Multiple sequence alignment - TraesCS6A01G028000

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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 TraesCS6A01G028000 chr6A 100.000 4935 0 0 1 4935 14367434 14372368 0.000000e+00 9114.0
1 TraesCS6A01G028000 chr6A 96.725 794 20 4 44 834 16618389 16619179 0.000000e+00 1317.0
2 TraesCS6A01G028000 chr6A 91.803 183 14 1 841 1022 16618572 16618390 2.280000e-63 254.0
3 TraesCS6A01G028000 chr6A 91.758 182 14 1 841 1022 14367658 14367478 8.200000e-63 252.0
4 TraesCS6A01G028000 chr6A 91.758 182 14 1 45 225 14368455 14368274 8.200000e-63 252.0
5 TraesCS6A01G028000 chr6A 100.000 44 0 0 1 44 14359015 14359058 1.140000e-11 82.4
6 TraesCS6A01G028000 chr6A 97.674 43 1 0 1023 1065 14359049 14359091 1.910000e-09 75.0
7 TraesCS6A01G028000 chr6B 93.299 985 50 10 2529 3497 23646508 23645524 0.000000e+00 1439.0
8 TraesCS6A01G028000 chr6B 92.818 905 45 8 3498 4391 23645489 23644594 0.000000e+00 1293.0
9 TraesCS6A01G028000 chr6B 89.989 909 74 9 1590 2487 23647767 23646865 0.000000e+00 1158.0
10 TraesCS6A01G028000 chr6B 94.472 199 11 0 4495 4693 23644597 23644399 1.730000e-79 307.0
11 TraesCS6A01G028000 chr6B 87.281 228 13 4 4711 4935 23644411 23644197 3.820000e-61 246.0
12 TraesCS6A01G028000 chr6D 83.799 1611 149 42 1023 2590 13090267 13091808 0.000000e+00 1426.0
13 TraesCS6A01G028000 chr6D 94.256 766 36 5 3499 4258 13092992 13093755 0.000000e+00 1164.0
14 TraesCS6A01G028000 chr6D 94.305 439 17 5 4263 4693 13095614 13096052 0.000000e+00 665.0
15 TraesCS6A01G028000 chr6D 84.330 619 71 11 2899 3497 13092344 13092956 2.560000e-162 582.0
16 TraesCS6A01G028000 chr6D 77.126 988 146 53 2712 3656 27734731 27733781 2.650000e-137 499.0
17 TraesCS6A01G028000 chr6D 93.013 229 12 4 4711 4935 13096040 13096268 1.020000e-86 331.0
18 TraesCS6A01G028000 chr6D 81.288 326 46 8 2585 2898 13091961 13092283 2.950000e-62 250.0
19 TraesCS6A01G028000 chr7A 97.851 791 16 1 45 834 110223706 110222916 0.000000e+00 1365.0
20 TraesCS6A01G028000 chr7A 82.034 590 76 20 3508 4087 254901081 254900512 4.470000e-130 475.0
21 TraesCS6A01G028000 chr7A 78.887 701 107 28 2712 3393 254901915 254901237 2.110000e-118 436.0
22 TraesCS6A01G028000 chr7A 78.807 486 84 12 1778 2256 254903148 254902675 4.800000e-80 309.0
23 TraesCS6A01G028000 chr7A 95.789 190 8 0 833 1022 110222771 110222582 1.730000e-79 307.0
24 TraesCS6A01G028000 chr7A 92.308 182 14 0 841 1022 110223525 110223706 4.900000e-65 259.0
25 TraesCS6A01G028000 chr7A 91.257 183 15 1 44 225 110222581 110222763 1.060000e-61 248.0
26 TraesCS6A01G028000 chr2B 97.100 793 20 3 44 834 283012329 283013120 0.000000e+00 1334.0
27 TraesCS6A01G028000 chr2B 96.316 190 7 0 833 1022 283013265 283013454 3.710000e-81 313.0
28 TraesCS6A01G028000 chr2B 92.308 182 13 1 45 225 283013454 283013273 1.760000e-64 257.0
29 TraesCS6A01G028000 chr2B 91.209 182 15 1 841 1022 283012510 283012330 3.820000e-61 246.0
30 TraesCS6A01G028000 chr4A 94.987 798 33 2 38 834 314689961 314690752 0.000000e+00 1245.0
31 TraesCS6A01G028000 chr4A 96.277 188 7 0 833 1020 314690897 314691084 4.800000e-80 309.0
32 TraesCS6A01G028000 chr4A 92.308 182 14 0 841 1022 314690149 314689968 4.900000e-65 259.0
33 TraesCS6A01G028000 chr4A 90.556 180 16 1 47 225 314691084 314690905 2.300000e-58 237.0
34 TraesCS6A01G028000 chr4A 79.359 281 48 10 2626 2901 678782278 678782003 6.520000e-44 189.0
35 TraesCS6A01G028000 chr7B 83.701 589 67 16 3508 4087 218538851 218539419 3.380000e-146 529.0
36 TraesCS6A01G028000 chr7B 80.031 651 103 21 2753 3394 218538062 218538694 1.620000e-124 457.0
37 TraesCS6A01G028000 chr7B 80.795 453 70 9 1815 2256 218536701 218537147 6.120000e-89 339.0
38 TraesCS6A01G028000 chr7B 77.397 146 24 7 2564 2702 218537834 218537977 1.470000e-10 78.7
39 TraesCS6A01G028000 chr7D 87.900 438 44 8 3508 3940 242778737 242779170 1.590000e-139 507.0
40 TraesCS6A01G028000 chr7D 78.807 637 103 22 2753 3372 242777958 242778579 2.770000e-107 399.0
41 TraesCS6A01G028000 chr7D 79.150 494 81 16 1774 2256 242776683 242777165 6.160000e-84 322.0
42 TraesCS6A01G028000 chr7D 79.178 365 62 12 2542 2899 404239352 404238995 1.780000e-59 241.0
43 TraesCS6A01G028000 chr2D 89.899 396 22 3 444 834 25877601 25877983 1.230000e-135 494.0
44 TraesCS6A01G028000 chr1A 92.440 291 17 2 47 336 552495720 552495434 1.280000e-110 411.0
45 TraesCS6A01G028000 chr1A 87.778 180 18 2 841 1020 552495545 552495720 1.800000e-49 207.0
46 TraesCS6A01G028000 chr1A 82.018 228 37 2 1705 1928 525146539 525146312 1.810000e-44 191.0
47 TraesCS6A01G028000 chr1A 97.590 83 2 0 329 411 552495224 552495142 5.150000e-30 143.0
48 TraesCS6A01G028000 chr1A 100.000 50 0 0 785 834 552495140 552495091 5.260000e-15 93.5
49 TraesCS6A01G028000 chr1A 92.453 53 4 0 1876 1928 272607810 272607862 5.300000e-10 76.8
50 TraesCS6A01G028000 chr1B 80.223 359 60 7 2548 2899 572150279 572150633 4.900000e-65 259.0
51 TraesCS6A01G028000 chr4D 79.396 364 62 11 2542 2899 43407704 43408060 1.370000e-60 244.0
52 TraesCS6A01G028000 chr5D 76.966 356 67 11 2550 2899 108957787 108957441 6.520000e-44 189.0
53 TraesCS6A01G028000 chr3A 78.417 278 42 12 2542 2805 679754302 679754029 1.100000e-36 165.0


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 TraesCS6A01G028000 chr6A 14367434 14372368 4934 False 9114.000000 9114 100.000000 1 4935 1 chr6A.!!$F1 4934
1 TraesCS6A01G028000 chr6A 16618389 16619179 790 False 1317.000000 1317 96.725000 44 834 1 chr6A.!!$F2 790
2 TraesCS6A01G028000 chr6A 14367478 14368455 977 True 252.000000 252 91.758000 45 1022 2 chr6A.!!$R2 977
3 TraesCS6A01G028000 chr6B 23644197 23647767 3570 True 888.600000 1439 91.571800 1590 4935 5 chr6B.!!$R1 3345
4 TraesCS6A01G028000 chr6D 13090267 13096268 6001 False 736.333333 1426 88.498500 1023 4935 6 chr6D.!!$F1 3912
5 TraesCS6A01G028000 chr6D 27733781 27734731 950 True 499.000000 499 77.126000 2712 3656 1 chr6D.!!$R1 944
6 TraesCS6A01G028000 chr7A 110222582 110223706 1124 True 836.000000 1365 96.820000 45 1022 2 chr7A.!!$R1 977
7 TraesCS6A01G028000 chr7A 254900512 254903148 2636 True 406.666667 475 79.909333 1778 4087 3 chr7A.!!$R2 2309
8 TraesCS6A01G028000 chr7A 110222581 110223706 1125 False 253.500000 259 91.782500 44 1022 2 chr7A.!!$F1 978
9 TraesCS6A01G028000 chr2B 283012329 283013454 1125 False 823.500000 1334 96.708000 44 1022 2 chr2B.!!$F1 978
10 TraesCS6A01G028000 chr2B 283012330 283013454 1124 True 251.500000 257 91.758500 45 1022 2 chr2B.!!$R1 977
11 TraesCS6A01G028000 chr4A 314689961 314691084 1123 False 777.000000 1245 95.632000 38 1020 2 chr4A.!!$F1 982
12 TraesCS6A01G028000 chr4A 314689968 314691084 1116 True 248.000000 259 91.432000 47 1022 2 chr4A.!!$R2 975
13 TraesCS6A01G028000 chr7B 218536701 218539419 2718 False 350.925000 529 80.481000 1815 4087 4 chr7B.!!$F1 2272
14 TraesCS6A01G028000 chr7D 242776683 242779170 2487 False 409.333333 507 81.952333 1774 3940 3 chr7D.!!$F1 2166
15 TraesCS6A01G028000 chr1A 552495091 552495720 629 True 215.833333 411 96.676667 47 834 3 chr1A.!!$R2 787

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
415 1138 0.950836 TGACTCAACCGGTGCATTTG 59.049 50.0 8.52 1.28 0.00 2.32 F
1043 2059 0.038159 AGAAACTCTTCACCGCCGAG 60.038 55.0 0.00 0.00 33.64 4.63 F
1365 2411 0.250513 GAGGTCAGGCTCGGTGATTT 59.749 55.0 0.00 0.00 0.00 2.17 F
1759 2833 0.471591 TGTTTTGGCCCCTCTGCATT 60.472 50.0 0.00 0.00 0.00 3.56 F
2496 4003 0.399833 GATCCATGCCTCTCTTCCCC 59.600 60.0 0.00 0.00 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 3009 0.169009 GAACAGAAACGGAGCATGGC 59.831 55.000 0.0 0.0 0.00 4.40 R
2494 4001 0.110295 TCATTGAGTGTGTGTGGGGG 59.890 55.000 0.0 0.0 0.00 5.40 R
2497 4004 1.267806 GCCTTCATTGAGTGTGTGTGG 59.732 52.381 0.0 0.0 0.00 4.17 R
3684 5871 1.556911 GGAGCTGAGGGAACTTCATCA 59.443 52.381 0.0 0.0 44.43 3.07 R
4476 8535 0.250234 CAGGAGACGGATGCTTTCCA 59.750 55.000 7.0 0.0 45.78 3.53 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
29 30 9.825109 TTTATTGGAAAAAGAAAACAACCTAGG 57.175 29.630 7.41 7.41 0.00 3.02
30 31 7.669089 ATTGGAAAAAGAAAACAACCTAGGA 57.331 32.000 17.98 0.00 0.00 2.94
31 32 6.709018 TGGAAAAAGAAAACAACCTAGGAG 57.291 37.500 17.98 10.18 0.00 3.69
32 33 6.192044 TGGAAAAAGAAAACAACCTAGGAGT 58.808 36.000 17.98 10.89 0.00 3.85
33 34 7.348033 TGGAAAAAGAAAACAACCTAGGAGTA 58.652 34.615 17.98 0.00 0.00 2.59
34 35 7.835181 TGGAAAAAGAAAACAACCTAGGAGTAA 59.165 33.333 17.98 0.00 0.00 2.24
35 36 8.689061 GGAAAAAGAAAACAACCTAGGAGTAAA 58.311 33.333 17.98 0.00 0.00 2.01
38 39 9.470399 AAAAGAAAACAACCTAGGAGTAAAAGA 57.530 29.630 17.98 0.00 0.00 2.52
39 40 9.470399 AAAGAAAACAACCTAGGAGTAAAAGAA 57.530 29.630 17.98 0.00 0.00 2.52
40 41 9.470399 AAGAAAACAACCTAGGAGTAAAAGAAA 57.530 29.630 17.98 0.00 0.00 2.52
41 42 8.900781 AGAAAACAACCTAGGAGTAAAAGAAAC 58.099 33.333 17.98 0.00 0.00 2.78
42 43 8.818622 AAAACAACCTAGGAGTAAAAGAAACT 57.181 30.769 17.98 0.00 0.00 2.66
101 103 5.336690 GGAGTTGATGATTTGCCTGCTTTAA 60.337 40.000 0.00 0.00 0.00 1.52
140 142 7.742556 TTTGCCCCATTTTTCTTTAATCTTG 57.257 32.000 0.00 0.00 0.00 3.02
407 1130 1.165907 TGCAAAGCTGACTCAACCGG 61.166 55.000 0.00 0.00 0.00 5.28
411 1134 2.280797 GCTGACTCAACCGGTGCA 60.281 61.111 8.52 0.64 0.00 4.57
415 1138 0.950836 TGACTCAACCGGTGCATTTG 59.049 50.000 8.52 1.28 0.00 2.32
537 1261 2.693762 CGGCGGAGTAACGGACAGA 61.694 63.158 0.00 0.00 0.00 3.41
599 1323 8.539117 TCTTATTTGTCTGATCTGATACTCCA 57.461 34.615 5.52 0.00 0.00 3.86
622 1346 6.836527 CCATATTTGGTTACAAGGGGATACAA 59.163 38.462 0.00 0.00 37.97 2.41
659 1383 1.529152 TAGCTTCACGTCCAAGCCGA 61.529 55.000 20.32 9.88 46.41 5.54
838 1854 1.968493 TGACCAAGGTGACTACTGTCC 59.032 52.381 0.00 0.00 42.68 4.02
984 2000 3.698040 ACTAAAGCAGGGCAAATCATCAG 59.302 43.478 0.00 0.00 0.00 2.90
1000 2016 9.342308 CAAATCATCAGCTCCCTAAATAAAGTA 57.658 33.333 0.00 0.00 0.00 2.24
1025 2041 4.442472 GGCAAATGATCCAATCTCCCAAAG 60.442 45.833 0.00 0.00 0.00 2.77
1043 2059 0.038159 AGAAACTCTTCACCGCCGAG 60.038 55.000 0.00 0.00 33.64 4.63
1144 2168 1.070445 CGTGGATCTGGCCTCATCC 59.930 63.158 21.09 21.09 39.38 3.51
1197 2243 3.003173 CTCCTCCTTCCGCCACCA 61.003 66.667 0.00 0.00 0.00 4.17
1258 2304 1.874019 CCGATTCGGTGCAGTCTCG 60.874 63.158 17.08 0.00 42.73 4.04
1270 2316 0.532862 CAGTCTCGTGGTGGTGCTTT 60.533 55.000 0.00 0.00 0.00 3.51
1282 2328 2.283101 TGCTTTGGCGGGCATCTT 60.283 55.556 4.64 0.00 42.25 2.40
1303 2349 4.208686 GTCTCCGAGCCGCCGAAT 62.209 66.667 3.21 0.00 0.00 3.34
1308 2354 3.022914 CGAGCCGCCGAATACGAC 61.023 66.667 0.00 0.00 42.66 4.34
1339 2385 2.018544 CGGCGCCGATTCCATTTTA 58.981 52.632 44.86 0.00 42.83 1.52
1351 2397 5.292101 CGATTCCATTTTACAGTGAGAGGTC 59.708 44.000 0.00 0.00 0.00 3.85
1352 2398 5.560722 TTCCATTTTACAGTGAGAGGTCA 57.439 39.130 0.00 0.00 0.00 4.02
1353 2399 5.152623 TCCATTTTACAGTGAGAGGTCAG 57.847 43.478 0.00 0.00 31.53 3.51
1354 2400 4.020218 TCCATTTTACAGTGAGAGGTCAGG 60.020 45.833 0.00 0.00 31.53 3.86
1355 2401 3.402628 TTTTACAGTGAGAGGTCAGGC 57.597 47.619 0.00 0.00 31.53 4.85
1356 2402 2.310779 TTACAGTGAGAGGTCAGGCT 57.689 50.000 0.00 0.00 31.53 4.58
1357 2403 1.840737 TACAGTGAGAGGTCAGGCTC 58.159 55.000 0.00 0.00 31.53 4.70
1358 2404 1.247419 ACAGTGAGAGGTCAGGCTCG 61.247 60.000 0.00 0.00 33.89 5.03
1359 2405 1.680651 AGTGAGAGGTCAGGCTCGG 60.681 63.158 0.00 0.00 33.89 4.63
1360 2406 1.979693 GTGAGAGGTCAGGCTCGGT 60.980 63.158 0.00 0.00 33.89 4.69
1361 2407 1.979155 TGAGAGGTCAGGCTCGGTG 60.979 63.158 0.00 0.00 33.89 4.94
1362 2408 1.679305 GAGAGGTCAGGCTCGGTGA 60.679 63.158 0.00 0.00 0.00 4.02
1363 2409 1.000993 AGAGGTCAGGCTCGGTGAT 59.999 57.895 0.00 0.00 0.00 3.06
1364 2410 0.616111 AGAGGTCAGGCTCGGTGATT 60.616 55.000 0.00 0.00 0.00 2.57
1365 2411 0.250513 GAGGTCAGGCTCGGTGATTT 59.749 55.000 0.00 0.00 0.00 2.17
1366 2412 1.480954 GAGGTCAGGCTCGGTGATTTA 59.519 52.381 0.00 0.00 0.00 1.40
1367 2413 1.207329 AGGTCAGGCTCGGTGATTTAC 59.793 52.381 0.00 0.00 0.00 2.01
1368 2414 1.207329 GGTCAGGCTCGGTGATTTACT 59.793 52.381 0.00 0.00 0.00 2.24
1369 2415 2.271800 GTCAGGCTCGGTGATTTACTG 58.728 52.381 0.00 0.00 36.99 2.74
1370 2416 2.094182 GTCAGGCTCGGTGATTTACTGA 60.094 50.000 0.00 0.00 42.36 3.41
1371 2417 2.094182 TCAGGCTCGGTGATTTACTGAC 60.094 50.000 0.00 0.00 39.75 3.51
1372 2418 2.093973 CAGGCTCGGTGATTTACTGACT 60.094 50.000 0.00 0.00 39.75 3.41
1373 2419 2.093973 AGGCTCGGTGATTTACTGACTG 60.094 50.000 0.00 0.00 39.75 3.51
1374 2420 2.094182 GGCTCGGTGATTTACTGACTGA 60.094 50.000 0.00 0.00 39.75 3.41
1375 2421 3.585862 GCTCGGTGATTTACTGACTGAA 58.414 45.455 0.00 0.00 39.75 3.02
1376 2422 3.368236 GCTCGGTGATTTACTGACTGAAC 59.632 47.826 0.00 0.00 39.75 3.18
1377 2423 4.810790 CTCGGTGATTTACTGACTGAACT 58.189 43.478 0.00 0.00 39.75 3.01
1378 2424 5.621555 GCTCGGTGATTTACTGACTGAACTA 60.622 44.000 0.00 0.00 39.75 2.24
1379 2425 5.950883 TCGGTGATTTACTGACTGAACTAG 58.049 41.667 0.00 0.00 39.75 2.57
1380 2426 4.563184 CGGTGATTTACTGACTGAACTAGC 59.437 45.833 0.00 0.00 37.93 3.42
1381 2427 5.622460 CGGTGATTTACTGACTGAACTAGCT 60.622 44.000 0.00 0.00 37.93 3.32
1382 2428 6.166982 GGTGATTTACTGACTGAACTAGCTT 58.833 40.000 0.00 0.00 0.00 3.74
1383 2429 6.091441 GGTGATTTACTGACTGAACTAGCTTG 59.909 42.308 0.00 0.00 0.00 4.01
1384 2430 5.639506 TGATTTACTGACTGAACTAGCTTGC 59.360 40.000 0.00 0.00 0.00 4.01
1455 2528 5.345472 TGCAAGATATTGTGAATTTGTTGCG 59.655 36.000 13.15 0.00 45.40 4.85
1460 2533 3.724508 TTGTGAATTTGTTGCGGATGT 57.275 38.095 0.00 0.00 0.00 3.06
1485 2558 3.476552 TCCGAAGAACTTTGCATCAAGT 58.523 40.909 0.00 0.00 0.00 3.16
1491 2564 7.077605 CGAAGAACTTTGCATCAAGTTTCATA 58.922 34.615 15.77 0.00 0.00 2.15
1494 2567 7.715657 AGAACTTTGCATCAAGTTTCATACAA 58.284 30.769 15.77 0.00 0.00 2.41
1500 2573 7.872163 TGCATCAAGTTTCATACAAATGTTC 57.128 32.000 0.00 0.00 34.50 3.18
1501 2574 7.660112 TGCATCAAGTTTCATACAAATGTTCT 58.340 30.769 0.00 0.00 34.50 3.01
1502 2575 8.791675 TGCATCAAGTTTCATACAAATGTTCTA 58.208 29.630 0.00 0.00 34.50 2.10
1534 2607 7.764443 AGTTTAACCTTTTCTTTTCTTGCTTCC 59.236 33.333 0.00 0.00 0.00 3.46
1555 2628 3.007940 CCTACAGTTGACCTGACCATTGA 59.992 47.826 0.00 0.00 44.49 2.57
1561 2634 3.057969 TGACCTGACCATTGATCACAC 57.942 47.619 0.00 0.00 0.00 3.82
1570 2643 3.696051 ACCATTGATCACACCTTGTATGC 59.304 43.478 0.00 0.00 0.00 3.14
1575 2648 5.612725 TGATCACACCTTGTATGCTCATA 57.387 39.130 0.00 0.00 0.00 2.15
1583 2656 5.931146 CACCTTGTATGCTCATATCCTCTTC 59.069 44.000 0.00 0.00 0.00 2.87
1602 2675 7.560262 TCCTCTTCGAAAGATCCTTAATAGTGA 59.440 37.037 0.00 0.00 41.60 3.41
1603 2676 8.198109 CCTCTTCGAAAGATCCTTAATAGTGAA 58.802 37.037 0.00 0.00 41.60 3.18
1627 2700 5.147032 TGAACTCAATTTCCCCACAATCTT 58.853 37.500 0.00 0.00 0.00 2.40
1631 2704 6.256053 ACTCAATTTCCCCACAATCTTGTAT 58.744 36.000 0.00 0.00 39.91 2.29
1632 2705 6.153340 ACTCAATTTCCCCACAATCTTGTATG 59.847 38.462 0.00 0.00 39.91 2.39
1633 2706 6.015918 TCAATTTCCCCACAATCTTGTATGT 58.984 36.000 0.00 0.00 39.91 2.29
1634 2707 7.178573 TCAATTTCCCCACAATCTTGTATGTA 58.821 34.615 0.00 0.00 39.91 2.29
1635 2708 7.339212 TCAATTTCCCCACAATCTTGTATGTAG 59.661 37.037 0.00 0.00 39.91 2.74
1636 2709 5.772393 TTCCCCACAATCTTGTATGTAGT 57.228 39.130 0.00 0.00 39.91 2.73
1637 2710 5.353394 TCCCCACAATCTTGTATGTAGTC 57.647 43.478 0.00 0.00 39.91 2.59
1668 2741 3.697166 TGCTGGTATGAGTGTCTGACTA 58.303 45.455 9.51 0.00 33.83 2.59
1756 2830 0.613012 ATCTGTTTTGGCCCCTCTGC 60.613 55.000 0.00 0.00 0.00 4.26
1759 2833 0.471591 TGTTTTGGCCCCTCTGCATT 60.472 50.000 0.00 0.00 0.00 3.56
1767 2841 1.755179 CCCCTCTGCATTTGGTGTAG 58.245 55.000 0.00 0.00 41.39 2.74
1775 2849 4.019771 TCTGCATTTGGTGTAGTATGGTGA 60.020 41.667 0.00 0.00 40.91 4.02
1920 2994 5.452077 CCCATGTAAGTGTAGCTCCTCTAAC 60.452 48.000 0.00 0.00 0.00 2.34
1924 2998 5.778750 TGTAAGTGTAGCTCCTCTAACCTTT 59.221 40.000 0.00 0.00 0.00 3.11
1935 3009 6.675728 GCTCCTCTAACCTTTTTAGATTTGCG 60.676 42.308 0.00 0.00 31.36 4.85
1967 3041 3.398954 TTCTGTTCAACGTTTGAGCAC 57.601 42.857 0.00 0.00 44.33 4.40
1996 3077 5.304614 TGTTCTGTAACTTAGCTGGAGAAGT 59.695 40.000 0.00 0.00 37.50 3.01
2007 3088 7.616150 ACTTAGCTGGAGAAGTAAGATACAGAA 59.384 37.037 0.00 0.00 34.13 3.02
2035 3116 5.830912 TGTGAATCCTTTTGCTGTTGTTAG 58.169 37.500 0.00 0.00 0.00 2.34
2106 3188 6.931243 TGTTTTTGTTCAGTTTTAACGGAC 57.069 33.333 0.00 0.00 32.93 4.79
2108 3190 5.542616 TTTTGTTCAGTTTTAACGGACGA 57.457 34.783 0.00 0.00 32.93 4.20
2115 3197 1.060122 GTTTTAACGGACGATCGCTGG 59.940 52.381 16.60 6.68 0.00 4.85
2169 3254 3.357919 GCATGTGCTGGCACTGAA 58.642 55.556 23.30 6.93 46.30 3.02
2188 3273 3.932710 TGAAAGCCTCTAATTGCAGTACG 59.067 43.478 0.00 0.00 0.00 3.67
2214 3299 0.548031 CAGCCAGGGAGCTATTGGAA 59.452 55.000 13.29 0.00 42.61 3.53
2281 3367 3.475566 TGGGTTTCTGTGTTCTCAGAG 57.524 47.619 0.00 0.00 43.85 3.35
2328 3414 9.913310 TTGGGAATATTAATATGTTGACTGTGA 57.087 29.630 8.74 0.00 0.00 3.58
2374 3467 3.057526 GCTAACATTTGTTGAGGACCCAC 60.058 47.826 6.21 0.00 38.90 4.61
2382 3475 6.739331 TTTGTTGAGGACCCACAATTTTAT 57.261 33.333 2.43 0.00 0.00 1.40
2446 3953 6.036577 TCCCCTTGCATATTTGAAGTTTTC 57.963 37.500 0.00 0.00 0.00 2.29
2453 3960 5.477984 TGCATATTTGAAGTTTTCCTGAGCT 59.522 36.000 0.00 0.00 0.00 4.09
2488 3995 0.749049 GCCCTTTTGATCCATGCCTC 59.251 55.000 0.00 0.00 0.00 4.70
2489 3996 1.687368 GCCCTTTTGATCCATGCCTCT 60.687 52.381 0.00 0.00 0.00 3.69
2490 3997 2.305009 CCCTTTTGATCCATGCCTCTC 58.695 52.381 0.00 0.00 0.00 3.20
2491 3998 2.091994 CCCTTTTGATCCATGCCTCTCT 60.092 50.000 0.00 0.00 0.00 3.10
2493 4000 3.631227 CCTTTTGATCCATGCCTCTCTTC 59.369 47.826 0.00 0.00 0.00 2.87
2494 4001 3.287867 TTTGATCCATGCCTCTCTTCC 57.712 47.619 0.00 0.00 0.00 3.46
2495 4002 1.135094 TGATCCATGCCTCTCTTCCC 58.865 55.000 0.00 0.00 0.00 3.97
2496 4003 0.399833 GATCCATGCCTCTCTTCCCC 59.600 60.000 0.00 0.00 0.00 4.81
2497 4004 1.064824 ATCCATGCCTCTCTTCCCCC 61.065 60.000 0.00 0.00 0.00 5.40
2521 4038 2.555325 CACACACTCAATGAAGGCATGT 59.445 45.455 0.00 0.00 34.26 3.21
2526 4043 5.124297 CACACTCAATGAAGGCATGTCAATA 59.876 40.000 0.00 0.00 34.26 1.90
2629 4610 9.924650 TCTTACTTGACAAGAGAAACCTTATAC 57.075 33.333 21.95 0.00 0.00 1.47
2646 4630 6.670233 CCTTATACGAGGTTCAGAGTATGTC 58.330 44.000 0.00 0.00 32.71 3.06
2702 4732 7.312415 TGATGATGAGAATGTCTGGTCATAT 57.688 36.000 0.00 0.00 31.42 1.78
2707 4737 9.716531 TGATGAGAATGTCTGGTCATATTAATC 57.283 33.333 0.00 0.00 29.66 1.75
2857 4887 3.571119 GCACTAGCTGCCACACTG 58.429 61.111 0.00 0.00 40.42 3.66
2921 5015 1.623811 GCTGTCCCCACTCTCTGTTTA 59.376 52.381 0.00 0.00 0.00 2.01
3009 5111 7.345691 TCCATTACTATCTTTTGGATGCAGAA 58.654 34.615 0.00 0.00 35.98 3.02
3244 5364 7.765360 AGCAGTCATGATAGAAAAGAAAGAGAG 59.235 37.037 0.00 0.00 0.00 3.20
3252 5372 5.482163 AGAAAAGAAAGAGAGACTGGAGG 57.518 43.478 0.00 0.00 0.00 4.30
3412 5540 7.805071 CCAGTTTACTGATTTGTTCATTGACTC 59.195 37.037 11.35 0.00 46.59 3.36
3413 5541 8.344831 CAGTTTACTGATTTGTTCATTGACTCA 58.655 33.333 3.80 0.00 46.59 3.41
3414 5542 8.345565 AGTTTACTGATTTGTTCATTGACTCAC 58.654 33.333 0.00 0.00 32.72 3.51
3423 5560 2.771089 TCATTGACTCACCTTGCTGTC 58.229 47.619 0.00 0.00 0.00 3.51
3456 5598 9.712305 AGTGTAGGTATAATCAATGCTATGTTC 57.288 33.333 0.00 0.00 0.00 3.18
3468 5611 7.799784 TCAATGCTATGTTCGATCATTACATG 58.200 34.615 13.88 11.62 34.55 3.21
3510 5689 6.157994 AGACCTAAGCATTTATACTTGGTGGA 59.842 38.462 0.00 0.00 31.68 4.02
3592 5774 3.664276 CGAAATGGTTGACTTAGCACGTG 60.664 47.826 12.28 12.28 0.00 4.49
3601 5783 1.613925 ACTTAGCACGTGAGCTGAAGA 59.386 47.619 22.23 0.00 46.11 2.87
3630 5812 3.618019 GCCTTGTAGTGAACCAATCCGTA 60.618 47.826 0.00 0.00 0.00 4.02
3670 5852 3.131046 AGGTTTTTCTGTTGCCTTGTGAG 59.869 43.478 0.00 0.00 0.00 3.51
3684 5871 4.142381 GCCTTGTGAGTTGTTTCTTCTGTT 60.142 41.667 0.00 0.00 0.00 3.16
3709 5896 1.450360 AGTTCCCTCAGCTCCCTTTT 58.550 50.000 0.00 0.00 0.00 2.27
3880 6069 1.251251 GCTTCCAGTGGTTGCTCATT 58.749 50.000 9.54 0.00 0.00 2.57
3961 6150 1.082756 GCTGCGACCACTGAAAACG 60.083 57.895 0.00 0.00 0.00 3.60
4031 6225 5.120399 TCTGAACATAAACACGAACCAGTT 58.880 37.500 0.00 0.00 0.00 3.16
4149 6343 4.197750 AGAGCTCTGAATATTGTGGCTTG 58.802 43.478 17.42 0.00 0.00 4.01
4223 6417 5.828299 AACATTCTTCGTCCTTGTTTTCA 57.172 34.783 0.00 0.00 0.00 2.69
4299 8347 2.237643 TGTGCTACCATTCCCATTACGT 59.762 45.455 0.00 0.00 0.00 3.57
4394 8445 7.438160 GGGACTTTCAACTTCGAAATGAATTTT 59.562 33.333 20.43 11.55 35.63 1.82
4454 8505 7.171337 GCATACATGGACTTCAACAAAAACATT 59.829 33.333 0.00 0.00 0.00 2.71
4456 8507 6.048509 ACATGGACTTCAACAAAAACATTCC 58.951 36.000 0.00 0.00 0.00 3.01
4476 8535 1.739067 GGAAGTATGAAGTTGCCGCT 58.261 50.000 0.00 0.00 0.00 5.52
4503 8562 2.095718 GCATCCGTCTCCTGAAACAAAC 60.096 50.000 0.00 0.00 0.00 2.93
4514 8573 6.826231 TCTCCTGAAACAAACTAACATCAACA 59.174 34.615 0.00 0.00 0.00 3.33
4516 8575 7.479980 TCCTGAAACAAACTAACATCAACAAG 58.520 34.615 0.00 0.00 0.00 3.16
4547 8606 3.443681 CCATGTGTAACCAATCAGTTCCC 59.556 47.826 0.00 0.00 34.36 3.97
4573 8632 6.653526 ATCACCTGATAAGAGTCTGATGAG 57.346 41.667 0.00 0.00 32.01 2.90
4719 8778 4.712122 TTTTTGCGAAAGTTCCTTGACT 57.288 36.364 0.00 0.00 0.00 3.41
4720 8779 4.712122 TTTTGCGAAAGTTCCTTGACTT 57.288 36.364 0.00 0.00 41.44 3.01
4760 8819 7.227049 AGAATGGTGAATTTGTCGGTTTTAT 57.773 32.000 0.00 0.00 0.00 1.40
4787 8846 3.947196 ACTTGAGACACTTTGTGAATGCA 59.053 39.130 4.61 0.00 36.96 3.96
4834 8894 8.902806 TGCCAGACTACATTTTCATTTATAAGG 58.097 33.333 0.00 0.00 0.00 2.69
4885 8946 2.988010 TTGGATTCCAGATCCACTCG 57.012 50.000 5.36 0.00 46.90 4.18
4894 8956 2.027385 CAGATCCACTCGAGATCACCA 58.973 52.381 21.68 0.00 42.19 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.825109 CCTAGGTTGTTTTCTTTTTCCAATAAA 57.175 29.630 0.00 0.00 0.00 1.40
4 5 9.203163 TCCTAGGTTGTTTTCTTTTTCCAATAA 57.797 29.630 9.08 0.00 0.00 1.40
5 6 8.770010 TCCTAGGTTGTTTTCTTTTTCCAATA 57.230 30.769 9.08 0.00 0.00 1.90
6 7 7.344612 ACTCCTAGGTTGTTTTCTTTTTCCAAT 59.655 33.333 9.08 0.00 0.00 3.16
7 8 6.666113 ACTCCTAGGTTGTTTTCTTTTTCCAA 59.334 34.615 9.08 0.00 0.00 3.53
8 9 6.192044 ACTCCTAGGTTGTTTTCTTTTTCCA 58.808 36.000 9.08 0.00 0.00 3.53
9 10 6.710597 ACTCCTAGGTTGTTTTCTTTTTCC 57.289 37.500 9.08 0.00 0.00 3.13
12 13 9.470399 TCTTTTACTCCTAGGTTGTTTTCTTTT 57.530 29.630 9.08 0.00 0.00 2.27
13 14 9.470399 TTCTTTTACTCCTAGGTTGTTTTCTTT 57.530 29.630 9.08 0.00 0.00 2.52
14 15 9.470399 TTTCTTTTACTCCTAGGTTGTTTTCTT 57.530 29.630 9.08 0.00 0.00 2.52
15 16 8.900781 GTTTCTTTTACTCCTAGGTTGTTTTCT 58.099 33.333 9.08 0.00 0.00 2.52
16 17 8.900781 AGTTTCTTTTACTCCTAGGTTGTTTTC 58.099 33.333 9.08 0.00 0.00 2.29
17 18 8.818622 AGTTTCTTTTACTCCTAGGTTGTTTT 57.181 30.769 9.08 0.00 0.00 2.43
18 19 7.226128 CGAGTTTCTTTTACTCCTAGGTTGTTT 59.774 37.037 9.08 0.00 39.03 2.83
19 20 6.704937 CGAGTTTCTTTTACTCCTAGGTTGTT 59.295 38.462 9.08 0.00 39.03 2.83
20 21 6.221659 CGAGTTTCTTTTACTCCTAGGTTGT 58.778 40.000 9.08 11.57 39.03 3.32
21 22 5.638234 CCGAGTTTCTTTTACTCCTAGGTTG 59.362 44.000 9.08 5.84 39.03 3.77
22 23 5.279859 CCCGAGTTTCTTTTACTCCTAGGTT 60.280 44.000 9.08 0.00 39.03 3.50
23 24 4.222366 CCCGAGTTTCTTTTACTCCTAGGT 59.778 45.833 9.08 0.00 39.03 3.08
24 25 4.465305 TCCCGAGTTTCTTTTACTCCTAGG 59.535 45.833 0.82 0.82 39.03 3.02
25 26 5.418209 TCTCCCGAGTTTCTTTTACTCCTAG 59.582 44.000 0.00 0.00 39.03 3.02
26 27 5.327732 TCTCCCGAGTTTCTTTTACTCCTA 58.672 41.667 0.00 0.00 39.03 2.94
27 28 4.158015 TCTCCCGAGTTTCTTTTACTCCT 58.842 43.478 0.00 0.00 39.03 3.69
28 29 4.532314 TCTCCCGAGTTTCTTTTACTCC 57.468 45.455 0.00 0.00 39.03 3.85
29 30 5.351740 CCAATCTCCCGAGTTTCTTTTACTC 59.648 44.000 0.00 0.00 38.88 2.59
30 31 5.012768 TCCAATCTCCCGAGTTTCTTTTACT 59.987 40.000 0.00 0.00 0.00 2.24
31 32 5.243207 TCCAATCTCCCGAGTTTCTTTTAC 58.757 41.667 0.00 0.00 0.00 2.01
32 33 5.492855 TCCAATCTCCCGAGTTTCTTTTA 57.507 39.130 0.00 0.00 0.00 1.52
33 34 4.367039 TCCAATCTCCCGAGTTTCTTTT 57.633 40.909 0.00 0.00 0.00 2.27
34 35 4.019321 TGATCCAATCTCCCGAGTTTCTTT 60.019 41.667 0.00 0.00 0.00 2.52
35 36 3.519510 TGATCCAATCTCCCGAGTTTCTT 59.480 43.478 0.00 0.00 0.00 2.52
36 37 3.107601 TGATCCAATCTCCCGAGTTTCT 58.892 45.455 0.00 0.00 0.00 2.52
37 38 3.543680 TGATCCAATCTCCCGAGTTTC 57.456 47.619 0.00 0.00 0.00 2.78
38 39 4.510167 AATGATCCAATCTCCCGAGTTT 57.490 40.909 0.00 0.00 0.00 2.66
39 40 4.202441 CAAATGATCCAATCTCCCGAGTT 58.798 43.478 0.00 0.00 0.00 3.01
40 41 3.813443 CAAATGATCCAATCTCCCGAGT 58.187 45.455 0.00 0.00 0.00 4.18
41 42 2.551459 GCAAATGATCCAATCTCCCGAG 59.449 50.000 0.00 0.00 0.00 4.63
42 43 2.575532 GCAAATGATCCAATCTCCCGA 58.424 47.619 0.00 0.00 0.00 5.14
101 103 6.266131 TGGGGCAAATGATCTAACTCTAAT 57.734 37.500 0.00 0.00 0.00 1.73
140 142 6.212888 ACAGAAATTAGGGCAAATGATCAC 57.787 37.500 0.00 0.00 0.00 3.06
369 1091 2.035832 GCATGTAGTGTTTGCCCTTTGT 59.964 45.455 0.00 0.00 0.00 2.83
407 1130 0.386838 GCCCTGCCTATCAAATGCAC 59.613 55.000 0.00 0.00 0.00 4.57
411 1134 2.025037 TGACTTGCCCTGCCTATCAAAT 60.025 45.455 0.00 0.00 0.00 2.32
415 1138 1.133976 ACATGACTTGCCCTGCCTATC 60.134 52.381 0.00 0.00 0.00 2.08
527 1251 1.601162 GCGTGAGTGTTCTGTCCGTTA 60.601 52.381 0.00 0.00 0.00 3.18
537 1261 1.062002 CTGTGTTTTCGCGTGAGTGTT 59.938 47.619 5.77 0.00 43.46 3.32
599 1323 7.563556 CCTTTGTATCCCCTTGTAACCAAATAT 59.436 37.037 0.00 0.00 0.00 1.28
622 1346 2.034812 GCTAGCTGCTACGTACATCCTT 59.965 50.000 7.70 0.00 38.95 3.36
659 1383 1.816074 ATTAACCACGCGTCCATGTT 58.184 45.000 9.86 13.16 0.00 2.71
984 2000 6.709018 TTTGCCATACTTTATTTAGGGAGC 57.291 37.500 0.00 0.00 0.00 4.70
1000 2016 3.236896 GGGAGATTGGATCATTTGCCAT 58.763 45.455 0.00 0.00 33.46 4.40
1025 2041 1.014564 CCTCGGCGGTGAAGAGTTTC 61.015 60.000 7.21 0.00 0.00 2.78
1070 2094 3.483869 CTCTACAGGGGGCAGGCC 61.484 72.222 3.77 3.77 0.00 5.19
1174 2198 2.125512 CGGAAGGAGGAGCGGTTG 60.126 66.667 0.00 0.00 0.00 3.77
1197 2243 2.496070 TCTCGTCCCGTCAGATTGAATT 59.504 45.455 0.00 0.00 0.00 2.17
1252 2298 0.532862 CAAAGCACCACCACGAGACT 60.533 55.000 0.00 0.00 0.00 3.24
1258 2304 3.977244 CCGCCAAAGCACCACCAC 61.977 66.667 0.00 0.00 39.83 4.16
1270 2316 3.371097 GACGAGAAGATGCCCGCCA 62.371 63.158 0.00 0.00 0.00 5.69
1296 2342 0.663568 GGGATCTGTCGTATTCGGCG 60.664 60.000 0.00 0.00 45.30 6.46
1303 2349 2.420568 GCGGGTGGGATCTGTCGTA 61.421 63.158 0.00 0.00 0.00 3.43
1330 2376 5.513094 CCTGACCTCTCACTGTAAAATGGAA 60.513 44.000 0.00 0.00 0.00 3.53
1337 2383 2.171840 GAGCCTGACCTCTCACTGTAA 58.828 52.381 0.00 0.00 0.00 2.41
1339 2385 1.247419 CGAGCCTGACCTCTCACTGT 61.247 60.000 0.00 0.00 0.00 3.55
1351 2397 2.093973 AGTCAGTAAATCACCGAGCCTG 60.094 50.000 0.00 0.00 0.00 4.85
1352 2398 2.093973 CAGTCAGTAAATCACCGAGCCT 60.094 50.000 0.00 0.00 0.00 4.58
1353 2399 2.094182 TCAGTCAGTAAATCACCGAGCC 60.094 50.000 0.00 0.00 0.00 4.70
1354 2400 3.232213 TCAGTCAGTAAATCACCGAGC 57.768 47.619 0.00 0.00 0.00 5.03
1355 2401 4.810790 AGTTCAGTCAGTAAATCACCGAG 58.189 43.478 0.00 0.00 0.00 4.63
1356 2402 4.866508 AGTTCAGTCAGTAAATCACCGA 57.133 40.909 0.00 0.00 0.00 4.69
1357 2403 4.563184 GCTAGTTCAGTCAGTAAATCACCG 59.437 45.833 0.00 0.00 0.00 4.94
1358 2404 5.725362 AGCTAGTTCAGTCAGTAAATCACC 58.275 41.667 0.00 0.00 0.00 4.02
1359 2405 6.401581 GCAAGCTAGTTCAGTCAGTAAATCAC 60.402 42.308 0.00 0.00 0.00 3.06
1360 2406 5.639506 GCAAGCTAGTTCAGTCAGTAAATCA 59.360 40.000 0.00 0.00 0.00 2.57
1361 2407 5.872070 AGCAAGCTAGTTCAGTCAGTAAATC 59.128 40.000 0.00 0.00 0.00 2.17
1362 2408 5.799213 AGCAAGCTAGTTCAGTCAGTAAAT 58.201 37.500 0.00 0.00 0.00 1.40
1363 2409 5.215252 AGCAAGCTAGTTCAGTCAGTAAA 57.785 39.130 0.00 0.00 0.00 2.01
1364 2410 4.873746 AGCAAGCTAGTTCAGTCAGTAA 57.126 40.909 0.00 0.00 0.00 2.24
1365 2411 7.825331 ATATAGCAAGCTAGTTCAGTCAGTA 57.175 36.000 7.91 0.00 31.45 2.74
1366 2412 6.723298 ATATAGCAAGCTAGTTCAGTCAGT 57.277 37.500 7.91 0.00 31.45 3.41
1367 2413 7.205992 TGAATATAGCAAGCTAGTTCAGTCAG 58.794 38.462 19.86 0.00 34.82 3.51
1368 2414 7.112452 TGAATATAGCAAGCTAGTTCAGTCA 57.888 36.000 19.86 12.02 34.82 3.41
1369 2415 7.869937 TGATGAATATAGCAAGCTAGTTCAGTC 59.130 37.037 24.17 21.33 38.85 3.51
1370 2416 7.730084 TGATGAATATAGCAAGCTAGTTCAGT 58.270 34.615 24.17 17.21 38.85 3.41
1371 2417 8.087136 TCTGATGAATATAGCAAGCTAGTTCAG 58.913 37.037 24.17 18.84 38.85 3.02
1372 2418 7.955918 TCTGATGAATATAGCAAGCTAGTTCA 58.044 34.615 23.16 23.16 39.30 3.18
1373 2419 9.434420 AATCTGATGAATATAGCAAGCTAGTTC 57.566 33.333 16.65 16.65 32.49 3.01
1374 2420 9.790344 AAATCTGATGAATATAGCAAGCTAGTT 57.210 29.630 7.91 5.27 31.45 2.24
1379 2425 9.784680 CCAATAAATCTGATGAATATAGCAAGC 57.215 33.333 0.00 0.00 0.00 4.01
1401 2447 6.496565 TGAATCCAACCACTGATTTAACCAAT 59.503 34.615 0.00 0.00 31.56 3.16
1407 2453 6.375174 CACATCTGAATCCAACCACTGATTTA 59.625 38.462 0.00 0.00 31.56 1.40
1409 2455 4.703575 CACATCTGAATCCAACCACTGATT 59.296 41.667 0.00 0.00 34.02 2.57
1455 2528 4.201822 GCAAAGTTCTTCGGATACACATCC 60.202 45.833 0.00 0.00 46.51 3.51
1460 2533 4.574892 TGATGCAAAGTTCTTCGGATACA 58.425 39.130 0.00 0.00 0.00 2.29
1516 2589 7.032377 ACTGTAGGAAGCAAGAAAAGAAAAG 57.968 36.000 0.00 0.00 0.00 2.27
1517 2590 7.122055 TCAACTGTAGGAAGCAAGAAAAGAAAA 59.878 33.333 0.00 0.00 0.00 2.29
1521 2594 5.278022 GGTCAACTGTAGGAAGCAAGAAAAG 60.278 44.000 0.00 0.00 0.00 2.27
1555 2628 5.309020 AGGATATGAGCATACAAGGTGTGAT 59.691 40.000 0.00 0.00 0.00 3.06
1561 2634 5.047731 TCGAAGAGGATATGAGCATACAAGG 60.048 44.000 0.00 0.00 0.00 3.61
1570 2643 6.588719 AGGATCTTTCGAAGAGGATATGAG 57.411 41.667 0.00 0.00 41.61 2.90
1575 2648 8.364142 CACTATTAAGGATCTTTCGAAGAGGAT 58.636 37.037 0.00 4.13 41.61 3.24
1583 2656 9.319143 AGTTCATTCACTATTAAGGATCTTTCG 57.681 33.333 0.00 0.00 0.00 3.46
1602 2675 5.781818 AGATTGTGGGGAAATTGAGTTCATT 59.218 36.000 0.00 0.00 0.00 2.57
1603 2676 5.336102 AGATTGTGGGGAAATTGAGTTCAT 58.664 37.500 0.00 0.00 0.00 2.57
1611 2684 7.182060 ACTACATACAAGATTGTGGGGAAATT 58.818 34.615 8.46 0.00 42.31 1.82
1627 2700 4.711846 AGCAATGGTGAGAGACTACATACA 59.288 41.667 0.00 0.00 0.00 2.29
1631 2704 2.234661 CCAGCAATGGTGAGAGACTACA 59.765 50.000 14.64 0.00 32.22 2.74
1632 2705 2.234908 ACCAGCAATGGTGAGAGACTAC 59.765 50.000 14.64 0.00 41.33 2.73
1633 2706 2.540383 ACCAGCAATGGTGAGAGACTA 58.460 47.619 14.64 0.00 41.33 2.59
1634 2707 1.356124 ACCAGCAATGGTGAGAGACT 58.644 50.000 14.64 0.00 41.33 3.24
1635 2708 3.118629 TCATACCAGCAATGGTGAGAGAC 60.119 47.826 14.64 0.00 43.03 3.36
1636 2709 3.106827 TCATACCAGCAATGGTGAGAGA 58.893 45.455 14.64 3.65 43.03 3.10
1637 2710 3.118482 ACTCATACCAGCAATGGTGAGAG 60.118 47.826 14.64 20.26 43.03 3.20
1654 2727 5.654209 TGCTACAGAATAGTCAGACACTCAT 59.346 40.000 2.66 0.00 36.43 2.90
1668 2741 6.047511 ACAATCAGAGAAGTGCTACAGAAT 57.952 37.500 0.00 0.00 0.00 2.40
1746 2820 2.037847 ACCAAATGCAGAGGGGCC 59.962 61.111 0.00 0.00 0.00 5.80
1756 2830 3.627577 GGCTCACCATACTACACCAAATG 59.372 47.826 0.00 0.00 35.26 2.32
1759 2833 1.557832 GGGCTCACCATACTACACCAA 59.442 52.381 0.00 0.00 39.85 3.67
1775 2849 4.032310 TGCTGAATCATTTAAATGGGGCT 58.968 39.130 24.40 9.41 37.03 5.19
1807 2881 2.636830 CTGAACACCATGATCAGGACC 58.363 52.381 9.37 0.00 41.71 4.46
1808 2882 2.012673 GCTGAACACCATGATCAGGAC 58.987 52.381 9.37 3.24 44.40 3.85
1809 2883 1.629861 TGCTGAACACCATGATCAGGA 59.370 47.619 9.37 11.09 44.40 3.86
1920 2994 2.604462 GCATGGCGCAAATCTAAAAAGG 59.396 45.455 10.83 0.00 41.79 3.11
1924 2998 1.405105 GGAGCATGGCGCAAATCTAAA 59.595 47.619 10.83 0.00 46.13 1.85
1935 3009 0.169009 GAACAGAAACGGAGCATGGC 59.831 55.000 0.00 0.00 0.00 4.40
2007 3088 4.666512 ACAGCAAAAGGATTCACAGGTAT 58.333 39.130 0.00 0.00 0.00 2.73
2106 3188 3.906998 AGAGAATATTCACCAGCGATCG 58.093 45.455 17.56 11.69 0.00 3.69
2108 3190 5.543507 AAGAGAGAATATTCACCAGCGAT 57.456 39.130 17.56 0.00 0.00 4.58
2143 3226 2.360350 AGCACATGCCGGACCAAG 60.360 61.111 5.05 0.00 43.38 3.61
2169 3254 3.611766 ACGTACTGCAATTAGAGGCTT 57.388 42.857 0.00 0.00 0.00 4.35
2176 3261 4.116961 GCTGTGGATACGTACTGCAATTA 58.883 43.478 11.71 0.00 40.23 1.40
2188 3273 1.147153 GCTCCCTGGCTGTGGATAC 59.853 63.158 0.00 0.00 0.00 2.24
2214 3299 3.754965 TGTAATTTCTGCTCCAAGCTGT 58.245 40.909 0.11 0.00 42.97 4.40
2281 3367 6.099341 CCAAAAGGCATACAAAACTATGTCC 58.901 40.000 0.00 0.00 34.75 4.02
2328 3414 2.795231 ACACAGATTGCAGGCTGTAT 57.205 45.000 19.17 10.05 43.06 2.29
2424 3930 5.046376 AGGAAAACTTCAAATATGCAAGGGG 60.046 40.000 0.00 0.00 0.00 4.79
2446 3953 0.610174 TCAGCCAGTGTAAGCTCAGG 59.390 55.000 0.00 0.00 37.18 3.86
2453 3960 4.354155 GCACGTCAGCCAGTGTAA 57.646 55.556 0.00 0.00 40.26 2.41
2494 4001 0.110295 TCATTGAGTGTGTGTGGGGG 59.890 55.000 0.00 0.00 0.00 5.40
2495 4002 1.881973 CTTCATTGAGTGTGTGTGGGG 59.118 52.381 0.00 0.00 0.00 4.96
2496 4003 1.881973 CCTTCATTGAGTGTGTGTGGG 59.118 52.381 0.00 0.00 0.00 4.61
2497 4004 1.267806 GCCTTCATTGAGTGTGTGTGG 59.732 52.381 0.00 0.00 0.00 4.17
2498 4005 1.948834 TGCCTTCATTGAGTGTGTGTG 59.051 47.619 0.00 0.00 0.00 3.82
2499 4006 2.346766 TGCCTTCATTGAGTGTGTGT 57.653 45.000 0.00 0.00 0.00 3.72
2500 4007 2.555325 ACATGCCTTCATTGAGTGTGTG 59.445 45.455 0.00 0.00 0.00 3.82
2503 4010 3.144657 TGACATGCCTTCATTGAGTGT 57.855 42.857 0.00 0.00 0.00 3.55
2521 4038 7.039784 CCAAAAGAAAAGGAGTGTCCATATTGA 60.040 37.037 0.00 0.00 39.61 2.57
2526 4043 4.803452 TCCAAAAGAAAAGGAGTGTCCAT 58.197 39.130 0.00 0.00 39.61 3.41
2569 4391 9.436957 CCTTACATATACGCTATCCAGATTTTT 57.563 33.333 0.00 0.00 0.00 1.94
2601 4580 9.847224 ATAAGGTTTCTCTTGTCAAGTAAGAAA 57.153 29.630 18.64 18.64 34.07 2.52
2629 4610 6.693545 GTCATAAAGACATACTCTGAACCTCG 59.306 42.308 0.00 0.00 46.77 4.63
2646 4630 4.946157 AGCACTGAATGGAAGGTCATAAAG 59.054 41.667 0.00 0.00 0.00 1.85
2702 4732 4.654262 ACTTTGCTATCCTCCGGAGATTAA 59.346 41.667 33.39 15.00 34.05 1.40
2707 4737 2.990066 AACTTTGCTATCCTCCGGAG 57.010 50.000 25.36 25.36 34.05 4.63
2715 4745 5.703876 ACAGCAAAAGCTAACTTTGCTATC 58.296 37.500 27.78 6.58 45.48 2.08
2807 4837 6.842437 TTCTGAATACTCACTGAGCTTAGT 57.158 37.500 5.11 5.11 32.04 2.24
2857 4887 3.942130 AAAAATACCACTGAAGCAGCC 57.058 42.857 0.00 0.00 34.37 4.85
2885 4917 6.838090 TGGGGACAGCATAAATATGAATCAAA 59.162 34.615 4.63 0.00 33.82 2.69
2905 4937 3.072476 CCAGTTTAAACAGAGAGTGGGGA 59.928 47.826 20.06 0.00 0.00 4.81
2921 5015 6.174720 TGTACTGATCTGAGAAACCAGTTT 57.825 37.500 16.55 0.00 38.76 2.66
3009 5111 8.863086 TCTCATCAACTGGATTTTCATTTTCTT 58.137 29.630 0.00 0.00 32.57 2.52
3166 5277 9.403110 CTTATTTGCATCCATTAGTTCATTAGC 57.597 33.333 0.00 0.00 0.00 3.09
3244 5364 4.141251 TCCAATTTAATAGGCCCTCCAGTC 60.141 45.833 0.00 0.00 33.74 3.51
3252 5372 5.776744 CTTCTGCATCCAATTTAATAGGCC 58.223 41.667 0.00 0.00 0.00 5.19
3364 5492 7.281774 ACTGGTTACTCATGCAGATAAAAGATG 59.718 37.037 0.00 0.00 0.00 2.90
3412 5540 3.067180 ACACTTTTCATGACAGCAAGGTG 59.933 43.478 14.96 14.96 0.00 4.00
3413 5541 3.290710 ACACTTTTCATGACAGCAAGGT 58.709 40.909 0.00 0.00 0.00 3.50
3414 5542 3.996150 ACACTTTTCATGACAGCAAGG 57.004 42.857 0.00 0.00 0.00 3.61
3423 5560 9.669353 GCATTGATTATACCTACACTTTTCATG 57.331 33.333 0.00 0.00 0.00 3.07
3468 5611 7.803659 GCTTAGGTCTTAAAACATCACAAGAAC 59.196 37.037 0.00 0.00 35.41 3.01
3510 5689 8.095452 AGAAATCCAACACAGTAAGAGGATAT 57.905 34.615 0.00 0.00 34.95 1.63
3592 5774 4.068599 ACAAGGCTACTTTTCTTCAGCTC 58.931 43.478 0.00 0.00 33.81 4.09
3601 5783 5.043737 TGGTTCACTACAAGGCTACTTTT 57.956 39.130 0.00 0.00 33.81 2.27
3630 5812 6.936968 AAACCTACCTTCTCTGTATCTTGT 57.063 37.500 0.00 0.00 0.00 3.16
3670 5852 6.693113 GGAACTTCATCAACAGAAGAAACAAC 59.307 38.462 9.65 0.00 44.00 3.32
3684 5871 1.556911 GGAGCTGAGGGAACTTCATCA 59.443 52.381 0.00 0.00 44.43 3.07
3709 5896 5.376625 AGCTTTCTCAGTAAACATCCACAA 58.623 37.500 0.00 0.00 0.00 3.33
3880 6069 4.341806 ACAAACATGCAGGTCATCAGAAAA 59.658 37.500 3.65 0.00 31.79 2.29
3961 6150 2.953466 TAACGGCTACTGATGACACC 57.047 50.000 0.00 0.00 0.00 4.16
4031 6225 3.507233 AGAAGCAATGCTCATTTCGGAAA 59.493 39.130 8.71 5.52 38.25 3.13
4056 6250 1.859398 GCGAACTGCACAATGACGA 59.141 52.632 0.00 0.00 45.45 4.20
4130 6324 4.194640 TCTCAAGCCACAATATTCAGAGC 58.805 43.478 0.00 0.00 0.00 4.09
4223 6417 6.474630 TGATTTATGGCCAAAGAGCAAAAAT 58.525 32.000 10.96 6.00 0.00 1.82
4442 8493 6.442952 TCATACTTCCGGAATGTTTTTGTTG 58.557 36.000 19.21 10.72 0.00 3.33
4454 8505 1.404986 CGGCAACTTCATACTTCCGGA 60.405 52.381 0.00 0.00 32.55 5.14
4456 8507 0.373716 GCGGCAACTTCATACTTCCG 59.626 55.000 0.00 0.00 38.51 4.30
4476 8535 0.250234 CAGGAGACGGATGCTTTCCA 59.750 55.000 7.00 0.00 45.78 3.53
4503 8562 3.123621 GTCCAGTCGCTTGTTGATGTTAG 59.876 47.826 0.00 0.00 0.00 2.34
4514 8573 0.973632 TACACATGGTCCAGTCGCTT 59.026 50.000 0.00 0.00 0.00 4.68
4516 8575 1.076332 GTTACACATGGTCCAGTCGC 58.924 55.000 0.00 0.00 0.00 5.19
4620 8679 1.203994 GACGAGCACTAGGTTAGCCAA 59.796 52.381 0.00 0.00 37.19 4.52
4709 8768 7.148457 CGAAGGGTCTATTAAAAGTCAAGGAAC 60.148 40.741 0.00 0.00 0.00 3.62
4710 8769 6.877322 CGAAGGGTCTATTAAAAGTCAAGGAA 59.123 38.462 0.00 0.00 0.00 3.36
4711 8770 6.211986 TCGAAGGGTCTATTAAAAGTCAAGGA 59.788 38.462 0.00 0.00 0.00 3.36
4712 8771 6.403878 TCGAAGGGTCTATTAAAAGTCAAGG 58.596 40.000 0.00 0.00 0.00 3.61
4713 8772 7.321153 TCTCGAAGGGTCTATTAAAAGTCAAG 58.679 38.462 0.00 0.00 0.00 3.02
4714 8773 7.235935 TCTCGAAGGGTCTATTAAAAGTCAA 57.764 36.000 0.00 0.00 0.00 3.18
4715 8774 6.845758 TCTCGAAGGGTCTATTAAAAGTCA 57.154 37.500 0.00 0.00 0.00 3.41
4716 8775 7.224949 CCATTCTCGAAGGGTCTATTAAAAGTC 59.775 40.741 2.34 0.00 37.47 3.01
4717 8776 7.048512 CCATTCTCGAAGGGTCTATTAAAAGT 58.951 38.462 2.34 0.00 37.47 2.66
4718 8777 7.484035 CCATTCTCGAAGGGTCTATTAAAAG 57.516 40.000 2.34 0.00 37.47 2.27
4760 8819 4.574892 TCACAAAGTGTCTCAAGTGACAA 58.425 39.130 6.55 0.00 46.77 3.18
4779 8838 5.643664 TGCTCAACAAATATCTGCATTCAC 58.356 37.500 0.00 0.00 0.00 3.18
4894 8956 5.969423 CATTATTTGCAGACCAAAGACCAT 58.031 37.500 0.00 0.00 45.87 3.55


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

AutoCloner maintained by Alex Coulton.