Multiple sequence alignment - TraesCS4B01G210200

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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 TraesCS4B01G210200 chr4B 100.000 2537 0 0 1 2537 448886911 448884375 0.000000e+00 4686.0
1 TraesCS4B01G210200 chr4B 83.128 243 31 4 397 637 51632169 51631935 1.980000e-51 213.0
2 TraesCS4B01G210200 chr4A 92.562 1089 64 7 915 1995 101954792 101955871 0.000000e+00 1546.0
3 TraesCS4B01G210200 chr4A 80.745 483 47 12 1 456 101946961 101947424 4.040000e-88 335.0
4 TraesCS4B01G210200 chr4A 84.615 260 32 7 507 764 101954170 101954423 4.190000e-63 252.0
5 TraesCS4B01G210200 chr4A 92.593 135 7 3 2302 2436 101957956 101958087 9.260000e-45 191.0
6 TraesCS4B01G210200 chr4A 93.220 59 2 1 832 888 101954442 101954500 4.500000e-13 86.1
7 TraesCS4B01G210200 chr4A 96.970 33 1 0 790 822 101954431 101954463 3.530000e-04 56.5
8 TraesCS4B01G210200 chr4D 91.437 981 55 17 832 1798 363582523 363581558 0.000000e+00 1319.0
9 TraesCS4B01G210200 chr4D 84.085 798 77 18 1 770 363583313 363582538 0.000000e+00 725.0
10 TraesCS4B01G210200 chr4D 90.431 209 14 2 1885 2093 363581521 363581319 1.160000e-68 270.0
11 TraesCS4B01G210200 chr4D 85.106 235 26 3 397 630 477176804 477177030 5.460000e-57 231.0
12 TraesCS4B01G210200 chr4D 87.097 155 19 1 486 639 315266390 315266544 9.330000e-40 174.0
13 TraesCS4B01G210200 chr4D 93.407 91 5 1 2153 2243 363581311 363581222 1.580000e-27 134.0
14 TraesCS4B01G210200 chr4D 94.872 39 2 0 784 822 363582540 363582502 7.580000e-06 62.1
15 TraesCS4B01G210200 chr5B 84.524 252 27 8 397 646 674377468 674377709 3.260000e-59 239.0
16 TraesCS4B01G210200 chr2B 84.898 245 27 4 397 639 175454307 175454543 3.260000e-59 239.0
17 TraesCS4B01G210200 chr2B 83.607 244 30 6 398 639 480072588 480072823 1.180000e-53 220.0
18 TraesCS4B01G210200 chr2B 85.864 191 27 0 1361 1551 456589747 456589937 1.190000e-48 204.0
19 TraesCS4B01G210200 chr2B 85.185 81 7 4 2457 2534 310493972 310494050 7.520000e-11 78.7
20 TraesCS4B01G210200 chr1B 84.016 244 31 2 397 639 94009429 94009193 7.060000e-56 228.0
21 TraesCS4B01G210200 chr1B 84.016 244 31 5 397 639 569517368 569517604 7.060000e-56 228.0
22 TraesCS4B01G210200 chr2D 83.740 246 30 4 397 639 13933416 13933654 9.130000e-55 224.0
23 TraesCS4B01G210200 chr2D 82.857 245 32 4 397 639 68736852 68736616 7.110000e-51 211.0
24 TraesCS4B01G210200 chr2D 86.458 192 24 2 1361 1551 385569562 385569752 2.560000e-50 209.0
25 TraesCS4B01G210200 chr7B 83.267 251 31 7 397 646 27613143 27613383 1.180000e-53 220.0
26 TraesCS4B01G210200 chr6B 82.061 262 35 8 390 649 692727699 692727448 1.980000e-51 213.0
27 TraesCS4B01G210200 chr7D 82.917 240 30 7 397 634 79975282 79975512 3.310000e-49 206.0
28 TraesCS4B01G210200 chr2A 81.675 191 35 0 1361 1551 521507705 521507895 2.610000e-35 159.0
29 TraesCS4B01G210200 chr5A 78.175 252 38 14 398 645 639596257 639596019 7.310000e-31 145.0
30 TraesCS4B01G210200 chr3A 87.640 89 9 2 1464 1551 494432684 494432771 4.470000e-18 102.0
31 TraesCS4B01G210200 chr3A 85.393 89 11 2 1464 1551 503056135 503056222 9.670000e-15 91.6
32 TraesCS4B01G210200 chr1A 87.640 89 9 2 1464 1551 280001504 280001591 4.470000e-18 102.0


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 TraesCS4B01G210200 chr4B 448884375 448886911 2536 True 4686.00 4686 100.0000 1 2537 1 chr4B.!!$R2 2536
1 TraesCS4B01G210200 chr4A 101954170 101958087 3917 False 426.32 1546 91.9920 507 2436 5 chr4A.!!$F2 1929
2 TraesCS4B01G210200 chr4D 363581222 363583313 2091 True 502.02 1319 90.8464 1 2243 5 chr4D.!!$R1 2242

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
811 839 0.029834 GCATAATCAAGTGCGGGCTG 59.97 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 4709 0.04109 CCAACCCCTAAATGGTGGCT 59.959 55.0 0.0 0.0 35.88 4.75 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
63 64 2.545532 CCGCCATTGCTGTGAAAAAGAA 60.546 45.455 0.00 0.00 34.43 2.52
69 70 6.369615 GCCATTGCTGTGAAAAAGAATTGTAT 59.630 34.615 0.00 0.00 33.53 2.29
70 71 7.095102 GCCATTGCTGTGAAAAAGAATTGTATT 60.095 33.333 0.00 0.00 33.53 1.89
104 106 8.664669 AAATCTGACAAAATATACAAAGGGGT 57.335 30.769 0.00 0.00 0.00 4.95
139 141 1.097547 GGTGGGAGTTGATGCGATGG 61.098 60.000 0.00 0.00 0.00 3.51
154 179 3.989817 TGCGATGGTAATGAATCGATGAG 59.010 43.478 0.00 0.00 46.70 2.90
180 205 6.224584 GTGAACAAGAGCCTTCTACTAGTTT 58.775 40.000 0.00 0.00 31.96 2.66
182 207 6.706270 TGAACAAGAGCCTTCTACTAGTTTTG 59.294 38.462 0.00 0.00 31.96 2.44
190 215 4.505039 CCTTCTACTAGTTTTGGTGTGGCT 60.505 45.833 0.00 0.00 0.00 4.75
211 236 0.313987 CGGTTGTGAAAGGCTTTCCC 59.686 55.000 31.17 23.31 38.90 3.97
224 249 1.860676 CTTTCCCGACGACTTGTTGA 58.139 50.000 0.00 0.00 33.36 3.18
229 254 1.269621 CCCGACGACTTGTTGAGAGTT 60.270 52.381 0.00 0.00 33.36 3.01
231 256 2.543031 CCGACGACTTGTTGAGAGTTGA 60.543 50.000 0.00 0.00 33.36 3.18
232 257 3.309388 CGACGACTTGTTGAGAGTTGAT 58.691 45.455 0.00 0.00 33.36 2.57
233 258 3.120286 CGACGACTTGTTGAGAGTTGATG 59.880 47.826 0.00 0.00 33.36 3.07
234 259 4.051922 GACGACTTGTTGAGAGTTGATGT 58.948 43.478 0.00 0.00 33.58 3.06
235 260 4.442706 ACGACTTGTTGAGAGTTGATGTT 58.557 39.130 0.00 0.00 33.58 2.71
236 261 4.876107 ACGACTTGTTGAGAGTTGATGTTT 59.124 37.500 0.00 0.00 33.58 2.83
237 262 5.006746 ACGACTTGTTGAGAGTTGATGTTTC 59.993 40.000 0.00 0.00 33.58 2.78
238 263 5.559035 CGACTTGTTGAGAGTTGATGTTTCC 60.559 44.000 0.00 0.00 31.41 3.13
239 264 5.440610 ACTTGTTGAGAGTTGATGTTTCCT 58.559 37.500 0.00 0.00 0.00 3.36
240 265 5.888161 ACTTGTTGAGAGTTGATGTTTCCTT 59.112 36.000 0.00 0.00 0.00 3.36
241 266 6.038714 ACTTGTTGAGAGTTGATGTTTCCTTC 59.961 38.462 0.00 0.00 0.00 3.46
242 267 5.684704 TGTTGAGAGTTGATGTTTCCTTCT 58.315 37.500 0.00 0.00 0.00 2.85
243 268 6.826668 TGTTGAGAGTTGATGTTTCCTTCTA 58.173 36.000 0.00 0.00 0.00 2.10
244 269 7.279615 TGTTGAGAGTTGATGTTTCCTTCTAA 58.720 34.615 0.00 0.00 0.00 2.10
245 270 7.773224 TGTTGAGAGTTGATGTTTCCTTCTAAA 59.227 33.333 0.00 0.00 0.00 1.85
258 283 4.606457 CCTTCTAAAGGCATCTTCAACG 57.394 45.455 0.00 0.00 42.78 4.10
259 284 3.181506 CCTTCTAAAGGCATCTTCAACGC 60.182 47.826 0.00 0.00 42.78 4.84
264 289 2.750888 GGCATCTTCAACGCGGACC 61.751 63.158 12.47 0.00 0.00 4.46
271 296 1.868498 CTTCAACGCGGACCTAAAACA 59.132 47.619 12.47 0.00 0.00 2.83
287 312 5.799936 CCTAAAACAGTTCGCATATGTTTGG 59.200 40.000 4.29 0.00 44.18 3.28
298 323 0.250381 TATGTTTGGACCGCGGTGTT 60.250 50.000 39.65 12.23 0.00 3.32
299 324 1.104577 ATGTTTGGACCGCGGTGTTT 61.105 50.000 39.65 11.74 0.00 2.83
304 329 1.184431 TGGACCGCGGTGTTTAGATA 58.816 50.000 39.65 9.39 0.00 1.98
321 346 6.558771 TTAGATATTTTGTGCCATCCATCG 57.441 37.500 0.00 0.00 0.00 3.84
330 355 2.537560 CCATCCATCGCGGTCTTGC 61.538 63.158 6.13 0.00 35.57 4.01
340 365 2.264794 GGTCTTGCATCGGTCCGT 59.735 61.111 11.88 0.00 0.00 4.69
353 378 1.812235 GGTCCGTAAAATGGTTCGGT 58.188 50.000 0.00 0.00 42.95 4.69
354 379 2.153645 GGTCCGTAAAATGGTTCGGTT 58.846 47.619 0.00 0.00 42.95 4.44
367 392 2.549349 GGTTCGGTTGCACTTTCTCCTA 60.549 50.000 0.00 0.00 0.00 2.94
392 417 8.935614 ACAAACTAAAAATAAAGTAGAGGCCT 57.064 30.769 3.86 3.86 0.00 5.19
440 466 5.605564 TCGTTCAACGACAATGAATTCAT 57.394 34.783 15.36 15.36 46.73 2.57
451 477 6.904011 CGACAATGAATTCATCTTTAGTGAGC 59.096 38.462 20.95 10.74 35.10 4.26
458 484 6.939132 ATTCATCTTTAGTGAGCCATCTTG 57.061 37.500 0.00 0.00 0.00 3.02
466 492 1.144936 GAGCCATCTTGGAGGTCCG 59.855 63.158 0.00 0.00 40.96 4.79
545 572 7.926555 GGTGATCCGTCATCTTTTTCTTAGATA 59.073 37.037 0.00 0.00 36.60 1.98
561 588 1.699634 AGATAACTGCTGTGGTGGTGT 59.300 47.619 0.00 0.00 0.00 4.16
562 589 2.106511 AGATAACTGCTGTGGTGGTGTT 59.893 45.455 0.00 0.00 0.00 3.32
563 590 1.961793 TAACTGCTGTGGTGGTGTTC 58.038 50.000 0.00 0.00 0.00 3.18
578 605 2.158957 GGTGTTCAAGACAGGTGACAGA 60.159 50.000 0.00 0.00 39.39 3.41
601 628 4.237724 CGTTTGTGTCAAGCTCAGAGATA 58.762 43.478 0.00 0.00 0.00 1.98
634 661 6.491394 TCTTTTCAGTTTTGTTATGTCCGTG 58.509 36.000 0.00 0.00 0.00 4.94
679 706 6.745116 TGAATGAGACATGTATTACCGGTAG 58.255 40.000 15.20 4.52 0.00 3.18
680 707 5.723672 ATGAGACATGTATTACCGGTAGG 57.276 43.478 15.20 0.00 45.13 3.18
681 708 4.795469 TGAGACATGTATTACCGGTAGGA 58.205 43.478 15.20 0.64 41.02 2.94
682 709 5.202765 TGAGACATGTATTACCGGTAGGAA 58.797 41.667 15.20 1.99 41.02 3.36
683 710 5.301045 TGAGACATGTATTACCGGTAGGAAG 59.699 44.000 15.20 6.84 41.02 3.46
684 711 5.452255 AGACATGTATTACCGGTAGGAAGA 58.548 41.667 15.20 0.00 41.02 2.87
721 749 1.959085 CCGGCATATACGTACGGGT 59.041 57.895 21.06 10.00 40.79 5.28
771 799 1.791662 CGTTAACCGCCACATGACC 59.208 57.895 0.00 0.00 0.00 4.02
772 800 1.641123 CGTTAACCGCCACATGACCC 61.641 60.000 0.00 0.00 0.00 4.46
773 801 1.376166 TTAACCGCCACATGACCCG 60.376 57.895 0.00 0.00 0.00 5.28
774 802 3.961838 TAACCGCCACATGACCCGC 62.962 63.158 0.00 0.00 0.00 6.13
777 805 2.125310 CGCCACATGACCCGCTTA 60.125 61.111 0.00 0.00 0.00 3.09
778 806 2.173669 CGCCACATGACCCGCTTAG 61.174 63.158 0.00 0.00 0.00 2.18
779 807 1.220749 GCCACATGACCCGCTTAGA 59.779 57.895 0.00 0.00 0.00 2.10
810 838 2.408333 GCATAATCAAGTGCGGGCT 58.592 52.632 0.00 0.00 0.00 5.19
811 839 0.029834 GCATAATCAAGTGCGGGCTG 59.970 55.000 0.00 0.00 0.00 4.85
812 840 1.382522 CATAATCAAGTGCGGGCTGT 58.617 50.000 0.00 0.00 0.00 4.40
813 841 1.331756 CATAATCAAGTGCGGGCTGTC 59.668 52.381 0.00 0.00 0.00 3.51
814 842 0.392461 TAATCAAGTGCGGGCTGTCC 60.392 55.000 0.00 0.00 0.00 4.02
823 851 4.475135 GGGCTGTCCGCTTCCCTC 62.475 72.222 0.00 0.00 39.13 4.30
824 852 3.706373 GGCTGTCCGCTTCCCTCA 61.706 66.667 0.00 0.00 39.13 3.86
825 853 2.347490 GCTGTCCGCTTCCCTCAA 59.653 61.111 0.00 0.00 35.14 3.02
826 854 1.302511 GCTGTCCGCTTCCCTCAAA 60.303 57.895 0.00 0.00 35.14 2.69
827 855 0.889186 GCTGTCCGCTTCCCTCAAAA 60.889 55.000 0.00 0.00 35.14 2.44
828 856 1.604604 CTGTCCGCTTCCCTCAAAAA 58.395 50.000 0.00 0.00 0.00 1.94
880 908 4.098914 TCCTGATCTAGAAGGCTCTCTC 57.901 50.000 5.68 0.00 33.25 3.20
904 1211 5.205821 TCTATATTCGTCCTGGAGGTTCAA 58.794 41.667 15.40 4.16 36.34 2.69
907 1214 3.604875 TTCGTCCTGGAGGTTCAATAC 57.395 47.619 15.40 0.00 36.34 1.89
908 1215 2.531771 TCGTCCTGGAGGTTCAATACA 58.468 47.619 15.40 0.00 36.34 2.29
913 1225 5.501156 GTCCTGGAGGTTCAATACAAATCT 58.499 41.667 0.00 0.00 36.34 2.40
959 1271 3.370104 TCTTGCAAAAAGAAACCCTCCA 58.630 40.909 0.00 0.00 0.00 3.86
967 1279 6.570571 GCAAAAAGAAACCCTCCATTACTCTC 60.571 42.308 0.00 0.00 0.00 3.20
974 1286 4.145807 ACCCTCCATTACTCTCTCGTATG 58.854 47.826 0.00 0.00 0.00 2.39
1029 1341 1.153628 GTGGTGGGATTCCGACGAG 60.154 63.158 11.21 0.00 35.24 4.18
1074 1386 0.748005 CCTATGTTGGCAACCTCCCG 60.748 60.000 26.31 10.76 0.00 5.14
1111 1423 1.067213 GCTCGCTCAAGGACTTCTTCT 60.067 52.381 0.00 0.00 32.41 2.85
1112 1424 2.874849 CTCGCTCAAGGACTTCTTCTC 58.125 52.381 0.00 0.00 32.41 2.87
1113 1425 1.546476 TCGCTCAAGGACTTCTTCTCC 59.454 52.381 0.00 0.00 32.41 3.71
1120 1432 3.724732 AGGACTTCTTCTCCGACTACT 57.275 47.619 0.00 0.00 32.45 2.57
1125 1437 0.039180 TCTTCTCCGACTACTGCCCA 59.961 55.000 0.00 0.00 0.00 5.36
1159 1471 4.036380 ACGTGAGTGGGTTTCAGATTTTTC 59.964 41.667 0.00 0.00 46.97 2.29
1197 1511 5.105957 CGATGGTGCTAGCTAGACTATGATT 60.106 44.000 25.15 3.18 0.00 2.57
1206 1520 9.103861 GCTAGCTAGACTATGATTCTTTTGTTT 57.896 33.333 25.15 0.00 0.00 2.83
1215 1529 2.600470 TTCTTTTGTTTGCTGCTGGG 57.400 45.000 0.00 0.00 0.00 4.45
1242 1556 4.365723 TCTGTACAGTTTTCCTCGTTGTC 58.634 43.478 21.99 0.00 0.00 3.18
1275 1594 3.866379 TTCAGCCTGGCCGCATTGT 62.866 57.895 16.57 0.00 0.00 2.71
1298 1617 6.421202 TGTTTTTGCTTGTTAGTCGTTTGTTT 59.579 30.769 0.00 0.00 0.00 2.83
1315 1634 9.804758 TCGTTTGTTTCTGTAATTATTTGGTTT 57.195 25.926 0.00 0.00 0.00 3.27
1336 1655 9.527157 TGGTTTAATTTCCATCTGTCTAATTCA 57.473 29.630 0.00 0.00 0.00 2.57
1346 1665 6.422100 CCATCTGTCTAATTCAATCGTACTGG 59.578 42.308 0.00 0.00 0.00 4.00
1565 1884 0.178950 AGGAGATCTATCTGCCCGCA 60.179 55.000 7.75 0.00 45.17 5.69
1654 1973 5.293324 TCGTGAAATTGAACCTATCGATTGG 59.707 40.000 22.18 22.18 40.61 3.16
1660 1979 0.814010 AACCTATCGATTGGCCGTGC 60.814 55.000 23.45 0.00 0.00 5.34
1719 2038 7.849804 AGTCTTTACATACATTGCAGTAAGG 57.150 36.000 0.00 0.00 0.00 2.69
1730 2049 6.681777 ACATTGCAGTAAGGAAAGAACAATC 58.318 36.000 0.00 0.00 0.00 2.67
1788 2135 6.763355 TCTAATTGAGAGATAACATCCCAGC 58.237 40.000 0.00 0.00 0.00 4.85
1791 2138 3.562182 TGAGAGATAACATCCCAGCGTA 58.438 45.455 0.00 0.00 0.00 4.42
1933 2282 1.668419 AAAACAAGACGCACTGAGCT 58.332 45.000 0.00 0.00 42.61 4.09
1939 2288 0.523966 AGACGCACTGAGCTACTGAC 59.476 55.000 0.00 0.00 42.61 3.51
1962 2311 2.178912 TCTTGTCCGGCTACCAAAAG 57.821 50.000 0.00 0.00 0.00 2.27
1964 2313 2.105134 TCTTGTCCGGCTACCAAAAGAA 59.895 45.455 0.00 0.00 0.00 2.52
2000 2641 2.423185 CGGCTGCAAATTAAGGATGTCA 59.577 45.455 0.50 0.00 0.00 3.58
2001 2642 3.067180 CGGCTGCAAATTAAGGATGTCAT 59.933 43.478 0.50 0.00 0.00 3.06
2002 2643 4.275689 CGGCTGCAAATTAAGGATGTCATA 59.724 41.667 0.50 0.00 0.00 2.15
2003 2644 5.523369 GGCTGCAAATTAAGGATGTCATAC 58.477 41.667 0.50 0.00 0.00 2.39
2012 2653 3.751479 AGGATGTCATACGCTGCATTA 57.249 42.857 0.00 0.00 0.00 1.90
2025 2666 0.621082 TGCATTAACATCCGGGGTGA 59.379 50.000 15.67 0.00 0.00 4.02
2040 2681 1.228245 GTGAGGCAAGGGAGCAACA 60.228 57.895 0.00 0.00 35.83 3.33
2094 2735 4.577246 GTAGCAGGCCGGCGAGAG 62.577 72.222 22.54 11.07 39.27 3.20
2119 2760 4.293648 CGTGGTCGCTGGTGTGGA 62.294 66.667 0.00 0.00 0.00 4.02
2120 2761 2.110213 GTGGTCGCTGGTGTGGAA 59.890 61.111 0.00 0.00 0.00 3.53
2121 2762 2.110213 TGGTCGCTGGTGTGGAAC 59.890 61.111 0.00 0.00 37.35 3.62
2129 2770 3.795905 GGTGTGGAACCTCCCGTA 58.204 61.111 0.00 0.00 46.55 4.02
2130 2771 2.293877 GGTGTGGAACCTCCCGTAT 58.706 57.895 0.00 0.00 46.55 3.06
2131 2772 0.107848 GGTGTGGAACCTCCCGTATG 60.108 60.000 0.00 0.00 46.55 2.39
2132 2773 0.899720 GTGTGGAACCTCCCGTATGA 59.100 55.000 0.00 0.00 35.03 2.15
2133 2774 0.899720 TGTGGAACCTCCCGTATGAC 59.100 55.000 0.00 0.00 35.03 3.06
2134 2775 0.179119 GTGGAACCTCCCGTATGACG 60.179 60.000 0.00 0.00 42.11 4.35
2135 2776 0.612732 TGGAACCTCCCGTATGACGT 60.613 55.000 0.00 0.00 40.58 4.34
2136 2777 0.179119 GGAACCTCCCGTATGACGTG 60.179 60.000 0.00 0.00 40.58 4.49
2137 2778 0.179119 GAACCTCCCGTATGACGTGG 60.179 60.000 0.00 0.00 40.58 4.94
2138 2779 2.106332 CCTCCCGTATGACGTGGC 59.894 66.667 0.00 0.00 40.58 5.01
2139 2780 2.423898 CCTCCCGTATGACGTGGCT 61.424 63.158 0.00 0.00 40.58 4.75
2140 2781 1.226974 CTCCCGTATGACGTGGCTG 60.227 63.158 0.00 0.00 40.58 4.85
2141 2782 2.890474 CCCGTATGACGTGGCTGC 60.890 66.667 0.00 0.00 40.58 5.25
2142 2783 2.890474 CCGTATGACGTGGCTGCC 60.890 66.667 12.87 12.87 40.58 4.85
2143 2784 3.254654 CGTATGACGTGGCTGCCG 61.255 66.667 14.98 5.41 36.74 5.69
2144 2785 3.564027 GTATGACGTGGCTGCCGC 61.564 66.667 22.00 22.00 0.00 6.53
2145 2786 3.770040 TATGACGTGGCTGCCGCT 61.770 61.111 27.76 15.91 36.09 5.52
2178 2819 1.275657 CGTTCGTGACTGTGTTGCC 59.724 57.895 0.00 0.00 0.00 4.52
2230 2871 3.329093 GCAGAAGCCCCTCCATCT 58.671 61.111 0.00 0.00 33.58 2.90
2248 2889 4.942090 CACGATTTGTGTGTGGGC 57.058 55.556 0.00 0.00 43.88 5.36
2249 2890 1.082169 CACGATTTGTGTGTGGGCG 60.082 57.895 0.00 0.00 43.88 6.13
2250 2891 1.227704 ACGATTTGTGTGTGGGCGA 60.228 52.632 0.00 0.00 0.00 5.54
2251 2892 0.605319 ACGATTTGTGTGTGGGCGAT 60.605 50.000 0.00 0.00 0.00 4.58
2252 2893 0.521291 CGATTTGTGTGTGGGCGATT 59.479 50.000 0.00 0.00 0.00 3.34
2253 2894 1.735018 CGATTTGTGTGTGGGCGATTA 59.265 47.619 0.00 0.00 0.00 1.75
2254 2895 2.354510 CGATTTGTGTGTGGGCGATTAT 59.645 45.455 0.00 0.00 0.00 1.28
2255 2896 3.546020 CGATTTGTGTGTGGGCGATTATC 60.546 47.826 0.00 0.00 0.00 1.75
2256 2897 2.779755 TTGTGTGTGGGCGATTATCT 57.220 45.000 0.00 0.00 0.00 1.98
2257 2898 2.779755 TGTGTGTGGGCGATTATCTT 57.220 45.000 0.00 0.00 0.00 2.40
2258 2899 3.066291 TGTGTGTGGGCGATTATCTTT 57.934 42.857 0.00 0.00 0.00 2.52
2259 2900 3.417101 TGTGTGTGGGCGATTATCTTTT 58.583 40.909 0.00 0.00 0.00 2.27
2260 2901 3.438781 TGTGTGTGGGCGATTATCTTTTC 59.561 43.478 0.00 0.00 0.00 2.29
2261 2902 3.013921 TGTGTGGGCGATTATCTTTTCC 58.986 45.455 0.00 0.00 0.00 3.13
2262 2903 2.357952 GTGTGGGCGATTATCTTTTCCC 59.642 50.000 0.00 0.00 0.00 3.97
2263 2904 2.241176 TGTGGGCGATTATCTTTTCCCT 59.759 45.455 9.04 0.00 34.89 4.20
2264 2905 2.618709 GTGGGCGATTATCTTTTCCCTG 59.381 50.000 9.04 0.00 34.89 4.45
2265 2906 1.609072 GGGCGATTATCTTTTCCCTGC 59.391 52.381 0.00 0.00 0.00 4.85
2266 2907 1.264288 GGCGATTATCTTTTCCCTGCG 59.736 52.381 0.00 0.00 0.00 5.18
2267 2908 1.334149 GCGATTATCTTTTCCCTGCGC 60.334 52.381 0.00 0.00 35.08 6.09
2268 2909 2.213499 CGATTATCTTTTCCCTGCGCT 58.787 47.619 9.73 0.00 0.00 5.92
2269 2910 2.032549 CGATTATCTTTTCCCTGCGCTG 60.033 50.000 9.73 8.47 0.00 5.18
2270 2911 1.094785 TTATCTTTTCCCTGCGCTGC 58.905 50.000 9.73 0.00 0.00 5.25
2271 2912 1.089481 TATCTTTTCCCTGCGCTGCG 61.089 55.000 19.17 19.17 0.00 5.18
2288 2929 2.927477 CTGCGCCGAACAACTATTCTTA 59.073 45.455 4.18 0.00 0.00 2.10
2292 2933 5.106475 TGCGCCGAACAACTATTCTTATTTT 60.106 36.000 4.18 0.00 0.00 1.82
2295 2936 7.163682 GCGCCGAACAACTATTCTTATTTTTAG 59.836 37.037 0.00 0.00 0.00 1.85
2297 2938 9.704098 GCCGAACAACTATTCTTATTTTTAGAG 57.296 33.333 0.00 0.00 0.00 2.43
2332 4646 4.631377 TGTGATTGAACGGAGATGACATTC 59.369 41.667 0.00 0.00 0.00 2.67
2335 4649 4.535526 TTGAACGGAGATGACATTCTGA 57.464 40.909 11.21 0.00 0.00 3.27
2361 4675 2.287644 CAGCTGACAAACATGAACGACA 59.712 45.455 8.42 0.00 0.00 4.35
2409 4723 7.781324 ATAATTAATGAGCCACCATTTAGGG 57.219 36.000 0.00 0.00 43.89 3.53
2428 4742 2.100197 GGGTTGGGCTCATTACCTTTC 58.900 52.381 7.38 0.00 0.00 2.62
2430 4744 3.017442 GGTTGGGCTCATTACCTTTCTC 58.983 50.000 0.00 0.00 0.00 2.87
2431 4745 3.308473 GGTTGGGCTCATTACCTTTCTCT 60.308 47.826 0.00 0.00 0.00 3.10
2432 4746 3.634397 TGGGCTCATTACCTTTCTCTG 57.366 47.619 0.00 0.00 0.00 3.35
2433 4747 2.912956 TGGGCTCATTACCTTTCTCTGT 59.087 45.455 0.00 0.00 0.00 3.41
2434 4748 4.101114 TGGGCTCATTACCTTTCTCTGTA 58.899 43.478 0.00 0.00 0.00 2.74
2435 4749 4.081087 TGGGCTCATTACCTTTCTCTGTAC 60.081 45.833 0.00 0.00 0.00 2.90
2436 4750 4.162509 GGGCTCATTACCTTTCTCTGTACT 59.837 45.833 0.00 0.00 0.00 2.73
2437 4751 5.363005 GGGCTCATTACCTTTCTCTGTACTA 59.637 44.000 0.00 0.00 0.00 1.82
2438 4752 6.274579 GGCTCATTACCTTTCTCTGTACTAC 58.725 44.000 0.00 0.00 0.00 2.73
2439 4753 6.274579 GCTCATTACCTTTCTCTGTACTACC 58.725 44.000 0.00 0.00 0.00 3.18
2440 4754 6.446781 TCATTACCTTTCTCTGTACTACCG 57.553 41.667 0.00 0.00 0.00 4.02
2441 4755 6.182627 TCATTACCTTTCTCTGTACTACCGA 58.817 40.000 0.00 0.00 0.00 4.69
2442 4756 6.318144 TCATTACCTTTCTCTGTACTACCGAG 59.682 42.308 2.05 2.05 31.74 4.63
2443 4757 2.754002 ACCTTTCTCTGTACTACCGAGC 59.246 50.000 3.37 0.00 30.75 5.03
2444 4758 2.223294 CCTTTCTCTGTACTACCGAGCG 60.223 54.545 3.37 0.00 30.75 5.03
2445 4759 0.731417 TTCTCTGTACTACCGAGCGC 59.269 55.000 0.00 0.00 30.75 5.92
2446 4760 1.094073 TCTCTGTACTACCGAGCGCC 61.094 60.000 2.29 0.00 30.75 6.53
2447 4761 1.077930 TCTGTACTACCGAGCGCCT 60.078 57.895 2.29 0.00 0.00 5.52
2448 4762 0.178767 TCTGTACTACCGAGCGCCTA 59.821 55.000 2.29 0.00 0.00 3.93
2449 4763 0.587285 CTGTACTACCGAGCGCCTAG 59.413 60.000 2.29 0.22 0.00 3.02
2459 4773 2.580867 GCGCCTAGCTCACACGAG 60.581 66.667 0.00 0.00 44.04 4.18
2460 4774 3.052620 GCGCCTAGCTCACACGAGA 62.053 63.158 0.00 0.00 42.34 4.04
2461 4775 1.063327 CGCCTAGCTCACACGAGAG 59.937 63.158 0.00 0.00 42.34 3.20
2480 4794 5.024785 AGAGTATTTCTCCCTTTAAGCGG 57.975 43.478 0.00 0.00 43.71 5.52
2481 4795 4.715297 AGAGTATTTCTCCCTTTAAGCGGA 59.285 41.667 3.00 3.00 43.71 5.54
2482 4796 5.024785 AGTATTTCTCCCTTTAAGCGGAG 57.975 43.478 17.66 17.66 46.07 4.63
2487 4801 2.762535 TCCCTTTAAGCGGAGACAAG 57.237 50.000 0.00 0.00 0.00 3.16
2488 4802 1.087501 CCCTTTAAGCGGAGACAAGC 58.912 55.000 0.00 0.00 0.00 4.01
2489 4803 1.339151 CCCTTTAAGCGGAGACAAGCT 60.339 52.381 0.00 0.00 46.97 3.74
2493 4807 2.746359 AGCGGAGACAAGCTTGCT 59.254 55.556 26.27 22.21 41.52 3.91
2494 4808 1.375268 AGCGGAGACAAGCTTGCTC 60.375 57.895 28.27 28.27 41.52 4.26
2495 4809 1.375268 GCGGAGACAAGCTTGCTCT 60.375 57.895 31.50 27.66 34.22 4.09
2496 4810 1.357991 GCGGAGACAAGCTTGCTCTC 61.358 60.000 31.50 31.06 36.00 3.20
2497 4811 1.075425 CGGAGACAAGCTTGCTCTCG 61.075 60.000 31.50 28.66 36.79 4.04
2498 4812 1.357991 GGAGACAAGCTTGCTCTCGC 61.358 60.000 31.50 24.90 36.79 5.03
2499 4813 0.389687 GAGACAAGCTTGCTCTCGCT 60.390 55.000 28.59 17.47 38.30 4.93
2500 4814 0.669932 AGACAAGCTTGCTCTCGCTG 60.670 55.000 26.27 0.00 36.45 5.18
2501 4815 0.668706 GACAAGCTTGCTCTCGCTGA 60.669 55.000 26.27 0.00 36.45 4.26
2502 4816 0.250038 ACAAGCTTGCTCTCGCTGAA 60.250 50.000 26.27 0.00 36.45 3.02
2503 4817 0.443088 CAAGCTTGCTCTCGCTGAAG 59.557 55.000 14.65 0.00 36.45 3.02
2504 4818 0.673022 AAGCTTGCTCTCGCTGAAGG 60.673 55.000 0.00 0.00 36.45 3.46
2505 4819 1.079543 GCTTGCTCTCGCTGAAGGA 60.080 57.895 0.00 0.00 36.97 3.36
2506 4820 0.671781 GCTTGCTCTCGCTGAAGGAA 60.672 55.000 0.00 0.00 36.97 3.36
2507 4821 2.011046 GCTTGCTCTCGCTGAAGGAAT 61.011 52.381 0.00 0.00 36.97 3.01
2508 4822 2.354259 CTTGCTCTCGCTGAAGGAATT 58.646 47.619 0.00 0.00 36.97 2.17
2509 4823 2.479566 TGCTCTCGCTGAAGGAATTT 57.520 45.000 0.00 0.00 36.97 1.82
2510 4824 2.783135 TGCTCTCGCTGAAGGAATTTT 58.217 42.857 0.00 0.00 36.97 1.82
2511 4825 2.485426 TGCTCTCGCTGAAGGAATTTTG 59.515 45.455 0.00 0.00 36.97 2.44
2512 4826 2.730402 GCTCTCGCTGAAGGAATTTTGC 60.730 50.000 0.00 0.00 0.00 3.68
2513 4827 2.746362 CTCTCGCTGAAGGAATTTTGCT 59.254 45.455 0.00 0.00 0.00 3.91
2514 4828 2.744202 TCTCGCTGAAGGAATTTTGCTC 59.256 45.455 0.00 0.00 0.00 4.26
2515 4829 2.746362 CTCGCTGAAGGAATTTTGCTCT 59.254 45.455 0.00 0.00 0.00 4.09
2516 4830 2.744202 TCGCTGAAGGAATTTTGCTCTC 59.256 45.455 0.00 0.00 0.00 3.20
2517 4831 2.475187 CGCTGAAGGAATTTTGCTCTCG 60.475 50.000 0.00 0.00 0.00 4.04
2518 4832 2.730402 GCTGAAGGAATTTTGCTCTCGC 60.730 50.000 0.00 0.00 0.00 5.03
2519 4833 1.464608 TGAAGGAATTTTGCTCTCGCG 59.535 47.619 0.00 0.00 39.65 5.87
2520 4834 1.464997 GAAGGAATTTTGCTCTCGCGT 59.535 47.619 5.77 0.00 39.65 6.01
2521 4835 2.380084 AGGAATTTTGCTCTCGCGTA 57.620 45.000 5.77 0.00 39.65 4.42
2522 4836 2.906354 AGGAATTTTGCTCTCGCGTAT 58.094 42.857 5.77 0.00 39.65 3.06
2523 4837 2.609459 AGGAATTTTGCTCTCGCGTATG 59.391 45.455 5.77 0.00 39.65 2.39
2524 4838 2.607635 GGAATTTTGCTCTCGCGTATGA 59.392 45.455 5.77 2.38 39.65 2.15
2525 4839 3.063452 GGAATTTTGCTCTCGCGTATGAA 59.937 43.478 5.77 0.00 39.65 2.57
2526 4840 4.260784 GGAATTTTGCTCTCGCGTATGAAT 60.261 41.667 5.77 0.00 39.65 2.57
2527 4841 3.925688 TTTTGCTCTCGCGTATGAATC 57.074 42.857 5.77 0.00 39.65 2.52
2528 4842 1.477105 TTGCTCTCGCGTATGAATCG 58.523 50.000 5.77 0.00 39.65 3.34
2529 4843 0.317854 TGCTCTCGCGTATGAATCGG 60.318 55.000 5.77 0.00 39.65 4.18
2530 4844 1.004277 GCTCTCGCGTATGAATCGGG 61.004 60.000 5.77 0.00 41.36 5.14
2531 4845 1.004277 CTCTCGCGTATGAATCGGGC 61.004 60.000 5.77 0.00 40.19 6.13
2532 4846 2.022129 CTCGCGTATGAATCGGGCC 61.022 63.158 5.77 0.00 40.19 5.80
2533 4847 3.403057 CGCGTATGAATCGGGCCG 61.403 66.667 22.51 22.51 34.88 6.13
2534 4848 2.279918 GCGTATGAATCGGGCCGT 60.280 61.111 27.32 7.44 0.00 5.68
2535 4849 2.308039 GCGTATGAATCGGGCCGTC 61.308 63.158 27.32 17.77 0.00 4.79
2536 4850 1.663702 CGTATGAATCGGGCCGTCC 60.664 63.158 27.32 16.03 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 115 4.388499 CAACTCCCACCGTCCGGG 62.388 72.222 10.91 0.00 46.03 5.73
116 118 1.745489 GCATCAACTCCCACCGTCC 60.745 63.158 0.00 0.00 0.00 4.79
139 141 5.116180 TGTTCACCCTCATCGATTCATTAC 58.884 41.667 0.00 0.00 0.00 1.89
154 179 2.303311 AGTAGAAGGCTCTTGTTCACCC 59.697 50.000 0.00 0.00 32.70 4.61
180 205 2.203280 CAACCGGAGCCACACCAA 60.203 61.111 9.46 0.00 0.00 3.67
182 207 2.951475 TTCACAACCGGAGCCACACC 62.951 60.000 9.46 0.00 0.00 4.16
190 215 1.314730 GAAAGCCTTTCACAACCGGA 58.685 50.000 9.46 0.00 39.45 5.14
211 236 2.727777 TCAACTCTCAACAAGTCGTCG 58.272 47.619 0.00 0.00 0.00 5.12
238 263 3.484229 CGCGTTGAAGATGCCTTTAGAAG 60.484 47.826 0.00 0.00 36.93 2.85
239 264 2.415168 CGCGTTGAAGATGCCTTTAGAA 59.585 45.455 0.00 0.00 36.93 2.10
240 265 1.999735 CGCGTTGAAGATGCCTTTAGA 59.000 47.619 0.00 0.00 36.93 2.10
241 266 1.062587 CCGCGTTGAAGATGCCTTTAG 59.937 52.381 4.92 0.00 36.93 1.85
242 267 1.083489 CCGCGTTGAAGATGCCTTTA 58.917 50.000 4.92 0.00 36.93 1.85
243 268 0.605319 TCCGCGTTGAAGATGCCTTT 60.605 50.000 4.92 0.00 36.93 3.11
244 269 1.003839 TCCGCGTTGAAGATGCCTT 60.004 52.632 4.92 0.00 36.93 4.35
245 270 1.741770 GTCCGCGTTGAAGATGCCT 60.742 57.895 4.92 0.00 36.93 4.75
254 279 1.223187 ACTGTTTTAGGTCCGCGTTG 58.777 50.000 4.92 0.00 0.00 4.10
258 283 0.165295 GCGAACTGTTTTAGGTCCGC 59.835 55.000 5.07 5.07 40.16 5.54
259 284 1.504359 TGCGAACTGTTTTAGGTCCG 58.496 50.000 0.00 0.00 40.16 4.79
264 289 6.523201 GTCCAAACATATGCGAACTGTTTTAG 59.477 38.462 1.58 0.47 40.19 1.85
271 296 2.006888 CGGTCCAAACATATGCGAACT 58.993 47.619 1.58 0.00 0.00 3.01
287 312 4.093850 ACAAAATATCTAAACACCGCGGTC 59.906 41.667 31.80 0.00 0.00 4.79
321 346 3.195698 GGACCGATGCAAGACCGC 61.196 66.667 0.00 0.00 0.00 5.68
330 355 2.029970 CGAACCATTTTACGGACCGATG 59.970 50.000 23.38 13.46 0.00 3.84
340 365 4.339814 AGAAAGTGCAACCGAACCATTTTA 59.660 37.500 0.00 0.00 37.80 1.52
353 378 7.633193 TTTTAGTTTGTAGGAGAAAGTGCAA 57.367 32.000 0.00 0.00 0.00 4.08
354 379 7.633193 TTTTTAGTTTGTAGGAGAAAGTGCA 57.367 32.000 0.00 0.00 0.00 4.57
367 392 8.935614 AGGCCTCTACTTTATTTTTAGTTTGT 57.064 30.769 0.00 0.00 0.00 2.83
383 408 2.124695 CCCCGCAAAGGCCTCTAC 60.125 66.667 5.23 0.00 39.21 2.59
384 409 2.609610 ACCCCGCAAAGGCCTCTA 60.610 61.111 5.23 0.00 39.21 2.43
385 410 4.351054 CACCCCGCAAAGGCCTCT 62.351 66.667 5.23 0.00 39.21 3.69
386 411 4.660938 ACACCCCGCAAAGGCCTC 62.661 66.667 5.23 0.00 39.21 4.70
387 412 4.218686 AACACCCCGCAAAGGCCT 62.219 61.111 0.00 0.00 39.21 5.19
388 413 3.989787 CAACACCCCGCAAAGGCC 61.990 66.667 0.00 0.00 39.21 5.19
390 415 2.912025 AGCAACACCCCGCAAAGG 60.912 61.111 0.00 0.00 40.63 3.11
392 417 2.909965 GGAGCAACACCCCGCAAA 60.910 61.111 0.00 0.00 0.00 3.68
434 460 6.320672 CCAAGATGGCTCACTAAAGATGAATT 59.679 38.462 0.00 0.00 0.00 2.17
435 461 5.826737 CCAAGATGGCTCACTAAAGATGAAT 59.173 40.000 0.00 0.00 0.00 2.57
440 466 3.198635 CCTCCAAGATGGCTCACTAAAGA 59.801 47.826 0.00 0.00 37.47 2.52
451 477 0.322456 TTTGCGGACCTCCAAGATGG 60.322 55.000 0.00 0.00 39.43 3.51
458 484 3.435186 GCAGCTTTGCGGACCTCC 61.435 66.667 0.00 0.00 0.00 4.30
466 492 3.058708 TGATCGCTAATATGCAGCTTTGC 60.059 43.478 7.71 0.00 36.86 3.68
505 531 1.280421 GATCACCTCCTCACCAAGCTT 59.720 52.381 0.00 0.00 0.00 3.74
527 553 8.940952 ACAGCAGTTATCTAAGAAAAAGATGAC 58.059 33.333 0.00 0.00 39.19 3.06
532 559 7.301054 CACCACAGCAGTTATCTAAGAAAAAG 58.699 38.462 0.00 0.00 0.00 2.27
545 572 0.034574 TGAACACCACCACAGCAGTT 60.035 50.000 0.00 0.00 0.00 3.16
561 588 1.754803 ACGTCTGTCACCTGTCTTGAA 59.245 47.619 0.00 0.00 0.00 2.69
562 589 1.399714 ACGTCTGTCACCTGTCTTGA 58.600 50.000 0.00 0.00 0.00 3.02
563 590 2.225068 AACGTCTGTCACCTGTCTTG 57.775 50.000 0.00 0.00 0.00 3.02
578 605 2.159099 TCTCTGAGCTTGACACAAACGT 60.159 45.455 0.00 0.00 0.00 3.99
607 634 8.504005 ACGGACATAACAAAACTGAAAAGATAG 58.496 33.333 0.00 0.00 0.00 2.08
625 652 3.708890 CCACGTAATAAGCACGGACATA 58.291 45.455 0.00 0.00 43.59 2.29
634 661 5.470368 TCATATCTGAGCCACGTAATAAGC 58.530 41.667 0.00 0.00 0.00 3.09
762 790 0.462047 GGTCTAAGCGGGTCATGTGG 60.462 60.000 0.00 0.00 0.00 4.17
764 792 1.515954 CGGTCTAAGCGGGTCATGT 59.484 57.895 0.00 0.00 35.16 3.21
765 793 1.883084 GCGGTCTAAGCGGGTCATG 60.883 63.158 0.49 0.00 39.82 3.07
766 794 2.499685 GCGGTCTAAGCGGGTCAT 59.500 61.111 0.49 0.00 39.82 3.06
773 801 3.551915 GGCGTTCGCGGTCTAAGC 61.552 66.667 6.13 3.76 41.67 3.09
774 802 2.884207 GGGCGTTCGCGGTCTAAG 60.884 66.667 6.13 0.00 41.67 2.18
775 803 4.781959 CGGGCGTTCGCGGTCTAA 62.782 66.667 6.13 0.00 43.76 2.10
809 837 1.604604 TTTTTGAGGGAAGCGGACAG 58.395 50.000 0.00 0.00 0.00 3.51
810 838 3.811031 TTTTTGAGGGAAGCGGACA 57.189 47.368 0.00 0.00 0.00 4.02
828 856 3.443588 GGACAGCCCGCACTTTTT 58.556 55.556 0.00 0.00 0.00 1.94
880 908 4.827835 TGAACCTCCAGGACGAATATAGAG 59.172 45.833 0.00 0.00 38.94 2.43
904 1211 4.452890 GCGTGATGCGTTAGATTTGTAT 57.547 40.909 0.00 0.00 43.66 2.29
933 1245 4.711846 AGGGTTTCTTTTTGCAAGAAGACT 59.288 37.500 26.94 19.03 37.54 3.24
959 1271 3.478509 AGCCGTCATACGAGAGAGTAAT 58.521 45.455 0.15 0.00 46.05 1.89
967 1279 1.030457 AACCCTAGCCGTCATACGAG 58.970 55.000 0.15 0.00 46.05 4.18
974 1286 3.505293 ACTATCGATAAACCCTAGCCGTC 59.495 47.826 6.58 0.00 0.00 4.79
1029 1341 3.316573 CTCAACCCCAGAGCGGTCC 62.317 68.421 11.73 0.00 31.48 4.46
1074 1386 4.436998 CTCTCGTCGGTGCCCCAC 62.437 72.222 0.00 0.00 0.00 4.61
1111 1423 0.541063 TTGAGTGGGCAGTAGTCGGA 60.541 55.000 0.00 0.00 0.00 4.55
1112 1424 0.389948 GTTGAGTGGGCAGTAGTCGG 60.390 60.000 0.00 0.00 0.00 4.79
1113 1425 0.732880 CGTTGAGTGGGCAGTAGTCG 60.733 60.000 0.00 0.00 0.00 4.18
1120 1432 4.980805 GTCGGCGTTGAGTGGGCA 62.981 66.667 6.85 0.00 0.00 5.36
1159 1471 0.041576 CCATCGAGCATGCATCAACG 60.042 55.000 21.98 16.05 0.00 4.10
1197 1511 1.136695 CACCCAGCAGCAAACAAAAGA 59.863 47.619 0.00 0.00 0.00 2.52
1206 1520 0.909133 TACAGATCCACCCAGCAGCA 60.909 55.000 0.00 0.00 0.00 4.41
1215 1529 3.927142 CGAGGAAAACTGTACAGATCCAC 59.073 47.826 30.43 26.19 34.28 4.02
1242 1556 5.363939 CAGGCTGAATCTAAACCCTAGAAG 58.636 45.833 9.42 0.00 0.00 2.85
1275 1594 6.864165 AGAAACAAACGACTAACAAGCAAAAA 59.136 30.769 0.00 0.00 0.00 1.94
1315 1634 9.613428 ACGATTGAATTAGACAGATGGAAATTA 57.387 29.630 0.00 0.00 0.00 1.40
1321 1640 6.422100 CCAGTACGATTGAATTAGACAGATGG 59.578 42.308 0.00 0.00 0.00 3.51
1346 1665 8.356526 CGATCTGATAAATTATCGTAACACGTC 58.643 37.037 8.30 0.00 43.14 4.34
1565 1884 2.093869 ACACTATAACGTGAATGCCCGT 60.094 45.455 0.00 0.00 38.27 5.28
1730 2049 3.067106 TGGCTTCGAGAAAACAAGCTAG 58.933 45.455 3.28 0.00 41.94 3.42
1788 2135 6.238022 GGTTGGTTCCGAATAGAAGAAATACG 60.238 42.308 0.00 0.00 0.00 3.06
1814 2161 7.308049 GGCCTCGATTCTTAATAAAACATCTCC 60.308 40.741 0.00 0.00 0.00 3.71
1933 2282 1.135199 GCCGGACAAGAATCGTCAGTA 60.135 52.381 5.05 0.00 34.97 2.74
1939 2288 0.174845 TGGTAGCCGGACAAGAATCG 59.825 55.000 5.05 0.00 0.00 3.34
2000 2641 2.143122 CCGGATGTTAATGCAGCGTAT 58.857 47.619 0.00 0.00 0.00 3.06
2001 2642 1.577468 CCGGATGTTAATGCAGCGTA 58.423 50.000 0.00 0.00 0.00 4.42
2002 2643 1.095228 CCCGGATGTTAATGCAGCGT 61.095 55.000 0.73 0.00 0.00 5.07
2003 2644 1.648720 CCCGGATGTTAATGCAGCG 59.351 57.895 0.73 0.00 0.00 5.18
2012 2653 2.484287 CTTGCCTCACCCCGGATGTT 62.484 60.000 0.73 0.00 0.00 2.71
2025 2666 2.281761 CGTGTTGCTCCCTTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
2102 2743 3.800685 TTCCACACCAGCGACCACG 62.801 63.158 0.00 0.00 42.93 4.94
2103 2744 2.110213 TTCCACACCAGCGACCAC 59.890 61.111 0.00 0.00 0.00 4.16
2104 2745 2.110213 GTTCCACACCAGCGACCA 59.890 61.111 0.00 0.00 0.00 4.02
2105 2746 2.668550 GGTTCCACACCAGCGACC 60.669 66.667 0.00 0.00 46.42 4.79
2113 2754 0.899720 TCATACGGGAGGTTCCACAC 59.100 55.000 0.00 0.00 38.64 3.82
2114 2755 0.899720 GTCATACGGGAGGTTCCACA 59.100 55.000 0.00 0.00 38.64 4.17
2115 2756 0.179119 CGTCATACGGGAGGTTCCAC 60.179 60.000 0.00 0.00 38.64 4.02
2116 2757 2.195389 CGTCATACGGGAGGTTCCA 58.805 57.895 0.00 0.00 38.64 3.53
2127 2768 3.564027 GCGGCAGCCACGTCATAC 61.564 66.667 13.30 0.00 37.42 2.39
2128 2769 3.770040 AGCGGCAGCCACGTCATA 61.770 61.111 13.30 0.00 46.67 2.15
2135 2776 4.783621 GATGGTCAGCGGCAGCCA 62.784 66.667 13.30 7.70 46.67 4.75
2136 2777 4.783621 TGATGGTCAGCGGCAGCC 62.784 66.667 4.82 0.00 46.67 4.85
2137 2778 3.503363 GTGATGGTCAGCGGCAGC 61.503 66.667 0.00 0.00 45.58 5.25
2138 2779 2.821366 GGTGATGGTCAGCGGCAG 60.821 66.667 1.45 0.00 35.04 4.85
2143 2784 2.100631 CGGTTCGGTGATGGTCAGC 61.101 63.158 0.00 0.00 41.16 4.26
2144 2785 0.320421 AACGGTTCGGTGATGGTCAG 60.320 55.000 0.00 0.00 0.00 3.51
2145 2786 0.320073 GAACGGTTCGGTGATGGTCA 60.320 55.000 4.94 0.00 0.00 4.02
2197 2838 1.902508 TCTGCCGTGGAGAAAGAGAAT 59.097 47.619 0.00 0.00 0.00 2.40
2243 2884 2.618709 CAGGGAAAAGATAATCGCCCAC 59.381 50.000 0.00 0.00 38.04 4.61
2244 2885 2.930950 CAGGGAAAAGATAATCGCCCA 58.069 47.619 0.00 0.00 38.04 5.36
2245 2886 1.609072 GCAGGGAAAAGATAATCGCCC 59.391 52.381 0.00 0.00 35.79 6.13
2246 2887 1.264288 CGCAGGGAAAAGATAATCGCC 59.736 52.381 0.00 0.00 0.00 5.54
2247 2888 1.334149 GCGCAGGGAAAAGATAATCGC 60.334 52.381 0.30 0.00 0.00 4.58
2248 2889 2.032549 CAGCGCAGGGAAAAGATAATCG 60.033 50.000 11.47 0.00 0.00 3.34
2249 2890 2.287248 GCAGCGCAGGGAAAAGATAATC 60.287 50.000 11.47 0.00 0.00 1.75
2250 2891 1.678101 GCAGCGCAGGGAAAAGATAAT 59.322 47.619 11.47 0.00 0.00 1.28
2251 2892 1.094785 GCAGCGCAGGGAAAAGATAA 58.905 50.000 11.47 0.00 0.00 1.75
2252 2893 1.089481 CGCAGCGCAGGGAAAAGATA 61.089 55.000 11.47 0.00 0.00 1.98
2253 2894 2.401766 CGCAGCGCAGGGAAAAGAT 61.402 57.895 11.47 0.00 0.00 2.40
2254 2895 3.049674 CGCAGCGCAGGGAAAAGA 61.050 61.111 11.47 0.00 0.00 2.52
2267 2908 1.359848 AGAATAGTTGTTCGGCGCAG 58.640 50.000 10.83 5.07 33.36 5.18
2268 2909 1.803334 AAGAATAGTTGTTCGGCGCA 58.197 45.000 10.83 0.00 33.36 6.09
2269 2910 4.531659 AATAAGAATAGTTGTTCGGCGC 57.468 40.909 0.00 0.00 33.36 6.53
2270 2911 8.385111 TCTAAAAATAAGAATAGTTGTTCGGCG 58.615 33.333 0.00 0.00 33.36 6.46
2271 2912 9.704098 CTCTAAAAATAAGAATAGTTGTTCGGC 57.296 33.333 0.00 0.00 33.36 5.54
2288 2929 8.934023 TCACAAATCTTGGTACCTCTAAAAAT 57.066 30.769 14.36 0.00 34.12 1.82
2292 2933 7.685481 TCAATCACAAATCTTGGTACCTCTAA 58.315 34.615 14.36 0.00 34.12 2.10
2295 2936 6.612306 GTTCAATCACAAATCTTGGTACCTC 58.388 40.000 14.36 0.00 34.12 3.85
2297 2938 5.390613 CGTTCAATCACAAATCTTGGTACC 58.609 41.667 4.43 4.43 34.12 3.34
2301 2942 4.455533 TCTCCGTTCAATCACAAATCTTGG 59.544 41.667 0.00 0.00 34.12 3.61
2302 2943 5.611796 TCTCCGTTCAATCACAAATCTTG 57.388 39.130 0.00 0.00 0.00 3.02
2303 2944 5.939883 TCATCTCCGTTCAATCACAAATCTT 59.060 36.000 0.00 0.00 0.00 2.40
2304 2945 5.352569 GTCATCTCCGTTCAATCACAAATCT 59.647 40.000 0.00 0.00 0.00 2.40
2305 2946 5.122239 TGTCATCTCCGTTCAATCACAAATC 59.878 40.000 0.00 0.00 0.00 2.17
2308 2949 4.001618 TGTCATCTCCGTTCAATCACAA 57.998 40.909 0.00 0.00 0.00 3.33
2311 2952 4.872124 CAGAATGTCATCTCCGTTCAATCA 59.128 41.667 0.00 0.00 31.61 2.57
2395 4709 0.041090 CCAACCCCTAAATGGTGGCT 59.959 55.000 0.00 0.00 35.88 4.75
2400 4714 0.334676 TGAGCCCAACCCCTAAATGG 59.665 55.000 0.00 0.00 0.00 3.16
2409 4723 3.017442 GAGAAAGGTAATGAGCCCAACC 58.983 50.000 0.00 0.00 0.00 3.77
2428 4742 1.096386 AGGCGCTCGGTAGTACAGAG 61.096 60.000 21.88 21.88 42.19 3.35
2430 4744 0.587285 CTAGGCGCTCGGTAGTACAG 59.413 60.000 7.64 0.00 0.00 2.74
2431 4745 1.442526 GCTAGGCGCTCGGTAGTACA 61.443 60.000 7.64 0.00 35.14 2.90
2432 4746 1.282265 GCTAGGCGCTCGGTAGTAC 59.718 63.158 7.64 0.00 35.14 2.73
2433 4747 3.741860 GCTAGGCGCTCGGTAGTA 58.258 61.111 7.64 0.00 35.14 1.82
2442 4756 2.580867 CTCGTGTGAGCTAGGCGC 60.581 66.667 0.00 0.00 34.96 6.53
2443 4757 1.063327 CTCTCGTGTGAGCTAGGCG 59.937 63.158 0.00 0.00 42.26 5.52
2444 4758 1.380524 TACTCTCGTGTGAGCTAGGC 58.619 55.000 0.00 0.00 42.26 3.93
2445 4759 4.336993 AGAAATACTCTCGTGTGAGCTAGG 59.663 45.833 0.00 0.00 42.26 3.02
2446 4760 5.493133 AGAAATACTCTCGTGTGAGCTAG 57.507 43.478 0.00 0.00 42.26 3.42
2447 4761 5.487153 GAGAAATACTCTCGTGTGAGCTA 57.513 43.478 0.00 0.00 41.34 3.32
2448 4762 4.364415 GAGAAATACTCTCGTGTGAGCT 57.636 45.455 0.00 0.00 41.34 4.09
2458 4772 4.715297 TCCGCTTAAAGGGAGAAATACTCT 59.285 41.667 0.00 0.00 44.37 3.24
2459 4773 5.019785 TCCGCTTAAAGGGAGAAATACTC 57.980 43.478 0.00 0.00 44.24 2.59
2468 4782 1.338769 GCTTGTCTCCGCTTAAAGGGA 60.339 52.381 0.00 0.00 0.00 4.20
2469 4783 1.087501 GCTTGTCTCCGCTTAAAGGG 58.912 55.000 0.00 0.00 0.00 3.95
2470 4784 2.100605 AGCTTGTCTCCGCTTAAAGG 57.899 50.000 0.00 0.00 31.17 3.11
2471 4785 2.413371 GCAAGCTTGTCTCCGCTTAAAG 60.413 50.000 26.55 0.00 44.06 1.85
2472 4786 1.535462 GCAAGCTTGTCTCCGCTTAAA 59.465 47.619 26.55 0.00 44.06 1.52
2473 4787 1.156736 GCAAGCTTGTCTCCGCTTAA 58.843 50.000 26.55 0.00 44.06 1.85
2474 4788 0.321671 AGCAAGCTTGTCTCCGCTTA 59.678 50.000 26.55 0.00 44.06 3.09
2475 4789 0.952984 GAGCAAGCTTGTCTCCGCTT 60.953 55.000 26.98 8.10 46.59 4.68
2476 4790 1.375268 GAGCAAGCTTGTCTCCGCT 60.375 57.895 26.98 18.88 36.51 5.52
2477 4791 1.357991 GAGAGCAAGCTTGTCTCCGC 61.358 60.000 30.46 23.61 34.24 5.54
2478 4792 1.075425 CGAGAGCAAGCTTGTCTCCG 61.075 60.000 31.30 28.65 34.64 4.63
2479 4793 2.748268 CGAGAGCAAGCTTGTCTCC 58.252 57.895 31.30 24.72 34.64 3.71
2492 4806 2.746362 AGCAAAATTCCTTCAGCGAGAG 59.254 45.455 0.00 0.00 0.00 3.20
2493 4807 2.744202 GAGCAAAATTCCTTCAGCGAGA 59.256 45.455 0.00 0.00 0.00 4.04
2494 4808 2.746362 AGAGCAAAATTCCTTCAGCGAG 59.254 45.455 0.00 0.00 0.00 5.03
2495 4809 2.744202 GAGAGCAAAATTCCTTCAGCGA 59.256 45.455 0.00 0.00 0.00 4.93
2496 4810 2.475187 CGAGAGCAAAATTCCTTCAGCG 60.475 50.000 0.00 0.00 0.00 5.18
2497 4811 3.128465 CGAGAGCAAAATTCCTTCAGC 57.872 47.619 0.00 0.00 0.00 4.26
2512 4826 1.004277 GCCCGATTCATACGCGAGAG 61.004 60.000 15.93 0.78 0.00 3.20
2513 4827 1.007734 GCCCGATTCATACGCGAGA 60.008 57.895 15.93 4.59 0.00 4.04
2514 4828 2.022129 GGCCCGATTCATACGCGAG 61.022 63.158 15.93 1.66 0.00 5.03
2515 4829 2.028484 GGCCCGATTCATACGCGA 59.972 61.111 15.93 0.00 0.00 5.87
2516 4830 3.403057 CGGCCCGATTCATACGCG 61.403 66.667 3.53 3.53 0.00 6.01
2517 4831 2.279918 ACGGCCCGATTCATACGC 60.280 61.111 11.71 0.00 0.00 4.42
2518 4832 1.663702 GGACGGCCCGATTCATACG 60.664 63.158 11.71 0.00 0.00 3.06
2519 4833 4.355925 GGACGGCCCGATTCATAC 57.644 61.111 11.71 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.