Multiple sequence alignment - TraesCS5B01G467700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G467700 chr5B 100.000 5890 0 0 1 5890 641405433 641399544 0.000000e+00 10877.0
1 TraesCS5B01G467700 chr5B 77.701 1157 204 35 3744 4879 641412979 641411856 0.000000e+00 658.0
2 TraesCS5B01G467700 chr5B 77.661 1137 200 30 3761 4879 641805368 641806468 1.380000e-180 643.0
3 TraesCS5B01G467700 chr5B 76.716 1151 220 33 3744 4879 641428270 641427153 1.090000e-166 597.0
4 TraesCS5B01G467700 chr5B 85.687 524 68 5 3745 4263 641161450 641160929 4.010000e-151 545.0
5 TraesCS5B01G467700 chr5B 84.596 396 41 6 338 713 641412980 641412585 5.570000e-100 375.0
6 TraesCS5B01G467700 chr5B 82.500 400 44 13 337 713 641805349 641805745 1.580000e-85 327.0
7 TraesCS5B01G467700 chr5B 80.442 317 46 12 2818 3123 641413771 641413460 1.650000e-55 228.0
8 TraesCS5B01G467700 chr5B 84.277 159 20 3 797 950 576865353 576865511 3.680000e-32 150.0
9 TraesCS5B01G467700 chr5B 90.541 74 2 1 1557 1625 641400222 641400149 6.280000e-15 93.5
10 TraesCS5B01G467700 chr5B 90.541 74 2 1 5212 5285 641403877 641403809 6.280000e-15 93.5
11 TraesCS5B01G467700 chr5D 95.431 2364 88 9 3280 5636 510389497 510387147 0.000000e+00 3749.0
12 TraesCS5B01G467700 chr5D 95.282 2374 72 18 3280 5648 510626786 510624448 0.000000e+00 3727.0
13 TraesCS5B01G467700 chr5D 96.680 1205 33 5 2055 3253 510628081 510626878 0.000000e+00 1997.0
14 TraesCS5B01G467700 chr5D 95.120 1209 49 7 2054 3253 510494231 510493024 0.000000e+00 1897.0
15 TraesCS5B01G467700 chr5D 83.945 1881 234 33 3280 5113 510492919 510491060 0.000000e+00 1738.0
16 TraesCS5B01G467700 chr5D 89.140 1105 81 16 497 1575 510496100 510495009 0.000000e+00 1339.0
17 TraesCS5B01G467700 chr5D 94.489 871 37 4 2387 3253 510390464 510389601 0.000000e+00 1332.0
18 TraesCS5B01G467700 chr5D 86.022 1023 125 12 4272 5287 510407666 510406655 0.000000e+00 1081.0
19 TraesCS5B01G467700 chr5D 86.108 799 72 17 594 1360 510629813 510629022 0.000000e+00 824.0
20 TraesCS5B01G467700 chr5D 92.756 566 39 2 10 573 510406144 510405579 0.000000e+00 817.0
21 TraesCS5B01G467700 chr5D 89.952 627 37 14 1101 1714 510405506 510404893 0.000000e+00 785.0
22 TraesCS5B01G467700 chr5D 94.389 499 21 4 10 501 510504059 510503561 0.000000e+00 760.0
23 TraesCS5B01G467700 chr5D 90.240 584 40 10 1 573 510631026 510630449 0.000000e+00 747.0
24 TraesCS5B01G467700 chr5D 80.709 959 156 21 3744 4679 510353960 510353008 0.000000e+00 719.0
25 TraesCS5B01G467700 chr5D 76.832 1269 231 40 3761 5011 510904586 510905809 0.000000e+00 656.0
26 TraesCS5B01G467700 chr5D 75.589 1274 236 51 3763 5011 510465992 510464769 1.430000e-155 560.0
27 TraesCS5B01G467700 chr5D 95.677 347 14 1 1714 2059 510404850 510404504 1.850000e-154 556.0
28 TraesCS5B01G467700 chr5D 95.362 345 15 1 1714 2058 510494705 510494362 1.120000e-151 547.0
29 TraesCS5B01G467700 chr5D 74.826 1291 248 52 3745 5007 510599630 510598389 4.070000e-141 512.0
30 TraesCS5B01G467700 chr5D 93.275 342 15 4 2055 2389 510404370 510404030 1.140000e-136 497.0
31 TraesCS5B01G467700 chr5D 89.000 400 41 2 3744 4140 510440172 510439773 5.300000e-135 492.0
32 TraesCS5B01G467700 chr5D 92.733 344 14 3 1357 1698 510628990 510628656 2.470000e-133 486.0
33 TraesCS5B01G467700 chr5D 90.435 345 12 1 1714 2058 510628539 510628216 9.060000e-118 435.0
34 TraesCS5B01G467700 chr5D 82.000 400 46 13 337 713 510904567 510904963 3.430000e-82 316.0
35 TraesCS5B01G467700 chr5D 88.406 207 23 1 5674 5880 510624453 510624248 1.270000e-61 248.0
36 TraesCS5B01G467700 chr5D 95.946 148 3 2 1567 1714 510494892 510494748 2.740000e-58 237.0
37 TraesCS5B01G467700 chr5D 92.079 101 7 1 5698 5798 510369836 510369737 2.210000e-29 141.0
38 TraesCS5B01G467700 chr5D 100.000 45 0 0 1654 1698 510405011 510404967 3.780000e-12 84.2
39 TraesCS5B01G467700 chr5D 90.164 61 1 1 5212 5272 510405061 510405006 2.280000e-09 75.0
40 TraesCS5B01G467700 chr5A 94.615 1207 53 11 2054 3253 638764966 638763765 0.000000e+00 1858.0
41 TraesCS5B01G467700 chr5A 83.998 1881 231 34 3280 5113 638763660 638761803 0.000000e+00 1742.0
42 TraesCS5B01G467700 chr5A 88.558 1276 105 21 10 1257 638807218 638805956 0.000000e+00 1509.0
43 TraesCS5B01G467700 chr5A 77.768 1138 197 33 3761 4879 639098444 639099544 0.000000e+00 649.0
44 TraesCS5B01G467700 chr5A 77.257 1152 205 34 3746 4879 638812425 638811313 1.800000e-174 623.0
45 TraesCS5B01G467700 chr5A 94.783 345 17 1 1714 2058 638790596 638790253 2.420000e-148 536.0
46 TraesCS5B01G467700 chr5A 91.520 342 17 4 1357 1698 638791042 638790713 1.500000e-125 460.0
47 TraesCS5B01G467700 chr5A 83.249 394 44 9 341 713 638812425 638812033 5.650000e-90 342.0
48 TraesCS5B01G467700 chr5A 82.368 397 50 7 337 713 639098425 639098821 1.580000e-85 327.0
49 TraesCS5B01G467700 chr5A 77.193 627 99 26 3763 4373 638641832 638641234 5.690000e-85 326.0
50 TraesCS5B01G467700 chr5A 94.444 108 6 0 1253 1360 638791181 638791074 3.650000e-37 167.0
51 TraesCS5B01G467700 chr7B 84.277 159 20 3 797 950 657424988 657425146 3.680000e-32 150.0
52 TraesCS5B01G467700 chr7B 79.245 159 26 5 797 949 702228550 702228393 2.900000e-18 104.0
53 TraesCS5B01G467700 chr4A 84.277 159 20 3 797 950 718820025 718820183 3.680000e-32 150.0
54 TraesCS5B01G467700 chr2A 83.333 162 22 3 797 953 761542428 761542267 1.710000e-30 145.0
55 TraesCS5B01G467700 chr2A 80.892 157 25 3 797 948 623336019 623336175 1.040000e-22 119.0


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 TraesCS5B01G467700 chr5B 641399544 641405433 5889 True 10877.000000 10877 100.000000 1 5890 1 chr5B.!!$R2 5889
1 TraesCS5B01G467700 chr5B 641427153 641428270 1117 True 597.000000 597 76.716000 3744 4879 1 chr5B.!!$R3 1135
2 TraesCS5B01G467700 chr5B 641160929 641161450 521 True 545.000000 545 85.687000 3745 4263 1 chr5B.!!$R1 518
3 TraesCS5B01G467700 chr5B 641805349 641806468 1119 False 485.000000 643 80.080500 337 4879 2 chr5B.!!$F2 4542
4 TraesCS5B01G467700 chr5B 641411856 641413771 1915 True 420.333333 658 80.913000 338 4879 3 chr5B.!!$R5 4541
5 TraesCS5B01G467700 chr5D 510387147 510390464 3317 True 2540.500000 3749 94.960000 2387 5636 2 chr5D.!!$R7 3249
6 TraesCS5B01G467700 chr5D 510624248 510631026 6778 True 1209.142857 3727 91.412000 1 5880 7 chr5D.!!$R10 5879
7 TraesCS5B01G467700 chr5D 510491060 510496100 5040 True 1151.600000 1897 91.902600 497 5113 5 chr5D.!!$R9 4616
8 TraesCS5B01G467700 chr5D 510353008 510353960 952 True 719.000000 719 80.709000 3744 4679 1 chr5D.!!$R1 935
9 TraesCS5B01G467700 chr5D 510464769 510465992 1223 True 560.000000 560 75.589000 3763 5011 1 chr5D.!!$R4 1248
10 TraesCS5B01G467700 chr5D 510404030 510407666 3636 True 556.457143 1081 92.549429 10 5287 7 chr5D.!!$R8 5277
11 TraesCS5B01G467700 chr5D 510598389 510599630 1241 True 512.000000 512 74.826000 3745 5007 1 chr5D.!!$R6 1262
12 TraesCS5B01G467700 chr5D 510904567 510905809 1242 False 486.000000 656 79.416000 337 5011 2 chr5D.!!$F1 4674
13 TraesCS5B01G467700 chr5A 638761803 638764966 3163 True 1800.000000 1858 89.306500 2054 5113 2 chr5A.!!$R3 3059
14 TraesCS5B01G467700 chr5A 638805956 638807218 1262 True 1509.000000 1509 88.558000 10 1257 1 chr5A.!!$R2 1247
15 TraesCS5B01G467700 chr5A 639098425 639099544 1119 False 488.000000 649 80.068000 337 4879 2 chr5A.!!$F1 4542
16 TraesCS5B01G467700 chr5A 638811313 638812425 1112 True 482.500000 623 80.253000 341 4879 2 chr5A.!!$R5 4538
17 TraesCS5B01G467700 chr5A 638790253 638791181 928 True 387.666667 536 93.582333 1253 2058 3 chr5A.!!$R4 805
18 TraesCS5B01G467700 chr5A 638641234 638641832 598 True 326.000000 326 77.193000 3763 4373 1 chr5A.!!$R1 610

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
495 2011 0.035915 GCTCCCAAGAACTCCTGTCC 60.036 60.0 0.00 0.00 0.00 4.02 F
1011 2552 0.035630 AGGTTGTCATGAGCTCCTGC 60.036 55.0 12.15 8.63 40.05 4.85 F
1322 2864 0.899720 GGTAGGGGATGTCACGAACA 59.100 55.0 0.00 0.00 43.51 3.18 F
2953 4899 0.608856 ATGCCGCATGTTTGTCCTCA 60.609 50.0 4.68 0.00 0.00 3.86 F
3225 5187 0.600557 CTGTCTCAGCTTCTCACGGT 59.399 55.0 0.00 0.00 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 3050 0.393820 ACCGGCCGAAAAGACAAGTA 59.606 50.000 30.73 0.00 0.00 2.24 R
2889 4835 1.510480 GGGAGCTCACCGCATAATGC 61.510 60.000 17.19 0.00 42.61 3.56 R
3194 5156 1.813178 CTGAGACAGGTGCTAACTCGA 59.187 52.381 0.00 0.00 0.00 4.04 R
4183 10817 4.362932 TCGAAACACAACTCAAATGCAA 57.637 36.364 0.00 0.00 0.00 4.08 R
5148 12032 2.675348 TGTGCGCACGATATTCATTCAA 59.325 40.909 33.22 10.12 0.00 2.69 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
43 1559 7.033185 GTCATGGTTTTTAGTGTGAAAGTTGT 58.967 34.615 0.00 0.00 0.00 3.32
182 1698 5.239087 TCCGGTTAATCGTTAAATTATGGGC 59.761 40.000 7.46 0.00 0.00 5.36
187 1703 8.303876 GGTTAATCGTTAAATTATGGGCATCAT 58.696 33.333 0.00 0.00 39.78 2.45
205 1721 6.037610 GGCATCATTACTTCTTGTAGTTCTGG 59.962 42.308 0.00 0.00 32.08 3.86
220 1736 9.485206 TTGTAGTTCTGGATAAACACTAAGTTC 57.515 33.333 0.00 0.00 40.26 3.01
320 1836 8.067189 GTGTTTTCAACAACAACAAAAACTCAT 58.933 29.630 9.56 0.00 44.16 2.90
352 1868 3.309121 CCTTGTTAGGGGATGACCACAAT 60.309 47.826 0.00 0.00 43.15 2.71
353 1869 4.344104 CTTGTTAGGGGATGACCACAATT 58.656 43.478 0.00 0.00 43.15 2.32
415 1931 1.243902 CCGCTTAAGTCCTTTTGCCA 58.756 50.000 4.02 0.00 0.00 4.92
419 1935 3.920412 CGCTTAAGTCCTTTTGCCATTTC 59.080 43.478 4.02 0.00 0.00 2.17
420 1936 4.558496 CGCTTAAGTCCTTTTGCCATTTCA 60.558 41.667 4.02 0.00 0.00 2.69
421 1937 4.925646 GCTTAAGTCCTTTTGCCATTTCAG 59.074 41.667 4.02 0.00 0.00 3.02
422 1938 5.278957 GCTTAAGTCCTTTTGCCATTTCAGA 60.279 40.000 4.02 0.00 0.00 3.27
463 1979 0.105593 GCCTTCTCATCTGATCCGCA 59.894 55.000 0.00 0.00 0.00 5.69
464 1980 1.863267 CCTTCTCATCTGATCCGCAC 58.137 55.000 0.00 0.00 0.00 5.34
465 1981 1.411977 CCTTCTCATCTGATCCGCACT 59.588 52.381 0.00 0.00 0.00 4.40
466 1982 2.625314 CCTTCTCATCTGATCCGCACTA 59.375 50.000 0.00 0.00 0.00 2.74
467 1983 3.551863 CCTTCTCATCTGATCCGCACTAC 60.552 52.174 0.00 0.00 0.00 2.73
468 1984 1.957177 TCTCATCTGATCCGCACTACC 59.043 52.381 0.00 0.00 0.00 3.18
469 1985 0.668535 TCATCTGATCCGCACTACCG 59.331 55.000 0.00 0.00 0.00 4.02
470 1986 0.941463 CATCTGATCCGCACTACCGC 60.941 60.000 0.00 0.00 0.00 5.68
471 1987 2.088674 ATCTGATCCGCACTACCGCC 62.089 60.000 0.00 0.00 0.00 6.13
472 1988 3.071837 TGATCCGCACTACCGCCA 61.072 61.111 0.00 0.00 0.00 5.69
473 1989 2.279517 GATCCGCACTACCGCCAG 60.280 66.667 0.00 0.00 0.00 4.85
474 1990 2.758327 ATCCGCACTACCGCCAGA 60.758 61.111 0.00 0.00 0.00 3.86
475 1991 2.292794 GATCCGCACTACCGCCAGAA 62.293 60.000 0.00 0.00 0.00 3.02
476 1992 2.298158 ATCCGCACTACCGCCAGAAG 62.298 60.000 0.00 0.00 0.00 2.85
477 1993 3.188786 CGCACTACCGCCAGAAGC 61.189 66.667 0.00 0.00 38.52 3.86
478 1994 2.266055 GCACTACCGCCAGAAGCT 59.734 61.111 0.00 0.00 40.39 3.74
479 1995 1.811679 GCACTACCGCCAGAAGCTC 60.812 63.158 0.00 0.00 40.39 4.09
480 1996 1.153549 CACTACCGCCAGAAGCTCC 60.154 63.158 0.00 0.00 40.39 4.70
481 1997 2.359967 ACTACCGCCAGAAGCTCCC 61.360 63.158 0.00 0.00 40.39 4.30
482 1998 2.284331 TACCGCCAGAAGCTCCCA 60.284 61.111 0.00 0.00 40.39 4.37
483 1999 1.899437 CTACCGCCAGAAGCTCCCAA 61.899 60.000 0.00 0.00 40.39 4.12
484 2000 1.899437 TACCGCCAGAAGCTCCCAAG 61.899 60.000 0.00 0.00 40.39 3.61
485 2001 2.665000 CGCCAGAAGCTCCCAAGA 59.335 61.111 0.00 0.00 40.39 3.02
486 2002 1.003355 CGCCAGAAGCTCCCAAGAA 60.003 57.895 0.00 0.00 40.39 2.52
487 2003 1.301677 CGCCAGAAGCTCCCAAGAAC 61.302 60.000 0.00 0.00 40.39 3.01
488 2004 0.037447 GCCAGAAGCTCCCAAGAACT 59.963 55.000 0.00 0.00 38.99 3.01
489 2005 1.948144 GCCAGAAGCTCCCAAGAACTC 60.948 57.143 0.00 0.00 38.99 3.01
490 2006 1.339535 CCAGAAGCTCCCAAGAACTCC 60.340 57.143 0.00 0.00 0.00 3.85
491 2007 1.627834 CAGAAGCTCCCAAGAACTCCT 59.372 52.381 0.00 0.00 0.00 3.69
492 2008 1.627834 AGAAGCTCCCAAGAACTCCTG 59.372 52.381 0.00 0.00 0.00 3.86
493 2009 1.349357 GAAGCTCCCAAGAACTCCTGT 59.651 52.381 0.00 0.00 0.00 4.00
494 2010 0.980423 AGCTCCCAAGAACTCCTGTC 59.020 55.000 0.00 0.00 0.00 3.51
495 2011 0.035915 GCTCCCAAGAACTCCTGTCC 60.036 60.000 0.00 0.00 0.00 4.02
573 2089 6.537453 CCTCGAGTGATAGGGATATTGATT 57.463 41.667 12.31 0.00 0.00 2.57
574 2090 6.940739 CCTCGAGTGATAGGGATATTGATTT 58.059 40.000 12.31 0.00 0.00 2.17
575 2091 7.390027 CCTCGAGTGATAGGGATATTGATTTT 58.610 38.462 12.31 0.00 0.00 1.82
576 2092 7.332926 CCTCGAGTGATAGGGATATTGATTTTG 59.667 40.741 12.31 0.00 0.00 2.44
578 2094 7.657354 TCGAGTGATAGGGATATTGATTTTGTG 59.343 37.037 0.00 0.00 0.00 3.33
581 2097 8.439971 AGTGATAGGGATATTGATTTTGTGCTA 58.560 33.333 0.00 0.00 0.00 3.49
582 2098 9.236006 GTGATAGGGATATTGATTTTGTGCTAT 57.764 33.333 0.00 0.00 0.00 2.97
584 2100 9.236006 GATAGGGATATTGATTTTGTGCTATGT 57.764 33.333 0.00 0.00 0.00 2.29
586 2102 7.719483 AGGGATATTGATTTTGTGCTATGTTG 58.281 34.615 0.00 0.00 0.00 3.33
587 2103 7.560991 AGGGATATTGATTTTGTGCTATGTTGA 59.439 33.333 0.00 0.00 0.00 3.18
588 2104 8.362639 GGGATATTGATTTTGTGCTATGTTGAT 58.637 33.333 0.00 0.00 0.00 2.57
589 2105 9.403110 GGATATTGATTTTGTGCTATGTTGATC 57.597 33.333 0.00 0.00 0.00 2.92
592 2108 7.451501 TTGATTTTGTGCTATGTTGATCTCA 57.548 32.000 0.00 0.00 0.00 3.27
599 2135 6.172630 TGTGCTATGTTGATCTCAAGCTTAA 58.827 36.000 0.00 0.00 36.39 1.85
605 2141 6.605471 TGTTGATCTCAAGCTTAAGGACTA 57.395 37.500 0.00 0.00 36.39 2.59
608 2144 6.605471 TGATCTCAAGCTTAAGGACTACAA 57.395 37.500 0.00 0.00 0.00 2.41
609 2145 6.398918 TGATCTCAAGCTTAAGGACTACAAC 58.601 40.000 0.00 0.00 0.00 3.32
635 2171 6.757897 TGGCCTACTTCTTTGTTATCATTG 57.242 37.500 3.32 0.00 0.00 2.82
701 2237 4.074970 CCAGCAACTAAAGAGTGGATTGT 58.925 43.478 0.00 0.00 35.52 2.71
717 2253 6.543831 AGTGGATTGTACTTCCAGATATTTGC 59.456 38.462 15.72 4.96 43.78 3.68
718 2254 6.543831 GTGGATTGTACTTCCAGATATTTGCT 59.456 38.462 15.72 0.00 43.78 3.91
724 2260 6.818644 TGTACTTCCAGATATTTGCTGTTCTC 59.181 38.462 0.00 0.00 0.00 2.87
746 2282 9.513906 TTCTCAGGTTGTGTTTTGATCATTATA 57.486 29.630 0.00 0.00 0.00 0.98
747 2283 9.166173 TCTCAGGTTGTGTTTTGATCATTATAG 57.834 33.333 0.00 0.00 0.00 1.31
753 2289 9.979270 GTTGTGTTTTGATCATTATAGTCTCAG 57.021 33.333 0.00 0.00 0.00 3.35
767 2303 4.717233 AGTCTCAGCACTTCTATGTCTG 57.283 45.455 0.00 0.00 0.00 3.51
768 2304 3.119173 AGTCTCAGCACTTCTATGTCTGC 60.119 47.826 0.00 0.00 0.00 4.26
773 2309 5.005740 TCAGCACTTCTATGTCTGCAAATT 58.994 37.500 0.00 0.00 31.71 1.82
778 2314 6.348786 GCACTTCTATGTCTGCAAATTTGAGA 60.349 38.462 22.31 16.86 0.00 3.27
779 2315 7.627939 GCACTTCTATGTCTGCAAATTTGAGAT 60.628 37.037 22.31 7.68 0.00 2.75
793 2329 7.632245 GCAAATTTGAGATAATCTTGAGCCCTT 60.632 37.037 22.31 0.00 0.00 3.95
813 2350 0.326238 ATAGGGTGGACATGGTCGGT 60.326 55.000 0.00 0.00 32.65 4.69
856 2393 2.047655 CGTTTGGACTGGCCGCTA 60.048 61.111 0.00 0.00 40.66 4.26
878 2415 4.570663 GCTGGATCGGACCGGACG 62.571 72.222 15.25 13.27 38.49 4.79
888 2425 1.978617 GACCGGACGGACCAACCTA 60.979 63.158 18.80 0.00 38.90 3.08
891 2428 2.183555 GGACGGACCAACCTAGCG 59.816 66.667 0.00 0.00 38.79 4.26
902 2439 1.804748 CAACCTAGCGGTCCTGTTTTC 59.195 52.381 0.00 0.00 44.73 2.29
918 2455 4.631740 TCAGGGACCGGACCAGCA 62.632 66.667 24.44 4.11 0.00 4.41
920 2457 2.852075 AGGGACCGGACCAGCAAA 60.852 61.111 24.44 0.00 0.00 3.68
1011 2552 0.035630 AGGTTGTCATGAGCTCCTGC 60.036 55.000 12.15 8.63 40.05 4.85
1014 2555 3.260483 GTCATGAGCTCCTGCGCG 61.260 66.667 12.15 0.00 45.42 6.86
1040 2581 2.659610 GAGGCACAGGAACGAGCT 59.340 61.111 0.00 0.00 0.00 4.09
1066 2607 2.587753 CACGAACGGCACACCAGT 60.588 61.111 0.00 0.00 34.57 4.00
1121 2663 2.375766 GGCAGAAGCTCACGACACG 61.376 63.158 0.00 0.00 41.70 4.49
1124 2666 1.004277 CAGAAGCTCACGACACGTCC 61.004 60.000 0.00 0.00 38.32 4.79
1150 2692 2.288825 CGAGACCTTGTGCACCTCTTTA 60.289 50.000 15.69 0.00 0.00 1.85
1234 2776 2.065899 ACTTTTGTGTGCCAGCCTTA 57.934 45.000 0.00 0.00 0.00 2.69
1246 2788 4.755123 GTGCCAGCCTTACGTGATTATTAT 59.245 41.667 0.00 0.00 0.00 1.28
1305 2847 1.078848 GACGCAGAAGCTGGATGGT 60.079 57.895 0.00 0.00 39.10 3.55
1322 2864 0.899720 GGTAGGGGATGTCACGAACA 59.100 55.000 0.00 0.00 43.51 3.18
1368 2945 2.744741 GCTCTCTCTGTTTTAGGCAACC 59.255 50.000 0.00 0.00 37.17 3.77
1394 2971 8.177322 GAATTCCTATTCCTATGGGCCTTCCA 62.177 46.154 4.53 0.00 40.96 3.53
1466 3043 4.841443 TCGTGTGAACTGTATGTAGTGT 57.159 40.909 0.00 0.00 0.00 3.55
1467 3044 5.945466 TCGTGTGAACTGTATGTAGTGTA 57.055 39.130 0.00 0.00 0.00 2.90
1468 3045 6.505044 TCGTGTGAACTGTATGTAGTGTAT 57.495 37.500 0.00 0.00 0.00 2.29
1469 3046 6.319399 TCGTGTGAACTGTATGTAGTGTATG 58.681 40.000 0.00 0.00 0.00 2.39
1470 3047 6.072342 TCGTGTGAACTGTATGTAGTGTATGT 60.072 38.462 0.00 0.00 0.00 2.29
1471 3048 7.119553 TCGTGTGAACTGTATGTAGTGTATGTA 59.880 37.037 0.00 0.00 0.00 2.29
1472 3049 7.428472 CGTGTGAACTGTATGTAGTGTATGTAG 59.572 40.741 0.00 0.00 0.00 2.74
1473 3050 8.242053 GTGTGAACTGTATGTAGTGTATGTAGT 58.758 37.037 0.00 0.00 0.00 2.73
1604 3305 2.033675 TGTGACTGTTTCAATGCTGCTG 59.966 45.455 0.00 0.00 35.39 4.41
1676 3377 2.485814 GCAGTCCATCTTTGACTTGTCC 59.514 50.000 0.00 0.00 41.02 4.02
1777 3579 5.407387 GTCTGTTTAAACATAGGAGCGTCAA 59.593 40.000 20.83 0.00 38.41 3.18
1795 3597 2.682856 TCAACTGTTCAACTTCTGTGGC 59.317 45.455 0.00 0.00 0.00 5.01
1831 3633 2.704190 AGAAGGTTGGAGTCTCCTGA 57.296 50.000 19.82 5.98 37.46 3.86
1898 3700 4.154918 CCGAAAATTACTTCAAGCTCTGCT 59.845 41.667 0.00 0.00 42.56 4.24
1946 3748 3.807209 GCCAAAGCTCAAGGAGAGTAACA 60.807 47.826 3.44 0.00 46.47 2.41
2029 3831 2.412089 CCAAGGACTTAAACTTCGAGCG 59.588 50.000 0.00 0.00 0.00 5.03
2035 3837 6.338937 AGGACTTAAACTTCGAGCGAATATT 58.661 36.000 5.73 6.95 33.28 1.28
2045 3847 6.253727 ACTTCGAGCGAATATTGTAGTCTTTG 59.746 38.462 5.73 0.00 33.28 2.77
2134 4073 6.216456 ACCCCTCTTGATATCTTTGAGACTTT 59.784 38.462 16.27 2.34 0.00 2.66
2201 4142 5.123186 TGTGCATAGGTTGTTTACTGCATAC 59.877 40.000 0.00 0.00 41.17 2.39
2231 4172 7.227711 TGAACGAGATTTTGTAAATGACTCCAA 59.772 33.333 0.00 0.00 0.00 3.53
2487 4431 6.239396 TGTTACAACGATAGGGATCCAAAAA 58.761 36.000 15.23 0.00 43.77 1.94
2708 4654 8.728596 TTTCCCTTATCCCTTTATCTCTAGAG 57.271 38.462 13.98 13.98 0.00 2.43
2763 4709 6.058553 TGATTCAGATTCAACACATCCTCT 57.941 37.500 0.00 0.00 0.00 3.69
2844 4790 2.358737 CCTCCGCAGCCTCGTTTT 60.359 61.111 0.00 0.00 0.00 2.43
2889 4835 1.515736 GCCGACGACCCGAAGTAAG 60.516 63.158 0.00 0.00 0.00 2.34
2895 4841 3.714391 GACGACCCGAAGTAAGCATTAT 58.286 45.455 0.00 0.00 30.46 1.28
2953 4899 0.608856 ATGCCGCATGTTTGTCCTCA 60.609 50.000 4.68 0.00 0.00 3.86
3191 5153 2.041620 TCTTGACTTGCCCTGGCTTATT 59.958 45.455 9.97 0.00 42.51 1.40
3194 5156 2.041620 TGACTTGCCCTGGCTTATTTCT 59.958 45.455 9.97 0.00 42.51 2.52
3225 5187 0.600557 CTGTCTCAGCTTCTCACGGT 59.399 55.000 0.00 0.00 0.00 4.83
3295 5335 2.810274 CAAGGATGGATGGCGATGTAAG 59.190 50.000 0.00 0.00 0.00 2.34
3391 5434 0.673644 GTGAATCCCTGTGACCCACG 60.674 60.000 0.00 0.00 37.14 4.94
3392 5435 1.125093 TGAATCCCTGTGACCCACGT 61.125 55.000 0.00 0.00 37.14 4.49
3431 5474 5.622233 GCCCATACCAAATCTGTTCTTTCAC 60.622 44.000 0.00 0.00 0.00 3.18
3545 5590 6.203723 TGAACATGATCACATACGTTTCAACA 59.796 34.615 0.83 0.00 35.09 3.33
3654 5815 8.654997 TGGATTTTAATTTTTGGGTTCAGATGA 58.345 29.630 0.00 0.00 0.00 2.92
3666 5827 4.759693 GGGTTCAGATGATGTTTACACACA 59.240 41.667 0.00 0.00 35.03 3.72
3779 5974 3.952323 GTGTACTACCTGATGAGCTGGTA 59.048 47.826 6.33 6.33 45.85 3.25
4183 10817 3.953775 CCCGGCCCGCTCCAATAT 61.954 66.667 0.00 0.00 0.00 1.28
4884 11763 0.318955 CAAGTTTCCAGCTTTGGCCG 60.319 55.000 0.00 0.00 39.73 6.13
4894 11773 0.038618 GCTTTGGCCGGTTAAAGGTG 60.039 55.000 24.35 9.15 35.10 4.00
4915 11794 6.488006 AGGTGTGAGGATGAATTATGTTATGC 59.512 38.462 0.00 0.00 0.00 3.14
5067 11951 2.673833 CCTTATCGGCCGATCAACTAC 58.326 52.381 42.11 0.00 36.17 2.73
5074 11958 2.412977 CGGCCGATCAACTACTATCGAG 60.413 54.545 24.07 0.00 46.08 4.04
5148 12032 8.585471 AGATTTTATGAACATGTGGAGTGAAT 57.415 30.769 0.00 0.00 0.00 2.57
5160 12044 8.627403 ACATGTGGAGTGAATTGAATGAATATC 58.373 33.333 0.00 0.00 0.00 1.63
5161 12045 7.250445 TGTGGAGTGAATTGAATGAATATCG 57.750 36.000 0.00 0.00 0.00 2.92
5166 12050 4.376861 GTGAATTGAATGAATATCGTGCGC 59.623 41.667 0.00 0.00 0.00 6.09
5167 12051 4.034975 TGAATTGAATGAATATCGTGCGCA 59.965 37.500 5.66 5.66 0.00 6.09
5168 12052 3.317744 TTGAATGAATATCGTGCGCAC 57.682 42.857 30.42 30.42 0.00 5.34
5287 12171 1.066645 TGCAGCTGACCATGTACAGAG 60.067 52.381 20.43 10.73 36.38 3.35
5307 12191 4.126437 GAGGAATAGCTGGCTTTCTTCTC 58.874 47.826 0.00 4.86 0.00 2.87
5323 12208 7.596749 TTTCTTCTCGTTAGCTTCTTTATGG 57.403 36.000 0.00 0.00 0.00 2.74
5414 12299 2.319747 TCACCCTTTCCCCCACTATAGA 59.680 50.000 6.78 0.00 0.00 1.98
5424 12309 8.632731 TTTCCCCCACTATAGAAATTCTTCTA 57.367 34.615 6.78 0.00 45.93 2.10
5513 12398 3.427573 TGTTCTGAATCTCCGTGGTCTA 58.572 45.455 0.00 0.00 0.00 2.59
5514 12399 4.023980 TGTTCTGAATCTCCGTGGTCTAT 58.976 43.478 0.00 0.00 0.00 1.98
5515 12400 4.466370 TGTTCTGAATCTCCGTGGTCTATT 59.534 41.667 0.00 0.00 0.00 1.73
5516 12401 5.046591 TGTTCTGAATCTCCGTGGTCTATTT 60.047 40.000 0.00 0.00 0.00 1.40
5610 12499 0.462937 CCGGGATGTACCAAATCGCA 60.463 55.000 0.00 0.00 41.20 5.10
5644 12533 4.291783 GTTTAGTCGGAGATCCTCATTCG 58.708 47.826 0.00 0.00 40.67 3.34
5648 12537 2.297597 GTCGGAGATCCTCATTCGGATT 59.702 50.000 0.00 0.00 43.71 3.01
5649 12538 2.558795 TCGGAGATCCTCATTCGGATTC 59.441 50.000 0.00 0.00 43.71 2.52
5650 12539 2.297315 CGGAGATCCTCATTCGGATTCA 59.703 50.000 0.00 0.00 43.71 2.57
5651 12540 3.658709 GGAGATCCTCATTCGGATTCAC 58.341 50.000 0.00 0.00 43.71 3.18
5652 12541 3.556004 GGAGATCCTCATTCGGATTCACC 60.556 52.174 0.00 0.00 43.71 4.02
5653 12542 6.871603 GGAGATCCTCATTCGGATTCACCG 62.872 54.167 0.00 0.00 46.71 4.94
5665 12554 3.650139 GGATTCACCGTTATCGCATAGT 58.350 45.455 0.00 0.00 35.54 2.12
5666 12555 4.056050 GGATTCACCGTTATCGCATAGTT 58.944 43.478 0.00 0.00 35.54 2.24
5667 12556 4.150098 GGATTCACCGTTATCGCATAGTTC 59.850 45.833 0.00 0.00 35.54 3.01
5668 12557 2.723209 TCACCGTTATCGCATAGTTCG 58.277 47.619 0.00 0.00 35.54 3.95
5669 12558 2.097954 TCACCGTTATCGCATAGTTCGT 59.902 45.455 0.00 0.00 35.54 3.85
5670 12559 2.215587 CACCGTTATCGCATAGTTCGTG 59.784 50.000 0.00 0.00 35.54 4.35
5671 12560 1.189446 CCGTTATCGCATAGTTCGTGC 59.811 52.381 0.00 0.00 39.18 5.34
5672 12561 1.189446 CGTTATCGCATAGTTCGTGCC 59.811 52.381 0.00 0.00 39.39 5.01
5673 12562 2.470821 GTTATCGCATAGTTCGTGCCT 58.529 47.619 0.00 0.00 39.39 4.75
5674 12563 2.417339 TATCGCATAGTTCGTGCCTC 57.583 50.000 0.00 0.00 39.39 4.70
5675 12564 0.249489 ATCGCATAGTTCGTGCCTCC 60.249 55.000 0.00 0.00 39.39 4.30
5676 12565 2.230940 CGCATAGTTCGTGCCTCCG 61.231 63.158 0.00 0.00 39.39 4.63
5677 12566 1.883084 GCATAGTTCGTGCCTCCGG 60.883 63.158 0.00 0.00 36.61 5.14
5678 12567 1.515954 CATAGTTCGTGCCTCCGGT 59.484 57.895 0.00 0.00 0.00 5.28
5685 12574 2.743928 GTGCCTCCGGTGCTGAAG 60.744 66.667 17.33 0.00 0.00 3.02
5735 12624 9.517609 CTAAAAGTACTCATACTGTCATACACC 57.482 37.037 0.00 0.00 41.00 4.16
5746 12635 2.095110 TGTCATACACCGTAACCTGACG 60.095 50.000 0.00 0.00 42.55 4.35
5747 12636 1.135315 TCATACACCGTAACCTGACGC 60.135 52.381 0.00 0.00 41.56 5.19
5751 12640 1.080974 ACCGTAACCTGACGCGAAG 60.081 57.895 15.93 10.12 41.56 3.79
5754 12643 1.411394 CGTAACCTGACGCGAAGAAA 58.589 50.000 15.93 0.00 35.79 2.52
5757 12646 0.942252 AACCTGACGCGAAGAAAACC 59.058 50.000 15.93 0.00 0.00 3.27
5790 12679 4.160252 GGAGAAATGAATTGGCTTGCCTTA 59.840 41.667 13.18 1.57 0.00 2.69
5791 12680 5.334724 AGAAATGAATTGGCTTGCCTTAG 57.665 39.130 13.18 0.00 0.00 2.18
5801 12690 2.027100 GGCTTGCCTTAGTTACCTCTGT 60.027 50.000 4.11 0.00 0.00 3.41
5805 12694 3.236047 TGCCTTAGTTACCTCTGTGACA 58.764 45.455 0.00 0.00 33.62 3.58
5807 12696 3.995048 GCCTTAGTTACCTCTGTGACAAC 59.005 47.826 0.00 0.00 33.62 3.32
5810 12699 3.753294 AGTTACCTCTGTGACAACCTG 57.247 47.619 0.00 0.00 33.62 4.00
5827 12716 1.650528 CTGAGGAGAACCACCCTTCT 58.349 55.000 0.00 0.00 38.94 2.85
5834 12723 3.134262 GGAGAACCACCCTTCTATACCAC 59.866 52.174 0.00 0.00 35.97 4.16
5853 12742 5.914085 CCACGAGAGATGGTTTGATTATC 57.086 43.478 0.00 0.00 32.08 1.75
5855 12744 5.994054 CCACGAGAGATGGTTTGATTATCAT 59.006 40.000 0.00 0.00 32.08 2.45
5859 12748 7.554118 ACGAGAGATGGTTTGATTATCATGTTT 59.446 33.333 0.00 0.00 0.00 2.83
5861 12750 9.512435 GAGAGATGGTTTGATTATCATGTTTTG 57.488 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 1559 9.066892 GGATGCCATTTGAACTGAAATACTATA 57.933 33.333 0.00 0.00 0.00 1.31
182 1698 8.954950 ATCCAGAACTACAAGAAGTAATGATG 57.045 34.615 0.00 0.00 30.92 3.07
187 1703 9.485206 GTGTTTATCCAGAACTACAAGAAGTAA 57.515 33.333 0.00 0.00 30.92 2.24
299 1815 7.831753 TCCTATGAGTTTTTGTTGTTGTTGAA 58.168 30.769 0.00 0.00 0.00 2.69
320 1836 5.492565 TCCCCTAACAAGGTTATCTCCTA 57.507 43.478 0.00 0.00 36.74 2.94
352 1868 3.513912 CACCAGGTCATCAGGTAGTACAA 59.486 47.826 2.06 0.00 33.49 2.41
353 1869 3.096852 CACCAGGTCATCAGGTAGTACA 58.903 50.000 2.06 0.00 33.49 2.90
401 1917 5.774690 ACATCTGAAATGGCAAAAGGACTTA 59.225 36.000 0.00 0.00 0.00 2.24
469 1985 0.037447 AGTTCTTGGGAGCTTCTGGC 59.963 55.000 0.00 0.00 42.19 4.85
470 1986 1.339535 GGAGTTCTTGGGAGCTTCTGG 60.340 57.143 0.00 0.00 33.21 3.86
471 1987 1.627834 AGGAGTTCTTGGGAGCTTCTG 59.372 52.381 0.00 0.00 37.27 3.02
472 1988 1.627834 CAGGAGTTCTTGGGAGCTTCT 59.372 52.381 0.00 0.00 38.87 2.85
473 1989 1.349357 ACAGGAGTTCTTGGGAGCTTC 59.651 52.381 0.00 0.00 33.21 3.86
474 1990 1.349357 GACAGGAGTTCTTGGGAGCTT 59.651 52.381 0.00 0.00 33.21 3.74
475 1991 0.980423 GACAGGAGTTCTTGGGAGCT 59.020 55.000 0.00 0.00 35.74 4.09
476 1992 0.035915 GGACAGGAGTTCTTGGGAGC 60.036 60.000 0.00 0.00 0.00 4.70
477 1993 0.247736 CGGACAGGAGTTCTTGGGAG 59.752 60.000 0.00 0.00 0.00 4.30
478 1994 0.471211 ACGGACAGGAGTTCTTGGGA 60.471 55.000 0.00 0.00 0.00 4.37
479 1995 0.037232 GACGGACAGGAGTTCTTGGG 60.037 60.000 0.00 0.00 0.00 4.12
480 1996 0.969894 AGACGGACAGGAGTTCTTGG 59.030 55.000 0.00 0.00 0.00 3.61
481 1997 1.067495 GGAGACGGACAGGAGTTCTTG 60.067 57.143 0.00 0.00 0.00 3.02
482 1998 1.203075 AGGAGACGGACAGGAGTTCTT 60.203 52.381 0.00 0.00 0.00 2.52
483 1999 0.406361 AGGAGACGGACAGGAGTTCT 59.594 55.000 0.00 0.00 0.00 3.01
484 2000 0.812549 GAGGAGACGGACAGGAGTTC 59.187 60.000 0.00 0.00 0.00 3.01
485 2001 0.406361 AGAGGAGACGGACAGGAGTT 59.594 55.000 0.00 0.00 0.00 3.01
486 2002 1.065272 GTAGAGGAGACGGACAGGAGT 60.065 57.143 0.00 0.00 0.00 3.85
487 2003 1.670791 GTAGAGGAGACGGACAGGAG 58.329 60.000 0.00 0.00 0.00 3.69
488 2004 0.255318 GGTAGAGGAGACGGACAGGA 59.745 60.000 0.00 0.00 0.00 3.86
489 2005 0.034380 TGGTAGAGGAGACGGACAGG 60.034 60.000 0.00 0.00 0.00 4.00
490 2006 1.835494 TTGGTAGAGGAGACGGACAG 58.165 55.000 0.00 0.00 0.00 3.51
491 2007 2.297698 TTTGGTAGAGGAGACGGACA 57.702 50.000 0.00 0.00 0.00 4.02
492 2008 3.586892 CTTTTTGGTAGAGGAGACGGAC 58.413 50.000 0.00 0.00 0.00 4.79
493 2009 2.565834 CCTTTTTGGTAGAGGAGACGGA 59.434 50.000 0.00 0.00 32.11 4.69
494 2010 2.973945 CCTTTTTGGTAGAGGAGACGG 58.026 52.381 0.00 0.00 32.11 4.79
554 2070 7.446625 AGCACAAAATCAATATCCCTATCACTC 59.553 37.037 0.00 0.00 0.00 3.51
555 2071 7.293073 AGCACAAAATCAATATCCCTATCACT 58.707 34.615 0.00 0.00 0.00 3.41
573 2089 5.005740 AGCTTGAGATCAACATAGCACAAA 58.994 37.500 18.45 0.00 0.00 2.83
574 2090 4.582869 AGCTTGAGATCAACATAGCACAA 58.417 39.130 18.45 0.00 0.00 3.33
575 2091 4.212143 AGCTTGAGATCAACATAGCACA 57.788 40.909 18.45 0.00 0.00 4.57
576 2092 6.238320 CCTTAAGCTTGAGATCAACATAGCAC 60.238 42.308 19.19 0.00 0.00 4.40
578 2094 6.018343 GTCCTTAAGCTTGAGATCAACATAGC 60.018 42.308 19.19 7.11 0.00 2.97
581 2097 6.059787 AGTCCTTAAGCTTGAGATCAACAT 57.940 37.500 19.19 0.00 0.00 2.71
582 2098 5.489792 AGTCCTTAAGCTTGAGATCAACA 57.510 39.130 19.19 0.00 0.00 3.33
584 2100 6.605471 TGTAGTCCTTAAGCTTGAGATCAA 57.395 37.500 19.19 0.00 0.00 2.57
586 2102 6.398918 TGTTGTAGTCCTTAAGCTTGAGATC 58.601 40.000 19.19 11.16 0.00 2.75
587 2103 6.360370 TGTTGTAGTCCTTAAGCTTGAGAT 57.640 37.500 19.19 7.63 0.00 2.75
588 2104 5.801531 TGTTGTAGTCCTTAAGCTTGAGA 57.198 39.130 19.19 5.38 0.00 3.27
589 2105 6.128172 CCATTGTTGTAGTCCTTAAGCTTGAG 60.128 42.308 9.86 10.61 0.00 3.02
590 2106 5.705441 CCATTGTTGTAGTCCTTAAGCTTGA 59.295 40.000 9.86 0.00 0.00 3.02
592 2108 4.459337 GCCATTGTTGTAGTCCTTAAGCTT 59.541 41.667 3.48 3.48 0.00 3.74
599 2135 3.182152 AGTAGGCCATTGTTGTAGTCCT 58.818 45.455 5.01 0.00 0.00 3.85
605 2141 4.215109 ACAAAGAAGTAGGCCATTGTTGT 58.785 39.130 5.01 6.83 0.00 3.32
608 2144 6.245408 TGATAACAAAGAAGTAGGCCATTGT 58.755 36.000 5.01 1.50 32.78 2.71
609 2145 6.757897 TGATAACAAAGAAGTAGGCCATTG 57.242 37.500 5.01 0.84 0.00 2.82
691 2227 7.254932 GCAAATATCTGGAAGTACAATCCACTC 60.255 40.741 14.49 0.00 41.98 3.51
701 2237 6.946340 TGAGAACAGCAAATATCTGGAAGTA 58.054 36.000 0.00 0.00 35.94 2.24
717 2253 4.963276 TCAAAACACAACCTGAGAACAG 57.037 40.909 0.00 0.00 43.12 3.16
718 2254 4.946772 TGATCAAAACACAACCTGAGAACA 59.053 37.500 0.00 0.00 0.00 3.18
724 2260 8.950210 AGACTATAATGATCAAAACACAACCTG 58.050 33.333 0.00 0.00 0.00 4.00
746 2282 3.119173 GCAGACATAGAAGTGCTGAGACT 60.119 47.826 0.00 0.00 32.97 3.24
747 2283 3.186119 GCAGACATAGAAGTGCTGAGAC 58.814 50.000 0.00 0.00 32.97 3.36
753 2289 5.702865 TCAAATTTGCAGACATAGAAGTGC 58.297 37.500 13.54 0.00 36.42 4.40
767 2303 5.981915 GGGCTCAAGATTATCTCAAATTTGC 59.018 40.000 13.54 0.00 0.00 3.68
768 2304 7.344095 AGGGCTCAAGATTATCTCAAATTTG 57.656 36.000 12.15 12.15 0.00 2.32
773 2309 7.911651 CCTATAAGGGCTCAAGATTATCTCAA 58.088 38.462 0.00 0.00 0.00 3.02
793 2329 1.062734 ACCGACCATGTCCACCCTATA 60.063 52.381 0.00 0.00 0.00 1.31
803 2339 3.387947 GGACCGGACCGACCATGT 61.388 66.667 17.49 3.54 38.90 3.21
822 2359 4.083862 GGTGGCTCGGTCAGGGAC 62.084 72.222 0.00 0.00 0.00 4.46
867 2404 4.972733 TTGGTCCGTCCGGTCCGA 62.973 66.667 14.39 11.77 44.64 4.55
888 2425 1.073199 CCCTGAAAACAGGACCGCT 59.927 57.895 16.53 0.00 45.00 5.52
902 2439 2.690653 TTTTGCTGGTCCGGTCCCTG 62.691 60.000 15.53 14.04 0.00 4.45
909 2446 0.388907 CCATGCTTTTTGCTGGTCCG 60.389 55.000 0.00 0.00 43.37 4.79
925 2466 2.765807 CCTCTCGGTCCAGCCCAT 60.766 66.667 0.00 0.00 0.00 4.00
926 2467 3.992641 TCCTCTCGGTCCAGCCCA 61.993 66.667 0.00 0.00 0.00 5.36
948 2489 2.390599 CCACATCGCCACTTGTCGG 61.391 63.158 0.00 0.00 0.00 4.79
949 2490 1.667830 ACCACATCGCCACTTGTCG 60.668 57.895 0.00 0.00 0.00 4.35
950 2491 0.602638 TCACCACATCGCCACTTGTC 60.603 55.000 0.00 0.00 0.00 3.18
951 2492 0.884704 GTCACCACATCGCCACTTGT 60.885 55.000 0.00 0.00 0.00 3.16
985 2526 1.677217 GCTCATGACAACCTCCTCCAC 60.677 57.143 0.00 0.00 0.00 4.02
988 2529 1.134551 GGAGCTCATGACAACCTCCTC 60.135 57.143 17.19 4.22 39.15 3.71
996 2537 2.125391 GCGCAGGAGCTCATGACA 60.125 61.111 31.20 0.00 39.10 3.58
1062 2603 4.034258 CGTTGCTGCTGCCACTGG 62.034 66.667 16.05 0.00 38.71 4.00
1064 2605 3.282157 CACGTTGCTGCTGCCACT 61.282 61.111 16.05 2.94 38.71 4.00
1095 2636 2.607750 AGCTTCTGCCTCCCGGAA 60.608 61.111 0.73 0.00 40.80 4.30
1165 2707 0.455815 GCATGGGGCTAAGAAAACGG 59.544 55.000 0.00 0.00 40.25 4.44
1227 2769 7.387673 TGATCCAATAATAATCACGTAAGGCTG 59.612 37.037 0.00 0.00 46.39 4.85
1234 2776 7.445096 TCATGCTTGATCCAATAATAATCACGT 59.555 33.333 0.00 0.00 0.00 4.49
1246 2788 3.284617 CTCCACATCATGCTTGATCCAA 58.715 45.455 11.92 0.00 40.70 3.53
1305 2847 3.576982 GGATATGTTCGTGACATCCCCTA 59.423 47.826 9.77 0.00 45.88 3.53
1322 2864 2.151502 AGATGGGCTCGATCGGATAT 57.848 50.000 16.41 3.27 0.00 1.63
1368 2945 3.264450 AGGCCCATAGGAATAGGAATTCG 59.736 47.826 0.00 0.00 42.16 3.34
1465 3042 5.290400 GGCCGAAAAGACAAGTACTACATAC 59.710 44.000 0.00 0.00 0.00 2.39
1466 3043 5.413499 GGCCGAAAAGACAAGTACTACATA 58.587 41.667 0.00 0.00 0.00 2.29
1467 3044 4.251268 GGCCGAAAAGACAAGTACTACAT 58.749 43.478 0.00 0.00 0.00 2.29
1468 3045 3.656559 GGCCGAAAAGACAAGTACTACA 58.343 45.455 0.00 0.00 0.00 2.74
1469 3046 2.665052 CGGCCGAAAAGACAAGTACTAC 59.335 50.000 24.07 0.00 0.00 2.73
1470 3047 2.353011 CCGGCCGAAAAGACAAGTACTA 60.353 50.000 30.73 0.00 0.00 1.82
1471 3048 1.607251 CCGGCCGAAAAGACAAGTACT 60.607 52.381 30.73 0.00 0.00 2.73
1472 3049 0.794473 CCGGCCGAAAAGACAAGTAC 59.206 55.000 30.73 0.00 0.00 2.73
1473 3050 0.393820 ACCGGCCGAAAAGACAAGTA 59.606 50.000 30.73 0.00 0.00 2.24
1604 3305 1.078214 TACATGGTCAGCTGCAGCC 60.078 57.895 34.39 19.67 43.38 4.85
1676 3377 3.875727 CAGCCTGATTCACCTACATTCTG 59.124 47.826 0.00 0.00 0.00 3.02
1777 3579 2.418368 TGCCACAGAAGTTGAACAGT 57.582 45.000 0.00 0.00 0.00 3.55
1795 3597 4.226168 ACCTTCTAAGAGTCCCCAGAAATG 59.774 45.833 0.00 0.00 0.00 2.32
1898 3700 4.579869 GAATCCAAGCTCAACCACTAAGA 58.420 43.478 0.00 0.00 0.00 2.10
1946 3748 4.338118 CACCAACAACCACAGAAACATAGT 59.662 41.667 0.00 0.00 0.00 2.12
2029 3831 6.653320 TGGACCACACAAAGACTACAATATTC 59.347 38.462 0.00 0.00 0.00 1.75
2035 3837 3.916359 TTGGACCACACAAAGACTACA 57.084 42.857 0.00 0.00 0.00 2.74
2134 4073 1.974957 TCCGACCAACTGAAAGGATCA 59.025 47.619 0.00 0.00 39.30 2.92
2178 4117 4.701956 ATGCAGTAAACAACCTATGCAC 57.298 40.909 0.00 0.00 45.42 4.57
2201 4142 8.017373 AGTCATTTACAAAATCTCGTTCATGTG 58.983 33.333 0.00 0.00 0.00 3.21
2231 4172 3.319122 GCAATCCCTTTGTGACAGAAGTT 59.681 43.478 6.71 0.00 37.65 2.66
2596 4542 5.070580 ACCCCACCGAACAAAATTATTTTCA 59.929 36.000 0.00 0.00 0.00 2.69
2666 4612 3.842925 AAGCACGCGGGACCACATT 62.843 57.895 15.48 0.00 0.00 2.71
2736 4682 5.649395 GGATGTGTTGAATCTGAATCAAGGA 59.351 40.000 8.35 0.00 37.46 3.36
2763 4709 2.997463 CCTAGAGAGAAGGGGGATAGGA 59.003 54.545 0.00 0.00 31.83 2.94
2886 4832 2.483876 GAGCTCACCGCATAATGCTTA 58.516 47.619 9.40 0.00 42.25 3.09
2889 4835 1.510480 GGGAGCTCACCGCATAATGC 61.510 60.000 17.19 0.00 42.61 3.56
2953 4899 6.233434 TGAGCTCAGATTAGAAACAACACAT 58.767 36.000 13.74 0.00 0.00 3.21
3191 5153 2.488545 GAGACAGGTGCTAACTCGAGAA 59.511 50.000 21.68 5.71 0.00 2.87
3194 5156 1.813178 CTGAGACAGGTGCTAACTCGA 59.187 52.381 0.00 0.00 0.00 4.04
3225 5187 8.901841 TCTATAATCCTAAGGACCTATCAGACA 58.098 37.037 0.00 0.00 32.98 3.41
3295 5335 6.375945 AAAATGACCAAGTTTTTCCAATGC 57.624 33.333 0.00 0.00 0.00 3.56
3431 5474 2.094675 GTGGGTCACAGGGATTCAATG 58.905 52.381 0.00 0.00 34.08 2.82
3545 5590 4.392138 GCTTGAATTAGTAAACGAGTGGCT 59.608 41.667 0.00 0.00 0.00 4.75
3717 5884 7.795534 ATCTAGGATCTGAACTTATCTGCAT 57.204 36.000 0.00 0.00 0.00 3.96
3852 6047 5.221028 GCCGATAGTATGGATGAGATGAGAG 60.221 48.000 0.00 0.00 0.00 3.20
4183 10817 4.362932 TCGAAACACAACTCAAATGCAA 57.637 36.364 0.00 0.00 0.00 4.08
4837 11709 5.131067 AGTACGGCACATAGAATAGACTGA 58.869 41.667 0.00 0.00 0.00 3.41
4884 11763 7.339466 ACATAATTCATCCTCACACCTTTAACC 59.661 37.037 0.00 0.00 0.00 2.85
4894 11773 7.502120 ACAGCATAACATAATTCATCCTCAC 57.498 36.000 0.00 0.00 0.00 3.51
4915 11794 7.093988 ACAGAGCTGATAGCATAATAGGTACAG 60.094 40.741 4.21 0.00 45.56 2.74
5074 11958 4.552166 TCCAAATTAAGCGAGCATAAGC 57.448 40.909 0.00 0.00 42.56 3.09
5116 12000 7.120579 TCCACATGTTCATAAAATCTACACCAC 59.879 37.037 0.00 0.00 0.00 4.16
5148 12032 2.675348 TGTGCGCACGATATTCATTCAA 59.325 40.909 33.22 10.12 0.00 2.69
5166 12050 4.801891 AGCAAATTAGTTCAGCACATGTG 58.198 39.130 21.83 21.83 0.00 3.21
5167 12051 4.520111 TGAGCAAATTAGTTCAGCACATGT 59.480 37.500 0.00 0.00 0.00 3.21
5168 12052 5.050644 TGAGCAAATTAGTTCAGCACATG 57.949 39.130 0.00 0.00 0.00 3.21
5242 12126 2.689471 AGCAGCATTGAAACAGTCACAA 59.311 40.909 0.00 0.00 35.39 3.33
5287 12171 2.869192 CGAGAAGAAAGCCAGCTATTCC 59.131 50.000 0.00 0.00 0.00 3.01
5307 12191 4.636206 AGGAAAGCCATAAAGAAGCTAACG 59.364 41.667 0.00 0.00 35.30 3.18
5323 12208 4.808414 AAATAGCCAAAGGAAGGAAAGC 57.192 40.909 0.00 0.00 0.00 3.51
5451 12336 4.576463 CAGAAGTTAGAACAGTTGGTGCTT 59.424 41.667 0.00 0.00 36.51 3.91
5541 12430 6.203526 ACGGGTCTCTTCTCCTAAGTATAT 57.796 41.667 0.00 0.00 0.00 0.86
5551 12440 0.179142 GCGGTTACGGGTCTCTTCTC 60.179 60.000 0.00 0.00 41.36 2.87
5593 12482 3.013921 TCTTTGCGATTTGGTACATCCC 58.986 45.455 0.00 0.00 39.30 3.85
5596 12485 4.759693 TGTCTTCTTTGCGATTTGGTACAT 59.240 37.500 0.00 0.00 39.30 2.29
5610 12499 5.070047 TCTCCGACTAAACCTTGTCTTCTTT 59.930 40.000 0.00 0.00 0.00 2.52
5644 12533 3.650139 ACTATGCGATAACGGTGAATCC 58.350 45.455 0.00 0.00 40.15 3.01
5648 12537 2.097954 ACGAACTATGCGATAACGGTGA 59.902 45.455 0.00 0.00 40.15 4.02
5649 12538 2.215587 CACGAACTATGCGATAACGGTG 59.784 50.000 0.00 0.00 40.15 4.94
5650 12539 2.456989 CACGAACTATGCGATAACGGT 58.543 47.619 0.00 0.00 40.15 4.83
5651 12540 1.189446 GCACGAACTATGCGATAACGG 59.811 52.381 0.00 0.00 40.15 4.44
5652 12541 1.189446 GGCACGAACTATGCGATAACG 59.811 52.381 0.00 0.00 44.37 3.18
5653 12542 2.470821 AGGCACGAACTATGCGATAAC 58.529 47.619 0.00 0.00 44.37 1.89
5654 12543 2.545113 GGAGGCACGAACTATGCGATAA 60.545 50.000 0.00 0.00 44.37 1.75
5655 12544 1.000607 GGAGGCACGAACTATGCGATA 60.001 52.381 0.00 0.00 44.37 2.92
5656 12545 0.249489 GGAGGCACGAACTATGCGAT 60.249 55.000 0.00 0.00 44.37 4.58
5657 12546 1.141019 GGAGGCACGAACTATGCGA 59.859 57.895 0.00 0.00 44.37 5.10
5658 12547 2.230940 CGGAGGCACGAACTATGCG 61.231 63.158 0.00 0.00 44.37 4.73
5659 12548 1.883084 CCGGAGGCACGAACTATGC 60.883 63.158 0.00 0.00 46.14 3.14
5660 12549 4.420143 CCGGAGGCACGAACTATG 57.580 61.111 0.00 0.00 46.14 2.23
5723 12612 3.057033 GTCAGGTTACGGTGTATGACAGT 60.057 47.826 10.66 0.00 37.56 3.55
5735 12624 1.411394 TTTCTTCGCGTCAGGTTACG 58.589 50.000 5.77 0.00 45.58 3.18
5746 12635 1.404035 AGTTGGTGTGGTTTTCTTCGC 59.596 47.619 0.00 0.00 0.00 4.70
5747 12636 2.223479 CCAGTTGGTGTGGTTTTCTTCG 60.223 50.000 0.00 0.00 0.00 3.79
5751 12640 2.650322 TCTCCAGTTGGTGTGGTTTTC 58.350 47.619 0.00 0.00 36.37 2.29
5754 12643 2.818751 TTTCTCCAGTTGGTGTGGTT 57.181 45.000 0.00 0.00 36.37 3.67
5757 12646 5.224888 CAATTCATTTCTCCAGTTGGTGTG 58.775 41.667 0.00 0.00 36.34 3.82
5791 12680 3.555168 CCTCAGGTTGTCACAGAGGTAAC 60.555 52.174 3.11 0.00 39.89 2.50
5801 12690 1.416401 GTGGTTCTCCTCAGGTTGTCA 59.584 52.381 0.00 0.00 34.23 3.58
5805 12694 0.104409 AGGGTGGTTCTCCTCAGGTT 60.104 55.000 0.00 0.00 34.23 3.50
5807 12696 0.615850 GAAGGGTGGTTCTCCTCAGG 59.384 60.000 0.00 0.00 32.02 3.86
5810 12699 3.642377 GGTATAGAAGGGTGGTTCTCCTC 59.358 52.174 0.00 0.00 37.89 3.71
5834 12723 7.488187 AACATGATAATCAAACCATCTCTCG 57.512 36.000 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.