Multiple sequence alignment - TraesCS7A01G145600

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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 TraesCS7A01G145600 chr7A 100.000 3515 0 0 1 3515 97024436 97020922 0.000000e+00 6492.0
1 TraesCS7A01G145600 chr7A 90.636 2232 139 37 471 2675 96816586 96814398 0.000000e+00 2900.0
2 TraesCS7A01G145600 chr7A 89.100 211 16 3 3235 3445 96814016 96813813 4.500000e-64 255.0
3 TraesCS7A01G145600 chr7A 88.068 176 18 2 2792 2966 96814336 96814163 4.600000e-49 206.0
4 TraesCS7A01G145600 chr7D 88.743 2585 182 48 130 2673 93883150 93880634 0.000000e+00 3061.0
5 TraesCS7A01G145600 chr7D 89.100 211 16 3 3235 3445 93880243 93880040 4.500000e-64 255.0
6 TraesCS7A01G145600 chr7D 88.710 186 20 1 2792 2976 93880570 93880385 3.530000e-55 226.0
7 TraesCS7A01G145600 chr7B 91.223 2085 124 27 625 2675 47604957 47602898 0.000000e+00 2782.0
8 TraesCS7A01G145600 chr7B 91.630 1601 83 24 467 2048 47341931 47340363 0.000000e+00 2167.0
9 TraesCS7A01G145600 chr7B 96.000 1300 52 0 2049 3348 47340401 47339102 0.000000e+00 2113.0
10 TraesCS7A01G145600 chr7B 92.358 615 38 8 1 613 47609250 47608643 0.000000e+00 867.0
11 TraesCS7A01G145600 chr7B 74.000 400 94 8 1156 1551 595531031 595531424 1.690000e-33 154.0
12 TraesCS7A01G145600 chr7B 85.321 109 15 1 1 109 747835414 747835521 1.030000e-20 111.0
13 TraesCS7A01G145600 chr6B 93.684 95 6 0 2697 2791 216509753 216509847 3.660000e-30 143.0
14 TraesCS7A01G145600 chr6B 88.679 106 9 2 1 105 661840416 661840313 3.680000e-25 126.0
15 TraesCS7A01G145600 chr3B 92.857 98 7 0 2697 2794 621334487 621334390 3.660000e-30 143.0
16 TraesCS7A01G145600 chr1B 94.624 93 4 1 2701 2793 320588049 320588140 3.660000e-30 143.0
17 TraesCS7A01G145600 chr1B 88.073 109 13 0 1 109 656202675 656202783 2.850000e-26 130.0
18 TraesCS7A01G145600 chr6D 93.684 95 5 1 2702 2796 59623259 59623166 1.320000e-29 141.0
19 TraesCS7A01G145600 chr6D 81.818 99 14 4 2244 2340 395369990 395369894 2.910000e-11 80.5
20 TraesCS7A01G145600 chr6D 82.609 92 12 4 2251 2340 395094249 395094160 1.050000e-10 78.7
21 TraesCS7A01G145600 chr5D 89.908 109 11 0 1 109 367755539 367755431 1.320000e-29 141.0
22 TraesCS7A01G145600 chr3D 90.476 105 10 0 2689 2793 400336924 400336820 4.730000e-29 139.0
23 TraesCS7A01G145600 chr1D 92.000 100 7 1 2702 2800 473970181 473970280 4.730000e-29 139.0
24 TraesCS7A01G145600 chr1D 90.426 94 9 0 1 94 203165988 203166081 1.320000e-24 124.0
25 TraesCS7A01G145600 chr1D 85.849 106 12 3 1 105 27990188 27990291 3.710000e-20 110.0
26 TraesCS7A01G145600 chr2D 91.176 102 7 2 2686 2786 574413515 574413615 1.700000e-28 137.0
27 TraesCS7A01G145600 chr2D 90.385 104 9 1 2687 2789 317889776 317889879 6.120000e-28 135.0
28 TraesCS7A01G145600 chr2D 81.818 99 14 4 2244 2340 17831540 17831636 2.910000e-11 80.5
29 TraesCS7A01G145600 chr2D 86.885 61 6 2 2245 2304 17956153 17956212 2.260000e-07 67.6
30 TraesCS7A01G145600 chr4D 87.156 109 14 0 1 109 448468737 448468845 1.320000e-24 124.0
31 TraesCS7A01G145600 chr4A 87.500 104 11 2 1 104 710672328 710672429 6.160000e-23 119.0
32 TraesCS7A01G145600 chr2A 75.152 165 35 5 2244 2407 19126178 19126337 4.870000e-09 73.1


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 TraesCS7A01G145600 chr7A 97020922 97024436 3514 True 6492.000000 6492 100.0000 1 3515 1 chr7A.!!$R1 3514
1 TraesCS7A01G145600 chr7A 96813813 96816586 2773 True 1120.333333 2900 89.2680 471 3445 3 chr7A.!!$R2 2974
2 TraesCS7A01G145600 chr7D 93880040 93883150 3110 True 1180.666667 3061 88.8510 130 3445 3 chr7D.!!$R1 3315
3 TraesCS7A01G145600 chr7B 47339102 47341931 2829 True 2140.000000 2167 93.8150 467 3348 2 chr7B.!!$R1 2881
4 TraesCS7A01G145600 chr7B 47602898 47609250 6352 True 1824.500000 2782 91.7905 1 2675 2 chr7B.!!$R2 2674

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
376 391 0.608035 TAGAAGTTGCGGGGCCAAAG 60.608 55.0 4.39 0.0 0.00 2.77 F
1039 4773 0.032130 CGTCGTGGGTAGCAGCATAT 59.968 55.0 0.00 0.0 0.00 1.78 F
1042 4776 0.392706 CGTGGGTAGCAGCATATCCA 59.607 55.0 0.00 0.0 33.38 3.41 F
1059 4793 0.468029 CCAGGTGTTTGGCCTTGTCT 60.468 55.0 3.32 0.0 33.31 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 5340 0.662085 GGCGTAGGGAAGTCGACTAG 59.338 60.000 20.39 5.79 0.00 2.57 R
2091 5837 1.205893 GGTTTCAGCCTCGACAGATCT 59.794 52.381 0.00 0.00 0.00 2.75 R
2170 5916 2.034001 CGTCAAACTTGTCGGTGAAGAC 60.034 50.000 1.83 0.00 41.30 3.01 R
2647 6393 3.266636 CGTGCCACATAAATGTACCTCA 58.733 45.455 0.00 0.00 39.39 3.86 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
49 50 3.474570 GTCGGGCCCTCAGATGCT 61.475 66.667 22.43 0.00 0.00 3.79
50 51 3.157252 TCGGGCCCTCAGATGCTC 61.157 66.667 22.43 0.00 0.00 4.26
144 145 9.953697 TTAATGCTTACGTTGTATTTGACTTTT 57.046 25.926 0.00 0.00 0.00 2.27
145 146 8.502161 AATGCTTACGTTGTATTTGACTTTTC 57.498 30.769 0.00 0.00 0.00 2.29
319 334 8.658840 AAATGTAGGGAATTAAGTTTTAGGCA 57.341 30.769 0.00 0.00 0.00 4.75
371 386 3.313012 AAATTTTAGAAGTTGCGGGGC 57.687 42.857 0.00 0.00 0.00 5.80
376 391 0.608035 TAGAAGTTGCGGGGCCAAAG 60.608 55.000 4.39 0.00 0.00 2.77
431 446 6.062749 AGTTTTGGAAGGAGGTTCTAGAAAC 58.937 40.000 12.89 12.89 35.25 2.78
454 469 8.794335 AACTAAGTTTTATGAAAGGGCTAGAG 57.206 34.615 0.00 0.00 0.00 2.43
621 4321 2.592308 GCCAATCTCCTCGGGCTT 59.408 61.111 0.00 0.00 43.09 4.35
708 4420 1.287041 GAACGAAACGGAGGGGAACG 61.287 60.000 0.00 0.00 0.00 3.95
750 4462 3.889815 TCCTCCATCCAGCAAATAACAG 58.110 45.455 0.00 0.00 0.00 3.16
758 4470 5.659440 TCCAGCAAATAACAGAAAATCCC 57.341 39.130 0.00 0.00 0.00 3.85
759 4471 4.157656 TCCAGCAAATAACAGAAAATCCCG 59.842 41.667 0.00 0.00 0.00 5.14
813 4526 2.188837 GGAAATCAAATTCCGGCGAC 57.811 50.000 9.30 0.00 39.54 5.19
855 4568 1.135139 GATCTGCTTCACCTACGAGCA 59.865 52.381 0.00 0.00 43.56 4.26
893 4613 7.754851 TGGCGTTCTATAAGTATCATACAGA 57.245 36.000 0.00 0.00 0.00 3.41
901 4621 9.463902 TCTATAAGTATCATACAGAAGCCTACC 57.536 37.037 0.00 0.00 0.00 3.18
918 4638 3.655211 CCCTGCCTGCCCTCTGTT 61.655 66.667 0.00 0.00 0.00 3.16
922 4642 2.282745 GCCTGCCCTCTGTTGCTT 60.283 61.111 0.00 0.00 0.00 3.91
974 4708 0.766288 GGAGAGGGAGATTGGGGAGG 60.766 65.000 0.00 0.00 0.00 4.30
1021 4755 2.890474 CGCCGTCTGGAATTCCCG 60.890 66.667 21.90 15.69 37.49 5.14
1039 4773 0.032130 CGTCGTGGGTAGCAGCATAT 59.968 55.000 0.00 0.00 0.00 1.78
1042 4776 0.392706 CGTGGGTAGCAGCATATCCA 59.607 55.000 0.00 0.00 33.38 3.41
1059 4793 0.468029 CCAGGTGTTTGGCCTTGTCT 60.468 55.000 3.32 0.00 33.31 3.41
1077 4811 0.859232 CTGGTGTGCTGACAACGTAC 59.141 55.000 0.00 0.00 43.43 3.67
1117 4851 3.263503 CTCGCCGTTCACCGTCTGA 62.264 63.158 0.00 0.00 33.66 3.27
1128 4862 1.360551 CCGTCTGATACCCAGCGAG 59.639 63.158 0.00 0.00 42.62 5.03
1340 5074 1.078848 AATCTGCCGGTGAGAGTGC 60.079 57.895 1.90 0.00 0.00 4.40
1383 5117 5.390885 CGTGGAGAACAAATCCTACACATTG 60.391 44.000 0.00 0.00 42.83 2.82
1683 5429 4.858935 TCTTTGAGAAGGCATTTTTGTCG 58.141 39.130 0.00 0.00 33.56 4.35
1731 5477 3.792401 TGTGGTACTCAAGCATAATCCG 58.208 45.455 0.00 0.00 38.03 4.18
1732 5478 2.544267 GTGGTACTCAAGCATAATCCGC 59.456 50.000 0.00 0.00 38.03 5.54
2013 5759 2.384828 AGAAACTGTTTGGGTTGGGAC 58.615 47.619 11.03 0.00 0.00 4.46
2059 5805 0.644380 TGAGGATGGGGAGGATGAGT 59.356 55.000 0.00 0.00 0.00 3.41
2067 5813 2.434336 TGGGGAGGATGAGTACATTTCG 59.566 50.000 0.00 0.00 36.82 3.46
2082 5828 3.569701 ACATTTCGGAACACAAGCTTGAT 59.430 39.130 32.50 16.97 0.00 2.57
2091 5837 1.465777 CACAAGCTTGATGATGCGACA 59.534 47.619 32.50 0.00 0.00 4.35
2138 5884 4.202367 GGATAGGGAGGATGACGATGTTTT 60.202 45.833 0.00 0.00 0.00 2.43
2143 5889 3.947834 GGAGGATGACGATGTTTTGGAAT 59.052 43.478 0.00 0.00 0.00 3.01
2170 5916 1.193323 AGGCTCTGACTCTCATGTGG 58.807 55.000 0.00 0.00 0.00 4.17
2178 5924 2.300152 TGACTCTCATGTGGTCTTCACC 59.700 50.000 13.73 0.00 45.48 4.02
2394 6140 3.449018 AGAGTCAGCGTGATATTGGAGTT 59.551 43.478 0.00 0.00 0.00 3.01
2414 6160 5.385198 AGTTCTCAACCTTGGAAATTGCTA 58.615 37.500 0.00 0.00 0.00 3.49
2452 6198 0.550914 ACCTCAGCTTTGGTCCAACA 59.449 50.000 2.98 0.00 29.18 3.33
2529 6275 3.813443 TGATTAGCCAGAAGATGCTTCC 58.187 45.455 3.71 0.00 39.00 3.46
2710 6484 4.223953 TGTGACAGTTTTCTACTCCCTCT 58.776 43.478 0.00 0.00 33.85 3.69
2728 6502 6.875469 TCCCTCTGTCCCATAATATAAGAGT 58.125 40.000 0.00 0.00 0.00 3.24
2780 6554 7.941431 ACACTCTTATATTATAGGACGGAGG 57.059 40.000 0.00 0.00 0.00 4.30
3042 6817 6.259550 AGTTGTTTCCAGATTGCTAATGTC 57.740 37.500 0.00 0.00 0.00 3.06
3045 6820 4.701651 TGTTTCCAGATTGCTAATGTCCAG 59.298 41.667 0.00 0.00 0.00 3.86
3061 6836 3.744940 TCCAGAAGGGATTTGCATCTT 57.255 42.857 0.00 0.00 42.15 2.40
3078 6853 3.851458 TCTTCATGACCTGCATATGCT 57.149 42.857 27.13 8.49 42.66 3.79
3273 7048 1.625315 AGAGCATGTAGACTGCCACAA 59.375 47.619 0.00 0.00 40.56 3.33
3357 7132 0.842635 GCCTGAGGATGACAGGGATT 59.157 55.000 0.65 0.00 0.00 3.01
3361 7136 3.054139 CCTGAGGATGACAGGGATTGAAA 60.054 47.826 0.00 0.00 0.00 2.69
3366 7141 4.977739 AGGATGACAGGGATTGAAAGGATA 59.022 41.667 0.00 0.00 0.00 2.59
3367 7142 5.066593 GGATGACAGGGATTGAAAGGATAC 58.933 45.833 0.00 0.00 0.00 2.24
3368 7143 4.503714 TGACAGGGATTGAAAGGATACC 57.496 45.455 0.00 0.00 37.17 2.73
3369 7144 3.849574 TGACAGGGATTGAAAGGATACCA 59.150 43.478 0.00 0.00 29.18 3.25
3370 7145 4.080356 TGACAGGGATTGAAAGGATACCAG 60.080 45.833 0.00 0.00 29.18 4.00
3371 7146 3.217626 CAGGGATTGAAAGGATACCAGC 58.782 50.000 0.00 0.00 29.18 4.85
3372 7147 2.852449 AGGGATTGAAAGGATACCAGCA 59.148 45.455 0.00 0.00 29.18 4.41
3377 7152 1.210478 TGAAAGGATACCAGCAGGAGC 59.790 52.381 0.35 0.00 38.69 4.70
3398 7173 3.803715 GCTACCTCACTGAGTTTTGCTGA 60.804 47.826 5.32 0.00 0.00 4.26
3410 7185 6.808829 TGAGTTTTGCTGAAAGAATGTCATT 58.191 32.000 0.00 0.00 27.44 2.57
3430 7205 8.405531 TGTCATTTTTGATATAACAAGCTAGGC 58.594 33.333 0.00 0.00 0.00 3.93
3438 7213 0.393077 AACAAGCTAGGCGACAGTGT 59.607 50.000 0.00 0.00 0.00 3.55
3445 7220 1.478510 CTAGGCGACAGTGTGATTCCT 59.521 52.381 0.00 4.03 0.00 3.36
3446 7221 0.036952 AGGCGACAGTGTGATTCCTG 60.037 55.000 0.00 0.00 34.82 3.86
3447 7222 0.037326 GGCGACAGTGTGATTCCTGA 60.037 55.000 0.00 0.00 32.93 3.86
3448 7223 1.354040 GCGACAGTGTGATTCCTGAG 58.646 55.000 0.00 0.00 32.93 3.35
3449 7224 1.337260 GCGACAGTGTGATTCCTGAGT 60.337 52.381 0.00 0.00 32.93 3.41
3450 7225 2.094700 GCGACAGTGTGATTCCTGAGTA 60.095 50.000 0.00 0.00 32.93 2.59
3451 7226 3.502920 CGACAGTGTGATTCCTGAGTAC 58.497 50.000 0.00 0.00 32.93 2.73
3452 7227 3.191581 CGACAGTGTGATTCCTGAGTACT 59.808 47.826 0.00 0.00 32.93 2.73
3453 7228 4.489810 GACAGTGTGATTCCTGAGTACTG 58.510 47.826 0.00 0.00 39.77 2.74
3454 7229 4.152647 ACAGTGTGATTCCTGAGTACTGA 58.847 43.478 0.00 0.00 37.91 3.41
3455 7230 4.774726 ACAGTGTGATTCCTGAGTACTGAT 59.225 41.667 0.00 0.00 37.91 2.90
3456 7231 5.247110 ACAGTGTGATTCCTGAGTACTGATT 59.753 40.000 0.00 0.00 37.91 2.57
3457 7232 5.809562 CAGTGTGATTCCTGAGTACTGATTC 59.190 44.000 0.00 0.00 36.96 2.52
3458 7233 5.481824 AGTGTGATTCCTGAGTACTGATTCA 59.518 40.000 0.00 1.24 0.00 2.57
3459 7234 6.155910 AGTGTGATTCCTGAGTACTGATTCAT 59.844 38.462 0.00 0.00 0.00 2.57
3460 7235 6.478344 GTGTGATTCCTGAGTACTGATTCATC 59.522 42.308 0.00 0.00 0.00 2.92
3461 7236 6.382282 TGTGATTCCTGAGTACTGATTCATCT 59.618 38.462 0.00 0.00 0.00 2.90
3462 7237 7.093156 TGTGATTCCTGAGTACTGATTCATCTT 60.093 37.037 0.00 0.00 0.00 2.40
3463 7238 7.437862 GTGATTCCTGAGTACTGATTCATCTTC 59.562 40.741 0.00 0.00 0.00 2.87
3464 7239 7.344093 TGATTCCTGAGTACTGATTCATCTTCT 59.656 37.037 0.00 0.00 0.00 2.85
3465 7240 7.487822 TTCCTGAGTACTGATTCATCTTCTT 57.512 36.000 0.00 0.00 0.00 2.52
3466 7241 7.487822 TCCTGAGTACTGATTCATCTTCTTT 57.512 36.000 0.00 0.00 0.00 2.52
3467 7242 7.326454 TCCTGAGTACTGATTCATCTTCTTTG 58.674 38.462 0.00 0.00 0.00 2.77
3468 7243 7.038729 TCCTGAGTACTGATTCATCTTCTTTGT 60.039 37.037 0.00 0.00 0.00 2.83
3469 7244 7.605691 CCTGAGTACTGATTCATCTTCTTTGTT 59.394 37.037 0.00 0.00 0.00 2.83
3470 7245 8.315391 TGAGTACTGATTCATCTTCTTTGTTG 57.685 34.615 0.00 0.00 0.00 3.33
3471 7246 7.933577 TGAGTACTGATTCATCTTCTTTGTTGT 59.066 33.333 0.00 0.00 0.00 3.32
3472 7247 8.682936 AGTACTGATTCATCTTCTTTGTTGTT 57.317 30.769 0.00 0.00 0.00 2.83
3473 7248 9.125026 AGTACTGATTCATCTTCTTTGTTGTTT 57.875 29.630 0.00 0.00 0.00 2.83
3474 7249 9.387123 GTACTGATTCATCTTCTTTGTTGTTTC 57.613 33.333 0.00 0.00 0.00 2.78
3475 7250 8.230472 ACTGATTCATCTTCTTTGTTGTTTCT 57.770 30.769 0.00 0.00 0.00 2.52
3476 7251 8.133627 ACTGATTCATCTTCTTTGTTGTTTCTG 58.866 33.333 0.00 0.00 0.00 3.02
3477 7252 6.919662 TGATTCATCTTCTTTGTTGTTTCTGC 59.080 34.615 0.00 0.00 0.00 4.26
3478 7253 6.455360 TTCATCTTCTTTGTTGTTTCTGCT 57.545 33.333 0.00 0.00 0.00 4.24
3479 7254 5.824429 TCATCTTCTTTGTTGTTTCTGCTG 58.176 37.500 0.00 0.00 0.00 4.41
3480 7255 5.589855 TCATCTTCTTTGTTGTTTCTGCTGA 59.410 36.000 0.00 0.00 0.00 4.26
3481 7256 6.263842 TCATCTTCTTTGTTGTTTCTGCTGAT 59.736 34.615 0.00 0.00 0.00 2.90
3482 7257 5.824429 TCTTCTTTGTTGTTTCTGCTGATG 58.176 37.500 0.00 0.00 0.00 3.07
3483 7258 5.589855 TCTTCTTTGTTGTTTCTGCTGATGA 59.410 36.000 0.00 0.00 0.00 2.92
3484 7259 6.263842 TCTTCTTTGTTGTTTCTGCTGATGAT 59.736 34.615 0.00 0.00 0.00 2.45
3485 7260 7.445096 TCTTCTTTGTTGTTTCTGCTGATGATA 59.555 33.333 0.00 0.00 0.00 2.15
3486 7261 7.137490 TCTTTGTTGTTTCTGCTGATGATAG 57.863 36.000 0.00 0.00 0.00 2.08
3487 7262 4.952262 TGTTGTTTCTGCTGATGATAGC 57.048 40.909 0.00 0.00 43.95 2.97
3488 7263 4.582869 TGTTGTTTCTGCTGATGATAGCT 58.417 39.130 0.00 0.00 44.01 3.32
3489 7264 5.005740 TGTTGTTTCTGCTGATGATAGCTT 58.994 37.500 0.00 0.00 44.01 3.74
3490 7265 5.106436 TGTTGTTTCTGCTGATGATAGCTTG 60.106 40.000 0.00 0.00 44.01 4.01
3491 7266 4.582869 TGTTTCTGCTGATGATAGCTTGT 58.417 39.130 0.00 0.00 44.01 3.16
3492 7267 4.633126 TGTTTCTGCTGATGATAGCTTGTC 59.367 41.667 0.00 0.00 44.01 3.18
3493 7268 4.750021 TTCTGCTGATGATAGCTTGTCT 57.250 40.909 0.00 0.00 44.01 3.41
3494 7269 4.750021 TCTGCTGATGATAGCTTGTCTT 57.250 40.909 0.00 0.00 44.01 3.01
3495 7270 5.095145 TCTGCTGATGATAGCTTGTCTTT 57.905 39.130 0.00 0.00 44.01 2.52
3496 7271 5.494724 TCTGCTGATGATAGCTTGTCTTTT 58.505 37.500 0.00 0.00 44.01 2.27
3497 7272 5.942236 TCTGCTGATGATAGCTTGTCTTTTT 59.058 36.000 0.00 0.00 44.01 1.94
3498 7273 6.093219 TCTGCTGATGATAGCTTGTCTTTTTC 59.907 38.462 0.00 0.00 44.01 2.29
3499 7274 5.942236 TGCTGATGATAGCTTGTCTTTTTCT 59.058 36.000 0.00 0.00 44.01 2.52
3500 7275 6.128090 TGCTGATGATAGCTTGTCTTTTTCTG 60.128 38.462 0.00 0.00 44.01 3.02
3501 7276 6.677431 GCTGATGATAGCTTGTCTTTTTCTGG 60.677 42.308 0.00 0.00 40.52 3.86
3502 7277 6.475504 TGATGATAGCTTGTCTTTTTCTGGA 58.524 36.000 0.00 0.00 0.00 3.86
3503 7278 7.114754 TGATGATAGCTTGTCTTTTTCTGGAT 58.885 34.615 0.00 0.00 0.00 3.41
3504 7279 6.748333 TGATAGCTTGTCTTTTTCTGGATG 57.252 37.500 0.00 0.00 0.00 3.51
3505 7280 5.649395 TGATAGCTTGTCTTTTTCTGGATGG 59.351 40.000 0.00 0.00 0.00 3.51
3506 7281 4.104383 AGCTTGTCTTTTTCTGGATGGA 57.896 40.909 0.00 0.00 0.00 3.41
3507 7282 4.077822 AGCTTGTCTTTTTCTGGATGGAG 58.922 43.478 0.00 0.00 0.00 3.86
3508 7283 3.823304 GCTTGTCTTTTTCTGGATGGAGT 59.177 43.478 0.00 0.00 0.00 3.85
3509 7284 5.003804 GCTTGTCTTTTTCTGGATGGAGTA 58.996 41.667 0.00 0.00 0.00 2.59
3510 7285 5.473504 GCTTGTCTTTTTCTGGATGGAGTAA 59.526 40.000 0.00 0.00 0.00 2.24
3511 7286 6.348868 GCTTGTCTTTTTCTGGATGGAGTAAG 60.349 42.308 0.00 0.00 0.00 2.34
3512 7287 6.433847 TGTCTTTTTCTGGATGGAGTAAGA 57.566 37.500 0.00 0.00 0.00 2.10
3513 7288 6.467677 TGTCTTTTTCTGGATGGAGTAAGAG 58.532 40.000 0.00 0.00 0.00 2.85
3514 7289 6.043243 TGTCTTTTTCTGGATGGAGTAAGAGT 59.957 38.462 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.157252 GAGCATCTGAGGGCCCGA 61.157 66.667 18.44 8.48 0.00 5.14
49 50 0.108804 CGAAGGCAGGAGCTTTACGA 60.109 55.000 0.00 0.00 40.49 3.43
50 51 1.696832 GCGAAGGCAGGAGCTTTACG 61.697 60.000 0.00 0.00 40.49 3.18
100 101 4.758773 TTAAGTAATAACTGACCGGGGG 57.241 45.455 6.32 0.00 35.62 5.40
319 334 7.122799 GTCTAAATTATCTTCACTTGGCCCTTT 59.877 37.037 0.00 0.00 0.00 3.11
328 343 9.981460 ATTTTGAGGGTCTAAATTATCTTCACT 57.019 29.630 0.00 0.00 29.89 3.41
359 374 2.650778 CTTTGGCCCCGCAACTTC 59.349 61.111 0.00 0.00 0.00 3.01
371 386 4.392921 TCTCTCTCGAAATAGGCTTTGG 57.607 45.455 0.00 0.00 0.00 3.28
431 446 9.050601 CATCTCTAGCCCTTTCATAAAACTTAG 57.949 37.037 0.00 0.00 0.00 2.18
454 469 2.284190 GTGGAGGACAGCTTAAGCATC 58.716 52.381 28.39 22.99 45.16 3.91
520 538 2.342648 GTTTCGCGGTGAGGGTCT 59.657 61.111 6.13 0.00 0.00 3.85
576 595 1.528309 GAGAGGAGGAGGAGGAGCG 60.528 68.421 0.00 0.00 0.00 5.03
708 4420 0.179189 CGAGCTTCCACAAATTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
750 4462 4.096532 GGTCAGGAAAAGATCGGGATTTTC 59.903 45.833 8.62 8.62 42.19 2.29
758 4470 0.736325 ACGCGGTCAGGAAAAGATCG 60.736 55.000 12.47 0.00 42.26 3.69
759 4471 1.000145 GACGCGGTCAGGAAAAGATC 59.000 55.000 12.47 0.00 32.09 2.75
893 4613 3.732849 GCAGGCAGGGGTAGGCTT 61.733 66.667 0.00 0.00 40.22 4.35
901 4621 3.655211 AACAGAGGGCAGGCAGGG 61.655 66.667 0.00 0.00 0.00 4.45
922 4642 4.078639 TGATCTCTCTCGTAGATGCAGA 57.921 45.455 0.00 0.00 33.82 4.26
1021 4755 1.605712 GGATATGCTGCTACCCACGAC 60.606 57.143 0.00 0.00 0.00 4.34
1039 4773 0.467290 GACAAGGCCAAACACCTGGA 60.467 55.000 5.01 0.00 38.96 3.86
1042 4776 0.468029 CCAGACAAGGCCAAACACCT 60.468 55.000 5.01 0.00 40.02 4.00
1059 4793 0.872451 CGTACGTTGTCAGCACACCA 60.872 55.000 7.22 0.00 29.76 4.17
1077 4811 2.859273 ATTCGGCAAGCCTCTGTCCG 62.859 60.000 9.73 0.00 37.35 4.79
1117 4851 2.972589 ATCTGGGGCTCGCTGGGTAT 62.973 60.000 0.00 0.00 0.00 2.73
1606 5340 0.662085 GGCGTAGGGAAGTCGACTAG 59.338 60.000 20.39 5.79 0.00 2.57
1731 5477 3.446799 TGCAAATGAAAGTTGTGACTGC 58.553 40.909 0.00 0.00 45.01 4.40
1732 5478 5.342433 TCTTGCAAATGAAAGTTGTGACTG 58.658 37.500 0.00 0.00 45.01 3.51
2034 5780 2.002977 CTCCCCATCCTCAAGCCCA 61.003 63.158 0.00 0.00 0.00 5.36
2059 5805 4.130857 TCAAGCTTGTGTTCCGAAATGTA 58.869 39.130 25.19 0.00 0.00 2.29
2067 5813 2.730090 CGCATCATCAAGCTTGTGTTCC 60.730 50.000 25.19 10.22 0.00 3.62
2091 5837 1.205893 GGTTTCAGCCTCGACAGATCT 59.794 52.381 0.00 0.00 0.00 2.75
2101 5847 2.122768 CCTATCCTCAGGTTTCAGCCT 58.877 52.381 0.00 0.00 39.99 4.58
2170 5916 2.034001 CGTCAAACTTGTCGGTGAAGAC 60.034 50.000 1.83 0.00 41.30 3.01
2178 5924 6.572254 CCACTTTAAATACGTCAAACTTGTCG 59.428 38.462 0.00 7.40 43.47 4.35
2220 5966 6.815641 CACATGAGCTAGTTATGTCTTCAAGT 59.184 38.462 0.00 0.00 33.06 3.16
2394 6140 5.324409 ACATAGCAATTTCCAAGGTTGAGA 58.676 37.500 0.00 0.00 0.00 3.27
2414 6160 7.362401 GCTGAGGTGATACAATTCTTTCAACAT 60.362 37.037 0.00 0.00 0.00 2.71
2452 6198 4.371417 CCACACAGGGGCTGGCAT 62.371 66.667 2.88 0.00 35.51 4.40
2645 6391 4.006989 GTGCCACATAAATGTACCTCACA 58.993 43.478 0.00 0.00 39.39 3.58
2647 6393 3.266636 CGTGCCACATAAATGTACCTCA 58.733 45.455 0.00 0.00 39.39 3.86
2758 6532 7.036717 ACTCCCTCCGTCCTATAATATAAGAGT 60.037 40.741 0.00 0.00 0.00 3.24
2775 6549 6.992715 ACATCTGAAAAATAATACTCCCTCCG 59.007 38.462 0.00 0.00 0.00 4.63
2780 6554 8.286097 GCTAGCACATCTGAAAAATAATACTCC 58.714 37.037 10.63 0.00 0.00 3.85
2856 6631 5.711976 AGCAAATAAACTGTAGCAATGGAGT 59.288 36.000 0.00 0.00 0.00 3.85
3042 6817 3.359033 TGAAGATGCAAATCCCTTCTGG 58.641 45.455 0.00 0.00 36.78 3.86
3045 6820 4.202090 GGTCATGAAGATGCAAATCCCTTC 60.202 45.833 0.00 0.00 36.48 3.46
3061 6836 3.473625 CTTCAGCATATGCAGGTCATGA 58.526 45.455 28.62 18.78 45.16 3.07
3078 6853 4.391869 CTGCAAGGAGCTGCTTCA 57.608 55.556 18.64 16.65 45.94 3.02
3085 6860 1.403780 CCAAATCTTGCTGCAAGGAGC 60.404 52.381 34.49 6.62 41.33 4.70
3317 7092 1.226491 GCATGGTGATTGAGTGCGC 60.226 57.895 0.00 0.00 0.00 6.09
3357 7132 1.210478 GCTCCTGCTGGTATCCTTTCA 59.790 52.381 9.73 0.00 36.03 2.69
3377 7152 3.995199 TCAGCAAAACTCAGTGAGGTAG 58.005 45.455 23.79 14.56 33.35 3.18
3381 7156 5.490139 TTCTTTCAGCAAAACTCAGTGAG 57.510 39.130 18.83 18.83 35.52 3.51
3410 7185 6.110033 TGTCGCCTAGCTTGTTATATCAAAA 58.890 36.000 0.00 0.00 0.00 2.44
3430 7205 2.732412 ACTCAGGAATCACACTGTCG 57.268 50.000 0.00 0.00 36.17 4.35
3438 7213 7.344093 AGAAGATGAATCAGTACTCAGGAATCA 59.656 37.037 0.00 0.00 0.00 2.57
3445 7220 7.933577 ACAACAAAGAAGATGAATCAGTACTCA 59.066 33.333 0.00 0.00 0.00 3.41
3446 7221 8.316640 ACAACAAAGAAGATGAATCAGTACTC 57.683 34.615 0.00 0.00 0.00 2.59
3447 7222 8.682936 AACAACAAAGAAGATGAATCAGTACT 57.317 30.769 0.00 0.00 0.00 2.73
3448 7223 9.387123 GAAACAACAAAGAAGATGAATCAGTAC 57.613 33.333 0.00 0.00 0.00 2.73
3449 7224 9.342308 AGAAACAACAAAGAAGATGAATCAGTA 57.658 29.630 0.00 0.00 0.00 2.74
3450 7225 8.133627 CAGAAACAACAAAGAAGATGAATCAGT 58.866 33.333 0.00 0.00 0.00 3.41
3451 7226 7.114529 GCAGAAACAACAAAGAAGATGAATCAG 59.885 37.037 0.00 0.00 0.00 2.90
3452 7227 6.919662 GCAGAAACAACAAAGAAGATGAATCA 59.080 34.615 0.00 0.00 0.00 2.57
3453 7228 7.114529 CAGCAGAAACAACAAAGAAGATGAATC 59.885 37.037 0.00 0.00 0.00 2.52
3454 7229 6.921857 CAGCAGAAACAACAAAGAAGATGAAT 59.078 34.615 0.00 0.00 0.00 2.57
3455 7230 6.095300 TCAGCAGAAACAACAAAGAAGATGAA 59.905 34.615 0.00 0.00 0.00 2.57
3456 7231 5.589855 TCAGCAGAAACAACAAAGAAGATGA 59.410 36.000 0.00 0.00 0.00 2.92
3457 7232 5.824429 TCAGCAGAAACAACAAAGAAGATG 58.176 37.500 0.00 0.00 0.00 2.90
3458 7233 6.263842 TCATCAGCAGAAACAACAAAGAAGAT 59.736 34.615 0.00 0.00 0.00 2.40
3459 7234 5.589855 TCATCAGCAGAAACAACAAAGAAGA 59.410 36.000 0.00 0.00 0.00 2.87
3460 7235 5.824429 TCATCAGCAGAAACAACAAAGAAG 58.176 37.500 0.00 0.00 0.00 2.85
3461 7236 5.833406 TCATCAGCAGAAACAACAAAGAA 57.167 34.783 0.00 0.00 0.00 2.52
3462 7237 6.348786 GCTATCATCAGCAGAAACAACAAAGA 60.349 38.462 0.00 0.00 41.40 2.52
3463 7238 5.798934 GCTATCATCAGCAGAAACAACAAAG 59.201 40.000 0.00 0.00 41.40 2.77
3464 7239 5.474532 AGCTATCATCAGCAGAAACAACAAA 59.525 36.000 0.00 0.00 44.35 2.83
3465 7240 5.005740 AGCTATCATCAGCAGAAACAACAA 58.994 37.500 0.00 0.00 44.35 2.83
3466 7241 4.582869 AGCTATCATCAGCAGAAACAACA 58.417 39.130 0.00 0.00 44.35 3.33
3467 7242 5.106396 ACAAGCTATCATCAGCAGAAACAAC 60.106 40.000 0.00 0.00 44.35 3.32
3468 7243 5.005740 ACAAGCTATCATCAGCAGAAACAA 58.994 37.500 0.00 0.00 44.35 2.83
3469 7244 4.582869 ACAAGCTATCATCAGCAGAAACA 58.417 39.130 0.00 0.00 44.35 2.83
3470 7245 4.874966 AGACAAGCTATCATCAGCAGAAAC 59.125 41.667 0.00 0.00 44.35 2.78
3471 7246 5.095145 AGACAAGCTATCATCAGCAGAAA 57.905 39.130 0.00 0.00 44.35 2.52
3472 7247 4.750021 AGACAAGCTATCATCAGCAGAA 57.250 40.909 0.00 0.00 44.35 3.02
3473 7248 4.750021 AAGACAAGCTATCATCAGCAGA 57.250 40.909 0.00 0.00 44.35 4.26
3474 7249 5.814764 AAAAGACAAGCTATCATCAGCAG 57.185 39.130 0.00 0.00 44.35 4.24
3475 7250 5.942236 AGAAAAAGACAAGCTATCATCAGCA 59.058 36.000 0.00 0.00 44.35 4.41
3476 7251 6.256686 CAGAAAAAGACAAGCTATCATCAGC 58.743 40.000 0.00 0.00 42.12 4.26
3477 7252 6.596888 TCCAGAAAAAGACAAGCTATCATCAG 59.403 38.462 0.00 0.00 0.00 2.90
3478 7253 6.475504 TCCAGAAAAAGACAAGCTATCATCA 58.524 36.000 0.00 0.00 0.00 3.07
3479 7254 6.992063 TCCAGAAAAAGACAAGCTATCATC 57.008 37.500 0.00 0.00 0.00 2.92
3480 7255 6.320672 CCATCCAGAAAAAGACAAGCTATCAT 59.679 38.462 0.00 0.00 0.00 2.45
3481 7256 5.649395 CCATCCAGAAAAAGACAAGCTATCA 59.351 40.000 0.00 0.00 0.00 2.15
3482 7257 5.882557 TCCATCCAGAAAAAGACAAGCTATC 59.117 40.000 0.00 0.00 0.00 2.08
3483 7258 5.819991 TCCATCCAGAAAAAGACAAGCTAT 58.180 37.500 0.00 0.00 0.00 2.97
3484 7259 5.221925 ACTCCATCCAGAAAAAGACAAGCTA 60.222 40.000 0.00 0.00 0.00 3.32
3485 7260 4.077822 CTCCATCCAGAAAAAGACAAGCT 58.922 43.478 0.00 0.00 0.00 3.74
3486 7261 3.823304 ACTCCATCCAGAAAAAGACAAGC 59.177 43.478 0.00 0.00 0.00 4.01
3487 7262 6.936900 TCTTACTCCATCCAGAAAAAGACAAG 59.063 38.462 0.00 0.00 0.00 3.16
3488 7263 6.837312 TCTTACTCCATCCAGAAAAAGACAA 58.163 36.000 0.00 0.00 0.00 3.18
3489 7264 6.043243 ACTCTTACTCCATCCAGAAAAAGACA 59.957 38.462 0.00 0.00 0.00 3.41
3490 7265 6.468543 ACTCTTACTCCATCCAGAAAAAGAC 58.531 40.000 0.00 0.00 0.00 3.01
3491 7266 6.688073 ACTCTTACTCCATCCAGAAAAAGA 57.312 37.500 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.