Multiple sequence alignment - TraesCS7A01G217200

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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 TraesCS7A01G217200 chr7A 100.000 7463 0 0 1 7463 183718156 183710694 0.000000e+00 13782.0
1 TraesCS7A01G217200 chr7A 85.061 3367 304 105 950 4179 30810493 30813797 0.000000e+00 3247.0
2 TraesCS7A01G217200 chr7A 86.498 1385 134 23 4316 5686 30813929 30815274 0.000000e+00 1472.0
3 TraesCS7A01G217200 chr7A 83.555 602 65 18 6163 6740 30816528 30817119 3.960000e-147 532.0
4 TraesCS7A01G217200 chr7A 85.882 85 2 6 5674 5752 30816227 30816307 1.730000e-11 82.4
5 TraesCS7A01G217200 chr7A 100.000 42 0 0 6672 6713 183651672 183651631 2.230000e-10 78.7
6 TraesCS7A01G217200 chr7D 94.716 5791 226 28 1 5754 179188833 179183086 0.000000e+00 8925.0
7 TraesCS7A01G217200 chr7D 85.278 3179 300 88 1121 4184 30304558 30307683 0.000000e+00 3123.0
8 TraesCS7A01G217200 chr7D 91.892 1258 42 22 5845 7071 179183079 179181851 0.000000e+00 1703.0
9 TraesCS7A01G217200 chr7D 86.812 1380 130 22 4321 5686 30307816 30309157 0.000000e+00 1493.0
10 TraesCS7A01G217200 chr7D 84.808 599 59 17 6134 6707 30310581 30311172 2.340000e-159 573.0
11 TraesCS7A01G217200 chr7D 94.059 101 5 1 7087 7186 179181729 179181629 1.300000e-32 152.0
12 TraesCS7A01G217200 chr7D 87.313 134 7 3 950 1083 30304282 30304405 2.170000e-30 145.0
13 TraesCS7A01G217200 chr7D 92.222 90 7 0 25 114 356895689 356895600 2.190000e-25 128.0
14 TraesCS7A01G217200 chr7D 87.059 85 4 3 5674 5752 30310273 30310356 1.030000e-13 89.8
15 TraesCS7A01G217200 chr7B 93.115 3413 167 36 2669 6043 145374794 145371412 0.000000e+00 4939.0
16 TraesCS7A01G217200 chr7B 94.620 1301 63 5 1307 2603 145376271 145374974 0.000000e+00 2008.0
17 TraesCS7A01G217200 chr7B 89.406 1095 43 24 6134 7199 145371415 145370365 0.000000e+00 1312.0
18 TraesCS7A01G217200 chr7B 87.349 332 24 6 952 1279 145377633 145377316 1.530000e-96 364.0
19 TraesCS7A01G217200 chr7B 98.077 52 1 0 2620 2671 145374926 145374875 2.870000e-14 91.6
20 TraesCS7A01G217200 chr7B 94.444 54 2 1 62 114 733613883 733613830 1.730000e-11 82.4
21 TraesCS7A01G217200 chr4A 86.143 1898 180 40 1114 2946 698427201 698429080 0.000000e+00 1971.0
22 TraesCS7A01G217200 chr4A 86.630 1451 143 22 4317 5752 698430572 698431986 0.000000e+00 1557.0
23 TraesCS7A01G217200 chr4A 85.290 1278 102 43 2951 4179 698429202 698430442 0.000000e+00 1240.0
24 TraesCS7A01G217200 chr4A 86.015 522 56 15 6134 6646 698432211 698432724 1.830000e-150 544.0
25 TraesCS7A01G217200 chr4A 83.988 331 41 10 6323 6646 698462805 698463130 2.620000e-79 307.0
26 TraesCS7A01G217200 chr4A 89.691 194 16 3 6134 6326 698462202 698462392 2.080000e-60 244.0
27 TraesCS7A01G217200 chr4A 89.815 108 8 2 969 1076 698426841 698426945 1.310000e-27 135.0
28 TraesCS7A01G217200 chr4A 86.905 84 5 3 5674 5752 698456628 698456710 1.030000e-13 89.8
29 TraesCS7A01G217200 chr1A 76.443 849 156 35 1388 2208 367436751 367435919 3.220000e-113 420.0
30 TraesCS7A01G217200 chr1A 80.289 553 86 17 3006 3541 367435245 367434699 5.430000e-106 396.0
31 TraesCS7A01G217200 chr1A 81.586 353 45 11 4424 4775 367433926 367433593 2.650000e-69 274.0
32 TraesCS7A01G217200 chr1A 81.098 328 51 7 5287 5609 367432997 367432676 1.240000e-62 252.0
33 TraesCS7A01G217200 chr1A 92.857 112 8 0 3950 4061 367434421 367434310 5.990000e-36 163.0
34 TraesCS7A01G217200 chr1A 85.401 137 16 4 2430 2565 367435669 367435536 1.010000e-28 139.0
35 TraesCS7A01G217200 chr1A 92.857 98 4 3 6040 6135 532672892 532672796 1.010000e-28 139.0
36 TraesCS7A01G217200 chr1D 80.576 556 84 15 3006 3542 294467971 294467421 2.510000e-109 407.0
37 TraesCS7A01G217200 chr1D 82.203 354 41 12 4424 4775 294466513 294466180 1.230000e-72 285.0
38 TraesCS7A01G217200 chr1D 91.736 121 9 1 3942 4061 294467049 294466929 4.630000e-37 167.0
39 TraesCS7A01G217200 chr1D 93.750 80 5 0 7384 7463 416282773 416282694 3.660000e-23 121.0
40 TraesCS7A01G217200 chr1B 79.603 554 91 16 3006 3542 396148804 396148256 1.970000e-100 377.0
41 TraesCS7A01G217200 chr1B 75.361 832 163 33 1403 2208 396150291 396149476 5.500000e-96 363.0
42 TraesCS7A01G217200 chr1B 82.153 353 43 10 4424 4775 396147350 396147017 1.230000e-72 285.0
43 TraesCS7A01G217200 chr1B 90.909 121 10 1 3942 4061 396147888 396147768 2.150000e-35 161.0
44 TraesCS7A01G217200 chr1B 91.346 104 6 3 6039 6140 56752489 56752387 1.010000e-28 139.0
45 TraesCS7A01G217200 chr1B 89.583 48 3 1 534 579 188444519 188444566 8.090000e-05 60.2
46 TraesCS7A01G217200 chrUn 92.746 193 9 2 7189 7381 62520223 62520036 2.650000e-69 274.0
47 TraesCS7A01G217200 chrUn 92.746 193 9 2 7189 7381 62579581 62579394 2.650000e-69 274.0
48 TraesCS7A01G217200 chrUn 92.746 193 9 2 7189 7381 363886199 363886012 2.650000e-69 274.0
49 TraesCS7A01G217200 chrUn 91.710 193 11 2 7189 7381 62523173 62522986 5.740000e-66 263.0
50 TraesCS7A01G217200 chrUn 91.192 193 12 2 7189 7381 62395499 62395312 2.670000e-64 257.0
51 TraesCS7A01G217200 chrUn 91.192 193 12 2 7189 7381 62451143 62450956 2.670000e-64 257.0
52 TraesCS7A01G217200 chrUn 89.583 48 3 1 534 579 79709179 79709226 8.090000e-05 60.2
53 TraesCS7A01G217200 chr6A 93.158 190 8 2 7189 7378 4426497 4426681 2.650000e-69 274.0
54 TraesCS7A01G217200 chr6A 92.632 190 9 2 7189 7378 4297581 4297765 1.230000e-67 268.0
55 TraesCS7A01G217200 chr4B 92.935 184 8 2 7189 7372 637366807 637366629 5.740000e-66 263.0
56 TraesCS7A01G217200 chr6D 93.878 98 3 3 6040 6135 464266281 464266185 2.170000e-30 145.0
57 TraesCS7A01G217200 chr2D 93.750 96 6 0 6040 6135 643762841 643762746 2.170000e-30 145.0
58 TraesCS7A01G217200 chr2D 93.902 82 5 0 7382 7463 493165421 493165502 2.830000e-24 124.0
59 TraesCS7A01G217200 chr5D 92.784 97 6 1 6040 6135 65990491 65990587 1.010000e-28 139.0
60 TraesCS7A01G217200 chr5D 90.476 105 7 3 6040 6143 558970435 558970537 1.310000e-27 135.0
61 TraesCS7A01G217200 chr5D 91.489 47 3 1 534 579 51196094 51196048 6.250000e-06 63.9
62 TraesCS7A01G217200 chr5D 89.583 48 3 1 534 579 51119184 51119137 8.090000e-05 60.2
63 TraesCS7A01G217200 chr5D 89.583 48 3 1 534 579 51156603 51156556 8.090000e-05 60.2
64 TraesCS7A01G217200 chr5D 89.583 48 3 1 534 579 51177107 51177060 8.090000e-05 60.2
65 TraesCS7A01G217200 chr5D 89.583 48 3 1 534 579 339303537 339303490 8.090000e-05 60.2
66 TraesCS7A01G217200 chr3D 92.784 97 6 1 6040 6135 138076336 138076240 1.010000e-28 139.0
67 TraesCS7A01G217200 chr3D 87.912 91 9 2 25 114 75769504 75769415 1.020000e-18 106.0
68 TraesCS7A01G217200 chr5A 91.089 101 8 1 6037 6136 593472224 593472324 1.310000e-27 135.0
69 TraesCS7A01G217200 chr5A 95.000 80 4 0 7384 7463 528554867 528554946 7.860000e-25 126.0
70 TraesCS7A01G217200 chr6B 96.203 79 3 0 7384 7462 134208724 134208646 6.080000e-26 130.0
71 TraesCS7A01G217200 chr5B 95.000 80 4 0 7384 7463 318172800 318172879 7.860000e-25 126.0
72 TraesCS7A01G217200 chr5B 96.000 50 2 0 28 77 60971449 60971498 1.730000e-11 82.4
73 TraesCS7A01G217200 chr5B 89.583 48 3 1 534 579 60976530 60976577 8.090000e-05 60.2
74 TraesCS7A01G217200 chr4D 92.222 90 5 2 7374 7463 363245695 363245782 7.860000e-25 126.0
75 TraesCS7A01G217200 chr2B 90.625 96 6 3 21 114 182355128 182355222 2.830000e-24 124.0
76 TraesCS7A01G217200 chr2B 89.655 58 5 1 7 64 182355064 182355120 1.040000e-08 73.1
77 TraesCS7A01G217200 chr2B 94.595 37 0 1 5754 5788 501008285 501008249 1.000000e-03 56.5
78 TraesCS7A01G217200 chr2A 93.671 79 5 0 7385 7463 673281614 673281692 1.320000e-22 119.0
79 TraesCS7A01G217200 chr2A 89.024 82 6 3 29 108 71077439 71077519 1.710000e-16 99.0
80 TraesCS7A01G217200 chr3A 91.463 82 7 0 7382 7463 458189180 458189261 6.120000e-21 113.0
81 TraesCS7A01G217200 chr3A 87.500 96 9 3 21 114 323383396 323383490 2.850000e-19 108.0
82 TraesCS7A01G217200 chr3B 89.011 91 7 3 7374 7463 106026393 106026481 7.920000e-20 110.0


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 TraesCS7A01G217200 chr7A 183710694 183718156 7462 True 13782.000000 13782 100.000000 1 7463 1 chr7A.!!$R2 7462
1 TraesCS7A01G217200 chr7A 30810493 30817119 6626 False 1333.350000 3247 85.249000 950 6740 4 chr7A.!!$F1 5790
2 TraesCS7A01G217200 chr7D 179181629 179188833 7204 True 3593.333333 8925 93.555667 1 7186 3 chr7D.!!$R2 7185
3 TraesCS7A01G217200 chr7D 30304282 30311172 6890 False 1084.760000 3123 86.254000 950 6707 5 chr7D.!!$F1 5757
4 TraesCS7A01G217200 chr7B 145370365 145377633 7268 True 1742.920000 4939 92.513400 952 7199 5 chr7B.!!$R2 6247
5 TraesCS7A01G217200 chr4A 698426841 698432724 5883 False 1089.400000 1971 86.778600 969 6646 5 chr4A.!!$F2 5677
6 TraesCS7A01G217200 chr4A 698462202 698463130 928 False 275.500000 307 86.839500 6134 6646 2 chr4A.!!$F3 512
7 TraesCS7A01G217200 chr1A 367432676 367436751 4075 True 274.000000 420 82.945667 1388 5609 6 chr1A.!!$R2 4221
8 TraesCS7A01G217200 chr1D 294466180 294467971 1791 True 286.333333 407 84.838333 3006 4775 3 chr1D.!!$R2 1769
9 TraesCS7A01G217200 chr1B 396147017 396150291 3274 True 296.500000 377 82.006500 1403 4775 4 chr1B.!!$R2 3372
10 TraesCS7A01G217200 chrUn 62520036 62523173 3137 True 268.500000 274 92.228000 7189 7381 2 chrUn.!!$R5 192


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
175 176 0.108662 CGACCTGCACATGCTCTGTA 60.109 55.0 5.31 0.00 42.66 2.74 F
767 782 0.250901 ACTTGATGGTCCTGGTGCAC 60.251 55.0 8.80 8.80 0.00 4.57 F
1676 2979 0.749091 TGGATGGAGCTTCAATGCCG 60.749 55.0 0.00 0.00 0.00 5.69 F
3142 4803 2.092375 AGTAACCCCTGCTAGAATTGCC 60.092 50.0 0.00 0.00 0.00 4.52 F
3199 4860 2.341846 TGGGTGTTCAAGTCCTTGTC 57.658 50.0 6.90 3.34 41.16 3.18 F
4907 6840 0.250166 GCTACCAAGTGTGAACCGGT 60.250 55.0 0.00 0.00 0.00 5.28 F
5678 7733 1.379527 GCTATGTTGCGTAGGCCTTT 58.620 50.0 12.58 0.00 38.85 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1193 1440 0.179032 ACTTGACGATGTTGGCCACA 60.179 50.000 3.88 7.85 40.71 4.17 R
2247 3595 2.911819 ACGCCACCAAAATCAATACG 57.088 45.000 0.00 0.00 0.00 3.06 R
3199 4860 2.170187 CTCCAGTTCCCTTGGATCAGAG 59.830 54.545 0.00 0.00 43.46 3.35 R
4269 6105 2.174319 GGTAAGCTGCTACGCTGGC 61.174 63.158 0.90 0.00 40.79 4.85 R
5181 7179 3.721087 ATTCACCGACCAGGAAAGAAT 57.279 42.857 0.00 0.00 45.00 2.40 R
6035 9281 1.192146 TGGGACACAGGGAGTAGCAC 61.192 60.000 0.00 0.00 0.00 4.40 R
7285 14084 1.030457 CCCACGTTCGGCTATACTCT 58.970 55.000 0.00 0.00 0.00 3.24 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
93 94 4.514577 CCCCGCGCTCCTGTACAG 62.515 72.222 16.34 16.34 0.00 2.74
136 137 1.525077 GTTCACAACTGCCCCACGA 60.525 57.895 0.00 0.00 0.00 4.35
175 176 0.108662 CGACCTGCACATGCTCTGTA 60.109 55.000 5.31 0.00 42.66 2.74
176 177 1.472201 CGACCTGCACATGCTCTGTAT 60.472 52.381 5.31 0.00 42.66 2.29
177 178 2.636830 GACCTGCACATGCTCTGTATT 58.363 47.619 5.31 0.00 42.66 1.89
190 191 3.682858 GCTCTGTATTAAACCACTTGCGA 59.317 43.478 0.00 0.00 0.00 5.10
197 198 8.583810 TGTATTAAACCACTTGCGATCTATAC 57.416 34.615 0.00 0.00 0.00 1.47
198 199 8.198778 TGTATTAAACCACTTGCGATCTATACA 58.801 33.333 0.00 0.00 0.00 2.29
199 200 9.204570 GTATTAAACCACTTGCGATCTATACAT 57.795 33.333 0.00 0.00 0.00 2.29
200 201 5.991328 AAACCACTTGCGATCTATACATG 57.009 39.130 0.00 0.00 0.00 3.21
214 218 5.389520 TCTATACATGCTAGCAGAAGAGGT 58.610 41.667 23.89 14.96 0.00 3.85
224 228 4.249638 AGCAGAAGAGGTCTAGTCTGAT 57.750 45.455 11.36 3.88 39.94 2.90
228 232 4.035091 CAGAAGAGGTCTAGTCTGATGACG 59.965 50.000 3.48 0.00 40.50 4.35
229 233 6.143061 CAGAAGAGGTCTAGTCTGATGACGA 61.143 48.000 3.48 0.00 40.50 4.20
231 235 9.265135 CAGAAGAGGTCTAGTCTGATGACGAAG 62.265 48.148 3.48 0.00 40.50 3.79
244 248 4.621460 TGATGACGAAGAAAGCTTTAGTCG 59.379 41.667 28.86 28.86 41.15 4.18
245 249 3.973657 TGACGAAGAAAGCTTTAGTCGT 58.026 40.909 33.05 33.05 41.15 4.34
258 273 3.416119 TTAGTCGTGAGCAATAGTCCG 57.584 47.619 0.00 0.00 0.00 4.79
276 291 1.852895 CCGTGAAGTCGCTATTGCTAC 59.147 52.381 0.00 0.00 36.97 3.58
284 299 0.940126 CGCTATTGCTACCAAGGCAG 59.060 55.000 0.00 0.00 40.90 4.85
311 326 2.408271 TGCACATCCTGATCTTCACC 57.592 50.000 0.00 0.00 0.00 4.02
334 349 0.907486 CTGTCATTGGAGCTCCCTGA 59.093 55.000 29.95 26.61 35.38 3.86
342 357 3.582998 TGGAGCTCCCTGATTTTATGG 57.417 47.619 29.95 0.00 35.38 2.74
351 366 4.104738 TCCCTGATTTTATGGAGGGTGATC 59.895 45.833 0.00 0.00 44.99 2.92
419 434 0.883814 GCCTCTCATTCGCCCAGATG 60.884 60.000 0.00 0.00 0.00 2.90
437 452 3.303135 TTGGAGCCTCGTCGCACT 61.303 61.111 0.00 0.00 0.00 4.40
438 453 2.867855 TTGGAGCCTCGTCGCACTT 61.868 57.895 0.00 0.00 0.00 3.16
458 473 2.111384 TGCTGGGTCATTCTCTACCTC 58.889 52.381 0.00 0.00 35.97 3.85
459 474 2.292521 TGCTGGGTCATTCTCTACCTCT 60.293 50.000 0.00 0.00 35.97 3.69
460 475 2.769095 GCTGGGTCATTCTCTACCTCTT 59.231 50.000 0.00 0.00 35.97 2.85
461 476 3.198853 GCTGGGTCATTCTCTACCTCTTT 59.801 47.826 0.00 0.00 35.97 2.52
462 477 4.682050 GCTGGGTCATTCTCTACCTCTTTC 60.682 50.000 0.00 0.00 35.97 2.62
463 478 4.689062 TGGGTCATTCTCTACCTCTTTCT 58.311 43.478 0.00 0.00 35.97 2.52
464 479 4.712337 TGGGTCATTCTCTACCTCTTTCTC 59.288 45.833 0.00 0.00 35.97 2.87
465 480 4.959839 GGGTCATTCTCTACCTCTTTCTCT 59.040 45.833 0.00 0.00 35.97 3.10
466 481 6.130569 GGGTCATTCTCTACCTCTTTCTCTA 58.869 44.000 0.00 0.00 35.97 2.43
467 482 6.040054 GGGTCATTCTCTACCTCTTTCTCTAC 59.960 46.154 0.00 0.00 35.97 2.59
468 483 6.040054 GGTCATTCTCTACCTCTTTCTCTACC 59.960 46.154 0.00 0.00 32.72 3.18
469 484 6.831868 GTCATTCTCTACCTCTTTCTCTACCT 59.168 42.308 0.00 0.00 0.00 3.08
470 485 7.012989 GTCATTCTCTACCTCTTTCTCTACCTC 59.987 44.444 0.00 0.00 0.00 3.85
519 534 4.838486 CGGAGCCTCGTCGCACTC 62.838 72.222 0.00 0.00 0.00 3.51
572 587 2.452600 TTGGTCAGGAATTATGCCCC 57.547 50.000 0.00 0.00 0.00 5.80
592 607 9.605951 ATGCCCCTATATAATTTGACTGAAAAT 57.394 29.630 0.00 0.00 0.00 1.82
621 636 9.738832 GATGTCTTAGACTATCTCAAAGTAACC 57.261 37.037 13.86 0.00 33.15 2.85
633 648 5.610982 TCTCAAAGTAACCATGCCCCTATAT 59.389 40.000 0.00 0.00 0.00 0.86
637 652 7.888021 TCAAAGTAACCATGCCCCTATATAATG 59.112 37.037 0.00 0.00 0.00 1.90
646 661 5.609782 TGCCCCTATATAATGGGACTGTAT 58.390 41.667 17.50 0.00 46.15 2.29
671 686 2.431057 GGTAGACTGTGTGGACTATGGG 59.569 54.545 0.00 0.00 0.00 4.00
674 689 2.108168 GACTGTGTGGACTATGGGCTA 58.892 52.381 0.00 0.00 0.00 3.93
679 694 6.082031 ACTGTGTGGACTATGGGCTATAATA 58.918 40.000 0.00 0.00 0.00 0.98
767 782 0.250901 ACTTGATGGTCCTGGTGCAC 60.251 55.000 8.80 8.80 0.00 4.57
774 789 0.954452 GGTCCTGGTGCACTTTTCTG 59.046 55.000 17.98 3.83 0.00 3.02
808 823 9.530633 GTAGTACTATATAAACTGCTTTGTGCT 57.469 33.333 5.75 0.00 43.37 4.40
844 859 9.046296 ACTAACAAACTATATGAACAGCATAGC 57.954 33.333 0.00 0.00 42.45 2.97
1071 1093 1.224592 GGATGTCCGCACCCAGAAT 59.775 57.895 0.00 0.00 0.00 2.40
1257 1516 1.269936 ACAAGGTACGTTCCTTCCACG 60.270 52.381 22.18 14.02 44.87 4.94
1284 1557 5.679906 CAAACGAATCCTGTTACTGAAGTG 58.320 41.667 0.00 0.00 0.00 3.16
1319 2604 4.017407 AGGATCAGTGGAGTAGACAGGTTA 60.017 45.833 0.00 0.00 0.00 2.85
1330 2615 5.219739 AGTAGACAGGTTATGGATCCACAT 58.780 41.667 18.99 4.55 34.90 3.21
1341 2626 7.201821 GGTTATGGATCCACATTAGTTTTGAGG 60.202 40.741 18.99 0.00 32.39 3.86
1343 2629 5.500234 TGGATCCACATTAGTTTTGAGGAG 58.500 41.667 11.44 0.00 37.29 3.69
1469 2755 1.153349 GTTGGAGGTCGAGCATCCC 60.153 63.158 18.15 14.54 46.85 3.85
1542 2842 7.951530 ACCATTGCTTTGTTCTTAGATTTTG 57.048 32.000 0.00 0.00 0.00 2.44
1676 2979 0.749091 TGGATGGAGCTTCAATGCCG 60.749 55.000 0.00 0.00 0.00 5.69
1683 2986 2.414691 GGAGCTTCAATGCCGAGTTTTC 60.415 50.000 0.00 0.00 0.00 2.29
1738 3049 7.014615 ACACATGATGCTCCTTTTCTTTTTACT 59.985 33.333 0.00 0.00 0.00 2.24
1851 3179 4.587262 AGTACCCCTTCCATTTTGAACAAC 59.413 41.667 0.00 0.00 0.00 3.32
1950 3287 4.705507 AGTATGTCGAGGAAAAGCTGTCTA 59.294 41.667 0.00 0.00 0.00 2.59
2175 3514 4.777366 TCCTATGGTCATGTGTTCTTCAGA 59.223 41.667 0.00 0.00 0.00 3.27
2237 3585 3.128242 GTGGAGCTCAGAAATTGATGGTG 59.872 47.826 17.19 0.00 34.68 4.17
2247 3595 3.648339 AATTGATGGTGCAGTTGTCAC 57.352 42.857 0.00 0.00 0.00 3.67
2442 3830 4.737054 CCTTGGCTGAAACAATGTGATAC 58.263 43.478 0.00 0.00 0.00 2.24
2730 4264 8.983724 GGCAAAATTTATTTACAACTTGTGCTA 58.016 29.630 4.57 0.00 33.83 3.49
2833 4368 9.578439 GTAATCTTACGTCTACCTTAATGTTGT 57.422 33.333 0.00 0.00 0.00 3.32
2956 4617 5.650266 TGATTCATTTAACATGCGGTTAGGT 59.350 36.000 0.00 0.00 42.63 3.08
3142 4803 2.092375 AGTAACCCCTGCTAGAATTGCC 60.092 50.000 0.00 0.00 0.00 4.52
3168 4829 7.000472 TGTCTTGATTTCAACCTTCAGAAGAT 59.000 34.615 12.14 0.00 0.00 2.40
3199 4860 2.341846 TGGGTGTTCAAGTCCTTGTC 57.658 50.000 6.90 3.34 41.16 3.18
3244 4905 6.432783 AGAAGATCCGTGAGAGGTATATTCAG 59.567 42.308 0.00 0.00 29.63 3.02
3350 5034 6.084326 TCCTGTTTGTTTCTAATTTCCTGC 57.916 37.500 0.00 0.00 0.00 4.85
3356 5040 4.331968 TGTTTCTAATTTCCTGCGATGGT 58.668 39.130 0.00 0.00 0.00 3.55
3360 5044 5.607939 TCTAATTTCCTGCGATGGTTCTA 57.392 39.130 0.00 0.00 0.00 2.10
3543 5252 8.611757 TGATATGTCATTGAAGGTATGTTTTCG 58.388 33.333 0.00 0.00 0.00 3.46
3803 5541 3.418047 CACCTTACGTTCCCTTCCAATT 58.582 45.455 0.00 0.00 0.00 2.32
3888 5653 6.980593 TGAATTTGAAAAGATGTACTGGGTG 58.019 36.000 0.00 0.00 0.00 4.61
3921 5687 7.280876 GTGTATGTGGATATCACTTGTGTTGAT 59.719 37.037 4.83 0.00 46.20 2.57
4079 5845 9.420118 TGGTATGGCTTATTTCTTCATATTGTT 57.580 29.630 0.00 0.00 0.00 2.83
4153 5937 4.880120 TCTTGAATCTCATCCATGACTTGC 59.120 41.667 0.00 0.00 32.50 4.01
4154 5938 3.548770 TGAATCTCATCCATGACTTGCC 58.451 45.455 0.00 0.00 32.50 4.52
4155 5939 3.201487 TGAATCTCATCCATGACTTGCCT 59.799 43.478 0.00 0.00 32.50 4.75
4156 5940 2.704464 TCTCATCCATGACTTGCCTG 57.296 50.000 0.00 0.00 32.50 4.85
4311 6180 5.691754 CAGTCTTTTGTTTTGCAATAGGACC 59.308 40.000 0.00 0.00 36.96 4.46
4313 6182 5.920840 GTCTTTTGTTTTGCAATAGGACCTC 59.079 40.000 0.00 0.00 36.96 3.85
4335 6207 8.985805 ACCTCGTTAGTAATAAAACAACTTCTG 58.014 33.333 0.00 0.00 0.00 3.02
4349 6221 5.380043 ACAACTTCTGTCATTGATGTTCCT 58.620 37.500 0.00 0.00 29.87 3.36
4352 6224 7.041098 ACAACTTCTGTCATTGATGTTCCTAAC 60.041 37.037 0.00 0.00 29.87 2.34
4400 6272 6.664515 TCAAGCCAAAATTAACTACTTGTCG 58.335 36.000 0.00 0.00 35.64 4.35
4612 6533 3.729716 GCTAGCTTTACTACGACGAATGG 59.270 47.826 7.70 0.00 0.00 3.16
4640 6561 5.645497 CAGCATTAGTTTGAAAGCTAGAGGT 59.355 40.000 0.00 0.00 0.00 3.85
4641 6562 5.645497 AGCATTAGTTTGAAAGCTAGAGGTG 59.355 40.000 0.00 0.00 0.00 4.00
4824 6745 1.141254 TGTCGCCTTGTTGTTTCCCTA 59.859 47.619 0.00 0.00 0.00 3.53
4907 6840 0.250166 GCTACCAAGTGTGAACCGGT 60.250 55.000 0.00 0.00 0.00 5.28
5000 6939 6.553953 TTCTTGTTGCTGGTCCATACTATA 57.446 37.500 0.00 0.00 0.00 1.31
5003 6942 3.389983 TGTTGCTGGTCCATACTATACCC 59.610 47.826 0.00 0.00 31.97 3.69
5171 7167 5.528690 TCTGCCATTTCACATAATAGTGCTC 59.471 40.000 0.00 0.00 39.35 4.26
5181 7179 7.826690 TCACATAATAGTGCTCGCATTAGATA 58.173 34.615 0.00 0.00 39.35 1.98
5234 7266 8.891671 TGTAAGTTATCGTTTTCTTGTAGGTT 57.108 30.769 0.00 0.00 0.00 3.50
5236 7268 8.981647 GTAAGTTATCGTTTTCTTGTAGGTTGA 58.018 33.333 0.00 0.00 0.00 3.18
5243 7275 8.441312 TCGTTTTCTTGTAGGTTGAAACTAAT 57.559 30.769 0.00 0.00 30.66 1.73
5244 7276 8.895737 TCGTTTTCTTGTAGGTTGAAACTAATT 58.104 29.630 0.00 0.00 30.66 1.40
5348 7398 2.271800 GTGTACCTGGAGAATCTTGCG 58.728 52.381 0.00 0.00 33.73 4.85
5438 7490 5.695851 AGGTTTGCTCAGTTATCTTTGTG 57.304 39.130 0.00 0.00 0.00 3.33
5488 7543 5.762179 TGATATACTAATGGGAGCAAGGG 57.238 43.478 0.00 0.00 0.00 3.95
5495 7550 1.719063 ATGGGAGCAAGGGTGTGTGT 61.719 55.000 0.00 0.00 0.00 3.72
5678 7733 1.379527 GCTATGTTGCGTAGGCCTTT 58.620 50.000 12.58 0.00 38.85 3.11
5765 8988 8.441311 AGCAATGATATACTCCCTCTATCAAA 57.559 34.615 0.00 0.00 35.96 2.69
5767 8990 9.678260 GCAATGATATACTCCCTCTATCAAAAT 57.322 33.333 0.00 0.00 35.96 1.82
5899 9140 3.758554 AGCTTTCTTTTGTATCGCACCAT 59.241 39.130 0.00 0.00 0.00 3.55
6035 9281 0.175302 TGCCCACTGCTGTTTTGTTG 59.825 50.000 0.00 0.00 42.00 3.33
6047 9293 2.948979 TGTTTTGTTGTGCTACTCCCTG 59.051 45.455 0.00 0.00 0.00 4.45
6063 9309 4.600111 ACTCCCTGTGTCCCAAAATAACTA 59.400 41.667 0.00 0.00 0.00 2.24
6066 9312 5.491078 TCCCTGTGTCCCAAAATAACTATCT 59.509 40.000 0.00 0.00 0.00 1.98
6067 9313 5.823045 CCCTGTGTCCCAAAATAACTATCTC 59.177 44.000 0.00 0.00 0.00 2.75
6114 9360 5.599999 AGTTGTACTGAAGTTGAGACACT 57.400 39.130 0.00 0.00 0.00 3.55
6115 9361 5.978814 AGTTGTACTGAAGTTGAGACACTT 58.021 37.500 0.00 0.00 39.84 3.16
6161 9409 4.336433 CACATGTTCAGTTTGTGTCTTCCT 59.664 41.667 0.00 0.00 36.77 3.36
6165 9413 6.174720 TGTTCAGTTTGTGTCTTCCTCTAT 57.825 37.500 0.00 0.00 0.00 1.98
6301 9583 1.478105 GATCATTCAGGTTGGTTGGCC 59.522 52.381 0.00 0.00 0.00 5.36
6458 10159 1.349357 GGAAGAGTCTGGCCAAGAAGT 59.651 52.381 7.01 0.00 36.40 3.01
6488 10189 0.668535 GCCATTTTACGATCCCTGGC 59.331 55.000 7.17 7.17 42.00 4.85
6527 10230 1.414181 GGCTGGCTGCTTATAGACTCA 59.586 52.381 16.14 0.00 42.39 3.41
6627 10336 5.046376 TGGATGTATGAGTGATTGAGTGTGT 60.046 40.000 0.00 0.00 0.00 3.72
6655 10370 1.101331 GTGTGGGTAGTAGGACTCGG 58.899 60.000 0.00 0.00 0.00 4.63
6778 10514 5.460646 CATCATGTTCGGCCCAATTAATAC 58.539 41.667 0.00 0.00 0.00 1.89
6815 10553 8.892723 TGGTTTAATATGTGAGCAATTAGACAG 58.107 33.333 0.00 0.00 0.00 3.51
6929 10673 6.506500 TTTTACACCTTTTCCACGTTTGTA 57.493 33.333 0.00 0.00 0.00 2.41
6937 10681 5.470777 CCTTTTCCACGTTTGTATTGGTAGA 59.529 40.000 0.00 0.00 0.00 2.59
7136 10986 5.682212 GCAACCTTGTTTCTTTTGGATCAGT 60.682 40.000 0.00 0.00 0.00 3.41
7175 11026 3.255642 TCTTTTCTTTTGCGGGAAGATGG 59.744 43.478 0.00 0.00 33.48 3.51
7187 11038 2.755103 GGGAAGATGGACATGTTTCACC 59.245 50.000 0.00 0.00 0.00 4.02
7207 11058 1.363744 GAGAAGTGCATCCCTGAACG 58.636 55.000 0.00 0.00 35.89 3.95
7283 14082 3.146618 TCAGCTAAGCGTGCTAGTTAC 57.853 47.619 0.00 0.00 38.92 2.50
7284 14083 2.753452 TCAGCTAAGCGTGCTAGTTACT 59.247 45.455 0.00 0.00 38.92 2.24
7285 14084 3.943381 TCAGCTAAGCGTGCTAGTTACTA 59.057 43.478 0.00 0.00 38.92 1.82
7302 14101 5.236047 AGTTACTAGAGTATAGCCGAACGTG 59.764 44.000 0.00 0.00 0.00 4.49
7331 14130 5.522460 AGCAAACTGAAACGTATATGCGTAT 59.478 36.000 19.28 7.17 45.00 3.06
7346 14145 3.482436 TGCGTATTCAAAGGACCAAACT 58.518 40.909 0.00 0.00 0.00 2.66
7378 14177 1.291877 CTGACACAAGCAGGGTACGC 61.292 60.000 0.77 0.77 30.42 4.42
7381 14180 4.308458 ACAAGCAGGGTACGCGCA 62.308 61.111 21.71 0.00 0.00 6.09
7382 14181 3.788766 CAAGCAGGGTACGCGCAC 61.789 66.667 21.71 2.26 0.00 5.34
7389 14188 4.015382 GGTACGCGCACGGCAAAA 62.015 61.111 5.73 0.00 46.04 2.44
7390 14189 2.174835 GTACGCGCACGGCAAAAT 59.825 55.556 5.73 0.00 46.04 1.82
7391 14190 1.441349 GTACGCGCACGGCAAAATT 60.441 52.632 5.73 0.00 46.04 1.82
7392 14191 1.441182 TACGCGCACGGCAAAATTG 60.441 52.632 5.73 0.00 46.04 2.32
7393 14192 1.842698 TACGCGCACGGCAAAATTGA 61.843 50.000 5.73 0.00 46.04 2.57
7394 14193 1.801113 CGCGCACGGCAAAATTGAT 60.801 52.632 8.75 0.00 43.84 2.57
7395 14194 0.522286 CGCGCACGGCAAAATTGATA 60.522 50.000 8.75 0.00 43.84 2.15
7396 14195 1.623359 GCGCACGGCAAAATTGATAA 58.377 45.000 0.30 0.00 42.87 1.75
7397 14196 1.989165 GCGCACGGCAAAATTGATAAA 59.011 42.857 0.30 0.00 42.87 1.40
7398 14197 2.602660 GCGCACGGCAAAATTGATAAAT 59.397 40.909 0.30 0.00 42.87 1.40
7399 14198 3.061965 GCGCACGGCAAAATTGATAAATT 59.938 39.130 0.30 0.00 42.87 1.82
7400 14199 4.435386 GCGCACGGCAAAATTGATAAATTT 60.435 37.500 0.30 0.00 42.87 1.82
7401 14200 5.014483 CGCACGGCAAAATTGATAAATTTG 58.986 37.500 1.29 0.00 37.17 2.32
7402 14201 5.164012 CGCACGGCAAAATTGATAAATTTGA 60.164 36.000 1.29 0.00 36.41 2.69
7403 14202 6.014898 GCACGGCAAAATTGATAAATTTGAC 58.985 36.000 1.29 2.84 38.43 3.18
7404 14203 6.533185 CACGGCAAAATTGATAAATTTGACC 58.467 36.000 1.29 5.81 38.55 4.02
7405 14204 6.368516 CACGGCAAAATTGATAAATTTGACCT 59.631 34.615 13.98 3.76 38.55 3.85
7406 14205 7.543868 CACGGCAAAATTGATAAATTTGACCTA 59.456 33.333 13.98 0.00 38.55 3.08
7407 14206 8.257306 ACGGCAAAATTGATAAATTTGACCTAT 58.743 29.630 13.98 4.24 38.55 2.57
7408 14207 8.542132 CGGCAAAATTGATAAATTTGACCTATG 58.458 33.333 13.98 5.22 38.55 2.23
7409 14208 9.598517 GGCAAAATTGATAAATTTGACCTATGA 57.401 29.630 1.29 0.00 36.32 2.15
7424 14223 9.474920 TTTGACCTATGAACAAAATCAAATCAC 57.525 29.630 0.00 0.00 31.51 3.06
7425 14224 8.175925 TGACCTATGAACAAAATCAAATCACA 57.824 30.769 0.00 0.00 32.06 3.58
7426 14225 8.298854 TGACCTATGAACAAAATCAAATCACAG 58.701 33.333 0.00 0.00 32.06 3.66
7427 14226 8.408043 ACCTATGAACAAAATCAAATCACAGA 57.592 30.769 0.00 0.00 32.06 3.41
7428 14227 8.859090 ACCTATGAACAAAATCAAATCACAGAA 58.141 29.630 0.00 0.00 32.06 3.02
7429 14228 9.865321 CCTATGAACAAAATCAAATCACAGAAT 57.135 29.630 0.00 0.00 32.06 2.40
7432 14231 9.767228 ATGAACAAAATCAAATCACAGAATGAA 57.233 25.926 0.00 0.00 35.17 2.57
7433 14232 9.033481 TGAACAAAATCAAATCACAGAATGAAC 57.967 29.630 0.00 0.00 41.93 3.18
7434 14233 9.252962 GAACAAAATCAAATCACAGAATGAACT 57.747 29.630 0.00 0.00 41.93 3.01
7435 14234 8.583810 ACAAAATCAAATCACAGAATGAACTG 57.416 30.769 0.00 0.00 41.93 3.16
7436 14235 8.415553 ACAAAATCAAATCACAGAATGAACTGA 58.584 29.630 0.00 0.00 41.93 3.41
7437 14236 8.697067 CAAAATCAAATCACAGAATGAACTGAC 58.303 33.333 0.00 0.00 41.93 3.51
7438 14237 5.947228 TCAAATCACAGAATGAACTGACC 57.053 39.130 0.00 0.00 41.93 4.02
7439 14238 4.452114 TCAAATCACAGAATGAACTGACCG 59.548 41.667 0.00 0.00 41.93 4.79
7440 14239 3.685139 ATCACAGAATGAACTGACCGT 57.315 42.857 0.00 0.00 41.93 4.83
7441 14240 2.754472 TCACAGAATGAACTGACCGTG 58.246 47.619 0.00 0.00 39.69 4.94
7442 14241 2.364002 TCACAGAATGAACTGACCGTGA 59.636 45.455 0.00 0.00 39.69 4.35
7443 14242 3.130633 CACAGAATGAACTGACCGTGAA 58.869 45.455 0.00 0.00 39.69 3.18
7444 14243 3.559655 CACAGAATGAACTGACCGTGAAA 59.440 43.478 0.00 0.00 39.69 2.69
7445 14244 3.560068 ACAGAATGAACTGACCGTGAAAC 59.440 43.478 0.00 0.00 39.69 2.78
7446 14245 3.809832 CAGAATGAACTGACCGTGAAACT 59.190 43.478 0.00 0.00 39.69 2.66
7447 14246 4.988540 CAGAATGAACTGACCGTGAAACTA 59.011 41.667 0.00 0.00 39.69 2.24
7448 14247 5.639506 CAGAATGAACTGACCGTGAAACTAT 59.360 40.000 0.00 0.00 39.69 2.12
7449 14248 6.147821 CAGAATGAACTGACCGTGAAACTATT 59.852 38.462 0.00 0.00 39.69 1.73
7450 14249 6.710744 AGAATGAACTGACCGTGAAACTATTT 59.289 34.615 0.00 0.00 31.75 1.40
7451 14250 6.877611 ATGAACTGACCGTGAAACTATTTT 57.122 33.333 0.00 0.00 31.75 1.82
7452 14251 7.972832 ATGAACTGACCGTGAAACTATTTTA 57.027 32.000 0.00 0.00 31.75 1.52
7453 14252 7.181143 TGAACTGACCGTGAAACTATTTTAC 57.819 36.000 0.00 0.00 31.75 2.01
7455 14254 4.151157 ACTGACCGTGAAACTATTTTACGC 59.849 41.667 11.74 2.47 46.98 4.42
7456 14255 3.121611 TGACCGTGAAACTATTTTACGCG 59.878 43.478 3.53 3.53 46.98 6.01
7457 14256 2.412770 ACCGTGAAACTATTTTACGCGG 59.587 45.455 12.47 18.86 46.98 6.46
7458 14257 2.424341 CGTGAAACTATTTTACGCGGC 58.576 47.619 12.47 0.00 43.78 6.53
7459 14258 2.093152 CGTGAAACTATTTTACGCGGCT 59.907 45.455 12.47 0.00 43.78 5.52
7460 14259 3.413558 GTGAAACTATTTTACGCGGCTG 58.586 45.455 12.47 0.00 0.00 4.85
7461 14260 3.123959 GTGAAACTATTTTACGCGGCTGA 59.876 43.478 12.47 0.00 0.00 4.26
7462 14261 3.123959 TGAAACTATTTTACGCGGCTGAC 59.876 43.478 12.47 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 2.425592 CTCGTGGGGCAGTTGTGA 59.574 61.111 0.00 0.00 0.00 3.58
175 176 7.307989 GCATGTATAGATCGCAAGTGGTTTAAT 60.308 37.037 0.00 0.00 39.48 1.40
176 177 6.018262 GCATGTATAGATCGCAAGTGGTTTAA 60.018 38.462 0.00 0.00 39.48 1.52
177 178 5.465390 GCATGTATAGATCGCAAGTGGTTTA 59.535 40.000 0.00 0.00 39.48 2.01
190 191 6.015918 ACCTCTTCTGCTAGCATGTATAGAT 58.984 40.000 19.72 0.00 0.00 1.98
197 198 3.636300 ACTAGACCTCTTCTGCTAGCATG 59.364 47.826 19.72 12.53 35.55 4.06
198 199 3.888930 GACTAGACCTCTTCTGCTAGCAT 59.111 47.826 19.72 0.07 35.55 3.79
199 200 3.053991 AGACTAGACCTCTTCTGCTAGCA 60.054 47.826 18.22 18.22 35.55 3.49
200 201 3.315191 CAGACTAGACCTCTTCTGCTAGC 59.685 52.174 8.10 8.10 35.55 3.42
214 218 4.702612 AGCTTTCTTCGTCATCAGACTAGA 59.297 41.667 0.00 0.00 42.73 2.43
224 228 3.734231 CACGACTAAAGCTTTCTTCGTCA 59.266 43.478 30.56 9.49 36.34 4.35
228 232 3.741344 TGCTCACGACTAAAGCTTTCTTC 59.259 43.478 16.57 12.00 36.96 2.87
229 233 3.728845 TGCTCACGACTAAAGCTTTCTT 58.271 40.909 16.57 3.27 36.96 2.52
231 235 4.670227 ATTGCTCACGACTAAAGCTTTC 57.330 40.909 16.57 0.00 36.96 2.62
232 236 5.238583 ACTATTGCTCACGACTAAAGCTTT 58.761 37.500 17.30 17.30 36.96 3.51
240 244 1.135373 CACGGACTATTGCTCACGACT 60.135 52.381 0.00 0.00 0.00 4.18
244 248 2.924290 GACTTCACGGACTATTGCTCAC 59.076 50.000 0.00 0.00 0.00 3.51
245 249 2.415491 CGACTTCACGGACTATTGCTCA 60.415 50.000 0.00 0.00 0.00 4.26
292 307 1.629861 TGGTGAAGATCAGGATGTGCA 59.370 47.619 0.00 0.00 37.40 4.57
296 311 2.879026 CAGCATGGTGAAGATCAGGATG 59.121 50.000 20.20 0.00 37.54 3.51
302 317 3.066342 CCAATGACAGCATGGTGAAGATC 59.934 47.826 30.46 17.52 43.62 2.75
308 323 0.454600 GCTCCAATGACAGCATGGTG 59.545 55.000 22.91 22.91 43.62 4.17
311 326 1.022735 GGAGCTCCAATGACAGCATG 58.977 55.000 28.43 0.00 38.18 4.06
379 394 0.111253 CCTGGCCTTGTTGTCCTTCT 59.889 55.000 3.32 0.00 0.00 2.85
380 395 0.110486 TCCTGGCCTTGTTGTCCTTC 59.890 55.000 3.32 0.00 0.00 3.46
381 396 0.111253 CTCCTGGCCTTGTTGTCCTT 59.889 55.000 3.32 0.00 0.00 3.36
419 434 3.112709 GTGCGACGAGGCTCCAAC 61.113 66.667 9.32 0.00 0.00 3.77
437 452 2.501723 GAGGTAGAGAATGACCCAGCAA 59.498 50.000 0.00 0.00 36.27 3.91
438 453 2.111384 GAGGTAGAGAATGACCCAGCA 58.889 52.381 0.00 0.00 36.27 4.41
458 473 6.183360 CCTTGAGCTTAGAGAGGTAGAGAAAG 60.183 46.154 0.00 0.00 35.91 2.62
459 474 5.654650 CCTTGAGCTTAGAGAGGTAGAGAAA 59.345 44.000 0.00 0.00 35.91 2.52
460 475 5.197451 CCTTGAGCTTAGAGAGGTAGAGAA 58.803 45.833 0.00 0.00 35.91 2.87
461 476 4.385865 CCCTTGAGCTTAGAGAGGTAGAGA 60.386 50.000 0.00 0.00 35.91 3.10
462 477 3.888930 CCCTTGAGCTTAGAGAGGTAGAG 59.111 52.174 0.00 0.00 35.91 2.43
463 478 3.269906 ACCCTTGAGCTTAGAGAGGTAGA 59.730 47.826 0.00 0.00 35.91 2.59
464 479 3.383185 CACCCTTGAGCTTAGAGAGGTAG 59.617 52.174 0.00 0.00 35.91 3.18
465 480 3.366396 CACCCTTGAGCTTAGAGAGGTA 58.634 50.000 0.00 0.00 35.91 3.08
466 481 2.183679 CACCCTTGAGCTTAGAGAGGT 58.816 52.381 0.00 0.00 39.22 3.85
467 482 1.484240 CCACCCTTGAGCTTAGAGAGG 59.516 57.143 0.00 0.00 0.00 3.69
468 483 2.430332 CTCCACCCTTGAGCTTAGAGAG 59.570 54.545 0.00 0.00 0.00 3.20
469 484 2.225394 ACTCCACCCTTGAGCTTAGAGA 60.225 50.000 0.00 0.00 32.98 3.10
470 485 2.093764 CACTCCACCCTTGAGCTTAGAG 60.094 54.545 0.00 0.00 32.98 2.43
519 534 6.851222 ATATGGTCAGAAATTAACAGAGCG 57.149 37.500 0.00 0.00 0.00 5.03
555 570 5.717119 ATATAGGGGCATAATTCCTGACC 57.283 43.478 4.52 4.52 41.46 4.02
558 573 9.699410 TCAAATTATATAGGGGCATAATTCCTG 57.301 33.333 0.00 0.00 36.68 3.86
592 607 8.815565 ACTTTGAGATAGTCTAAGACATCTCA 57.184 34.615 19.59 19.59 44.66 3.27
633 648 7.787904 ACAGTCTACCATAATACAGTCCCATTA 59.212 37.037 0.00 0.00 0.00 1.90
637 652 5.363005 ACACAGTCTACCATAATACAGTCCC 59.637 44.000 0.00 0.00 0.00 4.46
646 661 5.362717 CCATAGTCCACACAGTCTACCATAA 59.637 44.000 0.00 0.00 0.00 1.90
679 694 7.847711 AGACATAGGCACAAATCTAGTCTAT 57.152 36.000 0.00 0.00 32.58 1.98
861 877 2.026822 ACCAGGATCATCAAGTCCACAC 60.027 50.000 0.00 0.00 36.96 3.82
1071 1093 2.188947 AGGGGGAGGGGAGTTACCA 61.189 63.158 0.00 0.00 41.20 3.25
1097 1344 2.100631 CCGTGGAATCTGGCGTGAC 61.101 63.158 0.00 0.00 0.00 3.67
1193 1440 0.179032 ACTTGACGATGTTGGCCACA 60.179 50.000 3.88 7.85 40.71 4.17
1232 1479 1.613836 AGGAACGTACCTTGTCGAGT 58.386 50.000 0.00 0.00 36.86 4.18
1257 1516 4.024387 TCAGTAACAGGATTCGTTTGCAAC 60.024 41.667 0.00 0.00 0.00 4.17
1269 1528 2.571653 CCCATCCACTTCAGTAACAGGA 59.428 50.000 0.00 0.00 0.00 3.86
1284 1557 0.689623 CTGATCCTGGCTACCCATCC 59.310 60.000 0.00 0.00 41.21 3.51
1319 2604 6.069440 TCTCCTCAAAACTAATGTGGATCCAT 60.069 38.462 19.62 4.39 39.12 3.41
1330 2615 2.979678 AGGGCTGTCTCCTCAAAACTAA 59.020 45.455 0.00 0.00 0.00 2.24
1341 2626 2.613223 GGACTGTAACAAGGGCTGTCTC 60.613 54.545 0.00 0.00 37.23 3.36
1343 2629 1.071699 TGGACTGTAACAAGGGCTGTC 59.928 52.381 0.00 0.00 37.23 3.51
1495 2791 3.807622 TCAAACAAAACGAGGTCAGCTAG 59.192 43.478 0.00 0.00 0.00 3.42
1676 2979 7.875554 AGAGAAACTCATAGACAAGGAAAACTC 59.124 37.037 0.00 0.00 32.06 3.01
1683 2986 4.869297 CAGCAGAGAAACTCATAGACAAGG 59.131 45.833 0.00 0.00 32.06 3.61
1738 3049 4.323028 CCTCACAAGTTCATTGGCTCTCTA 60.323 45.833 0.00 0.00 43.68 2.43
1882 3218 5.951747 AGCTGGCAGAATATGAAGGTAAAAA 59.048 36.000 20.86 0.00 0.00 1.94
2237 3585 4.616802 CCAAAATCAATACGTGACAACTGC 59.383 41.667 0.00 0.00 39.72 4.40
2247 3595 2.911819 ACGCCACCAAAATCAATACG 57.088 45.000 0.00 0.00 0.00 3.06
2455 3843 6.430000 GCTTCTACAACCTAAGAAACCATTGA 59.570 38.462 0.00 0.00 31.61 2.57
2718 4246 5.009854 AGCAAAACAATAGCACAAGTTGT 57.990 34.783 1.64 1.64 37.66 3.32
2720 4248 7.307337 GCATAAAGCAAAACAATAGCACAAGTT 60.307 33.333 0.00 0.00 44.79 2.66
2755 4289 6.713903 ATGTCTAATACATCCAGCAGGAAATG 59.286 38.462 0.32 0.00 46.15 2.32
2833 4368 5.178096 TGAATATCAGGAAAAGGACAGCA 57.822 39.130 0.00 0.00 0.00 4.41
2881 4420 9.555727 GGCATTACAGTATTAATACAGGAGAAA 57.444 33.333 24.05 11.89 35.74 2.52
2919 4463 4.411256 AATGAATCAAACATCATGGCCC 57.589 40.909 0.00 0.00 36.44 5.80
2956 4617 4.734398 AAGTGGCACAAAGAACAATTCA 57.266 36.364 21.41 0.00 44.16 2.57
3142 4803 6.484643 TCTTCTGAAGGTTGAAATCAAGACAG 59.515 38.462 16.83 4.78 36.39 3.51
3168 4829 4.412796 TGAACACCCATTTGCATTTTCA 57.587 36.364 0.00 0.00 0.00 2.69
3199 4860 2.170187 CTCCAGTTCCCTTGGATCAGAG 59.830 54.545 0.00 0.00 43.46 3.35
3299 4978 5.055144 TGAGAGAGCATATTCATTGCAGAC 58.945 41.667 0.00 0.00 42.62 3.51
3350 5034 3.731867 GCAAAAGGCATGTAGAACCATCG 60.732 47.826 0.00 0.00 43.97 3.84
3423 5130 5.471456 ACGTCAGATTCTCTGCAAAAAGAAT 59.529 36.000 15.00 15.00 43.95 2.40
3446 5155 3.508762 TCTCAATTCGCTCCTTCGTTAC 58.491 45.455 0.00 0.00 0.00 2.50
3543 5252 7.757941 AATTATCTAACTCTACCCGAGGTAC 57.242 40.000 0.00 0.00 44.33 3.34
3803 5541 7.054124 AGGACAAAAACTTCAGATTGAGTACA 58.946 34.615 0.00 0.00 0.00 2.90
3888 5653 6.119144 GTGATATCCACATACACAACAACC 57.881 41.667 0.00 0.00 45.03 3.77
3921 5687 7.663905 ACACCAATACAGCAGATTTAGTTACAA 59.336 33.333 0.00 0.00 0.00 2.41
4134 5909 3.564644 CAGGCAAGTCATGGATGAGATTC 59.435 47.826 0.00 0.00 37.51 2.52
4181 5985 6.145535 AGAATCTTTTAAACAGAAGCAAGCG 58.854 36.000 0.00 0.00 0.00 4.68
4269 6105 2.174319 GGTAAGCTGCTACGCTGGC 61.174 63.158 0.90 0.00 40.79 4.85
4335 6207 9.884465 GCATTATTAGTTAGGAACATCAATGAC 57.116 33.333 0.00 0.00 0.00 3.06
4400 6272 7.769044 TGCAGATTCTTGTTACTTTAGGATACC 59.231 37.037 0.00 0.00 37.17 2.73
4612 6533 4.301628 AGCTTTCAAACTAATGCTGTTGC 58.698 39.130 0.00 0.00 38.15 4.17
4640 6561 6.760298 TGCATAAAAGAAAAGCAATTGTGACA 59.240 30.769 7.40 0.00 31.42 3.58
4641 6562 7.176285 TGCATAAAAGAAAAGCAATTGTGAC 57.824 32.000 7.40 0.00 31.42 3.67
4978 6917 5.163343 GGTATAGTATGGACCAGCAACAAGA 60.163 44.000 0.00 0.00 33.16 3.02
5017 6985 3.817709 TTGAAAACAAGGCCTCAAAGG 57.182 42.857 5.23 0.00 38.80 3.11
5074 7043 8.437575 ACTTTTAACTGTTCCTATTCTCCTCAA 58.562 33.333 0.00 0.00 0.00 3.02
5076 7045 8.095169 TGACTTTTAACTGTTCCTATTCTCCTC 58.905 37.037 0.00 0.00 0.00 3.71
5171 7167 5.119279 CGACCAGGAAAGAATATCTAATGCG 59.881 44.000 0.00 0.00 0.00 4.73
5181 7179 3.721087 ATTCACCGACCAGGAAAGAAT 57.279 42.857 0.00 0.00 45.00 2.40
5265 7315 5.047590 CCTGCATGCATGACCAATATACATT 60.048 40.000 30.64 0.00 0.00 2.71
5278 7328 1.100510 AGCAACTACCTGCATGCATG 58.899 50.000 22.97 22.70 45.18 4.06
5279 7329 1.100510 CAGCAACTACCTGCATGCAT 58.899 50.000 22.97 10.26 45.18 3.96
5280 7330 0.961857 CCAGCAACTACCTGCATGCA 60.962 55.000 21.29 21.29 45.18 3.96
5281 7331 0.962356 ACCAGCAACTACCTGCATGC 60.962 55.000 11.82 11.82 45.18 4.06
5348 7398 1.909302 TCCCTGGATCCAAGAGTTGTC 59.091 52.381 17.00 0.00 0.00 3.18
5438 7490 5.409826 GGTTCAGTATGCAAGTATCATAGGC 59.590 44.000 0.00 0.00 34.76 3.93
5488 7543 1.583054 GAGGACCTGTCAACACACAC 58.417 55.000 0.00 0.00 0.00 3.82
5495 7550 1.334160 TAACAGCGAGGACCTGTCAA 58.666 50.000 0.00 0.00 42.37 3.18
5635 7690 4.429108 GAGCCATAATCCGCTTAGATCTC 58.571 47.826 0.00 0.00 34.84 2.75
5669 7724 5.408909 GTGAAACTAGTCTTCAAAGGCCTAC 59.591 44.000 5.16 0.00 34.68 3.18
5678 7733 3.314693 AGGGTGGTGAAACTAGTCTTCA 58.685 45.455 13.22 13.22 36.74 3.02
5817 9056 7.281100 GGAAACCAAGGAGATATTGTCTTACAG 59.719 40.741 0.00 0.00 37.29 2.74
5819 9058 7.339482 AGGAAACCAAGGAGATATTGTCTTAC 58.661 38.462 0.00 0.00 37.29 2.34
5823 9062 6.539103 GTGTAGGAAACCAAGGAGATATTGTC 59.461 42.308 0.00 0.00 0.00 3.18
5922 9165 4.624452 GTGCACTTACCTAACGACTTAAGG 59.376 45.833 10.32 0.00 0.00 2.69
6035 9281 1.192146 TGGGACACAGGGAGTAGCAC 61.192 60.000 0.00 0.00 0.00 4.40
6047 9293 7.923414 AGTTGAGATAGTTATTTTGGGACAC 57.077 36.000 0.00 0.00 39.29 3.67
6114 9360 4.641868 AGTACTCCCTCCATCCCAAATAA 58.358 43.478 0.00 0.00 0.00 1.40
6115 9361 4.295905 AGTACTCCCTCCATCCCAAATA 57.704 45.455 0.00 0.00 0.00 1.40
6161 9409 6.389830 ACAAAGTTGAACATGTGCAATAGA 57.610 33.333 22.15 0.00 0.00 1.98
6165 9413 5.233225 TCAAACAAAGTTGAACATGTGCAA 58.767 33.333 15.66 15.66 34.59 4.08
6362 10059 1.862827 CAAACTGCAGAGCAAAAAGGC 59.137 47.619 23.35 0.00 38.41 4.35
6458 10159 2.421775 CGTAAAATGGCATGTGGCTACA 59.578 45.455 4.99 4.99 44.01 2.74
6488 10189 2.883574 CCATGGCATAACAAACAGCAG 58.116 47.619 0.00 0.00 0.00 4.24
6527 10230 4.082026 GGAAAATCACAAGCAGCAACCTAT 60.082 41.667 0.00 0.00 0.00 2.57
6627 10336 7.302948 AGTCCTACTACCCACACATAATGATA 58.697 38.462 0.00 0.00 0.00 2.15
6815 10553 5.105063 GGCTAAACATCCTTTTCATCAAGC 58.895 41.667 0.00 0.00 0.00 4.01
6929 10673 8.706322 AAAACAAACCTACAGAATCTACCAAT 57.294 30.769 0.00 0.00 0.00 3.16
6937 10681 8.664669 ATTATGGGAAAACAAACCTACAGAAT 57.335 30.769 0.00 0.00 0.00 2.40
7105 10955 5.606348 AAAGAAACAAGGTTGCCAACATA 57.394 34.783 10.18 0.00 0.00 2.29
7136 10986 3.435105 AAGAAACGCAAACATGCTCAA 57.565 38.095 0.00 0.00 0.00 3.02
7149 10999 3.073144 TCCCGCAAAAGAAAAGAAACG 57.927 42.857 0.00 0.00 0.00 3.60
7175 11026 2.096218 GCACTTCTCGGTGAAACATGTC 60.096 50.000 0.00 0.00 39.98 3.06
7187 11038 1.363744 GTTCAGGGATGCACTTCTCG 58.636 55.000 0.00 0.00 0.00 4.04
7283 14082 2.225963 CCCACGTTCGGCTATACTCTAG 59.774 54.545 0.00 0.00 0.00 2.43
7284 14083 2.158769 TCCCACGTTCGGCTATACTCTA 60.159 50.000 0.00 0.00 0.00 2.43
7285 14084 1.030457 CCCACGTTCGGCTATACTCT 58.970 55.000 0.00 0.00 0.00 3.24
7302 14101 1.594331 ACGTTTCAGTTTGCTCTCCC 58.406 50.000 0.00 0.00 0.00 4.30
7331 14130 3.445805 GGTGTCAAGTTTGGTCCTTTGAA 59.554 43.478 0.00 0.00 31.98 2.69
7346 14145 3.274095 TGTGTCAGATTGTGGTGTCAA 57.726 42.857 0.00 0.00 0.00 3.18
7378 14177 4.838665 AATTTATCAATTTTGCCGTGCG 57.161 36.364 0.00 0.00 0.00 5.34
7381 14180 6.463360 AGGTCAAATTTATCAATTTTGCCGT 58.537 32.000 0.00 0.00 40.09 5.68
7382 14181 6.966435 AGGTCAAATTTATCAATTTTGCCG 57.034 33.333 0.00 0.00 40.09 5.69
7383 14182 9.598517 TCATAGGTCAAATTTATCAATTTTGCC 57.401 29.630 0.00 1.90 40.09 4.52
7398 14197 9.474920 GTGATTTGATTTTGTTCATAGGTCAAA 57.525 29.630 0.00 0.00 38.14 2.69
7399 14198 8.637099 TGTGATTTGATTTTGTTCATAGGTCAA 58.363 29.630 0.00 0.00 0.00 3.18
7400 14199 8.175925 TGTGATTTGATTTTGTTCATAGGTCA 57.824 30.769 0.00 0.00 0.00 4.02
7401 14200 8.514594 TCTGTGATTTGATTTTGTTCATAGGTC 58.485 33.333 0.00 0.00 0.00 3.85
7402 14201 8.408043 TCTGTGATTTGATTTTGTTCATAGGT 57.592 30.769 0.00 0.00 0.00 3.08
7403 14202 9.865321 ATTCTGTGATTTGATTTTGTTCATAGG 57.135 29.630 0.00 0.00 0.00 2.57
7406 14205 9.767228 TTCATTCTGTGATTTGATTTTGTTCAT 57.233 25.926 0.00 0.00 36.54 2.57
7407 14206 9.033481 GTTCATTCTGTGATTTGATTTTGTTCA 57.967 29.630 0.00 0.00 36.54 3.18
7408 14207 9.252962 AGTTCATTCTGTGATTTGATTTTGTTC 57.747 29.630 0.00 0.00 36.54 3.18
7409 14208 9.037737 CAGTTCATTCTGTGATTTGATTTTGTT 57.962 29.630 0.00 0.00 36.54 2.83
7410 14209 8.415553 TCAGTTCATTCTGTGATTTGATTTTGT 58.584 29.630 0.00 0.00 36.54 2.83
7411 14210 8.697067 GTCAGTTCATTCTGTGATTTGATTTTG 58.303 33.333 0.00 0.00 36.54 2.44
7412 14211 7.869429 GGTCAGTTCATTCTGTGATTTGATTTT 59.131 33.333 0.00 0.00 36.54 1.82
7413 14212 7.373493 GGTCAGTTCATTCTGTGATTTGATTT 58.627 34.615 0.00 0.00 36.54 2.17
7414 14213 6.348786 CGGTCAGTTCATTCTGTGATTTGATT 60.349 38.462 0.00 0.00 36.54 2.57
7415 14214 5.122869 CGGTCAGTTCATTCTGTGATTTGAT 59.877 40.000 0.00 0.00 36.54 2.57
7416 14215 4.452114 CGGTCAGTTCATTCTGTGATTTGA 59.548 41.667 0.00 0.00 36.54 2.69
7417 14216 4.214119 ACGGTCAGTTCATTCTGTGATTTG 59.786 41.667 0.00 0.00 36.54 2.32
7418 14217 4.214119 CACGGTCAGTTCATTCTGTGATTT 59.786 41.667 0.00 0.00 38.86 2.17
7419 14218 3.748048 CACGGTCAGTTCATTCTGTGATT 59.252 43.478 0.00 0.00 38.86 2.57
7420 14219 3.006859 TCACGGTCAGTTCATTCTGTGAT 59.993 43.478 0.00 0.00 40.00 3.06
7421 14220 2.364002 TCACGGTCAGTTCATTCTGTGA 59.636 45.455 0.00 0.00 41.77 3.58
7422 14221 2.754472 TCACGGTCAGTTCATTCTGTG 58.246 47.619 0.00 0.00 38.19 3.66
7423 14222 3.469008 TTCACGGTCAGTTCATTCTGT 57.531 42.857 0.00 0.00 36.85 3.41
7424 14223 3.809832 AGTTTCACGGTCAGTTCATTCTG 59.190 43.478 0.00 0.00 36.85 3.02
7425 14224 4.073293 AGTTTCACGGTCAGTTCATTCT 57.927 40.909 0.00 0.00 0.00 2.40
7426 14225 6.481954 AATAGTTTCACGGTCAGTTCATTC 57.518 37.500 0.00 0.00 0.00 2.67
7427 14226 6.877611 AAATAGTTTCACGGTCAGTTCATT 57.122 33.333 0.00 0.00 0.00 2.57
7428 14227 6.877611 AAAATAGTTTCACGGTCAGTTCAT 57.122 33.333 0.00 0.00 0.00 2.57
7429 14228 6.074195 CGTAAAATAGTTTCACGGTCAGTTCA 60.074 38.462 0.00 0.00 0.00 3.18
7430 14229 6.294363 CGTAAAATAGTTTCACGGTCAGTTC 58.706 40.000 0.00 0.00 0.00 3.01
7431 14230 5.333568 GCGTAAAATAGTTTCACGGTCAGTT 60.334 40.000 14.63 0.00 33.39 3.16
7432 14231 4.151157 GCGTAAAATAGTTTCACGGTCAGT 59.849 41.667 14.63 0.00 33.39 3.41
7433 14232 4.634991 GCGTAAAATAGTTTCACGGTCAG 58.365 43.478 14.63 0.00 33.39 3.51
7434 14233 3.121611 CGCGTAAAATAGTTTCACGGTCA 59.878 43.478 0.00 0.00 33.39 4.02
7435 14234 3.482436 CCGCGTAAAATAGTTTCACGGTC 60.482 47.826 4.92 2.62 34.41 4.79
7436 14235 2.412770 CCGCGTAAAATAGTTTCACGGT 59.587 45.455 4.92 0.00 34.41 4.83
7437 14236 2.785342 GCCGCGTAAAATAGTTTCACGG 60.785 50.000 15.43 15.43 38.56 4.94
7438 14237 2.093152 AGCCGCGTAAAATAGTTTCACG 59.907 45.455 4.92 10.93 35.78 4.35
7439 14238 3.123959 TCAGCCGCGTAAAATAGTTTCAC 59.876 43.478 4.92 0.00 0.00 3.18
7440 14239 3.123959 GTCAGCCGCGTAAAATAGTTTCA 59.876 43.478 4.92 0.00 0.00 2.69
7441 14240 3.667050 GTCAGCCGCGTAAAATAGTTTC 58.333 45.455 4.92 0.00 0.00 2.78
7442 14241 3.734776 GTCAGCCGCGTAAAATAGTTT 57.265 42.857 4.92 0.00 0.00 2.66



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

AutoCloner maintained by Alex Coulton.