Multiple sequence alignment - TraesCS5D01G146600

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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 TraesCS5D01G146600 chr5D 100.000 5211 0 0 1 5211 233154427 233159637 0.000000e+00 9624.0
1 TraesCS5D01G146600 chr5D 92.982 114 3 5 4473 4586 519411635 519411743 1.500000e-35 161.0
2 TraesCS5D01G146600 chr5D 94.667 75 4 0 2192 2266 233156546 233156620 3.300000e-22 117.0
3 TraesCS5D01G146600 chr5D 94.667 75 4 0 2120 2194 233156618 233156692 3.300000e-22 117.0
4 TraesCS5D01G146600 chr5B 91.167 2253 101 46 1 2194 271918553 271916340 0.000000e+00 2968.0
5 TraesCS5D01G146600 chr5B 96.750 923 27 3 2192 3113 271916414 271915494 0.000000e+00 1535.0
6 TraesCS5D01G146600 chr5B 93.369 739 33 9 3619 4346 271910843 271910110 0.000000e+00 1079.0
7 TraesCS5D01G146600 chr5B 96.718 457 15 0 3158 3614 271914137 271913681 0.000000e+00 761.0
8 TraesCS5D01G146600 chr5A 93.718 1942 81 16 266 2194 321895566 321893653 0.000000e+00 2872.0
9 TraesCS5D01G146600 chr5A 91.003 1734 69 35 2974 4681 321893250 321891578 0.000000e+00 2257.0
10 TraesCS5D01G146600 chr5A 96.567 466 15 1 2192 2657 321893727 321893263 0.000000e+00 771.0
11 TraesCS5D01G146600 chr5A 89.140 442 22 10 4548 4973 321890726 321890295 1.290000e-145 527.0
12 TraesCS5D01G146600 chr5A 88.914 442 23 10 4548 4973 321891607 321891176 5.980000e-144 521.0
13 TraesCS5D01G146600 chr5A 91.429 315 23 3 4886 5198 321880058 321879746 3.730000e-116 429.0
14 TraesCS5D01G146600 chr5A 95.259 232 7 2 4659 4889 321889383 321889155 1.070000e-96 364.0
15 TraesCS5D01G146600 chr5A 92.609 230 12 4 4973 5200 321890046 321889820 5.030000e-85 326.0
16 TraesCS5D01G146600 chr5A 88.688 221 12 8 4767 4979 321890705 321890490 1.860000e-64 257.0
17 TraesCS5D01G146600 chr5A 88.688 221 12 8 4767 4979 321891586 321891371 1.860000e-64 257.0
18 TraesCS5D01G146600 chr5A 91.803 122 5 5 4474 4594 645980646 645980763 1.160000e-36 165.0
19 TraesCS5D01G146600 chr5A 93.976 83 1 3 4973 5054 321890927 321890848 7.090000e-24 122.0
20 TraesCS5D01G146600 chr1D 82.991 535 56 20 1547 2076 269501957 269502461 7.960000e-123 451.0
21 TraesCS5D01G146600 chr1A 82.824 524 56 19 1602 2120 333508377 333507883 6.200000e-119 438.0
22 TraesCS5D01G146600 chr4D 89.032 155 8 9 4471 4622 102160828 102160976 3.200000e-42 183.0
23 TraesCS5D01G146600 chr4D 95.413 109 2 3 4478 4586 442900966 442901071 2.500000e-38 171.0
24 TraesCS5D01G146600 chr4D 90.909 55 5 0 3390 3444 102159439 102159493 2.010000e-09 75.0
25 TraesCS5D01G146600 chr4B 92.562 121 3 6 4478 4595 552025502 552025619 8.970000e-38 169.0
26 TraesCS5D01G146600 chr4B 79.832 119 20 3 3390 3506 146488848 146488964 3.340000e-12 84.2
27 TraesCS5D01G146600 chr7D 96.907 97 3 0 4473 4569 483915543 483915447 4.180000e-36 163.0
28 TraesCS5D01G146600 chr4A 91.597 119 5 4 4478 4594 24759819 24759704 5.400000e-35 159.0
29 TraesCS5D01G146600 chr7B 93.396 106 6 1 4472 4576 509559637 509559532 6.990000e-34 156.0


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 TraesCS5D01G146600 chr5D 233154427 233159637 5210 False 3286.00 9624 96.444667 1 5211 3 chr5D.!!$F2 5210
1 TraesCS5D01G146600 chr5B 271910110 271918553 8443 True 1585.75 2968 94.501000 1 4346 4 chr5B.!!$R1 4345
2 TraesCS5D01G146600 chr5A 321889155 321895566 6411 True 827.40 2872 91.856200 266 5200 10 chr5A.!!$R2 4934
3 TraesCS5D01G146600 chr1D 269501957 269502461 504 False 451.00 451 82.991000 1547 2076 1 chr1D.!!$F1 529

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
161 168 0.395586 TCCCGGCCCAAATTCATCTG 60.396 55.0 0.00 0.0 0.00 2.90 F
164 171 0.531657 CGGCCCAAATTCATCTGCAA 59.468 50.0 0.00 0.0 0.00 4.08 F
1823 1904 0.761187 TGGCCTCTGACCTGCATATC 59.239 55.0 3.32 0.0 0.00 1.63 F
2644 2725 0.912486 ACATCAACCCCAGAGGCTAC 59.088 55.0 0.00 0.0 40.58 3.58 F
3910 8149 0.678048 GCACCAACATCAGGGTCTCC 60.678 60.0 0.00 0.0 34.45 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1844 1.867233 CCAAATCCCGCTGTCTAATCG 59.133 52.381 0.0 0.0 0.00 3.34 R
2104 2185 4.451096 TGTCTGAAGAAAAATACTCACGGC 59.549 41.667 0.0 0.0 0.00 5.68 R
3364 4765 0.243907 CACGAAGAGAAGGAAGCGGA 59.756 55.000 0.0 0.0 0.00 5.54 R
4105 8344 0.040067 GCGCAAACTCAAACCTGGAG 60.040 55.000 0.3 0.0 38.36 3.86 R
5178 10946 1.310904 TTTTGCCGGCGTCTTACTTT 58.689 45.000 23.9 0.0 0.00 2.66 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
27 28 4.684623 CCCTTAAGGCCATGGTGG 57.315 61.111 16.70 6.36 41.55 4.61
49 50 5.181245 TGGCGGAATGAGAAAAGTAAGAAAG 59.819 40.000 0.00 0.00 0.00 2.62
56 57 6.613755 TGAGAAAAGTAAGAAAGGGAAACG 57.386 37.500 0.00 0.00 0.00 3.60
67 68 5.469479 AGAAAGGGAAACGTATTTGCATTG 58.531 37.500 0.00 0.00 38.92 2.82
77 84 8.825667 AAACGTATTTGCATTGGAGTAATTTT 57.174 26.923 0.00 0.00 0.00 1.82
99 106 3.268334 TGCTAGGGTTCTTCTCTCTCTCT 59.732 47.826 0.00 0.00 0.00 3.10
100 107 4.264172 TGCTAGGGTTCTTCTCTCTCTCTT 60.264 45.833 0.00 0.00 0.00 2.85
102 109 3.708451 AGGGTTCTTCTCTCTCTCTTCC 58.292 50.000 0.00 0.00 0.00 3.46
103 110 3.336694 AGGGTTCTTCTCTCTCTCTTCCT 59.663 47.826 0.00 0.00 0.00 3.36
104 111 3.699538 GGGTTCTTCTCTCTCTCTTCCTC 59.300 52.174 0.00 0.00 0.00 3.71
105 112 4.569865 GGGTTCTTCTCTCTCTCTTCCTCT 60.570 50.000 0.00 0.00 0.00 3.69
106 113 4.399303 GGTTCTTCTCTCTCTCTTCCTCTG 59.601 50.000 0.00 0.00 0.00 3.35
107 114 4.927267 TCTTCTCTCTCTCTTCCTCTGT 57.073 45.455 0.00 0.00 0.00 3.41
108 115 6.177610 GTTCTTCTCTCTCTCTTCCTCTGTA 58.822 44.000 0.00 0.00 0.00 2.74
109 116 6.575244 TCTTCTCTCTCTCTTCCTCTGTAT 57.425 41.667 0.00 0.00 0.00 2.29
110 117 6.591935 TCTTCTCTCTCTCTTCCTCTGTATC 58.408 44.000 0.00 0.00 0.00 2.24
111 118 5.304686 TCTCTCTCTCTTCCTCTGTATCC 57.695 47.826 0.00 0.00 0.00 2.59
112 119 4.104102 TCTCTCTCTCTTCCTCTGTATCCC 59.896 50.000 0.00 0.00 0.00 3.85
113 120 3.139397 TCTCTCTCTTCCTCTGTATCCCC 59.861 52.174 0.00 0.00 0.00 4.81
114 121 2.859404 TCTCTCTTCCTCTGTATCCCCA 59.141 50.000 0.00 0.00 0.00 4.96
141 148 0.745128 AAACCACGAACACCAGCGAA 60.745 50.000 0.00 0.00 0.00 4.70
148 155 4.778143 ACACCAGCGAATCCCGGC 62.778 66.667 0.00 0.00 39.04 6.13
161 168 0.395586 TCCCGGCCCAAATTCATCTG 60.396 55.000 0.00 0.00 0.00 2.90
163 170 1.321805 CCGGCCCAAATTCATCTGCA 61.322 55.000 0.00 0.00 0.00 4.41
164 171 0.531657 CGGCCCAAATTCATCTGCAA 59.468 50.000 0.00 0.00 0.00 4.08
174 194 3.409851 TTCATCTGCAAATTAGCTGCG 57.590 42.857 0.00 0.00 42.97 5.18
184 204 4.798574 CAAATTAGCTGCGGAATATTCCC 58.201 43.478 25.60 18.88 44.67 3.97
191 211 3.142174 CTGCGGAATATTCCCTCCTTTC 58.858 50.000 25.60 9.05 44.67 2.62
207 228 3.049344 CCTTTCCCCAGTAGCCTAGATT 58.951 50.000 0.00 0.00 0.00 2.40
215 236 3.515316 TAGCCTAGATTGCGCGGGC 62.515 63.158 18.81 18.81 42.74 6.13
230 251 3.195698 GGCCGCGGCAAAGAGTAG 61.196 66.667 46.88 10.06 44.11 2.57
234 255 3.118454 GCGGCAAAGAGTAGCGCA 61.118 61.111 11.47 0.00 33.03 6.09
235 256 2.677003 GCGGCAAAGAGTAGCGCAA 61.677 57.895 11.47 0.00 33.03 4.85
240 261 2.663119 GGCAAAGAGTAGCGCAATTTTG 59.337 45.455 11.47 13.45 0.00 2.44
242 263 2.636768 AAGAGTAGCGCAATTTTGGC 57.363 45.000 11.47 0.00 0.00 4.52
271 314 1.649664 CTCGTCCTTGCTCAATCCTG 58.350 55.000 0.00 0.00 0.00 3.86
281 324 1.742268 GCTCAATCCTGCCTGTTTCTC 59.258 52.381 0.00 0.00 0.00 2.87
410 456 6.670077 TTTTTCTTTTGTTGAAATTCGGGG 57.330 33.333 0.00 0.00 34.04 5.73
449 501 2.949714 CGTTTCATCGCTTGTCTGTT 57.050 45.000 0.00 0.00 0.00 3.16
451 503 3.978759 CGTTTCATCGCTTGTCTGTTAG 58.021 45.455 0.00 0.00 0.00 2.34
463 515 2.288579 TGTCTGTTAGCGTGGTCGATTT 60.289 45.455 0.00 0.00 39.71 2.17
471 523 4.336532 AGCGTGGTCGATTTGTTTTATC 57.663 40.909 0.00 0.00 39.71 1.75
472 524 4.000988 AGCGTGGTCGATTTGTTTTATCT 58.999 39.130 0.00 0.00 39.71 1.98
473 525 5.172934 AGCGTGGTCGATTTGTTTTATCTA 58.827 37.500 0.00 0.00 39.71 1.98
474 526 5.291128 AGCGTGGTCGATTTGTTTTATCTAG 59.709 40.000 0.00 0.00 39.71 2.43
475 527 5.063060 GCGTGGTCGATTTGTTTTATCTAGT 59.937 40.000 0.00 0.00 39.71 2.57
476 528 6.254157 GCGTGGTCGATTTGTTTTATCTAGTA 59.746 38.462 0.00 0.00 39.71 1.82
477 529 7.201461 GCGTGGTCGATTTGTTTTATCTAGTAA 60.201 37.037 0.00 0.00 39.71 2.24
478 530 8.318876 CGTGGTCGATTTGTTTTATCTAGTAAG 58.681 37.037 0.00 0.00 39.71 2.34
479 531 9.148104 GTGGTCGATTTGTTTTATCTAGTAAGT 57.852 33.333 0.00 0.00 0.00 2.24
514 572 5.751509 GCTCATGTATGAACGGTAACATGTA 59.248 40.000 17.65 8.14 45.94 2.29
585 647 5.826586 AGTATCAGTCTACATCTTCTTGCG 58.173 41.667 0.00 0.00 0.00 4.85
626 695 6.116126 ACCTATTTATCTGAGACCTTGCAAC 58.884 40.000 0.00 0.00 0.00 4.17
627 696 6.069963 ACCTATTTATCTGAGACCTTGCAACT 60.070 38.462 0.00 0.00 0.00 3.16
628 697 6.825721 CCTATTTATCTGAGACCTTGCAACTT 59.174 38.462 0.00 0.00 0.00 2.66
629 698 7.337942 CCTATTTATCTGAGACCTTGCAACTTT 59.662 37.037 0.00 0.00 0.00 2.66
630 699 5.947228 TTATCTGAGACCTTGCAACTTTG 57.053 39.130 0.00 0.00 0.00 2.77
667 736 5.067283 GTGTGTTAAGATTGTTCCACCAACT 59.933 40.000 0.00 0.00 35.79 3.16
669 738 6.261381 TGTGTTAAGATTGTTCCACCAACTAC 59.739 38.462 0.00 0.00 35.79 2.73
826 900 7.713764 ATGGTCTTTGTTTTGCATTCTTTAC 57.286 32.000 0.00 0.00 0.00 2.01
907 984 6.699642 TGGCTAATTTGTAGTTTTGCACTTTC 59.300 34.615 0.00 0.00 36.88 2.62
988 1065 5.842874 TGATCATCTCTCTCTCTCTCTCTCT 59.157 44.000 0.00 0.00 0.00 3.10
1042 1119 2.997315 TGCTGCTGCTACCTCCGT 60.997 61.111 17.00 0.00 40.48 4.69
1082 1159 4.017407 TCTCTTCTCCTACCTGTACACCAT 60.017 45.833 0.00 0.00 0.00 3.55
1143 1220 1.779061 GCCAAGGAGTGAAGGGTCCA 61.779 60.000 0.00 0.00 35.02 4.02
1207 1284 1.455383 CCAGAAACTTGCCACGCCTT 61.455 55.000 0.00 0.00 0.00 4.35
1262 1339 4.524802 TCTCCTCAAATTATGTGGCCAT 57.475 40.909 9.72 0.00 41.53 4.40
1342 1419 9.096823 TGTAGATAGTTTCAGTAAGGAAGGAAA 57.903 33.333 0.00 0.00 0.00 3.13
1509 1586 7.768120 GGGGAATGCACAATTATAATCACAAAA 59.232 33.333 0.00 0.00 0.00 2.44
1537 1614 3.457234 GAGGCCTTTTGTTGTTTCAAGG 58.543 45.455 6.77 0.00 39.15 3.61
1595 1673 7.252612 TGTTCTTTGATGAGGACCTGTTATA 57.747 36.000 0.00 0.00 0.00 0.98
1600 1678 6.425210 TTGATGAGGACCTGTTATATCCTG 57.575 41.667 0.00 0.00 43.12 3.86
1814 1895 3.825328 ACATGGATAAATGGCCTCTGAC 58.175 45.455 3.32 0.00 31.46 3.51
1823 1904 0.761187 TGGCCTCTGACCTGCATATC 59.239 55.000 3.32 0.00 0.00 1.63
2094 2175 6.235664 TCTTCATGGACAAGGTTAAGGTAAC 58.764 40.000 0.00 0.00 37.94 2.50
2194 2275 5.982516 TGGTGTTGTTCAACAATAATGCTTC 59.017 36.000 17.98 4.75 41.17 3.86
2195 2276 5.982516 GGTGTTGTTCAACAATAATGCTTCA 59.017 36.000 17.98 0.00 40.59 3.02
2196 2277 6.144402 GGTGTTGTTCAACAATAATGCTTCAG 59.856 38.462 17.98 0.00 40.59 3.02
2197 2278 6.917477 GTGTTGTTCAACAATAATGCTTCAGA 59.083 34.615 17.98 0.00 40.59 3.27
2198 2279 6.917477 TGTTGTTCAACAATAATGCTTCAGAC 59.083 34.615 14.73 0.00 40.59 3.51
2199 2280 6.631971 TGTTCAACAATAATGCTTCAGACA 57.368 33.333 0.00 0.00 0.00 3.41
2200 2281 6.437928 TGTTCAACAATAATGCTTCAGACAC 58.562 36.000 0.00 0.00 0.00 3.67
2201 2282 5.281693 TCAACAATAATGCTTCAGACACG 57.718 39.130 0.00 0.00 0.00 4.49
2202 2283 3.747099 ACAATAATGCTTCAGACACGC 57.253 42.857 0.00 0.00 0.00 5.34
2203 2284 3.338249 ACAATAATGCTTCAGACACGCT 58.662 40.909 0.00 0.00 0.00 5.07
2204 2285 3.753272 ACAATAATGCTTCAGACACGCTT 59.247 39.130 0.00 0.00 0.00 4.68
2205 2286 4.216257 ACAATAATGCTTCAGACACGCTTT 59.784 37.500 0.00 0.00 0.00 3.51
2206 2287 5.156355 CAATAATGCTTCAGACACGCTTTT 58.844 37.500 0.00 0.00 0.00 2.27
2207 2288 3.715628 AATGCTTCAGACACGCTTTTT 57.284 38.095 0.00 0.00 0.00 1.94
2229 2310 6.843069 TTTTTAGGCAAAAATGCTTCAGAC 57.157 33.333 0.40 0.00 38.42 3.51
2230 2311 5.528043 TTTAGGCAAAAATGCTTCAGACA 57.472 34.783 0.40 0.00 34.73 3.41
2231 2312 3.655276 AGGCAAAAATGCTTCAGACAG 57.345 42.857 0.40 0.00 34.73 3.51
2232 2313 2.961062 AGGCAAAAATGCTTCAGACAGT 59.039 40.909 0.40 0.00 34.73 3.55
2233 2314 3.054878 GGCAAAAATGCTTCAGACAGTG 58.945 45.455 0.40 0.00 34.73 3.66
2234 2315 3.491447 GGCAAAAATGCTTCAGACAGTGT 60.491 43.478 0.00 0.00 34.73 3.55
2235 2316 4.114794 GCAAAAATGCTTCAGACAGTGTT 58.885 39.130 0.00 0.00 0.00 3.32
2236 2317 4.567959 GCAAAAATGCTTCAGACAGTGTTT 59.432 37.500 0.00 0.00 0.00 2.83
2237 2318 5.063817 GCAAAAATGCTTCAGACAGTGTTTT 59.936 36.000 0.00 0.00 0.00 2.43
2238 2319 6.402442 GCAAAAATGCTTCAGACAGTGTTTTT 60.402 34.615 0.00 0.00 0.00 1.94
2261 2342 9.877178 TTTTTCATGGTGTTGTTAAACAGTAAT 57.123 25.926 0.00 0.00 46.79 1.89
2262 2343 8.864069 TTTCATGGTGTTGTTAAACAGTAATG 57.136 30.769 0.00 0.00 46.79 1.90
2263 2344 6.442952 TCATGGTGTTGTTAAACAGTAATGC 58.557 36.000 0.00 0.00 46.79 3.56
2264 2345 6.264292 TCATGGTGTTGTTAAACAGTAATGCT 59.736 34.615 0.00 0.00 46.79 3.79
2265 2346 6.458232 TGGTGTTGTTAAACAGTAATGCTT 57.542 33.333 0.00 0.00 46.79 3.91
2266 2347 6.269315 TGGTGTTGTTAAACAGTAATGCTTG 58.731 36.000 0.00 0.00 46.79 4.01
2267 2348 5.174943 GGTGTTGTTAAACAGTAATGCTTGC 59.825 40.000 0.00 0.00 46.79 4.01
2268 2349 5.977129 GTGTTGTTAAACAGTAATGCTTGCT 59.023 36.000 0.00 0.00 46.79 3.91
2309 2390 6.149474 ACATGCACCATTAGACTAAACTTGAC 59.851 38.462 0.00 0.00 0.00 3.18
2417 2498 1.148048 GGAGGCAGGGCAGAGATTC 59.852 63.158 0.00 0.00 0.00 2.52
2434 2515 8.194104 GCAGAGATTCTAGTTGATGAGTTCTTA 58.806 37.037 0.00 0.00 0.00 2.10
2473 2554 8.281893 GCTGATGTTATATCAAGAGCTTCTTTC 58.718 37.037 0.00 0.00 33.78 2.62
2644 2725 0.912486 ACATCAACCCCAGAGGCTAC 59.088 55.000 0.00 0.00 40.58 3.58
2738 2819 6.655848 ACTGTATAGTTTATGCGTTTGGGAAA 59.344 34.615 0.00 0.00 31.66 3.13
2745 2826 1.610363 TGCGTTTGGGAAATAGCACA 58.390 45.000 0.00 0.00 33.92 4.57
2765 2846 8.532977 AGCACAAATTTTCCAATAACATGTAC 57.467 30.769 0.00 0.00 0.00 2.90
2809 2890 6.405953 CGGTCAGTACCTGTCTCAGATATTTT 60.406 42.308 0.00 0.00 44.35 1.82
2846 2927 4.380531 TCCGCCAGTATCAGATTCATTTC 58.619 43.478 0.00 0.00 0.00 2.17
2852 2933 6.125029 CCAGTATCAGATTCATTTCAGGGTT 58.875 40.000 0.00 0.00 0.00 4.11
2948 3030 4.746115 TGCTTCACAATTTTCATGCAAGTC 59.254 37.500 0.00 0.00 0.00 3.01
3055 3141 4.521639 AGTATACCGAAGTTGAGTGTCACA 59.478 41.667 5.62 0.00 0.00 3.58
3058 3144 2.128035 CCGAAGTTGAGTGTCACAGAC 58.872 52.381 5.62 0.78 0.00 3.51
3206 4607 2.157834 TGCTTGAATTTTGCTGCTGG 57.842 45.000 0.00 0.00 0.00 4.85
3237 4638 9.886132 AACAGATATTTACCGACAAAGAGTAAT 57.114 29.630 0.00 0.00 0.00 1.89
3364 4765 6.125029 CACTCCATCATTGAGGGTTCTAAAT 58.875 40.000 16.41 0.00 34.82 1.40
3429 4830 5.050091 CGACAACTGCAAGAACATCTACTTT 60.050 40.000 0.00 0.00 37.43 2.66
3621 5022 6.920817 TCGCTCTTGTAAATGAGAGAGTTTA 58.079 36.000 4.66 0.00 38.28 2.01
3698 7934 5.623956 TTTCTGAGTAACCAAACCTCTGA 57.376 39.130 0.00 0.00 33.21 3.27
3699 7935 5.825593 TTCTGAGTAACCAAACCTCTGAT 57.174 39.130 0.00 0.00 34.51 2.90
3745 7981 0.746063 TTTGCTTGCCTTGTGACTGG 59.254 50.000 0.00 0.00 0.00 4.00
3769 8005 5.762045 CTTGTGCAAAGTGCTAATACAAGT 58.238 37.500 16.83 0.00 43.10 3.16
3910 8149 0.678048 GCACCAACATCAGGGTCTCC 60.678 60.000 0.00 0.00 34.45 3.71
3976 8215 2.611971 CGACAAGTTTGATCCGGGAAGA 60.612 50.000 0.00 0.00 0.00 2.87
4105 8344 3.786586 GTGCTGTCGCTGCTGCTC 61.787 66.667 14.03 7.27 36.97 4.26
4162 8401 1.546589 ATCGGCCCGTGTTCAGGTTA 61.547 55.000 1.63 0.00 0.00 2.85
4232 8472 3.596310 TGATGGTCCGTTCATCGTTTA 57.404 42.857 0.00 0.00 42.73 2.01
4235 8475 3.322211 TGGTCCGTTCATCGTTTATGT 57.678 42.857 0.00 0.00 36.89 2.29
4365 8614 5.293814 TCACTTTGACATGGTGCAAAATTTG 59.706 36.000 0.57 0.57 34.01 2.32
4399 8648 1.066136 GGTACGTTCAAGAAGGCGTC 58.934 55.000 0.00 0.00 38.56 5.19
4401 8650 1.454653 GTACGTTCAAGAAGGCGTCAC 59.545 52.381 2.69 0.00 38.56 3.67
4405 8654 2.599848 CGTTCAAGAAGGCGTCACTTTG 60.600 50.000 2.69 0.00 0.00 2.77
4406 8655 0.944386 TCAAGAAGGCGTCACTTTGC 59.056 50.000 2.69 0.00 0.00 3.68
4408 8657 1.267806 CAAGAAGGCGTCACTTTGCAT 59.732 47.619 2.69 0.00 0.00 3.96
4409 8658 1.609208 AGAAGGCGTCACTTTGCATT 58.391 45.000 2.69 0.00 37.87 3.56
4410 8659 1.969103 GAAGGCGTCACTTTGCATTC 58.031 50.000 0.00 0.00 43.37 2.67
4412 8661 1.154225 GGCGTCACTTTGCATTCCG 60.154 57.895 0.00 0.00 0.00 4.30
4413 8662 1.574428 GCGTCACTTTGCATTCCGT 59.426 52.632 0.00 0.00 0.00 4.69
4414 8663 0.725784 GCGTCACTTTGCATTCCGTG 60.726 55.000 0.00 0.00 0.00 4.94
4415 8664 0.586319 CGTCACTTTGCATTCCGTGT 59.414 50.000 0.00 0.00 0.00 4.49
4416 8665 1.795872 CGTCACTTTGCATTCCGTGTA 59.204 47.619 0.00 0.00 0.00 2.90
4417 8666 2.159841 CGTCACTTTGCATTCCGTGTAG 60.160 50.000 0.00 0.00 0.00 2.74
4418 8667 1.804151 TCACTTTGCATTCCGTGTAGC 59.196 47.619 0.00 0.00 0.00 3.58
4419 8668 1.806542 CACTTTGCATTCCGTGTAGCT 59.193 47.619 0.00 0.00 0.00 3.32
4420 8669 2.226437 CACTTTGCATTCCGTGTAGCTT 59.774 45.455 0.00 0.00 0.00 3.74
4421 8670 2.226437 ACTTTGCATTCCGTGTAGCTTG 59.774 45.455 0.00 0.00 0.00 4.01
4422 8671 1.890876 TTGCATTCCGTGTAGCTTGT 58.109 45.000 0.00 0.00 0.00 3.16
4423 8672 1.890876 TGCATTCCGTGTAGCTTGTT 58.109 45.000 0.00 0.00 0.00 2.83
4424 8673 2.226330 TGCATTCCGTGTAGCTTGTTT 58.774 42.857 0.00 0.00 0.00 2.83
4425 8674 2.621055 TGCATTCCGTGTAGCTTGTTTT 59.379 40.909 0.00 0.00 0.00 2.43
4426 8675 3.234386 GCATTCCGTGTAGCTTGTTTTC 58.766 45.455 0.00 0.00 0.00 2.29
4427 8676 3.821841 CATTCCGTGTAGCTTGTTTTCC 58.178 45.455 0.00 0.00 0.00 3.13
4428 8677 2.623878 TCCGTGTAGCTTGTTTTCCA 57.376 45.000 0.00 0.00 0.00 3.53
4429 8678 2.920524 TCCGTGTAGCTTGTTTTCCAA 58.079 42.857 0.00 0.00 0.00 3.53
4430 8679 3.280295 TCCGTGTAGCTTGTTTTCCAAA 58.720 40.909 0.00 0.00 31.20 3.28
4431 8680 3.886505 TCCGTGTAGCTTGTTTTCCAAAT 59.113 39.130 0.00 0.00 31.20 2.32
4432 8681 5.064558 TCCGTGTAGCTTGTTTTCCAAATA 58.935 37.500 0.00 0.00 31.20 1.40
4436 8685 6.512741 CGTGTAGCTTGTTTTCCAAATACTGT 60.513 38.462 0.00 0.00 31.34 3.55
4437 8686 7.200455 GTGTAGCTTGTTTTCCAAATACTGTT 58.800 34.615 0.00 0.00 31.34 3.16
4567 8816 3.909732 TCAAACCCCACTTCTGACAAAT 58.090 40.909 0.00 0.00 0.00 2.32
4572 8821 5.982890 ACCCCACTTCTGACAAATTAATG 57.017 39.130 0.00 0.00 0.00 1.90
4597 8846 8.658609 TGTTTTGCATTTTTCTTCTTCTTTGAG 58.341 29.630 0.00 0.00 0.00 3.02
4603 8852 9.313118 GCATTTTTCTTCTTCTTTGAGGTTTAA 57.687 29.630 0.00 0.00 0.00 1.52
4612 8861 8.816640 TCTTCTTTGAGGTTTAATTTTGCATC 57.183 30.769 0.00 0.00 0.00 3.91
4627 8876 5.458041 TTTGCATCTCTTTTCCTTCCTTG 57.542 39.130 0.00 0.00 0.00 3.61
4630 8879 4.264083 TGCATCTCTTTTCCTTCCTTGGAT 60.264 41.667 0.00 0.00 35.83 3.41
4631 8880 4.097589 GCATCTCTTTTCCTTCCTTGGATG 59.902 45.833 0.00 0.00 35.83 3.51
4633 8882 5.324832 TCTCTTTTCCTTCCTTGGATGTT 57.675 39.130 0.00 0.00 35.83 2.71
4634 8883 5.705400 TCTCTTTTCCTTCCTTGGATGTTT 58.295 37.500 0.00 0.00 35.83 2.83
4753 9135 3.055675 CCTTGTTTCCATTCATGCATGGT 60.056 43.478 25.97 12.77 43.94 3.55
4754 9136 3.596310 TGTTTCCATTCATGCATGGTG 57.404 42.857 25.97 22.32 43.94 4.17
4771 9154 7.109501 TGCATGGTGTATACTTTCACTAATGT 58.890 34.615 4.17 0.00 34.47 2.71
4825 9763 6.539826 AGTTTTGCATTTCTTTTCCTTCCTTG 59.460 34.615 0.00 0.00 0.00 3.61
4863 9925 6.380846 TGCATATATTTCTTCCTTGCCAAACT 59.619 34.615 0.00 0.00 0.00 2.66
4937 10198 9.337396 ACGTTTTATATTGCATATTCTCTTCCA 57.663 29.630 0.00 0.00 0.00 3.53
4951 10212 5.488262 TCTCTTCCATGTTCTCATTCACA 57.512 39.130 0.00 0.00 31.15 3.58
4973 10234 8.318412 TCACACATGGTGTATACTTTCACTAAT 58.682 33.333 4.17 0.00 45.65 1.73
4974 10235 8.390354 CACACATGGTGTATACTTTCACTAATG 58.610 37.037 4.17 5.49 45.65 1.90
4975 10236 8.100791 ACACATGGTGTATACTTTCACTAATGT 58.899 33.333 4.17 6.01 45.56 2.71
5071 10581 2.361230 CGAGCCCCCAAAGAACCC 60.361 66.667 0.00 0.00 0.00 4.11
5081 10591 3.270877 CCCAAAGAACCCGTATCTCAAG 58.729 50.000 0.00 0.00 0.00 3.02
5087 10597 7.335924 CCAAAGAACCCGTATCTCAAGAAAATA 59.664 37.037 0.00 0.00 0.00 1.40
5091 10601 7.711339 AGAACCCGTATCTCAAGAAAATATCAC 59.289 37.037 0.00 0.00 0.00 3.06
5106 10616 4.920640 ATATCACTGGTGTAGGAGAACG 57.079 45.455 0.53 0.00 0.00 3.95
5107 10617 1.254026 TCACTGGTGTAGGAGAACGG 58.746 55.000 0.53 0.00 0.00 4.44
5117 10627 1.123928 AGGAGAACGGGGCATAAGAG 58.876 55.000 0.00 0.00 0.00 2.85
5190 10958 5.293814 GGGATAAGAGAAAAAGTAAGACGCC 59.706 44.000 0.00 0.00 0.00 5.68
5193 10961 1.128136 GAGAAAAAGTAAGACGCCGGC 59.872 52.381 19.07 19.07 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.392057 CCCTTTCTTACTTTTCTCATTCCGC 60.392 44.000 0.00 0.00 0.00 5.54
28 29 5.938125 TCCCTTTCTTACTTTTCTCATTCCG 59.062 40.000 0.00 0.00 0.00 4.30
49 50 3.192633 ACTCCAATGCAAATACGTTTCCC 59.807 43.478 0.00 0.00 0.00 3.97
56 57 7.832503 AGCAAAATTACTCCAATGCAAATAC 57.167 32.000 0.00 0.00 36.30 1.89
67 68 6.181190 AGAAGAACCCTAGCAAAATTACTCC 58.819 40.000 0.00 0.00 0.00 3.85
77 84 3.268334 AGAGAGAGAGAAGAACCCTAGCA 59.732 47.826 0.00 0.00 0.00 3.49
99 106 1.776662 CGAGTGGGGATACAGAGGAA 58.223 55.000 0.00 0.00 39.74 3.36
100 107 0.755698 GCGAGTGGGGATACAGAGGA 60.756 60.000 0.00 0.00 39.74 3.71
102 109 1.101635 TCGCGAGTGGGGATACAGAG 61.102 60.000 3.71 0.00 39.74 3.35
103 110 0.681887 TTCGCGAGTGGGGATACAGA 60.682 55.000 9.59 0.00 37.45 3.41
104 111 0.174845 TTTCGCGAGTGGGGATACAG 59.825 55.000 9.59 0.00 37.45 2.74
105 112 0.609151 TTTTCGCGAGTGGGGATACA 59.391 50.000 9.59 0.00 37.45 2.29
106 113 1.004595 GTTTTCGCGAGTGGGGATAC 58.995 55.000 9.59 0.00 37.45 2.24
107 114 0.108041 GGTTTTCGCGAGTGGGGATA 60.108 55.000 9.59 0.00 37.45 2.59
108 115 1.376812 GGTTTTCGCGAGTGGGGAT 60.377 57.895 9.59 0.00 37.45 3.85
109 116 2.031465 GGTTTTCGCGAGTGGGGA 59.969 61.111 9.59 0.00 35.54 4.81
110 117 2.281208 TGGTTTTCGCGAGTGGGG 60.281 61.111 9.59 0.00 0.00 4.96
111 118 2.943653 GTGGTTTTCGCGAGTGGG 59.056 61.111 9.59 0.00 0.00 4.61
141 148 0.557729 AGATGAATTTGGGCCGGGAT 59.442 50.000 2.18 0.00 0.00 3.85
148 155 5.522460 CAGCTAATTTGCAGATGAATTTGGG 59.478 40.000 14.27 0.00 30.98 4.12
161 168 4.229876 GGAATATTCCGCAGCTAATTTGC 58.770 43.478 18.61 3.49 37.65 3.68
174 194 2.789399 TGGGGAAAGGAGGGAATATTCC 59.211 50.000 24.14 24.14 46.82 3.01
184 204 2.043227 CTAGGCTACTGGGGAAAGGAG 58.957 57.143 0.00 0.00 0.00 3.69
191 211 0.034059 CGCAATCTAGGCTACTGGGG 59.966 60.000 0.00 0.00 0.00 4.96
215 236 3.554692 CGCTACTCTTTGCCGCGG 61.555 66.667 24.05 24.05 40.11 6.46
249 270 2.029904 GATTGAGCAAGGACGAGCGC 62.030 60.000 0.00 0.00 35.48 5.92
261 304 1.742268 GAGAAACAGGCAGGATTGAGC 59.258 52.381 0.00 0.00 0.00 4.26
271 314 3.131400 CCTGTAGGACTAGAGAAACAGGC 59.869 52.174 18.93 0.00 45.25 4.85
322 365 8.434589 AAATAGACTCATTCCCCAAATCAAAA 57.565 30.769 0.00 0.00 0.00 2.44
351 394 9.896645 ATTGAAACTGAAGATAGAGCAGATAAA 57.103 29.630 0.00 0.00 33.94 1.40
392 436 3.059166 CTGCCCCGAATTTCAACAAAAG 58.941 45.455 0.00 0.00 0.00 2.27
394 438 1.270041 GCTGCCCCGAATTTCAACAAA 60.270 47.619 0.00 0.00 0.00 2.83
397 441 1.154035 CGCTGCCCCGAATTTCAAC 60.154 57.895 0.00 0.00 0.00 3.18
401 445 3.134127 GAGCGCTGCCCCGAATTT 61.134 61.111 18.48 0.00 0.00 1.82
440 486 1.060713 CGACCACGCTAACAGACAAG 58.939 55.000 0.00 0.00 0.00 3.16
444 490 2.288579 ACAAATCGACCACGCTAACAGA 60.289 45.455 0.00 0.00 39.58 3.41
449 501 5.172934 AGATAAAACAAATCGACCACGCTA 58.827 37.500 0.00 0.00 39.58 4.26
451 503 4.336532 AGATAAAACAAATCGACCACGC 57.663 40.909 0.00 0.00 39.58 5.34
453 505 9.148104 ACTTACTAGATAAAACAAATCGACCAC 57.852 33.333 0.00 0.00 0.00 4.16
471 523 8.198109 ACATGAGCATGGTTACTAACTTACTAG 58.802 37.037 14.35 0.00 42.91 2.57
472 524 8.074613 ACATGAGCATGGTTACTAACTTACTA 57.925 34.615 14.35 0.00 42.91 1.82
473 525 6.947464 ACATGAGCATGGTTACTAACTTACT 58.053 36.000 14.35 0.00 42.91 2.24
474 526 8.765219 CATACATGAGCATGGTTACTAACTTAC 58.235 37.037 14.35 0.00 42.91 2.34
475 527 8.700973 TCATACATGAGCATGGTTACTAACTTA 58.299 33.333 14.35 0.00 42.91 2.24
476 528 7.564793 TCATACATGAGCATGGTTACTAACTT 58.435 34.615 14.35 0.00 42.91 2.66
477 529 7.124573 TCATACATGAGCATGGTTACTAACT 57.875 36.000 14.35 0.00 42.91 2.24
478 530 7.516785 CGTTCATACATGAGCATGGTTACTAAC 60.517 40.741 14.35 9.36 42.91 2.34
479 531 6.478673 CGTTCATACATGAGCATGGTTACTAA 59.521 38.462 14.35 0.00 42.91 2.24
514 572 1.107114 CGGCAGAGTATCAGTCCTGT 58.893 55.000 0.00 0.00 37.82 4.00
627 696 1.134753 CACACTCAACCTGCTTGCAAA 59.865 47.619 0.00 0.00 0.00 3.68
628 697 0.740149 CACACTCAACCTGCTTGCAA 59.260 50.000 0.00 0.00 0.00 4.08
629 698 0.394216 ACACACTCAACCTGCTTGCA 60.394 50.000 0.00 0.00 0.00 4.08
630 699 0.740737 AACACACTCAACCTGCTTGC 59.259 50.000 0.00 0.00 0.00 4.01
631 700 3.876914 TCTTAACACACTCAACCTGCTTG 59.123 43.478 0.00 0.00 0.00 4.01
632 701 4.150897 TCTTAACACACTCAACCTGCTT 57.849 40.909 0.00 0.00 0.00 3.91
633 702 3.838244 TCTTAACACACTCAACCTGCT 57.162 42.857 0.00 0.00 0.00 4.24
667 736 1.101635 CGGGTGAGGAGATGCTCGTA 61.102 60.000 0.00 0.00 0.00 3.43
669 738 2.415010 CGGGTGAGGAGATGCTCG 59.585 66.667 0.00 0.00 0.00 5.03
721 794 0.393537 GAGAGCACCCCCATCACAAG 60.394 60.000 0.00 0.00 0.00 3.16
826 900 8.233190 CAGTGCCAGTTTTCTAGAAGAAATAAG 58.767 37.037 5.12 0.75 43.06 1.73
988 1065 4.095211 GAGAGGATCATCATCATGAGGGA 58.905 47.826 10.44 4.91 42.53 4.20
1042 1119 7.027874 AGAAGAGAAGAGTAGAGAGGAAGAA 57.972 40.000 0.00 0.00 0.00 2.52
1143 1220 2.784347 CCGAAGAGGAAAGAAGGCTTT 58.216 47.619 0.00 0.00 46.62 3.51
1173 1250 5.279685 AGTTTCTGGATTCTCCTCATCTCT 58.720 41.667 0.00 0.00 37.46 3.10
1207 1284 2.402564 CCCTGCTCCCTCTTCTTGATA 58.597 52.381 0.00 0.00 0.00 2.15
1262 1339 3.326880 GTGGAGGAAGTAAGGGAACAGAA 59.673 47.826 0.00 0.00 0.00 3.02
1342 1419 6.767423 AGCAACCAAACAAATTCAAGCTAAAT 59.233 30.769 0.00 0.00 0.00 1.40
1420 1497 8.912988 AGATATCTCTTTCTACAGGAAGACTTG 58.087 37.037 0.00 0.00 35.16 3.16
1509 1586 4.400529 ACAACAAAAGGCCTCGATTTTT 57.599 36.364 5.23 0.00 0.00 1.94
1528 1605 2.301870 ACCATCTACTCGCCTTGAAACA 59.698 45.455 0.00 0.00 0.00 2.83
1537 1614 2.924454 GCATCTAGCACCATCTACTCGC 60.924 54.545 0.00 0.00 44.79 5.03
1538 1615 2.940147 GCATCTAGCACCATCTACTCG 58.060 52.381 0.00 0.00 44.79 4.18
1595 1673 4.467198 AACGACTACGAAATTCCAGGAT 57.533 40.909 0.00 0.00 42.66 3.24
1600 1678 7.222224 ACATCATCTAAACGACTACGAAATTCC 59.778 37.037 0.00 0.00 42.66 3.01
1765 1844 1.867233 CCAAATCCCGCTGTCTAATCG 59.133 52.381 0.00 0.00 0.00 3.34
1814 1895 4.641989 ACTTGCAAGGTTTAGATATGCAGG 59.358 41.667 29.18 6.62 46.44 4.85
2104 2185 4.451096 TGTCTGAAGAAAAATACTCACGGC 59.549 41.667 0.00 0.00 0.00 5.68
2141 2222 4.989279 ACACTGTCTGAAGCATTTTTGT 57.011 36.364 0.00 0.00 0.00 2.83
2206 2287 6.344500 TGTCTGAAGCATTTTTGCCTAAAAA 58.656 32.000 0.00 0.00 46.42 1.94
2207 2288 5.911752 TGTCTGAAGCATTTTTGCCTAAAA 58.088 33.333 0.00 0.00 39.88 1.52
2208 2289 5.068987 ACTGTCTGAAGCATTTTTGCCTAAA 59.931 36.000 0.00 0.00 34.90 1.85
2209 2290 4.584325 ACTGTCTGAAGCATTTTTGCCTAA 59.416 37.500 0.00 0.00 34.90 2.69
2210 2291 4.022935 CACTGTCTGAAGCATTTTTGCCTA 60.023 41.667 0.00 0.00 34.90 3.93
2211 2292 2.961062 ACTGTCTGAAGCATTTTTGCCT 59.039 40.909 0.00 0.00 34.90 4.75
2212 2293 3.054878 CACTGTCTGAAGCATTTTTGCC 58.945 45.455 0.00 0.00 34.90 4.52
2213 2294 3.709987 ACACTGTCTGAAGCATTTTTGC 58.290 40.909 0.00 0.00 0.00 3.68
2214 2295 6.651755 AAAACACTGTCTGAAGCATTTTTG 57.348 33.333 0.00 0.00 0.00 2.44
2235 2316 9.877178 ATTACTGTTTAACAACACCATGAAAAA 57.123 25.926 0.00 0.00 38.03 1.94
2236 2317 9.307121 CATTACTGTTTAACAACACCATGAAAA 57.693 29.630 0.00 0.00 38.03 2.29
2237 2318 7.436673 GCATTACTGTTTAACAACACCATGAAA 59.563 33.333 0.00 0.00 38.03 2.69
2238 2319 6.920758 GCATTACTGTTTAACAACACCATGAA 59.079 34.615 0.00 0.00 38.03 2.57
2239 2320 6.264292 AGCATTACTGTTTAACAACACCATGA 59.736 34.615 0.00 0.00 38.03 3.07
2240 2321 6.446318 AGCATTACTGTTTAACAACACCATG 58.554 36.000 0.00 0.00 38.03 3.66
2241 2322 6.648879 AGCATTACTGTTTAACAACACCAT 57.351 33.333 0.00 0.00 38.03 3.55
2242 2323 6.269315 CAAGCATTACTGTTTAACAACACCA 58.731 36.000 0.00 0.00 38.03 4.17
2243 2324 5.174943 GCAAGCATTACTGTTTAACAACACC 59.825 40.000 0.00 0.00 38.03 4.16
2244 2325 5.977129 AGCAAGCATTACTGTTTAACAACAC 59.023 36.000 0.00 0.00 38.03 3.32
2245 2326 6.142818 AGCAAGCATTACTGTTTAACAACA 57.857 33.333 0.00 0.00 40.82 3.33
2246 2327 7.463469 AAAGCAAGCATTACTGTTTAACAAC 57.537 32.000 0.00 0.00 0.00 3.32
2247 2328 9.587772 TTTAAAGCAAGCATTACTGTTTAACAA 57.412 25.926 0.00 0.00 0.00 2.83
2248 2329 9.587772 TTTTAAAGCAAGCATTACTGTTTAACA 57.412 25.926 0.00 0.00 0.00 2.41
2252 2333 8.069574 GCATTTTTAAAGCAAGCATTACTGTTT 58.930 29.630 0.00 0.00 0.00 2.83
2253 2334 7.442062 AGCATTTTTAAAGCAAGCATTACTGTT 59.558 29.630 0.00 0.00 0.00 3.16
2254 2335 6.930722 AGCATTTTTAAAGCAAGCATTACTGT 59.069 30.769 0.00 0.00 0.00 3.55
2255 2336 7.355332 AGCATTTTTAAAGCAAGCATTACTG 57.645 32.000 0.00 0.00 0.00 2.74
2256 2337 7.967890 AAGCATTTTTAAAGCAAGCATTACT 57.032 28.000 0.00 0.00 0.00 2.24
2257 2338 8.925700 AGTAAGCATTTTTAAAGCAAGCATTAC 58.074 29.630 0.00 8.37 0.00 1.89
2259 2340 7.967890 AGTAAGCATTTTTAAAGCAAGCATT 57.032 28.000 0.00 0.00 0.00 3.56
2260 2341 8.087750 TGTAGTAAGCATTTTTAAAGCAAGCAT 58.912 29.630 0.00 0.00 0.00 3.79
2261 2342 7.429633 TGTAGTAAGCATTTTTAAAGCAAGCA 58.570 30.769 0.00 0.00 0.00 3.91
2262 2343 7.867445 TGTAGTAAGCATTTTTAAAGCAAGC 57.133 32.000 1.36 0.00 0.00 4.01
2263 2344 8.375465 GCATGTAGTAAGCATTTTTAAAGCAAG 58.625 33.333 0.00 0.00 0.00 4.01
2264 2345 7.869937 TGCATGTAGTAAGCATTTTTAAAGCAA 59.130 29.630 0.00 0.00 32.55 3.91
2265 2346 7.328249 GTGCATGTAGTAAGCATTTTTAAAGCA 59.672 33.333 0.00 0.00 40.78 3.91
2266 2347 7.201435 GGTGCATGTAGTAAGCATTTTTAAAGC 60.201 37.037 0.00 0.00 40.78 3.51
2267 2348 7.812191 TGGTGCATGTAGTAAGCATTTTTAAAG 59.188 33.333 0.00 0.00 40.78 1.85
2268 2349 7.661968 TGGTGCATGTAGTAAGCATTTTTAAA 58.338 30.769 0.00 0.00 40.78 1.52
2434 2515 1.620819 ACATCAGCTGAGAAGTTCCGT 59.379 47.619 22.96 5.88 0.00 4.69
2473 2554 1.069906 CCTTCGACAAAACTGCTTCCG 60.070 52.381 0.00 0.00 0.00 4.30
2644 2725 6.705302 AGCCATCATGGTATAGTATGTGAAG 58.295 40.000 5.31 0.00 40.46 3.02
2729 2810 6.484977 TGGAAAATTTGTGCTATTTCCCAAAC 59.515 34.615 12.21 0.00 46.57 2.93
2765 2846 5.693104 TGACCGTTGTTAGCTTAAGTACTTG 59.307 40.000 18.56 3.44 0.00 3.16
2809 2890 3.218453 TGGCGGAAACTTTCTGAATTCA 58.782 40.909 13.66 8.12 38.34 2.57
2846 2927 8.294954 AGGACATATATATCGAAGTAACCCTG 57.705 38.462 0.00 0.00 0.00 4.45
2912 2993 4.424061 TGTGAAGCATTGCATGTAGAAC 57.576 40.909 11.91 0.22 0.00 3.01
2918 3000 5.599359 TGAAAATTGTGAAGCATTGCATG 57.401 34.783 11.91 0.00 0.00 4.06
2930 3012 4.992319 ACATGGACTTGCATGAAAATTGTG 59.008 37.500 16.67 0.00 33.38 3.33
3038 3124 2.128035 GTCTGTGACACTCAACTTCGG 58.872 52.381 7.20 0.00 32.09 4.30
3067 3153 5.298989 TGTTGGAGTAGTGGCTAGAAAAA 57.701 39.130 0.00 0.00 0.00 1.94
3116 3202 9.709495 ATGAAAATCATGCTACTGCTTTAAAAA 57.291 25.926 0.00 0.00 35.43 1.94
3117 3203 9.142515 CATGAAAATCATGCTACTGCTTTAAAA 57.857 29.630 7.35 0.00 46.37 1.52
3118 3204 8.692110 CATGAAAATCATGCTACTGCTTTAAA 57.308 30.769 7.35 0.00 46.37 1.52
3237 4638 3.115390 CCCCAGGTTCCAAATCTCTCTA 58.885 50.000 0.00 0.00 0.00 2.43
3364 4765 0.243907 CACGAAGAGAAGGAAGCGGA 59.756 55.000 0.00 0.00 0.00 5.54
3429 4830 1.003839 GGTTGTCTCATGTCCCGCA 60.004 57.895 0.00 0.00 0.00 5.69
3678 7914 8.475639 GTTATATCAGAGGTTTGGTTACTCAGA 58.524 37.037 0.00 0.00 33.76 3.27
3720 7956 2.892852 TCACAAGGCAAGCAAAAGCTAT 59.107 40.909 0.00 0.00 0.00 2.97
3769 8005 8.809066 ACCATCGTTAGCTGTAATACCATTATA 58.191 33.333 0.00 0.00 0.00 0.98
3910 8149 2.184830 CCGGTGAGCCAGCATGATG 61.185 63.158 3.34 3.34 39.69 3.07
4105 8344 0.040067 GCGCAAACTCAAACCTGGAG 60.040 55.000 0.30 0.00 38.36 3.86
4147 8386 1.571215 CGGTTAACCTGAACACGGGC 61.571 60.000 22.12 0.00 33.65 6.13
4232 8472 2.965572 AACAACAAGCAACAGCACAT 57.034 40.000 0.00 0.00 0.00 3.21
4235 8475 3.192422 ACAGTAAACAACAAGCAACAGCA 59.808 39.130 0.00 0.00 0.00 4.41
4365 8614 5.978919 TGAACGTACCATATTTGATACGACC 59.021 40.000 15.86 7.90 42.27 4.79
4399 8648 1.806542 AGCTACACGGAATGCAAAGTG 59.193 47.619 11.07 11.07 40.17 3.16
4401 8650 2.226437 ACAAGCTACACGGAATGCAAAG 59.774 45.455 0.00 0.00 0.00 2.77
4405 8654 2.989422 AAACAAGCTACACGGAATGC 57.011 45.000 0.00 0.00 0.00 3.56
4406 8655 3.252215 TGGAAAACAAGCTACACGGAATG 59.748 43.478 0.00 0.00 0.00 2.67
4408 8657 2.920524 TGGAAAACAAGCTACACGGAA 58.079 42.857 0.00 0.00 0.00 4.30
4409 8658 2.623878 TGGAAAACAAGCTACACGGA 57.376 45.000 0.00 0.00 0.00 4.69
4410 8659 3.701532 TTTGGAAAACAAGCTACACGG 57.298 42.857 0.00 0.00 40.82 4.94
4412 8661 6.735130 ACAGTATTTGGAAAACAAGCTACAC 58.265 36.000 0.00 0.00 40.82 2.90
4413 8662 6.952773 ACAGTATTTGGAAAACAAGCTACA 57.047 33.333 0.00 0.00 40.82 2.74
4414 8663 9.908152 AATAACAGTATTTGGAAAACAAGCTAC 57.092 29.630 0.00 0.00 40.82 3.58
4455 8704 8.514330 TTGTTTGTTGTGGAAGAGTATAAACT 57.486 30.769 0.00 0.00 39.21 2.66
4456 8705 8.403236 ACTTGTTTGTTGTGGAAGAGTATAAAC 58.597 33.333 0.00 0.00 0.00 2.01
4464 8713 3.694072 CCTGACTTGTTTGTTGTGGAAGA 59.306 43.478 0.00 0.00 0.00 2.87
4472 8721 1.963515 GGCCATCCTGACTTGTTTGTT 59.036 47.619 0.00 0.00 0.00 2.83
4473 8722 1.620822 GGCCATCCTGACTTGTTTGT 58.379 50.000 0.00 0.00 0.00 2.83
4572 8821 8.118607 CCTCAAAGAAGAAGAAAAATGCAAAAC 58.881 33.333 0.00 0.00 0.00 2.43
4584 8833 8.474025 TGCAAAATTAAACCTCAAAGAAGAAGA 58.526 29.630 0.00 0.00 0.00 2.87
4597 8846 8.607441 AAGGAAAAGAGATGCAAAATTAAACC 57.393 30.769 0.00 0.00 0.00 3.27
4603 8852 6.461640 CAAGGAAGGAAAAGAGATGCAAAAT 58.538 36.000 0.00 0.00 0.00 1.82
4612 8861 6.410942 AAAACATCCAAGGAAGGAAAAGAG 57.589 37.500 0.00 0.00 41.92 2.85
4627 8876 7.781056 TGGCAAGGAAGAAATATAAAACATCC 58.219 34.615 0.00 0.00 0.00 3.51
4630 8879 7.875554 GGTTTGGCAAGGAAGAAATATAAAACA 59.124 33.333 0.00 0.00 0.00 2.83
4631 8880 7.333423 GGGTTTGGCAAGGAAGAAATATAAAAC 59.667 37.037 0.00 0.00 0.00 2.43
4633 8882 6.070481 GGGGTTTGGCAAGGAAGAAATATAAA 60.070 38.462 0.00 0.00 0.00 1.40
4634 8883 5.423931 GGGGTTTGGCAAGGAAGAAATATAA 59.576 40.000 0.00 0.00 0.00 0.98
4694 9076 9.305925 GCAATATAAAACATTCAAGAAAGAGGG 57.694 33.333 0.00 0.00 0.00 4.30
4708 9090 9.920946 AAGGAAGAGAATAGGCAATATAAAACA 57.079 29.630 0.00 0.00 0.00 2.83
4771 9154 7.330700 ACGTCAAAGAAGAAGAAAAATGCAAAA 59.669 29.630 0.00 0.00 0.00 2.44
4951 10212 9.515226 AAACATTAGTGAAAGTATACACCATGT 57.485 29.630 5.50 0.00 40.20 3.21
4957 10218 9.802039 AGGGAAAAACATTAGTGAAAGTATACA 57.198 29.630 5.50 0.00 0.00 2.29
5029 10539 6.542370 GCCACAAATAACTTCTGCCTATAAGA 59.458 38.462 0.00 0.00 0.00 2.10
5030 10540 6.511767 CGCCACAAATAACTTCTGCCTATAAG 60.512 42.308 0.00 0.00 0.00 1.73
5071 10581 7.492669 ACACCAGTGATATTTTCTTGAGATACG 59.507 37.037 4.48 0.00 0.00 3.06
5081 10591 6.255887 CGTTCTCCTACACCAGTGATATTTTC 59.744 42.308 4.48 0.00 0.00 2.29
5087 10597 1.825474 CCGTTCTCCTACACCAGTGAT 59.175 52.381 4.48 0.00 0.00 3.06
5091 10601 1.898154 CCCCGTTCTCCTACACCAG 59.102 63.158 0.00 0.00 0.00 4.00
5106 10616 2.422093 CCCTCTTGTTCTCTTATGCCCC 60.422 54.545 0.00 0.00 0.00 5.80
5107 10617 2.422093 CCCCTCTTGTTCTCTTATGCCC 60.422 54.545 0.00 0.00 0.00 5.36
5117 10627 4.023291 TGAATAATTGCCCCCTCTTGTTC 58.977 43.478 0.00 0.00 0.00 3.18
5178 10946 1.310904 TTTTGCCGGCGTCTTACTTT 58.689 45.000 23.90 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.