Multiple sequence alignment - TraesCS7D01G043200

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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 TraesCS7D01G043200 chr7D 100.000 3070 0 0 1 3070 22271309 22268240 0.000000e+00 5670.0
1 TraesCS7D01G043200 chr7D 89.017 1211 77 31 870 2053 22523186 22522005 0.000000e+00 1448.0
2 TraesCS7D01G043200 chr7D 90.111 991 56 16 881 1853 22509997 22509031 0.000000e+00 1249.0
3 TraesCS7D01G043200 chr7D 78.478 381 63 15 412 790 457215720 457216083 6.620000e-57 231.0
4 TraesCS7D01G043200 chr7D 81.230 309 24 10 1753 2053 22509094 22508812 5.150000e-53 219.0
5 TraesCS7D01G043200 chr7D 100.000 28 0 0 2310 2337 22268620 22268593 6.000000e-03 52.8
6 TraesCS7D01G043200 chr7D 100.000 28 0 0 2690 2717 22269000 22268973 6.000000e-03 52.8
7 TraesCS7D01G043200 chr4A 89.493 1656 67 42 882 2514 704808055 704806484 0.000000e+00 1995.0
8 TraesCS7D01G043200 chr4A 87.177 1162 64 28 882 2026 705055328 705054235 0.000000e+00 1242.0
9 TraesCS7D01G043200 chr4A 85.532 1175 79 45 880 2026 705170666 705169555 0.000000e+00 1144.0
10 TraesCS7D01G043200 chr4A 93.580 514 28 2 2561 3070 704806479 704805967 0.000000e+00 761.0
11 TraesCS7D01G043200 chr4A 83.333 162 24 3 2770 2928 705053517 705053356 2.470000e-31 147.0
12 TraesCS7D01G043200 chr7A 88.156 1714 115 42 1 1679 22899415 22897755 0.000000e+00 1960.0
13 TraesCS7D01G043200 chr7A 87.830 871 77 12 2221 3070 22897263 22896401 0.000000e+00 994.0
14 TraesCS7D01G043200 chr7A 85.628 988 69 41 882 1853 22916649 22915719 0.000000e+00 970.0
15 TraesCS7D01G043200 chr7A 91.265 332 9 6 1741 2060 22897735 22897412 4.700000e-118 435.0
16 TraesCS7D01G043200 chr7A 81.293 294 22 9 1767 2053 22915767 22915500 1.120000e-49 207.0
17 TraesCS7D01G043200 chr7A 84.314 204 29 3 2852 3053 22897190 22896988 2.410000e-46 196.0
18 TraesCS7D01G043200 chr7A 83.333 186 22 7 427 612 641347052 641346876 2.450000e-36 163.0
19 TraesCS7D01G043200 chr7A 80.978 184 29 4 2857 3036 22915274 22915093 1.150000e-29 141.0
20 TraesCS7D01G043200 chr5B 88.998 509 39 5 1088 1594 469337832 469338325 5.630000e-172 614.0
21 TraesCS7D01G043200 chr6B 88.432 389 23 12 1791 2173 138522465 138522837 1.680000e-122 449.0
22 TraesCS7D01G043200 chr6B 86.283 226 19 5 1225 1450 138522223 138522436 5.120000e-58 235.0
23 TraesCS7D01G043200 chr6B 76.991 226 38 7 412 632 653583000 653583216 1.930000e-22 117.0
24 TraesCS7D01G043200 chr7B 81.003 379 51 11 412 778 583976144 583975775 6.480000e-72 281.0
25 TraesCS7D01G043200 chr7B 77.409 301 49 13 483 782 246018507 246018789 8.810000e-36 161.0
26 TraesCS7D01G043200 chr2A 82.449 245 26 12 1100 1341 4322555 4322325 6.710000e-47 198.0
27 TraesCS7D01G043200 chr2A 77.143 210 37 8 574 782 751011650 751011849 9.000000e-21 111.0
28 TraesCS7D01G043200 chr6D 78.808 302 45 16 483 782 56208407 56208123 5.230000e-43 185.0
29 TraesCS7D01G043200 chr6D 81.538 195 24 8 590 782 414434270 414434086 1.910000e-32 150.0
30 TraesCS7D01G043200 chr2D 78.652 267 47 10 519 782 93093000 93093259 5.260000e-38 169.0
31 TraesCS7D01G043200 chr2D 82.418 182 27 4 605 782 590057970 590057790 1.470000e-33 154.0
32 TraesCS7D01G043200 chr2D 76.190 294 53 14 485 777 35778205 35778482 4.130000e-29 139.0
33 TraesCS7D01G043200 chr4B 78.761 226 35 8 411 632 76050596 76050380 4.130000e-29 139.0
34 TraesCS7D01G043200 chr3B 78.125 224 37 7 412 632 809608905 809608691 6.910000e-27 132.0
35 TraesCS7D01G043200 chr3B 77.434 226 36 9 412 632 171086484 171086699 1.500000e-23 121.0
36 TraesCS7D01G043200 chr1A 100.000 61 0 0 1601 1661 27383214 27383154 2.500000e-21 113.0
37 TraesCS7D01G043200 chr1A 98.361 61 1 0 1601 1661 442726932 442726872 1.160000e-19 108.0
38 TraesCS7D01G043200 chr5D 85.714 105 15 0 412 516 375469388 375469284 9.000000e-21 111.0
39 TraesCS7D01G043200 chr5D 94.000 50 3 0 799 848 486260410 486260361 3.280000e-10 76.8
40 TraesCS7D01G043200 chr4D 91.837 49 4 0 799 847 484735524 484735476 5.490000e-08 69.4
41 TraesCS7D01G043200 chr3A 93.333 45 3 0 799 843 267040140 267040184 1.980000e-07 67.6
42 TraesCS7D01G043200 chr2B 84.000 75 7 4 785 857 98394162 98394233 1.980000e-07 67.6


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 TraesCS7D01G043200 chr7D 22268240 22271309 3069 True 1925.200000 5670 100.00000 1 3070 3 chr7D.!!$R2 3069
1 TraesCS7D01G043200 chr7D 22522005 22523186 1181 True 1448.000000 1448 89.01700 870 2053 1 chr7D.!!$R1 1183
2 TraesCS7D01G043200 chr7D 22508812 22509997 1185 True 734.000000 1249 85.67050 881 2053 2 chr7D.!!$R3 1172
3 TraesCS7D01G043200 chr4A 704805967 704808055 2088 True 1378.000000 1995 91.53650 882 3070 2 chr4A.!!$R2 2188
4 TraesCS7D01G043200 chr4A 705169555 705170666 1111 True 1144.000000 1144 85.53200 880 2026 1 chr4A.!!$R1 1146
5 TraesCS7D01G043200 chr4A 705053356 705055328 1972 True 694.500000 1242 85.25500 882 2928 2 chr4A.!!$R3 2046
6 TraesCS7D01G043200 chr7A 22896401 22899415 3014 True 896.250000 1960 87.89125 1 3070 4 chr7A.!!$R2 3069
7 TraesCS7D01G043200 chr7A 22915093 22916649 1556 True 439.333333 970 82.63300 882 3036 3 chr7A.!!$R3 2154
8 TraesCS7D01G043200 chr6B 138522223 138522837 614 False 342.000000 449 87.35750 1225 2173 2 chr6B.!!$F2 948

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
352 373 0.105593 AGGCGCATAGACATGAGTGG 59.894 55.0 10.83 0.0 34.70 4.00 F
1882 2003 0.319555 CCGAGGTCGAAGCACTGAAA 60.320 55.0 0.00 0.0 43.02 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2008 0.174845 TGGAAACGAGCACCTATCCG 59.825 55.0 0.0 0.0 0.0 4.18 R
2891 4228 1.209128 AGAAACAGCGTCGAACACAG 58.791 50.0 0.0 0.0 0.0 3.66 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
23 24 3.853831 TTGAAGATGCATGCGTGAAAT 57.146 38.095 19.18 1.32 0.00 2.17
31 32 5.697633 AGATGCATGCGTGAAATTTTCTTTT 59.302 32.000 19.18 0.00 0.00 2.27
119 122 2.043248 TAGGACGTGCCCTCTCCC 60.043 66.667 2.38 0.00 37.74 4.30
130 133 0.824759 CCCTCTCCCACTTTAGTCGG 59.175 60.000 0.00 0.00 0.00 4.79
131 134 0.824759 CCTCTCCCACTTTAGTCGGG 59.175 60.000 9.72 9.72 37.57 5.14
181 186 5.790593 TCTCACCAGGACAAGTTTATGTAC 58.209 41.667 0.00 0.00 34.14 2.90
184 189 6.694447 TCACCAGGACAAGTTTATGTACTAC 58.306 40.000 0.00 0.00 42.70 2.73
187 192 7.117812 CACCAGGACAAGTTTATGTACTACTTG 59.882 40.741 19.59 19.59 42.70 3.16
276 288 1.751544 GGATACAACAACGGGCCCC 60.752 63.158 18.66 0.00 0.00 5.80
277 289 1.001887 GATACAACAACGGGCCCCA 60.002 57.895 18.66 0.00 0.00 4.96
279 291 2.774687 ATACAACAACGGGCCCCACC 62.775 60.000 18.66 0.00 37.93 4.61
280 292 4.596585 CAACAACGGGCCCCACCT 62.597 66.667 18.66 0.00 39.10 4.00
288 309 4.106925 GGCCCCACCTGCAGAGAG 62.107 72.222 17.39 0.15 34.51 3.20
290 311 3.028921 GCCCCACCTGCAGAGAGAG 62.029 68.421 17.39 0.00 0.00 3.20
292 313 1.329171 CCCCACCTGCAGAGAGAGAG 61.329 65.000 17.39 0.00 0.00 3.20
299 320 1.945394 CTGCAGAGAGAGAGAGAGAGC 59.055 57.143 8.42 0.00 0.00 4.09
300 321 1.312815 GCAGAGAGAGAGAGAGAGCC 58.687 60.000 0.00 0.00 0.00 4.70
306 327 0.178992 AGAGAGAGAGAGCCGGATGG 60.179 60.000 5.05 0.00 38.77 3.51
352 373 0.105593 AGGCGCATAGACATGAGTGG 59.894 55.000 10.83 0.00 34.70 4.00
356 377 2.205074 CGCATAGACATGAGTGGGAAC 58.795 52.381 0.00 0.00 33.67 3.62
359 380 3.711086 CATAGACATGAGTGGGAACGAG 58.289 50.000 0.00 0.00 33.67 4.18
362 383 0.608640 ACATGAGTGGGAACGAGACC 59.391 55.000 0.00 0.00 0.00 3.85
364 385 1.605058 ATGAGTGGGAACGAGACCGG 61.605 60.000 0.00 0.00 40.78 5.28
366 387 4.754667 GTGGGAACGAGACCGGCC 62.755 72.222 0.00 0.00 40.78 6.13
373 394 4.697756 CGAGACCGGCCTGCCAAA 62.698 66.667 0.00 0.00 35.37 3.28
374 395 2.044946 GAGACCGGCCTGCCAAAT 60.045 61.111 0.00 0.00 35.37 2.32
375 396 2.361610 AGACCGGCCTGCCAAATG 60.362 61.111 0.00 0.00 35.37 2.32
376 397 3.451894 GACCGGCCTGCCAAATGG 61.452 66.667 0.00 3.66 35.37 3.16
377 398 4.299796 ACCGGCCTGCCAAATGGT 62.300 61.111 0.00 4.33 37.57 3.55
378 399 2.044451 CCGGCCTGCCAAATGGTA 60.044 61.111 9.17 0.00 37.57 3.25
379 400 2.414785 CCGGCCTGCCAAATGGTAC 61.415 63.158 9.17 0.00 37.57 3.34
380 401 2.414785 CGGCCTGCCAAATGGTACC 61.415 63.158 4.43 4.43 37.57 3.34
381 402 2.058001 GGCCTGCCAAATGGTACCC 61.058 63.158 10.07 0.00 37.57 3.69
382 403 1.304879 GCCTGCCAAATGGTACCCA 60.305 57.895 10.07 0.00 38.19 4.51
383 404 1.322538 GCCTGCCAAATGGTACCCAG 61.323 60.000 10.07 8.00 36.75 4.45
384 405 0.331278 CCTGCCAAATGGTACCCAGA 59.669 55.000 10.07 0.00 36.75 3.86
385 406 1.463674 CTGCCAAATGGTACCCAGAC 58.536 55.000 10.07 0.00 36.75 3.51
386 407 0.774276 TGCCAAATGGTACCCAGACA 59.226 50.000 10.07 0.00 36.75 3.41
387 408 1.173913 GCCAAATGGTACCCAGACAC 58.826 55.000 10.07 0.00 36.75 3.67
388 409 1.546773 GCCAAATGGTACCCAGACACA 60.547 52.381 10.07 0.00 36.75 3.72
389 410 2.883888 GCCAAATGGTACCCAGACACAT 60.884 50.000 10.07 0.00 36.75 3.21
390 411 3.623703 GCCAAATGGTACCCAGACACATA 60.624 47.826 10.07 0.00 36.75 2.29
391 412 3.945285 CCAAATGGTACCCAGACACATAC 59.055 47.826 10.07 0.00 36.75 2.39
392 413 4.566697 CCAAATGGTACCCAGACACATACA 60.567 45.833 10.07 0.00 36.75 2.29
393 414 5.192927 CAAATGGTACCCAGACACATACAT 58.807 41.667 10.07 0.00 36.75 2.29
418 439 0.976073 GGGGCTCCCGCATATAGCTA 60.976 60.000 0.00 0.00 42.61 3.32
425 446 2.571653 TCCCGCATATAGCTAGCCAAAT 59.428 45.455 12.13 5.58 42.61 2.32
551 572 4.596585 CCTGGGCCGTGTTTGGGT 62.597 66.667 0.00 0.00 0.00 4.51
570 591 4.498520 GCTAGGCTGAGCACGCGA 62.499 66.667 15.93 0.00 42.36 5.87
639 660 5.138276 TCTATATGGCCTAATACTAGCCCG 58.862 45.833 3.32 0.00 46.55 6.13
640 661 2.320681 ATGGCCTAATACTAGCCCGA 57.679 50.000 3.32 0.00 46.55 5.14
684 709 1.616725 CCCAATAGGCCAAACAGCAGA 60.617 52.381 5.01 0.00 0.00 4.26
736 761 1.607612 CCCGATTACCAGTTGGGCT 59.392 57.895 2.79 0.00 42.05 5.19
814 839 2.555325 CGATTGCCAGGCATGATTACAT 59.445 45.455 17.09 3.11 38.76 2.29
1032 1081 1.127343 CAATCCTCCCTCCTCACCTC 58.873 60.000 0.00 0.00 0.00 3.85
1065 1116 1.549620 CAGAGCAGCAGAGAGAAAGGA 59.450 52.381 0.00 0.00 0.00 3.36
1086 1137 2.432628 CCGGAGCAACAGGTCGAC 60.433 66.667 7.13 7.13 0.00 4.20
1102 1155 0.523966 CGACGAGGAAGACTTCAGCT 59.476 55.000 16.85 5.67 0.00 4.24
1369 1427 4.344865 GCCCTCCGCCAAGTCCAA 62.345 66.667 0.00 0.00 0.00 3.53
1370 1428 2.359975 CCCTCCGCCAAGTCCAAC 60.360 66.667 0.00 0.00 0.00 3.77
1371 1429 2.359975 CCTCCGCCAAGTCCAACC 60.360 66.667 0.00 0.00 0.00 3.77
1377 1435 1.908299 GCCAAGTCCAACCCCAAGG 60.908 63.158 0.00 0.00 40.04 3.61
1380 1438 2.091283 AAGTCCAACCCCAAGGCCT 61.091 57.895 0.00 0.00 36.11 5.19
1460 1527 4.808238 GGCTCCGACGACGACGAC 62.808 72.222 20.63 7.02 42.66 4.34
1478 1545 3.519930 GACTCCGAGGACGAGGCC 61.520 72.222 0.00 0.00 42.66 5.19
1719 1786 2.529619 GCGCCGATGAGGAAGAAGC 61.530 63.158 0.00 0.00 45.00 3.86
1796 1863 1.003233 GCTGAAGAGGAAGGCGGTT 60.003 57.895 0.00 0.00 0.00 4.44
1881 2002 1.289066 CCGAGGTCGAAGCACTGAA 59.711 57.895 0.00 0.00 43.02 3.02
1882 2003 0.319555 CCGAGGTCGAAGCACTGAAA 60.320 55.000 0.00 0.00 43.02 2.69
1883 2004 0.784778 CGAGGTCGAAGCACTGAAAC 59.215 55.000 0.00 0.00 43.02 2.78
1884 2005 1.603172 CGAGGTCGAAGCACTGAAACT 60.603 52.381 0.00 0.00 43.02 2.66
1885 2006 1.795286 GAGGTCGAAGCACTGAAACTG 59.205 52.381 0.00 0.00 0.00 3.16
1886 2007 1.412710 AGGTCGAAGCACTGAAACTGA 59.587 47.619 0.00 0.00 0.00 3.41
1887 2008 1.527311 GGTCGAAGCACTGAAACTGAC 59.473 52.381 0.00 0.00 0.00 3.51
2027 2723 4.142609 TGGAATCTAGTGTCATGCTTCC 57.857 45.455 0.00 0.00 33.02 3.46
2028 2724 3.519107 TGGAATCTAGTGTCATGCTTCCA 59.481 43.478 0.00 0.00 38.58 3.53
2029 2725 4.164796 TGGAATCTAGTGTCATGCTTCCAT 59.835 41.667 0.00 0.00 36.62 3.41
2030 2726 7.190410 ATGGAATCTAGTGTCATGCTTCCATG 61.190 42.308 11.89 0.00 45.52 3.66
2031 2727 9.489776 ATGGAATCTAGTGTCATGCTTCCATGT 62.490 40.741 11.89 0.00 45.52 3.21
2040 2736 4.976224 CATGCTTCCATGTCTGAATCAA 57.024 40.909 0.00 0.00 43.07 2.57
2041 2737 5.319140 CATGCTTCCATGTCTGAATCAAA 57.681 39.130 0.00 0.00 43.07 2.69
2042 2738 5.902681 CATGCTTCCATGTCTGAATCAAAT 58.097 37.500 0.00 0.00 43.07 2.32
2043 2739 5.571784 TGCTTCCATGTCTGAATCAAATC 57.428 39.130 0.00 0.00 0.00 2.17
2044 2740 4.400251 TGCTTCCATGTCTGAATCAAATCC 59.600 41.667 0.00 0.00 0.00 3.01
2045 2741 4.202090 GCTTCCATGTCTGAATCAAATCCC 60.202 45.833 0.00 0.00 0.00 3.85
2046 2742 4.868172 TCCATGTCTGAATCAAATCCCT 57.132 40.909 0.00 0.00 0.00 4.20
2047 2743 4.785301 TCCATGTCTGAATCAAATCCCTC 58.215 43.478 0.00 0.00 0.00 4.30
2048 2744 3.887716 CCATGTCTGAATCAAATCCCTCC 59.112 47.826 0.00 0.00 0.00 4.30
2049 2745 4.529897 CATGTCTGAATCAAATCCCTCCA 58.470 43.478 0.00 0.00 0.00 3.86
2050 2746 4.656100 TGTCTGAATCAAATCCCTCCAA 57.344 40.909 0.00 0.00 0.00 3.53
2051 2747 4.996793 TGTCTGAATCAAATCCCTCCAAA 58.003 39.130 0.00 0.00 0.00 3.28
2052 2748 5.582953 TGTCTGAATCAAATCCCTCCAAAT 58.417 37.500 0.00 0.00 0.00 2.32
2053 2749 6.730447 TGTCTGAATCAAATCCCTCCAAATA 58.270 36.000 0.00 0.00 0.00 1.40
2054 2750 7.356680 TGTCTGAATCAAATCCCTCCAAATAT 58.643 34.615 0.00 0.00 0.00 1.28
2055 2751 8.501904 TGTCTGAATCAAATCCCTCCAAATATA 58.498 33.333 0.00 0.00 0.00 0.86
2056 2752 9.525826 GTCTGAATCAAATCCCTCCAAATATAT 57.474 33.333 0.00 0.00 0.00 0.86
2057 2753 9.524496 TCTGAATCAAATCCCTCCAAATATATG 57.476 33.333 0.00 0.00 0.00 1.78
2058 2754 9.305555 CTGAATCAAATCCCTCCAAATATATGT 57.694 33.333 0.00 0.00 0.00 2.29
2059 2755 9.300681 TGAATCAAATCCCTCCAAATATATGTC 57.699 33.333 0.00 0.00 0.00 3.06
2060 2756 9.300681 GAATCAAATCCCTCCAAATATATGTCA 57.699 33.333 0.00 0.00 0.00 3.58
2061 2757 9.833179 AATCAAATCCCTCCAAATATATGTCAT 57.167 29.630 0.00 0.00 0.00 3.06
2062 2758 8.640063 TCAAATCCCTCCAAATATATGTCATG 57.360 34.615 0.00 0.00 0.00 3.07
2063 2759 7.177216 TCAAATCCCTCCAAATATATGTCATGC 59.823 37.037 0.00 0.00 0.00 4.06
2064 2760 4.922206 TCCCTCCAAATATATGTCATGCC 58.078 43.478 0.00 0.00 0.00 4.40
2065 2761 4.353489 TCCCTCCAAATATATGTCATGCCA 59.647 41.667 0.00 0.00 0.00 4.92
2066 2762 5.015497 TCCCTCCAAATATATGTCATGCCAT 59.985 40.000 0.00 0.00 0.00 4.40
2067 2763 5.126545 CCCTCCAAATATATGTCATGCCATG 59.873 44.000 0.00 0.00 0.00 3.66
2068 2764 5.713389 CCTCCAAATATATGTCATGCCATGT 59.287 40.000 4.31 0.00 0.00 3.21
2069 2765 6.209986 CCTCCAAATATATGTCATGCCATGTT 59.790 38.462 4.31 0.00 0.00 2.71
2070 2766 7.256048 CCTCCAAATATATGTCATGCCATGTTT 60.256 37.037 4.31 0.00 0.00 2.83
2071 2767 7.660112 TCCAAATATATGTCATGCCATGTTTC 58.340 34.615 4.31 0.00 0.00 2.78
2072 2768 7.506599 TCCAAATATATGTCATGCCATGTTTCT 59.493 33.333 4.31 0.00 0.00 2.52
2073 2769 8.145767 CCAAATATATGTCATGCCATGTTTCTT 58.854 33.333 4.31 0.00 0.00 2.52
2074 2770 9.537192 CAAATATATGTCATGCCATGTTTCTTT 57.463 29.630 4.31 0.00 0.00 2.52
2075 2771 9.754382 AAATATATGTCATGCCATGTTTCTTTC 57.246 29.630 4.31 0.00 0.00 2.62
2076 2772 8.701908 ATATATGTCATGCCATGTTTCTTTCT 57.298 30.769 4.31 0.00 0.00 2.52
2077 2773 9.797642 ATATATGTCATGCCATGTTTCTTTCTA 57.202 29.630 4.31 0.00 0.00 2.10
2078 2774 5.885230 TGTCATGCCATGTTTCTTTCTAG 57.115 39.130 4.31 0.00 0.00 2.43
2079 2775 5.316167 TGTCATGCCATGTTTCTTTCTAGT 58.684 37.500 4.31 0.00 0.00 2.57
2080 2776 6.472016 TGTCATGCCATGTTTCTTTCTAGTA 58.528 36.000 4.31 0.00 0.00 1.82
2081 2777 6.595326 TGTCATGCCATGTTTCTTTCTAGTAG 59.405 38.462 4.31 0.00 0.00 2.57
2082 2778 6.595716 GTCATGCCATGTTTCTTTCTAGTAGT 59.404 38.462 4.31 0.00 0.00 2.73
2083 2779 7.764443 GTCATGCCATGTTTCTTTCTAGTAGTA 59.236 37.037 4.31 0.00 0.00 1.82
2084 2780 8.486210 TCATGCCATGTTTCTTTCTAGTAGTAT 58.514 33.333 4.31 0.00 0.00 2.12
2085 2781 9.764363 CATGCCATGTTTCTTTCTAGTAGTATA 57.236 33.333 0.00 0.00 0.00 1.47
2087 2783 9.982651 TGCCATGTTTCTTTCTAGTAGTATATC 57.017 33.333 0.00 0.00 0.00 1.63
2111 2807 9.942526 ATCTAAATCAAATCCCCTGAAAGTATT 57.057 29.630 0.00 0.00 0.00 1.89
2112 2808 9.189156 TCTAAATCAAATCCCCTGAAAGTATTG 57.811 33.333 0.00 0.00 0.00 1.90
2113 2809 7.797121 AAATCAAATCCCCTGAAAGTATTGT 57.203 32.000 0.00 0.00 0.00 2.71
2114 2810 7.410120 AATCAAATCCCCTGAAAGTATTGTC 57.590 36.000 0.00 0.00 0.00 3.18
2115 2811 6.139679 TCAAATCCCCTGAAAGTATTGTCT 57.860 37.500 0.00 0.00 0.00 3.41
2116 2812 5.945784 TCAAATCCCCTGAAAGTATTGTCTG 59.054 40.000 0.00 0.00 0.00 3.51
2117 2813 5.779241 AATCCCCTGAAAGTATTGTCTGA 57.221 39.130 0.00 0.00 0.00 3.27
2118 2814 5.983333 ATCCCCTGAAAGTATTGTCTGAT 57.017 39.130 0.00 0.00 0.00 2.90
2119 2815 5.359194 TCCCCTGAAAGTATTGTCTGATC 57.641 43.478 0.00 0.00 0.00 2.92
2120 2816 4.782691 TCCCCTGAAAGTATTGTCTGATCA 59.217 41.667 0.00 0.00 0.00 2.92
2121 2817 5.250543 TCCCCTGAAAGTATTGTCTGATCAA 59.749 40.000 0.00 0.00 0.00 2.57
2122 2818 5.355350 CCCCTGAAAGTATTGTCTGATCAAC 59.645 44.000 0.00 0.00 0.00 3.18
2123 2819 6.176183 CCCTGAAAGTATTGTCTGATCAACT 58.824 40.000 0.00 0.00 0.00 3.16
2124 2820 6.314896 CCCTGAAAGTATTGTCTGATCAACTC 59.685 42.308 0.00 0.00 0.00 3.01
2125 2821 7.102346 CCTGAAAGTATTGTCTGATCAACTCT 58.898 38.462 0.00 0.00 0.00 3.24
2126 2822 7.064371 CCTGAAAGTATTGTCTGATCAACTCTG 59.936 40.741 0.00 0.00 0.00 3.35
2127 2823 7.670364 TGAAAGTATTGTCTGATCAACTCTGA 58.330 34.615 0.00 0.00 35.56 3.27
2128 2824 8.150296 TGAAAGTATTGTCTGATCAACTCTGAA 58.850 33.333 0.00 0.00 34.49 3.02
2129 2825 9.160496 GAAAGTATTGTCTGATCAACTCTGAAT 57.840 33.333 0.00 0.00 34.49 2.57
2130 2826 9.512588 AAAGTATTGTCTGATCAACTCTGAATT 57.487 29.630 0.00 0.00 34.49 2.17
2173 2869 7.284034 TCCTGCTTTGATATCTGAAAATCTTCC 59.716 37.037 3.98 0.00 0.00 3.46
2174 2870 7.284944 CCTGCTTTGATATCTGAAAATCTTCCT 59.715 37.037 3.98 0.00 0.00 3.36
2175 2871 9.334947 CTGCTTTGATATCTGAAAATCTTCCTA 57.665 33.333 3.98 0.00 0.00 2.94
2176 2872 9.685276 TGCTTTGATATCTGAAAATCTTCCTAA 57.315 29.630 3.98 0.00 0.00 2.69
2190 2886 8.702163 AAATCTTCCTAAAATAACAAATGCGG 57.298 30.769 0.00 0.00 0.00 5.69
2191 2887 6.827586 TCTTCCTAAAATAACAAATGCGGT 57.172 33.333 0.00 0.00 0.00 5.68
2192 2888 7.925043 TCTTCCTAAAATAACAAATGCGGTA 57.075 32.000 0.00 0.00 0.00 4.02
2193 2889 8.514330 TCTTCCTAAAATAACAAATGCGGTAT 57.486 30.769 0.00 0.00 0.00 2.73
2194 2890 8.962679 TCTTCCTAAAATAACAAATGCGGTATT 58.037 29.630 0.00 0.00 0.00 1.89
2195 2891 8.918961 TTCCTAAAATAACAAATGCGGTATTG 57.081 30.769 0.00 0.00 0.00 1.90
2196 2892 8.282455 TCCTAAAATAACAAATGCGGTATTGA 57.718 30.769 0.00 0.00 0.00 2.57
2197 2893 8.402472 TCCTAAAATAACAAATGCGGTATTGAG 58.598 33.333 0.00 0.00 0.00 3.02
2198 2894 7.647715 CCTAAAATAACAAATGCGGTATTGAGG 59.352 37.037 0.00 0.00 0.00 3.86
2199 2895 6.524101 AAATAACAAATGCGGTATTGAGGT 57.476 33.333 0.00 0.00 0.00 3.85
2200 2896 3.848272 AACAAATGCGGTATTGAGGTG 57.152 42.857 0.00 0.00 0.00 4.00
2201 2897 2.790433 ACAAATGCGGTATTGAGGTGT 58.210 42.857 0.00 0.00 0.00 4.16
2202 2898 2.487762 ACAAATGCGGTATTGAGGTGTG 59.512 45.455 0.00 0.00 0.00 3.82
2203 2899 1.750193 AATGCGGTATTGAGGTGTGG 58.250 50.000 0.00 0.00 0.00 4.17
2204 2900 0.748005 ATGCGGTATTGAGGTGTGGC 60.748 55.000 0.00 0.00 0.00 5.01
2205 2901 2.112815 GCGGTATTGAGGTGTGGCC 61.113 63.158 0.00 0.00 37.58 5.36
2214 2910 4.326255 GGTGTGGCCTTGGAGATG 57.674 61.111 3.32 0.00 0.00 2.90
2215 2911 1.380302 GGTGTGGCCTTGGAGATGT 59.620 57.895 3.32 0.00 0.00 3.06
2216 2912 0.251341 GGTGTGGCCTTGGAGATGTT 60.251 55.000 3.32 0.00 0.00 2.71
2217 2913 1.620822 GTGTGGCCTTGGAGATGTTT 58.379 50.000 3.32 0.00 0.00 2.83
2218 2914 1.541588 GTGTGGCCTTGGAGATGTTTC 59.458 52.381 3.32 0.00 0.00 2.78
2219 2915 1.144708 TGTGGCCTTGGAGATGTTTCA 59.855 47.619 3.32 0.00 0.00 2.69
2220 2916 2.225091 TGTGGCCTTGGAGATGTTTCAT 60.225 45.455 3.32 0.00 0.00 2.57
2221 2917 2.827921 GTGGCCTTGGAGATGTTTCATT 59.172 45.455 3.32 0.00 0.00 2.57
2222 2918 3.259123 GTGGCCTTGGAGATGTTTCATTT 59.741 43.478 3.32 0.00 0.00 2.32
2223 2919 4.462483 GTGGCCTTGGAGATGTTTCATTTA 59.538 41.667 3.32 0.00 0.00 1.40
2229 2925 7.704047 GCCTTGGAGATGTTTCATTTATTTCTC 59.296 37.037 0.00 0.00 0.00 2.87
2273 2969 3.801698 CATCGTCTGATCAACCCTGAAT 58.198 45.455 0.00 0.00 34.49 2.57
2274 2970 3.981071 TCGTCTGATCAACCCTGAATT 57.019 42.857 0.00 0.00 34.49 2.17
2276 2972 5.011090 TCGTCTGATCAACCCTGAATTAG 57.989 43.478 0.00 0.00 34.49 1.73
2283 2979 7.987458 TCTGATCAACCCTGAATTAGTATGTTC 59.013 37.037 0.00 0.00 34.49 3.18
2290 2986 7.690256 ACCCTGAATTAGTATGTTCTTGAAGT 58.310 34.615 0.00 0.00 0.00 3.01
2291 2987 8.822805 ACCCTGAATTAGTATGTTCTTGAAGTA 58.177 33.333 0.00 0.00 0.00 2.24
2307 3003 9.747898 TTCTTGAAGTAAAGCCCTGAAATAATA 57.252 29.630 0.00 0.00 0.00 0.98
2319 3015 9.965902 AGCCCTGAAATAATATAATAGTTCCTG 57.034 33.333 5.74 0.47 30.83 3.86
2335 3031 6.672266 AGTTCCTGTACTGAGATCTGAAAA 57.328 37.500 0.00 0.00 0.00 2.29
2338 3034 5.423015 TCCTGTACTGAGATCTGAAAATGC 58.577 41.667 0.00 0.00 0.00 3.56
2341 3037 6.041423 TGTACTGAGATCTGAAAATGCTCA 57.959 37.500 0.00 0.00 34.71 4.26
2353 3049 5.224888 TGAAAATGCTCAATGCTGTTTCTC 58.775 37.500 13.36 6.41 41.41 2.87
2374 3070 9.734620 TTTCTCACATTTTGTTTATCAGTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
2375 3071 8.450578 TCTCACATTTTGTTTATCAGTTCAGT 57.549 30.769 0.00 0.00 0.00 3.41
2385 3081 8.256611 TGTTTATCAGTTCAGTTGAAGCTATC 57.743 34.615 0.00 0.00 34.27 2.08
2386 3082 8.097038 TGTTTATCAGTTCAGTTGAAGCTATCT 58.903 33.333 0.00 0.00 34.27 1.98
2392 3088 6.203530 CAGTTCAGTTGAAGCTATCTTGTGAA 59.796 38.462 0.00 0.00 34.27 3.18
2393 3089 6.203723 AGTTCAGTTGAAGCTATCTTGTGAAC 59.796 38.462 15.00 15.00 36.64 3.18
2410 3106 7.548427 TCTTGTGAACTGCAAAATGAATTCAAA 59.452 29.630 13.09 0.00 0.00 2.69
2416 3112 6.432107 ACTGCAAAATGAATTCAAATGCAAC 58.568 32.000 29.69 13.76 40.01 4.17
2421 3117 5.486735 AATGAATTCAAATGCAACTCCCA 57.513 34.783 13.09 0.00 0.00 4.37
2449 3146 6.054941 TGTTGTTGCTACTGAGATCTGAAAA 58.945 36.000 0.00 0.00 0.00 2.29
2452 3149 5.122869 TGTTGCTACTGAGATCTGAAAATGC 59.877 40.000 0.00 0.00 0.00 3.56
2453 3150 4.194640 TGCTACTGAGATCTGAAAATGCC 58.805 43.478 0.00 0.00 0.00 4.40
2454 3151 4.080695 TGCTACTGAGATCTGAAAATGCCT 60.081 41.667 0.00 0.00 0.00 4.75
2479 3177 8.519492 TTTTTCTTGCTTATGTTTGATGCTAC 57.481 30.769 0.00 0.00 0.00 3.58
2480 3178 7.452880 TTTCTTGCTTATGTTTGATGCTACT 57.547 32.000 0.00 0.00 0.00 2.57
2482 3180 6.845302 TCTTGCTTATGTTTGATGCTACTTG 58.155 36.000 0.00 0.00 0.00 3.16
2485 3183 7.864108 TGCTTATGTTTGATGCTACTTGTAT 57.136 32.000 0.00 0.00 0.00 2.29
2501 3199 9.730420 GCTACTTGTATTAACATTATGTTTGGG 57.270 33.333 16.08 3.40 41.45 4.12
2503 3201 8.887264 ACTTGTATTAACATTATGTTTGGGGA 57.113 30.769 16.08 0.00 41.45 4.81
2504 3202 8.966868 ACTTGTATTAACATTATGTTTGGGGAG 58.033 33.333 16.08 9.78 41.45 4.30
2506 3204 7.415086 TGTATTAACATTATGTTTGGGGAGGT 58.585 34.615 16.08 0.00 41.45 3.85
2507 3205 7.558444 TGTATTAACATTATGTTTGGGGAGGTC 59.442 37.037 16.08 0.00 41.45 3.85
2508 3206 2.999331 ACATTATGTTTGGGGAGGTCG 58.001 47.619 0.00 0.00 0.00 4.79
2545 3245 1.135315 CGTTCCATGTGCAATTCCAGG 60.135 52.381 0.00 0.00 0.00 4.45
2553 3268 0.961019 TGCAATTCCAGGTCTGTTGC 59.039 50.000 14.10 14.10 43.93 4.17
2556 3271 2.787994 CAATTCCAGGTCTGTTGCTCT 58.212 47.619 0.00 0.00 0.00 4.09
2559 3274 2.604912 TCCAGGTCTGTTGCTCTAGA 57.395 50.000 0.00 0.00 0.00 2.43
2586 3301 2.575279 AGGTGTGATCTTTGAGATGCCT 59.425 45.455 0.00 0.00 34.53 4.75
2593 3308 6.317140 TGTGATCTTTGAGATGCCTTATGTTC 59.683 38.462 0.00 0.00 34.53 3.18
2596 3311 4.870426 TCTTTGAGATGCCTTATGTTCGTC 59.130 41.667 0.00 0.00 0.00 4.20
2621 3336 6.808212 CGAAATGCTGGAATGAAAAGTAATGT 59.192 34.615 0.00 0.00 0.00 2.71
2627 3342 7.092716 GCTGGAATGAAAAGTAATGTCATGTT 58.907 34.615 0.00 0.00 32.38 2.71
2629 3344 9.132521 CTGGAATGAAAAGTAATGTCATGTTTC 57.867 33.333 0.00 0.00 32.38 2.78
2630 3345 8.859090 TGGAATGAAAAGTAATGTCATGTTTCT 58.141 29.630 0.00 0.00 32.38 2.52
2791 4124 5.094429 TGTGTGTTCATCGAAATGTTGAG 57.906 39.130 0.00 0.00 34.32 3.02
2901 4238 4.051922 ACTGAAATCTGACTGTGTTCGAC 58.948 43.478 0.00 0.00 0.00 4.20
3009 4346 6.839124 TGTTGGTGCTGAGATATGAAAATT 57.161 33.333 0.00 0.00 0.00 1.82
3036 4373 5.691305 GTGTTTCTTGCTTATGTTTGATGCA 59.309 36.000 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 5.833131 ACGAATGGGCATATGAACCTATTTT 59.167 36.000 6.97 1.74 37.27 1.82
86 89 3.067106 GTCCTACACGAATGGGCATATG 58.933 50.000 0.00 0.00 0.00 1.78
119 122 7.255491 AGAACTTAAAAACCCGACTAAAGTG 57.745 36.000 0.00 0.00 0.00 3.16
258 270 1.751544 GGGGCCCGTTGTTGTATCC 60.752 63.158 17.79 0.00 0.00 2.59
272 284 3.005539 TCTCTCTGCAGGTGGGGC 61.006 66.667 15.13 0.00 0.00 5.80
276 288 2.019249 CTCTCTCTCTCTCTGCAGGTG 58.981 57.143 15.13 7.59 0.00 4.00
277 289 1.915489 TCTCTCTCTCTCTCTGCAGGT 59.085 52.381 15.13 0.00 0.00 4.00
279 291 1.945394 GCTCTCTCTCTCTCTCTGCAG 59.055 57.143 7.63 7.63 0.00 4.41
280 292 1.408683 GGCTCTCTCTCTCTCTCTGCA 60.409 57.143 0.00 0.00 0.00 4.41
284 305 0.468226 TCCGGCTCTCTCTCTCTCTC 59.532 60.000 0.00 0.00 0.00 3.20
286 307 1.238439 CATCCGGCTCTCTCTCTCTC 58.762 60.000 0.00 0.00 0.00 3.20
288 309 1.178534 CCCATCCGGCTCTCTCTCTC 61.179 65.000 0.00 0.00 0.00 3.20
290 311 1.456705 ACCCATCCGGCTCTCTCTC 60.457 63.158 0.00 0.00 33.26 3.20
292 313 1.743321 CTCACCCATCCGGCTCTCTC 61.743 65.000 0.00 0.00 33.26 3.20
299 320 0.328258 AAGTTTCCTCACCCATCCGG 59.672 55.000 0.00 0.00 37.81 5.14
300 321 1.679032 GGAAGTTTCCTCACCCATCCG 60.679 57.143 3.63 0.00 44.11 4.18
306 327 1.529865 CGTTTCGGAAGTTTCCTCACC 59.470 52.381 9.11 0.00 45.33 4.02
326 347 4.189580 TCTATGCGCCTTGGCCCC 62.190 66.667 4.18 0.00 0.00 5.80
332 353 1.473965 CCACTCATGTCTATGCGCCTT 60.474 52.381 4.18 0.00 34.21 4.35
335 356 0.104855 TCCCACTCATGTCTATGCGC 59.895 55.000 0.00 0.00 34.21 6.09
342 363 1.404315 GGTCTCGTTCCCACTCATGTC 60.404 57.143 0.00 0.00 0.00 3.06
344 365 0.458543 CGGTCTCGTTCCCACTCATG 60.459 60.000 0.00 0.00 0.00 3.07
356 377 3.976701 ATTTGGCAGGCCGGTCTCG 62.977 63.158 5.00 2.86 39.42 4.04
359 380 2.830186 TACCATTTGGCAGGCCGGTC 62.830 60.000 10.34 0.00 39.32 4.79
362 383 2.414785 GGTACCATTTGGCAGGCCG 61.415 63.158 7.15 0.00 39.32 6.13
376 397 5.221461 CCCTTCTATGTATGTGTCTGGGTAC 60.221 48.000 0.00 0.00 0.00 3.34
377 398 4.899457 CCCTTCTATGTATGTGTCTGGGTA 59.101 45.833 0.00 0.00 0.00 3.69
378 399 3.711704 CCCTTCTATGTATGTGTCTGGGT 59.288 47.826 0.00 0.00 0.00 4.51
379 400 3.071602 CCCCTTCTATGTATGTGTCTGGG 59.928 52.174 0.00 0.00 0.00 4.45
380 401 3.071602 CCCCCTTCTATGTATGTGTCTGG 59.928 52.174 0.00 0.00 0.00 3.86
381 402 3.495100 GCCCCCTTCTATGTATGTGTCTG 60.495 52.174 0.00 0.00 0.00 3.51
382 403 2.706190 GCCCCCTTCTATGTATGTGTCT 59.294 50.000 0.00 0.00 0.00 3.41
383 404 2.706190 AGCCCCCTTCTATGTATGTGTC 59.294 50.000 0.00 0.00 0.00 3.67
384 405 2.706190 GAGCCCCCTTCTATGTATGTGT 59.294 50.000 0.00 0.00 0.00 3.72
385 406 2.039084 GGAGCCCCCTTCTATGTATGTG 59.961 54.545 0.00 0.00 0.00 3.21
386 407 2.339769 GGAGCCCCCTTCTATGTATGT 58.660 52.381 0.00 0.00 0.00 2.29
458 479 4.388499 ATGGTGGGTCGTGTCGGC 62.388 66.667 0.00 0.00 0.00 5.54
493 514 2.361865 GGCATGGCCCGTTTACCA 60.362 61.111 8.35 0.00 44.06 3.25
545 566 0.609131 GCTCAGCCTAGCAACCCAAA 60.609 55.000 3.11 0.00 42.30 3.28
1032 1081 0.835276 TGCTCTGTGGATCTGGATGG 59.165 55.000 0.00 0.00 0.00 3.51
1065 1116 3.665675 GACCTGTTGCTCCGGCGAT 62.666 63.158 9.30 0.00 42.25 4.58
1086 1137 1.202359 GGCTAGCTGAAGTCTTCCTCG 60.202 57.143 15.72 0.39 0.00 4.63
1102 1155 1.112113 GGTGACTTGAGATCCGGCTA 58.888 55.000 0.00 0.00 0.00 3.93
1353 1411 2.359975 GTTGGACTTGGCGGAGGG 60.360 66.667 0.00 0.00 0.00 4.30
1360 1418 1.908299 GCCTTGGGGTTGGACTTGG 60.908 63.158 0.00 0.00 34.45 3.61
1361 1419 1.908299 GGCCTTGGGGTTGGACTTG 60.908 63.158 0.00 0.00 34.45 3.16
1362 1420 2.081585 GAGGCCTTGGGGTTGGACTT 62.082 60.000 6.77 0.00 42.77 3.01
1363 1421 2.452491 AGGCCTTGGGGTTGGACT 60.452 61.111 0.00 0.00 36.75 3.85
1364 1422 2.035783 GAGGCCTTGGGGTTGGAC 59.964 66.667 6.77 0.00 34.45 4.02
1365 1423 3.264845 GGAGGCCTTGGGGTTGGA 61.265 66.667 6.77 0.00 34.45 3.53
1366 1424 3.159104 TTGGAGGCCTTGGGGTTGG 62.159 63.158 6.77 0.00 34.45 3.77
1367 1425 1.607467 CTTGGAGGCCTTGGGGTTG 60.607 63.158 6.77 0.00 34.45 3.77
1368 1426 2.854076 CTTGGAGGCCTTGGGGTT 59.146 61.111 6.77 0.00 34.45 4.11
1369 1427 3.268032 CCTTGGAGGCCTTGGGGT 61.268 66.667 6.77 0.00 34.45 4.95
1380 1438 4.344865 GCGGACCTTGGCCTTGGA 62.345 66.667 19.10 0.00 0.00 3.53
1460 1527 3.878519 GCCTCGTCCTCGGAGTCG 61.879 72.222 4.02 8.61 37.69 4.18
1461 1528 3.519930 GGCCTCGTCCTCGGAGTC 61.520 72.222 4.02 0.00 37.69 3.36
1599 1666 3.181967 CTTCCTGACGCGCTTCCG 61.182 66.667 11.76 4.79 37.57 4.30
1707 1774 0.394080 GCAGCAGGCTTCTTCCTCAT 60.394 55.000 0.00 0.00 40.25 2.90
1807 1874 0.612174 CCTCTTCGGTGAGGTCCTCA 60.612 60.000 18.15 18.15 46.33 3.86
1881 2002 0.456221 CGAGCACCTATCCGTCAGTT 59.544 55.000 0.00 0.00 0.00 3.16
1882 2003 0.680280 ACGAGCACCTATCCGTCAGT 60.680 55.000 0.00 0.00 0.00 3.41
1883 2004 0.456221 AACGAGCACCTATCCGTCAG 59.544 55.000 0.00 0.00 33.84 3.51
1884 2005 0.892755 AAACGAGCACCTATCCGTCA 59.107 50.000 0.00 0.00 33.84 4.35
1885 2006 1.557651 GAAACGAGCACCTATCCGTC 58.442 55.000 0.00 0.00 33.84 4.79
1886 2007 0.175073 GGAAACGAGCACCTATCCGT 59.825 55.000 0.00 0.00 36.77 4.69
1887 2008 0.174845 TGGAAACGAGCACCTATCCG 59.825 55.000 0.00 0.00 0.00 4.18
2027 2723 4.529897 TGGAGGGATTTGATTCAGACATG 58.470 43.478 0.00 0.00 0.00 3.21
2028 2724 4.868172 TGGAGGGATTTGATTCAGACAT 57.132 40.909 0.00 0.00 0.00 3.06
2029 2725 4.656100 TTGGAGGGATTTGATTCAGACA 57.344 40.909 0.00 0.00 0.00 3.41
2030 2726 7.830099 ATATTTGGAGGGATTTGATTCAGAC 57.170 36.000 0.00 0.00 0.00 3.51
2031 2727 9.524496 CATATATTTGGAGGGATTTGATTCAGA 57.476 33.333 0.00 0.00 0.00 3.27
2032 2728 9.305555 ACATATATTTGGAGGGATTTGATTCAG 57.694 33.333 0.00 0.00 0.00 3.02
2033 2729 9.300681 GACATATATTTGGAGGGATTTGATTCA 57.699 33.333 0.00 0.00 0.00 2.57
2034 2730 9.300681 TGACATATATTTGGAGGGATTTGATTC 57.699 33.333 0.00 0.00 0.00 2.52
2035 2731 9.833179 ATGACATATATTTGGAGGGATTTGATT 57.167 29.630 0.00 0.00 0.00 2.57
2036 2732 9.251440 CATGACATATATTTGGAGGGATTTGAT 57.749 33.333 0.00 0.00 0.00 2.57
2037 2733 7.177216 GCATGACATATATTTGGAGGGATTTGA 59.823 37.037 0.00 0.00 0.00 2.69
2038 2734 7.318141 GCATGACATATATTTGGAGGGATTTG 58.682 38.462 0.00 0.00 0.00 2.32
2039 2735 6.438425 GGCATGACATATATTTGGAGGGATTT 59.562 38.462 0.00 0.00 0.00 2.17
2040 2736 5.954150 GGCATGACATATATTTGGAGGGATT 59.046 40.000 0.00 0.00 0.00 3.01
2041 2737 5.015497 TGGCATGACATATATTTGGAGGGAT 59.985 40.000 0.00 0.00 0.00 3.85
2042 2738 4.353489 TGGCATGACATATATTTGGAGGGA 59.647 41.667 0.00 0.00 0.00 4.20
2043 2739 4.665451 TGGCATGACATATATTTGGAGGG 58.335 43.478 0.00 0.00 0.00 4.30
2044 2740 5.713389 ACATGGCATGACATATATTTGGAGG 59.287 40.000 32.74 0.00 0.00 4.30
2045 2741 6.829229 ACATGGCATGACATATATTTGGAG 57.171 37.500 32.74 0.50 0.00 3.86
2046 2742 7.506599 AGAAACATGGCATGACATATATTTGGA 59.493 33.333 32.74 0.00 0.00 3.53
2047 2743 7.663827 AGAAACATGGCATGACATATATTTGG 58.336 34.615 32.74 2.12 0.00 3.28
2048 2744 9.537192 AAAGAAACATGGCATGACATATATTTG 57.463 29.630 32.74 4.68 0.00 2.32
2049 2745 9.754382 GAAAGAAACATGGCATGACATATATTT 57.246 29.630 32.74 19.80 0.00 1.40
2050 2746 9.139734 AGAAAGAAACATGGCATGACATATATT 57.860 29.630 32.74 17.17 0.00 1.28
2051 2747 8.701908 AGAAAGAAACATGGCATGACATATAT 57.298 30.769 32.74 13.18 0.00 0.86
2052 2748 9.276590 CTAGAAAGAAACATGGCATGACATATA 57.723 33.333 32.74 15.13 0.00 0.86
2053 2749 7.776969 ACTAGAAAGAAACATGGCATGACATAT 59.223 33.333 32.74 0.00 0.00 1.78
2054 2750 7.112122 ACTAGAAAGAAACATGGCATGACATA 58.888 34.615 32.74 12.33 0.00 2.29
2055 2751 5.948162 ACTAGAAAGAAACATGGCATGACAT 59.052 36.000 32.74 8.71 0.00 3.06
2056 2752 5.316167 ACTAGAAAGAAACATGGCATGACA 58.684 37.500 32.74 2.18 0.00 3.58
2057 2753 5.886960 ACTAGAAAGAAACATGGCATGAC 57.113 39.130 32.74 21.26 0.00 3.06
2058 2754 6.711277 ACTACTAGAAAGAAACATGGCATGA 58.289 36.000 32.74 7.00 0.00 3.07
2059 2755 6.992063 ACTACTAGAAAGAAACATGGCATG 57.008 37.500 25.31 25.31 0.00 4.06
2061 2757 9.982651 GATATACTACTAGAAAGAAACATGGCA 57.017 33.333 0.00 0.00 0.00 4.92
2085 2781 9.942526 AATACTTTCAGGGGATTTGATTTAGAT 57.057 29.630 0.00 0.00 0.00 1.98
2086 2782 9.189156 CAATACTTTCAGGGGATTTGATTTAGA 57.811 33.333 0.00 0.00 0.00 2.10
2087 2783 8.971073 ACAATACTTTCAGGGGATTTGATTTAG 58.029 33.333 0.00 0.00 0.00 1.85
2088 2784 8.893563 ACAATACTTTCAGGGGATTTGATTTA 57.106 30.769 0.00 0.00 0.00 1.40
2089 2785 7.675619 AGACAATACTTTCAGGGGATTTGATTT 59.324 33.333 0.00 0.00 0.00 2.17
2090 2786 7.123247 CAGACAATACTTTCAGGGGATTTGATT 59.877 37.037 0.00 0.00 0.00 2.57
2091 2787 6.604795 CAGACAATACTTTCAGGGGATTTGAT 59.395 38.462 0.00 0.00 0.00 2.57
2092 2788 5.945784 CAGACAATACTTTCAGGGGATTTGA 59.054 40.000 0.00 0.00 0.00 2.69
2093 2789 5.945784 TCAGACAATACTTTCAGGGGATTTG 59.054 40.000 0.00 0.00 0.00 2.32
2094 2790 6.139679 TCAGACAATACTTTCAGGGGATTT 57.860 37.500 0.00 0.00 0.00 2.17
2095 2791 5.779241 TCAGACAATACTTTCAGGGGATT 57.221 39.130 0.00 0.00 0.00 3.01
2096 2792 5.429762 TGATCAGACAATACTTTCAGGGGAT 59.570 40.000 0.00 0.00 0.00 3.85
2097 2793 4.782691 TGATCAGACAATACTTTCAGGGGA 59.217 41.667 0.00 0.00 0.00 4.81
2098 2794 5.102953 TGATCAGACAATACTTTCAGGGG 57.897 43.478 0.00 0.00 0.00 4.79
2099 2795 6.176183 AGTTGATCAGACAATACTTTCAGGG 58.824 40.000 0.00 0.00 32.36 4.45
2100 2796 7.064371 CAGAGTTGATCAGACAATACTTTCAGG 59.936 40.741 0.00 0.00 32.36 3.86
2101 2797 7.816513 TCAGAGTTGATCAGACAATACTTTCAG 59.183 37.037 0.00 0.00 32.36 3.02
2102 2798 7.670364 TCAGAGTTGATCAGACAATACTTTCA 58.330 34.615 0.00 0.00 32.36 2.69
2103 2799 8.539770 TTCAGAGTTGATCAGACAATACTTTC 57.460 34.615 0.00 0.00 32.27 2.62
2104 2800 9.512588 AATTCAGAGTTGATCAGACAATACTTT 57.487 29.630 0.00 0.00 32.27 2.66
2109 2805 9.902684 AGAATAATTCAGAGTTGATCAGACAAT 57.097 29.630 0.00 0.00 32.27 2.71
2110 2806 9.159364 CAGAATAATTCAGAGTTGATCAGACAA 57.841 33.333 0.00 0.00 32.27 3.18
2111 2807 8.534496 TCAGAATAATTCAGAGTTGATCAGACA 58.466 33.333 0.00 0.00 32.27 3.41
2112 2808 8.939201 TCAGAATAATTCAGAGTTGATCAGAC 57.061 34.615 0.00 0.00 32.27 3.51
2113 2809 9.948964 TTTCAGAATAATTCAGAGTTGATCAGA 57.051 29.630 0.00 0.00 32.27 3.27
2145 2841 5.824904 TTTTCAGATATCAAAGCAGGAGC 57.175 39.130 5.32 0.00 42.56 4.70
2173 2869 8.188139 ACCTCAATACCGCATTTGTTATTTTAG 58.812 33.333 0.00 0.00 0.00 1.85
2174 2870 7.971168 CACCTCAATACCGCATTTGTTATTTTA 59.029 33.333 0.00 0.00 0.00 1.52
2175 2871 6.811170 CACCTCAATACCGCATTTGTTATTTT 59.189 34.615 0.00 0.00 0.00 1.82
2176 2872 6.071616 ACACCTCAATACCGCATTTGTTATTT 60.072 34.615 0.00 0.00 0.00 1.40
2177 2873 5.417580 ACACCTCAATACCGCATTTGTTATT 59.582 36.000 0.00 0.00 0.00 1.40
2178 2874 4.947388 ACACCTCAATACCGCATTTGTTAT 59.053 37.500 0.00 0.00 0.00 1.89
2179 2875 4.155099 CACACCTCAATACCGCATTTGTTA 59.845 41.667 0.00 0.00 0.00 2.41
2180 2876 3.057596 CACACCTCAATACCGCATTTGTT 60.058 43.478 0.00 0.00 0.00 2.83
2181 2877 2.487762 CACACCTCAATACCGCATTTGT 59.512 45.455 0.00 0.00 0.00 2.83
2182 2878 2.159393 CCACACCTCAATACCGCATTTG 60.159 50.000 0.00 0.00 0.00 2.32
2183 2879 2.091541 CCACACCTCAATACCGCATTT 58.908 47.619 0.00 0.00 0.00 2.32
2184 2880 1.750193 CCACACCTCAATACCGCATT 58.250 50.000 0.00 0.00 0.00 3.56
2185 2881 0.748005 GCCACACCTCAATACCGCAT 60.748 55.000 0.00 0.00 0.00 4.73
2186 2882 1.376683 GCCACACCTCAATACCGCA 60.377 57.895 0.00 0.00 0.00 5.69
2187 2883 2.112815 GGCCACACCTCAATACCGC 61.113 63.158 0.00 0.00 34.51 5.68
2188 2884 4.218722 GGCCACACCTCAATACCG 57.781 61.111 0.00 0.00 34.51 4.02
2197 2893 0.251341 AACATCTCCAAGGCCACACC 60.251 55.000 5.01 0.00 39.61 4.16
2198 2894 1.541588 GAAACATCTCCAAGGCCACAC 59.458 52.381 5.01 0.00 0.00 3.82
2199 2895 1.144708 TGAAACATCTCCAAGGCCACA 59.855 47.619 5.01 0.00 0.00 4.17
2200 2896 1.909700 TGAAACATCTCCAAGGCCAC 58.090 50.000 5.01 0.00 0.00 5.01
2201 2897 2.905415 ATGAAACATCTCCAAGGCCA 57.095 45.000 5.01 0.00 0.00 5.36
2202 2898 5.859205 ATAAATGAAACATCTCCAAGGCC 57.141 39.130 0.00 0.00 0.00 5.19
2203 2899 7.550712 AGAAATAAATGAAACATCTCCAAGGC 58.449 34.615 0.00 0.00 0.00 4.35
2204 2900 8.964772 AGAGAAATAAATGAAACATCTCCAAGG 58.035 33.333 0.00 0.00 33.92 3.61
2229 2925 7.563888 TGCTTGAAGGATTTGATTCAGATAG 57.436 36.000 0.00 0.00 36.81 2.08
2246 2942 3.002791 GGTTGATCAGACGATGCTTGAA 58.997 45.455 0.00 0.00 29.66 2.69
2273 2969 7.606456 CAGGGCTTTACTTCAAGAACATACTAA 59.394 37.037 0.00 0.00 0.00 2.24
2274 2970 7.038587 TCAGGGCTTTACTTCAAGAACATACTA 60.039 37.037 0.00 0.00 0.00 1.82
2276 2972 5.938125 TCAGGGCTTTACTTCAAGAACATAC 59.062 40.000 0.00 0.00 0.00 2.39
2294 2990 9.740710 ACAGGAACTATTATATTATTTCAGGGC 57.259 33.333 6.92 0.00 36.02 5.19
2307 3003 9.647918 TTCAGATCTCAGTACAGGAACTATTAT 57.352 33.333 0.00 0.00 36.02 1.28
2310 3006 7.962995 TTTCAGATCTCAGTACAGGAACTAT 57.037 36.000 0.00 0.00 36.02 2.12
2311 3007 7.776618 TTTTCAGATCTCAGTACAGGAACTA 57.223 36.000 0.00 0.00 36.02 2.24
2319 3015 6.974932 TTGAGCATTTTCAGATCTCAGTAC 57.025 37.500 0.00 0.00 35.52 2.73
2338 3034 5.981315 ACAAAATGTGAGAAACAGCATTGAG 59.019 36.000 0.00 0.00 43.64 3.02
2341 3037 8.891671 ATAAACAAAATGTGAGAAACAGCATT 57.108 26.923 0.00 0.00 43.64 3.56
2353 3049 8.854979 TCAACTGAACTGATAAACAAAATGTG 57.145 30.769 0.00 0.00 0.00 3.21
2374 3070 4.214119 TGCAGTTCACAAGATAGCTTCAAC 59.786 41.667 0.00 0.00 30.14 3.18
2375 3071 4.388485 TGCAGTTCACAAGATAGCTTCAA 58.612 39.130 0.00 0.00 30.14 2.69
2385 3081 6.831727 TGAATTCATTTTGCAGTTCACAAG 57.168 33.333 3.38 0.00 0.00 3.16
2386 3082 7.606858 TTTGAATTCATTTTGCAGTTCACAA 57.393 28.000 9.40 0.00 0.00 3.33
2392 3088 6.261381 AGTTGCATTTGAATTCATTTTGCAGT 59.739 30.769 26.01 19.53 36.99 4.40
2393 3089 6.664515 AGTTGCATTTGAATTCATTTTGCAG 58.335 32.000 26.01 10.40 36.99 4.41
2410 3106 2.880443 ACAACAGATTGGGAGTTGCAT 58.120 42.857 0.00 0.00 44.77 3.96
2416 3112 3.438087 CAGTAGCAACAACAGATTGGGAG 59.562 47.826 0.00 0.00 40.42 4.30
2421 3117 5.873712 CAGATCTCAGTAGCAACAACAGATT 59.126 40.000 0.00 0.00 0.00 2.40
2449 3146 6.523840 TCAAACATAAGCAAGAAAAAGGCAT 58.476 32.000 0.00 0.00 0.00 4.40
2452 3149 6.647895 AGCATCAAACATAAGCAAGAAAAAGG 59.352 34.615 0.00 0.00 0.00 3.11
2453 3150 7.647907 AGCATCAAACATAAGCAAGAAAAAG 57.352 32.000 0.00 0.00 0.00 2.27
2454 3151 8.359642 AGTAGCATCAAACATAAGCAAGAAAAA 58.640 29.630 0.00 0.00 0.00 1.94
2459 3157 6.615088 ACAAGTAGCATCAAACATAAGCAAG 58.385 36.000 0.00 0.00 0.00 4.01
2479 3177 8.413229 CCTCCCCAAACATAATGTTAATACAAG 58.587 37.037 0.00 0.00 40.14 3.16
2480 3178 7.896496 ACCTCCCCAAACATAATGTTAATACAA 59.104 33.333 0.00 0.00 40.14 2.41
2482 3180 7.255001 CGACCTCCCCAAACATAATGTTAATAC 60.255 40.741 0.00 0.00 40.14 1.89
2485 3183 4.944930 CGACCTCCCCAAACATAATGTTAA 59.055 41.667 0.00 0.00 40.14 2.01
2493 3191 1.991230 CCTCGACCTCCCCAAACAT 59.009 57.895 0.00 0.00 0.00 2.71
2494 3192 2.890766 GCCTCGACCTCCCCAAACA 61.891 63.158 0.00 0.00 0.00 2.83
2495 3193 2.046217 GCCTCGACCTCCCCAAAC 60.046 66.667 0.00 0.00 0.00 2.93
2496 3194 2.528127 TGCCTCGACCTCCCCAAA 60.528 61.111 0.00 0.00 0.00 3.28
2499 3197 3.775654 CAGTGCCTCGACCTCCCC 61.776 72.222 0.00 0.00 0.00 4.81
2500 3198 2.060980 ATCAGTGCCTCGACCTCCC 61.061 63.158 0.00 0.00 0.00 4.30
2501 3199 1.142748 CATCAGTGCCTCGACCTCC 59.857 63.158 0.00 0.00 0.00 4.30
2502 3200 1.142748 CCATCAGTGCCTCGACCTC 59.857 63.158 0.00 0.00 0.00 3.85
2503 3201 1.610673 ACCATCAGTGCCTCGACCT 60.611 57.895 0.00 0.00 0.00 3.85
2504 3202 1.448540 CACCATCAGTGCCTCGACC 60.449 63.158 0.00 0.00 40.28 4.79
2523 3223 1.811965 TGGAATTGCACATGGAACGAG 59.188 47.619 0.00 0.00 0.00 4.18
2545 3245 4.159506 ACCTCAATCTCTAGAGCAACAGAC 59.840 45.833 15.35 0.00 0.00 3.51
2553 3268 6.713762 AAGATCACACCTCAATCTCTAGAG 57.286 41.667 13.98 13.98 0.00 2.43
2556 3271 6.665248 TCTCAAAGATCACACCTCAATCTCTA 59.335 38.462 0.00 0.00 0.00 2.43
2559 3274 5.752036 TCTCAAAGATCACACCTCAATCT 57.248 39.130 0.00 0.00 0.00 2.40
2586 3301 3.591023 TCCAGCATTTCGACGAACATAA 58.409 40.909 10.38 0.00 0.00 1.90
2593 3308 3.469899 TTTCATTCCAGCATTTCGACG 57.530 42.857 0.00 0.00 0.00 5.12
2596 3311 6.808212 ACATTACTTTTCATTCCAGCATTTCG 59.192 34.615 0.00 0.00 0.00 3.46
2638 3353 7.174599 CAGACATATTTCTGGAGGGATTTGATC 59.825 40.741 10.52 0.00 39.59 2.92
2791 4124 7.659652 AGAAAGAAACATGACACTACTTAGC 57.340 36.000 0.00 0.00 0.00 3.09
2891 4228 1.209128 AGAAACAGCGTCGAACACAG 58.791 50.000 0.00 0.00 0.00 3.66
2892 4229 1.647346 AAGAAACAGCGTCGAACACA 58.353 45.000 0.00 0.00 0.00 3.72
2901 4238 8.500837 TGATAAACAAAATGTAAGAAACAGCG 57.499 30.769 0.00 0.00 42.70 5.18
2953 4290 6.205270 GGGAATTGCATTTGAATTCAGTTTGT 59.795 34.615 8.41 0.00 40.26 2.83
3009 4346 6.125327 TCAAACATAAGCAAGAAACACGAA 57.875 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.