Multiple sequence alignment - TraesCS7B01G259300

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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 TraesCS7B01G259300 chr7B 100.000 4298 0 0 1 4298 479780012 479784309 0.000000e+00 7938.0
1 TraesCS7B01G259300 chr7B 94.872 117 6 0 4180 4296 437689953 437689837 2.640000e-42 183.0
2 TraesCS7B01G259300 chr7B 87.719 114 10 4 486 598 652932535 652932425 3.490000e-26 130.0
3 TraesCS7B01G259300 chr7A 91.865 2139 113 39 1939 4033 542709746 542707625 0.000000e+00 2929.0
4 TraesCS7B01G259300 chr7A 84.205 994 77 31 768 1712 542711033 542710071 0.000000e+00 893.0
5 TraesCS7B01G259300 chr7A 86.335 161 7 7 4033 4182 542707262 542707106 1.240000e-35 161.0
6 TraesCS7B01G259300 chr7A 89.720 107 10 1 468 573 704612827 704612933 7.500000e-28 135.0
7 TraesCS7B01G259300 chr7A 95.238 42 2 0 1732 1773 542710073 542710032 2.770000e-07 67.6
8 TraesCS7B01G259300 chr7D 88.861 1212 70 25 767 1923 458010584 458011785 0.000000e+00 1430.0
9 TraesCS7B01G259300 chr7D 86.775 862 79 20 2505 3347 458012462 458013307 0.000000e+00 928.0
10 TraesCS7B01G259300 chr7D 88.956 498 33 10 1 480 458009630 458010123 2.860000e-166 595.0
11 TraesCS7B01G259300 chr7D 84.437 302 23 14 3899 4186 458013664 458013955 4.230000e-70 276.0
12 TraesCS7B01G259300 chrUn 87.597 1032 70 24 2488 3484 92185022 92184014 0.000000e+00 1144.0
13 TraesCS7B01G259300 chrUn 91.703 229 7 7 3962 4189 92184019 92183802 1.500000e-79 307.0
14 TraesCS7B01G259300 chr4B 96.667 120 4 0 4177 4296 532721336 532721455 2.620000e-47 200.0
15 TraesCS7B01G259300 chr4B 95.833 120 5 0 4177 4296 515059363 515059244 1.220000e-45 195.0
16 TraesCS7B01G259300 chr4B 94.872 117 6 0 4180 4296 447273468 447273352 2.640000e-42 183.0
17 TraesCS7B01G259300 chr1B 94.444 126 6 1 4172 4296 301794444 301794569 4.390000e-45 193.0
18 TraesCS7B01G259300 chr2B 95.082 122 5 1 4176 4296 213340209 213340330 1.580000e-44 191.0
19 TraesCS7B01G259300 chr2B 90.196 102 8 2 483 583 699185509 699185609 9.700000e-27 132.0
20 TraesCS7B01G259300 chr2B 78.995 219 25 9 3503 3701 387087653 387087436 3.490000e-26 130.0
21 TraesCS7B01G259300 chr5B 95.726 117 5 0 4180 4296 207359709 207359593 5.670000e-44 189.0
22 TraesCS7B01G259300 chr5B 93.600 125 7 1 4172 4296 604637586 604637463 7.340000e-43 185.0
23 TraesCS7B01G259300 chr5B 94.872 117 6 0 4180 4296 444191384 444191268 2.640000e-42 183.0
24 TraesCS7B01G259300 chr2D 80.889 225 22 11 3503 3709 318561433 318561212 1.600000e-34 158.0
25 TraesCS7B01G259300 chr2D 89.583 48 5 0 3504 3551 561215987 561215940 1.290000e-05 62.1
26 TraesCS7B01G259300 chr2A 93.684 95 6 0 480 574 34104339 34104433 4.480000e-30 143.0
27 TraesCS7B01G259300 chr6D 93.548 93 5 1 482 573 4701409 4701317 2.080000e-28 137.0
28 TraesCS7B01G259300 chr3B 89.720 107 10 1 485 590 256530600 256530494 7.500000e-28 135.0
29 TraesCS7B01G259300 chr3D 88.596 114 8 5 486 595 475298912 475298800 2.700000e-27 134.0
30 TraesCS7B01G259300 chr3D 87.288 118 12 2 478 592 611167349 611167232 9.700000e-27 132.0
31 TraesCS7B01G259300 chr4A 90.816 98 7 2 476 571 584048371 584048468 3.490000e-26 130.0


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 TraesCS7B01G259300 chr7B 479780012 479784309 4297 False 7938.00 7938 100.00000 1 4298 1 chr7B.!!$F1 4297
1 TraesCS7B01G259300 chr7A 542707106 542711033 3927 True 1012.65 2929 89.41075 768 4182 4 chr7A.!!$R1 3414
2 TraesCS7B01G259300 chr7D 458009630 458013955 4325 False 807.25 1430 87.25725 1 4186 4 chr7D.!!$F1 4185
3 TraesCS7B01G259300 chrUn 92183802 92185022 1220 True 725.50 1144 89.65000 2488 4189 2 chrUn.!!$R1 1701

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
143 144 0.538287 GAAAGCAAGTGGGTGAGCCT 60.538 55.0 1.06 0.0 34.45 4.58 F
1282 1589 0.467804 GCCTCCTCTGATCTGGGTTC 59.532 60.0 0.00 0.0 0.00 3.62 F
2332 2845 0.329931 TGGGTTTGTCCGTGGCATAT 59.670 50.0 0.00 0.0 37.00 1.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2148 0.036010 ATGGTTCTGCAGAAGGACGG 60.036 55.0 29.13 0.0 34.84 4.79 R
2692 3312 0.110823 GCAAGTGCTTGGTAACGTCG 60.111 55.0 13.07 0.0 40.74 5.12 R
4184 5439 0.179108 GTTACTCCCACTGCGGCTAG 60.179 60.0 0.00 0.0 0.00 3.42 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
25 26 1.202099 TTCCATGGACGGCCTTACCA 61.202 55.000 15.91 13.28 39.03 3.25
28 29 1.308998 CATGGACGGCCTTACCAATC 58.691 55.000 9.82 0.00 39.03 2.67
103 104 9.965824 AAAAAGGTTGTCTAATTACTTGATGTG 57.034 29.630 0.00 0.00 0.00 3.21
117 118 6.575162 ACTTGATGTGGGTTTATCTTTCAC 57.425 37.500 0.00 0.00 0.00 3.18
143 144 0.538287 GAAAGCAAGTGGGTGAGCCT 60.538 55.000 1.06 0.00 34.45 4.58
175 176 0.898320 TCAACCTAGAGCAGCCTCAC 59.102 55.000 0.00 0.00 40.68 3.51
203 204 4.770874 GCGAAACTAGGCCGGCCA 62.771 66.667 45.13 29.46 38.92 5.36
204 205 2.818274 CGAAACTAGGCCGGCCAC 60.818 66.667 45.13 25.77 38.92 5.01
205 206 2.349755 GAAACTAGGCCGGCCACA 59.650 61.111 45.13 31.11 38.92 4.17
206 207 1.302993 GAAACTAGGCCGGCCACAA 60.303 57.895 45.13 28.82 38.92 3.33
213 232 3.894947 GCCGGCCACAACGTTTGT 61.895 61.111 18.11 0.00 46.75 2.83
220 239 2.219903 GGCCACAACGTTTGTTTTATGC 59.780 45.455 0.00 0.00 43.23 3.14
221 240 3.120041 GCCACAACGTTTGTTTTATGCT 58.880 40.909 0.00 0.00 43.23 3.79
497 516 8.671384 TTTTGAAATATAATACTCCCTCCGTG 57.329 34.615 0.00 0.00 0.00 4.94
498 517 7.606135 TTGAAATATAATACTCCCTCCGTGA 57.394 36.000 0.00 0.00 0.00 4.35
499 518 7.606135 TGAAATATAATACTCCCTCCGTGAA 57.394 36.000 0.00 0.00 0.00 3.18
500 519 7.439381 TGAAATATAATACTCCCTCCGTGAAC 58.561 38.462 0.00 0.00 0.00 3.18
501 520 7.289317 TGAAATATAATACTCCCTCCGTGAACT 59.711 37.037 0.00 0.00 0.00 3.01
502 521 8.716674 AAATATAATACTCCCTCCGTGAACTA 57.283 34.615 0.00 0.00 0.00 2.24
503 522 8.716674 AATATAATACTCCCTCCGTGAACTAA 57.283 34.615 0.00 0.00 0.00 2.24
504 523 8.896722 ATATAATACTCCCTCCGTGAACTAAT 57.103 34.615 0.00 0.00 0.00 1.73
505 524 4.939052 ATACTCCCTCCGTGAACTAATG 57.061 45.455 0.00 0.00 0.00 1.90
506 525 2.537143 ACTCCCTCCGTGAACTAATGT 58.463 47.619 0.00 0.00 0.00 2.71
507 526 3.705051 ACTCCCTCCGTGAACTAATGTA 58.295 45.455 0.00 0.00 0.00 2.29
508 527 4.091549 ACTCCCTCCGTGAACTAATGTAA 58.908 43.478 0.00 0.00 0.00 2.41
509 528 4.159879 ACTCCCTCCGTGAACTAATGTAAG 59.840 45.833 0.00 0.00 0.00 2.34
510 529 4.346730 TCCCTCCGTGAACTAATGTAAGA 58.653 43.478 0.00 0.00 0.00 2.10
511 530 4.401519 TCCCTCCGTGAACTAATGTAAGAG 59.598 45.833 0.00 0.00 0.00 2.85
512 531 4.113354 CCTCCGTGAACTAATGTAAGAGC 58.887 47.826 0.00 0.00 0.00 4.09
513 532 4.381612 CCTCCGTGAACTAATGTAAGAGCA 60.382 45.833 0.00 0.00 0.00 4.26
514 533 5.339008 TCCGTGAACTAATGTAAGAGCAT 57.661 39.130 0.00 0.00 0.00 3.79
515 534 5.730550 TCCGTGAACTAATGTAAGAGCATT 58.269 37.500 0.00 0.00 41.42 3.56
516 535 6.170506 TCCGTGAACTAATGTAAGAGCATTT 58.829 36.000 0.00 0.00 39.50 2.32
517 536 7.324935 TCCGTGAACTAATGTAAGAGCATTTA 58.675 34.615 0.00 0.00 39.50 1.40
518 537 7.491372 TCCGTGAACTAATGTAAGAGCATTTAG 59.509 37.037 0.00 0.00 39.50 1.85
519 538 7.491372 CCGTGAACTAATGTAAGAGCATTTAGA 59.509 37.037 0.00 0.00 39.50 2.10
520 539 8.869897 CGTGAACTAATGTAAGAGCATTTAGAA 58.130 33.333 0.00 0.00 39.50 2.10
534 553 9.959721 AGAGCATTTAGAATACTAAAAAGGTGA 57.040 29.630 0.00 0.00 46.90 4.02
543 562 8.880750 AGAATACTAAAAAGGTGATCTAAACGC 58.119 33.333 0.00 0.00 0.00 4.84
544 563 8.788325 AATACTAAAAAGGTGATCTAAACGCT 57.212 30.769 0.00 0.00 0.00 5.07
545 564 6.723131 ACTAAAAAGGTGATCTAAACGCTC 57.277 37.500 0.00 0.00 0.00 5.03
546 565 6.465084 ACTAAAAAGGTGATCTAAACGCTCT 58.535 36.000 0.00 0.00 0.00 4.09
547 566 6.935208 ACTAAAAAGGTGATCTAAACGCTCTT 59.065 34.615 0.00 0.00 0.00 2.85
548 567 8.092687 ACTAAAAAGGTGATCTAAACGCTCTTA 58.907 33.333 0.00 0.00 0.00 2.10
549 568 7.923414 AAAAAGGTGATCTAAACGCTCTTAT 57.077 32.000 0.00 0.00 0.00 1.73
551 570 9.614792 AAAAAGGTGATCTAAACGCTCTTATAT 57.385 29.630 0.00 0.00 0.00 0.86
552 571 9.614792 AAAAGGTGATCTAAACGCTCTTATATT 57.385 29.630 0.00 0.00 0.00 1.28
554 573 9.915629 AAGGTGATCTAAACGCTCTTATATTAG 57.084 33.333 0.00 0.00 0.00 1.73
555 574 9.080097 AGGTGATCTAAACGCTCTTATATTAGT 57.920 33.333 0.00 0.00 0.00 2.24
556 575 9.694137 GGTGATCTAAACGCTCTTATATTAGTT 57.306 33.333 0.00 0.00 0.00 2.24
561 580 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
562 581 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
563 582 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
564 583 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
565 584 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
566 585 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
567 586 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
958 1262 1.384525 GGTATAAATGGTGGTGCGCA 58.615 50.000 5.66 5.66 0.00 6.09
1059 1366 2.185350 CGGTCATTGAGAGGCGCT 59.815 61.111 7.64 0.00 0.00 5.92
1168 1475 2.508439 GCCTTCGCCATCGACGAA 60.508 61.111 0.00 8.76 45.43 3.85
1282 1589 0.467804 GCCTCCTCTGATCTGGGTTC 59.532 60.000 0.00 0.00 0.00 3.62
1284 1591 0.749649 CTCCTCTGATCTGGGTTCCG 59.250 60.000 0.00 0.00 0.00 4.30
1490 1823 9.887964 CCCAGAGGAGAGGTAACTTGATTGAAC 62.888 48.148 0.00 0.00 42.35 3.18
1506 1839 2.172483 GAACTGGCGCTCTTCTCCCA 62.172 60.000 7.64 0.00 0.00 4.37
1515 1863 2.795329 GCTCTTCTCCCAATTGGTTCA 58.205 47.619 22.91 5.84 34.77 3.18
1529 1877 2.524306 TGGTTCATTGTAGCCCCAAAG 58.476 47.619 0.00 0.00 0.00 2.77
1530 1878 1.204704 GGTTCATTGTAGCCCCAAAGC 59.795 52.381 0.00 0.00 0.00 3.51
1551 1899 1.604593 CCCTGTTTCCACTGCCCAG 60.605 63.158 0.00 0.00 0.00 4.45
1692 2059 8.458573 TTGGCTTAGAAGTTCATTCTTAAACA 57.541 30.769 5.50 0.00 46.49 2.83
1773 2140 5.415701 TGTGGAAATCAGCTCCTGTTTATTC 59.584 40.000 0.00 0.00 33.77 1.75
1774 2141 4.949856 TGGAAATCAGCTCCTGTTTATTCC 59.050 41.667 0.00 0.00 34.25 3.01
1775 2142 5.196695 GGAAATCAGCTCCTGTTTATTCCT 58.803 41.667 0.00 0.00 32.76 3.36
1776 2143 5.654209 GGAAATCAGCTCCTGTTTATTCCTT 59.346 40.000 0.00 0.00 32.76 3.36
1777 2144 6.183360 GGAAATCAGCTCCTGTTTATTCCTTC 60.183 42.308 0.00 0.00 32.76 3.46
1779 2146 4.836825 TCAGCTCCTGTTTATTCCTTCAG 58.163 43.478 0.00 0.00 32.61 3.02
1780 2147 3.944015 CAGCTCCTGTTTATTCCTTCAGG 59.056 47.826 0.00 0.00 46.00 3.86
1781 2148 2.685388 GCTCCTGTTTATTCCTTCAGGC 59.315 50.000 5.33 0.00 44.76 4.85
1782 2149 3.282885 CTCCTGTTTATTCCTTCAGGCC 58.717 50.000 0.00 0.00 44.76 5.19
1783 2150 2.017049 CCTGTTTATTCCTTCAGGCCG 58.983 52.381 0.00 0.00 40.43 6.13
1803 2244 3.535561 CGTCCTTCTGCAGAACCATTAT 58.464 45.455 25.16 0.00 0.00 1.28
1813 2254 5.713025 TGCAGAACCATTATGCTTTTCTTC 58.287 37.500 9.34 0.00 40.62 2.87
1841 2291 7.226441 AGCAACAGCATACTATCATTGGATTA 58.774 34.615 0.00 0.00 34.89 1.75
1859 2320 4.035675 GGATTATTCTGTTCTTTCGCCCTG 59.964 45.833 0.00 0.00 0.00 4.45
1863 2324 0.593128 CTGTTCTTTCGCCCTGGTTG 59.407 55.000 0.00 0.00 0.00 3.77
1878 2339 1.510480 GGTTGTCAGGCAGCACTGTC 61.510 60.000 9.83 0.00 39.48 3.51
1880 2341 2.026945 TTGTCAGGCAGCACTGTCGA 62.027 55.000 9.83 3.39 40.75 4.20
1923 2384 6.067263 ACGTAGAGATGATTTACTGCTCTC 57.933 41.667 0.00 0.00 37.20 3.20
1931 2392 6.544197 AGATGATTTACTGCTCTCTTCGTCTA 59.456 38.462 0.00 0.00 0.00 2.59
1932 2393 5.881447 TGATTTACTGCTCTCTTCGTCTAC 58.119 41.667 0.00 0.00 0.00 2.59
1933 2394 4.337985 TTTACTGCTCTCTTCGTCTACG 57.662 45.455 0.00 0.00 41.45 3.51
1934 2395 1.810959 ACTGCTCTCTTCGTCTACGT 58.189 50.000 2.02 0.00 40.80 3.57
1935 2396 2.969990 ACTGCTCTCTTCGTCTACGTA 58.030 47.619 2.02 0.00 40.80 3.57
1937 2398 4.691175 ACTGCTCTCTTCGTCTACGTATA 58.309 43.478 0.00 0.00 40.80 1.47
1987 2486 7.823745 AGGAGACTGCTTTTCATTTTCTTAA 57.176 32.000 0.00 0.00 41.13 1.85
1988 2487 8.237811 AGGAGACTGCTTTTCATTTTCTTAAA 57.762 30.769 0.00 0.00 41.13 1.52
1989 2488 8.695456 AGGAGACTGCTTTTCATTTTCTTAAAA 58.305 29.630 0.00 0.00 41.13 1.52
2092 2591 3.675698 TCAAACCACGAAAGCAACAAAAC 59.324 39.130 0.00 0.00 0.00 2.43
2094 2593 3.305398 ACCACGAAAGCAACAAAACAA 57.695 38.095 0.00 0.00 0.00 2.83
2119 2620 7.954666 ATATTGAGAGCTAGGATTAGAGTCC 57.045 40.000 0.00 0.00 38.62 3.85
2208 2709 1.301293 GCCCTCTTGAACCCAGAGG 59.699 63.158 8.77 8.77 46.46 3.69
2223 2724 3.380637 CCCAGAGGATGAGCTTCATTTTG 59.619 47.826 0.00 0.00 37.20 2.44
2276 2789 3.916989 ACTGAAAGGTTCCCCTAGTTGAT 59.083 43.478 0.00 0.00 41.56 2.57
2287 2800 4.544152 TCCCCTAGTTGATTCCTTCCAAAT 59.456 41.667 0.00 0.00 0.00 2.32
2308 2821 7.308710 CCAAATTTCCCAAATCACCAAAATGAG 60.309 37.037 0.00 0.00 30.46 2.90
2320 2833 3.007182 ACCAAAATGAGCATCTGGGTTTG 59.993 43.478 13.18 6.91 34.92 2.93
2332 2845 0.329931 TGGGTTTGTCCGTGGCATAT 59.670 50.000 0.00 0.00 37.00 1.78
2405 2932 3.624861 CAGTTCCCAGTCAAGACATATGC 59.375 47.826 1.58 0.00 0.00 3.14
2421 3023 6.758886 AGACATATGCTTTCTAGTACTTGTGC 59.241 38.462 0.00 6.72 0.00 4.57
2446 3048 6.093771 CAGTGAGTAGTTACTAGGTCGAATGT 59.906 42.308 0.00 0.00 36.50 2.71
2475 3077 3.980646 TCACCATTTCCTGTTTGAACG 57.019 42.857 0.00 0.00 0.00 3.95
2479 3081 2.351738 CCATTTCCTGTTTGAACGCCTC 60.352 50.000 0.00 0.00 0.00 4.70
2493 3095 9.509855 GTTTGAACGCCTCTATCTATATCTATG 57.490 37.037 0.00 0.00 0.00 2.23
2557 3163 4.400884 TGTTGTTCTGTGCCACTTATTTGT 59.599 37.500 0.00 0.00 0.00 2.83
2645 3261 8.671028 GTTCCACGTTTTATACCTTTGTCATAT 58.329 33.333 0.00 0.00 0.00 1.78
2670 3287 6.741992 TGTGTCATTCTTGTAATCATGGAC 57.258 37.500 0.00 0.00 0.00 4.02
2675 3292 9.112725 TGTCATTCTTGTAATCATGGACATTAG 57.887 33.333 0.00 0.00 0.00 1.73
2689 3306 5.804639 TGGACATTAGTAGCAACATGAACT 58.195 37.500 0.00 0.00 0.00 3.01
2692 3312 6.256757 GGACATTAGTAGCAACATGAACTCTC 59.743 42.308 0.00 0.00 0.00 3.20
2726 3346 7.118680 CCAAGCACTTGCAATTCATATTTTTCT 59.881 33.333 0.00 0.00 45.16 2.52
2773 3394 7.716799 AACACTATCACTCTCTCTGATTCTT 57.283 36.000 0.00 0.00 30.76 2.52
2869 3490 0.251033 ACATGCAGCAAGCTCTGGAA 60.251 50.000 0.00 0.00 45.94 3.53
2872 3493 1.174712 TGCAGCAAGCTCTGGAAACC 61.175 55.000 0.00 0.00 45.94 3.27
2875 3496 0.538287 AGCAAGCTCTGGAAACCACC 60.538 55.000 0.00 0.00 0.00 4.61
3315 3954 4.346730 TGAAATGGTCGTACTCCCTCTTA 58.653 43.478 0.00 0.00 0.00 2.10
3318 3957 2.569059 TGGTCGTACTCCCTCTTATCG 58.431 52.381 0.00 0.00 0.00 2.92
3502 4355 1.021202 TTCAACTGTGGTTTCTGCCG 58.979 50.000 0.00 0.00 32.73 5.69
3523 4376 2.495669 GGAAATTGCTTTTGGATCCCGA 59.504 45.455 9.90 0.00 0.00 5.14
3547 4400 2.042842 TCCATGGAGCCTGGATTTTTGA 59.957 45.455 11.44 0.00 37.87 2.69
3549 4402 3.261390 CCATGGAGCCTGGATTTTTGAAA 59.739 43.478 5.56 0.00 35.70 2.69
3606 4473 5.899631 AAAGTTACACTTGAACCTAGGGA 57.100 39.130 14.81 0.00 38.66 4.20
3622 4489 6.737608 ACCTAGGGATGTATTCTAGATCTCC 58.262 44.000 14.81 0.00 34.09 3.71
3623 4490 6.278239 ACCTAGGGATGTATTCTAGATCTCCA 59.722 42.308 14.81 0.00 34.09 3.86
3928 4796 3.249917 CTGGCTTCTTCTCTCGAGTTTC 58.750 50.000 13.13 0.00 0.00 2.78
3929 4797 2.255316 GGCTTCTTCTCTCGAGTTTCG 58.745 52.381 13.13 0.41 42.10 3.46
3953 4829 5.995897 GGAGAAGTAAACCTACATGTTGTGT 59.004 40.000 2.30 0.00 44.95 3.72
3957 4833 6.613755 AGTAAACCTACATGTTGTGTTGTC 57.386 37.500 2.30 6.09 42.29 3.18
3977 4853 4.240096 GTCGAGAGAATTTACCGTCCAAA 58.760 43.478 0.00 0.00 45.01 3.28
3995 4871 9.337091 CCGTCCAAATTATTTTACACTGTAAAG 57.663 33.333 12.94 2.39 0.00 1.85
3996 4872 9.887406 CGTCCAAATTATTTTACACTGTAAAGT 57.113 29.630 12.94 12.82 0.00 2.66
4051 5294 3.338250 ACATGGATGGGGCGTGGT 61.338 61.111 0.00 0.00 0.00 4.16
4052 5295 1.978455 GACATGGATGGGGCGTGGTA 61.978 60.000 0.00 0.00 0.00 3.25
4053 5296 1.525995 CATGGATGGGGCGTGGTAC 60.526 63.158 0.00 0.00 0.00 3.34
4124 5377 1.667151 CATGTGCCCACCTTGTTGG 59.333 57.895 0.00 0.00 42.93 3.77
4182 5437 6.623486 TGAATCCAGATTGCAAACACATAAG 58.377 36.000 1.71 0.00 0.00 1.73
4183 5438 6.433716 TGAATCCAGATTGCAAACACATAAGA 59.566 34.615 1.71 0.00 0.00 2.10
4184 5439 5.627499 TCCAGATTGCAAACACATAAGAC 57.373 39.130 1.71 0.00 0.00 3.01
4186 5441 6.472016 TCCAGATTGCAAACACATAAGACTA 58.528 36.000 1.71 0.00 0.00 2.59
4187 5442 6.595326 TCCAGATTGCAAACACATAAGACTAG 59.405 38.462 1.71 0.00 0.00 2.57
4188 5443 6.253746 CAGATTGCAAACACATAAGACTAGC 58.746 40.000 1.71 0.00 0.00 3.42
4189 5444 5.355350 AGATTGCAAACACATAAGACTAGCC 59.645 40.000 1.71 0.00 0.00 3.93
4190 5445 3.000041 TGCAAACACATAAGACTAGCCG 59.000 45.455 0.00 0.00 0.00 5.52
4191 5446 2.223044 GCAAACACATAAGACTAGCCGC 60.223 50.000 0.00 0.00 0.00 6.53
4192 5447 3.000041 CAAACACATAAGACTAGCCGCA 59.000 45.455 0.00 0.00 0.00 5.69
4193 5448 2.586258 ACACATAAGACTAGCCGCAG 57.414 50.000 0.00 0.00 0.00 5.18
4194 5449 1.825474 ACACATAAGACTAGCCGCAGT 59.175 47.619 0.00 0.00 0.00 4.40
4195 5450 2.196749 CACATAAGACTAGCCGCAGTG 58.803 52.381 0.00 0.00 0.00 3.66
4196 5451 1.137086 ACATAAGACTAGCCGCAGTGG 59.863 52.381 0.00 0.00 42.50 4.00
4197 5452 0.753262 ATAAGACTAGCCGCAGTGGG 59.247 55.000 1.11 0.00 38.63 4.61
4198 5453 0.323999 TAAGACTAGCCGCAGTGGGA 60.324 55.000 9.09 0.00 38.63 4.37
4199 5454 1.608717 AAGACTAGCCGCAGTGGGAG 61.609 60.000 9.09 0.67 38.63 4.30
4200 5455 2.283966 ACTAGCCGCAGTGGGAGT 60.284 61.111 9.09 1.34 38.63 3.85
4201 5456 1.000019 ACTAGCCGCAGTGGGAGTA 60.000 57.895 9.09 0.00 38.63 2.59
4202 5457 0.613853 ACTAGCCGCAGTGGGAGTAA 60.614 55.000 9.09 0.00 38.63 2.24
4203 5458 0.179108 CTAGCCGCAGTGGGAGTAAC 60.179 60.000 9.09 0.00 38.63 2.50
4204 5459 0.613853 TAGCCGCAGTGGGAGTAACT 60.614 55.000 9.09 0.96 38.63 2.24
4205 5460 1.003718 GCCGCAGTGGGAGTAACTT 60.004 57.895 9.09 0.00 38.63 2.66
4206 5461 1.019805 GCCGCAGTGGGAGTAACTTC 61.020 60.000 9.09 0.00 38.63 3.01
4207 5462 0.320374 CCGCAGTGGGAGTAACTTCA 59.680 55.000 9.09 0.00 0.00 3.02
4208 5463 1.673033 CCGCAGTGGGAGTAACTTCAG 60.673 57.143 9.09 0.00 0.00 3.02
4209 5464 1.443802 GCAGTGGGAGTAACTTCAGC 58.556 55.000 0.00 0.00 0.00 4.26
4210 5465 1.270839 GCAGTGGGAGTAACTTCAGCA 60.271 52.381 0.00 0.00 0.00 4.41
4211 5466 2.693069 CAGTGGGAGTAACTTCAGCAG 58.307 52.381 0.00 0.00 0.00 4.24
4212 5467 2.037772 CAGTGGGAGTAACTTCAGCAGT 59.962 50.000 0.00 0.00 37.30 4.40
4213 5468 3.258372 CAGTGGGAGTAACTTCAGCAGTA 59.742 47.826 0.00 0.00 32.94 2.74
4214 5469 3.901844 AGTGGGAGTAACTTCAGCAGTAA 59.098 43.478 0.00 0.00 32.94 2.24
4215 5470 4.347000 AGTGGGAGTAACTTCAGCAGTAAA 59.653 41.667 0.00 0.00 32.94 2.01
4216 5471 5.013183 AGTGGGAGTAACTTCAGCAGTAAAT 59.987 40.000 0.00 0.00 32.94 1.40
4217 5472 5.705905 GTGGGAGTAACTTCAGCAGTAAATT 59.294 40.000 0.00 0.00 32.94 1.82
4218 5473 6.206829 GTGGGAGTAACTTCAGCAGTAAATTT 59.793 38.462 0.00 0.00 32.94 1.82
4219 5474 6.206634 TGGGAGTAACTTCAGCAGTAAATTTG 59.793 38.462 0.00 0.00 32.94 2.32
4220 5475 6.430000 GGGAGTAACTTCAGCAGTAAATTTGA 59.570 38.462 0.00 0.00 32.94 2.69
4221 5476 7.361286 GGGAGTAACTTCAGCAGTAAATTTGAG 60.361 40.741 0.00 0.00 32.94 3.02
4222 5477 7.173390 GGAGTAACTTCAGCAGTAAATTTGAGT 59.827 37.037 0.00 0.00 32.94 3.41
4223 5478 8.089115 AGTAACTTCAGCAGTAAATTTGAGTC 57.911 34.615 0.00 0.00 32.94 3.36
4224 5479 5.948992 ACTTCAGCAGTAAATTTGAGTCC 57.051 39.130 0.00 0.00 31.97 3.85
4225 5480 5.376625 ACTTCAGCAGTAAATTTGAGTCCA 58.623 37.500 0.00 0.00 31.97 4.02
4226 5481 5.827797 ACTTCAGCAGTAAATTTGAGTCCAA 59.172 36.000 0.00 0.00 31.97 3.53
4227 5482 5.689383 TCAGCAGTAAATTTGAGTCCAAC 57.311 39.130 0.00 0.00 30.88 3.77
4228 5483 5.376625 TCAGCAGTAAATTTGAGTCCAACT 58.623 37.500 0.00 0.00 30.88 3.16
4229 5484 5.470098 TCAGCAGTAAATTTGAGTCCAACTC 59.530 40.000 0.00 0.08 45.26 3.01
4240 5495 3.311966 GAGTCCAACTCAGCAAATTTGC 58.688 45.455 31.36 31.36 44.45 3.68
4253 5508 4.914312 CAAATTTGCTTATGTGGCAGTG 57.086 40.909 5.01 0.00 40.90 3.66
4254 5509 4.558178 CAAATTTGCTTATGTGGCAGTGA 58.442 39.130 5.01 0.00 40.90 3.41
4255 5510 4.445452 AATTTGCTTATGTGGCAGTGAG 57.555 40.909 0.00 0.00 40.90 3.51
4256 5511 2.566833 TTGCTTATGTGGCAGTGAGT 57.433 45.000 0.00 0.00 40.90 3.41
4257 5512 2.566833 TGCTTATGTGGCAGTGAGTT 57.433 45.000 0.00 0.00 34.56 3.01
4258 5513 3.694043 TGCTTATGTGGCAGTGAGTTA 57.306 42.857 0.00 0.00 34.56 2.24
4259 5514 4.014569 TGCTTATGTGGCAGTGAGTTAA 57.985 40.909 0.00 0.00 34.56 2.01
4260 5515 4.588899 TGCTTATGTGGCAGTGAGTTAAT 58.411 39.130 0.00 0.00 34.56 1.40
4261 5516 4.395854 TGCTTATGTGGCAGTGAGTTAATG 59.604 41.667 0.00 0.00 34.56 1.90
4262 5517 4.635765 GCTTATGTGGCAGTGAGTTAATGA 59.364 41.667 0.00 0.00 0.00 2.57
4263 5518 5.220739 GCTTATGTGGCAGTGAGTTAATGAG 60.221 44.000 0.00 0.00 0.00 2.90
4264 5519 3.057969 TGTGGCAGTGAGTTAATGAGG 57.942 47.619 0.00 0.00 0.00 3.86
4265 5520 2.637382 TGTGGCAGTGAGTTAATGAGGA 59.363 45.455 0.00 0.00 0.00 3.71
4266 5521 3.265791 GTGGCAGTGAGTTAATGAGGAG 58.734 50.000 0.00 0.00 0.00 3.69
4267 5522 3.055819 GTGGCAGTGAGTTAATGAGGAGA 60.056 47.826 0.00 0.00 0.00 3.71
4268 5523 3.196469 TGGCAGTGAGTTAATGAGGAGAG 59.804 47.826 0.00 0.00 0.00 3.20
4269 5524 3.449018 GGCAGTGAGTTAATGAGGAGAGA 59.551 47.826 0.00 0.00 0.00 3.10
4270 5525 4.441356 GGCAGTGAGTTAATGAGGAGAGAG 60.441 50.000 0.00 0.00 0.00 3.20
4271 5526 4.400884 GCAGTGAGTTAATGAGGAGAGAGA 59.599 45.833 0.00 0.00 0.00 3.10
4272 5527 5.068987 GCAGTGAGTTAATGAGGAGAGAGAT 59.931 44.000 0.00 0.00 0.00 2.75
4273 5528 6.264292 GCAGTGAGTTAATGAGGAGAGAGATA 59.736 42.308 0.00 0.00 0.00 1.98
4274 5529 7.522073 GCAGTGAGTTAATGAGGAGAGAGATAG 60.522 44.444 0.00 0.00 0.00 2.08
4275 5530 7.502226 CAGTGAGTTAATGAGGAGAGAGATAGT 59.498 40.741 0.00 0.00 0.00 2.12
4276 5531 8.058847 AGTGAGTTAATGAGGAGAGAGATAGTT 58.941 37.037 0.00 0.00 0.00 2.24
4277 5532 9.344772 GTGAGTTAATGAGGAGAGAGATAGTTA 57.655 37.037 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.480954 TCTCTGATTGGTAAGGCCGTC 59.519 52.381 0.00 0.00 41.21 4.79
17 18 8.589338 TCTTAGATATTCTCTGATTGGTAAGGC 58.411 37.037 0.00 0.00 35.28 4.35
77 78 9.965824 CACATCAAGTAATTAGACAACCTTTTT 57.034 29.630 0.00 0.00 0.00 1.94
80 81 6.659242 CCCACATCAAGTAATTAGACAACCTT 59.341 38.462 0.00 0.00 0.00 3.50
102 103 4.020928 TCAGCTACGTGAAAGATAAACCCA 60.021 41.667 0.00 0.00 0.00 4.51
103 104 4.501071 TCAGCTACGTGAAAGATAAACCC 58.499 43.478 0.00 0.00 0.00 4.11
117 118 0.798776 CCCACTTGCTTTCAGCTACG 59.201 55.000 0.00 0.00 42.97 3.51
140 141 9.262358 CTCTAGGTTGAATACAATAAACTAGGC 57.738 37.037 0.00 0.00 38.32 3.93
143 144 9.817809 CTGCTCTAGGTTGAATACAATAAACTA 57.182 33.333 0.00 0.00 38.32 2.24
181 182 3.255379 GGCCTAGTTTCGCGCTCG 61.255 66.667 5.56 0.00 0.00 5.03
189 190 1.602605 GTTGTGGCCGGCCTAGTTT 60.603 57.895 43.34 0.00 36.94 2.66
424 443 9.342308 ACATACAAATGTTCCTGATGTATAAGG 57.658 33.333 0.00 0.00 44.07 2.69
476 495 7.668492 AGTTCACGGAGGGAGTATTATATTTC 58.332 38.462 0.00 0.00 0.00 2.17
480 499 7.727186 ACATTAGTTCACGGAGGGAGTATTATA 59.273 37.037 0.00 0.00 0.00 0.98
482 501 5.895534 ACATTAGTTCACGGAGGGAGTATTA 59.104 40.000 0.00 0.00 0.00 0.98
483 502 4.715297 ACATTAGTTCACGGAGGGAGTATT 59.285 41.667 0.00 0.00 0.00 1.89
485 504 3.705051 ACATTAGTTCACGGAGGGAGTA 58.295 45.455 0.00 0.00 0.00 2.59
486 505 2.537143 ACATTAGTTCACGGAGGGAGT 58.463 47.619 0.00 0.00 0.00 3.85
487 506 4.401519 TCTTACATTAGTTCACGGAGGGAG 59.598 45.833 0.00 0.00 0.00 4.30
488 507 4.346730 TCTTACATTAGTTCACGGAGGGA 58.653 43.478 0.00 0.00 0.00 4.20
489 508 4.683832 CTCTTACATTAGTTCACGGAGGG 58.316 47.826 0.00 0.00 0.00 4.30
490 509 4.113354 GCTCTTACATTAGTTCACGGAGG 58.887 47.826 0.00 0.00 0.00 4.30
491 510 4.744570 TGCTCTTACATTAGTTCACGGAG 58.255 43.478 0.00 0.00 0.00 4.63
492 511 4.794278 TGCTCTTACATTAGTTCACGGA 57.206 40.909 0.00 0.00 0.00 4.69
493 512 6.422776 AAATGCTCTTACATTAGTTCACGG 57.577 37.500 0.00 0.00 39.32 4.94
494 513 8.407457 TCTAAATGCTCTTACATTAGTTCACG 57.593 34.615 0.00 0.00 39.32 4.35
508 527 9.959721 TCACCTTTTTAGTATTCTAAATGCTCT 57.040 29.630 5.49 0.00 43.05 4.09
517 536 8.880750 GCGTTTAGATCACCTTTTTAGTATTCT 58.119 33.333 0.00 0.00 0.00 2.40
518 537 8.880750 AGCGTTTAGATCACCTTTTTAGTATTC 58.119 33.333 0.00 0.00 0.00 1.75
519 538 8.788325 AGCGTTTAGATCACCTTTTTAGTATT 57.212 30.769 0.00 0.00 0.00 1.89
520 539 8.258708 AGAGCGTTTAGATCACCTTTTTAGTAT 58.741 33.333 0.00 0.00 37.82 2.12
521 540 7.609056 AGAGCGTTTAGATCACCTTTTTAGTA 58.391 34.615 0.00 0.00 37.82 1.82
522 541 6.465084 AGAGCGTTTAGATCACCTTTTTAGT 58.535 36.000 0.00 0.00 37.82 2.24
523 542 6.969828 AGAGCGTTTAGATCACCTTTTTAG 57.030 37.500 0.00 0.00 37.82 1.85
525 544 7.923414 ATAAGAGCGTTTAGATCACCTTTTT 57.077 32.000 0.00 0.00 37.82 1.94
526 545 9.614792 AATATAAGAGCGTTTAGATCACCTTTT 57.385 29.630 0.00 0.00 37.82 2.27
528 547 9.915629 CTAATATAAGAGCGTTTAGATCACCTT 57.084 33.333 0.00 0.00 37.82 3.50
529 548 9.080097 ACTAATATAAGAGCGTTTAGATCACCT 57.920 33.333 0.00 0.00 37.82 4.00
530 549 9.694137 AACTAATATAAGAGCGTTTAGATCACC 57.306 33.333 0.00 0.00 37.82 4.02
535 554 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
536 555 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
537 556 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
538 557 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
539 558 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
540 559 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
541 560 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
542 561 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
543 562 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
550 569 8.953223 AAGATATACTCCCTCCGTAAACTAAT 57.047 34.615 0.00 0.00 0.00 1.73
551 570 8.773033 AAAGATATACTCCCTCCGTAAACTAA 57.227 34.615 0.00 0.00 0.00 2.24
552 571 8.636213 CAAAAGATATACTCCCTCCGTAAACTA 58.364 37.037 0.00 0.00 0.00 2.24
553 572 7.343833 TCAAAAGATATACTCCCTCCGTAAACT 59.656 37.037 0.00 0.00 0.00 2.66
554 573 7.495055 TCAAAAGATATACTCCCTCCGTAAAC 58.505 38.462 0.00 0.00 0.00 2.01
555 574 7.664552 TCAAAAGATATACTCCCTCCGTAAA 57.335 36.000 0.00 0.00 0.00 2.01
556 575 7.289317 ACATCAAAAGATATACTCCCTCCGTAA 59.711 37.037 0.00 0.00 0.00 3.18
557 576 6.781014 ACATCAAAAGATATACTCCCTCCGTA 59.219 38.462 0.00 0.00 0.00 4.02
558 577 5.602978 ACATCAAAAGATATACTCCCTCCGT 59.397 40.000 0.00 0.00 0.00 4.69
559 578 6.015010 AGACATCAAAAGATATACTCCCTCCG 60.015 42.308 0.00 0.00 0.00 4.63
560 579 7.309770 AGACATCAAAAGATATACTCCCTCC 57.690 40.000 0.00 0.00 0.00 4.30
720 739 0.314935 CAGTGGTTTTCTGCGGCATT 59.685 50.000 1.75 0.00 0.00 3.56
721 740 1.959085 CAGTGGTTTTCTGCGGCAT 59.041 52.632 1.75 0.00 0.00 4.40
722 741 2.844451 GCAGTGGTTTTCTGCGGCA 61.844 57.895 1.29 1.29 46.39 5.69
723 742 2.050077 GCAGTGGTTTTCTGCGGC 60.050 61.111 2.28 0.00 46.39 6.53
875 1155 3.509967 TGTGGTCTATGTCGACATTCTGT 59.490 43.478 34.06 14.87 37.76 3.41
978 1282 2.933878 TTTGGGAAGACAGTGCGCGT 62.934 55.000 8.43 0.00 0.00 6.01
1168 1475 1.081376 CGCCTCGAAGACGTTGACT 60.081 57.895 0.00 0.00 40.69 3.41
1282 1589 0.905357 ATCAGAGAAGTGGGGAACGG 59.095 55.000 0.00 0.00 0.00 4.44
1284 1591 4.145052 ACAAAATCAGAGAAGTGGGGAAC 58.855 43.478 0.00 0.00 0.00 3.62
1291 1599 4.985409 GTCAGACGACAAAATCAGAGAAGT 59.015 41.667 0.00 0.00 42.13 3.01
1490 1823 0.393537 AATTGGGAGAAGAGCGCCAG 60.394 55.000 2.29 0.00 38.36 4.85
1506 1839 3.182887 TGGGGCTACAATGAACCAATT 57.817 42.857 0.00 0.00 0.00 2.32
1515 1863 1.689258 GGGATGCTTTGGGGCTACAAT 60.689 52.381 0.00 0.00 0.00 2.71
1529 1877 1.598701 GGCAGTGGAAACAGGGATGC 61.599 60.000 0.00 0.00 44.46 3.91
1530 1878 0.967380 GGGCAGTGGAAACAGGGATG 60.967 60.000 0.00 0.00 44.46 3.51
1551 1899 2.268730 GCACTAGCTTCAATGGCAAC 57.731 50.000 0.00 0.00 37.91 4.17
1713 2080 6.044046 TGCTTGTTGAAACGTCTAAGACTTA 58.956 36.000 0.00 0.00 0.00 2.24
1714 2081 4.873827 TGCTTGTTGAAACGTCTAAGACTT 59.126 37.500 0.00 0.00 0.00 3.01
1718 2085 4.795970 ACTGCTTGTTGAAACGTCTAAG 57.204 40.909 0.00 0.00 0.00 2.18
1720 2087 4.393680 ACAAACTGCTTGTTGAAACGTCTA 59.606 37.500 0.00 0.00 46.49 2.59
1721 2088 3.190535 ACAAACTGCTTGTTGAAACGTCT 59.809 39.130 0.00 0.00 46.49 4.18
1722 2089 3.498082 ACAAACTGCTTGTTGAAACGTC 58.502 40.909 0.00 0.00 46.49 4.34
1723 2090 3.569250 ACAAACTGCTTGTTGAAACGT 57.431 38.095 0.00 0.00 46.49 3.99
1724 2091 4.904116 TCTACAAACTGCTTGTTGAAACG 58.096 39.130 1.35 0.00 46.49 3.60
1729 2096 5.459762 CCACAATTCTACAAACTGCTTGTTG 59.540 40.000 1.35 0.60 46.49 3.33
1730 2097 5.359576 TCCACAATTCTACAAACTGCTTGTT 59.640 36.000 1.35 0.00 46.49 2.83
1732 2099 5.437289 TCCACAATTCTACAAACTGCTTG 57.563 39.130 0.00 0.00 41.19 4.01
1773 2140 1.078848 CAGAAGGACGGCCTGAAGG 60.079 63.158 12.91 0.00 46.28 3.46
1774 2141 1.743252 GCAGAAGGACGGCCTGAAG 60.743 63.158 12.91 4.28 46.28 3.02
1775 2142 2.347490 GCAGAAGGACGGCCTGAA 59.653 61.111 12.91 0.00 46.28 3.02
1776 2143 2.922503 TGCAGAAGGACGGCCTGA 60.923 61.111 12.91 0.00 46.28 3.86
1777 2144 2.435586 CTGCAGAAGGACGGCCTG 60.436 66.667 12.91 0.00 46.28 4.85
1779 2146 2.035442 GTTCTGCAGAAGGACGGCC 61.035 63.158 29.13 12.00 38.85 6.13
1780 2147 2.035442 GGTTCTGCAGAAGGACGGC 61.035 63.158 29.13 15.76 34.84 5.68
1781 2148 0.036010 ATGGTTCTGCAGAAGGACGG 60.036 55.000 29.13 0.00 34.84 4.79
1782 2149 1.813513 AATGGTTCTGCAGAAGGACG 58.186 50.000 29.13 0.00 34.84 4.79
1783 2150 3.065925 GCATAATGGTTCTGCAGAAGGAC 59.934 47.826 29.13 21.08 35.96 3.85
1803 2244 3.569277 TGCTGTTGCTATGAAGAAAAGCA 59.431 39.130 0.00 0.00 44.15 3.91
1813 2254 6.652062 TCCAATGATAGTATGCTGTTGCTATG 59.348 38.462 0.00 0.00 40.48 2.23
1841 2291 1.073923 ACCAGGGCGAAAGAACAGAAT 59.926 47.619 0.00 0.00 0.00 2.40
1859 2320 1.510480 GACAGTGCTGCCTGACAACC 61.510 60.000 20.14 5.09 36.30 3.77
1863 2324 1.735920 CTCGACAGTGCTGCCTGAC 60.736 63.158 20.14 14.53 36.30 3.51
1880 2341 5.893501 ACGTAGTACCCTGCATTAAGCACT 61.894 45.833 0.00 0.00 46.08 4.40
1896 2357 7.932491 AGAGCAGTAAATCATCTCTACGTAGTA 59.068 37.037 21.53 11.96 45.11 1.82
1947 2446 4.348168 AGTCTCCTGACATAACCAAGTGTT 59.652 41.667 0.00 0.00 45.20 3.32
2010 2509 7.451566 ACCCTTTGGCATTAATATAGTCAATCC 59.548 37.037 0.00 0.00 33.59 3.01
2025 2524 0.471591 TTTCCAGCACCCTTTGGCAT 60.472 50.000 0.00 0.00 34.38 4.40
2092 2591 9.638239 GACTCTAATCCTAGCTCTCAATATTTG 57.362 37.037 0.00 0.00 0.00 2.32
2094 2593 7.122055 CGGACTCTAATCCTAGCTCTCAATATT 59.878 40.741 0.00 0.00 36.52 1.28
2119 2620 3.247173 GTGCTGCATAATTCTTCCTCTCG 59.753 47.826 5.27 0.00 0.00 4.04
2136 2637 1.328680 GATGACGTGCCATAAGTGCTG 59.671 52.381 0.00 0.00 0.00 4.41
2196 2697 1.661463 AGCTCATCCTCTGGGTTCAA 58.339 50.000 0.00 0.00 0.00 2.69
2208 2709 5.642919 ACTCTCACTCAAAATGAAGCTCATC 59.357 40.000 0.00 0.00 35.76 2.92
2223 2724 6.928492 AGAAATCTTTTGACTGACTCTCACTC 59.072 38.462 0.00 0.00 0.00 3.51
2276 2789 5.221823 GGTGATTTGGGAAATTTGGAAGGAA 60.222 40.000 0.00 0.00 0.00 3.36
2287 2800 4.102210 TGCTCATTTTGGTGATTTGGGAAA 59.898 37.500 0.00 0.00 0.00 3.13
2308 2821 1.586154 CCACGGACAAACCCAGATGC 61.586 60.000 0.00 0.00 34.64 3.91
2320 2833 5.470098 AGATATGACAAAATATGCCACGGAC 59.530 40.000 0.00 0.00 0.00 4.79
2379 2903 2.158623 TGTCTTGACTGGGAACTGCAAT 60.159 45.455 2.35 0.00 0.00 3.56
2405 2932 5.533482 ACTCACTGCACAAGTACTAGAAAG 58.467 41.667 0.00 0.00 36.83 2.62
2421 3023 6.093771 ACATTCGACCTAGTAACTACTCACTG 59.906 42.308 0.00 0.00 37.73 3.66
2475 3077 8.463930 AGAAGCACATAGATATAGATAGAGGC 57.536 38.462 0.00 0.00 0.00 4.70
2493 3095 7.518731 TTCAAACATTTTTGTGTAGAAGCAC 57.481 32.000 4.35 0.00 42.51 4.40
2557 3163 7.039082 CCCAAAAAGGTTCAAGAAATAGATGGA 60.039 37.037 0.00 0.00 34.66 3.41
2645 3261 7.230309 TGTCCATGATTACAAGAATGACACAAA 59.770 33.333 0.00 0.00 0.00 2.83
2670 3287 6.020281 GTCGAGAGTTCATGTTGCTACTAATG 60.020 42.308 0.00 0.00 0.00 1.90
2675 3292 2.594654 CGTCGAGAGTTCATGTTGCTAC 59.405 50.000 0.00 0.00 0.00 3.58
2689 3306 0.956633 AGTGCTTGGTAACGTCGAGA 59.043 50.000 0.00 0.00 42.51 4.04
2692 3312 0.110823 GCAAGTGCTTGGTAACGTCG 60.111 55.000 13.07 0.00 40.74 5.12
2726 3346 8.318412 TGTTAGGTCAGCAAGTAATTAAGATCA 58.682 33.333 0.00 0.00 0.00 2.92
2773 3394 1.951209 TCAAGGCAGGATGTCCTACA 58.049 50.000 0.32 0.00 46.31 2.74
2869 3490 1.890489 GGGTTTATGCTTTCGGTGGTT 59.110 47.619 0.00 0.00 0.00 3.67
2872 3493 2.432444 TCTGGGTTTATGCTTTCGGTG 58.568 47.619 0.00 0.00 0.00 4.94
2875 3496 5.811399 TTGTATCTGGGTTTATGCTTTCG 57.189 39.130 0.00 0.00 0.00 3.46
2968 3604 3.205784 AGCCTCTTGGTTGATATGCTC 57.794 47.619 0.00 0.00 35.27 4.26
3315 3954 1.608590 CTCAAACACAAACCCAGCGAT 59.391 47.619 0.00 0.00 0.00 4.58
3318 3957 0.389025 CCCTCAAACACAAACCCAGC 59.611 55.000 0.00 0.00 0.00 4.85
3502 4355 2.495669 TCGGGATCCAAAAGCAATTTCC 59.504 45.455 15.23 0.00 0.00 3.13
3557 4410 8.592105 TCAGAATTTTGAAACTTTAAGGCATG 57.408 30.769 0.00 0.00 0.00 4.06
3558 4411 9.612066 TTTCAGAATTTTGAAACTTTAAGGCAT 57.388 25.926 17.59 0.00 40.95 4.40
3559 4412 9.442047 TTTTCAGAATTTTGAAACTTTAAGGCA 57.558 25.926 20.37 3.78 44.33 4.75
3587 4453 5.161943 ACATCCCTAGGTTCAAGTGTAAC 57.838 43.478 8.29 0.00 0.00 2.50
3590 4456 5.726793 AGAATACATCCCTAGGTTCAAGTGT 59.273 40.000 8.29 5.73 0.00 3.55
3594 4461 8.235230 AGATCTAGAATACATCCCTAGGTTCAA 58.765 37.037 8.29 0.00 32.79 2.69
3637 4505 4.622740 GCAGCTTGAACCACAATGTATTTC 59.377 41.667 0.00 0.00 37.88 2.17
3641 4509 2.293122 GTGCAGCTTGAACCACAATGTA 59.707 45.455 0.00 0.00 37.88 2.29
3642 4510 1.067516 GTGCAGCTTGAACCACAATGT 59.932 47.619 0.00 0.00 37.88 2.71
3643 4511 1.067364 TGTGCAGCTTGAACCACAATG 59.933 47.619 0.00 0.00 37.88 2.82
3644 4512 1.401761 TGTGCAGCTTGAACCACAAT 58.598 45.000 0.00 0.00 37.88 2.71
3787 4655 3.880047 AGAAATGCACATGGACATTGG 57.120 42.857 14.08 0.00 36.64 3.16
3793 4661 5.244402 ACAAATCTGAAGAAATGCACATGGA 59.756 36.000 0.00 0.00 0.00 3.41
3855 4723 1.467920 CTCCATGGAGCCCTGTTTTC 58.532 55.000 28.45 0.00 35.31 2.29
3928 4796 5.120208 CACAACATGTAGGTTTACTTCTCCG 59.880 44.000 0.00 0.00 0.00 4.63
3929 4797 5.995897 ACACAACATGTAGGTTTACTTCTCC 59.004 40.000 0.00 0.00 40.88 3.71
3953 4829 3.256383 TGGACGGTAAATTCTCTCGACAA 59.744 43.478 0.00 0.00 0.00 3.18
3957 4833 5.796350 AATTTGGACGGTAAATTCTCTCG 57.204 39.130 0.00 0.00 33.70 4.04
3995 4871 6.127730 CCAAATCCCTTGTCCAAATACAGTAC 60.128 42.308 0.00 0.00 32.65 2.73
3996 4872 5.949354 CCAAATCCCTTGTCCAAATACAGTA 59.051 40.000 0.00 0.00 32.65 2.74
3997 4873 4.772100 CCAAATCCCTTGTCCAAATACAGT 59.228 41.667 0.00 0.00 32.65 3.55
3998 4874 4.160252 CCCAAATCCCTTGTCCAAATACAG 59.840 45.833 0.00 0.00 32.65 2.74
3999 4875 4.093011 CCCAAATCCCTTGTCCAAATACA 58.907 43.478 0.00 0.00 32.65 2.29
4000 4876 3.450817 CCCCAAATCCCTTGTCCAAATAC 59.549 47.826 0.00 0.00 32.65 1.89
4051 5294 6.200114 AGTACCCTTCCTTGTGCTTATAGTA 58.800 40.000 0.00 0.00 0.00 1.82
4052 5295 5.030820 AGTACCCTTCCTTGTGCTTATAGT 58.969 41.667 0.00 0.00 0.00 2.12
4053 5296 5.615925 AGTACCCTTCCTTGTGCTTATAG 57.384 43.478 0.00 0.00 0.00 1.31
4124 5377 3.736759 GCCTCGTGCTATTTTACTCTAGC 59.263 47.826 0.00 0.00 40.60 3.42
4182 5437 1.035932 TACTCCCACTGCGGCTAGTC 61.036 60.000 0.00 0.00 33.04 2.59
4183 5438 0.613853 TTACTCCCACTGCGGCTAGT 60.614 55.000 0.00 0.12 34.69 2.57
4184 5439 0.179108 GTTACTCCCACTGCGGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
4186 5441 1.481056 AAGTTACTCCCACTGCGGCT 61.481 55.000 0.00 0.00 0.00 5.52
4187 5442 1.003718 AAGTTACTCCCACTGCGGC 60.004 57.895 0.00 0.00 0.00 6.53
4188 5443 0.320374 TGAAGTTACTCCCACTGCGG 59.680 55.000 0.00 0.00 0.00 5.69
4189 5444 1.714794 CTGAAGTTACTCCCACTGCG 58.285 55.000 0.00 0.00 0.00 5.18
4190 5445 1.270839 TGCTGAAGTTACTCCCACTGC 60.271 52.381 0.00 0.00 0.00 4.40
4191 5446 2.037772 ACTGCTGAAGTTACTCCCACTG 59.962 50.000 0.00 0.00 34.57 3.66
4192 5447 2.330216 ACTGCTGAAGTTACTCCCACT 58.670 47.619 0.00 0.00 34.57 4.00
4193 5448 2.841442 ACTGCTGAAGTTACTCCCAC 57.159 50.000 0.00 0.00 34.57 4.61
4194 5449 4.967084 TTTACTGCTGAAGTTACTCCCA 57.033 40.909 0.00 0.00 40.56 4.37
4195 5450 6.430000 TCAAATTTACTGCTGAAGTTACTCCC 59.570 38.462 0.00 0.00 40.56 4.30
4196 5451 7.173390 ACTCAAATTTACTGCTGAAGTTACTCC 59.827 37.037 0.00 0.00 40.56 3.85
4197 5452 8.089115 ACTCAAATTTACTGCTGAAGTTACTC 57.911 34.615 0.00 0.00 40.56 2.59
4198 5453 7.173390 GGACTCAAATTTACTGCTGAAGTTACT 59.827 37.037 0.00 0.00 40.56 2.24
4199 5454 7.041372 TGGACTCAAATTTACTGCTGAAGTTAC 60.041 37.037 0.00 0.00 40.56 2.50
4200 5455 6.995686 TGGACTCAAATTTACTGCTGAAGTTA 59.004 34.615 0.00 0.00 40.56 2.24
4201 5456 5.827797 TGGACTCAAATTTACTGCTGAAGTT 59.172 36.000 0.00 0.00 40.56 2.66
4202 5457 5.376625 TGGACTCAAATTTACTGCTGAAGT 58.623 37.500 0.00 0.00 43.40 3.01
4203 5458 5.947228 TGGACTCAAATTTACTGCTGAAG 57.053 39.130 0.00 0.00 0.00 3.02
4204 5459 5.827797 AGTTGGACTCAAATTTACTGCTGAA 59.172 36.000 0.00 0.00 34.28 3.02
4205 5460 5.376625 AGTTGGACTCAAATTTACTGCTGA 58.623 37.500 0.00 0.00 34.28 4.26
4206 5461 5.693814 GAGTTGGACTCAAATTTACTGCTG 58.306 41.667 3.33 0.00 44.45 4.41
4207 5462 5.948992 GAGTTGGACTCAAATTTACTGCT 57.051 39.130 3.33 0.00 44.45 4.24
4232 5487 4.558178 TCACTGCCACATAAGCAAATTTG 58.442 39.130 14.03 14.03 40.35 2.32
4233 5488 4.281688 ACTCACTGCCACATAAGCAAATTT 59.718 37.500 0.00 0.00 40.35 1.82
4234 5489 3.828451 ACTCACTGCCACATAAGCAAATT 59.172 39.130 0.00 0.00 40.35 1.82
4235 5490 3.424703 ACTCACTGCCACATAAGCAAAT 58.575 40.909 0.00 0.00 40.35 2.32
4236 5491 2.862541 ACTCACTGCCACATAAGCAAA 58.137 42.857 0.00 0.00 40.35 3.68
4237 5492 2.566833 ACTCACTGCCACATAAGCAA 57.433 45.000 0.00 0.00 40.35 3.91
4238 5493 2.566833 AACTCACTGCCACATAAGCA 57.433 45.000 0.00 0.00 38.82 3.91
4239 5494 4.635765 TCATTAACTCACTGCCACATAAGC 59.364 41.667 0.00 0.00 0.00 3.09
4240 5495 5.295292 CCTCATTAACTCACTGCCACATAAG 59.705 44.000 0.00 0.00 0.00 1.73
4241 5496 5.045942 TCCTCATTAACTCACTGCCACATAA 60.046 40.000 0.00 0.00 0.00 1.90
4242 5497 4.469586 TCCTCATTAACTCACTGCCACATA 59.530 41.667 0.00 0.00 0.00 2.29
4243 5498 3.264193 TCCTCATTAACTCACTGCCACAT 59.736 43.478 0.00 0.00 0.00 3.21
4244 5499 2.637382 TCCTCATTAACTCACTGCCACA 59.363 45.455 0.00 0.00 0.00 4.17
4245 5500 3.055819 TCTCCTCATTAACTCACTGCCAC 60.056 47.826 0.00 0.00 0.00 5.01
4246 5501 3.173151 TCTCCTCATTAACTCACTGCCA 58.827 45.455 0.00 0.00 0.00 4.92
4247 5502 3.449018 TCTCTCCTCATTAACTCACTGCC 59.551 47.826 0.00 0.00 0.00 4.85
4248 5503 4.400884 TCTCTCTCCTCATTAACTCACTGC 59.599 45.833 0.00 0.00 0.00 4.40
4249 5504 6.713762 ATCTCTCTCCTCATTAACTCACTG 57.286 41.667 0.00 0.00 0.00 3.66
4250 5505 7.582719 ACTATCTCTCTCCTCATTAACTCACT 58.417 38.462 0.00 0.00 0.00 3.41
4251 5506 7.817418 ACTATCTCTCTCCTCATTAACTCAC 57.183 40.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.