Multiple sequence alignment - TraesCS1B01G385200

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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 TraesCS1B01G385200 chr1B 100.000 3311 0 0 1 3311 618699922 618696612 0.000000e+00 6115.0
1 TraesCS1B01G385200 chr1B 84.763 1306 167 24 953 2243 618542948 618544236 0.000000e+00 1280.0
2 TraesCS1B01G385200 chr1B 82.880 1472 179 40 598 2033 618908457 618907023 0.000000e+00 1254.0
3 TraesCS1B01G385200 chr1B 87.224 1088 125 6 952 2029 619095617 619094534 0.000000e+00 1227.0
4 TraesCS1B01G385200 chr1B 86.993 1084 127 8 985 2064 618196959 618198032 0.000000e+00 1208.0
5 TraesCS1B01G385200 chr1B 76.703 279 39 17 606 862 619096002 619095728 7.460000e-27 132.0
6 TraesCS1B01G385200 chr1B 95.000 60 2 1 2959 3017 619093918 619093859 3.520000e-15 93.5
7 TraesCS1B01G385200 chr1D 87.922 1689 151 21 585 2259 451036108 451034459 0.000000e+00 1940.0
8 TraesCS1B01G385200 chr1D 85.216 1691 162 44 608 2259 450758024 450756383 0.000000e+00 1657.0
9 TraesCS1B01G385200 chr1D 82.646 1648 223 37 641 2244 450578830 450580458 0.000000e+00 1400.0
10 TraesCS1B01G385200 chr1D 85.142 1299 160 25 862 2145 450739108 450740388 0.000000e+00 1299.0
11 TraesCS1B01G385200 chr1D 85.188 1276 138 27 728 1981 451063376 451062130 0.000000e+00 1262.0
12 TraesCS1B01G385200 chr1D 85.185 810 64 34 2504 3296 451034257 451033487 0.000000e+00 780.0
13 TraesCS1B01G385200 chr1D 86.074 517 28 17 2542 3053 450756161 450755684 1.760000e-142 516.0
14 TraesCS1B01G385200 chr1D 82.452 473 43 17 99 546 451036750 451036293 8.670000e-101 377.0
15 TraesCS1B01G385200 chr1D 92.000 250 18 2 3063 3311 450610832 450610584 1.890000e-92 350.0
16 TraesCS1B01G385200 chr1D 91.983 237 18 1 3076 3311 450754509 450754273 6.850000e-87 331.0
17 TraesCS1B01G385200 chr1D 89.272 261 20 5 99 352 450758650 450758391 1.480000e-83 320.0
18 TraesCS1B01G385200 chr1D 83.333 180 9 12 384 551 450758394 450758224 2.660000e-31 147.0
19 TraesCS1B01G385200 chr1D 92.771 83 5 1 2972 3053 450611191 450611109 5.800000e-23 119.0
20 TraesCS1B01G385200 chr1D 96.296 54 1 1 2959 3011 451061416 451061363 1.640000e-13 87.9
21 TraesCS1B01G385200 chr1A 87.055 1684 148 37 585 2232 545764365 545762716 0.000000e+00 1838.0
22 TraesCS1B01G385200 chr1A 83.251 1421 180 35 642 2014 545778680 545777270 0.000000e+00 1253.0
23 TraesCS1B01G385200 chr1A 85.690 1188 147 16 954 2128 545751980 545753157 0.000000e+00 1230.0
24 TraesCS1B01G385200 chr1A 87.219 579 48 12 2504 3070 545762450 545761886 1.300000e-178 636.0
25 TraesCS1B01G385200 chr1A 79.630 216 17 12 596 793 545856577 545856371 2.680000e-26 130.0
26 TraesCS1B01G385200 chr7D 100.000 88 0 0 2259 2346 121937432 121937345 2.640000e-36 163.0
27 TraesCS1B01G385200 chr7D 94.186 86 5 0 2259 2344 151326529 151326444 7.460000e-27 132.0
28 TraesCS1B01G385200 chr7D 94.186 86 5 0 2259 2344 446245090 446245005 7.460000e-27 132.0
29 TraesCS1B01G385200 chr6B 96.471 85 3 0 2259 2343 403192304 403192220 1.240000e-29 141.0
30 TraesCS1B01G385200 chr5D 92.632 95 6 1 2259 2352 533641625 533641719 5.760000e-28 135.0
31 TraesCS1B01G385200 chr5D 94.186 86 5 0 2259 2344 439641841 439641756 7.460000e-27 132.0
32 TraesCS1B01G385200 chr7B 89.720 107 8 3 2248 2352 462733983 462734088 2.070000e-27 134.0
33 TraesCS1B01G385200 chr4D 94.253 87 5 0 2259 2345 453044642 453044728 2.070000e-27 134.0
34 TraesCS1B01G385200 chr4A 91.579 95 7 1 2259 2352 638216786 638216692 2.680000e-26 130.0


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 TraesCS1B01G385200 chr1B 618696612 618699922 3310 True 6115.000000 6115 100.000000 1 3311 1 chr1B.!!$R1 3310
1 TraesCS1B01G385200 chr1B 618542948 618544236 1288 False 1280.000000 1280 84.763000 953 2243 1 chr1B.!!$F2 1290
2 TraesCS1B01G385200 chr1B 618907023 618908457 1434 True 1254.000000 1254 82.880000 598 2033 1 chr1B.!!$R2 1435
3 TraesCS1B01G385200 chr1B 618196959 618198032 1073 False 1208.000000 1208 86.993000 985 2064 1 chr1B.!!$F1 1079
4 TraesCS1B01G385200 chr1B 619093859 619096002 2143 True 484.166667 1227 86.309000 606 3017 3 chr1B.!!$R3 2411
5 TraesCS1B01G385200 chr1D 450578830 450580458 1628 False 1400.000000 1400 82.646000 641 2244 1 chr1D.!!$F1 1603
6 TraesCS1B01G385200 chr1D 450739108 450740388 1280 False 1299.000000 1299 85.142000 862 2145 1 chr1D.!!$F2 1283
7 TraesCS1B01G385200 chr1D 451033487 451036750 3263 True 1032.333333 1940 85.186333 99 3296 3 chr1D.!!$R3 3197
8 TraesCS1B01G385200 chr1D 451061363 451063376 2013 True 674.950000 1262 90.742000 728 3011 2 chr1D.!!$R4 2283
9 TraesCS1B01G385200 chr1D 450754273 450758650 4377 True 594.200000 1657 87.175600 99 3311 5 chr1D.!!$R2 3212
10 TraesCS1B01G385200 chr1D 450610584 450611191 607 True 234.500000 350 92.385500 2972 3311 2 chr1D.!!$R1 339
11 TraesCS1B01G385200 chr1A 545777270 545778680 1410 True 1253.000000 1253 83.251000 642 2014 1 chr1A.!!$R1 1372
12 TraesCS1B01G385200 chr1A 545761886 545764365 2479 True 1237.000000 1838 87.137000 585 3070 2 chr1A.!!$R3 2485
13 TraesCS1B01G385200 chr1A 545751980 545753157 1177 False 1230.000000 1230 85.690000 954 2128 1 chr1A.!!$F1 1174

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
44 45 0.107831 GCCTACATATGCACGGGGAA 59.892 55.0 1.58 0.0 0.00 3.97 F
476 497 0.591170 GCGCCGCACCATAATACAAT 59.409 50.0 3.15 0.0 0.00 2.71 F
2097 2489 0.392193 ATGCAGAGTCCGGCTTTCTG 60.392 55.0 19.30 19.3 40.93 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1577 1.139947 GGCGAACTCGAGGAAGAGG 59.860 63.158 18.41 0.73 42.31 3.69 R
2104 2496 0.240145 CTGTGCTCTACGTCAACGGA 59.760 55.000 7.53 0.00 44.95 4.69 R
3083 5123 0.949105 ATCGTGTTTGTCCTCGTGCC 60.949 55.000 0.00 0.00 0.00 5.01 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
37 38 3.678921 GGACGTGCCTACATATGCA 57.321 52.632 1.58 0.00 34.54 3.96
42 43 1.449782 TGCCTACATATGCACGGGG 59.550 57.895 1.58 0.00 31.31 5.73
43 44 1.051556 TGCCTACATATGCACGGGGA 61.052 55.000 1.58 0.00 31.31 4.81
44 45 0.107831 GCCTACATATGCACGGGGAA 59.892 55.000 1.58 0.00 0.00 3.97
45 46 1.271379 GCCTACATATGCACGGGGAAT 60.271 52.381 1.58 0.00 0.00 3.01
46 47 2.699954 CCTACATATGCACGGGGAATC 58.300 52.381 1.58 0.00 0.00 2.52
47 48 2.337583 CTACATATGCACGGGGAATCG 58.662 52.381 1.58 0.00 0.00 3.34
48 49 0.756294 ACATATGCACGGGGAATCGA 59.244 50.000 1.58 0.00 0.00 3.59
49 50 1.140052 ACATATGCACGGGGAATCGAA 59.860 47.619 1.58 0.00 0.00 3.71
50 51 2.224523 ACATATGCACGGGGAATCGAAT 60.225 45.455 1.58 0.00 0.00 3.34
51 52 3.007506 ACATATGCACGGGGAATCGAATA 59.992 43.478 1.58 0.00 0.00 1.75
52 53 2.859165 ATGCACGGGGAATCGAATAT 57.141 45.000 0.00 0.00 0.00 1.28
53 54 2.631160 TGCACGGGGAATCGAATATT 57.369 45.000 0.00 0.00 0.00 1.28
54 55 2.489971 TGCACGGGGAATCGAATATTC 58.510 47.619 5.30 5.30 0.00 1.75
95 96 9.822185 AATACAAATATTCTTCCAATTTCAGGC 57.178 29.630 0.00 0.00 0.00 4.85
96 97 6.643388 ACAAATATTCTTCCAATTTCAGGCC 58.357 36.000 0.00 0.00 0.00 5.19
97 98 5.520376 AATATTCTTCCAATTTCAGGCCG 57.480 39.130 0.00 0.00 0.00 6.13
165 172 3.909137 GCGCGCGAGATATTTACTG 57.091 52.632 37.18 0.00 0.00 2.74
183 191 1.834263 CTGGGAATCTTCTCTCCGGTT 59.166 52.381 0.00 0.00 31.97 4.44
276 295 2.812011 ACCGTAACCAGCTGTGAAATTC 59.188 45.455 13.81 0.00 0.00 2.17
279 298 3.423123 CGTAACCAGCTGTGAAATTCGAC 60.423 47.826 13.81 0.00 0.00 4.20
294 313 4.492160 GACGGATCGCGCCTGTGA 62.492 66.667 15.67 0.00 39.32 3.58
309 328 2.624838 CCTGTGAACCAGCTGTGAATTT 59.375 45.455 13.81 0.00 40.06 1.82
312 331 4.681744 TGTGAACCAGCTGTGAATTTTTC 58.318 39.130 13.81 4.62 0.00 2.29
315 334 4.037923 TGAACCAGCTGTGAATTTTTCCTC 59.962 41.667 13.81 0.00 0.00 3.71
320 339 1.818674 CTGTGAATTTTTCCTCCGGGG 59.181 52.381 0.00 0.00 0.00 5.73
325 344 4.281435 GTGAATTTTTCCTCCGGGGTAAAA 59.719 41.667 20.54 20.54 44.43 1.52
369 389 8.484008 GTCGCTAAGATTAGTTCAGAAATGATC 58.516 37.037 7.17 7.17 33.32 2.92
370 390 7.379797 TCGCTAAGATTAGTTCAGAAATGATCG 59.620 37.037 9.08 0.08 33.32 3.69
371 391 7.168302 CGCTAAGATTAGTTCAGAAATGATCGT 59.832 37.037 9.08 8.75 33.32 3.73
372 392 8.821894 GCTAAGATTAGTTCAGAAATGATCGTT 58.178 33.333 8.63 0.00 33.32 3.85
374 394 7.009568 AGATTAGTTCAGAAATGATCGTTGC 57.990 36.000 9.08 0.00 0.00 4.17
375 395 6.820656 AGATTAGTTCAGAAATGATCGTTGCT 59.179 34.615 1.89 1.89 0.00 3.91
376 396 4.675190 AGTTCAGAAATGATCGTTGCTG 57.325 40.909 24.71 24.71 0.00 4.41
384 404 3.702334 GATCGTTGCTGCCGCGTTC 62.702 63.158 4.92 9.52 39.65 3.95
475 496 1.440938 GGCGCCGCACCATAATACAA 61.441 55.000 12.58 0.00 0.00 2.41
476 497 0.591170 GCGCCGCACCATAATACAAT 59.409 50.000 3.15 0.00 0.00 2.71
477 498 1.001815 GCGCCGCACCATAATACAATT 60.002 47.619 3.15 0.00 0.00 2.32
478 499 2.649516 CGCCGCACCATAATACAATTG 58.350 47.619 3.24 3.24 0.00 2.32
480 501 3.606846 CGCCGCACCATAATACAATTGAG 60.607 47.826 13.59 0.00 0.00 3.02
485 520 5.277490 CGCACCATAATACAATTGAGAGTGG 60.277 44.000 13.59 14.56 0.00 4.00
486 521 5.009010 GCACCATAATACAATTGAGAGTGGG 59.991 44.000 13.59 9.12 0.00 4.61
546 582 1.977544 CGACCAACCGAGGAGACCT 60.978 63.158 0.00 0.00 36.03 3.85
547 583 1.891616 GACCAACCGAGGAGACCTC 59.108 63.158 7.65 7.65 46.44 3.85
566 765 4.103311 ACCTCCCATAATCCTAGCTCAAAC 59.897 45.833 0.00 0.00 0.00 2.93
590 802 1.060713 CGCGCCATTAGATAAGTCGG 58.939 55.000 0.00 0.00 0.00 4.79
810 1084 2.460853 CCTAATCCGGCCCCCACAT 61.461 63.158 0.00 0.00 0.00 3.21
812 1086 1.994885 CTAATCCGGCCCCCACATGT 61.995 60.000 0.00 0.00 0.00 3.21
840 1114 5.043248 CACTTTCACCATGTTCCAAACTTC 58.957 41.667 0.00 0.00 0.00 3.01
853 1131 3.073062 TCCAAACTTCTCTTCTCCCCAAG 59.927 47.826 0.00 0.00 0.00 3.61
882 1188 4.440250 GGCTCCCTATATATACACAGCACG 60.440 50.000 11.51 0.00 0.00 5.34
929 1251 4.748679 CGGCACAAGCAAGCTCGC 62.749 66.667 0.00 0.00 44.61 5.03
946 1268 1.346395 TCGCCAACACAGAGTACCAAT 59.654 47.619 0.00 0.00 0.00 3.16
949 1271 2.678336 GCCAACACAGAGTACCAATAGC 59.322 50.000 0.00 0.00 0.00 2.97
963 1305 2.159393 CCAATAGCAACCACCACAATCG 60.159 50.000 0.00 0.00 0.00 3.34
965 1307 1.295357 TAGCAACCACCACAATCGCG 61.295 55.000 0.00 0.00 0.00 5.87
997 1341 4.560819 CACAGATTACAGAAGAGAAGACGC 59.439 45.833 0.00 0.00 0.00 5.19
1230 1577 2.279517 CGCGATGGCTCCTACCAC 60.280 66.667 0.00 0.00 44.17 4.16
1401 1748 3.538201 GCGCGCAACGTCGTGATA 61.538 61.111 29.10 0.00 46.11 2.15
1575 1925 3.060000 ACGGTCGTCGAGATGGCA 61.060 61.111 0.00 0.00 42.43 4.92
1650 2000 1.248785 GGATCGGCTATACGGAGGCA 61.249 60.000 8.21 0.00 42.01 4.75
1970 2353 3.610669 CGAGGAGGGCTGGATCGG 61.611 72.222 0.00 0.00 0.00 4.18
2069 2458 3.589988 ACGCTATCACAAGTGAAGAAGG 58.410 45.455 7.02 0.00 43.58 3.46
2097 2489 0.392193 ATGCAGAGTCCGGCTTTCTG 60.392 55.000 19.30 19.30 40.93 3.02
2215 2619 8.129496 TCAGTTTTTGAAGGGTTTAGTTTCTT 57.871 30.769 0.00 0.00 31.34 2.52
2219 2623 2.882137 TGAAGGGTTTAGTTTCTTGCCG 59.118 45.455 0.00 0.00 0.00 5.69
2268 2675 2.824341 ACAAACAGTACTACTCCCTCCG 59.176 50.000 0.00 0.00 0.00 4.63
2269 2676 3.087031 CAAACAGTACTACTCCCTCCGA 58.913 50.000 0.00 0.00 0.00 4.55
2270 2677 3.666345 AACAGTACTACTCCCTCCGAT 57.334 47.619 0.00 0.00 0.00 4.18
2271 2678 3.211718 ACAGTACTACTCCCTCCGATC 57.788 52.381 0.00 0.00 0.00 3.69
2272 2679 2.158638 ACAGTACTACTCCCTCCGATCC 60.159 54.545 0.00 0.00 0.00 3.36
2273 2680 2.133520 AGTACTACTCCCTCCGATCCA 58.866 52.381 0.00 0.00 0.00 3.41
2274 2681 2.512896 AGTACTACTCCCTCCGATCCAA 59.487 50.000 0.00 0.00 0.00 3.53
2275 2682 2.544844 ACTACTCCCTCCGATCCAAA 57.455 50.000 0.00 0.00 0.00 3.28
2276 2683 3.047695 ACTACTCCCTCCGATCCAAAT 57.952 47.619 0.00 0.00 0.00 2.32
2277 2684 3.385115 ACTACTCCCTCCGATCCAAATT 58.615 45.455 0.00 0.00 0.00 1.82
2278 2685 4.553678 ACTACTCCCTCCGATCCAAATTA 58.446 43.478 0.00 0.00 0.00 1.40
2279 2686 5.155905 ACTACTCCCTCCGATCCAAATTAT 58.844 41.667 0.00 0.00 0.00 1.28
2280 2687 5.607171 ACTACTCCCTCCGATCCAAATTATT 59.393 40.000 0.00 0.00 0.00 1.40
2281 2688 5.388599 ACTCCCTCCGATCCAAATTATTT 57.611 39.130 0.00 0.00 0.00 1.40
2282 2689 5.133221 ACTCCCTCCGATCCAAATTATTTG 58.867 41.667 10.46 10.46 40.32 2.32
2283 2690 5.124036 TCCCTCCGATCCAAATTATTTGT 57.876 39.130 15.40 0.00 38.98 2.83
2284 2691 5.130350 TCCCTCCGATCCAAATTATTTGTC 58.870 41.667 15.40 7.40 38.98 3.18
2285 2692 4.024048 CCCTCCGATCCAAATTATTTGTCG 60.024 45.833 17.86 17.86 38.27 4.35
2286 2693 4.527564 CTCCGATCCAAATTATTTGTCGC 58.472 43.478 18.82 7.58 37.64 5.19
2287 2694 3.942115 TCCGATCCAAATTATTTGTCGCA 59.058 39.130 18.82 7.42 37.64 5.10
2288 2695 4.035091 TCCGATCCAAATTATTTGTCGCAG 59.965 41.667 18.82 10.65 37.64 5.18
2289 2696 3.725740 CGATCCAAATTATTTGTCGCAGC 59.274 43.478 15.40 0.59 38.98 5.25
2290 2697 4.496341 CGATCCAAATTATTTGTCGCAGCT 60.496 41.667 15.40 0.00 38.98 4.24
2291 2698 4.782019 TCCAAATTATTTGTCGCAGCTT 57.218 36.364 15.40 0.00 38.98 3.74
2292 2699 5.132897 TCCAAATTATTTGTCGCAGCTTT 57.867 34.783 15.40 0.00 38.98 3.51
2293 2700 6.260870 TCCAAATTATTTGTCGCAGCTTTA 57.739 33.333 15.40 0.00 38.98 1.85
2294 2701 6.321717 TCCAAATTATTTGTCGCAGCTTTAG 58.678 36.000 15.40 0.00 38.98 1.85
2295 2702 6.072175 TCCAAATTATTTGTCGCAGCTTTAGT 60.072 34.615 15.40 0.00 38.98 2.24
2296 2703 7.119992 TCCAAATTATTTGTCGCAGCTTTAGTA 59.880 33.333 15.40 0.00 38.98 1.82
2297 2704 7.218204 CCAAATTATTTGTCGCAGCTTTAGTAC 59.782 37.037 15.40 0.00 38.98 2.73
2298 2705 6.978343 ATTATTTGTCGCAGCTTTAGTACA 57.022 33.333 0.00 0.00 0.00 2.90
2299 2706 6.788684 TTATTTGTCGCAGCTTTAGTACAA 57.211 33.333 0.00 0.00 0.00 2.41
2300 2707 4.461992 TTTGTCGCAGCTTTAGTACAAC 57.538 40.909 0.00 0.00 0.00 3.32
2301 2708 3.380479 TGTCGCAGCTTTAGTACAACT 57.620 42.857 0.00 0.00 0.00 3.16
2302 2709 3.724374 TGTCGCAGCTTTAGTACAACTT 58.276 40.909 0.00 0.00 0.00 2.66
2303 2710 4.124238 TGTCGCAGCTTTAGTACAACTTT 58.876 39.130 0.00 0.00 0.00 2.66
2304 2711 4.025229 TGTCGCAGCTTTAGTACAACTTTG 60.025 41.667 0.00 0.00 0.00 2.77
2305 2712 4.025145 GTCGCAGCTTTAGTACAACTTTGT 60.025 41.667 0.00 0.00 44.86 2.83
2306 2713 5.176223 GTCGCAGCTTTAGTACAACTTTGTA 59.824 40.000 0.00 0.00 42.35 2.41
2317 2724 4.468095 ACAACTTTGTACTAAAGCTGCG 57.532 40.909 15.20 7.39 40.16 5.18
2318 2725 4.124238 ACAACTTTGTACTAAAGCTGCGA 58.876 39.130 15.20 0.00 40.16 5.10
2319 2726 4.025145 ACAACTTTGTACTAAAGCTGCGAC 60.025 41.667 15.20 0.00 40.16 5.19
2320 2727 3.724374 ACTTTGTACTAAAGCTGCGACA 58.276 40.909 14.06 0.00 0.00 4.35
2321 2728 4.124238 ACTTTGTACTAAAGCTGCGACAA 58.876 39.130 14.06 0.00 0.00 3.18
2322 2729 4.755123 ACTTTGTACTAAAGCTGCGACAAT 59.245 37.500 14.06 0.00 0.00 2.71
2323 2730 5.238650 ACTTTGTACTAAAGCTGCGACAATT 59.761 36.000 14.06 0.00 0.00 2.32
2324 2731 6.425721 ACTTTGTACTAAAGCTGCGACAATTA 59.574 34.615 14.06 0.00 0.00 1.40
2325 2732 6.788684 TTGTACTAAAGCTGCGACAATTAA 57.211 33.333 0.00 0.00 0.00 1.40
2326 2733 6.978343 TGTACTAAAGCTGCGACAATTAAT 57.022 33.333 0.00 0.00 0.00 1.40
2327 2734 8.481974 TTGTACTAAAGCTGCGACAATTAATA 57.518 30.769 0.00 0.00 0.00 0.98
2328 2735 8.657074 TGTACTAAAGCTGCGACAATTAATAT 57.343 30.769 0.00 0.00 0.00 1.28
2329 2736 8.547894 TGTACTAAAGCTGCGACAATTAATATG 58.452 33.333 0.00 0.00 0.00 1.78
2330 2737 6.959361 ACTAAAGCTGCGACAATTAATATGG 58.041 36.000 0.00 0.00 0.00 2.74
2331 2738 6.765989 ACTAAAGCTGCGACAATTAATATGGA 59.234 34.615 0.00 0.00 0.00 3.41
2332 2739 6.639632 AAAGCTGCGACAATTAATATGGAT 57.360 33.333 0.00 0.00 0.00 3.41
2333 2740 5.869753 AGCTGCGACAATTAATATGGATC 57.130 39.130 0.00 0.00 0.00 3.36
2334 2741 4.389992 AGCTGCGACAATTAATATGGATCG 59.610 41.667 0.00 0.00 0.00 3.69
2335 2742 4.436050 GCTGCGACAATTAATATGGATCGG 60.436 45.833 0.00 0.00 0.00 4.18
2336 2743 4.888917 TGCGACAATTAATATGGATCGGA 58.111 39.130 0.00 0.00 0.00 4.55
2337 2744 4.929211 TGCGACAATTAATATGGATCGGAG 59.071 41.667 0.00 0.00 0.00 4.63
2338 2745 4.330074 GCGACAATTAATATGGATCGGAGG 59.670 45.833 0.00 0.00 0.00 4.30
2339 2746 4.870426 CGACAATTAATATGGATCGGAGGG 59.130 45.833 0.00 0.00 0.00 4.30
2340 2747 5.337250 CGACAATTAATATGGATCGGAGGGA 60.337 44.000 0.00 0.00 0.00 4.20
2341 2748 6.054860 ACAATTAATATGGATCGGAGGGAG 57.945 41.667 0.00 0.00 0.00 4.30
2342 2749 5.548056 ACAATTAATATGGATCGGAGGGAGT 59.452 40.000 0.00 0.00 0.00 3.85
2343 2750 6.729100 ACAATTAATATGGATCGGAGGGAGTA 59.271 38.462 0.00 0.00 0.00 2.59
2344 2751 6.793505 ATTAATATGGATCGGAGGGAGTAC 57.206 41.667 0.00 0.00 0.00 2.73
2345 2752 4.405756 AATATGGATCGGAGGGAGTACT 57.594 45.455 0.00 0.00 0.00 2.73
2363 2770 7.362920 GGGAGTACTGTTTTGCAACATAATCAT 60.363 37.037 0.00 0.00 42.21 2.45
2397 2804 3.840890 TTCGTTCTTGCACAAACAGTT 57.159 38.095 10.17 0.00 0.00 3.16
2398 2805 3.840890 TCGTTCTTGCACAAACAGTTT 57.159 38.095 10.17 0.00 0.00 2.66
2406 2842 2.159254 TGCACAAACAGTTTTCCTGCTC 60.159 45.455 16.08 0.00 45.68 4.26
2425 2861 3.491652 GCGCCGCTCCTCTGTTTC 61.492 66.667 0.00 0.00 0.00 2.78
2426 2862 2.048222 CGCCGCTCCTCTGTTTCA 60.048 61.111 0.00 0.00 0.00 2.69
2427 2863 2.383527 CGCCGCTCCTCTGTTTCAC 61.384 63.158 0.00 0.00 0.00 3.18
2429 2865 1.738099 CCGCTCCTCTGTTTCACCG 60.738 63.158 0.00 0.00 0.00 4.94
2446 2896 2.594592 GTGCTCCCCGTTGCAACT 60.595 61.111 26.09 0.00 41.10 3.16
2450 2984 1.244019 GCTCCCCGTTGCAACTGATT 61.244 55.000 26.09 0.00 0.00 2.57
2483 3017 4.202245 TCGGAGGAAAATTAGGTCACAG 57.798 45.455 0.00 0.00 0.00 3.66
2484 3018 3.835978 TCGGAGGAAAATTAGGTCACAGA 59.164 43.478 0.00 0.00 0.00 3.41
2486 3020 5.001232 CGGAGGAAAATTAGGTCACAGAAA 58.999 41.667 0.00 0.00 0.00 2.52
2489 3023 6.264518 GGAGGAAAATTAGGTCACAGAAACAA 59.735 38.462 0.00 0.00 0.00 2.83
2490 3024 7.201875 GGAGGAAAATTAGGTCACAGAAACAAA 60.202 37.037 0.00 0.00 0.00 2.83
2491 3025 7.489160 AGGAAAATTAGGTCACAGAAACAAAC 58.511 34.615 0.00 0.00 0.00 2.93
2492 3026 7.123547 AGGAAAATTAGGTCACAGAAACAAACA 59.876 33.333 0.00 0.00 0.00 2.83
2493 3027 7.762159 GGAAAATTAGGTCACAGAAACAAACAA 59.238 33.333 0.00 0.00 0.00 2.83
2494 3028 9.145865 GAAAATTAGGTCACAGAAACAAACAAA 57.854 29.630 0.00 0.00 0.00 2.83
2495 3029 8.474006 AAATTAGGTCACAGAAACAAACAAAC 57.526 30.769 0.00 0.00 0.00 2.93
2496 3030 6.576662 TTAGGTCACAGAAACAAACAAACA 57.423 33.333 0.00 0.00 0.00 2.83
2497 3031 5.461032 AGGTCACAGAAACAAACAAACAA 57.539 34.783 0.00 0.00 0.00 2.83
2501 3035 6.018669 GGTCACAGAAACAAACAAACAAACAA 60.019 34.615 0.00 0.00 0.00 2.83
2509 3043 9.364110 GAAACAAACAAACAAACAAACAGTAAG 57.636 29.630 0.00 0.00 0.00 2.34
2557 3091 4.913126 CGGAGGAAAGGAAGTCCG 57.087 61.111 0.00 0.00 45.48 4.79
2713 3252 2.794631 GCACGGTCAAAAACCTCTTGTG 60.795 50.000 0.00 0.00 46.87 3.33
2728 3274 1.262151 CTTGTGTTTTACGTGGGTCCG 59.738 52.381 0.00 0.00 0.00 4.79
2960 3540 3.461982 CAGCGCAGTCGACACGTC 61.462 66.667 25.33 19.01 38.10 4.34
3023 3629 0.035725 CTGATGAGAACTGGCAGGCA 60.036 55.000 20.34 11.38 0.00 4.75
3065 5105 0.032952 GAGTTAGTCCACACGGCACA 59.967 55.000 0.00 0.00 0.00 4.57
3066 5106 0.249741 AGTTAGTCCACACGGCACAC 60.250 55.000 0.00 0.00 0.00 3.82
3245 5286 4.558860 GCGCATATTCTGTTTTCTTTGGAC 59.441 41.667 0.30 0.00 0.00 4.02
3248 5289 7.526608 CGCATATTCTGTTTTCTTTGGACTTA 58.473 34.615 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.019673 TATGTAGGCACGTCCTCGAC 58.980 55.000 9.44 5.29 43.20 4.20
15 16 1.607148 CATATGTAGGCACGTCCTCGA 59.393 52.381 9.44 0.00 43.20 4.04
16 17 1.930817 GCATATGTAGGCACGTCCTCG 60.931 57.143 9.44 0.00 43.20 4.63
17 18 1.068588 TGCATATGTAGGCACGTCCTC 59.931 52.381 9.44 4.08 43.20 3.71
19 20 3.678921 TGCATATGTAGGCACGTCC 57.321 52.632 4.29 0.00 38.15 4.79
24 25 1.051556 TCCCCGTGCATATGTAGGCA 61.052 55.000 7.86 0.00 41.05 4.75
25 26 0.107831 TTCCCCGTGCATATGTAGGC 59.892 55.000 7.86 0.00 0.00 3.93
26 27 2.699954 GATTCCCCGTGCATATGTAGG 58.300 52.381 4.29 5.53 0.00 3.18
27 28 2.029380 TCGATTCCCCGTGCATATGTAG 60.029 50.000 4.29 0.00 0.00 2.74
28 29 1.964933 TCGATTCCCCGTGCATATGTA 59.035 47.619 4.29 0.00 0.00 2.29
29 30 0.756294 TCGATTCCCCGTGCATATGT 59.244 50.000 4.29 0.00 0.00 2.29
30 31 1.877637 TTCGATTCCCCGTGCATATG 58.122 50.000 0.00 0.00 0.00 1.78
31 32 2.859165 ATTCGATTCCCCGTGCATAT 57.141 45.000 0.00 0.00 0.00 1.78
32 33 3.973206 ATATTCGATTCCCCGTGCATA 57.027 42.857 0.00 0.00 0.00 3.14
33 34 2.859165 ATATTCGATTCCCCGTGCAT 57.141 45.000 0.00 0.00 0.00 3.96
34 35 2.489971 GAATATTCGATTCCCCGTGCA 58.510 47.619 0.00 0.00 0.00 4.57
69 70 9.822185 GCCTGAAATTGGAAGAATATTTGTATT 57.178 29.630 0.00 0.00 0.00 1.89
70 71 8.424133 GGCCTGAAATTGGAAGAATATTTGTAT 58.576 33.333 0.00 0.00 0.00 2.29
71 72 7.416213 CGGCCTGAAATTGGAAGAATATTTGTA 60.416 37.037 0.00 0.00 0.00 2.41
72 73 6.627953 CGGCCTGAAATTGGAAGAATATTTGT 60.628 38.462 0.00 0.00 0.00 2.83
73 74 5.750067 CGGCCTGAAATTGGAAGAATATTTG 59.250 40.000 0.00 0.00 0.00 2.32
74 75 5.682212 GCGGCCTGAAATTGGAAGAATATTT 60.682 40.000 0.00 0.00 0.00 1.40
75 76 4.202151 GCGGCCTGAAATTGGAAGAATATT 60.202 41.667 0.00 0.00 0.00 1.28
76 77 3.319122 GCGGCCTGAAATTGGAAGAATAT 59.681 43.478 0.00 0.00 0.00 1.28
77 78 2.687935 GCGGCCTGAAATTGGAAGAATA 59.312 45.455 0.00 0.00 0.00 1.75
78 79 1.478105 GCGGCCTGAAATTGGAAGAAT 59.522 47.619 0.00 0.00 0.00 2.40
79 80 0.887933 GCGGCCTGAAATTGGAAGAA 59.112 50.000 0.00 0.00 0.00 2.52
80 81 0.965363 GGCGGCCTGAAATTGGAAGA 60.965 55.000 12.87 0.00 0.00 2.87
81 82 0.967380 AGGCGGCCTGAAATTGGAAG 60.967 55.000 23.19 0.00 29.57 3.46
82 83 0.329931 TAGGCGGCCTGAAATTGGAA 59.670 50.000 31.26 4.89 34.61 3.53
83 84 0.550914 ATAGGCGGCCTGAAATTGGA 59.449 50.000 31.26 9.18 34.61 3.53
84 85 1.338020 GAATAGGCGGCCTGAAATTGG 59.662 52.381 31.26 0.00 34.61 3.16
85 86 1.338020 GGAATAGGCGGCCTGAAATTG 59.662 52.381 31.26 0.00 34.61 2.32
86 87 1.692411 GGAATAGGCGGCCTGAAATT 58.308 50.000 31.26 21.95 34.61 1.82
87 88 0.535102 CGGAATAGGCGGCCTGAAAT 60.535 55.000 31.26 14.39 34.61 2.17
88 89 1.153249 CGGAATAGGCGGCCTGAAA 60.153 57.895 31.26 12.46 34.61 2.69
89 90 1.407656 ATCGGAATAGGCGGCCTGAA 61.408 55.000 31.26 13.29 34.61 3.02
90 91 1.837051 ATCGGAATAGGCGGCCTGA 60.837 57.895 31.26 19.25 34.61 3.86
91 92 1.669115 CATCGGAATAGGCGGCCTG 60.669 63.158 31.26 14.26 34.61 4.85
92 93 2.140792 ACATCGGAATAGGCGGCCT 61.141 57.895 26.95 26.95 37.71 5.19
93 94 1.961277 CACATCGGAATAGGCGGCC 60.961 63.158 12.11 12.11 0.00 6.13
94 95 1.961277 CCACATCGGAATAGGCGGC 60.961 63.158 0.00 0.00 36.56 6.53
95 96 1.301716 CCCACATCGGAATAGGCGG 60.302 63.158 0.00 0.00 36.56 6.13
96 97 1.301716 CCCCACATCGGAATAGGCG 60.302 63.158 0.00 0.00 36.56 5.52
97 98 0.472471 TTCCCCACATCGGAATAGGC 59.528 55.000 0.00 0.00 34.40 3.93
123 130 4.541482 TCGTCCGCGGCATCGTAC 62.541 66.667 23.51 11.71 38.89 3.67
165 172 2.112190 AGAACCGGAGAGAAGATTCCC 58.888 52.381 9.46 0.00 0.00 3.97
183 191 1.748122 GGTGGCTCCTCGACGTAGA 60.748 63.158 0.00 0.00 0.00 2.59
207 215 0.790814 GGAAAGAAAGCTCGTCGTGG 59.209 55.000 0.00 0.00 0.00 4.94
279 298 3.554692 GTTCACAGGCGCGATCCG 61.555 66.667 12.10 1.53 40.75 4.18
294 313 3.321968 GGAGGAAAAATTCACAGCTGGTT 59.678 43.478 19.93 4.40 0.00 3.67
325 344 1.228033 CGTCCCGACCCCAGTTTTT 60.228 57.895 0.00 0.00 0.00 1.94
349 369 7.335422 AGCAACGATCATTTCTGAACTAATCTT 59.665 33.333 0.00 0.00 34.37 2.40
351 371 6.904011 CAGCAACGATCATTTCTGAACTAATC 59.096 38.462 0.00 0.00 34.37 1.75
355 375 3.120060 GCAGCAACGATCATTTCTGAACT 60.120 43.478 5.34 0.00 34.37 3.01
356 376 3.166657 GCAGCAACGATCATTTCTGAAC 58.833 45.455 5.34 0.00 34.37 3.18
369 389 4.724697 CTGAACGCGGCAGCAACG 62.725 66.667 12.47 4.85 45.49 4.10
370 390 4.389576 CCTGAACGCGGCAGCAAC 62.390 66.667 21.31 0.00 45.49 4.17
371 391 4.617520 TCCTGAACGCGGCAGCAA 62.618 61.111 21.31 11.44 45.49 3.91
373 393 2.907897 ATACTCCTGAACGCGGCAGC 62.908 60.000 21.31 0.00 40.74 5.25
374 394 0.460284 AATACTCCTGAACGCGGCAG 60.460 55.000 20.19 20.19 0.00 4.85
375 395 0.036765 AAATACTCCTGAACGCGGCA 60.037 50.000 12.47 7.49 0.00 5.69
376 396 0.651031 GAAATACTCCTGAACGCGGC 59.349 55.000 12.47 1.95 0.00 6.53
384 404 1.749634 AGACGGACGGAAATACTCCTG 59.250 52.381 0.00 0.00 42.85 3.86
400 420 4.392921 ACATCCATCTAGAACCAAGACG 57.607 45.455 0.00 0.00 0.00 4.18
475 496 2.270205 CCGCAGCCCACTCTCAAT 59.730 61.111 0.00 0.00 0.00 2.57
476 497 4.704833 GCCGCAGCCCACTCTCAA 62.705 66.667 0.00 0.00 0.00 3.02
504 539 1.239296 CCACTGTGACTGTGGCATGG 61.239 60.000 25.22 5.32 44.09 3.66
546 582 4.044308 TGGTTTGAGCTAGGATTATGGGA 58.956 43.478 0.00 0.00 0.00 4.37
547 583 4.137543 GTGGTTTGAGCTAGGATTATGGG 58.862 47.826 0.00 0.00 0.00 4.00
548 584 5.041191 AGTGGTTTGAGCTAGGATTATGG 57.959 43.478 0.00 0.00 0.00 2.74
550 586 4.740934 GCGAGTGGTTTGAGCTAGGATTAT 60.741 45.833 0.00 0.00 0.00 1.28
551 587 3.430374 GCGAGTGGTTTGAGCTAGGATTA 60.430 47.826 0.00 0.00 0.00 1.75
552 588 2.678190 GCGAGTGGTTTGAGCTAGGATT 60.678 50.000 0.00 0.00 0.00 3.01
553 589 1.134670 GCGAGTGGTTTGAGCTAGGAT 60.135 52.381 0.00 0.00 0.00 3.24
554 590 0.246635 GCGAGTGGTTTGAGCTAGGA 59.753 55.000 0.00 0.00 0.00 2.94
555 591 1.078759 CGCGAGTGGTTTGAGCTAGG 61.079 60.000 0.00 0.00 0.00 3.02
556 592 1.687494 GCGCGAGTGGTTTGAGCTAG 61.687 60.000 12.10 0.00 33.58 3.42
557 593 1.736645 GCGCGAGTGGTTTGAGCTA 60.737 57.895 12.10 0.00 33.58 3.32
566 765 2.061773 CTTATCTAATGGCGCGAGTGG 58.938 52.381 12.10 0.00 0.00 4.00
590 802 2.666596 AAATCTCTCGCATCCCGGGC 62.667 60.000 18.49 2.63 37.34 6.13
715 939 0.322816 CCCTCCTGTGATTGTGGGTG 60.323 60.000 0.00 0.00 0.00 4.61
716 940 0.475632 TCCCTCCTGTGATTGTGGGT 60.476 55.000 0.00 0.00 36.23 4.51
717 941 0.035056 GTCCCTCCTGTGATTGTGGG 60.035 60.000 0.00 0.00 36.14 4.61
718 942 0.391661 CGTCCCTCCTGTGATTGTGG 60.392 60.000 0.00 0.00 0.00 4.17
719 943 1.021390 GCGTCCCTCCTGTGATTGTG 61.021 60.000 0.00 0.00 0.00 3.33
720 944 1.296715 GCGTCCCTCCTGTGATTGT 59.703 57.895 0.00 0.00 0.00 2.71
723 947 3.461773 CGGCGTCCCTCCTGTGAT 61.462 66.667 0.00 0.00 0.00 3.06
810 1084 4.142271 GGAACATGGTGAAAGTGTTTGACA 60.142 41.667 0.00 0.00 36.30 3.58
812 1086 4.019858 TGGAACATGGTGAAAGTGTTTGA 58.980 39.130 0.00 0.00 36.30 2.69
840 1114 2.355209 GCCTTGTACTTGGGGAGAAGAG 60.355 54.545 0.00 0.00 0.00 2.85
853 1131 7.630944 GCTGTGTATATATAGGGAGCCTTGTAC 60.631 44.444 0.00 0.00 34.61 2.90
913 1229 4.410743 GGCGAGCTTGCTTGTGCC 62.411 66.667 25.01 15.05 38.71 5.01
929 1251 3.937814 TGCTATTGGTACTCTGTGTTGG 58.062 45.455 0.00 0.00 0.00 3.77
946 1268 1.295357 CGCGATTGTGGTGGTTGCTA 61.295 55.000 0.00 0.00 0.00 3.49
949 1271 0.521291 AATCGCGATTGTGGTGGTTG 59.479 50.000 32.07 0.00 0.00 3.77
963 1305 1.523095 GTAATCTGTGCTCGGAATCGC 59.477 52.381 0.65 0.00 36.13 4.58
965 1307 4.046938 TCTGTAATCTGTGCTCGGAATC 57.953 45.455 0.65 0.00 32.29 2.52
1180 1527 3.749064 GAGGCAGGAGACGACGCA 61.749 66.667 0.00 0.00 0.00 5.24
1212 1559 4.221422 TGGTAGGAGCCATCGCGC 62.221 66.667 0.00 0.00 41.18 6.86
1230 1577 1.139947 GGCGAACTCGAGGAAGAGG 59.860 63.158 18.41 0.73 42.31 3.69
1650 2000 2.530151 TGGGGCAGCTCAGGAACT 60.530 61.111 0.00 0.00 43.88 3.01
1802 2158 1.374758 GACACCCACTTGCTCTCCG 60.375 63.158 0.00 0.00 0.00 4.63
2026 2409 2.024163 CGCGATGATGACGGTCGA 59.976 61.111 0.00 0.00 37.55 4.20
2069 2458 1.068885 CGGACTCTGCATCTACCGATC 60.069 57.143 14.33 0.00 42.40 3.69
2097 2489 2.921754 CTCTACGTCAACGGAAATGTCC 59.078 50.000 7.53 0.00 44.95 4.02
2104 2496 0.240145 CTGTGCTCTACGTCAACGGA 59.760 55.000 7.53 0.00 44.95 4.69
2178 2582 0.877071 AAAACTGATCGCTGCCAGTG 59.123 50.000 10.15 0.00 42.25 3.66
2180 2584 1.536766 TCAAAAACTGATCGCTGCCAG 59.463 47.619 3.32 3.32 36.53 4.85
2181 2585 1.603456 TCAAAAACTGATCGCTGCCA 58.397 45.000 0.00 0.00 0.00 4.92
2182 2586 2.589014 CTTCAAAAACTGATCGCTGCC 58.411 47.619 0.00 0.00 32.78 4.85
2183 2587 2.589014 CCTTCAAAAACTGATCGCTGC 58.411 47.619 0.00 0.00 32.78 5.25
2184 2588 2.554032 ACCCTTCAAAAACTGATCGCTG 59.446 45.455 0.00 0.00 32.78 5.18
2185 2589 2.863809 ACCCTTCAAAAACTGATCGCT 58.136 42.857 0.00 0.00 32.78 4.93
2186 2590 3.643159 AACCCTTCAAAAACTGATCGC 57.357 42.857 0.00 0.00 32.78 4.58
2187 2591 6.313744 ACTAAACCCTTCAAAAACTGATCG 57.686 37.500 0.00 0.00 32.78 3.69
2188 2592 8.414003 AGAAACTAAACCCTTCAAAAACTGATC 58.586 33.333 0.00 0.00 32.78 2.92
2215 2619 5.645929 ACAATTTACATGACACTAATCGGCA 59.354 36.000 0.00 0.00 0.00 5.69
2259 2666 5.133221 CAAATAATTTGGATCGGAGGGAGT 58.867 41.667 0.00 0.00 37.01 3.85
2260 2667 5.133221 ACAAATAATTTGGATCGGAGGGAG 58.867 41.667 0.00 0.00 44.81 4.30
2261 2668 5.124036 ACAAATAATTTGGATCGGAGGGA 57.876 39.130 0.00 0.00 44.81 4.20
2262 2669 4.024048 CGACAAATAATTTGGATCGGAGGG 60.024 45.833 0.00 0.00 44.81 4.30
2263 2670 4.554723 GCGACAAATAATTTGGATCGGAGG 60.555 45.833 0.00 0.00 44.81 4.30
2264 2671 4.035091 TGCGACAAATAATTTGGATCGGAG 59.965 41.667 0.00 0.00 44.81 4.63
2265 2672 3.942115 TGCGACAAATAATTTGGATCGGA 59.058 39.130 0.00 0.00 44.81 4.55
2266 2673 4.282068 CTGCGACAAATAATTTGGATCGG 58.718 43.478 0.00 0.00 44.81 4.18
2267 2674 3.725740 GCTGCGACAAATAATTTGGATCG 59.274 43.478 0.00 0.00 44.81 3.69
2268 2675 4.925068 AGCTGCGACAAATAATTTGGATC 58.075 39.130 0.00 0.00 44.81 3.36
2269 2676 4.989279 AGCTGCGACAAATAATTTGGAT 57.011 36.364 0.00 0.00 44.81 3.41
2270 2677 4.782019 AAGCTGCGACAAATAATTTGGA 57.218 36.364 0.00 0.00 44.81 3.53
2271 2678 6.092748 ACTAAAGCTGCGACAAATAATTTGG 58.907 36.000 0.00 0.00 44.81 3.28
2272 2679 7.748683 TGTACTAAAGCTGCGACAAATAATTTG 59.251 33.333 0.00 0.00 45.95 2.32
2273 2680 7.812648 TGTACTAAAGCTGCGACAAATAATTT 58.187 30.769 0.00 0.00 0.00 1.82
2274 2681 7.372451 TGTACTAAAGCTGCGACAAATAATT 57.628 32.000 0.00 0.00 0.00 1.40
2275 2682 6.978343 TGTACTAAAGCTGCGACAAATAAT 57.022 33.333 0.00 0.00 0.00 1.28
2276 2683 6.425721 AGTTGTACTAAAGCTGCGACAAATAA 59.574 34.615 0.00 0.00 0.00 1.40
2277 2684 5.929992 AGTTGTACTAAAGCTGCGACAAATA 59.070 36.000 0.00 0.00 0.00 1.40
2278 2685 4.755123 AGTTGTACTAAAGCTGCGACAAAT 59.245 37.500 0.00 0.00 0.00 2.32
2279 2686 4.124238 AGTTGTACTAAAGCTGCGACAAA 58.876 39.130 0.00 0.00 0.00 2.83
2280 2687 3.724374 AGTTGTACTAAAGCTGCGACAA 58.276 40.909 0.00 0.00 0.00 3.18
2281 2688 3.380479 AGTTGTACTAAAGCTGCGACA 57.620 42.857 0.00 0.00 0.00 4.35
2282 2689 4.025145 ACAAAGTTGTACTAAAGCTGCGAC 60.025 41.667 0.00 0.00 40.16 5.19
2283 2690 4.124238 ACAAAGTTGTACTAAAGCTGCGA 58.876 39.130 0.00 0.00 40.16 5.10
2284 2691 4.468095 ACAAAGTTGTACTAAAGCTGCG 57.532 40.909 0.00 0.00 40.16 5.18
2295 2702 5.176223 GTCGCAGCTTTAGTACAAAGTTGTA 59.824 40.000 22.56 14.87 42.35 2.41
2296 2703 4.025145 GTCGCAGCTTTAGTACAAAGTTGT 60.025 41.667 22.56 1.75 44.86 3.32
2297 2704 4.025229 TGTCGCAGCTTTAGTACAAAGTTG 60.025 41.667 20.03 20.03 40.14 3.16
2298 2705 4.124238 TGTCGCAGCTTTAGTACAAAGTT 58.876 39.130 14.90 9.23 0.00 2.66
2299 2706 3.724374 TGTCGCAGCTTTAGTACAAAGT 58.276 40.909 14.90 4.55 0.00 2.66
2300 2707 4.725556 TTGTCGCAGCTTTAGTACAAAG 57.274 40.909 11.27 11.27 0.00 2.77
2301 2708 5.682943 AATTGTCGCAGCTTTAGTACAAA 57.317 34.783 0.00 0.00 31.33 2.83
2302 2709 6.788684 TTAATTGTCGCAGCTTTAGTACAA 57.211 33.333 0.00 0.00 0.00 2.41
2303 2710 6.978343 ATTAATTGTCGCAGCTTTAGTACA 57.022 33.333 0.00 0.00 0.00 2.90
2304 2711 8.009974 CCATATTAATTGTCGCAGCTTTAGTAC 58.990 37.037 0.00 0.00 0.00 2.73
2305 2712 7.929245 TCCATATTAATTGTCGCAGCTTTAGTA 59.071 33.333 0.00 0.00 0.00 1.82
2306 2713 6.765989 TCCATATTAATTGTCGCAGCTTTAGT 59.234 34.615 0.00 0.00 0.00 2.24
2307 2714 7.189693 TCCATATTAATTGTCGCAGCTTTAG 57.810 36.000 0.00 0.00 0.00 1.85
2308 2715 7.360017 CGATCCATATTAATTGTCGCAGCTTTA 60.360 37.037 0.00 0.00 0.00 1.85
2309 2716 6.566564 CGATCCATATTAATTGTCGCAGCTTT 60.567 38.462 0.00 0.00 0.00 3.51
2310 2717 5.106948 CGATCCATATTAATTGTCGCAGCTT 60.107 40.000 0.00 0.00 0.00 3.74
2311 2718 4.389992 CGATCCATATTAATTGTCGCAGCT 59.610 41.667 0.00 0.00 0.00 4.24
2312 2719 4.436050 CCGATCCATATTAATTGTCGCAGC 60.436 45.833 0.00 0.00 0.00 5.25
2313 2720 4.929211 TCCGATCCATATTAATTGTCGCAG 59.071 41.667 0.00 0.00 0.00 5.18
2314 2721 4.888917 TCCGATCCATATTAATTGTCGCA 58.111 39.130 0.00 0.00 0.00 5.10
2315 2722 4.330074 CCTCCGATCCATATTAATTGTCGC 59.670 45.833 0.00 0.00 0.00 5.19
2316 2723 4.870426 CCCTCCGATCCATATTAATTGTCG 59.130 45.833 0.00 0.00 0.00 4.35
2317 2724 6.049955 TCCCTCCGATCCATATTAATTGTC 57.950 41.667 0.00 0.00 0.00 3.18
2318 2725 5.548056 ACTCCCTCCGATCCATATTAATTGT 59.452 40.000 0.00 0.00 0.00 2.71
2319 2726 6.054860 ACTCCCTCCGATCCATATTAATTG 57.945 41.667 0.00 0.00 0.00 2.32
2320 2727 6.960542 AGTACTCCCTCCGATCCATATTAATT 59.039 38.462 0.00 0.00 0.00 1.40
2321 2728 6.381420 CAGTACTCCCTCCGATCCATATTAAT 59.619 42.308 0.00 0.00 0.00 1.40
2322 2729 5.715279 CAGTACTCCCTCCGATCCATATTAA 59.285 44.000 0.00 0.00 0.00 1.40
2323 2730 5.222275 ACAGTACTCCCTCCGATCCATATTA 60.222 44.000 0.00 0.00 0.00 0.98
2324 2731 4.090090 CAGTACTCCCTCCGATCCATATT 58.910 47.826 0.00 0.00 0.00 1.28
2325 2732 3.076182 ACAGTACTCCCTCCGATCCATAT 59.924 47.826 0.00 0.00 0.00 1.78
2326 2733 2.445905 ACAGTACTCCCTCCGATCCATA 59.554 50.000 0.00 0.00 0.00 2.74
2327 2734 1.218196 ACAGTACTCCCTCCGATCCAT 59.782 52.381 0.00 0.00 0.00 3.41
2328 2735 0.629596 ACAGTACTCCCTCCGATCCA 59.370 55.000 0.00 0.00 0.00 3.41
2329 2736 1.777941 AACAGTACTCCCTCCGATCC 58.222 55.000 0.00 0.00 0.00 3.36
2330 2737 3.522553 CAAAACAGTACTCCCTCCGATC 58.477 50.000 0.00 0.00 0.00 3.69
2331 2738 2.354805 GCAAAACAGTACTCCCTCCGAT 60.355 50.000 0.00 0.00 0.00 4.18
2332 2739 1.001633 GCAAAACAGTACTCCCTCCGA 59.998 52.381 0.00 0.00 0.00 4.55
2333 2740 1.270625 TGCAAAACAGTACTCCCTCCG 60.271 52.381 0.00 0.00 0.00 4.63
2334 2741 2.552743 GTTGCAAAACAGTACTCCCTCC 59.447 50.000 0.00 0.00 0.00 4.30
2335 2742 3.211045 TGTTGCAAAACAGTACTCCCTC 58.789 45.455 0.00 0.00 0.00 4.30
2336 2743 3.290948 TGTTGCAAAACAGTACTCCCT 57.709 42.857 0.00 0.00 0.00 4.20
2337 2744 5.699097 TTATGTTGCAAAACAGTACTCCC 57.301 39.130 0.00 0.00 35.95 4.30
2338 2745 6.908825 TGATTATGTTGCAAAACAGTACTCC 58.091 36.000 0.00 0.00 35.95 3.85
2339 2746 8.236586 TGATGATTATGTTGCAAAACAGTACTC 58.763 33.333 0.00 0.00 35.95 2.59
2340 2747 8.109705 TGATGATTATGTTGCAAAACAGTACT 57.890 30.769 0.00 0.00 35.95 2.73
2341 2748 8.741101 TTGATGATTATGTTGCAAAACAGTAC 57.259 30.769 0.00 0.00 35.95 2.73
2342 2749 9.356433 CATTGATGATTATGTTGCAAAACAGTA 57.644 29.630 0.00 0.00 35.95 2.74
2343 2750 7.148540 GCATTGATGATTATGTTGCAAAACAGT 60.149 33.333 0.00 0.00 35.95 3.55
2344 2751 7.148557 TGCATTGATGATTATGTTGCAAAACAG 60.149 33.333 0.00 0.00 35.85 3.16
2345 2752 6.649557 TGCATTGATGATTATGTTGCAAAACA 59.350 30.769 0.00 0.00 35.85 2.83
2363 2770 4.944962 AGAACGAAATCGATTGCATTGA 57.055 36.364 16.41 0.00 43.02 2.57
2429 2865 2.594592 AGTTGCAACGGGGAGCAC 60.595 61.111 23.21 0.00 41.05 4.40
2446 2896 2.613595 CTCCGAATTTGCCGATCAATCA 59.386 45.455 0.00 0.00 34.12 2.57
2450 2984 0.539518 TCCTCCGAATTTGCCGATCA 59.460 50.000 0.00 0.00 0.00 2.92
2483 3017 9.364110 CTTACTGTTTGTTTGTTTGTTTGTTTC 57.636 29.630 0.00 0.00 0.00 2.78
2484 3018 8.884726 ACTTACTGTTTGTTTGTTTGTTTGTTT 58.115 25.926 0.00 0.00 0.00 2.83
2486 3020 9.187455 CTACTTACTGTTTGTTTGTTTGTTTGT 57.813 29.630 0.00 0.00 0.00 2.83
2489 3023 7.371936 TGCTACTTACTGTTTGTTTGTTTGTT 58.628 30.769 0.00 0.00 0.00 2.83
2490 3024 6.915349 TGCTACTTACTGTTTGTTTGTTTGT 58.085 32.000 0.00 0.00 0.00 2.83
2491 3025 6.020678 GCTGCTACTTACTGTTTGTTTGTTTG 60.021 38.462 0.00 0.00 0.00 2.93
2492 3026 6.033966 GCTGCTACTTACTGTTTGTTTGTTT 58.966 36.000 0.00 0.00 0.00 2.83
2493 3027 5.124776 TGCTGCTACTTACTGTTTGTTTGTT 59.875 36.000 0.00 0.00 0.00 2.83
2494 3028 4.638421 TGCTGCTACTTACTGTTTGTTTGT 59.362 37.500 0.00 0.00 0.00 2.83
2495 3029 4.970003 GTGCTGCTACTTACTGTTTGTTTG 59.030 41.667 0.00 0.00 0.00 2.93
2496 3030 4.260620 CGTGCTGCTACTTACTGTTTGTTT 60.261 41.667 0.00 0.00 0.00 2.83
2497 3031 3.247648 CGTGCTGCTACTTACTGTTTGTT 59.752 43.478 0.00 0.00 0.00 2.83
2501 3035 2.673833 GACGTGCTGCTACTTACTGTT 58.326 47.619 0.00 0.00 0.00 3.16
2537 3071 1.448013 GACTTCCTTTCCTCCGCCG 60.448 63.158 0.00 0.00 0.00 6.46
2539 3073 1.448013 CGGACTTCCTTTCCTCCGC 60.448 63.158 0.00 0.00 39.32 5.54
2557 3091 1.986575 GCAAGCTCTGAATCCACGCC 61.987 60.000 0.00 0.00 0.00 5.68
2651 3185 1.883084 CCATTCGAGCAGTACGCCC 60.883 63.158 6.15 0.00 44.04 6.13
2713 3252 1.571215 CTGCCGGACCCACGTAAAAC 61.571 60.000 5.05 0.00 0.00 2.43
2728 3274 2.105128 CCGTCGACTCCATCTGCC 59.895 66.667 14.70 0.00 0.00 4.85
2775 3329 0.462759 GAAGCAATCTCTGGACGGGG 60.463 60.000 0.00 0.00 0.00 5.73
2885 3465 4.457496 AGCCGACACGCCATCCAG 62.457 66.667 0.00 0.00 0.00 3.86
2960 3540 2.048877 GTGTGGGGGTACGTGTCG 60.049 66.667 0.00 0.00 0.00 4.35
2961 3541 1.833787 ATGGTGTGGGGGTACGTGTC 61.834 60.000 0.00 0.00 0.00 3.67
2962 3542 1.844289 ATGGTGTGGGGGTACGTGT 60.844 57.895 0.00 0.00 0.00 4.49
2963 3543 1.376683 CATGGTGTGGGGGTACGTG 60.377 63.158 0.00 0.00 0.00 4.49
2964 3544 3.074281 CATGGTGTGGGGGTACGT 58.926 61.111 0.00 0.00 0.00 3.57
2965 3545 2.437716 GCATGGTGTGGGGGTACG 60.438 66.667 0.00 0.00 0.00 3.67
2966 3546 1.077716 GAGCATGGTGTGGGGGTAC 60.078 63.158 0.00 0.00 0.00 3.34
2967 3547 2.305607 GGAGCATGGTGTGGGGGTA 61.306 63.158 0.00 0.00 0.00 3.69
3023 3629 6.291377 TCAACAGAGAAACAGATAAGCACTT 58.709 36.000 0.00 0.00 0.00 3.16
3083 5123 0.949105 ATCGTGTTTGTCCTCGTGCC 60.949 55.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.