Multiple sequence alignment - TraesCS6D01G303000

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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 TraesCS6D01G303000 chr6D 100.000 4909 0 0 984 5892 411800896 411805804 0.000000e+00 9066.0
1 TraesCS6D01G303000 chr6D 100.000 587 0 0 1 587 411799913 411800499 0.000000e+00 1085.0
2 TraesCS6D01G303000 chr6D 95.652 92 4 0 5633 5724 132304798 132304707 1.320000e-31 148.0
3 TraesCS6D01G303000 chr6D 83.750 80 6 4 3779 3855 411803661 411803736 1.060000e-07 69.4
4 TraesCS6D01G303000 chr6D 83.750 80 6 4 3749 3824 411803691 411803767 1.060000e-07 69.4
5 TraesCS6D01G303000 chr6B 94.315 4714 180 35 987 5646 619525784 619530463 0.000000e+00 7140.0
6 TraesCS6D01G303000 chr6B 85.644 613 44 25 2 587 619525195 619525790 6.530000e-169 604.0
7 TraesCS6D01G303000 chr6B 85.833 120 4 3 5715 5834 619530393 619530499 1.340000e-21 115.0
8 TraesCS6D01G303000 chr6B 83.750 80 6 6 3779 3855 619528556 619528631 1.060000e-07 69.4
9 TraesCS6D01G303000 chr6B 83.750 80 6 4 3749 3824 619528586 619528662 1.060000e-07 69.4
10 TraesCS6D01G303000 chr6A 94.163 2193 96 10 3478 5646 556742255 556744439 0.000000e+00 3312.0
11 TraesCS6D01G303000 chr6A 91.558 1149 45 21 984 2101 556740199 556741326 0.000000e+00 1537.0
12 TraesCS6D01G303000 chr6A 95.376 930 36 3 2144 3071 556741320 556742244 0.000000e+00 1472.0
13 TraesCS6D01G303000 chr6A 83.422 561 39 24 42 583 556739683 556740208 6.910000e-129 472.0
14 TraesCS6D01G303000 chr6A 81.065 169 6 5 5718 5886 556744375 556744517 1.740000e-20 111.0
15 TraesCS6D01G303000 chr6A 90.411 73 7 0 2668 2740 556742663 556742735 4.860000e-16 97.1
16 TraesCS6D01G303000 chr6A 84.337 83 6 5 3780 3859 556742527 556742605 2.280000e-09 75.0
17 TraesCS6D01G303000 chr7B 85.806 310 38 4 4632 4940 52981314 52981618 2.050000e-84 324.0
18 TraesCS6D01G303000 chr7B 85.197 304 39 5 4638 4940 52948379 52948081 2.060000e-79 307.0
19 TraesCS6D01G303000 chr5A 90.517 116 4 4 5777 5892 153180838 153180730 4.760000e-31 147.0
20 TraesCS6D01G303000 chr2D 96.552 87 3 0 5633 5719 97402376 97402462 1.710000e-30 145.0
21 TraesCS6D01G303000 chr2D 98.750 80 1 0 5633 5712 35309485 35309406 6.150000e-30 143.0
22 TraesCS6D01G303000 chr2D 97.500 80 2 0 5633 5712 569807385 569807464 2.860000e-28 137.0
23 TraesCS6D01G303000 chr5D 98.750 80 1 0 5633 5712 10032404 10032325 6.150000e-30 143.0
24 TraesCS6D01G303000 chr5D 98.750 80 1 0 5633 5712 10034043 10033964 6.150000e-30 143.0
25 TraesCS6D01G303000 chr5D 95.402 87 4 0 5633 5719 551407285 551407199 7.960000e-29 139.0
26 TraesCS6D01G303000 chr4D 97.500 80 2 0 5633 5712 83289712 83289791 2.860000e-28 137.0
27 TraesCS6D01G303000 chr4D 90.741 54 5 0 4790 4843 322857925 322857872 8.190000e-09 73.1
28 TraesCS6D01G303000 chr1D 91.753 97 6 2 5633 5728 362782310 362782215 3.700000e-27 134.0
29 TraesCS6D01G303000 chr4A 87.097 62 6 2 4782 4843 29086963 29086904 1.060000e-07 69.4
30 TraesCS6D01G303000 chr4A 88.889 54 6 0 4790 4843 149649026 149649079 3.810000e-07 67.6
31 TraesCS6D01G303000 chr4B 88.889 54 6 0 4790 4843 398233398 398233451 3.810000e-07 67.6


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 TraesCS6D01G303000 chr6D 411799913 411805804 5891 False 2572.450000 9066 91.875000 1 5892 4 chr6D.!!$F1 5891
1 TraesCS6D01G303000 chr6B 619525195 619530499 5304 False 1599.560000 7140 86.658400 2 5834 5 chr6B.!!$F1 5832
2 TraesCS6D01G303000 chr6A 556739683 556744517 4834 False 1010.871429 3312 88.618857 42 5886 7 chr6A.!!$F1 5844

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
390 418 0.250295 TCAGTTGGTTTCGCTCCCAG 60.250 55.0 0.0 0.0 31.04 4.45 F
1449 1517 0.100146 CCGAGTCCAGTAACGCTACC 59.900 60.0 0.0 0.0 0.00 3.18 F
3154 3237 0.039527 GCGACACAATCCCCACAAAC 60.040 55.0 0.0 0.0 0.00 2.93 F
3202 3285 0.179056 ATTGCCCCGATACACCGAAG 60.179 55.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2222 0.033504 GCTTCTTCGTCTGACCACCA 59.966 55.0 1.55 0.0 0.00 4.17 R
3156 3239 1.217916 TGTGAAGGACAGGGGTTTGA 58.782 50.0 0.00 0.0 0.00 2.69 R
4825 4910 0.968393 GGAGCTCGTTCCAGGAGTCT 60.968 60.0 7.83 0.0 37.20 3.24 R
5047 5140 5.308237 AGAGTTCCTGTTGGTAATGAGAGTT 59.692 40.0 0.00 0.0 34.23 3.01 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
23 24 5.266242 CGAATATGCTCTTGTTTTAGCCAC 58.734 41.667 0.00 0.00 37.97 5.01
29 30 0.958822 CTTGTTTTAGCCACGGCCTT 59.041 50.000 3.95 0.00 43.17 4.35
39 40 1.656818 CCACGGCCTTGCATGGTAAG 61.657 60.000 19.05 12.86 33.45 2.34
40 41 0.960364 CACGGCCTTGCATGGTAAGT 60.960 55.000 19.05 13.42 0.00 2.24
44 45 1.256812 GCCTTGCATGGTAAGTTGGT 58.743 50.000 19.05 0.00 0.00 3.67
54 55 2.158928 TGGTAAGTTGGTAACGCAGTGT 60.159 45.455 0.00 0.00 45.00 3.55
56 57 4.057432 GGTAAGTTGGTAACGCAGTGTTA 58.943 43.478 2.21 2.21 45.00 2.41
65 68 4.634443 GGTAACGCAGTGTTATTTCCTCAT 59.366 41.667 9.78 0.00 45.00 2.90
103 106 4.968259 TGATCACCGGAGAAGAAGAAAAA 58.032 39.130 9.46 0.00 0.00 1.94
164 189 2.822561 TGCCAATCAAATTAACGCCAGA 59.177 40.909 0.00 0.00 0.00 3.86
224 249 2.250939 ACATCGCACCACACCAACG 61.251 57.895 0.00 0.00 0.00 4.10
225 250 1.958715 CATCGCACCACACCAACGA 60.959 57.895 0.00 0.00 37.15 3.85
226 251 1.667830 ATCGCACCACACCAACGAG 60.668 57.895 0.00 0.00 36.05 4.18
238 264 1.202770 ACCAACGAGGAAGAAACCCAG 60.203 52.381 5.70 0.00 41.22 4.45
239 265 1.071699 CCAACGAGGAAGAAACCCAGA 59.928 52.381 0.00 0.00 41.22 3.86
275 301 1.804151 GCGTTGACAGCCAATCAAGTA 59.196 47.619 0.00 0.00 36.76 2.24
306 332 2.279918 ATTATCGCGTCGTGGGGC 60.280 61.111 5.77 0.00 0.00 5.80
323 349 2.919494 GCCCACGCAAAACCCAGAG 61.919 63.158 0.00 0.00 34.03 3.35
390 418 0.250295 TCAGTTGGTTTCGCTCCCAG 60.250 55.000 0.00 0.00 31.04 4.45
488 522 2.347490 CACTAACCACCCGCAGCT 59.653 61.111 0.00 0.00 0.00 4.24
490 524 2.214216 ACTAACCACCCGCAGCTCA 61.214 57.895 0.00 0.00 0.00 4.26
492 526 3.248446 TAACCACCCGCAGCTCACC 62.248 63.158 0.00 0.00 0.00 4.02
1281 1322 4.410400 CCCGCCAACTCCTCCCAC 62.410 72.222 0.00 0.00 0.00 4.61
1286 1327 1.904990 GCCAACTCCTCCCACTCCTC 61.905 65.000 0.00 0.00 0.00 3.71
1289 1330 0.494095 AACTCCTCCCACTCCTCCTT 59.506 55.000 0.00 0.00 0.00 3.36
1293 1334 1.690985 CTCCCACTCCTCCTTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
1406 1447 1.300620 CAACTGCGGTTCGTCCTCA 60.301 57.895 8.28 0.00 32.73 3.86
1449 1517 0.100146 CCGAGTCCAGTAACGCTACC 59.900 60.000 0.00 0.00 0.00 3.18
1509 1583 3.154473 CAATCGGGAGGCGGAGGA 61.154 66.667 0.00 0.00 0.00 3.71
1926 2003 0.251341 ATCCAGGCAAGAACCACACC 60.251 55.000 0.00 0.00 0.00 4.16
2145 2222 1.255667 CCAAAGAGGCTGCCAATGCT 61.256 55.000 22.65 9.40 38.71 3.79
2155 2232 1.303561 GCCAATGCTGGTGGTCAGA 60.304 57.895 0.00 0.00 46.18 3.27
2244 2321 0.179936 ACTCGTACCCTCTCTACCCG 59.820 60.000 0.00 0.00 0.00 5.28
2443 2523 3.873361 ACAGATTCAGTTATGTGATGGCG 59.127 43.478 0.00 0.00 0.00 5.69
2459 2539 0.815213 GGCGTGATGCTGATGCCTTA 60.815 55.000 0.00 0.00 45.43 2.69
2553 2633 3.118075 TCAACAGAAACATGTGGGAGTCA 60.118 43.478 0.00 0.00 32.52 3.41
2556 2636 3.070018 CAGAAACATGTGGGAGTCACTC 58.930 50.000 0.00 0.00 46.20 3.51
2573 2653 2.414481 CACTCGTTTGCATCTTGAGGAG 59.586 50.000 9.61 6.68 0.00 3.69
2580 2660 4.890158 TTGCATCTTGAGGAGTTCTGTA 57.110 40.909 0.00 0.00 0.00 2.74
2705 2787 4.470334 TTTTGCTGCTTTCCTTCAAAGT 57.530 36.364 0.00 0.00 43.29 2.66
2713 2795 4.218417 TGCTTTCCTTCAAAGTTGCTATCC 59.782 41.667 0.00 0.00 43.29 2.59
2790 2872 9.184523 CCCAGATTTACAATAATAGAAACCACA 57.815 33.333 0.00 0.00 0.00 4.17
2836 2918 7.287696 ACCAAACAGGAAAGTAACTCATCATTT 59.712 33.333 0.00 0.00 41.22 2.32
2943 3025 3.193479 GGCCTCCATTCTTTCGAATTGTT 59.807 43.478 0.00 0.00 37.77 2.83
2948 3030 6.072508 CCTCCATTCTTTCGAATTGTTGAAGA 60.073 38.462 0.00 0.00 37.77 2.87
3090 3173 1.933853 GGGATACACTACTGCTTTGCG 59.066 52.381 0.00 0.00 39.74 4.85
3144 3227 1.229428 CACCAGAACAGCGACACAAT 58.771 50.000 0.00 0.00 0.00 2.71
3148 3231 0.321653 AGAACAGCGACACAATCCCC 60.322 55.000 0.00 0.00 0.00 4.81
3149 3232 0.605319 GAACAGCGACACAATCCCCA 60.605 55.000 0.00 0.00 0.00 4.96
3150 3233 0.889186 AACAGCGACACAATCCCCAC 60.889 55.000 0.00 0.00 0.00 4.61
3151 3234 1.302431 CAGCGACACAATCCCCACA 60.302 57.895 0.00 0.00 0.00 4.17
3152 3235 0.888736 CAGCGACACAATCCCCACAA 60.889 55.000 0.00 0.00 0.00 3.33
3153 3236 0.179004 AGCGACACAATCCCCACAAA 60.179 50.000 0.00 0.00 0.00 2.83
3154 3237 0.039527 GCGACACAATCCCCACAAAC 60.040 55.000 0.00 0.00 0.00 2.93
3155 3238 1.313772 CGACACAATCCCCACAAACA 58.686 50.000 0.00 0.00 0.00 2.83
3156 3239 1.885887 CGACACAATCCCCACAAACAT 59.114 47.619 0.00 0.00 0.00 2.71
3157 3240 2.095263 CGACACAATCCCCACAAACATC 60.095 50.000 0.00 0.00 0.00 3.06
3158 3241 2.890311 GACACAATCCCCACAAACATCA 59.110 45.455 0.00 0.00 0.00 3.07
3159 3242 3.303938 ACACAATCCCCACAAACATCAA 58.696 40.909 0.00 0.00 0.00 2.57
3160 3243 3.708631 ACACAATCCCCACAAACATCAAA 59.291 39.130 0.00 0.00 0.00 2.69
3161 3244 4.057432 CACAATCCCCACAAACATCAAAC 58.943 43.478 0.00 0.00 0.00 2.93
3162 3245 3.070878 ACAATCCCCACAAACATCAAACC 59.929 43.478 0.00 0.00 0.00 3.27
3163 3246 1.710816 TCCCCACAAACATCAAACCC 58.289 50.000 0.00 0.00 0.00 4.11
3164 3247 0.684535 CCCCACAAACATCAAACCCC 59.315 55.000 0.00 0.00 0.00 4.95
3165 3248 1.715785 CCCACAAACATCAAACCCCT 58.284 50.000 0.00 0.00 0.00 4.79
3198 3281 1.470051 AAACATTGCCCCGATACACC 58.530 50.000 0.00 0.00 0.00 4.16
3202 3285 0.179056 ATTGCCCCGATACACCGAAG 60.179 55.000 0.00 0.00 0.00 3.79
3236 3320 5.241506 CCAATTCTAGGCAAAGTCTGAACAA 59.758 40.000 0.00 0.00 0.00 2.83
3252 3336 5.184864 TCTGAACAAAAACACACAGTTGGAT 59.815 36.000 0.00 0.00 41.19 3.41
3262 3346 9.656040 AAAACACACAGTTGGATATAATACGTA 57.344 29.630 0.00 0.00 41.19 3.57
3280 3364 2.028404 CGTAAATCGTTTAGTCGTGGCC 59.972 50.000 0.00 0.00 34.52 5.36
3297 3381 2.290008 TGGCCACAGAAATGACACGTAT 60.290 45.455 0.00 0.00 0.00 3.06
3336 3420 4.267536 TCTCTGAATCAGATTGCCTTTGG 58.732 43.478 13.93 0.00 39.92 3.28
3342 3426 5.246656 TGAATCAGATTGCCTTTGGTCAAAT 59.753 36.000 0.00 0.00 0.00 2.32
3363 3448 1.771854 TCTTTTCTGTACCACCAGCCA 59.228 47.619 0.00 0.00 32.32 4.75
3464 3549 1.807814 TTCCCCTGCCTATCTTCTCC 58.192 55.000 0.00 0.00 0.00 3.71
3554 3639 7.756722 ACATTCTTAGATCCTTTTCATTTTGCG 59.243 33.333 0.00 0.00 0.00 4.85
3563 3648 2.575694 TTCATTTTGCGCAACACAGT 57.424 40.000 24.99 1.78 0.00 3.55
3680 3765 6.475402 ACGAAATTCCACTGAATCAAAACAAC 59.525 34.615 0.00 0.00 40.34 3.32
3725 3810 8.408601 GTCATGAAAATAGGAGCATTAACACAT 58.591 33.333 0.00 0.00 0.00 3.21
3763 3848 4.043812 ACCATTAGCAGATCAGGGCATAAT 59.956 41.667 0.00 0.54 0.00 1.28
3864 3949 1.911357 AGTCAGAGCATGAATGTGGGA 59.089 47.619 0.00 0.00 40.43 4.37
3975 4060 8.071177 AGGATGAAAGCTTATGTGCTAAATTT 57.929 30.769 0.00 0.00 43.24 1.82
4175 4260 3.253432 GGTGGACACATGAGAAAACTTCC 59.747 47.826 0.00 0.00 0.00 3.46
4189 4274 2.881111 ACTTCCCTTGGGTAAGCTTC 57.119 50.000 0.00 0.00 32.40 3.86
4260 4345 6.016192 TGCATTTCAATTGTTCCTTACCGTTA 60.016 34.615 5.13 0.00 0.00 3.18
4356 4441 2.548295 CGCCTACCGGAGAGCTCTC 61.548 68.421 31.89 31.89 42.14 3.20
4816 4901 2.856000 AGCCACTGGTGCCTTCCT 60.856 61.111 0.00 0.00 0.00 3.36
4819 4904 2.528818 CCACTGGTGCCTTCCTGGA 61.529 63.158 0.00 0.00 38.35 3.86
4825 4910 2.853542 TGCCTTCCTGGAGTGCCA 60.854 61.111 14.53 0.00 43.47 4.92
4894 4979 6.932356 CATCAGATGCTACACCAATAAAGT 57.068 37.500 0.00 0.00 0.00 2.66
5025 5116 7.630242 TTTGGAATCCTTGCATAGAGTAAAG 57.370 36.000 0.00 0.00 0.00 1.85
5032 5123 5.188948 TCCTTGCATAGAGTAAAGTAGGCAA 59.811 40.000 0.00 0.00 42.03 4.52
5054 5147 8.965819 GGCAATCTATCAGATATCTAACTCTCA 58.034 37.037 4.54 0.00 32.89 3.27
5241 5334 3.567164 AGTGAGCATTCTTTGAGTTGGTG 59.433 43.478 0.00 0.00 0.00 4.17
5276 5369 8.978472 AGTATAGTAAGAAAAGTGGCTGTATGA 58.022 33.333 0.00 0.00 0.00 2.15
5306 5399 8.443953 AGCAATCCTTGTATTAGTTCTGAATC 57.556 34.615 0.00 0.00 0.00 2.52
5399 5492 1.693083 GATCAACGTGCGGTACAGCC 61.693 60.000 15.58 6.02 36.02 4.85
5419 5512 4.999950 AGCCGATTTTGAAGCCTAGATATG 59.000 41.667 0.00 0.00 0.00 1.78
5521 5614 7.775053 ATCCACAATATGTTTTACAGTTGGT 57.225 32.000 10.47 0.00 34.18 3.67
5617 5734 2.666272 TTACATGGCAAAGGTGGACA 57.334 45.000 0.00 0.00 0.00 4.02
5618 5735 2.198827 TACATGGCAAAGGTGGACAG 57.801 50.000 0.00 0.00 0.00 3.51
5619 5736 0.478072 ACATGGCAAAGGTGGACAGA 59.522 50.000 0.00 0.00 0.00 3.41
5620 5737 1.133513 ACATGGCAAAGGTGGACAGAA 60.134 47.619 0.00 0.00 0.00 3.02
5621 5738 1.270550 CATGGCAAAGGTGGACAGAAC 59.729 52.381 0.00 0.00 0.00 3.01
5622 5739 0.467290 TGGCAAAGGTGGACAGAACC 60.467 55.000 0.00 0.00 38.03 3.62
5623 5740 0.467290 GGCAAAGGTGGACAGAACCA 60.467 55.000 0.00 0.00 40.40 3.67
5634 5751 5.004922 TGGACAGAACCACAAATTTCAAC 57.995 39.130 0.00 0.00 34.77 3.18
5635 5752 4.464244 TGGACAGAACCACAAATTTCAACA 59.536 37.500 0.00 0.00 34.77 3.33
5636 5753 5.043248 GGACAGAACCACAAATTTCAACAG 58.957 41.667 0.00 0.00 0.00 3.16
5637 5754 4.432712 ACAGAACCACAAATTTCAACAGC 58.567 39.130 0.00 0.00 0.00 4.40
5638 5755 3.803778 CAGAACCACAAATTTCAACAGCC 59.196 43.478 0.00 0.00 0.00 4.85
5639 5756 2.507339 ACCACAAATTTCAACAGCCG 57.493 45.000 0.00 0.00 0.00 5.52
5640 5757 1.139163 CCACAAATTTCAACAGCCGC 58.861 50.000 0.00 0.00 0.00 6.53
5641 5758 1.269726 CCACAAATTTCAACAGCCGCT 60.270 47.619 0.00 0.00 0.00 5.52
5642 5759 2.053627 CACAAATTTCAACAGCCGCTC 58.946 47.619 0.00 0.00 0.00 5.03
5643 5760 1.000274 ACAAATTTCAACAGCCGCTCC 60.000 47.619 0.00 0.00 0.00 4.70
5644 5761 1.000385 CAAATTTCAACAGCCGCTCCA 60.000 47.619 0.00 0.00 0.00 3.86
5645 5762 0.598065 AATTTCAACAGCCGCTCCAC 59.402 50.000 0.00 0.00 0.00 4.02
5646 5763 0.537143 ATTTCAACAGCCGCTCCACA 60.537 50.000 0.00 0.00 0.00 4.17
5647 5764 0.749818 TTTCAACAGCCGCTCCACAA 60.750 50.000 0.00 0.00 0.00 3.33
5648 5765 0.749818 TTCAACAGCCGCTCCACAAA 60.750 50.000 0.00 0.00 0.00 2.83
5649 5766 0.537143 TCAACAGCCGCTCCACAAAT 60.537 50.000 0.00 0.00 0.00 2.32
5650 5767 0.314935 CAACAGCCGCTCCACAAATT 59.685 50.000 0.00 0.00 0.00 1.82
5651 5768 1.039856 AACAGCCGCTCCACAAATTT 58.960 45.000 0.00 0.00 0.00 1.82
5652 5769 0.598065 ACAGCCGCTCCACAAATTTC 59.402 50.000 0.00 0.00 0.00 2.17
5653 5770 0.597568 CAGCCGCTCCACAAATTTCA 59.402 50.000 0.00 0.00 0.00 2.69
5654 5771 1.000385 CAGCCGCTCCACAAATTTCAA 60.000 47.619 0.00 0.00 0.00 2.69
5655 5772 1.000274 AGCCGCTCCACAAATTTCAAC 60.000 47.619 0.00 0.00 0.00 3.18
5656 5773 1.000274 GCCGCTCCACAAATTTCAACT 60.000 47.619 0.00 0.00 0.00 3.16
5657 5774 2.227865 GCCGCTCCACAAATTTCAACTA 59.772 45.455 0.00 0.00 0.00 2.24
5658 5775 3.821841 CCGCTCCACAAATTTCAACTAC 58.178 45.455 0.00 0.00 0.00 2.73
5659 5776 3.479006 CGCTCCACAAATTTCAACTACG 58.521 45.455 0.00 0.00 0.00 3.51
5660 5777 3.185594 CGCTCCACAAATTTCAACTACGA 59.814 43.478 0.00 0.00 0.00 3.43
5661 5778 4.464112 GCTCCACAAATTTCAACTACGAC 58.536 43.478 0.00 0.00 0.00 4.34
5662 5779 4.213482 GCTCCACAAATTTCAACTACGACT 59.787 41.667 0.00 0.00 0.00 4.18
5663 5780 5.614887 GCTCCACAAATTTCAACTACGACTC 60.615 44.000 0.00 0.00 0.00 3.36
5664 5781 4.753107 TCCACAAATTTCAACTACGACTCC 59.247 41.667 0.00 0.00 0.00 3.85
5665 5782 4.513692 CCACAAATTTCAACTACGACTCCA 59.486 41.667 0.00 0.00 0.00 3.86
5666 5783 5.440685 CACAAATTTCAACTACGACTCCAC 58.559 41.667 0.00 0.00 0.00 4.02
5667 5784 4.514066 ACAAATTTCAACTACGACTCCACC 59.486 41.667 0.00 0.00 0.00 4.61
5668 5785 4.618920 AATTTCAACTACGACTCCACCT 57.381 40.909 0.00 0.00 0.00 4.00
5669 5786 3.380479 TTTCAACTACGACTCCACCTG 57.620 47.619 0.00 0.00 0.00 4.00
5670 5787 0.601558 TCAACTACGACTCCACCTGC 59.398 55.000 0.00 0.00 0.00 4.85
5671 5788 0.603569 CAACTACGACTCCACCTGCT 59.396 55.000 0.00 0.00 0.00 4.24
5672 5789 0.889306 AACTACGACTCCACCTGCTC 59.111 55.000 0.00 0.00 0.00 4.26
5673 5790 0.966370 ACTACGACTCCACCTGCTCC 60.966 60.000 0.00 0.00 0.00 4.70
5674 5791 1.994507 CTACGACTCCACCTGCTCCG 61.995 65.000 0.00 0.00 0.00 4.63
5675 5792 4.135153 CGACTCCACCTGCTCCGG 62.135 72.222 0.00 0.00 0.00 5.14
5676 5793 3.775654 GACTCCACCTGCTCCGGG 61.776 72.222 0.00 0.00 35.68 5.73
5677 5794 4.316823 ACTCCACCTGCTCCGGGA 62.317 66.667 0.00 0.00 33.36 5.14
5678 5795 3.465403 CTCCACCTGCTCCGGGAG 61.465 72.222 19.95 19.95 40.82 4.30
5679 5796 4.316823 TCCACCTGCTCCGGGAGT 62.317 66.667 24.30 3.27 33.36 3.85
5680 5797 4.087892 CCACCTGCTCCGGGAGTG 62.088 72.222 24.30 15.23 33.36 3.51
5681 5798 4.087892 CACCTGCTCCGGGAGTGG 62.088 72.222 24.30 25.22 33.36 4.00
5682 5799 4.316823 ACCTGCTCCGGGAGTGGA 62.317 66.667 30.83 15.36 36.37 4.02
5691 5808 4.154347 GGGAGTGGAGCTGCGGAG 62.154 72.222 0.00 0.00 36.30 4.63
5711 5828 2.200052 GGAGTACCTCCGAACAGGG 58.800 63.158 0.00 0.00 41.08 4.45
5712 5829 0.614134 GGAGTACCTCCGAACAGGGT 60.614 60.000 0.00 0.00 41.08 4.34
5713 5830 0.816373 GAGTACCTCCGAACAGGGTC 59.184 60.000 0.00 0.00 41.52 4.46
5758 5875 1.917872 TTACATGGCAAAGGTGGACC 58.082 50.000 0.00 0.00 0.00 4.46
5770 5887 3.900966 AGGTGGACCGAACCTAATAAC 57.099 47.619 1.55 0.00 46.44 1.89
5771 5888 3.175594 AGGTGGACCGAACCTAATAACA 58.824 45.455 1.55 0.00 46.44 2.41
5772 5889 3.583966 AGGTGGACCGAACCTAATAACAA 59.416 43.478 1.55 0.00 46.44 2.83
5773 5890 3.686241 GGTGGACCGAACCTAATAACAAC 59.314 47.826 0.00 0.00 34.66 3.32
5774 5891 3.368843 GTGGACCGAACCTAATAACAACG 59.631 47.826 0.00 0.00 0.00 4.10
5775 5892 3.257873 TGGACCGAACCTAATAACAACGA 59.742 43.478 0.00 0.00 0.00 3.85
5776 5893 3.861689 GGACCGAACCTAATAACAACGAG 59.138 47.826 0.00 0.00 0.00 4.18
5835 5952 2.039405 GTCTGGCTTCAGCTGCAGG 61.039 63.158 17.12 5.84 41.70 4.85
5836 5953 3.441290 CTGGCTTCAGCTGCAGGC 61.441 66.667 28.71 28.71 41.70 4.85
5852 5969 4.702081 GCTGCAGCTGCTGTGCAC 62.702 66.667 36.19 21.62 45.96 4.57
5857 5974 1.660575 CAGCTGCTGTGCACTTTGC 60.661 57.895 21.21 18.73 45.29 3.68
5873 5990 3.189287 ACTTTGCCTGAAGTTATCTTGCG 59.811 43.478 0.00 0.00 36.49 4.85
5877 5994 3.056107 TGCCTGAAGTTATCTTGCGTACT 60.056 43.478 0.00 0.00 33.64 2.73
5882 5999 6.812160 CCTGAAGTTATCTTGCGTACTTACTT 59.188 38.462 0.00 0.00 33.64 2.24
5886 6003 8.684973 AAGTTATCTTGCGTACTTACTTACTG 57.315 34.615 0.00 0.00 32.09 2.74
5887 6004 8.048534 AGTTATCTTGCGTACTTACTTACTGA 57.951 34.615 0.00 0.00 0.00 3.41
5888 6005 8.517878 AGTTATCTTGCGTACTTACTTACTGAA 58.482 33.333 0.00 0.00 0.00 3.02
5889 6006 9.132521 GTTATCTTGCGTACTTACTTACTGAAA 57.867 33.333 0.00 0.00 0.00 2.69
5890 6007 6.998258 TCTTGCGTACTTACTTACTGAAAC 57.002 37.500 0.00 0.00 0.00 2.78
5891 6008 6.506147 TCTTGCGTACTTACTTACTGAAACA 58.494 36.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.266242 GTGGCTAAAACAAGAGCATATTCG 58.734 41.667 0.00 0.00 40.64 3.34
7 8 0.109735 GCCGTGGCTAAAACAAGAGC 60.110 55.000 2.98 0.00 38.26 4.09
23 24 0.171007 CAACTTACCATGCAAGGCCG 59.829 55.000 8.15 0.00 0.00 6.13
29 30 1.807742 GCGTTACCAACTTACCATGCA 59.192 47.619 0.00 0.00 0.00 3.96
36 37 6.073112 GGAAATAACACTGCGTTACCAACTTA 60.073 38.462 0.00 0.00 42.82 2.24
39 40 4.214758 AGGAAATAACACTGCGTTACCAAC 59.785 41.667 0.00 0.00 42.82 3.77
40 41 4.391155 AGGAAATAACACTGCGTTACCAA 58.609 39.130 0.00 0.00 42.82 3.67
44 45 4.565166 CGATGAGGAAATAACACTGCGTTA 59.435 41.667 0.00 0.00 44.12 3.18
103 106 2.045926 GGCCACGCTCTGGATGTT 60.046 61.111 0.00 0.00 43.95 2.71
104 107 4.457496 CGGCCACGCTCTGGATGT 62.457 66.667 2.24 0.00 43.95 3.06
105 108 3.664025 TTCGGCCACGCTCTGGATG 62.664 63.158 2.24 0.00 43.95 3.51
106 109 2.257409 ATTTCGGCCACGCTCTGGAT 62.257 55.000 2.24 0.00 43.95 3.41
107 110 2.463589 AATTTCGGCCACGCTCTGGA 62.464 55.000 2.24 0.00 43.95 3.86
164 189 1.984026 CCCTGAAATTTGGCCGCCT 60.984 57.895 11.61 0.00 0.00 5.52
199 224 4.617520 TGGTGCGATGTGCCGTGT 62.618 61.111 0.00 0.00 45.60 4.49
224 249 3.990959 ATCACTCTGGGTTTCTTCCTC 57.009 47.619 0.00 0.00 0.00 3.71
225 250 4.104738 TCAAATCACTCTGGGTTTCTTCCT 59.895 41.667 0.00 0.00 0.00 3.36
226 251 4.216472 GTCAAATCACTCTGGGTTTCTTCC 59.784 45.833 0.00 0.00 0.00 3.46
238 264 1.532868 ACGCAGCAAGTCAAATCACTC 59.467 47.619 0.00 0.00 0.00 3.51
239 265 1.597742 ACGCAGCAAGTCAAATCACT 58.402 45.000 0.00 0.00 0.00 3.41
275 301 2.036089 GCGATAATCTCTCGGGGAGTTT 59.964 50.000 4.52 5.61 42.40 2.66
306 332 0.821711 TTCTCTGGGTTTTGCGTGGG 60.822 55.000 0.00 0.00 0.00 4.61
323 349 3.310652 CTCCCCTCCCGGAGTTTC 58.689 66.667 13.62 0.00 43.94 2.78
1279 1320 3.083997 CCCGGGGAAGGAGGAGTG 61.084 72.222 14.71 0.00 0.00 3.51
1433 1501 1.509923 GCGGTAGCGTTACTGGACT 59.490 57.895 18.43 0.00 36.78 3.85
1489 1563 4.161295 TCCGCCTCCCGATTGCTG 62.161 66.667 0.00 0.00 40.02 4.41
1511 1585 2.437716 AATTGCCGCCTGGTACCG 60.438 61.111 7.57 1.95 37.67 4.02
1557 1631 2.125832 GCAGCAGCGTTACCGGTA 60.126 61.111 11.16 11.16 44.18 4.02
1827 1901 3.134458 GGTCTGATTGACGGATGGAATC 58.866 50.000 0.00 0.00 46.24 2.52
2145 2222 0.033504 GCTTCTTCGTCTGACCACCA 59.966 55.000 1.55 0.00 0.00 4.17
2155 2232 2.729467 CGATCGAGTGAAGCTTCTTCGT 60.729 50.000 32.76 25.52 36.80 3.85
2188 2265 0.846401 CCGTAGAACATGTCGCATCG 59.154 55.000 0.00 1.25 0.00 3.84
2371 2448 1.830477 ACACAAACTGCATGGGTGTTT 59.170 42.857 7.50 2.20 39.48 2.83
2443 2523 5.300286 ACCTAAAATAAGGCATCAGCATCAC 59.700 40.000 0.00 0.00 44.61 3.06
2553 2633 2.037772 ACTCCTCAAGATGCAAACGAGT 59.962 45.455 0.00 0.00 0.00 4.18
2556 2636 3.070018 AGAACTCCTCAAGATGCAAACG 58.930 45.455 0.00 0.00 0.00 3.60
2573 2653 4.998033 CCCTCCTCTTGTCTTTTACAGAAC 59.002 45.833 0.00 0.00 39.87 3.01
2580 2660 5.269189 TCAAAAACCCTCCTCTTGTCTTTT 58.731 37.500 0.00 0.00 0.00 2.27
2713 2795 3.436704 TCCTAAATGCTGAAACAAGCTCG 59.563 43.478 0.00 0.00 43.90 5.03
2790 2872 8.774586 GTTTGGTATCAAGATTATGTAGCGAAT 58.225 33.333 0.00 0.00 33.98 3.34
2836 2918 2.376109 TGTTTCGGGGTTGTTGCTAAA 58.624 42.857 0.00 0.00 0.00 1.85
2840 2922 3.586100 ATTATGTTTCGGGGTTGTTGC 57.414 42.857 0.00 0.00 0.00 4.17
2930 3012 5.238650 GGGAAGTCTTCAACAATTCGAAAGA 59.761 40.000 14.49 0.00 39.20 2.52
2943 3025 2.270352 AATTGCACGGGAAGTCTTCA 57.730 45.000 14.49 0.00 0.00 3.02
3090 3173 1.997606 GGAATGCTGCATGTTTTGAGC 59.002 47.619 17.00 0.00 0.00 4.26
3144 3227 1.710816 GGGTTTGATGTTTGTGGGGA 58.289 50.000 0.00 0.00 0.00 4.81
3148 3231 2.035832 GGACAGGGGTTTGATGTTTGTG 59.964 50.000 0.00 0.00 0.00 3.33
3149 3232 2.091333 AGGACAGGGGTTTGATGTTTGT 60.091 45.455 0.00 0.00 0.00 2.83
3150 3233 2.597455 AGGACAGGGGTTTGATGTTTG 58.403 47.619 0.00 0.00 0.00 2.93
3151 3234 3.230976 GAAGGACAGGGGTTTGATGTTT 58.769 45.455 0.00 0.00 0.00 2.83
3152 3235 2.176798 TGAAGGACAGGGGTTTGATGTT 59.823 45.455 0.00 0.00 0.00 2.71
3153 3236 1.780309 TGAAGGACAGGGGTTTGATGT 59.220 47.619 0.00 0.00 0.00 3.06
3154 3237 2.162681 GTGAAGGACAGGGGTTTGATG 58.837 52.381 0.00 0.00 0.00 3.07
3155 3238 1.780309 TGTGAAGGACAGGGGTTTGAT 59.220 47.619 0.00 0.00 0.00 2.57
3156 3239 1.217916 TGTGAAGGACAGGGGTTTGA 58.782 50.000 0.00 0.00 0.00 2.69
3157 3240 1.956477 CTTGTGAAGGACAGGGGTTTG 59.044 52.381 0.00 0.00 35.44 2.93
3158 3241 1.850345 TCTTGTGAAGGACAGGGGTTT 59.150 47.619 0.00 0.00 35.44 3.27
3159 3242 1.518367 TCTTGTGAAGGACAGGGGTT 58.482 50.000 0.00 0.00 35.44 4.11
3160 3243 1.518367 TTCTTGTGAAGGACAGGGGT 58.482 50.000 0.00 0.00 35.44 4.95
3161 3244 2.623416 GTTTTCTTGTGAAGGACAGGGG 59.377 50.000 0.00 0.00 35.44 4.79
3162 3245 3.287222 TGTTTTCTTGTGAAGGACAGGG 58.713 45.455 0.00 0.00 35.44 4.45
3163 3246 5.284079 CAATGTTTTCTTGTGAAGGACAGG 58.716 41.667 0.00 0.00 35.29 4.00
3164 3247 4.741676 GCAATGTTTTCTTGTGAAGGACAG 59.258 41.667 0.00 0.00 35.29 3.51
3165 3248 4.441356 GGCAATGTTTTCTTGTGAAGGACA 60.441 41.667 0.00 0.00 35.83 4.02
3198 3281 5.982516 CCTAGAATTGGAGATGAACTCTTCG 59.017 44.000 0.00 0.00 44.37 3.79
3202 3285 5.028549 TGCCTAGAATTGGAGATGAACTC 57.971 43.478 0.00 0.00 44.24 3.01
3236 3320 8.556213 ACGTATTATATCCAACTGTGTGTTTT 57.444 30.769 0.00 0.00 36.63 2.43
3262 3346 1.802365 GTGGCCACGACTAAACGATTT 59.198 47.619 22.49 0.00 37.03 2.17
3278 3362 4.034048 CCTTATACGTGTCATTTCTGTGGC 59.966 45.833 0.00 0.00 0.00 5.01
3280 3364 4.034048 GGCCTTATACGTGTCATTTCTGTG 59.966 45.833 0.00 0.00 0.00 3.66
3317 3401 3.760151 TGACCAAAGGCAATCTGATTCAG 59.240 43.478 7.38 7.38 0.00 3.02
3336 3420 6.385649 TGGTGGTACAGAAAAGAATTTGAC 57.614 37.500 0.00 0.00 41.80 3.18
3342 3426 2.173782 TGGCTGGTGGTACAGAAAAGAA 59.826 45.455 0.00 0.00 41.80 2.52
3389 3474 9.052759 GTACCTGACATGAGAAAAGAGTAAAAA 57.947 33.333 0.00 0.00 0.00 1.94
3390 3475 8.208224 TGTACCTGACATGAGAAAAGAGTAAAA 58.792 33.333 0.00 0.00 31.20 1.52
3464 3549 6.944234 AGAGTCTTAAAGTTTTGAAGGGTG 57.056 37.500 0.00 0.00 0.00 4.61
3554 3639 7.760131 ATATGCATGAAATAAACTGTGTTGC 57.240 32.000 10.16 0.00 0.00 4.17
3586 3671 6.986817 TGTAAGTTCAGAGTCAGAAAAGGAAG 59.013 38.462 0.00 0.00 0.00 3.46
3617 3702 3.496884 TGTACGGTGCAAGAAGTGAATTC 59.503 43.478 0.00 0.00 38.28 2.17
3680 3765 5.611796 TGACAAAAATGTTCTGATCTCGG 57.388 39.130 0.00 0.00 0.00 4.63
3725 3810 6.286758 TGCTAATGGTTTGCTTCATTGAAAA 58.713 32.000 0.01 0.00 35.50 2.29
3975 4060 9.696572 AGTACAATTGTAGTCCTAGACAAGATA 57.303 33.333 18.56 0.00 38.86 1.98
3978 4063 7.542477 CACAGTACAATTGTAGTCCTAGACAAG 59.458 40.741 20.73 10.44 38.86 3.16
4175 4260 2.872858 GCGAATAGAAGCTTACCCAAGG 59.127 50.000 0.00 0.00 31.96 3.61
4260 4345 5.412594 CCTGTAGCACATTTGACATACTTGT 59.587 40.000 0.00 0.00 39.32 3.16
4314 4399 3.319137 TGGACATTCAGCTGACTGTAC 57.681 47.619 32.26 32.26 44.77 2.90
4431 4516 3.194968 TCTCTACGAACCTGAAATGGGAC 59.805 47.826 0.00 0.00 0.00 4.46
4608 4693 3.477530 GGGTATGGCATGAGGTACTTTC 58.522 50.000 10.98 0.00 41.55 2.62
4825 4910 0.968393 GGAGCTCGTTCCAGGAGTCT 60.968 60.000 7.83 0.00 37.20 3.24
5047 5140 5.308237 AGAGTTCCTGTTGGTAATGAGAGTT 59.692 40.000 0.00 0.00 34.23 3.01
5230 5323 9.214957 CTATACTATTCAACACACCAACTCAAA 57.785 33.333 0.00 0.00 0.00 2.69
5306 5399 4.095334 TGCACAGCATCAAAAGCACTATAG 59.905 41.667 0.00 0.00 31.71 1.31
5399 5492 4.143030 CGGCATATCTAGGCTTCAAAATCG 60.143 45.833 0.00 0.00 32.84 3.34
5404 5497 3.803715 GCTTCGGCATATCTAGGCTTCAA 60.804 47.826 0.00 0.00 41.33 2.69
5419 5512 1.739562 CTCACCAGAGTGCTTCGGC 60.740 63.158 0.00 0.00 44.16 5.54
5460 5553 3.114616 CACAGCGCCCTTCGACTG 61.115 66.667 2.29 0.00 43.17 3.51
5464 5557 2.887568 CTAGCACAGCGCCCTTCG 60.888 66.667 2.29 0.00 44.04 3.79
5617 5734 3.490761 CGGCTGTTGAAATTTGTGGTTCT 60.491 43.478 0.00 0.00 0.00 3.01
5618 5735 2.794350 CGGCTGTTGAAATTTGTGGTTC 59.206 45.455 0.00 0.00 0.00 3.62
5619 5736 2.820330 CGGCTGTTGAAATTTGTGGTT 58.180 42.857 0.00 0.00 0.00 3.67
5620 5737 1.537990 GCGGCTGTTGAAATTTGTGGT 60.538 47.619 0.00 0.00 0.00 4.16
5621 5738 1.139163 GCGGCTGTTGAAATTTGTGG 58.861 50.000 0.00 0.00 0.00 4.17
5622 5739 2.053627 GAGCGGCTGTTGAAATTTGTG 58.946 47.619 7.50 0.00 0.00 3.33
5623 5740 1.000274 GGAGCGGCTGTTGAAATTTGT 60.000 47.619 7.50 0.00 0.00 2.83
5624 5741 1.000385 TGGAGCGGCTGTTGAAATTTG 60.000 47.619 7.50 0.00 0.00 2.32
5625 5742 1.000274 GTGGAGCGGCTGTTGAAATTT 60.000 47.619 7.50 0.00 0.00 1.82
5626 5743 0.598065 GTGGAGCGGCTGTTGAAATT 59.402 50.000 7.50 0.00 0.00 1.82
5627 5744 0.537143 TGTGGAGCGGCTGTTGAAAT 60.537 50.000 7.50 0.00 0.00 2.17
5628 5745 0.749818 TTGTGGAGCGGCTGTTGAAA 60.750 50.000 7.50 0.00 0.00 2.69
5629 5746 0.749818 TTTGTGGAGCGGCTGTTGAA 60.750 50.000 7.50 0.00 0.00 2.69
5630 5747 0.537143 ATTTGTGGAGCGGCTGTTGA 60.537 50.000 7.50 0.00 0.00 3.18
5631 5748 0.314935 AATTTGTGGAGCGGCTGTTG 59.685 50.000 7.50 0.00 0.00 3.33
5632 5749 1.000274 GAAATTTGTGGAGCGGCTGTT 60.000 47.619 7.50 0.00 0.00 3.16
5633 5750 0.598065 GAAATTTGTGGAGCGGCTGT 59.402 50.000 7.50 0.00 0.00 4.40
5634 5751 0.597568 TGAAATTTGTGGAGCGGCTG 59.402 50.000 7.50 0.00 0.00 4.85
5635 5752 1.000274 GTTGAAATTTGTGGAGCGGCT 60.000 47.619 0.00 0.00 0.00 5.52
5636 5753 1.000274 AGTTGAAATTTGTGGAGCGGC 60.000 47.619 0.00 0.00 0.00 6.53
5637 5754 3.666902 CGTAGTTGAAATTTGTGGAGCGG 60.667 47.826 0.00 0.00 0.00 5.52
5638 5755 3.185594 TCGTAGTTGAAATTTGTGGAGCG 59.814 43.478 0.00 0.00 0.00 5.03
5639 5756 4.213482 AGTCGTAGTTGAAATTTGTGGAGC 59.787 41.667 0.00 0.00 0.00 4.70
5640 5757 5.107065 GGAGTCGTAGTTGAAATTTGTGGAG 60.107 44.000 0.00 0.00 0.00 3.86
5641 5758 4.753107 GGAGTCGTAGTTGAAATTTGTGGA 59.247 41.667 0.00 0.00 0.00 4.02
5642 5759 4.513692 TGGAGTCGTAGTTGAAATTTGTGG 59.486 41.667 0.00 0.00 0.00 4.17
5643 5760 5.440685 GTGGAGTCGTAGTTGAAATTTGTG 58.559 41.667 0.00 0.00 0.00 3.33
5644 5761 4.514066 GGTGGAGTCGTAGTTGAAATTTGT 59.486 41.667 0.00 0.00 0.00 2.83
5645 5762 4.755123 AGGTGGAGTCGTAGTTGAAATTTG 59.245 41.667 0.00 0.00 0.00 2.32
5646 5763 4.755123 CAGGTGGAGTCGTAGTTGAAATTT 59.245 41.667 0.00 0.00 0.00 1.82
5647 5764 4.315803 CAGGTGGAGTCGTAGTTGAAATT 58.684 43.478 0.00 0.00 0.00 1.82
5648 5765 3.864921 GCAGGTGGAGTCGTAGTTGAAAT 60.865 47.826 0.00 0.00 0.00 2.17
5649 5766 2.547218 GCAGGTGGAGTCGTAGTTGAAA 60.547 50.000 0.00 0.00 0.00 2.69
5650 5767 1.000506 GCAGGTGGAGTCGTAGTTGAA 59.999 52.381 0.00 0.00 0.00 2.69
5651 5768 0.601558 GCAGGTGGAGTCGTAGTTGA 59.398 55.000 0.00 0.00 0.00 3.18
5652 5769 0.603569 AGCAGGTGGAGTCGTAGTTG 59.396 55.000 0.00 0.00 0.00 3.16
5653 5770 0.889306 GAGCAGGTGGAGTCGTAGTT 59.111 55.000 0.00 0.00 0.00 2.24
5654 5771 0.966370 GGAGCAGGTGGAGTCGTAGT 60.966 60.000 0.00 0.00 0.00 2.73
5655 5772 1.810532 GGAGCAGGTGGAGTCGTAG 59.189 63.158 0.00 0.00 0.00 3.51
5656 5773 2.044555 CGGAGCAGGTGGAGTCGTA 61.045 63.158 0.00 0.00 0.00 3.43
5657 5774 3.374402 CGGAGCAGGTGGAGTCGT 61.374 66.667 0.00 0.00 0.00 4.34
5658 5775 4.135153 CCGGAGCAGGTGGAGTCG 62.135 72.222 0.00 0.00 0.00 4.18
5659 5776 3.775654 CCCGGAGCAGGTGGAGTC 61.776 72.222 0.73 0.00 0.00 3.36
5660 5777 4.316823 TCCCGGAGCAGGTGGAGT 62.317 66.667 0.73 0.00 0.00 3.85
5661 5778 3.465403 CTCCCGGAGCAGGTGGAG 61.465 72.222 0.73 0.00 38.56 3.86
5662 5779 4.316823 ACTCCCGGAGCAGGTGGA 62.317 66.667 14.86 0.00 32.04 4.02
5663 5780 4.087892 CACTCCCGGAGCAGGTGG 62.088 72.222 14.86 0.00 32.04 4.61
5664 5781 4.087892 CCACTCCCGGAGCAGGTG 62.088 72.222 14.86 5.98 32.04 4.00
5665 5782 4.316823 TCCACTCCCGGAGCAGGT 62.317 66.667 20.53 0.00 32.38 4.00
5666 5783 3.465403 CTCCACTCCCGGAGCAGG 61.465 72.222 14.86 16.08 45.95 4.85
5674 5791 4.154347 CTCCGCAGCTCCACTCCC 62.154 72.222 0.00 0.00 0.00 4.30
5675 5792 4.828925 GCTCCGCAGCTCCACTCC 62.829 72.222 0.00 0.00 43.09 3.85
5681 5798 3.518998 TACTCCGCTCCGCAGCTC 61.519 66.667 0.00 0.00 44.40 4.09
5682 5799 3.827898 GTACTCCGCTCCGCAGCT 61.828 66.667 0.00 0.00 44.40 4.24
5683 5800 4.874977 GGTACTCCGCTCCGCAGC 62.875 72.222 0.00 0.00 42.96 5.25
5684 5801 3.141488 AGGTACTCCGCTCCGCAG 61.141 66.667 0.00 0.00 39.05 5.18
5695 5812 3.617988 ACGACCCTGTTCGGAGGTACT 62.618 57.143 0.00 0.00 43.58 2.73
5696 5813 1.246737 ACGACCCTGTTCGGAGGTAC 61.247 60.000 0.00 0.00 43.58 3.34
5697 5814 0.327924 TACGACCCTGTTCGGAGGTA 59.672 55.000 0.00 0.00 43.58 3.08
5698 5815 0.540365 TTACGACCCTGTTCGGAGGT 60.540 55.000 0.00 0.00 43.58 3.85
5699 5816 0.822164 ATTACGACCCTGTTCGGAGG 59.178 55.000 0.00 0.00 43.58 4.30
5700 5817 5.640189 ATATATTACGACCCTGTTCGGAG 57.360 43.478 0.00 0.00 43.58 4.63
5701 5818 6.885918 TCATATATATTACGACCCTGTTCGGA 59.114 38.462 0.00 0.00 43.58 4.55
5702 5819 7.092137 TCATATATATTACGACCCTGTTCGG 57.908 40.000 0.00 0.00 43.58 4.30
5703 5820 8.975410 TTTCATATATATTACGACCCTGTTCG 57.025 34.615 0.00 0.00 44.87 3.95
5736 5853 3.632145 GGTCCACCTTTGCCATGTAATAG 59.368 47.826 0.00 0.00 0.00 1.73
5739 5856 1.884497 CGGTCCACCTTTGCCATGTAA 60.884 52.381 0.00 0.00 0.00 2.41
5758 5875 9.075519 TGTTATTACTCGTTGTTATTAGGTTCG 57.924 33.333 0.00 0.00 0.00 3.95
5765 5882 8.430063 CGTCAGTTGTTATTACTCGTTGTTATT 58.570 33.333 0.00 0.00 0.00 1.40
5766 5883 7.411157 GCGTCAGTTGTTATTACTCGTTGTTAT 60.411 37.037 0.00 0.00 0.00 1.89
5767 5884 6.129115 GCGTCAGTTGTTATTACTCGTTGTTA 60.129 38.462 0.00 0.00 0.00 2.41
5768 5885 5.332808 GCGTCAGTTGTTATTACTCGTTGTT 60.333 40.000 0.00 0.00 0.00 2.83
5769 5886 4.149396 GCGTCAGTTGTTATTACTCGTTGT 59.851 41.667 0.00 0.00 0.00 3.32
5770 5887 4.384846 AGCGTCAGTTGTTATTACTCGTTG 59.615 41.667 0.00 0.00 0.00 4.10
5771 5888 4.553323 AGCGTCAGTTGTTATTACTCGTT 58.447 39.130 0.00 0.00 0.00 3.85
5772 5889 4.164294 GAGCGTCAGTTGTTATTACTCGT 58.836 43.478 0.00 0.00 0.00 4.18
5773 5890 3.546670 GGAGCGTCAGTTGTTATTACTCG 59.453 47.826 0.00 0.00 0.00 4.18
5774 5891 4.326548 GTGGAGCGTCAGTTGTTATTACTC 59.673 45.833 0.00 0.00 0.00 2.59
5775 5892 4.243270 GTGGAGCGTCAGTTGTTATTACT 58.757 43.478 0.00 0.00 0.00 2.24
5776 5893 3.370061 GGTGGAGCGTCAGTTGTTATTAC 59.630 47.826 0.00 0.00 0.00 1.89
5835 5952 4.702081 GTGCACAGCAGCTGCAGC 62.702 66.667 38.24 34.23 45.22 5.25
5836 5953 2.071844 AAAGTGCACAGCAGCTGCAG 62.072 55.000 38.24 32.87 45.22 4.41
5837 5954 2.122797 AAAGTGCACAGCAGCTGCA 61.123 52.632 38.24 17.62 45.16 4.41
5838 5955 1.660575 CAAAGTGCACAGCAGCTGC 60.661 57.895 31.53 31.53 40.08 5.25
5839 5956 1.660575 GCAAAGTGCACAGCAGCTG 60.661 57.895 21.54 21.54 44.26 4.24
5840 5957 2.726274 GCAAAGTGCACAGCAGCT 59.274 55.556 21.04 0.00 44.26 4.24
5852 5969 3.189287 ACGCAAGATAACTTCAGGCAAAG 59.811 43.478 0.00 0.00 43.62 2.77
5857 5974 6.331061 AGTAAGTACGCAAGATAACTTCAGG 58.669 40.000 0.00 0.00 38.53 3.86


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

AutoCloner maintained by Alex Coulton.