Multiple sequence alignment - TraesCS6D01G227800

Loading Multiple Alignment...

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 TraesCS6D01G227800 chr6D 100.000 7484 0 0 1 7484 318967099 318959616 0.000000e+00 13821.0
1 TraesCS6D01G227800 chr6A 97.171 2828 66 7 2982 5799 456765968 456763145 0.000000e+00 4767.0
2 TraesCS6D01G227800 chr6A 93.243 2812 83 31 238 2986 456768990 456766223 0.000000e+00 4041.0
3 TraesCS6D01G227800 chr6A 96.218 899 25 4 5795 6685 456763058 456762161 0.000000e+00 1463.0
4 TraesCS6D01G227800 chr6A 97.365 759 16 1 6730 7484 456762165 456761407 0.000000e+00 1288.0
5 TraesCS6D01G227800 chr6A 95.062 243 9 3 1 242 456769259 456769019 5.480000e-101 379.0
6 TraesCS6D01G227800 chr1A 90.446 314 24 3 3179 3487 208894200 208893888 6.990000e-110 409.0
7 TraesCS6D01G227800 chr2D 90.127 314 26 2 3179 3487 373896852 373896539 3.250000e-108 403.0
8 TraesCS6D01G227800 chr2B 89.130 322 29 3 3172 3487 367688119 367687798 5.440000e-106 396.0
9 TraesCS6D01G227800 chr2B 88.043 92 11 0 6854 6945 765923030 765923121 7.940000e-20 110.0
10 TraesCS6D01G227800 chr1D 89.490 314 27 3 3179 3487 150941454 150941766 7.040000e-105 392.0
11 TraesCS6D01G227800 chr1D 81.013 79 8 3 4393 4471 19440068 19440139 1.000000e-03 56.5
12 TraesCS6D01G227800 chr4D 88.854 323 28 5 3171 3487 502760438 502760758 2.530000e-104 390.0
13 TraesCS6D01G227800 chr4A 89.062 320 27 4 3173 3487 45682456 45682772 2.530000e-104 390.0
14 TraesCS6D01G227800 chr4A 88.854 323 28 5 3171 3487 681672252 681671932 2.530000e-104 390.0
15 TraesCS6D01G227800 chr2A 88.450 329 31 4 3169 3491 13020815 13020488 2.530000e-104 390.0
16 TraesCS6D01G227800 chr6B 89.575 259 20 2 7233 7484 504309017 504309275 9.370000e-84 322.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G227800 chr6D 318959616 318967099 7483 True 13821.0 13821 100.0000 1 7484 1 chr6D.!!$R1 7483
1 TraesCS6D01G227800 chr6A 456761407 456769259 7852 True 2387.6 4767 95.8118 1 7484 5 chr6A.!!$R1 7483

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
689 744 0.597568 TTGTGCAATTTCCTCCGCTG 59.402 50.0 0.00 0.0 0.00 5.18 F
1618 1683 0.166814 GACTCGCACAACTCATTGCC 59.833 55.0 0.00 0.0 39.66 4.52 F
2182 2277 0.257039 CAGGCTAAGGCAGGATGGTT 59.743 55.0 0.00 0.0 40.87 3.67 F
3448 3805 0.593773 CCAACGCAACCAAAAGTCCG 60.594 55.0 0.00 0.0 0.00 4.79 F
4568 4926 0.320946 TACCAAAACGAGAAGGGGCG 60.321 55.0 0.00 0.0 0.00 6.13 F
5540 5907 0.620556 CTGGTTCTGGCCTGGTGTAT 59.379 55.0 10.07 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2556 2651 0.110056 CTGAAGATGGTGTTGTGCGC 60.110 55.0 0.00 0.0 0.00 6.09 R
3197 3554 0.661020 AGTTCGGACTTTTGGTTGCG 59.339 50.0 0.00 0.0 29.87 4.85 R
3907 4265 0.813610 TCCTGTGTGGCTTTGTCACG 60.814 55.0 0.00 0.0 41.53 4.35 R
4968 5335 0.107017 CCTCCTCCCGAATTGCATGT 60.107 55.0 0.00 0.0 0.00 3.21 R
5663 6030 0.393537 GAGGCTTGTGGGAGTGGATG 60.394 60.0 0.00 0.0 0.00 3.51 R
6687 7153 0.538516 GGAGCGGCAGATAGAGAGGA 60.539 60.0 1.45 0.0 0.00 3.71 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
41 42 4.657814 ATGGATTGGTCCCGCTTATAAT 57.342 40.909 0.00 0.00 44.41 1.28
59 60 7.616103 TTATAATTGTGCACGTGACAAAAAG 57.384 32.000 26.08 0.11 36.90 2.27
97 98 3.006859 GGCCAACCAAAGCTACAAGATTT 59.993 43.478 0.00 0.00 33.58 2.17
100 101 4.475944 CAACCAAAGCTACAAGATTTCCG 58.524 43.478 0.00 0.00 30.47 4.30
132 133 7.555914 AGTGGTCAAAAAGTGCCAAAAATAATT 59.444 29.630 0.00 0.00 35.87 1.40
137 138 8.960591 TCAAAAAGTGCCAAAAATAATTCCAAA 58.039 25.926 0.00 0.00 0.00 3.28
155 156 7.563724 TTCCAAACCAGTACTAGATAAAGGT 57.436 36.000 0.00 0.00 0.00 3.50
258 293 2.051334 TATTTTCCGGGCCATCACTG 57.949 50.000 4.39 0.00 0.00 3.66
386 430 7.801716 ATATTAATTGTTTTAGCTGGCGAGA 57.198 32.000 0.00 0.00 0.00 4.04
412 456 3.924073 TGTGACCATTAGAAATCGTGTCG 59.076 43.478 0.00 0.00 0.00 4.35
512 566 8.467402 AATACTCCGAATTATAAGATCTTGCG 57.533 34.615 18.47 10.86 0.00 4.85
517 571 6.641314 TCCGAATTATAAGATCTTGCGAGTTC 59.359 38.462 18.47 12.80 0.00 3.01
522 576 9.832445 AATTATAAGATCTTGCGAGTTCCTTTA 57.168 29.630 18.47 3.19 0.00 1.85
528 582 8.738645 AGATCTTGCGAGTTCCTTTATTAAAT 57.261 30.769 8.21 0.00 0.00 1.40
530 584 7.000575 TCTTGCGAGTTCCTTTATTAAATCG 57.999 36.000 0.00 0.00 43.70 3.34
536 590 6.300354 AGTTCCTTTATTAAATCGGATGCG 57.700 37.500 0.00 0.00 0.00 4.73
540 594 7.359262 TCCTTTATTAAATCGGATGCGTATG 57.641 36.000 6.49 0.00 0.00 2.39
623 678 6.959311 CCCAAACGTCTTATAATTCGAAACAG 59.041 38.462 0.00 0.00 0.00 3.16
632 687 9.967346 TCTTATAATTCGAAACAGAGGTGATAG 57.033 33.333 0.00 0.00 0.00 2.08
660 715 7.908827 ATTATGTGCAAAATTGAAATCAGCA 57.091 28.000 0.00 0.00 0.00 4.41
689 744 0.597568 TTGTGCAATTTCCTCCGCTG 59.402 50.000 0.00 0.00 0.00 5.18
701 756 0.891373 CTCCGCTGGAAGAGAAGACA 59.109 55.000 0.00 0.00 34.81 3.41
714 769 2.872858 GAGAAGACAAGGTCGTTTTGCT 59.127 45.455 0.00 0.00 37.67 3.91
723 778 4.383602 CGTTTTGCTCGGGGCGTG 62.384 66.667 0.00 0.00 45.43 5.34
793 851 2.514458 AAATCGAAGCTCCACCCATT 57.486 45.000 0.00 0.00 0.00 3.16
839 897 3.618780 CTGAGTCCACCTGGCTGGC 62.619 68.421 10.71 0.00 40.22 4.85
840 898 3.325753 GAGTCCACCTGGCTGGCT 61.326 66.667 10.71 9.77 40.22 4.75
841 899 3.322318 GAGTCCACCTGGCTGGCTC 62.322 68.421 10.71 15.94 40.22 4.70
842 900 4.416738 GTCCACCTGGCTGGCTCC 62.417 72.222 10.71 0.00 40.22 4.70
843 901 4.980592 TCCACCTGGCTGGCTCCA 62.981 66.667 10.71 0.00 40.22 3.86
844 902 4.729918 CCACCTGGCTGGCTCCAC 62.730 72.222 10.71 0.00 40.22 4.02
902 966 2.262915 CAGCGACCACCTGGAGTC 59.737 66.667 0.00 6.13 38.94 3.36
1068 1132 2.279120 CTCAGCTCATCGACGGGC 60.279 66.667 0.00 0.00 0.00 6.13
1129 1193 3.058351 CGGTGTTCGTCGCGTTAG 58.942 61.111 5.77 0.00 0.00 2.34
1151 1215 1.067776 AGACGATGTCAACGAAGGGAC 60.068 52.381 9.70 0.00 34.60 4.46
1244 1308 1.446099 CCACACGATCGACCCACAG 60.446 63.158 24.34 4.77 0.00 3.66
1302 1366 6.873605 CAGGTGAATTTTGGGTTATCTTTTCC 59.126 38.462 0.00 0.00 0.00 3.13
1306 1370 8.463607 GTGAATTTTGGGTTATCTTTTCCGATA 58.536 33.333 0.00 0.00 0.00 2.92
1354 1419 0.747283 GGCAGCATGAGACCAGAAGG 60.747 60.000 0.00 0.00 39.69 3.46
1389 1454 3.139077 AGAAACTTACAGCGGGACAAAG 58.861 45.455 0.00 0.00 0.00 2.77
1408 1473 1.064166 AGCAGGGAAGAACATGGATGG 60.064 52.381 0.00 0.00 0.00 3.51
1464 1529 7.334858 AGATCTAGAGGTTCAACTCAATTTCC 58.665 38.462 0.00 0.00 39.97 3.13
1491 1556 3.705072 CCGGTCAATACCTTTCTACCTCT 59.295 47.826 0.00 0.00 44.35 3.69
1492 1557 4.441634 CCGGTCAATACCTTTCTACCTCTG 60.442 50.000 0.00 0.00 44.35 3.35
1493 1558 4.441634 CGGTCAATACCTTTCTACCTCTGG 60.442 50.000 0.00 0.00 44.35 3.86
1494 1559 4.443621 GTCAATACCTTTCTACCTCTGGC 58.556 47.826 0.00 0.00 0.00 4.85
1495 1560 4.162509 GTCAATACCTTTCTACCTCTGGCT 59.837 45.833 0.00 0.00 0.00 4.75
1496 1561 5.363005 GTCAATACCTTTCTACCTCTGGCTA 59.637 44.000 0.00 0.00 0.00 3.93
1497 1562 5.363005 TCAATACCTTTCTACCTCTGGCTAC 59.637 44.000 0.00 0.00 0.00 3.58
1498 1563 2.100989 ACCTTTCTACCTCTGGCTACG 58.899 52.381 0.00 0.00 0.00 3.51
1499 1564 2.100989 CCTTTCTACCTCTGGCTACGT 58.899 52.381 0.00 0.00 0.00 3.57
1500 1565 2.099427 CCTTTCTACCTCTGGCTACGTC 59.901 54.545 0.00 0.00 0.00 4.34
1501 1566 1.760192 TTCTACCTCTGGCTACGTCC 58.240 55.000 0.00 0.00 0.00 4.79
1502 1567 0.622136 TCTACCTCTGGCTACGTCCA 59.378 55.000 0.00 0.00 34.42 4.02
1503 1568 1.214673 TCTACCTCTGGCTACGTCCAT 59.785 52.381 0.00 0.00 35.22 3.41
1533 1598 4.659111 TTCAGTTCAAGACTAACGTGGA 57.341 40.909 0.00 0.00 36.65 4.02
1558 1623 5.365025 ACACACTCTACTATGCCAGATTGAT 59.635 40.000 0.00 0.00 0.00 2.57
1618 1683 0.166814 GACTCGCACAACTCATTGCC 59.833 55.000 0.00 0.00 39.66 4.52
1682 1747 5.114081 ACCAACACTACTCAAAGTACACAC 58.886 41.667 0.00 0.00 0.00 3.82
1745 1811 6.587608 CCTACTGTTTTTCTCATGCCAATTTC 59.412 38.462 0.00 0.00 0.00 2.17
1801 1867 7.822822 GGGACTAACTGTATTTTCAGTACATGT 59.177 37.037 2.69 2.69 46.25 3.21
1811 1877 9.005777 GTATTTTCAGTACATGTGGTCCTTTTA 57.994 33.333 9.11 0.00 0.00 1.52
2000 2069 8.296713 ACTTAACGTTAACGGATAACTCTGTTA 58.703 33.333 29.81 13.24 46.79 2.41
2053 2122 9.440773 TCAGATTGATATATACTGCAATCCAAC 57.559 33.333 20.32 6.93 44.64 3.77
2057 2126 8.837788 TTGATATATACTGCAATCCAACTCAG 57.162 34.615 0.00 0.00 0.00 3.35
2152 2247 8.974060 TTTTCCTAACAAGTAGTGAAATGAGT 57.026 30.769 0.00 0.00 33.10 3.41
2155 2250 9.653287 TTCCTAACAAGTAGTGAAATGAGTATG 57.347 33.333 0.00 0.00 0.00 2.39
2156 2251 7.764443 TCCTAACAAGTAGTGAAATGAGTATGC 59.236 37.037 0.00 0.00 0.00 3.14
2157 2252 7.766278 CCTAACAAGTAGTGAAATGAGTATGCT 59.234 37.037 0.00 0.00 0.00 3.79
2158 2253 6.974932 ACAAGTAGTGAAATGAGTATGCTG 57.025 37.500 0.00 0.00 0.00 4.41
2159 2254 6.467677 ACAAGTAGTGAAATGAGTATGCTGT 58.532 36.000 0.00 0.00 0.00 4.40
2160 2255 6.936900 ACAAGTAGTGAAATGAGTATGCTGTT 59.063 34.615 0.00 0.00 0.00 3.16
2161 2256 8.094548 ACAAGTAGTGAAATGAGTATGCTGTTA 58.905 33.333 0.00 0.00 0.00 2.41
2162 2257 8.598924 CAAGTAGTGAAATGAGTATGCTGTTAG 58.401 37.037 0.00 0.00 0.00 2.34
2163 2258 6.758886 AGTAGTGAAATGAGTATGCTGTTAGC 59.241 38.462 0.00 0.00 42.82 3.09
2177 2272 0.541863 GTTAGCAGGCTAAGGCAGGA 59.458 55.000 13.66 0.00 38.95 3.86
2179 2274 0.761187 TAGCAGGCTAAGGCAGGATG 59.239 55.000 0.00 0.00 40.87 3.51
2180 2275 1.527844 GCAGGCTAAGGCAGGATGG 60.528 63.158 0.00 0.00 40.87 3.51
2181 2276 1.918253 CAGGCTAAGGCAGGATGGT 59.082 57.895 0.00 0.00 40.87 3.55
2182 2277 0.257039 CAGGCTAAGGCAGGATGGTT 59.743 55.000 0.00 0.00 40.87 3.67
2184 2279 1.064389 AGGCTAAGGCAGGATGGTTTC 60.064 52.381 0.00 0.00 40.87 2.78
2185 2280 1.064389 GGCTAAGGCAGGATGGTTTCT 60.064 52.381 0.00 0.00 40.87 2.52
2186 2281 2.621668 GGCTAAGGCAGGATGGTTTCTT 60.622 50.000 0.00 0.00 40.87 2.52
2187 2282 3.092301 GCTAAGGCAGGATGGTTTCTTT 58.908 45.455 0.00 0.00 38.54 2.52
2188 2283 3.119352 GCTAAGGCAGGATGGTTTCTTTG 60.119 47.826 0.00 0.00 38.54 2.77
2189 2284 2.978156 AGGCAGGATGGTTTCTTTGA 57.022 45.000 0.00 0.00 35.86 2.69
2190 2285 3.463048 AGGCAGGATGGTTTCTTTGAT 57.537 42.857 0.00 0.00 35.86 2.57
2191 2286 3.782992 AGGCAGGATGGTTTCTTTGATT 58.217 40.909 0.00 0.00 35.86 2.57
2192 2287 4.934356 AGGCAGGATGGTTTCTTTGATTA 58.066 39.130 0.00 0.00 35.86 1.75
2193 2288 5.332743 AGGCAGGATGGTTTCTTTGATTAA 58.667 37.500 0.00 0.00 35.86 1.40
2194 2289 5.960202 AGGCAGGATGGTTTCTTTGATTAAT 59.040 36.000 0.00 0.00 35.86 1.40
2195 2290 6.097412 AGGCAGGATGGTTTCTTTGATTAATC 59.903 38.462 8.60 8.60 35.86 1.75
2212 2307 9.941325 TTGATTAATCCAAACTTATGCACAATT 57.059 25.926 12.90 0.00 0.00 2.32
2246 2341 9.020731 GTTCTCAACCTATAGGGAAATGAAAAA 57.979 33.333 22.91 13.56 40.27 1.94
2342 2437 3.073062 GGGCATCTGATATGTACCAGGTT 59.927 47.826 0.00 0.00 0.00 3.50
2492 2587 4.630894 ACTCGTGCAAATGACTGAAAAA 57.369 36.364 0.00 0.00 0.00 1.94
2556 2651 1.771565 TATCCCCGTCACCTGTACAG 58.228 55.000 16.34 16.34 0.00 2.74
2637 2732 5.118642 AGAATGAAGAAGCAAGCTCAAAC 57.881 39.130 0.00 0.00 0.00 2.93
2930 3028 6.873605 CCATTTAAAGAATCCAAAGGGTTCAC 59.126 38.462 11.32 0.00 30.48 3.18
3053 3410 7.202526 TGTTAAAATTGTTGAAGCTCAGAAGG 58.797 34.615 0.00 0.00 0.00 3.46
3111 3468 3.264193 ACATTGTGGAGGTAGCAGATCAA 59.736 43.478 0.00 0.00 0.00 2.57
3137 3494 9.744468 AAACAACCATTTTTAGTTCTATGTGTC 57.256 29.630 0.00 0.00 0.00 3.67
3166 3523 3.141398 TGTTTCCTCATGTGAACAGAGC 58.859 45.455 0.00 0.00 0.00 4.09
3197 3554 1.399791 GAGCTTCATGCACTAGCCAAC 59.600 52.381 11.63 2.91 45.94 3.77
3255 3612 8.846943 AGACAATTCACATATACACTTCAACA 57.153 30.769 0.00 0.00 0.00 3.33
3289 3646 2.654912 GACGCGGGAAGACAACACG 61.655 63.158 12.47 0.00 0.00 4.49
3415 3772 5.540337 CCTTAGGCTCTGATACCATGTTAGA 59.460 44.000 0.00 0.00 0.00 2.10
3448 3805 0.593773 CCAACGCAACCAAAAGTCCG 60.594 55.000 0.00 0.00 0.00 4.79
3462 3819 5.472137 CCAAAAGTCCGAACTTATGGAAAGA 59.528 40.000 0.00 0.00 45.07 2.52
3463 3820 6.016610 CCAAAAGTCCGAACTTATGGAAAGAA 60.017 38.462 0.00 0.00 45.07 2.52
3596 3954 6.937465 GGGAAAAGACCACTTATATCTCATCC 59.063 42.308 0.00 0.00 35.05 3.51
3615 3973 1.568606 CAGGACAGATGATGCAGTCG 58.431 55.000 0.00 0.00 31.93 4.18
3620 3978 3.312828 GACAGATGATGCAGTCGGTATC 58.687 50.000 0.00 0.00 38.90 2.24
3722 4080 3.070576 GGCATCCACTTGGTGCCC 61.071 66.667 21.91 10.67 46.88 5.36
3753 4111 4.613925 ATGGTATGGTCATCTGTGCTAG 57.386 45.455 0.00 0.00 0.00 3.42
3820 4178 5.023533 TGGTATCATACAGGAAGAAGCAC 57.976 43.478 0.00 0.00 0.00 4.40
3823 4181 6.183360 TGGTATCATACAGGAAGAAGCACTAC 60.183 42.308 0.00 0.00 0.00 2.73
3907 4265 4.935808 AGGGACATGACGAATCTAACAAAC 59.064 41.667 0.00 0.00 0.00 2.93
3919 4277 3.271729 TCTAACAAACGTGACAAAGCCA 58.728 40.909 0.00 0.00 0.00 4.75
3922 4280 1.135517 ACAAACGTGACAAAGCCACAC 60.136 47.619 0.00 0.00 34.36 3.82
3923 4281 1.135546 CAAACGTGACAAAGCCACACA 60.136 47.619 0.00 0.00 34.36 3.72
3924 4282 0.732571 AACGTGACAAAGCCACACAG 59.267 50.000 0.00 0.00 34.36 3.66
4019 4377 6.426646 AGTAGCATCCCTTTTATAGACCAG 57.573 41.667 0.00 0.00 0.00 4.00
4078 4436 4.773323 AAGAATGTTCTTGCAGGCTAAC 57.227 40.909 7.18 0.00 45.27 2.34
4091 4449 3.437049 GCAGGCTAACGTTTCAGAAGATT 59.563 43.478 5.91 0.00 0.00 2.40
4141 4499 7.556844 GGAAACAGATTGAGGAGATACTTACA 58.443 38.462 0.00 0.00 0.00 2.41
4178 4536 7.228507 TGGAGATTGACGAAATGAAAAGAAGAA 59.771 33.333 0.00 0.00 0.00 2.52
4184 4542 8.771920 TGACGAAATGAAAAGAAGAAGCTATA 57.228 30.769 0.00 0.00 0.00 1.31
4411 4769 3.012518 TCTTTAGTACTCCCTCCGTTCG 58.987 50.000 0.00 0.00 0.00 3.95
4428 4786 3.685058 GTTCGGAAATAAGTGATGCTGC 58.315 45.455 0.00 0.00 0.00 5.25
4464 4822 3.602390 AAACAACGTCACTCATTTCCG 57.398 42.857 0.00 0.00 0.00 4.30
4467 4825 2.542595 ACAACGTCACTCATTTCCGAAC 59.457 45.455 0.00 0.00 0.00 3.95
4471 4829 1.993370 GTCACTCATTTCCGAACGGAG 59.007 52.381 15.34 6.93 46.06 4.63
4483 4841 7.581213 TTTCCGAACGGAGGTAATAGTATAA 57.419 36.000 15.34 0.97 46.06 0.98
4512 4870 8.840867 CAACTTAGAAGTGCGTGAATAAAATTC 58.159 33.333 0.00 0.00 39.66 2.17
4568 4926 0.320946 TACCAAAACGAGAAGGGGCG 60.321 55.000 0.00 0.00 0.00 6.13
4677 5035 9.346725 GAGCTAAAAGATTTAAAGGAACACATG 57.653 33.333 0.00 0.00 0.00 3.21
4682 5040 6.899393 AGATTTAAAGGAACACATGCTCAA 57.101 33.333 0.00 0.00 0.00 3.02
4756 5114 9.689976 ATGAGATCGTATAGAAAATCTGACTTG 57.310 33.333 0.00 0.00 0.00 3.16
4781 5148 4.813296 CTTTATTAAGGATGTGCCCGAC 57.187 45.455 0.00 0.00 37.37 4.79
4847 5214 8.267183 TCAGCTCTTGAAATGGTAAGATATTGA 58.733 33.333 0.00 0.00 32.92 2.57
4914 5281 7.769044 TGTGGATTGCTCTTATAGGTTAAAGAC 59.231 37.037 0.00 0.00 0.00 3.01
4926 5293 3.809905 GGTTAAAGACCTAGAGCATGGG 58.190 50.000 0.00 0.00 45.55 4.00
4949 5316 2.168326 TTGCGTGAGATGAGAAAGCA 57.832 45.000 0.00 0.00 0.00 3.91
4955 5322 4.240888 CGTGAGATGAGAAAGCAGAAAGA 58.759 43.478 0.00 0.00 0.00 2.52
4968 5335 1.349026 CAGAAAGAAGTGGAGGAGGCA 59.651 52.381 0.00 0.00 0.00 4.75
5006 5373 4.889409 GGAGGAAATTCAGGCAATGATACA 59.111 41.667 0.00 0.00 37.89 2.29
5071 5438 5.894807 AGTCGGCCATAAAATTTCATGAAG 58.105 37.500 8.41 0.00 0.00 3.02
5163 5530 2.099921 AGATACTGCAGTAACAGAGGCG 59.900 50.000 29.26 0.00 40.25 5.52
5224 5591 2.030371 TCTCACTATCTGAGCTGCAGG 58.970 52.381 17.12 0.00 45.64 4.85
5347 5714 3.795150 GCTTCATTGTCAACGCCTTCAAA 60.795 43.478 0.00 0.00 0.00 2.69
5516 5883 4.454678 TGTTTATAGGAGCATGCCAAGAG 58.545 43.478 15.66 0.00 0.00 2.85
5540 5907 0.620556 CTGGTTCTGGCCTGGTGTAT 59.379 55.000 10.07 0.00 0.00 2.29
5663 6030 1.717194 TATGGTCGGCTTTGACGTTC 58.283 50.000 0.00 0.00 39.83 3.95
5696 6063 1.302907 AGCCTCTCCCCATTGTTCAT 58.697 50.000 0.00 0.00 0.00 2.57
5717 6084 2.007608 GGTGATCTAAAGCCGGACAAC 58.992 52.381 5.05 0.00 0.00 3.32
5759 6126 4.077300 TGTGAGCAAGTTGAGAATCTGT 57.923 40.909 7.16 0.00 34.92 3.41
5777 6144 3.818773 TCTGTCAGGTTTCGAAAAATCCC 59.181 43.478 13.10 9.62 0.00 3.85
5862 6320 3.181507 CGATGTGTACTCCTTTGGCATTG 60.182 47.826 0.00 0.00 0.00 2.82
5912 6370 1.529438 TCGCAAAAGATCGTTGTGACC 59.471 47.619 18.70 2.50 39.82 4.02
5933 6391 3.682858 CCGTAGAAAAAGCGATGGAGAAA 59.317 43.478 0.00 0.00 0.00 2.52
5992 6450 2.828549 GCCATACCAACAGGCCGG 60.829 66.667 0.00 0.00 42.58 6.13
6012 6470 2.046892 AGCTTGCGCGTCTTGGAT 60.047 55.556 8.43 0.00 42.32 3.41
6040 6498 0.846693 ACCAACTTGAGTGGGAAGCT 59.153 50.000 11.54 0.00 41.85 3.74
6058 6516 5.512232 GGAAGCTCCAACCAGATCTTATAGG 60.512 48.000 0.00 0.00 36.28 2.57
6077 6535 2.936032 GGGGTGTGGGGAGAGCTT 60.936 66.667 0.00 0.00 0.00 3.74
6102 6560 3.764160 CTGATGAAGGCCGCCTCCC 62.764 68.421 13.72 8.59 30.89 4.30
6159 6617 0.531753 TGACACACACACACCATCCG 60.532 55.000 0.00 0.00 0.00 4.18
6181 6639 2.159734 GCTTTGTCTGTGCAATCTCTCG 60.160 50.000 0.00 0.00 0.00 4.04
6209 6667 4.702131 AGTAAGGATTCACAAACTGCATCC 59.298 41.667 0.00 0.00 34.64 3.51
6296 6754 0.036732 GGTGAACAGGAGGTGATGCA 59.963 55.000 0.00 0.00 0.00 3.96
6303 6761 0.622738 AGGAGGTGATGCATGACCCT 60.623 55.000 28.98 18.22 34.31 4.34
6426 6884 1.026718 GCGATCTCACCCCAAACAGG 61.027 60.000 0.00 0.00 37.03 4.00
6441 6899 4.473520 AGGGCACTCCATTCGGCG 62.474 66.667 0.00 0.00 38.24 6.46
6502 6960 4.991153 TGACTACATGAGGATCTGTCAC 57.009 45.455 0.00 0.00 34.92 3.67
6503 6961 3.378427 TGACTACATGAGGATCTGTCACG 59.622 47.826 0.00 0.00 34.92 4.35
6513 6979 2.610433 GATCTGTCACGAACTGCATCA 58.390 47.619 0.00 0.00 0.00 3.07
6604 7070 1.803334 TACGCAAGCAAAACCGATCT 58.197 45.000 0.00 0.00 45.62 2.75
6617 7083 6.296026 CAAAACCGATCTATTCATTCCCCTA 58.704 40.000 0.00 0.00 0.00 3.53
6620 7086 3.838317 CCGATCTATTCATTCCCCTACCA 59.162 47.826 0.00 0.00 0.00 3.25
6682 7148 3.461773 CCGATGAGCCCGTGGACT 61.462 66.667 0.00 0.00 0.00 3.85
6683 7149 2.105128 CGATGAGCCCGTGGACTC 59.895 66.667 0.00 0.00 0.00 3.36
6684 7150 2.710902 CGATGAGCCCGTGGACTCA 61.711 63.158 7.39 7.39 46.34 3.41
6685 7151 1.153549 GATGAGCCCGTGGACTCAC 60.154 63.158 7.08 0.00 45.19 3.51
6686 7152 2.579684 GATGAGCCCGTGGACTCACC 62.580 65.000 7.08 0.00 45.19 4.02
6687 7153 2.997897 GAGCCCGTGGACTCACCT 60.998 66.667 0.00 0.00 40.65 4.00
6688 7154 2.997897 AGCCCGTGGACTCACCTC 60.998 66.667 0.00 0.00 40.65 3.85
6689 7155 4.083862 GCCCGTGGACTCACCTCC 62.084 72.222 0.00 0.00 40.65 4.30
6690 7156 2.283966 CCCGTGGACTCACCTCCT 60.284 66.667 0.00 0.00 40.65 3.69
6691 7157 2.352032 CCCGTGGACTCACCTCCTC 61.352 68.421 0.00 0.00 40.65 3.71
6692 7158 1.304547 CCGTGGACTCACCTCCTCT 60.305 63.158 0.00 0.00 40.65 3.69
6693 7159 1.316706 CCGTGGACTCACCTCCTCTC 61.317 65.000 0.00 0.00 40.65 3.20
6694 7160 0.322997 CGTGGACTCACCTCCTCTCT 60.323 60.000 0.00 0.00 40.65 3.10
6695 7161 1.065345 CGTGGACTCACCTCCTCTCTA 60.065 57.143 0.00 0.00 40.65 2.43
6696 7162 2.422235 CGTGGACTCACCTCCTCTCTAT 60.422 54.545 0.00 0.00 40.65 1.98
6697 7163 3.219281 GTGGACTCACCTCCTCTCTATC 58.781 54.545 0.00 0.00 37.92 2.08
6698 7164 3.117663 GTGGACTCACCTCCTCTCTATCT 60.118 52.174 0.00 0.00 37.92 1.98
6699 7165 3.117701 TGGACTCACCTCCTCTCTATCTG 60.118 52.174 0.00 0.00 39.86 2.90
6700 7166 2.884639 GACTCACCTCCTCTCTATCTGC 59.115 54.545 0.00 0.00 0.00 4.26
6701 7167 2.238521 CTCACCTCCTCTCTATCTGCC 58.761 57.143 0.00 0.00 0.00 4.85
6702 7168 0.958091 CACCTCCTCTCTATCTGCCG 59.042 60.000 0.00 0.00 0.00 5.69
6703 7169 0.825840 ACCTCCTCTCTATCTGCCGC 60.826 60.000 0.00 0.00 0.00 6.53
6704 7170 0.539438 CCTCCTCTCTATCTGCCGCT 60.539 60.000 0.00 0.00 0.00 5.52
6705 7171 0.881118 CTCCTCTCTATCTGCCGCTC 59.119 60.000 0.00 0.00 0.00 5.03
6706 7172 0.538516 TCCTCTCTATCTGCCGCTCC 60.539 60.000 0.00 0.00 0.00 4.70
6707 7173 0.825425 CCTCTCTATCTGCCGCTCCA 60.825 60.000 0.00 0.00 0.00 3.86
6708 7174 0.597568 CTCTCTATCTGCCGCTCCAG 59.402 60.000 0.00 0.00 0.00 3.86
6709 7175 1.006337 CTCTATCTGCCGCTCCAGC 60.006 63.158 0.00 0.00 32.87 4.85
6798 7264 8.950007 AAGATAAAAACCAAACAGATCCCTAA 57.050 30.769 0.00 0.00 0.00 2.69
6875 7341 2.294512 CACTTCCTTGGCTGAGAAAACC 59.705 50.000 0.00 0.00 0.00 3.27
6944 7410 9.502091 TCAAAGTATGCAAACACTCTTACTAAT 57.498 29.630 0.00 0.00 0.00 1.73
7056 7522 5.014202 AGGGTTGTATTATGAACGGCTTTT 58.986 37.500 0.00 0.00 0.00 2.27
7136 7602 2.986728 AGACAAGTTCAGGGGGTAATGT 59.013 45.455 0.00 0.00 0.00 2.71
7284 7754 0.952497 CTTGTGCAGCTCCGACATGT 60.952 55.000 0.00 0.00 0.00 3.21
7285 7755 1.229975 TTGTGCAGCTCCGACATGTG 61.230 55.000 1.15 0.00 0.00 3.21
7306 7776 2.610232 GGGCGAACTCAAAAACATGCAT 60.610 45.455 0.00 0.00 0.00 3.96
7409 7879 1.215244 CATCATGCTCCTGTACTGCG 58.785 55.000 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.999507 ACTTTTTGTCACGTGCACAA 57.000 40.000 21.64 21.64 31.76 3.33
97 98 4.573201 CACTTTTTGACCACTAGTTTCGGA 59.427 41.667 4.80 0.00 0.00 4.55
100 101 4.097286 TGGCACTTTTTGACCACTAGTTTC 59.903 41.667 0.00 0.00 28.00 2.78
132 133 8.701895 CATACCTTTATCTAGTACTGGTTTGGA 58.298 37.037 5.39 0.00 0.00 3.53
207 209 9.905713 AGCTTAGTTGGTTCATTCAGATTATTA 57.094 29.630 0.00 0.00 0.00 0.98
210 212 7.769044 GGTAGCTTAGTTGGTTCATTCAGATTA 59.231 37.037 0.00 0.00 0.00 1.75
217 219 8.823220 AATATTGGTAGCTTAGTTGGTTCATT 57.177 30.769 0.00 0.00 0.00 2.57
224 226 6.238648 CCCGGAAAATATTGGTAGCTTAGTTG 60.239 42.308 0.73 0.00 0.00 3.16
296 331 7.711772 AGTTGCTCATTCAATGTTTTGATTCAA 59.288 29.630 0.00 0.00 41.38 2.69
297 332 7.211573 AGTTGCTCATTCAATGTTTTGATTCA 58.788 30.769 0.00 0.00 41.38 2.57
307 342 8.922058 AAAAAGCTATAGTTGCTCATTCAATG 57.078 30.769 0.84 0.00 40.22 2.82
386 430 6.115446 ACACGATTTCTAATGGTCACATCAT 58.885 36.000 0.00 0.00 35.94 2.45
412 456 6.538021 GCTCCAATCCATCATATGACTATGTC 59.462 42.308 7.78 0.00 36.80 3.06
512 566 6.018180 ACGCATCCGATTTAATAAAGGAACTC 60.018 38.462 0.00 0.00 36.19 3.01
517 571 6.370442 TCCATACGCATCCGATTTAATAAAGG 59.630 38.462 0.00 0.00 38.29 3.11
522 576 5.122239 CACATCCATACGCATCCGATTTAAT 59.878 40.000 0.00 0.00 38.29 1.40
523 577 4.450757 CACATCCATACGCATCCGATTTAA 59.549 41.667 0.00 0.00 38.29 1.52
528 582 0.750249 ACACATCCATACGCATCCGA 59.250 50.000 0.00 0.00 38.29 4.55
530 584 4.574828 ACTAAAACACATCCATACGCATCC 59.425 41.667 0.00 0.00 0.00 3.51
536 590 7.589954 GTGAAACACACTAAAACACATCCATAC 59.410 37.037 0.00 0.00 45.13 2.39
650 705 5.293814 CACAAACCACAAATTGCTGATTTCA 59.706 36.000 0.00 0.00 35.79 2.69
652 707 4.035441 GCACAAACCACAAATTGCTGATTT 59.965 37.500 0.00 0.00 38.49 2.17
653 708 3.560896 GCACAAACCACAAATTGCTGATT 59.439 39.130 0.00 0.00 0.00 2.57
659 714 5.066246 AGGAAATTGCACAAACCACAAATTG 59.934 36.000 0.00 0.00 0.00 2.32
660 715 5.192176 AGGAAATTGCACAAACCACAAATT 58.808 33.333 0.00 0.00 0.00 1.82
689 744 3.388345 AACGACCTTGTCTTCTCTTCC 57.612 47.619 0.00 0.00 0.00 3.46
701 756 1.599797 CCCCGAGCAAAACGACCTT 60.600 57.895 0.00 0.00 0.00 3.50
723 778 0.947180 CAGCAACAGCAACCATTGGC 60.947 55.000 1.54 0.00 0.00 4.52
793 851 0.950836 CAAATGTTGGTCGCACCTCA 59.049 50.000 6.83 6.57 39.58 3.86
821 879 2.667418 CCAGCCAGGTGGACTCAG 59.333 66.667 10.40 0.00 40.44 3.35
839 897 3.177194 TTGCCGTGTGGAGGTGGAG 62.177 63.158 0.00 0.00 37.49 3.86
840 898 3.164977 TTGCCGTGTGGAGGTGGA 61.165 61.111 0.00 0.00 37.49 4.02
841 899 2.978010 GTTGCCGTGTGGAGGTGG 60.978 66.667 0.00 0.00 37.49 4.61
842 900 1.600636 ATGTTGCCGTGTGGAGGTG 60.601 57.895 0.00 0.00 37.49 4.00
843 901 1.600636 CATGTTGCCGTGTGGAGGT 60.601 57.895 0.00 0.00 37.49 3.85
844 902 1.172180 AACATGTTGCCGTGTGGAGG 61.172 55.000 11.07 0.00 39.93 4.30
902 966 5.035443 GGTCAGTGCTCAGTATACTTAACG 58.965 45.833 1.56 0.00 0.00 3.18
957 1021 1.474478 GATGAGAGAGCCGTGTGAGAA 59.526 52.381 0.00 0.00 0.00 2.87
1021 1085 1.773496 CGCTCCAAAACGTCTCGTC 59.227 57.895 0.00 0.00 39.99 4.20
1050 1114 2.415010 CCCGTCGATGAGCTGAGG 59.585 66.667 6.11 0.00 0.00 3.86
1129 1193 0.716108 CCTTCGTTGACATCGTCTGC 59.284 55.000 5.86 0.00 33.15 4.26
1302 1366 2.710096 ACCCCCACTGAAACATATCG 57.290 50.000 0.00 0.00 0.00 2.92
1306 1370 2.897326 GCTTTTACCCCCACTGAAACAT 59.103 45.455 0.00 0.00 0.00 2.71
1354 1419 5.880332 TGTAAGTTTCTATGATTGCTGACCC 59.120 40.000 0.00 0.00 0.00 4.46
1389 1454 1.064463 TCCATCCATGTTCTTCCCTGC 60.064 52.381 0.00 0.00 0.00 4.85
1408 1473 1.599542 GTTTCGCTGTCAGGGCATATC 59.400 52.381 11.94 0.00 0.00 1.63
1437 1502 8.558973 AAATTGAGTTGAACCTCTAGATCTTG 57.441 34.615 0.00 0.00 32.50 3.02
1491 1556 0.678684 TCGAGTGATGGACGTAGCCA 60.679 55.000 0.00 0.00 43.23 4.75
1492 1557 0.454600 TTCGAGTGATGGACGTAGCC 59.545 55.000 0.00 0.00 0.00 3.93
1493 1558 2.493713 ATTCGAGTGATGGACGTAGC 57.506 50.000 0.00 0.00 0.00 3.58
1494 1559 4.028852 TGAATTCGAGTGATGGACGTAG 57.971 45.455 0.04 0.00 0.00 3.51
1495 1560 3.442625 ACTGAATTCGAGTGATGGACGTA 59.557 43.478 9.00 0.00 0.00 3.57
1496 1561 2.231478 ACTGAATTCGAGTGATGGACGT 59.769 45.455 9.00 0.00 0.00 4.34
1497 1562 2.881074 ACTGAATTCGAGTGATGGACG 58.119 47.619 9.00 0.00 0.00 4.79
1498 1563 4.245660 TGAACTGAATTCGAGTGATGGAC 58.754 43.478 10.14 0.00 40.56 4.02
1499 1564 4.535526 TGAACTGAATTCGAGTGATGGA 57.464 40.909 10.14 0.00 40.56 3.41
1500 1565 4.931601 TCTTGAACTGAATTCGAGTGATGG 59.068 41.667 10.14 4.39 45.82 3.51
1501 1566 5.636965 AGTCTTGAACTGAATTCGAGTGATG 59.363 40.000 10.14 5.02 45.82 3.07
1502 1567 5.788450 AGTCTTGAACTGAATTCGAGTGAT 58.212 37.500 10.14 0.00 45.82 3.06
1503 1568 5.201713 AGTCTTGAACTGAATTCGAGTGA 57.798 39.130 10.14 3.02 45.82 3.41
1533 1598 5.187772 TCAATCTGGCATAGTAGAGTGTGTT 59.812 40.000 0.00 0.00 39.34 3.32
1558 1623 4.971939 TCTCAATCACCACTTCATCACAA 58.028 39.130 0.00 0.00 0.00 3.33
1637 1702 0.737219 GCAGCTGCTCCCATTACAAG 59.263 55.000 31.33 0.00 38.21 3.16
1700 1765 3.933879 CCTTTTGGGGGAAATGCAC 57.066 52.632 0.00 0.00 35.46 4.57
1720 1785 5.649782 ATTGGCATGAGAAAAACAGTAGG 57.350 39.130 0.00 0.00 0.00 3.18
1723 1789 5.987347 CAGAAATTGGCATGAGAAAAACAGT 59.013 36.000 0.00 0.00 0.00 3.55
1745 1811 2.481952 GTGCTGCCTGTTCTAGAAACAG 59.518 50.000 19.75 19.75 45.33 3.16
1801 1867 0.752054 ACCGTGTCGTAAAAGGACCA 59.248 50.000 0.00 0.00 32.42 4.02
1811 1877 5.063180 TCTATGTTGAAATACCGTGTCGT 57.937 39.130 0.00 0.00 0.00 4.34
1891 1957 6.542852 GCTTCATCACTTAATTTTACTCGCA 58.457 36.000 0.00 0.00 0.00 5.10
1892 1958 5.672856 CGCTTCATCACTTAATTTTACTCGC 59.327 40.000 0.00 0.00 0.00 5.03
2034 2103 7.875041 ACACTGAGTTGGATTGCAGTATATATC 59.125 37.037 0.00 0.00 39.40 1.63
2099 2194 8.621532 AGTTTGAAAATGCAGTCTCTACATTA 57.378 30.769 0.00 0.00 33.01 1.90
2103 2198 8.634475 AAAAAGTTTGAAAATGCAGTCTCTAC 57.366 30.769 0.00 0.00 0.00 2.59
2152 2247 5.016069 TGCCTTAGCCTGCTAACAGCATA 62.016 47.826 19.99 6.49 43.63 3.14
2153 2248 4.337184 TGCCTTAGCCTGCTAACAGCAT 62.337 50.000 19.99 0.00 43.63 3.79
2154 2249 3.062852 TGCCTTAGCCTGCTAACAGCA 62.063 52.381 19.99 19.99 44.01 4.41
2155 2250 0.392998 TGCCTTAGCCTGCTAACAGC 60.393 55.000 16.63 16.63 43.02 4.40
2156 2251 1.661341 CTGCCTTAGCCTGCTAACAG 58.339 55.000 7.49 10.38 44.05 3.16
2157 2252 0.253044 CCTGCCTTAGCCTGCTAACA 59.747 55.000 7.49 5.05 38.69 2.41
2158 2253 0.541863 TCCTGCCTTAGCCTGCTAAC 59.458 55.000 7.49 0.71 38.69 2.34
2159 2254 1.141657 CATCCTGCCTTAGCCTGCTAA 59.858 52.381 10.89 10.89 38.69 3.09
2160 2255 0.761187 CATCCTGCCTTAGCCTGCTA 59.239 55.000 0.00 0.00 38.69 3.49
2161 2256 1.530771 CATCCTGCCTTAGCCTGCT 59.469 57.895 0.00 0.00 38.69 4.24
2162 2257 1.527844 CCATCCTGCCTTAGCCTGC 60.528 63.158 0.00 0.00 38.69 4.85
2163 2258 0.257039 AACCATCCTGCCTTAGCCTG 59.743 55.000 0.00 0.00 38.69 4.85
2182 2277 9.638239 GTGCATAAGTTTGGATTAATCAAAGAA 57.362 29.630 17.07 3.42 35.16 2.52
2184 2279 8.984891 TGTGCATAAGTTTGGATTAATCAAAG 57.015 30.769 17.07 0.96 35.16 2.77
2185 2280 9.941325 ATTGTGCATAAGTTTGGATTAATCAAA 57.059 25.926 17.07 9.48 0.00 2.69
2186 2281 9.941325 AATTGTGCATAAGTTTGGATTAATCAA 57.059 25.926 17.07 2.74 0.00 2.57
2187 2282 9.941325 AAATTGTGCATAAGTTTGGATTAATCA 57.059 25.926 17.07 1.07 0.00 2.57
2192 2287 9.553064 TTGTTAAATTGTGCATAAGTTTGGATT 57.447 25.926 14.00 0.00 0.00 3.01
2193 2288 9.723601 ATTGTTAAATTGTGCATAAGTTTGGAT 57.276 25.926 14.00 2.27 0.00 3.41
2194 2289 8.986847 CATTGTTAAATTGTGCATAAGTTTGGA 58.013 29.630 14.00 0.00 0.00 3.53
2195 2290 8.772705 ACATTGTTAAATTGTGCATAAGTTTGG 58.227 29.630 14.00 1.83 0.00 3.28
2212 2307 8.153221 TCCCTATAGGTTGAGAACATTGTTAA 57.847 34.615 17.72 0.00 36.75 2.01
2216 2311 7.775093 TCATTTCCCTATAGGTTGAGAACATTG 59.225 37.037 17.72 10.45 36.75 2.82
2246 2341 0.600255 CGCTGTCTTGGACTTCGGTT 60.600 55.000 0.00 0.00 33.15 4.44
2342 2437 3.454812 GGGATGGACCTTGCTCTACTTTA 59.545 47.826 0.00 0.00 38.98 1.85
2432 2527 8.383175 CAATAAATTGGTCCCTAGGCTAATCTA 58.617 37.037 2.05 0.00 34.22 1.98
2435 2530 6.777580 CACAATAAATTGGTCCCTAGGCTAAT 59.222 38.462 2.05 0.00 41.96 1.73
2492 2587 1.982226 TGCACAGGTATGGTTAGTGGT 59.018 47.619 0.00 0.00 0.00 4.16
2531 2626 0.469917 AGGTGACGGGGATATTGCAG 59.530 55.000 0.00 0.00 0.00 4.41
2556 2651 0.110056 CTGAAGATGGTGTTGTGCGC 60.110 55.000 0.00 0.00 0.00 6.09
2637 2732 6.712241 AACGATGAAGCTGAATTATATCCG 57.288 37.500 0.00 0.00 0.00 4.18
2830 2926 9.471084 AATTTTGGTCCTTTTTCTTGTAATACG 57.529 29.630 0.00 0.00 0.00 3.06
2904 3002 6.556874 TGAACCCTTTGGATTCTTTAAATGGT 59.443 34.615 0.00 0.00 34.97 3.55
2930 3028 7.932120 AAACATAGATCTCCGAGTTTATTCG 57.068 36.000 0.00 0.00 40.18 3.34
3053 3410 7.608761 TGTTGGTTAATTTCTATGGTGTAGACC 59.391 37.037 1.06 1.06 43.48 3.85
3091 3448 4.574674 TTTGATCTGCTACCTCCACAAT 57.425 40.909 0.00 0.00 0.00 2.71
3092 3449 4.072131 GTTTTGATCTGCTACCTCCACAA 58.928 43.478 0.00 0.00 0.00 3.33
3093 3450 3.072330 TGTTTTGATCTGCTACCTCCACA 59.928 43.478 0.00 0.00 0.00 4.17
3111 3468 9.744468 GACACATAGAACTAAAAATGGTTGTTT 57.256 29.630 0.00 0.00 0.00 2.83
3137 3494 5.611796 TCACATGAGGAAACATTTTCTCG 57.388 39.130 0.00 0.00 44.19 4.04
3166 3523 6.154445 AGTGCATGAAGCTCTACAATTTTTG 58.846 36.000 0.00 0.00 44.69 2.44
3197 3554 0.661020 AGTTCGGACTTTTGGTTGCG 59.339 50.000 0.00 0.00 29.87 4.85
3255 3612 2.200370 TCACACGTGAGAGGGGGT 59.800 61.111 25.01 0.00 34.14 4.95
3289 3646 6.902771 TGAGCCATACCTCTAAGTCTATTC 57.097 41.667 0.00 0.00 33.02 1.75
3320 3677 3.100207 CCCCCTTTGTGTCCATGTATT 57.900 47.619 0.00 0.00 0.00 1.89
3368 3725 5.532779 GGTCTTGAGTTCAAATCCTGACTTT 59.467 40.000 7.09 0.00 35.15 2.66
3415 3772 1.133025 GCGTTGGCTAATGCATGAAGT 59.867 47.619 20.82 0.00 45.91 3.01
3448 3805 7.656137 TGTGTGTCTAGTTCTTTCCATAAGTTC 59.344 37.037 0.00 0.00 0.00 3.01
3462 3819 9.371136 CATTGAAGTGTATATGTGTGTCTAGTT 57.629 33.333 0.00 0.00 0.00 2.24
3463 3820 8.749354 TCATTGAAGTGTATATGTGTGTCTAGT 58.251 33.333 0.00 0.00 0.00 2.57
3497 3854 7.393515 GGAGAAAAGGTAAACAGTATGACCAAT 59.606 37.037 0.00 0.00 39.69 3.16
3596 3954 1.568606 CGACTGCATCATCTGTCCTG 58.431 55.000 0.00 0.00 33.18 3.86
3615 3973 1.834263 AGTTGTGGCTCCAGAGATACC 59.166 52.381 0.00 0.00 0.00 2.73
3620 3978 2.039084 AGGTAAAGTTGTGGCTCCAGAG 59.961 50.000 0.00 0.00 0.00 3.35
3722 4080 6.312180 CAGATGACCATACCATATGACATTCG 59.688 42.308 3.65 0.00 35.83 3.34
3823 4181 7.017645 CCGAAATGTGTTTCTTCATCTACAAG 58.982 38.462 0.00 0.00 41.24 3.16
3907 4265 0.813610 TCCTGTGTGGCTTTGTCACG 60.814 55.000 0.00 0.00 41.53 4.35
4019 4377 6.687604 TGGCTAAAAGAGAAACTAATTTGGC 58.312 36.000 0.00 0.00 34.39 4.52
4141 4499 3.181471 CGTCAATCTCCAGCCTCTGTATT 60.181 47.826 0.00 0.00 0.00 1.89
4178 4536 7.937649 TGTAGTTCATCATGTAACGTATAGCT 58.062 34.615 0.00 0.00 0.00 3.32
4184 4542 5.654603 TCCTGTAGTTCATCATGTAACGT 57.345 39.130 0.00 0.00 0.00 3.99
4411 4769 6.442513 ACTAAAGCAGCATCACTTATTTCC 57.557 37.500 0.00 0.00 0.00 3.13
4464 4822 9.978044 AGTTGAATTATACTATTACCTCCGTTC 57.022 33.333 0.00 0.00 0.00 3.95
4483 4841 7.667043 TTATTCACGCACTTCTAAGTTGAAT 57.333 32.000 18.28 18.28 42.30 2.57
4512 4870 3.068590 CCCTGGCCTGCAATAATAGTTTG 59.931 47.826 3.32 0.00 0.00 2.93
4568 4926 1.134521 TCACATCCATGTCTAACCGCC 60.135 52.381 0.00 0.00 39.39 6.13
4774 5141 0.675083 TCTGTTAGTTTCGTCGGGCA 59.325 50.000 0.00 0.00 0.00 5.36
4778 5145 5.117287 CCTTCTTCTTCTGTTAGTTTCGTCG 59.883 44.000 0.00 0.00 0.00 5.12
4781 5148 4.152580 GCCCTTCTTCTTCTGTTAGTTTCG 59.847 45.833 0.00 0.00 0.00 3.46
4847 5214 5.079643 AGTTTGTAACTGGGAGCAATGAAT 58.920 37.500 0.00 0.00 41.01 2.57
4914 5281 1.605710 CGCAAAATCCCATGCTCTAGG 59.394 52.381 0.00 0.00 40.39 3.02
4926 5293 4.094212 GCTTTCTCATCTCACGCAAAATC 58.906 43.478 0.00 0.00 0.00 2.17
4949 5316 1.349357 GTGCCTCCTCCACTTCTTTCT 59.651 52.381 0.00 0.00 0.00 2.52
4955 5322 1.001641 GCATGTGCCTCCTCCACTT 60.002 57.895 0.00 0.00 34.38 3.16
4968 5335 0.107017 CCTCCTCCCGAATTGCATGT 60.107 55.000 0.00 0.00 0.00 3.21
5006 5373 4.843220 GCATTTATATCTGCCAGCTGTT 57.157 40.909 13.81 0.00 32.15 3.16
5052 5419 6.478016 GCTCTTCTTCATGAAATTTTATGGCC 59.522 38.462 19.47 0.00 33.79 5.36
5071 5438 4.737279 GTGTTTGCTCTTTTCAAGCTCTTC 59.263 41.667 0.00 0.00 40.50 2.87
5163 5530 6.670689 GCTTATTCTTTTGCCGCAATTCTTTC 60.671 38.462 6.64 0.00 0.00 2.62
5347 5714 5.709164 CCTCTTGATGGAATTCTTGTTGTCT 59.291 40.000 5.23 0.00 0.00 3.41
5419 5786 6.203530 CGATGCCATGATGATGTTACTACTTT 59.796 38.462 0.00 0.00 0.00 2.66
5420 5787 5.698089 CGATGCCATGATGATGTTACTACTT 59.302 40.000 0.00 0.00 0.00 2.24
5516 5883 1.676967 CAGGCCAGAACCAGAAGCC 60.677 63.158 5.01 0.00 44.20 4.35
5663 6030 0.393537 GAGGCTTGTGGGAGTGGATG 60.394 60.000 0.00 0.00 0.00 3.51
5696 6063 1.271856 TGTCCGGCTTTAGATCACCA 58.728 50.000 0.00 0.00 0.00 4.17
5717 6084 7.077605 TCACAAAATTAGCGTCAAGAAGAATG 58.922 34.615 0.00 0.00 0.00 2.67
5759 6126 3.153919 CCTGGGATTTTTCGAAACCTGA 58.846 45.455 10.79 0.00 0.00 3.86
5777 6144 2.270352 TAGTGTTCTTTGTGGCCCTG 57.730 50.000 0.00 0.00 0.00 4.45
5862 6320 0.528684 GTCAGCAGGCGTAGGATGAC 60.529 60.000 5.31 5.31 42.29 3.06
5912 6370 4.201724 CCTTTCTCCATCGCTTTTTCTACG 60.202 45.833 0.00 0.00 0.00 3.51
5933 6391 0.630673 TAATGGAATGCAGGTGCCCT 59.369 50.000 0.00 0.00 41.18 5.19
6006 6464 3.087031 AGTTGGTGCATCTCAATCCAAG 58.913 45.455 0.00 0.00 38.57 3.61
6012 6470 2.880268 CACTCAAGTTGGTGCATCTCAA 59.120 45.455 2.34 0.00 0.00 3.02
6040 6498 3.598264 CCCCCTATAAGATCTGGTTGGA 58.402 50.000 0.00 0.00 0.00 3.53
6077 6535 1.300963 GGCCTTCATCAGTGGCTCA 59.699 57.895 0.00 0.00 45.45 4.26
6159 6617 2.157738 AGAGATTGCACAGACAAAGCC 58.842 47.619 0.00 0.00 32.27 4.35
6181 6639 5.106277 GCAGTTTGTGAATCCTTACTAACCC 60.106 44.000 0.00 0.00 34.55 4.11
6268 6726 0.602638 TCCTGTTCACCGTGCATCAC 60.603 55.000 0.00 0.00 0.00 3.06
6296 6754 0.622136 TGCTGCAATCTGAGGGTCAT 59.378 50.000 0.00 0.00 0.00 3.06
6303 6761 0.622136 ACCCATCTGCTGCAATCTGA 59.378 50.000 3.02 0.00 0.00 3.27
6350 6808 2.430921 GTCCACTGTCGAGCCACG 60.431 66.667 0.00 0.00 44.09 4.94
6381 6839 2.839486 TGAGCTTCAGGTTCGTCATT 57.161 45.000 0.00 0.00 0.00 2.57
6426 6884 1.776034 GAATCGCCGAATGGAGTGCC 61.776 60.000 0.00 0.00 37.49 5.01
6429 6887 3.669354 GAGAATCGCCGAATGGAGT 57.331 52.632 0.00 0.00 37.49 3.85
6441 6899 0.723981 GCTGTTGCCACTCGAGAATC 59.276 55.000 21.68 7.50 0.00 2.52
6502 6960 4.260661 CCTTCATGAATCTGATGCAGTTCG 60.261 45.833 8.96 0.00 32.61 3.95
6503 6961 4.880120 TCCTTCATGAATCTGATGCAGTTC 59.120 41.667 8.96 0.00 32.61 3.01
6513 6979 8.032045 AGATGAATGTACTCCTTCATGAATCT 57.968 34.615 8.96 1.15 41.07 2.40
6604 7070 2.436542 CACCGTGGTAGGGGAATGAATA 59.563 50.000 0.00 0.00 36.61 1.75
6638 7104 1.484240 CTCGAGGGAAGGAAGCTTCAT 59.516 52.381 27.02 18.73 35.19 2.57
6680 7146 2.424234 GGCAGATAGAGAGGAGGTGAGT 60.424 54.545 0.00 0.00 0.00 3.41
6681 7147 2.238521 GGCAGATAGAGAGGAGGTGAG 58.761 57.143 0.00 0.00 0.00 3.51
6682 7148 1.477740 CGGCAGATAGAGAGGAGGTGA 60.478 57.143 0.00 0.00 0.00 4.02
6683 7149 0.958091 CGGCAGATAGAGAGGAGGTG 59.042 60.000 0.00 0.00 0.00 4.00
6684 7150 0.825840 GCGGCAGATAGAGAGGAGGT 60.826 60.000 0.00 0.00 0.00 3.85
6685 7151 0.539438 AGCGGCAGATAGAGAGGAGG 60.539 60.000 1.45 0.00 0.00 4.30
6686 7152 0.881118 GAGCGGCAGATAGAGAGGAG 59.119 60.000 1.45 0.00 0.00 3.69
6687 7153 0.538516 GGAGCGGCAGATAGAGAGGA 60.539 60.000 1.45 0.00 0.00 3.71
6688 7154 0.825425 TGGAGCGGCAGATAGAGAGG 60.825 60.000 1.45 0.00 0.00 3.69
6689 7155 0.597568 CTGGAGCGGCAGATAGAGAG 59.402 60.000 1.45 0.00 0.00 3.20
6690 7156 1.459455 GCTGGAGCGGCAGATAGAGA 61.459 60.000 1.45 0.00 35.55 3.10
6691 7157 1.006337 GCTGGAGCGGCAGATAGAG 60.006 63.158 1.45 0.00 35.55 2.43
6692 7158 3.133014 GCTGGAGCGGCAGATAGA 58.867 61.111 1.45 0.00 35.55 1.98
6713 7179 4.410400 GTTCCCTCCCCACTGCCG 62.410 72.222 0.00 0.00 0.00 5.69
6714 7180 2.936032 AGTTCCCTCCCCACTGCC 60.936 66.667 0.00 0.00 0.00 4.85
6715 7181 1.779061 TTGAGTTCCCTCCCCACTGC 61.779 60.000 0.00 0.00 36.86 4.40
6716 7182 0.771127 TTTGAGTTCCCTCCCCACTG 59.229 55.000 0.00 0.00 36.86 3.66
6717 7183 1.355720 CATTTGAGTTCCCTCCCCACT 59.644 52.381 0.00 0.00 36.86 4.00
6718 7184 1.075536 ACATTTGAGTTCCCTCCCCAC 59.924 52.381 0.00 0.00 36.86 4.61
6719 7185 1.075374 CACATTTGAGTTCCCTCCCCA 59.925 52.381 0.00 0.00 36.86 4.96
6720 7186 1.354368 TCACATTTGAGTTCCCTCCCC 59.646 52.381 0.00 0.00 36.86 4.81
6721 7187 2.716217 CTCACATTTGAGTTCCCTCCC 58.284 52.381 0.40 0.00 43.95 4.30
6763 7229 8.696374 TGTTTGGTTTTTATCTTTCCACACATA 58.304 29.630 0.00 0.00 35.07 2.29
6798 7264 4.164988 AGTGAGCTAGTCCAAAGGCATAAT 59.835 41.667 0.00 0.00 0.00 1.28
6893 7359 2.831526 GGGGTCAACATTGCTGGTTAAT 59.168 45.455 0.00 0.00 0.00 1.40
6906 7372 4.021544 TGCATACTTTGAATTGGGGTCAAC 60.022 41.667 0.00 0.00 34.78 3.18
6944 7410 6.180472 GTTCTCAGGACAAAATTCTCCCATA 58.820 40.000 0.00 0.00 0.00 2.74
7024 7490 7.709182 CGTTCATAATACAACCCTGAGATGTAA 59.291 37.037 0.00 0.00 33.63 2.41
7056 7522 6.183360 GGTTCAAATTTCACCCTCCAAGTTTA 60.183 38.462 5.12 0.00 0.00 2.01
7136 7602 4.789159 TCTAAGTCTGGGGAGAGAAGTCTA 59.211 45.833 0.00 0.00 30.97 2.59
7284 7754 1.269517 GCATGTTTTTGAGTTCGCCCA 60.270 47.619 0.00 0.00 0.00 5.36
7285 7755 1.269517 TGCATGTTTTTGAGTTCGCCC 60.270 47.619 0.00 0.00 0.00 6.13
7348 7818 2.320587 ACGCGACGAGTACGACCTT 61.321 57.895 15.93 0.00 42.66 3.50


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

AutoCloner maintained by Alex Coulton.