Multiple sequence alignment - TraesCS5D01G556700

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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 TraesCS5D01G556700 chr5D 100.000 4187 0 0 1 4187 559731740 559727554 0.000000e+00 7733.0
1 TraesCS5D01G556700 chr5D 89.189 148 12 4 2224 2369 60901485 60901340 9.250000e-42 182.0
2 TraesCS5D01G556700 chr5D 89.041 146 15 1 2221 2365 547601081 547601226 3.330000e-41 180.0
3 TraesCS5D01G556700 chr5D 82.540 189 22 2 1 189 339383643 339383466 5.600000e-34 156.0
4 TraesCS5D01G556700 chr5B 91.381 1195 56 18 994 2147 693995529 693994341 0.000000e+00 1592.0
5 TraesCS5D01G556700 chr5B 96.262 856 25 2 2442 3290 693993117 693992262 0.000000e+00 1397.0
6 TraesCS5D01G556700 chr5B 95.669 254 8 3 3498 3748 693991162 693990909 5.040000e-109 405.0
7 TraesCS5D01G556700 chr5B 84.507 355 44 4 1781 2134 522054660 522054316 1.440000e-89 340.0
8 TraesCS5D01G556700 chr5B 90.286 175 10 2 3297 3471 693991451 693991284 5.450000e-54 222.0
9 TraesCS5D01G556700 chr5B 84.232 241 22 7 701 932 693995768 693995535 1.960000e-53 220.0
10 TraesCS5D01G556700 chr5B 84.211 190 19 2 1 190 693996494 693996316 1.550000e-39 174.0
11 TraesCS5D01G556700 chr5B 80.804 224 17 7 1376 1599 519188492 519188689 7.250000e-33 152.0
12 TraesCS5D01G556700 chr5B 94.915 59 2 1 2376 2434 693993204 693993147 1.600000e-14 91.6
13 TraesCS5D01G556700 chr5B 93.220 59 3 1 2374 2432 693988234 693988177 7.460000e-13 86.1
14 TraesCS5D01G556700 chr4A 93.679 791 47 2 2502 3292 613320515 613319728 0.000000e+00 1181.0
15 TraesCS5D01G556700 chr4A 82.407 972 67 38 642 1599 613322958 613322077 0.000000e+00 752.0
16 TraesCS5D01G556700 chr4A 80.635 630 45 29 3587 4186 613317959 613317377 2.330000e-112 416.0
17 TraesCS5D01G556700 chr4A 84.783 414 44 10 1659 2063 613321996 613321593 8.430000e-107 398.0
18 TraesCS5D01G556700 chr4A 94.211 190 9 1 1 190 613325408 613325221 5.300000e-74 289.0
19 TraesCS5D01G556700 chr4A 79.393 461 39 23 186 608 604196260 604195818 1.480000e-69 274.0
20 TraesCS5D01G556700 chr4A 92.920 113 7 1 669 781 604195800 604195689 3.350000e-36 163.0
21 TraesCS5D01G556700 chr4A 97.143 70 2 0 2151 2220 613320964 613320895 7.350000e-23 119.0
22 TraesCS5D01G556700 chr4A 89.474 95 5 4 2367 2459 613320902 613320811 9.510000e-22 115.0
23 TraesCS5D01G556700 chr4A 80.000 135 15 5 241 365 322882965 322882833 5.770000e-14 89.8
24 TraesCS5D01G556700 chr2D 80.167 958 102 48 197 1112 403809555 403808644 1.640000e-178 636.0
25 TraesCS5D01G556700 chr2D 80.628 191 23 9 191 376 147702491 147702310 7.300000e-28 135.0
26 TraesCS5D01G556700 chr6A 82.097 782 72 36 313 1077 307920847 307921577 1.290000e-169 606.0
27 TraesCS5D01G556700 chr6A 96.875 32 1 0 2335 2366 5699729 5699760 2.000000e-03 54.7
28 TraesCS5D01G556700 chr6B 79.913 921 95 48 197 1075 46306621 46305749 1.000000e-165 593.0
29 TraesCS5D01G556700 chr6B 80.818 782 82 31 313 1077 83867845 83867115 6.120000e-153 551.0
30 TraesCS5D01G556700 chr6B 77.990 418 41 26 636 1029 671659008 671658618 9.120000e-52 215.0
31 TraesCS5D01G556700 chr6B 82.979 188 21 8 3 190 76225752 76225928 4.330000e-35 159.0
32 TraesCS5D01G556700 chr1A 81.586 782 76 31 313 1077 236392813 236392083 6.030000e-163 584.0
33 TraesCS5D01G556700 chr1A 79.554 269 37 10 1 257 479639341 479639603 4.300000e-40 176.0
34 TraesCS5D01G556700 chrUn 81.515 779 76 25 313 1074 87514330 87515057 2.810000e-161 579.0
35 TraesCS5D01G556700 chrUn 80.616 779 81 34 313 1074 87504506 87505231 4.760000e-149 538.0
36 TraesCS5D01G556700 chr7A 81.458 782 77 33 313 1077 395515325 395514595 2.810000e-161 579.0
37 TraesCS5D01G556700 chr7A 90.052 191 13 2 1659 1846 487485955 487486142 4.180000e-60 243.0
38 TraesCS5D01G556700 chr7A 80.804 224 17 7 1376 1599 487485677 487485874 7.250000e-33 152.0
39 TraesCS5D01G556700 chr4B 81.202 782 79 28 313 1077 552797830 552797100 6.070000e-158 568.0
40 TraesCS5D01G556700 chr4B 80.946 782 81 35 313 1077 636566971 636566241 1.310000e-154 556.0
41 TraesCS5D01G556700 chr4B 86.735 98 7 5 1809 1900 16689909 16690006 2.060000e-18 104.0
42 TraesCS5D01G556700 chr4B 82.906 117 13 4 1659 1775 16689814 16689923 9.580000e-17 99.0
43 TraesCS5D01G556700 chr3B 81.202 782 79 33 313 1077 746228 745498 6.070000e-158 568.0
44 TraesCS5D01G556700 chr3B 81.226 783 77 39 313 1077 817688145 817687415 6.070000e-158 568.0
45 TraesCS5D01G556700 chr3B 76.611 419 45 27 636 1029 748486884 748486494 9.250000e-42 182.0
46 TraesCS5D01G556700 chr3B 93.056 72 5 0 1663 1734 761144036 761144107 5.730000e-19 106.0
47 TraesCS5D01G556700 chr3B 91.429 70 4 2 1663 1731 761168401 761168469 1.240000e-15 95.3
48 TraesCS5D01G556700 chr7B 80.946 782 80 34 313 1077 681954823 681954094 4.730000e-154 555.0
49 TraesCS5D01G556700 chr7B 80.435 782 85 33 313 1077 695574377 695575107 6.160000e-148 534.0
50 TraesCS5D01G556700 chr7B 89.005 191 15 2 1659 1846 336661732 336661919 9.050000e-57 231.0
51 TraesCS5D01G556700 chr7B 89.041 146 15 1 2222 2366 375197180 375197035 3.330000e-41 180.0
52 TraesCS5D01G556700 chr7B 88.000 100 9 1 1500 1599 336661555 336661651 9.510000e-22 115.0
53 TraesCS5D01G556700 chr7B 93.056 72 4 1 1663 1734 644283834 644283904 2.060000e-18 104.0
54 TraesCS5D01G556700 chr7B 89.189 74 8 0 1794 1867 642054221 642054148 4.460000e-15 93.5
55 TraesCS5D01G556700 chr1B 84.211 342 42 6 1794 2134 337426293 337425963 5.220000e-84 322.0
56 TraesCS5D01G556700 chr1B 82.319 345 50 3 1791 2134 600849781 600850115 5.300000e-74 289.0
57 TraesCS5D01G556700 chr1B 82.164 342 50 3 1794 2134 657829893 657829562 2.460000e-72 283.0
58 TraesCS5D01G556700 chr1B 84.795 171 15 2 1 171 151148578 151148737 1.200000e-35 161.0
59 TraesCS5D01G556700 chr1B 77.835 194 21 9 191 373 151148943 151149125 2.660000e-17 100.0
60 TraesCS5D01G556700 chr2A 81.053 380 42 19 313 675 290320106 290319740 4.120000e-70 276.0
61 TraesCS5D01G556700 chr2A 88.079 151 17 1 2222 2371 748821119 748821269 1.200000e-40 178.0
62 TraesCS5D01G556700 chr4D 78.696 460 44 26 186 608 60091427 60090985 1.490000e-64 257.0
63 TraesCS5D01G556700 chr4D 85.200 250 26 4 1781 2029 142309497 142309258 3.230000e-61 246.0
64 TraesCS5D01G556700 chr4D 85.811 148 20 1 2221 2367 288633810 288633663 5.600000e-34 156.0
65 TraesCS5D01G556700 chr4D 81.152 191 22 11 191 376 332130661 332130480 1.570000e-29 141.0
66 TraesCS5D01G556700 chr2B 80.702 342 27 16 191 509 306849035 306849360 3.260000e-56 230.0
67 TraesCS5D01G556700 chr3D 77.238 391 54 21 1 373 231532634 231533007 3.300000e-46 196.0
68 TraesCS5D01G556700 chr3D 88.889 117 10 3 2253 2367 447575904 447575789 1.570000e-29 141.0
69 TraesCS5D01G556700 chr3D 80.272 147 27 2 2220 2366 263344667 263344811 4.430000e-20 110.0
70 TraesCS5D01G556700 chr5A 87.719 171 14 1 1781 1951 168349576 168349739 4.270000e-45 193.0
71 TraesCS5D01G556700 chr7D 82.540 189 22 2 1 189 594652103 594651926 5.600000e-34 156.0
72 TraesCS5D01G556700 chr6D 82.540 189 22 2 1 189 73253217 73253394 5.600000e-34 156.0
73 TraesCS5D01G556700 chr6D 83.125 160 15 11 220 373 73253481 73253634 7.300000e-28 135.0
74 TraesCS5D01G556700 chr1D 92.771 83 6 0 2221 2303 11348780 11348698 2.040000e-23 121.0


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 TraesCS5D01G556700 chr5D 559727554 559731740 4186 True 7733.000000 7733 100.000000 1 4187 1 chr5D.!!$R3 4186
1 TraesCS5D01G556700 chr5B 693988177 693996494 8317 True 523.462500 1592 91.272000 1 3748 8 chr5B.!!$R2 3747
2 TraesCS5D01G556700 chr4A 613317377 613325408 8031 True 467.142857 1181 88.904571 1 4186 7 chr4A.!!$R3 4185
3 TraesCS5D01G556700 chr4A 604195689 604196260 571 True 218.500000 274 86.156500 186 781 2 chr4A.!!$R2 595
4 TraesCS5D01G556700 chr2D 403808644 403809555 911 True 636.000000 636 80.167000 197 1112 1 chr2D.!!$R2 915
5 TraesCS5D01G556700 chr6A 307920847 307921577 730 False 606.000000 606 82.097000 313 1077 1 chr6A.!!$F2 764
6 TraesCS5D01G556700 chr6B 46305749 46306621 872 True 593.000000 593 79.913000 197 1075 1 chr6B.!!$R1 878
7 TraesCS5D01G556700 chr6B 83867115 83867845 730 True 551.000000 551 80.818000 313 1077 1 chr6B.!!$R2 764
8 TraesCS5D01G556700 chr1A 236392083 236392813 730 True 584.000000 584 81.586000 313 1077 1 chr1A.!!$R1 764
9 TraesCS5D01G556700 chrUn 87514330 87515057 727 False 579.000000 579 81.515000 313 1074 1 chrUn.!!$F2 761
10 TraesCS5D01G556700 chrUn 87504506 87505231 725 False 538.000000 538 80.616000 313 1074 1 chrUn.!!$F1 761
11 TraesCS5D01G556700 chr7A 395514595 395515325 730 True 579.000000 579 81.458000 313 1077 1 chr7A.!!$R1 764
12 TraesCS5D01G556700 chr4B 552797100 552797830 730 True 568.000000 568 81.202000 313 1077 1 chr4B.!!$R1 764
13 TraesCS5D01G556700 chr4B 636566241 636566971 730 True 556.000000 556 80.946000 313 1077 1 chr4B.!!$R2 764
14 TraesCS5D01G556700 chr3B 745498 746228 730 True 568.000000 568 81.202000 313 1077 1 chr3B.!!$R1 764
15 TraesCS5D01G556700 chr3B 817687415 817688145 730 True 568.000000 568 81.226000 313 1077 1 chr3B.!!$R3 764
16 TraesCS5D01G556700 chr7B 681954094 681954823 729 True 555.000000 555 80.946000 313 1077 1 chr7B.!!$R3 764
17 TraesCS5D01G556700 chr7B 695574377 695575107 730 False 534.000000 534 80.435000 313 1077 1 chr7B.!!$F2 764

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
568 2401 0.248621 GCACCCAAATACTCATGCGC 60.249 55.0 0.0 0.0 0.0 6.09 F
2267 5373 0.038744 ACCTGCCAATGTGCTAAGCT 59.961 50.0 0.0 0.0 0.0 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 5461 0.036010 CACAAGGACTAGGGGTGCAG 60.036 60.0 0.00 0.0 38.81 4.41 R
3817 8781 0.319383 ATCTGCGCTGATGACGATCC 60.319 55.0 26.49 0.0 0.00 3.36 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
120 121 8.023021 ACACTTGATTAGATATAAGCAGTGGA 57.977 34.615 21.02 1.86 33.32 4.02
151 152 4.494350 TCTTCAAATCACAAGCTCTTGC 57.506 40.909 9.36 0.00 44.03 4.01
211 265 2.354704 CGCCACTGGGAGATTGTAGAAA 60.355 50.000 0.00 0.00 35.76 2.52
217 271 7.437748 CCACTGGGAGATTGTAGAAATACTAG 58.562 42.308 0.00 0.00 35.59 2.57
232 286 8.950208 AGAAATACTAGTTAGAATGCCAGAAC 57.050 34.615 0.00 0.00 0.00 3.01
234 288 3.522553 ACTAGTTAGAATGCCAGAACGC 58.477 45.455 0.00 0.00 0.00 4.84
235 457 2.472695 AGTTAGAATGCCAGAACGCA 57.527 45.000 0.00 0.00 44.35 5.24
254 476 5.883661 ACGCAAGAATGGATAAAACAGATG 58.116 37.500 0.00 0.00 43.62 2.90
257 479 6.625740 CGCAAGAATGGATAAAACAGATGGTT 60.626 38.462 0.00 0.00 40.59 3.67
258 480 6.532657 GCAAGAATGGATAAAACAGATGGTTG 59.467 38.462 0.00 0.00 40.35 3.77
266 488 7.121168 TGGATAAAACAGATGGTTGATGTTCTC 59.879 37.037 0.00 0.00 40.35 2.87
357 1590 1.000896 CCAGAAGGACGGGCCATTT 60.001 57.895 4.39 0.00 40.02 2.32
360 1593 1.753078 GAAGGACGGGCCATTTCCC 60.753 63.158 4.39 0.00 43.02 3.97
362 1595 2.036572 GGACGGGCCATTTCCCAA 59.963 61.111 4.39 0.00 46.92 4.12
371 1615 2.613725 GGCCATTTCCCAAGCTTTGAAG 60.614 50.000 0.00 0.00 0.00 3.02
397 1644 6.875948 ACATAACAAACTCATGCAGTAACA 57.124 33.333 0.00 0.00 32.30 2.41
428 2233 5.500234 AGCATCTAAAACAGAAGTGGCATA 58.500 37.500 0.00 0.00 36.67 3.14
433 2239 7.202016 TCTAAAACAGAAGTGGCATAAACAG 57.798 36.000 0.00 0.00 0.00 3.16
435 2241 3.508845 ACAGAAGTGGCATAAACAGGT 57.491 42.857 0.00 0.00 0.00 4.00
440 2246 5.824624 CAGAAGTGGCATAAACAGGTATCAT 59.175 40.000 0.00 0.00 0.00 2.45
456 2265 5.944007 AGGTATCATTTGTTTACCTCACCAC 59.056 40.000 8.31 0.00 41.44 4.16
457 2266 5.708230 GGTATCATTTGTTTACCTCACCACA 59.292 40.000 0.00 0.00 33.95 4.17
458 2267 6.207810 GGTATCATTTGTTTACCTCACCACAA 59.792 38.462 0.00 0.00 33.95 3.33
459 2268 5.508200 TCATTTGTTTACCTCACCACAAC 57.492 39.130 0.00 0.00 0.00 3.32
460 2269 5.197451 TCATTTGTTTACCTCACCACAACT 58.803 37.500 0.00 0.00 0.00 3.16
461 2270 5.298276 TCATTTGTTTACCTCACCACAACTC 59.702 40.000 0.00 0.00 0.00 3.01
462 2271 4.497291 TTGTTTACCTCACCACAACTCT 57.503 40.909 0.00 0.00 0.00 3.24
463 2272 5.617528 TTGTTTACCTCACCACAACTCTA 57.382 39.130 0.00 0.00 0.00 2.43
510 2323 3.879295 CAGCTTATTCGGTGACAATGGAT 59.121 43.478 0.00 0.00 34.46 3.41
511 2324 3.879295 AGCTTATTCGGTGACAATGGATG 59.121 43.478 0.00 0.00 0.00 3.51
513 2326 4.260784 GCTTATTCGGTGACAATGGATGAC 60.261 45.833 0.00 0.00 0.00 3.06
529 2359 7.716799 ATGGATGACTAAAACCTAATTGCAA 57.283 32.000 0.00 0.00 0.00 4.08
532 2362 8.087750 TGGATGACTAAAACCTAATTGCAAAAG 58.912 33.333 1.71 4.05 0.00 2.27
533 2363 7.545615 GGATGACTAAAACCTAATTGCAAAAGG 59.454 37.037 23.09 23.09 36.42 3.11
543 2376 8.336801 ACCTAATTGCAAAAGGTTCTTACTAG 57.663 34.615 24.17 1.25 40.82 2.57
544 2377 7.094334 ACCTAATTGCAAAAGGTTCTTACTAGC 60.094 37.037 24.17 0.00 40.82 3.42
545 2378 6.648879 AATTGCAAAAGGTTCTTACTAGCA 57.351 33.333 1.71 0.00 0.00 3.49
546 2379 5.689383 TTGCAAAAGGTTCTTACTAGCAG 57.311 39.130 0.00 0.00 0.00 4.24
567 2400 1.382522 AGCACCCAAATACTCATGCG 58.617 50.000 0.00 0.00 38.12 4.73
568 2401 0.248621 GCACCCAAATACTCATGCGC 60.249 55.000 0.00 0.00 0.00 6.09
719 2615 2.433604 TGTTTGCTTCCCAAATGCAAGA 59.566 40.909 0.00 0.00 45.52 3.02
914 2819 1.200103 CGCAGCAATACATCGAGCG 59.800 57.895 0.00 0.00 37.68 5.03
931 2836 1.721487 CGCAATCGCTAAGGGTTGG 59.279 57.895 0.00 0.00 35.30 3.77
964 2874 3.753434 CAGCCGAGCCGAGTGAGT 61.753 66.667 0.00 0.00 0.00 3.41
965 2875 2.992114 AGCCGAGCCGAGTGAGTT 60.992 61.111 0.00 0.00 0.00 3.01
966 2876 2.811317 GCCGAGCCGAGTGAGTTG 60.811 66.667 0.00 0.00 0.00 3.16
967 2877 2.125912 CCGAGCCGAGTGAGTTGG 60.126 66.667 0.00 0.00 0.00 3.77
1016 2928 4.947147 TGGCGTGGTTCCAGGTGC 62.947 66.667 12.15 7.51 0.00 5.01
1264 3192 2.668212 CGCTTCGCTGGGGTTTCA 60.668 61.111 0.00 0.00 0.00 2.69
1327 3272 4.704965 GGGAAGCCCTAGTAATGTAGTTG 58.295 47.826 0.00 0.00 41.34 3.16
1331 3276 6.097981 GGAAGCCCTAGTAATGTAGTTGTAGT 59.902 42.308 0.00 0.00 0.00 2.73
1347 3292 3.715287 TGTAGTTACACTCTGGCCCATA 58.285 45.455 0.00 0.00 0.00 2.74
1349 3294 3.116096 AGTTACACTCTGGCCCATAGA 57.884 47.619 2.71 0.00 0.00 1.98
1350 3295 3.658725 AGTTACACTCTGGCCCATAGAT 58.341 45.455 2.71 0.00 0.00 1.98
1419 3368 4.457496 CACTGTCTCGGCGGCCAT 62.457 66.667 20.71 0.00 0.00 4.40
1466 3415 0.179004 ATCTCTCTCCGCCGATGACT 60.179 55.000 0.00 0.00 0.00 3.41
1552 3507 1.134371 GTAATCCACCTGCACCTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
1554 3509 2.770868 ATCCACCTGCACCTCCTCCA 62.771 60.000 0.00 0.00 0.00 3.86
1555 3510 2.528818 CCACCTGCACCTCCTCCAA 61.529 63.158 0.00 0.00 0.00 3.53
1556 3511 1.687612 CACCTGCACCTCCTCCAAT 59.312 57.895 0.00 0.00 0.00 3.16
1607 3616 0.804989 GTCAGAGGCCGATTTGGTTG 59.195 55.000 0.00 0.00 41.21 3.77
1609 3618 1.073125 TCAGAGGCCGATTTGGTTGAA 59.927 47.619 0.00 0.00 41.21 2.69
1641 3650 1.231221 TTTTGGTCGAATCCCGTGTG 58.769 50.000 0.00 0.00 39.75 3.82
1704 3713 3.329889 TGCAAGGGAGCCGTCCAT 61.330 61.111 0.00 0.00 46.07 3.41
1712 3721 3.982372 GAGCCGTCCATTCGTCGCA 62.982 63.158 0.00 0.00 0.00 5.10
2078 4092 6.903883 TGTTCAGTCTTGTGTTTTCTAGAC 57.096 37.500 0.00 0.00 37.79 2.59
2107 4121 3.745975 TGTGACTGGAGATTGTTAAAGCG 59.254 43.478 0.00 0.00 0.00 4.68
2144 4158 0.104304 AGATACTGCGGCGTTTAGGG 59.896 55.000 9.37 0.00 0.00 3.53
2179 5285 6.704937 GCGATTAGTTATGCCTAACCTAAGTT 59.295 38.462 8.11 0.00 38.40 2.66
2220 5326 6.126863 TCACTGAAGGTTGATGTCCTTATT 57.873 37.500 0.00 0.00 44.19 1.40
2221 5327 7.252612 TCACTGAAGGTTGATGTCCTTATTA 57.747 36.000 0.00 0.00 44.19 0.98
2222 5328 7.331026 TCACTGAAGGTTGATGTCCTTATTAG 58.669 38.462 0.00 0.00 44.19 1.73
2223 5329 6.540189 CACTGAAGGTTGATGTCCTTATTAGG 59.460 42.308 0.00 0.00 44.19 2.69
2224 5330 6.001449 TGAAGGTTGATGTCCTTATTAGGG 57.999 41.667 0.00 0.00 44.19 3.53
2225 5331 5.104109 TGAAGGTTGATGTCCTTATTAGGGG 60.104 44.000 0.00 0.00 44.19 4.79
2226 5332 4.380791 AGGTTGATGTCCTTATTAGGGGT 58.619 43.478 0.00 0.00 42.26 4.95
2227 5333 4.166144 AGGTTGATGTCCTTATTAGGGGTG 59.834 45.833 0.00 0.00 42.26 4.61
2228 5334 3.857157 TGATGTCCTTATTAGGGGTGC 57.143 47.619 0.00 0.00 42.26 5.01
2229 5335 3.119319 TGATGTCCTTATTAGGGGTGCA 58.881 45.455 0.00 0.00 42.26 4.57
2230 5336 3.136443 TGATGTCCTTATTAGGGGTGCAG 59.864 47.826 0.00 0.00 42.26 4.41
2231 5337 1.843851 TGTCCTTATTAGGGGTGCAGG 59.156 52.381 0.00 0.00 42.26 4.85
2232 5338 1.143073 GTCCTTATTAGGGGTGCAGGG 59.857 57.143 0.00 0.00 42.26 4.45
2233 5339 1.222567 CCTTATTAGGGGTGCAGGGT 58.777 55.000 0.00 0.00 37.94 4.34
2234 5340 1.133792 CCTTATTAGGGGTGCAGGGTG 60.134 57.143 0.00 0.00 37.94 4.61
2235 5341 0.923358 TTATTAGGGGTGCAGGGTGG 59.077 55.000 0.00 0.00 0.00 4.61
2236 5342 1.641552 TATTAGGGGTGCAGGGTGGC 61.642 60.000 0.00 0.00 0.00 5.01
2252 5358 2.743928 GCGTCCTGCCAAGACCTG 60.744 66.667 0.00 0.00 37.76 4.00
2253 5359 2.743928 CGTCCTGCCAAGACCTGC 60.744 66.667 0.00 0.00 0.00 4.85
2254 5360 2.360475 GTCCTGCCAAGACCTGCC 60.360 66.667 0.00 0.00 0.00 4.85
2255 5361 2.853542 TCCTGCCAAGACCTGCCA 60.854 61.111 0.00 0.00 0.00 4.92
2256 5362 2.115910 CCTGCCAAGACCTGCCAA 59.884 61.111 0.00 0.00 0.00 4.52
2257 5363 1.304713 CCTGCCAAGACCTGCCAAT 60.305 57.895 0.00 0.00 0.00 3.16
2258 5364 1.601419 CCTGCCAAGACCTGCCAATG 61.601 60.000 0.00 0.00 0.00 2.82
2259 5365 0.896940 CTGCCAAGACCTGCCAATGT 60.897 55.000 0.00 0.00 0.00 2.71
2260 5366 1.180456 TGCCAAGACCTGCCAATGTG 61.180 55.000 0.00 0.00 0.00 3.21
2261 5367 1.588082 CCAAGACCTGCCAATGTGC 59.412 57.895 0.00 0.00 0.00 4.57
2262 5368 0.896940 CCAAGACCTGCCAATGTGCT 60.897 55.000 0.00 0.00 0.00 4.40
2263 5369 1.614051 CCAAGACCTGCCAATGTGCTA 60.614 52.381 0.00 0.00 0.00 3.49
2264 5370 2.161855 CAAGACCTGCCAATGTGCTAA 58.838 47.619 0.00 0.00 0.00 3.09
2265 5371 2.119801 AGACCTGCCAATGTGCTAAG 57.880 50.000 0.00 0.00 0.00 2.18
2266 5372 0.453390 GACCTGCCAATGTGCTAAGC 59.547 55.000 0.00 0.00 0.00 3.09
2267 5373 0.038744 ACCTGCCAATGTGCTAAGCT 59.961 50.000 0.00 0.00 0.00 3.74
2268 5374 1.281867 ACCTGCCAATGTGCTAAGCTA 59.718 47.619 0.00 0.00 0.00 3.32
2269 5375 1.945394 CCTGCCAATGTGCTAAGCTAG 59.055 52.381 0.00 0.00 0.00 3.42
2289 5395 6.257169 CTAGCACAAATTGTACTAGCGTAC 57.743 41.667 17.45 0.00 44.95 3.67
2290 5396 4.817517 AGCACAAATTGTACTAGCGTACT 58.182 39.130 0.00 0.00 44.97 2.73
2291 5397 4.625742 AGCACAAATTGTACTAGCGTACTG 59.374 41.667 0.00 0.00 44.97 2.74
2292 5398 4.201685 GCACAAATTGTACTAGCGTACTGG 60.202 45.833 0.00 0.00 44.97 4.00
2293 5399 5.165676 CACAAATTGTACTAGCGTACTGGA 58.834 41.667 0.00 0.00 44.97 3.86
2294 5400 5.636121 CACAAATTGTACTAGCGTACTGGAA 59.364 40.000 0.00 0.00 44.97 3.53
2295 5401 6.312918 CACAAATTGTACTAGCGTACTGGAAT 59.687 38.462 0.00 0.00 44.97 3.01
2296 5402 6.534079 ACAAATTGTACTAGCGTACTGGAATC 59.466 38.462 0.00 0.00 44.97 2.52
2297 5403 4.644103 TTGTACTAGCGTACTGGAATCC 57.356 45.455 0.00 0.00 44.97 3.01
2298 5404 3.623703 TGTACTAGCGTACTGGAATCCA 58.376 45.455 0.48 0.48 44.97 3.41
2315 5421 9.566432 CTGGAATCCAGCTATAACTAGAAATTT 57.434 33.333 17.25 0.00 45.13 1.82
2316 5422 9.920946 TGGAATCCAGCTATAACTAGAAATTTT 57.079 29.630 0.00 0.00 0.00 1.82
2337 5443 9.889128 AATTTTCATTTTGTATATGAAGTGGGG 57.111 29.630 0.00 0.00 41.53 4.96
2338 5444 6.463995 TTCATTTTGTATATGAAGTGGGGC 57.536 37.500 0.00 0.00 37.15 5.80
2339 5445 4.578516 TCATTTTGTATATGAAGTGGGGCG 59.421 41.667 0.00 0.00 0.00 6.13
2340 5446 2.631160 TTGTATATGAAGTGGGGCGG 57.369 50.000 0.00 0.00 0.00 6.13
2341 5447 0.762418 TGTATATGAAGTGGGGCGGG 59.238 55.000 0.00 0.00 0.00 6.13
2342 5448 0.763035 GTATATGAAGTGGGGCGGGT 59.237 55.000 0.00 0.00 0.00 5.28
2343 5449 1.142262 GTATATGAAGTGGGGCGGGTT 59.858 52.381 0.00 0.00 0.00 4.11
2344 5450 0.182775 ATATGAAGTGGGGCGGGTTC 59.817 55.000 0.00 0.00 0.00 3.62
2345 5451 2.246761 TATGAAGTGGGGCGGGTTCG 62.247 60.000 0.00 0.00 39.81 3.95
2366 5472 4.537433 GCCGCTCTGCACCCCTAG 62.537 72.222 0.00 0.00 0.00 3.02
2367 5473 3.077556 CCGCTCTGCACCCCTAGT 61.078 66.667 0.00 0.00 0.00 2.57
2368 5474 2.496817 CGCTCTGCACCCCTAGTC 59.503 66.667 0.00 0.00 0.00 2.59
2369 5475 2.904131 GCTCTGCACCCCTAGTCC 59.096 66.667 0.00 0.00 0.00 3.85
2370 5476 1.687493 GCTCTGCACCCCTAGTCCT 60.687 63.158 0.00 0.00 0.00 3.85
2371 5477 1.268283 GCTCTGCACCCCTAGTCCTT 61.268 60.000 0.00 0.00 0.00 3.36
2372 5478 0.539051 CTCTGCACCCCTAGTCCTTG 59.461 60.000 0.00 0.00 0.00 3.61
2373 5479 0.178903 TCTGCACCCCTAGTCCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
2423 5536 5.074115 TGTGGGATTTCCGTTTATTCAGTT 58.926 37.500 0.00 0.00 38.76 3.16
2425 5538 4.461081 TGGGATTTCCGTTTATTCAGTTGG 59.539 41.667 0.00 0.00 38.76 3.77
2444 5557 2.430367 GGGTCCTTGCACGGTTCT 59.570 61.111 9.36 0.00 0.00 3.01
2445 5558 1.966451 GGGTCCTTGCACGGTTCTG 60.966 63.158 9.36 0.00 0.00 3.02
2446 5559 1.227853 GGTCCTTGCACGGTTCTGT 60.228 57.895 9.36 0.00 0.00 3.41
2447 5560 0.034337 GGTCCTTGCACGGTTCTGTA 59.966 55.000 9.36 0.00 0.00 2.74
2448 5561 1.429463 GTCCTTGCACGGTTCTGTAG 58.571 55.000 9.36 0.00 0.00 2.74
2466 5633 5.417894 TCTGTAGTTAGAGAAGCCGAAATGA 59.582 40.000 0.00 0.00 0.00 2.57
2489 5656 1.932511 GCTAGCTCAGTGAGTGCATTC 59.067 52.381 21.06 1.56 39.15 2.67
2493 5660 4.277515 AGCTCAGTGAGTGCATTCTAAA 57.722 40.909 21.06 0.00 39.15 1.85
2497 5664 3.691118 TCAGTGAGTGCATTCTAAATGGC 59.309 43.478 10.82 0.00 0.00 4.40
2505 5893 3.118702 TGCATTCTAAATGGCATGGGTTG 60.119 43.478 0.00 0.00 0.00 3.77
2598 5986 6.073058 TCACTGTCAGTTGCATTTGATCTAAC 60.073 38.462 1.67 0.00 0.00 2.34
2631 6019 1.882623 GTGTTCCTCTGCCTTCCTTTG 59.117 52.381 0.00 0.00 0.00 2.77
2652 6040 1.920574 CCGAGCTATTGTTCTGTGTCG 59.079 52.381 0.00 0.00 0.00 4.35
2890 6286 7.566658 AAAGATCCTATTCTTCCTGATAGGG 57.433 40.000 8.98 0.00 37.37 3.53
2956 6352 2.093973 CGACTGGGACATACTTTCTGCT 60.094 50.000 0.00 0.00 38.20 4.24
3097 6493 3.191162 CGCTTGGATTGTTCTTGGATTCA 59.809 43.478 0.00 0.00 0.00 2.57
3193 6589 5.757808 GCTTTGGTAAAATTTTGCTCCAGAA 59.242 36.000 16.98 14.02 0.00 3.02
3264 6660 1.134818 TGCATACATGACGACCCTGAC 60.135 52.381 0.00 0.00 0.00 3.51
3292 6688 2.579410 TGCATCCATGATGATCCTGG 57.421 50.000 10.12 10.12 42.09 4.45
3293 6689 2.059490 TGCATCCATGATGATCCTGGA 58.941 47.619 19.46 19.46 43.61 3.86
3295 7868 2.040012 GCATCCATGATGATCCTGGAGT 59.960 50.000 21.20 9.65 42.92 3.85
3305 7878 6.233434 TGATGATCCTGGAGTTACATATTGC 58.767 40.000 1.52 0.00 0.00 3.56
3333 7934 4.049186 TCTTCGTGTTTTTCTCTCTTCCG 58.951 43.478 0.00 0.00 0.00 4.30
3340 7941 6.136743 GTGTTTTTCTCTCTTCCGTTTCATC 58.863 40.000 0.00 0.00 0.00 2.92
3341 7942 5.050363 TGTTTTTCTCTCTTCCGTTTCATCG 60.050 40.000 0.00 0.00 0.00 3.84
3342 7943 4.514781 TTTCTCTCTTCCGTTTCATCGA 57.485 40.909 0.00 0.00 0.00 3.59
3384 7985 5.508153 CGATATTCTACCAGACCAGGTTCAG 60.508 48.000 0.00 0.00 43.08 3.02
3410 8133 6.096705 CCACTCATCTCACTCTCTCAACTAAT 59.903 42.308 0.00 0.00 0.00 1.73
3411 8134 7.195646 CACTCATCTCACTCTCTCAACTAATC 58.804 42.308 0.00 0.00 0.00 1.75
3412 8135 6.889177 ACTCATCTCACTCTCTCAACTAATCA 59.111 38.462 0.00 0.00 0.00 2.57
3413 8136 7.395772 ACTCATCTCACTCTCTCAACTAATCAA 59.604 37.037 0.00 0.00 0.00 2.57
3482 8353 1.334243 GCTCTTCATGCTTCATCAGGC 59.666 52.381 0.00 0.00 0.00 4.85
3497 8368 4.043200 GGCACTCCAAGGTTGCGC 62.043 66.667 0.00 0.00 0.00 6.09
3508 8379 0.179045 AGGTTGCGCCTCCATCATAC 60.179 55.000 17.84 0.00 46.96 2.39
3713 8677 8.180267 GTCCCACTATATGTACATACGTATGTC 58.820 40.741 37.31 28.13 45.11 3.06
3736 8700 4.082787 CGTCATGGCCTAAAAGAACAACAT 60.083 41.667 3.32 0.00 0.00 2.71
3772 8736 2.827800 ACATATGCACGATGGAGGAG 57.172 50.000 13.51 0.00 0.00 3.69
3773 8737 1.345741 ACATATGCACGATGGAGGAGG 59.654 52.381 13.51 0.00 0.00 4.30
3774 8738 0.979665 ATATGCACGATGGAGGAGGG 59.020 55.000 0.00 0.00 0.00 4.30
3775 8739 1.758440 TATGCACGATGGAGGAGGGC 61.758 60.000 0.00 0.00 0.00 5.19
3776 8740 4.554036 GCACGATGGAGGAGGGCC 62.554 72.222 0.00 0.00 0.00 5.80
3812 8776 3.198417 GGACCTAACATTCTTACCGGGAA 59.802 47.826 6.32 0.97 0.00 3.97
3814 8778 5.032327 ACCTAACATTCTTACCGGGAATC 57.968 43.478 6.32 0.00 31.90 2.52
3815 8779 4.141551 ACCTAACATTCTTACCGGGAATCC 60.142 45.833 6.32 0.00 31.90 3.01
3826 8790 2.058675 GGGAATCCGGGATCGTCAT 58.941 57.895 10.56 0.00 33.95 3.06
3827 8791 0.037232 GGGAATCCGGGATCGTCATC 60.037 60.000 10.56 3.52 33.95 2.92
3828 8792 0.679505 GGAATCCGGGATCGTCATCA 59.320 55.000 10.56 0.00 33.95 3.07
3829 8793 1.337260 GGAATCCGGGATCGTCATCAG 60.337 57.143 10.56 0.00 33.95 2.90
3830 8794 0.034059 AATCCGGGATCGTCATCAGC 59.966 55.000 10.56 0.00 33.95 4.26
3831 8795 2.147315 ATCCGGGATCGTCATCAGCG 62.147 60.000 2.97 0.00 33.95 5.18
3832 8796 3.032609 CGGGATCGTCATCAGCGC 61.033 66.667 0.00 0.00 0.00 5.92
3833 8797 2.106938 GGGATCGTCATCAGCGCA 59.893 61.111 11.47 0.00 0.00 6.09
3857 8821 7.119846 GCAGATTAATCAAGTCCGGCTATAATT 59.880 37.037 17.56 0.00 0.00 1.40
3859 8823 9.654663 AGATTAATCAAGTCCGGCTATAATTAC 57.345 33.333 17.56 0.00 0.00 1.89
3866 8830 5.365619 AGTCCGGCTATAATTACCAAACAG 58.634 41.667 0.00 0.00 0.00 3.16
3885 8849 9.846248 CCAAACAGGAAATAGAATAAGAACAAG 57.154 33.333 0.00 0.00 41.22 3.16
3898 8872 7.554476 AGAATAAGAACAAGAATAACCCTGCTC 59.446 37.037 0.00 0.00 0.00 4.26
3933 8907 4.813027 TCGTGTCACAAGAATAACCCTAC 58.187 43.478 3.42 0.00 0.00 3.18
3935 8909 4.625742 CGTGTCACAAGAATAACCCTACAG 59.374 45.833 3.42 0.00 0.00 2.74
3953 8934 6.708285 CCTACAGTGGGAATACTACAAAAGT 58.292 40.000 0.00 0.00 42.62 2.66
3954 8935 7.166167 CCTACAGTGGGAATACTACAAAAGTT 58.834 38.462 0.00 0.00 39.80 2.66
3955 8936 8.316214 CCTACAGTGGGAATACTACAAAAGTTA 58.684 37.037 0.00 0.00 39.80 2.24
3956 8937 9.715121 CTACAGTGGGAATACTACAAAAGTTAA 57.285 33.333 0.00 0.00 39.80 2.01
3976 8963 2.012937 TAAACCATAAGACACGCGGG 57.987 50.000 6.92 6.92 0.00 6.13
3983 8970 1.930567 TAAGACACGCGGGAAATAGC 58.069 50.000 19.19 0.00 0.00 2.97
3990 8977 0.738389 CGCGGGAAATAGCCACATTT 59.262 50.000 0.00 0.00 0.00 2.32
3998 8985 4.537015 GAAATAGCCACATTTATGTCGCC 58.463 43.478 8.53 0.00 44.40 5.54
3999 8986 3.492102 ATAGCCACATTTATGTCGCCT 57.508 42.857 8.53 1.65 44.40 5.52
4002 8989 2.093181 AGCCACATTTATGTCGCCTGTA 60.093 45.455 8.53 0.00 44.40 2.74
4004 8991 2.872245 CCACATTTATGTCGCCTGTAGG 59.128 50.000 0.00 0.00 39.39 3.18
4120 9107 7.248437 GGTACCACTTGCAAATGTTATACTTC 58.752 38.462 7.15 0.00 0.00 3.01
4173 9160 2.865119 TGAGGTGCATCACTTGTCAT 57.135 45.000 0.00 0.00 34.40 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 8.746530 AGCTTGTGATTTGAAGATCATGTAATT 58.253 29.630 0.00 0.00 38.25 1.40
151 152 9.119329 GATGCGATACTACTGTTTGTATCTAAG 57.881 37.037 20.67 12.58 41.45 2.18
159 160 9.794685 ATATCTATGATGCGATACTACTGTTTG 57.205 33.333 0.00 0.00 0.00 2.93
211 265 5.163447 TGCGTTCTGGCATTCTAACTAGTAT 60.163 40.000 0.00 0.00 38.17 2.12
217 271 2.742053 TCTTGCGTTCTGGCATTCTAAC 59.258 45.455 0.00 0.00 43.52 2.34
232 286 5.163622 ACCATCTGTTTTATCCATTCTTGCG 60.164 40.000 0.00 0.00 0.00 4.85
234 288 7.829725 TCAACCATCTGTTTTATCCATTCTTG 58.170 34.615 0.00 0.00 34.00 3.02
235 457 8.472413 CATCAACCATCTGTTTTATCCATTCTT 58.528 33.333 0.00 0.00 34.00 2.52
254 476 1.541588 GGCACTTGGAGAACATCAACC 59.458 52.381 0.00 0.00 0.00 3.77
257 479 2.040145 TCATGGCACTTGGAGAACATCA 59.960 45.455 0.00 0.00 0.00 3.07
258 480 2.715046 TCATGGCACTTGGAGAACATC 58.285 47.619 0.00 0.00 0.00 3.06
266 488 0.524862 GCTCACTTCATGGCACTTGG 59.475 55.000 0.00 0.00 0.00 3.61
357 1590 5.596361 TGTTATGTTTCTTCAAAGCTTGGGA 59.404 36.000 0.00 0.00 0.00 4.37
360 1593 8.411318 AGTTTGTTATGTTTCTTCAAAGCTTG 57.589 30.769 0.00 0.00 0.00 4.01
362 1595 7.771183 TGAGTTTGTTATGTTTCTTCAAAGCT 58.229 30.769 0.00 0.00 0.00 3.74
371 1615 7.860373 TGTTACTGCATGAGTTTGTTATGTTTC 59.140 33.333 0.00 0.00 35.96 2.78
397 1644 7.864379 CACTTCTGTTTTAGATGCTCAATGTTT 59.136 33.333 0.00 0.00 34.80 2.83
433 2239 5.708230 TGTGGTGAGGTAAACAAATGATACC 59.292 40.000 10.26 10.26 39.51 2.73
435 2241 7.001674 AGTTGTGGTGAGGTAAACAAATGATA 58.998 34.615 0.00 0.00 34.54 2.15
440 2246 4.850680 AGAGTTGTGGTGAGGTAAACAAA 58.149 39.130 0.00 0.00 34.54 2.83
456 2265 4.815269 GCTATGATAGCCACCTAGAGTTG 58.185 47.826 13.37 0.00 45.95 3.16
510 2323 7.354751 ACCTTTTGCAATTAGGTTTTAGTCA 57.645 32.000 21.83 0.00 39.19 3.41
529 2359 5.480205 GTGCTACTGCTAGTAAGAACCTTT 58.520 41.667 2.05 0.00 40.48 3.11
532 2362 3.430513 GGGTGCTACTGCTAGTAAGAACC 60.431 52.174 1.82 1.82 40.48 3.62
533 2363 3.194968 TGGGTGCTACTGCTAGTAAGAAC 59.805 47.826 2.05 0.00 40.48 3.01
541 2374 3.772572 TGAGTATTTGGGTGCTACTGCTA 59.227 43.478 0.00 0.00 40.48 3.49
542 2375 2.571653 TGAGTATTTGGGTGCTACTGCT 59.428 45.455 0.00 0.00 40.48 4.24
543 2376 2.985896 TGAGTATTTGGGTGCTACTGC 58.014 47.619 0.00 0.00 40.20 4.40
544 2377 3.313526 GCATGAGTATTTGGGTGCTACTG 59.686 47.826 0.00 0.00 0.00 2.74
545 2378 3.545703 GCATGAGTATTTGGGTGCTACT 58.454 45.455 0.00 0.00 0.00 2.57
546 2379 2.287915 CGCATGAGTATTTGGGTGCTAC 59.712 50.000 0.00 0.00 0.00 3.58
567 2400 2.090400 TGCTCAACTCAGTGATCTGC 57.910 50.000 0.00 0.00 41.10 4.26
568 2401 4.565962 GTGTATGCTCAACTCAGTGATCTG 59.434 45.833 0.00 0.00 42.54 2.90
632 2468 9.181805 CGTACTCTTGTATATCAATACCAGTTG 57.818 37.037 0.00 0.00 37.72 3.16
634 2470 7.523380 GCCGTACTCTTGTATATCAATACCAGT 60.523 40.741 0.00 0.00 37.72 4.00
699 2594 3.110447 TCTTGCATTTGGGAAGCAAAC 57.890 42.857 0.00 0.00 46.30 2.93
719 2615 3.321968 CCTCTTTTTAGTGCCTTGGCTTT 59.678 43.478 13.18 3.73 0.00 3.51
888 2793 0.521291 TGTATTGCTGCGGCTTTGAC 59.479 50.000 20.27 11.72 39.59 3.18
889 2794 1.401552 GATGTATTGCTGCGGCTTTGA 59.598 47.619 20.27 2.40 39.59 2.69
890 2795 1.831343 GATGTATTGCTGCGGCTTTG 58.169 50.000 20.27 0.00 39.59 2.77
891 2796 0.378257 CGATGTATTGCTGCGGCTTT 59.622 50.000 20.27 8.55 39.59 3.51
914 2819 0.451783 CACCAACCCTTAGCGATTGC 59.548 55.000 0.00 0.00 43.24 3.56
978 2888 2.443390 TACCCTACTCGCCCTGCC 60.443 66.667 0.00 0.00 0.00 4.85
979 2889 2.794028 GGTACCCTACTCGCCCTGC 61.794 68.421 0.00 0.00 0.00 4.85
980 2890 0.686769 AAGGTACCCTACTCGCCCTG 60.687 60.000 8.74 0.00 31.13 4.45
981 2891 0.686769 CAAGGTACCCTACTCGCCCT 60.687 60.000 8.74 0.00 31.13 5.19
984 2894 1.143401 GCCAAGGTACCCTACTCGC 59.857 63.158 8.74 0.00 31.13 5.03
1264 3192 1.610673 TCTTGGGCTTCTCTCGGCT 60.611 57.895 0.00 0.00 0.00 5.52
1331 3276 5.074746 TCTATCTATGGGCCAGAGTGTAA 57.925 43.478 26.25 8.88 0.00 2.41
1347 3292 7.310485 GGACGGACCCAAATGTAATATCTATCT 60.310 40.741 0.00 0.00 0.00 1.98
1349 3294 6.271391 TGGACGGACCCAAATGTAATATCTAT 59.729 38.462 0.00 0.00 38.00 1.98
1350 3295 5.603395 TGGACGGACCCAAATGTAATATCTA 59.397 40.000 0.00 0.00 38.00 1.98
1552 3507 1.543429 GCGTATTGAGGGGGAGATTGG 60.543 57.143 0.00 0.00 0.00 3.16
1554 3509 1.694696 GAGCGTATTGAGGGGGAGATT 59.305 52.381 0.00 0.00 0.00 2.40
1555 3510 1.343069 GAGCGTATTGAGGGGGAGAT 58.657 55.000 0.00 0.00 0.00 2.75
1556 3511 1.107538 CGAGCGTATTGAGGGGGAGA 61.108 60.000 0.00 0.00 0.00 3.71
1590 3556 1.533625 TTCAACCAAATCGGCCTCTG 58.466 50.000 0.00 0.00 39.03 3.35
1725 3734 2.358737 GACAACCCCGACCAGCAG 60.359 66.667 0.00 0.00 0.00 4.24
1739 3748 3.677527 GGTTCCTCGACCTCGACA 58.322 61.111 0.00 0.00 44.22 4.35
1994 4007 6.709643 CAATACTCATCAAACGACCTTCATC 58.290 40.000 0.00 0.00 0.00 2.92
2063 4077 6.688385 CACACATGTTGTCTAGAAAACACAAG 59.312 38.462 27.12 21.33 39.00 3.16
2078 4092 3.817084 ACAATCTCCAGTCACACATGTTG 59.183 43.478 0.00 0.00 0.00 3.33
2107 4121 7.217070 GCAGTATCTGATTCGAACAAACAAATC 59.783 37.037 0.00 0.00 32.44 2.17
2144 4158 8.040716 AGGCATAACTAATCGCATTATTTACC 57.959 34.615 0.00 0.00 0.00 2.85
2179 5285 5.070001 CAGTGAACAGGTTAAATCTGGGAA 58.930 41.667 10.60 0.00 36.62 3.97
2235 5341 2.743928 CAGGTCTTGGCAGGACGC 60.744 66.667 21.47 14.90 41.28 5.19
2236 5342 2.743928 GCAGGTCTTGGCAGGACG 60.744 66.667 21.47 11.24 34.82 4.79
2243 5349 0.896940 AGCACATTGGCAGGTCTTGG 60.897 55.000 0.00 0.00 35.83 3.61
2244 5350 1.825090 TAGCACATTGGCAGGTCTTG 58.175 50.000 0.00 0.00 35.83 3.02
2245 5351 2.440409 CTTAGCACATTGGCAGGTCTT 58.560 47.619 0.00 0.00 35.83 3.01
2246 5352 1.952367 GCTTAGCACATTGGCAGGTCT 60.952 52.381 0.00 0.00 35.83 3.85
2247 5353 0.453390 GCTTAGCACATTGGCAGGTC 59.547 55.000 0.00 0.00 35.83 3.85
2248 5354 0.038744 AGCTTAGCACATTGGCAGGT 59.961 50.000 7.07 0.00 35.83 4.00
2249 5355 1.945394 CTAGCTTAGCACATTGGCAGG 59.055 52.381 7.07 0.00 35.83 4.85
2290 5396 9.920946 AAAATTTCTAGTTATAGCTGGATTCCA 57.079 29.630 5.05 5.05 0.00 3.53
2311 5417 9.889128 CCCCACTTCATATACAAAATGAAAATT 57.111 29.630 0.74 0.00 41.50 1.82
2312 5418 7.986889 GCCCCACTTCATATACAAAATGAAAAT 59.013 33.333 0.74 0.00 41.50 1.82
2313 5419 7.327214 GCCCCACTTCATATACAAAATGAAAA 58.673 34.615 0.74 0.00 41.50 2.29
2314 5420 6.405286 CGCCCCACTTCATATACAAAATGAAA 60.405 38.462 0.74 0.00 41.50 2.69
2315 5421 5.067153 CGCCCCACTTCATATACAAAATGAA 59.933 40.000 0.00 0.00 40.21 2.57
2316 5422 4.578516 CGCCCCACTTCATATACAAAATGA 59.421 41.667 0.00 0.00 0.00 2.57
2317 5423 4.261572 CCGCCCCACTTCATATACAAAATG 60.262 45.833 0.00 0.00 0.00 2.32
2318 5424 3.888930 CCGCCCCACTTCATATACAAAAT 59.111 43.478 0.00 0.00 0.00 1.82
2319 5425 3.283751 CCGCCCCACTTCATATACAAAA 58.716 45.455 0.00 0.00 0.00 2.44
2320 5426 2.422235 CCCGCCCCACTTCATATACAAA 60.422 50.000 0.00 0.00 0.00 2.83
2321 5427 1.142060 CCCGCCCCACTTCATATACAA 59.858 52.381 0.00 0.00 0.00 2.41
2322 5428 0.762418 CCCGCCCCACTTCATATACA 59.238 55.000 0.00 0.00 0.00 2.29
2323 5429 0.763035 ACCCGCCCCACTTCATATAC 59.237 55.000 0.00 0.00 0.00 1.47
2324 5430 1.418637 GAACCCGCCCCACTTCATATA 59.581 52.381 0.00 0.00 0.00 0.86
2325 5431 0.182775 GAACCCGCCCCACTTCATAT 59.817 55.000 0.00 0.00 0.00 1.78
2326 5432 1.605453 GAACCCGCCCCACTTCATA 59.395 57.895 0.00 0.00 0.00 2.15
2327 5433 2.355115 GAACCCGCCCCACTTCAT 59.645 61.111 0.00 0.00 0.00 2.57
2328 5434 4.323477 CGAACCCGCCCCACTTCA 62.323 66.667 0.00 0.00 0.00 3.02
2349 5455 4.537433 CTAGGGGTGCAGAGCGGC 62.537 72.222 0.00 0.00 0.00 6.53
2350 5456 3.077556 ACTAGGGGTGCAGAGCGG 61.078 66.667 0.00 0.00 0.00 5.52
2351 5457 2.496817 GACTAGGGGTGCAGAGCG 59.503 66.667 0.00 0.00 0.00 5.03
2352 5458 1.268283 AAGGACTAGGGGTGCAGAGC 61.268 60.000 0.00 0.00 38.81 4.09
2353 5459 0.539051 CAAGGACTAGGGGTGCAGAG 59.461 60.000 0.00 0.00 38.81 3.35
2354 5460 0.178903 ACAAGGACTAGGGGTGCAGA 60.179 55.000 0.00 0.00 38.81 4.26
2355 5461 0.036010 CACAAGGACTAGGGGTGCAG 60.036 60.000 0.00 0.00 38.81 4.41
2356 5462 2.066340 CACAAGGACTAGGGGTGCA 58.934 57.895 0.00 0.00 38.81 4.57
2357 5463 1.377333 GCACAAGGACTAGGGGTGC 60.377 63.158 0.00 0.00 46.53 5.01
2358 5464 0.620556 ATGCACAAGGACTAGGGGTG 59.379 55.000 0.00 0.00 0.00 4.61
2359 5465 0.912486 GATGCACAAGGACTAGGGGT 59.088 55.000 0.00 0.00 0.00 4.95
2360 5466 0.911769 TGATGCACAAGGACTAGGGG 59.088 55.000 0.00 0.00 0.00 4.79
2361 5467 2.787473 TTGATGCACAAGGACTAGGG 57.213 50.000 0.00 0.00 34.20 3.53
2362 5468 6.057533 TGATATTTGATGCACAAGGACTAGG 58.942 40.000 0.00 0.00 39.77 3.02
2363 5469 7.281774 AGTTGATATTTGATGCACAAGGACTAG 59.718 37.037 0.00 0.00 39.77 2.57
2364 5470 7.112122 AGTTGATATTTGATGCACAAGGACTA 58.888 34.615 0.00 0.00 39.77 2.59
2365 5471 5.948162 AGTTGATATTTGATGCACAAGGACT 59.052 36.000 0.00 0.00 39.77 3.85
2366 5472 6.199937 AGTTGATATTTGATGCACAAGGAC 57.800 37.500 0.00 0.00 39.77 3.85
2367 5473 6.543465 CCTAGTTGATATTTGATGCACAAGGA 59.457 38.462 0.00 0.00 39.77 3.36
2368 5474 6.238842 CCCTAGTTGATATTTGATGCACAAGG 60.239 42.308 0.00 0.00 39.77 3.61
2369 5475 6.543465 TCCCTAGTTGATATTTGATGCACAAG 59.457 38.462 0.00 0.00 39.77 3.16
2370 5476 6.422333 TCCCTAGTTGATATTTGATGCACAA 58.578 36.000 0.00 0.00 36.65 3.33
2371 5477 6.000246 TCCCTAGTTGATATTTGATGCACA 58.000 37.500 0.00 0.00 0.00 4.57
2372 5478 6.291377 TCTCCCTAGTTGATATTTGATGCAC 58.709 40.000 0.00 0.00 0.00 4.57
2373 5479 6.327365 TCTCTCCCTAGTTGATATTTGATGCA 59.673 38.462 0.00 0.00 0.00 3.96
2423 5536 4.263572 CCGTGCAAGGACCCACCA 62.264 66.667 14.14 0.00 42.04 4.17
2425 5538 2.203294 AACCGTGCAAGGACCCAC 60.203 61.111 26.25 0.00 34.73 4.61
2444 5557 5.185249 ACTCATTTCGGCTTCTCTAACTACA 59.815 40.000 0.00 0.00 0.00 2.74
2445 5558 5.517054 CACTCATTTCGGCTTCTCTAACTAC 59.483 44.000 0.00 0.00 0.00 2.73
2446 5559 5.651530 CACTCATTTCGGCTTCTCTAACTA 58.348 41.667 0.00 0.00 0.00 2.24
2447 5560 4.499183 CACTCATTTCGGCTTCTCTAACT 58.501 43.478 0.00 0.00 0.00 2.24
2448 5561 3.062774 GCACTCATTTCGGCTTCTCTAAC 59.937 47.826 0.00 0.00 0.00 2.34
2466 5633 0.246086 GCACTCACTGAGCTAGCACT 59.754 55.000 18.83 0.00 32.04 4.40
2480 5647 3.243636 CCCATGCCATTTAGAATGCACTC 60.244 47.826 0.00 0.00 36.41 3.51
2489 5656 4.019174 AGTTCTCAACCCATGCCATTTAG 58.981 43.478 0.00 0.00 0.00 1.85
2493 5660 1.355381 TGAGTTCTCAACCCATGCCAT 59.645 47.619 0.00 0.00 0.00 4.40
2497 5664 6.633500 TTAAAACTGAGTTCTCAACCCATG 57.367 37.500 0.00 0.00 0.00 3.66
2505 5893 7.608376 AGAGCCCTTAATTAAAACTGAGTTCTC 59.392 37.037 0.00 0.00 0.00 2.87
2578 5966 7.484007 CAGATTGTTAGATCAAATGCAACTGAC 59.516 37.037 3.40 0.00 0.00 3.51
2598 5986 0.445436 GGAACACGCAGAGCAGATTG 59.555 55.000 0.00 0.00 0.00 2.67
2631 6019 1.661112 GACACAGAACAATAGCTCGGC 59.339 52.381 0.00 0.00 0.00 5.54
2652 6040 3.911661 AGAAAGCATGCTGTCTTTCAC 57.088 42.857 31.10 9.12 46.36 3.18
2890 6286 4.935630 GCCGTGGCACAGTAAAAC 57.064 55.556 19.09 0.00 41.80 2.43
3193 6589 5.063880 GGCGGATGAACCAAGATACTAAAT 58.936 41.667 0.00 0.00 38.90 1.40
3264 6660 1.947146 CATGGATGCAAATGCGCCG 60.947 57.895 4.18 0.00 45.83 6.46
3292 6688 6.531948 ACGAAGAACTGAGCAATATGTAACTC 59.468 38.462 0.00 0.00 0.00 3.01
3293 6689 6.311445 CACGAAGAACTGAGCAATATGTAACT 59.689 38.462 0.00 0.00 0.00 2.24
3295 7868 6.163476 ACACGAAGAACTGAGCAATATGTAA 58.837 36.000 0.00 0.00 0.00 2.41
3305 7878 5.751028 AGAGAGAAAAACACGAAGAACTGAG 59.249 40.000 0.00 0.00 0.00 3.35
3340 7941 3.855379 TCGTAACTGGATTCGTTTCATCG 59.145 43.478 0.00 0.00 0.00 3.84
3341 7942 5.968387 ATCGTAACTGGATTCGTTTCATC 57.032 39.130 0.00 0.00 0.00 2.92
3342 7943 7.926555 AGAATATCGTAACTGGATTCGTTTCAT 59.073 33.333 0.00 0.00 32.85 2.57
3352 7953 5.533903 GGTCTGGTAGAATATCGTAACTGGA 59.466 44.000 0.00 0.00 0.00 3.86
3384 7985 2.098614 TGAGAGAGTGAGATGAGTGGC 58.901 52.381 0.00 0.00 0.00 5.01
3410 8133 2.687935 GCAAGACAACTTTGGTCCTTGA 59.312 45.455 17.57 0.00 36.87 3.02
3411 8134 2.689983 AGCAAGACAACTTTGGTCCTTG 59.310 45.455 12.65 12.65 37.32 3.61
3412 8135 3.018423 AGCAAGACAACTTTGGTCCTT 57.982 42.857 0.00 0.00 35.89 3.36
3413 8136 2.736670 AGCAAGACAACTTTGGTCCT 57.263 45.000 0.00 0.00 35.89 3.85
3458 8329 1.003759 GATGAAGCATGAAGAGCAGCG 60.004 52.381 0.00 0.00 0.00 5.18
3459 8330 2.014857 TGATGAAGCATGAAGAGCAGC 58.985 47.619 0.00 0.00 0.00 5.25
3497 8368 5.332707 CGACGTACATATGTATGATGGAGG 58.667 45.833 32.29 14.21 39.30 4.30
3508 8379 2.328473 CATGGAGCCGACGTACATATG 58.672 52.381 0.00 0.00 0.00 1.78
3713 8677 3.252215 TGTTGTTCTTTTAGGCCATGACG 59.748 43.478 5.01 0.00 0.00 4.35
3748 8712 5.906073 TCCTCCATCGTGCATATGTATATG 58.094 41.667 4.29 8.08 42.30 1.78
3749 8713 5.069648 CCTCCTCCATCGTGCATATGTATAT 59.930 44.000 4.29 0.00 0.00 0.86
3750 8714 4.402474 CCTCCTCCATCGTGCATATGTATA 59.598 45.833 4.29 0.00 0.00 1.47
3751 8715 3.196469 CCTCCTCCATCGTGCATATGTAT 59.804 47.826 4.29 0.00 0.00 2.29
3752 8716 2.562738 CCTCCTCCATCGTGCATATGTA 59.437 50.000 4.29 0.00 0.00 2.29
3753 8717 1.345741 CCTCCTCCATCGTGCATATGT 59.654 52.381 4.29 0.00 0.00 2.29
3754 8718 1.338484 CCCTCCTCCATCGTGCATATG 60.338 57.143 0.00 0.00 0.00 1.78
3755 8719 0.979665 CCCTCCTCCATCGTGCATAT 59.020 55.000 0.00 0.00 0.00 1.78
3756 8720 1.758440 GCCCTCCTCCATCGTGCATA 61.758 60.000 0.00 0.00 0.00 3.14
3757 8721 3.112205 GCCCTCCTCCATCGTGCAT 62.112 63.158 0.00 0.00 0.00 3.96
3775 8739 3.807839 TCCATGCATGTCCCCCGG 61.808 66.667 24.58 8.25 0.00 5.73
3776 8740 2.516930 GTCCATGCATGTCCCCCG 60.517 66.667 24.58 8.85 0.00 5.73
3812 8776 1.668294 GCTGATGACGATCCCGGAT 59.332 57.895 0.73 0.00 40.78 4.18
3814 8778 2.355126 CGCTGATGACGATCCCGG 60.355 66.667 0.00 0.00 40.78 5.73
3815 8779 3.032609 GCGCTGATGACGATCCCG 61.033 66.667 0.00 0.00 42.50 5.14
3817 8781 0.319383 ATCTGCGCTGATGACGATCC 60.319 55.000 26.49 0.00 0.00 3.36
3818 8782 1.495878 AATCTGCGCTGATGACGATC 58.504 50.000 27.53 0.00 0.00 3.69
3819 8783 2.800881 TAATCTGCGCTGATGACGAT 57.199 45.000 27.53 15.39 0.00 3.73
3820 8784 2.577449 TTAATCTGCGCTGATGACGA 57.423 45.000 27.53 12.55 0.00 4.20
3821 8785 2.796593 TGATTAATCTGCGCTGATGACG 59.203 45.455 27.53 0.00 0.00 4.35
3822 8786 4.272018 ACTTGATTAATCTGCGCTGATGAC 59.728 41.667 27.53 18.64 0.00 3.06
3823 8787 4.445453 ACTTGATTAATCTGCGCTGATGA 58.555 39.130 27.53 19.27 0.00 2.92
3826 8790 3.198068 GGACTTGATTAATCTGCGCTGA 58.802 45.455 19.70 19.70 0.00 4.26
3827 8791 2.033407 CGGACTTGATTAATCTGCGCTG 60.033 50.000 16.24 8.88 0.00 5.18
3828 8792 2.205074 CGGACTTGATTAATCTGCGCT 58.795 47.619 16.24 0.00 0.00 5.92
3829 8793 1.261619 CCGGACTTGATTAATCTGCGC 59.738 52.381 16.24 0.00 0.00 6.09
3830 8794 1.261619 GCCGGACTTGATTAATCTGCG 59.738 52.381 16.24 12.40 0.00 5.18
3831 8795 2.565841 AGCCGGACTTGATTAATCTGC 58.434 47.619 16.24 7.58 0.00 4.26
3832 8796 8.553459 AATTATAGCCGGACTTGATTAATCTG 57.447 34.615 16.24 11.22 0.00 2.90
3833 8797 9.654663 GTAATTATAGCCGGACTTGATTAATCT 57.345 33.333 16.24 0.00 0.00 2.40
3859 8823 9.846248 CTTGTTCTTATTCTATTTCCTGTTTGG 57.154 33.333 0.00 0.00 37.10 3.28
3876 8840 6.374417 AGAGCAGGGTTATTCTTGTTCTTA 57.626 37.500 0.00 0.00 0.00 2.10
3882 8846 8.506168 TTAACATTAGAGCAGGGTTATTCTTG 57.494 34.615 0.00 0.00 0.00 3.02
3885 8849 7.054751 ACCTTAACATTAGAGCAGGGTTATTC 58.945 38.462 0.00 0.00 0.00 1.75
3886 8850 6.970191 ACCTTAACATTAGAGCAGGGTTATT 58.030 36.000 0.00 0.00 0.00 1.40
3887 8851 6.576778 ACCTTAACATTAGAGCAGGGTTAT 57.423 37.500 0.00 0.00 0.00 1.89
3889 8853 4.929146 ACCTTAACATTAGAGCAGGGTT 57.071 40.909 0.00 0.00 0.00 4.11
3890 8854 4.623171 CGAACCTTAACATTAGAGCAGGGT 60.623 45.833 0.00 0.00 0.00 4.34
3898 8872 6.422701 TCTTGTGACACGAACCTTAACATTAG 59.577 38.462 0.22 0.00 0.00 1.73
3953 8934 4.571580 CCCGCGTGTCTTATGGTTTATTAA 59.428 41.667 4.92 0.00 0.00 1.40
3954 8935 4.121317 CCCGCGTGTCTTATGGTTTATTA 58.879 43.478 4.92 0.00 0.00 0.98
3955 8936 2.940410 CCCGCGTGTCTTATGGTTTATT 59.060 45.455 4.92 0.00 0.00 1.40
3956 8937 2.168936 TCCCGCGTGTCTTATGGTTTAT 59.831 45.455 4.92 0.00 0.00 1.40
3969 8956 1.095228 ATGTGGCTATTTCCCGCGTG 61.095 55.000 4.92 0.00 35.64 5.34
3971 8958 0.738389 AAATGTGGCTATTTCCCGCG 59.262 50.000 0.00 0.00 35.64 6.46
3983 8970 2.872245 CCTACAGGCGACATAAATGTGG 59.128 50.000 0.00 0.28 41.95 4.17
3990 8977 2.829720 AGTGAAACCTACAGGCGACATA 59.170 45.455 0.00 0.00 37.80 2.29
3998 8985 5.178797 CCCAATGTAGAGTGAAACCTACAG 58.821 45.833 0.00 0.00 46.26 2.74
3999 8986 4.564821 GCCCAATGTAGAGTGAAACCTACA 60.565 45.833 0.00 0.00 46.72 2.74
4002 8989 2.644798 AGCCCAATGTAGAGTGAAACCT 59.355 45.455 0.00 0.00 37.80 3.50
4004 8991 3.674997 TGAGCCCAATGTAGAGTGAAAC 58.325 45.455 0.00 0.00 0.00 2.78
4050 9037 8.910666 CACTATCTATTTATCGACAGAAGCAAG 58.089 37.037 0.00 0.00 0.00 4.01
4092 9079 2.238521 ACATTTGCAAGTGGTACCCTG 58.761 47.619 23.78 5.41 0.00 4.45
4141 9128 0.673333 CACCTCATGTGCGCCACTAA 60.673 55.000 4.18 0.00 38.34 2.24


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

AutoCloner maintained by Alex Coulton.