Multiple sequence alignment - TraesCS1B01G260400

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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 TraesCS1B01G260400 chr1B 100.000 4721 0 0 1 4721 457861895 457866615 0.000000e+00 8719.0
1 TraesCS1B01G260400 chr1B 80.760 1315 162 50 2307 3597 458007606 458008853 0.000000e+00 942.0
2 TraesCS1B01G260400 chr1B 84.726 419 46 12 1745 2155 458006798 458007206 2.050000e-108 403.0
3 TraesCS1B01G260400 chr1B 78.598 542 90 17 2306 2841 458165650 458166171 7.570000e-88 335.0
4 TraesCS1B01G260400 chr1B 82.099 162 26 2 1063 1221 458011707 458011868 8.240000e-28 135.0
5 TraesCS1B01G260400 chr1D 94.092 1608 71 13 2161 3756 342069993 342071588 0.000000e+00 2422.0
6 TraesCS1B01G260400 chr1D 93.774 1317 57 10 848 2160 342068627 342069922 0.000000e+00 1954.0
7 TraesCS1B01G260400 chr1D 79.932 1460 189 68 2313 3732 342077145 342078540 0.000000e+00 977.0
8 TraesCS1B01G260400 chr1D 79.631 1463 190 60 2307 3732 342129757 342131148 0.000000e+00 952.0
9 TraesCS1B01G260400 chr1D 89.295 738 51 18 3031 3756 342113794 342114515 0.000000e+00 900.0
10 TraesCS1B01G260400 chr1D 81.085 719 85 29 1 710 342065124 342065800 1.160000e-145 527.0
11 TraesCS1B01G260400 chr1D 80.102 588 88 18 2306 2888 342168048 342168611 1.220000e-110 411.0
12 TraesCS1B01G260400 chr1D 84.346 428 44 17 1741 2155 342128948 342129365 9.520000e-107 398.0
13 TraesCS1B01G260400 chr1D 87.719 342 27 9 1824 2160 342076614 342076945 7.410000e-103 385.0
14 TraesCS1B01G260400 chr1D 86.111 180 24 1 1852 2030 342166311 342166490 4.820000e-45 193.0
15 TraesCS1B01G260400 chr1D 82.099 162 26 2 1063 1221 342165838 342165999 8.240000e-28 135.0
16 TraesCS1B01G260400 chr1D 97.222 36 0 1 1302 1337 342166079 342166113 5.100000e-05 60.2
17 TraesCS1B01G260400 chr1A 93.614 1613 77 17 2161 3756 441765172 441766775 0.000000e+00 2385.0
18 TraesCS1B01G260400 chr1A 80.076 1315 161 53 2307 3597 441799292 441800529 0.000000e+00 883.0
19 TraesCS1B01G260400 chr1A 81.981 949 150 13 3783 4712 58300568 58301514 0.000000e+00 785.0
20 TraesCS1B01G260400 chr1A 91.549 568 31 10 779 1340 441763746 441764302 0.000000e+00 767.0
21 TraesCS1B01G260400 chr1A 90.957 564 35 7 3204 3756 441775625 441776183 0.000000e+00 745.0
22 TraesCS1B01G260400 chr1A 88.621 580 59 5 2313 2888 441769402 441769978 0.000000e+00 699.0
23 TraesCS1B01G260400 chr1A 90.419 501 26 5 1668 2160 441764612 441765098 1.430000e-179 640.0
24 TraesCS1B01G260400 chr1A 84.941 425 44 15 1741 2155 441798498 441798912 3.400000e-111 412.0
25 TraesCS1B01G260400 chr1A 83.043 460 61 13 1713 2160 441768749 441769203 7.360000e-108 401.0
26 TraesCS1B01G260400 chr1A 79.231 520 58 29 3246 3732 441770494 441770996 2.740000e-82 316.0
27 TraesCS1B01G260400 chr1A 90.476 210 11 8 562 768 441762621 441762824 7.790000e-68 268.0
28 TraesCS1B01G260400 chr1A 84.916 179 26 1 1853 2030 441835829 441836007 3.750000e-41 180.0
29 TraesCS1B01G260400 chr1A 94.521 73 3 1 3032 3104 441773194 441773265 1.390000e-20 111.0
30 TraesCS1B01G260400 chr1A 93.333 75 4 1 3100 3174 441773609 441773682 4.990000e-20 110.0
31 TraesCS1B01G260400 chr1A 88.679 53 6 0 1582 1634 441764559 441764611 1.100000e-06 65.8
32 TraesCS1B01G260400 chr2B 83.838 990 136 15 3744 4712 798184334 798185320 0.000000e+00 920.0
33 TraesCS1B01G260400 chr2D 82.794 988 145 17 3745 4712 57209350 57210332 0.000000e+00 859.0
34 TraesCS1B01G260400 chr5D 82.139 991 149 21 3746 4718 439300555 439301535 0.000000e+00 824.0
35 TraesCS1B01G260400 chr7D 81.571 993 154 19 3748 4718 180223903 180224888 0.000000e+00 793.0
36 TraesCS1B01G260400 chr7D 80.427 797 142 10 3777 4562 19016051 19016844 3.140000e-166 595.0
37 TraesCS1B01G260400 chr4D 81.319 1001 161 18 3738 4718 461381481 461382475 0.000000e+00 789.0
38 TraesCS1B01G260400 chr4D 81.780 944 147 17 3796 4718 374331327 374330388 0.000000e+00 767.0
39 TraesCS1B01G260400 chr4D 81.224 948 146 20 3791 4718 397374636 397375571 0.000000e+00 736.0
40 TraesCS1B01G260400 chr6D 81.149 992 163 14 3747 4718 464428911 464427924 0.000000e+00 774.0
41 TraesCS1B01G260400 chr3A 88.608 79 8 1 2778 2856 46840305 46840228 1.400000e-15 95.3
42 TraesCS1B01G260400 chr3B 92.683 41 3 0 2770 2810 59044993 59044953 5.100000e-05 60.2


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 TraesCS1B01G260400 chr1B 457861895 457866615 4720 False 8719.000000 8719 100.000000 1 4721 1 chr1B.!!$F1 4720
1 TraesCS1B01G260400 chr1B 458006798 458011868 5070 False 493.333333 942 82.528333 1063 3597 3 chr1B.!!$F3 2534
2 TraesCS1B01G260400 chr1B 458165650 458166171 521 False 335.000000 335 78.598000 2306 2841 1 chr1B.!!$F2 535
3 TraesCS1B01G260400 chr1D 342065124 342071588 6464 False 1634.333333 2422 89.650333 1 3756 3 chr1D.!!$F2 3755
4 TraesCS1B01G260400 chr1D 342113794 342114515 721 False 900.000000 900 89.295000 3031 3756 1 chr1D.!!$F1 725
5 TraesCS1B01G260400 chr1D 342076614 342078540 1926 False 681.000000 977 83.825500 1824 3732 2 chr1D.!!$F3 1908
6 TraesCS1B01G260400 chr1D 342128948 342131148 2200 False 675.000000 952 81.988500 1741 3732 2 chr1D.!!$F4 1991
7 TraesCS1B01G260400 chr1A 58300568 58301514 946 False 785.000000 785 81.981000 3783 4712 1 chr1A.!!$F1 929
8 TraesCS1B01G260400 chr1A 441798498 441800529 2031 False 647.500000 883 82.508500 1741 3597 2 chr1A.!!$F4 1856
9 TraesCS1B01G260400 chr1A 441762621 441776183 13562 False 591.618182 2385 89.494818 562 3756 11 chr1A.!!$F3 3194
10 TraesCS1B01G260400 chr2B 798184334 798185320 986 False 920.000000 920 83.838000 3744 4712 1 chr2B.!!$F1 968
11 TraesCS1B01G260400 chr2D 57209350 57210332 982 False 859.000000 859 82.794000 3745 4712 1 chr2D.!!$F1 967
12 TraesCS1B01G260400 chr5D 439300555 439301535 980 False 824.000000 824 82.139000 3746 4718 1 chr5D.!!$F1 972
13 TraesCS1B01G260400 chr7D 180223903 180224888 985 False 793.000000 793 81.571000 3748 4718 1 chr7D.!!$F2 970
14 TraesCS1B01G260400 chr7D 19016051 19016844 793 False 595.000000 595 80.427000 3777 4562 1 chr7D.!!$F1 785
15 TraesCS1B01G260400 chr4D 461381481 461382475 994 False 789.000000 789 81.319000 3738 4718 1 chr4D.!!$F2 980
16 TraesCS1B01G260400 chr4D 374330388 374331327 939 True 767.000000 767 81.780000 3796 4718 1 chr4D.!!$R1 922
17 TraesCS1B01G260400 chr4D 397374636 397375571 935 False 736.000000 736 81.224000 3791 4718 1 chr4D.!!$F1 927
18 TraesCS1B01G260400 chr6D 464427924 464428911 987 True 774.000000 774 81.149000 3747 4718 1 chr6D.!!$R1 971

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
774 783 0.254747 TGTGATTTAGCCCCCTTCGG 59.745 55.000 0.00 0.0 0.0 4.30 F
1616 4507 1.078759 GTGGAAGTCGATCTGCACGG 61.079 60.000 5.77 0.0 0.0 4.94 F
2215 9300 1.210967 TCCTGTTCTTCCACCAACGTT 59.789 47.619 0.00 0.0 0.0 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 10002 0.394899 GGGGCATTTCACCTCTGAGG 60.395 60.0 22.00 22.00 42.49 3.86 R
3509 11083 1.111277 ATTACAAAAGGATGGCCGCC 58.889 50.0 1.04 1.04 39.96 6.13 R
3932 16713 0.831711 TGGCTGACACTAGAGGCACA 60.832 55.0 0.00 0.00 39.65 4.57 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 4.150627 CGAGTGTAATGTGTTCCTTGACTG 59.849 45.833 0.00 0.00 0.00 3.51
25 26 4.102524 AGTGTAATGTGTTCCTTGACTGGA 59.897 41.667 0.00 0.00 0.00 3.86
36 37 0.770499 TTGACTGGATGCTCAACCCA 59.230 50.000 0.00 0.00 0.00 4.51
37 38 0.770499 TGACTGGATGCTCAACCCAA 59.230 50.000 0.00 0.00 0.00 4.12
38 39 1.144708 TGACTGGATGCTCAACCCAAA 59.855 47.619 0.00 0.00 0.00 3.28
39 40 1.815003 GACTGGATGCTCAACCCAAAG 59.185 52.381 0.00 0.00 0.00 2.77
43 44 3.509442 TGGATGCTCAACCCAAAGAAAT 58.491 40.909 0.00 0.00 0.00 2.17
44 45 3.511146 TGGATGCTCAACCCAAAGAAATC 59.489 43.478 0.00 0.00 0.00 2.17
50 51 4.559502 GCTCAACCCAAAGAAATCTTCCAC 60.560 45.833 0.00 0.00 34.61 4.02
77 78 8.289618 GTCTCACTTATGCATTTGTGACTTAAA 58.710 33.333 22.32 8.47 35.83 1.52
78 79 9.013229 TCTCACTTATGCATTTGTGACTTAAAT 57.987 29.630 22.32 0.00 35.83 1.40
82 83 9.935682 ACTTATGCATTTGTGACTTAAATATCG 57.064 29.630 3.54 0.00 0.00 2.92
89 90 8.840321 CATTTGTGACTTAAATATCGAATCCCT 58.160 33.333 0.00 0.00 0.00 4.20
117 119 9.672086 TCTTTTAGTTCGGTTTGAAATTATGTG 57.328 29.630 0.00 0.00 38.60 3.21
129 131 5.076182 TGAAATTATGTGTTGCTCCTCCAA 58.924 37.500 0.00 0.00 0.00 3.53
138 140 2.665000 CTCCTCCAAGCCAGCGAA 59.335 61.111 0.00 0.00 0.00 4.70
152 154 3.283684 CGAAGCCCCGCAACACAA 61.284 61.111 0.00 0.00 0.00 3.33
153 155 2.625823 CGAAGCCCCGCAACACAAT 61.626 57.895 0.00 0.00 0.00 2.71
157 159 2.990967 CCCCGCAACACAATGCCT 60.991 61.111 0.00 0.00 43.47 4.75
167 169 4.012374 CAACACAATGCCTAGATGAACCT 58.988 43.478 0.00 0.00 0.00 3.50
174 176 1.950828 CCTAGATGAACCTGCTGCAG 58.049 55.000 22.44 22.44 0.00 4.41
191 197 1.470098 GCAGCAACATGGGTCAACTAG 59.530 52.381 0.00 0.00 0.00 2.57
203 209 1.993370 GTCAACTAGTAGCGGCAACAG 59.007 52.381 1.45 0.00 0.00 3.16
207 213 1.067071 ACTAGTAGCGGCAACAGGTTC 60.067 52.381 1.45 0.00 0.00 3.62
222 228 3.119291 CAGGTTCTAGATCACGACATGC 58.881 50.000 0.00 0.00 0.00 4.06
225 231 3.511699 GTTCTAGATCACGACATGCACA 58.488 45.455 0.00 0.00 0.00 4.57
230 236 1.064505 GATCACGACATGCACAATGGG 59.935 52.381 0.00 0.00 40.94 4.00
233 239 0.597568 ACGACATGCACAATGGGTTG 59.402 50.000 0.00 0.00 40.94 3.77
262 268 3.441222 TCAGCCAACTTGCACTTATCATG 59.559 43.478 0.00 0.00 0.00 3.07
296 302 3.463944 CCTTGAGTAAGGTTGTCGTGTT 58.536 45.455 0.00 0.00 46.92 3.32
297 303 3.493503 CCTTGAGTAAGGTTGTCGTGTTC 59.506 47.826 0.00 0.00 46.92 3.18
340 346 5.146010 TGCTTTTATGGGTTTTTGCTAGG 57.854 39.130 0.00 0.00 0.00 3.02
343 349 6.267928 TGCTTTTATGGGTTTTTGCTAGGTTA 59.732 34.615 0.00 0.00 0.00 2.85
353 359 9.146984 GGGTTTTTGCTAGGTTATTTTTATGAC 57.853 33.333 0.00 0.00 0.00 3.06
374 380 4.843728 ACTTTTTCTGAGCCATAATCCGA 58.156 39.130 0.00 0.00 0.00 4.55
376 382 5.123979 ACTTTTTCTGAGCCATAATCCGAAC 59.876 40.000 0.00 0.00 0.00 3.95
377 383 4.487714 TTTCTGAGCCATAATCCGAACT 57.512 40.909 0.00 0.00 0.00 3.01
378 384 3.735237 TCTGAGCCATAATCCGAACTC 57.265 47.619 0.00 0.00 0.00 3.01
381 387 3.031013 TGAGCCATAATCCGAACTCTGA 58.969 45.455 0.00 0.00 0.00 3.27
384 390 3.706594 AGCCATAATCCGAACTCTGAAGA 59.293 43.478 0.00 0.00 0.00 2.87
386 392 4.202161 GCCATAATCCGAACTCTGAAGAGA 60.202 45.833 14.20 0.00 44.74 3.10
387 393 5.682471 GCCATAATCCGAACTCTGAAGAGAA 60.682 44.000 14.20 0.00 44.74 2.87
388 394 5.982516 CCATAATCCGAACTCTGAAGAGAAG 59.017 44.000 14.20 4.78 44.74 2.85
389 395 4.464069 AATCCGAACTCTGAAGAGAAGG 57.536 45.455 14.20 12.55 44.74 3.46
390 396 1.546476 TCCGAACTCTGAAGAGAAGGC 59.454 52.381 14.20 0.12 44.74 4.35
407 413 4.413520 AGAAGGCATAGGGATTTCTGCTAA 59.586 41.667 0.00 0.00 35.03 3.09
408 414 4.796110 AGGCATAGGGATTTCTGCTAAA 57.204 40.909 0.00 0.00 35.03 1.85
413 419 5.358160 GCATAGGGATTTCTGCTAAAGTGTT 59.642 40.000 0.00 0.00 0.00 3.32
434 440 3.402110 TGAGGTACTGCACATGTGAAAG 58.598 45.455 29.80 24.74 41.55 2.62
439 445 3.430042 ACTGCACATGTGAAAGGAGAT 57.570 42.857 29.80 6.96 0.00 2.75
443 449 2.615912 GCACATGTGAAAGGAGATAGGC 59.384 50.000 29.80 5.08 0.00 3.93
461 467 2.443255 AGGCAGGAAGAAGGACAAAGAA 59.557 45.455 0.00 0.00 0.00 2.52
463 469 3.829026 GGCAGGAAGAAGGACAAAGAAAT 59.171 43.478 0.00 0.00 0.00 2.17
464 470 5.010282 GGCAGGAAGAAGGACAAAGAAATA 58.990 41.667 0.00 0.00 0.00 1.40
465 471 5.124617 GGCAGGAAGAAGGACAAAGAAATAG 59.875 44.000 0.00 0.00 0.00 1.73
466 472 5.940470 GCAGGAAGAAGGACAAAGAAATAGA 59.060 40.000 0.00 0.00 0.00 1.98
467 473 6.431234 GCAGGAAGAAGGACAAAGAAATAGAA 59.569 38.462 0.00 0.00 0.00 2.10
468 474 7.040409 GCAGGAAGAAGGACAAAGAAATAGAAA 60.040 37.037 0.00 0.00 0.00 2.52
469 475 8.510505 CAGGAAGAAGGACAAAGAAATAGAAAG 58.489 37.037 0.00 0.00 0.00 2.62
470 476 8.440771 AGGAAGAAGGACAAAGAAATAGAAAGA 58.559 33.333 0.00 0.00 0.00 2.52
471 477 9.067986 GGAAGAAGGACAAAGAAATAGAAAGAA 57.932 33.333 0.00 0.00 0.00 2.52
473 479 8.628630 AGAAGGACAAAGAAATAGAAAGAAGG 57.371 34.615 0.00 0.00 0.00 3.46
474 480 8.440771 AGAAGGACAAAGAAATAGAAAGAAGGA 58.559 33.333 0.00 0.00 0.00 3.36
475 481 7.987750 AGGACAAAGAAATAGAAAGAAGGAC 57.012 36.000 0.00 0.00 0.00 3.85
476 482 7.518188 AGGACAAAGAAATAGAAAGAAGGACA 58.482 34.615 0.00 0.00 0.00 4.02
477 483 7.998964 AGGACAAAGAAATAGAAAGAAGGACAA 59.001 33.333 0.00 0.00 0.00 3.18
478 484 8.630037 GGACAAAGAAATAGAAAGAAGGACAAA 58.370 33.333 0.00 0.00 0.00 2.83
479 485 9.670719 GACAAAGAAATAGAAAGAAGGACAAAG 57.329 33.333 0.00 0.00 0.00 2.77
480 486 9.408648 ACAAAGAAATAGAAAGAAGGACAAAGA 57.591 29.630 0.00 0.00 0.00 2.52
481 487 9.890352 CAAAGAAATAGAAAGAAGGACAAAGAG 57.110 33.333 0.00 0.00 0.00 2.85
482 488 8.628630 AAGAAATAGAAAGAAGGACAAAGAGG 57.371 34.615 0.00 0.00 0.00 3.69
483 489 7.750655 AGAAATAGAAAGAAGGACAAAGAGGT 58.249 34.615 0.00 0.00 0.00 3.85
484 490 7.663493 AGAAATAGAAAGAAGGACAAAGAGGTG 59.337 37.037 0.00 0.00 0.00 4.00
485 491 3.481453 AGAAAGAAGGACAAAGAGGTGC 58.519 45.455 0.00 0.00 0.00 5.01
486 492 3.137360 AGAAAGAAGGACAAAGAGGTGCT 59.863 43.478 0.00 0.00 41.57 4.40
487 493 2.557920 AGAAGGACAAAGAGGTGCTG 57.442 50.000 0.00 0.00 39.56 4.41
502 508 1.727335 GTGCTGTTAGCGGTTTCTCTC 59.273 52.381 0.00 0.00 46.26 3.20
503 509 1.337823 TGCTGTTAGCGGTTTCTCTCC 60.338 52.381 0.00 0.00 46.26 3.71
515 521 3.067040 GGTTTCTCTCCGTCTAGACATCC 59.933 52.174 22.37 6.15 0.00 3.51
528 534 1.185315 GACATCCCACCCAAACATGG 58.815 55.000 0.00 0.00 35.59 3.66
530 536 1.362237 ACATCCCACCCAAACATGGAT 59.638 47.619 0.00 0.00 38.34 3.41
531 537 1.758280 CATCCCACCCAAACATGGATG 59.242 52.381 0.00 0.00 44.53 3.51
532 538 1.079796 TCCCACCCAAACATGGATGA 58.920 50.000 0.00 0.00 38.34 2.92
533 539 1.005805 TCCCACCCAAACATGGATGAG 59.994 52.381 0.00 0.00 38.34 2.90
538 544 1.684983 CCCAAACATGGATGAGATGGC 59.315 52.381 0.00 0.00 31.73 4.40
588 597 2.025981 CAGGGACATGATGTTCTCCCAA 60.026 50.000 19.41 0.00 35.13 4.12
717 726 6.476243 AACTAGATAATTGTTCGTGCGTTT 57.524 33.333 0.00 0.00 0.00 3.60
718 727 5.854157 ACTAGATAATTGTTCGTGCGTTTG 58.146 37.500 0.00 0.00 0.00 2.93
719 728 3.488489 AGATAATTGTTCGTGCGTTTGC 58.512 40.909 0.00 0.00 43.20 3.68
764 773 5.627499 TGGTGCTTTAGCTTGTGATTTAG 57.373 39.130 0.00 0.00 42.66 1.85
767 776 3.443681 TGCTTTAGCTTGTGATTTAGCCC 59.556 43.478 0.00 0.00 42.66 5.19
771 780 1.359130 AGCTTGTGATTTAGCCCCCTT 59.641 47.619 0.00 0.00 38.14 3.95
772 781 1.751351 GCTTGTGATTTAGCCCCCTTC 59.249 52.381 0.00 0.00 0.00 3.46
774 783 0.254747 TGTGATTTAGCCCCCTTCGG 59.745 55.000 0.00 0.00 0.00 4.30
777 786 1.766496 TGATTTAGCCCCCTTCGGTAG 59.234 52.381 0.00 0.00 0.00 3.18
812 3263 4.093850 GCATCAAAATCAAATTGGGTCAGC 59.906 41.667 0.00 0.00 0.00 4.26
993 3757 4.060667 CCTGGCCCCGTTCCCAAT 62.061 66.667 0.00 0.00 0.00 3.16
994 3758 2.440247 CTGGCCCCGTTCCCAATC 60.440 66.667 0.00 0.00 0.00 2.67
995 3759 4.055227 TGGCCCCGTTCCCAATCC 62.055 66.667 0.00 0.00 0.00 3.01
996 3760 4.833989 GGCCCCGTTCCCAATCCC 62.834 72.222 0.00 0.00 0.00 3.85
997 3761 4.055227 GCCCCGTTCCCAATCCCA 62.055 66.667 0.00 0.00 0.00 4.37
998 3762 2.767352 CCCCGTTCCCAATCCCAA 59.233 61.111 0.00 0.00 0.00 4.12
999 3763 1.309688 CCCCGTTCCCAATCCCAAT 59.690 57.895 0.00 0.00 0.00 3.16
1021 3785 2.100252 CCAATCTCATCGCCAAGCAATT 59.900 45.455 0.00 0.00 0.00 2.32
1022 3786 3.316029 CCAATCTCATCGCCAAGCAATTA 59.684 43.478 0.00 0.00 0.00 1.40
1023 3787 4.285292 CAATCTCATCGCCAAGCAATTAC 58.715 43.478 0.00 0.00 0.00 1.89
1024 3788 3.266510 TCTCATCGCCAAGCAATTACT 57.733 42.857 0.00 0.00 0.00 2.24
1025 3789 3.198068 TCTCATCGCCAAGCAATTACTC 58.802 45.455 0.00 0.00 0.00 2.59
1026 3790 2.288666 TCATCGCCAAGCAATTACTCC 58.711 47.619 0.00 0.00 0.00 3.85
1027 3791 2.016318 CATCGCCAAGCAATTACTCCA 58.984 47.619 0.00 0.00 0.00 3.86
1028 3792 1.737838 TCGCCAAGCAATTACTCCAG 58.262 50.000 0.00 0.00 0.00 3.86
1106 3880 4.344865 AACCCACCGGCGCTCAAT 62.345 61.111 7.64 0.00 0.00 2.57
1225 3999 3.294943 CCGACGTCTACGGTAATTGATC 58.705 50.000 14.70 0.00 44.57 2.92
1263 4039 5.279384 TCTCTATTCGTATTCAAGTTCGGC 58.721 41.667 0.00 0.00 0.00 5.54
1366 4142 3.693578 TGTTTGTGCTTTCTGACATCACA 59.306 39.130 0.00 0.00 36.07 3.58
1386 4162 8.924691 CATCACAAGTTTTGTTTTATACCCATG 58.075 33.333 0.00 0.00 43.23 3.66
1393 4169 8.576442 AGTTTTGTTTTATACCCATGTCTCTTG 58.424 33.333 0.00 0.00 0.00 3.02
1403 4179 3.629398 CCCATGTCTCTTGGTTTAGCATC 59.371 47.826 0.00 0.00 31.99 3.91
1406 4182 1.666189 GTCTCTTGGTTTAGCATCGGC 59.334 52.381 0.00 0.00 41.61 5.54
1491 4267 5.680594 AAATCATCAGGCCATTTAGCAAA 57.319 34.783 5.01 0.00 0.00 3.68
1543 4319 4.672862 CGAGTCGTGCATATTGTCTAGAAG 59.327 45.833 3.82 0.00 0.00 2.85
1610 4501 1.337260 GCTGTGTGTGGAAGTCGATCT 60.337 52.381 0.00 0.00 0.00 2.75
1616 4507 1.078759 GTGGAAGTCGATCTGCACGG 61.079 60.000 5.77 0.00 0.00 4.94
1758 4658 8.925700 CCAGCTGTTAATTTTTGAATAGTTTCC 58.074 33.333 13.81 0.00 0.00 3.13
1768 4668 6.633500 TTTGAATAGTTTCCTGTGGACTTG 57.367 37.500 0.00 0.00 0.00 3.16
2155 9166 8.362639 ACTTAGATTCGGACAGTGTTAACTAAA 58.637 33.333 7.22 0.00 33.79 1.85
2199 9283 4.872691 GGATACTGACTGATTGTTGTCCTG 59.127 45.833 0.00 0.00 32.67 3.86
2200 9284 3.845781 ACTGACTGATTGTTGTCCTGT 57.154 42.857 0.00 0.00 32.67 4.00
2215 9300 1.210967 TCCTGTTCTTCCACCAACGTT 59.789 47.619 0.00 0.00 0.00 3.99
2461 9759 7.096551 AGCACTGTTTTGTTTTGTTACATCTT 58.903 30.769 0.00 0.00 0.00 2.40
2470 9769 8.705048 TTGTTTTGTTACATCTTAACCCAAAC 57.295 30.769 9.82 9.82 34.07 2.93
2473 9773 8.410912 GTTTTGTTACATCTTAACCCAAACTCT 58.589 33.333 0.00 0.00 32.54 3.24
2484 9784 9.346005 TCTTAACCCAAACTCTTAAGGTTTAAG 57.654 33.333 16.67 15.61 41.06 1.85
2597 9897 3.364964 CGCACCCTTCATTTGTTACTGTC 60.365 47.826 0.00 0.00 0.00 3.51
2598 9898 3.568007 GCACCCTTCATTTGTTACTGTCA 59.432 43.478 0.00 0.00 0.00 3.58
2629 9930 6.306643 AGAAGGTAAAATCTCTCCTTGAGG 57.693 41.667 0.00 0.00 42.86 3.86
2634 9935 7.797062 AGGTAAAATCTCTCCTTGAGGATTAC 58.203 38.462 0.00 5.52 44.46 1.89
2647 9948 6.536582 CCTTGAGGATTACAGATACACACTTG 59.463 42.308 0.00 0.00 37.39 3.16
2701 10002 6.722301 TCTTACACTACGACATGTGCTATAC 58.278 40.000 1.15 0.00 37.68 1.47
2748 10049 1.871080 ACTTGGAGCTGAAACTGACG 58.129 50.000 0.00 0.00 0.00 4.35
2823 10134 4.019231 ACTCAGGGGTAAGTTCTCATTTCC 60.019 45.833 0.00 0.00 0.00 3.13
2845 10161 1.611491 GCAACCCGATCTTCAAACCAA 59.389 47.619 0.00 0.00 0.00 3.67
2906 10223 8.642908 AACAAAGGCTAAACTAATTGTCAAAC 57.357 30.769 0.00 0.00 31.19 2.93
2924 10241 1.604593 CTTGGAACTGCCCTGGTGG 60.605 63.158 0.00 0.00 34.97 4.61
2954 10272 1.973515 TCTGACCAGAATGCTGTCTGT 59.026 47.619 13.85 0.00 43.02 3.41
2960 10278 3.701040 ACCAGAATGCTGTCTGTTTGTTT 59.299 39.130 13.85 0.00 43.02 2.83
2967 10285 2.543653 GCTGTCTGTTTGTTTCGGCATT 60.544 45.455 0.00 0.00 0.00 3.56
2980 10298 2.609350 TCGGCATTACGTGTTTCTACC 58.391 47.619 0.00 0.00 34.94 3.18
3000 10318 6.906901 TCTACCTCCTTCCCAAATTATGTACT 59.093 38.462 0.00 0.00 0.00 2.73
3001 10319 8.069356 TCTACCTCCTTCCCAAATTATGTACTA 58.931 37.037 0.00 0.00 0.00 1.82
3002 10320 6.896883 ACCTCCTTCCCAAATTATGTACTAC 58.103 40.000 0.00 0.00 0.00 2.73
3003 10321 6.677076 ACCTCCTTCCCAAATTATGTACTACT 59.323 38.462 0.00 0.00 0.00 2.57
3022 10340 9.556030 GTACTACTAATTTGCCTTTTGATGTTC 57.444 33.333 0.00 0.00 0.00 3.18
3143 10557 7.238486 AGCTAGTGTTATTATCCATCTGAGG 57.762 40.000 0.00 0.00 0.00 3.86
3376 10950 6.233434 ACAGATTGCTCACTTTGTCAAGATA 58.767 36.000 0.00 0.00 33.72 1.98
3478 11052 1.398390 GCGGACATGATTGACTGGTTC 59.602 52.381 0.00 0.00 0.00 3.62
3509 11083 6.824305 ACCTCAAGTGAACCTAATGAATTG 57.176 37.500 0.00 0.00 0.00 2.32
3658 16413 3.738830 ATGTGTGTGCTTGCTCATTTT 57.261 38.095 0.73 0.00 0.00 1.82
3698 16461 5.237127 TGAACACTGAAACTATTGCACTCAG 59.763 40.000 0.00 0.00 39.53 3.35
3751 16514 4.954875 TGGCACTTTCCTGGTTATTTTTG 58.045 39.130 0.00 0.00 0.00 2.44
3756 16519 7.496263 GGCACTTTCCTGGTTATTTTTGTTTTA 59.504 33.333 0.00 0.00 0.00 1.52
3827 16594 7.823745 AAAGGTGAATGTTTACAGAACTCAT 57.176 32.000 0.00 0.00 0.00 2.90
3829 16596 6.533730 AGGTGAATGTTTACAGAACTCATGA 58.466 36.000 0.00 0.00 0.00 3.07
3833 16600 9.515020 GTGAATGTTTACAGAACTCATGAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
3869 16650 4.988598 CACAGCCCGGCGTGTTCT 62.989 66.667 19.88 0.00 32.05 3.01
3935 16716 8.637986 AGATCCTCTAGAATAGCTTTAACTGTG 58.362 37.037 0.00 0.00 38.99 3.66
3943 16724 5.941555 ATAGCTTTAACTGTGCCTCTAGT 57.058 39.130 0.00 0.00 0.00 2.57
3944 16725 3.931578 AGCTTTAACTGTGCCTCTAGTG 58.068 45.455 0.00 0.00 0.00 2.74
3951 16732 0.831711 TGTGCCTCTAGTGTCAGCCA 60.832 55.000 0.00 0.00 0.00 4.75
3994 16776 3.486383 TGTTCCTTGTGTCCCAGATTTC 58.514 45.455 0.00 0.00 0.00 2.17
4012 16794 5.671276 AGATTTCCCAGAGAATGAGAAGGAT 59.329 40.000 0.00 0.00 33.44 3.24
4148 16930 2.224066 CGGACAAGTGAAGAAGAGGTGT 60.224 50.000 0.00 0.00 0.00 4.16
4152 16934 5.041191 ACAAGTGAAGAAGAGGTGTTCAT 57.959 39.130 0.00 0.00 41.22 2.57
4175 16957 0.540365 CCTCCACAGGGTTGTTGCAT 60.540 55.000 0.00 0.00 35.89 3.96
4199 16981 1.528292 GACAGGTGTCCGAGCTCAGT 61.528 60.000 15.40 0.00 39.07 3.41
4278 17060 6.109359 CACCCGAAGATCATTACTTTCTTCT 58.891 40.000 9.46 0.00 41.96 2.85
4289 17071 1.494721 ACTTTCTTCTGCACCCTGGAA 59.505 47.619 0.00 0.00 0.00 3.53
4315 17330 2.429930 CAGGGCAAGAACGGGTCA 59.570 61.111 0.00 0.00 0.00 4.02
4317 17332 1.841556 AGGGCAAGAACGGGTCAGA 60.842 57.895 0.00 0.00 0.00 3.27
4335 17350 2.300152 CAGAGAGCTGGGTGTTAAGTGA 59.700 50.000 0.00 0.00 38.51 3.41
4350 17365 2.591144 TGATGCATATGCGCCGCA 60.591 55.556 16.69 16.69 45.83 5.69
4367 17382 2.606795 CCGCACGTGGTGAAATTTTCAT 60.607 45.455 18.88 0.00 42.47 2.57
4396 17593 2.636412 CCTCGTGTCCGGCTCTTGA 61.636 63.158 0.00 0.00 33.95 3.02
4403 17600 0.741915 GTCCGGCTCTTGAGAGGTAG 59.258 60.000 9.87 0.00 42.29 3.18
4404 17601 0.331954 TCCGGCTCTTGAGAGGTAGT 59.668 55.000 9.87 0.00 42.29 2.73
4407 17604 1.819288 CGGCTCTTGAGAGGTAGTGAA 59.181 52.381 9.87 0.00 42.29 3.18
4442 17862 7.170393 ACAAAGAGTTTAGAAAGGCAAGTTT 57.830 32.000 0.00 0.00 0.00 2.66
4445 17865 6.775594 AGAGTTTAGAAAGGCAAGTTTTGT 57.224 33.333 0.00 0.00 0.00 2.83
4540 17962 2.096248 TGTTTTGTGTGGTGGGAGAAC 58.904 47.619 0.00 0.00 0.00 3.01
4542 17964 2.494073 GTTTTGTGTGGTGGGAGAACAA 59.506 45.455 0.00 0.00 0.00 2.83
4555 17977 4.043561 TGGGAGAACAAAGCAGGGTAAATA 59.956 41.667 0.00 0.00 0.00 1.40
4557 17979 5.105877 GGGAGAACAAAGCAGGGTAAATAAC 60.106 44.000 0.00 0.00 0.00 1.89
4566 17995 3.370527 GCAGGGTAAATAACAGCTCAGGA 60.371 47.826 0.00 0.00 0.00 3.86
4638 18067 3.831333 AGCAGTGTGAAATCTCTCTCAGA 59.169 43.478 0.00 0.00 34.78 3.27
4680 19113 7.524717 AATAGTTTTTGCAAAGAAGGAGCTA 57.475 32.000 12.41 9.10 0.00 3.32
4682 19115 6.018589 AGTTTTTGCAAAGAAGGAGCTATC 57.981 37.500 12.41 0.00 0.00 2.08
4683 19116 5.772169 AGTTTTTGCAAAGAAGGAGCTATCT 59.228 36.000 12.41 0.00 0.00 1.98
4690 19138 5.221621 GCAAAGAAGGAGCTATCTCTACCAT 60.222 44.000 0.00 0.00 39.31 3.55
4699 19147 5.655394 AGCTATCTCTACCATACCCAATGA 58.345 41.667 0.00 0.00 37.86 2.57
4718 19166 4.332683 TGAGAAGTGGGGAGTAGTGTAT 57.667 45.455 0.00 0.00 0.00 2.29
4719 19167 4.684724 TGAGAAGTGGGGAGTAGTGTATT 58.315 43.478 0.00 0.00 0.00 1.89
4720 19168 5.834460 TGAGAAGTGGGGAGTAGTGTATTA 58.166 41.667 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.385825 TCCAGTCAAGGAACACATTACAC 58.614 43.478 0.00 0.00 33.93 2.90
13 14 2.553028 GGTTGAGCATCCAGTCAAGGAA 60.553 50.000 0.00 0.00 41.92 3.36
23 24 3.766051 AGATTTCTTTGGGTTGAGCATCC 59.234 43.478 0.00 0.00 0.00 3.51
25 26 4.221482 GGAAGATTTCTTTGGGTTGAGCAT 59.779 41.667 0.00 0.00 36.11 3.79
36 37 4.962155 AGTGAGACGTGGAAGATTTCTTT 58.038 39.130 0.00 0.00 36.11 2.52
37 38 4.608948 AGTGAGACGTGGAAGATTTCTT 57.391 40.909 0.00 0.00 39.23 2.52
38 39 4.608948 AAGTGAGACGTGGAAGATTTCT 57.391 40.909 0.00 0.00 0.00 2.52
39 40 5.220491 GCATAAGTGAGACGTGGAAGATTTC 60.220 44.000 0.00 0.00 0.00 2.17
43 44 2.560981 TGCATAAGTGAGACGTGGAAGA 59.439 45.455 0.00 0.00 0.00 2.87
44 45 2.959516 TGCATAAGTGAGACGTGGAAG 58.040 47.619 0.00 0.00 0.00 3.46
50 51 4.389992 AGTCACAAATGCATAAGTGAGACG 59.610 41.667 25.70 6.81 41.20 4.18
77 78 8.251721 CCGAACTAAAAGATAGGGATTCGATAT 58.748 37.037 4.74 0.00 39.94 1.63
78 79 7.232127 ACCGAACTAAAAGATAGGGATTCGATA 59.768 37.037 4.74 0.00 39.94 2.92
82 83 7.551617 TCAAACCGAACTAAAAGATAGGGATTC 59.448 37.037 0.00 0.00 0.00 2.52
83 84 7.399634 TCAAACCGAACTAAAAGATAGGGATT 58.600 34.615 0.00 0.00 0.00 3.01
91 92 9.672086 CACATAATTTCAAACCGAACTAAAAGA 57.328 29.630 0.00 0.00 31.73 2.52
96 97 6.858993 GCAACACATAATTTCAAACCGAACTA 59.141 34.615 0.00 0.00 31.73 2.24
101 102 4.621034 GGAGCAACACATAATTTCAAACCG 59.379 41.667 0.00 0.00 0.00 4.44
117 119 2.338785 GCTGGCTTGGAGGAGCAAC 61.339 63.158 0.00 0.00 44.49 4.17
138 140 3.683937 GCATTGTGTTGCGGGGCT 61.684 61.111 0.00 0.00 32.06 5.19
144 146 3.428045 GGTTCATCTAGGCATTGTGTTGC 60.428 47.826 0.00 0.00 42.01 4.17
146 148 4.012374 CAGGTTCATCTAGGCATTGTGTT 58.988 43.478 0.00 0.00 0.00 3.32
149 151 2.240667 AGCAGGTTCATCTAGGCATTGT 59.759 45.455 0.00 0.00 0.00 2.71
152 154 1.476471 GCAGCAGGTTCATCTAGGCAT 60.476 52.381 0.00 0.00 0.00 4.40
153 155 0.107508 GCAGCAGGTTCATCTAGGCA 60.108 55.000 0.00 0.00 0.00 4.75
157 159 3.465990 GCTGCAGCAGGTTCATCTA 57.534 52.632 33.36 0.00 41.59 1.98
174 176 2.678336 GCTACTAGTTGACCCATGTTGC 59.322 50.000 8.60 0.00 0.00 4.17
181 183 0.248289 TTGCCGCTACTAGTTGACCC 59.752 55.000 8.60 0.00 0.00 4.46
182 184 1.337447 TGTTGCCGCTACTAGTTGACC 60.337 52.381 8.60 0.00 0.00 4.02
183 185 1.993370 CTGTTGCCGCTACTAGTTGAC 59.007 52.381 8.60 0.00 0.00 3.18
191 197 1.203994 TCTAGAACCTGTTGCCGCTAC 59.796 52.381 0.00 0.00 0.00 3.58
203 209 2.860735 GTGCATGTCGTGATCTAGAACC 59.139 50.000 0.00 0.00 0.00 3.62
207 213 3.246936 CCATTGTGCATGTCGTGATCTAG 59.753 47.826 0.00 0.00 0.00 2.43
222 228 3.747529 GCTGAAAATTCCAACCCATTGTG 59.252 43.478 0.00 0.00 33.60 3.33
225 231 2.978278 TGGCTGAAAATTCCAACCCATT 59.022 40.909 0.00 0.00 0.00 3.16
233 239 2.802247 GTGCAAGTTGGCTGAAAATTCC 59.198 45.455 4.75 0.00 34.04 3.01
278 284 2.358582 TCGAACACGACAACCTTACTCA 59.641 45.455 0.00 0.00 0.00 3.41
316 322 6.172630 CCTAGCAAAAACCCATAAAAGCAAT 58.827 36.000 0.00 0.00 0.00 3.56
320 326 9.719355 AAATAACCTAGCAAAAACCCATAAAAG 57.281 29.630 0.00 0.00 0.00 2.27
325 331 9.665719 CATAAAAATAACCTAGCAAAAACCCAT 57.334 29.630 0.00 0.00 0.00 4.00
326 332 8.871125 TCATAAAAATAACCTAGCAAAAACCCA 58.129 29.630 0.00 0.00 0.00 4.51
327 333 9.146984 GTCATAAAAATAACCTAGCAAAAACCC 57.853 33.333 0.00 0.00 0.00 4.11
338 344 9.914131 GCTCAGAAAAAGTCATAAAAATAACCT 57.086 29.630 0.00 0.00 0.00 3.50
340 346 9.691362 TGGCTCAGAAAAAGTCATAAAAATAAC 57.309 29.630 0.00 0.00 0.00 1.89
353 359 5.355350 AGTTCGGATTATGGCTCAGAAAAAG 59.645 40.000 0.00 0.00 30.47 2.27
357 363 3.706594 AGAGTTCGGATTATGGCTCAGAA 59.293 43.478 0.00 0.00 0.00 3.02
368 374 3.368948 GCCTTCTCTTCAGAGTTCGGATT 60.369 47.826 3.73 0.00 42.60 3.01
369 375 2.167487 GCCTTCTCTTCAGAGTTCGGAT 59.833 50.000 3.73 0.00 42.60 4.18
374 380 3.454082 CCCTATGCCTTCTCTTCAGAGTT 59.546 47.826 3.73 0.00 42.60 3.01
376 382 3.303938 TCCCTATGCCTTCTCTTCAGAG 58.696 50.000 0.00 0.00 43.36 3.35
377 383 3.404869 TCCCTATGCCTTCTCTTCAGA 57.595 47.619 0.00 0.00 0.00 3.27
378 384 4.703379 AATCCCTATGCCTTCTCTTCAG 57.297 45.455 0.00 0.00 0.00 3.02
381 387 4.688321 GCAGAAATCCCTATGCCTTCTCTT 60.688 45.833 0.00 0.00 32.49 2.85
384 390 2.782341 AGCAGAAATCCCTATGCCTTCT 59.218 45.455 0.00 0.00 39.51 2.85
385 391 3.220674 AGCAGAAATCCCTATGCCTTC 57.779 47.619 0.00 0.00 39.51 3.46
386 392 4.796110 TTAGCAGAAATCCCTATGCCTT 57.204 40.909 0.00 0.00 39.51 4.35
387 393 4.166919 ACTTTAGCAGAAATCCCTATGCCT 59.833 41.667 0.00 0.00 39.51 4.75
388 394 4.276926 CACTTTAGCAGAAATCCCTATGCC 59.723 45.833 0.00 0.00 39.51 4.40
389 395 4.884164 ACACTTTAGCAGAAATCCCTATGC 59.116 41.667 0.00 0.00 38.97 3.14
390 396 6.599244 TCAACACTTTAGCAGAAATCCCTATG 59.401 38.462 0.00 0.00 0.00 2.23
407 413 3.141398 CATGTGCAGTACCTCAACACTT 58.859 45.455 0.00 0.00 32.49 3.16
408 414 2.104792 ACATGTGCAGTACCTCAACACT 59.895 45.455 0.00 0.00 32.49 3.55
413 419 3.402110 CTTTCACATGTGCAGTACCTCA 58.598 45.455 21.38 0.00 0.00 3.86
434 440 2.367241 GTCCTTCTTCCTGCCTATCTCC 59.633 54.545 0.00 0.00 0.00 3.71
439 445 3.248024 TCTTTGTCCTTCTTCCTGCCTA 58.752 45.455 0.00 0.00 0.00 3.93
443 449 7.986085 TTCTATTTCTTTGTCCTTCTTCCTG 57.014 36.000 0.00 0.00 0.00 3.86
461 467 5.707764 GCACCTCTTTGTCCTTCTTTCTATT 59.292 40.000 0.00 0.00 0.00 1.73
463 469 4.348168 AGCACCTCTTTGTCCTTCTTTCTA 59.652 41.667 0.00 0.00 0.00 2.10
464 470 3.137360 AGCACCTCTTTGTCCTTCTTTCT 59.863 43.478 0.00 0.00 0.00 2.52
465 471 3.251972 CAGCACCTCTTTGTCCTTCTTTC 59.748 47.826 0.00 0.00 0.00 2.62
466 472 3.217626 CAGCACCTCTTTGTCCTTCTTT 58.782 45.455 0.00 0.00 0.00 2.52
467 473 2.173569 ACAGCACCTCTTTGTCCTTCTT 59.826 45.455 0.00 0.00 0.00 2.52
468 474 1.771255 ACAGCACCTCTTTGTCCTTCT 59.229 47.619 0.00 0.00 0.00 2.85
469 475 2.262423 ACAGCACCTCTTTGTCCTTC 57.738 50.000 0.00 0.00 0.00 3.46
470 476 2.736670 AACAGCACCTCTTTGTCCTT 57.263 45.000 0.00 0.00 0.00 3.36
471 477 2.551071 GCTAACAGCACCTCTTTGTCCT 60.551 50.000 0.00 0.00 41.89 3.85
472 478 1.807142 GCTAACAGCACCTCTTTGTCC 59.193 52.381 0.00 0.00 41.89 4.02
473 479 1.461127 CGCTAACAGCACCTCTTTGTC 59.539 52.381 0.00 0.00 42.58 3.18
474 480 1.512926 CGCTAACAGCACCTCTTTGT 58.487 50.000 0.00 0.00 42.58 2.83
475 481 0.798776 CCGCTAACAGCACCTCTTTG 59.201 55.000 0.00 0.00 42.58 2.77
476 482 0.396811 ACCGCTAACAGCACCTCTTT 59.603 50.000 0.00 0.00 42.58 2.52
477 483 0.396811 AACCGCTAACAGCACCTCTT 59.603 50.000 0.00 0.00 42.58 2.85
478 484 0.396811 AAACCGCTAACAGCACCTCT 59.603 50.000 0.00 0.00 42.58 3.69
479 485 0.796927 GAAACCGCTAACAGCACCTC 59.203 55.000 0.00 0.00 42.58 3.85
480 486 0.396811 AGAAACCGCTAACAGCACCT 59.603 50.000 0.00 0.00 42.58 4.00
481 487 0.796927 GAGAAACCGCTAACAGCACC 59.203 55.000 0.00 0.00 42.58 5.01
482 488 1.727335 GAGAGAAACCGCTAACAGCAC 59.273 52.381 0.00 0.00 42.58 4.40
483 489 1.337823 GGAGAGAAACCGCTAACAGCA 60.338 52.381 0.00 0.00 42.58 4.41
484 490 1.360820 GGAGAGAAACCGCTAACAGC 58.639 55.000 0.00 0.00 38.02 4.40
485 491 1.630148 CGGAGAGAAACCGCTAACAG 58.370 55.000 0.00 0.00 43.74 3.16
486 492 3.806591 CGGAGAGAAACCGCTAACA 57.193 52.632 0.00 0.00 43.74 2.41
502 508 0.686441 TGGGTGGGATGTCTAGACGG 60.686 60.000 17.85 0.00 0.00 4.79
503 509 1.191535 TTGGGTGGGATGTCTAGACG 58.808 55.000 17.85 0.00 0.00 4.18
528 534 1.027357 ATTTGGTGCGCCATCTCATC 58.973 50.000 21.95 0.00 45.56 2.92
530 536 1.339535 TGTATTTGGTGCGCCATCTCA 60.340 47.619 21.95 13.97 45.56 3.27
531 537 1.378531 TGTATTTGGTGCGCCATCTC 58.621 50.000 21.95 11.54 45.56 2.75
532 538 2.057137 ATGTATTTGGTGCGCCATCT 57.943 45.000 21.95 12.93 45.56 2.90
533 539 3.980646 TTATGTATTTGGTGCGCCATC 57.019 42.857 21.95 11.55 45.56 3.51
548 554 4.019174 CCTGCCTTCACCTCAAATTATGT 58.981 43.478 0.00 0.00 0.00 2.29
552 558 1.428912 TCCCTGCCTTCACCTCAAATT 59.571 47.619 0.00 0.00 0.00 1.82
610 619 9.226345 GAAGCAATCAACTATTGTTATTGCTAC 57.774 33.333 27.70 13.55 46.78 3.58
624 633 3.930336 TCGATGACTGAAGCAATCAACT 58.070 40.909 0.00 0.00 37.67 3.16
636 645 4.611310 ACAGATTTGCAATCGATGACTG 57.389 40.909 0.00 5.39 0.00 3.51
710 719 5.409643 ACTATATCATTCTGCAAACGCAC 57.590 39.130 0.00 0.00 35.03 5.34
771 780 0.747255 GCTCTGCATCCTTCTACCGA 59.253 55.000 0.00 0.00 0.00 4.69
772 781 0.461548 TGCTCTGCATCCTTCTACCG 59.538 55.000 0.00 0.00 31.71 4.02
797 3248 3.087031 CTCACTGCTGACCCAATTTGAT 58.913 45.455 0.00 0.00 0.00 2.57
851 3603 0.896479 TTTGGGCCTTCGCTTTACCC 60.896 55.000 4.53 0.00 41.24 3.69
984 3736 1.846007 TTGGATTGGGATTGGGAACG 58.154 50.000 0.00 0.00 0.00 3.95
989 3753 3.504906 CGATGAGATTGGATTGGGATTGG 59.495 47.826 0.00 0.00 0.00 3.16
990 3754 3.057736 GCGATGAGATTGGATTGGGATTG 60.058 47.826 0.00 0.00 0.00 2.67
991 3755 3.152341 GCGATGAGATTGGATTGGGATT 58.848 45.455 0.00 0.00 0.00 3.01
992 3756 2.553904 GGCGATGAGATTGGATTGGGAT 60.554 50.000 0.00 0.00 0.00 3.85
993 3757 1.202806 GGCGATGAGATTGGATTGGGA 60.203 52.381 0.00 0.00 0.00 4.37
994 3758 1.242076 GGCGATGAGATTGGATTGGG 58.758 55.000 0.00 0.00 0.00 4.12
995 3759 1.971481 TGGCGATGAGATTGGATTGG 58.029 50.000 0.00 0.00 0.00 3.16
996 3760 2.287427 GCTTGGCGATGAGATTGGATTG 60.287 50.000 0.00 0.00 0.00 2.67
997 3761 1.952296 GCTTGGCGATGAGATTGGATT 59.048 47.619 0.00 0.00 0.00 3.01
998 3762 1.134007 TGCTTGGCGATGAGATTGGAT 60.134 47.619 0.00 0.00 0.00 3.41
999 3763 0.252761 TGCTTGGCGATGAGATTGGA 59.747 50.000 0.00 0.00 0.00 3.53
1021 3785 1.990060 GGGCTGGAGTGCTGGAGTA 60.990 63.158 0.00 0.00 0.00 2.59
1022 3786 3.325753 GGGCTGGAGTGCTGGAGT 61.326 66.667 0.00 0.00 0.00 3.85
1023 3787 3.007920 AGGGCTGGAGTGCTGGAG 61.008 66.667 0.00 0.00 0.00 3.86
1024 3788 3.005539 GAGGGCTGGAGTGCTGGA 61.006 66.667 0.00 0.00 0.00 3.86
1025 3789 4.106925 GGAGGGCTGGAGTGCTGG 62.107 72.222 0.00 0.00 0.00 4.85
1026 3790 4.106925 GGGAGGGCTGGAGTGCTG 62.107 72.222 0.00 0.00 0.00 4.41
1173 3947 2.047179 GGCGGCCTTCGACTCTTT 60.047 61.111 12.87 0.00 45.10 2.52
1225 3999 2.122783 AGAGAGGAGTTCTGGTCGAG 57.877 55.000 0.00 0.00 35.87 4.04
1263 4039 1.464376 ATCGTCACTATCCCCGGCAG 61.464 60.000 0.00 0.00 0.00 4.85
1366 4142 8.706322 AGAGACATGGGTATAAAACAAAACTT 57.294 30.769 0.00 0.00 0.00 2.66
1386 4162 1.666189 GCCGATGCTAAACCAAGAGAC 59.334 52.381 0.00 0.00 33.53 3.36
1393 4169 0.663153 GGACATGCCGATGCTAAACC 59.337 55.000 0.00 0.00 38.71 3.27
1418 4194 5.501156 GGGGACAAAACAGAATCTACTGAT 58.499 41.667 0.00 0.00 40.63 2.90
1421 4197 3.326880 ACGGGGACAAAACAGAATCTACT 59.673 43.478 0.00 0.00 0.00 2.57
1430 4206 1.817209 GCCAAACGGGGACAAAACA 59.183 52.632 0.00 0.00 37.04 2.83
1478 4254 2.687370 CAACACCTTTGCTAAATGGCC 58.313 47.619 0.00 0.00 34.62 5.36
1543 4319 1.200020 CTGAGGACGAAATTGCCCAAC 59.800 52.381 0.00 0.00 0.00 3.77
1610 4501 2.342279 CTTCGTCCTTCCCGTGCA 59.658 61.111 0.00 0.00 0.00 4.57
1616 4507 2.295885 TCGAGTATCCTTCGTCCTTCC 58.704 52.381 0.00 0.00 39.05 3.46
1729 4621 4.679373 TTCAAAAATTAACAGCTGGGCA 57.321 36.364 19.93 0.47 0.00 5.36
1758 4658 5.447279 GGCGTCATAAAATACAAGTCCACAG 60.447 44.000 0.00 0.00 0.00 3.66
1768 4668 2.032924 GGCACAGGGCGTCATAAAATAC 59.967 50.000 0.00 0.00 46.16 1.89
1822 8817 5.483583 AGGAAAGAAGCTACATCAGAACTCT 59.516 40.000 0.00 0.00 0.00 3.24
2194 9278 1.226746 CGTTGGTGGAAGAACAGGAC 58.773 55.000 0.00 0.00 0.00 3.85
2195 9279 0.834612 ACGTTGGTGGAAGAACAGGA 59.165 50.000 0.00 0.00 0.00 3.86
2199 9283 4.612939 GCTTATCAACGTTGGTGGAAGAAC 60.613 45.833 27.02 7.10 27.59 3.01
2200 9284 3.500680 GCTTATCAACGTTGGTGGAAGAA 59.499 43.478 27.02 10.65 27.59 2.52
2215 9300 2.023984 TCTGACCCAGGAGAGCTTATCA 60.024 50.000 0.00 0.00 31.51 2.15
2404 9697 0.965363 AATAACCTGCAGCCCCAACG 60.965 55.000 8.66 0.00 0.00 4.10
2461 9759 7.229907 CAGCTTAAACCTTAAGAGTTTGGGTTA 59.770 37.037 22.14 7.25 39.05 2.85
2470 9769 6.112994 GCTTAGCAGCTTAAACCTTAAGAG 57.887 41.667 0.00 0.00 43.51 2.85
2629 9930 9.151471 ACAATGTACAAGTGTGTATCTGTAATC 57.849 33.333 13.21 0.00 42.18 1.75
2634 9935 6.426633 TGGAACAATGTACAAGTGTGTATCTG 59.573 38.462 14.36 0.00 37.82 2.90
2647 9948 7.708752 TGAAACCTTTCAAATGGAACAATGTAC 59.291 33.333 0.00 0.00 43.05 2.90
2701 10002 0.394899 GGGGCATTTCACCTCTGAGG 60.395 60.000 22.00 22.00 42.49 3.86
2748 10049 3.023832 CCAATTCTGGTGGGGACATTAC 58.976 50.000 0.00 0.00 46.14 1.89
2775 10077 3.100671 AGGATAGAACCTGCTCGAACTT 58.899 45.455 0.00 0.00 39.01 2.66
2823 10134 1.200020 GGTTTGAAGATCGGGTTGCTG 59.800 52.381 0.00 0.00 0.00 4.41
2845 10161 7.603180 TCTATAGCTTGAGTACATCATGGTT 57.397 36.000 13.76 8.07 42.10 3.67
2906 10223 1.604593 CCACCAGGGCAGTTCCAAG 60.605 63.158 0.00 0.00 36.21 3.61
2924 10241 4.446371 CATTCTGGTCAGATACAGTTCCC 58.554 47.826 1.16 0.00 37.29 3.97
2954 10272 3.694535 AACACGTAATGCCGAAACAAA 57.305 38.095 0.00 0.00 0.00 2.83
2960 10278 2.231964 AGGTAGAAACACGTAATGCCGA 59.768 45.455 0.00 0.00 0.00 5.54
2967 10285 2.827921 GGGAAGGAGGTAGAAACACGTA 59.172 50.000 0.00 0.00 0.00 3.57
3000 10318 8.637986 ACTTGAACATCAAAAGGCAAATTAGTA 58.362 29.630 0.00 0.00 35.73 1.82
3001 10319 7.500141 ACTTGAACATCAAAAGGCAAATTAGT 58.500 30.769 0.00 0.00 35.73 2.24
3002 10320 7.951530 ACTTGAACATCAAAAGGCAAATTAG 57.048 32.000 0.00 0.00 35.73 1.73
3003 10321 8.087750 CCTACTTGAACATCAAAAGGCAAATTA 58.912 33.333 7.73 0.00 35.73 1.40
3022 10340 6.741992 TGCAAAATGTCTGATACCTACTTG 57.258 37.500 0.00 0.00 0.00 3.16
3143 10557 7.859875 CCTTCTCACTTTCAAGAAAACAAGATC 59.140 37.037 0.00 0.00 31.45 2.75
3250 10792 7.359598 GCACATTCTACTGTACTTTCTGACTTG 60.360 40.741 0.00 0.00 0.00 3.16
3376 10950 1.288932 CCATGAGAAACCCCAGGGAAT 59.711 52.381 7.25 0.00 36.42 3.01
3478 11052 3.947834 AGGTTCACTTGAGGTTCTTGTTG 59.052 43.478 0.00 0.00 0.00 3.33
3509 11083 1.111277 ATTACAAAAGGATGGCCGCC 58.889 50.000 1.04 1.04 39.96 6.13
3658 16413 1.993701 TTCAGCACAAGCAGACCCCA 61.994 55.000 0.00 0.00 45.49 4.96
3698 16461 8.987890 ACAAAACTGCAAATACCACATTTTATC 58.012 29.630 0.00 0.00 0.00 1.75
3751 16514 2.353307 CCCCCGGTGAGCATTTTAAAAC 60.353 50.000 1.97 0.00 0.00 2.43
3774 16537 4.870021 ATATTCAGGTGAGGAGCCTTTT 57.130 40.909 0.00 0.00 33.31 2.27
3784 16547 9.527157 TCACCTTTTTGAAATATATTCAGGTGA 57.473 29.630 21.40 21.40 42.55 4.02
3827 16594 5.418310 GTGATTTCCTCTCACGTTTTTCA 57.582 39.130 0.00 0.00 34.24 2.69
3869 16650 4.817517 GTCTCAGGACGGAATCACTAAAA 58.182 43.478 0.00 0.00 32.47 1.52
3932 16713 0.831711 TGGCTGACACTAGAGGCACA 60.832 55.000 0.00 0.00 39.65 4.57
3935 16716 4.921834 GTGGCTGACACTAGAGGC 57.078 61.111 6.34 0.00 46.72 4.70
3943 16724 2.325484 TCCAGAGTTTAGTGGCTGACA 58.675 47.619 0.00 0.00 33.43 3.58
3944 16725 3.402628 TTCCAGAGTTTAGTGGCTGAC 57.597 47.619 0.00 0.00 33.43 3.51
3982 16764 2.342406 TCTCTGGGAAATCTGGGACA 57.658 50.000 0.00 0.00 0.00 4.02
3994 16776 4.978438 ATGATCCTTCTCATTCTCTGGG 57.022 45.455 0.00 0.00 31.82 4.45
4012 16794 1.209504 CTTCAGTCCGCCCCTTTATGA 59.790 52.381 0.00 0.00 0.00 2.15
4073 16855 1.375551 GACCGCAATTCACCCGTATT 58.624 50.000 0.00 0.00 0.00 1.89
4077 16859 1.366111 ATTCGACCGCAATTCACCCG 61.366 55.000 0.00 0.00 0.00 5.28
4152 16934 0.991355 AACAACCCTGTGGAGGACCA 60.991 55.000 0.00 0.00 42.93 4.02
4165 16947 1.270550 CCTGTCCAAGATGCAACAACC 59.729 52.381 0.00 0.00 0.00 3.77
4190 16972 2.575694 AGAAGCACATACTGAGCTCG 57.424 50.000 9.64 6.63 43.33 5.03
4199 16981 3.056107 AGAACCTGCGTAAGAAGCACATA 60.056 43.478 0.00 0.00 43.86 2.29
4278 17060 0.541764 GTTTGGGATTCCAGGGTGCA 60.542 55.000 4.80 0.00 45.04 4.57
4315 17330 2.609747 TCACTTAACACCCAGCTCTCT 58.390 47.619 0.00 0.00 0.00 3.10
4317 17332 2.616510 GCATCACTTAACACCCAGCTCT 60.617 50.000 0.00 0.00 0.00 4.09
4335 17350 4.016629 CGTGCGGCGCATATGCAT 62.017 61.111 38.43 3.79 41.91 3.96
4350 17365 6.586082 GCTTAATGATGAAAATTTCACCACGT 59.414 34.615 10.91 2.18 43.48 4.49
4367 17382 1.405526 GGACACGAGGCTGCTTAATGA 60.406 52.381 0.00 0.00 0.00 2.57
4390 17587 6.279513 AGATGTTTCACTACCTCTCAAGAG 57.720 41.667 0.00 0.00 41.71 2.85
4393 17590 4.997395 GCAAGATGTTTCACTACCTCTCAA 59.003 41.667 0.00 0.00 0.00 3.02
4396 17593 4.623932 TGCAAGATGTTTCACTACCTCT 57.376 40.909 0.00 0.00 0.00 3.69
4403 17600 5.343249 ACTCTTTGTTGCAAGATGTTTCAC 58.657 37.500 0.00 0.00 0.00 3.18
4404 17601 5.581126 ACTCTTTGTTGCAAGATGTTTCA 57.419 34.783 0.00 0.00 0.00 2.69
4407 17604 7.333528 TCTAAACTCTTTGTTGCAAGATGTT 57.666 32.000 0.00 0.00 39.13 2.71
4442 17862 3.802329 GCTAACCACTACTGCAGTCACAA 60.802 47.826 25.56 4.47 34.26 3.33
4445 17865 1.067846 CGCTAACCACTACTGCAGTCA 60.068 52.381 25.56 9.17 34.26 3.41
4540 17962 4.458989 TGAGCTGTTATTTACCCTGCTTTG 59.541 41.667 0.00 0.00 30.58 2.77
4542 17964 4.265073 CTGAGCTGTTATTTACCCTGCTT 58.735 43.478 0.00 0.00 30.58 3.91
4566 17995 2.551270 TGGTTAGATCAGTGGCTCCTT 58.449 47.619 0.00 0.00 0.00 3.36
4575 18004 5.412904 GTCCACCTTCTTTTGGTTAGATCAG 59.587 44.000 0.00 0.00 35.28 2.90
4576 18005 5.073144 AGTCCACCTTCTTTTGGTTAGATCA 59.927 40.000 0.00 0.00 35.28 2.92
4617 18046 3.925913 GTCTGAGAGAGATTTCACACTGC 59.074 47.826 0.00 0.00 31.63 4.40
4623 18052 4.085009 TGCAGAGTCTGAGAGAGATTTCA 58.915 43.478 24.55 5.06 32.44 2.69
4680 19113 6.042552 CACTTCTCATTGGGTATGGTAGAGAT 59.957 42.308 0.00 0.00 34.85 2.75
4682 19115 5.453903 CCACTTCTCATTGGGTATGGTAGAG 60.454 48.000 0.00 0.00 34.85 2.43
4683 19116 4.408921 CCACTTCTCATTGGGTATGGTAGA 59.591 45.833 0.00 0.00 34.85 2.59


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

AutoCloner maintained by Alex Coulton.