Multiple sequence alignment - TraesCS2D01G155500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G155500 chr2D 100.000 2315 0 0 1474 3788 99131867 99129553 0.000000e+00 4276.0
1 TraesCS2D01G155500 chr2D 100.000 1084 0 0 1 1084 99133340 99132257 0.000000e+00 2002.0
2 TraesCS2D01G155500 chr2A 94.388 1087 43 13 1 1084 98137785 98136714 0.000000e+00 1653.0
3 TraesCS2D01G155500 chr2A 91.404 826 40 11 2179 2984 98135730 98134916 0.000000e+00 1103.0
4 TraesCS2D01G155500 chr2A 91.159 328 23 5 1474 1799 98136657 98136334 1.250000e-119 440.0
5 TraesCS2D01G155500 chr2A 85.308 422 35 10 1787 2181 98136377 98135956 9.790000e-111 411.0
6 TraesCS2D01G155500 chr2A 94.286 210 8 3 3556 3762 98124767 98124559 6.110000e-83 318.0
7 TraesCS2D01G155500 chr2B 93.619 1097 42 17 1 1084 150711407 150710326 0.000000e+00 1613.0
8 TraesCS2D01G155500 chr2B 90.765 1072 59 17 1787 2831 150709995 150708937 0.000000e+00 1395.0
9 TraesCS2D01G155500 chr2B 95.046 323 16 0 1477 1799 150710274 150709952 3.380000e-140 508.0
10 TraesCS2D01G155500 chr2B 84.691 307 16 12 3479 3762 150708304 150708006 1.040000e-70 278.0
11 TraesCS2D01G155500 chr2B 83.946 299 23 13 2836 3128 150708898 150708619 2.900000e-66 263.0
12 TraesCS2D01G155500 chr3D 94.357 638 22 8 24 661 284205043 284204420 0.000000e+00 966.0
13 TraesCS2D01G155500 chr7B 92.476 638 34 7 24 661 29704457 29705080 0.000000e+00 900.0
14 TraesCS2D01G155500 chr3B 93.139 583 24 10 80 661 245914580 245914013 0.000000e+00 841.0
15 TraesCS2D01G155500 chr6A 90.800 250 14 3 2732 2981 24832862 24833102 3.650000e-85 326.0
16 TraesCS2D01G155500 chr6A 92.442 172 12 1 897 1068 24832423 24832593 1.050000e-60 244.0
17 TraesCS2D01G155500 chr6A 95.968 124 5 0 2522 2645 24832741 24832864 6.420000e-48 202.0
18 TraesCS2D01G155500 chr6A 93.814 97 6 0 1623 1719 24832590 24832686 3.050000e-31 147.0
19 TraesCS2D01G155500 chr6A 97.297 37 1 0 2273 2309 24832681 24832717 3.160000e-06 63.9
20 TraesCS2D01G155500 chr6A 100.000 28 0 0 2418 2445 24832715 24832742 7.000000e-03 52.8
21 TraesCS2D01G155500 chr5D 97.674 43 1 0 3194 3236 456591587 456591545 1.460000e-09 75.0
22 TraesCS2D01G155500 chr5B 97.674 43 1 0 3194 3236 558283458 558283416 1.460000e-09 75.0


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 TraesCS2D01G155500 chr2D 99129553 99133340 3787 True 3139.00 4276 100.00000 1 3788 2 chr2D.!!$R1 3787
1 TraesCS2D01G155500 chr2A 98134916 98137785 2869 True 901.75 1653 90.56475 1 2984 4 chr2A.!!$R2 2983
2 TraesCS2D01G155500 chr2B 150708006 150711407 3401 True 811.40 1613 89.61340 1 3762 5 chr2B.!!$R1 3761
3 TraesCS2D01G155500 chr3D 284204420 284205043 623 True 966.00 966 94.35700 24 661 1 chr3D.!!$R1 637
4 TraesCS2D01G155500 chr7B 29704457 29705080 623 False 900.00 900 92.47600 24 661 1 chr7B.!!$F1 637
5 TraesCS2D01G155500 chr3B 245914013 245914580 567 True 841.00 841 93.13900 80 661 1 chr3B.!!$R1 581

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
709 713 0.110010 GCCGAGAGCTTGCTTTGAAC 60.110 55.0 0.00 0.0 38.99 3.18 F
720 730 0.511653 GCTTTGAACCGTTCGAGTCC 59.488 55.0 6.78 0.0 0.00 3.85 F
1080 1111 0.977395 CCGAGGTATCCATCTTCCCC 59.023 60.0 0.00 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1837 0.112412 ACACCATGAACAAGGACCCC 59.888 55.000 3.07 0.0 0.00 4.95 R
2574 2883 1.271379 GAAAGGGGGCTTTAACCAACG 59.729 52.381 0.00 0.0 0.00 4.10 R
3079 3426 1.010419 GTTGCAATGCTTGGGCTTCG 61.010 55.000 6.82 0.0 39.59 3.79 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
20 21 1.364626 GCATCACCTTCCACAGCTCG 61.365 60.000 0.00 0.00 0.00 5.03
122 123 1.819288 TCGAATATCTCCCTCGCCATC 59.181 52.381 0.00 0.00 32.66 3.51
128 129 4.770362 TCCCTCGCCATCCCGACA 62.770 66.667 0.00 0.00 33.12 4.35
204 205 1.736645 CGCATTCCGTCGAACACCT 60.737 57.895 0.00 0.00 0.00 4.00
205 206 1.787847 GCATTCCGTCGAACACCTG 59.212 57.895 0.00 0.00 0.00 4.00
601 605 3.764049 GGTGCTGACGACGAACGC 61.764 66.667 0.00 0.70 46.94 4.84
705 709 1.078848 ATCGCCGAGAGCTTGCTTT 60.079 52.632 0.00 0.00 40.39 3.51
709 713 0.110010 GCCGAGAGCTTGCTTTGAAC 60.110 55.000 0.00 0.00 38.99 3.18
719 729 1.214367 TGCTTTGAACCGTTCGAGTC 58.786 50.000 6.78 1.92 0.00 3.36
720 730 0.511653 GCTTTGAACCGTTCGAGTCC 59.488 55.000 6.78 0.00 0.00 3.85
721 731 1.872653 GCTTTGAACCGTTCGAGTCCT 60.873 52.381 6.78 0.00 0.00 3.85
722 732 2.480845 CTTTGAACCGTTCGAGTCCTT 58.519 47.619 6.78 0.00 0.00 3.36
723 733 2.144482 TTGAACCGTTCGAGTCCTTC 57.856 50.000 6.78 0.00 0.00 3.46
869 879 4.681978 GTGGAGCGACCGTGGCTT 62.682 66.667 9.60 0.00 41.72 4.35
874 884 4.070552 GCGACCGTGGCTTCTCCT 62.071 66.667 0.00 0.00 35.26 3.69
875 885 2.125912 CGACCGTGGCTTCTCCTG 60.126 66.667 0.00 0.00 35.26 3.86
876 886 2.435059 GACCGTGGCTTCTCCTGC 60.435 66.667 0.00 0.00 35.26 4.85
877 887 2.925170 ACCGTGGCTTCTCCTGCT 60.925 61.111 0.00 0.00 35.26 4.24
878 888 2.435586 CCGTGGCTTCTCCTGCTG 60.436 66.667 0.00 0.00 35.26 4.41
879 889 2.659016 CGTGGCTTCTCCTGCTGA 59.341 61.111 0.00 0.00 35.26 4.26
880 890 1.447489 CGTGGCTTCTCCTGCTGAG 60.447 63.158 0.00 0.00 42.90 3.35
989 1010 2.723995 CGATCGCGCGAGGAAGAG 60.724 66.667 36.99 19.41 0.00 2.85
996 1024 2.485795 CGCGAGGAAGAGAGGGAGG 61.486 68.421 0.00 0.00 0.00 4.30
1029 1057 1.834378 CGAGGCCATGGAGCTCCTA 60.834 63.158 32.28 19.38 36.82 2.94
1076 1107 2.330216 CCCTTCCGAGGTATCCATCTT 58.670 52.381 0.00 0.00 41.85 2.40
1080 1111 0.977395 CCGAGGTATCCATCTTCCCC 59.023 60.000 0.00 0.00 0.00 4.81
1082 1113 2.047061 CGAGGTATCCATCTTCCCCAA 58.953 52.381 0.00 0.00 0.00 4.12
1539 1570 2.679355 CTCCGACGAGCTAATCTCTG 57.321 55.000 0.00 0.00 39.70 3.35
1740 1771 4.213482 GTCAGGTACAAAACAGTCATGGTC 59.787 45.833 0.00 0.00 0.00 4.02
1783 1815 7.215789 TGATGTTTGTTATTTGCATGTTCCTT 58.784 30.769 0.00 0.00 0.00 3.36
1784 1816 6.841443 TGTTTGTTATTTGCATGTTCCTTG 57.159 33.333 0.00 0.00 0.00 3.61
1785 1817 6.344500 TGTTTGTTATTTGCATGTTCCTTGT 58.656 32.000 0.00 0.00 0.00 3.16
1786 1818 6.820656 TGTTTGTTATTTGCATGTTCCTTGTT 59.179 30.769 0.00 0.00 0.00 2.83
1787 1819 7.010923 TGTTTGTTATTTGCATGTTCCTTGTTC 59.989 33.333 0.00 0.00 0.00 3.18
1788 1820 6.154203 TGTTATTTGCATGTTCCTTGTTCA 57.846 33.333 0.00 0.00 0.00 3.18
1789 1821 6.757237 TGTTATTTGCATGTTCCTTGTTCAT 58.243 32.000 0.00 0.00 0.00 2.57
1790 1822 6.645827 TGTTATTTGCATGTTCCTTGTTCATG 59.354 34.615 0.00 0.00 40.98 3.07
1791 1823 3.663995 TTGCATGTTCCTTGTTCATGG 57.336 42.857 0.00 0.00 39.20 3.66
1792 1824 2.596346 TGCATGTTCCTTGTTCATGGT 58.404 42.857 0.00 0.00 39.20 3.55
1793 1825 2.296752 TGCATGTTCCTTGTTCATGGTG 59.703 45.455 0.00 0.00 39.20 4.17
1794 1826 2.297033 GCATGTTCCTTGTTCATGGTGT 59.703 45.455 0.00 0.00 39.20 4.16
1795 1827 3.243839 GCATGTTCCTTGTTCATGGTGTT 60.244 43.478 0.00 0.00 39.20 3.32
1796 1828 4.740334 GCATGTTCCTTGTTCATGGTGTTT 60.740 41.667 0.00 0.00 39.20 2.83
1797 1829 5.358922 CATGTTCCTTGTTCATGGTGTTTT 58.641 37.500 0.00 0.00 36.36 2.43
1798 1830 5.413309 TGTTCCTTGTTCATGGTGTTTTT 57.587 34.783 0.00 0.00 0.00 1.94
1876 1909 8.167345 CGAGTATTTAGCTTGATCATGCTAATG 58.833 37.037 36.86 24.65 46.45 1.90
1908 1943 4.261801 ACGTTTACCATGCTAATTGCTCT 58.738 39.130 0.00 0.00 43.37 4.09
1910 1945 5.163754 ACGTTTACCATGCTAATTGCTCTTC 60.164 40.000 0.00 0.00 43.37 2.87
1935 1970 6.635641 CCATAATTGAATCGCTGATGTCAAAG 59.364 38.462 13.77 0.00 33.93 2.77
1978 2032 8.911918 TTAATGTACTTACTGAGCTTTTGGAA 57.088 30.769 0.00 0.00 0.00 3.53
2004 2058 2.094894 CACGCTAATTGCTCTTCCACAG 59.905 50.000 0.00 0.00 40.11 3.66
2015 2069 5.543714 TGCTCTTCCACAGTTAAATCGTTA 58.456 37.500 0.00 0.00 0.00 3.18
2016 2070 5.637810 TGCTCTTCCACAGTTAAATCGTTAG 59.362 40.000 0.00 0.00 0.00 2.34
2067 2121 6.869206 AATGTAGTTCCTGAGCTTTAGGTA 57.131 37.500 15.25 5.72 36.67 3.08
2068 2122 5.916661 TGTAGTTCCTGAGCTTTAGGTAG 57.083 43.478 15.25 0.00 36.67 3.18
2097 2155 5.643348 TCAGCTTATGGACATATATTTGGCG 59.357 40.000 0.00 0.00 0.00 5.69
2103 2161 3.137544 TGGACATATATTTGGCGTTCCCT 59.862 43.478 0.00 0.00 0.00 4.20
2106 2164 5.512576 GGACATATATTTGGCGTTCCCTAGT 60.513 44.000 0.00 0.00 0.00 2.57
2110 2168 2.702592 TTTGGCGTTCCCTAGTATGG 57.297 50.000 0.00 0.00 0.00 2.74
2151 2209 7.928307 ATTTGAATGTGCTAACACTCATACT 57.072 32.000 0.00 0.00 41.80 2.12
2206 2492 1.916000 GTTTTCCGTACGAGGATCACG 59.084 52.381 18.76 9.40 40.48 4.35
2226 2512 6.845302 TCACGATCAATTTCCTGAATTTGAG 58.155 36.000 17.24 10.46 41.20 3.02
2234 2520 8.143835 TCAATTTCCTGAATTTGAGTTCTTTCC 58.856 33.333 11.25 0.00 36.41 3.13
2398 2707 7.073088 TGGTTTGACTGATGGGATTATGGTATA 59.927 37.037 0.00 0.00 0.00 1.47
2399 2708 8.109634 GGTTTGACTGATGGGATTATGGTATAT 58.890 37.037 0.00 0.00 0.00 0.86
2453 2762 6.556874 TGGGAACAGAATGGAAGGTAAATTTT 59.443 34.615 0.00 0.00 43.62 1.82
2454 2763 7.097192 GGGAACAGAATGGAAGGTAAATTTTC 58.903 38.462 0.00 0.00 43.62 2.29
2574 2883 4.571176 GGGATACGGAAGATCAAACAAGAC 59.429 45.833 0.00 0.00 37.60 3.01
2575 2884 4.267928 GGATACGGAAGATCAAACAAGACG 59.732 45.833 0.00 0.00 0.00 4.18
2620 2929 3.505680 TCATAATTTGTGCCGCAGTTTCT 59.494 39.130 0.00 0.00 0.00 2.52
2648 2957 1.534175 CCTACAGCGCTTCGAGGTAAG 60.534 57.143 7.50 0.00 0.00 2.34
2754 3063 1.173043 CATACCAGCGGCAAAAGGAA 58.827 50.000 1.45 0.00 0.00 3.36
2787 3096 6.054860 TCTCAGAACCCTTTTCTTCCATAG 57.945 41.667 0.00 0.00 0.00 2.23
2816 3125 5.196341 TCCATTGTACTGTCGATATCCAC 57.804 43.478 0.00 0.00 0.00 4.02
2817 3126 4.647399 TCCATTGTACTGTCGATATCCACA 59.353 41.667 3.05 3.05 0.00 4.17
2818 3127 5.304357 TCCATTGTACTGTCGATATCCACAT 59.696 40.000 3.49 0.00 0.00 3.21
2819 3128 6.492087 TCCATTGTACTGTCGATATCCACATA 59.508 38.462 3.49 0.00 0.00 2.29
2820 3129 7.178451 TCCATTGTACTGTCGATATCCACATAT 59.822 37.037 3.49 0.00 0.00 1.78
2821 3130 8.466798 CCATTGTACTGTCGATATCCACATATA 58.533 37.037 3.49 0.00 0.00 0.86
2892 3239 7.169645 GCAAAACAATCTCTGCACTGAATAAAA 59.830 33.333 0.00 0.00 34.87 1.52
2903 3250 5.047164 TGCACTGAATAAAAGCACCAATCAT 60.047 36.000 0.00 0.00 0.00 2.45
2917 3264 5.388682 GCACCAATCATTGTTTGTGATTTCG 60.389 40.000 8.88 0.00 42.08 3.46
2927 3274 7.969387 TTGTTTGTGATTTCGAAGAAAAGAG 57.031 32.000 0.00 0.00 45.90 2.85
2928 3275 6.494842 TGTTTGTGATTTCGAAGAAAAGAGG 58.505 36.000 0.00 0.00 45.90 3.69
2933 3280 4.156556 TGATTTCGAAGAAAAGAGGCATGG 59.843 41.667 0.00 0.00 45.90 3.66
2952 3299 6.880822 CATGGTTTGCAGATATTCAGTTTG 57.119 37.500 0.00 0.00 0.00 2.93
2988 3335 3.070576 GCTCCTGCGCCCCAAAAT 61.071 61.111 4.18 0.00 0.00 1.82
3000 3347 4.873259 GCGCCCCAAAATTACATTTACAAT 59.127 37.500 0.00 0.00 0.00 2.71
3002 3349 6.128145 GCGCCCCAAAATTACATTTACAATTT 60.128 34.615 0.00 0.00 36.22 1.82
3003 3350 7.064728 GCGCCCCAAAATTACATTTACAATTTA 59.935 33.333 0.00 0.00 34.17 1.40
3004 3351 8.384365 CGCCCCAAAATTACATTTACAATTTAC 58.616 33.333 0.00 0.00 34.17 2.01
3005 3352 9.220767 GCCCCAAAATTACATTTACAATTTACA 57.779 29.630 0.00 0.00 34.17 2.41
3050 3397 8.975410 ACAATTCAGACATGTAAATGTTCATG 57.025 30.769 0.00 1.15 44.56 3.07
3060 3407 8.176814 CATGTAAATGTTCATGTCCAAATGTC 57.823 34.615 0.00 0.00 37.31 3.06
3069 3416 5.795972 TCATGTCCAAATGTCATTTGCAAT 58.204 33.333 26.42 17.69 46.27 3.56
3165 3518 4.842531 TTGGGCATTTCTAGAGACATGA 57.157 40.909 9.38 0.00 34.96 3.07
3166 3519 5.378230 TTGGGCATTTCTAGAGACATGAT 57.622 39.130 9.38 0.00 34.96 2.45
3168 3521 6.499106 TGGGCATTTCTAGAGACATGATTA 57.501 37.500 9.38 0.00 34.96 1.75
3169 3522 6.899089 TGGGCATTTCTAGAGACATGATTAA 58.101 36.000 9.38 0.00 34.96 1.40
3170 3523 6.767902 TGGGCATTTCTAGAGACATGATTAAC 59.232 38.462 9.38 0.00 34.96 2.01
3173 3526 7.712639 GGCATTTCTAGAGACATGATTAACTGA 59.287 37.037 9.38 0.00 34.96 3.41
3174 3527 9.270640 GCATTTCTAGAGACATGATTAACTGAT 57.729 33.333 9.38 0.00 34.96 2.90
3179 3532 9.809096 TCTAGAGACATGATTAACTGATGAAAC 57.191 33.333 0.00 0.00 0.00 2.78
3180 3533 9.591792 CTAGAGACATGATTAACTGATGAAACA 57.408 33.333 0.00 0.00 0.00 2.83
3181 3534 8.261492 AGAGACATGATTAACTGATGAAACAC 57.739 34.615 0.00 0.00 0.00 3.32
3203 3563 4.450757 ACAAACACAACTGTTCCTTTTTGC 59.549 37.500 10.82 0.00 39.88 3.68
3204 3564 3.951775 ACACAACTGTTCCTTTTTGCA 57.048 38.095 0.00 0.00 0.00 4.08
3211 3571 6.598850 ACAACTGTTCCTTTTTGCATGAAAAT 59.401 30.769 0.00 0.00 33.46 1.82
3212 3572 7.121020 ACAACTGTTCCTTTTTGCATGAAAATT 59.879 29.630 0.00 0.00 33.46 1.82
3213 3573 7.018635 ACTGTTCCTTTTTGCATGAAAATTG 57.981 32.000 0.00 0.00 33.46 2.32
3214 3574 6.598850 ACTGTTCCTTTTTGCATGAAAATTGT 59.401 30.769 0.00 0.00 33.46 2.71
3215 3575 7.014092 TGTTCCTTTTTGCATGAAAATTGTC 57.986 32.000 0.00 0.00 33.46 3.18
3216 3576 6.596888 TGTTCCTTTTTGCATGAAAATTGTCA 59.403 30.769 0.00 0.00 33.46 3.58
3217 3577 7.120285 TGTTCCTTTTTGCATGAAAATTGTCAA 59.880 29.630 1.55 0.00 33.46 3.18
3218 3578 7.249186 TCCTTTTTGCATGAAAATTGTCAAG 57.751 32.000 1.55 0.00 33.46 3.02
3219 3579 7.046652 TCCTTTTTGCATGAAAATTGTCAAGA 58.953 30.769 1.55 0.00 33.46 3.02
3220 3580 7.551974 TCCTTTTTGCATGAAAATTGTCAAGAA 59.448 29.630 1.55 0.00 33.46 2.52
3221 3581 7.641020 CCTTTTTGCATGAAAATTGTCAAGAAC 59.359 33.333 1.55 0.00 33.46 3.01
3222 3582 7.606858 TTTTGCATGAAAATTGTCAAGAACA 57.393 28.000 1.55 0.00 35.59 3.18
3223 3583 6.586868 TTGCATGAAAATTGTCAAGAACAC 57.413 33.333 1.55 0.00 37.70 3.32
3224 3584 5.658468 TGCATGAAAATTGTCAAGAACACA 58.342 33.333 1.55 0.00 37.70 3.72
3225 3585 6.282167 TGCATGAAAATTGTCAAGAACACAT 58.718 32.000 1.55 0.00 37.70 3.21
3226 3586 6.421501 TGCATGAAAATTGTCAAGAACACATC 59.578 34.615 1.55 0.00 37.70 3.06
3227 3587 6.421501 GCATGAAAATTGTCAAGAACACATCA 59.578 34.615 1.55 0.00 37.70 3.07
3237 3597 8.669946 TGTCAAGAACACATCAAACACTAATA 57.330 30.769 0.00 0.00 31.20 0.98
3291 3660 4.554162 TTTGTTTGAGTTTTTGTTCGCG 57.446 36.364 0.00 0.00 0.00 5.87
3309 3710 1.741525 GCCAGGAGCTTTGTTTGCA 59.258 52.632 0.00 0.00 38.99 4.08
3313 3714 2.557924 CCAGGAGCTTTGTTTGCATGTA 59.442 45.455 0.00 0.00 0.00 2.29
3314 3715 3.194116 CCAGGAGCTTTGTTTGCATGTAT 59.806 43.478 0.00 0.00 0.00 2.29
3315 3716 4.398988 CCAGGAGCTTTGTTTGCATGTATA 59.601 41.667 0.00 0.00 0.00 1.47
3317 3718 6.406177 CCAGGAGCTTTGTTTGCATGTATATT 60.406 38.462 0.00 0.00 0.00 1.28
3318 3719 6.694411 CAGGAGCTTTGTTTGCATGTATATTC 59.306 38.462 0.00 0.00 0.00 1.75
3319 3720 6.604795 AGGAGCTTTGTTTGCATGTATATTCT 59.395 34.615 0.00 0.00 0.00 2.40
3320 3721 7.775093 AGGAGCTTTGTTTGCATGTATATTCTA 59.225 33.333 0.00 0.00 0.00 2.10
3321 3722 8.072567 GGAGCTTTGTTTGCATGTATATTCTAG 58.927 37.037 0.00 0.00 0.00 2.43
3322 3723 7.934457 AGCTTTGTTTGCATGTATATTCTAGG 58.066 34.615 0.00 0.00 0.00 3.02
3323 3724 7.775093 AGCTTTGTTTGCATGTATATTCTAGGA 59.225 33.333 0.00 0.00 0.00 2.94
3324 3725 8.072567 GCTTTGTTTGCATGTATATTCTAGGAG 58.927 37.037 0.00 0.00 0.00 3.69
3325 3726 9.113838 CTTTGTTTGCATGTATATTCTAGGAGT 57.886 33.333 0.00 0.00 0.00 3.85
3326 3727 8.437360 TTGTTTGCATGTATATTCTAGGAGTG 57.563 34.615 0.00 0.00 0.00 3.51
3327 3728 6.992123 TGTTTGCATGTATATTCTAGGAGTGG 59.008 38.462 0.00 0.00 0.00 4.00
3328 3729 5.745312 TGCATGTATATTCTAGGAGTGGG 57.255 43.478 0.00 0.00 0.00 4.61
3329 3730 5.155161 TGCATGTATATTCTAGGAGTGGGT 58.845 41.667 0.00 0.00 0.00 4.51
3330 3731 5.606749 TGCATGTATATTCTAGGAGTGGGTT 59.393 40.000 0.00 0.00 0.00 4.11
3331 3732 6.101150 TGCATGTATATTCTAGGAGTGGGTTT 59.899 38.462 0.00 0.00 0.00 3.27
3338 3739 4.993705 TCTAGGAGTGGGTTTTTGTGAT 57.006 40.909 0.00 0.00 0.00 3.06
3342 3743 4.285863 AGGAGTGGGTTTTTGTGATTTCA 58.714 39.130 0.00 0.00 0.00 2.69
3359 3760 5.427806 TGATTTCAGAGATCCATTCAGACCT 59.572 40.000 0.00 0.00 0.00 3.85
3361 3762 5.350504 TTCAGAGATCCATTCAGACCTTC 57.649 43.478 0.00 0.00 0.00 3.46
3362 3763 4.356436 TCAGAGATCCATTCAGACCTTCA 58.644 43.478 0.00 0.00 0.00 3.02
3363 3764 4.405036 TCAGAGATCCATTCAGACCTTCAG 59.595 45.833 0.00 0.00 0.00 3.02
3364 3765 4.405036 CAGAGATCCATTCAGACCTTCAGA 59.595 45.833 0.00 0.00 0.00 3.27
3367 3768 2.619931 TCCATTCAGACCTTCAGACCA 58.380 47.619 0.00 0.00 0.00 4.02
3368 3769 3.184628 TCCATTCAGACCTTCAGACCAT 58.815 45.455 0.00 0.00 0.00 3.55
3369 3770 3.054875 TCCATTCAGACCTTCAGACCATG 60.055 47.826 0.00 0.00 0.00 3.66
3370 3771 2.479566 TTCAGACCTTCAGACCATGC 57.520 50.000 0.00 0.00 0.00 4.06
3371 3772 0.247460 TCAGACCTTCAGACCATGCG 59.753 55.000 0.00 0.00 0.00 4.73
3372 3773 0.742281 CAGACCTTCAGACCATGCGG 60.742 60.000 0.00 0.00 38.77 5.69
3373 3774 0.904865 AGACCTTCAGACCATGCGGA 60.905 55.000 0.00 0.00 35.59 5.54
3374 3775 0.036388 GACCTTCAGACCATGCGGAA 60.036 55.000 0.00 0.00 35.59 4.30
3375 3776 0.036010 ACCTTCAGACCATGCGGAAG 60.036 55.000 6.34 6.34 39.02 3.46
3376 3777 0.250234 CCTTCAGACCATGCGGAAGA 59.750 55.000 12.46 0.00 40.88 2.87
3377 3778 1.134280 CCTTCAGACCATGCGGAAGAT 60.134 52.381 12.46 0.00 40.88 2.40
3378 3779 2.636830 CTTCAGACCATGCGGAAGATT 58.363 47.619 7.20 0.00 40.88 2.40
3379 3780 2.028420 TCAGACCATGCGGAAGATTG 57.972 50.000 0.00 0.00 35.59 2.67
3380 3781 1.019673 CAGACCATGCGGAAGATTGG 58.980 55.000 0.00 0.00 39.64 3.16
3381 3782 0.911769 AGACCATGCGGAAGATTGGA 59.088 50.000 0.89 0.00 37.87 3.53
3382 3783 1.492176 AGACCATGCGGAAGATTGGAT 59.508 47.619 0.89 0.00 37.87 3.41
3383 3784 1.876156 GACCATGCGGAAGATTGGATC 59.124 52.381 0.89 0.00 37.87 3.36
3384 3785 1.212688 ACCATGCGGAAGATTGGATCA 59.787 47.619 0.89 0.00 37.87 2.92
3385 3786 2.158564 ACCATGCGGAAGATTGGATCAT 60.159 45.455 0.89 0.00 37.87 2.45
3386 3787 3.072915 ACCATGCGGAAGATTGGATCATA 59.927 43.478 0.89 0.00 37.87 2.15
3387 3788 4.263639 ACCATGCGGAAGATTGGATCATAT 60.264 41.667 0.89 0.00 37.87 1.78
3388 3789 5.045651 ACCATGCGGAAGATTGGATCATATA 60.046 40.000 0.89 0.00 37.87 0.86
3395 3796 8.514594 GCGGAAGATTGGATCATATAAATTTCA 58.485 33.333 0.00 0.00 0.00 2.69
3412 3813 2.885135 TCAACATTCATGGACAGCCT 57.115 45.000 0.00 0.00 34.31 4.58
3421 3822 4.901197 TCATGGACAGCCTTTACTACAA 57.099 40.909 0.00 0.00 34.31 2.41
3422 3823 4.832248 TCATGGACAGCCTTTACTACAAG 58.168 43.478 0.00 0.00 34.31 3.16
3423 3824 4.530553 TCATGGACAGCCTTTACTACAAGA 59.469 41.667 0.00 0.00 34.31 3.02
3424 3825 4.267349 TGGACAGCCTTTACTACAAGAC 57.733 45.455 0.00 0.00 34.31 3.01
3425 3826 3.251571 GGACAGCCTTTACTACAAGACG 58.748 50.000 0.00 0.00 0.00 4.18
3426 3827 3.305881 GGACAGCCTTTACTACAAGACGT 60.306 47.826 0.00 0.00 0.00 4.34
3427 3828 4.304939 GACAGCCTTTACTACAAGACGTT 58.695 43.478 0.00 0.00 0.00 3.99
3428 3829 4.304939 ACAGCCTTTACTACAAGACGTTC 58.695 43.478 0.00 0.00 0.00 3.95
3429 3830 4.202182 ACAGCCTTTACTACAAGACGTTCA 60.202 41.667 0.00 0.00 0.00 3.18
3430 3831 4.748102 CAGCCTTTACTACAAGACGTTCAA 59.252 41.667 0.00 0.00 0.00 2.69
3431 3832 5.408604 CAGCCTTTACTACAAGACGTTCAAT 59.591 40.000 0.00 0.00 0.00 2.57
3432 3833 5.638234 AGCCTTTACTACAAGACGTTCAATC 59.362 40.000 0.00 0.00 0.00 2.67
3433 3834 5.638234 GCCTTTACTACAAGACGTTCAATCT 59.362 40.000 0.00 0.00 0.00 2.40
3434 3835 6.810182 GCCTTTACTACAAGACGTTCAATCTA 59.190 38.462 0.00 0.00 0.00 1.98
3438 3839 5.109903 ACTACAAGACGTTCAATCTATGCC 58.890 41.667 0.00 0.00 0.00 4.40
3439 3840 3.937814 ACAAGACGTTCAATCTATGCCA 58.062 40.909 0.00 0.00 0.00 4.92
3445 3846 6.924111 AGACGTTCAATCTATGCCAAAAATT 58.076 32.000 0.00 0.00 0.00 1.82
3446 3847 6.808212 AGACGTTCAATCTATGCCAAAAATTG 59.192 34.615 0.00 0.00 0.00 2.32
3459 3860 4.827692 CCAAAAATTGGTTTAGTAGGGGC 58.172 43.478 0.87 0.00 45.93 5.80
3460 3861 4.284746 CCAAAAATTGGTTTAGTAGGGGCA 59.715 41.667 0.87 0.00 45.93 5.36
3461 3862 5.045942 CCAAAAATTGGTTTAGTAGGGGCAT 60.046 40.000 0.87 0.00 45.93 4.40
3462 3863 6.155393 CCAAAAATTGGTTTAGTAGGGGCATA 59.845 38.462 0.87 0.00 45.93 3.14
3464 3865 6.785337 AAATTGGTTTAGTAGGGGCATAAC 57.215 37.500 0.00 0.00 0.00 1.89
3465 3866 4.931027 TTGGTTTAGTAGGGGCATAACA 57.069 40.909 0.00 0.00 0.00 2.41
3467 3868 5.459982 TGGTTTAGTAGGGGCATAACAAT 57.540 39.130 0.00 0.00 0.00 2.71
3468 3869 5.442391 TGGTTTAGTAGGGGCATAACAATC 58.558 41.667 0.00 0.00 0.00 2.67
3469 3870 5.192923 TGGTTTAGTAGGGGCATAACAATCT 59.807 40.000 0.00 0.00 0.00 2.40
3471 3872 6.039382 GGTTTAGTAGGGGCATAACAATCTTG 59.961 42.308 0.00 0.00 0.00 3.02
3472 3873 4.170468 AGTAGGGGCATAACAATCTTGG 57.830 45.455 0.00 0.00 0.00 3.61
3473 3874 1.780503 AGGGGCATAACAATCTTGGC 58.219 50.000 0.00 0.00 35.37 4.52
3474 3875 1.006998 AGGGGCATAACAATCTTGGCA 59.993 47.619 0.00 0.00 37.64 4.92
3475 3876 1.830477 GGGGCATAACAATCTTGGCAA 59.170 47.619 0.00 0.00 37.64 4.52
3476 3877 2.159057 GGGGCATAACAATCTTGGCAAG 60.159 50.000 21.17 21.17 37.64 4.01
3477 3878 2.159057 GGGCATAACAATCTTGGCAAGG 60.159 50.000 25.92 13.25 37.64 3.61
3483 3884 2.233271 ACAATCTTGGCAAGGACACAG 58.767 47.619 25.92 12.87 0.00 3.66
3494 3895 3.496331 CAAGGACACAGGGGTACAAATT 58.504 45.455 0.00 0.00 0.00 1.82
3497 3898 3.117284 AGGACACAGGGGTACAAATTGTT 60.117 43.478 3.17 0.00 0.00 2.83
3500 3901 3.888930 ACACAGGGGTACAAATTGTTGAG 59.111 43.478 3.17 0.00 38.20 3.02
3518 3919 6.554419 TGTTGAGAAGTTTGTCATGTTGAAG 58.446 36.000 0.00 0.00 30.05 3.02
3544 3945 7.280652 GCCATTTTGGTATCTTTTTACATGCAT 59.719 33.333 0.00 0.00 40.46 3.96
3552 3953 7.376866 GGTATCTTTTTACATGCATGATGAACG 59.623 37.037 32.75 18.49 35.80 3.95
3553 3954 5.639757 TCTTTTTACATGCATGATGAACGG 58.360 37.500 32.75 15.57 35.80 4.44
3554 3955 5.182950 TCTTTTTACATGCATGATGAACGGT 59.817 36.000 32.75 10.44 35.80 4.83
3559 3980 2.286359 CATGCATGATGAACGGTTACCG 60.286 50.000 22.59 23.18 43.14 4.02
3588 4009 3.369756 CGCTATAAAAGGCGTGAACAAGA 59.630 43.478 0.00 0.00 45.34 3.02
3591 4012 2.422276 AAAAGGCGTGAACAAGATGC 57.578 45.000 0.00 0.00 0.00 3.91
3649 4070 2.366590 TGATACCCAGCATCACTAGCAG 59.633 50.000 0.00 0.00 0.00 4.24
3653 4074 1.209019 CCCAGCATCACTAGCAGAAGT 59.791 52.381 0.00 0.00 0.00 3.01
3654 4075 2.432146 CCCAGCATCACTAGCAGAAGTA 59.568 50.000 0.00 0.00 0.00 2.24
3662 4083 7.036220 GCATCACTAGCAGAAGTAAAGAACTA 58.964 38.462 0.00 0.00 37.50 2.24
3689 4110 9.520515 AAGATAATTTACATTGACCACAGAAGT 57.479 29.630 0.00 0.00 0.00 3.01
3714 4138 8.730680 GTTTGTCATCATGGTTATTACAAGACT 58.269 33.333 0.00 0.00 0.00 3.24
3719 4143 4.785914 TCATGGTTATTACAAGACTCCCCA 59.214 41.667 0.00 0.00 0.00 4.96
3720 4144 4.837093 TGGTTATTACAAGACTCCCCAG 57.163 45.455 0.00 0.00 0.00 4.45
3721 4145 3.054655 TGGTTATTACAAGACTCCCCAGC 60.055 47.826 0.00 0.00 0.00 4.85
3722 4146 3.054655 GGTTATTACAAGACTCCCCAGCA 60.055 47.826 0.00 0.00 0.00 4.41
3723 4147 4.385310 GGTTATTACAAGACTCCCCAGCAT 60.385 45.833 0.00 0.00 0.00 3.79
3724 4148 3.567478 ATTACAAGACTCCCCAGCATC 57.433 47.619 0.00 0.00 0.00 3.91
3725 4149 1.204146 TACAAGACTCCCCAGCATCC 58.796 55.000 0.00 0.00 0.00 3.51
3726 4150 1.225704 CAAGACTCCCCAGCATCCC 59.774 63.158 0.00 0.00 0.00 3.85
3727 4151 2.370445 AAGACTCCCCAGCATCCCG 61.370 63.158 0.00 0.00 0.00 5.14
3733 4157 0.473694 TCCCCAGCATCCCGATGTAT 60.474 55.000 6.56 0.00 40.80 2.29
3762 4186 0.111253 CCCAACCTTTCCTCAGCAGT 59.889 55.000 0.00 0.00 0.00 4.40
3763 4187 1.479389 CCCAACCTTTCCTCAGCAGTT 60.479 52.381 0.00 0.00 0.00 3.16
3764 4188 2.224769 CCCAACCTTTCCTCAGCAGTTA 60.225 50.000 0.00 0.00 0.00 2.24
3765 4189 3.486383 CCAACCTTTCCTCAGCAGTTAA 58.514 45.455 0.00 0.00 0.00 2.01
3766 4190 3.253432 CCAACCTTTCCTCAGCAGTTAAC 59.747 47.826 0.00 0.00 0.00 2.01
3767 4191 4.137543 CAACCTTTCCTCAGCAGTTAACT 58.862 43.478 1.12 1.12 0.00 2.24
3768 4192 5.305585 CAACCTTTCCTCAGCAGTTAACTA 58.694 41.667 8.04 0.00 0.00 2.24
3769 4193 5.763876 ACCTTTCCTCAGCAGTTAACTAT 57.236 39.130 8.04 0.00 0.00 2.12
3770 4194 5.491982 ACCTTTCCTCAGCAGTTAACTATG 58.508 41.667 8.04 10.41 0.00 2.23
3771 4195 4.333926 CCTTTCCTCAGCAGTTAACTATGC 59.666 45.833 8.04 9.74 42.87 3.14
3778 4202 3.682372 GCAGTTAACTATGCTTCAGGC 57.318 47.619 8.04 0.25 39.38 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.821589 CGGTCCAAGGAGGCGCTC 62.822 72.222 7.64 2.45 37.29 5.03
122 123 2.786495 CGTGAGAGGGGATGTCGGG 61.786 68.421 0.00 0.00 0.00 5.14
128 129 2.125961 GTACGCCGTGAGAGGGGAT 61.126 63.158 0.00 0.00 45.92 3.85
184 185 1.735198 GTGTTCGACGGAATGCGGA 60.735 57.895 0.00 0.00 34.05 5.54
705 709 3.879912 GAAGGACTCGAACGGTTCA 57.120 52.632 19.91 7.16 0.00 3.18
860 870 2.925170 AGCAGGAGAAGCCACGGT 60.925 61.111 0.00 0.00 40.02 4.83
875 885 1.950098 GCTCGAACGAAGCACTCAGC 61.950 60.000 11.40 0.00 46.19 4.26
876 886 0.664466 TGCTCGAACGAAGCACTCAG 60.664 55.000 13.73 0.00 33.24 3.35
877 887 1.362355 TGCTCGAACGAAGCACTCA 59.638 52.632 13.73 0.00 33.24 3.41
878 888 4.245054 TGCTCGAACGAAGCACTC 57.755 55.556 13.73 0.00 33.24 3.51
959 976 2.125512 GATCGCACCGGACAAGCT 60.126 61.111 9.46 0.00 0.00 3.74
960 977 3.554692 CGATCGCACCGGACAAGC 61.555 66.667 9.46 5.59 0.00 4.01
961 982 3.554692 GCGATCGCACCGGACAAG 61.555 66.667 33.89 0.00 41.49 3.16
979 1000 2.131067 CCCTCCCTCTCTTCCTCGC 61.131 68.421 0.00 0.00 0.00 5.03
989 1010 0.831711 GCTCCTCATCTCCCTCCCTC 60.832 65.000 0.00 0.00 0.00 4.30
996 1024 1.363443 CTCGCTGCTCCTCATCTCC 59.637 63.158 0.00 0.00 0.00 3.71
1537 1568 5.450137 CCAAAATCCAGCAGAAATAGCTCAG 60.450 44.000 0.00 0.00 41.14 3.35
1539 1570 4.400567 ACCAAAATCCAGCAGAAATAGCTC 59.599 41.667 0.00 0.00 41.14 4.09
1603 1634 3.072184 ACCTGCAACAGAAGATTCAGAGT 59.928 43.478 0.00 0.00 32.44 3.24
1684 1715 0.459411 GACTCCGCTTGAGGCTTCTC 60.459 60.000 0.00 0.00 46.54 2.87
1698 1729 3.569701 TGACCTGCTTGAATTTTGACTCC 59.430 43.478 0.00 0.00 0.00 3.85
1740 1771 4.398358 ACATCATGATGCCTGAAGTTCTTG 59.602 41.667 31.17 8.44 42.39 3.02
1798 1830 0.747852 GAACAAGGACCCCGCAAAAA 59.252 50.000 0.00 0.00 0.00 1.94
1799 1831 0.395862 TGAACAAGGACCCCGCAAAA 60.396 50.000 0.00 0.00 0.00 2.44
1800 1832 0.178975 ATGAACAAGGACCCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
1801 1833 0.893270 CATGAACAAGGACCCCGCAA 60.893 55.000 0.00 0.00 0.00 4.85
1802 1834 1.303236 CATGAACAAGGACCCCGCA 60.303 57.895 0.00 0.00 0.00 5.69
1803 1835 2.046285 CCATGAACAAGGACCCCGC 61.046 63.158 0.00 0.00 0.00 6.13
1804 1836 0.960364 CACCATGAACAAGGACCCCG 60.960 60.000 3.07 0.00 0.00 5.73
1805 1837 0.112412 ACACCATGAACAAGGACCCC 59.888 55.000 3.07 0.00 0.00 4.95
1806 1838 1.995376 AACACCATGAACAAGGACCC 58.005 50.000 3.07 0.00 0.00 4.46
1807 1839 4.764823 TGAATAACACCATGAACAAGGACC 59.235 41.667 3.07 0.00 0.00 4.46
1808 1840 5.106157 CCTGAATAACACCATGAACAAGGAC 60.106 44.000 3.07 0.00 0.00 3.85
1809 1841 5.009631 CCTGAATAACACCATGAACAAGGA 58.990 41.667 3.07 0.00 0.00 3.36
1810 1842 4.380867 GCCTGAATAACACCATGAACAAGG 60.381 45.833 0.00 0.00 0.00 3.61
1811 1843 4.218200 TGCCTGAATAACACCATGAACAAG 59.782 41.667 0.00 0.00 0.00 3.16
1812 1844 4.148079 TGCCTGAATAACACCATGAACAA 58.852 39.130 0.00 0.00 0.00 2.83
1840 1872 7.039270 TCAAGCTAAATACTCGTCTAATTGCA 58.961 34.615 0.00 0.00 0.00 4.08
1876 1909 3.181575 GCATGGTAAACGTTGCTTCAAAC 59.818 43.478 0.00 0.00 0.00 2.93
1908 1943 5.821995 TGACATCAGCGATTCAATTATGGAA 59.178 36.000 0.00 0.00 0.00 3.53
1910 1945 5.678132 TGACATCAGCGATTCAATTATGG 57.322 39.130 0.00 0.00 0.00 2.74
1935 1970 7.959689 ACATTAAGATCACATCTATGCTCAC 57.040 36.000 0.00 0.00 39.08 3.51
2028 2082 9.988815 GGAACTACATTAAGATCACATCTATGT 57.011 33.333 0.00 6.98 40.13 2.29
2097 2155 7.281100 CACAAAATCTCTTCCATACTAGGGAAC 59.719 40.741 0.00 0.00 39.44 3.62
2103 2161 7.994425 TTTGCACAAAATCTCTTCCATACTA 57.006 32.000 0.00 0.00 0.00 1.82
2106 2164 8.366401 TCAAATTTGCACAAAATCTCTTCCATA 58.634 29.630 13.54 0.00 37.51 2.74
2110 2168 8.553696 ACATTCAAATTTGCACAAAATCTCTTC 58.446 29.630 13.54 0.00 37.51 2.87
2174 2232 5.699915 TCGTACGGAAAACCACATTCAAATA 59.300 36.000 16.52 0.00 0.00 1.40
2206 2492 9.702494 AAAGAACTCAAATTCAGGAAATTGATC 57.298 29.630 11.68 8.45 38.90 2.92
2226 2512 7.148967 GCTTTGATTACAATTGTCGGAAAGAAC 60.149 37.037 23.27 11.56 35.85 3.01
2234 2520 9.128107 ACAATTAAGCTTTGATTACAATTGTCG 57.872 29.630 20.66 5.95 39.60 4.35
2398 2707 2.255252 GCAAACCGCAACGAGCAT 59.745 55.556 0.00 0.00 46.13 3.79
2453 2762 6.395426 ACAACAAATCTGCATTCTGAAAGA 57.605 33.333 0.00 0.00 44.68 2.52
2454 2763 7.306983 GGAAACAACAAATCTGCATTCTGAAAG 60.307 37.037 0.00 0.00 0.00 2.62
2558 2867 3.564225 ACCAACGTCTTGTTTGATCTTCC 59.436 43.478 0.00 0.00 39.29 3.46
2574 2883 1.271379 GAAAGGGGGCTTTAACCAACG 59.729 52.381 0.00 0.00 0.00 4.10
2575 2884 2.299013 CAGAAAGGGGGCTTTAACCAAC 59.701 50.000 0.00 0.00 0.00 3.77
2620 2929 1.877443 GAAGCGCTGTAGGAACCAAAA 59.123 47.619 12.58 0.00 0.00 2.44
2666 2975 8.792830 TGTAGATCTTAATGTTTTCTCTTGGG 57.207 34.615 0.00 0.00 0.00 4.12
2754 3063 1.694696 GGGTTCTGAGAGGAACACACT 59.305 52.381 9.12 0.00 45.75 3.55
2846 3193 2.733026 GCATCTCAAATTGCAACACACC 59.267 45.455 0.00 0.00 38.72 4.16
2892 3239 4.877378 ATCACAAACAATGATTGGTGCT 57.123 36.364 10.27 0.00 32.77 4.40
2903 3250 6.972328 CCTCTTTTCTTCGAAATCACAAACAA 59.028 34.615 0.00 0.00 0.00 2.83
2933 3280 5.064441 AGCCAAACTGAATATCTGCAAAC 57.936 39.130 0.00 0.00 0.00 2.93
2938 3285 5.070981 TCCCTAGAGCCAAACTGAATATCTG 59.929 44.000 0.00 0.00 0.00 2.90
2943 3290 3.922171 CTCCCTAGAGCCAAACTGAAT 57.078 47.619 0.00 0.00 32.13 2.57
2969 3316 3.884704 TTTTGGGGCGCAGGAGCAT 62.885 57.895 10.83 0.00 42.27 3.79
2970 3317 3.884704 ATTTTGGGGCGCAGGAGCA 62.885 57.895 10.83 0.00 42.27 4.26
3024 3371 9.414295 CATGAACATTTACATGTCTGAATTGTT 57.586 29.630 15.08 15.08 43.34 2.83
3038 3385 8.761575 AATGACATTTGGACATGAACATTTAC 57.238 30.769 0.00 0.00 34.47 2.01
3079 3426 1.010419 GTTGCAATGCTTGGGCTTCG 61.010 55.000 6.82 0.00 39.59 3.79
3141 3494 6.009589 TCATGTCTCTAGAAATGCCCAAAAA 58.990 36.000 5.41 0.00 39.16 1.94
3142 3495 5.569355 TCATGTCTCTAGAAATGCCCAAAA 58.431 37.500 5.41 0.00 39.16 2.44
3143 3496 5.178096 TCATGTCTCTAGAAATGCCCAAA 57.822 39.130 5.41 0.00 39.16 3.28
3144 3497 4.842531 TCATGTCTCTAGAAATGCCCAA 57.157 40.909 5.41 0.00 39.16 4.12
3145 3498 5.378230 AATCATGTCTCTAGAAATGCCCA 57.622 39.130 5.41 0.00 39.16 5.36
3146 3499 6.995091 AGTTAATCATGTCTCTAGAAATGCCC 59.005 38.462 5.41 0.00 39.16 5.36
3160 3513 8.412456 TGTTTGTGTTTCATCAGTTAATCATGT 58.588 29.630 0.00 0.00 0.00 3.21
3161 3514 8.693504 GTGTTTGTGTTTCATCAGTTAATCATG 58.306 33.333 0.00 0.00 0.00 3.07
3162 3515 8.412456 TGTGTTTGTGTTTCATCAGTTAATCAT 58.588 29.630 0.00 0.00 0.00 2.45
3165 3518 8.250332 AGTTGTGTTTGTGTTTCATCAGTTAAT 58.750 29.630 0.00 0.00 0.00 1.40
3166 3519 7.540400 CAGTTGTGTTTGTGTTTCATCAGTTAA 59.460 33.333 0.00 0.00 0.00 2.01
3168 3521 5.863397 CAGTTGTGTTTGTGTTTCATCAGTT 59.137 36.000 0.00 0.00 0.00 3.16
3169 3522 5.048083 ACAGTTGTGTTTGTGTTTCATCAGT 60.048 36.000 0.00 0.00 30.30 3.41
3170 3523 5.401550 ACAGTTGTGTTTGTGTTTCATCAG 58.598 37.500 0.00 0.00 30.30 2.90
3203 3563 7.933728 TGATGTGTTCTTGACAATTTTCATG 57.066 32.000 0.00 0.00 40.65 3.07
3204 3564 8.819974 GTTTGATGTGTTCTTGACAATTTTCAT 58.180 29.630 0.00 0.00 40.65 2.57
3211 3571 5.895636 AGTGTTTGATGTGTTCTTGACAA 57.104 34.783 0.00 0.00 40.65 3.18
3212 3572 6.993786 TTAGTGTTTGATGTGTTCTTGACA 57.006 33.333 0.00 0.00 35.42 3.58
3264 3624 9.484326 GCGAACAAAAACTCAAACAAATATTTT 57.516 25.926 0.00 0.00 0.00 1.82
3265 3625 7.843686 CGCGAACAAAAACTCAAACAAATATTT 59.156 29.630 0.00 0.00 0.00 1.40
3266 3626 7.334009 CGCGAACAAAAACTCAAACAAATATT 58.666 30.769 0.00 0.00 0.00 1.28
3267 3627 6.561350 GCGCGAACAAAAACTCAAACAAATAT 60.561 34.615 12.10 0.00 0.00 1.28
3268 3628 5.275974 GCGCGAACAAAAACTCAAACAAATA 60.276 36.000 12.10 0.00 0.00 1.40
3277 3637 0.660300 CCTGGCGCGAACAAAAACTC 60.660 55.000 12.10 0.00 0.00 3.01
3291 3660 0.319405 ATGCAAACAAAGCTCCTGGC 59.681 50.000 0.00 0.00 42.19 4.85
3309 3710 8.557450 ACAAAAACCCACTCCTAGAATATACAT 58.443 33.333 0.00 0.00 0.00 2.29
3313 3714 7.027874 TCACAAAAACCCACTCCTAGAATAT 57.972 36.000 0.00 0.00 0.00 1.28
3314 3715 6.442541 TCACAAAAACCCACTCCTAGAATA 57.557 37.500 0.00 0.00 0.00 1.75
3315 3716 5.319043 TCACAAAAACCCACTCCTAGAAT 57.681 39.130 0.00 0.00 0.00 2.40
3317 3718 4.993705 ATCACAAAAACCCACTCCTAGA 57.006 40.909 0.00 0.00 0.00 2.43
3318 3719 5.534654 TGAAATCACAAAAACCCACTCCTAG 59.465 40.000 0.00 0.00 0.00 3.02
3319 3720 5.450453 TGAAATCACAAAAACCCACTCCTA 58.550 37.500 0.00 0.00 0.00 2.94
3320 3721 4.285863 TGAAATCACAAAAACCCACTCCT 58.714 39.130 0.00 0.00 0.00 3.69
3321 3722 4.340950 TCTGAAATCACAAAAACCCACTCC 59.659 41.667 0.00 0.00 0.00 3.85
3322 3723 5.299279 TCTCTGAAATCACAAAAACCCACTC 59.701 40.000 0.00 0.00 0.00 3.51
3323 3724 5.200483 TCTCTGAAATCACAAAAACCCACT 58.800 37.500 0.00 0.00 0.00 4.00
3324 3725 5.514274 TCTCTGAAATCACAAAAACCCAC 57.486 39.130 0.00 0.00 0.00 4.61
3325 3726 5.243730 GGATCTCTGAAATCACAAAAACCCA 59.756 40.000 0.00 0.00 0.00 4.51
3326 3727 5.243730 TGGATCTCTGAAATCACAAAAACCC 59.756 40.000 0.00 0.00 0.00 4.11
3327 3728 6.331369 TGGATCTCTGAAATCACAAAAACC 57.669 37.500 0.00 0.00 0.00 3.27
3328 3729 8.084073 TGAATGGATCTCTGAAATCACAAAAAC 58.916 33.333 0.00 0.00 0.00 2.43
3329 3730 8.180706 TGAATGGATCTCTGAAATCACAAAAA 57.819 30.769 0.00 0.00 0.00 1.94
3330 3731 7.666804 TCTGAATGGATCTCTGAAATCACAAAA 59.333 33.333 0.00 0.00 0.00 2.44
3331 3732 7.120285 GTCTGAATGGATCTCTGAAATCACAAA 59.880 37.037 0.00 0.00 0.00 2.83
3338 3739 5.249163 TGAAGGTCTGAATGGATCTCTGAAA 59.751 40.000 0.00 0.00 0.00 2.69
3342 3743 4.405358 GTCTGAAGGTCTGAATGGATCTCT 59.595 45.833 0.00 0.00 0.00 3.10
3359 3760 2.358957 CAATCTTCCGCATGGTCTGAA 58.641 47.619 0.00 0.00 36.30 3.02
3361 3762 1.019673 CCAATCTTCCGCATGGTCTG 58.980 55.000 0.00 0.00 36.30 3.51
3362 3763 0.911769 TCCAATCTTCCGCATGGTCT 59.088 50.000 0.00 0.00 36.30 3.85
3363 3764 1.876156 GATCCAATCTTCCGCATGGTC 59.124 52.381 0.00 0.00 36.30 4.02
3364 3765 1.212688 TGATCCAATCTTCCGCATGGT 59.787 47.619 0.00 0.00 36.30 3.55
3367 3768 8.585471 AATTTATATGATCCAATCTTCCGCAT 57.415 30.769 0.00 0.00 0.00 4.73
3368 3769 8.408043 AAATTTATATGATCCAATCTTCCGCA 57.592 30.769 0.00 0.00 0.00 5.69
3369 3770 8.514594 TGAAATTTATATGATCCAATCTTCCGC 58.485 33.333 0.00 0.00 0.00 5.54
3384 3785 9.754382 GCTGTCCATGAATGTTGAAATTTATAT 57.246 29.630 0.00 0.00 0.00 0.86
3385 3786 8.196771 GGCTGTCCATGAATGTTGAAATTTATA 58.803 33.333 0.00 0.00 0.00 0.98
3386 3787 7.043565 GGCTGTCCATGAATGTTGAAATTTAT 58.956 34.615 0.00 0.00 0.00 1.40
3387 3788 6.211184 AGGCTGTCCATGAATGTTGAAATTTA 59.789 34.615 0.00 0.00 33.74 1.40
3388 3789 5.012354 AGGCTGTCCATGAATGTTGAAATTT 59.988 36.000 0.00 0.00 33.74 1.82
3395 3796 4.666512 AGTAAAGGCTGTCCATGAATGTT 58.333 39.130 0.00 0.00 33.74 2.71
3396 3797 4.307032 AGTAAAGGCTGTCCATGAATGT 57.693 40.909 0.00 0.00 33.74 2.71
3412 3813 7.277098 GGCATAGATTGAACGTCTTGTAGTAAA 59.723 37.037 0.00 0.00 0.00 2.01
3421 3822 5.957842 TTTTTGGCATAGATTGAACGTCT 57.042 34.783 0.00 0.00 0.00 4.18
3422 3823 6.034898 CCAATTTTTGGCATAGATTGAACGTC 59.965 38.462 18.36 0.00 45.17 4.34
3423 3824 5.868801 CCAATTTTTGGCATAGATTGAACGT 59.131 36.000 18.36 0.00 45.17 3.99
3424 3825 6.335176 CCAATTTTTGGCATAGATTGAACG 57.665 37.500 18.36 3.31 45.17 3.95
3438 3839 5.476091 TGCCCCTACTAAACCAATTTTTG 57.524 39.130 0.00 0.00 0.00 2.44
3439 3840 7.235812 TGTTATGCCCCTACTAAACCAATTTTT 59.764 33.333 0.00 0.00 0.00 1.94
3445 3846 4.931027 TTGTTATGCCCCTACTAAACCA 57.069 40.909 0.00 0.00 0.00 3.67
3446 3847 5.691896 AGATTGTTATGCCCCTACTAAACC 58.308 41.667 0.00 0.00 0.00 3.27
3456 3857 2.159057 CCTTGCCAAGATTGTTATGCCC 60.159 50.000 5.89 0.00 0.00 5.36
3459 3860 4.218200 TGTGTCCTTGCCAAGATTGTTATG 59.782 41.667 5.89 0.00 0.00 1.90
3460 3861 4.406456 TGTGTCCTTGCCAAGATTGTTAT 58.594 39.130 5.89 0.00 0.00 1.89
3461 3862 3.820467 CTGTGTCCTTGCCAAGATTGTTA 59.180 43.478 5.89 0.00 0.00 2.41
3462 3863 2.624838 CTGTGTCCTTGCCAAGATTGTT 59.375 45.455 5.89 0.00 0.00 2.83
3464 3865 1.542915 CCTGTGTCCTTGCCAAGATTG 59.457 52.381 5.89 0.00 0.00 2.67
3465 3866 1.548582 CCCTGTGTCCTTGCCAAGATT 60.549 52.381 5.89 0.00 0.00 2.40
3467 3868 1.455849 CCCTGTGTCCTTGCCAAGA 59.544 57.895 5.89 0.00 0.00 3.02
3468 3869 1.604593 CCCCTGTGTCCTTGCCAAG 60.605 63.158 0.00 0.00 0.00 3.61
3469 3870 1.063070 TACCCCTGTGTCCTTGCCAA 61.063 55.000 0.00 0.00 0.00 4.52
3471 3872 1.002502 GTACCCCTGTGTCCTTGCC 60.003 63.158 0.00 0.00 0.00 4.52
3472 3873 0.109723 TTGTACCCCTGTGTCCTTGC 59.890 55.000 0.00 0.00 0.00 4.01
3473 3874 2.649531 TTTGTACCCCTGTGTCCTTG 57.350 50.000 0.00 0.00 0.00 3.61
3474 3875 3.117284 ACAATTTGTACCCCTGTGTCCTT 60.117 43.478 0.00 0.00 0.00 3.36
3475 3876 2.445525 ACAATTTGTACCCCTGTGTCCT 59.554 45.455 0.00 0.00 0.00 3.85
3476 3877 2.871453 ACAATTTGTACCCCTGTGTCC 58.129 47.619 0.00 0.00 0.00 4.02
3477 3878 3.886505 TCAACAATTTGTACCCCTGTGTC 59.113 43.478 1.76 0.00 34.02 3.67
3483 3884 5.784578 AACTTCTCAACAATTTGTACCCC 57.215 39.130 1.76 0.00 34.02 4.95
3494 3895 6.507958 TTCAACATGACAAACTTCTCAACA 57.492 33.333 0.00 0.00 0.00 3.33
3497 3898 4.036734 GGCTTCAACATGACAAACTTCTCA 59.963 41.667 0.00 0.00 0.00 3.27
3500 3901 4.305989 TGGCTTCAACATGACAAACTTC 57.694 40.909 0.00 0.00 0.00 3.01
3518 3919 6.593382 TGCATGTAAAAAGATACCAAAATGGC 59.407 34.615 0.00 0.00 42.67 4.40
3568 3989 5.266242 GCATCTTGTTCACGCCTTTTATAG 58.734 41.667 0.00 0.00 0.00 1.31
3591 4012 1.478916 TGCATTGCCTGTGATGATTGG 59.521 47.619 6.12 0.00 0.00 3.16
3603 4024 3.327626 TGATGTTGTGAATTGCATTGCC 58.672 40.909 6.12 0.00 0.00 4.52
3688 4109 8.730680 AGTCTTGTAATAACCATGATGACAAAC 58.269 33.333 0.00 0.00 0.00 2.93
3689 4110 8.862325 AGTCTTGTAATAACCATGATGACAAA 57.138 30.769 0.00 0.00 0.00 2.83
3714 4138 0.473694 ATACATCGGGATGCTGGGGA 60.474 55.000 8.53 0.00 42.39 4.81
3724 4148 1.276421 GGAGTCATCCCATACATCGGG 59.724 57.143 0.00 0.00 46.03 5.14
3725 4149 2.751166 GGAGTCATCCCATACATCGG 57.249 55.000 0.00 0.00 40.03 4.18


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

AutoCloner maintained by Alex Coulton.