Multiple sequence alignment - TraesCS7D01G334100

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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 TraesCS7D01G334100 chr7D 100.000 4125 0 0 1 4125 426155634 426151510 0.000000e+00 7618
1 TraesCS7D01G334100 chr7D 88.806 134 15 0 3551 3684 436459626 436459759 9.170000e-37 165
2 TraesCS7D01G334100 chr7B 93.245 3790 153 47 343 4081 443346361 443342624 0.000000e+00 5485
3 TraesCS7D01G334100 chr7B 77.558 303 40 13 71 348 443346794 443346495 1.540000e-34 158
4 TraesCS7D01G334100 chr7A 89.713 3101 165 68 442 3472 507171105 507174121 0.000000e+00 3818
5 TraesCS7D01G334100 chr3B 91.200 125 11 0 3560 3684 528176332 528176208 1.970000e-38 171
6 TraesCS7D01G334100 chr4B 88.806 134 15 0 3551 3684 106227560 106227427 9.170000e-37 165
7 TraesCS7D01G334100 chr3A 88.889 135 13 2 3551 3684 208074164 208074031 9.170000e-37 165
8 TraesCS7D01G334100 chr5D 88.889 135 12 2 3551 3682 233044594 233044460 3.300000e-36 163
9 TraesCS7D01G334100 chr2A 87.770 139 15 2 3548 3684 176673421 176673283 1.190000e-35 161
10 TraesCS7D01G334100 chr6B 86.806 144 13 6 3543 3684 502316237 502316376 5.520000e-34 156
11 TraesCS7D01G334100 chr5B 86.713 143 16 3 3544 3684 68901369 68901228 5.520000e-34 156
12 TraesCS7D01G334100 chr6D 85.821 134 17 2 3058 3189 61793420 61793553 1.550000e-29 141
13 TraesCS7D01G334100 chr6A 84.106 151 19 3 3058 3206 79088896 79089043 1.550000e-29 141


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 TraesCS7D01G334100 chr7D 426151510 426155634 4124 True 7618.0 7618 100.0000 1 4125 1 chr7D.!!$R1 4124
1 TraesCS7D01G334100 chr7B 443342624 443346794 4170 True 2821.5 5485 85.4015 71 4081 2 chr7B.!!$R1 4010
2 TraesCS7D01G334100 chr7A 507171105 507174121 3016 False 3818.0 3818 89.7130 442 3472 1 chr7A.!!$F1 3030

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
346 371 0.178958 AGGTTCGAGTCCTGAGTGGT 60.179 55.0 9.87 0.0 37.07 4.16 F
347 372 0.244178 GGTTCGAGTCCTGAGTGGTC 59.756 60.0 2.12 0.0 37.07 4.02 F
1087 1268 0.686441 CGATGACTCCCTACCACCCA 60.686 60.0 0.00 0.0 0.00 4.51 F
2131 2353 0.168788 CATGTGTAACGGCCTTGCTG 59.831 55.0 0.00 0.0 42.39 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 2245 0.034574 TTGTAATGGATGCTGCCGGT 60.035 50.0 1.90 0.0 0.00 5.28 R
2123 2345 0.520404 CATATCATCCGCAGCAAGGC 59.480 55.0 0.00 0.0 0.00 4.35 R
2910 3138 0.037447 GCTGTTCCTCTTCTTGCCCT 59.963 55.0 0.00 0.0 0.00 5.19 R
4030 4285 0.165727 CAAGTATTTGAGCACGCGCA 59.834 50.0 5.73 0.0 42.27 6.09 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
24 25 7.938140 AAACAAATAGTTGCTGATAGGCTAA 57.062 32.000 2.17 0.00 41.19 3.09
25 26 7.938140 AACAAATAGTTGCTGATAGGCTAAA 57.062 32.000 2.17 0.00 39.49 1.85
26 27 7.938140 ACAAATAGTTGCTGATAGGCTAAAA 57.062 32.000 2.17 0.00 38.39 1.52
27 28 8.348285 ACAAATAGTTGCTGATAGGCTAAAAA 57.652 30.769 2.17 0.00 38.39 1.94
66 67 5.804639 ACATCTAAATGTGCCTTAGTCACA 58.195 37.500 0.00 0.00 44.51 3.58
67 68 5.643777 ACATCTAAATGTGCCTTAGTCACAC 59.356 40.000 0.00 0.00 45.83 3.82
68 69 4.575885 TCTAAATGTGCCTTAGTCACACC 58.424 43.478 0.00 0.00 45.83 4.16
69 70 2.200373 AATGTGCCTTAGTCACACCC 57.800 50.000 0.00 0.00 45.83 4.61
74 75 3.136809 TGTGCCTTAGTCACACCCTTTTA 59.863 43.478 0.00 0.00 39.29 1.52
82 83 7.173390 CCTTAGTCACACCCTTTTAGAAAAGAG 59.827 40.741 14.88 5.64 46.39 2.85
84 85 5.132144 AGTCACACCCTTTTAGAAAAGAGGA 59.868 40.000 20.18 8.40 46.39 3.71
85 86 6.004574 GTCACACCCTTTTAGAAAAGAGGAT 58.995 40.000 20.18 10.70 46.39 3.24
86 87 6.003950 TCACACCCTTTTAGAAAAGAGGATG 58.996 40.000 20.18 17.47 46.39 3.51
89 90 6.183361 ACACCCTTTTAGAAAAGAGGATGACT 60.183 38.462 20.18 4.24 46.39 3.41
94 95 7.231519 CCTTTTAGAAAAGAGGATGACTTTGGT 59.768 37.037 14.88 0.00 46.39 3.67
96 97 7.745620 TTAGAAAAGAGGATGACTTTGGTTC 57.254 36.000 0.00 0.00 37.59 3.62
144 145 7.054751 TCTCCGTTCATTAGAATGTCTCTCTA 58.945 38.462 2.32 0.00 38.77 2.43
175 176 1.317613 ACTTGCTTCAACAATCGCCA 58.682 45.000 0.00 0.00 0.00 5.69
177 178 0.597568 TTGCTTCAACAATCGCCAGG 59.402 50.000 0.00 0.00 0.00 4.45
179 180 0.598065 GCTTCAACAATCGCCAGGTT 59.402 50.000 0.00 0.00 0.00 3.50
180 181 1.810151 GCTTCAACAATCGCCAGGTTA 59.190 47.619 0.00 0.00 0.00 2.85
181 182 2.414161 GCTTCAACAATCGCCAGGTTAC 60.414 50.000 0.00 0.00 0.00 2.50
182 183 2.552599 TCAACAATCGCCAGGTTACA 57.447 45.000 0.00 0.00 0.00 2.41
183 184 2.852449 TCAACAATCGCCAGGTTACAA 58.148 42.857 0.00 0.00 0.00 2.41
184 185 3.417101 TCAACAATCGCCAGGTTACAAT 58.583 40.909 0.00 0.00 0.00 2.71
186 187 5.004448 TCAACAATCGCCAGGTTACAATTA 58.996 37.500 0.00 0.00 0.00 1.40
187 188 4.957759 ACAATCGCCAGGTTACAATTAC 57.042 40.909 0.00 0.00 0.00 1.89
188 189 4.328536 ACAATCGCCAGGTTACAATTACA 58.671 39.130 0.00 0.00 0.00 2.41
194 218 5.473846 TCGCCAGGTTACAATTACAAAATGA 59.526 36.000 0.00 0.00 0.00 2.57
203 227 5.261216 ACAATTACAAAATGACGGGAGGAT 58.739 37.500 0.00 0.00 0.00 3.24
213 237 3.649843 TGACGGGAGGATAGGTAATGTT 58.350 45.455 0.00 0.00 0.00 2.71
237 262 9.486857 GTTCTGTAAGTTTGTACTCTTCAAAAC 57.513 33.333 0.00 0.00 36.71 2.43
242 267 9.836076 GTAAGTTTGTACTCTTCAAAACAACTT 57.164 29.630 6.91 0.00 36.71 2.66
260 285 7.141100 ACAACTTAAACATTATCCTCAACGG 57.859 36.000 0.00 0.00 0.00 4.44
270 295 7.609056 ACATTATCCTCAACGGGTATATGTAC 58.391 38.462 0.00 0.00 32.83 2.90
272 297 5.979288 ATCCTCAACGGGTATATGTACTC 57.021 43.478 0.00 0.00 0.00 2.59
273 298 4.147321 TCCTCAACGGGTATATGTACTCC 58.853 47.826 0.00 0.00 0.00 3.85
274 299 3.893200 CCTCAACGGGTATATGTACTCCA 59.107 47.826 0.00 0.00 0.00 3.86
275 300 4.342951 CCTCAACGGGTATATGTACTCCAA 59.657 45.833 0.00 0.00 0.00 3.53
282 307 5.395990 CGGGTATATGTACTCCAAACCAACT 60.396 44.000 0.00 0.00 0.00 3.16
305 330 1.222567 GGTTGGATGGGTAGGTGGAT 58.777 55.000 0.00 0.00 0.00 3.41
312 337 3.244911 GGATGGGTAGGTGGATAATGGTG 60.245 52.174 0.00 0.00 0.00 4.17
327 352 1.462928 GGTGTTCCCATCCCACCAA 59.537 57.895 3.28 0.00 46.33 3.67
333 358 1.378514 CCCATCCCACCAAGGTTCG 60.379 63.158 0.00 0.00 34.66 3.95
338 363 1.003718 CCCACCAAGGTTCGAGTCC 60.004 63.158 0.00 1.17 34.66 3.85
340 365 0.320771 CCACCAAGGTTCGAGTCCTG 60.321 60.000 11.14 4.00 35.27 3.86
341 366 0.679505 CACCAAGGTTCGAGTCCTGA 59.320 55.000 11.14 0.00 35.27 3.86
342 367 0.969894 ACCAAGGTTCGAGTCCTGAG 59.030 55.000 11.14 8.62 35.27 3.35
343 368 0.969894 CCAAGGTTCGAGTCCTGAGT 59.030 55.000 11.14 0.00 35.27 3.41
345 370 0.969894 AAGGTTCGAGTCCTGAGTGG 59.030 55.000 11.14 0.00 35.27 4.00
346 371 0.178958 AGGTTCGAGTCCTGAGTGGT 60.179 55.000 9.87 0.00 37.07 4.16
347 372 0.244178 GGTTCGAGTCCTGAGTGGTC 59.756 60.000 2.12 0.00 37.07 4.02
348 373 0.959553 GTTCGAGTCCTGAGTGGTCA 59.040 55.000 0.00 0.00 37.07 4.02
349 374 1.546476 GTTCGAGTCCTGAGTGGTCAT 59.454 52.381 0.00 0.00 37.07 3.06
350 375 2.753452 GTTCGAGTCCTGAGTGGTCATA 59.247 50.000 0.00 0.00 37.07 2.15
351 376 2.644676 TCGAGTCCTGAGTGGTCATAG 58.355 52.381 0.00 0.00 37.07 2.23
352 377 1.678627 CGAGTCCTGAGTGGTCATAGG 59.321 57.143 0.00 0.00 37.07 2.57
357 521 4.417183 AGTCCTGAGTGGTCATAGGATAGA 59.583 45.833 0.00 0.00 31.47 1.98
370 534 6.148976 GTCATAGGATAGAGTGTGCGTATGTA 59.851 42.308 0.00 0.00 33.34 2.29
375 539 5.983720 GGATAGAGTGTGCGTATGTATGTTT 59.016 40.000 0.00 0.00 0.00 2.83
381 545 7.652105 AGAGTGTGCGTATGTATGTTTATAAGG 59.348 37.037 0.00 0.00 0.00 2.69
411 575 9.051679 AGTGTATTTAATGTATATTTGAGCGCA 57.948 29.630 11.47 0.00 0.00 6.09
414 578 7.801547 ATTTAATGTATATTTGAGCGCATGC 57.198 32.000 11.47 7.91 43.24 4.06
426 590 1.330306 GCGCATGCTTTTGTACTGTG 58.670 50.000 17.13 0.00 38.39 3.66
433 597 6.344936 CGCATGCTTTTGTACTGTGTTAAAAG 60.345 38.462 17.13 15.47 40.98 2.27
436 600 9.081997 CATGCTTTTGTACTGTGTTAAAAGAAA 57.918 29.630 20.25 12.58 40.68 2.52
437 601 8.455598 TGCTTTTGTACTGTGTTAAAAGAAAC 57.544 30.769 20.25 10.06 40.68 2.78
438 602 7.271653 TGCTTTTGTACTGTGTTAAAAGAAACG 59.728 33.333 20.25 0.00 40.68 3.60
497 662 5.105473 ACGATGTACTAGGCACACAACTAAT 60.105 40.000 1.91 0.00 0.00 1.73
571 736 1.459450 AGTGGCAAGTGTCAACGTTT 58.541 45.000 0.00 0.00 0.00 3.60
584 749 2.100087 TCAACGTTTCCCTTTTGCTTCC 59.900 45.455 0.00 0.00 0.00 3.46
658 826 4.287585 TCCCACTCCAATTATATAACCCCG 59.712 45.833 0.00 0.00 0.00 5.73
659 827 4.287585 CCCACTCCAATTATATAACCCCGA 59.712 45.833 0.00 0.00 0.00 5.14
660 828 5.243207 CCACTCCAATTATATAACCCCGAC 58.757 45.833 0.00 0.00 0.00 4.79
661 829 5.243207 CACTCCAATTATATAACCCCGACC 58.757 45.833 0.00 0.00 0.00 4.79
674 842 1.969064 CCGACCCAACGGCAATCAA 60.969 57.895 0.00 0.00 46.20 2.57
675 843 1.209127 CGACCCAACGGCAATCAAC 59.791 57.895 0.00 0.00 0.00 3.18
679 852 1.482593 ACCCAACGGCAATCAACAAAA 59.517 42.857 0.00 0.00 0.00 2.44
722 895 5.726560 TCCCCAATTCCATGAGACTATAGA 58.273 41.667 6.78 0.00 0.00 1.98
767 940 5.239525 ACCAGTCTTGAAAACTAGTCAATGC 59.760 40.000 0.00 0.00 34.59 3.56
801 974 3.012722 GTCCATTCCCCCGTCCCA 61.013 66.667 0.00 0.00 0.00 4.37
816 989 5.708697 CCCCGTCCCATATTTTAATTCCTAC 59.291 44.000 0.00 0.00 0.00 3.18
817 990 6.466759 CCCCGTCCCATATTTTAATTCCTACT 60.467 42.308 0.00 0.00 0.00 2.57
818 991 7.256763 CCCCGTCCCATATTTTAATTCCTACTA 60.257 40.741 0.00 0.00 0.00 1.82
819 992 7.605309 CCCGTCCCATATTTTAATTCCTACTAC 59.395 40.741 0.00 0.00 0.00 2.73
956 1134 4.340666 CACATAGACTGCATGTAGAGAGGT 59.659 45.833 18.40 6.80 34.88 3.85
1032 1210 4.087892 GAGAAGGAGGCGCTGGCA 62.088 66.667 7.64 0.00 42.47 4.92
1033 1211 4.093291 AGAAGGAGGCGCTGGCAG 62.093 66.667 10.94 10.94 42.47 4.85
1047 1225 1.221840 GGCAGCGGAGATCCTTGAA 59.778 57.895 0.00 0.00 0.00 2.69
1087 1268 0.686441 CGATGACTCCCTACCACCCA 60.686 60.000 0.00 0.00 0.00 4.51
1105 1286 4.410400 CGGGGCTGGACCTCAACC 62.410 72.222 0.00 0.00 40.00 3.77
1121 1302 2.437359 CCAAGGCTTCAGCGAGGG 60.437 66.667 0.00 0.00 43.26 4.30
1476 1674 7.302524 TCGTGATCTAAACTTTTATTTGTGCC 58.697 34.615 0.00 0.00 0.00 5.01
1722 1928 8.939929 CAGATGTACAGAAGCAAAAAGATAGAA 58.060 33.333 0.33 0.00 0.00 2.10
1766 1972 3.624777 CAGCCATGTCCTCAGGTTATTT 58.375 45.455 0.00 0.00 0.00 1.40
1769 1975 6.533730 CAGCCATGTCCTCAGGTTATTTATA 58.466 40.000 0.00 0.00 0.00 0.98
1808 2015 7.738847 TGATGCTGGATATCTCACTATTTTCA 58.261 34.615 2.05 0.00 0.00 2.69
1809 2016 7.658982 TGATGCTGGATATCTCACTATTTTCAC 59.341 37.037 2.05 0.00 0.00 3.18
1810 2017 6.888105 TGCTGGATATCTCACTATTTTCACA 58.112 36.000 2.05 0.00 0.00 3.58
1826 2033 9.778993 CTATTTTCACACACTAGGAATTCATTG 57.221 33.333 7.93 3.73 0.00 2.82
1835 2042 5.297776 CACTAGGAATTCATTGTCATGACCC 59.702 44.000 22.85 13.50 39.28 4.46
2027 2245 0.988832 ATTTACGGGCTCCTCCAACA 59.011 50.000 0.00 0.00 36.21 3.33
2036 2254 4.641645 CCTCCAACACCGGCAGCA 62.642 66.667 0.00 0.00 0.00 4.41
2120 2342 4.943093 ACAGCATCTTACATGCATGTGTAA 59.057 37.500 36.72 24.58 46.77 2.41
2121 2343 5.163723 ACAGCATCTTACATGCATGTGTAAC 60.164 40.000 36.72 22.02 46.77 2.50
2123 2345 4.786292 GCATCTTACATGCATGTGTAACGG 60.786 45.833 36.72 23.06 44.00 4.44
2124 2346 2.675844 TCTTACATGCATGTGTAACGGC 59.324 45.455 36.72 0.00 42.39 5.68
2125 2347 1.374560 TACATGCATGTGTAACGGCC 58.625 50.000 36.72 0.00 42.39 6.13
2126 2348 0.322456 ACATGCATGTGTAACGGCCT 60.322 50.000 30.92 2.17 42.39 5.19
2127 2349 0.810648 CATGCATGTGTAACGGCCTT 59.189 50.000 18.91 0.00 42.39 4.35
2128 2350 0.810648 ATGCATGTGTAACGGCCTTG 59.189 50.000 0.00 0.00 42.39 3.61
2129 2351 1.154035 GCATGTGTAACGGCCTTGC 60.154 57.895 0.00 0.00 42.39 4.01
2130 2352 1.586154 GCATGTGTAACGGCCTTGCT 61.586 55.000 0.00 0.00 42.39 3.91
2131 2353 0.168788 CATGTGTAACGGCCTTGCTG 59.831 55.000 0.00 0.00 42.39 4.41
2133 2355 3.047280 TGTAACGGCCTTGCTGCG 61.047 61.111 0.00 0.00 38.71 5.18
2134 2356 3.799755 GTAACGGCCTTGCTGCGG 61.800 66.667 0.00 0.00 38.71 5.69
2135 2357 4.010224 TAACGGCCTTGCTGCGGA 62.010 61.111 0.00 0.00 38.71 5.54
2136 2358 3.323758 TAACGGCCTTGCTGCGGAT 62.324 57.895 0.00 0.25 38.71 4.18
2139 2361 2.517875 GGCCTTGCTGCGGATGAT 60.518 61.111 0.00 0.00 0.00 2.45
2140 2362 1.227943 GGCCTTGCTGCGGATGATA 60.228 57.895 0.00 0.00 0.00 2.15
2141 2363 0.607489 GGCCTTGCTGCGGATGATAT 60.607 55.000 0.00 0.00 0.00 1.63
2151 2373 4.734695 GCTGCGGATGATATGACGATCATA 60.735 45.833 0.00 9.22 44.78 2.15
2509 2737 1.134699 CACGCTCAGCTCCCATTTAGA 60.135 52.381 0.00 0.00 0.00 2.10
2660 2888 8.458052 ACACATTTTGCTTCGAATTGATACATA 58.542 29.630 0.00 0.00 0.00 2.29
2907 3135 2.970639 GGCGGCAGACACTGTAGA 59.029 61.111 3.07 0.00 33.43 2.59
2910 3138 1.508632 GCGGCAGACACTGTAGAAAA 58.491 50.000 0.00 0.00 33.43 2.29
3106 3334 4.532126 AGTACTTTGGATCTGACCATGTCA 59.468 41.667 0.00 0.00 40.50 3.58
3145 3373 5.346281 GTGAGATCTTTCAAGTACTTGTCCG 59.654 44.000 29.83 19.85 41.16 4.79
3287 3520 5.584253 TGTAGAGCTAGGATGACTGTTTC 57.416 43.478 0.00 0.00 0.00 2.78
3357 3606 4.217118 GCATGGTATCATTGGGCTTCTAAG 59.783 45.833 0.00 0.00 0.00 2.18
3369 3618 9.896645 CATTGGGCTTCTAAGTCATATATATGT 57.103 33.333 19.78 6.17 35.26 2.29
3480 3732 5.467705 GGTACATTAGGGCAGTCTTATACG 58.532 45.833 0.00 0.00 0.00 3.06
3485 3737 6.706270 ACATTAGGGCAGTCTTATACGAAATG 59.294 38.462 0.00 0.00 0.00 2.32
3495 3747 8.604035 CAGTCTTATACGAAATGCACACTTATT 58.396 33.333 0.00 0.00 0.00 1.40
3504 3756 6.803320 CGAAATGCACACTTATTGATCAAACT 59.197 34.615 13.09 0.00 0.00 2.66
3505 3757 7.007725 CGAAATGCACACTTATTGATCAAACTC 59.992 37.037 13.09 0.00 0.00 3.01
3558 3810 7.716799 AATGGCATTAATAAACACTCCTTCA 57.283 32.000 11.81 0.00 0.00 3.02
3573 3825 8.918202 ACACTCCTTCAGTTCACAAATATAAA 57.082 30.769 0.00 0.00 30.26 1.40
3598 3850 9.665719 AAATGTTTTGGGTATTTTCATATGGAC 57.334 29.630 2.13 0.00 0.00 4.02
3606 3858 8.092068 TGGGTATTTTCATATGGACTACATACG 58.908 37.037 2.13 0.00 44.41 3.06
3611 3863 5.959618 TCATATGGACTACATACGGACTG 57.040 43.478 2.13 0.00 44.41 3.51
3655 3907 9.634163 CACTAAAACGTGCCTATATACATATCA 57.366 33.333 0.00 0.00 0.00 2.15
3707 3959 7.170393 TCATCTTATATATGTGAACGGAGGG 57.830 40.000 0.00 0.00 0.00 4.30
3779 4031 4.515944 ACTGTCCTAGTGCACTATATCGTC 59.484 45.833 26.22 13.72 38.49 4.20
3835 4089 8.600449 ATTTAGTGTCTTTTGTGAGAGAAGAG 57.400 34.615 0.00 0.00 30.66 2.85
3876 4130 9.935241 GGATTTGTTGCTAAGATCTATATCTGA 57.065 33.333 0.00 0.00 41.81 3.27
3915 4169 6.989169 AGATATGGTTGATTTCTCTTTCCTCG 59.011 38.462 0.00 0.00 0.00 4.63
3929 4183 0.109532 TCCTCGTGAAATTGGGTGCA 59.890 50.000 0.00 0.00 0.00 4.57
3937 4191 3.928375 GTGAAATTGGGTGCAACATCATC 59.072 43.478 3.06 0.00 39.98 2.92
3941 4195 3.663995 TTGGGTGCAACATCATCTTTG 57.336 42.857 3.06 0.00 39.98 2.77
3952 4206 8.791675 TGCAACATCATCTTTGTAGTTATGAAA 58.208 29.630 0.00 0.00 32.47 2.69
3954 4208 9.559958 CAACATCATCTTTGTAGTTATGAAACC 57.440 33.333 0.00 0.00 36.15 3.27
3963 4217 6.677781 TGTAGTTATGAAACCATGCTAAGC 57.322 37.500 0.00 0.00 36.15 3.09
3970 4224 4.651778 TGAAACCATGCTAAGCTACAAGT 58.348 39.130 0.00 0.00 0.00 3.16
3972 4226 5.642063 TGAAACCATGCTAAGCTACAAGTAC 59.358 40.000 0.00 0.00 0.00 2.73
3981 4235 6.323996 TGCTAAGCTACAAGTACACATATCCT 59.676 38.462 0.00 0.00 0.00 3.24
3995 4249 9.537848 GTACACATATCCTTAAACTCGTTTTTG 57.462 33.333 0.00 0.00 34.23 2.44
3999 4254 4.904253 TCCTTAAACTCGTTTTTGGGTG 57.096 40.909 0.00 0.00 34.23 4.61
4028 4283 9.541143 AAATAAACTGGTTTAATTTGTCCTGTG 57.459 29.630 9.51 0.00 38.38 3.66
4030 4285 4.542697 ACTGGTTTAATTTGTCCTGTGGT 58.457 39.130 0.00 0.00 32.48 4.16
4033 4288 3.305110 GTTTAATTTGTCCTGTGGTGCG 58.695 45.455 0.00 0.00 0.00 5.34
4034 4289 0.878416 TAATTTGTCCTGTGGTGCGC 59.122 50.000 0.00 0.00 0.00 6.09
4035 4290 2.128853 AATTTGTCCTGTGGTGCGCG 62.129 55.000 0.00 0.00 0.00 6.86
4049 4304 0.165727 TGCGCGTGCTCAAATACTTG 59.834 50.000 23.16 0.00 43.34 3.16
4085 4340 8.532186 ACTAGATTAGGATGAGCAGTATATGG 57.468 38.462 0.00 0.00 0.00 2.74
4086 4341 8.340002 ACTAGATTAGGATGAGCAGTATATGGA 58.660 37.037 0.00 0.00 0.00 3.41
4087 4342 9.194972 CTAGATTAGGATGAGCAGTATATGGAA 57.805 37.037 0.00 0.00 0.00 3.53
4088 4343 8.076910 AGATTAGGATGAGCAGTATATGGAAG 57.923 38.462 0.00 0.00 0.00 3.46
4089 4344 6.611613 TTAGGATGAGCAGTATATGGAAGG 57.388 41.667 0.00 0.00 0.00 3.46
4090 4345 4.497516 AGGATGAGCAGTATATGGAAGGT 58.502 43.478 0.00 0.00 0.00 3.50
4091 4346 4.285517 AGGATGAGCAGTATATGGAAGGTG 59.714 45.833 0.00 0.00 0.00 4.00
4092 4347 4.284490 GGATGAGCAGTATATGGAAGGTGA 59.716 45.833 0.00 0.00 0.00 4.02
4093 4348 5.221722 GGATGAGCAGTATATGGAAGGTGAA 60.222 44.000 0.00 0.00 0.00 3.18
4094 4349 5.282055 TGAGCAGTATATGGAAGGTGAAG 57.718 43.478 0.00 0.00 0.00 3.02
4095 4350 4.061596 GAGCAGTATATGGAAGGTGAAGC 58.938 47.826 0.00 0.00 0.00 3.86
4096 4351 3.713764 AGCAGTATATGGAAGGTGAAGCT 59.286 43.478 0.00 0.00 0.00 3.74
4097 4352 4.901849 AGCAGTATATGGAAGGTGAAGCTA 59.098 41.667 0.00 0.00 0.00 3.32
4098 4353 4.991687 GCAGTATATGGAAGGTGAAGCTAC 59.008 45.833 0.00 0.00 0.00 3.58
4099 4354 5.221541 GCAGTATATGGAAGGTGAAGCTACT 60.222 44.000 0.00 0.00 0.00 2.57
4100 4355 6.686632 GCAGTATATGGAAGGTGAAGCTACTT 60.687 42.308 0.00 0.00 0.00 2.24
4101 4356 7.275920 CAGTATATGGAAGGTGAAGCTACTTT 58.724 38.462 0.00 0.00 0.00 2.66
4102 4357 7.439655 CAGTATATGGAAGGTGAAGCTACTTTC 59.560 40.741 3.49 3.49 36.32 2.62
4109 4364 7.506328 GAAGGTGAAGCTACTTTCCTAAAAA 57.494 36.000 1.04 0.00 32.39 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.938140 TTAGCCTATCAGCAACTATTTGTTT 57.062 32.000 0.00 0.00 36.63 2.83
1 2 7.938140 TTTAGCCTATCAGCAACTATTTGTT 57.062 32.000 0.00 0.00 39.92 2.83
2 3 7.938140 TTTTAGCCTATCAGCAACTATTTGT 57.062 32.000 0.00 0.00 34.90 2.83
43 44 5.643777 GTGTGACTAAGGCACATTTAGATGT 59.356 40.000 9.62 0.00 46.65 3.06
44 45 5.065218 GGTGTGACTAAGGCACATTTAGATG 59.935 44.000 9.62 0.00 46.65 2.90
45 46 5.186198 GGTGTGACTAAGGCACATTTAGAT 58.814 41.667 9.62 0.00 46.65 1.98
46 47 4.564821 GGGTGTGACTAAGGCACATTTAGA 60.565 45.833 9.62 0.00 46.65 2.10
47 48 3.689649 GGGTGTGACTAAGGCACATTTAG 59.310 47.826 9.62 0.00 46.65 1.85
48 49 3.329520 AGGGTGTGACTAAGGCACATTTA 59.670 43.478 9.62 0.00 46.65 1.40
49 50 2.108250 AGGGTGTGACTAAGGCACATTT 59.892 45.455 9.62 0.00 46.65 2.32
50 51 1.705186 AGGGTGTGACTAAGGCACATT 59.295 47.619 9.62 0.00 46.65 2.71
51 52 1.362224 AGGGTGTGACTAAGGCACAT 58.638 50.000 9.62 0.00 46.65 3.21
52 53 1.136828 AAGGGTGTGACTAAGGCACA 58.863 50.000 2.01 2.01 43.41 4.57
53 54 2.271944 AAAGGGTGTGACTAAGGCAC 57.728 50.000 0.00 0.00 36.81 5.01
54 55 3.649023 TCTAAAAGGGTGTGACTAAGGCA 59.351 43.478 0.00 0.00 0.00 4.75
55 56 4.281898 TCTAAAAGGGTGTGACTAAGGC 57.718 45.455 0.00 0.00 0.00 4.35
56 57 6.996282 TCTTTTCTAAAAGGGTGTGACTAAGG 59.004 38.462 13.69 0.00 44.22 2.69
57 58 7.173390 CCTCTTTTCTAAAAGGGTGTGACTAAG 59.827 40.741 12.77 1.83 43.41 2.18
58 59 6.996282 CCTCTTTTCTAAAAGGGTGTGACTAA 59.004 38.462 12.77 0.00 43.41 2.24
59 60 6.328148 TCCTCTTTTCTAAAAGGGTGTGACTA 59.672 38.462 12.77 0.00 43.41 2.59
60 61 5.132144 TCCTCTTTTCTAAAAGGGTGTGACT 59.868 40.000 12.77 0.00 43.41 3.41
61 62 5.374071 TCCTCTTTTCTAAAAGGGTGTGAC 58.626 41.667 12.77 0.00 43.41 3.67
62 63 5.640158 TCCTCTTTTCTAAAAGGGTGTGA 57.360 39.130 12.77 2.43 43.41 3.58
63 64 6.003950 TCATCCTCTTTTCTAAAAGGGTGTG 58.996 40.000 12.77 10.75 43.41 3.82
64 65 6.004574 GTCATCCTCTTTTCTAAAAGGGTGT 58.995 40.000 12.77 0.43 43.41 4.16
65 66 6.241645 AGTCATCCTCTTTTCTAAAAGGGTG 58.758 40.000 12.77 7.08 43.41 4.61
66 67 6.455690 AGTCATCCTCTTTTCTAAAAGGGT 57.544 37.500 12.77 0.00 43.41 4.34
67 68 7.309438 CCAAAGTCATCCTCTTTTCTAAAAGGG 60.309 40.741 13.69 10.91 44.30 3.95
68 69 7.231519 ACCAAAGTCATCCTCTTTTCTAAAAGG 59.768 37.037 13.69 1.86 44.22 3.11
69 70 8.171164 ACCAAAGTCATCCTCTTTTCTAAAAG 57.829 34.615 8.58 8.58 45.17 2.27
74 75 5.073428 GGAACCAAAGTCATCCTCTTTTCT 58.927 41.667 0.00 0.00 33.58 2.52
82 83 5.638596 ATTTTACGGAACCAAAGTCATCC 57.361 39.130 0.00 0.00 0.00 3.51
84 85 6.717997 ACCTAATTTTACGGAACCAAAGTCAT 59.282 34.615 0.00 0.00 0.00 3.06
85 86 6.063404 ACCTAATTTTACGGAACCAAAGTCA 58.937 36.000 0.00 0.00 0.00 3.41
86 87 6.564709 ACCTAATTTTACGGAACCAAAGTC 57.435 37.500 0.00 0.00 0.00 3.01
89 90 9.737844 AACTATACCTAATTTTACGGAACCAAA 57.262 29.630 0.00 0.00 0.00 3.28
164 165 3.848272 ATTGTAACCTGGCGATTGTTG 57.152 42.857 0.00 0.00 0.00 3.33
172 173 5.571357 CGTCATTTTGTAATTGTAACCTGGC 59.429 40.000 0.00 0.00 0.00 4.85
175 176 6.005198 TCCCGTCATTTTGTAATTGTAACCT 58.995 36.000 0.00 0.00 0.00 3.50
177 178 6.149807 TCCTCCCGTCATTTTGTAATTGTAAC 59.850 38.462 0.00 0.00 0.00 2.50
179 180 5.806818 TCCTCCCGTCATTTTGTAATTGTA 58.193 37.500 0.00 0.00 0.00 2.41
180 181 4.658063 TCCTCCCGTCATTTTGTAATTGT 58.342 39.130 0.00 0.00 0.00 2.71
181 182 5.835113 ATCCTCCCGTCATTTTGTAATTG 57.165 39.130 0.00 0.00 0.00 2.32
182 183 6.062095 CCTATCCTCCCGTCATTTTGTAATT 58.938 40.000 0.00 0.00 0.00 1.40
183 184 5.132144 ACCTATCCTCCCGTCATTTTGTAAT 59.868 40.000 0.00 0.00 0.00 1.89
184 185 4.472108 ACCTATCCTCCCGTCATTTTGTAA 59.528 41.667 0.00 0.00 0.00 2.41
186 187 2.844348 ACCTATCCTCCCGTCATTTTGT 59.156 45.455 0.00 0.00 0.00 2.83
187 188 3.560636 ACCTATCCTCCCGTCATTTTG 57.439 47.619 0.00 0.00 0.00 2.44
188 189 5.132144 ACATTACCTATCCTCCCGTCATTTT 59.868 40.000 0.00 0.00 0.00 1.82
194 218 3.641906 CAGAACATTACCTATCCTCCCGT 59.358 47.826 0.00 0.00 0.00 5.28
203 227 9.918630 GAGTACAAACTTACAGAACATTACCTA 57.081 33.333 0.00 0.00 35.56 3.08
213 237 8.780846 TGTTTTGAAGAGTACAAACTTACAGA 57.219 30.769 0.00 0.00 37.05 3.41
237 262 6.150474 ACCCGTTGAGGATAATGTTTAAGTTG 59.850 38.462 0.00 0.00 45.00 3.16
242 267 8.653191 ACATATACCCGTTGAGGATAATGTTTA 58.347 33.333 0.00 0.00 45.00 2.01
244 269 7.074653 ACATATACCCGTTGAGGATAATGTT 57.925 36.000 0.00 0.00 45.00 2.71
245 270 6.681729 ACATATACCCGTTGAGGATAATGT 57.318 37.500 0.00 0.00 45.00 2.71
246 271 7.837863 AGTACATATACCCGTTGAGGATAATG 58.162 38.462 0.00 0.00 45.00 1.90
247 272 7.123847 GGAGTACATATACCCGTTGAGGATAAT 59.876 40.741 0.00 0.00 45.00 1.28
248 273 6.435277 GGAGTACATATACCCGTTGAGGATAA 59.565 42.308 0.00 0.00 45.00 1.75
249 274 5.948162 GGAGTACATATACCCGTTGAGGATA 59.052 44.000 0.00 0.00 45.00 2.59
250 275 4.771054 GGAGTACATATACCCGTTGAGGAT 59.229 45.833 0.00 0.00 45.00 3.24
260 285 6.882678 ACAAGTTGGTTTGGAGTACATATACC 59.117 38.462 7.96 0.00 32.32 2.73
282 307 1.074727 CACCTACCCATCCAACCACAA 59.925 52.381 0.00 0.00 0.00 3.33
287 312 4.398319 CATTATCCACCTACCCATCCAAC 58.602 47.826 0.00 0.00 0.00 3.77
294 319 3.434596 GGAACACCATTATCCACCTACCC 60.435 52.174 0.00 0.00 33.30 3.69
296 321 3.201266 TGGGAACACCATTATCCACCTAC 59.799 47.826 0.00 0.00 46.80 3.18
312 337 0.114364 AACCTTGGTGGGATGGGAAC 59.886 55.000 0.00 0.00 41.11 3.62
319 344 1.477685 GGACTCGAACCTTGGTGGGA 61.478 60.000 0.00 0.00 41.11 4.37
327 352 0.178958 ACCACTCAGGACTCGAACCT 60.179 55.000 5.17 5.17 41.22 3.50
333 358 3.019799 TCCTATGACCACTCAGGACTC 57.980 52.381 0.00 0.00 41.22 3.36
338 363 5.009510 CACACTCTATCCTATGACCACTCAG 59.990 48.000 0.00 0.00 0.00 3.35
340 365 4.261825 GCACACTCTATCCTATGACCACTC 60.262 50.000 0.00 0.00 0.00 3.51
341 366 3.639094 GCACACTCTATCCTATGACCACT 59.361 47.826 0.00 0.00 0.00 4.00
342 367 3.551046 CGCACACTCTATCCTATGACCAC 60.551 52.174 0.00 0.00 0.00 4.16
343 368 2.623416 CGCACACTCTATCCTATGACCA 59.377 50.000 0.00 0.00 0.00 4.02
345 370 3.992260 ACGCACACTCTATCCTATGAC 57.008 47.619 0.00 0.00 0.00 3.06
346 371 5.070685 ACATACGCACACTCTATCCTATGA 58.929 41.667 0.00 0.00 0.00 2.15
347 372 5.378292 ACATACGCACACTCTATCCTATG 57.622 43.478 0.00 0.00 0.00 2.23
348 373 6.659668 ACATACATACGCACACTCTATCCTAT 59.340 38.462 0.00 0.00 0.00 2.57
349 374 6.002082 ACATACATACGCACACTCTATCCTA 58.998 40.000 0.00 0.00 0.00 2.94
350 375 4.827835 ACATACATACGCACACTCTATCCT 59.172 41.667 0.00 0.00 0.00 3.24
351 376 5.122512 ACATACATACGCACACTCTATCC 57.877 43.478 0.00 0.00 0.00 2.59
352 377 8.744008 ATAAACATACATACGCACACTCTATC 57.256 34.615 0.00 0.00 0.00 2.08
357 521 7.494211 TCCTTATAAACATACATACGCACACT 58.506 34.615 0.00 0.00 0.00 3.55
411 575 9.083080 GTTTCTTTTAACACAGTACAAAAGCAT 57.917 29.630 8.31 0.00 37.71 3.79
414 578 8.883789 TCGTTTCTTTTAACACAGTACAAAAG 57.116 30.769 7.27 7.27 38.66 2.27
415 579 8.505625 ACTCGTTTCTTTTAACACAGTACAAAA 58.494 29.630 0.00 0.00 0.00 2.44
433 597 8.922058 TCTTTCCAAGTACATATACTCGTTTC 57.078 34.615 0.00 0.00 41.00 2.78
436 600 9.314321 CAATTCTTTCCAAGTACATATACTCGT 57.686 33.333 0.00 0.00 41.00 4.18
437 601 9.314321 ACAATTCTTTCCAAGTACATATACTCG 57.686 33.333 0.00 0.00 41.00 4.18
516 681 0.178953 AACAACAGCTGCTCCCCATT 60.179 50.000 15.27 0.00 0.00 3.16
517 682 0.896940 CAACAACAGCTGCTCCCCAT 60.897 55.000 15.27 0.00 0.00 4.00
529 694 3.709653 AGACTCTTGTAGGGACAACAACA 59.290 43.478 0.00 0.00 40.72 3.33
571 736 1.219213 TGGGAAAGGAAGCAAAAGGGA 59.781 47.619 0.00 0.00 0.00 4.20
584 749 1.318576 GACTGGGTTGTGTGGGAAAG 58.681 55.000 0.00 0.00 0.00 2.62
635 803 4.287585 CGGGGTTATATAATTGGAGTGGGA 59.712 45.833 0.00 0.00 0.00 4.37
658 826 0.671251 TTGTTGATTGCCGTTGGGTC 59.329 50.000 0.00 0.00 34.97 4.46
659 827 1.115467 TTTGTTGATTGCCGTTGGGT 58.885 45.000 0.00 0.00 34.97 4.51
660 828 2.231215 TTTTGTTGATTGCCGTTGGG 57.769 45.000 0.00 0.00 0.00 4.12
661 829 4.747108 TGTTATTTTGTTGATTGCCGTTGG 59.253 37.500 0.00 0.00 0.00 3.77
679 852 7.359849 TGGGGAGTATACTACACTCTTGTTAT 58.640 38.462 18.37 0.00 41.78 1.89
767 940 4.196626 TGGACAAGTAGTAATTCCACCG 57.803 45.455 0.00 0.00 31.19 4.94
816 989 2.001812 AGCAAGCGAGTGATGTGTAG 57.998 50.000 0.00 0.00 0.00 2.74
817 990 2.455674 AAGCAAGCGAGTGATGTGTA 57.544 45.000 0.00 0.00 0.00 2.90
818 991 2.455674 TAAGCAAGCGAGTGATGTGT 57.544 45.000 0.00 0.00 0.00 3.72
819 992 2.538333 GCATAAGCAAGCGAGTGATGTG 60.538 50.000 0.00 0.00 41.58 3.21
956 1134 1.544691 GCTTGTCCTTGACCTCGTCTA 59.455 52.381 0.00 0.00 33.15 2.59
1032 1210 0.827368 GGTCTTCAAGGATCTCCGCT 59.173 55.000 0.00 0.00 42.08 5.52
1033 1211 0.537188 TGGTCTTCAAGGATCTCCGC 59.463 55.000 0.00 0.00 42.08 5.54
1034 1212 2.544694 CGATGGTCTTCAAGGATCTCCG 60.545 54.545 0.00 0.00 42.08 4.63
1047 1225 2.043227 GAAGATCCCTTCCGATGGTCT 58.957 52.381 0.00 0.00 42.24 3.85
1087 1268 3.637273 GTTGAGGTCCAGCCCCGT 61.637 66.667 0.00 0.00 38.26 5.28
1105 1286 1.003355 TTCCCTCGCTGAAGCCTTG 60.003 57.895 0.00 0.00 37.91 3.61
1121 1302 4.493747 CTCCCCCGTCGTCGCTTC 62.494 72.222 0.00 0.00 35.54 3.86
1476 1674 3.052036 CGTTGCTCCTGTCCAAAAATTG 58.948 45.455 0.00 0.00 0.00 2.32
1722 1928 2.910479 TCGTGGCTGGACTCGTGT 60.910 61.111 0.00 0.00 0.00 4.49
1808 2015 6.372659 GTCATGACAATGAATTCCTAGTGTGT 59.627 38.462 21.07 0.00 44.40 3.72
1809 2016 6.183360 GGTCATGACAATGAATTCCTAGTGTG 60.183 42.308 26.47 1.19 44.40 3.82
1810 2017 5.882557 GGTCATGACAATGAATTCCTAGTGT 59.117 40.000 26.47 0.50 44.40 3.55
1826 2033 9.803315 GAAATTAATAGGAAAAAGGGTCATGAC 57.197 33.333 17.91 17.91 0.00 3.06
1899 2108 3.338249 CTGGAAGAACATGTCGTGGAAT 58.662 45.455 0.00 0.00 34.07 3.01
1998 2216 1.663702 CCCGTAAATCCGGCTAGCG 60.664 63.158 9.00 4.07 46.71 4.26
2027 2245 0.034574 TTGTAATGGATGCTGCCGGT 60.035 50.000 1.90 0.00 0.00 5.28
2036 2254 5.556915 TGAAGTCGAAGGTTTGTAATGGAT 58.443 37.500 0.00 0.00 0.00 3.41
2091 2313 1.063027 CATGTAAGATGCTGTGTGGCG 59.937 52.381 0.00 0.00 34.52 5.69
2094 2316 3.128068 ACATGCATGTAAGATGCTGTGTG 59.872 43.478 30.50 0.42 44.79 3.82
2095 2317 3.128068 CACATGCATGTAAGATGCTGTGT 59.872 43.478 30.92 16.64 44.79 3.72
2121 2343 2.994387 TATCATCCGCAGCAAGGCCG 62.994 60.000 0.00 0.00 0.00 6.13
2123 2345 0.520404 CATATCATCCGCAGCAAGGC 59.480 55.000 0.00 0.00 0.00 4.35
2124 2346 1.802960 GTCATATCATCCGCAGCAAGG 59.197 52.381 0.00 0.00 0.00 3.61
2125 2347 1.458445 CGTCATATCATCCGCAGCAAG 59.542 52.381 0.00 0.00 0.00 4.01
2126 2348 1.068434 TCGTCATATCATCCGCAGCAA 59.932 47.619 0.00 0.00 0.00 3.91
2127 2349 0.673437 TCGTCATATCATCCGCAGCA 59.327 50.000 0.00 0.00 0.00 4.41
2128 2350 1.923204 GATCGTCATATCATCCGCAGC 59.077 52.381 0.00 0.00 0.00 5.25
2129 2351 3.221964 TGATCGTCATATCATCCGCAG 57.778 47.619 0.00 0.00 30.92 5.18
2130 2352 3.874392 ATGATCGTCATATCATCCGCA 57.126 42.857 0.00 0.00 41.71 5.69
2151 2373 4.628074 CATGTACGGATTAGGGTTTCGAT 58.372 43.478 0.00 0.00 0.00 3.59
2152 2374 3.738899 GCATGTACGGATTAGGGTTTCGA 60.739 47.826 0.00 0.00 0.00 3.71
2166 2388 1.200483 CCTAGACGCAAGCATGTACG 58.800 55.000 0.00 0.00 45.62 3.67
2447 2675 0.992802 GCCGACATTGTCTTCGAGAC 59.007 55.000 14.54 7.74 45.26 3.36
2660 2888 8.548721 GCTGCGAACTTATATATTTACAAGTGT 58.451 33.333 0.43 0.00 31.80 3.55
2673 2901 7.118535 TGTGACAAATTAAGCTGCGAACTTATA 59.881 33.333 0.00 0.00 30.07 0.98
2675 2903 5.237561 TGTGACAAATTAAGCTGCGAACTTA 59.762 36.000 0.00 0.00 0.00 2.24
2676 2904 4.036262 TGTGACAAATTAAGCTGCGAACTT 59.964 37.500 0.00 0.00 0.00 2.66
2677 2905 3.563808 TGTGACAAATTAAGCTGCGAACT 59.436 39.130 0.00 0.00 0.00 3.01
2678 2906 3.884169 TGTGACAAATTAAGCTGCGAAC 58.116 40.909 0.00 0.00 0.00 3.95
2679 2907 4.560136 TTGTGACAAATTAAGCTGCGAA 57.440 36.364 0.00 0.00 0.00 4.70
2711 2939 7.013274 GCACAGAGAGGCAACCATTATATTAAA 59.987 37.037 0.00 0.00 37.17 1.52
2860 3088 0.979665 TCAGGCTTAGCTGCAACTCT 59.020 50.000 3.59 0.00 34.04 3.24
2904 3132 4.104102 TGTTCCTCTTCTTGCCCTTTTCTA 59.896 41.667 0.00 0.00 0.00 2.10
2907 3135 3.225940 CTGTTCCTCTTCTTGCCCTTTT 58.774 45.455 0.00 0.00 0.00 2.27
2910 3138 0.037447 GCTGTTCCTCTTCTTGCCCT 59.963 55.000 0.00 0.00 0.00 5.19
3106 3334 3.726557 TCTCACTCCAATGCCTTGATT 57.273 42.857 2.97 0.00 34.04 2.57
3145 3373 1.412343 TGCAAGTTTTGGAAGGCCTTC 59.588 47.619 33.67 33.67 38.80 3.46
3249 3481 7.175347 AGCTCTACATGTCACTCAAGATAAA 57.825 36.000 0.00 0.00 0.00 1.40
3287 3520 3.365264 GCATGTGACCATATAATGTGGCG 60.365 47.826 0.00 0.00 40.49 5.69
3480 3732 8.025445 AGAGTTTGATCAATAAGTGTGCATTTC 58.975 33.333 9.40 0.00 0.00 2.17
3485 3737 9.495754 GATTAAGAGTTTGATCAATAAGTGTGC 57.504 33.333 9.40 0.00 31.51 4.57
3495 3747 9.617523 TGCATCTTATGATTAAGAGTTTGATCA 57.382 29.630 0.00 0.00 45.29 2.92
3535 3787 6.891908 ACTGAAGGAGTGTTTATTAATGCCAT 59.108 34.615 0.00 0.00 31.75 4.40
3543 3795 7.639113 TTTGTGAACTGAAGGAGTGTTTATT 57.361 32.000 0.00 0.00 34.02 1.40
3573 3825 9.045745 AGTCCATATGAAAATACCCAAAACATT 57.954 29.630 3.65 0.00 0.00 2.71
3583 3835 9.136952 GTCCGTATGTAGTCCATATGAAAATAC 57.863 37.037 3.65 6.52 43.11 1.89
3598 3850 5.891451 TCACTCATTTCAGTCCGTATGTAG 58.109 41.667 0.00 0.00 0.00 2.74
3606 3858 4.527564 CGTTTGTTCACTCATTTCAGTCC 58.472 43.478 0.00 0.00 0.00 3.85
3611 3863 3.952535 AGTGCGTTTGTTCACTCATTTC 58.047 40.909 0.00 0.00 39.11 2.17
3681 3933 8.914011 CCCTCCGTTCACATATATAAGATGATA 58.086 37.037 5.28 0.00 0.00 2.15
3682 3934 7.619698 TCCCTCCGTTCACATATATAAGATGAT 59.380 37.037 5.28 0.00 0.00 2.45
3683 3935 6.951778 TCCCTCCGTTCACATATATAAGATGA 59.048 38.462 5.28 0.00 0.00 2.92
3694 3946 2.526888 TCTACTCCCTCCGTTCACAT 57.473 50.000 0.00 0.00 0.00 3.21
3756 4008 4.462133 ACGATATAGTGCACTAGGACAGT 58.538 43.478 29.05 20.98 38.75 3.55
3759 4011 5.692613 AAGACGATATAGTGCACTAGGAC 57.307 43.478 29.05 20.21 36.16 3.85
3812 4066 7.113658 ACTCTTCTCTCACAAAAGACACTAA 57.886 36.000 0.00 0.00 0.00 2.24
3835 4089 9.807649 AGCAACAAATCCAAAATATCTCATAAC 57.192 29.630 0.00 0.00 0.00 1.89
3890 4144 6.989169 CGAGGAAAGAGAAATCAACCATATCT 59.011 38.462 0.00 0.00 0.00 1.98
3891 4145 6.763610 ACGAGGAAAGAGAAATCAACCATATC 59.236 38.462 0.00 0.00 0.00 1.63
3892 4146 6.540189 CACGAGGAAAGAGAAATCAACCATAT 59.460 38.462 0.00 0.00 0.00 1.78
3893 4147 5.874810 CACGAGGAAAGAGAAATCAACCATA 59.125 40.000 0.00 0.00 0.00 2.74
3894 4148 4.697352 CACGAGGAAAGAGAAATCAACCAT 59.303 41.667 0.00 0.00 0.00 3.55
3895 4149 4.065088 CACGAGGAAAGAGAAATCAACCA 58.935 43.478 0.00 0.00 0.00 3.67
3897 4151 5.924475 TTCACGAGGAAAGAGAAATCAAC 57.076 39.130 0.00 0.00 30.98 3.18
3915 4169 3.383620 TGATGTTGCACCCAATTTCAC 57.616 42.857 0.00 0.00 32.75 3.18
3929 4183 9.295825 TGGTTTCATAACTACAAAGATGATGTT 57.704 29.630 0.00 0.00 34.59 2.71
3937 4191 7.698130 GCTTAGCATGGTTTCATAACTACAAAG 59.302 37.037 1.12 0.00 34.59 2.77
3941 4195 6.927294 AGCTTAGCATGGTTTCATAACTAC 57.073 37.500 7.07 0.00 34.59 2.73
3952 4206 4.020573 TGTGTACTTGTAGCTTAGCATGGT 60.021 41.667 7.07 1.62 0.00 3.55
3954 4208 7.116948 GGATATGTGTACTTGTAGCTTAGCATG 59.883 40.741 7.07 0.00 0.00 4.06
3963 4217 9.234384 CGAGTTTAAGGATATGTGTACTTGTAG 57.766 37.037 0.00 0.00 0.00 2.74
3970 4224 8.723311 CCAAAAACGAGTTTAAGGATATGTGTA 58.277 33.333 11.54 0.00 31.95 2.90
3972 4226 7.027161 CCCAAAAACGAGTTTAAGGATATGTG 58.973 38.462 16.11 1.34 31.95 3.21
4027 4282 1.669437 TATTTGAGCACGCGCACCA 60.669 52.632 5.73 0.00 42.27 4.17
4028 4283 1.226018 GTATTTGAGCACGCGCACC 60.226 57.895 5.73 0.00 42.27 5.01
4030 4285 0.165727 CAAGTATTTGAGCACGCGCA 59.834 50.000 5.73 0.00 42.27 6.09
4033 4288 5.858581 AGAAAATTCAAGTATTTGAGCACGC 59.141 36.000 0.65 0.00 43.76 5.34
4074 4329 3.713764 AGCTTCACCTTCCATATACTGCT 59.286 43.478 0.00 0.00 0.00 4.24
4081 4336 4.783227 AGGAAAGTAGCTTCACCTTCCATA 59.217 41.667 16.10 0.00 30.49 2.74
4082 4337 3.589288 AGGAAAGTAGCTTCACCTTCCAT 59.411 43.478 16.10 2.92 30.49 3.41
4083 4338 2.979678 AGGAAAGTAGCTTCACCTTCCA 59.020 45.455 16.10 0.00 30.49 3.53
4084 4339 3.704800 AGGAAAGTAGCTTCACCTTCC 57.295 47.619 8.45 8.45 30.49 3.46
4085 4340 7.506328 TTTTTAGGAAAGTAGCTTCACCTTC 57.494 36.000 0.00 0.00 34.22 3.46


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

AutoCloner maintained by Alex Coulton.