Multiple sequence alignment - TraesCS6B01G471100

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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 TraesCS6B01G471100 chr6B 100.000 4467 0 0 1 4467 719411464 719406998 0.000000e+00 8250.0
1 TraesCS6B01G471100 chr6B 90.953 1857 97 20 1209 3039 719440171 719441982 0.000000e+00 2433.0
2 TraesCS6B01G471100 chr6B 91.559 853 46 11 3036 3869 719442030 719442875 0.000000e+00 1153.0
3 TraesCS6B01G471100 chr6B 94.954 218 10 1 685 901 719439911 719440128 1.540000e-89 340.0
4 TraesCS6B01G471100 chr6A 93.571 3282 149 25 350 3598 615971873 615975125 0.000000e+00 4835.0
5 TraesCS6B01G471100 chr6A 90.588 85 4 3 273 354 615971616 615971699 4.720000e-20 110.0
6 TraesCS6B01G471100 chr6A 97.297 37 0 1 3598 3633 592883021 592883057 1.340000e-05 62.1
7 TraesCS6B01G471100 chr6D 90.326 2605 151 33 1906 4448 471251356 471253921 0.000000e+00 3321.0
8 TraesCS6B01G471100 chr6D 94.805 1694 71 11 174 1858 471249653 471251338 0.000000e+00 2625.0
9 TraesCS6B01G471100 chr6D 89.130 138 14 1 7 144 13965363 13965227 2.140000e-38 171.0
10 TraesCS6B01G471100 chr7A 84.216 944 78 31 1861 2766 263718554 263719464 0.000000e+00 852.0
11 TraesCS6B01G471100 chr7A 81.528 720 97 24 1161 1860 263717773 263718476 1.090000e-155 560.0
12 TraesCS6B01G471100 chr7A 83.512 467 60 11 677 1141 263717241 263717692 1.920000e-113 420.0
13 TraesCS6B01G471100 chr7A 83.582 201 17 3 3310 3494 263727600 263727800 1.650000e-39 174.0
14 TraesCS6B01G471100 chr7D 83.228 948 77 39 1861 2766 246813314 246814221 0.000000e+00 795.0
15 TraesCS6B01G471100 chr7D 82.247 721 91 24 1161 1860 246812528 246813232 4.980000e-164 588.0
16 TraesCS6B01G471100 chr7D 83.047 466 62 14 678 1141 246812000 246812450 1.500000e-109 407.0
17 TraesCS6B01G471100 chr7D 86.127 173 12 1 3310 3470 246815012 246815184 4.590000e-40 176.0
18 TraesCS6B01G471100 chr7B 85.511 704 65 11 1908 2586 223176132 223176823 0.000000e+00 701.0
19 TraesCS6B01G471100 chr7B 83.533 668 81 19 1161 1809 223175292 223175949 8.270000e-167 597.0
20 TraesCS6B01G471100 chr7B 83.476 466 61 14 678 1141 223174760 223175211 1.920000e-113 420.0
21 TraesCS6B01G471100 chr7B 74.114 649 136 28 3782 4410 686984479 686985115 5.770000e-59 239.0
22 TraesCS6B01G471100 chr7B 92.969 128 6 1 2642 2766 223176849 223176976 2.740000e-42 183.0
23 TraesCS6B01G471100 chr7B 84.615 182 16 1 3301 3470 223178643 223178824 2.140000e-38 171.0
24 TraesCS6B01G471100 chr7B 89.552 134 13 1 10 143 482171569 482171437 7.680000e-38 169.0
25 TraesCS6B01G471100 chr5D 74.921 634 129 23 3794 4411 40908411 40909030 3.430000e-66 263.0
26 TraesCS6B01G471100 chr4B 76.015 542 109 18 3883 4410 632696095 632695561 1.230000e-65 261.0
27 TraesCS6B01G471100 chr4B 89.855 138 11 2 7 144 659399689 659399823 1.650000e-39 174.0
28 TraesCS6B01G471100 chr4B 88.571 140 15 1 7 145 291896455 291896594 7.680000e-38 169.0
29 TraesCS6B01G471100 chr1A 73.233 665 145 27 3794 4439 397266458 397267108 1.260000e-50 211.0
30 TraesCS6B01G471100 chr1A 97.222 36 0 1 3598 3633 337681793 337681759 4.830000e-05 60.2
31 TraesCS6B01G471100 chr5A 90.226 133 12 1 14 146 571461881 571461750 5.940000e-39 172.0
32 TraesCS6B01G471100 chr3B 88.971 136 13 2 9 142 830398595 830398460 2.760000e-37 167.0
33 TraesCS6B01G471100 chr3B 88.971 136 13 2 9 142 830685968 830685833 2.760000e-37 167.0
34 TraesCS6B01G471100 chr2D 88.028 142 15 2 7 147 403383278 403383418 2.760000e-37 167.0
35 TraesCS6B01G471100 chr2D 95.122 41 1 1 3598 3637 402307956 402307916 3.730000e-06 63.9
36 TraesCS6B01G471100 chr2D 92.857 42 0 3 3595 3633 189359730 189359771 1.740000e-04 58.4
37 TraesCS6B01G471100 chrUn 87.857 140 16 1 7 146 294935479 294935341 3.580000e-36 163.0
38 TraesCS6B01G471100 chrUn 97.297 37 0 1 3598 3633 102499753 102499717 1.340000e-05 62.1
39 TraesCS6B01G471100 chr3A 92.857 42 1 1 3594 3633 646291917 646291876 4.830000e-05 60.2
40 TraesCS6B01G471100 chr2A 93.023 43 0 2 3597 3636 257770124 257770166 4.830000e-05 60.2


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 TraesCS6B01G471100 chr6B 719406998 719411464 4466 True 8250.000000 8250 100.000000 1 4467 1 chr6B.!!$R1 4466
1 TraesCS6B01G471100 chr6B 719439911 719442875 2964 False 1308.666667 2433 92.488667 685 3869 3 chr6B.!!$F1 3184
2 TraesCS6B01G471100 chr6A 615971616 615975125 3509 False 2472.500000 4835 92.079500 273 3598 2 chr6A.!!$F2 3325
3 TraesCS6B01G471100 chr6D 471249653 471253921 4268 False 2973.000000 3321 92.565500 174 4448 2 chr6D.!!$F1 4274
4 TraesCS6B01G471100 chr7A 263717241 263719464 2223 False 610.666667 852 83.085333 677 2766 3 chr7A.!!$F2 2089
5 TraesCS6B01G471100 chr7D 246812000 246815184 3184 False 491.500000 795 83.662250 678 3470 4 chr7D.!!$F1 2792
6 TraesCS6B01G471100 chr7B 223174760 223178824 4064 False 414.400000 701 86.020800 678 3470 5 chr7B.!!$F2 2792
7 TraesCS6B01G471100 chr7B 686984479 686985115 636 False 239.000000 239 74.114000 3782 4410 1 chr7B.!!$F1 628
8 TraesCS6B01G471100 chr5D 40908411 40909030 619 False 263.000000 263 74.921000 3794 4411 1 chr5D.!!$F1 617
9 TraesCS6B01G471100 chr4B 632695561 632696095 534 True 261.000000 261 76.015000 3883 4410 1 chr4B.!!$R1 527
10 TraesCS6B01G471100 chr1A 397266458 397267108 650 False 211.000000 211 73.233000 3794 4439 1 chr1A.!!$F1 645

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
34 35 1.098050 GTTGTCATGATGGTGGCTCC 58.902 55.0 0.0 0.0 0.0 4.70 F
232 233 1.355718 ACCCCTGCCCATCATCGAAT 61.356 55.0 0.0 0.0 0.0 3.34 F
1775 2047 0.687427 AAGGTGGCTTTGGTGCTGTT 60.687 50.0 0.0 0.0 0.0 3.16 F
2968 3390 0.107508 AGATGCCATTGTCCGACCAG 60.108 55.0 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1683 2.632377 CTGACATGCCTCGTTGGTTAT 58.368 47.619 0.00 0.00 38.35 1.89 R
1824 2096 2.762887 TGTGGGTTTCTGAAATGCAACA 59.237 40.909 6.06 6.48 0.00 3.33 R
3061 3534 0.179119 GAGCCGGCTTAGCGTCTTTA 60.179 55.000 33.34 0.00 34.64 1.85 R
3940 5783 0.978667 GGGAAGGAGGAGGAGTGGAC 60.979 65.000 0.00 0.00 0.00 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.263941 GCTCCGGCGACAAATGTT 58.736 55.556 9.30 0.00 0.00 2.71
18 19 1.154225 GCTCCGGCGACAAATGTTG 60.154 57.895 9.30 0.00 0.00 3.33
30 31 4.524316 ACAAATGTTGTCATGATGGTGG 57.476 40.909 0.00 0.00 40.56 4.61
31 32 3.255725 CAAATGTTGTCATGATGGTGGC 58.744 45.455 0.00 0.00 34.19 5.01
32 33 2.519771 ATGTTGTCATGATGGTGGCT 57.480 45.000 0.00 0.00 32.51 4.75
33 34 1.825090 TGTTGTCATGATGGTGGCTC 58.175 50.000 0.00 0.00 0.00 4.70
34 35 1.098050 GTTGTCATGATGGTGGCTCC 58.902 55.000 0.00 0.00 0.00 4.70
35 36 5.472376 ATGTTGTCATGATGGTGGCTCCA 62.472 47.826 11.19 11.19 40.68 3.86
44 45 2.787473 TGGTGGCTCCAGACTTAATG 57.213 50.000 3.73 0.00 41.93 1.90
45 46 2.265367 TGGTGGCTCCAGACTTAATGA 58.735 47.619 3.73 0.00 41.93 2.57
46 47 2.846206 TGGTGGCTCCAGACTTAATGAT 59.154 45.455 3.73 0.00 41.93 2.45
47 48 3.209410 GGTGGCTCCAGACTTAATGATG 58.791 50.000 0.00 0.00 35.97 3.07
48 49 3.118261 GGTGGCTCCAGACTTAATGATGA 60.118 47.826 0.00 0.00 35.97 2.92
49 50 4.517285 GTGGCTCCAGACTTAATGATGAA 58.483 43.478 0.00 0.00 0.00 2.57
50 51 5.128919 GTGGCTCCAGACTTAATGATGAAT 58.871 41.667 0.00 0.00 0.00 2.57
51 52 5.591877 GTGGCTCCAGACTTAATGATGAATT 59.408 40.000 0.00 0.00 0.00 2.17
52 53 6.767902 GTGGCTCCAGACTTAATGATGAATTA 59.232 38.462 0.00 0.00 0.00 1.40
53 54 7.446625 GTGGCTCCAGACTTAATGATGAATTAT 59.553 37.037 0.00 0.00 30.74 1.28
54 55 8.000709 TGGCTCCAGACTTAATGATGAATTATT 58.999 33.333 0.00 0.00 30.74 1.40
55 56 8.854117 GGCTCCAGACTTAATGATGAATTATTT 58.146 33.333 0.00 0.00 30.74 1.40
105 106 2.437180 CTGCAAGCATCGCCCAGA 60.437 61.111 0.00 0.00 0.00 3.86
106 107 1.822613 CTGCAAGCATCGCCCAGAT 60.823 57.895 0.00 0.00 41.01 2.90
113 114 2.827423 ATCGCCCAGATGCAGAGG 59.173 61.111 0.00 0.00 38.36 3.69
114 115 3.472943 ATCGCCCAGATGCAGAGGC 62.473 63.158 8.59 8.59 42.18 4.70
117 118 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
118 119 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
119 120 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
125 126 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
136 137 2.899303 GGGGTCATCCTCCTTTTCAA 57.101 50.000 0.00 0.00 35.33 2.69
137 138 3.169512 GGGGTCATCCTCCTTTTCAAA 57.830 47.619 0.00 0.00 35.33 2.69
138 139 3.506398 GGGGTCATCCTCCTTTTCAAAA 58.494 45.455 0.00 0.00 35.33 2.44
139 140 3.511540 GGGGTCATCCTCCTTTTCAAAAG 59.488 47.826 2.55 2.55 35.33 2.27
140 141 4.407365 GGGTCATCCTCCTTTTCAAAAGA 58.593 43.478 11.73 0.00 0.00 2.52
141 142 4.832823 GGGTCATCCTCCTTTTCAAAAGAA 59.167 41.667 11.73 0.00 0.00 2.52
142 143 5.304357 GGGTCATCCTCCTTTTCAAAAGAAA 59.696 40.000 11.73 0.00 0.00 2.52
143 144 6.183360 GGGTCATCCTCCTTTTCAAAAGAAAA 60.183 38.462 11.73 3.79 33.58 2.29
144 145 7.272244 GGTCATCCTCCTTTTCAAAAGAAAAA 58.728 34.615 11.73 0.00 34.18 1.94
214 215 9.366216 ACTTGAAGTTTTAAAATTTCAGGACAC 57.634 29.630 34.45 14.51 42.79 3.67
215 216 8.710835 TTGAAGTTTTAAAATTTCAGGACACC 57.289 30.769 27.33 8.74 42.79 4.16
216 217 7.269316 TGAAGTTTTAAAATTTCAGGACACCC 58.731 34.615 26.08 6.73 38.96 4.61
217 218 6.169557 AGTTTTAAAATTTCAGGACACCCC 57.830 37.500 3.52 0.00 0.00 4.95
232 233 1.355718 ACCCCTGCCCATCATCGAAT 61.356 55.000 0.00 0.00 0.00 3.34
260 261 9.341078 ACACATGTATAATGTATTTCTGCATGA 57.659 29.630 16.81 0.00 36.19 3.07
374 556 9.206870 CAATGGAATGCAGTATACTTTGTTTTT 57.793 29.630 1.56 0.00 0.00 1.94
476 662 5.443185 ACCTGCATGATTAATGGAATTCG 57.557 39.130 0.00 0.00 36.01 3.34
478 664 4.321452 CCTGCATGATTAATGGAATTCGGG 60.321 45.833 0.00 0.00 36.01 5.14
549 735 8.532819 ACTCTCTACCTGGAAACTAGTTTAATG 58.467 37.037 20.58 12.52 32.11 1.90
606 792 7.496591 ACAAATTGAACTGAAATGCAACAATCT 59.503 29.630 0.00 0.00 30.37 2.40
644 830 4.532834 ACCATGTTGTTACAGTGGTCTTT 58.467 39.130 11.52 0.00 39.68 2.52
646 832 5.420739 ACCATGTTGTTACAGTGGTCTTTTT 59.579 36.000 11.52 0.00 39.68 1.94
655 841 5.505173 ACAGTGGTCTTTTTGAATGTCAG 57.495 39.130 0.00 0.00 0.00 3.51
663 849 6.295292 GGTCTTTTTGAATGTCAGGGCTTAAT 60.295 38.462 0.00 0.00 0.00 1.40
675 861 5.183904 GTCAGGGCTTAATTTGACTTGATGT 59.816 40.000 2.97 0.00 37.53 3.06
895 1085 4.574674 AAGTATCCCTCATCTTGTGCAA 57.425 40.909 0.00 0.00 0.00 4.08
904 1094 5.008331 CCTCATCTTGTGCAATATAGCCAT 58.992 41.667 0.00 0.00 0.00 4.40
916 1106 5.120830 GCAATATAGCCATACTTCGTCCTTG 59.879 44.000 0.00 0.00 0.00 3.61
971 1161 6.183360 TGTTTTGGGGAAGAAAAACTGGATAC 60.183 38.462 11.10 0.00 43.49 2.24
986 1176 5.628130 ACTGGATACTATTGTCGGCTACTA 58.372 41.667 0.00 0.00 37.61 1.82
991 1181 6.374894 GGATACTATTGTCGGCTACTATGAGT 59.625 42.308 0.00 0.74 0.00 3.41
1286 1541 6.821388 ACGATTTTCTGCTAGAAGGATATGT 58.179 36.000 0.00 0.00 35.37 2.29
1429 1696 4.251268 ACTTCAAGTATAACCAACGAGGC 58.749 43.478 0.00 0.00 43.14 4.70
1557 1827 7.467811 GCCTTGACTGATATTAATCACAACAGG 60.468 40.741 0.00 0.00 37.20 4.00
1692 1964 5.048782 GGCATTACAGTTGACAAATCAGTCA 60.049 40.000 0.00 0.00 46.12 3.41
1763 2035 4.220602 ACTCATAAAATTGGACAAGGTGGC 59.779 41.667 0.00 0.00 0.00 5.01
1775 2047 0.687427 AAGGTGGCTTTGGTGCTGTT 60.687 50.000 0.00 0.00 0.00 3.16
1813 2085 5.310451 TGTAGGCGAGGTTAGTTCAAAAAT 58.690 37.500 0.00 0.00 0.00 1.82
1814 2086 6.465948 TGTAGGCGAGGTTAGTTCAAAAATA 58.534 36.000 0.00 0.00 0.00 1.40
1818 2090 8.570068 AGGCGAGGTTAGTTCAAAAATAAATA 57.430 30.769 0.00 0.00 0.00 1.40
1849 2121 2.598589 CATTTCAGAAACCCACATGCG 58.401 47.619 0.00 0.00 0.00 4.73
1881 2234 5.072058 TGTGTACTTAACTAGGGGCTTGAAA 59.928 40.000 0.00 0.00 0.00 2.69
1887 2240 3.825908 ACTAGGGGCTTGAAAAATGGA 57.174 42.857 0.00 0.00 0.00 3.41
1982 2350 2.766263 TCTCTTGTGTTGTCCACTGTCT 59.234 45.455 0.00 0.00 44.81 3.41
1993 2361 0.247736 CCACTGTCTAGAAAGCCGCT 59.752 55.000 10.05 0.00 0.00 5.52
2065 2433 3.130340 AGGTTTTGACACATGTTCACCAC 59.870 43.478 0.00 3.51 0.00 4.16
2198 2589 5.694458 GGTTAATTTGCCGTTTCAATGTTCT 59.306 36.000 0.00 0.00 0.00 3.01
2201 2592 9.562583 GTTAATTTGCCGTTTCAATGTTCTATA 57.437 29.630 0.00 0.00 0.00 1.31
2312 2703 3.404224 TGCGTGGAACTGGTAATGTTA 57.596 42.857 0.00 0.00 31.75 2.41
2320 2711 5.193679 GGAACTGGTAATGTTATGCCTCTT 58.806 41.667 0.00 0.00 0.00 2.85
2345 2740 6.431543 TGAAATACCGAATGTGCCTTTTTCTA 59.568 34.615 0.00 0.00 0.00 2.10
2347 2742 2.482721 ACCGAATGTGCCTTTTTCTACG 59.517 45.455 0.00 0.00 0.00 3.51
2558 2954 5.415701 GTGCAAAGGTAGGAATGATTCAAGA 59.584 40.000 7.56 0.00 0.00 3.02
2650 3053 9.485206 AAGTAATGTTGTTTACGTGTATCTTCT 57.515 29.630 0.00 0.00 37.20 2.85
2673 3076 2.029918 GGTTGCAGATTTTGGTCTGACC 60.030 50.000 19.96 19.96 46.77 4.02
2766 3172 5.481122 AGAGTAGGTTTCCTGAACTTCTACC 59.519 44.000 0.00 0.00 35.40 3.18
2801 3219 9.739276 AGGAATGAACATCTACTTTTGTCATTA 57.261 29.630 0.00 0.00 30.72 1.90
2875 3297 2.264005 TGGTGTTGGCAGATACGTTT 57.736 45.000 0.00 0.00 0.00 3.60
2931 3353 1.539827 GCCTTTGGCGTTGTCTTGTAT 59.460 47.619 0.00 0.00 39.62 2.29
2968 3390 0.107508 AGATGCCATTGTCCGACCAG 60.108 55.000 0.00 0.00 0.00 4.00
2991 3413 2.748605 GATGGATCTGCTAGTGGTTCG 58.251 52.381 0.00 0.00 0.00 3.95
3028 3450 3.011818 CTGGTAATTGTGCATCTGAGCA 58.988 45.455 0.00 0.00 43.35 4.26
3061 3534 4.615588 ACTTTCTGCTCTAAGTGCTTCT 57.384 40.909 0.00 0.00 33.55 2.85
3062 3535 5.730296 ACTTTCTGCTCTAAGTGCTTCTA 57.270 39.130 0.00 0.00 33.55 2.10
3065 3538 6.648725 ACTTTCTGCTCTAAGTGCTTCTAAAG 59.351 38.462 0.00 0.00 33.55 1.85
3072 3558 6.263516 TCTAAGTGCTTCTAAAGACGCTAA 57.736 37.500 9.51 0.00 39.68 3.09
3081 4686 3.839432 AGACGCTAAGCCGGCTCC 61.839 66.667 32.93 19.85 44.84 4.70
3085 4690 2.203084 GCTAAGCCGGCTCCCTTC 60.203 66.667 32.93 13.69 0.00 3.46
3086 4691 3.031417 GCTAAGCCGGCTCCCTTCA 62.031 63.158 32.93 9.92 0.00 3.02
3091 4696 2.685380 CCGGCTCCCTTCAGGTCT 60.685 66.667 0.00 0.00 36.75 3.85
3117 4723 4.791088 GCTGAAGTTCTTTCTTTGGCTGTC 60.791 45.833 4.17 0.00 36.71 3.51
3119 4725 5.680619 TGAAGTTCTTTCTTTGGCTGTCTA 58.319 37.500 4.17 0.00 36.71 2.59
3176 4785 0.459237 GACTCTCACTGCACCGGATG 60.459 60.000 9.46 3.68 0.00 3.51
3470 5291 2.770802 CTCATGTCTGGGAGATGACCTT 59.229 50.000 3.73 0.00 37.41 3.50
3471 5292 2.502947 TCATGTCTGGGAGATGACCTTG 59.497 50.000 3.73 0.00 37.41 3.61
3687 5514 4.927782 TGTCACGCACACCAGGGC 62.928 66.667 0.00 0.00 0.00 5.19
3688 5515 4.927782 GTCACGCACACCAGGGCA 62.928 66.667 0.00 0.00 0.00 5.36
3689 5516 4.182433 TCACGCACACCAGGGCAA 62.182 61.111 0.00 0.00 0.00 4.52
3690 5517 3.964875 CACGCACACCAGGGCAAC 61.965 66.667 0.00 0.00 0.00 4.17
3715 5542 2.436646 GCACCGACCAGTGGGATG 60.437 66.667 15.21 6.97 38.24 3.51
3727 5558 1.690985 TGGGATGGTGCGATGGGTA 60.691 57.895 0.00 0.00 0.00 3.69
3759 5590 2.874086 CACATGACTGAAGTGAACAGCA 59.126 45.455 0.00 0.00 38.74 4.41
3802 5637 2.122056 AGAGGGGTTGGTAGCGGT 59.878 61.111 0.00 0.00 0.00 5.68
3913 5754 3.435275 TGCTCTTCCTCGCATATCCTAT 58.565 45.455 0.00 0.00 0.00 2.57
3917 5758 5.561919 GCTCTTCCTCGCATATCCTATATCG 60.562 48.000 0.00 0.00 0.00 2.92
3940 5783 2.169832 TTCTCCTTGTTCTTCCTGCG 57.830 50.000 0.00 0.00 0.00 5.18
4016 5880 3.454082 AGGTCAGAGATCCTGGATTCAAC 59.546 47.826 11.17 11.39 43.12 3.18
4040 5904 2.260434 GCGACCGTGCTACCAGAA 59.740 61.111 0.00 0.00 0.00 3.02
4088 5952 4.593864 GGACCAGATCGCCGCTCC 62.594 72.222 0.00 0.00 0.00 4.70
4089 5953 3.838271 GACCAGATCGCCGCTCCA 61.838 66.667 0.00 0.00 0.00 3.86
4091 5955 3.842923 CCAGATCGCCGCTCCAGT 61.843 66.667 0.00 0.00 0.00 4.00
4099 5963 2.962569 CCGCTCCAGTGAAGACGA 59.037 61.111 0.00 0.00 0.00 4.20
4104 5968 2.736719 CGCTCCAGTGAAGACGATCAAT 60.737 50.000 0.00 0.00 0.00 2.57
4117 5981 3.371097 ATCAATGACGGGCGCGTCT 62.371 57.895 42.65 30.28 39.41 4.18
4122 5986 4.814294 GACGGGCGCGTCTCCAAT 62.814 66.667 39.13 14.11 36.12 3.16
4147 6011 4.445699 GCCTCGAAGCGATCCAAT 57.554 55.556 0.00 0.00 34.61 3.16
4148 6012 2.695314 GCCTCGAAGCGATCCAATT 58.305 52.632 0.00 0.00 34.61 2.32
4203 6071 0.808755 TACATCAGCAGCTCGACGAA 59.191 50.000 0.00 0.00 0.00 3.85
4207 6075 1.372251 CAGCAGCTCGACGAACTGT 60.372 57.895 24.65 12.11 33.87 3.55
4229 6103 3.492353 CCAGGTGGGCCGGATCAT 61.492 66.667 5.05 0.00 40.50 2.45
4266 6140 2.894257 ATCGGCTCCAGCAACACCA 61.894 57.895 0.03 0.00 44.36 4.17
4274 6148 0.037303 CCAGCAACACCAGAGGATGT 59.963 55.000 0.00 0.00 0.00 3.06
4360 6234 0.460109 CGCAATCATCGACACTGGGA 60.460 55.000 0.00 0.00 0.00 4.37
4439 6314 4.768968 ACCAATCTCAATCCCACTTTTCTG 59.231 41.667 0.00 0.00 0.00 3.02
4440 6315 4.381292 CCAATCTCAATCCCACTTTTCTGC 60.381 45.833 0.00 0.00 0.00 4.26
4441 6316 3.795688 TCTCAATCCCACTTTTCTGCT 57.204 42.857 0.00 0.00 0.00 4.24
4442 6317 3.679389 TCTCAATCCCACTTTTCTGCTC 58.321 45.455 0.00 0.00 0.00 4.26
4444 6319 2.376518 TCAATCCCACTTTTCTGCTCCT 59.623 45.455 0.00 0.00 0.00 3.69
4445 6320 2.751806 CAATCCCACTTTTCTGCTCCTC 59.248 50.000 0.00 0.00 0.00 3.71
4447 6322 0.695347 CCCACTTTTCTGCTCCTCCT 59.305 55.000 0.00 0.00 0.00 3.69
4448 6323 1.612726 CCCACTTTTCTGCTCCTCCTG 60.613 57.143 0.00 0.00 0.00 3.86
4449 6324 1.349026 CCACTTTTCTGCTCCTCCTGA 59.651 52.381 0.00 0.00 0.00 3.86
4450 6325 2.026449 CCACTTTTCTGCTCCTCCTGAT 60.026 50.000 0.00 0.00 0.00 2.90
4451 6326 3.008330 CACTTTTCTGCTCCTCCTGATG 58.992 50.000 0.00 0.00 0.00 3.07
4452 6327 2.641815 ACTTTTCTGCTCCTCCTGATGT 59.358 45.455 0.00 0.00 0.00 3.06
4453 6328 3.840666 ACTTTTCTGCTCCTCCTGATGTA 59.159 43.478 0.00 0.00 0.00 2.29
4454 6329 4.081198 ACTTTTCTGCTCCTCCTGATGTAG 60.081 45.833 0.00 0.00 0.00 2.74
4455 6330 3.388552 TTCTGCTCCTCCTGATGTAGA 57.611 47.619 0.00 0.00 0.00 2.59
4456 6331 3.609256 TCTGCTCCTCCTGATGTAGAT 57.391 47.619 0.00 0.00 0.00 1.98
4457 6332 3.921104 TCTGCTCCTCCTGATGTAGATT 58.079 45.455 0.00 0.00 0.00 2.40
4458 6333 3.894427 TCTGCTCCTCCTGATGTAGATTC 59.106 47.826 0.00 0.00 0.00 2.52
4459 6334 2.625314 TGCTCCTCCTGATGTAGATTCG 59.375 50.000 0.00 0.00 0.00 3.34
4460 6335 2.887783 GCTCCTCCTGATGTAGATTCGA 59.112 50.000 0.00 0.00 0.00 3.71
4461 6336 3.057596 GCTCCTCCTGATGTAGATTCGAG 60.058 52.174 0.00 0.00 0.00 4.04
4462 6337 4.141287 CTCCTCCTGATGTAGATTCGAGT 58.859 47.826 0.00 0.00 0.00 4.18
4463 6338 5.306114 TCCTCCTGATGTAGATTCGAGTA 57.694 43.478 0.00 0.00 0.00 2.59
4464 6339 5.309638 TCCTCCTGATGTAGATTCGAGTAG 58.690 45.833 0.00 0.00 0.00 2.57
4465 6340 4.457603 CCTCCTGATGTAGATTCGAGTAGG 59.542 50.000 0.00 0.00 0.00 3.18
4466 6341 4.399219 TCCTGATGTAGATTCGAGTAGGG 58.601 47.826 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.154225 CAACATTTGTCGCCGGAGC 60.154 57.895 5.05 0.00 0.00 4.70
1 2 2.244000 ACAACATTTGTCGCCGGAG 58.756 52.632 5.05 0.00 40.56 4.63
2 3 4.466133 ACAACATTTGTCGCCGGA 57.534 50.000 5.05 0.00 40.56 5.14
10 11 3.056393 AGCCACCATCATGACAACATTTG 60.056 43.478 0.00 0.00 34.15 2.32
11 12 3.167485 AGCCACCATCATGACAACATTT 58.833 40.909 0.00 0.00 34.15 2.32
12 13 2.756760 GAGCCACCATCATGACAACATT 59.243 45.455 0.00 0.00 34.15 2.71
13 14 2.372264 GAGCCACCATCATGACAACAT 58.628 47.619 0.00 0.00 37.19 2.71
14 15 1.614051 GGAGCCACCATCATGACAACA 60.614 52.381 0.00 0.00 38.79 3.33
15 16 1.098050 GGAGCCACCATCATGACAAC 58.902 55.000 0.00 0.00 38.79 3.32
16 17 0.697658 TGGAGCCACCATCATGACAA 59.302 50.000 0.00 0.00 44.64 3.18
17 18 2.385777 TGGAGCCACCATCATGACA 58.614 52.632 0.00 0.00 44.64 3.58
26 27 3.118261 TCATCATTAAGTCTGGAGCCACC 60.118 47.826 0.00 0.00 39.54 4.61
27 28 4.142609 TCATCATTAAGTCTGGAGCCAC 57.857 45.455 0.00 0.00 0.00 5.01
28 29 4.842531 TTCATCATTAAGTCTGGAGCCA 57.157 40.909 0.00 0.00 0.00 4.75
29 30 7.992754 ATAATTCATCATTAAGTCTGGAGCC 57.007 36.000 0.00 0.00 30.78 4.70
69 70 9.264719 GCTTGCAGCCATTTTATTAATTATTCT 57.735 29.630 0.00 0.00 34.48 2.40
70 71 9.044150 TGCTTGCAGCCATTTTATTAATTATTC 57.956 29.630 0.00 0.00 41.51 1.75
71 72 8.961294 TGCTTGCAGCCATTTTATTAATTATT 57.039 26.923 0.00 0.00 41.51 1.40
72 73 9.211485 GATGCTTGCAGCCATTTTATTAATTAT 57.789 29.630 0.00 0.00 41.51 1.28
73 74 7.381948 CGATGCTTGCAGCCATTTTATTAATTA 59.618 33.333 5.25 0.00 41.51 1.40
74 75 6.201425 CGATGCTTGCAGCCATTTTATTAATT 59.799 34.615 5.25 0.00 41.51 1.40
75 76 5.693104 CGATGCTTGCAGCCATTTTATTAAT 59.307 36.000 5.25 0.00 41.51 1.40
76 77 5.042593 CGATGCTTGCAGCCATTTTATTAA 58.957 37.500 5.25 0.00 41.51 1.40
77 78 4.609947 CGATGCTTGCAGCCATTTTATTA 58.390 39.130 5.25 0.00 41.51 0.98
78 79 3.450578 CGATGCTTGCAGCCATTTTATT 58.549 40.909 5.25 0.00 41.51 1.40
79 80 2.800629 GCGATGCTTGCAGCCATTTTAT 60.801 45.455 5.25 0.00 41.51 1.40
80 81 1.469595 GCGATGCTTGCAGCCATTTTA 60.470 47.619 5.25 0.00 41.51 1.52
81 82 0.738412 GCGATGCTTGCAGCCATTTT 60.738 50.000 5.25 0.00 41.51 1.82
82 83 1.153706 GCGATGCTTGCAGCCATTT 60.154 52.632 5.25 0.00 41.51 2.32
83 84 2.493030 GCGATGCTTGCAGCCATT 59.507 55.556 5.25 0.00 41.51 3.16
87 88 4.189188 CTGGGCGATGCTTGCAGC 62.189 66.667 0.26 0.26 42.82 5.25
88 89 1.822613 ATCTGGGCGATGCTTGCAG 60.823 57.895 0.87 0.00 0.00 4.41
89 90 2.116533 CATCTGGGCGATGCTTGCA 61.117 57.895 0.00 0.00 42.75 4.08
90 91 2.719979 CATCTGGGCGATGCTTGC 59.280 61.111 0.00 0.00 42.75 4.01
96 97 2.827423 CCTCTGCATCTGGGCGAT 59.173 61.111 0.00 0.00 36.28 4.58
97 98 4.166888 GCCTCTGCATCTGGGCGA 62.167 66.667 0.00 0.00 37.47 5.54
100 101 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
101 102 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
102 103 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
108 109 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
114 115 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
115 116 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
116 117 0.999712 TGAAAAGGAGGATGACCCCC 59.000 55.000 0.00 0.00 36.73 5.40
117 118 2.899303 TTGAAAAGGAGGATGACCCC 57.101 50.000 0.00 0.00 36.73 4.95
118 119 4.407365 TCTTTTGAAAAGGAGGATGACCC 58.593 43.478 16.79 0.00 36.73 4.46
119 120 6.405278 TTTCTTTTGAAAAGGAGGATGACC 57.595 37.500 16.79 0.00 44.51 4.02
193 194 6.385759 AGGGGTGTCCTGAAATTTTAAAACTT 59.614 34.615 1.97 0.00 46.07 2.66
195 196 6.169557 AGGGGTGTCCTGAAATTTTAAAAC 57.830 37.500 1.97 0.00 46.07 2.43
210 211 1.152881 GATGATGGGCAGGGGTGTC 60.153 63.158 0.00 0.00 0.00 3.67
214 215 0.178981 AATTCGATGATGGGCAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
215 216 2.154462 GTAATTCGATGATGGGCAGGG 58.846 52.381 0.00 0.00 0.00 4.45
216 217 2.549754 GTGTAATTCGATGATGGGCAGG 59.450 50.000 0.00 0.00 0.00 4.85
217 218 3.205338 TGTGTAATTCGATGATGGGCAG 58.795 45.455 0.00 0.00 0.00 4.85
218 219 3.274095 TGTGTAATTCGATGATGGGCA 57.726 42.857 0.00 0.00 0.00 5.36
219 220 3.565482 ACATGTGTAATTCGATGATGGGC 59.435 43.478 0.00 0.00 0.00 5.36
374 556 7.186972 ACATATCGGGTAGTCCTTCCAATATA 58.813 38.462 0.00 0.00 0.00 0.86
378 560 3.649843 ACATATCGGGTAGTCCTTCCAA 58.350 45.455 0.00 0.00 0.00 3.53
384 566 5.717078 TCAATGTACATATCGGGTAGTCC 57.283 43.478 9.21 0.00 0.00 3.85
590 776 8.600625 CAAATGGATTAGATTGTTGCATTTCAG 58.399 33.333 0.00 0.00 38.72 3.02
596 782 7.407393 TCATCAAATGGATTAGATTGTTGCA 57.593 32.000 0.00 0.00 32.57 4.08
606 792 8.765488 ACAACATGGTATCATCAAATGGATTA 57.235 30.769 0.00 0.00 32.57 1.75
644 830 6.267471 AGTCAAATTAAGCCCTGACATTCAAA 59.733 34.615 8.09 0.00 40.53 2.69
646 832 5.324409 AGTCAAATTAAGCCCTGACATTCA 58.676 37.500 8.09 0.00 40.53 2.57
655 841 7.333528 TGATACATCAAGTCAAATTAAGCCC 57.666 36.000 0.00 0.00 33.08 5.19
675 861 8.147704 TCAACTCTCCGCAACATATAAATGATA 58.852 33.333 0.00 0.00 36.54 2.15
833 1023 8.510243 TGAGAATAAATGTAACATGCATGACT 57.490 30.769 32.75 20.24 0.00 3.41
848 1038 5.416639 TCAGCACAACTGCATGAGAATAAAT 59.583 36.000 0.00 0.00 46.97 1.40
947 1137 4.746535 TCCAGTTTTTCTTCCCCAAAAC 57.253 40.909 0.00 0.00 41.35 2.43
971 1161 5.690997 TCACTCATAGTAGCCGACAATAG 57.309 43.478 0.00 0.00 0.00 1.73
1286 1541 3.761897 CTTCAAACCACCCTAATCCACA 58.238 45.455 0.00 0.00 0.00 4.17
1406 1673 4.694037 GCCTCGTTGGTTATACTTGAAGTT 59.306 41.667 1.97 0.00 38.35 2.66
1416 1683 2.632377 CTGACATGCCTCGTTGGTTAT 58.368 47.619 0.00 0.00 38.35 1.89
1429 1696 8.415950 AAGTAGACTTATAGATCCCTGACATG 57.584 38.462 0.00 0.00 33.79 3.21
1557 1827 6.749923 AGTTCAGAAATAAGAAGGCACATC 57.250 37.500 0.00 0.00 0.00 3.06
1763 2035 5.953183 TCAGCATAATAAACAGCACCAAAG 58.047 37.500 0.00 0.00 0.00 2.77
1775 2047 4.058124 CGCCTACAAGCTCAGCATAATAA 58.942 43.478 0.00 0.00 0.00 1.40
1824 2096 2.762887 TGTGGGTTTCTGAAATGCAACA 59.237 40.909 6.06 6.48 0.00 3.33
1849 2121 7.574404 GCCCCTAGTTAAGTACACATGTTTTTC 60.574 40.741 0.00 0.00 0.00 2.29
1881 2234 9.739276 TCACAGAGTTATGTTATTCTTCCATTT 57.261 29.630 0.00 0.00 0.00 2.32
1887 2240 8.565896 TGCAATCACAGAGTTATGTTATTCTT 57.434 30.769 0.00 0.00 27.20 2.52
1982 2350 7.012044 GTCCATTTTCTTTATAGCGGCTTTCTA 59.988 37.037 8.26 0.00 0.00 2.10
1993 2361 5.893255 AGCCTGCATGTCCATTTTCTTTATA 59.107 36.000 0.00 0.00 0.00 0.98
2038 2406 6.983890 GGTGAACATGTGTCAAAACCTTTAAT 59.016 34.615 0.00 0.00 0.00 1.40
2065 2433 9.765795 ATAGAAGATTTACGAACCAGATTTAGG 57.234 33.333 0.00 0.00 0.00 2.69
2312 2703 4.336433 CACATTCGGTATTTCAAGAGGCAT 59.664 41.667 0.00 0.00 0.00 4.40
2320 2711 5.242838 AGAAAAAGGCACATTCGGTATTTCA 59.757 36.000 0.00 0.00 0.00 2.69
2589 2992 7.093354 ACATATAGAACACATGGATCGATGAC 58.907 38.462 22.78 11.24 0.00 3.06
2590 2993 7.232118 ACATATAGAACACATGGATCGATGA 57.768 36.000 22.78 1.15 0.00 2.92
2639 3042 4.371855 TCTGCAACCTAGAAGATACACG 57.628 45.455 0.00 0.00 0.00 4.49
2650 3053 4.072131 GTCAGACCAAAATCTGCAACCTA 58.928 43.478 0.00 0.00 44.94 3.08
2673 3076 3.003689 CACCACCAACTTCTGTAAGCTTG 59.996 47.826 9.86 0.00 36.05 4.01
2875 3297 6.263842 ACCTTACGAGAAATATCACCGTATCA 59.736 38.462 0.00 0.00 38.34 2.15
2931 3353 4.637534 GCATCTTTGGCTGAGATAAGTTCA 59.362 41.667 3.47 0.00 32.75 3.18
2968 3390 0.320247 CCACTAGCAGATCCATCGGC 60.320 60.000 3.71 3.71 46.24 5.54
2991 3413 2.197465 ACCAGATAAACCAGTCCCCTC 58.803 52.381 0.00 0.00 0.00 4.30
3061 3534 0.179119 GAGCCGGCTTAGCGTCTTTA 60.179 55.000 33.34 0.00 34.64 1.85
3062 3535 1.448013 GAGCCGGCTTAGCGTCTTT 60.448 57.895 33.34 3.09 34.64 2.52
3065 3538 4.893601 GGGAGCCGGCTTAGCGTC 62.894 72.222 33.34 17.00 34.64 5.19
3080 4685 2.276732 TTCAGCAAAGACCTGAAGGG 57.723 50.000 0.56 0.00 42.58 3.95
3085 4690 4.578105 AGAAAGAACTTCAGCAAAGACCTG 59.422 41.667 5.93 0.00 38.44 4.00
3086 4691 4.786425 AGAAAGAACTTCAGCAAAGACCT 58.214 39.130 5.93 0.54 38.44 3.85
3091 4696 4.160252 AGCCAAAGAAAGAACTTCAGCAAA 59.840 37.500 0.00 0.00 36.40 3.68
3176 4785 0.321653 TTCTGGAGGCCTTCTTTCGC 60.322 55.000 13.68 0.00 0.00 4.70
3470 5291 0.988832 GGGGAGACATGTGGGTAACA 59.011 55.000 1.15 0.00 44.79 2.41
3471 5292 1.065418 CAGGGGAGACATGTGGGTAAC 60.065 57.143 1.15 0.00 0.00 2.50
3727 5558 2.049526 TCATGTGCTCGTCGCGTT 60.050 55.556 5.77 0.00 43.27 4.84
3739 5570 3.198409 TGCTGTTCACTTCAGTCATGT 57.802 42.857 0.00 0.00 35.60 3.21
3759 5590 0.462581 CTGGGCAGCGATACACACAT 60.463 55.000 0.00 0.00 0.00 3.21
3802 5637 3.952508 ACCACCATGGCACGCAGA 61.953 61.111 13.04 0.00 42.67 4.26
3913 5754 4.504858 GAAGAACAAGGAGAAAGGCGATA 58.495 43.478 0.00 0.00 0.00 2.92
3917 5758 2.816672 CAGGAAGAACAAGGAGAAAGGC 59.183 50.000 0.00 0.00 0.00 4.35
3940 5783 0.978667 GGGAAGGAGGAGGAGTGGAC 60.979 65.000 0.00 0.00 0.00 4.02
4016 5880 2.412323 TAGCACGGTCGCTGGTAGG 61.412 63.158 13.07 0.00 43.68 3.18
4074 5938 3.842923 ACTGGAGCGGCGATCTGG 61.843 66.667 25.16 18.68 0.00 3.86
4088 5952 2.600420 CCGTCATTGATCGTCTTCACTG 59.400 50.000 0.00 0.00 0.00 3.66
4089 5953 2.417379 CCCGTCATTGATCGTCTTCACT 60.417 50.000 0.00 0.00 0.00 3.41
4091 5955 1.739035 GCCCGTCATTGATCGTCTTCA 60.739 52.381 0.00 0.00 0.00 3.02
4117 5981 4.467084 GAGGCGGGCGTCATTGGA 62.467 66.667 8.36 0.00 0.00 3.53
4242 6116 2.124983 GCTGGAGCCGATGCAAGA 60.125 61.111 0.00 0.00 41.13 3.02
4266 6140 2.665000 CGCACCACCACATCCTCT 59.335 61.111 0.00 0.00 0.00 3.69
4309 6183 4.814294 CCCGTGGTGCCTAGCGTC 62.814 72.222 0.00 0.00 0.00 5.19
4343 6217 3.065786 CCAAATCCCAGTGTCGATGATTG 59.934 47.826 0.00 0.00 0.00 2.67
4344 6218 3.282021 CCAAATCCCAGTGTCGATGATT 58.718 45.455 0.00 0.00 0.00 2.57
4360 6234 2.035626 CCACCCCGTGAGCCAAAT 59.964 61.111 0.00 0.00 35.23 2.32
4405 6280 1.202879 TGAGATTGGTTGACACACCCC 60.203 52.381 4.88 0.00 35.73 4.95
4411 6286 3.074390 AGTGGGATTGAGATTGGTTGACA 59.926 43.478 0.00 0.00 0.00 3.58
4439 6314 2.887783 TCGAATCTACATCAGGAGGAGC 59.112 50.000 0.00 0.00 0.00 4.70
4440 6315 4.141287 ACTCGAATCTACATCAGGAGGAG 58.859 47.826 0.00 0.00 0.00 3.69
4441 6316 4.171878 ACTCGAATCTACATCAGGAGGA 57.828 45.455 0.00 0.00 0.00 3.71
4442 6317 4.457603 CCTACTCGAATCTACATCAGGAGG 59.542 50.000 0.00 0.00 0.00 4.30
4444 6319 4.399219 CCCTACTCGAATCTACATCAGGA 58.601 47.826 0.00 0.00 0.00 3.86
4445 6320 4.775058 CCCTACTCGAATCTACATCAGG 57.225 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.