Multiple sequence alignment - TraesCS6B01G020100

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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 TraesCS6B01G020100 chr6B 100.000 4816 0 0 1 4816 12119806 12114991 0.000000e+00 8894.0
1 TraesCS6B01G020100 chr6D 90.675 2016 71 55 2186 4149 6573191 6571241 0.000000e+00 2573.0
2 TraesCS6B01G020100 chr6D 89.314 2115 109 53 125 2182 6575289 6573235 0.000000e+00 2545.0
3 TraesCS6B01G020100 chr6D 90.445 607 41 9 4220 4816 6570894 6570295 0.000000e+00 784.0
4 TraesCS6B01G020100 chr6D 94.595 74 2 2 1 73 6575467 6575395 3.940000e-21 113.0
5 TraesCS6B01G020100 chr6D 100.000 29 0 0 78 106 6575376 6575348 2.000000e-03 54.7
6 TraesCS6B01G020100 chr6A 91.211 1900 80 37 2186 4041 6191358 6193214 0.000000e+00 2503.0
7 TraesCS6B01G020100 chr6A 86.555 2142 143 70 126 2182 6189228 6191309 0.000000e+00 2226.0
8 TraesCS6B01G020100 chr6A 81.988 161 12 2 4146 4289 6196265 6196425 2.350000e-23 121.0
9 TraesCS6B01G020100 chr6A 86.441 59 2 1 4066 4124 6196067 6196119 5.210000e-05 60.2
10 TraesCS6B01G020100 chr1D 82.823 588 54 22 3254 3798 342121197 342120614 2.610000e-132 483.0
11 TraesCS6B01G020100 chr1D 78.545 275 52 5 3217 3489 231465068 231464799 1.780000e-39 174.0
12 TraesCS6B01G020100 chr1D 97.619 42 0 1 2312 2353 342121709 342121669 2.400000e-08 71.3
13 TraesCS6B01G020100 chr1B 81.920 448 65 10 3257 3691 457954775 457954331 9.850000e-97 364.0
14 TraesCS6B01G020100 chr1B 78.909 275 51 5 3217 3489 365021480 365021749 3.830000e-41 180.0
15 TraesCS6B01G020100 chr1B 97.619 42 0 1 2312 2353 458005509 458005469 2.400000e-08 71.3
16 TraesCS6B01G020100 chr1A 82.353 357 51 8 3310 3654 441794158 441793802 2.820000e-77 300.0
17 TraesCS6B01G020100 chr1A 78.545 275 52 5 3217 3489 317813383 317813652 1.780000e-39 174.0
18 TraesCS6B01G020100 chr1A 97.619 42 0 1 2312 2353 441797323 441797283 2.400000e-08 71.3
19 TraesCS6B01G020100 chr2D 77.338 278 56 6 3214 3489 492509718 492509446 1.790000e-34 158.0


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 TraesCS6B01G020100 chr6B 12114991 12119806 4815 True 8894.00 8894 100.00000 1 4816 1 chr6B.!!$R1 4815
1 TraesCS6B01G020100 chr6D 6570295 6575467 5172 True 1213.94 2573 93.00580 1 4816 5 chr6D.!!$R1 4815
2 TraesCS6B01G020100 chr6A 6189228 6196425 7197 False 1227.55 2503 86.54875 126 4289 4 chr6A.!!$F1 4163
3 TraesCS6B01G020100 chr1D 342120614 342121709 1095 True 277.15 483 90.22100 2312 3798 2 chr1D.!!$R2 1486

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
305 373 0.175760 TCACCGATCAAGGCAGCTAC 59.824 55.0 0.00 0.0 33.69 3.58 F
1053 1182 0.107508 AGCAGTTCATCATGGACGGG 60.108 55.0 0.00 0.0 0.00 5.28 F
1608 1758 0.883833 CCGCCATGAACTTCAAGCTT 59.116 50.0 12.76 0.0 30.37 3.74 F
3181 3598 0.106819 GAGCTGGTCCCCTACGAGTA 60.107 60.0 0.00 0.0 36.38 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1971 0.253630 ATTGTAGGGGGAGAAGGCCA 60.254 55.000 5.01 0.0 0.0 5.36 R
1859 2020 1.226888 CGGACGGACGGAGGAATTC 60.227 63.158 0.00 0.0 0.0 2.17 R
3538 3967 2.127232 GTGGCTTTGGTGCTGGTGT 61.127 57.895 0.00 0.0 0.0 4.16 R
4360 7948 0.034896 ATCGGCGTGTGTTCTTCCTT 59.965 50.000 6.85 0.0 0.0 3.36 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
55 56 3.579685 GCCTTGGGCTCTCGTTTC 58.420 61.111 0.80 0.00 46.69 2.78
73 74 9.967346 TCTCGTTTCATTATGGAGAGTTATTAG 57.033 33.333 0.00 0.00 30.75 1.73
74 75 9.967346 CTCGTTTCATTATGGAGAGTTATTAGA 57.033 33.333 0.00 0.00 0.00 2.10
116 131 5.521544 GGAGCTCGTCCTTAACTACATTAG 58.478 45.833 7.83 0.00 42.99 1.73
117 132 5.067544 GGAGCTCGTCCTTAACTACATTAGT 59.932 44.000 7.83 0.00 42.99 2.24
118 133 5.892568 AGCTCGTCCTTAACTACATTAGTG 58.107 41.667 0.00 0.00 39.39 2.74
119 134 5.651139 AGCTCGTCCTTAACTACATTAGTGA 59.349 40.000 0.00 0.00 39.39 3.41
120 135 5.742926 GCTCGTCCTTAACTACATTAGTGAC 59.257 44.000 0.00 0.00 39.39 3.67
121 136 6.199937 TCGTCCTTAACTACATTAGTGACC 57.800 41.667 0.00 0.00 39.39 4.02
122 137 5.126061 TCGTCCTTAACTACATTAGTGACCC 59.874 44.000 0.00 0.00 39.39 4.46
123 138 5.126707 CGTCCTTAACTACATTAGTGACCCT 59.873 44.000 0.00 0.00 39.39 4.34
165 220 0.676782 CTACCACAAGGGGAAAGCCG 60.677 60.000 0.00 0.00 42.91 5.52
187 242 2.143122 GAAGGTTGCACAGAATCGTCA 58.857 47.619 0.00 0.00 0.00 4.35
197 252 0.526662 AGAATCGTCACCGTCACCTC 59.473 55.000 0.00 0.00 35.01 3.85
206 261 3.374402 CGTCACCTCTCACGCCCT 61.374 66.667 0.00 0.00 0.00 5.19
227 282 3.945640 ATACCTAGCAACCCCGATTTT 57.054 42.857 0.00 0.00 0.00 1.82
228 283 1.834188 ACCTAGCAACCCCGATTTTG 58.166 50.000 0.00 0.00 0.00 2.44
292 360 1.144093 ACCTCAAATGGGTTTCACCGA 59.856 47.619 0.00 0.00 39.83 4.69
305 373 0.175760 TCACCGATCAAGGCAGCTAC 59.824 55.000 0.00 0.00 33.69 3.58
416 484 4.675029 AGCCGGAAACCGTCACCG 62.675 66.667 5.05 0.00 46.80 4.94
437 505 3.869246 CGATTACGGTTTCCATAGCAACT 59.131 43.478 0.00 0.00 35.72 3.16
473 541 6.306987 AGAGAAAAACATAGTTGACCATGGT 58.693 36.000 19.89 19.89 0.00 3.55
483 551 5.144159 AGTTGACCATGGTCTCTATCCTA 57.856 43.478 37.92 18.11 44.80 2.94
486 554 4.878968 TGACCATGGTCTCTATCCTAACA 58.121 43.478 37.92 16.81 44.80 2.41
489 557 6.179906 ACCATGGTCTCTATCCTAACATTG 57.820 41.667 13.00 0.00 0.00 2.82
491 559 6.844388 ACCATGGTCTCTATCCTAACATTGTA 59.156 38.462 13.00 0.00 0.00 2.41
492 560 7.347222 ACCATGGTCTCTATCCTAACATTGTAA 59.653 37.037 13.00 0.00 0.00 2.41
493 561 7.875041 CCATGGTCTCTATCCTAACATTGTAAG 59.125 40.741 2.57 0.00 0.00 2.34
494 562 7.973048 TGGTCTCTATCCTAACATTGTAAGT 57.027 36.000 0.00 0.00 0.00 2.24
497 565 9.134055 GGTCTCTATCCTAACATTGTAAGTAGT 57.866 37.037 0.00 0.00 0.00 2.73
575 644 6.015519 TCACATAAACAAAAGGGGAGATGTTG 60.016 38.462 0.00 0.00 36.23 3.33
576 645 5.838521 ACATAAACAAAAGGGGAGATGTTGT 59.161 36.000 0.00 0.00 36.23 3.32
646 722 2.106566 GACAAGGAGCAGGAGATGAGA 58.893 52.381 0.00 0.00 0.00 3.27
647 723 2.699846 GACAAGGAGCAGGAGATGAGAT 59.300 50.000 0.00 0.00 0.00 2.75
648 724 2.435069 ACAAGGAGCAGGAGATGAGATG 59.565 50.000 0.00 0.00 0.00 2.90
649 725 2.699321 CAAGGAGCAGGAGATGAGATGA 59.301 50.000 0.00 0.00 0.00 2.92
650 726 2.600790 AGGAGCAGGAGATGAGATGAG 58.399 52.381 0.00 0.00 0.00 2.90
651 727 1.001181 GGAGCAGGAGATGAGATGAGC 59.999 57.143 0.00 0.00 0.00 4.26
652 728 1.001181 GAGCAGGAGATGAGATGAGCC 59.999 57.143 0.00 0.00 0.00 4.70
653 729 0.757512 GCAGGAGATGAGATGAGCCA 59.242 55.000 0.00 0.00 0.00 4.75
654 730 1.348366 GCAGGAGATGAGATGAGCCAT 59.652 52.381 0.00 0.00 0.00 4.40
655 731 2.566279 GCAGGAGATGAGATGAGCCATA 59.434 50.000 0.00 0.00 0.00 2.74
656 732 3.007723 GCAGGAGATGAGATGAGCCATAA 59.992 47.826 0.00 0.00 0.00 1.90
657 733 4.504514 GCAGGAGATGAGATGAGCCATAAA 60.505 45.833 0.00 0.00 0.00 1.40
658 734 5.239351 CAGGAGATGAGATGAGCCATAAAG 58.761 45.833 0.00 0.00 0.00 1.85
659 735 4.286549 AGGAGATGAGATGAGCCATAAAGG 59.713 45.833 0.00 0.00 41.84 3.11
683 759 0.550914 GCACCCCATCCAGGAATACA 59.449 55.000 0.00 0.00 41.22 2.29
718 794 1.665442 CCTTTCCAAAACCGCCCAG 59.335 57.895 0.00 0.00 0.00 4.45
766 842 3.607084 ATGGAAACCAGCCCTGCCC 62.607 63.158 0.00 0.00 36.75 5.36
828 914 2.826725 CGGGTAGTCCATATCCTCTTCC 59.173 54.545 0.00 0.00 31.67 3.46
834 920 3.713764 AGTCCATATCCTCTTCCACCTTG 59.286 47.826 0.00 0.00 0.00 3.61
880 966 0.451783 GCTCGCATTTCAATTCCGGT 59.548 50.000 0.00 0.00 0.00 5.28
931 1017 1.664873 GGAGTAATTTCAGGTCGGGC 58.335 55.000 0.00 0.00 0.00 6.13
932 1018 1.287425 GAGTAATTTCAGGTCGGGCG 58.713 55.000 0.00 0.00 0.00 6.13
933 1019 0.899720 AGTAATTTCAGGTCGGGCGA 59.100 50.000 0.00 0.00 0.00 5.54
934 1020 1.134788 AGTAATTTCAGGTCGGGCGAG 60.135 52.381 0.00 0.00 0.00 5.03
935 1021 0.899720 TAATTTCAGGTCGGGCGAGT 59.100 50.000 0.00 0.00 0.00 4.18
936 1022 0.673644 AATTTCAGGTCGGGCGAGTG 60.674 55.000 0.00 0.00 0.00 3.51
937 1023 1.541310 ATTTCAGGTCGGGCGAGTGA 61.541 55.000 0.00 0.00 0.00 3.41
938 1024 2.154798 TTTCAGGTCGGGCGAGTGAG 62.155 60.000 0.00 0.00 0.00 3.51
939 1025 3.374402 CAGGTCGGGCGAGTGAGT 61.374 66.667 0.00 0.00 0.00 3.41
940 1026 3.374402 AGGTCGGGCGAGTGAGTG 61.374 66.667 0.00 0.00 0.00 3.51
941 1027 3.371063 GGTCGGGCGAGTGAGTGA 61.371 66.667 0.00 0.00 0.00 3.41
942 1028 2.179517 GTCGGGCGAGTGAGTGAG 59.820 66.667 0.00 0.00 0.00 3.51
943 1029 3.749064 TCGGGCGAGTGAGTGAGC 61.749 66.667 0.00 0.00 0.00 4.26
969 1055 2.434359 GAGCGGTGCTGGTGGTAC 60.434 66.667 0.00 0.00 39.88 3.34
1053 1182 0.107508 AGCAGTTCATCATGGACGGG 60.108 55.000 0.00 0.00 0.00 5.28
1476 1626 3.738246 CACCAGCAGCAGCAGCAG 61.738 66.667 12.92 3.65 45.49 4.24
1608 1758 0.883833 CCGCCATGAACTTCAAGCTT 59.116 50.000 12.76 0.00 30.37 3.74
1820 1971 3.066198 GTACGCCACCACCCTTCT 58.934 61.111 0.00 0.00 0.00 2.85
1821 1972 1.375523 GTACGCCACCACCCTTCTG 60.376 63.158 0.00 0.00 0.00 3.02
1822 1973 2.589157 TACGCCACCACCCTTCTGG 61.589 63.158 0.00 0.00 41.37 3.86
1826 1977 2.845345 CCACCACCCTTCTGGCCTT 61.845 63.158 3.32 0.00 37.83 4.35
1827 1978 1.303643 CACCACCCTTCTGGCCTTC 60.304 63.158 3.32 0.00 37.83 3.46
1831 1982 1.925972 ACCCTTCTGGCCTTCTCCC 60.926 63.158 3.32 0.00 37.83 4.30
1834 1985 1.617839 CTTCTGGCCTTCTCCCCCT 60.618 63.158 3.32 0.00 0.00 4.79
1874 2035 0.902531 ATGTGAATTCCTCCGTCCGT 59.097 50.000 2.27 0.00 0.00 4.69
1875 2036 0.245539 TGTGAATTCCTCCGTCCGTC 59.754 55.000 2.27 0.00 0.00 4.79
1876 2037 0.459759 GTGAATTCCTCCGTCCGTCC 60.460 60.000 2.27 0.00 0.00 4.79
1877 2038 1.226888 GAATTCCTCCGTCCGTCCG 60.227 63.158 0.00 0.00 0.00 4.79
1901 2062 2.111878 GGATCCACTCATGGCGGG 59.888 66.667 6.95 0.00 46.80 6.13
2085 2246 0.397941 TGATGCCGATGATTCCTCCC 59.602 55.000 0.00 0.00 0.00 4.30
2111 2281 4.105754 ACTTTTGCTCCCTTTTAGCTCT 57.894 40.909 0.00 0.00 40.73 4.09
2113 2283 2.789409 TTGCTCCCTTTTAGCTCTCC 57.211 50.000 0.00 0.00 40.73 3.71
2134 2304 5.000591 TCCTCTCATTACATCACGCAAAAA 58.999 37.500 0.00 0.00 0.00 1.94
2139 2309 5.927030 TCATTACATCACGCAAAAAGAGAC 58.073 37.500 0.00 0.00 0.00 3.36
2161 2336 2.228343 ACTCTTTTCTTGCTCTGCATGC 59.772 45.455 11.82 11.82 38.76 4.06
2182 2357 2.354303 CCACAATTTGCCATGCAGATGT 60.354 45.455 0.00 0.00 40.61 3.06
2183 2358 3.331150 CACAATTTGCCATGCAGATGTT 58.669 40.909 0.00 0.00 40.61 2.71
2184 2359 3.369756 CACAATTTGCCATGCAGATGTTC 59.630 43.478 0.00 0.00 40.61 3.18
2225 2446 5.713822 GATGAAATCCTTGCTTGAATTGC 57.286 39.130 0.00 0.00 37.38 3.56
2285 2506 6.717413 CAATTGGTTTGGTTTGTTCATCTTG 58.283 36.000 0.00 0.00 0.00 3.02
2286 2507 5.413309 TTGGTTTGGTTTGTTCATCTTGT 57.587 34.783 0.00 0.00 0.00 3.16
2287 2508 5.413309 TGGTTTGGTTTGTTCATCTTGTT 57.587 34.783 0.00 0.00 0.00 2.83
2289 2510 6.936279 TGGTTTGGTTTGTTCATCTTGTTTA 58.064 32.000 0.00 0.00 0.00 2.01
2290 2511 7.038659 TGGTTTGGTTTGTTCATCTTGTTTAG 58.961 34.615 0.00 0.00 0.00 1.85
2291 2512 6.478673 GGTTTGGTTTGTTCATCTTGTTTAGG 59.521 38.462 0.00 0.00 0.00 2.69
2292 2513 7.262048 GTTTGGTTTGTTCATCTTGTTTAGGA 58.738 34.615 0.00 0.00 0.00 2.94
2293 2514 6.385649 TGGTTTGTTCATCTTGTTTAGGAC 57.614 37.500 0.00 0.00 0.00 3.85
2294 2515 6.126409 TGGTTTGTTCATCTTGTTTAGGACT 58.874 36.000 0.00 0.00 0.00 3.85
2295 2516 7.284074 TGGTTTGTTCATCTTGTTTAGGACTA 58.716 34.615 0.00 0.00 0.00 2.59
2296 2517 7.776030 TGGTTTGTTCATCTTGTTTAGGACTAA 59.224 33.333 0.00 0.00 0.00 2.24
2297 2518 8.290325 GGTTTGTTCATCTTGTTTAGGACTAAG 58.710 37.037 0.00 0.00 0.00 2.18
2298 2519 8.837389 GTTTGTTCATCTTGTTTAGGACTAAGT 58.163 33.333 0.00 0.00 0.00 2.24
2300 2521 8.378172 TGTTCATCTTGTTTAGGACTAAGTTG 57.622 34.615 0.00 0.00 0.00 3.16
2301 2522 8.208224 TGTTCATCTTGTTTAGGACTAAGTTGA 58.792 33.333 0.00 0.00 31.23 3.18
2303 2524 9.793259 TTCATCTTGTTTAGGACTAAGTTGAAT 57.207 29.630 0.00 0.00 34.57 2.57
2305 2526 9.831737 CATCTTGTTTAGGACTAAGTTGAATTG 57.168 33.333 0.00 0.00 0.00 2.32
2307 2528 8.836413 TCTTGTTTAGGACTAAGTTGAATTGTG 58.164 33.333 0.00 0.00 0.00 3.33
2308 2529 7.504924 TGTTTAGGACTAAGTTGAATTGTGG 57.495 36.000 0.00 0.00 0.00 4.17
2309 2530 7.284074 TGTTTAGGACTAAGTTGAATTGTGGA 58.716 34.615 0.00 0.00 0.00 4.02
2310 2531 7.942341 TGTTTAGGACTAAGTTGAATTGTGGAT 59.058 33.333 0.00 0.00 0.00 3.41
2311 2532 8.793592 GTTTAGGACTAAGTTGAATTGTGGATT 58.206 33.333 0.00 0.00 0.00 3.01
2314 2535 7.661040 AGGACTAAGTTGAATTGTGGATTTTG 58.339 34.615 0.00 0.00 0.00 2.44
2315 2536 6.868339 GGACTAAGTTGAATTGTGGATTTTGG 59.132 38.462 0.00 0.00 0.00 3.28
2316 2537 7.360113 ACTAAGTTGAATTGTGGATTTTGGT 57.640 32.000 0.00 0.00 0.00 3.67
2705 3119 0.109226 CGAACACCTCGGAGACTTCC 60.109 60.000 6.58 0.00 44.20 3.46
3181 3598 0.106819 GAGCTGGTCCCCTACGAGTA 60.107 60.000 0.00 0.00 36.38 2.59
3182 3599 0.395448 AGCTGGTCCCCTACGAGTAC 60.395 60.000 0.00 0.00 36.38 2.73
3183 3600 1.722636 GCTGGTCCCCTACGAGTACG 61.723 65.000 0.00 0.00 45.75 3.67
3498 3915 2.123640 GCCTCTACTCCCGCTCCT 60.124 66.667 0.00 0.00 0.00 3.69
3499 3916 2.197605 GCCTCTACTCCCGCTCCTC 61.198 68.421 0.00 0.00 0.00 3.71
3500 3917 1.529713 CCTCTACTCCCGCTCCTCC 60.530 68.421 0.00 0.00 0.00 4.30
3563 4010 3.223589 ACCAAAGCCACCGCCAAC 61.224 61.111 0.00 0.00 34.57 3.77
3570 4017 2.748251 CCACCGCCAACGCCATAA 60.748 61.111 0.00 0.00 38.22 1.90
3800 4265 4.471726 GGGCACGACGACGACGAT 62.472 66.667 25.15 7.72 42.66 3.73
3801 4266 3.238241 GGCACGACGACGACGATG 61.238 66.667 25.15 18.64 42.66 3.84
3802 4267 2.202260 GCACGACGACGACGATGA 60.202 61.111 25.15 0.00 42.66 2.92
3803 4268 2.209076 GCACGACGACGACGATGAG 61.209 63.158 25.15 12.68 42.66 2.90
3837 4302 2.158943 AGCTTGATTAACTAGGACCGCC 60.159 50.000 0.00 0.00 0.00 6.13
3838 4303 2.470821 CTTGATTAACTAGGACCGCCG 58.529 52.381 0.00 0.00 39.96 6.46
3839 4304 0.103572 TGATTAACTAGGACCGCCGC 59.896 55.000 0.00 0.00 39.96 6.53
3840 4305 0.103572 GATTAACTAGGACCGCCGCA 59.896 55.000 0.00 0.00 39.96 5.69
3842 4307 0.179094 TTAACTAGGACCGCCGCATG 60.179 55.000 0.00 0.00 39.96 4.06
3843 4308 2.638330 TAACTAGGACCGCCGCATGC 62.638 60.000 7.91 7.91 39.96 4.06
3844 4309 4.227134 CTAGGACCGCCGCATGCT 62.227 66.667 17.13 0.00 39.96 3.79
3845 4310 3.740128 CTAGGACCGCCGCATGCTT 62.740 63.158 17.13 0.00 39.96 3.91
3846 4311 2.363711 CTAGGACCGCCGCATGCTTA 62.364 60.000 17.13 0.00 39.96 3.09
3847 4312 2.363711 TAGGACCGCCGCATGCTTAG 62.364 60.000 17.13 5.48 39.96 2.18
3848 4313 3.941836 GACCGCCGCATGCTTAGC 61.942 66.667 17.13 14.52 38.05 3.09
3863 4328 4.799564 GCTTAGCTAGCTAGGACATGAT 57.200 45.455 31.70 4.64 46.77 2.45
3864 4329 4.743493 GCTTAGCTAGCTAGGACATGATC 58.257 47.826 31.70 12.50 46.77 2.92
3867 4332 2.817258 AGCTAGCTAGGACATGATCGAC 59.183 50.000 17.69 0.96 0.00 4.20
3871 4336 1.335142 GCTAGGACATGATCGACCGAC 60.335 57.143 0.00 0.00 0.00 4.79
3874 4339 1.721664 GGACATGATCGACCGACCGA 61.722 60.000 0.00 1.90 43.16 4.69
3907 4374 9.881649 AGAAAATTTGCTTCTTTCTTCTTCTTT 57.118 25.926 0.00 0.00 36.27 2.52
3908 4375 9.911980 GAAAATTTGCTTCTTTCTTCTTCTTTG 57.088 29.630 0.00 0.00 0.00 2.77
3909 4376 7.474398 AATTTGCTTCTTTCTTCTTCTTTGC 57.526 32.000 0.00 0.00 0.00 3.68
3940 4407 2.687425 TGCTGCTTCTGCTTGTTGTTAA 59.313 40.909 0.00 0.00 40.48 2.01
3941 4408 3.318839 TGCTGCTTCTGCTTGTTGTTAAT 59.681 39.130 0.00 0.00 40.48 1.40
3942 4409 4.202141 TGCTGCTTCTGCTTGTTGTTAATT 60.202 37.500 0.00 0.00 40.48 1.40
3943 4410 5.009510 TGCTGCTTCTGCTTGTTGTTAATTA 59.990 36.000 0.00 0.00 40.48 1.40
3944 4411 5.570589 GCTGCTTCTGCTTGTTGTTAATTAG 59.429 40.000 0.00 0.00 40.48 1.73
3946 4413 5.241506 TGCTTCTGCTTGTTGTTAATTAGCT 59.758 36.000 0.83 0.00 40.48 3.32
3948 4415 6.743172 GCTTCTGCTTGTTGTTAATTAGCTAC 59.257 38.462 6.89 6.89 36.03 3.58
3949 4416 7.361286 GCTTCTGCTTGTTGTTAATTAGCTACT 60.361 37.037 13.21 0.00 36.03 2.57
3950 4417 9.151471 CTTCTGCTTGTTGTTAATTAGCTACTA 57.849 33.333 13.21 6.65 33.15 1.82
3951 4418 9.496873 TTCTGCTTGTTGTTAATTAGCTACTAA 57.503 29.630 13.21 6.89 33.15 2.24
3955 4422 9.922305 GCTTGTTGTTAATTAGCTACTAAGATG 57.078 33.333 18.85 5.89 29.02 2.90
4027 4500 9.896645 AGAAGATCAGCTTAATTAATCACTTCA 57.103 29.630 18.44 4.23 36.83 3.02
4041 4514 9.866655 ATTAATCACTTCAATAATCCCAAGCTA 57.133 29.630 0.00 0.00 0.00 3.32
4042 4515 7.814264 AATCACTTCAATAATCCCAAGCTAG 57.186 36.000 0.00 0.00 0.00 3.42
4043 4516 5.126067 TCACTTCAATAATCCCAAGCTAGC 58.874 41.667 6.62 6.62 0.00 3.42
4044 4517 5.104360 TCACTTCAATAATCCCAAGCTAGCT 60.104 40.000 12.68 12.68 0.00 3.32
4045 4518 6.099701 TCACTTCAATAATCCCAAGCTAGCTA 59.900 38.462 19.70 1.74 0.00 3.32
4064 7369 5.814314 GCTATAGCTCGTAGACATTTGTG 57.186 43.478 17.75 0.00 38.21 3.33
4070 7375 3.362986 GCTCGTAGACATTTGTGTGTGTG 60.363 47.826 0.00 0.00 31.16 3.82
4092 7397 0.032952 TCGACCATGGCCGCTTATAC 59.967 55.000 16.50 0.00 0.00 1.47
4093 7398 0.033504 CGACCATGGCCGCTTATACT 59.966 55.000 13.04 0.00 0.00 2.12
4094 7399 1.271379 CGACCATGGCCGCTTATACTA 59.729 52.381 13.04 0.00 0.00 1.82
4095 7400 2.685100 GACCATGGCCGCTTATACTAC 58.315 52.381 13.04 0.00 0.00 2.73
4096 7401 2.299297 GACCATGGCCGCTTATACTACT 59.701 50.000 13.04 0.00 0.00 2.57
4097 7402 3.503365 ACCATGGCCGCTTATACTACTA 58.497 45.455 13.04 0.00 0.00 1.82
4126 7434 6.149633 GCTGTTATTTTTGTAAGTGTGAGGG 58.850 40.000 0.00 0.00 0.00 4.30
4166 7611 3.599046 CAGTTGTCTTTGACTGTCTGC 57.401 47.619 9.51 0.00 38.70 4.26
4202 7647 3.006859 TCTGGACATAACTGTGGTCACTG 59.993 47.826 6.47 6.47 35.14 3.66
4204 7649 3.067106 GGACATAACTGTGGTCACTGTG 58.933 50.000 13.01 0.17 41.62 3.66
4205 7650 3.244078 GGACATAACTGTGGTCACTGTGA 60.244 47.826 6.36 6.36 41.62 3.58
4207 7652 5.337250 GGACATAACTGTGGTCACTGTGATA 60.337 44.000 14.37 3.74 41.62 2.15
4208 7653 5.724328 ACATAACTGTGGTCACTGTGATAG 58.276 41.667 14.37 12.03 41.62 2.08
4337 7925 3.070060 CGAAACCTCGCAGCGTAC 58.930 61.111 15.93 0.65 38.45 3.67
4353 7941 1.671845 CGTACCGGAAAGAGAGAGAGG 59.328 57.143 9.46 0.00 0.00 3.69
4354 7942 2.025898 GTACCGGAAAGAGAGAGAGGG 58.974 57.143 9.46 0.00 0.00 4.30
4355 7943 0.705253 ACCGGAAAGAGAGAGAGGGA 59.295 55.000 9.46 0.00 0.00 4.20
4360 7948 2.243736 GGAAAGAGAGAGAGGGAGGAGA 59.756 54.545 0.00 0.00 0.00 3.71
4388 7985 2.434884 CACGCCGATGAGCTTGGT 60.435 61.111 0.00 0.00 0.00 3.67
4400 7997 0.670546 AGCTTGGTGTCGATGAACGG 60.671 55.000 0.00 0.00 42.82 4.44
4433 8030 0.168128 CGGCAAATCGAGGTGGAAAC 59.832 55.000 0.00 0.00 0.00 2.78
4435 8032 0.168128 GCAAATCGAGGTGGAAACGG 59.832 55.000 0.00 0.00 0.00 4.44
4446 8043 2.297880 GGTGGAAACGGCTAATTTTGGT 59.702 45.455 0.00 0.00 0.00 3.67
4474 8071 1.493950 GCATCGAGAGGCAATGTCCG 61.494 60.000 4.77 0.00 38.12 4.79
4519 8117 1.607612 CAAGGGCGGTAGAATGGGT 59.392 57.895 0.00 0.00 0.00 4.51
4553 8151 4.452733 GAGCCCGGGAAGACGTGG 62.453 72.222 29.31 0.00 0.00 4.94
4564 8162 3.179265 GACGTGGTGGCGATGACG 61.179 66.667 0.00 0.00 42.93 4.35
4565 8163 4.735132 ACGTGGTGGCGATGACGG 62.735 66.667 7.26 0.00 40.15 4.79
4600 8198 2.029666 GCGAGGCCGATATGTGCT 59.970 61.111 0.00 0.00 38.22 4.40
4640 8238 2.456119 GCAGGCAACCGTCGAGATG 61.456 63.158 0.00 0.00 37.17 2.90
4650 8248 1.320344 CGTCGAGATGGAAGGGGACA 61.320 60.000 0.00 0.00 0.00 4.02
4664 8262 1.632422 GGGACAAAATTCATGCTGCG 58.368 50.000 0.00 0.00 0.00 5.18
4667 8265 2.352617 GGACAAAATTCATGCTGCGGAA 60.353 45.455 8.65 8.65 0.00 4.30
4707 8305 7.299586 GGTGCTTTGTGAACAATTATACGTTA 58.700 34.615 0.00 0.00 35.55 3.18
4709 8307 9.976255 GTGCTTTGTGAACAATTATACGTTATA 57.024 29.630 0.00 0.00 35.55 0.98
4732 8330 4.098349 AGCTTTGAATTTCAGTCAAGTGCA 59.902 37.500 9.79 0.00 38.05 4.57
4733 8331 4.986659 GCTTTGAATTTCAGTCAAGTGCAT 59.013 37.500 9.79 0.00 36.41 3.96
4741 8339 7.692460 ATTTCAGTCAAGTGCATATTTCTCA 57.308 32.000 0.00 0.00 0.00 3.27
4742 8340 6.486253 TTCAGTCAAGTGCATATTTCTCAC 57.514 37.500 0.00 0.00 0.00 3.51
4763 8361 3.259876 ACTTGTACGATAGCTTTGGACCA 59.740 43.478 0.00 0.00 42.67 4.02
4774 8372 1.139853 CTTTGGACCAGGCTAGCTAGG 59.860 57.143 22.10 18.25 0.00 3.02
4813 8411 4.832608 GGCCCCGACACGCCTAAG 62.833 72.222 0.00 0.00 42.21 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.205022 TGGTTGCTAGCTTGCAGATT 57.795 45.000 21.64 0.00 44.27 2.40
17 18 3.430929 GCTACTGTACATGGTTGCTAGCT 60.431 47.826 17.23 0.00 33.03 3.32
73 74 5.409214 GCTCCTTCATCTCATCTGCTTAATC 59.591 44.000 0.00 0.00 0.00 1.75
74 75 5.072058 AGCTCCTTCATCTCATCTGCTTAAT 59.928 40.000 0.00 0.00 0.00 1.40
106 121 8.426569 TGTAGTTAAGGGTCACTAATGTAGTT 57.573 34.615 0.00 0.00 36.76 2.24
107 122 8.605325 ATGTAGTTAAGGGTCACTAATGTAGT 57.395 34.615 0.00 0.00 40.28 2.73
111 126 9.314321 CACTAATGTAGTTAAGGGTCACTAATG 57.686 37.037 0.00 0.00 36.76 1.90
112 127 9.263446 TCACTAATGTAGTTAAGGGTCACTAAT 57.737 33.333 0.00 0.00 36.76 1.73
113 128 8.526147 GTCACTAATGTAGTTAAGGGTCACTAA 58.474 37.037 0.00 0.00 36.76 2.24
116 131 6.104665 GGTCACTAATGTAGTTAAGGGTCAC 58.895 44.000 0.00 0.00 36.76 3.67
117 132 5.188359 GGGTCACTAATGTAGTTAAGGGTCA 59.812 44.000 0.00 0.00 36.76 4.02
118 133 5.424573 AGGGTCACTAATGTAGTTAAGGGTC 59.575 44.000 0.00 0.00 36.76 4.46
119 134 5.347978 AGGGTCACTAATGTAGTTAAGGGT 58.652 41.667 0.00 0.00 36.76 4.34
120 135 5.952347 AGGGTCACTAATGTAGTTAAGGG 57.048 43.478 0.00 0.00 36.76 3.95
121 136 8.537858 AGTTAAGGGTCACTAATGTAGTTAAGG 58.462 37.037 0.00 0.00 36.76 2.69
165 220 1.873591 ACGATTCTGTGCAACCTTCAC 59.126 47.619 0.00 0.00 34.36 3.18
187 242 3.681835 GGCGTGAGAGGTGACGGT 61.682 66.667 0.00 0.00 36.09 4.83
197 252 1.617322 TGCTAGGTATAGGGCGTGAG 58.383 55.000 0.00 0.00 0.00 3.51
206 261 4.710324 CAAAATCGGGGTTGCTAGGTATA 58.290 43.478 0.00 0.00 0.00 1.47
227 282 3.071479 CCCTAAAACTTTAGTCGCAGCA 58.929 45.455 8.11 0.00 38.73 4.41
228 283 3.072211 ACCCTAAAACTTTAGTCGCAGC 58.928 45.455 8.11 0.00 38.73 5.25
292 360 3.201290 CTGAAATCGTAGCTGCCTTGAT 58.799 45.455 0.00 0.00 0.00 2.57
305 373 1.864750 CGCCGCTTTGCTGAAATCG 60.865 57.895 0.00 0.00 31.87 3.34
350 418 1.732259 CGCAATGTAGTTGTGGGTCTC 59.268 52.381 0.00 0.00 43.09 3.36
416 484 4.272748 GGAGTTGCTATGGAAACCGTAATC 59.727 45.833 0.00 0.00 31.40 1.75
452 520 6.431234 AGAGACCATGGTCAACTATGTTTTTC 59.569 38.462 39.38 25.14 46.76 2.29
458 526 5.541868 AGGATAGAGACCATGGTCAACTATG 59.458 44.000 38.88 12.00 46.76 2.23
459 527 5.721225 AGGATAGAGACCATGGTCAACTAT 58.279 41.667 36.77 36.77 46.76 2.12
460 528 5.144159 AGGATAGAGACCATGGTCAACTA 57.856 43.478 39.38 35.81 46.76 2.24
462 530 5.128827 TGTTAGGATAGAGACCATGGTCAAC 59.871 44.000 39.38 30.53 46.76 3.18
493 561 9.341899 GGATGTGTTTGATTTCAATTGTACTAC 57.658 33.333 5.13 0.00 35.55 2.73
494 562 8.519526 GGGATGTGTTTGATTTCAATTGTACTA 58.480 33.333 5.13 0.00 35.55 1.82
497 565 7.295322 TGGGATGTGTTTGATTTCAATTGTA 57.705 32.000 5.13 0.00 35.55 2.41
575 644 3.317430 GGAATGAATGGCCTCTCATCAAC 59.683 47.826 17.29 12.54 30.97 3.18
576 645 3.559069 GGAATGAATGGCCTCTCATCAA 58.441 45.455 17.29 0.00 30.97 2.57
611 680 1.539827 CTTGTCCCGGTTTCAATGGAC 59.460 52.381 0.00 0.00 45.99 4.02
618 687 0.955919 CTGCTCCTTGTCCCGGTTTC 60.956 60.000 0.00 0.00 0.00 2.78
646 722 1.570501 TGCCCTTCCTTTATGGCTCAT 59.429 47.619 0.00 0.00 44.32 2.90
647 723 0.998928 TGCCCTTCCTTTATGGCTCA 59.001 50.000 0.00 0.00 44.32 4.26
648 724 1.393603 GTGCCCTTCCTTTATGGCTC 58.606 55.000 0.00 0.00 44.32 4.70
649 725 0.033109 GGTGCCCTTCCTTTATGGCT 60.033 55.000 0.00 0.00 44.32 4.75
650 726 1.043116 GGGTGCCCTTCCTTTATGGC 61.043 60.000 0.00 0.00 44.27 4.40
651 727 0.397114 GGGGTGCCCTTCCTTTATGG 60.397 60.000 7.26 0.00 41.34 2.74
652 728 0.334676 TGGGGTGCCCTTCCTTTATG 59.665 55.000 7.26 0.00 45.70 1.90
653 729 1.217942 GATGGGGTGCCCTTCCTTTAT 59.782 52.381 7.26 0.00 45.70 1.40
654 730 0.629058 GATGGGGTGCCCTTCCTTTA 59.371 55.000 7.26 0.00 45.70 1.85
655 731 1.388133 GATGGGGTGCCCTTCCTTT 59.612 57.895 7.26 0.00 45.70 3.11
656 732 3.100111 GATGGGGTGCCCTTCCTT 58.900 61.111 7.26 0.00 45.70 3.36
659 735 2.276740 CTGGATGGGGTGCCCTTC 59.723 66.667 7.26 0.00 45.70 3.46
718 794 0.940833 GGCCGCTCAGCTTTATCTTC 59.059 55.000 0.00 0.00 0.00 2.87
766 842 2.043953 GGGTTAAGGGCAGGGCAG 60.044 66.667 0.00 0.00 0.00 4.85
834 920 2.679996 AATTTGGTGGGCGAGGGC 60.680 61.111 0.00 0.00 38.90 5.19
880 966 2.370459 ATTGGGGAACAGTGGCAGCA 62.370 55.000 0.00 0.00 0.00 4.41
931 1017 0.179202 CTCACTCGCTCACTCACTCG 60.179 60.000 0.00 0.00 0.00 4.18
932 1018 0.878416 ACTCACTCGCTCACTCACTC 59.122 55.000 0.00 0.00 0.00 3.51
933 1019 0.595588 CACTCACTCGCTCACTCACT 59.404 55.000 0.00 0.00 0.00 3.41
934 1020 0.593618 TCACTCACTCGCTCACTCAC 59.406 55.000 0.00 0.00 0.00 3.51
935 1021 0.877743 CTCACTCACTCGCTCACTCA 59.122 55.000 0.00 0.00 0.00 3.41
936 1022 0.455972 GCTCACTCACTCGCTCACTC 60.456 60.000 0.00 0.00 0.00 3.51
937 1023 1.583986 GCTCACTCACTCGCTCACT 59.416 57.895 0.00 0.00 0.00 3.41
938 1024 1.799519 CGCTCACTCACTCGCTCAC 60.800 63.158 0.00 0.00 0.00 3.51
939 1025 2.563427 CGCTCACTCACTCGCTCA 59.437 61.111 0.00 0.00 0.00 4.26
940 1026 2.202544 CCGCTCACTCACTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
941 1027 2.986413 ACCGCTCACTCACTCGCT 60.986 61.111 0.00 0.00 0.00 4.93
942 1028 2.807045 CACCGCTCACTCACTCGC 60.807 66.667 0.00 0.00 0.00 5.03
943 1029 2.807045 GCACCGCTCACTCACTCG 60.807 66.667 0.00 0.00 0.00 4.18
944 1030 1.735920 CAGCACCGCTCACTCACTC 60.736 63.158 0.00 0.00 36.40 3.51
969 1055 2.417719 GCAACTCCACTCCACAGTAAG 58.582 52.381 0.00 0.00 0.00 2.34
1476 1626 2.282391 TGGTGGTGGTGATGCTGC 60.282 61.111 0.00 0.00 0.00 5.25
1477 1627 2.338015 GCTGGTGGTGGTGATGCTG 61.338 63.158 0.00 0.00 0.00 4.41
1478 1628 2.034687 GCTGGTGGTGGTGATGCT 59.965 61.111 0.00 0.00 0.00 3.79
1479 1629 2.034687 AGCTGGTGGTGGTGATGC 59.965 61.111 0.00 0.00 0.00 3.91
1480 1630 3.991999 CAGCTGGTGGTGGTGATG 58.008 61.111 5.57 0.00 37.97 3.07
1810 1961 1.464198 AGAAGGCCAGAAGGGTGGT 60.464 57.895 5.01 0.00 40.09 4.16
1816 1967 0.326618 TAGGGGGAGAAGGCCAGAAG 60.327 60.000 5.01 0.00 0.00 2.85
1818 1969 1.003051 GTAGGGGGAGAAGGCCAGA 59.997 63.158 5.01 0.00 0.00 3.86
1820 1971 0.253630 ATTGTAGGGGGAGAAGGCCA 60.254 55.000 5.01 0.00 0.00 5.36
1821 1972 0.474614 GATTGTAGGGGGAGAAGGCC 59.525 60.000 0.00 0.00 0.00 5.19
1822 1973 0.474614 GGATTGTAGGGGGAGAAGGC 59.525 60.000 0.00 0.00 0.00 4.35
1823 1974 1.893315 TGGATTGTAGGGGGAGAAGG 58.107 55.000 0.00 0.00 0.00 3.46
1826 1977 1.296832 TGGATGGATTGTAGGGGGAGA 59.703 52.381 0.00 0.00 0.00 3.71
1827 1978 1.819753 TGGATGGATTGTAGGGGGAG 58.180 55.000 0.00 0.00 0.00 4.30
1859 2020 1.226888 CGGACGGACGGAGGAATTC 60.227 63.158 0.00 0.00 0.00 2.17
1878 2039 4.241555 ATGAGTGGATCCGGGCGC 62.242 66.667 7.39 0.00 0.00 6.53
1901 2062 3.110178 CTTTCCGTGTCCGTCGGC 61.110 66.667 6.34 2.31 46.49 5.54
1941 2102 1.402456 GCAGAGCCAACAAAGATGCAG 60.402 52.381 0.00 0.00 32.58 4.41
2085 2246 1.423584 AAAGGGAGCAAAAGTTGGGG 58.576 50.000 0.00 0.00 0.00 4.96
2097 2267 3.370104 TGAGAGGAGAGCTAAAAGGGAG 58.630 50.000 0.00 0.00 0.00 4.30
2111 2281 3.885724 TTGCGTGATGTAATGAGAGGA 57.114 42.857 0.00 0.00 0.00 3.71
2113 2283 6.091305 TCTCTTTTTGCGTGATGTAATGAGAG 59.909 38.462 8.36 8.36 35.17 3.20
2134 2304 4.630111 CAGAGCAAGAAAAGAGTGTCTCT 58.370 43.478 0.00 0.00 43.37 3.10
2139 2309 3.822996 CATGCAGAGCAAGAAAAGAGTG 58.177 45.455 0.00 0.00 43.62 3.51
2161 2336 2.276201 CATCTGCATGGCAAATTGTGG 58.724 47.619 0.00 0.00 38.41 4.17
2211 2432 3.604875 ATTGGAGCAATTCAAGCAAGG 57.395 42.857 0.00 0.00 28.76 3.61
2225 2446 5.504392 GCAAAAAGCAACAAGAAATTGGAG 58.496 37.500 0.00 0.00 44.79 3.86
2283 2504 7.776030 TCCACAATTCAACTTAGTCCTAAACAA 59.224 33.333 0.00 0.00 0.00 2.83
2285 2506 7.739498 TCCACAATTCAACTTAGTCCTAAAC 57.261 36.000 0.00 0.00 0.00 2.01
2286 2507 8.934023 AATCCACAATTCAACTTAGTCCTAAA 57.066 30.769 0.00 0.00 0.00 1.85
2287 2508 8.934023 AAATCCACAATTCAACTTAGTCCTAA 57.066 30.769 0.00 0.00 0.00 2.69
2289 2510 7.255942 CCAAAATCCACAATTCAACTTAGTCCT 60.256 37.037 0.00 0.00 0.00 3.85
2290 2511 6.868339 CCAAAATCCACAATTCAACTTAGTCC 59.132 38.462 0.00 0.00 0.00 3.85
2291 2512 7.382218 CACCAAAATCCACAATTCAACTTAGTC 59.618 37.037 0.00 0.00 0.00 2.59
2292 2513 7.147742 ACACCAAAATCCACAATTCAACTTAGT 60.148 33.333 0.00 0.00 0.00 2.24
2293 2514 7.169645 CACACCAAAATCCACAATTCAACTTAG 59.830 37.037 0.00 0.00 0.00 2.18
2294 2515 6.983307 CACACCAAAATCCACAATTCAACTTA 59.017 34.615 0.00 0.00 0.00 2.24
2295 2516 5.816777 CACACCAAAATCCACAATTCAACTT 59.183 36.000 0.00 0.00 0.00 2.66
2296 2517 5.128499 TCACACCAAAATCCACAATTCAACT 59.872 36.000 0.00 0.00 0.00 3.16
2297 2518 5.355596 TCACACCAAAATCCACAATTCAAC 58.644 37.500 0.00 0.00 0.00 3.18
2298 2519 5.604758 TCACACCAAAATCCACAATTCAA 57.395 34.783 0.00 0.00 0.00 2.69
2300 2521 5.782047 TCATCACACCAAAATCCACAATTC 58.218 37.500 0.00 0.00 0.00 2.17
2301 2522 5.804944 TCATCACACCAAAATCCACAATT 57.195 34.783 0.00 0.00 0.00 2.32
2303 2524 5.804944 AATCATCACACCAAAATCCACAA 57.195 34.783 0.00 0.00 0.00 3.33
2305 2526 5.406175 CACAAATCATCACACCAAAATCCAC 59.594 40.000 0.00 0.00 0.00 4.02
2307 2528 5.540911 ACACAAATCATCACACCAAAATCC 58.459 37.500 0.00 0.00 0.00 3.01
2308 2529 6.808212 CCTACACAAATCATCACACCAAAATC 59.192 38.462 0.00 0.00 0.00 2.17
2309 2530 6.493115 TCCTACACAAATCATCACACCAAAAT 59.507 34.615 0.00 0.00 0.00 1.82
2310 2531 5.830457 TCCTACACAAATCATCACACCAAAA 59.170 36.000 0.00 0.00 0.00 2.44
2311 2532 5.380900 TCCTACACAAATCATCACACCAAA 58.619 37.500 0.00 0.00 0.00 3.28
2314 2535 3.941483 CCTCCTACACAAATCATCACACC 59.059 47.826 0.00 0.00 0.00 4.16
2315 2536 3.375299 GCCTCCTACACAAATCATCACAC 59.625 47.826 0.00 0.00 0.00 3.82
2316 2537 3.609853 GCCTCCTACACAAATCATCACA 58.390 45.455 0.00 0.00 0.00 3.58
3236 3653 3.453070 GATCAGCGCCTCCACCTCC 62.453 68.421 2.29 0.00 0.00 4.30
3538 3967 2.127232 GTGGCTTTGGTGCTGGTGT 61.127 57.895 0.00 0.00 0.00 4.16
3539 3968 2.730094 GTGGCTTTGGTGCTGGTG 59.270 61.111 0.00 0.00 0.00 4.17
3540 3969 2.521708 GGTGGCTTTGGTGCTGGT 60.522 61.111 0.00 0.00 0.00 4.00
3746 4211 3.838271 TCGTCATGCTCCTCGCCC 61.838 66.667 0.00 0.00 38.05 6.13
3800 4265 3.954258 TCAAGCTCTAATGATCGTCCTCA 59.046 43.478 0.00 0.00 0.00 3.86
3801 4266 4.576216 TCAAGCTCTAATGATCGTCCTC 57.424 45.455 0.00 0.00 0.00 3.71
3802 4267 5.543507 AATCAAGCTCTAATGATCGTCCT 57.456 39.130 0.00 0.00 35.29 3.85
3803 4268 6.926272 AGTTAATCAAGCTCTAATGATCGTCC 59.074 38.462 0.00 0.00 35.29 4.79
3843 4308 4.697828 TCGATCATGTCCTAGCTAGCTAAG 59.302 45.833 24.20 18.77 0.00 2.18
3844 4309 4.456222 GTCGATCATGTCCTAGCTAGCTAA 59.544 45.833 24.20 10.87 0.00 3.09
3845 4310 4.004314 GTCGATCATGTCCTAGCTAGCTA 58.996 47.826 22.85 22.85 0.00 3.32
3846 4311 2.817258 GTCGATCATGTCCTAGCTAGCT 59.183 50.000 23.12 23.12 0.00 3.32
3847 4312 2.094957 GGTCGATCATGTCCTAGCTAGC 60.095 54.545 15.74 6.62 0.00 3.42
3848 4313 2.160615 CGGTCGATCATGTCCTAGCTAG 59.839 54.545 14.20 14.20 0.00 3.42
3874 4339 0.958822 AAGCAAATTTTCTCCGCCGT 59.041 45.000 0.00 0.00 0.00 5.68
3877 4342 4.550422 AGAAAGAAGCAAATTTTCTCCGC 58.450 39.130 0.00 0.00 36.68 5.54
3962 4429 9.950496 AGCAGTAGTAGTACTAACAAGTAAGTA 57.050 33.333 11.64 0.00 37.40 2.24
4041 4514 5.067936 ACACAAATGTCTACGAGCTATAGCT 59.932 40.000 27.21 27.21 45.68 3.32
4042 4515 5.174035 CACACAAATGTCTACGAGCTATAGC 59.826 44.000 17.33 17.33 36.72 2.97
4043 4516 6.197282 CACACACAAATGTCTACGAGCTATAG 59.803 42.308 0.00 0.00 36.72 1.31
4044 4517 6.033966 CACACACAAATGTCTACGAGCTATA 58.966 40.000 0.00 0.00 36.72 1.31
4045 4518 4.864806 CACACACAAATGTCTACGAGCTAT 59.135 41.667 0.00 0.00 36.72 2.97
4052 4537 4.550063 CGACACACACACACAAATGTCTAC 60.550 45.833 0.00 0.00 36.72 2.59
4061 7366 0.176910 ATGGTCGACACACACACACA 59.823 50.000 18.91 2.70 0.00 3.72
4062 7367 0.581529 CATGGTCGACACACACACAC 59.418 55.000 18.91 0.00 0.00 3.82
4063 7368 0.531753 CCATGGTCGACACACACACA 60.532 55.000 18.91 4.28 0.00 3.72
4064 7369 1.841663 GCCATGGTCGACACACACAC 61.842 60.000 18.91 0.00 0.00 3.82
4097 7402 9.593134 TCACACTTACAAAAATAACAGCAAAAT 57.407 25.926 0.00 0.00 0.00 1.82
4126 7434 0.676466 TCCCATTGACCATCACACGC 60.676 55.000 0.00 0.00 0.00 5.34
4166 7611 1.279496 TCCAGATCAAGGACCACAGG 58.721 55.000 3.01 0.00 0.00 4.00
4186 7631 4.568359 GCTATCACAGTGACCACAGTTATG 59.432 45.833 5.05 0.00 0.00 1.90
4193 7638 2.482142 GCTAGGCTATCACAGTGACCAC 60.482 54.545 5.05 0.00 0.00 4.16
4202 7647 6.105333 CCTCTCATTATTGCTAGGCTATCAC 58.895 44.000 0.00 0.00 0.00 3.06
4204 7649 6.105333 CACCTCTCATTATTGCTAGGCTATC 58.895 44.000 0.00 0.00 31.23 2.08
4205 7650 5.545723 ACACCTCTCATTATTGCTAGGCTAT 59.454 40.000 0.00 0.00 31.23 2.97
4207 7652 3.713764 ACACCTCTCATTATTGCTAGGCT 59.286 43.478 0.00 0.00 31.23 4.58
4208 7653 4.078639 ACACCTCTCATTATTGCTAGGC 57.921 45.455 0.00 0.00 31.23 3.93
4282 7870 3.302480 CGGCGAACATTGCTATGTAGAAC 60.302 47.826 14.19 4.89 44.14 3.01
4283 7871 2.863740 CGGCGAACATTGCTATGTAGAA 59.136 45.455 14.19 0.00 44.14 2.10
4337 7925 1.398692 CTCCCTCTCTCTCTTTCCGG 58.601 60.000 0.00 0.00 0.00 5.14
4353 7941 2.610727 CGTGTGTTCTTCCTTCTCCTCC 60.611 54.545 0.00 0.00 0.00 4.30
4354 7942 2.678324 CGTGTGTTCTTCCTTCTCCTC 58.322 52.381 0.00 0.00 0.00 3.71
4355 7943 1.270358 GCGTGTGTTCTTCCTTCTCCT 60.270 52.381 0.00 0.00 0.00 3.69
4360 7948 0.034896 ATCGGCGTGTGTTCTTCCTT 59.965 50.000 6.85 0.00 0.00 3.36
4388 7985 0.102300 ATCATCGCCGTTCATCGACA 59.898 50.000 0.00 0.00 42.86 4.35
4404 8001 1.498043 CGATTTGCCGCCGATCATCA 61.498 55.000 0.00 0.00 0.00 3.07
4433 8030 0.387878 TTGCGCACCAAAATTAGCCG 60.388 50.000 11.12 0.00 0.00 5.52
4435 8032 0.715551 GCTTGCGCACCAAAATTAGC 59.284 50.000 11.12 10.63 35.78 3.09
4474 8071 2.480555 CATTGACTTGCCGCCGAC 59.519 61.111 0.00 0.00 0.00 4.79
4519 8117 0.247460 CTCGGTCCTCTTGTGATGCA 59.753 55.000 0.00 0.00 0.00 3.96
4545 8143 1.374252 GTCATCGCCACCACGTCTT 60.374 57.895 0.00 0.00 0.00 3.01
4553 8151 2.404789 CATTGCCGTCATCGCCAC 59.595 61.111 0.00 0.00 35.54 5.01
4555 8153 3.585990 CCCATTGCCGTCATCGCC 61.586 66.667 0.00 0.00 35.54 5.54
4557 8155 1.449423 TCACCCATTGCCGTCATCG 60.449 57.895 0.00 0.00 0.00 3.84
4564 8162 0.819582 CCATTCAGTCACCCATTGCC 59.180 55.000 0.00 0.00 0.00 4.52
4565 8163 0.174162 GCCATTCAGTCACCCATTGC 59.826 55.000 0.00 0.00 0.00 3.56
4570 8168 1.450312 CCTCGCCATTCAGTCACCC 60.450 63.158 0.00 0.00 0.00 4.61
4620 8218 4.379243 CTCGACGGTTGCCTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
4624 8222 1.541310 TTCCATCTCGACGGTTGCCT 61.541 55.000 0.00 0.00 0.00 4.75
4631 8229 1.320344 TGTCCCCTTCCATCTCGACG 61.320 60.000 0.00 0.00 0.00 5.12
4632 8230 0.902531 TTGTCCCCTTCCATCTCGAC 59.097 55.000 0.00 0.00 0.00 4.20
4640 8238 2.833943 AGCATGAATTTTGTCCCCTTCC 59.166 45.455 0.00 0.00 0.00 3.46
4650 8248 3.059166 GTTGTTCCGCAGCATGAATTTT 58.941 40.909 0.00 0.00 39.69 1.82
4664 8262 1.206578 CGTGGCACGATGTTGTTCC 59.793 57.895 34.85 0.00 46.05 3.62
4667 8265 2.110213 ACCGTGGCACGATGTTGT 59.890 55.556 38.91 24.95 46.05 3.32
4707 8305 6.016024 TGCACTTGACTGAAATTCAAAGCTAT 60.016 34.615 5.97 0.00 36.11 2.97
4709 8307 4.098349 TGCACTTGACTGAAATTCAAAGCT 59.902 37.500 5.97 0.00 36.11 3.74
4732 8330 9.035607 CAAAGCTATCGTACAAGTGAGAAATAT 57.964 33.333 0.00 0.00 0.00 1.28
4733 8331 7.491372 CCAAAGCTATCGTACAAGTGAGAAATA 59.509 37.037 0.00 0.00 0.00 1.40
4741 8339 3.259876 TGGTCCAAAGCTATCGTACAAGT 59.740 43.478 0.00 0.00 0.00 3.16
4742 8340 3.857052 TGGTCCAAAGCTATCGTACAAG 58.143 45.455 0.00 0.00 0.00 3.16
4763 8361 1.118838 CAAGTCTGCCTAGCTAGCCT 58.881 55.000 15.74 1.20 0.00 4.58
4774 8372 4.161333 CGTCCAAAAATCATCAAGTCTGC 58.839 43.478 0.00 0.00 0.00 4.26
4775 8373 4.726416 CCGTCCAAAAATCATCAAGTCTG 58.274 43.478 0.00 0.00 0.00 3.51
4776 8374 3.191371 GCCGTCCAAAAATCATCAAGTCT 59.809 43.478 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.