Multiple sequence alignment - TraesCS5B01G232600

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 TraesCS5B01G232600 chr5B 100.000 3072 0 0 1 3072 410599876 410596805 0.000000e+00 5674.0
1 TraesCS5B01G232600 chr5B 95.621 845 36 1 1219 2062 410722621 410723465 0.000000e+00 1354.0
2 TraesCS5B01G232600 chr5B 82.807 285 37 8 2380 2657 398440388 398440667 8.510000e-61 244.0
3 TraesCS5B01G232600 chr5D 89.734 2182 142 37 91 2221 349982680 349980530 0.000000e+00 2713.0
4 TraesCS5B01G232600 chr5D 90.401 1073 80 17 1015 2073 350220217 350221280 0.000000e+00 1389.0
5 TraesCS5B01G232600 chr5A 94.139 1365 52 9 763 2114 450475116 450473767 0.000000e+00 2052.0
6 TraesCS5B01G232600 chr5A 89.897 1069 83 19 1015 2073 450540887 450541940 0.000000e+00 1352.0
7 TraesCS5B01G232600 chr5A 91.273 699 54 5 1 696 450477125 450476431 0.000000e+00 946.0
8 TraesCS5B01G232600 chr5A 78.445 283 29 24 2078 2335 450473763 450473488 4.100000e-34 156.0
9 TraesCS5B01G232600 chr5A 80.337 178 17 14 267 442 511969915 511969754 5.380000e-23 119.0
10 TraesCS5B01G232600 chr5A 94.286 35 2 0 390 424 105089542 105089508 2.000000e-03 54.7
11 TraesCS5B01G232600 chr6D 84.615 468 69 3 1454 1921 414256791 414256327 2.160000e-126 462.0
12 TraesCS5B01G232600 chr6B 84.848 462 65 5 1461 1921 624496390 624495933 7.760000e-126 460.0
13 TraesCS5B01G232600 chr6B 84.188 468 71 3 1454 1921 624018225 624017761 4.670000e-123 451.0
14 TraesCS5B01G232600 chr6B 84.255 470 67 6 1454 1921 624312758 624312294 4.670000e-123 451.0
15 TraesCS5B01G232600 chr6B 78.386 347 58 13 2380 2720 512209068 512209403 3.100000e-50 209.0
16 TraesCS5B01G232600 chr6B 83.030 165 13 10 281 442 674371953 674371801 5.340000e-28 135.0
17 TraesCS5B01G232600 chr3D 82.569 327 39 14 2398 2715 45967580 45967897 3.900000e-69 272.0
18 TraesCS5B01G232600 chr1B 80.702 342 50 13 2383 2720 597158289 597158618 5.080000e-63 252.0
19 TraesCS5B01G232600 chr3B 81.818 297 43 10 2380 2670 666511891 666512182 3.960000e-59 239.0
20 TraesCS5B01G232600 chr7B 81.849 292 44 8 2354 2641 70537400 70537114 1.420000e-58 237.0
21 TraesCS5B01G232600 chr7B 80.519 308 46 10 2355 2656 609174526 609174227 1.110000e-54 224.0
22 TraesCS5B01G232600 chr1A 81.724 290 40 11 2383 2663 483650494 483650209 2.380000e-56 230.0
23 TraesCS5B01G232600 chr1D 78.448 348 49 24 2388 2720 40873939 40873603 1.440000e-48 204.0
24 TraesCS5B01G232600 chr2B 79.330 179 32 4 255 431 791123868 791123693 1.500000e-23 121.0


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 TraesCS5B01G232600 chr5B 410596805 410599876 3071 True 5674.000000 5674 100.000000 1 3072 1 chr5B.!!$R1 3071
1 TraesCS5B01G232600 chr5B 410722621 410723465 844 False 1354.000000 1354 95.621000 1219 2062 1 chr5B.!!$F2 843
2 TraesCS5B01G232600 chr5D 349980530 349982680 2150 True 2713.000000 2713 89.734000 91 2221 1 chr5D.!!$R1 2130
3 TraesCS5B01G232600 chr5D 350220217 350221280 1063 False 1389.000000 1389 90.401000 1015 2073 1 chr5D.!!$F1 1058
4 TraesCS5B01G232600 chr5A 450540887 450541940 1053 False 1352.000000 1352 89.897000 1015 2073 1 chr5A.!!$F1 1058
5 TraesCS5B01G232600 chr5A 450473488 450477125 3637 True 1051.333333 2052 87.952333 1 2335 3 chr5A.!!$R3 2334

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
79 83 0.698818 ACAGATGGGAGGTGGGTTTC 59.301 55.0 0.00 0.0 0.0 2.78 F
558 575 0.886490 GGATGCCGGCCTATCAACTG 60.886 60.0 26.77 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1209 2505 0.041312 CACGCACCACCGAAAAAGAG 60.041 55.0 0.00 0.0 0.0 2.85 R
2167 3552 0.314618 TAGCTACCAAACACACGCGA 59.685 50.0 15.93 0.0 0.0 5.87 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
79 83 0.698818 ACAGATGGGAGGTGGGTTTC 59.301 55.000 0.00 0.00 0.00 2.78
103 107 8.093659 TCATATTTGCATAAAAATCGGATCGA 57.906 30.769 0.00 0.00 41.13 3.59
159 174 8.218338 AGGACATGCAGATTGAGTTTTAATAG 57.782 34.615 0.00 0.00 0.00 1.73
163 178 8.616076 ACATGCAGATTGAGTTTTAATAGTAGC 58.384 33.333 0.00 0.00 0.00 3.58
240 257 7.274250 GGAAAGTTGTGATTGTCATTCAATAGC 59.726 37.037 0.00 0.00 45.49 2.97
310 327 8.073467 TCTCAGTTTGTTTTGGAAGGTTATTT 57.927 30.769 0.00 0.00 0.00 1.40
351 368 5.878406 ATCTTTTAGGACGGTGATCTCAT 57.122 39.130 0.00 0.00 0.00 2.90
366 383 9.600646 CGGTGATCTCATATATATGACGTTATC 57.399 37.037 19.44 17.73 37.76 1.75
467 484 1.933853 GAGGGTCGGACGAATTGATTG 59.066 52.381 1.43 0.00 0.00 2.67
504 521 3.135994 GGTGAAAAACCTAGCGTGAAGA 58.864 45.455 0.00 0.00 46.55 2.87
558 575 0.886490 GGATGCCGGCCTATCAACTG 60.886 60.000 26.77 0.00 0.00 3.16
560 577 1.987807 ATGCCGGCCTATCAACTGCT 61.988 55.000 26.77 0.00 0.00 4.24
595 612 3.826729 AGATCCAACACTTTAAAGCCCAC 59.173 43.478 15.24 0.05 0.00 4.61
598 615 3.383185 TCCAACACTTTAAAGCCCACAAG 59.617 43.478 15.24 0.00 0.00 3.16
615 632 7.178983 AGCCCACAAGAATATCTTTGAAATTCA 59.821 33.333 0.00 0.00 33.78 2.57
647 664 9.283768 ACCATCATAATTTATTGCGTGATTCTA 57.716 29.630 0.00 0.00 0.00 2.10
710 736 8.915036 AGAGTACAATCTCCGTTTCATATTAGT 58.085 33.333 0.00 0.00 35.28 2.24
711 737 9.530633 GAGTACAATCTCCGTTTCATATTAGTT 57.469 33.333 0.00 0.00 0.00 2.24
712 738 9.886132 AGTACAATCTCCGTTTCATATTAGTTT 57.114 29.630 0.00 0.00 0.00 2.66
877 2146 2.171659 TCGAGGCTATAAATTGCACCCA 59.828 45.455 0.00 0.00 0.00 4.51
879 2148 3.003689 CGAGGCTATAAATTGCACCCAAG 59.996 47.826 0.00 0.00 33.80 3.61
1183 2479 8.001881 TCCTTATCGATCTATCCTTAATGCTC 57.998 38.462 0.00 0.00 0.00 4.26
1199 2495 2.300433 TGCTCATCTGCTCTCTCTCTC 58.700 52.381 0.00 0.00 0.00 3.20
1201 2497 2.551459 GCTCATCTGCTCTCTCTCTCTC 59.449 54.545 0.00 0.00 0.00 3.20
1203 2499 4.063689 CTCATCTGCTCTCTCTCTCTCTC 58.936 52.174 0.00 0.00 0.00 3.20
1205 2501 3.827008 TCTGCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
1206 2502 3.378512 TCTGCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
1207 2503 3.386078 TCTGCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
1208 2504 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
1209 2505 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
1210 2506 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
1211 2507 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
1268 2564 1.657751 CTCGACGGAGCTGATGGACA 61.658 60.000 0.00 0.00 32.61 4.02
1491 2787 1.524008 TTCGCGTCAGAGCTGGAGAA 61.524 55.000 5.77 0.00 34.40 2.87
1522 2818 2.969016 CTGCTCGACCTGCTCTGT 59.031 61.111 0.00 0.00 0.00 3.41
1885 3181 1.568504 TCGCATCCTTCTACAACCCT 58.431 50.000 0.00 0.00 0.00 4.34
1887 3183 1.743772 CGCATCCTTCTACAACCCTGG 60.744 57.143 0.00 0.00 0.00 4.45
2008 3316 2.484770 CCACAAGTTCGAGGACAAGGAA 60.485 50.000 0.00 0.00 0.00 3.36
2075 3383 1.270826 TCATCGCTACTGCATAGAGGC 59.729 52.381 7.19 0.00 39.64 4.70
2147 3532 0.872388 GGGTCGGTCATGTGTTTGTC 59.128 55.000 0.00 0.00 0.00 3.18
2148 3533 1.588674 GGTCGGTCATGTGTTTGTCA 58.411 50.000 0.00 0.00 0.00 3.58
2149 3534 1.263217 GGTCGGTCATGTGTTTGTCAC 59.737 52.381 0.00 0.00 46.31 3.67
2161 3546 5.312382 GTGTTTGTCACGAGTACTCTTTC 57.688 43.478 20.34 7.65 37.31 2.62
2162 3547 5.041940 GTGTTTGTCACGAGTACTCTTTCT 58.958 41.667 20.34 0.00 37.31 2.52
2163 3548 5.519206 GTGTTTGTCACGAGTACTCTTTCTT 59.481 40.000 20.34 0.00 37.31 2.52
2164 3549 6.035758 GTGTTTGTCACGAGTACTCTTTCTTT 59.964 38.462 20.34 0.00 37.31 2.52
2165 3550 6.592607 TGTTTGTCACGAGTACTCTTTCTTTT 59.407 34.615 20.34 0.00 0.00 2.27
2166 3551 6.823678 TTGTCACGAGTACTCTTTCTTTTC 57.176 37.500 20.34 4.16 0.00 2.29
2167 3552 6.145338 TGTCACGAGTACTCTTTCTTTTCT 57.855 37.500 20.34 0.00 0.00 2.52
2168 3553 6.207213 TGTCACGAGTACTCTTTCTTTTCTC 58.793 40.000 20.34 1.73 0.00 2.87
2169 3554 5.340138 GTCACGAGTACTCTTTCTTTTCTCG 59.660 44.000 20.34 6.28 45.35 4.04
2170 3555 4.088781 CACGAGTACTCTTTCTTTTCTCGC 59.911 45.833 20.34 0.00 44.26 5.03
2171 3556 3.298499 CGAGTACTCTTTCTTTTCTCGCG 59.702 47.826 20.34 0.00 37.20 5.87
2172 3557 4.228317 GAGTACTCTTTCTTTTCTCGCGT 58.772 43.478 15.91 0.00 0.00 6.01
2173 3558 3.982058 AGTACTCTTTCTTTTCTCGCGTG 59.018 43.478 5.77 3.13 0.00 5.34
2174 3559 2.822764 ACTCTTTCTTTTCTCGCGTGT 58.177 42.857 5.77 0.00 0.00 4.49
2175 3560 2.540101 ACTCTTTCTTTTCTCGCGTGTG 59.460 45.455 5.77 0.00 0.00 3.82
2176 3561 2.540101 CTCTTTCTTTTCTCGCGTGTGT 59.460 45.455 5.77 0.00 0.00 3.72
2210 3595 7.719689 AATTTATGCTTCGTTTTATGACGTG 57.280 32.000 0.00 0.00 43.23 4.49
2258 3684 5.220931 GGGAGATGTATCATGTTGTTTCTGC 60.221 44.000 0.00 0.00 0.00 4.26
2260 3686 6.763135 GGAGATGTATCATGTTGTTTCTGCTA 59.237 38.462 0.00 0.00 0.00 3.49
2261 3687 7.280876 GGAGATGTATCATGTTGTTTCTGCTAA 59.719 37.037 0.00 0.00 0.00 3.09
2262 3688 8.206325 AGATGTATCATGTTGTTTCTGCTAAG 57.794 34.615 0.00 0.00 0.00 2.18
2263 3689 6.182039 TGTATCATGTTGTTTCTGCTAAGC 57.818 37.500 0.00 0.00 0.00 3.09
2264 3690 3.811722 TCATGTTGTTTCTGCTAAGCG 57.188 42.857 0.00 0.00 0.00 4.68
2265 3691 3.398406 TCATGTTGTTTCTGCTAAGCGA 58.602 40.909 0.00 0.00 0.00 4.93
2266 3692 3.186409 TCATGTTGTTTCTGCTAAGCGAC 59.814 43.478 0.00 0.00 0.00 5.19
2268 3694 1.871039 GTTGTTTCTGCTAAGCGACCA 59.129 47.619 0.00 0.00 0.00 4.02
2281 3711 1.160137 GCGACCAATGCTCAAAGACT 58.840 50.000 0.00 0.00 0.00 3.24
2283 3713 2.742053 GCGACCAATGCTCAAAGACTAA 59.258 45.455 0.00 0.00 0.00 2.24
2284 3714 3.188460 GCGACCAATGCTCAAAGACTAAA 59.812 43.478 0.00 0.00 0.00 1.85
2285 3715 4.712763 CGACCAATGCTCAAAGACTAAAC 58.287 43.478 0.00 0.00 0.00 2.01
2286 3716 4.666655 CGACCAATGCTCAAAGACTAAACG 60.667 45.833 0.00 0.00 0.00 3.60
2287 3717 4.385825 ACCAATGCTCAAAGACTAAACGA 58.614 39.130 0.00 0.00 0.00 3.85
2288 3718 4.819630 ACCAATGCTCAAAGACTAAACGAA 59.180 37.500 0.00 0.00 0.00 3.85
2289 3719 5.049405 ACCAATGCTCAAAGACTAAACGAAG 60.049 40.000 0.00 0.00 0.00 3.79
2290 3720 4.670227 ATGCTCAAAGACTAAACGAAGC 57.330 40.909 0.00 0.00 0.00 3.86
2335 3765 4.963276 TTCATCCGATGCGATTTTTCTT 57.037 36.364 3.25 0.00 0.00 2.52
2336 3766 6.255215 GTTTCATCCGATGCGATTTTTCTTA 58.745 36.000 3.25 0.00 0.00 2.10
2337 3767 5.403897 TCATCCGATGCGATTTTTCTTAC 57.596 39.130 3.25 0.00 0.00 2.34
2338 3768 4.873259 TCATCCGATGCGATTTTTCTTACA 59.127 37.500 3.25 0.00 0.00 2.41
2339 3769 4.857871 TCCGATGCGATTTTTCTTACAG 57.142 40.909 0.00 0.00 0.00 2.74
2340 3770 4.250464 TCCGATGCGATTTTTCTTACAGT 58.750 39.130 0.00 0.00 0.00 3.55
2341 3771 4.693566 TCCGATGCGATTTTTCTTACAGTT 59.306 37.500 0.00 0.00 0.00 3.16
2342 3772 4.788100 CCGATGCGATTTTTCTTACAGTTG 59.212 41.667 0.00 0.00 0.00 3.16
2343 3773 5.390461 CCGATGCGATTTTTCTTACAGTTGA 60.390 40.000 0.00 0.00 0.00 3.18
2344 3774 6.077197 CGATGCGATTTTTCTTACAGTTGAA 58.923 36.000 0.00 0.00 0.00 2.69
2345 3775 6.577055 CGATGCGATTTTTCTTACAGTTGAAA 59.423 34.615 0.00 0.00 0.00 2.69
2346 3776 7.112844 CGATGCGATTTTTCTTACAGTTGAAAA 59.887 33.333 8.99 8.99 39.47 2.29
2382 3812 3.859411 AAAAACACTCTTCAAACGGCA 57.141 38.095 0.00 0.00 0.00 5.69
2383 3813 4.385358 AAAAACACTCTTCAAACGGCAT 57.615 36.364 0.00 0.00 0.00 4.40
2384 3814 4.385358 AAAACACTCTTCAAACGGCATT 57.615 36.364 0.00 0.00 0.00 3.56
2385 3815 4.385358 AAACACTCTTCAAACGGCATTT 57.615 36.364 0.00 0.00 0.00 2.32
2396 3826 4.809815 AAACGGCATTTGAAAAATGGTG 57.190 36.364 13.11 0.00 0.00 4.17
2397 3827 3.742433 ACGGCATTTGAAAAATGGTGA 57.258 38.095 13.11 0.00 0.00 4.02
2398 3828 4.065321 ACGGCATTTGAAAAATGGTGAA 57.935 36.364 13.11 0.00 0.00 3.18
2399 3829 3.807071 ACGGCATTTGAAAAATGGTGAAC 59.193 39.130 13.11 0.00 0.00 3.18
2400 3830 3.806521 CGGCATTTGAAAAATGGTGAACA 59.193 39.130 13.11 0.00 0.00 3.18
2401 3831 4.272018 CGGCATTTGAAAAATGGTGAACAA 59.728 37.500 13.11 0.00 0.00 2.83
2402 3832 5.558653 CGGCATTTGAAAAATGGTGAACAAG 60.559 40.000 13.11 0.00 0.00 3.16
2403 3833 5.296531 GGCATTTGAAAAATGGTGAACAAGT 59.703 36.000 13.11 0.00 0.00 3.16
2404 3834 6.481644 GGCATTTGAAAAATGGTGAACAAGTA 59.518 34.615 13.11 0.00 0.00 2.24
2405 3835 7.173047 GGCATTTGAAAAATGGTGAACAAGTAT 59.827 33.333 13.11 0.00 0.00 2.12
2406 3836 8.558700 GCATTTGAAAAATGGTGAACAAGTATT 58.441 29.630 13.11 0.00 0.00 1.89
2409 3839 9.658799 TTTGAAAAATGGTGAACAAGTATTTGA 57.341 25.926 4.81 0.00 37.73 2.69
2410 3840 9.658799 TTGAAAAATGGTGAACAAGTATTTGAA 57.341 25.926 4.81 0.00 37.73 2.69
2411 3841 9.658799 TGAAAAATGGTGAACAAGTATTTGAAA 57.341 25.926 4.81 0.00 37.73 2.69
2466 3896 9.872757 TGAACGAGTATTTAGAAAATGTTGAAC 57.127 29.630 0.00 0.00 0.00 3.18
2467 3897 9.872757 GAACGAGTATTTAGAAAATGTTGAACA 57.127 29.630 0.00 0.00 0.00 3.18
2469 3899 9.878599 ACGAGTATTTAGAAAATGTTGAACAAG 57.121 29.630 0.62 0.00 0.00 3.16
2470 3900 9.878599 CGAGTATTTAGAAAATGTTGAACAAGT 57.121 29.630 0.62 0.00 0.00 3.16
2479 3909 9.868277 AGAAAATGTTGAACAAGTATTTGAACA 57.132 25.926 0.62 5.69 37.73 3.18
2482 3912 7.678194 ATGTTGAACAAGTATTTGAACAACG 57.322 32.000 23.51 0.00 45.03 4.10
2483 3913 6.613233 TGTTGAACAAGTATTTGAACAACGT 58.387 32.000 23.51 0.00 45.03 3.99
2484 3914 7.085116 TGTTGAACAAGTATTTGAACAACGTT 58.915 30.769 23.51 0.00 45.03 3.99
2485 3915 7.061210 TGTTGAACAAGTATTTGAACAACGTTG 59.939 33.333 26.20 26.20 45.03 4.10
2486 3916 6.843208 TGAACAAGTATTTGAACAACGTTGA 58.157 32.000 33.66 12.23 37.73 3.18
2487 3917 7.306213 TGAACAAGTATTTGAACAACGTTGAA 58.694 30.769 33.66 17.94 37.73 2.69
2488 3918 7.271653 TGAACAAGTATTTGAACAACGTTGAAC 59.728 33.333 33.66 24.13 37.73 3.18
2489 3919 6.613233 ACAAGTATTTGAACAACGTTGAACA 58.387 32.000 33.66 26.14 37.73 3.18
2490 3920 7.085116 ACAAGTATTTGAACAACGTTGAACAA 58.915 30.769 33.66 29.38 37.73 2.83
2491 3921 7.272515 ACAAGTATTTGAACAACGTTGAACAAG 59.727 33.333 33.66 22.37 37.73 3.16
2492 3922 6.848451 AGTATTTGAACAACGTTGAACAAGT 58.152 32.000 33.66 29.12 32.50 3.16
2493 3923 7.976826 AGTATTTGAACAACGTTGAACAAGTA 58.023 30.769 33.66 28.30 32.50 2.24
2494 3924 8.617809 AGTATTTGAACAACGTTGAACAAGTAT 58.382 29.630 33.66 25.03 32.50 2.12
2495 3925 9.228636 GTATTTGAACAACGTTGAACAAGTATT 57.771 29.630 33.66 15.13 32.50 1.89
2496 3926 8.696410 ATTTGAACAACGTTGAACAAGTATTT 57.304 26.923 33.66 14.41 32.50 1.40
2497 3927 7.499438 TTGAACAACGTTGAACAAGTATTTG 57.501 32.000 33.66 4.28 40.24 2.32
2498 3928 6.843208 TGAACAACGTTGAACAAGTATTTGA 58.157 32.000 33.66 6.43 37.73 2.69
2499 3929 7.306213 TGAACAACGTTGAACAAGTATTTGAA 58.694 30.769 33.66 3.34 37.73 2.69
2500 3930 7.808381 TGAACAACGTTGAACAAGTATTTGAAA 59.192 29.630 33.66 4.85 37.73 2.69
2501 3931 8.522178 AACAACGTTGAACAAGTATTTGAAAA 57.478 26.923 33.66 0.00 37.73 2.29
2502 3932 8.522178 ACAACGTTGAACAAGTATTTGAAAAA 57.478 26.923 33.66 0.00 37.73 1.94
2503 3933 9.145865 ACAACGTTGAACAAGTATTTGAAAAAT 57.854 25.926 33.66 2.00 37.73 1.82
2504 3934 9.618410 CAACGTTGAACAAGTATTTGAAAAATC 57.382 29.630 23.90 0.00 37.73 2.17
2505 3935 9.581099 AACGTTGAACAAGTATTTGAAAAATCT 57.419 25.926 0.00 0.00 37.73 2.40
2506 3936 9.581099 ACGTTGAACAAGTATTTGAAAAATCTT 57.419 25.926 4.81 0.00 37.73 2.40
2639 4069 9.889128 ATTGAATGGGTATTTAGAAAAATGGTG 57.111 29.630 0.00 0.00 36.02 4.17
2640 4070 8.657387 TGAATGGGTATTTAGAAAAATGGTGA 57.343 30.769 0.00 0.00 36.02 4.02
2641 4071 9.265862 TGAATGGGTATTTAGAAAAATGGTGAT 57.734 29.630 0.00 0.00 36.02 3.06
2642 4072 9.750125 GAATGGGTATTTAGAAAAATGGTGATC 57.250 33.333 0.00 0.00 36.02 2.92
2643 4073 8.837099 ATGGGTATTTAGAAAAATGGTGATCA 57.163 30.769 0.00 0.00 36.02 2.92
2644 4074 8.837099 TGGGTATTTAGAAAAATGGTGATCAT 57.163 30.769 0.00 0.00 36.02 2.45
2645 4075 8.694540 TGGGTATTTAGAAAAATGGTGATCATG 58.305 33.333 0.00 0.00 36.02 3.07
2646 4076 8.695456 GGGTATTTAGAAAAATGGTGATCATGT 58.305 33.333 0.00 0.00 36.02 3.21
2690 4120 6.862711 AAAAACCAAACAAAAGAAAACCGA 57.137 29.167 0.00 0.00 0.00 4.69
2691 4121 6.862711 AAAACCAAACAAAAGAAAACCGAA 57.137 29.167 0.00 0.00 0.00 4.30
2692 4122 6.862711 AAACCAAACAAAAGAAAACCGAAA 57.137 29.167 0.00 0.00 0.00 3.46
2693 4123 6.862711 AACCAAACAAAAGAAAACCGAAAA 57.137 29.167 0.00 0.00 0.00 2.29
2694 4124 6.862711 ACCAAACAAAAGAAAACCGAAAAA 57.137 29.167 0.00 0.00 0.00 1.94
2695 4125 6.660722 ACCAAACAAAAGAAAACCGAAAAAC 58.339 32.000 0.00 0.00 0.00 2.43
2696 4126 6.260271 ACCAAACAAAAGAAAACCGAAAAACA 59.740 30.769 0.00 0.00 0.00 2.83
2697 4127 7.132863 CCAAACAAAAGAAAACCGAAAAACAA 58.867 30.769 0.00 0.00 0.00 2.83
2698 4128 7.644157 CCAAACAAAAGAAAACCGAAAAACAAA 59.356 29.630 0.00 0.00 0.00 2.83
2699 4129 8.465253 CAAACAAAAGAAAACCGAAAAACAAAC 58.535 29.630 0.00 0.00 0.00 2.93
2700 4130 7.247929 ACAAAAGAAAACCGAAAAACAAACA 57.752 28.000 0.00 0.00 0.00 2.83
2701 4131 7.694886 ACAAAAGAAAACCGAAAAACAAACAA 58.305 26.923 0.00 0.00 0.00 2.83
2702 4132 8.182227 ACAAAAGAAAACCGAAAAACAAACAAA 58.818 25.926 0.00 0.00 0.00 2.83
2703 4133 9.010366 CAAAAGAAAACCGAAAAACAAACAAAA 57.990 25.926 0.00 0.00 0.00 2.44
2704 4134 9.737427 AAAAGAAAACCGAAAAACAAACAAAAT 57.263 22.222 0.00 0.00 0.00 1.82
2710 4140 9.946165 AAACCGAAAAACAAACAAAATAAAACA 57.054 22.222 0.00 0.00 0.00 2.83
2711 4141 9.946165 AACCGAAAAACAAACAAAATAAAACAA 57.054 22.222 0.00 0.00 0.00 2.83
2712 4142 9.946165 ACCGAAAAACAAACAAAATAAAACAAA 57.054 22.222 0.00 0.00 0.00 2.83
2728 4158 9.454859 AATAAAACAAAGGAAAAATGTTGTCCA 57.545 25.926 0.14 0.00 37.36 4.02
2729 4159 7.936496 AAAACAAAGGAAAAATGTTGTCCAT 57.064 28.000 0.14 0.00 37.36 3.41
2730 4160 6.923928 AACAAAGGAAAAATGTTGTCCATG 57.076 33.333 0.14 1.76 36.03 3.66
2731 4161 5.988287 ACAAAGGAAAAATGTTGTCCATGT 58.012 33.333 0.14 2.31 32.82 3.21
2732 4162 7.118496 ACAAAGGAAAAATGTTGTCCATGTA 57.882 32.000 6.79 0.00 34.12 2.29
2733 4163 6.983890 ACAAAGGAAAAATGTTGTCCATGTAC 59.016 34.615 6.79 0.00 34.12 2.90
2734 4164 6.976934 AAGGAAAAATGTTGTCCATGTACT 57.023 33.333 0.14 0.00 32.82 2.73
2735 4165 8.356657 CAAAGGAAAAATGTTGTCCATGTACTA 58.643 33.333 0.14 0.00 32.82 1.82
2736 4166 8.472007 AAGGAAAAATGTTGTCCATGTACTAA 57.528 30.769 0.14 0.00 32.82 2.24
2737 4167 8.472007 AGGAAAAATGTTGTCCATGTACTAAA 57.528 30.769 0.14 0.00 32.82 1.85
2738 4168 8.919145 AGGAAAAATGTTGTCCATGTACTAAAA 58.081 29.630 0.14 0.00 32.82 1.52
2739 4169 9.535878 GGAAAAATGTTGTCCATGTACTAAAAA 57.464 29.630 0.00 0.00 32.82 1.94
2776 4206 9.994432 TTGCATTTGAAAAATAATGAAAAACGT 57.006 22.222 0.00 0.00 34.44 3.99
2777 4207 9.430838 TGCATTTGAAAAATAATGAAAAACGTG 57.569 25.926 0.00 0.00 34.44 4.49
2778 4208 9.432077 GCATTTGAAAAATAATGAAAAACGTGT 57.568 25.926 0.00 0.00 34.44 4.49
2827 4257 9.826574 AGTACAGAAATGTTAAACTTGTACTGA 57.173 29.630 12.10 0.00 38.58 3.41
2902 4332 9.665719 AATGTAGAATGAAAACCAAAACAAACT 57.334 25.926 0.00 0.00 0.00 2.66
2907 4337 9.936759 AGAATGAAAACCAAAACAAACTAAGAA 57.063 25.926 0.00 0.00 0.00 2.52
2911 4341 8.499967 TGAAAACCAAAACAAACTAAGAAAAGC 58.500 29.630 0.00 0.00 0.00 3.51
2912 4342 7.971183 AAACCAAAACAAACTAAGAAAAGCA 57.029 28.000 0.00 0.00 0.00 3.91
2913 4343 7.971183 AACCAAAACAAACTAAGAAAAGCAA 57.029 28.000 0.00 0.00 0.00 3.91
2914 4344 7.595311 ACCAAAACAAACTAAGAAAAGCAAG 57.405 32.000 0.00 0.00 0.00 4.01
2915 4345 6.593770 ACCAAAACAAACTAAGAAAAGCAAGG 59.406 34.615 0.00 0.00 0.00 3.61
2916 4346 6.816140 CCAAAACAAACTAAGAAAAGCAAGGA 59.184 34.615 0.00 0.00 0.00 3.36
2917 4347 7.333174 CCAAAACAAACTAAGAAAAGCAAGGAA 59.667 33.333 0.00 0.00 0.00 3.36
2918 4348 8.716909 CAAAACAAACTAAGAAAAGCAAGGAAA 58.283 29.630 0.00 0.00 0.00 3.13
2919 4349 9.448438 AAAACAAACTAAGAAAAGCAAGGAAAT 57.552 25.926 0.00 0.00 0.00 2.17
3047 4477 8.702163 AACAAAGTAAAACATGGAGAAAACTG 57.298 30.769 0.00 0.00 0.00 3.16
3048 4478 8.062065 ACAAAGTAAAACATGGAGAAAACTGA 57.938 30.769 0.00 0.00 0.00 3.41
3049 4479 8.527810 ACAAAGTAAAACATGGAGAAAACTGAA 58.472 29.630 0.00 0.00 0.00 3.02
3050 4480 9.533253 CAAAGTAAAACATGGAGAAAACTGAAT 57.467 29.630 0.00 0.00 0.00 2.57
3056 4486 9.883142 AAAACATGGAGAAAACTGAATAAAACA 57.117 25.926 0.00 0.00 0.00 2.83
3057 4487 9.533253 AAACATGGAGAAAACTGAATAAAACAG 57.467 29.630 0.00 0.00 40.68 3.16
3058 4488 8.463930 ACATGGAGAAAACTGAATAAAACAGA 57.536 30.769 0.00 0.00 38.55 3.41
3059 4489 8.912988 ACATGGAGAAAACTGAATAAAACAGAA 58.087 29.630 0.00 0.00 38.55 3.02
3060 4490 9.748708 CATGGAGAAAACTGAATAAAACAGAAA 57.251 29.630 0.00 0.00 38.55 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 5.812286 TCATAAAGAACTAACTTCCACCCC 58.188 41.667 0.00 0.00 0.00 4.95
61 62 0.698238 TGAAACCCACCTCCCATCTG 59.302 55.000 0.00 0.00 0.00 2.90
65 66 3.707316 CAAATATGAAACCCACCTCCCA 58.293 45.455 0.00 0.00 0.00 4.37
66 67 2.430694 GCAAATATGAAACCCACCTCCC 59.569 50.000 0.00 0.00 0.00 4.30
79 83 8.791605 CATCGATCCGATTTTTATGCAAATATG 58.208 33.333 0.00 0.00 44.59 1.78
103 107 1.561542 GAACACATCCTCCACTCCCAT 59.438 52.381 0.00 0.00 0.00 4.00
159 174 5.424121 ACCAAATCGCATATTTCAGCTAC 57.576 39.130 0.00 0.00 0.00 3.58
163 178 9.781834 TTTTACTTACCAAATCGCATATTTCAG 57.218 29.630 0.00 0.00 0.00 3.02
224 241 6.018425 ACGACATCTGCTATTGAATGACAATC 60.018 38.462 0.00 0.00 44.77 2.67
240 257 0.802222 CCCGCACACTACGACATCTG 60.802 60.000 0.00 0.00 0.00 2.90
290 307 8.710835 TTCTCAAATAACCTTCCAAAACAAAC 57.289 30.769 0.00 0.00 0.00 2.93
340 357 9.600646 GATAACGTCATATATATGAGATCACCG 57.399 37.037 22.97 21.67 42.84 4.94
395 412 5.421056 ACAGGTGCTGATTCAATTCAATCAT 59.579 36.000 5.13 0.00 41.06 2.45
467 484 1.133915 TCACCCTCACACTCAAAACCC 60.134 52.381 0.00 0.00 0.00 4.11
504 521 1.306654 TTACCTCCCGCCATCACCT 60.307 57.895 0.00 0.00 0.00 4.00
615 632 9.844790 CACGCAATAAATTATGATGGTCATATT 57.155 29.630 0.91 0.00 38.94 1.28
647 664 7.649306 GCGGTCATTATGCTAAATCTTTCAATT 59.351 33.333 0.00 0.00 0.00 2.32
671 688 9.562583 GGAGATTGTACTCTAGAATTATTAGCG 57.437 37.037 0.00 0.00 37.13 4.26
681 698 8.693120 ATATGAAACGGAGATTGTACTCTAGA 57.307 34.615 0.00 0.00 37.13 2.43
710 736 5.607477 AGAAATAATATGGAGCGGACGAAA 58.393 37.500 0.00 0.00 0.00 3.46
711 737 5.209818 AGAAATAATATGGAGCGGACGAA 57.790 39.130 0.00 0.00 0.00 3.85
712 738 4.615223 CGAGAAATAATATGGAGCGGACGA 60.615 45.833 0.00 0.00 0.00 4.20
713 739 3.608506 CGAGAAATAATATGGAGCGGACG 59.391 47.826 0.00 0.00 0.00 4.79
751 824 6.382282 GGTTGTACACCCCTCTAGTATTACTT 59.618 42.308 0.00 0.00 40.19 2.24
752 825 5.896106 GGTTGTACACCCCTCTAGTATTACT 59.104 44.000 0.00 1.30 40.19 2.24
753 826 5.658190 TGGTTGTACACCCCTCTAGTATTAC 59.342 44.000 7.02 0.00 46.68 1.89
754 827 5.841209 TGGTTGTACACCCCTCTAGTATTA 58.159 41.667 7.02 0.00 46.68 0.98
755 828 4.691238 TGGTTGTACACCCCTCTAGTATT 58.309 43.478 7.02 0.00 46.68 1.89
756 829 4.341863 TGGTTGTACACCCCTCTAGTAT 57.658 45.455 7.02 0.00 46.68 2.12
760 2025 2.262637 CCTTGGTTGTACACCCCTCTA 58.737 52.381 7.02 0.00 46.68 2.43
761 2026 1.064825 CCTTGGTTGTACACCCCTCT 58.935 55.000 7.02 0.00 46.68 3.69
899 2169 0.534412 ATGAAGGAGTCAGGAGTGCG 59.466 55.000 0.00 0.00 40.43 5.34
909 2179 2.158842 GCCTGATGCTGTATGAAGGAGT 60.159 50.000 7.87 0.00 36.87 3.85
1128 2415 5.614308 TCCTGTCAGATTATGCCATGTTAG 58.386 41.667 0.00 0.00 0.00 2.34
1183 2479 4.063689 GAGAGAGAGAGAGAGAGCAGATG 58.936 52.174 0.00 0.00 0.00 2.90
1199 2495 4.380444 CCACCGAAAAAGAGAGAGAGAGAG 60.380 50.000 0.00 0.00 0.00 3.20
1201 2497 3.257127 ACCACCGAAAAAGAGAGAGAGAG 59.743 47.826 0.00 0.00 0.00 3.20
1203 2499 3.321497 CACCACCGAAAAAGAGAGAGAG 58.679 50.000 0.00 0.00 0.00 3.20
1205 2501 1.801178 GCACCACCGAAAAAGAGAGAG 59.199 52.381 0.00 0.00 0.00 3.20
1206 2502 1.872237 CGCACCACCGAAAAAGAGAGA 60.872 52.381 0.00 0.00 0.00 3.10
1207 2503 0.512952 CGCACCACCGAAAAAGAGAG 59.487 55.000 0.00 0.00 0.00 3.20
1208 2504 0.179067 ACGCACCACCGAAAAAGAGA 60.179 50.000 0.00 0.00 0.00 3.10
1209 2505 0.041312 CACGCACCACCGAAAAAGAG 60.041 55.000 0.00 0.00 0.00 2.85
1210 2506 2.018544 CACGCACCACCGAAAAAGA 58.981 52.632 0.00 0.00 0.00 2.52
1211 2507 1.657181 GCACGCACCACCGAAAAAG 60.657 57.895 0.00 0.00 0.00 2.27
1268 2564 2.307098 CCTTGGTCATCTTCTCCACCTT 59.693 50.000 0.00 0.00 0.00 3.50
1510 2806 0.389166 GGTTCTCACAGAGCAGGTCG 60.389 60.000 0.00 0.00 0.00 4.79
1522 2818 2.035155 TCGAGGCCGAGGTTCTCA 59.965 61.111 0.00 1.67 40.30 3.27
1561 2857 2.045926 CCCTTGGAGCCACGGAAG 60.046 66.667 13.19 0.00 37.52 3.46
1627 2923 4.452733 CCCTTGACGAGGTCGGGC 62.453 72.222 8.01 0.00 44.71 6.13
2008 3316 2.529389 AAGGCCTCGAACCTGGGT 60.529 61.111 5.23 0.00 37.67 4.51
2075 3383 6.507023 ACACAGTTTTGAAGCTTTATTCAGG 58.493 36.000 0.00 0.00 40.16 3.86
2147 3532 4.088781 GCGAGAAAAGAAAGAGTACTCGTG 59.911 45.833 17.07 0.47 44.50 4.35
2148 3533 4.228317 GCGAGAAAAGAAAGAGTACTCGT 58.772 43.478 17.07 11.52 44.50 4.18
2149 3534 3.298499 CGCGAGAAAAGAAAGAGTACTCG 59.702 47.826 17.07 0.00 45.13 4.18
2150 3535 4.088781 CACGCGAGAAAAGAAAGAGTACTC 59.911 45.833 15.93 15.41 0.00 2.59
2151 3536 3.982058 CACGCGAGAAAAGAAAGAGTACT 59.018 43.478 15.93 0.00 0.00 2.73
2152 3537 3.734735 ACACGCGAGAAAAGAAAGAGTAC 59.265 43.478 15.93 0.00 0.00 2.73
2153 3538 3.734231 CACACGCGAGAAAAGAAAGAGTA 59.266 43.478 15.93 0.00 0.00 2.59
2154 3539 2.540101 CACACGCGAGAAAAGAAAGAGT 59.460 45.455 15.93 0.00 0.00 3.24
2155 3540 2.540101 ACACACGCGAGAAAAGAAAGAG 59.460 45.455 15.93 0.00 0.00 2.85
2156 3541 2.546778 ACACACGCGAGAAAAGAAAGA 58.453 42.857 15.93 0.00 0.00 2.52
2157 3542 3.319238 AACACACGCGAGAAAAGAAAG 57.681 42.857 15.93 0.00 0.00 2.62
2158 3543 3.421741 CAAACACACGCGAGAAAAGAAA 58.578 40.909 15.93 0.00 0.00 2.52
2159 3544 2.223157 CCAAACACACGCGAGAAAAGAA 60.223 45.455 15.93 0.00 0.00 2.52
2160 3545 1.329292 CCAAACACACGCGAGAAAAGA 59.671 47.619 15.93 0.00 0.00 2.52
2161 3546 1.063469 ACCAAACACACGCGAGAAAAG 59.937 47.619 15.93 0.53 0.00 2.27
2162 3547 1.088306 ACCAAACACACGCGAGAAAA 58.912 45.000 15.93 0.00 0.00 2.29
2163 3548 1.862201 CTACCAAACACACGCGAGAAA 59.138 47.619 15.93 0.00 0.00 2.52
2164 3549 1.493772 CTACCAAACACACGCGAGAA 58.506 50.000 15.93 0.00 0.00 2.87
2165 3550 0.942410 GCTACCAAACACACGCGAGA 60.942 55.000 15.93 0.00 0.00 4.04
2166 3551 0.944311 AGCTACCAAACACACGCGAG 60.944 55.000 15.93 7.88 0.00 5.03
2167 3552 0.314618 TAGCTACCAAACACACGCGA 59.685 50.000 15.93 0.00 0.00 5.87
2168 3553 1.141645 TTAGCTACCAAACACACGCG 58.858 50.000 3.53 3.53 0.00 6.01
2169 3554 3.824414 AATTAGCTACCAAACACACGC 57.176 42.857 0.00 0.00 0.00 5.34
2170 3555 5.737290 GCATAAATTAGCTACCAAACACACG 59.263 40.000 0.00 0.00 0.00 4.49
2171 3556 6.852664 AGCATAAATTAGCTACCAAACACAC 58.147 36.000 0.00 0.00 39.78 3.82
2172 3557 7.461182 AAGCATAAATTAGCTACCAAACACA 57.539 32.000 0.00 0.00 40.90 3.72
2173 3558 6.687105 CGAAGCATAAATTAGCTACCAAACAC 59.313 38.462 0.00 0.00 40.90 3.32
2174 3559 6.373216 ACGAAGCATAAATTAGCTACCAAACA 59.627 34.615 0.00 0.00 40.90 2.83
2175 3560 6.782150 ACGAAGCATAAATTAGCTACCAAAC 58.218 36.000 0.00 0.00 40.90 2.93
2176 3561 6.995511 ACGAAGCATAAATTAGCTACCAAA 57.004 33.333 0.00 0.00 40.90 3.28
2207 3592 5.508124 AAAAACAACAACAACATGACACG 57.492 34.783 0.00 0.00 0.00 4.49
2233 3659 5.007039 CAGAAACAACATGATACATCTCCCG 59.993 44.000 0.00 0.00 0.00 5.14
2258 3684 3.002791 TCTTTGAGCATTGGTCGCTTAG 58.997 45.455 10.98 5.88 40.63 2.18
2260 3686 1.537202 GTCTTTGAGCATTGGTCGCTT 59.463 47.619 10.98 0.00 40.63 4.68
2261 3687 1.160137 GTCTTTGAGCATTGGTCGCT 58.840 50.000 10.98 0.00 44.10 4.93
2262 3688 1.160137 AGTCTTTGAGCATTGGTCGC 58.840 50.000 10.98 0.11 32.15 5.19
2263 3689 4.666655 CGTTTAGTCTTTGAGCATTGGTCG 60.667 45.833 10.98 0.00 32.15 4.79
2264 3690 4.451096 TCGTTTAGTCTTTGAGCATTGGTC 59.549 41.667 8.91 8.91 0.00 4.02
2265 3691 4.385825 TCGTTTAGTCTTTGAGCATTGGT 58.614 39.130 0.00 0.00 0.00 3.67
2266 3692 5.356882 TTCGTTTAGTCTTTGAGCATTGG 57.643 39.130 0.00 0.00 0.00 3.16
2268 3694 4.083271 GGCTTCGTTTAGTCTTTGAGCATT 60.083 41.667 0.00 0.00 0.00 3.56
2281 3711 2.529780 TTCAACCGAGGCTTCGTTTA 57.470 45.000 17.52 1.00 45.28 2.01
2283 3713 1.156736 CATTCAACCGAGGCTTCGTT 58.843 50.000 17.52 8.64 45.28 3.85
2284 3714 0.320374 TCATTCAACCGAGGCTTCGT 59.680 50.000 17.52 2.54 45.28 3.85
2285 3715 1.328680 CATCATTCAACCGAGGCTTCG 59.671 52.381 11.85 11.85 46.29 3.79
2286 3716 2.352960 GACATCATTCAACCGAGGCTTC 59.647 50.000 0.00 0.00 0.00 3.86
2287 3717 2.290260 TGACATCATTCAACCGAGGCTT 60.290 45.455 0.00 0.00 0.00 4.35
2288 3718 1.278985 TGACATCATTCAACCGAGGCT 59.721 47.619 0.00 0.00 0.00 4.58
2289 3719 1.398390 GTGACATCATTCAACCGAGGC 59.602 52.381 0.00 0.00 0.00 4.70
2290 3720 2.009774 GGTGACATCATTCAACCGAGG 58.990 52.381 0.00 0.00 0.00 4.63
2362 3792 3.859411 TGCCGTTTGAAGAGTGTTTTT 57.141 38.095 0.00 0.00 0.00 1.94
2363 3793 4.385358 AATGCCGTTTGAAGAGTGTTTT 57.615 36.364 0.00 0.00 0.00 2.43
2364 3794 4.385358 AAATGCCGTTTGAAGAGTGTTT 57.615 36.364 0.00 0.00 0.00 2.83
2374 3804 4.272018 TCACCATTTTTCAAATGCCGTTTG 59.728 37.500 2.89 2.89 46.86 2.93
2375 3805 4.446371 TCACCATTTTTCAAATGCCGTTT 58.554 34.783 4.01 0.00 0.00 3.60
2376 3806 4.065321 TCACCATTTTTCAAATGCCGTT 57.935 36.364 4.01 0.00 0.00 4.44
2377 3807 3.742433 TCACCATTTTTCAAATGCCGT 57.258 38.095 4.01 0.00 0.00 5.68
2378 3808 3.806521 TGTTCACCATTTTTCAAATGCCG 59.193 39.130 4.01 0.00 0.00 5.69
2379 3809 5.296531 ACTTGTTCACCATTTTTCAAATGCC 59.703 36.000 4.01 0.00 0.00 4.40
2380 3810 6.362210 ACTTGTTCACCATTTTTCAAATGC 57.638 33.333 4.01 0.00 0.00 3.56
2383 3813 9.658799 TCAAATACTTGTTCACCATTTTTCAAA 57.341 25.926 0.00 0.00 33.94 2.69
2384 3814 9.658799 TTCAAATACTTGTTCACCATTTTTCAA 57.341 25.926 0.00 0.00 33.94 2.69
2385 3815 9.658799 TTTCAAATACTTGTTCACCATTTTTCA 57.341 25.926 0.00 0.00 33.94 2.69
2440 3870 9.872757 GTTCAACATTTTCTAAATACTCGTTCA 57.127 29.630 0.00 0.00 0.00 3.18
2441 3871 9.872757 TGTTCAACATTTTCTAAATACTCGTTC 57.127 29.630 0.00 0.00 0.00 3.95
2443 3873 9.878599 CTTGTTCAACATTTTCTAAATACTCGT 57.121 29.630 0.00 0.00 0.00 4.18
2444 3874 9.878599 ACTTGTTCAACATTTTCTAAATACTCG 57.121 29.630 0.00 0.00 0.00 4.18
2453 3883 9.868277 TGTTCAAATACTTGTTCAACATTTTCT 57.132 25.926 0.00 0.00 33.94 2.52
2456 3886 8.591312 CGTTGTTCAAATACTTGTTCAACATTT 58.409 29.630 18.40 0.00 41.42 2.32
2457 3887 7.757624 ACGTTGTTCAAATACTTGTTCAACATT 59.242 29.630 18.40 8.58 41.42 2.71
2458 3888 7.254852 ACGTTGTTCAAATACTTGTTCAACAT 58.745 30.769 18.40 7.97 41.42 2.71
2459 3889 6.613233 ACGTTGTTCAAATACTTGTTCAACA 58.387 32.000 18.40 6.65 41.42 3.33
2460 3890 7.271653 TCAACGTTGTTCAAATACTTGTTCAAC 59.728 33.333 26.47 12.82 40.00 3.18
2461 3891 7.306213 TCAACGTTGTTCAAATACTTGTTCAA 58.694 30.769 26.47 0.00 33.94 2.69
2462 3892 6.843208 TCAACGTTGTTCAAATACTTGTTCA 58.157 32.000 26.47 0.00 33.94 3.18
2463 3893 7.271653 TGTTCAACGTTGTTCAAATACTTGTTC 59.728 33.333 26.47 1.73 33.94 3.18
2464 3894 7.085116 TGTTCAACGTTGTTCAAATACTTGTT 58.915 30.769 26.47 0.00 33.94 2.83
2465 3895 6.613233 TGTTCAACGTTGTTCAAATACTTGT 58.387 32.000 26.47 0.00 33.94 3.16
2466 3896 7.272515 ACTTGTTCAACGTTGTTCAAATACTTG 59.727 33.333 26.47 18.66 0.00 3.16
2467 3897 7.309920 ACTTGTTCAACGTTGTTCAAATACTT 58.690 30.769 26.47 11.68 0.00 2.24
2468 3898 6.848451 ACTTGTTCAACGTTGTTCAAATACT 58.152 32.000 26.47 12.21 0.00 2.12
2469 3899 8.776680 ATACTTGTTCAACGTTGTTCAAATAC 57.223 30.769 26.47 14.19 0.00 1.89
2470 3900 9.790389 AAATACTTGTTCAACGTTGTTCAAATA 57.210 25.926 26.47 22.98 0.00 1.40
2471 3901 8.591312 CAAATACTTGTTCAACGTTGTTCAAAT 58.409 29.630 26.47 21.86 0.00 2.32
2472 3902 7.808381 TCAAATACTTGTTCAACGTTGTTCAAA 59.192 29.630 26.47 17.34 33.94 2.69
2473 3903 7.306213 TCAAATACTTGTTCAACGTTGTTCAA 58.694 30.769 26.47 25.98 33.94 2.69
2474 3904 6.843208 TCAAATACTTGTTCAACGTTGTTCA 58.157 32.000 26.47 21.79 33.94 3.18
2475 3905 7.728580 TTCAAATACTTGTTCAACGTTGTTC 57.271 32.000 26.47 19.75 33.94 3.18
2476 3906 8.522178 TTTTCAAATACTTGTTCAACGTTGTT 57.478 26.923 26.47 9.23 33.94 2.83
2477 3907 8.522178 TTTTTCAAATACTTGTTCAACGTTGT 57.478 26.923 26.47 9.92 33.94 3.32
2478 3908 9.618410 GATTTTTCAAATACTTGTTCAACGTTG 57.382 29.630 22.35 22.35 33.94 4.10
2479 3909 9.581099 AGATTTTTCAAATACTTGTTCAACGTT 57.419 25.926 0.00 0.00 33.94 3.99
2480 3910 9.581099 AAGATTTTTCAAATACTTGTTCAACGT 57.419 25.926 0.00 0.00 33.94 3.99
2613 4043 9.889128 CACCATTTTTCTAAATACCCATTCAAT 57.111 29.630 0.00 0.00 32.75 2.57
2614 4044 9.094578 TCACCATTTTTCTAAATACCCATTCAA 57.905 29.630 0.00 0.00 32.75 2.69
2615 4045 8.657387 TCACCATTTTTCTAAATACCCATTCA 57.343 30.769 0.00 0.00 32.75 2.57
2616 4046 9.750125 GATCACCATTTTTCTAAATACCCATTC 57.250 33.333 0.00 0.00 32.75 2.67
2617 4047 9.265862 TGATCACCATTTTTCTAAATACCCATT 57.734 29.630 0.00 0.00 32.75 3.16
2618 4048 8.837099 TGATCACCATTTTTCTAAATACCCAT 57.163 30.769 0.00 0.00 32.75 4.00
2619 4049 8.694540 CATGATCACCATTTTTCTAAATACCCA 58.305 33.333 0.00 0.00 32.75 4.51
2620 4050 8.695456 ACATGATCACCATTTTTCTAAATACCC 58.305 33.333 0.00 0.00 32.75 3.69
2667 4097 6.862711 TCGGTTTTCTTTTGTTTGGTTTTT 57.137 29.167 0.00 0.00 0.00 1.94
2668 4098 6.862711 TTCGGTTTTCTTTTGTTTGGTTTT 57.137 29.167 0.00 0.00 0.00 2.43
2669 4099 6.862711 TTTCGGTTTTCTTTTGTTTGGTTT 57.137 29.167 0.00 0.00 0.00 3.27
2670 4100 6.862711 TTTTCGGTTTTCTTTTGTTTGGTT 57.137 29.167 0.00 0.00 0.00 3.67
2671 4101 6.260271 TGTTTTTCGGTTTTCTTTTGTTTGGT 59.740 30.769 0.00 0.00 0.00 3.67
2672 4102 6.659776 TGTTTTTCGGTTTTCTTTTGTTTGG 58.340 32.000 0.00 0.00 0.00 3.28
2673 4103 8.465253 GTTTGTTTTTCGGTTTTCTTTTGTTTG 58.535 29.630 0.00 0.00 0.00 2.93
2674 4104 8.182227 TGTTTGTTTTTCGGTTTTCTTTTGTTT 58.818 25.926 0.00 0.00 0.00 2.83
2675 4105 7.694886 TGTTTGTTTTTCGGTTTTCTTTTGTT 58.305 26.923 0.00 0.00 0.00 2.83
2676 4106 7.247929 TGTTTGTTTTTCGGTTTTCTTTTGT 57.752 28.000 0.00 0.00 0.00 2.83
2677 4107 8.548433 TTTGTTTGTTTTTCGGTTTTCTTTTG 57.452 26.923 0.00 0.00 0.00 2.44
2678 4108 9.737427 ATTTTGTTTGTTTTTCGGTTTTCTTTT 57.263 22.222 0.00 0.00 0.00 2.27
2684 4114 9.946165 TGTTTTATTTTGTTTGTTTTTCGGTTT 57.054 22.222 0.00 0.00 0.00 3.27
2685 4115 9.946165 TTGTTTTATTTTGTTTGTTTTTCGGTT 57.054 22.222 0.00 0.00 0.00 4.44
2686 4116 9.946165 TTTGTTTTATTTTGTTTGTTTTTCGGT 57.054 22.222 0.00 0.00 0.00 4.69
2702 4132 9.454859 TGGACAACATTTTTCCTTTGTTTTATT 57.545 25.926 0.00 0.00 32.34 1.40
2703 4133 9.625747 ATGGACAACATTTTTCCTTTGTTTTAT 57.374 25.926 0.00 0.00 35.97 1.40
2704 4134 8.887717 CATGGACAACATTTTTCCTTTGTTTTA 58.112 29.630 0.00 0.00 37.84 1.52
2705 4135 7.392953 ACATGGACAACATTTTTCCTTTGTTTT 59.607 29.630 0.00 0.00 37.84 2.43
2706 4136 6.883756 ACATGGACAACATTTTTCCTTTGTTT 59.116 30.769 0.00 0.00 37.84 2.83
2707 4137 6.413892 ACATGGACAACATTTTTCCTTTGTT 58.586 32.000 0.00 0.00 37.84 2.83
2708 4138 5.988287 ACATGGACAACATTTTTCCTTTGT 58.012 33.333 0.00 0.00 37.84 2.83
2709 4139 7.209475 AGTACATGGACAACATTTTTCCTTTG 58.791 34.615 11.55 0.00 37.84 2.77
2710 4140 7.360113 AGTACATGGACAACATTTTTCCTTT 57.640 32.000 11.55 0.00 37.84 3.11
2711 4141 6.976934 AGTACATGGACAACATTTTTCCTT 57.023 33.333 11.55 0.00 37.84 3.36
2712 4142 8.472007 TTTAGTACATGGACAACATTTTTCCT 57.528 30.769 11.55 0.00 37.84 3.36
2713 4143 9.535878 TTTTTAGTACATGGACAACATTTTTCC 57.464 29.630 11.55 0.00 37.84 3.13
2750 4180 9.994432 ACGTTTTTCATTATTTTTCAAATGCAA 57.006 22.222 0.00 0.00 33.91 4.08
2751 4181 9.430838 CACGTTTTTCATTATTTTTCAAATGCA 57.569 25.926 0.00 0.00 33.91 3.96
2752 4182 9.432077 ACACGTTTTTCATTATTTTTCAAATGC 57.568 25.926 0.00 0.00 33.91 3.56
2801 4231 9.826574 TCAGTACAAGTTTAACATTTCTGTACT 57.173 29.630 14.84 14.84 40.00 2.73
2876 4306 9.665719 AGTTTGTTTTGGTTTTCATTCTACATT 57.334 25.926 0.00 0.00 0.00 2.71
2881 4311 9.936759 TTCTTAGTTTGTTTTGGTTTTCATTCT 57.063 25.926 0.00 0.00 0.00 2.40
2885 4315 8.499967 GCTTTTCTTAGTTTGTTTTGGTTTTCA 58.500 29.630 0.00 0.00 0.00 2.69
2886 4316 8.499967 TGCTTTTCTTAGTTTGTTTTGGTTTTC 58.500 29.630 0.00 0.00 0.00 2.29
2887 4317 8.384607 TGCTTTTCTTAGTTTGTTTTGGTTTT 57.615 26.923 0.00 0.00 0.00 2.43
2888 4318 7.971183 TGCTTTTCTTAGTTTGTTTTGGTTT 57.029 28.000 0.00 0.00 0.00 3.27
2889 4319 7.119116 CCTTGCTTTTCTTAGTTTGTTTTGGTT 59.881 33.333 0.00 0.00 0.00 3.67
2890 4320 6.593770 CCTTGCTTTTCTTAGTTTGTTTTGGT 59.406 34.615 0.00 0.00 0.00 3.67
2891 4321 6.816140 TCCTTGCTTTTCTTAGTTTGTTTTGG 59.184 34.615 0.00 0.00 0.00 3.28
2892 4322 7.826260 TCCTTGCTTTTCTTAGTTTGTTTTG 57.174 32.000 0.00 0.00 0.00 2.44
2893 4323 8.840833 TTTCCTTGCTTTTCTTAGTTTGTTTT 57.159 26.923 0.00 0.00 0.00 2.43
3021 4451 9.150348 CAGTTTTCTCCATGTTTTACTTTGTTT 57.850 29.630 0.00 0.00 0.00 2.83
3022 4452 8.527810 TCAGTTTTCTCCATGTTTTACTTTGTT 58.472 29.630 0.00 0.00 0.00 2.83
3023 4453 8.062065 TCAGTTTTCTCCATGTTTTACTTTGT 57.938 30.769 0.00 0.00 0.00 2.83
3024 4454 8.925161 TTCAGTTTTCTCCATGTTTTACTTTG 57.075 30.769 0.00 0.00 0.00 2.77
3030 4460 9.883142 TGTTTTATTCAGTTTTCTCCATGTTTT 57.117 25.926 0.00 0.00 0.00 2.43
3031 4461 9.533253 CTGTTTTATTCAGTTTTCTCCATGTTT 57.467 29.630 0.00 0.00 0.00 2.83
3032 4462 8.912988 TCTGTTTTATTCAGTTTTCTCCATGTT 58.087 29.630 0.00 0.00 34.86 2.71
3033 4463 8.463930 TCTGTTTTATTCAGTTTTCTCCATGT 57.536 30.769 0.00 0.00 34.86 3.21
3034 4464 9.748708 TTTCTGTTTTATTCAGTTTTCTCCATG 57.251 29.630 0.00 0.00 34.86 3.66


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

AutoCloner maintained by Alex Coulton.