Multiple sequence alignment - TraesCS6D01G042500

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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 TraesCS6D01G042500 chr6D 100.000 2219 0 0 1 2219 17316670 17318888 0.000000e+00 4098.0
1 TraesCS6D01G042500 chr6D 100.000 42 0 0 859 900 17317487 17317528 6.570000e-11 78.7
2 TraesCS6D01G042500 chr6D 100.000 42 0 0 818 859 17317528 17317569 6.570000e-11 78.7
3 TraesCS6D01G042500 chr6D 100.000 42 0 0 1 42 437965410 437965451 6.570000e-11 78.7
4 TraesCS6D01G042500 chr6A 94.498 618 26 6 1602 2213 17943946 17944561 0.000000e+00 946.0
5 TraesCS6D01G042500 chr6A 86.047 473 31 21 938 1375 17943150 17943622 1.990000e-130 475.0
6 TraesCS6D01G042500 chr6A 92.115 279 14 5 521 796 17942826 17943099 9.610000e-104 387.0
7 TraesCS6D01G042500 chr6A 85.256 156 16 6 208 357 17942430 17942584 1.060000e-33 154.0
8 TraesCS6D01G042500 chr6A 95.918 49 2 0 872 920 17943109 17943157 1.830000e-11 80.5
9 TraesCS6D01G042500 chr6A 97.778 45 1 0 2 46 84900156 84900112 6.570000e-11 78.7
10 TraesCS6D01G042500 chr6A 100.000 29 0 0 831 859 17943109 17943137 1.000000e-03 54.7
11 TraesCS6D01G042500 chr6B 87.453 534 30 8 859 1376 30323917 30324429 4.110000e-162 580.0
12 TraesCS6D01G042500 chr6B 86.751 317 23 9 547 859 30323657 30323958 3.530000e-88 335.0
13 TraesCS6D01G042500 chr6B 86.486 296 34 4 41 334 30312476 30312767 9.890000e-84 320.0
14 TraesCS6D01G042500 chr6B 85.660 265 32 3 41 305 30323340 30323598 7.810000e-70 274.0
15 TraesCS6D01G042500 chr6B 89.623 106 5 1 2114 2213 30324852 30324957 1.790000e-26 130.0
16 TraesCS6D01G042500 chr6B 85.366 123 14 4 1958 2076 30324726 30324848 8.320000e-25 124.0
17 TraesCS6D01G042500 chr6B 82.558 86 15 0 61 146 148068177 148068092 2.360000e-10 76.8
18 TraesCS6D01G042500 chr1A 89.474 209 16 3 991 1196 142101608 142101813 2.190000e-65 259.0
19 TraesCS6D01G042500 chr1B 88.517 209 18 3 991 1196 195102618 195102413 4.730000e-62 248.0
20 TraesCS6D01G042500 chr1D 88.038 209 19 3 991 1196 126972034 126972239 2.200000e-60 243.0
21 TraesCS6D01G042500 chr1D 96.581 117 4 0 352 468 116238380 116238496 6.250000e-46 195.0
22 TraesCS6D01G042500 chr1D 82.143 84 12 3 63 146 75934995 75934915 3.950000e-08 69.4
23 TraesCS6D01G042500 chr2B 97.436 117 3 0 352 468 378986033 378986149 1.340000e-47 200.0
24 TraesCS6D01G042500 chr2B 94.872 117 6 0 352 468 647309991 647309875 1.350000e-42 183.0
25 TraesCS6D01G042500 chr2B 80.583 103 18 1 61 163 21856126 21856226 6.570000e-11 78.7
26 TraesCS6D01G042500 chr5B 96.581 117 4 0 352 468 96878942 96879058 6.250000e-46 195.0
27 TraesCS6D01G042500 chr5B 94.355 124 6 1 345 468 252311137 252311015 2.910000e-44 189.0
28 TraesCS6D01G042500 chr2D 96.581 117 4 0 352 468 592468110 592467994 6.250000e-46 195.0
29 TraesCS6D01G042500 chr2D 96.581 117 4 0 352 468 645613051 645613167 6.250000e-46 195.0
30 TraesCS6D01G042500 chr4A 93.077 130 6 2 341 468 682683442 682683570 1.050000e-43 187.0
31 TraesCS6D01G042500 chr4A 95.745 47 2 0 2 48 107368887 107368841 2.360000e-10 76.8
32 TraesCS6D01G042500 chr2A 93.600 125 5 3 345 468 70030768 70030646 1.350000e-42 183.0
33 TraesCS6D01G042500 chr4B 100.000 44 0 0 2 45 74685726 74685769 5.080000e-12 82.4
34 TraesCS6D01G042500 chr4B 82.796 93 12 4 57 146 14844320 14844411 1.830000e-11 80.5
35 TraesCS6D01G042500 chr4B 82.105 95 13 4 54 145 15186278 15186371 6.570000e-11 78.7
36 TraesCS6D01G042500 chr7D 100.000 43 0 0 1 43 169823412 169823370 1.830000e-11 80.5
37 TraesCS6D01G042500 chr7D 97.826 46 0 1 2 47 51998813 51998857 6.570000e-11 78.7
38 TraesCS6D01G042500 chr7D 97.826 46 0 1 1 46 177106901 177106857 6.570000e-11 78.7
39 TraesCS6D01G042500 chr5D 97.778 45 1 0 1 45 293374967 293374923 6.570000e-11 78.7
40 TraesCS6D01G042500 chr5D 81.111 90 15 1 74 163 485395598 485395511 1.100000e-08 71.3
41 TraesCS6D01G042500 chr5D 78.505 107 21 1 57 163 485763901 485763797 3.950000e-08 69.4
42 TraesCS6D01G042500 chr4D 95.833 48 1 1 1 47 3719325 3719372 2.360000e-10 76.8


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 TraesCS6D01G042500 chr6D 17316670 17318888 2218 False 1418.466667 4098 100.000000 1 2219 3 chr6D.!!$F2 2218
1 TraesCS6D01G042500 chr6A 17942430 17944561 2131 False 349.533333 946 92.305667 208 2213 6 chr6A.!!$F1 2005
2 TraesCS6D01G042500 chr6B 30323340 30324957 1617 False 288.600000 580 86.970600 41 2213 5 chr6B.!!$F2 2172

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
374 380 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1640 0.550914 ACAAGACAAGGCTGAACCCA 59.449 50.0 0.0 0.0 40.58 4.51 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
26 27 7.435068 AGTGTCAAAAACGCTCTTATATTGT 57.565 32.000 0.00 0.00 45.69 2.71
27 28 7.298122 AGTGTCAAAAACGCTCTTATATTGTG 58.702 34.615 0.00 0.00 45.69 3.33
28 29 6.523201 GTGTCAAAAACGCTCTTATATTGTGG 59.477 38.462 0.00 0.00 35.42 4.17
29 30 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
30 31 5.941058 TCAAAAACGCTCTTATATTGTGGGA 59.059 36.000 0.00 0.00 0.00 4.37
31 32 5.813080 AAAACGCTCTTATATTGTGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
32 33 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
33 34 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
34 35 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
35 36 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
36 37 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
37 38 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
38 39 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
39 40 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
44 45 0.106116 GTGGGACGGAGGGAGTAGAT 60.106 60.000 0.00 0.00 0.00 1.98
50 51 3.306156 GGACGGAGGGAGTAGATAATTGC 60.306 52.174 0.00 0.00 0.00 3.56
55 56 5.301555 GGAGGGAGTAGATAATTGCTTGTC 58.698 45.833 0.00 0.00 0.00 3.18
57 58 4.721776 AGGGAGTAGATAATTGCTTGTCCA 59.278 41.667 0.00 0.00 0.00 4.02
65 66 1.246649 ATTGCTTGTCCATCGCAACA 58.753 45.000 0.00 0.00 45.19 3.33
78 79 7.066887 TGTCCATCGCAACAAGATACAAATATT 59.933 33.333 0.00 0.00 0.00 1.28
113 114 3.831323 TCGTGATTTCCATGCCCATATT 58.169 40.909 0.00 0.00 0.00 1.28
114 115 4.979335 TCGTGATTTCCATGCCCATATTA 58.021 39.130 0.00 0.00 0.00 0.98
115 116 4.759693 TCGTGATTTCCATGCCCATATTAC 59.240 41.667 0.00 0.00 0.00 1.89
119 120 2.183478 TCCATGCCCATATTACTGCG 57.817 50.000 0.00 0.00 0.00 5.18
131 132 7.094975 GCCCATATTACTGCGATTGTGTAAATA 60.095 37.037 0.00 0.00 31.25 1.40
165 166 3.949586 TGGTGAGCCCATGATTTATCA 57.050 42.857 0.00 0.00 38.72 2.15
167 168 4.806892 TGGTGAGCCCATGATTTATCAAT 58.193 39.130 0.00 0.00 40.69 2.57
168 169 4.828939 TGGTGAGCCCATGATTTATCAATC 59.171 41.667 0.00 0.00 40.69 2.67
171 172 6.888632 GGTGAGCCCATGATTTATCAATCTAT 59.111 38.462 0.00 0.00 40.69 1.98
172 173 8.049117 GGTGAGCCCATGATTTATCAATCTATA 58.951 37.037 0.00 0.00 40.69 1.31
173 174 9.453572 GTGAGCCCATGATTTATCAATCTATAA 57.546 33.333 0.00 0.00 40.69 0.98
232 233 5.071923 ACTTATGGGCTTATACCAGAGGAAC 59.928 44.000 0.00 0.00 42.15 3.62
234 235 2.124411 GGGCTTATACCAGAGGAACCA 58.876 52.381 0.00 0.00 0.00 3.67
242 243 0.244994 CCAGAGGAACCAGTGAGTCG 59.755 60.000 0.00 0.00 0.00 4.18
254 255 7.494625 GGAACCAGTGAGTCGATTAAATATGAA 59.505 37.037 0.00 0.00 0.00 2.57
309 313 2.418368 ATGCTGGATTCCGCACTAAA 57.582 45.000 19.58 2.82 36.35 1.85
315 319 1.810151 GGATTCCGCACTAAAGCACAA 59.190 47.619 0.00 0.00 0.00 3.33
358 364 8.833493 AGCTATAATGTGTAAAAACGTATTCCC 58.167 33.333 0.00 0.00 0.00 3.97
359 365 8.833493 GCTATAATGTGTAAAAACGTATTCCCT 58.167 33.333 0.00 0.00 0.00 4.20
361 367 6.505044 AATGTGTAAAAACGTATTCCCTCC 57.495 37.500 0.00 0.00 0.00 4.30
362 368 3.995705 TGTGTAAAAACGTATTCCCTCCG 59.004 43.478 0.00 0.00 0.00 4.63
363 369 3.996363 GTGTAAAAACGTATTCCCTCCGT 59.004 43.478 0.00 0.00 36.17 4.69
364 370 4.091945 GTGTAAAAACGTATTCCCTCCGTC 59.908 45.833 0.00 0.00 32.95 4.79
365 371 2.391616 AAAACGTATTCCCTCCGTCC 57.608 50.000 0.00 0.00 32.95 4.79
366 372 0.174162 AAACGTATTCCCTCCGTCCG 59.826 55.000 0.00 0.00 32.95 4.79
367 373 1.669999 AACGTATTCCCTCCGTCCGG 61.670 60.000 0.00 0.00 32.95 5.14
368 374 1.825191 CGTATTCCCTCCGTCCGGA 60.825 63.158 0.00 0.00 42.90 5.14
369 375 1.386525 CGTATTCCCTCCGTCCGGAA 61.387 60.000 5.23 0.00 44.66 4.30
370 376 0.826062 GTATTCCCTCCGTCCGGAAA 59.174 55.000 5.23 1.92 44.66 3.13
371 377 1.415289 GTATTCCCTCCGTCCGGAAAT 59.585 52.381 5.23 9.21 44.66 2.17
372 378 1.797320 ATTCCCTCCGTCCGGAAATA 58.203 50.000 5.23 0.00 44.66 1.40
373 379 0.826062 TTCCCTCCGTCCGGAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
374 380 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
375 381 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
376 382 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
377 383 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
378 384 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
379 385 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
380 386 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
381 387 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
382 388 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
383 389 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
384 390 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
385 391 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
386 392 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
387 393 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
388 394 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
389 395 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
390 396 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
398 404 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
399 405 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
400 406 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
401 407 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
402 408 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
403 409 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
406 412 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
458 464 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
465 471 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
466 472 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
467 473 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
468 474 7.485913 CCATTTTGATGACAAGTATTTTCGGAG 59.514 37.037 0.00 0.00 37.32 4.63
469 475 7.504924 TTTTGATGACAAGTATTTTCGGAGT 57.495 32.000 0.00 0.00 37.32 3.85
487 493 7.356089 TCGGAGTATTCAAATGTGGTAGTAT 57.644 36.000 0.00 0.00 0.00 2.12
489 495 8.262227 TCGGAGTATTCAAATGTGGTAGTATTT 58.738 33.333 0.00 0.00 0.00 1.40
518 524 6.532365 TTAATTTTTGAACCGAAATGTGGC 57.468 33.333 0.00 0.00 0.00 5.01
523 529 3.066291 TGAACCGAAATGTGGCAGTAT 57.934 42.857 0.00 0.00 0.00 2.12
525 531 3.190327 TGAACCGAAATGTGGCAGTATTG 59.810 43.478 0.00 0.00 0.00 1.90
528 534 3.572255 ACCGAAATGTGGCAGTATTGTTT 59.428 39.130 0.00 0.00 0.00 2.83
529 535 3.919804 CCGAAATGTGGCAGTATTGTTTG 59.080 43.478 0.00 0.00 0.00 2.93
534 736 7.422465 AAATGTGGCAGTATTGTTTGGATAT 57.578 32.000 0.00 0.00 0.00 1.63
539 741 7.039434 TGTGGCAGTATTGTTTGGATATTTTGA 60.039 33.333 0.00 0.00 0.00 2.69
588 790 0.387929 GGCATCATCCATGTGCCAAG 59.612 55.000 17.04 0.00 45.65 3.61
629 832 1.125093 TTGGGATCCGTCCTGTGTGT 61.125 55.000 5.45 0.00 44.44 3.72
654 857 0.608130 TGTCCTCTTCCCACGTGATG 59.392 55.000 19.30 7.99 0.00 3.07
663 866 2.573869 CACGTGATGGCGAGAGGT 59.426 61.111 10.90 0.00 35.59 3.85
698 903 1.609555 GACTCACGCCGATCTTATCCT 59.390 52.381 0.00 0.00 0.00 3.24
707 912 3.155501 CCGATCTTATCCTAACCTCCGT 58.844 50.000 0.00 0.00 0.00 4.69
750 955 3.293337 CCAGCAGATTCATCCATCCAAA 58.707 45.455 0.00 0.00 0.00 3.28
805 1010 2.117423 CCCCGGTTTGCTCCCTTT 59.883 61.111 0.00 0.00 0.00 3.11
806 1011 1.977009 CCCCGGTTTGCTCCCTTTC 60.977 63.158 0.00 0.00 0.00 2.62
847 1055 2.307686 TCCGATCCCCCATAAATAAGCC 59.692 50.000 0.00 0.00 0.00 4.35
848 1056 2.620627 CCGATCCCCCATAAATAAGCCC 60.621 54.545 0.00 0.00 0.00 5.19
849 1057 2.041081 CGATCCCCCATAAATAAGCCCA 59.959 50.000 0.00 0.00 0.00 5.36
850 1058 3.431415 GATCCCCCATAAATAAGCCCAC 58.569 50.000 0.00 0.00 0.00 4.61
851 1059 1.501604 TCCCCCATAAATAAGCCCACC 59.498 52.381 0.00 0.00 0.00 4.61
852 1060 1.219213 CCCCCATAAATAAGCCCACCA 59.781 52.381 0.00 0.00 0.00 4.17
853 1061 2.359781 CCCCCATAAATAAGCCCACCAA 60.360 50.000 0.00 0.00 0.00 3.67
854 1062 2.965147 CCCCATAAATAAGCCCACCAAG 59.035 50.000 0.00 0.00 0.00 3.61
855 1063 2.965147 CCCATAAATAAGCCCACCAAGG 59.035 50.000 0.00 0.00 37.03 3.61
856 1064 3.373658 CCCATAAATAAGCCCACCAAGGA 60.374 47.826 0.00 0.00 41.22 3.36
857 1065 4.285863 CCATAAATAAGCCCACCAAGGAA 58.714 43.478 0.00 0.00 41.22 3.36
858 1066 4.342092 CCATAAATAAGCCCACCAAGGAAG 59.658 45.833 0.00 0.00 41.22 3.46
859 1067 3.825908 AAATAAGCCCACCAAGGAAGA 57.174 42.857 0.00 0.00 41.22 2.87
860 1068 3.372440 AATAAGCCCACCAAGGAAGAG 57.628 47.619 0.00 0.00 41.22 2.85
861 1069 2.038863 TAAGCCCACCAAGGAAGAGA 57.961 50.000 0.00 0.00 41.22 3.10
862 1070 1.376649 AAGCCCACCAAGGAAGAGAT 58.623 50.000 0.00 0.00 41.22 2.75
863 1071 0.915364 AGCCCACCAAGGAAGAGATC 59.085 55.000 0.00 0.00 41.22 2.75
864 1072 0.915364 GCCCACCAAGGAAGAGATCT 59.085 55.000 0.00 0.00 41.22 2.75
865 1073 1.134250 GCCCACCAAGGAAGAGATCTC 60.134 57.143 15.29 15.29 41.22 2.75
866 1074 2.191400 CCCACCAAGGAAGAGATCTCA 58.809 52.381 24.39 0.00 41.22 3.27
867 1075 2.776536 CCCACCAAGGAAGAGATCTCAT 59.223 50.000 24.39 13.22 41.22 2.90
868 1076 3.181456 CCCACCAAGGAAGAGATCTCATC 60.181 52.174 24.39 20.93 41.22 2.92
869 1077 3.181456 CCACCAAGGAAGAGATCTCATCC 60.181 52.174 31.11 31.11 45.19 3.51
874 1082 3.866883 GGAAGAGATCTCATCCGATCC 57.133 52.381 26.59 17.44 40.50 3.36
875 1083 2.495669 GGAAGAGATCTCATCCGATCCC 59.504 54.545 26.59 8.07 40.50 3.85
876 1084 2.230130 AGAGATCTCATCCGATCCCC 57.770 55.000 24.39 0.00 40.50 4.81
877 1085 1.190643 GAGATCTCATCCGATCCCCC 58.809 60.000 18.11 0.00 40.50 5.40
878 1086 0.489117 AGATCTCATCCGATCCCCCA 59.511 55.000 0.00 0.00 40.50 4.96
879 1087 1.080161 AGATCTCATCCGATCCCCCAT 59.920 52.381 0.00 0.00 40.50 4.00
880 1088 2.316067 AGATCTCATCCGATCCCCCATA 59.684 50.000 0.00 0.00 40.50 2.74
881 1089 2.713828 TCTCATCCGATCCCCCATAA 57.286 50.000 0.00 0.00 0.00 1.90
882 1090 2.984672 TCTCATCCGATCCCCCATAAA 58.015 47.619 0.00 0.00 0.00 1.40
883 1091 3.531059 TCTCATCCGATCCCCCATAAAT 58.469 45.455 0.00 0.00 0.00 1.40
884 1092 4.694512 TCTCATCCGATCCCCCATAAATA 58.305 43.478 0.00 0.00 0.00 1.40
885 1093 5.097948 TCTCATCCGATCCCCCATAAATAA 58.902 41.667 0.00 0.00 0.00 1.40
886 1094 5.189736 TCTCATCCGATCCCCCATAAATAAG 59.810 44.000 0.00 0.00 0.00 1.73
887 1095 3.713826 TCCGATCCCCCATAAATAAGC 57.286 47.619 0.00 0.00 0.00 3.09
928 1136 3.806257 CGCATCGCATAGTGGTTTC 57.194 52.632 0.00 0.00 0.00 2.78
929 1137 0.304705 CGCATCGCATAGTGGTTTCC 59.695 55.000 0.00 0.00 0.00 3.13
930 1138 1.378531 GCATCGCATAGTGGTTTCCA 58.621 50.000 0.00 0.00 0.00 3.53
931 1139 1.949525 GCATCGCATAGTGGTTTCCAT 59.050 47.619 0.00 0.00 35.28 3.41
932 1140 2.031682 GCATCGCATAGTGGTTTCCATC 60.032 50.000 0.00 0.00 35.28 3.51
933 1141 2.325583 TCGCATAGTGGTTTCCATCC 57.674 50.000 0.00 0.00 35.28 3.51
964 1172 1.646189 CCTTTCTCTCGTTGCTAGGC 58.354 55.000 0.00 0.00 0.00 3.93
1221 1435 1.351350 GGCAAGAACAAGTCCTAGGGT 59.649 52.381 9.46 0.00 0.00 4.34
1229 1462 1.139853 CAAGTCCTAGGGTGATGCCTC 59.860 57.143 9.46 0.00 37.43 4.70
1318 1566 3.578272 GTCGTGGCGTGTTTGGCA 61.578 61.111 0.00 0.00 42.76 4.92
1347 1604 3.179443 TGATCTATTTCCAGTCGTGGC 57.821 47.619 0.00 0.00 44.60 5.01
1377 1634 0.613292 AGGTGTCTGGATCTCGCACT 60.613 55.000 0.00 0.00 0.00 4.40
1378 1635 1.103803 GGTGTCTGGATCTCGCACTA 58.896 55.000 0.00 0.00 0.00 2.74
1379 1636 1.476891 GGTGTCTGGATCTCGCACTAA 59.523 52.381 0.00 0.00 0.00 2.24
1380 1637 2.094182 GGTGTCTGGATCTCGCACTAAA 60.094 50.000 0.00 0.00 0.00 1.85
1381 1638 2.924290 GTGTCTGGATCTCGCACTAAAC 59.076 50.000 0.00 0.00 0.00 2.01
1382 1639 2.826128 TGTCTGGATCTCGCACTAAACT 59.174 45.455 0.00 0.00 0.00 2.66
1383 1640 3.258372 TGTCTGGATCTCGCACTAAACTT 59.742 43.478 0.00 0.00 0.00 2.66
1384 1641 3.614616 GTCTGGATCTCGCACTAAACTTG 59.385 47.826 0.00 0.00 0.00 3.16
1385 1642 2.932614 CTGGATCTCGCACTAAACTTGG 59.067 50.000 0.00 0.00 0.00 3.61
1386 1643 2.280628 GGATCTCGCACTAAACTTGGG 58.719 52.381 0.00 0.00 0.00 4.12
1387 1644 2.354805 GGATCTCGCACTAAACTTGGGT 60.355 50.000 0.00 0.00 0.00 4.51
1388 1645 2.922740 TCTCGCACTAAACTTGGGTT 57.077 45.000 0.00 0.00 37.24 4.11
1389 1646 2.762745 TCTCGCACTAAACTTGGGTTC 58.237 47.619 0.00 0.00 34.14 3.62
1390 1647 2.103432 TCTCGCACTAAACTTGGGTTCA 59.897 45.455 0.00 0.00 34.14 3.18
1391 1648 2.480419 CTCGCACTAAACTTGGGTTCAG 59.520 50.000 0.00 0.00 34.14 3.02
1392 1649 1.069227 CGCACTAAACTTGGGTTCAGC 60.069 52.381 0.00 0.00 34.14 4.26
1393 1650 1.269723 GCACTAAACTTGGGTTCAGCC 59.730 52.381 0.00 0.00 34.14 4.85
1394 1651 2.863809 CACTAAACTTGGGTTCAGCCT 58.136 47.619 0.00 0.00 37.43 4.58
1401 1658 1.610522 CTTGGGTTCAGCCTTGTCTTG 59.389 52.381 0.00 0.00 37.43 3.02
1409 1666 2.945008 TCAGCCTTGTCTTGTGTTTCTG 59.055 45.455 0.00 0.00 0.00 3.02
1420 1677 4.816385 TCTTGTGTTTCTGTCATCTTGGTC 59.184 41.667 0.00 0.00 0.00 4.02
1425 1682 3.744238 TTCTGTCATCTTGGTCGTTCA 57.256 42.857 0.00 0.00 0.00 3.18
1431 1688 4.245660 GTCATCTTGGTCGTTCATTCTGA 58.754 43.478 0.00 0.00 0.00 3.27
1445 1702 6.313252 GTTCATTCTGAGTTGATTTCTGCTC 58.687 40.000 0.00 0.00 0.00 4.26
1450 1707 6.889301 TCTGAGTTGATTTCTGCTCAATTT 57.111 33.333 0.00 0.00 37.50 1.82
1454 1711 8.169977 TGAGTTGATTTCTGCTCAATTTACTT 57.830 30.769 0.00 0.00 35.26 2.24
1456 1713 9.548208 GAGTTGATTTCTGCTCAATTTACTTAC 57.452 33.333 0.00 0.00 35.26 2.34
1458 1715 7.072177 TGATTTCTGCTCAATTTACTTACCG 57.928 36.000 0.00 0.00 0.00 4.02
1462 1719 5.041287 TCTGCTCAATTTACTTACCGATCG 58.959 41.667 8.51 8.51 0.00 3.69
1463 1720 5.001237 TGCTCAATTTACTTACCGATCGA 57.999 39.130 18.66 0.00 0.00 3.59
1464 1721 5.597806 TGCTCAATTTACTTACCGATCGAT 58.402 37.500 18.66 0.00 0.00 3.59
1467 1724 7.064064 GCTCAATTTACTTACCGATCGATTTC 58.936 38.462 18.66 0.00 0.00 2.17
1468 1725 7.473027 TCAATTTACTTACCGATCGATTTCC 57.527 36.000 18.66 0.00 0.00 3.13
1469 1726 7.270047 TCAATTTACTTACCGATCGATTTCCT 58.730 34.615 18.66 0.00 0.00 3.36
1470 1727 8.415553 TCAATTTACTTACCGATCGATTTCCTA 58.584 33.333 18.66 0.00 0.00 2.94
1473 1730 5.587388 ACTTACCGATCGATTTCCTACAA 57.413 39.130 18.66 0.00 0.00 2.41
1475 1732 3.454371 ACCGATCGATTTCCTACAAGG 57.546 47.619 18.66 0.00 36.46 3.61
1480 1795 4.021894 CGATCGATTTCCTACAAGGAGGAT 60.022 45.833 10.26 0.00 46.73 3.24
1484 1799 5.070047 TCGATTTCCTACAAGGAGGATTACC 59.930 44.000 0.97 0.00 46.73 2.85
1490 1805 5.911178 TCCTACAAGGAGGATTACCATGATT 59.089 40.000 0.00 0.00 40.06 2.57
1494 1809 6.125029 ACAAGGAGGATTACCATGATTTCTG 58.875 40.000 0.00 0.00 38.94 3.02
1497 1812 6.360618 AGGAGGATTACCATGATTTCTGAAC 58.639 40.000 0.00 0.00 38.94 3.18
1508 1823 1.888215 TTTCTGAACCAGCTGAGCAG 58.112 50.000 17.39 18.10 0.00 4.24
1546 1866 7.125792 TCCATAGGGATCACTTCTTTCTTAC 57.874 40.000 0.87 0.00 38.64 2.34
1550 1870 6.056090 AGGGATCACTTCTTTCTTACCTTC 57.944 41.667 0.00 0.00 0.00 3.46
1559 1879 4.084287 TCTTTCTTACCTTCGTCTGCCTA 58.916 43.478 0.00 0.00 0.00 3.93
1578 1898 4.421131 CCTACCTAGGCTGATCCATAGTT 58.579 47.826 9.30 0.00 36.53 2.24
1581 1901 6.497259 CCTACCTAGGCTGATCCATAGTTTAA 59.503 42.308 9.30 0.00 36.53 1.52
1582 1902 6.824958 ACCTAGGCTGATCCATAGTTTAAA 57.175 37.500 9.30 0.00 37.29 1.52
1583 1903 7.208064 ACCTAGGCTGATCCATAGTTTAAAA 57.792 36.000 9.30 0.00 37.29 1.52
1584 1904 7.639378 ACCTAGGCTGATCCATAGTTTAAAAA 58.361 34.615 9.30 0.00 37.29 1.94
1600 1920 0.758123 AAAAACCGGACCGACCTACA 59.242 50.000 17.49 0.00 36.31 2.74
1601 1921 0.758123 AAAACCGGACCGACCTACAA 59.242 50.000 17.49 0.00 36.31 2.41
1603 1923 0.978907 AACCGGACCGACCTACAATT 59.021 50.000 17.49 0.00 36.31 2.32
1605 1925 1.066645 ACCGGACCGACCTACAATTTC 60.067 52.381 17.49 0.00 36.31 2.17
1606 1926 1.066716 CCGGACCGACCTACAATTTCA 60.067 52.381 17.49 0.00 36.31 2.69
1648 2153 4.792521 ATCTCCAGTTACACAGTCTGAC 57.207 45.455 6.91 0.00 0.00 3.51
1670 2175 2.629617 ACAAAGATTGGAAACTGGCCAG 59.370 45.455 31.60 31.60 36.64 4.85
1773 2278 8.137437 ACAAACATTCATGAAACCAACTCTAAG 58.863 33.333 13.09 0.00 0.00 2.18
1781 2286 4.578928 TGAAACCAACTCTAAGCTGAAACC 59.421 41.667 0.00 0.00 0.00 3.27
1812 2317 5.181009 TCTGAAGACAGCACATAATTGAGG 58.819 41.667 0.00 0.00 43.17 3.86
1842 2347 1.350351 AGCATCAGAGGTGACAGCTTT 59.650 47.619 8.86 0.00 42.04 3.51
1886 2391 1.271379 TCAACTATCACTCGTTGGCGT 59.729 47.619 0.00 0.00 40.56 5.68
1888 2393 0.172803 ACTATCACTCGTTGGCGTCC 59.827 55.000 0.00 0.00 39.49 4.79
1935 2441 2.100991 GCATCGCCAAAGCTTCCG 59.899 61.111 0.00 3.48 36.60 4.30
1940 2446 2.563427 GCCAAAGCTTCCGAGTGC 59.437 61.111 0.00 0.00 35.50 4.40
1941 2447 2.863153 CCAAAGCTTCCGAGTGCG 59.137 61.111 0.00 0.00 37.24 5.34
1963 2469 1.002366 GCATCTGTTACACGCTCCAG 58.998 55.000 0.00 0.00 0.00 3.86
1966 2472 1.324383 TCTGTTACACGCTCCAGACA 58.676 50.000 0.00 0.00 0.00 3.41
1967 2473 1.269723 TCTGTTACACGCTCCAGACAG 59.730 52.381 0.00 0.00 36.68 3.51
1975 2481 2.183811 CTCCAGACAGCCTGCTCG 59.816 66.667 0.00 0.00 41.57 5.03
1977 2483 2.125753 CCAGACAGCCTGCTCGAC 60.126 66.667 0.00 0.00 41.57 4.20
2009 2515 4.394300 AGCGTTCCTTCTTCATTTCTGATG 59.606 41.667 0.00 0.00 0.00 3.07
2209 2730 2.042686 AGCTGCGGATTTGCTTGATA 57.957 45.000 0.00 0.00 32.61 2.15
2213 2734 4.580167 AGCTGCGGATTTGCTTGATAATTA 59.420 37.500 0.00 0.00 32.61 1.40
2214 2735 4.676924 GCTGCGGATTTGCTTGATAATTAC 59.323 41.667 0.00 0.00 35.36 1.89
2215 2736 5.506317 GCTGCGGATTTGCTTGATAATTACT 60.506 40.000 0.00 0.00 35.36 2.24
2216 2737 6.449635 TGCGGATTTGCTTGATAATTACTT 57.550 33.333 0.00 0.00 35.36 2.24
2217 2738 6.264832 TGCGGATTTGCTTGATAATTACTTG 58.735 36.000 0.00 0.00 35.36 3.16
2218 2739 5.687285 GCGGATTTGCTTGATAATTACTTGG 59.313 40.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.995220 ACAATATAAGAGCGTTTTTGACACTAA 58.005 29.630 0.00 0.00 0.00 2.24
1 2 8.440059 CACAATATAAGAGCGTTTTTGACACTA 58.560 33.333 0.00 0.00 0.00 2.74
2 3 7.298122 CACAATATAAGAGCGTTTTTGACACT 58.702 34.615 0.00 0.00 0.00 3.55
3 4 6.523201 CCACAATATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
4 5 6.348950 CCCACAATATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
5 6 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
6 7 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
7 8 6.027749 GTCCCACAATATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
8 9 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
9 10 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
10 11 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
11 12 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
12 13 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
13 14 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
14 15 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
15 16 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
16 17 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
17 18 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
18 19 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
19 20 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
20 21 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
21 22 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
22 23 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
23 24 0.613853 CTACTCCCTCCGTCCCACAA 60.614 60.000 0.00 0.00 0.00 3.33
24 25 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
25 26 0.106116 ATCTACTCCCTCCGTCCCAC 60.106 60.000 0.00 0.00 0.00 4.61
26 27 1.526315 TATCTACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
27 28 2.671896 TTATCTACTCCCTCCGTCCC 57.328 55.000 0.00 0.00 0.00 4.46
28 29 3.306156 GCAATTATCTACTCCCTCCGTCC 60.306 52.174 0.00 0.00 0.00 4.79
29 30 3.574826 AGCAATTATCTACTCCCTCCGTC 59.425 47.826 0.00 0.00 0.00 4.79
30 31 3.577919 AGCAATTATCTACTCCCTCCGT 58.422 45.455 0.00 0.00 0.00 4.69
31 32 4.202264 ACAAGCAATTATCTACTCCCTCCG 60.202 45.833 0.00 0.00 0.00 4.63
32 33 5.297569 ACAAGCAATTATCTACTCCCTCC 57.702 43.478 0.00 0.00 0.00 4.30
33 34 5.163301 TGGACAAGCAATTATCTACTCCCTC 60.163 44.000 0.00 0.00 0.00 4.30
34 35 4.721776 TGGACAAGCAATTATCTACTCCCT 59.278 41.667 0.00 0.00 0.00 4.20
35 36 5.036117 TGGACAAGCAATTATCTACTCCC 57.964 43.478 0.00 0.00 0.00 4.30
36 37 5.406780 CGATGGACAAGCAATTATCTACTCC 59.593 44.000 0.00 0.00 0.00 3.85
37 38 5.107298 GCGATGGACAAGCAATTATCTACTC 60.107 44.000 0.00 0.00 0.00 2.59
38 39 4.752101 GCGATGGACAAGCAATTATCTACT 59.248 41.667 0.00 0.00 0.00 2.57
39 40 4.511454 TGCGATGGACAAGCAATTATCTAC 59.489 41.667 3.86 0.00 38.01 2.59
55 56 7.642669 AGAATATTTGTATCTTGTTGCGATGG 58.357 34.615 0.00 0.00 0.00 3.51
57 58 9.547753 AGTAGAATATTTGTATCTTGTTGCGAT 57.452 29.630 0.00 0.00 0.00 4.58
89 90 3.289407 TGGGCATGGAAATCACGATTA 57.711 42.857 0.00 0.00 0.00 1.75
91 92 2.369983 ATGGGCATGGAAATCACGAT 57.630 45.000 0.00 0.00 0.00 3.73
94 95 5.565439 GCAGTAATATGGGCATGGAAATCAC 60.565 44.000 0.00 0.00 0.00 3.06
101 102 2.183478 TCGCAGTAATATGGGCATGG 57.817 50.000 0.00 0.00 33.41 3.66
131 132 7.673641 TGGGCTCACCATTTGATAAATATTT 57.326 32.000 5.89 5.89 46.80 1.40
224 225 1.248486 TCGACTCACTGGTTCCTCTG 58.752 55.000 0.00 0.00 0.00 3.35
337 343 6.313411 CGGAGGGAATACGTTTTTACACATTA 59.687 38.462 0.00 0.00 0.00 1.90
341 347 4.588805 CGGAGGGAATACGTTTTTACAC 57.411 45.455 0.00 0.00 0.00 2.90
352 358 1.797320 ATTTCCGGACGGAGGGAATA 58.203 50.000 13.64 0.00 46.06 1.75
353 359 1.415289 GTATTTCCGGACGGAGGGAAT 59.585 52.381 13.64 12.81 46.06 3.01
354 360 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.000 13.64 6.20 46.06 3.97
355 361 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
356 362 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
357 363 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
358 364 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
359 365 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
360 366 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
361 367 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
362 368 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
363 369 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
364 370 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
365 371 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
372 378 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
373 379 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
374 380 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
375 381 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
376 382 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
377 383 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
380 386 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
432 438 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
440 446 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
441 447 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
442 448 7.312154 TCCGAAAATACTTGTCATCAAAATGG 58.688 34.615 0.00 0.00 33.42 3.16
443 449 8.023128 ACTCCGAAAATACTTGTCATCAAAATG 58.977 33.333 0.00 0.00 32.87 2.32
444 450 8.110860 ACTCCGAAAATACTTGTCATCAAAAT 57.889 30.769 0.00 0.00 32.87 1.82
445 451 7.504924 ACTCCGAAAATACTTGTCATCAAAA 57.495 32.000 0.00 0.00 32.87 2.44
446 452 8.786826 ATACTCCGAAAATACTTGTCATCAAA 57.213 30.769 0.00 0.00 32.87 2.69
447 453 8.786826 AATACTCCGAAAATACTTGTCATCAA 57.213 30.769 0.00 0.00 0.00 2.57
448 454 8.038351 TGAATACTCCGAAAATACTTGTCATCA 58.962 33.333 0.00 0.00 0.00 3.07
449 455 8.420374 TGAATACTCCGAAAATACTTGTCATC 57.580 34.615 0.00 0.00 0.00 2.92
450 456 8.786826 TTGAATACTCCGAAAATACTTGTCAT 57.213 30.769 0.00 0.00 0.00 3.06
451 457 8.610248 TTTGAATACTCCGAAAATACTTGTCA 57.390 30.769 0.00 0.00 0.00 3.58
452 458 9.490663 CATTTGAATACTCCGAAAATACTTGTC 57.509 33.333 0.00 0.00 0.00 3.18
453 459 9.010029 ACATTTGAATACTCCGAAAATACTTGT 57.990 29.630 0.00 0.00 0.00 3.16
454 460 9.277565 CACATTTGAATACTCCGAAAATACTTG 57.722 33.333 0.00 0.00 0.00 3.16
455 461 8.458843 CCACATTTGAATACTCCGAAAATACTT 58.541 33.333 0.00 0.00 0.00 2.24
456 462 7.610305 ACCACATTTGAATACTCCGAAAATACT 59.390 33.333 0.00 0.00 0.00 2.12
457 463 7.758495 ACCACATTTGAATACTCCGAAAATAC 58.242 34.615 0.00 0.00 0.00 1.89
458 464 7.931578 ACCACATTTGAATACTCCGAAAATA 57.068 32.000 0.00 0.00 0.00 1.40
459 465 6.834168 ACCACATTTGAATACTCCGAAAAT 57.166 33.333 0.00 0.00 0.00 1.82
460 466 6.938030 ACTACCACATTTGAATACTCCGAAAA 59.062 34.615 0.00 0.00 0.00 2.29
461 467 6.469410 ACTACCACATTTGAATACTCCGAAA 58.531 36.000 0.00 0.00 0.00 3.46
462 468 6.045072 ACTACCACATTTGAATACTCCGAA 57.955 37.500 0.00 0.00 0.00 4.30
463 469 5.670792 ACTACCACATTTGAATACTCCGA 57.329 39.130 0.00 0.00 0.00 4.55
464 470 8.433421 AAATACTACCACATTTGAATACTCCG 57.567 34.615 0.00 0.00 0.00 4.63
493 499 7.227512 TGCCACATTTCGGTTCAAAAATTAAAT 59.772 29.630 0.00 0.00 0.00 1.40
494 500 6.538742 TGCCACATTTCGGTTCAAAAATTAAA 59.461 30.769 0.00 0.00 0.00 1.52
497 503 4.446371 TGCCACATTTCGGTTCAAAAATT 58.554 34.783 0.00 0.00 0.00 1.82
498 504 4.057432 CTGCCACATTTCGGTTCAAAAAT 58.943 39.130 0.00 0.00 0.00 1.82
499 505 3.118956 ACTGCCACATTTCGGTTCAAAAA 60.119 39.130 0.00 0.00 0.00 1.94
500 506 2.428890 ACTGCCACATTTCGGTTCAAAA 59.571 40.909 0.00 0.00 0.00 2.44
518 524 9.740239 CCATCTCAAAATATCCAAACAATACTG 57.260 33.333 0.00 0.00 0.00 2.74
523 529 5.417266 TCGCCATCTCAAAATATCCAAACAA 59.583 36.000 0.00 0.00 0.00 2.83
525 531 5.499139 TCGCCATCTCAAAATATCCAAAC 57.501 39.130 0.00 0.00 0.00 2.93
528 534 5.882000 CCATATCGCCATCTCAAAATATCCA 59.118 40.000 0.00 0.00 0.00 3.41
529 535 5.220931 GCCATATCGCCATCTCAAAATATCC 60.221 44.000 0.00 0.00 0.00 2.59
534 736 2.929641 TGCCATATCGCCATCTCAAAA 58.070 42.857 0.00 0.00 0.00 2.44
539 741 1.417517 TCACTTGCCATATCGCCATCT 59.582 47.619 0.00 0.00 0.00 2.90
570 772 3.959478 CTTGGCACATGGATGATGC 57.041 52.632 0.00 0.00 39.30 3.91
588 790 1.542915 TGAAAATCTTGAGCTGCAGCC 59.457 47.619 34.39 24.89 43.38 4.85
629 832 2.137528 TGGGAAGAGGACACGCACA 61.138 57.895 0.00 0.00 0.00 4.57
698 903 2.985282 ACGGTCGCACGGAGGTTA 60.985 61.111 3.77 0.00 38.39 2.85
750 955 0.816018 TTTGGCGACGTGTGTTGGAT 60.816 50.000 0.00 0.00 0.00 3.41
796 1001 2.614013 GGGAGGGGAAAGGGAGCA 60.614 66.667 0.00 0.00 0.00 4.26
803 1008 0.981277 GATCTCACGGGGAGGGGAAA 60.981 60.000 7.54 0.00 44.19 3.13
805 1010 2.282446 GATCTCACGGGGAGGGGA 59.718 66.667 7.54 0.00 44.19 4.81
806 1011 1.834822 GAGATCTCACGGGGAGGGG 60.835 68.421 18.11 0.00 44.19 4.79
847 1055 3.181456 GGATGAGATCTCTTCCTTGGTGG 60.181 52.174 34.61 0.00 45.37 4.61
848 1056 3.492309 CGGATGAGATCTCTTCCTTGGTG 60.492 52.174 36.33 24.74 46.14 4.17
849 1057 2.697751 CGGATGAGATCTCTTCCTTGGT 59.302 50.000 36.33 12.53 46.14 3.67
850 1058 2.961741 TCGGATGAGATCTCTTCCTTGG 59.038 50.000 36.33 27.18 46.14 3.61
851 1059 4.321899 GGATCGGATGAGATCTCTTCCTTG 60.322 50.000 36.33 27.68 46.14 3.61
852 1060 3.831911 GGATCGGATGAGATCTCTTCCTT 59.168 47.826 36.33 28.58 46.14 3.36
853 1061 3.430453 GGATCGGATGAGATCTCTTCCT 58.570 50.000 36.33 26.71 46.14 3.36
854 1062 2.495669 GGGATCGGATGAGATCTCTTCC 59.504 54.545 33.26 33.26 43.12 3.46
855 1063 2.495669 GGGGATCGGATGAGATCTCTTC 59.504 54.545 23.93 23.93 45.17 2.87
856 1064 2.534990 GGGGATCGGATGAGATCTCTT 58.465 52.381 22.95 17.01 45.17 2.85
857 1065 1.272985 GGGGGATCGGATGAGATCTCT 60.273 57.143 22.95 9.13 45.17 3.10
858 1066 1.190643 GGGGGATCGGATGAGATCTC 58.809 60.000 16.21 16.21 45.12 2.75
859 1067 0.489117 TGGGGGATCGGATGAGATCT 59.511 55.000 0.00 0.00 44.71 2.75
860 1068 1.577736 ATGGGGGATCGGATGAGATC 58.422 55.000 0.00 0.00 44.62 2.75
861 1069 2.948889 TATGGGGGATCGGATGAGAT 57.051 50.000 0.00 0.00 0.00 2.75
862 1070 2.713828 TTATGGGGGATCGGATGAGA 57.286 50.000 0.00 0.00 0.00 3.27
863 1071 5.431765 CTTATTTATGGGGGATCGGATGAG 58.568 45.833 0.00 0.00 0.00 2.90
864 1072 4.324254 GCTTATTTATGGGGGATCGGATGA 60.324 45.833 0.00 0.00 0.00 2.92
865 1073 3.947834 GCTTATTTATGGGGGATCGGATG 59.052 47.826 0.00 0.00 0.00 3.51
866 1074 3.053619 GGCTTATTTATGGGGGATCGGAT 60.054 47.826 0.00 0.00 0.00 4.18
867 1075 2.307686 GGCTTATTTATGGGGGATCGGA 59.692 50.000 0.00 0.00 0.00 4.55
868 1076 2.620627 GGGCTTATTTATGGGGGATCGG 60.621 54.545 0.00 0.00 0.00 4.18
869 1077 2.041081 TGGGCTTATTTATGGGGGATCG 59.959 50.000 0.00 0.00 0.00 3.69
870 1078 3.431415 GTGGGCTTATTTATGGGGGATC 58.569 50.000 0.00 0.00 0.00 3.36
871 1079 2.111792 GGTGGGCTTATTTATGGGGGAT 59.888 50.000 0.00 0.00 0.00 3.85
872 1080 1.501604 GGTGGGCTTATTTATGGGGGA 59.498 52.381 0.00 0.00 0.00 4.81
873 1081 1.219213 TGGTGGGCTTATTTATGGGGG 59.781 52.381 0.00 0.00 0.00 5.40
874 1082 2.765689 TGGTGGGCTTATTTATGGGG 57.234 50.000 0.00 0.00 0.00 4.96
875 1083 2.965147 CCTTGGTGGGCTTATTTATGGG 59.035 50.000 0.00 0.00 0.00 4.00
876 1084 3.909732 TCCTTGGTGGGCTTATTTATGG 58.090 45.455 0.00 0.00 36.20 2.74
877 1085 4.342092 CCTTCCTTGGTGGGCTTATTTATG 59.658 45.833 0.00 0.00 36.20 1.90
878 1086 4.231890 TCCTTCCTTGGTGGGCTTATTTAT 59.768 41.667 0.00 0.00 36.20 1.40
879 1087 3.594232 TCCTTCCTTGGTGGGCTTATTTA 59.406 43.478 0.00 0.00 36.20 1.40
880 1088 2.381961 TCCTTCCTTGGTGGGCTTATTT 59.618 45.455 0.00 0.00 36.20 1.40
881 1089 2.000048 TCCTTCCTTGGTGGGCTTATT 59.000 47.619 0.00 0.00 36.20 1.40
882 1090 1.681229 TCCTTCCTTGGTGGGCTTAT 58.319 50.000 0.00 0.00 36.20 1.73
883 1091 1.451449 TTCCTTCCTTGGTGGGCTTA 58.549 50.000 0.00 0.00 36.20 3.09
884 1092 0.560688 TTTCCTTCCTTGGTGGGCTT 59.439 50.000 0.00 0.00 36.20 4.35
885 1093 0.786435 ATTTCCTTCCTTGGTGGGCT 59.214 50.000 0.00 0.00 36.20 5.19
886 1094 1.186200 GATTTCCTTCCTTGGTGGGC 58.814 55.000 0.00 0.00 36.20 5.36
887 1095 2.603075 TGATTTCCTTCCTTGGTGGG 57.397 50.000 0.00 0.00 36.20 4.61
917 1125 4.169059 TGGATGGATGGAAACCACTATG 57.831 45.455 0.00 0.00 43.65 2.23
918 1126 4.202609 GGATGGATGGATGGAAACCACTAT 60.203 45.833 0.00 0.00 43.65 2.12
919 1127 3.138283 GGATGGATGGATGGAAACCACTA 59.862 47.826 0.00 0.00 43.65 2.74
920 1128 2.091665 GGATGGATGGATGGAAACCACT 60.092 50.000 0.00 0.00 43.65 4.00
921 1129 2.310538 GGATGGATGGATGGAAACCAC 58.689 52.381 0.00 0.00 43.65 4.16
922 1130 1.928785 TGGATGGATGGATGGAAACCA 59.071 47.619 0.00 0.00 45.53 3.67
923 1131 2.754012 TGGATGGATGGATGGAAACC 57.246 50.000 0.00 0.00 0.00 3.27
924 1132 3.160269 GGATGGATGGATGGATGGAAAC 58.840 50.000 0.00 0.00 0.00 2.78
925 1133 2.110543 GGGATGGATGGATGGATGGAAA 59.889 50.000 0.00 0.00 0.00 3.13
926 1134 1.712510 GGGATGGATGGATGGATGGAA 59.287 52.381 0.00 0.00 0.00 3.53
927 1135 1.131970 AGGGATGGATGGATGGATGGA 60.132 52.381 0.00 0.00 0.00 3.41
928 1136 1.379776 AGGGATGGATGGATGGATGG 58.620 55.000 0.00 0.00 0.00 3.51
929 1137 3.075582 AGAAAGGGATGGATGGATGGATG 59.924 47.826 0.00 0.00 0.00 3.51
930 1138 3.333082 GAGAAAGGGATGGATGGATGGAT 59.667 47.826 0.00 0.00 0.00 3.41
931 1139 2.713167 GAGAAAGGGATGGATGGATGGA 59.287 50.000 0.00 0.00 0.00 3.41
932 1140 2.715336 AGAGAAAGGGATGGATGGATGG 59.285 50.000 0.00 0.00 0.00 3.51
933 1141 3.556633 CGAGAGAAAGGGATGGATGGATG 60.557 52.174 0.00 0.00 0.00 3.51
964 1172 6.675002 GCAACAACAAGATCAAGATCTAGCTG 60.675 42.308 12.62 10.07 46.75 4.24
999 1207 1.815421 CTTCTTCCCGCCGTCCATG 60.815 63.158 0.00 0.00 0.00 3.66
1261 1498 9.302345 TCAACTCACACGATTTAGAAATCTATC 57.698 33.333 12.03 0.00 41.99 2.08
1281 1518 8.056571 CCACGACTCGATTTAATTATTCAACTC 58.943 37.037 5.20 0.00 0.00 3.01
1318 1566 8.807118 ACGACTGGAAATAGATCATATGTACAT 58.193 33.333 13.93 13.93 0.00 2.29
1347 1604 4.487714 TCCAGACACCTAATTAGCAAGG 57.512 45.455 6.99 0.00 38.93 3.61
1377 1634 3.117663 AGACAAGGCTGAACCCAAGTTTA 60.118 43.478 0.00 0.00 40.58 2.01
1378 1635 2.031870 GACAAGGCTGAACCCAAGTTT 58.968 47.619 0.00 0.00 40.58 2.66
1379 1636 1.215423 AGACAAGGCTGAACCCAAGTT 59.785 47.619 0.00 0.00 40.58 2.66
1380 1637 0.846693 AGACAAGGCTGAACCCAAGT 59.153 50.000 0.00 0.00 40.58 3.16
1381 1638 1.610522 CAAGACAAGGCTGAACCCAAG 59.389 52.381 0.00 0.00 40.58 3.61
1382 1639 1.064017 ACAAGACAAGGCTGAACCCAA 60.064 47.619 0.00 0.00 40.58 4.12
1383 1640 0.550914 ACAAGACAAGGCTGAACCCA 59.449 50.000 0.00 0.00 40.58 4.51
1384 1641 0.954452 CACAAGACAAGGCTGAACCC 59.046 55.000 0.00 0.00 40.58 4.11
1385 1642 1.680338 ACACAAGACAAGGCTGAACC 58.320 50.000 0.00 0.00 39.61 3.62
1386 1643 3.378427 AGAAACACAAGACAAGGCTGAAC 59.622 43.478 0.00 0.00 0.00 3.18
1387 1644 3.378112 CAGAAACACAAGACAAGGCTGAA 59.622 43.478 0.00 0.00 0.00 3.02
1388 1645 2.945008 CAGAAACACAAGACAAGGCTGA 59.055 45.455 0.00 0.00 0.00 4.26
1389 1646 2.684881 ACAGAAACACAAGACAAGGCTG 59.315 45.455 0.00 0.00 0.00 4.85
1390 1647 2.945668 GACAGAAACACAAGACAAGGCT 59.054 45.455 0.00 0.00 0.00 4.58
1391 1648 2.682856 TGACAGAAACACAAGACAAGGC 59.317 45.455 0.00 0.00 0.00 4.35
1392 1649 4.818546 AGATGACAGAAACACAAGACAAGG 59.181 41.667 0.00 0.00 0.00 3.61
1393 1650 5.998454 AGATGACAGAAACACAAGACAAG 57.002 39.130 0.00 0.00 0.00 3.16
1394 1651 5.066375 CCAAGATGACAGAAACACAAGACAA 59.934 40.000 0.00 0.00 0.00 3.18
1401 1658 3.131396 ACGACCAAGATGACAGAAACAC 58.869 45.455 0.00 0.00 0.00 3.32
1409 1666 4.245660 TCAGAATGAACGACCAAGATGAC 58.754 43.478 0.00 0.00 45.97 3.06
1425 1682 7.463961 AATTGAGCAGAAATCAACTCAGAAT 57.536 32.000 5.80 0.00 40.08 2.40
1431 1688 8.515414 GGTAAGTAAATTGAGCAGAAATCAACT 58.485 33.333 0.00 0.00 39.36 3.16
1445 1702 7.478520 AGGAAATCGATCGGTAAGTAAATTG 57.521 36.000 16.41 0.00 0.00 2.32
1450 1707 6.238842 CCTTGTAGGAAATCGATCGGTAAGTA 60.239 42.308 16.41 0.00 37.67 2.24
1454 1711 4.209538 TCCTTGTAGGAAATCGATCGGTA 58.790 43.478 16.41 0.00 42.51 4.02
1456 1713 3.553096 CCTCCTTGTAGGAAATCGATCGG 60.553 52.174 16.41 0.00 45.28 4.18
1458 1715 4.939052 TCCTCCTTGTAGGAAATCGATC 57.061 45.455 0.00 0.00 45.28 3.69
1467 1724 5.832539 ATCATGGTAATCCTCCTTGTAGG 57.167 43.478 0.00 0.00 38.06 3.18
1468 1725 7.443575 CAGAAATCATGGTAATCCTCCTTGTAG 59.556 40.741 0.00 0.00 33.61 2.74
1469 1726 7.127186 TCAGAAATCATGGTAATCCTCCTTGTA 59.873 37.037 0.00 0.00 33.61 2.41
1470 1727 6.069440 TCAGAAATCATGGTAATCCTCCTTGT 60.069 38.462 0.00 0.00 33.61 3.16
1473 1730 6.360618 GTTCAGAAATCATGGTAATCCTCCT 58.639 40.000 0.00 0.00 34.23 3.69
1475 1732 6.122277 TGGTTCAGAAATCATGGTAATCCTC 58.878 40.000 0.00 0.00 34.23 3.71
1480 1795 4.701651 CAGCTGGTTCAGAAATCATGGTAA 59.298 41.667 5.57 0.00 32.44 2.85
1484 1799 3.181499 GCTCAGCTGGTTCAGAAATCATG 60.181 47.826 15.13 0.00 32.44 3.07
1490 1805 1.051008 TCTGCTCAGCTGGTTCAGAA 58.949 50.000 22.22 5.98 32.44 3.02
1494 1809 2.008329 CATCTTCTGCTCAGCTGGTTC 58.992 52.381 15.13 3.86 0.00 3.62
1497 1812 2.093606 TCTTCATCTTCTGCTCAGCTGG 60.094 50.000 15.13 5.82 0.00 4.85
1508 1823 6.678568 TCCCTATGGATCTTCTTCATCTTC 57.321 41.667 0.00 0.00 35.03 2.87
1546 1866 1.033574 CCTAGGTAGGCAGACGAAGG 58.966 60.000 0.00 0.00 36.53 3.46
1559 1879 6.824958 TTTAAACTATGGATCAGCCTAGGT 57.175 37.500 11.31 0.00 37.63 3.08
1581 1901 0.758123 TGTAGGTCGGTCCGGTTTTT 59.242 50.000 12.29 0.00 41.99 1.94
1582 1902 0.758123 TTGTAGGTCGGTCCGGTTTT 59.242 50.000 12.29 0.00 41.99 2.43
1583 1903 0.978907 ATTGTAGGTCGGTCCGGTTT 59.021 50.000 12.29 0.00 41.99 3.27
1584 1904 0.978907 AATTGTAGGTCGGTCCGGTT 59.021 50.000 12.29 0.00 41.99 4.44
1585 1905 0.978907 AAATTGTAGGTCGGTCCGGT 59.021 50.000 12.29 0.00 41.99 5.28
1586 1906 1.066716 TGAAATTGTAGGTCGGTCCGG 60.067 52.381 12.29 0.00 41.99 5.14
1589 1909 6.586844 GCTATCTATGAAATTGTAGGTCGGTC 59.413 42.308 0.00 0.00 0.00 4.79
1590 1910 6.267928 AGCTATCTATGAAATTGTAGGTCGGT 59.732 38.462 0.00 0.00 0.00 4.69
1592 1912 7.116948 CCAAGCTATCTATGAAATTGTAGGTCG 59.883 40.741 0.00 0.00 0.00 4.79
1593 1913 7.095017 GCCAAGCTATCTATGAAATTGTAGGTC 60.095 40.741 0.00 0.00 0.00 3.85
1594 1914 6.712547 GCCAAGCTATCTATGAAATTGTAGGT 59.287 38.462 0.00 0.00 0.00 3.08
1596 1916 7.094890 CCAGCCAAGCTATCTATGAAATTGTAG 60.095 40.741 0.00 0.00 36.40 2.74
1597 1917 6.712095 CCAGCCAAGCTATCTATGAAATTGTA 59.288 38.462 0.00 0.00 36.40 2.41
1598 1918 5.533903 CCAGCCAAGCTATCTATGAAATTGT 59.466 40.000 0.00 0.00 36.40 2.71
1600 1920 5.767168 GTCCAGCCAAGCTATCTATGAAATT 59.233 40.000 0.00 0.00 36.40 1.82
1601 1921 5.163163 TGTCCAGCCAAGCTATCTATGAAAT 60.163 40.000 0.00 0.00 36.40 2.17
1603 1923 3.711190 TGTCCAGCCAAGCTATCTATGAA 59.289 43.478 0.00 0.00 36.40 2.57
1605 1925 3.758755 TGTCCAGCCAAGCTATCTATG 57.241 47.619 0.00 0.00 36.40 2.23
1606 1926 4.778213 TTTGTCCAGCCAAGCTATCTAT 57.222 40.909 0.00 0.00 36.40 1.98
1635 2140 5.527214 CCAATCTTTGTGTCAGACTGTGTAA 59.473 40.000 1.59 0.00 0.00 2.41
1648 2153 2.364970 TGGCCAGTTTCCAATCTTTGTG 59.635 45.455 0.00 0.00 0.00 3.33
1670 2175 5.442391 TGTAGGTACCTATGAAATTTGGCC 58.558 41.667 24.36 7.74 0.00 5.36
1728 2233 3.951979 GTGTTGAACACTGTCCAAGAG 57.048 47.619 20.39 0.00 45.27 2.85
1773 2278 3.325293 TCAGAGACATCAGGTTTCAGC 57.675 47.619 0.00 0.00 33.18 4.26
1799 2304 6.514048 GCTTATGACCTTCCTCAATTATGTGC 60.514 42.308 0.00 0.00 0.00 4.57
1803 2308 7.520798 TGATGCTTATGACCTTCCTCAATTAT 58.479 34.615 0.00 0.00 0.00 1.28
1807 2312 4.471025 TCTGATGCTTATGACCTTCCTCAA 59.529 41.667 0.00 0.00 0.00 3.02
1812 2317 4.125703 CACCTCTGATGCTTATGACCTTC 58.874 47.826 0.00 0.00 0.00 3.46
1886 2391 1.123077 ATGCAGCTAGTCGAATGGGA 58.877 50.000 0.00 0.00 0.00 4.37
1888 2393 2.286294 GTGAATGCAGCTAGTCGAATGG 59.714 50.000 0.00 0.00 0.00 3.16
1935 2441 0.721718 GTAACAGATGCACCGCACTC 59.278 55.000 0.00 0.00 43.04 3.51
1940 2446 1.014044 AGCGTGTAACAGATGCACCG 61.014 55.000 0.00 0.00 41.13 4.94
1941 2447 0.721718 GAGCGTGTAACAGATGCACC 59.278 55.000 0.00 0.00 41.13 5.01
1963 2469 2.125753 CTGGTCGAGCAGGCTGTC 60.126 66.667 32.01 11.19 0.00 3.51
1975 2481 1.739067 AGGAACGCTAATTGCTGGTC 58.261 50.000 0.00 0.00 40.11 4.02
1977 2483 2.359900 AGAAGGAACGCTAATTGCTGG 58.640 47.619 0.00 0.00 40.11 4.85
1989 2495 5.620879 GCACCATCAGAAATGAAGAAGGAAC 60.621 44.000 0.00 0.00 0.00 3.62
2009 2515 4.035102 GACTCCACCCCCAGCACC 62.035 72.222 0.00 0.00 0.00 5.01
2136 2650 5.756195 ATAATCGGGAACAATGTGACATG 57.244 39.130 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.