Multiple sequence alignment - TraesCS5D01G399100

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 TraesCS5D01G399100 chr5D 100.000 4594 0 0 1 4594 464989302 464993895 0.000000e+00 8484.0
1 TraesCS5D01G399100 chr5D 84.392 2377 281 55 1063 3398 464916642 464918969 0.000000e+00 2252.0
2 TraesCS5D01G399100 chr5D 81.517 633 90 17 1 612 63414526 63413900 3.190000e-136 496.0
3 TraesCS5D01G399100 chr5D 85.315 429 52 7 210 631 473950573 473950149 2.540000e-117 433.0
4 TraesCS5D01G399100 chr5D 83.110 373 53 7 3027 3394 464818155 464818522 9.530000e-87 331.0
5 TraesCS5D01G399100 chr5D 79.118 431 70 15 2974 3394 464605891 464606311 3.500000e-71 279.0
6 TraesCS5D01G399100 chr5D 95.833 168 7 0 3712 3879 559625934 559625767 5.860000e-69 272.0
7 TraesCS5D01G399100 chr5D 94.828 174 8 1 3713 3886 215255233 215255405 2.110000e-68 270.0
8 TraesCS5D01G399100 chr5D 81.373 306 45 12 1257 1556 464491671 464491970 5.940000e-59 239.0
9 TraesCS5D01G399100 chr5D 87.209 172 22 0 1167 1338 242502948 242502777 3.630000e-46 196.0
10 TraesCS5D01G399100 chr5D 83.799 179 29 0 1895 2073 464492224 464492402 2.200000e-38 171.0
11 TraesCS5D01G399100 chr5D 81.679 131 20 4 1089 1216 464491430 464491559 6.290000e-19 106.0
12 TraesCS5D01G399100 chr5D 78.035 173 24 8 4424 4594 473348057 473347897 3.780000e-16 97.1
13 TraesCS5D01G399100 chr5A 92.994 2769 125 30 749 3451 585396319 585399084 0.000000e+00 3975.0
14 TraesCS5D01G399100 chr5A 83.987 2373 266 66 1063 3398 585234394 585236689 0.000000e+00 2172.0
15 TraesCS5D01G399100 chr5A 82.000 600 54 20 4044 4594 585399683 585400277 1.160000e-125 460.0
16 TraesCS5D01G399100 chr5A 82.574 373 55 7 3027 3394 585216219 585216586 2.060000e-83 320.0
17 TraesCS5D01G399100 chr5A 91.064 235 15 5 3479 3708 585399217 585399450 3.450000e-81 313.0
18 TraesCS5D01G399100 chr5A 79.350 431 69 14 2974 3394 585021010 585021430 7.520000e-73 285.0
19 TraesCS5D01G399100 chr5A 81.046 306 46 12 1257 1556 584965915 584966214 2.760000e-57 233.0
20 TraesCS5D01G399100 chr5A 87.791 172 17 2 3876 4045 585399455 585399624 1.010000e-46 198.0
21 TraesCS5D01G399100 chr5A 84.358 179 28 0 1895 2073 584966441 584966619 4.720000e-40 176.0
22 TraesCS5D01G399100 chr5A 77.358 159 30 5 3891 4044 448293372 448293215 6.330000e-14 89.8
23 TraesCS5D01G399100 chr5B 91.803 2879 166 39 610 3451 572341351 572344196 0.000000e+00 3945.0
24 TraesCS5D01G399100 chr5B 84.399 2378 292 51 1063 3398 572141865 572144205 0.000000e+00 2263.0
25 TraesCS5D01G399100 chr5B 94.805 231 7 3 3479 3706 572344339 572344567 5.650000e-94 355.0
26 TraesCS5D01G399100 chr5B 82.447 376 56 8 3027 3397 571555016 571554646 2.060000e-83 320.0
27 TraesCS5D01G399100 chr5B 87.008 254 30 2 4342 4594 572347025 572347276 2.710000e-72 283.0
28 TraesCS5D01G399100 chr5B 88.987 227 20 2 1 227 572328597 572328818 4.530000e-70 276.0
29 TraesCS5D01G399100 chr5B 81.250 304 45 12 1260 1557 571836668 571836371 7.680000e-58 235.0
30 TraesCS5D01G399100 chr5B 80.645 217 38 4 1895 2109 571836089 571835875 1.020000e-36 165.0
31 TraesCS5D01G399100 chr2D 84.689 627 85 8 1 625 27553700 27553083 2.350000e-172 616.0
32 TraesCS5D01G399100 chr2D 89.423 208 22 0 1 208 572644771 572644978 3.520000e-66 263.0
33 TraesCS5D01G399100 chr2D 87.629 194 24 0 1362 1555 634257654 634257461 4.620000e-55 226.0
34 TraesCS5D01G399100 chr2D 82.581 155 26 1 3892 4045 437903738 437903584 8.020000e-28 135.0
35 TraesCS5D01G399100 chr2D 83.838 99 16 0 1118 1216 634258031 634257933 1.360000e-15 95.3
36 TraesCS5D01G399100 chr1D 83.520 625 80 13 1 623 112637751 112637148 3.100000e-156 562.0
37 TraesCS5D01G399100 chr1D 95.210 167 8 0 3712 3878 362597891 362598057 9.800000e-67 265.0
38 TraesCS5D01G399100 chr1D 76.316 114 22 4 4353 4465 472399837 472399728 6.420000e-04 56.5
39 TraesCS5D01G399100 chr2B 80.243 658 87 21 1 623 141702792 141702143 5.420000e-124 455.0
40 TraesCS5D01G399100 chr2B 88.144 194 23 0 1362 1555 777171090 777170897 9.940000e-57 231.0
41 TraesCS5D01G399100 chr2B 85.897 156 18 4 3892 4045 514346501 514346348 3.680000e-36 163.0
42 TraesCS5D01G399100 chr2B 82.828 99 17 0 1118 1216 777171498 777171400 6.330000e-14 89.8
43 TraesCS5D01G399100 chr3D 84.758 433 56 8 194 624 100849413 100849837 4.250000e-115 425.0
44 TraesCS5D01G399100 chr3D 88.636 220 25 0 1 220 517291061 517290842 7.580000e-68 268.0
45 TraesCS5D01G399100 chr3D 88.785 214 24 0 1 214 402499254 402499467 3.520000e-66 263.0
46 TraesCS5D01G399100 chr3D 93.220 177 12 0 3712 3888 550509597 550509421 1.270000e-65 261.0
47 TraesCS5D01G399100 chr3D 91.758 182 13 2 3713 3893 556141142 556140962 7.630000e-63 252.0
48 TraesCS5D01G399100 chr3D 89.529 191 18 2 3713 3903 98843491 98843679 1.650000e-59 241.0
49 TraesCS5D01G399100 chr3A 76.577 888 132 44 1948 2818 106300708 106301536 7.110000e-113 418.0
50 TraesCS5D01G399100 chr2A 76.603 889 130 43 1948 2818 613185192 613184364 7.110000e-113 418.0
51 TraesCS5D01G399100 chr2A 94.737 171 8 1 3712 3881 469790201 469790031 9.800000e-67 265.0
52 TraesCS5D01G399100 chr2A 77.124 153 19 7 3892 4044 550870792 550870928 1.770000e-09 75.0
53 TraesCS5D01G399100 chr4D 83.990 406 58 6 210 613 380527950 380528350 2.590000e-102 383.0
54 TraesCS5D01G399100 chr4D 82.212 416 61 8 202 613 483624159 483623753 3.400000e-91 346.0
55 TraesCS5D01G399100 chr4D 84.726 347 45 6 197 541 248917655 248917995 1.580000e-89 340.0
56 TraesCS5D01G399100 chr4D 91.803 183 13 2 3712 3893 93336683 93336864 2.120000e-63 254.0
57 TraesCS5D01G399100 chr7D 83.413 416 53 12 204 613 552158258 552158663 5.610000e-99 372.0
58 TraesCS5D01G399100 chrUn 82.679 433 60 10 203 623 90354621 90354192 2.020000e-98 370.0
59 TraesCS5D01G399100 chrUn 87.500 104 12 1 4492 4594 340858269 340858166 8.070000e-23 119.0
60 TraesCS5D01G399100 chr6D 83.208 399 64 3 200 597 451622854 451623250 3.380000e-96 363.0
61 TraesCS5D01G399100 chr6D 89.956 229 20 3 2 227 140019772 140020000 4.500000e-75 292.0
62 TraesCS5D01G399100 chr6D 88.837 215 23 1 1 214 451622616 451622830 3.520000e-66 263.0
63 TraesCS5D01G399100 chr3B 74.775 888 144 46 1948 2818 598041460 598042284 4.430000e-85 326.0
64 TraesCS5D01G399100 chr3B 94.675 169 8 1 3713 3881 368322279 368322446 1.270000e-65 261.0
65 TraesCS5D01G399100 chr3B 84.615 143 15 5 4053 4192 671382169 671382307 8.020000e-28 135.0
66 TraesCS5D01G399100 chr3B 95.349 43 2 0 3891 3933 819010789 819010831 8.250000e-08 69.4
67 TraesCS5D01G399100 chr7A 82.692 156 25 2 4055 4208 19509259 19509414 2.230000e-28 137.0
68 TraesCS5D01G399100 chr7A 86.170 94 13 0 4066 4159 131106540 131106447 8.130000e-18 102.0
69 TraesCS5D01G399100 chr7A 78.571 154 30 3 3893 4045 10875560 10875711 1.050000e-16 99.0
70 TraesCS5D01G399100 chr7A 81.356 118 21 1 4044 4160 131106575 131106692 1.360000e-15 95.3
71 TraesCS5D01G399100 chr4B 83.505 97 14 2 4055 4151 413872889 413872983 6.330000e-14 89.8
72 TraesCS5D01G399100 chr4B 80.000 130 14 7 3891 4016 489091941 489092062 8.190000e-13 86.1
73 TraesCS5D01G399100 chr6B 97.778 45 1 0 3890 3934 18723366 18723410 1.370000e-10 78.7


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 TraesCS5D01G399100 chr5D 464989302 464993895 4593 False 8484.000000 8484 100.000000 1 4594 1 chr5D.!!$F5 4593
1 TraesCS5D01G399100 chr5D 464916642 464918969 2327 False 2252.000000 2252 84.392000 1063 3398 1 chr5D.!!$F4 2335
2 TraesCS5D01G399100 chr5D 63413900 63414526 626 True 496.000000 496 81.517000 1 612 1 chr5D.!!$R1 611
3 TraesCS5D01G399100 chr5A 585234394 585236689 2295 False 2172.000000 2172 83.987000 1063 3398 1 chr5A.!!$F3 2335
4 TraesCS5D01G399100 chr5A 585396319 585400277 3958 False 1236.500000 3975 88.462250 749 4594 4 chr5A.!!$F5 3845
5 TraesCS5D01G399100 chr5A 584965915 584966619 704 False 204.500000 233 82.702000 1257 2073 2 chr5A.!!$F4 816
6 TraesCS5D01G399100 chr5B 572141865 572144205 2340 False 2263.000000 2263 84.399000 1063 3398 1 chr5B.!!$F1 2335
7 TraesCS5D01G399100 chr5B 572341351 572347276 5925 False 1527.666667 3945 91.205333 610 4594 3 chr5B.!!$F3 3984
8 TraesCS5D01G399100 chr2D 27553083 27553700 617 True 616.000000 616 84.689000 1 625 1 chr2D.!!$R1 624
9 TraesCS5D01G399100 chr1D 112637148 112637751 603 True 562.000000 562 83.520000 1 623 1 chr1D.!!$R1 622
10 TraesCS5D01G399100 chr2B 141702143 141702792 649 True 455.000000 455 80.243000 1 623 1 chr2B.!!$R1 622
11 TraesCS5D01G399100 chr3A 106300708 106301536 828 False 418.000000 418 76.577000 1948 2818 1 chr3A.!!$F1 870
12 TraesCS5D01G399100 chr2A 613184364 613185192 828 True 418.000000 418 76.603000 1948 2818 1 chr2A.!!$R2 870
13 TraesCS5D01G399100 chr6D 451622616 451623250 634 False 313.000000 363 86.022500 1 597 2 chr6D.!!$F2 596
14 TraesCS5D01G399100 chr3B 598041460 598042284 824 False 326.000000 326 74.775000 1948 2818 1 chr3B.!!$F2 870

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
456 538 0.312729 TCTAACAACAGCGACGCAGA 59.687 50.0 23.70 11.11 0.00 4.26 F
761 844 0.823356 TGGGGTCTTGCTTGCTTGTC 60.823 55.0 0.00 0.00 0.00 3.18 F
2164 2302 0.176910 TGCACTCGTGGTGTTCTTCA 59.823 50.0 11.43 0.87 46.86 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2303 0.035056 AGGAGCAAGAATCCAACGGG 60.035 55.000 0.0 0.0 39.47 5.28 R
2353 2539 0.110678 TCACAGAGTCAGTCTCCCGT 59.889 55.000 0.0 0.0 43.71 5.28 R
3708 4095 1.829222 TGGGAACGAAGGGAGTATGAC 59.171 52.381 0.0 0.0 0.00 3.06 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
48 50 5.300286 CCTGTAATGGGGAATTGATGAACTC 59.700 44.000 0.00 0.00 0.00 3.01
68 70 1.682684 TGTCGGAGGAGGAAGAGGC 60.683 63.158 0.00 0.00 0.00 4.70
103 105 1.758440 GATCAGCTCCGGCCATGGTA 61.758 60.000 14.67 0.00 39.73 3.25
157 159 0.768221 AAGGTTGGAGTGGGCTCAGA 60.768 55.000 0.00 0.00 43.37 3.27
165 167 0.607489 AGTGGGCTCAGACAATGTGC 60.607 55.000 0.00 0.00 45.62 4.57
170 172 2.487934 GGCTCAGACAATGTGCGATAT 58.512 47.619 0.00 0.00 46.97 1.63
203 210 8.310382 TCAGACAAGGATCTAAAGAAGAAGAAG 58.690 37.037 0.00 0.00 37.89 2.85
208 215 9.717942 CAAGGATCTAAAGAAGAAGAAGAAGAA 57.282 33.333 0.00 0.00 37.89 2.52
249 330 3.795623 TCCACCTAGTTAGCATCGTTC 57.204 47.619 0.00 0.00 0.00 3.95
266 347 4.975631 TCGTTCAACTTTCCCCTATTCAA 58.024 39.130 0.00 0.00 0.00 2.69
306 388 5.679734 AACTTGACTGTCATTTGCTAGTG 57.320 39.130 11.86 0.00 0.00 2.74
321 403 6.614694 TTGCTAGTGGTTAGGATAAACTGA 57.385 37.500 0.00 0.00 29.09 3.41
355 437 3.589988 AGCTAGGACAAGACAATGTTCG 58.410 45.455 0.00 0.00 33.81 3.95
369 451 2.892914 TTCGGTGTGCGTGTGGTG 60.893 61.111 0.00 0.00 0.00 4.17
418 500 4.626042 TCACATTTTTAGCCGTTTGCAAT 58.374 34.783 0.00 0.00 44.83 3.56
456 538 0.312729 TCTAACAACAGCGACGCAGA 59.687 50.000 23.70 11.11 0.00 4.26
496 579 4.423625 ACTAATTACTCCCCTCATGCAC 57.576 45.455 0.00 0.00 0.00 4.57
510 593 2.939781 TGCACGAAGCCTAATGCAA 58.060 47.368 0.00 0.00 44.72 4.08
511 594 1.242989 TGCACGAAGCCTAATGCAAA 58.757 45.000 0.00 0.00 44.72 3.68
536 619 7.441017 ACAACCAAACTACATGCAAATGTTAT 58.559 30.769 0.00 0.00 36.08 1.89
541 624 9.810231 CCAAACTACATGCAAATGTTATTTTTC 57.190 29.630 0.00 0.00 36.08 2.29
547 630 8.830201 ACATGCAAATGTTATTTTTCTAAGCA 57.170 26.923 0.00 0.00 0.00 3.91
597 680 2.273557 CAAGCATGCAAAATGCCCTAC 58.726 47.619 21.98 0.00 44.23 3.18
603 686 2.591923 TGCAAAATGCCCTACACAGAA 58.408 42.857 0.00 0.00 44.23 3.02
630 713 3.056328 GAACGCACCCTTGGAGGC 61.056 66.667 0.00 0.00 32.73 4.70
655 738 6.563010 CGCTCTTTATTCACATCCGAGAATTC 60.563 42.308 0.00 0.00 34.70 2.17
656 739 6.258727 GCTCTTTATTCACATCCGAGAATTCA 59.741 38.462 8.44 0.00 34.70 2.57
658 741 8.201554 TCTTTATTCACATCCGAGAATTCAAG 57.798 34.615 8.44 0.61 34.70 3.02
660 743 8.560355 TTTATTCACATCCGAGAATTCAAGAA 57.440 30.769 8.44 0.67 34.70 2.52
720 803 4.047125 CCCTTCGCACACCCCCAT 62.047 66.667 0.00 0.00 0.00 4.00
721 804 2.751436 CCTTCGCACACCCCCATG 60.751 66.667 0.00 0.00 0.00 3.66
761 844 0.823356 TGGGGTCTTGCTTGCTTGTC 60.823 55.000 0.00 0.00 0.00 3.18
822 905 6.376177 CGCATGTGCATAGATATGTTTGAAT 58.624 36.000 5.77 0.00 42.21 2.57
837 920 7.969536 ATGTTTGAATATCTAATCTGACCCG 57.030 36.000 0.00 0.00 0.00 5.28
1084 1168 3.194308 GCGCTCCTGCTCTTCTGC 61.194 66.667 0.00 0.00 36.97 4.26
1580 1668 6.551385 ACTAAATCTCTGAGCAACACTTTG 57.449 37.500 0.00 0.00 35.62 2.77
1584 1686 3.461061 TCTCTGAGCAACACTTTGTGAG 58.539 45.455 4.61 0.00 36.96 3.51
1593 1696 6.165577 AGCAACACTTTGTGAGTTTTGAATT 58.834 32.000 8.72 0.00 44.92 2.17
1639 1765 1.065199 CACCTGCTGCTTCCCTTATCA 60.065 52.381 0.00 0.00 0.00 2.15
2134 2272 6.616017 GCTCAAATTCCAGGTAGAAAAGAAG 58.384 40.000 0.00 0.00 0.00 2.85
2163 2301 1.295792 TTGCACTCGTGGTGTTCTTC 58.704 50.000 11.43 0.00 46.86 2.87
2164 2302 0.176910 TGCACTCGTGGTGTTCTTCA 59.823 50.000 11.43 0.87 46.86 3.02
2165 2303 0.582005 GCACTCGTGGTGTTCTTCAC 59.418 55.000 11.43 0.00 46.86 3.18
2182 2343 0.804989 CACCCGTTGGATTCTTGCTC 59.195 55.000 0.00 0.00 34.81 4.26
2186 2363 2.555199 CCGTTGGATTCTTGCTCCTAG 58.445 52.381 0.00 0.00 33.69 3.02
2196 2377 6.407979 GGATTCTTGCTCCTAGTCTTCAGATT 60.408 42.308 0.00 0.00 0.00 2.40
2214 2395 4.796830 CAGATTTTCAGATGTTCATTGCCG 59.203 41.667 0.00 0.00 0.00 5.69
2276 2457 0.178995 TGGGCATTGACAAGCTCACA 60.179 50.000 7.76 0.00 36.06 3.58
2351 2537 2.497138 CTTGACATGGTGAGCAAGACA 58.503 47.619 0.00 0.00 36.32 3.41
2352 2538 2.174363 TGACATGGTGAGCAAGACAG 57.826 50.000 0.00 0.00 0.00 3.51
2353 2539 1.693606 TGACATGGTGAGCAAGACAGA 59.306 47.619 0.00 0.00 0.00 3.41
2355 2541 1.073964 CATGGTGAGCAAGACAGACG 58.926 55.000 0.00 0.00 0.00 4.18
2356 2542 0.036952 ATGGTGAGCAAGACAGACGG 60.037 55.000 0.00 0.00 0.00 4.79
2357 2543 1.374758 GGTGAGCAAGACAGACGGG 60.375 63.158 0.00 0.00 0.00 5.28
2358 2544 1.666011 GTGAGCAAGACAGACGGGA 59.334 57.895 0.00 0.00 0.00 5.14
2359 2545 0.389166 GTGAGCAAGACAGACGGGAG 60.389 60.000 0.00 0.00 0.00 4.30
2360 2546 0.539669 TGAGCAAGACAGACGGGAGA 60.540 55.000 0.00 0.00 0.00 3.71
2361 2547 0.109039 GAGCAAGACAGACGGGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
2369 2555 3.257935 AGACGGGAGACTGACTCTG 57.742 57.895 7.06 3.42 44.37 3.35
2370 2556 0.402504 AGACGGGAGACTGACTCTGT 59.597 55.000 7.06 6.26 44.37 3.41
2400 2599 2.222027 GTAGTGTTGCTTGCTGAGGTT 58.778 47.619 0.00 0.00 0.00 3.50
2411 2626 2.783135 TGCTGAGGTTGATGTTTCTCC 58.217 47.619 0.00 0.00 0.00 3.71
2627 2853 4.221703 AGGTACTGACTGATGAAACTCTGG 59.778 45.833 0.00 0.00 37.18 3.86
2629 2855 5.185249 GGTACTGACTGATGAAACTCTGGTA 59.815 44.000 0.00 0.00 0.00 3.25
2643 2869 7.442364 TGAAACTCTGGTACTGAATTCAGAAAG 59.558 37.037 36.15 25.31 46.59 2.62
2647 2873 5.470098 TCTGGTACTGAATTCAGAAAGTTGC 59.530 40.000 36.15 19.31 46.59 4.17
2649 2875 5.239306 TGGTACTGAATTCAGAAAGTTGCTG 59.761 40.000 36.15 11.75 46.59 4.41
2652 2878 2.030893 TGAATTCAGAAAGTTGCTGCCG 60.031 45.455 5.92 0.00 33.45 5.69
2653 2879 1.896220 ATTCAGAAAGTTGCTGCCGA 58.104 45.000 5.92 0.00 33.45 5.54
2654 2880 0.944386 TTCAGAAAGTTGCTGCCGAC 59.056 50.000 5.92 0.00 33.45 4.79
2656 2882 0.947244 CAGAAAGTTGCTGCCGACTT 59.053 50.000 11.31 11.31 45.53 3.01
2657 2883 1.069636 CAGAAAGTTGCTGCCGACTTC 60.070 52.381 15.75 10.85 43.36 3.01
2658 2884 0.944386 GAAAGTTGCTGCCGACTTCA 59.056 50.000 15.75 0.00 43.36 3.02
2660 2886 0.106708 AAGTTGCTGCCGACTTCAGA 59.893 50.000 11.31 0.00 40.88 3.27
2661 2887 0.106708 AGTTGCTGCCGACTTCAGAA 59.893 50.000 0.00 0.00 31.43 3.02
2663 2889 1.537202 GTTGCTGCCGACTTCAGAATT 59.463 47.619 0.00 0.00 33.54 2.17
2664 2890 1.896220 TGCTGCCGACTTCAGAATTT 58.104 45.000 0.00 0.00 33.54 1.82
2666 2892 2.622942 TGCTGCCGACTTCAGAATTTTT 59.377 40.909 0.00 0.00 33.54 1.94
2687 2930 3.430042 TGCTTGAGCTCCTGAATTCTT 57.570 42.857 12.15 0.00 42.66 2.52
2837 3101 2.125106 GCGCCCAAGATCCTCGTT 60.125 61.111 0.00 0.00 0.00 3.85
3622 4001 9.944376 GAAGCTATGGTAAATGTATCCTCATTA 57.056 33.333 0.00 0.00 37.09 1.90
3681 4065 4.457949 AGTTACTACCATTCCCGCAAAAAG 59.542 41.667 0.00 0.00 0.00 2.27
3689 4076 5.011635 ACCATTCCCGCAAAAAGAAAATACT 59.988 36.000 0.00 0.00 0.00 2.12
3695 4082 6.033966 CCCGCAAAAAGAAAATACTACCATC 58.966 40.000 0.00 0.00 0.00 3.51
3711 4098 7.504926 ACTACCATCATAAAACTTAGGGTCA 57.495 36.000 0.00 0.00 0.00 4.02
3712 4099 8.102484 ACTACCATCATAAAACTTAGGGTCAT 57.898 34.615 0.00 0.00 0.00 3.06
3713 4100 9.220906 ACTACCATCATAAAACTTAGGGTCATA 57.779 33.333 0.00 0.00 0.00 2.15
3714 4101 9.490379 CTACCATCATAAAACTTAGGGTCATAC 57.510 37.037 0.00 0.00 0.00 2.39
3715 4102 8.102484 ACCATCATAAAACTTAGGGTCATACT 57.898 34.615 0.00 0.00 0.00 2.12
3716 4103 8.211629 ACCATCATAAAACTTAGGGTCATACTC 58.788 37.037 0.00 0.00 0.00 2.59
3717 4104 7.661847 CCATCATAAAACTTAGGGTCATACTCC 59.338 40.741 0.00 0.00 0.00 3.85
3718 4105 7.133133 TCATAAAACTTAGGGTCATACTCCC 57.867 40.000 0.00 0.00 44.90 4.30
3725 4112 2.598686 GGGTCATACTCCCTTCGTTC 57.401 55.000 0.00 0.00 41.58 3.95
3726 4113 1.138464 GGGTCATACTCCCTTCGTTCC 59.862 57.143 0.00 0.00 41.58 3.62
3727 4114 1.138464 GGTCATACTCCCTTCGTTCCC 59.862 57.143 0.00 0.00 0.00 3.97
3728 4115 1.829222 GTCATACTCCCTTCGTTCCCA 59.171 52.381 0.00 0.00 0.00 4.37
3729 4116 2.235402 GTCATACTCCCTTCGTTCCCAA 59.765 50.000 0.00 0.00 0.00 4.12
3730 4117 2.907696 TCATACTCCCTTCGTTCCCAAA 59.092 45.455 0.00 0.00 0.00 3.28
3731 4118 3.521937 TCATACTCCCTTCGTTCCCAAAT 59.478 43.478 0.00 0.00 0.00 2.32
3732 4119 4.717778 TCATACTCCCTTCGTTCCCAAATA 59.282 41.667 0.00 0.00 0.00 1.40
3733 4120 5.368523 TCATACTCCCTTCGTTCCCAAATAT 59.631 40.000 0.00 0.00 0.00 1.28
3734 4121 6.555738 TCATACTCCCTTCGTTCCCAAATATA 59.444 38.462 0.00 0.00 0.00 0.86
3735 4122 5.703730 ACTCCCTTCGTTCCCAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
3736 4123 5.681639 ACTCCCTTCGTTCCCAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
3737 4124 5.191124 ACTCCCTTCGTTCCCAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
3738 4125 5.677567 TCCCTTCGTTCCCAAATATAAGTC 58.322 41.667 0.00 0.00 0.00 3.01
3739 4126 5.190132 TCCCTTCGTTCCCAAATATAAGTCA 59.810 40.000 0.00 0.00 0.00 3.41
3740 4127 6.062095 CCCTTCGTTCCCAAATATAAGTCAT 58.938 40.000 0.00 0.00 0.00 3.06
3741 4128 6.546034 CCCTTCGTTCCCAAATATAAGTCATT 59.454 38.462 0.00 0.00 0.00 2.57
3742 4129 7.068226 CCCTTCGTTCCCAAATATAAGTCATTT 59.932 37.037 0.00 0.00 0.00 2.32
3743 4130 8.466798 CCTTCGTTCCCAAATATAAGTCATTTT 58.533 33.333 0.00 0.00 0.00 1.82
3746 4133 9.893634 TCGTTCCCAAATATAAGTCATTTTAGA 57.106 29.630 0.00 0.00 0.00 2.10
3770 4157 9.302345 AGATATTTCAACAAGTGACTACATACG 57.698 33.333 0.00 0.00 35.39 3.06
3771 4158 9.297586 GATATTTCAACAAGTGACTACATACGA 57.702 33.333 0.00 0.00 35.39 3.43
3772 4159 7.956420 ATTTCAACAAGTGACTACATACGAA 57.044 32.000 0.00 0.00 35.39 3.85
3773 4160 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
3774 4161 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
3775 4162 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
3776 4163 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3777 4164 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
3778 4165 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3779 4166 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3780 4167 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
3781 4168 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3782 4169 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3783 4170 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
3784 4171 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3785 4172 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3786 4173 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3787 4174 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3788 4175 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3789 4176 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
3790 4177 5.039480 ACGAAGCAAAATGAGTGAATCTG 57.961 39.130 0.00 0.00 0.00 2.90
3791 4178 3.850273 CGAAGCAAAATGAGTGAATCTGC 59.150 43.478 0.00 0.00 0.00 4.26
3792 4179 4.614306 CGAAGCAAAATGAGTGAATCTGCA 60.614 41.667 0.00 0.00 0.00 4.41
3793 4180 4.170292 AGCAAAATGAGTGAATCTGCAC 57.830 40.909 0.00 0.00 39.05 4.57
3806 4193 8.430801 AGTGAATCTGCACTCTAAAATATGTC 57.569 34.615 0.00 0.00 45.54 3.06
3807 4194 8.263640 AGTGAATCTGCACTCTAAAATATGTCT 58.736 33.333 0.00 0.00 45.54 3.41
3808 4195 9.534565 GTGAATCTGCACTCTAAAATATGTCTA 57.465 33.333 0.00 0.00 35.91 2.59
3809 4196 9.534565 TGAATCTGCACTCTAAAATATGTCTAC 57.465 33.333 0.00 0.00 0.00 2.59
3810 4197 9.534565 GAATCTGCACTCTAAAATATGTCTACA 57.465 33.333 0.00 0.00 0.00 2.74
3813 4200 9.967346 TCTGCACTCTAAAATATGTCTACATAC 57.033 33.333 4.98 0.00 41.15 2.39
3814 4201 9.750125 CTGCACTCTAAAATATGTCTACATACA 57.250 33.333 4.98 0.00 41.15 2.29
3832 4219 5.838529 CATACATCCGTATGTTGTAGTCCA 58.161 41.667 0.00 0.00 46.70 4.02
3833 4220 6.455647 CATACATCCGTATGTTGTAGTCCAT 58.544 40.000 0.00 0.00 46.70 3.41
3834 4221 5.353394 ACATCCGTATGTTGTAGTCCATT 57.647 39.130 0.00 0.00 44.07 3.16
3835 4222 5.741011 ACATCCGTATGTTGTAGTCCATTT 58.259 37.500 0.00 0.00 44.07 2.32
3836 4223 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
3837 4224 5.408880 TCCGTATGTTGTAGTCCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
3838 4225 5.795972 TCCGTATGTTGTAGTCCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
3839 4226 6.231951 TCCGTATGTTGTAGTCCATTTGAAA 58.768 36.000 0.00 0.00 0.00 2.69
3840 4227 6.882140 TCCGTATGTTGTAGTCCATTTGAAAT 59.118 34.615 0.00 0.00 0.00 2.17
3841 4228 6.966632 CCGTATGTTGTAGTCCATTTGAAATG 59.033 38.462 10.84 10.84 0.00 2.32
3842 4229 6.468956 CGTATGTTGTAGTCCATTTGAAATGC 59.531 38.462 12.26 0.23 0.00 3.56
3843 4230 5.132897 TGTTGTAGTCCATTTGAAATGCC 57.867 39.130 12.26 5.23 0.00 4.40
3844 4231 4.832266 TGTTGTAGTCCATTTGAAATGCCT 59.168 37.500 12.26 11.73 0.00 4.75
3845 4232 6.007076 TGTTGTAGTCCATTTGAAATGCCTA 58.993 36.000 12.26 10.85 0.00 3.93
3846 4233 6.491745 TGTTGTAGTCCATTTGAAATGCCTAA 59.508 34.615 12.26 1.00 0.00 2.69
3847 4234 7.014711 TGTTGTAGTCCATTTGAAATGCCTAAA 59.985 33.333 12.26 6.93 0.00 1.85
3848 4235 7.531857 TGTAGTCCATTTGAAATGCCTAAAA 57.468 32.000 12.26 4.58 0.00 1.52
3849 4236 7.957002 TGTAGTCCATTTGAAATGCCTAAAAA 58.043 30.769 12.26 2.62 0.00 1.94
3850 4237 8.087750 TGTAGTCCATTTGAAATGCCTAAAAAG 58.912 33.333 12.26 0.00 0.00 2.27
3851 4238 7.301868 AGTCCATTTGAAATGCCTAAAAAGA 57.698 32.000 12.26 0.00 0.00 2.52
3852 4239 7.154656 AGTCCATTTGAAATGCCTAAAAAGAC 58.845 34.615 12.26 10.86 0.00 3.01
3853 4240 7.015584 AGTCCATTTGAAATGCCTAAAAAGACT 59.984 33.333 12.26 12.67 31.00 3.24
3854 4241 7.657354 GTCCATTTGAAATGCCTAAAAAGACTT 59.343 33.333 12.26 0.00 0.00 3.01
3855 4242 8.865090 TCCATTTGAAATGCCTAAAAAGACTTA 58.135 29.630 12.26 0.00 0.00 2.24
3856 4243 9.657419 CCATTTGAAATGCCTAAAAAGACTTAT 57.343 29.630 12.26 0.00 0.00 1.73
4127 5724 7.828717 TCCATCATCATACTTTACACACATGTT 59.171 33.333 0.00 0.00 40.48 2.71
4250 5870 0.838122 CCCGATCCAATCTAGGGGCT 60.838 60.000 0.00 0.00 38.44 5.19
4256 5876 3.089874 AATCTAGGGGCTGCCGCA 61.090 61.111 33.32 19.69 39.05 5.69
4323 5943 3.877450 GGATGATGCTGGCGGGGA 61.877 66.667 0.00 0.00 0.00 4.81
4359 6758 4.438346 GCAGTCGCGGTGGATATT 57.562 55.556 6.13 0.00 0.00 1.28
4378 6777 2.594592 GCACGGGTGTCCTGCTTT 60.595 61.111 0.25 0.00 35.63 3.51
4385 6784 1.507141 GGTGTCCTGCTTTGACGTGG 61.507 60.000 0.00 0.00 35.46 4.94
4386 6785 1.891919 TGTCCTGCTTTGACGTGGC 60.892 57.895 0.00 0.00 35.46 5.01
4406 6806 4.077184 CCTCCGGCGTTAGTGGCA 62.077 66.667 6.01 0.00 0.00 4.92
4427 6827 2.002586 CAACGATGCAGATTCTTCCGT 58.997 47.619 0.00 0.00 0.00 4.69
4436 6836 2.014857 AGATTCTTCCGTCGTCGATGA 58.985 47.619 16.06 2.39 39.71 2.92
4539 6939 1.176527 CATGGGGTGTGTTGGATGAC 58.823 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.263639 ACAGGATCCAGTTGTGAATGATGT 60.264 41.667 15.82 1.30 0.00 3.06
48 50 1.658686 CCTCTTCCTCCTCCGACACG 61.659 65.000 0.00 0.00 0.00 4.49
68 70 2.027385 TGATCACCTCATCAGGAGTCG 58.973 52.381 0.00 0.00 43.65 4.18
103 105 2.198827 TCATTGTCAAACGCCTCCAT 57.801 45.000 0.00 0.00 0.00 3.41
157 159 3.132824 TGACCTCTGATATCGCACATTGT 59.867 43.478 0.00 0.00 0.00 2.71
165 167 3.885901 TCCTTGTCTGACCTCTGATATCG 59.114 47.826 5.17 0.00 0.00 2.92
170 172 3.464720 AGATCCTTGTCTGACCTCTGA 57.535 47.619 5.17 0.00 0.00 3.27
203 210 8.665643 AGTTCATCATCATCATCTTCTTCTTC 57.334 34.615 0.00 0.00 0.00 2.87
208 215 6.766944 GTGGAAGTTCATCATCATCATCTTCT 59.233 38.462 5.01 0.00 33.14 2.85
214 236 4.849813 AGGTGGAAGTTCATCATCATCA 57.150 40.909 5.01 0.00 0.00 3.07
217 280 5.762179 AACTAGGTGGAAGTTCATCATCA 57.238 39.130 5.01 0.00 31.56 3.07
249 330 7.417797 CCAATATGGTTGAATAGGGGAAAGTTG 60.418 40.741 0.00 0.00 31.35 3.16
266 347 8.275040 AGTCAAGTTATTAAGAGCCAATATGGT 58.725 33.333 0.00 0.00 40.46 3.55
306 388 9.406828 GAAAACAAATGTCAGTTTATCCTAACC 57.593 33.333 0.00 0.00 36.98 2.85
321 403 7.173390 GTCTTGTCCTAGCTAGAAAACAAATGT 59.827 37.037 22.70 0.00 0.00 2.71
355 437 2.972505 CCTCACCACACGCACACC 60.973 66.667 0.00 0.00 0.00 4.16
386 468 5.868801 CGGCTAAAAATGTGATCACCATTTT 59.131 36.000 27.53 27.53 39.36 1.82
389 471 4.016444 ACGGCTAAAAATGTGATCACCAT 58.984 39.130 22.85 13.15 0.00 3.55
456 538 1.064952 GTTAGCACGCTGTTTGGTTGT 59.935 47.619 0.72 0.00 0.00 3.32
496 579 2.030363 TGGTTGTTTGCATTAGGCTTCG 60.030 45.455 0.00 0.00 45.15 3.79
510 593 5.669477 ACATTTGCATGTAGTTTGGTTGTT 58.331 33.333 0.00 0.00 42.24 2.83
511 594 5.275067 ACATTTGCATGTAGTTTGGTTGT 57.725 34.783 0.00 0.00 42.24 3.32
536 619 8.977505 GTTTGAACTAATGCATGCTTAGAAAAA 58.022 29.630 28.41 22.62 31.89 1.94
541 624 6.032094 CCTGTTTGAACTAATGCATGCTTAG 58.968 40.000 23.75 23.75 33.36 2.18
543 626 4.281688 ACCTGTTTGAACTAATGCATGCTT 59.718 37.500 20.33 10.16 0.00 3.91
547 630 4.406456 TGGACCTGTTTGAACTAATGCAT 58.594 39.130 0.00 0.00 0.00 3.96
603 686 1.512156 GGGTGCGTTCGGTTCACATT 61.512 55.000 0.00 0.00 32.69 2.71
630 713 3.706698 TCTCGGATGTGAATAAAGAGCG 58.293 45.455 0.00 0.00 0.00 5.03
658 741 9.046296 GGGGAAATTTTCTTTTCTCTTCTTTTC 57.954 33.333 8.93 0.00 36.51 2.29
660 743 8.324191 AGGGGAAATTTTCTTTTCTCTTCTTT 57.676 30.769 8.93 0.00 36.51 2.52
703 786 4.047125 ATGGGGGTGTGCGAAGGG 62.047 66.667 0.00 0.00 0.00 3.95
737 820 0.032540 GCAAGCAAGACCCCAAACTG 59.967 55.000 0.00 0.00 0.00 3.16
738 821 0.106015 AGCAAGCAAGACCCCAAACT 60.106 50.000 0.00 0.00 0.00 2.66
739 822 0.752658 AAGCAAGCAAGACCCCAAAC 59.247 50.000 0.00 0.00 0.00 2.93
740 823 0.752054 CAAGCAAGCAAGACCCCAAA 59.248 50.000 0.00 0.00 0.00 3.28
743 826 1.527433 GGACAAGCAAGCAAGACCCC 61.527 60.000 0.00 0.00 0.00 4.95
837 920 1.565156 TTGACAACGGCGCATCTGTC 61.565 55.000 21.36 21.36 38.91 3.51
844 927 2.535934 TGAATTATTGACAACGGCGC 57.464 45.000 6.90 0.00 0.00 6.53
1307 1394 4.838152 CATGTCCGCCCACTCCCG 62.838 72.222 0.00 0.00 0.00 5.14
1308 1395 4.489771 CCATGTCCGCCCACTCCC 62.490 72.222 0.00 0.00 0.00 4.30
1470 1557 1.144936 CCGATCCTCTTCACCAGGC 59.855 63.158 0.00 0.00 0.00 4.85
1580 1668 3.302415 GGCAAACGCAATTCAAAACTCAC 60.302 43.478 0.00 0.00 0.00 3.51
1584 1686 1.855360 TCGGCAAACGCAATTCAAAAC 59.145 42.857 0.00 0.00 43.86 2.43
1593 1696 2.593148 ATGGTGTCGGCAAACGCA 60.593 55.556 0.00 0.00 43.86 5.24
1639 1765 2.355513 GGATCTCTGCACACCTGTTCAT 60.356 50.000 0.00 0.00 0.00 2.57
2134 2272 2.393764 CACGAGTGCAATTGTTTTCCC 58.606 47.619 3.81 0.00 0.00 3.97
2163 2301 0.804989 GAGCAAGAATCCAACGGGTG 59.195 55.000 0.00 0.00 34.93 4.61
2164 2302 0.322546 GGAGCAAGAATCCAACGGGT 60.323 55.000 0.00 0.00 36.79 5.28
2165 2303 0.035056 AGGAGCAAGAATCCAACGGG 60.035 55.000 0.00 0.00 39.47 5.28
2167 2305 3.118956 AGACTAGGAGCAAGAATCCAACG 60.119 47.826 0.00 0.00 39.47 4.10
2168 2306 4.479786 AGACTAGGAGCAAGAATCCAAC 57.520 45.455 0.00 0.00 39.47 3.77
2170 2308 4.096681 TGAAGACTAGGAGCAAGAATCCA 58.903 43.478 0.00 0.00 39.47 3.41
2171 2309 4.404073 TCTGAAGACTAGGAGCAAGAATCC 59.596 45.833 0.00 0.00 37.07 3.01
2172 2310 5.590530 TCTGAAGACTAGGAGCAAGAATC 57.409 43.478 0.00 0.00 0.00 2.52
2182 2343 7.821359 TGAACATCTGAAAATCTGAAGACTAGG 59.179 37.037 0.00 0.00 0.00 3.02
2186 2363 7.272948 GCAATGAACATCTGAAAATCTGAAGAC 59.727 37.037 0.00 0.00 0.00 3.01
2196 2377 3.317711 ACAACGGCAATGAACATCTGAAA 59.682 39.130 0.00 0.00 0.00 2.69
2214 2395 0.867746 TGCAGTCAAGATGCGACAAC 59.132 50.000 0.00 0.00 46.87 3.32
2351 2537 0.402504 ACAGAGTCAGTCTCCCGTCT 59.597 55.000 0.00 0.00 43.71 4.18
2352 2538 0.523966 CACAGAGTCAGTCTCCCGTC 59.476 60.000 0.00 0.00 43.71 4.79
2353 2539 0.110678 TCACAGAGTCAGTCTCCCGT 59.889 55.000 0.00 0.00 43.71 5.28
2355 2541 2.094286 CACATCACAGAGTCAGTCTCCC 60.094 54.545 0.00 0.00 43.71 4.30
2356 2542 2.822561 TCACATCACAGAGTCAGTCTCC 59.177 50.000 0.00 0.00 43.71 3.71
2357 2543 4.511617 TTCACATCACAGAGTCAGTCTC 57.488 45.455 0.00 0.00 43.05 3.36
2358 2544 4.282957 ACATTCACATCACAGAGTCAGTCT 59.717 41.667 0.00 0.00 35.00 3.24
2359 2545 4.564041 ACATTCACATCACAGAGTCAGTC 58.436 43.478 0.00 0.00 0.00 3.51
2360 2546 4.613925 ACATTCACATCACAGAGTCAGT 57.386 40.909 0.00 0.00 0.00 3.41
2361 2547 5.575995 CACTACATTCACATCACAGAGTCAG 59.424 44.000 0.00 0.00 0.00 3.51
2365 2551 5.390251 GCAACACTACATTCACATCACAGAG 60.390 44.000 0.00 0.00 0.00 3.35
2367 2553 4.453478 AGCAACACTACATTCACATCACAG 59.547 41.667 0.00 0.00 0.00 3.66
2368 2554 4.388485 AGCAACACTACATTCACATCACA 58.612 39.130 0.00 0.00 0.00 3.58
2369 2555 5.149273 CAAGCAACACTACATTCACATCAC 58.851 41.667 0.00 0.00 0.00 3.06
2370 2556 4.320421 GCAAGCAACACTACATTCACATCA 60.320 41.667 0.00 0.00 0.00 3.07
2400 2599 3.753815 TGCAACATCAGGAGAAACATCA 58.246 40.909 0.00 0.00 0.00 3.07
2411 2626 2.223502 GCACCATGATCTGCAACATCAG 60.224 50.000 12.34 4.35 33.74 2.90
2614 2840 6.768483 TGAATTCAGTACCAGAGTTTCATCA 58.232 36.000 3.38 0.00 0.00 3.07
2627 2853 5.149977 GCAGCAACTTTCTGAATTCAGTAC 58.850 41.667 29.80 12.10 44.12 2.73
2629 2855 3.005155 GGCAGCAACTTTCTGAATTCAGT 59.995 43.478 29.80 12.96 44.12 3.41
2643 2869 1.160137 ATTCTGAAGTCGGCAGCAAC 58.840 50.000 0.00 0.00 33.45 4.17
2663 2889 4.586001 AGAATTCAGGAGCTCAAGCAAAAA 59.414 37.500 17.19 0.00 45.16 1.94
2664 2890 4.147321 AGAATTCAGGAGCTCAAGCAAAA 58.853 39.130 17.19 1.02 45.16 2.44
2666 2892 3.430042 AGAATTCAGGAGCTCAAGCAA 57.570 42.857 17.19 2.54 45.16 3.91
2668 2894 3.341823 TCAAGAATTCAGGAGCTCAAGC 58.658 45.455 17.19 0.00 42.49 4.01
2669 2895 6.512342 AAATCAAGAATTCAGGAGCTCAAG 57.488 37.500 17.19 7.20 0.00 3.02
2670 2896 7.067859 CCATAAATCAAGAATTCAGGAGCTCAA 59.932 37.037 17.19 1.16 0.00 3.02
2671 2897 6.544931 CCATAAATCAAGAATTCAGGAGCTCA 59.455 38.462 17.19 0.00 0.00 4.26
2672 2898 6.545298 ACCATAAATCAAGAATTCAGGAGCTC 59.455 38.462 4.71 4.71 0.00 4.09
2673 2899 6.320672 CACCATAAATCAAGAATTCAGGAGCT 59.679 38.462 8.44 0.00 0.00 4.09
2687 2930 4.220693 AGTAGCAGCACACCATAAATCA 57.779 40.909 0.00 0.00 0.00 2.57
2926 3190 3.822192 CGGCGTCGAGGATGGTGA 61.822 66.667 1.44 0.00 39.00 4.02
3010 3274 2.718073 TAGGAGAAGCCGCCGTTCC 61.718 63.158 0.00 0.00 43.43 3.62
3474 3834 2.738846 CTCCGTCTGGTGAAAAGTGATG 59.261 50.000 0.00 0.00 36.30 3.07
3475 3835 2.872038 GCTCCGTCTGGTGAAAAGTGAT 60.872 50.000 0.00 0.00 36.30 3.06
3595 3974 7.373617 TGAGGATACATTTACCATAGCTTCA 57.626 36.000 0.00 0.00 41.41 3.02
3689 4076 9.220906 AGTATGACCCTAAGTTTTATGATGGTA 57.779 33.333 0.00 0.00 0.00 3.25
3708 4095 1.829222 TGGGAACGAAGGGAGTATGAC 59.171 52.381 0.00 0.00 0.00 3.06
3711 4098 5.906772 ATATTTGGGAACGAAGGGAGTAT 57.093 39.130 0.00 0.00 37.08 2.12
3712 4099 6.384886 ACTTATATTTGGGAACGAAGGGAGTA 59.615 38.462 0.00 0.00 37.08 2.59
3713 4100 5.191124 ACTTATATTTGGGAACGAAGGGAGT 59.809 40.000 0.00 0.00 37.08 3.85
3714 4101 5.681639 ACTTATATTTGGGAACGAAGGGAG 58.318 41.667 0.00 0.00 37.08 4.30
3715 4102 5.190132 TGACTTATATTTGGGAACGAAGGGA 59.810 40.000 0.00 0.00 37.08 4.20
3716 4103 5.433526 TGACTTATATTTGGGAACGAAGGG 58.566 41.667 0.00 0.00 37.08 3.95
3717 4104 7.568199 AATGACTTATATTTGGGAACGAAGG 57.432 36.000 0.00 0.00 37.08 3.46
3720 4107 9.893634 TCTAAAATGACTTATATTTGGGAACGA 57.106 29.630 0.00 0.00 0.00 3.85
3744 4131 9.302345 CGTATGTAGTCACTTGTTGAAATATCT 57.698 33.333 0.00 0.00 35.39 1.98
3745 4132 9.297586 TCGTATGTAGTCACTTGTTGAAATATC 57.702 33.333 0.00 0.00 35.39 1.63
3746 4133 9.647797 TTCGTATGTAGTCACTTGTTGAAATAT 57.352 29.630 0.00 0.00 35.39 1.28
3747 4134 9.135843 CTTCGTATGTAGTCACTTGTTGAAATA 57.864 33.333 0.00 0.00 35.39 1.40
3748 4135 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
3749 4136 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
3750 4137 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
3751 4138 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
3752 4139 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
3753 4140 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3754 4141 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3755 4142 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3756 4143 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3757 4144 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3758 4145 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3759 4146 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
3760 4147 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3761 4148 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3762 4149 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3763 4150 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3764 4151 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
3765 4152 6.685828 CAGATTCACTCATTTTGCTTCGTATG 59.314 38.462 0.00 0.00 0.00 2.39
3766 4153 6.676456 GCAGATTCACTCATTTTGCTTCGTAT 60.676 38.462 0.00 0.00 0.00 3.06
3767 4154 5.390885 GCAGATTCACTCATTTTGCTTCGTA 60.391 40.000 0.00 0.00 0.00 3.43
3768 4155 4.614535 GCAGATTCACTCATTTTGCTTCGT 60.615 41.667 0.00 0.00 0.00 3.85
3769 4156 3.850273 GCAGATTCACTCATTTTGCTTCG 59.150 43.478 0.00 0.00 0.00 3.79
3770 4157 4.620184 GTGCAGATTCACTCATTTTGCTTC 59.380 41.667 0.00 0.00 34.29 3.86
3771 4158 4.280174 AGTGCAGATTCACTCATTTTGCTT 59.720 37.500 0.00 0.00 43.28 3.91
3772 4159 3.825014 AGTGCAGATTCACTCATTTTGCT 59.175 39.130 0.00 0.00 43.28 3.91
3773 4160 4.170292 AGTGCAGATTCACTCATTTTGC 57.830 40.909 0.00 0.00 43.28 3.68
3782 4169 8.430801 AGACATATTTTAGAGTGCAGATTCAC 57.569 34.615 0.00 0.00 37.24 3.18
3783 4170 9.534565 GTAGACATATTTTAGAGTGCAGATTCA 57.465 33.333 0.00 0.00 0.00 2.57
3784 4171 9.534565 TGTAGACATATTTTAGAGTGCAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
3787 4174 9.967346 GTATGTAGACATATTTTAGAGTGCAGA 57.033 33.333 5.69 0.00 40.53 4.26
3788 4175 9.750125 TGTATGTAGACATATTTTAGAGTGCAG 57.250 33.333 5.69 0.00 40.53 4.41
3810 4197 6.665992 ATGGACTACAACATACGGATGTAT 57.334 37.500 15.10 8.21 45.93 2.29
3811 4198 6.474140 AATGGACTACAACATACGGATGTA 57.526 37.500 15.10 0.00 45.93 2.29
3813 4200 5.815222 TCAAATGGACTACAACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
3814 4201 5.984725 TCAAATGGACTACAACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
3815 4202 5.408880 TCAAATGGACTACAACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
3816 4203 6.489127 TTTCAAATGGACTACAACATACGG 57.511 37.500 0.00 0.00 0.00 4.02
3817 4204 6.468956 GCATTTCAAATGGACTACAACATACG 59.531 38.462 12.14 0.00 0.00 3.06
3818 4205 6.751888 GGCATTTCAAATGGACTACAACATAC 59.248 38.462 12.14 0.00 0.00 2.39
3819 4206 6.663093 AGGCATTTCAAATGGACTACAACATA 59.337 34.615 12.14 0.00 0.00 2.29
3820 4207 5.481473 AGGCATTTCAAATGGACTACAACAT 59.519 36.000 12.14 0.00 0.00 2.71
3821 4208 4.832266 AGGCATTTCAAATGGACTACAACA 59.168 37.500 12.14 0.00 0.00 3.33
3822 4209 5.391312 AGGCATTTCAAATGGACTACAAC 57.609 39.130 12.14 0.00 0.00 3.32
3823 4210 7.531857 TTTAGGCATTTCAAATGGACTACAA 57.468 32.000 12.14 1.11 0.00 2.41
3824 4211 7.531857 TTTTAGGCATTTCAAATGGACTACA 57.468 32.000 12.14 0.00 0.00 2.74
3825 4212 8.303876 TCTTTTTAGGCATTTCAAATGGACTAC 58.696 33.333 12.14 0.00 0.00 2.73
3826 4213 8.303876 GTCTTTTTAGGCATTTCAAATGGACTA 58.696 33.333 12.14 2.16 0.00 2.59
3827 4214 7.015584 AGTCTTTTTAGGCATTTCAAATGGACT 59.984 33.333 12.14 9.71 0.00 3.85
3828 4215 7.154656 AGTCTTTTTAGGCATTTCAAATGGAC 58.845 34.615 12.14 7.77 0.00 4.02
3829 4216 7.301868 AGTCTTTTTAGGCATTTCAAATGGA 57.698 32.000 12.14 0.00 0.00 3.41
3830 4217 7.967890 AAGTCTTTTTAGGCATTTCAAATGG 57.032 32.000 12.14 0.00 0.00 3.16
3849 4236 9.890915 ACTCTCTCCATTCCTAAATATAAGTCT 57.109 33.333 0.00 0.00 0.00 3.24
3860 4247 9.877222 TGTAACAATATACTCTCTCCATTCCTA 57.123 33.333 0.00 0.00 0.00 2.94
3861 4248 8.783660 TGTAACAATATACTCTCTCCATTCCT 57.216 34.615 0.00 0.00 0.00 3.36
3862 4249 9.482627 CTTGTAACAATATACTCTCTCCATTCC 57.517 37.037 0.00 0.00 0.00 3.01
3864 4251 9.823647 CACTTGTAACAATATACTCTCTCCATT 57.176 33.333 0.00 0.00 0.00 3.16
3865 4252 9.201989 TCACTTGTAACAATATACTCTCTCCAT 57.798 33.333 0.00 0.00 0.00 3.41
3866 4253 8.589701 TCACTTGTAACAATATACTCTCTCCA 57.410 34.615 0.00 0.00 0.00 3.86
3867 4254 9.871238 TTTCACTTGTAACAATATACTCTCTCC 57.129 33.333 0.00 0.00 0.00 3.71
3975 5512 5.803552 TGTATGAATGTGTGTGATCCTTCA 58.196 37.500 0.00 0.00 0.00 3.02
3979 5516 5.819379 ACATCTGTATGAATGTGTGTGATCC 59.181 40.000 0.00 0.00 36.54 3.36
4216 5816 2.284151 GGGAGGGAGGGAGGAGAC 59.716 72.222 0.00 0.00 0.00 3.36
4256 5876 2.034221 GCGACAAGGAAAGGGGCT 59.966 61.111 0.00 0.00 0.00 5.19
4332 5952 2.476499 GCGACTGCGAAAGGAAGC 59.524 61.111 0.00 0.00 40.82 3.86
4356 6755 1.216977 CAGGACACCCGTGCGAATA 59.783 57.895 0.00 0.00 38.75 1.75
4365 6764 1.227853 ACGTCAAAGCAGGACACCC 60.228 57.895 3.81 0.00 34.97 4.61
4390 6790 2.813908 GTGCCACTAACGCCGGAG 60.814 66.667 5.05 3.72 0.00 4.63
4399 6799 0.320050 TCTGCATCGTTGTGCCACTA 59.680 50.000 0.00 0.00 44.43 2.74
4400 6800 0.321919 ATCTGCATCGTTGTGCCACT 60.322 50.000 0.00 0.00 44.43 4.00
4406 6806 2.002586 CGGAAGAATCTGCATCGTTGT 58.997 47.619 0.00 0.00 0.00 3.32
4416 6816 2.014857 TCATCGACGACGGAAGAATCT 58.985 47.619 7.55 0.00 40.21 2.40
4427 6827 1.313091 CCTGGGTGAGTCATCGACGA 61.313 60.000 0.00 0.00 37.67 4.20
4460 6860 3.991051 AGCGGTGTCACGACCCAG 61.991 66.667 0.00 0.00 35.47 4.45
4461 6861 4.293648 CAGCGGTGTCACGACCCA 62.294 66.667 6.41 0.00 35.47 4.51
4531 6931 1.264749 CCTCCTCCACCGTCATCCAA 61.265 60.000 0.00 0.00 0.00 3.53
4539 6939 1.381872 ACCAGATCCTCCTCCACCG 60.382 63.158 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.