Multiple sequence alignment - TraesCS5B01G020100

Loading Multiple Alignment...

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 TraesCS5B01G020100 chr5B 100.000 4862 0 0 1 4862 19588872 19593733 0.000000e+00 8979.0
1 TraesCS5B01G020100 chr5B 83.472 3957 537 64 710 4607 19575408 19579306 0.000000e+00 3576.0
2 TraesCS5B01G020100 chr5B 85.616 2176 270 23 2206 4359 19672389 19674543 0.000000e+00 2244.0
3 TraesCS5B01G020100 chr5B 81.980 1182 178 26 979 2148 19629327 19630485 0.000000e+00 970.0
4 TraesCS5B01G020100 chr5B 82.021 940 133 28 3575 4484 19678065 19678998 0.000000e+00 767.0
5 TraesCS5B01G020100 chr5B 84.067 659 88 11 986 1634 20814345 20813694 1.920000e-173 619.0
6 TraesCS5B01G020100 chr5B 81.818 539 73 12 979 1492 19677526 19678064 3.480000e-116 429.0
7 TraesCS5B01G020100 chr5B 83.013 312 34 10 404 704 447268307 447268610 1.040000e-66 265.0
8 TraesCS5B01G020100 chr5B 88.479 217 12 5 490 706 441103790 441103993 2.910000e-62 250.0
9 TraesCS5B01G020100 chr5B 80.156 257 50 1 1723 1978 20359938 20360194 1.790000e-44 191.0
10 TraesCS5B01G020100 chr5B 83.333 120 12 2 286 405 271164012 271163901 2.390000e-18 104.0
11 TraesCS5B01G020100 chr5B 89.474 76 8 0 1 76 19575333 19575408 4.010000e-16 97.1
12 TraesCS5B01G020100 chr5B 94.444 54 3 0 352 405 441101048 441101101 3.120000e-12 84.2
13 TraesCS5B01G020100 chr5A 84.020 3035 403 51 1097 4096 18788996 18791983 0.000000e+00 2843.0
14 TraesCS5B01G020100 chr5A 80.910 2902 442 72 1735 4576 18709652 18712501 0.000000e+00 2187.0
15 TraesCS5B01G020100 chr5A 81.996 1683 270 17 2368 4042 19106660 19108317 0.000000e+00 1399.0
16 TraesCS5B01G020100 chr5A 83.346 1267 192 11 986 2241 19105487 19106745 0.000000e+00 1153.0
17 TraesCS5B01G020100 chr5A 88.261 230 19 1 176 405 642138779 642139000 8.020000e-68 268.0
18 TraesCS5B01G020100 chr5A 86.486 222 22 5 486 706 642141159 642141373 2.260000e-58 237.0
19 TraesCS5B01G020100 chr5A 85.000 120 10 2 286 405 30770999 30771110 1.110000e-21 115.0
20 TraesCS5B01G020100 chr5D 83.435 2777 400 36 979 3725 27436941 27439687 0.000000e+00 2525.0
21 TraesCS5B01G020100 chr5D 84.518 2280 311 23 1097 3358 27458253 27460508 0.000000e+00 2217.0
22 TraesCS5B01G020100 chr5D 92.506 1361 70 13 3519 4862 27310760 27312105 0.000000e+00 1919.0
23 TraesCS5B01G020100 chr5D 82.326 2167 294 56 2463 4596 27432599 27434709 0.000000e+00 1797.0
24 TraesCS5B01G020100 chr5D 82.115 1683 268 18 2368 4042 28481644 28483301 0.000000e+00 1410.0
25 TraesCS5B01G020100 chr5D 81.687 1731 272 32 979 2679 27399168 27400883 0.000000e+00 1399.0
26 TraesCS5B01G020100 chr5D 83.741 1267 187 11 986 2241 28480471 28481729 0.000000e+00 1181.0
27 TraesCS5B01G020100 chr5D 83.799 1216 153 29 3169 4359 27426833 27428029 0.000000e+00 1114.0
28 TraesCS5B01G020100 chr5D 81.980 1121 161 19 1296 2394 27431501 27432602 0.000000e+00 913.0
29 TraesCS5B01G020100 chr5D 82.802 878 133 8 1147 2007 27278997 27279873 0.000000e+00 769.0
30 TraesCS5B01G020100 chr5D 79.908 1090 155 37 3341 4411 27460690 27461734 0.000000e+00 741.0
31 TraesCS5B01G020100 chr5D 84.469 367 35 13 979 1328 27431115 27431476 4.660000e-90 342.0
32 TraesCS5B01G020100 chr3D 77.412 3431 650 87 993 4359 12809432 12806063 0.000000e+00 1927.0
33 TraesCS5B01G020100 chr3D 78.705 2193 375 54 2432 4588 12751425 12749289 0.000000e+00 1378.0
34 TraesCS5B01G020100 chr3D 78.817 1978 331 54 2434 4359 12505236 12503295 0.000000e+00 1251.0
35 TraesCS5B01G020100 chr3D 78.672 783 120 28 3705 4459 12710902 12711665 1.220000e-130 477.0
36 TraesCS5B01G020100 chr1B 83.720 1812 238 32 1296 3085 631119455 631117679 0.000000e+00 1659.0
37 TraesCS5B01G020100 chr3A 79.095 1923 328 49 2434 4315 24605978 24607867 0.000000e+00 1256.0
38 TraesCS5B01G020100 chr3A 86.469 303 28 6 404 704 746320462 746320753 2.180000e-83 320.0
39 TraesCS5B01G020100 chr6A 87.009 331 26 4 78 405 203218699 203219015 1.660000e-94 357.0
40 TraesCS5B01G020100 chr6A 89.333 225 15 6 482 706 203220010 203220225 1.720000e-69 274.0
41 TraesCS5B01G020100 chr2B 84.894 331 42 5 78 405 136957909 136957584 1.300000e-85 327.0
42 TraesCS5B01G020100 chr2B 83.283 329 38 11 78 405 64997872 64998184 2.210000e-73 287.0
43 TraesCS5B01G020100 chr2B 87.556 225 15 6 481 705 415337405 415337616 1.050000e-61 248.0
44 TraesCS5B01G020100 chr2A 85.938 320 25 11 78 393 126567073 126566770 1.690000e-84 324.0
45 TraesCS5B01G020100 chr2A 88.210 229 18 5 482 709 126566098 126565878 1.040000e-66 265.0
46 TraesCS5B01G020100 chr7B 84.731 334 38 8 78 405 687546421 687546095 6.070000e-84 322.0
47 TraesCS5B01G020100 chr7B 85.484 310 29 7 404 704 687546021 687545719 4.730000e-80 309.0
48 TraesCS5B01G020100 chr7D 84.412 340 35 8 78 405 530907016 530906683 7.850000e-83 318.0
49 TraesCS5B01G020100 chr7D 81.004 279 31 14 78 354 611263757 611264015 8.250000e-48 202.0
50 TraesCS5B01G020100 chr1D 84.985 333 29 12 86 405 369912553 369912229 7.850000e-83 318.0
51 TraesCS5B01G020100 chr1D 88.125 160 11 5 78 232 472419883 472420039 2.990000e-42 183.0
52 TraesCS5B01G020100 chr1D 87.975 158 11 1 248 405 472420168 472420317 3.870000e-41 180.0
53 TraesCS5B01G020100 chr7A 88.210 229 21 3 481 709 108748812 108748590 8.020000e-68 268.0


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 TraesCS5B01G020100 chr5B 19588872 19593733 4861 False 8979.000000 8979 100.000000 1 4862 1 chr5B.!!$F1 4861
1 TraesCS5B01G020100 chr5B 19575333 19579306 3973 False 1836.550000 3576 86.473000 1 4607 2 chr5B.!!$F5 4606
2 TraesCS5B01G020100 chr5B 19672389 19678998 6609 False 1146.666667 2244 83.151667 979 4484 3 chr5B.!!$F6 3505
3 TraesCS5B01G020100 chr5B 19629327 19630485 1158 False 970.000000 970 81.980000 979 2148 1 chr5B.!!$F2 1169
4 TraesCS5B01G020100 chr5B 20813694 20814345 651 True 619.000000 619 84.067000 986 1634 1 chr5B.!!$R1 648
5 TraesCS5B01G020100 chr5A 18788996 18791983 2987 False 2843.000000 2843 84.020000 1097 4096 1 chr5A.!!$F2 2999
6 TraesCS5B01G020100 chr5A 18709652 18712501 2849 False 2187.000000 2187 80.910000 1735 4576 1 chr5A.!!$F1 2841
7 TraesCS5B01G020100 chr5A 19105487 19108317 2830 False 1276.000000 1399 82.671000 986 4042 2 chr5A.!!$F4 3056
8 TraesCS5B01G020100 chr5A 642138779 642141373 2594 False 252.500000 268 87.373500 176 706 2 chr5A.!!$F5 530
9 TraesCS5B01G020100 chr5D 27310760 27312105 1345 False 1919.000000 1919 92.506000 3519 4862 1 chr5D.!!$F2 1343
10 TraesCS5B01G020100 chr5D 27458253 27461734 3481 False 1479.000000 2217 82.213000 1097 4411 2 chr5D.!!$F5 3314
11 TraesCS5B01G020100 chr5D 27399168 27400883 1715 False 1399.000000 1399 81.687000 979 2679 1 chr5D.!!$F3 1700
12 TraesCS5B01G020100 chr5D 27426833 27439687 12854 False 1338.200000 2525 83.201800 979 4596 5 chr5D.!!$F4 3617
13 TraesCS5B01G020100 chr5D 28480471 28483301 2830 False 1295.500000 1410 82.928000 986 4042 2 chr5D.!!$F6 3056
14 TraesCS5B01G020100 chr5D 27278997 27279873 876 False 769.000000 769 82.802000 1147 2007 1 chr5D.!!$F1 860
15 TraesCS5B01G020100 chr3D 12806063 12809432 3369 True 1927.000000 1927 77.412000 993 4359 1 chr3D.!!$R3 3366
16 TraesCS5B01G020100 chr3D 12749289 12751425 2136 True 1378.000000 1378 78.705000 2432 4588 1 chr3D.!!$R2 2156
17 TraesCS5B01G020100 chr3D 12503295 12505236 1941 True 1251.000000 1251 78.817000 2434 4359 1 chr3D.!!$R1 1925
18 TraesCS5B01G020100 chr3D 12710902 12711665 763 False 477.000000 477 78.672000 3705 4459 1 chr3D.!!$F1 754
19 TraesCS5B01G020100 chr1B 631117679 631119455 1776 True 1659.000000 1659 83.720000 1296 3085 1 chr1B.!!$R1 1789
20 TraesCS5B01G020100 chr3A 24605978 24607867 1889 False 1256.000000 1256 79.095000 2434 4315 1 chr3A.!!$F1 1881
21 TraesCS5B01G020100 chr6A 203218699 203220225 1526 False 315.500000 357 88.171000 78 706 2 chr6A.!!$F1 628
22 TraesCS5B01G020100 chr2A 126565878 126567073 1195 True 294.500000 324 87.074000 78 709 2 chr2A.!!$R1 631
23 TraesCS5B01G020100 chr7B 687545719 687546421 702 True 315.500000 322 85.107500 78 704 2 chr7B.!!$R1 626

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
491 2600 0.101579 CCTTTCCCGCACAACGTTTT 59.898 50.0 0.00 0.00 41.42 2.43 F
895 3096 0.108138 GAATGACTGGGACTCCGTGG 60.108 60.0 0.00 0.00 35.24 4.94 F
1294 6110 0.971386 TACAAGTCCGGACCTTGACC 59.029 55.0 34.02 13.93 31.76 4.02 F
2164 7052 0.546122 TGACCTGTCCAGCAACAACT 59.454 50.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 6488 0.036388 CAACGTACCAGGCCAGTCAT 60.036 55.000 5.01 0.0 0.00 3.06 R
2090 6964 0.108520 TGGTAGCGTCCCGTTGAATC 60.109 55.000 0.00 0.0 0.00 2.52 R
3019 7910 1.141053 GGATTCTGGAATGTACCCGCT 59.859 52.381 0.17 0.0 0.00 5.52 R
3966 9082 0.731417 CTCTTGCTTGATGCTTCCGG 59.269 55.000 0.00 0.0 43.37 5.14 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
43 44 7.532571 TCAATCTCTTTTTGCTGTCATACATG 58.467 34.615 0.00 0.00 0.00 3.21
48 49 4.787260 TTTTGCTGTCATACATGCATGT 57.213 36.364 33.20 33.20 44.48 3.21
54 55 4.665212 CTGTCATACATGCATGTTGTTCC 58.335 43.478 35.45 19.89 41.97 3.62
61 62 3.321396 ACATGCATGTTGTTCCATGTTGA 59.679 39.130 26.61 0.00 44.05 3.18
147 148 9.661954 AGGGACTAGATTGTGAGAGATTATTAA 57.338 33.333 0.00 0.00 36.02 1.40
182 186 1.444895 GATCCCACGTACACGCGTT 60.445 57.895 10.22 3.81 43.83 4.84
216 220 0.462047 GTACAAGGCTGGTGATCGGG 60.462 60.000 4.33 0.00 0.00 5.14
237 241 4.177026 GGCCATAACTATCTACATCGCTG 58.823 47.826 0.00 0.00 0.00 5.18
242 246 1.676529 ACTATCTACATCGCTGCACGT 59.323 47.619 0.00 0.00 44.19 4.49
261 265 3.074094 ACGTCTCCATCTATACCTAGCCA 59.926 47.826 0.00 0.00 0.00 4.75
321 325 1.138859 AGGCGACGAATTCATCATCCA 59.861 47.619 6.22 0.00 0.00 3.41
323 327 1.070309 GCGACGAATTCATCATCCAGC 60.070 52.381 6.22 0.00 0.00 4.85
324 328 2.204237 CGACGAATTCATCATCCAGCA 58.796 47.619 6.22 0.00 0.00 4.41
354 365 2.352805 GCAAGTCAGGTCCCCAGG 59.647 66.667 0.00 0.00 0.00 4.45
356 367 1.679898 CAAGTCAGGTCCCCAGGTC 59.320 63.158 0.00 0.00 0.00 3.85
357 368 1.539124 AAGTCAGGTCCCCAGGTCC 60.539 63.158 0.00 0.00 0.00 4.46
358 369 3.009714 GTCAGGTCCCCAGGTCCC 61.010 72.222 0.00 0.00 31.29 4.46
359 370 4.348495 TCAGGTCCCCAGGTCCCC 62.348 72.222 0.00 0.00 31.29 4.81
361 372 4.354943 AGGTCCCCAGGTCCCCAG 62.355 72.222 0.00 0.00 31.29 4.45
369 380 1.997311 CAGGTCCCCAGCAGATCCA 60.997 63.158 0.00 0.00 0.00 3.41
406 417 2.512515 GGCTAGCCGCTCACAAGG 60.513 66.667 20.16 0.00 39.13 3.61
407 418 2.579201 GCTAGCCGCTCACAAGGA 59.421 61.111 2.29 0.00 35.14 3.36
409 420 0.878086 GCTAGCCGCTCACAAGGATC 60.878 60.000 2.29 0.00 35.14 3.36
413 424 0.872021 GCCGCTCACAAGGATCGTAG 60.872 60.000 0.00 0.00 33.44 3.51
414 425 0.872021 CCGCTCACAAGGATCGTAGC 60.872 60.000 0.00 0.00 33.44 3.58
415 426 0.179137 CGCTCACAAGGATCGTAGCA 60.179 55.000 8.24 0.00 30.81 3.49
416 427 1.735700 CGCTCACAAGGATCGTAGCAA 60.736 52.381 8.24 0.00 30.81 3.91
417 428 2.346803 GCTCACAAGGATCGTAGCAAA 58.653 47.619 3.59 0.00 0.00 3.68
420 431 3.531538 TCACAAGGATCGTAGCAAATCC 58.468 45.455 0.00 0.00 41.56 3.01
431 2479 8.283291 GGATCGTAGCAAATCCTACATAAAAAG 58.717 37.037 0.00 0.00 38.74 2.27
452 2528 4.662968 AGAGGATCGTAGCATCTAGCACG 61.663 52.174 0.00 0.00 44.21 5.34
472 2581 3.107017 GGCACCACGCATTCTTTTC 57.893 52.632 0.00 0.00 45.17 2.29
473 2582 0.388520 GGCACCACGCATTCTTTTCC 60.389 55.000 0.00 0.00 45.17 3.13
474 2583 0.598065 GCACCACGCATTCTTTTCCT 59.402 50.000 0.00 0.00 41.79 3.36
476 2585 2.545742 GCACCACGCATTCTTTTCCTTT 60.546 45.455 0.00 0.00 41.79 3.11
477 2586 3.308530 CACCACGCATTCTTTTCCTTTC 58.691 45.455 0.00 0.00 0.00 2.62
478 2587 2.296190 ACCACGCATTCTTTTCCTTTCC 59.704 45.455 0.00 0.00 0.00 3.13
480 2589 1.539827 ACGCATTCTTTTCCTTTCCCG 59.460 47.619 0.00 0.00 0.00 5.14
481 2590 1.732405 CGCATTCTTTTCCTTTCCCGC 60.732 52.381 0.00 0.00 0.00 6.13
482 2591 1.272212 GCATTCTTTTCCTTTCCCGCA 59.728 47.619 0.00 0.00 0.00 5.69
484 2593 2.060050 TTCTTTTCCTTTCCCGCACA 57.940 45.000 0.00 0.00 0.00 4.57
485 2594 2.060050 TCTTTTCCTTTCCCGCACAA 57.940 45.000 0.00 0.00 0.00 3.33
487 2596 0.382515 TTTTCCTTTCCCGCACAACG 59.617 50.000 0.00 0.00 43.15 4.10
489 2598 0.748729 TTCCTTTCCCGCACAACGTT 60.749 50.000 0.00 0.00 41.42 3.99
490 2599 0.748729 TCCTTTCCCGCACAACGTTT 60.749 50.000 0.00 0.00 41.42 3.60
491 2600 0.101579 CCTTTCCCGCACAACGTTTT 59.898 50.000 0.00 0.00 41.42 2.43
520 2629 3.570125 TCTTGGAGCGATCGATCAGTATT 59.430 43.478 31.78 5.16 31.28 1.89
551 2747 8.106247 TGTGTGTAGCAATCGATCTGTATATA 57.894 34.615 0.00 0.00 0.00 0.86
573 2769 0.242825 CGATCTGTGTACACGTGGGT 59.757 55.000 21.57 9.85 0.00 4.51
717 2915 3.070018 AGCCAATTCTGTCGAGTTTCAG 58.930 45.455 0.00 0.00 0.00 3.02
725 2923 5.959618 TCTGTCGAGTTTCAGAGACATTA 57.040 39.130 0.00 0.00 41.92 1.90
772 2971 2.568623 AACCGGCAGAGTTTCAATCT 57.431 45.000 0.00 0.00 0.00 2.40
855 3056 3.374745 CACAGTCAGTGCCACAAAATTC 58.625 45.455 0.00 0.00 42.15 2.17
858 3059 4.275936 ACAGTCAGTGCCACAAAATTCTAC 59.724 41.667 0.00 0.00 0.00 2.59
863 3064 3.252458 AGTGCCACAAAATTCTACGAACC 59.748 43.478 0.00 0.00 0.00 3.62
864 3065 3.003897 GTGCCACAAAATTCTACGAACCA 59.996 43.478 0.00 0.00 0.00 3.67
867 3068 4.498345 GCCACAAAATTCTACGAACCACAA 60.498 41.667 0.00 0.00 0.00 3.33
884 3085 5.835257 ACCACAAACTTGATTGAATGACTG 58.165 37.500 0.00 0.00 34.38 3.51
885 3086 5.221303 ACCACAAACTTGATTGAATGACTGG 60.221 40.000 0.00 0.00 34.38 4.00
890 3091 4.583871 ACTTGATTGAATGACTGGGACTC 58.416 43.478 0.00 0.00 0.00 3.36
891 3092 3.634397 TGATTGAATGACTGGGACTCC 57.366 47.619 0.00 0.00 0.00 3.85
894 3095 0.608130 TGAATGACTGGGACTCCGTG 59.392 55.000 0.00 0.00 35.24 4.94
895 3096 0.108138 GAATGACTGGGACTCCGTGG 60.108 60.000 0.00 0.00 35.24 4.94
897 3098 3.391382 GACTGGGACTCCGTGGGG 61.391 72.222 0.00 0.00 35.24 4.96
901 3102 3.155167 GGGACTCCGTGGGGCTAG 61.155 72.222 0.00 0.00 0.00 3.42
904 3105 2.683933 ACTCCGTGGGGCTAGTGG 60.684 66.667 0.00 0.00 0.00 4.00
905 3106 2.683933 CTCCGTGGGGCTAGTGGT 60.684 66.667 0.00 0.00 0.00 4.16
942 3150 2.168521 TCTTGTAGTATGGCTCTGGTGC 59.831 50.000 0.00 0.00 0.00 5.01
952 3160 1.943340 GGCTCTGGTGCATAGCTAAAC 59.057 52.381 0.00 0.00 34.64 2.01
953 3161 1.943340 GCTCTGGTGCATAGCTAAACC 59.057 52.381 13.93 13.93 32.09 3.27
958 3166 2.158813 TGGTGCATAGCTAAACCCTAGC 60.159 50.000 16.73 0.00 40.67 3.42
1007 5734 2.502142 TGTTCTTCCAGCATGCATCT 57.498 45.000 21.98 0.00 31.97 2.90
1014 5741 1.003928 TCCAGCATGCATCTCACAACT 59.996 47.619 21.98 0.00 31.97 3.16
1063 5803 9.269453 TCATCATAAGCATCACTTCATCTTTAG 57.731 33.333 0.00 0.00 39.97 1.85
1213 5963 1.925415 GCACGGACATGATTGCTGCA 61.925 55.000 0.00 0.00 32.00 4.41
1294 6110 0.971386 TACAAGTCCGGACCTTGACC 59.029 55.000 34.02 13.93 31.76 4.02
1304 6123 2.127708 GGACCTTGACCCCTATGATGT 58.872 52.381 0.00 0.00 0.00 3.06
1350 6171 1.539827 GGCGAGATAAGCTCCTCTCTC 59.460 57.143 18.29 12.82 40.70 3.20
1412 6236 4.382386 ACTGTTTAGGGCCAAATAGTGT 57.618 40.909 21.04 5.47 38.12 3.55
1509 6334 3.786553 TCCTTCTCAGCTTGGTAACCTA 58.213 45.455 0.00 0.00 0.00 3.08
1515 6340 7.202047 CCTTCTCAGCTTGGTAACCTATCTAAT 60.202 40.741 0.00 0.00 0.00 1.73
1538 6363 1.202268 GCAGCATCTTGATCTTGGCAC 60.202 52.381 0.00 0.00 0.00 5.01
1540 6365 1.065926 AGCATCTTGATCTTGGCACGA 60.066 47.619 0.00 0.00 0.00 4.35
1544 6375 2.688507 TCTTGATCTTGGCACGAGTTC 58.311 47.619 0.00 0.00 0.00 3.01
1556 6396 2.856557 GCACGAGTTCTTATTACGGGAC 59.143 50.000 0.00 0.00 0.00 4.46
1557 6397 3.674138 GCACGAGTTCTTATTACGGGACA 60.674 47.826 0.00 0.00 0.00 4.02
1623 6471 5.817816 GCAGTACCTTAGTATGAGCACAATT 59.182 40.000 0.00 0.00 0.00 2.32
1636 6484 5.188434 TGAGCACAATTAATCTCTCAAGGG 58.812 41.667 4.17 0.00 0.00 3.95
1638 6486 4.946157 AGCACAATTAATCTCTCAAGGGTG 59.054 41.667 0.00 0.00 0.00 4.61
1640 6488 5.500234 CACAATTAATCTCTCAAGGGTGGA 58.500 41.667 0.00 0.00 0.00 4.02
1671 6519 4.447724 CCTGGTACGTTGAATATGATTCCG 59.552 45.833 0.00 0.00 0.00 4.30
1679 6527 7.262772 ACGTTGAATATGATTCCGTCTCTAAA 58.737 34.615 0.00 0.00 0.00 1.85
1792 6640 3.815401 CGGGAATAATTTAGGCCACTCAG 59.185 47.826 5.01 0.00 0.00 3.35
1815 6663 3.791245 TGCATCAAGTTGGTTTTGGAAC 58.209 40.909 2.34 0.00 34.96 3.62
1821 6669 4.458295 TCAAGTTGGTTTTGGAACGTAACA 59.542 37.500 2.34 0.00 36.65 2.41
1837 6685 4.454504 ACGTAACAAGCCTCAAATACCTTG 59.545 41.667 0.00 0.00 40.26 3.61
1861 6721 3.839490 TCTTGGTGGGACTCGGTTATTTA 59.161 43.478 0.00 0.00 0.00 1.40
1862 6722 3.615224 TGGTGGGACTCGGTTATTTAC 57.385 47.619 0.00 0.00 0.00 2.01
1893 6753 3.997021 CAGACACACTAGGAAACATGACC 59.003 47.826 0.00 0.00 0.00 4.02
1924 6784 5.625150 AGGTACTTGATTTGTCAGAAAGCT 58.375 37.500 0.00 0.00 27.25 3.74
1925 6785 5.703130 AGGTACTTGATTTGTCAGAAAGCTC 59.297 40.000 0.00 0.00 27.25 4.09
1936 6805 3.195396 GTCAGAAAGCTCTCTGGATGAGT 59.805 47.826 16.95 0.00 42.68 3.41
1956 6825 6.289064 TGAGTCTGGAAACCTTAAAAGTCTC 58.711 40.000 0.00 0.00 0.00 3.36
2013 6882 7.184862 ACCTCTCTGGAAATTTTATGAATGGT 58.815 34.615 0.00 0.00 39.71 3.55
2026 6898 7.609760 TTTATGAATGGTGATATACGGATGC 57.390 36.000 0.00 0.00 0.00 3.91
2027 6899 3.937814 TGAATGGTGATATACGGATGCC 58.062 45.455 0.00 0.00 0.00 4.40
2089 6963 2.231964 GAGCTGCATTTCCATGGAAACA 59.768 45.455 36.31 28.61 45.34 2.83
2130 7018 7.675161 ACCAAATTTTATAGGGGAATTCAGG 57.325 36.000 7.93 0.00 0.00 3.86
2133 7021 7.565029 CCAAATTTTATAGGGGAATTCAGGAGT 59.435 37.037 7.93 0.00 0.00 3.85
2139 7027 2.989571 AGGGGAATTCAGGAGTTTGAGT 59.010 45.455 7.93 0.00 0.00 3.41
2140 7028 3.084786 GGGGAATTCAGGAGTTTGAGTG 58.915 50.000 7.93 0.00 0.00 3.51
2164 7052 0.546122 TGACCTGTCCAGCAACAACT 59.454 50.000 0.00 0.00 0.00 3.16
2226 7114 5.351465 GCGTTTAACCAATCTTGATCTCAGA 59.649 40.000 0.00 0.00 0.00 3.27
2242 7130 8.071177 TGATCTCAGACAGAATCAACTCAATA 57.929 34.615 0.00 0.00 33.62 1.90
2252 7143 8.497745 ACAGAATCAACTCAATAGGATACCAAT 58.502 33.333 0.00 0.00 37.17 3.16
2253 7144 8.997323 CAGAATCAACTCAATAGGATACCAATC 58.003 37.037 0.00 0.00 37.17 2.67
2297 7188 4.019411 TCTGACTTATTTGGACATGAGCCA 60.019 41.667 0.00 3.54 0.00 4.75
2366 7257 4.756135 GCATTTGGCATTCCTTTTTCTTGA 59.244 37.500 0.00 0.00 43.97 3.02
2377 7268 7.883229 TTCCTTTTTCTTGAAGACAACAAAC 57.117 32.000 0.00 0.00 32.27 2.93
2416 7307 5.711976 CCACCAGAGGTTATGAATTCAACTT 59.288 40.000 13.09 3.26 31.02 2.66
2449 7340 4.479056 TCCTAGACCTCTCCAGTAATCACT 59.521 45.833 0.00 0.00 34.42 3.41
2525 7416 5.657302 TGGACCTAAGCAAAAACAACCTTAA 59.343 36.000 0.00 0.00 0.00 1.85
2544 7435 2.680312 ATGGTGTGATCACGGAAGAG 57.320 50.000 20.54 0.00 44.68 2.85
2574 7465 8.592105 TTGCAAATCTAAAAGGTTTGAAGATG 57.408 30.769 15.12 0.00 35.43 2.90
2631 7522 2.019984 GATTCAAATTGGCGCTCTCCT 58.980 47.619 7.64 0.00 0.00 3.69
2651 7542 3.307059 CCTTTTAGGCTACAGTCTGCAGT 60.307 47.826 14.67 0.00 0.00 4.40
2686 7577 3.397618 TCAAATGGGTCCTCTCTTTCCAA 59.602 43.478 0.00 0.00 0.00 3.53
2758 7649 5.307196 ACAGCTTTAGAGGACAAGTTTCCTA 59.693 40.000 6.59 0.00 46.80 2.94
2785 7676 7.589958 TGGTTTTGGTATACATTTTCACAGT 57.410 32.000 5.01 0.00 0.00 3.55
2823 7714 7.458397 ACATCTCTAACAACCAAATAAGTGGA 58.542 34.615 0.00 0.00 41.65 4.02
2834 7725 3.439857 AATAAGTGGAAGCTTGCCAGA 57.560 42.857 15.98 6.15 35.77 3.86
2835 7726 2.479566 TAAGTGGAAGCTTGCCAGAG 57.520 50.000 15.98 0.00 35.77 3.35
2852 7743 1.990327 AGAGCATATGGATGGCATGGA 59.010 47.619 3.81 0.00 33.26 3.41
2910 7801 2.614057 CGGGTCAATACCTTCATTGCTC 59.386 50.000 0.00 0.00 45.95 4.26
2957 7848 6.840780 ATCCAACAATAACTTTTCAGGAGG 57.159 37.500 0.00 0.00 0.00 4.30
3067 7958 6.651755 GCAAATTGCAGCAACTATTGTATT 57.348 33.333 21.91 6.35 44.26 1.89
3085 7976 5.764131 TGTATTTGGATTTGTCGAACAACC 58.236 37.500 0.00 0.00 37.90 3.77
3117 8008 4.996758 GGTGAAATTCCTCAATGTTTTGGG 59.003 41.667 0.00 0.00 33.44 4.12
3264 8155 4.820775 TGCCTACTTGGATAGGAGATCTT 58.179 43.478 0.00 0.00 44.12 2.40
3268 8159 5.480073 CCTACTTGGATAGGAGATCTTGAGG 59.520 48.000 0.00 0.00 44.12 3.86
3314 8205 6.421801 GGCCACAATGCATTTTCTGATAATAC 59.578 38.462 9.83 0.00 0.00 1.89
3341 8232 3.195661 CCGACATAACAAGCCTTAGGTC 58.804 50.000 0.00 0.00 35.17 3.85
3342 8432 3.195661 CGACATAACAAGCCTTAGGTCC 58.804 50.000 0.00 0.00 35.10 4.46
3352 8442 2.434702 AGCCTTAGGTCCCTTCAATACG 59.565 50.000 0.00 0.00 0.00 3.06
3474 8567 9.956640 GATGATAGATTTATTGGAACCTCAGAT 57.043 33.333 0.00 0.00 0.00 2.90
3488 8581 7.567250 TGGAACCTCAGATATTCATGGTAGTTA 59.433 37.037 0.00 0.00 0.00 2.24
3492 8585 8.370940 ACCTCAGATATTCATGGTAGTTACATG 58.629 37.037 0.00 0.00 45.39 3.21
3493 8586 7.821359 CCTCAGATATTCATGGTAGTTACATGG 59.179 40.741 0.00 0.00 44.42 3.66
3494 8587 8.491045 TCAGATATTCATGGTAGTTACATGGA 57.509 34.615 0.00 0.00 44.42 3.41
3495 8588 8.933653 TCAGATATTCATGGTAGTTACATGGAA 58.066 33.333 0.00 0.00 44.42 3.53
3496 8589 9.730705 CAGATATTCATGGTAGTTACATGGAAT 57.269 33.333 0.00 6.85 44.42 3.01
3500 8593 5.690865 TCATGGTAGTTACATGGAATTCCC 58.309 41.667 21.90 5.06 44.42 3.97
3501 8594 5.431731 TCATGGTAGTTACATGGAATTCCCT 59.568 40.000 21.90 9.42 44.42 4.20
3502 8595 5.110814 TGGTAGTTACATGGAATTCCCTG 57.889 43.478 23.66 23.66 37.61 4.45
3503 8596 4.538490 TGGTAGTTACATGGAATTCCCTGT 59.462 41.667 30.42 30.42 45.02 4.00
3537 8630 5.069251 AGGTCACCTAGGAGAAATATTGTCG 59.931 44.000 17.98 0.00 28.47 4.35
3628 8727 5.763204 TCAGTAAACTCCTTGATTGGTGAAC 59.237 40.000 0.00 0.00 0.00 3.18
3633 8732 2.040278 CTCCTTGATTGGTGAACTCCCA 59.960 50.000 0.00 0.00 0.00 4.37
3697 8796 7.773489 TTATCATCCAACAAATTGAGTGGAA 57.227 32.000 20.67 10.53 38.13 3.53
3774 8873 4.518211 CAGAACAAGCTCTCTGGTGAAATT 59.482 41.667 10.99 0.00 36.27 1.82
3825 8924 1.722011 CCGCGTTGAACTTGTCCTAT 58.278 50.000 4.92 0.00 0.00 2.57
3865 8978 2.337359 ACCCTCTAGCCCTTAACACA 57.663 50.000 0.00 0.00 0.00 3.72
4000 9116 2.746472 GCAAGAGTTTGACCCACTGACT 60.746 50.000 0.00 0.00 36.36 3.41
4019 9135 6.657541 ACTGACTTTTTACTTTGGTCTTGTGA 59.342 34.615 0.00 0.00 0.00 3.58
4132 9248 7.316640 AGGCGTATGATCAACTCTATGTATTC 58.683 38.462 0.00 0.00 0.00 1.75
4188 9304 6.215845 ACACAACCACAGAATAAGCATTTTC 58.784 36.000 0.00 0.00 0.00 2.29
4189 9305 5.634859 CACAACCACAGAATAAGCATTTTCC 59.365 40.000 0.00 0.00 0.00 3.13
4224 9345 1.601759 GTGTCTGTGCTGCACCCAT 60.602 57.895 28.17 0.00 32.73 4.00
4225 9346 1.601477 TGTCTGTGCTGCACCCATG 60.601 57.895 28.17 15.93 32.73 3.66
4377 9546 9.938280 ACTATTGTAGTACATGCAAGACTTAAA 57.062 29.630 3.28 0.00 36.91 1.52
4519 9694 5.351189 GTGTTTTTCTTTGTTGCAAGATGGT 59.649 36.000 0.00 0.00 0.00 3.55
4607 9836 4.606210 TGTGAGGTACTGCTCCATTACTA 58.394 43.478 0.00 0.00 41.55 1.82
4639 9868 4.290711 TGCTTGGATCATTCAGACTTCA 57.709 40.909 0.00 0.00 0.00 3.02
4698 9929 5.464168 ACTTGGATGAAAATTTTGCTCTCG 58.536 37.500 8.47 1.34 0.00 4.04
4703 9934 3.836949 TGAAAATTTTGCTCTCGCCATC 58.163 40.909 8.47 0.00 34.43 3.51
4725 9956 5.771469 TCTGCAGAAACCAATTTATGTGTG 58.229 37.500 15.67 0.00 38.92 3.82
4766 9997 9.457436 GATTGGGTTTTCTCTGGTAATTAAGTA 57.543 33.333 0.00 0.00 0.00 2.24
4791 11246 3.264193 TGTGCTTGGTATTCAGATCAGGT 59.736 43.478 0.00 0.00 0.00 4.00
4796 11251 1.473257 GGTATTCAGATCAGGTGCGCA 60.473 52.381 5.66 5.66 0.00 6.09
4822 11277 8.428063 ACTCCCAATCTATGAAACATAAGAGAG 58.572 37.037 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.866480 TGACAGCAAAAAGAGATTGAAAACT 58.134 32.000 0.00 0.00 0.00 2.66
14 15 7.704789 ATGACAGCAAAAAGAGATTGAAAAC 57.295 32.000 0.00 0.00 0.00 2.43
54 55 6.646653 TCAGCTGTACTAGAGTTTTCAACATG 59.353 38.462 14.67 0.00 0.00 3.21
142 143 9.574516 GGATCTTCTTTTTCCCTAGCATTAATA 57.425 33.333 0.00 0.00 0.00 0.98
147 148 4.797743 GGGATCTTCTTTTTCCCTAGCAT 58.202 43.478 0.00 0.00 44.86 3.79
182 186 5.659525 AGCCTTGTACCTGTACATGTATACA 59.340 40.000 9.18 8.27 44.54 2.29
205 209 0.469917 AGTTATGGCCCGATCACCAG 59.530 55.000 0.00 0.00 39.88 4.00
216 220 3.614616 GCAGCGATGTAGATAGTTATGGC 59.385 47.826 1.22 0.00 0.00 4.40
237 241 3.119779 GCTAGGTATAGATGGAGACGTGC 60.120 52.174 0.00 0.00 0.00 5.34
242 246 5.222337 TGTGATGGCTAGGTATAGATGGAGA 60.222 44.000 0.00 0.00 0.00 3.71
261 265 1.747709 GCTGCCTGATGAGTTGTGAT 58.252 50.000 0.00 0.00 0.00 3.06
284 288 2.365105 TAGGGTTGAGGAGGCGGG 60.365 66.667 0.00 0.00 0.00 6.13
354 365 1.341383 ACATTTGGATCTGCTGGGGAC 60.341 52.381 0.00 0.00 0.00 4.46
356 367 1.753073 GAACATTTGGATCTGCTGGGG 59.247 52.381 0.00 0.00 0.00 4.96
357 368 2.426024 CTGAACATTTGGATCTGCTGGG 59.574 50.000 0.00 0.00 0.00 4.45
358 369 2.426024 CCTGAACATTTGGATCTGCTGG 59.574 50.000 0.00 0.00 0.00 4.85
359 370 2.159282 GCCTGAACATTTGGATCTGCTG 60.159 50.000 0.00 0.00 0.00 4.41
361 372 1.202222 CGCCTGAACATTTGGATCTGC 60.202 52.381 0.00 0.00 0.00 4.26
406 417 9.042008 TCTTTTTATGTAGGATTTGCTACGATC 57.958 33.333 5.02 0.00 0.00 3.69
407 418 8.958119 TCTTTTTATGTAGGATTTGCTACGAT 57.042 30.769 5.02 3.28 0.00 3.73
409 420 7.494625 TCCTCTTTTTATGTAGGATTTGCTACG 59.505 37.037 5.02 0.00 33.18 3.51
413 424 7.012421 ACGATCCTCTTTTTATGTAGGATTTGC 59.988 37.037 4.33 0.00 46.48 3.68
414 425 8.438676 ACGATCCTCTTTTTATGTAGGATTTG 57.561 34.615 4.33 3.75 46.48 2.32
415 426 9.765795 CTACGATCCTCTTTTTATGTAGGATTT 57.234 33.333 4.33 0.00 46.48 2.17
416 427 7.873505 GCTACGATCCTCTTTTTATGTAGGATT 59.126 37.037 4.33 0.00 46.48 3.01
420 431 8.085296 AGATGCTACGATCCTCTTTTTATGTAG 58.915 37.037 0.00 0.00 33.09 2.74
422 433 6.821388 AGATGCTACGATCCTCTTTTTATGT 58.179 36.000 0.00 0.00 0.00 2.29
423 434 7.062839 GCTAGATGCTACGATCCTCTTTTTATG 59.937 40.741 0.00 0.00 38.95 1.90
431 2479 2.413502 CGTGCTAGATGCTACGATCCTC 60.414 54.545 0.00 0.00 43.50 3.71
452 2528 1.815817 AAAAGAATGCGTGGTGCCCC 61.816 55.000 0.00 0.00 45.60 5.80
464 2573 2.593026 TGTGCGGGAAAGGAAAAGAAT 58.407 42.857 0.00 0.00 0.00 2.40
467 2576 1.599419 CGTTGTGCGGGAAAGGAAAAG 60.599 52.381 0.00 0.00 36.85 2.27
469 2578 0.748729 ACGTTGTGCGGGAAAGGAAA 60.749 50.000 0.00 0.00 46.52 3.13
470 2579 0.748729 AACGTTGTGCGGGAAAGGAA 60.749 50.000 0.00 0.00 46.52 3.36
471 2580 0.748729 AAACGTTGTGCGGGAAAGGA 60.749 50.000 0.00 0.00 46.52 3.36
472 2581 0.101579 AAAACGTTGTGCGGGAAAGG 59.898 50.000 0.00 0.00 46.52 3.11
473 2582 1.064952 AGAAAACGTTGTGCGGGAAAG 59.935 47.619 0.00 0.00 46.52 2.62
474 2583 1.096416 AGAAAACGTTGTGCGGGAAA 58.904 45.000 0.00 0.00 46.52 3.13
476 2585 1.096416 AAAGAAAACGTTGTGCGGGA 58.904 45.000 0.00 0.00 46.52 5.14
477 2586 1.849829 GAAAAGAAAACGTTGTGCGGG 59.150 47.619 0.00 0.00 46.52 6.13
478 2587 2.781646 GAGAAAAGAAAACGTTGTGCGG 59.218 45.455 0.00 0.00 46.52 5.69
480 2589 4.265320 CCAAGAGAAAAGAAAACGTTGTGC 59.735 41.667 0.00 0.00 0.00 4.57
481 2590 5.636837 TCCAAGAGAAAAGAAAACGTTGTG 58.363 37.500 0.00 0.00 0.00 3.33
482 2591 5.676331 GCTCCAAGAGAAAAGAAAACGTTGT 60.676 40.000 0.00 0.00 0.00 3.32
484 2593 4.495844 CGCTCCAAGAGAAAAGAAAACGTT 60.496 41.667 0.00 0.00 0.00 3.99
485 2594 3.002348 CGCTCCAAGAGAAAAGAAAACGT 59.998 43.478 0.00 0.00 0.00 3.99
487 2596 4.813296 TCGCTCCAAGAGAAAAGAAAAC 57.187 40.909 0.00 0.00 0.00 2.43
489 2598 3.679980 CGATCGCTCCAAGAGAAAAGAAA 59.320 43.478 0.26 0.00 0.00 2.52
490 2599 3.056821 TCGATCGCTCCAAGAGAAAAGAA 60.057 43.478 11.09 0.00 0.00 2.52
491 2600 2.492088 TCGATCGCTCCAAGAGAAAAGA 59.508 45.455 11.09 0.00 0.00 2.52
520 2629 3.723260 TCGATTGCTACACACAGAACAA 58.277 40.909 0.00 0.00 0.00 2.83
551 2747 2.098607 CCCACGTGTACACAGATCGTAT 59.901 50.000 24.98 0.00 33.49 3.06
553 2749 0.242825 CCCACGTGTACACAGATCGT 59.757 55.000 24.98 14.08 35.12 3.73
557 2753 0.390124 GGAACCCACGTGTACACAGA 59.610 55.000 24.98 0.00 0.00 3.41
573 2769 4.526650 GTGCTAGGGGAAAATGAAAAGGAA 59.473 41.667 0.00 0.00 0.00 3.36
698 2896 4.387256 GTCTCTGAAACTCGACAGAATTGG 59.613 45.833 5.15 0.00 41.58 3.16
706 2904 8.912787 TTCTTATAATGTCTCTGAAACTCGAC 57.087 34.615 0.00 0.00 0.00 4.20
736 2934 3.687698 CCGGTTAGTGTATTCCACCAAAG 59.312 47.826 0.00 0.00 45.74 2.77
746 2944 3.259876 TGAAACTCTGCCGGTTAGTGTAT 59.740 43.478 1.90 0.00 0.00 2.29
749 2947 2.163818 TGAAACTCTGCCGGTTAGTG 57.836 50.000 1.90 5.86 0.00 2.74
750 2948 2.922740 TTGAAACTCTGCCGGTTAGT 57.077 45.000 1.90 0.93 0.00 2.24
757 2956 4.074970 TCCAAAGAGATTGAAACTCTGCC 58.925 43.478 5.72 0.00 42.85 4.85
772 2971 8.413229 CCTAAACATTCTCTTTTTGTCCAAAGA 58.587 33.333 0.00 0.00 39.91 2.52
855 3056 5.666969 TCAATCAAGTTTGTGGTTCGTAG 57.333 39.130 0.00 0.00 0.00 3.51
858 3059 5.399301 GTCATTCAATCAAGTTTGTGGTTCG 59.601 40.000 0.00 0.00 0.00 3.95
863 3064 5.009911 TCCCAGTCATTCAATCAAGTTTGTG 59.990 40.000 0.00 0.00 0.00 3.33
864 3065 5.010012 GTCCCAGTCATTCAATCAAGTTTGT 59.990 40.000 0.00 0.00 0.00 2.83
867 3068 4.990526 AGTCCCAGTCATTCAATCAAGTT 58.009 39.130 0.00 0.00 0.00 2.66
884 3085 3.155167 CTAGCCCCACGGAGTCCC 61.155 72.222 2.80 0.00 41.61 4.46
885 3086 2.363925 ACTAGCCCCACGGAGTCC 60.364 66.667 0.00 0.00 41.61 3.85
890 3091 1.275291 CATATACCACTAGCCCCACGG 59.725 57.143 0.00 0.00 0.00 4.94
891 3092 1.275291 CCATATACCACTAGCCCCACG 59.725 57.143 0.00 0.00 0.00 4.94
894 3095 0.618981 GGCCATATACCACTAGCCCC 59.381 60.000 0.00 0.00 34.23 5.80
895 3096 1.358152 TGGCCATATACCACTAGCCC 58.642 55.000 0.00 0.00 39.72 5.19
897 3098 3.815809 TGTTTGGCCATATACCACTAGC 58.184 45.455 6.09 0.00 36.76 3.42
899 3100 5.606749 AGAGATGTTTGGCCATATACCACTA 59.393 40.000 6.09 0.00 36.76 2.74
901 3102 4.718961 AGAGATGTTTGGCCATATACCAC 58.281 43.478 6.09 2.81 36.76 4.16
904 3105 6.992715 ACTACAAGAGATGTTTGGCCATATAC 59.007 38.462 6.09 6.22 43.63 1.47
905 3106 7.136822 ACTACAAGAGATGTTTGGCCATATA 57.863 36.000 6.09 0.00 43.63 0.86
942 3150 1.608283 GGCGGCTAGGGTTTAGCTATG 60.608 57.143 0.00 0.00 40.25 2.23
976 3184 2.087646 GGAAGAACAAGAGATGGGTGC 58.912 52.381 0.00 0.00 0.00 5.01
1007 5734 5.758296 GTGGTGAACAAGAGATTAGTTGTGA 59.242 40.000 0.00 0.00 36.98 3.58
1014 5741 5.560722 TGAAGGTGGTGAACAAGAGATTA 57.439 39.130 0.00 0.00 0.00 1.75
1213 5963 2.231380 AATGAACGCCCCTCCACCT 61.231 57.895 0.00 0.00 0.00 4.00
1294 6110 2.531522 TCATCGCACACATCATAGGG 57.468 50.000 0.00 0.00 0.00 3.53
1304 6123 4.261280 CCAATGAATTAGCATCATCGCACA 60.261 41.667 0.00 0.00 36.53 4.57
1350 6171 3.876320 GCTCTAGATGCTTCAAGGAAAGG 59.124 47.826 2.07 0.00 0.00 3.11
1412 6236 3.054361 GGAGCCCAAGAACTGAGGAATAA 60.054 47.826 0.00 0.00 0.00 1.40
1509 6334 7.426410 CAAGATCAAGATGCTGCAAATTAGAT 58.574 34.615 6.36 7.03 0.00 1.98
1515 6340 2.094390 GCCAAGATCAAGATGCTGCAAA 60.094 45.455 6.36 0.00 0.00 3.68
1538 6363 7.143340 TGAATATGTCCCGTAATAAGAACTCG 58.857 38.462 0.00 0.00 0.00 4.18
1540 6365 9.273016 CATTGAATATGTCCCGTAATAAGAACT 57.727 33.333 0.00 0.00 0.00 3.01
1544 6375 8.792830 ATCCATTGAATATGTCCCGTAATAAG 57.207 34.615 0.00 0.00 0.00 1.73
1623 6471 4.406972 CAGTCATCCACCCTTGAGAGATTA 59.593 45.833 0.00 0.00 0.00 1.75
1636 6484 0.107654 GTACCAGGCCAGTCATCCAC 60.108 60.000 5.01 0.00 0.00 4.02
1638 6486 1.144057 CGTACCAGGCCAGTCATCC 59.856 63.158 5.01 0.00 0.00 3.51
1640 6488 0.036388 CAACGTACCAGGCCAGTCAT 60.036 55.000 5.01 0.00 0.00 3.06
1671 6519 7.466590 GCAGCAAGATTGATAACCTTTAGAGAC 60.467 40.741 0.00 0.00 0.00 3.36
1679 6527 3.067742 GCATGCAGCAAGATTGATAACCT 59.932 43.478 14.21 0.00 44.79 3.50
1792 6640 3.791245 TCCAAAACCAACTTGATGCAAC 58.209 40.909 0.00 0.00 0.00 4.17
1815 6663 4.142687 CCAAGGTATTTGAGGCTTGTTACG 60.143 45.833 0.00 0.00 39.21 3.18
1821 6669 4.082125 CAAGACCAAGGTATTTGAGGCTT 58.918 43.478 9.25 0.00 39.21 4.35
1837 6685 1.765597 AACCGAGTCCCACCAAGACC 61.766 60.000 0.00 0.00 34.67 3.85
1861 6721 5.690865 TCCTAGTGTGTCTGGAAATTTTGT 58.309 37.500 0.00 0.00 0.00 2.83
1862 6722 6.633500 TTCCTAGTGTGTCTGGAAATTTTG 57.367 37.500 0.00 0.00 33.66 2.44
1936 6805 5.906772 AGGAGACTTTTAAGGTTTCCAGA 57.093 39.130 16.70 0.00 39.51 3.86
1956 6825 7.784633 TTCCAAACAGCAAAGATTTTTAAGG 57.215 32.000 0.00 0.00 0.00 2.69
2026 6898 4.113815 TGGCAAGCCCTCCATCGG 62.114 66.667 8.89 0.00 34.56 4.18
2027 6899 2.825836 GTGGCAAGCCCTCCATCG 60.826 66.667 8.89 0.00 34.47 3.84
2037 6909 2.277692 CATGCGCATCGTGGCAAG 60.278 61.111 22.51 2.32 43.26 4.01
2065 6939 1.033746 CCATGGAAATGCAGCTCCGT 61.034 55.000 5.56 8.66 34.14 4.69
2089 6963 0.175073 GGTAGCGTCCCGTTGAATCT 59.825 55.000 0.00 0.00 0.00 2.40
2090 6964 0.108520 TGGTAGCGTCCCGTTGAATC 60.109 55.000 0.00 0.00 0.00 2.52
2096 6970 1.900245 AAAATTTGGTAGCGTCCCGT 58.100 45.000 0.00 0.00 0.00 5.28
2103 6991 8.245195 TGAATTCCCCTATAAAATTTGGTAGC 57.755 34.615 2.27 0.00 0.00 3.58
2130 7018 2.289002 CAGGTCAAGCACACTCAAACTC 59.711 50.000 0.00 0.00 0.00 3.01
2133 7021 2.288666 GACAGGTCAAGCACACTCAAA 58.711 47.619 0.00 0.00 0.00 2.69
2164 7052 1.271108 TGGCGGTATGAGCTCAACAAA 60.271 47.619 22.50 3.83 34.52 2.83
2171 7059 3.866582 GCCCTGGCGGTATGAGCT 61.867 66.667 0.00 0.00 34.52 4.09
2226 7114 7.437713 TGGTATCCTATTGAGTTGATTCTGT 57.562 36.000 0.00 0.00 0.00 3.41
2297 7188 5.701290 GCTATACTTCCAGTCAAGTTGTTGT 59.299 40.000 2.11 0.00 37.75 3.32
2320 7211 2.226437 TCAATTTTCCAAGCTCGACTGC 59.774 45.455 0.00 0.00 0.00 4.40
2324 7215 2.884012 TGCTTCAATTTTCCAAGCTCGA 59.116 40.909 4.65 0.00 42.60 4.04
2352 7243 8.314021 AGTTTGTTGTCTTCAAGAAAAAGGAAT 58.686 29.630 0.00 0.00 44.34 3.01
2354 7245 7.227049 AGTTTGTTGTCTTCAAGAAAAAGGA 57.773 32.000 0.00 0.00 44.34 3.36
2360 7251 6.882140 TCCAGTAAGTTTGTTGTCTTCAAGAA 59.118 34.615 0.00 0.00 35.53 2.52
2366 7257 4.850680 TGGTCCAGTAAGTTTGTTGTCTT 58.149 39.130 0.00 0.00 0.00 3.01
2377 7268 3.517901 TCTGGTGGTATTGGTCCAGTAAG 59.482 47.826 9.39 0.00 45.18 2.34
2416 7307 4.024670 GAGAGGTCTAGGAAGGTTAAGCA 58.975 47.826 7.52 0.00 0.00 3.91
2525 7416 1.406069 GCTCTTCCGTGATCACACCAT 60.406 52.381 24.93 0.00 43.34 3.55
2544 7435 6.257630 TCAAACCTTTTAGATTTGCAAAGTGC 59.742 34.615 18.19 9.41 45.29 4.40
2610 7501 1.745087 GGAGAGCGCCAATTTGAATCA 59.255 47.619 2.29 0.00 0.00 2.57
2617 7508 2.369394 CCTAAAAGGAGAGCGCCAATT 58.631 47.619 2.29 0.00 37.67 2.32
2631 7522 4.351874 AACTGCAGACTGTAGCCTAAAA 57.648 40.909 23.35 0.00 33.13 1.52
2656 7547 3.588842 AGAGGACCCATTTGACAAGATGA 59.411 43.478 10.21 0.00 0.00 2.92
2664 7555 2.986019 TGGAAAGAGAGGACCCATTTGA 59.014 45.455 0.00 0.00 0.00 2.69
2758 7649 9.487790 CTGTGAAAATGTATACCAAAACCAATT 57.512 29.630 0.00 0.00 0.00 2.32
2785 7676 9.371136 GTTGTTAGAGATGTTGAGATATGTTGA 57.629 33.333 0.00 0.00 0.00 3.18
2834 7725 1.709115 AGTCCATGCCATCCATATGCT 59.291 47.619 0.00 0.00 31.47 3.79
2835 7726 2.211250 AGTCCATGCCATCCATATGC 57.789 50.000 0.00 0.00 31.47 3.14
2852 7743 6.995364 GAACTTAGGTAGAGTTCTTCCAAGT 58.005 40.000 9.16 10.41 45.94 3.16
2934 7825 6.552008 TCCTCCTGAAAAGTTATTGTTGGAT 58.448 36.000 0.00 0.00 0.00 3.41
2957 7848 6.758416 GGAGGCTTCAAAATTTGATGGTATTC 59.242 38.462 18.94 9.17 39.84 1.75
3019 7910 1.141053 GGATTCTGGAATGTACCCGCT 59.859 52.381 0.17 0.00 0.00 5.52
3054 7945 7.247728 TCGACAAATCCAAATACAATAGTTGC 58.752 34.615 0.00 0.00 32.82 4.17
3067 7958 4.993029 AAAGGTTGTTCGACAAATCCAA 57.007 36.364 2.65 0.00 40.15 3.53
3085 7976 7.177392 ACATTGAGGAATTTCACCCTCTAAAAG 59.823 37.037 11.15 0.72 46.94 2.27
3117 8008 9.428097 AGCAGAAGAAATTGTAATTTTTGGATC 57.572 29.630 4.27 0.00 38.64 3.36
3249 8140 8.567198 TTAATTCCTCAAGATCTCCTATCCAA 57.433 34.615 0.00 0.00 0.00 3.53
3268 8159 9.093970 GTGGCCCAATAATACAAAACTTAATTC 57.906 33.333 0.00 0.00 0.00 2.17
3289 8180 2.747396 TCAGAAAATGCATTGTGGCC 57.253 45.000 13.82 0.00 0.00 5.36
3314 8205 1.009829 GCTTGTTATGTCGGCTGGAG 58.990 55.000 0.00 0.00 0.00 3.86
3341 8232 5.468540 TGATAGATCCACGTATTGAAGGG 57.531 43.478 0.00 0.00 0.00 3.95
3342 8432 5.349817 GCATGATAGATCCACGTATTGAAGG 59.650 44.000 0.00 0.00 0.00 3.46
3352 8442 7.013083 AGAGAAATTGTTGCATGATAGATCCAC 59.987 37.037 0.00 0.00 0.00 4.02
3469 8562 8.491045 TCCATGTAACTACCATGAATATCTGA 57.509 34.615 0.00 0.00 0.00 3.27
3474 8567 7.942341 GGGAATTCCATGTAACTACCATGAATA 59.058 37.037 25.67 0.00 37.91 1.75
3476 8569 6.069088 AGGGAATTCCATGTAACTACCATGAA 60.069 38.462 25.67 0.00 38.24 2.57
3478 8571 5.532406 CAGGGAATTCCATGTAACTACCATG 59.468 44.000 27.23 1.64 42.43 3.66
3498 8591 4.133373 CCTGCCCCCATCACAGGG 62.133 72.222 0.19 0.00 45.97 4.45
3500 8593 2.273449 GACCTGCCCCCATCACAG 59.727 66.667 0.00 0.00 0.00 3.66
3501 8594 2.531428 TGACCTGCCCCCATCACA 60.531 61.111 0.00 0.00 0.00 3.58
3502 8595 2.044946 GTGACCTGCCCCCATCAC 60.045 66.667 0.00 0.00 35.12 3.06
3503 8596 2.484868 TAGGTGACCTGCCCCCATCA 62.485 60.000 15.83 0.00 34.61 3.07
3510 8603 1.276622 TTTCTCCTAGGTGACCTGCC 58.723 55.000 15.83 0.00 34.61 4.85
3513 8606 5.069251 CGACAATATTTCTCCTAGGTGACCT 59.931 44.000 13.11 10.00 37.71 3.85
3537 8630 4.820173 AGTTGCTGTCCTTTTGTTACTACC 59.180 41.667 0.00 0.00 0.00 3.18
3608 8707 5.313712 GGAGTTCACCAATCAAGGAGTTTA 58.686 41.667 0.00 0.00 0.00 2.01
3609 8708 4.145052 GGAGTTCACCAATCAAGGAGTTT 58.855 43.478 0.00 0.00 0.00 2.66
3620 8719 1.562008 TGTCTGTTGGGAGTTCACCAA 59.438 47.619 0.00 0.00 45.25 3.67
3628 8727 2.616510 GGGAAGTGATGTCTGTTGGGAG 60.617 54.545 0.00 0.00 0.00 4.30
3633 8732 2.107204 AGCAAGGGAAGTGATGTCTGTT 59.893 45.455 0.00 0.00 0.00 3.16
3774 8873 4.966005 CTTGACAAGCTCGACGGA 57.034 55.556 1.43 0.00 0.00 4.69
3810 8909 9.180678 CACAAATTGTTATAGGACAAGTTCAAC 57.819 33.333 0.00 0.00 43.45 3.18
3825 8924 5.712917 GGGTATCCTTCCACACAAATTGTTA 59.287 40.000 0.00 0.00 35.67 2.41
3865 8978 5.755409 TGTACATAAGTGATGGGTTGTCT 57.245 39.130 0.00 0.00 40.18 3.41
3966 9082 0.731417 CTCTTGCTTGATGCTTCCGG 59.269 55.000 0.00 0.00 43.37 5.14
4000 9116 5.894393 TCCCATCACAAGACCAAAGTAAAAA 59.106 36.000 0.00 0.00 0.00 1.94
4019 9135 1.228862 GCCCAACCACAAGTCCCAT 60.229 57.895 0.00 0.00 0.00 4.00
4132 9248 1.745087 CTTCCCCATTTCACGACCATG 59.255 52.381 0.00 0.00 0.00 3.66
4188 9304 2.157738 CACTGCCTCCTTCAGAAAAGG 58.842 52.381 6.83 6.83 38.78 3.11
4189 9305 2.810852 GACACTGCCTCCTTCAGAAAAG 59.189 50.000 0.00 0.00 35.61 2.27
4220 9341 3.294038 AATCCAGAGCTCTTTCATGGG 57.706 47.619 15.27 11.47 0.00 4.00
4224 9345 6.957631 TGGTTAATAATCCAGAGCTCTTTCA 58.042 36.000 15.27 0.34 0.00 2.69
4519 9694 8.675705 TTACTGATTCAGTTCAGATGACAAAA 57.324 30.769 23.53 5.52 42.59 2.44
4590 9765 7.331193 CCGATTAAATAGTAATGGAGCAGTACC 59.669 40.741 0.00 0.00 35.84 3.34
4607 9836 6.096705 TGAATGATCCAAGCAACCGATTAAAT 59.903 34.615 0.00 0.00 0.00 1.40
4639 9868 9.277783 GCAGAAATTTCAGGACATACAGTATAT 57.722 33.333 19.99 0.00 0.00 0.86
4698 9929 3.323751 AAATTGGTTTCTGCAGATGGC 57.676 42.857 19.04 10.46 45.13 4.40
4703 9934 4.925054 CCACACATAAATTGGTTTCTGCAG 59.075 41.667 7.63 7.63 0.00 4.41
4725 9956 1.539827 CCAATCAACTGAAACCGACCC 59.460 52.381 0.00 0.00 0.00 4.46
4766 9997 5.359009 CCTGATCTGAATACCAAGCACAATT 59.641 40.000 0.38 0.00 0.00 2.32
4772 10003 2.615912 GCACCTGATCTGAATACCAAGC 59.384 50.000 0.38 0.00 0.00 4.01
4791 11246 0.829990 TCATAGATTGGGAGTGCGCA 59.170 50.000 5.66 5.66 34.89 6.09
4796 11251 8.324191 TCTCTTATGTTTCATAGATTGGGAGT 57.676 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.