGGACGAGCA 60.866 50.000 8.33 0.00 0.00 4.26
4328 7049 1.583054 AACTGAGTTGGACGAGCAAC 58.417 50.000 0.00 0.00 0.00 4.17
4348 7069 0.302890 GCTGGCGTCATGAGATTTCG 59.697 55.000 0.00 0.00 0.00 3.46
4353 7074 1.926561 CGTCATGAGATTTCGCTCCA 58.073 50.000 0.00 0.00 33.95 3.86
4355 7076 2.029728 CGTCATGAGATTTCGCTCCAAC 59.970 50.000 0.00 0.00 33.95 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.502962 AGCTGCTTGATACTCTTTCTGAC 58.497 43.478 0.00 0.00 0.00 3.51
156 157 1.760613 TCATTAGGGGAGCTACAACCG 59.239 52.381 0.00 0.00 0.00 4.44
162 163 1.760613 CCGTTGTCATTAGGGGAGCTA 59.239 52.381 0.00 0.00 0.00 3.32
228 229 2.990479 GGTGACCCCCTGCTACAG 59.010 66.667 0.00 0.00 0.00 2.74
275 276 2.813179 GCGGCGTTCCATGCTACAG 61.813 63.158 9.37 0.00 0.00 2.74
315 316 0.035439 CGACCCCTGCTACAACCATT 60.035 55.000 0.00 0.00 0.00 3.16
339 340 0.249398 CGTTAGGGTAGCTGCAACCT 59.751 55.000 12.23 12.23 37.18 3.50
395 396 0.536460 GAAGGCGGAAACTGGAACCA 60.536 55.000 0.00 0.00 0.00 3.67
412 413 0.749818 TTGGTGAAGCTGCAACCGAA 60.750 50.000 7.45 0.00 0.00 4.30
425 426 1.000052 TGTTGCGACTATCGTTGGTGA 60.000 47.619 5.50 0.00 42.81 4.02
443 444 0.865769 GAAACTGACACCGCGAATGT 59.134 50.000 8.23 12.31 0.00 2.71
455 456 1.913778 ATGTGCATGCTGGAAACTGA 58.086 45.000 20.33 0.00 0.00 3.41
506 562 2.577112 CTGCGTCCGTCGTGCTAG 60.577 66.667 0.00 0.00 42.13 3.42
512 568 3.112075 ATTGTGCTGCGTCCGTCG 61.112 61.111 0.00 0.00 43.12 5.12
518 574 2.677524 ATGGCCATTGTGCTGCGT 60.678 55.556 14.09 0.00 0.00 5.24
607 663 1.907255 ACAACCTTGACTACTAGGGGC 59.093 52.381 0.00 0.00 41.91 5.80
626 3060 3.191078 CTTCCTCATCTGGATGGACAC 57.809 52.381 10.22 0.00 39.24 3.67
632 3066 3.428063 TCCTTCCTTCCTCATCTGGAT 57.572 47.619 0.00 0.00 35.83 3.41
636 3070 2.703007 CCGATTCCTTCCTTCCTCATCT 59.297 50.000 0.00 0.00 0.00 2.90
640 3074 2.633488 CAACCGATTCCTTCCTTCCTC 58.367 52.381 0.00 0.00 0.00 3.71
839 3273 4.534824 GGACGGGGATCGAGGGGA 62.535 72.222 0.00 0.00 42.43 4.81
900 3347 1.179174 GCGGAATTTATGGGAGGGGC 61.179 60.000 0.00 0.00 0.00 5.80
927 3374 0.621082 CTTCCCAGTTTCCCTCCCTC 59.379 60.000 0.00 0.00 0.00 4.30
928 3375 1.501654 GCTTCCCAGTTTCCCTCCCT 61.502 60.000 0.00 0.00 0.00 4.20
930 3377 0.322906 CTGCTTCCCAGTTTCCCTCC 60.323 60.000 0.00 0.00 36.79 4.30
931 3378 3.256281 CTGCTTCCCAGTTTCCCTC 57.744 57.895 0.00 0.00 36.79 4.30
958 3406 1.429463 GAATCGCTGGTGTTTCGAGT 58.571 50.000 0.00 0.00 35.61 4.18
967 3415 4.514577 CCGAGCCGAATCGCTGGT 62.515 66.667 0.00 0.00 39.87 4.00
1098 3546 2.811317 CGGAAGAGGACAGCGTGC 60.811 66.667 0.00 0.00 0.00 5.34
1116 3564 2.665603 GCGCAAGAGGGAGGAACT 59.334 61.111 0.30 0.00 42.32 3.01
1117 3565 2.815647 CGCGCAAGAGGGAGGAAC 60.816 66.667 8.75 0.00 43.02 3.62
1118 3566 4.760047 GCGCGCAAGAGGGAGGAA 62.760 66.667 29.10 0.00 43.02 3.36
1130 3578 4.500568 GTAAGAACGGCAGCGCGC 62.501 66.667 26.66 26.66 41.28 6.86
1131 3579 1.897398 AAAGTAAGAACGGCAGCGCG 61.897 55.000 0.00 0.00 0.00 6.86
1132 3580 0.452784 CAAAGTAAGAACGGCAGCGC 60.453 55.000 0.00 0.00 0.00 5.92
1133 3581 0.865769 ACAAAGTAAGAACGGCAGCG 59.134 50.000 0.00 0.00 0.00 5.18
1194 3642 5.425941 CGCAGCAATCAATAAAGAAACAC 57.574 39.130 0.00 0.00 0.00 3.32
1306 3772 1.319172 CGAAATCGCGATCTAGACGG 58.681 55.000 23.92 4.08 0.00 4.79
1328 3794 1.755179 ATCTGGCCACCAAAATCGAG 58.245 50.000 0.00 0.00 30.80 4.04
1361 3827 9.638239 AAACATTGTTAAATATCGTGCTTCATT 57.362 25.926 1.76 0.00 0.00 2.57
1391 3860 7.888021 AGAATTTGGTCAGTTGATAACATGGTA 59.112 33.333 0.00 0.00 0.00 3.25
1398 3867 5.774690 AGGCAAGAATTTGGTCAGTTGATAA 59.225 36.000 0.00 0.00 34.79 1.75
1421 3890 5.774630 TGCCGAGGTTTACCAAAATAAAAG 58.225 37.500 1.13 0.00 38.89 2.27
1426 3895 4.882842 ATTTGCCGAGGTTTACCAAAAT 57.117 36.364 1.13 0.00 38.89 1.82
1462 3934 3.327626 TGGCGAGATTAAAGCGTACAAA 58.672 40.909 0.00 0.00 0.00 2.83
1464 3936 2.658373 TGGCGAGATTAAAGCGTACA 57.342 45.000 0.00 0.00 0.00 2.90
1536 4061 8.911918 TTGTAGACAAATAAAAGCTGGAGTTA 57.088 30.769 0.00 0.00 32.11 2.24
1542 4067 9.394477 GGTAAACTTGTAGACAAATAAAAGCTG 57.606 33.333 0.00 0.00 35.15 4.24
1568 4097 9.667107 TCCAACCAGAAAAGAGTACATAAATAG 57.333 33.333 0.00 0.00 0.00 1.73
1574 4103 7.839680 AAATTCCAACCAGAAAAGAGTACAT 57.160 32.000 0.00 0.00 0.00 2.29
1575 4104 8.934023 ATAAATTCCAACCAGAAAAGAGTACA 57.066 30.769 0.00 0.00 0.00 2.90
1607 4136 1.135859 CAAAGATCAGTCTTGCACGGC 60.136 52.381 0.00 0.00 43.80 5.68
1613 4142 7.021790 CACATGATGAACAAAGATCAGTCTTG 58.978 38.462 0.00 0.00 43.80 3.02
1624 4153 6.653526 ATCAAGGAACACATGATGAACAAA 57.346 33.333 0.00 0.00 32.77 2.83
1649 4178 6.337356 GCCTTGTAGCTATTGGCAAAATAAA 58.663 36.000 21.77 0.00 44.79 1.40
1704 4233 0.318614 CAATCCGTGTTTGGCACCAC 60.319 55.000 6.44 6.44 44.97 4.16
1840 4369 9.725019 TGTGATGATGTTAACTGTCTTCTTATT 57.275 29.630 18.75 0.00 0.00 1.40
1914 4443 0.110678 ACGAGTCAGACTGGTGGAGA 59.889 55.000 16.80 0.00 35.80 3.71
1928 4457 5.224888 TGAAGCAAAGTATTACGAACGAGT 58.775 37.500 0.14 0.00 0.00 4.18
1969 4562 3.230743 ACTTTTTCCACACAACAGCAC 57.769 42.857 0.00 0.00 0.00 4.40
1984 4577 8.813282 GTGTGGTTAAATTTTGATCGAACTTTT 58.187 29.630 14.26 10.67 0.00 2.27
1991 4584 8.450964 ACTCTATGTGTGGTTAAATTTTGATCG 58.549 33.333 0.00 0.00 0.00 3.69
1995 4588 9.180678 GTGAACTCTATGTGTGGTTAAATTTTG 57.819 33.333 0.00 0.00 0.00 2.44
1996 4589 9.131791 AGTGAACTCTATGTGTGGTTAAATTTT 57.868 29.630 0.00 0.00 0.00 1.82
2058 4651 7.225734 CGAAACCTGGTTAACATTCCAAATTTT 59.774 33.333 13.37 0.00 33.06 1.82
2071 4664 4.512571 GTGCTTCTTACGAAACCTGGTTAA 59.487 41.667 13.37 2.36 0.00 2.01
2097 4690 4.693283 TCATAGCCTTCATACCGACTTTG 58.307 43.478 0.00 0.00 0.00 2.77
2169 4762 3.055530 CCCTATGAATAATCGCTGGCTCT 60.056 47.826 0.00 0.00 0.00 4.09
2196 4789 9.507280 CCATTTATGAATATGTTGTCACACTTC 57.493 33.333 0.00 0.00 35.03 3.01
2686 5283 3.317711 ACATTGGACGAAAATCAGTTGCA 59.682 39.130 0.00 0.00 0.00 4.08
2827 5431 5.590663 GTCTTTCTGGAGGAAACAGTTCTTT 59.409 40.000 0.00 0.00 38.81 2.52
2868 5478 1.137872 AGACTGAAATAGGAGGCGCAG 59.862 52.381 10.83 0.00 0.00 5.18
2869 5479 1.137086 GAGACTGAAATAGGAGGCGCA 59.863 52.381 10.83 0.00 0.00 6.09
2870 5480 1.410882 AGAGACTGAAATAGGAGGCGC 59.589 52.381 0.00 0.00 0.00 6.53
2871 5481 2.955660 AGAGAGACTGAAATAGGAGGCG 59.044 50.000 0.00 0.00 0.00 5.52
3001 5611 4.164988 CCACTGGGATCAGGAAATCTTAGT 59.835 45.833 0.00 0.00 44.99 2.24
3034 5644 2.944129 TGAAAGAGGTTTCTTGGGTGG 58.056 47.619 0.01 0.00 42.80 4.61
3070 5681 9.466497 ACAATTTTGATGTGTCAGTATAGGATT 57.534 29.630 0.00 0.00 35.39 3.01
3130 5741 2.092968 GCTGGTATCTTGGTCCACATCA 60.093 50.000 0.00 0.00 0.00 3.07
3378 5993 2.174854 ACACTAGCTTGGGGAAAACAGT 59.825 45.455 1.66 0.00 0.00 3.55
3382 5997 5.013704 TGAAGATACACTAGCTTGGGGAAAA 59.986 40.000 1.66 0.00 34.04 2.29
3463 6080 1.346395 ACATCGAGTGGGCACTGTAAA 59.654 47.619 0.00 0.00 42.66 2.01
3556 6173 5.988310 TCGAACTACCTCCAACTGATAAA 57.012 39.130 0.00 0.00 0.00 1.40
3558 6175 5.421056 ACATTCGAACTACCTCCAACTGATA 59.579 40.000 0.00 0.00 0.00 2.15
3569 6186 3.329929 AAGGGACACATTCGAACTACC 57.670 47.619 0.00 0.01 0.00 3.18
3594 6211 9.612066 ATTGGATTGAACACAACAACTTAAAAT 57.388 25.926 0.00 0.00 0.00 1.82
3697 6315 5.958987 AGTTACAAGAATACCACTAGAGGCT 59.041 40.000 6.07 0.00 0.00 4.58
3699 6317 7.406031 TGAGTTACAAGAATACCACTAGAGG 57.594 40.000 4.44 4.44 0.00 3.69
3700 6318 9.877178 AAATGAGTTACAAGAATACCACTAGAG 57.123 33.333 0.00 0.00 0.00 2.43
3703 6321 9.787435 ACAAAATGAGTTACAAGAATACCACTA 57.213 29.630 0.00 0.00 0.00 2.74
3704 6322 8.691661 ACAAAATGAGTTACAAGAATACCACT 57.308 30.769 0.00 0.00 0.00 4.00
3718 6336 5.300752 AGAGACATCGTGACAAAATGAGTT 58.699 37.500 5.54 0.00 0.00 3.01
3739 6357 9.913310 TCTCTATATTTGAAGACTTCTGAGAGA 57.087 33.333 16.02 16.99 0.00 3.10
3829 6508 5.736951 TTTAATGGGTGGAGAATGTTTGG 57.263 39.130 0.00 0.00 0.00 3.28
3857 6537 7.120138 CCCGTAAACTCACACTTTATGGTTATT 59.880 37.037 7.90 0.00 38.09 1.40
3858 6538 6.596497 CCCGTAAACTCACACTTTATGGTTAT 59.404 38.462 7.90 0.00 38.09 1.89
3859 6539 5.933463 CCCGTAAACTCACACTTTATGGTTA 59.067 40.000 7.90 0.00 38.09 2.85
3860 6540 4.758165 CCCGTAAACTCACACTTTATGGTT 59.242 41.667 7.90 0.00 38.09 3.67
3861 6541 4.202388 ACCCGTAAACTCACACTTTATGGT 60.202 41.667 7.90 0.00 38.09 3.55
3862 6542 4.320870 ACCCGTAAACTCACACTTTATGG 58.679 43.478 0.00 0.00 38.93 2.74
3863 6543 4.992319 TGACCCGTAAACTCACACTTTATG 59.008 41.667 0.00 0.00 0.00 1.90
3864 6544 5.217978 TGACCCGTAAACTCACACTTTAT 57.782 39.130 0.00 0.00 0.00 1.40
3898 6578 0.765510 AACGGAGGCACTTCTTTCCT 59.234 50.000 0.00 0.00 41.55 3.36
3905 6585 1.981256 ATTTGTGAACGGAGGCACTT 58.019 45.000 0.00 0.00 41.55 3.16
3908 6588 5.092554 TCTTATATTTGTGAACGGAGGCA 57.907 39.130 0.00 0.00 0.00 4.75
3909 6589 5.527582 ACATCTTATATTTGTGAACGGAGGC 59.472 40.000 0.00 0.00 0.00 4.70
3939 6639 6.806739 CGGCTGTGTCAATTAATATAGATCGA 59.193 38.462 0.00 0.00 0.00 3.59
4027 6733 0.944311 ACACTAAAGCGTGCCTGTCG 60.944 55.000 0.00 0.00 38.45 4.35
4030 6748 0.944386 AACACACTAAAGCGTGCCTG 59.056 50.000 0.00 0.00 38.45 4.85
4328 7049 0.302890 GAAATCTCATGACGCCAGCG 59.697 55.000 11.05 11.05 46.03 5.18


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

AutoCloner maintained by Alex Coulton.