Multiple sequence alignment - TraesCS3B01G388900

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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 TraesCS3B01G388900 chr3B 100.000 2656 0 0 1 2656 612097448 612100103 0.000000e+00 4905.0
1 TraesCS3B01G388900 chr3B 100.000 1543 0 0 4312 5854 612101759 612103301 0.000000e+00 2850.0
2 TraesCS3B01G388900 chr3B 100.000 1131 0 0 2944 4074 612100391 612101521 0.000000e+00 2089.0
3 TraesCS3B01G388900 chr3D 87.902 2364 151 49 373 2656 461307304 461309612 0.000000e+00 2656.0
4 TraesCS3B01G388900 chr3D 89.875 1600 97 28 4312 5854 461311043 461312634 0.000000e+00 1997.0
5 TraesCS3B01G388900 chr3D 93.785 1062 40 9 2944 4003 461309644 461310681 0.000000e+00 1572.0
6 TraesCS3B01G388900 chr3D 90.130 385 35 2 1 385 461306906 461307287 1.130000e-136 497.0
7 TraesCS3B01G388900 chr3D 85.580 319 35 8 1648 1958 609468509 609468824 2.030000e-84 324.0
8 TraesCS3B01G388900 chr3A 89.244 1813 100 36 895 2656 603807879 603809647 0.000000e+00 2180.0
9 TraesCS3B01G388900 chr3A 90.138 1592 92 27 4312 5854 603811141 603812716 0.000000e+00 2010.0
10 TraesCS3B01G388900 chr3A 94.552 1138 29 10 2944 4074 603809992 603811103 0.000000e+00 1727.0
11 TraesCS3B01G388900 chr3A 94.161 137 8 0 2185 2321 579913585 579913449 5.940000e-50 209.0
12 TraesCS3B01G388900 chr3A 91.398 93 8 0 998 1090 698010704 698010796 1.710000e-25 128.0
13 TraesCS3B01G388900 chr7A 85.804 317 39 6 1648 1962 85260554 85260242 1.220000e-86 331.0
14 TraesCS3B01G388900 chr7A 90.323 93 9 0 998 1090 512022506 512022598 7.970000e-24 122.0
15 TraesCS3B01G388900 chr7A 85.217 115 7 1 1546 1650 98746413 98746299 6.200000e-20 110.0
16 TraesCS3B01G388900 chr1D 85.942 313 38 4 1650 1961 483359287 483358980 4.370000e-86 329.0
17 TraesCS3B01G388900 chr1D 83.486 327 42 10 1635 1958 10148367 10148050 1.600000e-75 294.0
18 TraesCS3B01G388900 chr1D 93.431 137 9 0 2185 2321 336732510 336732374 2.770000e-48 204.0
19 TraesCS3B01G388900 chr1D 81.349 252 36 11 4463 4709 383314983 383314738 1.660000e-45 195.0
20 TraesCS3B01G388900 chr1D 78.623 276 33 16 3629 3898 383315365 383315110 6.070000e-35 159.0
21 TraesCS3B01G388900 chr1D 90.164 61 2 4 5342 5402 20971877 20971933 6.290000e-10 76.8
22 TraesCS3B01G388900 chr6D 85.079 315 40 5 1648 1958 456280787 456280476 1.220000e-81 315.0
23 TraesCS3B01G388900 chr6D 83.962 106 14 1 1497 1602 3559553 3559655 1.340000e-16 99.0
24 TraesCS3B01G388900 chr6D 92.308 52 4 0 5361 5412 422072066 422072117 2.260000e-09 75.0
25 TraesCS3B01G388900 chr2A 84.839 310 43 3 1648 1956 771597476 771597782 5.700000e-80 309.0
26 TraesCS3B01G388900 chr2A 76.832 505 69 24 1498 1961 11645891 11646388 2.110000e-59 241.0
27 TraesCS3B01G388900 chr2A 75.050 501 75 24 1496 1957 1544295 1544784 2.790000e-43 187.0
28 TraesCS3B01G388900 chr1B 84.543 317 44 3 1648 1961 291968061 291967747 5.700000e-80 309.0
29 TraesCS3B01G388900 chr1B 81.323 257 35 12 4450 4703 513540263 513540017 4.630000e-46 196.0
30 TraesCS3B01G388900 chr1B 78.986 276 32 16 3629 3898 513540633 513540378 1.310000e-36 165.0
31 TraesCS3B01G388900 chr1B 83.750 160 12 7 1502 1650 603297038 603297194 7.910000e-29 139.0
32 TraesCS3B01G388900 chr1B 94.118 51 3 0 5361 5411 394410714 394410664 1.750000e-10 78.7
33 TraesCS3B01G388900 chr2B 90.099 202 20 0 2124 2325 316299177 316298976 4.500000e-66 263.0
34 TraesCS3B01G388900 chr2B 79.121 273 50 6 1687 1957 164093876 164093609 1.300000e-41 182.0
35 TraesCS3B01G388900 chr2B 80.357 168 18 7 1498 1650 683761317 683761484 4.790000e-21 113.0
36 TraesCS3B01G388900 chr2B 88.136 59 5 2 5362 5419 451828108 451828165 1.050000e-07 69.4
37 TraesCS3B01G388900 chr1A 81.887 265 37 11 4450 4709 483027390 483027132 4.600000e-51 213.0
38 TraesCS3B01G388900 chr1A 94.074 135 8 0 2187 2321 54873575 54873441 7.690000e-49 206.0
39 TraesCS3B01G388900 chr1A 79.496 278 30 16 3629 3898 483027763 483027505 7.800000e-39 172.0
40 TraesCS3B01G388900 chr1A 92.308 78 6 0 3245 3322 483028169 483028092 1.720000e-20 111.0
41 TraesCS3B01G388900 chr4D 94.161 137 8 0 2185 2321 196908967 196909103 5.940000e-50 209.0
42 TraesCS3B01G388900 chr4D 90.164 61 2 4 5342 5402 73385823 73385879 6.290000e-10 76.8
43 TraesCS3B01G388900 chr5D 94.074 135 8 0 2187 2321 364017583 364017449 7.690000e-49 206.0
44 TraesCS3B01G388900 chr5D 90.526 95 9 0 996 1090 524586647 524586741 6.160000e-25 126.0
45 TraesCS3B01G388900 chr5A 94.074 135 8 0 2187 2321 501874745 501874879 7.690000e-49 206.0
46 TraesCS3B01G388900 chr5A 91.089 101 8 1 996 1096 650834309 650834408 1.020000e-27 135.0
47 TraesCS3B01G388900 chr5A 85.965 114 6 4 1546 1649 520090865 520090752 4.790000e-21 113.0
48 TraesCS3B01G388900 chr7B 84.375 160 11 8 1502 1650 28932470 28932626 1.700000e-30 145.0
49 TraesCS3B01G388900 chr7B 84.466 103 12 2 1502 1603 740002250 740002349 1.340000e-16 99.0
50 TraesCS3B01G388900 chr5B 95.122 82 4 0 996 1077 659169297 659169378 4.760000e-26 130.0
51 TraesCS3B01G388900 chr6A 90.323 93 9 0 998 1090 57134578 57134486 7.970000e-24 122.0
52 TraesCS3B01G388900 chr6B 89.583 96 9 1 996 1091 693281157 693281251 2.870000e-23 121.0
53 TraesCS3B01G388900 chr4A 85.366 123 6 3 1539 1650 491693647 491693526 3.710000e-22 117.0
54 TraesCS3B01G388900 chrUn 80.606 165 16 9 1497 1650 42056524 42056365 4.790000e-21 113.0
55 TraesCS3B01G388900 chrUn 80.220 91 15 2 1496 1586 126882244 126882157 1.360000e-06 65.8
56 TraesCS3B01G388900 chr7D 85.088 114 7 1 1546 1649 594147626 594147513 2.230000e-19 108.0
57 TraesCS3B01G388900 chr2D 100.000 42 0 0 5361 5402 164389736 164389777 1.750000e-10 78.7
58 TraesCS3B01G388900 chr4B 90.385 52 5 0 5351 5402 255392151 255392202 1.050000e-07 69.4


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 TraesCS3B01G388900 chr3B 612097448 612103301 5853 False 3281.333333 4905 100.000000 1 5854 3 chr3B.!!$F1 5853
1 TraesCS3B01G388900 chr3D 461306906 461312634 5728 False 1680.500000 2656 90.423000 1 5854 4 chr3D.!!$F2 5853
2 TraesCS3B01G388900 chr3A 603807879 603812716 4837 False 1972.333333 2180 91.311333 895 5854 3 chr3A.!!$F2 4959

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
201 202 0.251341 GGGTGTTGGGCTCATGAACT 60.251 55.0 0.00 0.0 0.00 3.01 F
218 219 0.319728 ACTCAGTCTGCAAGCACGAT 59.680 50.0 0.00 0.0 0.00 3.73 F
1544 1614 0.179073 CCTGACCCGAGCTGGTTATG 60.179 60.0 0.00 0.0 39.24 1.90 F
1872 1981 0.393537 GGCTGTGTGCATCCTAGCTT 60.394 55.0 12.70 0.0 45.15 3.74 F
3414 3600 0.690762 TTGGGACTGTCTGCCCTTAC 59.309 55.0 7.85 0.0 44.96 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1595 0.179073 CATAACCAGCTCGGGTCAGG 60.179 60.000 0.0 0.0 41.32 3.86 R
1680 1789 0.750249 ATGACACCACACAGTCGACA 59.250 50.000 19.5 0.0 37.58 4.35 R
2999 3183 1.618343 CCCAGTTCTTTTGGCCGATTT 59.382 47.619 0.0 0.0 34.26 2.17 R
3547 3733 0.658536 GCACAGAGCGAAACAAGCAC 60.659 55.000 0.0 0.0 37.01 4.40 R
5208 5673 0.324368 AGGACGGCAGGTACTCATCA 60.324 55.000 0.0 0.0 33.10 3.07 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
35 36 4.494350 TTCTGTACGACACCACTTCTAC 57.506 45.455 0.00 0.00 0.00 2.59
36 37 2.816087 TCTGTACGACACCACTTCTACC 59.184 50.000 0.00 0.00 0.00 3.18
57 58 6.017400 ACCATTCAAACACAGCTATCAAAG 57.983 37.500 0.00 0.00 0.00 2.77
158 159 2.757868 TGGTTTCTCCACAAGGTTGTTG 59.242 45.455 0.00 0.00 41.93 3.33
172 173 5.422214 AGGTTGTTGGAGTCGATAAGAAT 57.578 39.130 0.00 0.00 0.00 2.40
192 193 2.360475 GCAGAGAGGGTGTTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
193 194 2.900106 GCAGAGAGGGTGTTGGGCT 61.900 63.158 0.00 0.00 0.00 5.19
195 196 1.152030 AGAGAGGGTGTTGGGCTCA 60.152 57.895 0.00 0.00 0.00 4.26
201 202 0.251341 GGGTGTTGGGCTCATGAACT 60.251 55.000 0.00 0.00 0.00 3.01
204 205 1.808945 GTGTTGGGCTCATGAACTCAG 59.191 52.381 0.00 0.00 0.00 3.35
208 209 1.277273 TGGGCTCATGAACTCAGTCTG 59.723 52.381 0.00 0.00 0.00 3.51
218 219 0.319728 ACTCAGTCTGCAAGCACGAT 59.680 50.000 0.00 0.00 0.00 3.73
225 226 0.877071 CTGCAAGCACGATCCAAAGT 59.123 50.000 0.00 0.00 0.00 2.66
231 232 0.734889 GCACGATCCAAAGTCCCATG 59.265 55.000 0.00 0.00 0.00 3.66
245 246 1.203162 TCCCATGGAGGCAACAACATT 60.203 47.619 15.22 0.00 41.41 2.71
256 257 5.876357 AGGCAACAACATTAACTAGGAGAA 58.124 37.500 0.00 0.00 41.41 2.87
291 292 4.936891 ACTTGCAATTGACTCAAAACTCC 58.063 39.130 10.34 0.00 0.00 3.85
294 295 3.569701 TGCAATTGACTCAAAACTCCCTC 59.430 43.478 10.34 0.00 0.00 4.30
301 302 4.097892 TGACTCAAAACTCCCTCAAAAAGC 59.902 41.667 0.00 0.00 0.00 3.51
306 307 0.606673 ACTCCCTCAAAAAGCGAGCC 60.607 55.000 0.00 0.00 33.85 4.70
309 310 0.606401 CCCTCAAAAAGCGAGCCTGA 60.606 55.000 0.00 0.00 0.00 3.86
313 314 0.386478 CAAAAAGCGAGCCTGACAGC 60.386 55.000 0.00 0.00 0.00 4.40
358 359 7.004555 TGTCCTGAATAGTGAAAAGCTCTAA 57.995 36.000 0.00 0.00 0.00 2.10
359 360 6.874134 TGTCCTGAATAGTGAAAAGCTCTAAC 59.126 38.462 0.00 0.00 0.00 2.34
360 361 7.100409 GTCCTGAATAGTGAAAAGCTCTAACT 58.900 38.462 0.00 0.00 0.00 2.24
361 362 7.064016 GTCCTGAATAGTGAAAAGCTCTAACTG 59.936 40.741 0.00 0.00 0.00 3.16
379 380 8.918202 TCTAACTGAAACAAACCTAACATCAT 57.082 30.769 0.00 0.00 0.00 2.45
385 386 6.038825 TGAAACAAACCTAACATCATCGTTGT 59.961 34.615 0.00 0.00 0.00 3.32
387 388 4.151689 ACAAACCTAACATCATCGTTGTCG 59.848 41.667 0.00 0.00 38.55 4.35
388 389 3.587797 ACCTAACATCATCGTTGTCGT 57.412 42.857 0.00 0.00 38.33 4.34
389 390 3.508762 ACCTAACATCATCGTTGTCGTC 58.491 45.455 0.00 0.00 38.33 4.20
390 391 3.057104 ACCTAACATCATCGTTGTCGTCA 60.057 43.478 0.00 0.00 38.33 4.35
391 392 3.303495 CCTAACATCATCGTTGTCGTCAC 59.697 47.826 0.00 0.00 38.33 3.67
396 426 0.598942 CATCGTTGTCGTCACCACCA 60.599 55.000 0.00 0.00 38.33 4.17
397 427 0.320374 ATCGTTGTCGTCACCACCAT 59.680 50.000 0.00 0.00 38.33 3.55
408 438 2.756760 GTCACCACCATCAAATCATGCT 59.243 45.455 0.00 0.00 0.00 3.79
414 444 3.130516 CACCATCAAATCATGCTGAAGCT 59.869 43.478 3.61 0.00 42.66 3.74
432 462 1.724082 GCTCTTGACGAGAACTTGCTC 59.276 52.381 0.00 0.00 42.62 4.26
439 469 3.450028 GAGAACTTGCTCGGATGCT 57.550 52.632 0.00 0.00 0.00 3.79
442 472 0.723981 GAACTTGCTCGGATGCTGAC 59.276 55.000 0.00 0.00 0.00 3.51
446 476 2.512515 GCTCGGATGCTGACCCAC 60.513 66.667 0.00 0.00 0.00 4.61
447 477 2.202797 CTCGGATGCTGACCCACG 60.203 66.667 0.00 0.00 0.00 4.94
448 478 2.678580 TCGGATGCTGACCCACGA 60.679 61.111 0.00 0.00 0.00 4.35
457 487 0.464735 CTGACCCACGACCAAAACCA 60.465 55.000 0.00 0.00 0.00 3.67
459 489 1.778027 GACCCACGACCAAAACCACG 61.778 60.000 0.00 0.00 0.00 4.94
472 502 2.674796 AACCACGAGTGCTCCTTATC 57.325 50.000 0.00 0.00 0.00 1.75
474 504 1.478510 ACCACGAGTGCTCCTTATCAG 59.521 52.381 0.00 0.00 0.00 2.90
475 505 1.478510 CCACGAGTGCTCCTTATCAGT 59.521 52.381 0.00 0.00 0.00 3.41
476 506 2.480416 CCACGAGTGCTCCTTATCAGTC 60.480 54.545 0.00 0.00 0.00 3.51
478 508 1.402259 CGAGTGCTCCTTATCAGTCGT 59.598 52.381 10.29 0.00 45.72 4.34
479 509 2.792890 CGAGTGCTCCTTATCAGTCGTG 60.793 54.545 10.29 0.00 45.72 4.35
480 510 2.423892 GAGTGCTCCTTATCAGTCGTGA 59.576 50.000 0.00 0.00 37.02 4.35
482 512 1.476891 TGCTCCTTATCAGTCGTGACC 59.523 52.381 0.00 0.00 34.75 4.02
485 515 1.822990 TCCTTATCAGTCGTGACCACC 59.177 52.381 0.00 0.00 34.75 4.61
498 531 0.600255 GACCACCACACGAGGACAAG 60.600 60.000 0.00 0.00 0.00 3.16
511 544 1.586154 GGACAAGCATGGAACCGTGG 61.586 60.000 13.87 1.67 33.81 4.94
528 561 1.755380 GTGGGACTGTTATACGCCTCT 59.245 52.381 0.00 0.00 0.00 3.69
530 563 2.954318 TGGGACTGTTATACGCCTCTAC 59.046 50.000 0.00 0.00 0.00 2.59
535 568 5.242393 GGACTGTTATACGCCTCTACCATTA 59.758 44.000 0.00 0.00 0.00 1.90
536 569 6.328641 ACTGTTATACGCCTCTACCATTAG 57.671 41.667 0.00 0.00 0.00 1.73
543 576 2.225963 CGCCTCTACCATTAGGACGTAG 59.774 54.545 0.00 0.00 38.69 3.51
550 583 2.505167 ATTAGGACGTAGCCGCCCC 61.505 63.158 0.00 0.00 37.31 5.80
616 662 3.136626 TGCTTCCTCTCCTTTTATAGGGC 59.863 47.826 0.00 0.00 44.86 5.19
619 665 5.616270 CTTCCTCTCCTTTTATAGGGCTTC 58.384 45.833 0.00 0.00 44.86 3.86
627 673 7.027874 TCCTTTTATAGGGCTTCTTTCTTCA 57.972 36.000 0.00 0.00 44.86 3.02
651 697 4.142249 CCTTTTGGTTCAAAGAAAGGTCGT 60.142 41.667 5.73 0.00 41.90 4.34
757 803 4.072131 TCACAGTCTTGACCAAAATAGCC 58.928 43.478 0.00 0.00 0.00 3.93
758 804 3.191371 CACAGTCTTGACCAAAATAGCCC 59.809 47.826 0.00 0.00 0.00 5.19
759 805 2.755103 CAGTCTTGACCAAAATAGCCCC 59.245 50.000 0.00 0.00 0.00 5.80
760 806 2.649816 AGTCTTGACCAAAATAGCCCCT 59.350 45.455 0.00 0.00 0.00 4.79
761 807 3.017442 GTCTTGACCAAAATAGCCCCTC 58.983 50.000 0.00 0.00 0.00 4.30
762 808 2.919602 TCTTGACCAAAATAGCCCCTCT 59.080 45.455 0.00 0.00 0.00 3.69
763 809 3.054361 TCTTGACCAAAATAGCCCCTCTC 60.054 47.826 0.00 0.00 0.00 3.20
764 810 2.562296 TGACCAAAATAGCCCCTCTCT 58.438 47.619 0.00 0.00 0.00 3.10
765 811 2.505819 TGACCAAAATAGCCCCTCTCTC 59.494 50.000 0.00 0.00 0.00 3.20
766 812 2.774809 GACCAAAATAGCCCCTCTCTCT 59.225 50.000 0.00 0.00 0.00 3.10
767 813 2.774809 ACCAAAATAGCCCCTCTCTCTC 59.225 50.000 0.00 0.00 0.00 3.20
768 814 3.044894 CCAAAATAGCCCCTCTCTCTCT 58.955 50.000 0.00 0.00 0.00 3.10
769 815 3.070878 CCAAAATAGCCCCTCTCTCTCTC 59.929 52.174 0.00 0.00 0.00 3.20
770 816 3.966665 CAAAATAGCCCCTCTCTCTCTCT 59.033 47.826 0.00 0.00 0.00 3.10
863 912 4.217159 CGTCCCCGTCCCCGATTC 62.217 72.222 0.00 0.00 35.63 2.52
864 913 4.217159 GTCCCCGTCCCCGATTCG 62.217 72.222 0.00 0.00 35.63 3.34
865 914 4.445710 TCCCCGTCCCCGATTCGA 62.446 66.667 7.83 0.00 35.63 3.71
866 915 3.231736 CCCCGTCCCCGATTCGAT 61.232 66.667 7.83 0.00 35.63 3.59
867 916 2.803817 CCCCGTCCCCGATTCGATT 61.804 63.158 7.83 0.00 35.63 3.34
957 1019 3.080300 TCACACCTCTCTCTTCTCTCC 57.920 52.381 0.00 0.00 0.00 3.71
1103 1170 2.318908 CTGCTCCTCCTGCTAGATCTT 58.681 52.381 0.00 0.00 0.00 2.40
1132 1199 4.752879 GCCGCGGGCTTCTGTACA 62.753 66.667 29.38 0.00 46.69 2.90
1157 1224 1.312371 GCGCAATGGTTAGCAAGGGA 61.312 55.000 0.30 0.00 0.00 4.20
1174 1241 7.220030 AGCAAGGGAATGATAGTTGTGTATAG 58.780 38.462 0.00 0.00 0.00 1.31
1175 1242 7.071196 AGCAAGGGAATGATAGTTGTGTATAGA 59.929 37.037 0.00 0.00 0.00 1.98
1176 1243 7.880195 GCAAGGGAATGATAGTTGTGTATAGAT 59.120 37.037 0.00 0.00 0.00 1.98
1249 1316 5.182380 TGGCTTGGTTGCTTGTAAGTTATAC 59.818 40.000 0.00 0.00 0.00 1.47
1250 1317 5.414765 GGCTTGGTTGCTTGTAAGTTATACT 59.585 40.000 0.00 0.00 0.00 2.12
1251 1318 6.596497 GGCTTGGTTGCTTGTAAGTTATACTA 59.404 38.462 0.00 0.00 0.00 1.82
1265 1332 6.597832 AGTTATACTAGATGGATGGACTGC 57.402 41.667 0.00 0.00 0.00 4.40
1273 1340 3.197766 AGATGGATGGACTGCTCGTTTTA 59.802 43.478 0.00 0.00 0.00 1.52
1282 1349 4.143094 GGACTGCTCGTTTTAGTAGCTTTG 60.143 45.833 0.00 0.00 37.16 2.77
1292 1359 5.545658 TTTAGTAGCTTTGATTTGCTCCG 57.454 39.130 0.00 0.00 40.35 4.63
1315 1382 3.607078 GCGGATTGATAAAAGCCTAAGCG 60.607 47.826 0.00 0.00 46.67 4.68
1398 1468 1.308998 AGTTTCTTGGTGAACTGCCG 58.691 50.000 0.00 0.00 33.88 5.69
1470 1540 6.305877 GTCAGAAACTGTAGGCGATATAATCG 59.694 42.308 4.97 4.97 42.80 3.34
1488 1558 1.544691 TCGAAGCTGTAGGTGGAGAAC 59.455 52.381 0.00 0.00 0.00 3.01
1532 1602 1.224870 GAAAGCCTAGGCCTGACCC 59.775 63.158 30.42 10.01 43.17 4.46
1544 1614 0.179073 CCTGACCCGAGCTGGTTATG 60.179 60.000 0.00 0.00 39.24 1.90
1680 1789 2.159296 GGCGTTGTTGTTGAAGAACCTT 60.159 45.455 2.62 0.00 32.86 3.50
1683 1792 4.095610 CGTTGTTGTTGAAGAACCTTGTC 58.904 43.478 2.62 0.00 32.86 3.18
1685 1794 3.601435 TGTTGTTGAAGAACCTTGTCGA 58.399 40.909 2.62 0.00 0.00 4.20
1775 1884 7.392113 TCTGATCGCTTTGGGTTTTTCTTTATA 59.608 33.333 0.00 0.00 0.00 0.98
1803 1912 6.155827 TGCCAATGCATAGTTTTTGTCTTAC 58.844 36.000 0.00 0.00 44.23 2.34
1822 1931 3.492421 ACATGACTTTGCTATTTGCCG 57.508 42.857 0.00 0.00 42.00 5.69
1872 1981 0.393537 GGCTGTGTGCATCCTAGCTT 60.394 55.000 12.70 0.00 45.15 3.74
1882 1991 1.134159 CATCCTAGCTTTGCAGAGGCT 60.134 52.381 6.36 10.38 41.91 4.58
1941 2050 6.535963 CTCCCTTTTGAGCCAATAAAATCT 57.464 37.500 0.00 0.00 0.00 2.40
1952 2061 5.357032 AGCCAATAAAATCTACCCTTTGTCG 59.643 40.000 0.00 0.00 0.00 4.35
1974 2083 5.881443 TCGAAAAAGGTGGAGAACTTTTACA 59.119 36.000 0.00 0.00 43.81 2.41
2114 2223 3.481112 AGTTCGTGGTGTTTGTGAAAC 57.519 42.857 0.00 0.00 41.73 2.78
2131 2240 5.362717 TGTGAAACGGTATCCTGTGATATCT 59.637 40.000 3.98 0.00 42.39 1.98
2191 2302 3.230976 CCTTGTAGAAGGGGTGCTTTTT 58.769 45.455 10.88 0.00 44.76 1.94
2250 2361 4.081406 TGGCAGCATCTAGTTGTTTTGAT 58.919 39.130 0.00 0.00 0.00 2.57
2322 2433 4.787551 TGTACAGGACACCAATTCACTTT 58.212 39.130 0.00 0.00 31.20 2.66
2325 2436 4.787551 ACAGGACACCAATTCACTTTGTA 58.212 39.130 0.00 0.00 0.00 2.41
2326 2437 4.578928 ACAGGACACCAATTCACTTTGTAC 59.421 41.667 0.00 0.00 0.00 2.90
2327 2438 3.813166 AGGACACCAATTCACTTTGTACG 59.187 43.478 0.00 0.00 0.00 3.67
2329 2440 3.810941 GACACCAATTCACTTTGTACGGA 59.189 43.478 0.00 0.00 0.00 4.69
2330 2441 4.200874 ACACCAATTCACTTTGTACGGAA 58.799 39.130 0.00 0.00 0.00 4.30
2331 2442 4.274950 ACACCAATTCACTTTGTACGGAAG 59.725 41.667 7.13 7.13 0.00 3.46
2354 2475 3.631686 TGTGTGTGACTGAAAATGGGAAG 59.368 43.478 0.00 0.00 0.00 3.46
2462 2588 3.058432 CAGTCAAAGCTGTCTTGTGGATG 60.058 47.826 0.00 0.00 31.78 3.51
2478 2604 4.080919 TGTGGATGTACTCCTTTCTGGATG 60.081 45.833 11.21 0.00 45.16 3.51
2498 2625 6.381133 TGGATGTATTCTGTGTGTATGAGACT 59.619 38.462 0.00 0.00 0.00 3.24
2536 2663 5.509622 GCGAGAAAACTAATCAATTGTGAGC 59.490 40.000 5.13 0.00 37.14 4.26
2548 2675 6.613755 TCAATTGTGAGCTATGATGACATG 57.386 37.500 5.13 0.00 37.87 3.21
2643 2770 5.974158 CGTTTAATTTTGGTGTGATGTGTCA 59.026 36.000 0.00 0.00 0.00 3.58
2972 3156 5.734855 TTTGACAATCCTAGCTATTTCGC 57.265 39.130 0.00 0.00 0.00 4.70
2999 3183 3.774766 TCCGATTCTCAAGATTCTGGGAA 59.225 43.478 0.00 0.00 40.07 3.97
3050 3234 9.647918 ATCTCTTCTGGTAGTATATGAGTTTGA 57.352 33.333 0.00 0.00 0.00 2.69
3051 3235 8.904834 TCTCTTCTGGTAGTATATGAGTTTGAC 58.095 37.037 0.00 0.00 0.00 3.18
3052 3236 7.704271 TCTTCTGGTAGTATATGAGTTTGACG 58.296 38.462 0.00 0.00 0.00 4.35
3053 3237 7.555195 TCTTCTGGTAGTATATGAGTTTGACGA 59.445 37.037 0.00 0.00 0.00 4.20
3054 3238 7.260558 TCTGGTAGTATATGAGTTTGACGAG 57.739 40.000 0.00 0.00 0.00 4.18
3055 3239 6.827251 TCTGGTAGTATATGAGTTTGACGAGT 59.173 38.462 0.00 0.00 0.00 4.18
3136 3320 5.911752 TCATAGGACTCATGCTTCTCTTTC 58.088 41.667 0.00 0.00 0.00 2.62
3137 3321 5.423290 TCATAGGACTCATGCTTCTCTTTCA 59.577 40.000 0.00 0.00 0.00 2.69
3138 3322 3.936564 AGGACTCATGCTTCTCTTTCAC 58.063 45.455 0.00 0.00 0.00 3.18
3139 3323 3.582208 AGGACTCATGCTTCTCTTTCACT 59.418 43.478 0.00 0.00 0.00 3.41
3140 3324 3.932089 GGACTCATGCTTCTCTTTCACTC 59.068 47.826 0.00 0.00 0.00 3.51
3141 3325 4.322650 GGACTCATGCTTCTCTTTCACTCT 60.323 45.833 0.00 0.00 0.00 3.24
3142 3326 5.226194 ACTCATGCTTCTCTTTCACTCTT 57.774 39.130 0.00 0.00 0.00 2.85
3143 3327 5.619220 ACTCATGCTTCTCTTTCACTCTTT 58.381 37.500 0.00 0.00 0.00 2.52
3144 3328 5.469421 ACTCATGCTTCTCTTTCACTCTTTG 59.531 40.000 0.00 0.00 0.00 2.77
3145 3329 5.371526 TCATGCTTCTCTTTCACTCTTTGT 58.628 37.500 0.00 0.00 0.00 2.83
3211 3395 6.650807 CACTCTATTCTTTTGCCAACTCACTA 59.349 38.462 0.00 0.00 0.00 2.74
3355 3541 7.426929 TCAGAAGCTTTCTAGTTTTCATCAC 57.573 36.000 0.00 0.00 38.11 3.06
3413 3599 1.440618 TTTGGGACTGTCTGCCCTTA 58.559 50.000 7.85 0.00 44.96 2.69
3414 3600 0.690762 TTGGGACTGTCTGCCCTTAC 59.309 55.000 7.85 0.00 44.96 2.34
3547 3733 1.469940 GGACTATCACGACAGGTGCAG 60.470 57.143 0.00 0.00 46.56 4.41
3550 3736 0.389817 TATCACGACAGGTGCAGTGC 60.390 55.000 8.58 8.58 46.56 4.40
3742 3928 8.349568 TCTTCAAGCTTCAGTGTAGATAACTA 57.650 34.615 0.00 0.00 0.00 2.24
3908 4095 5.599242 AGAGTAAAAGGGTACTGATCTAGGC 59.401 44.000 0.00 0.00 34.40 3.93
3909 4096 5.278061 AGTAAAAGGGTACTGATCTAGGCA 58.722 41.667 0.00 0.00 32.97 4.75
3910 4097 5.905913 AGTAAAAGGGTACTGATCTAGGCAT 59.094 40.000 0.00 0.00 32.97 4.40
3950 4137 7.834068 TGTTATCTGCTGTTCTTATTGTCTC 57.166 36.000 0.00 0.00 0.00 3.36
4029 4467 6.071108 GCATGTAGAGAAGATTATAGCCCTCA 60.071 42.308 0.00 0.00 0.00 3.86
4381 4822 4.748277 ATGAAATGCAAGAAGGAATGGG 57.252 40.909 0.00 0.00 0.00 4.00
4382 4823 2.234414 TGAAATGCAAGAAGGAATGGGC 59.766 45.455 0.00 0.00 0.00 5.36
4401 4842 3.306818 GGCGGAGTAATACTTAGAAGCG 58.693 50.000 0.00 0.00 0.00 4.68
4442 4883 8.345565 GTTCATTTGGTATTATTAGCTCACAGG 58.654 37.037 0.00 0.00 0.00 4.00
4448 4895 6.183360 TGGTATTATTAGCTCACAGGTCTGTC 60.183 42.308 0.00 0.00 42.83 3.51
4491 4938 2.040278 TCTACTGCAAAGGGACAAGCAT 59.960 45.455 0.00 0.00 36.28 3.79
4550 4997 3.508744 AGTTGTTGTGCTGAAGGTTTG 57.491 42.857 0.00 0.00 0.00 2.93
4724 5172 3.312697 GGTCATACCGAGCATTTTTCCTC 59.687 47.826 0.00 0.00 41.98 3.71
4741 5189 8.702163 TTTTTCCTCTGTTGATTTGAACTTTC 57.298 30.769 0.00 0.00 0.00 2.62
4863 5311 2.236146 TGTGGCTCATGAGGAATACGTT 59.764 45.455 23.89 0.00 0.00 3.99
4892 5340 4.156008 CACTACCATGGGCTGTTTTAACTC 59.844 45.833 18.09 0.00 0.00 3.01
4932 5380 8.322091 ACTGTCAGCTTGTTATTATAGGAACTT 58.678 33.333 0.00 0.00 41.75 2.66
4970 5418 7.099764 AGATGACTATGTTGTGGTTGTTCTAG 58.900 38.462 0.00 0.00 0.00 2.43
5064 5512 4.159879 TGATTGCATGTTGTATTGCCATCA 59.840 37.500 7.36 7.36 44.17 3.07
5087 5542 6.592994 TCATGAGAACTTTCTGCTGATGTAAG 59.407 38.462 0.00 0.00 37.73 2.34
5138 5593 4.523943 TGCTACATCTGCAAAACTCCATTT 59.476 37.500 0.00 0.00 37.51 2.32
5139 5594 4.860907 GCTACATCTGCAAAACTCCATTTG 59.139 41.667 0.00 0.00 42.01 2.32
5144 5608 0.599728 GCAAAACTCCATTTGGCGCA 60.600 50.000 10.83 0.00 37.48 6.09
5167 5632 5.128992 TCGTGCTACACTTAGTTGAATGA 57.871 39.130 0.00 0.00 31.34 2.57
5183 5648 3.181437 TGAATGATGCACTAGCCATGGAT 60.181 43.478 18.40 13.25 41.13 3.41
5191 5656 4.640201 TGCACTAGCCATGGATAACTTTTC 59.360 41.667 18.40 0.42 41.13 2.29
5192 5657 4.640201 GCACTAGCCATGGATAACTTTTCA 59.360 41.667 18.40 0.00 33.58 2.69
5198 5663 4.036852 GCCATGGATAACTTTTCACTAGGC 59.963 45.833 18.40 0.00 0.00 3.93
5200 5665 5.529060 CCATGGATAACTTTTCACTAGGCTC 59.471 44.000 5.56 0.00 0.00 4.70
5206 5671 4.984146 ACTTTTCACTAGGCTCCTTTCT 57.016 40.909 0.00 0.00 0.00 2.52
5208 5673 4.595350 ACTTTTCACTAGGCTCCTTTCTCT 59.405 41.667 0.00 0.00 0.00 3.10
5215 5680 2.831565 AGGCTCCTTTCTCTGATGAGT 58.168 47.619 0.00 0.00 40.98 3.41
5219 5684 3.704061 GCTCCTTTCTCTGATGAGTACCT 59.296 47.826 0.00 0.00 40.98 3.08
5223 5688 1.393603 TCTCTGATGAGTACCTGCCG 58.606 55.000 0.00 0.00 40.98 5.69
5242 5707 2.470821 CGTCCTTCGGTGGATAATGAC 58.529 52.381 0.96 0.00 38.52 3.06
5245 5710 2.434336 TCCTTCGGTGGATAATGACTGG 59.566 50.000 0.00 0.00 0.00 4.00
5246 5711 2.170607 CCTTCGGTGGATAATGACTGGT 59.829 50.000 0.00 0.00 0.00 4.00
5299 5764 4.003648 CGAGGAAGTTAATTTGAGCACCT 58.996 43.478 0.00 0.00 0.00 4.00
5303 5768 6.749139 AGGAAGTTAATTTGAGCACCTTTTC 58.251 36.000 0.00 0.00 0.00 2.29
5305 5770 6.462347 GGAAGTTAATTTGAGCACCTTTTCCA 60.462 38.462 0.00 0.00 31.78 3.53
5306 5771 6.670695 AGTTAATTTGAGCACCTTTTCCAT 57.329 33.333 0.00 0.00 0.00 3.41
5349 5815 9.175312 TGAATTGCAAACATGCCAATAATATTT 57.825 25.926 1.71 0.00 0.00 1.40
5402 5869 7.792364 AACATCTTATATTATGGGACGGAGA 57.208 36.000 0.00 0.00 0.00 3.71
5403 5870 7.979786 ACATCTTATATTATGGGACGGAGAT 57.020 36.000 0.00 0.00 0.00 2.75
5413 5880 2.091499 TGGGACGGAGATAGTACCATGT 60.091 50.000 0.00 0.00 46.98 3.21
5414 5881 2.296471 GGGACGGAGATAGTACCATGTG 59.704 54.545 0.00 0.00 42.20 3.21
5417 5884 4.765856 GGACGGAGATAGTACCATGTGTAT 59.234 45.833 0.00 0.00 0.00 2.29
5420 5887 5.010719 ACGGAGATAGTACCATGTGTATTGG 59.989 44.000 0.00 0.00 40.26 3.16
5426 5893 7.787904 AGATAGTACCATGTGTATTGGGTTAGA 59.212 37.037 0.00 0.00 38.64 2.10
5439 5906 4.216411 TGGGTTAGACTATGCCAACTTC 57.784 45.455 6.11 0.00 0.00 3.01
5443 5910 4.329256 GGTTAGACTATGCCAACTTCGTTC 59.671 45.833 0.25 0.00 0.00 3.95
5444 5911 3.678056 AGACTATGCCAACTTCGTTCA 57.322 42.857 0.00 0.00 0.00 3.18
5445 5912 3.589988 AGACTATGCCAACTTCGTTCAG 58.410 45.455 0.00 0.00 0.00 3.02
5489 5956 4.323868 GGTAGAGTTTGTCTTTGATCGTCG 59.676 45.833 0.00 0.00 36.64 5.12
5526 5993 5.419788 CCACCTGAATTCCTGAATGATGAAA 59.580 40.000 2.27 0.00 0.00 2.69
5543 6010 6.380995 TGATGAAAACATGTTATGTGTGCTC 58.619 36.000 12.39 2.37 44.07 4.26
5549 6016 4.252878 ACATGTTATGTGTGCTCGAATGA 58.747 39.130 0.00 0.00 43.01 2.57
5564 6031 2.947652 CGAATGATTCCATGGACTGCTT 59.052 45.455 15.91 6.22 32.36 3.91
5584 6051 7.023197 TGCTTTAGACCTTGTTTTGTTCTAC 57.977 36.000 0.00 0.00 0.00 2.59
5585 6052 6.826741 TGCTTTAGACCTTGTTTTGTTCTACT 59.173 34.615 0.00 0.00 0.00 2.57
5586 6053 7.988599 TGCTTTAGACCTTGTTTTGTTCTACTA 59.011 33.333 0.00 0.00 0.00 1.82
5587 6054 9.000486 GCTTTAGACCTTGTTTTGTTCTACTAT 58.000 33.333 0.00 0.00 0.00 2.12
5618 6085 2.093306 TGTTTAGATGTGCCGGTGAG 57.907 50.000 1.90 0.00 0.00 3.51
5629 6096 3.135994 GTGCCGGTGAGAAGTTAGAAAA 58.864 45.455 1.90 0.00 0.00 2.29
5653 6120 7.079182 ACGTCTTTGAACTGTTGAATGTTTA 57.921 32.000 0.00 0.00 0.00 2.01
5677 6147 4.223320 TCCTTGCGTTCAGTTTTCATTC 57.777 40.909 0.00 0.00 0.00 2.67
5682 6152 4.786507 TGCGTTCAGTTTTCATTCATCTG 58.213 39.130 0.00 0.00 0.00 2.90
5699 6169 9.447040 CATTCATCTGTTAAGAATGCAATACAG 57.553 33.333 0.00 0.00 41.24 2.74
5705 6175 9.719355 TCTGTTAAGAATGCAATACAGAAGTTA 57.281 29.630 3.18 0.00 39.06 2.24
5742 6212 0.109597 GCAAGCAGAATGGGTTGACG 60.110 55.000 9.05 0.00 46.36 4.35
5850 6343 7.156876 TGACTTTGTGTTCTGAAGAAAATGT 57.843 32.000 8.22 8.22 35.58 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.285990 AGTGGTGTCGTACAGAATAAAAGTT 58.714 36.000 0.00 0.00 0.00 2.66
17 18 2.585330 TGGTAGAAGTGGTGTCGTACA 58.415 47.619 0.00 0.00 0.00 2.90
22 23 4.819630 TGTTTGAATGGTAGAAGTGGTGTC 59.180 41.667 0.00 0.00 0.00 3.67
35 36 6.088824 GTCTTTGATAGCTGTGTTTGAATGG 58.911 40.000 0.00 0.00 0.00 3.16
36 37 6.671190 TGTCTTTGATAGCTGTGTTTGAATG 58.329 36.000 0.00 0.00 0.00 2.67
57 58 9.034544 AGCTTTTCTATTTTGTGTTCATTTGTC 57.965 29.630 0.00 0.00 0.00 3.18
106 107 5.509670 GGAAAAAGAGGTGAAGAAACCATGG 60.510 44.000 11.19 11.19 43.20 3.66
107 108 5.302823 AGGAAAAAGAGGTGAAGAAACCATG 59.697 40.000 0.00 0.00 43.20 3.66
148 149 4.566004 TCTTATCGACTCCAACAACCTTG 58.434 43.478 0.00 0.00 0.00 3.61
149 150 4.884668 TCTTATCGACTCCAACAACCTT 57.115 40.909 0.00 0.00 0.00 3.50
172 173 2.583441 CCAACACCCTCTCTGCCGA 61.583 63.158 0.00 0.00 0.00 5.54
175 176 2.360475 GCCCAACACCCTCTCTGC 60.360 66.667 0.00 0.00 0.00 4.26
192 193 2.415857 GCTTGCAGACTGAGTTCATGAG 59.584 50.000 6.65 0.00 0.00 2.90
193 194 2.224354 TGCTTGCAGACTGAGTTCATGA 60.224 45.455 6.65 0.00 0.00 3.07
195 196 2.149578 GTGCTTGCAGACTGAGTTCAT 58.850 47.619 6.65 0.00 0.00 2.57
201 202 0.390340 GGATCGTGCTTGCAGACTGA 60.390 55.000 6.65 0.00 0.00 3.41
204 205 0.874390 TTTGGATCGTGCTTGCAGAC 59.126 50.000 0.00 0.00 0.00 3.51
208 209 0.169009 GGACTTTGGATCGTGCTTGC 59.831 55.000 0.00 0.00 0.00 4.01
218 219 1.139498 TGCCTCCATGGGACTTTGGA 61.139 55.000 13.02 0.00 38.60 3.53
225 226 0.409092 ATGTTGTTGCCTCCATGGGA 59.591 50.000 13.02 0.00 36.00 4.37
231 232 4.585879 TCCTAGTTAATGTTGTTGCCTCC 58.414 43.478 0.00 0.00 0.00 4.30
245 246 4.405680 TGCAGCTTAGCATTCTCCTAGTTA 59.594 41.667 7.07 0.00 40.11 2.24
291 292 0.519077 GTCAGGCTCGCTTTTTGAGG 59.481 55.000 0.00 0.00 33.99 3.86
294 295 0.386478 GCTGTCAGGCTCGCTTTTTG 60.386 55.000 1.14 0.00 0.00 2.44
301 302 1.812922 GTCATGGCTGTCAGGCTCG 60.813 63.158 25.17 16.44 41.96 5.03
330 331 4.096984 GCTTTTCACTATTCAGGACATGGG 59.903 45.833 0.00 0.00 0.00 4.00
331 332 4.946157 AGCTTTTCACTATTCAGGACATGG 59.054 41.667 0.00 0.00 0.00 3.66
337 338 7.099764 TCAGTTAGAGCTTTTCACTATTCAGG 58.900 38.462 0.00 0.00 0.00 3.86
358 359 5.763204 ACGATGATGTTAGGTTTGTTTCAGT 59.237 36.000 0.00 0.00 0.00 3.41
359 360 6.241207 ACGATGATGTTAGGTTTGTTTCAG 57.759 37.500 0.00 0.00 0.00 3.02
360 361 6.038825 ACAACGATGATGTTAGGTTTGTTTCA 59.961 34.615 0.00 0.00 0.00 2.69
361 362 6.435428 ACAACGATGATGTTAGGTTTGTTTC 58.565 36.000 0.00 0.00 0.00 2.78
379 380 0.319211 GATGGTGGTGACGACAACGA 60.319 55.000 0.00 0.00 42.66 3.85
385 386 2.849294 TGATTTGATGGTGGTGACGA 57.151 45.000 0.00 0.00 0.00 4.20
387 388 2.756760 AGCATGATTTGATGGTGGTGAC 59.243 45.455 0.00 0.00 32.82 3.67
388 389 2.756207 CAGCATGATTTGATGGTGGTGA 59.244 45.455 0.00 0.00 44.55 4.02
389 390 3.159353 CAGCATGATTTGATGGTGGTG 57.841 47.619 0.00 0.00 44.55 4.17
432 462 2.509336 GTCGTGGGTCAGCATCCG 60.509 66.667 0.00 0.00 0.00 4.18
435 465 0.179004 TTTTGGTCGTGGGTCAGCAT 60.179 50.000 0.00 0.00 0.00 3.79
439 469 0.748729 GTGGTTTTGGTCGTGGGTCA 60.749 55.000 0.00 0.00 0.00 4.02
442 472 1.503818 CTCGTGGTTTTGGTCGTGGG 61.504 60.000 0.00 0.00 0.00 4.61
446 476 1.157870 AGCACTCGTGGTTTTGGTCG 61.158 55.000 0.00 0.00 38.24 4.79
447 477 0.586802 GAGCACTCGTGGTTTTGGTC 59.413 55.000 3.05 0.00 41.93 4.02
448 478 0.818040 GGAGCACTCGTGGTTTTGGT 60.818 55.000 3.05 0.00 41.93 3.67
457 487 1.402259 CGACTGATAAGGAGCACTCGT 59.598 52.381 0.00 0.00 0.00 4.18
459 489 2.423892 TCACGACTGATAAGGAGCACTC 59.576 50.000 0.00 0.00 0.00 3.51
478 508 1.331399 TTGTCCTCGTGTGGTGGTCA 61.331 55.000 0.00 0.00 0.00 4.02
479 509 0.600255 CTTGTCCTCGTGTGGTGGTC 60.600 60.000 0.00 0.00 0.00 4.02
480 510 1.445942 CTTGTCCTCGTGTGGTGGT 59.554 57.895 0.00 0.00 0.00 4.16
482 512 0.603707 ATGCTTGTCCTCGTGTGGTG 60.604 55.000 0.00 0.00 0.00 4.17
485 515 0.320683 TCCATGCTTGTCCTCGTGTG 60.321 55.000 0.00 0.00 0.00 3.82
490 523 0.321653 ACGGTTCCATGCTTGTCCTC 60.322 55.000 0.00 0.00 0.00 3.71
498 531 2.040544 CAGTCCCACGGTTCCATGC 61.041 63.158 0.00 0.00 0.00 4.06
511 544 2.954318 TGGTAGAGGCGTATAACAGTCC 59.046 50.000 0.00 0.00 0.00 3.85
528 561 0.670162 GCGGCTACGTCCTAATGGTA 59.330 55.000 0.00 0.00 43.45 3.25
530 563 1.300697 GGCGGCTACGTCCTAATGG 60.301 63.158 0.00 0.00 43.45 3.16
543 576 1.801771 GTTTTGTTTATTTGGGGCGGC 59.198 47.619 0.00 0.00 0.00 6.53
616 662 6.207691 TGAACCAAAAGGTGAAGAAAGAAG 57.792 37.500 0.00 0.00 0.00 2.85
619 665 6.630071 TCTTTGAACCAAAAGGTGAAGAAAG 58.370 36.000 0.00 0.00 37.67 2.62
651 697 3.706373 GCAGGTTCTGGCCTCCGA 61.706 66.667 3.32 0.00 36.58 4.55
704 750 1.358152 TGAGGGAGTTTTGGGTCGAT 58.642 50.000 0.00 0.00 0.00 3.59
757 803 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
758 804 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
759 805 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
760 806 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
761 807 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
762 808 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
763 809 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
764 810 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
765 811 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
766 812 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
767 813 4.039004 CAGGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
768 814 3.963374 CAGGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
769 815 3.494048 GCAGGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
770 816 2.435805 GCAGGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
804 850 2.386661 ATCGTAGGAACAGGCTTGTG 57.613 50.000 0.65 0.00 37.67 3.33
805 851 2.159282 CGTATCGTAGGAACAGGCTTGT 60.159 50.000 0.00 0.00 39.87 3.16
806 852 2.098607 TCGTATCGTAGGAACAGGCTTG 59.901 50.000 0.00 0.00 0.00 4.01
807 853 2.372264 TCGTATCGTAGGAACAGGCTT 58.628 47.619 0.00 0.00 0.00 4.35
809 855 2.553172 AGATCGTATCGTAGGAACAGGC 59.447 50.000 0.00 0.00 0.00 4.85
863 912 1.060713 CGGGGAATCGAATCGAATCG 58.939 55.000 16.66 16.66 39.99 3.34
864 913 0.790814 GCGGGGAATCGAATCGAATC 59.209 55.000 10.12 11.13 39.99 2.52
865 914 0.105964 TGCGGGGAATCGAATCGAAT 59.894 50.000 10.12 0.00 39.99 3.34
866 915 0.105964 ATGCGGGGAATCGAATCGAA 59.894 50.000 10.12 0.00 39.99 3.71
867 916 0.319555 GATGCGGGGAATCGAATCGA 60.320 55.000 8.12 8.12 35.75 3.59
896 958 4.760047 ACATCGGCGGAGTGTGGC 62.760 66.667 7.21 0.00 0.00 5.01
1132 1199 1.635663 GCTAACCATTGCGCACTCGT 61.636 55.000 11.12 0.00 38.14 4.18
1174 1241 2.064762 CGCAGCAAGCCAGTCTATATC 58.935 52.381 0.00 0.00 41.38 1.63
1175 1242 1.414181 ACGCAGCAAGCCAGTCTATAT 59.586 47.619 0.00 0.00 41.38 0.86
1176 1243 0.824109 ACGCAGCAAGCCAGTCTATA 59.176 50.000 0.00 0.00 41.38 1.31
1177 1244 0.460987 GACGCAGCAAGCCAGTCTAT 60.461 55.000 0.00 0.00 41.38 1.98
1178 1245 1.079819 GACGCAGCAAGCCAGTCTA 60.080 57.895 0.00 0.00 41.38 2.59
1179 1246 2.358003 GACGCAGCAAGCCAGTCT 60.358 61.111 0.00 0.00 41.38 3.24
1180 1247 2.358003 AGACGCAGCAAGCCAGTC 60.358 61.111 0.00 4.66 41.38 3.51
1229 1296 9.378551 CATCTAGTATAACTTACAAGCAACCAA 57.621 33.333 0.00 0.00 0.00 3.67
1249 1316 1.959985 ACGAGCAGTCCATCCATCTAG 59.040 52.381 0.00 0.00 0.00 2.43
1250 1317 2.073252 ACGAGCAGTCCATCCATCTA 57.927 50.000 0.00 0.00 0.00 1.98
1251 1318 1.198713 AACGAGCAGTCCATCCATCT 58.801 50.000 0.00 0.00 0.00 2.90
1265 1332 6.603095 AGCAAATCAAAGCTACTAAAACGAG 58.397 36.000 0.00 0.00 39.78 4.18
1273 1340 2.359900 CCGGAGCAAATCAAAGCTACT 58.640 47.619 0.00 0.00 42.04 2.57
1282 1349 1.095228 TCAATCCGCCGGAGCAAATC 61.095 55.000 13.12 0.00 39.83 2.17
1292 1359 3.304726 GCTTAGGCTTTTATCAATCCGCC 60.305 47.826 0.00 0.00 37.80 6.13
1351 1421 1.478510 AGCATACTGGTGACTTCCTCG 59.521 52.381 0.00 0.00 0.00 4.63
1398 1468 1.657822 GACGCTGAAATCCCTTCCTC 58.342 55.000 0.00 0.00 32.53 3.71
1428 1498 0.319641 GACTTTCCAGAGCGTTCGGT 60.320 55.000 9.22 0.00 0.00 4.69
1470 1540 3.686916 AAGTTCTCCACCTACAGCTTC 57.313 47.619 0.00 0.00 0.00 3.86
1509 1579 2.275748 GGCCTAGGCTTTCACCCC 59.724 66.667 32.18 10.15 41.60 4.95
1525 1595 0.179073 CATAACCAGCTCGGGTCAGG 60.179 60.000 0.00 0.00 41.32 3.86
1532 1602 2.182842 GCCAGGCATAACCAGCTCG 61.183 63.158 6.55 0.00 43.14 5.03
1583 1654 1.065102 CAATCCGAGCAATGCCTTCAG 59.935 52.381 0.00 0.00 0.00 3.02
1680 1789 0.750249 ATGACACCACACAGTCGACA 59.250 50.000 19.50 0.00 37.58 4.35
1683 1792 1.422388 CTCATGACACCACACAGTCG 58.578 55.000 0.00 0.00 37.58 4.18
1685 1794 0.761187 AGCTCATGACACCACACAGT 59.239 50.000 0.00 0.00 0.00 3.55
1790 1899 7.100458 AGCAAAGTCATGTAAGACAAAAACT 57.900 32.000 0.00 0.00 40.98 2.66
1796 1905 6.611381 GCAAATAGCAAAGTCATGTAAGACA 58.389 36.000 0.00 0.00 44.79 3.41
1839 1948 1.821759 CAGCCAACACCAACGGACA 60.822 57.895 0.00 0.00 0.00 4.02
1872 1981 2.113774 CACACCCAGCCTCTGCAA 59.886 61.111 0.00 0.00 41.13 4.08
1882 1991 1.227823 CCGAAAGAGCACACACCCA 60.228 57.895 0.00 0.00 0.00 4.51
1952 2061 8.194769 TGATTGTAAAAGTTCTCCACCTTTTTC 58.805 33.333 3.08 0.00 40.39 2.29
1974 2083 5.936956 GTCAAGAGTCATTCCTCTGTTGATT 59.063 40.000 7.72 0.00 42.67 2.57
1994 2103 3.958798 GGCATCCAGTAGGTAGTAGTCAA 59.041 47.826 0.00 0.00 35.89 3.18
2114 2223 3.990469 GCAACAGATATCACAGGATACCG 59.010 47.826 5.32 0.00 38.76 4.02
2131 2240 1.106351 AAACGCATCAGTGGGCAACA 61.106 50.000 0.00 0.00 41.64 3.33
2250 2361 2.826128 GCCGAGTATATCATGAGGACCA 59.174 50.000 0.09 0.00 0.00 4.02
2322 2433 1.752498 AGTCACACACACTTCCGTACA 59.248 47.619 0.00 0.00 0.00 2.90
2325 2436 0.821517 TCAGTCACACACACTTCCGT 59.178 50.000 0.00 0.00 0.00 4.69
2326 2437 1.934589 TTCAGTCACACACACTTCCG 58.065 50.000 0.00 0.00 0.00 4.30
2327 2438 4.498009 CCATTTTCAGTCACACACACTTCC 60.498 45.833 0.00 0.00 0.00 3.46
2329 2440 3.381272 CCCATTTTCAGTCACACACACTT 59.619 43.478 0.00 0.00 0.00 3.16
2330 2441 2.951642 CCCATTTTCAGTCACACACACT 59.048 45.455 0.00 0.00 0.00 3.55
2331 2442 2.948979 TCCCATTTTCAGTCACACACAC 59.051 45.455 0.00 0.00 0.00 3.82
2478 2604 4.735822 GCGAGTCTCATACACACAGAATAC 59.264 45.833 0.00 0.00 0.00 1.89
2548 2675 3.125146 TGACGAGTAACAATGCTGATTGC 59.875 43.478 0.00 0.00 42.54 3.56
2972 3156 3.067461 AGAATCTTGAGAATCGGACCTCG 59.933 47.826 0.00 0.00 38.61 4.63
2999 3183 1.618343 CCCAGTTCTTTTGGCCGATTT 59.382 47.619 0.00 0.00 34.26 2.17
3050 3234 4.330944 TGTCCAATAGTGTCAAACTCGT 57.669 40.909 0.00 0.00 40.56 4.18
3051 3235 5.862924 AATGTCCAATAGTGTCAAACTCG 57.137 39.130 0.00 0.00 40.56 4.18
3052 3236 5.858581 GCAAATGTCCAATAGTGTCAAACTC 59.141 40.000 0.00 0.00 40.56 3.01
3053 3237 5.301551 TGCAAATGTCCAATAGTGTCAAACT 59.698 36.000 0.00 0.00 43.40 2.66
3054 3238 5.527951 TGCAAATGTCCAATAGTGTCAAAC 58.472 37.500 0.00 0.00 0.00 2.93
3055 3239 5.781210 TGCAAATGTCCAATAGTGTCAAA 57.219 34.783 0.00 0.00 0.00 2.69
3136 3320 5.814705 ACAAGACTGAGAAAGACAAAGAGTG 59.185 40.000 0.00 0.00 0.00 3.51
3137 3321 5.983540 ACAAGACTGAGAAAGACAAAGAGT 58.016 37.500 0.00 0.00 0.00 3.24
3138 3322 8.494347 CAATACAAGACTGAGAAAGACAAAGAG 58.506 37.037 0.00 0.00 0.00 2.85
3139 3323 8.204160 TCAATACAAGACTGAGAAAGACAAAGA 58.796 33.333 0.00 0.00 0.00 2.52
3140 3324 8.370493 TCAATACAAGACTGAGAAAGACAAAG 57.630 34.615 0.00 0.00 0.00 2.77
3141 3325 8.908786 ATCAATACAAGACTGAGAAAGACAAA 57.091 30.769 0.00 0.00 0.00 2.83
3142 3326 9.645059 CTATCAATACAAGACTGAGAAAGACAA 57.355 33.333 0.00 0.00 0.00 3.18
3143 3327 8.807118 ACTATCAATACAAGACTGAGAAAGACA 58.193 33.333 0.00 0.00 0.00 3.41
3144 3328 9.646427 AACTATCAATACAAGACTGAGAAAGAC 57.354 33.333 0.00 0.00 0.00 3.01
3327 3511 7.807977 TGAAAACTAGAAAGCTTCTGAACAT 57.192 32.000 0.00 0.00 40.94 2.71
3547 3733 0.658536 GCACAGAGCGAAACAAGCAC 60.659 55.000 0.00 0.00 37.01 4.40
3908 4095 8.640651 CAGATAACATATAGAGGGAGGATGATG 58.359 40.741 0.00 0.00 0.00 3.07
3909 4096 7.289782 GCAGATAACATATAGAGGGAGGATGAT 59.710 40.741 0.00 0.00 0.00 2.45
3910 4097 6.609212 GCAGATAACATATAGAGGGAGGATGA 59.391 42.308 0.00 0.00 0.00 2.92
3949 4136 4.546674 TGATGCATTCACTAGGGAGTAGA 58.453 43.478 0.00 0.00 33.32 2.59
3950 4137 4.944619 TGATGCATTCACTAGGGAGTAG 57.055 45.455 0.00 0.00 33.32 2.57
4029 4467 6.824958 TCCAAAGGTGATAAGTAGCCTAAT 57.175 37.500 0.00 0.00 0.00 1.73
4044 4485 4.850680 TGTTAGACACAACTTCCAAAGGT 58.149 39.130 0.00 0.00 29.87 3.50
4381 4822 3.243334 ACCGCTTCTAAGTATTACTCCGC 60.243 47.826 0.00 0.00 0.00 5.54
4382 4823 4.275443 AGACCGCTTCTAAGTATTACTCCG 59.725 45.833 0.00 0.00 30.17 4.63
4401 4842 5.440685 CAAATGAACAACAGTACGAAGACC 58.559 41.667 0.00 0.00 0.00 3.85
4442 4883 4.737054 CCTGCAATAACAATTGGACAGAC 58.263 43.478 10.83 0.00 32.43 3.51
4448 4895 3.598019 ACAGCCTGCAATAACAATTGG 57.402 42.857 10.83 0.00 32.43 3.16
4724 5172 8.652810 AATCCAAAGAAAGTTCAAATCAACAG 57.347 30.769 0.00 0.00 0.00 3.16
4863 5311 1.278985 CAGCCCATGGTAGTGAAGTCA 59.721 52.381 11.73 0.00 0.00 3.41
4892 5340 9.155975 ACAAGCTGACAGTAATAAACAGATAAG 57.844 33.333 3.99 0.00 0.00 1.73
4970 5418 8.726988 TGCAAAGAATATAGAAGGTAACACAAC 58.273 33.333 0.00 0.00 41.41 3.32
5029 5477 3.956199 ACATGCAATCACCCCTAGAAATG 59.044 43.478 0.00 0.00 0.00 2.32
5064 5512 6.370994 CACTTACATCAGCAGAAAGTTCTCAT 59.629 38.462 0.00 0.00 34.74 2.90
5144 5608 5.720202 TCATTCAACTAAGTGTAGCACGAT 58.280 37.500 0.00 0.00 39.64 3.73
5167 5632 4.443978 AAGTTATCCATGGCTAGTGCAT 57.556 40.909 6.96 0.00 41.91 3.96
5183 5648 6.270231 AGAGAAAGGAGCCTAGTGAAAAGTTA 59.730 38.462 0.00 0.00 0.00 2.24
5191 5656 3.703556 TCATCAGAGAAAGGAGCCTAGTG 59.296 47.826 0.00 0.00 0.00 2.74
5192 5657 3.960102 CTCATCAGAGAAAGGAGCCTAGT 59.040 47.826 0.00 0.00 44.98 2.57
5198 5663 4.441356 GCAGGTACTCATCAGAGAAAGGAG 60.441 50.000 0.00 0.00 44.98 3.69
5200 5665 3.431486 GGCAGGTACTCATCAGAGAAAGG 60.431 52.174 0.00 0.00 44.98 3.11
5206 5671 1.103803 GACGGCAGGTACTCATCAGA 58.896 55.000 0.00 0.00 34.60 3.27
5208 5673 0.324368 AGGACGGCAGGTACTCATCA 60.324 55.000 0.00 0.00 33.10 3.07
5242 5707 6.798482 TGCTTGCTCAAATAATTATGACCAG 58.202 36.000 0.00 0.00 0.00 4.00
5246 5711 9.872721 TGATTTTGCTTGCTCAAATAATTATGA 57.127 25.926 0.00 0.00 36.04 2.15
5275 5740 4.933400 GGTGCTCAAATTAACTTCCTCGTA 59.067 41.667 0.00 0.00 0.00 3.43
5276 5741 3.751698 GGTGCTCAAATTAACTTCCTCGT 59.248 43.478 0.00 0.00 0.00 4.18
5349 5815 7.903145 ACAACCAATATGTGACAGAGTAGTAA 58.097 34.615 0.00 0.00 0.00 2.24
5354 5820 9.162764 GTTATTACAACCAATATGTGACAGAGT 57.837 33.333 0.00 0.00 32.27 3.24
5358 5825 9.679661 AGATGTTATTACAACCAATATGTGACA 57.320 29.630 0.00 0.00 37.91 3.58
5402 5869 7.567622 AGTCTAACCCAATACACATGGTACTAT 59.432 37.037 0.00 0.00 36.14 2.12
5403 5870 6.899075 AGTCTAACCCAATACACATGGTACTA 59.101 38.462 0.00 0.00 36.14 1.82
5413 5880 5.190925 AGTTGGCATAGTCTAACCCAATACA 59.809 40.000 14.28 0.00 37.82 2.29
5414 5881 5.681639 AGTTGGCATAGTCTAACCCAATAC 58.318 41.667 14.28 6.79 37.82 1.89
5417 5884 4.585879 GAAGTTGGCATAGTCTAACCCAA 58.414 43.478 9.41 9.41 33.47 4.12
5420 5887 3.858247 ACGAAGTTGGCATAGTCTAACC 58.142 45.455 0.00 0.00 37.78 2.85
5439 5906 1.493772 TACAAGGCACGAACTGAACG 58.506 50.000 0.00 0.00 0.00 3.95
5443 5910 3.201726 CCATTTACAAGGCACGAACTG 57.798 47.619 0.00 0.00 0.00 3.16
5464 5931 3.612860 CGATCAAAGACAAACTCTACCCG 59.387 47.826 0.00 0.00 0.00 5.28
5511 5978 8.805175 ACATAACATGTTTTCATCATTCAGGAA 58.195 29.630 17.78 0.00 41.63 3.36
5526 5993 4.694982 TCATTCGAGCACACATAACATGTT 59.305 37.500 16.68 16.68 42.70 2.71
5543 6010 2.569059 AGCAGTCCATGGAATCATTCG 58.431 47.619 18.20 3.85 0.00 3.34
5549 6016 3.525199 AGGTCTAAAGCAGTCCATGGAAT 59.475 43.478 18.20 13.77 35.12 3.01
5587 6054 8.822855 CGGCACATCTAAACAAGTATAAACATA 58.177 33.333 0.00 0.00 0.00 2.29
5588 6055 7.201696 CCGGCACATCTAAACAAGTATAAACAT 60.202 37.037 0.00 0.00 0.00 2.71
5590 6057 6.093082 ACCGGCACATCTAAACAAGTATAAAC 59.907 38.462 0.00 0.00 0.00 2.01
5591 6058 6.092944 CACCGGCACATCTAAACAAGTATAAA 59.907 38.462 0.00 0.00 0.00 1.40
5593 6060 5.105269 TCACCGGCACATCTAAACAAGTATA 60.105 40.000 0.00 0.00 0.00 1.47
5594 6061 3.938963 CACCGGCACATCTAAACAAGTAT 59.061 43.478 0.00 0.00 0.00 2.12
5618 6085 7.461918 ACAGTTCAAAGACGTTTTCTAACTTC 58.538 34.615 13.02 0.00 32.51 3.01
5629 6096 5.560966 AACATTCAACAGTTCAAAGACGT 57.439 34.783 0.00 0.00 0.00 4.34
5653 6120 4.647424 TGAAAACTGAACGCAAGGAAAT 57.353 36.364 0.00 0.00 46.39 2.17
5677 6147 8.671921 ACTTCTGTATTGCATTCTTAACAGATG 58.328 33.333 16.08 16.08 41.94 2.90
5762 6232 0.759959 TTCAAAGCGGGGTACAGTCA 59.240 50.000 0.00 0.00 0.00 3.41
5763 6233 1.886886 TTTCAAAGCGGGGTACAGTC 58.113 50.000 0.00 0.00 0.00 3.51
5764 6234 2.159382 CATTTCAAAGCGGGGTACAGT 58.841 47.619 0.00 0.00 0.00 3.55
5765 6235 2.159382 ACATTTCAAAGCGGGGTACAG 58.841 47.619 0.00 0.00 0.00 2.74
5766 6236 2.156098 GACATTTCAAAGCGGGGTACA 58.844 47.619 0.00 0.00 0.00 2.90
5770 6261 3.385193 AAAAGACATTTCAAAGCGGGG 57.615 42.857 0.00 0.00 0.00 5.73
5796 6287 8.452989 ACAGACATTTCAATTTATTTCTTCGC 57.547 30.769 0.00 0.00 0.00 4.70
5797 6288 9.611284 TGACAGACATTTCAATTTATTTCTTCG 57.389 29.630 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.