Multiple sequence alignment - TraesCS7A01G266900

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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 TraesCS7A01G266900 chr7A 100.000 8300 0 0 1 8300 269965966 269957667 0.000000e+00 15328.0
1 TraesCS7A01G266900 chr7A 88.855 2315 161 47 5644 7908 269280695 269278428 0.000000e+00 2756.0
2 TraesCS7A01G266900 chr7A 87.291 1613 118 38 864 2401 269283369 269281769 0.000000e+00 1762.0
3 TraesCS7A01G266900 chr7A 88.701 708 61 12 4776 5477 269281775 269281081 0.000000e+00 846.0
4 TraesCS7A01G266900 chr7A 97.479 119 1 2 5532 5648 133053346 133053228 1.410000e-47 202.0
5 TraesCS7A01G266900 chr7A 87.050 139 8 3 7912 8045 269278489 269278356 1.870000e-31 148.0
6 TraesCS7A01G266900 chr7A 94.737 38 2 0 8063 8100 269277956 269277919 9.000000e-05 60.2
7 TraesCS7A01G266900 chr7B 93.026 2667 114 21 5644 8249 228391718 228394373 0.000000e+00 3829.0
8 TraesCS7A01G266900 chr7B 88.875 2319 165 43 5644 7908 228784778 228787057 0.000000e+00 2767.0
9 TraesCS7A01G266900 chr7B 90.596 1744 92 12 67 1770 228387462 228389173 0.000000e+00 2246.0
10 TraesCS7A01G266900 chr7B 96.452 620 19 2 1761 2380 228390236 228390852 0.000000e+00 1020.0
11 TraesCS7A01G266900 chr7B 89.987 789 40 16 4776 5542 228390950 228391721 0.000000e+00 983.0
12 TraesCS7A01G266900 chr7B 93.543 604 30 7 1610 2211 228782926 228783522 0.000000e+00 891.0
13 TraesCS7A01G266900 chr7B 86.675 773 61 22 4776 5542 228784045 228784781 0.000000e+00 819.0
14 TraesCS7A01G266900 chr7B 88.654 520 48 8 1093 1606 228782373 228782887 2.540000e-174 623.0
15 TraesCS7A01G266900 chr7B 92.453 265 19 1 493 756 711736956 711737220 2.190000e-100 377.0
16 TraesCS7A01G266900 chr7B 86.364 264 15 8 871 1116 228782103 228782363 1.370000e-67 268.0
17 TraesCS7A01G266900 chr7B 98.261 115 2 0 5533 5647 559142187 559142301 1.410000e-47 202.0
18 TraesCS7A01G266900 chr7B 96.154 52 2 0 8249 8300 228394405 228394456 1.480000e-12 86.1
19 TraesCS7A01G266900 chr7B 100.000 35 0 0 1 35 228385703 228385737 1.930000e-06 65.8
20 TraesCS7A01G266900 chr7D 94.741 2415 101 7 1 2402 251505212 251507613 0.000000e+00 3733.0
21 TraesCS7A01G266900 chr7D 93.910 2299 121 17 2446 4733 90628348 90626058 0.000000e+00 3452.0
22 TraesCS7A01G266900 chr7D 95.789 1781 44 9 5644 7415 251508367 251510125 0.000000e+00 2844.0
23 TraesCS7A01G266900 chr7D 88.683 2315 169 36 5644 7908 252029431 252031702 0.000000e+00 2737.0
24 TraesCS7A01G266900 chr7D 92.697 1520 99 6 3276 4784 521574678 521573160 0.000000e+00 2182.0
25 TraesCS7A01G266900 chr7D 97.653 767 16 1 4776 5542 251507606 251508370 0.000000e+00 1315.0
26 TraesCS7A01G266900 chr7D 91.609 870 28 11 7408 8249 251516227 251517079 0.000000e+00 1160.0
27 TraesCS7A01G266900 chr7D 89.521 773 66 13 4776 5542 252028671 252029434 0.000000e+00 965.0
28 TraesCS7A01G266900 chr7D 93.377 604 33 6 1610 2211 252027549 252028147 0.000000e+00 887.0
29 TraesCS7A01G266900 chr7D 85.861 778 60 17 871 1606 252026741 252027510 0.000000e+00 782.0
30 TraesCS7A01G266900 chr7D 92.674 546 31 7 4198 4737 631692569 631692027 0.000000e+00 778.0
31 TraesCS7A01G266900 chr7D 85.972 720 74 14 2421 3135 167247896 167248593 0.000000e+00 745.0
32 TraesCS7A01G266900 chr7D 94.461 343 19 0 4433 4775 572553692 572553350 5.710000e-146 529.0
33 TraesCS7A01G266900 chr7D 94.203 345 18 1 4433 4775 110568754 110569098 7.380000e-145 525.0
34 TraesCS7A01G266900 chr7D 96.337 273 10 0 4503 4775 496155683 496155955 4.570000e-122 449.0
35 TraesCS7A01G266900 chr7D 91.795 195 16 0 2207 2401 252028483 252028677 1.060000e-68 272.0
36 TraesCS7A01G266900 chr7D 88.732 142 9 3 7908 8042 252031637 252031778 5.150000e-37 167.0
37 TraesCS7A01G266900 chr7D 94.231 52 3 0 8249 8300 251517111 251517162 6.910000e-11 80.5
38 TraesCS7A01G266900 chr4D 93.916 2334 127 10 2446 4775 455184140 455186462 0.000000e+00 3509.0
39 TraesCS7A01G266900 chr2A 93.528 2333 98 12 2446 4775 628732133 628734415 0.000000e+00 3422.0
40 TraesCS7A01G266900 chr2A 99.145 117 0 1 5537 5652 555342219 555342335 8.440000e-50 209.0
41 TraesCS7A01G266900 chr5D 92.670 2333 104 14 2446 4775 371789235 371791503 0.000000e+00 3299.0
42 TraesCS7A01G266900 chr5D 92.087 2338 137 17 2442 4775 387112336 387110043 0.000000e+00 3249.0
43 TraesCS7A01G266900 chr5D 92.284 1944 108 12 2837 4778 323024330 323022427 0.000000e+00 2721.0
44 TraesCS7A01G266900 chr5D 92.520 254 19 0 493 746 369105934 369106187 1.700000e-96 364.0
45 TraesCS7A01G266900 chrUn 92.019 2343 146 19 2437 4775 26911208 26908903 0.000000e+00 3253.0
46 TraesCS7A01G266900 chrUn 92.015 263 21 0 496 758 98340455 98340193 3.660000e-98 370.0
47 TraesCS7A01G266900 chr2D 92.532 2263 141 20 2445 4698 349731726 349729483 0.000000e+00 3217.0
48 TraesCS7A01G266900 chr2D 95.044 343 17 0 4433 4775 209029269 209029611 2.640000e-149 540.0
49 TraesCS7A01G266900 chr6D 91.493 2351 169 17 2437 4782 322585327 322583003 0.000000e+00 3205.0
50 TraesCS7A01G266900 chr3A 87.903 1645 153 23 2421 4059 251347161 251345557 0.000000e+00 1893.0
51 TraesCS7A01G266900 chr3A 87.933 721 64 8 2421 3135 17850630 17849927 0.000000e+00 828.0
52 TraesCS7A01G266900 chr3A 91.951 410 29 4 2402 2810 594024234 594024640 9.350000e-159 571.0
53 TraesCS7A01G266900 chr3A 93.539 356 19 2 2401 2755 675345975 675345623 2.050000e-145 527.0
54 TraesCS7A01G266900 chr3A 80.831 313 22 18 2401 2682 33831877 33831572 2.350000e-50 211.0
55 TraesCS7A01G266900 chr3A 95.935 123 3 2 5537 5658 571176983 571177104 1.830000e-46 198.0
56 TraesCS7A01G266900 chr6B 89.861 503 37 9 4248 4746 329771781 329771289 1.180000e-177 634.0
57 TraesCS7A01G266900 chr1A 96.210 343 13 0 4433 4775 423918131 423918473 5.620000e-156 562.0
58 TraesCS7A01G266900 chr1A 95.349 129 3 2 5540 5668 343396803 343396678 1.410000e-47 202.0
59 TraesCS7A01G266900 chr3B 91.316 380 30 3 2421 2798 823256884 823256506 4.440000e-142 516.0
60 TraesCS7A01G266900 chr3B 91.950 323 22 2 2401 2722 418063485 418063166 4.570000e-122 449.0
61 TraesCS7A01G266900 chr3B 89.443 341 30 4 2421 2759 322287812 322288148 7.700000e-115 425.0
62 TraesCS7A01G266900 chr3B 90.977 266 19 3 493 758 822004634 822004374 3.690000e-93 353.0
63 TraesCS7A01G266900 chr5A 93.233 266 15 1 493 758 471305839 471305577 1.010000e-103 388.0
64 TraesCS7A01G266900 chr5A 92.045 264 20 1 493 756 471402339 471402601 3.660000e-98 370.0
65 TraesCS7A01G266900 chr5A 98.246 114 2 0 5540 5653 69844895 69844782 5.080000e-47 200.0
66 TraesCS7A01G266900 chr2B 93.182 264 18 0 494 757 731334117 731334380 1.010000e-103 388.0
67 TraesCS7A01G266900 chr1D 97.458 118 3 0 5530 5647 247521075 247520958 1.410000e-47 202.0
68 TraesCS7A01G266900 chr1B 96.694 121 3 1 5527 5647 624663038 624662919 5.080000e-47 200.0
69 TraesCS7A01G266900 chr1B 95.935 123 4 1 5525 5647 687253928 687254049 1.830000e-46 198.0
70 TraesCS7A01G266900 chr3D 77.872 235 27 15 4554 4775 418436718 418436940 1.130000e-23 122.0


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 TraesCS7A01G266900 chr7A 269957667 269965966 8299 True 15328.000000 15328 100.000000 1 8300 1 chr7A.!!$R2 8299
1 TraesCS7A01G266900 chr7A 269277919 269283369 5450 True 1114.440000 2756 89.326800 864 8100 5 chr7A.!!$R3 7236
2 TraesCS7A01G266900 chr7B 228385703 228394456 8753 False 1371.650000 3829 94.369167 1 8300 6 chr7B.!!$F3 8299
3 TraesCS7A01G266900 chr7B 228782103 228787057 4954 False 1073.600000 2767 88.822200 871 7908 5 chr7B.!!$F4 7037
4 TraesCS7A01G266900 chr7D 90626058 90628348 2290 True 3452.000000 3452 93.910000 2446 4733 1 chr7D.!!$R1 2287
5 TraesCS7A01G266900 chr7D 251505212 251510125 4913 False 2630.666667 3733 96.061000 1 7415 3 chr7D.!!$F4 7414
6 TraesCS7A01G266900 chr7D 521573160 521574678 1518 True 2182.000000 2182 92.697000 3276 4784 1 chr7D.!!$R2 1508
7 TraesCS7A01G266900 chr7D 252026741 252031778 5037 False 968.333333 2737 89.661500 871 8042 6 chr7D.!!$F6 7171
8 TraesCS7A01G266900 chr7D 631692027 631692569 542 True 778.000000 778 92.674000 4198 4737 1 chr7D.!!$R4 539
9 TraesCS7A01G266900 chr7D 167247896 167248593 697 False 745.000000 745 85.972000 2421 3135 1 chr7D.!!$F2 714
10 TraesCS7A01G266900 chr7D 251516227 251517162 935 False 620.250000 1160 92.920000 7408 8300 2 chr7D.!!$F5 892
11 TraesCS7A01G266900 chr4D 455184140 455186462 2322 False 3509.000000 3509 93.916000 2446 4775 1 chr4D.!!$F1 2329
12 TraesCS7A01G266900 chr2A 628732133 628734415 2282 False 3422.000000 3422 93.528000 2446 4775 1 chr2A.!!$F2 2329
13 TraesCS7A01G266900 chr5D 371789235 371791503 2268 False 3299.000000 3299 92.670000 2446 4775 1 chr5D.!!$F2 2329
14 TraesCS7A01G266900 chr5D 387110043 387112336 2293 True 3249.000000 3249 92.087000 2442 4775 1 chr5D.!!$R2 2333
15 TraesCS7A01G266900 chr5D 323022427 323024330 1903 True 2721.000000 2721 92.284000 2837 4778 1 chr5D.!!$R1 1941
16 TraesCS7A01G266900 chrUn 26908903 26911208 2305 True 3253.000000 3253 92.019000 2437 4775 1 chrUn.!!$R1 2338
17 TraesCS7A01G266900 chr2D 349729483 349731726 2243 True 3217.000000 3217 92.532000 2445 4698 1 chr2D.!!$R1 2253
18 TraesCS7A01G266900 chr6D 322583003 322585327 2324 True 3205.000000 3205 91.493000 2437 4782 1 chr6D.!!$R1 2345
19 TraesCS7A01G266900 chr3A 251345557 251347161 1604 True 1893.000000 1893 87.903000 2421 4059 1 chr3A.!!$R3 1638
20 TraesCS7A01G266900 chr3A 17849927 17850630 703 True 828.000000 828 87.933000 2421 3135 1 chr3A.!!$R1 714

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
271 1965 0.829990 TATGAACCAGATGCGAGCCA 59.170 50.000 0.0 0.0 0.00 4.75 F
1491 3264 0.339162 TAGGACCCGTGGTTCCCATA 59.661 55.000 0.0 0.0 35.25 2.74 F
1495 3268 2.021457 GACCCGTGGTTCCCATATTTG 58.979 52.381 0.0 0.0 35.25 2.32 F
1647 3456 2.432510 TGTGGTACTGTGTGTGACATGA 59.567 45.455 0.0 0.0 32.74 3.07 F
2963 6284 0.671781 AACAGATGACCAGCACGCTC 60.672 55.000 0.0 0.0 0.00 5.03 F
3349 6673 0.760567 CTCCCGATCCATCAGGTCCA 60.761 60.000 0.0 0.0 35.89 4.02 F
4353 7681 0.535102 AGAAGGTGTTTGACGCTGGG 60.535 55.000 0.0 0.0 0.00 4.45 F
4647 8023 0.031010 CCCTAGCCACCTCTAACCCT 60.031 60.000 0.0 0.0 0.00 4.34 F
4651 8027 0.691413 AGCCACCTCTAACCCTAGCC 60.691 60.000 0.0 0.0 0.00 3.93 F
5568 9343 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.0 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 4935 0.823356 TTGCCTGCAAACCACTCCTC 60.823 55.000 1.31 0.00 32.44 3.71 R
2404 5715 0.395312 GCCTAGCTAAACCGGCCATA 59.605 55.000 10.00 0.00 36.56 2.74 R
2405 5716 1.148498 GCCTAGCTAAACCGGCCAT 59.852 57.895 10.00 0.00 36.56 4.40 R
3528 6852 1.226802 CGTGTCGAGATGGCTCAGG 60.227 63.158 0.00 0.00 41.36 3.86 R
4353 7681 0.248702 GAACTCCTCGAGGCGATCAC 60.249 60.000 27.68 12.02 34.61 3.06 R
4614 7967 1.196012 CTAGGGTTTCGGCTCCTCTT 58.804 55.000 0.00 0.00 32.46 2.85 R
5631 9406 0.467659 ATCCTACTCCCTCCGTTCCG 60.468 60.000 0.00 0.00 0.00 4.30 R
5640 9415 0.551396 CCCCACCAAATCCTACTCCC 59.449 60.000 0.00 0.00 0.00 4.30 R
5641 9416 1.212195 GTCCCCACCAAATCCTACTCC 59.788 57.143 0.00 0.00 0.00 3.85 R
7367 11197 0.036732 AGCTCAACAAATCCCGCAGA 59.963 50.000 0.00 0.00 0.00 4.26 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
38 502 1.745489 CGCCGAAGAAGAAAGGGGG 60.745 63.158 0.00 0.00 33.69 5.40
56 520 2.698797 GGGGTCGAGATTTGGTAGATGA 59.301 50.000 0.00 0.00 0.00 2.92
135 1829 2.596346 TCATGTTTGCCAAGTGTCCAT 58.404 42.857 0.00 0.00 0.00 3.41
158 1852 5.807909 TCAATGAACAAGGTCTCATGATGA 58.192 37.500 0.00 0.00 32.60 2.92
220 1914 7.361894 TCATCATCATATTATTGTTGTTGGCG 58.638 34.615 0.00 0.00 0.00 5.69
221 1915 5.518812 TCATCATATTATTGTTGTTGGCGC 58.481 37.500 0.00 0.00 0.00 6.53
247 1941 1.134401 ACCGTGATCCATGTCATCCAC 60.134 52.381 0.00 0.00 0.00 4.02
252 1946 4.458397 GTGATCCATGTCATCCACAGAAT 58.542 43.478 0.00 0.00 38.85 2.40
271 1965 0.829990 TATGAACCAGATGCGAGCCA 59.170 50.000 0.00 0.00 0.00 4.75
278 1972 1.506493 CAGATGCGAGCCAATCCTAC 58.494 55.000 0.00 0.00 0.00 3.18
302 1996 3.599343 AGTGTATCATTGTCGTGCACAT 58.401 40.909 18.64 3.12 33.90 3.21
316 2010 4.940654 TCGTGCACATTAATTCTTCATGGA 59.059 37.500 18.64 0.00 0.00 3.41
348 2042 5.528690 GTGCTGGATAAACATTATCAGCTGA 59.471 40.000 20.79 20.79 33.45 4.26
391 2085 6.000891 TCATGAACATTGTGTTTGCTCTAC 57.999 37.500 0.00 0.00 41.28 2.59
393 2087 5.826601 TGAACATTGTGTTTGCTCTACAA 57.173 34.783 0.00 0.00 41.28 2.41
410 2104 3.940209 ACAACGAAGTATGTCCCGTTA 57.060 42.857 0.00 0.00 45.00 3.18
427 2121 1.777030 TTACACGTTGCAAGGCACGG 61.777 55.000 18.61 8.73 38.71 4.94
478 2172 6.059484 CCTATGCGGGTTCCTAAAGAAATAA 58.941 40.000 0.00 0.00 35.85 1.40
485 2179 7.093992 CGGGTTCCTAAAGAAATAATGCAAAA 58.906 34.615 0.00 0.00 35.85 2.44
486 2180 7.763985 CGGGTTCCTAAAGAAATAATGCAAAAT 59.236 33.333 0.00 0.00 35.85 1.82
531 2225 5.428457 TCCTTTAGATCTTGGTATGAAGGCA 59.572 40.000 0.00 0.00 33.99 4.75
535 2229 4.036518 AGATCTTGGTATGAAGGCAGTCT 58.963 43.478 0.00 0.00 0.00 3.24
583 2277 1.442148 GTAGGAGGACGATGGTGGC 59.558 63.158 0.00 0.00 0.00 5.01
587 2281 2.764128 AGGACGATGGTGGCCGAT 60.764 61.111 0.00 0.00 0.00 4.18
829 2538 3.057104 GCAGGGGCTTACGTGTTAATTTT 60.057 43.478 0.00 0.00 36.96 1.82
1053 2781 2.677848 GGACCCAAAGGAGAGGCC 59.322 66.667 0.00 0.00 36.73 5.19
1139 2900 1.078823 TGGAGGTAGAGGGAAGAAGCA 59.921 52.381 0.00 0.00 0.00 3.91
1335 3102 3.260269 TCCTAGGACTGGGATGGTATG 57.740 52.381 7.62 0.00 35.16 2.39
1336 3103 1.625818 CCTAGGACTGGGATGGTATGC 59.374 57.143 1.05 0.00 32.26 3.14
1408 3181 3.555586 GCCCAAGCTGTTTGATGAAATGT 60.556 43.478 5.77 0.00 39.21 2.71
1491 3264 0.339162 TAGGACCCGTGGTTCCCATA 59.661 55.000 0.00 0.00 35.25 2.74
1495 3268 2.021457 GACCCGTGGTTCCCATATTTG 58.979 52.381 0.00 0.00 35.25 2.32
1555 3329 8.764524 ACTGTTTTGTTTTATTGTAGTTTGCA 57.235 26.923 0.00 0.00 0.00 4.08
1647 3456 2.432510 TGTGGTACTGTGTGTGACATGA 59.567 45.455 0.00 0.00 32.74 3.07
1749 3558 2.917713 AATAAATGCCCCACAGGTGA 57.082 45.000 0.00 0.00 38.26 4.02
1928 4813 5.808042 ATGTTGCACATGATAGTTCACTC 57.192 39.130 0.00 0.00 37.45 3.51
2242 5470 7.609056 TCTTGAATTACCAGACTACTGTTACC 58.391 38.462 0.00 0.00 42.05 2.85
2397 5708 7.284919 TCGAGTATGTGCCATCTATTTTAGA 57.715 36.000 0.00 0.00 39.50 2.10
2398 5709 7.896811 TCGAGTATGTGCCATCTATTTTAGAT 58.103 34.615 0.00 0.00 46.06 1.98
2399 5710 8.367911 TCGAGTATGTGCCATCTATTTTAGATT 58.632 33.333 0.00 0.00 42.70 2.40
2400 5711 8.438513 CGAGTATGTGCCATCTATTTTAGATTG 58.561 37.037 0.00 0.00 42.70 2.67
2401 5712 9.277783 GAGTATGTGCCATCTATTTTAGATTGT 57.722 33.333 0.00 0.00 42.70 2.71
2402 5713 9.060347 AGTATGTGCCATCTATTTTAGATTGTG 57.940 33.333 0.00 0.00 42.70 3.33
2403 5714 7.886629 ATGTGCCATCTATTTTAGATTGTGT 57.113 32.000 0.00 0.00 42.70 3.72
2404 5715 7.701539 TGTGCCATCTATTTTAGATTGTGTT 57.298 32.000 0.00 0.00 42.70 3.32
2405 5716 8.800370 TGTGCCATCTATTTTAGATTGTGTTA 57.200 30.769 0.00 0.00 42.70 2.41
2406 5717 9.407380 TGTGCCATCTATTTTAGATTGTGTTAT 57.593 29.630 0.00 0.00 42.70 1.89
2407 5718 9.669353 GTGCCATCTATTTTAGATTGTGTTATG 57.331 33.333 0.00 0.00 42.70 1.90
2408 5719 8.849168 TGCCATCTATTTTAGATTGTGTTATGG 58.151 33.333 0.00 0.00 42.70 2.74
2409 5720 7.809806 GCCATCTATTTTAGATTGTGTTATGGC 59.190 37.037 0.00 0.00 42.70 4.40
2410 5721 8.299570 CCATCTATTTTAGATTGTGTTATGGCC 58.700 37.037 0.00 0.00 42.70 5.36
2411 5722 7.490962 TCTATTTTAGATTGTGTTATGGCCG 57.509 36.000 0.00 0.00 0.00 6.13
2412 5723 4.974368 TTTTAGATTGTGTTATGGCCGG 57.026 40.909 0.00 0.00 0.00 6.13
2413 5724 3.637911 TTAGATTGTGTTATGGCCGGT 57.362 42.857 1.90 0.00 0.00 5.28
2414 5725 2.507407 AGATTGTGTTATGGCCGGTT 57.493 45.000 1.90 0.00 0.00 4.44
2415 5726 2.802719 AGATTGTGTTATGGCCGGTTT 58.197 42.857 1.90 0.00 0.00 3.27
2416 5727 3.958018 AGATTGTGTTATGGCCGGTTTA 58.042 40.909 1.90 0.00 0.00 2.01
2417 5728 3.945285 AGATTGTGTTATGGCCGGTTTAG 59.055 43.478 1.90 0.00 0.00 1.85
2418 5729 1.455248 TGTGTTATGGCCGGTTTAGC 58.545 50.000 1.90 0.00 0.00 3.09
2419 5730 1.003812 TGTGTTATGGCCGGTTTAGCT 59.996 47.619 1.90 0.00 0.00 3.32
2578 5892 2.666098 GGAGCCGAAACCCTAGCCA 61.666 63.158 0.00 0.00 0.00 4.75
2592 5906 1.964933 CTAGCCACCTCTAACCCTAGC 59.035 57.143 0.00 0.00 0.00 3.42
2593 5907 0.691413 AGCCACCTCTAACCCTAGCC 60.691 60.000 0.00 0.00 0.00 3.93
2794 6114 4.459089 GCTGCCCGTCTCCACCTC 62.459 72.222 0.00 0.00 0.00 3.85
2963 6284 0.671781 AACAGATGACCAGCACGCTC 60.672 55.000 0.00 0.00 0.00 5.03
3030 6351 2.176273 CAGTACATGGCAGGAGCGC 61.176 63.158 5.99 0.00 43.41 5.92
3349 6673 0.760567 CTCCCGATCCATCAGGTCCA 60.761 60.000 0.00 0.00 35.89 4.02
4070 7398 3.011517 AGCAGGAATCACCGCCCT 61.012 61.111 0.00 0.00 44.74 5.19
4353 7681 0.535102 AGAAGGTGTTTGACGCTGGG 60.535 55.000 0.00 0.00 0.00 4.45
4614 7967 3.488569 CCCTATTGCCCGGCTCCA 61.489 66.667 11.61 0.00 0.00 3.86
4636 8012 2.666098 GGAGCCGAAACCCTAGCCA 61.666 63.158 0.00 0.00 0.00 4.75
4637 8013 1.449778 GAGCCGAAACCCTAGCCAC 60.450 63.158 0.00 0.00 0.00 5.01
4638 8014 2.437895 GCCGAAACCCTAGCCACC 60.438 66.667 0.00 0.00 0.00 4.61
4639 8015 2.967946 GCCGAAACCCTAGCCACCT 61.968 63.158 0.00 0.00 0.00 4.00
4640 8016 1.221021 CCGAAACCCTAGCCACCTC 59.779 63.158 0.00 0.00 0.00 3.85
4641 8017 1.265454 CCGAAACCCTAGCCACCTCT 61.265 60.000 0.00 0.00 0.00 3.69
4642 8018 1.481871 CGAAACCCTAGCCACCTCTA 58.518 55.000 0.00 0.00 0.00 2.43
4643 8019 1.829222 CGAAACCCTAGCCACCTCTAA 59.171 52.381 0.00 0.00 0.00 2.10
4644 8020 2.418334 CGAAACCCTAGCCACCTCTAAC 60.418 54.545 0.00 0.00 0.00 2.34
4645 8021 1.581223 AACCCTAGCCACCTCTAACC 58.419 55.000 0.00 0.00 0.00 2.85
4646 8022 0.326332 ACCCTAGCCACCTCTAACCC 60.326 60.000 0.00 0.00 0.00 4.11
4647 8023 0.031010 CCCTAGCCACCTCTAACCCT 60.031 60.000 0.00 0.00 0.00 4.34
4648 8024 1.219724 CCCTAGCCACCTCTAACCCTA 59.780 57.143 0.00 0.00 0.00 3.53
4649 8025 2.599677 CCTAGCCACCTCTAACCCTAG 58.400 57.143 0.00 0.00 0.00 3.02
4650 8026 1.964933 CTAGCCACCTCTAACCCTAGC 59.035 57.143 0.00 0.00 0.00 3.42
4651 8027 0.691413 AGCCACCTCTAACCCTAGCC 60.691 60.000 0.00 0.00 0.00 3.93
4652 8028 2.029307 GCCACCTCTAACCCTAGCCG 62.029 65.000 0.00 0.00 0.00 5.52
4653 8029 1.442148 CACCTCTAACCCTAGCCGC 59.558 63.158 0.00 0.00 0.00 6.53
4654 8030 1.761271 ACCTCTAACCCTAGCCGCC 60.761 63.158 0.00 0.00 0.00 6.13
5096 8529 9.626045 CTCTAAATTAATTTCCTGACAAACACC 57.374 33.333 16.56 0.00 0.00 4.16
5385 8836 6.579666 AATGTTGTGTGCTGAGAACATTAT 57.420 33.333 16.76 1.50 43.98 1.28
5542 9317 5.461078 TGTGTTTGCGAGTCTAAAGAAGTAC 59.539 40.000 0.00 0.00 0.00 2.73
5543 9318 5.690857 GTGTTTGCGAGTCTAAAGAAGTACT 59.309 40.000 0.00 0.00 0.00 2.73
5544 9319 5.919141 TGTTTGCGAGTCTAAAGAAGTACTC 59.081 40.000 0.00 0.00 35.97 2.59
5545 9320 4.698583 TGCGAGTCTAAAGAAGTACTCC 57.301 45.455 0.00 0.00 35.93 3.85
5546 9321 3.442977 TGCGAGTCTAAAGAAGTACTCCC 59.557 47.826 0.00 0.00 35.93 4.30
5548 9323 4.201940 GCGAGTCTAAAGAAGTACTCCCTC 60.202 50.000 0.00 0.00 35.93 4.30
5549 9324 4.336153 CGAGTCTAAAGAAGTACTCCCTCC 59.664 50.000 0.00 0.00 35.93 4.30
5550 9325 4.271661 AGTCTAAAGAAGTACTCCCTCCG 58.728 47.826 0.00 0.00 0.00 4.63
5551 9326 4.015764 GTCTAAAGAAGTACTCCCTCCGT 58.984 47.826 0.00 0.00 0.00 4.69
5552 9327 4.462132 GTCTAAAGAAGTACTCCCTCCGTT 59.538 45.833 0.00 0.00 0.00 4.44
5553 9328 3.957591 AAAGAAGTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 0.00 3.95
5554 9329 1.849977 AGAAGTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 0.00 3.62
5555 9330 1.076677 AGAAGTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 0.00 3.53
5556 9331 1.897802 GAAGTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
5557 9332 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
5558 9333 2.547990 AGTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
5559 9334 2.910977 AGTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
5560 9335 4.098894 AGTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
5561 9336 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
5562 9337 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
5563 9338 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
5564 9339 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
5565 9340 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
5566 9341 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
5567 9342 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
5568 9343 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
5569 9344 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
5570 9345 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
5571 9346 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
5572 9347 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
5573 9348 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
5574 9349 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
5575 9350 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
5576 9351 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
5577 9352 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
5578 9353 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
5579 9354 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
5580 9355 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
5581 9356 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
5582 9357 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
5583 9358 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
5584 9359 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
5585 9360 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
5586 9361 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
5587 9362 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
5588 9363 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
5589 9364 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
5590 9365 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
5591 9366 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
5592 9367 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
5593 9368 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
5619 9394 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
5620 9395 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
5621 9396 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
5622 9397 3.944055 AGATACATCCATACCTGCGAC 57.056 47.619 0.00 0.00 0.00 5.19
5623 9398 3.230976 AGATACATCCATACCTGCGACA 58.769 45.455 0.00 0.00 0.00 4.35
5624 9399 3.641436 AGATACATCCATACCTGCGACAA 59.359 43.478 0.00 0.00 0.00 3.18
5625 9400 2.315925 ACATCCATACCTGCGACAAG 57.684 50.000 0.00 0.00 0.00 3.16
5626 9401 1.555075 ACATCCATACCTGCGACAAGT 59.445 47.619 0.00 0.00 0.00 3.16
5627 9402 2.764010 ACATCCATACCTGCGACAAGTA 59.236 45.455 0.00 0.00 0.00 2.24
5628 9403 3.196901 ACATCCATACCTGCGACAAGTAA 59.803 43.478 0.00 0.00 0.00 2.24
5629 9404 4.141711 ACATCCATACCTGCGACAAGTAAT 60.142 41.667 0.00 0.00 0.00 1.89
5630 9405 4.481368 TCCATACCTGCGACAAGTAATT 57.519 40.909 0.00 0.00 0.00 1.40
5631 9406 4.439057 TCCATACCTGCGACAAGTAATTC 58.561 43.478 0.00 0.00 0.00 2.17
5632 9407 3.245284 CCATACCTGCGACAAGTAATTCG 59.755 47.826 0.00 0.00 38.31 3.34
5633 9408 1.722011 ACCTGCGACAAGTAATTCGG 58.278 50.000 0.00 0.00 35.73 4.30
5634 9409 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
5635 9410 2.289195 ACCTGCGACAAGTAATTCGGAA 60.289 45.455 0.00 0.00 35.02 4.30
5636 9411 2.093783 CCTGCGACAAGTAATTCGGAAC 59.906 50.000 0.00 0.00 35.02 3.62
5650 9425 3.535574 GGAACGGAGGGAGTAGGAT 57.464 57.895 0.00 0.00 0.00 3.24
5651 9426 1.790818 GGAACGGAGGGAGTAGGATT 58.209 55.000 0.00 0.00 0.00 3.01
5652 9427 2.117051 GGAACGGAGGGAGTAGGATTT 58.883 52.381 0.00 0.00 0.00 2.17
5653 9428 2.158943 GGAACGGAGGGAGTAGGATTTG 60.159 54.545 0.00 0.00 0.00 2.32
5654 9429 1.497161 ACGGAGGGAGTAGGATTTGG 58.503 55.000 0.00 0.00 0.00 3.28
5655 9430 1.273666 ACGGAGGGAGTAGGATTTGGT 60.274 52.381 0.00 0.00 0.00 3.67
5656 9431 1.139058 CGGAGGGAGTAGGATTTGGTG 59.861 57.143 0.00 0.00 0.00 4.17
5668 9444 3.582647 AGGATTTGGTGGGGACATTTTTC 59.417 43.478 0.00 0.00 46.14 2.29
5716 9492 1.196808 CCAACGCCTTCATGTGTACAC 59.803 52.381 19.36 19.36 0.00 2.90
5828 9609 5.117592 GTGCATTTATGACAGTCAAACTTGC 59.882 40.000 7.50 14.54 0.00 4.01
5961 9742 4.037446 GGAATGTTTGTGTGTTCTTGCCTA 59.963 41.667 0.00 0.00 0.00 3.93
6074 9863 3.742433 AGGATATCTCGAACAGGCAAG 57.258 47.619 2.05 0.00 0.00 4.01
6165 9954 4.070716 GGTATCTGAGATGCCAAATGGAG 58.929 47.826 22.42 0.00 37.39 3.86
6171 9960 6.236409 TCTGAGATGCCAAATGGAGATATTC 58.764 40.000 2.98 0.00 37.39 1.75
6206 9995 8.791327 AACAACCTGATCTTTTTGAAATTGTT 57.209 26.923 7.48 0.00 33.08 2.83
6310 10099 6.656632 TTTACAAGAGAGACATGTCAGAGT 57.343 37.500 27.02 17.07 32.58 3.24
6546 10346 9.880064 GAAAAACTAACAATACCTTGTCTTCTC 57.120 33.333 0.00 0.00 44.83 2.87
6549 10349 7.784470 ACTAACAATACCTTGTCTTCTCTCT 57.216 36.000 0.00 0.00 44.83 3.10
6560 10360 2.028203 GTCTTCTCTCTGCTGGCTTCTT 60.028 50.000 0.00 0.00 0.00 2.52
6647 10447 9.256228 ACAGATTAGTGTCAGAGGTAATTTCTA 57.744 33.333 0.00 0.00 0.00 2.10
6680 10480 5.990386 ACTGATGACTGATGCTACATGATTC 59.010 40.000 0.00 0.00 0.00 2.52
6721 10521 6.038936 TGGTGTAGTTTCAACTTTAAAGCTCC 59.961 38.462 15.24 6.50 40.37 4.70
6836 10636 4.214310 TCTTGGTTTGAATTGCTTCCTGA 58.786 39.130 0.00 0.00 0.00 3.86
7140 10954 0.750850 AAGGTGCGTGCTATATCGGT 59.249 50.000 0.00 0.00 0.00 4.69
7357 11187 3.499737 GTGATGCTTCGGGTGCGG 61.500 66.667 0.00 0.00 0.00 5.69
7367 11197 2.190841 CGGGTGCGGAAGTTTGGTT 61.191 57.895 0.00 0.00 0.00 3.67
7381 11211 1.698506 TTGGTTCTGCGGGATTTGTT 58.301 45.000 0.00 0.00 0.00 2.83
7463 11294 5.133221 AGATTAGCAGTTTGTGGAAGTGTT 58.867 37.500 0.00 0.00 40.21 3.32
7501 11332 4.790246 CCCAAGGAATGATATGGATAGGGA 59.210 45.833 0.00 0.00 34.82 4.20
7502 11333 5.253798 CCCAAGGAATGATATGGATAGGGAA 59.746 44.000 0.00 0.00 34.82 3.97
7503 11334 6.240556 CCCAAGGAATGATATGGATAGGGAAA 60.241 42.308 0.00 0.00 34.82 3.13
7504 11335 7.416731 CCAAGGAATGATATGGATAGGGAAAT 58.583 38.462 0.00 0.00 34.82 2.17
7505 11336 7.897565 CCAAGGAATGATATGGATAGGGAAATT 59.102 37.037 0.00 0.00 34.82 1.82
7506 11337 9.317827 CAAGGAATGATATGGATAGGGAAATTT 57.682 33.333 0.00 0.00 0.00 1.82
7507 11338 9.903190 AAGGAATGATATGGATAGGGAAATTTT 57.097 29.630 0.00 0.00 0.00 1.82
7512 11343 6.714810 TGATATGGATAGGGAAATTTTGTCGG 59.285 38.462 0.00 0.00 0.00 4.79
7516 11347 2.391926 AGGGAAATTTTGTCGGGGTT 57.608 45.000 0.00 0.00 0.00 4.11
7537 11369 3.994931 TTGCCTTCCCTAGGTAGTTTC 57.005 47.619 8.29 0.00 46.61 2.78
7664 11497 4.284485 AGTTTTGTCGCGGTTTTACAATC 58.716 39.130 6.13 5.85 33.44 2.67
7665 11498 3.965292 TTTGTCGCGGTTTTACAATCA 57.035 38.095 6.13 0.00 33.44 2.57
7689 11539 5.957774 ACATAAACAGGCATATCTTTGGGTT 59.042 36.000 0.00 0.00 0.00 4.11
7755 11608 2.811101 CAGCCGAGGAGAATCGCT 59.189 61.111 0.00 0.00 41.37 4.93
7883 11737 4.328118 AAAGCTCCAAGGATCTTCCAAT 57.672 40.909 5.74 0.00 39.61 3.16
7888 11742 6.777782 AGCTCCAAGGATCTTCCAATAATAG 58.222 40.000 0.00 0.00 39.61 1.73
7941 11800 3.441572 ACATTCCAAAAGCTGATCTTCCG 59.558 43.478 0.00 0.00 32.88 4.30
8144 12391 5.906443 TAGTCATCAACTCGTGCAATGCAC 61.906 45.833 26.87 26.87 45.98 4.57
8156 12403 1.131126 GCAATGCACGTGCTAGTGATT 59.869 47.619 37.59 25.83 44.43 2.57
8178 12425 6.969828 TTTTTGTCAAATTGGTAAAGCGTT 57.030 29.167 0.00 0.00 0.00 4.84
8186 12433 1.320507 TGGTAAAGCGTTTCAACCCC 58.679 50.000 12.08 0.00 0.00 4.95
8191 12438 0.458260 AAGCGTTTCAACCCCAACAC 59.542 50.000 0.00 0.00 0.00 3.32
8206 12453 1.895020 AACACTGGAGCCCGCGATTA 61.895 55.000 8.23 0.00 0.00 1.75
8217 12464 1.202651 CCCGCGATTATTGAGAGGGTT 60.203 52.381 8.23 0.00 39.67 4.11
8277 12556 2.167900 ACGACCTCCACTGCTATTAACC 59.832 50.000 0.00 0.00 0.00 2.85
8281 12560 4.621769 ACCTCCACTGCTATTAACCTACT 58.378 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 502 4.339814 AGTCCTCATCTACCAAATCTCGAC 59.660 45.833 0.00 0.00 0.00 4.20
56 520 2.299297 ACAGTAACAAAGCGCTAGTCCT 59.701 45.455 12.05 9.54 0.00 3.85
135 1829 5.807909 TCATCATGAGACCTTGTTCATTGA 58.192 37.500 0.09 0.00 31.91 2.57
158 1852 0.171903 CGACCCGGATCGTACACTTT 59.828 55.000 11.07 0.00 37.33 2.66
247 1941 3.186001 GCTCGCATCTGGTTCATATTCTG 59.814 47.826 0.00 0.00 0.00 3.02
252 1946 0.829990 TGGCTCGCATCTGGTTCATA 59.170 50.000 0.00 0.00 0.00 2.15
271 1965 6.096987 ACGACAATGATACACTCTGTAGGATT 59.903 38.462 0.00 0.00 36.14 3.01
278 1972 3.061295 GTGCACGACAATGATACACTCTG 59.939 47.826 0.00 0.00 0.00 3.35
302 1996 6.806249 GCACGAACATTTCCATGAAGAATTAA 59.194 34.615 0.00 0.00 34.11 1.40
316 2010 5.643379 ATGTTTATCCAGCACGAACATTT 57.357 34.783 0.00 0.00 37.59 2.32
391 2085 3.365820 GTGTAACGGGACATACTTCGTTG 59.634 47.826 9.71 0.00 38.42 4.10
393 2087 3.221964 GTGTAACGGGACATACTTCGT 57.778 47.619 0.00 0.00 37.45 3.85
410 2104 3.582120 CCGTGCCTTGCAACGTGT 61.582 61.111 7.78 0.00 41.47 4.49
511 2205 5.663106 AGACTGCCTTCATACCAAGATCTAA 59.337 40.000 0.00 0.00 0.00 2.10
566 2260 1.760875 GGCCACCATCGTCCTCCTA 60.761 63.158 0.00 0.00 0.00 2.94
583 2277 4.114997 GCCACGCCCAAACATCGG 62.115 66.667 0.00 0.00 0.00 4.18
587 2281 2.755876 TTGTGCCACGCCCAAACA 60.756 55.556 0.00 0.00 0.00 2.83
1053 2781 1.514443 GTCGCTCCGTTTCCTCTCG 60.514 63.158 0.00 0.00 0.00 4.04
1064 2792 4.373116 TTCCCTGTGCGTCGCTCC 62.373 66.667 19.50 9.54 0.00 4.70
1139 2900 5.946486 AGATGAAAACCTCCTTGTTCTTCT 58.054 37.500 0.00 0.00 32.59 2.85
1335 3102 4.094294 TCAACTAAGCAACATAATCCGTGC 59.906 41.667 0.00 0.00 0.00 5.34
1336 3103 5.794687 TCAACTAAGCAACATAATCCGTG 57.205 39.130 0.00 0.00 0.00 4.94
1408 3181 4.200838 TCAATGTCGAAACCTATCAGCA 57.799 40.909 0.00 0.00 0.00 4.41
1491 3264 4.925054 CAGTTTCCAATCGATGCAACAAAT 59.075 37.500 0.00 0.00 0.00 2.32
1495 3268 2.487762 TCCAGTTTCCAATCGATGCAAC 59.512 45.455 0.00 0.00 0.00 4.17
1555 3329 5.239744 CAGATAACGTCTATGCTGGTCTACT 59.760 44.000 0.00 0.00 34.69 2.57
1647 3456 1.353022 TGCCCCCTAAAATTCGACAGT 59.647 47.619 0.00 0.00 0.00 3.55
1909 4794 6.878389 TGTATTGAGTGAACTATCATGTGCAA 59.122 34.615 0.00 0.00 38.01 4.08
1928 4813 7.116233 GCCATTGAGTACCTTTTTGTTGTATTG 59.884 37.037 0.00 0.00 0.00 1.90
1967 4852 8.950210 TCAAAAGATTGAAGTTATCAGCTAAGG 58.050 33.333 0.00 0.00 42.47 2.69
2049 4935 0.823356 TTGCCTGCAAACCACTCCTC 60.823 55.000 1.31 0.00 32.44 3.71
2111 4997 3.112263 CCCCAGAACATTACCTAGACCA 58.888 50.000 0.00 0.00 0.00 4.02
2242 5470 7.425606 AGAAACTAAAACAATGTAACTGCAGG 58.574 34.615 19.93 0.00 0.00 4.85
2397 5708 2.425668 GCTAAACCGGCCATAACACAAT 59.574 45.455 0.00 0.00 0.00 2.71
2398 5709 1.813786 GCTAAACCGGCCATAACACAA 59.186 47.619 0.00 0.00 0.00 3.33
2399 5710 1.003812 AGCTAAACCGGCCATAACACA 59.996 47.619 0.00 0.00 0.00 3.72
2400 5711 1.746470 AGCTAAACCGGCCATAACAC 58.254 50.000 0.00 0.00 0.00 3.32
2401 5712 2.158871 CCTAGCTAAACCGGCCATAACA 60.159 50.000 0.00 0.00 0.00 2.41
2402 5713 2.490991 CCTAGCTAAACCGGCCATAAC 58.509 52.381 0.00 0.00 0.00 1.89
2403 5714 1.202722 GCCTAGCTAAACCGGCCATAA 60.203 52.381 10.00 0.00 36.56 1.90
2404 5715 0.395312 GCCTAGCTAAACCGGCCATA 59.605 55.000 10.00 0.00 36.56 2.74
2405 5716 1.148498 GCCTAGCTAAACCGGCCAT 59.852 57.895 10.00 0.00 36.56 4.40
2406 5717 2.587889 GCCTAGCTAAACCGGCCA 59.412 61.111 10.00 0.00 36.56 5.36
2408 5719 2.203167 GGGCCTAGCTAAACCGGC 60.203 66.667 12.25 12.25 41.75 6.13
2409 5720 1.153229 GTGGGCCTAGCTAAACCGG 60.153 63.158 4.53 0.00 0.00 5.28
2410 5721 1.153229 GGTGGGCCTAGCTAAACCG 60.153 63.158 11.59 0.00 0.00 4.44
2411 5722 1.153229 CGGTGGGCCTAGCTAAACC 60.153 63.158 16.80 0.14 0.00 3.27
2412 5723 1.153229 CCGGTGGGCCTAGCTAAAC 60.153 63.158 16.80 0.00 0.00 2.01
2413 5724 2.372074 CCCGGTGGGCCTAGCTAAA 61.372 63.158 16.80 0.00 35.35 1.85
2414 5725 2.766651 CCCGGTGGGCCTAGCTAA 60.767 66.667 16.80 0.00 35.35 3.09
2578 5892 1.761271 GGCGGCTAGGGTTAGAGGT 60.761 63.158 0.00 0.00 0.00 3.85
2738 6055 4.213564 AGAAGACATGATCAGACCCAAC 57.786 45.455 0.00 0.00 0.00 3.77
3528 6852 1.226802 CGTGTCGAGATGGCTCAGG 60.227 63.158 0.00 0.00 41.36 3.86
3783 7109 0.606401 CCAAAGCGAAGGAGGCAGAA 60.606 55.000 0.00 0.00 0.00 3.02
3975 7301 3.090532 GGGTCCCCGAAGCTCCAT 61.091 66.667 0.00 0.00 0.00 3.41
4353 7681 0.248702 GAACTCCTCGAGGCGATCAC 60.249 60.000 27.68 12.02 34.61 3.06
4557 7908 8.822652 ATTGCTTAATTCCAAAAAGAGTCTTG 57.177 30.769 6.06 0.00 0.00 3.02
4614 7967 1.196012 CTAGGGTTTCGGCTCCTCTT 58.804 55.000 0.00 0.00 32.46 2.85
4625 7978 1.914108 GGTTAGAGGTGGCTAGGGTTT 59.086 52.381 0.00 0.00 0.00 3.27
4636 8012 1.761271 GGCGGCTAGGGTTAGAGGT 60.761 63.158 0.00 0.00 0.00 3.85
4637 8013 2.857744 CGGCGGCTAGGGTTAGAGG 61.858 68.421 7.61 0.00 0.00 3.69
4638 8014 2.728817 CGGCGGCTAGGGTTAGAG 59.271 66.667 7.61 0.00 0.00 2.43
4639 8015 3.534056 GCGGCGGCTAGGGTTAGA 61.534 66.667 9.78 0.00 35.83 2.10
4640 8016 4.603946 GGCGGCGGCTAGGGTTAG 62.604 72.222 27.22 0.00 39.81 2.34
4775 8179 9.599866 CTCAACCATATTACAAGTGACAATCTA 57.400 33.333 0.00 0.00 0.00 1.98
5078 8511 4.498345 GCAACGGTGTTTGTCAGGAAATTA 60.498 41.667 0.66 0.00 0.00 1.40
5096 8529 7.278868 AGGTAAGAAAATTAGAGATGAGCAACG 59.721 37.037 0.00 0.00 0.00 4.10
5385 8836 9.806203 CATTTTATATTGTCCAGAAATGAGCAA 57.194 29.630 0.00 0.00 36.89 3.91
5427 8878 1.553706 AACCGGTCGAACAGGACTAT 58.446 50.000 8.04 0.00 36.90 2.12
5542 9317 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
5543 9318 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
5544 9319 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
5545 9320 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
5546 9321 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
5548 9323 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
5549 9324 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
5550 9325 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
5551 9326 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
5552 9327 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
5553 9328 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
5554 9329 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
5555 9330 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
5556 9331 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
5557 9332 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
5558 9333 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
5559 9334 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
5560 9335 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
5561 9336 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
5562 9337 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
5563 9338 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
5564 9339 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
5565 9340 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
5566 9341 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
5567 9342 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
5593 9368 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
5594 9369 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
5595 9370 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
5596 9371 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
5597 9372 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
5598 9373 5.358442 GTCGCAGGTATGGATGTATCTAGAT 59.642 44.000 10.73 10.73 0.00 1.98
5599 9374 4.700692 GTCGCAGGTATGGATGTATCTAGA 59.299 45.833 0.00 0.00 0.00 2.43
5600 9375 4.459337 TGTCGCAGGTATGGATGTATCTAG 59.541 45.833 0.00 0.00 0.00 2.43
5601 9376 4.403734 TGTCGCAGGTATGGATGTATCTA 58.596 43.478 0.00 0.00 0.00 1.98
5602 9377 3.230976 TGTCGCAGGTATGGATGTATCT 58.769 45.455 0.00 0.00 0.00 1.98
5603 9378 3.660501 TGTCGCAGGTATGGATGTATC 57.339 47.619 0.00 0.00 0.00 2.24
5604 9379 3.388024 ACTTGTCGCAGGTATGGATGTAT 59.612 43.478 0.00 0.00 0.00 2.29
5605 9380 2.764010 ACTTGTCGCAGGTATGGATGTA 59.236 45.455 0.00 0.00 0.00 2.29
5606 9381 1.555075 ACTTGTCGCAGGTATGGATGT 59.445 47.619 0.00 0.00 0.00 3.06
5607 9382 2.315925 ACTTGTCGCAGGTATGGATG 57.684 50.000 0.00 0.00 0.00 3.51
5608 9383 4.689612 ATTACTTGTCGCAGGTATGGAT 57.310 40.909 3.46 0.00 0.00 3.41
5609 9384 4.439057 GAATTACTTGTCGCAGGTATGGA 58.561 43.478 3.46 0.00 0.00 3.41
5610 9385 3.245284 CGAATTACTTGTCGCAGGTATGG 59.755 47.826 3.46 0.00 0.00 2.74
5611 9386 3.245284 CCGAATTACTTGTCGCAGGTATG 59.755 47.826 3.46 0.00 35.93 2.39
5612 9387 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
5613 9388 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
5614 9389 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
5615 9390 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
5616 9391 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
5617 9392 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
5618 9393 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
5619 9394 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
5620 9395 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5621 9396 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5622 9397 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5623 9398 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
5624 9399 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
5625 9400 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
5626 9401 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
5627 9402 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
5628 9403 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
5629 9404 0.682209 CCTACTCCCTCCGTTCCGAA 60.682 60.000 0.00 0.00 0.00 4.30
5630 9405 1.077212 CCTACTCCCTCCGTTCCGA 60.077 63.158 0.00 0.00 0.00 4.55
5631 9406 0.467659 ATCCTACTCCCTCCGTTCCG 60.468 60.000 0.00 0.00 0.00 4.30
5632 9407 1.790818 AATCCTACTCCCTCCGTTCC 58.209 55.000 0.00 0.00 0.00 3.62
5633 9408 2.158943 CCAAATCCTACTCCCTCCGTTC 60.159 54.545 0.00 0.00 0.00 3.95
5634 9409 1.838077 CCAAATCCTACTCCCTCCGTT 59.162 52.381 0.00 0.00 0.00 4.44
5635 9410 1.273666 ACCAAATCCTACTCCCTCCGT 60.274 52.381 0.00 0.00 0.00 4.69
5636 9411 1.139058 CACCAAATCCTACTCCCTCCG 59.861 57.143 0.00 0.00 0.00 4.63
5637 9412 1.490910 CCACCAAATCCTACTCCCTCC 59.509 57.143 0.00 0.00 0.00 4.30
5638 9413 1.490910 CCCACCAAATCCTACTCCCTC 59.509 57.143 0.00 0.00 0.00 4.30
5639 9414 1.596496 CCCACCAAATCCTACTCCCT 58.404 55.000 0.00 0.00 0.00 4.20
5640 9415 0.551396 CCCCACCAAATCCTACTCCC 59.449 60.000 0.00 0.00 0.00 4.30
5641 9416 1.212195 GTCCCCACCAAATCCTACTCC 59.788 57.143 0.00 0.00 0.00 3.85
5642 9417 1.913419 TGTCCCCACCAAATCCTACTC 59.087 52.381 0.00 0.00 0.00 2.59
5643 9418 2.053747 TGTCCCCACCAAATCCTACT 57.946 50.000 0.00 0.00 0.00 2.57
5644 9419 3.382083 AATGTCCCCACCAAATCCTAC 57.618 47.619 0.00 0.00 0.00 3.18
5645 9420 4.412060 AAAATGTCCCCACCAAATCCTA 57.588 40.909 0.00 0.00 0.00 2.94
5646 9421 3.274281 AAAATGTCCCCACCAAATCCT 57.726 42.857 0.00 0.00 0.00 3.24
5647 9422 3.582647 AGAAAAATGTCCCCACCAAATCC 59.417 43.478 0.00 0.00 0.00 3.01
5648 9423 4.890158 AGAAAAATGTCCCCACCAAATC 57.110 40.909 0.00 0.00 0.00 2.17
5649 9424 6.755542 TTAAGAAAAATGTCCCCACCAAAT 57.244 33.333 0.00 0.00 0.00 2.32
5650 9425 6.561519 TTTAAGAAAAATGTCCCCACCAAA 57.438 33.333 0.00 0.00 0.00 3.28
5651 9426 6.465035 CCATTTAAGAAAAATGTCCCCACCAA 60.465 38.462 9.03 0.00 36.24 3.67
5652 9427 5.012561 CCATTTAAGAAAAATGTCCCCACCA 59.987 40.000 9.03 0.00 36.24 4.17
5653 9428 5.487433 CCATTTAAGAAAAATGTCCCCACC 58.513 41.667 9.03 0.00 36.24 4.61
5654 9429 4.935205 GCCATTTAAGAAAAATGTCCCCAC 59.065 41.667 9.03 0.00 36.24 4.61
5655 9430 4.594920 TGCCATTTAAGAAAAATGTCCCCA 59.405 37.500 9.03 0.41 36.24 4.96
5656 9431 5.159273 TGCCATTTAAGAAAAATGTCCCC 57.841 39.130 9.03 0.00 36.24 4.81
5668 9444 7.555087 TCACCAAGGATTTTATGCCATTTAAG 58.445 34.615 0.00 0.00 0.00 1.85
6074 9863 3.056328 GCACTTTCCGGAGCCACC 61.056 66.667 3.34 0.00 0.00 4.61
6165 9954 6.592607 TCAGGTTGTTCGTGTTTAGGAATATC 59.407 38.462 0.00 0.00 33.73 1.63
6171 9960 4.315803 AGATCAGGTTGTTCGTGTTTAGG 58.684 43.478 0.00 0.00 34.10 2.69
6337 10135 9.642327 CAACCAATCAAGATGACATTCAATTTA 57.358 29.630 0.00 0.00 0.00 1.40
6546 10346 3.722728 AAACAAAAGAAGCCAGCAGAG 57.277 42.857 0.00 0.00 0.00 3.35
6549 10349 2.278854 GCAAAACAAAAGAAGCCAGCA 58.721 42.857 0.00 0.00 0.00 4.41
6560 10360 2.397044 ATCCCTCCCTGCAAAACAAA 57.603 45.000 0.00 0.00 0.00 2.83
6647 10447 4.634883 GCATCAGTCATCAGTCTGACAATT 59.365 41.667 10.88 0.00 46.45 2.32
6680 10480 2.034558 ACACCATCTCAAGCCAAAAACG 59.965 45.455 0.00 0.00 0.00 3.60
6721 10521 0.868406 GGCCTTCACAAACAGAGTCG 59.132 55.000 0.00 0.00 0.00 4.18
6805 10605 5.863935 GCAATTCAAACCAAGAAGTACATCC 59.136 40.000 0.00 0.00 0.00 3.51
7140 10954 9.515226 AACTGGAAAAGAACATAGCATTAGTTA 57.485 29.630 0.00 0.00 0.00 2.24
7357 11187 1.534729 ATCCCGCAGAACCAAACTTC 58.465 50.000 0.00 0.00 0.00 3.01
7367 11197 0.036732 AGCTCAACAAATCCCGCAGA 59.963 50.000 0.00 0.00 0.00 4.26
7381 11211 0.884704 GAAAGCACCGGTGAAGCTCA 60.885 55.000 38.30 0.00 37.70 4.26
7463 11294 1.066908 CTTGGGCGCTTGTTGAAAAGA 59.933 47.619 7.64 0.00 0.00 2.52
7501 11332 2.171659 AGGCAAAACCCCGACAAAATTT 59.828 40.909 0.00 0.00 40.58 1.82
7502 11333 1.765904 AGGCAAAACCCCGACAAAATT 59.234 42.857 0.00 0.00 40.58 1.82
7503 11334 1.419381 AGGCAAAACCCCGACAAAAT 58.581 45.000 0.00 0.00 40.58 1.82
7504 11335 1.137282 GAAGGCAAAACCCCGACAAAA 59.863 47.619 0.00 0.00 40.58 2.44
7505 11336 0.747852 GAAGGCAAAACCCCGACAAA 59.252 50.000 0.00 0.00 40.58 2.83
7506 11337 1.110518 GGAAGGCAAAACCCCGACAA 61.111 55.000 0.00 0.00 40.58 3.18
7507 11338 1.529713 GGAAGGCAAAACCCCGACA 60.530 57.895 0.00 0.00 40.58 4.35
7510 11341 0.679960 CTAGGGAAGGCAAAACCCCG 60.680 60.000 0.00 0.00 44.21 5.73
7512 11343 3.283020 CCTAGGGAAGGCAAAACCC 57.717 57.895 0.00 0.00 38.97 4.11
7537 11369 6.093495 TGCCTAAAGTCTGACAAAATTATCGG 59.907 38.462 10.88 4.30 0.00 4.18
7664 11497 5.360714 ACCCAAAGATATGCCTGTTTATGTG 59.639 40.000 0.00 0.00 0.00 3.21
7665 11498 5.518865 ACCCAAAGATATGCCTGTTTATGT 58.481 37.500 0.00 0.00 0.00 2.29
7689 11539 6.611613 AGTGTCTGGAAGTTGATCTAATCA 57.388 37.500 0.00 0.00 37.55 2.57
7704 11554 4.256920 AGCAAAGCAACTATAGTGTCTGG 58.743 43.478 6.06 4.63 0.00 3.86
7755 11608 2.355108 GCTGCAAGGGACAGAGACATTA 60.355 50.000 0.00 0.00 37.32 1.90
7789 11642 2.032681 GCTCGTGGAGTGGGCTTT 59.967 61.111 0.00 0.00 31.39 3.51
7790 11643 2.129555 ATTGCTCGTGGAGTGGGCTT 62.130 55.000 0.00 0.00 31.39 4.35
7883 11737 6.719370 TCTTGCTTTGGGCTTCTTTTCTATTA 59.281 34.615 0.00 0.00 42.39 0.98
7888 11742 3.733443 TCTTGCTTTGGGCTTCTTTTC 57.267 42.857 0.00 0.00 42.39 2.29
8112 12359 8.793592 TGCACGAGTTGATGACTAGTATATATT 58.206 33.333 0.00 0.00 41.53 1.28
8144 12391 6.129115 CCAATTTGACAAAAATCACTAGCACG 60.129 38.462 4.41 0.00 0.00 5.34
8145 12392 6.701400 ACCAATTTGACAAAAATCACTAGCAC 59.299 34.615 4.41 0.00 0.00 4.40
8156 12403 6.590292 TGAAACGCTTTACCAATTTGACAAAA 59.410 30.769 4.41 0.00 0.00 2.44
8178 12425 3.819245 CTCCAGTGTTGGGGTTGAA 57.181 52.632 0.00 0.00 45.10 2.69
8186 12433 3.958147 ATCGCGGGCTCCAGTGTTG 62.958 63.158 6.13 0.00 0.00 3.33
8191 12438 0.249868 TCAATAATCGCGGGCTCCAG 60.250 55.000 6.13 0.00 0.00 3.86
8217 12464 0.263765 AGCCGGTACCCATAGGAGAA 59.736 55.000 6.25 0.00 36.73 2.87
8277 12556 3.705043 ACTAACGCCCGTCATTAGTAG 57.295 47.619 2.79 0.00 37.38 2.57


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

AutoCloner maintained by Alex Coulton.