Multiple sequence alignment - TraesCS2D01G283300

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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 TraesCS2D01G283300 chr2D 100.000 7663 0 0 1 7663 356525783 356533445 0.000000e+00 14151
1 TraesCS2D01G283300 chr2D 83.957 187 30 0 143 329 502525970 502525784 6.110000e-41 180
2 TraesCS2D01G283300 chr2D 86.567 134 18 0 5388 5521 32802255 32802388 1.720000e-31 148
3 TraesCS2D01G283300 chr2A 95.582 7401 245 39 1 7339 477001963 477009343 0.000000e+00 11780
4 TraesCS2D01G283300 chr2A 95.222 293 6 8 7368 7657 477009453 477009740 2.520000e-124 457
5 TraesCS2D01G283300 chr2A 88.060 134 16 0 5388 5521 36051539 36051672 7.960000e-35 159
6 TraesCS2D01G283300 chr2B 95.469 4282 109 24 660 4895 424326286 424330528 0.000000e+00 6754
7 TraesCS2D01G283300 chr2B 93.210 2327 92 27 5030 7339 424330867 424333144 0.000000e+00 3362
8 TraesCS2D01G283300 chr2B 78.635 1451 278 22 1108 2539 54545157 54546594 0.000000e+00 933
9 TraesCS2D01G283300 chr2B 92.401 329 13 6 7335 7654 424333173 424333498 7.010000e-125 459
10 TraesCS2D01G283300 chr2B 87.313 134 17 0 5388 5521 54548848 54548981 3.700000e-33 154
11 TraesCS2D01G283300 chr2B 78.210 257 33 10 368 615 136428952 136429194 8.020000e-30 143
12 TraesCS2D01G283300 chr6D 81.876 469 63 13 1 452 329839672 329840135 7.260000e-100 375
13 TraesCS2D01G283300 chr3B 79.452 511 60 21 115 624 52798186 52798652 3.450000e-83 320
14 TraesCS2D01G283300 chr6B 79.227 414 65 11 23 426 680687955 680687553 1.270000e-67 268
15 TraesCS2D01G283300 chr6B 81.985 272 30 11 221 475 352416481 352416212 6.020000e-51 213
16 TraesCS2D01G283300 chr4A 78.737 475 48 25 153 624 120568238 120568662 1.270000e-67 268
17 TraesCS2D01G283300 chr5B 85.057 261 35 3 106 363 590380561 590380302 5.900000e-66 263
18 TraesCS2D01G283300 chr5D 78.523 447 61 13 12 427 358596283 358595841 2.120000e-65 261
19 TraesCS2D01G283300 chr4D 81.410 312 50 8 55 363 365203022 365203328 1.650000e-61 248
20 TraesCS2D01G283300 chr5A 82.558 258 35 6 127 384 104975514 104975761 1.290000e-52 219
21 TraesCS2D01G283300 chr7D 88.060 134 11 2 368 496 109317305 109317438 3.700000e-33 154
22 TraesCS2D01G283300 chr7A 88.060 134 11 2 368 496 115265615 115265748 3.700000e-33 154


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 TraesCS2D01G283300 chr2D 356525783 356533445 7662 False 14151.0 14151 100.000000 1 7663 1 chr2D.!!$F2 7662
1 TraesCS2D01G283300 chr2A 477001963 477009740 7777 False 6118.5 11780 95.402000 1 7657 2 chr2A.!!$F2 7656
2 TraesCS2D01G283300 chr2B 424326286 424333498 7212 False 3525.0 6754 93.693333 660 7654 3 chr2B.!!$F3 6994
3 TraesCS2D01G283300 chr2B 54545157 54548981 3824 False 543.5 933 82.974000 1108 5521 2 chr2B.!!$F2 4413

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
484 485 0.036765 TGTGGAACTACGGTGATGGC 60.037 55.000 0.00 0.00 38.04 4.40 F
504 505 0.739462 TATGACGCGAAGGCTTGTGG 60.739 55.000 15.93 0.00 36.88 4.17 F
943 975 0.906775 TCTTGGATCGGTACCCCAAC 59.093 55.000 15.01 1.40 35.25 3.77 F
1722 1760 1.066303 GACAGGCTCATCTGGAGTACG 59.934 57.143 0.00 0.00 45.88 3.67 F
2740 2906 0.037232 ACTGTGAGCCTTAAGACGCC 60.037 55.000 3.36 0.00 0.00 5.68 F
3906 4098 0.039472 TTGGCATGCTAAGGCTCCAA 59.961 50.000 18.92 7.64 39.04 3.53 F
4983 5665 0.999406 CCTGTTCGCATGACCTAACG 59.001 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1814 0.681733 TCAGTGTCTCTGCACCTTCC 59.318 55.000 0.00 0.00 43.32 3.46 R
1785 1823 4.614475 TCATACCAGGAATCAGTGTCTCT 58.386 43.478 0.00 0.00 0.00 3.10 R
2539 2577 2.856988 GGGGTGGGGTCTGGACAA 60.857 66.667 3.10 0.00 0.00 3.18 R
3291 3481 0.877743 TCAATCATTTGGCGACGCAA 59.122 45.000 23.09 7.74 33.44 4.85 R
4015 4207 0.396060 TGTCTGCTACACATGCCACA 59.604 50.000 0.00 0.00 31.43 4.17 R
5374 6059 3.883489 CACTCATCTGCAATCATGGACAT 59.117 43.478 0.00 0.00 0.00 3.06 R
6780 7475 0.096454 GACCGTTTCTAATGTGCGGC 59.904 55.000 0.00 0.00 45.53 6.53 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
21 22 2.107141 GGACGATGAGGCCGGAAG 59.893 66.667 5.05 0.00 38.99 3.46
27 28 1.977293 GATGAGGCCGGAAGCTCCTT 61.977 60.000 5.05 0.00 43.05 3.36
38 39 1.331399 AAGCTCCTTCTACGCCCTCC 61.331 60.000 0.00 0.00 0.00 4.30
137 138 0.387202 CTCGGGCAGATGTTCGATCT 59.613 55.000 0.00 0.00 0.00 2.75
138 139 0.103026 TCGGGCAGATGTTCGATCTG 59.897 55.000 9.67 9.67 46.12 2.90
145 146 2.045524 AGATGTTCGATCTGCCCATCT 58.954 47.619 7.72 7.72 37.89 2.90
262 263 2.177950 GAGTACCAACTCGCCTCGA 58.822 57.895 0.00 0.00 42.66 4.04
263 264 0.179169 GAGTACCAACTCGCCTCGAC 60.179 60.000 0.00 0.00 42.66 4.20
270 271 3.213402 CTCGCCTCGACCCTCTCC 61.213 72.222 0.00 0.00 0.00 3.71
275 276 3.827898 CTCGACCCTCTCCGGCAC 61.828 72.222 0.00 0.00 0.00 5.01
299 300 0.976073 ATCTACCACACCCTCCACGG 60.976 60.000 0.00 0.00 0.00 4.94
303 304 2.978010 CACACCCTCCACGGCAAC 60.978 66.667 0.00 0.00 0.00 4.17
359 360 1.859703 CGACGACGAGTAGATGCTAGT 59.140 52.381 0.00 0.00 42.66 2.57
402 403 7.545965 AGTTGTTTCAGTTTGACCTATCTATCG 59.454 37.037 0.00 0.00 0.00 2.92
473 474 9.162764 GTATGTATGAACTATGTTTGTGGAACT 57.837 33.333 0.00 0.00 39.08 3.01
484 485 0.036765 TGTGGAACTACGGTGATGGC 60.037 55.000 0.00 0.00 38.04 4.40
488 489 2.102420 TGGAACTACGGTGATGGCTATG 59.898 50.000 0.00 0.00 0.00 2.23
489 490 2.364324 GGAACTACGGTGATGGCTATGA 59.636 50.000 0.00 0.00 0.00 2.15
504 505 0.739462 TATGACGCGAAGGCTTGTGG 60.739 55.000 15.93 0.00 36.88 4.17
506 507 2.357517 ACGCGAAGGCTTGTGGAG 60.358 61.111 15.93 0.00 36.88 3.86
525 526 6.479990 TGTGGAGCTATCTATGTTTGAAATCG 59.520 38.462 0.00 0.00 0.00 3.34
529 530 8.082852 GGAGCTATCTATGTTTGAAATCGAGTA 58.917 37.037 0.00 0.00 0.00 2.59
536 537 9.653287 TCTATGTTTGAAATCGAGTACAAATCT 57.347 29.630 13.69 8.83 35.31 2.40
540 541 6.389622 TTGAAATCGAGTACAAATCTGACG 57.610 37.500 0.00 0.00 0.00 4.35
552 553 8.832521 AGTACAAATCTGACGACATTTAACAAA 58.167 29.630 0.00 0.00 0.00 2.83
555 556 9.180678 ACAAATCTGACGACATTTAACAAAATC 57.819 29.630 0.00 0.00 0.00 2.17
562 563 9.986833 TGACGACATTTAACAAAATCTATCATG 57.013 29.630 0.00 0.00 0.00 3.07
564 565 7.639850 ACGACATTTAACAAAATCTATCATGCG 59.360 33.333 0.00 0.00 0.00 4.73
567 568 8.131100 ACATTTAACAAAATCTATCATGCGAGG 58.869 33.333 0.00 0.00 0.00 4.63
573 574 1.080230 CTATCATGCGAGGAGGCCG 60.080 63.158 0.00 0.00 0.00 6.13
628 629 9.755064 CTATAAACGAAATTTACAGGACAGTTG 57.245 33.333 0.00 0.00 35.57 3.16
632 633 8.836268 AACGAAATTTACAGGACAGTTGTATA 57.164 30.769 0.00 0.00 31.60 1.47
636 637 2.667473 ACAGGACAGTTGTATACCGC 57.333 50.000 0.00 0.00 0.00 5.68
637 638 2.176889 ACAGGACAGTTGTATACCGCT 58.823 47.619 0.00 0.00 0.00 5.52
638 639 2.165845 ACAGGACAGTTGTATACCGCTC 59.834 50.000 0.00 0.00 0.00 5.03
639 640 2.427453 CAGGACAGTTGTATACCGCTCT 59.573 50.000 0.00 0.00 0.00 4.09
640 641 3.630769 CAGGACAGTTGTATACCGCTCTA 59.369 47.826 0.00 0.00 0.00 2.43
641 642 4.097437 CAGGACAGTTGTATACCGCTCTAA 59.903 45.833 0.00 0.00 0.00 2.10
642 643 4.338682 AGGACAGTTGTATACCGCTCTAAG 59.661 45.833 0.00 0.00 0.00 2.18
643 644 4.043037 ACAGTTGTATACCGCTCTAAGC 57.957 45.455 0.00 0.00 38.02 3.09
645 646 4.099573 ACAGTTGTATACCGCTCTAAGCAT 59.900 41.667 0.00 0.00 42.58 3.79
646 647 4.681942 CAGTTGTATACCGCTCTAAGCATC 59.318 45.833 0.00 0.00 42.58 3.91
647 648 4.341235 AGTTGTATACCGCTCTAAGCATCA 59.659 41.667 0.00 0.00 42.58 3.07
648 649 4.238761 TGTATACCGCTCTAAGCATCAC 57.761 45.455 0.00 0.00 42.58 3.06
649 650 3.634910 TGTATACCGCTCTAAGCATCACA 59.365 43.478 0.00 0.00 42.58 3.58
650 651 4.280929 TGTATACCGCTCTAAGCATCACAT 59.719 41.667 0.00 0.00 42.58 3.21
651 652 5.475564 TGTATACCGCTCTAAGCATCACATA 59.524 40.000 0.00 0.00 42.58 2.29
652 653 3.819564 ACCGCTCTAAGCATCACATAA 57.180 42.857 0.00 0.00 42.58 1.90
735 756 1.265635 TGTTCGCGAAAACATCCAAGG 59.734 47.619 25.24 0.00 34.31 3.61
739 760 2.031508 TCGCGAAAACATCCAAGGAAAC 60.032 45.455 6.20 0.00 0.00 2.78
759 780 7.846823 AGGAAACTATCGAATATATCCCCATCT 59.153 37.037 0.00 0.00 40.61 2.90
883 915 3.208594 ACGAACCCTAACTTGTTTGGAC 58.791 45.455 13.89 5.92 31.42 4.02
943 975 0.906775 TCTTGGATCGGTACCCCAAC 59.093 55.000 15.01 1.40 35.25 3.77
1722 1760 1.066303 GACAGGCTCATCTGGAGTACG 59.934 57.143 0.00 0.00 45.88 3.67
1767 1805 2.186826 GTGGACCACTGCAAAGCGT 61.187 57.895 17.84 0.00 0.00 5.07
1776 1814 2.429069 GCAAAGCGTTTCGGCCTG 60.429 61.111 0.00 0.00 0.00 4.85
2539 2577 5.044402 ACCCAGCCTAAAATGTACAAGGTAT 60.044 40.000 11.97 0.63 0.00 2.73
2546 2584 7.415206 GCCTAAAATGTACAAGGTATTGTCCAG 60.415 40.741 11.97 0.00 46.90 3.86
2673 2839 8.794335 AGTCCTGATTATTCCTTACTTTTGAC 57.206 34.615 0.00 0.00 0.00 3.18
2733 2899 7.949690 TTAGTAGACATAACTGTGAGCCTTA 57.050 36.000 0.00 0.00 35.14 2.69
2734 2900 6.852420 AGTAGACATAACTGTGAGCCTTAA 57.148 37.500 0.00 0.00 35.14 1.85
2735 2901 6.868622 AGTAGACATAACTGTGAGCCTTAAG 58.131 40.000 0.00 0.00 35.14 1.85
2736 2902 6.663953 AGTAGACATAACTGTGAGCCTTAAGA 59.336 38.462 3.36 0.00 35.14 2.10
2737 2903 5.725362 AGACATAACTGTGAGCCTTAAGAC 58.275 41.667 3.36 0.00 35.14 3.01
2738 2904 4.495422 ACATAACTGTGAGCCTTAAGACG 58.505 43.478 3.36 0.00 33.22 4.18
2739 2905 1.797025 AACTGTGAGCCTTAAGACGC 58.203 50.000 3.36 0.00 0.00 5.19
2740 2906 0.037232 ACTGTGAGCCTTAAGACGCC 60.037 55.000 3.36 0.00 0.00 5.68
2741 2907 0.247736 CTGTGAGCCTTAAGACGCCT 59.752 55.000 3.36 0.00 0.00 5.52
3131 3321 5.947663 TGATTCTTTCCTTCCAGTTTGGTA 58.052 37.500 0.00 0.00 39.03 3.25
3254 3444 2.121291 TGACAACACTGCCAGAAACA 57.879 45.000 0.00 0.00 0.00 2.83
3291 3481 5.541484 AGGGCTGTCAAGAAGATTTTTGATT 59.459 36.000 2.34 0.00 35.91 2.57
3901 4093 1.292992 GCAATTTGGCATGCTAAGGC 58.707 50.000 18.92 17.64 39.46 4.35
3906 4098 0.039472 TTGGCATGCTAAGGCTCCAA 59.961 50.000 18.92 7.64 39.04 3.53
3987 4179 2.430465 CAGCTGAGGTATGCAACAAGT 58.570 47.619 8.42 0.00 0.00 3.16
3996 4188 5.137551 AGGTATGCAACAAGTTTTGTACCT 58.862 37.500 7.28 7.28 44.59 3.08
4015 4207 2.230508 CCTGTTGAATTGAGCAGCACAT 59.769 45.455 3.23 0.00 0.00 3.21
4081 4273 9.835389 ATGGCTAAATGCATGTTGTATAATTTT 57.165 25.926 0.00 0.00 45.15 1.82
4238 4430 5.409826 ACTGTTAAGAAAATCTGAAGCGAGG 59.590 40.000 0.00 0.00 0.00 4.63
4242 4434 5.363979 AAGAAAATCTGAAGCGAGGAAAC 57.636 39.130 0.00 0.00 0.00 2.78
4259 4451 6.035112 CGAGGAAACGAAGAGGAAATTCTTAG 59.965 42.308 0.00 0.00 37.53 2.18
4321 4524 6.734104 TTTAGGTAGAGACTACTTGACGAC 57.266 41.667 8.48 0.00 0.00 4.34
4459 4843 5.066375 TCACCTGATGTGTGCTATAATTTGC 59.934 40.000 0.00 0.00 45.61 3.68
4500 4904 2.158682 TGCTGTTCTGGGCTTTGAGTTA 60.159 45.455 0.00 0.00 0.00 2.24
4554 4958 1.544724 TATGGGAAGCACAGTTTGGC 58.455 50.000 0.00 0.00 0.00 4.52
4886 5292 3.616219 GAACTGCCATAACCATACACCA 58.384 45.455 0.00 0.00 0.00 4.17
4889 5295 2.682856 CTGCCATAACCATACACCACAC 59.317 50.000 0.00 0.00 0.00 3.82
4983 5665 0.999406 CCTGTTCGCATGACCTAACG 59.001 55.000 0.00 0.00 0.00 3.18
5081 5763 5.416326 GTGCTTCCTCTACTTCTGAGTTCTA 59.584 44.000 0.00 0.00 37.33 2.10
5103 5787 7.446769 TCTATAGAAAGTTGCAACTACACCAA 58.553 34.615 31.31 15.48 38.57 3.67
5184 5868 3.065925 GTGAGAGCCAAAATCCATGTAGC 59.934 47.826 0.00 0.00 0.00 3.58
5588 6273 1.851021 CGCAACCATCTTTCGGTGCA 61.851 55.000 0.00 0.00 36.67 4.57
5669 6354 5.115480 GTGATGTCTCCAAAGAATCTCCTC 58.885 45.833 0.00 0.00 31.93 3.71
5984 6669 1.134551 TCGGATTCCAATGATGTCGCA 60.135 47.619 3.09 0.00 0.00 5.10
6020 6705 2.053244 CAGCTCTGTCCATTCCCCTAT 58.947 52.381 0.00 0.00 0.00 2.57
6035 6720 1.506493 CCTATGACCTCATTCAGCGC 58.494 55.000 0.00 0.00 37.76 5.92
6142 6827 5.607477 TCTCTTCGTGAAAACATACAAGGT 58.393 37.500 0.00 0.00 0.00 3.50
6154 6839 4.662278 ACATACAAGGTTTGCATGTAGGT 58.338 39.130 8.47 8.47 43.83 3.08
6158 6843 5.179452 ACAAGGTTTGCATGTAGGTAGAT 57.821 39.130 0.00 0.00 0.00 1.98
6170 6855 8.630917 TGCATGTAGGTAGATAAACTCTTCTAC 58.369 37.037 0.00 2.26 42.27 2.59
6500 7195 1.220206 CAATCCTCGCCTGCTGACT 59.780 57.895 0.00 0.00 0.00 3.41
6548 7243 7.551974 GGCAGCATAGATGATATCAAGTATGTT 59.448 37.037 24.70 20.37 32.50 2.71
6560 7255 0.552615 AGTATGTTGGAAGGGCCCCT 60.553 55.000 21.43 4.78 34.97 4.79
6730 7425 4.441913 CCATGCAGAAAAACAACAGGTCTT 60.442 41.667 0.00 0.00 0.00 3.01
6738 7433 9.965824 CAGAAAAACAACAGGTCTTAATTACAT 57.034 29.630 0.00 0.00 0.00 2.29
6768 7463 6.738114 CAGCCATTTGGTGAATAATCGTTAT 58.262 36.000 0.00 0.00 45.48 1.89
6780 7475 3.763097 AATCGTTATGCATGTGTGGTG 57.237 42.857 10.16 0.00 0.00 4.17
6858 7557 6.323739 TCAAAGCTTTTTGGTCTACATCCTTT 59.676 34.615 9.53 0.00 32.99 3.11
6958 7657 3.249320 TGTATGTATGTCCTACGAGACGC 59.751 47.826 0.00 0.00 39.77 5.19
7006 7705 6.707440 TTATGATTCCAGTCTGTCTCTCTC 57.293 41.667 0.00 0.00 0.00 3.20
7038 7749 6.650120 TGGAAAGAAACTAGTTCAGTGAAGT 58.350 36.000 17.14 17.14 38.86 3.01
7039 7750 7.788026 TGGAAAGAAACTAGTTCAGTGAAGTA 58.212 34.615 17.52 17.52 38.86 2.24
7040 7751 7.709613 TGGAAAGAAACTAGTTCAGTGAAGTAC 59.290 37.037 15.13 7.04 38.86 2.73
7041 7752 7.927092 GGAAAGAAACTAGTTCAGTGAAGTACT 59.073 37.037 15.13 8.51 41.36 2.73
7063 7774 2.273449 CACCATCTCCCAGGCCAC 59.727 66.667 5.01 0.00 0.00 5.01
7158 7869 2.623416 CTGGCCGTTTTCTTTCTTTCCT 59.377 45.455 0.00 0.00 0.00 3.36
7163 7874 4.506654 GCCGTTTTCTTTCTTTCCTTTTCC 59.493 41.667 0.00 0.00 0.00 3.13
7167 7878 7.010183 CCGTTTTCTTTCTTTCCTTTTCCTTTC 59.990 37.037 0.00 0.00 0.00 2.62
7193 7904 3.114606 TGGAAGATCCATGACTTGCCTA 58.885 45.455 12.83 0.00 42.67 3.93
7245 7957 9.093458 AGAAATTTTCAATCTTGTAACCCTCAT 57.907 29.630 11.53 0.00 0.00 2.90
7253 7965 6.747414 ATCTTGTAACCCTCATGTGCTATA 57.253 37.500 0.00 0.00 0.00 1.31
7302 8014 0.039618 GAGAAACTGGATTGGGGCCA 59.960 55.000 4.39 0.00 0.00 5.36
7343 8055 3.494850 GGGCCATAGCACTAGCAAA 57.505 52.632 4.39 0.00 45.49 3.68
7344 8056 1.762708 GGGCCATAGCACTAGCAAAA 58.237 50.000 4.39 0.00 45.49 2.44
7345 8057 1.678101 GGGCCATAGCACTAGCAAAAG 59.322 52.381 4.39 0.00 45.49 2.27
7347 8059 2.643551 GCCATAGCACTAGCAAAAGGA 58.356 47.619 0.00 0.00 45.49 3.36
7348 8060 2.356069 GCCATAGCACTAGCAAAAGGAC 59.644 50.000 0.00 0.00 45.49 3.85
7349 8061 3.609853 CCATAGCACTAGCAAAAGGACA 58.390 45.455 0.00 0.00 45.49 4.02
7350 8062 3.375299 CCATAGCACTAGCAAAAGGACAC 59.625 47.826 0.00 0.00 45.49 3.67
7351 8063 1.897560 AGCACTAGCAAAAGGACACC 58.102 50.000 0.00 0.00 45.49 4.16
7352 8064 0.517316 GCACTAGCAAAAGGACACCG 59.483 55.000 0.00 0.00 41.58 4.94
7353 8065 1.156736 CACTAGCAAAAGGACACCGG 58.843 55.000 0.00 0.00 0.00 5.28
7354 8066 0.036306 ACTAGCAAAAGGACACCGGG 59.964 55.000 6.32 0.00 0.00 5.73
7355 8067 0.323629 CTAGCAAAAGGACACCGGGA 59.676 55.000 6.32 0.00 0.00 5.14
7356 8068 0.766131 TAGCAAAAGGACACCGGGAA 59.234 50.000 6.32 0.00 0.00 3.97
7357 8069 0.106419 AGCAAAAGGACACCGGGAAA 60.106 50.000 6.32 0.00 0.00 3.13
7358 8070 0.966179 GCAAAAGGACACCGGGAAAT 59.034 50.000 6.32 0.00 0.00 2.17
7359 8071 2.164338 GCAAAAGGACACCGGGAAATA 58.836 47.619 6.32 0.00 0.00 1.40
7360 8072 2.559231 GCAAAAGGACACCGGGAAATAA 59.441 45.455 6.32 0.00 0.00 1.40
7364 8120 5.462530 AAAGGACACCGGGAAATAAAAAG 57.537 39.130 6.32 0.00 0.00 2.27
7372 8164 4.847512 ACCGGGAAATAAAAAGGGGAAAAT 59.152 37.500 6.32 0.00 0.00 1.82
7564 8360 5.888161 GGACAATGATAATCACTTGGTCCTT 59.112 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.107141 CTTCCGGCCTCATCGTCC 59.893 66.667 0.00 0.00 0.00 4.79
10 11 2.607750 AAGGAGCTTCCGGCCTCA 60.608 61.111 15.39 0.00 42.75 3.86
21 22 2.816012 GGAGGGCGTAGAAGGAGC 59.184 66.667 0.00 0.00 0.00 4.70
38 39 0.041312 CTTGTGCCTTTTCGACACCG 60.041 55.000 1.19 0.00 33.30 4.94
120 121 2.598045 CAGATCGAACATCTGCCCG 58.402 57.895 1.77 0.00 39.03 6.13
131 132 1.959848 CGCTAGATGGGCAGATCGA 59.040 57.895 0.00 0.00 0.00 3.59
262 263 4.753662 TAGCGTGCCGGAGAGGGT 62.754 66.667 5.05 4.43 41.48 4.34
263 264 2.701163 GATTAGCGTGCCGGAGAGGG 62.701 65.000 5.05 0.00 41.48 4.30
270 271 0.179121 TGTGGTAGATTAGCGTGCCG 60.179 55.000 0.00 0.00 0.00 5.69
275 276 1.068741 GGAGGGTGTGGTAGATTAGCG 59.931 57.143 0.00 0.00 0.00 4.26
279 280 0.902531 CGTGGAGGGTGTGGTAGATT 59.097 55.000 0.00 0.00 0.00 2.40
312 313 3.644399 GAAGTCGTCCTCACGGGGC 62.644 68.421 0.00 0.00 46.70 5.80
332 333 2.345502 CTACTCGTCGTCGGAGTCGC 62.346 65.000 7.33 0.00 39.21 5.19
340 341 4.685165 TCATACTAGCATCTACTCGTCGTC 59.315 45.833 0.00 0.00 0.00 4.20
342 343 5.177881 AGTTCATACTAGCATCTACTCGTCG 59.822 44.000 0.00 0.00 31.21 5.12
380 381 6.255887 CACCGATAGATAGGTCAAACTGAAAC 59.744 42.308 0.00 0.00 39.00 2.78
402 403 1.156736 AGTTTCGCACATAGCACACC 58.843 50.000 0.00 0.00 46.13 4.16
463 464 2.773487 CCATCACCGTAGTTCCACAAA 58.227 47.619 0.00 0.00 0.00 2.83
473 474 0.031585 GCGTCATAGCCATCACCGTA 59.968 55.000 0.00 0.00 0.00 4.02
484 485 0.647410 CACAAGCCTTCGCGTCATAG 59.353 55.000 5.77 0.00 41.18 2.23
488 489 2.357034 TCCACAAGCCTTCGCGTC 60.357 61.111 5.77 0.00 41.18 5.19
489 490 2.357517 CTCCACAAGCCTTCGCGT 60.358 61.111 5.77 0.00 41.18 6.01
504 505 7.938563 ACTCGATTTCAAACATAGATAGCTC 57.061 36.000 0.00 0.00 0.00 4.09
506 507 8.575565 TGTACTCGATTTCAAACATAGATAGC 57.424 34.615 0.00 0.00 0.00 2.97
515 516 6.732392 CGTCAGATTTGTACTCGATTTCAAAC 59.268 38.462 9.20 5.12 33.63 2.93
516 517 6.643360 TCGTCAGATTTGTACTCGATTTCAAA 59.357 34.615 9.39 9.39 34.95 2.69
525 526 8.014322 TGTTAAATGTCGTCAGATTTGTACTC 57.986 34.615 0.00 0.00 0.00 2.59
529 530 9.180678 GATTTTGTTAAATGTCGTCAGATTTGT 57.819 29.630 0.00 0.00 34.16 2.83
536 537 9.986833 CATGATAGATTTTGTTAAATGTCGTCA 57.013 29.630 0.00 0.00 34.16 4.35
540 541 9.162793 CTCGCATGATAGATTTTGTTAAATGTC 57.837 33.333 0.00 0.00 34.16 3.06
552 553 1.277557 GGCCTCCTCGCATGATAGATT 59.722 52.381 0.00 0.00 0.00 2.40
555 556 1.080230 CGGCCTCCTCGCATGATAG 60.080 63.158 0.00 0.00 0.00 2.08
573 574 6.015458 TTGTAAACAAAATTTACGGGACGGC 61.015 40.000 0.00 0.00 45.28 5.68
628 629 4.238761 TGTGATGCTTAGAGCGGTATAC 57.761 45.455 0.00 0.00 46.26 1.47
632 633 3.118775 TGTTATGTGATGCTTAGAGCGGT 60.119 43.478 0.00 0.00 46.26 5.68
636 637 7.615582 TCCTTTTGTTATGTGATGCTTAGAG 57.384 36.000 0.00 0.00 0.00 2.43
637 638 7.828717 TCATCCTTTTGTTATGTGATGCTTAGA 59.171 33.333 0.00 0.00 31.85 2.10
638 639 7.988737 TCATCCTTTTGTTATGTGATGCTTAG 58.011 34.615 0.00 0.00 31.85 2.18
639 640 7.936496 TCATCCTTTTGTTATGTGATGCTTA 57.064 32.000 0.00 0.00 31.85 3.09
640 641 6.839124 TCATCCTTTTGTTATGTGATGCTT 57.161 33.333 0.00 0.00 31.85 3.91
641 642 6.209192 TGTTCATCCTTTTGTTATGTGATGCT 59.791 34.615 0.00 0.00 31.85 3.79
642 643 6.389091 TGTTCATCCTTTTGTTATGTGATGC 58.611 36.000 0.00 0.00 31.85 3.91
643 644 8.991243 ATTGTTCATCCTTTTGTTATGTGATG 57.009 30.769 0.00 0.00 0.00 3.07
646 647 8.863049 GCTAATTGTTCATCCTTTTGTTATGTG 58.137 33.333 0.00 0.00 0.00 3.21
647 648 8.584157 TGCTAATTGTTCATCCTTTTGTTATGT 58.416 29.630 0.00 0.00 0.00 2.29
648 649 8.863049 GTGCTAATTGTTCATCCTTTTGTTATG 58.137 33.333 0.00 0.00 0.00 1.90
649 650 7.754924 CGTGCTAATTGTTCATCCTTTTGTTAT 59.245 33.333 0.00 0.00 0.00 1.89
650 651 7.081349 CGTGCTAATTGTTCATCCTTTTGTTA 58.919 34.615 0.00 0.00 0.00 2.41
651 652 5.920273 CGTGCTAATTGTTCATCCTTTTGTT 59.080 36.000 0.00 0.00 0.00 2.83
652 653 5.460646 CGTGCTAATTGTTCATCCTTTTGT 58.539 37.500 0.00 0.00 0.00 2.83
735 756 9.535878 GAAGATGGGGATATATTCGATAGTTTC 57.464 37.037 0.00 0.00 37.40 2.78
739 760 6.784969 AGGGAAGATGGGGATATATTCGATAG 59.215 42.308 0.00 0.00 30.91 2.08
759 780 3.521937 AGATGGACGTGGATAAAAGGGAA 59.478 43.478 0.00 0.00 0.00 3.97
883 915 2.167281 TCAGGAGAAAAGATCGGAGCAG 59.833 50.000 0.00 0.00 0.00 4.24
943 975 3.053896 GCGGAAAACTGGACGGGG 61.054 66.667 0.00 0.00 0.00 5.73
1362 1400 3.702048 TGGCCGCTCACCTGGTAC 61.702 66.667 0.00 0.00 0.00 3.34
1722 1760 2.297033 TGCCAGGAAATTCTCAAACTGC 59.703 45.455 0.00 0.00 0.00 4.40
1767 1805 2.282180 GCACCTTCCAGGCCGAAA 60.282 61.111 0.00 0.00 39.63 3.46
1776 1814 0.681733 TCAGTGTCTCTGCACCTTCC 59.318 55.000 0.00 0.00 43.32 3.46
1785 1823 4.614475 TCATACCAGGAATCAGTGTCTCT 58.386 43.478 0.00 0.00 0.00 3.10
2539 2577 2.856988 GGGGTGGGGTCTGGACAA 60.857 66.667 3.10 0.00 0.00 3.18
2657 2822 9.802039 ATGGTGTTTAGTCAAAAGTAAGGAATA 57.198 29.630 0.00 0.00 0.00 1.75
3131 3321 2.241176 TGTGGAGGGAAACACAGAAACT 59.759 45.455 0.00 0.00 42.20 2.66
3254 3444 1.145738 ACAGCCCTGTGAGGTTTGAAT 59.854 47.619 0.00 0.00 43.11 2.57
3291 3481 0.877743 TCAATCATTTGGCGACGCAA 59.122 45.000 23.09 7.74 33.44 4.85
3602 3794 7.259882 TGCTTATGGTGATTTCATGTTTCATC 58.740 34.615 0.00 0.00 0.00 2.92
3901 4093 5.467035 TGGCTAAGGACAAATTTTTGGAG 57.533 39.130 7.85 0.00 42.34 3.86
3987 4179 5.735922 GCTGCTCAATTCAACAGGTACAAAA 60.736 40.000 0.00 0.00 0.00 2.44
3996 4188 2.624364 ACATGTGCTGCTCAATTCAACA 59.376 40.909 8.59 0.00 0.00 3.33
4015 4207 0.396060 TGTCTGCTACACATGCCACA 59.604 50.000 0.00 0.00 31.43 4.17
4065 4257 7.775397 AATGCTCCAAAATTATACAACATGC 57.225 32.000 0.00 0.00 0.00 4.06
4081 4273 3.597182 TCCCAGGACATATAATGCTCCA 58.403 45.455 0.00 0.00 34.78 3.86
4096 4288 7.789202 TTCTATTTCTCTAGATCATCCCAGG 57.211 40.000 0.00 0.00 0.00 4.45
4124 4316 7.923414 ATTCCAAGATGGTGTTTAGTTAGTC 57.077 36.000 0.00 0.00 39.03 2.59
4238 4430 6.481954 TGCTAAGAATTTCCTCTTCGTTTC 57.518 37.500 0.00 0.00 36.95 2.78
4242 4434 7.308435 ACAATTTGCTAAGAATTTCCTCTTCG 58.692 34.615 0.00 0.00 36.95 3.79
4259 4451 9.495754 GTCAGTTCAGAGAATATAACAATTTGC 57.504 33.333 0.00 0.00 0.00 3.68
4317 4509 3.192844 AGATGACAAGGTTATGACGTCGT 59.807 43.478 15.78 15.78 36.53 4.34
4321 4524 7.953158 ATATTCAGATGACAAGGTTATGACG 57.047 36.000 0.00 0.00 0.00 4.35
4500 4904 4.946160 TGGGTTCTCCATTGAATAACCT 57.054 40.909 7.33 0.00 41.46 3.50
4554 4958 3.591196 TGAGCCCCATTTGAAAAATCG 57.409 42.857 0.00 0.00 0.00 3.34
4983 5665 6.931840 CCTATGAGGTATTTAGCTTTGTCCTC 59.068 42.308 13.82 13.82 39.97 3.71
5081 5763 6.546034 AGTTTGGTGTAGTTGCAACTTTCTAT 59.454 34.615 35.20 14.31 40.37 1.98
5103 5787 7.283329 ACAGAAGTCCAACTAAGAATCAAGTT 58.717 34.615 0.00 0.00 36.38 2.66
5184 5868 7.318141 ACTATCTTCAAAATGCTTCACCAATG 58.682 34.615 0.00 0.00 0.00 2.82
5374 6059 3.883489 CACTCATCTGCAATCATGGACAT 59.117 43.478 0.00 0.00 0.00 3.06
5588 6273 6.599638 GCAAACAGAGGAAGATACAGGTTAAT 59.400 38.462 0.00 0.00 0.00 1.40
5984 6669 5.128499 ACAGAGCTGCTCAACTCTACATATT 59.872 40.000 29.49 2.98 41.31 1.28
6020 6705 1.153765 CTCGCGCTGAATGAGGTCA 60.154 57.895 5.56 0.00 0.00 4.02
6035 6720 4.582701 ACTTGGATATCTCTTCAGCTCG 57.417 45.455 2.05 0.00 0.00 5.03
6142 6827 8.540388 AGAAGAGTTTATCTACCTACATGCAAA 58.460 33.333 0.00 0.00 37.23 3.68
6154 6839 8.639761 GGCATGTAAGGTAGAAGAGTTTATCTA 58.360 37.037 0.00 0.00 37.23 1.98
6158 6843 6.614694 TGGCATGTAAGGTAGAAGAGTTTA 57.385 37.500 0.00 0.00 0.00 2.01
6170 6855 9.991388 CATTTCAAATAAAATTGGCATGTAAGG 57.009 29.630 0.00 0.00 0.00 2.69
6611 7306 1.080501 CGCCTTCTTCACGAGCTCA 60.081 57.895 15.40 0.00 0.00 4.26
6730 7425 7.067372 CACCAAATGGCTGAAGAGATGTAATTA 59.933 37.037 0.00 0.00 39.32 1.40
6738 7433 3.507162 TTCACCAAATGGCTGAAGAGA 57.493 42.857 11.11 0.00 39.32 3.10
6780 7475 0.096454 GACCGTTTCTAATGTGCGGC 59.904 55.000 0.00 0.00 45.53 6.53
6787 7485 3.170717 TGGACCTCAGACCGTTTCTAAT 58.829 45.455 0.00 0.00 31.12 1.73
6845 7544 6.447162 CCAGAAAAACAAAAGGATGTAGACC 58.553 40.000 0.00 0.00 32.02 3.85
6858 7557 3.637769 ACCTTAGCACCCAGAAAAACAA 58.362 40.909 0.00 0.00 0.00 2.83
6982 7681 6.665248 TGAGAGAGACAGACTGGAATCATAAA 59.335 38.462 7.51 0.00 0.00 1.40
6983 7682 6.190587 TGAGAGAGACAGACTGGAATCATAA 58.809 40.000 7.51 0.00 0.00 1.90
7006 7705 9.884465 CTGAACTAGTTTCTTTCCAAGTATTTG 57.116 33.333 10.02 0.00 34.97 2.32
7038 7749 2.388735 CTGGGAGATGGTGTGCTAGTA 58.611 52.381 0.00 0.00 0.00 1.82
7039 7750 1.198713 CTGGGAGATGGTGTGCTAGT 58.801 55.000 0.00 0.00 0.00 2.57
7040 7751 0.467384 CCTGGGAGATGGTGTGCTAG 59.533 60.000 0.00 0.00 0.00 3.42
7041 7752 1.626356 GCCTGGGAGATGGTGTGCTA 61.626 60.000 0.00 0.00 0.00 3.49
7117 7828 6.072175 GGCCAGTTCAGACATAACAATAACAA 60.072 38.462 0.00 0.00 0.00 2.83
7158 7869 7.270832 TGGATCTTCCATCTAGAAAGGAAAA 57.729 36.000 22.88 15.22 42.67 2.29
7224 7936 6.516527 GCACATGAGGGTTACAAGATTGAAAA 60.517 38.462 0.00 0.00 0.00 2.29
7253 7965 4.380867 GGATGCCAATTCGATTTTCTGTGT 60.381 41.667 0.00 0.00 0.00 3.72
7257 7969 4.220382 TGTTGGATGCCAATTCGATTTTCT 59.780 37.500 1.79 0.00 45.80 2.52
7264 7976 1.198867 TCGTTGTTGGATGCCAATTCG 59.801 47.619 1.79 7.89 45.80 3.34
7302 8014 2.687566 CCGTTAGGAGGCCCAGGT 60.688 66.667 0.00 0.00 41.02 4.00
7339 8051 0.966179 ATTTCCCGGTGTCCTTTTGC 59.034 50.000 0.00 0.00 0.00 3.68
7342 8054 4.282449 CCTTTTTATTTCCCGGTGTCCTTT 59.718 41.667 0.00 0.00 0.00 3.11
7343 8055 3.830178 CCTTTTTATTTCCCGGTGTCCTT 59.170 43.478 0.00 0.00 0.00 3.36
7344 8056 3.427573 CCTTTTTATTTCCCGGTGTCCT 58.572 45.455 0.00 0.00 0.00 3.85
7345 8057 2.494471 CCCTTTTTATTTCCCGGTGTCC 59.506 50.000 0.00 0.00 0.00 4.02
7347 8059 2.110365 TCCCCTTTTTATTTCCCGGTGT 59.890 45.455 0.00 0.00 0.00 4.16
7348 8060 2.810164 TCCCCTTTTTATTTCCCGGTG 58.190 47.619 0.00 0.00 0.00 4.94
7349 8061 3.546429 TTCCCCTTTTTATTTCCCGGT 57.454 42.857 0.00 0.00 0.00 5.28
7350 8062 4.893829 TTTTCCCCTTTTTATTTCCCGG 57.106 40.909 0.00 0.00 0.00 5.73
7351 8063 5.872617 GTCATTTTCCCCTTTTTATTTCCCG 59.127 40.000 0.00 0.00 0.00 5.14
7352 8064 5.872617 CGTCATTTTCCCCTTTTTATTTCCC 59.127 40.000 0.00 0.00 0.00 3.97
7353 8065 6.693466 TCGTCATTTTCCCCTTTTTATTTCC 58.307 36.000 0.00 0.00 0.00 3.13
7354 8066 7.491372 GGATCGTCATTTTCCCCTTTTTATTTC 59.509 37.037 0.00 0.00 0.00 2.17
7355 8067 7.180229 AGGATCGTCATTTTCCCCTTTTTATTT 59.820 33.333 0.00 0.00 0.00 1.40
7356 8068 6.667848 AGGATCGTCATTTTCCCCTTTTTATT 59.332 34.615 0.00 0.00 0.00 1.40
7357 8069 6.194967 AGGATCGTCATTTTCCCCTTTTTAT 58.805 36.000 0.00 0.00 0.00 1.40
7358 8070 5.576128 AGGATCGTCATTTTCCCCTTTTTA 58.424 37.500 0.00 0.00 0.00 1.52
7359 8071 4.416516 AGGATCGTCATTTTCCCCTTTTT 58.583 39.130 0.00 0.00 0.00 1.94
7360 8072 4.047627 AGGATCGTCATTTTCCCCTTTT 57.952 40.909 0.00 0.00 0.00 2.27
7364 8120 2.480845 CGTAGGATCGTCATTTTCCCC 58.519 52.381 0.00 0.00 0.00 4.81
7372 8164 0.376152 GTCGAAGCGTAGGATCGTCA 59.624 55.000 9.75 0.00 37.79 4.35
7407 8200 2.485814 ACATCAAGCGCCTCTTCTTTTC 59.514 45.455 2.29 0.00 31.27 2.29
7411 8204 2.191128 AAACATCAAGCGCCTCTTCT 57.809 45.000 2.29 0.00 31.27 2.85
7412 8205 3.684788 TCTTAAACATCAAGCGCCTCTTC 59.315 43.478 2.29 0.00 31.27 2.87
7415 8208 3.188460 TGTTCTTAAACATCAAGCGCCTC 59.812 43.478 2.29 0.00 40.45 4.70
7418 8211 3.188460 TCCTGTTCTTAAACATCAAGCGC 59.812 43.478 0.00 0.00 44.18 5.92
7564 8360 1.064017 ACAAACAAGAGCCAGTTGGGA 60.064 47.619 0.00 0.00 40.01 4.37


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

AutoCloner maintained by Alex Coulton.